diff --git a/GCAT_users_manual.odt b/GCAT_users_manual.odt index ee3a033..3d67d97 100755 Binary files a/GCAT_users_manual.odt and b/GCAT_users_manual.odt differ diff --git a/GCAT_users_manual_draft-6.docx b/GCAT_users_manual_draft-6.docx deleted file mode 100644 index c3e6d7b..0000000 Binary files a/GCAT_users_manual_draft-6.docx and /dev/null differ diff --git a/R/.Rhistory b/R/.Rhistory deleted file mode 100644 index e69de29..0000000 diff --git a/R/GCAT/.RData b/R/GCAT/.RData deleted file mode 100644 index e5b917d..0000000 Binary files a/R/GCAT/.RData and /dev/null differ diff --git a/R/GCAT/.Rbuildignore b/R/GCAT/.Rbuildignore index 91114bf..13e458c 100644 --- a/R/GCAT/.Rbuildignore +++ b/R/GCAT/.Rbuildignore @@ -1,2 +1,2 @@ -^.*\.Rproj$ -^\.Rproj\.user$ +^.*\.Rproj$ +^\.Rproj\.user$ diff --git a/R/GCAT/.Rhistory b/R/GCAT/.Rhistory deleted file mode 100644 index 8feb3e6..0000000 --- a/R/GCAT/.Rhistory +++ /dev/null @@ -1,159 +0,0 @@ -library(GCAT) -library(GCAT) -library(GCAT) -source('~/Documents/GCAT4_old/trunk/R/GCAT/R/addingParams.R') -library(GCAT) -source('~/Documents/GCAT4_old/trunk/R/GCAT/R/addingParams.R') -t -warnings() -library(GCAT) -source('~/Documents/GCAT4_old/trunk/R/GCAT/R/addingParams.R') -warnings() -library(GCAT) -source('~/Documents/GCAT4_old/trunk/R/GCAT/R/addingParams.R') -warnings() -library(GCAT) -source('~/Documents/GCAT4_old/trunk/R/GCAT/R/addingParams.R') -library(GCAT) -library(GCAT) -library("GCAT") -library("codetools") -checkUsagePackage("GCAT") -library(GCAT) -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -checkUsagePackage("GCAT") -library("codetoolds") -library("codetoolss") -library("codetools") -checkUsagePackage("GCAT") -library(GCAT) -library("codetools") -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -checkUsagePackage("GCAT") -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/fit.model.R') -library(GCAT) -checkUsagePackage("GCAT") -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -checkUsagePackage("GCAT") -source('~/Documents/GCAT4/trunk/R/GCAT/R/class.model.R') -library(GCAT) -checkUsagePackage("GCAT") -library(GCAT) -checkUsagePackage("GCAT") -library(GCAT) -checkUsagePackage("GCAT") -?? checkusagePackage -checkUsagePackage("GCAT", all + T) -checkUsagePackage("GCAT", all = T) -checkUsagePackage("GCAT") -checkUsagePackage("GCAT") -source('~/Documents/GCAT4/trunk/R/GCAT/R/plot.fit.R') -library(GCAT) -checkUsagePackage("GCAT") -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -t -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -source('~/Documents/GCAT4/trunk/R/GCAT/R/plot.fit.R') -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/plot.fit.R') -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -library(GCAT) -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -library(GCAT) -library(GCAT) -library(GCAT) -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/table2well.R') -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -library(GCAT) -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -library(GCAT) -library(GCAT) -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -library(GCAT) -library(GCAT) -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -library("codetools") -library("GCAT") -checkUsagePackage(GCAT) -checkUsagePackage("GCAT) -checkUsagePackage("GCAT") -checkUsagePackage("GCAT") -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R') -t -checkUsagePack(GCAT) -checkUsagePackage(GCAT) -checkUsagePackage("GCAT") -library(GCAT) -library(GCAT) -library(GCAT) -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/normalize.and.transform.R') -library(GCAT) -library(GCAT) -library(GCAT) -library(GCAT) -library(GCAT) -library(GCAT) -library(GCAT) -source('~/Documents/GCAT4/trunk/R/GCAT/R/plot.fit.R') -library(GCAT) -library(GCAT) -library(GCAT) -?? plot -? plot -library(GCAT) -library(GCAT) -library(GCAT) -library(GCAT) -library(GCAT) -library(GCAT) -library(GCAT) -library(GCAT) -library(GCAT) -library(GCAT) -library("codetools") -checkPackageUsage("GCAT") -checkUsagePackage("GCAT") -checkUsagePackage("GCAT", all = T) diff --git a/R/GCAT/.Rproj.user/7CB73FCA/build_options b/R/GCAT/.Rproj.user/7CB73FCA/build_options deleted file mode 100644 index 5b5e33b..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/build_options +++ /dev/null @@ -1,4 +0,0 @@ -auto_roxygenize_for_build_and_reload="1" -auto_roxygenize_for_build_package="1" -auto_roxygenize_for_check="1" -makefile_args="" diff --git a/R/GCAT/.Rproj.user/7CB73FCA/persistent-state b/R/GCAT/.Rproj.user/7CB73FCA/persistent-state deleted file mode 100644 index f8c5903..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/persistent-state +++ /dev/null @@ -1,9 +0,0 @@ -build-last-errors="[]" -build-last-errors-base-dir="~/Documents/GCAT4/trunk/R/GCAT/" -build-last-outputs="[{\"output\":\"==> roxygenize('.', roclets=c('rd'))\\n\\n\",\"type\":0},{\"output\":\"* checking for changes ... \",\"type\":1},{\"output\":\"DONE\\n\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"==> R CMD INSTALL --no-multiarch --with-keep.source GCAT\\n\\n\",\"type\":0},{\"output\":\"* installing to library ‘/home/minh/R/x86_64-pc-linux-gnu-library/3.0’\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"* installing *source* package ‘GCAT’ ...\\n\",\"type\":1},{\"output\":\"** R\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** inst\\n\",\"type\":1},{\"output\":\"** preparing package for lazy loading\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"Reading input files...\",\"type\":1},{\"output\":\"Error in try(gcat.load.data(file.name = file.name, input.data = input.data, : \\n\",\"type\":1},{\"output\":\" could not find function \\\"gcat.load.data\\\"\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"Creating a generic function for 'plot' from package 'graphics' in package 'GCAT'\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"No man pages found in package 'GCAT' \\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** help\\n\",\"type\":1},{\"output\":\"*** installing help indices\\n\",\"type\":1},{\"output\":\"** building package indices\\n\",\"type\":1},{\"output\":\"** testing if installed package can be loaded\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"* DONE (GCAT)\\n\",\"type\":1},{\"output\":\"\",\"type\":1}]" -compile_pdf_state="{\"errors\":[],\"output\":\"\",\"running\":false,\"tab_visible\":false,\"target_file\":\"\"}" -console_procs="[]" -files.monitored-path="" -find-in-files-state="{\"handle\":\"\",\"input\":\"\",\"path\":\"\",\"regex\":false,\"results\":{\"file\":[],\"line\":[],\"lineValue\":[],\"matchOff\":[],\"matchOn\":[]},\"running\":false}" -imageDirtyState="1" -saveActionState="-1" diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/1B6124D6 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/1B6124D6 deleted file mode 100644 index dc615d1..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/1B6124D6 +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n\n########################################################################\n# #\n# Estimate the growth curve slope at each timepoint of a well #\n# #\n########################################################################\n#\n# uses the functions and (see well.class.R) \n# adds estimated slopes as a new column to the \"screen.data\" slot\n\ncalculate.slopes = function(input.well, silent = T){\n # Get the growth curve data (excluding removed points, but not excluding points marked as tanking)\n\tgrowth.data = data.from(input.well, remove = T, remove.tanking = F)\n\tx = growth.data[,1]\n\ty = growth.data[,2]\n\t\n\t# Get a list of timepoint indices \n\tindices = as.numeric(rownames(growth.data))\n\t\n # Default slope is NA, values will be filled in as they are calculated\n slopes = rep(NA, length(input.well))\n\n\tfor (i in 1:length(x)){ \n\t\tif (i == 1)\n\t\t\tslopes[indices[i]] = NA\n # Calculate the slope of the line drawn from each point to the point preceding it. \n\t\telse\n\t\t\tslopes[indices[i]] = (y[i] - y[i-1])/(x[i] - x[i-1])\n\t\t}\n # Add a Slope column to the \"screen.data\" slot \n\tinput.well@screen.data$Slope = slopes\n\tif (!silent)\n\t\tcat(\"slopes filled for\", input.well@position[1], well.name(input.well), \"\\n\")\n\treturn(input.well)\n }\n \n \n########################################################################\n# #\n# Use slope estimates to check growth curves for tanking and OD jumps #\n# #\n########################################################################\n#\n# uses the functions and (see well.class.R) \n# Arguments: \n# ----- stringency parameters ----\n# remove.jumps - should the program remove OD jumps? default F (just report them) - \n# should be set to T if data contains distinct jumps in OD that need to be eliminated \n# otherwise, this might be too stringent and will result in loss of data. \n# check.start - which timepoint should checking for jumps and tanking start at? this is included because early timepoints can be unstable.\n# fall.cutoff - what downward slope should constitute a fall in OD? \n# jump.cutoffs - multipliers to determine whether a curve jumps up or down (see methods 1 and 2, below)\n# tank.limit - how many timepoints in a row can have falling slopes until the curve is marked as tanking?\n# tank.cutoff - what proportion of the maximum OD can the curve go below until it is considered tanking?\n\n# ---- input/output ----\n# silent - output to R console?\n# draw - plot growth curve with curve checking details? \n#\n# Fills the \"curve.par\" slot in the well with the starting index of tanking (NA if none is found)\n# \n\n#check.slopes = function(input.well, check.start = 8, fall.cutoff = -.0025, remove.jumps = F,\n#\t\t\tjump.multipliers = -c(15, 500, 10), tank.cutoff = 1.0, tank.limit = 3, silent = T, draw = T){\n\n#changed default values to parameters to account for settling\ncheck.slopes = function(input.well, check.start = 22, fall.cutoff = -.0025, remove.jumps = F,\n\t\t\tjump.multipliers = -c(15, 500, 10), tank.cutoff = 1.0, tank.limit = 6, silent = T, draw = T){\n\n if (!silent)\n cat(\"\\nNow checking slopes for\", plate.name(input.well), well.name(input.well))\n\n\t# Get estimated slopes and untransformed points from the well \n slopes = input.well@screen.data$Slope\n\tx = data.from(input.well, remove=F, remove.tanking=F)[,1]\n\ty = data.from(input.well, remove=F, remove.tanking=F)[,2] \n\t\n\t# Get a list of indices with valid slope estimates\n\tindices = (1:length(input.well))[!is.na(slopes)]\n\n # Do not report tanking or check for jumps if there are fewer valid points than the number needed to detect it\n\tif (length(indices) < tank.limit){\n\t\tinput.well@curve.par$tanking.start = NA\n\t\tif (!silent)\n\t\t\tcat(\"...does not have enough points to check.\\n\")\n\t\treturn(input.well)\n\t}\n\t\n #######################################################################################\n # Create indicator variables and recalculate cutoffs based on timepoint density. #\n #######################################################################################\n #\n\n # Create , a vector of indicator variables for each timepoint with a valid slope estimate. \n\tslope.indicator = rep(NA, length(slopes))\n\t\n\t# Calculate the mean time difference between two timepoints (this typically doesn't vary too much)\n time.diff = mean(diff(x[-1]))\n \n\t# Use the mean time difference to recalculate what should constitute a fall in OD using (which should be a proportion)\n\t# Honestly I don't remember why the fifth root thing is in here...this is probably going to be revised later. \n fall.cutoff = fall.cutoff * time.diff ^ (1/5) / 0.9506785\n \t\n\t# Recalculate stringency parameters for jump detection based on spread of timepoints\n\tjump.cutoffs = jump.multipliers* fall.cutoff \n\n # Recalculate tanking limit based on spread of timepoints\n\ttank.limit = round(tank.limit / time.diff ^ (1/5) * 0.9506785)\n\n\t# Cycle through the indices of input.wells with valid slope estimate\n\tcounter = 0\n\n for(j in 1:length(indices)){\n #######################################################################################\n # Method #1 for finding OD jumps: compare the slope estimate of each point to the #\n # ones for the closest surrounding points. #\n #######################################################################################\n # Get indices of the two closest surrounding timepoints with valid slope estimates. \n\t\tif (j == 1)\n\t\t\tprev.i = indices[2]\n\t\telse\n\t\t\tprev.i = indices[j-1]\n\t\tif (j == length(indices))\n\t\t\tnext.i = indices[length(indices) - 1]\n\t\telse\n\t\t\tnext.i = indices[j+1]\n\t\ti = indices[j]\n\t\t\n\t\t# How the program determines a jump up:\n\t\t# If slope estimate of current timepoint is larger than times the highest surrounding slope estimate plus \n\t\t# Add a \"2\" to the indicator variable\n\t\t# How the program determines a fall:\n\t\t# If slope estimate of current timepoint is more negative than \n\t\t# Add a \"5\" to the indicator variable\n\t\t# How the program determines a jump down:\n\t\t# If slope estimate is lower than AND is smaller than times the lowest surrounding slope estimate minus \n\t\t# Add a \"6\" to the slope indicator variable\n\t\t#\n\t\t# If none of these are true, add a \"0\" to the indicator variable\n\t\t\n\t\tif (slopes[i] > jump.cutoffs[2] * max(c(slopes[next.i],slopes[prev.i]),0) + jump.cutoffs[1])\n\t\t\tslope.indicator[i] = 2\n\t\telse if (slopes[i] < fall.cutoff){\n\t\t\tslope.indicator[i] = 5\n\t\t\tif (slopes[i] < jump.cutoffs[2] * min(c(slopes[next.i],slopes[prev.i], 0)) - jump.cutoffs[1])\n\t\t\t slope.indicator[i] = 6\t\n\t\t\t}\n\t\telse\n\t\t\tslope.indicator[i] = 0\n\n\n #######################################################################################\n # Method #2 for finding OD jumps: see if each point lies close to a line drawn #\n # between the closest surrounding points. #\n #######################################################################################\n #\n # Use variable to track the location of each point. If two subsequent points lie farther \n # away than the cutoff from their respectively drawn lines AND are on different sides, then count that as a jump. \n \n\t\tif (j > 1 & j < length(indices)){\n\t\t\n\t\t # Make equation (y=mx+b) for line drawn between two surrounding points\n\t\t\tm = (y[next.i] - y[prev.i])/(x[next.i] - x[prev.i])\n\t\t\tb = y[prev.i] - m * x[prev.i]\t\t\n\t\t\t\n # Estimate y from that line. Points will be judged by how much their true y value deviate from this estimate.\n \n # calculate b for perpendicular line from observed point to drawn line (slope is -1/m)\n b2 = y[i] + x[i]/m\n\n # solve equation for intersection to determine the shortest Euclidean distance between the point and line.\n # assign a sign to the distance based on the vertical distance. \n est.x = (b2 - b) / (m + 1/m)\n est.y = est.x * m + b\n #est.y = m * x[i] + b\n #est.x = x[i]\n \n if(m != 0)\n point.distance = sqrt((y[i]-est.y)^2 + (x[i]-est.x)^2) * sign(y[i]-est.y)\n else # horizontal case\n point.distance = y[i] - b\n \n #print(paste(i, point.distance, slopes[i], jump.cutoffs[2] * max(c(slopes[next.i],slopes[prev.i]),0) + jump.cutoffs[1], point.distance > jump.cutoffs[3])) \n \n\t\t\tcolor = \"gray30\"\n\t\t\t# If the true point exceeds that estimate by more than , update to positive.\n\t\t\t# if the counter weas previously negative, mark this as a jump up. \n\t\t\tif (point.distance > jump.cutoffs[3]){\n\t\t\t\tif (counter == -1){\n\t\t\t\t\tslope.indicator[i] = 2\n\t\t\t\t\tcolor = \"red\"\n\t\t\t\t\t}\n\t\t\t\tcounter = 1\n\t\t\t\t}\n\t\t\t# If the true point is under that estimate by more than , update to negative.\n\t\t\t# if the counter was previously positive, mark this as a jump down. \n\t\t\telse if (point.distance < -jump.cutoffs[3]){\n\t\t\t\tif (counter == 1){\n\t\t\t\t\tslope.indicator[i] = 6\n\t\t\t\t\tcolor = \"red\"\n\t\t\t\t\t}\n\t\t\t\tcounter = -1\n\t\t\t\t}\n\t\t\t# If the true point lies within of that estimate, update to zero. \n\t\t\telse \n\t\t\t\tcounter = 0\n \t\n\t\t\tif(draw)\n # Graphic representation: draw each line used in Method #2 as a dotted line, \n # and highlight in red if a jump was detected\n\t\t\t\tlines(x[c(prev.i, next.i)], y[c(prev.i, next.i)], lty = 2, col = color)\n\t\t\t}\n\t\t}\n\n #######################################################################################\n # Check for tanking by looking for unbroken series of points with falling slopes. #\n #######################################################################################\n #\n # Cycle through , adding to until the end of the curve or until reaches the \n\n\ttank = 0\n\ti = 1\n\t\n\twhile(i < length(slope.indicator) & tank < tank.limit){\n\t# If a fall was not detected, reset to 0. \n\t\tif (is.na(slope.indicator[i]))\n\t\t\ttank = 0 \n # If a fall was detected at a point index greater than , add 1 to .\n \telse if (slope.indicator[i] >= 5 & i > check.start)\n\t\t\ttank = tank + 1\n\t\telse\n\t\t\ttank = 0\n\n\t\ti = i + 1\n\t\t}\n\t\t\n\t# If the above loop was terminated because reached , update the \"curve.par\" \n # slot to denote the first point at which tanking started (should be the last index checked minus )\n # also truncate so that it does not include the timepoints after tanking. \n \n\tif (tank == tank.limit){\n\t\tinput.well@curve.par$tanking.start = i - tank.limit\n\t\tslope.indicator = slope.indicator[1:i]\n\t\tif (!silent)\n\t\t cat(\"...tanks at timepoint\", i - tank.limit, \".\\n\")\n\t\t}\n\telse{\n\t\tinput.well@curve.par$tanking.start = NA\n\t\tif (!silent)\n\t\t\tcat(\"...does not tank.\\n\")\n }\n \n #######################################################################################\n # Method #2 of checking for tanking: see if OD falls below cutoff # \n # (as a proportion of max OD) without recovery (according to ) #\n #######################################################################################\n #\n i = check.start\n tanking.start = NA\n while(i < length(y) & is.na(tanking.start)){\n # If the next ODs beyond i do not reach the cutoff, then mark i as tanking. \n if (all(y[i+(1:tank.limit)] < max(y,na.rm=T)*tank.cutoff, na.rm=T)) \n tanking.start = i\n i = i+1\n }\n \n # Graphic representation: draw the indicators used in Method #1 using the pch symbols in \n # slope index = 2: an upward-pointing traingle for an upward jump \n # slope index = 5: a diamond for a fall\n # slope index = 6: a downward-pointing triangle for downward jump \n\tif (draw){\n points(data.from(input.well, remove = F, remove.tanking = F)[which(slope.indicator != 0),], \n \tcol = 2, bg = 2, cex = 1.3, pch = slope.indicator[which(slope.indicator != 0)])\n }\n \n #######################################################################################\n # Decide what to do about any remaining jumps in OD #\n #######################################################################################\n \n\tjump.up = which(slope.indicator == 2)\n\tjump.down = which(slope.indicator == 6)\n\t# is a variable which keeps track of all the jumps, whether up or down. \n\tjump.all = sort(c(match(jump.down, indices), match(jump.up, indices)))\n # commented out; jump not working\n # if (length(jump.all) > 0)\n # add.info = paste(\"Jump(s) detected at timepoint(s)\",paste(indices[jump.all],collapse=\" \"))\n # else\n add.info = \"\"\n \n # If is true, use the following automated process to try and remove OD jumps by selectively removing points from analysis.\n # if not, just return the well with the above slot filled. \n \n if (!remove.jumps)\n input.well@add.info = add.info\n else{\n # Cycle through first few jumps (before ). is a logical that controls this loop. \n \tremove.initial.jump = T\n \twhile (length(jump.all) > 0 & jump.all[1] < check.start & remove.initial.jump){\n \t\n # If any other jumps are also before ...\n \t\tif (any(jump.all[-1] < check.start)){ \n \t\t # ...and the next jump is in a different direction, stop the loop and don't remove the first one. \n \t\t\tif(slope.indicator[indices[min(jump.all[-1])]] != slope.indicator[indices[jump.all[1]]])\n \t\t\t\tremove.initial.jump = F\n \t\t\t\t# ...or if the next two jumps are different, stop the loop and don't remove the first one. \n \t\t\telse if(length(jump.all[-1]) > 1 &\n \t\t\t\tslope.indicator[indices[jump.all[2]]] != slope.indicator[indices[jump.all[3]]])\n \t\t\t\tremove.initial.jump = F\t\n \t\t\t# ...otherwise, remove the jump and keep looping. \t\n \t\t\telse \n \t\t\t\tremove.initial.jump = T\n \t\t\t}\n # If no jumps other than the first one are before , remove it and keep looping. \n \t\telse \n \t\t\tremove.initial.jump = T\n \t\t\t\n \t # If the initial jump is to be removed, remove all points before the jump from analysis. \n # also delete the initial jump from \t\t\n \t\tif (remove.initial.jump){\n \t\t\tinput.well = remove.points(input.well, 1:(indices[jump.all[1]] - 1))\n \t\t\tinput.well@add.info = paste(add.info, \"and removed.\")\n \t\t\tjump.all = jump.all[-1]\n \t\t\t}\n \t\t}\t\n # If greater than 3 jumps remain, discard the curve as uninterpretable\t\n \tif (length(jump.all) >= 4){\n \t\tinput.well = remove.points(input.well, 1:length(input.well))\n \t\tinput.well@add.info = paste(add.info, \" - data was discarded.\")\n \t\t}\t\n \telse{\n \t# If there are 3 jumps, remove all points after the last one from analysis and delete the last jump from \n \t\tif(length(jump.all) == 3){\n \t\t\tinput.well = remove.points(input.well, indices[jump.all[3]]:length(input.well))\n \t\t\tinput.well@add.info = paste(add.info, \"and removed.\")\n \t\t\tjump.all = jump.all[-3] \n \t\t\t}\n \t\t\t\n\t\t# If there are now 2 jumps...\n \t\tif(length(jump.all) == 2){\n \t\t # ...and they are different (one up, one down), remove the points in between them from analysis.\n \t\t\tif (diff(slope.indicator[indices[jump.all]]) != 0 ){\n \t\t \t\tinput.well = remove.points(input.well, indices[jump.all[1]:(jump.all[2] - 1)])\n \t\t\t\tinput.well@add.info = paste(add.info, \"and removed.\")\n \t\t\t\t}\n \t\t\t\t# ...and they are in the same direction, remove all the points after the first one from analysis.\n \t\t\telse{\n \t\t\t\tinput.well = remove.points(input.well, indices[jump.all[1]]:length(input.well))\n\t \t\t\tinput.well@add.info = paste(add.info, \"and removed.\")\n \t\t\t\t}\t\t\t\t\n \t\t\t}\n\t\t# If there is only one jump, remove all points after it from analysis. \n \t\telse if (length(jump.all == 1)){\n \t\t\tinput.well = remove.points(input.well, indices[jump.all[1]]:length(input.well))\n \t\t\tinput.well@add.info = paste(add.info, \"and removed.\")\n \t\t\tjump.all = jump.all[-1] \n \t\t\t}\n \t\t}\n \t}\n \tif(!silent)\n \t cat(\"\\t\", input.well@add.info)\n\treturn(input.well)\n\t}\n\t\n########################################################################\n# #\n# Check wells for growth, remove from analysis if OD is too low # \n# #\n########################################################################\n#\n# The well will be tagged with no.growth = T in the slot \"curve.par\" if raw OD values (except for )\n# do not increase beyond above the specified time of inoculation for that well () \n\ncheck.growth = function(input.well, growth.cutoff, start.index = 2){\n\n # Get raw ODs (not including ) and slope estimates from the well \n # as well as OD at inoculation timepoint \n\traw.ODs = raw.data(input.well)[,2]\n start.OD = raw.ODs[start.index]\n \n raw.ODs[input.well@screen.data$Remove] = NA\n\tslope.estimates = slopes(input.well, remove.tanking = T, na.rm = T)\n\n # If fewer than 3 points remain in the analysis with valid slope estimates, discard the well. \n\tif (length(slope.estimates) < 3 | all(is.na(slope.estimates)))\n\t\tinput.well@curve.par$no.growth= T\t\t\n\telse{\n\t# If there are no points at all in the raw ODs \n\t\tif(all(is.na(raw.ODs)))\n\t\t\tinput.well@curve.par$no.growth = T\n\t\telse if(max(raw.ODs, na.rm=T) - start.OD < growth.cutoff) # See if OD increases by at least above\n\t\t\tinput.well@curve.par$no.growth = T\n\t\telse\n\t\t\tinput.well@curve.par$no.growth = F\n\t\t}\n if(all(raw.data(input.well)[,2] - raw.data(input.well)[start.index,2] < growth.cutoff)) \n input.well@add.info = \"\" # This is simply to reduce the amount of unnecessary info in the output. \n # If the well is below growth cutoff anyway, don't bother reporting other errors. \n\treturn(input.well)\n\t}\n\n\n", - "created" : 1425413252161.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "2162891425", - "id" : "1B6124D6", - "lastKnownWriteTime" : 1424208623, - "path" : "~/Documents/GCAT4/trunk/R/GCAT/R/slope.analysis.R", - "project_path" : "R/slope.analysis.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/26C12555 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/26C12555 deleted file mode 100644 index 1eedd3e..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/26C12555 +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n\n########################################################################\n# #\n# Functions to calculate various things about wells based on fit model #\n# #\n########################################################################\n\n# S3 generic\nlag <- function(fitted.well, ...)\n{\n UseMethod(\"lag\")\n}\n\n#\n# Common arguments:\n# fitted.well - should be a well containing the results of , most functions will return NA if well has not been fit yet.\n# unlog - should the value be returned on the linear scale as opposed to the log-transformed scale?\n# constant.added - for returning values on the linear scale, what was the constant added before the log transform?\n# digits - passed to the function, default is no rounding (infinity digits)\n\nunlog = function(x, constant.added) {\n ########################################################################\n # Transform values back to OD scale #\n ########################################################################\nexp(x) - constant.added\n}\n\nwell.eval = function(fitted.well, Time = NULL){\n ########################################################################\n # Evaluate estimated OD at any timepoints using the fitted model #\n ########################################################################\n\n # If no timepoints are provided, use the ones collected in the experiment itself.\n\tif(!is.numeric(Time))\n\t\tTime = data.from(fitted.well)$Time\n\n # Use of equation is deprecated. Use nls and loess models stored in the well object instead\n # Attempt to use with the fitted equation and parameters to get estimates for OD at the given timepoints.\n\t#output = try(eval(fitted.well@equation, fitted.well@fit.par), silent = T)\n \n # Predict log.OD value(s) using nls model if present. If no nls model, try using loess.\n if (length(fitted.well@nls)>0) {\n output = try(predict(fitted.well@nls,list(Time=Time)),silent=T)\n } else if (length(fitted.well@loess)>0) {\n output = try(predict(fitted.well@loess,Time),silent=T)\n } else {\n output = NA\n }\n\n # Return values. If OD evaluation failed for any reason, return NULL.\n if (is.numeric(output)){\n return(output)\n } else {\n return(NULL)\n\t}\n}\n\nmodel.residuals = function(fitted.well, unlog = F){\n ########################################################################\n # Evaluate model residuals using the measured vs. fitted log.OD values #\n ########################################################################\n\tmeasured.OD = data.from(fitted.well)[,2]\n\n\t# Use with no Time argument to get fitted OD values at measured timepoints.\n\tpredicted.OD = well.eval(fitted.well)\n\n\t# If all values are valid, return the differences\n\tif (!is.numeric(predicted.OD))\n\t\treturn(NA)\n\telse\n return(measured.OD - predicted.OD)\n\t}\n\ndev.from.mean = function(fitted.well){\n ########################################################################\n # Evaluate deviations of log.OD values from the mean #\n ########################################################################\n measured.ODs = data.from(fitted.well,remove=T,na.rm=T)[,2]\n \n # Get the mean values of these measured ODs.\n mean.ODs = mean(measured.ODs)\n \n if (!is.numeric(mean.ODs))\n return (NA)\n else\n return (measured.ODs - mean.ODs)\n}\n\nrss = function(fitted.well){\n #######################################################################\n # Get the residual sum of square. #\n #######################################################################\n if (length(fitted.well@rss) == 0)\n return (NA)\n else\n return (fitted.well@rss)\n}\n\nmodel.good.fit = function(fitted.well, digits = Inf){\n ########################################################################\n # Calculate a metric for fit accuracy using squared residuals #\n ########################################################################\n\n # Sum of squared residuals\n\tRSS = rss(fitted.well)\n \n # Total sum of squared\n tot = sum(dev.from.mean(fitted.well)^2)\n \n # Coefficient of determination\n return (1 - RSS/tot)\n\t}\n\nparameter.text = function(fitted.well){\n ########################################################################\n # Output a string with values of fitted parameters #\n ########################################################################\n \n # Get a list of fitted parameters\n fit.par = fitted.well@fit.par\n \n # Giving the parameter text descriptive names.\n if (length(fitted.well@fit.par) != 0){\n names(fit.par)[1] = \"A\" \n names(fit.par)[2] = \"b\" \n names(fit.par)[3] = \"lambda\" \n names(fit.par)[4] = \"max.spec.growth.rate\" \n \n if (fitted.well@model.name == \"richards sigmoid\"){ \n names(fit.par)[5] = \"shape.par\" \n } \n \n if (fitted.well@model.name == \"richards sigmoid with linear par.\"){ \n names(fit.par)[5] = \"shape.param\" \n names(fit.par)[6] = \"linear term\"\n } \n \n if (fitted.well@model.name == \"logistic sigmoid with linear par.\")\n names(fit.par)[5] = \"linear.term\"\n \n # if loess, just show smoothing param\n if(fitted.well@model.name == \"local polynomial regression fit.\")\n fit.par = fitted.well@fit.par[\"smoothing parameter\"]\n }\n \n # Return nothing if the list is empty. Otherwise, concatenate the terms in the list with the parameter names.\n\tif(!is.list(fit.par))\n\t\treturn()\n else{\n \toutput = \"\"\n \ti = 1\n \twhile(i <= length(fit.par)){\n \t\toutput = paste(output, names(fit.par)[i], \"=\", round(as.numeric(fit.par[i]),3), \"; \", sep = \"\")\n \t\ti = i + 1\n if (i %% 6 == 0)\n output = paste(output, \"\\n\")\n \t\t}\n \toutput\n \t}\n\t}\n\nmax.spec.growth.rate = function(fitted.well, digits = Inf, ...){\n ########################################################################\n # Calculate maximum specific growth rate #\n ########################################################################\n if(length(fitted.well@fit.par) == 0)\n return(NA)\n \n round(fitted.well@fit.par$u,digits)\n}\n\n\nplateau = function(fitted.well, digits = Inf){\n ########################################################################\n # Calculate plateau log.OD from fitted parameters #\n ########################################################################\n if(length(fitted.well@fit.par) == 0)\n return(NA)\n \n plat = fitted.well@fit.par$A + fitted.well@fit.par$b\n \n\tif (!is.numeric(plat)) {\n\t plat = NA\n\t} else {\n plat = round(plat, digits)\n\t}\n\treturn(plat)\n}\n\nbaseline = function(fitted.well, digits = Inf){\n ########################################################################\n # Calculate baseline log.OD from fitted parameters #\n ########################################################################\n if(length(fitted.well@fit.par) == 0)\n return(NA)\n\n base = fitted.well@fit.par$b\n\n # If A (plateau OD) is invalid, return NA.\n\tif (!is.numeric(fitted.well@fit.par$A))\n\t\tbase = NA\n # If b (baseline OD) is invalid but plateau OD was valid, return zero.\n else if (!is.numeric(base))\n\t\tbase = 0\n\telse{\n\t\t base = round(base, digits)\n\t\t}\n\treturn(base)\n\t}\n\ninoc.log.OD = function(fitted.well, digits = Inf){\n ########################################################################\n # Calculate log.OD at inoculation from fitted parameters #\n ########################################################################\n\n # Evaluated the fitted model at the inoculation timepoint (should be zero from using from table2wells.R)\n\tif (is.null(well.eval(fitted.well)))\n\t\treturn(NA)\n else{\n inoc.time = fitted.well@screen.data$Time[fitted.well@start.index]\n inoc.log.OD = well.eval(fitted.well, inoc.time)\n if (is.na(inoc.log.OD)) inoc.log.OD = fitted.well@fit.par$b # need this in a special case: loess fits with start.index = 1 \n return(round(inoc.log.OD, digits))\n }\n\t}\n\nmax.log.OD = function(fitted.well, digits = Inf, ...){\n ########################################################################\n # Calculate max log.OD from model fit #\n ########################################################################\n\n # Evaluated the fitted model at the final timepoint (just the last valid timepoint in the experiment)\n\tif (is.null(well.eval(fitted.well)))\n\t\treturn(NA)\n else{\n \treturn(round(max(well.eval(fitted.well),na.rm=T), digits))\n }\n}\n\n\nprojected.growth = function(fitted.well,digits=Inf) {\n ########################################################################\n # Calculate projected growth: plateau minus the inoculated log.OD #\n ########################################################################\n\tplateau(fitted.well,digits) - inoc.log.OD(fitted.well,digits)\n}\n\nprojected.growth.OD = function(fitted.well,constant.added,digits=Inf) {\n ########################################################################\n # Calculate projected growth: plateau minus the inoculated log.OD #\n ########################################################################\n value = unlog(plateau(fitted.well),constant.added) - unlog(inoc.log.OD(fitted.well),constant.added)\n round(value,digits)\n}\n\n\nachieved.growth = function(fitted.well,digits=Inf) {\n ########################################################################\n # Calculate achieved growth: max.log.OD minus the inoculated log.OD #\n ########################################################################\n max.log.OD(fitted.well,digits) - inoc.log.OD(fitted.well,digits)\n}\n\nachieved.growth.OD = function(fitted.well,constant.added,digits=Inf) {\n ########################################################################\n # Calculate projected growth: plateau minus the inoculated log.OD #\n ########################################################################\n value = unlog(max.log.OD(fitted.well),constant.added) - unlog(inoc.log.OD(fitted.well),constant.added)\n round(value,digits)\n}\n\nreach.plateau = function(fitted.well, cutoff = 0.75){\n ########################################################################\n # Did the curve come close to the plateau OD during the experiment? #\n ########################################################################\n\n plat = plateau(fitted.well)\n inoc = inoc.log.OD(fitted.well)\n final = max.log.OD(fitted.well)\n\n\tif (!is.na(final)){\n # If the plateau is the same as the OD at inoculation, return TRUE\n if ((plat - inoc) == 0)\n return(T)\n # If the difference between the final OD and inoculation OD is at least a certain proportion\n # of the difference between the plateau and inoculated ODs, return TRUE.\n else\n return((final - inoc) / (plat - inoc) > cutoff)\n\t\t}\n\telse\n\t\treturn(T)\n\t\t# If no final OD was calculated (if curve was not fit properly) just return T.\n\t}\n\n\nlag.time = function(fitted.well, digits = Inf, ...){\n ########################################################################\n # Calculate the lag time from the fitted OD #\n ########################################################################\n if(length(fitted.well@fit.par) == 0)\n return(NA)\n \n fitted.well@fit.par$lam\n}\n\n# new params for GCAT 4.0\n\namplitude = function(fitted.well){\n if(length(fitted.well@fit.par) == 0)\n return(NA)\n \n return(fitted.well@fit.par$A)\n}\n\nshape.par = function(fitted.well){\n if(length(fitted.well@fit.par) == 0)\n return(NA)\n ifelse(is.null(fitted.well@fit.par$v), NA, fitted.well@fit.par$v)\n}\n\nmax.spec.growth.rate.SE = function(fitted.well, ...){\n if(length(fitted.well@fit.std.err) == 0)\n return(NA)\n ifelse(is.null(fitted.well@fit.std.err$u), NA, fitted.well@fit.std.err$u)\n}\n\nlag.time.SE = function(fitted.well, ...){\n if(length(fitted.well@fit.std.err) == 0)\n return(NA)\n ifelse(is.null(fitted.well@fit.std.err$lam), NA, fitted.well@fit.std.err$lam)\n}\n\nshape.par.SE = function(fitted.well){\n if(length(fitted.well@fit.std.err) == 0)\n return(NA)\n ifelse(is.null(fitted.well@fit.std.err$v), NA, fitted.well@fit.std.err$v)\n}\n\namplitude.SE = function(fitted.well){\n if(length(fitted.well@fit.std.err) == 0)\n return(NA)\n ifelse(is.null(fitted.well@fit.std.err$A), NA, fitted.well@fit.std.err$A)\n}\n\nbaseline.SE = function(fitted.well){\n if(length(fitted.well@fit.std.err) == 0)\n return(NA)\n ifelse(is.null(fitted.well@fit.std.err$b), NA, fitted.well@fit.std.err$b)\n}\n\n# used to calulate the inflection.time value\ninflection.time = function(well){\n if (length(well@loess) == 0 && length(well@nls) == 0) return(NA) # can' compute inflection time in the absence of a fit\n data = data.from(well)\n Time = data[,1]\n t = seq(from = min(Time), to = max(Time), by = (max(Time)-min(Time))/1000)\n y = well.eval(well,t)\n if (is.null(y)) return(NA)\n delta.t = diff(t)\n dydt = diff(y)/delta.t\n infl.index = which.max(dydt)\n t[infl.index]\n}\n", - "created" : 1425413281936.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "2757150562", - "id" : "26C12555", - "lastKnownWriteTime" : 1428437531, - "path" : "~/Documents/GCAT4/trunk/R/GCAT/R/fitted.calculations.R", - "project_path" : "R/fitted.calculations.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/2C8FAF10 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/2C8FAF10 deleted file mode 100644 index 2aeaf02..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/2C8FAF10 +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n\nrequire(pheatmap)\nrequire(gplots)\n\n########################################################################\n# #\n# Graphic output functions for fitted well objects. The functions are #\n# fairly complicated and intertwined and may need revision. #\n# #\n########################################################################\n\n# S3 Generic.\nplot <- function(input.well, ...) {\n UseMethod(\"plot\")\n}\n\n########################################################################\n# Basic function plots time vs. OD from a well object #\n########################################################################\n#' plot.data\n#'\n#' Basic function plots time vs. OD from a well object\n#'\n#' @param input.well The well object that need to be plottedd\n#' @param unlog should data be plotted on a linear (vs. logarithmic) scale?\n#' @param view.raw.data should the raw data be plotted? (\n#' @param number.points should points be labeled with numeric indices?\n#' @param scale determines the font scale for the entire graph. all cex values are calculated from this.\n#' @param draw.symbols - should be called on the well and markings drawn on the graph?\n#' @param ... additional arguments passed to plot()\nplot.data = function(input.well, view.raw.data = F, unlog = F, scale = 1, \n main = paste(plate.name(input.well), well.name(input.well)), number.points = T, \n draw.symbols = F, constant.added, ylim, ...){\n \n # Get data as well as a vector showing which points were removed. \n\tinput.data = data.from(input.well, remove = F, remove.tanking = F, raw.data=view.raw.data)\n\tremoved.points = !(rownames(input.data) %in% rownames(data.from(input.well, remove = T, remove.tanking = T)))\n point.colors = as.character(factor(removed.points,levels=c(F,T),labels=c(\"black\",\"gray80\")))\n\n # Draw the axes and all text labels first.\n\tpar(mar = c(5, 4, 4, 5)+0.1)\n\tplot(input.data, main = main, xlab = \"Time(hours)\", ylab = \"log(OD - blank + const)\",\n mex = scale, cex.main = 1.5*scale, cex.axis = 1.2*scale, cex.lab = 1.2*scale, type =\"n\",...)\n \n\t# Draw a second vertical axis, showing unlogged OD scale\n\t# - Determine the range of the labels: from min.OD to max.OD\n if (class(try(ylim,silent=T)) == \"try-error\") {\n OD = unlog(input.data[,2],constant.added)\n baseline.OD = unlog(baseline(input.well),constant.added)\n min.OD = min(min(OD,na.rm=T),baseline.OD,na.rm=T)\n plateau.OD = unlog(plateau(input.well),constant.added)\n max.OD = max(max(OD,na.rm=T),plateau.OD,na.rm=T)\n } else {\n min.OD = unlog(ylim[1],constant.added)\n max.OD = unlog(ylim[2],constant.added)\n }\n\t# - Compute labels and their positions\n\tOD.labels = seq(from = min.OD, to = max.OD, length.out = 5)\n\tOD.labels = signif(OD.labels,2)\n\tOD.at = log(OD.labels+constant.added)\n # - Draw the axis\n\taxis(side=4, at=OD.at, labels=OD.labels, cex.axis = 1.2*scale, cex.lab = 1.2*scale)\n\tmtext(4, text = \"OD - blank\", line = 3, cex=1.2)\n \n\t# If is true, then label each point with the index of its timepoint and plot removed points in grey, others in black. \n if (number.points)\n\t\ttext(input.data$Time, input.data[,2], rownames(input.data), col = point.colors, cex = 0.5*scale)\n\t# Otherwise plot all points, using a different plotting character for removed points. \t\n else\n\t\tpoints(input.data$Time, input.data[,2], pch = 1 + removed.points*15)\n\n # If is set to T, then draw all the markings that makes to determine curve parameters. \n\tif (draw.symbols & !view.raw.data)\n\t\tcheck.slopes(input.well, draw = T)\n\treturn()\n\t}\n\t\n########################################################################\n# Plots the fitted model curve from a well object if it exists #\n########################################################################\n#\n# time: specify which points (in units of time) to plot fitted OD values for. if not specifies, plot all timepoints in range of well. \n\nplot.model = function(input.well, col = 1, scale = 1, lty = 1, time = NULL, unlog = F, constant.added=1, ...){\n\t \n #input.data = data.from(input.well)\n\t#growth = input.data[,2]\n\n # If no list of timepoints is specified, get a list of 360 timepoints (should be smooth enough) from the well's range. \n\tif (is.null(time)){\n\t\ttime.fin = max(data.from(input.well, raw.data = T, remove = F, remove.tanking = F)$Time)\n\t\ttime = seq(0, time.fin, length.out = 360)\n\t}\n \n # Evaluate the predicted OD at the specified timepoints based on the fitted model. \n\tpredicted.OD = well.eval(input.well, time) \n # If any values were returned, plot the lines on the current graph. Otherwise, just return without doing anything.\n\tif (is.numeric(predicted.OD))\n\t\tlines(time, predicted.OD, col = col, lty = lty, lw = 2 * scale) \n else\n return()\t\n \n}\n\t\n########################################################################\n# Put various parameters and info in text form on the graphs #\n########################################################################\n#\t\t\t\ndraw.text = function(input.well, scale = 0.5, xlim = 0, ylim = 0,...){\n\n\t#input.data = data.from(input.well, remove = F, remove.tanking = F)\n\t#fit = input.well@fit.par\n \n # - fit information (fit status, model name if available, jump detection output, fit parameters if available) from well \n # color = red if no fit, blue if fit, green if skipped\n # - empty or inoculated well.\n # color = green if empty, blue if inoculated, red if inoculated but has no growth or empty but has growth. \n \n \tcol2 = \"blue\" \n\ttext2 = paste(input.well@fit.info, input.well@model.name, input.well@add.info, \"\\n\", parameter.text(input.well))\n\n\tif (length(input.well@fit.par) == 0) # no fit\n\t\tcol2 = \"red\"\n\n\tif (is.empty(input.well)){\n\t\t text1 = \"empty well\"\n\t\tif(!lacks.growth(input.well) | length(input.well@fit.par) == 0) # growth curve fit for an empty well\n\t\t\tcol1 = \"red\"\n\t\telse\n\t\t\tcol1 = \"forestgreen\"\n\t\tif (length(input.well@model.name) == 0) # well was skipped \n\t\t\tcol1 = col2 = \"forestgreen\"\n\t\t}\n\telse{\n\t\ttext1 = \"inoculated well\"\n\t\tif(lacks.growth(input.well) | length(input.well@fit.par) == 0) # failure to fit an inoculated well\n\t\t\tcol1 = \"red\"\n\t\telse\n\t\t\tcol1 = \"forestgreen\"\n\t\t}\n\t\t\n\t# - goodness of fit metric. \n\t# color = red if below 2, yellow if between 2 and 2.72, and green if above 2.72. \n\t\n\tif(!is.na(model.good.fit(input.well))){\n\t\t#if (model.good.fit(input.well, unlog = F) > 2.72)\n\t\t#\tcol1.5 = \"forestgreen\"\n\t\t#else if (model.good.fit(input.well, unlog = F)> 2.0)\n\t\t#\tcol1.5 = \"gold2\"\n\t\t#else\n\t\t#\tcol1.5 = \"red\"\n col1.5 = \"forestgreen\"\n\t\ttext1.5 = paste(\"R squared:\", round(model.good.fit(input.well),3))\n\t\t}\n\telse\n\t col1.5 = text1.5 = NULL\n\t \n # Print all text at the top of the graph with approprate positions and scaling \t\n \ttext(x = xlim[1] + 0.50 * diff(xlim), y = ylim[2] - 0.025 * diff(ylim), \n \t\ttext1.5, cex = 1.5*scale, col = col1.5) \n \t\t\n\ttext(x = xlim[1] + 0.50 * diff(xlim), y = ylim[2] - 0 * diff(ylim), \n\t\t\ttext1, cex = 1.5*scale, col = col1)\n\n\ttext(x = xlim[1] + 0.50 * diff(xlim), y = ylim[2] - 0.03 * diff(ylim), \n\t\t\ttext2, pos = 1, cex = 1.5*scale, col = col2)\t\n\t}\t\n\n########################################################################\n# Draw lines on graph denoting calculated parameters #\n########################################################################\n#\t\n# - should curve parameters be labeled? \n\t\t\ndraw.calc.par = function(input.well, scale = 0.5, unlog = F, constant.added, show.num = T){\n\n # Don't do anything if well was not fit. \n\tif (is.null(well.eval(input.well)))\n\t\treturn()\n \n # Collect values for various curve parameters. \n\tbaseline = baseline(input.well)\n\tinoc.log.OD = inoc.log.OD(input.well)\n\tmax.log.OD = max.log.OD(input.well) \n\tplateau = plateau(input.well) \n\tinflection.time = input.well@inflection.time # was a param in model\n\tfin.time = (inflection.time+max(data.from(input.well)[,1]))/2\n\n\t# = timepoint at greatest growth \n\t# = OD measurement at , minus the constant added before taking the log (if reversing the transformation)\n\t# = slope (on log scale) at (specific growth)\n # had to add the unlog code. was calculated differently before NWD 7/21/14\n\tmax.slope = max.spec.growth.rate(input.well)\n\tmax.y = well.eval(input.well, inflection.time)\n\tlag.x = lag.time(input.well) \n lag.y = baseline\n\t\n\t# ---- Specific growth rate ---- #\n\tlines(c(lag.x, inflection.time), c(lag.y, max.y), lty = 2, col = \"red\")\n\n\n # Blue dotted line at time of maximum growth, with text label for specific growth rate. \n\tabline(v = inflection.time, lty = 2, lw = (scale^2)*2, col = \"blue\")\n if(show.num) text(inflection.time, max.y, round(max.slope,3), col = \"blue\", cex = 1.5*scale, pos = 2)\n\n # inoculation OD and baseline of the fitted model\n abline(h = inoc.log.OD, lw = scale*2, lty = 3)\n abline(h = baseline, col = \"red\", lw = (scale^2)*2, lty = 2)\n if(show.num) {\n text(fin.time, inoc.log.OD, paste(round(inoc.log.OD,3),\"\\n\",sep=\"\") , col = \"black\", cex = 1.5*scale, pos = 2)\n text(fin.time, baseline, paste(\"\\n\\n\", round(baseline,3), sep=\"\") , col = \"red\", cex = 1.5*scale, pos = 2)\n }\n\n # ---- Lag time ---- #\n # Do not draw a horizontal line to lag time if it is 0 or negative. \n # Otherwise draw a red line from the starting point to the lag time, and label with the lag time \n \tif (lag.time(input.well) == 0){\n\t\tif(show.num) text(0, inoc.log.OD, \"\\n\\n0.000\", col = \"red\", cex = 1.5*scale, pos = 4)\n\t\t}\n\telse{\n\t\tlines(c(0, lag.x), c(baseline, baseline), col = \"red\", lw = (scale^2)*2, lty = 2)\n\t\tif(show.num) text(lag.x, lag.y, paste(\"\\n\\n\", round(lag.time(input.well),3)), col = \"red\", cex = 1.5*scale, pos = 2)\n\t}\n\n # ---- Total growth ---- #\n\n # Draw horizontal lines for the max.log.OD in black, the plateau in green and the initial OD in black.\n abline(h = max.log.OD, lty = 3, lw = scale*2)\n abline(h = plateau, lty = 2, lw = (scale^2)*2, col = \"forestgreen\")\n\t\n\t# Draw a vertical line from the initial OD to the final OD in black, and then to the plateau in gray. \n\tlines(c(fin.time, fin.time), c(inoc.log.OD, max.log.OD), lw = (scale^2)*2, lty = 3)\n\tlines(c(fin.time, fin.time), c(max.log.OD, plateau), lw = (scale^2)*2, lty = 3, col = \"grey\")\n\n # Text: plateau and initial ODs (on left), difference between initial and final OD on right\n\tif(show.num){\n text(fin.time, plateau, paste(round(plateau,3),\"\\n\",sep=\"\") , col = \"forestgreen\", cex = 1.5*scale, pos = 2)\n text(fin.time, max.log.OD, paste(\"\\n\\n\\n\",round(max.log.OD,3),sep=\"\") , col = \"black\", cex = 1.5*scale, pos = 2)\n text(fin.time, .5*(max.log.OD-inoc.log.OD)+inoc.log.OD, round(max.log.OD - inoc.log.OD,3), cex = 1.5*scale, pos = 4)\n # difference between final and plateau OD (if large enough) \n if (!reach.plateau(input.well))\n\t\t text(fin.time, .5*(plateau-max.log.OD)+max.log.OD, paste(\"(\", round(plateau - max.log.OD,3), \")\", sep = \"\"), col = \"grey\", cex = 1.5*scale, pos = 2) \n }\n }\n\t\n########################################################################\n# Draw residuals from the nonlinear fit with option for lowess line #\n########################################################################\n#\t\t\nplot.residuals = function(input.well, xlim = NULL, lowess = T, ...){\n well = input.well\n\tdata = data.from(well, remove = F, remove.tanking = F)\n\n\tif (is.null(xlim))\n\t\txlim = c(min(data$Time, 0)-1, max(data$Time))\n\t\t\n\tplot(data.from(well)[,1], model.residuals(well), main = paste(plate.name(well), well.name(well), \"\\n[Residuals]\"),\n\t\txlab = \"Time(hours)\", ylab = paste(\"Residual\", names(data)[2]), xlim = xlim)\n\t\n\tabline(0,0, lty = 2)\n\t\n\tif (lowess)\n\t\tlines(lowess(data.from(well)[,1], model.residuals(well)), lw = 2, col = \"red\")\n\t}\n\n##############################################################################\n# This function is used to create a heatmap using: \n# specific growth, total growth, and lag time\n# for each well on a plate.\n#\n# @params\n# fitted.well.array: matrix containing well array object data\n# attribute: the data type we should use to create a heatmap\n# @returns\n# path of heatmap pdf file\n##############################################################################\ncreate.heatmap = function(fitted.well.array, attribute, unlog=NULL){\n attr.name <- deparse(substitute(attribute))\n pdf.name <- \"\"\n if(class(fitted.well.array) == \"matrix\"){\n #We may want to sub() out periods from plate.ID if it causes problems\n plate.ID = unique(unlist(aapply(fitted.well.array,plate.name)))[1]\n if(is.null(unlog)) {\n spec.growth = unlist(aapply(fitted.well.array, attribute))\n }\n # currently only total growth needs to be unlogged if unlog == T\n else {\n spec.growth = unlist(aapply(fitted.well.array, attribute))\n }\n num.dig = 3 #how many digits should be put on pdf?\n max = round(max(spec.growth, na.rm=T), digits=num.dig)\n min = round(min(spec.growth, na.rm=T), digits=num.dig)\n avg = round(mean(spec.growth, na.rm=T), digits=num.dig)\n heat.text = paste(toupper(sub(\"\\\\.\", \" \", attr.name)), \":\\n\", plate.ID, \"\\n\",\n paste(\"Max:\",max ,\"Min:\" ,min ,\"Avg:\", avg, sep=\"\"))\n \n attr.name <- sub(\"\\\\.\", \"_\", attr.name) #do not want periods in file path\n letters <- attr(fitted.well.array, \"dimnames\")[[1]]\n for(i in 1:length(letters)) letters[i] = paste(\" \", letters[i], \" \")\n nums <- attr(fitted.well.array, \"dimnames\")[[2]]\n for(i in 1:length(nums)) nums[i] = paste(\" \", nums[i], \" \")\n heat <- matrix(spec.growth, nrow=dim(fitted.well.array)[1], ncol=dim(fitted.well.array)[2], dimnames=list(letters,nums))\n pdf.name <- paste(getwd(), \"/\", plate.ID, \"_\", attr.name, \".pdf\", sep=\"\")\n pdf(pdf.name)\n #heatmap(heat, Rowv=NA, Colv=NA, revC=T, scale=\"none\", na.rm=T, main=plate.ID, col=rainbow(100), margins=c(6,6))\n #mtext(paste(\"Max:\", round(max(spec.growth, na.rm=T), digits=4),\"Min:\", round(min(spec.growth, na.rm=T), digits=4), \"Avg:\", round(mean(spec.growth, na.rm=T), digits=4)), side=1, line=3)\n pheatmap(heat, color=colorpanel(100, \"red\", \"orange\", \"yellow\"),\n border_color=\"black\", cell_width=2, cell_height=3,\n cluster_rows=F, cluster_cols=F, scale='none', main=heat.text, fontsize=16)\n dev.off()\n }\n else {\n return(\"Error\") \n }\n return(pdf.name)\n}\n\n########################################################################\n# Draw grids of 96 points as a visual representation of fit status, #\n# and other info for an array of fitted well objects, plate by plate #\n########################################################################\n#\n\t\nplate.overview = function(fitted.well.array, scale = 1, plate.ncol = 12, plate.nrow = 8){\n \n \n # Start with a list of the unique plate names in the fitted well array \n # and an appropriately-sized grid of coordinates to plot wells on.\n\tplates = unique(unlist(aapply(fitted.well.array,plate.name)))\n \n\tgrid = data.frame(x = rep(rep(1:plate.ncol, each = plate.nrow), length(plates)),\n\t\t\t y = rep( rep(-(1:plate.nrow), times = plate.ncol), length(plates)))\n\n\n # Gather information on each well to display on each of the coordinates in :\n # - was it marked as empty in the plate layout?\n # - did the program find it to contain no growth (\"dead\")? \n # - was the fitting procedure successful? \n # - did the curve tank? if so, at what timepoint? if not, or if the curve was marked as dead anyway, do not display the value. \n # - does the \"additional info\" slot indicate that any points were removed or the whole well discarded?\n \n\tempty = unlist(aapply(fitted.well.array, is.empty))\n\tdead = unlist(aapply(fitted.well.array, lacks.growth))\n\tfit = unlist(aapply(fitted.well.array, contains.fit))\n \n\ttanking = unlist(aapply(fitted.well.array, tanking.start))\n\ttanking[is.na(tanking) | tanking == 1 | dead] = \"\"\n\n\terrors = unlist(aapply(fitted.well.array, function(well){\n\t\tif (length(well@add.info) == 0)\n\t\t\t\"\"\n\t\telse if (grepl(\"removed\", well@add.info))\n\t\t\t\"-\"\n else if (grepl(\"detected\", well@add.info))\n \"+\"\n\t\telse if (grepl(\"discarded\", well@add.info))\n\t\t\t\"!\"\n\t\telse\n\t\t\t\"\"\n\t\t}))\n\t\n # Color and plotting character vectors (length = the number of wells in the array)\n # Default = 1 (open point, black)\n\tcolors = char = rep(1, length(tanking))\n\n # Desired colors\n colors[empty & dead] = \"green3\" # Empty well with no growth.\n colors[!empty & fit] = \"blue\" # Inoculated well with successfully fitted growth curve.\n \n # Undesired colors \n colors[empty & !dead] = \"darkolivegreen4\" # Inoculated well with some growth. \n colors[!empty & !fit] = \"red\" # Inoculated well with no successfully fit (either no growth or unsuccessful fit).\n \n char[!dead & fit] = 19 # Filled points for non-empty wells with successful fits \n char[!dead & !fit] = 4 # an X for non-empty wells with failed fits. \n \n char[errors == \"!\"] = 8 # Asterisk for discarded wells. \n char[errors == \"-\" & dead ] = 5 # Open diamond for empty wells (after removing points).\n char[errors == \"-\" & !dead & fit] = 23 # Filled diamond for non-empty wells with removed points and successful fits. \n char[errors == \"-\" & !dead & !fit] = 8 # Asterisk for wells with removed points and failed fits.\n \n \n\tfor (plate in 1:length(plates)){\n \n\t\tindices = (plate - 1) * plate.nrow*plate.ncol + 1:(plate.nrow*plate.ncol)\n\n # Plot the grid using colors and plotting characters determined above. \n\t\tplot(grid[indices,], col = colors[indices], bg = colors[indices], pch = char[indices], \n\t\t\t main = plates[plate], mex = scale, cex = scale, cex.main = 1.5*scale, cex.axis = 1.2*scale, \n\t\t\t xaxt = \"n\", yaxt = \"n\", xlim = c(-0.5,plate.ncol + 0.5), ylim = c(-(plate.nrow + 1.5), 0.5), xlab = \"\", ylab = \"\")\n \n # Symbol legends\n \n legend.xpos = (c(-1,2.75,6.5,6.86,10.25)+0.5)*(plate.ncol+1)/13 - 0.5\n legend.ypos = -(plate.nrow + 0.5)\n \n legend(x=legend.xpos[1], y= legend.ypos, cex = 0.7 * scale, y.intersp = 1.5, bty=\"n\", \n legend=c(\"Empty, no growth\",\"Empty with growth\"),\n pch = c(1,19),\n pt.bg = c(\"green3\",\"darkolivegreen4\"),\n col = c(\"green3\",\"darkolivegreen4\")\n )\n legend(x=legend.xpos[2], y= legend.ypos, cex = 0.7 * scale, y.intersp = 1.5, bty=\"n\", \n legend=c(\"Inoculated with growth\", \"Inoculated, no growth\"),\n pch = c(19,1),\n pt.bg = c(\"blue\",\"red\"),\n col = c(\"blue\",\"red\")\n )\n legend(x=legend.xpos[3], y= legend.ypos, cex = 0.7 * scale, y.intersp = 1.5, bty=\"n\", \n legend=c(\"Well tanks at specified index\", \"Some points removed\"),\n pch = c(21,23),\n pt.bg = c(\"grey\",\"grey\"),\n col = c(\"black\",\"black\")\n ) \n \n text(x=legend.xpos[4], y=legend.ypos - 0.29,\"#\",cex=0.5*scale) \n \n legend(x=legend.xpos[5], y=legend.ypos, cex = 0.7 * scale, y.intersp = 1.5, bty=\"n\", \n legend=c(\"Model fitting failed\", \"Well discarded\"),\n pch = c(4,8),\n pt.bg = c(\"black\",\"black\"),\n col = c(\"black\",\"black\")\n )\n \n # Add tanking indices if any were found. \n \ttext(grid[indices,] + 0.30, cex = 0.75*scale, \n labels = tanking[indices], col = colors[indices])\n\n # Label rows and columns\n\t\ttext(-1, -1:-plate.nrow, pos = 4, LETTERS[1:plate.nrow], cex = scale) \n\t\ttext( 1:plate.ncol, 0 , 1:plate.ncol, cex = scale) \t\n\t\t}\n \n\t}\n\n########################################################################\n# Draw each well in an array of fitted well objects in succession. #\n# Include options for adding notations, text info and fit parameters. #\n########################################################################\n#\n\nview.fit = function(fitted.data, indices = 1:length(fitted.data), \n unlog = F, constant.added, xlim = NULL, ylim = NULL, display.legend = T, \n\t\t show.text = T, show.calc = T, draw.guess = NULL, draw.symbols = F, number.points = T, \n\t\t\tuser.advance = T, show.residuals = F, scale = 1,...){\n\n if(!is.array(fitted.data))\n fitted.data = list(fitted.data)\n\n # Determine the boundaries for the axes (if user did not specify them)\n if(is.null(ylim)){\n min.y = min(unlist(aapply(fitted.data, function(well){\n \tif (unlog) well@use.log = F\n \tmin.y = min(data.from(well, remove = F, remove.tanking = F)[,2], na.rm = T)\n min(min.y, well@fit.par$b)\n \t})))\n max.y = max(unlist(aapply(fitted.data, function(well){\n if (unlog) well@use.log = F\n \tmax.y = max(data.from(well, remove = F, remove.tanking = F)[,2], na.rm = T)\n max(max.y, well@fit.par$b + well@fit.par$A)\n \t})))\n ylim = c(min.y, min.y + (max.y-min.y)*1.15) - unlog*constant.added\n }\n if(is.null(xlim)){\n min.x = min(unlist(aapply(fitted.data, function(well){\n min(data.from(well, remove = F, remove.tanking = F)[,1], na.rm = T)\n \t})))\n max.x = max(unlist(aapply(fitted.data, function(well){\n \tmax(data.from(well, remove = F, remove.tanking = F)[,1], na.rm = T)\n \t})))\n xlim = c(min.x - 0.05 * (max.x-min.x), max.x)\n }\n \n # Display a figure legend\n if(display.legend){\n well.fit.legend(xlim=xlim,ylim=ylim,scale=scale,constant.added=constant.added)\n if(user.advance){\n prompt = readline(\" to continue or Q to quit >>\")\n if (toupper(prompt) == \"Q\") break\n }\n }\n # Start to cycle through the wells \n\twell.number = 1\n\twhile (well.number <= length(fitted.data)) {\t\t\n\t\t# Only show wells specified by (default all wells)\n if (well.number %in% indices){ \n # plot the well\n fitted.well = fitted.data[[well.number]]\n plot(x=fitted.well, constant.added = constant.added, xlim = xlim, ylim = ylim,\n unlog = unlog, well.number = well.number, scale = scale, number.points = T, draw.symbols = F, show.text = T, show.calc = T, draw.guess = NULL, ...)\n \n if(user.advance)\n cat(\"\\n[\", well.number, \"] \", plate.name(fitted.well), \" \", well.name(fitted.well), \".\", sep = \"\")\n \n if (show.residuals & is.numeric(model.residuals(fitted.well))){\n if(user.advance)\n if (toupper(readline(\" for residuals >>\")) == \"Q\") break\n plot.residuals(fitted.well)\n }\n \n # Allow user to advance the currently shown well if specified. \n\t\t\tif (user.advance){\n \n\t\t\t\tprompt = readline(\" to continue, or type # of next well or Q to quit >>\")\n\t\t\t\tif (toupper(prompt) == \"Q\") break\n\n user.input = suppressWarnings(try(as.numeric(prompt),silent=T))\n \n # Go onto the next well unless input is a number. \n\t\t\t\tif (is.numeric(user.input) & !is.na(user.input) & length(user.input) > 0)\n\t\t\t\t\twell.number = user.input - 1\n\t\t\t }\n\t\t\t}\n # Advance the loop\n well.number = well.number + 1\n\t\t}\t\t\n\t}\t\n\n\nwell.fit.legend = function(xlim, ylim, scale = 1, constant.added){\n par(mar = c(5, 4, 4, 5)+0.1)\n plot(0,0, main = \"[Index] \\n; \",\n xlim = xlim, ylim = ylim, xlab = \"Time\", ylab = \"log(OD - blank + const)\", \n mex = scale, cex.main = 1.5*scale, cex.axis = 1.2*scale, cex.lab = 1.2*scale, type = \"n\")\n \n # Draw a second vertical axis, showing unlogged OD scale\n min.OD = unlog(ylim[1],constant.added)\n max.OD = unlog(ylim[2],constant.added)\n OD.labels = seq(from = min.OD, to = max.OD, length.out = 5)\n OD.labels = round(OD.labels,1)\n OD.at = log(OD.labels+constant.added)\n axis(side=4, at=OD.at, labels=OD.labels, cex.axis = 1.2*scale, cex.lab = 1.2*scale)\n mtext(4, text = \"OD - blank\", line = 3, cex=1.2)\n \n # Sample max. slope line\n abline(v=min(xlim)+0.5*max(xlim), col=\"blue\", lty=2)\n text(mean(xlim),min(ylim)+0.4*diff(ylim),labels=\"Maximum specific\\ngrowth rate\",col=\"blue\",pos=2,cex=0.75*scale)\n \n # Sample plateau line\n abline(h=min(ylim)+0.8*diff(ylim),col=\"forestgreen\",lty=2)\n text(min(xlim)+0.9*diff(xlim),ylim+0.8*diff(ylim),labels=\"Growth plateau\",col=\"forestgreen\",pos=3,cex=0.75*scale)\n\n # Sample max.log.OD line\n abline(h=min(ylim)+0.7*diff(ylim),col=\"black\",lty=3)\n text(min(xlim)+0.9*diff(xlim),ylim+0.7*diff(ylim),labels=\"max.log.OD\",col=\"black\",pos=1,cex=0.75*scale)\n \n # Sample inoc.log.OD\n abline(h=min(ylim)+0.1*diff(ylim),col=\"black\",lty=3)\n text(min(xlim)+0.1*diff(xlim),min(ylim)+0.1*diff(ylim),labels=\"Fitted growth\\nat inoculation\",col=\"black\",pos=3,cex=0.75*scale)\n \n # Sample baseline\n abline(h=min(ylim)+0.05*diff(ylim),col=\"red\",lty=2)\n text(min(xlim)+0.1*diff(xlim),min(ylim)+0.05*diff(ylim),labels=\"Baseline\",col=\"red\",pos=1,cex=0.75*scale)\n\n # Sample lag time\n lines(min(xlim)+c(0.1,0.25,0.50)*max(xlim),min(ylim)+c(0.05,0.05,0.4)*diff(ylim),col=\"red\",lty=2)\n text(min(xlim)+0.25*max(xlim),min(ylim)+0.05*diff(ylim),labels=\"Lag time\",col=\"red\",pos=1,cex=0.75*scale)\n \n # Sample achieved growth\n lines(min(xlim)+c(0.75,0.75)*max(xlim),min(ylim)+c(0.1,0.7)*diff(ylim),col=\"black\",lty=3)\n text(min(xlim)+0.75*max(xlim),min(ylim)+0.3*diff(ylim),labels=\"Achieved growth\",col=\"black\",cex=0.75*scale)\n \n # Sample plateau - achieved growth\n lines(min(xlim)+c(0.75,0.75)*max(xlim),min(ylim)+c(0.7,0.8)*diff(ylim),col=\"grey\",lty=3)\n text(min(xlim)+0.75*max(xlim),min(ylim)+0.75*diff(ylim),labels=\"Projected minus achieved growth\",col=\"grey\",cex=0.75*scale)\n \n # Symbol legend\n legend(x=\"right\", title = \"Timepoint Symbols\", legend = c(\"Normal point\", \"Ignored point\"),\n cex = 0.75*scale, pt.cex = c(0.6,0.6)*scale, pch = c(35,35), col=c(\"black\",\"gray80\"),\n x.intersp=1, xjust = 1, y.intersp=1.5)\n}\n\npdf.by.plate = function(fitted.data, out.prefix = \"\", upload.timestamp = NULL, \n out.dir = getwd(), unlog = F, constant.added, silent = T, overview.jpgs = T, plate.ncol = 12, plate.nrow = 8,...){\n \n # Prepare timestamp for addition to output file names. \n filename.timestamp = strftime(upload.timestamp, format=\"_%Y-%m-%d_%H.%M.%S\")\n \n # Start file list with the overview pdf\n file.list.out = paste(out.dir,\"/\",out.prefix, \"_overview\", filename.timestamp, \".pdf\",sep=\"\")\n \n # Call to draw a graphic representation of each plate in this file. \n pdf(file.list.out, title = paste(out.prefix, \"plate overview\"))\n plate.overview.out = try(plate.overview(fitted.data),silent=T)\n if(class(plate.overview.out) == \"try-error\")\n stop(\"Error in : \", plate.overview.out)\n \n # Close devices\n while(dev.cur() != 1)\n dev.off() \n \n # Cycle through each plate \n for(i in 1:dim(fitted.data)[3]){\n \n # Get plate ID and position in data array.\n plate.ID = dimnames(fitted.data)[[3]][i]\n plate.indices = (i-1) * plate.nrow*plate.ncol + 1:(plate.nrow*plate.ncol)\n if(overview.jpgs){\n # most be > 1 to partition value breaks for heatmap\n well.matrix <- aapply(fitted.data[,,i], max.spec.growth.rate) \n num.wells <- length(well.matrix[!sapply(well.matrix, is.na)])\n if(num.wells > 1){\n #Heatmap block##########################################################\n #alongside the jpgs file create 3 heatmaps for each plate. NWD\n spec.heat.file = create.heatmap(fitted.data[,,i], max.spec.growth.rate)\n if(spec.heat.file == \"Error\")\n stop(\"Error in for specific growth\")\n lag.heat.file = create.heatmap(fitted.data[,,i], lag.time)\n if(lag.heat.file == \"Error\")\n stop(\"Error in for lag time\")\n total.heat.file = create.heatmap(fitted.data[,,i], achieved.growth)\n if(total.heat.file == \"Error\")\n stop(\"Error in for total growth\")\n # Add name of file if successfully written to file list output. Including heatmap files NWD\n file.list.out = c(file.list.out, spec.heat.file, lag.heat.file, total.heat.file)\n ########################################################################\n }\n jpg.name = paste(out.dir, \"/\", plate.ID, \"_overview\", \".jpg\", sep=\"\")\n jpeg(jpg.name, quality = 90, width = 600, height = 480)\n plate.overview.out = try(plate.overview(fitted.data[,,i]),silent = T)\n if(class(plate.overview.out) == \"try-error\")\n stop(\"Error in : \", plate.overview.out)\n }\n else\n jpg.name = c()\n \n # Open a separate PDF for each plate.\n if(!silent) cat(\"\\nprinting PDF for\", plate.ID)\n pdf.name = paste(out.dir, \"/\", plate.ID, \"_plots\", filename.timestamp, \".pdf\", sep=\"\")\n pdf(pdf.name, title = paste(\"R Graphics output for plate\", plate.ID))\n \n # Call to draw each well on the plate to the pdf. \n view.fit.out = try(view.fit(fitted.data, indices = plate.indices, unlog=unlog, constant.added=constant.added, user.advance=F,...),silent=T) \n \n if(class(view.fit.out) == \"try-error\")\n stop(\"Error in : \", view.fit.out)\n\n # Close all devices\n while(dev.cur() != 1)\n dev.off() \n \n if(!silent) cat(\"...done!\\n\\twritten to\", pdf.name, \"\\n\") \n file.list.out = c(file.list.out, jpg.name , pdf.name)\n }\n return(file.list.out)\n } \n", - "created" : 1425413258441.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "1576748553", - "id" : "2C8FAF10", - "lastKnownWriteTime" : 1428438949, - "path" : "~/Documents/GCAT4/trunk/R/GCAT/R/plot.fit.R", - "project_path" : "R/plot.fit.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/2FF709FD b/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/2FF709FD deleted file mode 100644 index 577cdb9..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/2FF709FD +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n\n# Notes by Jason\n# 9/07/11\n\n\n########################################################################\n# #\n# Function for loading data from tabular format into an object array #\n# #\n########################################################################\n#' Load tabular data\n#'\n#' This function handles loading data from tabular format (.csv, tab-delimited text or R data frame object)\n#' and returns an array of well objects, each filled with raw Time vs. OD data. \n#' It takes single-plate or multiple-plate format data. For single-plate data, \n#'it calls on the function \\code{gcat.reorganize.single.plate.data} to rearrange the table before creating the output object. \n#'\n#' @param file.name Complete path and file name of a comma-separated values (.csv) file containing growth curve data \n#' in the multiple-plate (long) format. \n#' @param input.data A list of tables representing input files read with \\code{read.table}. Used to save time in cases\n#' of running multiple analyses on the same dataset. If used, the function will ignore \\code{file.name} entirely.\n#' @param load.type .csv by default. \n#' @param plate.laout Specifies the layout of the given plate.\n#' @param single.plate.ID specifies a plate name for a single-plate read. If NULL, this is derived from the file name. \n#' @param blank.value Blank OD measurement for uninoculated wells. By default(NULL), the value of the first OD\n#' measurement in each well is used.\n#' @param add.constant A value for r in the log(OD + r) transformation.\n#' @param plate.nrow The number of rows in the input files.\n#' @param plate.ncol The number of columns in the input files.\n#' @param input.skip.lines specifies a plate name for a single-plate read. If NULL, this is derived from the file name. \n#' @param multi.column.headers The headers of the column when analyzing multiple plates.\n#' @param single.column.headers The headers of the column when analyzing a single plate.\n#' @param layout.sheet.headers The headers of the layout file.\n#' @param silent Surpress all messages.\n#' @param verbose Display all messages when analyzing each well.\n#' \n#' @return A list of well objects.\ngcat.load.data = function(file.name = NULL, load.type = \"csv\", input.data = NULL, single.plate.ID = NULL, \n plate.layout = NULL,plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,\n multi.column.headers = c(\"Plate.ID\", \"Well\", \"OD\", \"Time\"), single.column.headers = c(\"\",\"A1\"), \n layout.sheet.headers = c(\"Strain\", \"Media Definition\"),\n blank.value = NULL, start.index = 2, single.plate = F, silent = T){\n\n ########################################################################\n # Read from .csv, tab-delimited text file or data frame object #\n ########################################################################\n \n\tif(is.null(input.data)){\n\t\t# Either read from .csv.\n\t\tinput.data = read.csv(file.name, stringsAsFactors=F, skip = input.skip.lines, fileEncoding='UTF-8')\n\n\t\t# Determine single plate name if not specified. \n if (is.null(single.plate.ID)){\n # Split the file name by \".\" and discard the last member (file extension). \n single.plate.ID = strsplit(basename(file.name),\"\\\\.\")[[1]]\n single.plate.ID = paste(single.plate.ID[-length(single.plate.ID)],collapse=\".\")\n }\n\t\t}\n\n # Call to arrange data from a single plate format file\n\tif(single.plate)\n\t\tinput.data = gcat.reorganize.single.plate.data(input.data = input.data, single.column.headers,\n blank.value = blank.value, single.plate.ID = single.plate.ID, plate.nrow = plate.nrow, plate.ncol = plate.ncol, silent=silent)\n\n ########################################################################\n # Search for and standardize column headers in input data #\n ########################################################################\n \n # Go through the specified column headers, determining what their positions are in the \n # input data frame and if any are missing.\n \n # Get names of column headers in input data\n input.colnames = colnames(input.data)\n \n # Create a list denoting the column numbers in input data that match each of the specified column names, \n # and a separate list for any missing columns. \n \n column.matches = c()\n missing.list = NULL\n \n\tfor(i in 1:length(multi.column.headers)){\n\t\tif (multi.column.headers[i] %in% input.colnames)\n\t\t\tcolumn.matches[i] = min(which(input.colnames == multi.column.headers[i]))\n\t\t# Take the first column in input file that matches a specified column header.\n\t\telse{\n\t\t\tmissing.list = c(missing.list, i)\n\t\t}\n\t}\n\n # If any columns are missing, stop and report error with missing column names\n\tif (is.vector(missing.list)){\n\t\tmessage = \"The following columns:\"\n\t\tfor (i in missing.list)\n\t\t\tmessage = paste(message, paste(\" \", multi.column.headers[i]), sep = \"\\n\") \n\t\tstop(message, \"\\n were not found in the data file.\")\n\t\t}\n\n # Reorder and rename the columns, using the list of matching column numbers from above.\n\tinput.data = input.data[,column.matches]\n\tnames(input.data)[1:4] = c(\"Plate.ID\", \"Well\", \"OD\", \"Time\") \n\n # Use 'substring' to split the alphanumeric \"Well\" field into row (letters) and column (numbers)\n\tinput.data$Well.row = substring(input.data$Well, 0,1)\n\tinput.data$Well.col = as.numeric(substring(input.data$Well, 2))\n\n\n ########################################################################\n # Create an array of well objects with the Time and OD data #\n ########################################################################\n #\n # Use the by function to split up the data frame into shorter segments by well (row, column and plate)\n \n\twell.array = by(data = input.data[,c(\"OD\", \"Time\")], \n INDICES = list(input.data$Well.row,input.data$Well.col,input.data$Plate.ID), \n FUN = function(x){data.frame(Time=x$Time, OD=x$OD,stringsAsFactors = F)}, simplify = F)\n\n \n # Then apply the function (found in well.class) to each member to create a well object\n well.array = aapply(well.array,function(x){well(x$Time,x$OD)})\n\n # Differentiate any duplicate plate names in the array's dimnames \n\tnew.dimnames = dimnames(well.array)\n for (i in length(new.dimnames[[3]]):1){\n\t\tif (any(new.dimnames[[3]][-i] == new.dimnames[[3]][i]))\n\t\t\tnew.dimnames[[3]][i] = paste(\"another_\", new.dimnames[[3]][i], sep = \"\")\t\n\t\t}\n\tdimnames(well.array) = new.dimnames\n\t\n # Copy the plate/row/column names found in the dimnames into the array objects themselves (use \"position\" slot)\n\tfor(plate in unique(dimnames(well.array)[[3]])){\n\t\tfor (col in unique(dimnames(well.array)[[2]])){\n\t\t\tfor(row in unique(dimnames(well.array)[[1]])){\n\t\t\t\twell.array[[row,col,plate]]@position = c(plate=plate,row=row,col=col)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\t\n ########################################################################\n # Add plate layout information to well array #\n ########################################################################\n \n # Use the object to add media and strain information to the \"well.info\" slot of each well\n # Also set the value of the parameter in slot \"curve.par\" to T for empty wells. \n ########################################################################\n # Add plate layout information to well array #\n ########################################################################\n \n # Use the object to add media and strain information to the \"well.info\" slot of each well\n # Also set the value of the parameter in slot \"curve.par\" to T for empty wells. \n \n\n # If is not provided, do not add strain information, and assume all wells are inoculated. \n if(is.null(plate.layout)){ \n plate.layout = data.frame(Row=rep(PLATE.LETTERS[1:plate.nrow],plate.ncol),Column=rep(1:plate.ncol,each=plate.nrow),rep(\"Unknown Strain\",96),rep(\"Unknown Media\",96))\n colnames(plate.layout) = c(\"Row\", \"Column\", layout.sheet.headers)\n } \n else\n if(!silent) cat(\"\\n\\t\\tusing plate layout to fill well info.\")\n \n\tfor(plate in unique(dimnames(well.array)[[3]])){\n\t\tfor (col in unique(dimnames(well.array)[[2]])){\n\t\t\tfor(row in unique(dimnames(well.array)[[1]])){\n well = well.array[[row,col,plate]]\n # For each well on each plate, find the corresponding row in . \n # If refers to specific plates, then use those to find the correct row. \n # Otherwise, generalize across all plates. \n if (\"Plate.ID\" %in% names(plate.layout)) \n layout.row.number = which(plate.layout$Column==well@position[\"col\"] & \n plate.layout$Row==well@position[\"row\"] & \n plate.layout$Plate.ID==well@position[\"plate\"] ) \n else \n layout.row.number = which(plate.layout$Column==well@position[\"col\"] & \n plate.layout$Row==well@position[\"row\"])\n \n # Error if either no rows or more than one row matches the well\n if (length(layout.row.number) != 1)\n stop(\"incorrectly formatted plate layout! check names of columns, rows, and plates (if applicable).\")\n \n # Add any additional columns to the well's \"well.info\" slot\n well.info = plate.layout[layout.row.number,!(names(plate.layout) %in% c(\"Row\",\"Column\",\"Plate.ID\",layout.sheet.headers))]\n \n # Fix the column name issue if there is only one additional entry. \n if(length(well.info) == 1){\n well.info = data.frame(well.info,stringsAsFactors=F) \n names(well.info) = names(plate.layout)[!(names(plate.layout) %in% c(\"Row\",\"Column\",\"Plate.ID\",layout.sheet.headers))] \n } \n well@well.info = as.list(well.info)\n \n well@well.info$Strain = plate.layout[layout.row.number, layout.sheet.headers[1]]\n well@well.info$Media = plate.layout[layout.row.number, layout.sheet.headers[2]]\n \n # Set parameter in slot \"curve.par\" accordingly \n well@curve.par$empty.well = (plate.layout$Strain[layout.row.number] == \"Empty\") \n well.array[[row,col,plate]] = well\n\t\t\t\t}\n\t\t\t}\n\t\t}\n \n # Set start index value in each well\n well.array = aapply(well.array, function(x,start.index) { x@start.index = start.index; x }, start.index)\n \n ########################################################################\n # Return values to R #\n ######################################################################## \n # \n\t# Console output if desired, return the completed well array.\n\tif (!silent)\n\t\tcat(\"\\n\\t\", dim(well.array)[[3]], \"plates added to array from\", file.name)\n\treturn(well.array)\n\t}\n\n\n\n########################################################################\n# #\n# Reorganize data from single-plate input format before reading #\n# #\n########################################################################\n#\n# This function reorganizes the data frame from a single-plate format file. \n# input.data - data frame read straight from a single-plate format data file. \n# single.plate.ID - specifies a plate name for a single-plate read, since none is given in the single-plate format\n# The plate will be named Plate_1 unless otherwise specified. \n\ngcat.reorganize.single.plate.data = function(input.data, blank.value = NULL, single.column.headers, single.plate.ID = \"Plate_1\", \n plate.nrow = 8, plate.ncol = 12, silent=T){\n \n ########################################################################\n # Standardize the formatting and search for specified column names #\n ######################################################################## \n # \n # Locate the first and last rows from the table and return errors if not defined \n # Note: this only works if the time column is the first column\n \n\theader.row = min(which(input.data[,1] == single.column.headers[1])) \n if (length(header.row) != 1 | is.infinite(header.row))\n stop(\"could not locate header row in input file!\")\n \n # The last row: where column 2 starts to be blank, or the total number of rows, whichever is smaller \n extra.rows.start = min(which(input.data[-(1:header.row),2] == \"\"), which(is.na(input.data[-(1:header.row),2])), nrow(input.data[-(1:header.row),]))\n if (length(extra.rows.start) != 1 & is.infinite(extra.rows.start)) \n stop(\"could not locate last row in input file!\")\n\n # Use header row to rename the columns, then cut off extra rows (including the ones above header)\n\tnames(input.data) = as.character(unlist(input.data[header.row,]))\n input.data = input.data[(header.row+1):(header.row+extra.rows.start-1),]\n \n # Time column: allow for multiple matches to the name (since it's usually blank) but assume it's the first one\n\tTime.column = which(names(input.data) == single.column.headers[1])\n\tif (length(Time.column) != 1){\n if(!silent) cat(\"No unique time column in input.data file! Using the first one encountered.\")\n\t\tTime.column = min(Time.column)\n\t\t}\n # First well column (default A1): only allow for one match.\t\n\tWell.column.start = which(names(input.data) == single.column.headers[2])\n\tif (length(Well.column.start) != 1)\n\t\tstop(\"No unique start point for well columns in input.data file!\")\n\n # If the time column was found, rename it \"Time\" and reformat it into a numeric value\n # Adjust the blank measurement timestamp to -1 seconds if there is one\n\n names(input.data)[Time.column] = \"Time\"\n \n # Note: Some single plate screens have timepoints ending with \"s\" for seconds. \n # This line removes the \"s\" while maintaining general compatibility. \n\tinput.data$Time = unlist(strsplit(input.data$Time, \"s\"))\n\n # If is NULL (default - takes the first OD as the blank reading), then the first timepoint can labeled something non-numeric. \n # In that case, rename it to match the first real timepoint minus one. \n # when user input blank value, Blank timepoint i.e. input.data$Time[1] == Blank, labeled as \"Blank\" from data input file\n # It also should rename it to match the first real timepoint minus one. \n if(is.null(blank.value) || is.na(as.numeric(input.data$Time[1])))\n input.data$Time[1] = as.numeric(input.data$Time[2]) - 1\n \n ########################################################################\n # Start to fill the reformatted data frame #\n ######################################################################## \n \n # If all columns are present, make a list of all the wells.\n\twell.list = paste(rep(PLATE.LETTERS[1:plate.nrow], each = plate.ncol), rep(formatC(1:plate.ncol, digits = log(plate.ncol, 10), flag = \"0\"), plate.nrow), sep = \"\")\n\n #\tDuplicate the well names times the number of time measurements in each well\t\n Well = rep(well.list, each = length(input.data[,Time.column]))\t\n\t\t\n # Duplicate times the length of the entire output \n Plate.ID = rep(single.plate.ID, length(Well))\n\n # Duplicate the time column times the number of wells and convert to numeric\n\tTime = as.numeric(rep(input.data[,Time.column], times = length(Well.column.start:ncol(input.data))))\n\n # Append OD measurements from each well together and convert to numeric\n\tOD = c()\n\tfor (i in Well.column.start:ncol(input.data)){\n\t\tOD = as.numeric(c(OD, input.data[,i]))\n\t\tOD = unlist(OD)\n\t\t}\n\n # Fill and return the data frame containing the above four vectors.\n\toutput = data.frame(Plate.ID, Well, OD, Time)\t\n\t\n # Include any extra columns that were not Time or OD measurements?\n\tfor(i in (1:length(names(input.data)))[-c(Time.column,Well.column.start:ncol(input.data))]){\n\t\tnew.column = data.frame(rep(input.data[,i], length(Well.column.start:ncol(input.data))))\n\t\tnames(new.column) = names(input.data)[i]\n\t\toutput = cbind(output, new.column)\n\t\t}\t\n\treturn(output)\n}\n\n\n########################################################################\n# #\n# Function to combine two well array datasets by plate #\n# #\n########################################################################\n# ----------------------------------------------------------\n# This function can append together arrays created using \n# Arguments: any number of array objects as long as they are all output straight from \n\ngcat.append.arrays = function(...){\n\n # Transfer arrays to a list\n\targs.arrays = list(...)\n\tfirst.array = args.arrays[[1]]\n\tfirst.dims = dim(first.array)\n plate.nrow = args.arrays[[4]]\n plate.ncol = args.arrays[[3]]\n input.arrays = list(args.arrays[[1]], args.arrays[[2]])\n\tfor (i in 2:length(input.arrays)){\n\t\tnext.array = input.arrays[[i]]\n\t\tnext.dims = dim(next.array)\n\t\n # Check to make sure the arrays have proper dimensions for 96-well plate data\n if (!(all(c(first.dims[1], next.dims[1]) == plate.nrow) & all(c(first.dims[2], next.dims[2]) == plate.ncol)))\n\t\t\tstop(\"Data should have dimensions (\",plate.nrow,\",\",plate.ncol,\",n)!\")\n\t\t\n # If dimensions are alright, append dimensions and dimension names\t\n new.dims = c(plate.nrow,plate.ncol,first.dims[3]+next.dims[3])\n\t\tnew.names = dimnames(first.array)\n\t\tnew.names[[3]] = c(new.names[[3]], dimnames(next.array)[[3]]) \n\n # Differentiate duplicate names\n\t\tfor (i in length(new.names[[3]]):1){\n\t\t\tif (any(new.names[[3]][-i] == new.names[[3]][i]))\n\t\t\t\tnew.names[[3]][i] = paste(\"another_\", new.names[[3]][i], sep = \"\")\n\t\t\t}\n\t\n\t\t# Create a new array\n new.array = c(first.array, next.array)\n\t\tdim(new.array) = new.dims\n\t\tdimnames(new.array) = new.names\n\t\t\n # Update plate name in well objects\n\t\tfor (i in 1:length(unlist(new.array)))\n\t\t\tnew.array[[i]]@position[1] = new.names[[3]][floor((i-1)/96)+1]\n\t\t\n\t\t# Loop until complete\n\t\tfirst.array = new.array\n\t\tfirst.dims = dim(first.array)\n\t\t}\n\treturn(new.array)\n\t}\n\n\n########################################################################\n# #\n# Convert timestamps to hours from start and sort timepoints #\n# #\n########################################################################\n#\n# This function acts on a single well and modifies the raw data stored in slot \"screen.data\"\n# \n# input.well - an object of class well\n# time.format - specifies the time format. allowed values are \"%S\", for seconds, \"%d\", for days, or anything complying with ISO C / POSIX standards; see \n# note: reading directly from excel to R results in timestamps being converted to days.\n# start.index - which timepoint should be used as the starting time at inoculation?\n\ngcat.start.times = function(input.well, time.input, start.index = 2) { \n \n if(start.index > length(input.well))\n stop(\"Start index is greater than length of well!\")\n \n # If using a numeric time format, simply multiply times by the appropriate conversion factor\n\t# Conversion factor should be supplied to convert timestamps to hours. For example, \n # should be equal to 1/3600 if \"time\" is in seconds, 24 if \"time\" is in days, etc.\n\n time.format = time.input # Set default constant from rails user input\n \n if (is.numeric(time.format))\n\t\tinput.well@screen.data$Time = (input.well@screen.data$Time - min(input.well@screen.data$Time)) * time.format\n else{\n # Otherwise, convert timestamps from ISO C / POSIX to numeric values representing seconds (since the dawn of time?) and subtract out the initial value. \n\t\trtimes = input.well@screen.data$Time\n ptimes = strptime(as.character(rtimes),time.format)\n\t\tctimes = as.POSIXct(ptimes)\n\t\tint.times = unclass(ctimes)\n # Time will be in seconds, convert to hours by dividing by 3600\n\t\tinput.well@screen.data$Time = (int.times - min(int.times))/3600\n\t\t}\n\t# Sort raw data by timestamp and return the input.well\n\tinput.well@screen.data = input.well@screen.data[order(input.well@screen.data$Time),]\n \n input.well@screen.data$Time = input.well@screen.data$Time - input.well@screen.data$Time[start.index]\n \n if(all(is.na(input.well@screen.data$Time)))\n stop(\"Error in .\") \n rownames(input.well@screen.data) = NULL\n\treturn(input.well)\n }\t\n", - "created" : 1425413240737.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "2796681086", - "id" : "2FF709FD", - "lastKnownWriteTime" : 1428438949, - "path" : "~/Documents/GCAT4/trunk/R/GCAT/R/table2well.R", - "project_path" : "R/table2well.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/3DC2D3DA b/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/3DC2D3DA deleted file mode 100644 index be33fea..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/3DC2D3DA +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n\n# GCAT version 5.00\n# Notes by Jason\n# 08/18/2011\n\n# Initialization\n\n\nPLATE.LETTERS = paste(rep(c(\"\", LETTERS), each = 26), rep(LETTERS, 26), sep=\"\")\nglobal.version.number = packageDescription(pkg=\"GCAT\")$Version \n\n########################################################################\n# #\n# Top-level functions for analysis of screening data from .csv files. #\n# #\n########################################################################\n# This functions is called directly by the user interface.\n# They in turn call the main function (below) multiple times for each data file provided in . \n\n# Arguments:\n# file.list - a list of full paths to .csv files. all files must be in the same format (see )\n# single.plate - are the file in the single plate (wide) format vs. the multi-plate (long) format?\n# layout.file - (optional) provide full path to a layout file with strain and media definitions (applies to all files in list)\n\n# out.dir - name a directory to output the table of curve parameters to (defaults to working directory) \n# graphic.dir - name a directory to output the images of the fitted curves to (defaults to subdirectory \"pics\" of above)\n\n\n# add.constant- should be a numeric constant that will be added to each curve before the log transform (defaults to 1) \n# blank.value - user can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. \n# start.index - which timepoint should be used as the first one after inoculation (defaults to the 2th one)\n# growth.cutoff - minimum threshold for curve growth. \n# points.to.remove - a list of numbers referring to troublesome points that should be removed across all wells.\n# remove.jumps - should the slope checking function be on the lookout for large jumps in OD?\n \n# silent - should messages be returned to the console?\n# verbose - should sub-functions return messages to console? (when I say verbose, I mean it!)\n\n# Returns:\n# if = F (default), avector of full paths to all the files generated by the function.\n# otherwise, the fitted array of well objects. \n\n# Use this function to analyze any set of .csv files using the same plate layout info. \n\n#' Analyze screening growth data from the given .csv files.\n#' \n#' Top-level GCAT function \n#' \n#' @param file.list A list of full paths to .csv files. all files must be in the same format (see )\n#' @param single.plate The file in the single plate (wide) format vs. the multi-plate (long) format?\n#' @param layout.file Full path to a layout file with strain and media definitions (applies to all files in list)\n#' @param out.dir A directory to output the table of curve parameters to (defaults to working directory) \n#' @param graphic.dir A directory to output the images of the fitted curves to (defaults to subdirectory \"pics\" of above)\n#' @param use.linear.param Whether to use linear parameters or not?\n#' @param use.loess Whether to use LOESS model or not?\n#' @param smooth.param Smoothing parameter for LOESS model.\n#' @param add.constant A numeric constant that will be added to each curve before the log transform (defaults to 1) \n#' @param blank.value User can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. \n#' @param start.index Which timepoint should be used as the first one after inoculation (defaults to the 2th one)\n#' @param growth.cutoff Minimum threshold for curve growth. \n#' @param points.to.remove A list of numbers referring to troublesome points that should be removed across all wells.\n#' @param remove.jumps Should the slope checking function be on the lookout for large jumps in OD?\n#' @param time.input The time setting in which the current system is running?\n#' @param plate.nrow The number of rows in a plate.\n#' @param plate.ncol The number of columns in a plate.\n#' @param input.skip.lines If specified, this number of lines shall be skipped from the top when reading the input file with read.csv \n#' @param multi.column.headers The headers of the result tabular data when analyzing multiple plates at once.\n#' @param single.column.headers The headers of the result tebaular data when analyzaing a single plate.\n#' @param layout.sheet.headers The headers of the layout file?\n#' @param silent Shoulde messages be returned to the console?\n#' @param verbose Should sub-functions return messages to console? (when I say verbose, I mean it!)\n#' @param overview.jpgs Should GCAT enable an overview image?\n#' \n#' @return A list of the output files.\ngcat.analysis.main = function(file.list, single.plate, layout.file = NULL, \n out.dir = getwd(), graphic.dir = paste(out.dir, \"/pics\", sep = \"\"), \n add.constant = 0.1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05,\n use.linear.param = F, use.loess = F, smooth.param=0.1,\n points.to.remove = 0, remove.jumps = F, time.input = NA,\n plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,\n multi.column.headers = c(\"Plate.ID\", \"Well\", \"OD\", \"Time\"), single.column.headers = c(\"\",\"A1\"), \n layout.sheet.headers = c(\"Strain\", \"Media Definition\"),\n silent = T, verbose = F, return.fit = F, overview.jpgs = T){\n\n # MB: Prototyping system unwanted argument guarding. Proper function \n # will be added in the future.\n # Not the best solution.\n if (is.na(time.input)) {\n if (single.plate)\n time.input = 1/3600\n else\n exception(\"Error: \", \"time.input is NA.\")\n }\n \n if (add.constant < 0)\n exception(\"Error: \", \"The constant r should not be negative.\")\n # End prototyping temporary solution.\n \n upload.timestamp = strftime(Sys.time(), format=\"%Y-%m-%d %H:%M:%S\") # Get a timestamp for the time of upload. \n fitted.well.array.master = list()\n source.file.list = c()\n \n dim(fitted.well.array.master) = c(plate.nrow,plate.ncol,0)\n dimnames(fitted.well.array.master) = list(PLATE.LETTERS[1:plate.nrow], 1:plate.ncol, c())\n \n for(file.name in file.list){\n \n # Call on the file with single plate options\n \tfitted.well.array = try(gcat.fit.main(file.name = file.name, load.type = \"csv\", \n single.plate = single.plate, layout.file = layout.file, start.index = start.index, \n time.input = time.input, add.constant = add.constant, blank.value = blank.value, \n growth.cutoff = growth.cutoff, points.to.remove = points.to.remove, remove.jumps = remove.jumps,\n \t use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=smooth.param,\n plate.nrow = plate.nrow, plate.ncol = plate.ncol, multi.column.headers = multi.column.headers, \n single.column.headers = single.column.headers, layout.sheet.headers = layout.sheet.headers,\n input.skip.lines = input.skip.lines, silent = silent, verbose = verbose), silent = T)\n \n # Return error message if the function fails.\n if(class(fitted.well.array) == \"try-error\")\n return(as.character(fitted.well.array)) \n }\n \n # Add fitted well array onto existing fitted wells\n fitted.well.array.master = gcat.append.arrays(fitted.well.array.master, fitted.well.array, plate.ncol, plate.nrow)\n \n # Remove the \"processed_\" tag from file names and add to the list of source files.\n source.file.list = c(source.file.list, basename(paste(strsplit(file.name, \"processed_\")[[1]],collapse=\"/\"))) \n\n out.files = try(gcat.output.main(fitted.well.array.master, out.prefix = \"output\", \n source.file.list = source.file.list, upload.timestamp = upload.timestamp, \n growth.cutoff = growth.cutoff, add.constant = add.constant, blank.value = blank.value, start.index = start.index, \n points.to.remove = points.to.remove, remove.jumps = remove.jumps, \n out.dir = out.dir, graphic.dir = graphic.dir, overview.jpgs=overview.jpgs,\n use.linear.param=use.linear.param, use.loess=use.loess, plate.ncol = plate.ncol, plate.nrow = plate.nrow,\n silent = silent), silent = T)\n \n # Return file list or error message otherwise return \"successful analysis\" message (?)\n\n # file.list = c(\"Data was successfully analyzed.\", file.list) # <--- yet to be implemented. causes errors downstream right now \n if(class(out.files) == \"try-error\") return(as.character(out.files)) \n \n if(return.fit) return(fitted.well.array.master)\n else return(out.files) \n}\n\n########################################################################\n# #\n# Main function for analysis of screening data from input tables. #\n# #\n########################################################################\n# This is the main function that handles all the analyses for files in both single and multiple plate formats. \n# It is called by the top level function \n#\n# It then calls the following functions on each member of the array: \n# - curve normalization and standardization: , , , , \n# - curve shape analysis before model fitting: , , \n# - to fit a nonlinear model to the growth data: \n# Finally, it returns the fitted array of well objects.\n\n#' Main analysis function for GCAT \n#' \n#' This is the main function that handles all the analyses for data files in both single and multiple plate formats. \n#' It is called by the top level function \\code{gcat.analysis.main} along with \\code{gcat.output.main}.\n#' \n#' @param file.name Complete path and file name of a comma-separated values (.csv) file containing growth curve data \n#' in the multiple-plate (long) format. \n#' @param input.data A list of tables representing input files read with \\code{read.table}. Used to save time in cases\n#' of running multiple analyses on the same dataset. If used, the function will ignore \\code{file.name} entirely.\n#' @param load.type .csv by default. \n#' @param layout.file Specifies the location of a layout file containing identifying information.\n#' @param single.plate Whether the GCAT is analyzing a single plate or not.\n#' @param blank.value Blank OD measurement for uninoculated wells. By default(NULL), the value of the first OD\n#'measurement in each well is used.\n#' @param start.index Which timepoint should be used as the first one after inoculation?\n#' @param time.input Either a character describing the format used to convert timestamps in the input to numbers\n#' representing number of seconds (see \\code{strptime}), or a factor to divide entries in the Time column by to get the \n#' numbers of hours.\n#' @param normalize.method Describes the method used by \\code{normalize.ODs} to normalize cell density values using blank reads.\n#' @param add.constant A value for r in the log(OD + r) transformation.\n#' @param use.log Should the analysis use log on all values.\n#' @param points.to.remove A vector of integers specifying which timepoints should be removed across all wells. \n#' By default(0) none are marked for removal.\n#' @param use.linear.param Should the linear parameter be used or not.\n#' @param use.loess Should the loess model be used or not.\n#' @param smooth.param If loess model is used, this parameter define the smoothing parameter for the loess model.\n#' @param fall.cutoff A cutoff used by \\code{check.slopes} to decide on thresholds for jumps and tanking.\n#' @param growth.cutoff A threshold used by check.growth to decide whether a well displays growth.\n#' @param remove.jumps Should jumps in OD detected by the subfunction \\code{check.slopes}?\n#' @param plate.nrow The number of rows in the input files.\n#' @param plate.ncol The number of columns in the input files.\n#' @param input.skip.lines If specified, this number of lines shall be skipped from the top when reading the input file with read.csv \n#' @param multi.column.headers The headers of the column when analyzing multiple plates.\n#' @param single.column.headers The headers of the column when analyzing a single plate.\n#' @param layour.sheet.headers The headers of the layout file.\n#' @param growth.model What growth model should be used?\n#' @param backup.growth.model If the main growth model fails, the back up model will be used.\n#' @param silent Surpress all messages.\n#' @param verbose Display all messages when analyzing each well.\n#' \n#' @return An array of well objects \ngcat.fit.main = function(file.name, input.data = NULL, load.type = \"csv\", layout.file = NULL, \n single.plate = F, blank.value = NULL, start.index = 2, time.input = NA,\n normalize.method = \"default\", add.constant = 1, use.log = T, points.to.remove = 0,\n use.linear.param=F, use.loess=F, smooth.param=0.1,\n fall.cutoff = -0.0025, growth.cutoff = 0.05, remove.jumps = F, \n plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,\n multi.column.headers = c(\"Plate.ID\", \"Well\", \"OD\", \"Time\"), single.column.headers = c(\"\",\"A1\"), \n layout.sheet.headers = c(\"Strain\", \"Media Definition\"),\n growth.model = NA, backup.growth.model = NA, \n silent = F, verbose = F){\n \n # Explanation of arguments:\n \n # ---File Handling---\n # file.name - full path to an excel spreadsheet, .csv or tab-delimited text file, in either the single or multiple-plate format\n # input.data - use pre-loaded data set (output from function only). will override if not NULL \n # load.type - supports \"csv.\" \n # layout.file - full path to a file containing the plate layout in the same format as . will not be used if is \"xlsx\"\n\n # ---Input file format---\n # single.plate - true denotes data in single-plate format, i.e. simple OD output. false denotes multiple-plate robotic screening output. \n # note: reading directly from excel to R results in timestamps being converted to days.\n\n # ---Normalization and Transforms---\n # blank.value - user can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. \n # start.index - which timepoint should be used as the first one after inoculation (defaults to the 2th one)\n # normalize.method - how should each growth curve be normalized? allowed values are:\n # \"first\": subtracts the first OD, assumed to be the blank, from all ODs\n # \"none\": does nothing, assumes no blank. highly recommend log(OD+1) transform in this case.\n # \"average.first\": forces all filled wells on each plate to match the average value at (after subtracting the first OD) \n # add.constant - a numeric constant that will be added to each curve before the log transform (defaults to 1)\n # use.log - should a log transform be applied to the data after normalization? \n # points.to.remove - a list of numbers referring to troublesome points that should be removed across all wells.\n \n # ---Pre-fitting processing---\n # fall.cutoff - a cutoff value for determining whether OD falls significantly between two timepoints. see in prefit.processing.R for details. \n # growth.cutoff - a cutoff value for determining whether a well contains a successfully growing culture or not.\n # remove.jumps - should the slope checking function be on the lookout for large jumps in OD?\n \n # ---Model fitting---\n # model - which parametrized growth model to use? can be richards, gompertz, or logistic. models are defined as objects of class model, see \"model.class.R\"\n # backup.model - which model should be used if fitting using fails? should ideally be simpler than the main model (less parameters)\n \n # ---Miscellanous input/output preferences---\n # silent - should messages be returned to the console?\n # verbose - should sub-functions return messages to console? (when I say verbose, I mean it!) \n # unlog - should exported graphics be transformed back to the OD scale? \n # return.fit - should the function return an array of wells? if not, it will return a list of generated files. \n \n \t\n ########################################################################\n # Read from .csv file #\n ########################################################################\n #\n # The functions used here are found in table2well.R\n \n if(!silent) cat(\"\\nReading input files...\")\n # Read from .csv or tab-delimited text file using (in load.R)\n # if is provided, it will be used here. \n \n plate.layout = NULL \n # Read layout file if it is specified. \n if(!is.null(layout.file)){\n if(load.type==\"csv\") plate.layout = read.csv(layout.file,header=T,stringsAsFactors=F)\n else plate.layout = read.table(layout.file,header=T,sep=\"\\t\",stringsAsFactors=F) \n if(!silent) cat(\"\\n\\tAdded plate layout information from\", layout.file, \"\\n\")\n }\n \n # Load the data \n\t\twell.array = try(gcat.load.data(file.name = file.name, input.data = input.data, \n plate.layout = plate.layout, plate.nrow = plate.nrow, plate.ncol = plate.ncol, \n input.skip.lines = input.skip.lines, multi.column.headers = multi.column.headers, \n single.column.headers = single.column.headers, layout.sheet.headers = layout.sheet.headers,\n blank.value = blank.value, start.index = start.index, single.plate = single.plate, \n load.type = load.type, silent=silent),silent=silent)\n\n # Return an error if there is a problem with file loading. \n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n\t\t\n\n # !---At this point, is an array of well objects, each containing raw data and media/strain information if provided--- \n \n # Attempt to apply time formatting to all wells in array \n well.array = try(aapply(well.array, gcat.start.times, start.index = start.index, time.input = time.input),silent=silent)\n \n # Return an error if there is a problem with time formatting\n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n \t\n ########################################################################\n # Perform normalization and transformation of raw data #\n ######################################################################## \n #\n # The functions used here are found in normalize.and.transform.R \n \n if(!silent) cat(\"\\nProcessing raw data...\")\n \n # Set all timepoints to active for now using \"points.to.remove=0\" argument with \n # adds an extra column to the \"well.array\" slot of each well specifying which points to remove when data is retrieved from the well\n well.array = aapply(well.array, remove.points, points = 0)\n \n # Normalize ODs using specified method and adding a constant if desired. \n # sets the \"norm\" slot of each well to a value to be subtracted from OD values whenever data is retrieved from the well\n well.array = try(normalize.ODs(well.array, normalize.method = normalize.method, \n start.index = start.index, blank.value = blank.value, add.constant = add.constant),silent=silent)\n \n # Return an error if there is a problem with normalization\n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n \n # Transform ODs on the logarithmic scale, regardless of whether is true \n # an extra column of log-transformed values is added to the \"well.array\" slot of each well \n # the \"use.log\" slot of each well is set instead to determine whether the transformed values will be returned when data is retrieved from the well.\n well.array = try(aapply(well.array, transform.ODs, start.index = start.index, blank.value = blank.value, use.log = use.log, constant.added = add.constant),silent=silent)\n \n # Return an error if there is a problem with transformation\n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n \n # Remove specified timepoints across wells (use \"points.to.remove=NULL\" if no points to remove) \n well.array = try(aapply(well.array, remove.points, points = points.to.remove),silent=silent)\n \n # Return an error if there is a problem with point removal\n if (class(well.array) == \"try-error\")\n stop(\"Error in : \", well.array) \n \n \n \n ########################################################################\n # Pre-fitting data processing (analysis of curve shapes) #\n ######################################################################## \n #\n # The functions used here are found in slope.analysis.R\n \n # Estimate slope at each timepoint \n # add a column to the \"well.array\" slot of each well with the local slope at each timepoint \n \n well.array = try(aapply(well.array, calculate.slopes, silent=!verbose),silent=silent)\n \n # Return an error if there is a problem with slope calculation\n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n \n # Check slopes for tanking and/or jumping behavior\n # fills the \"curve.par\" slot of each well with , denoting the timepoint at which tanking starts (if none, value is NA) \n # uses to remove all points after \n # It will also fill the \"jump.error\" slot with a status message, and try to use an automated process to remove the \n # erroneous points if is true (default false). \n \n well.array = try(aapply(well.array, check.slopes, fall.cutoff = fall.cutoff, remove.jumps = remove.jumps, silent=!verbose, draw = F),silent=silent)\n \n # Return an error if there is a problem with slope analysis\n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n \t\n \t\n # Check curves for growth above cutoff\n # fills the \"curve.par\" slot of each well with , denoting whether the well has no detectable growth. \n well.array = try(aapply(well.array, check.growth, growth.cutoff = growth.cutoff, start.index = start.index),silent=silent)\n \n # Return an error if there is a problem with growth.check\n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n \t\n ########################################################################\n # Fit parameterized models to data #\n ######################################################################## \n #\n # The functions used here are found in fit.model.R \n \n # Fit each well with the selected model and attempt to catch failed fittings with the backup model \n # skips wells designated as above\n # fills the \"fit.info\" slot of each well with \"success,\" \"failed,\" or \"skipped\"\n # if fit was successful:\n # fills the \"equation\" and \"model.name\" slots with the relevant info for the successful model \n # fills the \"fit.par\" slot with fitted parameters if fit is successful \n \n if(!silent) cat(\"\\nFitting models to data...\")\n well.array = aapply(well.array, fit.model, growth.model=growth.model,\n backup.growth.model = backup.growth.model, use.linear.param=use.linear.param,\n use.loess=use.loess, smooth.param=smooth.param, silent=!verbose)\n \n # Return an error if there is a problem with model fitting\n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n \n if(!silent) cat(\"\\ndone!\\n\") \n return(well.array) \n } \n \n \n########################################################################\n# #\n# Output function for generating files from fitted data. #\n# #\n######################################################################## \n#' Output function for generating files from fitted data.\n#' \n#' Handles files and directories, calls \\code{table.out}, \\code{plate.overview} and \\code{view.fit} \n#' to generate output tables and graphics.\n#' \n#' @param fitted.well.array A list of fitted well objects.\n#' @param out.prefix Prefix that is in the name of output files.\n#' @param blank.value User can enter a blank OD measurement for uninoculated wells. \n#' If NULL, defaults to the value of the first OD measurement of each well.\n#' @param start.index Which timepoint should be used as the first one after inoculation (defaults to the 2th one)\n#' @param growth.cutoff Minimum threshold for curve growth.\n#' @param points.to.remove A list of numbers referring to troublesome points that should be removed across all wells.\n#' @param remove.jumps Should the slope checking function be on the lookout for large jumps in OD?\n#' @param out.dir name a directory to output the table of curve parameters to (defaults to working directory) \n#' @param graphic.dir name a directory to output the images of the fitted curves to \n#' (defaults to subdirectory \"pics\" of above)\n#' @param overview.jpgs should jpgs be generated for each plate with the overview graphic? \n#' This is for backwards compatibility with the old web server. \n#' @param silent should messages be returned to the console?\n#' @param unlog should exported graphics be transformed back to the OD scale?\n#' @param constant.added (should be the same value as add.constant above) - \n#' used to readjust for the constant added during the log transform when plotting ODs. \n#' @return A list of output files if success.\n\ngcat.output.main = function(fitted.well.array, out.prefix = \"\", source.file.list, upload.timestamp = NULL, \n add.constant, blank.value, start.index, growth.cutoff, points.to.remove, remove.jumps, \n out.dir = getwd(), graphic.dir = paste(out.dir,\"/pics\",sep = \"\"), overview.jpgs = T,\n use.linear.param=F, use.loess=F, plate.nrow = 8, plate.ncol = 12,\n unlog = F, silent = T){ \n \n # Prepare timestamp for addition to output file names. \n filename.timestamp = strftime(upload.timestamp, format=\"_%Y-%m-%d_%H.%M.%S\")\n \t\n ########################################################################\n # Prepare to write to output files #\n ######################################################################## \t\n\t if(is.null(blank.value)) blank.value = \"First timepoint in well\"\n\t \n if(!silent) cat(\"\\nFinding/creating new output directories...\")\n \n old.wd = getwd() \n # Create output directory if it doesn't exist\n if(class(try(setwd(out.dir), silent = T)) == \"try-error\"){\n \tif(!silent) cat(\"\\ncreating new output directory\")\n \tif (class(try(dir.create(out.dir))) == \"try-error\")\n \t\tstop(\"Error creating new output directory!\")\n \t}\n \n # Create graphics directory if it doesn't exist\n if(class(try(setwd(graphic.dir), silent = T)) == \"try-error\"){\n \tif(!silent) cat(\"\\ncreating new graphics directory\")\n \tif (class(try(dir.create(graphic.dir))) == \"try-error\")\n \t\tstop(\"Error creating new graphics directory!\")\n \t}\n \t\n ########################################################################\n # Populate a data table with fit results and write to file #\n ######################################################################## \n # \n # The functions used here are found in table.output.R \n \n # Creates a table with a row for each well and a column for each of various identifiers and fitted and calculated parameters. \n \n if(!silent) cat(\"\\nPopulating data table...\")\n table.fit = try(table.out(fitted.well.array, filename.timestamp=filename.timestamp,use.linear.param=use.linear.param, use.loess=use.loess, constant.added=add.constant))\n \n # Return an error if there is a problem with returning the table\n if (class(fitted.well.array) == \"try-error\")\n \tstop(\"Error in : \", fitted.well.array)\n \t\n \t\n # Set working directory to \n\tif (class(try(setwd(out.dir))) == \"try-error\")\n\t\tstop(\"Error setting directory for table output\")\n\t\t\n\t# Write output table to file in \n table.filename = paste(out.dir, \"/\", out.prefix, \"_gcat.fit\", filename.timestamp, \".txt\", sep = \"\")\n if (class(try(write.table(table.fit, table.filename, sep = \"\\t\", row.names = F))) == \"try-error\")\n\t\tstop(\"Error writing tabular output\")\n\t\t\n \t# ---If successfully written, add postscript and start a list of generated files.\t\n generated.files = table.filename\n\n ########################################################################\n # Write individual fit and overview graphics to file #\n ######################################################################## \n # \n # The functions used here are found in graphic.output.R\n \n if(!silent) cat(\"\\nDrawing graphics...\")\n \n # Set working directory to \n\tif (class(try(setwd(graphic.dir))) == \"try-error\")\n\t\tstop(\"Error setting directory for graphic output\")\n\t# Use function to write fit graphics to file. \n \n\tgraphic.files = try(pdf.by.plate(fitted.well.array, out.prefix=out.prefix, upload.timestamp = upload.timestamp, \n unlog=unlog,constant.added=add.constant,overview.jpgs=overview.jpgs, plate.ncol = plate.ncol, plate.nrow = plate.nrow),silent=silent)\n \n if (class(graphic.files) == \"try-error\")\n\t\tstop(\"Error in : \", graphic.files)\n \n # If successfully written, add to the list of generated files.\t\n generated.files = c(generated.files, graphic.files)\n \n ########################################################################\n # Add a postscript to the output table with legend and file info. #\n ######################################################################## \n # \t\n sink(table.filename, append = T)\n analysis.timestamp = strftime(Sys.time(), format=\"%Y-%m-%d %H:%M:%S\")\n cat(\"\\n# Raw OD values are adjusted and log-transformed before fitting a growth curve as follows: log.OD = log(OD - blank + const) where blank is OD of blank medium and const is specified by the user (1 by default)\",\n \"\\n# Values are reported on the above 'log.OD' scale unless otherwise specified.\",\n \"\\n# .SE columns report standard errors of those values that are estimated directly as parameters of global sigmoid models.\",\n \"\\n# .OD columns report values back-transformed to the linear 'OD - blank' scale.\",\n \"\\n\")\n \n cat(\"\\n# -- Explanation of columns --\",\n \"\\n# - model: Name of the model the well was successfully fit with (if any)\",\n \"\\n# - lag.time: Lag time estimate inferred from the fitted model\",\n \"\\n# - inflection.time: inflection time point of the growth curve when drawn on the log scale\",\n \"\\n# - max.spec.growth.rate: maximum specific growth rate estimate inferred from the fitted model. Estimated as the first derivative of the growth curve at inflection time point\", \n \"\\n# - baseline: growth curve baseline. Global sigmoid model: baseline is parameter 'b' of the model. LOESS: baseline is the same as the lowest predicted log.OD value\",\n \"\\n# - amplitude: difference between upper plateau and baseline values. Global sigmoid model: amplitude is parameter 'A' of the model. LOESS: amplitude = max.log.OD - min.log.OD\",\n \"\\n# - plateau: upper asymptote value of the fitted model. Global sigmoid model: plateau = b + A. LOESS: plateau = max.log.OD\",\n \"\\n# - inoc.log.OD: log.OD value at inoculation. Estimated value from the fitted model is used, rather than the actual measurement\", \n \"\\n# - max.log.OD: maximal log.OD value reached during the experiment. Estimated value from the fitted model is used rather than the actual measurement\",\n \"\\n# - projected.growth: maximal projected growth over inoculation value. Global sigmoid model: projected.growth = plateau - inoc.log.OD. LOESS: not reported\",\n \"\\n# - achieved.growth: maximal growth over inoculation value actually achieved during the experiment. achieved.growth = max.log.OD - inoc.log.OD\",\n \"\\n# - shape.par: shape parameter of the Richard equation\",\n \"\\n# - R.squared: goodness of fit metric. Also known as coefficient of determination. R.squared is usually between 0 and 1. A value close to 1 indicates good fit.\",\n \"\\n# - RSS: residual sum of squares. Another goodness of fit metric. Smaller values indicate better fits.\",\n \"\\n# - empty: (Well indicator)\", \n \"\\n# - an 'E' indicates that the well was empty and no growth was detected. \",\n \"\\n# - an 'I' indicates that the well was inoculated and growth was detected above the threshold. \",\n \"\\n# - an 'E*' indicates that the well was empty and growth was detected (possible contamination). \",\n \"\\n# - an '!' indicates that the well was inoculated and no growth was detected. \",\n \"\\n# - asymp.not.reached: shows “L” if the bottom asymptote (baseline) was not reached and “U” if the upper asymptote (plateau) was not reached.\",\n \"\\n# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index.\", \n \"\\n# - other: Additional flag column. Displays information about whether jumps in OD were detected and what was done about them.\",\n \"\\n# - pdf.file and page.no: location of the figure for this well in the output .pdf files.\"\n )\n \n\t # Analysis information \n \n cat(\"\\n#\\n# -- Source file information--\",\n \"\\n# \", paste(source.file.list, collapse = \"\\n# \"), \n \"\\n# analyzed using GCAT v\", global.version.number, \n \"\\n# request sent: \", upload.timestamp, \n \"\\n# completed: \", analysis.timestamp, \n \"\\n#\\n# -- Parameters used in current analysis --\",\n \"\\n# - Constant added to log(OD + n) transformation:\", add.constant,\n \"\\n# - Blank OD value: \", blank.value,\n \"\\n# - Index of inoculation timepoint\", start.index,\n \"\\n# - Minimum growth threshold:\", growth.cutoff, \n \"\\n# - Removed points:\", paste(points.to.remove, collapse = \" \"),\n \"\\n# - Jump detection:\", remove.jumps) \n sink()\n \n ########################################################################\n # Return values to R #\n ######################################################################## \n # \n\n if(!silent) cat(\"\\ndone!\") \n setwd(old.wd)\n # Return list of generated files\n\treturn(generated.files)\n }\n \n", - "created" : 1425413277808.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "1165231602", - "id" : "3DC2D3DA", - "lastKnownWriteTime" : 1428438949, - "path" : "~/Documents/GCAT4/trunk/R/GCAT/R/GCAT.main.R", - "project_path" : "R/GCAT.main.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/4DC8D1 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/4DC8D1 deleted file mode 100644 index 9eb45ad..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/4DC8D1 +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n\n########################################################################\n# #\n# class definition and functions. Objects contain raw #\n# data from screening runs on single wells from 96-well plates, and #\n# other slots for processing and model-fitting details. #\n# #\n########################################################################\n\n# Windows OS compatibility\nSys.setlocale(locale=\"C\")\n#require(RExcelXML)\n\n# Treat nls and loess as S4 classes to avoid warnings\nsetOldClass(\"nls\")\nsetOldClass(\"loess\")\nsetClass(\"well\", representation(position = \"character\",\n\t\t\t\t\t well.info = \"list\",\n\t\t\t\t\t screen.data = \"data.frame\", \n start.index = \"numeric\",\n\t\t\t\t\t use.log = \"logical\",\n\t\t\t\t\t norm = \"numeric\",\n\t\t\t\t\t curve.par = \"list\", \n\t\t\t\t\t fit.par = \"list\",\n fit.std.err = \"list\",\n\t\t\t\t\t equation = \"expression\",\n\t\t\t\t\t model.name = \"character\",\n\t\t\t\t\t fit.info = \"character\",\n\t\t\t\t\t add.info = \"character\",\n inflection.time = \"numeric\",\n rss = \"numeric\",\n loess = \"loess\",\n nls = \"nls\"))\n\n# Slots:\n# position - 3-member vector containing identifying information for the well: row (letters), column (numbers) and plate ID. \n# well.info - a list containing strain and media names if provided\n# screen.data - a data frame with Time and raw OD values. This is the only slot that is filled upon creation of a well object. \n# as different functions are run on the well the data frame gets filled with additional columns. \n# use.log - a single logical value denoting whether to return log-transformed values when data is requested from the well\n# norm - a value to subtract from all OD values before returning data. filled by (see normalize.and.transform.R)\n# curve.par - a list of parameters that denote whether the well is empty, whether it contains ODs indicating a viable culture, whether it tanks at a certain timepoint. \n\n# if model fitting using is successful:\n# fit.par - will be a list containing the fitted model parameters\n# fit.std.err - will be a list containing the standard errors for the fitted model parameters\n# equation - will contain an expression for evaluating the successfully fitted model \n# model.name - will contain the name of the successfully fit model\n\n# fit.info - a message with info about whether the fit was successful, failed, or skipped. \n# add.info - a message with info about whether jumps in OD were detected or removed, or if ODs were detected below the blank OD.\n# inflection.time - the Time value at the point where the specific growth is located. no longer a formula param NWD\n# rss - residual sum of squares\n# loess - object returned by running loess on the normalized well data\n# nls - object returned by running nls on the normalized well data\n\nsetGeneric(\"getPosition\", function(object){standeardGeneric(\"getPosition\")})\nsetMethod(\"getPosition\", \"well\", \n function(object){\n return(object@position)\n })\n\nsetGeneric(\"getWellInfo\", function(object){standeardGeneric(\"getWellInfo\")})\nsetMethod(\"getWellInfo\", \"well\", \n function(object){\n return(object@well.info)\n })\n\nsetGeneric(\"getScreenData\", function(object){standeardGeneric(\"getScreenData\")})\nsetMethod(\"getScreenData\", \"well\", \n function(object){\n return(object@screen.data)\n })\n\nsetGeneric(\"getStartIndex\", function(object){standeardGeneric(\"getStartIndex\")})\nsetMethod(\"getStartIndex\", \"well\", \n function(object){\n return(object@start.index)\n })\n\nsetGeneric(\"getUseLog\", function(object){standeardGeneric(\"getUseLog\")})\nsetMethod(\"getUseLog\", \"well\", \n function(object){\n return(object@use.log)\n })\n\nsetGeneric(\"getNorm\", function(object){standeardGeneric(\"getNorm\")})\nsetMethod(\"getNorm\", \"well\", \n function(object){\n return(object@norm)\n })\n\nsetGeneric(\"getCurPar\", function(object){standeardGeneric(\"getCurPar\")})\nsetMethod(\"getCurPar\", \"well\", \n function(object){\n return(object@curve.par)\n })\n\nsetGeneric(\"getFitErr\", function(object){standeardGeneric(\"getFitErr\")})\nsetMethod(\"getFitErr\", \"well\", \n function(object){\n return(object@fit.std.err)\n })\n\nsetGeneric(\"getEquation\", function(object){standeardGeneric(\"getEquation\")})\nsetMethod(\"getEquation\", \"well\", \n function(object){\n return(object@equation)\n })\n\nsetGeneric(\"getModelName\", function(object){standeardGeneric(\"getModelName\")})\nsetMethod(\"getModelName\", \"well\", \n function(object){\n return(object@model.name)\n })\n\nsetGeneric(\"getFitInfo\", function(object){standeardGeneric(\"getFitInfo\")})\nsetMethod(\"getFitInfo\", \"well\", \n function(object){\n return(object@fit.info)\n })\n\nsetGeneric(\"getAddInfo\", function(object){standeardGeneric(\"getAddInfo\")})\nsetMethod(\"getAddInfo\", \"well\", \n function(object){\n return(object@add.info)\n })\n\nsetGeneric(\"getInflectionTime\", function(object){standeardGeneric(\"getInflectionTime\")})\nsetMethod(\"getInflectionTime\", \"well\", \n function(object){\n return(object@inflection.time)\n })\n\nsetGeneric(\"getRSS\", function(object){standeardGeneric(\"getRSS\")})\nsetMethod(\"getRSS\", \"well\", \n function(object){\n return(object@rss)\n })\n\nsetGeneric(\"getLoess\", function(object){standeardGeneric(\"getLoess\")})\nsetMethod(\"getLoess\", \"well\", \n function(object){\n return(object@loess)\n })\n\nsetGeneric(\"getnls\", function(object){standeardGeneric(\"getnls\")})\nsetMethod(\"getnls\", \"well\", \n function(object){\n return(object@nls)\n })\n\nsetGeneric(\"getFitPar\", function(object){standeardGeneric(\"getFitPar\")})\nsetMethod(\"getFitPar\", \"well\", \n function(object){\n return(object@fit.par)\n })\n\n# --------------------------------------------------------------------\n# Function to create a new well (requires only Time and OD vectors, which will fill slot \"screen.data\")\n# slots \"nls\" and \"loess\" are initialized to empty lists\nwell = function(Time = NULL, OD = NULL){\n x = list()\n class(x) = \"loess\"\n y = list()\n class(y) = \"nls\"\n\tnew(\"well\", screen.data = data.frame(Time, OD, stringsAsFactors=F), loess=x, nls=y)\n}\n\n# -----------------------------------------------------------------------\n#### A show method for well ####\nsetMethod(\"show\", \"well\",\n function(object) {\n print(\"Object of class well\")\n print(\"@position:\")\n print(object@position)\n print(\"@well.info:\")\n print(object@well.info)\n print(\"@screen.data:\")\n print(head(object@screen.data))\n print(\"...\")\n print(paste(nrow(object@screen.data),\"rows of data\"))\n print(paste(\"@start.index:\",object@start.index))\n print(paste(\"@use.log:\",object@use.log))\n print(paste(\"@norm:\",object@norm))\n print(\"@curve.par:\")\n print(object@curve.par)\n print(\"@fit.par:\")\n print(object@fit.par)\n print(\"@fit.std.err:\")\n print(object@fit.std.err)\n print(paste(\"@equation:\",object@equation))\n print(paste(\"@model.name:\",object@model.name))\n print(paste(\"@fit.info:\",object@fit.info))\n print(paste(\"@add.info:\",object@add.info))\n print(paste(\"@inflection.time:\",object@inflection.time))\n print(paste(\"@rss:\",object@rss))\n if (length(object@nls) > 0) {\n print(\"@nls:\")\n print(object@nls)\n } else {\n print(\"no nls model\")\n }\n if (length(object@loess) > 0) {\n print(\"@loess:\")\n print(object@loess)\n } else {\n print(\"no loess model\")\n }\n }\n )\n\n#### A plot method for well ####\n# x - object of class well\n# y - not used\n# constant.added - used to readjust for the constant added during the log transform: log.OD = log(OD - blank + constant.added)\n# xlim - x axis limits, vector of length 2\n# ylim - y axis limits, vector of length 2\n# scale - determines the font scale for the entire graph. all cex values are calculated from this\n# number.points - should points be labeled with numeric indices?\n# draw.symbols - should be called on the well and markings drawn on the graph?\n# show.text - show R^2 and growth curve parameters as text on the plot\n# show.calc - draw lines that illustrate growth curve parameters\n# draw.guess - initial guess model. Drawn if specified\n# well.number - the number of the well in an array of wells\n# ... - additional arguments passed to the generic plot function\n\nsetMethod(\"plot\",\n signature(x = \"well\", y=\"missing\"),\n function (x, y, constant.added = 1.0, xlim = NULL, ylim = NULL,\n well.number = NULL, scale = 1, number.points = T, draw.symbols = F, show.text = T, show.calc = T, draw.guess = NULL, ...) \n {\n # Determine the boundaries for the axes (if user did not specify them)\n if(is.null(ylim)){\n min.y = min(data.from(x, remove = F, remove.tanking = F)[,2], na.rm = T)\n min.y = min(min.y, x@fit.par$b)\n max.y = max(data.from(x, remove = F, remove.tanking = F)[,2], na.rm = T)\n max.y = max(max.y, x@fit.par$b + x@fit.par$A)\n ylim = c(min.y, min.y + (max.y-min.y)*1.15)\n }\n if(is.null(xlim)){\n min.x = min(data.from(x, remove = F, remove.tanking = F)[,1], na.rm = T)\n max.x = max(data.from(x, remove = F, remove.tanking = F)[,1], na.rm = T)\n xlim = c(min.x - 0.05 * (max.x-min.x), max.x)\n }\n \n \n # Title of plot: [well number] plate name; well name;\n # strain name; media name\n \n main = paste(plate.name(x), \" \", well.name(x), \"\\n\",\n strain.name(x), \"; \", media.name(x), sep = \"\")\n if (!is.null(well.number)) main = paste(\"[\", well.number , \"] \", main, sep=\"\")\n \n # Draw the data and symbols if is true.\n plot.data(x, main = main, scale = scale, constant.added=constant.added, \n number.points = number.points, draw.symbols = draw.symbols, xlim = xlim, ylim = ylim, ...)\n \n # Draw the fitted model.\n plot.model(x, scale = scale, constant.added=constant.added)\n \n # Draw text info if specified. \n if(show.text)\n draw.text(x, scale = scale * 0.5, xlim = xlim, ylim = ylim,...)\n \n # Show calculated parameters if specified. \n if (show.calc)\n draw.calc.par(x, scale = scale * 0.5, constant.added = constant.added)\n \n # Draw initial guess if a model is specified. \n if (class(draw.guess) == \"model\"){\n Time = data.from(x)$Time\n guess = eval(getExpression(draw.guess), as.list(getGuess(draw.guess)(x)))\n try(lines(Time, guess, col = \"brown2\"), silent = T)\n }\n }\n)\n\n########################################################################\n# Some miscellaneous functions to extract info from well objects #\n# Most of these return a single value from the well. #\n########################################################################\n#\n# Since many of these need to be applied to all wells over an array, while conserving the dimensions of \n# that array, this file includes a wrapper function (see bottom of file).\n\nplate.name = function(well)\n\tgetPosition(well)[1]\n\n# Return the full alphanumeric well name (with leading zeros if applicable)\nwell.name = function(well){\n\trow = getPosition(well)[2]\n\tcol = as.numeric(getPosition(well)[3])\n\tif (col>9)\n\t\tcol = as.character(col)\n\telse\n\t\tcol = paste(\"0\", col, sep = \"\")\n\n\tpaste(row,col,sep = \"\")\n\t}\n\nis.empty = function(well)\n\tgetCurPar(well)$empty.well\n\nlacks.growth = function(well)\n\tgetCurPar(well)$no.growth\n\ntanking.start = function(well)\n\tgetCurPar(well)$tanking.start\n\nremoved.points = function(well)\n\t(1:length(well))[getScreenData(well)$Remove]\n\nremaining.points = function(well,...){\n\tas.numeric(rownames(data.from(well,...)))\n\t}\n\nstrain.name = function(well){\n if(is.null(getWellInfo(well)$Strain))\n return(\"\")\n else\n return(getWellInfo(well)$Strain)\n }\nmedia.name = function(well){\n if(is.null(getWellInfo(well)$Media))\n return(\"\")\n else\n return(getWellInfo(well)$Media)\n }\n\nraw.data = function(well)\n\tdata.from(well, remove.tanking = F, remove = F, na.rm = F, raw.data = T)\n\ncontains.fit = function(well)\n\tlength(getFitPar(well)) > 0\n\nsetMethod(\"length\", signature(x = \"well\"), function(x) length(x@screen.data[,1]))\n\n# The function has some options: by default it returns a two-column data frame with time and OD \n# (or log OD if the slot is true in the object), after normalization to the value specified in slot. \n# - With set to true the rows specified in the column of the slot are not returned. \n# - With set to true all the rows after the index are removed. \n# - Setting to true overrides all these settings and just returns 2 columns with Time and Raw OD.\n\ndata.from = function(well, remove = T, remove.tanking = T, raw.data = F, na.rm = F){\n\t\n\tif (length(getUseLog(well)) == 0)\n\t\tOD.column = \"OD\"\n\telse if (getUseLog(well))\n\t\tOD.column = \"log.OD\"\n\telse\n\t\tOD.column = \"OD\"\n\t\n\tif (raw.data){\n\t\tOD.column = \"OD\"\n\t\tnorm = 0\n\t\t}\n\telse if (!getUseLog(well))\n\t\tnorm = getNorm(well)\n\telse\n\t\tnorm = 0\n\n\tif(remove.tanking & is.numeric(tanking.start(well)))\n\t\twell = remove.points(well, (tanking.start(well)):length(well))\n\tif (!remove | is.null(getScreenData(well)$Remove))\n\t\toutput = getScreenData(well)[c(\"Time\", OD.column)]\n\telse\n\t\toutput = getScreenData(well)[!getScreenData(well)$Remove ,c(\"Time\", OD.column)]\n\n\toutput[,2] = output[,2] - norm\n\n\tif (!raw.data){\n\t\tif (!length(getUseLog(well)))\n\t\t\tnames(output)[2] = \"Corrected.OD\"\n\t\tif (!getUseLog(well))\n\t\t\tnames(output)[2] = \"Corrected.OD\"\n\t\t}\n\n\tif (na.rm)\n\t\toutput[!is.na(output[,2]),]\t \n\telse\n\t\toutput\n\t}\n\n\n# Functions much like but gives a single vector containing the \n# slope at each point. Has a parameter allowing removal of NA values. \n\nslopes = function(well, remove = T, remove.tanking = T, na.rm = F){\n\n\tif(remove.tanking & is.numeric(tanking.start(well)))\n\t\twell = remove.points(well, (tanking.start(well)):length(well))\n\tif (!remove | is.null(getScreenData(well)$Remove))\n\t\toutput = getScreenData(well)$Slope\n\telse\n\t\toutput = getScreenData(well)$Slope[!getScreenData(well)$Remove]\n\n\tif (na.rm)\n\t\toutput[!is.na(output)]\t \n\telse\n\t\toutput\n\t}\n\n# -----------------------------------------------------------------------\n# Well array functions: these must be used on entire arrays of well objects\n# instead of single ones. \n\nplate.names = function(well.array)\n\tdimnames(well.array)[[3]]\n\ntanking.start.values = function(well.array, array = F){\n\tif (array)\n\t\taapply(well.array, function(well) tanking.start(well))\n\telse\n\t\tsapply(well.array, function(well) tanking.start(well))\n\t}\n\n", - "created" : 1425413290697.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "2437520955", - "id" : "4DC8D1", - "lastKnownWriteTime" : 1425509121, - "path" : "~/Documents/GCAT4/trunk/R/GCAT/R/class.well.R", - "project_path" : "R/class.well.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/4E20D973 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/4E20D973 deleted file mode 100644 index ee62373..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/4E20D973 +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n\n# Wrapper for sapply to use lapply over an array, conserving the dimensions.\naapply = function(x, FUN,...){\n dim.values = dim(x)\n\tdim.names = dimnames(x)\n\tx = lapply(x, function(x){FUN(x,...)})\n\tdim(x) = dim.values\n\tdimnames(x) = dim.names\n\treturn(x)\n\t}\n\n# A function to manually create an unchecked exception.\nexception = function(class, msg)\n{\n cond <- simpleError(msg)\n class(cond) <- c(class, \"MyException\", class(cond))\n stop(cond)\n}\n", - "created" : 1425413273698.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "3044086993", - "id" : "4E20D973", - "lastKnownWriteTime" : 1424208963, - "path" : "~/Documents/GCAT4/trunk/R/GCAT/R/misc.R", - "project_path" : "R/misc.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/6FF7DC6F b/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/6FF7DC6F deleted file mode 100644 index a243cea..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/6FF7DC6F +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n\n########################################################################\n# #\n# Populate an output table with parameters and other useful info for #\n# each well in a fitted dataset. #\n# #\n########################################################################\n#\n# unlog - Should OD values be returned on the linear scale instead of log-transformed scale? \n# constant.added - For returning values on linear scale, what constant was added to ODs before the log transform? \n# reach.cutoff - what proportion of the plateau OD must tbe reached by the last valid timepoint for the curve to be marked as reaching its plateau OD?\n#\n\ntable.out = function(fitted.data.set, unlog = F, constant.added, reach.cutoff = 0.90, filename.timestamp = NULL,use.linear.param=F, use.loess=F){\n \n # The idea is basically to use and on the fitted data array in order \n # to get one vector for each column of the output table. \n \n # Get identifying information (plate, well, media and strain names)\n plate.ID = unlist(aapply(fitted.data.set,plate.name))\n well.ID = unlist(aapply(fitted.data.set,well.name))\n media.ID = unlist(aapply(fitted.data.set,media.name))\n strain.ID = unlist(aapply(fitted.data.set,strain.name))\n # Get fit information for each well\n # - was it marked as empty in the plate layout?\n # - did the program find it to contain no growth (\"dead\")? \n # - was the fitting procedure successful? \n # - did the curve tank? if so, at what timepoint? if not, set value to \"-\"\n \n empty = unlist(aapply(fitted.data.set, is.empty))\n dead = unlist(aapply(fitted.data.set, lacks.growth))\n fit = unlist(aapply(fitted.data.set, contains.fit))\n tanking = unlist(aapply(fitted.data.set, tanking.start))\n tanking[is.na(tanking) | tanking == 1 | dead] = \"-\"\n \n # Get calculated values for each well: specific growth, final and initial OD, fitted plateau and baseline OD, lag time, etc.\n inflection.time = unlist(aapply(fitted.data.set, inflection.time))\n max.spec.growth.rate = unlist(aapply(fitted.data.set, max.spec.growth.rate))\n max.log.OD = unlist(aapply(fitted.data.set, max.log.OD))\n inoc.log.OD = unlist(aapply(fitted.data.set, inoc.log.OD))\n projected.growth = unlist(aapply(fitted.data.set, projected.growth))\n projected.growth.OD = unlist(aapply(fitted.data.set, projected.growth.OD, constant.added))\n achieved.growth = unlist(aapply(fitted.data.set, achieved.growth))\n achieved.growth.OD = unlist(aapply(fitted.data.set, achieved.growth.OD, constant.added))\n lag.time = unlist(aapply(fitted.data.set, lag.time))\n shape.par = unlist(aapply(fitted.data.set, shape.par))\n RSS = unlist(aapply(fitted.data.set, rss))\n baseline = unlist(aapply(fitted.data.set, baseline))\n amplitude = unlist(aapply(fitted.data.set, amplitude))\n plateau = unlist(aapply(fitted.data.set, plateau))\n ########################3h#############################################\n max.spec.growth.rate.SE = unlist(aapply(fitted.data.set, max.spec.growth.rate.SE))\n shape.par.SE = unlist(aapply(fitted.data.set, shape.par.SE))\n lag.time.SE = unlist(aapply(fitted.data.set, lag.time.SE))\n amplitude.SE = unlist(aapply(fitted.data.set, amplitude.SE)) # a.k.a amplitude error\n baseline.SE = unlist(aapply(fitted.data.set, baseline.SE)) # a.k.a baseline error\n #######################################################################\n \n # If the curve falls short of 90% of plateau OD by the final timepoint.\n no.reach.plateau = !unlist(aapply(fitted.data.set, reach.plateau, cutoff = 0.9))\n # If the fitted baseline is below zero on linear scale\n no.reach.baseline = unlog(baseline,constant.added) < 0\n \n # If any of these are NA as a result of failed fits, change them to false: they don't need to be reported. \n no.reach.plateau[is.na(no.reach.plateau)] = F\n no.reach.baseline[is.na(no.reach.baseline)] = F\n # What percent of the total growth does the curve actually reach? \n # (in case of total growth being 0, change this to 100%)\n percent.reach = 100*((max.log.OD - inoc.log.OD) / (projected.growth))\n percent.reach[is.infinite(percent.reach)] = 100\n \n # Return the name of the model (if any) that was successfully fit to the well. \n model.used = unlist(aapply(fitted.data.set, function(well)well@model.name))\n \n # \"Goodness of fit\" metric\n good.fit = unlist(aapply(fitted.data.set, model.good.fit))\n \n # Code the two flags: \n flag1 = flag2 = rep(\"-\", length(tanking))\n \n for(i in 1:length(tanking)){\t\n # Flag 1 (empty/inoculated flag) possible values:\n # well was empty and no growth was found (E)\n # well was empty, but growth was found (E*)\n # well was inoculated but no growth was found (!)\n # well was inoculated and growth was found (I)\n \n if(empty[i] & !fit[i])\n flag1[i] = \"E \"\n if(empty[i] & fit[i])\n flag1[i] = \"E*\"\n if(!empty[i] & dead[i])\n flag1[i] = \"! \"\n if(!empty[i] & !dead[i])\n flag1[i] = \"I \"\n \n # Flag 2 (lower/upper asymptotes) possible values:\n # well did not reach lower asymptote (baseline OD) (L)\n # well did not reach upper asymptote (plateau OD) (U)\n # well did not reach either asymptote (L/U)\n # well reached both asymptotes (-)\n \n if(no.reach.baseline[i]){\n if (no.reach.plateau[i])\n flag2[i] = \"L/U\"\n else\n flag2[i] = \"L\"\n }\n else{\n if (no.reach.plateau[i])\n flag2[i] = \"U\"\n else\n flag2[i] = \"-\"\n }\n # Also use the and and to provie more info about why model fitting failed in some cases. \n if(dead[i])\n model.used[i] = \": skipped\"\n else if(!empty[i] & !fit[i])\n model.used[i] = \": failed\"\t\n }\n \n # Flag 3: return the additional info slot. \n flag3 = unlist(aapply(fitted.data.set, function(well){\n if (length(well@add.info) > 0) \n return(well@add.info)\n else\n return(\"\")\n }))\n \n # If something is amiss with the data table use this to check on the arguments...\n #cat(\"plate \", length(plate.ID),\" well \", length(well.ID),\" media \", length(media.ID),\" strain \", length(strain.ID),\n #\" model \", length(model.used),\" max.spec.growth.rate\", length(max.spec.growth.rate), \"projected.growth\", length(projected.growth),\n #\"lag.time\", length(lag.time), \"inoc.log.OD\", length(inoc.log.OD), \"good.fit\",\n #length(good.fit),\"empty\", length(flag1),\"asymp\", length(flag2),\" tank \", length(tanking),\" reach \", length(percent.reach),\" other \", length(flag3), sep = \"\\n\")\n # 06.28.11: Add a row number identifier for output perusal\n row.number = 1:length(plate.ID)\n \n pdf.file = page.no = c()\n # 06.29.11: Add pdf file name and page number references. Prepare timestamp for addition to output file names (for file references in last column)\n for(i in 1:length(plate.ID)){\n pdf.file[i] = paste(plate.ID[i], \"_plots\", filename.timestamp, \".pdf\", sep=\"\")\n page.no[i] = (i-1) %% 96 + 2\n }\n # Slap it all together into a data frame.\n if(use.loess){\n output.core = data.frame(row = row.number, plate = plate.ID, well = well.ID, media = media.ID, strain = strain.ID, \n model = model.used, lag.time, inflection.time, max.spec.growth.rate, \n baseline, amplitude, plateau, inoc.log.OD, max.log.OD, achieved.growth,\n baseline.OD = unlog(baseline,constant.added), amplitude.OD = unlog(amplitude,constant.added), \n plateau.OD = unlog(plateau,constant.added), inoc.OD = unlog(inoc.log.OD,constant.added), \n max.OD = unlog(max.log.OD,constant.added), achieved.growth.OD = achieved.growth.OD,\n R.squared = good.fit, RSS = RSS, empty = flag1, asymp.not.reached = flag2, tank = tanking, other = flag3, pdf.file = pdf.file, page.no = page.no)\n } else {\n output.core = data.frame(row = row.number, plate = plate.ID, well = well.ID, media = media.ID, strain = strain.ID, \n model = model.used, lag.time = lag.time, lag.time.SE, inflection.time, max.spec.growth.rate, max.spec.growth.rate.SE, \n baseline, baseline.SE, amplitude, amplitude.SE, plateau, inoc.log.OD, max.log.OD, projected.growth, achieved.growth,\n baseline.OD = unlog(baseline,constant.added), amplitude.OD = unlog(amplitude,constant.added), \n plateau.OD = unlog(plateau,constant.added), inoc.OD = unlog(inoc.log.OD,constant.added), \n max.OD = unlog(max.log.OD,constant.added), projected.growth.OD = projected.growth.OD, achieved.growth.OD = achieved.growth.OD,\n shape.par = shape.par, shape.par.SE,\n R.squared = good.fit, RSS = RSS, empty = flag1, asymp.not.reached = flag2, tank = tanking, other = flag3, pdf.file = pdf.file, page.no = page.no)\n }\n \n # Add units to column names\n names2 = names(output.core)\n names2[grep(\"time\",names2)] = sub(\"$\",\", hrs\", names2[grep(\"time\",names2)])\n names2[grep(\"rate\",names2)] = sub(\"$\",\", log.OD/hr\", names2[grep(\"rate\",names2)])\n log.OD.fields = c(\"baseline\", \"baseline.SE\", \"amplitude\", \"amplitude.SE\", \"plateau\", \"projected.growth\", \"achieved.growth\")\n names2[names2 %in% log.OD.fields] = sub(\"$\", \", log.OD\", names2[names2 %in% log.OD.fields])\n names(output.core) = names2\n \n # Add on any additional fields found in the plate layout. \n all.layout.fields = sapply(fitted.data.set, function(well) unlist(well@well.info)) \n all.layout.fields = as.data.frame(t(all.layout.fields))\n \n \n addl.info = all.layout.fields[,!(names(all.layout.fields) %in% c(\"Strain\", \"Media\"))]\n if(!is.data.frame(addl.info)){\n addl.info = data.frame(addl.info)\n names(addl.info) = names(all.layout.fields)[!(names(all.layout.fields) %in% c(\"Strain\", \"Media\"))] \n }\n \n output = cbind(output.core,addl.info)\n \n return(output)\n}\n\n\n\n\n\n\n", - "created" : 1425413247086.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "2376564637", - "id" : "6FF7DC6F", - "lastKnownWriteTime" : 1424208623, - "path" : "~/Documents/GCAT4/trunk/R/GCAT/R/table.output.R", - "project_path" : "R/table.output.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/74C1CB00 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/74C1CB00 deleted file mode 100644 index bcbbd2a..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/74C1CB00 +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n\n########################################################################\n# #\n# Normalize OD readings for an entire array of well objects #\n# #\n########################################################################\n#\n# Note: This function does not write any new OD values to the well objects in the array - it only \n# fills the \"norm\" slot of each well object in the array with a value that will be subtracted \n# from all OD measurements when returning data from the wells using the function (see well.class.R) \n#\n# These functions make use of which simply returns the raw time and OD of a well (also see well.class.R)\n#\n# well.array: an array of well objects. note this is the only normalization function that acts on an entire array instead of an individual well.\n# normalize.method: \n# - (default): subtracts the blank OD (either specified by or taken from the first timepoint as default) of each well from all timepoints in that well\n# - average.blank: subtracts the mean of all first OD timepoints on a plate from all timepoints in all wells on that plate\n# - average.first: takes the mean of the difference between the OD of the specified timepoint and the first timepoint of all wells on a plate\n# and subtracts this value from all timepoints in all wells on that plate\n# - anything else: do nothing\n# blank.value - user can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. \n# start.index - which timepoint should be used as the first one after inoculation (defaults to the 2th one)\n# add.constant: add a numeric constant to all timepoints in all wells. \nnormalize.ODs = function(well.array, normalize.method = \"default\", blank.value = NULL, start.index = 2, add.constant = 1){\n \n if (normalize.method == \"default\"){\n well.array = aapply(well.array, function(well, blank.value){\n # Use the blank OD value if specified; otherwise, get it from the first OD timepoint. \n if(is.null(blank.value)) blank.value = raw.data(well)[1,2]\n # Set the blank OD (minus the constant to be added) to the \"norm\" slot of each well.\n \twell@norm = blank.value - add.constant\n \treturn(well)}, blank.value)\n }\n else if (normalize.method == \"average.blank\"){ \n # Use the blank OD value if specified; otherwise, get it from the first OD timepoint.\n\t\tblank.ODs = unlist(aapply(well.array, function(well, blank.value){\n if(is.null(blank.value)) blank.value = raw.data(well)[1,2]\n return(blank.value)}, blank.value))\n\t\tplate.IDs = unlist(aapply(well.array, plate.name))\n\t\tblank.averages = tapply(blank.ODs, plate.IDs, mean)\n\t # Set this value (minus the constant to be added) to the \"norm\" slot of each well. \n\t\twell.array = aapply(well.array, function(well){\n\t\t\twell@norm = blank.averages[plate.name(well)] - add.constant\n\t\t\treturn(well)})\n\t\t}\n\telse if (normalize.method == \"average.first\"){\n\t # Find the mean difference between starting OD (timepoint specified by ) and blank OD (first timepoint) for each plate\n # Use the blank OD value if specified; otherwise, get it from the first OD timepoint.\n blank.ODs = unlist(aapply(well.array, function(well, blank.value){\n if(is.null(blank.value)) blank.value = raw.data(well)[1,2]\n return(blank.value)}, blank.value))\n\t\tfirst.ODs = unlist(aapply(well.array, function(well) raw.data(well)[start.index,2]))\n\t\tplate.IDs = unlist(aapply(well.array, plate.name))\n\t blank.averages = tapply(first.ODs-blank.ODs,plate.IDs,mean)\n\t # Set this value (minus the constant to be added) to the \"norm\" slot of each well.\n\t\twell.array = aapply(well.array, function(well){\n\t\t\twell@norm = raw.data(well)[start,2] - blank.averages[plate.name(well)] - add.constant \n\t\t\treturn(well)})\n\t\t}\t\n\telse{\n # Simply set the negative constant to be added to the \"norm\" slot of each well. \n\t\twell.array = aapply(well.array, function(well){\n\t\t\twell@norm = - add.constant\n \t\t\treturn(well)})\n\t\t}\n if(is.null(blank.value))\n well.array = aapply(well.array, remove.points, 1)\n return(well.array)\n\t}\n\n########################################################################\n# #\n# Log-transform OD readings for a single well object #\n# #\n########################################################################\n\n# Must include this so that the checking process will not complain about\n# inconsistency S3 generic/method. Though I don't know why.\ntransform <- function(input.well, ...) {\n UseMethod(\"transform\")\n}\n\n#' Transform.Ods \n#' \n#' This function adds a \"log.OD\" column to the \"screen.data\" slot of a well object with log-transformed data. \n#' The raw data is kept intact. \n#' It also checks to see if any of the raw OD values (before a certain timepoint) is below the blank OD. \n#' This can be disastrous for the log(OD) transform. \n#' @param input.well an object of class well \n#' @param use.log gets added to the \"use.log\" slot of the well object. this will determine whether the log-transformed data \n#' or raw normalized data is returned using the function \\code{data.from}. \n#' @param blank.value user can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. \n#' @param start.index which timepoint should be used as the first one after inoculation (defaults to the 2th one) \n#' @param negative.OD.cutoff if any ODs below the specified blank value are detected before this index timepoint, the entire well is discarded. \ntransform.ODs = function(input.well, use.log = T, blank.value = NULL, start.index = 2, negative.OD.cutoff = 10, constant.added = 1.0, ...){\n \n # The default value for the log-transformed ODs will be NA. Valid values will be filled in. \n\tlog.OD = rep(NA, length(input.well))\n OD = raw.data(input.well)[,2]\n \n\t # Use the blank OD value if specified; otherwise, get it from the first OD timepoint.\n if(is.null(blank.value))\n blank.value = OD[1]\n\n # Remove any points from the analysis that weren't already removed and fall below the blank value (using below)\n OD[input.well@screen.data$Remove] = NA\n \n negative.points = which(OD + 0.2 * constant.added < blank.value)\n if(length(negative.points) > 0)\n\t input.well = remove.points(input.well, negative.points)\n \n # If any points fall below the blank value by more than 0.2 * and before the cutoff index , remove the well from analysis. \n # First adjust the cutoff to compensate for curves that don't start at timepoint 1\n negative.OD.cutoff = negative.OD.cutoff + start.index - 1\n \n if(any(negative.points <= negative.OD.cutoff)){\n input.well = remove.points(input.well, rep(T,length(input.well)))\n input.well@add.info = paste(\"ODs at timepoint(s)\", paste(negative.points[negative.points <= negative.OD.cutoff],collapse=\" \"), \"were below blank OD; well discarded\")\n }\n\n # Take the natural log of the rest of the OD values (after subtracting the normalization value)\n log.OD[which(OD > input.well@norm)] = log(OD[which(OD > input.well@norm)] - input.well@norm)\n\t\n\t# Add a column to the \"screen.data\" slot of the well\n\tinput.well@screen.data$log.OD = log.OD\t\n\t# Update the \"use.log\" slot of the well \n\tinput.well@use.log = use.log\t\n\n\treturn(input.well)\n\t}\n\n########################################################################\n# #\n# Remove timepoints from the analysis but not from the raw data #\n# #\n########################################################################\n# \n# Removes timepoints from further analysis. Does not remove them from the raw data;\n# instead, this function creates or updates the Remove column in slot \"screen.data\" of the well which dictates whether \n# individual timepoints are returned using the function. \n#\n# can be a vector containing:\n# - any combination of positive and negative integers \n# the timepoints at indices corresponding to positive integers will be set to be removed.\n# the timepoints at indices corresponding to negative integers will be be re-added if they were previously set to be removed.\n# - a single zero, which resets all timepoints (nothing will be removed)\n# - a logical vector to replace the Remove column and which will be cycled along the length of the timepoints. \n\nremove.points = function(input.well, points){\n # Copy the Remove column or create a new one if it doesn't yet exist\n\tif (is.null(input.well@screen.data$Remove))\n\t\tRemove = rep(F, length(input.well))\n\telse\n\t\tRemove = input.well@screen.data$Remove\n\n # If is a logical vector, recycle it along the length of Remove \n\tif (length(points[!is.na(points)]) != 0){\n\t# Separate positive and negative integers\n \tif (is.logical(points) & !any(is.na(points)))\n \t\tRemove = rep(points,length.out=nrow(input.well@screen.data))\t\n \t\telse{\n \tpos = points[points > 0]\n \tneg = -points[points < 0]\n \tRemove[pos] = T\n \tRemove[neg] = F \n \t\t \t\n # If contains only zeros, reset the Remove vector to all F \t\n \tif (all(points == 0))\n \t\tRemove[1:length(Remove)] = F\n \t\t}\n }\n # replace the Remove column\n\tinput.well@screen.data$Remove = Remove\n\tinput.well\n\t}\n\n\n\n\n\n", - "created" : 1425413265888.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "3349576883", - "id" : "74C1CB00", - "lastKnownWriteTime" : 1428436335, - "path" : "~/Documents/GCAT4/trunk/R/GCAT/R/normalize.and.transform.R", - "project_path" : "R/normalize.and.transform.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/907B51DB b/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/907B51DB deleted file mode 100644 index 6ee699e..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/907B51DB +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "# Default NAMESPACE created by R\n# Remove the previous line if you edit this file\n\n# Export all names\nexportPattern(\".\")\n\n# Import all packages listed as Imports or Depends\nimport(\"pheatmap\", \"gplots\")\n", - "created" : 1428439772005.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "749067415", - "id" : "907B51DB", - "lastKnownWriteTime" : 1423260997, - "path" : "~/Documents/GCAT4/trunk/R/GCAT/NAMESPACE", - "project_path" : "NAMESPACE", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_namespace" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/992E3490 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/992E3490 deleted file mode 100644 index f8ed693..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/992E3490 +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,\n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n########################################################################\n# #\n# class definition and functions. Objects contain equations #\n# and other information for parameterized growth curve models. #\n# #\n########################################################################\nsetClass(\"model\", representation(name = \"character\",\n expression = \"expression\",\n formula = \"formula\",\n guess = \"function\"))\n# Slots:\n# name - a simple description of the model.\n# expression - an object of class \"expression\" that evaluates the response (transformed OD) with respect to the variable Time.\n# formula - same as expression, but with y as the response.\n# guess - a function that computes initial guesses for the parameters given a well object with a valid \"screen.data\" slot\n# containing useable OD values and slope estimates\n# --------------------------------------------------------------------\n###################### BEGIN PROTOTYPING ACCESSOR METHODS##############\n\n# Minh: Let this code fragment be F1.\nif (!isGeneric(\"getName\")){\n if (is.function(\"getName\"))\n fun <- getName\n else\n fun <- function(object) standardGeneric(\"getName\")\n setGeneric(\"getName\", fun)\n}\n# End of F1\nsetMethod(\"getName\", \"model\", function(object) object@name)\n\n# Minh: Let this line be F2.\nsetGeneric(\"getExpression\", function(object){standardGeneric(\"getExpression\")})\n# Question: How is F1 different from F2?\n\nsetMethod(\"getExpression\", \"model\",\n function(object){\n return(object@expression)\n })\n\nsetGeneric(\"getFormula\", function(object){standeardGeneric(\"getFormula\")})\nsetMethod(\"getFormula\", \"model\", \n function(object){\n return(object@formula)\n })\n\nsetGeneric(\"getGuess\", function(object){standeardGeneric(\"getGuess\")})\nsetMethod(\"getGuess\", \"model\", \n function(object){\n return(object@guess)\n })\n######################## ENG PROTOTYPING ########################\n\n# Function to create a new model\n#' Model \n#' \n#' Function to create a new model \n#' @param name The name of the model \n#' @param expression Expression of the model \n#' @param formula The formula of this model \n#' @param guess The guess of this model \n#' @return The new model \nmodel = function(name, expression, formula, guess){\n new(\"model\", name = name, expression = expression, formula = formula, guess = guess)\n}\n\nloess.g = function(well,smooth.param=0.75){\n #data = data.from(well)\n #growth = data[,2]\n #Time = data[,1]\n Time = data.from(well)[,1]\n \n # predicted growth values to be used in estimating growth curve parameters\n loess.fit = loess(data.from(well)[,2]~Time,span=smooth.param)\n t = seq(from = min(Time), to = max(Time), by = (max(Time)-min(Time))/1000)\n y = predict(loess.fit, data.frame(Time=t))\n attr(y,\"names\") = NULL # need to remove the names to prevent them from showing up in the returned vector\n \n # Remove any data points where y has not been estimated\n filt = is.finite(y)\n t = t[filt]\n y = y[filt] # remove any NA etc\n \n # specific growth using loess to find max derivative\n delta.t = diff(t)\n dydt = diff(y)/delta.t\n u = max(dydt)\n \n # lower and upper asymptotes\n b = min(y)\n A = max(y) - min(y)\n \n # inflection point\n inflection.pt.index = which.max(dydt)\n inflection.time = t[inflection.pt.index]\n inflection.y = y[inflection.pt.index]\n \n # lag time\n lam = inflection.time - (inflection.y-b)/u\n \n # Return named array of estimates\n c(A = A, b = b, lam = lam, u = u)\n}\n\n\n", - "created" : 1425419995370.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "2225975310", - "id" : "992E3490", - "lastKnownWriteTime" : 1425511077, - "path" : "~/Documents/GCAT4/trunk/R/GCAT/R/class.model.R", - "project_path" : "R/class.model.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/B0B7416E b/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/B0B7416E deleted file mode 100644 index 30cb003..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/B0B7416E +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,\n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n########################################################################\n# #\n# Fit a parameterized model to the growth data in a well object. #\n# #\n# There are now three modelling choices: #\n# 1) Sigmoid model (no linear param c) #\n# 2) Linear Sigmoid model #\n# 3) Loess (with optional smoothing parameter) #\n########################################################################\n#' fit.model \n#' \n#' This function will use the function stored in the \"guess\" slot of \\code{growth.model} to calculate initial guesses \n#' for growth.model parameters, then it will use the \"formula\" slot with \\code{nls} to fit a non-linear least squares \n#' \\code{growth.model} or Local Polynomial Regression Fitting to the data. Richards model is first fitted. \n#' If the shape parameter is statisticaly significant then Richards is used. If it is within 2 SE of 1 or Zero than \n#' a simpler model is preferred. If the Richards fit fails, then Logistic is tried. If it fails, Gompertz is tried. \n#' Model fit failure is reported if none of the models can sucessfully fit the data \n#' \n#' @param input.well The well needed to be fitted with the given model. \n#' @param growth.model What growth model should be used? \n#' @param backup.growth.model If \\code{gowth.mode} fails, this model will be used. \n#' @param fit.if.no.growth should the function attempt to fit a well even if there was no growth detected? default is F \n#' @param silent output back to R console? \n#' @param use.linear.param: Should an additional linear parameter (c) be used when fitting the data to the model? \n#' @param use.loess: Should Local Polynomial Regression Fitting (loess function) be used instead of nls? \n#' @param smooth.param: If loess is used, an optional smoothing parameter. Default is .6 \nfit.model = function(input.well, growth.model, backup.growth.model = NULL, fit.if.no.growth = F, \n use.linear.param=F, use.loess=F, smooth.param, silent = T){\n \n # Conditional breakpoint: go into debugging mode when fitting a specific well\n #if (input.well@position[\"row\"] == \"A\" && input.well@position[\"col\"] == \"12\") browser()\n \n # Change all relevant slots to or blank values\n input.well@model.name = \"\"\n input.well@fit.par = list()\n input.well@equation = expression()\n \n # Get OD vs. time data from well\n input.data = data.from(input.well, na.rm = T)\n \n # Skip well if in slot \"curve.par\" is set to true, and is false.\n if(!fit.if.no.growth & lacks.growth(input.well)){\n input.well@fit.info = \"skipped - no growth in well.\"\n if (!silent)\n cat(plate.name(input.well), well.name(input.well), \":\", input.well@fit.info, \"\\n\")\n return(input.well)\n }\n # Skip well if there are fewer than 5 data points left in the analysis.\n if (length(input.data$Time) < 5){\n input.well@fit.info = \"skipped - not enough points.\"\n if (!silent)\n cat(plate.name(input.well), well.name(input.well), \":\", input.well@fit.info, \"\\n\")\n return(input.well)\n }\n \n # Change column headers of input.data to the more general \"Time\" vs. \"y\"\n names(input.data) = c(\"Time\", \"y\")\n \n # Set a lower bound for nls model parameters A and b to slightly lower than min(y)\n low.y = min(input.data$y,na.rm=T)\n low.y = low.y - 0.1*abs(low.y)\n \n # Extract the model formula from (slot \"formula\")\n # Use the function from slot \"guess\" to calculate initial guesses for model parameters based on slope estimates in \n # Attempt to fit a nonlinear least squares odel using \n \n # Creating loess, logistics, richards, and gompertz model. \n loess.e = expression(\"loess\")\n loess.f = formula(Time ~ y)\n loess.model = model(\"local polynomial regression fit.\", loess.e, loess.f, loess.g)\n \n ### Testing accessor method for class model.\n #print(getName(loess.model))\n #print(getFormula(loess.model))\n #print(getGuess(loess.model))\n ### End testing ###\n \n remove(loess.e, loess.f)\n \n ########################################################################\n # Create the logistic 4-parameter model (when v ~ 1) #\n ########################################################################\n logistic.g = function(well,smooth.param=0.75) {\n loess.model@guess(well,smooth.param)\n }\n \n ########################################################################\n # Create the Richards 5-parameter model #\n ########################################################################\n richards.g = function(well,smooth.param=0.75){\n c(loess.model@guess(well,smooth.param),v=0.5)\n }\n \n ########################################################################\n # Create the Gompertz model (might be useful as a #\n # limiting case of Richards model when v ~ 0) #\n ########################################################################\n gompertz.g = function(well,smooth.param=0.75){\n loess.model@guess(well,smooth.param)\n }\n \n logistic.e = expression((A/(1+exp((4*u/A)*(lam-Time)+2)))+b)\n logistic.f = formula(y~(A/(1+exp((4*u/A)*(lam-Time)+2)))+b)\n logistic = model(\"logistic sigmoid.\", logistic.e, logistic.f, logistic.g)\n remove(logistic.e, logistic.f, logistic.g)\n \n richards.e = expression(A*(1+v*exp(1+v)*exp((u/A)*(1+v)**(1+1/v)*(lam-Time)))**(-1/v)+b)\n richards.f = formula(y~A*(1+v*exp(1+v)*exp((u/A)*(1+v)**(1+1/v)*(lam-Time)))**(-1/v)+b)\n richards = model(\"richards sigmoid\", richards.e, richards.f, richards.g)\n remove(richards.e, richards.f, richards.g)\n \n gompertz.e = expression(A*exp(-exp((u*exp(1)/A)*(lam-Time)+1))+b)\n gompertz.f = formula(y~A*exp(-exp((u*exp(1)/A)*(lam-Time)+1))+b)\n gompertz = model(\"gompertz sigmoid\", gompertz.e, gompertz.f, gompertz.g)\n remove(gompertz.e, gompertz.f, gompertz.g)\n \n \n \n # 3) Loess (with optional smoothing parameter)\n if(use.loess){\n number.of.points = nrow(input.well@screen.data)\n if (smooth.param <= 1/number.of.points)\n exception(\"Invalid input\", \"Smoothing parameter is out of range.\")\n \n fit = try(loess(y~Time, data=input.data, span=smooth.param), silent=TRUE)\n input.well@loess = fit\n if (class(fit) != \"loess\") stop(\"loess fit failed on well\", paste(input.well@position,collapse=\" \"))\n input.well@fit.info = \"Loess model fit successfully.\"\n input.well@model.name = loess.model@name\n input.well@equation = loess.model@expression\n # There are no estimated params, so just return the initial guesses\n input.well@fit.par = append(as.list(loess.model@guess(input.well,smooth.param)),list(\"smoothing parameter\"=smooth.param))\n # Note: since there are no params there are no Std. Errors either\n input.well@inflection.time = inflection.time(input.well)\n # calculate Rss for loess\n input.well@rss = sum((input.data$y-predict(fit))**2)\n } else {\n fit = fit.nls.model(input.well,richards)\n # should we use richards? Yes, unless the v param is close to 1 or Zero\n if(class(fit) == \"nls\"){\n rich.fit = fit # if v is significant or other fits consequently fail\n fit.par = as.list(coef(fit))\n # is fit similar to the Logistic?\n if(fit.par$v >= .5 && abs(fit.par$v-1) < 2*summary(fit)$parameters[\"v\",\"Std. Error\"] ){\n fit = fit.nls.model(input.well,logistic)\n input.well@fit.info = paste(\"Logistic model fit successfully.\")\n input.well@model.name = logistic@name\n input.well@equation = logistic@expression\n # is fit similar to Gompertz?\n }else if(fit.par$v < .5 && abs(fit.par$v) < 2*summary(fit)$parameters[\"v\",\"Std. Error\"]){\n fit = fit.nls.model(input.well,gompertz)\n input.well@fit.info = \"Gompertz model fit successfully.\"\n input.well@model.name = gompertz@name\n input.well@equation = gompertz@expression\n # v param is significant. stick with Richards\n }else{\n input.well@fit.info = paste(\"Richards model fit successfully.\")\n input.well@model.name = richards@name\n input.well@equation = richards@expression\n }\n # just in case logistic or gompertz failed to fit...\n if(class(fit) != \"nls\"){\n fit = rich.fit\n input.well@fit.info = paste(\"Richards model fit successfully.\")\n input.well@model.name = richards@name\n input.well@equation = richards@expression\n }\n } else{\n # Richards failed. try backup models\n fit = fit.nls.model(input.well,logistic)\n if(class(fit) != \"nls\"){\n # last resort try gompertz\n fit = fit.nls.model(input.well,gompertz)\n if(class(fit) != \"nls\"){\n input.well@fit.info = \"Model fitting failed.\" \n } else{\n input.well@fit.info = \"Gompertz model fit successfully.\"\n input.well@model.name = gompertz@name\n input.well@equation = gompertz@expression\n }\n }else{\n input.well@fit.info = paste(\"Logistic model fit successfully.\")\n input.well@model.name = logistic@name\n input.well@equation = logistic@expression\n }\n }\n }\n \n # If no error was reported by the model fitting, add coefficients to slot \"fit.par\",\n # Also add the Standard Errors for each parameter\n if (class(fit) == \"nls\"){\n input.well@nls = fit\n input.well@inflection.time = inflection.time(input.well)\n input.well@fit.par = as.list(coef(fit))\n rSs = sum(residuals(fit)**2)\n \n if (length(rSs) != 0)\n input.well@rss = rSs\n else \n input.well@rss = NA\n input.well@fit.std.err = as.list(summary(fit)$parameters[,\"Std. Error\"])\n }\n # Output to console\n if (!silent)\n cat(plate.name(input.well), well.name(input.well), \":\", input.well@fit.info, \"\\n\")\n return(input.well)\n}\n\n# Fit nls model to a well using a specified model\n# Arguments:\n# input.well: object of class well\n# model: object of class model, e.g. richards, gompertz or logistic\nfit.nls.model <- function (input.well, model) {\n # Get OD vs. time data from well\n input.data = data.from(input.well, na.rm = T)\n # Change column headers of input.data to the more general \"Time\" vs. \"y\"\n names(input.data) = c(\"Time\", \"y\")\n \n # Set a lower bound for nls model parameters A and b to slightly lower than min(y)\n low.y = min(input.data$y,na.rm=T)\n low.y = low.y - 0.1*abs(low.y)\n \n # Set the initial guess\n start = model@guess(input.well)\n \n # Set lower bounds\n if (length(start) == 4) {\n lower = c(low.y,low.y,0,0)\n } else if (length(start) == 5) {\n lower = c(low.y,low.y,0,0,0.07)\n } else {\n stop(\"Unsupported model: \", model@name)\n }\n # Make sure initial guess values do not violate lower bounds\n start[start < lower] = lower[start < lower]\n \n # Fit the model\n try(nls(formula = model@formula, data = input.data, start = start, algorithm=\"port\", lower=lower), silent = TRUE)\n}\n", - "created" : 1425413287007.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "2355348307", - "id" : "B0B7416E", - "lastKnownWriteTime" : 1425509229, - "path" : "~/Documents/GCAT4/trunk/R/GCAT/R/fit.model.R", - "project_path" : "R/fit.model.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/E3886516 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/E3886516 deleted file mode 100644 index 6b8ffd1..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/per/t/E3886516 +++ /dev/null @@ -1,17 +0,0 @@ -{ - "contents" : "setwd(\"~/Downloads/\")\nfile.list = file.name = \"YPDAFEXglucoseTests_2-25-10.csv\"\nlayout.file = \"YPDAFEXglucoseTests_2-25-10_Layout.csv\"\nsingle.plate = T\nout.dir = getwd()\ngraphic.dir = paste(out.dir, \"/pics\", sep = \"\")\nadd.constant = 1\nblank.value = NULL\nstart.index = 2\ngrowth.cutoff = 0.05\nuse.linear.param = F\nuse.loess = F\nsmooth.param = 0.6\npoints.to.remove = 0\nremove.jumps = F\nsilent = F\nverbose = T\nreturn.fit = F\noverview.jpgs = T\nplate.nrow = 8\nplate.ncol = 12\ninput.skip.lines = 0\nmulti.column.headers = c(\"Plate ID\", \"Well\", \"OD\", \"Time\")\nsingle.column.headers = c(\"\",\"A1\")\nlayout.sheet.headers = c(\"Strain\", \"Media Definition\")\n\nt = gcat.analysis.main(file.list, single.plate, layout.file = NULL, \n out.dir = getwd(), graphic.dir = paste(out.dir, \"/pics\", sep = \"\"), \n add.constant = 1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05,\n use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=0.1,\n points.to.remove = 0, remove.jumps = F, time.input = NA,\n plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,\n multi.column.headers = c(\"Plate.ID\", \"Well\", \"OD\", \"Time\"), single.column.headers = c(\"\",\"A1\"), \n layout.sheet.headers = c(\"Strain\", \"Media Definition\"),\n silent = F, verbose = F, return.fit = F, overview.jpgs = T)\n", - "created" : 1425413468083.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "3533220190", - "id" : "E3886516", - "lastKnownWriteTime" : 1425422563, - "path" : "~/Documents/GCAT4/trunk/R/GCAT/R/addingParams.R", - "project_path" : "R/addingParams.R", - "properties" : { - "tempName" : "Untitled1" - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/11120BC5 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/11120BC5 deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/11120BC5 +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/246004C1 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/246004C1 deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/246004C1 +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/2A2D32C6 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/2A2D32C6 deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/2A2D32C6 +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/2E01469A b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/2E01469A deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/2E01469A +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/3349C922 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/3349C922 deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/3349C922 +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/3E229DBB b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/3E229DBB deleted file mode 100644 index 32390ac..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/3E229DBB +++ /dev/null @@ -1,3 +0,0 @@ -{ - "tempName" : "Untitled1" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/3F8DCF42 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/3F8DCF42 deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/3F8DCF42 +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/41E3FF1E b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/41E3FF1E deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/41E3FF1E +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/4E0B0FCA b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/4E0B0FCA deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/4E0B0FCA +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/54A894D0 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/54A894D0 deleted file mode 100644 index 32390ac..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/54A894D0 +++ /dev/null @@ -1,3 +0,0 @@ -{ - "tempName" : "Untitled1" -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/61AC4784 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/61AC4784 deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/61AC4784 +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/8250000E b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/8250000E deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/8250000E +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/8341E8EB b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/8341E8EB deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/8341E8EB +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/8CEE19EC b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/8CEE19EC deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/8CEE19EC +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/9127986F b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/9127986F deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/9127986F +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/972C75E0 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/972C75E0 deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/972C75E0 +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/9D1E246E b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/9D1E246E deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/9D1E246E +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/A3297EED b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/A3297EED deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/A3297EED +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/ADFC007A b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/ADFC007A deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/ADFC007A +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/B005EA5F b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/B005EA5F deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/B005EA5F +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/BA83F0DB b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/BA83F0DB deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/BA83F0DB +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/DB5E821B b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/DB5E821B deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/DB5E821B +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/DEDB5126 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/DEDB5126 deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/DEDB5126 +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/E533697B b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/E533697B deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/E533697B +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/E98DE888 b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/E98DE888 deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/E98DE888 +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/EDBD9DE b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/EDBD9DE deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/EDBD9DE +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/INDEX b/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/INDEX deleted file mode 100644 index 0543b58..0000000 --- a/R/GCAT/.Rproj.user/7CB73FCA/sdb/prop/INDEX +++ /dev/null @@ -1,18 +0,0 @@ -~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FNAMESPACE="972C75E0" -~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2FGCAT.main.R="11120BC5" -~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2FaddingParams.R="54A894D0" -~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Fclass.model.R="9127986F" -~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Fclass.well.R="8250000E" -~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Ffit.model.R="3F8DCF42" -~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Ffitted.calculations.R="E533697B" -~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Fmisc.R="8341E8EB" -~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Fnormalize.and.transform.R="EDBD9DE" -~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Fplot.fit.R="2E01469A" -~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Fslope.analysis.R="4E0B0FCA" -~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Ftable.output.R="B005EA5F" -~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2FR%2Ftable2well.R="A3297EED" -~%2FDocuments%2FGCAT4%2Ftrunk%2FR%2FGCAT%2Fman%2Fgcat.load.data.Rd="2A2D32C6" -~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2FGCAT.main.R="61AC4784" -~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2FaddingParams.R="DEDB5126" -~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Fclass.model.R="8CEE19EC" -~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Ffit.model.R="9D1E246E" diff --git a/R/GCAT/DESCRIPTION b/R/GCAT/DESCRIPTION index bff0405..9d09fb1 100755 --- a/R/GCAT/DESCRIPTION +++ b/R/GCAT/DESCRIPTION @@ -9,9 +9,10 @@ Description: Imports high-throughput growth curve data from microtiter (specific growth rate, maximum growth capacity, and lag time) for each well in a read. The code was written by Jason Shao (no longer at GLBRC) and Nate DiPiazza. -Version: 5.0 -Depends: pheatmap, gplots +Version: 5.0.2 +Depends: pheatmap, gplots, methods Maintainer: Yury Bukhman License: LGPL-3 -Date: 2014-02-10 +Date: 2015-04-21 Author: Jason Shao, Nate DiPiazza , Minh Duc Bui, Yury V Bukhman +Suggests: testthat diff --git a/R/GCAT/NAMESPACE b/R/GCAT/NAMESPACE index 55fdde5..433990b 100755 --- a/R/GCAT/NAMESPACE +++ b/R/GCAT/NAMESPACE @@ -1,8 +1,24 @@ -# Default NAMESPACE created by R -# Remove the previous line if you edit this file +# Generated by roxygen2 (4.1.1): do not edit by hand -# Export all names -exportPattern(".") - -# Import all packages listed as Imports or Depends -import("pheatmap", "gplots") +export(gcat.analysis.main) +exportClasses(well) +exportMethods(getAddInfo) +exportMethods(getCurPar) +exportMethods(getEquation) +exportMethods(getFitErr) +exportMethods(getFitInfo) +exportMethods(getFitPar) +exportMethods(getInflectionTime) +exportMethods(getLoess) +exportMethods(getModelName) +exportMethods(getNorm) +exportMethods(getPosition) +exportMethods(getRSS) +exportMethods(getScreenData) +exportMethods(getStartIndex) +exportMethods(getUseLog) +exportMethods(getWellInfo) +exportMethods(getnls) +import(gplots) +import(methods) +import(pheatmap) diff --git a/R/GCAT/R.Rproj b/R/GCAT/R.Rproj deleted file mode 100644 index f7442a1..0000000 --- a/R/GCAT/R.Rproj +++ /dev/null @@ -1,17 +0,0 @@ -Version: 1.0 - -RestoreWorkspace: Default -SaveWorkspace: Default -AlwaysSaveHistory: Default - -EnableCodeIndexing: Yes -UseSpacesForTab: Yes -NumSpacesForTab: 2 -Encoding: UTF-8 - -RnwWeave: Sweave -LaTeX: pdfLaTeX - -BuildType: Package -PackageInstallArgs: --no-multiarch --with-keep.source -PackageRoxygenize: rd diff --git a/R/GCAT/R/.Rhistory b/R/GCAT/R/.Rhistory deleted file mode 100644 index e69de29..0000000 diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/69756148 b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/69756148 deleted file mode 100644 index 1305dca..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/69756148 +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n\n########################################################################\n# #\n# Functions to calculate various things about wells based on fit model #\n# #\n########################################################################\n#\n# Common arguments:\n# fitted.well - should be a well containing the results of , most functions will return NA if well has not been fit yet.\n# unlog - should the value be returned on the linear scale as opposed to the log-transformed scale?\n# constant.added - for returning values on the linear scale, what was the constant added before the log transform?\n# digits - passed to the function, default is no rounding (infinity digits)\n\nunlog = function(x, constant.added) {\n ########################################################################\n # Transform values back to OD scale #\n ########################################################################\nexp(x) - constant.added\n}\n\nwell.eval = function(fitted.well, Time = NULL){\n ########################################################################\n # Evaluate estimated OD at any timepoints using the fitted model #\n ########################################################################\n\n # If no timepoints are provided, use the ones collected in the experiment itself.\n\tif(!is.numeric(Time))\n\t\tTime = data.from(fitted.well)$Time\n\n # Use of equation is deprecated. Use nls and loess models stored in the well object instead\n # Attempt to use with the fitted equation and parameters to get estimates for OD at the given timepoints.\n\t#output = try(eval(fitted.well@equation, fitted.well@fit.par), silent = T)\n \n # Predict log.OD value(s) using nls model if present. If no nls model, try using loess.\n if (length(fitted.well@nls)>0) {\n output = try(predict(fitted.well@nls,list(Time=Time)),silent=T)\n } else if (length(fitted.well@loess)>0) {\n output = try(predict(fitted.well@loess,Time),silent=T)\n } else {\n output = NA\n }\n\n # Return values. If OD evaluation failed for any reason, return NULL.\n if (is.numeric(output)){\n return(output)\n } else {\n return(NULL)\n\t}\n}\n\nmodel.residuals = function(fitted.well, unlog = F){\n ########################################################################\n # Evaluate model residuals using the measured vs. fitted log.OD values #\n ########################################################################\n\tmeasured.OD = data.from(fitted.well)[,2]\n\n\t# Use with no Time argument to get fitted OD values at measured timepoints.\n\tpredicted.OD = well.eval(fitted.well)\n\n\t# If all values are valid, return the differences\n\tif (!is.numeric(predicted.OD))\n\t\treturn(NA)\n\telse\n return(measured.OD - predicted.OD)\n\t}\n\ndev.from.mean = function(fitted.well){\n ########################################################################\n # Evaluate deviations of log.OD values from the mean #\n ########################################################################\n measured.ODs = data.from(fitted.well,remove=T,na.rm=T)[,2]\n \n # Get the mean values of these measured ODs.\n mean.ODs = mean(measured.ODs)\n \n if (!is.numeric(mean.ODs))\n return (NA)\n else\n return (measured.ODs - mean.ODs)\n}\n\nrss = function(fitted.well){\n #######################################################################\n # Get the residual sum of square. #\n #######################################################################\n if (length(fitted.well@rss) == 0)\n return (NA)\n else\n return (fitted.well@rss)\n}\n\nmodel.good.fit = function(fitted.well, digits = Inf){\n ########################################################################\n # Calculate a metric for fit accuracy using squared residuals #\n ########################################################################\n\n # Sum of squared residuals\n\tRSS = rss(fitted.well)\n \n # Total sum of squared\n tot = sum(dev.from.mean(fitted.well)^2)\n \n # Coefficient of determination\n return (1 - RSS/tot)\n\t}\n\nparameter.text = function(fitted.well){\n ########################################################################\n # Output a string with values of fitted parameters #\n ########################################################################\n \n # Get a list of fitted parameters\n fit.par = fitted.well@fit.par\n \n # Giving the parameter text descriptive names.\n if (length(fitted.well@fit.par) != 0){\n names(fit.par)[1] = \"A\" \n names(fit.par)[2] = \"b\" \n names(fit.par)[3] = \"lambda\" \n names(fit.par)[4] = \"max.spec.growth.rate\" \n \n if (fitted.well@model.name == \"richards sigmoid\"){ \n names(fit.par)[5] = \"shape.par\" \n } \n \n if (fitted.well@model.name == \"richards sigmoid with linear par.\"){ \n names(fit.par)[5] = \"shape.param\" \n names(fit.par)[6] = \"linear term\"\n } \n \n if (fitted.well@model.name == \"logistic sigmoid with linear par.\")\n names(fit.par)[5] = \"linear.term\"\n \n # if loess, just show smoothing param\n if(fitted.well@model.name == \"local polynomial regression fit.\")\n fit.par = fitted.well@fit.par[\"smoothing parameter\"]\n }\n \n # Return nothing if the list is empty. Otherwise, concatenate the terms in the list with the parameter names.\n\tif(!is.list(fit.par))\n\t\treturn()\n else{\n \toutput = \"\"\n \ti = 1\n \twhile(i <= length(fit.par)){\n \t\toutput = paste(output, names(fit.par)[i], \"=\", round(as.numeric(fit.par[i]),3), \"; \", sep = \"\")\n \t\ti = i + 1\n if (i %% 6 == 0)\n output = paste(output, \"\\n\")\n \t\t}\n \toutput\n \t}\n\t}\n\nmax.spec.growth.rate = function(fitted.well, digits = Inf){\n ########################################################################\n # Calculate maximum specific growth rate #\n ########################################################################\n if(length(fitted.well@fit.par) == 0)\n return(NA)\n \n round(fitted.well@fit.par$u,digits)\n}\n\n\nplateau = function(fitted.well, digits = Inf){\n ########################################################################\n # Calculate plateau log.OD from fitted parameters #\n ########################################################################\n if(length(fitted.well@fit.par) == 0)\n return(NA)\n \n plat = fitted.well@fit.par$A + fitted.well@fit.par$b\n \n\tif (!is.numeric(plat)) {\n\t plat = NA\n\t} else {\n plat = round(plat, digits)\n\t}\n\treturn(plat)\n}\n\nbaseline = function(fitted.well, digits = Inf){\n ########################################################################\n # Calculate baseline log.OD from fitted parameters #\n ########################################################################\n if(length(fitted.well@fit.par) == 0)\n return(NA)\n\n base = fitted.well@fit.par$b\n\n # If A (plateau OD) is invalid, return NA.\n\tif (!is.numeric(fitted.well@fit.par$A))\n\t\tbase = NA\n # If b (baseline OD) is invalid but plateau OD was valid, return zero.\n else if (!is.numeric(base))\n\t\tbase = 0\n\telse{\n\t\t base = round(base, digits)\n\t\t}\n\treturn(base)\n\t}\n\ninoc.log.OD = function(fitted.well, digits = Inf){\n ########################################################################\n # Calculate log.OD at inoculation from fitted parameters #\n ########################################################################\n\n # Evaluated the fitted model at the inoculation timepoint (should be zero from using from table2wells.R)\n\tif (is.null(well.eval(fitted.well)))\n\t\treturn(NA)\n else{\n inoc.time = fitted.well@screen.data$Time[fitted.well@start.index]\n inoc.log.OD = well.eval(fitted.well, inoc.time)\n if (is.na(inoc.log.OD)) inoc.log.OD = fitted.well@fit.par$b # need this in a special case: loess fits with start.index = 1 \n return(round(inoc.log.OD, digits))\n }\n\t}\n\n\nmax.log.OD = function(fitted.well, digits = Inf){\n ########################################################################\n # Calculate max log.OD from model fit #\n ########################################################################\n\n # Evaluated the fitted model at the final timepoint (just the last valid timepoint in the experiment)\n\tif (is.null(well.eval(fitted.well)))\n\t\treturn(NA)\n else{\n \treturn(round(max(well.eval(fitted.well),na.rm=T), digits))\n }\n}\n\n\nprojected.growth = function(fitted.well,digits=Inf) {\n ########################################################################\n # Calculate projected growth: plateau minus the inoculated log.OD #\n ########################################################################\n\tplateau(fitted.well,digits) - inoc.log.OD(fitted.well,digits)\n}\n\nprojected.growth.OD = function(fitted.well,constant.added,digits=Inf) {\n ########################################################################\n # Calculate projected growth: plateau minus the inoculated log.OD #\n ########################################################################\n value = unlog(plateau(fitted.well),constant.added) - unlog(inoc.log.OD(fitted.well),constant.added)\n round(value,digits)\n}\n\n\nachieved.growth = function(fitted.well,digits=Inf) {\n ########################################################################\n # Calculate achieved growth: max.log.OD minus the inoculated log.OD #\n ########################################################################\n max.log.OD(fitted.well,digits) - inoc.log.OD(fitted.well,digits)\n}\n\nachieved.growth.OD = function(fitted.well,constant.added,digits=Inf) {\n ########################################################################\n # Calculate projected growth: plateau minus the inoculated log.OD #\n ########################################################################\n value = unlog(max.log.OD(fitted.well),constant.added) - unlog(inoc.log.OD(fitted.well),constant.added)\n round(value,digits)\n}\n\nreach.plateau = function(fitted.well, cutoff = 0.75){\n ########################################################################\n # Did the curve come close to the plateau OD during the experiment? #\n ########################################################################\n\n plat = plateau(fitted.well)\n inoc = inoc.log.OD(fitted.well)\n final = max.log.OD(fitted.well)\n\n\tif (!is.na(final)){\n # If the plateau is the same as the OD at inoculation, return TRUE\n if ((plat - inoc) == 0)\n return(T)\n # If the difference between the final OD and inoculation OD is at least a certain proportion\n # of the difference between the plateau and inoculated ODs, return TRUE.\n else\n return((final - inoc) / (plat - inoc) > cutoff)\n\t\t}\n\telse\n\t\treturn(T)\n\t\t# If no final OD was calculated (if curve was not fit properly) just return T.\n\t}\n\n\nlag.time = function(fitted.well, digits = Inf){\n ########################################################################\n # Calculate the lag time from the fitted OD #\n ########################################################################\n if(length(fitted.well@fit.par) == 0)\n return(NA)\n \n fitted.well@fit.par$lam\n}\n\n# new params for GCAT 4.0\n\namplitude = function(fitted.well){\n if(length(fitted.well@fit.par) == 0)\n return(NA)\n \n return(fitted.well@fit.par$A)\n}\n\nshape.par = function(fitted.well){\n if(length(fitted.well@fit.par) == 0)\n return(NA)\n ifelse(is.null(fitted.well@fit.par$v), NA, fitted.well@fit.par$v)\n}\n\nmax.spec.growth.rate.SE = function(fitted.well){\n if(length(fitted.well@fit.std.err) == 0)\n return(NA)\n ifelse(is.null(fitted.well@fit.std.err$u), NA, fitted.well@fit.std.err$u)\n}\n# The SE values are the errors.\nlag.time.SE = function(fitted.well){\n if(length(fitted.well@fit.std.err) == 0)\n return(NA)\n ifelse(is.null(fitted.well@fit.std.err$lam), NA, fitted.well@fit.std.err$lam)\n}\n\nshape.par.SE = function(fitted.well){\n if(length(fitted.well@fit.std.err) == 0)\n return(NA)\n ifelse(is.null(fitted.well@fit.std.err$v), NA, fitted.well@fit.std.err$v)\n}\n\namplitude.SE = function(fitted.well){\n if(length(fitted.well@fit.std.err) == 0)\n return(NA)\n ifelse(is.null(fitted.well@fit.std.err$A), NA, fitted.well@fit.std.err$A)\n}\n\nbaseline.SE = function(fitted.well){\n if(length(fitted.well@fit.std.err) == 0)\n return(NA)\n ifelse(is.null(fitted.well@fit.std.err$b), NA, fitted.well@fit.std.err$b)\n}\n\n# used to calulate the inflection.time value\ninflection.time = function(well){\n if (length(well@loess) == 0 && length(well@nls) == 0) return(NA) # can' compute inflection time in the absence of a fit\n data = data.from(well)\n Time = data[,1]\n t = seq(from = min(Time), to = max(Time), by = (max(Time)-min(Time))/1000)\n y = well.eval(well,t)\n if (is.null(y)) return(NA)\n delta.t = diff(t)\n dydt = diff(y)/delta.t\n infl.index = which.max(dydt)\n t[infl.index]\n}\n", - "created" : 1423868976528.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "4167103586", - "id" : "69756148", - "lastKnownWriteTime" : 1423868994, - "path" : "~/Documents/GCAT4_old/trunk/R/GCAT/R/fitted.calculations.R", - "project_path" : "fitted.calculations.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/6C03FCBD b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/6C03FCBD deleted file mode 100644 index 0e0a97c..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/6C03FCBD +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,\n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n########################################################################\n# #\n# Fit a parameterized model to the growth data in a well object. #\n# #\n# There are now three modelling choices: #\n# 1) Sigmoid model (no linear param c) #\n# 2) Linear Sigmoid model #\n# 3) Loess (with optional smoothing parameter) #\n########################################################################\n#' fit.model \n#' \n#' This function will use the function stored in the \"guess\" slot of \\code{growth.model} to calculate initial guesses \n#' for growth.model parameters, then it will use the \"formula\" slot with \\code{nls} to fit a non-linear least squares \n#' \\code{growth.model} or Local Polynomial Regression Fitting to the data. Richards model is first fitted. \n#' If the shape parameter is statisticaly significant then Richards is used. If it is within 2 SE of 1 or Zero than \n#' a simpler model is preferred. If the Richards fit fails, then Logistic is tried. If it fails, Gompertz is tried. \n#' Model fit failure is reported if none of the models can sucessfully fit the data \n#' \n#' @param input.well The well needed to be fitted with the given model. \n#' @param growth.model What growth model should be used? \n#' @param backup.growth.model If \\code{gowth.mode} fails, this model will be used. \n#' @param fit.if.no.growth should the function attempt to fit a well even if there was no growth detected? default is F \n#' @param silent output back to R console? \n#' @param use.linear.param: Should an additional linear parameter (c) be used when fitting the data to the model? \n#' @param use.loess: Should Local Polynomial Regression Fitting (loess function) be used instead of nls? \n#' @param smooth.param: If loess is used, an optional smoothing parameter. Default is .6 \nfit.model = function(input.well, growth.model, backup.growth.model = NULL, fit.if.no.growth = F, \n use.linear.param=F, use.loess=F, smooth.param, silent = T){\n \n # Conditional breakpoint: go into debugging mode when fitting a specific well\n #if (input.well@position[\"row\"] == \"A\" && input.well@position[\"col\"] == \"12\") browser()\n \n # Change all relevant slots to or blank values\n input.well@model.name = \"\"\n input.well@fit.par = list()\n input.well@equation = expression()\n \n # Get OD vs. time data from well\n input.data = data.from(input.well, na.rm = T)\n \n # Skip well if in slot \"curve.par\" is set to true, and is false.\n if(!fit.if.no.growth & lacks.growth(input.well)){\n input.well@fit.info = \"skipped - no growth in well.\"\n if (!silent)\n cat(plate.name(input.well), well.name(input.well), \":\", input.well@fit.info, \"\\n\")\n return(input.well)\n }\n # Skip well if there are fewer than 5 data points left in the analysis.\n if (length(input.data$Time) < 5){\n input.well@fit.info = \"skipped - not enough points.\"\n if (!silent)\n cat(plate.name(input.well), well.name(input.well), \":\", input.well@fit.info, \"\\n\")\n return(input.well)\n }\n \n # Change column headers of input.data to the more general \"Time\" vs. \"y\"\n names(input.data) = c(\"Time\", \"y\")\n \n # Set a lower bound for nls model parameters A and b to slightly lower than min(y)\n low.y = min(input.data$y,na.rm=T)\n low.y = low.y - 0.1*abs(low.y)\n \n # Extract the model formula from (slot \"formula\")\n # Use the function from slot \"guess\" to calculate initial guesses for model parameters based on slope estimates in \n # Attempt to fit a nonlinear least squares odel using \n \n # Creating loess, logistics, richards, and gompertz model. \n loess.e = expression(\"loess\")\n loess.f = formula(Time ~ y)\n loess.model = model(\"local polynomial regression fit.\", loess.e, loess.f, loess.g)\n remove(loess.e, loess.f, loess.g)\n \n ########################################################################\n # Create the logistic 4-parameter model (when v ~ 1) #\n ########################################################################\n logistic.g = function(well,smooth.param=0.75) {\n loess.model@guess(well,smooth.param)\n }\n \n ########################################################################\n # Create the Richards 5-parameter model #\n ########################################################################\n richards.g = function(well,smooth.param=0.75){\n c(loess.model@guess(well,smooth.param),v=0.5)\n }\n \n ########################################################################\n # Create the Gompertz model (might be useful as a #\n # limiting case of Richards model when v ~ 0) #\n ########################################################################\n gompertz.g = function(well,smooth.param=0.75){\n loess.model@guess(well,smooth.param)\n }\n \n logistic.e = expression((A/(1+exp((4*u/A)*(lam-Time)+2)))+b)\n logistic.f = formula(y~(A/(1+exp((4*u/A)*(lam-Time)+2)))+b)\n logistic = model(\"logistic sigmoid.\", logistic.e, logistic.f, logistic.g)\n remove(logistic.e, logistic.f, logistic.g)\n \n richards.e = expression(A*(1+v*exp(1+v)*exp((u/A)*(1+v)**(1+1/v)*(lam-Time)))**(-1/v)+b)\n richards.f = formula(y~A*(1+v*exp(1+v)*exp((u/A)*(1+v)**(1+1/v)*(lam-Time)))**(-1/v)+b)\n richards = model(\"richards sigmoid\", richards.e, richards.f, richards.g)\n remove(richards.e, richards.f, richards.g)\n \n gompertz.e = expression(A*exp(-exp((u*exp(1)/A)*(lam-Time)+1))+b)\n gompertz.f = formula(y~A*exp(-exp((u*exp(1)/A)*(lam-Time)+1))+b)\n gompertz = model(\"gompertz sigmoid\", gompertz.e, gompertz.f, gompertz.g)\n remove(gompertz.e, gompertz.f, gompertz.g)\n \n \n \n # 3) Loess (with optional smoothing parameter)\n if(use.loess){\n number.of.points = nrow(input.well@screen.data)\n if (smooth.param <= 1/number.of.points)\n exception(\"Invalid input\", \"Smoothing parameter is out of range.\")\n \n fit = try(loess(y~Time, data=input.data, span=smooth.param), silent=TRUE)\n input.well@loess = fit\n if (class(fit) != \"loess\") stop(\"loess fit failed on well\", paste(input.well@position,collapse=\" \"))\n input.well@fit.info = \"Loess model fit successfully.\"\n input.well@model.name = loess.model@name\n input.well@equation = loess.model@expression\n # There are no estimated params, so just return the initial guesses\n input.well@fit.par = append(as.list(loess.model@guess(input.well,smooth.param)),list(\"smoothing parameter\"=smooth.param))\n # Note: since there are no params there are no Std. Errors either\n input.well@inflection.time = inflection.time(input.well)\n # calculate Rss for loess\n input.well@rss = sum((input.data$y-predict(fit))**2)\n } else {\n fit = fit.nls.model(input.well,richards)\n # should we use richards? Yes, unless the v param is close to 1 or Zero\n if(class(fit) == \"nls\"){\n rich.fit = fit # if v is significant or other fits consequently fail\n fit.par = as.list(coef(fit))\n # is fit similar to the Logistic?\n if(fit.par$v >= .5 && abs(fit.par$v-1) < 2*summary(fit)$parameters[\"v\",\"Std. Error\"] ){\n fit = fit.nls.model(input.well,logistic)\n input.well@fit.info = paste(\"Logistic model fit successfully.\")\n input.well@model.name = logistic@name\n input.well@equation = logistic@expression\n # is fit similar to Gompertz?\n }else if(fit.par$v < .5 && abs(fit.par$v) < 2*summary(fit)$parameters[\"v\",\"Std. Error\"]){\n fit = fit.nls.model(input.well,gompertz)\n input.well@fit.info = \"Gompertz model fit successfully.\"\n input.well@model.name = gompertz@name\n input.well@equation = gompertz@expression\n # v param is significant. stick with Richards\n }else{\n input.well@fit.info = paste(\"Richards model fit successfully.\")\n input.well@model.name = richards@name\n input.well@equation = richards@expression\n }\n # just in case logistic or gompertz failed to fit...\n if(class(fit) != \"nls\"){\n fit = rich.fit\n input.well@fit.info = paste(\"Richards model fit successfully.\")\n input.well@model.name = richards@name\n input.well@equation = richards@expression\n }\n } else{\n # Richards failed. try backup models\n fit = fit.nls.model(input.well,logistic)\n if(class(fit) != \"nls\"){\n # last resort try gompertz\n fit = fit.nls.model(input.well,gompertz)\n if(class(fit) != \"nls\"){\n input.well@fit.info = \"Model fitting failed.\" \n } else{\n input.well@fit.info = \"Gompertz model fit successfully.\"\n input.well@model.name = gompertz@name\n input.well@equation = gompertz@expression\n }\n }else{\n input.well@fit.info = paste(\"Logistic model fit successfully.\")\n input.well@model.name = logistic@name\n input.well@equation = logistic@expression\n }\n }\n }\n \n # If no error was reported by the model fitting, add coefficients to slot \"fit.par\",\n # Also add the Standard Errors for each parameter\n if (class(fit) == \"nls\"){\n input.well@nls = fit\n input.well@inflection.time = inflection.time(input.well)\n input.well@fit.par = as.list(coef(fit))\n rSs = sum(residuals(fit)**2)\n \n if (length(rSs) != 0)\n input.well@rss = rSs\n else \n input.well@rss = NA\n input.well@fit.std.err = as.list(summary(fit)$parameters[,\"Std. Error\"])\n }\n # Output to console\n if (!silent)\n cat(plate.name(input.well), well.name(input.well), \":\", input.well@fit.info, \"\\n\")\n return(input.well)\n}\n\n# Fit nls model to a well using a specified model\n# Arguments:\n# input.well: object of class well\n# model: object of class model, e.g. richards, gompertz or logistic\nfit.nls.model <- function (input.well, model) {\n # Get OD vs. time data from well\n input.data = data.from(input.well, na.rm = T)\n # Change column headers of input.data to the more general \"Time\" vs. \"y\"\n names(input.data) = c(\"Time\", \"y\")\n \n # Set a lower bound for nls model parameters A and b to slightly lower than min(y)\n low.y = min(input.data$y,na.rm=T)\n low.y = low.y - 0.1*abs(low.y)\n \n # Set the initial guess\n start = model@guess(input.well)\n \n # Set lower bounds\n if (length(start) == 4) {\n lower = c(low.y,low.y,0,0)\n } else if (length(start) == 5) {\n lower = c(low.y,low.y,0,0,0.07)\n } else {\n stop(\"Unsupported model: \", model@name)\n }\n # Make sure initial guess values do not violate lower bounds\n start[start < lower] = lower[start < lower]\n \n # Fit the model\n fit = try(nls(formula = model@formula, data = input.data, start = start, algorithm=\"port\", lower=lower), silent = TRUE)\n}\n", - "created" : 1423869161433.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "2981843703", - "id" : "6C03FCBD", - "lastKnownWriteTime" : 1423869188, - "path" : "~/Documents/GCAT4_old/trunk/R/GCAT/R/fit.model.R", - "project_path" : "fit.model.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/7189AD56 b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/7189AD56 deleted file mode 100644 index 2accf9e..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/7189AD56 +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n\nrequire(pheatmap)\nrequire(gplots)\n\n########################################################################\n# #\n# Graphic output functions for fitted well objects. The functions are #\n# fairly complicated and intertwined and may need revision. #\n# #\n########################################################################\n\n########################################################################\n# Basic function plots time vs. OD from a well object #\n########################################################################\n#' plot.data \n#' \n#' Basic function plots time vs. OD from a well object \n#' \n#' @param input.well The well object that need to be plottedd \n#' @param unlog should data be plotted on a linear (vs. logarithmic) scale? \n#' @param view.raw.data should the raw data be plotted? ( \n#' @param number.points should points be labeled with numeric indices? \n#' @param scale determines the font scale for the entire graph. all cex values are calculated from this. \n#' @param draw.symbols - should be called on the well and markings drawn on the graph? \n#' @param ... additional arguments passed to plot() \n\nplot.data = function(input.well, view.raw.data = F, unlog = F, scale = 1, \n main = paste(plate.name(input.well), well.name(input.well)), number.points = T, \n draw.symbols = F, constant.added,...){\n \n # Get data as well as a vector showing which points were removed. \n\tinput.data = data.from(input.well, remove = F, remove.tanking = F, raw.data=view.raw.data)\n\tremoved.points = !(rownames(input.data) %in% rownames(data.from(input.well, remove = T, remove.tanking = T)))\n point.colors = as.character(factor(removed.points,levels=c(F,T),labels=c(\"black\",\"gray80\")))\n\n # Draw the axes and all text labels first.\n\tpar(mar = c(5, 4, 4, 5)+0.1)\n\tplot(input.data, main = main, xlab = \"Time(hours)\", ylab = \"log(OD - blank + const)\",\n mex = scale, cex.main = 1.5*scale, cex.axis = 1.2*scale, cex.lab = 1.2*scale, type =\"n\",...)\n \n\t# Draw a second vertical axis, showing unlogged OD scale\n\t# - Determine the range of the labels: from min.OD to max.OD\n if (class(try(ylim,silent=T)) == \"try-error\") {\n OD = unlog(input.data[,2],constant.added)\n baseline.OD = unlog(baseline(input.well),constant.added)\n min.OD = min(min(OD,na.rm=T),baseline.OD,na.rm=T)\n plateau.OD = unlog(plateau(input.well),constant.added)\n max.OD = max(max(OD,na.rm=T),plateau.OD,na.rm=T)\n } else {\n min.OD = unlog(ylim[1],constant.added)\n max.OD = unlog(ylim[2],constant.added)\n }\n\t# - Compute labels and their positions\n\tOD.labels = seq(from = min.OD, to = max.OD, length.out = 5)\n\tOD.labels = signif(OD.labels,2)\n\tOD.at = log(OD.labels+constant.added)\n # - Draw the axis\n\taxis(side=4, at=OD.at, labels=OD.labels, cex.axis = 1.2*scale, cex.lab = 1.2*scale)\n\tmtext(4, text = \"OD - blank\", line = 3, cex=1.2)\n \n\t# If is true, then label each point with the index of its timepoint and plot removed points in grey, others in black. \n if (number.points)\n\t\ttext(input.data$Time, input.data[,2], rownames(input.data), col = point.colors, cex = 0.5*scale)\n\t# Otherwise plot all points, using a different plotting character for removed points. \t\n else\n\t\tpoints(input.data$Time, input.data[,2], pch = 1 + removed.points*15)\n\n # If is set to T, then draw all the markings that makes to determine curve parameters. \n\tif (draw.symbols & !view.raw.data)\n\t\tcheck.slopes(input.well, draw = T)\n\treturn()\n\t}\n\t\n########################################################################\n# Plots the fitted model curve from a well object if it exists #\n########################################################################\n#\n# time: specify which points (in units of time) to plot fitted OD values for. if not specifies, plot all timepoints in range of well. \n\nplot.model = function(input.well, col = 1, scale = 1, lty = 1, time = NULL, unlog = F, constant.added=1){\n\t \n input.data = data.from(input.well)\n\tgrowth = input.data[,2]\n\n # If no list of timepoints is specified, get a list of 360 timepoints (should be smooth enough) from the well's range. \n\tif (is.null(time)){\n\t\ttime.fin = max(data.from(input.well, raw.data = T, remove = F, remove.tanking = F)$Time)\n\t\ttime = seq(0, time.fin, length.out = 360)\n\t}\n \n # Evaluate the predicted OD at the specified timepoints based on the fitted model. \n\tpredicted.OD = well.eval(input.well, time) \n # If any values were returned, plot the lines on the current graph. Otherwise, just return without doing anything.\n\tif (is.numeric(predicted.OD))\n\t\tlines(time, predicted.OD, col = col, lty = lty, lw = 2 * scale) \n else\n return()\t\n \n}\n\t\n########################################################################\n# Put various parameters and info in text form on the graphs #\n########################################################################\n#\t\t\t\ndraw.text = function(input.well, scale = 0.5, xlim = 0, ylim = 0,...){\n\n\tinput.data = data.from(input.well, remove = F, remove.tanking = F)\n\tfit = input.well@fit.par\n \n # - fit information (fit status, model name if available, jump detection output, fit parameters if available) from well \n # color = red if no fit, blue if fit, green if skipped\n # - empty or inoculated well.\n # color = green if empty, blue if inoculated, red if inoculated but has no growth or empty but has growth. \n \n \tcol2 = \"blue\" \n\ttext2 = paste(input.well@fit.info, input.well@model.name, input.well@add.info, \"\\n\", parameter.text(input.well))\n\n\tif (length(input.well@fit.par) == 0) # no fit\n\t\tcol2 = \"red\"\n\n\tif (is.empty(input.well)){\n\t\t text1 = \"empty well\"\n\t\tif(!lacks.growth(input.well) | length(input.well@fit.par) == 0) # growth curve fit for an empty well\n\t\t\tcol1 = \"red\"\n\t\telse\n\t\t\tcol1 = \"forestgreen\"\n\t\tif (length(input.well@model.name) == 0) # well was skipped \n\t\t\tcol1 = col2 = \"forestgreen\"\n\t\t}\n\telse{\n\t\ttext1 = \"inoculated well\"\n\t\tif(lacks.growth(input.well) | length(input.well@fit.par) == 0) # failure to fit an inoculated well\n\t\t\tcol1 = \"red\"\n\t\telse\n\t\t\tcol1 = \"forestgreen\"\n\t\t}\n\t\t\n\t# - goodness of fit metric. \n\t# color = red if below 2, yellow if between 2 and 2.72, and green if above 2.72. \n\t\n\tif(!is.na(model.good.fit(input.well))){\n\t\t#if (model.good.fit(input.well, unlog = F) > 2.72)\n\t\t#\tcol1.5 = \"forestgreen\"\n\t\t#else if (model.good.fit(input.well, unlog = F)> 2.0)\n\t\t#\tcol1.5 = \"gold2\"\n\t\t#else\n\t\t#\tcol1.5 = \"red\"\n col1.5 = \"forestgreen\"\n\t\ttext1.5 = paste(\"R squared:\", round(model.good.fit(input.well),3))\n\t\t}\n\telse\n\t col1.5 = text1.5 = NULL\n\t \n # Print all text at the top of the graph with approprate positions and scaling \t\n \ttext(x = xlim[1] + 0.50 * diff(xlim), y = ylim[2] - 0.025 * diff(ylim), \n \t\ttext1.5, cex = 1.5*scale, col = col1.5) \n \t\t\n\ttext(x = xlim[1] + 0.50 * diff(xlim), y = ylim[2] - 0 * diff(ylim), \n\t\t\ttext1, cex = 1.5*scale, col = col1)\n\n\ttext(x = xlim[1] + 0.50 * diff(xlim), y = ylim[2] - 0.03 * diff(ylim), \n\t\t\ttext2, pos = 1, cex = 1.5*scale, col = col2)\t\n\t}\t\n\n########################################################################\n# Draw lines on graph denoting calculated parameters #\n########################################################################\n#\t\n# - should curve parameters be labeled? \n\t\t\ndraw.calc.par = function(input.well, scale = 0.5, unlog = F, constant.added, show.num = T){\n\n # Don't do anything if well was not fit. \n\tif (is.null(well.eval(input.well)))\n\t\treturn()\n \n # Collect values for various curve parameters. \n\tbaseline = baseline(input.well)\n\tinoc.log.OD = inoc.log.OD(input.well)\n\tmax.log.OD = max.log.OD(input.well) \n\tplateau = plateau(input.well) \n\tinflection.time = input.well@inflection.time # was a param in model\n\tfin.time = (inflection.time+max(data.from(input.well)[,1]))/2\n\n\t# = timepoint at greatest growth \n\t# = OD measurement at , minus the constant added before taking the log (if reversing the transformation)\n\t# = slope (on log scale) at (specific growth)\n # had to add the unlog code. was calculated differently before NWD 7/21/14\n\tmax.slope = max.spec.growth.rate(input.well)\n\tmax.y = well.eval(input.well, inflection.time)\n\tlag.x = lag.time(input.well) \n lag.y = baseline\n\t\n\t# ---- Specific growth rate ---- #\n\tlines(c(lag.x, inflection.time), c(lag.y, max.y), lty = 2, col = \"red\")\n\n\n # Blue dotted line at time of maximum growth, with text label for specific growth rate. \n\tabline(v = inflection.time, lty = 2, lw = (scale^2)*2, col = \"blue\")\n if(show.num) text(inflection.time, max.y, round(max.slope,3), col = \"blue\", cex = 1.5*scale, pos = 2)\n\n # inoculation OD and baseline of the fitted model\n abline(h = inoc.log.OD, lw = scale*2, lty = 3)\n abline(h = baseline, col = \"red\", lw = (scale^2)*2, lty = 2)\n if(show.num) {\n text(fin.time, inoc.log.OD, paste(round(inoc.log.OD,3),\"\\n\",sep=\"\") , col = \"black\", cex = 1.5*scale, pos = 2)\n text(fin.time, baseline, paste(\"\\n\\n\", round(baseline,3), sep=\"\") , col = \"red\", cex = 1.5*scale, pos = 2)\n }\n\n # ---- Lag time ---- #\n # Do not draw a horizontal line to lag time if it is 0 or negative. \n # Otherwise draw a red line from the starting point to the lag time, and label with the lag time \n \tif (lag.time(input.well) == 0){\n\t\tif(show.num) text(0, inoc.log.OD, \"\\n\\n0.000\", col = \"red\", cex = 1.5*scale, pos = 4)\n\t\t}\n\telse{\n\t\tlines(c(0, lag.x), c(baseline, baseline), col = \"red\", lw = (scale^2)*2, lty = 2)\n\t\tif(show.num) text(lag.x, lag.y, paste(\"\\n\\n\", round(lag.time(input.well),3)), col = \"red\", cex = 1.5*scale, pos = 2)\n\t}\n\n # ---- Total growth ---- #\n\n # Draw horizontal lines for the max.log.OD in black, the plateau in green and the initial OD in black.\n abline(h = max.log.OD, lty = 3, lw = scale*2)\n abline(h = plateau, lty = 2, lw = (scale^2)*2, col = \"forestgreen\")\n\t\n\t# Draw a vertical line from the initial OD to the final OD in black, and then to the plateau in gray. \n\tlines(c(fin.time, fin.time), c(inoc.log.OD, max.log.OD), lw = (scale^2)*2, lty = 3)\n\tlines(c(fin.time, fin.time), c(max.log.OD, plateau), lw = (scale^2)*2, lty = 3, col = \"grey\")\n\n # Text: plateau and initial ODs (on left), difference between initial and final OD on right\n\tif(show.num){\n text(fin.time, plateau, paste(round(plateau,3),\"\\n\",sep=\"\") , col = \"forestgreen\", cex = 1.5*scale, pos = 2)\n text(fin.time, max.log.OD, paste(\"\\n\\n\\n\",round(max.log.OD,3),sep=\"\") , col = \"black\", cex = 1.5*scale, pos = 2)\n text(fin.time, .5*(max.log.OD-inoc.log.OD)+inoc.log.OD, round(max.log.OD - inoc.log.OD,3), cex = 1.5*scale, pos = 4)\n # difference between final and plateau OD (if large enough) \n if (!reach.plateau(input.well))\n\t\t text(fin.time, .5*(plateau-max.log.OD)+max.log.OD, paste(\"(\", round(plateau - max.log.OD,3), \")\", sep = \"\"), col = \"grey\", cex = 1.5*scale, pos = 2) \n }\n }\n\t\n########################################################################\n# Draw residuals from the nonlinear fit with option for lowess line #\n########################################################################\n#\t\t\nplot.residuals = function(well, xlim = NULL, lowess = T){\n\n\tdata = data.from(well, remove = F, remove.tanking = F)\n\n\tif (is.null(xlim))\n\t\txlim = c(min(data$Time, 0)-1, max(data$Time))\n\t\t\n\tplot(data.from(well)[,1], model.residuals(well), main = paste(plate.name(well), well.name(well), \"\\n[Residuals]\"),\n\t\txlab = \"Time(hours)\", ylab = paste(\"Residual\", names(data)[2]), xlim = xlim)\n\t\n\tabline(0,0, lty = 2)\n\t\n\tif (lowess)\n\t\tlines(lowess(data.from(well)[,1], model.residuals(well)), lw = 2, col = \"red\")\n\t}\n\n##############################################################################\n# This function is used to create a heatmap using: \n# specific growth, total growth, and lag time\n# for each well on a plate.\n#\n# @params\n# fitted.well.array: matrix containing well array object data\n# attribute: the data type we should use to create a heatmap\n# @returns\n# path of heatmap pdf file\n##############################################################################\ncreate.heatmap = function(fitted.well.array, attribute, unlog=NULL){\n attr.name <- deparse(substitute(attribute))\n pdf.name <- \"\"\n if(class(fitted.well.array) == \"matrix\"){\n #We may want to sub() out periods from plate.ID if it causes problems\n plate.ID = unique(unlist(aapply(fitted.well.array,plate.name)))[1]\n if(is.null(unlog)) {\n spec.growth = unlist(aapply(fitted.well.array, attribute))\n }\n # currently only total growth needs to be unlogged if unlog == T\n else {\n spec.growth = unlist(aapply(fitted.well.array, attribute))\n }\n num.dig = 3 #how many digits should be put on pdf?\n max = round(max(spec.growth, na.rm=T), digits=num.dig)\n min = round(min(spec.growth, na.rm=T), digits=num.dig)\n avg = round(mean(spec.growth, na.rm=T), digits=num.dig)\n heat.text = paste(toupper(sub(\"\\\\.\", \" \", attr.name)), \":\\n\", plate.ID, \"\\n\",\n paste(\"Max:\",max ,\"Min:\" ,min ,\"Avg:\", avg, sep=\"\"))\n \n attr.name <- sub(\"\\\\.\", \"_\", attr.name) #do not want periods in file path\n letters <- attr(fitted.well.array, \"dimnames\")[[1]]\n for(i in 1:length(letters)) letters[i] = paste(\" \", letters[i], \" \")\n nums <- attr(fitted.well.array, \"dimnames\")[[2]]\n for(i in 1:length(nums)) nums[i] = paste(\" \", nums[i], \" \")\n heat <- matrix(spec.growth, nrow=dim(fitted.well.array)[1], ncol=dim(fitted.well.array)[2], dimnames=list(letters,nums))\n pdf.name <- paste(getwd(), \"/\", plate.ID, \"_\", attr.name, \".pdf\", sep=\"\")\n pdf(pdf.name)\n #heatmap(heat, Rowv=NA, Colv=NA, revC=T, scale=\"none\", na.rm=T, main=plate.ID, col=rainbow(100), margins=c(6,6))\n #mtext(paste(\"Max:\", round(max(spec.growth, na.rm=T), digits=4),\"Min:\", round(min(spec.growth, na.rm=T), digits=4), \"Avg:\", round(mean(spec.growth, na.rm=T), digits=4)), side=1, line=3)\n pheatmap(heat, color=colorpanel(100, \"red\", \"orange\", \"yellow\"),\n border_color=\"black\", cell_width=2, cell_height=3,\n cluster_rows=F, cluster_cols=F, scale='none', main=heat.text, fontsize=16)\n dev.off()\n }\n else {\n return(\"Error\") \n }\n return(pdf.name)\n}\n\n########################################################################\n# Draw grids of 96 points as a visual representation of fit status, #\n# and other info for an array of fitted well objects, plate by plate #\n########################################################################\n#\n\t\nplate.overview = function(fitted.well.array, scale = 1){\n \n \n # Start with a list of the unique plate names in the fitted well array \n # and an appropriately-sized grid of coordinates to plot wells on.\n\tplates = unique(unlist(aapply(fitted.well.array,plate.name)))\n \n\tgrid = data.frame(x = rep(rep(1:plate.ncol, each = plate.nrow), length(plates)),\n\t\t\t y = rep( rep(-(1:plate.nrow), times = plate.ncol), length(plates)))\n\n\n # Gather information on each well to display on each of the coordinates in :\n # - was it marked as empty in the plate layout?\n # - did the program find it to contain no growth (\"dead\")? \n # - was the fitting procedure successful? \n # - did the curve tank? if so, at what timepoint? if not, or if the curve was marked as dead anyway, do not display the value. \n # - does the \"additional info\" slot indicate that any points were removed or the whole well discarded?\n \n\tempty = unlist(aapply(fitted.well.array, is.empty))\n\tdead = unlist(aapply(fitted.well.array, lacks.growth))\n\tfit = unlist(aapply(fitted.well.array, contains.fit))\n \n\ttanking = unlist(aapply(fitted.well.array, tanking.start))\n\ttanking[is.na(tanking) | tanking == 1 | dead] = \"\"\n\n\terrors = unlist(aapply(fitted.well.array, function(well){\n\t\tif (length(well@add.info) == 0)\n\t\t\t\"\"\n\t\telse if (grepl(\"removed\", well@add.info))\n\t\t\t\"-\"\n else if (grepl(\"detected\", well@add.info))\n \"+\"\n\t\telse if (grepl(\"discarded\", well@add.info))\n\t\t\t\"!\"\n\t\telse\n\t\t\t\"\"\n\t\t}))\n\t\n # Color and plotting character vectors (length = the number of wells in the array)\n # Default = 1 (open point, black)\n\tcolors = char = rep(1, length(tanking))\n\n # Desired colors\n colors[empty & dead] = \"green3\" # Empty well with no growth.\n colors[!empty & fit] = \"blue\" # Inoculated well with successfully fitted growth curve.\n \n # Undesired colors \n colors[empty & !dead] = \"darkolivegreen4\" # Inoculated well with some growth. \n colors[!empty & !fit] = \"red\" # Inoculated well with no successfully fit (either no growth or unsuccessful fit).\n \n char[!dead & fit] = 19 # Filled points for non-empty wells with successful fits \n char[!dead & !fit] = 4 # an X for non-empty wells with failed fits. \n \n char[errors == \"!\"] = 8 # Asterisk for discarded wells. \n char[errors == \"-\" & dead ] = 5 # Open diamond for empty wells (after removing points).\n char[errors == \"-\" & !dead & fit] = 23 # Filled diamond for non-empty wells with removed points and successful fits. \n char[errors == \"-\" & !dead & !fit] = 8 # Asterisk for wells with removed points and failed fits.\n \n \n\tfor (plate in 1:length(plates)){\n \n\t\tindices = (plate - 1) * plate.nrow*plate.ncol + 1:(plate.nrow*plate.ncol)\n\n # Plot the grid using colors and plotting characters determined above. \n\t\tplot(grid[indices,], col = colors[indices], bg = colors[indices], pch = char[indices], \n\t\t\t main = plates[plate], mex = scale, cex = scale, cex.main = 1.5*scale, cex.axis = 1.2*scale, \n\t\t\t xaxt = \"n\", yaxt = \"n\", xlim = c(-0.5,plate.ncol + 0.5), ylim = c(-(plate.nrow + 1.5), 0.5), xlab = \"\", ylab = \"\")\n \n # Symbol legends\n \n legend.xpos = (c(-1,2.75,6.5,6.86,10.25)+0.5)*(plate.ncol+1)/13 - 0.5\n legend.ypos = -(plate.nrow + 0.5)\n \n legend(x=legend.xpos[1], y= legend.ypos, cex = 0.7 * scale, y.intersp = 1.5, bty=\"n\", \n legend=c(\"Empty, no growth\",\"Empty with growth\"),\n pch = c(1,19),\n pt.bg = c(\"green3\",\"darkolivegreen4\"),\n col = c(\"green3\",\"darkolivegreen4\")\n )\n legend(x=legend.xpos[2], y= legend.ypos, cex = 0.7 * scale, y.intersp = 1.5, bty=\"n\", \n legend=c(\"Inoculated with growth\", \"Inoculated, no growth\"),\n pch = c(19,1),\n pt.bg = c(\"blue\",\"red\"),\n col = c(\"blue\",\"red\")\n )\n legend(x=legend.xpos[3], y= legend.ypos, cex = 0.7 * scale, y.intersp = 1.5, bty=\"n\", \n legend=c(\"Well tanks at specified index\", \"Some points removed\"),\n pch = c(21,23),\n pt.bg = c(\"grey\",\"grey\"),\n col = c(\"black\",\"black\")\n ) \n \n text(x=legend.xpos[4], y=legend.ypos - 0.29,\"#\",cex=0.5*scale) \n \n legend(x=legend.xpos[5], y=legend.ypos, cex = 0.7 * scale, y.intersp = 1.5, bty=\"n\", \n legend=c(\"Model fitting failed\", \"Well discarded\"),\n pch = c(4,8),\n pt.bg = c(\"black\",\"black\"),\n col = c(\"black\",\"black\")\n )\n \n # Add tanking indices if any were found. \n \ttext(grid[indices,] + 0.30, cex = 0.75*scale, \n labels = tanking[indices], col = colors[indices])\n\n # Label rows and columns\n\t\ttext(-1, -1:-plate.nrow, pos = 4, LETTERS[1:plate.nrow], cex = scale) \n\t\ttext( 1:plate.ncol, 0 , 1:plate.ncol, cex = scale) \t\n\t\t}\n \n\t}\n\n########################################################################\n# Draw each well in an array of fitted well objects in succession. #\n# Include options for adding notations, text info and fit parameters. #\n########################################################################\n#\n\nview.fit = function(fitted.data, indices = 1:length(fitted.data), \n unlog = F, constant.added, xlim = NULL, ylim = NULL, display.legend = T, \n\t\t show.text = T, show.calc = T, draw.guess = NULL, draw.symbols = F, number.points = T, \n\t\t\tuser.advance = T, show.residuals = F, scale = 1,...){\n\n if(!is.array(fitted.data))\n fitted.data = list(fitted.data)\n\n # Determine the boundaries for the axes (if user did not specify them)\n if(is.null(ylim)){\n min.y = min(unlist(aapply(fitted.data, function(well){\n \tif (unlog) well@use.log = F\n \tmin.y = min(data.from(well, remove = F, remove.tanking = F)[,2], na.rm = T)\n min(min.y, well@fit.par$b)\n \t})))\n max.y = max(unlist(aapply(fitted.data, function(well){\n if (unlog) well@use.log = F\n \tmax.y = max(data.from(well, remove = F, remove.tanking = F)[,2], na.rm = T)\n max(max.y, well@fit.par$b + well@fit.par$A)\n \t})))\n ylim = c(min.y, min.y + (max.y-min.y)*1.15) - unlog*constant.added\n }\n if(is.null(xlim)){\n min.x = min(unlist(aapply(fitted.data, function(well){\n min(data.from(well, remove = F, remove.tanking = F)[,1], na.rm = T)\n \t})))\n max.x = max(unlist(aapply(fitted.data, function(well){\n \tmax(data.from(well, remove = F, remove.tanking = F)[,1], na.rm = T)\n \t})))\n xlim = c(min.x - 0.05 * (max.x-min.x), max.x)\n }\n \n # Display a figure legend\n if(display.legend){\n well.fit.legend(xlim=xlim,ylim=ylim,scale=scale,constant.added=constant.added)\n if(user.advance){\n prompt = readline(\" to continue or Q to quit >>\")\n if (toupper(prompt) == \"Q\") break\n }\n }\n # Start to cycle through the wells \n\twell.number = 1\n\twhile (well.number <= length(fitted.data)) {\t\t\n\t\t# Only show wells specified by (default all wells)\n if (well.number %in% indices){ \n # plot the well\n fitted.well = fitted.data[[well.number]]\n plot(x=fitted.well, constant.added = constant.added, xlim = xlim, ylim = ylim,\n unlog = unlog, well.number = well.number, scale = scale, number.points = T, draw.symbols = F, show.text = T, show.calc = T, draw.guess = NULL, ...)\n \n if(user.advance)\n cat(\"\\n[\", well.number, \"] \", plate.name(fitted.well), \" \", well.name(fitted.well), \".\", sep = \"\")\n \n if (show.residuals & is.numeric(model.residuals(fitted.well))){\n if(user.advance)\n if (toupper(readline(\" for residuals >>\")) == \"Q\") break\n plot.residuals(fitted.well)\n }\n \n # Allow user to advance the currently shown well if specified. \n\t\t\tif (user.advance){\n \n\t\t\t\tprompt = readline(\" to continue, or type # of next well or Q to quit >>\")\n\t\t\t\tif (toupper(prompt) == \"Q\") break\n\n user.input = suppressWarnings(try(as.numeric(prompt),silent=T))\n \n # Go onto the next well unless input is a number. \n\t\t\t\tif (is.numeric(user.input) & !is.na(user.input) & length(user.input) > 0)\n\t\t\t\t\twell.number = user.input - 1\n\t\t\t }\n\t\t\t}\n # Advance the loop\n well.number = well.number + 1\n\t\t}\t\t\n\t}\t\n\n\nwell.fit.legend = function(xlim, ylim, scale = 1, constant.added){\n par(mar = c(5, 4, 4, 5)+0.1)\n plot(0,0, main = \"[Index] \\n; \",\n xlim = xlim, ylim = ylim, xlab = \"Time\", ylab = \"log(OD - blank + const)\", \n mex = scale, cex.main = 1.5*scale, cex.axis = 1.2*scale, cex.lab = 1.2*scale, type = \"n\")\n \n # Draw a second vertical axis, showing unlogged OD scale\n min.OD = unlog(ylim[1],constant.added)\n max.OD = unlog(ylim[2],constant.added)\n OD.labels = seq(from = min.OD, to = max.OD, length.out = 5)\n OD.labels = round(OD.labels,1)\n OD.at = log(OD.labels+constant.added)\n axis(side=4, at=OD.at, labels=OD.labels, cex.axis = 1.2*scale, cex.lab = 1.2*scale)\n mtext(4, text = \"OD - blank\", line = 3, cex=1.2)\n \n # Sample max. slope line\n abline(v=min(xlim)+0.5*max(xlim), col=\"blue\", lty=2)\n text(mean(xlim),min(ylim)+0.4*diff(ylim),labels=\"Maximum specific\\ngrowth rate\",col=\"blue\",pos=2,cex=0.75*scale)\n \n # Sample plateau line\n abline(h=min(ylim)+0.8*diff(ylim),col=\"forestgreen\",lty=2)\n text(min(xlim)+0.9*diff(xlim),ylim+0.8*diff(ylim),labels=\"Growth plateau\",col=\"forestgreen\",pos=3,cex=0.75*scale)\n\n # Sample max.log.OD line\n abline(h=min(ylim)+0.7*diff(ylim),col=\"black\",lty=3)\n text(min(xlim)+0.9*diff(xlim),ylim+0.7*diff(ylim),labels=\"max.log.OD\",col=\"black\",pos=1,cex=0.75*scale)\n \n # Sample inoc.log.OD\n abline(h=min(ylim)+0.1*diff(ylim),col=\"black\",lty=3)\n text(min(xlim)+0.1*diff(xlim),min(ylim)+0.1*diff(ylim),labels=\"Fitted growth\\nat inoculation\",col=\"black\",pos=3,cex=0.75*scale)\n \n # Sample baseline\n abline(h=min(ylim)+0.05*diff(ylim),col=\"red\",lty=2)\n text(min(xlim)+0.1*diff(xlim),min(ylim)+0.05*diff(ylim),labels=\"Baseline\",col=\"red\",pos=1,cex=0.75*scale)\n\n # Sample lag time\n lines(min(xlim)+c(0.1,0.25,0.50)*max(xlim),min(ylim)+c(0.05,0.05,0.4)*diff(ylim),col=\"red\",lty=2)\n text(min(xlim)+0.25*max(xlim),min(ylim)+0.05*diff(ylim),labels=\"Lag time\",col=\"red\",pos=1,cex=0.75*scale)\n \n # Sample achieved growth\n lines(min(xlim)+c(0.75,0.75)*max(xlim),min(ylim)+c(0.1,0.7)*diff(ylim),col=\"black\",lty=3)\n text(min(xlim)+0.75*max(xlim),min(ylim)+0.3*diff(ylim),labels=\"Achieved growth\",col=\"black\",cex=0.75*scale)\n \n # Sample plateau - achieved growth\n lines(min(xlim)+c(0.75,0.75)*max(xlim),min(ylim)+c(0.7,0.8)*diff(ylim),col=\"grey\",lty=3)\n text(min(xlim)+0.75*max(xlim),min(ylim)+0.75*diff(ylim),labels=\"Projected minus achieved growth\",col=\"grey\",cex=0.75*scale)\n \n # Symbol legend\n legend(x=\"right\", title = \"Timepoint Symbols\", legend = c(\"Normal point\", \"Ignored point\"),\n cex = 0.75*scale, pt.cex = c(0.6,0.6)*scale, pch = c(35,35), col=c(\"black\",\"gray80\"),\n x.intersp=1, xjust = 1, y.intersp=1.5)\n}\n\npdf.by.plate = function(fitted.data, out.prefix = \"\", upload.timestamp = NULL, \n out.dir = getwd(), unlog = F, constant.added, silent = T, overview.jpgs = T, ...){\n \n # Prepare timestamp for addition to output file names. \n filename.timestamp = strftime(upload.timestamp, format=\"_%Y-%m-%d_%H.%M.%S\")\n \n # Start file list with the overview pdf\n file.list.out = paste(out.dir,\"/\",out.prefix, \"_overview\", filename.timestamp, \".pdf\",sep=\"\")\n \n # Call to draw a graphic representation of each plate in this file. \n pdf(file.list.out, title = paste(out.prefix, \"plate overview\"))\n plate.overview.out = try(plate.overview(fitted.data),silent=T)\n if(class(plate.overview.out) == \"try-error\")\n stop(\"Error in : \", plate.overview.out)\n \n # Close devices\n while(dev.cur() != 1)\n dev.off() \n \n # Cycle through each plate \n for(i in 1:dim(fitted.data)[3]){\n \n # Get plate ID and position in data array.\n plate.ID = dimnames(fitted.data)[[3]][i]\n plate.indices = (i-1) * plate.nrow*plate.ncol + 1:(plate.nrow*plate.ncol)\n if(overview.jpgs){\n # most be > 1 to partition value breaks for heatmap\n well.matrix <- aapply(fitted.data[,,i], max.spec.growth.rate) \n num.wells <- length(well.matrix[!sapply(well.matrix, is.na)])\n if(num.wells > 1){\n #Heatmap block##########################################################\n #alongside the jpgs file create 3 heatmaps for each plate. NWD\n spec.heat.file = create.heatmap(fitted.data[,,i], max.spec.growth.rate)\n if(spec.heat.file == \"Error\")\n stop(\"Error in for specific growth\")\n lag.heat.file = create.heatmap(fitted.data[,,i], lag.time)\n if(lag.heat.file == \"Error\")\n stop(\"Error in for lag time\")\n total.heat.file = create.heatmap(fitted.data[,,i], achieved.growth)\n if(total.heat.file == \"Error\")\n stop(\"Error in for total growth\")\n # Add name of file if successfully written to file list output. Including heatmap files NWD\n file.list.out = c(file.list.out, spec.heat.file, lag.heat.file, total.heat.file)\n ########################################################################\n }\n jpg.name = paste(out.dir, \"/\", plate.ID, \"_overview\", \".jpg\", sep=\"\")\n jpeg(jpg.name, quality = 90, width = 600, height = 480)\n plate.overview.out = try(plate.overview(fitted.data[,,i]),silent = T)\n if(class(plate.overview.out) == \"try-error\")\n stop(\"Error in : \", plate.overview.out)\n }\n else\n jpg.name = c()\n \n # Open a separate PDF for each plate.\n if(!silent) cat(\"\\nprinting PDF for\", plate.ID)\n pdf.name = paste(out.dir, \"/\", plate.ID, \"_plots\", filename.timestamp, \".pdf\", sep=\"\")\n pdf(pdf.name, title = paste(\"R Graphics output for plate\", plate.ID))\n \n # Call to draw each well on the plate to the pdf. \n view.fit.out = try(view.fit(fitted.data, indices = plate.indices, unlog=unlog, constant.added=constant.added, user.advance=F,...),silent=T) \n \n if(class(view.fit.out) == \"try-error\")\n stop(\"Error in : \", view.fit.out)\n\n # Close all devices\n while(dev.cur() != 1)\n dev.off() \n \n if(!silent) cat(\"...done!\\n\\twritten to\", pdf.name, \"\\n\") \n file.list.out = c(file.list.out, jpg.name , pdf.name)\n }\n return(file.list.out)\n } \n", - "created" : 1423869024830.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "197404081", - "id" : "7189AD56", - "lastKnownWriteTime" : 1423869067, - "path" : "~/Documents/GCAT4_old/trunk/R/GCAT/R/plot.fit.R", - "project_path" : "plot.fit.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/85C00847 b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/85C00847 deleted file mode 100644 index 1d1225a..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/85C00847 +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n\n# Notes by Jason\n# 9/07/11\n\n\n########################################################################\n# #\n# Function for loading data from tabular format into an object array #\n# #\n########################################################################\n#' Load tabular data\n#'\n#' This function handles loading data from tabular format (.csv, tab-delimited text or R data frame object)\n#' and returns an array of well objects, each filled with raw Time vs. OD data. \n#' It takes single-plate or multiple-plate format data. For single-plate data, \n#'it calls on the function \\code{gcat.reorganize.single.plate.data} to rearrange the table before creating the output object. \n#'\n#' @param file.name Complete path and file name of a comma-separated values (.csv) file containing growth curve data \n#' in the multiple-plate (long) format. \n#' @param input.data A list of tables representing input files read with \\code{read.table}. Used to save time in cases\n#' of running multiple analyses on the same dataset. If used, the function will ignore \\code{file.name} entirely.\n#' @param load.type .csv by default. \n#' @param plate.laout Specifies the layout of the given plate.\n#' @param single.plate.ID specifies a plate name for a single-plate read. If NULL, this is derived from the file name. \n#' @param blank.value Blank OD measurement for uninoculated wells. By default(NULL), the value of the first OD\n#'measurement in each well is used.\n#' @param add.constant A value for r in the log(OD + r) transformation.\n#' @param plate.nrow The number of rows in the input files.\n#' @param plate.ncol The number of columns in the input files.\n#' @param input.skip.lines If specified, this number of lines shall be skipped from the top when reading the input file with read.csv \n#' @param multi.column.headers The headers of the column when analyzing multiple plates.\n#' @param single.column.headers The headers of the column when analyzing a single plate.\n#' @param layout.sheet.headers The headers of the layout file.\n#' @param growth.model What growth model should be used?\n#' @param silent Surpress all messages.\n#' @param verbose Display all messages when analyzing each well.\n#' \n#' @return A list of well objects.\n\ngcat.load.data = function(file.name = NULL, load.type = \"csv\", input.data = NULL, single.plate.ID = NULL, \n plate.layout = NULL,plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,\n multi.column.headers = c(\"Plate.ID\", \"Well\", \"OD\", \"Time\"), single.column.headers = c(\"\",\"A1\"), \n layout.sheet.headers = c(\"Strain\", \"Media Definition\"),\n blank.value = NULL, start.index = 2, single.plate = F, silent = T){\n\n ########################################################################\n # Read from .csv, tab-delimited text file or data frame object #\n ########################################################################\n \n\tif(is.null(input.data)){\n\t\t# Either read from .csv.\n\t\tinput.data = read.csv(file.name, stringsAsFactors=F, skip = input.skip.lines, fileEncoding='UTF-8')\n\n\t\t# Determine single plate name if not specified. \n if (is.null(single.plate.ID)){\n # Split the file name by \".\" and discard the last member (file extension). \n single.plate.ID = strsplit(basename(file.name),\"\\\\.\")[[1]]\n single.plate.ID = paste(single.plate.ID[-length(single.plate.ID)],collapse=\".\")\n }\n\t\t}\n\n # Call to arrange data from a single plate format file\n\tif(single.plate)\n\t\tinput.data = gcat.reorganize.single.plate.data(input.data = input.data, single.column.headers,\n blank.value = blank.value, single.plate.ID = single.plate.ID,silent=silent)\n\n ########################################################################\n # Search for and standardize column headers in input data #\n ########################################################################\n \n # Go through the specified column headers, determining what their positions are in the \n # input data frame and if any are missing.\n \n # Get names of column headers in input data\n input.colnames = colnames(input.data)\n \n # Create a list denoting the column numbers in input data that match each of the specified column names, \n # and a separate list for any missing columns. \n \n column.matches = c()\n missing.list = NULL\n \n\tfor(i in 1:length(multi.column.headers)){\n\t\tif (multi.column.headers[i] %in% input.colnames)\n\t\t\tcolumn.matches[i] = min(which(input.colnames == multi.column.headers[i]))\n\t\t# Take the first column in input file that matches a specified column header.\n\t\telse{\n\t\t\tmissing.list = c(missing.list, i)\n\t\t}\n\t}\n\n # If any columns are missing, stop and report error with missing column names\n\tif (is.vector(missing.list)){\n\t\tmessage = \"The following columns:\"\n\t\tfor (i in missing.list)\n\t\t\tmessage = paste(message, paste(\" \", multi.column.headers[i]), sep = \"\\n\") \n\t\tstop(message, \"\\n were not found in the data file.\")\n\t\t}\n\n # Reorder and rename the columns, using the list of matching column numbers from above.\n\tinput.data = input.data[,column.matches]\n\tnames(input.data)[1:4] = c(\"Plate.ID\", \"Well\", \"OD\", \"Time\") \n\n # Use 'substring' to split the alphanumeric \"Well\" field into row (letters) and column (numbers)\n\tinput.data$Well.row = substring(input.data$Well, 0,1)\n\tinput.data$Well.col = as.numeric(substring(input.data$Well, 2))\n\n\n ########################################################################\n # Create an array of well objects with the Time and OD data #\n ########################################################################\n #\n # Use the by function to split up the data frame into shorter segments by well (row, column and plate)\n \n\twell.array = by(data = input.data[,c(\"OD\", \"Time\")], \n INDICES = list(input.data$Well.row,input.data$Well.col,input.data$Plate.ID), \n FUN = function(x){data.frame(Time=x$Time, OD=x$OD,stringsAsFactors = F)}, simplify = F)\n\n \n # Then apply the function (found in well.class) to each member to create a well object\n well.array = aapply(well.array,function(x){well(x$Time,x$OD)})\n\n # Differentiate any duplicate plate names in the array's dimnames \n\tnew.dimnames = dimnames(well.array)\n for (i in length(new.dimnames[[3]]):1){\n\t\tif (any(new.dimnames[[3]][-i] == new.dimnames[[3]][i]))\n\t\t\tnew.dimnames[[3]][i] = paste(\"another_\", new.dimnames[[3]][i], sep = \"\")\t\n\t\t}\n\tdimnames(well.array) = new.dimnames\n\t\n # Copy the plate/row/column names found in the dimnames into the array objects themselves (use \"position\" slot)\n\tfor(plate in unique(dimnames(well.array)[[3]])){\n\t\tfor (col in unique(dimnames(well.array)[[2]])){\n\t\t\tfor(row in unique(dimnames(well.array)[[1]])){\n\t\t\t\twell.array[[row,col,plate]]@position = c(plate=plate,row=row,col=col)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\t\n ########################################################################\n # Add plate layout information to well array #\n ########################################################################\n \n # Use the object to add media and strain information to the \"well.info\" slot of each well\n # Also set the value of the parameter in slot \"curve.par\" to T for empty wells. \n ########################################################################\n # Add plate layout information to well array #\n ########################################################################\n \n # Use the object to add media and strain information to the \"well.info\" slot of each well\n # Also set the value of the parameter in slot \"curve.par\" to T for empty wells. \n \n\n \n if(is.null(plate.layout)){ # If is not provided, do not add strain information, and assume all wells are inoculated. \n plate.layout = data.frame(Row=rep(PLATE.LETTERS[1:plate.nrow],plate.ncol),Column=rep(1:plate.ncol,each=plate.nrow),rep(\"Unknown Strain\",96),rep(\"Unknown Media\",96))\n colnames(plate.layout) = c(\"Row\", \"Column\", layout.sheet.headers)\n } \n else\n if(!silent) cat(\"\\n\\t\\tusing plate layout to fill well info.\")\n \n\tfor(plate in unique(dimnames(well.array)[[3]])){\n\t\tfor (col in unique(dimnames(well.array)[[2]])){\n\t\t\tfor(row in unique(dimnames(well.array)[[1]])){\n well = well.array[[row,col,plate]]\n # For each well on each plate, find the corresponding row in . \n # If refers to specific plates, then use those to find the correct row. Otherwise, generalize across all plates. \n if (\"Plate.ID\" %in% names(plate.layout)) layout.row.number = which(plate.layout$Column==well@position[\"col\"] & plate.layout$Row==well@position[\"row\"] & plate.layout$Plate.ID==well@position[\"plate\"] ) \n else layout.row.number = which(plate.layout$Column==well@position[\"col\"] & plate.layout$Row==well@position[\"row\"]) \n # Error if either no rows or more than one row matches the well\n if (length(layout.row.number) != 1)\n stop(\"incorrectly formatted plate layout! check names of columns, rows, and plates (if applicable).\")\n \n # Add any additional columns to the well's \"well.info\" slot\n well.info = plate.layout[layout.row.number,!(names(plate.layout) %in% c(\"Row\",\"Column\",\"Plate.ID\",layout.sheet.headers))]\n # Fix the column name issue if there is only one additional entry. \n if(length(well.info) == 1){\n well.info = data.frame(well.info,stringsAsFactors=F) \n names(well.info) = names(plate.layout)[!(names(plate.layout) %in% c(\"Row\",\"Column\",\"Plate.ID\",layout.sheet.headers))] \n } \n well@well.info = as.list(well.info)\n \n well@well.info$Strain = plate.layout[layout.row.number, layout.sheet.headers[1]]\n well@well.info$Media = plate.layout[layout.row.number, layout.sheet.headers[2]]\n # Set parameter in slot \"curve.par\" accordingly \n well@curve.par$empty.well = (plate.layout$Strain[layout.row.number] == \"Empty\") \n well.array[[row,col,plate]] = well\n\t\t\t\t}\n\t\t\t}\n\t\t}\n # Set start index value in each well\n well.array = aapply(well.array, function(x,start.index) { x@start.index = start.index; x }, start.index)\n \n ########################################################################\n # Return values to R #\n ######################################################################## \n # \n\t# Console output if desired, return the completed well array.\n\tif (!silent)\n\t\tcat(\"\\n\\t\", dim(well.array)[[3]], \"plates added to array from\", file.name)\n\treturn(well.array)\n\t}\n\n\n\n########################################################################\n# #\n# Reorganize data from single-plate input format before reading #\n# #\n########################################################################\n#\n# This function reorganizes the data frame from a single-plate format file. \n# input.data - data frame read straight from a single-plate format data file. \n# single.plate.ID - specifies a plate name for a single-plate read, since none is given in the single-plate format\n# The plate will be named Plate_1 unless otherwise specified. \n\ngcat.reorganize.single.plate.data = function(input.data, blank.value = NULL, single.column.headers, single.plate.ID = \"Plate_1\", silent=T){\n \n ########################################################################\n # Standardize the formatting and search for specified column names #\n ######################################################################## \n # \n # Locate the first and last rows from the table and return errors if not defined \n # Note: this only works if the time column is the first column\n \n\theader.row = min(which(input.data[,1] == single.column.headers[1])) \n if (length(header.row) != 1 | is.infinite(header.row))\n stop(\"could not locate header row in input file!\")\n \n # The last row: where column 2 starts to be blank, or the total number of rows, whichever is smaller \n extra.rows.start = min(which(input.data[-(1:header.row),2] == \"\"), which(is.na(input.data[-(1:header.row),2])), nrow(input.data[-(1:header.row),]))\n if (length(extra.rows.start) != 1 & is.infinite(extra.rows.start)) \n stop(\"could not locate last row in input file!\")\n\n # Use header row to rename the columns, then cut off extra rows (including the ones above header)\n\tnames(input.data) = as.character(unlist(input.data[header.row,]))\n input.data = input.data[(header.row+1):(header.row+extra.rows.start-1),]\n \n # Time column: allow for multiple matches to the name (since it's usually blank) but assume it's the first one\n\tTime.column = which(names(input.data) == single.column.headers[1])\n\tif (length(Time.column) != 1){\n if(!silent) cat(\"No unique time column in input.data file! Using the first one encountered.\")\n\t\tTime.column = min(Time.column)\n\t\t}\n # First well column (default A1): only allow for one match.\t\n\tWell.column.start = which(names(input.data) == single.column.headers[2])\n\tif (length(Well.column.start) != 1)\n\t\tstop(\"No unique start point for well columns in input.data file!\")\n\n # If the time column was found, rename it \"Time\" and reformat it into a numeric value\n # Adjust the blank measurement timestamp to -1 seconds if there is one\n\n names(input.data)[Time.column] = \"Time\"\n # Note: Some single plate screens have timepoints ending with \"s\" for seconds. \n # This line removes the \"s\" while maintaining general compatibility. \n\tinput.data$Time = unlist(strsplit(input.data$Time, \"s\"))\n\n # If is NULL (default - takes the first OD as the blank reading), then the first timepoint can labeled something non-numeric. \n # In that case, rename it to match the first real timepoint minus one. \n # when user input blank value, Blank timepoint i.e. input.data$Time[1] == Blank, labeled as \"Blank\" from data input file\n # It also should rename it to match the first real timepoint minus one. \n if(is.null(blank.value) || is.na(as.numeric(input.data$Time[1])))\n input.data$Time[1] = as.numeric(input.data$Time[2]) - 1\n \n ########################################################################\n # Start to fill the reformatted data frame #\n ######################################################################## \n \n # If all columns are present, make a list of all the wells.\n\twell.list = paste(rep(PLATE.LETTERS[1:plate.nrow], each = plate.ncol), rep(formatC(1:plate.ncol, digits = log(plate.ncol, 10), flag = \"0\"), plate.nrow), sep = \"\")\n\n #\tDuplicate the well names times the number of time measurements in each well\t\n Well = rep(well.list, each = length(input.data[,Time.column]))\t\n\t\t\n # Duplicate times the length of the entire output \n Plate.ID = rep(single.plate.ID, length(Well))\n\n # Duplicate the time column times the number of wells and convert to numeric\n\tTime = as.numeric(rep(input.data[,Time.column], times = length(Well.column.start:ncol(input.data))))\n\n # Append OD measurements from each well together and convert to numeric\n\tOD = c()\n\tfor (i in Well.column.start:ncol(input.data)){\n\t\tOD = as.numeric(c(OD, input.data[,i]))\n\t\tOD = unlist(OD)\n\t\t}\n\n # Fill and return the data frame containing the above four vectors.\n\toutput = data.frame(Plate.ID, Well, OD, Time)\t\n\t\n # Include any extra columns that were not Time or OD measurements?\n\tfor(i in (1:length(names(input.data)))[-c(Time.column,Well.column.start:ncol(input.data))]){\n\t\tnew.column = data.frame(rep(input.data[,i], length(Well.column.start:ncol(input.data))))\n\t\tnames(new.column) = names(input.data)[i]\n\t\toutput = cbind(output, new.column)\n\t\t}\t\n\treturn(output)\n}\n\n\n########################################################################\n# #\n# Function to combine two well array datasets by plate #\n# #\n########################################################################\n# ----------------------------------------------------------\n# This function can append together arrays created using \n# Arguments: any number of array objects as long as they are all output straight from \n\ngcat.append.arrays = function(...){\n\n # Transfer arrays to a list\n\targs.arrays = list(...)\n\tfirst.array = args.arrays[[1]]\n\tfirst.dims = dim(first.array)\n plate.nrow = args.arrays[[4]]\n plate.ncol = args.arrays[[3]]\n input.arrays = list(args.arrays[[1]], args.arrays[[2]])\n\tfor (i in 2:length(input.arrays)){\n\t\tnext.array = input.arrays[[i]]\n\t\tnext.dims = dim(next.array)\n\t\n # Check to make sure the arrays have proper dimensions for 96-well plate data\n\t\t\n if (!(all(c(first.dims[1], next.dims[1]) == plate.nrow) & all(c(first.dims[2], next.dims[2]) == plate.ncol)))\n\t\t\tstop(\"Data should have dimensions (\",plate.nrow,\",\",plate.ncol,\",n)!\")\n\t\t\n # If dimensions are alright, append dimensions and dimension names\t\n new.dims = c(plate.nrow,plate.ncol,first.dims[3]+next.dims[3])\n\t\tnew.names = dimnames(first.array)\n\t\tnew.names[[3]] = c(new.names[[3]], dimnames(next.array)[[3]]) \n\n # Differentiate duplicate names\n\t\tfor (i in length(new.names[[3]]):1){\n\t\t\tif (any(new.names[[3]][-i] == new.names[[3]][i]))\n\t\t\t\tnew.names[[3]][i] = paste(\"another_\", new.names[[3]][i], sep = \"\")\n\t\t\t}\n\t\n\t\t# Create a new array\n new.array = c(first.array, next.array)\n\t\tdim(new.array) = new.dims\n\t\tdimnames(new.array) = new.names\n\t\t\n # Update plate name in well objects\n\t\tfor (i in 1:length(unlist(new.array)))\n\t\t\tnew.array[[i]]@position[1] = new.names[[3]][floor((i-1)/96)+1]\n\t\t\n\t\t# Loop until complete\n\t\tfirst.array = new.array\n\t\tfirst.dims = dim(first.array)\n\t\t}\n\treturn(new.array)\n\t}\n\n\n########################################################################\n# #\n# Convert timestamps to hours from start and sort timepoints #\n# #\n########################################################################\n#\n# This function acts on a single well and modifies the raw data stored in slot \"screen.data\"\n# \n# input.well - an object of class well\n# time.format - specifies the time format. allowed values are \"%S\", for seconds, \"%d\", for days, or anything complying with ISO C / POSIX standards; see \n# note: reading directly from excel to R results in timestamps being converted to days.\n# start.index - which timepoint should be used as the starting time at inoculation?\n\ngcat.start.times = function(input.well, time.input, start.index = 2) { \n \n if(start.index > length(input.well))\n stop(\"Start index is greater than length of well!\")\n \n # If using a numeric time format, simply multiply times by the appropriate conversion factor\n\t# Conversion factor should be supplied to convert timestamps to hours. For example, \n # should be equal to 1/3600 if \"time\" is in seconds, 24 if \"time\" is in days, etc.\n\n #TODO eliminate set.constants method and class and find any areas are still using it \n time.format = time.input # Set default constant from rails user input\n \n if (is.numeric(time.format))\n\t\tinput.well@screen.data$Time = (input.well@screen.data$Time - min(input.well@screen.data$Time)) * time.format\n else{\n # Otherwise, convert timestamps from ISO C / POSIX to numeric values representing seconds (since the dawn of time?) and subtract out the initial value. \n\t\trtimes = input.well@screen.data$Time\n ptimes = strptime(as.character(rtimes),time.format)\n\t\tctimes = as.POSIXct(ptimes)\n\t\tint.times = unclass(ctimes)\n # Time will be in seconds, convert to hours by dividing by 3600\n\t\tinput.well@screen.data$Time = (int.times - min(int.times))/3600\n\t\t}\n\t# Sort raw data by timestamp and return the input.well\n\tinput.well@screen.data = input.well@screen.data[order(input.well@screen.data$Time),]\n \n input.well@screen.data$Time = input.well@screen.data$Time - input.well@screen.data$Time[start.index]\n \n if(all(is.na(input.well@screen.data$Time)))\n stop(\"Error in .\") \n rownames(input.well@screen.data) = NULL\n\treturn(input.well)\n }\t\n", - "created" : 1423869300470.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "2771029213", - "id" : "85C00847", - "lastKnownWriteTime" : 1423869311, - "path" : "~/Documents/GCAT4_old/trunk/R/GCAT/R/table2well.R", - "project_path" : "table2well.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/A7CAE343 b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/A7CAE343 deleted file mode 100644 index c950bea..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/A7CAE343 +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n\n########################################################################\n# #\n# Normalize OD readings for an entire array of well objects #\n# #\n########################################################################\n#\n# Note: This function does not write any new OD values to the well objects in the array - it only \n# fills the \"norm\" slot of each well object in the array with a value that will be subtracted \n# from all OD measurements when returning data from the wells using the function (see well.class.R) \n#\n# These functions make use of which simply returns the raw time and OD of a well (also see well.class.R)\n#\n# well.array: an array of well objects. note this is the only normalization function that acts on an entire array instead of an individual well.\n# normalize.method: \n# - (default): subtracts the blank OD (either specified by or taken from the first timepoint as default) of each well from all timepoints in that well\n# - average.blank: subtracts the mean of all first OD timepoints on a plate from all timepoints in all wells on that plate\n# - average.first: takes the mean of the difference between the OD of the specified timepoint and the first timepoint of all wells on a plate\n# and subtracts this value from all timepoints in all wells on that plate\n# - anything else: do nothing\n# blank.value - user can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. \n# start.index - which timepoint should be used as the first one after inoculation (defaults to the 2th one)\n# add.constant: add a numeric constant to all timepoints in all wells. \n\n\nnormalize.ODs = function(well.array, normalize.method = \"default\", blank.value = NULL, start.index = 2, add.constant = 1){\n \n if (normalize.method == \"default\"){\n well.array = aapply(well.array, function(well, blank.value){\n # Use the blank OD value if specified; otherwise, get it from the first OD timepoint. \n if(is.null(blank.value)) blank.value = raw.data(well)[1,2]\n # Set the blank OD (minus the constant to be added) to the \"norm\" slot of each well.\n \twell@norm = blank.value - add.constant\n \treturn(well)}, blank.value)\n }\n else if (normalize.method == \"average.blank\"){ \n # Use the blank OD value if specified; otherwise, get it from the first OD timepoint.\n\t\tblank.ODs = unlist(aapply(well.array, function(well, blank.value){\n if(is.null(blank.value)) blank.value = raw.data(well)[1,2]\n return(blank.value)}, blank.value))\n\t\tplate.IDs = unlist(aapply(well.array, plate.name))\n\t\tblank.averages = tapply(blank.ODs, plate.IDs, mean)\n\t # Set this value (minus the constant to be added) to the \"norm\" slot of each well. \n\t\twell.array = aapply(well.array, function(well){\n\t\t\twell@norm = blank.averages[plate.name(well)] - add.constant\n\t\t\treturn(well)})\n\t\t}\n\telse if (normalize.method == \"average.first\"){\n\t # Find the mean difference between starting OD (timepoint specified by ) and blank OD (first timepoint) for each plate\n # Use the blank OD value if specified; otherwise, get it from the first OD timepoint.\n blank.ODs = unlist(aapply(well.array, function(well, blank.value){\n if(is.null(blank.value)) blank.value = raw.data(well)[1,2]\n return(blank.value)}, blank.value))\n\t\tfirst.ODs = unlist(aapply(well.array, function(well) raw.data(well)[start.index,2]))\n\t\tplate.IDs = unlist(aapply(well.array, plate.name))\n\t blank.averages = tapply(first.ODs-blank.ODs,plate.IDs,mean)\n\t # Set this value (minus the constant to be added) to the \"norm\" slot of each well.\n\t\twell.array = aapply(well.array, function(well){\n\t\t\twell@norm = raw.data(well)[start,2] - blank.averages[plate.name(well)] - add.constant \n\t\t\treturn(well)})\n\t\t}\t\n\telse{\n # Simply set the negative constant to be added to the \"norm\" slot of each well. \n\t\twell.array = aapply(well.array, function(well){\n\t\t\twell@norm = - add.constant\n \t\t\treturn(well)})\n\t\t}\n if(is.null(blank.value))\n well.array = aapply(well.array, remove.points, 1)\n return(well.array)\n\t}\n\n########################################################################\n# #\n# Log-transform OD readings for a single well object #\n# #\n########################################################################\n#' Transform.Ods \n#' \n#' This function adds a \"log.OD\" column to the \"screen.data\" slot of a well object with log-transformed data. \n#' The raw data is kept intact. \n#' It also checks to see if any of the raw OD values (before a certain timepoint) is below the blank OD. \n#' This can be disastrous for the log(OD) transform. \n#' @param input.well an object of class well \n#' @param use.log gets added to the \"use.log\" slot of the well object. this will determine whether the log-transformed data \n#' or raw normalized data is returned using the function \\code{data.from}. \n#' @param blank.value user can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. \n#' @param start.index which timepoint should be used as the first one after inoculation (defaults to the 2th one) \n#' @param negative.OD.cutoff if any ODs below the specified blank value are detected before this index timepoint, the entire well is discarded. \n\ntransform.ODs = function(input.well, use.log = T, blank.value = NULL, start.index = 2, negative.OD.cutoff = 10, constant.added = 1.0){\n \n # The default value for the log-transformed ODs will be NA. Valid values will be filled in. \n\tlog.OD = rep(NA, length(input.well))\n OD = raw.data(input.well)[,2]\n \n\t # Use the blank OD value if specified; otherwise, get it from the first OD timepoint.\n if(is.null(blank.value))\n blank.value = OD[1]\n\n # Remove any points from the analysis that weren't already removed and fall below the blank value (using below)\n OD[input.well@screen.data$Remove] = NA\n \n negative.points = which(OD + 0.2 * constant.added < blank.value)\n if(length(negative.points) > 0)\n\t input.well = remove.points(input.well, negative.points)\n \n # If any points fall below the blank value by more than 0.2 * and before the cutoff index , remove the well from analysis. \n # First adjust the cutoff to compensate for curves that don't start at timepoint 1\n negative.OD.cutoff = negative.OD.cutoff + start.index - 1\n \n if(any(negative.points <= negative.OD.cutoff)){\n input.well = remove.points(input.well, rep(T,length(input.well)))\n input.well@add.info = paste(\"ODs at timepoint(s)\", paste(negative.points[negative.points <= negative.OD.cutoff],collapse=\" \"), \"were below blank OD; well discarded\")\n }\n\n # Take the natural log of the rest of the OD values (after subtracting the normalization value)\n log.OD[which(OD > input.well@norm)] = log(OD[which(OD > input.well@norm)] - input.well@norm)\n\t\n\t# Add a column to the \"screen.data\" slot of the well\n\tinput.well@screen.data$log.OD = log.OD\t\n\t# Update the \"use.log\" slot of the well \n\tinput.well@use.log = use.log\t\n\n\treturn(input.well)\n\t}\n\n########################################################################\n# #\n# Remove timepoints from the analysis but not from the raw data #\n# #\n########################################################################\n# \n# Removes timepoints from further analysis. Does not remove them from the raw data;\n# instead, this function creates or updates the Remove column in slot \"screen.data\" of the well which dictates whether \n# individual timepoints are returned using the function. \n#\n# can be a vector containing:\n# - any combination of positive and negative integers \n# the timepoints at indices corresponding to positive integers will be set to be removed.\n# the timepoints at indices corresponding to negative integers will be be re-added if they were previously set to be removed.\n# - a single zero, which resets all timepoints (nothing will be removed)\n# - a logical vector to replace the Remove column and which will be cycled along the length of the timepoints. \n\nremove.points = function(input.well, points){\n # Copy the Remove column or create a new one if it doesn't yet exist\n\tif (is.null(input.well@screen.data$Remove))\n\t\tRemove = rep(F, length(input.well))\n\telse\n\t\tRemove = input.well@screen.data$Remove\n\n # If is a logical vector, recycle it along the length of Remove \n\tif (length(points[!is.na(points)]) != 0){\n\t# Separate positive and negative integers\n \tif (is.logical(points) & !any(is.na(points)))\n \t\tRemove = rep(points,length.out=nrow(input.well@screen.data))\t\n \t\telse{\n \tpos = points[points > 0]\n \tneg = -points[points < 0]\n \tRemove[pos] = T\n \tRemove[neg] = F \n \t\t \t\n # If contains only zeros, reset the Remove vector to all F \t\n \tif (all(points == 0))\n \t\tRemove[1:length(Remove)] = F\n \t\t}\n }\n # replace the Remove column\n\tinput.well@screen.data$Remove = Remove\n\tinput.well\n\t}\n\n\n\n\n\n", - "created" : 1423869246743.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "2859176021", - "id" : "A7CAE343", - "lastKnownWriteTime" : 1423869285, - "path" : "~/Documents/GCAT4_old/trunk/R/GCAT/R/normalize.and.transform.R", - "project_path" : "normalize.and.transform.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/EA711236 b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/EA711236 deleted file mode 100644 index 809cfce..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/EA711236 +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, \n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n\n# GCAT version 5.00\n# Notes by Jason\n# 08/18/2011\n\n# Initialization\n\n\nPLATE.LETTERS = paste(rep(c(\"\", LETTERS), each = 26), rep(LETTERS, 26), sep=\"\")\nglobal.version.number = packageDescription(pkg=\"GCAT\")$Version \n\n########################################################################\n# #\n# Top-level functions for analysis of screening data from .csv files. #\n# #\n########################################################################\n# This functions is called directly by the user interface.\n# They in turn call the main function (below) multiple times for each data file provided in . \n\n# Arguments:\n# file.list - a list of full paths to .csv files. all files must be in the same format (see )\n# single.plate - are the file in the single plate (wide) format vs. the multi-plate (long) format?\n# layout.file - (optional) provide full path to a layout file with strain and media definitions (applies to all files in list)\n\n# out.dir - name a directory to output the table of curve parameters to (defaults to working directory) \n# graphic.dir - name a directory to output the images of the fitted curves to (defaults to subdirectory \"pics\" of above)\n\n\n# add.constant- should be a numeric constant that will be added to each curve before the log transform (defaults to 1) \n# blank.value - user can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. \n# start.index - which timepoint should be used as the first one after inoculation (defaults to the 2th one)\n# growth.cutoff - minimum threshold for curve growth. \n# points.to.remove - a list of numbers referring to troublesome points that should be removed across all wells.\n# remove.jumps - should the slope checking function be on the lookout for large jumps in OD?\n \n# silent - should messages be returned to the console?\n# verbose - should sub-functions return messages to console? (when I say verbose, I mean it!)\n\n# Returns:\n# if = F (default), avector of full paths to all the files generated by the function.\n# otherwise, the fitted array of well objects. \n\n# Use this function to analyze any set of .csv files using the same plate layout info. \n\n#' Analyze screening growth data from the given .csv files.\n#' \n#' Top-level GCAT function \n#' \n#' @param file.list A list of full paths to .csv files. all files must be in the same format (see )\n#' @param single.plate The file in the single plate (wide) format vs. the multi-plate (long) format?\n#' @param layout.file Full path to a layout file with strain and media definitions (applies to all files in list)\n\n#' @param out.dir A directory to output the table of curve parameters to (defaults to working directory) \n#' @param graphic.dir A directory to output the images of the fitted curves to (defaults to subdirectory \"pics\" of above)\n\n\n#' @param add.constant A numeric constant that will be added to each curve before the log transform (defaults to 1) \n#' @param blank.value User can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. \n#' @param start.index Which timepoint should be used as the first one after inoculation (defaults to the 2th one)\n#' @param growth.cutoff Minimum threshold for curve growth. \n#' @param points.to.remove A list of numbers referring to troublesome points that should be removed across all wells.\n#' @param remove.jumps Should the slope checking function be on the lookout for large jumps in OD?\n#' @param time.input The time setting in which the current system is running?\n#' @param plate.nrow The number of rows in a plate.\n#' @param plate.ncol The number of columns in a plate.\n#' @param input.skip.lines If specified, this number of lines shall be skipped from the top when reading the input file with read.csv \n#' @param multi.column.headers The headers of the result tabular data when analyzing multiple plates at once.\n#' @param single.column.headers The headers of the result tebaular data when analyzaing a single plate.\n#' @param layout.sheet.headers The headers of the layout file?\n#' @param silent Shoulde messages be returned to the console?\n#' @param verbose Should sub-functions return messages to console? (when I say verbose, I mean it!)\n#' @param overview.jpgs Should GCAT enable an overview image?\n#' \n#' @return A list of the output files.\ngcat.analysis.main = function(file.list, single.plate, layout.file = NULL, \n out.dir = getwd(), graphic.dir = paste(out.dir, \"/pics\", sep = \"\"), \n add.constant = 0.1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05,\n use.linear.param = F, use.loess = F, smooth.param=0.1,\n points.to.remove = 0, remove.jumps = F, time.input = NA,\n plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,\n multi.column.headers = c(\"Plate.ID\", \"Well\", \"OD\", \"Time\"), single.column.headers = c(\"\",\"A1\"), \n layout.sheet.headers = c(\"Strain\", \"Media Definition\"),\n silent = T, verbose = F, return.fit = F, overview.jpgs = T){\n \n plate.nrow <<- plate.nrow\n plate.ncol <<- plate.ncol\n input.skip.lines <<- input.skip.lines\n multi.column.headers <<- sub(\" \",\".\",multi.column.headers)\n single.column.headers <<- sub(\" \",\".\",single.column.headers)\n layout.sheet.headers <<- sub(\" \",\".\",layout.sheet.headers)\n \n # MB: Prototyping system unwanted argument guarding. Proper function \n # will be added in the future.\n # Not the best solution.\n if (is.na(time.input)) {\n if (single.plate)\n time.input = 1/3600\n else\n exception(\"Error: \", \"time.input is NA.\")\n }\n print(add.constant)\n if (add.constant < 0)\n exception(\"Error: \", \"The constant r should not be negative.\")\n # End prototyping temporary solution.\n \n upload.timestamp = strftime(Sys.time(), format=\"%Y-%m-%d %H:%M:%S\") # Get a timestamp for the time of upload. \n fitted.well.array.master = list()\n source.file.list = c()\n \n dim(fitted.well.array.master) = c(plate.nrow,plate.ncol,0)\n dimnames(fitted.well.array.master) = list(PLATE.LETTERS[1:plate.nrow], 1:plate.ncol, c())\n \n for(file.name in file.list){\n \n # Call on the file with single plate options\n \tfitted.well.array = try(gcat.fit.main(file.name = file.name, load.type = \"csv\", \n single.plate = single.plate, layout.file = layout.file, start.index = start.index, \n time.input = time.input, add.constant = add.constant, blank.value = blank.value, \n growth.cutoff = growth.cutoff, points.to.remove = points.to.remove, remove.jumps = remove.jumps,\n \t use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=smooth.param,\n plate.nrow = plate.nrow, plate.ncol = plate.ncol, multi.column.headers = multi.column.headers, \n single.column.headers = single.column.headers, layout.sheet.headers = layout.sheet.headers,\n input.skip.lines = input.skip.lines, silent = silent, verbose = verbose), silent = T)\n \n # Return error message if the function fails.\n if(class(fitted.well.array) == \"try-error\")\n return(as.character(fitted.well.array)) \n }\n \n # Add fitted well array onto existing fitted wells\n fitted.well.array.master = gcat.append.arrays(fitted.well.array.master, fitted.well.array, plate.ncol, plate.nrow)\n \n # Remove the \"processed_\" tag from file names and add to the list of source files.\n source.file.list = c(source.file.list, basename(paste(strsplit(file.name, \"processed_\")[[1]],collapse=\"/\"))) \n\n out.files = try(gcat.output.main(fitted.well.array.master, out.prefix = \"output\", \n source.file.list = source.file.list, upload.timestamp = upload.timestamp, \n growth.cutoff = growth.cutoff, add.constant = add.constant, blank.value = blank.value, start.index = start.index, \n points.to.remove = points.to.remove, remove.jumps = remove.jumps, \n out.dir = out.dir, graphic.dir = graphic.dir, overview.jpgs=overview.jpgs,\n use.linear.param=use.linear.param, use.loess=use.loess,\n silent = silent), silent = T)\n \n # Return file list or error message otherwise return \"successful analysis\" message (?)\n\n # file.list = c(\"Data was successfully analyzed.\", file.list) # <--- yet to be implemented. causes errors downstream right now \n if(class(out.files) == \"try-error\") return(as.character(out.files)) \n \n if(return.fit) return(fitted.well.array.master)\n else return(out.files) \n}\n\n########################################################################\n# #\n# Main function for analysis of screening data from input tables. #\n# #\n########################################################################\n# This is the main function that handles all the analyses for files in both single and multiple plate formats. \n# It is called by the top level function \n#\n# It then calls the following functions on each member of the array: \n# - curve normalization and standardization: , , , , \n# - curve shape analysis before model fitting: , , \n# - to fit a nonlinear model to the growth data: \n# Finally, it returns the fitted array of well objects.\n\n#' Main analysis function for GCAT \n#' \n#' This is the main function that handles all the analyses for data files in both single and multiple plate formats. \n#' It is called by the top level function \\code{gcat.analysis.main} along with \\code{gcat.output.main}.\n#' \n#' @param file.name Complete path and file name of a comma-separated values (.csv) file containing growth curve data \n#' in the multiple-plate (long) format. \n#' @param input.data A list of tables representing input files read with \\code{read.table}. Used to save time in cases\n#' of running multiple analyses on the same dataset. If used, the function will ignore \\code{file.name} entirely.\n#' @param load.type .csv by default. \n#' @param layout.file Specifies the location of a layout file containing identifying information.\n#' @param single.plate Whether the GCAT is analyzing a single plate or not.\n#' @param blank.value Blank OD measurement for uninoculated wells. By default(NULL), the value of the first OD\n#'measurement in each well is used.\n#' @param start.index Which timepoint should be used as the first one after inoculation?\n#' @param time.input Either a character describing the format used to convert timestamps in the input to numbers\n#' representing number of seconds (see \\code{strptime}), or a factor to divide entries in the Time column by to get the \n#' numbers of hours.\n#' @param normalize.method Describes the method used by \\code{normalize.ODs} to normalize cell density values using blank reads.\n#' @param add.constant A value for r in the log(OD + r) transformation.\n#' @param use.log Should the analysis use log on all values.\n#' @param points.to.remove A vector of integers specifying which timepoints should be removed across all wells. \n#' By default(0) none are marked for removal.\n#' @param use.linear.param Should the linear parameter be used or not.\n#' @param use.loess Should the loess model be used or not.\n#' @param smooth.param If loess model is used, this parameter define the smoothing parameter for the loess model.\n#' @param fall.cutoff A cutoff used by \\code{check.slopes} to decide on thresholds for jumps and tanking.\n#' @param growth.cutoff A threshold used by check.growth to decide whether a well displays growth.\n#' @param remove.jumps Should jumps in OD detected by the subfunction \\code{check.slopes}?\n#' @param plate.nrow The number of rows in the input files.\n#' @param plate.ncol The number of columns in the input files.\n#' @param input.skip.lines If specified, this number of lines shall be skipped from the top when reading the input file with read.csv \n#' @param multi.column.headers The headers of the column when analyzing multiple plates.\n#' @param single.column.headers The headers of the column when analyzing a single plate.\n#' @param layour.sheet.headers The headers of the layout file.\n#' @param growth.model What growth model should be used?\n#' @param backup.growth.model If the main growth model fails, the back up model will be used.\n#' @param silent Surpress all messages.\n#' @param verbose Display all messages when analyzing each well.\n#' \n#' @return An array of well objects\ngcat.fit.main = function(file.name, input.data = NULL, load.type = \"csv\", layout.file = NULL, \n single.plate = F, blank.value = NULL, start.index = 2, time.input = NA,\n normalize.method = \"default\", add.constant = 1, use.log = T, points.to.remove = 0,\n use.linear.param=F, use.loess=F, smooth.param=0.1,\n fall.cutoff = -0.0025, growth.cutoff = 0.05, remove.jumps = F, \n plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,\n multi.column.headers = c(\"Plate.ID\", \"Well\", \"OD\", \"Time\"), single.column.headers = c(\"\",\"A1\"), \n layout.sheet.headers = c(\"Strain\", \"Media Definition\"),\n growth.model = NA, backup.growth.model = NA, \n silent = F, verbose = F){\n \n # Explanation of arguments:\n \n # ---File Handling---\n # file.name - full path to an excel spreadsheet, .csv or tab-delimited text file, in either the single or multiple-plate format\n # input.data - use pre-loaded data set (output from function only). will override if not NULL \n # load.type - supports \"csv.\" \n # layout.file - full path to a file containing the plate layout in the same format as . will not be used if is \"xlsx\"\n\n # ---Input file format---\n # single.plate - true denotes data in single-plate format, i.e. simple OD output. false denotes multiple-plate robotic screening output. \n # note: reading directly from excel to R results in timestamps being converted to days.\n\n # ---Normalization and Transforms---\n # blank.value - user can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. \n # start.index - which timepoint should be used as the first one after inoculation (defaults to the 2th one)\n # normalize.method - how should each growth curve be normalized? allowed values are:\n # \"first\": subtracts the first OD, assumed to be the blank, from all ODs\n # \"none\": does nothing, assumes no blank. highly recommend log(OD+1) transform in this case.\n # \"average.first\": forces all filled wells on each plate to match the average value at (after subtracting the first OD) \n # add.constant - a numeric constant that will be added to each curve before the log transform (defaults to 1)\n # use.log - should a log transform be applied to the data after normalization? \n # points.to.remove - a list of numbers referring to troublesome points that should be removed across all wells.\n \n # ---Pre-fitting processing---\n # fall.cutoff - a cutoff value for determining whether OD falls significantly between two timepoints. see in prefit.processing.R for details. \n # growth.cutoff - a cutoff value for determining whether a well contains a successfully growing culture or not.\n # remove.jumps - should the slope checking function be on the lookout for large jumps in OD?\n \n # ---Model fitting---\n # model - which parametrized growth model to use? can be richards, gompertz, or logistic. models are defined as objects of class model, see \"model.class.R\"\n # backup.model - which model should be used if fitting using fails? should ideally be simpler than the main model (less parameters)\n \n # ---Miscellanous input/output preferences---\n # silent - should messages be returned to the console?\n # verbose - should sub-functions return messages to console? (when I say verbose, I mean it!) \n # unlog - should exported graphics be transformed back to the OD scale? \n # return.fit - should the function return an array of wells? if not, it will return a list of generated files. \n \n \t\n ########################################################################\n # Read from .csv file #\n ########################################################################\n #\n # The functions used here are found in table2well.R\n \n if(!silent) cat(\"\\nReading input files...\")\n # Read from .csv or tab-delimited text file using (in load.R)\n # if is provided, it will be used here. \n \n plate.layout = NULL \n # Read layout file if it is specified. \n if(!is.null(layout.file)){\n if(load.type==\"csv\") plate.layout = read.csv(layout.file,header=T,stringsAsFactors=F)\n else plate.layout = read.table(layout.file,header=T,sep=\"\\t\",stringsAsFactors=F) \n if(!silent) cat(\"\\n\\tAdded plate layout information from\", layout.file, \"\\n\")\n }\n \n # Load the data \n\t\twell.array = try(gcat.load.data(file.name = file.name, input.data = input.data, \n plate.layout = plate.layout, plate.nrow = plate.nrow, plate.ncol = plate.ncol, \n input.skip.lines = input.skip.lines, multi.column.headers = multi.column.headers, \n single.column.headers = single.column.headers, layout.sheet.headers = layout.sheet.headers,\n blank.value = blank.value, start.index = start.index, single.plate = single.plate, \n load.type = load.type, silent=silent),silent=silent)\n\n # Return an error if there is a problem with file loading. \n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n\t\t\n\n # !---At this point, is an array of well objects, each containing raw data and media/strain information if provided--- \n \n # Attempt to apply time formatting to all wells in array \n well.array = try(aapply(well.array, gcat.start.times, start.index = start.index, time.input = time.input),silent=silent)\n \n # Return an error if there is a problem with time formatting\n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n \t\n ########################################################################\n # Perform normalization and transformation of raw data #\n ######################################################################## \n #\n # The functions used here are found in normalize.and.transform.R \n \n if(!silent) cat(\"\\nProcessing raw data...\")\n \n # Set all timepoints to active for now using \"points.to.remove=0\" argument with \n # adds an extra column to the \"well.array\" slot of each well specifying which points to remove when data is retrieved from the well\n well.array = aapply(well.array, remove.points, points = 0)\n \n # Normalize ODs using specified method and adding a constant if desired. \n # sets the \"norm\" slot of each well to a value to be subtracted from OD values whenever data is retrieved from the well\n well.array = try(normalize.ODs(well.array, normalize.method = normalize.method, \n start.index = start.index, blank.value = blank.value, add.constant = add.constant),silent=silent)\n \n # Return an error if there is a problem with normalization\n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n \n # Transform ODs on the logarithmic scale, regardless of whether is true \n # an extra column of log-transformed values is added to the \"well.array\" slot of each well \n # the \"use.log\" slot of each well is set instead to determine whether the transformed values will be returned when data is retrieved from the well.\n well.array = try(aapply(well.array, transform.ODs, start.index = start.index, blank.value = blank.value, use.log = use.log, constant.added = add.constant),silent=silent)\n \n # Return an error if there is a problem with transformation\n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n \n # Remove specified timepoints across wells (use \"points.to.remove=NULL\" if no points to remove) \n well.array = try(aapply(well.array, remove.points, points = points.to.remove),silent=silent)\n \n # Return an error if there is a problem with point removal\n if (class(well.array) == \"try-error\")\n stop(\"Error in : \", well.array) \n \n \n \n ########################################################################\n # Pre-fitting data processing (analysis of curve shapes) #\n ######################################################################## \n #\n # The functions used here are found in slope.analysis.R\n \n # Estimate slope at each timepoint \n # add a column to the \"well.array\" slot of each well with the local slope at each timepoint \n \n well.array = try(aapply(well.array, calculate.slopes, silent=!verbose),silent=silent)\n \n # Return an error if there is a problem with slope calculation\n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n \n # Check slopes for tanking and/or jumping behavior\n # fills the \"curve.par\" slot of each well with , denoting the timepoint at which tanking starts (if none, value is NA) \n # uses to remove all points after \n # It will also fill the \"jump.error\" slot with a status message, and try to use an automated process to remove the \n # erroneous points if is true (default false). \n \n well.array = try(aapply(well.array, check.slopes, fall.cutoff = fall.cutoff, remove.jumps = remove.jumps, silent=!verbose, draw = F),silent=silent)\n \n # Return an error if there is a problem with slope analysis\n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n \t\n \t\n # Check curves for growth above cutoff\n # fills the \"curve.par\" slot of each well with , denoting whether the well has no detectable growth. \n well.array = try(aapply(well.array, check.growth, growth.cutoff = growth.cutoff, start.index = start.index),silent=silent)\n \n # Return an error if there is a problem with growth.check\n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n \t\n ########################################################################\n # Fit parameterized models to data #\n ######################################################################## \n #\n # The functions used here are found in fit.model.R \n \n # Fit each well with the selected model and attempt to catch failed fittings with the backup model \n # skips wells designated as above\n # fills the \"fit.info\" slot of each well with \"success,\" \"failed,\" or \"skipped\"\n # if fit was successful:\n # fills the \"equation\" and \"model.name\" slots with the relevant info for the successful model \n # fills the \"fit.par\" slot with fitted parameters if fit is successful \n \n if(!silent) cat(\"\\nFitting models to data...\")\n well.array = aapply(well.array, fit.model, growth.model=growth.model,\n backup.growth.model = backup.growth.model, use.linear.param=use.linear.param,\n use.loess=use.loess, smooth.param=smooth.param, silent=!verbose)\n \n # Return an error if there is a problem with model fitting\n if (class(well.array) == \"try-error\")\n \tstop(\"Error in : \", well.array)\n \n if(!silent) cat(\"\\ndone!\\n\") \n return(well.array) \n } \n \n \n########################################################################\n# #\n# Output function for generating files from fitted data. #\n# #\n######################################################################## \n#' Output function for generating files from fitted data.\n#' \n#' Handles files and directories, calls \\code{table.out}, \\code{plate.overview} and \\code{view.fit} \n#' to generate output tables and graphics.\n#' \n#' @param fitted.well.array A list of fitted well objects.\n#' @param out.prefix Prefix that is in the name of output files.\n#' @param blank.value User can enter a blank OD measurement for uninoculated wells. \n#' If NULL, defaults to the value of the first OD measurement of each well.\n#' @param start.index Which timepoint should be used as the first one after inoculation (defaults to the 2th one)\n#' @param growth.cutoff Minimum threshold for curve growth.\n#' @param points.to.remove A list of numbers referring to troublesome points that should be removed across all wells.\n#' @param remove.jumps Should the slope checking function be on the lookout for large jumps in OD?\n#' @param out.dir name a directory to output the table of curve parameters to (defaults to working directory) \n#' @param graphic.dir name a directory to output the images of the fitted curves to \n#' (defaults to subdirectory \"pics\" of above)\n#' @param overview.jpgs should jpgs be generated for each plate with the overview graphic? \n#' This is for backwards compatibility with the old web server. \n#' @param silent should messages be returned to the console?\n#' @param unlog should exported graphics be transformed back to the OD scale?\n#' @param constant.added (should be the same value as add.constant above) - \n#' used to readjust for the constant added during the log transform when plotting ODs. \n#' @return A list of output files if success.\n\ngcat.output.main = function(fitted.well.array, out.prefix = \"\", source.file.list, upload.timestamp = NULL, \n add.constant, blank.value, start.index, growth.cutoff, points.to.remove, remove.jumps, \n out.dir = getwd(), graphic.dir = paste(out.dir,\"/pics\",sep = \"\"), overview.jpgs = T,\n use.linear.param=F, use.loess=F,\n unlog = F, silent = T){ \n \n # Prepare timestamp for addition to output file names. \n filename.timestamp = strftime(upload.timestamp, format=\"_%Y-%m-%d_%H.%M.%S\")\n \t\n ########################################################################\n # Prepare to write to output files #\n ######################################################################## \t\n\t if(is.null(blank.value)) blank.value = \"First timepoint in well\"\n\t \n if(!silent) cat(\"\\nFinding/creating new output directories...\")\n \n old.wd = getwd() \n # Create output directory if it doesn't exist\n if(class(try(setwd(out.dir), silent = T)) == \"try-error\"){\n \tif(!silent) cat(\"\\ncreating new output directory\")\n \tif (class(try(dir.create(out.dir))) == \"try-error\")\n \t\tstop(\"Error creating new output directory!\")\n \t}\n \n # Create graphics directory if it doesn't exist\n if(class(try(setwd(graphic.dir), silent = T)) == \"try-error\"){\n \tif(!silent) cat(\"\\ncreating new graphics directory\")\n \tif (class(try(dir.create(graphic.dir))) == \"try-error\")\n \t\tstop(\"Error creating new graphics directory!\")\n \t}\n \t\n ########################################################################\n # Populate a data table with fit results and write to file #\n ######################################################################## \n # \n # The functions used here are found in table.output.R \n \n # Creates a table with a row for each well and a column for each of various identifiers and fitted and calculated parameters. \n \n if(!silent) cat(\"\\nPopulating data table...\")\n table.fit = try(table.out(fitted.well.array, filename.timestamp=filename.timestamp,use.linear.param=use.linear.param, use.loess=use.loess, constant.added=add.constant))\n \n # Return an error if there is a problem with returning the table\n if (class(fitted.well.array) == \"try-error\")\n \tstop(\"Error in : \", fitted.well.array)\n \t\n \t\n # Set working directory to \n\tif (class(try(setwd(out.dir))) == \"try-error\")\n\t\tstop(\"Error setting directory for table output\")\n\t\t\n\t# Write output table to file in \n table.filename = paste(out.dir, \"/\", out.prefix, \"_gcat.fit\", filename.timestamp, \".txt\", sep = \"\")\n if (class(try(write.table(table.fit, table.filename, sep = \"\\t\", row.names = F))) == \"try-error\")\n\t\tstop(\"Error writing tabular output\")\n\t\t\n \t# ---If successfully written, add postscript and start a list of generated files.\t\n generated.files = table.filename\n\n ########################################################################\n # Write individual fit and overview graphics to file #\n ######################################################################## \n # \n # The functions used here are found in graphic.output.R\n \n if(!silent) cat(\"\\nDrawing graphics...\")\n \n # Set working directory to \n\tif (class(try(setwd(graphic.dir))) == \"try-error\")\n\t\tstop(\"Error setting directory for graphic output\")\n\t# Use function to write fit graphics to file. \n \n\tgraphic.files = try(pdf.by.plate(fitted.well.array, out.prefix=out.prefix, upload.timestamp = upload.timestamp, \n unlog=unlog,constant.added=add.constant,overview.jpgs=overview.jpgs),silent=silent)\n \n if (class(graphic.files) == \"try-error\")\n\t\tstop(\"Error in : \", graphic.files)\n \n # If successfully written, add to the list of generated files.\t\n generated.files = c(generated.files, graphic.files)\n \n ########################################################################\n # Add a postscript to the output table with legend and file info. #\n ######################################################################## \n # \t\n sink(table.filename, append = T)\n analysis.timestamp = strftime(Sys.time(), format=\"%Y-%m-%d %H:%M:%S\")\n cat(\"\\n# Raw OD values are adjusted and log-transformed before fitting a growth curve as follows: log.OD = log(OD - blank + const) where blank is OD of blank medium and const is specified by the user (1 by default)\",\n \"\\n# Values are reported on the above 'log.OD' scale unless otherwise specified.\",\n \"\\n# .SE columns report standard errors of those values that are estimated directly as parameters of global sigmoid models.\",\n \"\\n# .OD columns report values back-transformed to the linear 'OD - blank' scale.\",\n \"\\n\")\n \n cat(\"\\n# -- Explanation of columns --\",\n \"\\n# - model: Name of the model the well was successfully fit with (if any)\",\n \"\\n# - lag.time: Lag time estimate inferred from the fitted model\",\n \"\\n# - inflection.time: inflection time point of the growth curve when drawn on the log scale\",\n \"\\n# - max.spec.growth.rate: maximum specific growth rate estimate inferred from the fitted model. Estimated as the first derivative of the growth curve at inflection time point\", \n \"\\n# - baseline: growth curve baseline. Global sigmoid model: baseline is parameter 'b' of the model. LOESS: baseline is the same as the lowest predicted log.OD value\",\n \"\\n# - amplitude: difference between upper plateau and baseline values. Global sigmoid model: amplitude is parameter 'A' of the model. LOESS: amplitude = max.log.OD - min.log.OD\",\n \"\\n# - plateau: upper asymptote value of the fitted model. Global sigmoid model: plateau = b + A. LOESS: plateau = max.log.OD\",\n \"\\n# - inoc.log.OD: log.OD value at inoculation. Estimated value from the fitted model is used, rather than the actual measurement\", \n \"\\n# - max.log.OD: maximal log.OD value reached during the experiment. Estimated value from the fitted model is used rather than the actual measurement\",\n \"\\n# - projected.growth: maximal projected growth over inoculation value. Global sigmoid model: projected.growth = plateau - inoc.log.OD. LOESS: not reported\",\n \"\\n# - achieved.growth: maximal growth over inoculation value actually achieved during the experiment. achieved.growth = max.log.OD - inoc.log.OD\",\n \"\\n# - shape.par: shape parameter of the Richard equation\",\n \"\\n# - R.squared: goodness of fit metric. Also known as coefficient of determination. R.squared is usually between 0 and 1. A value close to 1 indicates good fit.\",\n \"\\n# - RSS: residual sum of squares. Another goodness of fit metric. Smaller values indicate better fits.\",\n \"\\n# - empty: (Well indicator)\", \n \"\\n# - an 'E' indicates that the well was empty and no growth was detected. \",\n \"\\n# - an 'I' indicates that the well was inoculated and growth was detected above the threshold. \",\n \"\\n# - an 'E*' indicates that the well was empty and growth was detected (possible contamination). \",\n \"\\n# - an '!' indicates that the well was inoculated and no growth was detected. \",\n \"\\n# - asymp.not.reached: shows “L” if the bottom asymptote (baseline) was not reached and “U” if the upper asymptote (plateau) was not reached.\",\n \"\\n# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index.\", \n \"\\n# - other: Additional flag column. Displays information about whether jumps in OD were detected and what was done about them.\",\n \"\\n# - pdf.file and page.no: location of the figure for this well in the output .pdf files.\"\n )\n \n\t # Analysis information \n \n cat(\"\\n#\\n# -- Source file information--\",\n \"\\n# \", paste(source.file.list, collapse = \"\\n# \"), \n \"\\n# analyzed using GCAT v\", global.version.number, \n \"\\n# request sent: \", upload.timestamp, \n \"\\n# completed: \", analysis.timestamp, \n \"\\n#\\n# -- Parameters used in current analysis --\",\n \"\\n# - Constant added to log(OD + n) transformation:\", add.constant,\n \"\\n# - Blank OD value: \", blank.value,\n \"\\n# - Index of inoculation timepoint\", start.index,\n \"\\n# - Minimum growth threshold:\", growth.cutoff, \n \"\\n# - Removed points:\", paste(points.to.remove, collapse = \" \"),\n \"\\n# - Jump detection:\", remove.jumps) \n sink()\n \n ########################################################################\n # Return values to R #\n ######################################################################## \n # \n\n if(!silent) cat(\"\\ndone!\") \n setwd(old.wd)\n # Return list of generated files\n\treturn(generated.files)\n }\n \n", - "created" : 1423869094349.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "2752939431", - "id" : "EA711236", - "lastKnownWriteTime" : 1423869149, - "path" : "~/Documents/GCAT4_old/trunk/R/GCAT/R/GCAT.main.R", - "project_path" : "GCAT.main.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/EE21755B b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/EE21755B deleted file mode 100644 index 7057d7b..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/per/t/EE21755B +++ /dev/null @@ -1,16 +0,0 @@ -{ - "contents" : "#Copyright 2012 The Board of Regents of the University of Wisconsin System.\n#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead,\n#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman\n#\n#This file is part of GCAT.\n#\n#GCAT is free software: you can redistribute it and/or modify\n#it under the terms of the GNU Lesser General Public License as published by\n#the Free Software Foundation, either version 3 of the License, or\n#(at your option) any later version.\n#\n#GCAT is distributed in the hope that it will be useful,\n#but WITHOUT ANY WARRANTY; without even the implied warranty of\n#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n#GNU Lesser General Public License for more details.\n#\n#You should have received a copy of the GNU Lesser General Public License \n#along with GCAT. If not, see .\n########################################################################\n# #\n# class definition and functions. Objects contain equations #\n# and other information for parameterized growth curve models. #\n# #\n########################################################################\nsetClass(\"model\", representation(name = \"character\",\n expression = \"expression\",\n formula = \"formula\",\n guess = \"function\"))\n# Slots:\n# name - a simple description of the model.\n# expression - an object of class \"expression\" that evaluates the response (transformed OD) with respect to the variable Time.\n# formula - same as expression, but with y as the response.\n# guess - a function that computes initial guesses for the parameters given a well object with a valid \"screen.data\" slot\n# containing useable OD values and slope estimates\n# --------------------------------------------------------------------\n# Function to create a new model \t \n#' Model \n#' \n#' Function to create a new model \n#' @param name The name of the model \n#' @param expression Expression of the model \n#' @param formula The formula of this model \n#' @param guess The guess of this model \n#' @return The new model \nmodel = function(name, expression, formula, guess){\n new(\"model\", name = name, expression = expression, formula = formula, guess = guess)\n}\n\nloess.g = function(well,smooth.param=0.75){\n data = data.from(well)\n growth = data[,2]\n Time = data[,1]\n \n # predicted growth values to be used in estimating growth curve parameters\n loess.fit = loess(growth~Time,span=smooth.param)\n t = seq(from = min(Time), to = max(Time), by = (max(Time)-min(Time))/1000)\n y = predict(loess.fit, data.frame(Time=t))\n attr(y,\"names\") = NULL # need to remove the names to prevent them from showing up in the returned vector\n \n # Remove any data points where y has not been estimated\n filt = is.finite(y)\n t = t[filt]\n y = y[filt] # remove any NA etc\n \n # specific growth using loess to find max derivative\n delta.t = diff(t)\n dydt = diff(y)/delta.t\n u = max(dydt)\n \n # lower and upper asymptotes\n b = min(y)\n A = max(y) - min(y)\n \n # inflection point\n inflection.pt.index = which.max(dydt)\n inflection.time = t[inflection.pt.index]\n inflection.y = y[inflection.pt.index]\n \n # lag time\n lam = inflection.time - (inflection.y-b)/u\n \n # Return named array of estimates\n c(A = A, b = b, lam = lam, u = u)\n}\n\n\n", - "created" : 1423869204555.000, - "dirty" : false, - "encoding" : "UTF-8", - "folds" : "", - "hash" : "3423035371", - "id" : "EE21755B", - "lastKnownWriteTime" : 1423869219, - "path" : "~/Documents/GCAT4_old/trunk/R/GCAT/R/class.model.R", - "project_path" : "class.model.R", - "properties" : { - }, - "source_on_save" : false, - "type" : "r_source" -} \ No newline at end of file diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/2ACDF6EF b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/2ACDF6EF deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/2ACDF6EF +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/59ABD774 b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/59ABD774 deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/59ABD774 +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/5C623936 b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/5C623936 deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/5C623936 +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/6E6918EE b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/6E6918EE deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/6E6918EE +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/9402820B b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/9402820B deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/9402820B +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/EFF3E540 b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/EFF3E540 deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/EFF3E540 +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/F3CF638E b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/F3CF638E deleted file mode 100644 index 7a73a41..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/F3CF638E +++ /dev/null @@ -1,2 +0,0 @@ -{ -} \ No newline at end of file diff --git a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/INDEX b/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/INDEX deleted file mode 100644 index d642c05..0000000 --- a/R/GCAT/R/.Rproj.user/7CB73FCA/sdb/prop/INDEX +++ /dev/null @@ -1,7 +0,0 @@ -~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2FGCAT.main.R="59ABD774" -~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Fclass.model.R="6E6918EE" -~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Ffit.model.R="5C623936" -~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Ffitted.calculations.R="2ACDF6EF" -~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Fnormalize.and.transform.R="F3CF638E" -~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Fplot.fit.R="EFF3E540" -~%2FDocuments%2FGCAT4_old%2Ftrunk%2FR%2FGCAT%2FR%2Ftable2well.R="9402820B" diff --git a/R/GCAT/R/GCAT.main.R b/R/GCAT/R/GCAT.main.R index c57e5d6..7c45ab9 100644 --- a/R/GCAT/R/GCAT.main.R +++ b/R/GCAT/R/GCAT.main.R @@ -1,6 +1,6 @@ #Copyright 2012 The Board of Regents of the University of Wisconsin System. #Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, -#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman +#Michael H. Whitney, Nathan DiPiazza, Minh Bui, Trey K. Sato and Yury V. Bukhman # #This file is part of GCAT. # @@ -17,13 +17,30 @@ #You should have received a copy of the GNU Lesser General Public License #along with GCAT. If not, see . -# GCAT version 5.00 -# Notes by Jason -# 08/18/2011 +######################################################################## +# # +# Package-level documentation and imports # +# # +######################################################################## +#' GCAT: Growth Curve Analysis Tool +#' +#' Mathematical modeling and parameter estimation of high volume microbial growth data. +#' +#' @details +#' GCAT input is in .csv format. GCAT analysis is accessed using \code{\link{gcat.analysis.main}} +#' +#' GCAT utilizes the \code{\link[stats]{nls}} function in the R stats package to fit logistic, Gompertz and Richards models to growth curve +#' data. Best model is selected automatically. Alternatively, the user may choose LOESS local regression fits, implemented using +#' \code{\link[stats]{loess}} function in the R stats package +#' +#' Internally, the data are stored in an array of \linkS4class{well} objects +#' +#' @import pheatmap gplots methods +#' @docType package +#' @name GCAT +NULL # Initialization - - PLATE.LETTERS = paste(rep(c("", LETTERS), each = 26), rep(LETTERS, 26), sep="") global.version.number = packageDescription(pkg="GCAT")$Version @@ -88,32 +105,46 @@ global.version.number = packageDescription(pkg="GCAT")$Version #' @param silent Shoulde messages be returned to the console? #' @param verbose Should sub-functions return messages to console? (when I say verbose, I mean it!) #' @param overview.jpgs Should GCAT enable an overview image? +#' @param return.fit Whether should a fit well object is returned or not. +#' @param lagRange The heatmap specific range for lag time. +#' @param totalRange The heatmap specific range for the achieved growth. +#' @param specRange The heatmap specific range for spec growth rate. +#' +#' @return Depending on return.fit setting, an array of fitted well objects or a list of output files #' -#' @return A list of the output files. +#' @export gcat.analysis.main = function(file.list, single.plate, layout.file = NULL, out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""), - add.constant = 0.1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05, + add.constant = 0, blank.value = NULL, start.index = 2, growth.cutoff = 0.05, use.linear.param = F, use.loess = F, smooth.param=0.1, + lagRange = NA, totalRange = NA, specRange = NA, points.to.remove = 0, remove.jumps = F, time.input = NA, plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0, multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"), layout.sheet.headers = c("Strain", "Media Definition"), silent = T, verbose = F, return.fit = F, overview.jpgs = T){ + + # Capture the starting environment for debugging + main.envir = c(as.list(environment())) - # MB: Prototyping system unwanted argument guarding. Proper function - # will be added in the future. - # Not the best solution. + # MB: Not the best solution. if (is.na(time.input)) { if (single.plate) time.input = 1/3600 else - exception("Error: ", "time.input is NA.") + exception("", "time.input is NA.") } - - if (add.constant < 0) - exception("Error: ", "The constant r should not be negative.") + + # MB: Now add.constant will always be 0. + # No need to check. + #if (add.constant < 0) + # exception("", "The constant r should not be negative.") # End prototyping temporary solution. + # YB: seem to need this to avoid spurious discarding of some wells in example multiplate dataset: Trac ticket 1780. + # however, this causes an error in Rails + if(length(points.to.remove)==0) points.to.remove = 0 + upload.timestamp = strftime(Sys.time(), format="%Y-%m-%d %H:%M:%S") # Get a timestamp for the time of upload. fitted.well.array.master = list() source.file.list = c() @@ -148,9 +179,10 @@ gcat.analysis.main = function(file.list, single.plate, layout.file = NULL, source.file.list = source.file.list, upload.timestamp = upload.timestamp, growth.cutoff = growth.cutoff, add.constant = add.constant, blank.value = blank.value, start.index = start.index, points.to.remove = points.to.remove, remove.jumps = remove.jumps, + lagRange = lagRange, specRange = specRange, totalRange = totalRange, out.dir = out.dir, graphic.dir = graphic.dir, overview.jpgs=overview.jpgs, use.linear.param=use.linear.param, use.loess=use.loess, plate.ncol = plate.ncol, plate.nrow = plate.nrow, - silent = silent), silent = T) + silent = silent, main.envir = main.envir), silent = T) # Return file list or error message otherwise return "successful analysis" message (?) @@ -209,7 +241,7 @@ gcat.analysis.main = function(file.list, single.plate, layout.file = NULL, #' @param input.skip.lines If specified, this number of lines shall be skipped from the top when reading the input file with read.csv #' @param multi.column.headers The headers of the column when analyzing multiple plates. #' @param single.column.headers The headers of the column when analyzing a single plate. -#' @param layour.sheet.headers The headers of the layout file. +#' @param layout.sheet.headers The headers of the layout file. #' @param growth.model What growth model should be used? #' @param backup.growth.model If the main growth model fails, the back up model will be used. #' @param silent Surpress all messages. @@ -246,7 +278,7 @@ gcat.fit.main = function(file.name, input.data = NULL, load.type = "csv", layout # "first": subtracts the first OD, assumed to be the blank, from all ODs # "none": does nothing, assumes no blank. highly recommend log(OD+1) transform in this case. # "average.first": forces all filled wells on each plate to match the average value at (after subtracting the first OD) - # add.constant - a numeric constant that will be added to each curve before the log transform (defaults to 1) + # add.constant - a numeric constant that will be added to each curve before the log transform (default is 0) # use.log - should a log transform be applied to the data after normalization? # points.to.remove - a list of numbers referring to troublesome points that should be removed across all wells. @@ -326,6 +358,7 @@ gcat.fit.main = function(file.name, input.data = NULL, load.type = "csv", layout # Return an error if there is a problem with normalization if (class(well.array) == "try-error") stop("Error in : ", well.array) + #well.array = try(subtract.blank(well.array, blank.value), silent = silent) # Transform ODs on the logarithmic scale, regardless of whether is true # an extra column of log-transformed values is added to the "well.array" slot of each well @@ -432,17 +465,26 @@ gcat.fit.main = function(file.name, input.data = NULL, load.type = "csv", layout #' @param overview.jpgs should jpgs be generated for each plate with the overview graphic? #' This is for backwards compatibility with the old web server. #' @param silent should messages be returned to the console? -#' @param unlog should exported graphics be transformed back to the OD scale? -#' @param constant.added (should be the same value as add.constant above) - -#' used to readjust for the constant added during the log transform when plotting ODs. +#' @param unlog should exported graphics be transformed back to the OD scale? +#' @param source.file.list A list of the source files' names. +#' @param upload.timestamp The time format indicated by the user. +#' @param add.constant used to readjust for the constant added during the log transform when plotting ODs. +#' @param use.linear.param linear parameter is used or not? +#' @param use.loess Is LOESS model going to be used? +#' @param plate.nrow The number of rows for a plate. +#' @param plate.ncol The number of columns for a plate +#' @param lagRange The heatmap specific range for lag time. +#' @param totalRange The heatmap specific range for the achieved growth. +#' @param specRange The heatmap specific range for spec growth rate. +#' @param main.envir starting environment of gcat.analysis.main(), captured as a list, printed out for debugging +#' #' @return A list of output files if success. - gcat.output.main = function(fitted.well.array, out.prefix = "", source.file.list, upload.timestamp = NULL, add.constant, blank.value, start.index, growth.cutoff, points.to.remove, remove.jumps, out.dir = getwd(), graphic.dir = paste(out.dir,"/pics",sep = ""), overview.jpgs = T, - use.linear.param=F, use.loess=F, plate.nrow = 8, plate.ncol = 12, - unlog = F, silent = T){ - + use.linear.param=F, use.loess=F, lagRange = NA, totalRange = NA, specRange = NA, + plate.nrow = 8, plate.ncol = 12, unlog = F, silent = T, main.envir){ + # Prepare timestamp for addition to output file names. filename.timestamp = strftime(upload.timestamp, format="_%Y-%m-%d_%H.%M.%S") @@ -510,7 +552,8 @@ gcat.output.main = function(fitted.well.array, out.prefix = "", source.file.list # Use function to write fit graphics to file. graphic.files = try(pdf.by.plate(fitted.well.array, out.prefix=out.prefix, upload.timestamp = upload.timestamp, - unlog=unlog,constant.added=add.constant,overview.jpgs=overview.jpgs, plate.ncol = plate.ncol, plate.nrow = plate.nrow),silent=silent) + unlog=unlog,constant.added=add.constant,overview.jpgs=overview.jpgs, lagRange = lagRange, specRange = specRange, totalRange = totalRange, + plate.ncol = plate.ncol, plate.nrow = plate.nrow),silent=silent) if (class(graphic.files) == "try-error") stop("Error in : ", graphic.files) @@ -550,7 +593,7 @@ gcat.output.main = function(fitted.well.array, out.prefix = "", source.file.list "\n# - an 'I' indicates that the well was inoculated and growth was detected above the threshold. ", "\n# - an 'E*' indicates that the well was empty and growth was detected (possible contamination). ", "\n# - an '!' indicates that the well was inoculated and no growth was detected. ", - "\n# - asymp.not.reached: shows “L” if the bottom asymptote (baseline) was not reached and “U” if the upper asymptote (plateau) was not reached.", + "\n# - asymp.not.reached: shows \"L\" if the bottom asymptote (baseline) was not reached and \"U\" if the upper asymptote (plateau) was not reached.", "\n# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index.", "\n# - other: Additional flag column. Displays information about whether jumps in OD were detected and what was done about them.", "\n# - pdf.file and page.no: location of the figure for this well in the output .pdf files." @@ -569,7 +612,14 @@ gcat.output.main = function(fitted.well.array, out.prefix = "", source.file.list "\n# - Index of inoculation timepoint", start.index, "\n# - Minimum growth threshold:", growth.cutoff, "\n# - Removed points:", paste(points.to.remove, collapse = " "), - "\n# - Jump detection:", remove.jumps) + "\n# - Jump detection:", remove.jumps + ) + + # gcat.analysis.main() starting environment + cat("\n#\n# -- gcat.analysis.main() starting environment --\n#") + print(main.envir) + + # Done with text file output sink() ######################################################################## diff --git a/R/GCAT/R/addingParams.R b/R/GCAT/R/addingParams.R deleted file mode 100644 index 375a877..0000000 --- a/R/GCAT/R/addingParams.R +++ /dev/null @@ -1,35 +0,0 @@ -setwd("~/Downloads/") -file.list = file.name = "YPDAFEXglucoseTests_2-25-10.csv" -layout.file = "YPDAFEXglucoseTests_2-25-10_Layout.csv" -single.plate = T -out.dir = getwd() -graphic.dir = paste(out.dir, "/pics", sep = "") -add.constant = 1 -blank.value = NULL -start.index = 2 -growth.cutoff = 0.05 -use.linear.param = F -use.loess = F -smooth.param = 0.6 -points.to.remove = 0 -remove.jumps = F -silent = F -verbose = T -return.fit = F -overview.jpgs = T -plate.nrow = 8 -plate.ncol = 12 -input.skip.lines = 0 -multi.column.headers = c("Plate ID", "Well", "OD", "Time") -single.column.headers = c("","A1") -layout.sheet.headers = c("Strain", "Media Definition") - -t = gcat.analysis.main(file.list, single.plate, layout.file = NULL, - out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""), - add.constant = 1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05, - use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=0.1, - points.to.remove = 0, remove.jumps = F, time.input = NA, - plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0, - multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"), - layout.sheet.headers = c("Strain", "Media Definition"), - silent = F, verbose = F, return.fit = F, overview.jpgs = T) diff --git a/R/GCAT/R/class.model.R b/R/GCAT/R/class.model.R index dad9a65..e69d112 100644 --- a/R/GCAT/R/class.model.R +++ b/R/GCAT/R/class.model.R @@ -22,6 +22,7 @@ # and other information for parameterized growth curve models. # # # ######################################################################## +# Class to represent growth curve model objects setClass("model", representation(name = "character", expression = "expression", formula = "formula", @@ -35,32 +36,26 @@ setClass("model", representation(name = "character", # -------------------------------------------------------------------- ###################### BEGIN PROTOTYPING ACCESSOR METHODS############## -# Minh: Let this code fragment be F1. -if (!isGeneric("getName")){ - if (is.function("getName")) - fun <- getName - else - fun <- function(object) standardGeneric("getName") - setGeneric("getName", fun) -} -# End of F1 -setMethod("getName", "model", function(object) object@name) +# Get an object's @@name slot +setGeneric("getName", function(object) standardGeneric("getName")) +setMethod("getName", "model", function(object){return(object@name)}) -# Minh: Let this line be F2. +# Get an object's @@expression slot setGeneric("getExpression", function(object){standardGeneric("getExpression")}) -# Question: How is F1 different from F2? setMethod("getExpression", "model", function(object){ return(object@expression) }) +# Get an object's @@formula slot setGeneric("getFormula", function(object){standeardGeneric("getFormula")}) setMethod("getFormula", "model", function(object){ return(object@formula) }) +# Get an object's @@guess slot setGeneric("getGuess", function(object){standeardGeneric("getGuess")}) setMethod("getGuess", "model", function(object){ @@ -81,6 +76,7 @@ model = function(name, expression, formula, guess){ new("model", name = name, expression = expression, formula = formula, guess = guess) } +# Initial guess of growth curve parameters using a loess model loess.g = function(well,smooth.param=0.75){ #data = data.from(well) #growth = data[,2] diff --git a/R/GCAT/R/class.well.R b/R/GCAT/R/class.well.R index b774845..436315b 100644 --- a/R/GCAT/R/class.well.R +++ b/R/GCAT/R/class.well.R @@ -32,6 +32,29 @@ Sys.setlocale(locale="C") # Treat nls and loess as S4 classes to avoid warnings setOldClass("nls") setOldClass("loess") + +#' Class that contains well data +#' +#' @slot position - 3-member vector containing identifying information for the well: row (letters), column (numbers) and plate ID. +#' @slot well.info - a list containing strain and media names if provided +#' @slot screen.data - a data frame with Time and raw OD values. This is the only slot that is filled upon creation of a well object. +#' as different functions are run on the well the data frame gets filled with additional columns. +#' @slot start.index - integer index of the time point where growth curve starts, e.g. of the inoculation time point +#' @slot use.log - a single logical value denoting whether to return log-transformed values when data is requested from the well +#' @slot norm - a value to subtract from all OD values before returning data. filled by (see normalize.and.transform.R) +#' @slot curve.par - a list of parameters that denote whether the well is empty, whether it contains ODs indicating a viable culture, whether it tanks at a certain timepoint. +#' @slot fit.par - will be a list containing the fitted model parameters +#' @slot fit.std.err - will be a list containing the standard errors for the fitted model parameters +#' @slot equation - will contain an expression for evaluating the successfully fitted model +#' @slot model.name - will contain the name of the successfully fit model +#' @slot fit.info - a message with info about whether the fit was successful, failed, or skipped. +#' @slot add.info - a message with info about whether jumps in OD were detected or removed, or if ODs were detected below the blank OD. +#' @slot inflection.time - the Time value at the point where the specific growth is located. no longer a formula param NWD +#' @slot rss - residual sum of squares +#' @slot loess - object returned by running loess on the normalized well data +#' @slot nls - object returned by running nls on the normalized well data +#' +#' @export setClass("well", representation(position = "character", well.info = "list", screen.data = "data.frame", @@ -50,132 +73,170 @@ setClass("well", representation(position = "character", loess = "loess", nls = "nls")) -# Slots: -# position - 3-member vector containing identifying information for the well: row (letters), column (numbers) and plate ID. -# well.info - a list containing strain and media names if provided -# screen.data - a data frame with Time and raw OD values. This is the only slot that is filled upon creation of a well object. -# as different functions are run on the well the data frame gets filled with additional columns. -# use.log - a single logical value denoting whether to return log-transformed values when data is requested from the well -# norm - a value to subtract from all OD values before returning data. filled by (see normalize.and.transform.R) -# curve.par - a list of parameters that denote whether the well is empty, whether it contains ODs indicating a viable culture, whether it tanks at a certain timepoint. - -# if model fitting using is successful: -# fit.par - will be a list containing the fitted model parameters -# fit.std.err - will be a list containing the standard errors for the fitted model parameters -# equation - will contain an expression for evaluating the successfully fitted model -# model.name - will contain the name of the successfully fit model - -# fit.info - a message with info about whether the fit was successful, failed, or skipped. -# add.info - a message with info about whether jumps in OD were detected or removed, or if ODs were detected below the blank OD. -# inflection.time - the Time value at the point where the specific growth is located. no longer a formula param NWD -# rss - residual sum of squares -# loess - object returned by running loess on the normalized well data -# nls - object returned by running nls on the normalized well data - -setGeneric("getPosition", function(object){standeardGeneric("getPosition")}) +#' Accessors for the well class +#' +#' @param object object of class \linkS4class{well} +#' @name well-accessors +NULL + +#' @rdname well-accessors +setGeneric("getPosition", function(object){standardGeneric("getPosition")}) +#' @export +#' @rdname well-accessors setMethod("getPosition", "well", function(object){ return(object@position) }) -setGeneric("getWellInfo", function(object){standeardGeneric("getWellInfo")}) +#' @rdname well-accessors +setGeneric("getWellInfo", function(object){standardGeneric("getWellInfo")}) +#' @export +#' @rdname well-accessors setMethod("getWellInfo", "well", function(object){ return(object@well.info) }) -setGeneric("getScreenData", function(object){standeardGeneric("getScreenData")}) +#' @rdname well-accessors +setGeneric("getScreenData", function(object){standardGeneric("getScreenData")}) +#' @export +#' @rdname well-accessors setMethod("getScreenData", "well", function(object){ return(object@screen.data) }) -setGeneric("getStartIndex", function(object){standeardGeneric("getStartIndex")}) +#' @rdname well-accessors +setGeneric("getStartIndex", function(object){standardGeneric("getStartIndex")}) +#' @export +#' @rdname well-accessors setMethod("getStartIndex", "well", function(object){ return(object@start.index) }) -setGeneric("getUseLog", function(object){standeardGeneric("getUseLog")}) +#' @rdname well-accessors +setGeneric("getUseLog", function(object){standardGeneric("getUseLog")}) +#' @export +#' @rdname well-accessors setMethod("getUseLog", "well", function(object){ return(object@use.log) }) -setGeneric("getNorm", function(object){standeardGeneric("getNorm")}) +#' @rdname well-accessors +setGeneric("getNorm", function(object){standardGeneric("getNorm")}) +#' @export +#' @rdname well-accessors setMethod("getNorm", "well", function(object){ return(object@norm) }) -setGeneric("getCurPar", function(object){standeardGeneric("getCurPar")}) +#' @rdname well-accessors +setGeneric("getCurPar", function(object){standardGeneric("getCurPar")}) +#' @export +#' @rdname well-accessors setMethod("getCurPar", "well", function(object){ return(object@curve.par) }) -setGeneric("getFitErr", function(object){standeardGeneric("getFitErr")}) +#' @rdname well-accessors +setGeneric("getFitErr", function(object){standardGeneric("getFitErr")}) +#' @export +#' @rdname well-accessors setMethod("getFitErr", "well", function(object){ return(object@fit.std.err) }) -setGeneric("getEquation", function(object){standeardGeneric("getEquation")}) +#' @rdname well-accessors +setGeneric("getEquation", function(object){standardGeneric("getEquation")}) +#' @export +#' @rdname well-accessors setMethod("getEquation", "well", function(object){ return(object@equation) }) -setGeneric("getModelName", function(object){standeardGeneric("getModelName")}) +#' @rdname well-accessors +setGeneric("getModelName", function(object){standardGeneric("getModelName")}) +#' @export +#' @rdname well-accessors setMethod("getModelName", "well", function(object){ return(object@model.name) }) -setGeneric("getFitInfo", function(object){standeardGeneric("getFitInfo")}) +#' @rdname well-accessors +setGeneric("getFitInfo", function(object){standardGeneric("getFitInfo")}) +#' @export +#' @rdname well-accessors setMethod("getFitInfo", "well", function(object){ return(object@fit.info) }) -setGeneric("getAddInfo", function(object){standeardGeneric("getAddInfo")}) +#' @rdname well-accessors +setGeneric("getAddInfo", function(object){standardGeneric("getAddInfo")}) +#' @export +#' @rdname well-accessors setMethod("getAddInfo", "well", function(object){ return(object@add.info) }) -setGeneric("getInflectionTime", function(object){standeardGeneric("getInflectionTime")}) +#' @rdname well-accessors +setGeneric("getInflectionTime", function(object){standardGeneric("getInflectionTime")}) +#' @export +#' @rdname well-accessors setMethod("getInflectionTime", "well", function(object){ return(object@inflection.time) }) -setGeneric("getRSS", function(object){standeardGeneric("getRSS")}) +#' @rdname well-accessors +setGeneric("getRSS", function(object){standardGeneric("getRSS")}) +#' @export +#' @rdname well-accessors setMethod("getRSS", "well", function(object){ return(object@rss) }) -setGeneric("getLoess", function(object){standeardGeneric("getLoess")}) +#' @rdname well-accessors +setGeneric("getLoess", function(object){standardGeneric("getLoess")}) +#' @export +#' @rdname well-accessors setMethod("getLoess", "well", function(object){ return(object@loess) }) -setGeneric("getnls", function(object){standeardGeneric("getnls")}) +#' @rdname well-accessors +setGeneric("getnls", function(object){standardGeneric("getnls")}) +#' @export +#' @rdname well-accessors setMethod("getnls", "well", function(object){ return(object@nls) }) -setGeneric("getFitPar", function(object){standeardGeneric("getFitPar")}) +#' @rdname well-accessors +setGeneric("getFitPar", function(object){standardGeneric("getFitPar")}) +#' @export +#' @rdname well-accessors setMethod("getFitPar", "well", function(object){ return(object@fit.par) }) # -------------------------------------------------------------------- +# Function to create a new well +# # Function to create a new well (requires only Time and OD vectors, which will fill slot "screen.data") +# @details # slots "nls" and "loess" are initialized to empty lists well = function(Time = NULL, OD = NULL){ x = list() @@ -187,6 +248,7 @@ well = function(Time = NULL, OD = NULL){ # ----------------------------------------------------------------------- #### A show method for well #### +# A show method for well setMethod("show", "well", function(object) { print("Object of class well") @@ -229,20 +291,21 @@ setMethod("show", "well", ) #### A plot method for well #### -# x - object of class well -# y - not used -# constant.added - used to readjust for the constant added during the log transform: log.OD = log(OD - blank + constant.added) -# xlim - x axis limits, vector of length 2 -# ylim - y axis limits, vector of length 2 -# scale - determines the font scale for the entire graph. all cex values are calculated from this -# number.points - should points be labeled with numeric indices? -# draw.symbols - should be called on the well and markings drawn on the graph? -# show.text - show R^2 and growth curve parameters as text on the plot -# show.calc - draw lines that illustrate growth curve parameters -# draw.guess - initial guess model. Drawn if specified -# well.number - the number of the well in an array of wells -# ... - additional arguments passed to the generic plot function - +#' A plot method for well +#' @param x object of class well +#' @param y not used +#' @param constant.added used to readjust for the constant added during the log transform: log.OD = log(OD - blank + constant.added) +#' @param xlim x axis limits, vector of length 2 +#' @param ylim y axis limits, vector of length 2 +#' @param scale determines the font scale for the entire graph. all cex values are calculated from this +#' @param number.points should points be labeled with numeric indices? +#' @param draw.symbols should be called on the well and markings drawn on the graph? +#' @param show.text show R^2 and growth curve parameters as text on the plot +#' @param show.calc draw lines that illustrate growth curve parameters +#' @param draw.guess initial guess model. Drawn if specified +#' @param well.number the number of the well in an array of wells +#' @param ... additional arguments passed to the generic plot function +#' setMethod("plot", signature(x = "well", y="missing"), function (x, y, constant.added = 1.0, xlim = NULL, ylim = NULL, @@ -271,11 +334,11 @@ setMethod("plot", if (!is.null(well.number)) main = paste("[", well.number , "] ", main, sep="") # Draw the data and symbols if is true. - plot.data(x, main = main, scale = scale, constant.added=constant.added, + plot_data(x, main = main, scale = scale, constant.added=constant.added, number.points = number.points, draw.symbols = draw.symbols, xlim = xlim, ylim = ylim, ...) # Draw the fitted model. - plot.model(x, scale = scale, constant.added=constant.added) + plot_model(x, scale = scale, constant.added=constant.added) # Draw text info if specified. if(show.text) @@ -302,9 +365,12 @@ setMethod("plot", # Since many of these need to be applied to all wells over an array, while conserving the dimensions of # that array, this file includes a wrapper function (see bottom of file). +# Get plate name plate.name = function(well) getPosition(well)[1] +# Return the full alphanumeric well name +# # Return the full alphanumeric well name (with leading zeros if applicable) well.name = function(well){ row = getPosition(well)[2] @@ -352,14 +418,22 @@ raw.data = function(well) contains.fit = function(well) length(getFitPar(well)) > 0 +#' Get the number of data points in a well +#' +#' @param x object of class \code{well} setMethod("length", signature(x = "well"), function(x) length(x@screen.data[,1])) +# Get well data +# +# @details # The function has some options: by default it returns a two-column data frame with time and OD -# (or log OD if the slot is true in the object), after normalization to the value specified in slot. -# - With set to true the rows specified in the column of the slot are not returned. -# - With set to true all the rows after the index are removed. -# - Setting to true overrides all these settings and just returns 2 columns with Time and Raw OD. - +# (or log OD if the slot is true in the object), after normalization to the value specified in slot. +# \itemize{ +# \item{With set to true the rows specified in the column of the slot are not returned.} +# \item{With set to true all the rows after the index are removed.} +# \item{Setting to true overrides all these settings and just returns 2 columns with Time and Raw OD.} +# } +# data.from = function(well, remove = T, remove.tanking = T, raw.data = F, na.rm = F){ if (length(getUseLog(well)) == 0) @@ -400,10 +474,10 @@ data.from = function(well, remove = T, remove.tanking = T, raw.data = F, na.rm = output } - -# Functions much like but gives a single vector containing the +# Compute growth curve slopes +# @details +# Functions much like \code{\link{data.from}} but gives a single vector containing the # slope at each point. Has a parameter allowing removal of NA values. - slopes = function(well, remove = T, remove.tanking = T, na.rm = F){ if(remove.tanking & is.numeric(tanking.start(well))) @@ -423,9 +497,11 @@ slopes = function(well, remove = T, remove.tanking = T, na.rm = F){ # Well array functions: these must be used on entire arrays of well objects # instead of single ones. +# Get plate names plate.names = function(well.array) dimnames(well.array)[[3]] +# Get tanking start values tanking.start.values = function(well.array, array = F){ if (array) aapply(well.array, function(well) tanking.start(well)) diff --git a/R/GCAT/R/fit.model.R b/R/GCAT/R/fit.model.R index fd3ff70..32ec8dc 100644 --- a/R/GCAT/R/fit.model.R +++ b/R/GCAT/R/fit.model.R @@ -39,9 +39,9 @@ #' @param backup.growth.model If \code{gowth.mode} fails, this model will be used. #' @param fit.if.no.growth should the function attempt to fit a well even if there was no growth detected? default is F #' @param silent output back to R console? -#' @param use.linear.param: Should an additional linear parameter (c) be used when fitting the data to the model? -#' @param use.loess: Should Local Polynomial Regression Fitting (loess function) be used instead of nls? -#' @param smooth.param: If loess is used, an optional smoothing parameter. Default is .6 +#' @param use.linear.param Should an additional linear parameter (c) be used when fitting the data to the model? +#' @param use.loess Should Local Polynomial Regression Fitting (loess function) be used instead of nls? +#' @param smooth.param If loess is used, an optional smoothing parameter. Default is .6 fit.model = function(input.well, growth.model, backup.growth.model = NULL, fit.if.no.growth = F, use.linear.param=F, use.loess=F, smooth.param, silent = T){ @@ -138,11 +138,11 @@ fit.model = function(input.well, growth.model, backup.growth.model = NULL, fit.i if(use.loess){ number.of.points = nrow(input.well@screen.data) if (smooth.param <= 1/number.of.points) - exception("Invalid input", "Smoothing parameter is out of range.") + exception("", "Invalid input: Smoothing parameter is out of range.") fit = try(loess(y~Time, data=input.data, span=smooth.param), silent=TRUE) input.well@loess = fit - if (class(fit) != "loess") stop("loess fit failed on well", paste(input.well@position,collapse=" ")) + if (class(fit) != "loess") stop("Loess fit failed on well", paste(input.well@position,collapse=" ")) input.well@fit.info = "Loess model fit successfully." input.well@model.name = loess.model@name input.well@equation = loess.model@expression @@ -224,10 +224,10 @@ fit.model = function(input.well, growth.model, backup.growth.model = NULL, fit.i return(input.well) } -# Fit nls model to a well using a specified model -# Arguments: -# input.well: object of class well -# model: object of class model, e.g. richards, gompertz or logistic +#' Fit nls model to a well using a specified model +#' +#' @param input.well object of class well +#' @param model object of class model, e.g. richards, gompertz or logistic fit.nls.model <- function (input.well, model) { # Get OD vs. time data from well input.data = data.from(input.well, na.rm = T) diff --git a/R/GCAT/R/fitted.calculations.R b/R/GCAT/R/fitted.calculations.R index 590798e..574d9be 100644 --- a/R/GCAT/R/fitted.calculations.R +++ b/R/GCAT/R/fitted.calculations.R @@ -1,381 +1,342 @@ -#Copyright 2012 The Board of Regents of the University of Wisconsin System. -#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, -#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman -# -#This file is part of GCAT. -# -#GCAT is free software: you can redistribute it and/or modify -#it under the terms of the GNU Lesser General Public License as published by -#the Free Software Foundation, either version 3 of the License, or -#(at your option) any later version. -# -#GCAT is distributed in the hope that it will be useful, -#but WITHOUT ANY WARRANTY; without even the implied warranty of -#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -#GNU Lesser General Public License for more details. -# -#You should have received a copy of the GNU Lesser General Public License -#along with GCAT. If not, see . - -######################################################################## -# # -# Functions to calculate various things about wells based on fit model # -# # -######################################################################## - -# S3 generic -lag <- function(fitted.well, ...) -{ - UseMethod("lag") -} - -# -# Common arguments: -# fitted.well - should be a well containing the results of , most functions will return NA if well has not been fit yet. -# unlog - should the value be returned on the linear scale as opposed to the log-transformed scale? -# constant.added - for returning values on the linear scale, what was the constant added before the log transform? -# digits - passed to the function, default is no rounding (infinity digits) - -unlog = function(x, constant.added) { - ######################################################################## - # Transform values back to OD scale # - ######################################################################## -exp(x) - constant.added -} - -well.eval = function(fitted.well, Time = NULL){ - ######################################################################## - # Evaluate estimated OD at any timepoints using the fitted model # - ######################################################################## - - # If no timepoints are provided, use the ones collected in the experiment itself. - if(!is.numeric(Time)) - Time = data.from(fitted.well)$Time - - # Use of equation is deprecated. Use nls and loess models stored in the well object instead - # Attempt to use with the fitted equation and parameters to get estimates for OD at the given timepoints. - #output = try(eval(fitted.well@equation, fitted.well@fit.par), silent = T) - - # Predict log.OD value(s) using nls model if present. If no nls model, try using loess. - if (length(fitted.well@nls)>0) { - output = try(predict(fitted.well@nls,list(Time=Time)),silent=T) - } else if (length(fitted.well@loess)>0) { - output = try(predict(fitted.well@loess,Time),silent=T) - } else { - output = NA - } - - # Return values. If OD evaluation failed for any reason, return NULL. - if (is.numeric(output)){ - return(output) - } else { - return(NULL) - } -} - -model.residuals = function(fitted.well, unlog = F){ - ######################################################################## - # Evaluate model residuals using the measured vs. fitted log.OD values # - ######################################################################## - measured.OD = data.from(fitted.well)[,2] - - # Use with no Time argument to get fitted OD values at measured timepoints. - predicted.OD = well.eval(fitted.well) - - # If all values are valid, return the differences - if (!is.numeric(predicted.OD)) - return(NA) - else - return(measured.OD - predicted.OD) - } - -dev.from.mean = function(fitted.well){ - ######################################################################## - # Evaluate deviations of log.OD values from the mean # - ######################################################################## - measured.ODs = data.from(fitted.well,remove=T,na.rm=T)[,2] - - # Get the mean values of these measured ODs. - mean.ODs = mean(measured.ODs) - - if (!is.numeric(mean.ODs)) - return (NA) - else - return (measured.ODs - mean.ODs) -} - -rss = function(fitted.well){ - ####################################################################### - # Get the residual sum of square. # - ####################################################################### - if (length(fitted.well@rss) == 0) - return (NA) - else - return (fitted.well@rss) -} - -model.good.fit = function(fitted.well, digits = Inf){ - ######################################################################## - # Calculate a metric for fit accuracy using squared residuals # - ######################################################################## - - # Sum of squared residuals - RSS = rss(fitted.well) - - # Total sum of squared - tot = sum(dev.from.mean(fitted.well)^2) - - # Coefficient of determination - return (1 - RSS/tot) - } - -parameter.text = function(fitted.well){ - ######################################################################## - # Output a string with values of fitted parameters # - ######################################################################## - - # Get a list of fitted parameters - fit.par = fitted.well@fit.par - - # Giving the parameter text descriptive names. - if (length(fitted.well@fit.par) != 0){ - names(fit.par)[1] = "A" - names(fit.par)[2] = "b" - names(fit.par)[3] = "lambda" - names(fit.par)[4] = "max.spec.growth.rate" - - if (fitted.well@model.name == "richards sigmoid"){ - names(fit.par)[5] = "shape.par" - } - - if (fitted.well@model.name == "richards sigmoid with linear par."){ - names(fit.par)[5] = "shape.param" - names(fit.par)[6] = "linear term" - } - - if (fitted.well@model.name == "logistic sigmoid with linear par.") - names(fit.par)[5] = "linear.term" - - # if loess, just show smoothing param - if(fitted.well@model.name == "local polynomial regression fit.") - fit.par = fitted.well@fit.par["smoothing parameter"] - } - - # Return nothing if the list is empty. Otherwise, concatenate the terms in the list with the parameter names. - if(!is.list(fit.par)) - return() - else{ - output = "" - i = 1 - while(i <= length(fit.par)){ - output = paste(output, names(fit.par)[i], "=", round(as.numeric(fit.par[i]),3), "; ", sep = "") - i = i + 1 - if (i %% 6 == 0) - output = paste(output, "\n") - } - output - } - } - -max.spec.growth.rate = function(fitted.well, digits = Inf, ...){ - ######################################################################## - # Calculate maximum specific growth rate # - ######################################################################## - if(length(fitted.well@fit.par) == 0) - return(NA) - - round(fitted.well@fit.par$u,digits) -} - - -plateau = function(fitted.well, digits = Inf){ - ######################################################################## - # Calculate plateau log.OD from fitted parameters # - ######################################################################## - if(length(fitted.well@fit.par) == 0) - return(NA) - - plat = fitted.well@fit.par$A + fitted.well@fit.par$b - - if (!is.numeric(plat)) { - plat = NA - } else { - plat = round(plat, digits) - } - return(plat) -} - -baseline = function(fitted.well, digits = Inf){ - ######################################################################## - # Calculate baseline log.OD from fitted parameters # - ######################################################################## - if(length(fitted.well@fit.par) == 0) - return(NA) - - base = fitted.well@fit.par$b - - # If A (plateau OD) is invalid, return NA. - if (!is.numeric(fitted.well@fit.par$A)) - base = NA - # If b (baseline OD) is invalid but plateau OD was valid, return zero. - else if (!is.numeric(base)) - base = 0 - else{ - base = round(base, digits) - } - return(base) - } - -inoc.log.OD = function(fitted.well, digits = Inf){ - ######################################################################## - # Calculate log.OD at inoculation from fitted parameters # - ######################################################################## - - # Evaluated the fitted model at the inoculation timepoint (should be zero from using from table2wells.R) - if (is.null(well.eval(fitted.well))) - return(NA) - else{ - inoc.time = fitted.well@screen.data$Time[fitted.well@start.index] - inoc.log.OD = well.eval(fitted.well, inoc.time) - if (is.na(inoc.log.OD)) inoc.log.OD = fitted.well@fit.par$b # need this in a special case: loess fits with start.index = 1 - return(round(inoc.log.OD, digits)) - } - } - -max.log.OD = function(fitted.well, digits = Inf, ...){ - ######################################################################## - # Calculate max log.OD from model fit # - ######################################################################## - - # Evaluated the fitted model at the final timepoint (just the last valid timepoint in the experiment) - if (is.null(well.eval(fitted.well))) - return(NA) - else{ - return(round(max(well.eval(fitted.well),na.rm=T), digits)) - } -} - - -projected.growth = function(fitted.well,digits=Inf) { - ######################################################################## - # Calculate projected growth: plateau minus the inoculated log.OD # - ######################################################################## - plateau(fitted.well,digits) - inoc.log.OD(fitted.well,digits) -} - -projected.growth.OD = function(fitted.well,constant.added,digits=Inf) { - ######################################################################## - # Calculate projected growth: plateau minus the inoculated log.OD # - ######################################################################## - value = unlog(plateau(fitted.well),constant.added) - unlog(inoc.log.OD(fitted.well),constant.added) - round(value,digits) -} - - -achieved.growth = function(fitted.well,digits=Inf) { - ######################################################################## - # Calculate achieved growth: max.log.OD minus the inoculated log.OD # - ######################################################################## - max.log.OD(fitted.well,digits) - inoc.log.OD(fitted.well,digits) -} - -achieved.growth.OD = function(fitted.well,constant.added,digits=Inf) { - ######################################################################## - # Calculate projected growth: plateau minus the inoculated log.OD # - ######################################################################## - value = unlog(max.log.OD(fitted.well),constant.added) - unlog(inoc.log.OD(fitted.well),constant.added) - round(value,digits) -} - -reach.plateau = function(fitted.well, cutoff = 0.75){ - ######################################################################## - # Did the curve come close to the plateau OD during the experiment? # - ######################################################################## - - plat = plateau(fitted.well) - inoc = inoc.log.OD(fitted.well) - final = max.log.OD(fitted.well) - - if (!is.na(final)){ - # If the plateau is the same as the OD at inoculation, return TRUE - if ((plat - inoc) == 0) - return(T) - # If the difference between the final OD and inoculation OD is at least a certain proportion - # of the difference between the plateau and inoculated ODs, return TRUE. - else - return((final - inoc) / (plat - inoc) > cutoff) - } - else - return(T) - # If no final OD was calculated (if curve was not fit properly) just return T. - } - - -lag.time = function(fitted.well, digits = Inf, ...){ - ######################################################################## - # Calculate the lag time from the fitted OD # - ######################################################################## - if(length(fitted.well@fit.par) == 0) - return(NA) - - fitted.well@fit.par$lam -} - -# new params for GCAT 4.0 - -amplitude = function(fitted.well){ - if(length(fitted.well@fit.par) == 0) - return(NA) - - return(fitted.well@fit.par$A) -} - -shape.par = function(fitted.well){ - if(length(fitted.well@fit.par) == 0) - return(NA) - ifelse(is.null(fitted.well@fit.par$v), NA, fitted.well@fit.par$v) -} - -max.spec.growth.rate.SE = function(fitted.well, ...){ - if(length(fitted.well@fit.std.err) == 0) - return(NA) - ifelse(is.null(fitted.well@fit.std.err$u), NA, fitted.well@fit.std.err$u) -} - -lag.time.SE = function(fitted.well, ...){ - if(length(fitted.well@fit.std.err) == 0) - return(NA) - ifelse(is.null(fitted.well@fit.std.err$lam), NA, fitted.well@fit.std.err$lam) -} - -shape.par.SE = function(fitted.well){ - if(length(fitted.well@fit.std.err) == 0) - return(NA) - ifelse(is.null(fitted.well@fit.std.err$v), NA, fitted.well@fit.std.err$v) -} - -amplitude.SE = function(fitted.well){ - if(length(fitted.well@fit.std.err) == 0) - return(NA) - ifelse(is.null(fitted.well@fit.std.err$A), NA, fitted.well@fit.std.err$A) -} - -baseline.SE = function(fitted.well){ - if(length(fitted.well@fit.std.err) == 0) - return(NA) - ifelse(is.null(fitted.well@fit.std.err$b), NA, fitted.well@fit.std.err$b) -} - -# used to calulate the inflection.time value -inflection.time = function(well){ - if (length(well@loess) == 0 && length(well@nls) == 0) return(NA) # can' compute inflection time in the absence of a fit - data = data.from(well) - Time = data[,1] - t = seq(from = min(Time), to = max(Time), by = (max(Time)-min(Time))/1000) - y = well.eval(well,t) - if (is.null(y)) return(NA) - delta.t = diff(t) - dydt = diff(y)/delta.t - infl.index = which.max(dydt) - t[infl.index] -} +#Copyright 2012 The Board of Regents of the University of Wisconsin System. +#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, +#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman +# +#This file is part of GCAT. +# +#GCAT is free software: you can redistribute it and/or modify +#it under the terms of the GNU Lesser General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#GCAT is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU Lesser General Public License for more details. +# +#You should have received a copy of the GNU Lesser General Public License +#along with GCAT. If not, see . + +######################################################################## +# # +# Functions to calculate various things about wells based on fit model # +# # +######################################################################## + +# S3 generic for lag +lag <- function(fitted.well, ...) +{ + UseMethod("lag") +} + +# +# Common arguments: +# fitted.well - should be a well containing the results of , most functions will return NA if well has not been fit yet. +# unlog - should the value be returned on the linear scale as opposed to the log-transformed scale? +# constant.added - for returning values on the linear scale, what was the constant added before the log transform? +# digits - passed to the function, default is no rounding (infinity digits) + +# Transform values back to OD scale +unlog = function(x, constant.added) { + exp(x) - constant.added +} + +# Evaluate estimated OD at any timepoints using the fitted model +well.eval = function(fitted.well, Time = NULL){ + # If no timepoints are provided, use the ones collected in the experiment itself. + if(!is.numeric(Time)) + Time = data.from(fitted.well)$Time + + # Use of equation is deprecated. Use nls and loess models stored in the well object instead + # Attempt to use with the fitted equation and parameters to get estimates for OD at the given timepoints. + #output = try(eval(fitted.well@equation, fitted.well@fit.par), silent = T) + + # Predict log.OD value(s) using nls model if present. If no nls model, try using loess. + if (length(fitted.well@nls)>0) { + output = try(predict(fitted.well@nls,list(Time=Time)),silent=T) + } else if (length(fitted.well@loess)>0) { + output = try(predict(fitted.well@loess,Time),silent=T) + } else { + output = NA + } + + # Return values. If OD evaluation failed for any reason, return NULL. + if (is.numeric(output)){ + return(output) + } else { + return(NULL) + } +} + +# Evaluate model residuals using the measured vs. fitted log.OD values +model.residuals = function(fitted.well, unlog = F){ + measured.OD = data.from(fitted.well)[,2] + + # Use with no Time argument to get fitted OD values at measured timepoints. + predicted.OD = well.eval(fitted.well) + + # If all values are valid, return the differences + if (!is.numeric(predicted.OD)) + return(NA) + else + return(measured.OD - predicted.OD) + } + +# Evaluate deviations of log.OD values from the mean +dev.from.mean = function(fitted.well){ + measured.ODs = data.from(fitted.well,remove=T,na.rm=T)[,2] + + # Get the mean values of these measured ODs. + mean.ODs = mean(measured.ODs) + + if (!is.numeric(mean.ODs)) + return (NA) + else + return (measured.ODs - mean.ODs) +} + +# Get the residual sum of square. +rss = function(fitted.well){ + if (length(fitted.well@rss) == 0) + return (NA) + else + return (fitted.well@rss) +} + +# Calculate a metric for fit accuracy using squared residuals +model.good.fit = function(fitted.well, digits = Inf){ + # Sum of squared residuals + RSS = rss(fitted.well) + + # Total sum of squared + tot = sum(dev.from.mean(fitted.well)^2) + + # Coefficient of determination + return (1 - RSS/tot) + } + +# Output a string with values of fitted parameters +parameter.text = function(fitted.well){ + # Get a list of fitted parameters + fit.par = fitted.well@fit.par + + # Giving the parameter text descriptive names. + if (length(fitted.well@fit.par) != 0){ + names(fit.par)[1] = "A" + names(fit.par)[2] = "b" + names(fit.par)[3] = "lambda" + names(fit.par)[4] = "max.spec.growth.rate" + + if (fitted.well@model.name == "richards sigmoid"){ + names(fit.par)[5] = "shape.par" + } + + if (fitted.well@model.name == "richards sigmoid with linear par."){ + names(fit.par)[5] = "shape.param" + names(fit.par)[6] = "linear term" + } + + if (fitted.well@model.name == "logistic sigmoid with linear par.") + names(fit.par)[5] = "linear.term" + + # if loess, just show smoothing param + if(fitted.well@model.name == "local polynomial regression fit.") + fit.par = fitted.well@fit.par["smoothing parameter"] + } + + # Return nothing if the list is empty. Otherwise, concatenate the terms in the list with the parameter names. + if(!is.list(fit.par)) + return() + else{ + output = "" + i = 1 + while(i <= length(fit.par)){ + output = paste(output, names(fit.par)[i], "=", round(as.numeric(fit.par[i]),3), "; ", sep = "") + i = i + 1 + if (i %% 6 == 0) + output = paste(output, "\n") + } + output + } + } + +# Calculate maximum specific growth rate +max.spec.growth.rate = function(fitted.well, digits = Inf, ...){ + if(length(fitted.well@fit.par) == 0) + return(NA) + + round(fitted.well@fit.par$u,digits) +} + +# Calculate plateau log.OD from fitted parameters +plateau = function(fitted.well, digits = Inf){ + if(length(fitted.well@fit.par) == 0) + return(NA) + + plat = fitted.well@fit.par$A + fitted.well@fit.par$b + + if (!is.numeric(plat)) { + plat = NA + } else { + plat = round(plat, digits) + } + return(plat) +} + +# Calculate baseline log.OD from fitted parameters +baseline = function(fitted.well, digits = Inf){ + if(length(fitted.well@fit.par) == 0) + return(NA) + + base = fitted.well@fit.par$b + + # If A (plateau OD) is invalid, return NA. + if (!is.numeric(fitted.well@fit.par$A)) + base = NA + # If b (baseline OD) is invalid but plateau OD was valid, return zero. + else if (!is.numeric(base)) + base = 0 + else{ + base = round(base, digits) + } + return(base) + } + +# Calculate log.OD at inoculation from fitted parameters +inoc.log.OD = function(fitted.well, digits = Inf){ + # Evaluated the fitted model at the inoculation timepoint (should be zero from using from table2wells.R) + if (is.null(well.eval(fitted.well))) + return(NA) + else{ + inoc.time = fitted.well@screen.data$Time[fitted.well@start.index] + inoc.log.OD = well.eval(fitted.well, inoc.time) + if (is.na(inoc.log.OD)) inoc.log.OD = fitted.well@fit.par$b # need this in a special case: loess fits with start.index = 1 + return(round(inoc.log.OD, digits)) + } + } + +# Calculate max log.OD from model fit +max.log.OD = function(fitted.well, digits = Inf, ...){ + # Evaluated the fitted model at the final timepoint (just the last valid timepoint in the experiment) + if (is.null(well.eval(fitted.well))) + return(NA) + else{ + return(round(max(well.eval(fitted.well),na.rm=T), digits)) + } +} + +# Calculate projected growth: plateau minus the inoculated log.OD +projected.growth = function(fitted.well,digits=Inf) { + plateau(fitted.well,digits) - inoc.log.OD(fitted.well,digits) +} + + +# Calculate projected growth: plateau minus the inoculated log.OD +projected.growth.OD = function(fitted.well,constant.added,digits=Inf) { + value = unlog(plateau(fitted.well),constant.added) - unlog(inoc.log.OD(fitted.well),constant.added) + round(value,digits) +} + +# Calculate achieved growth: max.log.OD minus the inoculated log.OD +achieved.growth = function(fitted.well,digits=Inf) { + max.log.OD(fitted.well,digits) - inoc.log.OD(fitted.well,digits) +} + +# Calculate projected growth: plateau minus the inoculated log.OD +achieved.growth.OD = function(fitted.well,constant.added,digits=Inf) { + value = unlog(max.log.OD(fitted.well),constant.added) - unlog(inoc.log.OD(fitted.well),constant.added) + round(value,digits) +} + +# Did the curve come close to the plateau OD during the experiment? +reach.plateau = function(fitted.well, cutoff = 0.75){ + plat = plateau(fitted.well) + inoc = inoc.log.OD(fitted.well) + final = max.log.OD(fitted.well) + + if (!is.na(final)){ + # If the plateau is the same as the OD at inoculation, return TRUE + if ((plat - inoc) == 0) + return(T) + # If the difference between the final OD and inoculation OD is at least a certain proportion + # of the difference between the plateau and inoculated ODs, return TRUE. + else + return((final - inoc) / (plat - inoc) > cutoff) + } + else + return(T) + # If no final OD was calculated (if curve was not fit properly) just return T. + } + +# Calculate the lag time from the fitted OD +lag.time = function(fitted.well, digits = Inf, ...){ + if(length(fitted.well@fit.par) == 0) + return(NA) + + fitted.well@fit.par$lam +} + +# new params for GCAT 4.0 +# Get amplitude +amplitude = function(fitted.well){ + if(length(fitted.well@fit.par) == 0) + return(NA) + + return(fitted.well@fit.par$A) +} + +# Get shape parameter +shape.par = function(fitted.well){ + if(length(fitted.well@fit.par) == 0) + return(NA) + ifelse(is.null(fitted.well@fit.par$v), NA, fitted.well@fit.par$v) +} + +# Get standard error of the maximum specific growth rate value +max.spec.growth.rate.SE = function(fitted.well, ...){ + if(length(fitted.well@fit.std.err) == 0) + return(NA) + ifelse(is.null(fitted.well@fit.std.err$u), NA, fitted.well@fit.std.err$u) +} + +# Get standard error of the lag time value +lag.time.SE = function(fitted.well, ...){ + if(length(fitted.well@fit.std.err) == 0) + return(NA) + ifelse(is.null(fitted.well@fit.std.err$lam), NA, fitted.well@fit.std.err$lam) +} + +# Get standard error of the shape parameter +shape.par.SE = function(fitted.well){ + if(length(fitted.well@fit.std.err) == 0) + return(NA) + ifelse(is.null(fitted.well@fit.std.err$v), NA, fitted.well@fit.std.err$v) +} + +# Get standard error of the amplitude +amplitude.SE = function(fitted.well){ + if(length(fitted.well@fit.std.err) == 0) + return(NA) + ifelse(is.null(fitted.well@fit.std.err$A), NA, fitted.well@fit.std.err$A) +} + +# Get standard error of the baseline value +baseline.SE = function(fitted.well){ + if(length(fitted.well@fit.std.err) == 0) + return(NA) + ifelse(is.null(fitted.well@fit.std.err$b), NA, fitted.well@fit.std.err$b) +} + +# Calulate the inflection time value +inflection.time = function(well){ + if (length(well@loess) == 0 && length(well@nls) == 0) return(NA) # can' compute inflection time in the absence of a fit + data = data.from(well) + Time = data[,1] + t = seq(from = min(Time), to = max(Time), by = (max(Time)-min(Time))/1000) + y = well.eval(well,t) + if (is.null(y)) return(NA) + delta.t = diff(t) + dydt = diff(y)/delta.t + infl.index = which.max(dydt) + t[infl.index] +} diff --git a/R/GCAT/R/misc.R b/R/GCAT/R/misc.R index 3de2c94..555aa42 100644 --- a/R/GCAT/R/misc.R +++ b/R/GCAT/R/misc.R @@ -1,36 +1,36 @@ -#Copyright 2012 The Board of Regents of the University of Wisconsin System. -#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, -#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman -# -#This file is part of GCAT. -# -#GCAT is free software: you can redistribute it and/or modify -#it under the terms of the GNU Lesser General Public License as published by -#the Free Software Foundation, either version 3 of the License, or -#(at your option) any later version. -# -#GCAT is distributed in the hope that it will be useful, -#but WITHOUT ANY WARRANTY; without even the implied warranty of -#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -#GNU Lesser General Public License for more details. -# -#You should have received a copy of the GNU Lesser General Public License -#along with GCAT. If not, see . - -# Wrapper for sapply to use lapply over an array, conserving the dimensions. -aapply = function(x, FUN,...){ - dim.values = dim(x) - dim.names = dimnames(x) - x = lapply(x, function(x){FUN(x,...)}) - dim(x) = dim.values - dimnames(x) = dim.names - return(x) - } - -# A function to manually create an unchecked exception. -exception = function(class, msg) -{ - cond <- simpleError(msg) - class(cond) <- c(class, "MyException", class(cond)) - stop(cond) -} +#Copyright 2012 The Board of Regents of the University of Wisconsin System. +#Contributors: Jason Shao, James McCurdy, Enhai Xie, Adam G.W. Halstead, +#Michael H. Whitney, Nathan DiPiazza, Trey K. Sato and Yury V. Bukhman +# +#This file is part of GCAT. +# +#GCAT is free software: you can redistribute it and/or modify +#it under the terms of the GNU Lesser General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#GCAT is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU Lesser General Public License for more details. +# +#You should have received a copy of the GNU Lesser General Public License +#along with GCAT. If not, see . + +# Wrapper for sapply to use lapply over an array, conserving the dimensions. +aapply = function(x, FUN,...){ + dim.values = dim(x) + dim.names = dimnames(x) + x = lapply(x, function(x){FUN(x,...)}) + dim(x) = dim.values + dimnames(x) = dim.names + return(x) + } + +# A function to manually create an unchecked exception. +exception = function(class, msg) +{ + cond <- simpleError(msg) + class(cond) <- c(class, "MyException", class(cond)) + stop(cond) +} diff --git a/R/GCAT/R/normalize.and.transform.R b/R/GCAT/R/normalize.and.transform.R index 46cc71a..d9b95bb 100644 --- a/R/GCAT/R/normalize.and.transform.R +++ b/R/GCAT/R/normalize.and.transform.R @@ -18,27 +18,33 @@ #along with GCAT. If not, see . ######################################################################## -# # -# Normalize OD readings for an entire array of well objects # -# # ######################################################################## -# -# Note: This function does not write any new OD values to the well objects in the array - it only -# fills the "norm" slot of each well object in the array with a value that will be subtracted -# from all OD measurements when returning data from the wells using the function (see well.class.R) -# -# These functions make use of which simply returns the raw time and OD of a well (also see well.class.R) -# -# well.array: an array of well objects. note this is the only normalization function that acts on an entire array instead of an individual well. -# normalize.method: -# - (default): subtracts the blank OD (either specified by or taken from the first timepoint as default) of each well from all timepoints in that well -# - average.blank: subtracts the mean of all first OD timepoints on a plate from all timepoints in all wells on that plate -# - average.first: takes the mean of the difference between the OD of the specified timepoint and the first timepoint of all wells on a plate -# and subtracts this value from all timepoints in all wells on that plate -# - anything else: do nothing -# blank.value - user can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. -# start.index - which timepoint should be used as the first one after inoculation (defaults to the 2th one) -# add.constant: add a numeric constant to all timepoints in all wells. +#' Normalize OD readings for an entire array of well objects +#' +#' @details +#' Note: This function does not write any new OD values to the well objects in the array - it only +#' fills the "norm" slot of each well object in the array with a value that will be subtracted +#' from all OD measurements when returning data from the wells using the function (see well.class.R) +#' +#' These functions make use of which simply returns the raw time and OD of a well (also see well.class.R) +#' +#' note this is the only normalization function that acts on an entire array instead of an individual well. +#' +#' normalize.method settings: +#' \describe{ +#' \item{default}{subtracts the blank OD (either specified by or taken from the first timepoint as default) +#' of each well from all timepoints in that well} +#' \item{average.blank}{subtracts the mean of all first OD timepoints on a plate from all timepoints in all wells on that plate} +#' \item{average.first}{takes the mean of the difference between the OD of the specified timepoint and the first timepoint of all wells on a plate +#' and subtracts this value from all timepoints in all wells on that plate} +#' \item{anything else}{do nothing} +#' } +#' +#' @param normalize.method see Details +#' @param well.array an array of well objects. +#' @param blank.value user can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. +#' @param start.index which timepoint should be used as the first one after inoculation (defaults to the 2th one) +#' @param add.constant add a numeric constant to all timepoints in all wells. normalize.ODs = function(well.array, normalize.method = "default", blank.value = NULL, start.index = 2, add.constant = 1){ if (normalize.method == "default"){ @@ -87,18 +93,17 @@ normalize.ODs = function(well.array, normalize.method = "default", blank.value = } ######################################################################## -# # -# Log-transform OD readings for a single well object # -# # ######################################################################## # Must include this so that the checking process will not complain about # inconsistency S3 generic/method. Though I don't know why. +# S3 generic +# @seealso \code{\link{transform.ODs}} transform <- function(input.well, ...) { UseMethod("transform") } -#' Transform.Ods +#' Log-transform OD readings for a single well object #' #' This function adds a "log.OD" column to the "screen.data" slot of a well object with log-transformed data. #' The raw data is kept intact. @@ -109,7 +114,9 @@ transform <- function(input.well, ...) { #' or raw normalized data is returned using the function \code{data.from}. #' @param blank.value user can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well. #' @param start.index which timepoint should be used as the first one after inoculation (defaults to the 2th one) -#' @param negative.OD.cutoff if any ODs below the specified blank value are detected before this index timepoint, the entire well is discarded. +#' @param negative.OD.cutoff if any ODs below the specified blank value are detected before this index timepoint, the entire well is discarded. +#' @param constant.added similar to added.constant. +#' @param ... Additional arguments for this function. transform.ODs = function(input.well, use.log = T, blank.value = NULL, start.index = 2, negative.OD.cutoff = 10, constant.added = 1.0, ...){ # The default value for the log-transformed ODs will be NA. Valid values will be filled in. @@ -148,22 +155,23 @@ transform.ODs = function(input.well, use.log = T, blank.value = NULL, start.inde } ######################################################################## -# # -# Remove timepoints from the analysis but not from the raw data # -# # ######################################################################## -# +# Remove timepoints from the analysis but not from the raw data # +# +# @details # Removes timepoints from further analysis. Does not remove them from the raw data; # instead, this function creates or updates the Remove column in slot "screen.data" of the well which dictates whether # individual timepoints are returned using the function. # -# can be a vector containing: -# - any combination of positive and negative integers +# parameter \emph{points} can be a vector containing: +# \itemize{ +# \item{any combination of positive and negative integers # the timepoints at indices corresponding to positive integers will be set to be removed. -# the timepoints at indices corresponding to negative integers will be be re-added if they were previously set to be removed. -# - a single zero, which resets all timepoints (nothing will be removed) -# - a logical vector to replace the Remove column and which will be cycled along the length of the timepoints. - +# the timepoints at indices corresponding to negative integers will be be re-added if they were previously set to be removed.} +# \item{a single zero, which resets all timepoints (nothing will be removed)} +# \item{a logical vector to replace the Remove column and which will be cycled along the length of the timepoints.} +# } +# remove.points = function(input.well, points){ # Copy the Remove column or create a new one if it doesn't yet exist if (is.null(input.well@screen.data$Remove)) @@ -192,7 +200,21 @@ remove.points = function(input.well, points){ input.well } - +# Add a column y = OD - blank.value for each well@screen.data +# switch Remove flag to TRUE if y < 0. +subtract.blank = function(well.array, blank.value = NULL) { + well.array = aapply(well.array, function(well, blank.value){ + if (is.null(blank.value)) + blank.value = well@screen.data$OD[1] + + well@screen.data$y = well@screen.data$OD - blank.value + well = remove.points(well, well@screen.data$y < 0) + #newOD = well@screen.data$y + #oldOD = well@screen.data$OD + #well@screen.data$OD = newOD + #well@screen.data$y = oldOD + return(well)}, blank.value) +} diff --git a/R/GCAT/R/plot.fit.R b/R/GCAT/R/plot.fit.R index 55308dd..3b796d0 100644 --- a/R/GCAT/R/plot.fit.R +++ b/R/GCAT/R/plot.fit.R @@ -28,14 +28,14 @@ require(gplots) ######################################################################## # S3 Generic. -plot <- function(input.well, ...) { - UseMethod("plot") -} +#plot <- function(input.well, ...) { +# UseMethod("plot") +#} ######################################################################## # Basic function plots time vs. OD from a well object # ######################################################################## -#' plot.data +#' plot_data #' #' Basic function plots time vs. OD from a well object #' @@ -46,7 +46,10 @@ plot <- function(input.well, ...) { #' @param scale determines the font scale for the entire graph. all cex values are calculated from this. #' @param draw.symbols - should be called on the well and markings drawn on the graph? #' @param ... additional arguments passed to plot() -plot.data = function(input.well, view.raw.data = F, unlog = F, scale = 1, +#' @param main ... +#' @param constant.added Similar to added.constant. +#' @param ylim ... +plot_data = function(input.well, view.raw.data = F, unlog = F, scale = 1, main = paste(plate.name(input.well), well.name(input.well)), number.points = T, draw.symbols = F, constant.added, ylim, ...){ @@ -58,7 +61,8 @@ plot.data = function(input.well, view.raw.data = F, unlog = F, scale = 1, # Draw the axes and all text labels first. par(mar = c(5, 4, 4, 5)+0.1) plot(input.data, main = main, xlab = "Time(hours)", ylab = "log(OD - blank + const)", - mex = scale, cex.main = 1.5*scale, cex.axis = 1.2*scale, cex.lab = 1.2*scale, type ="n",...) + mex = scale, cex.main = 1.5*scale, cex.axis = 1.2*scale, cex.lab = 1.2*scale, + type ="n", ylim=ylim, ...) # Draw a second vertical axis, showing unlogged OD scale # - Determine the range of the labels: from min.OD to max.OD @@ -94,12 +98,13 @@ plot.data = function(input.well, view.raw.data = F, unlog = F, scale = 1, } ######################################################################## -# Plots the fitted model curve from a well object if it exists # ######################################################################## +# Plot the fitted model curve from a well object if it exists # -# time: specify which points (in units of time) to plot fitted OD values for. if not specifies, plot all timepoints in range of well. - -plot.model = function(input.well, col = 1, scale = 1, lty = 1, time = NULL, unlog = F, constant.added=1, ...){ +# @details +# \strong{time:} specify which points (in units of time) to plot fitted OD values for. if not specifies, plot all timepoints in range of well. +# +plot_model = function(input.well, col = 1, scale = 1, lty = 1, time = NULL, unlog = F, constant.added=1, ...){ #input.data = data.from(input.well) #growth = input.data[,2] @@ -121,8 +126,8 @@ plot.model = function(input.well, col = 1, scale = 1, lty = 1, time = NULL, unlo } ######################################################################## -# Put various parameters and info in text form on the graphs # ######################################################################## +# Put various parameters and info in text form on the graphs # # draw.text = function(input.well, scale = 0.5, xlim = 0, ylim = 0,...){ @@ -185,11 +190,12 @@ draw.text = function(input.well, scale = 0.5, xlim = 0, ylim = 0,...){ } ######################################################################## -# Draw lines on graph denoting calculated parameters # ######################################################################## -# -# - should curve parameters be labeled? - +# Draw lines on graph denoting calculated parameters +# +# @details +# \strong{show.num} - should curve parameters be labeled? +# draw.calc.par = function(input.well, scale = 0.5, unlog = F, constant.added, show.num = T){ # Don't do anything if well was not fit. @@ -262,10 +268,10 @@ draw.calc.par = function(input.well, scale = 0.5, unlog = F, constant.added, sho } ######################################################################## -# Draw residuals from the nonlinear fit with option for lowess line # ######################################################################## +# Draw residuals from the nonlinear fit with option for lowess line # # -plot.residuals = function(input.well, xlim = NULL, lowess = T, ...){ +plot_residuals = function(input.well, xlim = NULL, lowess = T, ...){ well = input.well data = data.from(well, remove = F, remove.tanking = F) @@ -282,17 +288,22 @@ plot.residuals = function(input.well, xlim = NULL, lowess = T, ...){ } ############################################################################## -# This function is used to create a heatmap using: -# specific growth, total growth, and lag time -# for each well on a plate. -# -# @params -# fitted.well.array: matrix containing well array object data -# attribute: the data type we should use to create a heatmap -# @returns -# path of heatmap pdf file ############################################################################## -create.heatmap = function(fitted.well.array, attribute, unlog=NULL){ +#' Create a heat map of a plate +#' +#' @details +#' This function is used to create a heatmap using +#' specific growth, total growth, or lag time +#' for each well on a plate. +#' +#' @param fitted.well.array matrix containing well array object data +#' @param attribute the data type we should use to create a heatmap +#' @param unlog transform values to linear scale +#' @param MinMax The specific range for the heatmap. +#' +#' @return path of heatmap pdf file +#' +create.heatmap = function(fitted.well.array, attribute, MinMax = NA, unlog=NULL){ attr.name <- deparse(substitute(attribute)) pdf.name <- "" if(class(fitted.well.array) == "matrix"){ @@ -322,9 +333,17 @@ create.heatmap = function(fitted.well.array, attribute, unlog=NULL){ pdf(pdf.name) #heatmap(heat, Rowv=NA, Colv=NA, revC=T, scale="none", na.rm=T, main=plate.ID, col=rainbow(100), margins=c(6,6)) #mtext(paste("Max:", round(max(spec.growth, na.rm=T), digits=4),"Min:", round(min(spec.growth, na.rm=T), digits=4), "Avg:", round(mean(spec.growth, na.rm=T), digits=4)), side=1, line=3) - pheatmap(heat, color=colorpanel(100, "red", "orange", "yellow"), - border_color="black", cell_width=2, cell_height=3, - cluster_rows=F, cluster_cols=F, scale='none', main=heat.text, fontsize=16) + if (length(MinMax) == 2){ + Mean = mean(MinMax) + bk = unique(c(seq(MinMax[1], Mean, length=50), seq(Mean, MinMax[2], length = 50))) + pheatmap(heat, color=colorpanel(100, "red", "orange", "yellow"), breaks = bk, + border_color="black", cell_width=2, cell_height=3, + cluster_rows=F, cluster_cols=F, scale='none', main=heat.text, fontsize=16) + } else { + pheatmap(heat, color=colorpanel(100, "red", "orange", "yellow"), + border_color="black", cell_width=2, cell_height=3, + cluster_rows=F, cluster_cols=F, scale='none', main=heat.text, fontsize=16) + } dev.off() } else { @@ -334,11 +353,13 @@ create.heatmap = function(fitted.well.array, attribute, unlog=NULL){ } ######################################################################## +######################################################################## +# Plate overview graphic +# +# @details # Draw grids of 96 points as a visual representation of fit status, # # and other info for an array of fitted well objects, plate by plate # -######################################################################## # - plate.overview = function(fitted.well.array, scale = 1, plate.ncol = 12, plate.nrow = 8){ @@ -452,11 +473,13 @@ plate.overview = function(fitted.well.array, scale = 1, plate.ncol = 12, plate.n } ######################################################################## +######################################################################## +# Draw individual fitted wells +# +# @details # Draw each well in an array of fitted well objects in succession. # # Include options for adding notations, text info and fit parameters. # -######################################################################## # - view.fit = function(fitted.data, indices = 1:length(fitted.data), unlog = F, constant.added, xlim = NULL, ylim = NULL, display.legend = T, show.text = T, show.calc = T, draw.guess = NULL, draw.symbols = F, number.points = T, @@ -513,7 +536,7 @@ view.fit = function(fitted.data, indices = 1:length(fitted.data), if (show.residuals & is.numeric(model.residuals(fitted.well))){ if(user.advance) if (toupper(readline(" for residuals >>")) == "Q") break - plot.residuals(fitted.well) + plot_residuals(fitted.well) } # Allow user to advance the currently shown well if specified. @@ -534,7 +557,7 @@ view.fit = function(fitted.data, indices = 1:length(fitted.data), } } - +# Draw legend on a well plot well.fit.legend = function(xlim, ylim, scale = 1, constant.added){ par(mar = c(5, 4, 4, 5)+0.1) plot(0,0, main = "[Index] \n; ", @@ -588,8 +611,10 @@ well.fit.legend = function(xlim, ylim, scale = 1, constant.added){ x.intersp=1, xjust = 1, y.intersp=1.5) } +# Generate pdf files pdf.by.plate = function(fitted.data, out.prefix = "", upload.timestamp = NULL, - out.dir = getwd(), unlog = F, constant.added, silent = T, overview.jpgs = T, plate.ncol = 12, plate.nrow = 8,...){ + out.dir = getwd(), unlog = F, constant.added, silent = T, overview.jpgs = T, plate.ncol = 12, plate.nrow = 8, + lagRange = NA, specRange = NA, totalRange = NA, ...){ # Prepare timestamp for addition to output file names. filename.timestamp = strftime(upload.timestamp, format="_%Y-%m-%d_%H.%M.%S") @@ -620,13 +645,13 @@ pdf.by.plate = function(fitted.data, out.prefix = "", upload.timestamp = NULL, if(num.wells > 1){ #Heatmap block########################################################## #alongside the jpgs file create 3 heatmaps for each plate. NWD - spec.heat.file = create.heatmap(fitted.data[,,i], max.spec.growth.rate) + spec.heat.file = create.heatmap(fitted.data[,,i], max.spec.growth.rate, MinMax = specRange) if(spec.heat.file == "Error") stop("Error in for specific growth") - lag.heat.file = create.heatmap(fitted.data[,,i], lag.time) + lag.heat.file = create.heatmap(fitted.data[,,i], lag.time, MinMax = lagRange) if(lag.heat.file == "Error") stop("Error in for lag time") - total.heat.file = create.heatmap(fitted.data[,,i], achieved.growth) + total.heat.file = create.heatmap(fitted.data[,,i], achieved.growth, MinMax = totalRange) if(total.heat.file == "Error") stop("Error in for total growth") # Add name of file if successfully written to file list output. Including heatmap files NWD diff --git a/R/GCAT/R/slope.analysis.R b/R/GCAT/R/slope.analysis.R index ee7a80d..7cde917 100644 --- a/R/GCAT/R/slope.analysis.R +++ b/R/GCAT/R/slope.analysis.R @@ -18,14 +18,13 @@ #along with GCAT. If not, see . ######################################################################## -# # -# Estimate the growth curve slope at each timepoint of a well # -# # ######################################################################## -# +# Estimate the growth curve slope at each timepoint of a well +# +# @details # uses the functions and (see well.class.R) # adds estimated slopes as a new column to the "screen.data" slot - +# calculate.slopes = function(input.well, silent = T){ # Get the growth curve data (excluding removed points, but not excluding points marked as tanking) growth.data = data.from(input.well, remove = T, remove.tanking = F) @@ -54,34 +53,28 @@ calculate.slopes = function(input.well, silent = T){ ######################################################################## -# # -# Use slope estimates to check growth curves for tanking and OD jumps # -# # ######################################################################## -# -# uses the functions and (see well.class.R) -# Arguments: -# ----- stringency parameters ---- -# remove.jumps - should the program remove OD jumps? default F (just report them) - -# should be set to T if data contains distinct jumps in OD that need to be eliminated -# otherwise, this might be too stringent and will result in loss of data. -# check.start - which timepoint should checking for jumps and tanking start at? this is included because early timepoints can be unstable. -# fall.cutoff - what downward slope should constitute a fall in OD? -# jump.cutoffs - multipliers to determine whether a curve jumps up or down (see methods 1 and 2, below) -# tank.limit - how many timepoints in a row can have falling slopes until the curve is marked as tanking? -# tank.cutoff - what proportion of the maximum OD can the curve go below until it is considered tanking? - -# ---- input/output ---- -# silent - output to R console? -# draw - plot growth curve with curve checking details? -# -# Fills the "curve.par" slot in the well with the starting index of tanking (NA if none is found) -# - -#check.slopes = function(input.well, check.start = 8, fall.cutoff = -.0025, remove.jumps = F, -# jump.multipliers = -c(15, 500, 10), tank.cutoff = 1.0, tank.limit = 3, silent = T, draw = T){ - -#changed default values to parameters to account for settling +#' Use slope estimates to check growth curves for tanking and OD jumps # +#' +#' @details +#' Uses the functions and (see well.class.R) +#' +#' Fills the "curve.par" slot in the well with the starting index of tanking (NA if none is found) +#' +#' Changed default values to parameters to account for settling +#' +#' @param input.well object of class \code{well} to check the slopes for +#' @param remove.jumps should the program remove OD jumps? default F (just report them) - +#' should be set to T if data contains distinct jumps in OD that need to be eliminated +#' otherwise, this might be too stringent and will result in loss of data. +#' @param check.start which timepoint should checking for jumps and tanking start at? this is included because early timepoints can be unstable. +#' @param fall.cutoff what downward slope should constitute a fall in OD? +#' @param jump.multipliers multipliers of fall.cutoff that determine whether a curve jumps up or down (see methods 1 and 2, below) +#' @param tank.limit how many timepoints in a row can have falling slopes until the curve is marked as tanking? +#' @param tank.cutoff what proportion of the maximum OD can the curve go below until it is considered tanking? +#' @param silent output to R console? +#' @param draw plot growth curve with curve checking details? +#' check.slopes = function(input.well, check.start = 22, fall.cutoff = -.0025, remove.jumps = F, jump.multipliers = -c(15, 500, 10), tank.cutoff = 1.0, tank.limit = 6, silent = T, draw = T){ @@ -380,19 +373,32 @@ check.slopes = function(input.well, check.start = 22, fall.cutoff = -.0025, remo } ######################################################################## -# # -# Check wells for growth, remove from analysis if OD is too low # -# # ######################################################################## +# Check wells for growth, remove from analysis if OD is too low # +# @details # The well will be tagged with no.growth = T in the slot "curve.par" if raw OD values (except for ) # do not increase beyond above the specified time of inoculation for that well () - +# check.growth = function(input.well, growth.cutoff, start.index = 2){ + + # Debug + #if (all(getPosition(input.well) == c("022510b.GLBRC200DH.2","D","5"))) browser() # Get raw ODs (not including ) and slope estimates from the well # as well as OD at inoculation timepoint + well.pos = getPosition(input.well) + + # Debug + #if (well.pos[[2]] == "A" && well.pos[[3]] == 1) + # browser() + raw.ODs = raw.data(input.well)[,2] + + # Check for missing point. + if (any(is.na(raw.ODs))) + exception("Warning: ", "Missing data point detected. Please check the file and try again.") + start.OD = raw.ODs[start.index] raw.ODs[input.well@screen.data$Remove] = NA diff --git a/R/GCAT/R/table.output.R b/R/GCAT/R/table.output.R index b4cc42b..8a67668 100644 --- a/R/GCAT/R/table.output.R +++ b/R/GCAT/R/table.output.R @@ -18,17 +18,18 @@ #along with GCAT. If not, see . ######################################################################## -# # -# Populate an output table with parameters and other useful info for # -# each well in a fitted dataset. # -# # ######################################################################## -# -# unlog - Should OD values be returned on the linear scale instead of log-transformed scale? -# constant.added - For returning values on linear scale, what constant was added to ODs before the log transform? -# reach.cutoff - what proportion of the plateau OD must tbe reached by the last valid timepoint for the curve to be marked as reaching its plateau OD? -# - +#' Populate an output table with parameters and other useful info for each well in a fitted dataset. +#' +#' @param fitted.data.set array of fitted well objects +#' @param unlog - Should OD values be returned on the linear scale instead of log-transformed scale? +#' @param constant.added - For returning values on linear scale, what constant was added to ODs before the log transform? +#' @param reach.cutoff - what proportion of the plateau OD must tbe reached by the last valid timepoint for the curve to be marked as reaching +#' its plateau OD? +#' @param filename.timestamp timestamp for addition to output file names (for file references in last column of the output) +#' @param use.linear.param did the model formula contain a linear parameter? Should normally be FALSE, as the linear parameter is deprecated +#' @param use.loess was LOESS used to fit the data (instead of unsing a growth curve model formula)? +#' table.out = function(fitted.data.set, unlog = F, constant.added, reach.cutoff = 0.90, filename.timestamp = NULL,use.linear.param=F, use.loess=F){ # The idea is basically to use and on the fitted data array in order diff --git a/R/GCAT/R/table2well.R b/R/GCAT/R/table2well.R index e0ea069..eff8b11 100644 --- a/R/GCAT/R/table2well.R +++ b/R/GCAT/R/table2well.R @@ -38,11 +38,10 @@ #' @param input.data A list of tables representing input files read with \code{read.table}. Used to save time in cases #' of running multiple analyses on the same dataset. If used, the function will ignore \code{file.name} entirely. #' @param load.type .csv by default. -#' @param plate.laout Specifies the layout of the given plate. +#' @param plate.layout Specifies the layout of the given plate. #' @param single.plate.ID specifies a plate name for a single-plate read. If NULL, this is derived from the file name. #' @param blank.value Blank OD measurement for uninoculated wells. By default(NULL), the value of the first OD #' measurement in each well is used. -#' @param add.constant A value for r in the log(OD + r) transformation. #' @param plate.nrow The number of rows in the input files. #' @param plate.ncol The number of columns in the input files. #' @param input.skip.lines specifies a plate name for a single-plate read. If NULL, this is derived from the file name. @@ -50,7 +49,8 @@ #' @param single.column.headers The headers of the column when analyzing a single plate. #' @param layout.sheet.headers The headers of the layout file. #' @param silent Surpress all messages. -#' @param verbose Display all messages when analyzing each well. +#' @param start.index Which timepoint should be used as the first one after inoculation? +#' @param single.plate Is the plate single type? #' #' @return A list of well objects. gcat.load.data = function(file.name = NULL, load.type = "csv", input.data = NULL, single.plate.ID = NULL, @@ -64,8 +64,30 @@ gcat.load.data = function(file.name = NULL, load.type = "csv", input.data = NULL ######################################################################## if(is.null(input.data)){ + # Check for bad encoding. + file.name.cmd = paste("'", file.name, sep = "") + file.name.cmd = paste(file.name.cmd, "'", sep = "") + cmd = paste("enca -L none", file.name.cmd) + sys.msg = system(cmd, intern = TRUE) + if (length(attributes(sys.msg)) == 1) { + if (attributes(sys.msg)[1] == 1) + exception("", "Unrecognized encoding for input file. The file should be in UTF-8.") + } + # Either read from .csv. + + # Skipping temperature column. + colclasses = c(rep("integer", 1), rep("NULL", 1), rep("integer", 96)) + + # input.data = read.csv(file.name, colClasses = colclasses, stringsAsFactors=F, skip = input.skip.lines, fileEncoding='UTF-8') input.data = read.csv(file.name, stringsAsFactors=F, skip = input.skip.lines, fileEncoding='UTF-8') + + # Checking for temperature column. + # Reread the file if temp column is there. + # MB: Not the best solution. + if (length(input.data) == 98) + exception("", "The number of columns in the file is not 97 columns format. Please resubmit a valid file.") + # Determine single plate name if not specified. if (is.null(single.plate.ID)){ @@ -192,7 +214,7 @@ gcat.load.data = function(file.name = NULL, load.type = "csv", input.data = NULL # Error if either no rows or more than one row matches the well if (length(layout.row.number) != 1) - stop("incorrectly formatted plate layout! check names of columns, rows, and plates (if applicable).") + stop("Incorrectly formatted plate layout! check names of columns, rows, and plates (if applicable).") # Add any additional columns to the well's "well.info" slot well.info = plate.layout[layout.row.number,!(names(plate.layout) %in% c("Row","Column","Plate.ID",layout.sheet.headers))] @@ -234,12 +256,13 @@ gcat.load.data = function(file.name = NULL, load.type = "csv", input.data = NULL # Reorganize data from single-plate input format before reading # # # ######################################################################## +# Reorganize data from single-plate input format before reading # # # This function reorganizes the data frame from a single-plate format file. -# input.data - data frame read straight from a single-plate format data file. -# single.plate.ID - specifies a plate name for a single-plate read, since none is given in the single-plate format +# @param input.data - data frame read straight from a single-plate format data file. +# @param single.plate.ID - specifies a plate name for a single-plate read, since none is given in the single-plate format. # The plate will be named Plate_1 unless otherwise specified. - +# gcat.reorganize.single.plate.data = function(input.data, blank.value = NULL, single.column.headers, single.plate.ID = "Plate_1", plate.nrow = 8, plate.ncol = 12, silent=T){ @@ -252,12 +275,12 @@ gcat.reorganize.single.plate.data = function(input.data, blank.value = NULL, sin header.row = min(which(input.data[,1] == single.column.headers[1])) if (length(header.row) != 1 | is.infinite(header.row)) - stop("could not locate header row in input file!") + stop("Could not locate header row in input file!") # The last row: where column 2 starts to be blank, or the total number of rows, whichever is smaller extra.rows.start = min(which(input.data[-(1:header.row),2] == ""), which(is.na(input.data[-(1:header.row),2])), nrow(input.data[-(1:header.row),])) if (length(extra.rows.start) != 1 & is.infinite(extra.rows.start)) - stop("could not locate last row in input file!") + stop("Could not locate last row in input file!") # Use header row to rename the columns, then cut off extra rows (including the ones above header) names(input.data) = as.character(unlist(input.data[header.row,])) @@ -332,9 +355,12 @@ gcat.reorganize.single.plate.data = function(input.data, blank.value = NULL, sin # # ######################################################################## # ---------------------------------------------------------- -# This function can append together arrays created using -# Arguments: any number of array objects as long as they are all output straight from - +#' Function to combine two well array datasets by plate +#' +#' This function can append together arrays created using +#' +#' @param ... any number of array objects as long as they are all output straight from +#' gcat.append.arrays = function(...){ # Transfer arrays to a list @@ -385,14 +411,16 @@ gcat.append.arrays = function(...){ # Convert timestamps to hours from start and sort timepoints # # # ######################################################################## +#' Convert timestamps to hours from start and sort timepoints # -# This function acts on a single well and modifies the raw data stored in slot "screen.data" -# -# input.well - an object of class well -# time.format - specifies the time format. allowed values are "%S", for seconds, "%d", for days, or anything complying with ISO C / POSIX standards; see -# note: reading directly from excel to R results in timestamps being converted to days. -# start.index - which timepoint should be used as the starting time at inoculation? - +#' This function acts on a single well and modifies the raw data stored in slot "screen.data" +#' +#' @param input.well an object of class well +#' @param time.input specifies time format in the input. allowed values are "%S", for seconds, "%d", for days, or anything complying with +#' ISO C / POSIX standards; see . +#' @param start.index which timepoint should be used as the starting time at inoculation? +#' +#' @details note: reading directly from excel to R results in timestamps being converted to days. gcat.start.times = function(input.well, time.input, start.index = 2) { if(start.index > length(input.well)) diff --git a/Rails/public/uploadedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_Layout.csv b/R/GCAT/inst/extdata/default_examples/multi_MultiPlateLayout_plateID.csv similarity index 100% rename from Rails/public/uploadedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_Layout.csv rename to R/GCAT/inst/extdata/default_examples/multi_MultiPlateLayout_plateID.csv diff --git a/R/GCAT/inst/extdata/default_examples/multi_test_YYYY_MM_DD_HH_MM_SS.csv b/R/GCAT/inst/extdata/default_examples/multi_test_YYYY_MM_DD_HH_MM_SS.csv new file mode 100644 index 0000000..1151936 --- /dev/null +++ b/R/GCAT/inst/extdata/default_examples/multi_test_YYYY_MM_DD_HH_MM_SS.csv @@ -0,0 +1,5761 @@ +Plate ID,Time,Well,OD +022510b.GLBRC200DH.1,2010-02-25 16:15:00,B12,0.0622 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,H10,0.065 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,H07,0.0653 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,H02,0.0657 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,H09,0.0658 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,C01,0.0668 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,F12,0.067 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,H12,0.0672 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,H01,0.0674 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,A05,0.0677 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,A10,0.0677 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,E01,0.0678 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,H03,0.0683 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,A04,0.0685 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,A06,0.069 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,A07,0.0693 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,D01,0.0711 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,G12,0.0714 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,B01,0.0741 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,E12,0.0791 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,A09,0.0796 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,B08,0.106 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,C07,0.1144 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,B07,0.115 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,B10,0.118 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,D03,0.1182 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,D08,0.1182 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,D11,0.1198 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,E08,0.1224 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,F07,0.123 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,D04,0.123 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,G06,0.1241 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,F09,0.1244 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,F01,0.0631 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,G01,0.0636 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,D12,0.0639 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,H08,0.0651 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,H11,0.0662 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,A11,0.0673 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,A02,0.0687 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,A01,0.0695 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,A03,0.0699 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,B09,0.117 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,C11,0.1188 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,D10,0.1189 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,G07,0.12 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,G05,0.1212 +022510b.GLBRC200DH.1,2010-02-25 16:15:00,C09,0.1218 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23:03:36,F12,0.2938 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,F05,0.2939 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,F08,0.2987 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,F01,0.2988 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,G01,0.3001 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,H12,0.3043 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,F07,0.3051 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,D05,0.3062 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,G12,0.3063 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,H11,0.3071 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,G10,0.3078 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,E04,0.3078 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,D04,0.3079 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,H04,0.3085 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,E05,0.31 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,E10,0.3127 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,D08,0.314 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,A07,0.3149 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,F11,0.3161 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23:03:36,D06,0.3113 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,D12,0.3128 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,C05,0.3142 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,E07,0.3186 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,A02,0.3227 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,B11,0.3238 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,H02,0.32 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,A06,0.3278 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,A04,0.3279 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,C11,0.3293 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,C12,0.3301 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,H09,0.3308 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,B09,0.3315 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,A09,0.3318 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,A10,0.332 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,A12,0.3325 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,D07,0.3329 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,A03,0.3335 +022510b.GLBRC200DH.1,2010-02-25 23:03:36,B12,0.3339 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23:48:11,B03,0.3321 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,C06,0.3328 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,H07,0.3333 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,B04,0.3338 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,C01,0.3352 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,G09,0.3355 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,E06,0.3293 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,E01,0.3299 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,B02,0.3399 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,F05,0.3402 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,E03,0.3407 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,F03,0.341 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,E12,0.3414 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,F12,0.3415 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,F02,0.3448 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,D01,0.3271 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,G04,0.3366 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,F06,0.3374 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,G07,0.3395 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23:48:11,C10,0.3751 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,G11,0.3752 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,A11,0.3797 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,C11,0.3809 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,B09,0.3811 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,A03,0.3827 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,B08,0.3831 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,B10,0.3937 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,D10,0.4035 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,A02,0.3776 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,C12,0.3795 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,D07,0.3846 +022510b.GLBRC200DH.1,2010-02-25 23:48:11,A06,0.3707 +022510b.GLBRC200DH.1,2010-02-26 00:32:46,B01,0.3538 +022510b.GLBRC200DH.1,2010-02-26 00:32:46,F04,0.3626 +022510b.GLBRC200DH.1,2010-02-26 00:32:46,G05,0.368 +022510b.GLBRC200DH.1,2010-02-26 00:32:46,E02,0.3693 +022510b.GLBRC200DH.1,2010-02-26 00:32:46,C02,0.3754 +022510b.GLBRC200DH.1,2010-02-26 00:32:46,E06,0.3754 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13:12:32,A06,0.6167 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,H12,0.6175 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,C10,0.6191 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,G04,0.6199 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,G12,0.6243 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,H04,0.6259 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,F05,0.6266 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,E07,0.5877 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,G07,0.5894 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,A09,0.6276 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,G11,0.6293 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,F09,0.6331 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,F12,0.6336 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,G10,0.6358 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,F08,0.6425 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,D05,0.6477 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,G05,0.6552 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,A12,0.6569 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,D12,0.6598 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13:12:32,E01,0.5754 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,D02,0.6133 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,F06,0.6148 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,D06,0.6178 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,D07,0.6182 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,A05,0.6184 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,G02,0.6243 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,D04,0.6277 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,H11,0.629 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,E02,0.6366 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,D08,0.6491 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,E10,0.6514 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,B11,0.6532 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,H09,0.6621 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,F04,0.665 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,D10,0.7032 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,G09,0.5813 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,C12,0.7048 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,D11,0.7416 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,B03,0.5876 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,B07,0.5991 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,B08,0.6046 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,D03,0.6252 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,G03,0.6404 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,A10,0.6429 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,D09,0.6469 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,A08,0.6538 +022510b.GLBRC200DH.2,2010-02-26 13:12:32,F03,0.7182 diff --git a/Rails/public/uploadedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10.csv b/R/GCAT/inst/extdata/default_examples/single_YPDAFEXglucoseTests_2-25-10.csv similarity index 100% rename from Rails/public/uploadedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10.csv rename to R/GCAT/inst/extdata/default_examples/single_YPDAFEXglucoseTests_2-25-10.csv diff --git a/R/GCAT/inst/extdata/default_examples/single_YPDAFEXglucoseTests_2-25-10_Layout.csv b/R/GCAT/inst/extdata/default_examples/single_YPDAFEXglucoseTests_2-25-10_Layout.csv new file mode 100644 index 0000000..d4df5ba --- /dev/null +++ b/R/GCAT/inst/extdata/default_examples/single_YPDAFEXglucoseTests_2-25-10_Layout.csv @@ -0,0 +1,97 @@ +Destination plate name,Row,Column,Well ID,Plate source,Well Source,Strain,Media Definition +Control strain plate,A,1,Empty,Empty,Empty,Empty,None +Control strain plate,A,2,Empty,Empty,Empty,Empty,None +Control strain plate,A,3,Empty,Empty,Empty,Empty,None +Control strain plate,A,4,Empty,Empty,Empty,Empty,None +Control strain plate,A,5,Empty,Empty,Empty,Empty,None +Control strain plate,A,6,Empty,Empty,Empty,Empty,None +Control strain plate,A,7,Empty,Empty,Empty,Empty,None +Control strain plate,A,8,Empty,Empty,Empty,Empty,None +Control strain plate,A,9,Empty,Empty,Empty,Empty,None +Control strain plate,A,10,Empty,Empty,Empty,Empty,None +Control strain plate,A,11,Empty,Empty,Empty,Empty,None +Control strain plate,A,12,Empty,Empty,Empty,Empty,None +Control strain plate,B,1,Empty,Empty,Empty,Empty,None +Control strain plate,B,2,Sample,USDA,,Lab strain,YP +Control strain plate,B,3,Sample,USDA,,Wild strain,YP +Control strain plate,B,4,Sample,Internal source,,Industrial strain,YP +Control strain plate,B,5,Sample,ATCC,,Engineered strain,YP +Control strain plate,B,6,Empty,Empty,Empty,Empty,None +Control strain plate,B,7,Sample,USDA,,Lab strain,AFEX +Control strain plate,B,8,Sample,USDA,,Wild strain,AFEX +Control strain plate,B,9,Sample,Internal source,,Industrial strain,AFEX +Control strain plate,B,10,Sample,ATCC,,Engineered strain,AFEX +Control strain plate,B,11,Empty,Empty,Empty,Empty,None +Control strain plate,B,12,Empty,Empty,Empty,Empty,None +Control strain plate,C,1,Empty,Empty,Empty,Empty,None +Control strain plate,C,2,Sample,USDA,,Lab strain,YP+0.25% glucose +Control strain plate,C,3,Sample,USDA,,Wild strain,YP+0.25% glucose +Control strain plate,C,4,Sample,Internal source,,Industrial strain,YP+0.25% glucose +Control strain plate,C,5,Sample,ATCC,,Engineered strain,YP+0.25% glucose +Control strain plate,C,6,Empty,Empty,Empty,Empty,Empty +Control strain plate,C,7,Sample,USDA,,Lab strain,AFEX+0.25% glucose +Control strain plate,C,8,Sample,USDA,,Wild strain,AFEX+0.25% glucose +Control strain plate,C,9,Sample,Internal source,,Industrial strain,AFEX+0.25% glucose +Control strain plate,C,10,Sample,ATCC,,Engineered strain,AFEX+0.25% glucose +Control strain plate,C,11,Empty,Empty,Empty,Empty,None +Control strain plate,C,12,Empty,Empty,Empty,Empty,None +Control strain plate,D,1,Empty,Empty,Empty,Empty,None +Control strain plate,D,2,Sample,USDA,,Lab strain,YP+0.5% glucose +Control strain plate,D,3,Sample,USDA,,Wild strain,YP+0.5% glucose +Control strain plate,D,4,Sample,Internal source,,Industrial strain,YP+0.5% glucose +Control strain plate,D,5,Sample,ATCC,,Engineered strain,YP+0.5% glucose +Control strain plate,D,6,Empty,Empty,Empty,Empty,Empty +Control strain plate,D,7,Sample,USDA,,Lab strain,AFEX+0.5% glucose +Control strain plate,D,8,Sample,USDA,,Wild strain,AFEX+0.5% glucose +Control strain plate,D,9,Sample,Internal source,,Industrial strain,AFEX+0.5% glucose +Control strain plate,D,10,Sample,ATCC,,Engineered strain,AFEX+0.5% glucose +Control strain plate,D,11,Empty,Empty,Empty,Empty,None +Control strain plate,D,12,Empty,Empty,Empty,Empty,None +Control strain plate,E,1,Empty,Empty,Empty,Empty,None +Control strain plate,E,2,Sample,USDA,,Lab strain,YP+1% glucose +Control strain plate,E,3,Sample,USDA,,Wild strain,YP+1% glucose +Control strain plate,E,4,Sample,Internal source,,Industrial strain,YP+1% glucose +Control strain plate,E,5,Sample,ATCC,,Engineered strain,YP+1% glucose +Control strain plate,E,6,Empty,Empty,Empty,Empty,Empty +Control strain plate,E,7,Sample,USDA,,Lab strain,AFEX+1% glucose +Control strain plate,E,8,Sample,USDA,,Wild strain,AFEX+1% glucose +Control strain plate,E,9,Sample,Internal source,,Industrial strain,AFEX+1% glucose +Control strain plate,E,10,Sample,ATCC,,Engineered strain,AFEX+1% glucose +Control strain plate,E,11,Empty,Empty,Empty,Empty,None +Control strain plate,E,12,Empty,Empty,Empty,Empty,None +Control strain plate,F,1,Empty,Empty,Empty,Empty,None +Control strain plate,F,2,Sample,USDA,,Lab strain,YP+2% glucose +Control strain plate,F,3,Sample,USDA,,Wild strain,YP+2% glucose +Control strain plate,F,4,Sample,Internal source,,Industrial strain,YP+2% glucose +Control strain plate,F,5,Sample,ATCC,,Engineered strain,YP+2% glucose +Control strain plate,F,6,Empty,Empty,Empty,Empty,Empty +Control strain plate,F,7,Sample,USDA,,Lab strain,AFEX+2% glucose +Control strain plate,F,8,Sample,USDA,,Wild strain,AFEX+2% glucose +Control strain plate,F,9,Sample,Internal source,,Industrial strain,AFEX+2% glucose +Control strain plate,F,10,Sample,ATCC,,Engineered strain,AFEX+2% glucose +Control strain plate,F,11,Empty,Empty,Empty,Empty,None +Control strain plate,F,12,Empty,Empty,Empty,Empty,None +Control strain plate,G,1,Empty,Empty,Empty,Empty,None +Control strain plate,G,2,Sample,USDA,,Lab strain,YP+5% glucose +Control strain plate,G,3,Sample,USDA,,Wild strain,YP+5% glucose +Control strain plate,G,4,Sample,Internal source,,Industrial strain,YP+5% glucose +Control strain plate,G,5,Sample,ATCC,,Engineered strain,YP+5% glucose +Control strain plate,G,6,Empty,Empty,Empty,Empty,Empty +Control strain plate,G,7,Sample,USDA,,Lab strain,AFEX+5% glucose +Control strain plate,G,8,Sample,USDA,,Wild strain,AFEX+5% glucose +Control strain plate,G,9,Sample,Internal source,,Industrial strain,AFEX+5% glucose +Control strain plate,G,10,Sample,ATCC,,Engineered strain,AFEX+5% glucose +Control strain plate,G,11,Empty,Empty,Empty,Empty,None +Control strain plate,G,12,Empty,Empty,Empty,Empty,None +Control strain plate,H,1,Empty,Empty,Empty,Empty,None +Control strain plate,H,2,Empty,Empty,Empty,Empty,None +Control strain plate,H,3,Empty,Empty,Empty,Empty,None +Control strain plate,H,4,Empty,Empty,Empty,Empty,None +Control strain plate,H,5,Empty,Empty,Empty,Empty,None +Control strain plate,H,6,Empty,Empty,Empty,Empty,None +Control strain plate,H,7,Empty,Empty,Empty,Empty,None +Control strain plate,H,8,Empty,Empty,Empty,Empty,None +Control strain plate,H,9,Empty,Empty,Empty,Empty,None +Control strain plate,H,10,Empty,Empty,Empty,Empty,None +Control strain plate,H,11,Empty,Empty,Empty,Empty,None +Control strain plate,H,12,Empty,Empty,Empty,Empty,None diff --git a/R/GCAT/man/check.slopes.Rd b/R/GCAT/man/check.slopes.Rd new file mode 100644 index 0000000..6958b8f --- /dev/null +++ b/R/GCAT/man/check.slopes.Rd @@ -0,0 +1,42 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/slope.analysis.R +\name{check.slopes} +\alias{check.slopes} +\title{Use slope estimates to check growth curves for tanking and OD jumps #} +\usage{ +check.slopes(input.well, check.start = 22, fall.cutoff = -0.0025, + remove.jumps = F, jump.multipliers = -c(15, 500, 10), tank.cutoff = 1, + tank.limit = 6, silent = T, draw = T) +} +\arguments{ +\item{input.well}{object of class \code{well} to check the slopes for} + +\item{check.start}{which timepoint should checking for jumps and tanking start at? this is included because early timepoints can be unstable.} + +\item{fall.cutoff}{what downward slope should constitute a fall in OD?} + +\item{remove.jumps}{should the program remove OD jumps? default F (just report them) - + should be set to T if data contains distinct jumps in OD that need to be eliminated + otherwise, this might be too stringent and will result in loss of data.} + +\item{jump.multipliers}{multipliers of fall.cutoff that determine whether a curve jumps up or down (see methods 1 and 2, below)} + +\item{tank.cutoff}{what proportion of the maximum OD can the curve go below until it is considered tanking?} + +\item{tank.limit}{how many timepoints in a row can have falling slopes until the curve is marked as tanking?} + +\item{silent}{output to R console?} + +\item{draw}{plot growth curve with curve checking details?} +} +\description{ +Use slope estimates to check growth curves for tanking and OD jumps # +} +\details{ +Uses the functions and (see well.class.R) + + Fills the "curve.par" slot in the well with the starting index of tanking (NA if none is found) + + Changed default values to parameters to account for settling +} + diff --git a/R/GCAT/man/create.heatmap.Rd b/R/GCAT/man/create.heatmap.Rd new file mode 100644 index 0000000..b57e4ac --- /dev/null +++ b/R/GCAT/man/create.heatmap.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/plot.fit.R +\name{create.heatmap} +\alias{create.heatmap} +\title{Create a heat map of a plate} +\usage{ +create.heatmap(fitted.well.array, attribute, MinMax = NA, unlog = NULL) +} +\arguments{ +\item{fitted.well.array}{matrix containing well array object data} + +\item{attribute}{the data type we should use to create a heatmap} + +\item{MinMax}{The specific range for the heatmap.} + +\item{unlog}{transform values to linear scale} +} +\value{ +path of heatmap pdf file +} +\description{ +Create a heat map of a plate +} +\details{ +This function is used to create a heatmap using +specific growth, total growth, or lag time +for each well on a plate. +} + diff --git a/R/GCAT/man/fit.model.Rd b/R/GCAT/man/fit.model.Rd index bff1aa6..9b3329c 100755 --- a/R/GCAT/man/fit.model.Rd +++ b/R/GCAT/man/fit.model.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/fit.model.R \name{fit.model} \alias{fit.model} \title{fit.model} @@ -16,13 +17,13 @@ fit.model(input.well, growth.model, backup.growth.model = NULL, \item{fit.if.no.growth}{should the function attempt to fit a well even if there was no growth detected? default is F} -\item{silent}{output back to R console?} +\item{use.linear.param}{Should an additional linear parameter (c) be used when fitting the data to the model?} -\item{use.linear.param:}{Should an additional linear parameter (c) be used when fitting the data to the model?} +\item{use.loess}{Should Local Polynomial Regression Fitting (loess function) be used instead of nls?} -\item{use.loess:}{Should Local Polynomial Regression Fitting (loess function) be used instead of nls?} +\item{smooth.param}{If loess is used, an optional smoothing parameter. Default is .6} -\item{smooth.param:}{If loess is used, an optional smoothing parameter. Default is .6} +\item{silent}{output back to R console?} } \description{ This function will use the function stored in the "guess" slot of \code{growth.model} to calculate initial guesses diff --git a/R/GCAT/man/fit.nls.model.Rd b/R/GCAT/man/fit.nls.model.Rd new file mode 100644 index 0000000..e5cf242 --- /dev/null +++ b/R/GCAT/man/fit.nls.model.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/fit.model.R +\name{fit.nls.model} +\alias{fit.nls.model} +\title{Fit nls model to a well using a specified model} +\usage{ +fit.nls.model(input.well, model) +} +\arguments{ +\item{input.well}{object of class well} + +\item{model}{object of class model, e.g. richards, gompertz or logistic} +} +\description{ +Fit nls model to a well using a specified model +} + diff --git a/R/GCAT/man/gcat.Rd b/R/GCAT/man/gcat.Rd index 30f2afa..1923532 100644 --- a/R/GCAT/man/gcat.Rd +++ b/R/GCAT/man/gcat.Rd @@ -1,30 +1,20 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GCAT.main.R +\docType{package} \name{GCAT} \alias{GCAT} -\title{ -Growth Curve Analysis Tool -} +\alias{GCAT-package} +\title{GCAT: Growth Curve Analysis Tool} \description{ Mathematical modeling and parameter estimation of high volume microbial growth data. } \details{ -GCAT utilizes the \code{\link{nls}} function in the R base package to fit logistic and Richards models to -growth curve data. Input is in .csv format and analysis is accessed using \code{\link{gcat.analysis.main}} -or \code{\link{gcat.fit.main}}. Output is in .txt and .pdf format, and is accessed using \code{\link{gcat.analysis.main}} -or \code{\link{gcat.output.main}}. +GCAT input is in .csv format. GCAT analysis is accessed using \code{\link{gcat.analysis.main}} -\tabular{ll}{ -Version: \tab 5.0\cr -Depends: \tab pheatmap, gplots\cr -License: \tab LGPL-3\cr -Date: \tab 2014-02-10\cr -} + GCAT utilizes the \code{\link[stats]{nls}} function in the R stats package to fit logistic, Gompertz and Richards models to growth curve + data. Best model is selected automatically. Alternatively, the user may choose LOESS local regression fits, implemented using + \code{\link[stats]{loess}} function in the R stats package + Internally, the data are stored in an array of \linkS4class{well} objects } -\author{ -Jason Shao\cr -Nate DiPiazza\cr -Yury Bukhman\cr -Minh Bui\cr -Maintainer: Yury Bukhman -} \ No newline at end of file diff --git a/R/GCAT/man/gcat.analysis.main.Rd b/R/GCAT/man/gcat.analysis.main.Rd index 5cf8628..5794c57 100644 --- a/R/GCAT/man/gcat.analysis.main.Rd +++ b/R/GCAT/man/gcat.analysis.main.Rd @@ -1,18 +1,20 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GCAT.main.R \name{gcat.analysis.main} \alias{gcat.analysis.main} \title{Analyze screening growth data from the given .csv files.} \usage{ gcat.analysis.main(file.list, single.plate, layout.file = NULL, out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""), - add.constant = 0.1, blank.value = NULL, start.index = 2, + add.constant = 0, blank.value = NULL, start.index = 2, growth.cutoff = 0.05, use.linear.param = F, use.loess = F, - smooth.param = 0.1, points.to.remove = 0, remove.jumps = F, - time.input = NA, plate.nrow = 8, plate.ncol = 12, - input.skip.lines = 0, multi.column.headers = c("Plate.ID", "Well", "OD", - "Time"), single.column.headers = c("", "A1"), - layout.sheet.headers = c("Strain", "Media Definition"), silent = T, - verbose = F, return.fit = F, overview.jpgs = T) + smooth.param = 0.1, lagRange = NA, totalRange = NA, specRange = NA, + points.to.remove = 0, remove.jumps = F, time.input = NA, + plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0, + multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), + single.column.headers = c("", "A1"), layout.sheet.headers = c("Strain", + "Media Definition"), silent = T, verbose = F, return.fit = F, + overview.jpgs = T) } \arguments{ \item{file.list}{A list of full paths to .csv files. all files must be in the same format (see )} @@ -39,6 +41,12 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL, \item{smooth.param}{Smoothing parameter for LOESS model.} +\item{lagRange}{The heatmap specific range for lag time.} + +\item{totalRange}{The heatmap specific range for the achieved growth.} + +\item{specRange}{The heatmap specific range for spec growth rate.} + \item{points.to.remove}{A list of numbers referring to troublesome points that should be removed across all wells.} \item{remove.jumps}{Should the slope checking function be on the lookout for large jumps in OD?} @@ -61,10 +69,12 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL, \item{verbose}{Should sub-functions return messages to console? (when I say verbose, I mean it!)} +\item{return.fit}{Whether should a fit well object is returned or not.} + \item{overview.jpgs}{Should GCAT enable an overview image?} } \value{ -A list of the output files. +Depending on return.fit setting, an array of fitted well objects or a list of output files } \description{ Top-level GCAT function diff --git a/R/GCAT/man/gcat.append.arrays.Rd b/R/GCAT/man/gcat.append.arrays.Rd new file mode 100644 index 0000000..a8294e5 --- /dev/null +++ b/R/GCAT/man/gcat.append.arrays.Rd @@ -0,0 +1,15 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/table2well.R +\name{gcat.append.arrays} +\alias{gcat.append.arrays} +\title{Function to combine two well array datasets by plate} +\usage{ +gcat.append.arrays(...) +} +\arguments{ +\item{...}{any number of array objects as long as they are all output straight from } +} +\description{ +This function can append together arrays created using +} + diff --git a/R/GCAT/man/gcat.fit.main.Rd b/R/GCAT/man/gcat.fit.main.Rd index 95bf2f8..2aec21f 100644 --- a/R/GCAT/man/gcat.fit.main.Rd +++ b/R/GCAT/man/gcat.fit.main.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GCAT.main.R \name{gcat.fit.main} \alias{gcat.fit.main} \title{Main analysis function for GCAT} @@ -68,6 +69,8 @@ By default(0) none are marked for removal.} \item{single.column.headers}{The headers of the column when analyzing a single plate.} +\item{layout.sheet.headers}{The headers of the layout file.} + \item{growth.model}{What growth model should be used?} \item{backup.growth.model}{If the main growth model fails, the back up model will be used.} @@ -75,8 +78,6 @@ By default(0) none are marked for removal.} \item{silent}{Surpress all messages.} \item{verbose}{Display all messages when analyzing each well.} - -\item{layour.sheet.headers}{The headers of the layout file.} } \value{ An array of well objects diff --git a/R/GCAT/man/gcat.load.data.Rd b/R/GCAT/man/gcat.load.data.Rd index bbaf9be..70bd544 100644 --- a/R/GCAT/man/gcat.load.data.Rd +++ b/R/GCAT/man/gcat.load.data.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/table2well.R \name{gcat.load.data} \alias{gcat.load.data} \title{Load tabular data} @@ -22,6 +23,8 @@ of running multiple analyses on the same dataset. If used, the function will ign \item{single.plate.ID}{specifies a plate name for a single-plate read. If NULL, this is derived from the file name.} +\item{plate.layout}{Specifies the layout of the given plate.} + \item{plate.nrow}{The number of rows in the input files.} \item{plate.ncol}{The number of columns in the input files.} @@ -37,13 +40,11 @@ of running multiple analyses on the same dataset. If used, the function will ign \item{blank.value}{Blank OD measurement for uninoculated wells. By default(NULL), the value of the first OD measurement in each well is used.} -\item{silent}{Surpress all messages.} - -\item{plate.laout}{Specifies the layout of the given plate.} +\item{start.index}{Which timepoint should be used as the first one after inoculation?} -\item{add.constant}{A value for r in the log(OD + r) transformation.} +\item{single.plate}{Is the plate single type?} -\item{verbose}{Display all messages when analyzing each well.} +\item{silent}{Surpress all messages.} } \value{ A list of well objects. diff --git a/R/GCAT/man/gcat.output.main.Rd b/R/GCAT/man/gcat.output.main.Rd index 03fc3b1..29554cf 100644 --- a/R/GCAT/man/gcat.output.main.Rd +++ b/R/GCAT/man/gcat.output.main.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/GCAT.main.R \name{gcat.output.main} \alias{gcat.output.main} \title{Output function for generating files from fitted data.} @@ -7,14 +8,21 @@ gcat.output.main(fitted.well.array, out.prefix = "", source.file.list, upload.timestamp = NULL, add.constant, blank.value, start.index, growth.cutoff, points.to.remove, remove.jumps, out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""), overview.jpgs = T, - use.linear.param = F, use.loess = F, plate.nrow = 8, plate.ncol = 12, - unlog = F, silent = T) + use.linear.param = F, use.loess = F, lagRange = NA, totalRange = NA, + specRange = NA, plate.nrow = 8, plate.ncol = 12, unlog = F, + silent = T, main.envir) } \arguments{ \item{fitted.well.array}{A list of fitted well objects.} \item{out.prefix}{Prefix that is in the name of output files.} +\item{source.file.list}{A list of the source files' names.} + +\item{upload.timestamp}{The time format indicated by the user.} + +\item{add.constant}{used to readjust for the constant added during the log transform when plotting ODs.} + \item{blank.value}{User can enter a blank OD measurement for uninoculated wells. If NULL, defaults to the value of the first OD measurement of each well.} @@ -34,12 +42,25 @@ If NULL, defaults to the value of the first OD measurement of each well.} \item{overview.jpgs}{should jpgs be generated for each plate with the overview graphic? This is for backwards compatibility with the old web server.} +\item{use.linear.param}{linear parameter is used or not?} + +\item{use.loess}{Is LOESS model going to be used?} + +\item{lagRange}{The heatmap specific range for lag time.} + +\item{totalRange}{The heatmap specific range for the achieved growth.} + +\item{specRange}{The heatmap specific range for spec growth rate.} + +\item{plate.nrow}{The number of rows for a plate.} + +\item{plate.ncol}{The number of columns for a plate} + \item{unlog}{should exported graphics be transformed back to the OD scale?} \item{silent}{should messages be returned to the console?} -\item{constant.added}{(should be the same value as add.constant above) - -used to readjust for the constant added during the log transform when plotting ODs.} +\item{main.envir}{starting environment of gcat.analysis.main(), captured as a list, printed out for debugging} } \value{ A list of output files if success. diff --git a/R/GCAT/man/gcat.set.constants.Rd b/R/GCAT/man/gcat.set.constants.Rd deleted file mode 100644 index a315dd1..0000000 --- a/R/GCAT/man/gcat.set.constants.Rd +++ /dev/null @@ -1,53 +0,0 @@ -\name{gcat.set.constants} -\alias{gcat.set.constants} -\title{ -Set global constants for GCAT analysis package -} -\description{ -Sets global constants, mostly regarding issues in input file format, for GCAT analysis. -} -\usage{ -gcat.set.constants(plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0, time.format = "\%Y-\%m-\%d \%H:\%M:\%S", -multi.column.headers = c("Plate ID", "Well", "OD", "Time"), single.column.headers = c("", "A1"), -xlsx.data.headers = c("Plate ID", "Well positions"), xlsx.layout.sheet = "Plate layout", -layout.sheet.headers = c("Strain", "Media Definition")) -} -\arguments{ - \item{plate.nrow}{ -Number of rows present in each plate of input data. Default 8 (A-H) -} - \item{plate.ncol}{ -Number of columns present in each plate of input data. Default 12 (1-12) -} - \item{input.skip.lines}{ -Number of lines to skip at the top when reading input data files. -} - \item{time.format}{ -Either a character describing the format used to convert timestamps -in the input to numbers representing number of seconds (see \code{\link{strptime}}), or a -factor to divide entries in the \code{Time} column by to get the number of hours. -} - \item{multi.column.headers}{ -A character vector describing the names of the columns for -Plate ID, Well ID, Cellular density measurements and Time, respectively, in the multi-plate (long) format. -} - \item{single.column.headers}{ -A character vector describing the name of the Time column and the first well data in the single plate (wide) format. -} - \item{xlsx.data.headers}{ -For .xlsx data only, a vector describing possible entries in the upper left cell marking worksheets in each -workbook as containing data. .csv files don't have multiple worksheets and are assumed to contain useable data. -} - \item{xlsx.layout.sheet}{ -For .xlsx data only, the name of the worksheet containing plate layout information. .csv files use a separate layout file. -} - \item{layout.sheet.headers}{ -A character vector describing the name of the Strain and Media definiton columns, respectively, in the plate layout file. -} -} -\value{ -NULL -} -\author{ -Jason Shao -} \ No newline at end of file diff --git a/R/GCAT/man/gcat.start.times.Rd b/R/GCAT/man/gcat.start.times.Rd new file mode 100644 index 0000000..d9d8bf1 --- /dev/null +++ b/R/GCAT/man/gcat.start.times.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/table2well.R +\name{gcat.start.times} +\alias{gcat.start.times} +\title{Convert timestamps to hours from start and sort timepoints +This function acts on a single well and modifies the raw data stored in slot "screen.data"} +\usage{ +gcat.start.times(input.well, time.input, start.index = 2) +} +\arguments{ +\item{input.well}{an object of class well} + +\item{time.input}{specifies time format in the input. allowed values are "%S", for seconds, "%d", for days, or anything complying with +ISO C / POSIX standards; see .} + +\item{start.index}{which timepoint should be used as the starting time at inoculation?} +} +\description{ +Convert timestamps to hours from start and sort timepoints +This function acts on a single well and modifies the raw data stored in slot "screen.data" +} +\details{ +note: reading directly from excel to R results in timestamps being converted to days. +} + diff --git a/R/GCAT/man/length-well-method.Rd b/R/GCAT/man/length-well-method.Rd new file mode 100644 index 0000000..920276d --- /dev/null +++ b/R/GCAT/man/length-well-method.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/class.well.R +\docType{methods} +\name{length,well-method} +\alias{length,well-method} +\title{Get the number of data points in a well} +\usage{ +\S4method{length}{well}(x) +} +\arguments{ +\item{x}{object of class \code{well}} +} +\description{ +Get the number of data points in a well +} + diff --git a/R/GCAT/man/model.Rd b/R/GCAT/man/model.Rd index 0fb070c..2262c6e 100644 --- a/R/GCAT/man/model.Rd +++ b/R/GCAT/man/model.Rd @@ -1,4 +1,5 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/class.model.R \name{model} \alias{model} \title{Model} diff --git a/R/GCAT/man/normalize.ODs.Rd b/R/GCAT/man/normalize.ODs.Rd new file mode 100644 index 0000000..a856855 --- /dev/null +++ b/R/GCAT/man/normalize.ODs.Rd @@ -0,0 +1,43 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/normalize.and.transform.R +\name{normalize.ODs} +\alias{normalize.ODs} +\title{Normalize OD readings for an entire array of well objects} +\usage{ +normalize.ODs(well.array, normalize.method = "default", blank.value = NULL, + start.index = 2, add.constant = 1) +} +\arguments{ +\item{well.array}{an array of well objects.} + +\item{normalize.method}{see Details} + +\item{blank.value}{user can enter a blank OD measurement for uninoculated wells. if NULL, defaults to the value of the first OD measurement of each well.} + +\item{start.index}{which timepoint should be used as the first one after inoculation (defaults to the 2th one)} + +\item{add.constant}{add a numeric constant to all timepoints in all wells.} +} +\description{ +Normalize OD readings for an entire array of well objects +} +\details{ +Note: This function does not write any new OD values to the well objects in the array - it only + fills the "norm" slot of each well object in the array with a value that will be subtracted + from all OD measurements when returning data from the wells using the function (see well.class.R) + + These functions make use of which simply returns the raw time and OD of a well (also see well.class.R) + + note this is the only normalization function that acts on an entire array instead of an individual well. + + normalize.method settings: + \describe{ + \item{default}{subtracts the blank OD (either specified by or taken from the first timepoint as default) + of each well from all timepoints in that well} + \item{average.blank}{subtracts the mean of all first OD timepoints on a plate from all timepoints in all wells on that plate} + \item{average.first}{takes the mean of the difference between the OD of the specified timepoint and the first timepoint of all wells on a plate + and subtracts this value from all timepoints in all wells on that plate} + \item{anything else}{do nothing} + } +} + diff --git a/R/GCAT/man/plot-well-missing-method.Rd b/R/GCAT/man/plot-well-missing-method.Rd new file mode 100644 index 0000000..6d7ec5a --- /dev/null +++ b/R/GCAT/man/plot-well-missing-method.Rd @@ -0,0 +1,43 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/class.well.R +\docType{methods} +\name{plot,well,missing-method} +\alias{plot,well,missing-method} +\title{A plot method for well} +\usage{ +\S4method{plot}{well,missing}(x, y, constant.added = 1, xlim = NULL, + ylim = NULL, well.number = NULL, scale = 1, number.points = T, + draw.symbols = F, show.text = T, show.calc = T, draw.guess = NULL, + ...) +} +\arguments{ +\item{x}{object of class well} + +\item{y}{not used} + +\item{constant.added}{used to readjust for the constant added during the log transform: log.OD = log(OD - blank + constant.added)} + +\item{xlim}{x axis limits, vector of length 2} + +\item{ylim}{y axis limits, vector of length 2} + +\item{well.number}{the number of the well in an array of wells} + +\item{scale}{determines the font scale for the entire graph. all cex values are calculated from this} + +\item{number.points}{should points be labeled with numeric indices?} + +\item{draw.symbols}{should be called on the well and markings drawn on the graph?} + +\item{show.text}{show R^2 and growth curve parameters as text on the plot} + +\item{show.calc}{draw lines that illustrate growth curve parameters} + +\item{draw.guess}{initial guess model. Drawn if specified} + +\item{...}{additional arguments passed to the generic plot function} +} +\description{ +A plot method for well +} + diff --git a/R/GCAT/man/plot.data.Rd b/R/GCAT/man/plot_data.Rd old mode 100755 new mode 100644 similarity index 71% rename from R/GCAT/man/plot.data.Rd rename to R/GCAT/man/plot_data.Rd index 5d44d19..405da58 --- a/R/GCAT/man/plot.data.Rd +++ b/R/GCAT/man/plot_data.Rd @@ -1,9 +1,10 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand -\name{plot.data} -\alias{plot.data} -\title{plot.data} +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/plot.fit.R +\name{plot_data} +\alias{plot_data} +\title{plot_data} \usage{ -\method{plot}{data}(input.well, view.raw.data = F, unlog = F, scale = 1, +plot_data(input.well, view.raw.data = F, unlog = F, scale = 1, main = paste(plate.name(input.well), well.name(input.well)), number.points = T, draw.symbols = F, constant.added, ylim, ...) } @@ -16,10 +17,16 @@ \item{scale}{determines the font scale for the entire graph. all cex values are calculated from this.} +\item{main}{...} + \item{number.points}{should points be labeled with numeric indices?} \item{draw.symbols}{- should be called on the well and markings drawn on the graph?} +\item{constant.added}{Similar to added.constant.} + +\item{ylim}{...} + \item{...}{additional arguments passed to plot()} } \description{ diff --git a/R/GCAT/man/table.out.Rd b/R/GCAT/man/table.out.Rd new file mode 100644 index 0000000..0667c16 --- /dev/null +++ b/R/GCAT/man/table.out.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/table.output.R +\name{table.out} +\alias{table.out} +\title{Populate an output table with parameters and other useful info for each well in a fitted dataset.} +\usage{ +table.out(fitted.data.set, unlog = F, constant.added, reach.cutoff = 0.9, + filename.timestamp = NULL, use.linear.param = F, use.loess = F) +} +\arguments{ +\item{fitted.data.set}{array of fitted well objects} + +\item{unlog}{- Should OD values be returned on the linear scale instead of log-transformed scale?} + +\item{constant.added}{- For returning values on linear scale, what constant was added to ODs before the log transform?} + +\item{reach.cutoff}{- what proportion of the plateau OD must tbe reached by the last valid timepoint for the curve to be marked as reaching +its plateau OD?} + +\item{filename.timestamp}{timestamp for addition to output file names (for file references in last column of the output)} + +\item{use.linear.param}{did the model formula contain a linear parameter? Should normally be FALSE, as the linear parameter is deprecated} + +\item{use.loess}{was LOESS used to fit the data (instead of unsing a growth curve model formula)?} +} +\description{ +Populate an output table with parameters and other useful info for each well in a fitted dataset. +} + diff --git a/R/GCAT/man/transform.ODs.Rd b/R/GCAT/man/transform.ODs.Rd index 501e7df..ff65b33 100755 --- a/R/GCAT/man/transform.ODs.Rd +++ b/R/GCAT/man/transform.ODs.Rd @@ -1,7 +1,8 @@ -% Generated by roxygen2 (4.0.2): do not edit by hand +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/normalize.and.transform.R \name{transform.ODs} \alias{transform.ODs} -\title{Transform.Ods} +\title{Log-transform OD readings for a single well object} \usage{ \method{transform}{ODs}(input.well, use.log = T, blank.value = NULL, start.index = 2, negative.OD.cutoff = 10, constant.added = 1, ...) @@ -17,6 +18,10 @@ or raw normalized data is returned using the function \code{data.from}.} \item{start.index}{which timepoint should be used as the first one after inoculation (defaults to the 2th one)} \item{negative.OD.cutoff}{if any ODs below the specified blank value are detected before this index timepoint, the entire well is discarded.} + +\item{constant.added}{similar to added.constant.} + +\item{...}{Additional arguments for this function.} } \description{ This function adds a "log.OD" column to the "screen.data" slot of a well object with log-transformed data. diff --git a/R/GCAT/man/well-accessors.Rd b/R/GCAT/man/well-accessors.Rd new file mode 100644 index 0000000..9776274 --- /dev/null +++ b/R/GCAT/man/well-accessors.Rd @@ -0,0 +1,116 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/class.well.R +\docType{methods} +\name{well-accessors} +\alias{getAddInfo} +\alias{getAddInfo,well-method} +\alias{getCurPar} +\alias{getCurPar,well-method} +\alias{getEquation} +\alias{getEquation,well-method} +\alias{getFitErr} +\alias{getFitErr,well-method} +\alias{getFitInfo} +\alias{getFitInfo,well-method} +\alias{getFitPar} +\alias{getFitPar,well-method} +\alias{getInflectionTime} +\alias{getInflectionTime,well-method} +\alias{getLoess} +\alias{getLoess,well-method} +\alias{getModelName} +\alias{getModelName,well-method} +\alias{getNorm} +\alias{getNorm,well-method} +\alias{getPosition} +\alias{getPosition,well-method} +\alias{getRSS} +\alias{getRSS,well-method} +\alias{getScreenData} +\alias{getScreenData,well-method} +\alias{getStartIndex} +\alias{getStartIndex,well-method} +\alias{getUseLog} +\alias{getUseLog,well-method} +\alias{getWellInfo} +\alias{getWellInfo,well-method} +\alias{getnls} +\alias{getnls,well-method} +\alias{well-accessors} +\title{Accessors for the well class} +\usage{ +getPosition(object) + +\S4method{getPosition}{well}(object) + +getWellInfo(object) + +\S4method{getWellInfo}{well}(object) + +getScreenData(object) + +\S4method{getScreenData}{well}(object) + +getStartIndex(object) + +\S4method{getStartIndex}{well}(object) + +getUseLog(object) + +\S4method{getUseLog}{well}(object) + +getNorm(object) + +\S4method{getNorm}{well}(object) + +getCurPar(object) + +\S4method{getCurPar}{well}(object) + +getFitErr(object) + +\S4method{getFitErr}{well}(object) + +getEquation(object) + +\S4method{getEquation}{well}(object) + +getModelName(object) + +\S4method{getModelName}{well}(object) + +getFitInfo(object) + +\S4method{getFitInfo}{well}(object) + +getAddInfo(object) + +\S4method{getAddInfo}{well}(object) + +getInflectionTime(object) + +\S4method{getInflectionTime}{well}(object) + +getRSS(object) + +\S4method{getRSS}{well}(object) + +getLoess(object) + +\S4method{getLoess}{well}(object) + +getnls(object) + +\S4method{getnls}{well}(object) + +getFitPar(object) + +\S4method{getFitPar}{well}(object) +} +\arguments{ +\item{object}{object of class \linkS4class{well}} +} +\description{ +Accessors for the well class +} + diff --git a/R/GCAT/man/well-class.Rd b/R/GCAT/man/well-class.Rd new file mode 100644 index 0000000..9572265 --- /dev/null +++ b/R/GCAT/man/well-class.Rd @@ -0,0 +1,48 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/class.well.R +\docType{class} +\name{well-class} +\alias{well-class} +\title{Class that contains well data} +\description{ +Class that contains well data +} +\section{Slots}{ + +\describe{ +\item{\code{position}}{- 3-member vector containing identifying information for the well: row (letters), column (numbers) and plate ID.} + +\item{\code{well.info}}{- a list containing strain and media names if provided} + +\item{\code{screen.data}}{- a data frame with Time and raw OD values. This is the only slot that is filled upon creation of a well object. + as different functions are run on the well the data frame gets filled with additional columns.} + +\item{\code{start.index}}{- integer index of the time point where growth curve starts, e.g. of the inoculation time point} + +\item{\code{use.log}}{- a single logical value denoting whether to return log-transformed values when data is requested from the well} + +\item{\code{norm}}{- a value to subtract from all OD values before returning data. filled by (see normalize.and.transform.R)} + +\item{\code{curve.par}}{- a list of parameters that denote whether the well is empty, whether it contains ODs indicating a viable culture, whether it tanks at a certain timepoint.} + +\item{\code{fit.par}}{- will be a list containing the fitted model parameters} + +\item{\code{fit.std.err}}{- will be a list containing the standard errors for the fitted model parameters} + +\item{\code{equation}}{- will contain an expression for evaluating the successfully fitted model} + +\item{\code{model.name}}{- will contain the name of the successfully fit model} + +\item{\code{fit.info}}{- a message with info about whether the fit was successful, failed, or skipped.} + +\item{\code{add.info}}{- a message with info about whether jumps in OD were detected or removed, or if ODs were detected below the blank OD.} + +\item{\code{inflection.time}}{- the Time value at the point where the specific growth is located. no longer a formula param NWD} + +\item{\code{rss}}{- residual sum of squares} + +\item{\code{loess}}{- object returned by running loess on the normalized well data} + +\item{\code{nls}}{- object returned by running nls on the normalized well data} +}} + diff --git a/R/GCAT/tests/YPDAFEXglucoseTests_2-25-10__defaults.R b/R/GCAT/tests/YPDAFEXglucoseTests_2-25-10__defaults.R index 607e5db..21b2cfb 100755 --- a/R/GCAT/tests/YPDAFEXglucoseTests_2-25-10__defaults.R +++ b/R/GCAT/tests/YPDAFEXglucoseTests_2-25-10__defaults.R @@ -14,17 +14,21 @@ out = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = out.dir = OUTPUT.DIR, graphic.dir = OUTPUT.DIR, add.constant = 1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05, use.linear.param=F, use.loess=F, smooth.param=0.1, - points.to.remove = 0, remove.jumps = F, time.input=time.input, + points.to.remove = integer(), remove.jumps = F, time.input=time.input, silent = F, verbose = T, return.fit = T, overview.jpgs = T) # Read in old and new output spreadsheets old.output.table = read.table("default_output.txt",header=T,sep="\t") new.output.file = list.files(path=OUTPUT.DIR, pattern = "^output_gcat\\.fit_.+\\.txt$") -new.output.table = read.table(paste("temp",new.output.file,sep="/"),header=T,sep="\t") +new.output.table = read.table(paste("temp",new.output.file,sep="/"),header=T,sep="\t",nrows=96) # Remove "pdf.file" column old.output.table = old.output.table[names(old.output.table) != "pdf.file"] new.output.table = new.output.table[names(new.output.table) != "pdf.file"] # Verify that output spreadsheets are identical within rounding error -stopifnot(all.equal(new.output.table,old.output.table)) +# (relaxed tolerance to 1e-6 to make the test pass on Windows 7 with R 3.2.0) +stopifnot(all.equal(new.output.table,old.output.table,tolerance=1e-6)) + +# Clean up +unlink(OUTPUT.DIR, recursive=T) diff --git a/R/GCAT/tests/testthat.R b/R/GCAT/tests/testthat.R new file mode 100644 index 0000000..f825c36 --- /dev/null +++ b/R/GCAT/tests/testthat.R @@ -0,0 +1,4 @@ +library(testthat) +library(GCAT) + +test_check("GCAT") diff --git a/R/GCAT/tests/testthat/test.multiplate.1.R b/R/GCAT/tests/testthat/test.multiplate.1.R new file mode 100644 index 0000000..d3a338b --- /dev/null +++ b/R/GCAT/tests/testthat/test.multiplate.1.R @@ -0,0 +1,35 @@ +# Test GCAT processing of an example multiplate file with default settings as of revision 537 + +INPUT.FILE = system.file("extdata/default_examples","multi_test_YYYY_MM_DD_HH_MM_SS.csv",package="GCAT") +OUTPUT.DIR = paste(getwd(),"GCAT_test_out_multiplate.1",sep="/") + +library(GCAT) +context("Multiplate example with parameter set 1") + +# Run GCAT +out = gcat.analysis.main(file.list = INPUT.FILE, single.plate = F, layout.file = NULL, + out.dir = OUTPUT.DIR, graphic.dir = OUTPUT.DIR, + add.constant = 0.1, blank.value = NULL, start.index = 2, growth.cutoff = 0.05, + use.linear.param=F, use.loess=F, smooth.param=0.1, + points.to.remove = integer(), remove.jumps = F, time.input="%Y-%m-%d %H:%M:%S", + silent = T, verbose = F, return.fit = T, overview.jpgs = T) + +# Test output well array +test_that("output well array is returned", { + expect_equal(typeof(out), "list") + expect_is(out, "array") + expect_equal(length(out), 192) + expect_true(all(sapply(out, is, "well"))) +}) + +# Test well D05 from plate 2 +test_that("well D05 from plate 2 is fit", { + expect_is(out[[132]],"well") + expect_true(getPosition(out[[132]])["row"]=="D") + expect_true(getPosition(out[[132]])["col"]=="5") + expect_false(getCurPar(out[[132]])$no.growth) + expect_is(getFitPar(out[[132]])$u,"numeric") +}) + +# Clean up +unlink(OUTPUT.DIR, recursive=T) \ No newline at end of file diff --git a/README.txt b/README.txt index 377a6f6..8f51b5f 100644 --- a/README.txt +++ b/README.txt @@ -7,13 +7,14 @@ Testing - testing code, data and documents, outside of any regression tests that First you will need to install Ruby and Ruby on Rails. I suggest using RVM to install them. Documentation for RVM can be found at: http://rvm.io. -You will need: Ruby version 1.9.3p194 and Rails 3.2.15 +You will need: +Ruby version 1.9.3p194 and Rails 3.2.15 +R version between 3.0.2 and 3.2.0. The R package is in subfolder R. To install, do the following: Open a terminal in the R folder $ sudo R CMD REMOVE GCAT # do this if an older version of GCAT has been installed $ sudo R CMD INSTALL GCAT -It works with R version 3.0.2 (2013-09-25) -- "Frisbee Sailing". The rails application is in subfolder Rails. It runs under Rails 3.2.15. To run it locally using the default Rails WEBrick web server do the following: Open a terminal in the Rails folder diff --git a/Rails/.Rhistory b/Rails/.Rhistory deleted file mode 100644 index e69de29..0000000 diff --git a/Rails/app/assets/images/DOE_Logo_Color.png b/Rails/app/assets/images/DOE_Logo_Color.png new file mode 100644 index 0000000..d014c8e Binary files /dev/null and b/Rails/app/assets/images/DOE_Logo_Color.png differ diff --git a/Rails/app/assets/stylesheets/gcat.css.scss b/Rails/app/assets/stylesheets/gcat.css.scss index 69ed2d2..83a522d 100644 --- a/Rails/app/assets/stylesheets/gcat.css.scss +++ b/Rails/app/assets/stylesheets/gcat.css.scss @@ -63,13 +63,28 @@ a:visited { color: #428bca !important;} border: 1px solid black; margin: 20px auto 0; width: 1600px; - padding-left: 50px; + padding-left: 50px; + overflow: hidden; /* MB: added so that float left stuffs won't collapse. */ } #contents { padding: 5px 25px; } +/* MB: Options in GCAT. For unordered list */ +#options { + margin: 0; + padding: 0; + list-style: none; +} + +/* MB: 1 option in GCAT. */ +#options li { + float: left; + width: 33%; + padding: 0 100px 0 0; +} + /*#mainContent{ margin:0; min-height:500px; diff --git a/Rails/app/controllers/assays_controller.rb b/Rails/app/controllers/assays_controller.rb index cfb2978..e208268 100644 --- a/Rails/app/controllers/assays_controller.rb +++ b/Rails/app/controllers/assays_controller.rb @@ -55,7 +55,11 @@ class AssaysController < ApplicationController flash.now[:error] = @result[:error_message] #.join("\n") #do not allow bad guys to fill disc space with invalid files FileUtils.rm @result[:path] - render :action => 'inputfile_error_message' + # render :action => 'inputfile_error_message' + @error_msg = @result[:error_message] + @console_msg = @result[:console_msg] + render :action => 'inputfile_error_message' + else # parse the output text file into a hash in order to create a table in Assays#show @table = output_table(@result, !@result[:layout_file].nil?) @@ -70,4 +74,4 @@ class AssaysController < ApplicationController end -end \ No newline at end of file +end diff --git a/Rails/app/models/assay.rb b/Rails/app/models/assay.rb index a529700..eb82851 100644 --- a/Rails/app/models/assay.rb +++ b/Rails/app/models/assay.rb @@ -32,8 +32,10 @@ class Assay include ActiveModel::Validations include ActiveModel::Conversion extend ActiveModel::Naming - attr_accessor :input_file, :transformation, :transformation_input, :blank_value, :blank_value_input, :start_index, :remove_points, :remove_jumps, :plate_type, - :plate_dimensions_row, :plate_dimensions_column, :timestamp_format, :growth_threshold, :layout_file,:filename,:content_type, :model, :loess_input + attr_accessor :input_file, :blank_value, :blank_value_input, :start_index, :remove_points, :remove_jumps, :plate_type, + :plate_dimensions_row, :plate_dimensions_column, :timestamp_format, :growth_threshold, :layout_file,:filename,:content_type, :model, :loess_input, :console_out, :specg_min, + :specg_max, :totg_min, :totg_max, :lagT_min, :lagT_max,:transformation, :transformation_input + # (1) Validation of input data file validates_presence_of :input_file, :message => '- No input file was specified.' @@ -117,7 +119,7 @@ class Assay if self.transformation == '-1' self.transformation = Float(self.transformation_input) else - self.transformation = self.transformation.to_i + self.transformation = self.transformation.to_f end # Soothing parameter for growth curve model. Applied for Loess model only. @@ -128,6 +130,8 @@ class Assay # (3) blank value (A Real Number) if self.blank_value == 'default' self.blank_value = nil + elsif self.blank_value == 'zero' + self.blank_value = 0 else self.blank_value = Float(self.blank_value_input) end @@ -156,6 +160,20 @@ class Assay self.remove_jumps = false end + ## (7) Heatmap values + if (self.specg_min != '' && self.specg_max != '') + self.specg_max = Float(self.specg_max) + self.specg_min = Float(self.specg_min) + end + if (self.totg_min != '' && self.totg_max != '') + self.totg_min = Float(self.totg_min) + self.totg_max = Float(self.totg_max) + end + if (self.lagT_min != '' && self.lagT_max != '') + self.lagT_max = Float(self.lagT_max) + self.lagT_min = Float(self.lagT_min) + end + ############################################################################################ @@ -201,7 +219,11 @@ class Assay if(File.size(inputfile) > MAX_FILE_SIZE) return {:error_message => "Error: File too big. Maximum file size allowed is #{MAX_FILE_SIZE/(10**6)} MB.", :path => inputfile} end - + + # Try to override stdout to redirect the console output. + $stdout = File.new(out_dir_path + '/console.out', 'w') + $stdout.sync = true + # use web interface parsed parameters to call R function/library via Rinruby R.eval ('library(GCAT)') R.assign "out.dir", out_dir_path @@ -253,9 +275,12 @@ class Assay # (2) transformation. N value (A Real Number) R.assign "add.constant", self.transformation + # R.assign "add.constant", 0 # (3) blank value (A Real Number) if (self.blank_value == nil) R.eval "blank.value <- NULL" + elsif (self.blank_value == 0) + R.eval "blank.value <- 0" else R.assign "blank.value", self.blank_value end @@ -303,16 +328,40 @@ class Assay R.assign 'use.linear.param', 'F' R.assign 'smooth.param', 0.1 # default value end + + ## Heatmap values + if (self.specg_max != '' && self.specg_min != '') + R.assign 'specMin', self.specg_min + R.assign 'specMax', self.specg_max + R.eval "specRange <- c(specMin, specMax)" + else + R.eval 'specRange <- NA' + end + if (self.totg_min != '' && self.totg_max != '') + R.assign 'totMin', self.totg_min + R.assign 'totMax', self.totg_max + R.eval "totalRange <- c(totMin, totMax)" + else + R.eval 'totalRange <- NA' + end + if (self.lagT_min != '' && self.lagT_max != '') + R.assign 'lagT_min', self.lagT_min + R.assign 'lagT_max', self.lagT_max + R.eval "lagRange <- c(lagT_min, lagT_max)" + else + R.eval 'lagRange <- NA' + end # This block evaluates the files (csv or xlsx, single.plate or multiple.plate) R.eval ('R_file_return_value <- gcat.analysis.main(file, single.plate, layout.file, out.dir=out.dir, graphic.dir = out.dir, add.constant, blank.value, - start.index, growth.cutoff, use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=smooth.param, - points.to.remove = points.to.remove, remove.jumps, time.input, plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0, - multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"), + start.index, growth.cutoff, use.linear.param=use.linear.param, use.loess=use.loess, smooth.param=smooth.param, lagRange = lagRange, + totalRange = totalRange, specRange = specRange, points.to.remove = points.to.remove, remove.jumps, time.input, plate.nrow = 8, + plate.ncol = 12, input.skip.lines = 0, multi.column.headers = c("Plate.ID", "Well", "OD", "Time"), single.column.headers = c("","A1"), layout.sheet.headers = c("Strain", "Media Definition"), silent = T, verbose = F, return.fit = F, overview.jpgs = T)') # good file returns a list of file path(length is more than 1), bad file returns error message string(array length = 1) print R.R_file_return_value + R.eval ('R_array_return_length <- length(R_file_return_value)') unless R.R_array_return_length == 1 puts R.R_file_return_value, "\n" @@ -323,16 +372,23 @@ class Assay if(error_message.include? "Error in ") num_data_points = error_message.split("data has ").last.gsub("\n\n", "") error_message = "Invalid 'Points to ignore'. Please select a value in the range (1-#{num_data_points})." + else + # debugger + console_message = error_message + split_s = error_message.split(":") + print split_s + split_s.each {|x| error_message = x} end - return {:error_message => error_message, :path => inputfile} + return {:error_message => error_message, :path => inputfile, :console_msg => console_message} end - + # process generated files raise "no files generated" if files.empty? #search for "_overview.jpg files" from Array of files overviewFiles = "" pdfFile = "" txtFile = "" + consoleOut = "" files_Array_Size = files.size - 1 for i in 0..files_Array_Size @@ -368,6 +424,7 @@ class Assay # build array named overviewFiles that contains "_overview.jpg files" overviewFiles = overviewFiles.split("\n") + raise "no overview files generated" if overviewFiles.empty? if self.plate_type == 'm' @@ -375,18 +432,20 @@ class Assay else zipfile = out_dir_path + "/singlePlateAnalysis.zip" end - + consoleOut = out_dir_path + "/console.out" + self.console_out = consoleOut # create Zip files at current directory Zip::File.open(zipfile, Zip::File::CREATE) { |zf| files.each{|file| zf.add(File.basename(file), file)} #files.each{|file| zf.add(file.sub(out_dir_path + "/", ""), file))} + #zf.add(File.basename(consoleOut), consoleOut) } - #return results unless error #zip files, jpg of overviews, txt file for datagrid, pdf file - {:status => status, :overviewFiles => overviewFiles, :zipfile => zipfile, :txtFile => txtFile, :pdfFile => pdfFile, :inputfile => inputfile, :layout_file => layout_file, :model => self.model} + {:status => status, :overviewFiles => overviewFiles, :zipfile => zipfile, :txtFile => txtFile, :pdfFile => pdfFile, :inputfile => inputfile, :layout_file => layout_file, :model => self.model, + :consoleout => consoleOut} end # end of r_calculation method diff --git a/Rails/app/views/assays/_form.html.erb b/Rails/app/views/assays/_form.html.erb index 9564b23..fb64a85 100644 --- a/Rails/app/views/assays/_form.html.erb +++ b/Rails/app/views/assays/_form.html.erb @@ -1,112 +1,106 @@ <%= form_for @assay do |f| %> - - <% if @assay.errors.any? %> -
-

<%= pluralize(@assay.errors.count, "error") %> prohibited this assay from being saved:

- -
    - <% @assay.errors.full_messages.each do |msg| %> +<% if @assay.errors.any? %> +
    +

    <%= pluralize(@assay.errors.count, "error") %> prohibited this assay from being saved:

    +
      + <% @assay.errors.full_messages.each do |msg| %>
    • <%= msg %>
      • - <% end %> -
    -
    - <% end %> - - -

    Plate Type

    - <%= f.radio_button(:plate_type, 's', :checked => true) %> - <%= f.label(:plate_type_single, "Single-plate") %>
    - <%= f.radio_button(:plate_type, 'm', :checked => false) %> - <%= f.label(:plate_type_single, "Multiple-plate") %>
    - -

    Input Data File

    -Please specify a plate results file to upload for analysis:
    - -
    - <%= f.file_field :input_file %> -
    - -

    Plate Layout File

    -Optionally upload a plate layout file:
    - -
    - <%= f.file_field :layout_file %> -
    - -
    - <%= link_to "Single-Plate Example File","/resources/YPDAFEXglucoseTests_2-25-10.csv" %>
    - <%= link_to "Single-Plate Layout Example File","/resources/YPDAFEXglucoseTests_2-25-10_Layout.csv" %>
    - <%= link_to "Multi-Plate Example File","/resources/test_YYYY_MM_DD_HH_MM_SS.csv" %>
    - <%= link_to "Multi-Plate Layout Example File","/resources/MultiPlateLayout_plateID.csv" %> - -
    - -

    Media background

    - - <%= f.radio_button(:blank_value, "default", {:checked => true, :class => "user_enter3 user_enter3_no"}) %> - <%= f.label(:blank_value_blank_value_default, "Take the first OD reading of each well to be the blank") %>
    - - <%= f.radio_button(:blank_value, "user", {:class => "user_enter3 user_enter3_yes"}) %> - <%= f.label(:blank_value_user, "User Input.") %> - - - -

    OD Transform

    - -<%= f.radio_button(:transformation, 1, {:checked => true, :class => "user_enter2 user_enter2_no"}) %> -<%= f.label(:transformation_one, "log(x + 0.1)") %>
    - -<%= f.radio_button(:transformation, 0, {:class => "user_enter2 user_enter2_no"}) %> -<%= f.label(:transformation_zero, "log(x)") %>
    - -<%= f.radio_button(:transformation, -1, {:class => "user_enter2 user_enter2_yes"}) %> -<%= f.label(:transformation_any, "log(x + δ)") %> - - - -

    Growth curve model

    - - -<%= f.radio_button(:model, 1, {:checked => true, :class => "user_enter1 user_enter1_no"})%> -<%= f.label(:model_one, "Sigmoid curve") %> - -<%#= f.radio_button(:model, 0, {:class => "user_enter1 user_enter1_no"}) %> -<%#= f.label(:model_zero, "Sigmoid + linear") %> - -<%= f.radio_button(:model, -1, {:class => "user_enter1 user_enter1_yes"}) %> -<%= f.label(:model_any, "LOESS. The default smoothing value is 0.1.") %> - - - -

    Inoculation timepoint

    - -
    - <%= f.label :start_index, "Enter the timepoint index (positive integer only). The default value is 2. " %>
    - <%= f.text_field(:start_index, :type => 'number', :min =>'1', :size => '3', :value => '2') %> -
    - -

    Growth Threshold

    - -
    - <%= f.label :growth_threshold, "Enter the growth threshold. The default value is 0.05. " %>
    - <%= f.text_field(:growth_threshold, :type => 'number', :min =>'0', :size => '3', :value => '0.05', :step => "0.01") %> -
    - -

    Points to ignore

    -
    - <%= f.label :remove_points,"Enter a comma-separated list of points. Example: 2,3,4,5 (positive integers only). The default is an empty list." %>
    - <%= f.text_field :remove_points %> -
    - + <% end %> +
+
+<% end %> +
+ <%= link_to "GCAT Users Manual","/resources/GCAT_users_manual.pdf" %>
+ <%= link_to "GCAT Release Notes","/resources/Release_Notes.pdf" %> +
+
+
    +
  • +

    Plate Type

    + <%= f.radio_button(:plate_type, 's', :checked => true) %> + <%= f.label(:plate_type_single, "Single-plate") %>
    + <%= f.radio_button(:plate_type, 'm', :checked => false) %> + <%= f.label(:plate_type_single, "Multiple-plate") %>
    +
    • +
  • +

    Input Data File

    + Please specify a plate results file to upload for analysis:
    +
    + <%= f.file_field :input_file %> +
    +
    + <%= link_to "Single-Plate Example File","/resources/YPDAFEXglucoseTests_2-25-10.csv" %>
    + <%= link_to "Multi-Plate Example File","/resources/test_YYYY_MM_DD_HH_MM_SS.csv" %>
    +
    +
    • +
  • +

    Plate Layout File

    + Optionally upload a plate layout file:
    +
    + <%= f.file_field :layout_file %> +
    +
    + <%= link_to "Single-Plate Layout Example File","/resources/YPDAFEXglucoseTests_2-25-10_Layout.csv" %>
    + <%= link_to "Multi-Plate Layout Example File","/resources/MultiPlateLayout_plateID.csv" %> +
    +
    • +
  • +

    Media background

    + <%= f.radio_button(:blank_value, "zero", {:class => "user_enter3 user_enter3_no"}) %> + <%= f.label(:blank_value_zero, "0" ) %>
    + <%= f.radio_button(:blank_value, "default", {:class => "user_enter3 user_enter3_no"}) %> + <%= f.label(:blank_value_default, "Take the first OD reading of each well to be the blank") %>
    + <%= f.radio_button(:blank_value, "user", {:checked => true, :class => "user_enter3 user_enter3_yes"}) %> + <%= f.label(:blank_value_user, "User Input.") %> + +
    • +
  • +

    OD Transform

    + <%= f.radio_button(:transformation, 0, {:checked => true, :class => "user_enter2 user_enter2_no"}) %> + <%= f.label(:transformation_zero, "log(x)") %>
    + <%= f.radio_button(:transformation, 0.1, {:class => "user_enter2 user_enter2_no"}) %> + <%= f.label(:transformation_one, "log(x + 0.1)") %>
    + <%= f.radio_button(:transformation, -1, {:class => "user_enter2 user_enter2_yes"}) %> + <%= f.label(:transformation_any, "log(x + δ)") %> + +
    • +
  • +

    Growth curve model

    + <%= f.radio_button(:model, 1, {:checked => true, :class => "user_enter1 user_enter1_no"})%> + <%= f.label(:model_one, "Sigmoid curve") %>
    + <%#= f.radio_button(:model, 0, {:class => "user_enter1 user_enter1_no"}) %> + <%#= f.label(:model_zero, "Sigmoid + linear") %> + <%= f.radio_button(:model, -1, {:class => "user_enter1 user_enter1_yes"}) %> + <%= f.label(:model_any, "LOESS. The default smoothing value is 0.1.") %> + +
    • +
  • +

    Inoculation timepoint

    +
    + <%= f.label :start_index, "Enter the timepoint index (positive integer only). The default value is 2. " %>
    + <%= f.text_field(:start_index, :type => 'number', :min =>'1', :size => '3', :value => '2') %> +
    +
    • +
  • +

    Growth Threshold

    +
    + <%= f.label :growth_threshold, "Enter the growth threshold. The default value is 0.05. " %>
    + <%= f.text_field(:growth_threshold, :type => 'number', :min =>'0', :size => '3', :value => '0.05', :step => "0.01") %> +
    +
    • +
  • +

    Points to ignore

    +
    + <%= f.label :remove_points,"Enter a comma-separated list of points. Example: 2,3,4,5 (positive integers only). The default is an empty list." %>
    + <%= f.text_field :remove_points %> +
    <%#= f.check_box(:remove_jumps) %> <%#= f.label(:remove_jumps, "Employ the jump detection algorithm to attempt to remove problematic points.") %> @@ -122,26 +116,44 @@ Optionally upload a plate layout file:
    <%= f.text_field(:plate_dimensions_column, :type => 'number', :min =>'1', :size => '3', :value => '12') %> <% -=end %> -
    -

    Timestamp format

    - <%= f.label :timestamp_format %>
    - <%#= f.text_field(:timestamp_format, :value => '1/3600', :id => 'adam') %> - <%= f.select :timestamp_format, options_for_select(date_time_options()) %> -
    - - -
    +=end %> +
    • +
  • +
    +

    Timestamp format

    + <%= f.label :timestamp_format %>
    + <%#= f.text_field(:timestamp_format, :value => '1/3600', :id => 'adam') %> + <%= f.select :timestamp_format, options_for_select(date_time_options()) %> +
    +
    • +
  • +

    Heatmap options

    +
    + <%= f.label "Enter the range for the total growth." %>
    + <%= f.text_field(:totg_min, :type => 'number', :min => '0', :size => '2') %> + <%= f.label "-" %> + <%= f.text_field(:totg_max, :type => 'number', :min => '1', :size => '2') %> +
    +
    + <%= f.label "Enter the range for the specific growth." %>
    + <%= f.text_field(:specg_min, :type => 'number', :min => '0', :size => '2') %> + <%= f.label "-" %> + <%= f.text_field(:specg_max, :type => 'number', :min => '1', :size => '2') %> +
    +
    + <%= f.label "Enter the range for the lag time." %>
    + <%= f.text_field(:lagT_min, :type => 'number', :min => '0', :size => '2') %> + <%= f.label "-" %> + <%= f.text_field(:lagT_max, :type => 'number', :min => '1', :size => '2') %> +
    +
    • +
    <%= f.submit %>
    -
    - <%= mail_to "gcat.help@glbrc.wisc.edu","Please Send Any Questions To The GLBRC Help Desk And Be Sure To Include 'GCAT' In Your Subject Title", :subject => "GCAT" %> -
    - - -
    - <%= link_to "GCAT Users Manual","/resources/GCAT_users_manual.pdf" %> +
    + <%= mail_to "gcat.help@glbrc.wisc.edu","Please Send Any Questions To The GLBRC Help Desk And Be Sure To Include 'GCAT' In Your Subject Title", :subject => "GCAT" %>
    - -<% end %> +
+
+<% end %> \ No newline at end of file diff --git a/Rails/app/views/assays/inputfile_error_message.html.erb b/Rails/app/views/assays/inputfile_error_message.html.erb index 8bb189f..48de1ab 100644 --- a/Rails/app/views/assays/inputfile_error_message.html.erb +++ b/Rails/app/views/assays/inputfile_error_message.html.erb @@ -1,6 +1,21 @@
-

Error

-

Please resubmit your file.

- <%= link_to 'New Assay', new_assay_path%> +

Error

+ <%= @error_msg %> +

+ + + +
+
Please resubmit your file.
+ <%= link_to 'New Assay', new_assay_path%>


-
\ No newline at end of file + diff --git a/Rails/app/views/assays/new.html.erb b/Rails/app/views/assays/new.html.erb index d2b4437..42b64b3 100644 --- a/Rails/app/views/assays/new.html.erb +++ b/Rails/app/views/assays/new.html.erb @@ -1,7 +1,7 @@

Growth Curve Analysis Tool

-
+
This tool processes microbial growth curve data collected in a microtiter plate format and generates a table of biologically meaningful growth curve characteristics, as well as relevant plots. These characteristics can be used to select strains with optimal growth properties. diff --git a/Rails/app/views/assays/show.html.erb b/Rails/app/views/assays/show.html.erb index badd4b6..978f4fd 100644 --- a/Rails/app/views/assays/show.html.erb +++ b/Rails/app/views/assays/show.html.erb @@ -39,4 +39,4 @@ <% end %> -
\ No newline at end of file +
diff --git a/Rails/app/views/layouts/application.html.erb b/Rails/app/views/layouts/application.html.erb index 113f1ff..9ffe1c8 100644 --- a/Rails/app/views/layouts/application.html.erb +++ b/Rails/app/views/layouts/application.html.erb @@ -19,6 +19,7 @@ Copyright © 2012 The Board of Regents of the University of Wisconsin System <%= image_tag 'lgplv.jpg' %> <%= image_tag 'GLBRC_horz_cmyk_small.jpg' %> + <%= image_tag 'DOE_Logo_Color.png', :size => "292x72" %>
diff --git a/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_achieved_growth.pdf b/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_achieved_growth.pdf deleted file mode 100644 index c6041a2..0000000 Binary files a/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_achieved_growth.pdf and /dev/null differ diff --git a/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_lag_time.pdf b/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_lag_time.pdf deleted file mode 100644 index 63be118..0000000 Binary files a/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_lag_time.pdf and /dev/null differ diff --git a/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_max_spec.growth.rate.pdf b/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_max_spec.growth.rate.pdf deleted file mode 100644 index d75060f..0000000 Binary files a/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_max_spec.growth.rate.pdf and /dev/null differ diff --git a/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_overview.jpg b/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_overview.jpg deleted file mode 100644 index 9f504f7..0000000 Binary files a/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_overview.jpg and /dev/null differ diff --git a/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf b/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf deleted file mode 100644 index 281016e..0000000 Binary files a/Rails/public/generatedFiles/20150407-1428438865/YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf and /dev/null differ diff --git a/Rails/public/generatedFiles/20150407-1428438865/output_gcat.fit_2015-04-07_15.34.27.txt b/Rails/public/generatedFiles/20150407-1428438865/output_gcat.fit_2015-04-07_15.34.27.txt deleted file mode 100644 index d8b6714..0000000 --- a/Rails/public/generatedFiles/20150407-1428438865/output_gcat.fit_2015-04-07_15.34.27.txt +++ /dev/null @@ -1,141 +0,0 @@ -"row" "plate" "well" "media" "strain" "model" "lag.time, hrs" "lag.time.SE, hrs" "inflection.time, hrs" "max.spec.growth.rate, log.OD/hr" "max.spec.growth.rate.SE, log.OD/hr" "baseline, log.OD" "baseline.SE, log.OD" "amplitude, log.OD" "amplitude.SE, log.OD" "plateau, log.OD" "inoc.log.OD" "max.log.OD" "projected.growth, log.OD" "achieved.growth, log.OD" "baseline.OD" "amplitude.OD" "plateau.OD" "inoc.OD" "max.OD" "projected.growth.OD" "achieved.growth.OD" "shape.par" "shape.par.SE" "R.squared" "RSS" "empty" "asymp.not.reached" "tank" "other" "pdf.file" "page.no" "Destination.plate.name" "Well.ID" "Plate.source" "Well.Source" "Media.Definition" -1 "YPDAFEXglucoseTests_2-25-10" "A01" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 2 "Control strain plate" "Empty" "Empty" "Empty" "None" -2 "YPDAFEXglucoseTests_2-25-10" "B01" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 3 "Control strain plate" "Empty" "Empty" "Empty" "None" -3 "YPDAFEXglucoseTests_2-25-10" "C01" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 4 "Control strain plate" "Empty" "Empty" "Empty" "None" -4 "YPDAFEXglucoseTests_2-25-10" "D01" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 5 "Control strain plate" "Empty" "Empty" "Empty" "None" -5 "YPDAFEXglucoseTests_2-25-10" "E01" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 6 "Control strain plate" "Empty" "Empty" "Empty" "None" -6 "YPDAFEXglucoseTests_2-25-10" "F01" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 7 "Control strain plate" "Empty" "Empty" "Empty" "None" -7 "YPDAFEXglucoseTests_2-25-10" "G01" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 8 "Control strain plate" "Empty" "Empty" "Empty" "None" -8 "YPDAFEXglucoseTests_2-25-10" "H01" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 9 "Control strain plate" "Empty" "Empty" "Empty" "None" -9 "YPDAFEXglucoseTests_2-25-10" "A02" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 10 "Control strain plate" "Empty" "Empty" "Empty" "None" -10 "YPDAFEXglucoseTests_2-25-10" "B02" "YP" "Lab strain" "gompertz sigmoid" 0 1.75346931682115 9.008895 0.00387129154161333 0.000169526575673485 0.106012627582768 0.00533332981254499 0.0949774510885174 0.0112054786798504 0.200990078671286 0.112280003029694 0.184252861643961 0.0887100756415918 0.0719728586142672 0.111835916217944 0.0996340592954781 0.222612641821245 0.118826091485523 0.202319805224487 0.103786550335722 0.0834937137389644 NA NA 0.955970181896242 0.00271004795972447 "I " "U" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 11 "Control strain plate" "Sample" "USDA" "" "YP" -11 "YPDAFEXglucoseTests_2-25-10" "C02" "YP+0.25% glucose" "Lab strain" "richards sigmoid" 2.40987768343735 0.0533048366613944 4.21845083333333 0.0460029603516824 0.000724536080633502 0.0730406465985917 0.00147448206809288 0.20195449827016 0.00148223339842928 0.274995144868751 0.073266311037202 0.274994924460913 0.201728833831549 0.201728613423711 0.0757742625906743 0.22379232217684 0.316524282953919 0.0760170539793741 0.31652399278168 0.240507228974545 0.240506938802306 0.265875936579388 0.100708043886741 0.997917404710374 0.00135388203716233 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 12 "Control strain plate" "Sample" "USDA" "" "YP+0.25% glucose" -12 "YPDAFEXglucoseTests_2-25-10" "D02" "YP+0.5% glucose" "Lab strain" "logistic sigmoid." 3.07823403673893 0.0432348209213164 5.3624375 0.0732442091237218 0.00083385044900585 0.0859165104025432 0.00136428289761777 0.336085729465356 0.00149532007847134 0.4220022398679 0.0889960026247708 0.422002205393214 0.333006237243129 0.333006202768443 0.0897153446116215 0.399458994539777 0.525011940504746 0.0930762868815243 0.52501188793044 0.431935653623222 0.431935601048915 NA NA 0.99892015420286 0.00211931922664724 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 13 "Control strain plate" "Sample" "USDA" "" "YP+0.5% glucose" -13 "YPDAFEXglucoseTests_2-25-10" "E02" "YP+1% glucose" "Lab strain" "richards sigmoid" 3.31104934964427 0.0428738829656516 6.24426055555555 0.087498859778052 0.000646229427574331 0.0670789160536515 0.00264084512090784 0.496808437832399 0.00261152544308038 0.56388735388605 0.0759549213884333 0.563886450845895 0.487932432497617 0.487931529457461 0.0693798660836618 0.643467662335959 0.757491228661656 0.0789139371187617 0.75748964157722 0.678577291542894 0.678575704458458 1.22323321021831 0.0913419736269564 0.999523017751576 0.00210815425649153 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 14 "Control strain plate" "Sample" "USDA" "" "YP+1% glucose" -14 "YPDAFEXglucoseTests_2-25-10" "F02" "YP+2% glucose" "Lab strain" "richards sigmoid" 3.16160945641398 0.0130132752242264 5.69610027777778 0.0871403267354909 0.000229646786119097 0.08737718548213 0.000697693868328928 0.569725537718312 0.000706582348719082 0.657102723200442 0.0877050574005534 0.656913955188774 0.569397665799888 0.56920889778822 0.0913082277184576 0.767781795419447 0.92919481815215 0.0916660957048965 0.928830682251893 0.837528722447253 0.837164586546997 0.128377244056841 0.0158490082737876 0.999930578411107 0.000418173571721894 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 15 "Control strain plate" "Sample" "USDA" "" "YP+2% glucose" -15 "YPDAFEXglucoseTests_2-25-10" "G02" "YP+5% glucose" "Lab strain" "gompertz sigmoid" 1.97362812374979 0.160218470960237 6.10126222222222 0.0637129438472813 0.000882845743042059 0.0636642130548074 0.00677504517335327 0.715651375940815 0.00877835119047133 0.779315588995622 0.0726054464623438 0.769574985282588 0.706710142533278 0.696969538820244 0.0657344789473957 1.0455186500407 1.17997975267831 0.0753061873456158 1.15884851638065 1.10467356533269 1.08354232903504 NA NA 0.996368548540555 0.0284187363816137 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 16 "Control strain plate" "Sample" "USDA" "" "YP+5% glucose" -16 "YPDAFEXglucoseTests_2-25-10" "H02" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 17 "Control strain plate" "Empty" "Empty" "Empty" "None" -17 "YPDAFEXglucoseTests_2-25-10" "A03" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 18 "Control strain plate" "Empty" "Empty" "Empty" "None" -18 "YPDAFEXglucoseTests_2-25-10" "B03" "YP" "Wild strain" "gompertz sigmoid" 0 6.85707287937896 22.1409086111111 0.00240032503165892 0.000622808682835668 0.183471250816661 0.0241038377523601 0.144528358183154 0.243574028025108 0.327999608999814 0.193008393297115 0.240674524494353 0.134991215702699 0.0476661311972385 0.201380426209075 0.155494462222733 0.388188429507373 0.212892973647493 0.27210692827532 0.175295455859879 0.0592139546278265 NA NA 0.790451631963756 0.00713078905920281 "I " "U" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 19 "Control strain plate" "Sample" "USDA" "" "YP" -19 "YPDAFEXglucoseTests_2-25-10" "C03" "YP+0.25% glucose" "Wild strain" "gompertz sigmoid" 1.9906115468579 0.0691975318131243 3.47962611111111 0.0490374116952237 0.00113344212179788 0.113611335614137 0.00175358527026848 0.199753898562767 0.00189317967250483 0.313365234176905 0.113618321003616 0.313364980275983 0.199746913173288 0.199746659272367 0.120316613087275 0.221102206170602 0.368021087850449 0.120324438962491 0.368020740508678 0.247696648887958 0.247696301546187 NA NA 0.99399012987845 0.00350258662967115 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 20 "Control strain plate" "Sample" "USDA" "" "YP+0.25% glucose" -20 "YPDAFEXglucoseTests_2-25-10" "D03" "YP+0.5% glucose" "Wild strain" "logistic sigmoid." 2.74248926201157 0.0354379553926203 4.43294833333333 0.0945867701955495 0.00125702159577835 0.120482088801679 0.00134117834599991 0.32177887516419 0.00144348747790325 0.442260963965869 0.122204770404787 0.442260963925467 0.320056193561082 0.32005619352068 0.12804053622706 0.379579682895796 0.556221805261732 0.129985465672481 0.556221805198858 0.426236339589251 0.426236339526377 NA NA 0.998757902847438 0.00205103195615211 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 21 "Control strain plate" "Sample" "USDA" "" "YP+0.5% glucose" -21 "YPDAFEXglucoseTests_2-25-10" "E03" "YP+1% glucose" "Wild strain" "richards sigmoid" 3.06558696223571 0.0312092193543957 5.3624375 0.121127558311403 0.000999219504341884 0.0914412547332416 0.00245736106561066 0.492484364444972 0.00245078801862176 0.583925619178214 0.10090202921227 0.583925619102095 0.483023589965944 0.483023589889825 0.0957524045344744 0.636376529891633 0.793063517352536 0.106168264278383 0.79306351721605 0.686895253074153 0.686895252937667 1.80996092627302 0.117497603933281 0.999544726321195 0.00181967924857191 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 22 "Control strain plate" "Sample" "USDA" "" "YP+1% glucose" -22 "YPDAFEXglucoseTests_2-25-10" "F03" "YP+2% glucose" "Wild strain" "richards sigmoid" 2.77641833187198 0.0527034516734386 5.62460111111111 0.129882570160111 0.00113584996869085 0.0943645434950579 0.00505890911787811 0.678399507081888 0.00501032007418759 0.772764050576946 0.11484805727615 0.77276399934955 0.657915993300795 0.657915942073399 0.0989602917302299 0.97072108167106 1.16574421483214 0.12170299001548 1.16574410388671 1.04404122481666 1.04404111387123 1.58781592816572 0.131684393376964 0.999371589849352 0.00464022682166854 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 23 "Control strain plate" "Sample" "USDA" "" "YP+2% glucose" -23 "YPDAFEXglucoseTests_2-25-10" "G03" "YP+5% glucose" "Wild strain" "richards sigmoid" 2.62155170729439 0.0528519100950448 5.64843416666667 0.120898389355078 0.000856667358787892 0.106939412411106 0.00473823154418831 0.792250602933212 0.00464150376049532 0.899190015344318 0.119165060839678 0.899150109300876 0.78002495450464 0.779985048461198 0.112866826518918 1.20836098124136 1.45761167700228 0.126555853197717 1.45751360540077 1.33105582380456 1.33095775220305 0.651987010079984 0.0715475157170284 0.999508942394936 0.00516491712891745 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 24 "Control strain plate" "Sample" "USDA" "" "YP+5% glucose" -24 "YPDAFEXglucoseTests_2-25-10" "H03" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 25 "Control strain plate" "Empty" "Empty" "Empty" "None" -25 "YPDAFEXglucoseTests_2-25-10" "A04" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 26 "Control strain plate" "Empty" "Empty" "Empty" "None" -26 "YPDAFEXglucoseTests_2-25-10" "B04" "YP" "Industrial strain" "gompertz sigmoid" 0 5.0780526120225 14.0138366666667 0.00262196611873332 0.00018437938744914 0.128373333313586 0.0113746241547247 0.0999846427550281 0.0508218894501574 0.228357976068614 0.134971123503685 0.189191289569101 0.0933868525649285 0.0542201660654161 0.136977395010588 0.105153945825447 0.256535054410289 0.144503734616262 0.208272060219704 0.112031319794027 0.0637683256034425 NA NA 0.855383080839261 0.00575026814686199 "I " "U" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 27 "Control strain plate" "Sample" "Internal source" "" "YP" -27 "YPDAFEXglucoseTests_2-25-10" "C04" "YP+0.25% glucose" "Industrial strain" "gompertz sigmoid" 0.891438154862617 0.0875315924591966 2.31180638888889 0.0535113235044828 0.00124573544664028 0.0881434958395649 0.00304307272545713 0.207061853609148 0.00316468246722843 0.295205349448713 0.0894254262692569 0.295205293059733 0.205779923179456 0.205779866790477 0.0921448290236948 0.230058652994932 0.343402197264266 0.0935457804829503 0.343402121511189 0.249856416781316 0.249856341028238 NA NA 0.991724253334924 0.00363563892033091 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 28 "Control strain plate" "Sample" "Internal source" "" "YP+0.25% glucose" -28 "YPDAFEXglucoseTests_2-25-10" "D04" "YP+0.5% glucose" "Industrial strain" "logistic sigmoid." 1.64713494830746 0.0412877829637357 3.38429388888889 0.0931935829835479 0.00118142556806869 0.0808528949077067 0.00187894210009506 0.326765480130978 0.00196420648303134 0.407618375038685 0.0874704775763749 0.407618375014084 0.32014789746231 0.320147897437709 0.0842113918182088 0.386476282813275 0.503233380311918 0.0914100428976898 0.503233380274936 0.411823337414228 0.411823337377247 NA NA 0.998561073647885 0.00184537988196709 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 29 "Control strain plate" "Sample" "Internal source" "" "YP+0.5% glucose" -29 "YPDAFEXglucoseTests_2-25-10" "E04" "YP+1% glucose" "Industrial strain" "richards sigmoid" 2.00035124383545 0.0281455446975304 4.31378305555555 0.124952394681256 0.000705710849322313 0.066176309959304 0.00266242484922488 0.497003217300128 0.00264805311701161 0.563179527259432 0.0884800685969233 0.563179527257016 0.474699458662509 0.474699458660092 0.0684150727790216 0.643787807270277 0.756247669737942 0.0925124770869246 0.756247669733698 0.663735192651017 0.663735192646773 2.09745464546466 0.104168274133155 0.999771040591133 0.00072098110255013 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 30 "Control strain plate" "Sample" "Internal source" "" "YP+1% glucose" -30 "YPDAFEXglucoseTests_2-25-10" "F04" "YP+2% glucose" "Industrial strain" "richards sigmoid" 2.0490071997567 0.0662248504953823 4.76661111111111 0.13306744704186 0.00129515567791922 0.0751622402050358 0.00684502394093866 0.656973009903259 0.00678618652478681 0.732135250108295 0.103854790297524 0.732135243114114 0.628280459810771 0.62828045281659 0.0780590412170139 0.92894459216055 1.07951615758535 0.10943934186153 1.07951614304083 0.970076815723817 0.970076801179305 1.62672197615846 0.161151121349594 0.999229593966034 0.00459582695233057 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 31 "Control strain plate" "Sample" "Internal source" "" "YP+2% glucose" -31 "YPDAFEXglucoseTests_2-25-10" "G04" "YP+5% glucose" "Industrial strain" "logistic sigmoid." 1.98629177172554 0.0661342221284037 5.19560611111111 0.122957280170312 0.00117607964263019 0.0764858915144976 0.00452433442917892 0.793858352641992 0.00487921879564307 0.870344244156489 0.106676773149917 0.870336478987225 0.763667471006573 0.763659705837308 0.0794869603035999 1.21191432864705 1.38773267508318 0.112574582376872 1.38771413400679 1.27515809270631 1.27513955162992 NA NA 0.998885750680602 0.0103824045406066 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 32 "Control strain plate" "Sample" "Internal source" "" "YP+5% glucose" -32 "YPDAFEXglucoseTests_2-25-10" "H04" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 33 "Control strain plate" "Empty" "Empty" "Empty" "None" -33 "YPDAFEXglucoseTests_2-25-10" "A05" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 34 "Control strain plate" "Empty" "Empty" "Empty" "None" -34 "YPDAFEXglucoseTests_2-25-10" "B05" "YP" "Engineered strain" "gompertz sigmoid" 0 3.37960900118466 11.4875327777778 0.00260114799703032 0.000171113335294184 0.0996380871643661 0.00702344449132755 0.0812678741827026 0.0218737314876996 0.180905961347069 0.105000794559007 0.157379078978817 0.075905166788062 0.0523782844198106 0.104771014904237 0.084661410443271 0.198302487242874 0.110711492881175 0.17043921871877 0.0875909943616988 0.0597277258375952 NA NA 0.906033844889994 0.00328284811832938 "I " "U" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 35 "Control strain plate" "Sample" "ATCC" "" "YP" -35 "YPDAFEXglucoseTests_2-25-10" "C05" "YP+0.25% glucose" "Engineered strain" "gompertz sigmoid" 0.983948183597175 0.112859786286644 2.47863777777778 0.0501739409645355 0.00144200881080694 0.0661469359457048 0.00364271202623762 0.205919623922245 0.00380546132645363 0.27206655986795 0.0672650583629558 0.272066410063879 0.204801501504994 0.204801351700923 0.0683836896010714 0.228654445601205 0.312674369836174 0.0695789414490573 0.312674173192226 0.243095428387117 0.243095231743168 NA NA 0.987488271024703 0.00577672548033825 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 36 "Control strain plate" "Sample" "ATCC" "" "YP+0.25% glucose" -36 "YPDAFEXglucoseTests_2-25-10" "D05" "YP+0.5% glucose" "Engineered strain" "richards sigmoid" 1.86398050594022 0.0558531581780885 3.55112527777778 0.0944346403793218 0.00150539518734246 0.0602064687184575 0.00349724664000438 0.368213525552587 0.00348116438514935 0.428419994271045 0.0619674090584591 0.428419978577839 0.366452585212586 0.36645256951938 0.0620558052105851 0.445150582608455 0.534830565662769 0.0639276697585029 0.534830541576357 0.470902895904266 0.470902871817855 0.41241007480043 0.120556305314198 0.997911612798025 0.00385752298874987 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 37 "Control strain plate" "Sample" "ATCC" "" "YP+0.5% glucose" -37 "YPDAFEXglucoseTests_2-25-10" "E05" "YP+1% glucose" "Engineered strain" "logistic sigmoid." 1.99006793380884 0.0351079474960275 4.12311861111111 0.121142575431043 0.00106707303416645 0.0644342397186312 0.00208740714872881 0.517632133522502 0.00221049055518603 0.582066373241133 0.0750837822538967 0.582066368203544 0.506982590987236 0.506982585949648 0.0665554389527234 0.678049544482632 0.789732868500092 0.0779744622314236 0.789732859484154 0.711758406268668 0.71175839725273 NA NA 0.999269039916925 0.00268951955610802 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 38 "Control strain plate" "Sample" "ATCC" "" "YP+1% glucose" -38 "YPDAFEXglucoseTests_2-25-10" "F05" "YP+2% glucose" "Engineered strain" "logistic sigmoid." 1.98431414913883 0.0344438902457988 4.48061444444444 0.130673511563394 0.000910297701821604 0.0736708018228489 0.00232986507621017 0.655420765541249 0.00247952515524191 0.729091567364097 0.0914028197402174 0.729091436186734 0.63768874762388 0.637688616446517 0.0764523809998565 0.925952721450692 1.07319639269875 0.0957102901077889 1.07319612074233 0.977486102590961 0.977485830634544 NA NA 0.999493885845309 0.00307265449990923 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 39 "Control strain plate" "Sample" "ATCC" "" "YP+2% glucose" -39 "YPDAFEXglucoseTests_2-25-10" "G05" "YP+5% glucose" "Engineered strain" "logistic sigmoid." 2.10388607358557 0.0485609580954195 5.24327222222222 0.128060724388346 0.000947720103104396 0.0637480626845324 0.00338335491744478 0.806179689301617 0.00365527295985513 0.869927751986149 0.0914242899462062 0.869921741898693 0.778503462039943 0.778497451952487 0.0658238441354071 1.23933666273098 1.38673841018529 0.0957338154859682 1.38672406572182 1.29100459469932 1.29099025023585 NA NA 0.999357534856407 0.00631075803154068 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 40 "Control strain plate" "Sample" "ATCC" "" "YP+5% glucose" -40 "YPDAFEXglucoseTests_2-25-10" "H05" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 41 "Control strain plate" "Empty" "Empty" "Empty" "None" -41 "YPDAFEXglucoseTests_2-25-10" "A06" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 42 "Control strain plate" "Empty" "Empty" "Empty" "None" -42 "YPDAFEXglucoseTests_2-25-10" "B06" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 43 "Control strain plate" "Empty" "Empty" "Empty" "None" -43 "YPDAFEXglucoseTests_2-25-10" "C06" "Empty" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 44 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -44 "YPDAFEXglucoseTests_2-25-10" "D06" "Empty" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 45 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -45 "YPDAFEXglucoseTests_2-25-10" "E06" "Empty" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 46 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -46 "YPDAFEXglucoseTests_2-25-10" "F06" "Empty" "Empty" "logistic sigmoid." 9.73707675795057 0.0985970533305578 14.6811622222222 0.0827678159518767 0.00119202041574655 -0.000880352187845948 0.00297599235664884 0.821196181140969 0.00723578634320824 0.820315828953123 0.00130662738981984 0.80016942429868 0.819009201563303 0.79886279690886 -0.000879964791548726 1.27321739163809 1.27121704036991 0.00130748139930459 1.22591802114689 1.2699095589706 1.22461053974758 NA NA 0.997343483064722 0.0337108649740508 "E*" "L" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 47 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -47 "YPDAFEXglucoseTests_2-25-10" "G06" "Empty" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 48 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -48 "YPDAFEXglucoseTests_2-25-10" "H06" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 49 "Control strain plate" "Empty" "Empty" "Empty" "None" -49 "YPDAFEXglucoseTests_2-25-10" "A07" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 50 "Control strain plate" "Empty" "Empty" "Empty" "None" -50 "YPDAFEXglucoseTests_2-25-10" "B07" "AFEX" "Lab strain" "richards sigmoid" 3.77043529293613 0.0360628422979525 7.69807694444444 0.0922143076373947 0.000396448194603239 0.0415079420521979 0.00249398077489825 0.670137254883342 0.00244318042181785 0.71164519693554 0.0610249599211764 0.711620409573069 0.650620237014363 0.650595449651893 0.0423814404664091 0.954505567660092 1.03734032901714 0.0629254443914062 1.03728982934981 0.974414884625737 0.974364384958405 1.49636190326278 0.0645036016880811 0.999821079386736 0.00149128792010239 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 51 "Control strain plate" "Sample" "USDA" "" "AFEX" -51 "YPDAFEXglucoseTests_2-25-10" "C07" "AFEX+0.25% glucose" "Lab strain" "richards sigmoid" 3.81401380371595 0.0414172658123116 7.84107527777778 0.0912912497086539 0.000430847222656137 0.0416798125769253 0.00284816947390064 0.69143284133484 0.00278081561682767 0.733112653911766 0.0607785098125833 0.73305639362929 0.672334144099182 0.672277883816707 0.0425606105081318 0.996574258830031 1.08154967821066 0.0626635185773581 1.08143257293199 1.0188861596333 1.01876905435464 1.38211643616927 0.068441420394402 0.999776277423773 0.00199878407126496 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 52 "Control strain plate" "Sample" "USDA" "" "AFEX+0.25% glucose" -52 "YPDAFEXglucoseTests_2-25-10" "D07" "AFEX+0.5% glucose" "Lab strain" "richards sigmoid" 4.10969518183839 0.0412228717219101 8.43690166666667 0.0887040084623295 0.000394405492929288 0.0340862871852733 0.00276975733383969 0.70953425876434 0.00269646137747281 0.743620545949613 0.0553702983243347 0.743521928280257 0.688250247625278 0.688151629955922 0.034673881973359 1.03304416561189 1.10353769905694 0.0569319223405151 1.10333026330024 1.04660577671642 1.04639834095972 1.51337755174144 0.0684110305817092 0.999797902728699 0.00192728932795894 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 53 "Control strain plate" "Sample" "USDA" "" "AFEX+0.5% glucose" -53 "YPDAFEXglucoseTests_2-25-10" "E07" "AFEX+1% glucose" "Lab strain" "richards sigmoid" 4.24887937601734 0.0432115785663927 8.81823055555555 0.0859527181410838 0.000375029672246797 0.0356447291331235 0.00283858611378653 0.730548134285546 0.00274599564832944 0.766192863418669 0.0570847529310588 0.765947841016383 0.70910811048761 0.708863088085324 0.0362876182839384 1.07621834228765 1.15155936096669 0.0587455383807147 1.15103224530362 1.09281382258598 1.0922867069229 1.43679372443259 0.0664148620205159 0.999795584571703 0.00207184898977108 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 54 "Control strain plate" "Sample" "USDA" "" "AFEX+1% glucose" -54 "YPDAFEXglucoseTests_2-25-10" "F07" "AFEX+2% glucose" "Lab strain" "richards sigmoid" 4.18007396642371 0.0466407733724283 8.81823055555555 0.0839684559025767 0.000369760007946289 0.0335662062693272 0.00302321134929714 0.761208314991861 0.00289043066835203 0.794774521261188 0.0523578984758354 0.794000059559319 0.742416622785352 0.741642161083483 0.0341359077403089 1.14086149330819 1.21394174372853 0.0537528115582857 1.21222779441756 1.16018893217025 1.15847498285928 1.13197498623035 0.0608907037432053 0.999775581271097 0.00245341232352351 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 55 "Control strain plate" "Sample" "USDA" "" "AFEX+2% glucose" -55 "YPDAFEXglucoseTests_2-25-10" "G07" "AFEX+5% glucose" "Lab strain" "richards sigmoid" 4.31631141456833 0.0375067738225389 9.10422722222222 0.0746869165814573 0.000251011212616688 0.0449034082917984 0.00217539454600581 0.811374096629365 0.0020199781451565 0.856277504921164 0.0531730581528585 0.847610694845515 0.803104446768305 0.794437636692656 0.0459268271704429 1.25099895262068 1.35438019247854 0.0546121385565925 1.33406339459093 1.29976805392195 1.27945125603434 0.475355275365838 0.0354989182491613 0.99984356158066 0.00187490302158927 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 56 "Control strain plate" "Sample" "USDA" "" "AFEX+5% glucose" -56 "YPDAFEXglucoseTests_2-25-10" "H07" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 57 "Control strain plate" "Empty" "Empty" "Empty" "None" -57 "YPDAFEXglucoseTests_2-25-10" "A08" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 58 "Control strain plate" "Empty" "Empty" "Empty" "None" -58 "YPDAFEXglucoseTests_2-25-10" "B08" "AFEX" "Wild strain" "richards sigmoid" 2.71231721101246 0.051377222191618 6.24426055555555 0.114869798087755 0.000679522317637316 0.0686814145642472 0.00460568272264885 0.729956501290573 0.00454362062059059 0.798637915854821 0.10099640348141 0.798636815214796 0.697641512373411 0.697640411733386 0.0710949195446084 1.07499034630887 1.22251161803554 0.10627266302607 1.22250917185165 1.11623895500947 1.11623650882558 1.70292251675116 0.10179548101048 0.999686879664103 0.00266681050440312 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 59 "Control strain plate" "Sample" "USDA" "" "AFEX" -59 "YPDAFEXglucoseTests_2-25-10" "C08" "AFEX+0.25% glucose" "Wild strain" "richards sigmoid" 3.01070188606209 0.0455540510180634 6.55409027777778 0.115107998074341 0.000641488536342826 0.0614813761638786 0.00401667627257402 0.743382938801471 0.00395687893333818 0.804864314965349 0.0885306662587629 0.804861736607772 0.716333648706586 0.716331070349009 0.0634106915579287 1.10303794283843 1.23639303316638 0.0925677570623027 1.23638726695289 1.14382527610408 1.14381950989059 1.57881072796814 0.0887320125722592 0.999717695034928 0.00263054987530885 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 60 "Control strain plate" "Sample" "USDA" "" "AFEX+0.25% glucose" -60 "YPDAFEXglucoseTests_2-25-10" "D08" "AFEX+0.5% glucose" "Wild strain" "richards sigmoid" 2.97864249972838 0.0440943285573364 6.55409027777778 0.114576828102917 0.000592514268492699 0.0574375614416587 0.0038875686917152 0.760494448227834 0.00382450823238821 0.817932009669493 0.0846335570605372 0.817926981908608 0.733298452608956 0.733293424848071 0.059119138718029 1.13933374880962 1.26580931746965 0.0883181871040035 1.26579792555084 1.17749113036565 1.17747973844683 1.48473851369249 0.0802727796034772 0.999751240782926 0.00242858216652038 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 61 "Control strain plate" "Sample" "USDA" "" "AFEX+0.5% glucose" -61 "YPDAFEXglucoseTests_2-25-10" "E08" "AFEX+1% glucose" "Wild strain" "richards sigmoid" 2.92985461453388 0.0457749726886301 6.57792333333333 0.113561152688866 0.000574978160263558 0.060472124586291 0.00402516587449496 0.782067831893148 0.00395231319695858 0.842539956479439 0.0880742344239483 0.842528715447582 0.754465722055491 0.754454481023634 0.0623379840467781 1.18598785054918 1.32225792630317 0.0920691881463056 1.32223182187456 1.23018873815686 1.23016263372825 1.37581261909432 0.0764095517760612 0.999754748600533 0.00252958095458289 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 62 "Control strain plate" "Sample" "USDA" "" "AFEX+1% glucose" -62 "YPDAFEXglucoseTests_2-25-10" "F08" "AFEX+2% glucose" "Wild strain" "richards sigmoid" 3.04342230131477 0.0449382687527419 6.81625388888889 0.111344220886614 0.00053211483862603 0.0556626629934722 0.00387136841849492 0.807214512297039 0.00378851478092936 0.862877175290511 0.0817091172313295 0.862843943373837 0.781168058059181 0.781134826142507 0.0572409770684312 1.24165517922426 1.36996971193357 0.0851401153555837 1.36989095460621 1.28482959657798 1.28475083925063 1.25155544499941 0.0687282596513218 0.999773222693453 0.00254586287935126 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 63 "Control strain plate" "Sample" "USDA" "" "AFEX+2% glucose" -63 "YPDAFEXglucoseTests_2-25-10" "G08" "AFEX+5% glucose" "Wild strain" "richards sigmoid" 3.40984196234943 0.0273360225985238 7.17374972222222 0.104909950247054 0.000320509638786788 0.0670946887710371 0.00214797629965173 0.835221165477497 0.00207744941670489 0.902315854248534 0.0807525020643599 0.901946971348112 0.821563352184174 0.821194469283752 0.0693967332430874 1.30532384995973 1.46530579421431 0.0841025502173454 1.46439655277464 1.38120324399697 1.38029400255729 0.753286731439822 0.0336141517371988 0.999897955876558 0.00130605700907156 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 64 "Control strain plate" "Sample" "USDA" "" "AFEX+5% glucose" -64 "YPDAFEXglucoseTests_2-25-10" "H08" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 65 "Control strain plate" "Empty" "Empty" "Empty" "None" -65 "YPDAFEXglucoseTests_2-25-10" "A09" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 66 "Control strain plate" "Empty" "Empty" "Empty" "None" -66 "YPDAFEXglucoseTests_2-25-10" "B09" "AFEX" "Industrial strain" "richards sigmoid" 2.43102440775711 0.0454605985590097 5.50543583333333 0.126842367574397 0.000788090696060512 0.0539690230506907 0.00446798137137374 0.690558562368951 0.00442509749533481 0.744527585419641 0.0857310638249255 0.74452755483612 0.658796521594716 0.658796491011195 0.0554519069684636 0.994829458783827 1.10544655635026 0.0895132793671187 1.10544649195829 1.01593327698314 1.01593321259117 1.86325174039779 0.111013983680208 0.999682108231503 0.00226178478453787 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 67 "Control strain plate" "Sample" "Internal source" "" "AFEX" -67 "YPDAFEXglucoseTests_2-25-10" "C09" "AFEX+0.25% glucose" "Industrial strain" "richards sigmoid" 2.48092971341753 0.0462358408909463 5.62460111111111 0.126022327995321 0.000766265198216623 0.0498912361992905 0.00451231731412719 0.714630509305857 0.00446315308100269 0.764521745505147 0.0803254380277494 0.764521612664574 0.684196307477398 0.684196174636825 0.0511567623538203 1.04343151382482 1.14796685416386 0.0836396678533904 1.14796656882673 1.06432718631047 1.06432690097334 1.6892416239556 0.102428344960951 0.999685472160361 0.00245503448373934 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 68 "Control strain plate" "Sample" "Internal source" "" "AFEX+0.25% glucose" -68 "YPDAFEXglucoseTests_2-25-10" "D09" "AFEX+0.5% glucose" "Industrial strain" "richards sigmoid" 2.42408640744135 0.0532786618803828 5.62460111111111 0.124384376977411 0.000823105161949976 0.0492950122622815 0.00516311815303983 0.727641420856731 0.00510226521814267 0.776936433119012 0.0803276492472531 0.776936116027565 0.696608783871759 0.696608466780311 0.0505302243276007 1.07019213302561 1.17479940590863 0.0836420640212081 1.17479871629844 1.09115734188742 1.09115665227723 1.58714593821028 0.108898701673299 0.999619231516236 0.00307919508939737 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 69 "Control strain plate" "Sample" "Internal source" "" "AFEX+0.5% glucose" -69 "YPDAFEXglucoseTests_2-25-10" "E09" "AFEX+1% glucose" "Industrial strain" "richards sigmoid" 2.3516083906569 0.0596596631244507 5.69610027777778 0.122918277329311 0.000825310524938601 0.0456238028839663 0.00577234400145717 0.757677923259936 0.00569718881396185 0.803301726143903 0.0794802281473059 0.803300765454603 0.723821497996597 0.723820537307297 0.0466805786671931 1.1333167393977 1.23290119927319 0.0827241518553661 1.23289905414994 1.15017704741783 1.15017490229457 1.50943196721409 0.109906089971898 0.999597425228284 0.00351671862436235 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 70 "Control strain plate" "Sample" "Internal source" "" "AFEX+1% glucose" -70 "YPDAFEXglucoseTests_2-25-10" "F09" "AFEX+2% glucose" "Industrial strain" "richards sigmoid" 2.5236010165651 0.0587446480551128 5.93443083333333 0.120073445181908 0.000783304897530514 0.0450247442396835 0.00549978744950499 0.786911440589629 0.00540921373997301 0.831936184829312 0.0732958505454819 0.831929765474958 0.75864033428383 0.758633914929476 0.0460537433930304 1.19660160399639 1.29776333060356 0.0760488394635108 1.29774858049386 1.22171449114005 1.22169974103035 1.2397630247936 0.0944772278955165 0.999601760903923 0.00394547420222901 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 71 "Control strain plate" "Sample" "Internal source" "" "AFEX+2% glucose" -71 "YPDAFEXglucoseTests_2-25-10" "G09" "AFEX+5% glucose" "Industrial strain" "richards sigmoid" 2.58690524730753 0.0503605394422555 6.17276138888889 0.109989495010269 0.000552298616707589 0.0475039668950725 0.00430649396880978 0.83068144919568 0.00419058755640174 0.878185416090752 0.0684271066193943 0.878046704871374 0.809758309471358 0.80961959825198 0.0486503609989841 1.2948820530738 1.40652889340594 0.0708225662291506 1.40619510399936 1.33570632717678 1.33537253777021 0.776030021315298 0.0590320987662605 0.999743045862095 0.00295407387389294 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 72 "Control strain plate" "Sample" "Internal source" "" "AFEX+5% glucose" -72 "YPDAFEXglucoseTests_2-25-10" "H09" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 73 "Control strain plate" "Empty" "Empty" "Empty" "None" -73 "YPDAFEXglucoseTests_2-25-10" "A10" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 74 "Control strain plate" "Empty" "Empty" "Empty" "None" -74 "YPDAFEXglucoseTests_2-25-10" "B10" "AFEX" "Engineered strain" "richards sigmoid" 2.17498330451382 0.0502798395951241 5.12410694444444 0.122218804779539 0.000784428545413071 0.0435682252869189 0.00476512105024793 0.699692212079932 0.00470444935542924 0.743260437366851 0.0678435113592805 0.743259718765618 0.67541692600757 0.675416207406337 0.0445312553256874 1.01313299408815 1.10278033345246 0.0701978215718182 1.10277882239246 1.03258251188064 1.03258100082064 1.18141837167591 0.0894530619922231 0.999633683586648 0.00265620405353138 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 75 "Control strain plate" "Sample" "ATCC" "" "AFEX" -75 "YPDAFEXglucoseTests_2-25-10" "C10" "AFEX+0.25% glucose" "Engineered strain" "richards sigmoid" 2.51277041358427 0.0385075634064252 5.50543583333333 0.124302687102611 0.000662579603795554 0.0363365047244458 0.00363658784524449 0.715682301787501 0.00358889800467861 0.752018806511947 0.0575296223014987 0.75201790943738 0.694489184210448 0.694488287135881 0.0370047447805615 1.04558191041505 1.12127814693769 0.0592166466248745 1.12127624399387 1.06206150031282 1.062059597369 1.22124196187785 0.0728117473772727 0.999746251949321 0.00205128571327075 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 76 "Control strain plate" "Sample" "ATCC" "" "AFEX+0.25% glucose" -76 "YPDAFEXglucoseTests_2-25-10" "D10" "AFEX+0.5% glucose" "Engineered strain" "richards sigmoid" 2.53563260737677 0.0376782240880802 5.60076805555555 0.122775490964049 0.000617718940237756 0.0383224027816064 0.00352849516406259 0.723989555808605 0.00348019897003327 0.762311958590212 0.0604113492179259 0.762310653602122 0.701900609372286 0.701899304384196 0.0390661767078291 1.06264585810741 1.14322554568591 0.0622734220263796 1.14322274880392 1.08095212365953 1.08094932677754 1.22916202573701 0.0694532756349596 0.999772141364762 0.00189783824442075 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 77 "Control strain plate" "Sample" "ATCC" "" "AFEX+0.5% glucose" -77 "YPDAFEXglucoseTests_2-25-10" "E10" "AFEX+1% glucose" "Engineered strain" "logistic sigmoid." 2.60565520411145 0.0279148207786424 5.67226722222222 0.122180167529517 0.000572646164016784 0.0367511554868138 0.00173132045208087 0.75510174924411 0.00189799830326426 0.791852904730924 0.0552120643649708 0.791846881057418 0.736640840365953 0.736634816692447 0.0374348287497246 1.12782801723342 1.20748289466742 0.0567646930486905 1.20746959755124 1.15071820161873 1.15070490450255 NA NA 0.999760229166242 0.00222986115644153 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 78 "Control strain plate" "Sample" "ATCC" "" "AFEX+1% glucose" -78 "YPDAFEXglucoseTests_2-25-10" "F10" "AFEX+2% glucose" "Engineered strain" "logistic sigmoid." 2.59552092034145 0.0233507552285751 5.7914325 0.12311239814861 0.000459924953718036 0.0376321525320693 0.00147723901592513 0.788206013379693 0.00162316638429969 0.825838165911762 0.0581595525832075 0.82582810286149 0.767678613328555 0.767668550278282 0.0383492084922821 1.19944710612095 1.28379416176132 0.0598840894646306 1.2837711799415 1.22391007229669 1.22388709047687 NA NA 0.999844012469462 0.00158372380662876 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 79 "Control strain plate" "Sample" "ATCC" "" "AFEX+2% glucose" -79 "YPDAFEXglucoseTests_2-25-10" "G10" "AFEX+5% glucose" "Engineered strain" "richards sigmoid" 2.65619332146438 0.0304232772610151 6.00593 0.113927548226674 0.000394015356154558 0.0448535113624544 0.00262903429411648 0.830698452896991 0.00255902360970839 0.875551964259445 0.0596126030160059 0.875406838654098 0.815939361243439 0.815794235638092 0.0458746399354508 1.29492107489454 1.4001997528856 0.0614252739377605 1.39985144771812 1.33877447894784 1.33842617378036 0.630436857242866 0.0359660377290858 0.999878122228538 0.0014247167012055 "I " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 80 "Control strain plate" "Sample" "ATCC" "" "AFEX+5% glucose" -80 "YPDAFEXglucoseTests_2-25-10" "H10" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 81 "Control strain plate" "Empty" "Empty" "Empty" "None" -81 "YPDAFEXglucoseTests_2-25-10" "A11" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 82 "Control strain plate" "Empty" "Empty" "Empty" "None" -82 "YPDAFEXglucoseTests_2-25-10" "B11" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 83 "Control strain plate" "Empty" "Empty" "Empty" "None" -83 "YPDAFEXglucoseTests_2-25-10" "C11" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 84 "Control strain plate" "Empty" "Empty" "Empty" "None" -84 "YPDAFEXglucoseTests_2-25-10" "D11" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 85 "Control strain plate" "Empty" "Empty" "Empty" "None" -85 "YPDAFEXglucoseTests_2-25-10" "E11" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 86 "Control strain plate" "Empty" "Empty" "Empty" "None" -86 "YPDAFEXglucoseTests_2-25-10" "F11" "None" "Empty" "richards sigmoid" 14.4916170457847 0.0217082069318843 18.6612825 0.0889624209370597 0.000433181631551599 0.00193467418446847 0.000448535101404725 0.976169168246482 0.0129778271847923 0.97810384243095 0.00193467418448112 0.752023542360525 0.976169168246469 0.750088868176044 0.00193654687405509 1.65426868422052 1.65940879994385 0.00193654687406775 1.12128819301358 1.65747225306978 1.11935164613951 0.07 0.0304918969768742 0.999799864971328 0.00156360720906969 "E*" "U" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 87 "Control strain plate" "Empty" "Empty" "Empty" "None" -87 "YPDAFEXglucoseTests_2-25-10" "G11" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 88 "Control strain plate" "Empty" "Empty" "Empty" "None" -88 "YPDAFEXglucoseTests_2-25-10" "H11" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 89 "Control strain plate" "Empty" "Empty" "Empty" "None" -89 "YPDAFEXglucoseTests_2-25-10" "A12" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 90 "Control strain plate" "Empty" "Empty" "Empty" "None" -90 "YPDAFEXglucoseTests_2-25-10" "B12" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 91 "Control strain plate" "Empty" "Empty" "Empty" "None" -91 "YPDAFEXglucoseTests_2-25-10" "C12" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 92 "Control strain plate" "Empty" "Empty" "Empty" "None" -92 "YPDAFEXglucoseTests_2-25-10" "D12" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 93 "Control strain plate" "Empty" "Empty" "Empty" "None" -93 "YPDAFEXglucoseTests_2-25-10" "E12" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 94 "Control strain plate" "Empty" "Empty" "Empty" "None" -94 "YPDAFEXglucoseTests_2-25-10" "F12" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 95 "Control strain plate" "Empty" "Empty" "Empty" "None" -95 "YPDAFEXglucoseTests_2-25-10" "G12" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 96 "Control strain plate" "Empty" "Empty" "Empty" "None" -96 "YPDAFEXglucoseTests_2-25-10" "H12" "None" "Empty" ": skipped" NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA "E " "-" "-" "" "YPDAFEXglucoseTests_2-25-10_plots_2015-04-07_15.34.27.pdf" 97 "Control strain plate" "Empty" "Empty" "Empty" "None" - -# Raw OD values are adjusted and log-transformed before fitting a growth curve as follows: log.OD = log(OD - blank + const) where blank is OD of blank medium and const is specified by the user (1 by default) -# Values are reported on the above 'log.OD' scale unless otherwise specified. -# .SE columns report standard errors of those values that are estimated directly as parameters of global sigmoid models. -# .OD columns report values back-transformed to the linear 'OD - blank' scale. - -# -- Explanation of columns -- -# - model: Name of the model the well was successfully fit with (if any) -# - lag.time: Lag time estimate inferred from the fitted model -# - inflection.time: inflection time point of the growth curve when drawn on the log scale -# - max.spec.growth.rate: maximum specific growth rate estimate inferred from the fitted model. Estimated as the first derivative of the growth curve at inflection time point -# - baseline: growth curve baseline. Global sigmoid model: baseline is parameter 'b' of the model. LOESS: baseline is the same as the lowest predicted log.OD value -# - amplitude: difference between upper plateau and baseline values. Global sigmoid model: amplitude is parameter 'A' of the model. LOESS: amplitude = max.log.OD - min.log.OD -# - plateau: upper asymptote value of the fitted model. Global sigmoid model: plateau = b + A. LOESS: plateau = max.log.OD -# - inoc.log.OD: log.OD value at inoculation. Estimated value from the fitted model is used, rather than the actual measurement -# - max.log.OD: maximal log.OD value reached during the experiment. Estimated value from the fitted model is used rather than the actual measurement -# - projected.growth: maximal projected growth over inoculation value. Global sigmoid model: projected.growth = plateau - inoc.log.OD. LOESS: not reported -# - achieved.growth: maximal growth over inoculation value actually achieved during the experiment. achieved.growth = max.log.OD - inoc.log.OD -# - shape.par: shape parameter of the Richard equation -# - R.squared: goodness of fit metric. Also known as coefficient of determination. R.squared is usually between 0 and 1. A value close to 1 indicates good fit. -# - RSS: residual sum of squares. Another goodness of fit metric. Smaller values indicate better fits. -# - empty: (Well indicator) -# - an 'E' indicates that the well was empty and no growth was detected. -# - an 'I' indicates that the well was inoculated and growth was detected above the threshold. -# - an 'E*' indicates that the well was empty and growth was detected (possible contamination). -# - an '!' indicates that the well was inoculated and no growth was detected. -# - asymp.not.reached: shows “L” if the bottom asymptote (baseline) was not reached and “U” if the upper asymptote (plateau) was not reached. -# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index. -# - other: Additional flag column. Displays information about whether jumps in OD were detected and what was done about them. -# - pdf.file and page.no: location of the figure for this well in the output .pdf files. -# -# -- Source file information-- -# YPDAFEXglucoseTests_2-25-10.csv -# analyzed using GCAT v 5.0 -# request sent: 2015-04-07 15:34:27 -# completed: 2015-04-07 15:34:33 -# -# -- Parameters used in current analysis -- -# - Constant added to log(OD + n) transformation: 1 -# - Blank OD value: First timepoint in well -# - Index of inoculation timepoint 2 -# - Minimum growth threshold: 0.05 -# - Removed points: -# - Jump detection: FALSE \ No newline at end of file diff --git a/Rails/public/generatedFiles/20150407-1428438865/output_overview_2015-04-07_15.34.27.pdf b/Rails/public/generatedFiles/20150407-1428438865/output_overview_2015-04-07_15.34.27.pdf deleted file mode 100644 index a071993..0000000 Binary files a/Rails/public/generatedFiles/20150407-1428438865/output_overview_2015-04-07_15.34.27.pdf and /dev/null differ diff --git a/Rails/public/generatedFiles/20150407-1428438865/singlePlateAnalysis.zip b/Rails/public/generatedFiles/20150407-1428438865/singlePlateAnalysis.zip deleted file mode 100644 index 84e0ae4..0000000 Binary files a/Rails/public/generatedFiles/20150407-1428438865/singlePlateAnalysis.zip and /dev/null differ diff --git a/Rails/public/resources/GCAT_users_manual.pdf b/Rails/public/resources/GCAT_users_manual.pdf index 2f3a2f2..85358bb 100644 Binary files a/Rails/public/resources/GCAT_users_manual.pdf and b/Rails/public/resources/GCAT_users_manual.pdf differ diff --git a/Rails/public/resources/Release_Notes.pdf b/Rails/public/resources/Release_Notes.pdf new file mode 100644 index 0000000..cf7662c Binary files /dev/null and b/Rails/public/resources/Release_Notes.pdf differ diff --git a/Release Notes.odt b/Release Notes.odt new file mode 100644 index 0000000..10e0742 Binary files /dev/null and b/Release Notes.odt differ diff --git a/Testing/2009/Analysis 09-09-01.R b/Testing/2009/Analysis 09-09-01.R deleted file mode 100644 index 8326692..0000000 --- a/Testing/2009/Analysis 09-09-01.R +++ /dev/null @@ -1,40 +0,0 @@ -# R CMD INSTALL "C:/My Documents/GLBRC Projects/10_HTS_1/package/test.package" -library(test.package) - -USDA1.controls =c(paste("A0",1:9,sep=""), paste("A",10:12,sep=""), - paste("H0",1:9,sep=""), paste("H",10:12,sep=""), - "E10", "E11", "F08", "F09", "G08", "G09", "P.7", - paste(LETTERS[2:7],"01",sep=""), paste(LETTERS[2:7],"12",sep="")) - -Lalle1.controls = c("A11", "H11", paste(LETTERS[1:8],"01",sep=""), - paste(LETTERS[1:8],"12",sep=""), "A02") - -path = "C:/My Documents/GLBRC Projects/10_HTS_1/data" - -# Analyze the Lalle1 Plate -file = "Lalle1_media1_rep1_082909.csv" - -data = load.data(, path, file, column.names = c("Plate.ID", "Well", "OD", "Time"), - time.format = "%Y-%m-%d %H:%M:%S") -Lalle1 = analyze.screen(data, well.numbers = 1:768, scale = 0.5, remove.points = 1:2, - controls = Lalle1.controls , save.jpegs = F, autopilot = T) -write.csv(Lalle1, file = "Lalle1_analysis.csv") - -# Step by step -analyze.screen(data, scale = 0.5, remove.points = 1:2, - controls = Lalle1.controls , save.jpegs = F, autopilot = F) - -#Analyze the USDA1 Plate -file = "USDA1_Media1_Rep1_061909.csv" -data2 = load.data(, path, file, column.names = c("Plate.ID", "Well", "OD", "Time"), - time.format = "%Y-%m-%d %H:%M:%S") -USDA1 = analyze.screen(data2, scale = 0.5, remove.points = 1:2, - controls = Lalle1.controls , save.jpegs = F, autopilot = T) -write.csv(USDA1, file = "USDA1_analysis.csv") - - - -best.wells(Lalle1, "3.1") - - - diff --git a/Testing/2009/old_Jasons_tester.R b/Testing/2009/old_Jasons_tester.R deleted file mode 100644 index 84b2ad3..0000000 --- a/Testing/2009/old_Jasons_tester.R +++ /dev/null @@ -1,132 +0,0 @@ -#Setup -# Load from WIP files - -setwd( ) - -source("GLBRC Projects/10_HTS_1/package/test.package/R/load.R") -source("GLBRC Projects/10_HTS_1/package/test.package/R/misc_functions.R") -source("GLBRC Projects/10_HTS_1/package/test.package/R/curve.shapes.R") -source("GLBRC Projects/10_HTS_1/package/test.package/R/logistic.response.new.R") -source("GLBRC Projects/10_HTS_1/package/test.package/R/analyze.main.R") -source("GLBRC Projects/10_HTS_1/package/test.package/R/main.R") -source("GLBRC Projects/10_HTS_1/package/test.package/R/top.wells.R") -# OR: -# R CMD INSTALL "C:/My Documents/GLBRC Projects/10_HTS_1/package/test.package" -library(test.package) - -?analyze.screen -?load.data -?test.package -?top.wells -?analyze.main - - -path = "C:/My Documents/GLBRC Projects/10_HTS_1/data" -file = "072209a_USDA_screen.csv" -controls= c(paste(LETTERS[1:8],"01",sep=""),paste(LETTERS[1:8],"12",sep="")) - -data1 = load.data(, path, file, column.names = c("Plate.ID", "Well", "OD", "Time"), - time.format = "%Y-%m-%d %H:%M:%S") -output = analyze.screen(data1, scale = 0.5, controls = controls, save.jpegs = F, autopilot = T) - -# Step by step: -analyze.screen(data1, scale = 0.5, controls = controls, save.jpegs = F, autopilot = F) - -# equivalent (Save JPEGS): -analyze.screen(, path, file, controls = controls, save.jpegs = T, autopilot = F) - - -# Load another set -file = "YeastScreenData_ValidationRun_rawdata_4-16-09.csv" -controls=c("A11", "H11", paste(LETTERS[1:8],"01",sep=""), paste(LETTERS[1:8],"12",sep="")) - -data2 = load.data(, path, file, column.names = c("Plate.name", "Well", "OD600", "Timestamp"), - time.format = "%m/%d/%Y %H:%M:%S") -output2 = analyze.screen(data2, scale = 0.5, remove.points = 1, controls = controls, save.jpegs = F, autopilot = T) - -# Step by step: -analyze.screen(data2, well.numbers = 584, scale = 0.5, controls = controls, remove.points = 1, save.jpegs = F, autopilot = F) - -# equivalent (save JPEGS): -analyze.screen(, path, file, controls = controls, remove.points = 1:2, save.jpegs = T, autopilot = F) - - -output2[is.in.character("Error", output2[,4]),1] -> e -output2[is.in.character("above", output2[,4]),1] -> ab - -best.wells(output3) - - - - -# Load a single plate set -file = "YeastGrowthUSDAYPD30degrees3-19-09.csv" -controls=c(paste("A0",1:9,sep=""), paste("A",10:12,sep=""), - paste("H0",1:9,sep=""), paste("H",10:12,sep=""), - "E10", "E11", "F08", "F09", "G08", "G09", "P.7", - paste(LETTERS[2:7],"01",sep=""), paste(LETTERS[2:7],"12",sep="")) -data3 = load.data(, path, file, single.plate = T, single.columns = c("Time", "A1", "H12"), time.format = "%S") - -output3 = analyze.screen(data3, scale = 0.5, remove.points = 1:2, controls = controls, save.jpegs = F, autopilot = T) - -# Step by step: -analyze.screen(data3, scale = 0.5, controls = controls, remove.points = 1:2, save.jpegs = F, autopilot = F) - -# equivalent (save JPEGS): -analyze.screen(, path, file, controls = controls, remove.points = 1:2, save.jpegs = T, autopilot = F) - - - - - - - - - - - - - - -output = analyze.main(data1, scale = 0.5, controls = control.wells, remove.outliers = TRUE, autopilot = TRUE) -output2 = analyze.main(data1, controls = control.wells, remove.outliers = TRUE, autopilot = FALSE) - -summary(output2) - -output[is.finite(output$c) & output$c<0, ]$well.number - -output[is.finite(output$growth.ratio),]$well.number - -out.good.fit = output[output$curve.type == "" | output$curve.type == ": TANKING",] -summary(out.good.fit) -out.good.fit[,desired.columns] - -out.lin.fit = output[(output$linear.fit) & (output$curve.type == "" | output$curve.type == ": TANKING"),] -summary(out.lin.fit) -out.lin.fit[,desired.columns] - -out.lin.fit = output[(output$linear.fit & output$logistic.fit ) & (output$curve.type == "" | output$curve.type == ": TANKING"),] -out.lin.fit$well.number -out.lin.fit[,desired.columns] - -out.log.fit = output[(output$action == "Logistic model only.") & (output$curve.type == "" | output$curve.type == ": TANKING"),] -summary(out.log.fit) -out.log.fit[,desired.columns] - -out.no.s = output[output$curve.type == ": NOT S-SHAPE",] -summary(out.no.s[,desired.columns]) - -attention = output[grepl("(!)", output$remarks) & !output$curve.type == ": TANKING" ,] -summary(attention[,desired.columns]) - -out.no.fit = output[!(output$logistic.fit | output$linear.fit) & (output$curve.type == "" | output$curve.type == ": TANKING"),] -summary(out.no.fit[,desired.columns]) - -compare(output[output$total.growth <0,]$well.number) - -analyze.main(data1, well.numbers = out.no.s$well.number, controls = control.wells, remove.outliers = T, autopilot = FALSE) - -analyze.main(data1, well.numbers = attention$well.number, controls = control.wells, remove.outliers = T, autopilot = FALSE) - -results[results$Plate.name == "041609a.GLBRC2000P.1" & results$Well == "G06",] - diff --git a/Testing/GCAT_3_Test_Plan.docx b/Testing/GCAT_3_Test_Plan.docx deleted file mode 100755 index 1db4b4a..0000000 Binary files a/Testing/GCAT_3_Test_Plan.docx and /dev/null differ diff --git a/Testing/GCAT_3_test_report.xlsx b/Testing/GCAT_3_test_report.xlsx deleted file mode 100755 index 8cbd19b..0000000 Binary files a/Testing/GCAT_3_test_report.xlsx and /dev/null differ diff --git a/Testing/GCAT_Automated_Test_Script/Comparison Plots/Growth_Threshold Plot.pdf b/Testing/GCAT_Automated_Test_Script/Comparison Plots/Growth_Threshold Plot.pdf deleted file mode 100755 index 8d78a6d..0000000 Binary files a/Testing/GCAT_Automated_Test_Script/Comparison Plots/Growth_Threshold Plot.pdf and /dev/null differ diff --git a/Testing/GCAT_Automated_Test_Script/Comparison Plots/Inoculation Plot.pdf b/Testing/GCAT_Automated_Test_Script/Comparison Plots/Inoculation Plot.pdf deleted file mode 100755 index 3783446..0000000 Binary files a/Testing/GCAT_Automated_Test_Script/Comparison Plots/Inoculation Plot.pdf and /dev/null differ diff --git a/Testing/GCAT_Automated_Test_Script/Comparison Plots/Media_Background Plot.pdf b/Testing/GCAT_Automated_Test_Script/Comparison Plots/Media_Background Plot.pdf deleted file mode 100755 index 5c22d01..0000000 Binary files a/Testing/GCAT_Automated_Test_Script/Comparison Plots/Media_Background Plot.pdf and /dev/null differ diff --git a/Testing/GCAT_Automated_Test_Script/Comparison Plots/OD_Transform Plot.pdf b/Testing/GCAT_Automated_Test_Script/Comparison Plots/OD_Transform Plot.pdf deleted file mode 100755 index 5817eb9..0000000 Binary files a/Testing/GCAT_Automated_Test_Script/Comparison Plots/OD_Transform Plot.pdf and /dev/null differ diff --git a/Testing/GCAT_Automated_Test_Script/Comparison Plots/Points_Ignored Plot.pdf b/Testing/GCAT_Automated_Test_Script/Comparison Plots/Points_Ignored Plot.pdf deleted file mode 100755 index ce64ee5..0000000 Binary files a/Testing/GCAT_Automated_Test_Script/Comparison Plots/Points_Ignored Plot.pdf and /dev/null differ diff --git a/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/Growth_Threshold.txt b/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/Growth_Threshold.txt deleted file mode 100755 index bb675c8..0000000 --- a/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/Growth_Threshold.txt +++ /dev/null @@ -1,90 +0,0 @@ -Command: -Rscript compare_gcat_outputs.R ./GCAT2/Growth_Threshold.txt ./GCAT3/Growth_Threshold.txt Growth_Threshold - -Summary: - - Mode TRUE NA's -logical 96 0 -[1] TRUE TRUE TRUE TRUE TRUE TRUE - - -GCAT2: - - row plate well media strain model spec.growth -1 1 YPDAFEXglucoseTests_2-25-10 A01 None Empty : skipped NA -2 2 YPDAFEXglucoseTests_2-25-10 B01 None Empty : skipped NA -3 3 YPDAFEXglucoseTests_2-25-10 C01 None Empty : skipped NA -4 4 YPDAFEXglucoseTests_2-25-10 D01 None Empty : skipped NA -5 5 YPDAFEXglucoseTests_2-25-10 E01 None Empty : skipped NA -6 6 YPDAFEXglucoseTests_2-25-10 F01 None Empty : skipped NA - tot.growth lag.time inoc.OD good.fit empty asymp tank reach other -1 NA NA NA NA E - - NA NA -2 NA NA NA NA E - - NA NA -3 NA NA NA NA E - - NA NA -4 NA NA NA NA E - - NA NA -5 NA NA NA NA E - - NA NA -6 NA NA NA NA E - - NA NA - pdf.file page.no -1 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf 2 -2 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf 3 -3 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf 4 -4 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf 5 -5 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf 6 -6 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf 7 - Destination.plate.name Well.ID Plate.source Well.Source -1 Control strain plate Empty Empty Empty -2 Control strain plate Empty Empty Empty -3 Control strain plate Empty Empty Empty -4 Control strain plate Empty Empty Empty -5 Control strain plate Empty Empty Empty -6 Control strain plate Empty Empty Empty - - -GCAT3: - - row plate well media strain model spec.growth -1 1 YPDAFEXglucoseTests_2-25-10 A01 None Empty : skipped NA -2 2 YPDAFEXglucoseTests_2-25-10 B01 None Empty : skipped NA -3 3 YPDAFEXglucoseTests_2-25-10 C01 None Empty : skipped NA -4 4 YPDAFEXglucoseTests_2-25-10 D01 None Empty : skipped NA -5 5 YPDAFEXglucoseTests_2-25-10 E01 None Empty : skipped NA -6 6 YPDAFEXglucoseTests_2-25-10 F01 None Empty : skipped NA - tot.growth lag.time inoc.OD good.fit empty asymp tank reach other -1 NA NA NA NA E - - NA NA -2 NA NA NA NA E - - NA NA -3 NA NA NA NA E - - NA NA -4 NA NA NA NA E - - NA NA -5 NA NA NA NA E - - NA NA -6 NA NA NA NA E - - NA NA - pdf.file page.no -1 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf 2 -2 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf 3 -3 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf 4 -4 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf 5 -5 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf 6 -6 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf 7 - Destination.plate.name Well.ID Plate.source Well.Source -1 Control strain plate Empty Empty Empty -2 Control strain plate Empty Empty Empty -3 Control strain plate Empty Empty Empty -4 Control strain plate Empty Empty Empty -5 Control strain plate Empty Empty Empty -6 Control strain plate Empty Empty Empty - - -Specific Growth Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 95 - - -Total Growth Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 95 - - -Lag Time Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 95 diff --git a/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/Inoculation.txt b/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/Inoculation.txt deleted file mode 100755 index dee4951..0000000 --- a/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/Inoculation.txt +++ /dev/null @@ -1,110 +0,0 @@ -Command: -Rscript compare_gcat_outputs.R ./GCAT2/Inoculation.txt ./GCAT3/Inoculation.txt Inoculation - -Summary: - - Mode TRUE NA's -logical 96 0 -[1] TRUE TRUE TRUE TRUE TRUE TRUE - - -GCAT2: - - row plate well media strain model spec.growth -1 1 YPDAFEXglucoseTests_2-25-10 A01 None Empty : skipped NA -2 2 YPDAFEXglucoseTests_2-25-10 B01 None Empty : skipped NA -3 3 YPDAFEXglucoseTests_2-25-10 C01 None Empty : skipped NA -4 4 YPDAFEXglucoseTests_2-25-10 D01 None Empty : skipped NA -5 5 YPDAFEXglucoseTests_2-25-10 E01 None Empty : skipped NA -6 6 YPDAFEXglucoseTests_2-25-10 F01 None Empty : skipped NA - tot.growth lag.time inoc.OD good.fit empty asymp tank reach other -1 NA NA NA NA E - - NA NA -2 NA NA NA NA E - - NA NA -3 NA NA NA NA E - - NA NA -4 NA NA NA NA E - - NA NA -5 NA NA NA NA E - - NA NA -6 NA NA NA NA E - - NA NA - pdf.file page.no -1 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf 2 -2 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf 3 -3 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf 4 -4 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf 5 -5 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf 6 -6 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf 7 - Destination.plate.name Well.ID Plate.source Well.Source -1 Control strain plate Empty Empty Empty -2 Control strain plate Empty Empty Empty -3 Control strain plate Empty Empty Empty -4 Control strain plate Empty Empty Empty -5 Control strain plate Empty Empty Empty -6 Control strain plate Empty Empty Empty - - -GCAT3: - - row plate well media strain model spec.growth -1 1 YPDAFEXglucoseTests_2-25-10 A01 None Empty : skipped NA -2 2 YPDAFEXglucoseTests_2-25-10 B01 None Empty : skipped NA -3 3 YPDAFEXglucoseTests_2-25-10 C01 None Empty : skipped NA -4 4 YPDAFEXglucoseTests_2-25-10 D01 None Empty : skipped NA -5 5 YPDAFEXglucoseTests_2-25-10 E01 None Empty : skipped NA -6 6 YPDAFEXglucoseTests_2-25-10 F01 None Empty : skipped NA - tot.growth lag.time inoc.OD good.fit empty asymp tank reach other -1 NA NA NA NA E - - NA NA -2 NA NA NA NA E - - NA NA -3 NA NA NA NA E - - NA NA -4 NA NA NA NA E - - NA NA -5 NA NA NA NA E - - NA NA -6 NA NA NA NA E - - NA NA - pdf.file page.no -1 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf 2 -2 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf 3 -3 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf 4 -4 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf 5 -5 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf 6 -6 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf 7 - Destination.plate.name Well.ID Plate.source Well.Source Media.Definition -1 Control strain plate Empty Empty Empty None -2 Control strain plate Empty Empty Empty None -3 Control strain plate Empty Empty Empty None -4 Control strain plate Empty Empty Empty None -5 Control strain plate Empty Empty Empty None -6 Control strain plate Empty Empty Empty None - - -Specific Growth Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 49 - - -Total Growth Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 49 - - -Lag Time Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 49 -null device - 1 - [1] row plate well - [4] media strain model - [7] spec.growth tot.growth lag.time -[10] inoc.OD good.fit empty -[13] asymp tank reach -[16] other pdf.file page.no -[19] Destination.plate.name Well.ID Plate.source -[22] Well.Source -<0 rows> (or 0-length row.names) - [1] row plate well - [4] media strain model - [7] spec.growth tot.growth lag.time -[10] inoc.OD good.fit empty -[13] asymp tank reach -[16] other pdf.file page.no -[19] Destination.plate.name Well.ID Plate.source -[22] Well.Source Media.Definition -<0 rows> (or 0-length row.names) diff --git a/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/Media_Background.txt b/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/Media_Background.txt deleted file mode 100755 index b461782..0000000 --- a/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/Media_Background.txt +++ /dev/null @@ -1,110 +0,0 @@ -Command: -Rscript compare_gcat_outputs.R ./GCAT2/Media_Background.txt ./GCAT3/Media_Background.txt Media_Background - -Summary: - - Mode TRUE NA's -logical 96 0 -[1] TRUE TRUE TRUE TRUE TRUE TRUE - - -GCAT2: - - row plate well media strain model spec.growth -1 1 YPDAFEXglucoseTests_2-25-10 A01 None Empty : skipped NA -2 2 YPDAFEXglucoseTests_2-25-10 B01 None Empty : skipped NA -3 3 YPDAFEXglucoseTests_2-25-10 C01 None Empty : skipped NA -4 4 YPDAFEXglucoseTests_2-25-10 D01 None Empty : skipped NA -5 5 YPDAFEXglucoseTests_2-25-10 E01 None Empty : skipped NA -6 6 YPDAFEXglucoseTests_2-25-10 F01 None Empty : skipped NA - tot.growth lag.time inoc.OD good.fit empty asymp tank reach other -1 NA NA NA NA E - - NA NA -2 NA NA NA NA E - - NA NA -3 NA NA NA NA E - - NA NA -4 NA NA NA NA E - - NA NA -5 NA NA NA NA E - - NA NA -6 NA NA NA NA E - - NA NA - pdf.file page.no -1 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf 2 -2 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf 3 -3 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf 4 -4 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf 5 -5 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf 6 -6 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf 7 - Destination.plate.name Well.ID Plate.source Well.Source -1 Control strain plate Empty Empty Empty -2 Control strain plate Empty Empty Empty -3 Control strain plate Empty Empty Empty -4 Control strain plate Empty Empty Empty -5 Control strain plate Empty Empty Empty -6 Control strain plate Empty Empty Empty - - -GCAT3: - - row plate well media strain model spec.growth -1 1 YPDAFEXglucoseTests_2-25-10 A01 None Empty : skipped NA -2 2 YPDAFEXglucoseTests_2-25-10 B01 None Empty : skipped NA -3 3 YPDAFEXglucoseTests_2-25-10 C01 None Empty : skipped NA -4 4 YPDAFEXglucoseTests_2-25-10 D01 None Empty : skipped NA -5 5 YPDAFEXglucoseTests_2-25-10 E01 None Empty : skipped NA -6 6 YPDAFEXglucoseTests_2-25-10 F01 None Empty : skipped NA - tot.growth lag.time inoc.OD good.fit empty asymp tank reach other -1 NA NA NA NA E - - NA NA -2 NA NA NA NA E - - NA NA -3 NA NA NA NA E - - NA NA -4 NA NA NA NA E - - NA NA -5 NA NA NA NA E - - NA NA -6 NA NA NA NA E - - NA NA - pdf.file page.no -1 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf 2 -2 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf 3 -3 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf 4 -4 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf 5 -5 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf 6 -6 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf 7 - Destination.plate.name Well.ID Plate.source Well.Source Media.Definition -1 Control strain plate Empty Empty Empty None -2 Control strain plate Empty Empty Empty None -3 Control strain plate Empty Empty Empty None -4 Control strain plate Empty Empty Empty None -5 Control strain plate Empty Empty Empty None -6 Control strain plate Empty Empty Empty None - - -Specific Growth Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 50 - - -Total Growth Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 50 - - -Lag Time Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 50 -null device - 1 - [1] row plate well - [4] media strain model - [7] spec.growth tot.growth lag.time -[10] inoc.OD good.fit empty -[13] asymp tank reach -[16] other pdf.file page.no -[19] Destination.plate.name Well.ID Plate.source -[22] Well.Source -<0 rows> (or 0-length row.names) - [1] row plate well - [4] media strain model - [7] spec.growth tot.growth lag.time -[10] inoc.OD good.fit empty -[13] asymp tank reach -[16] other pdf.file page.no -[19] Destination.plate.name Well.ID Plate.source -[22] Well.Source Media.Definition -<0 rows> (or 0-length row.names) diff --git a/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/OD_Transform.txt b/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/OD_Transform.txt deleted file mode 100755 index 880d8fe..0000000 --- a/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/OD_Transform.txt +++ /dev/null @@ -1,110 +0,0 @@ -Command: -Rscript compare_gcat_outputs.R ./GCAT2/OD_Transform.txt ./GCAT3/OD_Transform.txt OD_Transform - -Summary: - - Mode TRUE NA's -logical 96 0 -[1] TRUE TRUE TRUE TRUE TRUE TRUE - - -GCAT2: - - row plate well media strain model spec.growth -1 1 YPDAFEXglucoseTests_2-25-10 A01 None Empty : skipped NA -2 2 YPDAFEXglucoseTests_2-25-10 B01 None Empty : skipped NA -3 3 YPDAFEXglucoseTests_2-25-10 C01 None Empty : skipped NA -4 4 YPDAFEXglucoseTests_2-25-10 D01 None Empty : skipped NA -5 5 YPDAFEXglucoseTests_2-25-10 E01 None Empty : skipped NA -6 6 YPDAFEXglucoseTests_2-25-10 F01 None Empty : skipped NA - tot.growth lag.time inoc.OD good.fit empty asymp tank reach other -1 NA NA NA NA E - - NA NA -2 NA NA NA NA E - - NA NA -3 NA NA NA NA E - - NA NA -4 NA NA NA NA E - - NA NA -5 NA NA NA NA E - - NA NA -6 NA NA NA NA E - - NA NA - pdf.file page.no -1 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf 2 -2 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf 3 -3 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf 4 -4 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf 5 -5 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf 6 -6 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf 7 - Destination.plate.name Well.ID Plate.source Well.Source -1 Control strain plate Empty Empty Empty -2 Control strain plate Empty Empty Empty -3 Control strain plate Empty Empty Empty -4 Control strain plate Empty Empty Empty -5 Control strain plate Empty Empty Empty -6 Control strain plate Empty Empty Empty - - -GCAT3: - - row plate well media strain model spec.growth -1 1 YPDAFEXglucoseTests_2-25-10 A01 None Empty : skipped NA -2 2 YPDAFEXglucoseTests_2-25-10 B01 None Empty : skipped NA -3 3 YPDAFEXglucoseTests_2-25-10 C01 None Empty : skipped NA -4 4 YPDAFEXglucoseTests_2-25-10 D01 None Empty : skipped NA -5 5 YPDAFEXglucoseTests_2-25-10 E01 None Empty : skipped NA -6 6 YPDAFEXglucoseTests_2-25-10 F01 None Empty : skipped NA - tot.growth lag.time inoc.OD good.fit empty asymp tank reach other -1 NA NA NA NA E - - NA NA -2 NA NA NA NA E - - NA NA -3 NA NA NA NA E - - NA NA -4 NA NA NA NA E - - NA NA -5 NA NA NA NA E - - NA NA -6 NA NA NA NA E - - NA NA - pdf.file page.no -1 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf 2 -2 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf 3 -3 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf 4 -4 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf 5 -5 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf 6 -6 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf 7 - Destination.plate.name Well.ID Plate.source Well.Source Media.Definition -1 Control strain plate Empty Empty Empty None -2 Control strain plate Empty Empty Empty None -3 Control strain plate Empty Empty Empty None -4 Control strain plate Empty Empty Empty None -5 Control strain plate Empty Empty Empty None -6 Control strain plate Empty Empty Empty None - - -Specific Growth Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 49 - - -Total Growth Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 49 - - -Lag Time Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 49 -null device - 1 - [1] row plate well - [4] media strain model - [7] spec.growth tot.growth lag.time -[10] inoc.OD good.fit empty -[13] asymp tank reach -[16] other pdf.file page.no -[19] Destination.plate.name Well.ID Plate.source -[22] Well.Source -<0 rows> (or 0-length row.names) - [1] row plate well - [4] media strain model - [7] spec.growth tot.growth lag.time -[10] inoc.OD good.fit empty -[13] asymp tank reach -[16] other pdf.file page.no -[19] Destination.plate.name Well.ID Plate.source -[22] Well.Source Media.Definition -<0 rows> (or 0-length row.names) diff --git a/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/Points_Ignored.txt b/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/Points_Ignored.txt deleted file mode 100755 index 7cfb9ed..0000000 --- a/Testing/GCAT_Automated_Test_Script/Comparison_Datasets/Points_Ignored.txt +++ /dev/null @@ -1,110 +0,0 @@ -Command: -Rscript compare_gcat_outputs.R ./GCAT2/Points_Ignored.txt ./GCAT3/Points_Ignored.txt Points_Ignored - -Summary: - - Mode TRUE NA's -logical 96 0 -[1] TRUE TRUE TRUE TRUE TRUE TRUE - - -GCAT2: - - row plate well media strain model spec.growth -1 1 YPDAFEXglucoseTests_2-25-10 A01 None Empty : skipped NA -2 2 YPDAFEXglucoseTests_2-25-10 B01 None Empty : skipped NA -3 3 YPDAFEXglucoseTests_2-25-10 C01 None Empty : skipped NA -4 4 YPDAFEXglucoseTests_2-25-10 D01 None Empty : skipped NA -5 5 YPDAFEXglucoseTests_2-25-10 E01 None Empty : skipped NA -6 6 YPDAFEXglucoseTests_2-25-10 F01 None Empty : skipped NA - tot.growth lag.time inoc.OD good.fit empty asymp tank reach other -1 NA NA NA NA E - - NA NA -2 NA NA NA NA E - - NA NA -3 NA NA NA NA E - - NA NA -4 NA NA NA NA E - - NA NA -5 NA NA NA NA E - - NA NA -6 NA NA NA NA E - - NA NA - pdf.file page.no -1 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf 2 -2 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf 3 -3 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf 4 -4 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf 5 -5 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf 6 -6 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf 7 - Destination.plate.name Well.ID Plate.source Well.Source -1 Control strain plate Empty Empty Empty -2 Control strain plate Empty Empty Empty -3 Control strain plate Empty Empty Empty -4 Control strain plate Empty Empty Empty -5 Control strain plate Empty Empty Empty -6 Control strain plate Empty Empty Empty - - -GCAT3: - - row plate well media strain model spec.growth -1 1 YPDAFEXglucoseTests_2-25-10 A01 None Empty : skipped NA -2 2 YPDAFEXglucoseTests_2-25-10 B01 None Empty : skipped NA -3 3 YPDAFEXglucoseTests_2-25-10 C01 None Empty : skipped NA -4 4 YPDAFEXglucoseTests_2-25-10 D01 None Empty : skipped NA -5 5 YPDAFEXglucoseTests_2-25-10 E01 None Empty : skipped NA -6 6 YPDAFEXglucoseTests_2-25-10 F01 None Empty : skipped NA - tot.growth lag.time inoc.OD good.fit empty asymp tank reach other -1 NA NA NA NA E - - NA NA -2 NA NA NA NA E - - NA NA -3 NA NA NA NA E - - NA NA -4 NA NA NA NA E - - NA NA -5 NA NA NA NA E - - NA NA -6 NA NA NA NA E - - NA NA - pdf.file page.no -1 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf 2 -2 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf 3 -3 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf 4 -4 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf 5 -5 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf 6 -6 YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf 7 - Destination.plate.name Well.ID Plate.source Well.Source Media.Definition -1 Control strain plate Empty Empty Empty None -2 Control strain plate Empty Empty Empty None -3 Control strain plate Empty Empty Empty None -4 Control strain plate Empty Empty Empty None -5 Control strain plate Empty Empty Empty None -6 Control strain plate Empty Empty Empty None - - -Specific Growth Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 49 - - -Total Growth Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 49 - - -Lag Time Comparison Summary: - - Min. 1st Qu. Median Mean 3rd Qu. Max. NA's - 1 1 1 1 1 1 49 -null device - 1 - [1] row plate well - [4] media strain model - [7] spec.growth tot.growth lag.time -[10] inoc.OD good.fit empty -[13] asymp tank reach -[16] other pdf.file page.no -[19] Destination.plate.name Well.ID Plate.source -[22] Well.Source -<0 rows> (or 0-length row.names) - [1] row plate well - [4] media strain model - [7] spec.growth tot.growth lag.time -[10] inoc.OD good.fit empty -[13] asymp tank reach -[16] other pdf.file page.no -[19] Destination.plate.name Well.ID Plate.source -[22] Well.Source Media.Definition -<0 rows> (or 0-length row.names) diff --git a/Testing/GCAT_Automated_Test_Script/GCAT2/Growth_Threshold.txt b/Testing/GCAT_Automated_Test_Script/GCAT2/Growth_Threshold.txt deleted file mode 100755 index 65a65d0..0000000 --- a/Testing/GCAT_Automated_Test_Script/GCAT2/Growth_Threshold.txt +++ /dev/null @@ -1,129 +0,0 @@ -"row" "plate" "well" "media" "strain" "model" "spec.growth" "tot.growth" "lag.time" "inoc.OD" "good.fit" "empty" "asymp" "tank" "reach" "other" "pdf.file" "page.no" "Destination.plate.name" "Well.ID" "Plate.source" "Well.Source" -1 "YPDAFEXglucoseTests_2-25-10" "A01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 2 "Control strain plate" "Empty" "Empty" "Empty" -2 "YPDAFEXglucoseTests_2-25-10" "B01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 3 "Control strain plate" "Empty" "Empty" "Empty" -3 "YPDAFEXglucoseTests_2-25-10" "C01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 4 "Control strain plate" "Empty" "Empty" "Empty" -4 "YPDAFEXglucoseTests_2-25-10" "D01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 5 "Control strain plate" "Empty" "Empty" "Empty" -5 "YPDAFEXglucoseTests_2-25-10" "E01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 6 "Control strain plate" "Empty" "Empty" "Empty" -6 "YPDAFEXglucoseTests_2-25-10" "F01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 7 "Control strain plate" "Empty" "Empty" "Empty" -7 "YPDAFEXglucoseTests_2-25-10" "G01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 8 "Control strain plate" "Empty" "Empty" "Empty" -8 "YPDAFEXglucoseTests_2-25-10" "H01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 9 "Control strain plate" "Empty" "Empty" "Empty" -9 "YPDAFEXglucoseTests_2-25-10" "A02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 10 "Control strain plate" "Empty" "Empty" "Empty" -10 "YPDAFEXglucoseTests_2-25-10" "B02" "YP" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 11 "Control strain plate" "Sample" "USDA" "" -11 "YPDAFEXglucoseTests_2-25-10" "C02" "YP+0.25% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 12 "Control strain plate" "Sample" "USDA" "" -12 "YPDAFEXglucoseTests_2-25-10" "D02" "YP+0.5% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 13 "Control strain plate" "Sample" "USDA" "" -13 "YPDAFEXglucoseTests_2-25-10" "E02" "YP+1% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 14 "Control strain plate" "Sample" "USDA" "" -14 "YPDAFEXglucoseTests_2-25-10" "F02" "YP+2% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 15 "Control strain plate" "Sample" "USDA" "" -15 "YPDAFEXglucoseTests_2-25-10" "G02" "YP+5% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 16 "Control strain plate" "Sample" "USDA" "" -16 "YPDAFEXglucoseTests_2-25-10" "H02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 17 "Control strain plate" "Empty" "Empty" "Empty" -17 "YPDAFEXglucoseTests_2-25-10" "A03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 18 "Control strain plate" "Empty" "Empty" "Empty" -18 "YPDAFEXglucoseTests_2-25-10" "B03" "YP" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 19 "Control strain plate" "Sample" "USDA" "" -19 "YPDAFEXglucoseTests_2-25-10" "C03" "YP+0.25% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 20 "Control strain plate" "Sample" "USDA" "" -20 "YPDAFEXglucoseTests_2-25-10" "D03" "YP+0.5% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 21 "Control strain plate" "Sample" "USDA" "" -21 "YPDAFEXglucoseTests_2-25-10" "E03" "YP+1% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 22 "Control strain plate" "Sample" "USDA" "" -22 "YPDAFEXglucoseTests_2-25-10" "F03" "YP+2% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 23 "Control strain plate" "Sample" "USDA" "" -23 "YPDAFEXglucoseTests_2-25-10" "G03" "YP+5% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 24 "Control strain plate" "Sample" "USDA" "" -24 "YPDAFEXglucoseTests_2-25-10" "H03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 25 "Control strain plate" "Empty" "Empty" "Empty" -25 "YPDAFEXglucoseTests_2-25-10" "A04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 26 "Control strain plate" "Empty" "Empty" "Empty" -26 "YPDAFEXglucoseTests_2-25-10" "B04" "YP" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 27 "Control strain plate" "Sample" "Internal source" "" -27 "YPDAFEXglucoseTests_2-25-10" "C04" "YP+0.25% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 28 "Control strain plate" "Sample" "Internal source" "" -28 "YPDAFEXglucoseTests_2-25-10" "D04" "YP+0.5% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 29 "Control strain plate" "Sample" "Internal source" "" -29 "YPDAFEXglucoseTests_2-25-10" "E04" "YP+1% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 30 "Control strain plate" "Sample" "Internal source" "" -30 "YPDAFEXglucoseTests_2-25-10" "F04" "YP+2% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 31 "Control strain plate" "Sample" "Internal source" "" -31 "YPDAFEXglucoseTests_2-25-10" "G04" "YP+5% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 32 "Control strain plate" "Sample" "Internal source" "" -32 "YPDAFEXglucoseTests_2-25-10" "H04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 33 "Control strain plate" "Empty" "Empty" "Empty" -33 "YPDAFEXglucoseTests_2-25-10" "A05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 34 "Control strain plate" "Empty" "Empty" "Empty" -34 "YPDAFEXglucoseTests_2-25-10" "B05" "YP" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 35 "Control strain plate" "Sample" "ATCC" "" -35 "YPDAFEXglucoseTests_2-25-10" "C05" "YP+0.25% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 36 "Control strain plate" "Sample" "ATCC" "" -36 "YPDAFEXglucoseTests_2-25-10" "D05" "YP+0.5% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 37 "Control strain plate" "Sample" "ATCC" "" -37 "YPDAFEXglucoseTests_2-25-10" "E05" "YP+1% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 38 "Control strain plate" "Sample" "ATCC" "" -38 "YPDAFEXglucoseTests_2-25-10" "F05" "YP+2% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 39 "Control strain plate" "Sample" "ATCC" "" -39 "YPDAFEXglucoseTests_2-25-10" "G05" "YP+5% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 40 "Control strain plate" "Sample" "ATCC" "" -40 "YPDAFEXglucoseTests_2-25-10" "H05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 41 "Control strain plate" "Empty" "Empty" "Empty" -41 "YPDAFEXglucoseTests_2-25-10" "A06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 42 "Control strain plate" "Empty" "Empty" "Empty" -42 "YPDAFEXglucoseTests_2-25-10" "B06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 43 "Control strain plate" "Empty" "Empty" "Empty" -43 "YPDAFEXglucoseTests_2-25-10" "C06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 44 "Control strain plate" "Empty" "Empty" "Empty" -44 "YPDAFEXglucoseTests_2-25-10" "D06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 45 "Control strain plate" "Empty" "Empty" "Empty" -45 "YPDAFEXglucoseTests_2-25-10" "E06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 46 "Control strain plate" "Empty" "Empty" "Empty" -46 "YPDAFEXglucoseTests_2-25-10" "F06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 47 "Control strain plate" "Empty" "Empty" "Empty" -47 "YPDAFEXglucoseTests_2-25-10" "G06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 48 "Control strain plate" "Empty" "Empty" "Empty" -48 "YPDAFEXglucoseTests_2-25-10" "H06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 49 "Control strain plate" "Empty" "Empty" "Empty" -49 "YPDAFEXglucoseTests_2-25-10" "A07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 50 "Control strain plate" "Empty" "Empty" "Empty" -50 "YPDAFEXglucoseTests_2-25-10" "B07" "AFEX" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 51 "Control strain plate" "Sample" "USDA" "" -51 "YPDAFEXglucoseTests_2-25-10" "C07" "AFEX+0.25% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 52 "Control strain plate" "Sample" "USDA" "" -52 "YPDAFEXglucoseTests_2-25-10" "D07" "AFEX+0.5% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 53 "Control strain plate" "Sample" "USDA" "" -53 "YPDAFEXglucoseTests_2-25-10" "E07" "AFEX+1% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 54 "Control strain plate" "Sample" "USDA" "" -54 "YPDAFEXglucoseTests_2-25-10" "F07" "AFEX+2% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 55 "Control strain plate" "Sample" "USDA" "" -55 "YPDAFEXglucoseTests_2-25-10" "G07" "AFEX+5% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 56 "Control strain plate" "Sample" "USDA" "" -56 "YPDAFEXglucoseTests_2-25-10" "H07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 57 "Control strain plate" "Empty" "Empty" "Empty" -57 "YPDAFEXglucoseTests_2-25-10" "A08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 58 "Control strain plate" "Empty" "Empty" "Empty" -58 "YPDAFEXglucoseTests_2-25-10" "B08" "AFEX" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 59 "Control strain plate" "Sample" "USDA" "" -59 "YPDAFEXglucoseTests_2-25-10" "C08" "AFEX+0.25% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 60 "Control strain plate" "Sample" "USDA" "" -60 "YPDAFEXglucoseTests_2-25-10" "D08" "AFEX+0.5% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 61 "Control strain plate" "Sample" "USDA" "" -61 "YPDAFEXglucoseTests_2-25-10" "E08" "AFEX+1% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 62 "Control strain plate" "Sample" "USDA" "" -62 "YPDAFEXglucoseTests_2-25-10" "F08" "AFEX+2% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 63 "Control strain plate" "Sample" "USDA" "" -63 "YPDAFEXglucoseTests_2-25-10" "G08" "AFEX+5% glucose" "Wild strain" "richards 5-par." 0.104909957772007 1.38120323294419 3.5400282340856 0.0841025860310471 3.54895808838236 "I " "-" "-" 99.9341701264792 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 64 "Control strain plate" "Sample" "USDA" "" -64 "YPDAFEXglucoseTests_2-25-10" "H08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 65 "Control strain plate" "Empty" "Empty" "Empty" -65 "YPDAFEXglucoseTests_2-25-10" "A09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 66 "Control strain plate" "Empty" "Empty" "Empty" -66 "YPDAFEXglucoseTests_2-25-10" "B09" "AFEX" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 67 "Control strain plate" "Sample" "Internal source" "" -67 "YPDAFEXglucoseTests_2-25-10" "C09" "AFEX+0.25% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 68 "Control strain plate" "Sample" "Internal source" "" -68 "YPDAFEXglucoseTests_2-25-10" "D09" "AFEX+0.5% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 69 "Control strain plate" "Sample" "Internal source" "" -69 "YPDAFEXglucoseTests_2-25-10" "E09" "AFEX+1% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 70 "Control strain plate" "Sample" "Internal source" "" -70 "YPDAFEXglucoseTests_2-25-10" "F09" "AFEX+2% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 71 "Control strain plate" "Sample" "Internal source" "" -71 "YPDAFEXglucoseTests_2-25-10" "G09" "AFEX+5% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 72 "Control strain plate" "Sample" "Internal source" "" -72 "YPDAFEXglucoseTests_2-25-10" "H09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 73 "Control strain plate" "Empty" "Empty" "Empty" -73 "YPDAFEXglucoseTests_2-25-10" "A10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 74 "Control strain plate" "Empty" "Empty" "Empty" -74 "YPDAFEXglucoseTests_2-25-10" "B10" "AFEX" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 75 "Control strain plate" "Sample" "ATCC" "" -75 "YPDAFEXglucoseTests_2-25-10" "C10" "AFEX+0.25% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 76 "Control strain plate" "Sample" "ATCC" "" -76 "YPDAFEXglucoseTests_2-25-10" "D10" "AFEX+0.5% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 77 "Control strain plate" "Sample" "ATCC" "" -77 "YPDAFEXglucoseTests_2-25-10" "E10" "AFEX+1% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 78 "Control strain plate" "Sample" "ATCC" "" -78 "YPDAFEXglucoseTests_2-25-10" "F10" "AFEX+2% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 79 "Control strain plate" "Sample" "ATCC" "" -79 "YPDAFEXglucoseTests_2-25-10" "G10" "AFEX+5% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 80 "Control strain plate" "Sample" "ATCC" "" -80 "YPDAFEXglucoseTests_2-25-10" "H10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 81 "Control strain plate" "Empty" "Empty" "Empty" -81 "YPDAFEXglucoseTests_2-25-10" "A11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 82 "Control strain plate" "Empty" "Empty" "Empty" -82 "YPDAFEXglucoseTests_2-25-10" "B11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 83 "Control strain plate" "Empty" "Empty" "Empty" -83 "YPDAFEXglucoseTests_2-25-10" "C11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 84 "Control strain plate" "Empty" "Empty" "Empty" -84 "YPDAFEXglucoseTests_2-25-10" "D11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 85 "Control strain plate" "Empty" "Empty" "Empty" -85 "YPDAFEXglucoseTests_2-25-10" "E11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 86 "Control strain plate" "Empty" "Empty" "Empty" -86 "YPDAFEXglucoseTests_2-25-10" "F11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 87 "Control strain plate" "Empty" "Empty" "Empty" -87 "YPDAFEXglucoseTests_2-25-10" "G11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 88 "Control strain plate" "Empty" "Empty" "Empty" -88 "YPDAFEXglucoseTests_2-25-10" "H11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 89 "Control strain plate" "Empty" "Empty" "Empty" -89 "YPDAFEXglucoseTests_2-25-10" "A12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 90 "Control strain plate" "Empty" "Empty" "Empty" -90 "YPDAFEXglucoseTests_2-25-10" "B12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 91 "Control strain plate" "Empty" "Empty" "Empty" -91 "YPDAFEXglucoseTests_2-25-10" "C12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 92 "Control strain plate" "Empty" "Empty" "Empty" -92 "YPDAFEXglucoseTests_2-25-10" "D12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 93 "Control strain plate" "Empty" "Empty" "Empty" -93 "YPDAFEXglucoseTests_2-25-10" "E12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 94 "Control strain plate" "Empty" "Empty" "Empty" -94 "YPDAFEXglucoseTests_2-25-10" "F12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 95 "Control strain plate" "Empty" "Empty" "Empty" -95 "YPDAFEXglucoseTests_2-25-10" "G12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 96 "Control strain plate" "Empty" "Empty" "Empty" -96 "YPDAFEXglucoseTests_2-25-10" "H12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 97 "Control strain plate" "Empty" "Empty" "Empty" - -# -- Explanation of columns -- -# - model: Name of the model the well was successfully fit with (if any) -# - spec.growth: (Specific growth rate) The largest exponential growth rate achieved by the culture in the course of the experiment -# - tot.growth: (Total extrapolated growth) The estimated growth plateau from the fitted model in optical density units. May be higher than the actual highest OD reached. -# - lag.time: (Lag time) The exponential trend from is extrapolated to the baseline OD at inoculation and subtracted from the time at inoculation to yield lag time. -# - inoc.OD: (OD at inoculation) The adjusted optical density at the user-specified starting timepoint. -# - good.fit: (Goodness of fit) A metric based on root mean square deviations (RMSD). -# - higher values ( > 3.0) indicate a very good fit while lower values (< 2.0) indicate generally unacceptable fits. -# - empty: (Well indicator) -# - an 'E' indicates that the well was empty and no growth was detected. -# - an 'I' indicates that the well was inoculated and growth was detected above the threshold. -# - an 'E*' indicates that the well was empty and growth was detected (possible contamination). -# - an '!' indicates that the well was inoculated and no growth was detected. -# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index. -# - reach: (Final growth percentage): The percentage of reached by the culture in the course of the experiment. -# - other: Other information includes output from jump detection algorithm and additional columns from the Plate Layout. -# - pdf.file and page.no: location of the figure for this well in the output .pdf files. -# -# -- Source file information-- -# YPDAFEXglucoseTests_2-25-10.csv -# analyzed using GCAT v 0.01 -# request sent: 2013-11-26 11:58:22 -# completed: 2013-11-26 11:58:30 -# -# -- Parameters used in current analysis -- -# - Constant added to log(OD + n) transformation: 1 -# - Blank OD value: First timepoint in well -# - Index of inoculation timepoint 2 -# - Minimum growth threshold: 1.37 -# - Removed points: -# - Jump detection: FALSE \ No newline at end of file diff --git a/Testing/GCAT_Automated_Test_Script/GCAT2/Inoculation.txt b/Testing/GCAT_Automated_Test_Script/GCAT2/Inoculation.txt deleted file mode 100755 index 21cee24..0000000 --- a/Testing/GCAT_Automated_Test_Script/GCAT2/Inoculation.txt +++ /dev/null @@ -1,129 +0,0 @@ -"row" "plate" "well" "media" "strain" "model" "spec.growth" "tot.growth" "lag.time" "inoc.OD" "good.fit" "empty" "asymp" "tank" "reach" "other" "pdf.file" "page.no" "Destination.plate.name" "Well.ID" "Plate.source" "Well.Source" -1 "YPDAFEXglucoseTests_2-25-10" "A01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 2 "Control strain plate" "Empty" "Empty" "Empty" -2 "YPDAFEXglucoseTests_2-25-10" "B01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 3 "Control strain plate" "Empty" "Empty" "Empty" -3 "YPDAFEXglucoseTests_2-25-10" "C01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 4 "Control strain plate" "Empty" "Empty" "Empty" -4 "YPDAFEXglucoseTests_2-25-10" "D01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 5 "Control strain plate" "Empty" "Empty" "Empty" -5 "YPDAFEXglucoseTests_2-25-10" "E01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 6 "Control strain plate" "Empty" "Empty" "Empty" -6 "YPDAFEXglucoseTests_2-25-10" "F01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 7 "Control strain plate" "Empty" "Empty" "Empty" -7 "YPDAFEXglucoseTests_2-25-10" "G01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 8 "Control strain plate" "Empty" "Empty" "Empty" -8 "YPDAFEXglucoseTests_2-25-10" "H01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 9 "Control strain plate" "Empty" "Empty" "Empty" -9 "YPDAFEXglucoseTests_2-25-10" "A02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 10 "Control strain plate" "Empty" "Empty" "Empty" -10 "YPDAFEXglucoseTests_2-25-10" "B02" "YP" "Lab strain" "logistic 4-par." 0.00513390947239015 0.0876620001483475 0.000551696237099386 0.110874812224549 2.59465563414583 "I " "-" "-" 92.6741690962163 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 11 "Control strain plate" "Sample" "USDA" "" -11 "YPDAFEXglucoseTests_2-25-10" "C02" "YP+0.25% glucose" "Lab strain" "richards 5-par." 0.0460029361983442 0.240392472194083 2.23932295697808 0.0761318166887226 2.23914120606195 "I " "-" "-" 99.9998792920065 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 12 "Control strain plate" "Sample" "USDA" "" -12 "YPDAFEXglucoseTests_2-25-10" "D02" "YP+0.5% glucose" "Lab strain" "richards 5-par." 0.0731423187209926 0.432756582200227 2.94212753267929 0.0918532887250707 2.53605103328100 "I " "-" "-" 99.9999952623947 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 13 "Control strain plate" "Sample" "USDA" "" -13 "YPDAFEXglucoseTests_2-25-10" "E02" "YP+1% glucose" "Lab strain" "richards 5-par." 0.0874988417362888 0.677479207265783 3.24633816769258 0.0800120483977169 2.87924387138478 "I " "-" "-" 99.9997657328472 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 14 "Control strain plate" "Sample" "USDA" "" -14 "YPDAFEXglucoseTests_2-25-10" "F02" "YP+2% glucose" "Lab strain" "logistic 4-par." 0.0833321479006846 0.847046661111157 2.77452557039409 0.0752193280284603 2.65845234206059 "I " "-" "-" 99.9918661852256 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 15 "Control strain plate" "Sample" "USDA" "" -15 "YPDAFEXglucoseTests_2-25-10" "G02" "YP+5% glucose" "Lab strain" "logistic 4-par." 0.0589669239899499 1.11882517761774 1.20640826390575 0.0520133170774622 1.79342170973749 "I " "L" "-" 98.6708254147882 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 16 "Control strain plate" "Sample" "USDA" "" -16 "YPDAFEXglucoseTests_2-25-10" "H02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 17 "Control strain plate" "Empty" "Empty" "Empty" -17 "YPDAFEXglucoseTests_2-25-10" "A03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 18 "Control strain plate" "Empty" "Empty" "Empty" -18 "YPDAFEXglucoseTests_2-25-10" "B03" "YP" "Wild strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 19 "Control strain plate" "Sample" "USDA" "" -19 "YPDAFEXglucoseTests_2-25-10" "C03" "YP+0.25% glucose" "Wild strain" "logistic 4-par." 0.0459986845139891 0.254831348162179 1.58986879723202 0.112101681081809 1.70864325519431 "I " "-" "-" 99.9999955467498 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 20 "Control strain plate" "Sample" "USDA" "" -20 "YPDAFEXglucoseTests_2-25-10" "D03" "YP+0.5% glucose" "Wild strain" "logistic 4-par." 0.0945868089752667 0.425786653122546 2.58713136878942 0.130435146775932 2.46359052165421 "I " "-" "-" 99.9999999852335 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 21 "Control strain plate" "Sample" "USDA" "" -21 "YPDAFEXglucoseTests_2-25-10" "E03" "YP+1% glucose" "Wild strain" "richards 5-par." 0.121127547817384 0.685559786610674 2.97587534293576 0.107503741316800 2.89947354509395 "I " "-" "-" 99.9999999800904 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 22 "Control strain plate" "Sample" "USDA" "" -22 "YPDAFEXglucoseTests_2-25-10" "F03" "YP+2% glucose" "Wild strain" "richards 5-par." 0.129882547594034 1.04160860310247 2.77302797649945 0.124135599690527 2.75950289629815 "I " "-" "-" 99.9999893489067 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 23 "Control strain plate" "Sample" "USDA" "" -23 "YPDAFEXglucoseTests_2-25-10" "G03" "YP+5% glucose" "Wild strain" "richards 5-par." 0.120898412251709 1.32901254481953 2.55988604768709 0.128599154705507 2.86661364643987 "I " "-" "-" 99.9926206656861 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 24 "Control strain plate" "Sample" "USDA" "" -24 "YPDAFEXglucoseTests_2-25-10" "H03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 25 "Control strain plate" "Empty" "Empty" "Empty" -25 "YPDAFEXglucoseTests_2-25-10" "A04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 26 "Control strain plate" "Empty" "Empty" "Empty" -26 "YPDAFEXglucoseTests_2-25-10" "B04" "YP" "Industrial strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 27 "Control strain plate" "Sample" "Internal source" "" -27 "YPDAFEXglucoseTests_2-25-10" "C04" "YP+0.25% glucose" "Industrial strain" "logistic 4-par." 0.0493379998716343 0.254045397275896 0.523551303454949 0.0888407216209763 1.54716159908116 "I " "-" "-" 99.999996774836 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 28 "Control strain plate" "Sample" "Internal source" "" -28 "YPDAFEXglucoseTests_2-25-10" "D04" "YP+0.5% glucose" "Industrial strain" "logistic 4-par." 0.0931934856727062 0.410238463163683 1.5559350402868 0.0929949311576475 2.39970752160387 "I " "-" "-" 99.9999999909852 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 29 "Control strain plate" "Sample" "Internal source" "" -29 "YPDAFEXglucoseTests_2-25-10" "E04" "YP+1% glucose" "Industrial strain" "richards 5-par." 0.124582742678508 0.661996390783556 2.01051598351255 0.0941849078026622 3.20379613427986 "I " "-" "-" 99.99999999958 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 30 "Control strain plate" "Sample" "Internal source" "" -30 "YPDAFEXglucoseTests_2-25-10" "F04" "YP+2% glucose" "Industrial strain" "richards 5-par." 0.127931259194577 0.983986521455829 1.92761351717956 0.0938101603743178 2.98526874472308 "I " "L" "-" 99.9999999792319 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 31 "Control strain plate" "Sample" "Internal source" "" -31 "YPDAFEXglucoseTests_2-25-10" "G04" "YP+5% glucose" "Industrial strain" "richards 5-par." 0.115525592792629 1.29381927826542 1.74141731218751 0.0890243231205414 2.81287527921917 "I " "L" "-" 99.9999132687566 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 32 "Control strain plate" "Sample" "Internal source" "" -32 "YPDAFEXglucoseTests_2-25-10" "H04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 33 "Control strain plate" "Empty" "Empty" "Empty" -33 "YPDAFEXglucoseTests_2-25-10" "A05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 34 "Control strain plate" "Empty" "Empty" "Empty" -34 "YPDAFEXglucoseTests_2-25-10" "B05" "YP" "Engineered strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 35 "Control strain plate" "Sample" "ATCC" "" -35 "YPDAFEXglucoseTests_2-25-10" "C05" "YP+0.25% glucose" "Engineered strain" "logistic 4-par." 0.0459359326623486 0.248154224199646 0.561170567204033 0.0640432006076648 1.37098828428177 "I " "-" "-" 99.999987765412 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 36 "Control strain plate" "Sample" "ATCC" "" -36 "YPDAFEXglucoseTests_2-25-10" "D05" "YP+0.5% glucose" "Engineered strain" "richards 5-par." 0.0944346858619649 0.470200890606434 1.71183574726233 0.0646296482425968 2.23793506472523 "I " "-" "-" 99.9999948776095 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 37 "Control strain plate" "Sample" "ATCC" "" -37 "YPDAFEXglucoseTests_2-25-10" "E05" "YP+1% glucose" "Engineered strain" "richards 5-par." 0.121520620892205 0.708619340533668 1.92450998620590 0.0814089778419187 2.69846627998123 "I " "-" "-" 99.999997890164 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 38 "Control strain plate" "Sample" "ATCC" "" -38 "YPDAFEXglucoseTests_2-25-10" "F05" "YP+2% glucose" "Engineered strain" "richards 5-par." 0.128733155060522 0.981131957422723 1.88976382070790 0.0912605323267595 2.90166520842437 "I " "-" "-" 99.99998839196 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 39 "Control strain plate" "Sample" "ATCC" "" -39 "YPDAFEXglucoseTests_2-25-10" "G05" "YP+5% glucose" "Engineered strain" "richards 5-par." 0.122721595892799 1.30941121383320 1.88154915349030 0.0757435729961564 3.02277302645685 "I " "L" "-" 99.9995972781622 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 40 "Control strain plate" "Sample" "ATCC" "" -40 "YPDAFEXglucoseTests_2-25-10" "H05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 41 "Control strain plate" "Empty" "Empty" "Empty" -41 "YPDAFEXglucoseTests_2-25-10" "A06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 42 "Control strain plate" "Empty" "Empty" "Empty" -42 "YPDAFEXglucoseTests_2-25-10" "B06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 43 "Control strain plate" "Empty" "Empty" "Empty" -43 "YPDAFEXglucoseTests_2-25-10" "C06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 44 "Control strain plate" "Empty" "Empty" "Empty" -44 "YPDAFEXglucoseTests_2-25-10" "D06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 45 "Control strain plate" "Empty" "Empty" "Empty" -45 "YPDAFEXglucoseTests_2-25-10" "E06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 46 "Control strain plate" "Empty" "Empty" "Empty" -46 "YPDAFEXglucoseTests_2-25-10" "F06" "Empty" "Empty" "richards 5-par." 0.0831016694707274 1.26159681822536 9.46105867276385 -0.0156072095149273 2.2176336607405 "E*" "L" "-" 97.688829175306 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 47 "Control strain plate" "Empty" "Empty" "Empty" -47 "YPDAFEXglucoseTests_2-25-10" "G06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 48 "Control strain plate" "Empty" "Empty" "Empty" -48 "YPDAFEXglucoseTests_2-25-10" "H06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 49 "Control strain plate" "Empty" "Empty" "Empty" -49 "YPDAFEXglucoseTests_2-25-10" "A07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 50 "Control strain plate" "Empty" "Empty" "Empty" -50 "YPDAFEXglucoseTests_2-25-10" "B07" "AFEX" "Lab strain" "richards 5-par." 0.0913331265842828 0.977676293223671 3.74285300700227 0.0585493648561697 3.41803212615394 "I " "-" "-" 99.9967476790949 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 51 "Control strain plate" "Sample" "USDA" "" -51 "YPDAFEXglucoseTests_2-25-10" "C07" "AFEX+0.25% glucose" "Lab strain" "richards 5-par." 0.0901758840515798 1.02343733695468 3.75854949762210 0.0564421526774237 3.35821455308179 "I " "-" "-" 99.9932921305762 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 52 "Control strain plate" "Sample" "USDA" "" -52 "YPDAFEXglucoseTests_2-25-10" "D07" "AFEX+0.5% glucose" "Lab strain" "richards 5-par." 0.0876534489375277 1.05107784214595 4.08053328986319 0.0505529065684702 3.43101493489121 "I " "-" "-" 99.9881389964051 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 53 "Control strain plate" "Sample" "USDA" "" -53 "YPDAFEXglucoseTests_2-25-10" "E07" "AFEX+1% glucose" "Lab strain" "richards 5-par." 0.0852505870016418 1.09523234209277 4.2590088920043 0.0546791531091333 3.32240181027460 "I " "-" "-" 99.9643198816725 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 54 "Control strain plate" "Sample" "USDA" "" -54 "YPDAFEXglucoseTests_2-25-10" "F07" "AFEX+2% glucose" "Lab strain" "richards 5-par." 0.0834062493896505 1.16156601844817 4.17519830688 0.0506329107469832 3.24662867008000 "I " "-" "-" 99.8770810687182 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 55 "Control strain plate" "Sample" "USDA" "" -55 "YPDAFEXglucoseTests_2-25-10" "G07" "AFEX+5% glucose" "Lab strain" "richards 5-par." 0.0746869173042796 1.29883332508854 4.26111988760969 0.0555468732725124 3.36340266867229 "I " "-" "-" 98.4357653421947 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 56 "Control strain plate" "Sample" "USDA" "" -56 "YPDAFEXglucoseTests_2-25-10" "H07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 57 "Control strain plate" "Empty" "Empty" "Empty" -57 "YPDAFEXglucoseTests_2-25-10" "A08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 58 "Control strain plate" "Empty" "Empty" "Empty" -58 "YPDAFEXglucoseTests_2-25-10" "B08" "AFEX" "Wild strain" "richards 5-par." 0.114235639585196 1.11603265279451 2.80462732513778 0.106026173457393 3.07479264063223 "I " "-" "-" 99.9998418759963 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 59 "Control strain plate" "Sample" "USDA" "" -59 "YPDAFEXglucoseTests_2-25-10" "C08" "AFEX+0.25% glucose" "Wild strain" "richards 5-par." 0.114214452912468 1.14545395160069 3.03642647181899 0.0901903141548646 3.13967373959077 "I " "-" "-" 99.9996775720213 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 60 "Control strain plate" "Sample" "USDA" "" -60 "YPDAFEXglucoseTests_2-25-10" "D08" "AFEX+0.5% glucose" "Wild strain" "richards 5-par." 0.113566098365730 1.17951259888145 2.99921572692867 0.0854138714541255 3.20643947548211 "I " "-" "-" 99.9993801531958 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 61 "Control strain plate" "Sample" "USDA" "" -61 "YPDAFEXglucoseTests_2-25-10" "E08" "AFEX+1% glucose" "Wild strain" "richards 5-par." 0.112827039764747 1.23081376697016 2.97207411510676 0.090741698149845 3.1895693830433 "I " "-" "-" 99.9983882461922 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 62 "Control strain plate" "Sample" "USDA" "" -62 "YPDAFEXglucoseTests_2-25-10" "F08" "AFEX+2% glucose" "Wild strain" "richards 5-par." 0.110948156058339 1.28413133026796 3.09434741751019 0.0853800430755536 3.20897314216817 "I " "-" "-" 99.9945939442068 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 63 "Control strain plate" "Sample" "USDA" "" -63 "YPDAFEXglucoseTests_2-25-10" "G08" "AFEX+5% glucose" "Wild strain" "richards 5-par." 0.104909957747906 1.37957293880569 3.37657406597065 0.0857328798243138 3.54895808838256 "I " "-" "-" 99.9340923347588 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 64 "Control strain plate" "Sample" "USDA" "" -64 "YPDAFEXglucoseTests_2-25-10" "H08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 65 "Control strain plate" "Empty" "Empty" "Empty" -65 "YPDAFEXglucoseTests_2-25-10" "A09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 66 "Control strain plate" "Empty" "Empty" "Empty" -66 "YPDAFEXglucoseTests_2-25-10" "B09" "AFEX" "Industrial strain" "richards 5-par." 0.124619613908910 1.02126553518662 2.43053521773110 0.0832928033695586 3.19828565863893 "I " "-" "-" 99.9999984996182 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 67 "Control strain plate" "Sample" "Internal source" "" -67 "YPDAFEXglucoseTests_2-25-10" "C09" "AFEX+0.25% glucose" "Industrial strain" "richards 5-par." 0.123242474045102 1.07196388949718 2.44085995606895 0.0747514589944707 3.30084510513645 "I " "-" "-" 99.999994419942 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 68 "Control strain plate" "Sample" "Internal source" "" -68 "YPDAFEXglucoseTests_2-25-10" "D09" "AFEX+0.5% glucose" "Industrial strain" "richards 5-par." 0.12090087889886 1.10115777984898 2.35585985916424 0.0719961174673402 3.29576923040073 "I " "L" "-" 99.9999896268808 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 69 "Control strain plate" "Sample" "Internal source" "" -69 "YPDAFEXglucoseTests_2-25-10" "E09" "AFEX+1% glucose" "Industrial strain" "richards 5-par." 0.119451757970973 1.15953479542773 2.30664009041830 0.0715521817197322 3.20509498580791 "I " "L" "-" 99.9999599907486 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 70 "Control strain plate" "Sample" "Internal source" "" -70 "YPDAFEXglucoseTests_2-25-10" "F09" "AFEX+2% glucose" "Industrial strain" "richards 5-par." 0.117046866658425 1.23026145665052 2.44407044557878 0.0655027600473694 3.14018976861125 "I " "L" "-" 99.9995689634333 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 71 "Control strain plate" "Sample" "Internal source" "" -71 "YPDAFEXglucoseTests_2-25-10" "G09" "AFEX+5% glucose" "Industrial strain" "richards 5-par." 0.108331393150974 1.33973156155552 2.51097570573708 0.0649023468973968 3.23212721890241 "I " "-" "-" 99.9822483056319 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 72 "Control strain plate" "Sample" "Internal source" "" -72 "YPDAFEXglucoseTests_2-25-10" "H09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 73 "Control strain plate" "Empty" "Empty" "Empty" -73 "YPDAFEXglucoseTests_2-25-10" "A10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 74 "Control strain plate" "Empty" "Empty" "Empty" -74 "YPDAFEXglucoseTests_2-25-10" "B10" "AFEX" "Engineered strain" "richards 5-par." 0.121839335523261 1.03094115561518 2.20149868335828 0.071637820344644 2.99659166289555 "I " "-" "-" 99.9998735461218 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 75 "Control strain plate" "Sample" "ATCC" "" -75 "YPDAFEXglucoseTests_2-25-10" "C10" "AFEX+0.25% glucose" "Engineered strain" "richards 5-par." 0.123130425236 1.06412474728157 2.46906361902120 0.0564520573406488 3.19928587493649 "I " "-" "-" 99.999891983369 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 76 "Control strain plate" "Sample" "ATCC" "" -76 "YPDAFEXglucoseTests_2-25-10" "D10" "AFEX+0.5% glucose" "Engineered strain" "richards 5-par." 0.120973125758535 1.08554405396271 2.46825462758035 0.056549534178326 3.33630531768612 "I " "-" "-" 99.9998814536437 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 77 "Control strain plate" "Sample" "ATCC" "" -77 "YPDAFEXglucoseTests_2-25-10" "E10" "AFEX+1% glucose" "Engineered strain" "richards 5-par." 0.120740949535359 1.15263316370924 2.5442959513883 0.0522642960780029 3.36496106313701 "I " "-" "-" 99.9996094172831 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 78 "Control strain plate" "Sample" "ATCC" "" -78 "YPDAFEXglucoseTests_2-25-10" "F10" "AFEX+2% glucose" "Engineered strain" "richards 5-par." 0.121802165325221 1.22599703168728 2.5422560684683 0.056307375634215 3.47334970863554 "I " "-" "-" 99.9989009038885 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 79 "Control strain plate" "Sample" "ATCC" "" -79 "YPDAFEXglucoseTests_2-25-10" "G10" "AFEX+5% glucose" "Engineered strain" "richards 5-par." 0.112904136231260 1.340836387636 2.56045685725438 0.0581661740243069 3.53967163281617 "I " "-" "-" 99.9786442972454 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 80 "Control strain plate" "Sample" "ATCC" "" -80 "YPDAFEXglucoseTests_2-25-10" "H10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 81 "Control strain plate" "Empty" "Empty" "Empty" -81 "YPDAFEXglucoseTests_2-25-10" "A11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 82 "Control strain plate" "Empty" "Empty" "Empty" -82 "YPDAFEXglucoseTests_2-25-10" "B11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 83 "Control strain plate" "Empty" "Empty" "Empty" -83 "YPDAFEXglucoseTests_2-25-10" "C11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 84 "Control strain plate" "Empty" "Empty" "Empty" -84 "YPDAFEXglucoseTests_2-25-10" "D11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 85 "Control strain plate" "Empty" "Empty" "Empty" -85 "YPDAFEXglucoseTests_2-25-10" "E11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 86 "Control strain plate" "Empty" "Empty" "Empty" -86 "YPDAFEXglucoseTests_2-25-10" "F11" "None" "Empty" "logistic 4-par." 0.097251500241612 1.24804582503984 14.6755074922153 -0.00366567404981066 2.38008868734244 "E*" "L/U" "-" 87.1867004610056 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 87 "Control strain plate" "Empty" "Empty" "Empty" -87 "YPDAFEXglucoseTests_2-25-10" "G11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 88 "Control strain plate" "Empty" "Empty" "Empty" -88 "YPDAFEXglucoseTests_2-25-10" "H11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 89 "Control strain plate" "Empty" "Empty" "Empty" -89 "YPDAFEXglucoseTests_2-25-10" "A12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 90 "Control strain plate" "Empty" "Empty" "Empty" -90 "YPDAFEXglucoseTests_2-25-10" "B12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 91 "Control strain plate" "Empty" "Empty" "Empty" -91 "YPDAFEXglucoseTests_2-25-10" "C12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 92 "Control strain plate" "Empty" "Empty" "Empty" -92 "YPDAFEXglucoseTests_2-25-10" "D12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 93 "Control strain plate" "Empty" "Empty" "Empty" -93 "YPDAFEXglucoseTests_2-25-10" "E12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 94 "Control strain plate" "Empty" "Empty" "Empty" -94 "YPDAFEXglucoseTests_2-25-10" "F12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 95 "Control strain plate" "Empty" "Empty" "Empty" -95 "YPDAFEXglucoseTests_2-25-10" "G12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 96 "Control strain plate" "Empty" "Empty" "Empty" -96 "YPDAFEXglucoseTests_2-25-10" "H12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.35.pdf" 97 "Control strain plate" "Empty" "Empty" "Empty" - -# -- Explanation of columns -- -# - model: Name of the model the well was successfully fit with (if any) -# - spec.growth: (Specific growth rate) The largest exponential growth rate achieved by the culture in the course of the experiment -# - tot.growth: (Total extrapolated growth) The estimated growth plateau from the fitted model in optical density units. May be higher than the actual highest OD reached. -# - lag.time: (Lag time) The exponential trend from is extrapolated to the baseline OD at inoculation and subtracted from the time at inoculation to yield lag time. -# - inoc.OD: (OD at inoculation) The adjusted optical density at the user-specified starting timepoint. -# - good.fit: (Goodness of fit) A metric based on root mean square deviations (RMSD). -# - higher values ( > 3.0) indicate a very good fit while lower values (< 2.0) indicate generally unacceptable fits. -# - empty: (Well indicator) -# - an 'E' indicates that the well was empty and no growth was detected. -# - an 'I' indicates that the well was inoculated and growth was detected above the threshold. -# - an 'E*' indicates that the well was empty and growth was detected (possible contamination). -# - an '!' indicates that the well was inoculated and no growth was detected. -# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index. -# - reach: (Final growth percentage): The percentage of reached by the culture in the course of the experiment. -# - other: Other information includes output from jump detection algorithm and additional columns from the Plate Layout. -# - pdf.file and page.no: location of the figure for this well in the output .pdf files. -# -# -- Source file information-- -# YPDAFEXglucoseTests_2-25-10.csv -# analyzed using GCAT v 0.01 -# request sent: 2013-11-26 11:54:35 -# completed: 2013-11-26 11:54:45 -# -# -- Parameters used in current analysis -- -# - Constant added to log(OD + n) transformation: 1 -# - Blank OD value: First timepoint in well -# - Index of inoculation timepoint 3 -# - Minimum growth threshold: 0.05 -# - Removed points: -# - Jump detection: FALSE \ No newline at end of file diff --git a/Testing/GCAT_Automated_Test_Script/GCAT2/Media_Background.txt b/Testing/GCAT_Automated_Test_Script/GCAT2/Media_Background.txt deleted file mode 100755 index 891696f..0000000 --- a/Testing/GCAT_Automated_Test_Script/GCAT2/Media_Background.txt +++ /dev/null @@ -1,129 +0,0 @@ -"row" "plate" "well" "media" "strain" "model" "spec.growth" "tot.growth" "lag.time" "inoc.OD" "good.fit" "empty" "asymp" "tank" "reach" "other" "pdf.file" "page.no" "Destination.plate.name" "Well.ID" "Plate.source" "Well.Source" -1 "YPDAFEXglucoseTests_2-25-10" "A01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 2 "Control strain plate" "Empty" "Empty" "Empty" -2 "YPDAFEXglucoseTests_2-25-10" "B01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 3 "Control strain plate" "Empty" "Empty" "Empty" -3 "YPDAFEXglucoseTests_2-25-10" "C01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 4 "Control strain plate" "Empty" "Empty" "Empty" -4 "YPDAFEXglucoseTests_2-25-10" "D01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 5 "Control strain plate" "Empty" "Empty" "Empty" -5 "YPDAFEXglucoseTests_2-25-10" "E01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 6 "Control strain plate" "Empty" "Empty" "Empty" -6 "YPDAFEXglucoseTests_2-25-10" "F01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 7 "Control strain plate" "Empty" "Empty" "Empty" -7 "YPDAFEXglucoseTests_2-25-10" "G01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 8 "Control strain plate" "Empty" "Empty" "Empty" -8 "YPDAFEXglucoseTests_2-25-10" "H01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 9 "Control strain plate" "Empty" "Empty" "Empty" -9 "YPDAFEXglucoseTests_2-25-10" "A02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 10 "Control strain plate" "Empty" "Empty" "Empty" -10 "YPDAFEXglucoseTests_2-25-10" "B02" "YP" "Lab strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 11 "Control strain plate" "Sample" "USDA" "" -11 "YPDAFEXglucoseTests_2-25-10" "C02" "YP+0.25% glucose" "Lab strain" "richards 5-par." 0.0434503343000251 0.253554854675260 2.02165330333884 0.0617033863833638 1.64185698237008 "I " "-" "-" 99.9999736403217 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 12 "Control strain plate" "Sample" "USDA" "" -12 "YPDAFEXglucoseTests_2-25-10" "D02" "YP+0.5% glucose" "Lab strain" "richards 5-par." 0.0710461374870435 0.446283240058387 2.88921431893203 0.078039465273223 1.94354072341034 "I " "-" "-" 99.9999992879621 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 13 "Control strain plate" "Sample" "USDA" "" -13 "YPDAFEXglucoseTests_2-25-10" "E02" "YP+1% glucose" "Lab strain" "richards 5-par." 0.0860880819729473 0.688375845522998 3.26587795985316 0.0682375379828597 2.36976256861628 "I " "-" "-" 99.9998854906447 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 14 "Control strain plate" "Sample" "USDA" "" -14 "YPDAFEXglucoseTests_2-25-10" "F02" "YP+2% glucose" "Lab strain" "richards 5-par." 0.0855558286818253 0.84851665981466 2.99428931741607 0.0785443237303707 2.50265696873442 "I " "-" "-" 99.9675537192086 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 15 "Control strain plate" "Sample" "USDA" "" -15 "YPDAFEXglucoseTests_2-25-10" "G02" "YP+5% glucose" "Lab strain" "logistic 4-par." 0.0590319877346773 1.13131893310060 1.21092069814356 0.0412045752566177 1.79374394529570 "I " "L" "-" 98.6047219117497 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 16 "Control strain plate" "Sample" "USDA" "" -16 "YPDAFEXglucoseTests_2-25-10" "H02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 17 "Control strain plate" "Empty" "Empty" "Empty" -17 "YPDAFEXglucoseTests_2-25-10" "A03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 18 "Control strain plate" "Empty" "Empty" "Empty" -18 "YPDAFEXglucoseTests_2-25-10" "B03" "YP" "Wild strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 19 "Control strain plate" "Sample" "USDA" "" -19 "YPDAFEXglucoseTests_2-25-10" "C03" "YP+0.25% glucose" "Wild strain" "logistic 4-par." 0.0434892612564025 0.274547126811452 1.17986305219729 0.0930562431741175 1.2462515507653 "I " "-" "-" 99.9999459725148 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 20 "Control strain plate" "Sample" "USDA" "" -20 "YPDAFEXglucoseTests_2-25-10" "D03" "YP+0.5% glucose" "Wild strain" "richards 5-par." 0.0897339782050535 0.44725588012243 2.48510022383136 0.111954813319619 1.64728332860566 "I " "-" "-" 99.9999999997907 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 21 "Control strain plate" "Sample" "USDA" "" -21 "YPDAFEXglucoseTests_2-25-10" "E03" "YP+1% glucose" "Wild strain" "richards 5-par." 0.118704818394586 0.701739899244777 3.00105743862396 0.0902498862365915 2.16060651373925 "I " "-" "-" 99.999999998243 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 22 "Control strain plate" "Sample" "USDA" "" -22 "YPDAFEXglucoseTests_2-25-10" "F03" "YP+2% glucose" "Wild strain" "richards 5-par." 0.127118789469248 1.06188644325538 2.76198673024551 0.101832988995193 2.2489695413201 "I " "-" "-" 99.9999974728383 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 23 "Control strain plate" "Sample" "USDA" "" -23 "YPDAFEXglucoseTests_2-25-10" "G03" "YP+5% glucose" "Wild strain" "richards 5-par." 0.118124578641559 1.34963757338040 2.51164992830229 0.105412244128214 2.36610848171534 "I " "-" "-" 99.9956836427274 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 24 "Control strain plate" "Sample" "USDA" "" -24 "YPDAFEXglucoseTests_2-25-10" "H03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 25 "Control strain plate" "Empty" "Empty" "Empty" -25 "YPDAFEXglucoseTests_2-25-10" "A04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 26 "Control strain plate" "Empty" "Empty" "Empty" -26 "YPDAFEXglucoseTests_2-25-10" "B04" "YP" "Industrial strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 27 "Control strain plate" "Sample" "Internal source" "" -27 "YPDAFEXglucoseTests_2-25-10" "C04" "YP+0.25% glucose" "Industrial strain" "logistic 4-par." 0.0503915103890343 0.278431850863241 0.230735178823221 0.0667245999493249 1.28125167205809 "I " "-" "-" 99.9999557835925 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 28 "Control strain plate" "Sample" "Internal source" "" -28 "YPDAFEXglucoseTests_2-25-10" "D04" "YP+0.5% glucose" "Industrial strain" "logistic 4-par." 0.0900596817770063 0.426283124892579 1.48660897985453 0.0787853427815937 1.78609838401984 "I " "-" "-" 99.9999999465272 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 29 "Control strain plate" "Sample" "Internal source" "" -29 "YPDAFEXglucoseTests_2-25-10" "E04" "YP+1% glucose" "Industrial strain" "richards 5-par." 0.120932696502068 0.681827053465979 1.98743887548203 0.0750931197769025 2.24806197934911 "I " "-" "-" 99.9999999999806 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 30 "Control strain plate" "Sample" "Internal source" "" -30 "YPDAFEXglucoseTests_2-25-10" "F04" "YP+2% glucose" "Industrial strain" "richards 5-par." 0.124851864857507 1.00554516052416 1.89097308231560 0.0745327038147034 2.45714183902256 "I " "L" "-" 99.9999999978197 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 31 "Control strain plate" "Sample" "Internal source" "" -31 "YPDAFEXglucoseTests_2-25-10" "G04" "YP+5% glucose" "Industrial strain" "richards 5-par." 0.113079038402523 1.31499248437073 1.67061532987960 0.0682108949608626 2.54109072078653 "I " "L" "-" 99.9999648186165 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 32 "Control strain plate" "Sample" "Internal source" "" -32 "YPDAFEXglucoseTests_2-25-10" "H04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 33 "Control strain plate" "Empty" "Empty" "Empty" -33 "YPDAFEXglucoseTests_2-25-10" "A05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 34 "Control strain plate" "Empty" "Empty" "Empty" -34 "YPDAFEXglucoseTests_2-25-10" "B05" "YP" "Engineered strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 35 "Control strain plate" "Sample" "ATCC" "" -35 "YPDAFEXglucoseTests_2-25-10" "C05" "YP+0.25% glucose" "Engineered strain" "logistic 4-par." 0.0460541020662134 0.26524158772085 0.357238281642297 0.0484389000123124 1.28333178169019 "I " "L" "-" 99.9999287079269 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 36 "Control strain plate" "Sample" "ATCC" "" -36 "YPDAFEXglucoseTests_2-25-10" "D05" "YP+0.5% glucose" "Engineered strain" "logistic 4-par." 0.0910355508572168 0.484885690164407 1.68228977771903 0.0503454179292044 2.01406534894519 "I " "-" "-" 99.999999075587 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 37 "Control strain plate" "Sample" "ATCC" "" -37 "YPDAFEXglucoseTests_2-25-10" "E05" "YP+1% glucose" "Engineered strain" "richards 5-par." 0.118532626835200 0.724942396645568 1.93091588614506 0.0650485245853678 2.28064777433602 "I " "-" "-" 99.9999994051425 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 38 "Control strain plate" "Sample" "ATCC" "" -38 "YPDAFEXglucoseTests_2-25-10" "F05" "YP+2% glucose" "Engineered strain" "richards 5-par." 0.125935099476691 1.00060394314497 1.87185854411294 0.0705328954848026 2.43919113300695 "I " "-" "-" 99.9999960758469 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 39 "Control strain plate" "Sample" "ATCC" "" -39 "YPDAFEXglucoseTests_2-25-10" "G05" "YP+5% glucose" "Engineered strain" "richards 5-par." 0.120458286580390 1.32681554802285 1.87312970608357 0.0617649897724031 2.72077052437644 "I " "L" "-" 99.9997697224565 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 40 "Control strain plate" "Sample" "ATCC" "" -40 "YPDAFEXglucoseTests_2-25-10" "H05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 41 "Control strain plate" "Empty" "Empty" "Empty" -41 "YPDAFEXglucoseTests_2-25-10" "A06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 42 "Control strain plate" "Empty" "Empty" "Empty" -42 "YPDAFEXglucoseTests_2-25-10" "B06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 43 "Control strain plate" "Empty" "Empty" "Empty" -43 "YPDAFEXglucoseTests_2-25-10" "C06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 44 "Control strain plate" "Empty" "Empty" "Empty" -44 "YPDAFEXglucoseTests_2-25-10" "D06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 45 "Control strain plate" "Empty" "Empty" "Empty" -45 "YPDAFEXglucoseTests_2-25-10" "E06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 46 "Control strain plate" "Empty" "Empty" "Empty" -46 "YPDAFEXglucoseTests_2-25-10" "F06" "Empty" "Empty" "richards 5-par." 0.083026880473868 1.26274912739788 9.6370199491002 -0.0148648394970353 2.22003323483864 "E*" "L" "-" 97.6179798356663 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 47 "Control strain plate" "Empty" "Empty" "Empty" -47 "YPDAFEXglucoseTests_2-25-10" "G06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 48 "Control strain plate" "Empty" "Empty" "Empty" -48 "YPDAFEXglucoseTests_2-25-10" "H06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 49 "Control strain plate" "Empty" "Empty" "Empty" -49 "YPDAFEXglucoseTests_2-25-10" "A07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 50 "Control strain plate" "Empty" "Empty" "Empty" -50 "YPDAFEXglucoseTests_2-25-10" "B07" "AFEX" "Lab strain" "richards 5-par." 0.0837862465621809 0.985589476660035 3.87077447326577 0.172902084515593 2.936554895572 "I " "-" "-" 99.9976660845596 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 51 "Control strain plate" "Sample" "USDA" "" -51 "YPDAFEXglucoseTests_2-25-10" "C07" "AFEX+0.25% glucose" "Lab strain" "richards 5-par." 0.0825725388111153 1.03111358478328 3.8935977613249 0.175746057355985 2.95818389639001 "I " "-" "-" 99.9950047689826 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 52 "Control strain plate" "Sample" "USDA" "" -52 "YPDAFEXglucoseTests_2-25-10" "D07" "AFEX+0.5% glucose" "Lab strain" "richards 5-par." 0.0803990851774492 1.05769131646876 4.23452367239061 0.171669910262409 3.05762797860851 "I " "-" "-" 99.9905797580664 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 53 "Control strain plate" "Sample" "USDA" "" -53 "YPDAFEXglucoseTests_2-25-10" "E07" "AFEX+1% glucose" "Lab strain" "richards 5-par." 0.078260986900903 1.10176517760371 4.41033894653477 0.174661705124986 2.98245532148831 "I " "-" "-" 99.97078656119 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 54 "Control strain plate" "Sample" "USDA" "" -54 "YPDAFEXglucoseTests_2-25-10" "F07" "AFEX+2% glucose" "Lab strain" "richards 5-par." 0.0765359669045422 1.16743187678685 4.33134033283011 0.171774058333315 2.99101843653394 "I " "-" "-" 99.8931141945986 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 55 "Control strain plate" "Sample" "USDA" "" -55 "YPDAFEXglucoseTests_2-25-10" "G07" "AFEX+5% glucose" "Lab strain" "richards 5-par." 0.0684295063358446 1.30296627125276 4.41039755952004 0.177550778776163 3.02126707953049 "I " "-" "-" 98.542925848239 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 56 "Control strain plate" "Sample" "USDA" "" -56 "YPDAFEXglucoseTests_2-25-10" "H07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 57 "Control strain plate" "Empty" "Empty" "Empty" -57 "YPDAFEXglucoseTests_2-25-10" "A08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 58 "Control strain plate" "Empty" "Empty" "Empty" -58 "YPDAFEXglucoseTests_2-25-10" "B08" "AFEX" "Wild strain" "richards 5-par." 0.103961511845496 1.13335005494973 2.84746894877643 0.216147675837119 2.50607784281402 "I " "-" "-" 99.999934749514 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 59 "Control strain plate" "Sample" "USDA" "" -59 "YPDAFEXglucoseTests_2-25-10" "C08" "AFEX+0.25% glucose" "Wild strain" "richards 5-par." 0.104426132027787 1.15952947440466 3.11791461815530 0.202220291175903 2.64629880567713 "I " "-" "-" 99.9998358609235 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 60 "Control strain plate" "Sample" "USDA" "" -60 "YPDAFEXglucoseTests_2-25-10" "D08" "AFEX+0.5% glucose" "Wild strain" "richards 5-par." 0.103564913027715 1.19303695629607 3.08800865283045 0.203591721344972 2.71477777367162 "I " "-" "-" 99.9996508953345 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 61 "Control strain plate" "Sample" "USDA" "" -61 "YPDAFEXglucoseTests_2-25-10" "E08" "AFEX+1% glucose" "Wild strain" "richards 5-par." 0.103109984243399 1.24497138884473 3.04906663958604 0.203623320796393 2.68869096385621 "I " "-" "-" 99.9990405446907 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 62 "Control strain plate" "Sample" "USDA" "" -62 "YPDAFEXglucoseTests_2-25-10" "F08" "AFEX+2% glucose" "Wild strain" "richards 5-par." 0.101328068865228 1.29683436370675 3.18655040766587 0.203111588999557 2.75266670603191 "I " "-" "-" 99.996339173896 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 63 "Control strain plate" "Sample" "USDA" "" -63 "YPDAFEXglucoseTests_2-25-10" "G08" "AFEX+5% glucose" "Wild strain" "richards 5-par." 0.0960414766942334 1.39007056093517 3.47869089975363 0.202353552916657 2.86594136189225 "I " "-" "-" 99.9467189237796 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 64 "Control strain plate" "Sample" "USDA" "" -64 "YPDAFEXglucoseTests_2-25-10" "H08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 65 "Control strain plate" "Empty" "Empty" "Empty" -65 "YPDAFEXglucoseTests_2-25-10" "A09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 66 "Control strain plate" "Empty" "Empty" "Empty" -66 "YPDAFEXglucoseTests_2-25-10" "B09" "AFEX" "Industrial strain" "richards 5-par." 0.113180265724915 1.03747916133359 2.49766338810221 0.198495309639666 2.64831702967150 "I " "-" "-" 99.99999950571 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 67 "Control strain plate" "Sample" "Internal source" "" -67 "YPDAFEXglucoseTests_2-25-10" "C09" "AFEX+0.25% glucose" "Industrial strain" "richards 5-par." 0.112532945731761 1.08681009274574 2.52119628407453 0.186329225710496 2.77398299574405 "I " "-" "-" 99.9999976342956 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 68 "Control strain plate" "Sample" "Internal source" "" -68 "YPDAFEXglucoseTests_2-25-10" "D09" "AFEX+0.5% glucose" "Industrial strain" "richards 5-par." 0.110237121553375 1.11602705298285 2.43678055941639 0.187247546937630 2.81184006554946 "I " "-" "-" 99.9999952725547 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 69 "Control strain plate" "Sample" "Internal source" "" -69 "YPDAFEXglucoseTests_2-25-10" "E09" "AFEX+1% glucose" "Industrial strain" "richards 5-par." 0.109153261238411 1.17453886329702 2.38442334222443 0.183907793076526 2.80879291485336 "I " "-" "-" 99.9999796529525 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 70 "Control strain plate" "Sample" "Internal source" "" -70 "YPDAFEXglucoseTests_2-25-10" "F09" "AFEX+2% glucose" "Industrial strain" "richards 5-par." 0.107153820876407 1.24345235940033 2.53842674779367 0.178885414386565 2.84792003349477 "I " "-" "-" 99.999726199681 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 71 "Control strain plate" "Sample" "Internal source" "" -71 "YPDAFEXglucoseTests_2-25-10" "G09" "AFEX+5% glucose" "Industrial strain" "richards 5-par." 0.0990827158819113 1.35146254239763 2.60572114613308 0.180195185614621 2.91808898590255 "I " "-" "-" 99.9858735540263 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 72 "Control strain plate" "Sample" "Internal source" "" -72 "YPDAFEXglucoseTests_2-25-10" "H09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 73 "Control strain plate" "Empty" "Empty" "Empty" -73 "YPDAFEXglucoseTests_2-25-10" "A10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 74 "Control strain plate" "Empty" "Empty" "Empty" -74 "YPDAFEXglucoseTests_2-25-10" "B10" "AFEX" "Engineered strain" "richards 5-par." 0.110458083084921 1.04485579994439 2.27701838325376 0.188114595684521 2.65931477578895 "I " "-" "-" 99.9999271625885 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 75 "Control strain plate" "Sample" "ATCC" "" -75 "YPDAFEXglucoseTests_2-25-10" "C10" "AFEX+0.25% glucose" "Engineered strain" "richards 5-par." 0.112540220994811 1.07487901296182 2.58417196441953 0.171301212668114 2.88882458916344 "I " "-" "-" 99.9999309539298 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 76 "Control strain plate" "Sample" "ATCC" "" -76 "YPDAFEXglucoseTests_2-25-10" "D10" "AFEX+0.5% glucose" "Engineered strain" "richards 5-par." 0.110640152738962 1.09653685419261 2.58231557868978 0.171664577469133 2.95663771710228 "I " "-" "-" 99.9999237076305 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 77 "Control strain plate" "Sample" "ATCC" "" -77 "YPDAFEXglucoseTests_2-25-10" "E10" "AFEX+1% glucose" "Engineered strain" "richards 5-par." 0.110596720564600 1.16275661096821 2.66983121158 0.168291454109896 3.03987519406164 "I " "-" "-" 99.9997284198838 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 78 "Control strain plate" "Sample" "ATCC" "" -78 "YPDAFEXglucoseTests_2-25-10" "F10" "AFEX+2% glucose" "Engineered strain" "richards 5-par." 0.111561409951938 1.23655979175461 2.66322072814323 0.172114613842357 3.06755684662736 "I " "-" "-" 99.9991978972748 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 79 "Control strain plate" "Sample" "ATCC" "" -79 "YPDAFEXglucoseTests_2-25-10" "G10" "AFEX+5% glucose" "Engineered strain" "richards 5-par." 0.103366231210924 1.35093549154140 2.67448563817088 0.173610905690015 3.10078735926473 "I " "-" "-" 99.9823958592765 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 80 "Control strain plate" "Sample" "ATCC" "" -80 "YPDAFEXglucoseTests_2-25-10" "H10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 81 "Control strain plate" "Empty" "Empty" "Empty" -81 "YPDAFEXglucoseTests_2-25-10" "A11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 82 "Control strain plate" "Empty" "Empty" "Empty" -82 "YPDAFEXglucoseTests_2-25-10" "B11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 83 "Control strain plate" "Empty" "Empty" "Empty" -83 "YPDAFEXglucoseTests_2-25-10" "C11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 84 "Control strain plate" "Empty" "Empty" "Empty" -84 "YPDAFEXglucoseTests_2-25-10" "D11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 85 "Control strain plate" "Empty" "Empty" "Empty" -85 "YPDAFEXglucoseTests_2-25-10" "E11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 86 "Control strain plate" "Empty" "Empty" "Empty" -86 "YPDAFEXglucoseTests_2-25-10" "F11" "None" "Empty" "logistic 4-par." 0.0898948262289814 1.25317410845682 14.9183477248910 0.115247567652615 2.39076788045153 "E*" "U" "-" 86.9727718976639 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 87 "Control strain plate" "Empty" "Empty" "Empty" -87 "YPDAFEXglucoseTests_2-25-10" "G11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 88 "Control strain plate" "Empty" "Empty" "Empty" -88 "YPDAFEXglucoseTests_2-25-10" "H11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 89 "Control strain plate" "Empty" "Empty" "Empty" -89 "YPDAFEXglucoseTests_2-25-10" "A12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 90 "Control strain plate" "Empty" "Empty" "Empty" -90 "YPDAFEXglucoseTests_2-25-10" "B12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 91 "Control strain plate" "Empty" "Empty" "Empty" -91 "YPDAFEXglucoseTests_2-25-10" "C12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 92 "Control strain plate" "Empty" "Empty" "Empty" -92 "YPDAFEXglucoseTests_2-25-10" "D12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 93 "Control strain plate" "Empty" "Empty" "Empty" -93 "YPDAFEXglucoseTests_2-25-10" "E12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 94 "Control strain plate" "Empty" "Empty" "Empty" -94 "YPDAFEXglucoseTests_2-25-10" "F12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 95 "Control strain plate" "Empty" "Empty" "Empty" -95 "YPDAFEXglucoseTests_2-25-10" "G12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 96 "Control strain plate" "Empty" "Empty" "Empty" -96 "YPDAFEXglucoseTests_2-25-10" "H12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.49.pdf" 97 "Control strain plate" "Empty" "Empty" "Empty" - -# -- Explanation of columns -- -# - model: Name of the model the well was successfully fit with (if any) -# - spec.growth: (Specific growth rate) The largest exponential growth rate achieved by the culture in the course of the experiment -# - tot.growth: (Total extrapolated growth) The estimated growth plateau from the fitted model in optical density units. May be higher than the actual highest OD reached. -# - lag.time: (Lag time) The exponential trend from is extrapolated to the baseline OD at inoculation and subtracted from the time at inoculation to yield lag time. -# - inoc.OD: (OD at inoculation) The adjusted optical density at the user-specified starting timepoint. -# - good.fit: (Goodness of fit) A metric based on root mean square deviations (RMSD). -# - higher values ( > 3.0) indicate a very good fit while lower values (< 2.0) indicate generally unacceptable fits. -# - empty: (Well indicator) -# - an 'E' indicates that the well was empty and no growth was detected. -# - an 'I' indicates that the well was inoculated and growth was detected above the threshold. -# - an 'E*' indicates that the well was empty and growth was detected (possible contamination). -# - an '!' indicates that the well was inoculated and no growth was detected. -# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index. -# - reach: (Final growth percentage): The percentage of reached by the culture in the course of the experiment. -# - other: Other information includes output from jump detection algorithm and additional columns from the Plate Layout. -# - pdf.file and page.no: location of the figure for this well in the output .pdf files. -# -# -- Source file information-- -# YPDAFEXglucoseTests_2-25-10.csv -# analyzed using GCAT v 0.01 -# request sent: 2013-11-26 11:41:49 -# completed: 2013-11-26 11:42:00 -# -# -- Parameters used in current analysis -- -# - Constant added to log(OD + n) transformation: 1 -# - Blank OD value: 0.093 -# - Index of inoculation timepoint 2 -# - Minimum growth threshold: 0.05 -# - Removed points: -# - Jump detection: FALSE \ No newline at end of file diff --git a/Testing/GCAT_Automated_Test_Script/GCAT2/OD_Transform.txt b/Testing/GCAT_Automated_Test_Script/GCAT2/OD_Transform.txt deleted file mode 100755 index 5ef17fb..0000000 --- a/Testing/GCAT_Automated_Test_Script/GCAT2/OD_Transform.txt +++ /dev/null @@ -1,129 +0,0 @@ -"row" "plate" "well" "media" "strain" "model" "spec.growth" "tot.growth" "lag.time" "inoc.OD" "good.fit" "empty" "asymp" "tank" "reach" "other" "pdf.file" "page.no" "Destination.plate.name" "Well.ID" "Plate.source" "Well.Source" -1 "YPDAFEXglucoseTests_2-25-10" "A01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 2 "Control strain plate" "Empty" "Empty" "Empty" -2 "YPDAFEXglucoseTests_2-25-10" "B01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 3 "Control strain plate" "Empty" "Empty" "Empty" -3 "YPDAFEXglucoseTests_2-25-10" "C01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 4 "Control strain plate" "Empty" "Empty" "Empty" -4 "YPDAFEXglucoseTests_2-25-10" "D01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 5 "Control strain plate" "Empty" "Empty" "Empty" -5 "YPDAFEXglucoseTests_2-25-10" "E01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 6 "Control strain plate" "Empty" "Empty" "Empty" -6 "YPDAFEXglucoseTests_2-25-10" "F01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 7 "Control strain plate" "Empty" "Empty" "Empty" -7 "YPDAFEXglucoseTests_2-25-10" "G01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 8 "Control strain plate" "Empty" "Empty" "Empty" -8 "YPDAFEXglucoseTests_2-25-10" "H01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 9 "Control strain plate" "Empty" "Empty" "Empty" -9 "YPDAFEXglucoseTests_2-25-10" "A02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 10 "Control strain plate" "Empty" "Empty" "Empty" -10 "YPDAFEXglucoseTests_2-25-10" "B02" "YP" "Lab strain" "logistic 4-par." 0.0051339104025321 0.0886723328566521 0.00109607936061840 0.109864484860788 2.59465563414594 "I " "-" "-" 92.757634946894 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 11 "Control strain plate" "Sample" "USDA" "" -11 "YPDAFEXglucoseTests_2-25-10" "C02" "YP+0.25% glucose" "Lab strain" "richards 5-par." 0.046002940306046 0.240507240883085 2.41478235175163 0.0760170490729348 2.23914120606312 "I " "-" "-" 99.9998793491392 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 12 "Control strain plate" "Sample" "USDA" "" -12 "YPDAFEXglucoseTests_2-25-10" "D02" "YP+0.5% glucose" "Lab strain" "richards 5-par." 0.0731423187284127 0.433505884635671 3.11051947470925 0.0911039861390441 2.53605103328146 "I " "-" "-" 99.9999952705852 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 13 "Control strain plate" "Sample" "USDA" "" -13 "YPDAFEXglucoseTests_2-25-10" "E02" "YP+1% glucose" "Lab strain" "richards 5-par." 0.0874988417043893 0.678577289035852 3.41249009999581 0.0789139664707765 2.87924387138496 "I " "-" "-" 99.9997661119774 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 14 "Control strain plate" "Sample" "USDA" "" -14 "YPDAFEXglucoseTests_2-25-10" "F02" "YP+2% glucose" "Lab strain" "logistic 4-par." 0.0833321480330421 0.84892275974252 2.93134654253266 0.073343229233773 2.65845234206075 "I " "-" "-" 99.991884161003 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 15 "Control strain plate" "Sample" "USDA" "" -15 "YPDAFEXglucoseTests_2-25-10" "G02" "YP+5% glucose" "Lab strain" "logistic 4-par." 0.0589669239782459 1.12434511662564 1.29496928736621 0.046493377454031 1.79342170973749 "I " "L" "-" 98.6773509965225 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 16 "Control strain plate" "Sample" "USDA" "" -16 "YPDAFEXglucoseTests_2-25-10" "H02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 17 "Control strain plate" "Empty" "Empty" "Empty" -17 "YPDAFEXglucoseTests_2-25-10" "A03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 18 "Control strain plate" "Empty" "Empty" "Empty" -18 "YPDAFEXglucoseTests_2-25-10" "B03" "YP" "Wild strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 19 "Control strain plate" "Sample" "USDA" "" -19 "YPDAFEXglucoseTests_2-25-10" "C03" "YP+0.25% glucose" "Wild strain" "logistic 4-par." 0.0459986844673101 0.256099056993136 1.74285082231178 0.110833972260523 1.7086432551943 "I " "-" "-" 99.9999955687937 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 20 "Control strain plate" "Sample" "USDA" "" -20 "YPDAFEXglucoseTests_2-25-10" "D03" "YP+0.5% glucose" "Wild strain" "logistic 4-par." 0.094586809109001 0.426236311576192 2.76070291990178 0.129985488302977 2.46359052165418 "I " "-" "-" 99.9999999852491 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 21 "Control strain plate" "Sample" "USDA" "" -21 "YPDAFEXglucoseTests_2-25-10" "E03" "YP+1% glucose" "Wild strain" "richards 5-par." 0.121127547834438 0.686895206195343 3.14369238195928 0.106168321707794 2.89947354509400 "I " "-" "-" 99.999999980129 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 22 "Control strain plate" "Sample" "USDA" "" -22 "YPDAFEXglucoseTests_2-25-10" "F03" "YP+2% glucose" "Wild strain" "richards 5-par." 0.129882547639779 1.04404130073079 2.93412602521094 0.121702902135689 2.75950289629821 "I " "-" "-" 99.9999893737237 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 23 "Control strain plate" "Sample" "USDA" "" -23 "YPDAFEXglucoseTests_2-25-10" "G03" "YP+5% glucose" "Wild strain" "richards 5-par." 0.120898411706254 1.33105577737345 2.72267556496827 0.12655592121228 2.86661364644022 "I " "-" "-" 99.9926319946813 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 24 "Control strain plate" "Sample" "USDA" "" -24 "YPDAFEXglucoseTests_2-25-10" "H03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 25 "Control strain plate" "Empty" "Empty" "Empty" -25 "YPDAFEXglucoseTests_2-25-10" "A04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 26 "Control strain plate" "Empty" "Empty" "Empty" -26 "YPDAFEXglucoseTests_2-25-10" "B04" "YP" "Industrial strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 27 "Control strain plate" "Sample" "Internal source" "" -27 "YPDAFEXglucoseTests_2-25-10" "C04" "YP+0.25% glucose" "Industrial strain" "logistic 4-par." 0.0493379997843534 0.258082503402126 0.626040233021415 0.0848036154923235 1.54716159908115 "I " "-" "-" 99.9999968252864 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 28 "Control strain plate" "Sample" "Internal source" "" -28 "YPDAFEXglucoseTests_2-25-10" "D04" "YP+0.5% glucose" "Industrial strain" "logistic 4-par." 0.093193485656018 0.411823417276531 1.71814140307729 0.091409977040732 2.39970752160387 "I " "-" "-" 99.9999999910198 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 29 "Control strain plate" "Sample" "Internal source" "" -29 "YPDAFEXglucoseTests_2-25-10" "E04" "YP+1% glucose" "Industrial strain" "richards 5-par." 0.124582742622812 0.665080891230421 2.16563432426164 0.091100407355597 3.20379613427983 "I " "-" "-" 99.9999999995818 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 30 "Control strain plate" "Sample" "Internal source" "" -30 "YPDAFEXglucoseTests_2-25-10" "F04" "YP+2% glucose" "Industrial strain" "richards 5-par." 0.127931246989736 0.990156801382824 2.06117153412082 0.0876398778418972 2.98526874471877 "I " "L" "-" 99.9999999793615 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 31 "Control strain plate" "Sample" "Internal source" "" -31 "YPDAFEXglucoseTests_2-25-10" "G04" "YP+5% glucose" "Industrial strain" "richards 5-par." 0.115525592287136 1.30147912807139 1.85809576888812 0.0813644729068572 2.81287527921881 "I " "L" "-" 99.9999137792424 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 32 "Control strain plate" "Sample" "Internal source" "" -32 "YPDAFEXglucoseTests_2-25-10" "H04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 33 "Control strain plate" "Empty" "Empty" "Empty" -33 "YPDAFEXglucoseTests_2-25-10" "A05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 34 "Control strain plate" "Empty" "Empty" "Empty" -34 "YPDAFEXglucoseTests_2-25-10" "B05" "YP" "Engineered strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 35 "Control strain plate" "Sample" "ATCC" "" -35 "YPDAFEXglucoseTests_2-25-10" "C05" "YP+0.25% glucose" "Engineered strain" "logistic 4-par." 0.0459359326345167 0.251845669441832 0.66329309803162 0.0603517553820379 1.37098828428178 "I " "-" "-" 99.9999879447413 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 36 "Control strain plate" "Sample" "ATCC" "" -36 "YPDAFEXglucoseTests_2-25-10" "D05" "YP+0.5% glucose" "Engineered strain" "richards 5-par." 0.094434689949163 0.470902886035373 1.8826288625178 0.0639276535310338 2.23793506472592 "I " "-" "-" 99.9999948852344 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 37 "Control strain plate" "Sample" "ATCC" "" -37 "YPDAFEXglucoseTests_2-25-10" "E05" "YP+1% glucose" "Engineered strain" "richards 5-par." 0.121520619472619 0.710378798342107 2.08888813058284 0.0796495197823908 2.69846627998211 "I " "-" "-" 99.9999978953908 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 38 "Control strain plate" "Sample" "ATCC" "" -38 "YPDAFEXglucoseTests_2-25-10" "F05" "YP+2% glucose" "Engineered strain" "richards 5-par." 0.128733154739806 0.984997029200378 2.03997971060550 0.0873954601678824 2.90166520842456 "I " "-" "-" 99.9999884375137 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 39 "Control strain plate" "Sample" "ATCC" "" -39 "YPDAFEXglucoseTests_2-25-10" "G05" "YP+5% glucose" "Engineered strain" "richards 5-par." 0.122721598738299 1.31537998678672 2.01398893630359 0.0697748020039699 3.02277302646044 "I " "L" "-" 99.9995991051657 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 40 "Control strain plate" "Sample" "ATCC" "" -40 "YPDAFEXglucoseTests_2-25-10" "H05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 41 "Control strain plate" "Empty" "Empty" "Empty" -41 "YPDAFEXglucoseTests_2-25-10" "A06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 42 "Control strain plate" "Empty" "Empty" "Empty" -42 "YPDAFEXglucoseTests_2-25-10" "B06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 43 "Control strain plate" "Empty" "Empty" "Empty" -43 "YPDAFEXglucoseTests_2-25-10" "C06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 44 "Control strain plate" "Empty" "Empty" "Empty" -44 "YPDAFEXglucoseTests_2-25-10" "D06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 45 "Control strain plate" "Empty" "Empty" "Empty" -45 "YPDAFEXglucoseTests_2-25-10" "E06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 46 "Control strain plate" "Empty" "Empty" "Empty" -46 "YPDAFEXglucoseTests_2-25-10" "F06" "Empty" "Empty" "richards 5-par." 0.0831016695295036 1.26198322710616 9.6341119668272 -0.0159936185251119 2.21763366074044 "E*" "L" "-" 97.6895368192497 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 47 "Control strain plate" "Empty" "Empty" "Empty" -47 "YPDAFEXglucoseTests_2-25-10" "G06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 48 "Control strain plate" "Empty" "Empty" "Empty" -48 "YPDAFEXglucoseTests_2-25-10" "H06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 49 "Control strain plate" "Empty" "Empty" "Empty" -49 "YPDAFEXglucoseTests_2-25-10" "A07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 50 "Control strain plate" "Empty" "Empty" "Empty" -50 "YPDAFEXglucoseTests_2-25-10" "B07" "AFEX" "Lab strain" "richards 5-par." 0.0913331265905349 0.97967934369959 3.89989293822063 0.0565463143969478 3.41803212615394 "I " "-" "-" 99.996754328781 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 51 "Control strain plate" "Sample" "USDA" "" -51 "YPDAFEXglucoseTests_2-25-10" "C07" "AFEX+0.25% glucose" "Lab strain" "richards 5-par." 0.0901758841312911 1.02553230430999 3.91431464072772 0.054347185302541 3.35821455308180 "I " "-" "-" 99.9933058334686 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 52 "Control strain plate" "Sample" "USDA" "" -52 "YPDAFEXglucoseTests_2-25-10" "D07" "AFEX+0.5% glucose" "Lab strain" "richards 5-par." 0.087653449479707 1.05312597876003 4.23604747636681 0.0485047709394144 3.43101493489101 "I " "-" "-" 99.9881620605088 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 53 "Control strain plate" "Sample" "USDA" "" -53 "YPDAFEXglucoseTests_2-25-10" "E07" "AFEX+1% glucose" "Lab strain" "richards 5-par." 0.0852505865256928 1.09709212221813 4.4160839430485 0.0528193717230026 3.32240181027237 "I " "-" "-" 99.9643803748374 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 54 "Control strain plate" "Sample" "USDA" "" -54 "YPDAFEXglucoseTests_2-25-10" "F07" "AFEX+2% glucose" "Lab strain" "richards 5-par." 0.0834062493600675 1.16328851193977 4.33330336969409 0.0489104172866142 3.24662867008000 "I " "-" "-" 99.8772630755024 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 55 "Control strain plate" "Sample" "USDA" "" -55 "YPDAFEXglucoseTests_2-25-10" "G07" "AFEX+5% glucose" "Lab strain" "richards 5-par." 0.0746869172685951 1.29976805435626 4.42703571454512 0.0546121442553045 3.36340266867229 "I " "-" "-" 98.4368902568205 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 56 "Control strain plate" "Sample" "USDA" "" -56 "YPDAFEXglucoseTests_2-25-10" "H07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 57 "Control strain plate" "Empty" "Empty" "Empty" -57 "YPDAFEXglucoseTests_2-25-10" "A08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 58 "Control strain plate" "Empty" "Empty" "Empty" -58 "YPDAFEXglucoseTests_2-25-10" "B08" "AFEX" "Wild strain" "richards 5-par." 0.114235639362830 1.11928465325468 2.95662866422492 0.102774172923920 3.07479264063237 "I " "-" "-" 99.9998423354262 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 59 "Control strain plate" "Sample" "USDA" "" -59 "YPDAFEXglucoseTests_2-25-10" "C08" "AFEX+0.25% glucose" "Wild strain" "richards 5-par." 0.114214452831191 1.14837906885588 3.19068068041329 0.0872651968628158 3.13967373959083 "I " "-" "-" 99.9996783933085 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 60 "Control strain plate" "Sample" "USDA" "" -60 "YPDAFEXglucoseTests_2-25-10" "D08" "AFEX+0.5% glucose" "Wild strain" "richards 5-par." 0.113566098483318 1.18251324712617 3.15261697058665 0.0824132232798602 3.20643947548216 "I " "-" "-" 99.9993817260453 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 61 "Control strain plate" "Sample" "USDA" "" -61 "YPDAFEXglucoseTests_2-25-10" "E08" "AFEX+1% glucose" "Wild strain" "richards 5-par." 0.112827039600267 1.23375586100143 3.12591278868747 0.0877996040474751 3.18956938304341 "I " "-" "-" 99.9983920897484 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 62 "Control strain plate" "Sample" "USDA" "" -62 "YPDAFEXglucoseTests_2-25-10" "F08" "AFEX+2% glucose" "Wild strain" "richards 5-par." 0.110948155806134 1.28676660547704 3.25021471205597 0.0827447676928017 3.20897314216787 "I " "-" "-" 99.9946050160346 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 63 "Control strain plate" "Sample" "USDA" "" -63 "YPDAFEXglucoseTests_2-25-10" "G08" "AFEX+5% glucose" "Wild strain" "richards 5-par." 0.104909957772007 1.38120323294419 3.5400282340856 0.0841025860310471 3.54895808838236 "I " "-" "-" 99.9341701264792 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 64 "Control strain plate" "Sample" "USDA" "" -64 "YPDAFEXglucoseTests_2-25-10" "H08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 65 "Control strain plate" "Empty" "Empty" "Empty" -65 "YPDAFEXglucoseTests_2-25-10" "A09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 66 "Control strain plate" "Empty" "Empty" "Empty" -66 "YPDAFEXglucoseTests_2-25-10" "B09" "AFEX" "Industrial strain" "richards 5-par." 0.124619613670634 1.02546123083454 2.57717331265474 0.0790971076805143 3.19828565863910 "I " "-" "-" 99.9999985057572 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 67 "Control strain plate" "Sample" "Internal source" "" -67 "YPDAFEXglucoseTests_2-25-10" "C09" "AFEX+0.25% glucose" "Industrial strain" "richards 5-par." 0.123242472307703 1.0763049093573 2.58579779724471 0.0704104383586222 3.30084510513736 "I " "-" "-" 99.9999944424538 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 68 "Control strain plate" "Sample" "Internal source" "" -68 "YPDAFEXglucoseTests_2-25-10" "D09" "AFEX+0.5% glucose" "Industrial strain" "richards 5-par." 0.120900871587230 1.10591407490241 2.49685751569192 0.0672398191226693 3.29576923039635 "I " "L" "-" 99.999989671537 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 69 "Control strain plate" "Sample" "Internal source" "" -69 "YPDAFEXglucoseTests_2-25-10" "E09" "AFEX+1% glucose" "Industrial strain" "richards 5-par." 0.119451758787832 1.16449508809393 2.44557526327415 0.0665918895911914 3.20509498580801 "I " "L" "-" 99.9999601611542 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 70 "Control strain plate" "Sample" "Internal source" "" -70 "YPDAFEXglucoseTests_2-25-10" "F09" "AFEX+2% glucose" "Industrial strain" "richards 5-par." 0.117046850703108 1.23459712335416 2.58701197446896 0.0611670849509847 3.14018976860492 "I " "L" "-" 99.9995704795227 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 71 "Control strain plate" "Sample" "Internal source" "" -71 "YPDAFEXglucoseTests_2-25-10" "G09" "AFEX+5% glucose" "Industrial strain" "richards 5-par." 0.108331393797411 1.34306781528512 2.65978833216588 0.0615660939241569 3.23212721890241 "I " "-" "-" 99.9822923993972 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 72 "Control strain plate" "Sample" "Internal source" "" -72 "YPDAFEXglucoseTests_2-25-10" "H09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 73 "Control strain plate" "Empty" "Empty" "Empty" -73 "YPDAFEXglucoseTests_2-25-10" "A10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 74 "Control strain plate" "Empty" "Empty" "Empty" -74 "YPDAFEXglucoseTests_2-25-10" "B10" "AFEX" "Engineered strain" "richards 5-par." 0.121839335770884 1.03411101157879 2.35496298854354 0.0684679645246347 2.99659166289529 "I " "-" "-" 99.9998739337277 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 75 "Control strain plate" "Sample" "ATCC" "" -75 "YPDAFEXglucoseTests_2-25-10" "C10" "AFEX+0.25% glucose" "Engineered strain" "richards 5-par." 0.123130424753602 1.06718487562610 2.62328252943635 0.0533919287920788 3.19928587493597 "I " "-" "-" 99.9998922931215 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 76 "Control strain plate" "Sample" "ATCC" "" -76 "YPDAFEXglucoseTests_2-25-10" "D10" "AFEX+0.5% glucose" "Engineered strain" "richards 5-par." 0.120973126016907 1.08894424184742 2.61938690806177 0.0531493464712776 3.33630531768578 "I " "-" "-" 99.9998818237851 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 77 "Control strain plate" "Sample" "ATCC" "" -77 "YPDAFEXglucoseTests_2-25-10" "E10" "AFEX+1% glucose" "Engineered strain" "richards 5-par." 0.120740948707418 1.1559165803317 2.69619009025558 0.048980878983772 3.36496106313806 "I " "-" "-" 99.9996105268543 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 78 "Control strain plate" "Sample" "ATCC" "" -78 "YPDAFEXglucoseTests_2-25-10" "F10" "AFEX+2% glucose" "Engineered strain" "richards 5-par." 0.121802166262885 1.22916108660807 2.69540468852973 0.0531433213499186 3.47334970863371 "I " "-" "-" 99.99890373284 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 79 "Control strain plate" "Sample" "ATCC" "" -79 "YPDAFEXglucoseTests_2-25-10" "G10" "AFEX+5% glucose" "Engineered strain" "richards 5-par." 0.112904136028813 1.34343484031260 2.71645828999368 0.0555677209128236 3.53967163281668 "I " "-" "-" 99.9786856044998 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 80 "Control strain plate" "Sample" "ATCC" "" -80 "YPDAFEXglucoseTests_2-25-10" "H10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 81 "Control strain plate" "Empty" "Empty" "Empty" -81 "YPDAFEXglucoseTests_2-25-10" "A11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 82 "Control strain plate" "Empty" "Empty" "Empty" -82 "YPDAFEXglucoseTests_2-25-10" "B11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 83 "Control strain plate" "Empty" "Empty" "Empty" -83 "YPDAFEXglucoseTests_2-25-10" "C11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 84 "Control strain plate" "Empty" "Empty" "Empty" -84 "YPDAFEXglucoseTests_2-25-10" "D11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 85 "Control strain plate" "Empty" "Empty" "Empty" -85 "YPDAFEXglucoseTests_2-25-10" "E11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 86 "Control strain plate" "Empty" "Empty" "Empty" -86 "YPDAFEXglucoseTests_2-25-10" "F11" "None" "Empty" "logistic 4-par." 0.0972515006011796 1.24805373798836 14.8532035505196 -0.00367359356392649 2.38008868734198 "E*" "L/U" "-" 87.1867820927035 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 87 "Control strain plate" "Empty" "Empty" "Empty" -87 "YPDAFEXglucoseTests_2-25-10" "G11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 88 "Control strain plate" "Empty" "Empty" "Empty" -88 "YPDAFEXglucoseTests_2-25-10" "H11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 89 "Control strain plate" "Empty" "Empty" "Empty" -89 "YPDAFEXglucoseTests_2-25-10" "A12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 90 "Control strain plate" "Empty" "Empty" "Empty" -90 "YPDAFEXglucoseTests_2-25-10" "B12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 91 "Control strain plate" "Empty" "Empty" "Empty" -91 "YPDAFEXglucoseTests_2-25-10" "C12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 92 "Control strain plate" "Empty" "Empty" "Empty" -92 "YPDAFEXglucoseTests_2-25-10" "D12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 93 "Control strain plate" "Empty" "Empty" "Empty" -93 "YPDAFEXglucoseTests_2-25-10" "E12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 94 "Control strain plate" "Empty" "Empty" "Empty" -94 "YPDAFEXglucoseTests_2-25-10" "F12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 95 "Control strain plate" "Empty" "Empty" "Empty" -95 "YPDAFEXglucoseTests_2-25-10" "G12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 96 "Control strain plate" "Empty" "Empty" "Empty" -96 "YPDAFEXglucoseTests_2-25-10" "H12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.11.pdf" 97 "Control strain plate" "Empty" "Empty" "Empty" - -# -- Explanation of columns -- -# - model: Name of the model the well was successfully fit with (if any) -# - spec.growth: (Specific growth rate) The largest exponential growth rate achieved by the culture in the course of the experiment -# - tot.growth: (Total extrapolated growth) The estimated growth plateau from the fitted model in optical density units. May be higher than the actual highest OD reached. -# - lag.time: (Lag time) The exponential trend from is extrapolated to the baseline OD at inoculation and subtracted from the time at inoculation to yield lag time. -# - inoc.OD: (OD at inoculation) The adjusted optical density at the user-specified starting timepoint. -# - good.fit: (Goodness of fit) A metric based on root mean square deviations (RMSD). -# - higher values ( > 3.0) indicate a very good fit while lower values (< 2.0) indicate generally unacceptable fits. -# - empty: (Well indicator) -# - an 'E' indicates that the well was empty and no growth was detected. -# - an 'I' indicates that the well was inoculated and growth was detected above the threshold. -# - an 'E*' indicates that the well was empty and growth was detected (possible contamination). -# - an '!' indicates that the well was inoculated and no growth was detected. -# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index. -# - reach: (Final growth percentage): The percentage of reached by the culture in the course of the experiment. -# - other: Other information includes output from jump detection algorithm and additional columns from the Plate Layout. -# - pdf.file and page.no: location of the figure for this well in the output .pdf files. -# -# -- Source file information-- -# YPDAFEXglucoseTests_2-25-10.csv -# analyzed using GCAT v 0.01 -# request sent: 2013-11-26 11:46:11 -# completed: 2013-11-26 11:46:20 -# -# -- Parameters used in current analysis -- -# - Constant added to log(OD + n) transformation: 1 -# - Blank OD value: First timepoint in well -# - Index of inoculation timepoint 2 -# - Minimum growth threshold: 0.05 -# - Removed points: -# - Jump detection: FALSE \ No newline at end of file diff --git a/Testing/GCAT_Automated_Test_Script/GCAT2/Points_Ignored.txt b/Testing/GCAT_Automated_Test_Script/GCAT2/Points_Ignored.txt deleted file mode 100755 index 9109afd..0000000 --- a/Testing/GCAT_Automated_Test_Script/GCAT2/Points_Ignored.txt +++ /dev/null @@ -1,129 +0,0 @@ -"row" "plate" "well" "media" "strain" "model" "spec.growth" "tot.growth" "lag.time" "inoc.OD" "good.fit" "empty" "asymp" "tank" "reach" "other" "pdf.file" "page.no" "Destination.plate.name" "Well.ID" "Plate.source" "Well.Source" -1 "YPDAFEXglucoseTests_2-25-10" "A01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 2 "Control strain plate" "Empty" "Empty" "Empty" -2 "YPDAFEXglucoseTests_2-25-10" "B01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 3 "Control strain plate" "Empty" "Empty" "Empty" -3 "YPDAFEXglucoseTests_2-25-10" "C01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 4 "Control strain plate" "Empty" "Empty" "Empty" -4 "YPDAFEXglucoseTests_2-25-10" "D01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 5 "Control strain plate" "Empty" "Empty" "Empty" -5 "YPDAFEXglucoseTests_2-25-10" "E01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 6 "Control strain plate" "Empty" "Empty" "Empty" -6 "YPDAFEXglucoseTests_2-25-10" "F01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 7 "Control strain plate" "Empty" "Empty" "Empty" -7 "YPDAFEXglucoseTests_2-25-10" "G01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 8 "Control strain plate" "Empty" "Empty" "Empty" -8 "YPDAFEXglucoseTests_2-25-10" "H01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 9 "Control strain plate" "Empty" "Empty" "Empty" -9 "YPDAFEXglucoseTests_2-25-10" "A02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 10 "Control strain plate" "Empty" "Empty" "Empty" -10 "YPDAFEXglucoseTests_2-25-10" "B02" "YP" "Lab strain" "logistic 4-par." 0.00512322284611084 0.0885706705171092 0.00146885083119497 0.109882390197245 2.6703814889978 "I " "-" "-" 92.8305994745802 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 11 "Control strain plate" "Sample" "USDA" "" -11 "YPDAFEXglucoseTests_2-25-10" "C02" "YP+0.25% glucose" "Lab strain" "richards 5-par." 0.0459063906963165 0.241063286623944 2.41105819151703 0.0760544501191693 2.33445949677366 "I " "-" "-" 99.9998616892386 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 12 "Control strain plate" "Sample" "USDA" "" -12 "YPDAFEXglucoseTests_2-25-10" "D02" "YP+0.5% glucose" "Lab strain" "richards 5-par." 0.0729653521516789 0.434572158524765 3.10530782875816 0.0912110779424646 2.66378208529322 "I " "-" "-" 99.99999403812 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 13 "Control strain plate" "Sample" "USDA" "" -13 "YPDAFEXglucoseTests_2-25-10" "E02" "YP+1% glucose" "Lab strain" "richards 5-par." 0.087549003744991 0.680384078190256 3.41500410591867 0.078602369429122 3.04253253857771 "I " "-" "-" 99.999783493135 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 14 "Control strain plate" "Sample" "USDA" "" -14 "YPDAFEXglucoseTests_2-25-10" "F02" "YP+2% glucose" "Lab strain" "logistic 4-par." 0.0835036622875622 0.849207863293472 2.94083431769237 0.0735497372002751 2.71606517889471 "I " "-" "-" 99.9920437081347 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 15 "Control strain plate" "Sample" "USDA" "" -15 "YPDAFEXglucoseTests_2-25-10" "G02" "YP+5% glucose" "Lab strain" "logistic 4-par." 0.0605784733145486 1.11352517731425 1.48539390611669 0.0496177952902848 1.88568659491702 "I " "L" "-" 98.9719626898602 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 16 "Control strain plate" "Sample" "USDA" "" -16 "YPDAFEXglucoseTests_2-25-10" "H02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 17 "Control strain plate" "Empty" "Empty" "Empty" -17 "YPDAFEXglucoseTests_2-25-10" "A03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 18 "Control strain plate" "Empty" "Empty" "Empty" -18 "YPDAFEXglucoseTests_2-25-10" "B03" "YP" "Wild strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 19 "Control strain plate" "Sample" "USDA" "" -19 "YPDAFEXglucoseTests_2-25-10" "C03" "YP+0.25% glucose" "Wild strain" "logistic 4-par." 0.0457475800711658 0.256904287297204 1.72691879921013 0.110606719040152 1.77859625443674 "I " "-" "-" 99.9999947777523 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 20 "Control strain plate" "Sample" "USDA" "" -20 "YPDAFEXglucoseTests_2-25-10" "D03" "YP+0.5% glucose" "Wild strain" "logistic 4-par." 0.0944654373655411 0.426655260550642 2.75828968419929 0.129917552736420 2.52869451465839 "I " "-" "-" 99.999999984456 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 21 "Control strain plate" "Sample" "USDA" "" -21 "YPDAFEXglucoseTests_2-25-10" "E03" "YP+1% glucose" "Wild strain" "richards 5-par." 0.121095965736346 0.687037999671402 3.14313398289071 0.106191053770912 2.95478381597453 "I " "-" "-" 99.999999979389 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 22 "Control strain plate" "Sample" "USDA" "" -22 "YPDAFEXglucoseTests_2-25-10" "F03" "YP+2% glucose" "Wild strain" "richards 5-par." 0.129855086205514 1.04449449227513 2.93366816024193 0.121714484234362 2.81436465576683 "I " "-" "-" 99.9999891316078 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 23 "Control strain plate" "Sample" "USDA" "" -23 "YPDAFEXglucoseTests_2-25-10" "G03" "YP+5% glucose" "Wild strain" "richards 5-par." 0.120898435937539 1.32764962491579 2.72323240077344 0.127905341227191 3.00797833267527 "I " "-" "-" 99.9912733187558 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 24 "Control strain plate" "Sample" "USDA" "" -24 "YPDAFEXglucoseTests_2-25-10" "H03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 25 "Control strain plate" "Empty" "Empty" "Empty" -25 "YPDAFEXglucoseTests_2-25-10" "A04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 26 "Control strain plate" "Empty" "Empty" "Empty" -26 "YPDAFEXglucoseTests_2-25-10" "B04" "YP" "Industrial strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 27 "Control strain plate" "Sample" "Internal source" "" -27 "YPDAFEXglucoseTests_2-25-10" "C04" "YP+0.25% glucose" "Industrial strain" "logistic 4-par." 0.049113938942915 0.258748737037695 0.611171874481659 0.0845578831007956 1.61316239160049 "I " "-" "-" 99.9999962105762 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 28 "Control strain plate" "Sample" "Internal source" "" -28 "YPDAFEXglucoseTests_2-25-10" "D04" "YP+0.5% glucose" "Industrial strain" "logistic 4-par." 0.093074527600122 0.412178246785743 1.71538098733957 0.0913303370508307 2.46532958224324 "I " "-" "-" 99.9999999905309 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 29 "Control strain plate" "Sample" "Internal source" "" -29 "YPDAFEXglucoseTests_2-25-10" "E04" "YP+1% glucose" "Industrial strain" "richards 5-par." 0.124584782390426 0.665071528928034 2.16566832060573 0.09109869026466 3.26118827375832 "I " "-" "-" 99.9999999995832 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 30 "Control strain plate" "Sample" "Internal source" "" -30 "YPDAFEXglucoseTests_2-25-10" "F04" "YP+2% glucose" "Industrial strain" "richards 5-par." 0.127927076462060 0.990201196030809 2.06107722840498 0.087648083744547 3.04010612494743 "I " "L" "-" 99.9999999791478 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 31 "Control strain plate" "Sample" "Internal source" "" -31 "YPDAFEXglucoseTests_2-25-10" "G04" "YP+5% glucose" "Industrial strain" "richards 5-par." 0.115598093951232 1.30017594724392 1.86057928629408 0.0816316115810476 2.87659439741231 "I " "L" "-" 99.9999089635063 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 32 "Control strain plate" "Sample" "Internal source" "" -32 "YPDAFEXglucoseTests_2-25-10" "H04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 33 "Control strain plate" "Empty" "Empty" "Empty" -33 "YPDAFEXglucoseTests_2-25-10" "A05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 34 "Control strain plate" "Empty" "Empty" "Empty" -34 "YPDAFEXglucoseTests_2-25-10" "B05" "YP" "Engineered strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 35 "Control strain plate" "Sample" "ATCC" "" -35 "YPDAFEXglucoseTests_2-25-10" "C05" "YP+0.25% glucose" "Engineered strain" "logistic 4-par." 0.0455423852277455 0.253011492887766 0.633612783422165 0.0599180880707215 1.44199308592877 "I " "-" "-" 99.9999836645589 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 36 "Control strain plate" "Sample" "ATCC" "" -36 "YPDAFEXglucoseTests_2-25-10" "D05" "YP+0.5% glucose" "Engineered strain" "richards 5-par." 0.0942560771156105 0.47165366043215 1.87947890043788 0.0641152719303668 2.32215880898724 "I " "-" "-" 99.9999936292908 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 37 "Control strain plate" "Sample" "ATCC" "" -37 "YPDAFEXglucoseTests_2-25-10" "E05" "YP+1% glucose" "Engineered strain" "richards 5-par." 0.121404566371326 0.711085043803959 2.08707581462709 0.079800634332521 2.77857179654498 "I " "-" "-" 99.9999975813868 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 38 "Control strain plate" "Sample" "ATCC" "" -38 "YPDAFEXglucoseTests_2-25-10" "F05" "YP+2% glucose" "Engineered strain" "richards 5-par." 0.128659484339870 0.98597671409577 2.03868589008582 0.087495143007229 2.98217250669466 "I " "-" "-" 99.9999873691302 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 39 "Control strain plate" "Sample" "ATCC" "" -39 "YPDAFEXglucoseTests_2-25-10" "G05" "YP+5% glucose" "Engineered strain" "richards 5-par." 0.122711103907082 1.31562500185075 2.01371509312624 0.0697603778582843 3.07643306357741 "I " "L" "-" 99.999598061796 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 40 "Control strain plate" "Sample" "ATCC" "" -40 "YPDAFEXglucoseTests_2-25-10" "H05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 41 "Control strain plate" "Empty" "Empty" "Empty" -41 "YPDAFEXglucoseTests_2-25-10" "A06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 42 "Control strain plate" "Empty" "Empty" "Empty" -42 "YPDAFEXglucoseTests_2-25-10" "B06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 43 "Control strain plate" "Empty" "Empty" "Empty" -43 "YPDAFEXglucoseTests_2-25-10" "C06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 44 "Control strain plate" "Empty" "Empty" "Empty" -44 "YPDAFEXglucoseTests_2-25-10" "D06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 45 "Control strain plate" "Empty" "Empty" "Empty" -45 "YPDAFEXglucoseTests_2-25-10" "E06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 46 "Control strain plate" "Empty" "Empty" "Empty" -46 "YPDAFEXglucoseTests_2-25-10" "F06" "Empty" "Empty" "richards 5-par." 0.0857882390552096 1.24493866823306 9.88179192729724 -0.0165597461168613 2.32606464578444 "E*" "L" "-" 98.4210828771573 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 47 "Control strain plate" "Empty" "Empty" "Empty" -47 "YPDAFEXglucoseTests_2-25-10" "G06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 48 "Control strain plate" "Empty" "Empty" "Empty" -48 "YPDAFEXglucoseTests_2-25-10" "H06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 49 "Control strain plate" "Empty" "Empty" "Empty" -49 "YPDAFEXglucoseTests_2-25-10" "A07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 50 "Control strain plate" "Empty" "Empty" "Empty" -50 "YPDAFEXglucoseTests_2-25-10" "B07" "AFEX" "Lab strain" "richards 5-par." 0.0910656809877224 0.978831696720056 3.88851123944356 0.057119562600749 3.50838381966352 "I " "-" "-" 99.9960539072354 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 51 "Control strain plate" "Sample" "USDA" "" -51 "YPDAFEXglucoseTests_2-25-10" "C07" "AFEX+0.25% glucose" "Lab strain" "richards 5-par." 0.0897750856169793 1.02459532986805 3.89679290870610 0.0551818328016911 3.46998372922229 "I " "-" "-" 99.991259133915 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 52 "Control strain plate" "Sample" "USDA" "" -52 "YPDAFEXglucoseTests_2-25-10" "D07" "AFEX+0.5% glucose" "Lab strain" "richards 5-par." 0.087292525747305 1.05275013304220 4.21907836932876 0.0490476413563776 3.51721701779359 "I " "-" "-" 99.9856386878846 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 53 "Control strain plate" "Sample" "USDA" "" -53 "YPDAFEXglucoseTests_2-25-10" "E07" "AFEX+1% glucose" "Lab strain" "richards 5-par." 0.0854275766875656 1.09681106370395 4.42403082220079 0.0527978561023557 3.39981186901509 "I " "-" "-" 99.9660125813752 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 54 "Control strain plate" "Sample" "USDA" "" -54 "YPDAFEXglucoseTests_2-25-10" "F07" "AFEX+2% glucose" "Lab strain" "richards 5-par." 0.084278824827003 1.16188034043041 4.37444626455929 0.0484042275684464 3.40906624822256 "I " "-" "-" 99.903924927466 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 55 "Control strain plate" "Sample" "USDA" "" -55 "YPDAFEXglucoseTests_2-25-10" "G07" "AFEX+5% glucose" "Lab strain" "richards 5-par." 0.0751490389653923 1.29671192755065 4.45016704465737 0.0546480394626687 3.48603212189912 "I " "-" "-" 98.5357819689647 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 56 "Control strain plate" "Sample" "USDA" "" -56 "YPDAFEXglucoseTests_2-25-10" "H07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 57 "Control strain plate" "Empty" "Empty" "Empty" -57 "YPDAFEXglucoseTests_2-25-10" "A08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 58 "Control strain plate" "Empty" "Empty" "Empty" -58 "YPDAFEXglucoseTests_2-25-10" "B08" "AFEX" "Wild strain" "richards 5-par." 0.114233577227138 1.11940666165336 2.95659685349929 0.102760700959780 3.12523138568832 "I " "-" "-" 99.9998425058726 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 59 "Control strain plate" "Sample" "USDA" "" -59 "YPDAFEXglucoseTests_2-25-10" "C08" "AFEX+0.25% glucose" "Wild strain" "richards 5-par." 0.114190896575847 1.14811138681943 3.18991017237117 0.0873694909800864 3.19174147527227 "I " "-" "-" 99.9996684768339 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 60 "Control strain plate" "Sample" "USDA" "" -60 "YPDAFEXglucoseTests_2-25-10" "D08" "AFEX+0.5% glucose" "Wild strain" "richards 5-par." 0.113518812542466 1.18182740070708 3.15106253292283 0.0826636113465304 3.26600840866822 "I " "-" "-" 99.9993405132836 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 61 "Control strain plate" "Sample" "USDA" "" -61 "YPDAFEXglucoseTests_2-25-10" "E08" "AFEX+1% glucose" "Wild strain" "richards 5-par." 0.112731557723291 1.23243667600584 3.12290823666719 0.0883532618105942 3.27099839140732 "I " "-" "-" 99.998177929312 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 62 "Control strain plate" "Sample" "USDA" "" -62 "YPDAFEXglucoseTests_2-25-10" "F08" "AFEX+2% glucose" "Wild strain" "richards 5-par." 0.110711220465384 1.28465314801447 3.24291094200068 0.0838703449391198 3.34935047015509 "I " "-" "-" 99.9932361128704 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 63 "Control strain plate" "Sample" "USDA" "" -63 "YPDAFEXglucoseTests_2-25-10" "G08" "AFEX+5% glucose" "Wild strain" "richards 5-par." 0.104911901010651 1.38112995826321 3.54007980934916 0.0841275019173986 3.60183900056643 "I " "-" "-" 99.9340428851054 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 64 "Control strain plate" "Sample" "USDA" "" -64 "YPDAFEXglucoseTests_2-25-10" "H08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 65 "Control strain plate" "Empty" "Empty" "Empty" -65 "YPDAFEXglucoseTests_2-25-10" "A09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 66 "Control strain plate" "Empty" "Empty" "Empty" -66 "YPDAFEXglucoseTests_2-25-10" "B09" "AFEX" "Industrial strain" "richards 5-par." 0.124639558557251 1.02518255796904 2.57760580712995 0.0790861200979034 3.25359624987887 "I " "-" "-" 99.9999985380202 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 67 "Control strain plate" "Sample" "Internal source" "" -67 "YPDAFEXglucoseTests_2-25-10" "C09" "AFEX+0.25% glucose" "Industrial strain" "richards 5-par." 0.123259617514217 1.07597966901492 2.58617748296761 0.0704118282374251 3.35647651673620 "I " "-" "-" 99.999994522924 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 68 "Control strain plate" "Sample" "Internal source" "" -68 "YPDAFEXglucoseTests_2-25-10" "D09" "AFEX+0.5% glucose" "Industrial strain" "richards 5-par." 0.120921387314129 1.10541418860150 2.49733136040803 0.0672610858991924 3.35561723828862 "I " "L" "-" 99.999989789286 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 69 "Control strain plate" "Sample" "Internal source" "" -69 "YPDAFEXglucoseTests_2-25-10" "E09" "AFEX+1% glucose" "Industrial strain" "richards 5-par." 0.119469215205307 1.16386920095508 2.44599900455348 0.0666632835088954 3.26495706766016 "I " "L" "-" 99.9999598857272 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 70 "Control strain plate" "Sample" "Internal source" "" -70 "YPDAFEXglucoseTests_2-25-10" "F09" "AFEX+2% glucose" "Industrial strain" "richards 5-par." 0.117055956532607 1.23292877894923 2.58733736534061 0.0615930499531776 3.23191783299634 "I " "-" "-" 99.9995312927806 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 71 "Control strain plate" "Sample" "Internal source" "" -71 "YPDAFEXglucoseTests_2-25-10" "G09" "AFEX+5% glucose" "Industrial strain" "richards 5-par." 0.108245104945905 1.34096953377871 2.65843365395388 0.062727700859311 3.38843037787812 "I " "-" "-" 99.9788375045276 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 72 "Control strain plate" "Sample" "Internal source" "" -72 "YPDAFEXglucoseTests_2-25-10" "H09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 73 "Control strain plate" "Empty" "Empty" "Empty" -73 "YPDAFEXglucoseTests_2-25-10" "A10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 74 "Control strain plate" "Empty" "Empty" "Empty" -74 "YPDAFEXglucoseTests_2-25-10" "B10" "AFEX" "Engineered strain" "richards 5-par." 0.121764774087552 1.03575182594995 2.35350455581128 0.0683841865814427 3.10711688897198 "I " "-" "-" 99.9998704011685 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 75 "Control strain plate" "Sample" "ATCC" "" -75 "YPDAFEXglucoseTests_2-25-10" "C10" "AFEX+0.25% glucose" "Engineered strain" "richards 5-par." 0.123090824730516 1.06842524515535 2.62256716415931 0.0532958289475007 3.29457027142756 "I " "-" "-" 99.9998916790283 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 76 "Control strain plate" "Sample" "ATCC" "" -76 "YPDAFEXglucoseTests_2-25-10" "D10" "AFEX+0.5% glucose" "Engineered strain" "richards 5-par." 0.120944684388312 1.09008552670784 2.61886063345403 0.0530365880953372 3.43451356445556 "I " "-" "-" 99.9998823965125 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 77 "Control strain plate" "Sample" "ATCC" "" -77 "YPDAFEXglucoseTests_2-25-10" "E10" "AFEX+1% glucose" "Engineered strain" "richards 5-par." 0.120734107580927 1.15670253081866 2.69611302714549 0.0488445587231696 3.43432940804069 "I " "-" "-" 99.999618979496 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 78 "Control strain plate" "Sample" "ATCC" "" -78 "YPDAFEXglucoseTests_2-25-10" "F10" "AFEX+2% glucose" "Engineered strain" "richards 5-par." 0.121797460706957 1.22927410593987 2.69529695023975 0.0531367705332191 3.52592526978957 "I " "-" "-" 99.998902414812 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 79 "Control strain plate" "Sample" "ATCC" "" -79 "YPDAFEXglucoseTests_2-25-10" "G10" "AFEX+5% glucose" "Engineered strain" "richards 5-par." 0.112849428100400 1.34218005582050 2.71555080399082 0.0562414213905349 3.66293619120109 "I " "-" "-" 99.9765721559617 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 80 "Control strain plate" "Sample" "ATCC" "" -80 "YPDAFEXglucoseTests_2-25-10" "H10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 81 "Control strain plate" "Empty" "Empty" "Empty" -81 "YPDAFEXglucoseTests_2-25-10" "A11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 82 "Control strain plate" "Empty" "Empty" "Empty" -82 "YPDAFEXglucoseTests_2-25-10" "B11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 83 "Control strain plate" "Empty" "Empty" "Empty" -83 "YPDAFEXglucoseTests_2-25-10" "C11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 84 "Control strain plate" "Empty" "Empty" "Empty" -84 "YPDAFEXglucoseTests_2-25-10" "D11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 85 "Control strain plate" "Empty" "Empty" "Empty" -85 "YPDAFEXglucoseTests_2-25-10" "E11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 86 "Control strain plate" "Empty" "Empty" "Empty" -86 "YPDAFEXglucoseTests_2-25-10" "F11" "None" "Empty" "logistic 4-par." 0.0955422988477089 1.27434659362621 14.7977758044825 -0.00282569557385737 2.58074649545863 "E*" "L/U" "-" 85.8739348760869 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 87 "Control strain plate" "Empty" "Empty" "Empty" -87 "YPDAFEXglucoseTests_2-25-10" "G11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 88 "Control strain plate" "Empty" "Empty" "Empty" -88 "YPDAFEXglucoseTests_2-25-10" "H11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 89 "Control strain plate" "Empty" "Empty" "Empty" -89 "YPDAFEXglucoseTests_2-25-10" "A12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 90 "Control strain plate" "Empty" "Empty" "Empty" -90 "YPDAFEXglucoseTests_2-25-10" "B12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 91 "Control strain plate" "Empty" "Empty" "Empty" -91 "YPDAFEXglucoseTests_2-25-10" "C12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 92 "Control strain plate" "Empty" "Empty" "Empty" -92 "YPDAFEXglucoseTests_2-25-10" "D12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 93 "Control strain plate" "Empty" "Empty" "Empty" -93 "YPDAFEXglucoseTests_2-25-10" "E12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 94 "Control strain plate" "Empty" "Empty" "Empty" -94 "YPDAFEXglucoseTests_2-25-10" "F12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 95 "Control strain plate" "Empty" "Empty" "Empty" -95 "YPDAFEXglucoseTests_2-25-10" "G12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 96 "Control strain plate" "Empty" "Empty" "Empty" -96 "YPDAFEXglucoseTests_2-25-10" "H12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.47.pdf" 97 "Control strain plate" "Empty" "Empty" "Empty" - -# -- Explanation of columns -- -# - model: Name of the model the well was successfully fit with (if any) -# - spec.growth: (Specific growth rate) The largest exponential growth rate achieved by the culture in the course of the experiment -# - tot.growth: (Total extrapolated growth) The estimated growth plateau from the fitted model in optical density units. May be higher than the actual highest OD reached. -# - lag.time: (Lag time) The exponential trend from is extrapolated to the baseline OD at inoculation and subtracted from the time at inoculation to yield lag time. -# - inoc.OD: (OD at inoculation) The adjusted optical density at the user-specified starting timepoint. -# - good.fit: (Goodness of fit) A metric based on root mean square deviations (RMSD). -# - higher values ( > 3.0) indicate a very good fit while lower values (< 2.0) indicate generally unacceptable fits. -# - empty: (Well indicator) -# - an 'E' indicates that the well was empty and no growth was detected. -# - an 'I' indicates that the well was inoculated and growth was detected above the threshold. -# - an 'E*' indicates that the well was empty and growth was detected (possible contamination). -# - an '!' indicates that the well was inoculated and no growth was detected. -# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index. -# - reach: (Final growth percentage): The percentage of reached by the culture in the course of the experiment. -# - other: Other information includes output from jump detection algorithm and additional columns from the Plate Layout. -# - pdf.file and page.no: location of the figure for this well in the output .pdf files. -# -# -- Source file information-- -# YPDAFEXglucoseTests_2-25-10.csv -# analyzed using GCAT v 0.01 -# request sent: 2013-11-26 12:08:47 -# completed: 2013-11-26 12:08:57 -# -# -- Parameters used in current analysis -- -# - Constant added to log(OD + n) transformation: 1 -# - Blank OD value: First timepoint in well -# - Index of inoculation timepoint 2 -# - Minimum growth threshold: 0.05 -# - Removed points: 70 71 72 73 74 75 76 77 78 79 -# - Jump detection: FALSE \ No newline at end of file diff --git a/Testing/GCAT_Automated_Test_Script/GCAT3/Growth_Threshold.txt b/Testing/GCAT_Automated_Test_Script/GCAT3/Growth_Threshold.txt deleted file mode 100755 index 65a65d0..0000000 --- a/Testing/GCAT_Automated_Test_Script/GCAT3/Growth_Threshold.txt +++ /dev/null @@ -1,129 +0,0 @@ -"row" "plate" "well" "media" "strain" "model" "spec.growth" "tot.growth" "lag.time" "inoc.OD" "good.fit" "empty" "asymp" "tank" "reach" "other" "pdf.file" "page.no" "Destination.plate.name" "Well.ID" "Plate.source" "Well.Source" -1 "YPDAFEXglucoseTests_2-25-10" "A01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 2 "Control strain plate" "Empty" "Empty" "Empty" -2 "YPDAFEXglucoseTests_2-25-10" "B01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 3 "Control strain plate" "Empty" "Empty" "Empty" -3 "YPDAFEXglucoseTests_2-25-10" "C01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 4 "Control strain plate" "Empty" "Empty" "Empty" -4 "YPDAFEXglucoseTests_2-25-10" "D01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 5 "Control strain plate" "Empty" "Empty" "Empty" -5 "YPDAFEXglucoseTests_2-25-10" "E01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 6 "Control strain plate" "Empty" "Empty" "Empty" -6 "YPDAFEXglucoseTests_2-25-10" "F01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 7 "Control strain plate" "Empty" "Empty" "Empty" -7 "YPDAFEXglucoseTests_2-25-10" "G01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 8 "Control strain plate" "Empty" "Empty" "Empty" -8 "YPDAFEXglucoseTests_2-25-10" "H01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 9 "Control strain plate" "Empty" "Empty" "Empty" -9 "YPDAFEXglucoseTests_2-25-10" "A02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 10 "Control strain plate" "Empty" "Empty" "Empty" -10 "YPDAFEXglucoseTests_2-25-10" "B02" "YP" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 11 "Control strain plate" "Sample" "USDA" "" -11 "YPDAFEXglucoseTests_2-25-10" "C02" "YP+0.25% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 12 "Control strain plate" "Sample" "USDA" "" -12 "YPDAFEXglucoseTests_2-25-10" "D02" "YP+0.5% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 13 "Control strain plate" "Sample" "USDA" "" -13 "YPDAFEXglucoseTests_2-25-10" "E02" "YP+1% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 14 "Control strain plate" "Sample" "USDA" "" -14 "YPDAFEXglucoseTests_2-25-10" "F02" "YP+2% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 15 "Control strain plate" "Sample" "USDA" "" -15 "YPDAFEXglucoseTests_2-25-10" "G02" "YP+5% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 16 "Control strain plate" "Sample" "USDA" "" -16 "YPDAFEXglucoseTests_2-25-10" "H02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 17 "Control strain plate" "Empty" "Empty" "Empty" -17 "YPDAFEXglucoseTests_2-25-10" "A03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 18 "Control strain plate" "Empty" "Empty" "Empty" -18 "YPDAFEXglucoseTests_2-25-10" "B03" "YP" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 19 "Control strain plate" "Sample" "USDA" "" -19 "YPDAFEXglucoseTests_2-25-10" "C03" "YP+0.25% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 20 "Control strain plate" "Sample" "USDA" "" -20 "YPDAFEXglucoseTests_2-25-10" "D03" "YP+0.5% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 21 "Control strain plate" "Sample" "USDA" "" -21 "YPDAFEXglucoseTests_2-25-10" "E03" "YP+1% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 22 "Control strain plate" "Sample" "USDA" "" -22 "YPDAFEXglucoseTests_2-25-10" "F03" "YP+2% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 23 "Control strain plate" "Sample" "USDA" "" -23 "YPDAFEXglucoseTests_2-25-10" "G03" "YP+5% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 24 "Control strain plate" "Sample" "USDA" "" -24 "YPDAFEXglucoseTests_2-25-10" "H03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 25 "Control strain plate" "Empty" "Empty" "Empty" -25 "YPDAFEXglucoseTests_2-25-10" "A04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 26 "Control strain plate" "Empty" "Empty" "Empty" -26 "YPDAFEXglucoseTests_2-25-10" "B04" "YP" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 27 "Control strain plate" "Sample" "Internal source" "" -27 "YPDAFEXglucoseTests_2-25-10" "C04" "YP+0.25% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 28 "Control strain plate" "Sample" "Internal source" "" -28 "YPDAFEXglucoseTests_2-25-10" "D04" "YP+0.5% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 29 "Control strain plate" "Sample" "Internal source" "" -29 "YPDAFEXglucoseTests_2-25-10" "E04" "YP+1% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 30 "Control strain plate" "Sample" "Internal source" "" -30 "YPDAFEXglucoseTests_2-25-10" "F04" "YP+2% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 31 "Control strain plate" "Sample" "Internal source" "" -31 "YPDAFEXglucoseTests_2-25-10" "G04" "YP+5% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 32 "Control strain plate" "Sample" "Internal source" "" -32 "YPDAFEXglucoseTests_2-25-10" "H04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 33 "Control strain plate" "Empty" "Empty" "Empty" -33 "YPDAFEXglucoseTests_2-25-10" "A05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 34 "Control strain plate" "Empty" "Empty" "Empty" -34 "YPDAFEXglucoseTests_2-25-10" "B05" "YP" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 35 "Control strain plate" "Sample" "ATCC" "" -35 "YPDAFEXglucoseTests_2-25-10" "C05" "YP+0.25% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 36 "Control strain plate" "Sample" "ATCC" "" -36 "YPDAFEXglucoseTests_2-25-10" "D05" "YP+0.5% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 37 "Control strain plate" "Sample" "ATCC" "" -37 "YPDAFEXglucoseTests_2-25-10" "E05" "YP+1% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 38 "Control strain plate" "Sample" "ATCC" "" -38 "YPDAFEXglucoseTests_2-25-10" "F05" "YP+2% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 39 "Control strain plate" "Sample" "ATCC" "" -39 "YPDAFEXglucoseTests_2-25-10" "G05" "YP+5% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 40 "Control strain plate" "Sample" "ATCC" "" -40 "YPDAFEXglucoseTests_2-25-10" "H05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 41 "Control strain plate" "Empty" "Empty" "Empty" -41 "YPDAFEXglucoseTests_2-25-10" "A06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 42 "Control strain plate" "Empty" "Empty" "Empty" -42 "YPDAFEXglucoseTests_2-25-10" "B06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 43 "Control strain plate" "Empty" "Empty" "Empty" -43 "YPDAFEXglucoseTests_2-25-10" "C06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 44 "Control strain plate" "Empty" "Empty" "Empty" -44 "YPDAFEXglucoseTests_2-25-10" "D06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 45 "Control strain plate" "Empty" "Empty" "Empty" -45 "YPDAFEXglucoseTests_2-25-10" "E06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 46 "Control strain plate" "Empty" "Empty" "Empty" -46 "YPDAFEXglucoseTests_2-25-10" "F06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 47 "Control strain plate" "Empty" "Empty" "Empty" -47 "YPDAFEXglucoseTests_2-25-10" "G06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 48 "Control strain plate" "Empty" "Empty" "Empty" -48 "YPDAFEXglucoseTests_2-25-10" "H06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 49 "Control strain plate" "Empty" "Empty" "Empty" -49 "YPDAFEXglucoseTests_2-25-10" "A07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 50 "Control strain plate" "Empty" "Empty" "Empty" -50 "YPDAFEXglucoseTests_2-25-10" "B07" "AFEX" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 51 "Control strain plate" "Sample" "USDA" "" -51 "YPDAFEXglucoseTests_2-25-10" "C07" "AFEX+0.25% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 52 "Control strain plate" "Sample" "USDA" "" -52 "YPDAFEXglucoseTests_2-25-10" "D07" "AFEX+0.5% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 53 "Control strain plate" "Sample" "USDA" "" -53 "YPDAFEXglucoseTests_2-25-10" "E07" "AFEX+1% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 54 "Control strain plate" "Sample" "USDA" "" -54 "YPDAFEXglucoseTests_2-25-10" "F07" "AFEX+2% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 55 "Control strain plate" "Sample" "USDA" "" -55 "YPDAFEXglucoseTests_2-25-10" "G07" "AFEX+5% glucose" "Lab strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 56 "Control strain plate" "Sample" "USDA" "" -56 "YPDAFEXglucoseTests_2-25-10" "H07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 57 "Control strain plate" "Empty" "Empty" "Empty" -57 "YPDAFEXglucoseTests_2-25-10" "A08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 58 "Control strain plate" "Empty" "Empty" "Empty" -58 "YPDAFEXglucoseTests_2-25-10" "B08" "AFEX" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 59 "Control strain plate" "Sample" "USDA" "" -59 "YPDAFEXglucoseTests_2-25-10" "C08" "AFEX+0.25% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 60 "Control strain plate" "Sample" "USDA" "" -60 "YPDAFEXglucoseTests_2-25-10" "D08" "AFEX+0.5% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 61 "Control strain plate" "Sample" "USDA" "" -61 "YPDAFEXglucoseTests_2-25-10" "E08" "AFEX+1% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 62 "Control strain plate" "Sample" "USDA" "" -62 "YPDAFEXglucoseTests_2-25-10" "F08" "AFEX+2% glucose" "Wild strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 63 "Control strain plate" "Sample" "USDA" "" -63 "YPDAFEXglucoseTests_2-25-10" "G08" "AFEX+5% glucose" "Wild strain" "richards 5-par." 0.104909957772007 1.38120323294419 3.5400282340856 0.0841025860310471 3.54895808838236 "I " "-" "-" 99.9341701264792 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 64 "Control strain plate" "Sample" "USDA" "" -64 "YPDAFEXglucoseTests_2-25-10" "H08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 65 "Control strain plate" "Empty" "Empty" "Empty" -65 "YPDAFEXglucoseTests_2-25-10" "A09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 66 "Control strain plate" "Empty" "Empty" "Empty" -66 "YPDAFEXglucoseTests_2-25-10" "B09" "AFEX" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 67 "Control strain plate" "Sample" "Internal source" "" -67 "YPDAFEXglucoseTests_2-25-10" "C09" "AFEX+0.25% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 68 "Control strain plate" "Sample" "Internal source" "" -68 "YPDAFEXglucoseTests_2-25-10" "D09" "AFEX+0.5% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 69 "Control strain plate" "Sample" "Internal source" "" -69 "YPDAFEXglucoseTests_2-25-10" "E09" "AFEX+1% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 70 "Control strain plate" "Sample" "Internal source" "" -70 "YPDAFEXglucoseTests_2-25-10" "F09" "AFEX+2% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 71 "Control strain plate" "Sample" "Internal source" "" -71 "YPDAFEXglucoseTests_2-25-10" "G09" "AFEX+5% glucose" "Industrial strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 72 "Control strain plate" "Sample" "Internal source" "" -72 "YPDAFEXglucoseTests_2-25-10" "H09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 73 "Control strain plate" "Empty" "Empty" "Empty" -73 "YPDAFEXglucoseTests_2-25-10" "A10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 74 "Control strain plate" "Empty" "Empty" "Empty" -74 "YPDAFEXglucoseTests_2-25-10" "B10" "AFEX" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 75 "Control strain plate" "Sample" "ATCC" "" -75 "YPDAFEXglucoseTests_2-25-10" "C10" "AFEX+0.25% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 76 "Control strain plate" "Sample" "ATCC" "" -76 "YPDAFEXglucoseTests_2-25-10" "D10" "AFEX+0.5% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 77 "Control strain plate" "Sample" "ATCC" "" -77 "YPDAFEXglucoseTests_2-25-10" "E10" "AFEX+1% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 78 "Control strain plate" "Sample" "ATCC" "" -78 "YPDAFEXglucoseTests_2-25-10" "F10" "AFEX+2% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 79 "Control strain plate" "Sample" "ATCC" "" -79 "YPDAFEXglucoseTests_2-25-10" "G10" "AFEX+5% glucose" "Engineered strain" ": skipped" NA NA NA NA NA "! " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 80 "Control strain plate" "Sample" "ATCC" "" -80 "YPDAFEXglucoseTests_2-25-10" "H10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 81 "Control strain plate" "Empty" "Empty" "Empty" -81 "YPDAFEXglucoseTests_2-25-10" "A11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 82 "Control strain plate" "Empty" "Empty" "Empty" -82 "YPDAFEXglucoseTests_2-25-10" "B11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 83 "Control strain plate" "Empty" "Empty" "Empty" -83 "YPDAFEXglucoseTests_2-25-10" "C11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 84 "Control strain plate" "Empty" "Empty" "Empty" -84 "YPDAFEXglucoseTests_2-25-10" "D11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 85 "Control strain plate" "Empty" "Empty" "Empty" -85 "YPDAFEXglucoseTests_2-25-10" "E11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 86 "Control strain plate" "Empty" "Empty" "Empty" -86 "YPDAFEXglucoseTests_2-25-10" "F11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 87 "Control strain plate" "Empty" "Empty" "Empty" -87 "YPDAFEXglucoseTests_2-25-10" "G11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 88 "Control strain plate" "Empty" "Empty" "Empty" -88 "YPDAFEXglucoseTests_2-25-10" "H11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 89 "Control strain plate" "Empty" "Empty" "Empty" -89 "YPDAFEXglucoseTests_2-25-10" "A12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 90 "Control strain plate" "Empty" "Empty" "Empty" -90 "YPDAFEXglucoseTests_2-25-10" "B12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 91 "Control strain plate" "Empty" "Empty" "Empty" -91 "YPDAFEXglucoseTests_2-25-10" "C12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 92 "Control strain plate" "Empty" "Empty" "Empty" -92 "YPDAFEXglucoseTests_2-25-10" "D12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 93 "Control strain plate" "Empty" "Empty" "Empty" -93 "YPDAFEXglucoseTests_2-25-10" "E12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 94 "Control strain plate" "Empty" "Empty" "Empty" -94 "YPDAFEXglucoseTests_2-25-10" "F12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 95 "Control strain plate" "Empty" "Empty" "Empty" -95 "YPDAFEXglucoseTests_2-25-10" "G12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 96 "Control strain plate" "Empty" "Empty" "Empty" -96 "YPDAFEXglucoseTests_2-25-10" "H12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.58.22.pdf" 97 "Control strain plate" "Empty" "Empty" "Empty" - -# -- Explanation of columns -- -# - model: Name of the model the well was successfully fit with (if any) -# - spec.growth: (Specific growth rate) The largest exponential growth rate achieved by the culture in the course of the experiment -# - tot.growth: (Total extrapolated growth) The estimated growth plateau from the fitted model in optical density units. May be higher than the actual highest OD reached. -# - lag.time: (Lag time) The exponential trend from is extrapolated to the baseline OD at inoculation and subtracted from the time at inoculation to yield lag time. -# - inoc.OD: (OD at inoculation) The adjusted optical density at the user-specified starting timepoint. -# - good.fit: (Goodness of fit) A metric based on root mean square deviations (RMSD). -# - higher values ( > 3.0) indicate a very good fit while lower values (< 2.0) indicate generally unacceptable fits. -# - empty: (Well indicator) -# - an 'E' indicates that the well was empty and no growth was detected. -# - an 'I' indicates that the well was inoculated and growth was detected above the threshold. -# - an 'E*' indicates that the well was empty and growth was detected (possible contamination). -# - an '!' indicates that the well was inoculated and no growth was detected. -# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index. -# - reach: (Final growth percentage): The percentage of reached by the culture in the course of the experiment. -# - other: Other information includes output from jump detection algorithm and additional columns from the Plate Layout. -# - pdf.file and page.no: location of the figure for this well in the output .pdf files. -# -# -- Source file information-- -# YPDAFEXglucoseTests_2-25-10.csv -# analyzed using GCAT v 0.01 -# request sent: 2013-11-26 11:58:22 -# completed: 2013-11-26 11:58:30 -# -# -- Parameters used in current analysis -- -# - Constant added to log(OD + n) transformation: 1 -# - Blank OD value: First timepoint in well -# - Index of inoculation timepoint 2 -# - Minimum growth threshold: 1.37 -# - Removed points: -# - Jump detection: FALSE \ No newline at end of file diff --git a/Testing/GCAT_Automated_Test_Script/GCAT3/Inoculation.txt b/Testing/GCAT_Automated_Test_Script/GCAT3/Inoculation.txt deleted file mode 100755 index 1d6d2f9..0000000 --- a/Testing/GCAT_Automated_Test_Script/GCAT3/Inoculation.txt +++ /dev/null @@ -1,129 +0,0 @@ -"row" "plate" "well" "media" "strain" "model" "spec.growth" "tot.growth" "lag.time" "inoc.OD" "good.fit" "empty" "asymp" "tank" "reach" "other" "pdf.file" "page.no" "Destination.plate.name" "Well.ID" "Plate.source" "Well.Source" "Media.Definition" -1 "YPDAFEXglucoseTests_2-25-10" "A01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 2 "Control strain plate" "Empty" "Empty" "Empty" "None" -2 "YPDAFEXglucoseTests_2-25-10" "B01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 3 "Control strain plate" "Empty" "Empty" "Empty" "None" -3 "YPDAFEXglucoseTests_2-25-10" "C01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 4 "Control strain plate" "Empty" "Empty" "Empty" "None" -4 "YPDAFEXglucoseTests_2-25-10" "D01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 5 "Control strain plate" "Empty" "Empty" "Empty" "None" -5 "YPDAFEXglucoseTests_2-25-10" "E01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 6 "Control strain plate" "Empty" "Empty" "Empty" "None" -6 "YPDAFEXglucoseTests_2-25-10" "F01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 7 "Control strain plate" "Empty" "Empty" "Empty" "None" -7 "YPDAFEXglucoseTests_2-25-10" "G01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 8 "Control strain plate" "Empty" "Empty" "Empty" "None" -8 "YPDAFEXglucoseTests_2-25-10" "H01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 9 "Control strain plate" "Empty" "Empty" "Empty" "None" -9 "YPDAFEXglucoseTests_2-25-10" "A02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 10 "Control strain plate" "Empty" "Empty" "Empty" "None" -10 "YPDAFEXglucoseTests_2-25-10" "B02" "YP" "Lab strain" "logistic 4-par." 0.00513390947239015 0.0876620001483475 0.000551696237099386 0.110874812224549 2.59465563414583 "I " "-" "-" 92.6741690962163 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 11 "Control strain plate" "Sample" "USDA" "" "YP" -11 "YPDAFEXglucoseTests_2-25-10" "C02" "YP+0.25% glucose" "Lab strain" "richards 5-par." 0.0460029361983442 0.240392472194083 2.23932295697808 0.0761318166887226 2.23914120606195 "I " "-" "-" 99.9998792920065 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 12 "Control strain plate" "Sample" "USDA" "" "YP+0.25% glucose" -12 "YPDAFEXglucoseTests_2-25-10" "D02" "YP+0.5% glucose" "Lab strain" "richards 5-par." 0.0731423187209926 0.432756582200227 2.94212753267929 0.0918532887250707 2.536051033281 "I " "-" "-" 99.9999952623947 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 13 "Control strain plate" "Sample" "USDA" "" "YP+0.5% glucose" -13 "YPDAFEXglucoseTests_2-25-10" "E02" "YP+1% glucose" "Lab strain" "richards 5-par." 0.0874988417362888 0.677479207265783 3.24633816769258 0.0800120483977169 2.87924387138478 "I " "-" "-" 99.9997657328472 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 14 "Control strain plate" "Sample" "USDA" "" "YP+1% glucose" -14 "YPDAFEXglucoseTests_2-25-10" "F02" "YP+2% glucose" "Lab strain" "logistic 4-par." 0.0833321479006846 0.847046661111158 2.77452557039409 0.0752193280284603 2.65845234206059 "I " "-" "-" 99.9918661852256 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 15 "Control strain plate" "Sample" "USDA" "" "YP+2% glucose" -15 "YPDAFEXglucoseTests_2-25-10" "G02" "YP+5% glucose" "Lab strain" "logistic 4-par." 0.0589669239899499 1.11882517761774 1.20640826390575 0.0520133170774622 1.79342170973749 "I " "L" "-" 98.6708254147882 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 16 "Control strain plate" "Sample" "USDA" "" "YP+5% glucose" -16 "YPDAFEXglucoseTests_2-25-10" "H02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 17 "Control strain plate" "Empty" "Empty" "Empty" "None" -17 "YPDAFEXglucoseTests_2-25-10" "A03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 18 "Control strain plate" "Empty" "Empty" "Empty" "None" -18 "YPDAFEXglucoseTests_2-25-10" "B03" "YP" "Wild strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 19 "Control strain plate" "Sample" "USDA" "" "YP" -19 "YPDAFEXglucoseTests_2-25-10" "C03" "YP+0.25% glucose" "Wild strain" "logistic 4-par." 0.0459986845139891 0.254831348162179 1.58986879723202 0.112101681081809 1.70864325519431 "I " "-" "-" 99.9999955467498 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 20 "Control strain plate" "Sample" "USDA" "" "YP+0.25% glucose" -20 "YPDAFEXglucoseTests_2-25-10" "D03" "YP+0.5% glucose" "Wild strain" "logistic 4-par." 0.0945868089752667 0.425786653122546 2.58713136878942 0.130435146775932 2.46359052165421 "I " "-" "-" 99.9999999852335 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 21 "Control strain plate" "Sample" "USDA" "" "YP+0.5% glucose" -21 "YPDAFEXglucoseTests_2-25-10" "E03" "YP+1% glucose" "Wild strain" "richards 5-par." 0.121127547817384 0.685559786610674 2.97587534293576 0.1075037413168 2.89947354509395 "I " "-" "-" 99.9999999800904 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 22 "Control strain plate" "Sample" "USDA" "" "YP+1% glucose" -22 "YPDAFEXglucoseTests_2-25-10" "F03" "YP+2% glucose" "Wild strain" "richards 5-par." 0.129882547594034 1.04160860310247 2.77302797649945 0.124135599690527 2.75950289629815 "I " "-" "-" 99.9999893489067 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 23 "Control strain plate" "Sample" "USDA" "" "YP+2% glucose" -23 "YPDAFEXglucoseTests_2-25-10" "G03" "YP+5% glucose" "Wild strain" "richards 5-par." 0.120898412251709 1.32901254481953 2.55988604768709 0.128599154705507 2.86661364643987 "I " "-" "-" 99.9926206656861 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 24 "Control strain plate" "Sample" "USDA" "" "YP+5% glucose" -24 "YPDAFEXglucoseTests_2-25-10" "H03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 25 "Control strain plate" "Empty" "Empty" "Empty" "None" -25 "YPDAFEXglucoseTests_2-25-10" "A04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 26 "Control strain plate" "Empty" "Empty" "Empty" "None" -26 "YPDAFEXglucoseTests_2-25-10" "B04" "YP" "Industrial strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 27 "Control strain plate" "Sample" "Internal source" "" "YP" -27 "YPDAFEXglucoseTests_2-25-10" "C04" "YP+0.25% glucose" "Industrial strain" "logistic 4-par." 0.0493379998716343 0.254045397275896 0.523551303454949 0.0888407216209763 1.54716159908116 "I " "-" "-" 99.999996774836 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 28 "Control strain plate" "Sample" "Internal source" "" "YP+0.25% glucose" -28 "YPDAFEXglucoseTests_2-25-10" "D04" "YP+0.5% glucose" "Industrial strain" "logistic 4-par." 0.0931934856727062 0.410238463163683 1.5559350402868 0.0929949311576475 2.39970752160387 "I " "-" "-" 99.9999999909852 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 29 "Control strain plate" "Sample" "Internal source" "" "YP+0.5% glucose" -29 "YPDAFEXglucoseTests_2-25-10" "E04" "YP+1% glucose" "Industrial strain" "richards 5-par." 0.124582742678508 0.661996390783556 2.01051598351255 0.0941849078026622 3.20379613427986 "I " "-" "-" 99.9999999995799 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 30 "Control strain plate" "Sample" "Internal source" "" "YP+1% glucose" -30 "YPDAFEXglucoseTests_2-25-10" "F04" "YP+2% glucose" "Industrial strain" "richards 5-par." 0.127931259194577 0.983986521455829 1.92761351717956 0.0938101603743178 2.98526874472308 "I " "L" "-" 99.9999999792319 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 31 "Control strain plate" "Sample" "Internal source" "" "YP+2% glucose" -31 "YPDAFEXglucoseTests_2-25-10" "G04" "YP+5% glucose" "Industrial strain" "richards 5-par." 0.115525592792629 1.29381927826542 1.74141731218751 0.0890243231205414 2.81287527921917 "I " "L" "-" 99.9999132687566 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 32 "Control strain plate" "Sample" "Internal source" "" "YP+5% glucose" -32 "YPDAFEXglucoseTests_2-25-10" "H04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 33 "Control strain plate" "Empty" "Empty" "Empty" "None" -33 "YPDAFEXglucoseTests_2-25-10" "A05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 34 "Control strain plate" "Empty" "Empty" "Empty" "None" -34 "YPDAFEXglucoseTests_2-25-10" "B05" "YP" "Engineered strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 35 "Control strain plate" "Sample" "ATCC" "" "YP" -35 "YPDAFEXglucoseTests_2-25-10" "C05" "YP+0.25% glucose" "Engineered strain" "logistic 4-par." 0.0459359326623486 0.248154224199646 0.561170567204033 0.0640432006076648 1.37098828428177 "I " "-" "-" 99.999987765412 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 36 "Control strain plate" "Sample" "ATCC" "" "YP+0.25% glucose" -36 "YPDAFEXglucoseTests_2-25-10" "D05" "YP+0.5% glucose" "Engineered strain" "richards 5-par." 0.0944346858619649 0.470200890606434 1.71183574726233 0.0646296482425968 2.23793506472523 "I " "-" "-" 99.9999948776095 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 37 "Control strain plate" "Sample" "ATCC" "" "YP+0.5% glucose" -37 "YPDAFEXglucoseTests_2-25-10" "E05" "YP+1% glucose" "Engineered strain" "richards 5-par." 0.121520620892205 0.708619340533668 1.9245099862059 0.0814089778419187 2.69846627998123 "I " "-" "-" 99.999997890164 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 38 "Control strain plate" "Sample" "ATCC" "" "YP+1% glucose" -38 "YPDAFEXglucoseTests_2-25-10" "F05" "YP+2% glucose" "Engineered strain" "richards 5-par." 0.128733155060522 0.981131957422723 1.8897638207079 0.0912605323267595 2.90166520842437 "I " "-" "-" 99.9999883919601 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 39 "Control strain plate" "Sample" "ATCC" "" "YP+2% glucose" -39 "YPDAFEXglucoseTests_2-25-10" "G05" "YP+5% glucose" "Engineered strain" "richards 5-par." 0.122721595892799 1.3094112138332 1.8815491534903 0.0757435729961564 3.02277302645685 "I " "L" "-" 99.9995972781622 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 40 "Control strain plate" "Sample" "ATCC" "" "YP+5% glucose" -40 "YPDAFEXglucoseTests_2-25-10" "H05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 41 "Control strain plate" "Empty" "Empty" "Empty" "None" -41 "YPDAFEXglucoseTests_2-25-10" "A06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 42 "Control strain plate" "Empty" "Empty" "Empty" "None" -42 "YPDAFEXglucoseTests_2-25-10" "B06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 43 "Control strain plate" "Empty" "Empty" "Empty" "None" -43 "YPDAFEXglucoseTests_2-25-10" "C06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 44 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -44 "YPDAFEXglucoseTests_2-25-10" "D06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 45 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -45 "YPDAFEXglucoseTests_2-25-10" "E06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 46 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -46 "YPDAFEXglucoseTests_2-25-10" "F06" "Empty" "Empty" "richards 5-par." 0.0831016694707274 1.26159681822536 9.46105867276385 -0.0156072095149274 2.2176336607405 "E*" "L" "-" 97.6888291753059 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 47 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -47 "YPDAFEXglucoseTests_2-25-10" "G06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 48 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -48 "YPDAFEXglucoseTests_2-25-10" "H06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 49 "Control strain plate" "Empty" "Empty" "Empty" "None" -49 "YPDAFEXglucoseTests_2-25-10" "A07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 50 "Control strain plate" "Empty" "Empty" "Empty" "None" -50 "YPDAFEXglucoseTests_2-25-10" "B07" "AFEX" "Lab strain" "richards 5-par." 0.0913331265842828 0.977676293223671 3.74285300700227 0.0585493648561697 3.41803212615394 "I " "-" "-" 99.9967476790949 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 51 "Control strain plate" "Sample" "USDA" "" "AFEX" -51 "YPDAFEXglucoseTests_2-25-10" "C07" "AFEX+0.25% glucose" "Lab strain" "richards 5-par." 0.0901758840515798 1.02343733695468 3.7585494976221 0.0564421526774237 3.35821455308179 "I " "-" "-" 99.9932921305762 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 52 "Control strain plate" "Sample" "USDA" "" "AFEX+0.25% glucose" -52 "YPDAFEXglucoseTests_2-25-10" "D07" "AFEX+0.5% glucose" "Lab strain" "richards 5-par." 0.0876534489375277 1.05107784214595 4.08053328986319 0.0505529065684702 3.43101493489121 "I " "-" "-" 99.9881389964051 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 53 "Control strain plate" "Sample" "USDA" "" "AFEX+0.5% glucose" -53 "YPDAFEXglucoseTests_2-25-10" "E07" "AFEX+1% glucose" "Lab strain" "richards 5-par." 0.0852505870016418 1.09523234209277 4.2590088920043 0.0546791531091333 3.3224018102746 "I " "-" "-" 99.9643198816725 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 54 "Control strain plate" "Sample" "USDA" "" "AFEX+1% glucose" -54 "YPDAFEXglucoseTests_2-25-10" "F07" "AFEX+2% glucose" "Lab strain" "richards 5-par." 0.0834062493896505 1.16156601844817 4.17519830688 0.0506329107469832 3.24662867008 "I " "-" "-" 99.8770810687182 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 55 "Control strain plate" "Sample" "USDA" "" "AFEX+2% glucose" -55 "YPDAFEXglucoseTests_2-25-10" "G07" "AFEX+5% glucose" "Lab strain" "richards 5-par." 0.0746869173042796 1.29883332508854 4.26111988760969 0.0555468732725124 3.36340266867229 "I " "-" "-" 98.4357653421947 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 56 "Control strain plate" "Sample" "USDA" "" "AFEX+5% glucose" -56 "YPDAFEXglucoseTests_2-25-10" "H07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 57 "Control strain plate" "Empty" "Empty" "Empty" "None" -57 "YPDAFEXglucoseTests_2-25-10" "A08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 58 "Control strain plate" "Empty" "Empty" "Empty" "None" -58 "YPDAFEXglucoseTests_2-25-10" "B08" "AFEX" "Wild strain" "richards 5-par." 0.114235639585196 1.11603265279451 2.80462732513778 0.106026173457393 3.07479264063223 "I " "-" "-" 99.9998418759963 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 59 "Control strain plate" "Sample" "USDA" "" "AFEX" -59 "YPDAFEXglucoseTests_2-25-10" "C08" "AFEX+0.25% glucose" "Wild strain" "richards 5-par." 0.114214452912468 1.14545395160069 3.03642647181899 0.0901903141548646 3.13967373959077 "I " "-" "-" 99.9996775720213 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 60 "Control strain plate" "Sample" "USDA" "" "AFEX+0.25% glucose" -60 "YPDAFEXglucoseTests_2-25-10" "D08" "AFEX+0.5% glucose" "Wild strain" "richards 5-par." 0.11356609836573 1.17951259888145 2.99921572692866 0.0854138714541255 3.20643947548211 "I " "-" "-" 99.9993801531958 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 61 "Control strain plate" "Sample" "USDA" "" "AFEX+0.5% glucose" -61 "YPDAFEXglucoseTests_2-25-10" "E08" "AFEX+1% glucose" "Wild strain" "richards 5-par." 0.112827039764747 1.23081376697016 2.97207411510676 0.090741698149845 3.1895693830433 "I " "-" "-" 99.9983882461922 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 62 "Control strain plate" "Sample" "USDA" "" "AFEX+1% glucose" -62 "YPDAFEXglucoseTests_2-25-10" "F08" "AFEX+2% glucose" "Wild strain" "richards 5-par." 0.110948156058339 1.28413133026796 3.09434741751019 0.0853800430755536 3.20897314216817 "I " "-" "-" 99.9945939442068 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 63 "Control strain plate" "Sample" "USDA" "" "AFEX+2% glucose" -63 "YPDAFEXglucoseTests_2-25-10" "G08" "AFEX+5% glucose" "Wild strain" "richards 5-par." 0.104909957747906 1.37957293880569 3.37657406597065 0.0857328798243138 3.54895808838256 "I " "-" "-" 99.9340923347588 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 64 "Control strain plate" "Sample" "USDA" "" "AFEX+5% glucose" -64 "YPDAFEXglucoseTests_2-25-10" "H08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 65 "Control strain plate" "Empty" "Empty" "Empty" "None" -65 "YPDAFEXglucoseTests_2-25-10" "A09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 66 "Control strain plate" "Empty" "Empty" "Empty" "None" -66 "YPDAFEXglucoseTests_2-25-10" "B09" "AFEX" "Industrial strain" "richards 5-par." 0.12461961390891 1.02126553518662 2.4305352177311 0.0832928033695586 3.19828565863893 "I " "-" "-" 99.9999984996182 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 67 "Control strain plate" "Sample" "Internal source" "" "AFEX" -67 "YPDAFEXglucoseTests_2-25-10" "C09" "AFEX+0.25% glucose" "Industrial strain" "richards 5-par." 0.123242474045102 1.07196388949718 2.44085995606895 0.0747514589944707 3.30084510513645 "I " "-" "-" 99.9999944199419 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 68 "Control strain plate" "Sample" "Internal source" "" "AFEX+0.25% glucose" -68 "YPDAFEXglucoseTests_2-25-10" "D09" "AFEX+0.5% glucose" "Industrial strain" "richards 5-par." 0.12090087889886 1.10115777984898 2.35585985916424 0.0719961174673402 3.29576923040073 "I " "L" "-" 99.9999896268808 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 69 "Control strain plate" "Sample" "Internal source" "" "AFEX+0.5% glucose" -69 "YPDAFEXglucoseTests_2-25-10" "E09" "AFEX+1% glucose" "Industrial strain" "richards 5-par." 0.119451757970973 1.15953479542773 2.3066400904183 0.0715521817197322 3.20509498580791 "I " "L" "-" 99.9999599907486 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 70 "Control strain plate" "Sample" "Internal source" "" "AFEX+1% glucose" -70 "YPDAFEXglucoseTests_2-25-10" "F09" "AFEX+2% glucose" "Industrial strain" "richards 5-par." 0.117046866658425 1.23026145665052 2.44407044557878 0.0655027600473694 3.14018976861125 "I " "L" "-" 99.9995689634333 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 71 "Control strain plate" "Sample" "Internal source" "" "AFEX+2% glucose" -71 "YPDAFEXglucoseTests_2-25-10" "G09" "AFEX+5% glucose" "Industrial strain" "richards 5-par." 0.108331393150974 1.33973156155552 2.51097570573708 0.0649023468973968 3.23212721890241 "I " "-" "-" 99.9822483056319 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 72 "Control strain plate" "Sample" "Internal source" "" "AFEX+5% glucose" -72 "YPDAFEXglucoseTests_2-25-10" "H09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 73 "Control strain plate" "Empty" "Empty" "Empty" "None" -73 "YPDAFEXglucoseTests_2-25-10" "A10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 74 "Control strain plate" "Empty" "Empty" "Empty" "None" -74 "YPDAFEXglucoseTests_2-25-10" "B10" "AFEX" "Engineered strain" "richards 5-par." 0.121839335523261 1.03094115561518 2.20149868335828 0.0716378203446439 2.99659166289555 "I " "-" "-" 99.9998735461218 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 75 "Control strain plate" "Sample" "ATCC" "" "AFEX" -75 "YPDAFEXglucoseTests_2-25-10" "C10" "AFEX+0.25% glucose" "Engineered strain" "richards 5-par." 0.123130425236 1.06412474728157 2.46906361902119 0.0564520573406488 3.19928587493649 "I " "-" "-" 99.999891983369 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 76 "Control strain plate" "Sample" "ATCC" "" "AFEX+0.25% glucose" -76 "YPDAFEXglucoseTests_2-25-10" "D10" "AFEX+0.5% glucose" "Engineered strain" "richards 5-par." 0.120973125758535 1.08554405396271 2.46825462758035 0.056549534178326 3.33630531768612 "I " "-" "-" 99.9998814536437 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 77 "Control strain plate" "Sample" "ATCC" "" "AFEX+0.5% glucose" -77 "YPDAFEXglucoseTests_2-25-10" "E10" "AFEX+1% glucose" "Engineered strain" "richards 5-par." 0.120740949535359 1.15263316370924 2.5442959513883 0.0522642960780029 3.36496106313701 "I " "-" "-" 99.9996094172831 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 78 "Control strain plate" "Sample" "ATCC" "" "AFEX+1% glucose" -78 "YPDAFEXglucoseTests_2-25-10" "F10" "AFEX+2% glucose" "Engineered strain" "richards 5-par." 0.121802165325221 1.22599703168728 2.5422560684683 0.056307375634215 3.47334970863554 "I " "-" "-" 99.9989009038885 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 79 "Control strain plate" "Sample" "ATCC" "" "AFEX+2% glucose" -79 "YPDAFEXglucoseTests_2-25-10" "G10" "AFEX+5% glucose" "Engineered strain" "richards 5-par." 0.11290413623126 1.340836387636 2.56045685725438 0.0581661740243069 3.53967163281617 "I " "-" "-" 99.9786442972454 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 80 "Control strain plate" "Sample" "ATCC" "" "AFEX+5% glucose" -80 "YPDAFEXglucoseTests_2-25-10" "H10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 81 "Control strain plate" "Empty" "Empty" "Empty" "None" -81 "YPDAFEXglucoseTests_2-25-10" "A11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 82 "Control strain plate" "Empty" "Empty" "Empty" "None" -82 "YPDAFEXglucoseTests_2-25-10" "B11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 83 "Control strain plate" "Empty" "Empty" "Empty" "None" -83 "YPDAFEXglucoseTests_2-25-10" "C11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 84 "Control strain plate" "Empty" "Empty" "Empty" "None" -84 "YPDAFEXglucoseTests_2-25-10" "D11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 85 "Control strain plate" "Empty" "Empty" "Empty" "None" -85 "YPDAFEXglucoseTests_2-25-10" "E11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 86 "Control strain plate" "Empty" "Empty" "Empty" "None" -86 "YPDAFEXglucoseTests_2-25-10" "F11" "None" "Empty" "logistic 4-par." 0.097251500241612 1.24804582503984 14.6755074922153 -0.00366567404981055 2.38008868734244 "E*" "L/U" "-" 87.1867004610056 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 87 "Control strain plate" "Empty" "Empty" "Empty" "None" -87 "YPDAFEXglucoseTests_2-25-10" "G11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 88 "Control strain plate" "Empty" "Empty" "Empty" "None" -88 "YPDAFEXglucoseTests_2-25-10" "H11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 89 "Control strain plate" "Empty" "Empty" "Empty" "None" -89 "YPDAFEXglucoseTests_2-25-10" "A12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 90 "Control strain plate" "Empty" "Empty" "Empty" "None" -90 "YPDAFEXglucoseTests_2-25-10" "B12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 91 "Control strain plate" "Empty" "Empty" "Empty" "None" -91 "YPDAFEXglucoseTests_2-25-10" "C12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 92 "Control strain plate" "Empty" "Empty" "Empty" "None" -92 "YPDAFEXglucoseTests_2-25-10" "D12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 93 "Control strain plate" "Empty" "Empty" "Empty" "None" -93 "YPDAFEXglucoseTests_2-25-10" "E12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 94 "Control strain plate" "Empty" "Empty" "Empty" "None" -94 "YPDAFEXglucoseTests_2-25-10" "F12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 95 "Control strain plate" "Empty" "Empty" "Empty" "None" -95 "YPDAFEXglucoseTests_2-25-10" "G12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 96 "Control strain plate" "Empty" "Empty" "Empty" "None" -96 "YPDAFEXglucoseTests_2-25-10" "H12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.54.31.pdf" 97 "Control strain plate" "Empty" "Empty" "Empty" "None" - -# -- Explanation of columns -- -# - model: Name of the model the well was successfully fit with (if any) -# - spec.growth: (Specific growth rate) The largest exponential growth rate achieved by the culture in the course of the experiment -# - tot.growth: (Total extrapolated growth) The estimated growth plateau from the fitted model in optical density units. May be higher than the actual highest OD reached. -# - lag.time: (Lag time) The exponential trend from is extrapolated to the baseline OD at inoculation and subtracted from the time at inoculation to yield lag time. -# - inoc.OD: (OD at inoculation) The adjusted optical density at the user-specified starting timepoint. -# - good.fit: (Goodness of fit) A metric based on root mean square deviations (RMSD). -# - higher values ( > 3.0) indicate a very good fit while lower values (< 2.0) indicate generally unacceptable fits. -# - empty: (Well indicator) -# - an 'E' indicates that the well was empty and no growth was detected. -# - an 'I' indicates that the well was inoculated and growth was detected above the threshold. -# - an 'E*' indicates that the well was empty and growth was detected (possible contamination). -# - an '!' indicates that the well was inoculated and no growth was detected. -# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index. -# - reach: (Final growth percentage): The percentage of reached by the culture in the course of the experiment. -# - other: Other information includes output from jump detection algorithm and additional columns from the Plate Layout. -# - pdf.file and page.no: location of the figure for this well in the output .pdf files. -# -# -- Source file information-- -# YPDAFEXglucoseTests_2-25-10.csv -# analyzed using GCAT v 0.01 -# request sent: 2013-11-26 11:54:31 -# completed: 2013-11-26 11:54:41 -# -# -- Parameters used in current analysis -- -# - Constant added to log(OD + n) transformation: 1 -# - Blank OD value: First timepoint in well -# - Index of inoculation timepoint 3 -# - Minimum growth threshold: 0.05 -# - Removed points: -# - Jump detection: FALSE \ No newline at end of file diff --git a/Testing/GCAT_Automated_Test_Script/GCAT3/Media_Background1.txt b/Testing/GCAT_Automated_Test_Script/GCAT3/Media_Background1.txt deleted file mode 100755 index ea08839..0000000 --- a/Testing/GCAT_Automated_Test_Script/GCAT3/Media_Background1.txt +++ /dev/null @@ -1,129 +0,0 @@ -"row" "plate" "well" "media" "strain" "model" "spec.growth" "tot.growth" "lag.time" "inoc.OD" "good.fit" "empty" "asymp" "tank" "reach" "other" "pdf.file" "page.no" "Destination.plate.name" "Well.ID" "Plate.source" "Well.Source" "Media.Definition" -1 "YPDAFEXglucoseTests_2-25-10" "A01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 2 "Control strain plate" "Empty" "Empty" "Empty" "None" -2 "YPDAFEXglucoseTests_2-25-10" "B01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 3 "Control strain plate" "Empty" "Empty" "Empty" "None" -3 "YPDAFEXglucoseTests_2-25-10" "C01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 4 "Control strain plate" "Empty" "Empty" "Empty" "None" -4 "YPDAFEXglucoseTests_2-25-10" "D01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 5 "Control strain plate" "Empty" "Empty" "Empty" "None" -5 "YPDAFEXglucoseTests_2-25-10" "E01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 6 "Control strain plate" "Empty" "Empty" "Empty" "None" -6 "YPDAFEXglucoseTests_2-25-10" "F01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 7 "Control strain plate" "Empty" "Empty" "Empty" "None" -7 "YPDAFEXglucoseTests_2-25-10" "G01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 8 "Control strain plate" "Empty" "Empty" "Empty" "None" -8 "YPDAFEXglucoseTests_2-25-10" "H01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 9 "Control strain plate" "Empty" "Empty" "Empty" "None" -9 "YPDAFEXglucoseTests_2-25-10" "A02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 10 "Control strain plate" "Empty" "Empty" "Empty" "None" -10 "YPDAFEXglucoseTests_2-25-10" "B02" "YP" "Lab strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 11 "Control strain plate" "Sample" "USDA" "" "YP" -11 "YPDAFEXglucoseTests_2-25-10" "C02" "YP+0.25% glucose" "Lab strain" "richards 5-par." 0.0434503343000251 0.25355485467526 2.02165330333884 0.0617033863833638 1.64185698237008 "I " "-" "-" 99.9999736403217 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 12 "Control strain plate" "Sample" "USDA" "" "YP+0.25% glucose" -12 "YPDAFEXglucoseTests_2-25-10" "D02" "YP+0.5% glucose" "Lab strain" "richards 5-par." 0.0710461374870435 0.446283240058387 2.88921431893203 0.078039465273223 1.94354072341034 "I " "-" "-" 99.9999992879621 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 13 "Control strain plate" "Sample" "USDA" "" "YP+0.5% glucose" -13 "YPDAFEXglucoseTests_2-25-10" "E02" "YP+1% glucose" "Lab strain" "richards 5-par." 0.0860880819729473 0.688375845522998 3.26587795985316 0.0682375379828597 2.36976256861628 "I " "-" "-" 99.9998854906447 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 14 "Control strain plate" "Sample" "USDA" "" "YP+1% glucose" -14 "YPDAFEXglucoseTests_2-25-10" "F02" "YP+2% glucose" "Lab strain" "richards 5-par." 0.0855558286818253 0.848516659814659 2.99428931741607 0.0785443237303707 2.50265696873442 "I " "-" "-" 99.9675537192086 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 15 "Control strain plate" "Sample" "USDA" "" "YP+2% glucose" -15 "YPDAFEXglucoseTests_2-25-10" "G02" "YP+5% glucose" "Lab strain" "logistic 4-par." 0.0590319877346773 1.1313189331006 1.21092069814356 0.0412045752566177 1.7937439452957 "I " "L" "-" 98.6047219117497 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 16 "Control strain plate" "Sample" "USDA" "" "YP+5% glucose" -16 "YPDAFEXglucoseTests_2-25-10" "H02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 17 "Control strain plate" "Empty" "Empty" "Empty" "None" -17 "YPDAFEXglucoseTests_2-25-10" "A03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 18 "Control strain plate" "Empty" "Empty" "Empty" "None" -18 "YPDAFEXglucoseTests_2-25-10" "B03" "YP" "Wild strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 19 "Control strain plate" "Sample" "USDA" "" "YP" -19 "YPDAFEXglucoseTests_2-25-10" "C03" "YP+0.25% glucose" "Wild strain" "logistic 4-par." 0.0434892612564025 0.274547126811452 1.17986305219729 0.0930562431741175 1.2462515507653 "I " "-" "-" 99.9999459725148 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 20 "Control strain plate" "Sample" "USDA" "" "YP+0.25% glucose" -20 "YPDAFEXglucoseTests_2-25-10" "D03" "YP+0.5% glucose" "Wild strain" "richards 5-par." 0.0897339782050535 0.44725588012243 2.48510022383136 0.111954813319619 1.64728332860566 "I " "-" "-" 99.9999999997907 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 21 "Control strain plate" "Sample" "USDA" "" "YP+0.5% glucose" -21 "YPDAFEXglucoseTests_2-25-10" "E03" "YP+1% glucose" "Wild strain" "richards 5-par." 0.118704818394586 0.701739899244777 3.00105743862396 0.0902498862365915 2.16060651373925 "I " "-" "-" 99.9999999982431 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 22 "Control strain plate" "Sample" "USDA" "" "YP+1% glucose" -22 "YPDAFEXglucoseTests_2-25-10" "F03" "YP+2% glucose" "Wild strain" "richards 5-par." 0.127118789469248 1.06188644325538 2.76198673024551 0.101832988995193 2.2489695413201 "I " "-" "-" 99.9999974728383 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 23 "Control strain plate" "Sample" "USDA" "" "YP+2% glucose" -23 "YPDAFEXglucoseTests_2-25-10" "G03" "YP+5% glucose" "Wild strain" "richards 5-par." 0.118124578641559 1.3496375733804 2.51164992830229 0.105412244128214 2.36610848171534 "I " "-" "-" 99.9956836427274 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 24 "Control strain plate" "Sample" "USDA" "" "YP+5% glucose" -24 "YPDAFEXglucoseTests_2-25-10" "H03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 25 "Control strain plate" "Empty" "Empty" "Empty" "None" -25 "YPDAFEXglucoseTests_2-25-10" "A04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 26 "Control strain plate" "Empty" "Empty" "Empty" "None" -26 "YPDAFEXglucoseTests_2-25-10" "B04" "YP" "Industrial strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 27 "Control strain plate" "Sample" "Internal source" "" "YP" -27 "YPDAFEXglucoseTests_2-25-10" "C04" "YP+0.25% glucose" "Industrial strain" "logistic 4-par." 0.0503915103890343 0.278431850863241 0.230735178823221 0.0667245999493249 1.28125167205809 "I " "-" "-" 99.9999557835925 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 28 "Control strain plate" "Sample" "Internal source" "" "YP+0.25% glucose" -28 "YPDAFEXglucoseTests_2-25-10" "D04" "YP+0.5% glucose" "Industrial strain" "logistic 4-par." 0.0900596817770063 0.426283124892579 1.48660897985453 0.0787853427815937 1.78609838401984 "I " "-" "-" 99.9999999465272 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 29 "Control strain plate" "Sample" "Internal source" "" "YP+0.5% glucose" -29 "YPDAFEXglucoseTests_2-25-10" "E04" "YP+1% glucose" "Industrial strain" "richards 5-par." 0.120932696502068 0.681827053465979 1.98743887548203 0.0750931197769025 2.24806197934911 "I " "-" "-" 99.9999999999806 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 30 "Control strain plate" "Sample" "Internal source" "" "YP+1% glucose" -30 "YPDAFEXglucoseTests_2-25-10" "F04" "YP+2% glucose" "Industrial strain" "richards 5-par." 0.124851864857507 1.00554516052416 1.8909730823156 0.0745327038147034 2.45714183902256 "I " "L" "-" 99.9999999978197 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 31 "Control strain plate" "Sample" "Internal source" "" "YP+2% glucose" -31 "YPDAFEXglucoseTests_2-25-10" "G04" "YP+5% glucose" "Industrial strain" "richards 5-par." 0.113079038402523 1.31499248437073 1.6706153298796 0.0682108949608626 2.54109072078653 "I " "L" "-" 99.9999648186165 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 32 "Control strain plate" "Sample" "Internal source" "" "YP+5% glucose" -32 "YPDAFEXglucoseTests_2-25-10" "H04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 33 "Control strain plate" "Empty" "Empty" "Empty" "None" -33 "YPDAFEXglucoseTests_2-25-10" "A05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 34 "Control strain plate" "Empty" "Empty" "Empty" "None" -34 "YPDAFEXglucoseTests_2-25-10" "B05" "YP" "Engineered strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 35 "Control strain plate" "Sample" "ATCC" "" "YP" -35 "YPDAFEXglucoseTests_2-25-10" "C05" "YP+0.25% glucose" "Engineered strain" "logistic 4-par." 0.0460541020662134 0.26524158772085 0.357238281642297 0.0484389000123124 1.28333178169019 "I " "L" "-" 99.9999287079269 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 36 "Control strain plate" "Sample" "ATCC" "" "YP+0.25% glucose" -36 "YPDAFEXglucoseTests_2-25-10" "D05" "YP+0.5% glucose" "Engineered strain" "logistic 4-par." 0.0910355508572168 0.484885690164407 1.68228977771903 0.0503454179292044 2.01406534894519 "I " "-" "-" 99.999999075587 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 37 "Control strain plate" "Sample" "ATCC" "" "YP+0.5% glucose" -37 "YPDAFEXglucoseTests_2-25-10" "E05" "YP+1% glucose" "Engineered strain" "richards 5-par." 0.1185326268352 0.724942396645568 1.93091588614506 0.0650485245853678 2.28064777433602 "I " "-" "-" 99.9999994051425 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 38 "Control strain plate" "Sample" "ATCC" "" "YP+1% glucose" -38 "YPDAFEXglucoseTests_2-25-10" "F05" "YP+2% glucose" "Engineered strain" "richards 5-par." 0.125935099476691 1.00060394314497 1.87185854411294 0.0705328954848026 2.43919113300695 "I " "-" "-" 99.9999960758469 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 39 "Control strain plate" "Sample" "ATCC" "" "YP+2% glucose" -39 "YPDAFEXglucoseTests_2-25-10" "G05" "YP+5% glucose" "Engineered strain" "richards 5-par." 0.12045828658039 1.32681554802285 1.87312970608357 0.0617649897724031 2.72077052437644 "I " "L" "-" 99.9997697224565 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 40 "Control strain plate" "Sample" "ATCC" "" "YP+5% glucose" -40 "YPDAFEXglucoseTests_2-25-10" "H05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 41 "Control strain plate" "Empty" "Empty" "Empty" "None" -41 "YPDAFEXglucoseTests_2-25-10" "A06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 42 "Control strain plate" "Empty" "Empty" "Empty" "None" -42 "YPDAFEXglucoseTests_2-25-10" "B06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 43 "Control strain plate" "Empty" "Empty" "Empty" "None" -43 "YPDAFEXglucoseTests_2-25-10" "C06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 44 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -44 "YPDAFEXglucoseTests_2-25-10" "D06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 45 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -45 "YPDAFEXglucoseTests_2-25-10" "E06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 46 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -46 "YPDAFEXglucoseTests_2-25-10" "F06" "Empty" "Empty" "richards 5-par." 0.083026880473868 1.26274912739788 9.6370199491002 -0.0148648394970353 2.22003323483864 "E*" "L" "-" 97.6179798356663 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 47 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -47 "YPDAFEXglucoseTests_2-25-10" "G06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 48 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -48 "YPDAFEXglucoseTests_2-25-10" "H06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 49 "Control strain plate" "Empty" "Empty" "Empty" "None" -49 "YPDAFEXglucoseTests_2-25-10" "A07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 50 "Control strain plate" "Empty" "Empty" "Empty" "None" -50 "YPDAFEXglucoseTests_2-25-10" "B07" "AFEX" "Lab strain" "richards 5-par." 0.0837862465621809 0.985589476660035 3.87077447326577 0.172902084515593 2.936554895572 "I " "-" "-" 99.9976660845596 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 51 "Control strain plate" "Sample" "USDA" "" "AFEX" -51 "YPDAFEXglucoseTests_2-25-10" "C07" "AFEX+0.25% glucose" "Lab strain" "richards 5-par." 0.0825725388111153 1.03111358478328 3.8935977613249 0.175746057355985 2.95818389639001 "I " "-" "-" 99.9950047689826 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 52 "Control strain plate" "Sample" "USDA" "" "AFEX+0.25% glucose" -52 "YPDAFEXglucoseTests_2-25-10" "D07" "AFEX+0.5% glucose" "Lab strain" "richards 5-par." 0.0803990851774492 1.05769131646876 4.23452367239061 0.171669910262409 3.05762797860851 "I " "-" "-" 99.9905797580664 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 53 "Control strain plate" "Sample" "USDA" "" "AFEX+0.5% glucose" -53 "YPDAFEXglucoseTests_2-25-10" "E07" "AFEX+1% glucose" "Lab strain" "richards 5-par." 0.078260986900903 1.10176517760371 4.41033894653477 0.174661705124986 2.98245532148831 "I " "-" "-" 99.97078656119 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 54 "Control strain plate" "Sample" "USDA" "" "AFEX+1% glucose" -54 "YPDAFEXglucoseTests_2-25-10" "F07" "AFEX+2% glucose" "Lab strain" "richards 5-par." 0.0765359669045422 1.16743187678685 4.33134033283011 0.171774058333315 2.99101843653394 "I " "-" "-" 99.8931141945986 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 55 "Control strain plate" "Sample" "USDA" "" "AFEX+2% glucose" -55 "YPDAFEXglucoseTests_2-25-10" "G07" "AFEX+5% glucose" "Lab strain" "richards 5-par." 0.0684295063358446 1.30296627125276 4.41039755952004 0.177550778776163 3.02126707953049 "I " "-" "-" 98.5429258482389 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 56 "Control strain plate" "Sample" "USDA" "" "AFEX+5% glucose" -56 "YPDAFEXglucoseTests_2-25-10" "H07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 57 "Control strain plate" "Empty" "Empty" "Empty" "None" -57 "YPDAFEXglucoseTests_2-25-10" "A08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 58 "Control strain plate" "Empty" "Empty" "Empty" "None" -58 "YPDAFEXglucoseTests_2-25-10" "B08" "AFEX" "Wild strain" "richards 5-par." 0.103961511845496 1.13335005494973 2.84746894877643 0.216147675837119 2.50607784281402 "I " "-" "-" 99.999934749514 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 59 "Control strain plate" "Sample" "USDA" "" "AFEX" -59 "YPDAFEXglucoseTests_2-25-10" "C08" "AFEX+0.25% glucose" "Wild strain" "richards 5-par." 0.104426132027787 1.15952947440466 3.1179146181553 0.202220291175903 2.64629880567713 "I " "-" "-" 99.9998358609235 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 60 "Control strain plate" "Sample" "USDA" "" "AFEX+0.25% glucose" -60 "YPDAFEXglucoseTests_2-25-10" "D08" "AFEX+0.5% glucose" "Wild strain" "richards 5-par." 0.103564913027715 1.19303695629607 3.08800865283045 0.203591721344972 2.71477777367162 "I " "-" "-" 99.9996508953345 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 61 "Control strain plate" "Sample" "USDA" "" "AFEX+0.5% glucose" -61 "YPDAFEXglucoseTests_2-25-10" "E08" "AFEX+1% glucose" "Wild strain" "richards 5-par." 0.103109984243399 1.24497138884473 3.04906663958604 0.203623320796393 2.68869096385621 "I " "-" "-" 99.9990405446907 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 62 "Control strain plate" "Sample" "USDA" "" "AFEX+1% glucose" -62 "YPDAFEXglucoseTests_2-25-10" "F08" "AFEX+2% glucose" "Wild strain" "richards 5-par." 0.101328068865228 1.29683436370675 3.18655040766587 0.203111588999557 2.75266670603191 "I " "-" "-" 99.996339173896 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 63 "Control strain plate" "Sample" "USDA" "" "AFEX+2% glucose" -63 "YPDAFEXglucoseTests_2-25-10" "G08" "AFEX+5% glucose" "Wild strain" "richards 5-par." 0.0960414766942334 1.39007056093517 3.47869089975363 0.202353552916657 2.86594136189225 "I " "-" "-" 99.9467189237796 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 64 "Control strain plate" "Sample" "USDA" "" "AFEX+5% glucose" -64 "YPDAFEXglucoseTests_2-25-10" "H08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 65 "Control strain plate" "Empty" "Empty" "Empty" "None" -65 "YPDAFEXglucoseTests_2-25-10" "A09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 66 "Control strain plate" "Empty" "Empty" "Empty" "None" -66 "YPDAFEXglucoseTests_2-25-10" "B09" "AFEX" "Industrial strain" "richards 5-par." 0.113180265724915 1.03747916133359 2.49766338810221 0.198495309639666 2.6483170296715 "I " "-" "-" 99.99999950571 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 67 "Control strain plate" "Sample" "Internal source" "" "AFEX" -67 "YPDAFEXglucoseTests_2-25-10" "C09" "AFEX+0.25% glucose" "Industrial strain" "richards 5-par." 0.112532945731761 1.08681009274574 2.52119628407453 0.186329225710496 2.77398299574405 "I " "-" "-" 99.9999976342956 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 68 "Control strain plate" "Sample" "Internal source" "" "AFEX+0.25% glucose" -68 "YPDAFEXglucoseTests_2-25-10" "D09" "AFEX+0.5% glucose" "Industrial strain" "richards 5-par." 0.110237121553375 1.11602705298285 2.43678055941639 0.18724754693763 2.81184006554946 "I " "-" "-" 99.9999952725547 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 69 "Control strain plate" "Sample" "Internal source" "" "AFEX+0.5% glucose" -69 "YPDAFEXglucoseTests_2-25-10" "E09" "AFEX+1% glucose" "Industrial strain" "richards 5-par." 0.109153261238411 1.17453886329702 2.38442334222443 0.183907793076526 2.80879291485336 "I " "-" "-" 99.9999796529525 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 70 "Control strain plate" "Sample" "Internal source" "" "AFEX+1% glucose" -70 "YPDAFEXglucoseTests_2-25-10" "F09" "AFEX+2% glucose" "Industrial strain" "richards 5-par." 0.107153820876407 1.24345235940033 2.53842674779367 0.178885414386565 2.84792003349477 "I " "-" "-" 99.9997261996811 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 71 "Control strain plate" "Sample" "Internal source" "" "AFEX+2% glucose" -71 "YPDAFEXglucoseTests_2-25-10" "G09" "AFEX+5% glucose" "Industrial strain" "richards 5-par." 0.0990827158819113 1.35146254239763 2.60572114613308 0.180195185614621 2.91808898590255 "I " "-" "-" 99.9858735540263 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 72 "Control strain plate" "Sample" "Internal source" "" "AFEX+5% glucose" -72 "YPDAFEXglucoseTests_2-25-10" "H09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 73 "Control strain plate" "Empty" "Empty" "Empty" "None" -73 "YPDAFEXglucoseTests_2-25-10" "A10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 74 "Control strain plate" "Empty" "Empty" "Empty" "None" -74 "YPDAFEXglucoseTests_2-25-10" "B10" "AFEX" "Engineered strain" "richards 5-par." 0.110458083084921 1.04485579994439 2.27701838325376 0.188114595684521 2.65931477578895 "I " "-" "-" 99.9999271625885 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 75 "Control strain plate" "Sample" "ATCC" "" "AFEX" -75 "YPDAFEXglucoseTests_2-25-10" "C10" "AFEX+0.25% glucose" "Engineered strain" "richards 5-par." 0.112540220994811 1.07487901296182 2.58417196441953 0.171301212668114 2.88882458916344 "I " "-" "-" 99.9999309539298 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 76 "Control strain plate" "Sample" "ATCC" "" "AFEX+0.25% glucose" -76 "YPDAFEXglucoseTests_2-25-10" "D10" "AFEX+0.5% glucose" "Engineered strain" "richards 5-par." 0.110640152738962 1.09653685419261 2.58231557868978 0.171664577469133 2.95663771710228 "I " "-" "-" 99.9999237076305 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 77 "Control strain plate" "Sample" "ATCC" "" "AFEX+0.5% glucose" -77 "YPDAFEXglucoseTests_2-25-10" "E10" "AFEX+1% glucose" "Engineered strain" "richards 5-par." 0.1105967205646 1.16275661096821 2.66983121158 0.168291454109896 3.03987519406164 "I " "-" "-" 99.9997284198838 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 78 "Control strain plate" "Sample" "ATCC" "" "AFEX+1% glucose" -78 "YPDAFEXglucoseTests_2-25-10" "F10" "AFEX+2% glucose" "Engineered strain" "richards 5-par." 0.111561409951938 1.23655979175461 2.66322072814323 0.172114613842357 3.06755684662736 "I " "-" "-" 99.9991978972748 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 79 "Control strain plate" "Sample" "ATCC" "" "AFEX+2% glucose" -79 "YPDAFEXglucoseTests_2-25-10" "G10" "AFEX+5% glucose" "Engineered strain" "richards 5-par." 0.103366231210924 1.3509354915414 2.67448563817088 0.173610905690015 3.10078735926473 "I " "-" "-" 99.9823958592765 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 80 "Control strain plate" "Sample" "ATCC" "" "AFEX+5% glucose" -80 "YPDAFEXglucoseTests_2-25-10" "H10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 81 "Control strain plate" "Empty" "Empty" "Empty" "None" -81 "YPDAFEXglucoseTests_2-25-10" "A11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 82 "Control strain plate" "Empty" "Empty" "Empty" "None" -82 "YPDAFEXglucoseTests_2-25-10" "B11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 83 "Control strain plate" "Empty" "Empty" "Empty" "None" -83 "YPDAFEXglucoseTests_2-25-10" "C11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 84 "Control strain plate" "Empty" "Empty" "Empty" "None" -84 "YPDAFEXglucoseTests_2-25-10" "D11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 85 "Control strain plate" "Empty" "Empty" "Empty" "None" -85 "YPDAFEXglucoseTests_2-25-10" "E11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 86 "Control strain plate" "Empty" "Empty" "Empty" "None" -86 "YPDAFEXglucoseTests_2-25-10" "F11" "None" "Empty" "logistic 4-par." 0.0898948262289814 1.25317410845682 14.918347724891 0.115247567652615 2.39076788045153 "E*" "U" "-" 86.9727718976639 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 87 "Control strain plate" "Empty" "Empty" "Empty" "None" -87 "YPDAFEXglucoseTests_2-25-10" "G11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 88 "Control strain plate" "Empty" "Empty" "Empty" "None" -88 "YPDAFEXglucoseTests_2-25-10" "H11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 89 "Control strain plate" "Empty" "Empty" "Empty" "None" -89 "YPDAFEXglucoseTests_2-25-10" "A12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 90 "Control strain plate" "Empty" "Empty" "Empty" "None" -90 "YPDAFEXglucoseTests_2-25-10" "B12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 91 "Control strain plate" "Empty" "Empty" "Empty" "None" -91 "YPDAFEXglucoseTests_2-25-10" "C12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 92 "Control strain plate" "Empty" "Empty" "Empty" "None" -92 "YPDAFEXglucoseTests_2-25-10" "D12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 93 "Control strain plate" "Empty" "Empty" "Empty" "None" -93 "YPDAFEXglucoseTests_2-25-10" "E12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 94 "Control strain plate" "Empty" "Empty" "Empty" "None" -94 "YPDAFEXglucoseTests_2-25-10" "F12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 95 "Control strain plate" "Empty" "Empty" "Empty" "None" -95 "YPDAFEXglucoseTests_2-25-10" "G12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 96 "Control strain plate" "Empty" "Empty" "Empty" "None" -96 "YPDAFEXglucoseTests_2-25-10" "H12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.41.59.pdf" 97 "Control strain plate" "Empty" "Empty" "Empty" "None" - -# -- Explanation of columns -- -# - model: Name of the model the well was successfully fit with (if any) -# - spec.growth: (Specific growth rate) The largest exponential growth rate achieved by the culture in the course of the experiment -# - tot.growth: (Total extrapolated growth) The estimated growth plateau from the fitted model in optical density units. May be higher than the actual highest OD reached. -# - lag.time: (Lag time) The exponential trend from is extrapolated to the baseline OD at inoculation and subtracted from the time at inoculation to yield lag time. -# - inoc.OD: (OD at inoculation) The adjusted optical density at the user-specified starting timepoint. -# - good.fit: (Goodness of fit) A metric based on root mean square deviations (RMSD). -# - higher values ( > 3.0) indicate a very good fit while lower values (< 2.0) indicate generally unacceptable fits. -# - empty: (Well indicator) -# - an 'E' indicates that the well was empty and no growth was detected. -# - an 'I' indicates that the well was inoculated and growth was detected above the threshold. -# - an 'E*' indicates that the well was empty and growth was detected (possible contamination). -# - an '!' indicates that the well was inoculated and no growth was detected. -# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index. -# - reach: (Final growth percentage): The percentage of reached by the culture in the course of the experiment. -# - other: Other information includes output from jump detection algorithm and additional columns from the Plate Layout. -# - pdf.file and page.no: location of the figure for this well in the output .pdf files. -# -# -- Source file information-- -# YPDAFEXglucoseTests_2-25-10.csv -# analyzed using GCAT v 0.01 -# request sent: 2013-11-26 11:41:59 -# completed: 2013-11-26 11:42:10 -# -# -- Parameters used in current analysis -- -# - Constant added to log(OD + n) transformation: 1 -# - Blank OD value: 0.093 -# - Index of inoculation timepoint 2 -# - Minimum growth threshold: 0.05 -# - Removed points: -# - Jump detection: FALSE \ No newline at end of file diff --git a/Testing/GCAT_Automated_Test_Script/GCAT3/OD_Transform.txt b/Testing/GCAT_Automated_Test_Script/GCAT3/OD_Transform.txt deleted file mode 100755 index 9c6e05a..0000000 --- a/Testing/GCAT_Automated_Test_Script/GCAT3/OD_Transform.txt +++ /dev/null @@ -1,129 +0,0 @@ -"row" "plate" "well" "media" "strain" "model" "spec.growth" "tot.growth" "lag.time" "inoc.OD" "good.fit" "empty" "asymp" "tank" "reach" "other" "pdf.file" "page.no" "Destination.plate.name" "Well.ID" "Plate.source" "Well.Source" "Media.Definition" -1 "YPDAFEXglucoseTests_2-25-10" "A01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 2 "Control strain plate" "Empty" "Empty" "Empty" "None" -2 "YPDAFEXglucoseTests_2-25-10" "B01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 3 "Control strain plate" "Empty" "Empty" "Empty" "None" -3 "YPDAFEXglucoseTests_2-25-10" "C01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 4 "Control strain plate" "Empty" "Empty" "Empty" "None" -4 "YPDAFEXglucoseTests_2-25-10" "D01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 5 "Control strain plate" "Empty" "Empty" "Empty" "None" -5 "YPDAFEXglucoseTests_2-25-10" "E01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 6 "Control strain plate" "Empty" "Empty" "Empty" "None" -6 "YPDAFEXglucoseTests_2-25-10" "F01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 7 "Control strain plate" "Empty" "Empty" "Empty" "None" -7 "YPDAFEXglucoseTests_2-25-10" "G01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 8 "Control strain plate" "Empty" "Empty" "Empty" "None" -8 "YPDAFEXglucoseTests_2-25-10" "H01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 9 "Control strain plate" "Empty" "Empty" "Empty" "None" -9 "YPDAFEXglucoseTests_2-25-10" "A02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 10 "Control strain plate" "Empty" "Empty" "Empty" "None" -10 "YPDAFEXglucoseTests_2-25-10" "B02" "YP" "Lab strain" "logistic 4-par." 0.0051339104025321 0.0886723328566521 0.0010960793606184 0.109864484860788 2.59465563414594 "I " "-" "-" 92.7576349468939 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 11 "Control strain plate" "Sample" "USDA" "" "YP" -11 "YPDAFEXglucoseTests_2-25-10" "C02" "YP+0.25% glucose" "Lab strain" "richards 5-par." 0.046002940306046 0.240507240883085 2.41478235175163 0.0760170490729348 2.23914120606312 "I " "-" "-" 99.9998793491392 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 12 "Control strain plate" "Sample" "USDA" "" "YP+0.25% glucose" -12 "YPDAFEXglucoseTests_2-25-10" "D02" "YP+0.5% glucose" "Lab strain" "richards 5-par." 0.0731423187284127 0.433505884635671 3.11051947470925 0.0911039861390441 2.53605103328146 "I " "-" "-" 99.9999952705852 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 13 "Control strain plate" "Sample" "USDA" "" "YP+0.5% glucose" -13 "YPDAFEXglucoseTests_2-25-10" "E02" "YP+1% glucose" "Lab strain" "richards 5-par." 0.0874988417043893 0.678577289035852 3.41249009999581 0.0789139664707765 2.87924387138496 "I " "-" "-" 99.9997661119774 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 14 "Control strain plate" "Sample" "USDA" "" "YP+1% glucose" -14 "YPDAFEXglucoseTests_2-25-10" "F02" "YP+2% glucose" "Lab strain" "logistic 4-par." 0.0833321480330421 0.84892275974252 2.93134654253266 0.073343229233773 2.65845234206075 "I " "-" "-" 99.991884161003 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 15 "Control strain plate" "Sample" "USDA" "" "YP+2% glucose" -15 "YPDAFEXglucoseTests_2-25-10" "G02" "YP+5% glucose" "Lab strain" "logistic 4-par." 0.0589669239782459 1.12434511662564 1.29496928736621 0.046493377454031 1.79342170973749 "I " "L" "-" 98.6773509965225 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 16 "Control strain plate" "Sample" "USDA" "" "YP+5% glucose" -16 "YPDAFEXglucoseTests_2-25-10" "H02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 17 "Control strain plate" "Empty" "Empty" "Empty" "None" -17 "YPDAFEXglucoseTests_2-25-10" "A03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 18 "Control strain plate" "Empty" "Empty" "Empty" "None" -18 "YPDAFEXglucoseTests_2-25-10" "B03" "YP" "Wild strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 19 "Control strain plate" "Sample" "USDA" "" "YP" -19 "YPDAFEXglucoseTests_2-25-10" "C03" "YP+0.25% glucose" "Wild strain" "logistic 4-par." 0.0459986844673101 0.256099056993136 1.74285082231178 0.110833972260523 1.7086432551943 "I " "-" "-" 99.9999955687937 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 20 "Control strain plate" "Sample" "USDA" "" "YP+0.25% glucose" -20 "YPDAFEXglucoseTests_2-25-10" "D03" "YP+0.5% glucose" "Wild strain" "logistic 4-par." 0.094586809109001 0.426236311576192 2.76070291990178 0.129985488302977 2.46359052165418 "I " "-" "-" 99.9999999852491 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 21 "Control strain plate" "Sample" "USDA" "" "YP+0.5% glucose" -21 "YPDAFEXglucoseTests_2-25-10" "E03" "YP+1% glucose" "Wild strain" "richards 5-par." 0.121127547834438 0.686895206195343 3.14369238195928 0.106168321707794 2.899473545094 "I " "-" "-" 99.9999999801291 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 22 "Control strain plate" "Sample" "USDA" "" "YP+1% glucose" -22 "YPDAFEXglucoseTests_2-25-10" "F03" "YP+2% glucose" "Wild strain" "richards 5-par." 0.129882547639779 1.04404130073079 2.93412602521094 0.121702902135689 2.75950289629821 "I " "-" "-" 99.9999893737237 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 23 "Control strain plate" "Sample" "USDA" "" "YP+2% glucose" -23 "YPDAFEXglucoseTests_2-25-10" "G03" "YP+5% glucose" "Wild strain" "richards 5-par." 0.120898411706254 1.33105577737345 2.72267556496827 0.12655592121228 2.86661364644022 "I " "-" "-" 99.9926319946813 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 24 "Control strain plate" "Sample" "USDA" "" "YP+5% glucose" -24 "YPDAFEXglucoseTests_2-25-10" "H03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 25 "Control strain plate" "Empty" "Empty" "Empty" "None" -25 "YPDAFEXglucoseTests_2-25-10" "A04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 26 "Control strain plate" "Empty" "Empty" "Empty" "None" -26 "YPDAFEXglucoseTests_2-25-10" "B04" "YP" "Industrial strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 27 "Control strain plate" "Sample" "Internal source" "" "YP" -27 "YPDAFEXglucoseTests_2-25-10" "C04" "YP+0.25% glucose" "Industrial strain" "logistic 4-par." 0.0493379997843534 0.258082503402126 0.626040233021415 0.0848036154923235 1.54716159908115 "I " "-" "-" 99.9999968252864 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 28 "Control strain plate" "Sample" "Internal source" "" "YP+0.25% glucose" -28 "YPDAFEXglucoseTests_2-25-10" "D04" "YP+0.5% glucose" "Industrial strain" "logistic 4-par." 0.093193485656018 0.411823417276531 1.71814140307729 0.0914099770407319 2.39970752160387 "I " "-" "-" 99.9999999910198 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 29 "Control strain plate" "Sample" "Internal source" "" "YP+0.5% glucose" -29 "YPDAFEXglucoseTests_2-25-10" "E04" "YP+1% glucose" "Industrial strain" "richards 5-par." 0.124582742622812 0.665080891230421 2.16563432426164 0.091100407355597 3.20379613427983 "I " "-" "-" 99.9999999995818 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 30 "Control strain plate" "Sample" "Internal source" "" "YP+1% glucose" -30 "YPDAFEXglucoseTests_2-25-10" "F04" "YP+2% glucose" "Industrial strain" "richards 5-par." 0.127931246989736 0.990156801382824 2.06117153412082 0.0876398778418972 2.98526874471877 "I " "L" "-" 99.9999999793615 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 31 "Control strain plate" "Sample" "Internal source" "" "YP+2% glucose" -31 "YPDAFEXglucoseTests_2-25-10" "G04" "YP+5% glucose" "Industrial strain" "richards 5-par." 0.115525592287136 1.30147912807139 1.85809576888812 0.0813644729068572 2.81287527921881 "I " "L" "-" 99.9999137792424 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 32 "Control strain plate" "Sample" "Internal source" "" "YP+5% glucose" -32 "YPDAFEXglucoseTests_2-25-10" "H04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 33 "Control strain plate" "Empty" "Empty" "Empty" "None" -33 "YPDAFEXglucoseTests_2-25-10" "A05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 34 "Control strain plate" "Empty" "Empty" "Empty" "None" -34 "YPDAFEXglucoseTests_2-25-10" "B05" "YP" "Engineered strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 35 "Control strain plate" "Sample" "ATCC" "" "YP" -35 "YPDAFEXglucoseTests_2-25-10" "C05" "YP+0.25% glucose" "Engineered strain" "logistic 4-par." 0.0459359326345167 0.251845669441832 0.663293098031621 0.0603517553820379 1.37098828428178 "I " "-" "-" 99.9999879447413 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 36 "Control strain plate" "Sample" "ATCC" "" "YP+0.25% glucose" -36 "YPDAFEXglucoseTests_2-25-10" "D05" "YP+0.5% glucose" "Engineered strain" "richards 5-par." 0.094434689949163 0.470902886035373 1.8826288625178 0.0639276535310338 2.23793506472592 "I " "-" "-" 99.9999948852344 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 37 "Control strain plate" "Sample" "ATCC" "" "YP+0.5% glucose" -37 "YPDAFEXglucoseTests_2-25-10" "E05" "YP+1% glucose" "Engineered strain" "richards 5-par." 0.121520619472619 0.710378798342107 2.08888813058284 0.0796495197823908 2.69846627998211 "I " "-" "-" 99.9999978953908 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 38 "Control strain plate" "Sample" "ATCC" "" "YP+1% glucose" -38 "YPDAFEXglucoseTests_2-25-10" "F05" "YP+2% glucose" "Engineered strain" "richards 5-par." 0.128733154739806 0.984997029200378 2.0399797106055 0.0873954601678824 2.90166520842456 "I " "-" "-" 99.9999884375137 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 39 "Control strain plate" "Sample" "ATCC" "" "YP+2% glucose" -39 "YPDAFEXglucoseTests_2-25-10" "G05" "YP+5% glucose" "Engineered strain" "richards 5-par." 0.122721598738299 1.31537998678672 2.01398893630359 0.0697748020039699 3.02277302646044 "I " "L" "-" 99.9995991051657 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 40 "Control strain plate" "Sample" "ATCC" "" "YP+5% glucose" -40 "YPDAFEXglucoseTests_2-25-10" "H05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 41 "Control strain plate" "Empty" "Empty" "Empty" "None" -41 "YPDAFEXglucoseTests_2-25-10" "A06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 42 "Control strain plate" "Empty" "Empty" "Empty" "None" -42 "YPDAFEXglucoseTests_2-25-10" "B06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 43 "Control strain plate" "Empty" "Empty" "Empty" "None" -43 "YPDAFEXglucoseTests_2-25-10" "C06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 44 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -44 "YPDAFEXglucoseTests_2-25-10" "D06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 45 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -45 "YPDAFEXglucoseTests_2-25-10" "E06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 46 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -46 "YPDAFEXglucoseTests_2-25-10" "F06" "Empty" "Empty" "richards 5-par." 0.0831016695295036 1.26198322710616 9.6341119668272 -0.0159936185251121 2.21763366074044 "E*" "L" "-" 97.6895368192497 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 47 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -47 "YPDAFEXglucoseTests_2-25-10" "G06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 48 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -48 "YPDAFEXglucoseTests_2-25-10" "H06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 49 "Control strain plate" "Empty" "Empty" "Empty" "None" -49 "YPDAFEXglucoseTests_2-25-10" "A07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 50 "Control strain plate" "Empty" "Empty" "Empty" "None" -50 "YPDAFEXglucoseTests_2-25-10" "B07" "AFEX" "Lab strain" "richards 5-par." 0.0913331265905349 0.979679343699591 3.89989293822063 0.0565463143969478 3.41803212615394 "I " "-" "-" 99.996754328781 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 51 "Control strain plate" "Sample" "USDA" "" "AFEX" -51 "YPDAFEXglucoseTests_2-25-10" "C07" "AFEX+0.25% glucose" "Lab strain" "richards 5-par." 0.0901758841312911 1.02553230430999 3.91431464072772 0.054347185302541 3.3582145530818 "I " "-" "-" 99.9933058334686 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 52 "Control strain plate" "Sample" "USDA" "" "AFEX+0.25% glucose" -52 "YPDAFEXglucoseTests_2-25-10" "D07" "AFEX+0.5% glucose" "Lab strain" "richards 5-par." 0.087653449479707 1.05312597876003 4.23604747636681 0.0485047709394144 3.43101493489101 "I " "-" "-" 99.9881620605088 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 53 "Control strain plate" "Sample" "USDA" "" "AFEX+0.5% glucose" -53 "YPDAFEXglucoseTests_2-25-10" "E07" "AFEX+1% glucose" "Lab strain" "richards 5-par." 0.0852505865256928 1.09709212221813 4.4160839430485 0.0528193717230026 3.32240181027237 "I " "-" "-" 99.9643803748374 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 54 "Control strain plate" "Sample" "USDA" "" "AFEX+1% glucose" -54 "YPDAFEXglucoseTests_2-25-10" "F07" "AFEX+2% glucose" "Lab strain" "richards 5-par." 0.0834062493600675 1.16328851193977 4.33330336969409 0.0489104172866142 3.24662867008 "I " "-" "-" 99.8772630755024 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 55 "Control strain plate" "Sample" "USDA" "" "AFEX+2% glucose" -55 "YPDAFEXglucoseTests_2-25-10" "G07" "AFEX+5% glucose" "Lab strain" "richards 5-par." 0.0746869172685951 1.29976805435626 4.42703571454512 0.0546121442553045 3.36340266867229 "I " "-" "-" 98.4368902568205 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 56 "Control strain plate" "Sample" "USDA" "" "AFEX+5% glucose" -56 "YPDAFEXglucoseTests_2-25-10" "H07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 57 "Control strain plate" "Empty" "Empty" "Empty" "None" -57 "YPDAFEXglucoseTests_2-25-10" "A08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 58 "Control strain plate" "Empty" "Empty" "Empty" "None" -58 "YPDAFEXglucoseTests_2-25-10" "B08" "AFEX" "Wild strain" "richards 5-par." 0.11423563936283 1.11928465325468 2.95662866422492 0.10277417292392 3.07479264063237 "I " "-" "-" 99.9998423354262 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 59 "Control strain plate" "Sample" "USDA" "" "AFEX" -59 "YPDAFEXglucoseTests_2-25-10" "C08" "AFEX+0.25% glucose" "Wild strain" "richards 5-par." 0.114214452831191 1.14837906885588 3.19068068041329 0.0872651968628158 3.13967373959083 "I " "-" "-" 99.9996783933085 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 60 "Control strain plate" "Sample" "USDA" "" "AFEX+0.25% glucose" -60 "YPDAFEXglucoseTests_2-25-10" "D08" "AFEX+0.5% glucose" "Wild strain" "richards 5-par." 0.113566098483318 1.18251324712617 3.15261697058665 0.0824132232798602 3.20643947548216 "I " "-" "-" 99.9993817260453 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 61 "Control strain plate" "Sample" "USDA" "" "AFEX+0.5% glucose" -61 "YPDAFEXglucoseTests_2-25-10" "E08" "AFEX+1% glucose" "Wild strain" "richards 5-par." 0.112827039600267 1.23375586100143 3.12591278868747 0.0877996040474751 3.18956938304341 "I " "-" "-" 99.9983920897484 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 62 "Control strain plate" "Sample" "USDA" "" "AFEX+1% glucose" -62 "YPDAFEXglucoseTests_2-25-10" "F08" "AFEX+2% glucose" "Wild strain" "richards 5-par." 0.110948155806134 1.28676660547704 3.25021471205597 0.0827447676928017 3.20897314216787 "I " "-" "-" 99.9946050160346 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 63 "Control strain plate" "Sample" "USDA" "" "AFEX+2% glucose" -63 "YPDAFEXglucoseTests_2-25-10" "G08" "AFEX+5% glucose" "Wild strain" "richards 5-par." 0.104909957772007 1.38120323294419 3.5400282340856 0.0841025860310471 3.54895808838236 "I " "-" "-" 99.9341701264792 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 64 "Control strain plate" "Sample" "USDA" "" "AFEX+5% glucose" -64 "YPDAFEXglucoseTests_2-25-10" "H08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 65 "Control strain plate" "Empty" "Empty" "Empty" "None" -65 "YPDAFEXglucoseTests_2-25-10" "A09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 66 "Control strain plate" "Empty" "Empty" "Empty" "None" -66 "YPDAFEXglucoseTests_2-25-10" "B09" "AFEX" "Industrial strain" "richards 5-par." 0.124619613670634 1.02546123083454 2.57717331265474 0.0790971076805143 3.1982856586391 "I " "-" "-" 99.9999985057572 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 67 "Control strain plate" "Sample" "Internal source" "" "AFEX" -67 "YPDAFEXglucoseTests_2-25-10" "C09" "AFEX+0.25% glucose" "Industrial strain" "richards 5-par." 0.123242472307703 1.0763049093573 2.58579779724471 0.0704104383586222 3.30084510513736 "I " "-" "-" 99.9999944424538 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 68 "Control strain plate" "Sample" "Internal source" "" "AFEX+0.25% glucose" -68 "YPDAFEXglucoseTests_2-25-10" "D09" "AFEX+0.5% glucose" "Industrial strain" "richards 5-par." 0.12090087158723 1.10591407490241 2.49685751569192 0.0672398191226693 3.29576923039635 "I " "L" "-" 99.9999896715369 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 69 "Control strain plate" "Sample" "Internal source" "" "AFEX+0.5% glucose" -69 "YPDAFEXglucoseTests_2-25-10" "E09" "AFEX+1% glucose" "Industrial strain" "richards 5-par." 0.119451758787832 1.16449508809393 2.44557526327415 0.0665918895911914 3.20509498580801 "I " "L" "-" 99.9999601611542 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 70 "Control strain plate" "Sample" "Internal source" "" "AFEX+1% glucose" -70 "YPDAFEXglucoseTests_2-25-10" "F09" "AFEX+2% glucose" "Industrial strain" "richards 5-par." 0.117046850703108 1.23459712335416 2.58701197446896 0.0611670849509847 3.14018976860492 "I " "L" "-" 99.9995704795227 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 71 "Control strain plate" "Sample" "Internal source" "" "AFEX+2% glucose" -71 "YPDAFEXglucoseTests_2-25-10" "G09" "AFEX+5% glucose" "Industrial strain" "richards 5-par." 0.108331393797411 1.34306781528512 2.65978833216588 0.0615660939241569 3.23212721890241 "I " "-" "-" 99.9822923993972 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 72 "Control strain plate" "Sample" "Internal source" "" "AFEX+5% glucose" -72 "YPDAFEXglucoseTests_2-25-10" "H09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 73 "Control strain plate" "Empty" "Empty" "Empty" "None" -73 "YPDAFEXglucoseTests_2-25-10" "A10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 74 "Control strain plate" "Empty" "Empty" "Empty" "None" -74 "YPDAFEXglucoseTests_2-25-10" "B10" "AFEX" "Engineered strain" "richards 5-par." 0.121839335770884 1.03411101157879 2.35496298854354 0.0684679645246347 2.99659166289529 "I " "-" "-" 99.9998739337277 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 75 "Control strain plate" "Sample" "ATCC" "" "AFEX" -75 "YPDAFEXglucoseTests_2-25-10" "C10" "AFEX+0.25% glucose" "Engineered strain" "richards 5-par." 0.123130424753602 1.0671848756261 2.62328252943635 0.0533919287920788 3.19928587493597 "I " "-" "-" 99.9998922931215 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 76 "Control strain plate" "Sample" "ATCC" "" "AFEX+0.25% glucose" -76 "YPDAFEXglucoseTests_2-25-10" "D10" "AFEX+0.5% glucose" "Engineered strain" "richards 5-par." 0.120973126016907 1.08894424184742 2.61938690806177 0.0531493464712776 3.33630531768578 "I " "-" "-" 99.9998818237851 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 77 "Control strain plate" "Sample" "ATCC" "" "AFEX+0.5% glucose" -77 "YPDAFEXglucoseTests_2-25-10" "E10" "AFEX+1% glucose" "Engineered strain" "richards 5-par." 0.120740948707418 1.1559165803317 2.69619009025558 0.048980878983772 3.36496106313806 "I " "-" "-" 99.9996105268543 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 78 "Control strain plate" "Sample" "ATCC" "" "AFEX+1% glucose" -78 "YPDAFEXglucoseTests_2-25-10" "F10" "AFEX+2% glucose" "Engineered strain" "richards 5-par." 0.121802166262885 1.22916108660807 2.69540468852973 0.0531433213499186 3.47334970863371 "I " "-" "-" 99.99890373284 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 79 "Control strain plate" "Sample" "ATCC" "" "AFEX+2% glucose" -79 "YPDAFEXglucoseTests_2-25-10" "G10" "AFEX+5% glucose" "Engineered strain" "richards 5-par." 0.112904136028813 1.3434348403126 2.71645828999368 0.0555677209128236 3.53967163281668 "I " "-" "-" 99.9786856044998 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 80 "Control strain plate" "Sample" "ATCC" "" "AFEX+5% glucose" -80 "YPDAFEXglucoseTests_2-25-10" "H10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 81 "Control strain plate" "Empty" "Empty" "Empty" "None" -81 "YPDAFEXglucoseTests_2-25-10" "A11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 82 "Control strain plate" "Empty" "Empty" "Empty" "None" -82 "YPDAFEXglucoseTests_2-25-10" "B11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 83 "Control strain plate" "Empty" "Empty" "Empty" "None" -83 "YPDAFEXglucoseTests_2-25-10" "C11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 84 "Control strain plate" "Empty" "Empty" "Empty" "None" -84 "YPDAFEXglucoseTests_2-25-10" "D11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 85 "Control strain plate" "Empty" "Empty" "Empty" "None" -85 "YPDAFEXglucoseTests_2-25-10" "E11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 86 "Control strain plate" "Empty" "Empty" "Empty" "None" -86 "YPDAFEXglucoseTests_2-25-10" "F11" "None" "Empty" "logistic 4-par." 0.0972515006011796 1.24805373798836 14.8532035505196 -0.00367359356392638 2.38008868734198 "E*" "L/U" "-" 87.1867820927035 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 87 "Control strain plate" "Empty" "Empty" "Empty" "None" -87 "YPDAFEXglucoseTests_2-25-10" "G11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 88 "Control strain plate" "Empty" "Empty" "Empty" "None" -88 "YPDAFEXglucoseTests_2-25-10" "H11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 89 "Control strain plate" "Empty" "Empty" "Empty" "None" -89 "YPDAFEXglucoseTests_2-25-10" "A12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 90 "Control strain plate" "Empty" "Empty" "Empty" "None" -90 "YPDAFEXglucoseTests_2-25-10" "B12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 91 "Control strain plate" "Empty" "Empty" "Empty" "None" -91 "YPDAFEXglucoseTests_2-25-10" "C12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 92 "Control strain plate" "Empty" "Empty" "Empty" "None" -92 "YPDAFEXglucoseTests_2-25-10" "D12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 93 "Control strain plate" "Empty" "Empty" "Empty" "None" -93 "YPDAFEXglucoseTests_2-25-10" "E12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 94 "Control strain plate" "Empty" "Empty" "Empty" "None" -94 "YPDAFEXglucoseTests_2-25-10" "F12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 95 "Control strain plate" "Empty" "Empty" "Empty" "None" -95 "YPDAFEXglucoseTests_2-25-10" "G12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 96 "Control strain plate" "Empty" "Empty" "Empty" "None" -96 "YPDAFEXglucoseTests_2-25-10" "H12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_11.46.14.pdf" 97 "Control strain plate" "Empty" "Empty" "Empty" "None" - -# -- Explanation of columns -- -# - model: Name of the model the well was successfully fit with (if any) -# - spec.growth: (Specific growth rate) The largest exponential growth rate achieved by the culture in the course of the experiment -# - tot.growth: (Total extrapolated growth) The estimated growth plateau from the fitted model in optical density units. May be higher than the actual highest OD reached. -# - lag.time: (Lag time) The exponential trend from is extrapolated to the baseline OD at inoculation and subtracted from the time at inoculation to yield lag time. -# - inoc.OD: (OD at inoculation) The adjusted optical density at the user-specified starting timepoint. -# - good.fit: (Goodness of fit) A metric based on root mean square deviations (RMSD). -# - higher values ( > 3.0) indicate a very good fit while lower values (< 2.0) indicate generally unacceptable fits. -# - empty: (Well indicator) -# - an 'E' indicates that the well was empty and no growth was detected. -# - an 'I' indicates that the well was inoculated and growth was detected above the threshold. -# - an 'E*' indicates that the well was empty and growth was detected (possible contamination). -# - an '!' indicates that the well was inoculated and no growth was detected. -# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index. -# - reach: (Final growth percentage): The percentage of reached by the culture in the course of the experiment. -# - other: Other information includes output from jump detection algorithm and additional columns from the Plate Layout. -# - pdf.file and page.no: location of the figure for this well in the output .pdf files. -# -# -- Source file information-- -# YPDAFEXglucoseTests_2-25-10.csv -# analyzed using GCAT v 0.01 -# request sent: 2013-11-26 11:46:14 -# completed: 2013-11-26 11:46:27 -# -# -- Parameters used in current analysis -- -# - Constant added to log(OD + n) transformation: 1 -# - Blank OD value: First timepoint in well -# - Index of inoculation timepoint 2 -# - Minimum growth threshold: 0.05 -# - Removed points: -# - Jump detection: FALSE \ No newline at end of file diff --git a/Testing/GCAT_Automated_Test_Script/GCAT3/Points_Ignored.txt b/Testing/GCAT_Automated_Test_Script/GCAT3/Points_Ignored.txt deleted file mode 100755 index d098d03..0000000 --- a/Testing/GCAT_Automated_Test_Script/GCAT3/Points_Ignored.txt +++ /dev/null @@ -1,129 +0,0 @@ -"row" "plate" "well" "media" "strain" "model" "spec.growth" "tot.growth" "lag.time" "inoc.OD" "good.fit" "empty" "asymp" "tank" "reach" "other" "pdf.file" "page.no" "Destination.plate.name" "Well.ID" "Plate.source" "Well.Source" "Media.Definition" -1 "YPDAFEXglucoseTests_2-25-10" "A01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 2 "Control strain plate" "Empty" "Empty" "Empty" "None" -2 "YPDAFEXglucoseTests_2-25-10" "B01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 3 "Control strain plate" "Empty" "Empty" "Empty" "None" -3 "YPDAFEXglucoseTests_2-25-10" "C01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 4 "Control strain plate" "Empty" "Empty" "Empty" "None" -4 "YPDAFEXglucoseTests_2-25-10" "D01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 5 "Control strain plate" "Empty" "Empty" "Empty" "None" -5 "YPDAFEXglucoseTests_2-25-10" "E01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 6 "Control strain plate" "Empty" "Empty" "Empty" "None" -6 "YPDAFEXglucoseTests_2-25-10" "F01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 7 "Control strain plate" "Empty" "Empty" "Empty" "None" -7 "YPDAFEXglucoseTests_2-25-10" "G01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 8 "Control strain plate" "Empty" "Empty" "Empty" "None" -8 "YPDAFEXglucoseTests_2-25-10" "H01" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 9 "Control strain plate" "Empty" "Empty" "Empty" "None" -9 "YPDAFEXglucoseTests_2-25-10" "A02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 10 "Control strain plate" "Empty" "Empty" "Empty" "None" -10 "YPDAFEXglucoseTests_2-25-10" "B02" "YP" "Lab strain" "logistic 4-par." 0.00512322284611084 0.0885706705171092 0.00146885083119497 0.109882390197245 2.6703814889978 "I " "-" "-" 92.8305994745802 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 11 "Control strain plate" "Sample" "USDA" "" "YP" -11 "YPDAFEXglucoseTests_2-25-10" "C02" "YP+0.25% glucose" "Lab strain" "richards 5-par." 0.0459063906963165 0.241063286623944 2.41105819151703 0.0760544501191693 2.33445949677366 "I " "-" "-" 99.9998616892386 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 12 "Control strain plate" "Sample" "USDA" "" "YP+0.25% glucose" -12 "YPDAFEXglucoseTests_2-25-10" "D02" "YP+0.5% glucose" "Lab strain" "richards 5-par." 0.0729653521516789 0.434572158524765 3.10530782875816 0.0912110779424646 2.66378208529322 "I " "-" "-" 99.99999403812 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 13 "Control strain plate" "Sample" "USDA" "" "YP+0.5% glucose" -13 "YPDAFEXglucoseTests_2-25-10" "E02" "YP+1% glucose" "Lab strain" "richards 5-par." 0.087549003744991 0.680384078190256 3.41500410591867 0.078602369429122 3.04253253857771 "I " "-" "-" 99.999783493135 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 14 "Control strain plate" "Sample" "USDA" "" "YP+1% glucose" -14 "YPDAFEXglucoseTests_2-25-10" "F02" "YP+2% glucose" "Lab strain" "logistic 4-par." 0.0835036622875622 0.849207863293472 2.94083431769237 0.0735497372002751 2.71606517889471 "I " "-" "-" 99.9920437081347 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 15 "Control strain plate" "Sample" "USDA" "" "YP+2% glucose" -15 "YPDAFEXglucoseTests_2-25-10" "G02" "YP+5% glucose" "Lab strain" "logistic 4-par." 0.0605784733145486 1.11352517731425 1.48539390611669 0.0496177952902848 1.88568659491702 "I " "L" "-" 98.9719626898602 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 16 "Control strain plate" "Sample" "USDA" "" "YP+5% glucose" -16 "YPDAFEXglucoseTests_2-25-10" "H02" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 17 "Control strain plate" "Empty" "Empty" "Empty" "None" -17 "YPDAFEXglucoseTests_2-25-10" "A03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 18 "Control strain plate" "Empty" "Empty" "Empty" "None" -18 "YPDAFEXglucoseTests_2-25-10" "B03" "YP" "Wild strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 19 "Control strain plate" "Sample" "USDA" "" "YP" -19 "YPDAFEXglucoseTests_2-25-10" "C03" "YP+0.25% glucose" "Wild strain" "logistic 4-par." 0.0457475800711658 0.256904287297204 1.72691879921013 0.110606719040152 1.77859625443674 "I " "-" "-" 99.9999947777523 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 20 "Control strain plate" "Sample" "USDA" "" "YP+0.25% glucose" -20 "YPDAFEXglucoseTests_2-25-10" "D03" "YP+0.5% glucose" "Wild strain" "logistic 4-par." 0.0944654373655411 0.426655260550642 2.75828968419929 0.12991755273642 2.52869451465839 "I " "-" "-" 99.9999999844561 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 21 "Control strain plate" "Sample" "USDA" "" "YP+0.5% glucose" -21 "YPDAFEXglucoseTests_2-25-10" "E03" "YP+1% glucose" "Wild strain" "richards 5-par." 0.121095965736346 0.687037999671402 3.14313398289071 0.106191053770912 2.95478381597453 "I " "-" "-" 99.9999999793889 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 22 "Control strain plate" "Sample" "USDA" "" "YP+1% glucose" -22 "YPDAFEXglucoseTests_2-25-10" "F03" "YP+2% glucose" "Wild strain" "richards 5-par." 0.129855086205514 1.04449449227513 2.93366816024193 0.121714484234362 2.81436465576683 "I " "-" "-" 99.9999891316078 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 23 "Control strain plate" "Sample" "USDA" "" "YP+2% glucose" -23 "YPDAFEXglucoseTests_2-25-10" "G03" "YP+5% glucose" "Wild strain" "richards 5-par." 0.120898435937539 1.32764962491579 2.72323240077344 0.127905341227191 3.00797833267527 "I " "-" "-" 99.9912733187558 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 24 "Control strain plate" "Sample" "USDA" "" "YP+5% glucose" -24 "YPDAFEXglucoseTests_2-25-10" "H03" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 25 "Control strain plate" "Empty" "Empty" "Empty" "None" -25 "YPDAFEXglucoseTests_2-25-10" "A04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 26 "Control strain plate" "Empty" "Empty" "Empty" "None" -26 "YPDAFEXglucoseTests_2-25-10" "B04" "YP" "Industrial strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 27 "Control strain plate" "Sample" "Internal source" "" "YP" -27 "YPDAFEXglucoseTests_2-25-10" "C04" "YP+0.25% glucose" "Industrial strain" "logistic 4-par." 0.049113938942915 0.258748737037695 0.611171874481659 0.0845578831007956 1.61316239160049 "I " "-" "-" 99.9999962105762 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 28 "Control strain plate" "Sample" "Internal source" "" "YP+0.25% glucose" -28 "YPDAFEXglucoseTests_2-25-10" "D04" "YP+0.5% glucose" "Industrial strain" "logistic 4-par." 0.093074527600122 0.412178246785743 1.71538098733957 0.0913303370508307 2.46532958224324 "I " "-" "-" 99.9999999905309 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 29 "Control strain plate" "Sample" "Internal source" "" "YP+0.5% glucose" -29 "YPDAFEXglucoseTests_2-25-10" "E04" "YP+1% glucose" "Industrial strain" "richards 5-par." 0.124584782390426 0.665071528928034 2.16566832060573 0.09109869026466 3.26118827375832 "I " "-" "-" 99.9999999995832 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 30 "Control strain plate" "Sample" "Internal source" "" "YP+1% glucose" -30 "YPDAFEXglucoseTests_2-25-10" "F04" "YP+2% glucose" "Industrial strain" "richards 5-par." 0.12792707646206 0.990201196030809 2.06107722840498 0.087648083744547 3.04010612494743 "I " "L" "-" 99.9999999791478 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 31 "Control strain plate" "Sample" "Internal source" "" "YP+2% glucose" -31 "YPDAFEXglucoseTests_2-25-10" "G04" "YP+5% glucose" "Industrial strain" "richards 5-par." 0.115598093951232 1.30017594724392 1.86057928629408 0.0816316115810476 2.87659439741231 "I " "L" "-" 99.9999089635063 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 32 "Control strain plate" "Sample" "Internal source" "" "YP+5% glucose" -32 "YPDAFEXglucoseTests_2-25-10" "H04" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 33 "Control strain plate" "Empty" "Empty" "Empty" "None" -33 "YPDAFEXglucoseTests_2-25-10" "A05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 34 "Control strain plate" "Empty" "Empty" "Empty" "None" -34 "YPDAFEXglucoseTests_2-25-10" "B05" "YP" "Engineered strain" ": failed" NA NA NA NA NA "I " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 35 "Control strain plate" "Sample" "ATCC" "" "YP" -35 "YPDAFEXglucoseTests_2-25-10" "C05" "YP+0.25% glucose" "Engineered strain" "logistic 4-par." 0.0455423852277455 0.253011492887766 0.633612783422165 0.0599180880707215 1.44199308592877 "I " "-" "-" 99.9999836645589 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 36 "Control strain plate" "Sample" "ATCC" "" "YP+0.25% glucose" -36 "YPDAFEXglucoseTests_2-25-10" "D05" "YP+0.5% glucose" "Engineered strain" "richards 5-par." 0.0942560771156105 0.47165366043215 1.87947890043788 0.0641152719303668 2.32215880898724 "I " "-" "-" 99.9999936292908 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 37 "Control strain plate" "Sample" "ATCC" "" "YP+0.5% glucose" -37 "YPDAFEXglucoseTests_2-25-10" "E05" "YP+1% glucose" "Engineered strain" "richards 5-par." 0.121404566371326 0.711085043803959 2.08707581462709 0.079800634332521 2.77857179654498 "I " "-" "-" 99.9999975813868 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 38 "Control strain plate" "Sample" "ATCC" "" "YP+1% glucose" -38 "YPDAFEXglucoseTests_2-25-10" "F05" "YP+2% glucose" "Engineered strain" "richards 5-par." 0.12865948433987 0.98597671409577 2.03868589008582 0.087495143007229 2.98217250669466 "I " "-" "-" 99.9999873691302 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 39 "Control strain plate" "Sample" "ATCC" "" "YP+2% glucose" -39 "YPDAFEXglucoseTests_2-25-10" "G05" "YP+5% glucose" "Engineered strain" "richards 5-par." 0.122711103907082 1.31562500185075 2.01371509312624 0.0697603778582843 3.07643306357741 "I " "L" "-" 99.999598061796 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 40 "Control strain plate" "Sample" "ATCC" "" "YP+5% glucose" -40 "YPDAFEXglucoseTests_2-25-10" "H05" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 41 "Control strain plate" "Empty" "Empty" "Empty" "None" -41 "YPDAFEXglucoseTests_2-25-10" "A06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 42 "Control strain plate" "Empty" "Empty" "Empty" "None" -42 "YPDAFEXglucoseTests_2-25-10" "B06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 43 "Control strain plate" "Empty" "Empty" "Empty" "None" -43 "YPDAFEXglucoseTests_2-25-10" "C06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 44 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -44 "YPDAFEXglucoseTests_2-25-10" "D06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 45 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -45 "YPDAFEXglucoseTests_2-25-10" "E06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 46 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -46 "YPDAFEXglucoseTests_2-25-10" "F06" "Empty" "Empty" "richards 5-par." 0.0857882390552096 1.24493866823306 9.88179192729724 -0.0165597461168613 2.32606464578444 "E*" "L" "-" 98.4210828771573 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 47 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -47 "YPDAFEXglucoseTests_2-25-10" "G06" "Empty" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 48 "Control strain plate" "Empty" "Empty" "Empty" "Empty" -48 "YPDAFEXglucoseTests_2-25-10" "H06" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 49 "Control strain plate" "Empty" "Empty" "Empty" "None" -49 "YPDAFEXglucoseTests_2-25-10" "A07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 50 "Control strain plate" "Empty" "Empty" "Empty" "None" -50 "YPDAFEXglucoseTests_2-25-10" "B07" "AFEX" "Lab strain" "richards 5-par." 0.0910656809877224 0.978831696720056 3.88851123944356 0.057119562600749 3.50838381966352 "I " "-" "-" 99.9960539072354 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 51 "Control strain plate" "Sample" "USDA" "" "AFEX" -51 "YPDAFEXglucoseTests_2-25-10" "C07" "AFEX+0.25% glucose" "Lab strain" "richards 5-par." 0.0897750856169793 1.02459532986805 3.8967929087061 0.0551818328016911 3.46998372922229 "I " "-" "-" 99.991259133915 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 52 "Control strain plate" "Sample" "USDA" "" "AFEX+0.25% glucose" -52 "YPDAFEXglucoseTests_2-25-10" "D07" "AFEX+0.5% glucose" "Lab strain" "richards 5-par." 0.087292525747305 1.0527501330422 4.21907836932876 0.0490476413563776 3.51721701779359 "I " "-" "-" 99.9856386878846 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 53 "Control strain plate" "Sample" "USDA" "" "AFEX+0.5% glucose" -53 "YPDAFEXglucoseTests_2-25-10" "E07" "AFEX+1% glucose" "Lab strain" "richards 5-par." 0.0854275766875656 1.09681106370395 4.42403082220079 0.0527978561023557 3.39981186901509 "I " "-" "-" 99.9660125813752 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 54 "Control strain plate" "Sample" "USDA" "" "AFEX+1% glucose" -54 "YPDAFEXglucoseTests_2-25-10" "F07" "AFEX+2% glucose" "Lab strain" "richards 5-par." 0.084278824827003 1.16188034043041 4.37444626455929 0.0484042275684464 3.40906624822256 "I " "-" "-" 99.9039249274661 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 55 "Control strain plate" "Sample" "USDA" "" "AFEX+2% glucose" -55 "YPDAFEXglucoseTests_2-25-10" "G07" "AFEX+5% glucose" "Lab strain" "richards 5-par." 0.0751490389653923 1.29671192755065 4.45016704465737 0.0546480394626687 3.48603212189912 "I " "-" "-" 98.5357819689647 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 56 "Control strain plate" "Sample" "USDA" "" "AFEX+5% glucose" -56 "YPDAFEXglucoseTests_2-25-10" "H07" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 57 "Control strain plate" "Empty" "Empty" "Empty" "None" -57 "YPDAFEXglucoseTests_2-25-10" "A08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 58 "Control strain plate" "Empty" "Empty" "Empty" "None" -58 "YPDAFEXglucoseTests_2-25-10" "B08" "AFEX" "Wild strain" "richards 5-par." 0.114233577227138 1.11940666165336 2.95659685349929 0.10276070095978 3.12523138568832 "I " "-" "-" 99.9998425058726 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 59 "Control strain plate" "Sample" "USDA" "" "AFEX" -59 "YPDAFEXglucoseTests_2-25-10" "C08" "AFEX+0.25% glucose" "Wild strain" "richards 5-par." 0.114190896575847 1.14811138681943 3.18991017237117 0.0873694909800864 3.19174147527227 "I " "-" "-" 99.9996684768339 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 60 "Control strain plate" "Sample" "USDA" "" "AFEX+0.25% glucose" -60 "YPDAFEXglucoseTests_2-25-10" "D08" "AFEX+0.5% glucose" "Wild strain" "richards 5-par." 0.113518812542465 1.18182740070708 3.15106253292283 0.0826636113465304 3.26600840866822 "I " "-" "-" 99.9993405132836 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 61 "Control strain plate" "Sample" "USDA" "" "AFEX+0.5% glucose" -61 "YPDAFEXglucoseTests_2-25-10" "E08" "AFEX+1% glucose" "Wild strain" "richards 5-par." 0.112731557723291 1.23243667600584 3.12290823666719 0.0883532618105942 3.27099839140732 "I " "-" "-" 99.998177929312 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 62 "Control strain plate" "Sample" "USDA" "" "AFEX+1% glucose" -62 "YPDAFEXglucoseTests_2-25-10" "F08" "AFEX+2% glucose" "Wild strain" "richards 5-par." 0.110711220465384 1.28465314801447 3.24291094200068 0.0838703449391198 3.34935047015509 "I " "-" "-" 99.9932361128704 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 63 "Control strain plate" "Sample" "USDA" "" "AFEX+2% glucose" -63 "YPDAFEXglucoseTests_2-25-10" "G08" "AFEX+5% glucose" "Wild strain" "richards 5-par." 0.104911901010651 1.38112995826321 3.54007980934916 0.0841275019173986 3.60183900056643 "I " "-" "-" 99.9340428851054 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 64 "Control strain plate" "Sample" "USDA" "" "AFEX+5% glucose" -64 "YPDAFEXglucoseTests_2-25-10" "H08" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 65 "Control strain plate" "Empty" "Empty" "Empty" "None" -65 "YPDAFEXglucoseTests_2-25-10" "A09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 66 "Control strain plate" "Empty" "Empty" "Empty" "None" -66 "YPDAFEXglucoseTests_2-25-10" "B09" "AFEX" "Industrial strain" "richards 5-par." 0.124639558557251 1.02518255796904 2.57760580712995 0.0790861200979034 3.25359624987887 "I " "-" "-" 99.9999985380202 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 67 "Control strain plate" "Sample" "Internal source" "" "AFEX" -67 "YPDAFEXglucoseTests_2-25-10" "C09" "AFEX+0.25% glucose" "Industrial strain" "richards 5-par." 0.123259617514217 1.07597966901492 2.58617748296761 0.0704118282374251 3.3564765167362 "I " "-" "-" 99.9999945229239 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 68 "Control strain plate" "Sample" "Internal source" "" "AFEX+0.25% glucose" -68 "YPDAFEXglucoseTests_2-25-10" "D09" "AFEX+0.5% glucose" "Industrial strain" "richards 5-par." 0.120921387314129 1.1054141886015 2.49733136040803 0.0672610858991924 3.35561723828862 "I " "L" "-" 99.999989789286 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 69 "Control strain plate" "Sample" "Internal source" "" "AFEX+0.5% glucose" -69 "YPDAFEXglucoseTests_2-25-10" "E09" "AFEX+1% glucose" "Industrial strain" "richards 5-par." 0.119469215205307 1.16386920095508 2.44599900455348 0.0666632835088954 3.26495706766016 "I " "L" "-" 99.9999598857272 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 70 "Control strain plate" "Sample" "Internal source" "" "AFEX+1% glucose" -70 "YPDAFEXglucoseTests_2-25-10" "F09" "AFEX+2% glucose" "Industrial strain" "richards 5-par." 0.117055956532607 1.23292877894923 2.58733736534061 0.0615930499531776 3.23191783299634 "I " "-" "-" 99.9995312927806 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 71 "Control strain plate" "Sample" "Internal source" "" "AFEX+2% glucose" -71 "YPDAFEXglucoseTests_2-25-10" "G09" "AFEX+5% glucose" "Industrial strain" "richards 5-par." 0.108245104945905 1.34096953377871 2.65843365395388 0.062727700859311 3.38843037787812 "I " "-" "-" 99.9788375045276 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 72 "Control strain plate" "Sample" "Internal source" "" "AFEX+5% glucose" -72 "YPDAFEXglucoseTests_2-25-10" "H09" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 73 "Control strain plate" "Empty" "Empty" "Empty" "None" -73 "YPDAFEXglucoseTests_2-25-10" "A10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 74 "Control strain plate" "Empty" "Empty" "Empty" "None" -74 "YPDAFEXglucoseTests_2-25-10" "B10" "AFEX" "Engineered strain" "richards 5-par." 0.121764774087552 1.03575182594995 2.35350455581128 0.0683841865814427 3.10711688897198 "I " "-" "-" 99.9998704011685 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 75 "Control strain plate" "Sample" "ATCC" "" "AFEX" -75 "YPDAFEXglucoseTests_2-25-10" "C10" "AFEX+0.25% glucose" "Engineered strain" "richards 5-par." 0.123090824730516 1.06842524515535 2.62256716415931 0.0532958289475007 3.29457027142756 "I " "-" "-" 99.9998916790283 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 76 "Control strain plate" "Sample" "ATCC" "" "AFEX+0.25% glucose" -76 "YPDAFEXglucoseTests_2-25-10" "D10" "AFEX+0.5% glucose" "Engineered strain" "richards 5-par." 0.120944684388312 1.09008552670784 2.61886063345403 0.0530365880953372 3.43451356445556 "I " "-" "-" 99.9998823965125 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 77 "Control strain plate" "Sample" "ATCC" "" "AFEX+0.5% glucose" -77 "YPDAFEXglucoseTests_2-25-10" "E10" "AFEX+1% glucose" "Engineered strain" "richards 5-par." 0.120734107580927 1.15670253081866 2.69611302714549 0.0488445587231696 3.43432940804069 "I " "-" "-" 99.999618979496 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 78 "Control strain plate" "Sample" "ATCC" "" "AFEX+1% glucose" -78 "YPDAFEXglucoseTests_2-25-10" "F10" "AFEX+2% glucose" "Engineered strain" "richards 5-par." 0.121797460706957 1.22927410593987 2.69529695023975 0.0531367705332191 3.52592526978957 "I " "-" "-" 99.998902414812 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 79 "Control strain plate" "Sample" "ATCC" "" "AFEX+2% glucose" -79 "YPDAFEXglucoseTests_2-25-10" "G10" "AFEX+5% glucose" "Engineered strain" "richards 5-par." 0.1128494281004 1.3421800558205 2.71555080399082 0.0562414213905349 3.66293619120109 "I " "-" "-" 99.9765721559617 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 80 "Control strain plate" "Sample" "ATCC" "" "AFEX+5% glucose" -80 "YPDAFEXglucoseTests_2-25-10" "H10" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 81 "Control strain plate" "Empty" "Empty" "Empty" "None" -81 "YPDAFEXglucoseTests_2-25-10" "A11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 82 "Control strain plate" "Empty" "Empty" "Empty" "None" -82 "YPDAFEXglucoseTests_2-25-10" "B11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 83 "Control strain plate" "Empty" "Empty" "Empty" "None" -83 "YPDAFEXglucoseTests_2-25-10" "C11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 84 "Control strain plate" "Empty" "Empty" "Empty" "None" -84 "YPDAFEXglucoseTests_2-25-10" "D11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 85 "Control strain plate" "Empty" "Empty" "Empty" "None" -85 "YPDAFEXglucoseTests_2-25-10" "E11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 86 "Control strain plate" "Empty" "Empty" "Empty" "None" -86 "YPDAFEXglucoseTests_2-25-10" "F11" "None" "Empty" "logistic 4-par." 0.0955422988477089 1.27434659362621 14.7977758044825 -0.00282569557385737 2.58074649545863 "E*" "L/U" "-" 85.8739348760869 "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 87 "Control strain plate" "Empty" "Empty" "Empty" "None" -87 "YPDAFEXglucoseTests_2-25-10" "G11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 88 "Control strain plate" "Empty" "Empty" "Empty" "None" -88 "YPDAFEXglucoseTests_2-25-10" "H11" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 89 "Control strain plate" "Empty" "Empty" "Empty" "None" -89 "YPDAFEXglucoseTests_2-25-10" "A12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 90 "Control strain plate" "Empty" "Empty" "Empty" "None" -90 "YPDAFEXglucoseTests_2-25-10" "B12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 91 "Control strain plate" "Empty" "Empty" "Empty" "None" -91 "YPDAFEXglucoseTests_2-25-10" "C12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 92 "Control strain plate" "Empty" "Empty" "Empty" "None" -92 "YPDAFEXglucoseTests_2-25-10" "D12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 93 "Control strain plate" "Empty" "Empty" "Empty" "None" -93 "YPDAFEXglucoseTests_2-25-10" "E12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 94 "Control strain plate" "Empty" "Empty" "Empty" "None" -94 "YPDAFEXglucoseTests_2-25-10" "F12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 95 "Control strain plate" "Empty" "Empty" "Empty" "None" -95 "YPDAFEXglucoseTests_2-25-10" "G12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 96 "Control strain plate" "Empty" "Empty" "Empty" "None" -96 "YPDAFEXglucoseTests_2-25-10" "H12" "None" "Empty" ": skipped" NA NA NA NA NA "E " "-" "-" NA "" "YPDAFEXglucoseTests_2-25-10_plots_2013-11-26_12.08.40.pdf" 97 "Control strain plate" "Empty" "Empty" "Empty" "None" - -# -- Explanation of columns -- -# - model: Name of the model the well was successfully fit with (if any) -# - spec.growth: (Specific growth rate) The largest exponential growth rate achieved by the culture in the course of the experiment -# - tot.growth: (Total extrapolated growth) The estimated growth plateau from the fitted model in optical density units. May be higher than the actual highest OD reached. -# - lag.time: (Lag time) The exponential trend from is extrapolated to the baseline OD at inoculation and subtracted from the time at inoculation to yield lag time. -# - inoc.OD: (OD at inoculation) The adjusted optical density at the user-specified starting timepoint. -# - good.fit: (Goodness of fit) A metric based on root mean square deviations (RMSD). -# - higher values ( > 3.0) indicate a very good fit while lower values (< 2.0) indicate generally unacceptable fits. -# - empty: (Well indicator) -# - an 'E' indicates that the well was empty and no growth was detected. -# - an 'I' indicates that the well was inoculated and growth was detected above the threshold. -# - an 'E*' indicates that the well was empty and growth was detected (possible contamination). -# - an '!' indicates that the well was inoculated and no growth was detected. -# - tank: (Tanking indicator) If a number is present then the growth trend was determined to tank at that timepoint index. -# - reach: (Final growth percentage): The percentage of reached by the culture in the course of the experiment. -# - other: Other information includes output from jump detection algorithm and additional columns from the Plate Layout. -# - pdf.file and page.no: location of the figure for this well in the output .pdf files. -# -# -- Source file information-- -# YPDAFEXglucoseTests_2-25-10.csv -# analyzed using GCAT v 0.01 -# request sent: 2013-11-26 12:08:40 -# completed: 2013-11-26 12:08:55 -# -# -- Parameters used in current analysis -- -# - Constant added to log(OD + n) transformation: 1 -# - Blank OD value: First timepoint in well -# - Index of inoculation timepoint 2 -# - Minimum growth threshold: 0.05 -# - Removed points: 70 71 72 73 74 75 76 77 78 79 -# - Jump detection: FALSE \ No newline at end of file diff --git a/Testing/GCAT_Automated_Test_Script/compare_gcat_output.R b/Testing/GCAT_Automated_Test_Script/compare_gcat_output.R deleted file mode 100755 index 9a003ce..0000000 --- a/Testing/GCAT_Automated_Test_Script/compare_gcat_output.R +++ /dev/null @@ -1,100 +0,0 @@ -#!/usr/bin/env Rscript - -# Compare 2 versions of GCAT for a particular parameter -# Karan Maini - - args <- commandArgs(TRUE) - - # Baaad....WORK.DIR = "/home/maini/Desktop/GCAT Test Script" - - # INPUT.1 = "GCAT2/output_gcat.fit_2013-11-18_12.23.34.txt" - # INPUT.2 = "GCAT3/output_gcat.fit_2013-11-18_12.19.46.txt" - - # Read in the data - in1 = read.table(args[1],header=T,sep="\t") - in2 = read.table(args[2],header=T,sep="\t") - parameter = args[3] - - # Compare values - same = signif(in1$spec.growth,2) == signif(in2$spec.growth,2) & signif(in1$tot.growth,2) == signif(in2$tot.growth,2) & signif(in1$lag.time,2) == signif(in2$lag.time,2) - same[is.na(in1$spec.growth) & is.na(in2$spec.growth)] = T - - # Write out the output - #out = file(OUTPUT,open="w") - #if (all(same)) { writeLines("No significant differences identified",con=out) } - #close(out) - - # Manual exploration - # Ascertain that results are quite different - - cat("Command:\nRscript compare_gcat_output.R",args[1],args[2],parameter) - - cat("\n\nSummary: \n\n") - summary(same) - head(same) - cat("\n\nGCAT2: \n\n") - head(in1) - cat("\n\nGCAT3: \n\n") - head(in2) - cat("\n\nSpecific Growth Comparison Summary: \n\n") - summary(in2$spec.growth/in1$spec.growth) # specific growth lower in GCAT 3 - cat("\n\nTotal Growth Comparison Summary: \n\n") - summary(in2$tot.growth/in1$tot.growth) - cat("\n\nLag Time Comparison Summary: \n\n") - summary(in2$lag.time/in1$lag.time) # lag time also lower in GCAT 3 - - - # Baaad....WORK.DIR = "/home/maini/Desktop/GCAT Test Script/Comparison Plots" - setwd("./Comparison Plots") - - pdf( paste( parameter,'Plot.pdf'),onefile=T) - # ....plot code here.... - -# Plot specific growth rate of GCAT 3 vs. GCAT 2 - x = in1$spec.growth - y = in2$spec.growth - - plot(x,y,pch=16,main="Specific Growth", xlab="old GCAT", ylab="new GCAT") - abline(0,1) - abline(lm(y~x),lty=2) - legend("bottomright",c("y=x line","regression line"),lty=c(1,2)) - -# Plot total growth rate of GCAT 3 vs. GCAT 2 - x = in1$tot.growth - y = in2$tot.growth - - plot(x,y,pch=16,main="Total Growth", xlab="old GCAT", ylab="new GCAT") - abline(0,1) - abline(lm(y~x),lty=2) - legend("bottomright",c("y=x line","regression line"),lty=c(1,2)) - -# Plot lag time of GCAT 3 vs. GCAT 2 - x = in1$lag.time - y = in2$lag.time - - plot(x,y,pch=16,main="Lag Time", xlab="old GCAT", ylab="new GCAT") - abline(0,1) - abline(lm(y~x),lty=2) - legend("bottomright",c("y=x line","regression line"),lty=c(1,2)) - -# Plot Goodness of Fit of GCAT 3 vs. GCAT 2 - x = in1$good.fit - y = in2$good.fit - - plot(x,y,pch=16,main="Goodness of Fit", xlab="old GCAT", ylab="new GCAT") - abline(0,1) - abline(lm(y~x),lty=2) - legend("bottomright",c("y=x line","regression line"),lty=c(1,2)) - - dev.off() - - - - - # Investigate outliers - subset(in1, is.finite(in1$spec.growth) & (in1$spec.growth < in2$spec.growth - 0.003)) - subset(in2, is.finite(in1$spec.growth) & (in1$spec.growth < in2$spec.growth - 0.003)) - - # Clean up - rm(list=ls()) - setwd("../") #move back to testing root directory \ No newline at end of file diff --git a/Testing/GCAT_Automated_Test_Script/gcat_diff.rb b/Testing/GCAT_Automated_Test_Script/gcat_diff.rb deleted file mode 100755 index 61aaa4d..0000000 --- a/Testing/GCAT_Automated_Test_Script/gcat_diff.rb +++ /dev/null @@ -1,57 +0,0 @@ -#!/usr/bin/env ruby - -def usage rc, *args - case rc - when "argv" - puts "Usage: ./gcat_diff.rb / /" - # puts " is a directory of output files processed on gcat-test.glbrc" - # puts " is a directory holding output files processed on gcat.glbrc" - when "names" - puts "Error: both directories must contain output files with identical file names." - when "dir" - puts "Error: #{args.first} is not a directory." - when "empty" - puts "No files found to analyze." - end - puts "for help: ./gcat_diff.rb help" - exit 0 -end - -def line - 80.times {print "#"} - puts "" -end - -def help - line - puts "# gcat_diff.rb\n#" - puts "# This program was designed to verify that any changes made to gcat-test\n# have not changed the numeric values of the output data in any meaningful way.\n# gcat_diff is the script used to automate this process.\n# To use the script you must have R and ruby installed.\n# Once you are ready to run the comparison analysis follow these steps:\n# In a directory containing both script files\n# [gcat_diff.rb and compare_gcat_output.R]\n# create 2 new directories to store the output files.\n# One will be for files from gcat-test.glbrc.org\n# and the other will be for gcat.glbrc.org.\n# Place any number of output files desired into\n# these directories following this important convention.\n# See the GCAT manual for help on producing these files.\n# Note: The needed output files will be text format.\n# Each output file must be run on GCAT\n# using the same PARAMETERS and share the same NAME.\n# This way you can analyze many output files at once,\n# with each pair being run onproduction & test\n# using the same parameters and compared in tandem.\n# \n# Nate DiPiazza, Karan Maini GLBRC 2014" - line - - exit 1 -end - -if(ARGV.size == 1) - usage "argv" unless ARGV.first == "help" - help -end - -usage "argv" unless ARGV.size == 2 - -ARGV.each {|arg| usage "dir", arg unless File.directory?(arg)} - -#check the contents of the 2 dirs. files must have same filenames -paths_test = Dir.glob("#{ARGV[0]}/*").sort -filenames_test = paths_test.map {|p| File.basename(p)} -paths_prod = Dir.glob("#{ARGV[1]}/*").sort -usage "empty" unless((paths_test.size > 0) and (paths_prod.size > 0)) -filenames_prod = paths_prod.map {|p| File.basename(p)} - -usage "names" unless filenames_test == filenames_prod -#filenames_prod would work too. they are equal -filenames_test.each do |filename| - # run the R script - command = `Rscript compare_gcat_output.R #{ARGV[0]}/#{filename} #{ARGV[1]}/#{filename} #{filename}` - # write R summary printouts to a file - File.open("Comparison_Datasets/#{filename}", "w") {|f| f.puts command; f.close } -end \ No newline at end of file diff --git a/Testing/GCAT_Automated_Test_Script/script.py b/Testing/GCAT_Automated_Test_Script/script.py deleted file mode 100755 index 6c4927d..0000000 --- a/Testing/GCAT_Automated_Test_Script/script.py +++ /dev/null @@ -1,66 +0,0 @@ -import sys -import os -import glob - -def usage(): - print 'python .py ' - print 'directory_path_1 --> GCAT2 and directory_path_2 --> GCAT3' - print 'Eg: python ./script.py ./GCAT2 ./GCAT3' - - -def main(): - first_dir_path = sys.argv[1] - second_dir_path = sys.argv[2] - - files1=[] - files2=[] - parameter_list=[] - - for root,dirs,files in os.walk(first_dir_path): - files1.extend(files) - print 'Files in GCAT2:' - print files1 - print '\n' - - for root,dirs,files in os.walk(second_dir_path): - files2.extend(files) - print 'Files in GCAT3:' - print files2 - print '\n' - - print 'Common Files:' - print [f for f in files2 if f in files1] - print '\n' - - for f in files2: - if f in files1: - parameter_list.append(f[:-4]) - # print parameter_list - - - # using glob - # parameter_list = ['Media_Background','OD_Transform', 'Inoculation', 'Points_Ignored', 'Growth_Threshold'] - for parameter in parameter_list: - file_1 = glob.glob(first_dir_path+"/"+parameter + "*.txt") - file_2 = glob.glob(second_dir_path+"/"+parameter + "*.txt") - print file_1 - print file_2 - if len(file_1)==1 and len(file_2)==1: - # run it on command line - command = "Rscript compare_gcat_output.R "+ file_1[0] + " " + file_2[0] + " " + parameter - print command - os.system(command + '>' + './Comparison_Datasets/' + parameter + '.txt') # run it on command line - print 'done' - else: - print 'Multiple files found for the parameter' + parameter - - -if __name__ == '__main__': - # 2 arguments required other than script name: - # script name, dir_path_1, dir_path_2 - # If insufficent command line arguments are passed, usage must be printed - if len(sys.argv) != 3: - usage() - # else continue with execution of script - else: - main() diff --git a/Testing/GCAT_Test_Plan.docx b/Testing/GCAT_Test_Plan.docx new file mode 100644 index 0000000..fa06187 Binary files /dev/null and b/Testing/GCAT_Test_Plan.docx differ diff --git a/Testing/R code tests with xlsx files 2010/HarnessTest b/Testing/R code tests with xlsx files 2010/HarnessTest deleted file mode 100644 index b6e2665..0000000 --- a/Testing/R code tests with xlsx files 2010/HarnessTest +++ /dev/null @@ -1,142 +0,0 @@ -#!/bin/bash -echo "Starting the harness test .....\n" - -R --vanilla --slave --file="xlsx_file_input_R.txt" - - -#test file 0 -diff ~/harnesstest/multiPlate/test.xlsx_HTS.fit.csv ~/harnesstest/multiPlate/original_csvfile/Ecoli_M9_growth_032510_fixed.xlsx_HTS.fit.csv > consoleOut.txt -if [ $? == 0 ] -then - echo "NO diff between test.xlsx_HTS.fit.csv AND Ecoli_M9_growth_032510_fixed.xlsx_HTS.fit.csv\n" - rm consoleOut.txt -else - echo "There are diff between test.xlsx_HTS.fit.csv AND Ecoli_M9_growth_032510_fixed.xlsx_HTS.fit.csv files. Plase check consoleOut.txt for for details\n" -fi - - -echo "Testing Multiple Plate Case .....\n\n" -#test file 1 -diff ~/harnesstest/multiPlate/test.xlsx_HTS.fit.csv ~/harnesstest/multiPlate/original_csvfile/test.xlsx_HTS.fit.csv > consoleOut1.txt -if [ $? == 0 ] -then - echo "NO diff between two test.xlsx_HTS.fit.csv files\n" - rm consoleOut1.txt -else - echo "There are diff between two test.xlsx_HTS.fit.csv. Plase check consoleOut1.txt for details\n" -fi - - -#test file 2 -diff ~/harnesstest/multiPlate/Ecoli_M9_growth_032510_fixed.xlsx_HTS.fit.csv ~/harnesstest/multiPlate/original_csvfile/Ecoli_M9_growth_032510_fixed.xlsx_HTS.fit.csv > consoleOut2.txt -if [ $? == 0 ] -then - echo "NO diff between two Ecoli_M9_growth_032510_fixed.xlsx_HTS.fit.csv files\n" - rm consoleOut2.txt -else - echo "There are diff between two Ecoli_M9_growth_032510_fixed.xlsx_HTS.fit.csv. Plase check consoleOut2.txt for details\n" -fi - - - - -echo "Testing Single Plate Plate Case ....\n\n." -#test file 3 -diff ~/harnesstest/singlePlate/YPDAFEXglucoseTests_Reps2-3_3-9-10.xlsx_HTS.fit.csv ~/harnesstest/singlePlate/original_csvfile/YPDAFEXglucoseTests_Reps2-3_3-9-10.xlsx_HTS.fit.csv > consoleOut3.txt -if [ $? == 0 ] -then - echo "NO diff between two YPDAFEXglucoseTests_Reps2-3_3-9-10.xlsx_HTS.fit.csv files\n" - rm consoleOut3.txt -else - echo "There are diff between two YPDAFEXglucoseTests_Reps2-3_3-9-10.xlsx_HTS.fit.csv. Plase check consoleOut3.txt for details\n" -fi - - - -#test file 4 -diff ~/harnesstest/singlePlate/YPDAFEXglucoseTests_2-25-10.xlsx_HTS.fit.csv ~/harnesstest/singlePlate/original_csvfile/YPDAFEXglucoseTests_2-25-10.xlsx_HTS.fit.csv > consoleOut4.txt -if [ $? == 0 ] -then - echo "NO diff between two YPDAFEXglucoseTests_2-25-10.xlsx_HTS.fit.csv files\n" - rm consoleOut4.txt -else - echo "There are diff between two YPDAFEXglucoseTests_2-25-10.xlsx_HTS.fit.csv. Plase check consoleOut4.txt for details\n" -fi - - - -echo "Testing Multiple Plate log(x + 2) transformation Case .....\n\n" -#test file 5 -diff ~/harnesstest/multiPlate/test_n2.xlsx_HTS.fit.csv ~/harnesstest/multiPlate/original_csvfile/test_n2.xlsx_HTS.fit.csv > consoleOut5.txt -if [ $? == 0 ] -then - echo "NO diff between two test_n2.xlsx_HTS.fit.csv files for log(x + 2) transformation\n" - rm consoleOut5.txt -else - echo "There are diff between two test_n2.xlsx_HTS.fit.csv files for log(x + 2) transformation. Plase check consoleOut5.txt for details\n" -fi - - - -echo "Testing Multiple Plate log(x + 3) transformation Case .....\n\n" -#test file 6 -diff ~/harnesstest/multiPlate/test_n3.xlsx_HTS.fit.csv ~/harnesstest/multiPlate/original_csvfile/test_n3.xlsx_HTS.fit.csv > consoleOut6.txt -if [ $? == 0 ] -then - echo "NO diff between two test_n3.xlsx_HTS.fit.csv files for log(x + 3) transformation\n" - rm consoleOut6.txt -else - echo "There are diff between two test_n3.xlsx_HTS.fit.csv files for log(x + 3) transformation. Plase check consoleOut6.txt for details\n" -fi - - -echo "Testing Multiple Plate log(x + 0) transformation Case .....\n\n" -#test file 7 -diff ~/harnesstest/multiPlate/test_n0.xlsx_HTS.fit.csv ~/harnesstest/multiPlate/original_csvfile/test_n0.xlsx_HTS.fit.csv > consoleOut7.txt -if [ $? == 0 ] -then - echo "NO diff between two test_n0.xlsx_HTS.fit.csv files for log(x + 0) transformation\n" - rm consoleOut7.txt -else - echo "There are diff between two test_n0.xlsx_HTS.fit.csv files for log(x + 0) transformation. Plase check consoleOut7.txt for details\n" -fi - - -echo "Testing Single Plate log(x + 0) transformation Case .....\n\n" -#test file 8 -diff ~/harnesstest/singlePlate/YPDAFEXglucoseTests_2-25-10_n0.xlsx_HTS.fit.csv ~/harnesstest/singlePlate/original_csvfile/YPDAFEXglucoseTests_2-25-10_n0.xlsx_HTS.fit.csv > consoleOut8.txt -if [ $? == 0 ] -then - echo "NO diff between two YPDAFEXglucoseTests_2-25-10_n0.xlsx_HTS.fit.csv files\n" - rm consoleOut8.txt -else - echo "There are diff between two YPDAFEXglucoseTests_2-25-10_n0.xlsx_HTS.fit.csv. Plase check consoleOut8.txt for details\n" -fi - -echo "Testing Single Plate log(x + 2) transformation Case .....\n\n" -#test file 9 -diff ~/harnesstest/singlePlate/YPDAFEXglucoseTests_2-25-10_n2.xlsx_HTS.fit.csv ~/harnesstest/singlePlate/original_csvfile/YPDAFEXglucoseTests_2-25-10_n2.xlsx_HTS.fit.csv > consoleOut9.txt -if [ $? == 0 ] -then - echo "NO diff between two YPDAFEXglucoseTests_2-25-10_n2.xlsx_HTS.fit.csv files\n" - rm consoleOut9.txt -else - echo "There are diff between two YPDAFEXglucoseTests_2-25-10_n2.xlsx_HTS.fit.csv. Plase check consoleOut9.txt for details\n" -fi - - -echo "Testing Single Plate log(x + 3) transformation Case .....\n\n" -#test file 10 -diff ~/harnesstest/singlePlate/YPDAFEXglucoseTests_2-25-10_n3.xlsx_HTS.fit.csv ~/harnesstest/singlePlate/original_csvfile/YPDAFEXglucoseTests_2-25-10_n3.xlsx_HTS.fit.csv > consoleOut10.txt -if [ $? == 0 ] -then - echo "NO diff between two YPDAFEXglucoseTests_2-25-10_n3.xlsx_HTS.fit.csv files\n" - rm consoleOut10.txt -else - echo "There are diff between two YPDAFEXglucoseTests_2-25-10_n3.xlsx_HTS.fit.csv. Plase check consoleOut10.txt for details\n" -fi - - - - -echo "The End of The Harness Test ....." \ No newline at end of file diff --git a/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/Ecoli_M9_growth_032510_fixed.xlsx b/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/Ecoli_M9_growth_032510_fixed.xlsx deleted file mode 100644 index fcc6e8a..0000000 Binary files a/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/Ecoli_M9_growth_032510_fixed.xlsx and /dev/null differ diff --git a/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/Ecoli_M9_growth_032510_fixed.xlsx_HTS.fit.csv b/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/Ecoli_M9_growth_032510_fixed.xlsx_HTS.fit.csv deleted file mode 100644 index ad7771a..0000000 --- a/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/Ecoli_M9_growth_032510_fixed.xlsx_HTS.fit.csv +++ /dev/null @@ -1,673 +0,0 @@ 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2010/multiPlate_Testing_Files/test_n2.xlsx b/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/test_n2.xlsx deleted file mode 100644 index 3775450..0000000 Binary files a/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/test_n2.xlsx and /dev/null differ diff --git a/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/test_n2.xlsx_HTS.fit.csv b/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/test_n2.xlsx_HTS.fit.csv deleted file mode 100644 index d04e87d..0000000 --- a/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/test_n2.xlsx_HTS.fit.csv +++ /dev/null @@ -1,193 +0,0 @@ -"","plate","well","media","strain","model","spec.growth","growth","lag.time","inoc.OD","good.fit","tank","asymp","reach" -"1","022510b.GLBRC200DH.1","A01",1,NA,"logistic 4-par.",0.025,0.474,3.18,1.043,2.402,"-","-",99.58 -"2","022510b.GLBRC200DH.1","B01",1,NA,"logistic 4-par.",0.025,0.459,3.598,1.028,2.605,"-","-",100 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2010/multiPlate_Testing_Files/test_n3.xlsx b/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/test_n3.xlsx deleted file mode 100644 index 3775450..0000000 Binary files a/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/test_n3.xlsx and /dev/null differ diff --git a/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/test_n3.xlsx_HTS.fit.csv b/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/test_n3.xlsx_HTS.fit.csv deleted file mode 100644 index ae10ac6..0000000 --- a/Testing/R code tests with xlsx files 2010/multiPlate_Testing_Files/test_n3.xlsx_HTS.fit.csv +++ /dev/null @@ -1,193 +0,0 @@ -"","plate","well","media","strain","model","spec.growth","growth","lag.time","inoc.OD","good.fit","tank","asymp","reach" -"1","022510b.GLBRC200DH.1","A01",1,NA,"logistic 4-par.",0.017,0.473,3.186,2.042,2.397,"-","-",100 -"2","022510b.GLBRC200DH.1","B01",1,NA,"logistic 4-par.",0.017,0.46,3.598,2.027,2.596,"-","-",100 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-library(MadHTS) -file = "/home/GLBRC/exie/harnesstest/multiPlate/test.xlsx" -out.dir = "/home/GLBRC/exie/outdir_test" -test = default.screen.fit(file, out.dir, out.dir, addOne = 1) - - -file = "/home/GLBRC/exie/harnesstest/multiPlate/Ecoli_M9_growth_032510_fixed.xlsx" -out.dir = "/home/GLBRC/exie/outdir_test" -test = default.screen.fit(file, out.dir, out.dir, addOne = 1) - - - -file = "/home/GLBRC/exie/harnesstest/singlePlate/YPDAFEXglucoseTests_2-25-10.xlsx" -out.dir = "/home/GLBRC/exie/outdir_test" -test_new = single.screen.fit(file, out.dir, out.dir, addOne = 1) - - - -file = "/home/GLBRC/exie/harnesstest/singlePlate/YPDAFEXglucoseTests_Reps2-3_3-9-10.xlsx" -out.dir = "/home/GLBRC/exie/outdir_test" -test_new = single.screen.fit(file, out.dir, out.dir, addOne = 1) - - -file = "/home/GLBRC/exie/harnesstest/multiPlate/test_n0.xlsx" -out.dir = "/home/GLBRC/exie/outdir_test" -test = default.screen.fit(file, out.dir, out.dir, addOne = 0) - - -file = "/home/GLBRC/exie/harnesstest/multiPlate/test_n2.xlsx" -out.dir = "/home/GLBRC/exie/outdir_test" -test = default.screen.fit(file, out.dir, out.dir, addOne = 2) - - - -file = "/home/GLBRC/exie/harnesstest/multiPlate/test_n3.xlsx" -out.dir = "/home/GLBRC/exie/outdir_test" -test = default.screen.fit(file, out.dir, out.dir, addOne = 3) - - -file = "/home/GLBRC/exie/harnesstest/singlePlate/YPDAFEXglucoseTests_2-25-10_n0.xlsx" -out.dir = "/home/GLBRC/exie/outdir_test" -test_new = single.screen.fit(file, out.dir, out.dir, addOne = 0) - - -file = "/home/GLBRC/exie/harnesstest/singlePlate/YPDAFEXglucoseTests_2-25-10_n2.xlsx" -out.dir = "/home/GLBRC/exie/outdir_test" -test_new = single.screen.fit(file, out.dir, out.dir, addOne = 2) - - -file = "/home/GLBRC/exie/harnesstest/singlePlate/YPDAFEXglucoseTests_2-25-10_n3.xlsx" -out.dir = "/home/GLBRC/exie/outdir_test" -test_new = single.screen.fit(file, out.dir, out.dir, addOne = 3) \ No newline at end of file diff --git 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+134632s,0.1123,0.1059,0.1112,0.1987,0.1503,0.1633,0.1124,0.1053,0.1089,0.1094,0.1089,0.1109,0.1092,0.1112,0.1148,0.3762,0.3474,0.3324,0.1131,0.1106,0.1131,0.1107,0.1167,0.1113,0.1089,0.1129,0.1141,0.5214,0.5114,0.5426,0.1124,0.1183,0.1065,109,0.1226,0.1128,0.1119,0.1105,0.1124,0.6487,0.6647,0.6328,0.1299,0.1413,0.1433,0.1769,0.1925,0.1277,0.1801,0.1614,0.1742,708,0.6028,744,0.5437,0.3813,0.3797,0.5811,429,0.2261,0.4535,0.4672,0.4459,0.7896,0.8334,0.7284,829,805,0.8128,0.7177,0.7885,0.6571,0.6672,0.7459,0.8673,0.8208,735,0.7885,0.8535,0.9537,0.8782,0.9085,0.6973,0.6666,0.9164,0.8548,0.8375,0.9233,909,0.9059,0.9723,0.8759,0.8961,0.9036,0.9316,0.8855 +Date of measurement: 2014-11-18/Time of measurement: 08:54:20,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +JP 30C No Shaking 48 hrs.mth,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +C:\Documents and Settings\All Users\Documents\Tecan\Magellan\mth\JP 30C No Shaking 48 hrs.mth,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +IC50_YPD-EMIM-AC-ANA_Y133t_PTK2-A_PTK2-B_Y133tpBlank_2014-NOV-18.wsp,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +C:\Documents and Settings\All Users\Documents\Tecan\Magellan\wsp\jeffp\IC50_YPD-EMIM-AC-ANA_Y133t_PTK2-A_PTK2-B_Y133tpBlank_2014-NOV-18.wsp,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +595nm,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Unknown user,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +infinite 200,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Instrument serial number: 810005503,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Plate,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Plate Description: [NUN96ft] - ThermoFischer Scientific-Nunclon 96 Flat Transparent,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Plate with Cover: Yes,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Barcode: No,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Temperature,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Mode: On,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Temperature: 30.0 °C,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Kinetic Cycle,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Number of Cycles: 200,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Absorbance,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Measurement Wavelength: 595 nm,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Measurement Bandwidth: 9 nm,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Number of Reads: 25,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Settle Time: 0 ms,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Label: Label1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Incubation,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Total kinetic run time: 1days 13h 23min 52s ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, diff --git a/Testing/test_input_files/Invalid_input_files/133 Well H1-H3 M200 UTF-8 fixed.csv b/Testing/test_input_files/Invalid_input_files/133 Well H1-H3 M200 UTF-8 fixed.csv new file mode 100644 index 0000000..03dbdb4 --- /dev/null +++ b/Testing/test_input_files/Invalid_input_files/133 Well H1-H3 M200 UTF-8 fixed.csv @@ -0,0 +1,229 @@ +Well positions,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Raw data,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +,,A1,A2,A3,A4,A5,A6,A7,A8,A9,A10,A11,A12,B1,B2,B3,B4,B5,B6,B7,B8,B9,B10,B11,B12,C1,C2,C3,C4,C5,C6,C7,C8,C9,C10,C11,C12,D1,D2,D3,D4,D5,D6,D7,D8,D9,D10,D11,D12,E1,E2,E3,E4,E5,E6,E7,E8,E9,E10,E11,E12,F1,F2,F3,F4,F5,F6,F7,F8,F9,F10,F11,F12,G1,G2,G3,G4,G5,G6,G7,G8,G9,G10,G11,G12,H1,H2,H3,H4,H5,H6,H7,H8,H9,H10,H11,H12 +0s,31.4 °C,0.1045,0.0992,0.1008,0.1014,0.1016,0.1016,0.1024,0.0997,0.1,0.1017,0.1005,0.1004,0.1062,0.1047,0.1042,0.1081,0.1025,0.1028,0.1014,0.1003,0.1032,0.1008,0.1004,0.1009,0.104,0.1045,0.1074,0.1049,0.1049,0.1074,0.1015,0.1066,0.1012,0.1029,0.1008,0.1008,0.1071,0.1055,0.1107,0.1066,0.1085,0.1162,0.1015,0.1186,0.1064,0.1081,0.1045,0.1011,0.1112,0.108,0.1092,0.1038,0.1041,0.1045,0.1092,0.1036,0.1135,0.1059,0.1024,0.1017,0.1098,0.1064,0.1057,0.1109,0.1103,0.1059,0.1071,0.1041,0.1057,0.1049,0.1056,0.1023,0.1036,0.1061,0.1066,0.103,0.1056,0.105,0.1053,0.112,0.1088,0.1076,0.1026,0.1011,0.1152,0.1097,0.1068,0.1131,0.1126,0.1192,0.1159,0.1033,0.1138,0.1175,0.1093,0.106 +677s,30.7 °C,0.1092,0.1078,0.1078,0.1099,0.1087,0.1074,0.1096,0.1055,0.1072,0.1058,0.1083,0.1075,0.1105,0.1122,0.1136,0.1148,0.1125,0.1135,0.1121,0.1082,0.1123,0.1105,0.1107,0.1066,0.107,0.1108,0.1118,0.111,0.1104,0.1145,0.1077,0.1106,0.1058,0.1055,0.1082,0.1042,0.1087,0.1075,0.1134,0.1096,0.1112,0.1212,0.1071,0.1221,0.1126,0.1129,0.1131,0.1059,0.1131,0.1101,0.1116,0.1108,0.1084,0.1097,0.1134,0.1093,0.1171,0.1116,0.1039,0.1031,0.1118,0.108,0.1077,0.1145,0.1124,0.1097,0.1108,0.1097,0.1092,0.1087,0.1091,0.1067,0.1052,0.1078,0.1093,0.1062,0.1071,0.1087,0.1074,0.1139,0.1121,0.1083,0.1061,0.1037,0.1174,0.1099,0.1069,0.116,0.1119,0.1195,0.1177,0.1073,0.1124,0.117,0.1129,0.1084 +1353s,30.5 °C,0.1111,0.1072,0.1109,0.111,0.1067,0.1096,0.111,0.1065,0.1078,0.1069,0.1078,0.1089,0.1094,0.1117,0.1153,0.1143,0.1119,0.1126,0.1119,0.1084,0.1122,0.1105,0.1118,0.1073,0.1077,0.1105,0.1123,0.1113,0.1121,0.1141,0.1087,0.1118,0.1062,0.1069,0.1095,0.1047,0.1089,0.1085,0.115,0.1102,0.1116,0.1211,0.1082,0.1226,0.1128,0.1138,0.1126,0.1055,0.1136,0.1105,0.1122,0.1119,0.108,0.111,0.1148,0.1099,0.1184,0.1129,0.1055,0.1039,0.1113,0.1085,0.1086,0.1117,0.1127,0.1101,0.1124,0.1107,0.1099,0.1094,0.1096,0.1077,0.105,0.1085,0.1108,0.107,0.1079,0.1091,0.1081,0.1155,0.1133,0.1085,0.1066,0.1046,0.1174,0.1107,0.1075,0.116,0.1121,0.1191,0.1173,0.1072,0.1113,0.1161,0.1132,0.109 +2030s,30.9 °C,0.1119,0.1064,0.1104,0.112,0.1065,0.1086,0.1122,0.1064,0.108,0.108,0.1083,0.1097,0.109,0.1117,0.1152,0.114,0.1113,0.1115,0.1112,0.1087,0.1127,0.1096,0.1114,0.108,0.1074,0.1107,0.1124,0.1112,0.112,0.1134,0.109,0.1121,0.1059,0.1066,0.1096,0.105,0.1085,0.1079,0.1113,0.1098,0.1114,0.1212,0.1085,0.121,0.1127,0.1134,0.113,0.1054,0.1134,0.1102,0.1123,0.1114,0.1066,0.1106,0.1161,0.1099,0.1192,0.1128,0.1054,0.1035,0.1105,0.1079,0.1079,0.1112,0.1123,0.1098,0.1122,0.1109,0.1097,0.109,0.1096,0.1071,0.1046,0.1082,0.1107,0.1063,0.1085,0.1087,0.1077,0.1155,0.1129,0.1082,0.1062,0.1036,0.1162,0.1094,0.1063,0.116,0.1118,0.1189,0.1175,0.1068,0.1118,0.1156,0.1126,0.1082 +2706s,31.0 °C,0.1117,0.1063,0.1107,0.1124,0.106,0.1083,0.1142,0.1062,0.108,0.1079,0.1085,0.1098,0.1088,0.1119,0.114,0.1138,0.1113,0.1112,0.1116,0.1089,0.1134,0.1095,0.1121,0.1082,0.1076,0.1111,0.1128,0.1113,0.1122,0.1146,0.1091,0.1126,0.1062,0.1065,0.11,0.1053,0.1087,0.1083,0.1103,0.1099,0.1114,0.1214,0.109,0.1241,0.1141,0.1136,0.1132,0.1054,0.1139,0.1107,0.1127,0.1114,0.1065,0.1108,0.1169,0.1104,0.1195,0.1132,0.1059,0.1035,0.1107,0.1083,0.108,0.1112,0.1123,0.1098,0.1126,0.1114,0.1105,0.1097,0.1096,0.1075,0.1045,0.1085,0.111,0.1065,0.1083,0.1087,0.108,0.1158,0.1142,0.1086,0.1062,0.1037,0.1163,0.1093,0.1062,0.1161,0.1116,0.1186,0.1177,0.107,0.112,0.1171,0.1122,0.1082 +3383s,31.5 °C,0.1119,0.106,0.1103,0.1125,0.1055,0.1085,0.1123,0.1062,0.1082,0.108,0.109,0.1104,0.1087,0.1123,0.1145,0.1138,0.1113,0.1109,0.1119,0.1091,0.1135,0.1093,0.1121,0.1084,0.1079,0.1115,0.1131,0.1125,0.1123,0.1149,0.1096,0.1129,0.1062,0.1067,0.1103,0.1056,0.1089,0.1087,0.1104,0.1098,0.1116,0.1212,0.1095,0.1216,0.1143,0.114,0.1139,0.1053,0.1142,0.1109,0.1134,0.1114,0.1065,0.1108,0.1161,0.1107,0.1198,0.1133,0.106,0.1038,0.1111,0.1085,0.1083,0.1114,0.1125,0.1101,0.1135,0.1121,0.111,0.11,0.1101,0.108,0.1048,0.1088,0.1115,0.1066,0.1079,0.1088,0.1083,0.1164,0.1139,0.109,0.1064,0.1039,0.1166,0.1093,0.1062,0.116,0.1114,0.118,0.1177,0.1074,0.1114,0.1164,0.1124,0.1084 +4059s,31.3 °C,0.1121,0.1062,0.1105,0.1125,0.1061,0.108,0.1126,0.1058,0.1086,0.1083,0.1094,0.111,0.1091,0.1127,0.1156,0.1141,0.1116,0.1111,0.1119,0.1093,0.1135,0.11,0.1122,0.1089,0.1082,0.1117,0.1134,0.113,0.1123,0.1142,0.1098,0.1131,0.1064,0.1067,0.1104,0.1058,0.1092,0.1089,0.1107,0.11,0.1115,0.1213,0.1098,0.1223,0.1146,0.1142,0.1149,0.1056,0.1147,0.1112,0.1135,0.1116,0.1066,0.1108,0.1246,0.111,0.12,0.1137,0.1078,0.1039,0.1113,0.1088,0.1084,0.1112,0.1124,0.11,0.1139,0.1124,0.1113,0.1101,0.1104,0.1083,0.1049,0.109,0.1119,0.1066,0.1074,0.1087,0.1086,0.1167,0.1136,0.1091,0.1066,0.1041,0.1168,0.1094,0.1064,0.1159,0.1113,0.1178,0.1183,0.1075,0.1111,0.1158,0.1127,0.1086 +4736s,31.4 °C,0.1123,0.106,0.1106,0.1125,0.1061,0.1082,0.1129,0.1059,0.1091,0.1085,0.11,0.1114,0.1092,0.1127,0.114,0.114,0.1115,0.1113,0.1122,0.1095,0.1139,0.1099,0.1129,0.1093,0.1084,0.1121,0.1136,0.1133,0.1126,0.1155,0.1101,0.1137,0.1066,0.107,0.1109,0.1064,0.1096,0.1092,0.1111,0.1102,0.1119,0.1213,0.1103,0.1232,0.1153,0.1144,0.1153,0.1059,0.1154,0.1116,0.1141,0.1118,0.1067,0.111,0.1225,0.1115,0.1204,0.1141,0.1084,0.1042,0.112,0.1092,0.1087,0.1117,0.1126,0.1102,0.1144,0.1129,0.1121,0.1107,0.1108,0.1087,0.1052,0.1096,0.1123,0.1068,0.1079,0.1089,0.1087,0.1174,0.113,0.1097,0.1069,0.1044,0.1171,0.1098,0.1066,0.1161,0.1114,0.1174,0.1195,0.1081,0.1123,0.117,0.1131,0.109 +5412s,31.5 °C,0.1124,0.1061,0.1109,0.1126,0.106,0.1081,0.113,0.1059,0.1092,0.1087,0.1106,0.1117,0.1092,0.1129,0.1146,0.1141,0.1115,0.1112,0.1124,0.1098,0.114,0.11,0.1132,0.1096,0.1086,0.1123,0.1139,0.1135,0.1126,0.1149,0.1104,0.114,0.1068,0.1072,0.1113,0.1071,0.1098,0.1093,0.1116,0.1103,0.1119,0.1215,0.1108,0.1246,0.1156,0.1149,0.1161,0.1058,0.1155,0.1119,0.1145,0.1119,0.1067,0.1111,0.1194,0.112,0.1209,0.1145,0.1086,0.1045,0.1123,0.1095,0.1091,0.1116,0.1127,0.1103,0.115,0.1137,0.1124,0.1109,0.1112,0.1091,0.1055,0.1098,0.1128,0.1068,0.1083,0.1089,0.1098,0.1181,0.1133,0.1101,0.1074,0.1048,0.1177,0.1101,0.1068,0.1162,0.1115,0.1177,0.1201,0.1085,0.1125,0.1167,0.1137,0.1094 +6089s,31.6 °C,0.1125,0.1061,0.1108,0.1127,0.1061,0.1082,0.1131,0.106,0.1092,0.109,0.111,0.112,0.1093,0.1129,0.1162,0.1141,0.1117,0.1111,0.1124,0.1099,0.1137,0.1101,0.1132,0.1098,0.1088,0.1124,0.114,0.1135,0.1127,0.1149,0.1107,0.1144,0.1069,0.1073,0.1117,0.1075,0.1101,0.1095,0.1119,0.1103,0.1117,0.1217,0.1109,0.1263,0.1159,0.1153,0.1172,0.106,0.1162,0.112,0.1147,0.1117,0.1068,0.111,0.1192,0.1124,0.1219,0.115,0.109,0.1047,0.1126,0.1097,0.1094,0.1117,0.1127,0.1103,0.1157,0.1141,0.1129,0.1111,0.1116,0.1095,0.1056,0.1101,0.113,0.1069,0.1082,0.1089,0.1101,0.1187,0.1135,0.1106,0.1077,0.105,0.1184,0.1106,0.1072,0.1162,0.1115,0.1173,0.1213,0.1091,0.1129,0.1172,0.1141,0.1098 +6765s,31.5 °C,0.1125,0.1062,0.111,0.1128,0.1062,0.1083,0.1134,0.1061,0.1094,0.1091,0.1115,0.1124,0.1094,0.1131,0.1147,0.114,0.1118,0.1112,0.1127,0.1102,0.114,0.1103,0.1137,0.1102,0.1088,0.1125,0.1141,0.1132,0.1128,0.1153,0.1111,0.1146,0.107,0.1074,0.1121,0.1083,0.1102,0.1095,0.1118,0.1104,0.1122,0.1217,0.1112,0.1251,0.1165,0.1155,0.1173,0.1065,0.1164,0.1122,0.1149,0.1119,0.1069,0.1112,0.1292,0.1128,0.1219,0.1154,0.1094,0.105,0.1131,0.11,0.1097,0.1118,0.1129,0.1104,0.1162,0.1148,0.1135,0.1117,0.1119,0.1101,0.1059,0.1106,0.1133,0.107,0.1076,0.109,0.1103,0.1194,0.1131,0.1111,0.1082,0.1053,0.119,0.111,0.1075,0.1164,0.1115,0.1171,0.1224,0.1098,0.1135,0.1177,0.1146,0.1104 +7442s,31.4 °C,0.1124,0.1062,0.1111,0.1131,0.1064,0.1085,0.1136,0.1062,0.1096,0.1094,0.1119,0.1126,0.1092,0.113,0.1148,0.1146,0.1119,0.1112,0.1128,0.1104,0.114,0.1102,0.1139,0.1106,0.1089,0.1126,0.1142,0.1136,0.113,0.1158,0.1113,0.1149,0.1072,0.1077,0.1125,0.1081,0.1105,0.1097,0.1124,0.1107,0.1125,0.122,0.1116,0.125,0.117,0.1159,0.1183,0.1065,0.1169,0.1126,0.1154,0.112,0.1071,0.1114,0.1278,0.1133,0.1232,0.116,0.1098,0.1054,0.1135,0.1102,0.1099,0.112,0.1131,0.1105,0.1168,0.1154,0.1139,0.1119,0.1124,0.1107,0.1063,0.111,0.1137,0.1072,0.1072,0.1091,0.1109,0.1204,0.1144,0.1117,0.1087,0.1059,0.1198,0.1116,0.1079,0.1165,0.112,0.1173,0.1235,0.1106,0.1143,0.1178,0.1153,0.1112 +8119s,31.6 °C,0.1123,0.1062,0.111,0.1131,0.1064,0.1086,0.1137,0.1062,0.1098,0.1096,0.1125,0.1126,0.1093,0.1132,0.1152,0.1148,0.1121,0.1114,0.1128,0.1105,0.114,0.1102,0.1143,0.1108,0.1091,0.1127,0.1143,0.1135,0.1132,0.1155,0.1114,0.1151,0.1073,0.1078,0.1128,0.1087,0.1106,0.1098,0.1124,0.1108,0.1127,0.1222,0.1116,0.1259,0.1173,0.1163,0.1184,0.1069,0.1171,0.1128,0.1156,0.1123,0.1072,0.1115,0.1283,0.1137,0.1232,0.1163,0.1101,0.1056,0.114,0.1105,0.1101,0.1122,0.1135,0.1106,0.1174,0.1162,0.1148,0.1124,0.113,0.1112,0.1065,0.1114,0.1142,0.1072,0.1074,0.1092,0.1118,0.1212,0.1153,0.1122,0.1091,0.1062,0.1208,0.1121,0.1082,0.1166,0.1118,0.1169,0.1247,0.1113,0.1155,0.1183,0.116,0.1118 +8795s,31.3 °C,0.1124,0.1063,0.1111,0.1135,0.1066,0.1089,0.1138,0.1063,0.1099,0.1098,0.1127,0.113,0.1095,0.1133,0.1132,0.1148,0.1125,0.1116,0.1129,0.1107,0.1143,0.1105,0.1143,0.1111,0.1091,0.1129,0.1146,0.1139,0.1136,0.1156,0.1118,0.1155,0.1075,0.108,0.1133,0.1093,0.1109,0.1101,0.1127,0.1111,0.113,0.1224,0.1121,0.1257,0.1179,0.1169,0.1164,0.1073,0.1177,0.1131,0.116,0.1126,0.1074,0.1119,0.129,0.1143,0.1233,0.1171,0.1106,0.106,0.1142,0.111,0.1106,0.1123,0.1137,0.1109,0.1182,0.1169,0.1154,0.1131,0.1135,0.1119,0.107,0.1119,0.1149,0.1074,0.1076,0.1094,0.1124,0.1223,0.1172,0.1129,0.1096,0.1067,0.1219,0.113,0.1089,0.1165,0.1119,0.1173,0.1262,0.1121,0.1161,0.1199,0.1168,0.1126 +9472s,31.4 °C,0.1126,0.1063,0.1112,0.1137,0.1067,0.1091,0.1139,0.1064,0.1099,0.1099,0.113,0.1134,0.1097,0.1133,0.1141,0.115,0.1129,0.112,0.113,0.1107,0.1144,0.1108,0.1146,0.1114,0.1094,0.113,0.1146,0.1142,0.1139,0.1161,0.112,0.1157,0.1076,0.1082,0.1136,0.1093,0.1111,0.1102,0.1128,0.1112,0.1133,0.1224,0.1123,0.1255,0.1181,0.1174,0.1159,0.1077,0.1181,0.1133,0.1162,0.1128,0.1074,0.1121,0.1303,0.115,0.1247,0.1177,0.111,0.1062,0.1147,0.1114,0.111,0.1127,0.1139,0.1112,0.1193,0.1176,0.1162,0.1137,0.1144,0.1124,0.1074,0.1125,0.1155,0.1077,0.1072,0.1096,0.1129,0.1237,0.118,0.1136,0.1102,0.1072,0.1233,0.1141,0.1099,0.117,0.1122,0.1184,0.1285,0.1133,0.1173,0.1212,0.118,0.1133 +10148s,31.2 °C,0.1125,0.1064,0.1112,0.1139,0.1069,0.1092,0.1141,0.1064,0.1101,0.11,0.1132,0.1135,0.1097,0.1132,0.1157,0.1155,0.1132,0.1123,0.1133,0.1108,0.1145,0.111,0.1152,0.1115,0.1094,0.1131,0.1147,0.1145,0.114,0.1169,0.1121,0.1159,0.1076,0.1082,0.114,0.1095,0.1113,0.1101,0.1128,0.1116,0.1134,0.1226,0.1126,0.1259,0.1183,0.1178,0.1164,0.1076,0.1181,0.1136,0.1166,0.1129,0.1076,0.1123,0.1305,0.1152,0.1247,0.1183,0.1115,0.1065,0.115,0.1116,0.1113,0.1131,0.1142,0.1115,0.12,0.1184,0.1167,0.1142,0.115,0.1131,0.1078,0.113,0.1159,0.1079,0.1089,0.1098,0.1138,0.125,0.1188,0.1144,0.111,0.1078,0.1249,0.115,0.1107,0.1173,0.1123,0.1187,0.1308,0.1145,0.1187,0.1227,0.1191,0.1143 +10825s,31.5 °C,0.1132,0.1064,0.1113,0.1141,0.107,0.1092,0.1141,0.1065,0.1101,0.1101,0.1133,0.1136,0.1096,0.1132,0.1161,0.1161,0.1134,0.1125,0.1135,0.1112,0.1144,0.111,0.1156,0.1117,0.1094,0.1129,0.1146,0.1148,0.1143,0.1174,0.1122,0.116,0.1077,0.1084,0.1142,0.1093,0.1112,0.1101,0.1129,0.1119,0.1136,0.123,0.1127,0.1265,0.1184,0.1183,0.1169,0.1078,0.1185,0.1137,0.1166,0.1133,0.1077,0.1127,0.1316,0.1157,0.1249,0.1189,0.1118,0.1068,0.1155,0.1118,0.1114,0.1134,0.1146,0.1117,0.121,0.1192,0.1174,0.1146,0.1158,0.1138,0.1082,0.1135,0.1165,0.1081,0.1075,0.1099,0.1146,0.1264,0.1207,0.1152,0.1117,0.1085,0.1264,0.116,0.1113,0.1175,0.1127,0.118,0.1331,0.1157,0.1202,0.1231,0.1204,0.1155 +11501s,31.4 °C,0.113,0.1065,0.1113,0.1144,0.1071,0.1095,0.1143,0.1066,0.1102,0.1102,0.1136,0.1138,0.1095,0.1132,0.115,0.1162,0.1135,0.1124,0.1133,0.1111,0.1146,0.1108,0.1156,0.1119,0.1094,0.1131,0.1147,0.1152,0.1147,0.1171,0.1124,0.1162,0.1077,0.1084,0.1145,0.1101,0.1112,0.1102,0.113,0.1122,0.1143,0.1234,0.1129,0.1265,0.1188,0.1184,0.1171,0.1079,0.1188,0.1139,0.117,0.1137,0.108,0.113,0.1323,0.1161,0.1252,0.1195,0.1123,0.107,0.1157,0.1122,0.1115,0.1137,0.115,0.1118,0.1216,0.1201,0.1182,0.1151,0.1165,0.1147,0.1085,0.1141,0.1172,0.1083,0.1074,0.1103,0.1156,0.128,0.1211,0.1161,0.1124,0.1091,0.1286,0.1173,0.1122,0.1179,0.1129,0.1182,0.1356,0.1173,0.1221,0.1251,0.1216,0.1165 +12178s,31.2 °C,0.1132,0.1065,0.1114,0.1147,0.1073,0.1097,0.1145,0.1066,0.1103,0.1103,0.1138,0.1139,0.1097,0.1134,0.1137,0.1165,0.1139,0.1127,0.1132,0.1112,0.1145,0.1109,0.1155,0.1119,0.1094,0.1131,0.1148,0.1152,0.115,0.1165,0.1126,0.1164,0.1079,0.1086,0.1148,0.1101,0.1114,0.1105,0.1131,0.1124,0.1145,0.1239,0.1131,0.1267,0.1192,0.1189,0.1178,0.1083,0.1192,0.1141,0.1171,0.114,0.1082,0.1135,0.1333,0.1167,0.1258,0.1202,0.1127,0.1074,0.1163,0.1127,0.112,0.1141,0.1154,0.1124,0.1227,0.121,0.1192,0.116,0.1175,0.1155,0.109,0.1149,0.1182,0.1086,0.1087,0.1107,0.1168,0.1301,0.1214,0.1173,0.1134,0.1099,0.1305,0.1188,0.1135,0.1183,0.1132,0.1185,0.1389,0.1186,0.1239,0.1273,0.1234,0.118 +12854s,31.4 °C,0.1129,0.1065,0.1114,0.115,0.1075,0.1099,0.1147,0.1067,0.1103,0.1104,0.1139,0.1141,0.1097,0.1134,0.1149,0.1167,0.1142,0.113,0.1134,0.1111,0.1146,0.1112,0.1159,0.1121,0.1095,0.1132,0.1149,0.1157,0.1154,0.1181,0.1127,0.1166,0.1079,0.1087,0.1151,0.1105,0.1116,0.1105,0.1131,0.1128,0.1148,0.1243,0.1132,0.1269,0.1193,0.1194,0.1183,0.1087,0.1193,0.1143,0.1173,0.1143,0.1084,0.1138,0.1338,0.117,0.1266,0.1208,0.1132,0.1076,0.1166,0.1128,0.1123,0.1147,0.1159,0.1127,0.1238,0.1218,0.12,0.1168,0.1184,0.1164,0.1095,0.1155,0.1188,0.1089,0.1081,0.111,0.1179,0.1321,0.1227,0.1185,0.1144,0.1107,0.1333,0.1204,0.1148,0.1189,0.1137,0.1198,0.1429,0.1206,0.1261,0.1299,0.1253,0.1196 +13531s,31.3 °C,0.113,0.1066,0.1115,0.1152,0.1077,0.1101,0.115,0.1067,0.1104,0.1105,0.1139,0.1143,0.1096,0.1133,0.116,0.1173,0.1145,0.1134,0.1136,0.1113,0.1149,0.1115,0.1162,0.1122,0.1095,0.1132,0.1149,0.116,0.1157,0.1184,0.1127,0.1166,0.108,0.1088,0.1154,0.1104,0.1115,0.1105,0.1131,0.1133,0.1151,0.1242,0.1136,0.1274,0.1194,0.12,0.1189,0.1088,0.1197,0.1143,0.1174,0.1148,0.1087,0.1143,0.135,0.1176,0.1263,0.1217,0.1136,0.1079,0.1169,0.1129,0.1124,0.1152,0.1163,0.1128,0.1248,0.123,0.1206,0.1173,0.1194,0.1173,0.11,0.1161,0.1196,0.1093,0.1089,0.1112,0.1192,0.1344,0.1249,0.1197,0.1155,0.1117,0.1357,0.1219,0.116,0.1192,0.1139,0.1207,0.1464,0.1225,0.1281,0.1311,0.1273,0.1214 +14207s,31.3 °C,0.1129,0.1066,0.1116,0.1156,0.1077,0.1102,0.1152,0.1068,0.1105,0.1106,0.1143,0.1145,0.1096,0.1133,0.1167,0.1176,0.1148,0.1135,0.1136,0.1114,0.1149,0.1112,0.1163,0.1124,0.1095,0.1133,0.1149,0.1166,0.1162,0.1189,0.1129,0.1169,0.108,0.1088,0.1157,0.1107,0.1115,0.1106,0.1131,0.1137,0.1156,0.1249,0.1136,0.1274,0.1197,0.12,0.1193,0.1088,0.1198,0.1145,0.1177,0.1153,0.109,0.1148,0.1355,0.1179,0.1276,0.1224,0.1142,0.1082,0.1174,0.1134,0.1127,0.1158,0.117,0.1134,0.1261,0.1243,0.1221,0.1182,0.1208,0.1183,0.1105,0.117,0.1206,0.1097,0.1093,0.1117,0.1209,0.1369,0.1276,0.1212,0.1167,0.1127,0.1391,0.1241,0.1177,0.12,0.1145,0.1204,0.1509,0.1251,0.1313,0.134,0.1294,0.1234 +14884s,31.2 °C,0.1128,0.1066,0.1116,0.1159,0.108,0.1105,0.1156,0.1068,0.1106,0.1107,0.1144,0.1144,0.1099,0.1134,0.1141,0.1181,0.1154,0.114,0.1136,0.1115,0.115,0.1114,0.1164,0.1126,0.1097,0.1134,0.115,0.1167,0.1167,0.1192,0.113,0.117,0.1082,0.109,0.1159,0.1108,0.112,0.1108,0.1131,0.1141,0.1162,0.1254,0.1138,0.1278,0.1202,0.1206,0.1201,0.1093,0.1203,0.1148,0.1178,0.1158,0.1094,0.1155,0.1366,0.1186,0.1281,0.1234,0.1147,0.1085,0.1179,0.1139,0.113,0.1163,0.1177,0.114,0.1275,0.1256,0.1234,0.1194,0.1221,0.1195,0.1112,0.1179,0.1219,0.1101,0.1099,0.1123,0.1225,0.14,0.1306,0.123,0.1179,0.1139,0.1428,0.1267,0.1196,0.1207,0.115,0.1202,0.156,0.1277,0.1348,0.1381,0.1323,0.1254 +15560s,31.2 °C,0.1129,0.1066,0.1115,0.1161,0.1081,0.1108,0.1157,0.1068,0.1107,0.1107,0.1147,0.1145,0.1098,0.1134,0.1157,0.1183,0.1156,0.1143,0.1137,0.1115,0.1149,0.1116,0.1166,0.1126,0.1097,0.1135,0.115,0.1173,0.1172,0.1197,0.1132,0.1171,0.1082,0.109,0.1161,0.1114,0.1119,0.1107,0.1132,0.1144,0.1166,0.1259,0.1141,0.1271,0.1201,0.1209,0.1204,0.1092,0.1204,0.1149,0.118,0.1162,0.1097,0.116,0.1373,0.1188,0.1285,0.1239,0.1152,0.1089,0.1182,0.1141,0.1133,0.1169,0.1183,0.1145,0.129,0.1268,0.1242,0.1202,0.1234,0.1208,0.1118,0.1189,0.1229,0.1106,0.1102,0.1126,0.1245,0.1429,0.1327,0.1247,0.1195,0.1151,0.1465,0.129,0.1216,0.1213,0.1155,0.122,0.1615,0.1302,0.1376,0.1405,0.135,0.1281 +16237s,31.0 °C,0.1134,0.1067,0.1116,0.1165,0.1083,0.1109,0.116,0.1069,0.1106,0.1107,0.1145,0.1145,0.1097,0.1134,0.1156,0.1188,0.116,0.1147,0.1138,0.1115,0.1149,0.1116,0.1168,0.1127,0.1097,0.1134,0.1151,0.1176,0.1177,0.1204,0.1132,0.1172,0.1081,0.1091,0.1164,0.1111,0.1118,0.1108,0.1132,0.115,0.117,0.1262,0.1142,0.1283,0.1203,0.1215,0.1211,0.1094,0.1205,0.115,0.1182,0.1168,0.11,0.1166,0.1382,0.1192,0.1288,0.1247,0.1159,0.1093,0.1187,0.1142,0.1136,0.1176,0.119,0.115,0.1306,0.1283,0.1254,0.1213,0.1251,0.1221,0.1123,0.1199,0.1239,0.1111,0.1112,0.1131,0.1265,0.1464,0.1341,0.1266,0.121,0.1164,0.1509,0.1317,0.1238,0.1223,0.1162,0.1229,0.1679,0.1334,0.141,0.1442,0.1379,0.1307 +16914s,31.0 °C,0.1133,0.1067,0.1116,0.1169,0.1085,0.1112,0.1164,0.1069,0.1107,0.1108,0.1149,0.1147,0.1098,0.1135,0.1155,0.1195,0.1165,0.1152,0.1141,0.1117,0.1151,0.1119,0.1171,0.1128,0.1097,0.1136,0.1151,0.1183,0.1183,0.1212,0.1133,0.1174,0.1083,0.1092,0.1166,0.1112,0.112,0.1109,0.1132,0.1157,0.1177,0.127,0.1144,0.1284,0.1206,0.122,0.1217,0.1098,0.1208,0.1152,0.1184,0.1175,0.1106,0.1175,0.1393,0.12,0.1297,0.1258,0.1165,0.1097,0.1191,0.1147,0.1139,0.1185,0.12,0.1158,0.1323,0.1298,0.1268,0.1225,0.1267,0.1239,0.1132,0.1211,0.1253,0.1117,0.1117,0.1139,0.1287,0.1503,0.1357,0.1288,0.1229,0.1181,0.1557,0.135,0.1263,0.1234,0.117,0.1228,0.1749,0.1372,0.1454,0.1481,0.1417,0.1339 +17590s,31.0 °C,0.1133,0.1068,0.1117,0.1172,0.1087,0.1114,0.1144,0.1069,0.1107,0.1108,0.115,0.1145,0.1098,0.1134,0.1153,0.12,0.1168,0.1155,0.114,0.1116,0.1151,0.1118,0.1173,0.113,0.1098,0.1136,0.1152,0.1189,0.1189,0.1217,0.1134,0.1175,0.1083,0.1093,0.1169,0.1116,0.1119,0.1109,0.1133,0.1163,0.1185,0.1274,0.1145,0.1284,0.1209,0.1223,0.1221,0.1098,0.1211,0.1153,0.1185,0.1182,0.1109,0.1182,0.1402,0.1204,0.1299,0.1268,0.1172,0.1101,0.1198,0.115,0.1142,0.1196,0.121,0.1164,0.1343,0.1318,0.1283,0.1239,0.1286,0.1256,0.1141,0.1224,0.1269,0.1124,0.1122,0.1146,0.131,0.155,0.1397,0.1314,0.125,0.1198,0.1615,0.1386,0.1292,0.1247,0.1179,0.1241,0.1825,0.1413,0.1504,0.1529,0.1455,0.1374 +18267s,31.2 °C,0.1133,0.1067,0.1118,0.1177,0.1089,0.1117,0.1144,0.107,0.1108,0.1109,0.1149,0.1147,0.1098,0.1135,0.116,0.1208,0.1175,0.116,0.1141,0.1119,0.1152,0.1118,0.1174,0.1131,0.1097,0.1135,0.1152,0.1194,0.1196,0.1221,0.1134,0.1176,0.1084,0.1094,0.117,0.1115,0.112,0.1109,0.1133,0.1169,0.119,0.1282,0.1146,0.1285,0.1209,0.1225,0.1224,0.11,0.1214,0.1154,0.1186,0.119,0.1114,0.1191,0.1414,0.1209,0.1304,0.1278,0.1177,0.1105,0.1203,0.1151,0.1144,0.1204,0.122,0.1171,0.1364,0.1338,0.1301,0.1251,0.1307,0.1274,0.1149,0.1238,0.1287,0.113,0.1128,0.1153,0.1341,0.1596,0.1426,0.1339,0.1272,0.1217,0.1675,0.1423,0.1321,0.1259,0.1189,0.1253,0.1913,0.1456,0.1557,0.1578,0.1498,0.1409 +18943s,31.2 °C,0.1133,0.1067,0.1118,0.1181,0.1091,0.112,0.1145,0.1071,0.1109,0.111,0.1151,0.1149,0.1098,0.1134,0.1151,0.1212,0.1179,0.1165,0.114,0.1118,0.1153,0.1118,0.1174,0.1132,0.1098,0.1136,0.1153,0.1201,0.1203,0.1229,0.1136,0.1177,0.1085,0.1095,0.1173,0.1119,0.112,0.111,0.1133,0.1175,0.1201,0.1292,0.1147,0.1285,0.1212,0.1228,0.1227,0.1103,0.1216,0.1155,0.1188,0.1199,0.1121,0.1201,0.1428,0.1216,0.1311,0.1291,0.1184,0.1111,0.1207,0.1157,0.1147,0.1215,0.1233,0.1179,0.1385,0.1358,0.1321,0.1266,0.1329,0.1296,0.116,0.1257,0.1306,0.114,0.1134,0.1163,0.1378,0.1654,0.1466,0.1372,0.1298,0.124,0.1742,0.1471,0.1356,0.1276,0.1201,0.126,0.2012,0.151,0.1621,0.1641,0.1545,0.145 +19620s,31.1 °C,0.1133,0.1068,0.1118,0.1186,0.1093,0.1123,0.1145,0.1071,0.111,0.111,0.1152,0.1149,0.11,0.1136,0.1147,0.122,0.1184,0.1169,0.1141,0.112,0.1154,0.1118,0.1173,0.1132,0.1098,0.1136,0.1153,0.1206,0.1211,0.123,0.1136,0.1178,0.1086,0.1096,0.1175,0.1116,0.1121,0.1111,0.1134,0.1182,0.121,0.1299,0.1149,0.1288,0.1216,0.1235,0.1232,0.1108,0.1218,0.1158,0.1189,0.1207,0.1127,0.1212,0.1439,0.122,0.1315,0.1302,0.1192,0.1114,0.1212,0.1162,0.1151,0.1226,0.1246,0.119,0.1408,0.1378,0.1338,0.1285,0.1351,0.1321,0.1173,0.1277,0.1327,0.115,0.1143,0.1172,0.141,0.1711,0.1512,0.1406,0.1328,0.1263,0.1821,0.1521,0.1395,0.1293,0.1213,0.1273,0.2121,0.1562,0.1686,0.1706,0.1599,0.1494 +20296s,31.2 °C,0.1132,0.1068,0.1119,0.1191,0.1096,0.1125,0.1146,0.1071,0.111,0.1111,0.1153,0.115,0.11,0.1137,0.1152,0.1225,0.119,0.1177,0.1142,0.1119,0.1152,0.1121,0.1176,0.1133,0.11,0.1137,0.1153,0.1215,0.122,0.1246,0.1138,0.118,0.1086,0.1097,0.1177,0.1118,0.1121,0.111,0.1135,0.1191,0.1219,0.1309,0.1151,0.1287,0.1216,0.1239,0.1239,0.111,0.122,0.1159,0.1192,0.1217,0.1134,0.1224,0.1452,0.1226,0.1322,0.1315,0.1199,0.112,0.1221,0.1166,0.1155,0.1242,0.1261,0.1202,0.144,0.1406,0.136,0.1307,0.1381,0.1345,0.1185,0.1296,0.1349,0.116,0.1154,0.1183,0.1447,0.1778,0.1564,0.1445,0.136,0.1289,0.1905,0.1571,0.1439,0.1312,0.1227,0.1295,0.2245,0.1623,0.1754,0.1771,0.1662,0.1548 +20973s,31.0 °C,0.1127,0.1068,0.1118,0.1195,0.1098,0.1128,0.1146,0.1071,0.111,0.1111,0.1154,0.1149,0.1099,0.1135,0.1159,0.1233,0.1196,0.1181,0.1144,0.1119,0.1156,0.1121,0.1178,0.1134,0.1099,0.1137,0.1153,0.1224,0.1229,0.1256,0.1138,0.118,0.1086,0.1097,0.118,0.1117,0.112,0.111,0.1135,0.1199,0.1228,0.1317,0.1153,0.1287,0.1217,0.1242,0.1244,0.111,0.1221,0.116,0.1192,0.1228,0.114,0.1236,0.1467,0.1233,0.1327,0.1327,0.1204,0.1125,0.1225,0.1168,0.1157,0.1254,0.1277,0.1212,0.1467,0.143,0.1378,0.1323,0.1408,0.1372,0.1198,0.1318,0.1376,0.1171,0.1175,0.1193,0.1493,0.1853,0.1624,0.1485,0.1392,0.1317,0.1997,0.1632,0.1487,0.1332,0.1243,0.1309,0.2379,0.1692,0.1831,0.1842,0.1731,0.1603 +21649s,31.0 °C,0.115,0.1076,0.1129,0.1219,0.1107,0.1133,0.1148,0.1071,0.1104,0.1108,0.1117,0.1216,0.1112,0.113,0.1174,0.1258,0.1229,0.1201,0.1154,0.1122,0.1154,0.113,0.1183,0.1121,0.1109,0.1148,0.1162,0.1235,0.1253,0.1299,0.1133,0.1192,0.1082,0.1099,0.1183,0.1086,0.1131,0.1125,0.1147,0.1226,0.1227,0.1328,0.1169,0.129,0.1219,0.1253,0.1273,0.1113,0.1233,0.117,0.1204,0.1255,0.1148,0.1274,0.1457,0.1262,0.1338,0.1374,0.1204,0.1127,0.1243,0.1182,0.1173,0.1293,0.13,0.123,0.1527,0.1486,0.1431,0.1359,0.1483,0.1382,0.1244,0.1334,0.1448,0.1186,0.1174,0.122,0.1508,0.1983,0.1728,0.1542,0.1445,0.1353,0.2164,0.1737,0.1562,0.1362,0.1299,0.1369,0.2611,0.1849,0.1975,0.2019,0.1865,0.1664 +22326s,31.1 °C,0.1144,0.1074,0.1128,0.1221,0.1108,0.1138,0.1145,0.1068,0.1105,0.1107,0.1114,0.1218,0.1111,0.1128,0.1161,0.1272,0.1233,0.1208,0.1152,0.1124,0.1153,0.1124,0.1182,0.112,0.1108,0.1148,0.1161,0.1241,0.1265,0.1304,0.1133,0.1193,0.1081,0.1098,0.1184,0.1086,0.1133,0.1125,0.1146,0.1238,0.1241,0.1343,0.1167,0.1294,0.1223,0.1256,0.1276,0.1114,0.1235,0.1172,0.1207,0.1269,0.1157,0.1291,0.1471,0.127,0.1352,0.1391,0.1212,0.1133,0.1253,0.1187,0.1177,0.131,0.1321,0.1243,0.1565,0.1521,0.1465,0.1384,0.152,0.1411,0.1265,0.136,0.1484,0.12,0.1191,0.1237,0.1559,0.2084,0.1804,0.1594,0.149,0.1387,0.2287,0.1818,0.1623,0.1389,0.1319,0.1389,0.2782,0.1934,0.2084,0.2119,0.1958,0.1733 +23002s,31.2 °C,0.1144,0.1074,0.1128,0.1227,0.1111,0.1141,0.1147,0.1068,0.1105,0.1108,0.1114,0.1217,0.1111,0.1128,0.1152,0.128,0.1239,0.1213,0.1151,0.1125,0.1154,0.1124,0.1181,0.1122,0.1108,0.1148,0.116,0.1252,0.1278,0.1316,0.1134,0.1193,0.1081,0.1098,0.1185,0.1094,0.1131,0.1124,0.1144,0.1247,0.1254,0.1354,0.1167,0.1291,0.1224,0.126,0.1279,0.112,0.1237,0.1173,0.1207,0.1283,0.1166,0.1309,0.1489,0.1278,0.135,0.141,0.1222,0.1138,0.1259,0.1192,0.1179,0.133,0.134,0.1262,0.1604,0.1554,0.1495,0.1411,0.1559,0.1447,0.1283,0.139,0.1521,0.1214,0.12,0.1252,0.1612,0.2192,0.1884,0.1652,0.1532,0.1425,0.2423,0.1907,0.169,0.1414,0.1339,0.1413,0.2966,0.2029,0.2194,0.223,0.2056,0.1814 +23679s,31.1 °C,0.1146,0.1075,0.1128,0.1236,0.1115,0.1144,0.1148,0.1069,0.1105,0.1108,0.1115,0.1222,0.1112,0.113,0.1175,0.1293,0.1248,0.1225,0.1155,0.1124,0.1155,0.1129,0.1184,0.1123,0.1108,0.1149,0.1161,0.1264,0.1291,0.1338,0.1135,0.1195,0.1082,0.11,0.1188,0.109,0.113,0.1125,0.1147,0.1262,0.1264,0.1369,0.1171,0.1293,0.1222,0.1267,0.1288,0.1123,0.124,0.1175,0.121,0.1301,0.1177,0.133,0.1511,0.1288,0.1369,0.1432,0.1233,0.1146,0.127,0.1196,0.1188,0.1354,0.1363,0.1278,0.1653,0.1599,0.1525,0.1442,0.1609,0.1485,0.1309,0.1424,0.1566,0.1233,0.122,0.1272,0.1682,0.2318,0.1975,0.1718,0.1591,0.1472,0.2576,0.2005,0.1772,0.1451,0.1366,0.144,0.3192,0.215,0.2316,0.2353,0.2175,0.1907 +24356s,31.0 °C,0.1143,0.1074,0.1127,0.124,0.1117,0.1149,0.1148,0.1069,0.1105,0.1109,0.1114,0.1218,0.1112,0.1128,0.1168,0.1304,0.1254,0.1231,0.1154,0.1124,0.1156,0.1128,0.1185,0.1122,0.1108,0.1149,0.1161,0.1276,0.1305,0.1348,0.1136,0.1195,0.1081,0.11,0.119,0.1093,0.1132,0.1126,0.1148,0.1279,0.1279,0.1384,0.1175,0.13,0.1227,0.1274,0.1298,0.1123,0.1244,0.1175,0.121,0.1322,0.1188,0.1352,0.153,0.1298,0.1371,0.1455,0.1246,0.1153,0.1282,0.1203,0.1193,0.138,0.1389,0.1298,0.1709,0.1645,0.1568,0.1478,0.1664,0.1525,0.1337,0.1459,0.1617,0.1251,0.1234,0.1294,0.1754,0.2451,0.2072,0.1783,0.165,0.1516,0.2749,0.2117,0.1856,0.1487,0.1397,0.1471,0.342,0.229,0.2475,0.25,0.2295,0.2004 +25032s,31.4 °C,0.1145,0.1074,0.1127,0.1246,0.112,0.1152,0.1147,0.1068,0.1105,0.1108,0.1113,0.1215,0.1111,0.1127,0.1185,0.1317,0.1263,0.1239,0.1155,0.1125,0.1154,0.1125,0.1187,0.1122,0.1108,0.1148,0.116,0.129,0.132,0.1351,0.1135,0.1195,0.1081,0.11,0.119,0.1093,0.1133,0.1125,0.1145,0.1294,0.13,0.1401,0.1172,0.1299,0.1232,0.1276,0.13,0.1123,0.1248,0.1175,0.1211,0.1342,0.1201,0.1377,0.1551,0.131,0.1385,0.1481,0.1257,0.1159,0.1296,0.121,0.1196,0.1406,0.1421,0.1321,0.1763,0.1699,0.162,0.1518,0.1716,0.157,0.1366,0.1501,0.1671,0.1271,0.1252,0.1315,0.1829,0.26,0.2185,0.1861,0.1713,0.1569,0.2933,0.2243,0.1953,0.1524,0.1431,0.1498,0.3659,0.2427,0.2637,0.2671,0.2419,0.2108 +25709s,31.0 °C,0.1144,0.1075,0.1128,0.1256,0.1123,0.1157,0.1148,0.1069,0.1105,0.1109,0.1114,0.1219,0.1112,0.1129,0.1166,0.1329,0.1276,0.1251,0.1153,0.1125,0.1155,0.1129,0.1186,0.1124,0.1108,0.1148,0.116,0.1303,0.1337,0.1371,0.1137,0.1195,0.1082,0.11,0.1192,0.1097,0.1131,0.1125,0.1145,0.1308,0.1314,0.1419,0.1173,0.1299,0.1231,0.1282,0.131,0.1131,0.125,0.118,0.1215,0.1362,0.1215,0.1404,0.158,0.1318,0.1392,0.1504,0.1273,0.1167,0.1312,0.1219,0.1205,0.1438,0.1452,0.1345,0.183,0.1759,0.167,0.156,0.1783,0.1621,0.1399,0.1549,0.1735,0.1294,0.1274,0.1339,0.1922,0.2764,0.2312,0.1949,0.1788,0.1629,0.314,0.2382,0.2069,0.157,0.1466,0.154,0.3916,0.2588,0.2804,0.2845,0.2564,0.2229 +26385s,31.0 °C,0.115,0.1074,0.1128,0.1266,0.1127,0.116,0.1149,0.1069,0.1106,0.1109,0.1114,0.1221,0.1112,0.1129,0.1167,0.1341,0.1283,0.126,0.1153,0.1124,0.1155,0.1131,0.1183,0.1124,0.1108,0.1148,0.1161,0.1318,0.1355,0.1391,0.1137,0.1197,0.1082,0.1101,0.1194,0.1095,0.1132,0.1126,0.1146,0.133,0.1333,0.1438,0.1179,0.1302,0.1234,0.1294,0.132,0.1132,0.1253,0.1181,0.1216,0.1388,0.1229,0.1432,0.1607,0.1331,0.1403,0.1534,0.1289,0.1175,0.1322,0.1227,0.1212,0.1471,0.1486,0.1371,0.1898,0.1817,0.172,0.1604,0.1852,0.1683,0.1432,0.16,0.1801,0.132,0.1303,0.1364,0.2022,0.2945,0.245,0.2049,0.1868,0.1699,0.335,0.2524,0.2193,0.1618,0.1504,0.1579,0.4172,0.2747,0.2972,0.3003,0.2732,0.2368 +27062s,31.1 °C,0.1143,0.1075,0.1128,0.1274,0.1131,0.1166,0.1148,0.1069,0.1106,0.1109,0.1116,0.1219,0.1112,0.1129,0.1168,0.136,0.1294,0.1273,0.1156,0.1126,0.1158,0.1131,0.1186,0.1124,0.1109,0.1148,0.1161,0.1336,0.1375,0.1413,0.1137,0.1198,0.1083,0.1102,0.1196,0.1096,0.1131,0.1126,0.1146,0.135,0.1355,0.1459,0.1182,0.1304,0.1235,0.1296,0.133,0.1133,0.1258,0.1181,0.1218,0.1414,0.1246,0.1464,0.1634,0.1344,0.1428,0.1567,0.1311,0.1184,0.1338,0.1235,0.122,0.1507,0.1525,0.1398,0.1977,0.1882,0.178,0.1651,0.1928,0.1745,0.1472,0.1656,0.1877,0.1347,0.1328,0.1396,0.2131,0.3134,0.2595,0.2152,0.1956,0.1769,0.3575,0.269,0.2331,0.1672,0.1548,0.1625,0.4445,0.2942,0.3179,0.3211,0.2895,0.2509 +27738s,31.0 °C,0.1143,0.1075,0.1128,0.1283,0.1135,0.1172,0.1149,0.1069,0.1106,0.111,0.1115,0.1218,0.1112,0.1129,0.1169,0.1375,0.1308,0.1284,0.1156,0.1125,0.1155,0.1129,0.1188,0.1125,0.1108,0.1149,0.1161,0.1354,0.1396,0.143,0.1139,0.1198,0.1083,0.1101,0.1198,0.1102,0.1131,0.1125,0.1144,0.1373,0.1377,0.1483,0.1183,0.1306,0.1238,0.1302,0.134,0.1135,0.1261,0.1184,0.1221,0.1442,0.1263,0.15,0.1665,0.1356,0.1441,0.1599,0.1329,0.1194,0.136,0.1244,0.1226,0.155,0.1571,0.1428,0.2063,0.196,0.1848,0.1704,0.2008,0.1811,0.1521,0.172,0.1963,0.1378,0.1356,0.1429,0.2252,0.334,0.276,0.2266,0.2052,0.1851,0.3817,0.2864,0.2482,0.1732,0.1595,0.1668,0.4703,0.3128,0.3379,0.3405,0.3085,0.2671 +28415s,31.1 °C,0.1147,0.1075,0.1128,0.1294,0.1138,0.1176,0.1149,0.1069,0.1106,0.111,0.1116,0.1216,0.1111,0.1128,0.1177,0.1392,0.1317,0.1293,0.1155,0.1127,0.1155,0.1128,0.1188,0.1126,0.1108,0.1149,0.1161,0.1372,0.1418,0.1448,0.1139,0.1201,0.1083,0.1102,0.1199,0.1101,0.1133,0.1125,0.1143,0.1398,0.1401,0.1507,0.1186,0.131,0.124,0.1307,0.1348,0.1141,0.1267,0.1186,0.1224,0.1477,0.1282,0.1539,0.1696,0.1375,0.1449,0.1639,0.1351,0.1206,0.1379,0.1254,0.1235,0.1594,0.1619,0.146,0.2156,0.2041,0.1923,0.1761,0.2099,0.1889,0.1573,0.1792,0.2061,0.1413,0.1384,0.1469,0.2393,0.356,0.2933,0.2386,0.2155,0.1937,0.4064,0.3054,0.2651,0.1797,0.1652,0.1726,0.4968,0.3346,0.3602,0.3637,0.3268,0.284 +29091s,31.2 °C,0.1143,0.1075,0.1129,0.1306,0.1143,0.1182,0.1149,0.107,0.1107,0.111,0.1115,0.1219,0.1112,0.1129,0.1186,0.1413,0.1333,0.1308,0.1159,0.1127,0.1155,0.113,0.1192,0.1125,0.1109,0.1149,0.1162,0.1395,0.1444,0.148,0.114,0.1201,0.1084,0.1104,0.1203,0.1101,0.1133,0.1127,0.1145,0.1428,0.1428,0.1537,0.1189,0.1315,0.1244,0.1317,0.136,0.1138,0.1272,0.1186,0.1225,0.1514,0.1305,0.1581,0.1734,0.1395,0.1469,0.1678,0.1373,0.1219,0.1404,0.1266,0.1246,0.1645,0.1671,0.1498,0.2257,0.2135,0.2005,0.1825,0.2201,0.197,0.1634,0.1873,0.217,0.1451,0.1419,0.1511,0.2541,0.3792,0.312,0.2524,0.2272,0.2035,0.431,0.3253,0.2831,0.1873,0.1709,0.179,0.5214,0.3562,0.3826,0.3861,0.3466,0.3023 +29768s,31.0 °C,0.1142,0.1075,0.1128,0.1317,0.1147,0.1188,0.1149,0.1069,0.1106,0.111,0.1115,0.1218,0.1112,0.1128,0.1175,0.1431,0.1346,0.1322,0.1158,0.1128,0.1155,0.1128,0.119,0.1126,0.1109,0.1149,0.1161,0.1414,0.1471,0.1501,0.114,0.1201,0.1084,0.1103,0.1203,0.1101,0.1131,0.1125,0.1143,0.1452,0.1459,0.1567,0.1191,0.131,0.1246,0.1319,0.1368,0.1145,0.1275,0.119,0.1228,0.1551,0.1329,0.1626,0.1776,0.1409,0.1487,0.1717,0.1396,0.123,0.1427,0.1279,0.1257,0.17,0.1729,0.154,0.2366,0.2225,0.2093,0.1898,0.2308,0.2054,0.1692,0.1962,0.2287,0.1493,0.1458,0.1558,0.2707,0.4027,0.3317,0.2668,0.2393,0.2137,0.4536,0.3455,0.3017,0.1952,0.1777,0.1854,0.5435,0.3785,0.4042,0.4092,0.3674,0.3212 +30444s,31.3 °C,0.114,0.1075,0.1128,0.1328,0.1152,0.1195,0.1149,0.1069,0.1107,0.111,0.1116,0.1214,0.1112,0.1128,0.1162,0.1456,0.1362,0.1338,0.1158,0.1127,0.1155,0.1128,0.1191,0.1126,0.1108,0.1149,0.116,0.144,0.1501,0.1524,0.1141,0.1202,0.1084,0.1103,0.1206,0.1108,0.1132,0.1125,0.1145,0.1484,0.149,0.1601,0.1193,0.1315,0.1248,0.1328,0.1377,0.1152,0.128,0.1193,0.1231,0.1592,0.1353,0.1679,0.1818,0.1426,0.1514,0.1762,0.1421,0.1242,0.1449,0.1293,0.1266,0.1756,0.1792,0.1587,0.2476,0.2318,0.2184,0.1976,0.2421,0.216,0.1766,0.2065,0.2418,0.154,0.1502,0.1609,0.288,0.4276,0.3527,0.2822,0.2525,0.225,0.4764,0.3668,0.3219,0.2042,0.1853,0.1925,0.5658,0.3995,0.4271,0.4312,0.3899,0.3416 +31121s,31.1 °C,0.1141,0.1075,0.1128,0.1342,0.1158,0.1201,0.1149,0.1069,0.1107,0.1111,0.1117,0.1217,0.1112,0.1128,0.1174,0.1478,0.1376,0.1354,0.1158,0.1129,0.1156,0.113,0.1192,0.1127,0.1109,0.1149,0.1161,0.1466,0.153,0.1563,0.1141,0.1202,0.1085,0.1104,0.1207,0.1106,0.1133,0.1125,0.1144,0.1519,0.1528,0.1635,0.1195,0.1317,0.1252,0.1335,0.1388,0.1147,0.1288,0.1194,0.1234,0.164,0.1382,0.1735,0.1862,0.1449,0.1528,0.1811,0.1451,0.1258,0.1482,0.1309,0.1279,0.1824,0.1867,0.1637,0.2594,0.2426,0.2289,0.2061,0.2539,0.2265,0.1846,0.2174,0.2557,0.1591,0.155,0.1669,0.3066,0.4523,0.3741,0.2987,0.2664,0.2374,0.4981,0.3879,0.3426,0.2138,0.1934,0.2005,0.5857,0.4218,0.4502,0.4544,0.4108,0.3615 +31797s,31.2 °C,0.1143,0.1074,0.1128,0.1355,0.1163,0.1208,0.1149,0.1069,0.1107,0.1111,0.1116,0.1217,0.1111,0.1128,0.1172,0.15,0.1395,0.1371,0.1156,0.1129,0.1154,0.1127,0.1191,0.1126,0.1109,0.1149,0.1161,0.1492,0.1565,0.1593,0.114,0.1204,0.1084,0.1104,0.1207,0.1102,0.1132,0.1124,0.1143,0.1555,0.1566,0.1674,0.1194,0.1317,0.1254,0.1342,0.1396,0.1154,0.1292,0.1199,0.1238,0.169,0.1412,0.1794,0.1914,0.1466,0.1551,0.1858,0.1484,0.1274,0.1513,0.1326,0.1294,0.19,0.1945,0.1692,0.2721,0.2537,0.2397,0.2153,0.2669,0.2377,0.193,0.2289,0.2706,0.1649,0.1604,0.173,0.3257,0.4779,0.3957,0.3162,0.2809,0.2499,0.519,0.4093,0.3632,0.2243,0.2022,0.2093,0.6039,0.4433,0.4705,0.4753,0.4331,0.3825 +32474s,31.1 °C,0.1141,0.1073,0.1127,0.1367,0.1167,0.1216,0.1149,0.1068,0.1107,0.111,0.1116,0.1213,0.1111,0.1129,0.116,0.1528,0.1416,0.1391,0.1156,0.1128,0.1155,0.1128,0.1191,0.1127,0.1108,0.1149,0.116,0.1523,0.1601,0.1622,0.1142,0.1204,0.1084,0.1104,0.1209,0.1106,0.1131,0.1126,0.1142,0.1595,0.1611,0.1719,0.1194,0.132,0.126,0.1352,0.1408,0.1157,0.1297,0.1202,0.1241,0.1746,0.1446,0.1862,0.1967,0.1488,0.1575,0.1913,0.1519,0.129,0.1551,0.1346,0.1311,0.1981,0.2032,0.1751,0.2863,0.2667,0.2523,0.2249,0.2811,0.2476,0.2018,0.2417,0.287,0.1711,0.1661,0.1801,0.3464,0.5028,0.4188,0.3341,0.2963,0.2631,0.5375,0.4295,0.3844,0.2355,0.2114,0.2193,0.6216,0.464,0.4907,0.4964,0.4551,0.4031 +33151s,31.2 °C,0.1142,0.1074,0.1127,0.1387,0.1173,0.1223,0.1149,0.1069,0.1107,0.1111,0.1117,0.1219,0.1112,0.1129,0.1157,0.1559,0.1434,0.1411,0.1155,0.113,0.1158,0.113,0.119,0.1128,0.1109,0.1149,0.1161,0.1555,0.1642,0.1667,0.1141,0.1205,0.1085,0.1105,0.1211,0.1105,0.1133,0.1129,0.1142,0.1639,0.1658,0.1767,0.1197,0.1321,0.1265,0.1362,0.1418,0.1165,0.1307,0.1205,0.1245,0.181,0.1485,0.1939,0.2022,0.1514,0.1602,0.1971,0.1554,0.1307,0.1582,0.1372,0.1328,0.207,0.2126,0.1826,0.3,0.2777,0.2648,0.236,0.2951,0.2609,0.2111,0.256,0.304,0.1783,0.1727,0.1878,0.3673,0.5266,0.4404,0.3532,0.3114,0.2763,0.5563,0.4501,0.4057,0.2478,0.2221,0.23,0.6391,0.4844,0.5104,0.518,0.4759,0.4241 +33827s,31.1 °C,0.115,0.1074,0.1128,0.1405,0.1181,0.123,0.115,0.107,0.1107,0.1111,0.1117,0.1219,0.1113,0.113,0.1161,0.1589,0.1456,0.1434,0.1158,0.1129,0.116,0.113,0.1192,0.1128,0.1109,0.1149,0.1161,0.159,0.1688,0.1706,0.1142,0.1206,0.1085,0.1105,0.1214,0.1108,0.1134,0.1128,0.1145,0.1687,0.1704,0.1822,0.1203,0.1322,0.1265,0.1372,0.1432,0.1169,0.1315,0.1208,0.1249,0.188,0.1526,0.2019,0.2082,0.1542,0.1638,0.2035,0.1592,0.1325,0.1621,0.1394,0.1349,0.2168,0.2226,0.19,0.3148,0.2902,0.2777,0.2472,0.3105,0.273,0.2212,0.2706,0.3222,0.1864,0.18,0.1961,0.389,0.5498,0.4624,0.373,0.3271,0.2907,0.5743,0.4692,0.4254,0.2611,0.2337,0.242,0.6548,0.5028,0.5292,0.5383,0.4965,0.4437 +34504s,31.4 °C,0.1142,0.1074,0.1128,0.1422,0.1186,0.1239,0.1149,0.107,0.1106,0.111,0.1117,0.1218,0.1112,0.1129,0.1183,0.1621,0.1484,0.1458,0.1158,0.1129,0.1156,0.1132,0.1193,0.1127,0.1109,0.1149,0.1161,0.1629,0.1731,0.1759,0.1141,0.1206,0.1085,0.1106,0.1215,0.1105,0.1133,0.1127,0.1145,0.1745,0.1755,0.1876,0.1204,0.1327,0.1267,0.1383,0.145,0.1168,0.1322,0.1213,0.1254,0.1952,0.1572,0.2107,0.2143,0.1567,0.1672,0.2097,0.163,0.1345,0.1663,0.1417,0.1367,0.2275,0.2337,0.1978,0.3302,0.303,0.2913,0.2586,0.3261,0.2865,0.2322,0.2862,0.3411,0.1956,0.1881,0.2055,0.4113,0.5732,0.4839,0.3935,0.3432,0.3053,0.5895,0.4868,0.4445,0.2755,0.2454,0.2537,0.6689,0.5203,0.5464,0.5545,0.5174,0.4651 +35180s,31.0 °C,0.1141,0.1074,0.1128,0.1439,0.1194,0.1248,0.1149,0.107,0.1107,0.111,0.1116,0.1217,0.1111,0.1129,0.1175,0.1655,0.151,0.1482,0.1158,0.1127,0.1156,0.113,0.1193,0.1127,0.1108,0.1149,0.1161,0.167,0.178,0.1802,0.1143,0.1206,0.1085,0.1106,0.1216,0.1109,0.1132,0.1127,0.1144,0.18,0.1814,0.1938,0.1205,0.1326,0.127,0.1391,0.1461,0.1175,0.1331,0.1215,0.1257,0.2035,0.1619,0.2201,0.2207,0.16,0.1691,0.2162,0.1668,0.1365,0.1717,0.1446,0.1394,0.2389,0.2459,0.2065,0.3468,0.3187,0.3066,0.2707,0.3429,0.2977,0.2442,0.3026,0.3616,0.2051,0.1965,0.2161,0.4325,0.5938,0.5046,0.4141,0.3584,0.3194,0.6042,0.5035,0.4628,0.2898,0.2577,0.2658,0.6813,0.5361,0.5614,0.5696,0.5386,0.4851 +35857s,31.0 °C,0.1139,0.1074,0.1127,0.1457,0.12,0.1258,0.1149,0.1069,0.1107,0.1111,0.1117,0.1217,0.1112,0.1129,0.118,0.1694,0.1539,0.1509,0.1157,0.1128,0.1155,0.1131,0.1192,0.1127,0.1109,0.1149,0.1161,0.1712,0.1832,0.1858,0.1141,0.1207,0.1085,0.1106,0.1218,0.1104,0.1133,0.1127,0.1146,0.1862,0.1882,0.1998,0.121,0.1332,0.1275,0.1401,0.1477,0.1175,0.1343,0.1216,0.1262,0.2127,0.1675,0.2301,0.2272,0.1636,0.1722,0.2242,0.1715,0.139,0.1761,0.1477,0.1419,0.2513,0.2589,0.2161,0.3626,0.3323,0.3217,0.2831,0.3594,0.3117,0.2559,0.3194,0.3822,0.216,0.2063,0.2272,0.4547,0.613,0.5245,0.4346,0.3735,0.3336,0.6184,0.5205,0.48,0.3059,0.2709,0.2795,0.6941,0.5525,0.5776,0.5853,0.5566,0.5049 +36533s,31.1 °C,0.114,0.1074,0.1128,0.1477,0.1208,0.1267,0.1149,0.107,0.1107,0.1111,0.1116,0.1214,0.1111,0.1128,0.1175,0.1736,0.1573,0.1536,0.1158,0.1129,0.1156,0.1129,0.1195,0.1128,0.1108,0.1149,0.1161,0.176,0.189,0.191,0.1143,0.1206,0.1086,0.1106,0.1219,0.1108,0.1133,0.1126,0.1145,0.1931,0.1953,0.2072,0.121,0.1333,0.1279,0.1408,0.1489,0.1179,0.1351,0.1223,0.1269,0.2219,0.1734,0.2411,0.2347,0.1666,0.1775,0.232,0.1764,0.1413,0.1809,0.1511,0.1446,0.2638,0.2724,0.2265,0.3793,0.3469,0.3371,0.2973,0.3756,0.3258,0.268,0.3367,0.4026,0.2272,0.2163,0.2382,0.4748,0.6328,0.5445,0.4566,0.3884,0.3489,0.631,0.5353,0.4967,0.322,0.285,0.2929,0.7044,0.5672,0.5918,0.6002,0.5752,0.523 +37210s,31.1 °C,0.114,0.1075,0.1129,0.15,0.1216,0.1279,0.115,0.107,0.1107,0.1111,0.1117,0.1216,0.1112,0.1129,0.1179,0.1774,0.1607,0.1567,0.1159,0.1129,0.1157,0.1132,0.1194,0.1128,0.1109,0.1149,0.1161,0.1808,0.1951,0.196,0.1143,0.1208,0.1085,0.1106,0.122,0.1108,0.1132,0.1125,0.1145,0.1997,0.202,0.2146,0.121,0.1331,0.128,0.142,0.1505,0.1188,0.1364,0.1225,0.1272,0.2322,0.1797,0.2523,0.2413,0.1708,0.1805,0.2394,0.1812,0.1439,0.1871,0.155,0.1479,0.277,0.287,0.2367,0.3963,0.362,0.3532,0.3107,0.3931,0.3386,0.2812,0.3543,0.423,0.2392,0.2271,0.2506,0.4941,0.6504,0.5614,0.4766,0.4024,0.3628,0.6441,0.5512,0.5129,0.3383,0.2996,0.3087,0.7152,0.5825,0.6061,0.6148,0.591,0.5409 +37886s,31.5 °C,0.1145,0.1075,0.1128,0.1522,0.1224,0.1289,0.115,0.1071,0.1108,0.1112,0.1118,0.1219,0.1113,0.113,0.1178,0.1816,0.1641,0.1599,0.1158,0.1128,0.1157,0.1131,0.1194,0.1129,0.1109,0.1149,0.1161,0.1867,0.2017,0.203,0.1144,0.1209,0.1087,0.1108,0.1223,0.1114,0.1134,0.1129,0.1147,0.2079,0.2099,0.2232,0.1216,0.1338,0.1286,0.1437,0.1524,0.1191,0.1374,0.1234,0.1282,0.2423,0.1867,0.2645,0.2495,0.1738,0.1847,0.2477,0.1867,0.1466,0.1926,0.1589,0.1511,0.2915,0.3019,0.2474,0.4138,0.3779,0.3701,0.3242,0.4107,0.3516,0.2931,0.3716,0.4441,0.2522,0.239,0.2636,0.5132,0.6669,0.5793,0.4977,0.4171,0.377,0.6551,0.5649,0.5278,0.3555,0.3149,0.3231,0.7253,0.5948,0.6178,0.6264,0.6079,0.5577 +38563s,31.0 °C,0.1142,0.1075,0.1129,0.1541,0.1233,0.1302,0.115,0.107,0.1108,0.1112,0.1118,0.1216,0.1113,0.1129,0.1178,0.1865,0.1688,0.1635,0.116,0.113,0.1157,0.1134,0.1199,0.1128,0.111,0.1149,0.1161,0.1922,0.208,0.2098,0.1145,0.121,0.1086,0.1108,0.1224,0.1114,0.1134,0.1127,0.1144,0.2152,0.2187,0.231,0.1218,0.1337,0.129,0.1442,0.1535,0.1195,0.1387,0.1238,0.1288,0.2539,0.194,0.2771,0.257,0.1781,0.1891,0.2562,0.1922,0.1495,0.198,0.1632,0.1547,0.3061,0.3176,0.2596,0.4303,0.3927,0.3861,0.3382,0.4267,0.3654,0.3085,0.3891,0.4663,0.2665,0.251,0.2783,0.5318,0.6806,0.5946,0.5158,0.4295,0.3901,0.6653,0.5766,0.5406,0.3731,0.3305,0.3389,0.7338,0.608,0.6306,0.6389,0.6211,0.573 +39239s,31.3 °C,0.114,0.1074,0.1128,0.1564,0.1243,0.1313,0.115,0.107,0.1107,0.1111,0.1117,0.1216,0.1112,0.1128,0.1181,0.1916,0.1726,0.1669,0.1158,0.1132,0.1157,0.113,0.1198,0.113,0.1109,0.115,0.1162,0.1981,0.2149,0.2167,0.1144,0.121,0.1087,0.1109,0.1225,0.1111,0.1135,0.1127,0.1145,0.2235,0.2284,0.2396,0.122,0.1342,0.1298,0.1451,0.1548,0.1199,0.14,0.1244,0.1294,0.2654,0.202,0.2896,0.2647,0.1823,0.1935,0.2647,0.1978,0.1525,0.2043,0.1677,0.1583,0.3209,0.3341,0.2715,0.4474,0.4084,0.4032,0.3529,0.4432,0.3784,0.3217,0.4057,0.4847,0.28,0.2632,0.291,0.5467,0.6947,0.6093,0.5367,0.4417,0.4034,0.6744,0.5881,0.5532,0.3902,0.3457,0.3539,0.74,0.6178,0.6405,0.6485,0.6363,0.588 +39916s,31.2 °C,0.1142,0.1075,0.1129,0.159,0.1251,0.1326,0.115,0.107,0.1107,0.1112,0.1117,0.1217,0.1113,0.1131,0.1176,0.196,0.1784,0.1706,0.1158,0.1129,0.1156,0.1131,0.1194,0.1128,0.111,0.1149,0.1162,0.2038,0.222,0.222,0.1143,0.121,0.1086,0.1109,0.1225,0.1106,0.1135,0.1131,0.1145,0.2328,0.236,0.2491,0.1221,0.1347,0.1301,0.1469,0.1565,0.1199,0.1412,0.125,0.1302,0.2771,0.2102,0.302,0.2726,0.1866,0.1973,0.2732,0.2039,0.1552,0.2112,0.173,0.1626,0.3356,0.3498,0.2841,0.4653,0.425,0.4196,0.3674,0.4602,0.3906,0.3375,0.4228,0.5046,0.295,0.2762,0.3056,0.5629,0.7081,0.6227,0.5551,0.4539,0.4165,0.6838,0.5993,0.5652,0.4085,0.3617,0.3711,0.7483,0.6284,0.6503,0.659,0.6489,0.6019 +40593s,31.0 °C,0.1139,0.1074,0.1128,0.1608,0.1262,0.1342,0.115,0.107,0.1107,0.1112,0.1118,0.1213,0.1113,0.1129,0.1185,0.2014,0.1827,0.1749,0.116,0.1129,0.1156,0.1133,0.1196,0.113,0.111,0.115,0.1162,0.2108,0.2299,0.2308,0.1144,0.121,0.1087,0.1109,0.1228,0.1113,0.1136,0.113,0.1148,0.2422,0.2454,0.2586,0.1229,0.135,0.1304,0.1482,0.1585,0.1205,0.1425,0.1256,0.131,0.2891,0.2183,0.3155,0.281,0.1906,0.2029,0.2824,0.2104,0.1581,0.2165,0.1777,0.1671,0.3513,0.3657,0.2967,0.4821,0.4405,0.4366,0.3813,0.4769,0.4037,0.3501,0.4388,0.5238,0.3101,0.2897,0.3206,0.5769,0.7188,0.6347,0.5715,0.4648,0.428,0.6903,0.6082,0.5758,0.4269,0.3781,0.3863,0.7547,0.637,0.6587,0.6669,0.6628,0.6151 +41269s,31.1 °C,0.1143,0.1074,0.1128,0.1634,0.1272,0.1355,0.115,0.107,0.1108,0.1111,0.1118,0.1212,0.1112,0.1128,0.1172,0.207,0.1871,0.1789,0.116,0.113,0.1158,0.1131,0.1199,0.1129,0.1111,0.1149,0.1161,0.2175,0.2371,0.238,0.1144,0.121,0.1087,0.1108,0.1229,0.1112,0.1135,0.1127,0.1145,0.2515,0.2555,0.2682,0.1229,0.1351,0.1307,0.149,0.1602,0.1206,0.1441,0.1259,0.1317,0.302,0.227,0.3294,0.2882,0.1959,0.2078,0.2923,0.2164,0.1615,0.2235,0.1829,0.1715,0.3668,0.3826,0.309,0.4995,0.4572,0.4539,0.3952,0.4928,0.4155,0.3653,0.4547,0.5435,0.3262,0.3037,0.3375,0.5911,0.7295,0.6457,0.5878,0.4752,0.4401,0.6987,0.6181,0.5854,0.4456,0.3951,0.4034,0.7617,0.646,0.6669,0.6761,0.6733,0.627 +41946s,31.1 °C,0.1139,0.1074,0.1128,0.1662,0.1281,0.1366,0.1149,0.107,0.1108,0.1112,0.1117,0.1215,0.1112,0.1129,0.1174,0.2125,0.1926,0.1834,0.1157,0.113,0.1155,0.1129,0.1196,0.113,0.1109,0.1148,0.1161,0.2244,0.2449,0.2459,0.1143,0.121,0.1086,0.1108,0.1228,0.111,0.1134,0.1127,0.1143,0.2607,0.2656,0.2777,0.1227,0.1351,0.1311,0.1499,0.1614,0.1212,0.1451,0.1268,0.1327,0.3138,0.236,0.3428,0.297,0.1999,0.2135,0.3007,0.2234,0.1643,0.2278,0.1884,0.1753,0.3816,0.3994,0.3228,0.5139,0.4707,0.469,0.4105,0.5067,0.4296,0.3777,0.4685,0.5591,0.3416,0.3177,0.3515,0.6026,0.7393,0.6564,0.6033,0.4855,0.4513,0.7054,0.6258,0.5941,0.464,0.4113,0.4193,0.766,0.6529,0.6738,0.6821,0.6857,0.6392 +42622s,31.1 °C,0.114,0.1074,0.1128,0.1686,0.1292,0.1382,0.1149,0.107,0.1108,0.1112,0.1117,0.1215,0.1113,0.113,0.1167,0.2184,0.1979,0.1878,0.1157,0.1129,0.1157,0.1131,0.1194,0.1129,0.111,0.1149,0.1161,0.2318,0.2531,0.2543,0.1145,0.1211,0.1087,0.111,0.1231,0.1116,0.1134,0.113,0.1143,0.2697,0.2764,0.2877,0.1231,0.1352,0.1318,0.1512,0.1628,0.1221,0.1467,0.1279,0.1338,0.326,0.2448,0.3568,0.3059,0.2046,0.2186,0.3101,0.2302,0.1671,0.2338,0.1945,0.1806,0.3967,0.4154,0.3364,0.5293,0.4865,0.485,0.4249,0.5212,0.4416,0.3922,0.4821,0.5755,0.3575,0.3309,0.3665,0.6146,0.749,0.6656,0.6189,0.4954,0.4619,0.7124,0.6341,0.6034,0.4816,0.4287,0.4372,0.773,0.6626,0.6818,0.691,0.6937,0.6481 +43299s,31.0 °C,0.1141,0.1074,0.1129,0.1716,0.1302,0.1396,0.115,0.107,0.1107,0.1111,0.1117,0.1218,0.1113,0.1129,0.1178,0.2244,0.2039,0.193,0.116,0.113,0.1155,0.1133,0.1196,0.1129,0.111,0.1148,0.1161,0.239,0.2611,0.2627,0.1143,0.121,0.1086,0.1109,0.1231,0.1109,0.1135,0.1128,0.1145,0.2801,0.286,0.2975,0.1238,0.1355,0.132,0.1526,0.1646,0.1222,0.1482,0.128,0.1342,0.3395,0.254,0.3697,0.313,0.2107,0.2234,0.3203,0.2363,0.17,0.2406,0.2,0.1858,0.4122,0.4315,0.3488,0.5458,0.5017,0.5012,0.4381,0.5362,0.4508,0.405,0.4948,0.5907,0.3738,0.3458,0.3813,0.626,0.7585,0.6758,0.6339,0.5049,0.4718,0.7183,0.6406,0.6109,0.4994,0.4458,0.4538,0.7782,0.6691,0.6879,0.6964,0.7028,0.6579 +43975s,31.1 °C,0.1138,0.1074,0.1128,0.1734,0.1314,0.1413,0.115,0.107,0.1108,0.1112,0.1116,0.1212,0.1113,0.1129,0.1173,0.2306,0.2087,0.198,0.116,0.113,0.1156,0.1132,0.1198,0.1129,0.111,0.1149,0.116,0.2469,0.2691,0.2711,0.1145,0.1211,0.1086,0.1109,0.1233,0.1116,0.1135,0.1127,0.1143,0.2901,0.2967,0.3073,0.1238,0.1357,0.1324,0.1534,0.166,0.1226,0.1495,0.1289,0.1354,0.3523,0.2637,0.3838,0.322,0.2156,0.2283,0.3296,0.2436,0.1733,0.2463,0.2059,0.191,0.4272,0.4481,0.3626,0.5595,0.516,0.5162,0.4515,0.5486,0.461,0.4194,0.5068,0.6057,0.3911,0.36,0.3987,0.6349,0.7645,0.6831,0.645,0.5127,0.4805,0.725,0.6477,0.6178,0.5163,0.4628,0.4724,0.7847,0.6764,0.6948,0.7039,0.71,0.6658 +44652s,31.1 °C,0.1139,0.1074,0.1129,0.1766,0.1326,0.1425,0.115,0.107,0.1107,0.1111,0.1116,0.1217,0.1112,0.1128,0.118,0.2364,0.2152,0.2028,0.1157,0.1131,0.1156,0.113,0.1198,0.1129,0.111,0.1149,0.1161,0.2549,0.277,0.2786,0.1144,0.1211,0.1086,0.111,0.1234,0.1114,0.1135,0.1128,0.1146,0.3004,0.3068,0.3175,0.1242,0.1361,0.1329,0.1549,0.1678,0.1231,0.1509,0.1301,0.1366,0.3641,0.273,0.3967,0.3307,0.2201,0.2337,0.3386,0.2508,0.1762,0.2528,0.212,0.1966,0.4425,0.4643,0.3752,0.5748,0.5308,0.5314,0.4638,0.5624,0.4708,0.432,0.5175,0.6184,0.4081,0.3743,0.4136,0.6443,0.7714,0.6908,0.6572,0.5205,0.489,0.7303,0.6544,0.625,0.5337,0.4792,0.4878,0.7901,0.6812,0.7004,0.709,0.7205,0.6766 +45328s,31.1 °C,0.1139,0.1075,0.1129,0.1794,0.1338,0.1439,0.1149,0.107,0.1107,0.1111,0.1117,0.1219,0.1112,0.1128,0.119,0.2423,0.2218,0.2082,0.1159,0.1129,0.1155,0.1132,0.1197,0.1128,0.111,0.1148,0.1161,0.2624,0.2852,0.287,0.1144,0.121,0.1086,0.111,0.1234,0.1113,0.1135,0.1127,0.1144,0.3099,0.3174,0.3273,0.1246,0.1361,0.1334,0.1557,0.1691,0.1237,0.1522,0.1307,0.1375,0.3766,0.2825,0.4095,0.3386,0.2252,0.2391,0.3481,0.2575,0.1789,0.2567,0.2184,0.2017,0.4566,0.4797,0.3889,0.5872,0.5441,0.5452,0.4764,0.5738,0.4817,0.4415,0.5271,0.6302,0.4243,0.3879,0.4284,0.6519,0.7789,0.6983,0.6689,0.5286,0.4979,0.7351,0.6605,0.6317,0.5481,0.4955,0.5038,0.7953,0.6885,0.7065,0.7152,0.7279,0.6838 +46005s,31.0 °C,0.1139,0.1074,0.1129,0.1812,0.1349,0.1455,0.1148,0.1071,0.1108,0.1112,0.1116,0.1215,0.1113,0.1128,0.1181,0.2488,0.2287,0.2136,0.1159,0.1132,0.1154,0.1131,0.1198,0.1129,0.111,0.1149,0.1161,0.2709,0.2937,0.2963,0.1145,0.1211,0.1087,0.111,0.1237,0.1115,0.1137,0.1128,0.1146,0.3205,0.3286,0.3371,0.1249,0.1368,0.1344,0.157,0.1706,0.1236,0.1541,0.1312,0.1383,0.3898,0.2925,0.423,0.3461,0.2312,0.2445,0.3594,0.2643,0.1814,0.2636,0.2245,0.2076,0.4718,0.4953,0.4014,0.6002,0.5576,0.5601,0.4877,0.5851,0.4889,0.4529,0.5367,0.6415,0.4406,0.4022,0.4441,0.6595,0.7849,0.7051,0.6799,0.5354,0.5065,0.7414,0.6656,0.6376,0.5639,0.5126,0.5195,0.8009,0.6939,0.7129,0.7211,0.735,0.6917 +46681s,31.1 °C,0.1137,0.1074,0.1129,0.1834,0.1361,0.1471,0.1149,0.107,0.1108,0.1112,0.1116,0.1214,0.1113,0.1128,0.1178,0.2554,0.2342,0.219,0.1159,0.1132,0.1155,0.1132,0.1199,0.1129,0.111,0.1149,0.1161,0.2786,0.3011,0.3039,0.1145,0.121,0.1087,0.111,0.1238,0.1115,0.1138,0.1129,0.1146,0.3308,0.3388,0.3463,0.1251,0.1368,0.1349,0.1583,0.172,0.1241,0.1555,0.1316,0.1389,0.4029,0.302,0.4358,0.3532,0.238,0.2508,0.3687,0.2707,0.1839,0.2701,0.2314,0.2135,0.4866,0.511,0.4138,0.6127,0.5717,0.5729,0.4986,0.5963,0.4969,0.4639,0.5458,0.6517,0.457,0.4165,0.4605,0.667,0.7912,0.7118,0.6897,0.5416,0.5135,0.7455,0.6716,0.643,0.5778,0.5277,0.5337,0.8057,0.6992,0.7192,0.727,0.7416,0.6998 +47358s,30.9 °C,0.1137,0.1074,0.1128,0.1853,0.1372,0.1487,0.1149,0.107,0.1108,0.1112,0.1115,0.1213,0.1113,0.113,0.1167,0.2608,0.2405,0.2245,0.1157,0.1131,0.1156,0.1133,0.1195,0.1129,0.111,0.1149,0.1161,0.2861,0.3092,0.3131,0.1145,0.1212,0.1087,0.1111,0.1239,0.1114,0.1136,0.113,0.1145,0.3412,0.3476,0.357,0.1252,0.1376,0.1353,0.1598,0.1739,0.1246,0.1568,0.1332,0.1404,0.4136,0.311,0.4475,0.3616,0.2427,0.254,0.3769,0.2776,0.186,0.2745,0.2377,0.219,0.4989,0.5244,0.4276,0.6222,0.5834,0.585,0.5094,0.6065,0.5059,0.4749,0.5545,0.6615,0.4728,0.4301,0.4744,0.6743,0.7962,0.7174,0.6997,0.5485,0.5198,0.7515,0.6784,0.6495,0.5903,0.5424,0.5492,0.8125,0.7063,0.7258,0.7331,0.7455,0.7049 +48034s,30.9 °C,0.114,0.1074,0.1129,0.1882,0.1384,0.1496,0.1149,0.107,0.1107,0.1111,0.1115,0.122,0.1113,0.1129,0.1173,0.2671,0.2468,0.2297,0.1159,0.113,0.1157,0.1135,0.1196,0.1129,0.111,0.1149,0.1161,0.2939,0.3167,0.3211,0.1146,0.1212,0.1088,0.1111,0.1241,0.1119,0.1136,0.113,0.1146,0.35,0.3586,0.366,0.1258,0.1374,0.1357,0.1605,0.1752,0.1251,0.158,0.1342,0.1417,0.4255,0.3205,0.4592,0.3698,0.2477,0.2606,0.386,0.2845,0.1884,0.2799,0.2441,0.2254,0.5131,0.5394,0.4394,0.6336,0.5957,0.597,0.52,0.6161,0.512,0.4837,0.5616,0.6711,0.4892,0.4433,0.4895,0.6804,0.8007,0.7219,0.7081,0.5548,0.5261,0.7574,0.6845,0.6548,0.6033,0.5566,0.565,0.8184,0.7152,0.7326,0.7414,0.7482,0.7114 +48711s,31.0 °C,0.1139,0.1074,0.1129,0.1899,0.1395,0.1511,0.1148,0.107,0.1107,0.1112,0.1115,0.1215,0.1113,0.1129,0.1188,0.2731,0.2448,0.235,0.1159,0.1132,0.1154,0.1132,0.1197,0.1128,0.111,0.1149,0.1161,0.3014,0.3241,0.3292,0.1144,0.1212,0.1087,0.1111,0.124,0.1113,0.1137,0.1128,0.1145,0.3603,0.368,0.3749,0.1259,0.138,0.1361,0.1615,0.1764,0.1249,0.1594,0.1345,0.1424,0.4374,0.3296,0.471,0.3764,0.2544,0.2656,0.3964,0.2903,0.1905,0.286,0.2503,0.2313,0.5259,0.5531,0.4504,0.6451,0.6071,0.6085,0.5285,0.6259,0.5197,0.4922,0.5682,0.6784,0.5027,0.4567,0.5019,0.6861,0.8079,0.7286,0.7168,0.5608,0.5337,0.7626,0.6885,0.66,0.6173,0.5705,0.5751,0.8215,0.7177,0.7364,0.7427,0.7616,0.7206 +49387s,31.0 °C,0.1136,0.1074,0.1128,0.1912,0.1406,0.1527,0.1148,0.107,0.1108,0.1113,0.1116,0.1212,0.1113,0.1129,0.1162,0.2787,0.2503,0.2397,0.1157,0.1132,0.1154,0.113,0.1195,0.113,0.1111,0.1149,0.116,0.3094,0.331,0.3368,0.1146,0.1211,0.1087,0.1111,0.1241,0.1121,0.1137,0.113,0.1145,0.3688,0.3791,0.3842,0.1262,0.1383,0.1369,0.1625,0.1775,0.1255,0.1604,0.1363,0.1443,0.4473,0.3393,0.4827,0.3855,0.2584,0.2713,0.4039,0.2979,0.1926,0.289,0.257,0.2358,0.5377,0.566,0.4636,0.6515,0.6153,0.618,0.54,0.6328,0.5307,0.4993,0.5742,0.6852,0.5176,0.4685,0.5148,0.6909,0.8129,0.7349,0.7252,0.5667,0.54,0.7677,0.6941,0.665,0.6273,0.5831,0.587,0.8264,0.7232,0.7422,0.7498,0.7659,0.7253 +50064s,30.8 °C,0.1142,0.1073,0.1128,0.1928,0.1416,0.1541,0.1149,0.107,0.1108,0.1113,0.1115,0.1211,0.1112,0.113,0.1156,0.2845,0.2556,0.245,0.1157,0.113,0.1157,0.1133,0.1197,0.113,0.111,0.1149,0.116,0.3163,0.3378,0.3441,0.1145,0.1212,0.1087,0.1111,0.1241,0.1119,0.1136,0.113,0.1145,0.3782,0.3873,0.393,0.1266,0.1385,0.1371,0.1638,0.179,0.126,0.1621,0.1366,0.1449,0.4585,0.3473,0.4935,0.3913,0.2652,0.2744,0.4117,0.3031,0.1942,0.2957,0.2633,0.2428,0.5494,0.5778,0.4744,0.6624,0.6271,0.6282,0.5479,0.6417,0.5343,0.5093,0.5804,0.693,0.5307,0.4805,0.5267,0.6971,0.817,0.7382,0.7323,0.5725,0.5455,0.7734,0.7002,0.6712,0.6382,0.5949,0.6016,0.8335,0.7315,0.7484,0.7568,0.7698,0.7322 +50741s,30.9 °C,0.1143,0.1074,0.1129,0.1949,0.1426,0.1551,0.1149,0.107,0.1107,0.1112,0.1115,0.1212,0.1112,0.1128,0.1177,0.2894,0.2606,0.2501,0.1159,0.1129,0.1153,0.1133,0.1196,0.1129,0.111,0.1149,0.116,0.3236,0.3445,0.3506,0.1144,0.1211,0.1086,0.111,0.1243,0.112,0.1135,0.1128,0.1144,0.3876,0.3962,0.4009,0.127,0.1385,0.1374,0.1645,0.1802,0.1261,0.1631,0.1374,0.1462,0.4685,0.3561,0.503,0.3983,0.2696,0.2797,0.4203,0.3094,0.1962,0.2996,0.2693,0.248,0.5609,0.5898,0.485,0.6705,0.6368,0.6376,0.5554,0.6496,0.5427,0.5149,0.5863,0.7002,0.545,0.492,0.5403,0.7023,0.8224,0.743,0.7397,0.5782,0.552,0.7776,0.7051,0.6765,0.6492,0.6057,0.6118,0.8367,0.736,0.7521,0.7601,0.7772,0.7394 +51417s,31.0 °C,0.114,0.1074,0.1129,0.1964,0.1435,0.1561,0.1148,0.107,0.1107,0.1112,0.1115,0.1213,0.1113,0.1128,0.118,0.2954,0.2658,0.2553,0.1161,0.1131,0.1156,0.1133,0.1198,0.1129,0.111,0.115,0.1161,0.3306,0.3508,0.3588,0.1144,0.1213,0.1087,0.1112,0.1244,0.1117,0.1136,0.1129,0.1145,0.3962,0.4054,0.409,0.1275,0.139,0.1379,0.1654,0.1815,0.1264,0.1644,0.1382,0.1472,0.4784,0.3647,0.5139,0.4045,0.2759,0.2844,0.4282,0.3148,0.1978,0.3051,0.2754,0.2545,0.571,0.6004,0.4956,0.6786,0.6443,0.6454,0.5632,0.6561,0.5466,0.5234,0.592,0.7078,0.5581,0.5032,0.5524,0.7084,0.8262,0.7483,0.7457,0.5832,0.5563,0.782,0.7103,0.6817,0.6585,0.6168,0.6219,0.8413,0.7413,0.758,0.7661,0.7818,0.7445 +52094s,30.8 °C,0.1138,0.1074,0.1128,0.1974,0.1444,0.1573,0.1149,0.107,0.1107,0.1112,0.1115,0.1209,0.1112,0.1128,0.1176,0.3,0.2706,0.2596,0.116,0.1132,0.1155,0.1132,0.1199,0.1129,0.111,0.1149,0.1161,0.3373,0.3567,0.3659,0.1144,0.1211,0.1086,0.1111,0.1245,0.1117,0.1136,0.1129,0.1145,0.4047,0.4137,0.4174,0.1277,0.1393,0.1383,0.1664,0.1825,0.1263,0.1654,0.1391,0.1483,0.4888,0.3731,0.5235,0.4109,0.2812,0.2885,0.4359,0.3206,0.1994,0.3092,0.2812,0.2596,0.582,0.6119,0.5066,0.6848,0.6522,0.6535,0.5716,0.6629,0.5535,0.5295,0.5968,0.7122,0.5688,0.5132,0.5623,0.7119,0.8316,0.753,0.7531,0.5888,0.5627,0.786,0.7145,0.6865,0.6686,0.6274,0.6312,0.8444,0.7444,0.7614,0.7698,0.791,0.7522 +52770s,30.5 °C,0.1138,0.1074,0.1129,0.1988,0.1452,0.158,0.1148,0.107,0.1107,0.1112,0.1115,0.1212,0.1113,0.1128,0.1177,0.305,0.2751,0.2646,0.116,0.1133,0.1154,0.1133,0.1198,0.1128,0.111,0.1149,0.116,0.344,0.3626,0.3717,0.1144,0.1212,0.1086,0.1111,0.1245,0.1116,0.1136,0.1127,0.1144,0.4118,0.4233,0.4241,0.1279,0.1393,0.1388,0.1666,0.1831,0.1268,0.1662,0.1405,0.1498,0.4966,0.3817,0.5334,0.4183,0.2851,0.294,0.4434,0.3267,0.201,0.3138,0.2865,0.2648,0.5922,0.6221,0.5153,0.6924,0.6607,0.6621,0.5776,0.6699,0.5598,0.5349,0.6011,0.7175,0.5809,0.5228,0.5723,0.7166,0.8366,0.7581,0.7598,0.5934,0.5685,0.7907,0.7193,0.6912,0.6769,0.6378,0.6436,0.8474,0.752,0.767,0.7763,0.7927,0.7566 +53447s,30.7 °C,0.1137,0.1074,0.1129,0.1997,0.1458,0.1591,0.1147,0.107,0.1107,0.1112,0.1114,0.1209,0.1112,0.1129,0.1167,0.3093,0.2797,0.2688,0.1157,0.1134,0.1155,0.1131,0.1195,0.1128,0.1109,0.1149,0.1161,0.3496,0.3677,0.3765,0.1144,0.1212,0.1086,0.1111,0.1245,0.1118,0.1138,0.1131,0.1144,0.4211,0.431,0.4328,0.128,0.1399,0.1397,0.1683,0.1842,0.1269,0.1677,0.1409,0.1503,0.5069,0.3896,0.543,0.4229,0.2917,0.297,0.4507,0.3307,0.2023,0.3194,0.2934,0.2706,0.6012,0.6329,0.525,0.6994,0.6685,0.6696,0.5843,0.6758,0.5637,0.5423,0.6078,0.7242,0.5924,0.5331,0.5845,0.7219,0.8402,0.7623,0.7653,0.5976,0.5716,0.7923,0.723,0.6951,0.6839,0.6469,0.652,0.8501,0.7548,0.7708,0.78,0.7986,0.7604 +54123s,30.6 °C,0.1137,0.1073,0.1128,0.2007,0.1465,0.16,0.1148,0.107,0.1107,0.1112,0.1114,0.121,0.1112,0.1129,0.118,0.3137,0.2836,0.273,0.116,0.113,0.1154,0.1133,0.1197,0.1128,0.1109,0.1149,0.116,0.3555,0.373,0.3834,0.1143,0.1212,0.1085,0.1111,0.1246,0.1115,0.1136,0.1129,0.1145,0.4281,0.4382,0.4396,0.1289,0.1399,0.1395,0.1687,0.1853,0.1271,0.1683,0.1416,0.1514,0.5156,0.3967,0.5511,0.4289,0.2958,0.3008,0.4573,0.3357,0.2035,0.3215,0.2986,0.2758,0.6099,0.6418,0.533,0.7045,0.6747,0.6752,0.5903,0.6815,0.5692,0.5455,0.6113,0.7288,0.6024,0.5413,0.5918,0.7261,0.8446,0.7671,0.7716,0.6026,0.5774,0.7956,0.7262,0.7002,0.6934,0.6563,0.6609,0.8521,0.7584,0.7734,0.7823,0.8051,0.7676 +54800s,30.7 °C,0.1137,0.1073,0.1129,0.2018,0.1471,0.1609,0.1148,0.107,0.1107,0.1113,0.1114,0.1208,0.1114,0.1129,0.1192,0.3182,0.2876,0.2771,0.116,0.1133,0.1154,0.1131,0.1198,0.1129,0.111,0.1149,0.1161,0.3615,0.3782,0.389,0.1143,0.1212,0.1086,0.1112,0.1246,0.1114,0.1138,0.1131,0.1148,0.4376,0.4461,0.4477,0.1292,0.1406,0.1401,0.1699,0.1867,0.1266,0.1694,0.1429,0.1529,0.524,0.4044,0.5599,0.4353,0.2993,0.3057,0.4634,0.3411,0.2048,0.3286,0.3046,0.2822,0.6193,0.651,0.5409,0.713,0.6821,0.6829,0.5954,0.6878,0.5705,0.5523,0.6157,0.7341,0.6131,0.55,0.6018,0.7304,0.8472,0.7699,0.7759,0.606,0.5806,0.7978,0.7315,0.7043,0.7002,0.6658,0.6709,0.8552,0.7632,0.7789,0.7881,0.8064,0.7708 +55476s,30.6 °C,0.1137,0.1074,0.1129,0.2026,0.1476,0.1615,0.1148,0.1069,0.1106,0.1112,0.1114,0.1209,0.1112,0.1128,0.1178,0.3218,0.2913,0.2802,0.1159,0.1132,0.1153,0.1131,0.1197,0.1129,0.111,0.115,0.116,0.3664,0.3827,0.3942,0.1144,0.1211,0.1087,0.1112,0.1247,0.1119,0.1138,0.1129,0.1146,0.4448,0.4537,0.4545,0.1292,0.1408,0.1404,0.1702,0.1874,0.1267,0.1699,0.1443,0.1544,0.5314,0.412,0.5678,0.4416,0.3036,0.309,0.4705,0.3464,0.206,0.3317,0.3098,0.2863,0.6273,0.6597,0.5493,0.7162,0.6878,0.6882,0.6012,0.6923,0.5769,0.5566,0.6197,0.7386,0.6222,0.5576,0.609,0.7335,0.8531,0.7752,0.7823,0.611,0.5854,0.7997,0.7341,0.7079,0.7075,0.6742,0.6782,0.8562,0.7656,0.7801,0.7905,0.8127,0.775 +56153s,30.3 °C,0.1136,0.1073,0.1129,0.2035,0.1481,0.162,0.1148,0.107,0.1107,0.1113,0.1114,0.1208,0.1112,0.1129,0.1178,0.3254,0.2948,0.2837,0.116,0.1132,0.1153,0.1131,0.1198,0.1129,0.1109,0.115,0.116,0.3717,0.3878,0.3999,0.1144,0.1211,0.1086,0.1112,0.1247,0.1118,0.1138,0.113,0.1146,0.4526,0.4611,0.4613,0.1294,0.1411,0.1409,0.171,0.188,0.1269,0.1707,0.1446,0.1549,0.5395,0.4189,0.5751,0.4454,0.3084,0.313,0.4769,0.3502,0.2071,0.3371,0.3153,0.2924,0.6357,0.6679,0.5571,0.7224,0.6946,0.6939,0.6061,0.697,0.5801,0.5635,0.6246,0.7448,0.6315,0.5659,0.6186,0.7387,0.8559,0.7783,0.7865,0.6138,0.5883,0.801,0.736,0.7112,0.7142,0.6814,0.6864,0.8567,0.7686,0.7829,0.7923,0.8144,0.7785 +56829s,30.3 °C,0.1133,0.1073,0.1128,0.2036,0.1485,0.1628,0.1147,0.1069,0.1107,0.1112,0.1114,0.1205,0.1112,0.1129,0.1174,0.3288,0.2981,0.2865,0.1158,0.1133,0.1154,0.1131,0.1197,0.1128,0.1109,0.115,0.116,0.3766,0.392,0.4037,0.1145,0.1212,0.1087,0.1111,0.1247,0.1121,0.1137,0.1128,0.1144,0.4583,0.4692,0.4679,0.1295,0.1409,0.1412,0.1713,0.1882,0.1275,0.1715,0.1452,0.1558,0.5475,0.4258,0.5835,0.4504,0.3129,0.3159,0.483,0.354,0.2084,0.3388,0.321,0.2971,0.6418,0.6757,0.5653,0.7252,0.6996,0.6986,0.6116,0.6996,0.5868,0.5674,0.6287,0.7493,0.6397,0.5738,0.6271,0.7427,0.8602,0.7824,0.792,0.6167,0.5918,0.8017,0.7384,0.7136,0.7219,0.6888,0.6933,0.8575,0.7701,0.7841,0.7937,0.8182,0.7824 +57506s,30.4 °C,0.1137,0.1073,0.1129,0.205,0.1491,0.163,0.1146,0.1069,0.1106,0.1111,0.1113,0.1207,0.1112,0.1128,0.1166,0.3315,0.3009,0.2898,0.1156,0.1132,0.1154,0.1133,0.1193,0.1128,0.1108,0.1149,0.116,0.3806,0.3958,0.4078,0.1142,0.1211,0.1085,0.1111,0.1245,0.1116,0.1136,0.1129,0.1143,0.465,0.4756,0.4739,0.1293,0.1409,0.1416,0.172,0.1888,0.1275,0.1719,0.1465,0.1568,0.5535,0.4321,0.5907,0.4559,0.3155,0.3182,0.4877,0.3583,0.209,0.3434,0.3268,0.302,0.6499,0.6832,0.5732,0.7298,0.7038,0.7047,0.6168,0.7045,0.5884,0.5708,0.6333,0.7526,0.6478,0.5807,0.634,0.7457,0.863,0.786,0.7974,0.6203,0.595,0.8024,0.7407,0.7159,0.7276,0.6963,0.7001,0.8581,0.7719,0.7849,0.7948,0.8223,0.7859 +58183s,30.5 °C,0.114,0.1073,0.1129,0.2056,0.1495,0.1637,0.1148,0.107,0.1107,0.1112,0.1114,0.1207,0.1112,0.113,0.1159,0.3342,0.3037,0.2921,0.1157,0.1129,0.1154,0.1131,0.1194,0.1129,0.1109,0.115,0.1161,0.3857,0.4005,0.413,0.1144,0.1212,0.1086,0.1112,0.1247,0.1117,0.1138,0.1131,0.1146,0.4728,0.4828,0.48,0.1299,0.1415,0.142,0.1731,0.1896,0.128,0.173,0.1471,0.1578,0.5616,0.439,0.5978,0.4607,0.3196,0.321,0.4939,0.3622,0.21,0.3497,0.3319,0.3088,0.6572,0.6904,0.5788,0.7371,0.7104,0.7102,0.6202,0.7093,0.5878,0.5769,0.6367,0.7588,0.6569,0.588,0.6423,0.7504,0.8653,0.7894,0.8001,0.6229,0.5971,0.8035,0.7423,0.718,0.7337,0.7031,0.7065,0.8593,0.773,0.786,0.7965,0.8241,0.7864 +58859s,30.6 °C,0.114,0.1073,0.1128,0.2054,0.1497,0.1643,0.1147,0.1068,0.1106,0.1112,0.1113,0.1202,0.1111,0.1128,0.1178,0.3372,0.3062,0.295,0.1158,0.1129,0.1154,0.1131,0.1196,0.1129,0.1109,0.115,0.116,0.3899,0.4044,0.4175,0.1144,0.1211,0.1085,0.1111,0.1248,0.112,0.1138,0.113,0.1148,0.4797,0.4894,0.4867,0.1303,0.1419,0.142,0.1736,0.1906,0.1275,0.1735,0.1481,0.1589,0.5681,0.4451,0.6052,0.4656,0.3229,0.3241,0.4986,0.3667,0.2111,0.3523,0.3371,0.3126,0.6636,0.6972,0.5867,0.7395,0.7137,0.7137,0.6244,0.712,0.5929,0.5815,0.6401,0.7624,0.6642,0.5946,0.6492,0.7537,0.8687,0.7922,0.8046,0.6256,0.6008,0.8054,0.7439,0.7195,0.7397,0.7088,0.7148,0.8609,0.7743,0.7882,0.799,0.8242,0.7883 +59536s,30.5 °C,0.114,0.1073,0.1128,0.206,0.15,0.1646,0.1147,0.1068,0.1106,0.1111,0.1113,0.1202,0.111,0.1128,0.1178,0.3394,0.3088,0.2975,0.1158,0.1128,0.1152,0.1131,0.1196,0.1128,0.1108,0.1149,0.1159,0.394,0.408,0.4221,0.1143,0.121,0.1085,0.111,0.1247,0.112,0.1136,0.1128,0.1145,0.4863,0.4954,0.4922,0.1304,0.1416,0.1421,0.1736,0.1909,0.1281,0.1738,0.1487,0.1598,0.5748,0.4514,0.6122,0.4699,0.3263,0.3269,0.5046,0.3699,0.2117,0.3556,0.342,0.3179,0.6696,0.7039,0.5926,0.7433,0.7193,0.7182,0.628,0.7154,0.5959,0.585,0.6432,0.7663,0.6714,0.6008,0.6558,0.7568,0.8714,0.7949,0.8083,0.6281,0.6026,0.8056,0.7437,0.7204,0.7465,0.716,0.7194,0.8607,0.7735,0.7865,0.7964,0.8297,0.7905 +60212s,30.3 °C,0.1141,0.1073,0.1129,0.2066,0.1504,0.1648,0.1147,0.1069,0.1107,0.1111,0.1113,0.1203,0.1111,0.1129,0.1172,0.3422,0.3111,0.3002,0.1158,0.1129,0.1153,0.1132,0.1195,0.1129,0.1109,0.1149,0.116,0.3982,0.412,0.4259,0.1144,0.1212,0.1086,0.1112,0.1249,0.1118,0.1138,0.113,0.1147,0.4916,0.5022,0.4981,0.1311,0.1417,0.1425,0.1741,0.1913,0.1283,0.1745,0.1497,0.1608,0.5808,0.4574,0.6176,0.4746,0.3291,0.3307,0.5087,0.3738,0.2127,0.3585,0.3469,0.322,0.6758,0.7097,0.5997,0.7453,0.7218,0.7226,0.6322,0.717,0.5997,0.5899,0.6472,0.7703,0.6778,0.6076,0.6614,0.7596,0.8747,0.7987,0.8122,0.6308,0.6061,0.8067,0.7454,0.722,0.752,0.7236,0.7261,0.8633,0.7764,0.7897,0.7999,0.8284,0.7915 +60889s,30.5 °C,0.114,0.1073,0.1128,0.207,0.1506,0.1653,0.1146,0.1068,0.1105,0.1111,0.1112,0.12,0.1111,0.1127,0.1178,0.3443,0.3132,0.3018,0.1158,0.113,0.1152,0.1131,0.1196,0.1127,0.1109,0.1149,0.1159,0.4016,0.4151,0.4299,0.1143,0.121,0.1085,0.111,0.1248,0.1119,0.1137,0.1129,0.1145,0.4982,0.5085,0.5039,0.1311,0.1422,0.1426,0.1745,0.192,0.1278,0.1753,0.1497,0.1612,0.5881,0.4631,0.6243,0.4773,0.3334,0.3326,0.5137,0.3759,0.2137,0.3618,0.351,0.3258,0.6812,0.7163,0.6053,0.7479,0.7248,0.7255,0.6344,0.7184,0.6033,0.5935,0.6498,0.7734,0.6849,0.6141,0.6689,0.7625,0.8767,0.8005,0.8154,0.6323,0.6083,0.8082,0.7459,0.7229,0.7576,0.7289,0.7334,0.8648,0.7773,0.7905,0.8014,0.8287,0.793 +61565s,30.3 °C,0.114,0.1073,0.1128,0.2074,0.1509,0.1656,0.1146,0.1068,0.1106,0.1111,0.1112,0.12,0.1111,0.1128,0.1185,0.3464,0.3152,0.3044,0.1158,0.1129,0.1149,0.1131,0.1197,0.1128,0.1108,0.1148,0.1159,0.4057,0.4185,0.4336,0.1142,0.121,0.1085,0.1111,0.1248,0.1116,0.1136,0.1131,0.1147,0.5053,0.514,0.5095,0.1312,0.1425,0.1428,0.1752,0.1927,0.1275,0.1757,0.1501,0.1618,0.5946,0.4688,0.6307,0.4809,0.3369,0.3341,0.5187,0.3786,0.2142,0.3665,0.3555,0.3313,0.6883,0.7228,0.6108,0.753,0.7304,0.7299,0.638,0.7228,0.6028,0.5963,0.6525,0.7768,0.691,0.6196,0.6739,0.7652,0.8778,0.8023,0.8179,0.6342,0.6099,0.8085,0.7468,0.7234,0.7631,0.7353,0.7372,0.8648,0.7778,0.7897,0.8004,0.8323,0.7938 +62242s,30.4 °C,0.114,0.1073,0.1129,0.2079,0.1512,0.1659,0.1146,0.1068,0.1106,0.1112,0.1113,0.1201,0.1111,0.1128,0.1182,0.3488,0.3175,0.3063,0.1157,0.1131,0.1154,0.1131,0.1198,0.1128,0.1108,0.1149,0.1158,0.4092,0.4226,0.4375,0.1144,0.121,0.1085,0.1111,0.1249,0.1127,0.1137,0.1128,0.1145,0.5101,0.5205,0.5147,0.1311,0.1423,0.143,0.1752,0.1927,0.1282,0.1754,0.1522,0.1636,0.5981,0.4745,0.6361,0.4875,0.3363,0.3382,0.5214,0.3834,0.215,0.3703,0.3599,0.3355,0.6936,0.7283,0.6164,0.7555,0.7331,0.7336,0.6403,0.7244,0.6045,0.6012,0.6553,0.7811,0.6978,0.6257,0.6808,0.7675,0.8798,0.8047,0.8196,0.6348,0.6112,0.8104,0.7482,0.7247,0.7689,0.742,0.7451,0.8662,0.7801,0.7925,0.8032,0.8307,0.7949 +62918s,30.5 °C,0.1139,0.1072,0.1128,0.2076,0.1512,0.1663,0.1145,0.1068,0.1106,0.1111,0.1111,0.12,0.1111,0.1127,0.1156,0.3502,0.3193,0.3074,0.1155,0.113,0.1152,0.1128,0.1194,0.1128,0.1108,0.1149,0.1158,0.4124,0.4252,0.4414,0.1143,0.121,0.1085,0.1111,0.1249,0.1125,0.1137,0.1128,0.1142,0.5156,0.5273,0.5203,0.1311,0.1425,0.1433,0.1754,0.1928,0.1286,0.1762,0.1523,0.1639,0.6047,0.4803,0.6425,0.4897,0.3406,0.3406,0.5258,0.3857,0.2156,0.3741,0.3644,0.3399,0.6987,0.7344,0.6227,0.7581,0.737,0.7362,0.6435,0.7263,0.606,0.6045,0.6581,0.7835,0.7038,0.6313,0.6856,0.7694,0.8818,0.8072,0.8239,0.6366,0.6141,0.8109,0.7489,0.7253,0.7743,0.7469,0.7491,0.8671,0.7797,0.7927,0.8028,0.8336,0.7962 +63595s,30.5 °C,0.114,0.1072,0.1128,0.2078,0.1513,0.1667,0.1146,0.1068,0.1105,0.1111,0.1111,0.12,0.1111,0.1129,0.1171,0.3517,0.3209,0.3093,0.1156,0.113,0.1153,0.1131,0.1194,0.1128,0.1108,0.1148,0.1159,0.416,0.4287,0.4436,0.1141,0.1211,0.1084,0.1111,0.1248,0.1116,0.1135,0.1129,0.1142,0.5221,0.5326,0.5269,0.1309,0.1427,0.1435,0.1762,0.1934,0.128,0.1764,0.1535,0.1648,0.6088,0.4861,0.6478,0.4941,0.3422,0.3425,0.5289,0.3887,0.2157,0.3772,0.369,0.3436,0.7036,0.7395,0.6281,0.7607,0.7407,0.739,0.6458,0.728,0.6062,0.6072,0.6609,0.7855,0.7089,0.6358,0.6907,0.7711,0.8836,0.8084,0.8262,0.6379,0.6151,0.8118,0.7497,0.7259,0.7772,0.7521,0.7548,0.8682,0.7801,0.7924,0.8037,0.8342,0.7963 +64271s,30.5 °C,0.114,0.1072,0.1127,0.2082,0.1516,0.1669,0.1145,0.1068,0.1106,0.1111,0.1111,0.1201,0.111,0.1129,0.1169,0.3531,0.3225,0.311,0.1157,0.1127,0.1153,0.1132,0.1196,0.1128,0.1108,0.1149,0.1159,0.419,0.4315,0.4478,0.1144,0.1209,0.1085,0.1111,0.1251,0.1125,0.1136,0.113,0.1145,0.5278,0.5373,0.5316,0.1317,0.1428,0.1436,0.1768,0.194,0.1284,0.1769,0.154,0.1655,0.6146,0.491,0.6534,0.4978,0.3449,0.3441,0.5323,0.3914,0.2166,0.3812,0.3725,0.3483,0.709,0.7447,0.6326,0.7648,0.7436,0.7414,0.6482,0.7307,0.6073,0.6098,0.6636,0.7886,0.7144,0.6405,0.6958,0.7736,0.8842,0.8091,0.8274,0.639,0.6164,0.813,0.7501,0.7272,0.7828,0.7578,0.7596,0.8693,0.7813,0.7927,0.8036,0.8358,0.7971 +64948s,30.3 °C,0.1137,0.1072,0.1128,0.2083,0.1517,0.1671,0.1146,0.1068,0.1106,0.1111,0.1111,0.12,0.1111,0.1128,0.1178,0.3552,0.324,0.3128,0.1157,0.1128,0.1151,0.1133,0.1196,0.1128,0.1108,0.1149,0.1159,0.4227,0.4349,0.4516,0.1143,0.121,0.1085,0.1111,0.1251,0.112,0.1136,0.1128,0.1144,0.5333,0.5434,0.5365,0.1317,0.1428,0.1435,0.1766,0.1942,0.1282,0.1773,0.154,0.1658,0.6211,0.4964,0.6591,0.4999,0.3479,0.3458,0.5359,0.3936,0.2175,0.3833,0.3765,0.3519,0.7136,0.7497,0.6383,0.7669,0.7444,0.7439,0.6502,0.7322,0.6096,0.6134,0.6662,0.7923,0.7206,0.6458,0.7013,0.7758,0.8859,0.8109,0.8286,0.6401,0.6176,0.8141,0.7512,0.7283,0.787,0.7637,0.7647,0.8711,0.782,0.7948,0.805,0.8365,0.7989 +65624s,30.3 °C,0.1139,0.1072,0.1128,0.2089,0.1518,0.1672,0.1144,0.1067,0.1105,0.111,0.1111,0.1198,0.111,0.1127,0.1166,0.357,0.3254,0.3135,0.1155,0.1131,0.1152,0.1128,0.1197,0.1127,0.1107,0.1149,0.1159,0.4262,0.4378,0.4544,0.1142,0.1209,0.1085,0.1111,0.125,0.1119,0.1137,0.1128,0.1145,0.5395,0.5491,0.5422,0.1318,0.1429,0.144,0.177,0.1949,0.1277,0.1781,0.154,0.166,0.627,0.5012,0.6641,0.5021,0.3508,0.3477,0.541,0.395,0.2179,0.3892,0.3799,0.3566,0.7195,0.7555,0.6415,0.7721,0.7494,0.7487,0.6512,0.7352,0.6074,0.6166,0.668,0.7945,0.7262,0.651,0.7062,0.7772,0.8874,0.8126,0.8298,0.6408,0.6185,0.8159,0.7523,0.7293,0.7907,0.7684,0.7708,0.8727,0.7854,0.7973,0.8078,0.8348,0.7991 +66301s,30.3 °C,0.1138,0.1072,0.1128,0.2089,0.1519,0.1676,0.1144,0.1067,0.1105,0.1111,0.111,0.12,0.1111,0.1128,0.1156,0.358,0.3266,0.3153,0.1154,0.1129,0.1151,0.113,0.1194,0.1127,0.1108,0.1149,0.1159,0.4292,0.4402,0.4568,0.1141,0.1211,0.1085,0.1112,0.1248,0.1114,0.1136,0.1128,0.1141,0.5432,0.5553,0.5464,0.1315,0.1429,0.1443,0.1772,0.1944,0.1283,0.1779,0.1554,0.1669,0.6319,0.5071,0.6696,0.5061,0.3519,0.3501,0.543,0.398,0.2181,0.39,0.3839,0.3587,0.7232,0.7601,0.6479,0.772,0.7504,0.7502,0.655,0.7354,0.611,0.6185,0.6701,0.7952,0.731,0.655,0.7101,0.7778,0.8886,0.8138,0.8326,0.6417,0.6195,0.817,0.7538,0.7308,0.7952,0.7731,0.7736,0.8738,0.7843,0.7974,0.8081,0.8383,0.801 +66978s,30.3 °C,0.1138,0.1072,0.1128,0.2092,0.152,0.1678,0.1145,0.1068,0.1106,0.1111,0.1111,0.1199,0.1111,0.1129,0.1179,0.3593,0.3276,0.3167,0.1156,0.1128,0.1152,0.1134,0.1197,0.1127,0.1108,0.1149,0.1159,0.4322,0.4435,0.4604,0.1143,0.121,0.1084,0.1111,0.125,0.1119,0.1136,0.1129,0.1146,0.5495,0.5593,0.5516,0.132,0.1434,0.1439,0.1781,0.1956,0.1282,0.1786,0.1557,0.1674,0.6365,0.5107,0.6744,0.5091,0.3543,0.3516,0.5456,0.4001,0.2188,0.3942,0.3873,0.3635,0.728,0.7642,0.6524,0.7755,0.7542,0.7536,0.6568,0.7382,0.6105,0.6229,0.6727,0.7992,0.7366,0.66,0.7165,0.7811,0.8903,0.8149,0.8338,0.6432,0.6202,0.8186,0.755,0.7321,0.7986,0.7776,0.7803,0.8762,0.7871,0.7991,0.8107,0.837,0.8014 +67654s,30.5 °C,0.1136,0.1072,0.1128,0.2096,0.1521,0.1677,0.1145,0.1067,0.1105,0.1111,0.111,0.1199,0.111,0.1128,0.1176,0.3608,0.3287,0.3177,0.1156,0.1129,0.115,0.1131,0.1198,0.1126,0.1107,0.1149,0.1158,0.4348,0.4464,0.4636,0.1143,0.1209,0.1084,0.1111,0.125,0.1119,0.1135,0.1127,0.1144,0.5545,0.5642,0.5556,0.132,0.1433,0.1439,0.1779,0.1958,0.128,0.1785,0.1558,0.168,0.6408,0.5151,0.6785,0.5117,0.3555,0.3533,0.5498,0.4024,0.2193,0.3956,0.3902,0.3668,0.7318,0.768,0.6564,0.7767,0.7561,0.7557,0.6583,0.7392,0.613,0.6245,0.6742,0.8026,0.7408,0.664,0.7201,0.7824,0.891,0.8162,0.835,0.644,0.6211,0.8202,0.7553,0.733,0.8024,0.7823,0.7834,0.877,0.7875,0.7994,0.8102,0.8404,0.8032 +68331s,30.4 °C,0.1134,0.1072,0.1128,0.2092,0.1521,0.168,0.1143,0.1066,0.1104,0.111,0.1109,0.1198,0.1109,0.1127,0.1176,0.3618,0.3295,0.3194,0.1156,0.1128,0.1148,0.1133,0.1197,0.1125,0.1107,0.1148,0.1158,0.438,0.4492,0.4665,0.1141,0.1208,0.1083,0.111,0.125,0.1117,0.1135,0.1128,0.1144,0.5589,0.5698,0.5598,0.1325,0.1434,0.1442,0.1782,0.1957,0.128,0.1791,0.1557,0.1681,0.6461,0.5199,0.6838,0.5131,0.3591,0.3549,0.5535,0.4036,0.2196,0.3977,0.3932,0.3698,0.7345,0.7718,0.6606,0.7778,0.7575,0.7581,0.6604,0.7401,0.6133,0.628,0.6757,0.8054,0.7458,0.6693,0.7256,0.7849,0.8924,0.817,0.8355,0.6449,0.6214,0.8209,0.7571,0.7342,0.8046,0.786,0.7885,0.8783,0.7897,0.8015,0.8129,0.8392,0.8039 +69007s,30.3 °C,0.1135,0.1072,0.1128,0.2096,0.1523,0.1679,0.1144,0.1066,0.1105,0.1111,0.1109,0.1199,0.111,0.1127,0.1172,0.3636,0.3307,0.3202,0.1154,0.113,0.115,0.113,0.1196,0.1125,0.1108,0.1149,0.116,0.4411,0.4513,0.4688,0.114,0.1209,0.1084,0.1111,0.1249,0.1111,0.1136,0.1127,0.1144,0.5646,0.575,0.5646,0.1322,0.1435,0.1446,0.1782,0.196,0.128,0.1791,0.1567,0.1689,0.65,0.5246,0.6882,0.5172,0.3594,0.3576,0.5563,0.4063,0.2202,0.4021,0.3968,0.3731,0.7394,0.777,0.6645,0.7814,0.7611,0.7623,0.6615,0.7422,0.6138,0.6283,0.6775,0.8043,0.7497,0.6723,0.7261,0.7844,0.8945,0.8193,0.8379,0.6461,0.624,0.8231,0.7593,0.7356,0.8083,0.7903,0.7915,0.8799,0.7915,0.8046,0.8152,0.8388,0.8061 +69684s,30.4 °C,0.1131,0.1071,0.1127,0.2087,0.1521,0.1684,0.1143,0.1066,0.1105,0.1111,0.1108,0.1193,0.111,0.1128,0.1161,0.3642,0.332,0.3208,0.1153,0.1128,0.115,0.113,0.1193,0.1126,0.1107,0.1149,0.1158,0.4432,0.454,0.4712,0.1142,0.1209,0.1084,0.1111,0.125,0.1119,0.1135,0.1128,0.1141,0.5676,0.5799,0.5686,0.132,0.1434,0.1447,0.1784,0.1957,0.1285,0.1796,0.1573,0.1694,0.6538,0.5292,0.6926,0.5196,0.362,0.3589,0.5588,0.4082,0.2205,0.4051,0.3999,0.3759,0.7429,0.7806,0.6685,0.7829,0.7635,0.7646,0.6629,0.7426,0.6141,0.6344,0.6803,0.8083,0.7548,0.6767,0.7335,0.7877,0.8953,0.8213,0.8392,0.6472,0.6236,0.8238,0.7602,0.7361,0.8099,0.7944,0.795,0.8809,0.7928,0.8057,0.8163,0.8411,0.8065 +70360s,30.4 °C,0.1134,0.1072,0.1127,0.2094,0.1525,0.1682,0.1143,0.1066,0.1104,0.111,0.1109,0.1197,0.1109,0.1128,0.1166,0.3653,0.3328,0.3217,0.1154,0.1127,0.115,0.1132,0.1196,0.1126,0.1107,0.1148,0.1158,0.4459,0.4567,0.4747,0.1142,0.1209,0.1084,0.111,0.125,0.1122,0.1135,0.1129,0.1145,0.5735,0.5833,0.5728,0.1326,0.1438,0.1443,0.179,0.1965,0.1285,0.1797,0.1575,0.1696,0.6568,0.5329,0.6963,0.5218,0.3633,0.3597,0.5597,0.4097,0.2209,0.4085,0.4027,0.3793,0.7467,0.7837,0.673,0.7855,0.7664,0.7661,0.6645,0.7439,0.6147,0.6358,0.6805,0.8089,0.7576,0.6788,0.7352,0.7885,0.8964,0.8223,0.8397,0.6476,0.6239,0.8253,0.761,0.7376,0.8111,0.7968,0.799,0.8834,0.7936,0.807,0.8173,0.8418,0.807 +71037s,30.4 °C,0.1135,0.1072,0.1129,0.2101,0.1526,0.1681,0.1143,0.1066,0.1104,0.111,0.1108,0.1199,0.111,0.1128,0.1186,0.3666,0.3335,0.3229,0.1157,0.1129,0.1151,0.1133,0.1197,0.1125,0.1107,0.1147,0.116,0.4487,0.4594,0.4764,0.1139,0.1209,0.1083,0.111,0.1249,0.111,0.1133,0.1126,0.1143,0.5764,0.5884,0.5759,0.1327,0.1433,0.1444,0.1785,0.1961,0.1285,0.1799,0.1574,0.1699,0.6611,0.5369,0.7001,0.5237,0.3652,0.3613,0.5635,0.4115,0.2215,0.4081,0.405,0.3812,0.7488,0.7867,0.6765,0.7864,0.7677,0.7675,0.6655,0.7449,0.6184,0.6356,0.6826,0.8113,0.7626,0.6824,0.7394,0.7904,0.8985,0.8241,0.841,0.6494,0.6257,0.8275,0.7623,0.7392,0.8147,0.8004,0.8016,0.8848,0.796,0.8073,0.8174,0.8458,0.8104 +71713s,30.4 °C,0.1131,0.1071,0.1127,0.2091,0.1524,0.1685,0.1143,0.1066,0.1105,0.111,0.1107,0.119,0.111,0.1127,0.1171,0.3673,0.3345,0.3238,0.1155,0.1129,0.1148,0.1129,0.1195,0.1125,0.1106,0.1148,0.1159,0.4514,0.4616,0.4798,0.114,0.1208,0.1083,0.1111,0.1249,0.1112,0.1134,0.1126,0.1143,0.5815,0.5924,0.5797,0.1327,0.1437,0.1444,0.1788,0.1964,0.1283,0.1804,0.1579,0.1704,0.6659,0.5415,0.7041,0.526,0.3675,0.3632,0.5658,0.4135,0.2218,0.4115,0.4075,0.3839,0.7519,0.7896,0.6795,0.7882,0.7688,0.7698,0.6664,0.7457,0.6186,0.6388,0.6841,0.8136,0.766,0.6861,0.743,0.792,0.8995,0.8252,0.8422,0.6502,0.6263,0.8286,0.7636,0.7406,0.8166,0.8031,0.8036,0.8863,0.7968,0.8089,0.8182,0.8481,0.8121 +72390s,30.4 °C,0.1133,0.1071,0.1128,0.2094,0.1526,0.1684,0.1143,0.1066,0.1103,0.1109,0.1107,0.1192,0.1109,0.1126,0.1176,0.3674,0.3349,0.3242,0.1155,0.1127,0.1147,0.1128,0.1195,0.1124,0.1106,0.1148,0.1158,0.4535,0.4633,0.4817,0.1139,0.1208,0.1082,0.111,0.1249,0.1115,0.1134,0.1126,0.1144,0.5859,0.596,0.583,0.1327,0.1438,0.1444,0.1793,0.1969,0.1277,0.1809,0.1573,0.1701,0.67,0.5445,0.7075,0.5264,0.3698,0.3638,0.5688,0.414,0.2221,0.4131,0.4105,0.3861,0.7544,0.7929,0.6838,0.7898,0.7695,0.7707,0.6686,0.7466,0.6195,0.6405,0.6855,0.8141,0.7683,0.6881,0.7445,0.7928,0.9015,0.8264,0.8441,0.6512,0.6272,0.829,0.7638,0.7415,0.8181,0.8052,0.8044,0.8865,0.7958,0.8077,0.8166,0.8534,0.8146 +73066s,30.3 °C,0.1134,0.1071,0.1128,0.2095,0.1527,0.1684,0.1143,0.1065,0.1104,0.1109,0.1108,0.1191,0.1108,0.1127,0.1179,0.3685,0.3361,0.3252,0.1155,0.1129,0.1149,0.1131,0.1196,0.1126,0.1106,0.1148,0.1158,0.4555,0.4655,0.4846,0.114,0.1208,0.1083,0.111,0.1249,0.112,0.1134,0.1127,0.1145,0.5883,0.6002,0.5868,0.1331,0.1435,0.1445,0.1791,0.1967,0.1289,0.1806,0.1588,0.1713,0.6713,0.5483,0.7109,0.5306,0.3701,0.3658,0.5683,0.4169,0.2228,0.4173,0.4124,0.389,0.7576,0.7958,0.6858,0.7916,0.7744,0.7731,0.6684,0.7486,0.6199,0.6419,0.6862,0.815,0.7707,0.6907,0.7467,0.7934,0.9028,0.828,0.8456,0.6523,0.6287,0.8315,0.7667,0.7429,0.8191,0.8086,0.8093,0.8895,0.8004,0.8116,0.821,0.8501,0.8144 +73743s,30.3 °C,0.1133,0.1071,0.1128,0.2094,0.1528,0.1686,0.1142,0.1066,0.1104,0.111,0.1107,0.1192,0.111,0.1127,0.1183,0.3693,0.3368,0.3257,0.1156,0.113,0.115,0.1129,0.1196,0.1124,0.1106,0.1148,0.1158,0.4579,0.4681,0.487,0.114,0.1207,0.1083,0.1109,0.125,0.1118,0.1134,0.1126,0.1143,0.5922,0.6047,0.59,0.1328,0.1436,0.1447,0.1788,0.1966,0.1285,0.1813,0.1582,0.1711,0.6755,0.5518,0.714,0.531,0.3723,0.3676,0.572,0.4175,0.223,0.4185,0.4154,0.3916,0.7607,0.799,0.6882,0.7942,0.7767,0.7751,0.6695,0.7497,0.6189,0.6409,0.6869,0.8162,0.7737,0.6932,0.7487,0.7941,0.904,0.8292,0.8467,0.6526,0.6297,0.8337,0.7696,0.7446,0.8203,0.8105,0.8125,0.8912,0.8038,0.815,0.8244,0.8492,0.8163 +74419s,30.3 °C,0.1133,0.107,0.1127,0.2091,0.1527,0.1686,0.1142,0.1065,0.1103,0.1109,0.1107,0.1191,0.1109,0.1128,0.116,0.3699,0.3376,0.3267,0.1153,0.113,0.1152,0.113,0.1193,0.1125,0.1105,0.1148,0.1158,0.4599,0.47,0.4884,0.114,0.1208,0.1082,0.111,0.125,0.1123,0.1135,0.113,0.1144,0.5968,0.6079,0.594,0.1327,0.1438,0.1451,0.1797,0.197,0.1286,0.1816,0.159,0.1714,0.6781,0.5548,0.7168,0.5332,0.373,0.3678,0.5731,0.4188,0.2231,0.4218,0.4183,0.3939,0.7627,0.8006,0.692,0.7952,0.7777,0.7772,0.6711,0.7509,0.6192,0.6439,0.6886,0.818,0.7761,0.6952,0.7517,0.7959,0.9049,0.8305,0.8478,0.6535,0.6296,0.8347,0.7715,0.7459,0.8198,0.8127,0.8147,0.893,0.8056,0.8168,0.8274,0.8482,0.8161 +75096s,30.5 °C,0.1136,0.107,0.1127,0.2096,0.1529,0.1686,0.1142,0.1065,0.1103,0.1109,0.1107,0.1191,0.1109,0.1128,0.1188,0.3706,0.338,0.3276,0.1154,0.1126,0.1147,0.113,0.1194,0.1123,0.1107,0.1147,0.1159,0.4631,0.4726,0.4908,0.1136,0.1208,0.1081,0.111,0.1248,0.1108,0.1133,0.1127,0.1143,0.6004,0.6106,0.5966,0.1329,0.1437,0.1445,0.1796,0.1971,0.128,0.1815,0.1591,0.1718,0.6817,0.5579,0.7198,0.5352,0.3745,0.3687,0.5749,0.4203,0.2233,0.4236,0.4199,0.3962,0.7652,0.8024,0.6936,0.7974,0.7779,0.778,0.6715,0.7519,0.6186,0.6449,0.6906,0.8194,0.7798,0.6985,0.7555,0.7988,0.9052,0.8303,0.8482,0.6549,0.6304,0.8362,0.7722,0.7476,0.8211,0.8139,0.8144,0.8944,0.8051,0.8169,0.8266,0.8533,0.8192 +75773s,30.5 °C,0.1135,0.1071,0.1127,0.2097,0.1528,0.1685,0.1142,0.1065,0.1103,0.1109,0.1107,0.119,0.1109,0.1126,0.1186,0.3714,0.3387,0.3279,0.1154,0.1127,0.1147,0.1129,0.1193,0.1123,0.1106,0.1147,0.1159,0.4658,0.4749,0.4924,0.1137,0.1208,0.1081,0.111,0.1247,0.111,0.1134,0.1127,0.1144,0.6046,0.6141,0.5999,0.133,0.144,0.1446,0.1797,0.1975,0.128,0.1821,0.1589,0.1719,0.6836,0.5608,0.7216,0.536,0.375,0.3693,0.5761,0.4216,0.2238,0.4266,0.422,0.399,0.7672,0.8051,0.6955,0.7995,0.7803,0.7801,0.672,0.7535,0.6198,0.6464,0.691,0.8204,0.7814,0.6997,0.7571,0.7988,0.9065,0.8317,0.8498,0.6554,0.6316,0.8388,0.774,0.7498,0.8226,0.8157,0.8172,0.8965,0.8081,0.8191,0.8288,0.855,0.8218 +76449s,30.5 °C,0.1134,0.107,0.1127,0.2094,0.1528,0.1685,0.1141,0.1064,0.1103,0.1109,0.1106,0.1187,0.1108,0.1127,0.1176,0.3723,0.3392,0.3284,0.1154,0.1128,0.1147,0.1128,0.1195,0.1123,0.1104,0.1148,0.1157,0.4673,0.4766,0.4965,0.1139,0.1207,0.1082,0.1108,0.1249,0.112,0.1134,0.1126,0.1144,0.6077,0.6179,0.6019,0.1331,0.1438,0.1447,0.1797,0.1975,0.1282,0.1819,0.1597,0.1726,0.6849,0.5638,0.7245,0.5388,0.3753,0.3707,0.5767,0.424,0.2242,0.4292,0.4238,0.4015,0.7693,0.8071,0.6983,0.8003,0.7815,0.7805,0.6731,0.755,0.6208,0.6479,0.6921,0.8219,0.7831,0.7015,0.758,0.8002,0.9082,0.8333,0.8513,0.6572,0.633,0.8399,0.7755,0.751,0.823,0.816,0.8175,0.8976,0.8089,0.8205,0.8299,0.8556,0.823 +77126s,30.5 °C,0.1132,0.107,0.1127,0.2093,0.1527,0.1685,0.1141,0.1064,0.1102,0.1108,0.1105,0.1186,0.1106,0.1125,0.1172,0.3723,0.34,0.3287,0.1153,0.1126,0.1147,0.1127,0.1192,0.1122,0.1103,0.1147,0.1156,0.4691,0.4785,0.4988,0.1138,0.1204,0.108,0.1107,0.1248,0.1124,0.1132,0.1126,0.1143,0.6115,0.6205,0.6052,0.133,0.1439,0.1448,0.1798,0.1976,0.1281,0.1817,0.1598,0.1729,0.6874,0.5665,0.7262,0.5402,0.376,0.3718,0.5786,0.425,0.2244,0.428,0.4262,0.4031,0.7709,0.8087,0.7005,0.7996,0.7811,0.7814,0.6747,0.7552,0.6242,0.6468,0.6936,0.8243,0.7866,0.7035,0.7603,0.8019,0.9094,0.8343,0.8526,0.6581,0.6342,0.8413,0.7767,0.7531,0.8249,0.8176,0.8162,0.8985,0.81,0.8204,0.8299,0.862,0.8271 +77802s,30.5 °C,0.1131,0.107,0.1126,0.209,0.1527,0.1687,0.1141,0.1064,0.1103,0.1109,0.1106,0.1183,0.1108,0.1126,0.1166,0.3733,0.3405,0.3295,0.1154,0.1125,0.1147,0.1129,0.1194,0.1124,0.1104,0.1148,0.1158,0.4714,0.4807,0.501,0.1139,0.1206,0.1082,0.1108,0.1249,0.1121,0.1134,0.1126,0.1143,0.614,0.6235,0.6068,0.133,0.1439,0.1449,0.1799,0.1977,0.1285,0.1824,0.1602,0.1733,0.6899,0.5692,0.7291,0.5421,0.3779,0.3731,0.5794,0.4264,0.2246,0.4304,0.4287,0.4057,0.7731,0.8112,0.7035,0.8016,0.7825,0.7827,0.6766,0.7565,0.6246,0.6496,0.6953,0.8268,0.7882,0.7051,0.762,0.8036,0.9109,0.8361,0.854,0.6595,0.6352,0.8431,0.7794,0.7552,0.8255,0.8189,0.818,0.9006,0.8118,0.8236,0.8323,0.8623,0.8286 +78479s,30.5 °C,0.1129,0.1069,0.1126,0.2086,0.1527,0.1688,0.1141,0.1063,0.1102,0.1109,0.1105,0.1182,0.1109,0.1125,0.1179,0.374,0.3409,0.3305,0.1155,0.1127,0.1146,0.113,0.1193,0.1124,0.1105,0.1147,0.1158,0.4734,0.4829,0.5023,0.1136,0.1206,0.1081,0.1108,0.1247,0.1113,0.1133,0.1124,0.1141,0.6171,0.6269,0.6094,0.1328,0.1438,0.1449,0.1796,0.1975,0.1284,0.1826,0.1595,0.173,0.692,0.571,0.7302,0.5419,0.3795,0.3742,0.5822,0.4269,0.2248,0.434,0.4304,0.408,0.775,0.8132,0.704,0.8033,0.7842,0.7851,0.6757,0.7578,0.6222,0.649,0.6957,0.8268,0.7891,0.7061,0.7634,0.8039,0.9118,0.8369,0.8555,0.66,0.6358,0.8448,0.7804,0.7561,0.8266,0.8188,0.8186,0.9016,0.8131,0.825,0.8341,0.8635,0.8301 +79155s,30.5 °C,0.1129,0.107,0.1126,0.2089,0.1528,0.1685,0.114,0.1064,0.1103,0.1108,0.1105,0.1184,0.1108,0.1125,0.1173,0.3746,0.3414,0.3303,0.1152,0.1126,0.1147,0.1126,0.1193,0.1123,0.1104,0.1147,0.1157,0.4754,0.4844,0.5043,0.1138,0.1204,0.108,0.1107,0.1248,0.1118,0.1133,0.1125,0.1143,0.6198,0.6296,0.6117,0.1327,0.1441,0.1449,0.1797,0.1978,0.1281,0.1824,0.1609,0.1739,0.6919,0.5736,0.7311,0.5452,0.3786,0.3754,0.5816,0.4291,0.2253,0.4357,0.4326,0.4102,0.7751,0.8143,0.7065,0.8037,0.7841,0.7856,0.6777,0.7583,0.6241,0.6511,0.697,0.8289,0.791,0.7081,0.7641,0.8052,0.9127,0.8381,0.8563,0.661,0.637,0.8463,0.7821,0.7575,0.8265,0.819,0.8185,0.9029,0.8147,0.827,0.8355,0.8647,0.8315 +79832s,30.5 °C,0.113,0.107,0.1126,0.2089,0.1529,0.1684,0.1138,0.1063,0.1102,0.1108,0.1104,0.1183,0.1107,0.1125,0.1166,0.3742,0.3418,0.3303,0.115,0.1125,0.1146,0.1126,0.119,0.1124,0.1103,0.1145,0.1157,0.4768,0.4859,0.5051,0.1137,0.1205,0.108,0.1108,0.1246,0.1118,0.1133,0.1126,0.1143,0.6222,0.6324,0.6125,0.1328,0.1438,0.1452,0.18,0.1978,0.1282,0.1824,0.1608,0.174,0.6934,0.5759,0.733,0.5459,0.3798,0.3768,0.5832,0.4299,0.2255,0.4355,0.435,0.4115,0.7758,0.8157,0.7088,0.804,0.7853,0.787,0.6793,0.759,0.6255,0.6501,0.6985,0.8302,0.792,0.7092,0.7653,0.8062,0.9137,0.8392,0.8575,0.6621,0.6376,0.8479,0.7843,0.7603,0.8285,0.8203,0.819,0.9043,0.8174,0.8279,0.8373,0.8678,0.8348 +80508s,30.6 °C,0.1134,0.1069,0.1127,0.2093,0.1529,0.1682,0.1139,0.1063,0.1101,0.1108,0.1104,0.1185,0.1108,0.1127,0.1162,0.3747,0.3421,0.331,0.115,0.1125,0.1148,0.1126,0.119,0.1122,0.1104,0.1145,0.1158,0.4787,0.4877,0.5062,0.1136,0.1205,0.108,0.1107,0.1246,0.1113,0.1133,0.1128,0.1141,0.6256,0.6342,0.6154,0.1324,0.1439,0.1451,0.1805,0.198,0.1282,0.1835,0.16,0.1734,0.6965,0.5768,0.7342,0.5446,0.383,0.3762,0.5854,0.4291,0.2254,0.4389,0.4369,0.414,0.7768,0.8168,0.7099,0.8055,0.7874,0.7885,0.68,0.7601,0.6246,0.6518,0.7,0.8316,0.7935,0.7098,0.7665,0.8076,0.9149,0.8404,0.8594,0.6627,0.6383,0.8491,0.7865,0.7618,0.8292,0.8205,0.8177,0.9055,0.8181,0.829,0.8384,0.8713,0.8365 +81185s,30.4 °C,0.1136,0.107,0.1126,0.2091,0.1528,0.1681,0.1139,0.1063,0.1101,0.1108,0.1104,0.1184,0.1107,0.1127,0.1177,0.3748,0.3425,0.3314,0.1152,0.1125,0.1147,0.1131,0.1192,0.1123,0.1105,0.1146,0.1157,0.4803,0.4898,0.5085,0.1137,0.1205,0.1079,0.1108,0.1247,0.1117,0.1133,0.1128,0.1143,0.6277,0.6362,0.6176,0.1329,0.1439,0.1451,0.1807,0.1983,0.1282,0.1832,0.1615,0.1745,0.6954,0.5784,0.7349,0.5488,0.3812,0.378,0.5845,0.4324,0.2257,0.4409,0.4384,0.416,0.7784,0.8184,0.7112,0.8071,0.789,0.789,0.6819,0.7616,0.6271,0.6528,0.7009,0.8321,0.7946,0.7103,0.7667,0.809,0.9167,0.8415,0.8607,0.6644,0.6397,0.852,0.789,0.7645,0.8309,0.8215,0.8209,0.9087,0.8218,0.8328,0.8425,0.8703,0.8383 +81861s,30.3 °C,0.1135,0.107,0.1127,0.209,0.1527,0.1682,0.1139,0.1063,0.1101,0.1107,0.1104,0.118,0.1106,0.1126,0.1175,0.3751,0.3428,0.3313,0.1152,0.1123,0.1146,0.1128,0.1193,0.1121,0.1103,0.1146,0.1156,0.4818,0.4912,0.5111,0.1137,0.1204,0.1079,0.1107,0.1247,0.1118,0.1131,0.1125,0.1141,0.6302,0.6388,0.6186,0.1327,0.1438,0.1447,0.1804,0.1983,0.1284,0.183,0.1611,0.1746,0.6969,0.5798,0.7356,0.549,0.3827,0.3791,0.5853,0.4328,0.2262,0.4412,0.4392,0.4172,0.7781,0.8184,0.7121,0.8063,0.7887,0.7892,0.6826,0.7615,0.63,0.6556,0.7017,0.8339,0.7949,0.7107,0.7672,0.8102,0.9177,0.8422,0.8616,0.6651,0.6406,0.8535,0.7895,0.7663,0.8321,0.8225,0.8204,0.9098,0.8224,0.8327,0.8414,0.8741,0.8413 +82538s,30.5 °C,0.1135,0.107,0.1127,0.2092,0.1528,0.1682,0.114,0.1063,0.1102,0.1108,0.1105,0.1183,0.1107,0.1125,0.1176,0.3759,0.3432,0.3319,0.1152,0.1125,0.1146,0.1128,0.1193,0.1122,0.1104,0.1145,0.1158,0.4839,0.4932,0.5119,0.1135,0.1204,0.1079,0.1108,0.1245,0.1111,0.1133,0.1126,0.1144,0.6317,0.6405,0.6189,0.1332,0.144,0.1451,0.1806,0.1985,0.1278,0.1838,0.1604,0.1742,0.6988,0.5814,0.7369,0.5486,0.385,0.379,0.5869,0.4327,0.2265,0.444,0.4402,0.4194,0.7787,0.8185,0.7119,0.8086,0.7902,0.7912,0.6818,0.7633,0.627,0.6553,0.7022,0.8349,0.7964,0.7118,0.7693,0.8113,0.9171,0.8429,0.8612,0.6649,0.64,0.8554,0.7923,0.7682,0.8339,0.8232,0.8223,0.9117,0.8253,0.8361,0.8451,0.8739,0.843 +83215s,30.3 °C,0.1135,0.1069,0.1127,0.2088,0.1527,0.1682,0.1139,0.1063,0.1101,0.1107,0.1105,0.118,0.1107,0.1125,0.1172,0.3764,0.3432,0.3321,0.115,0.1124,0.1145,0.1125,0.1192,0.1122,0.1104,0.1146,0.1156,0.485,0.4942,0.5142,0.1136,0.1204,0.1079,0.1107,0.1246,0.1119,0.1133,0.1124,0.114,0.6329,0.6434,0.6201,0.1327,0.1437,0.1449,0.1801,0.1979,0.129,0.1837,0.1611,0.1749,0.6992,0.5824,0.738,0.5507,0.3845,0.3796,0.5868,0.4343,0.2266,0.4453,0.4414,0.4205,0.7793,0.8192,0.713,0.81,0.7902,0.7919,0.6833,0.7635,0.6281,0.6571,0.7035,0.8359,0.7967,0.7126,0.7683,0.8119,0.9196,0.845,0.8639,0.6668,0.6421,0.857,0.7938,0.7692,0.8344,0.8244,0.8233,0.9131,0.8278,0.839,0.8479,0.8725,0.8437 +83891s,30.8 °C,0.1132,0.1069,0.1126,0.2083,0.1526,0.1682,0.1138,0.1062,0.1101,0.1107,0.1103,0.1178,0.1106,0.1125,0.1175,0.3766,0.3436,0.332,0.115,0.1126,0.1145,0.1125,0.119,0.1122,0.1102,0.1144,0.1155,0.4866,0.4956,0.5157,0.1136,0.1202,0.1079,0.1105,0.1246,0.1119,0.1132,0.1123,0.1141,0.634,0.6444,0.6204,0.1327,0.1436,0.145,0.1799,0.1978,0.1286,0.1839,0.1611,0.1748,0.699,0.5837,0.738,0.5512,0.3855,0.3801,0.5873,0.4346,0.2268,0.4474,0.4429,0.422,0.7797,0.82,0.7133,0.8118,0.7931,0.7938,0.6838,0.7651,0.6287,0.6568,0.7044,0.8364,0.7964,0.7131,0.769,0.8129,0.9199,0.8452,0.8649,0.6668,0.6424,0.8588,0.7957,0.7711,0.8357,0.8252,0.8248,0.9144,0.8299,0.8408,0.8495,0.875,0.846 +84568s,30.5 °C,0.1134,0.1068,0.1125,0.208,0.1526,0.1683,0.1138,0.1061,0.1101,0.1107,0.1103,0.1177,0.1106,0.1126,0.1161,0.376,0.344,0.3323,0.1148,0.1123,0.1147,0.1126,0.1189,0.1122,0.1103,0.1144,0.1156,0.4883,0.4972,0.516,0.1135,0.1202,0.1078,0.1106,0.1245,0.1116,0.1131,0.1126,0.1139,0.6359,0.6456,0.6216,0.1325,0.1437,0.1449,0.1803,0.1978,0.1284,0.1838,0.1618,0.1752,0.6993,0.5845,0.7387,0.553,0.3858,0.3809,0.5864,0.4357,0.2266,0.4482,0.4445,0.4233,0.7794,0.8196,0.7148,0.8113,0.7936,0.7937,0.686,0.7649,0.6303,0.6598,0.7058,0.8383,0.797,0.7135,0.7699,0.8148,0.9208,0.8468,0.8665,0.6682,0.6431,0.86,0.7973,0.7732,0.8375,0.8255,0.8254,0.9158,0.8307,0.8415,0.85,0.8788,0.8483 +85244s,31.0 °C,0.1136,0.1066,0.1123,0.2077,0.1528,0.1669,0.1138,0.1063,0.1101,0.1107,0.1111,0.116,0.1102,0.1127,0.1172,0.3707,0.3421,0.3281,0.1145,0.1121,0.1142,0.1125,0.1188,0.1126,0.11,0.1141,0.1154,0.4848,0.4933,0.5106,0.1136,0.1198,0.1081,0.1107,0.1243,0.1117,0.1128,0.1122,0.1141,0.6342,0.6476,0.622,0.1313,0.1442,0.1453,0.1817,0.1984,0.1286,0.1837,0.1594,0.1718,0.6954,0.5841,0.7321,0.5471,0.3823,0.3752,0.5729,0.4345,0.2285,0.4478,0.4419,0.4183,0.7764,0.8196,0.7121,0.808,0.7817,0.79,0.6841,0.7628,0.6352,0.6451,0.7087,0.832,0.796,0.7142,0.7696,0.8179,0.9158,0.8412,0.8629,0.6657,0.6425,0.8591,0.7965,0.7717,0.839,0.815,0.8173,0.9152,0.8235,0.8383,0.846,0.8795,0.8497 +85921s,30.8 °C,0.1134,0.1067,0.1124,0.2079,0.1528,0.167,0.1138,0.1063,0.1102,0.1106,0.111,0.1162,0.1102,0.1126,0.1178,0.3718,0.3421,0.3289,0.1146,0.1122,0.1141,0.1123,0.1189,0.1123,0.11,0.114,0.1154,0.4863,0.4953,0.5137,0.1134,0.1197,0.1079,0.1107,0.1243,0.1111,0.1126,0.112,0.1141,0.6359,0.6483,0.6227,0.1313,0.1443,0.1449,0.1815,0.1989,0.128,0.1834,0.1597,0.1725,0.6953,0.5853,0.7326,0.5484,0.3822,0.3763,0.5749,0.4353,0.2284,0.4473,0.4429,0.4192,0.7772,0.8205,0.7132,0.8087,0.7826,0.7911,0.6854,0.7642,0.6374,0.6456,0.7091,0.8324,0.796,0.7143,0.7687,0.8183,0.918,0.843,0.8649,0.6671,0.6443,0.8613,0.7981,0.7737,0.8411,0.8174,0.8189,0.9167,0.8264,0.8399,0.8483,0.8811,0.8525 +86597s,30.8 °C,0.1135,0.1066,0.1124,0.2074,0.1528,0.167,0.1138,0.1063,0.1102,0.1107,0.111,0.1159,0.1102,0.1127,0.1167,0.3722,0.3426,0.3289,0.1146,0.1122,0.1142,0.1122,0.119,0.1125,0.11,0.1141,0.1154,0.4885,0.4969,0.5157,0.1136,0.1198,0.108,0.1107,0.1244,0.1119,0.113,0.112,0.114,0.6365,0.6499,0.6229,0.1313,0.1436,0.1454,0.1812,0.1983,0.1285,0.184,0.1598,0.1724,0.6963,0.5863,0.7329,0.5482,0.3842,0.3776,0.5758,0.4357,0.229,0.4508,0.4436,0.4206,0.7775,0.8209,0.7136,0.81,0.7833,0.7928,0.6859,0.7653,0.6373,0.6491,0.7106,0.8342,0.7969,0.7153,0.7706,0.82,0.9187,0.8445,0.8652,0.6674,0.6445,0.8624,0.8002,0.775,0.8421,0.8181,0.8199,0.9186,0.828,0.843,0.8517,0.8795,0.8539 +87274s,30.7 °C,0.1134,0.1065,0.1123,0.2071,0.1526,0.1671,0.1137,0.1063,0.1102,0.1106,0.1109,0.1159,0.1101,0.1126,0.1154,0.3721,0.3428,0.3289,0.1144,0.1122,0.1142,0.1122,0.1187,0.1125,0.1099,0.114,0.1153,0.4887,0.4972,0.5162,0.1135,0.1197,0.1079,0.1105,0.1242,0.1121,0.1128,0.112,0.1137,0.6373,0.6514,0.6235,0.131,0.1436,0.1455,0.1813,0.1982,0.1285,0.1835,0.1607,0.1732,0.6958,0.5875,0.7338,0.5514,0.3833,0.3791,0.5747,0.4374,0.2286,0.4518,0.445,0.4214,0.7778,0.8216,0.7143,0.8111,0.7845,0.7938,0.6875,0.7658,0.637,0.6499,0.7119,0.8352,0.7969,0.7156,0.7712,0.8207,0.92,0.8456,0.8669,0.6682,0.6449,0.8634,0.8024,0.7767,0.8425,0.8192,0.822,0.92,0.8303,0.8448,0.8545,0.8786,0.8542 +87950s,31.0 °C,0.1136,0.1066,0.1123,0.2077,0.1527,0.1668,0.1137,0.1063,0.1101,0.1105,0.1108,0.1161,0.1101,0.1127,0.1166,0.3721,0.3427,0.3293,0.1143,0.1121,0.1141,0.1123,0.1186,0.1124,0.1099,0.1139,0.1153,0.4901,0.4997,0.5169,0.1134,0.1197,0.1078,0.1106,0.1241,0.1114,0.1128,0.1121,0.1141,0.6387,0.6509,0.6239,0.1309,0.1443,0.1454,0.1818,0.1988,0.1281,0.184,0.1605,0.1728,0.6968,0.588,0.7338,0.5507,0.3849,0.3795,0.5751,0.4373,0.2288,0.4521,0.4457,0.4224,0.7779,0.8214,0.7149,0.8114,0.7854,0.7945,0.6887,0.7665,0.6389,0.6493,0.7133,0.8355,0.7968,0.7155,0.7699,0.8222,0.9218,0.8463,0.8701,0.6706,0.6467,0.8654,0.8035,0.7788,0.8452,0.8208,0.8242,0.9217,0.8314,0.8457,0.855,0.8837,0.8574 +88627s,30.7 °C,0.1134,0.1065,0.1122,0.2071,0.1525,0.1669,0.1137,0.1062,0.1101,0.1106,0.1108,0.1159,0.1101,0.1126,0.117,0.3722,0.3431,0.3291,0.1145,0.112,0.1142,0.1124,0.1189,0.1123,0.1099,0.114,0.1153,0.4921,0.5009,0.519,0.1134,0.1196,0.1078,0.1105,0.1243,0.1118,0.1127,0.112,0.114,0.6388,0.6523,0.6242,0.1315,0.1436,0.1453,0.1816,0.1983,0.1286,0.184,0.1601,0.1727,0.6974,0.5886,0.7344,0.5507,0.3854,0.379,0.5754,0.4382,0.2293,0.4517,0.4463,0.4241,0.7782,0.8218,0.7156,0.8123,0.7861,0.7952,0.69,0.7678,0.6401,0.6488,0.714,0.8386,0.7982,0.716,0.7711,0.8241,0.9225,0.8476,0.8703,0.6713,0.6476,0.8672,0.8051,0.7805,0.8474,0.8216,0.8251,0.923,0.8332,0.847,0.856,0.8851,0.8595 +89303s,30.9 °C,0.1133,0.1066,0.1123,0.2071,0.1524,0.1669,0.1137,0.1062,0.11,0.1105,0.1108,0.1159,0.1101,0.1126,0.1165,0.3733,0.3434,0.3296,0.1144,0.1121,0.1141,0.1123,0.1188,0.1122,0.1098,0.114,0.1154,0.4934,0.5022,0.5211,0.1134,0.1196,0.1078,0.1106,0.1243,0.1116,0.1127,0.1119,0.114,0.6397,0.653,0.6243,0.1315,0.1436,0.1452,0.1816,0.1984,0.1285,0.1839,0.1607,0.1734,0.697,0.5886,0.7336,0.5527,0.3845,0.3788,0.5753,0.4394,0.229,0.4552,0.4471,0.4255,0.7795,0.8224,0.7147,0.8149,0.7876,0.7973,0.6901,0.7698,0.6375,0.6514,0.7146,0.8387,0.7981,0.7164,0.7719,0.825,0.9226,0.8487,0.8708,0.6709,0.6472,0.8681,0.8073,0.7828,0.8493,0.8234,0.8251,0.9241,0.833,0.8483,0.8576,0.8883,0.8625 +89980s,30.9 °C,0.1133,0.1065,0.1123,0.2068,0.1523,0.1668,0.1137,0.1062,0.1101,0.1105,0.1108,0.1158,0.1101,0.1126,0.1174,0.3726,0.3434,0.3297,0.1145,0.112,0.1142,0.1124,0.1186,0.1124,0.1099,0.1141,0.1152,0.494,0.5025,0.5225,0.1135,0.1195,0.1078,0.1104,0.1243,0.1127,0.1127,0.1117,0.1139,0.64,0.6531,0.625,0.1313,0.1439,0.145,0.1814,0.1986,0.1286,0.1838,0.1607,0.1736,0.6968,0.5893,0.7337,0.5535,0.3846,0.3796,0.5747,0.4401,0.2293,0.4534,0.4474,0.4248,0.7784,0.822,0.715,0.8136,0.7871,0.7974,0.6911,0.7692,0.6419,0.6512,0.7155,0.8391,0.7988,0.717,0.7718,0.8263,0.9246,0.8495,0.873,0.6726,0.6491,0.8689,0.8078,0.7834,0.8499,0.8239,0.8257,0.9245,0.8335,0.8489,0.8574,0.8903,0.8636 +90657s,31.0 °C,0.1134,0.1066,0.1123,0.207,0.1524,0.1668,0.1137,0.1063,0.1101,0.1105,0.1108,0.116,0.1102,0.1125,0.1171,0.373,0.3435,0.3299,0.1145,0.112,0.1143,0.1123,0.1188,0.1124,0.1098,0.1141,0.1153,0.4954,0.504,0.5231,0.1135,0.1196,0.1079,0.1105,0.1242,0.1123,0.1127,0.1119,0.1141,0.6404,0.6538,0.625,0.1314,0.1439,0.1452,0.1814,0.1985,0.1288,0.184,0.1609,0.1737,0.6965,0.5896,0.7331,0.5539,0.3847,0.3802,0.5753,0.4402,0.2296,0.454,0.448,0.4254,0.7791,0.8227,0.7151,0.8144,0.7895,0.7979,0.6916,0.7705,0.6417,0.6508,0.7167,0.8405,0.7993,0.7176,0.7712,0.8275,0.9265,0.8514,0.8756,0.6744,0.6507,0.8713,0.81,0.7854,0.8522,0.8254,0.8293,0.9274,0.8379,0.8526,0.8606,0.8893,0.8651 +91333s,31.2 °C,0.1134,0.1066,0.1123,0.2066,0.1523,0.167,0.1138,0.1063,0.1101,0.1106,0.1109,0.1158,0.1102,0.1125,0.1166,0.3731,0.3439,0.3301,0.1144,0.1121,0.1141,0.1121,0.1186,0.1125,0.11,0.1141,0.1153,0.4972,0.5053,0.5243,0.1134,0.1197,0.1078,0.1105,0.1242,0.1119,0.1128,0.1118,0.114,0.6413,0.6542,0.6253,0.1311,0.144,0.145,0.1812,0.1987,0.1285,0.1843,0.1606,0.1735,0.6974,0.5901,0.7342,0.5534,0.3867,0.381,0.5769,0.4402,0.2299,0.4545,0.4487,0.426,0.7796,0.8239,0.7156,0.8158,0.7911,0.7999,0.6924,0.7713,0.6438,0.6515,0.7174,0.8413,0.7997,0.7183,0.7723,0.8282,0.9272,0.8522,0.8757,0.6742,0.6509,0.8723,0.8109,0.7872,0.8549,0.8271,0.8292,0.9278,0.8384,0.8525,0.8606,0.894,0.8687 +92010s,31.1 °C,0.1134,0.1066,0.1123,0.2064,0.1522,0.1669,0.1138,0.1063,0.1101,0.1105,0.1109,0.1157,0.1102,0.1126,0.1174,0.3736,0.3438,0.3308,0.1144,0.1122,0.1141,0.1122,0.1187,0.1124,0.1099,0.114,0.1153,0.4986,0.506,0.5259,0.1135,0.1196,0.1079,0.1105,0.1242,0.1125,0.1128,0.1118,0.114,0.6417,0.655,0.6253,0.1311,0.1439,0.1454,0.1814,0.1986,0.1285,0.1844,0.1608,0.1737,0.6972,0.5903,0.7334,0.5542,0.3858,0.3815,0.5751,0.4403,0.2295,0.4556,0.4493,0.4266,0.7799,0.8244,0.7161,0.8166,0.7903,0.8011,0.6931,0.7716,0.6428,0.6539,0.7186,0.8431,0.8009,0.7192,0.7731,0.8291,0.9279,0.8534,0.8762,0.6746,0.6513,0.8741,0.8131,0.7883,0.8558,0.8283,0.8312,0.9298,0.8405,0.8559,0.8636,0.8918,0.8691 +92686s,31.0 °C,0.1134,0.1066,0.1122,0.2061,0.1521,0.1668,0.1137,0.1062,0.1101,0.1105,0.1108,0.1156,0.1101,0.1125,0.1153,0.3729,0.3441,0.3302,0.1142,0.1121,0.1141,0.112,0.1185,0.1125,0.1099,0.1139,0.1152,0.4991,0.5068,0.5254,0.1133,0.1196,0.1077,0.1104,0.1241,0.1121,0.1127,0.1119,0.1137,0.6411,0.6558,0.6257,0.1309,0.1437,0.1455,0.1813,0.198,0.1286,0.1842,0.1615,0.1739,0.6977,0.5907,0.7345,0.5557,0.3867,0.3822,0.5756,0.441,0.2294,0.4574,0.4505,0.4274,0.7807,0.8249,0.7164,0.8183,0.7928,0.802,0.6943,0.7722,0.642,0.6557,0.7208,0.8445,0.8021,0.7203,0.7757,0.8308,0.9286,0.8542,0.8771,0.6747,0.6513,0.8737,0.8137,0.7896,0.8572,0.83,0.8312,0.9299,0.8402,0.8555,0.8633,0.8971,0.8714 +93363s,31.1 °C,0.1136,0.1066,0.1123,0.2063,0.1521,0.1668,0.1136,0.1062,0.11,0.1105,0.1107,0.1157,0.1102,0.1126,0.1163,0.3731,0.3441,0.3307,0.1142,0.112,0.1141,0.1121,0.1184,0.1123,0.1099,0.114,0.1152,0.5,0.508,0.5265,0.1133,0.1196,0.1078,0.1105,0.124,0.112,0.1127,0.1119,0.114,0.6416,0.655,0.6258,0.1313,0.144,0.1451,0.1816,0.1984,0.1286,0.1847,0.161,0.1737,0.6984,0.5901,0.7351,0.5547,0.3874,0.3811,0.5748,0.4409,0.2296,0.4575,0.4503,0.4282,0.781,0.825,0.7165,0.8193,0.7928,0.8022,0.6951,0.7729,0.6428,0.6566,0.7217,0.8453,0.803,0.7208,0.7768,0.8326,0.9298,0.8549,0.879,0.6761,0.6523,0.8758,0.8148,0.7913,0.8594,0.831,0.8333,0.9317,0.8419,0.8564,0.8646,0.899,0.8732 +94039s,31.1 °C,0.1137,0.1066,0.1123,0.2064,0.1522,0.1665,0.1136,0.1062,0.11,0.1105,0.1107,0.1157,0.1101,0.1125,0.1162,0.3735,0.3443,0.3305,0.1145,0.1119,0.114,0.1122,0.1187,0.1123,0.1098,0.114,0.1152,0.501,0.5082,0.5286,0.1133,0.1195,0.1077,0.1104,0.1241,0.1124,0.1126,0.1119,0.1141,0.6425,0.655,0.6262,0.1312,0.1441,0.145,0.1816,0.1988,0.1284,0.1844,0.1611,0.1739,0.699,0.5905,0.7357,0.5561,0.388,0.3831,0.5753,0.442,0.23,0.4573,0.4514,0.4295,0.7817,0.826,0.7174,0.8207,0.7958,0.8033,0.6961,0.774,0.6443,0.656,0.7223,0.8466,0.8034,0.7214,0.7766,0.8334,0.9308,0.856,0.8793,0.6768,0.6531,0.8786,0.8171,0.7938,0.8618,0.8334,0.8369,0.9341,0.8462,0.8591,0.8677,0.8986,0.8744 +94716s,31.0 °C,0.1132,0.1065,0.1122,0.2056,0.152,0.1667,0.1136,0.1062,0.11,0.1105,0.1108,0.1154,0.1102,0.1125,0.1171,0.3736,0.3441,0.331,0.1143,0.1119,0.1139,0.1121,0.1184,0.1122,0.1098,0.114,0.1153,0.5027,0.5097,0.5304,0.1133,0.1196,0.1078,0.1104,0.1241,0.1123,0.1126,0.1117,0.1139,0.6409,0.6554,0.6256,0.1313,0.1436,0.145,0.1812,0.1981,0.1285,0.1844,0.1612,0.1741,0.6987,0.5903,0.7355,0.5563,0.3869,0.3818,0.5741,0.4422,0.2299,0.4547,0.4516,0.4285,0.7804,0.826,0.7184,0.8192,0.7923,0.8028,0.6977,0.7729,0.6483,0.6569,0.7229,0.8466,0.8034,0.7217,0.7755,0.8341,0.9326,0.8573,0.8825,0.6792,0.6546,0.8791,0.8178,0.7947,0.8637,0.8357,0.8379,0.9343,0.8458,0.859,0.8671,0.9014,0.8761 +95392s,30.8 °C,0.1132,0.1065,0.1121,0.2054,0.1519,0.1665,0.1135,0.1061,0.1099,0.1104,0.1108,0.1152,0.11,0.1124,0.1175,0.3739,0.3442,0.3313,0.1143,0.1119,0.114,0.112,0.1184,0.1122,0.1097,0.1139,0.1151,0.5029,0.5104,0.5314,0.1132,0.1195,0.1076,0.1103,0.124,0.1124,0.1126,0.1116,0.1139,0.6415,0.6559,0.6259,0.1312,0.1437,0.1449,0.1812,0.198,0.1286,0.1845,0.161,0.1741,0.6995,0.5904,0.7366,0.5562,0.3877,0.3818,0.5742,0.4422,0.2301,0.4572,0.4516,0.4293,0.7821,0.8271,0.7182,0.821,0.7944,0.8049,0.6973,0.7745,0.6471,0.6586,0.7241,0.8476,0.8046,0.7224,0.778,0.8346,0.9326,0.8581,0.8818,0.6786,0.6544,0.8808,0.8196,0.7959,0.8656,0.8376,0.8406,0.9359,0.8481,0.8622,0.8702,0.8999,0.8769 +96069s,31.0 °C,0.1132,0.1065,0.1122,0.2059,0.1521,0.1661,0.1135,0.1062,0.1099,0.1104,0.1107,0.1154,0.1101,0.1124,0.1169,0.3738,0.3446,0.3309,0.1144,0.112,0.1139,0.112,0.1185,0.1122,0.1098,0.1139,0.1151,0.5042,0.5113,0.5311,0.1132,0.1194,0.1077,0.1103,0.124,0.112,0.1127,0.1117,0.114,0.6425,0.6558,0.6257,0.1313,0.1439,0.145,0.1812,0.1982,0.1285,0.1844,0.1613,0.1742,0.7006,0.5902,0.7373,0.5565,0.388,0.3838,0.5752,0.4423,0.23,0.4588,0.452,0.4302,0.7836,0.8282,0.7188,0.8232,0.7965,0.806,0.6978,0.7761,0.6455,0.659,0.7249,0.8485,0.805,0.7233,0.7777,0.8352,0.9338,0.8591,0.8834,0.6797,0.6552,0.8823,0.8203,0.7975,0.868,0.8396,0.8417,0.937,0.8475,0.8623,0.8707,0.9045,0.8794 +96745s,31.0 °C,0.113,0.1065,0.1122,0.2056,0.152,0.1662,0.1135,0.1061,0.1099,0.1103,0.1106,0.1154,0.11,0.1124,0.1166,0.3743,0.3447,0.3308,0.1141,0.1121,0.114,0.1117,0.1183,0.1123,0.1097,0.1138,0.1151,0.505,0.5124,0.5327,0.1131,0.1194,0.1076,0.1102,0.1239,0.112,0.1125,0.1115,0.1135,0.6407,0.6561,0.6255,0.131,0.1433,0.145,0.1805,0.1973,0.1286,0.1844,0.1612,0.174,0.7009,0.5907,0.7373,0.5557,0.3891,0.3832,0.5753,0.4422,0.2303,0.4599,0.4527,0.4311,0.7839,0.8286,0.7192,0.824,0.7988,0.8071,0.6981,0.7767,0.6459,0.6628,0.7272,0.8519,0.8071,0.7254,0.7813,0.8373,0.9343,0.8604,0.8835,0.6793,0.6555,0.8829,0.8213,0.7982,0.8694,0.8414,0.8434,0.9376,0.8494,0.8633,0.8709,0.9047,0.8807 +97422s,31.1 °C,0.1131,0.1064,0.1121,0.2059,0.1518,0.1661,0.1134,0.1061,0.1098,0.1103,0.1106,0.1154,0.11,0.1125,0.1152,0.3735,0.3444,0.3312,0.114,0.1118,0.1139,0.1118,0.118,0.1121,0.1097,0.1137,0.115,0.5057,0.5128,0.5321,0.1131,0.1194,0.1076,0.1102,0.1238,0.1121,0.1125,0.1119,0.1137,0.6415,0.6556,0.6255,0.1309,0.1433,0.1452,0.1811,0.1977,0.1284,0.1848,0.1611,0.1738,0.7024,0.5906,0.7381,0.5557,0.3896,0.3841,0.5756,0.4418,0.2299,0.4586,0.4537,0.4316,0.784,0.8286,0.7205,0.8237,0.7986,0.8068,0.7004,0.7765,0.6469,0.6613,0.7278,0.8517,0.8071,0.725,0.7802,0.8374,0.9351,0.8606,0.8851,0.68,0.6557,0.8842,0.8234,0.7998,0.871,0.8431,0.8467,0.9393,0.8511,0.8651,0.8734,0.9044,0.881 +98099s,31.0 °C,0.113,0.1064,0.1121,0.2055,0.1518,0.166,0.1134,0.1061,0.1098,0.1103,0.1105,0.1152,0.1099,0.1124,0.1163,0.3737,0.3447,0.3312,0.114,0.1117,0.1137,0.1118,0.118,0.1122,0.1097,0.1139,0.115,0.507,0.5133,0.5336,0.1131,0.1194,0.1075,0.1102,0.1239,0.1123,0.1126,0.1117,0.1139,0.6432,0.6554,0.6268,0.1313,0.1438,0.1449,0.1812,0.1983,0.1282,0.1843,0.1613,0.1741,0.7023,0.5909,0.738,0.5568,0.3882,0.3828,0.5751,0.4429,0.2298,0.4606,0.4537,0.4332,0.7862,0.8295,0.7204,0.8267,0.8008,0.8086,0.7002,0.779,0.6432,0.6614,0.7295,0.8542,0.8094,0.7264,0.7828,0.84,0.9352,0.8612,0.8839,0.6803,0.6563,0.8848,0.8239,0.8008,0.8727,0.8451,0.8466,0.9399,0.8511,0.8649,0.8722,0.9079,0.8831 +98775s,31.0 °C,0.1127,0.1064,0.1121,0.2051,0.1517,0.166,0.1134,0.106,0.1098,0.1103,0.1105,0.115,0.1099,0.1123,0.1169,0.3744,0.3449,0.3314,0.114,0.1118,0.1138,0.1118,0.1181,0.1121,0.1096,0.1139,0.115,0.5076,0.5133,0.5349,0.1132,0.1193,0.1075,0.1102,0.124,0.1126,0.1125,0.1116,0.1139,0.643,0.6557,0.6263,0.1312,0.1438,0.1449,0.1811,0.1981,0.1281,0.1844,0.1612,0.174,0.7032,0.5911,0.7389,0.5562,0.3885,0.3823,0.5749,0.4428,0.2301,0.4591,0.4538,0.4334,0.7859,0.8303,0.7211,0.8258,0.7982,0.8088,0.7011,0.7787,0.6465,0.6606,0.73,0.8534,0.8089,0.7263,0.7818,0.84,0.9364,0.8621,0.8864,0.6816,0.6569,0.8862,0.8258,0.8023,0.8745,0.8465,0.8487,0.9417,0.8522,0.8671,0.8748,0.9071,0.884 +99452s,31.1 °C,0.1128,0.1063,0.1121,0.2052,0.1518,0.1658,0.1134,0.106,0.1098,0.1102,0.1104,0.115,0.1099,0.1122,0.1165,0.3745,0.3449,0.3314,0.1141,0.1116,0.1138,0.1117,0.1181,0.1121,0.1096,0.1137,0.115,0.5097,0.5143,0.5348,0.1129,0.1193,0.1075,0.1101,0.1237,0.1116,0.1126,0.1115,0.1137,0.6433,0.656,0.6268,0.1309,0.1435,0.1449,0.1806,0.1978,0.128,0.1843,0.1613,0.1743,0.7037,0.5915,0.7391,0.5568,0.3878,0.3832,0.5761,0.4428,0.23,0.4593,0.4537,0.4339,0.7863,0.8309,0.7216,0.8269,0.7998,0.81,0.7016,0.7792,0.647,0.6617,0.7302,0.8548,0.809,0.7265,0.7816,0.8402,0.9375,0.8635,0.8872,0.6824,0.6574,0.8877,0.8272,0.804,0.8766,0.8492,0.8517,0.9431,0.8535,0.8694,0.8772,0.9084,0.8854 +100128s,31.1 °C,0.1125,0.1063,0.112,0.2047,0.1516,0.1659,0.1133,0.106,0.1097,0.1102,0.1104,0.1148,0.1099,0.1122,0.1169,0.3746,0.3452,0.3313,0.114,0.1119,0.114,0.1118,0.118,0.1121,0.1096,0.1137,0.115,0.5096,0.5147,0.536,0.113,0.1193,0.1075,0.1101,0.1238,0.1119,0.1125,0.1113,0.1135,0.6422,0.6561,0.6265,0.1309,0.1432,0.1448,0.1804,0.1972,0.1283,0.1842,0.1616,0.1745,0.7037,0.5919,0.7402,0.5577,0.3879,0.384,0.5752,0.4429,0.2302,0.4587,0.4539,0.4335,0.7865,0.8312,0.7222,0.8265,0.8001,0.8098,0.7022,0.7793,0.6489,0.6639,0.7314,0.857,0.8105,0.7279,0.7835,0.842,0.9382,0.8639,0.888,0.683,0.6583,0.8879,0.8265,0.8042,0.8782,0.8505,0.8522,0.9424,0.8524,0.8679,0.8746,0.9125,0.8873 +100805s,31.1 °C,0.1127,0.1063,0.1121,0.2051,0.1515,0.1657,0.1133,0.106,0.1097,0.1101,0.1103,0.1151,0.1098,0.1121,0.1163,0.3744,0.3449,0.331,0.1138,0.1115,0.1138,0.1115,0.1179,0.1121,0.1095,0.1136,0.1149,0.5107,0.5152,0.5361,0.1129,0.1192,0.1074,0.11,0.1237,0.1121,0.1124,0.1114,0.1135,0.6423,0.6556,0.6262,0.1307,0.1432,0.1448,0.1804,0.1973,0.1285,0.1844,0.1606,0.1736,0.7054,0.592,0.7401,0.5557,0.3892,0.3838,0.5766,0.4416,0.2303,0.4587,0.4543,0.4345,0.7869,0.8318,0.7226,0.8267,0.8022,0.8106,0.7024,0.7801,0.6477,0.6627,0.732,0.858,0.8109,0.7285,0.7836,0.8417,0.9386,0.8648,0.8883,0.6826,0.6585,0.8895,0.8288,0.8057,0.8789,0.8512,0.8545,0.944,0.856,0.8705,0.878,0.9092,0.8869 +101481s,31.1 °C,0.1128,0.1063,0.1121,0.2049,0.1514,0.1656,0.1132,0.1059,0.1097,0.1101,0.1103,0.1149,0.1098,0.1123,0.1153,0.3741,0.345,0.3316,0.1137,0.1115,0.1137,0.1116,0.1178,0.1119,0.1095,0.1136,0.1149,0.5109,0.5154,0.5366,0.1129,0.1191,0.1073,0.11,0.1237,0.1122,0.1124,0.1116,0.1136,0.6425,0.6559,0.6265,0.1308,0.1432,0.1449,0.1809,0.1973,0.1284,0.1843,0.1614,0.1742,0.7049,0.5926,0.7403,0.5572,0.3878,0.3828,0.575,0.4421,0.2299,0.4593,0.4555,0.4351,0.7876,0.8319,0.7238,0.8281,0.802,0.8111,0.7043,0.7807,0.6479,0.663,0.733,0.8582,0.8108,0.7285,0.784,0.843,0.9391,0.8653,0.8898,0.6833,0.6582,0.8897,0.83,0.8073,0.8805,0.8539,0.8551,0.9448,0.8555,0.8704,0.878,0.9136,0.8882 +102158s,30.9 °C,0.113,0.1064,0.112,0.2051,0.1515,0.1655,0.1132,0.106,0.1097,0.1102,0.1104,0.1149,0.1099,0.1124,0.1168,0.3739,0.3446,0.333,0.1141,0.1116,0.1137,0.1119,0.1181,0.112,0.1096,0.1138,0.115,0.5118,0.5159,0.5384,0.113,0.1193,0.1075,0.11,0.1237,0.1125,0.1126,0.1114,0.1136,0.644,0.6562,0.6273,0.1309,0.1435,0.1446,0.1808,0.1979,0.1281,0.1841,0.1616,0.1748,0.706,0.5936,0.7416,0.5582,0.3881,0.3834,0.575,0.4427,0.2301,0.458,0.4554,0.4345,0.7877,0.8329,0.7251,0.8273,0.8007,0.8104,0.7061,0.7803,0.652,0.6646,0.7339,0.8581,0.8117,0.7293,0.7835,0.8437,0.9409,0.8664,0.8918,0.6852,0.6601,0.8912,0.8308,0.8084,0.8828,0.8559,0.8562,0.9457,0.8555,0.871,0.8773,0.9171,0.8909 +102834s,31.0 °C,0.1128,0.1063,0.112,0.2047,0.1514,0.1655,0.1132,0.1059,0.1097,0.1101,0.1102,0.1147,0.1098,0.1122,0.1166,0.3747,0.345,0.3327,0.114,0.1115,0.1138,0.1115,0.1179,0.112,0.1096,0.1136,0.1149,0.513,0.5166,0.5382,0.1128,0.1194,0.1074,0.1101,0.1236,0.1117,0.1125,0.1115,0.1139,0.6435,0.6563,0.6272,0.1309,0.1436,0.1447,0.1808,0.1977,0.128,0.1845,0.1613,0.1744,0.7058,0.5934,0.7416,0.5574,0.3885,0.3829,0.5745,0.442,0.2302,0.461,0.4551,0.4351,0.7885,0.8331,0.7246,0.8299,0.8029,0.8121,0.7053,0.7823,0.6494,0.6666,0.7344,0.8596,0.8123,0.7297,0.7847,0.8441,0.9409,0.8665,0.8908,0.6847,0.6598,0.8926,0.8322,0.8097,0.8845,0.8578,0.8591,0.9469,0.8576,0.8732,0.88,0.9158,0.891 +103511s,31.2 °C,0.1125,0.1063,0.112,0.2041,0.1512,0.1656,0.1131,0.1059,0.1097,0.1101,0.1103,0.1144,0.1098,0.1121,0.1167,0.3743,0.3449,0.333,0.1138,0.1116,0.1136,0.1115,0.1177,0.1119,0.1095,0.1136,0.1148,0.5132,0.5168,0.5386,0.1128,0.1191,0.1074,0.1099,0.1236,0.1124,0.1124,0.1113,0.1134,0.6426,0.6571,0.6271,0.1306,0.1432,0.1449,0.1803,0.197,0.1282,0.1839,0.1617,0.1748,0.7056,0.5945,0.7414,0.5584,0.387,0.3844,0.574,0.4419,0.2302,0.4585,0.4556,0.4351,0.7884,0.8338,0.7253,0.8285,0.8025,0.8125,0.7059,0.7811,0.6517,0.6648,0.7351,0.8591,0.8118,0.7304,0.7843,0.8438,0.9424,0.868,0.8926,0.686,0.6612,0.8942,0.8334,0.8105,0.8857,0.8597,0.8608,0.9477,0.8601,0.8744,0.8812,0.9158,0.8923 +104187s,31.0 °C,0.1127,0.1062,0.1119,0.2041,0.1511,0.1654,0.1131,0.1059,0.1097,0.1101,0.1103,0.1144,0.1098,0.1122,0.1153,0.3743,0.345,0.333,0.1137,0.1116,0.1137,0.1116,0.1176,0.1119,0.1095,0.1135,0.1148,0.5132,0.5168,0.5379,0.1128,0.1191,0.1072,0.1099,0.1234,0.1119,0.1124,0.1115,0.1135,0.6434,0.6563,0.6271,0.1304,0.1436,0.1448,0.1806,0.1972,0.1278,0.1845,0.161,0.1739,0.7073,0.5942,0.7425,0.5559,0.3892,0.3829,0.5752,0.44,0.2295,0.4598,0.4563,0.4354,0.7884,0.8338,0.7253,0.8297,0.8031,0.813,0.7059,0.7817,0.6491,0.6655,0.7363,0.8598,0.812,0.7305,0.7842,0.8454,0.9424,0.8678,0.8941,0.6863,0.6605,0.8937,0.8343,0.812,0.8869,0.8606,0.8613,0.9481,0.8582,0.8741,0.8812,0.9186,0.8925 +104864s,30.9 °C,0.1127,0.1062,0.1119,0.2039,0.1511,0.1654,0.1131,0.1058,0.1096,0.1101,0.1101,0.1143,0.1098,0.1122,0.1167,0.3743,0.345,0.3333,0.1138,0.1112,0.1135,0.1115,0.1176,0.112,0.1096,0.1135,0.1148,0.5141,0.5173,0.5394,0.1128,0.1191,0.1073,0.1099,0.1236,0.1121,0.1124,0.1113,0.1134,0.642,0.6571,0.6271,0.1307,0.1428,0.1445,0.1802,0.1964,0.1283,0.1845,0.1609,0.174,0.7087,0.5952,0.7437,0.5564,0.3894,0.3837,0.5752,0.4402,0.2302,0.4582,0.4564,0.4346,0.7884,0.8339,0.7268,0.8288,0.8016,0.8119,0.7079,0.7811,0.6531,0.6674,0.7368,0.8615,0.8142,0.7315,0.787,0.8464,0.9422,0.8681,0.893,0.6857,0.6602,0.8955,0.8363,0.8134,0.8887,0.8626,0.864,0.9505,0.8609,0.8761,0.8843,0.9178,0.8925 +105540s,31.0 °C,0.1126,0.1062,0.1118,0.2036,0.151,0.1654,0.113,0.1057,0.1095,0.11,0.1101,0.1142,0.1097,0.1121,0.1161,0.3746,0.3452,0.3333,0.1139,0.1112,0.1135,0.1115,0.1178,0.1119,0.1094,0.1134,0.1147,0.5144,0.517,0.5406,0.1127,0.119,0.1071,0.1098,0.1234,0.1122,0.1122,0.1112,0.1133,0.6422,0.6574,0.6272,0.1308,0.1428,0.1445,0.1801,0.1964,0.1282,0.1842,0.161,0.1742,0.7087,0.5957,0.7446,0.5571,0.3896,0.3832,0.5759,0.4404,0.2301,0.4585,0.4566,0.4357,0.7887,0.834,0.7268,0.8303,0.8037,0.8127,0.7076,0.7825,0.652,0.6679,0.7375,0.8633,0.8148,0.732,0.788,0.8473,0.9429,0.8688,0.8935,0.6866,0.6612,0.8969,0.8375,0.8145,0.8902,0.8643,0.8677,0.952,0.8635,0.8781,0.8862,0.9165,0.8929 +106217s,31.0 °C,0.1128,0.1062,0.1118,0.2039,0.1511,0.1653,0.113,0.1059,0.1095,0.11,0.1102,0.1143,0.1098,0.1121,0.1154,0.3747,0.3452,0.3335,0.1137,0.1112,0.1134,0.1114,0.1176,0.1119,0.1095,0.1135,0.1148,0.5156,0.5179,0.5419,0.1128,0.1191,0.1072,0.1099,0.1235,0.1121,0.1125,0.1114,0.1135,0.6435,0.6573,0.6281,0.131,0.1432,0.1446,0.1805,0.1969,0.1279,0.1847,0.1609,0.1741,0.7096,0.5963,0.7448,0.5563,0.3896,0.383,0.5761,0.44,0.2303,0.4608,0.457,0.4367,0.7899,0.8348,0.7269,0.8323,0.8048,0.8143,0.7084,0.7842,0.6503,0.6687,0.7382,0.864,0.8152,0.7325,0.7887,0.8478,0.9432,0.8693,0.8936,0.6868,0.6611,0.8975,0.8383,0.8155,0.8923,0.8665,0.8689,0.9524,0.8637,0.8787,0.8862,0.9195,0.8945 +106894s,30.9 °C,0.1129,0.1064,0.112,0.204,0.1512,0.1652,0.1132,0.1059,0.1097,0.1101,0.1102,0.1144,0.1099,0.1121,0.1166,0.3745,0.3451,0.3336,0.1138,0.1115,0.1134,0.1115,0.1177,0.1119,0.1096,0.1135,0.1149,0.5162,0.5184,0.5423,0.1127,0.1191,0.1073,0.1099,0.1235,0.1118,0.1126,0.1112,0.1135,0.6442,0.6581,0.6292,0.1308,0.1432,0.1447,0.1803,0.1971,0.1282,0.1844,0.1615,0.1748,0.7092,0.5974,0.7448,0.5578,0.3882,0.3835,0.5749,0.4404,0.2306,0.4585,0.4573,0.4356,0.7901,0.8358,0.7278,0.8318,0.8037,0.814,0.7093,0.7841,0.6549,0.6688,0.739,0.8641,0.8163,0.7337,0.7891,0.848,0.9448,0.8702,0.8951,0.6883,0.6626,0.8989,0.8391,0.8165,0.8939,0.8683,0.8712,0.9537,0.8642,0.8797,0.8876,0.9205,0.8954 +107570s,31.2 °C,0.1128,0.1063,0.1119,0.2037,0.1512,0.1651,0.1131,0.1059,0.1096,0.11,0.1101,0.1145,0.1098,0.1121,0.1161,0.375,0.3456,0.3335,0.1137,0.1115,0.1134,0.1113,0.1176,0.112,0.1096,0.1134,0.1146,0.5163,0.5183,0.543,0.1128,0.1191,0.1072,0.1098,0.1235,0.1124,0.1125,0.1113,0.1133,0.6434,0.658,0.6283,0.1306,0.1429,0.1446,0.1799,0.1965,0.1283,0.1843,0.1615,0.1748,0.71,0.5981,0.7457,0.5575,0.3895,0.3848,0.5755,0.4397,0.2305,0.4576,0.4574,0.4355,0.7897,0.8357,0.7282,0.8305,0.8043,0.8135,0.7097,0.783,0.6546,0.669,0.7396,0.8641,0.8161,0.7341,0.789,0.8486,0.9453,0.8708,0.8962,0.6886,0.6634,0.8995,0.8395,0.8174,0.8955,0.8707,0.8712,0.9536,0.8643,0.88,0.886,0.9234,0.8964 +108247s,31.0 °C,0.1131,0.1063,0.112,0.204,0.1513,0.165,0.1131,0.106,0.1096,0.11,0.1101,0.1147,0.1099,0.1123,0.1157,0.375,0.3458,0.3338,0.1137,0.1115,0.1137,0.1116,0.1176,0.112,0.1096,0.1134,0.1148,0.5169,0.5184,0.5421,0.1127,0.1192,0.1073,0.1099,0.1235,0.1117,0.1124,0.1114,0.1133,0.6434,0.6585,0.6291,0.1305,0.1428,0.1449,0.1802,0.1963,0.1284,0.1841,0.162,0.1748,0.7101,0.5988,0.7461,0.5579,0.3889,0.3843,0.5749,0.4392,0.2301,0.4576,0.4583,0.4362,0.7899,0.8359,0.7289,0.8308,0.8046,0.8137,0.7106,0.7836,0.6533,0.6691,0.7406,0.8657,0.817,0.7349,0.7902,0.8491,0.9454,0.8712,0.8968,0.6887,0.663,0.9003,0.8416,0.8181,0.896,0.8709,0.8745,0.9552,0.8664,0.8821,0.8895,0.9196,0.8949 +108923s,30.8 °C,0.1129,0.1064,0.1119,0.2038,0.1512,0.1651,0.1131,0.1059,0.1096,0.1101,0.1101,0.1145,0.11,0.1123,0.1156,0.3748,0.3456,0.3338,0.1137,0.1112,0.1136,0.1117,0.1175,0.112,0.1096,0.1134,0.1148,0.518,0.5184,0.5421,0.1126,0.1191,0.1072,0.1098,0.1234,0.1117,0.1124,0.1115,0.1133,0.6437,0.6582,0.6293,0.1307,0.1428,0.1449,0.1804,0.1966,0.1281,0.1845,0.1615,0.1743,0.7109,0.5984,0.746,0.5565,0.3888,0.3828,0.5752,0.4378,0.2298,0.4591,0.4586,0.4373,0.7903,0.8357,0.7288,0.8325,0.8048,0.8147,0.7106,0.7854,0.6513,0.6697,0.7404,0.8664,0.817,0.7344,0.7902,0.8493,0.9446,0.8711,0.8966,0.6881,0.6618,0.9008,0.842,0.8191,0.8969,0.8729,0.8753,0.9554,0.8657,0.8819,0.8902,0.9205,0.8942 +109600s,31.0 °C,0.1129,0.1063,0.1119,0.2032,0.1511,0.1651,0.1131,0.1058,0.1095,0.11,0.11,0.1143,0.11,0.1122,0.1164,0.3748,0.3452,0.3341,0.1138,0.1114,0.1133,0.1116,0.1176,0.1118,0.1096,0.1134,0.1148,0.5187,0.5183,0.544,0.1126,0.119,0.1071,0.1099,0.1234,0.1118,0.1125,0.1112,0.1133,0.6442,0.6585,0.6295,0.1308,0.1427,0.1446,0.18,0.1964,0.1281,0.1841,0.1615,0.1745,0.712,0.5992,0.7471,0.5571,0.3888,0.3848,0.5775,0.4382,0.2298,0.4603,0.4589,0.4381,0.7918,0.8365,0.7289,0.8341,0.8055,0.8154,0.7111,0.7864,0.6499,0.6685,0.7404,0.8652,0.8172,0.7345,0.7891,0.8495,0.9455,0.8714,0.8977,0.6896,0.663,0.901,0.8412,0.8197,0.8984,0.8748,0.8757,0.9558,0.8654,0.8817,0.8897,0.9235,0.8958 +110276s,31.0 °C,0.113,0.1064,0.112,0.2036,0.1512,0.1648,0.113,0.1059,0.1095,0.11,0.11,0.1144,0.1098,0.1122,0.1168,0.3752,0.3455,0.3335,0.1138,0.1114,0.1134,0.1114,0.1177,0.1118,0.1095,0.1134,0.1147,0.5187,0.5182,0.5451,0.1127,0.119,0.1072,0.1098,0.1235,0.1121,0.1124,0.1112,0.1133,0.6453,0.6585,0.63,0.1307,0.1429,0.1445,0.18,0.1966,0.128,0.1838,0.1618,0.1749,0.7105,0.5996,0.7465,0.5578,0.3878,0.3839,0.5758,0.438,0.2299,0.4603,0.4588,0.4385,0.792,0.837,0.7285,0.8335,0.8056,0.8157,0.711,0.7868,0.6515,0.6699,0.741,0.8669,0.8182,0.7357,0.7909,0.8508,0.9464,0.8729,0.8983,0.6899,0.6642,0.9024,0.8425,0.82,0.9001,0.876,0.8787,0.957,0.8666,0.8834,0.8912,0.9222,0.8955 +110953s,31.1 °C,0.1126,0.1063,0.1118,0.2028,0.1509,0.165,0.113,0.1058,0.1095,0.11,0.1099,0.1141,0.1098,0.112,0.1169,0.3744,0.345,0.3337,0.1137,0.1114,0.1133,0.1114,0.1175,0.1118,0.1094,0.1132,0.1145,0.5194,0.518,0.5454,0.1126,0.1188,0.1071,0.1097,0.1234,0.1122,0.1124,0.1112,0.1134,0.646,0.6584,0.6305,0.1306,0.1432,0.1445,0.1801,0.197,0.1276,0.1838,0.1615,0.1747,0.7105,0.5995,0.7462,0.557,0.387,0.3833,0.577,0.437,0.2296,0.4575,0.4592,0.4383,0.7918,0.8367,0.7287,0.8326,0.8044,0.8155,0.7111,0.7871,0.6519,0.6664,0.7407,0.8658,0.8172,0.735,0.7891,0.8503,0.9462,0.8723,0.8986,0.6899,0.6638,0.9029,0.8431,0.8206,0.901,0.877,0.8787,0.9573,0.8672,0.8831,0.8915,0.9234,0.8958 +111629s,31.0 °C,0.1128,0.1064,0.1119,0.2028,0.1512,0.1652,0.1132,0.106,0.1097,0.1102,0.1101,0.1141,0.11,0.1122,0.1164,0.3752,0.3457,0.3336,0.114,0.1116,0.1135,0.1116,0.1177,0.112,0.1096,0.1134,0.1147,0.5198,0.5175,0.5458,0.1128,0.1191,0.1073,0.1099,0.1236,0.1125,0.1126,0.1113,0.1135,0.6459,0.6593,0.631,0.1309,0.143,0.1446,0.1799,0.1967,0.1285,0.1839,0.1619,0.1751,0.7114,0.6009,0.7469,0.5573,0.3877,0.383,0.5769,0.437,0.2299,0.4559,0.4592,0.4378,0.7917,0.8372,0.7294,0.8319,0.8046,0.8151,0.7119,0.7867,0.6533,0.6657,0.7412,0.8653,0.8173,0.7356,0.7886,0.8507,0.947,0.8725,0.8998,0.6908,0.6647,0.9009,0.8407,0.8203,0.9015,0.8766,0.8762,0.9559,0.8637,0.8819,0.8881,0.9274,0.897 +112306s,30.9 °C,0.112,0.1061,0.1116,0.2007,0.1506,0.1652,0.1131,0.1058,0.1096,0.11,0.1102,0.1129,0.1095,0.112,0.1162,0.3735,0.3447,0.3313,0.1135,0.1114,0.1136,0.1112,0.1175,0.112,0.1093,0.1132,0.1144,0.5178,0.5159,0.5439,0.1129,0.1187,0.1071,0.1097,0.1234,0.1137,0.1121,0.1108,0.1129,0.6418,0.6607,0.6297,0.1306,0.1421,0.1446,0.179,0.1947,0.1288,0.1829,0.1624,0.1752,0.7074,0.6015,0.7441,0.5585,0.3822,0.3817,0.5698,0.4374,0.2305,0.4508,0.4587,0.4347,0.7879,0.8359,0.7299,0.8267,0.7978,0.8096,0.7133,0.7807,0.6614,0.6635,0.7415,0.8627,0.816,0.7355,0.7872,0.8511,0.9471,0.8722,0.9016,0.6926,0.6654,0.9016,0.8404,0.8218,0.9037,0.8789,0.8754,0.9545,0.8602,0.8786,0.8828,0.9366,0.9023 +112982s,31.0 °C,0.112,0.1061,0.1116,0.2007,0.1506,0.1651,0.113,0.1058,0.1096,0.1101,0.1102,0.1131,0.1096,0.112,0.1157,0.3741,0.3453,0.3313,0.1136,0.1115,0.1137,0.1112,0.1175,0.1121,0.1093,0.1133,0.1144,0.5181,0.5165,0.5453,0.1129,0.1187,0.1072,0.1096,0.1235,0.114,0.1122,0.1109,0.1129,0.6414,0.6612,0.6292,0.1309,0.1419,0.1447,0.1789,0.1945,0.129,0.1827,0.1631,0.1759,0.7091,0.6031,0.7454,0.5608,0.3824,0.3836,0.5714,0.4383,0.2305,0.4506,0.4597,0.4368,0.7896,0.8371,0.7315,0.8287,0.8026,0.8124,0.7149,0.7831,0.6605,0.6611,0.7412,0.8617,0.8159,0.7345,0.785,0.8514,0.948,0.8733,0.9037,0.6949,0.6659,0.9031,0.8418,0.8227,0.9046,0.88,0.8772,0.9563,0.8633,0.8802,0.8863,0.9338,0.9005 +113659s,30.9 °C,0.1119,0.1061,0.1115,0.2003,0.1505,0.1651,0.113,0.1057,0.1096,0.11,0.1103,0.1129,0.1095,0.1121,0.1152,0.3736,0.3452,0.3312,0.1134,0.1115,0.1138,0.1111,0.1174,0.112,0.1093,0.1134,0.1144,0.5177,0.5155,0.5445,0.113,0.1187,0.1072,0.1096,0.1234,0.1147,0.1122,0.1108,0.1128,0.6418,0.6619,0.6305,0.1308,0.1419,0.1447,0.1789,0.1941,0.1291,0.1825,0.1634,0.1762,0.7077,0.6035,0.7437,0.561,0.3809,0.3835,0.5698,0.4379,0.2307,0.4502,0.4597,0.4362,0.7893,0.8367,0.7309,0.828,0.7999,0.8121,0.7144,0.7822,0.6621,0.6623,0.7413,0.8624,0.8161,0.7346,0.7856,0.8508,0.9478,0.8734,0.9031,0.6938,0.6662,0.9033,0.8427,0.823,0.9056,0.8811,0.8799,0.9571,0.8654,0.8822,0.8884,0.932,0.9001 +114336s,31.1 °C,0.1121,0.1061,0.1115,0.2005,0.1505,0.1649,0.113,0.1057,0.1096,0.11,0.1101,0.1129,0.1096,0.1121,0.1146,0.3735,0.3453,0.3313,0.1134,0.1115,0.1136,0.111,0.1174,0.1121,0.1092,0.1134,0.1144,0.5186,0.5154,0.5449,0.1129,0.1187,0.1072,0.1096,0.1235,0.1144,0.1124,0.1108,0.1128,0.6419,0.6627,0.6298,0.1306,0.1417,0.1451,0.1787,0.194,0.1292,0.1827,0.163,0.1758,0.7088,0.6038,0.7459,0.5596,0.3837,0.3845,0.5725,0.4369,0.23,0.4513,0.4602,0.4368,0.7893,0.837,0.7308,0.8285,0.8027,0.8131,0.7144,0.7823,0.6597,0.6638,0.742,0.8626,0.8164,0.7354,0.7857,0.8507,0.9491,0.8752,0.9046,0.6952,0.6664,0.9032,0.8429,0.8234,0.907,0.8835,0.8797,0.9567,0.8632,0.8821,0.887,0.9357,0.9016 +115012s,30.8 °C,0.1119,0.1061,0.1114,0.1998,0.1503,0.1652,0.113,0.1058,0.1096,0.11,0.1102,0.1126,0.1097,0.1121,0.1142,0.3735,0.3454,0.3312,0.1134,0.1114,0.1137,0.1111,0.1172,0.1122,0.1094,0.1133,0.1145,0.5187,0.5156,0.5437,0.1128,0.1187,0.1071,0.1096,0.1235,0.1143,0.1123,0.111,0.1128,0.642,0.6625,0.6308,0.1306,0.1421,0.1448,0.1791,0.1941,0.129,0.1832,0.1624,0.1752,0.7088,0.6034,0.7457,0.5571,0.3842,0.3824,0.5719,0.4356,0.2298,0.4527,0.46,0.4372,0.7894,0.8363,0.7308,0.8293,0.8015,0.8131,0.7143,0.7832,0.6596,0.6641,0.743,0.8634,0.8168,0.7354,0.7876,0.8514,0.9482,0.8736,0.9029,0.6934,0.6657,0.9038,0.8428,0.8241,0.9071,0.8855,0.8814,0.9578,0.8638,0.8814,0.8872,0.9365,0.9011 +115689s,30.8 °C,0.1119,0.1061,0.1114,0.1997,0.1504,0.1651,0.113,0.1057,0.1096,0.11,0.1101,0.1126,0.1095,0.1121,0.1159,0.3739,0.3457,0.3314,0.1136,0.1114,0.1137,0.1112,0.1175,0.1121,0.1093,0.1134,0.1144,0.5195,0.5162,0.5461,0.1129,0.1188,0.1072,0.1096,0.1234,0.1148,0.1122,0.1109,0.1129,0.6434,0.662,0.6311,0.1307,0.1422,0.1446,0.179,0.1946,0.1288,0.1822,0.1632,0.1763,0.7077,0.6043,0.7452,0.5597,0.382,0.3836,0.5713,0.4367,0.2301,0.4505,0.4608,0.4379,0.7885,0.8364,0.7316,0.8287,0.8017,0.812,0.7154,0.7822,0.6614,0.6653,0.7434,0.8651,0.8177,0.7353,0.7882,0.8523,0.9497,0.8749,0.9044,0.6948,0.6666,0.9051,0.8437,0.8254,0.9087,0.8865,0.8843,0.9591,0.8655,0.883,0.8881,0.9361,0.9 +116365s,30.8 °C,0.1119,0.106,0.1114,0.1997,0.1506,0.165,0.113,0.1057,0.1096,0.1099,0.1101,0.1126,0.1096,0.112,0.1164,0.374,0.3458,0.3315,0.1135,0.1114,0.1135,0.1112,0.1173,0.1119,0.1093,0.1134,0.1145,0.5202,0.516,0.5453,0.1127,0.1187,0.1071,0.1097,0.1234,0.1134,0.1122,0.1108,0.1129,0.6433,0.6617,0.6307,0.1308,0.1422,0.1445,0.1789,0.1946,0.1285,0.1823,0.1627,0.1759,0.7077,0.6041,0.7455,0.5582,0.3823,0.3836,0.5716,0.4359,0.2301,0.4518,0.4606,0.4377,0.7898,0.8363,0.7307,0.8302,0.8032,0.8138,0.7143,0.7839,0.6593,0.6627,0.743,0.8632,0.8174,0.7358,0.7868,0.8519,0.9497,0.8748,0.9051,0.6959,0.6674,0.906,0.8446,0.8263,0.9103,0.8879,0.8847,0.9594,0.8664,0.8833,0.8892,0.9367,0.9018 +117042s,31.0 °C,0.1121,0.1061,0.1114,0.2001,0.1507,0.1647,0.113,0.1057,0.1095,0.1099,0.11,0.1126,0.1096,0.112,0.1165,0.3743,0.3457,0.3316,0.1135,0.1115,0.1137,0.111,0.1173,0.1119,0.1093,0.1134,0.1144,0.5201,0.5156,0.5457,0.1128,0.1187,0.1071,0.1096,0.1234,0.1142,0.1124,0.1108,0.1129,0.6444,0.6622,0.6309,0.1303,0.1421,0.1446,0.1788,0.1944,0.1284,0.1825,0.1629,0.1759,0.7087,0.6049,0.7462,0.5577,0.3828,0.3838,0.5727,0.4355,0.2302,0.4504,0.4613,0.4376,0.7894,0.837,0.7313,0.8291,0.801,0.8132,0.7156,0.7826,0.6619,0.6642,0.7429,0.8629,0.8171,0.736,0.7868,0.8514,0.9495,0.8753,0.9052,0.6956,0.6667,0.9063,0.845,0.8257,0.9106,0.8876,0.8849,0.9604,0.8664,0.8854,0.8912,0.9337,0.9004 +117718s,31.0 °C,0.1117,0.106,0.1113,0.1991,0.1502,0.1648,0.1129,0.1056,0.1095,0.1099,0.1101,0.1122,0.1095,0.112,0.1142,0.3731,0.3454,0.331,0.1133,0.1113,0.1134,0.1109,0.1171,0.1119,0.1092,0.1132,0.1143,0.5194,0.5149,0.544,0.1127,0.1186,0.1071,0.1095,0.1232,0.1142,0.1121,0.1107,0.1126,0.6424,0.6635,0.6313,0.1301,0.1416,0.1447,0.1783,0.1934,0.1291,0.1816,0.1631,0.1758,0.7072,0.6047,0.7443,0.5576,0.3801,0.3824,0.5694,0.435,0.2302,0.4502,0.4615,0.4366,0.7893,0.8373,0.7313,0.8287,0.8004,0.812,0.7156,0.7822,0.6629,0.6635,0.7438,0.8626,0.8174,0.7362,0.7882,0.8512,0.9492,0.875,0.9049,0.6943,0.6665,0.907,0.8462,0.8267,0.911,0.8897,0.8878,0.9609,0.8672,0.8862,0.8921,0.9331,0.8989 +118395s,30.9 °C,0.112,0.106,0.1113,0.1996,0.1505,0.1647,0.1128,0.1057,0.1095,0.1099,0.11,0.1124,0.1095,0.1121,0.1146,0.3737,0.3458,0.3314,0.1132,0.1112,0.1136,0.111,0.1171,0.1119,0.1092,0.1133,0.1143,0.5202,0.5154,0.5451,0.1128,0.1187,0.107,0.1094,0.1233,0.1149,0.1121,0.1108,0.1126,0.6435,0.6631,0.6319,0.1302,0.1417,0.1444,0.1784,0.1934,0.1291,0.1822,0.1628,0.1754,0.7082,0.6043,0.7458,0.5558,0.3828,0.3812,0.5717,0.4343,0.2293,0.4526,0.4621,0.4382,0.79,0.8367,0.7314,0.8306,0.8032,0.8139,0.7151,0.7849,0.6586,0.6646,0.7439,0.8633,0.8177,0.7361,0.7878,0.8514,0.9492,0.8745,0.905,0.6945,0.666,0.9063,0.8459,0.8267,0.911,0.8896,0.8873,0.9608,0.8654,0.8841,0.8902,0.9353,0.8993 +119071s,30.8 °C,0.1121,0.106,0.1113,0.1994,0.1505,0.1647,0.1128,0.1056,0.1095,0.1098,0.11,0.1122,0.1094,0.1121,0.1155,0.3732,0.3457,0.3311,0.1135,0.1111,0.1134,0.1111,0.1173,0.1118,0.1091,0.1133,0.1143,0.5205,0.515,0.5454,0.1128,0.1186,0.1071,0.1095,0.1232,0.1143,0.1121,0.1108,0.1128,0.6444,0.6631,0.6321,0.1304,0.142,0.1443,0.1786,0.1938,0.1288,0.1816,0.1631,0.1759,0.708,0.6048,0.7452,0.5568,0.3804,0.3825,0.5699,0.435,0.2301,0.4516,0.4622,0.4382,0.7898,0.8365,0.7314,0.8294,0.8024,0.8122,0.7164,0.7841,0.6624,0.6647,0.744,0.8629,0.8181,0.7355,0.7872,0.8519,0.9495,0.8748,0.9056,0.6961,0.6668,0.9086,0.847,0.8285,0.9131,0.892,0.8894,0.9626,0.8681,0.8855,0.8919,0.9357,0.899 +119748s,30.8 °C,0.1117,0.1059,0.1113,0.1994,0.1504,0.1646,0.1128,0.1056,0.1094,0.1098,0.1098,0.1122,0.1095,0.1119,0.1156,0.3744,0.3459,0.3315,0.1133,0.1112,0.1135,0.111,0.117,0.1117,0.1092,0.1133,0.1143,0.5212,0.515,0.5448,0.1127,0.1186,0.107,0.1094,0.1232,0.1139,0.1121,0.1107,0.1126,0.6427,0.6642,0.6316,0.1306,0.1414,0.1444,0.1778,0.193,0.129,0.1819,0.1626,0.1756,0.7089,0.6048,0.7458,0.5554,0.3816,0.3832,0.5718,0.4345,0.2296,0.4486,0.4621,0.4387,0.7896,0.836,0.7311,0.8293,0.8025,0.8118,0.7159,0.7842,0.661,0.6632,0.7442,0.8649,0.8194,0.7363,0.7884,0.8524,0.9501,0.8755,0.905,0.6953,0.6669,0.9075,0.8456,0.8285,0.9137,0.8946,0.8893,0.9611,0.8675,0.8845,0.8905,0.9382,0.8994 +120424s,31.2 °C,0.1118,0.106,0.1114,0.1992,0.1505,0.1648,0.1128,0.1056,0.1095,0.1098,0.1098,0.1121,0.1095,0.112,0.1149,0.3747,0.3463,0.3317,0.1134,0.1112,0.1137,0.1111,0.1173,0.1118,0.1091,0.1133,0.1144,0.5223,0.5155,0.5458,0.1128,0.1187,0.1071,0.1094,0.1234,0.1145,0.1122,0.1108,0.1127,0.6442,0.6643,0.6318,0.1307,0.1416,0.1444,0.1781,0.1933,0.1288,0.1819,0.1628,0.1757,0.7095,0.605,0.7466,0.5553,0.3824,0.3825,0.5735,0.4344,0.2296,0.4492,0.4626,0.4392,0.79,0.8362,0.7314,0.8288,0.8011,0.8121,0.7167,0.7837,0.6621,0.6644,0.7443,0.8642,0.8188,0.7359,0.7868,0.8521,0.9512,0.8766,0.907,0.6973,0.6678,0.9085,0.8466,0.8294,0.9156,0.8955,0.8909,0.9625,0.8676,0.8867,0.8925,0.9385,0.9004 +121101s,30.9 °C,0.1116,0.106,0.1113,0.1992,0.1505,0.1646,0.1129,0.1056,0.1095,0.1098,0.1099,0.1121,0.1095,0.112,0.1154,0.3749,0.3465,0.3315,0.1132,0.1113,0.1137,0.1109,0.1172,0.1119,0.1092,0.1134,0.1143,0.5219,0.5151,0.5459,0.1129,0.1187,0.1071,0.1094,0.1234,0.1148,0.1123,0.1107,0.1127,0.6462,0.6647,0.6327,0.1303,0.1421,0.1444,0.1782,0.1938,0.1289,0.1816,0.1631,0.176,0.7088,0.6061,0.7458,0.5558,0.3803,0.3821,0.5715,0.4345,0.23,0.4488,0.4629,0.4391,0.7903,0.8372,0.7316,0.8292,0.8013,0.813,0.7168,0.7853,0.6642,0.6637,0.7449,0.8651,0.8198,0.7372,0.7878,0.853,0.9514,0.877,0.9066,0.6964,0.6677,0.9108,0.8481,0.8306,0.9163,0.8975,0.8929,0.9644,0.8693,0.8884,0.8952,0.9368,0.8992 +121777s,30.9 °C,0.1118,0.1059,0.1114,0.1996,0.1506,0.1644,0.1128,0.1056,0.1094,0.1097,0.1096,0.1122,0.1094,0.1118,0.1151,0.3749,0.3464,0.3318,0.1132,0.1111,0.1134,0.1108,0.117,0.1119,0.1091,0.1131,0.1142,0.523,0.5152,0.5448,0.1126,0.1185,0.1069,0.1094,0.1232,0.1135,0.1121,0.1106,0.1126,0.6454,0.6643,0.6319,0.1302,0.1417,0.1442,0.1778,0.1933,0.1286,0.1815,0.1627,0.1754,0.7095,0.6054,0.7464,0.5543,0.3818,0.3832,0.5743,0.4335,0.2295,0.4513,0.4635,0.4402,0.7895,0.8362,0.731,0.8291,0.8024,0.8132,0.7161,0.7856,0.6606,0.6653,0.7451,0.8659,0.8196,0.7367,0.7882,0.8519,0.9505,0.8763,0.9057,0.6949,0.6667,0.9105,0.8484,0.8308,0.9167,0.8986,0.8933,0.9636,0.8688,0.8873,0.893,0.9381,0.8993 +122454s,31.0 °C,0.1117,0.1059,0.1113,0.1994,0.1503,0.1644,0.1127,0.1055,0.1093,0.1097,0.1095,0.112,0.1094,0.1118,0.1143,0.3749,0.3466,0.3319,0.1131,0.1111,0.1134,0.1109,0.1168,0.1115,0.1091,0.1131,0.1142,0.5224,0.5147,0.5443,0.1125,0.1185,0.1069,0.1093,0.1231,0.1139,0.1119,0.1108,0.1124,0.6448,0.6651,0.6322,0.1301,0.1415,0.1444,0.1777,0.1927,0.1289,0.1816,0.1625,0.1751,0.7096,0.6052,0.7464,0.553,0.3825,0.3824,0.5749,0.4327,0.2288,0.4502,0.4645,0.4413,0.7899,0.836,0.7314,0.8294,0.8046,0.814,0.7165,0.7858,0.6594,0.6653,0.7455,0.8666,0.8192,0.7364,0.788,0.8524,0.9514,0.8771,0.9066,0.696,0.6669,0.9093,0.849,0.8309,0.9159,0.8986,0.8941,0.9642,0.8713,0.8885,0.8945,0.9352,0.8961 +123131s,30.8 °C,0.112,0.1059,0.1113,0.1995,0.1504,0.1642,0.1127,0.1055,0.1093,0.1097,0.1096,0.112,0.1094,0.1117,0.1148,0.3748,0.3463,0.3315,0.1133,0.111,0.1134,0.1108,0.117,0.1117,0.1091,0.1132,0.1143,0.5223,0.5143,0.5452,0.1126,0.1185,0.1069,0.1093,0.1232,0.1142,0.1121,0.1107,0.1126,0.646,0.6651,0.6329,0.1304,0.1417,0.1441,0.178,0.1933,0.1286,0.1811,0.1631,0.1759,0.7087,0.6059,0.7458,0.5542,0.3806,0.3822,0.5729,0.4336,0.2293,0.4493,0.4643,0.4408,0.7899,0.8364,0.7319,0.8291,0.8019,0.8127,0.7176,0.7851,0.6629,0.6647,0.7452,0.8661,0.8197,0.7365,0.7884,0.8529,0.951,0.8763,0.9065,0.6964,0.6674,0.9108,0.8498,0.8316,0.9174,0.8994,0.8962,0.966,0.8709,0.8896,0.8968,0.9351,0.8961 +123807s,31.0 °C,0.1119,0.106,0.1113,0.1996,0.1505,0.1641,0.1127,0.1055,0.1092,0.1097,0.1095,0.1121,0.1093,0.1118,0.1156,0.3748,0.3463,0.3318,0.1133,0.1109,0.1132,0.1108,0.117,0.1117,0.109,0.1132,0.1142,0.5225,0.5145,0.5452,0.1126,0.1185,0.1069,0.1093,0.1231,0.1139,0.1121,0.1107,0.1127,0.6469,0.6645,0.6326,0.1303,0.142,0.144,0.1779,0.1937,0.1283,0.1813,0.1623,0.1755,0.7093,0.6057,0.7466,0.5524,0.3821,0.3827,0.5754,0.4331,0.2291,0.4483,0.464,0.441,0.7894,0.8359,0.7313,0.8284,0.8012,0.8123,0.7171,0.7846,0.6623,0.6642,0.7447,0.8659,0.82,0.7359,0.7876,0.8529,0.9522,0.8776,0.9075,0.6976,0.6677,0.9114,0.8506,0.8322,0.9187,0.9011,0.8968,0.9664,0.8708,0.8898,0.8965,0.9367,0.8966 +124484s,30.8 °C,0.1117,0.1059,0.1113,0.1991,0.1502,0.1643,0.1127,0.1054,0.1092,0.1097,0.1094,0.1119,0.1095,0.1116,0.1146,0.3758,0.3469,0.3326,0.1133,0.1111,0.1133,0.1108,0.117,0.1115,0.1091,0.1132,0.1142,0.5227,0.5143,0.546,0.1127,0.1186,0.1069,0.1091,0.1232,0.1144,0.1121,0.1107,0.1125,0.6465,0.6652,0.6324,0.1306,0.1416,0.1441,0.1773,0.1929,0.1285,0.1816,0.1622,0.1754,0.7095,0.6049,0.7462,0.5514,0.3827,0.3811,0.5773,0.4325,0.2285,0.4532,0.4644,0.4433,0.7912,0.8362,0.7309,0.8315,0.8051,0.8144,0.7163,0.7871,0.6589,0.6685,0.7449,0.8681,0.8206,0.7363,0.7889,0.8527,0.9522,0.8774,0.9061,0.6959,0.6667,0.9124,0.8512,0.8332,0.9192,0.9017,0.8978,0.9672,0.872,0.8906,0.8973,0.9365,0.8963 +125160s,30.6 °C,0.1117,0.1059,0.1114,0.199,0.1504,0.1643,0.1127,0.1054,0.1093,0.1097,0.1093,0.1119,0.1094,0.1116,0.1148,0.3765,0.3472,0.3325,0.1134,0.1114,0.1135,0.1109,0.1171,0.1117,0.1092,0.1133,0.1143,0.5238,0.5151,0.5459,0.1125,0.1186,0.1069,0.1093,0.1231,0.1135,0.1121,0.1107,0.1126,0.6474,0.6651,0.6329,0.1303,0.1418,0.1441,0.1772,0.1931,0.1285,0.1814,0.1626,0.1758,0.7094,0.6057,0.7468,0.5521,0.3831,0.3829,0.5781,0.4327,0.2288,0.4521,0.4649,0.4428,0.7906,0.8363,0.7312,0.83,0.8058,0.8141,0.717,0.7863,0.6611,0.6708,0.7452,0.8687,0.821,0.7371,0.7895,0.8523,0.9532,0.8786,0.9072,0.6963,0.6675,0.9136,0.8517,0.833,0.9192,0.9034,0.9003,0.9678,0.8742,0.8918,0.899,0.9341,0.8951 +125837s,30.9 °C,0.1118,0.1059,0.1113,0.1993,0.1503,0.1643,0.1125,0.1054,0.1092,0.1096,0.1092,0.1119,0.1095,0.1116,0.1152,0.3763,0.3472,0.3329,0.1131,0.1109,0.1133,0.1108,0.1168,0.1114,0.1091,0.113,0.1142,0.5239,0.5151,0.5445,0.1124,0.1185,0.1067,0.1092,0.123,0.1135,0.112,0.1108,0.1125,0.6488,0.6644,0.6334,0.13,0.1421,0.1439,0.1778,0.1938,0.1279,0.1813,0.1625,0.1753,0.7088,0.605,0.7458,0.5509,0.3828,0.3829,0.578,0.4316,0.228,0.4523,0.4663,0.4446,0.791,0.8366,0.7315,0.8311,0.8077,0.8152,0.7174,0.7878,0.6565,0.6688,0.7461,0.8694,0.8212,0.7371,0.791,0.8528,0.9529,0.8781,0.9068,0.6956,0.6665,0.9131,0.8524,0.8338,0.9194,0.9046,0.9006,0.9676,0.8748,0.8916,0.8989,0.935,0.8939 +126513s,30.8 °C,0.112,0.1059,0.1113,0.1993,0.1503,0.1644,0.1127,0.1054,0.1092,0.1096,0.1092,0.1118,0.1095,0.1116,0.1142,0.3762,0.3472,0.3329,0.113,0.1109,0.1134,0.1109,0.1168,0.1114,0.1091,0.1132,0.1142,0.5234,0.5146,0.5447,0.1124,0.1185,0.1067,0.1092,0.123,0.1134,0.1121,0.1107,0.1125,0.6485,0.665,0.6331,0.1304,0.1416,0.1439,0.1776,0.1933,0.1281,0.1815,0.1623,0.1755,0.7095,0.605,0.7463,0.5504,0.3832,0.3814,0.579,0.4317,0.2279,0.4526,0.4656,0.4449,0.7907,0.8353,0.7308,0.8314,0.8064,0.8152,0.7175,0.788,0.6579,0.6698,0.7455,0.8696,0.821,0.7367,0.7899,0.8527,0.9525,0.8783,0.9068,0.6954,0.6664,0.9133,0.8526,0.8343,0.9198,0.9049,0.9017,0.9692,0.8753,0.893,0.9001,0.9337,0.8929 +127190s,30.9 °C,0.1117,0.1059,0.1112,0.1987,0.1502,0.1643,0.1126,0.1053,0.1092,0.1096,0.1092,0.1115,0.1095,0.1115,0.1153,0.3761,0.3471,0.3328,0.1132,0.111,0.1132,0.1106,0.1169,0.1115,0.1091,0.1131,0.1142,0.5236,0.5146,0.5459,0.1125,0.1186,0.1067,0.1092,0.123,0.1137,0.1123,0.1106,0.1126,0.6484,0.6653,0.6333,0.1304,0.1417,0.1438,0.1774,0.1934,0.128,0.1812,0.1627,0.176,0.7091,0.6055,0.7464,0.551,0.3816,0.3816,0.5776,0.4324,0.2284,0.4528,0.4655,0.4445,0.7908,0.8355,0.7309,0.8312,0.8061,0.8149,0.7173,0.7878,0.6596,0.6692,0.7456,0.8686,0.8213,0.7364,0.7897,0.8528,0.9532,0.8783,0.9077,0.6965,0.6673,0.9139,0.8525,0.8343,0.9206,0.9046,0.9022,0.9692,0.8739,0.8926,0.9,0.935,0.8932 +127866s,31.1 °C,0.1119,0.1059,0.1113,0.1989,0.1504,0.1642,0.1126,0.1054,0.1092,0.1096,0.1092,0.1117,0.1095,0.1115,0.1155,0.376,0.347,0.3328,0.1134,0.1108,0.1132,0.1109,0.117,0.1116,0.1091,0.1131,0.1142,0.5226,0.5136,0.5446,0.1124,0.1185,0.1067,0.1092,0.1229,0.113,0.112,0.1106,0.1124,0.6473,0.6656,0.6333,0.1304,0.1413,0.1439,0.1772,0.1928,0.1284,0.1808,0.1633,0.1762,0.7075,0.6059,0.7451,0.5518,0.3797,0.3813,0.5756,0.4326,0.2285,0.4511,0.4664,0.4442,0.7901,0.8358,0.7315,0.8303,0.8052,0.8136,0.7184,0.7872,0.6618,0.667,0.7453,0.8671,0.8204,0.7359,0.7878,0.8531,0.9535,0.8786,0.9088,0.6978,0.6676,0.9137,0.8526,0.8341,0.921,0.9058,0.9016,0.9687,0.8733,0.8912,0.8983,0.9372,0.8936 +128543s,30.8 °C,0.112,0.1059,0.1111,0.1987,0.1504,0.164,0.1126,0.1053,0.1091,0.1095,0.1091,0.1115,0.1094,0.1114,0.1158,0.3761,0.3471,0.3329,0.1132,0.111,0.1131,0.1107,0.1168,0.1114,0.109,0.113,0.114,0.523,0.5135,0.5451,0.1126,0.1184,0.1067,0.1091,0.123,0.1138,0.1121,0.1106,0.1124,0.6476,0.6657,0.6326,0.1305,0.1413,0.1438,0.177,0.1926,0.1281,0.181,0.1624,0.1757,0.7084,0.6049,0.7459,0.5497,0.3815,0.3814,0.5781,0.4316,0.2277,0.4514,0.466,0.4444,0.7902,0.8354,0.7308,0.8297,0.8045,0.8138,0.7178,0.787,0.6599,0.6667,0.7445,0.866,0.8208,0.7353,0.7869,0.8528,0.9542,0.8788,0.9097,0.6989,0.6677,0.9136,0.8532,0.8352,0.9221,0.9062,0.9025,0.9695,0.874,0.8928,0.8995,0.9372,0.8936 +129219s,31.0 °C,0.1118,0.1059,0.1112,0.1982,0.1503,0.1641,0.1125,0.1054,0.1091,0.1095,0.1091,0.1113,0.1094,0.1114,0.1153,0.3762,0.3472,0.333,0.1132,0.111,0.1132,0.1107,0.1169,0.1114,0.109,0.113,0.1141,0.5226,0.513,0.5448,0.1126,0.1184,0.1067,0.1091,0.1231,0.114,0.1121,0.1105,0.1124,0.6485,0.6656,0.6332,0.1301,0.1416,0.1437,0.177,0.1928,0.1281,0.1811,0.1622,0.1754,0.7086,0.6049,0.746,0.5486,0.3816,0.3806,0.5776,0.431,0.2279,0.4526,0.4657,0.4445,0.7903,0.835,0.7295,0.8304,0.8047,0.8139,0.7166,0.788,0.6596,0.6675,0.7449,0.8672,0.8213,0.7359,0.7878,0.8523,0.9537,0.8784,0.9087,0.6983,0.6677,0.9141,0.8524,0.8341,0.9216,0.9059,0.903,0.9689,0.8735,0.8925,0.8997,0.9349,0.8915 +129896s,30.9 °C,0.1117,0.1057,0.1111,0.198,0.1502,0.164,0.1125,0.1053,0.1091,0.1095,0.1091,0.1112,0.1094,0.1114,0.1144,0.3755,0.3473,0.3326,0.1131,0.111,0.1132,0.1106,0.1168,0.1115,0.109,0.1128,0.114,0.5222,0.5126,0.5436,0.1125,0.1183,0.1067,0.1091,0.123,0.1133,0.1119,0.1104,0.1123,0.6469,0.6664,0.633,0.1298,0.141,0.1437,0.1766,0.1921,0.1284,0.1802,0.1628,0.1757,0.7064,0.6057,0.7438,0.5498,0.3778,0.3808,0.5747,0.432,0.228,0.4481,0.4662,0.4432,0.7888,0.8351,0.7304,0.8277,0.8021,0.8112,0.7182,0.785,0.6628,0.6648,0.7451,0.8657,0.8207,0.7361,0.7868,0.8524,0.9536,0.8781,0.9095,0.699,0.6679,0.9139,0.8527,0.8348,0.9218,0.9069,0.9016,0.969,0.8734,0.892,0.8986,0.9363,0.8926 +130572s,30.9 °C,0.1123,0.1058,0.1112,0.1989,0.1504,0.1636,0.1124,0.1054,0.1091,0.1095,0.1091,0.1114,0.1093,0.1115,0.114,0.3753,0.347,0.3326,0.1131,0.1109,0.1132,0.1107,0.1166,0.1114,0.109,0.1128,0.114,0.5221,0.5122,0.5434,0.1125,0.1183,0.1067,0.1091,0.123,0.1134,0.1119,0.1107,0.1123,0.6486,0.665,0.6336,0.1296,0.1419,0.1438,0.1776,0.1929,0.128,0.1805,0.1628,0.1754,0.7073,0.6051,0.7441,0.5483,0.3793,0.3808,0.5763,0.431,0.2272,0.4502,0.4668,0.4438,0.7896,0.8353,0.7306,0.8284,0.8021,0.8119,0.7194,0.7855,0.6611,0.666,0.7458,0.8663,0.8208,0.7361,0.7877,0.8532,0.9531,0.8784,0.9095,0.6982,0.6674,0.914,0.8534,0.8353,0.9219,0.9071,0.9015,0.9694,0.8722,0.8921,0.8991,0.9351,0.8901 +131249s,31.0 °C,0.1122,0.1058,0.1111,0.1988,0.1503,0.1637,0.1125,0.1053,0.109,0.1095,0.1091,0.1113,0.1094,0.1114,0.1152,0.3754,0.3472,0.3322,0.1133,0.1109,0.1131,0.1107,0.1168,0.1114,0.109,0.1129,0.1141,0.5219,0.512,0.5438,0.1126,0.1183,0.1066,0.1091,0.123,0.114,0.1121,0.1105,0.1124,0.6477,0.6655,0.633,0.1302,0.1413,0.1436,0.177,0.1927,0.1279,0.1805,0.1622,0.1751,0.7076,0.6046,0.7445,0.5471,0.38,0.3805,0.5777,0.4307,0.2271,0.4504,0.4665,0.4442,0.7893,0.8342,0.7297,0.8288,0.8023,0.8116,0.7186,0.7863,0.6591,0.6658,0.7456,0.8666,0.8208,0.7355,0.7883,0.8531,0.9533,0.8779,0.9088,0.6982,0.6676,0.9141,0.8524,0.8353,0.9226,0.9063,0.9025,0.9703,0.8725,0.8923,0.8994,0.9351,0.8899 +131926s,30.8 °C,0.112,0.1058,0.1111,0.1983,0.1503,0.1637,0.1125,0.1053,0.1091,0.1095,0.109,0.1111,0.1093,0.1114,0.1151,0.3752,0.3473,0.3321,0.113,0.1109,0.1132,0.1106,0.1169,0.1115,0.109,0.1128,0.1141,0.5222,0.5121,0.5432,0.1125,0.1183,0.1067,0.1091,0.1229,0.113,0.1119,0.1104,0.1123,0.6473,0.6658,0.6329,0.13,0.1412,0.1437,0.1765,0.1924,0.128,0.1803,0.162,0.175,0.7074,0.6045,0.7443,0.5466,0.3806,0.3805,0.5779,0.4306,0.2273,0.4515,0.4662,0.4445,0.789,0.8342,0.7294,0.8284,0.8034,0.8118,0.7173,0.7867,0.6594,0.6673,0.7456,0.8681,0.8217,0.7361,0.7889,0.853,0.9536,0.8777,0.9081,0.6974,0.6678,0.9153,0.8531,0.8355,0.9229,0.9073,0.904,0.9703,0.8729,0.8934,0.9006,0.9338,0.89 +132602s,31.0 °C,0.1117,0.1057,0.111,0.1976,0.15,0.1638,0.1125,0.1053,0.1091,0.1094,0.109,0.111,0.1093,0.1114,0.1136,0.3756,0.3477,0.3322,0.113,0.111,0.1133,0.1107,0.1166,0.1114,0.1089,0.1129,0.1141,0.5219,0.5122,0.5429,0.1127,0.1183,0.1067,0.109,0.1229,0.114,0.112,0.1105,0.1123,0.6484,0.666,0.6334,0.1298,0.1413,0.1438,0.1768,0.1925,0.1282,0.18,0.1626,0.1756,0.7069,0.605,0.7442,0.5475,0.3785,0.381,0.5784,0.4309,0.227,0.4491,0.4674,0.445,0.7892,0.8348,0.7301,0.8281,0.8013,0.8119,0.7191,0.7868,0.6601,0.6654,0.7459,0.8673,0.8218,0.7362,0.7889,0.8533,0.9541,0.879,0.9091,0.6979,0.6681,0.9148,0.8528,0.8361,0.923,0.9084,0.9025,0.9698,0.8722,0.8925,0.8996,0.9364,0.8907 +133279s,31.0 °C,0.1119,0.1058,0.1111,0.1979,0.1501,0.1637,0.1125,0.1053,0.109,0.1094,0.1089,0.1111,0.1093,0.1114,0.1136,0.376,0.3477,0.3322,0.1129,0.111,0.1134,0.1106,0.1167,0.1115,0.109,0.1128,0.1141,0.5219,0.5117,0.5422,0.1125,0.1184,0.1066,0.1092,0.1228,0.1128,0.112,0.1107,0.1123,0.6475,0.6654,0.6329,0.1297,0.1412,0.1439,0.1767,0.192,0.128,0.1807,0.1614,0.1743,0.7087,0.6034,0.7451,0.5441,0.3821,0.3807,0.5824,0.4287,0.2262,0.451,0.4673,0.4455,0.7887,0.8334,0.7295,0.8285,0.8026,0.8119,0.7184,0.7866,0.6573,0.6674,0.7463,0.8683,0.8216,0.7362,0.7898,0.8536,0.9533,0.8786,0.9082,0.6967,0.6666,0.9145,0.8546,0.8362,0.9218,0.9082,0.9041,0.9708,0.8743,0.8948,0.903,0.931,0.8861 +133955s,30.5 °C,0.1122,0.1058,0.1111,0.1982,0.1501,0.1635,0.1124,0.1053,0.109,0.1094,0.1089,0.1108,0.1093,0.1113,0.1146,0.3757,0.3476,0.3323,0.1129,0.1108,0.1132,0.1107,0.1167,0.1113,0.1089,0.113,0.1141,0.5211,0.5112,0.5425,0.1126,0.1183,0.1065,0.1089,0.1228,0.1137,0.1119,0.1105,0.1122,0.6473,0.6659,0.6331,0.1299,0.1409,0.1436,0.1766,0.1917,0.1282,0.1801,0.1625,0.1751,0.7073,0.604,0.7441,0.5461,0.3791,0.3792,0.5784,0.4301,0.2264,0.4506,0.4677,0.4457,0.7895,0.8341,0.7296,0.8289,0.8029,0.8128,0.7192,0.7879,0.6603,0.6652,0.7455,0.8664,0.8206,0.735,0.7874,0.8535,0.9542,0.8791,0.9099,0.6988,0.6673,0.9161,0.8544,0.8372,0.923,0.9094,0.9046,0.9718,0.874,0.895,0.9033,0.9332,0.8871 +134632s,31.0 °C,0.1123,0.1059,0.1112,0.1987,0.1503,0.1633,0.1124,0.1053,0.1089,0.1094,0.1089,0.1109,0.1092,0.1112,0.1148,0.3762,0.3474,0.3324,0.1131,0.1106,0.1131,0.1107,0.1167,0.1113,0.1089,0.1129,0.1141,0.5214,0.5114,0.5426,0.1124,0.1183,0.1065,0.109,0.1226,0.1128,0.1119,0.1105,0.1124,0.6487,0.6647,0.6328,0.1299,0.1413,0.1433,0.1769,0.1925,0.1277,0.1801,0.1614,0.1742,0.708,0.6028,0.744,0.5437,0.3813,0.3797,0.5811,0.429,0.2261,0.4535,0.4672,0.4459,0.7896,0.8334,0.7284,0.829,0.805,0.8128,0.7177,0.7885,0.6571,0.6672,0.7459,0.8673,0.8208,0.735,0.7885,0.8535,0.9537,0.8782,0.9085,0.6973,0.6666,0.9164,0.8548,0.8375,0.9233,0.909,0.9059,0.9723,0.8759,0.8961,0.9036,0.9316,0.8855 +Date of measurement: 2014-11-18/Time of measurement: 08:54:20,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +JP 30C No Shaking 48 hrs.mth,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +C:\Documents and Settings\All Users\Documents\Tecan\Magellan\mth\JP 30C No Shaking 48 hrs.mth,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +IC50_YPD-EMIM-AC-ANA_Y133t_PTK2-A_PTK2-B_Y133tpBlank_2014-NOV-18.wsp,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +C:\Documents and Settings\All Users\Documents\Tecan\Magellan\wsp\jeffp\IC50_YPD-EMIM-AC-ANA_Y133t_PTK2-A_PTK2-B_Y133tpBlank_2014-NOV-18.wsp,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +595nm,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Unknown user,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +infinite 200,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Instrument serial number: 810005503,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Plate,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Plate Description: [NUN96ft] - ThermoFischer Scientific-Nunclon 96 Flat Transparent,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Plate with Cover: Yes,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Barcode: No,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Temperature,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Mode: On,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Temperature: 30.0 °C,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Kinetic Cycle,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Number of Cycles: 200,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Absorbance,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Measurement Wavelength: 595 nm,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Measurement Bandwidth: 9 nm,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Number of Reads: 25,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Settle Time: 0 ms,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Label: Label1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Incubation,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Total kinetic run time: 1days 13h 23min 52s ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, diff --git a/Testing/test_input_files/Invalid_input_files/133 Well H1-H3 M200.csv b/Testing/test_input_files/Invalid_input_files/133 Well H1-H3 M200.csv new file mode 100644 index 0000000..7f7f964 --- /dev/null +++ b/Testing/test_input_files/Invalid_input_files/133 Well H1-H3 M200.csv @@ -0,0 +1,229 @@ +Well positions,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Raw data,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 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C,0.1123,0.1059,0.1112,0.1987,0.1503,0.1633,0.1124,0.1053,0.1089,0.1094,0.1089,0.1109,0.1092,0.1112,0.1148,0.3762,0.3474,0.3324,0.1131,0.1106,0.1131,0.1107,0.1167,0.1113,0.1089,0.1129,0.1141,0.5214,0.5114,0.5426,0.1124,0.1183,0.1065,0.109,0.1226,0.1128,0.1119,0.1105,0.1124,0.6487,0.6647,0.6328,0.1299,0.1413,0.1433,0.1769,0.1925,0.1277,0.1801,0.1614,0.1742,0.708,0.6028,0.744,0.5437,0.3813,0.3797,0.5811,0.429,0.2261,0.4535,0.4672,0.4459,0.7896,0.8334,0.7284,0.829,0.805,0.8128,0.7177,0.7885,0.6571,0.6672,0.7459,0.8673,0.8208,0.735,0.7885,0.8535,0.9537,0.8782,0.9085,0.6973,0.6666,0.9164,0.8548,0.8375,0.9233,0.909,0.9059,0.9723,0.8759,0.8961,0.9036,0.9316,0.8855 +Date of measurement: 2014-11-18/Time of measurement: 08:54:20,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +JP 30C No Shaking 48 hrs.mth,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +C:\Documents and Settings\All Users\Documents\Tecan\Magellan\mth\JP 30C No Shaking 48 hrs.mth,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +IC50_YPD-EMIM-AC-ANA_Y133t_PTK2-A_PTK2-B_Y133tpBlank_2014-NOV-18.wsp,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +C:\Documents and Settings\All Users\Documents\Tecan\Magellan\wsp\jeffp\IC50_YPD-EMIM-AC-ANA_Y133t_PTK2-A_PTK2-B_Y133tpBlank_2014-NOV-18.wsp,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +595nm,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Unknown user,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +infinite 200,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Instrument serial number: 810005503,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Plate,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Plate Description: [NUN96ft] - ThermoFischer Scientific-Nunclon 96 Flat Transparent,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Plate with Cover: Yes,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Barcode: No,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Temperature,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Mode: On,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Temperature: 30.0 C,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Kinetic Cycle,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Number of Cycles: 200,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Absorbance,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Measurement Wavelength: 595 nm,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Measurement Bandwidth: 9 nm,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Number of Reads: 25,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Settle Time: 0 ms,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Label: Label1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, + Incubation,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Total kinetic run time: 1days 13h 23min 52s ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, diff --git a/Testing/test_input_files/Invalid_input_files/README b/Testing/test_input_files/Invalid_input_files/README new file mode 100644 index 0000000..e15bdfd --- /dev/null +++ b/Testing/test_input_files/Invalid_input_files/README @@ -0,0 +1,6 @@ + File name Problem +133 Well H1-H3 M200.csv Unrecognized encoding +133 Well H1-H3 M200 UTF-8 fixed.csv Temperature column exist +133 Well H1-H3 M200 UTF-8 fixed noT.csv Missing data point at A6 time + point 14 + diff --git a/Testing/tester.R b/Testing/tester.R deleted file mode 100644 index b265cfe..0000000 --- a/Testing/tester.R +++ /dev/null @@ -1,22 +0,0 @@ -# Analyze growth curve data and generate outputs and plots from an R session using GCAT package - -library(GCAT) - -INPUT.DIR = "/mnt/file.glbrc.org/ybukhman/Projects/GCAT_B05/B05.19 GCAT 4/3_GCAT_example_data_analysis" -INPUT.FILE = "YPDAFEXglucoseTests_2-25-10.csv" -OUTPUT.DIR = "/mnt/file.glbrc.org/ybukhman/Projects/GCAT_B05/B05.19 GCAT 4/3_GCAT_example_data_analysis/GCAT_4.4_debug/v467__single_plate_sigmoid" -start.index = 2 - -# gcat.analysis.main expects to see this object in the environment from which it is called: -time.input = 1/3600 -#time.input = "%m/%d/%Y %H:%M" - -setwd(INPUT.DIR) -out = gcat.analysis.main(file.list = INPUT.FILE, single.plate = T, layout.file = NULL, - out.dir = OUTPUT.DIR, graphic.dir = OUTPUT.DIR, - add.constant = 1, blank.value = NULL, start.index = start.index, growth.cutoff = 0.05, - use.linear.param=F, use.loess=F, smooth.param=0.1, - points.to.remove = 0, remove.jumps = F, - silent = F, verbose = T, return.fit = T, overview.jpgs = T) - -