Updated master to SVN trunk revision 572

2015-06-26 15:04:35 -05:00
parent 67544a10e6
commit 2d658405a1
184 changed files with 8236 additions and 6182 deletions
@@ -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 <data.from> and <well.name> (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
+}
+
@@ -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.
+}
+
@@ -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{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{smooth.param}{If loess is used, an optional smoothing parameter. Default is .6}
+
 \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.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}
 }
 \description{
 This function will use the function stored in the "guess" slot of \code{growth.model} to calculate initial guesses
@@ -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
+}
+
@@ -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
-}
@@ -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 <single.plate>)}
@@ -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
@@ -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 <load.data>}
+}
+\description{
+This function can append together arrays created using <load.data>
+}
+
@@ -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
@@ -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{start.index}{Which timepoint should be used as the first one after inoculation?}
+
+\item{single.plate}{Is the plate single type?}
+
 \item{silent}{Surpress all messages.}
-
-\item{plate.laout}{Specifies the layout of the given plate.}
-
-\item{add.constant}{A value for r in the log(OD + r) transformation.}
-
-\item{verbose}{Display all messages when analyzing each well.}
 }
 \value{
 A list of well objects.
@@ -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.
@@ -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
-}
@@ -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 <strptime>.}
+
+\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.
+}
+
@@ -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
+}
+
@@ -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}
@@ -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 <data.from> (see well.class.R)
+
+ These functions make use of <raw.data> 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 <blank.value> 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 <start> 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}
+ }
+}
+
@@ -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 <check.slopes> 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
+}
+
@@ -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 <check.slopes> 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{
@@ -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.
+}
+
@@ -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.
@@ -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
+}
+
@@ -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 <normalize.ODs> (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}
+}}
+