Updated master to SVN trunk revision 572

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.