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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Please edit documentation in R/GCAT.main.R
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\name{gcat.output.main}
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\alias{gcat.output.main}
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\title{Output function for generating files from fitted data.}
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\usage{
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gcat.output.main(fitted.well.array, out.prefix = "", source.file.list,
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upload.timestamp = NULL, add.constant, blank.value, start.index,
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growth.cutoff, points.to.remove, remove.jumps, out.dir = getwd(),
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graphic.dir = paste(out.dir, "/pics", sep = ""), overview.jpgs = T,
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sranges = NA, use.linear.param = F, use.loess = F, lagRange = NA,
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totalRange = NA, totalODRange = NA, specRange = NA, plate.nrow = 8,
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plate.ncol = 12, unlog = F, silent = T, main.envir)
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}
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\arguments{
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\item{fitted.well.array}{A list of fitted well objects.}
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\item{out.prefix}{Prefix that is in the name of output files.}
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\item{source.file.list}{A list of the source files' names.}
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\item{upload.timestamp}{The time format indicated by the user.}
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\item{add.constant}{used to readjust for the constant added during the log transform when plotting ODs.}
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\item{blank.value}{User can enter a blank OD measurement for uninoculated wells.
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If NULL, defaults to the value of the first OD measurement of each well.}
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\item{start.index}{Which timepoint should be used as the first one after inoculation (defaults to the 2th one)}
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\item{growth.cutoff}{Minimum threshold for curve growth.}
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\item{points.to.remove}{A list of numbers referring to troublesome points that should be removed across all wells.}
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\item{remove.jumps}{Should the slope checking function be on the lookout for large jumps in OD?}
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\item{out.dir}{name a directory to output the table of curve parameters to (defaults to working directory)}
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\item{graphic.dir}{name a directory to output the images of the fitted curves to
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(defaults to subdirectory "pics" of <out.dir> above)}
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\item{overview.jpgs}{should jpgs be generated for each plate with the overview graphic?
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This is for backwards compatibility with the old web server.}
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\item{sranges}{The 2 boundaries for calculating the area under the curve.}
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\item{use.linear.param}{linear parameter is used or not?}
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\item{use.loess}{Is LOESS model going to be used?}
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\item{lagRange}{The heatmap specific range for lag time.}
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\item{totalRange}{The heatmap specific range for the achieved growth.}
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\item{totalODRange}{The heatmap specific range for the achieved growth on linear (OD) scale.}
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\item{specRange}{The heatmap specific range for spec growth rate.}
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\item{plate.nrow}{The number of rows for a plate.}
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\item{plate.ncol}{The number of columns for a plate}
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\item{unlog}{should exported graphics be transformed back to the OD scale?}
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\item{silent}{should messages be returned to the console?}
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\item{main.envir}{starting environment of gcat.analysis.main(), captured as a list, printed out for debugging}
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}
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\value{
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A list of output files if success.
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}
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\description{
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Handles files and directories, calls \code{table.out}, \code{plate.overview} and \code{view.fit}
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to generate output tables and graphics.
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}
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