RSCABS: Rao-Scott Cochran-Armitage by Slices Trend Test
Version 0.9.2

Performs the Rao-Scott Cochran-Armitage by Slices trend test (RSCABS) used in analysis of histopathological endpoints, built to be used with either a GUI or by a command line. The RSCABS method is detailed in "Statistical analysis of histopathological endpoints" by John Green et. al. (2014) .

Browse man pages Browse package API and functions Browse package files

AuthorJoe Swintek [aut, cre], Kevin Flynn [ctb]
Date of publication2017-04-26 17:47:29 UTC
MaintainerJoe Swintek <swintek.joe@epa.gov>
LicenseCC0
Version0.9.2
URL https://CRAN.R-project.org/package=RSCABS
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RSCABS")

Man pages

addHistoSpec: Specify data parameters
checkPlot: Check the selection for plotting
checkSelction: Checks user inputs
convert2Score: Converts any object that is not zero or a positive number to...
detailedResults2HTML: Saves results as an HTML file
detailedResults2Output: Print results to the GUI window
exampleHistData: Example histology data
filterData: Filters problematic data
getDir: Attain the name of a directory
Histopath: GUI for analysis of histopathological data
openCB: Open a csv file
otherPath: Other analyses for histopathological endpoints
plotPath: Plot histopathological data
plotRSCABS: Plots histopathological data.
popMessage: Pops up a message
prepDataRSCABS: Prepares data for an RSCABS analysis
RSCABK: Runs the kth slice of RSCABS
RSCABSMain: Cleans data and runs RSCABS when called from the GUI...
RSCABS-package: Runs the Rao-Scott adjusted Cochran-Armitage trend test by...
runDetailedResults: Attain detailed results on an endpoint
runEffectSelect: Runs a detailed analysis on an endpoint
runRSCABS: Runs RSCABS
runStdSubset: Subset the data used in Histopath
saveCB: Attain the name of a file to be saved
saveFile: Saves a data set
selectPara: Window to declare the names of variables and values
setPlotParms: Sets the default plotting parameters for RSCABS
stepDownRSCABS: Performs the step down aspect of RSCABS
stepKRSCABS: Steps through the severity score for a given effect
subsetDataKeep: Subsets data

Functions

Histopath Man page Source code
RSCABK Man page Source code
RSCABS Man page
RSCABS-package Man page
RSCABSMain Man page Source code
addHistoSpec Man page Source code
checkPlot Man page Source code
checkSelction Man page Source code
convert2Score Man page Source code
detailedResults2HTML Man page Source code
detailedResults2Output Man page Source code
exampleHistData Man page
filterData Man page Source code
getDir Man page Source code
onAttach Source code
onLoad Source code
openCB Man page Source code
otherPath Man page Source code
plotPath Man page Source code
plotRSCABS Man page Source code
popMessage Man page Source code
prepDataRSCABS Man page Source code
runDetailedResults Man page Source code
runEffectSelect Man page Source code
runRSCABS Man page Source code
runStdSubset Man page Source code
saveCB Man page Source code
saveFile Man page Source code
selectPara Man page Source code
setPlotParms Man page Source code
stepDownRSCABS Man page Source code
stepKRSCABS Man page Source code
subsetDataKeep Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/RSCABS.R
inst/doc/RSCABS.pdf
inst/doc/RSCABS.Rnw
NAMESPACE
data
data/exampleHistData.rda
R
R/runRSCABS.R
R/checkPlot.r
R/otherPath.R
R/stepKRSCABS.R
R/selectPara.r
R/plotPath.r
R/RSCABSMain.R
R/RSCABK.R
R/saveCB.R
R/convert2Score.R
R/subsetDataKeep.R
R/stepDownRSCABS.R
R/getDir.R
R/runStdSubset.R
R/popMessage.R
R/detailedResults2HTML.R
R/runDetailedResults.R
R/addHistoSpec.R
R/checkSelction.R
R/detailedResults2Output.R
R/filterData.R
R/zzz.r
R/plotRSCABS.r
R/setPlotParms.r
R/runEffectSelect.R
R/RSCABS-internal.R
R/saveFile.R
R/openCB.R
R/prepDataRSCABS.R
R/Histopath.R
vignettes
vignettes/dialogue1.png
vignettes/OtherPath4.png
vignettes/RSCABS1.png
vignettes/GTK2.png
vignettes/OtherPath2.png
vignettes/OtherPath1.png
vignettes/data
vignettes/data/exampleHistData.rda
vignettes/GTK1.png
vignettes/R
vignettes/R/runRSCABS.R
vignettes/R/stepKRSCABS.R
vignettes/R/RSCABK.R
vignettes/R/convert2Score.R
vignettes/R/stepDownRSCABS.R
vignettes/R/filterData.R
vignettes/R/prepDataRSCABS.R
vignettes/PlotPath2.png
vignettes/RSCABS4.png
vignettes/RSCABS.Rnw
vignettes/ExampleData.png
vignettes/HistoSpec1.png
vignettes/PlotPath1.png
vignettes/PlotPath3.png
vignettes/ExampleData2.png
vignettes/HistoSpec2.png
vignettes/OtherPath3.png
vignettes/RSCABS2.png
vignettes/RSCABS3.png
MD5
build
build/vignette.rds
DESCRIPTION
man
man/RSCABS-package.Rd
man/checkPlot.Rd
man/plotRSCABS.Rd
man/popMessage.Rd
man/exampleHistData.Rd
man/Histopath.Rd
man/openCB.Rd
man/otherPath.Rd
man/prepDataRSCABS.Rd
man/selectPara.Rd
man/runRSCABS.Rd
man/runDetailedResults.Rd
man/saveCB.Rd
man/runEffectSelect.Rd
man/RSCABK.Rd
man/plotPath.Rd
man/detailedResults2HTML.Rd
man/getDir.Rd
man/detailedResults2Output.Rd
man/stepKRSCABS.Rd
man/saveFile.Rd
man/setPlotParms.Rd
man/filterData.Rd
man/runStdSubset.Rd
man/addHistoSpec.Rd
man/RSCABSMain.Rd
man/convert2Score.Rd
man/subsetDataKeep.Rd
man/checkSelction.Rd
man/stepDownRSCABS.Rd
INDEX
RSCABS documentation built on May 19, 2017, 11:08 p.m.