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

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Performs the Rao-Scott Cochran-Armitage by Slices trend test (RSCABS) used in analysis of histopathological endpoints. It has functions for both command line operations along with a built in GUI.

Author
Joe Swintek [aut, cre], Kevin Flynn [ctb]
Date of publication
2016-08-12 16:50:59
Maintainer
Joe Swintek <swintek.joe@epa.gov>
License
CC0
Version
0.9.0
URLs

View on CRAN

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

Files in this package

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