Files in DarioS/ClassifyR
A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing
.Rbuildignore
.gitignore
ClassifyR.Rproj
DESCRIPTION
NAMESPACE
R/ROCplot.R
R/available.R
R/calcPerformance.R
R/classes.R
R/constants.R
R/crissCrossValidate.R
R/crossValidate.R
R/data.R
R/distribution.R
R/edgesToHubNetworks.R
R/featureSetSummary.R
R/getLocationsAndScales.R
R/interactorDifferences.R
R/interfaceClassify.R
R/interfaceCoxPH.R
R/interfaceCoxnet.R
R/interfaceDLDA.R
R/interfaceFisherDiscriminant.R
R/interfaceGLM.R
R/interfaceKNN.R
R/interfaceKTSPclassifier.R
R/interfaceMerge.R
R/interfaceMixModels.R
R/interfaceNSC.R
R/interfaceNaiveBayesKernel.R
R/interfacePCA.R
R/interfacePenalisedGLM.R
R/interfacePrevalidation.R
R/interfaceRandomForest.R
R/interfaceRandomForestSurvival.R
R/interfaceSVM.R
R/interfaceXGB.R
R/performancePlot.R
R/plotFeatureClasses.R
R/precisionPathways.R
R/prepareData.R
R/previousSelection.R
R/previousTrained.R
R/randomSelection.R
R/rankingBartlett.R
R/rankingCoxPH.R
R/rankingDMD.R
R/rankingDifferentMeans.R
R/rankingEdgeR.R
R/rankingKolmogorovSmirnov.R
R/rankingKullbackLeibler.R
R/rankingLevene.R
R/rankingLikelihoodRatio.R
R/rankingLimma.R
R/rankingPairsDifferences.R
R/rankingPlot.R
R/runTest.R
R/runTests.R
R/samplesMetricMap.R
R/selectMulti.R
R/selectionPlot.R
R/simpleParams.R
R/subtractFromLocation.R
R/utilities.R
README.md
_pkgdown.yml
data/HuRI.RData
data/METABRICclinical.RData
data/asthma.RData
docs/404.html
docs/articles/ClassifyR.html
docs/articles/ClassifyR_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/ClassifyR_files/figure-html/unnamed-chunk-11-1.png
docs/articles/ClassifyR_files/figure-html/unnamed-chunk-14-1.png
docs/articles/ClassifyR_files/figure-html/unnamed-chunk-15-1.png
docs/articles/ClassifyR_files/figure-html/unnamed-chunk-16-1.png
docs/articles/ClassifyR_files/figure-html/unnamed-chunk-17-1.png
docs/articles/ClassifyR_files/figure-html/unnamed-chunk-18-1.png
docs/articles/ClassifyR_files/figure-html/unnamed-chunk-5-1.png
docs/articles/ClassifyR_files/figure-html/unnamed-chunk-6-1.png
docs/articles/ClassifyR_files/figure-html/unnamed-chunk-7-1.png
docs/articles/ClassifyR_files/figure-html/unnamed-chunk-8-1.png
docs/articles/DevelopersGuide.html
docs/articles/DevelopersGuide_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/images/Cindex.png
docs/articles/images/ClassifyRprocedure.png
docs/articles/images/accessors.png
docs/articles/images/balancedAccuracy.png
docs/articles/images/leave2out.png
docs/articles/images/microMacro.png
docs/articles/images/permuteFold.png
docs/articles/images/permutePercentSplit.png
docs/articles/incorporateNew.html
docs/articles/incorporateNew_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/index.html
docs/articles/introduction.html
docs/articles/introduction_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/multiViewMethods.html
docs/articles/multiViewMethods_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/performanceEvaluation.html
docs/articles/performanceEvaluation_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/presets.html
docs/articles/presets_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/style.css
docs/articles/survival.html
docs/articles/survival_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/survival_files/figure-html/unnamed-chunk-3-1.png
docs/articles/survival_files/figure-html/unnamed-chunk-4-1.png
docs/articles/survival_files/figure-html/unnamed-chunk-5-1.png
docs/authors.html
docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js
docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.1.3/bootstrap.min.css
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.2.2/bootstrap.min.css
docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js
docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.3.1/bootstrap.min.css
docs/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js
docs/deps/clipboard.js-2.0.11/clipboard.min.js
docs/deps/data-deps.txt
docs/deps/font-awesome-6.5.2/css/all.css
docs/deps/font-awesome-6.5.2/css/all.min.css
docs/deps/font-awesome-6.5.2/css/v4-shims.css
docs/deps/font-awesome-6.5.2/css/v4-shims.min.css
docs/deps/font-awesome-6.5.2/webfonts/fa-brands-400.ttf
docs/deps/font-awesome-6.5.2/webfonts/fa-brands-400.woff2
docs/deps/font-awesome-6.5.2/webfonts/fa-regular-400.ttf
docs/deps/font-awesome-6.5.2/webfonts/fa-regular-400.woff2
docs/deps/font-awesome-6.5.2/webfonts/fa-solid-900.ttf
docs/deps/font-awesome-6.5.2/webfonts/fa-solid-900.woff2
docs/deps/font-awesome-6.5.2/webfonts/fa-v4compatibility.ttf
docs/deps/font-awesome-6.5.2/webfonts/fa-v4compatibility.woff2
docs/deps/headroom-0.11.0/headroom.min.js
docs/deps/headroom-0.11.0/jQuery.headroom.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/deps/search-1.0.0/autocomplete.jquery.min.js
docs/deps/search-1.0.0/fuse.min.js
docs/deps/search-1.0.0/mark.min.js
docs/extra.css
docs/index.html
docs/katex-auto.js
docs/lightswitch.js
docs/link.svg
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/ClassifyResult-class.html
docs/reference/CrossValParams-class.html
docs/reference/FeatureSetCollection.html
docs/reference/HuRI.html
docs/reference/METABRICclinical.html
docs/reference/ModellingParams-class.html
docs/reference/PredictParams-class.html
docs/reference/ROCplot-1.png
docs/reference/ROCplot.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/Rplot003.png
docs/reference/Rplot004.png
docs/reference/SelectParams-class.html
docs/reference/TrainParams-class.html
docs/reference/TransformParams-class.html
docs/reference/asthma.html
docs/reference/available.html
docs/reference/calcPerformance.html
docs/reference/colCoxTests.html
docs/reference/crissCrossPlot.html
docs/reference/crissCrossValidate.html
docs/reference/crossValidate-1.png
docs/reference/crossValidate.html
docs/reference/distribution-1.png
docs/reference/distribution.html
docs/reference/edgesToHubNetworks.html
docs/reference/featureSetSummary.html
docs/reference/figures/ClassifyRsticker.png
docs/reference/generateCrossValParams.html
docs/reference/generateModellingParams.html
docs/reference/index.html
docs/reference/interactorDifferences.html
docs/reference/performancePlot-1.png
docs/reference/performancePlot.html
docs/reference/plotFeatureClasses-1.png
docs/reference/plotFeatureClasses-2.png
docs/reference/plotFeatureClasses-3.png
docs/reference/plotFeatureClasses.html
docs/reference/precisionPathways.html
docs/reference/precisionPathwaysEvaluations.html
docs/reference/prepareData.html
docs/reference/rankingPlot-1.png
docs/reference/rankingPlot.html
docs/reference/runTest.html
docs/reference/runTests.html
docs/reference/samplesMetricMap-1.png
docs/reference/samplesMetricMap.html
docs/reference/samplesSplitting.html
docs/reference/selectionPlot-1.png
docs/reference/selectionPlot-2.png
docs/reference/selectionPlot-3.png
docs/reference/selectionPlot-4.png
docs/reference/selectionPlot.html
docs/search.json
docs/sitemap.xml
inst/CITATION
inst/NEWS.Rd
man/ClassifyResult-class.Rd
man/CrossValParams-class.Rd
man/FeatureSetCollection.Rd
man/HuRI.Rd
man/METABRICclinical.Rd
man/ModellingParams-class.Rd
man/PredictParams-class.Rd
man/ROCplot.Rd
man/SelectParams-class.Rd
man/TrainParams-class.Rd
man/TransformParams-class.Rd
man/asthma.Rd
man/available.Rd
man/calcPerformance.Rd
man/colCoxTests.Rd
man/crissCrossPlot.Rd
man/crissCrossValidate.Rd
man/crossValidate.Rd
man/distribution.Rd
man/edgesToHubNetworks.Rd
man/featureSetSummary.Rd
man/figures/ClassifyRsticker.png
man/interactorDifferences.Rd
man/performancePlot.Rd
man/plotFeatureClasses.Rd
man/precisionPathways.Rd
man/precisionPathwaysEvaluations.Rd
man/prepareData.Rd
man/rankingPlot.Rd
man/runTest.Rd
man/runTests.Rd
man/samplesMetricMap.Rd
man/samplesSplitting.Rd
man/selectionPlot.Rd
pkgdown/extra.css
src/Makevars
src/coxformatrices.cpp
src/survS.h
src/survproto.h
vignettes/ClassifyR.Rmd
vignettes/DevelopersGuide.Rmd
vignettes/images/Cindex.png
vignettes/images/ClassifyRprocedure.png
vignettes/images/accessors.png
vignettes/images/balancedAccuracy.png
vignettes/images/leave2out.png
vignettes/images/microMacro.png
vignettes/images/permuteFold.png
vignettes/images/permutePercentSplit.png
vignettes/incorporateNew.Rmd
vignettes/introduction.Rmd
vignettes/multiViewMethods.Rmd
vignettes/performanceEvaluation.Rmd
vignettes/presets.Rmd
vignettes/style.css
vignettes/survival.Rmd
