DESCRIPTION

Package: ClassifyR
Type: Package
Title: A framework for cross-validated classification problems, with
       applications to differential variability and differential
       distribution testing
Version: 3.11.6
Date: 2024-12-19
Authors@R:
    c(
    person(given = "Dario", family = "Strbenac", email = "dario.strbenac@sydney.edu.au", role = c("aut", "cre")),
    person(given = "Ellis", family = "Patrick", role = "aut"),
    person(given = "Sourish", family = "Iyengar", role = "aut"),
    person(given = "Harry", family = "Robertson", role = "aut"),
    person(given = "Andy", family = "Tran", role = "aut"),
    person(given = "John", family = "Ormerod", role = "aut"),
    person(given = "Graham", family = "Mann", role = "aut"),
    person(given = "Jean", family = "Yang", email = "jean.yang@sydney.edu.au", role = "aut")
    )
VignetteBuilder: knitr
Encoding: UTF-8
biocViews: Classification, Survival
Depends: R (>= 4.1.0), generics, methods, S4Vectors, MultiAssayExperiment, BiocParallel, survival
Imports: grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2 (>= 3.0.0), ggpubr, reshape2, ggupset, broom, dcanr
Suggests: limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot,
        BiocStyle, pamr, PoiClaClu, knitr, htmltools, gtable,
        scales, e1071, rmarkdown, IRanges, robustbase, glmnet, class, randomForestSRC,
        MatrixModels, xgboost, data.tree, ggnewscale
Description: The software formalises a framework for classification and survival model evaluation
             in R. There are four stages; Data transformation, feature selection, model training,
             and prediction. The requirements of variable types and variable order are
             fixed, but specialised variables for functions can also be provided.
             The framework is wrapped in a driver loop that reproducibly carries out a
             number of cross-validation schemes. Functions for differential mean, differential variability,
             and differential distribution are included. Additional functions
             may be developed by the user, by creating an interface to the framework.
License: GPL-3
Packaged: 2014-10-18 11:16:55 UTC; dario
RoxygenNote: 7.3.2
NeedsCompilation: yes
Collate:
    'ROCplot.R'
    'available.R'
    'classes.R'
    'calcPerformance.R'
    'constants.R'
    'crissCrossValidate.R'
    'crossValidate.R'
    'data.R'
    'distribution.R'
    'edgesToHubNetworks.R'
    'featureSetSummary.R'
    'getLocationsAndScales.R'
    'interactorDifferences.R'
    'interfaceClassify.R'
    'interfaceCoxPH.R'
    'interfaceCoxnet.R'
    'interfaceDLDA.R'
    'interfaceFisherDiscriminant.R'
    'interfaceGLM.R'
    'interfaceKNN.R'
    'interfaceKTSPclassifier.R'
    'interfaceMerge.R'
    'interfaceMixModels.R'
    'interfaceNSC.R'
    'interfaceNaiveBayesKernel.R'
    'interfacePCA.R'
    'interfacePenalisedGLM.R'
    'interfacePrevalidation.R'
    'interfaceRandomForest.R'
    'interfaceRandomForestSurvival.R'
    'interfaceSVM.R'
    'interfaceXGB.R'
    'performancePlot.R'
    'plotFeatureClasses.R'
    'precisionPathways.R'
    'prepareData.R'
    'previousSelection.R'
    'previousTrained.R'
    'randomSelection.R'
    'rankingBartlett.R'
    'rankingCoxPH.R'
    'rankingDMD.R'
    'rankingDifferentMeans.R'
    'rankingEdgeR.R'
    'rankingKolmogorovSmirnov.R'
    'rankingKullbackLeibler.R'
    'rankingLevene.R'
    'rankingLikelihoodRatio.R'
    'rankingLimma.R'
    'rankingPairsDifferences.R'
    'rankingPlot.R'
    'runTest.R'
    'runTests.R'
    'samplesMetricMap.R'
    'selectMulti.R'
    'selectionPlot.R'
    'simpleParams.R'
    'subtractFromLocation.R'
    'utilities.R'
URL: https://sydneybiox.github.io/ClassifyR/