ClassifyR

Package: ClassifyR
Type: Package
Title: A framework for two-class classification problems, with
applications to differential variability and differential
distribution testing
Version: 1.6.2
Date: 2016-03-08
Author: Dario Strbenac, John Ormerod, Graham Mann, Jean Yang
Maintainer: Dario Strbenac <dario.strbenac@sydney.edu.au>
VignetteBuilder: knitr
biocViews: Classification, Survival
Depends: R (>= 3.0.3), methods, Biobase, BiocParallel
Imports: locfit, ROCR, grid
Suggests: limma, edgeR, car, Rmixmod, ggplot2 (>= 2.0.0), gridExtra (>=
2.0.0), BiocStyle, pamr, sparsediscrim, PoiClaClu,
curatedOvarianData, parathyroidSE, knitr, klaR, gtable, scales,
e1071, rmarkdown, IRanges
Description: The software formalises a framework for classification in R.
There are four stages; Data transformation, feature selection, classifier training,
and prediction. The requirements of variable types and names are
fixed, but specialised variables for functions can also be provided.
The classification framework is wrapped in a driver loop, that
reproducibly carries out a number of cross-validation schemes.
Functions for differential expression, differential variability,
and differential distribution are included. Additional functions
may be developed by the user, by creating an interface to the framework.
Collate: bartlettSelection.R classes.R utilities.R calcPerformance.R
classifyInterface.R DMDselection.R edgeRselection.R errorMap.R
fisherDiscriminant.R distribution.R getLocationsAndScales.R
KolmogorovSmirnovSelection.R KullbackLeiblerSelection.R
leveneSelection.R likelihoodRatioSelection.R limmaSelection.R
mixmodels.R naiveBayesKernel.R
nearestShrunkenCentroidSelectionInterface.R
nearestShrunkenCentroidTrainInterface.R
nearestShrunkenCentroidPredictInterface.R performancePlot.R
plotFeatureClasses.R previousSelection.R rankingPlot.R
ROCplot.R runTest.R runTests.R selectionPlot.R
subtractFromLocation.R
License: GPL-3
Packaged: 2016-05-16 04:45:32 UTC; biocbuild
NeedsCompilation: no

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ClassifyR' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'performance' in package 'ClassifyR'
** help
*** installing help indices
  converting help for package 'ClassifyR'
    finding HTML links ... done
    ClassifyResult-class                    html  
    DMDselection                            html  
    finding level-2 HTML links ... done

    KolmogorovSmirnovSelection              html  
    KullbackLeiblerSelection                html  
    PredictParams-class                     html  
    ROCplot                                 html  
    ResubstituteParams-class                html  
    SelectParams-class                      html  
Rd warning: /tmp/RtmpfaCKXy/R.INSTALL7f8d1ec868c/ClassifyR/man/SelectParams-class.Rd:30: missing file link 'ExpressionSet'
    SelectResult-class                      html  
    TrainParams-class                       html  
    TransformParams-class                   html  
Rd warning: /tmp/RtmpfaCKXy/R.INSTALL7f8d1ec868c/ClassifyR/man/TransformParams-class.Rd:22: missing file link 'ExpressionSet'
    bartlettSelection                       html  
    calcPerformance                         html  
    classifyInterface                       html  
    distribution                            html  
Rd warning: /tmp/RtmpfaCKXy/R.INSTALL7f8d1ec868c/ClassifyR/man/distribution.Rd:32: missing file link 'stat_density'
    edgeRselection                          html  
Rd warning: /tmp/RtmpfaCKXy/R.INSTALL7f8d1ec868c/ClassifyR/man/edgeRselection.Rd:27: missing file link 'glmFit'
Rd warning: /tmp/RtmpfaCKXy/R.INSTALL7f8d1ec868c/ClassifyR/man/edgeRselection.Rd:40: missing file link 'edgeR'
    errorMap                                html  
    fisherDiscriminant                      html  
    functionOrList-class                    html  
    getLocationsAndScales                   html  
    leveneSelection                         html  
    likelihoodRatioSelection                html  
    limmaSelection                          html  
    mixmodels                               html  
    naiveBayesKernel                        html  
    nearestShrunkenCentroidPredictInterface
                                            html  
    nearestShrunkenCentroidSelectionInterface
                                            html  
    nearestShrunkenCentroidTrainInterface   html  
    pamrtrained-class                       html  
    performancePlot                         html  
    plotFeatureClasses                      html  
    previousSelection                       html  
    rankingPlot                             html  
    runTest                                 html  
    runTests                                html  
    selectionPlot                           html  
    subtractFromLocation                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ClassifyR)
Making 'packages.html' ... done