nlcv: Nested Loop Cross Validation

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Nested loop cross validation for classification purposes

Author
Willem Talloen, Tobias Verbeke
Date of publication
2012-03-23 22:31:47
Maintainer
Tobias Verbeke <tobias.verbeke@openanalytics.eu>
License
GPL-3
Version
0.2-2

View on R-Forge

Man pages

classify
Wrapper to run all classifiers for one run
confusionMatrix
compute a confusion matrix for the optimal number of features...
inTrainingSample
Function to define a learning sample based on balanced...
limmaTwoGroups
Wrapper around limma for the comparison of two groups
mcrPlot
Misclassification Rate Plot
nlcv
Nested Loop Cross-Validation
nlcvData
Simulated Datasets to Demonstrate nlcv Functionality
nldaI
new MLInterfaces schema for lda from MASS
pamrI
Instance of a learnerSchema for pamr models
pamrML
Wrapper function around the pamr.* functions
pamrTrain
Function providing a formula interface to pamr.train
rankDistributionPlot
Plot the Distribution of Ranks of Features Across nlcv Runs
rocPlot
Produce a ROC plot for a classification model belonging to a...
scoresPlot
Function to Plot a Scores Plot
topTable-methods
Methods for topTable
xtable.confusionMatrix
xtable method for confusionMatrix objects
xtable.summary.mcrPlot
xtable method for summary.mcrPlot objects

Files in this package

nlcv
nlcv/data
nlcv/data/datalist
nlcv/data/nlcvRF_WS.rda
nlcv/data/nlcvRF_WHS.rda
nlcv/data/nlcvTT_WHS.rda
nlcv/data/nlcvTT_SHS.rda
nlcv/data/nlcvTT_SS.rda
nlcv/data/nlcvRF_R.rda
nlcv/data/nlcvTT_R.rda
nlcv/data/nlcvRF_SS.rda
nlcv/data/nlcvRF_SHS.rda
nlcv/data/nlcvTT_WS.rda
nlcv/R
nlcv/R/compareOrig.R
nlcv/R/topTable.R
nlcv/R/confusionMatrix.R
nlcv/R/nldaI.R
nlcv/R/pamrI.R
nlcv/R/classify.R
nlcv/R/zzz.R
nlcv/R/mcrPlot.R
nlcv/R/classify_bioc_2.2.R
nlcv/R/rankDistributionPlot.R
nlcv/R/xtable.confusionMatrix.R
nlcv/R/xtable.summary.mcrPlot.R
nlcv/R/limma.R
nlcv/R/inTrainingSample.R
nlcv/R/scoresPlot.R
nlcv/R/rocPlot.R
nlcv/R/nlcv.R
nlcv/R/classify_bioc_2.3.R
nlcv/NAMESPACE
nlcv/tests
nlcv/tests/test.scoresPlot.R
nlcv/tests/test.MLInterfaces.R
nlcv/tests/test.mcrPlot.R
nlcv/inst
nlcv/inst/unitTests
nlcv/inst/unitTests/runTests.R
nlcv/inst/unitTests/runit.nlcv.R
nlcv/inst/unitTests/Makefile
nlcv/inst/generateData.R
nlcv/inst/TODO
nlcv/inst/doc
nlcv/inst/doc/vignetteNLCV.bib
nlcv/inst/doc/nlcv.pdf
nlcv/inst/doc/graphs
nlcv/inst/doc/graphs/plotGeneSS.pdf
nlcv/inst/doc/graphs/ScoresPlot_nlcv_SHS3.pdf
nlcv/inst/doc/graphs/mcrPlot_nlcv_SS.pdf
nlcv/inst/doc/graphs/mcrPlot_nlcv_R.pdf
nlcv/inst/doc/graphs/ScoresPlot_nlcv_WHS2.pdf
nlcv/inst/doc/graphs/ScoresPlot_nlcv_WHS.pdf
nlcv/inst/doc/graphs/mcrPlot_nlcv_SHS.pdf
nlcv/inst/doc/graphs/ScoresPlot_nlcv_R.pdf
nlcv/inst/doc/graphs/mcrPlot_nlcv_SHS_3C_5R.pdf
nlcv/inst/doc/graphs/mcrPlot_nlcv_WS.pdf
nlcv/inst/doc/graphs/ScoresPlot_nlcv_SHS.pdf
nlcv/inst/doc/graphs/plotGeneWS.pdf
nlcv/inst/doc/graphs/plotGeneSHS.pdf
nlcv/inst/doc/graphs/ScoresPlot_nlcv_WHS3.pdf
nlcv/inst/doc/graphs/ScoresPlot_nlcv_SHS_3C_5R.pdf
nlcv/inst/doc/graphs/ScoresPlot_nlcv_WHS0.pdf
nlcv/inst/doc/graphs/ScoresPlot_nlcv_SHS_5C_5R.pdf
nlcv/inst/doc/graphs/ScoresPlot_nlcv_SS.pdf
nlcv/inst/doc/graphs/ScoresPlot_nlcv_WS.pdf
nlcv/inst/doc/graphs/Ranking_NL.pdf
nlcv/inst/doc/graphs/mcrPlot_nlcv_SHS_5C_5R.pdf
nlcv/inst/doc/graphs/NestedLoop.pdf
nlcv/inst/doc/graphs/mcrPlot_nlcv_WHS.pdf
nlcv/inst/doc/graphs/plotGeneWHS.pdf
nlcv/inst/doc/graphs/ScoresPlot_nlcv_SHS2.pdf
nlcv/inst/doc/nlcv.Rnw
nlcv/inst/NEWS
nlcv/DESCRIPTION
nlcv/man
nlcv/man/confusionMatrix.Rd
nlcv/man/pamrI.Rd
nlcv/man/xtable.summary.mcrPlot.Rd
nlcv/man/mcrPlot.Rd
nlcv/man/topTable-methods.Rd
nlcv/man/classify.Rd
nlcv/man/rocPlot.Rd
nlcv/man/scoresPlot.Rd
nlcv/man/xtable.confusionMatrix.Rd
nlcv/man/nldaI.Rd
nlcv/man/nlcvData.Rd
nlcv/man/pamrTrain.Rd
nlcv/man/nlcv.Rd
nlcv/man/pamrML.Rd
nlcv/man/rankDistributionPlot.Rd
nlcv/man/inTrainingSample.Rd
nlcv/man/limmaTwoGroups.Rd