nlcv: Nested Loop Cross Validation
Version 0.2-2

Nested loop cross validation for classification purposes

Browse man pages Browse package API and functions Browse package files

AuthorWillem Talloen, Tobias Verbeke
Date of publication2012-03-23 22:31:47
MaintainerTobias Verbeke <tobias.verbeke@openanalytics.eu>
LicenseGPL-3
Version0.2-2
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("nlcv", repos="http://R-Forge.R-project.org")

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

Functions

MLIConverter.nlda Source code
classify Man page Source code
classify_bioc_2.2 Source code
classify_bioc_2.3 Source code
compareOrig Source code
confusionMatrix.nlcv Man page Source code
inTrainingSample Man page Source code
limmaTwoGroups Man page Source code
mcrPlot Man page Source code
nlcv Man page Source code
nlcvRF_R Man page
nlcvRF_SHS Man page
nlcvRF_SS Man page
nlcvRF_WHS Man page
nlcvRF_WS Man page
nlcvTT_R Man page
nlcvTT_SHS Man page
nlcvTT_SS Man page
nlcvTT_WHS Man page
nlcvTT_WS Man page
nldaI Man page
onAttach Source code
pamrI Man page
pamrIconverter Source code
pamrML Man page Source code
pamrTrain Man page Source code
predict.pamrML Man page Source code
print.nlcvConfusionMatrix Man page Source code
print.pamrML Man page Source code
print.summary.mcrPlot Man page Source code
rankDistributionPlot Man page Source code
rocPlot Man page Source code
scoresPlot Man page Source code
summary.mcrPlot Man page Source code
topTable Man page
topTable,nlcv-method Man page
topTable-methods Man page
xtable.confusionMatrix Man page Source code
xtable.summary.mcrPlot Man page Source code

Files

data
data/datalist
data/nlcvRF_WS.rda
data/nlcvRF_WHS.rda
data/nlcvTT_WHS.rda
data/nlcvTT_SHS.rda
data/nlcvTT_SS.rda
data/nlcvRF_R.rda
data/nlcvTT_R.rda
data/nlcvRF_SS.rda
data/nlcvRF_SHS.rda
data/nlcvTT_WS.rda
R
R/compareOrig.R
R/topTable.R
R/confusionMatrix.R
R/nldaI.R
R/pamrI.R
R/classify.R
R/zzz.R
R/mcrPlot.R
R/classify_bioc_2.2.R
R/rankDistributionPlot.R
R/xtable.confusionMatrix.R
R/xtable.summary.mcrPlot.R
R/limma.R
R/inTrainingSample.R
R/scoresPlot.R
R/rocPlot.R
R/nlcv.R
R/classify_bioc_2.3.R
NAMESPACE
tests
tests/test.scoresPlot.R
tests/test.MLInterfaces.R
tests/test.mcrPlot.R
inst
inst/unitTests
inst/unitTests/runTests.R
inst/unitTests/runit.nlcv.R
inst/unitTests/Makefile
inst/generateData.R
inst/TODO
inst/doc
inst/doc/vignetteNLCV.bib
inst/doc/nlcv.pdf
inst/doc/graphs
inst/doc/graphs/plotGeneSS.pdf
inst/doc/graphs/ScoresPlot_nlcv_SHS3.pdf
inst/doc/graphs/mcrPlot_nlcv_SS.pdf
inst/doc/graphs/mcrPlot_nlcv_R.pdf
inst/doc/graphs/ScoresPlot_nlcv_WHS2.pdf
inst/doc/graphs/ScoresPlot_nlcv_WHS.pdf
inst/doc/graphs/mcrPlot_nlcv_SHS.pdf
inst/doc/graphs/ScoresPlot_nlcv_R.pdf
inst/doc/graphs/mcrPlot_nlcv_SHS_3C_5R.pdf
inst/doc/graphs/mcrPlot_nlcv_WS.pdf
inst/doc/graphs/ScoresPlot_nlcv_SHS.pdf
inst/doc/graphs/plotGeneWS.pdf
inst/doc/graphs/plotGeneSHS.pdf
inst/doc/graphs/ScoresPlot_nlcv_WHS3.pdf
inst/doc/graphs/ScoresPlot_nlcv_SHS_3C_5R.pdf
inst/doc/graphs/ScoresPlot_nlcv_WHS0.pdf
inst/doc/graphs/ScoresPlot_nlcv_SHS_5C_5R.pdf
inst/doc/graphs/ScoresPlot_nlcv_SS.pdf
inst/doc/graphs/ScoresPlot_nlcv_WS.pdf
inst/doc/graphs/Ranking_NL.pdf
inst/doc/graphs/mcrPlot_nlcv_SHS_5C_5R.pdf
inst/doc/graphs/NestedLoop.pdf
inst/doc/graphs/mcrPlot_nlcv_WHS.pdf
inst/doc/graphs/plotGeneWHS.pdf
inst/doc/graphs/ScoresPlot_nlcv_SHS2.pdf
inst/doc/nlcv.Rnw
inst/NEWS
DESCRIPTION
man
man/confusionMatrix.Rd
man/pamrI.Rd
man/xtable.summary.mcrPlot.Rd
man/mcrPlot.Rd
man/topTable-methods.Rd
man/classify.Rd
man/rocPlot.Rd
man/scoresPlot.Rd
man/xtable.confusionMatrix.Rd
man/nldaI.Rd
man/nlcvData.Rd
man/pamrTrain.Rd
man/nlcv.Rd
man/pamrML.Rd
man/rankDistributionPlot.Rd
man/inTrainingSample.Rd
man/limmaTwoGroups.Rd
nlcv documentation built on May 21, 2017, 12:53 a.m.