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commit da723259afd7e7c90eb3d13a74438cf91a22f26f
Merge: d5b8b59 4bd0fc5
Author: Andreas Tille <tille at debian.org>
Date: Tue Nov 29 14:09:24 2016 +0100
Merge tag 'upstream/6.0-73+dfsg1'
Upstream version 6.0-73+dfsg1
.Rinstignore | 1 +
DESCRIPTION | 30 +-
MD5 | 397 +++---
NAMESPACE | 952 ++++++-------
R/BoxCoxTrans.R | 85 +-
R/aaa.R | 415 +++---
R/adaptive.R | 85 +-
R/additive.R | 1 +
R/aucRoc.R | 15 -
R/avNNet.R | 110 +-
R/bag.R | 189 ++-
R/bagEarth.R | 183 ++-
R/bagFDA.R | 137 +-
R/calibration.R | 216 ++-
R/caret-package.R | 373 +++++
R/caretTheme.R | 1 +
R/classDist.R | 85 +-
R/classLevels.R | 30 +-
R/common_code.R | 25 +
R/confusionMatrix.R | 729 +++++++---
R/createDataPartition.R | 240 +++-
R/createFolds.R | 73 -
R/createModel.R | 54 +-
R/createResample.R | 6 +-
R/createTimeSlices.R | 41 -
R/dotplot.varImp.train.R | 28 +
R/dummyVar.R | 333 +++--
R/expoTrans.R | 8 +-
R/extractPrediction.R | 4 +-
R/extractProb.R | 15 +-
R/featurePlot.R | 31 +
R/filterVarImp.R | 221 ++-
R/findCorrelation.R | 149 +-
R/findLinearCombos.R | 51 +
R/format.bagEarth.R | 40 +
R/gafs.R | 848 +++++++----
R/getTrainPerf.R | 1 +
R/ggplot.R | 227 ++-
R/heldout.R | 11 +-
R/icr.R | 66 +-
R/knn3.R | 151 ++
R/knn3Train.R | 58 -
R/knnreg.R | 94 +-
R/lattice.train.R | 78 +-
R/learning_curve.R | 138 ++
R/lift.R | 255 +++-
R/maxDissim.R | 93 ++
R/misc.R | 341 +++--
R/modelLookup.R | 125 +-
R/nearZeroVar.R | 159 ++-
R/negPredValue.R | 9 +-
R/panel.needle.R | 24 +
R/pcaNNet.R | 96 +-
R/plot.train.R | 75 +
R/plot.varImp.train.R | 64 +
R/plotClassProbs.R | 64 +
R/plotObsVsPred.R | 79 ++
R/plsda.R | 121 +-
R/posPredValue.R | 10 +-
R/postResample.R | 200 +++
R/preProcess.R | 1091 ++++++++++----
R/prec_rec.R | 239 ++++
R/predict.train.R | 165 ++-
R/predictionFunction.R | 5 +-
R/predictors.R | 35 +
R/print.confusionMatrix.R | 95 --
R/print.train.R | 273 +++-
R/print.varImp.train.R | 2 +
R/probFunction.R | 6 +-
R/reg_sims.R | 32 +-
R/resampleHist.R | 38 +-
R/resampleSummary.R | 27 +
R/resampleWrapper.R | 2 +
R/resamples.R | 600 +++++++-
R/rfe.R | 1489 +++++++++++++-------
R/roc.R | 21 -
R/rocPoint.R | 19 -
R/safs.R | 765 ++++++++--
R/sampling.R | 39 +-
R/selectByFilter.R | 1045 +++++++++-----
R/selection.R | 116 +-
R/sensitivity.R | 138 ++
R/sortImp.R | 3 +
R/spatialSign.R | 37 +-
R/specificity.R | 4 +
R/splsda.R | 7 +-
R/train.default.R | 413 +++++-
R/trainControl.R | 191 ++-
R/trim.R | 5 +-
R/twoClassSim.R | 173 ++-
R/updates.R | 48 +
R/varImp.R | 367 +++--
R/varImp.train.R | 9 +-
R/workflows.R | 794 ++++++-----
build/vignette.rds | Bin 224 -> 225 bytes
data/Sacramento.RData | Bin 0 -> 23504 bytes
data/datalist | 2 +
data/scat.RData | Bin 0 -> 5091 bytes
inst/NEWS.Rd | 184 ++-
inst/doc/caret.R | 2 +-
inst/doc/caret.Rnw | 6 +-
inst/models/models.RData | Bin 1532539 -> 2324347 bytes
inst/models/sampling.RData | Bin 0 -> 1030 bytes
man/BloodBrain.Rd | 38 +-
man/BoxCoxTrans.Rd | 121 +-
man/GermanCredit.Rd | 32 +-
man/Sacramento.Rd | 37 +
...usionMatrix.Rd => as.matrix.confusionMatrix.Rd} | 44 +-
man/avNNet.Rd | 126 +-
man/bag.Rd | 154 +-
man/bagEarth.Rd | 106 +-
man/bagFDA.Rd | 105 +-
man/calibration.Rd | 127 +-
man/caret-internal.Rd | 86 +-
man/{rfeFunctions.Rd => caretFuncs.Rd} | 119 +-
man/caretSBF.Rd | 60 +
man/cars.Rd | 29 +-
man/classDist.Rd | 96 +-
man/confusionMatrix.Rd | 180 ++-
man/confusionMatrix.train.Rd | 71 +-
man/cox2.Rd | 51 +-
man/createDataPartition.Rd | 143 +-
man/densityplot.rfe.Rd | 88 ++
man/dhfr.Rd | 36 +-
man/diff.resamples.Rd | 118 +-
man/{dotplot.varImp.train.Rd => dotPlot.Rd} | 29 +-
man/dotplot.diff.resamples.Rd | 74 +
man/downSample.Rd | 57 +-
man/dummyVars.Rd | 190 ++-
man/extractPrediction.Rd | 99 --
man/featurePlot.Rd | 54 +-
man/filterVarImp.Rd | 81 +-
man/findCorrelation.Rd | 100 +-
man/findLinearCombos.Rd | 45 +-
man/format.bagEarth.Rd | 34 +-
man/ga_functions.Rd | 111 --
man/gafs.default.Rd | 180 ++-
man/gafs_initial.Rd | 129 ++
man/getSamplingInfo.Rd | 25 +
man/histogram.train.Rd | 89 ++
man/icr.Rd | 99 --
man/icr.formula.Rd | 82 ++
man/index2vec.Rd | 34 +-
man/knn3.Rd | 130 +-
man/knnreg.Rd | 108 +-
man/lattice.Rd | 70 -
man/lattice.diff.resamples.Rd | 64 -
man/lattice.resamples.Rd | 95 --
man/lattice.rfe.Rd | 73 -
man/learing_curve_dat.Rd | 81 ++
man/lift.Rd | 177 ++-
man/maxDissim.Rd | 78 +-
man/mdrr.Rd | 63 +-
man/modelLookup.Rd | 98 +-
man/models.Rd | 505 ++++++-
man/nearZeroVar.Rd | 110 +-
man/nullModel.Rd | 79 +-
man/oil.Rd | 40 +-
man/oneSE.Rd | 140 ++
man/panel.lift.Rd | 64 -
man/panel.lift2.Rd | 69 +
man/panel.needle.Rd | 65 +-
man/pcaNNet.Rd | 154 +-
man/plot.gafs.Rd | 72 +-
man/plot.rfe.Rd | 79 +-
man/plot.train.Rd | 136 +-
man/plot.varImp.train.Rd | 52 +-
man/plotClassProbs.Rd | 56 +-
man/plotObsVsPred.Rd | 53 +-
man/plsda.Rd | 105 +-
man/postResample.Rd | 147 +-
man/pottery.Rd | 26 +-
man/prcomp.resamples.Rd | 118 +-
man/preProcess.Rd | 247 +++-
man/predict.bagEarth.Rd | 52 +-
man/predict.gafs.Rd | 47 +-
man/predict.knn3.Rd | 47 +-
man/predict.knnreg.Rd | 35 +-
man/predict.train.Rd | 131 ++
man/predictors.Rd | 65 +-
man/print.confusionMatrix.Rd | 38 +-
man/print.train.Rd | 64 +-
man/recall.Rd | 138 ++
man/resampleHist.Rd | 42 +-
man/resampleSummary.Rd | 50 +-
man/resamples.Rd | 121 +-
man/rf_seq.Rd | 43 -
man/rfe.Rd | 162 ++-
man/rfeControl.Rd | 237 ++--
man/sa_functions.Rd | 117 --
man/safs.Rd | 147 ++
man/safs.default.Rd | 97 --
man/safsControl.Rd | 246 ++--
man/safs_initial.Rd | 157 +++
man/sbf.Rd | 128 +-
man/sbfControl.Rd | 194 +--
man/sbfFunctions.Rd | 50 -
man/scat.Rd | 25 +
man/segmentationData.Rd | 54 +-
man/selection.Rd | 88 --
man/sensitivity.Rd | 179 ++-
man/spatialSign.Rd | 39 +-
man/summary.bagEarth.Rd | 41 +-
man/tecator.Rd | 67 +-
man/train.Rd | 226 +--
man/trainControl.Rd | 257 +++-
man/twoClassSim.Rd | 262 ++--
man/update.safs.Rd | 60 +-
man/update.train.Rd | 59 +-
man/varImp.Rd | 387 ++---
man/varImp.gafs.Rd | 56 +-
man/var_seq.Rd | 41 +
man/xyplot.resamples.Rd | 139 ++
tests/testthat/preProcess_methods.R | 323 +++++
tests/testthat/test_BoxCox.R | 31 +
tests/testthat/test_Dummies.R | 117 ++
tests/testthat/test_bad_class_options.R | 46 +
tests/testthat/test_confusionMatrix.R | 2 +-
tests/testthat/test_glmnet_varImp.R | 24 +
tests/testthat/test_mnLogLoss.R | 29 +-
tests/testthat/test_models_bagEarth.R | 1 +
tests/testthat/test_nearZeroVar.R | 23 +
tests/testthat/test_sampling_options.R | 86 ++
tests/testthat/test_twoClassSummary.R | 35 +
vignettes/algorithm.tex | 22 +
vignettes/caret.Rnw | 6 +-
226 files changed, 20334 insertions(+), 8859 deletions(-)
--
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