[r-cran-caret] branch master updated (d5b8b59 -> f5adb8b)
Andreas Tille
tille at debian.org
Tue Nov 29 13:35:55 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository r-cran-caret.
from d5b8b59 Update changelog
adds 4bd0fc5 New upstream version 6.0-73+dfsg1
new da72325 Merge tag 'upstream/6.0-73+dfsg1'
new d935c6a New upstream version
new 5df5e7c cme fix dpkg-control
new b0eafa9 Remove redundant Build-Depends: r-base-core
new 581de6d Enhance description
new 48200ed Convert to dh-r
new 45dfc87 Canonical homepage for CRAN, Enhance metadata in d/copyright
new e5e895b debhelper 10
new d58c150 d/watch: version=4
new e5530a3 Add autopkgtest
new f5adb8b TODO: New Build-Depends: r-cran-modelmetrics
The 11 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.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
debian/README.test | 9 +
debian/changelog | 17 +
debian/compat | 2 +-
debian/control | 38 +-
debian/copyright | 15 +-
debian/docs | 3 +
debian/rules | 5 +-
debian/tests/control | 3 +
debian/tests/run-unit-test | 13 +
debian/watch | 2 +-
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 +-
236 files changed, 20415 insertions(+), 8885 deletions(-)
delete mode 100644 R/aucRoc.R
create mode 100644 R/caret-package.R
delete mode 100644 R/createFolds.R
delete mode 100644 R/createTimeSlices.R
delete mode 100644 R/knn3Train.R
create mode 100644 R/learning_curve.R
create mode 100644 R/prec_rec.R
delete mode 100644 R/print.confusionMatrix.R
delete mode 100644 R/roc.R
delete mode 100644 R/rocPoint.R
create mode 100644 data/Sacramento.RData
create mode 100644 data/scat.RData
create mode 100644 debian/README.test
create mode 100644 debian/docs
create mode 100644 debian/tests/control
create mode 100644 debian/tests/run-unit-test
create mode 100644 inst/models/sampling.RData
create mode 100644 man/Sacramento.Rd
rename man/{as.table.confusionMatrix.Rd => as.matrix.confusionMatrix.Rd} (67%)
rename man/{rfeFunctions.Rd => caretFuncs.Rd} (56%)
create mode 100644 man/caretSBF.Rd
create mode 100644 man/densityplot.rfe.Rd
rename man/{dotplot.varImp.train.Rd => dotPlot.Rd} (54%)
create mode 100644 man/dotplot.diff.resamples.Rd
delete mode 100644 man/extractPrediction.Rd
delete mode 100644 man/ga_functions.Rd
create mode 100644 man/gafs_initial.Rd
create mode 100644 man/getSamplingInfo.Rd
create mode 100644 man/histogram.train.Rd
delete mode 100644 man/icr.Rd
create mode 100644 man/icr.formula.Rd
delete mode 100644 man/lattice.Rd
delete mode 100644 man/lattice.diff.resamples.Rd
delete mode 100644 man/lattice.resamples.Rd
delete mode 100644 man/lattice.rfe.Rd
create mode 100644 man/learing_curve_dat.Rd
create mode 100644 man/oneSE.Rd
delete mode 100644 man/panel.lift.Rd
create mode 100644 man/panel.lift2.Rd
create mode 100644 man/predict.train.Rd
create mode 100644 man/recall.Rd
delete mode 100644 man/rf_seq.Rd
delete mode 100644 man/sa_functions.Rd
create mode 100644 man/safs.Rd
delete mode 100644 man/safs.default.Rd
create mode 100644 man/safs_initial.Rd
delete mode 100644 man/sbfFunctions.Rd
create mode 100644 man/scat.Rd
delete mode 100644 man/selection.Rd
create mode 100644 man/var_seq.Rd
create mode 100644 man/xyplot.resamples.Rd
create mode 100644 tests/testthat/preProcess_methods.R
create mode 100644 tests/testthat/test_BoxCox.R
create mode 100644 tests/testthat/test_Dummies.R
create mode 100644 tests/testthat/test_bad_class_options.R
create mode 100644 tests/testthat/test_glmnet_varImp.R
create mode 100644 tests/testthat/test_nearZeroVar.R
create mode 100644 tests/testthat/test_sampling_options.R
create mode 100644 tests/testthat/test_twoClassSummary.R
create mode 100644 vignettes/algorithm.tex
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