Title: Zero-Inflated Poisson Hidden (Semi-)Markov Models
Description: Fit zero-inflated Poisson hidden (semi-)Markov models with or without covariates by directly minimizing the negative log likelihood function using the gradient descent algorithm. Multiple starting values should be used to avoid local minima.
Author: Zekun (Jack) Xu, Ye Liu
Maintainer: Zekun (Jack) Xu <zekunxu@gmail.com>
Diff between ziphsmm versions 2.0.1 dated 2018-01-05 and 2.0.2 dated 2018-03-10
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/dist_learn.R | 11 ++++++----- R/dist_learn2.R | 11 ++++++----- R/package.R | 6 ++---- man/dist_learn.Rd | 2 +- man/dist_learn2.Rd | 4 ++-- man/package-ziphsmm.Rd | 8 ++------ 8 files changed, 31 insertions(+), 35 deletions(-)
Title: Widen, Process, then Re-Tidy Data
Description: Encapsulates the pattern of untidying data into a wide matrix,
performing some processing, then turning it back into a tidy form. This
is useful for several operations such as co-occurrence counts,
correlations, or clustering that are mathematically convenient on wide matrices.
Author: David Robinson [aut, cre],
Kanishka Misra [ctb]
Maintainer: David Robinson <admiral.david@gmail.com>
Diff between widyr versions 0.1.0 dated 2017-08-14 and 0.1.1 dated 2018-03-10
DESCRIPTION | 18 ++-- MD5 | 27 ++++--- NAMESPACE | 6 + NEWS.md | 7 + R/pairwise_count.R | 2 R/pairwise_delta.R |only R/pairwise_pmi.R |only R/widely.R | 2 R/widely_svd.R |only README.md | 9 ++ build/vignette.rds |binary inst/doc/intro.html | 140 +++++++++++++++++++------------------ inst/doc/united_nations.html | 106 ++++++++++++++-------------- man/pairwise_count.Rd | 2 man/pairwise_delta.Rd |only man/pairwise_pmi.Rd |only man/widely_svd.Rd |only tests/testthat/test-pairwise-pmi.R |only 18 files changed, 179 insertions(+), 140 deletions(-)
Title: Penalized Elastic Net S/MM-Estimator of Regression
Description: Robust penalized elastic net S and MM estimator for linear
regression. The method is described in detail in
Cohen Freue, G. V., Kepplinger, D., Salibian-Barrera, M., and Smucler, E.
(2017) <https://gcohenfr.github.io/pdfs/PENSE_manuscript.pdf>.
Author: David Kepplinger [aut, cre],
Matias Salibian-Barrera [aut],
Gabriela Cohen Freue [aut],
Derek Cho [ctb]
Maintainer: David Kepplinger <david.kepplinger@gmail.com>
Diff between pense versions 1.0.8 dated 2017-11-03 and 1.2.0 dated 2018-03-10
pense-1.0.8/pense/TODO |only pense-1.2.0/pense/DESCRIPTION | 16 +- pense-1.2.0/pense/MD5 | 46 ++++---- pense-1.2.0/pense/NAMESPACE | 3 pense-1.2.0/pense/NEWS.md | 6 + pense-1.2.0/pense/R/additional-options.R | 5 pense-1.2.0/pense/R/build_lambda_grid.R | 151 ++++++++++++++++++++++++-- pense-1.2.0/pense/R/coef-methods.R | 20 +-- pense-1.2.0/pense/R/elnet.R | 45 +++---- pense-1.2.0/pense/R/pense.R | 25 ++-- pense-1.2.0/pense/R/pense_coldwarm.R | 2 pense-1.2.0/pense/R/pensem.R | 155 +++++++-------------------- pense-1.2.0/pense/R/utilities.R | 19 +++ pense-1.2.0/pense/configure | 18 +-- pense-1.2.0/pense/configure.ac | 2 pense-1.2.0/pense/src/BLAS.h | 9 + pense-1.2.0/pense/src/ENDal.cpp | 11 + pense-1.2.0/pense/src/ENLars.cpp | 2 pense-1.2.0/pense/src/MStep.cpp | 21 +-- pense-1.2.0/pense/src/PENSEreg.cpp | 39 ++++-- pense-1.2.0/pense/src/PSCxx.cpp | 14 -- pense-1.2.0/pense/src/Rinterface.cpp | 129 ++++++++++++++++------ pense-1.2.0/pense/src/Rinterface.hpp | 10 + pense-1.2.0/pense/src/autoconfig.win.h | 4 pense-1.2.0/pense/tests/testthat/test.0mad.R |only 25 files changed, 464 insertions(+), 288 deletions(-)
Title: Machine Learning in R
Description: Interface to a large number of classification and regression
techniques, including machine-readable parameter descriptions. There is
also an experimental extension for survival analysis, clustering and
general, example-specific cost-sensitive learning. Generic resampling,
including cross-validation, bootstrapping and subsampling. Hyperparameter
tuning with modern optimization techniques, for single- and multi-objective
problems. Filter and wrapper methods for feature selection. Extension of
basic learners with additional operations common in machine learning, also
allowing for easy nested resampling. Most operations can be parallelized.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Lars Kotthoff [aut],
Julia Schiffner [aut],
Jakob Richter [aut],
Zachary Jones [aut],
Giuseppe Casalicchio [aut],
Mason Gallo [aut],
Jakob Bossek [ctb],
Erich Studerus [ctb],
Leonard Judt [ctb],
Tobias Kuehn [ctb],
Pascal Kerschke [ctb],
Florian Fendt [ctb],
Philipp Probst [ctb],
Xudong Sun [ctb],
Janek Thomas [ctb],
Bruno Vieira [ctb],
Laura Beggel [ctb],
Quay Au [ctb],
Martin Binder [ctb],
Florian Pfisterer [ctb],
Stefan Coors [ctb],
Patrick Schratz [ctb],
Steve Bronder [ctb]
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between mlr versions 2.11 dated 2017-03-15 and 2.12 dated 2018-03-10
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mlr-2.12/mlr/man/getBMRLearnerShortNames.Rd | 4 mlr-2.12/mlr/man/getBMRLearners.Rd | 4 mlr-2.12/mlr/man/getBMRMeasureIds.Rd | 4 mlr-2.12/mlr/man/getBMRMeasures.Rd | 4 mlr-2.12/mlr/man/getBMRModels.Rd | 16 mlr-2.12/mlr/man/getBMRPerformances.Rd | 18 mlr-2.12/mlr/man/getBMRPredictions.Rd | 22 mlr-2.12/mlr/man/getBMRTaskDescriptions.Rd | 6 mlr-2.12/mlr/man/getBMRTaskDescs.Rd | 6 mlr-2.12/mlr/man/getBMRTaskIds.Rd | 4 mlr-2.12/mlr/man/getBMRTuneResults.Rd | 18 mlr-2.12/mlr/man/getCaretParamSet.Rd | 20 mlr-2.12/mlr/man/getClassWeightParam.Rd | 13 mlr-2.12/mlr/man/getConfMatrix.Rd | 11 mlr-2.12/mlr/man/getDefaultMeasure.Rd | 24 mlr-2.12/mlr/man/getFailureModelDump.Rd | 6 mlr-2.12/mlr/man/getFailureModelMsg.Rd | 6 mlr-2.12/mlr/man/getFeatSelResult.Rd | 6 mlr-2.12/mlr/man/getFeatureImportance.Rd | 34 mlr-2.12/mlr/man/getFeatureImportanceLearner.Rd | 14 mlr-2.12/mlr/man/getFilterValues.Rd | 23 mlr-2.12/mlr/man/getFilteredFeatures.Rd | 10 mlr-2.12/mlr/man/getHyperPars.Rd | 16 mlr-2.12/mlr/man/getLearnerId.Rd | 11 mlr-2.12/mlr/man/getLearnerModel.Rd | 12 mlr-2.12/mlr/man/getLearnerPackages.Rd | 11 mlr-2.12/mlr/man/getLearnerParVals.Rd | 17 mlr-2.12/mlr/man/getLearnerParamSet.Rd | 13 mlr-2.12/mlr/man/getLearnerPredictType.Rd | 11 mlr-2.12/mlr/man/getLearnerShortName.Rd | 15 mlr-2.12/mlr/man/getLearnerType.Rd | 10 mlr-2.12/mlr/man/getMlrOptions.Rd | 2 mlr-2.12/mlr/man/getMultilabelBinaryPerformances.Rd | 6 mlr-2.12/mlr/man/getNestedTuneResultsOptPathDf.Rd | 8 mlr-2.12/mlr/man/getNestedTuneResultsX.Rd | 6 mlr-2.12/mlr/man/getOOBPreds.Rd | 20 mlr-2.12/mlr/man/getOOBPredsLearner.Rd | 8 mlr-2.12/mlr/man/getParamSet.Rd | 8 mlr-2.12/mlr/man/getPredictionDump.Rd | 6 mlr-2.12/mlr/man/getPredictionProbabilities.Rd | 10 mlr-2.12/mlr/man/getPredictionResponse.Rd | 18 mlr-2.12/mlr/man/getPredictionTaskDesc.Rd |only mlr-2.12/mlr/man/getRRDump.Rd | 8 mlr-2.12/mlr/man/getRRPredictionList.Rd | 14 mlr-2.12/mlr/man/getRRPredictions.Rd | 6 mlr-2.12/mlr/man/getRRTaskDesc.Rd | 6 mlr-2.12/mlr/man/getRRTaskDescription.Rd | 6 mlr-2.12/mlr/man/getStackedBaseLearnerPredictions.Rd | 4 mlr-2.12/mlr/man/getTaskClassLevels.Rd | 6 mlr-2.12/mlr/man/getTaskCosts.Rd | 10 mlr-2.12/mlr/man/getTaskData.Rd | 26 mlr-2.12/mlr/man/getTaskDesc.Rd | 6 mlr-2.12/mlr/man/getTaskDescription.Rd | 6 mlr-2.12/mlr/man/getTaskFeatureNames.Rd | 4 mlr-2.12/mlr/man/getTaskFormula.Rd | 10 mlr-2.12/mlr/man/getTaskId.Rd | 6 mlr-2.12/mlr/man/getTaskNFeats.Rd | 6 mlr-2.12/mlr/man/getTaskSize.Rd | 6 mlr-2.12/mlr/man/getTaskTargetNames.Rd | 6 mlr-2.12/mlr/man/getTaskTargets.Rd | 19 mlr-2.12/mlr/man/getTaskType.Rd | 6 mlr-2.12/mlr/man/getTuneResult.Rd | 6 mlr-2.12/mlr/man/getTuneResultOptPath.Rd |only mlr-2.12/mlr/man/gunpoint.task.Rd |only mlr-2.12/mlr/man/hasFunctionalFeatures.Rd |only mlr-2.12/mlr/man/helpLearner.Rd |only mlr-2.12/mlr/man/helpLearnerParam.Rd |only mlr-2.12/mlr/man/imputations.Rd | 52 mlr-2.12/mlr/man/impute.Rd | 48 mlr-2.12/mlr/man/iris.task.Rd | 2 mlr-2.12/mlr/man/isFailureModel.Rd | 6 mlr-2.12/mlr/man/joinClassLevels.Rd | 6 mlr-2.12/mlr/man/learnerArgsToControl.Rd | 4 mlr-2.12/mlr/man/learners.Rd | 2 mlr-2.12/mlr/man/listFilterMethods.Rd | 18 mlr-2.12/mlr/man/listLearnerProperties.Rd | 4 mlr-2.12/mlr/man/listLearners.Rd | 40 mlr-2.12/mlr/man/listMeasureProperties.Rd | 2 mlr-2.12/mlr/man/listMeasures.Rd | 20 mlr-2.12/mlr/man/listTaskTypes.Rd | 2 mlr-2.12/mlr/man/lung.task.Rd | 4 mlr-2.12/mlr/man/makeAggregation.Rd | 40 mlr-2.12/mlr/man/makeBaggingWrapper.Rd | 22 mlr-2.12/mlr/man/makeBaseWrapper.Rd |only mlr-2.12/mlr/man/makeChainModel.Rd |only mlr-2.12/mlr/man/makeClassificationViaRegressionWrapper.Rd |only mlr-2.12/mlr/man/makeConstantClassWrapper.Rd | 10 mlr-2.12/mlr/man/makeCostMeasure.Rd | 33 mlr-2.12/mlr/man/makeCostSensClassifWrapper.Rd | 10 mlr-2.12/mlr/man/makeCostSensRegrWrapper.Rd | 10 mlr-2.12/mlr/man/makeCostSensWeightedPairsWrapper.Rd | 10 mlr-2.12/mlr/man/makeCustomResampledMeasure.Rd | 62 mlr-2.12/mlr/man/makeDownsampleWrapper.Rd | 16 mlr-2.12/mlr/man/makeDummyFeaturesWrapper.Rd | 18 mlr-2.12/mlr/man/makeExtractFDAFeatMethod.Rd |only mlr-2.12/mlr/man/makeExtractFDAFeatsWrapper.Rd |only mlr-2.12/mlr/man/makeFeatSelWrapper.Rd | 28 mlr-2.12/mlr/man/makeFilter.Rd | 62 mlr-2.12/mlr/man/makeFilterWrapper.Rd | 30 mlr-2.12/mlr/man/makeFixedHoldoutInstance.Rd | 8 mlr-2.12/mlr/man/makeFunctionalData.Rd |only mlr-2.12/mlr/man/makeImputeMethod.Rd | 6 mlr-2.12/mlr/man/makeImputeWrapper.Rd | 26 mlr-2.12/mlr/man/makeLearner.Rd | 37 mlr-2.12/mlr/man/makeLearners.Rd | 18 mlr-2.12/mlr/man/makeMeasure.Rd | 77 mlr-2.12/mlr/man/makeModelMultiplexer.Rd | 10 mlr-2.12/mlr/man/makeModelMultiplexerParamSet.Rd | 10 mlr-2.12/mlr/man/makeMulticlassWrapper.Rd | 10 mlr-2.12/mlr/man/makeMultilabelBinaryRelevanceWrapper.Rd | 14 mlr-2.12/mlr/man/makeMultilabelClassifierChainsWrapper.Rd | 14 mlr-2.12/mlr/man/makeMultilabelDBRWrapper.Rd | 10 mlr-2.12/mlr/man/makeMultilabelNestedStackingWrapper.Rd | 18 mlr-2.12/mlr/man/makeMultilabelStackingWrapper.Rd | 14 mlr-2.12/mlr/man/makeOverBaggingWrapper.Rd | 18 mlr-2.12/mlr/man/makePreprocWrapper.Rd | 18 mlr-2.12/mlr/man/makePreprocWrapperCaret.Rd | 20 mlr-2.12/mlr/man/makeRLearner.classif.fdausc.glm.Rd |only mlr-2.12/mlr/man/makeRLearner.classif.fdausc.kernel.Rd |only mlr-2.12/mlr/man/makeRLearner.classif.fdausc.np.Rd |only mlr-2.12/mlr/man/makeRemoveConstantFeaturesWrapper.Rd | 18 mlr-2.12/mlr/man/makeResampleDesc.Rd | 73 mlr-2.12/mlr/man/makeResampleInstance.Rd | 28 mlr-2.12/mlr/man/makeSMOTEWrapper.Rd | 18 mlr-2.12/mlr/man/makeStackedLearner.Rd | 64 mlr-2.12/mlr/man/makeTaskDesc.Rd |only mlr-2.12/mlr/man/makeTaskDescInternal.Rd |only mlr-2.12/mlr/man/makeTuneControlCMAES.Rd | 40 mlr-2.12/mlr/man/makeTuneControlDesign.Rd | 28 mlr-2.12/mlr/man/makeTuneControlGenSA.Rd | 42 mlr-2.12/mlr/man/makeTuneControlGrid.Rd | 38 mlr-2.12/mlr/man/makeTuneControlIrace.Rd | 46 mlr-2.12/mlr/man/makeTuneControlMBO.Rd | 64 mlr-2.12/mlr/man/makeTuneControlRandom.Rd | 30 mlr-2.12/mlr/man/makeTuneWrapper.Rd | 30 mlr-2.12/mlr/man/makeUndersampleWrapper.Rd | 18 mlr-2.12/mlr/man/makeWeightedClassesWrapper.Rd | 12 mlr-2.12/mlr/man/makeWrappedModel.Rd | 22 mlr-2.12/mlr/man/measures.Rd | 55 mlr-2.12/mlr/man/mergeBenchmarkResults.Rd | 14 mlr-2.12/mlr/man/mergeSmallFactorLevels.Rd | 8 mlr-2.12/mlr/man/mlrFamilies.Rd | 24 mlr-2.12/mlr/man/mtcars.task.Rd | 2 mlr-2.12/mlr/man/normalizeFeatures.Rd | 28 mlr-2.12/mlr/man/oversample.Rd | 8 mlr-2.12/mlr/man/parallelization.Rd | 24 mlr-2.12/mlr/man/performance.Rd | 22 mlr-2.12/mlr/man/phoneme.task.Rd |only mlr-2.12/mlr/man/pid.task.Rd | 4 mlr-2.12/mlr/man/plotBMRBoxplots.Rd | 20 mlr-2.12/mlr/man/plotBMRRanksAsBarChart.Rd | 24 mlr-2.12/mlr/man/plotBMRSummary.Rd | 24 mlr-2.12/mlr/man/plotCalibration.Rd | 18 mlr-2.12/mlr/man/plotCritDifferences.Rd | 12 mlr-2.12/mlr/man/plotFilterValues.Rd | 15 mlr-2.12/mlr/man/plotHyperParsEffect.Rd | 32 mlr-2.12/mlr/man/plotLearnerPrediction.Rd | 40 mlr-2.12/mlr/man/plotLearningCurve.Rd | 19 mlr-2.12/mlr/man/plotPartialDependence.Rd | 31 mlr-2.12/mlr/man/plotROCCurves.Rd | 31 mlr-2.12/mlr/man/plotResiduals.Rd | 14 mlr-2.12/mlr/man/plotThreshVsPerf.Rd | 31 mlr-2.12/mlr/man/plotTuneMultiCritResult.Rd | 17 mlr-2.12/mlr/man/predict.WrappedModel.Rd | 24 mlr-2.12/mlr/man/predictLearner.Rd | 42 mlr-2.12/mlr/man/reduceBatchmarkResults.Rd | 22 mlr-2.12/mlr/man/reextractFDAFeatures.Rd |only mlr-2.12/mlr/man/regr.randomForest.Rd | 44 mlr-2.12/mlr/man/reimpute.Rd | 20 mlr-2.12/mlr/man/removeConstantFeatures.Rd | 16 mlr-2.12/mlr/man/removeHyperPars.Rd | 17 mlr-2.12/mlr/man/resample.Rd | 69 mlr-2.12/mlr/man/selectFeatures.Rd | 28 mlr-2.12/mlr/man/setAggregation.Rd | 20 mlr-2.12/mlr/man/setHyperPars.Rd | 17 mlr-2.12/mlr/man/setHyperPars2.Rd | 4 mlr-2.12/mlr/man/setId.Rd | 15 mlr-2.12/mlr/man/setLearnerId.Rd | 13 mlr-2.12/mlr/man/setMeasurePars.Rd |only mlr-2.12/mlr/man/setPredictThreshold.Rd | 19 mlr-2.12/mlr/man/setPredictType.Rd | 15 mlr-2.12/mlr/man/setThreshold.Rd | 8 mlr-2.12/mlr/man/simplifyMeasureNames.Rd | 4 mlr-2.12/mlr/man/smote.Rd | 14 mlr-2.12/mlr/man/sonar.task.Rd | 2 mlr-2.12/mlr/man/spam.task.Rd |only mlr-2.12/mlr/man/spatial.task.Rd |only mlr-2.12/mlr/man/subsetTask.Rd | 14 mlr-2.12/mlr/man/summarizeColumns.Rd | 28 mlr-2.12/mlr/man/summarizeLevels.Rd | 6 mlr-2.12/mlr/man/train.Rd | 24 mlr-2.12/mlr/man/trainLearner.Rd | 14 mlr-2.12/mlr/man/tuneParams.Rd | 40 mlr-2.12/mlr/man/tuneParamsMultiCrit.Rd | 35 mlr-2.12/mlr/man/tuneThreshold.Rd | 22 mlr-2.12/mlr/man/wpbc.task.Rd | 4 mlr-2.12/mlr/man/yeast.task.Rd | 2 mlr-2.12/mlr/tests/run-base.R | 2 mlr-2.12/mlr/tests/run-basenocran.R |only mlr-2.12/mlr/tests/run-classif1.R |only mlr-2.12/mlr/tests/run-classif2.R |only mlr-2.12/mlr/tests/run-lint.R |only mlr-2.12/mlr/tests/testthat/helper_helpers.R | 141 mlr-2.12/mlr/tests/testthat/helper_learners_all.R | 14 mlr-2.12/mlr/tests/testthat/helper_lint.R |only mlr-2.12/mlr/tests/testthat/helper_mock_learners.R | 55 mlr-2.12/mlr/tests/testthat/helper_objects.R | 81 mlr-2.12/mlr/tests/testthat/helper_zzz.R | 4 mlr-2.12/mlr/tests/testthat/test_base_BaggingWrapper.R | 9 mlr-2.12/mlr/tests/testthat/test_base_BaseWrapper.R | 49 mlr-2.12/mlr/tests/testthat/test_base_ClassificationViaRegressionWrapper.R |only mlr-2.12/mlr/tests/testthat/test_base_FailureModel.R | 4 mlr-2.12/mlr/tests/testthat/test_base_Learner_properties.R | 14 mlr-2.12/mlr/tests/testthat/test_base_MulticlassWrapper.R | 6 mlr-2.12/mlr/tests/testthat/test_base_PreprocWrapper.R | 51 mlr-2.12/mlr/tests/testthat/test_base_PreprocWrapperCaret.R | 37 mlr-2.12/mlr/tests/testthat/test_base_SupervisedTask.R | 25 mlr-2.12/mlr/tests/testthat/test_base_TaskDesc.R | 12 mlr-2.12/mlr/tests/testthat/test_base_TuneWrapper.R | 26 mlr-2.12/mlr/tests/testthat/test_base_UnsupervisedTask.R | 13 mlr-2.12/mlr/tests/testthat/test_base_aggregations.R | 14 mlr-2.12/mlr/tests/testthat/test_base_benchmark.R | 12 mlr-2.12/mlr/tests/testthat/test_base_blocking.R | 14 mlr-2.12/mlr/tests/testthat/test_base_calculateConfusionMatrix.R | 107 mlr-2.12/mlr/tests/testthat/test_base_calculateROCMeasures.R | 10 mlr-2.12/mlr/tests/testthat/test_base_capLargeValues.R | 6 mlr-2.12/mlr/tests/testthat/test_base_chains.R | 4 mlr-2.12/mlr/tests/testthat/test_base_checkData.R | 26 mlr-2.12/mlr/tests/testthat/test_base_checkTaskLearner.R | 4 mlr-2.12/mlr/tests/testthat/test_base_checkTaskSubset.R | 7 mlr-2.12/mlr/tests/testthat/test_base_clustering.R | 6 mlr-2.12/mlr/tests/testthat/test_base_convertBMRToRankMatrix.R | 8 mlr-2.12/mlr/tests/testthat/test_base_convertMLBenchObjToTask.R | 2 mlr-2.12/mlr/tests/testthat/test_base_costs.R | 2 mlr-2.12/mlr/tests/testthat/test_base_costsens.R | 2 mlr-2.12/mlr/tests/testthat/test_base_createDummyFeatures.R | 4 mlr-2.12/mlr/tests/testthat/test_base_downsample.R | 10 mlr-2.12/mlr/tests/testthat/test_base_fda.R |only mlr-2.12/mlr/tests/testthat/test_base_fda_extractFDAFeatures.R |only mlr-2.12/mlr/tests/testthat/test_base_fda_extractFDAFeaturesWrapper.R |only mlr-2.12/mlr/tests/testthat/test_base_generateCalibration.R | 2 mlr-2.12/mlr/tests/testthat/test_base_generateFeatureImportanceData.R | 2 mlr-2.12/mlr/tests/testthat/test_base_generateFilterValuesData.R | 29 mlr-2.12/mlr/tests/testthat/test_base_generateHyperParsEffect.R | 36 mlr-2.12/mlr/tests/testthat/test_base_generateLearningCurve.R | 3 mlr-2.12/mlr/tests/testthat/test_base_generatePartialDependence.R | 251 - mlr-2.12/mlr/tests/testthat/test_base_generateThreshVsPerf.R | 43 mlr-2.12/mlr/tests/testthat/test_base_getFeatureImportance.R | 18 mlr-2.12/mlr/tests/testthat/test_base_getHyperPars.R | 6 mlr-2.12/mlr/tests/testthat/test_base_getOOBPreds.R | 28 mlr-2.12/mlr/tests/testthat/test_base_getParamSet.R | 2 mlr-2.12/mlr/tests/testthat/test_base_getTaskData.R | 24 mlr-2.12/mlr/tests/testthat/test_base_getTaskFormula.R | 24 mlr-2.12/mlr/tests/testthat/test_base_helpLearner.R |only mlr-2.12/mlr/tests/testthat/test_base_helpers.R | 4 mlr-2.12/mlr/tests/testthat/test_base_hyperpars.R | 4 mlr-2.12/mlr/tests/testthat/test_base_imbal_overbagging.R | 4 mlr-2.12/mlr/tests/testthat/test_base_imbal_overundersample.R | 46 mlr-2.12/mlr/tests/testthat/test_base_imbal_smote.R | 32 mlr-2.12/mlr/tests/testthat/test_base_impute.R | 20 mlr-2.12/mlr/tests/testthat/test_base_learnerArgsToControl.R | 34 mlr-2.12/mlr/tests/testthat/test_base_listLearners.R | 9 mlr-2.12/mlr/tests/testthat/test_base_makeTask.R |only mlr-2.12/mlr/tests/testthat/test_base_measures.R | 324 + mlr-2.12/mlr/tests/testthat/test_base_multilabel.R | 12 mlr-2.12/mlr/tests/testthat/test_base_multilabelWrapperIds.R |only mlr-2.12/mlr/tests/testthat/test_base_normalizeFeatures.R | 8 mlr-2.12/mlr/tests/testthat/test_base_orderedfactors.R | 2 mlr-2.12/mlr/tests/testthat/test_base_performance.R | 2 mlr-2.12/mlr/tests/testthat/test_base_plotBMRBoxplots.R | 6 mlr-2.12/mlr/tests/testthat/test_base_plotBMRSummary.R | 8 mlr-2.12/mlr/tests/testthat/test_base_plotCritDifferences.R | 6 mlr-2.12/mlr/tests/testthat/test_base_plotLearnerPrediction.R | 4 mlr-2.12/mlr/tests/testthat/test_base_plotResiduals.R | 4 mlr-2.12/mlr/tests/testthat/test_base_predict.R | 23 mlr-2.12/mlr/tests/testthat/test_base_relativeOverfitting.R | 66 mlr-2.12/mlr/tests/testthat/test_base_removeConstantFeatures.R | 2 mlr-2.12/mlr/tests/testthat/test_base_resample.R | 43 mlr-2.12/mlr/tests/testthat/test_base_resample_b632.R | 16 mlr-2.12/mlr/tests/testthat/test_base_resample_b632plus.R | 4 mlr-2.12/mlr/tests/testthat/test_base_resample_bs.R | 2 mlr-2.12/mlr/tests/testthat/test_base_resample_cv.R | 4 mlr-2.12/mlr/tests/testthat/test_base_resample_fixedwindowcv.R |only mlr-2.12/mlr/tests/testthat/test_base_resample_growingwindowcv.R |only mlr-2.12/mlr/tests/testthat/test_base_resample_holdout.R | 4 mlr-2.12/mlr/tests/testthat/test_base_resample_loo.R | 8 mlr-2.12/mlr/tests/testthat/test_base_resample_makeResampleDesc.R | 6 mlr-2.12/mlr/tests/testthat/test_base_resample_operators.R | 22 mlr-2.12/mlr/tests/testthat/test_base_resample_repcv.R | 15 mlr-2.12/mlr/tests/testthat/test_base_resample_stratify.R | 32 mlr-2.12/mlr/tests/testthat/test_base_selectFeatures.R | 3 mlr-2.12/mlr/tests/testthat/test_base_spcv.R |only mlr-2.12/mlr/tests/testthat/test_base_summarizeColumns.R | 2 mlr-2.12/mlr/tests/testthat/test_base_summarizeLevels.R | 6 mlr-2.12/mlr/tests/testthat/test_base_tuning.R | 33 mlr-2.12/mlr/tests/testthat/test_base_weights.R | 22 mlr-2.12/mlr/tests/testthat/test_basenocran_batchmark.R |only mlr-2.12/mlr/tests/testthat/test_classif_C50.R | 2 mlr-2.12/mlr/tests/testthat/test_classif_IBk.R | 8 mlr-2.12/mlr/tests/testthat/test_classif_J48.R | 26 mlr-2.12/mlr/tests/testthat/test_classif_JRip.R | 26 mlr-2.12/mlr/tests/testthat/test_classif_LibLineaRMultiClassSVC.R | 2 mlr-2.12/mlr/tests/testthat/test_classif_LiblineaRL1L2SVC.R | 2 mlr-2.12/mlr/tests/testthat/test_classif_LiblineaRL1LogReg.R | 4 mlr-2.12/mlr/tests/testthat/test_classif_LiblineaRL2L1SVC.R | 2 mlr-2.12/mlr/tests/testthat/test_classif_LiblineaRL2LogReg.R | 4 mlr-2.12/mlr/tests/testthat/test_classif_LiblineaRL2SVC.R | 6 mlr-2.12/mlr/tests/testthat/test_classif_OneR.R | 20 mlr-2.12/mlr/tests/testthat/test_classif_PART.R | 8 mlr-2.12/mlr/tests/testthat/test_classif_RRF.R | 26 mlr-2.12/mlr/tests/testthat/test_classif_ada.R | 8 mlr-2.12/mlr/tests/testthat/test_classif_adaboostm1.R |only mlr-2.12/mlr/tests/testthat/test_classif_bartMachine.R | 12 mlr-2.12/mlr/tests/testthat/test_classif_binomial.R | 10 mlr-2.12/mlr/tests/testthat/test_classif_blackboost.R | 14 mlr-2.12/mlr/tests/testthat/test_classif_boost.R | 12 mlr-2.12/mlr/tests/testthat/test_classif_bst.R | 2 mlr-2.12/mlr/tests/testthat/test_classif_cforest.R | 6 mlr-2.12/mlr/tests/testthat/test_classif_clusterSVM.R | 16 mlr-2.12/mlr/tests/testthat/test_classif_ctree.R | 12 mlr-2.12/mlr/tests/testthat/test_classif_cvglmnet.R | 4 mlr-2.12/mlr/tests/testthat/test_classif_dbnDNN.R | 24 mlr-2.12/mlr/tests/testthat/test_classif_dcSVM.R | 30 mlr-2.12/mlr/tests/testthat/test_classif_earth.R | 18 mlr-2.12/mlr/tests/testthat/test_classif_evtree.R | 6 mlr-2.12/mlr/tests/testthat/test_classif_extraTrees.R | 4 mlr-2.12/mlr/tests/testthat/test_classif_fdausc.glm.R |only mlr-2.12/mlr/tests/testthat/test_classif_fdausc.kernel.R |only mlr-2.12/mlr/tests/testthat/test_classif_fdausc.knn.R |only mlr-2.12/mlr/tests/testthat/test_classif_fdausc.np.R |only mlr-2.12/mlr/tests/testthat/test_classif_fnn.R | 22 mlr-2.12/mlr/tests/testthat/test_classif_gamboost.R | 16 mlr-2.12/mlr/tests/testthat/test_classif_gaterSVM.R | 6 mlr-2.12/mlr/tests/testthat/test_classif_gausspr.R | 16 mlr-2.12/mlr/tests/testthat/test_classif_gbm.R | 10 mlr-2.12/mlr/tests/testthat/test_classif_geoDA.R | 14 mlr-2.12/mlr/tests/testthat/test_classif_glmboost.R | 23 mlr-2.12/mlr/tests/testthat/test_classif_glmnet.R | 10 mlr-2.12/mlr/tests/testthat/test_classif_h2odeeplearning.R | 17 mlr-2.12/mlr/tests/testthat/test_classif_h2ogbm.R | 17 mlr-2.12/mlr/tests/testthat/test_classif_h2oglm.R | 17 mlr-2.12/mlr/tests/testthat/test_classif_h2orandomForest.R | 17 mlr-2.12/mlr/tests/testthat/test_classif_kknn.R | 4 mlr-2.12/mlr/tests/testthat/test_classif_knn.R | 4 mlr-2.12/mlr/tests/testthat/test_classif_ksvm.R | 26 mlr-2.12/mlr/tests/testthat/test_classif_lda.R | 2 mlr-2.12/mlr/tests/testthat/test_classif_linDA.R | 14 mlr-2.12/mlr/tests/testthat/test_classif_logreg.R | 4 mlr-2.12/mlr/tests/testthat/test_classif_lqa.R | 12 mlr-2.12/mlr/tests/testthat/test_classif_lssvm.R | 24 mlr-2.12/mlr/tests/testthat/test_classif_mda.R | 6 mlr-2.12/mlr/tests/testthat/test_classif_mlp.R | 23 mlr-2.12/mlr/tests/testthat/test_classif_multinom.R | 14 mlr-2.12/mlr/tests/testthat/test_classif_naiveBayes.R | 12 mlr-2.12/mlr/tests/testthat/test_classif_neuralnet.R | 42 mlr-2.12/mlr/tests/testthat/test_classif_nnTrain.R | 32 mlr-2.12/mlr/tests/testthat/test_classif_nnet.R | 17 mlr-2.12/mlr/tests/testthat/test_classif_nodeHarvest.R | 4 mlr-2.12/mlr/tests/testthat/test_classif_pamr.R | 4 mlr-2.12/mlr/tests/testthat/test_classif_penalized.R |only mlr-2.12/mlr/tests/testthat/test_classif_plr.R | 4 mlr-2.12/mlr/tests/testthat/test_classif_plsdaCaret.R | 6 mlr-2.12/mlr/tests/testthat/test_classif_probit.R | 4 mlr-2.12/mlr/tests/testthat/test_classif_qda.R | 6 mlr-2.12/mlr/tests/testthat/test_classif_quaDA.R | 10 mlr-2.12/mlr/tests/testthat/test_classif_rFerns.R | 2 mlr-2.12/mlr/tests/testthat/test_classif_randomForest.R | 26 mlr-2.12/mlr/tests/testthat/test_classif_randomForestSRC.R | 14 mlr-2.12/mlr/tests/testthat/test_classif_ranger.R | 6 mlr-2.12/mlr/tests/testthat/test_classif_rda.R | 20 mlr-2.12/mlr/tests/testthat/test_classif_rknn.R | 6 mlr-2.12/mlr/tests/testthat/test_classif_rotationForest.R | 2 mlr-2.12/mlr/tests/testthat/test_classif_rpart.R | 4 mlr-2.12/mlr/tests/testthat/test_classif_saeDNN.R | 28 mlr-2.12/mlr/tests/testthat/test_classif_sda.R | 2 mlr-2.12/mlr/tests/testthat/test_classif_sparseLDA.R | 4 mlr-2.12/mlr/tests/testthat/test_classif_svm.R | 20 mlr-2.12/mlr/tests/testthat/test_classif_xgboost.R | 20 mlr-2.12/mlr/tests/testthat/test_cluster_Cobweb.R | 2 mlr-2.12/mlr/tests/testthat/test_cluster_EM.R | 6 mlr-2.12/mlr/tests/testthat/test_cluster_FarthestFirst.R | 4 mlr-2.12/mlr/tests/testthat/test_cluster_SimpleKMeans.R | 2 mlr-2.12/mlr/tests/testthat/test_cluster_XMeans.R | 2 mlr-2.12/mlr/tests/testthat/test_cluster_cmeans.R | 8 mlr-2.12/mlr/tests/testthat/test_cluster_dbscan.R | 2 mlr-2.12/mlr/tests/testthat/test_cluster_kkmeans.R | 12 mlr-2.12/mlr/tests/testthat/test_cluster_kmeans.R | 8 mlr-2.12/mlr/tests/testthat/test_featsel_analyzeFeatSelResult.R | 10 mlr-2.12/mlr/tests/testthat/test_featsel_filters.R | 36 mlr-2.12/mlr/tests/testthat/test_learners_all_classif.R | 23 mlr-2.12/mlr/tests/testthat/test_learners_all_clusters.R | 4 mlr-2.12/mlr/tests/testthat/test_learners_all_multilabel.R | 10 mlr-2.12/mlr/tests/testthat/test_learners_all_regr.R | 24 mlr-2.12/mlr/tests/testthat/test_learners_all_surv.R | 14 mlr-2.12/mlr/tests/testthat/test_learners_classiflabelswitch.R | 18 mlr-2.12/mlr/tests/testthat/test_lint.R |only mlr-2.12/mlr/tests/testthat/test_multilabel_cforest.R | 12 mlr-2.12/mlr/tests/testthat/test_multilabel_randomForestSRC.R | 6 mlr-2.12/mlr/tests/testthat/test_parallel_all.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_FDboost.R |only mlr-2.12/mlr/tests/testthat/test_regr_GPfit.R | 18 mlr-2.12/mlr/tests/testthat/test_regr_IBk.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_LiblineaRL2L1SVR.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_LiblineaRL2L2SVR.R | 6 mlr-2.12/mlr/tests/testthat/test_regr_RRF.R | 8 mlr-2.12/mlr/tests/testthat/test_regr_bartMachine.R | 17 mlr-2.12/mlr/tests/testthat/test_regr_bcart.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_bgp.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_bgpllm.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_blackboost.R | 22 mlr-2.12/mlr/tests/testthat/test_regr_blm.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_brnn.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_bst.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_btgp.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_btgpllm.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_btlm.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_cforest.R | 4 mlr-2.12/mlr/tests/testthat/test_regr_crs.R | 4 mlr-2.12/mlr/tests/testthat/test_regr_ctree.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_cubist.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_cvglmnet.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_earth.R | 10 mlr-2.12/mlr/tests/testthat/test_regr_elmNN.R | 8 mlr-2.12/mlr/tests/testthat/test_regr_evtree.R | 4 mlr-2.12/mlr/tests/testthat/test_regr_extraTrees.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_featureless.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_fnn.R | 26 mlr-2.12/mlr/tests/testthat/test_regr_frbs.R | 4 mlr-2.12/mlr/tests/testthat/test_regr_gamboost.R | 18 mlr-2.12/mlr/tests/testthat/test_regr_gausspr.R | 10 mlr-2.12/mlr/tests/testthat/test_regr_gbm.R | 14 mlr-2.12/mlr/tests/testthat/test_regr_glm.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_glmboost.R | 20 mlr-2.12/mlr/tests/testthat/test_regr_glmnet.R | 6 mlr-2.12/mlr/tests/testthat/test_regr_h2odeeplearning.R | 4 mlr-2.12/mlr/tests/testthat/test_regr_h2ogbm.R | 4 mlr-2.12/mlr/tests/testthat/test_regr_h2oglm.R | 4 mlr-2.12/mlr/tests/testthat/test_regr_h2orandomForest.R | 4 mlr-2.12/mlr/tests/testthat/test_regr_kknn.R | 4 mlr-2.12/mlr/tests/testthat/test_regr_km.R | 16 mlr-2.12/mlr/tests/testthat/test_regr_ksvm.R | 16 mlr-2.12/mlr/tests/testthat/test_regr_laGP.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_lm.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_mob.R | 26 mlr-2.12/mlr/tests/testthat/test_regr_nnet.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_nodeHarvest.R | 4 mlr-2.12/mlr/tests/testthat/test_regr_penalized.R |only mlr-2.12/mlr/tests/testthat/test_regr_plsr.R | 4 mlr-2.12/mlr/tests/testthat/test_regr_randomForest.R | 6 mlr-2.12/mlr/tests/testthat/test_regr_randomForestSRC.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_ranger.R | 31 mlr-2.12/mlr/tests/testthat/test_regr_rknn.R | 8 mlr-2.12/mlr/tests/testthat/test_regr_rpart.R | 16 mlr-2.12/mlr/tests/testthat/test_regr_rsm.R | 4 mlr-2.12/mlr/tests/testthat/test_regr_slim.R | 4 mlr-2.12/mlr/tests/testthat/test_regr_svm.R | 2 mlr-2.12/mlr/tests/testthat/test_regr_xgboost.R | 18 mlr-2.12/mlr/tests/testthat/test_stack.R | 6 mlr-2.12/mlr/tests/testthat/test_surv_CoxBoost.R | 4 mlr-2.12/mlr/tests/testthat/test_surv_cforest.R | 7 mlr-2.12/mlr/tests/testthat/test_surv_coxph.R | 2 mlr-2.12/mlr/tests/testthat/test_surv_cv.CoxBoost.R | 21 mlr-2.12/mlr/tests/testthat/test_surv_cvglmnet.R | 6 mlr-2.12/mlr/tests/testthat/test_surv_gamboost.R | 18 mlr-2.12/mlr/tests/testthat/test_surv_gbm.R | 8 mlr-2.12/mlr/tests/testthat/test_surv_glmboost.R | 10 mlr-2.12/mlr/tests/testthat/test_surv_glmnet.R | 8 mlr-2.12/mlr/tests/testthat/test_surv_measures.R |only mlr-2.12/mlr/tests/testthat/test_surv_randomForestSRC.R | 2 mlr-2.12/mlr/tests/testthat/test_surv_ranger.R | 4 mlr-2.12/mlr/tests/testthat/test_surv_rpart.R | 10 mlr-2.12/mlr/tests/testthat/test_tuneParams.R | 12 mlr-2.12/mlr/tests/testthat/test_tune_ModelMultiplexer.R | 38 mlr-2.12/mlr/tests/testthat/test_tune_getTuneResultOptPath.R |only mlr-2.12/mlr/tests/testthat/test_tune_tuneCMAES.R | 13 mlr-2.12/mlr/tests/testthat/test_tune_tuneDesign.R | 8 mlr-2.12/mlr/tests/testthat/test_tune_tuneGenSA.R | 14 mlr-2.12/mlr/tests/testthat/test_tune_tuneGrid.R | 18 mlr-2.12/mlr/tests/testthat/test_tune_tuneIrace.R | 22 mlr-2.12/mlr/tests/testthat/test_tune_tuneMBO.R | 24 mlr-2.12/mlr/tests/testthat/test_tune_tuneParamsMultiCrit.R | 79 mlr-2.12/mlr/tests/testthat/test_tune_tuneRandom.R | 8 mlr-2.12/mlr/tests/testthat/test_tune_tuneThreshold.R | 6 992 files changed, 10904 insertions(+), 9482 deletions(-)
Title: A Statistically Sound 'data.frame' Processor/Conditioner
Description: A 'data.frame' processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner.
'vtreat' prepares variables so that data has fewer exceptional cases, making
it easier to safely use models in production. Common problems 'vtreat' defends
against: 'Inf', 'NA', too many categorical levels, rare categorical levels, and new
categorical levels (levels seen during application, but not during training). Reference:
"'vtreat': a data.frame Processor for Predictive Modeling", 'Zumel', 'Mount', 2016, DOI:10.5281/zenodo.1173314.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 1.0.2 dated 2018-01-20 and 1.0.3 dated 2018-03-10
DESCRIPTION | 12 +- MD5 | 49 ++++---- NAMESPACE | 3 NEWS.md | 5 R/indicatorTreatment.R | 93 ++++++++++++--- R/outOfSample.R | 61 ++++++++++ R/vtreat.R | 136 ++++++++++++++++++++++- R/vtreatImpl.R | 145 ++++++++++++++++++------ README.md | 100 ++++++++--------- inst/doc/SavingTreamentPlans.html | 14 +- inst/doc/vtreat.html | 222 +++++++++++++++++++------------------- inst/doc/vtreatCrossFrames.html | 59 +++++----- inst/doc/vtreatGrouping.html | 10 - inst/doc/vtreatOverfit.html | 43 +++---- inst/doc/vtreatRareLevels.Rmd | 2 inst/doc/vtreatRareLevels.html | 42 +++---- inst/doc/vtreatScaleMode.html | 78 +++++++------ inst/doc/vtreatSignificance.html | 22 +-- inst/doc/vtreatSplitting.html | 8 - inst/doc/vtreatVariableTypes.html | 150 ++++++++++++------------- man/kWayStratifiedYReplace.Rd |only man/mkCrossFrameCExperiment.Rd | 6 - man/mkCrossFrameNExperiment.Rd | 6 - man/novel_value_summary.Rd |only man/prepare.Rd | 4 man/track_values.Rd |only vignettes/vtreatRareLevels.Rmd | 2 27 files changed, 811 insertions(+), 461 deletions(-)
Title: Spatial and Spatiotemporal Relative Risk
Description: Provides functions to estimate kernel-smoothed spatial and spatio-temporal densities and relative risk functions, and perform subsequent inference. Methodological details can be found in the accompanying tutorial: Davies et al. (2018) <DOI:10.1002/sim.7577>.
Author: Tilman M. Davies [aut, cre],
Jonathan C. Marshall [aut]
Maintainer: Tilman M. Davies <tdavies@maths.otago.ac.nz>
Diff between sparr versions 2.2-1 dated 2018-02-22 and 2.2-11 dated 2018-03-10
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NEWS | 8 ++++++++ R/NS.R | 6 +++--- R/package.R | 15 +++++++++++---- R/zzz.R | 2 +- README.md | 3 +-- inst/CITATION | 7 ++++--- man/NS.Rd | 6 +++--- man/figures/README-pbc-example-1.png |binary man/sparr-package.Rd | 19 +++++++++++++------ 11 files changed, 59 insertions(+), 37 deletions(-)
Title: Tools for Multivariate Nonparametrics
Description: Tools for multivariate nonparametrics, as location tests based on marginal ranks, spatial median and spatial signs computation, Hotelling's T-test, estimates of shape are implemented.
Author: Klaus Nordhausen, Seija Sirkia, Hannu Oja, David E. Tyler
Maintainer: Klaus Nordhausen <klaus.nordhausen@tuwien.ac.at>
Diff between ICSNP versions 1.1-0 dated 2015-09-22 and 1.1-1 dated 2018-03-10
DESCRIPTION | 10 ++++----- MD5 | 51 +++++++++++++++++++++++------------------------ NAMESPACE | 2 - data/pulmonary.rda |binary inst/ChangeLog | 8 ++++++- man/HP.loc.test.Rd | 2 - man/HP1.shape.Rd | 2 - man/HR.Mest.Rd | 2 - man/HotellingsT.Rd | 2 - man/ICSNP-package.Rd | 6 ++--- man/duembgen.shape.Rd | 4 ++- man/duembgen.shape.wt.Rd | 2 - man/hl.loc.Rd | 2 - man/ind.ctest.Rd | 2 - man/ind.ictest.Rd | 5 ++-- man/pair.diff.Rd | 2 - man/pair.prod.Rd | 2 - man/pair.sum.Rd | 2 - man/rank.ctest.Rd | 2 - man/rank.ictest.Rd | 2 - man/spatial.median.Rd | 2 - man/spatial.sign.Rd | 2 - man/symm.huber.Rd | 2 - man/symm.huber.wt.Rd | 2 - man/tyler.shape.Rd | 4 ++- man/vdw.loc.Rd | 2 - src/aa.c |only 27 files changed, 68 insertions(+), 56 deletions(-)
Title: Fast Computation of Multivariate M-Estimators
Description: Implements the new algorithm for fast computation of M-scatter matrices using a partial Newton-Raphson procedure for several estimators. The algorithm is described in Duembgen, Nordhausen and Schuhmacher (2016) <doi:10.1016/j.jmva.2015.11.009>.
Author: Lutz Duembgen, Klaus Nordhausen, Heike Schuhmacher
Maintainer: Klaus Nordhausen <klaus.nordhausen@tuwien.ac.at>
Diff between fastM versions 0.0-2 dated 2014-04-12 and 0.0-3 dated 2018-03-10
DESCRIPTION | 14 +++++++------- MD5 | 30 ++++++++++++++++-------------- NAMESPACE | 6 ++++-- R/MVTMLE0wrap.R | 2 +- R/MVTMLEsymm1wrap.R | 2 +- R/MVTMLEsymm2wrap.R | 2 +- build |only inst/ChangeLog | 11 ++++++++--- man/DUEMBGENshape.Rd | 5 +++-- man/MVTMLE.Rd | 2 +- man/MVTMLE0r.Rd | 2 +- man/MVTMLEsymm.Rd | 2 +- man/TYLERshape.Rd | 4 ++-- man/fastM-package.Rd | 12 ++++++------ src/MVTMLE.cpp | 6 +++--- src/MVTMLE.h | 6 +++--- src/aa.c |only 17 files changed, 58 insertions(+), 48 deletions(-)
Title: Genotype Simulations for Rare or Common Variants Using
Haplotypes from 1000 Genomes
Description: Generates realistic simulated genetic data in families or unrelated individuals.
Author: Apostolos Dimitromanolakis <apostolis@live.ca>,
Jingxiong Xu <jingxiong.xu@mail.utoronto.ca>,
Agnieszka Krol <krol@lunenfeld.ca>,
Laurent Briollais <laurent@lunenfeld.ca>
Maintainer: Apostolos Dimitromanolakis <apostolis@live.ca>
Diff between sim1000G versions 1.38 dated 2018-02-18 and 1.39 dated 2018-03-10
sim1000G-1.38/sim1000G/inst/doc/getting-started.html |only sim1000G-1.38/sim1000G/inst/examples/sim1000G-timings.log.R |only sim1000G-1.39/sim1000G/DESCRIPTION | 8 sim1000G-1.39/sim1000G/MD5 | 17 sim1000G-1.39/sim1000G/R/recombination.R | 7 sim1000G-1.39/sim1000G/R/simulation.R | 2 sim1000G-1.39/sim1000G/inst/doc/ExtractingRegionsForSimulation.html | 81 +- sim1000G-1.39/sim1000G/inst/doc/SimulatingFamilyData.html | 284 +++------- sim1000G-1.39/sim1000G/inst/examples/amelia |only sim1000G-1.39/sim1000G/man/downloadGeneticMap.Rd | 2 sim1000G-1.39/sim1000G/man/setRecombinationModel.Rd | 2 11 files changed, 146 insertions(+), 257 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou and Kleanthi Lakiotaki
Maintainer: Manos Papadakis <papadakm95@gmail.com>
Diff between Rfast versions 1.8.6 dated 2017-11-17 and 1.8.8 dated 2018-03-10
Rfast-1.8.6/Rfast/src/Hash_list.cpp |only Rfast-1.8.6/Rfast/src/Lbeta.cpp |only Rfast-1.8.6/Rfast/src/Lchoose.cpp |only Rfast-1.8.6/Rfast/src/bcdcor.cpp |only Rfast-1.8.6/Rfast/src/check_aliases.cpp |only Rfast-1.8.6/Rfast/src/check_namespace.cpp |only Rfast-1.8.6/Rfast/src/col_diffs.cpp |only Rfast-1.8.6/Rfast/src/col_max_p.cpp |only Rfast-1.8.6/Rfast/src/col_mean_p.cpp |only Rfast-1.8.6/Rfast/src/col_min_p.cpp |only Rfast-1.8.6/Rfast/src/col_row_all.cpp |only Rfast-1.8.6/Rfast/src/col_row_all_p.cpp |only Rfast-1.8.6/Rfast/src/col_row_any.cpp |only Rfast-1.8.6/Rfast/src/col_row_count_values.cpp |only Rfast-1.8.6/Rfast/src/col_row_count_values_p.cpp |only Rfast-1.8.6/Rfast/src/col_row_false.cpp |only Rfast-1.8.6/Rfast/src/col_row_len_sort_un_int.cpp |only Rfast-1.8.6/Rfast/src/col_row_mads.cpp |only Rfast-1.8.6/Rfast/src/col_row_mads_p.cpp |only Rfast-1.8.6/Rfast/src/col_row_max.cpp |only Rfast-1.8.6/Rfast/src/col_row_means.cpp |only Rfast-1.8.6/Rfast/src/col_row_meds.cpp |only Rfast-1.8.6/Rfast/src/col_row_meds_p.cpp |only Rfast-1.8.6/Rfast/src/col_row_min.cpp |only Rfast-1.8.6/Rfast/src/col_row_min_max.cpp |only Rfast-1.8.6/Rfast/src/col_row_nth.cpp |only Rfast-1.8.6/Rfast/src/col_row_nth_p.cpp |only Rfast-1.8.6/Rfast/src/col_row_order.cpp |only Rfast-1.8.6/Rfast/src/col_row_order_p.cpp |only Rfast-1.8.6/Rfast/src/col_row_prods.cpp |only Rfast-1.8.6/Rfast/src/col_row_ranks.cpp |only Rfast-1.8.6/Rfast/src/col_row_ranks_p.cpp |only Rfast-1.8.6/Rfast/src/col_row_shuffle.cpp |only Rfast-1.8.6/Rfast/src/col_row_sums.cpp |only Rfast-1.8.6/Rfast/src/col_row_tabulate.cpp |only Rfast-1.8.6/Rfast/src/col_row_true.cpp |only Rfast-1.8.6/Rfast/src/col_row_true_false.cpp |only Rfast-1.8.6/Rfast/src/col_sum_p.cpp |only Rfast-1.8.6/Rfast/src/dcor.cpp |only Rfast-1.8.6/Rfast/src/dcov.cpp |only Rfast-1.8.6/Rfast/src/dvar.cpp |only Rfast-1.8.6/Rfast/src/edist.cpp |only Rfast-1.8.6/Rfast/src/glm_logistic.cpp |only Rfast-1.8.6/Rfast/src/glm_poisson.cpp |only Rfast-1.8.6/Rfast/src/gold_rat2.cpp |only Rfast-1.8.6/Rfast/src/gold_rat3.cpp |only Rfast-1.8.6/Rfast/src/group_all.cpp |only Rfast-1.8.6/Rfast/src/group_any.cpp |only Rfast-1.8.6/Rfast/src/group_mad.cpp |only Rfast-1.8.6/Rfast/src/group_max.cpp |only Rfast-1.8.6/Rfast/src/group_mean.cpp |only Rfast-1.8.6/Rfast/src/group_med.cpp |only Rfast-1.8.6/Rfast/src/group_min.cpp |only Rfast-1.8.6/Rfast/src/group_min_max.cpp |only Rfast-1.8.6/Rfast/src/group_sum.cpp |only Rfast-1.8.6/Rfast/src/group_var.cpp |only Rfast-1.8.6/Rfast/src/hash2list.cpp |only Rfast-1.8.6/Rfast/src/hash_find.cpp |only Rfast-1.8.6/Rfast/src/is_element.cpp |only Rfast-1.8.6/Rfast/src/k_nn_cv.cpp |only Rfast-1.8.6/Rfast/src/len_sort_unique.cpp |only Rfast-1.8.6/Rfast/src/lower_tri.cpp |only Rfast-1.8.6/Rfast/src/pmax.cpp |only Rfast-1.8.6/Rfast/src/pmin.cpp |only Rfast-1.8.6/Rfast/src/prop_reg.cpp |only Rfast-1.8.6/Rfast/src/prop_regs.cpp |only Rfast-1.8.6/Rfast/src/qpois_reg.cpp |only Rfast-1.8.6/Rfast/src/qpois_regs.cpp |only Rfast-1.8.6/Rfast/src/rank.cpp |only Rfast-1.8.6/Rfast/src/read_directory.cpp |only Rfast-1.8.6/Rfast/src/read_examples.cpp |only Rfast-1.8.6/Rfast/src/rint_mle.cpp |only Rfast-1.8.6/Rfast/src/rint_reg.cpp |only Rfast-1.8.6/Rfast/src/rint_regs.cpp |only Rfast-1.8.6/Rfast/src/sort_mat_stable.cpp |only Rfast-1.8.6/Rfast/src/sort_mat_stable_p.cpp |only Rfast-1.8.6/Rfast/src/spml_mle.cpp |only Rfast-1.8.6/Rfast/src/spml_reg.cpp |only Rfast-1.8.6/Rfast/src/spml_regs.cpp |only Rfast-1.8.6/Rfast/src/stable_sort.cpp |only Rfast-1.8.6/Rfast/src/sum_eachrow.cpp |only Rfast-1.8.6/Rfast/src/sum_x_op_x.cpp |only Rfast-1.8.6/Rfast/src/sum_x_op_y.cpp |only Rfast-1.8.6/Rfast/src/upper_tri.cpp |only Rfast-1.8.8/Rfast/DESCRIPTION | 8 Rfast-1.8.8/Rfast/MD5 | 514 +++++++------- Rfast-1.8.8/Rfast/NAMESPACE | 2 Rfast-1.8.8/Rfast/NEWS.md | 122 +-- Rfast-1.8.8/Rfast/R/Match.R | 6 Rfast-1.8.8/Rfast/R/Pmax.R | 4 Rfast-1.8.8/Rfast/R/Pmin.R | 4 Rfast-1.8.8/Rfast/R/Pmin_Pmax.R |only Rfast-1.8.8/Rfast/R/Sort.R | 8 Rfast-1.8.8/Rfast/R/Table.R | 23 Rfast-1.8.8/Rfast/R/Table.sign.R |only Rfast-1.8.8/Rfast/R/allttests.R | 73 +- Rfast-1.8.8/Rfast/R/ancova1.R | 3 Rfast-1.8.8/Rfast/R/ancovas.R | 1 Rfast-1.8.8/Rfast/R/anova1.R | 1 Rfast-1.8.8/Rfast/R/anova_quasipois.reg.R |only Rfast-1.8.8/Rfast/R/anovas.R | 1 Rfast-1.8.8/Rfast/R/ar1.R |only Rfast-1.8.8/Rfast/R/as_integer.R |only Rfast-1.8.8/Rfast/R/auc.R |only Rfast-1.8.8/Rfast/R/bc.R |only Rfast-1.8.8/Rfast/R/boot.ttest2.R |only Rfast-1.8.8/Rfast/R/cat.goftests.R | 1 Rfast-1.8.8/Rfast/R/checkExamples.R | 14 Rfast-1.8.8/Rfast/R/checkTF.R |only Rfast-1.8.8/Rfast/R/col.coxpoisrat.R |only Rfast-1.8.8/Rfast/R/col.yule.R |only Rfast-1.8.8/Rfast/R/colPmax.R |only Rfast-1.8.8/Rfast/R/colPmin.R |only Rfast-1.8.8/Rfast/R/colanovas.R |only Rfast-1.8.8/Rfast/R/colar1.R |only Rfast-1.8.8/Rfast/R/colhameans.R | 4 Rfast-1.8.8/Rfast/R/colnormlog.mle.R |only Rfast-1.8.8/Rfast/R/colsums.R | 6 Rfast-1.8.8/Rfast/R/columns.R |only Rfast-1.8.8/Rfast/R/colvarcomps.mom.R | 1 Rfast-1.8.8/Rfast/R/cor.fsreg.R | 45 - Rfast-1.8.8/Rfast/R/countNA.R |only Rfast-1.8.8/Rfast/R/cox.poisrat.R |only Rfast-1.8.8/Rfast/R/data.frame.to_matrix.R | 17 Rfast-1.8.8/Rfast/R/diri.nr2.R | 2 Rfast-1.8.8/Rfast/R/eachcol.apply.R |only Rfast-1.8.8/Rfast/R/eachrow.R | 8 Rfast-1.8.8/Rfast/R/freq.max.R |only Rfast-1.8.8/Rfast/R/freq.min.R |only Rfast-1.8.8/Rfast/R/ftest.R | 1 Rfast-1.8.8/Rfast/R/ftests.R | 1 Rfast-1.8.8/Rfast/R/gammanb.R |only Rfast-1.8.8/Rfast/R/gammanb.pred.R |only Rfast-1.8.8/Rfast/R/gaussian.nb.R | 1 Rfast-1.8.8/Rfast/R/geom.anova.R | 1 Rfast-1.8.8/Rfast/R/geom.anovas.R | 1 Rfast-1.8.8/Rfast/R/geom.nb.R | 1 Rfast-1.8.8/Rfast/R/geomnb.pred.R |only Rfast-1.8.8/Rfast/R/ginis.R |only Rfast-1.8.8/Rfast/R/group.max.R | 4 Rfast-1.8.8/Rfast/R/groupcolVars.R | 1 Rfast-1.8.8/Rfast/R/hd.eigen.R | 44 - Rfast-1.8.8/Rfast/R/is_integer.R |only Rfast-1.8.8/Rfast/R/knn.cv.R | 17 Rfast-1.8.8/Rfast/R/kruskaltest.R | 1 Rfast-1.8.8/Rfast/R/kruskaltests.R | 1 Rfast-1.8.8/Rfast/R/mad2.R | 4 Rfast-1.8.8/Rfast/R/multinom.nb.R | 5 Rfast-1.8.8/Rfast/R/multinom.regs.R | 4 Rfast-1.8.8/Rfast/R/nth.R | 6 Rfast-1.8.8/Rfast/R/omp.R |only Rfast-1.8.8/Rfast/R/ompr.R | 29 Rfast-1.8.8/Rfast/R/pc.skel.R | 10 Rfast-1.8.8/Rfast/R/permcor.R |only Rfast-1.8.8/Rfast/R/permutation.R | 4 Rfast-1.8.8/Rfast/R/permutation.next.R | 4 Rfast-1.8.8/Rfast/R/permutation.prev.R | 4 Rfast-1.8.8/Rfast/R/poisson.anova.R | 3 Rfast-1.8.8/Rfast/R/poisson.anovas.R | 1 Rfast-1.8.8/Rfast/R/prop.reg.R | 2 Rfast-1.8.8/Rfast/R/prop.regs.R | 4 Rfast-1.8.8/Rfast/R/qpois.reg.R | 6 Rfast-1.8.8/Rfast/R/quasi.poisson_only.R |only Rfast-1.8.8/Rfast/R/quasipoisson.anova.R |only Rfast-1.8.8/Rfast/R/quasipoisson.anovas.R |only Rfast-1.8.8/Rfast/R/rbing.R |only Rfast-1.8.8/Rfast/R/rbingham.R |only Rfast-1.8.8/Rfast/R/regression.R | 1 Rfast-1.8.8/Rfast/R/rmdp.R | 18 Rfast-1.8.8/Rfast/R/rowhameans.R | 4 Rfast-1.8.8/Rfast/R/rows.R |only Rfast-1.8.8/Rfast/R/rowsums.R | 8 Rfast-1.8.8/Rfast/R/sourceR.R | 2 Rfast-1.8.8/Rfast/R/standardise.R | 7 Rfast-1.8.8/Rfast/R/tobit.mle.R | 4 Rfast-1.8.8/Rfast/R/topological_sort.R |only Rfast-1.8.8/Rfast/R/univglms.R | 31 Rfast-1.8.8/Rfast/R/univglms2.R |only Rfast-1.8.8/Rfast/R/varcomps.mle.R | 2 Rfast-1.8.8/Rfast/R/yule.R |only Rfast-1.8.8/Rfast/man/AddToNamespace.Rd | 10 Rfast-1.8.8/Rfast/man/Match.Rd | 7 Rfast-1.8.8/Rfast/man/Norm.Rd | 2 Rfast-1.8.8/Rfast/man/Pmax.Rd | 30 Rfast-1.8.8/Rfast/man/Rfast-package.Rd | 27 Rfast-1.8.8/Rfast/man/Sort.Rd | 14 Rfast-1.8.8/Rfast/man/Table.Rd | 78 +- Rfast-1.8.8/Rfast/man/XopY.sum.Rd | 44 - Rfast-1.8.8/Rfast/man/ancovas.Rd | 2 Rfast-1.8.8/Rfast/man/anova_propreg.Rd | 2 Rfast-1.8.8/Rfast/man/anova_quasipois.reg.Rd |only Rfast-1.8.8/Rfast/man/ar1.Rd |only Rfast-1.8.8/Rfast/man/bc.Rd |only Rfast-1.8.8/Rfast/man/boot.ttest2.Rd |only Rfast-1.8.8/Rfast/man/checkNamespace.Rd | 46 + Rfast-1.8.8/Rfast/man/col.yule.Rd |only Rfast-1.8.8/Rfast/man/colPmax.Rd |only Rfast-1.8.8/Rfast/man/colTrue.Rd | 6 Rfast-1.8.8/Rfast/man/colanovas.Rd |only Rfast-1.8.8/Rfast/man/colaucs.Rd | 18 Rfast-1.8.8/Rfast/man/colnormal.mle.Rd | 4 Rfast-1.8.8/Rfast/man/colnth.Rd | 5 Rfast-1.8.8/Rfast/man/colsums.Rd | 13 Rfast-1.8.8/Rfast/man/columns.Rd |only Rfast-1.8.8/Rfast/man/colvarcomps.mom.Rd | 1 Rfast-1.8.8/Rfast/man/count_value.Rd | 6 Rfast-1.8.8/Rfast/man/cox.poisrat.Rd |only Rfast-1.8.8/Rfast/man/data.frame.to_matrix.Rd | 10 Rfast-1.8.8/Rfast/man/design_matrix.Rd | 2 Rfast-1.8.8/Rfast/man/edist.Rd | 2 Rfast-1.8.8/Rfast/man/freq.min.Rd |only Rfast-1.8.8/Rfast/man/gaussian.nb.Rd | 33 Rfast-1.8.8/Rfast/man/gaussiannb.pred.Rd | 14 Rfast-1.8.8/Rfast/man/ginis.Rd |only Rfast-1.8.8/Rfast/man/group.var.Rd | 5 Rfast-1.8.8/Rfast/man/hd.eigen.Rd | 36 - Rfast-1.8.8/Rfast/man/is_integer.Rd |only Rfast-1.8.8/Rfast/man/mad2.Rd | 11 Rfast-1.8.8/Rfast/man/mahala.Rd | 2 Rfast-1.8.8/Rfast/man/multinom.regs.Rd | 5 Rfast-1.8.8/Rfast/man/normal.mle.Rd | 3 Rfast-1.8.8/Rfast/man/odds.ratio.Rd | 1 Rfast-1.8.8/Rfast/man/ompr.Rd | 27 Rfast-1.8.8/Rfast/man/pc.skel.Rd | 14 Rfast-1.8.8/Rfast/man/permcor.Rd |only Rfast-1.8.8/Rfast/man/permutation.Rd | 24 Rfast-1.8.8/Rfast/man/poisson.anova.Rd | 14 Rfast-1.8.8/Rfast/man/poisson.anovas.Rd | 9 Rfast-1.8.8/Rfast/man/prop.reg.Rd | 2 Rfast-1.8.8/Rfast/man/qpois.reg.Rd | 5 Rfast-1.8.8/Rfast/man/quasi.poisson_only.Rd |only Rfast-1.8.8/Rfast/man/rbing.Rd |only Rfast-1.8.8/Rfast/man/rbingham.Rd |only Rfast-1.8.8/Rfast/man/topological_sort.Rd |only Rfast-1.8.8/Rfast/man/univglms.Rd | 29 Rfast-1.8.8/Rfast/man/yule.Rd |only Rfast-1.8.8/Rfast/src/Choose.cpp | 43 + Rfast-1.8.8/Rfast/src/Diag.cpp | 13 Rfast-1.8.8/Rfast/src/Log.cpp | 44 + Rfast-1.8.8/Rfast/src/Match.cpp | 17 Rfast-1.8.8/Rfast/src/Norm.cpp | 45 - Rfast-1.8.8/Rfast/src/Order.cpp | 22 Rfast-1.8.8/Rfast/src/Outer.cpp |only Rfast-1.8.8/Rfast/src/Rank.cpp |only Rfast-1.8.8/Rfast/src/Sort.cpp | 103 ++ Rfast-1.8.8/Rfast/src/Table.cpp | 236 +++++- Rfast-1.8.8/Rfast/src/Var.cpp | 2 Rfast-1.8.8/Rfast/src/add_to_namespace.cpp | 6 Rfast-1.8.8/Rfast/src/as_integer.cpp |only Rfast-1.8.8/Rfast/src/bic_fs_reg.cpp | 2 Rfast-1.8.8/Rfast/src/binarysearch.cpp | 8 Rfast-1.8.8/Rfast/src/bincomb.cpp | 2 Rfast-1.8.8/Rfast/src/calc_pc_skel.cpp | 105 +- Rfast-1.8.8/Rfast/src/calc_pc_skel.h | 5 Rfast-1.8.8/Rfast/src/calc_perm_cor.cpp |only Rfast-1.8.8/Rfast/src/calc_perm_cor.h |only Rfast-1.8.8/Rfast/src/calc_qpois_regs.cpp | 11 Rfast-1.8.8/Rfast/src/check.cpp |only Rfast-1.8.8/Rfast/src/col_row_utilities.cpp |only Rfast-1.8.8/Rfast/src/col_row_utilities_p.cpp |only Rfast-1.8.8/Rfast/src/col_row_zero.cpp | 1 Rfast-1.8.8/Rfast/src/col_statistical.cpp |only Rfast-1.8.8/Rfast/src/colrint_mle.cpp | 115 ++- Rfast-1.8.8/Rfast/src/columns_rows.cpp |only Rfast-1.8.8/Rfast/src/colweibull_mle.cpp | 43 - Rfast-1.8.8/Rfast/src/combn.cpp | 4 Rfast-1.8.8/Rfast/src/count_value.cpp | 44 + Rfast-1.8.8/Rfast/src/cts.cpp | 130 --- Rfast-1.8.8/Rfast/src/cts.h | 7 Rfast-1.8.8/Rfast/src/design_matrix.cpp | 4 Rfast-1.8.8/Rfast/src/dir_knn.cpp | 65 + Rfast-1.8.8/Rfast/src/diri_nr_type2.cpp | 19 Rfast-1.8.8/Rfast/src/dista.cpp | 21 Rfast-1.8.8/Rfast/src/dists.cpp | 19 Rfast-1.8.8/Rfast/src/dists_vec.cpp | 55 + Rfast-1.8.8/Rfast/src/eachcol_apply.cpp |only Rfast-1.8.8/Rfast/src/eachrow.cpp | 97 +- Rfast-1.8.8/Rfast/src/energy.cpp |only Rfast-1.8.8/Rfast/src/floyd_john.cpp | 3 Rfast-1.8.8/Rfast/src/frame_to_matrix.cpp | 33 Rfast-1.8.8/Rfast/src/gamma.cpp | 3 Rfast-1.8.8/Rfast/src/geom_regs.cpp | 122 ++- Rfast-1.8.8/Rfast/src/glm.cpp |only Rfast-1.8.8/Rfast/src/group.cpp |only Rfast-1.8.8/Rfast/src/hash.cpp |only Rfast-1.8.8/Rfast/src/init.c | 137 ++- Rfast-1.8.8/Rfast/src/is.cpp |only Rfast-1.8.8/Rfast/src/k_nn.cpp | 30 Rfast-1.8.8/Rfast/src/logistic_only.cpp | 205 +++-- Rfast-1.8.8/Rfast/src/lower_upper_tri.cpp |only Rfast-1.8.8/Rfast/src/mad2.cpp | 26 Rfast-1.8.8/Rfast/src/mat_mat.cpp | 1 Rfast-1.8.8/Rfast/src/matrix_sum.cpp | 6 Rfast-1.8.8/Rfast/src/med.cpp | 3 Rfast-1.8.8/Rfast/src/min_max.cpp | 137 +++ Rfast-1.8.8/Rfast/src/min_max_freq.cpp |only Rfast-1.8.8/Rfast/src/mn.cpp | 350 ++------- Rfast-1.8.8/Rfast/src/mn.h | 34 Rfast-1.8.8/Rfast/src/multinom_regs.cpp | 219 ++---- Rfast-1.8.8/Rfast/src/my_k_sorted_array.cpp | 11 Rfast-1.8.8/Rfast/src/normlog_reg.cpp | 2 Rfast-1.8.8/Rfast/src/normlog_regs.cpp | 142 ++- Rfast-1.8.8/Rfast/src/nth.cpp | 71 + Rfast-1.8.8/Rfast/src/odds_helper.cpp | 3 Rfast-1.8.8/Rfast/src/only_glm.cpp | 38 - Rfast-1.8.8/Rfast/src/only_glm.h | 4 Rfast-1.8.8/Rfast/src/partial_sort.cpp | 16 Rfast-1.8.8/Rfast/src/pc_skel.cpp | 19 Rfast-1.8.8/Rfast/src/perm_cor.cpp |only Rfast-1.8.8/Rfast/src/permutation.cpp | 99 +- Rfast-1.8.8/Rfast/src/poisson_only.cpp | 2 Rfast-1.8.8/Rfast/src/prop.cpp |only Rfast-1.8.8/Rfast/src/qpois.cpp |only Rfast-1.8.8/Rfast/src/quasi_poisson_only.cpp |only Rfast-1.8.8/Rfast/src/rbing.cpp |only Rfast-1.8.8/Rfast/src/read.cpp |only Rfast-1.8.8/Rfast/src/reg_lib.cpp | 273 ++++--- Rfast-1.8.8/Rfast/src/reg_lib.h | 20 Rfast-1.8.8/Rfast/src/reg_lib2.cpp | 124 +++ Rfast-1.8.8/Rfast/src/reg_lib2.h | 10 Rfast-1.8.8/Rfast/src/rep.cpp | 15 Rfast-1.8.8/Rfast/src/rint.cpp |only Rfast-1.8.8/Rfast/src/rmdp.cpp | 1 Rfast-1.8.8/Rfast/src/sort_mat.cpp | 75 +- Rfast-1.8.8/Rfast/src/sort_mat_p.cpp | 88 ++ Rfast-1.8.8/Rfast/src/sort_unique.cpp | 197 ++++- Rfast-1.8.8/Rfast/src/spat_med.cpp | 1 Rfast-1.8.8/Rfast/src/spml.cpp |only Rfast-1.8.8/Rfast/src/squareform.cpp | 10 Rfast-1.8.8/Rfast/src/submatrix.cpp | 1 Rfast-1.8.8/Rfast/src/sum_mat_op_mat.cpp |only Rfast-1.8.8/Rfast/src/symmetric.cpp | 1 Rfast-1.8.8/Rfast/src/system_files.cpp | 225 ++++-- Rfast-1.8.8/Rfast/src/system_files.h | 31 Rfast-1.8.8/Rfast/src/templates.h | 791 +++++++++++++++++++++- Rfast-1.8.8/Rfast/src/topological_sort.cpp |only Rfast-1.8.8/Rfast/src/total_dista.cpp | 11 Rfast-1.8.8/Rfast/src/total_dists.cpp | 31 Rfast-1.8.8/Rfast/src/transpose.cpp | 7 Rfast-1.8.8/Rfast/src/varcomps_mle.cpp | 9 Rfast-1.8.8/Rfast/src/weib_reg.cpp | 5 Rfast-1.8.8/Rfast/src/which_isFactor.cpp | 7 342 files changed, 4370 insertions(+), 2235 deletions(-)
Title: A Monadic Pipeline System
Description: A monadic solution to pipeline analysis. All operations -- and the errors,
warnings and messages they emit -- are merged into a directed graph. Infix
binary operators mediate when values are stored, how exceptions are
handled, and where pipelines branch and merge. The resulting structure may
be queried for debugging or report generation. 'rmonad' complements, rather
than competes with, non-monadic pipeline packages like 'magrittr' or
'pipeR'. This work is funded by the NSF (award number 1546858).
Author: Zebulun Arendsee [aut, cre]
Maintainer: Zebulun Arendsee <zbwrnz@gmail.com>
Diff between rmonad versions 0.4.0 dated 2017-12-20 and 0.5.0 dated 2018-03-10
rmonad-0.4.0/rmonad/man/make_local_cacher.Rd |only rmonad-0.5.0/rmonad/DESCRIPTION | 11 rmonad-0.5.0/rmonad/MD5 | 149 +- rmonad-0.5.0/rmonad/NAMESPACE | 16 rmonad-0.5.0/rmonad/NEWS.md | 86 + rmonad-0.5.0/rmonad/R/access.R | 301 +++- rmonad-0.5.0/rmonad/R/bind.R | 97 + rmonad-0.5.0/rmonad/R/cache.R | 179 ++ rmonad-0.5.0/rmonad/R/classes.R | 30 rmonad-0.5.0/rmonad/R/from-monad.R | 13 rmonad-0.5.0/rmonad/R/generics.R | 18 rmonad-0.5.0/rmonad/R/graph.R | 67 rmonad-0.5.0/rmonad/R/metadata.R | 25 rmonad-0.5.0/rmonad/R/onload.R |only rmonad-0.5.0/rmonad/R/operators.R | 15 rmonad-0.5.0/rmonad/R/parallel.R |only rmonad-0.5.0/rmonad/R/rmonad.R | 6 rmonad-0.5.0/rmonad/R/splice.R | 5 rmonad-0.5.0/rmonad/R/to-monad.R | 87 + rmonad-0.5.0/rmonad/R/util.R | 42 rmonad-0.5.0/rmonad/build/vignette.rds |binary rmonad-0.5.0/rmonad/inst/JOSS |only rmonad-0.5.0/rmonad/inst/doc/cheatsheet.html | 92 - rmonad-0.5.0/rmonad/inst/doc/gff-processing.R | 126 + rmonad-0.5.0/rmonad/inst/doc/gff-processing.Rmd | 192 ++ rmonad-0.5.0/rmonad/inst/doc/gff-processing.html | 1278 +++++++++++-------- rmonad-0.5.0/rmonad/inst/doc/introduction.R | 28 rmonad-0.5.0/rmonad/inst/doc/introduction.Rmd | 37 rmonad-0.5.0/rmonad/inst/doc/introduction.html | 399 +++-- rmonad-0.5.0/rmonad/inst/doc/nozzle.R |only rmonad-0.5.0/rmonad/inst/doc/nozzle.Rmd |only rmonad-0.5.0/rmonad/inst/doc/nozzle.html |only rmonad-0.5.0/rmonad/inst/doc/theory_monad.html | 18 rmonad-0.5.0/rmonad/inst/extdata |only rmonad-0.5.0/rmonad/man/bind.Rd | 4 rmonad-0.5.0/rmonad/man/clear_cache.Rd | 11 rmonad-0.5.0/rmonad/man/crunch.Rd |only rmonad-0.5.0/rmonad/man/esc.Rd | 6 rmonad-0.5.0/rmonad/man/fail_cache.Rd |only rmonad-0.5.0/rmonad/man/infix.Rd | 14 rmonad-0.5.0/rmonad/man/loop.Rd |only rmonad-0.5.0/rmonad/man/make_cacher.Rd |only rmonad-0.5.0/rmonad/man/make_recacher.Rd | 6 rmonad-0.5.0/rmonad/man/memory_cache.Rd | 6 rmonad-0.5.0/rmonad/man/missues.Rd | 5 rmonad-0.5.0/rmonad/man/mtabulate.Rd | 5 rmonad-0.5.0/rmonad/man/no_cache.Rd | 6 rmonad-0.5.0/rmonad/man/print.Rmonad.Rd | 9 rmonad-0.5.0/rmonad/man/reexports.Rd |only rmonad-0.5.0/rmonad/man/rmonad_checkers.Rd | 31 rmonad-0.5.0/rmonad/man/rmonad_getters.Rd | 76 - rmonad-0.5.0/rmonad/man/size.Rd | 4 rmonad-0.5.0/rmonad/man/tag.Rd |only rmonad-0.5.0/rmonad/man/view.Rd |only rmonad-0.5.0/rmonad/man/viewID.Rd |only rmonad-0.5.0/rmonad/man/viewIDs.Rd |only rmonad-0.5.0/rmonad/man/views.Rd |only rmonad-0.5.0/rmonad/man/void_cache.Rd | 6 rmonad-0.5.0/rmonad/man/x_to_monad.Rd | 12 rmonad-0.5.0/rmonad/tests/testthat/test-binops.R | 44 rmonad-0.5.0/rmonad/tests/testthat/test-branch.R | 6 rmonad-0.5.0/rmonad/tests/testthat/test-cache.R | 76 - rmonad-0.5.0/rmonad/tests/testthat/test-codestr.R | 3 rmonad-0.5.0/rmonad/tests/testthat/test-combine.R | 49 rmonad-0.5.0/rmonad/tests/testthat/test-issues.R | 4 rmonad-0.5.0/rmonad/tests/testthat/test-key.R |only rmonad-0.5.0/rmonad/tests/testthat/test-m-star.R | 66 rmonad-0.5.0/rmonad/tests/testthat/test-monad-laws.R |only rmonad-0.5.0/rmonad/tests/testthat/test-nest.R | 15 rmonad-0.5.0/rmonad/tests/testthat/test-nse.R | 72 - rmonad-0.5.0/rmonad/tests/testthat/test-parallel.R |only rmonad-0.5.0/rmonad/tests/testthat/test-tag.R |only rmonad-0.5.0/rmonad/tests/testthat/test-utilities.R |only rmonad-0.5.0/rmonad/tests/testthat/test-view.R |only rmonad-0.5.0/rmonad/vignettes/gff-processing.Rmd | 192 ++ rmonad-0.5.0/rmonad/vignettes/introduction.Rmd | 37 rmonad-0.5.0/rmonad/vignettes/nozzle.Rmd |only 77 files changed, 2895 insertions(+), 1187 deletions(-)
Title: Simultaneous Generation of Count and Continuous Data
Description: Generation of count (assuming Poisson distribution) and continuous data (using Fleishman polynomials) simultaneously.
Author: Hakan Demirtas, Yaru Shi, Rawan Allozi
Maintainer: Rawan Allozi <ralloz2@uic.edu>
Diff between PoisNonNor versions 1.4 dated 2018-01-10 and 1.5 dated 2018-03-10
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++++++++-- R |only man/PoisNonNor-package.Rd | 4 ++-- 4 files changed, 20 insertions(+), 8 deletions(-)
Title: Data Analysis in Ecology
Description: Tools for spatial analysis and model selection in ecology.
Author: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Maintainer: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Diff between pgirmess versions 1.6.7 dated 2017-03-27 and 1.6.8 dated 2018-03-10
DESCRIPTION | 10 +++++----- MD5 | 19 +++++++++++-------- NAMESPACE | 4 ++-- R/thintrack.r | 24 ++++++++++++------------ R/writecn.delim.r |only README.md |only data/preybiom.rda |binary data/siegelp179.rda |binary man/thintrack.rd | 6 +++--- man/transLines2pix.rd | 4 ++-- man/write.delim.rd | 8 ++++---- man/writecn.delim.rd |only 12 files changed, 39 insertions(+), 36 deletions(-)
Title: Landscape Meteorology Tools
Description: Functions to estimate weather variables at any position of a landscape.
Author: Miquel De Cáceres [aut, cre],
Nicolas Martin [aut],
VÃctor Granda [aut],
Antoine Cabon [aut]
Maintainer: Miquel De Cáceres <miquelcaceres@gmail.com>
Diff between meteoland versions 0.6.7 dated 2017-11-15 and 0.7.1 dated 2018-03-10
meteoland-0.6.7/meteoland/R/correctiongrid.R |only meteoland-0.6.7/meteoland/R/downloadAEMETpoints.R |only meteoland-0.6.7/meteoland/R/downloadAEMETstationdata.R |only meteoland-0.6.7/meteoland/man/correctiongrid.Rd |only meteoland-0.6.7/meteoland/man/downloadAEMETpoints.Rd |only meteoland-0.7.1/meteoland/DESCRIPTION | 10 meteoland-0.7.1/meteoland/MD5 | 108 +++-- meteoland-0.7.1/meteoland/NAMESPACE | 21 - meteoland-0.7.1/meteoland/NEWS | 21 + meteoland-0.7.1/meteoland/R/DefineSpatialDataClasses.R | 31 + meteoland-0.7.1/meteoland/R/RcppExports.R | 8 meteoland-0.7.1/meteoland/R/SpatialPixelsMeteorology.R |only meteoland-0.7.1/meteoland/R/SpatialPixelsTopography.R |only meteoland-0.7.1/meteoland/R/SpatialPointsMeteorology.R | 56 +- meteoland-0.7.1/meteoland/R/SpatialPointsTopography.R | 37 + meteoland-0.7.1/meteoland/R/correctionpoints.R | 11 meteoland-0.7.1/meteoland/R/correctionpoints.errors.R | 23 - meteoland-0.7.1/meteoland/R/defaultCorrectionParams.R | 1 meteoland-0.7.1/meteoland/R/defaultInterpolationParams.R | 48 +- meteoland-0.7.1/meteoland/R/downloadAEMETcurrentday.R | 194 ++++------ meteoland-0.7.1/meteoland/R/downloadAEMEThistorical.R |only meteoland-0.7.1/meteoland/R/downloadAEMEThistoricalstationlist.R |only meteoland-0.7.1/meteoland/R/extractNetCDF.R | 5 meteoland-0.7.1/meteoland/R/extractgridpoints.R | 29 + meteoland-0.7.1/meteoland/R/interpolation.calibration.R | 102 +++++ meteoland-0.7.1/meteoland/R/interpolationgrid.R | 2 meteoland-0.7.1/meteoland/R/interpolationpixels.R |only meteoland-0.7.1/meteoland/R/meteoplot.R | 18 meteoland-0.7.1/meteoland/R/readmeteorologypixels.R |only meteoland-0.7.1/meteoland/R/summarygrid.R | 23 - meteoland-0.7.1/meteoland/R/summarypixels.R |only meteoland-0.7.1/meteoland/R/utils.R | 90 ++-- meteoland-0.7.1/meteoland/R/writemeteorologygrid.R | 142 +++---- meteoland-0.7.1/meteoland/R/writemeteorologypixels.R |only meteoland-0.7.1/meteoland/build/vignette.rds |binary meteoland-0.7.1/meteoland/data/examplecorrectiondata.rda |binary meteoland-0.7.1/meteoland/inst/doc/Meteorology.R | 52 +- meteoland-0.7.1/meteoland/inst/doc/Meteorology.Rnw | 88 ++-- meteoland-0.7.1/meteoland/inst/doc/Meteorology.pdf |binary meteoland-0.7.1/meteoland/inst/include/meteoland_RcppExports.h | 16 meteoland-0.7.1/meteoland/man/SpatialPixelsMeteorology-class.Rd |only meteoland-0.7.1/meteoland/man/SpatialPixelsMeteorology.Rd |only meteoland-0.7.1/meteoland/man/SpatialPixelsTopography-class.Rd |only meteoland-0.7.1/meteoland/man/SpatialPixelsTopography.Rd |only meteoland-0.7.1/meteoland/man/SpatialPointsTopography.Rd | 78 ++-- meteoland-0.7.1/meteoland/man/defaultCorrectionParams.Rd | 1 meteoland-0.7.1/meteoland/man/defaultInterpolationParams.Rd | 88 ++-- meteoland-0.7.1/meteoland/man/downloadAEMET.Rd |only meteoland-0.7.1/meteoland/man/extractNetCDF.Rd | 2 meteoland-0.7.1/meteoland/man/extractpointdates.Rd | 2 meteoland-0.7.1/meteoland/man/interpolation.cv.Rd | 5 meteoland-0.7.1/meteoland/man/interpolationpixels.Rd |only meteoland-0.7.1/meteoland/man/meteoplot.Rd | 8 meteoland-0.7.1/meteoland/man/radiation.Rd | 4 meteoland-0.7.1/meteoland/man/readmeteorologygrid.Rd | 80 ++-- meteoland-0.7.1/meteoland/man/spplot.Rd | 76 ++- meteoland-0.7.1/meteoland/man/summarypoints.Rd | 7 meteoland-0.7.1/meteoland/man/writemeteorologypixels.Rd |only meteoland-0.7.1/meteoland/src/RcppExports.cpp | 32 - meteoland-0.7.1/meteoland/src/precipitation.cpp | 11 meteoland-0.7.1/meteoland/src/radiation.cpp | 71 ++- meteoland-0.7.1/meteoland/src/radiation.h | 4 meteoland-0.7.1/meteoland/vignettes/Meteorology-008.pdf |only meteoland-0.7.1/meteoland/vignettes/Meteorology-009.pdf |only meteoland-0.7.1/meteoland/vignettes/Meteorology-011.pdf |only meteoland-0.7.1/meteoland/vignettes/Meteorology-020.pdf |only meteoland-0.7.1/meteoland/vignettes/Meteorology.Rnw | 88 ++-- 67 files changed, 972 insertions(+), 721 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc]
(<https://orcid.org/0000-0002-0734-2199>),
Christoph Burow [aut, trl, dtc]
(<https://orcid.org/0000-0002-5023-4046>),
Michael Dietze [aut] (<https://orcid.org/0000-0001-6063-1726>),
Margret C. Fuchs [aut],
Christoph Schmidt [aut] (<https://orcid.org/0000-0002-2309-3209>),
Manfred Fischer [aut, trl],
Johannes Friedrich [aut],
Norbert Mercier [ctb],
Rachel K. Smedley [ctb] (<https://orcid.org/0000-0001-7773-5193>),
Claire Christophe [ctb],
Antoine Zink [ctb],
Julie Durcan [ctb] (<https://orcid.org/0000-0001-8724-8022>),
Georgina E. King [ctb, dtc] (<https://orcid.org/0000-0003-1059-8192>),
Anne Philippe [ctb],
Guillaume Guerin [ctb],
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Diff between Luminescence versions 0.7.5 dated 2017-06-29 and 0.8.2 dated 2018-03-10
Luminescence-0.7.5/Luminescence/data/BaseDataSet.CosmicDoseRate.RData |only Luminescence-0.7.5/Luminescence/data/ExampleData.BINfileData.RData |only Luminescence-0.7.5/Luminescence/data/ExampleData.CW_OSL_Curve.RData |only Luminescence-0.7.5/Luminescence/data/ExampleData.DeValues.RData |only Luminescence-0.7.5/Luminescence/data/ExampleData.Fading.RData |only Luminescence-0.7.5/Luminescence/data/ExampleData.FittingLM.RData |only Luminescence-0.7.5/Luminescence/data/ExampleData.LxTxData.RData |only Luminescence-0.7.5/Luminescence/data/ExampleData.LxTxOSLData.RData |only Luminescence-0.7.5/Luminescence/data/ExampleData.RLum.Analysis.RData |only Luminescence-0.7.5/Luminescence/data/ExampleData.RLum.Data.Image.RData |only Luminescence-0.7.5/Luminescence/data/ExampleData.XSYG.RData |only Luminescence-0.7.5/Luminescence/data/ExampleData.portableOSL.RData |only Luminescence-0.7.5/Luminescence/inst/doc/index.html |only Luminescence-0.7.5/Luminescence/src/analyse_IRSARRF_SRS.cpp |only Luminescence-0.7.5/Luminescence/src/create_RLumDataCurve_matrix.cpp |only Luminescence-0.7.5/Luminescence/tests/testthat/test_calc_Kars2008.R |only Luminescence-0.8.2/Luminescence/DESCRIPTION | 123 - Luminescence-0.8.2/Luminescence/MD5 | 639 ++++--- Luminescence-0.8.2/Luminescence/NAMESPACE | 10 Luminescence-0.8.2/Luminescence/NEWS | 629 ++----- Luminescence-0.8.2/Luminescence/R/Analyse_SAR.OSLdata.R | 161 +- Luminescence-0.8.2/Luminescence/R/CW2pHMi.R | 149 + Luminescence-0.8.2/Luminescence/R/CW2pLM.R | 71 Luminescence-0.8.2/Luminescence/R/CW2pLMi.R | 124 + Luminescence-0.8.2/Luminescence/R/CW2pPMi.R | 139 + Luminescence-0.8.2/Luminescence/R/Luminescence-package.R | 802 +++++++--- Luminescence-0.8.2/Luminescence/R/PSL2Risoe.BINfileData.R | 29 Luminescence-0.8.2/Luminescence/R/RLum-class.R | 51 Luminescence-0.8.2/Luminescence/R/RLum.Analysis-class.R | 304 ++- Luminescence-0.8.2/Luminescence/R/RLum.Data-class.R | 16 Luminescence-0.8.2/Luminescence/R/RLum.Data.Curve-class.R | 211 +- Luminescence-0.8.2/Luminescence/R/RLum.Data.Image-class.R | 117 - Luminescence-0.8.2/Luminescence/R/RLum.Data.Spectrum-class.R | 119 - Luminescence-0.8.2/Luminescence/R/RLum.Results-class.R | 126 - Luminescence-0.8.2/Luminescence/R/RcppExports.R | 16 Luminescence-0.8.2/Luminescence/R/Risoe.BINfileData2RLum.Analysis.R | 102 - Luminescence-0.8.2/Luminescence/R/Risoe.BINfileData2RLum.Data.Curve.R | 74 Luminescence-0.8.2/Luminescence/R/RisoeBINfileData-class.R | 274 +-- Luminescence-0.8.2/Luminescence/R/Second2Gray.R | 79 Luminescence-0.8.2/Luminescence/R/addins_RLum.R |only Luminescence-0.8.2/Luminescence/R/analyse_Al2O3C_CrossTalk.R |only Luminescence-0.8.2/Luminescence/R/analyse_Al2O3C_ITC.R |only Luminescence-0.8.2/Luminescence/R/analyse_Al2O3C_Measurement.R |only Luminescence-0.8.2/Luminescence/R/analyse_FadingMeasurement.R | 115 - Luminescence-0.8.2/Luminescence/R/analyse_IRSAR.RF.R | 531 +++--- Luminescence-0.8.2/Luminescence/R/analyse_SAR.CWOSL.R | 359 ++-- Luminescence-0.8.2/Luminescence/R/analyse_SAR.TL.R | 117 - Luminescence-0.8.2/Luminescence/R/analyse_baSAR.R | 463 +++-- Luminescence-0.8.2/Luminescence/R/analyse_pIRIRSequence.R | 163 +- Luminescence-0.8.2/Luminescence/R/analyse_portableOSL.R | 34 Luminescence-0.8.2/Luminescence/R/app_RLum.R | 12 Luminescence-0.8.2/Luminescence/R/apply_CosmicRayRemoval.R | 107 - Luminescence-0.8.2/Luminescence/R/apply_EfficiencyCorrection.R | 29 Luminescence-0.8.2/Luminescence/R/bin_RLum.Data.R | 17 Luminescence-0.8.2/Luminescence/R/calc_AliquotSize.R | 138 - Luminescence-0.8.2/Luminescence/R/calc_AverageDose.R | 312 +-- Luminescence-0.8.2/Luminescence/R/calc_CentralDose.R | 108 - Luminescence-0.8.2/Luminescence/R/calc_CommonDose.R | 94 - Luminescence-0.8.2/Luminescence/R/calc_CosmicDoseRate.R | 153 + Luminescence-0.8.2/Luminescence/R/calc_FadingCorr.R | 106 - Luminescence-0.8.2/Luminescence/R/calc_FastRatio.R | 92 - Luminescence-0.8.2/Luminescence/R/calc_FiniteMixture.R | 190 +- Luminescence-0.8.2/Luminescence/R/calc_FuchsLang2001.R | 102 - Luminescence-0.8.2/Luminescence/R/calc_HomogeneityTest.R | 132 - Luminescence-0.8.2/Luminescence/R/calc_Huntley2006.R |only Luminescence-0.8.2/Luminescence/R/calc_IEU.R | 72 Luminescence-0.8.2/Luminescence/R/calc_Kars2008.R | 702 -------- Luminescence-0.8.2/Luminescence/R/calc_Lamothe2003.R |only Luminescence-0.8.2/Luminescence/R/calc_MaxDose.R | 113 - Luminescence-0.8.2/Luminescence/R/calc_MinDose.R | 399 ++-- Luminescence-0.8.2/Luminescence/R/calc_OSLLxTxRatio.R | 205 +- Luminescence-0.8.2/Luminescence/R/calc_SourceDoseRate.R | 133 - Luminescence-0.8.2/Luminescence/R/calc_Statistics.R | 43 Luminescence-0.8.2/Luminescence/R/calc_TLLxTxRatio.R | 83 - Luminescence-0.8.2/Luminescence/R/calc_ThermalLifetime.R | 115 - Luminescence-0.8.2/Luminescence/R/calc_WodaFuchs2008.R |only Luminescence-0.8.2/Luminescence/R/calc_gSGC.R | 66 Luminescence-0.8.2/Luminescence/R/convert_Activity2Concentration.R |only Luminescence-0.8.2/Luminescence/R/convert_BIN2CSV.R | 30 Luminescence-0.8.2/Luminescence/R/convert_Daybreak2CSV.R | 30 Luminescence-0.8.2/Luminescence/R/convert_PSL2CSV.R | 24 Luminescence-0.8.2/Luminescence/R/convert_RLum2Risoe.BINfileData.R |only Luminescence-0.8.2/Luminescence/R/convert_XSYG2CSV.R | 30 Luminescence-0.8.2/Luminescence/R/extract_IrradiationTimes.R | 108 - Luminescence-0.8.2/Luminescence/R/fit_CWCurve.R | 271 ++- Luminescence-0.8.2/Luminescence/R/fit_LMCurve.R | 250 +-- Luminescence-0.8.2/Luminescence/R/fit_SurfaceExposure.R |only Luminescence-0.8.2/Luminescence/R/get_Layout.R | 22 Luminescence-0.8.2/Luminescence/R/get_Quote.R | 19 Luminescence-0.8.2/Luminescence/R/get_RLum.R | 101 - Luminescence-0.8.2/Luminescence/R/get_Risoe.BINfileData.R | 29 Luminescence-0.8.2/Luminescence/R/get_rightAnswer.R | 5 Luminescence-0.8.2/Luminescence/R/github.R | 64 Luminescence-0.8.2/Luminescence/R/install_DevelopmentVersion.R | 16 Luminescence-0.8.2/Luminescence/R/internal_as.latex.table.R | 189 +- Luminescence-0.8.2/Luminescence/R/internals_RLum.R | 181 ++ Luminescence-0.8.2/Luminescence/R/length_RLum.R | 22 Luminescence-0.8.2/Luminescence/R/merge_RLum.Analysis.R | 49 Luminescence-0.8.2/Luminescence/R/merge_RLum.Data.Curve.R | 96 - Luminescence-0.8.2/Luminescence/R/merge_RLum.R | 35 Luminescence-0.8.2/Luminescence/R/merge_RLum.Results.R | 16 Luminescence-0.8.2/Luminescence/R/merge_Risoe.BINfileData.R | 69 Luminescence-0.8.2/Luminescence/R/methods_DRAC.R | 18 Luminescence-0.8.2/Luminescence/R/methods_RLum.R | 74 Luminescence-0.8.2/Luminescence/R/model_LuminescenceSignals.R | 34 Luminescence-0.8.2/Luminescence/R/names_RLum.R | 56 Luminescence-0.8.2/Luminescence/R/plot_AbanicoPlot.R | 370 ++-- Luminescence-0.8.2/Luminescence/R/plot_DRTResults.R | 293 +-- Luminescence-0.8.2/Luminescence/R/plot_DetPlot.R | 119 - Luminescence-0.8.2/Luminescence/R/plot_FilterCombinations.R | 128 - Luminescence-0.8.2/Luminescence/R/plot_GrowthCurve.R | 644 +++++--- Luminescence-0.8.2/Luminescence/R/plot_Histogram.R | 132 - Luminescence-0.8.2/Luminescence/R/plot_KDE.R | 150 - Luminescence-0.8.2/Luminescence/R/plot_NRt.R | 45 Luminescence-0.8.2/Luminescence/R/plot_RLum.Analysis.R | 111 - Luminescence-0.8.2/Luminescence/R/plot_RLum.Data.Curve.R | 36 Luminescence-0.8.2/Luminescence/R/plot_RLum.Data.Image.R | 84 - Luminescence-0.8.2/Luminescence/R/plot_RLum.Data.Spectrum.R | 201 +- Luminescence-0.8.2/Luminescence/R/plot_RLum.R | 74 Luminescence-0.8.2/Luminescence/R/plot_RLum.Results.R | 557 +++--- Luminescence-0.8.2/Luminescence/R/plot_RadialPlot.R | 194 +- Luminescence-0.8.2/Luminescence/R/plot_Risoe.BINfileData.R | 108 - Luminescence-0.8.2/Luminescence/R/plot_ViolinPlot.R | 94 - Luminescence-0.8.2/Luminescence/R/read_BIN2R.R | 204 +- Luminescence-0.8.2/Luminescence/R/read_Daybreak2R.R | 62 Luminescence-0.8.2/Luminescence/R/read_PSL2R.R | 62 Luminescence-0.8.2/Luminescence/R/read_SPE2R.R | 130 + Luminescence-0.8.2/Luminescence/R/read_XSYG2R.R | 319 ++- Luminescence-0.8.2/Luminescence/R/replicate_RLum.R | 17 Luminescence-0.8.2/Luminescence/R/report_RLum.R | 104 - Luminescence-0.8.2/Luminescence/R/set_RLum.R | 61 Luminescence-0.8.2/Luminescence/R/set_Risoe.BINfileData.R | 21 Luminescence-0.8.2/Luminescence/R/smooth_RLum.R | 33 Luminescence-0.8.2/Luminescence/R/structure_RLum.R | 51 Luminescence-0.8.2/Luminescence/R/template_DRAC.R | 467 +++-- Luminescence-0.8.2/Luminescence/R/tune_Data.R | 29 Luminescence-0.8.2/Luminescence/R/use_DRAC.R | 89 - Luminescence-0.8.2/Luminescence/R/utils_DRAC.R |only Luminescence-0.8.2/Luminescence/R/verify_SingleGrainData.R | 132 - Luminescence-0.8.2/Luminescence/R/write_R2BIN.R | 159 + Luminescence-0.8.2/Luminescence/R/write_RLum2CSV.R | 56 Luminescence-0.8.2/Luminescence/R/zzz.R | 27 Luminescence-0.8.2/Luminescence/build |only Luminescence-0.8.2/Luminescence/data/BaseDataSet.CosmicDoseRate.rda 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Luminescence-0.8.2/Luminescence/man/calc_CommonDose.Rd | 83 - Luminescence-0.8.2/Luminescence/man/calc_CosmicDoseRate.Rd | 123 - Luminescence-0.8.2/Luminescence/man/calc_FadingCorr.Rd | 103 - Luminescence-0.8.2/Luminescence/man/calc_FastRatio.Rd | 100 - Luminescence-0.8.2/Luminescence/man/calc_FiniteMixture.Rd | 151 + Luminescence-0.8.2/Luminescence/man/calc_FuchsLang2001.Rd | 77 Luminescence-0.8.2/Luminescence/man/calc_HomogeneityTest.Rd | 41 Luminescence-0.8.2/Luminescence/man/calc_Huntley2006.Rd |only Luminescence-0.8.2/Luminescence/man/calc_IEU.Rd | 64 Luminescence-0.8.2/Luminescence/man/calc_Kars2008.Rd | 137 - Luminescence-0.8.2/Luminescence/man/calc_Lamothe2003.Rd |only Luminescence-0.8.2/Luminescence/man/calc_MaxDose.Rd | 114 - Luminescence-0.8.2/Luminescence/man/calc_MinDose.Rd | 191 +- Luminescence-0.8.2/Luminescence/man/calc_OSLLxTxRatio.Rd | 165 +- Luminescence-0.8.2/Luminescence/man/calc_SourceDoseRate.Rd | 112 - Luminescence-0.8.2/Luminescence/man/calc_Statistics.Rd | 40 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Luminescence-0.8.2/Luminescence/man/get_Layout.Rd | 17 Luminescence-0.8.2/Luminescence/man/get_Quote.Rd | 12 Luminescence-0.8.2/Luminescence/man/get_RLum.Rd | 47 Luminescence-0.8.2/Luminescence/man/get_Risoe.BINfileData.Rd | 24 Luminescence-0.8.2/Luminescence/man/get_rightAnswer.Rd | 4 Luminescence-0.8.2/Luminescence/man/install_DevelopmentVersion.Rd | 12 Luminescence-0.8.2/Luminescence/man/length_RLum.Rd | 25 Luminescence-0.8.2/Luminescence/man/merge_RLum.Analysis.Rd | 55 Luminescence-0.8.2/Luminescence/man/merge_RLum.Data.Curve.Rd | 94 - Luminescence-0.8.2/Luminescence/man/merge_RLum.Rd | 46 Luminescence-0.8.2/Luminescence/man/merge_RLum.Results.Rd | 15 Luminescence-0.8.2/Luminescence/man/merge_Risoe.BINfileData.Rd | 56 Luminescence-0.8.2/Luminescence/man/methods_RLum.Rd | 65 Luminescence-0.8.2/Luminescence/man/model_LuminescenceSignals.Rd | 18 Luminescence-0.8.2/Luminescence/man/names_RLum.Rd | 38 Luminescence-0.8.2/Luminescence/man/plot_AbanicoPlot.Rd | 289 ++- Luminescence-0.8.2/Luminescence/man/plot_DRTResults.Rd | 115 - Luminescence-0.8.2/Luminescence/man/plot_DetPlot.Rd | 101 - Luminescence-0.8.2/Luminescence/man/plot_FilterCombinations.Rd | 108 - Luminescence-0.8.2/Luminescence/man/plot_GrowthCurve.Rd | 287 ++- Luminescence-0.8.2/Luminescence/man/plot_Histogram.Rd | 99 - Luminescence-0.8.2/Luminescence/man/plot_KDE.Rd | 101 - Luminescence-0.8.2/Luminescence/man/plot_NRt.Rd | 40 Luminescence-0.8.2/Luminescence/man/plot_RLum.Analysis.Rd | 96 - Luminescence-0.8.2/Luminescence/man/plot_RLum.Data.Curve.Rd | 47 Luminescence-0.8.2/Luminescence/man/plot_RLum.Data.Image.Rd | 67 Luminescence-0.8.2/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 179 +- Luminescence-0.8.2/Luminescence/man/plot_RLum.Rd | 66 Luminescence-0.8.2/Luminescence/man/plot_RLum.Results.Rd | 39 Luminescence-0.8.2/Luminescence/man/plot_RadialPlot.Rd | 177 +- Luminescence-0.8.2/Luminescence/man/plot_Risoe.BINfileData.Rd | 82 - Luminescence-0.8.2/Luminescence/man/plot_ViolinPlot.Rd | 65 Luminescence-0.8.2/Luminescence/man/read_BIN2R.Rd | 128 - Luminescence-0.8.2/Luminescence/man/read_Daybreak2R.Rd | 57 Luminescence-0.8.2/Luminescence/man/read_PSL2R.Rd | 63 Luminescence-0.8.2/Luminescence/man/read_SPE2R.Rd | 61 Luminescence-0.8.2/Luminescence/man/read_XSYG2R.Rd | 154 + Luminescence-0.8.2/Luminescence/man/replicate_RLum.Rd | 18 Luminescence-0.8.2/Luminescence/man/report_RLum.Rd | 68 Luminescence-0.8.2/Luminescence/man/sTeve.Rd | 28 Luminescence-0.8.2/Luminescence/man/set_RLum.Rd | 53 Luminescence-0.8.2/Luminescence/man/set_Risoe.BINfileData.Rd | 16 Luminescence-0.8.2/Luminescence/man/smooth_RLum.Rd | 27 Luminescence-0.8.2/Luminescence/man/structure_RLum.Rd | 40 Luminescence-0.8.2/Luminescence/man/template_DRAC.Rd | 46 Luminescence-0.8.2/Luminescence/man/tune_Data.Rd | 36 Luminescence-0.8.2/Luminescence/man/use_DRAC.Rd | 58 Luminescence-0.8.2/Luminescence/man/verify_SingleGrainData.Rd | 134 - Luminescence-0.8.2/Luminescence/man/write_R2BIN.Rd | 68 Luminescence-0.8.2/Luminescence/man/write_RLum2CSV.Rd | 59 Luminescence-0.8.2/Luminescence/src/Luminescence_init.c | 28 Luminescence-0.8.2/Luminescence/src/Makevars |only Luminescence-0.8.2/Luminescence/src/RcppExports.cpp | 23 Luminescence-0.8.2/Luminescence/src/create_UID.cpp | 14 Luminescence-0.8.2/Luminescence/src/src_analyse_IRSARRF_SRS.cpp |only Luminescence-0.8.2/Luminescence/src/src_create_RLumDataCurve_matrix.cpp |only Luminescence-0.8.2/Luminescence/src/src_get_XSYG_curve_values.cpp |only Luminescence-0.8.2/Luminescence/tests/testthat/test_Analyse_SAROSLdata.R | 30 Luminescence-0.8.2/Luminescence/tests/testthat/test_RLum.Analysis-class.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_RLum.Data.Curve.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_RLum.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_RisoeBINfileData-class.R | 5 Luminescence-0.8.2/Luminescence/tests/testthat/test_analyse_Al2O3C_CrossTalk.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_analyse_Al2O3C_ITC.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_analyse_Al2O3C_Measurement.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_analyse_IRSARRF.R | 6 Luminescence-0.8.2/Luminescence/tests/testthat/test_analyse_baSAR.R | 10 Luminescence-0.8.2/Luminescence/tests/testthat/test_app_RLum.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_apply_CosmicRayRemoval.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_apply_EfficiencyCorrection.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_as_latex_table.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_calc_AliquotSize.R | 12 Luminescence-0.8.2/Luminescence/tests/testthat/test_calc_HomogeneityTest.R | 26 Luminescence-0.8.2/Luminescence/tests/testthat/test_calc_Huntley2008.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_calc_IEU.R | 54 Luminescence-0.8.2/Luminescence/tests/testthat/test_calc_Lamothe2003.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_calc_MaxDose.R | 16 Luminescence-0.8.2/Luminescence/tests/testthat/test_calc_OSLLxTxRatio.R | 274 +++ Luminescence-0.8.2/Luminescence/tests/testthat/test_calc_SourceDoseRate.R | 48 Luminescence-0.8.2/Luminescence/tests/testthat/test_calc_Statistics.R | 6 Luminescence-0.8.2/Luminescence/tests/testthat/test_calc_ThermalLifetime.R | 23 Luminescence-0.8.2/Luminescence/tests/testthat/test_calc_WodaFuchs2008.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_calc_gSGC.R | 28 Luminescence-0.8.2/Luminescence/tests/testthat/test_convert_Activity2Concentration.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_convert_PSL2CSV.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_convert_RLum2Risoe.BINfileData.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_extract_IrradiationTimes.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_fit_CWCurve.R | 6 Luminescence-0.8.2/Luminescence/tests/testthat/test_fit_LMCurve.R | 16 Luminescence-0.8.2/Luminescence/tests/testthat/test_fit_SurfaceExposure.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_get_RLum.R | 11 Luminescence-0.8.2/Luminescence/tests/testthat/test_github.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_internals.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_methods_DRAC.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_model_LuminescenceSignals.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_plot_AbanicoPlot.R | 11 Luminescence-0.8.2/Luminescence/tests/testthat/test_plot_Functions.R | 12 Luminescence-0.8.2/Luminescence/tests/testthat/test_plot_GrowthCurve.R | 16 Luminescence-0.8.2/Luminescence/tests/testthat/test_plot_RLum.Analysis.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_read_BIN2R.R | 3 Luminescence-0.8.2/Luminescence/tests/testthat/test_read_Daybreak2R.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_read_PSL2R.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_read_SPE2R.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_read_XSYG2R.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_replicate_RLum.R | 1 Luminescence-0.8.2/Luminescence/tests/testthat/test_report_RLum.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_smooth_RLum.R | 14 Luminescence-0.8.2/Luminescence/tests/testthat/test_subset_RLum.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_template_DRAC.R | 28 Luminescence-0.8.2/Luminescence/tests/testthat/test_use_DRAC.R |only Luminescence-0.8.2/Luminescence/tests/testthat/test_verify_SingleGrainData.R | 12 Luminescence-0.8.2/Luminescence/tests/testthat/test_write_R2BIN.R | 91 - Luminescence-0.8.2/Luminescence/tests/testthat/test_zzz.R | 14 Luminescence-0.8.2/Luminescence/vignettes |only 363 files changed, 15428 insertions(+), 12788 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating random
and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between igraph versions 1.1.2 dated 2017-07-21 and 1.2.1 dated 2018-03-10
igraph-1.1.2/igraph/R/mgclust.R |only igraph-1.1.2/igraph/man/gclust.app.Rd |only igraph-1.1.2/igraph/man/gclust.rsvt.Rd |only igraph-1.1.2/igraph/man/getAICc.Rd |only igraph-1.1.2/igraph/src/glpk |only igraph-1.2.1/igraph/DESCRIPTION | 31 igraph-1.2.1/igraph/MD5 | 352 ++----- igraph-1.2.1/igraph/NAMESPACE | 5 igraph-1.2.1/igraph/R/community.R | 51 - igraph-1.2.1/igraph/R/conversion.R | 4 igraph-1.2.1/igraph/R/foreign.R | 7 igraph-1.2.1/igraph/R/games.R | 13 igraph-1.2.1/igraph/R/iterators.R | 2 igraph-1.2.1/igraph/R/nexus.R | 5 igraph-1.2.1/igraph/R/palette.R | 9 igraph-1.2.1/igraph/R/plot.R | 4 igraph-1.2.1/igraph/R/print.R | 2 igraph-1.2.1/igraph/R/structural.properties.R | 2 igraph-1.2.1/igraph/R/tkplot.R | 15 igraph-1.2.1/igraph/configure | 105 +- igraph-1.2.1/igraph/configure.ac | 32 igraph-1.2.1/igraph/inst/NEWS.md | 9 igraph-1.2.1/igraph/man/as_graphnel.Rd | 1 igraph-1.2.1/igraph/man/categorical_pal.Rd | 10 igraph-1.2.1/igraph/man/cluster_infomap.Rd | 2 igraph-1.2.1/igraph/man/cluster_optimal.Rd | 27 igraph-1.2.1/igraph/man/cluster_spinglass.Rd | 6 igraph-1.2.1/igraph/man/graph_from_graphdb.Rd | 5 igraph-1.2.1/igraph/man/graph_from_graphnel.Rd | 1 igraph-1.2.1/igraph/man/igraph-es-indexing.Rd | 2 igraph-1.2.1/igraph/man/nexus.Rd | 7 igraph-1.2.1/igraph/man/plot.igraph.Rd | 4 igraph-1.2.1/igraph/man/print.igraph.Rd | 2 igraph-1.2.1/igraph/man/reciprocity.Rd | 2 igraph-1.2.1/igraph/man/sample_islands.Rd | 5 igraph-1.2.1/igraph/man/tkplot.Rd | 18 igraph-1.2.1/igraph/src/Makevars.in | 6 igraph-1.2.1/igraph/src/Makevars.win | 6 igraph-1.2.1/igraph/src/bipartite.c | 13 igraph-1.2.1/igraph/src/bliss/graph.cc | 3 igraph-1.2.1/igraph/src/centrality.c | 84 + igraph-1.2.1/igraph/src/coloring.c |only igraph-1.2.1/igraph/src/community.c | 16 igraph-1.2.1/igraph/src/conversion.c | 1 igraph-1.2.1/igraph/src/cs/cs_amd.c | 3 igraph-1.2.1/igraph/src/cs/cs_lu.c | 2 igraph-1.2.1/igraph/src/cs/cs_malloc.c | 2 igraph-1.2.1/igraph/src/cs/cs_qr.c | 2 igraph-1.2.1/igraph/src/cs/cs_randperm.c | 2 igraph-1.2.1/igraph/src/decomposition.c | 5 igraph-1.2.1/igraph/src/foreign-dl-lexer.c | 313 +++--- igraph-1.2.1/igraph/src/foreign-dl-lexer.l | 12 igraph-1.2.1/igraph/src/foreign-dl-parser.c | 261 ++--- igraph-1.2.1/igraph/src/foreign-dl-parser.h | 8 igraph-1.2.1/igraph/src/foreign-dl-parser.y | 6 igraph-1.2.1/igraph/src/foreign-gml-lexer.c | 53 - igraph-1.2.1/igraph/src/foreign-gml-lexer.l | 13 igraph-1.2.1/igraph/src/foreign-gml-parser.c | 103 +- igraph-1.2.1/igraph/src/foreign-gml-parser.h | 8 igraph-1.2.1/igraph/src/foreign-gml-parser.y | 10 igraph-1.2.1/igraph/src/foreign-graphml.c | 10 igraph-1.2.1/igraph/src/foreign-lgl-lexer.c | 45 igraph-1.2.1/igraph/src/foreign-lgl-lexer.l | 13 igraph-1.2.1/igraph/src/foreign-lgl-parser.c | 64 - igraph-1.2.1/igraph/src/foreign-lgl-parser.h | 8 igraph-1.2.1/igraph/src/foreign-lgl-parser.y | 10 igraph-1.2.1/igraph/src/foreign-ncol-lexer.c | 40 igraph-1.2.1/igraph/src/foreign-ncol-lexer.l | 14 igraph-1.2.1/igraph/src/foreign-ncol-parser.c | 52 - igraph-1.2.1/igraph/src/foreign-ncol-parser.h | 8 igraph-1.2.1/igraph/src/foreign-ncol-parser.y | 6 igraph-1.2.1/igraph/src/foreign-pajek-lexer.c | 125 +- igraph-1.2.1/igraph/src/foreign-pajek-lexer.l | 14 igraph-1.2.1/igraph/src/foreign-pajek-parser.c | 583 +++++------- igraph-1.2.1/igraph/src/foreign-pajek-parser.h | 150 +-- igraph-1.2.1/igraph/src/foreign-pajek-parser.y | 18 igraph-1.2.1/igraph/src/foreign.c | 2 igraph-1.2.1/igraph/src/games.c | 20 igraph-1.2.1/igraph/src/glpk_support.c | 9 igraph-1.2.1/igraph/src/igraph_hrg.cc | 18 igraph-1.2.1/igraph/src/igraph_math.h | 11 igraph-1.2.1/igraph/src/igraph_version.h | 2 igraph-1.2.1/igraph/src/include/igraph.h | 1 igraph-1.2.1/igraph/src/include/igraph_adjlist.h | 2 igraph-1.2.1/igraph/src/include/igraph_coloring.h |only igraph-1.2.1/igraph/src/include/igraph_eigen.h | 1 igraph-1.2.1/igraph/src/include/igraph_matrix_pmt.h | 4 igraph-1.2.1/igraph/src/include/igraph_paths.h | 7 igraph-1.2.1/igraph/src/include/igraph_vector_pmt.h | 4 igraph-1.2.1/igraph/src/lad.c | 3 igraph-1.2.1/igraph/src/math.c | 62 + igraph-1.2.1/igraph/src/matrix.pmt | 4 igraph-1.2.1/igraph/src/microscopic_update.c | 4 igraph-1.2.1/igraph/src/qsort.c | 5 igraph-1.2.1/igraph/src/random.c | 26 igraph-1.2.1/igraph/src/random_walk.c | 173 +++ igraph-1.2.1/igraph/src/rinterface.c | 4 igraph-1.2.1/igraph/src/separators.c | 4 igraph-1.2.1/igraph/src/spectral_properties.c | 2 igraph-1.2.1/igraph/src/structural_properties.c | 37 igraph-1.2.1/igraph/src/structural_properties_internal.h | 6 igraph-1.2.1/igraph/src/structure_generators.c | 7 igraph-1.2.1/igraph/src/vector.pmt | 9 igraph-1.2.1/igraph/tests/testthat/helper.R |only igraph-1.2.1/igraph/tests/testthat/test_authority.score.R | 3 igraph-1.2.1/igraph/tests/testthat/test_communities.R | 5 igraph-1.2.1/igraph/tests/testthat/test_optimal.community.R | 4 107 files changed, 1784 insertions(+), 1487 deletions(-)
Title: Pretty Time of Day
Description: Implements an S3 class for storing and formatting time-of-day
values, based on the 'difftime' class.
Author: Kirill Müller [aut, cre],
The R Consortium [fnd]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between hms versions 0.4.1 dated 2018-01-24 and 0.4.2 dated 2018-03-10
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ man/hms.Rd | 1 - tests/testthat/out/hm.txt | 10 +++++----- tests/testthat/out/hms.txt | 18 +++++++++--------- tests/testthat/out/hmss.txt | 18 +++++++++--------- tests/testthat/out/ms.txt | 10 +++++----- tests/testthat/out/mss.txt | 14 +++++++------- 9 files changed, 53 insertions(+), 49 deletions(-)
Title: Utilities for Dates and Times
Description: Utilities for handling dates and times, such
as selecting particular days of the week or month,
formatting timestamps as required by RSS feeds, or
converting timestamp representations of other software
(such as 'MATLAB' and 'Excel') to R. The package is
lightweight (no dependencies, pure R implementations) and
relies only on R's standard classes to represent dates
and times ('Date' and 'POSIXt'); it aims to provide
efficient implementations, through vectorisation and the
use of R's native numeric representations of timestamps
where possible.
Author: Enrico Schumann [aut, cre] (<https://orcid.org/0000-0001-7601-6576>)
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between datetimeutils versions 0.2-7 dated 2017-08-28 and 0.2-12 dated 2018-03-10
datetimeutils-0.2-12/datetimeutils/DESCRIPTION | 13 datetimeutils-0.2-12/datetimeutils/MD5 | 50 datetimeutils-0.2-12/datetimeutils/NAMESPACE | 61 datetimeutils-0.2-12/datetimeutils/NEWS | 189 +- datetimeutils-0.2-12/datetimeutils/R/functions.R | 778 +++++----- datetimeutils-0.2-12/datetimeutils/README.md | 80 - datetimeutils-0.2-12/datetimeutils/build/partial.rdb |binary datetimeutils-0.2-12/datetimeutils/build/vignette.rds |binary datetimeutils-0.2-12/datetimeutils/inst/doc/datetimeutils_examples.R | 107 - datetimeutils-0.2-12/datetimeutils/inst/doc/datetimeutils_examples.Rnw | 175 +- datetimeutils-0.2-12/datetimeutils/inst/doc/datetimeutils_examples.pdf |binary datetimeutils-0.2-12/datetimeutils/inst/unitTests/runTests.R | 44 datetimeutils-0.2-12/datetimeutils/inst/unitTests/test_results.txt | 65 datetimeutils-0.2-12/datetimeutils/inst/unitTests/ut_datetime.R | 626 ++++---- datetimeutils-0.2-12/datetimeutils/man/business_days.Rd | 164 +- datetimeutils-0.2-12/datetimeutils/man/convertDate.Rd | 96 - datetimeutils-0.2-12/datetimeutils/man/convertTZ.Rd | 116 - datetimeutils-0.2-12/datetimeutils/man/datetimeutils-package.Rd | 52 datetimeutils-0.2-12/datetimeutils/man/end_of_period.Rd | 193 +- datetimeutils-0.2-12/datetimeutils/man/guess_datetime.Rd | 164 +- datetimeutils-0.2-12/datetimeutils/man/lastWeekday.Rd | 168 +- datetimeutils-0.2-12/datetimeutils/man/nth_day.Rd |only datetimeutils-0.2-12/datetimeutils/man/rfc822t.Rd | 88 - datetimeutils-0.2-12/datetimeutils/man/roundPOSIXt.Rd | 112 - datetimeutils-0.2-12/datetimeutils/man/timegrid.Rd | 181 +- datetimeutils-0.2-12/datetimeutils/vignettes/datetimeutils_examples.Rnw | 175 +- datetimeutils-0.2-7/datetimeutils/ChangeLog |only 27 files changed, 1960 insertions(+), 1737 deletions(-)
Title: Relational Query Generator for Data Manipulation at Scale
Description: A 'SQL' query generator based on Edgar F. Codd's relational
algebra and experience using 'SQL' and 'dplyr' at big data
scale. The design represents an attempt to make 'SQL' more teachable by
denoting composition by a sequential pipeline notation instead of nested
queries or functions. The implementation delivers reliable high
performance data processing on large data systems such as `Spark`
and databases. Package features include: data processing trees
or pipelines as observable objects (able to report both columns
produced and columns used), optimized 'SQL' generation as an explicit
user visible modeling step, and convenience methods for applying query
trees to in-memory 'data.frame's.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rquery versions 0.3.1 dated 2018-02-10 and 0.4.0 dated 2018-03-10
rquery-0.3.1/rquery/man/execute_data_frame.Rd |only rquery-0.3.1/rquery/man/to_pre_sql.Rd |only rquery-0.4.0/rquery/DESCRIPTION | 28 + rquery-0.4.0/rquery/MD5 | 97 ++++-- rquery-0.4.0/rquery/NAMESPACE | 27 + rquery-0.4.0/rquery/NEWS.md | 13 rquery-0.4.0/rquery/R/ex_data_frame.R | 187 +++++++------ rquery-0.4.0/rquery/R/extend.R | 26 + rquery-0.4.0/rquery/R/materialize.R | 240 +++++++++++++++-- rquery-0.4.0/rquery/R/natural_join.R | 38 +- rquery-0.4.0/rquery/R/non_sql_node.R |only rquery-0.4.0/rquery/R/order_by.R | 27 + rquery-0.4.0/rquery/R/package.R | 5 rquery-0.4.0/rquery/R/pre_sql.R | 3 rquery-0.4.0/rquery/R/project.R | 87 ++++-- rquery-0.4.0/rquery/R/relop.R | 49 +-- rquery-0.4.0/rquery/R/rename.R | 21 - rquery-0.4.0/rquery/R/rsummary.R |only rquery-0.4.0/rquery/R/select_columns.R | 21 - rquery-0.4.0/rquery/R/select_rows.R | 23 - rquery-0.4.0/rquery/R/sql_node.R | 186 ++++++++++--- rquery-0.4.0/rquery/R/table_source.R | 70 +--- rquery-0.4.0/rquery/R/theta_join.R | 40 +- rquery-0.4.0/rquery/R/tokenize_for_sql.R | 125 ++++++-- rquery-0.4.0/rquery/R/utils.R | 55 --- rquery-0.4.0/rquery/R/work_with_NULLs.R |only rquery-0.4.0/rquery/README.md | 31 -- rquery-0.4.0/rquery/build/vignette.rds |binary rquery-0.4.0/rquery/inst/doc/AssigmentPartitioner.html | 5 rquery-0.4.0/rquery/inst/doc/QueryGeneration.R | 9 rquery-0.4.0/rquery/inst/doc/QueryGeneration.Rmd | 9 rquery-0.4.0/rquery/inst/doc/QueryGeneration.html | 4 rquery-0.4.0/rquery/inst/doc/rquery_intro.R |only rquery-0.4.0/rquery/inst/doc/rquery_intro.Rmd |only rquery-0.4.0/rquery/inst/doc/rquery_intro.html |only rquery-0.4.0/rquery/man/count_null_cols.Rd |only rquery-0.4.0/rquery/man/dbi_table.Rd | 3 rquery-0.4.0/rquery/man/execute.Rd |only rquery-0.4.0/rquery/man/mark_null_cols.Rd |only rquery-0.4.0/rquery/man/materialize.Rd | 15 - rquery-0.4.0/rquery/man/materialize_node.Rd |only rquery-0.4.0/rquery/man/non_sql_node.Rd |only rquery-0.4.0/rquery/man/project_nse.Rd | 32 +- rquery-0.4.0/rquery/man/project_se.Rd | 32 +- rquery-0.4.0/rquery/man/replace_null_cols.Rd |only rquery-0.4.0/rquery/man/rquery_apply_to_data_frame.Rd | 31 -- rquery-0.4.0/rquery/man/rsummary.Rd |only rquery-0.4.0/rquery/man/rsummary_node.Rd |only rquery-0.4.0/rquery/man/sql_node.Rd | 66 +++- rquery-0.4.0/rquery/man/table_source.Rd | 4 rquery-0.4.0/rquery/man/tables_used.Rd | 2 rquery-0.4.0/rquery/man/to_sql.Rd | 4 rquery-0.4.0/rquery/man/tokenize_for_SQL.Rd | 2 rquery-0.4.0/rquery/man/wrapr_function.relop.Rd |only rquery-0.4.0/rquery/tests/testthat/test_parse.R | 8 rquery-0.4.0/rquery/tests/testthat/test_translation.R |only rquery-0.4.0/rquery/vignettes/QueryGeneration.Rmd | 9 rquery-0.4.0/rquery/vignettes/narrow.png |only rquery-0.4.0/rquery/vignettes/rquery_intro.Rmd |only rquery-0.4.0/rquery/vignettes/runtimes_1.png |only 60 files changed, 1044 insertions(+), 590 deletions(-)
Title: Dynamic Ensembles for Time Series Forecasting
Description: A framework for dynamically combining forecasting models for time series forecasting predictive tasks. It leverages machine learning models from other packages to automatically combine expert advice using metalearning and other state-of-the-art forecasting combination approaches. The predictive methods receive a data matrix as input, representing an embedded time series, and return a predictive ensemble model. The ensemble use generic functions 'predict()' and 'forecast()' to forecast future values of the time series. Moreover, an ensemble can be updated using methods, such as 'update_weights()' or 'update_base_models()'. A complete description of the methods can be found in: Cerqueira, V., Torgo, L., Pinto, F., and Soares, C. "Arbitrated Ensemble for Time Series Forecasting." to appear at: Joint European Conference on Machine Learning and Knowledge Discovery in Databases. Springer International Publishing, 2017; and Cerqueira, V., Torgo, L., and Soares, C.: "Arbitrated Ensemble for Solar Radiation Forecasting." International Work-Conference on Artificial Neural Networks. Springer, 2017 <doi:10.1007/978-3-319-59153-7_62>.
Author: Vitor Cerqueira [aut, cre],
Luis Torgo [ctb],
Carlos Soares [ctb]
Maintainer: Vitor Cerqueira <cerqueira.vitormanuel@gmail.com>
Diff between tsensembler versions 0.0.2 dated 2017-08-28 and 0.0.3 dated 2018-03-10
DESCRIPTION | 12 - MD5 | 77 +++++--- NAMESPACE | 17 + R/all-classes.r | 98 +++++++++- R/arbitration-methods.r | 58 +++--- R/base-models.r | 341 ++++++++++++++++++++++++++++++++----- R/build-base-ensemble.r | 4 R/ensembling-pipes.R | 37 ++-- R/forecast.R | 29 ++- R/meta-modeling.R |only R/metrics.r | 4 R/out-of-bag-pipes.r | 16 + R/predict-methods.r | 76 ++++++-- R/sequential-reweight.R |only R/ts-preprocess.R | 12 + R/utils.R | 29 ++- README.md | 2 man/ADE-class.Rd | 21 ++ man/ADE.Rd | 22 ++ man/DETS-class.Rd | 5 man/DETS.Rd | 7 man/ae.Rd | 2 man/arima_offline_forecast.Rd |only man/arima_online_forecast.Rd |only man/base_models_loss.Rd | 4 man/blocked_prequential.Rd | 2 man/bm_auto_arima.Rd |only man/intraining_estimations.Rd | 5 man/loss_meta_learn.Rd |only man/meta_gp.Rd |only man/meta_gp_predict.Rd |only man/meta_lasso.Rd |only man/meta_lasso_predict.Rd |only man/meta_predict.Rd |only man/meta_rf.Rd |only man/meta_rf_predict.Rd |only man/predict_pls_pcr.Rd |only man/se.Rd | 2 man/sequential_reweighting.Rd |only man/sliding_similarity.Rd |only man/soft.completion.Rd |only man/train_ade.Rd | 4 tests/testthat/test-ade.r | 10 - tests/testthat/test-erfc.R | 24 +- tests/testthat/test-fifo.R | 2 tests/testthat/test-predict.r | 2 tests/testthat/test-recentseries.R | 2 tests/testthat/test-selectbest.r | 2 48 files changed, 742 insertions(+), 186 deletions(-)
Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other
'dplyr' inspired syntactic style when calculating summary statistics on survey
data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre],
Thomas Lumley [ctb]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>
Diff between srvyr versions 0.3.0 dated 2018-01-23 and 0.3.1 dated 2018-03-10
DESCRIPTION | 8 MD5 | 39 +- NEWS.md | 9 R/lazy_tbl.r | 24 + R/tbl-svy.r | 2 inst/doc/extending-srvyr.html | 4 inst/doc/srvyr-database.R | 355 +++++++++++++------------- inst/doc/srvyr-database.Rmd | 13 inst/doc/srvyr-database.html | 290 ++++++++++++++++++--- inst/doc/srvyr-vs-survey.html | 22 - tests/testthat/test_as_survey_twophase.r | 5 tests/testthat/test_basic_example.r | 1 tests/testthat/test_cascade.r | 4 tests/testthat/test_database.R | 45 ++- tests/testthat/test_survey_mean_factor.r | 5 tests/testthat/test_survey_package.r | 3 tests/testthat/test_survey_proportion.R | 5 tests/testthat/test_survey_statistics.r | 9 tests/testthat/test_survey_statistics_basic.r | 5 tests/testthat/utilities.R |only vignettes/srvyr-database.Rmd | 13 21 files changed, 582 insertions(+), 279 deletions(-)
Title: Pediatric Complex Chronic Conditions
Description: An implementation of the pediatric complex chronic conditions (CCC)
classification system using R and C++.
Author: Peter DeWitt [aut],
Tell Bennett [aut],
James Feinstein [aut],
Seth Russell [aut, cre]
Maintainer: Seth Russell <seth.russell@ucdenver.edu>
Diff between pccc versions 1.0.0 dated 2017-12-13 and 1.0.1 dated 2018-03-10
DESCRIPTION | 6 MD5 | 13 - NEWS.md | 4 R/ccc.R | 6 inst/doc/pccc-example.html | 24 +- inst/doc/pccc-icd-codes.html | 180 +++++++-------- inst/doc/pccc-overview.html | 40 +-- inst/pccc_references/ccc_version2_updated01_2018_sas.sas |only 8 files changed, 141 insertions(+), 132 deletions(-)
Title: Database Query Interfaces
Description: Wrapper to 'RODBC'. Supports parameterised, multi-statement, 'SQL' scripts, with embedded 'R'. Implicit handling of connection channels and communication parameters.
Author: Mike Lee
Maintainer: Mike Lee <random.deviate@gmail.com>
Diff between SQRL versions 0.2.0 dated 2018-03-08 and 0.2.1 dated 2018-03-10
DESCRIPTION | 8 +-- MD5 | 10 ++-- R/SQRL.R | 114 +++++++++++++++++++++++++--------------------------- build/partial.rdb |binary man/SQRL-package.Rd | 3 - man/sqrlOff.Rd | 2 6 files changed, 65 insertions(+), 72 deletions(-)
Title: Datasets for Spatial Analysis
Description: Diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis.
It includes R data of class sf (defined by the package 'sf'), Spatial ('sp'), and nb ('spdep').
Unlike other spatial data packages such as 'rnaturalearth' and 'maps',
it also contains data stored in a range of file formats including GeoJSON, ESRI Shapefile and GeoPackage.
Some of the datasets are designed to illustrate specific analysis techniques.
cycle_hire and cycle_hire_osm, for example, is designed to illustrate point pattern analysis techniques.
Author: Roger Bivand [aut] (<https://orcid.org/0000-0003-2392-6140>),
Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between spData versions 0.2.7.4 dated 2018-02-11 and 0.2.8.1 dated 2018-03-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/lnd.R | 2 +- R/zzz.R | 22 ++++++++++++++++------ man/lnd.Rd | 2 +- 5 files changed, 26 insertions(+), 16 deletions(-)
Title: D3 JavaScript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive
features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre],
Kent Russell [aut, ctb],
Mike Bostock [aut, cph] (d3.js library, http://d3js.org),
Susie Lu [aut, cph] (d3-legend library, http://d3-legend.susielu.com/),
Speros Kokenes [aut, cph] (d3-lasso-plugin library,
https://github.com/skokenes/D3-Lasso-Plugin)
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between scatterD3 versions 0.8.1 dated 2016-12-13 and 0.8.2 dated 2018-03-10
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Title: Tools to Support Evidence Synthesis
Description: Researchers commonly need to summarize scientific information, a process known as 'evidence synthesis'. The first stage of a synthesis process (such as a systematic review or meta-analysis) is to download a list of references from academic search engines such as 'Web of Knowledge' or 'Scopus'. This information can be sorted manually (the traditional approach to systematic review), or the user can draw on tools from machine learning to help them visualise patterns in the corpus. 'revtools' uses topic models to render ordinations of text drawn from article titles, keywords and abstracts, and allows the user to interactively select or exclude individual references, words or topics. 'revtools' does not currently provide tools for analysis of data drawn from those references, features that are available in other packages such as 'metagear' or 'metafor'.
Author: Martin J. Westgate <martinjwestgate@gmail.com>
Maintainer: Martin J. Westgate <martinjwestgate@gmail.com>
Diff between revtools versions 0.2.1 dated 2018-02-06 and 0.2.2 dated 2018-03-10
DESCRIPTION | 13 +++----- MD5 | 16 +++++----- R/internal_functions.R | 6 +-- R/make_DTM.R | 2 - R/read_bibliography.R | 9 +++++ R/revtools_ui.R | 6 ++- R/start_review_window.R | 71 ++++++++++++++++++++++++++++++++++----------- README.md | 2 - man/start_review_window.Rd | 5 +-- 9 files changed, 90 insertions(+), 40 deletions(-)
Title: Relative Importance of Regressors in Linear Models
Description: Provides several metrics for assessing relative importance in linear models. These can be printed, plotted and bootstrapped. The recommended metric is lmg, which provides a decomposition of the model explained variance into non-negative contributions. There is a version of this package available that additionally provides a new and also recommended metric called pmvd. If you are a non-US user, you can download this extended version from Ulrike Groempings web site.
Author: Ulrike Groemping [aut, cre],
Lehrkamp Matthias [ctb]
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>
Diff between relaimpo versions 2.2-2 dated 2013-09-11 and 2.2-3 dated 2018-03-10
DESCRIPTION | 16 ++++++++-------- MD5 | 20 ++++++++++---------- NAMESPACE | 6 +++++- R/alltype.R | 1 + R/zzz.R | 1 + inst/NEWS | 8 +++++++- man/booteval.relimp.Rd | 6 +++--- man/calc.relimp.Rd | 4 ++-- man/classesmethods.relaimpo.Rd | 2 +- man/mianalyze.relimp.Rd | 4 ++-- man/relaimpo-package.Rd | 4 ++-- 11 files changed, 42 insertions(+), 30 deletions(-)
Title: Tools for Combinatorics and Computational Mathematics
Description: Provides optimized functions implemented in C++ with 'Rcpp' for
solving problems in combinatorics and computational mathematics. There is
a combination function and a permutation function that are both flexible as
well as efficient with respect to speed and memory. There are optional
constraint parameters that when utilized, generate all combinations/
permutations of a vector meeting specific criteria (e.g. finding all
combinations such that the sum is less than a bound). Both functions are
capable of handling multisets as well. Additionally, there are several
highly efficient number theoretic functions that are useful for problems
common in computational mathematics. These include various sieving
functions that can quickly generate the following: prime numbers, number of
coprime elements, number of divisors, prime factorizations, and complete
factorizations. Some of these functions make use of the fast integer
division library 'libdivide' by <http://ridiculousfish.com>. The primeSieve
function is based on the segmented sieve of Eratosthenes implementation by
Kim Walisch. It is capable of generating all primes less than a billion in
just over 1 second. It can also quickly generate prime numbers over a range
(e.g. primeSieve(10^13, 10^13+10^9)). There are stand-alone vectorized
functions for general factoring (e.g. all divisors of number), primality
testing, as well as prime factoring (this function implements a non-gmp
variant of Pollard's rho algorithm). Finally, there is a prime counting
function that implements a simple variation of Legendre's formula based off
of the algorithm by Kim Walisch. It is capable of returning the number of
primes below a trillion in under 0.5 seconds.
Author: Joseph Wood
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between RcppAlgos versions 1.0.0 dated 2018-03-07 and 1.0.1 dated 2018-03-10
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS | 8 ++++++++ man/RcppAlgos-package.Rd |only man/isPrimeRcpp.Rd | 2 +- man/primeFactorizeSieve.Rd | 8 ++++---- src/PollardRho.cpp | 8 +++----- 7 files changed, 25 insertions(+), 18 deletions(-)
Title: Parse 'Java' Properties Files for 'R Service Bus' Applications
Description: Allows to parse 'Java' properties files in the context of
'R Service Bus' applications.
Author: Tobias Verbeke, Daan Seynaeve, based on read.dcf by R Core Development Team
Maintainer: Daan Seynaeve <daan.seynaeve@openanalytics.eu>
Diff between properties versions 0.0-8 dated 2015-12-02 and 0.0-9 dated 2018-03-10
DESCRIPTION | 23 ++++++++++++----------- MD5 | 13 ++++++++----- NAMESPACE | 3 ++- R/read.properties.R | 6 +++++- R/write.properties.R |only inst/NEWS | 3 +++ man/read.properties.Rd | 12 +++++++++--- man/write.properties.Rd |only tests/test.write.properties.R |only 9 files changed, 39 insertions(+), 21 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Description: Manage the R packages your project depends
on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, Aron Atkins, JJ Allaire
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between packrat versions 0.4.8-1 dated 2016-09-07 and 0.4.9 dated 2018-03-10
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Title: Tools for Working with ICD-9 and ICD-10 Codes, and Finding
Comorbidities
Description: Calculate comorbidities, Charlson scores, perform fast and accurate
validation, conversion, manipulation, filtering and comparison of ICD-9 and
ICD-10 codes. Common ambiguities and code formats are handled. This
package enables a work flow from raw lists of ICD codes in hospital
billing databases to comorbidities. ICD-9 and ICD-10 comorbidity mappings
from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included. This
package replaces 'icd9', which should be uninstalled.
Author: Jack O. Wasey [aut, cre, cph],
William Murphy [ctb] (Van Walraven scores),
Anobel Odisho [ctb] (Hierarchical Condition Codes),
Ed Lee [ctb] (explain codes in table format),
Kevin Ushey [ctb] (Code adapted for fast factor generation),
R Core Team [ctb, cph] (m4 macro for OpenMP detection in configure)
Maintainer: Jack O. Wasey <jack@jackwasey.com>
Diff between icd versions 2.3.1 dated 2017-10-12 and 2.4.1 dated 2018-03-10
icd-2.3.1/icd/man/my_test_check.Rd |only icd-2.3.1/icd/man/set_full_test_options.Rd |only icd-2.3.1/icd/man/setup_test_check.Rd |only icd-2.3.1/icd/man/show_test_options.Rd |only icd-2.3.1/icd/tests/testthat/test-who-icd10.R |only icd-2.4.1/icd/.Rinstignore | 1 icd-2.4.1/icd/DESCRIPTION | 12 icd-2.4.1/icd/MD5 | 387 +++++----- icd-2.4.1/icd/NAMESPACE | 2 icd-2.4.1/icd/R/RcppExports.R | 246 +++--- icd-2.4.1/icd/R/as_char_no_warn.R | 2 icd-2.4.1/icd/R/attr.R | 4 icd-2.4.1/icd/R/catch-routine-registration.R |only icd-2.4.1/icd/R/children.R | 14 icd-2.4.1/icd/R/children_alt.R |only icd-2.4.1/icd/R/class.R | 15 icd-2.4.1/icd/R/comorbid.R | 182 ---- icd-2.4.1/icd/R/comorbid_alt.R |only icd-2.4.1/icd/R/condense.R | 2 icd-2.4.1/icd/R/convert.R | 11 icd-2.4.1/icd/R/datadocs.R | 2 icd-2.4.1/icd/R/diff_comorbid.R | 2 icd-2.4.1/icd/R/env.R | 2 icd-2.4.1/icd/R/explain-table.R | 3 icd-2.4.1/icd/R/explain.R | 25 icd-2.4.1/icd/R/filter.R | 2 icd-2.4.1/icd/R/generate_mappings.R | 2 icd-2.4.1/icd/R/generate_sysdata.R | 2 icd-2.4.1/icd/R/guess.R | 2 icd-2.4.1/icd/R/hcc.R |only icd-2.4.1/icd/R/icd-package.R | 4 icd-2.4.1/icd/R/manip.R | 2 icd-2.4.1/icd/R/parse-comorbid.R | 208 ----- icd-2.4.1/icd/R/parse-icd10.R | 2 icd-2.4.1/icd/R/parse-icd10cm-xml.R | 2 icd-2.4.1/icd/R/parse-rtf.R | 2 icd-2.4.1/icd/R/parse.R | 4 icd-2.4.1/icd/R/parse_hcc.R |only icd-2.4.1/icd/R/print.icd_comorbidity_map.R | 2 icd-2.4.1/icd/R/ranges.R | 2 icd-2.4.1/icd/R/ranges_alt.R |only icd-2.4.1/icd/R/real.R | 2 icd-2.4.1/icd/R/sas.R | 2 icd-2.4.1/icd/R/save_in_data_dir.R | 2 icd-2.4.1/icd/R/score.R | 14 icd-2.4.1/icd/R/sort.R | 13 icd-2.4.1/icd/R/sort_alt.R |only icd-2.4.1/icd/R/to_data_raw.R | 10 icd-2.4.1/icd/R/unzip_single.R | 2 icd-2.4.1/icd/R/util-file.R | 2 icd-2.4.1/icd/R/util-test.R | 91 -- icd-2.4.1/icd/R/util.R | 12 icd-2.4.1/icd/R/valid.R | 4 icd-2.4.1/icd/R/zzz.R | 7 icd-2.4.1/icd/README.md | 206 +++-- icd-2.4.1/icd/build/vignette.rds |binary icd-2.4.1/icd/configure | 4 icd-2.4.1/icd/data/icd10_map_ahrq.RData |binary icd-2.4.1/icd/data/icd10_map_cc.RData |binary icd-2.4.1/icd/data/icd10_map_elix.RData |binary icd-2.4.1/icd/data/icd10_map_quan_deyo.RData |binary icd-2.4.1/icd/data/icd10_map_quan_elix.RData |binary icd-2.4.1/icd/data/icd10_sub_chapters.RData |binary icd-2.4.1/icd/data/icd10cm2016.RData |binary icd-2.4.1/icd/data/icd9_majors.RData |binary icd-2.4.1/icd/data/icd9_map_ahrq.RData |binary icd-2.4.1/icd/data/icd9_map_cc.RData |binary icd-2.4.1/icd/data/icd9_map_elix.RData |binary icd-2.4.1/icd/data/icd9_map_quan_deyo.RData |binary icd-2.4.1/icd/data/icd9_map_quan_elix.RData |binary icd-2.4.1/icd/data/icd9_sources.RData |binary icd-2.4.1/icd/data/icd9_sub_chapters.RData |binary icd-2.4.1/icd/data/icd9cm_billable.RData |binary icd-2.4.1/icd/data/icd9cm_hierarchy.RData |binary icd-2.4.1/icd/data/icd_chapters.rda |binary icd-2.4.1/icd/data/icd_map_cc_hcc.RData |binary icd-2.4.1/icd/data/mappingNames.rda |binary icd-2.4.1/icd/data/uranium_pathology.RData |binary icd-2.4.1/icd/data/vermont_dx.RData |binary icd-2.4.1/icd/inst/doc/Charlson_and_other_scores.Rmd | 2 icd-2.4.1/icd/inst/doc/Charlson_and_other_scores.html | 217 +++++ icd-2.4.1/icd/inst/doc/Comparing_Comorbidity_Mappings_Vignette.R |only icd-2.4.1/icd/inst/doc/Comparing_Comorbidity_Mappings_Vignette.Rmd |only icd-2.4.1/icd/inst/doc/Comparing_Comorbidity_Mappings_Vignette.html |only icd-2.4.1/icd/inst/doc/Using_Hierarchical_Condition_Codes.R |only icd-2.4.1/icd/inst/doc/Using_Hierarchical_Condition_Codes.Rmd |only icd-2.4.1/icd/inst/doc/Using_Hierarchical_Condition_Codes.html |only icd-2.4.1/icd/inst/doc/icd-10.Rmd | 2 icd-2.4.1/icd/inst/doc/icd-10.html | 219 +++++ icd-2.4.1/icd/inst/doc/introduction.R | 6 icd-2.4.1/icd/inst/doc/introduction.Rmd | 8 icd-2.4.1/icd/inst/doc/introduction.html | 223 +++++ icd-2.4.1/icd/inst/include/icd_RcppExports.h | 292 +++---- icd-2.4.1/icd/man/as.icd_short_diag.Rd | 8 icd-2.4.1/icd/man/attr_decimal_diag.Rd |only icd-2.4.1/icd/man/combine.Rd | 7 icd-2.4.1/icd/man/icd-package.Rd | 2 icd-2.4.1/icd/man/icd10_comorbid_parent_search.Rd | 2 icd-2.4.1/icd/man/icd10_comorbid_parent_search_cpp.Rd | 6 icd-2.4.1/icd/man/icd10_parse_cc.Rd | 2 icd-2.4.1/icd/man/icd9AddLeadingZeroesMajorSingle.Rd |only icd-2.4.1/icd/man/icd9AddLeadingZeroesShortSingle.Rd |only icd-2.4.1/icd/man/icd9ChildrenShort11.Rd | 6 icd-2.4.1/icd/man/icd9_add_leading_zeroes_cpp.Rd | 19 icd-2.4.1/icd/man/icd9_order_short.Rd | 11 icd-2.4.1/icd/man/icd9_parse_cc.Rd | 8 icd-2.4.1/icd/man/icd9_parse_leaf_desc_ver.Rd | 2 icd-2.4.1/icd/man/icd_charlson.Rd | 12 icd-2.4.1/icd/man/icd_children.Rd | 13 icd-2.4.1/icd/man/icd_comorbid.Rd | 39 - 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icd-2.4.1/icd/src/ranges.h | 3 icd-2.4.1/icd/src/ranges_alt.cpp | 40 - icd-2.4.1/icd/src/registration.c | 2 icd-2.4.1/icd/src/test-cpp.cpp | 23 icd-2.4.1/icd/src/test-runner.cpp | 7 icd-2.4.1/icd/src/util.cpp | 17 icd-2.4.1/icd/src/util.h | 15 icd-2.4.1/icd/tests/test-all.R | 7 icd-2.4.1/icd/tests/testthat/github133-b.rds |only icd-2.4.1/icd/tests/testthat/github133_tiny_slice.txt |only icd-2.4.1/icd/tests/testthat/helper-base.R | 37 icd-2.4.1/icd/tests/testthat/helper-icd10.R | 6 icd-2.4.1/icd/tests/testthat/test-attr.R | 4 icd-2.4.1/icd/tests/testthat/test-billable.R | 4 icd-2.4.1/icd/tests/testthat/test-children-icd10.R | 3 icd-2.4.1/icd/tests/testthat/test-class.R | 76 - icd-2.4.1/icd/tests/testthat/test-comorbid-calcs-icd10.R | 3 icd-2.4.1/icd/tests/testthat/test-comorbid-calcs-icd9.R | 11 icd-2.4.1/icd/tests/testthat/test-comorbid-maps-icd10.R | 7 icd-2.4.1/icd/tests/testthat/test-comorbid-maps-icd9.R | 18 icd-2.4.1/icd/tests/testthat/test-condense.R | 2 icd-2.4.1/icd/tests/testthat/test-convert.R | 14 icd-2.4.1/icd/tests/testthat/test-cpp.R | 38 icd-2.4.1/icd/tests/testthat/test-examples.R | 4 icd-2.4.1/icd/tests/testthat/test-explain-table.R | 8 icd-2.4.1/icd/tests/testthat/test-explain.R | 9 icd-2.4.1/icd/tests/testthat/test-filter-icd10.R | 2 icd-2.4.1/icd/tests/testthat/test-filter-poa.R | 2 icd-2.4.1/icd/tests/testthat/test-future-explain-icd10.R | 10 icd-2.4.1/icd/tests/testthat/test-github133.R |only icd-2.4.1/icd/tests/testthat/test-hcc.R | 32 icd-2.4.1/icd/tests/testthat/test-hierarchy.R | 2 icd-2.4.1/icd/tests/testthat/test-is.R | 2 icd-2.4.1/icd/tests/testthat/test-lints.R | 7 icd-2.4.1/icd/tests/testthat/test-longtowide.R | 2 icd-2.4.1/icd/tests/testthat/test-manip.R | 2 icd-2.4.1/icd/tests/testthat/test-openmp.R | 15 icd-2.4.1/icd/tests/testthat/test-parse-icd10.R | 9 icd-2.4.1/icd/tests/testthat/test-parse-icd9.R | 2 icd-2.4.1/icd/tests/testthat/test-parse.R | 84 +- icd-2.4.1/icd/tests/testthat/test-ranges-icd10.R | 2 icd-2.4.1/icd/tests/testthat/test-ranges.R | 6 icd-2.4.1/icd/tests/testthat/test-reshape.R | 2 icd-2.4.1/icd/tests/testthat/test-sample-data.R | 2 icd-2.4.1/icd/tests/testthat/test-sas.R | 2 icd-2.4.1/icd/tests/testthat/test-score.R | 2 icd-2.4.1/icd/tests/testthat/test-sort.R | 2 icd-2.4.1/icd/tests/testthat/test-spell.R | 2 icd-2.4.1/icd/tests/testthat/test-util.R | 2 icd-2.4.1/icd/tests/testthat/test-valid-icd10.R | 3 icd-2.4.1/icd/tests/testthat/test-valid.R | 2 icd-2.4.1/icd/vignettes/Charlson_and_other_scores.Rmd | 2 icd-2.4.1/icd/vignettes/Comparing_Comorbidity_Mappings_Vignette.Rmd |only icd-2.4.1/icd/vignettes/Using_Hierarchical_Condition_Codes.Rmd |only icd-2.4.1/icd/vignettes/icd-10.Rmd | 2 icd-2.4.1/icd/vignettes/introduction.Rmd | 8 210 files changed, 2100 insertions(+), 1815 deletions(-)
Title: Get WHO Tuberculosis Data
Description: Facilitates easy import of analysis ready World Health Organisation Tuberculosis data and provides plotting functions for exploratory data analysis.
Author: Sam Abbott [aut, cre]
Maintainer: Sam Abbott <contact@samabbott.co.uk>
Diff between getTBinR versions 0.5.2 dated 2018-02-13 and 0.5.3 dated 2018-03-10
DESCRIPTION | 6 - MD5 | 58 ++++++------ NAMESPACE | 1 NEWS.md | 17 +++ R/get_data.R | 49 ++++++++-- R/map_tb_burden.R | 54 +++++++++-- R/plot_tb_burden.R | 21 +++- R/plot_tb_burden_overview.R | 11 +- README.md | 16 +-- build/vignette.rds |binary inst/doc/case_fatality_rate.R |only inst/doc/case_fatality_rate.Rmd |only inst/doc/case_fatality_rate.html |only inst/doc/case_study_global_trends.html | 6 - inst/doc/intro.html | 134 ++++++++++++++++++----------- man/figure/map-tb-incidence-eur-1.png |binary man/figure/plot-tb-incidence-eur-1.png |binary man/figure/plot-tb-incidence-eur-per-1.png |binary man/figure/plot-tb-incidence-uk-1.png |binary man/get_data.Rd | 9 + man/get_data_dict.Rd | 4 man/get_tb_burden.Rd | 4 man/map_tb_burden.Rd | 28 ++++-- man/plot_tb_burden.Rd | 13 ++ man/plot_tb_burden_overview.Rd | 13 ++ tests/testthat/test-get_data.R | 18 +++ tests/testthat/test-get_data_dict.R | 22 ++-- tests/testthat/test-get_tb_burden.R | 21 ++-- tests/testthat/test-map_tb_burden.R | 27 +++++ tests/testthat/test-prepare_df_plot.R | 32 ++++-- tests/testthat/test-search_data_dict.R | 15 +-- vignettes/case_fatality_rate.Rmd |only 32 files changed, 398 insertions(+), 181 deletions(-)
Title: Handy File and String Manipulation
Description: Convenient functions for moving files, deleting directories,
and a variety of string operations that facilitate manipulating files
and extracting information from strings.
Author: Rory Nolan [aut, cre, cph],
Sergi Padilla-Parra [ths]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between filesstrings versions 2.0.4 dated 2018-02-09 and 2.1.0 dated 2018-03-10
filesstrings-2.0.4/filesstrings/src/init.c |only filesstrings-2.1.0/filesstrings/DESCRIPTION | 6 filesstrings-2.1.0/filesstrings/MD5 | 26 +-- filesstrings-2.1.0/filesstrings/NAMESPACE | 1 filesstrings-2.1.0/filesstrings/NEWS.md | 6 filesstrings-2.1.0/filesstrings/R/RcppExports.R | 4 filesstrings-2.1.0/filesstrings/R/utils.R | 104 ++++++++++++ filesstrings-2.1.0/filesstrings/README.md | 4 filesstrings-2.1.0/filesstrings/build/partial.rdb |binary filesstrings-2.1.0/filesstrings/inst/doc/files.html | 28 +-- filesstrings-2.1.0/filesstrings/inst/doc/strings.html | 52 +++--- filesstrings-2.1.0/filesstrings/man/match_arg.Rd |only filesstrings-2.1.0/filesstrings/src/RcppExports.cpp | 33 +++ filesstrings-2.1.0/filesstrings/src/strings.cpp | 54 ++++++ filesstrings-2.1.0/filesstrings/tests/testthat/test_utils.R | 31 +++ 15 files changed, 292 insertions(+), 57 deletions(-)
Title: Dynamic Model Averaging
Description: Dynamic model averaging for binary and continuous
outcomes.
Author: Tyler H. McCormick, Adrian Raftery, David Madigan
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between dma versions 1.3-0 dated 2017-06-15 and 1.3-1 dated 2018-03-10
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/dma.R | 2 +- R/dma.default.R | 2 +- R/makf4.R | 6 +++--- man/dma-package.Rd | 4 ++-- man/dma.Rd | 4 ++-- man/logistic.dma.Rd | 1 + 9 files changed, 26 insertions(+), 21 deletions(-)
Title: Some Functions to be Used as Shortcuts in 'RStudio'
Description: 'RStudio' as of recently offers the option to define addins and assign shortcuts to them. This package contains addins for a few most frequently used functions in a data scientist's (at least mine) daily work (like str(), example(), plot(), head(), view(), Desc()). Most of these functions will use the current selection in the editor window and send the specific command to the console while instantly executing it. Assigning shortcuts to these addins will save you quite a few keystrokes.
Author: Andri Signorell
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescToolsAddIns versions 0.9.2 dated 2017-11-25 and 1.0 dated 2018-03-10
DESCRIPTION | 8 +++---- MD5 | 15 +++++++------ NAMESPACE | 2 - NEWS | 10 +++++++- R/AddIns.R | 52 ++++++++++++++++++++++++++++++++++++++++++++++ inst/rstudio/addins.dcf | 11 +++++++++ man/DescToolsAddIns.Rd | 28 +++++++++++++++--------- man/figures/AddIns.png |binary man/figures/Shortcuts.png |only 9 files changed, 102 insertions(+), 24 deletions(-)
More information about DescToolsAddIns at CRAN
Permanent link
Title: Fast and URL-Safe Base64 Encoder and Decoder
Description: In contrast to RFC3548, the 62nd character ("+") is replaced with
"-", the 63rd character ("/") is replaced with "_". Furthermore, the encoder
does not fill the string with trailing "=". The resulting encoded strings
comply to the regular expression pattern "[A-Za-z0-9_-]" and thus are
safe to use in URLs or for file names.
The package also comes with a simple base32 encoder/decoder suited for
case insensitive file systems.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Apache Foundation [ctb, cph],
Free Software Foundation [ctb, cph]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between base64url versions 1.2 dated 2017-06-14 and 1.3 dated 2018-03-10
DESCRIPTION | 11 - MD5 | 28 +-- NEWS.md | 4 R/base32.R | 2 R/base64.R | 2 build/vignette.rds |binary inst/doc/Benchmarks.R | 2 inst/doc/Benchmarks.Rmd | 2 inst/doc/Benchmarks.html | 396 ++++++++++++++++++++++++++++++++----------- src/base32.c | 8 src/base64.c | 8 tests/testthat/helper.R | 7 tests/testthat/test_base32.R | 9 tests/testthat/test_base64.R | 11 - vignettes/Benchmarks.Rmd | 2 15 files changed, 353 insertions(+), 139 deletions(-)
Title: Object Pooling
Description: Enables the creation of object pools, which make it less
computationally expensive to fetch a new object. Currently the
only supported pooled objects are 'DBI' connections.
Author: Barbara Borges [aut, cre],
RStudio [cph]
Maintainer: Barbara Borges <barbara@rstudio.com>
Diff between pool versions 0.1.2 dated 2017-11-03 and 0.1.4 dated 2018-03-10
DESCRIPTION | 6 - MD5 | 32 ++++---- NEWS.md | 10 ++ R/DBI-connection-quote.R | 34 -------- R/DBI-connection-transaction.R | 59 ++++++++------- R/DBI-connection.R | 73 ++++++++++-------- R/DBI-object.R | 35 +++++---- R/DBI.R | 35 +++++---- R/dbplyr.R | 47 ++++++------ man/DBI-connection-quote.Rd | 17 +--- man/DBI-connection.Rd | 91 ++++++++++++----------- man/DBI-object.Rd | 35 +++++---- man/dbPool.Rd | 35 +++++---- man/dplyr-db-methods.Rd | 47 ++++++------ man/pool.Rd | 26 ------ man/poolWithTransaction.Rd | 59 ++++++++------- tests/testthat/test-dplyr.R | 159 ++++++++++++++++++++--------------------- 17 files changed, 399 insertions(+), 401 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <http://glottolog.org> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <http://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://ropensci.github.io/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and others.
Author: George Moroz
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.0.11 dated 2018-01-14 and 1.0.12 dated 2018-03-10
DESCRIPTION | 6 - MD5 | 77 +++++++------- NAMESPACE | 3 NEWS | 17 ++- R/abvd.feature.R | 4 R/afbo.feature.R | 15 ++ R/atlas.database.R |only R/autotyp.feature.R | 5 R/is.glottolog.R | 2 R/map.feature.R | 132 ++++++++++++++++++++++--- R/phoible.feature.R | 13 ++ R/polygon.points.R | 8 + R/sails.feature.R | 3 R/wals.feature.R | 15 ++ build/vignette.rds |binary data/abvd.RData |binary data/circassian.RData |binary data/countries.RData |binary data/ejective_and_n_consonants.RData |binary data/glottolog.modified.RData |binary data/glottolog.original.RData |binary data/wals.RData |binary inst/CITATION | 2 inst/doc/lingtypology_creating_maps.R | 43 ++++---- inst/doc/lingtypology_creating_maps.Rmd | 126 +++++++++++++---------- inst/doc/lingtypology_creating_maps.html | 113 ++++++++++++--------- inst/doc/lingtypology_db_API.html | 4 inst/doc/lingtypology_dplyr.R | 65 +++++++++++- inst/doc/lingtypology_dplyr.Rmd | 118 +++++++++++++++++++++- inst/doc/lingtypology_dplyr.html | 85 +++++++++++++++- inst/doc/lingtypology_glottolog_functions.Rmd | 1 inst/doc/lingtypology_glottolog_functions.html | 5 inst/doc/lingtypology_intro.html | 8 - inst/doc/manual/lingtypology.pdf |binary man/atlas.database.Rd |only man/imports.Rd |only man/map.feature.Rd | 46 ++++++-- tests/testthat/test-mapfeature.R | 7 + vignettes/lingtypology_creating_maps.Rmd | 126 +++++++++++++---------- vignettes/lingtypology_dplyr.Rmd | 118 +++++++++++++++++++++- vignettes/lingtypology_glottolog_functions.Rmd | 1 41 files changed, 888 insertions(+), 280 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-23 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-04-25 1.02
2009-09-28 1.01
2009-03-26 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-03 0.4