Title: Visualize Alpha-Helical Peptide Sequences
Description: Create pretty visualizations of alpha-helical
peptide sequences in R. The amino acid type (polar, hydrophobic, etc.) is
denoted by color. This package allows creation of helical wheels, and the
newer Wenxiang diagrams. Future versions aim to include increased
customizability of the two existing visualizations, as well as a
visualization for the helical net diagram.
Author: Raoul Wadhwa [cre, aut],
Regina Stevens-Truss [aut]
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>
Diff between helixvis versions 0.1.0 dated 2017-06-26 and 0.2.0 dated 2018-02-04
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/draw_func.R | 4 ---- R/zzz.R | 10 ++++++++++ README.md | 12 ++++++++++-- inst/doc/Visualization.Rmd | 2 -- inst/doc/Visualization.html | 18 +++++++++++------- vignettes/Visualization.Rmd | 2 -- 8 files changed, 43 insertions(+), 29 deletions(-)
Title: Univariate GARCH Models
Description: ARFIMA, in-mean, external regressors and various GARCH flavors, with methods for fit, forecast, simulation, inference and plotting.
Author: Alexios Ghalanos [aut, cre]
Maintainer: Alexios Ghalanos <alexios@4dscape.com>
Diff between rugarch versions 1.3-8 dated 2017-10-08 and 1.4-0 dated 2018-02-04
rugarch-1.3-8/rugarch/src/Makevars |only rugarch-1.3-8/rugarch/src/Makevars.win |only rugarch-1.3-8/rugarch/vignettes/Introduction_to_the_rugarch_package.tex |only rugarch-1.4-0/rugarch/ChangeLog | 10 rugarch-1.4-0/rugarch/DESCRIPTION | 24 rugarch-1.4-0/rugarch/MD5 | 83 +- rugarch-1.4-0/rugarch/R/arfima-main.R | 379 ++++------ rugarch-1.4-0/rugarch/R/rugarch-aparch.R | 6 rugarch-1.4-0/rugarch/R/rugarch-csgarch.R | 6 rugarch-1.4-0/rugarch/R/rugarch-cwrappers.R | 10 rugarch-1.4-0/rugarch/R/rugarch-egarch.R | 6 rugarch-1.4-0/rugarch/R/rugarch-fgarch.R | 6 rugarch-1.4-0/rugarch/R/rugarch-figarch.R |only rugarch-1.4-0/rugarch/R/rugarch-gjrgarch.R | 6 rugarch-1.4-0/rugarch/R/rugarch-helperfn.R | 97 +- rugarch-1.4-0/rugarch/R/rugarch-igarch.R | 6 rugarch-1.4-0/rugarch/R/rugarch-mcsgarch.R | 6 rugarch-1.4-0/rugarch/R/rugarch-methods.R | 58 + rugarch-1.4-0/rugarch/R/rugarch-numderiv.R | 14 rugarch-1.4-0/rugarch/R/rugarch-plots.R | 240 +++--- rugarch-1.4-0/rugarch/R/rugarch-realgarch.R | 6 rugarch-1.4-0/rugarch/R/rugarch-sgarch.R | 5 rugarch-1.4-0/rugarch/R/rugarch-solvers.R | 88 +- rugarch-1.4-0/rugarch/R/rugarch-startpars.R | 280 +++++-- rugarch-1.4-0/rugarch/R/rugarch-tests.R | 188 ++-- rugarch-1.4-0/rugarch/data/dji30ret.rda |binary rugarch-1.4-0/rugarch/inst/doc/Introduction_to_the_rugarch_package.Rnw | 3 rugarch-1.4-0/rugarch/inst/doc/Introduction_to_the_rugarch_package.pdf |binary rugarch-1.4-0/rugarch/inst/rugarch.tests/rugarch.test14.R |only rugarch-1.4-0/rugarch/man/ugarchfilter-methods.Rd | 48 - rugarch-1.4-0/rugarch/man/ugarchfit-methods.Rd | 111 +- rugarch-1.4-0/rugarch/man/ugarchforecast-methods.Rd | 64 - rugarch-1.4-0/rugarch/man/ugarchpath-methods.Rd | 59 - rugarch-1.4-0/rugarch/src/distributions.c | 25 rugarch-1.4-0/rugarch/src/filters.c | 29 rugarch-1.4-0/rugarch/src/filters.h | 2 rugarch-1.4-0/rugarch/src/fracdiff.c | 44 + rugarch-1.4-0/rugarch/src/fracdiff.h | 2 rugarch-1.4-0/rugarch/src/garchmodels.c | 51 + rugarch-1.4-0/rugarch/src/garchsim.cpp | 1 rugarch-1.4-0/rugarch/src/rugarch.c | 8 rugarch-1.4-0/rugarch/src/rugarch.h | 10 rugarch-1.4-0/rugarch/vignettes/Introduction_to_the_rugarch_package.Rnw | 3 rugarch-1.4-0/rugarch/vignettes/rugarch.tex | 90 +- rugarch-1.4-0/rugarch/vignettes/rugarchbib.bib | 57 + 45 files changed, 1318 insertions(+), 813 deletions(-)
Title: Modeling, Analysis, Validation and Visualization of Observer
Performance Studies in Diagnostic Radiology
Description: Tools for quantitative assessment of medical imaging systems, radiologists or computer aided ('CAD') algorithms. Implements methods described in a book: 'Chakraborty' 'DP' (2017), "Observer Performance Methods for Diagnostic Imaging - Foundations, Modeling, and Applications with R-Based Examples", Taylor-Francis <https://www.crcpress.com/9781482214840>. Data collection paradigms include receiver operating characteristic ('ROC') and its location specific extensions, primarily free-response 'ROC' ('FROC'). 'ROC' data consists of a single rating per image, where the rating is the perceived confidence level the image is of a diseased patient. 'FROC' data consists of a variable number (including zero) of mark-rating pairs per image, where a mark is the location of a clinically reportable suspicious region and the rating is the corresponding confidence level that it is a true lesion. The software supersedes the current Windows version of 'JAFROC' software <http://www.devchakraborty.com>. 'RJafroc' is derived from it being an enhanced R version of original Windows 'JAFROC'. Implemented are a number of figures of merit quantifying performance, functions for visualizing operating characteristics; three ROC ratings data curve-fitting algorithms: the 'binormal' model ('BM'), the contaminated binormal model ('CBM') and the radiological search model ('RSM'). Unlike the 'BM', the 'CBM' and the 'RSM' predict proper ROC curves that do not cross the chance diagonal or display inappropriate hooks near the upper right corner of the plots. 'RSM' fitting additionally yields measures of search and lesion-classification performances, in addition to the usual case-classification performance measured by the area under the 'ROC' curve. Search performance is the ability to find lesions while avoiding finding non-lesions. Lesion-classification performance is the ability to discriminate between found lesions and non-lesions. For fully crossed study designs, termed multiple-reader multiple-case, significance testing of reader-averaged figure-of-merit differences between modalities is implemented via both 'Dorfman', 'Berbaum' and 'Metz' ('DBM') and the 'Obuchowski' and 'Rockette' ('OR') methods. Single treatment analysis allows comparison of performance of a group of radiologists to a specified value, or comparison of 'CAD' performance to a group of radiologists interpreting the same cases. Sample size estimation tools are provided for 'ROC' and 'FROC' studies that allow estimation of relevant variances from a pilot study to predict required numbers of readers and cases in a pivotal study. Utility and data file manipulation functions allow data to be read in any of the currently used input formats, including Excel, and the results of the analysis can be viewed in text or Excel output files. The package is used extensively in the online appendices of the cited book. Directions for accessing the online material are available by following the software tab of <http://www.devchakraborty.com>.
Author: Dev Chakraborty [cre, aut, cph],
Xuetong Zhai [aut, cph],
Lucy D'Agostino McGowan [ctb]
Maintainer: Dev Chakraborty <dpc10ster@gmail.com>
Diff between RJafroc versions 0.1.1 dated 2015-08-14 and 1.0.0 dated 2018-02-04
RJafroc-0.1.1/RJafroc/R/CalculateAFROCPoints.R |only RJafroc-0.1.1/RJafroc/R/CalculateAvgAFROCPoints.R |only RJafroc-0.1.1/RJafroc/R/CalculateAvgFROCPoints.R |only RJafroc-0.1.1/RJafroc/R/CalculateAvgROCPoints.R |only RJafroc-0.1.1/RJafroc/R/CalculateFROCPoints.R |only RJafroc-0.1.1/RJafroc/R/CalculateROCPoints.R |only RJafroc-0.1.1/RJafroc/R/CalculateTrapezoidalArea.R |only RJafroc-0.1.1/RJafroc/R/CalculateTrapezoidalAreaWeighted.R |only RJafroc-0.1.1/RJafroc/R/DBMHAnalysis.R |only RJafroc-0.1.1/RJafroc/R/EmpiricalOpCharac.R |only RJafroc-0.1.1/RJafroc/R/EstimateVarCov.R |only RJafroc-0.1.1/RJafroc/R/FROC2HrROC.R |only RJafroc-0.1.1/RJafroc/R/FigureOfMerit.R |only RJafroc-0.1.1/RJafroc/R/FindOptimalCutoffs.R |only RJafroc-0.1.1/RJafroc/R/GlobalVariables.R |only RJafroc-0.1.1/RJafroc/R/MyFOM.R |only RJafroc-0.1.1/RJafroc/R/ORHAnalysis.R |only RJafroc-0.1.1/RJafroc/R/OutputReport.R |only RJafroc-0.1.1/RJafroc/R/PlotAFROC.R |only RJafroc-0.1.1/RJafroc/R/PlotFROC.R |only RJafroc-0.1.1/RJafroc/R/PlotROC.R |only RJafroc-0.1.1/RJafroc/R/PowerGivenJK.R |only RJafroc-0.1.1/RJafroc/R/PowerTable.R |only RJafroc-0.1.1/RJafroc/R/RJafrocGui.R |only RJafroc-0.1.1/RJafroc/R/ReadDataFile.R |only RJafroc-0.1.1/RJafroc/R/ReadImrmc.R |only RJafroc-0.1.1/RJafroc/R/ReadJAFROC.R |only RJafroc-0.1.1/RJafroc/R/ReadLrc.R |only RJafroc-0.1.1/RJafroc/R/ResamplingEstimateVarCovs.R |only RJafroc-0.1.1/RJafroc/R/SampleSizeGivenJ.R |only RJafroc-0.1.1/RJafroc/R/SaveDataFile.R |only RJafroc-0.1.1/RJafroc/R/SaveImrmc.R |only RJafroc-0.1.1/RJafroc/R/SaveJAFROC.R |only RJafroc-0.1.1/RJafroc/R/SaveLrc.R |only RJafroc-0.1.1/RJafroc/R/SaveOrDbmMrmc.R |only RJafroc-0.1.1/RJafroc/R/VarCovs.R |only RJafroc-0.1.1/RJafroc/R/frocData.R |only RJafroc-0.1.1/RJafroc/R/rocData.R |only RJafroc-0.1.1/RJafroc/R/roiData.R |only RJafroc-0.1.1/RJafroc/build |only RJafroc-0.1.1/RJafroc/data/frocData.rda |only RJafroc-0.1.1/RJafroc/data/rocData.rda |only RJafroc-0.1.1/RJafroc/data/roiData.rda |only RJafroc-0.1.1/RJafroc/inst/GUI |only RJafroc-0.1.1/RJafroc/inst/doc |only RJafroc-0.1.1/RJafroc/inst/tests |only RJafroc-0.1.1/RJafroc/man/DBMHAnalysis.Rd |only RJafroc-0.1.1/RJafroc/man/EmpiricalOpCharac.Rd |only RJafroc-0.1.1/RJafroc/man/FROC2HrROC.Rd |only RJafroc-0.1.1/RJafroc/man/FigureOfMerit.Rd |only RJafroc-0.1.1/RJafroc/man/ORHAnalysis.Rd |only RJafroc-0.1.1/RJafroc/man/OutputReport.Rd |only RJafroc-0.1.1/RJafroc/man/PowerGivenJK.Rd |only RJafroc-0.1.1/RJafroc/man/PowerTable.Rd |only RJafroc-0.1.1/RJafroc/man/RJafrocGui.Rd |only RJafroc-0.1.1/RJafroc/man/ReadDataFile.Rd |only RJafroc-0.1.1/RJafroc/man/SampleSizeGivenJ.Rd |only RJafroc-0.1.1/RJafroc/man/SaveDataFile.Rd |only RJafroc-0.1.1/RJafroc/man/frocData.Rd |only RJafroc-0.1.1/RJafroc/man/rocData.Rd |only RJafroc-0.1.1/RJafroc/man/roiData.Rd |only RJafroc-0.1.1/RJafroc/vignettes |only RJafroc-1.0.0/RJafroc/DESCRIPTION | 36 RJafroc-1.0.0/RJafroc/MD5 | 275 +++- RJafroc-1.0.0/RJafroc/NAMESPACE | 76 - RJafroc-1.0.0/RJafroc/R/BinningRelated.R |only RJafroc-1.0.0/RJafroc/R/ComBins.R |only RJafroc-1.0.0/RJafroc/R/Df2RJafrocDataset.R |only RJafroc-1.0.0/RJafroc/R/DfBinDataset.R |only RJafroc-1.0.0/RJafroc/R/DfExtractDataset.R |only RJafroc-1.0.0/RJafroc/R/DfFroc2Afroc.R |only RJafroc-1.0.0/RJafroc/R/DfFroc2Roc.R |only RJafroc-1.0.0/RJafroc/R/DfLroc2Roc.R |only RJafroc-1.0.0/RJafroc/R/DfReadCrossedModalities.R |only RJafroc-1.0.0/RJafroc/R/DfReadDataFile.R |only RJafroc-1.0.0/RJafroc/R/DfReadLrocDataFile.R |only RJafroc-1.0.0/RJafroc/R/DfSaveDataFile.R |only RJafroc-1.0.0/RJafroc/R/EnvironmentVariables.R |only RJafroc-1.0.0/RJafroc/R/ExampleCompare3ProperRocFits.R |only RJafroc-1.0.0/RJafroc/R/FitBinormalRoc.R |only RJafroc-1.0.0/RJafroc/R/FitCbmRoc.R |only RJafroc-1.0.0/RJafroc/R/FitRsmRoc.R |only RJafroc-1.0.0/RJafroc/R/PlotBinormalFit.R |only RJafroc-1.0.0/RJafroc/R/PlotCBMFit.R |only RJafroc-1.0.0/RJafroc/R/PlotEmpiricalOperatingCharacteristics.R |only RJafroc-1.0.0/RJafroc/R/PlotRsmOperatingCharacteristics.R |only RJafroc-1.0.0/RJafroc/R/RcppExports.R |only RJafroc-1.0.0/RJafroc/R/ReadOrDbmMrmc.R | 13 RJafroc-1.0.0/RJafroc/R/SimulateFrocDataset.R |only RJafroc-1.0.0/RJafroc/R/SimulateRocDataset.R |only RJafroc-1.0.0/RJafroc/R/SsFROCPowerGivenJK.R |only RJafroc-1.0.0/RJafroc/R/SsPowerGivenJK.R |only RJafroc-1.0.0/RJafroc/R/SsPowerTable.R |only RJafroc-1.0.0/RJafroc/R/SsSampleSizeKGivenJ.R |only RJafroc-1.0.0/RJafroc/R/StSignificanceTesting.R |only RJafroc-1.0.0/RJafroc/R/StSignificanceTestingCadVsRadiologists.R |only RJafroc-1.0.0/RJafroc/R/StSignificanceTestingCrossedModalities.R |only RJafroc-1.0.0/RJafroc/R/StSignificanceTestingSingleFixedFactor.R |only RJafroc-1.0.0/RJafroc/R/Transforms.R |only RJafroc-1.0.0/RJafroc/R/UtilAucBinormal.R |only RJafroc-1.0.0/RJafroc/R/UtilAucCBM.R |only RJafroc-1.0.0/RJafroc/R/UtilAucPROPROC.R |only RJafroc-1.0.0/RJafroc/R/UtilAucsRSM.R |only RJafroc-1.0.0/RJafroc/R/UtilFigureOfMerit.R |only RJafroc-1.0.0/RJafroc/R/UtilIntrinsic2PhysicalRSM.R |only RJafroc-1.0.0/RJafroc/R/UtilLesionDistribution.R |only RJafroc-1.0.0/RJafroc/R/UtilLesionWeights.R |only RJafroc-1.0.0/RJafroc/R/UtilMeanSquares.R |only RJafroc-1.0.0/RJafroc/R/UtilOutputReport.R |only RJafroc-1.0.0/RJafroc/R/UtilPhysical2IntrinsicRSM.R |only RJafroc-1.0.0/RJafroc/R/UtilPseudoValues.R |only RJafroc-1.0.0/RJafroc/R/UtilVarianceComponents.R |only RJafroc-1.0.0/RJafroc/R/addArguments.R |only RJafroc-1.0.0/RJafroc/R/datasets.R |only RJafroc-1.0.0/RJafroc/R/genericPlotLROC.R |only RJafroc-1.0.0/RJafroc/R/genericPlotROC.R |only RJafroc-1.0.0/RJafroc/R/gpfMyFOM.R |only RJafroc-1.0.0/RJafroc/R/testDf2RJafrocDataset.R |only RJafroc-1.0.0/RJafroc/R/testDfBinDataset.R |only RJafroc-1.0.0/RJafroc/data/dataset01.RData |only RJafroc-1.0.0/RJafroc/data/dataset02.RData |only RJafroc-1.0.0/RJafroc/data/dataset03.RData |only RJafroc-1.0.0/RJafroc/data/dataset04.RData |only RJafroc-1.0.0/RJafroc/data/dataset05.RData |only RJafroc-1.0.0/RJafroc/data/dataset06.RData |only RJafroc-1.0.0/RJafroc/data/dataset07.RData |only RJafroc-1.0.0/RJafroc/data/dataset08.RData |only RJafroc-1.0.0/RJafroc/data/dataset09.RData |only RJafroc-1.0.0/RJafroc/data/dataset10.RData |only RJafroc-1.0.0/RJafroc/data/dataset11.RData |only RJafroc-1.0.0/RJafroc/data/dataset12.RData |only RJafroc-1.0.0/RJafroc/data/dataset13.RData |only RJafroc-1.0.0/RJafroc/data/dataset14.RData |only RJafroc-1.0.0/RJafroc/data/datasetCadLroc.RData |only RJafroc-1.0.0/RJafroc/data/datasetCrossedModality.RData |only RJafroc-1.0.0/RJafroc/data/datasetDegenerate.RData |only RJafroc-1.0.0/RJafroc/inst/ANALYZED |only RJafroc-1.0.0/RJafroc/inst/MRMCRuns |only RJafroc-1.0.0/RJafroc/inst/extdata |only RJafroc-1.0.0/RJafroc/man/Df2RJafrocDataset.Rd |only RJafroc-1.0.0/RJafroc/man/DfBinDataset.Rd |only RJafroc-1.0.0/RJafroc/man/DfExtractDataset.Rd |only RJafroc-1.0.0/RJafroc/man/DfFroc2Afroc.Rd |only RJafroc-1.0.0/RJafroc/man/DfFroc2Roc.Rd |only RJafroc-1.0.0/RJafroc/man/DfLroc2Roc.Rd |only RJafroc-1.0.0/RJafroc/man/DfReadCrossedModalities.Rd |only RJafroc-1.0.0/RJafroc/man/DfReadDataFile.Rd |only RJafroc-1.0.0/RJafroc/man/DfReadLrocDataFile.Rd |only RJafroc-1.0.0/RJafroc/man/DfSaveDataFile.Rd |only RJafroc-1.0.0/RJafroc/man/ExampleCompare3ProperRocFits.Rd |only RJafroc-1.0.0/RJafroc/man/FitBinormalRoc.Rd |only RJafroc-1.0.0/RJafroc/man/FitCbmRoc.Rd |only RJafroc-1.0.0/RJafroc/man/FitRsmRoc.Rd |only RJafroc-1.0.0/RJafroc/man/PlotBinormalFit.Rd |only RJafroc-1.0.0/RJafroc/man/PlotCbmFit.Rd |only RJafroc-1.0.0/RJafroc/man/PlotEmpiricalOperatingCharacteristics.Rd |only RJafroc-1.0.0/RJafroc/man/PlotRsmOperatingCharacteristics.Rd |only RJafroc-1.0.0/RJafroc/man/RJafroc-package.Rd | 634 +++++++--- RJafroc-1.0.0/RJafroc/man/SimulateFrocDataset.Rd |only RJafroc-1.0.0/RJafroc/man/SimulateRocDataset.Rd |only RJafroc-1.0.0/RJafroc/man/SsFROCPowerGivenJK.Rd |only RJafroc-1.0.0/RJafroc/man/SsPowerGivenJK.Rd |only RJafroc-1.0.0/RJafroc/man/SsPowerTable.Rd |only RJafroc-1.0.0/RJafroc/man/SsSampleSizeKGivenJ.Rd |only RJafroc-1.0.0/RJafroc/man/StSignificanceTesting.Rd |only RJafroc-1.0.0/RJafroc/man/StSignificanceTestingCadVsRadiologists.Rd |only RJafroc-1.0.0/RJafroc/man/StSignificanceTestingCrossedModalities.Rd |only RJafroc-1.0.0/RJafroc/man/StSignificanceTestingSingleFixedFactor.Rd |only RJafroc-1.0.0/RJafroc/man/UtilAucBinormal.Rd |only RJafroc-1.0.0/RJafroc/man/UtilAucCBM.Rd |only RJafroc-1.0.0/RJafroc/man/UtilAucPROPROC.Rd |only RJafroc-1.0.0/RJafroc/man/UtilAucsRSM.Rd |only RJafroc-1.0.0/RJafroc/man/UtilFigureOfMerit.Rd |only RJafroc-1.0.0/RJafroc/man/UtilIntrinsic2PhysicalRSM.Rd |only RJafroc-1.0.0/RJafroc/man/UtilLesionDistribution.Rd |only RJafroc-1.0.0/RJafroc/man/UtilLesionWeights.Rd |only RJafroc-1.0.0/RJafroc/man/UtilMeanSquares.Rd |only RJafroc-1.0.0/RJafroc/man/UtilOutputReport.Rd |only RJafroc-1.0.0/RJafroc/man/UtilPhysical2IntrinsicRSM.Rd |only RJafroc-1.0.0/RJafroc/man/UtilPseudoValues.Rd |only RJafroc-1.0.0/RJafroc/man/dataset01.Rd |only RJafroc-1.0.0/RJafroc/man/dataset02.Rd |only RJafroc-1.0.0/RJafroc/man/dataset03.Rd |only RJafroc-1.0.0/RJafroc/man/dataset04.Rd |only RJafroc-1.0.0/RJafroc/man/dataset05.Rd |only RJafroc-1.0.0/RJafroc/man/dataset06.Rd |only RJafroc-1.0.0/RJafroc/man/dataset07.Rd |only RJafroc-1.0.0/RJafroc/man/dataset08.Rd |only RJafroc-1.0.0/RJafroc/man/dataset09.Rd |only RJafroc-1.0.0/RJafroc/man/dataset10.Rd |only RJafroc-1.0.0/RJafroc/man/dataset11.Rd |only RJafroc-1.0.0/RJafroc/man/dataset12.Rd |only RJafroc-1.0.0/RJafroc/man/dataset13.Rd |only RJafroc-1.0.0/RJafroc/man/dataset14.Rd |only RJafroc-1.0.0/RJafroc/man/datasetCadLroc.Rd |only RJafroc-1.0.0/RJafroc/man/datasetCrossedModality.Rd |only RJafroc-1.0.0/RJafroc/man/datasetDegenerate.Rd |only RJafroc-1.0.0/RJafroc/src |only 198 files changed, 786 insertions(+), 248 deletions(-)
Title: Classical Test Theory Functions
Description: A collection of common test and item analyses from a classical test theory (CTT) framework. Analyses can be applied to both dichotomous and polytomous data. Functions provide reliability analyses (alpha), item statistics, disctractor analyses, disattenuated correlations, scoring routines, and empirical ICCs.
Author: John T. Willse
Maintainer: John T. Willse <willse@uncg.edu>
Diff between CTT versions 2.3 dated 2017-11-03 and 2.3.2 dated 2018-02-04
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/distractorAnalysis.R | 27 +++++++++++++++++++++------ R/subscales.R | 2 +- man/distractorAnalysis.Rd | 8 +++++--- 5 files changed, 35 insertions(+), 18 deletions(-)
Title: Functions for Time Series Analysis
Description: Includes non-parametric estimators and tests for time series analysis. The functions are to test for presence of possibly non-monotonic trends and for synchronism of trends in multiple time series, using modern bootstrap techniques and robust non-parametric difference-based estimators.
Author: Vyacheslav Lyubchich [aut, cre],
Yulia R. Gel [aut],
Calvin Chu [ctb],
Xin Huang [ctb],
Ethan D. Schaeffer [ctb],
Xingyu Wang [ctb]
Maintainer: Vyacheslav Lyubchich <lyubchic@umces.edu>
Diff between funtimes versions 4.0 dated 2017-02-28 and 5.0 dated 2018-02-04
DESCRIPTION | 11 ++++++----- MD5 | 16 ++++++++++------ NAMESPACE | 1 - R/i.tails.R |only R/q.tails.R |only R/sync.test.R | 12 ++++++------ man/BICC.Rd | 2 +- man/Purity.Rd | 2 +- man/i.tails.Rd |only man/q.tails.Rd |only man/sync.test.Rd | 10 +++++++--- 11 files changed, 31 insertions(+), 23 deletions(-)
Title: Experimental Design and Analysis for Tree Improvement
Description: Provides data sets and R Codes for Williams, E.R., Matheson, A.C. and Harwood, C.E. (2002). Experimental Design and Analysis for Tree Improvement, CSIRO Publishing.
Author: Muhammad Yaseen [aut, cre],
Sami Ullah [aut, ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between eda4treeR versions 0.1.0 dated 2018-01-24 and 0.2.0 dated 2018-02-04
DESCRIPTION | 12 +++++---- MD5 | 28 +++++++++++++++++---- NAMESPACE | 3 ++ NEWS.md | 5 +++ R/DataExam4.3.R |only R/DataExam5.2.R | 64 ++++++++++++++++++++++++------------------------- R/DataExam6.2.R |only R/DataExam8.1.R |only R/Exam4.3.R |only R/Exam6.2.R |only R/Exam8.1.1.R |only R/Exam8.1.2.R |only R/Exam8.1.R |only data/DataExam4.3.RData |only data/DataExam6.2.RData |only data/DataExam8.1.RData |only man/DataExam4.3.Rd |only man/DataExam5.2.Rd | 2 - man/DataExam6.2.Rd |only man/DataExam8.1.Rd |only man/Exam4.3.Rd |only man/Exam8.1.1.Rd |only man/Exam8.1.2.Rd |only man/Exam8.1.Rd |only 24 files changed, 71 insertions(+), 43 deletions(-)
Title: Exploratory Data Analysis and Manipulation of Multi-Label Data
Sets
Description: Exploratory data analysis and manipulation functions for multi-
label data sets along with an interactive Shiny application to ease their use.
Author: David Charte [cre],
Francisco Charte [aut]
Maintainer: David Charte <fdavidcl@ugr.es>
Diff between mldr versions 0.3.22 dated 2016-01-16 and 0.4.0 dated 2018-02-04
mldr-0.3.22/mldr/inst/shiny/rsconnect |only mldr-0.4.0/mldr/DESCRIPTION | 16 - mldr-0.4.0/mldr/MD5 | 73 ++++--- mldr-0.4.0/mldr/NAMESPACE | 22 ++ mldr-0.4.0/mldr/R/evaluate.R | 271 ++++++++--------------------- mldr-0.4.0/mldr/R/evmetrics_av.R |only mldr-0.4.0/mldr/R/evmetrics_ml.R |only mldr-0.4.0/mldr/R/evmetrics_rk.R |only mldr-0.4.0/mldr/R/filters.R | 2 mldr-0.4.0/mldr/R/mldr.R | 10 - mldr-0.4.0/mldr/R/operators.R | 9 mldr-0.4.0/mldr/R/read.arff.R | 51 +++-- mldr-0.4.0/mldr/R/write.arff.R | 26 ++ mldr-0.4.0/mldr/README.md | 6 mldr-0.4.0/mldr/build/vignette.rds |binary mldr-0.4.0/mldr/inst/CITATION | 2 mldr-0.4.0/mldr/inst/doc/mldr.pdf |binary mldr-0.4.0/mldr/man/birds.Rd | 1 mldr-0.4.0/mldr/man/concurrenceReport.Rd | 1 mldr-0.4.0/mldr/man/emotions.Rd | 1 mldr-0.4.0/mldr/man/equals-.mldr.Rd | 1 mldr-0.4.0/mldr/man/evmetrics-av.Rd |only mldr-0.4.0/mldr/man/evmetrics-ml.Rd |only mldr-0.4.0/mldr/man/evmetrics-rk.Rd |only mldr-0.4.0/mldr/man/genbase.Rd | 1 mldr-0.4.0/mldr/man/labelInteractions.Rd | 1 mldr-0.4.0/mldr/man/mldr.Rd | 9 mldr-0.4.0/mldr/man/mldrGUI.Rd | 1 mldr-0.4.0/mldr/man/mldr_evaluate.Rd | 57 +++--- mldr-0.4.0/mldr/man/mldr_from_dataframe.Rd | 1 mldr-0.4.0/mldr/man/mldr_to_labels.Rd |only mldr-0.4.0/mldr/man/mldr_transform.Rd | 1 mldr-0.4.0/mldr/man/plot.mldr.Rd | 1 mldr-0.4.0/mldr/man/plus-.mldr.Rd | 1 mldr-0.4.0/mldr/man/print.mldr.Rd | 1 mldr-0.4.0/mldr/man/read.arff.Rd | 12 - mldr-0.4.0/mldr/man/remedial.Rd | 1 mldr-0.4.0/mldr/man/roc.mldr.Rd |only mldr-0.4.0/mldr/man/sub-.mldr.Rd | 1 mldr-0.4.0/mldr/man/summary.mldr.Rd | 1 mldr-0.4.0/mldr/man/write_arff.Rd | 13 - mldr-0.4.0/mldr/tests |only 42 files changed, 274 insertions(+), 320 deletions(-)
Title: R-Interface to Gene Drop Simulation from JPSGCS
Description: R-interface to gene drop programs from Alun Thomas' Java Programs for Statistical Genetics and Computational Statistics (JPSGCS).
Author: Sigal Blay [aut],
Jinko Graham [aut],
Brad McNeney [aut, cre],
Annick Nembot-Simo [aut],
Alun Thomas [ctb],
Hin-Tak Leung [ctb]
Maintainer: Brad McNeney <mcneney@sfu.ca>
Diff between rJPSGCS versions 0.2-7 dated 2014-12-04 and 0.2-8 dated 2018-02-04
DESCRIPTION | 15 ++++++------ MD5 | 32 +++++++++++++++---------- NAMESPACE | 19 ++++++++------- R/read.pedfile.R | 4 +-- R/write.pedfile.R | 8 +++--- R/zzz.R | 5 ++++ data/exdat.rda |binary inst/java/GeneDrops.java |only inst/java/jpsgcs |only java/JPSGCS.jar |only man/FitGMLD.Rd | 10 ++++---- man/GeneDrops.Rd | 5 ---- man/rJPSGCS-package.Rd | 58 +++++++++++++++++++++-------------------------- man/read.pedfile.Rd | 5 ---- man/write.parfile.Rd | 5 ---- man/write.pedfile.Rd | 5 ---- src/readPEDfile.c | 14 +++++------ src/registerR.c |only 18 files changed, 89 insertions(+), 96 deletions(-)
Title: Data for Trails in the United States from the Rails-to-Trails
Conservancy
Description: Rail trail data from the excellent 'TrailLink' website, sponsored by the
Rails-to-Trails Conservancy <https://www.traillink.com/>. Includes information
(such as name, length, surface, and reviews) 3,846 trails and 24,413 reviews in
every state in the United States. Data can be used for to better understand
recreational trail use in the United States and for examples / teaching,
particularly those involving hierarchical or repeated measures data.
Author: Joshua Rosenberg [aut, cre]
Maintainer: Joshua Rosenberg <jmichaelrosenberg@gmail.com>
Diff between railtrails versions 0.0.2 dated 2018-02-03 and 0.0.3 dated 2018-02-04
DESCRIPTION | 17 +++++++++-------- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ R/railtrails.R | 2 ++ README.md | 4 +++- data/railtrails.rda |binary inst/doc/intro_to_railtrails.Rmd | 6 ++++++ inst/doc/intro_to_railtrails.html | 29 +++++++++++++++++------------ man/railtrails.Rd | 2 ++ vignettes/intro_to_railtrails.Rmd | 6 ++++++ 10 files changed, 59 insertions(+), 30 deletions(-)
Title: Data Cloning and MCMC Tools for Maximum Likelihood Methods
Description: Low level functions for implementing
maximum likelihood estimating procedures for
complex models using data cloning and Bayesian
Markov chain Monte Carlo methods
as described in Solymos 2010 (R Journal 2(2):29--37).
Sequential and parallel MCMC support
for 'JAGS', 'WinBUGS' and 'OpenBUGS'.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between dclone versions 2.1-2 dated 2016-03-12 and 2.1-3 dated 2018-02-04
dclone-2.1-2/dclone/inst/ChangeLog |only dclone-2.1-3/dclone/DESCRIPTION | 13 dclone-2.1-3/dclone/MD5 | 53 +- dclone-2.1-3/dclone/R/bugs.parfit.R | 240 ++++++------ dclone-2.1-3/dclone/R/clean.jags.model.R | 15 dclone-2.1-3/dclone/R/dc.fit.R | 18 dclone-2.1-3/dclone/R/dc.parfit.R | 507 +++++++++++++-------------- dclone-2.1-3/dclone/R/dcFit.R | 29 + dclone-2.1-3/dclone/R/jags.parfit.R | 163 ++++---- dclone-2.1-3/dclone/R/parCodaSamples.R | 8 dclone-2.1-3/dclone/R/parJagsModel.R | 116 +++--- dclone-2.1-3/dclone/R/parUpdate.R | 64 +-- dclone-2.1-3/dclone/R/summary.mcmc.list.dc.R | 11 dclone-2.1-3/dclone/R/write.jags.model.R | 68 +-- dclone-2.1-3/dclone/inst/CITATION | 4 dclone-2.1-3/dclone/man/bugs.parfit.Rd | 56 +- dclone-2.1-3/dclone/man/clusterSplitSB.Rd | 40 +- dclone-2.1-3/dclone/man/dc.fit.Rd | 69 ++- dclone-2.1-3/dclone/man/dc.parfit.Rd | 126 +++--- dclone-2.1-3/dclone/man/dcFit.Rd | 60 +-- dclone-2.1-3/dclone/man/dclone-package.Rd | 34 - dclone-2.1-3/dclone/man/dclone.Rd | 64 +-- dclone-2.1-3/dclone/man/dctable.Rd | 64 +-- dclone-2.1-3/dclone/man/jags.parfit.Rd | 38 +- dclone-2.1-3/dclone/man/lambdamax.diag.Rd | 16 dclone-2.1-3/dclone/man/parDosa.Rd | 80 ++-- dclone-2.1-3/dclone/man/parUpdate.Rd | 5 dclone-2.1-3/dclone/man/write.jags.model.Rd | 32 - 28 files changed, 1028 insertions(+), 965 deletions(-)
Title: Collection of Convenient Functions for Common Statistical
Computations
Description: Collection of convenient functions for common statistical computations,
which are not directly provided by R's base or stats packages.
This package aims at providing, first, shortcuts for statistical
measures, which otherwise could only be calculated with additional
effort (like standard errors or root mean squared errors). Second,
these shortcut functions are generic (if appropriate), and can be
applied not only to vectors, but also to other objects as well
(e.g., the Coefficient of Variation can be computed for vectors,
linear models, or linear mixed models; the r2()-function returns
the r-squared value for 'lm', 'glm', 'merMod' or 'lme' objects).
The focus of most functions lies on summary statistics or fit
measures for regression models, including generalized linear
models and mixed effects models. However, some of the functions
also deal with other statistical measures, like Cronbach's Alpha,
Cramer's V, Phi etc.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjstats versions 0.14.0 dated 2018-01-14 and 0.14.1 dated 2018-02-04
DESCRIPTION | 16 MD5 | 142 ++++---- NAMESPACE | 572 ++++++++++++++++----------------- NEWS.md | 559 ++++++++++++++++---------------- R/HDI.R | 338 ++++++++++--------- R/boot_ci.R | 462 +++++++++++++-------------- R/gmd.R | 2 R/grpmean.R | 596 ++++++++++++++++++----------------- R/icc.R | 2 R/internal_consistency.R | 552 ++++++++++++++++---------------- R/mcse.R | 10 R/mwu.R | 320 +++++++++--------- R/n_eff.R | 4 R/pred_vars.R | 464 ++++++++++++++------------- R/svy_scale_weights.R | 18 - R/tidy_stan.R | 45 +- R/typical.R | 5 build/partial.rdb |binary build/vignette.rds |binary inst/doc/anova-statistics.R | 66 +-- inst/doc/anova-statistics.html | 342 ++++++++++---------- inst/doc/mixedmodels-statistics.R | 138 ++++---- inst/doc/mixedmodels-statistics.html | 552 ++++++++++++++++---------------- man/boot_ci.Rd | 304 ++++++++--------- man/bootstrap.Rd | 178 +++++----- man/check_assumptions.Rd | 286 ++++++++-------- man/chisq_gof.Rd | 118 +++--- man/cod.Rd | 90 ++--- man/converge_ok.Rd | 132 +++---- man/cv.Rd | 122 +++---- man/cv_error.Rd | 104 +++--- man/deff.Rd | 86 ++--- man/efc.Rd | 66 +-- man/eta_sq.Rd | 108 +++--- man/find_beta.Rd | 216 ++++++------ man/gmd.Rd | 78 ++-- man/grpmean.Rd | 120 +++---- man/hdi.Rd | 196 +++++------ man/hoslem_gof.Rd | 92 ++--- man/icc.Rd | 256 +++++++-------- man/inequ_trend.Rd | 140 ++++---- man/is_prime.Rd | 48 +- man/mean_n.Rd | 138 ++++---- man/mn.Rd | 72 ++-- man/mwu.Rd | 104 +++--- man/nhanes_sample.Rd | 30 - man/odds_to_rr.Rd | 154 ++++----- man/overdisp.Rd | 156 ++++----- man/p_value.Rd | 108 +++--- man/pca.Rd | 96 ++--- man/pred_accuracy.Rd | 126 +++---- man/pred_vars.Rd | 142 ++++---- man/prop.Rd | 224 ++++++------- man/r2.Rd | 242 +++++++------- man/re_var.Rd | 138 ++++---- man/reexports.Rd | 32 - man/reliab_test.Rd | 317 +++++++++--------- man/rmse.Rd | 152 ++++---- man/robust.Rd | 164 ++++----- man/scale_weights.Rd | 112 +++--- man/se.Rd | 276 ++++++++-------- man/se_ybar.Rd | 58 +-- man/smpsize_lmm.Rd | 136 +++---- man/std_beta.Rd | 140 ++++---- man/svyglm.nb.Rd | 140 ++++---- man/table_values.Rd | 72 ++-- man/tidy_stan.Rd | 156 ++++----- man/typical_value.Rd | 152 ++++---- man/var_pop.Rd | 78 ++-- man/weight.Rd | 114 +++--- man/wtd_sd.Rd | 118 +++--- man/xtab_statistics.Rd | 220 ++++++------ 72 files changed, 6127 insertions(+), 5985 deletions(-)
Title: 'R' 'Markdown' Format for 'shower' Presentations
Description: 'R' 'Markdown' format for 'shower' presentations, see
<https://github.com/shower/shower>.
Author: Vadim Makeev [aut, cph] (shower, https://github.com/shower/shower),
Oleg Jahson [aut, cph] (shower, https://github.com/shower/shower),
Slava Oliyanchuk [aut, cph] (shower, https://github.com/shower/shower),
Roman Komarov [aut, cph] (shower, https://github.com/shower/shower),
Artem Polikarpov [aut, cph] (shower, https://github.com/shower/shower),
Tony Ganch [aut, cph] (shower, https://github.com/shower/shower),
Denis Hananein [aut, cph] (shower, https://github.com/shower/shower),
Gábor Csárdi [aut],
Doug Ashton [aut, cre],
JJ Allaire [aut],
RStudio [cph],
Mango Solutions [cph]
Maintainer: Doug Ashton <dashton@mango-solutions.com>
Diff between rmdshower versions 2.0.0 dated 2016-06-06 and 2.1.1 dated 2018-02-04
rmdshower-2.0.0/rmdshower/inst/examples/mango.Rmd |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-mango |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-material/LICENSE.md |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-material/README.md |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-material/docs |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-material/fonts |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-material/images |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-material/index.html |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-material/package.json |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-material/pictures |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-material/styles |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-ribbon/LICENSE.md |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-ribbon/README.md |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-ribbon/fonts |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-ribbon/images |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-ribbon/index.html |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-ribbon/package.json |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-ribbon/pictures |only rmdshower-2.0.0/rmdshower/inst/node_modules/shower-ribbon/styles |only rmdshower-2.0.0/rmdshower/inst/style-mango.css |only rmdshower-2.1.1/rmdshower/DESCRIPTION | 19 - rmdshower-2.1.1/rmdshower/MD5 | 148 ++++------ rmdshower-2.1.1/rmdshower/NAMESPACE | 1 rmdshower-2.1.1/rmdshower/NEWS.md | 10 rmdshower-2.1.1/rmdshower/R/shower.R | 19 - rmdshower-2.1.1/rmdshower/R/theme.R |only rmdshower-2.1.1/rmdshower/build |only rmdshower-2.1.1/rmdshower/inst/doc |only rmdshower-2.1.1/rmdshower/inst/examples/skeleton.Rmd | 2 rmdshower-2.1.1/rmdshower/inst/node_modules/shower-material/package |only rmdshower-2.1.1/rmdshower/inst/node_modules/shower-material/style-override.css |only rmdshower-2.1.1/rmdshower/inst/node_modules/shower-ribbon/package |only rmdshower-2.1.1/rmdshower/inst/node_modules/shower-ribbon/style-override.css |only rmdshower-2.1.1/rmdshower/inst/package.json | 3 rmdshower-2.1.1/rmdshower/inst/rmarkdown/templates/shower/resources/default.html | 5 rmdshower-2.1.1/rmdshower/inst/rmarkdown/templates/shower/skeleton/skeleton.Rmd | 86 +++-- rmdshower-2.1.1/rmdshower/inst/style-earl2016.css |only rmdshower-2.1.1/rmdshower/man/shower_presentation.Rd | 12 rmdshower-2.1.1/rmdshower/vignettes |only 39 files changed, 166 insertions(+), 139 deletions(-)
Title: Quadratic Programming with Absolute Value Constraints
Description: Extends the quadprog package to solve quadratic programs with
absolute value constraints and absolute values in the objective function.
Author: Bob Harlow [aut, cre]
Maintainer: Bob Harlow <rharlow86@gmail.com>
Diff between quadprogXT versions 0.0.1 dated 2017-05-30 and 0.0.2 dated 2018-02-04
quadprogXT-0.0.1/quadprogXT/R/constraintConstructors.R |only quadprogXT-0.0.1/quadprogXT/R/equalityConstraints.R |only quadprogXT-0.0.1/quadprogXT/R/expandConstraints.R |only quadprogXT-0.0.1/quadprogXT/R/merge.R |only quadprogXT-0.0.2/quadprogXT/DESCRIPTION | 7 quadprogXT-0.0.2/quadprogXT/MD5 | 14 quadprogXT-0.0.2/quadprogXT/NAMESPACE | 5 quadprogXT-0.0.2/quadprogXT/R/solveQPXT.R | 224 +++++++++--- quadprogXT-0.0.2/quadprogXT/man/solveQPXT.Rd | 40 +- quadprogXT-0.0.2/quadprogXT/tests/testthat/test-solveQPXT.R | 20 + 10 files changed, 219 insertions(+), 91 deletions(-)
Title: Optimized Regression Discontinuity Designs
Description: Optimized inference in regression discontinuity designs, as proposed by Imbens and Wager (2017) <arXiv:1705.01677>.
Author: Guido Imbens [aut],
Stefan Wager [aut, cre]
Maintainer: Stefan Wager <swager@stanford.edu>
Diff between optrdd versions 0.9 dated 2017-08-24 and 1.0 dated 2018-02-04
optrdd-0.9/optrdd/tests/testthat/test_all.R |only optrdd-1.0/optrdd/DESCRIPTION | 8 +- optrdd-1.0/optrdd/MD5 | 8 +- optrdd-1.0/optrdd/R/optrdd.R | 86 ++++++++++++++++++----- optrdd-1.0/optrdd/man/optrdd.Rd | 28 ++++++- optrdd-1.0/optrdd/tests/testthat/test_for_cran.R |only 6 files changed, 102 insertions(+), 28 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch [aut],
Rodney Sparapani [aut, cre],
Robert Gramacy [aut],
Charles Spanbauer [aut],
Matthew Pratola [aut],
Jean-Sebastien Roy [ctb],
Makoto Matsumoto [ctb],
Takuji Nishimura [ctb],
Bill Venables [ctb],
Brian Ripley [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 1.3 dated 2017-09-21 and 1.4 dated 2018-02-04
.Rinstignore | 10 - DESCRIPTION | 20 ++ MD5 | 268 ++++++++++++++++++++++++-------------- NAMESPACE | 22 ++- NEWS | 30 +++- R/bartModelMatrix.R |only R/class.ind.R |only R/crisk.bart.R | 102 ++++++++++++-- R/lbart.R | 96 ++++++++++--- R/mbart.R | 166 ++++++++++++++++++++---- R/mc.crisk.bart.R | 79 ++++++----- R/mc.crisk.pwbart.R | 4 R/mc.lbart.R |only R/mc.mbart.R |only R/mc.pbart.R | 57 +++++--- R/mc.pwbart.R | 2 R/mc.recur.bart.R | 71 ++++++---- R/mc.recur.pwbart.R | 14 +- R/mc.surv.bart.R | 65 +++++---- R/mc.surv.pwbart.R | 15 +- R/mc.wbart.R | 49 +++++-- R/pbart.R | 89 +++++++++--- R/predict.criskbart.R | 4 R/predict.lbart.R | 14 +- R/predict.mbart.R |only R/predict.pbart.R | 14 +- R/predict.recurbart.R | 5 R/predict.survbart.R | 7 - R/predict.wbart.R | 2 R/pwbart.R | 2 R/recur.bart.R | 83 +++++++----- R/recur.pre.bart.R | 152 +++++++--------------- R/recur.pwbart.R | 14 +- R/rs.pbart.R |only R/stratrs.R |only R/surv.bart.R | 62 ++++++--- R/surv.pwbart.R | 15 +- R/wbart.R | 44 ++++-- build |only cleanup | 14 -- cleanup.win | 14 -- data/ACTG175.rda |binary data/arq.rda |binary data/bladder.rda |binary data/lung.rda |binary data/transplant.rda |binary data/xdm20.test.rda |binary data/xdm20.train.rda |binary data/ydm20.test.rda |binary data/ydm20.train.rda |binary demo/00Index | 20 ++ demo/aids.itr.lbart.R |only demo/aids.itr.pbart.R | 12 + demo/bladder.recur.bart.R |only demo/c.surv.bart.R |only demo/cal.recur.bart.R |only demo/cube.pbart.R | 42 ++++-- demo/data.recur.pre.bart.R |only demo/dm.recur.bart.R | 34 ++-- demo/ex.mbart.R |only demo/exp.recur.bart.R |only demo/geweke.recur.bart.R |only demo/geweke.rs.pbart.R |only demo/liver.crisk.bart.R | 27 +-- demo/lung.surv.bart.R | 70 +++++----- demo/lung.surv.lbart.R |only demo/nhanes.pbart1.R | 8 + demo/np.recur.bart.R |only demo/sparse.lbart.R |only demo/sparse.pbart.R |only demo/sparse.wbart.R |only inst/cxx-ex/Makefile | 18 ++ inst/cxx-ex/bart.cpp | 82 ++++++++++- inst/cxx-ex/bart.h | 23 ++- inst/cxx-ex/bartfuns.cpp | 79 ++++++++++- inst/cxx-ex/bartfuns.h | 3 inst/cxx-ex/bd.cpp | 7 - inst/cxx-ex/bd.h | 3 inst/cxx-ex/clbart.cpp | 163 ++++++++++++++++------- inst/cxx-ex/cmbart.cpp | 303 ++++++++++++++++++++++++++++++++++--------- inst/cxx-ex/cpbart.cpp | 167 ++++++++++++++++++------ inst/cxx-ex/cwbart.cpp | 117 +++++++++++++--- inst/cxx-ex/heterbart.cpp | 3 inst/cxx-ex/heterbd.cpp | 7 - inst/cxx-ex/heterbd.h | 3 inst/cxx-ex/lmain.cpp | 39 ++--- inst/cxx-ex/mmain.cpp |only inst/cxx-ex/pmain.cpp | 42 ++---- inst/cxx-ex/rn.h | 209 +++++++++++++++++++++++++++--- inst/cxx-ex/tree.cpp | 8 + inst/cxx-ex/tree.h | 1 inst/cxx-ex/wmain.cpp |only inst/doc |only man/ACTG175.Rd | 1 man/BART-package.Rd | 27 +-- man/bartModelMatrix.Rd |only man/bladder.Rd | 84 +++++++----- man/class.ind.Rd |only man/crisk.bart.Rd | 123 ++++++++++++----- man/lbart.Rd | 76 ++++++++--- man/lung.Rd | 3 man/mbart.Rd | 196 +++++++++++++++++++++++++++- man/mc.lbart.Rd |only man/mc.mbart.Rd |only man/mc.pbart.Rd | 74 +++++++--- man/mc.surv.pwbart.Rd | 17 +- man/mc.wbart.Rd | 50 +++++-- man/pbart.Rd | 64 +++++++-- man/predict.lbart.Rd |only man/predict.mbart.Rd |only man/predict.pbart.Rd |only man/predict.recurbart.Rd | 2 man/predict.wbart.Rd | 22 +-- man/recur.bart.Rd | 109 ++++++++++----- man/recur.pre.bart.Rd | 310 +++++++++++++++++++++------------------------ man/rs.pbart.Rd |only man/stratrs.Rd |only man/surv.bart.Rd | 219 +++++++++++++++++-------------- man/wbart.Rd | 52 ++++++- src/Makevars.in | 5 src/bart.cpp | 82 ++++++++++- src/bart.h | 23 ++- src/bartfuns.cpp | 79 ++++++++++- src/bartfuns.h | 3 src/bd.cpp | 7 - src/bd.h | 3 src/clbart.cpp | 163 ++++++++++++++++------- src/cmbart.cpp | 303 ++++++++++++++++++++++++++++++++++--------- src/cpbart.cpp | 167 ++++++++++++++++++------ src/cwbart.cpp | 117 +++++++++++++--- src/heterbart.cpp | 3 src/heterbd.cpp | 7 - src/heterbd.h | 3 src/init.c | 20 +- src/rn.h | 209 +++++++++++++++++++++++++++--- src/tree.cpp | 8 + src/tree.h | 1 vignettes |only 138 files changed, 4118 insertions(+), 1609 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-12-10 0.1.4
2013-03-29 0.1.3
2012-11-12 0.1.2
2010-04-09 0.1-0
Title: Roll Call Analysis Software
Description: Estimates Poole and Rosenthal W-NOMINATE scores from roll
call votes supplied though a 'rollcall' object from package
'pscl'.
Author: Keith Poole <ktpoole@uga.edu>, Jeffrey Lewis
<jblewis@ucla.edu>, James Lo <lojames@usc.edu> and Royce
Carroll <rcarroll@rice.edu>
Maintainer: ORPHANED
Diff between wnominate versions 1.2.1 dated 2018-02-01 and 1.2.2 dated 2018-02-04
wnominate-1.2.1/wnominate/src/Makevars.win |only wnominate-1.2.2/wnominate/DESCRIPTION | 8 +++++--- wnominate-1.2.2/wnominate/MD5 | 5 ++--- wnominate-1.2.2/wnominate/src/random_wrap.c | 2 +- 4 files changed, 8 insertions(+), 7 deletions(-)
Title: Hyper-Ensemble Smote Undersampled Random Forests
Description: Machine learning supervised method to learn rare genomic features in imbalanced genetic data sets. This method can be also applied to classify or rank examples characterized by a high imbalance between the minority and majority class. hyperSMURF adopts a hyper-ensemble (ensemble of ensembles) approach, undersampling of the majority class and oversampling of the minority class to learn highly imbalanced data. Both single-core and parallel multi-core version of hyperSMURF are implemented.
Author: Giorgio Valentini [aut, cre] - AnacletoLab, Dipartimento di Informatica, Universita' degli Studi di Milano;
Max Schubach [ctb] - Charite, Universitatsmedizin Berlin;
Matteo Re [ctb] - AnacletoLab, Dipartimento di Informatica, Universita' degli Studi di Milano;
Peter N Robinson [ctb] - The Jackson Laboratory for Genomic Medicine, Farmington CT, USA.
Maintainer: Giorgio Valentini <valentini@di.unimi.it>
Diff between hyperSMURF versions 1.1.2 dated 2016-08-18 and 1.1.3 dated 2018-02-04
hyperSMURF-1.1.2/hyperSMURF/R/hyperSMURF1.1.R |only hyperSMURF-1.1.3/hyperSMURF/DESCRIPTION | 8 ++-- hyperSMURF-1.1.3/hyperSMURF/MD5 | 18 +++++----- hyperSMURF-1.1.3/hyperSMURF/R/hyperSMURF1.2.R |only hyperSMURF-1.1.3/hyperSMURF/build/partial.rdb |binary hyperSMURF-1.1.3/hyperSMURF/inst/doc/hyperSMURF-manual.pdf |binary hyperSMURF-1.1.3/hyperSMURF/man/hyperSMURF-package.Rd | 5 ++ hyperSMURF-1.1.3/hyperSMURF/man/hyperSMURF.corr.cv.parallel.Rd | 7 +++ hyperSMURF-1.1.3/hyperSMURF/man/hyperSMURF.cv.Rd | 5 ++ hyperSMURF-1.1.3/hyperSMURF/man/hyperSMURF.test.Rd | 5 ++ hyperSMURF-1.1.3/hyperSMURF/man/hyperSMURF.train.Rd | 5 ++ 11 files changed, 39 insertions(+), 14 deletions(-)
Title: Canadian Census Data and Geography from the 'CensusMapper' API
Description: Integrated, convenient, and uniform access to Canadian
Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready
tidy data frames and spatial data in multiple formats, as well as convenience functions
for working with Census variables, variable hierarchies, and region selection. API
keys are freely available with free registration at <https://censusmapper.ca/api>.
Census data and boundary geometries are reproduced and distributed on an "as
is" basis with the permission of Statistics Canada (Statistics Canada 2006;
2011; 2016).
Author: Jens von Bergmann [aut] (API creator and maintainer),
Dmitry Shkolnik [aut, cre] (Package maintainer, responsible for
correspondence),
Aaron Jacobs [aut]
Maintainer: Dmitry Shkolnik <shkolnikd@gmail.com>
Diff between cancensus versions 0.1.6 dated 2018-01-24 and 0.1.7 dated 2018-02-04
cancensus-0.1.6/cancensus/inst/cache |only cancensus-0.1.7/cancensus/DESCRIPTION | 6 cancensus-0.1.7/cancensus/MD5 | 28 - cancensus-0.1.7/cancensus/NEWS.md | 52 +- cancensus-0.1.7/cancensus/R/cancensus.R | 28 + cancensus-0.1.7/cancensus/README.md | 10 cancensus-0.1.7/cancensus/inst/CITATION | 2 cancensus-0.1.7/cancensus/inst/doc/Making_maps_with_cancensus.html | 8 cancensus-0.1.7/cancensus/inst/doc/cancensus.R | 17 cancensus-0.1.7/cancensus/inst/doc/cancensus.Rmd | 24 - cancensus-0.1.7/cancensus/inst/doc/cancensus.html | 236 +++++----- cancensus-0.1.7/cancensus/vignettes/cancensus.Rmd | 24 - 12 files changed, 257 insertions(+), 178 deletions(-)
Title: Age-Depth Modelling using Bayesian Statistics
Description: Bacon is an approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information. See Blaauw & Christen (2011) <doi:10.1214/11-BA618>.
Author: Maarten Blaauw [aut, cre],
J. Andres Christen [aut],
Judith Esquivel Vazquez [ctb],
Ted Belding [cph],
James Theiler [cph],
Brian Gough [cph],
Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rbacon versions 2.3.1.2 dated 2018-01-03 and 2.3.2 dated 2018-02-04
rbacon-2.3.1.2/rbacon/man/add.date.Rd |only rbacon-2.3.1.2/rbacon/src/hist2.cpp |only rbacon-2.3.2/rbacon/DESCRIPTION | 8 rbacon-2.3.2/rbacon/MD5 | 38 rbacon-2.3.2/rbacon/NAMESPACE | 3 rbacon-2.3.2/rbacon/NEWS.md |only rbacon-2.3.2/rbacon/R/Bacon.R | 956 +++++++++++------------- rbacon-2.3.2/rbacon/R/RcppExports.R | 4 rbacon-2.3.2/rbacon/man/Bacon.Rd | 48 - rbacon-2.3.2/rbacon/man/Bacon.hist.Rd | 17 rbacon-2.3.2/rbacon/man/Bacon_runs.Rd | 5 rbacon-2.3.2/rbacon/man/accrate.age.Rd | 4 rbacon-2.3.2/rbacon/man/accrate.depth.ghost.Rd | 2 rbacon-2.3.2/rbacon/man/add.dates.Rd |only rbacon-2.3.2/rbacon/man/agedepth.Rd | 38 rbacon-2.3.2/rbacon/man/calib.plot.Rd | 14 rbacon-2.3.2/rbacon/man/copyCalibrationCurve.Rd | 4 rbacon-2.3.2/rbacon/man/pMC.age.Rd | 4 rbacon-2.3.2/rbacon/man/proxy.ghost.Rd | 15 rbacon-2.3.2/rbacon/man/rbacon.Rd | 2 rbacon-2.3.2/rbacon/src/RcppExports.cpp | 19 rbacon-2.3.2/rbacon/src/bacon.h | 6 22 files changed, 571 insertions(+), 616 deletions(-)
Title: Multiple Change-Point Detection for Nonstationary Time Series
Description: Implements detection for the number and locations of
the change-points in a time series using the Wild Binary Segmentation and
the Locally Stationary Wavelet model.
Author: Karolos Korkas and Piotr Fryzlewicz
Maintainer: Karolos Korkas <kkorkas@yahoo.co.uk>
Diff between wbsts versions 0.3 dated 2015-09-30 and 0.4 dated 2018-02-04
DESCRIPTION | 7 ++++--- MD5 | 13 ++++++++----- NAMESPACE | 2 +- R/post.processing.R | 2 +- R/uh.wbs.R | 19 +++++++++---------- man/pkg-internal-2.Rd |only man/pkg-internal.Rd |only man/wbs.lsw.Rd | 10 +++++----- src/init.c.c |only 9 files changed, 28 insertions(+), 25 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-25 0.1.3
2017-11-22 0.1.2
2017-07-12 0.1.1-1
2017-06-27 0.1.1
2017-06-25 0.1.0
Title: g-and-k and g-and-h Distribution Functions
Description: Functions for the g-and-k and generalised g-and-h distributions.
Author: Dennis Prangle [aut, cre, cph]
Maintainer: Dennis Prangle <dennis.prangle@gmail.com>
Diff between gk versions 0.5.0 dated 2017-06-21 and 0.5.1 dated 2018-02-04
DESCRIPTION | 10 +++--- MD5 | 55 ++++++++++++++++++------------------ R/fdsa.R | 5 +++ R/mcmc.R | 1 R/pgh.R | 2 - R/pgk.R | 2 - inst |only man/Qgh_deriv.Rd | 1 man/Qgh_log_deriv.Rd | 1 man/Qgk_deriv.Rd | 1 man/Qgk_log_deriv.Rd | 1 man/abc.Rd | 1 man/abc_batch.Rd | 1 man/fdsa.Rd | 1 man/fx.Rd | 1 man/g-and-h.Rd | 3 - man/g-and-k.Rd | 3 - man/improper_uniform_log_density.Rd | 1 man/isValid.Rd | 1 man/isValid_scalar.Rd | 1 man/logSumExp.Rd | 2 - man/mcmc.Rd | 1 man/momentEstimates.Rd | 1 man/orderstats.Rd | 1 man/pgh_scalar.Rd | 3 - man/pgk_scalar.Rd | 3 - man/project.Rd | 2 - man/z2gh.Rd | 1 man/z2gk.Rd | 1 29 files changed, 47 insertions(+), 60 deletions(-)