Title: Simple Variable Treatment
Description: 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 values, rare categorical values, new categorical values (levels seen during application, but not during training). 'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 0.5.21 dated 2015-11-10 and 0.5.22 dated 2016-01-07
DESCRIPTION | 8 MD5 | 62 + NAMESPACE | 2 R/cleanTreatment.R |only R/deviationFact.R |only R/effectTreatmentC.R |only R/effectTreatmentN.R |only R/indicatorTreatment.R |only R/isBadTreatment.R |only R/outOfSample.R |only R/prevalenceFact.R |only R/utils.R |only R/vtreat.R | 1398 +++++++--------------------------------- R/vtreatImpl.R |only README.md | 87 +- build/vignette.rds |binary inst/doc/vtreat.html | 272 +++---- inst/doc/vtreatOverfit.R | 5 inst/doc/vtreatOverfit.Rmd | 7 inst/doc/vtreatOverfit.html | 162 ++-- man/catScore.Rd | 2 man/designTreatmentsC.Rd | 11 man/designTreatmentsN.Rd | 11 man/designTreatmentsZ.Rd | 12 man/hold1OutMeans.Rd | 2 man/mkCrossFrameCExperiment.Rd |only man/mkCrossFrameNExperiment.Rd |only man/pressStatOfBestLinearFit.Rd | 2 man/vtreat-package.Rd | 8 tests/testthat/testBO.R | 2 tests/testthat/testCar.R | 2 tests/testthat/testDataTable.R | 2 tests/testthat/testNoY.R | 30 tests/testthat/testParallel.R | 2 tests/testthat/testStability.R |only tests/testthat/testUniqValue.R |only tests/testthat/testW1.R | 49 + tests/testthat/testWeirdTypes.R | 2 tests/testthat/testZW.R | 2 39 files changed, 658 insertions(+), 1484 deletions(-)
Title: Data Structures and Handling for Neuroimaging Data
Description: A collection of data structures that represent
volumetric brain imaging data. The focus is on basic data handling for 3D
and 4D neuroimaging data. In addition, there are function to read and write
NIFTI files and limited support for reading AFNI files.
Author: Bradley R. Buchsbaum
Maintainer: Bradley Buchsbaum <brad.buchsbaum@gmail.com>
Diff between neuroim versions 0.0.4 dated 2015-07-02 and 0.0.6 dated 2016-01-07
neuroim-0.0.4/neuroim/man/as.vector-BrainData-ANY-method.Rd |only neuroim-0.0.6/neuroim/DESCRIPTION | 27 neuroim-0.0.6/neuroim/MD5 | 430 +++++----- neuroim-0.0.6/neuroim/NAMESPACE | 31 neuroim-0.0.6/neuroim/R/AFNI_IO.R | 134 +++ neuroim-0.0.6/neuroim/R/AllClass.R | 174 +++- neuroim-0.0.6/neuroim/R/AllGeneric.R | 131 ++- neuroim-0.0.6/neuroim/R/Axis.R | 3 neuroim-0.0.6/neuroim/R/BinaryIO.R | 16 neuroim-0.0.6/neuroim/R/BrainData.R | 2 neuroim-0.0.6/neuroim/R/BrainFileDescriptor.R | 95 -- neuroim-0.0.6/neuroim/R/BrainMetaInfo.R | 114 ++ neuroim-0.0.6/neuroim/R/BrainRegion3D.R | 18 neuroim-0.0.6/neuroim/R/BrainSlice.R | 13 neuroim-0.0.6/neuroim/R/BrainSpace.R | 42 neuroim-0.0.6/neuroim/R/BrainSurface.R |only neuroim-0.0.6/neuroim/R/BrainVector.R | 24 neuroim-0.0.6/neuroim/R/BrainVolume.R | 26 neuroim-0.0.6/neuroim/R/Display.R | 151 +++ neuroim-0.0.6/neuroim/R/FREESURFER_IO.R |only neuroim-0.0.6/neuroim/R/SparseBrainVector.R | 15 neuroim-0.0.6/neuroim/R/common.R | 24 neuroim-0.0.6/neuroim/R/conncomp.R | 11 neuroim-0.0.6/neuroim/R/neuroim.R | 1 neuroim-0.0.6/neuroim/build/vignette.rds |binary neuroim-0.0.6/neuroim/man/AFNIFileDescriptor-class.Rd | 2 neuroim-0.0.6/neuroim/man/AFNIMetaInfo-class.Rd | 2 neuroim-0.0.6/neuroim/man/AxisSet-class.Rd | 2 neuroim-0.0.6/neuroim/man/AxisSet1D-class.Rd | 2 neuroim-0.0.6/neuroim/man/AxisSet2D-class.Rd | 2 neuroim-0.0.6/neuroim/man/AxisSet3D-class.Rd | 2 neuroim-0.0.6/neuroim/man/AxisSet4D-class.Rd | 2 neuroim-0.0.6/neuroim/man/AxisSet5D-class.Rd | 2 neuroim-0.0.6/neuroim/man/Base-class.Rd | 2 neuroim-0.0.6/neuroim/man/BaseMetaInfo-class.Rd | 2 neuroim-0.0.6/neuroim/man/BaseSource-class.Rd | 2 neuroim-0.0.6/neuroim/man/BinaryReader-class.Rd | 2 neuroim-0.0.6/neuroim/man/BinaryReader.Rd | 2 neuroim-0.0.6/neuroim/man/BinaryWriter-class.Rd | 2 neuroim-0.0.6/neuroim/man/BootstrapSearchlight.Rd | 2 neuroim-0.0.6/neuroim/man/BrainBucket-class.Rd | 2 neuroim-0.0.6/neuroim/man/BrainBucketSource-class.Rd | 2 neuroim-0.0.6/neuroim/man/BrainData-class.Rd | 2 neuroim-0.0.6/neuroim/man/BrainFileDescriptor-class.Rd | 2 neuroim-0.0.6/neuroim/man/BrainFileSource-class.Rd | 11 neuroim-0.0.6/neuroim/man/BrainMetaInfo-class.Rd | 12 neuroim-0.0.6/neuroim/man/BrainSlice-class.Rd | 2 neuroim-0.0.6/neuroim/man/BrainSlice.Rd | 10 neuroim-0.0.6/neuroim/man/BrainSource-class.Rd | 4 neuroim-0.0.6/neuroim/man/BrainSpace-class.Rd | 2 neuroim-0.0.6/neuroim/man/BrainSpace.Rd | 2 neuroim-0.0.6/neuroim/man/BrainSurface-class.Rd |only neuroim-0.0.6/neuroim/man/BrainSurfaceSource-class.Rd |only neuroim-0.0.6/neuroim/man/BrainSurfaceVector-class.Rd |only neuroim-0.0.6/neuroim/man/BrainSurfaceVectorSource-class.Rd |only neuroim-0.0.6/neuroim/man/BrainVector-class.Rd | 8 neuroim-0.0.6/neuroim/man/BrainVectorSource-class.Rd | 4 neuroim-0.0.6/neuroim/man/BrainVectorSource.Rd | 2 neuroim-0.0.6/neuroim/man/BrainVolume-class.Rd | 2 neuroim-0.0.6/neuroim/man/BrainVolume.Rd | 4 neuroim-0.0.6/neuroim/man/BrainVolumeSource-class.Rd | 10 neuroim-0.0.6/neuroim/man/ClusteredBrainVolume-class.Rd | 3 neuroim-0.0.6/neuroim/man/ColumnReader-class.Rd |only neuroim-0.0.6/neuroim/man/ColumnReader.Rd |only neuroim-0.0.6/neuroim/man/DenseBrainVector-class.Rd | 2 neuroim-0.0.6/neuroim/man/DenseBrainVolume-class.Rd | 2 neuroim-0.0.6/neuroim/man/FileMetaInfo-class.Rd | 4 neuroim-0.0.6/neuroim/man/FreeSurferSurfaceGeometryMetaInfo-class.Rd |only neuroim-0.0.6/neuroim/man/FreesurferAsciiSurfaceFileDescriptor-class.Rd |only neuroim-0.0.6/neuroim/man/IndexLookupVolume-class.Rd | 2 neuroim-0.0.6/neuroim/man/Kernel-class.Rd | 2 neuroim-0.0.6/neuroim/man/Kernel.Rd | 2 neuroim-0.0.6/neuroim/man/Layer-class.Rd | 6 neuroim-0.0.6/neuroim/man/Layer.Rd | 6 neuroim-0.0.6/neuroim/man/LogicalBrainVolume-class.Rd | 2 neuroim-0.0.6/neuroim/man/MNI_SPACE_1MM.Rd | 2 neuroim-0.0.6/neuroim/man/NIMLSurfaceDataMetaInfo-class.Rd |only neuroim-0.0.6/neuroim/man/NIMLSurfaceDataMetaInfo.Rd |only neuroim-0.0.6/neuroim/man/NIMLSurfaceFileDescriptor-class.Rd |only neuroim-0.0.6/neuroim/man/NIfTIFileDescriptor-class.Rd | 2 neuroim-0.0.6/neuroim/man/NIfTIMetaInfo-class.Rd | 2 neuroim-0.0.6/neuroim/man/NamedAxis-class.Rd | 2 neuroim-0.0.6/neuroim/man/NullMetaInfo-class.Rd | 2 neuroim-0.0.6/neuroim/man/ROIVolume-class.Rd | 2 neuroim-0.0.6/neuroim/man/ROIVolume.Rd | 2 neuroim-0.0.6/neuroim/man/RandomSearchlight.Rd | 2 neuroim-0.0.6/neuroim/man/RegionCube.Rd | 12 neuroim-0.0.6/neuroim/man/RegionSphere.Rd | 4 neuroim-0.0.6/neuroim/man/RegionSquare.Rd | 16 neuroim-0.0.6/neuroim/man/Searchlight.Rd | 2 neuroim-0.0.6/neuroim/man/SparseBrainVector-class.Rd | 5 neuroim-0.0.6/neuroim/man/SparseBrainVectorSource-class.Rd | 2 neuroim-0.0.6/neuroim/man/SparseBrainVolume-class.Rd | 10 neuroim-0.0.6/neuroim/man/SurfaceDataMetaInfo-class.Rd |only neuroim-0.0.6/neuroim/man/SurfaceDataMetaInfo.Rd |only neuroim-0.0.6/neuroim/man/SurfaceGeometryMetaInfo-class.Rd |only neuroim-0.0.6/neuroim/man/SurfaceGeometryMetaInfo.Rd |only neuroim-0.0.6/neuroim/man/addDim-methods.Rd | 2 neuroim-0.0.6/neuroim/man/as-methods.Rd | 2 neuroim-0.0.6/neuroim/man/as.array-BrainData-method.Rd | 2 neuroim-0.0.6/neuroim/man/as.list-methods.Rd | 16 neuroim-0.0.6/neuroim/man/as.logical-methods.Rd | 2 neuroim-0.0.6/neuroim/man/as.mask-methods.Rd | 2 neuroim-0.0.6/neuroim/man/as.matrix-BrainData-method.Rd | 2 neuroim-0.0.6/neuroim/man/as.matrix-methods.Rd | 16 neuroim-0.0.6/neuroim/man/as.numeric-methods.Rd | 2 neuroim-0.0.6/neuroim/man/as.raster-methods.Rd | 8 neuroim-0.0.6/neuroim/man/as.sparse-methods.Rd | 2 neuroim-0.0.6/neuroim/man/as.vector-BrainData-method.Rd |only neuroim-0.0.6/neuroim/man/axes-methods.Rd | 2 neuroim-0.0.6/neuroim/man/axisToIndex-methods.Rd | 2 neuroim-0.0.6/neuroim/man/bounds-methods.Rd | 2 neuroim-0.0.6/neuroim/man/close-methods.Rd | 2 neuroim-0.0.6/neuroim/man/clusterCenters-methods.Rd | 2 neuroim-0.0.6/neuroim/man/concat-methods.Rd | 13 neuroim-0.0.6/neuroim/man/connComp-methods.Rd | 2 neuroim-0.0.6/neuroim/man/connComp3D.Rd | 6 neuroim-0.0.6/neuroim/man/coordToGrid-methods.Rd | 2 neuroim-0.0.6/neuroim/man/coordToIndex-methods.Rd | 2 neuroim-0.0.6/neuroim/man/coords-methods.Rd | 8 neuroim-0.0.6/neuroim/man/dataFile-methods.Rd | 4 neuroim-0.0.6/neuroim/man/dataFileMatches-methods.Rd | 4 neuroim-0.0.6/neuroim/man/dataReader-methods.Rd | 5 neuroim-0.0.6/neuroim/man/dim-BrainData-method.Rd | 2 neuroim-0.0.6/neuroim/man/dim-BrainSpace-method.Rd | 2 neuroim-0.0.6/neuroim/man/dim-FileMetaInfo-method.Rd | 2 neuroim-0.0.6/neuroim/man/dropDim-methods.Rd | 5 neuroim-0.0.6/neuroim/man/eachSeries-methods.Rd | 8 neuroim-0.0.6/neuroim/man/eachSlice-methods.Rd | 2 neuroim-0.0.6/neuroim/man/eachVolume-methods.Rd | 34 neuroim-0.0.6/neuroim/man/fileMatches-methods.Rd | 4 neuroim-0.0.6/neuroim/man/fill-methods.Rd | 3 neuroim-0.0.6/neuroim/man/gridToCoord-methods.Rd | 6 neuroim-0.0.6/neuroim/man/gridToIndex-methods.Rd | 2 neuroim-0.0.6/neuroim/man/headerFile-methods.Rd | 4 neuroim-0.0.6/neuroim/man/headerFileMatches-methods.Rd | 4 neuroim-0.0.6/neuroim/man/image-methods.Rd | 4 neuroim-0.0.6/neuroim/man/imageGrid.Rd | 4 neuroim-0.0.6/neuroim/man/indexToCoord-methods.Rd | 2 neuroim-0.0.6/neuroim/man/indexToGrid-methods.Rd | 6 neuroim-0.0.6/neuroim/man/indices-methods.Rd | 8 neuroim-0.0.6/neuroim/man/internal-methods.Rd | 5 neuroim-0.0.6/neuroim/man/inverseTrans-methods.Rd | 2 neuroim-0.0.6/neuroim/man/length-methods.Rd | 2 neuroim-0.0.6/neuroim/man/loadBucket.Rd | 2 neuroim-0.0.6/neuroim/man/loadData-methods.Rd | 13 neuroim-0.0.6/neuroim/man/loadFSSurface.Rd |only neuroim-0.0.6/neuroim/man/loadSurface.Rd |only neuroim-0.0.6/neuroim/man/loadVector.Rd | 2 neuroim-0.0.6/neuroim/man/loadVolume.Rd | 7 neuroim-0.0.6/neuroim/man/loadVolumeList.Rd | 2 neuroim-0.0.6/neuroim/man/lookup-methods.Rd | 8 neuroim-0.0.6/neuroim/man/makeVector.Rd | 2 neuroim-0.0.6/neuroim/man/makeVolume.Rd | 2 neuroim-0.0.6/neuroim/man/map-methods.Rd | 2 neuroim-0.0.6/neuroim/man/mapToColors.Rd |only neuroim-0.0.6/neuroim/man/matchAnatomy2D.Rd | 2 neuroim-0.0.6/neuroim/man/matchAnatomy3D.Rd | 2 neuroim-0.0.6/neuroim/man/matrixToVolumeList.Rd | 2 neuroim-0.0.6/neuroim/man/mergePartitions-methods.Rd | 2 neuroim-0.0.6/neuroim/man/names-methods.Rd | 2 neuroim-0.0.6/neuroim/man/ndim-methods.Rd | 3 neuroim-0.0.6/neuroim/man/neuroim.Rd | 6 neuroim-0.0.6/neuroim/man/numClusters-methods.Rd | 2 neuroim-0.0.6/neuroim/man/origin-methods.Rd | 3 neuroim-0.0.6/neuroim/man/overlay-methods.Rd | 2 neuroim-0.0.6/neuroim/man/partition-methods.Rd | 2 neuroim-0.0.6/neuroim/man/permMat-methods.Rd | 2 neuroim-0.0.6/neuroim/man/pick-methods.Rd | 2 neuroim-0.0.6/neuroim/man/print-AxisSet2D-method.Rd | 2 neuroim-0.0.6/neuroim/man/print-AxisSet3D-method.Rd | 2 neuroim-0.0.6/neuroim/man/print-NamedAxis-method.Rd | 2 neuroim-0.0.6/neuroim/man/print-methods.Rd | 2 neuroim-0.0.6/neuroim/man/readAFNIHeader.Rd | 2 neuroim-0.0.6/neuroim/man/readColumns-methods.Rd |only neuroim-0.0.6/neuroim/man/readElements-methods.Rd | 2 neuroim-0.0.6/neuroim/man/readHeader.Rd | 2 neuroim-0.0.6/neuroim/man/readMetaInfo-methods.Rd | 10 neuroim-0.0.6/neuroim/man/render-methods.Rd |only neuroim-0.0.6/neuroim/man/renderSlice-methods.Rd |only neuroim-0.0.6/neuroim/man/scaleSeries-methods.Rd | 6 neuroim-0.0.6/neuroim/man/series-methods.Rd | 12 neuroim-0.0.6/neuroim/man/seriesIter.Rd | 15 neuroim-0.0.6/neuroim/man/show-AxisSet1D-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-AxisSet2D-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-AxisSet3D-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-AxisSet4D-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-BaseMetaInfo-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-BrainSpace-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-BrainVector-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-BrainVectorSource-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-BrainVolume-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-FileMetaInfo-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-NamedAxis-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-NullMetaInfo-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-ROIVolume-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-SparseBrainVector-method.Rd | 2 neuroim-0.0.6/neuroim/man/show-SurfaceDataMetaInfo-method.Rd |only neuroim-0.0.6/neuroim/man/show-SurfaceGeometryMetaInfo-method.Rd |only neuroim-0.0.6/neuroim/man/slice-methods.Rd | 2 neuroim-0.0.6/neuroim/man/sliceData.Rd |only neuroim-0.0.6/neuroim/man/space-methods.Rd | 3 neuroim-0.0.6/neuroim/man/spacing-methods.Rd | 2 neuroim-0.0.6/neuroim/man/splitFill-methods.Rd | 5 neuroim-0.0.6/neuroim/man/splitReduce-methods.Rd | 11 neuroim-0.0.6/neuroim/man/splitScale-methods.Rd | 5 neuroim-0.0.6/neuroim/man/stripExtension-methods.Rd | 4 neuroim-0.0.6/neuroim/man/sub-BrainBucket-index-missing-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-ROIVolume-numeric-missing-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVector-missing-missing-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVector-missing-numeric-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVector-numeric-missing-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVector-numeric-numeric-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVolume-matrix-missing-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVolume-missing-missing-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVolume-missing-numeric-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVolume-numeric-missing-missing-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-SparseBrainVolume-numeric-numeric-ANY-method.Rd | 2 neuroim-0.0.6/neuroim/man/sub-sub-BrainBucket-index-missing-method.Rd | 2 neuroim-0.0.6/neuroim/man/subVector-methods.Rd |only neuroim-0.0.6/neuroim/man/takeSeries-methods.Rd | 2 neuroim-0.0.6/neuroim/man/takeVolume-methods.Rd | 8 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Title: Stable Isotope Mixing Model
Description: Estimates diet contributions from isotopic sources using JAGS.
Includes estimation of concentration dependence and measurement error.
Author: Jake Ferguson and Jack Hopkins
Maintainer: Jake Ferguson <troutinthemilk@gmail.com>
Diff between IsotopeR versions 0.5.1 dated 2015-11-10 and 0.5.2 dated 2016-01-07
IsotopeR-0.5.1/IsotopeR/vignettes/Fig1.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig10.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig11.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig12.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig13.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig14.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig15.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig16.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig17.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig18.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig19.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig2.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig20.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig21.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig22.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig3.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig4.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig5.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig6.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig7.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig8.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Fig9.png |only IsotopeR-0.5.1/IsotopeR/vignettes/IsoScreen.png |only IsotopeR-0.5.1/IsotopeR/vignettes/IsotopeR.Rnw.backup |only IsotopeR-0.5.1/IsotopeR/vignettes/Screenshot-IsotopeR.eps |only IsotopeR-0.5.1/IsotopeR/vignettes/Screenshot-IsotopeR.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Screenshot-Load_Previous_Run.eps |only IsotopeR-0.5.1/IsotopeR/vignettes/Screenshot-Load_Previous_Run.png |only IsotopeR-0.5.1/IsotopeR/vignettes/Screenshot-New_Run.eps |only IsotopeR-0.5.1/IsotopeR/vignettes/Screenshot-New_Run.png |only IsotopeR-0.5.2/IsotopeR/DESCRIPTION | 8 IsotopeR-0.5.2/IsotopeR/MD5 | 77 - IsotopeR-0.5.2/IsotopeR/NAMESPACE | 3 IsotopeR-0.5.2/IsotopeR/NEWS | 6 IsotopeR-0.5.2/IsotopeR/R/IsotopeRgui.R | 86 - IsotopeR-0.5.2/IsotopeR/R/Plot_jags.R | 2 IsotopeR-0.5.2/IsotopeR/inst/doc/IsotopeR.Rnw | 555 ++++------ IsotopeR-0.5.2/IsotopeR/inst/doc/IsotopeR.pdf |binary IsotopeR-0.5.2/IsotopeR/man/IsoWrapper.Rd | 18 IsotopeR-0.5.2/IsotopeR/vignettes/Figures |only IsotopeR-0.5.2/IsotopeR/vignettes/IsotopeR.Rnw | 257 ++-- 41 files changed, 498 insertions(+), 514 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors. The package has been developed and tested for binary data from GENEActiv and GENEA devices and .csv-export data from Actigraph devices. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Severine Sabia [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>
Diff between GGIR versions 1.2-1 dated 2015-12-09 and 1.2-2 dated 2016-01-07
DESCRIPTION | 8 MD5 | 30 +- R/g.analyse.R | 1 R/g.calibrate.R | 29 ++ R/g.dotorcomma.R | 66 +++-- R/g.extractheadervars.R | 2 R/g.getbout.R | 2 R/g.getmeta.R | 76 +++++- R/g.inspectfile.R | 368 +++++++++++++++++--------------- R/g.part1.R | 547 ++++++++++++++++++++++++------------------------ R/g.part4.R | 11 R/g.report.part2.R | 2 R/g.shell.GGIR.R | 475 ++++++++++++++++++----------------------- inst/NEWS.Rd | 6 man/GGIR-package.Rd | 4 man/g.part4.Rd | 5 16 files changed, 855 insertions(+), 777 deletions(-)
Title: Tools for Analysis of Diversity and Similarity in Biological
Systems
Description: A set of tools for empirical analysis of diversity (a number and frequency of different types in population) and similarity (a number and frequency of shared types in two populations) in biological or ecological systems.
Author: Maciej Pietrzak, Michal Seweryn, Grzegorz Rempala
Maintainer: Maciej Pietrzak <pietrzak.20@osu.edu>
Diff between divo versions 0.1.1 dated 2015-02-03 and 0.1.2 dated 2016-01-07
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 5 ++++- R/divo.R | 2 +- build/vignette.rds |binary inst/DivO_DP.py | 2 +- inst/DivO_EnvCheck.py | 2 +- inst/DivO_Overlap.py | 2 +- inst/doc/divo-Manual.Rnw | 2 +- inst/doc/divo-Manual.pdf |binary inst/doc/divo-Vignette.Rnw | 2 +- inst/doc/divo-Vignette.pdf |binary vignettes/divo-Manual.Rnw | 2 +- vignettes/divo-Vignette.Rnw | 2 +- 14 files changed, 29 insertions(+), 26 deletions(-)
Title: General Purpose Interface to 'Elasticsearch'
Description: Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java'
Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' 'API'
(<https://www.elastic.co/products/elasticsearch>), including functions for
setting connection details to 'Elasticsearch' instances, loading bulk data,
searching for documents with both 'HTTP' query variables and 'JSON' based body
requests. In addition, 'elastic' provides functions for interacting with 'APIs'
for 'indices', documents, nodes, clusters, an interface to the cat 'API', and
more.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between elastic versions 0.5.0 dated 2015-07-02 and 0.6.0 dated 2016-01-07
elastic-0.5.0/elastic/R/mlt.R |only elastic-0.5.0/elastic/man/mlt.Rd |only elastic-0.5.0/elastic/tests/test-all.R |only elastic-0.6.0/elastic/DESCRIPTION | 26 + elastic-0.6.0/elastic/LICENSE | 2 elastic-0.6.0/elastic/MD5 | 193 ++++++++------ elastic-0.6.0/elastic/NAMESPACE | 13 elastic-0.6.0/elastic/NEWS.md | 83 ++++++ elastic-0.6.0/elastic/R/Search.R | 65 ++-- elastic-0.6.0/elastic/R/Search_uri.R | 38 +- elastic-0.6.0/elastic/R/alias.R | 17 - elastic-0.6.0/elastic/R/cat.r | 97 ++++--- elastic-0.6.0/elastic/R/cluster.R | 94 ++++++- elastic-0.6.0/elastic/R/connect.R | 123 +++++---- elastic-0.6.0/elastic/R/count.r | 5 elastic-0.6.0/elastic/R/defunct.R |only elastic-0.6.0/elastic/R/docs_bulk.r | 227 ++++++++++++++--- elastic-0.6.0/elastic/R/docs_create.R | 2 elastic-0.6.0/elastic/R/docs_delete.R | 2 elastic-0.6.0/elastic/R/docs_get.r | 4 elastic-0.6.0/elastic/R/docs_mget.r | 9 elastic-0.6.0/elastic/R/documents.R | 16 - elastic-0.6.0/elastic/R/elastic-package.r | 23 + elastic-0.6.0/elastic/R/explain.R | 11 elastic-0.6.0/elastic/R/field_stats.R |only elastic-0.6.0/elastic/R/httr-verbs.R | 138 ++++++++-- elastic-0.6.0/elastic/R/index.R | 79 +++-- elastic-0.6.0/elastic/R/mapping.R | 61 ++-- elastic-0.6.0/elastic/R/msearch.R |only elastic-0.6.0/elastic/R/nodes.R | 20 - 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elastic-0.6.0/elastic/inst/vign/elastic_intro.md | 40 +- elastic-0.6.0/elastic/inst/vign/search.md | 56 +--- elastic-0.6.0/elastic/man/Search.Rd | 167 +++++++----- elastic-0.6.0/elastic/man/Search_uri.Rd | 44 ++- elastic-0.6.0/elastic/man/alias.Rd | 13 elastic-0.6.0/elastic/man/cat.Rd | 75 ++--- elastic-0.6.0/elastic/man/cluster.Rd | 82 +++++- elastic-0.6.0/elastic/man/connect.Rd | 26 + elastic-0.6.0/elastic/man/count.Rd | 7 elastic-0.6.0/elastic/man/docs_bulk.Rd | 80 +++++ elastic-0.6.0/elastic/man/docs_create.Rd | 4 elastic-0.6.0/elastic/man/docs_delete.Rd | 4 elastic-0.6.0/elastic/man/docs_get.Rd | 4 elastic-0.6.0/elastic/man/docs_mget.Rd | 10 elastic-0.6.0/elastic/man/documents.Rd | 18 - elastic-0.6.0/elastic/man/elastic-defunct.Rd |only elastic-0.6.0/elastic/man/elastic.Rd | 24 + elastic-0.6.0/elastic/man/es_auth.Rd | 2 elastic-0.6.0/elastic/man/es_parse.Rd | 2 elastic-0.6.0/elastic/man/explain.Rd | 8 elastic-0.6.0/elastic/man/field_stats.Rd |only elastic-0.6.0/elastic/man/index.Rd | 52 ++- elastic-0.6.0/elastic/man/index_status-defunct.Rd |only elastic-0.6.0/elastic/man/mapping.Rd | 45 +-- elastic-0.6.0/elastic/man/mapping_delete-defunct.Rd |only elastic-0.6.0/elastic/man/mlt-defunct.Rd |only elastic-0.6.0/elastic/man/msearch.Rd |only elastic-0.6.0/elastic/man/nodes-defunct.Rd |only elastic-0.6.0/elastic/man/nodes.Rd | 19 - 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elastic-0.6.0/elastic/tests/testthat/test-search_uri.R | 13 elastic-0.6.0/elastic/vignettes/elastic_intro.Rmd | 40 +- elastic-0.6.0/elastic/vignettes/search.Rmd | 56 +--- 111 files changed, 1796 insertions(+), 1257 deletions(-)
Title: Low-Level R to Java Interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
Author: Simon Urbanek <simon.urbanek@r-project.org>
Maintainer: Simon Urbanek <simon.urbanek@r-project.org>
Diff between rJava versions 0.9-7 dated 2015-07-29 and 0.9-8 dated 2016-01-07
rJava-0.9-7/rJava/jri/REngine/REngine.jar |only rJava-0.9-7/rJava/jri/REngine/Rserve.jar |only rJava-0.9-8/rJava/DESCRIPTION | 6 rJava-0.9-8/rJava/MD5 | 102 rJava-0.9-8/rJava/NEWS | 8 rJava-0.9-8/rJava/R/zzz.R.in | 14 rJava-0.9-8/rJava/configure | 12 rJava-0.9-8/rJava/configure.ac | 12 rJava-0.9-8/rJava/inst/javadoc/ArrayDimensionException.html | 4 rJava-0.9-8/rJava/inst/javadoc/ArrayWrapper.html | 4 rJava-0.9-8/rJava/inst/javadoc/ArrayWrapper_Test.html | 4 rJava-0.9-8/rJava/inst/javadoc/DummyPoint.html | 4 rJava-0.9-8/rJava/inst/javadoc/FlatException.html | 4 rJava-0.9-8/rJava/inst/javadoc/NotAnArrayException.html | 4 rJava-0.9-8/rJava/inst/javadoc/NotComparableException.html | 4 rJava-0.9-8/rJava/inst/javadoc/ObjectArrayException.html | 4 rJava-0.9-8/rJava/inst/javadoc/PrimitiveArrayException.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaArrayIterator.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaArrayTools.ArrayDimensionMismatchException.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaArrayTools.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaArrayTools_Test.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaClassLoader.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaComparator.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaImport.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaTools.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaTools_Test.DummyNonStaticClass.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaTools_Test.TestException.html | 4 rJava-0.9-8/rJava/inst/javadoc/RJavaTools_Test.html | 4 rJava-0.9-8/rJava/inst/javadoc/RectangularArrayBuilder.html | 4 rJava-0.9-8/rJava/inst/javadoc/RectangularArrayBuilder_Test.html | 4 rJava-0.9-8/rJava/inst/javadoc/RectangularArrayExamples.html | 4 rJava-0.9-8/rJava/inst/javadoc/RectangularArraySummary.html | 4 rJava-0.9-8/rJava/inst/javadoc/TestException.html | 4 rJava-0.9-8/rJava/inst/javadoc/allclasses-frame.html | 4 rJava-0.9-8/rJava/inst/javadoc/allclasses-noframe.html | 4 rJava-0.9-8/rJava/inst/javadoc/constant-values.html | 4 rJava-0.9-8/rJava/inst/javadoc/deprecated-list.html | 4 rJava-0.9-8/rJava/inst/javadoc/help-doc.html | 4 rJava-0.9-8/rJava/inst/javadoc/index-all.html | 4 rJava-0.9-8/rJava/inst/javadoc/index.html | 2 rJava-0.9-8/rJava/inst/javadoc/overview-tree.html | 4 rJava-0.9-8/rJava/inst/javadoc/package-frame.html | 4 rJava-0.9-8/rJava/inst/javadoc/package-summary.html | 4 rJava-0.9-8/rJava/inst/javadoc/package-tree.html | 4 rJava-0.9-8/rJava/inst/javadoc/serialized-form.html | 4 rJava-0.9-8/rJava/inst/jri/JRIEngine.jar |binary rJava-0.9-8/rJava/inst/jri/REngine.jar |binary rJava-0.9-8/rJava/jri/configure | 4294 ++++------ rJava-0.9-8/rJava/jri/configure.ac | 7 rJava-0.9-8/rJava/jri/tools/config.guess | 1246 +- rJava-0.9-8/rJava/jri/tools/config.sub | 605 + rJava-0.9-8/rJava/jri/tools/install-sh | 708 + rJava-0.9-8/rJava/src/rJava.h | 2 53 files changed, 3957 insertions(+), 3205 deletions(-)
Title: Applied Geochemistry EDA
Description: Geological Survey of Canada (GSC) functions for exploratory data analysis with applied geochemical data, with special application to the estimation of background ranges and identification of outliers, 'anomalies', to support mineral exploration and environmental studies. Additional functions are provided to support analytical data QA/QC, ANOVA for investigations of field sampling and analytical variability, and utility tasks. NOTE: function caplot() for concentration-area plots employs package 'akima', however, 'akima' is only licensed for not-for-profit use. Therefore, not-for-profit users of 'rgr' will have to independently make package 'akima' available through library(....); and use of function caplot() by for-profit users will fail.
Author: Robert G. Garrett
Maintainer: Robert G. Garrett <robert.garrett@canada.ca>
Diff between rgr versions 1.1.11 dated 2015-05-04 and 1.1.13 dated 2016-01-07
rgr-1.1.11/rgr/inst/doc/What_is_in_rgr_1-1-11.pdf |only rgr-1.1.11/rgr/inst/doc/rgr_Overview_1-1-11.pdf |only rgr-1.1.11/rgr/inst/doc/rgr_func_list_1-1-11.pdf |only rgr-1.1.11/rgr/man/rgr_1.1.11-package.Rd |only rgr-1.1.13/rgr/DESCRIPTION | 10 +- rgr-1.1.13/rgr/MD5 | 82 +++++++++++----------- rgr-1.1.13/rgr/NAMESPACE | 10 +- rgr-1.1.13/rgr/R/ad.plot3.R | 41 ++++++----- rgr-1.1.13/rgr/R/ad.plot4.R | 2 rgr-1.1.13/rgr/R/caplot.R | 35 ++------- rgr-1.1.13/rgr/R/gx.hist.R | 6 + rgr-1.1.13/rgr/R/gx.mf.R |only rgr-1.1.13/rgr/R/gx.rma.R | 66 +++++++++++------ rgr-1.1.13/rgr/R/gx.t.test.R |only rgr-1.1.13/rgr/R/inset.R | 5 - rgr-1.1.13/rgr/R/shape.R | 5 + rgr-1.1.13/rgr/R/shape.alt.R |only rgr-1.1.13/rgr/data/ad.test.rda |binary rgr-1.1.13/rgr/data/crm.test.new.rda |binary rgr-1.1.13/rgr/data/crm.test.rda |binary rgr-1.1.13/rgr/data/fix.test.asis.rda |binary rgr-1.1.13/rgr/data/fix.test.rda |binary rgr-1.1.13/rgr/data/kola.c.rda |binary rgr-1.1.13/rgr/data/kola.o.rda |binary rgr-1.1.13/rgr/data/ms.data1.rda |binary rgr-1.1.13/rgr/data/ms.data2.rda |binary rgr-1.1.13/rgr/data/ms.data3.rda |binary rgr-1.1.13/rgr/data/ogrady.mat2open.rda |binary rgr-1.1.13/rgr/data/ogrady.rda |binary rgr-1.1.13/rgr/data/sind.mat2open.rda |binary rgr-1.1.13/rgr/data/sind.rda |binary rgr-1.1.13/rgr/data/triples.test1.rda |binary rgr-1.1.13/rgr/data/triples.test2.rda |binary rgr-1.1.13/rgr/inst/doc/What_is_in_rgr_1-1-13.pdf |only rgr-1.1.13/rgr/inst/doc/rgr_Overview_1-1-13.pdf |only rgr-1.1.13/rgr/inst/doc/rgr_func_list_1-1-13.pdf |only rgr-1.1.13/rgr/man/ad.plot3.Rd | 10 +- rgr-1.1.13/rgr/man/ad.plot4.Rd | 2 rgr-1.1.13/rgr/man/caplot.Rd | 14 +-- rgr-1.1.13/rgr/man/gx.hist.Rd | 10 +- rgr-1.1.13/rgr/man/gx.mf.Rd |only rgr-1.1.13/rgr/man/gx.mvalloc.Rd | 4 - rgr-1.1.13/rgr/man/gx.mvalloc.closed.Rd | 4 - rgr-1.1.13/rgr/man/gx.rma.Rd | 3 rgr-1.1.13/rgr/man/gx.t.test.Rd |only rgr-1.1.13/rgr/man/inset.Rd | 2 rgr-1.1.13/rgr/man/rgr_1.1.13-package.Rd |only rgr-1.1.13/rgr/man/shape.Rd | 6 - rgr-1.1.13/rgr/man/shape.alt.Rd |only 49 files changed, 172 insertions(+), 145 deletions(-)
Title: A Toolbox for the Analysis of Proteomics Data
Description: Tools for the statistical analysis and visualization of (relative and absolute) quantitative (LFQ,TMT,HRM) Proteomics data.
Author: Erik Ahrne
Maintainer: Erik Ahrne <erik.ahrne@unibas.ch>
Diff between SafeQuant versions 2.2.1 dated 2016-01-05 and 2.2.2 dated 2016-01-07
SafeQuant-2.2.1/SafeQuant/exec/commitToTPPServer.sh |only SafeQuant-2.2.1/SafeQuant/exec/createDocumentation.sh |only SafeQuant-2.2.1/SafeQuant/inst/version/TODO.txt |only SafeQuant-2.2.2/SafeQuant/DESCRIPTION | 6 SafeQuant-2.2.2/SafeQuant/MD5 | 25 +- SafeQuant-2.2.2/SafeQuant/README.md | 15 - SafeQuant-2.2.2/SafeQuant/exec/mFuzzClustering.R | 128 +++++++++-- SafeQuant-2.2.2/SafeQuant/inst/manuals/SafeQuant-man.pdf |binary SafeQuant-2.2.2/SafeQuant/inst/testData |only SafeQuant-2.2.2/SafeQuant/tests/initTestSession.R | 32 +- SafeQuant-2.2.2/SafeQuant/tests/testExpressionAnalysis.R | 52 ++-- SafeQuant-2.2.2/SafeQuant/tests/testIdentificationAnalysis.R | 10 SafeQuant-2.2.2/SafeQuant/tests/testParser.R | 2 SafeQuant-2.2.2/SafeQuant/tests/testTMT.R | 8 SafeQuant-2.2.2/SafeQuant/tests/testTargeted.R | 2 15 files changed, 184 insertions(+), 96 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre],
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Ben Baumer [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Jeff Arnold [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.11 dated 2015-08-14 and 1.12 dated 2016-01-07
DESCRIPTION | 35 +++++--- MD5 | 149 +++++++++++++++++++------------------- NAMESPACE | 4 + R/block.R | 103 ++++++++++++++++++-------- R/cache.R | 5 - R/citation.R | 12 ++- R/defaults.R | 1 R/engine.R | 65 +++++++++++++--- R/header.R | 2 R/highlight.R | 3 R/hooks-extra.R | 2 R/hooks-html.R | 43 +++++++--- R/hooks-latex.R | 36 ++++----- R/hooks-md.R | 68 ++++++++++++----- R/hooks-rst.R | 4 - R/hooks-textile.R | 3 R/hooks.R | 23 +++++ R/output.R | 16 +++- R/pandoc.R | 4 - R/plot.R | 43 ++++++++++ R/rocco.R | 12 +-- R/spin.R | 5 + R/table.R | 99 +++++++++++++++++++------ R/template.R | 2 R/themes.R | 2 R/utils-base64.R | 2 R/utils-conversion.R | 50 ++++++++++++ R/utils-sweave.R | 4 - R/utils.R | 81 +++++++++++++++++--- README.md | 5 - build/knitr.pdf |binary build/vignette.rds |binary inst/doc/docco-classic.html | 2 inst/doc/docco-linear.html | 2 inst/doc/knit_expand.html | 4 - inst/doc/knit_print.html | 124 ++++++++++++++++++------------- inst/doc/knitr-intro.html | 87 ++++++++++++++-------- inst/doc/knitr-markdown.html | 4 - inst/doc/knitr-refcard.pdf |binary inst/examples/knitr-beamer.Rnw | 2 inst/examples/knitr-graphics.Rnw | 24 +++--- inst/examples/knitr-listings.Rnw | 2 inst/examples/knitr-manual.Rnw | 7 + inst/examples/knitr-manual.bib | 8 +- inst/examples/knitr-manual.lyx | 34 ++++++-- inst/examples/knitr-minimal.Rnw | 2 inst/examples/knitr-packages.bib | 56 +++++++------- inst/examples/knitr-spin.html | 2 inst/examples/knitr-subfloats.Rnw | 4 - inst/examples/knitr-themes.Rnw | 4 - inst/examples/knitr-twocolumn.Rnw | 4 - inst/examples/upload-github.R | 11 +- man/all_patterns.Rd | 52 ------------- man/asis_output.Rd | 5 + man/chunk_hook.Rd | 2 man/hook_plot.Rd | 8 +- man/include_graphics.Rd |only man/kable.Rd | 7 + man/knit2html.Rd | 5 + man/knit_engines.Rd | 7 - man/knit_hooks.Rd | 7 - man/knit_patterns.Rd | 7 - man/knit_theme.Rd | 5 - man/knit_watch.Rd |only man/opts_chunk.Rd | 7 - man/opts_hooks.Rd |only man/opts_knit.Rd | 7 - man/opts_template.Rd | 7 - man/output_hooks.Rd | 8 +- man/rand_seed.Rd | 2 man/spin.Rd | 5 + man/write_bib.Rd | 12 ++- tests/testit/test-hooks.R | 15 +++ tests/testit/test-output.R | 28 +++++++ tests/testit/test-plot.R | 13 +++ tests/testit/test-table.R | 6 + tests/testit/test-utils.R | 8 ++ 77 files changed, 976 insertions(+), 513 deletions(-)
Title: Image Processing Library Based on CImg
Description: Fast image processing for images in up to 4 dimensions (two spatial
dimensions, one time/depth dimension, one colour dimension). Provides most
traditional image processing tools (filtering, morphology, transformations,
etc.) as well as various functions for easily analysing image data using R.
Author: Simon Barthelme [aut, cre],
Antoine Cecchi [ctb]
Maintainer: Simon Barthelme <simon.barthelme@gipsa-lab.fr>
Diff between imager versions 0.14 dated 2015-09-18 and 0.15 dated 2016-01-07
imager-0.14/imager/man/subim.Rd |only imager-0.15/imager/DESCRIPTION | 18 imager-0.15/imager/MD5 | 206 +-- imager-0.15/imager/NAMESPACE | 13 imager-0.15/imager/NEWS | 11 imager-0.15/imager/R/RcppExports.R | 118 -- imager-0.15/imager/R/cimg_class.R | 1509 +++----------------------- imager-0.15/imager/R/conversions.R |only imager-0.15/imager/R/coordinates.R |only imager-0.15/imager/R/imgen.R |only imager-0.15/imager/R/interpolation.R | 44 imager-0.15/imager/R/splitcombine.R |only imager-0.15/imager/R/stencils.R |only imager-0.15/imager/R/utils.R | 435 +++++++ imager-0.15/imager/README.md | 3 imager-0.15/imager/inst/include/CImg.h | 11 imager-0.15/imager/man/FFT.Rd | 6 imager-0.15/imager/man/add.colour.Rd | 2 imager-0.15/imager/man/as.cimg.Rd | 6 imager-0.15/imager/man/as.cimg.array.Rd | 4 imager-0.15/imager/man/as.cimg.data.frame.Rd | 4 imager-0.15/imager/man/as.cimg.function.Rd | 34 imager-0.15/imager/man/as.data.frame.cimg.Rd | 4 imager-0.15/imager/man/as.raster.cimg.Rd | 4 imager-0.15/imager/man/at.Rd | 2 imager-0.15/imager/man/autocrop.Rd | 2 imager-0.15/imager/man/blur_anisotropic.Rd | 4 imager-0.15/imager/man/boats.Rd | 2 imager-0.15/imager/man/boxblur.Rd | 2 imager-0.15/imager/man/boxblur_xy.Rd | 4 imager-0.15/imager/man/bucketfill.Rd | 6 imager-0.15/imager/man/capture.plot.Rd | 4 imager-0.15/imager/man/center.stencil.Rd | 4 imager-0.15/imager/man/channels.Rd | 2 imager-0.15/imager/man/cimg.Rd | 4 imager-0.15/imager/man/cimg.dimensions.Rd | 2 imager-0.15/imager/man/cimg.extract.Rd | 29 imager-0.15/imager/man/cimg2im.Rd | 4 imager-0.15/imager/man/convolve.Rd | 6 imager-0.15/imager/man/correlate.Rd | 6 imager-0.15/imager/man/deriche.Rd | 2 imager-0.15/imager/man/diffusion_tensors.Rd | 2 imager-0.15/imager/man/displacement.Rd | 2 imager-0.15/imager/man/display.Rd | 6 imager-0.15/imager/man/display_list.Rd | 2 imager-0.15/imager/man/distance_transform.Rd | 4 imager-0.15/imager/man/erode.Rd | 6 imager-0.15/imager/man/extract_patches.Rd | 4 imager-0.15/imager/man/frames.Rd | 2 imager-0.15/imager/man/get.locations.Rd | 5 imager-0.15/imager/man/get.stencil.Rd | 4 imager-0.15/imager/man/get_gradient.Rd | 2 imager-0.15/imager/man/get_hessian.Rd | 2 imager-0.15/imager/man/grayscale.Rd | 2 imager-0.15/imager/man/haar.Rd | 4 imager-0.15/imager/man/idply.Rd | 4 imager-0.15/imager/man/iiply.Rd | 7 imager-0.15/imager/man/ilply.Rd | 4 imager-0.15/imager/man/im2cimg.Rd | 2 imager-0.15/imager/man/im_split.Rd | 4 imager-0.15/imager/man/imager.Rd | 2 imager-0.15/imager/man/imager.colourspaces.Rd | 2 imager-0.15/imager/man/imager.combine.Rd | 21 imager-0.15/imager/man/imager.replace.Rd |only imager-0.15/imager/man/imappend.Rd | 2 imager-0.15/imager/man/imdirac.Rd | 8 imager-0.15/imager/man/imdraw.Rd | 6 imager-0.15/imager/man/imfill.Rd | 12 imager-0.15/imager/man/imgradient.Rd | 6 imager-0.15/imager/man/imhessian.Rd | 4 imager-0.15/imager/man/imnoise.Rd | 9 imager-0.15/imager/man/imrotate.Rd | 2 imager-0.15/imager/man/imsharpen.Rd | 3 imager-0.15/imager/man/imshift.Rd | 2 imager-0.15/imager/man/imsplit.Rd | 6 imager-0.15/imager/man/imsub.Rd |only imager-0.15/imager/man/imwarp.Rd | 10 imager-0.15/imager/man/interp.Rd | 2 imager-0.15/imager/man/isoblur.Rd | 2 imager-0.15/imager/man/label.Rd | 5 imager-0.15/imager/man/liply.Rd | 4 imager-0.15/imager/man/load.image.Rd | 6 imager-0.15/imager/man/medianblur.Rd | 2 imager-0.15/imager/man/mirror.Rd | 2 imager-0.15/imager/man/pad.Rd | 2 imager-0.15/imager/man/periodic.part.Rd | 5 imager-0.15/imager/man/permute_axes.Rd | 2 imager-0.15/imager/man/pixel.grid.Rd | 12 imager-0.15/imager/man/pixel.index.Rd | 4 imager-0.15/imager/man/play.Rd | 2 imager-0.15/imager/man/plot.cimg.Rd | 2 imager-0.15/imager/man/renorm.Rd | 4 imager-0.15/imager/man/resize.Rd | 2 imager-0.15/imager/man/resize_uniform.Rd | 4 imager-0.15/imager/man/rotate_xy.Rd | 2 imager-0.15/imager/man/save.image.Rd | 2 imager-0.15/imager/man/selectSimilar.Rd | 6 imager-0.15/imager/man/squeeze.Rd | 2 imager-0.15/imager/man/stencil.cross.Rd | 4 imager-0.15/imager/man/sub-.cimg.Rd | 2 imager-0.15/imager/man/threshold.Rd | 18 imager-0.15/imager/man/vanvliet.Rd | 12 imager-0.15/imager/man/warp.Rd | 2 imager-0.15/imager/man/watershed.Rd | 12 imager-0.15/imager/src/Makevars.win | 2 imager-0.15/imager/src/filtering.cpp | 81 - imager-0.15/imager/src/morphology.cpp | 15 imager-0.15/imager/src/transformations.cpp | 22 108 files changed, 1183 insertions(+), 1741 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits and imputation of censored data.
Author: Clifford Anderson-Bergman; the Eigen team for Eigen library included(for C++ matrix operations); uses Marloes Maathuis's HeightMap algorithm (MLEcens::reduc)
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.3.2 dated 2016-01-05 and 1.3.3 dated 2016-01-07
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS | 10 ++++++++++ src/icenReg_files/experimentalCode.cpp | 2 ++ src/icenReg_files/ic_sp_ch.cpp | 7 +++++-- src/icenReg_files/regressionTransforms.cpp | 2 +- 6 files changed, 28 insertions(+), 13 deletions(-)
Title: Kinship-Adjusted Survival SNP-Set Analysis
Description: SNP-set association testing for censored phenotypes in the presence of intrafamilial correlation.
Author: Martin Leclerc and Lajmi Lakhal Chaieb
Maintainer: Martin Leclerc <martin.leclerc.5@ulaval.ca>
Diff between gyriq versions 1.0.1 dated 2015-11-23 and 1.0.2 dated 2016-01-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/gyriq.R | 15 +++++++++++++-- R/testGyriq.R | 11 +++++++++++ man/gyriq-package.Rd | 15 +++++++++++++-- man/testGyriq.Rd | 11 +++++++++++ src/kernel_func.c | 7 ++++++- 7 files changed, 64 insertions(+), 15 deletions(-)
Title: Variable Selection Deviation Measures and Instability Tests for
High-Dimensional Generalized Linear Models
Description: Variable selection deviation (VSD) measures and instability tests for high-dimensional model selection methods such as LASSO, SCAD and MCP, etc., to decide whether the sparse patterns identified by those methods are reliable.
Author: Ying Nan <nanx0006@gmail.com>, Yanjia Yu <yuxxx748@umn.edu>, Yuhong Yang <yyang@stat.umn.edu>, Yi Yang <yi.yang6@mcgill.ca>
Maintainer: Yi Yang <yi.yang6@mcgill.ca>
Diff between glmvsd versions 1.3 dated 2015-07-25 and 1.4 dated 2016-01-07
ChangeLog | 6 + DESCRIPTION | 14 +-- MD5 | 30 +++---- NAMESPACE | 4 R/binomialfit.R | 24 ++--- R/gaussianfit.R | 24 ++--- R/glmvsd.R | 208 +++++++++++++++++++++++++++----------------------- R/logitARM.R | 90 +++++++++++---------- R/logitIC.R | 54 ++++++------ R/lsARM.R | 95 +++++++++++----------- R/lsIC.R | 6 - R/modelfit.R | 36 ++++---- R/stability.test.R | 103 ++++++++++++------------ R/tools.R | 11 -- man/glmvsd.Rd | 16 ++- man/stability.test.Rd | 8 + 16 files changed, 381 insertions(+), 348 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods such as principal component methods and clustering.
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between FactoMineR versions 1.31.4 dated 2015-10-09 and 1.31.5 dated 2016-01-07
DESCRIPTION | 10 MD5 | 32 +- NAMESPACE | 3 R/AovSum.r | 192 +++++++++-------- R/CA.R | 2 R/FAMD.R | 2 R/MFA.R | 2 R/catdes.r | 2 R/condes.r | 4 R/plot.FAMD.R | 5 R/plot.MFA.R | 14 - R/plotellipses.r | 48 ++-- R/summary.CA.r | 2 inst/doc/FactoMineR.pdf |binary inst/doc/clustering_and_pricipal_component_methods.pdf |binary man/plot.MFA.Rd | 2 man/plotellipses.Rd | 6 17 files changed, 175 insertions(+), 151 deletions(-)
Title: Dynamic Range Boxes
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>,
Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>,
Robert R. Junker <Robert.Junker@sbg.ac.at>,
Jonas Kuppler <Jonas.Kuppler@uni-duesseldorf.de>,
Arne Bathke <Arne.Bathke@sbg.ac.at>
Maintainer: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>
Diff between dynRB versions 0.5 dated 2015-12-24 and 0.6 dated 2016-01-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/unitTests/test_dynRB_VPa.R | 17 ----------------- man/dynRB-package.Rd | 4 ++-- tests/testthat/test_dynRB_VPa.R | 17 ----------------- 5 files changed, 9 insertions(+), 43 deletions(-)
Title: Arps Decline Curve Analysis in R
Description: Functions for Arps decline-curve analysis on oil and gas data. Includes exponential, hyperbolic, harmonic, and hyperbolic-to-exponential models as well as the preceding with initial curtailment. Functions included for computing rate, cumulative production, instantaneous decline, EUR, time to economic limit, and performing least-squares best fits.
Author: Derrick Turk [aut, cre, cph]
Maintainer: Derrick Turk <dwt@terminusdatascience.com>
Diff between aRpsDCA versions 1.0.1 dated 2015-06-22 and 1.0.2 dated 2016-01-07
DESCRIPTION | 9 +++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 2 ++ R/arps.R | 6 ++++-- R/bestfit.R | 2 +- R/curtail.R | 2 +- R/eur.R | 2 +- R/s3.R | 2 +- README.md | 9 +++++---- tests/fit_and_plot.R | 2 +- tests/fit_and_plot_from_Np.R | 2 +- 11 files changed, 32 insertions(+), 26 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.4.8 dated 2015-12-23 and 0.5.0 dated 2016-01-07
DESCRIPTION | 8 - MD5 | 34 ++--- NAMESPACE | 1 R/lin.ratio.R | 8 - R/vardchangannual.R |only R/vardchanges.R | 302 +++++++++++++++++++++++++++++++----------------- R/vardchangespoor.R | 51 +++++--- R/vardcros.R | 37 +++-- R/vardom.R | 4 inst/CITATION | 6 inst/COPYING | 2 inst/NEWS | 4 man/lin.ratio.Rd | 9 - man/vardchangannual.Rd |only man/vardchanges.Rd | 43 ++++++ man/vardchangespoor.Rd | 23 ++- man/vardcros.Rd | 8 - man/vardcrospoor.Rd | 1 man/vardpoor-package.Rd | 4 19 files changed, 364 insertions(+), 181 deletions(-)
Title: Estimating Mixed Graphical Models
Description: Estimation of Mixed Graphical model using L1-regularized neighborhood regression.
Author: Jonas Haslbeck
Maintainer: Jonas Haslbeck <jonashaslbeck@gmail.com>
Diff between mgm versions 1.1-3 dated 2016-01-06 and 1.1-4 dated 2016-01-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- man/mgm-package.Rd | 2 +- src/mMRFSampler_Ccore.cpp | 7 ++++++- 4 files changed, 13 insertions(+), 8 deletions(-)
Title: Analysis of Evolutionary Rates in an OU Framework
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between OUwie versions 1.46 dated 2015-09-05 and 1.48 dated 2016-01-07
DESCRIPTION | 10 - MD5 | 22 +-- NAMESPACE | 6 R/OUwie.R | 10 - R/OUwie.boot.R | 33 +++- R/OUwie.sim.R | 28 +++ R/OUwie.slice.R | 11 - R/hOUwie.R |only R/pathLike.R |only R/varcov.ou.R | 207 +++++++++++++++------------- R/weight.mat.R | 385 ++++++++++++++++++++++++++++------------------------- man/OUwie.sim.Rd | 5 man/OUwie.slice.Rd | 3 13 files changed, 404 insertions(+), 316 deletions(-)
Title: Multi-Model Inference
Description: Model selection and model averaging based on information criteria
(AICc and alike).
Author: Kamil Bartoń
Maintainer: Kamil Bartoń <kamil.barton@go2.pl>
Diff between MuMIn versions 1.15.1 dated 2015-07-03 and 1.15.6 dated 2016-01-07
MuMIn-1.15.1/MuMIn/R/glm-link-new.R |only MuMIn-1.15.1/MuMIn/R/predict-new.R |only MuMIn-1.15.6/MuMIn/DESCRIPTION | 19 MuMIn-1.15.6/MuMIn/MD5 | 63 - MuMIn-1.15.6/MuMIn/NAMESPACE | 14 MuMIn-1.15.6/MuMIn/NEWS | 373 ++++++----- MuMIn-1.15.6/MuMIn/R/Weights.R | 1 MuMIn-1.15.6/MuMIn/R/arm.glm.R | 24 MuMIn-1.15.6/MuMIn/R/coefTable.R | 159 ++++ MuMIn-1.15.6/MuMIn/R/coeffs.R | 14 MuMIn-1.15.6/MuMIn/R/dredge.R | 168 ++--- MuMIn-1.15.6/MuMIn/R/get.models.R | 14 MuMIn-1.15.6/MuMIn/R/makeArgs.R | 91 +- MuMIn-1.15.6/MuMIn/R/model.avg.R | 34 - MuMIn-1.15.6/MuMIn/R/modify.model.selection.R | 65 +- MuMIn-1.15.6/MuMIn/R/pdredge.R | 150 ++-- MuMIn-1.15.6/MuMIn/R/rbind.model.selection.R | 33 - MuMIn-1.15.6/MuMIn/R/substitution.R | 66 +- MuMIn-1.15.6/MuMIn/R/utils-misc.R | 9 MuMIn-1.15.6/MuMIn/R/utils-models.R | 135 +++- MuMIn-1.15.6/MuMIn/data/Beetle.rda |binary MuMIn-1.15.6/MuMIn/data/Cement.rda |binary MuMIn-1.15.6/MuMIn/data/GPA.rda |binary MuMIn-1.15.6/MuMIn/man/MuMIn-package.Rd | 6 MuMIn-1.15.6/MuMIn/man/data-Beetle.Rd | 65 -- MuMIn-1.15.6/MuMIn/man/data-GPA.Rd | 10 MuMIn-1.15.6/MuMIn/man/dredge.Rd | 116 +-- MuMIn-1.15.6/MuMIn/man/exprApply.Rd | 8 MuMIn-1.15.6/MuMIn/man/par.avg.Rd | 4 MuMIn-1.15.6/MuMIn/man/std.coef.Rd | 5 MuMIn-1.15.6/MuMIn/man/subset.model.selection.Rd | 2 MuMIn-1.15.6/MuMIn/man/supported-classes.Rd | 13 MuMIn-1.15.6/MuMIn/tests/classes.R | 732 ++++++++++------------- MuMIn-1.15.6/MuMIn/tests/gam-smooth-consitency.R |only 34 files changed, 1364 insertions(+), 1029 deletions(-)
Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between hisse versions 1.3 dated 2015-10-03 and 1.4 dated 2016-01-07
hisse-1.3/hisse/tests |only hisse-1.4/hisse/DESCRIPTION | 10 +++++----- hisse-1.4/hisse/MD5 | 9 +++------ hisse-1.4/hisse/R/hisseNull4.R | 4 ++-- hisse-1.4/hisse/R/plotHisse.R | 2 ++ 5 files changed, 12 insertions(+), 13 deletions(-)
Title: Calculate Generalized Eigenvalues, the Generalized Schur
Decomposition and the Generalized Singular Value Decomposition
of a Matrix Pair with Lapack
Description: Functions to compute generalized eigenvalues and eigenvectors,
the generalized Schur decomposition and
the generalized Singular Value Decomposition of a matrix pair,
using Lapack routines.
Author: Berend Hasselman [cre, aut],
Lapack authors [aut, cph]
Maintainer: Berend Hasselman <bhh@xs4all.nl>
Diff between geigen versions 1.8 dated 2015-11-02 and 1.9 dated 2016-01-07
DESCRIPTION | 8 MD5 | 32 +- NEWS | 5 R/gsvd.R | 43 ++ inst/COPYRIGHTS | 11 man/geigen.Rd | 2 man/gqz.Rd | 2 man/gsvd.Rd | 2 src/dggsvd3.f |only src/dggsvp3.f |only src/xdggsvd.f | 9 src/xzggsvd.f | 7 src/zggesall.f | 16 - src/zggevall.f | 8 src/zggevsdeps.f | 50 +-- src/zggsvdall.f | 761 +++++++++++++++++-------------------------------- tests/tgsvd4.R | 12 tests/tgsvd4.Rout.save | 39 +- 18 files changed, 424 insertions(+), 583 deletions(-)
Title: Analysis of Binary Character Evolution
Description: Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Jeffrey C. Oliver <jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between corHMM versions 1.17 dated 2015-10-29 and 1.18 dated 2016-01-07
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ancRECON.R | 9 ++++++--- 3 files changed, 12 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-22 0.3.0