Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
Author: Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>),
Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>),
Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>),
Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>),
Jeff Farrell [ctb],
Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>),
Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>),
Patrick Roelli [ctb]
Maintainer: Paul Hoffman <nygcSatijalab@nygenome.org>
Diff between Seurat versions 2.3.4 dated 2018-07-17 and 3.0.0 dated 2019-04-15
Seurat-2.3.4/Seurat/R/alignment.R |only Seurat-2.3.4/Seurat/R/as.R |only Seurat-2.3.4/Seurat/R/cluster_determination.R |only Seurat-2.3.4/Seurat/R/cluster_determination_internal.R |only Seurat-2.3.4/Seurat/R/cluster_validation.R |only Seurat-2.3.4/Seurat/R/conversion.R |only Seurat-2.3.4/Seurat/R/deprecated_functions.R |only Seurat-2.3.4/Seurat/R/differential_expression_internal.R |only Seurat-2.3.4/Seurat/R/dimensional_reduction_internal.R |only Seurat-2.3.4/Seurat/R/dimensional_reduction_utilities.R |only Seurat-2.3.4/Seurat/R/interaction.R |only Seurat-2.3.4/Seurat/R/jackstraw.R |only Seurat-2.3.4/Seurat/R/jackstraw_internal.R |only Seurat-2.3.4/Seurat/R/multi_modal.R |only Seurat-2.3.4/Seurat/R/not_used_yet.R |only Seurat-2.3.4/Seurat/R/plotting.R |only Seurat-2.3.4/Seurat/R/plotting_internal.R |only Seurat-2.3.4/Seurat/R/plotting_utilities.R |only Seurat-2.3.4/Seurat/R/preprocessing_internal.R |only Seurat-2.3.4/Seurat/R/printing_utilities.R |only Seurat-2.3.4/Seurat/R/scoring.R |only Seurat-2.3.4/Seurat/R/seurat.R |only Seurat-2.3.4/Seurat/R/snn.R |only Seurat-2.3.4/Seurat/R/spatial.R |only Seurat-2.3.4/Seurat/R/spatial_internal.R |only Seurat-2.3.4/Seurat/R/tSNE_project.R |only Seurat-2.3.4/Seurat/R/utilities_internal.R |only Seurat-2.3.4/Seurat/man/AddImputedScore.Rd |only Seurat-2.3.4/Seurat/man/AddSamples.Rd |only Seurat-2.3.4/Seurat/man/AddSmoothedScore.Rd |only Seurat-2.3.4/Seurat/man/AlignSubspace.Rd |only Seurat-2.3.4/Seurat/man/AssessNodes.Rd |only Seurat-2.3.4/Seurat/man/AssessSplit.Rd |only Seurat-2.3.4/Seurat/man/AverageDetectionRate.Rd |only Seurat-2.3.4/Seurat/man/AveragePCA.Rd |only Seurat-2.3.4/Seurat/man/BatchGene.Rd |only Seurat-2.3.4/Seurat/man/BlackAndWhite.Rd |only Seurat-2.3.4/Seurat/man/BuildRFClassifier.Rd |only Seurat-2.3.4/Seurat/man/BuildSNN.Rd |only Seurat-2.3.4/Seurat/man/CalcAlignmentMetric.Rd |only Seurat-2.3.4/Seurat/man/CalcVarExpRatio.Rd |only Seurat-2.3.4/Seurat/man/CellPlot.Rd |only Seurat-2.3.4/Seurat/man/ClassifyCells.Rd |only Seurat-2.3.4/Seurat/man/ColorTSNESplit.Rd |only Seurat-2.3.4/Seurat/man/CombineIdent.Rd |only Seurat-2.3.4/Seurat/man/Convert.Rd |only Seurat-2.3.4/Seurat/man/DBClustDimension.Rd |only Seurat-2.3.4/Seurat/man/DESeq2DETest.Rd |only Seurat-2.3.4/Seurat/man/DMEmbed.Rd |only Seurat-2.3.4/Seurat/man/DMPlot.Rd |only Seurat-2.3.4/Seurat/man/DarkTheme.Rd |only Seurat-2.3.4/Seurat/man/DiffExpTest.Rd |only Seurat-2.3.4/Seurat/man/DiffTTest.Rd |only Seurat-2.3.4/Seurat/man/DimElbowPlot.Rd |only Seurat-2.3.4/Seurat/man/DimTopCells.Rd |only Seurat-2.3.4/Seurat/man/DimTopGenes.Rd |only Seurat-2.3.4/Seurat/man/DoKMeans.Rd |only Seurat-2.3.4/Seurat/man/DotPlotOld.Rd |only Seurat-2.3.4/Seurat/man/ExtractField.Rd |only Seurat-2.3.4/Seurat/man/FastWhichCells.Rd |only Seurat-2.3.4/Seurat/man/FeatureHeatmap.Rd |only Seurat-2.3.4/Seurat/man/FeatureLocator.Rd |only Seurat-2.3.4/Seurat/man/FilterCells.Rd |only Seurat-2.3.4/Seurat/man/FindAllMarkersNode.Rd |only Seurat-2.3.4/Seurat/man/FindGeneTerms.Rd |only Seurat-2.3.4/Seurat/man/FindMarkersNode.Rd |only Seurat-2.3.4/Seurat/man/FindVariableGenes.Rd |only Seurat-2.3.4/Seurat/man/FitGeneK.Rd |only Seurat-2.3.4/Seurat/man/GenePlot.Rd |only Seurat-2.3.4/Seurat/man/GenesInCluster.Rd |only Seurat-2.3.4/Seurat/man/GetCellEmbeddings.Rd |only Seurat-2.3.4/Seurat/man/GetCentroids.Rd |only Seurat-2.3.4/Seurat/man/GetClusters.Rd |only Seurat-2.3.4/Seurat/man/GetDimReduction.Rd |only Seurat-2.3.4/Seurat/man/GetGeneLoadings.Rd |only Seurat-2.3.4/Seurat/man/GetIdent.Rd |only Seurat-2.3.4/Seurat/man/ICAEmbed.Rd |only Seurat-2.3.4/Seurat/man/ICALoad.Rd |only Seurat-2.3.4/Seurat/man/ICAPlot.Rd |only Seurat-2.3.4/Seurat/man/ICHeatmap.Rd |only Seurat-2.3.4/Seurat/man/ICTopCells.Rd |only Seurat-2.3.4/Seurat/man/ICTopGenes.Rd |only Seurat-2.3.4/Seurat/man/InitialMapping.Rd |only Seurat-2.3.4/Seurat/man/KClustDimension.Rd |only Seurat-2.3.4/Seurat/man/KMeansHeatmap.Rd |only Seurat-2.3.4/Seurat/man/MASTDETest.Rd |only Seurat-2.3.4/Seurat/man/MakeSparse.Rd |only Seurat-2.3.4/Seurat/man/MarkerTest.Rd |only Seurat-2.3.4/Seurat/man/MatrixRowShuffle.Rd |only Seurat-2.3.4/Seurat/man/MergeNode.Rd |only Seurat-2.3.4/Seurat/man/MergeSeurat.Rd |only Seurat-2.3.4/Seurat/man/MetageneBicorPlot.Rd |only Seurat-2.3.4/Seurat/man/MultiModal_CCA.Rd |only Seurat-2.3.4/Seurat/man/MultiModal_CIA.Rd |only Seurat-2.3.4/Seurat/man/NegBinomDETest.Rd |only Seurat-2.3.4/Seurat/man/NegBinomRegDETest.Rd |only Seurat-2.3.4/Seurat/man/NumberClusters.Rd |only Seurat-2.3.4/Seurat/man/OldDoHeatmap.Rd |only Seurat-2.3.4/Seurat/man/PCAEmbed.Rd |only Seurat-2.3.4/Seurat/man/PCALoad.Rd |only Seurat-2.3.4/Seurat/man/PCAPlot.Rd |only Seurat-2.3.4/Seurat/man/PCElbowPlot.Rd |only Seurat-2.3.4/Seurat/man/PCHeatmap.Rd |only Seurat-2.3.4/Seurat/man/PCTopCells.Rd |only Seurat-2.3.4/Seurat/man/PCTopGenes.Rd |only Seurat-2.3.4/Seurat/man/PoissonDETest.Rd |only Seurat-2.3.4/Seurat/man/PrintAlignSubspaceParams.Rd |only Seurat-2.3.4/Seurat/man/PrintCCAParams.Rd |only Seurat-2.3.4/Seurat/man/PrintCalcParams.Rd |only Seurat-2.3.4/Seurat/man/PrintCalcVarExpRatioParams.Rd |only Seurat-2.3.4/Seurat/man/PrintDMParams.Rd |only Seurat-2.3.4/Seurat/man/PrintDim.Rd |only Seurat-2.3.4/Seurat/man/PrintFindClustersParams.Rd |only Seurat-2.3.4/Seurat/man/PrintICA.Rd |only Seurat-2.3.4/Seurat/man/PrintICAParams.Rd |only Seurat-2.3.4/Seurat/man/PrintPCA.Rd |only Seurat-2.3.4/Seurat/man/PrintPCAParams.Rd |only Seurat-2.3.4/Seurat/man/PrintSNNParams.Rd |only Seurat-2.3.4/Seurat/man/PrintTSNEParams.Rd |only Seurat-2.3.4/Seurat/man/ProjectPCA.Rd |only Seurat-2.3.4/Seurat/man/PurpleAndYellow.Rd |only Seurat-2.3.4/Seurat/man/RefinedMapping.Rd |only Seurat-2.3.4/Seurat/man/RemoveFromTable.Rd |only Seurat-2.3.4/Seurat/man/RenameIdent.Rd |only Seurat-2.3.4/Seurat/man/ReorderIdent.Rd |only Seurat-2.3.4/Seurat/man/RunDiffusion.Rd |only Seurat-2.3.4/Seurat/man/RunMultiCCA.Rd |only Seurat-2.3.4/Seurat/man/RunPHATE.Rd |only Seurat-2.3.4/Seurat/man/SaveClusters.Rd |only Seurat-2.3.4/Seurat/man/ScaleDataR.Rd |only Seurat-2.3.4/Seurat/man/SetAllIdent.Rd |only Seurat-2.3.4/Seurat/man/SetClusters.Rd |only Seurat-2.3.4/Seurat/man/SetDimReduction.Rd |only Seurat-2.3.4/Seurat/man/SetIdent.Rd |only Seurat-2.3.4/Seurat/man/Seurat-deprecated.Rd |only Seurat-2.3.4/Seurat/man/Shuffle.Rd |only Seurat-2.3.4/Seurat/man/SplitDotPlotGG.Rd |only Seurat-2.3.4/Seurat/man/StashIdent.Rd |only Seurat-2.3.4/Seurat/man/SubsetByPredicate.Rd |only Seurat-2.3.4/Seurat/man/SubsetColumn.Rd |only Seurat-2.3.4/Seurat/man/SubsetRow.Rd |only Seurat-2.3.4/Seurat/man/TSNEPlot.Rd |only Seurat-2.3.4/Seurat/man/TobitTest.Rd |only Seurat-2.3.4/Seurat/man/TransferIdent.Rd |only Seurat-2.3.4/Seurat/man/ValidateClusters.Rd |only Seurat-2.3.4/Seurat/man/ValidateSpecificClusters.Rd |only Seurat-2.3.4/Seurat/man/VariableGenePlot.Rd |only Seurat-2.3.4/Seurat/man/VizDimReduction.Rd |only Seurat-2.3.4/Seurat/man/VizICA.Rd |only Seurat-2.3.4/Seurat/man/VizPCA.Rd |only Seurat-2.3.4/Seurat/man/WilcoxDETest.Rd |only Seurat-2.3.4/Seurat/man/seurat.Rd |only Seurat-2.3.4/Seurat/tests/testthat/test_alignment.R |only Seurat-2.3.4/Seurat/tests/testthat/test_cluster_determination.R |only Seurat-2.3.4/Seurat/tests/testthat/test_differential_expression.R |only Seurat-2.3.4/Seurat/tests/testthat/test_interaction.R |only Seurat-2.3.4/Seurat/tests/testthat/test_seurat_object.R |only Seurat-2.3.4/Seurat/tests/testthat/test_snn.R |only Seurat-3.0.0/Seurat/DESCRIPTION | 53 Seurat-3.0.0/Seurat/MD5 | 389 - Seurat-3.0.0/Seurat/NAMESPACE | 619 +- Seurat-3.0.0/Seurat/NEWS.md | 18 Seurat-3.0.0/Seurat/R/RcppExports.R | 40 Seurat-3.0.0/Seurat/R/clustering.R |only Seurat-3.0.0/Seurat/R/convenience.R |only Seurat-3.0.0/Seurat/R/data.R | 24 Seurat-3.0.0/Seurat/R/differential_expression.R | 2415 +++---- Seurat-3.0.0/Seurat/R/dimensional_reduction.R | 2881 +++++---- Seurat-3.0.0/Seurat/R/generics.R |only Seurat-3.0.0/Seurat/R/integration.R |only Seurat-3.0.0/Seurat/R/objects.R |only Seurat-3.0.0/Seurat/R/preprocessing.R | 3093 +++++++--- Seurat-3.0.0/Seurat/R/tree.R |only Seurat-3.0.0/Seurat/R/utilities.R | 1996 ++++-- Seurat-3.0.0/Seurat/R/visualization.R |only Seurat-3.0.0/Seurat/README.md | 21 Seurat-3.0.0/Seurat/data/pbmc_small.rda |binary Seurat-3.0.0/Seurat/inst/CITATION | 19 Seurat-3.0.0/Seurat/man/ALRAChooseKPlot.Rd |only Seurat-3.0.0/Seurat/man/AddMetaData.Rd | 48 Seurat-3.0.0/Seurat/man/AddModuleScore.Rd | 43 Seurat-3.0.0/Seurat/man/AnchorSet-class.Rd |only Seurat-3.0.0/Seurat/man/Assay-class.Rd |only Seurat-3.0.0/Seurat/man/AugmentPlot.Rd | 27 Seurat-3.0.0/Seurat/man/AverageExpression.Rd | 23 Seurat-3.0.0/Seurat/man/BarcodeInflectionsPlot.Rd |only Seurat-3.0.0/Seurat/man/BuildClusterTree.Rd | 29 Seurat-3.0.0/Seurat/man/CalculateBarcodeInflections.Rd |only Seurat-3.0.0/Seurat/man/CaseMatch.Rd | 2 Seurat-3.0.0/Seurat/man/CellCycleScoring.Rd | 19 Seurat-3.0.0/Seurat/man/CellScatter.Rd |only Seurat-3.0.0/Seurat/man/CellSelector.Rd |only Seurat-3.0.0/Seurat/man/Cells.Rd |only Seurat-3.0.0/Seurat/man/CollapseSpeciesExpressionMatrix.Rd | 25 Seurat-3.0.0/Seurat/man/CombinePlots.Rd |only Seurat-3.0.0/Seurat/man/Command.Rd |only Seurat-3.0.0/Seurat/man/CreateAssayObject.Rd |only Seurat-3.0.0/Seurat/man/CreateDimReducObject.Rd |only Seurat-3.0.0/Seurat/man/CreateGeneActivityMatrix.Rd |only Seurat-3.0.0/Seurat/man/CreateSeuratObject.Rd | 71 Seurat-3.0.0/Seurat/man/CustomPalette.Rd | 30 Seurat-3.0.0/Seurat/man/DefaultAssay.Rd |only Seurat-3.0.0/Seurat/man/DietSeurat.Rd |only Seurat-3.0.0/Seurat/man/DimHeatmap.Rd | 58 Seurat-3.0.0/Seurat/man/DimPlot.Rd | 111 Seurat-3.0.0/Seurat/man/DimReduc-class.Rd |only Seurat-3.0.0/Seurat/man/DoHeatmap.Rd | 72 Seurat-3.0.0/Seurat/man/DotPlot.Rd | 34 Seurat-3.0.0/Seurat/man/ElbowPlot.Rd |only Seurat-3.0.0/Seurat/man/Embeddings.Rd |only Seurat-3.0.0/Seurat/man/ExportToCellbrowser.Rd |only Seurat-3.0.0/Seurat/man/FeaturePlot.Rd | 89 Seurat-3.0.0/Seurat/man/FeatureScatter.Rd |only Seurat-3.0.0/Seurat/man/FetchData.Rd | 20 Seurat-3.0.0/Seurat/man/FindAllMarkers.Rd | 106 Seurat-3.0.0/Seurat/man/FindClusters.Rd | 94 Seurat-3.0.0/Seurat/man/FindConservedMarkers.Rd | 16 Seurat-3.0.0/Seurat/man/FindIntegrationAnchors.Rd |only Seurat-3.0.0/Seurat/man/FindMarkers.Rd | 159 Seurat-3.0.0/Seurat/man/FindNeighbors.Rd |only Seurat-3.0.0/Seurat/man/FindTransferAnchors.Rd |only Seurat-3.0.0/Seurat/man/FindVariableFeatures.Rd |only Seurat-3.0.0/Seurat/man/GetAssay.Rd |only Seurat-3.0.0/Seurat/man/GetAssayData.Rd | 43 Seurat-3.0.0/Seurat/man/GetIntegrationData.Rd |only Seurat-3.0.0/Seurat/man/Graph-class.Rd |only Seurat-3.0.0/Seurat/man/HTODemux.Rd | 42 Seurat-3.0.0/Seurat/man/HTOHeatmap.Rd | 25 Seurat-3.0.0/Seurat/man/HVFInfo.Rd |only Seurat-3.0.0/Seurat/man/HoverLocator.Rd | 20 Seurat-3.0.0/Seurat/man/Idents.Rd |only Seurat-3.0.0/Seurat/man/IntegrateData.Rd |only Seurat-3.0.0/Seurat/man/IntegrationData-class.Rd |only Seurat-3.0.0/Seurat/man/JS.Rd |only Seurat-3.0.0/Seurat/man/JackStraw.Rd | 29 Seurat-3.0.0/Seurat/man/JackStrawData-class.Rd |only Seurat-3.0.0/Seurat/man/JackStrawPlot.Rd | 28 Seurat-3.0.0/Seurat/man/Key.Rd |only Seurat-3.0.0/Seurat/man/L2CCA.Rd |only Seurat-3.0.0/Seurat/man/L2Dim.Rd |only Seurat-3.0.0/Seurat/man/LabelClusters.Rd |only Seurat-3.0.0/Seurat/man/LabelPoints.Rd |only Seurat-3.0.0/Seurat/man/Loadings.Rd |only Seurat-3.0.0/Seurat/man/LocalStruct.Rd |only Seurat-3.0.0/Seurat/man/LogNormalize.Rd | 6 Seurat-3.0.0/Seurat/man/MULTIseqDemux.Rd |only Seurat-3.0.0/Seurat/man/MetaFeature.Rd |only Seurat-3.0.0/Seurat/man/Misc.Rd |only Seurat-3.0.0/Seurat/man/MixingMetric.Rd |only Seurat-3.0.0/Seurat/man/NormalizeData.Rd | 52 Seurat-3.0.0/Seurat/man/OldWhichCells.Rd |only Seurat-3.0.0/Seurat/man/PCASigGenes.Rd | 7 Seurat-3.0.0/Seurat/man/PercentageFeatureSet.Rd |only Seurat-3.0.0/Seurat/man/PlotClusterTree.Rd | 9 Seurat-3.0.0/Seurat/man/PolyDimPlot.Rd |only Seurat-3.0.0/Seurat/man/PolyFeaturePlot.Rd |only Seurat-3.0.0/Seurat/man/Project.Rd |only Seurat-3.0.0/Seurat/man/ProjectDim.Rd | 31 Seurat-3.0.0/Seurat/man/Read10X.Rd | 22 Seurat-3.0.0/Seurat/man/Read10X_h5.Rd | 13 Seurat-3.0.0/Seurat/man/ReadAlevin.Rd |only Seurat-3.0.0/Seurat/man/ReadAlevinCsv.Rd |only Seurat-3.0.0/Seurat/man/RelativeCounts.Rd |only Seurat-3.0.0/Seurat/man/RenameCells.Rd | 48 Seurat-3.0.0/Seurat/man/RidgePlot.Rd | 56 Seurat-3.0.0/Seurat/man/RunALRA.Rd |only Seurat-3.0.0/Seurat/man/RunCCA.Rd | 70 Seurat-3.0.0/Seurat/man/RunICA.Rd | 67 Seurat-3.0.0/Seurat/man/RunLSI.Rd |only Seurat-3.0.0/Seurat/man/RunPCA.Rd | 69 Seurat-3.0.0/Seurat/man/RunTSNE.Rd | 71 Seurat-3.0.0/Seurat/man/RunUMAP.Rd | 143 Seurat-3.0.0/Seurat/man/SCTransform.Rd |only Seurat-3.0.0/Seurat/man/SampleUMI.Rd | 8 Seurat-3.0.0/Seurat/man/ScaleData.Rd | 82 Seurat-3.0.0/Seurat/man/ScoreJackStraw.Rd |only Seurat-3.0.0/Seurat/man/SelectIntegrationFeatures.Rd |only Seurat-3.0.0/Seurat/man/SetAssayData.Rd | 53 Seurat-3.0.0/Seurat/man/SetIntegrationData.Rd |only Seurat-3.0.0/Seurat/man/Seurat-class.Rd |only Seurat-3.0.0/Seurat/man/SeuratCommand-class.Rd |only Seurat-3.0.0/Seurat/man/SeuratTheme.Rd |only Seurat-3.0.0/Seurat/man/SplitObject.Rd | 12 Seurat-3.0.0/Seurat/man/Stdev.Rd |only Seurat-3.0.0/Seurat/man/StopCellbrowser.Rd |only Seurat-3.0.0/Seurat/man/SubsetByBarcodeInflections.Rd |only Seurat-3.0.0/Seurat/man/SubsetData.Rd | 56 Seurat-3.0.0/Seurat/man/TF.IDF.Rd |only Seurat-3.0.0/Seurat/man/Tool.Rd |only Seurat-3.0.0/Seurat/man/TopCells.Rd |only Seurat-3.0.0/Seurat/man/TopFeatures.Rd |only Seurat-3.0.0/Seurat/man/TransferData.Rd |only Seurat-3.0.0/Seurat/man/UpdateSeuratObject.Rd | 4 Seurat-3.0.0/Seurat/man/VariableFeaturePlot.Rd |only Seurat-3.0.0/Seurat/man/VariableFeatures.Rd |only Seurat-3.0.0/Seurat/man/VizDimLoadings.Rd |only Seurat-3.0.0/Seurat/man/VlnPlot.Rd | 67 Seurat-3.0.0/Seurat/man/WhichCells.Rd | 54 Seurat-3.0.0/Seurat/man/as.Graph.Rd |only Seurat-3.0.0/Seurat/man/as.Seurat.Rd |only Seurat-3.0.0/Seurat/man/as.SingleCellExperiment.Rd |only Seurat-3.0.0/Seurat/man/as.loom.Rd |only Seurat-3.0.0/Seurat/man/as.sparse.Rd |only Seurat-3.0.0/Seurat/man/h5ad.Rd |only Seurat-3.0.0/Seurat/man/merge.Seurat.Rd |only Seurat-3.0.0/Seurat/man/oldseurat-class.Rd |only Seurat-3.0.0/Seurat/man/print.DimReduc.Rd |only Seurat-3.0.0/Seurat/man/subset.Seurat.Rd |only Seurat-3.0.0/Seurat/src/RModularityOptimizer.cpp | 63 Seurat-3.0.0/Seurat/src/RcppExports.cpp | 163 Seurat-3.0.0/Seurat/src/data_manipulation.cpp | 148 Seurat-3.0.0/Seurat/src/data_manipulation.h | 17 Seurat-3.0.0/Seurat/src/integration.cpp |only Seurat-3.0.0/Seurat/src/integration.h |only Seurat-3.0.0/Seurat/tests/testdata/cr3.0 |only Seurat-3.0.0/Seurat/tests/testthat/test_data_manipulation.R | 63 Seurat-3.0.0/Seurat/tests/testthat/test_dimensional_reduction.R |only Seurat-3.0.0/Seurat/tests/testthat/test_load_10X.R |only Seurat-3.0.0/Seurat/tests/testthat/test_modularity_optimizer.R | 191 Seurat-3.0.0/Seurat/tests/testthat/test_objects.R |only Seurat-3.0.0/Seurat/tests/testthat/test_preprocessing.R | 403 - 321 files changed, 9051 insertions(+), 5828 deletions(-)
Title: Power in a Group Sequential Design
Description: Tools for the evaluation of interim analysis plans for sequentially
monitored trials on a survival endpoint; tools to construct efficacy and
futility boundaries, for deriving power of a sequential design at a specified
alternative, template for evaluating the performance of candidate plans at a
set of time varying alternatives. See Izmirlian, G. (2014) <doi:10.4310/SII.2014.v7.n1.a4>.
Author: Grant Izmirlian <izmirlig@mail.nih.gov>
Maintainer: Grant Izmirlian <izmirlig@mail.nih.gov>
Diff between PwrGSD versions 2.3 dated 2018-03-26 and 2.3.1 dated 2019-04-15
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- R/PwrGSD.R | 3 ++- build/vignette.rds |binary inst/doc/GrpSeqBnds-vignette.Rnw | 1 - inst/doc/GrpSeqBnds-vignette.pdf |binary inst/doc/PwrGSD-vignette.Rnw | 1 - inst/doc/PwrGSD-vignette.pdf |binary inst/doc/cpd-PwrGSD-vignette.Rnw | 1 - inst/doc/cpd-PwrGSD-vignette.pdf |binary src/WtdLogRank.c | 12 +++++++----- vignettes/GrpSeqBnds-vignette.Rnw | 1 - vignettes/PwrGSD-vignette.Rnw | 1 - vignettes/cpd-PwrGSD-vignette.Rnw | 1 - 14 files changed, 27 insertions(+), 30 deletions(-)
Title: Stochastic Island Biogeography Theory Made Easy
Description: Tools to develop stochastic models based on the Theory of Island
Biogeography (TIB) of MacArthur and Wilson (1967) <DOI:10.1023/A:1016393430551>
and extensions. The package implements methods to estimate colonization and
extinction rates (including environmental variables) given presence-absence
data, simulate community assembly, and perform model selection.
Author: Vicente Jimenez [aut, cre],
David Alonso [aut]
Maintainer: Vicente Jimenez <vicente.jimenez.ontiveros@gmail.com>
Diff between island versions 0.2.3 dated 2019-03-21 and 0.2.4 dated 2019-04-15
island-0.2.3/island/src/Parameter_Index_Checking_Order.c |only island-0.2.3/island/src/R_SHLIB___mle_NLLikelihood_Minimization.c |only island-0.2.4/island/DESCRIPTION | 10 island-0.2.4/island/MD5 | 95 +- island-0.2.4/island/NEWS.md | 5 island-0.2.4/island/R/da_MacKenzie_mle.R | 78 +- island-0.2.4/island/R/da_mle_cedp.R | 132 +-- island-0.2.4/island/R/da_upgma_AIC_cedp.R | 132 +-- island-0.2.4/island/build/vignette.rds |binary island-0.2.4/island/inst/CITATION | 4 island-0.2.4/island/inst/doc/IBDmodels.html | 4 island-0.2.4/island/inst/doc/detectability.html | 62 - island-0.2.4/island/inst/doc/island.html | 4 island-0.2.4/island/src/Counting_Type_of_Transitions.c | 1 island-0.2.4/island/src/GSL_MacKenzie_NLL_Uneven_Function.c | 63 - island-0.2.4/island/src/GSL_MacKenzie_NLLikelihood_Function.c | 29 island-0.2.4/island/src/GSL_Minimization_Simplex.c | 55 - island-0.2.4/island/src/GSL_NLL_Function_Uneven.c | 41 - island-0.2.4/island/src/GSL_NLLikelihood_Function.c | 130 +-- island-0.2.4/island/src/HEADERS.h | 6 island-0.2.4/island/src/IO_AKAIKE_Model_Selection.c | 170 ++-- island-0.2.4/island/src/IO_Missing_Values.c | 107 +- island-0.2.4/island/src/MODEL.h | 13 island-0.2.4/island/src/MODEL_Parameter_Space_STRUCT_DEF.h | 41 - island-0.2.4/island/src/MODEL_SELECTION_UPGMA_MacKENZIE_R_FUNCTION.c | 337 ++++---- island-0.2.4/island/src/MODEL_SELECTION_UPGMA_MacKENZIE_R_SHLIB.c | 370 ++++----- island-0.2.4/island/src/MODEL_SELECTION_UPGMA_R_FUNCTION.c | 284 +++---- island-0.2.4/island/src/MODEL_SELECTION_UPGMA_R_SHLIB.c | 388 +++++----- island-0.2.4/island/src/MODEL_SP_Matrix_Data_STRUCT_DEF.h | 50 - island-0.2.4/island/src/MacKenzie_NLLikelihood_Function.c | 273 +++---- island-0.2.4/island/src/Parameter_Model.c | 70 - island-0.2.4/island/src/Parameter_Space_R_SHLIB.c | 85 +- island-0.2.4/island/src/Probability_Rates.c | 2 island-0.2.4/island/src/R_SHLIB___mle_MacKenzie_NLL_Uneven_Minimization.c | 325 +++----- island-0.2.4/island/src/R_SHLIB___mle_MacKenzie_NLLikelihood_Minimization.c | 146 +-- island-0.2.4/island/src/R_SHLIB___mle_NLL_Uneven_Minimization.c |only island-0.2.4/island/src/SP_Matrix_Data.c | 29 island-0.2.4/island/src/UPGMA_CLUSTERING_PARTITION.c | 134 +-- island-0.2.4/island/src/da_IBT_Functions.h | 26 island-0.2.4/island/src/da_IBT_Optimization.h | 117 +-- island-0.2.4/island/src/init.c | 4 island-0.2.4/island/src/mle_Col_Ext_Uneven_Matrix_R_SHLIB.c | 123 +-- island-0.2.4/island/src/mle_MacKenzie_Uneven_Matrix_R_SHLIB.c | 98 +- island-0.2.4/island/src/upgma_clustering.c | 8 island-0.2.4/island/tests/testthat/test_detectability.R | 11 island-0.2.4/island/tests/testthat/test_environmental.R | 2 island-0.2.4/island/tests/testthat/test_general.R | 2 island-0.2.4/island/tests/testthat/test_ibd.R | 2 island-0.2.4/island/tests/testthat/test_irregular.R | 2 island-0.2.4/island/tests/testthat/test_regular.R | 2 50 files changed, 2051 insertions(+), 2021 deletions(-)
Title: Local Polynomial Density Estimation and Inference
Description: Without imposing stringent distributional assumptions or shape restrictions, nonparametric density estimation has been popular in economics and other social sciences for counterfactual analysis, program evaluation, and policy recommendations. This package implements a novel density estimator based on local polynomial regression, documented in Cattaneo, Jansson and Ma (2019) <arXiv:1811.11512>: lpdensity() to construct local polynomial based density (and derivatives) estimator; lpbwdensity() to perform data-driven bandwidth selection; and lpdensity.plot() for density plot with robust confidence interval.
Author: Matias D. Cattaneo, Michael Jansson, Xinwei Ma
Maintainer: Xinwei Ma <xinweima@umich.edu>
Diff between lpdensity versions 0.2.2 dated 2017-07-09 and 0.2.3 dated 2019-04-15
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/lpbwdensity.R | 12 ++++++------ R/lpdensity-package.R | 16 ++++++++-------- R/lpdensity.R | 12 ++++++------ R/lpdensity.plot.R | 12 ++++++------ man/lpbwdensity.Rd | 14 +++++++------- man/lpdensity-package.Rd | 10 +++++----- man/lpdensity.Rd | 12 ++++++------ man/lpdensity.plot.Rd | 11 ++++++----- 10 files changed, 64 insertions(+), 63 deletions(-)
Title: A Project Infrastructure for Researchers
Description: Provides a project infrastructure with a focus on
manuscript creation. Creates a project folder with a single command,
containing subdirectories for specific components, templates for
manuscripts, and so on.
Author: Nik Krieger [aut, cre],
Adam Perzynski [aut],
Jarrod Dalton [aut]
Maintainer: Nik Krieger <nk@case.edu>
Diff between projects versions 1.1.0 dated 2019-04-15 and 1.1.1 dated 2019-04-15
DESCRIPTION | 6 +- MD5 | 22 ++++---- NAMESPACE | 1 NEWS.md | 9 +++ R/edit.R | 32 +++++++----- R/file_management.R | 2 R/header.R | 7 ++ R/metadata_manipulation.R | 114 ++-------------------------------------------- R/setup.R | 13 ++--- R/update.R | 74 ----------------------------- R/utilities.R | 2 R/validation.R | 8 ++- 12 files changed, 67 insertions(+), 223 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description: Contains functions for multiple imputation which
complements existing functionality in R.
In particular, several imputation methods for the
mice package (van Buuren & Groothuis-Oudshoorn, 2011,
<doi:10.18637/jss.v045.i03>) are included.
Main features of the miceadds package include
plausible value imputation (Mislevy, 1991,
<doi:10.1007/BF02294457>), multilevel imputation for
variables at any level or with any number of hierarchical
and non-hierarchical levels (Grund, Luedtke & Robitzsch,
2018, <doi:10.1177/1094428117703686>; van Buuren, 2018,
Ch.7, <doi:10.1201/9780429492259>), imputation using
partial least squares (PLS) for high dimensional
predictors (Robitzsch, Pham & Yanagida, 2016),
nested multiple imputation (Rubin, 2003,
<doi:10.1111/1467-9574.00217>) and substantive model
compatible imputation (Bartlett et al., 2015,
<doi:10.1177/0962280214521348>).
Author: Alexander Robitzsch [aut, cre], Simon Grund [aut],
Thorsten Henke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 3.1-37 dated 2019-03-18 and 3.2-48 dated 2019-04-15
miceadds-3.1-37/miceadds/R/ma.wtd.aux.data.R |only miceadds-3.1-37/miceadds/R/mice.impute.2l.eap.R |only miceadds-3.1-37/miceadds/R/mice_impute_2l_lmer.R |only miceadds-3.1-37/miceadds/R/mice_impute_bygroup_modify_arguments.R |only miceadds-3.1-37/miceadds/R/mice_impute_create_type_vector.R |only miceadds-3.1-37/miceadds/man/mice.impute.eap.Rd |only miceadds-3.1-37/miceadds/man/mice_impute_2l_lmer.Rd |only miceadds-3.2-48/miceadds/DESCRIPTION | 25 - miceadds-3.2-48/miceadds/MD5 | 187 ++++--- miceadds-3.2-48/miceadds/NAMESPACE | 20 miceadds-3.2-48/miceadds/R/NMIcombine.R | 30 - miceadds-3.2-48/miceadds/R/NMIcombine_include_dimnames.R |only miceadds-3.2-48/miceadds/R/RcppExports.R | 66 +- miceadds-3.2-48/miceadds/R/cor_avoid_zero.R | 28 - miceadds-3.2-48/miceadds/R/create_interactions.R | 5 miceadds-3.2-48/miceadds/R/latent.regression.em.R | 78 --- miceadds-3.2-48/miceadds/R/latent_regression_em_sampling.R |only miceadds-3.2-48/miceadds/R/lmer_vcov.R | 4 miceadds-3.2-48/miceadds/R/ma.wtd.corNA.R | 4 miceadds-3.2-48/miceadds/R/ma.wtd.covNA.R | 4 miceadds-3.2-48/miceadds/R/ma.wtd.kurtosisNA.R | 9 miceadds-3.2-48/miceadds/R/ma.wtd.meanNA.R | 9 miceadds-3.2-48/miceadds/R/ma.wtd.quantileNA.R | 15 miceadds-3.2-48/miceadds/R/ma.wtd.sdNA.R | 11 miceadds-3.2-48/miceadds/R/ma.wtd.skewnessNA.R | 13 miceadds-3.2-48/miceadds/R/ma_lme4_formula_design_matrices.R | 4 miceadds-3.2-48/miceadds/R/ma_lme4_formula_terms.R | 12 miceadds-3.2-48/miceadds/R/ma_wtd_stat_prepare_data.R |only miceadds-3.2-48/miceadds/R/mice.impute.2l.binary.R | 4 miceadds-3.2-48/miceadds/R/mice.impute.2l.continuous.R | 6 miceadds-3.2-48/miceadds/R/mice.impute.2l.pmm.R | 12 miceadds-3.2-48/miceadds/R/mice.impute.2lonly.function.R | 20 miceadds-3.2-48/miceadds/R/mice.impute.bygroup.R | 28 - miceadds-3.2-48/miceadds/R/mice.impute.ml.lmer.R | 10 miceadds-3.2-48/miceadds/R/mice.impute.plausible.values.R | 5 miceadds-3.2-48/miceadds/R/mice.impute.pls.R | 28 - miceadds-3.2-48/miceadds/R/mice.impute.smcfcs.R |only miceadds-3.2-48/miceadds/R/mice.impute.weighted.norm.R | 8 miceadds-3.2-48/miceadds/R/mice.impute.weighted.pmm.R | 16 miceadds-3.2-48/miceadds/R/mice_imputation_2l_lmer.R |only miceadds-3.2-48/miceadds/R/mice_imputation_add_jitter.R |only miceadds-3.2-48/miceadds/R/mice_imputation_args_include_wy.R |only miceadds-3.2-48/miceadds/R/mice_imputation_bygroup_modify_arguments.R |only miceadds-3.2-48/miceadds/R/mice_imputation_create_interactions.R | 25 - miceadds-3.2-48/miceadds/R/mice_imputation_create_type_vector.R |only miceadds-3.2-48/miceadds/R/mice_imputation_define_wy.R |only miceadds-3.2-48/miceadds/R/mice_imputation_draw_bootstrap_sample.R |only miceadds-3.2-48/miceadds/R/mice_imputation_extract_arguments_list.R | 4 miceadds-3.2-48/miceadds/R/mice_imputation_extract_parameters_bc.R |only miceadds-3.2-48/miceadds/R/mice_imputation_extract_parameters_lm.R |only miceadds-3.2-48/miceadds/R/mice_imputation_extract_parameters_yj.R |only miceadds-3.2-48/miceadds/R/mice_imputation_get_states.R | 21 miceadds-3.2-48/miceadds/R/mice_imputation_multilevel_lmerControl_define_optimizer.R |only miceadds-3.2-48/miceadds/R/mice_imputation_new_proposal.R |only miceadds-3.2-48/miceadds/R/mice_imputation_pls_correlation_criteria.R | 10 miceadds-3.2-48/miceadds/R/mice_imputation_pls_do_impute.R | 20 miceadds-3.2-48/miceadds/R/mice_imputation_pls_estimate_pls_regression.R | 19 miceadds-3.2-48/miceadds/R/mice_imputation_pls_include_interactions.R | 30 - miceadds-3.2-48/miceadds/R/mice_imputation_pls_include_quadratics.R | 5 miceadds-3.2-48/miceadds/R/mice_imputation_pls_largest_correlations.R | 21 miceadds-3.2-48/miceadds/R/mice_imputation_pls_pca_reduction.R | 7 miceadds-3.2-48/miceadds/R/mice_imputation_pls_scale_x.R | 16 miceadds-3.2-48/miceadds/R/mice_imputation_prepare_2l_functions.R | 5 miceadds-3.2-48/miceadds/R/mice_imputation_refresh_update_factor.R |only miceadds-3.2-48/miceadds/R/mice_imputation_smcfcs_clean_input.R |only miceadds-3.2-48/miceadds/R/mice_imputation_smcfcs_estimate_model.R |only miceadds-3.2-48/miceadds/R/mice_imputation_smcfcs_evaluate_loglikelihood.R |only miceadds-3.2-48/miceadds/R/mice_imputation_smcfcs_evaluate_loglikelihood_model.R |only miceadds-3.2-48/miceadds/R/mice_imputation_smcfcs_require_namespace.R |only miceadds-3.2-48/miceadds/R/mice_imputation_weighted_norm_draw.R | 28 - miceadds-3.2-48/miceadds/R/mice_ml_lmer_extract_input.R | 2 miceadds-3.2-48/miceadds/R/mice_ml_lmer_include_cluster_means.R | 4 miceadds-3.2-48/miceadds/R/mice_ml_lmer_interactions_pls.R | 4 miceadds-3.2-48/miceadds/R/miceadds_ginv.R |only miceadds-3.2-48/miceadds/R/miceadds_weighted_centering.R |only miceadds-3.2-48/miceadds/R/miceadds_weighted_colMeans.R |only miceadds-3.2-48/miceadds/R/miceadds_weighted_scaling_y.R |only miceadds-3.2-48/miceadds/R/ml_mcmc.R | 9 miceadds-3.2-48/miceadds/R/ml_mcmc_fit.R | 11 miceadds-3.2-48/miceadds/R/ml_mcmc_proc_data.R | 2 miceadds-3.2-48/miceadds/R/pca.covridge.R | 19 miceadds-3.2-48/miceadds/R/plausible.value.imputation.R | 76 +-- miceadds-3.2-48/miceadds/R/pool.mi.R | 4 miceadds-3.2-48/miceadds/R/save.data.R | 7 miceadds-3.2-48/miceadds/R/with.datlist.R | 5 miceadds-3.2-48/miceadds/build/partial.rdb |binary miceadds-3.2-48/miceadds/inst/NEWS | 39 + miceadds-3.2-48/miceadds/inst/include/miceadds_RcppExports.h | 80 +-- miceadds-3.2-48/miceadds/man/datalist2mids.Rd | 4 miceadds-3.2-48/miceadds/man/draw.pv.ctt.Rd | 6 miceadds-3.2-48/miceadds/man/kernelpls.fit2.Rd | 5 miceadds-3.2-48/miceadds/man/mice.impute.2lonly.function.Rd | 13 miceadds-3.2-48/miceadds/man/mice.impute.bygroup.Rd | 5 miceadds-3.2-48/miceadds/man/mice.impute.ml.lmer.Rd | 6 miceadds-3.2-48/miceadds/man/mice.impute.plausible.values.Rd | 6 miceadds-3.2-48/miceadds/man/mice.impute.pls.Rd | 26 + miceadds-3.2-48/miceadds/man/mice.impute.smcfcs.Rd |only miceadds-3.2-48/miceadds/man/mice.impute.weighted.pmm.Rd | 11 miceadds-3.2-48/miceadds/man/mice_imputation_2l_lmer.Rd |only miceadds-3.2-48/miceadds/man/miceadds-defunct.Rd | 7 miceadds-3.2-48/miceadds/man/miceadds-utilities.Rd | 5 miceadds-3.2-48/miceadds/man/ml_mcmc.Rd | 16 miceadds-3.2-48/miceadds/man/pca.covridge.Rd | 5 miceadds-3.2-48/miceadds/man/source.all.Rd | 4 miceadds-3.2-48/miceadds/man/write.datlist.Rd | 4 miceadds-3.2-48/miceadds/man/write.pspp.Rd | 4 miceadds-3.2-48/miceadds/src/RcppExports.cpp | 235 ++++++---- miceadds-3.2-48/miceadds/src/miceadds_rcpp_create_interactions.cpp | 26 - miceadds-3.2-48/miceadds/src/miceadds_rcpp_ml_mcmc_sampler.cpp | 12 miceadds-3.2-48/miceadds/src/miceadds_rcpp_ml_mcmc_sub.cpp | 60 +- miceadds-3.2-48/miceadds/src/miceadds_rcpp_ml_mcmc_sub.h | 38 - miceadds-3.2-48/miceadds/src/miceadds_rcpp_weighted_cor.cpp |only miceadds-3.2-48/miceadds/src/miceadds_rcpp_weighted_pmm.cpp |only 113 files changed, 955 insertions(+), 677 deletions(-)
Title: Bayesian Analysis of Quantile Regression Models
Description: Bayesian estimation and variable selection for quantile regression models.
Author: Rahim Alhamzawi
Maintainer: Rahim Alhamzawi (University of Al-Qadisiyah) <rahim.alhamzawi@qu.edu.iq>
Diff between Brq versions 2.4 dated 2019-04-08 and 2.5 dated 2019-04-15
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NAMESPACE | 2 +- R/Brq1.R | 13 +++++++++++-- R/DIC.R |only man/Brq1.Rd | 4 ++-- man/DIC.Rd |only 7 files changed, 24 insertions(+), 13 deletions(-)
Title: An R Package for Creating Ternary Plots
Description: Plots ternary diagrams using the standard graphics functions.
An alternative to 'ggtern', which uses the 'ggplot2' family of plotting functions.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Ternary versions 1.0.2 dated 2018-10-30 and 1.1.0 dated 2019-04-15
DESCRIPTION | 13 +-- MD5 | 45 +++++++--- NAMESPACE | 19 ++++ NEWS.md | 29 ++++--- R/Contours.R |only R/Coordinates.R |only R/TernaryPlot.R | 157 +++++++++++--------------------------- README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Using-Ternary.R | 67 ++++++++++++++++ inst/doc/Using-Ternary.Rmd | 81 +++++++++++++++++++ inst/doc/Using-Ternary.html | 112 +++++++++++++++++++++++++-- man/AddToTernary.Rd | 4 man/ColourTernary.Rd |only man/OutsidePlot.Rd |only man/ReflectedEquivalents.Rd |only man/TernaryContour.Rd |only man/TernaryCoords.Rd | 3 man/TernaryDensityContour.Rd |only man/TernaryPlot.Rd | 48 ++++++----- man/TernaryPointValues.Rd |only man/TernaryTiles.Rd |only man/TernaryXRange.Rd | 9 +- man/TriangleCentres.Rd |only man/XYToTernary.Rd |only tests/testthat/test-Contours.R |only tests/testthat/test-Coordinates.R |only tests/testthat/test-ternary.R | 19 ++-- vignettes/Using-Ternary.Rmd | 81 +++++++++++++++++++ 30 files changed, 505 insertions(+), 186 deletions(-)
Title: Compositional Data Analysis
Description: Methods for analysis of compositional data including robust
methods, imputation, methods to replace rounded zeros, (robust) outlier
detection for compositional data, (robust) principal component analysis for
compositional data, (robust) factor analysis for compositional data, (robust)
discriminant analysis for compositional data (Fisher rule), robust regression
with compositional predictors and (robust) Anderson-Darling normality tests for
compositional data as well as popular log-ratio transformations (addLR, cenLR,
isomLR, and their inverse transformations). In addition, visualisation and
diagnostic tools are implemented as well as high and low-level plot functions
for the ternary diagram.
Author: Matthias Templ [aut, cre],
Karel Hron [aut],
Peter Filzmoser [aut],
Kamila Facevicova [ctb],
Petra Kynclova [ctb],
Jan Walach [ctb],
Veronika Pintar [ctb],
Jiajia Chen [ctb],
Dominika Miksova [ctb]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between robCompositions versions 2.0.10 dated 2019-02-19 and 2.1.0 dated 2019-04-15
DESCRIPTION | 14 ++--- MD5 | 24 +++++--- NAMESPACE | 7 ++ NEWS | 5 + R/cubeCoord.R |only R/dataSets.R | 91 +++++++++++++++++++++++++++++++++- R/tabCoord.R |only build/vignette.rds |binary data/employment2.rda |only data/manu_abs.rda |only inst/doc/imputation.pdf |binary inst/doc/robCompositions-overview.pdf |binary man/cubeCoord.Rd |only man/employment2.Rd |only man/gjovik.Rd | 66 ++++++++++++++++++++++++ man/manu_abs.Rd |only man/tabCoord.Rd |only 17 files changed, 191 insertions(+), 16 deletions(-)
More information about robCompositions at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-12 0.1.4
Title: Binary R server
Description: Rserve acts as a socket server (TCP/IP or local sockets)
which allows binary requests to be sent to R. Every
connection has a separate workspace and working
directory. Client-side implementations are available
for popular languages such as C/C++ and Java, allowing
any application to use facilities of R without the need of
linking to R code. Rserve supports remote connection,
user authentication and file transfer. A simple R client
is included in this package as well.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between Rserve versions 1.7-3 dated 2013-08-21 and 1.7-3.1 dated 2019-04-15
DESCRIPTION | 5 MD5 | 7 aclocal.m4 |only configure | 421 +++++++++++++++++++++++++++++++---------------------------- configure.ac | 9 - 5 files changed, 240 insertions(+), 202 deletions(-)
Title: Java Graphics Device
Description: Graphics device routing all graphics commands to a Java
program. The actual functionality of the JavaGD depends on the
Java-side implementation. Simple AWT and Swing implementations
are included.
Author: Simon Urbanek <Simon.Urbanek@R-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@R-project.org>
Diff between JavaGD versions 0.6-1 dated 2012-09-13 and 0.6-1.1 dated 2019-04-15
DESCRIPTION | 7 ++++--- MD5 | 6 +++--- configure | 6 ++++++ configure.ac | 5 +++-- 4 files changed, 16 insertions(+), 8 deletions(-)
Title: Fast Interactive Framework for Web Scripting Using R
Description: Infrastrcture for creating rich, dynamic web content using R scripts while maintaining very fast response time.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>, Jeffrey Horner <jeffrey.horner@gmail.com>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between FastRWeb versions 1.1-1 dated 2015-07-29 and 1.1-1.1 dated 2019-04-15
DESCRIPTION | 6 MD5 | 8 configure | 5487 ++++++++++++++++++++++----------------------------- configure.ac | 5 src/Rcgi/config.h.in | 18 5 files changed, 2471 insertions(+), 3053 deletions(-)
Title: A Framework for Reproducible and Collaborative Data Science
Description: Provides a workflow for your analysis projects by combining
literate programming ('knitr' and 'rmarkdown') and version control
('Git', via 'git2r') to generate a website containing time-stamped,
versioned, and documented results.
Author: John Blischak [aut, cre] (<https://orcid.org/0000-0003-2634-9879>),
Peter Carbonetto [aut] (<https://orcid.org/0000-0003-1144-6780>),
Matthew Stephens [aut] (<https://orcid.org/0000-0001-5397-9257>),
Luke Zappia [ctb] (Instructions for hosting with GitLab),
Pierre Formont [ctb] (Support for hosting with Shiny Server),
Tim Trice [ctb] (Instructions for sharing common code),
Jiaxiang Li [ctb] (Function wflow_toc() to create table of contents)
Maintainer: John Blischak <jdblischak@uchicago.edu>
Diff between workflowr versions 1.2.0 dated 2019-02-14 and 1.3.0 dated 2019-04-15
DESCRIPTION | 23 +- MD5 | 124 ++++++----- NAMESPACE | 2 NEWS.md | 89 ++++++- R/git.R | 34 ++- R/infrastructure.R | 8 R/report.R | 9 R/wflow_build.R | 7 R/wflow_git_config.R | 2 R/wflow_git_pull.R | 34 ++- R/wflow_git_push.R | 34 ++- R/wflow_html.R | 68 ++++-- R/wflow_open.R | 2 R/wflow_options.R | 2 R/wflow_publish_addin.R |only R/wflow_remove.R | 2 R/wflow_rename_proj.R |only R/wflow_start.R | 20 - R/wflow_status.R | 33 ++ R/wflow_toc.R |only R/wflow_update.R | 9 R/wflow_use_github.R | 4 R/wflow_use_gitlab.R | 4 build/vignette.rds |binary inst/WORDLIST |only inst/doc/wflow-01-getting-started.Rmd | 40 ++- inst/doc/wflow-01-getting-started.html | 63 +++-- inst/doc/wflow-02-customization.html | 11 inst/doc/wflow-03-migrating.html | 11 inst/doc/wflow-04-how-it-works.Rmd | 2 inst/doc/wflow-04-how-it-works.html | 13 - inst/doc/wflow-05-faq.Rmd | 78 ++++++ inst/doc/wflow-05-faq.html | 39 +++ inst/doc/wflow-06-gitlab.html | 11 inst/doc/wflow-07-common-code.html | 11 inst/doc/wflow-08-deploy.Rmd | 6 inst/doc/wflow-08-deploy.html | 17 - inst/rstudio/addins.dcf |only man/is_fig_path_ext.Rd | 2 man/wflow_git_config.Rd | 2 man/wflow_git_pull.Rd | 5 man/wflow_git_push.Rd | 5 man/wflow_html.Rd | 2 man/wflow_rename_proj.Rd |only man/wflow_start.Rd | 16 - man/wflow_status.Rd | 10 man/wflow_toc.Rd |only man/wflow_update.Rd | 9 man/wflow_use_github.Rd | 2 man/wflow_use_gitlab.Rd | 2 tests/spelling.R |only tests/system-info.R |only tests/testthat/files/test-wflow_html/collapse.Rmd |only tests/testthat/files/test-wflow_html/indent.Rmd |only tests/testthat/files/test-wflow_html/keep_md.Rmd |only tests/testthat/files/test-wflow_html/sessioninfo-spacing.Rmd |only tests/testthat/files/test-wflow_update/post/_workflowr.yml | 2 tests/testthat/test-obtain_existing_path.R | 3 tests/testthat/test-wflow_build.R | 35 ++- tests/testthat/test-wflow_git_push_pull.R | 78 ++++++ tests/testthat/test-wflow_html.R | 121 ++++++++-- tests/testthat/test-wflow_rename_proj-external.R |only tests/testthat/test-wflow_rename_proj.R |only tests/testthat/test-wflow_start.R | 10 tests/testthat/test-wflow_status.R | 36 +++ tests/testthat/test-wflow_toc.R |only tests/testthat/test-wflow_use_github.R | 3 vignettes/wflow-01-getting-started.Rmd | 40 ++- vignettes/wflow-04-how-it-works.Rmd | 2 vignettes/wflow-05-faq.Rmd | 78 ++++++ vignettes/wflow-08-deploy.Rmd | 6 71 files changed, 965 insertions(+), 316 deletions(-)
Title: MultiFractal Detrended Fluctuation Analysis
Description: Contains the MultiFractal Detrended Fluctuation Analysis (MFDFA),
MultiFractal Detrended Cross-Correlation Analysis (MFXDFA), and the Multiscale
Multifractal Analysis (MMA). The MFDFA() function proposed in this package was
used in Laib et al. (<doi:10.1016/j.chaos.2018.02.024> and <doi:10.1063/1.5022737>).
See references for more information. Interested users can find a parallel version of
the MFDFA() function on GitHub.
Author: Mohamed Laib [aut, cre],
Luciano Telesca [aut],
Mikhail Kanevski [aut]
Maintainer: Mohamed Laib <laib.med@gmail.com>
Diff between MFDFA versions 1.0 dated 2018-04-18 and 1.1 dated 2019-04-15
DESCRIPTION | 19 +++++++++++-------- MD5 | 16 ++++++++++------ NAMESPACE | 4 ++++ R/MFDFA.R | 54 ++++++++++++++++++++++++++++++++---------------------- R/MFXDFA.R |only R/MFsim.R | 29 ++++++++++++++++++++++++----- R/MMA.R |only man/MFDFA.Rd | 35 +++++++++++++---------------------- man/MFXDFA.Rd |only man/MFsim.Rd | 24 ++++++++++++++++++++---- man/MMA.Rd |only 11 files changed, 114 insertions(+), 67 deletions(-)
Title: A Basic Set of Functions for Compositional Data Analysis
Description: A minimum set of functions to perform compositional data analysis
using the log-ratio approach introduced by John Aitchison (1982) <http://www.jstor.org/stable/2345821>. Main functions
have been implemented in c++ for better performance.
Author: Marc Comas-Cufà [aut, cre]
Maintainer: Marc Comas-Cufà <mcomas@imae.udg.edu>
Diff between coda.base versions 0.1.11 dated 2019-01-15 and 0.1.12 dated 2019-04-15
DESCRIPTION | 8 MD5 | 18 - NEWS | 6 R/coordinates.R | 20 - build/vignette.rds |binary inst/doc/coordinates.Rmd | 14 inst/doc/coordinates.html | 746 ++++++++++++++++------------------------------ man/dist.Rd | 2 man/pb_basis.Rd | 6 vignettes/coordinates.Rmd | 14 10 files changed, 313 insertions(+), 521 deletions(-)
Title: Read and Write from the System Clipboard
Description: Simple utility functions to read from and write to
the Windows, OS X, and X11 clipboards.
Author: Matthew Lincoln [aut, cre] (<https://orcid.org/0000-0002-4387-3384>),
Louis Maddox [ctb],
Steve Simpson [ctb],
Jennifer Bryan [ctb]
Maintainer: Matthew Lincoln <matthew.d.lincoln@gmail.com>
Diff between clipr versions 0.5.0 dated 2019-01-11 and 0.6.0 dated 2019-04-15
DESCRIPTION | 10 ++-- MD5 | 38 ++++++++++------- NAMESPACE | 1 NEWS.md | 10 ++++ R/clipboard.R | 77 ++++++++++++++++++++--------------- R/clipr-package.R | 8 +-- R/flat_str.R | 16 +++---- R/read_clip_tbl.R | 31 +++++++++----- R/utils.R | 14 +++--- README.md | 92 ++++++++++--------------------------------- build |only inst/doc |only man/clear_clip.Rd | 4 - man/clipr.Rd | 8 +-- man/clipr_available.Rd | 14 +++--- man/read_clip.Rd | 8 +-- man/read_clip_tbl.Rd | 16 ++++--- man/write_clip.Rd | 38 ++++++++--------- man/write_last_clip.Rd |only tests/testthat/test_render.R | 52 +++++++++++++++++------- vignettes |only 21 files changed, 224 insertions(+), 213 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889>, Letac et al. (2018) <arXiv:1706.04416>, Dobra and Mohammadi (2018) <doi:10.1214/18-AOAS1164>, Mohammadi et al. (2017) <doi:10.1111/rssc.12171>. To speed up the computations, the BDMCMC sampling algorithms are implemented in parallel using OpenMP in C++.
Author: Reza Mohammadi [aut, cre] <https://orcid.org/0000-0001-9538-0648>,
Ernst Wit [aut] <https://orcid.org/0000-0002-3671-9610>,
Adrian Dobra [ctb]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between BDgraph versions 2.57 dated 2019-04-07 and 2.58 dated 2019-04-15
DESCRIPTION | 8 MD5 | 47 +- NAMESPACE | 19 - NEWS | 11 R/bdgraph.R | 831 ++++++++++++++++++++----------------------------- R/bdgraph.mpl.R | 48 -- R/bdgraph.sim.R | 18 - R/bdgraph.ts.R | 11 R/compare.R | 91 +---- R/detect_cores.R | 20 - R/get_things.R |only R/graph.sim.R | 24 - R/plinks.R | 1 R/select.R | 91 ++--- inst/doc/BDgraph.pdf |binary inst/doc/vignette.pdf |binary man/BDgraph-package.Rd | 11 man/bdgraph.Rd | 4 man/bdgraph.mpl.Rd | 2 man/plot.bdgraph.Rd | 4 man/plot.graph.Rd | 13 man/plot.sim.Rd | 6 man/plotcoda.Rd | 2 man/plotroc.Rd | 2 vignettes/BDgraph.pdf |binary 25 files changed, 536 insertions(+), 728 deletions(-)
Title: Tools for the Analysis of Animal Track Data
Description: Functions for accessing and manipulating spatial data for animal
tracking, with straightforward coercion from and to other formats. Filter
for speed and create time spent maps from animal track data. There are
coercion methods to convert between 'trip' and 'ltraj' from 'adehabitatLT',
and between 'trip' and 'psp' and 'ppp' from 'spatstat'. Trip objects
can be created from raw or grouped data frames, and from types in the 'sp',
'sf', 'amt', 'trackeR', 'mousetrap', and other packages.
Author: Michael D. Sumner [aut, cre],
Sebastian Luque [ctb],
Anthony Fischbach [ctb],
Tomislav Hengl [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between trip versions 1.5.0 dated 2016-10-18 and 1.6.0 dated 2019-04-15
trip-1.5.0/trip/ChangeLog |only trip-1.5.0/trip/NEWS |only trip-1.5.0/trip/R/interpequal.R |only trip-1.5.0/trip/R/speedDistanceAngle.R |only trip-1.5.0/trip/R/trip-package.r |only trip-1.5.0/trip/inst/triptopology.r |only trip-1.6.0/trip/DESCRIPTION | 31 trip-1.6.0/trip/MD5 | 125 +-- trip-1.6.0/trip/NAMESPACE | 8 trip-1.6.0/trip/NEWS.md |only trip-1.6.0/trip/R/AllClass.R | 15 trip-1.6.0/trip/R/AllMethod.R | 311 +++++++- trip-1.6.0/trip/R/algorithms.R |only trip-1.6.0/trip/R/angle.R |only trip-1.6.0/trip/R/as.trip.R | 36 trip-1.6.0/trip/R/coerce.R | 73 + trip-1.6.0/trip/R/colours.R | 8 trip-1.6.0/trip/R/distance.R | 114 +++ trip-1.6.0/trip/R/filter.R | 90 ++ trip-1.6.0/trip/R/grid.R | 21 trip-1.6.0/trip/R/read.R |only trip-1.6.0/trip/R/simulate.R |only trip-1.6.0/trip/R/sysdata.rda |only trip-1.6.0/trip/R/trip-package.R |only trip-1.6.0/trip/R/trip.R | 887 +----------------------- trip-1.6.0/trip/R/utils.R |only trip-1.6.0/trip/R/write_track_kml.R |only trip-1.6.0/trip/README.md | 138 +++ trip-1.6.0/trip/build/vignette.rds |binary trip-1.6.0/trip/inst/CITATION |only trip-1.6.0/trip/inst/ChangeLog |only trip-1.6.0/trip/inst/ONEWS |only trip-1.6.0/trip/inst/WORDLIST |only trip-1.6.0/trip/inst/doc/trip.R | 110 +- trip-1.6.0/trip/inst/doc/trip.Rmd | 192 +++-- trip-1.6.0/trip/inst/doc/trip.html | 721 +++++++++++++++---- trip-1.6.0/trip/inst/extdata |only trip-1.6.0/trip/inst/misc |only trip-1.6.0/trip/man/TimeOrderedRecords-class.Rd | 8 trip-1.6.0/trip/man/TimeOrderedRecords.Rd | 1 trip-1.6.0/trip/man/adjust.duplicateTimes.Rd | 2 trip-1.6.0/trip/man/argos.sigma.Rd | 1 trip-1.6.0/trip/man/as.Other.Rd | 33 trip-1.6.0/trip/man/as.trip-methods.Rd | 15 trip-1.6.0/trip/man/cut.trip.Rd | 35 trip-1.6.0/trip/man/filter.penSS.Rd | 7 trip-1.6.0/trip/man/forceCompliance.Rd | 1 trip-1.6.0/trip/man/homedist.Rd | 3 trip-1.6.0/trip/man/makeGridTopology.Rd | 5 trip-1.6.0/trip/man/oc.theme.Rd | 11 trip-1.6.0/trip/man/rasterize.Rd | 8 trip-1.6.0/trip/man/readArgos.Rd | 22 trip-1.6.0/trip/man/sda.Rd | 3 trip-1.6.0/trip/man/sepIdGaps.Rd | 4 trip-1.6.0/trip/man/speedfilter.Rd | 16 trip-1.6.0/trip/man/trackAngle.Rd | 5 trip-1.6.0/trip/man/trackDistance.Rd | 19 trip-1.6.0/trip/man/trip-accessors.Rd | 3 trip-1.6.0/trip/man/trip-class.Rd | 23 trip-1.6.0/trip/man/trip-internal.Rd | 30 trip-1.6.0/trip/man/trip-methods.Rd | 111 ++- trip-1.6.0/trip/man/trip-package.Rd | 11 trip-1.6.0/trip/man/trip.split.exact.Rd | 9 trip-1.6.0/trip/man/tripGrid.Rd | 1 trip-1.6.0/trip/man/tripGrid.interp.Rd | 11 trip-1.6.0/trip/man/walrus818.Rd | 9 trip-1.6.0/trip/man/write_track_kml.Rd |only trip-1.6.0/trip/tests/spelling.R |only trip-1.6.0/trip/tests/testthat/Rplots.pdf |only trip-1.6.0/trip/tests/testthat/test-algos.R |only trip-1.6.0/trip/tests/testthat/test-coerce.R |only trip-1.6.0/trip/tests/testthat/test-distances.R |only trip-1.6.0/trip/tests/testthat/test-methods.R |only trip-1.6.0/trip/tests/testthat/test-read.R |only trip-1.6.0/trip/tests/testthat/test-summary.R |only trip-1.6.0/trip/tests/testthat/test-trip.R | 156 ++++ trip-1.6.0/trip/tests/testthat/test-write.R |only trip-1.6.0/trip/vignettes/trip.Rmd | 192 +++-- 78 files changed, 2161 insertions(+), 1474 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.3.8.8 dated 2019-03-04 and 0.3.9 dated 2019-04-15
DESCRIPTION | 10 - MD5 | 54 +++---- NAMESPACE | 2 R/Dependence.R | 1 R/Multivariate_Regression.R | 14 + R/Partial_Moments.R | 48 ++++-- R/Partition_Map.R | 14 + R/Regression.R | 134 ++++++++++++++----- R/Stack.R | 26 ++- R/dy_d_wrt.R | 3 R/dy_dx.R | 3 R/gvload.R | 1 inst/doc/NNSvignette_Clustering_and_Regression.R | 4 inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 8 - inst/doc/NNSvignette_Clustering_and_Regression.html | 13 + inst/doc/NNSvignette_Correlation_and_Dependence.R | 4 inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 5 inst/doc/NNSvignette_Correlation_and_Dependence.html | 11 + inst/doc/NNSvignette_Forecasting.R | 4 inst/doc/NNSvignette_Forecasting.Rmd | 6 inst/doc/NNSvignette_Forecasting.html | 5 man/NNS.part.Rd | 4 man/NNS.reg.Rd | 51 ++++--- man/dy.d_.Rd | 3 man/dy.dx.Rd | 3 vignettes/NNSvignette_Clustering_and_Regression.Rmd | 8 - vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 5 vignettes/NNSvignette_Forecasting.Rmd | 6 28 files changed, 311 insertions(+), 139 deletions(-)
Title: Access 'Upwave' API
Description: 'Upwave' <https://www.upwave.io/> is a task management app
organising tasks on boards and cards. 'upwaver' is a wrapper
around the 'Upwave' API <https://upwavehq.github.io/api/> that
allows listing and updating those boards and cards.
Author: Adrian Staempfli, Christoph Strauss, Fabian Leuthold, Michael
Schmid
Maintainer: Adrian Staempfli <adrian.staempfli@fhsg.ch>
Diff between upwaver versions 1.1.0 dated 2018-04-24 and 1.2.0 dated 2019-04-15
DESCRIPTION | 10 +++---- MD5 | 33 +++++++++++++----------- NAMESPACE | 1 NEWS.md | 4 +++ R/board2excel.R |only R/burndown.R | 8 +++--- R/list_cards_pretty.R |only R/upwaver.R | 15 ++++++----- inst/doc/upwaver.R | 8 +++--- inst/doc/upwaver.Rmd | 8 +++--- inst/doc/upwaver.html | 44 +++++++++++++++++++++++++-------- man/board2excel.Rd |only man/board_details.Rd | 2 - man/list_boards.Rd | 2 - man/list_cards.Rd | 2 - man/storypoints_and_status.Rd | 2 - man/storypoints_and_status_released.Rd | 2 - tests/testthat/test-upwaver.R | 28 +++++++++------------ vignettes/upwaver.Rmd | 8 +++--- 19 files changed, 105 insertions(+), 72 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],
Srishti Vishwakarma [ctb],
Xingyu Wang [ctb]
Maintainer: Vyacheslav Lyubchich <lyubchic@umces.edu>
Diff between funtimes versions 6.0 dated 2019-02-17 and 6.1 dated 2019-04-15
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/mcusum.test.R | 35 ++++++++++++++++++++++++++++------- R/sync.cluster.R | 2 +- build/partial.rdb |binary man/mcusum.test.Rd | 18 +++++++++++++++--- man/sync.cluster.Rd | 2 +- 7 files changed, 56 insertions(+), 23 deletions(-)
Title: Downloads and Organizes Financial Data for Multiple Tickers
Description: Makes it easy to download a large number of trade data from Yahoo Finance <https://finance.yahoo.com/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between BatchGetSymbols versions 2.4 dated 2019-03-23 and 2.5 dated 2019-04-15
DESCRIPTION | 13 +-- MD5 | 26 +++--- NEWS.md | 7 + R/BatchGetSymbols.R | 123 +++++++++++++++------------------ R/GetSP500Stocks.R | 23 +++++- R/Get_Ibov_Stocks.R | 22 +++++ R/Utils.R | 4 - R/myGetSymbols.R | 76 ++++++++++++++++++-- README.md | 12 +-- inst/doc/BatchGetSymbols-vignette.html | 31 +++----- man/BatchGetSymbols.Rd | 4 - man/GetIbovStocks.Rd | 7 + man/GetSP500Stocks.Rd | 7 + man/myGetSymbols.Rd | 14 +++ 14 files changed, 244 insertions(+), 125 deletions(-)
More information about BatchGetSymbols at CRAN
Permanent link
Title: A Project Infrastructure for Researchers
Description: Provides a project infrastructure with a focus on
manuscript creation. Creates a project folder with a single command,
containing subdirectories for specific components, templates for
manuscripts, and so on.
Author: Nik Krieger [aut, cre],
Adam Perzynski [aut],
Jarrod Dalton [aut]
Maintainer: Nik Krieger <nk@case.edu>
Diff between projects versions 0.1.0 dated 2018-12-30 and 1.1.0 dated 2019-04-15
DESCRIPTION | 20 MD5 | 53 +- NAMESPACE | 73 ++- NEWS.md | 61 ++ R/class-projects_author.R |only R/class-projects_stage.R |only R/edit.R | 943 ++++++++++++++++++++++++++-------------------- R/file_management.R | 410 ++++++++++++++------ R/getters.R | 356 +++++++++-------- R/header.R | 309 +++++++++++++-- R/metadata_manipulation.R | 263 +++++++++--- R/new.R | 922 +++++++++++++++++++++++++++----------------- R/set_generics.R |only R/setup.R | 134 +++--- R/update.R |only R/utilities.R | 365 ++++------------- R/validation.R | 519 ++++++++++++++++--------- R/zzz.R | 22 - README.md | 541 ++++++++++++++++++++------ man/display_metadata.Rd | 258 ++++++------ man/file_management.Rd | 268 +++++++------ man/header.Rd | 143 +++--- man/new_edit_delete.Rd | 593 ++++++++++++++++------------ man/pipe.Rd | 24 - man/projects-package.Rd | 86 ++-- man/projects_author.Rd |only man/projects_folder.Rd | 49 +- man/projects_stage.Rd |only man/reordering.Rd | 212 +++++----- man/setup_projects.Rd | 177 ++++---- man/update_metadata.Rd |only 31 files changed, 4135 insertions(+), 2666 deletions(-)
Title: UK National River Flow Archive Data from R
Description: Utility functions to retrieve data from the UK National River Flow Archive (<http://nrfa.ceh.ac.uk/>). The package contains R wrappers to the UK NRFA data temporary-API. There are functions to retrieve stations falling in a bounding box, to generate a map and extracting time series and general information.
Author: Claudia Vitolo [aut, cre] (<https://orcid.org/0000-0002-4252-1176>),
Matthew Fry [ctb] (Matthew supervised the unofficial API integration.),
Wouter Buytaert [ctb] (This package is part of Claudia Vitolo's PhD
work and Wouter is the supervisor.),
Michael Spencer [ctb] (Michael updated the function osg_parse to work
with grid references of different lengths.),
Tobias Gauster [ctb] (Tobias improved the function osg_parse
introducing vectorisation)
Maintainer: Claudia Vitolo <cvitolodev@gmail.com>
Diff between rnrfa versions 1.5.0 dated 2018-11-20 and 2.0 dated 2019-04-15
rnrfa-1.5.0/rnrfa/data |only rnrfa-1.5.0/rnrfa/man/stationSummary.Rd |only rnrfa-2.0/rnrfa/DESCRIPTION | 22 - rnrfa-2.0/rnrfa/MD5 | 78 ++--- rnrfa-2.0/rnrfa/NAMESPACE | 12 rnrfa-2.0/rnrfa/NEWS.md |only rnrfa-2.0/rnrfa/R/catalogue.R | 249 +++++----------- rnrfa-2.0/rnrfa/R/cmr.R | 27 + rnrfa-2.0/rnrfa/R/convert_flow.R | 17 - rnrfa-2.0/rnrfa/R/gdf.R | 26 + rnrfa-2.0/rnrfa/R/get_ts.R | 181 ++++------- rnrfa-2.0/rnrfa/R/internals.R |only rnrfa-2.0/rnrfa/R/osg_parse.R | 75 ++-- rnrfa-2.0/rnrfa/R/plot_rain_flow.R | 13 rnrfa-2.0/rnrfa/R/plot_trend.R | 43 +- rnrfa-2.0/rnrfa/R/rnrfa-package.R | 64 ---- rnrfa-2.0/rnrfa/R/seasonal_averages.R | 53 +-- rnrfa-2.0/rnrfa/R/station_ids.R |only rnrfa-2.0/rnrfa/R/zzz.R | 25 - rnrfa-2.0/rnrfa/README.md | 196 ------------ rnrfa-2.0/rnrfa/build |only rnrfa-2.0/rnrfa/inst/CITATION | 9 rnrfa-2.0/rnrfa/inst/doc |only rnrfa-2.0/rnrfa/man/catalogue.Rd | 36 +- rnrfa-2.0/rnrfa/man/cmr.Rd | 23 + rnrfa-2.0/rnrfa/man/convert_flow.Rd | 9 rnrfa-2.0/rnrfa/man/gdf.Rd | 22 + rnrfa-2.0/rnrfa/man/get_ts.Rd | 51 ++- rnrfa-2.0/rnrfa/man/osg_parse.Rd | 20 - rnrfa-2.0/rnrfa/man/plot_rain_flow.Rd | 5 rnrfa-2.0/rnrfa/man/plot_trend.Rd | 13 rnrfa-2.0/rnrfa/man/rnrfa-package.Rd | 5 rnrfa-2.0/rnrfa/man/seasonal_averages.Rd | 20 - rnrfa-2.0/rnrfa/man/station_ids.Rd |only rnrfa-2.0/rnrfa/tests/testthat.R | 22 - rnrfa-2.0/rnrfa/tests/testthat/test-catalogue.R | 33 +- rnrfa-2.0/rnrfa/tests/testthat/test-cmr.R | 28 - rnrfa-2.0/rnrfa/tests/testthat/test-convert_flow.R | 2 rnrfa-2.0/rnrfa/tests/testthat/test-get_ts.R | 33 +- rnrfa-2.0/rnrfa/tests/testthat/test-internals.R |only rnrfa-2.0/rnrfa/tests/testthat/test-osg_parse.R | 129 +++----- rnrfa-2.0/rnrfa/tests/testthat/test-seasonal_averages.R | 10 rnrfa-2.0/rnrfa/tests/testthat/test-station_ids.R |only rnrfa-2.0/rnrfa/vignettes |only 44 files changed, 683 insertions(+), 868 deletions(-)
Title: Computing Word Alignment Using IBM Model 1 (and Symmetrization)
for a Given Parallel Corpus and Its Evaluation
Description: For a given Sentence-Aligned Parallel Corpus, it aligns words for each sentence pair. It considers one-to-many and symmetrization alignments. Moreover, it evaluates the quality of word alignment based on this package and some other software. It also builds an automatic dictionary of two languages based on given parallel corpus.
Author: Neda Daneshagr and Majid Sarmad.
Maintainer: Neda Daneshgar<ne_da978@stu-mail.um.ac.ir>
Diff between word.alignment versions 1.0.9 dated 2018-02-21 and 1.1 dated 2019-04-15
word.alignment-1.0.9/word.alignment/R/Evaluation1.R |only word.alignment-1.0.9/word.alignment/R/ExcelToR.R |only word.alignment-1.0.9/word.alignment/R/Symmetrization.R |only word.alignment-1.0.9/word.alignment/R/align_test.set.R |only word.alignment-1.0.9/word.alignment/R/cons.agn.R |only word.alignment-1.0.9/word.alignment/R/culf.R |only word.alignment-1.0.9/word.alignment/R/mydictionary.R |only word.alignment-1.0.9/word.alignment/R/prepareData.R |only word.alignment-1.0.9/word.alignment/R/squareN.R |only word.alignment-1.0.9/word.alignment/R/word_alignIBM1.R |only word.alignment-1.0.9/word.alignment/man/Evaluation1.Rd |only word.alignment-1.0.9/word.alignment/man/ExcelToR.Rd |only word.alignment-1.0.9/word.alignment/man/Symmetrization.Rd |only word.alignment-1.0.9/word.alignment/man/align_test.set.Rd |only word.alignment-1.0.9/word.alignment/man/cons.agn.Rd |only word.alignment-1.0.9/word.alignment/man/culf.Rd |only word.alignment-1.0.9/word.alignment/man/mydictionary.Rd |only word.alignment-1.0.9/word.alignment/man/prepareData.Rd |only word.alignment-1.0.9/word.alignment/man/squareN.Rd |only word.alignment-1.0.9/word.alignment/man/word_alignIBM1.Rd |only word.alignment-1.1/word.alignment/DESCRIPTION | 10 +- word.alignment-1.1/word.alignment/MD5 | 46 +++++----- word.alignment-1.1/word.alignment/NAMESPACE | 30 +++--- word.alignment-1.1/word.alignment/R/align.ibm1.R |only word.alignment-1.1/word.alignment/R/align.test.R |only word.alignment-1.1/word.alignment/R/bidictionary.R |only word.alignment-1.1/word.alignment/R/cross.table.R |only word.alignment-1.1/word.alignment/R/evaluation.R |only word.alignment-1.1/word.alignment/R/excel2rdata.R |only word.alignment-1.1/word.alignment/R/neighbor.R |only word.alignment-1.1/word.alignment/R/nfirst2lower.R |only word.alignment-1.1/word.alignment/R/prepare.data.R |only word.alignment-1.1/word.alignment/R/remove.punct.R |only word.alignment-1.1/word.alignment/man/align.ibm1.Rd |only word.alignment-1.1/word.alignment/man/align.test.Rd |only word.alignment-1.1/word.alignment/man/bidictionary.Rd |only word.alignment-1.1/word.alignment/man/cross.table.Rd |only word.alignment-1.1/word.alignment/man/evaluation.Rd |only word.alignment-1.1/word.alignment/man/excel2rdata.Rd |only word.alignment-1.1/word.alignment/man/neighbor.Rd |only word.alignment-1.1/word.alignment/man/nfirst2lower.Rd |only word.alignment-1.1/word.alignment/man/prepare.data.Rd |only word.alignment-1.1/word.alignment/man/remove.punct.Rd |only word.alignment-1.1/word.alignment/man/word.alignment-package.Rd | 16 +-- 44 files changed, 52 insertions(+), 50 deletions(-)
More information about word.alignment at CRAN
Permanent link
Title: Least-Squares Bilinear Clustering for Three-Way Data
Description: Functions for performing least-squares bilinear clustering of
three-way data. The method uses the bilinear decomposition (or bi-additive
model) to model two-way matrix slices while clustering over the third way.
Up to four different types of clusters are included, one for each term of the
bilinear decomposition. In this way, matrices are clustered simultaneously on
(a subset of) their overall means, row margins, column margins and row-column
interactions. The orthogonality of the bilinear model results in separability of
the joint clustering problem into four separate ones. Three of these sub-problems
are specific k-means problems, while a special algorithm is implemented for the
interactions. Plotting methods are provided, including biplots for the low-rank
approximations of the interactions.
Author: Pieter Schoonees [aut, cre],
Patrick Groenen [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between lsbclust versions 1.0.5 dated 2018-04-19 and 1.1 dated 2019-04-15
lsbclust-1.0.5/lsbclust/tests |only lsbclust-1.1/lsbclust/DESCRIPTION | 14 +++---- lsbclust-1.1/lsbclust/MD5 | 39 +++++++------------- lsbclust-1.1/lsbclust/R/plot.int.lsbclust.R | 47 ++++++++++++++++++------- lsbclust-1.1/lsbclust/data/dcars.rda |binary lsbclust-1.1/lsbclust/data/lov.rda |binary lsbclust-1.1/lsbclust/data/supermarkets.rda |binary lsbclust-1.1/lsbclust/man/KMeansW.Rd | 1 lsbclust-1.1/lsbclust/man/int.lsbclust.Rd | 9 ++-- lsbclust-1.1/lsbclust/man/lsbclust.Rd | 9 ++-- lsbclust-1.1/lsbclust/man/lsbclusttoclue.Rd | 2 - lsbclust-1.1/lsbclust/man/plot.T3Clusf.Rd | 3 + lsbclust-1.1/lsbclust/man/plot.bicomp.Rd | 5 +- lsbclust-1.1/lsbclust/man/plot.int.lsbclust.Rd | 32 ++++++++++------- lsbclust-1.1/lsbclust/man/rlsbclust.Rd | 4 +- lsbclust-1.1/lsbclust/man/sim_lsbclust.Rd | 12 +++--- lsbclust-1.1/lsbclust/man/step.lsbclust.Rd | 8 ++-- 17 files changed, 103 insertions(+), 82 deletions(-)
Title: Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM,
PBS/Torque)
Description: Evaluate arbitrary function calls using workers on HPC schedulers
in single line of code. All processing is done on the network without
accessing the file system. Remote schedulers are supported via SSH.
Author: Michael Schubert <mschu.dev@gmail.com>
Maintainer: Michael Schubert <mschu.dev@gmail.com>
Diff between clustermq versions 0.8.6 dated 2019-02-22 and 0.8.7 dated 2019-04-15
clustermq-0.8.6/clustermq/inst/doc/clustermq.R |only clustermq-0.8.6/clustermq/inst/doc/clustermq.Rmd |only clustermq-0.8.6/clustermq/inst/doc/clustermq.html |only clustermq-0.8.7/clustermq/DESCRIPTION | 10 clustermq-0.8.7/clustermq/MD5 | 89 - clustermq-0.8.7/clustermq/NEWS.md | 121 +- clustermq-0.8.7/clustermq/R/Q.r | 6 clustermq-0.8.7/clustermq/R/Q_rows.r | 13 clustermq-0.8.7/clustermq/R/foreach.r | 26 clustermq-0.8.7/clustermq/R/master.r | 39 clustermq-0.8.7/clustermq/R/qsys.r | 19 clustermq-0.8.7/clustermq/R/qsys_multicore.r | 18 clustermq-0.8.7/clustermq/R/qsys_ssh.r | 49 clustermq-0.8.7/clustermq/R/ssh_proxy.r | 102 - clustermq-0.8.7/clustermq/R/work_chunk.r | 8 clustermq-0.8.7/clustermq/R/worker.r | 14 clustermq-0.8.7/clustermq/R/workers.r | 5 clustermq-0.8.7/clustermq/R/zzz.r | 6 clustermq-0.8.7/clustermq/build/vignette.rds |binary clustermq-0.8.7/clustermq/inst/LSF.tmpl | 2 clustermq-0.8.7/clustermq/inst/PBS.tmpl | 2 clustermq-0.8.7/clustermq/inst/SGE.tmpl | 1 clustermq-0.8.7/clustermq/inst/SLURM.tmpl | 1 clustermq-0.8.7/clustermq/inst/SSH.tmpl |only clustermq-0.8.7/clustermq/inst/TORQUE.tmpl | 2 clustermq-0.8.7/clustermq/inst/doc/quickstart.R | 5 clustermq-0.8.7/clustermq/inst/doc/quickstart.Rmd | 26 clustermq-0.8.7/clustermq/inst/doc/quickstart.html | 478 +++++--- clustermq-0.8.7/clustermq/inst/doc/technicaldocs.Rmd | 2 clustermq-0.8.7/clustermq/inst/doc/technicaldocs.html | 484 +++++--- clustermq-0.8.7/clustermq/inst/doc/userguide.R | 5 clustermq-0.8.7/clustermq/inst/doc/userguide.Rmd | 10 clustermq-0.8.7/clustermq/inst/doc/userguide.html | 653 +++++++---- clustermq-0.8.7/clustermq/man/Q.Rd | 4 clustermq-0.8.7/clustermq/man/Q_rows.Rd | 5 clustermq-0.8.7/clustermq/man/dot-onLoad.Rd | 4 clustermq-0.8.7/clustermq/man/master.Rd | 4 clustermq-0.8.7/clustermq/man/work_chunk.Rd | 4 clustermq-0.8.7/clustermq/man/workers.Rd | 4 clustermq-0.8.7/clustermq/tests/testthat/helper-util.r | 18 clustermq-0.8.7/clustermq/tests/testthat/test-2-work_chunk.r | 2 clustermq-0.8.7/clustermq/tests/testthat/test-4-qsys.r | 47 clustermq-0.8.7/clustermq/tests/testthat/test-5-qsys_impl.r | 13 clustermq-0.8.7/clustermq/tests/testthat/test-6-ssh_proxy.r | 18 clustermq-0.8.7/clustermq/tests/testthat/test-7-foreach.r |only clustermq-0.8.7/clustermq/vignettes/quickstart.Rmd | 26 clustermq-0.8.7/clustermq/vignettes/technicaldocs.Rmd | 2 clustermq-0.8.7/clustermq/vignettes/userguide.Rmd | 10 48 files changed, 1608 insertions(+), 749 deletions(-)
Title: Construct Polygons Summarising the Location and Variability of
Point Sets
Description: Various applications in invasive species biology,
conservation biology, epidemiology and elsewhere involve
sampling of sets of 2D points from a posterior distribution.
The number of such point sets may be large, say 1000 or 10000.
This package facilitates visualisation of such output by
constructing seven nested polygons representing the location and
variability of the point sets. This can be used, for example, to
visualise the range boundary of a species, and uncertainty in
the location of that boundary.
Author: Jonathan Keith [aut, cre],
Ken Clarkson [aut],
Eric Hufschmid [ctb],
AT&T [cph]
Maintainer: Jonathan Keith <jonathan.keith@monash.edu>
Diff between pts2polys versions 0.1.0 dated 2019-04-14 and 0.1.1 dated 2019-04-15
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/pts2polys.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Regularized Linear Models
Description: Algorithms for fitting model-based penalized coefficient paths. Currently the models include penalized Poisson, negative binomial, zero-inflated Poisson and zero-inflated negative binomial regression models. The penalties include least absolute shrinkage and selection operator (LASSO), smoothly clipped absolute deviation (SCAD) and minimax concave penalty (MCP), and each possibly combining with L_2 penalty.
See Wang et al. (2014) <doi:10.1002/sim.6314>, Wang et al. (2015) <doi:10.1002/bimj.201400143>,
Wang et al. (2016) <doi:10.1177/0962280214530608>.
Author: Zhu Wang, with contributions from Achim Zeileis, Simon Jackman, Brian Ripley, Trevor Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Gil Chu and Patrick Breheny
Maintainer: Zhu Wang <wangz1@uthscsa.edu>
Diff between mpath versions 0.3-7 dated 2019-02-27 and 0.3-12 dated 2019-04-15
DESCRIPTION | 8 MD5 | 97 +++-- NEWS | 19 + R/glmreg.R | 29 - R/glmregNB.R | 15 R/nclreg.R | 167 ++++++++- R/predict.glmreg.R | 10 R/zipath.R | 721 +++++++++++++++---------------------------- build/vignette.rds |binary inst/doc/brcancer.R | 11 inst/doc/brcancer.Rnw | 16 inst/doc/brcancer.pdf |binary inst/doc/german.R | 54 +-- inst/doc/german.Rnw | 26 - inst/doc/german.pdf |binary inst/doc/kkt.Rnw |only inst/doc/kkt.pdf |only inst/doc/static_brcancer.pdf |binary inst/doc/static_german.pdf |binary man/breadReg.Rd | 2 man/estfunReg.Rd | 2 man/glmreg.Rd | 2 man/glmregNB.Rd | 27 - man/glmreg_fit.Rd | 14 man/hessianReg.Rd | 2 man/meatReg.Rd | 2 man/nclreg.Rd | 4 man/nclreg_fit.Rd | 17 - man/sandwichReg.Rd | 2 man/se.Rd | 2 man/zipath.Rd | 32 + src/activeset.f |only src/cfuns.c | 2 src/compute_h.f |only src/dnbinom.f |only src/dpois.f |only src/factorial.f |only src/gfunc.f |only src/glmreg_fit_fortran.f |only src/glmregnb_fortran.f |only src/gradient.f |only src/init.f |only src/lmax_zipath.f |only src/lmnetGaussian.f | 51 +-- src/loss.f |only src/midloop.f | 17 - src/midloopGLM.f | 36 +- src/mpath_init.c | 52 ++- src/mutil.f | 17 + src/nclreg_fortran.f |only src/outloop.f | 116 +++--- src/outprod.f |only src/theta_ml.f |only src/zi.f |only src/zipath_active.f |only src/zipath_nonactive.f |only vignettes/brcancer.Rnw | 16 vignettes/german.Rnw | 26 - vignettes/kkt.Rnw |only vignettes/mpath.bib | 20 + 60 files changed, 839 insertions(+), 795 deletions(-)
Title: Probability of Detection for Qualitative PCR Methods
Description: This tool computes the probability of detection (POD) curve and the limit of detection (LOD), i.e. the number of copies of the target DNA sequence required to ensure a 95 % probability of detection (LOD95). Other quantiles of the LOD can be specified.
This is a reimplementation of the mathematical-statistical modelling of the validation of qualitative polymerase chain reaction (PCR) methods within a single laboratory as provided by the commercial tool 'PROLab' <http://quodata.de/>. The modelling itself has been described by Uhlig et al. (2015) <doi:10.1007/s00769-015-1112-9>.
Author: Markus Boenn (State Office for Consumer Protection Saxony-Anhalt, Germany)
Maintainer: Markus Boenn <markus.boenn.sf@gmail.com>
Diff between POD versions 0.99.0 dated 2019-02-06 and 1.1.0 dated 2019-04-15
CHANGELOG |only DESCRIPTION | 9 ++++---- MD5 | 36 ++++++++++++++++++++------------ R/analyzeSingleLab.R | 53 ++++++++++++++++++++++++++---------------------- R/foreign.R | 7 +++--- R/plotPOD.R | 20 +++++++++++++----- R/printPod.R | 53 ++++++++++++++++++++++++++++-------------------- R/testdata.R | 2 - R/zzz.R | 17 +++++++++++---- README.md |only build |only inst/doc |only inst/pod.xlsm |binary man/analyzeSingleLab.Rd | 9 -------- man/foreign.Rd | 7 +++--- man/plotPOD.Rd | 7 +++++- man/print.pod.Rd | 3 ++ man/testdata.Rd | 2 - vignettes |only 19 files changed, 137 insertions(+), 88 deletions(-)
Title: Different Models of Posterior Distributions of Adjusted Odds
Ratio
Description: Generates different posterior distributions of adjusted odds ratio under different priors of sensitivity and specificity, and plots the models for comparison. It also provides estimations for the specifications of the models using diagnostics of exposure status with a non-linear mixed effects model. It implements the methods that are first proposed by Chu et al. (2006) <doi:10.1016/j.annepidem.2006.04.001> and Chu et al. (2010) <doi:10.1177/0272989X09353452>.
Author: Jinhui Yang, Haitao Chu, and Lifeng Lin
Maintainer: Jinhui Yang <yangj2@carleton.edu>
Diff between BayesSenMC versions 0.1.0 dated 2019-04-08 and 0.1.1 dated 2019-04-15
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/doc/BayesSenMC_demo.pdf |binary 3 files changed, 6 insertions(+), 6 deletions(-)
Title: A Computational Tool for Aerobiological Data
Description: Different tools for managing databases of airborne particles, elaborating the main calculations and visualization of results. In a first step, data are checked using tools for quality control and all missing gaps are completed. Then, the main parameters of the pollen season are calculated and represented graphically. Multiple graphical tools are available: pollen calendars, phenological plots, time series, tendencies, interactive plots, abundance plots...
Author: Jesus Rojo <Jesus.Rojo@uclm.es>, Antonio Picornell <picornell@uma.es>, Jose Oteros <OterosJose@gmail.com>
Maintainer: "Jose Oteros" <OterosJose@gmail.com>
Diff between AeRobiology versions 1.0.3 dated 2019-03-05 and 2.0 dated 2019-04-15
AeRobiology-1.0.3/AeRobiology/R/munich.R |only AeRobiology-1.0.3/AeRobiology/R/ps_plot.R |only AeRobiology-1.0.3/AeRobiology/R/qualitycontrol.R |only AeRobiology-1.0.3/AeRobiology/R/summary_normplot.R |only AeRobiology-1.0.3/AeRobiology/R/summary_plot.R |only AeRobiology-1.0.3/AeRobiology/R/trend_plot.R |only AeRobiology-1.0.3/AeRobiology/R/trends.R |only AeRobiology-1.0.3/AeRobiology/data/munich.rda |only AeRobiology-1.0.3/AeRobiology/man/munich.Rd |only AeRobiology-1.0.3/AeRobiology/man/ps_plot.Rd |only AeRobiology-1.0.3/AeRobiology/man/qualitycontrol.Rd |only AeRobiology-1.0.3/AeRobiology/man/summary_normplot.Rd |only AeRobiology-1.0.3/AeRobiology/man/summary_plot.Rd |only AeRobiology-1.0.3/AeRobiology/man/trend_plot.Rd |only AeRobiology-1.0.3/AeRobiology/man/trends.Rd |only AeRobiology-2.0/AeRobiology/DESCRIPTION | 18 AeRobiology-2.0/AeRobiology/MD5 | 85 - AeRobiology-2.0/AeRobiology/NAMESPACE | 24 AeRobiology-2.0/AeRobiology/NEWS.md | 61 AeRobiology-2.0/AeRobiology/R/AeRobiology.R | 2 AeRobiology-2.0/AeRobiology/R/POMO_pollen.R |only AeRobiology-2.0/AeRobiology/R/analyse_trend.R |only AeRobiology-2.0/AeRobiology/R/calculate_ps.R | 1149 +++++++++--------- AeRobiology-2.0/AeRobiology/R/interpollen.R | 83 - AeRobiology-2.0/AeRobiology/R/iplot_abundance.R | 37 AeRobiology-2.0/AeRobiology/R/iplot_pheno.R | 17 AeRobiology-2.0/AeRobiology/R/iplot_pollen.R | 21 AeRobiology-2.0/AeRobiology/R/iplot_years.R | 15 AeRobiology-2.0/AeRobiology/R/ma.R | 68 - AeRobiology-2.0/AeRobiology/R/munich_pollen.R |only AeRobiology-2.0/AeRobiology/R/plot_heathour.R |only AeRobiology-2.0/AeRobiology/R/plot_hour.R |only AeRobiology-2.0/AeRobiology/R/plot_normsummary.R |only AeRobiology-2.0/AeRobiology/R/plot_ps.R |only AeRobiology-2.0/AeRobiology/R/plot_summary.R |only AeRobiology-2.0/AeRobiology/R/plot_trend.R |only AeRobiology-2.0/AeRobiology/R/pollen_calendar.R | 64 - AeRobiology-2.0/AeRobiology/R/quality_control.R |only AeRobiology-2.0/AeRobiology/build |only AeRobiology-2.0/AeRobiology/data/POMO_pollen.rda |only AeRobiology-2.0/AeRobiology/data/munich_pollen.rda |only AeRobiology-2.0/AeRobiology/inst |only AeRobiology-2.0/AeRobiology/man/POMO_pollen.Rd |only AeRobiology-2.0/AeRobiology/man/analyse_trend.Rd |only AeRobiology-2.0/AeRobiology/man/calculate_ps.Rd | 24 AeRobiology-2.0/AeRobiology/man/interpollen.Rd | 12 AeRobiology-2.0/AeRobiology/man/iplot_abundance.Rd | 14 AeRobiology-2.0/AeRobiology/man/iplot_pheno.Rd | 4 AeRobiology-2.0/AeRobiology/man/iplot_pollen.Rd | 4 AeRobiology-2.0/AeRobiology/man/iplot_years.Rd | 4 AeRobiology-2.0/AeRobiology/man/ma.Rd | 4 AeRobiology-2.0/AeRobiology/man/munich_pollen.Rd |only AeRobiology-2.0/AeRobiology/man/plot_heathour.Rd |only AeRobiology-2.0/AeRobiology/man/plot_hour.Rd |only AeRobiology-2.0/AeRobiology/man/plot_normsummary.Rd |only AeRobiology-2.0/AeRobiology/man/plot_ps.Rd |only AeRobiology-2.0/AeRobiology/man/plot_summary.Rd |only AeRobiology-2.0/AeRobiology/man/plot_trend.Rd |only AeRobiology-2.0/AeRobiology/man/pollen_calendar.Rd | 12 AeRobiology-2.0/AeRobiology/man/quality_control.Rd |only AeRobiology-2.0/AeRobiology/tests |only AeRobiology-2.0/AeRobiology/vignettes |only 62 files changed, 970 insertions(+), 752 deletions(-)
Title: Tables, Labels and Some Useful Functions from Spreadsheets and
'SPSS' Statistics
Description: Package computes and displays tables with support for 'SPSS'-style
labels, multiple and nested banners, weights, multiple-response variables
and significance testing. There are facilities for nice output of tables
in 'knitr', 'Shiny', '*.xlsx' files, R and 'Jupyter' notebooks. Methods
for labelled variables add value labels support to base R functions and to
some functions from other packages. Additionally, the package brings
popular data transformation functions from 'SPSS' Statistics and 'Excel':
'RECODE', 'COUNT', 'COMPUTE', 'DO IF', 'COUNTIF', 'VLOOKUP' and etc.
These functions are very useful for data processing in marketing research
surveys. Package intended to help people to move data
processing from 'Excel' and 'SPSS' to R.
Author: Gregory Demin [aut, cre]
Maintainer: Gregory Demin <gdemin@gmail.com>
Diff between expss versions 0.8.10 dated 2018-12-11 and 0.8.11 dated 2019-04-15
expss-0.8.10/expss/R/modify.R |only expss-0.8.10/expss/man/modify.Rd |only expss-0.8.10/expss/tests/testthat/test_modify.R |only expss-0.8.10/expss/tests/testthat/test_subst.R |only expss-0.8.11/expss/DESCRIPTION | 29 expss-0.8.11/expss/MD5 | 347 expss-0.8.11/expss/NAMESPACE | 1438 - expss-0.8.11/expss/NEWS | 259 expss-0.8.11/expss/R/S3_methods.R | 44 expss-0.8.11/expss/R/aaa_utils.R | 24 expss-0.8.11/expss/R/common_table_utils.R | 12 expss-0.8.11/expss/R/compute.R |only expss-0.8.11/expss/R/cro.R | 17 expss-0.8.11/expss/R/cro_fun.R | 115 expss-0.8.11/expss/R/custom_tables.R | 35 expss-0.8.11/expss/R/custom_tables_significance.R | 69 expss-0.8.11/expss/R/html_table.R | 962 - expss-0.8.11/expss/R/if_val.R | 1120 - expss-0.8.11/expss/R/keep.R | 51 expss-0.8.11/expss/R/labels.R | 42 expss-0.8.11/expss/R/mrset.R | 33 expss-0.8.11/expss/R/qc.R | 78 expss-0.8.11/expss/R/selectors.R | 73 expss-0.8.11/expss/R/significance_cases.R | 9 expss-0.8.11/expss/R/significance_cell_chisq.R |only expss-0.8.11/expss/R/significance_cpct.R | 127 expss-0.8.11/expss/R/significance_pvalue.R | 188 expss-0.8.11/expss/R/split_by.R | 2 expss-0.8.11/expss/R/vlookup.R | 14 expss-0.8.11/expss/R/where.R | 30 expss-0.8.11/expss/R/write_labels.R | 31 expss-0.8.11/expss/R/xl_write.R | 1670 - expss-0.8.11/expss/R/zzz_experimental.R | 24 expss-0.8.11/expss/build/vignette.rds |binary expss-0.8.11/expss/inst/doc/labels-support.R | 262 expss-0.8.11/expss/inst/doc/labels-support.Rmd | 2 expss-0.8.11/expss/inst/doc/labels-support.html | 1282 - expss-0.8.11/expss/inst/doc/tables-with-labels.R | 950 - expss-0.8.11/expss/inst/doc/tables-with-labels.Rmd | 2 expss-0.8.11/expss/inst/doc/tables-with-labels.html | 9144 ++++++---- expss-0.8.11/expss/inst/doc/xlsx-export.R | 146 expss-0.8.11/expss/inst/doc/xlsx-export.html | 1171 - expss-0.8.11/expss/man/add_rows.Rd | 148 expss-0.8.11/expss/man/apply_labels.Rd | 122 expss-0.8.11/expss/man/as.category.Rd | 126 expss-0.8.11/expss/man/as.datatable_widget.Rd | 172 expss-0.8.11/expss/man/as.dichotomy.Rd | 234 expss-0.8.11/expss/man/as.etable.Rd | 72 expss-0.8.11/expss/man/as.labelled.Rd | 56 expss-0.8.11/expss/man/by_groups.Rd | 112 expss-0.8.11/expss/man/compare_proportions.Rd | 170 expss-0.8.11/expss/man/compute.Rd |only expss-0.8.11/expss/man/count_if.Rd | 646 expss-0.8.11/expss/man/criteria.Rd | 384 expss-0.8.11/expss/man/cro.Rd | 446 expss-0.8.11/expss/man/cro_fun.Rd | 552 expss-0.8.11/expss/man/default_dataset.Rd | 86 expss-0.8.11/expss/man/do_repeat.Rd | 194 expss-0.8.11/expss/man/drop_empty_rows.Rd | 142 expss-0.8.11/expss/man/experimental.Rd | 390 expss-0.8.11/expss/man/expss.Rd | 104 expss-0.8.11/expss/man/expss.options.Rd | 238 expss-0.8.11/expss/man/fctr.Rd | 94 expss-0.8.11/expss/man/fre.Rd | 158 expss-0.8.11/expss/man/htmlTable.etable.Rd | 234 expss-0.8.11/expss/man/if_na.Rd | 178 expss-0.8.11/expss/man/if_val.Rd | 460 expss-0.8.11/expss/man/info.Rd | 74 expss-0.8.11/expss/man/keep.Rd | 142 expss-0.8.11/expss/man/match_row.Rd | 136 expss-0.8.11/expss/man/merge.etable.Rd | 128 expss-0.8.11/expss/man/mrset.Rd | 132 expss-0.8.11/expss/man/na_if.Rd | 154 expss-0.8.11/expss/man/name_dots.Rd |only expss-0.8.11/expss/man/names2labels.Rd | 108 expss-0.8.11/expss/man/nest.Rd | 130 expss-0.8.11/expss/man/prepend_values.Rd | 180 expss-0.8.11/expss/man/product_test.Rd | 82 expss-0.8.11/expss/man/prop.Rd | 96 expss-0.8.11/expss/man/qc.Rd | 109 expss-0.8.11/expss/man/read_spss.Rd | 86 expss-0.8.11/expss/man/reexports.Rd | 166 expss-0.8.11/expss/man/ref.Rd | 134 expss-0.8.11/expss/man/set_caption.Rd | 96 expss-0.8.11/expss/man/sheet.Rd | 94 expss-0.8.11/expss/man/significance.Rd | 687 expss-0.8.11/expss/man/sort_asc.Rd | 106 expss-0.8.11/expss/man/split_by.Rd | 176 expss-0.8.11/expss/man/split_labels.Rd | 206 expss-0.8.11/expss/man/sum_row.Rd | 236 expss-0.8.11/expss/man/tab_sort_asc.Rd | 148 expss-0.8.11/expss/man/tables.Rd | 940 - 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expss-0.8.11/expss/tests/testthat/test_htmlTable.R | 365 expss-0.8.11/expss/tests/testthat/test_if_na.R | 2 expss-0.8.11/expss/tests/testthat/test_if_val.R | 1393 - expss-0.8.11/expss/tests/testthat/test_if_val_with_na.R | 2 expss-0.8.11/expss/tests/testthat/test_into.R | 61 expss-0.8.11/expss/tests/testthat/test_keep.R | 16 expss-0.8.11/expss/tests/testthat/test_labels.R | 6 expss-0.8.11/expss/tests/testthat/test_mean_if.R | 2 expss-0.8.11/expss/tests/testthat/test_mrset.R | 5 expss-0.8.11/expss/tests/testthat/test_na_if.R | 1 expss-0.8.11/expss/tests/testthat/test_parameter.R | 29 expss-0.8.11/expss/tests/testthat/test_prepend.R | 424 expss-0.8.11/expss/tests/testthat/test_ref.R | 2 expss-0.8.11/expss/tests/testthat/test_selectors.R | 30 expss-0.8.11/expss/tests/testthat/test_siginificance_cases.R | 350 expss-0.8.11/expss/tests/testthat/test_significance_cell_chisq.R |only expss-0.8.11/expss/tests/testthat/test_significance_cpct.R | 986 - expss-0.8.11/expss/tests/testthat/test_significance_means.R | 783 expss-0.8.11/expss/tests/testthat/test_sort.R | 1 expss-0.8.11/expss/tests/testthat/test_sum_if.R | 3 expss-0.8.11/expss/tests/testthat/test_text_expand.R |only expss-0.8.11/expss/tests/testthat/test_vlookup.R | 13 expss-0.8.11/expss/tests/testthat/test_weighted_stats.R | 2 expss-0.8.11/expss/tests/testthat/test_where.R | 1 expss-0.8.11/expss/tests/testthat/test_with_data.table.R | 2 expss-0.8.11/expss/tests/testthat/test_xl_write.R | 860 expss-0.8.11/expss/vignettes/labels-support.Rmd | 2 expss-0.8.11/expss/vignettes/tables-with-labels.Rmd | 2 182 files changed, 24705 insertions(+), 20679 deletions(-)