Title: Fit Text Inside a Box in 'ggplot2'
Description: Provides 'ggplot2' geoms to fit text into a box by growing, shrinking
or wrapping the text.
Author: David Wilkins [aut, cre]
Maintainer: David Wilkins <david@wilkox.org>
Diff between ggfittext versions 0.8.1 dated 2019-07-18 and 0.9.0 dated 2020-06-14
DESCRIPTION | 10 MD5 | 107 +++-- NAMESPACE | 1 NEWS.md | 31 + R/data.R | 13 R/geom_bar_text.R | 89 +++- R/geom_fit_text.R | 183 ++++++---- R/polar.R |only README.md | 36 + build/vignette.rds |binary data/gold.rda |only inst/doc/introduction-to-ggfittext.R | 40 +- inst/doc/introduction-to-ggfittext.Rmd | 37 +- inst/doc/introduction-to-ggfittext.html | 80 ++-- man/altitudes.Rd | 6 man/animals.Rd | 6 man/coffees.Rd | 6 man/figures/README-hero-1.png |binary man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |only man/figures/README-unnamed-chunk-14-1.png |only man/figures/README-unnamed-chunk-15-1.png |only man/figures/README-unnamed-chunk-16-1.png |only man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/geom_fit_text.Rd | 80 +++- man/ggfittext.Rd | 1 man/gold.Rd |only tests/figs/geom-bar-text |only tests/figs/visual-tests-of-plots/angles-and-basic-placement.svg | 18 tests/figs/visual-tests-of-plots/basic-bar-plot.svg | 10 tests/figs/visual-tests-of-plots/basic-placement.svg | 8 tests/figs/visual-tests-of-plots/blank-labels.svg | 14 tests/figs/visual-tests-of-plots/contrast-against-default-bar-colour.svg |only tests/figs/visual-tests-of-plots/contrasting-text.svg | 52 +- tests/figs/visual-tests-of-plots/contrasting-works-with-non-black-text.svg |only tests/figs/visual-tests-of-plots/dodged-and-flipped-bar-plot.svg | 22 - tests/figs/visual-tests-of-plots/frost-poem.svg |only tests/figs/visual-tests-of-plots/height-of-20-mm.svg |only tests/figs/visual-tests-of-plots/height-of-5-mm.svg |only tests/figs/visual-tests-of-plots/place-bottom.svg |only tests/figs/visual-tests-of-plots/place-centre.svg |only tests/figs/visual-tests-of-plots/place-top.svg |only tests/figs/visual-tests-of-plots/reflowing-and-growing.svg | 20 - tests/figs/visual-tests-of-plots/stacked-bar-plot.svg | 26 - tests/figs/visual-tests-of-plots/width-of-100-mm.svg |only tests/figs/visual-tests-of-plots/width-of-40-mm.svg |only tests/figs/visual-tests-of-plots/ymin-ymax.svg | 22 - tests/testthat/test-geom_bar_text.R | 18 tests/testthat/test-geom_fit_text.R | 32 + tests/testthat/test-polar.R |only tests/testthat/test_plots.R | 114 ++++++ vignettes/introduction-to-ggfittext.Rmd | 37 +- 59 files changed, 810 insertions(+), 309 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here this package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of the package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
it gives users more convenience and freedom to design figures for
better understanding complex patterns behind multiple dimensional data.
The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.4.9 dated 2020-04-30 and 0.4.10 dated 2020-06-14
DESCRIPTION | 10 MD5 | 115 +- NAMESPACE | 21 NEWS | 23 R/chordDiagram.R | 142 ++ R/circos.heatmap.R |only R/circos.nested.R | 13 R/genomic.R | 37 R/genomic_utils.R | 2 R/global.R | 106 + R/link.R | 9 R/low_level.R |only R/plot.R | 1947 ----------------------------------- R/utils.R | 328 +++++ inst/doc/circlize.Rmd | 2 inst/doc/circlize.html | 2 man/chordDiagram.Rd | 8 man/chordDiagramFromDataFrame.Rd | 12 man/chordDiagramFromMatrix.Rd | 10 man/circlize-package.Rd | 6 man/circos.barplot.Rd |only man/circos.boxplot.Rd |only man/circos.dendrogram.Rd | 6 man/circos.genomicDensity.Rd | 2 man/circos.genomicHeatmap.Rd | 2 man/circos.genomicIdeogram.Rd | 4 man/circos.genomicLabels.Rd | 4 man/circos.genomicLines.Rd | 4 man/circos.genomicLink.Rd | 2 man/circos.genomicRainfall.Rd | 2 man/circos.genomicRect.Rd | 2 man/circos.heatmap.Rd |only man/circos.heatmap.initialize.Rd |only man/circos.heatmap.link.Rd |only man/circos.info.Rd | 6 man/circos.initialize.Rd | 4 man/circos.initializeWithIdeogram.Rd | 2 man/circos.link.Rd | 8 man/circos.nested.Rd | 2 man/circos.par.Rd | 6 man/circos.text.Rd | 12 man/circos.trackHist.Rd | 12 man/circos.trackPlotRegion.Rd | 2 man/circos.triangle.Rd | 2 man/circos.violin.Rd |only man/cm_h.Rd |only man/cm_x.Rd |only man/cm_y.Rd |only man/convert_height.Rd | 3 man/convert_length.Rd | 2 man/convert_x.Rd | 18 man/convert_y.Rd | 2 man/cytoband.col.Rd | 3 man/draw.sector.Rd | 4 man/get.cell.meta.data.Rd | 8 man/highlight.sector.Rd | 2 man/inch_h.Rd |only man/inch_x.Rd |only man/inch_y.Rd |only man/inches_h.Rd |only man/inches_x.Rd |only man/inches_y.Rd |only man/mm_h.Rd |only man/mm_x.Rd |only man/mm_y.Rd |only man/read.chromInfo.Rd | 6 man/read.cytoband.Rd | 6 man/set_track_gap.Rd |only vignettes/circlize.Rmd | 2 69 files changed, 824 insertions(+), 2109 deletions(-)
Title: Moments of Folded and Doubly Truncated Multivariate
Distributions
Description: It computes arbitrary products moments (mean vector and variance-covariance matrix), for some double truncated (and folded) multivariate distributions. These distributions belong to the family of selection elliptical distributions, which includes well known skewed distributions as the unified skew-t distribution (SUT) and its particular cases as the extended skew-t (EST), skew-t (ST) and the symmetric student-t (T) distribution. Analogous normal cases unified skew-normal (SUN), extended skew-normal (ESN), skew-normal (SN), and symmetric normal (N) are also included. Density, probabilities and random deviates are also offered for these members.
References used for this package:
Arellano-Valle, R. B. & Genton, M. G. (2005). On fundamental skew distributions. Journal of Multivariate Analysis, 96, 93-116.
Galarza C.E., Matos L.A., Dey D.K. & Lachos V.H. (2019) On Moments of Folded and Truncated Multivariate Extended Skew-Normal Distributions. Technical report. ID 19-14. University of Connecticut. <https://stat.uconn.edu/tech-reports-2019/>.
Author: Christian E. Galarza, Raymond Kan and Victor H. Lachos
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>
Diff between MomTrunc versions 5.87 dated 2020-04-12 and 5.89 dated 2020-06-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/TN_mv_Vaida.R | 4 ++-- build/partial.rdb |binary 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Image Processing for Simulated Cameras
Description: Uses convolution-based techniques to generate simulated camera bokeh, depth of field, and other camera effects, using an image and an optional depth map. Accepts both filename inputs and in-memory array representations of images and matrices. Includes functions to perform 2D convolutions, reorient and resize images/matrices, add image overlays, generate camera vignette effects, and add titles to images.
Author: Tyler Morgan-Wall
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayimage versions 0.2.7 dated 2020-04-12 and 0.3.0 dated 2020-06-14
DESCRIPTION | 8 ++++---- MD5 | 30 ++++++++++++++++-------------- NAMESPACE | 1 + R/RcppExports.R | 4 ++++ R/calc_bokeh_size.R | 5 +++-- R/get_file_type.R | 4 ++-- R/interpolate_array.R |only R/plot_image.R | 4 ++-- R/render_bokeh.R | 28 +++++++++++++++++++--------- R/render_convolution.R | 4 +--- man/calc_bokeh_size.Rd | 2 +- man/dragon.Rd | 6 ++++-- man/dragondepth.Rd | 6 ++++-- man/interpolate_array.Rd |only man/render_bokeh.Rd | 7 +++++++ src/RcppExports.cpp | 14 ++++++++++++++ src/pointspread.cpp | 10 ++++++++++ 17 files changed, 92 insertions(+), 41 deletions(-)
Title: Morphometric Maps, Bone Landmarking and Cross Sectional Geometry
Description: Extract cross sections from long bone meshes at specified intervals along the diaphysis. Calculate two and three-dimensional morphometric maps, cross-sectional geometric parameters, and semilandmarks on the periosteal and endosteal contours of each cross section.
Author: Antonio Profico [aut, cre],
Luca Bondioli [aut],
Pasquale Raia [aut],
Julien Claude [ctb],
Paul O'Higgins [aut],
Damiano Marchi [aut]
Maintainer: Antonio Profico <antonio.profico@gmail.com>
Diff between morphomap versions 1.1 dated 2020-01-12 and 1.2 dated 2020-06-14
DESCRIPTION | 8 MD5 | 92 +++++---- NAMESPACE | 119 ++++++------ R/morphomap2Dmap.R | 13 + R/morphomap3Dmap.R | 4 R/morphomapArea.R | 3 R/morphomapArray2matrix.R |only R/morphomapCSG.R | 4 R/morphomapCore.R | 4 R/morphomapDF.R | 4 R/morphomapMatrix2array.R |only R/morphomapMoment.R | 3 R/morphomapPic.R | 38 ++-- R/morphomapPlotShape.R |only R/morphomapRaster.R | 4 R/morphomapReadMorphologika.R |only R/morphomapSegm.R | 7 R/morphomapShape.R | 353 +++++++++++++++++++------------------- R/morphomapThickness.R | 2 R/morphomapTri2sects.R |only R/morphomapTriangulate.R |only R/morphomapWriteMorphologika.R |only man/HomFem38023.Rd | 32 +-- man/PanFem27713.Rd | 32 +-- man/morphomap-package.Rd | 26 +- man/morphomap2Dmap.Rd | 207 ++++++++++++---------- man/morphomap3Dmap.Rd | 194 ++++++++++---------- man/morphomapArea.Rd | 59 +++--- man/morphomapArray2matrix.Rd |only man/morphomapCSG.Rd | 317 +++++++++++++++++----------------- man/morphomapCentroid.Rd | 64 +++--- man/morphomapCheck.Rd | 52 ++--- man/morphomapCircle.Rd | 56 +++--- man/morphomapCore.Rd | 202 +++++++++++---------- man/morphomapDF.Rd | 129 +++++++------ man/morphomapFlip.Rd | 97 +++++----- man/morphomapMatrix2array.Rd |only man/morphomapMirror.Rd | 64 +++--- man/morphomapMoment.Rd | 68 +++---- man/morphomapPic.Rd | 144 ++++++++------- man/morphomapPlotShape.Rd |only man/morphomapRaster.Rd | 82 ++++---- man/morphomapReadMorphologika.Rd |only man/morphomapRectangle.Rd | 60 +++--- man/morphomapRegradius.Rd | 68 +++---- man/morphomapSegm.Rd | 95 +++++----- man/morphomapShape.Rd | 196 ++++++++++----------- man/morphomapSort.Rd | 54 ++--- man/morphomapThickness.Rd | 84 ++++----- man/morphomapTranslate.Rd | 74 +++---- man/morphomapTri2sects.Rd |only man/morphomapTriangulate.Rd |only man/morphomapWriteMorphologika.Rd |only man/morphomapZmoment.Rd | 82 ++++---- 54 files changed, 1654 insertions(+), 1542 deletions(-)
Title: Quantitative Exploration of Elastic Net Families for Generalized
Linear Models
Description: Provides a quantitative toolkit to explore elastic net families and to uncover correlates contributing to prediction under a cross-validation framework. Fits linear, binomial (logistic), multinomial and Cox regression models. Candia J and Tsang JS, BMC Bioinformatics (2019) 20:189 <doi:10.1186/s12859-019-2778-5>.
Author: Julian Candia and John S. Tsang
Maintainer: Julian Candia <julian.candia@nih.gov>
Diff between eNetXplorer versions 1.1.0 dated 2019-09-20 and 1.1.1 dated 2020-06-14
ChangeLog | 3 ++ DESCRIPTION | 8 +++--- MD5 | 16 ++++++------- NAMESPACE | 2 - build/vignette.rds |binary inst/doc/eNetXplorer_vignette.R | 44 +++++++++++++++++++------------------- inst/doc/eNetXplorer_vignette.pdf |binary man/eNetXplorer-package.Rd | 6 ++--- man/plotContingency.Rd | 7 ------ 9 files changed, 40 insertions(+), 46 deletions(-)
Title: Simulation-Based Sensitivity Analysis for Causal Mediation
Studies
Description: Simulation-based sensitivity analysis for causal mediation studies. It numerically and graphically evaluates the sensitivity of causal mediation analysis results
to the presence of unmeasured pretreatment confounding. The proposed method has primary advantages over existing methods.
First, using an unmeasured pretreatment confounder conditional associations with the treatment, mediator, and outcome as
sensitivity parameters, the method enables users to intuitively assess sensitivity in reference to prior knowledge about the
strength of a potential unmeasured pretreatment confounder. Second, the method accurately reflects the influence of unmeasured
pretreatment confounding on the efficiency of estimation of the causal effects. Third, the method can be implemented in
different causal mediation analysis approaches, including regression-based, simulation-based, and propensity score-based
methods. It is applicable to both randomized experiments and observational studies.
Author: Xu Qin and Fan Yang
Maintainer: Xu Qin <xuqin@pitt.edu>
Diff between mediationsens versions 0.0.1 dated 2020-05-26 and 0.0.2 dated 2020-06-14
DESCRIPTION | 11 +++++------ MD5 | 6 +++--- R/mediationsens.R | 7 ++++--- man/sens.Rd | 16 +++++++++------- 4 files changed, 21 insertions(+), 19 deletions(-)
Title: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
Description: A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell
T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and
visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq)
and single-cell sequencing (scRNAseq). It implements most of the widely used AIRR analysis methods,
such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes
and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor
databases and clonotype tracking in vaccination and cancer studies. A successor to our
previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
Author: Vadim I. Nazarov [aut, cre],
Vasily O. Tsvetkov [aut],
Eugene Rumynskiy [aut],
Anna Lorenc [ctb],
Daniel J. Moore [ctb],
Victor Greiff [ctb],
ImmunoMind [cph, fnd]
Maintainer: Vadim I. Nazarov <vdm.nazarov@gmail.com>
Diff between immunarch versions 0.6.4 dated 2020-05-13 and 0.6.5 dated 2020-06-14
immunarch-0.6.4/immunarch/R/data.R |only immunarch-0.6.4/immunarch/R/processing.R |only immunarch-0.6.4/immunarch/R/search.R |only immunarch-0.6.4/immunarch/R/shared.R |only immunarch-0.6.4/immunarch/inst/doc/v1_introduction.R |only immunarch-0.6.4/immunarch/inst/doc/v3_basic_analysis.R |only immunarch-0.6.4/immunarch/inst/doc/v3_basic_analysis.Rmd |only immunarch-0.6.4/immunarch/inst/doc/v3_basic_analysis.html |only immunarch-0.6.4/immunarch/man/filter_barcodes.Rd |only immunarch-0.6.4/immunarch/man/vis_treemap.Rd |only immunarch-0.6.4/immunarch/vignettes/v3_basic_analysis.Rmd |only immunarch-0.6.5/immunarch/DESCRIPTION | 36 - immunarch-0.6.5/immunarch/MD5 | 129 ++--- immunarch-0.6.5/immunarch/NAMESPACE | 11 immunarch-0.6.5/immunarch/R/annotation.R |only immunarch-0.6.5/immunarch/R/data_docs.R | 35 + immunarch-0.6.5/immunarch/R/diversity.R | 2 immunarch-0.6.5/immunarch/R/immunr_data_format.R | 5 immunarch-0.6.5/immunarch/R/io.R | 257 ++++++---- immunarch-0.6.5/immunarch/R/preprocessing.R |only immunarch-0.6.5/immunarch/R/public.R |only immunarch-0.6.5/immunarch/R/sampling.R |only immunarch-0.6.5/immunarch/R/singlecell.R |only immunarch-0.6.5/immunarch/R/tools.R | 171 ------ immunarch-0.6.5/immunarch/R/vis.R | 145 +---- immunarch-0.6.5/immunarch/README.md | 36 - immunarch-0.6.5/immunarch/build/vignette.rds |binary immunarch-0.6.5/immunarch/data/datalist | 1 immunarch-0.6.5/immunarch/data/immdata.rda |binary immunarch-0.6.5/immunarch/data/scdata.rda |only immunarch-0.6.5/immunarch/inst/doc/v1_introduction.Rmd | 119 +--- immunarch-0.6.5/immunarch/inst/doc/v1_introduction.html | 122 ++-- immunarch-0.6.5/immunarch/inst/doc/v2_data.Rmd | 5 immunarch-0.6.5/immunarch/inst/doc/v2_data.html | 55 +- immunarch-0.6.5/immunarch/inst/extdata/sc |only immunarch-0.6.5/immunarch/man/coding.Rd | 2 immunarch-0.6.5/immunarch/man/dbAnnotate.Rd | 2 immunarch-0.6.5/immunarch/man/dbLoad.Rd | 2 immunarch-0.6.5/immunarch/man/immdata.Rd | 10 immunarch-0.6.5/immunarch/man/pubRep.Rd | 2 immunarch-0.6.5/immunarch/man/pubRepApply.Rd | 2 immunarch-0.6.5/immunarch/man/pubRepFilter.Rd | 2 immunarch-0.6.5/immunarch/man/pubRepStatistics.Rd | 2 immunarch-0.6.5/immunarch/man/public_matrix.Rd | 2 immunarch-0.6.5/immunarch/man/repLoad.Rd | 19 immunarch-0.6.5/immunarch/man/repSample.Rd | 2 immunarch-0.6.5/immunarch/man/repSave.Rd | 7 immunarch-0.6.5/immunarch/man/scdata.Rd |only immunarch-0.6.5/immunarch/man/select_barcodes.Rd |only immunarch-0.6.5/immunarch/man/select_clusters.Rd |only immunarch-0.6.5/immunarch/man/top.Rd | 2 immunarch-0.6.5/immunarch/man/vis.Rd | 2 immunarch-0.6.5/immunarch/man/vis.immunr_chao1.Rd | 1 immunarch-0.6.5/immunarch/man/vis.immunr_clonal_prop.Rd | 1 immunarch-0.6.5/immunarch/man/vis.immunr_gene_usage.Rd | 14 immunarch-0.6.5/immunarch/man/vis.immunr_hclust.Rd | 13 immunarch-0.6.5/immunarch/man/vis.immunr_kmeans.Rd | 6 immunarch-0.6.5/immunarch/man/vis.immunr_kmer_table.Rd | 3 immunarch-0.6.5/immunarch/man/vis.immunr_mds.Rd | 1 immunarch-0.6.5/immunarch/man/vis.immunr_ov_matrix.Rd | 1 immunarch-0.6.5/immunarch/man/vis.immunr_public_repertoire.Rd | 1 immunarch-0.6.5/immunarch/man/vis.immunr_public_statistics.Rd | 3 immunarch-0.6.5/immunarch/man/vis_bar.Rd | 1 immunarch-0.6.5/immunarch/man/vis_box.Rd | 1 immunarch-0.6.5/immunarch/man/vis_heatmap.Rd | 1 immunarch-0.6.5/immunarch/man/vis_heatmap2.Rd | 1 immunarch-0.6.5/immunarch/man/vis_hist.Rd | 3 immunarch-0.6.5/immunarch/man/vis_public_clonotypes.Rd | 5 immunarch-0.6.5/immunarch/vignettes/v1_introduction.Rmd | 119 +--- immunarch-0.6.5/immunarch/vignettes/v2_data.Rmd | 5 immunarch-0.6.5/immunarch/vignettes/web_only/v21_singlecell.Rmd |only immunarch-0.6.5/immunarch/vignettes/web_only/v3_basic_analysis.Rmd |only immunarch-0.6.5/immunarch/vignettes/web_only/v4_overlap.Rmd | 37 - immunarch-0.6.5/immunarch/vignettes/web_only/v5_gene_usage.Rmd | 50 - immunarch-0.6.5/immunarch/vignettes/web_only/v6_diversity.Rmd | 37 - immunarch-0.6.5/immunarch/vignettes/web_only/v8_tracking.Rmd | 34 - immunarch-0.6.5/immunarch/vignettes/web_only/v9_kmers.Rmd | 45 - 77 files changed, 687 insertions(+), 883 deletions(-)
Title: Genome-Wide Structural Equation Modeling
Description: Melds genome-wide association tests with structural
equation modeling (SEM) using 'OpenMx'. This package contains
low-level C/C++ code to rapidly read genetic data encoded in U.K.
Biobank or 'plink' formats. Prebuilt modeling options include one and
two factor models. Alternately, analyses may utilize arbitrary,
user-provided SEMs. See Verhulst, Maes, & Neale (2017)
<doi:10.1007/s10519-017-9842-6> for details. An updated manuscript is
in preparation.
Author: Joshua N. Pritikin [aut, cre],
Bradley Verhulst [cph],
Gavin Band [cph],
Yann Collet [cph],
Facebook, Inc. [cph],
Yuta Mori [cph],
Shaun Purcell [cph],
Christopher Chang [cph],
Wojciech Mula [cph],
Kim Walisch [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between gwsem versions 0.1.17 dated 2020-03-27 and 2.0.5 dated 2020-06-14
DESCRIPTION | 10 MD5 | 75 +++++-- R/model.R | 136 ++++++++----- R/report.R | 10 build/gwsem.pdf |binary build/vignette.rds |binary inst/doc/GeneEnvironmentInteraction.R |only inst/doc/GeneEnvironmentInteraction.Rmd |only inst/doc/GeneEnvironmentInteraction.html |only inst/doc/OneFactorModel.R |only inst/doc/OneFactorModel.Rmd |only inst/doc/OneFactorModel.html |only inst/doc/PostGWASprocessing.R |only inst/doc/PostGWASprocessing.Rmd |only inst/doc/PostGWASprocessing.html |only inst/doc/ResidualsModel.R |only inst/doc/ResidualsModel.Rmd |only inst/doc/ResidualsModel.html |only inst/doc/StandardGWAS.R |only inst/doc/StandardGWAS.Rmd |only inst/doc/StandardGWAS.html |only inst/doc/TwoFactorModel.R |only inst/doc/TwoFactorModel.Rmd |only inst/doc/TwoFactorModel.html |only inst/doc/UserSpecifiedGWASModels.R |only inst/doc/UserSpecifiedGWASModels.Rmd |only inst/doc/UserSpecifiedGWASModels.html |only inst/doc/growth.R | 3 inst/doc/growth.Rmd | 7 inst/doc/growth.html | 316 +++++-------------------------- inst/extdata/test2.pgen |only inst/extdata/test2.psam |only inst/extdata/test2.pvar |only man/GWAS.Rd | 30 ++ man/buildItem.Rd | 52 +++-- man/buildOneFac.Rd | 58 +++-- man/buildOneFacRes.Rd | 58 +++-- man/buildTwoFac.Rd | 66 ++++-- man/prepareComputePlan.Rd | 38 ++- man/setupExogenousCovariates.Rd | 6 man/setupThresholds.Rd | 6 tests/testthat/test-covariate.R | 2 tests/testthat/test-formats.R | 8 tests/testthat/test-model.R | 2 tools/build | 2 tools/vignetter | 4 vignettes/GeneEnvironmentInteraction.Rmd |only vignettes/OneFactorModel.Rmd |only vignettes/PostGWASprocessing.Rmd |only vignettes/ResidualsModel.Rmd |only vignettes/StandardGWAS.Rmd |only vignettes/TwoFactorModel.Rmd |only vignettes/UserSpecifiedGWASModels.Rmd |only vignettes/growth.Rmd | 7 54 files changed, 450 insertions(+), 446 deletions(-)
Title: Smoothed LASSO Regression via Nesterov Smoothing
Description: We provide full functionality to compute smoothed LASSO regression estimates. For this, the LASSO objective function is first smoothed using Nesterov smoothing (see Y. Nesterov (2005) <doi:10.1007/s10107-004-0552-5>), resulting in a modified LASSO objective function with explicit gradients everywhere. The smoothed objective function and its gradient are used to minimize it via BFGS, and the obtained minimizer is returned. Using Nesterov smoothing, the smoothed LASSO objective function can be made arbitrarily close to the original (unsmoothed) one. In particular, the Nesterov approach has the advantage that it comes with explicit accuracy bounds, both on the L1/L2 difference of the unsmoothed to the smoothed LASSO objective function as well as on their respective minimizers. A progressive smoothing approach is provided which iteratively smoothes the LASSO, resulting in more stable regression estimates.
Author: Georg Hahn [aut,cre], Sharon M. Lutz [ctb], Nilanjana Laha [ctb], Christoph Lange [ctb]
Maintainer: Georg Hahn <ghahn@hsph.harvard.edu>
Diff between smoothedLasso versions 1.2 dated 2020-06-01 and 1.3 dated 2020-06-14
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/smoothedLasso.r | 14 +++++++++----- man/solveSmoothedLASSOSequence.Rd | 6 +++--- 4 files changed, 20 insertions(+), 16 deletions(-)
Title: R Interface to 'lp_solve' Version 5.5.2.0
Description: The lpSolveAPI package provides an R interface to 'lp_solve',
a Mixed Integer Linear Programming (MILP) solver with support for pure
linear, (mixed) integer/binary, semi-continuous and special ordered sets
(SOS) models.
Author: lp_solve <http://lpsolve.sourceforge.net/> [aut],
Kjell Konis [aut],
Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between lpSolveAPI versions 5.5.2.0-17.6 dated 2020-01-10 and 5.5.2.0-17.7 dated 2020-06-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/lp_solve/commonlib.c | 7 ++----- src/lp_solve/lp_utils.c | 1 - 4 files changed, 8 insertions(+), 12 deletions(-)
Title: Fast Implementation of (Local) Population Stratification Methods
Description: Fast and fully sparse 'cpp' implementations to compute the genetic covariance matrix, the genomic relationship matrix, the Jaccard matrix, and the s-matrix of an input matrix. Full support for sparse matrices from the R-package 'Matrix'. Additionally, a 'cpp' implementation of the power method (von Mises iteration) algorithm to compute the largest eigenvector of a matrix is included, and a function to compute sliding windows.
Author: Georg Hahn [aut,cre], Sharon M. Lutz [ctb], Christoph Lange [ctb]
Maintainer: Georg Hahn <ghahn@hsph.harvard.edu>
Diff between locStra versions 1.3 dated 2020-02-26 and 1.4 dated 2020-06-14
locStra-1.3/locStra/src/Makevars |only locStra-1.3/locStra/src/Makevars.win |only locStra-1.4/locStra/DESCRIPTION | 10 +++++----- locStra-1.4/locStra/MD5 | 10 ++++------ locStra-1.4/locStra/R/localStrat.r | 4 ++-- locStra-1.4/locStra/man/sMatrix.Rd | 4 ++-- locStra-1.4/locStra/man/testdata-data.Rd | 4 +++- 7 files changed, 16 insertions(+), 16 deletions(-)
Title: Graphical Independence Networks
Description: Probability propagation in graphical independence networks, also
known as Bayesian networks or probabilistic expert systems.
Author: Søren Højsgaard <sorenh@math.aau.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between gRain versions 1.3-4 dated 2020-02-20 and 1.3-5 dated 2020-06-14
gRain-1.3-4/gRain/R/namespace.R |only gRain-1.3-5/gRain/DESCRIPTION | 10 gRain-1.3-5/gRain/MD5 | 29 +- gRain-1.3-5/gRain/NAMESPACE | 8 gRain-1.3-5/gRain/R/NAMESPACE.R |only gRain-1.3-5/gRain/R/cpt-pot-gather.R | 21 + gRain-1.3-5/gRain/R/grain-simulate.R | 112 +++------- gRain-1.3-5/gRain/R/loadSaveHuginNet.R | 14 + gRain-1.3-5/gRain/build/vignette.rds |binary gRain-1.3-5/gRain/inst/doc/grain-intro.pdf |binary gRain-1.3-5/gRain/inst/huginex/chest_clinic_short.net |only gRain-1.3-5/gRain/man/chest.Rd | 4 gRain-1.3-5/gRain/man/components_gather.Rd | 8 gRain-1.3-5/gRain/man/grain-simulate.Rd | 8 gRain-1.3-5/gRain/man/grass.Rd | 4 gRain-1.3-5/gRain/vignettes/figures/grain-chest-LS-1.pdf |binary gRain-1.3-5/gRain/vignettes/figures/grain-unnamed-chunk-33-1.pdf |binary 17 files changed, 112 insertions(+), 106 deletions(-)
Title: Import and Process Data from the 'Lattes' Curriculum Platform
Description: Tool for import and process data from 'Lattes' curriculum platform (<http://lattes.cnpq.br/>). The Brazilian government keeps an extensive base of curricula for academics from all over the country, with over 5 million registrations. The academic life of the Brazilian researcher, or related to Brazilian universities, is documented in 'Lattes'. Some information that can be obtained: professional formation, research area, publications, academics advisories, projects, etc. 'getLattes' package allows work with 'Lattes' data exported to XML format.
Author: Roney Fraga Souza [aut, cre] (<https://orcid.org/0000-0001-5750-489X>),
Winicius Sabino [aut]
Maintainer: Roney Fraga Souza <roneyfraga@gmail.com>
Diff between getLattes versions 0.1.0 dated 2020-06-12 and 0.1.1 dated 2020-06-14
DESCRIPTION | 6 MD5 | 9 NEWS.md | 7 README.md | 11 inst/CITATION |only inst/doc/introduction_getLattes.html | 770 +++++++++++++++++------------------ 6 files changed, 408 insertions(+), 395 deletions(-)
Title: Visualise Clusterings at Different Resolutions
Description: Deciding what resolution to use can be a difficult question when
approaching a clustering analysis. One way to approach this problem is to
look at how samples move as the number of clusters increases. This package
allows you to produce clustering trees, a visualisation for interrogating
clusterings as resolution increases.
Author: Luke Zappia [aut, cre] (<https://orcid.org/0000-0001-7744-8565>),
Alicia Oshlack [aut] (<https://orcid.org/0000-0001-9788-5690>),
Andrea Rau [ctb],
Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>)
Maintainer: Luke Zappia <luke@lazappi.id.au>
Diff between clustree versions 0.4.2 dated 2020-01-29 and 0.4.3 dated 2020-06-14
clustree-0.4.2/clustree/data/iris_clusts.rda |only clustree-0.4.2/clustree/man/iris_clusts.Rd |only clustree-0.4.3/clustree/DESCRIPTION | 12 clustree-0.4.3/clustree/MD5 | 46 clustree-0.4.3/clustree/NEWS.md | 51 clustree-0.4.3/clustree/R/clustree.R | 55 - clustree-0.4.3/clustree/R/clustree_overlay.R | 61 - clustree-0.4.3/clustree/R/datasets.R | 42 clustree-0.4.3/clustree/R/graph.R | 2 clustree-0.4.3/clustree/README.md | 2 clustree-0.4.3/clustree/data/nba_clusts.rda |only clustree-0.4.3/clustree/inst/WORDLIST | 16 clustree-0.4.3/clustree/inst/doc/clustree.R | 68 - clustree-0.4.3/clustree/inst/doc/clustree.Rmd | 147 +- clustree-0.4.3/clustree/inst/doc/clustree.html | 513 +++++----- clustree-0.4.3/clustree/man/clustree.Rd | 4 clustree-0.4.3/clustree/man/clustree_overlay.Rd | 4 clustree-0.4.3/clustree/man/nba_clusts.Rd |only clustree-0.4.3/clustree/man/sc_example.Rd | 6 clustree-0.4.3/clustree/tests/testthat/test-aesthetics.R | 74 - clustree-0.4.3/clustree/tests/testthat/test-clustree-overlay.R | 84 + clustree-0.4.3/clustree/tests/testthat/test-clustree.R | 83 + clustree-0.4.3/clustree/tests/testthat/test-layout.R | 6 clustree-0.4.3/clustree/tests/testthat/test-overlay-aesthetics.R | 18 clustree-0.4.3/clustree/tests/testthat/test-stability.R | 4 clustree-0.4.3/clustree/vignettes/clustree.Rmd | 147 +- 26 files changed, 793 insertions(+), 652 deletions(-)
Title: Build Tables for Publication
Description: A collection of functions to make building customized ready-to-export tables for publication purposes easier and creating summaries of large datasets for review a breeze.
Author: Eric Finnesgard [aut, cre],
Jennifer Grauberger [aut]
Maintainer: Eric Finnesgard <efinite@outlook.com>
Diff between utile.tables versions 0.2.0 dated 2020-05-01 and 0.2.1 dated 2020-06-14
DESCRIPTION | 11 MD5 | 38 - NAMESPACE | 20 NEWS.md | 19 R/build_model.R | 31 - R/build_row.R | 1057 +++++++++++++++++++++--------------------- R/build_table.R | 407 +++++++--------- R/reexports.R |only README.md | 22 man/build_model.Rd | 6 man/build_model.coxph.Rd | 8 man/build_row.Rd | 4 man/build_row.data.frame.Rd | 29 - man/build_row.factor.Rd | 16 man/build_row.logical.Rd | 16 man/build_row.numeric.Rd | 16 man/build_table.Rd | 3 man/build_table.coxph.Rd | 4 man/build_table.data.frame.Rd | 25 man/build_table.lm.Rd | 4 man/reexports.Rd |only 21 files changed, 896 insertions(+), 840 deletions(-)
Title: Classification with Mixture Modelling
Description: Interface of 'MIXMOD' software for supervised, unsupervised and
semi-supervised classification with mixture modelling.
Author: Florent Langrognet [aut],
Remi Lebret [aut],
Christian Poli [aut],
Serge Iovleff [aut],
Benjamin Auder [aut],
Parmeet Bhatia [ctb],
Anwuli Echenim [ctb],
Serge Iovleff [aut],
Christophe Biernacki [ctb],
Gilles Celeux [ctb],
Gerard Govaert [ctb],
Quentin Grimonprez [cre]
Maintainer: Quentin Grimonprez <quentin.grimonprez@inria.fr>
Diff between Rmixmod versions 2.1.4 dated 2020-05-30 and 2.1.5 dated 2020-06-14
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/mixmod/Utilities/Random.cpp | 12 +++++++----- 3 files changed, 13 insertions(+), 11 deletions(-)
Title: Geospatial Kriging with Metropolis Sampling
Description: Estimates kriging models for geographical point-referenced data. Method is described in Monogan and Gill (2016) <doi:10.1017/psrm.2015.5>.
Author: Jason S. Byers [aut, cre], Le Bao [aut], James E. Monogan III [aut], Jamie Carson [aut], Jeff Gill [aut]
Maintainer: Jason S. Byers <jaybyers55@gmail.com>
Diff between krige versions 0.5.4 dated 2020-06-13 and 0.5.5 dated 2020-06-14
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- configure | 12 ++++++------ 3 files changed, 13 insertions(+), 13 deletions(-)
Title: Protein Quantification in Mass Spectrometry-Based Proteomics
Description: An implementation of the maximal
peptide ratio extraction module of the MaxLFQ algorithm by
Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a complete
pipeline for processing proteomics data in data-independent acquisition mode
(Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>).
It offers additional options for protein quantification using the N most intense
fragment ions, using all
fragment ions, and a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).
Author: Thang Pham [aut, cre, cph, ctb]
(<https://orcid.org/0000-0003-0333-2492>),
Alex Henneman [ctb] (<https://orcid.org/0000-0002-3746-4410>)
Maintainer: Thang Pham <t.pham@amsterdamumc.nl>
Diff between iq versions 1.7 dated 2020-05-26 and 1.8 dated 2020-06-14
DESCRIPTION | 6 +- MD5 | 10 +-- build/vignette.rds |binary inst/doc/iq-fast.html | 136 +++++++++++++++++++++++++------------------------- inst/doc/iq.html | 6 +- src/iq.cpp | 7 +- 6 files changed, 84 insertions(+), 81 deletions(-)
Title: Modeling and Inferring Gene Networks
Description: Analyzes gene expression
(time series) data with focus on the inference of gene networks.
In particular, GeneNet implements the methods of Schaefer and
Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
for learning large-scale gene association networks (including
assignment of putative directions).
Author: Juliane Schaefer, Rainer Opgen-Rhein, and
Korbinian Strimmer.
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between GeneNet versions 1.2.14 dated 2020-02-06 and 1.2.15 dated 2020-06-14
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 7 +++++++ R/ggm.simulate.pcor.R | 18 ++++++++++++------ data/ecoli.rda |binary man/cor0.test.Rd | 6 +++--- man/ggm.estimate.pcor.Rd | 8 ++++---- man/ggm.simulate.pcor.Rd | 19 +++++++++++++------ 8 files changed, 50 insertions(+), 30 deletions(-)
Title: Animal Movement Tools
Description: Manage and analyze animal movement data. The functionality of 'amt' includes methods to calculate track statistics (e.g. step lengths, speed, or turning angles), prepare data for fitting habitat selection analyses (resource selection functions and step-selection functions <doi:10.1890/04-0953> and integrated step-selection functions <doi:10.1111/2041-210X.12528>), and simulation of space-use from fitted step-selection functions <doi:10.1002/ecs2.1771>.
Author: Johannes Signer [aut, cre],
Bjoern Reineking [ctb],
Brian Smith [ctb],
Ulrike Schlaegel [ctb],
Scott LaPoint [dtc]
Maintainer: Johannes Signer <jsigner@gwdg.de>
Diff between amt versions 0.1.1 dated 2020-04-28 and 0.1.2 dated 2020-06-14
DESCRIPTION | 13 - MD5 | 65 ++++---- NAMESPACE | 20 +- NEWS.md | 11 + R/amt.R | 5 R/as_track.R | 27 +++ R/distributions.R | 4 R/hr_area.R | 9 - R/hr_documentation.R | 2 R/hr_isopleths.R | 9 - R/hr_kde.R | 7 R/hr_locoh.R | 3 R/hr_mcp.R | 6 R/hr_plot.R | 12 + R/random_steps.R | 1 R/site_fidelity.R |only build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/p1_getting_started.html | 288 ++++++++++++++++++-------------------- inst/doc/p3_rsf.html | 224 ++++++++++++++--------------- inst/doc/p4_SSF.html | 258 ++++++++++++++++------------------ inst/doc/p5_other_packages.html | 230 ++++++++++++++---------------- inst/tinytest/test_as_track.R |only inst/tinytest/test_hr.R | 9 + inst/tinytest/test_random_steps.R | 4 man/amt_fisher.Rd | 6 man/amt_fisher_lu.Rd | 4 man/as_track.Rd | 3 man/deer.Rd | 6 man/hr.Rd | 18 ++ man/reexports.Rd | 4 man/sh.Rd | 6 man/sh_forest.Rd | 4 man/site_fidelity.Rd |only 35 files changed, 664 insertions(+), 597 deletions(-)
Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an efficient implementation
of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.
This package is its R interface. The package includes efficient linear
model solver and tree learning algorithms. The package can automatically
do parallel computation on a single machine which could be more than 10
times faster than existing gradient boosting packages. It supports
various objective functions, including regression, classification and ranking.
The package is made to be extensible, so that users are also allowed to define
their own objectives easily.
Author: Tianqi Chen [aut],
Tong He [aut, cre],
Michael Benesty [aut],
Vadim Khotilovich [aut],
Yuan Tang [aut] (<https://orcid.org/0000-0001-5243-233X>),
Hyunsu Cho [aut],
Kailong Chen [aut],
Rory Mitchell [aut],
Ignacio Cano [aut],
Tianyi Zhou [aut],
Mu Li [aut],
Junyuan Xie [aut],
Min Lin [aut],
Yifeng Geng [aut],
Yutian Li [aut],
XGBoost contributors [cph] (base XGBoost implementation)
Maintainer: Tong He <hetong007@gmail.com>
Diff between xgboost versions 1.0.0.2 dated 2020-03-25 and 1.1.1.1 dated 2020-06-14
xgboost-1.0.0.2/xgboost/src/dmlc-core/src/build_config.cc |only xgboost-1.0.0.2/xgboost/src/src/common/bitmap.h |only xgboost-1.0.0.2/xgboost/src/src/data/simple_csr_source.cc |only xgboost-1.0.0.2/xgboost/src/src/data/simple_csr_source.h |only xgboost-1.1.1.1/xgboost/DESCRIPTION | 10 xgboost-1.1.1.1/xgboost/MD5 | 318 +-- xgboost-1.1.1.1/xgboost/NAMESPACE | 5 xgboost-1.1.1.1/xgboost/R/utils.R | 6 xgboost-1.1.1.1/xgboost/R/xgb.Booster.R | 84 xgboost-1.1.1.1/xgboost/R/xgb.DMatrix.R | 17 xgboost-1.1.1.1/xgboost/R/xgb.cv.R | 2 xgboost-1.1.1.1/xgboost/R/xgb.load.R | 30 xgboost-1.1.1.1/xgboost/R/xgb.load.raw.R |only xgboost-1.1.1.1/xgboost/R/xgb.save.raw.R | 16 xgboost-1.1.1.1/xgboost/R/xgb.serialize.R |only xgboost-1.1.1.1/xgboost/R/xgb.train.R | 4 xgboost-1.1.1.1/xgboost/R/xgb.unserialize.R |only xgboost-1.1.1.1/xgboost/configure | 2 xgboost-1.1.1.1/xgboost/configure.ac | 2 xgboost-1.1.1.1/xgboost/demo/create_sparse_matrix.R | 6 xgboost-1.1.1.1/xgboost/inst/doc/discoverYourData.R | 6 xgboost-1.1.1.1/xgboost/inst/doc/discoverYourData.Rmd | 6 xgboost-1.1.1.1/xgboost/inst/doc/discoverYourData.html | 25 xgboost-1.1.1.1/xgboost/inst/doc/xgboost.pdf |binary xgboost-1.1.1.1/xgboost/inst/doc/xgboostPresentation.R | 2 xgboost-1.1.1.1/xgboost/inst/doc/xgboostPresentation.Rmd | 2 xgboost-1.1.1.1/xgboost/inst/doc/xgboostPresentation.html | 16 xgboost-1.1.1.1/xgboost/man/agaricus.test.Rd | 6 xgboost-1.1.1.1/xgboost/man/agaricus.train.Rd | 6 xgboost-1.1.1.1/xgboost/man/xgb.attr.Rd | 2 xgboost-1.1.1.1/xgboost/man/xgb.config.Rd |only xgboost-1.1.1.1/xgboost/man/xgb.cv.Rd | 2 xgboost-1.1.1.1/xgboost/man/xgb.load.raw.Rd |only xgboost-1.1.1.1/xgboost/man/xgb.save.raw.Rd | 6 xgboost-1.1.1.1/xgboost/man/xgb.serialize.Rd |only xgboost-1.1.1.1/xgboost/man/xgb.unserialize.Rd |only xgboost-1.1.1.1/xgboost/src/amalgamation/xgboost-all0.cc | 7 xgboost-1.1.1.1/xgboost/src/dmlc-core/include/dmlc/build_config_default.h | 1 xgboost-1.1.1.1/xgboost/src/dmlc-core/include/dmlc/concurrentqueue.h | 36 xgboost-1.1.1.1/xgboost/src/dmlc-core/include/dmlc/optional.h | 10 xgboost-1.1.1.1/xgboost/src/dmlc-core/src/data/csv_parser.h | 10 xgboost-1.1.1.1/xgboost/src/include/xgboost/base.h | 65 xgboost-1.1.1.1/xgboost/src/include/xgboost/c_api.h | 16 xgboost-1.1.1.1/xgboost/src/include/xgboost/data.h | 119 - xgboost-1.1.1.1/xgboost/src/include/xgboost/feature_map.h | 2 xgboost-1.1.1.1/xgboost/src/include/xgboost/gbm.h | 54 xgboost-1.1.1.1/xgboost/src/include/xgboost/generic_parameters.h | 8 xgboost-1.1.1.1/xgboost/src/include/xgboost/host_device_vector.h | 5 xgboost-1.1.1.1/xgboost/src/include/xgboost/json.h | 157 - xgboost-1.1.1.1/xgboost/src/include/xgboost/json_io.h | 5 xgboost-1.1.1.1/xgboost/src/include/xgboost/learner.h | 56 xgboost-1.1.1.1/xgboost/src/include/xgboost/linear_updater.h | 2 xgboost-1.1.1.1/xgboost/src/include/xgboost/logging.h | 4 xgboost-1.1.1.1/xgboost/src/include/xgboost/metric.h | 25 xgboost-1.1.1.1/xgboost/src/include/xgboost/objective.h | 2 xgboost-1.1.1.1/xgboost/src/include/xgboost/parameter.h | 2 xgboost-1.1.1.1/xgboost/src/include/xgboost/predictor.h | 140 - xgboost-1.1.1.1/xgboost/src/include/xgboost/span.h | 66 xgboost-1.1.1.1/xgboost/src/include/xgboost/tree_model.h | 99 xgboost-1.1.1.1/xgboost/src/include/xgboost/tree_updater.h | 10 xgboost-1.1.1.1/xgboost/src/include/xgboost/version_config.h | 4 xgboost-1.1.1.1/xgboost/src/init.c | 8 xgboost-1.1.1.1/xgboost/src/rabit/include/rabit/c_api.h | 2 xgboost-1.1.1.1/xgboost/src/src/CMakeLists.txt | 11 xgboost-1.1.1.1/xgboost/src/src/c_api/c_api.cc | 358 +-- xgboost-1.1.1.1/xgboost/src/src/c_api/c_api.cu | 88 xgboost-1.1.1.1/xgboost/src/src/cli_main.cc | 29 xgboost-1.1.1.1/xgboost/src/src/common/bitfield.h | 14 xgboost-1.1.1.1/xgboost/src/src/common/column_matrix.h | 325 ++- xgboost-1.1.1.1/xgboost/src/src/common/common.h | 14 xgboost-1.1.1.1/xgboost/src/src/common/compressed_iterator.h | 56 xgboost-1.1.1.1/xgboost/src/src/common/config.h | 10 xgboost-1.1.1.1/xgboost/src/src/common/device_helpers.cu | 16 xgboost-1.1.1.1/xgboost/src/src/common/device_helpers.cuh | 1049 ++-------- xgboost-1.1.1.1/xgboost/src/src/common/group_data.h | 20 xgboost-1.1.1.1/xgboost/src/src/common/hist_util.cc | 572 ++++- xgboost-1.1.1.1/xgboost/src/src/common/hist_util.cu | 828 +++---- xgboost-1.1.1.1/xgboost/src/src/common/hist_util.h | 331 +-- xgboost-1.1.1.1/xgboost/src/src/common/host_device_vector.cu | 1 xgboost-1.1.1.1/xgboost/src/src/common/json.cc | 58 xgboost-1.1.1.1/xgboost/src/src/common/observer.h | 41 xgboost-1.1.1.1/xgboost/src/src/common/probability_distribution.cc |only xgboost-1.1.1.1/xgboost/src/src/common/probability_distribution.h |only xgboost-1.1.1.1/xgboost/src/src/common/quantile.h | 6 xgboost-1.1.1.1/xgboost/src/src/common/row_set.h | 155 + xgboost-1.1.1.1/xgboost/src/src/common/survival_util.cc |only xgboost-1.1.1.1/xgboost/src/src/common/survival_util.h |only xgboost-1.1.1.1/xgboost/src/src/common/threading_utils.h | 12 xgboost-1.1.1.1/xgboost/src/src/common/timer.cc | 12 xgboost-1.1.1.1/xgboost/src/src/common/timer.cu | 4 xgboost-1.1.1.1/xgboost/src/src/common/timer.h | 12 xgboost-1.1.1.1/xgboost/src/src/common/transform.h | 18 xgboost-1.1.1.1/xgboost/src/src/data/adapter.h | 186 + xgboost-1.1.1.1/xgboost/src/src/data/array_interface.h | 5 xgboost-1.1.1.1/xgboost/src/src/data/data.cc | 198 + xgboost-1.1.1.1/xgboost/src/src/data/data.cu | 2 xgboost-1.1.1.1/xgboost/src/src/data/device_adapter.cuh | 65 xgboost-1.1.1.1/xgboost/src/src/data/device_dmatrix.cu |only xgboost-1.1.1.1/xgboost/src/src/data/device_dmatrix.h |only xgboost-1.1.1.1/xgboost/src/src/data/ellpack_page.cc | 16 xgboost-1.1.1.1/xgboost/src/src/data/ellpack_page.cu | 357 +-- xgboost-1.1.1.1/xgboost/src/src/data/ellpack_page.cuh | 272 +- xgboost-1.1.1.1/xgboost/src/src/data/ellpack_page_raw_format.cu | 31 xgboost-1.1.1.1/xgboost/src/src/data/ellpack_page_source.cc | 36 xgboost-1.1.1.1/xgboost/src/src/data/ellpack_page_source.cu | 145 - xgboost-1.1.1.1/xgboost/src/src/data/ellpack_page_source.h | 44 xgboost-1.1.1.1/xgboost/src/src/data/simple_dmatrix.cc | 112 - xgboost-1.1.1.1/xgboost/src/src/data/simple_dmatrix.cu | 48 xgboost-1.1.1.1/xgboost/src/src/data/simple_dmatrix.h | 39 xgboost-1.1.1.1/xgboost/src/src/data/sparse_page_dmatrix.cc | 76 xgboost-1.1.1.1/xgboost/src/src/data/sparse_page_dmatrix.h | 35 xgboost-1.1.1.1/xgboost/src/src/data/sparse_page_source.h | 341 ++- xgboost-1.1.1.1/xgboost/src/src/gbm/gblinear.cc | 106 - xgboost-1.1.1.1/xgboost/src/src/gbm/gblinear_model.h | 49 xgboost-1.1.1.1/xgboost/src/src/gbm/gbm.cc | 7 xgboost-1.1.1.1/xgboost/src/src/gbm/gbtree.cc | 186 + xgboost-1.1.1.1/xgboost/src/src/gbm/gbtree.h | 104 xgboost-1.1.1.1/xgboost/src/src/gbm/gbtree_model.cc | 4 xgboost-1.1.1.1/xgboost/src/src/gbm/gbtree_model.h | 6 xgboost-1.1.1.1/xgboost/src/src/learner.cc | 653 +++--- xgboost-1.1.1.1/xgboost/src/src/linear/coordinate_common.h | 26 xgboost-1.1.1.1/xgboost/src/src/linear/updater_coordinate.cc | 16 xgboost-1.1.1.1/xgboost/src/src/linear/updater_gpu_coordinate.cu | 60 xgboost-1.1.1.1/xgboost/src/src/linear/updater_shotgun.cc | 8 xgboost-1.1.1.1/xgboost/src/src/logging.cc | 6 xgboost-1.1.1.1/xgboost/src/src/metric/elementwise_metric.cu | 16 xgboost-1.1.1.1/xgboost/src/src/metric/metric.cc | 53 xgboost-1.1.1.1/xgboost/src/src/metric/metric_common.h | 61 xgboost-1.1.1.1/xgboost/src/src/metric/multiclass_metric.cu | 11 xgboost-1.1.1.1/xgboost/src/src/metric/rank_metric.cc | 490 ++-- xgboost-1.1.1.1/xgboost/src/src/metric/rank_metric.cu |only xgboost-1.1.1.1/xgboost/src/src/metric/survival_metric.cc |only xgboost-1.1.1.1/xgboost/src/src/objective/aft_obj.cc |only xgboost-1.1.1.1/xgboost/src/src/objective/multiclass_obj.cu | 4 xgboost-1.1.1.1/xgboost/src/src/objective/rank_obj.cu | 329 --- xgboost-1.1.1.1/xgboost/src/src/objective/regression_obj.cu | 53 xgboost-1.1.1.1/xgboost/src/src/predictor/cpu_predictor.cc | 440 ++-- xgboost-1.1.1.1/xgboost/src/src/predictor/gpu_predictor.cu | 554 +++-- xgboost-1.1.1.1/xgboost/src/src/predictor/predictor.cc | 48 xgboost-1.1.1.1/xgboost/src/src/tree/constraints.cc | 14 xgboost-1.1.1.1/xgboost/src/src/tree/constraints.cu | 48 xgboost-1.1.1.1/xgboost/src/src/tree/constraints.cuh | 20 xgboost-1.1.1.1/xgboost/src/src/tree/constraints.h | 2 xgboost-1.1.1.1/xgboost/src/src/tree/gpu_hist/gradient_based_sampler.cu |only xgboost-1.1.1.1/xgboost/src/src/tree/gpu_hist/gradient_based_sampler.cuh |only xgboost-1.1.1.1/xgboost/src/src/tree/gpu_hist/histogram.cu |only xgboost-1.1.1.1/xgboost/src/src/tree/gpu_hist/histogram.cuh |only xgboost-1.1.1.1/xgboost/src/src/tree/gpu_hist/row_partitioner.cu | 185 + xgboost-1.1.1.1/xgboost/src/src/tree/gpu_hist/row_partitioner.cuh | 64 xgboost-1.1.1.1/xgboost/src/src/tree/param.cc | 29 xgboost-1.1.1.1/xgboost/src/src/tree/param.h | 125 - xgboost-1.1.1.1/xgboost/src/src/tree/tree_model.cc | 119 - xgboost-1.1.1.1/xgboost/src/src/tree/updater_basemaker-inl.h | 7 xgboost-1.1.1.1/xgboost/src/src/tree/updater_colmaker.cc | 223 -- xgboost-1.1.1.1/xgboost/src/src/tree/updater_gpu_common.cuh | 91 xgboost-1.1.1.1/xgboost/src/src/tree/updater_gpu_hist.cu | 480 +--- xgboost-1.1.1.1/xgboost/src/src/tree/updater_histmaker.cc | 3 xgboost-1.1.1.1/xgboost/src/src/tree/updater_prune.cc | 43 xgboost-1.1.1.1/xgboost/src/src/tree/updater_quantile_hist.cc | 574 +++-- xgboost-1.1.1.1/xgboost/src/src/tree/updater_quantile_hist.h | 110 - xgboost-1.1.1.1/xgboost/src/src/tree/updater_refresh.cc | 9 xgboost-1.1.1.1/xgboost/src/src/tree/updater_skmaker.cc | 11 xgboost-1.1.1.1/xgboost/src/xgboost_R.cc | 54 xgboost-1.1.1.1/xgboost/src/xgboost_R.h | 32 xgboost-1.1.1.1/xgboost/tests/testthat/test_basic.R | 70 xgboost-1.1.1.1/xgboost/tests/testthat/test_callbacks.R | 67 xgboost-1.1.1.1/xgboost/tests/testthat/test_custom_objective.R | 17 xgboost-1.1.1.1/xgboost/tests/testthat/test_dmatrix.R | 8 xgboost-1.1.1.1/xgboost/tests/testthat/test_glm.R | 2 xgboost-1.1.1.1/xgboost/tests/testthat/test_interaction_constraints.R | 41 xgboost-1.1.1.1/xgboost/vignettes/discoverYourData.Rmd | 6 xgboost-1.1.1.1/xgboost/vignettes/xgboostPresentation.Rmd | 2 172 files changed, 7260 insertions(+), 6030 deletions(-)
Title: R Interface to the Vowpal Wabbit
Description: The 'Vowpal Wabbit' project is a fast out-of-core learning
system sponsored by Microsoft Research (having started at Yahoo! Research)
and written by John Langford along with a number of contributors. This R
package does not include the distributed computing implementation of the
cluster/ directory of the upstream sources. Use of the software as a network
service is also not directly supported as the aim is a simpler direct call
from R for validation and comparison. Note that this package contains an
embedded older version of 'Vowpal Wabbit'. The package 'rvw' at the GitHub
repo <https://github.com/eddelbuettel/rvw> can provide an alternative using
an external 'Vowpal Wabbit' library installation.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RVowpalWabbit versions 0.0.13 dated 2019-02-22 and 0.0.14 dated 2020-06-14
RVowpalWabbit-0.0.13/RVowpalWabbit/configure.in |only RVowpalWabbit-0.0.14/RVowpalWabbit/ChangeLog | 26 ++++ RVowpalWabbit-0.0.14/RVowpalWabbit/DESCRIPTION | 13 +- RVowpalWabbit-0.0.14/RVowpalWabbit/MD5 | 18 +-- RVowpalWabbit-0.0.14/RVowpalWabbit/README.md | 14 ++ RVowpalWabbit-0.0.14/RVowpalWabbit/configure | 105 +++++++------------ RVowpalWabbit-0.0.14/RVowpalWabbit/configure.ac |only RVowpalWabbit-0.0.14/RVowpalWabbit/src/Makevars.in | 2 RVowpalWabbit-0.0.14/RVowpalWabbit/src/accumulate.cc | 28 ++--- RVowpalWabbit-0.0.14/RVowpalWabbit/src/bfgs.cc | 34 +++--- RVowpalWabbit-0.0.14/RVowpalWabbit/src/vw.cc | 12 +- 11 files changed, 129 insertions(+), 123 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages. These
include e.g. measures like r-squared, intraclass correlation coefficient
(Nakagawa, Johnson & Schielzeth (2017) <doi:10.1098/rsif.2017.0213>),
root mean squared error or functions to check models for overdispersion,
singularity or zero-inflation and more. Functions apply to a large variety of
regression models, including generalized linear models, mixed effects models
and Bayesian models.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between performance versions 0.4.6 dated 2020-05-03 and 0.4.7 dated 2020-06-14
DESCRIPTION | 6 MD5 | 176 ++++++------- NAMESPACE | 79 +++++- NEWS.md | 17 + R/check_collinearity.R | 88 ++++++ R/check_convergence.R | 32 +- R/check_itemscale.R | 6 R/check_normality.R | 119 +++++++-- R/check_outliers.R | 2 R/check_overdispersion.R | 18 + R/compare_performance.R | 8 R/icc.R | 4 R/item_difficulty.R | 2 R/item_intercor.R | 2 R/model_performance.bayesian.R | 2 R/model_performance.lavaan.R | 2 R/model_performance.lm.R | 42 +++ R/model_performance.rma.R | 20 + R/performance_accuracy.R | 12 R/performance_aicc.R | 32 ++ R/performance_logloss.R | 15 + R/performance_mse.R | 46 +++ R/performance_pcp.R | 5 R/performance_roc.R | 17 - R/performance_score.R | 5 R/print-methods.R | 72 +---- R/r2.R | 40 +++ R/r2_coxsnell.R | 33 ++ R/r2_mcfadden.R | 33 ++ R/r2_mckelvey.R | 2 R/r2_nagelkerke.R | 33 ++ R/r2_nakagawa.R | 2 README.md | 14 - build/partial.rdb |binary inst/WORDLIST | 10 man/binned_residuals.Rd | 124 ++++----- man/check_autocorrelation.Rd | 72 ++--- man/check_collinearity.Rd | 159 +++++++----- man/check_convergence.Rd | 116 +++++--- man/check_distribution.Rd | 108 ++++---- man/check_heteroscedasticity.Rd | 62 ++-- man/check_homogeneity.Rd | 78 ++--- man/check_itemscale.Rd | 106 ++++---- man/check_model.Rd | 116 ++++---- man/check_normality.Rd | 96 +++---- man/check_outliers.Rd | 368 ++++++++++++++-------------- man/check_overdispersion.Rd | 142 +++++----- man/check_singularity.Rd | 150 +++++------ man/check_zeroinflation.Rd | 76 ++--- man/compare_performance.Rd | 160 ++++++------ man/cronbachs_alpha.Rd | 72 ++--- man/figures/unnamed-chunk-13-1.png |binary man/icc.Rd | 278 ++++++++++----------- man/item_difficulty.Rd | 68 ++--- man/item_intercor.Rd | 94 +++---- man/item_reliability.Rd | 86 +++--- man/item_split_half.Rd | 74 ++--- man/looic.Rd | 48 +-- man/model_performance.Rd | 82 +++--- man/model_performance.lavaan.Rd | 118 ++++---- man/model_performance.lm.Rd | 4 man/model_performance.merMod.Rd | 74 ++--- man/model_performance.rma.Rd | 90 +++--- man/model_performance.stanreg.Rd | 118 ++++---- man/performance_accuracy.Rd | 96 +++---- man/performance_aicc.Rd | 74 ++--- man/performance_hosmer.Rd | 66 ++--- man/performance_logloss.Rd | 72 ++--- man/performance_lrt.Rd | 58 ++-- man/performance_mse.Rd | 68 ++--- man/performance_pcp.Rd | 122 ++++----- man/performance_rmse.Rd | 94 +++---- man/performance_roc.Rd | 107 ++++---- man/performance_rse.Rd | 52 +-- man/performance_score.Rd | 130 ++++----- man/r2.Rd | 88 +++--- man/r2_bayes.Rd | 124 ++++----- man/r2_coxsnell.Rd | 74 ++--- man/r2_efron.Rd | 68 ++--- man/r2_kullback.Rd | 54 ++-- man/r2_loo.Rd | 56 ++-- man/r2_mcfadden.Rd | 66 ++--- man/r2_mckelvey.Rd | 82 +++--- man/r2_nagelkerke.Rd | 50 +-- man/r2_nakagawa.Rd | 96 +++---- man/r2_tjur.Rd | 56 ++-- man/r2_xu.Rd | 58 ++-- man/r2_zeroinflated.Rd | 80 +++--- tests/testthat/test-model_performance.rma.R | 6 89 files changed, 3327 insertions(+), 2705 deletions(-)
Title: Tidy Statistical Inference
Description: The objective of this package is to perform inference using an expressive statistical grammar that coheres with the tidy design framework.
Author: Andrew Bray [aut, cre],
Chester Ismay [aut],
Evgeni Chasnovski [aut],
Ben Baumer [aut],
Mine Cetinkaya-Rundel [aut],
Simon Couch [ctb],
Ted Laderas [ctb],
Nick Solomon [ctb],
Johanna Hardin [ctb],
Albert Y. Kim [ctb],
Neal Fultz [ctb],
Doug Friedman [ctb],
Richie Cotton [ctb],
Brian Fannin [ctb]
Maintainer: Andrew Bray <abray@reed.edu>
Diff between infer versions 0.5.1 dated 2019-11-19 and 0.5.2 dated 2020-06-14
infer-0.5.1/infer/build/infer.pdf |only infer-0.5.1/infer/inst/doc/chisq_test.R |only infer-0.5.1/infer/inst/doc/chisq_test.Rmd |only infer-0.5.1/infer/inst/doc/chisq_test.html |only infer-0.5.1/infer/inst/doc/flights_examples.R |only infer-0.5.1/infer/inst/doc/flights_examples.Rmd |only infer-0.5.1/infer/inst/doc/flights_examples.html |only infer-0.5.1/infer/inst/doc/mtcars_examples.R |only infer-0.5.1/infer/inst/doc/mtcars_examples.Rmd |only infer-0.5.1/infer/inst/doc/mtcars_examples.html |only infer-0.5.1/infer/inst/doc/two_sample_t.R |only infer-0.5.1/infer/inst/doc/two_sample_t.Rmd |only infer-0.5.1/infer/inst/doc/two_sample_t.html |only infer-0.5.1/infer/vignettes/chisq_test.Rmd |only infer-0.5.1/infer/vignettes/flights_examples.Rmd |only infer-0.5.1/infer/vignettes/mtcars_examples.Rmd |only infer-0.5.1/infer/vignettes/two_sample_t.Rmd |only infer-0.5.2/infer/DESCRIPTION | 16 infer-0.5.2/infer/MD5 | 202 - infer-0.5.2/infer/NAMESPACE | 3 infer-0.5.2/infer/NEWS.md | 27 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Title: A Package for Graphical Modelling in R
Description: The 'gRbase' package provides graphical modelling features
used by e.g. the packages 'gRain', 'gRim' and 'gRc'.
'gRbase' contains data sets relevant for use in connection with
graphical models (in particular all data sets used in the book Graphical
Models with R (2012)).
'gRbase' implements graph algorithms including
(i) maximum cardinality search (for marked and unmarked graphs).
(ii) moralize.
(iii) triangulate.
(iv) junction tree.
'gRbase' facilitates array operations,
'gRbase' implements functions for testing for conditional independence.
'gRbase' illustrates how hierarchical log-linear models may be
implemented and describes concept of graphical meta
data. These features, however, are not maintained anymore and
remains in 'gRbase' only because there exists a paper describing
these facilities: A Common Platform for Graphical Models in R:
The 'gRbase' Package, Journal of Statistical Software, Vol 14,
No 17, 2005.
NOTICE 'gRbase' requires that the packages graph,
'Rgraphviz' and 'RBGL' are installed from 'bioconductor'; for
installation instructions please refer to the web page given below.
Author: Søren Højsgaard <sorenh@math.aau.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between gRbase versions 1.8-6.4 dated 2020-02-18 and 1.8-6.6 dated 2020-06-14
gRbase-1.8-6.4/gRbase/R/namespace.R |only gRbase-1.8-6.4/gRbase/R/u_setops-c.R |only gRbase-1.8-6.4/gRbase/man/set_operations.Rd |only gRbase-1.8-6.4/gRbase/src/_u_setops.cpp |only gRbase-1.8-6.4/gRbase/src/_u_setops_c.c |only gRbase-1.8-6.4/gRbase/src/_utils_print.c |only gRbase-1.8-6.4/gRbase/src/_utils_print.h |only gRbase-1.8-6.4/gRbase/src/concatenate.h |only gRbase-1.8-6.4/gRbase/src/t_array_properties.cpp |only gRbase-1.8-6.4/gRbase/src/t_array_properties.h |only gRbase-1.8-6.6/gRbase/DESCRIPTION | 10 gRbase-1.8-6.6/gRbase/MD5 | 144 +- gRbase-1.8-6.6/gRbase/NAMESPACE | 6 gRbase-1.8-6.6/gRbase/NEWS | 17 gRbase-1.8-6.6/gRbase/R/NAMESPACE.R |only gRbase-1.8-6.6/gRbase/R/RcppExports.R | 122 + gRbase-1.8-6.6/gRbase/R/api_array_tabX.R | 28 gRbase-1.8-6.6/gRbase/R/api_array_tableX_bristol.R | 244 +++ gRbase-1.8-6.6/gRbase/R/api_setops.R |only gRbase-1.8-6.6/gRbase/R/api_setops_obsolete.R |only gRbase-1.8-6.6/gRbase/R/graph-coerce-xxx2yyy.R | 13 gRbase-1.8-6.6/gRbase/R/graph-mintriang.R | 10 gRbase-1.8-6.6/gRbase/R/graph-properties.R | 26 gRbase-1.8-6.6/gRbase/R/graph-rip.R | 6 gRbase-1.8-6.6/gRbase/R/graph-utilities.R | 3 gRbase-1.8-6.6/gRbase/R/grbase-utilities.R | 10 gRbase-1.8-6.6/gRbase/build/vignette.rds |binary gRbase-1.8-6.6/gRbase/inst/doc/arrays.R | 2 gRbase-1.8-6.6/gRbase/inst/doc/arrays.Rnw | 3 gRbase-1.8-6.6/gRbase/inst/doc/arrays.pdf |binary gRbase-1.8-6.6/gRbase/inst/doc/graphs.pdf |binary gRbase-1.8-6.6/gRbase/inst/include/gRbase.h | 2 gRbase-1.8-6.6/gRbase/inst/include/gRbase_RcppExports.h | 459 ++++--- gRbase-1.8-6.6/gRbase/man/all-subsets.Rd | 2 gRbase-1.8-6.6/gRbase/man/all_pairs.Rd | 2 gRbase-1.8-6.6/gRbase/man/api-array-07.Rd | 7 gRbase-1.8-6.6/gRbase/man/api-tabX.Rd | 16 gRbase-1.8-6.6/gRbase/man/api-tabX_.Rd | 13 gRbase-1.8-6.6/gRbase/man/data-BodyFat.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-Nutrimouse.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-ashtrees.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-breastcancer.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-cad.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-carcass.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-chestSim.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-dietox.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-dumping.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-lizard.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-mathmark.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-mildew.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-milkcomp.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-rats.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-reinis.Rd | 6 gRbase-1.8-6.6/gRbase/man/data-wine.Rd | 6 gRbase-1.8-6.6/gRbase/man/set-operations-obsolete.Rd |only gRbase-1.8-6.6/gRbase/man/set-operations.Rd |only gRbase-1.8-6.6/gRbase/src/Makevars | 2 gRbase-1.8-6.6/gRbase/src/R_like.cpp |only gRbase-1.8-6.6/gRbase/src/R_like.h |only gRbase-1.8-6.6/gRbase/src/RcppExports.cpp | 812 ++++++++----- gRbase-1.8-6.6/gRbase/src/_g_mcsMAT.cpp | 4 gRbase-1.8-6.6/gRbase/src/_g_mcsMAT2.cpp | 32 gRbase-1.8-6.6/gRbase/src/_g_mcsMAT2.h | 5 gRbase-1.8-6.6/gRbase/src/_g_rip-cliques.cpp | 90 - gRbase-1.8-6.6/gRbase/src/_m_coerce-dense-sparse.cpp | 2 gRbase-1.8-6.6/gRbase/src/_m_coerce-list2M.cpp | 203 ++- gRbase-1.8-6.6/gRbase/src/_m_colmat2list_etc.cpp | 2 gRbase-1.8-6.6/gRbase/src/_u_rowsums_etc.c | 2 gRbase-1.8-6.6/gRbase/src/api_array_cell.cpp | 2 gRbase-1.8-6.6/gRbase/src/api_array_tab_X.cpp | 514 ++++++-- gRbase-1.8-6.6/gRbase/src/api_setops.cpp |only gRbase-1.8-6.6/gRbase/src/api_setops_obsolete1.c |only gRbase-1.8-6.6/gRbase/src/api_setops_obsolete2.cpp |only gRbase-1.8-6.6/gRbase/src/array_properties.cpp |only gRbase-1.8-6.6/gRbase/src/array_properties.h |only gRbase-1.8-6.6/gRbase/src/combnC.c | 1 gRbase-1.8-6.6/gRbase/src/init.c | 80 - gRbase-1.8-6.6/gRbase/tests/testthat/test-graph-coercion.R |only gRbase-1.8-6.6/gRbase/tests/testthat/test-tabX.R | 70 + gRbase-1.8-6.6/gRbase/vignettes/arrays.Rnw | 3 gRbase-1.8-6.6/gRbase/vignettes/fig |only 81 files changed, 2134 insertions(+), 931 deletions(-)
Title: Goodness-of-Fit Tests for Copulae
Description: Several Goodness-of-Fit (GoF) tests for Copulae are provided. A new hybrid test, Zhang et al. (2016) <doi:10.1016/j.jeconom.2016.02.017> is implemented which supports all of the individual tests in the package, e.g. Genest et al. (2009) <doi:10.1016/j.insmatheco.2007.10.005>. Estimation methods for the margins are provided and all the tests support parameter estimation and predefined values. The parameters are estimated by pseudo maximum likelihood but if it fails the estimation switches automatically to inversion of Kendall's tau. For reproducibility of results, the functions support the definition of seeds. Also all the tests support automatized parallelization of the bootstrapping tasks. The package provides an interface to perform new GoF tests by submitting the test statistic.
Author: Ostap Okhrin <ostap.okhrin@tu-dresden.de>,
Simon Trimborn <trimborn.econometrics@gmail.com>,
Martin Waltz <martin.waltz@tu-dresden.de>
Maintainer: Simon Trimborn <trimborn.econometrics@gmail.com>
Diff between gofCopula versions 0.3-2 dated 2020-03-26 and 0.3-3 dated 2020-06-14
DESCRIPTION | 20 ++++++++++---------- MD5 | 42 +++++++++++++++++++++--------------------- NAMESPACE | 3 --- R/Tstats.R | 2 +- R/class_gofCOP.R | 11 ++--------- R/gofGetHybrid.R | 2 +- R/goftime.R | 2 +- R/margin_param_est.R | 4 ++-- R/test_HybridOutput.R | 2 +- R/tests.R | 6 ++++++ R/tests_CheckTime.R | 10 ++++++---- R/tests_CustomTest.R | 2 ++ R/tests_KendallCvM.R | 2 ++ R/tests_KendallKS.R | 2 ++ R/tests_White.R | 2 ++ R/tests_copula_helper.R | 5 ++++- R/tests_copula_new.R | 10 ++++++++++ R/tests_gof.R | 2 ++ R/tests_gofco.R | 2 ++ R/tests_hybrid.R | 6 +++--- R/tests_which.R | 11 ++++++----- man/CryptoCurrencies.Rd | 34 +++++++++++++++++----------------- 22 files changed, 103 insertions(+), 79 deletions(-)
Title: Fast Kalman Filter
Description: This is a fast and flexible implementation of the Kalman
filter, which can deal with NAs. It is entirely written in C
and relies fully on linear algebra subroutines contained in
BLAS and LAPACK. Due to the speed of the filter, the fitting of
high-dimensional linear state space models to large datasets
becomes possible. This package also contains a plot function
for the visualization of the state vector and graphical
diagnostics of the residuals.
Author: David Luethi [aut],
Philipp Erb [aut],
Simon Otziger [aut],
Paul Smith [cre] (<https://orcid.org/0000-0002-0034-3412>)
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between FKF versions 0.1.6 dated 2020-06-01 and 0.1.7 dated 2020-06-14
FKF-0.1.6/FKF/ChangeLog |only FKF-0.1.7/FKF/DESCRIPTION | 8 - FKF-0.1.7/FKF/MD5 | 26 +-- FKF-0.1.7/FKF/NEWS.md |only FKF-0.1.7/FKF/R/fkf.R | 258 +++++++++++++++++++-------------------- FKF-0.1.7/FKF/R/plot.fkf.R | 2 FKF-0.1.7/FKF/README.md | 21 ++- FKF-0.1.7/FKF/build/vignette.rds |binary FKF-0.1.7/FKF/demo/FKF-Ex.R | 4 FKF-0.1.7/FKF/inst/doc/FKF.R | 20 +-- FKF-0.1.7/FKF/inst/doc/FKF.Rmd | 23 +-- FKF-0.1.7/FKF/inst/doc/FKF.html | 93 ++++++-------- FKF-0.1.7/FKF/man/fkf.Rd | 14 -- FKF-0.1.7/FKF/man/plot.fkf.Rd | 2 FKF-0.1.7/FKF/vignettes/FKF.Rmd | 23 +-- 15 files changed, 244 insertions(+), 250 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu, Simon Firestone, Ryan Kyle, Johann Popp, Mathew Jay and Charles Reynard.
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 1.0-14 dated 2020-03-13 and 1.0-15 dated 2020-06-14
DESCRIPTION | 8 MD5 | 54 ++- NAMESPACE | 82 +++++ NEWS | 11 R/epi.2by2.R | 582 ++++++----------------------------------- R/epi.conf.R | 40 ++ R/epi.insthaz.R | 99 +++++- R/epi.sscc.R | 16 - R/epi.tests.R | 47 --- R/zARscore.R |only R/zARwald.R |only R/zMHRD.GR.R |only R/zMHRD.Sato.R |only R/zMHRD.Sato0.R |only R/zORcfield.R |only R/zORml.R |only R/zORscore.R |only R/zORwald.R |only R/zRRscore.R |only R/zRRtaylor.R |only R/zRRwald.R |only R/zincrate.R |only R/zincrisk.R |only R/zlimit.R |only R/zz2stat.R |only build/vignette.rds |binary inst/doc/epiR_descriptive.Rmd | 2 inst/doc/epiR_descriptive.html | 44 +-- man/epi.2by2.Rd | 6 man/epi.conf.Rd | 8 man/epi.insthaz.Rd | 98 ++++-- man/epi.sscc.Rd | 26 - man/epi.sscomps.Rd | 6 man/epi.ssdetect.Rd | 4 vignettes/epiR_descriptive.Rmd | 2 vignettes/epiR_descriptive.tex | 26 - 36 files changed, 500 insertions(+), 661 deletions(-)
Title: Tools for Case 1 Best-Worst Scaling (MaxDiff) Designs
Description: Tools to design best-worst scaling designs (i.e., balanced incomplete block designs) and
to analyze data from these designs, using aggregate and individual methods such as: difference
scores, Louviere, Lings, Islam, Gudergan, & Flynn (2013) <doi:10.1016/j.ijresmar.2012.10.002>;
analytical estimation, Lipovetsky & Conklin (2014) <doi:10.1016/j.jocm.2014.02.001>; empirical
Bayes, Lipovetsky & Conklin (2015) <doi:10.1142/S1793536915500028>; Elo, Hollis (2018)
<doi:10.3758/s13428-017-0898-2>; and network-based measures.
Author: Mark White [aut, cre]
Maintainer: Mark White <markhwhiteii@gmail.com>
Diff between bwsTools versions 1.1.0 dated 2020-03-19 and 1.1.1 dated 2020-06-14
DESCRIPTION | 10 MD5 | 40 +-- NEWS.md | 2 R/prscoring.R | 2 R/walkscoring.R | 2 build/vignette.rds |binary inst/doc/aggregate.R | 12 inst/doc/aggregate.Rmd | 12 inst/doc/aggregate.html | 456 +++++++++-------------------------- inst/doc/individual.html | 340 +++++--------------------- inst/doc/tidying_data.html | 567 +++++++++++++------------------------------- man/agg.Rd | 4 man/bibds.Rd | 4 man/e_bayescoring.Rd | 12 man/eloscoring.Rd | 3 man/indiv.Rd | 4 man/prscoring.Rd | 2 man/vdata.Rd | 4 man/walkscoring.Rd | 2 tests/testthat/test_get_M.R | 4 vignettes/aggregate.Rmd | 12 21 files changed, 445 insertions(+), 1049 deletions(-)
Title: Acquisition and Processing of MODIS Products
Description: Download and processing functionalities for the Moderate Resolution
Imaging Spectroradiometer (MODIS). The package provides automated access to the
global online data archives LP DAAC (<https://lpdaac.usgs.gov/>), LAADS
(<https://ladsweb.modaps.eosdis.nasa.gov/>) and NSIDC (<https://nsidc.org/>)
as well as processing capabilities such as file conversion, mosaicking,
subsetting and time series filtering.
Author: Matteo Mattiuzzi [aut],
Florian Detsch [cre, aut]
Maintainer: Florian Detsch <fdetsch@web.de>
Diff between MODIS versions 1.1.7 dated 2020-03-30 and 1.2.0 dated 2020-06-14
DESCRIPTION | 25 MD5 | 67 NAMESPACE | 1 NEWS | 11 R/MODIS-package.R | 68 R/MODISoptions.R | 1083 +++++------ R/aaa-classes.R | 3 R/arcStats.R | 554 +++--- R/checkIntegrity.R | 81 R/checkTools.R |only R/checkUtils.R | 194 +- R/doOptions.R | 472 ++--- R/gdalControls.R | 307 +-- R/getHdf.R | 823 ++++---- R/getSds.R | 231 -- R/getStruc.R | 398 ++-- R/getTile.R | 948 ++++++---- R/minorFuns.R | 486 ----- R/runGdal.R | 1105 ++++-------- R/runMrt.R | 900 ++++----- R/smoothSpline.R | 16 R/sysdata.rda |binary R/whittaker.R | 36 README.md | 98 - inst/external/MOD13A2.A2016145.h18v04.006.2016166145124.hdf |only inst/external/MODIS_Opts.R | 101 - inst/external/modis_latlonWGS84_grid_world.dbf |binary inst/external/modis_latlonWGS84_grid_world.shx |only man/MODISextent-class.Rd | 51 man/MODISoptions.Rd | 339 +-- man/getHdf.Rd | 210 +- man/getSds.Rd | 31 man/getTile.Rd | 285 +-- man/runGdal.Rd | 273 +- tests/testthat/test-getSds.R |only tests/testthat/test-getTile.R | 2 tests/testthat/test-minorFuns.R |only 37 files changed, 4382 insertions(+), 4817 deletions(-)
Title: Performance Assessment of Binary Classifier with Visualization
Description: Sensitivity (or recall or true positive rate), false positive rate, specificity, precision (or positive predictive value), negative predictive value, misclassification rate, accuracy, F-score- these are popular metrics for assessing performance of binary classifier for certain threshold. These metrics are calculated at certain threshold values. Receiver operating characteristic (ROC) curve is a common tool for assessing overall diagnostic ability of the binary classifier. Unlike depending on a certain threshold, area under ROC curve (also known as AUC), is a summary statistic about how well a binary classifier performs overall for the classification task. ROCit package provides flexibility to easily evaluate threshold-bound metrics. Also, ROC curve, along with AUC, can be obtained using different methods, such as empirical, binormal and non-parametric. ROCit encompasses a wide variety of methods for constructing confidence interval of ROC curve and AUC. ROCit also features the option of constructing empirical gains table, which is a handy tool for direct marketing. The package offers options for commonly used visualization, such as, ROC curve, KS plot, lift plot. Along with in-built default graphics setting, there are rooms for manual tweak by providing the necessary values as function arguments. ROCit is a powerful tool offering a range of things, yet it is very easy to use.
Author: Md Riaz Ahmed Khan [aut, cre],
Thomas Brandenburger [aut]
Maintainer: Md Riaz Ahmed Khan <mdriazahmed.khan@jacks.sdstate.edu>
Diff between ROCit versions 1.1.1 dated 2019-01-30 and 2.1.1 dated 2020-06-14
ROCit-1.1.1/ROCit/man/gettptnfpfn.Rd |only ROCit-1.1.1/ROCit/man/invlogit.Rd |only ROCit-1.1.1/ROCit/man/logit.Rd |only ROCit-2.1.1/ROCit/DESCRIPTION | 13 - ROCit-2.1.1/ROCit/MD5 | 94 ++++++----- ROCit-2.1.1/ROCit/NAMESPACE | 3 ROCit-2.1.1/ROCit/NEWS.md | 13 - ROCit-2.1.1/ROCit/R/Cartesian.R | 10 - ROCit-2.1.1/ROCit/R/ROCit-defunct.R |only ROCit-2.1.1/ROCit/R/ROCit-deprecated.R |only ROCit-2.1.1/ROCit/R/SummaryRocit.R | 25 +- ROCit-2.1.1/ROCit/R/aucCI.R | 55 ++++-- ROCit-2.1.1/ROCit/R/convertClass.R | 39 +++- ROCit-2.1.1/ROCit/R/gainstable.R | 2 ROCit-2.1.1/ROCit/R/getSurvival.R | 11 - ROCit-2.1.1/ROCit/R/getTPFPTNFN.R | 31 +-- ROCit-2.1.1/ROCit/R/ksplot.R | 63 +++---- ROCit-2.1.1/ROCit/R/logitInvLogit.R | 55 +++++- ROCit-2.1.1/ROCit/R/measureit.R | 97 ++++++++--- ROCit-2.1.1/ROCit/R/plotGainsTable.R | 47 ++--- ROCit-2.1.1/ROCit/R/plotROC.R | 15 - ROCit-2.1.1/ROCit/R/plot_ciROC.R | 11 - ROCit-2.1.1/ROCit/R/printMeasureit.R | 6 ROCit-2.1.1/ROCit/R/print_ROCit.R |only ROCit-2.1.1/ROCit/R/print_rocci.R |only ROCit-2.1.1/ROCit/R/rocCIbin.R | 4 ROCit-2.1.1/ROCit/R/rocCIemp.R | 4 ROCit-2.1.1/ROCit/R/rocit.R | 96 ++++++++--- ROCit-2.1.1/ROCit/R/trap_MLestimates.R | 11 - ROCit-2.1.1/ROCit/README.md | 16 + ROCit-2.1.1/ROCit/build/vignette.rds |binary ROCit-2.1.1/ROCit/inst/doc/my-vignette.R | 42 ++--- ROCit-2.1.1/ROCit/inst/doc/my-vignette.Rmd | 4 ROCit-2.1.1/ROCit/inst/doc/my-vignette.html | 226 ++++++++++++++------------- ROCit-2.1.1/ROCit/man/Diabetes.Rd | 6 ROCit-2.1.1/ROCit/man/Loan.Rd | 6 ROCit-2.1.1/ROCit/man/ROCit-defunct.Rd |only ROCit-2.1.1/ROCit/man/ROCit-deprecated.Rd |only ROCit-2.1.1/ROCit/man/ciAUC.rocit.Rd | 13 + ROCit-2.1.1/ROCit/man/convertclass.Rd | 89 +++++----- ROCit-2.1.1/ROCit/man/gainstable.default.Rd | 3 ROCit-2.1.1/ROCit/man/gettptnfpfn-defunct.Rd |only ROCit-2.1.1/ROCit/man/invlogit-deprecated.Rd |only ROCit-2.1.1/ROCit/man/ksplot.rocit.Rd | 14 + ROCit-2.1.1/ROCit/man/logit-deprecated.Rd |only ROCit-2.1.1/ROCit/man/measureit.default.Rd | 23 ++ ROCit-2.1.1/ROCit/man/plot.gainstable.Rd | 10 - ROCit-2.1.1/ROCit/man/plot.rocci.Rd | 13 + ROCit-2.1.1/ROCit/man/plot.rocit.Rd | 12 + ROCit-2.1.1/ROCit/man/print.rocci.Rd |only ROCit-2.1.1/ROCit/man/print.rocit.Rd |only ROCit-2.1.1/ROCit/man/rocit.Rd | 22 ++ ROCit-2.1.1/ROCit/man/summary.rocit.Rd | 3 ROCit-2.1.1/ROCit/tests/testthat.R | 8 ROCit-2.1.1/ROCit/vignettes/my-vignette.Rmd | 4 55 files changed, 736 insertions(+), 483 deletions(-)
Title: A Framework for Building HTTP API
Description: Allows to easily create high-performance full featured HTTP APIs from R
functions. Provides high-level classes such as 'Request', 'Response',
'Application', 'Middleware' in order to streamline server side
application development. Out of the box allows to serve requests using
'Rserve' package, but flexible enough to integrate with other HTTP servers
such as 'httpuv'.
Author: Dmitriy Selivanov [aut, cre] (<https://orcid.org/0000-0001-5413-1506>),
Artem Klevtsov [aut] (<https://orcid.org/0000-0003-0492-6647>),
rexy.ai [cph, fnd]
Maintainer: Dmitriy Selivanov <ds@rexy.ai>
Diff between RestRserve versions 0.2.2 dated 2020-04-12 and 0.3.0 dated 2020-06-14
RestRserve-0.2.2/RestRserve/vignettes/Benchmarks.R |only RestRserve-0.2.2/RestRserve/vignettes/Deployment.R |only RestRserve-0.2.2/RestRserve/vignettes/Overview.R |only RestRserve-0.2.2/RestRserve/vignettes/benchmarks/_Benchmarks-jmeter.Rmd |only RestRserve-0.2.2/RestRserve/vignettes/benchmarks/plumber-fib.R |only RestRserve-0.3.0/RestRserve/DESCRIPTION | 6 RestRserve-0.3.0/RestRserve/MD5 | 61 +- RestRserve-0.3.0/RestRserve/NEWS.md | 6 RestRserve-0.3.0/RestRserve/R/Application.R | 4 RestRserve-0.3.0/RestRserve/R/BackendRserve.R | 25 - RestRserve-0.3.0/RestRserve/R/HTTPError.R | 2 RestRserve-0.3.0/RestRserve/R/RcppExports.R | 4 RestRserve-0.3.0/RestRserve/R/Request.R | 5 RestRserve-0.3.0/RestRserve/R/Router.R | 9 RestRserve-0.3.0/RestRserve/R/utils.R | 31 + RestRserve-0.3.0/RestRserve/inst/doc/Authentication.R | 30 - RestRserve-0.3.0/RestRserve/inst/doc/Authentication.html | 248 ++++------ RestRserve-0.3.0/RestRserve/inst/doc/ContentHandlers.R | 32 - RestRserve-0.3.0/RestRserve/inst/doc/ContentHandlers.html | 220 ++++---- RestRserve-0.3.0/RestRserve/inst/doc/Logging.R | 16 RestRserve-0.3.0/RestRserve/inst/doc/Logging.html | 92 +-- RestRserve-0.3.0/RestRserve/inst/doc/Middleware.R | 18 RestRserve-0.3.0/RestRserve/inst/doc/Middleware.html | 204 +++----- RestRserve-0.3.0/RestRserve/inst/doc/RestRserve.R | 20 RestRserve-0.3.0/RestRserve/inst/doc/RestRserve.html | 158 +++--- RestRserve-0.3.0/RestRserve/inst/tinytest/test-cl-application.R | 2 RestRserve-0.3.0/RestRserve/inst/tinytest/test-cl-router.R | 7 RestRserve-0.3.0/RestRserve/man/Application.Rd | 4 RestRserve-0.3.0/RestRserve/man/BackendRserve.Rd | 7 RestRserve-0.3.0/RestRserve/src/RcppExports.cpp | 13 RestRserve-0.3.0/RestRserve/src/parse_multipart.cpp | 73 +- RestRserve-0.3.0/RestRserve/src/utils.h | 1 RestRserve-0.3.0/RestRserve/vignettes/benchmarks/Benchmarks.Rmd | 14 RestRserve-0.3.0/RestRserve/vignettes/img/bench-rps-no-keep-alive.png |binary 34 files changed, 689 insertions(+), 623 deletions(-)
Title: Local Projections Impulse Response Functions
Description: Provides functions to estimate and plot linear as well as nonlinear impulse
responses based on local projections by Jordà (2005) <doi:10.1257/0002828053828518>.
Author: Philipp Adämmer [aut, cre] (<https://orcid.org/0000-0003-3770-0097>),
James P. LeSage [ctb],
Mehmet Balcilar [ctb],
Jon Danielsson [ctb]
Maintainer: Philipp Adämmer <adaemmer@hsu-hh.de>
Diff between lpirfs versions 0.1.8 dated 2020-06-05 and 0.1.9 dated 2020-06-14
DESCRIPTION | 8 MD5 | 14 NEWS.md | 6 build/vignette.rds |binary inst/doc/lpirfs_vignette.R | 167 +++---- inst/doc/lpirfs_vignette.Rmd | 169 +++---- inst/doc/lpirfs_vignette.html | 890 ++++++++++++++++++++---------------------- vignettes/lpirfs_vignette.Rmd | 169 +++---- 8 files changed, 708 insertions(+), 715 deletions(-)
Title: Get Pedestrian Frequency Data from the 'Hystreet' Project
Description: An R API wrapper for the 'Hystreet' project <https://hystreet.com>. 'Hystreet' provides pedestrian counts in different cities in Germany.
Author: Johannes Friedrich [aut, cre]
Maintainer: Johannes Friedrich <Johannes.Friedrich@posteo.de>
Diff between hystReet versions 0.0.1 dated 2020-04-01 and 0.0.2 dated 2020-06-14
hystReet-0.0.1/hystReet/data/data.rda |only hystReet-0.0.1/hystReet/data/location_71.rda |only hystReet-0.0.1/hystReet/data/locations.rda |only hystReet-0.0.1/hystReet/data/ratio.rda |only hystReet-0.0.1/hystReet/man/data.Rd |only hystReet-0.0.2/hystReet/DESCRIPTION | 13 hystReet-0.0.2/hystReet/MD5 | 50 +-- hystReet-0.0.2/hystReet/R/create_hystreet_request.R | 5 hystReet-0.0.2/hystReet/R/get_hystreet_locations.R | 5 hystReet-0.0.2/hystReet/R/get_hystreet_station_data.R | 15 - hystReet-0.0.2/hystReet/R/get_hystreet_stats.R | 5 hystReet-0.0.2/hystReet/R/hystReet-package.R | 12 hystReet-0.0.2/hystReet/R/set_hystreet_token.R | 3 hystReet-0.0.2/hystReet/R/utils.R | 5 hystReet-0.0.2/hystReet/build/vignette.rds |binary hystReet-0.0.2/hystReet/data/corona_data_all.RData |only hystReet-0.0.2/hystReet/data/data_73_74.RData |only hystReet-0.0.2/hystReet/data/location_71.RData |only hystReet-0.0.2/hystReet/data/locations.RData |only hystReet-0.0.2/hystReet/data/ratio.RData |only hystReet-0.0.2/hystReet/inst/doc/Getting_started_with_the_R_package_hystReet.R | 49 ++- hystReet-0.0.2/hystReet/inst/doc/Getting_started_with_the_R_package_hystReet.Rmd | 58 +++- hystReet-0.0.2/hystReet/inst/doc/Getting_started_with_the_R_package_hystReet.html | 144 ++++++---- hystReet-0.0.2/hystReet/man/corona_data_all.Rd |only hystReet-0.0.2/hystReet/man/data_73_74.Rd |only hystReet-0.0.2/hystReet/man/dot-create_hystreet_request.Rd | 5 hystReet-0.0.2/hystReet/man/get_hystreet_locations.Rd | 7 hystReet-0.0.2/hystReet/man/get_hystreet_station_data.Rd | 17 - hystReet-0.0.2/hystReet/man/get_hystreet_stats.Rd | 7 hystReet-0.0.2/hystReet/man/hystReet-package.Rd | 2 hystReet-0.0.2/hystReet/man/set_hystreet_token.Rd | 5 hystReet-0.0.2/hystReet/vignettes/Getting_started_with_the_R_package_hystReet.Rmd | 58 +++- 32 files changed, 308 insertions(+), 157 deletions(-)
Title: Model-Free Functional Chi-Squared and Exact Tests
Description: Statistical hypothesis testing methods for
inferring model-free functional dependency using asymptotic
chi-squared or exact distributions. Functional test
statistics are asymmetric and functionally optimal, unique
from other related statistics. Tests in this package reveal
evidence for causality based on the
causality-by-functionality principle. They include
asymptotic functional chi-squared tests
(Zhang & Song 2013) <arXiv:1311.2707> and an exact
functional test (Zhong & Song 2019)
<doi:10.1109/TCBB.2018.2809743>. The normalized functional
chi-squared test was used by Best Performer 'NMSUSongLab'
in HPN-DREAM (DREAM8) Breast Cancer Network Inference
Challenges (Hill et al 2016) <doi:10.1038/nmeth.3773>. A
function index (Zhong & Song 2019)
<doi:10.1186/s12920-019-0565-9> (Kumar et al 2018)
<doi:10.1109/BIBM.2018.8621502> derived from the
functional test statistic offers a new effect size measure
for the strength of functional dependency, a better
alternative to conditional entropy in many aspects. For
continuous data, these tests offer an advantage over
regression analysis when a parametric functional form
cannot be assumed; for categorical data, they provide a
novel means to assess directional dependency not possible
with symmetrical Pearson's chi-squared or Fisher's exact
tests.
Author: Yang Zhang [aut],
Hua Zhong [aut] (<https://orcid.org/0000-0003-1962-2603>),
Hien Nguyen [aut] (<https://orcid.org/0000-0002-7237-4752>),
Ruby Sharma [aut],
Sajal Kumar [aut] (<https://orcid.org/0000-0003-0930-1582>),
Joe Song [aut, cre] (<https://orcid.org/0000-0002-6883-6547>)
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between FunChisq versions 2.5.0 dated 2020-04-24 and 2.5.1 dated 2020-06-14
DESCRIPTION | 8 MD5 | 36 - NEWS | 40 ++ R/simulate_tables.R | 785 +++++++++++++++++++++++------------------ README.md | 13 build/partial.rdb |binary build/vignette.rds |binary inst/doc/exact.fun.test.html | 74 +-- inst/doc/patterns.html | 298 +++++++-------- man/EFT.Rd | 12 man/FunChisq-deprecated.Rd | 7 man/FunChisq-package.Rd | 11 man/cond.fun.chisq.test.Rd | 37 - man/cp.fun.chisq.test.Rd | 23 - man/fun.chisq.test.Rd | 49 -- man/noise_model.Rd | 2 man/plot_table.Rd | 6 man/simulate_tables.Rd | 83 +++- tests/testthat/test_simulate.R | 161 ++++++++ 19 files changed, 987 insertions(+), 658 deletions(-)
Title: High Performance Container Data Types
Description: Provides high performance container data types such
as queues, stacks, deques, dicts and ordered dicts. Benchmarks
<https://randy3k.github.io/collections/articles/benchmark.html> have
shown that these containers are asymptotically more efficient than
those offered by other packages.
Author: Randy Lai [aut, cre],
Andrea Mazzoleni [cph] (tommy hash table library)
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between collections versions 0.3.2 dated 2020-06-01 and 0.3.3 dated 2020-06-14
DESCRIPTION | 8 ++--- MD5 | 12 ++++---- R/dict.R | 2 - README.md | 2 - man/dict.Rd | 2 - src/dict.c | 65 +++++++++++++++++++++++++++++++++++++++------ tests/testthat/test-dict.R | 26 +++++++++++++++--- 7 files changed, 92 insertions(+), 25 deletions(-)
Title: Generates Facts Sourced from the Wikipedia Main Page
Description: Displays random facts from the Wikipedia homepage.
Author: Keith McNulty [aut, cre] (<https://orcid.org/0000-0002-2332-1654>)
Maintainer: Keith McNulty <keith.mcnulty@gmail.com>
Diff between wikifacts versions 0.2 dated 2020-05-13 and 0.3.0 dated 2020-06-14
DESCRIPTION | 20 +++++++---- MD5 | 34 +++++++++++++------- NAMESPACE | 1 NEWS.md | 12 +++++++ R/globals.R |only R/wiki_didyouknow.R | 28 ++++++++++------ R/wiki_inthenews.R | 31 ++++++++++-------- R/wiki_onthisday.R | 27 +++++++++------- R/wiki_randomfact.R | 37 +++++++++++++++------- R/wiki_search.R |only README.md | 82 ++++++++++++++++++++++++------------------------- man/wiki_didyouknow.Rd | 16 +++++---- man/wiki_inthenews.Rd | 16 +++++---- man/wiki_onthisday.Rd | 14 +++++--- man/wiki_randomfact.Rd | 23 ++++++++++--- man/wiki_search.Rd |only tests |only 17 files changed, 211 insertions(+), 130 deletions(-)
Title: Quantity Calculus for R Vectors
Description: Integration of the 'units' and 'errors' packages for a complete
quantity calculus system for R vectors, matrices and arrays, with automatic
propagation, conversion, derivation and simplification of magnitudes and
uncertainties. Documentation about 'units' and 'errors' is provided in the
papers by Pebesma, Mailund & Hiebert (2016, <doi:10.32614/RJ-2016-061>) and
by Ucar, Pebesma & Azcorra (2018, <doi:10.32614/RJ-2018-075>), included in
those packages as vignettes; see 'citation("quantities")' for details.
Author: Iñaki Ucar [aut, cph, cre] (<https://orcid.org/0000-0001-6403-5550>)
Maintainer: Iñaki Ucar <iucar@fedoraproject.org>
Diff between quantities versions 0.1.4 dated 2020-06-06 and 0.1.5 dated 2020-06-14
quantities-0.1.4/quantities/man/tibble.Rd |only quantities-0.1.5/quantities/DESCRIPTION | 13 quantities-0.1.5/quantities/MD5 | 39 +- quantities-0.1.5/quantities/NAMESPACE | 7 quantities-0.1.5/quantities/NEWS.md | 6 quantities-0.1.5/quantities/R/errors.R | 8 quantities-0.1.5/quantities/R/init.R |only quantities-0.1.5/quantities/R/misc.R | 37 -- quantities-0.1.5/quantities/R/tidyverse.R |only quantities-0.1.5/quantities/R/units.R | 13 quantities-0.1.5/quantities/R/utils.R | 10 quantities-0.1.5/quantities/build/partial.rdb |binary quantities-0.1.5/quantities/inst/doc/introduction.R | 31 -- quantities-0.1.5/quantities/inst/doc/introduction.Rmd | 63 +--- quantities-0.1.5/quantities/inst/doc/introduction.html | 146 ++++------ quantities-0.1.5/quantities/inst/doc/parsing.html | 4 quantities-0.1.5/quantities/tests/testthat.R | 19 - quantities-0.1.5/quantities/tests/testthat/helper-quantities.R |only quantities-0.1.5/quantities/tests/testthat/test-misc.R | 17 - quantities-0.1.5/quantities/tests/testthat/test-quantities.R | 5 quantities-0.1.5/quantities/tests/testthat/test-tidyverse.R |only quantities-0.1.5/quantities/tests/testthat/test-utils.R | 5 quantities-0.1.5/quantities/vignettes/introduction.Rmd | 63 +--- 23 files changed, 177 insertions(+), 309 deletions(-)
Title: Meta-Analysis using Structural Equation Modeling
Description: A collection of functions for conducting meta-analysis using a
structural equation modeling (SEM) approach via the 'OpenMx' and
'lavaan' packages. It also implements various procedures to
perform meta-analytic structural equation modeling on the
correlation and covariance matrices.
Author: Mike Cheung [aut, cre] (<https://orcid.org/0000-0003-0113-0758>)
Maintainer: Mike Cheung <mikewlcheung@nus.edu.sg>
Diff between metaSEM versions 1.2.3.1 dated 2019-12-08 and 1.2.4 dated 2020-06-14
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Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>),
Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>),
Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>),
Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>),
Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>),
Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>),
Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>),
Stephanie Lobaugh [ctb]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 1.3.1 dated 2020-06-02 and 1.3.2 dated 2020-06-14
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