Title: An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE)
Solvers
Description: Provides a way to call the functions in 'SUNDIALS' C ODE solving library (<https://computing.llnl.gov/projects/sundials>). Currently the serial version of ODE solver, 'CVODE', sensitivity calculator 'CVODES' and differential algebraic solver 'IDA' from the 'SUNDIALS' library are implemented. The package requires ODE to be written as an 'R' or 'Rcpp' function and does not require the 'SUNDIALS' library to be installed on the local machine.
Author: Satyaprakash Nayak [aut, cre, cph]
,
Lawrence Livermore National Security [cph],
Southern Methodist University [cph]
Maintainer: Satyaprakash Nayak <satyaprakash.nayak@gmail.com>
Diff between sundialr versions 0.1.6.1 dated 2024-12-18 and 0.1.6.2 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS | 4 ++++ cleanup | 2 +- configure.ac | 8 ++++---- inst/doc/my-vignette.html | 8 ++++---- inst/include/sundials/sundials_config.h | 10 +++++----- src/scripts/sundials_download.sh | 19 ++++++++++++++----- src/sundials-mod-7.2.1.tar.gz |only tools/cmake_call.sh | 2 +- 10 files changed, 45 insertions(+), 31 deletions(-)
Title: Table Monster
Description: Provides a user friendly interface to
generation of booktab style tables using 'xtable'.
Author: Grant Izmirlian [aut, cre]
Maintainer: Grant Izmirlian <izmirlig@mail.nih.gov>
Diff between TableMonster versions 1.7.5 dated 2024-12-18 and 1.7.6 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/TableMonster.R | 7 +++++-- 3 files changed, 10 insertions(+), 7 deletions(-)
Title: Read and Write PNG Files with Configurable Decoder/Encoder
Options
Description: Read and write PNG images with arrays, rasters, native
rasters, numeric arrays, integer arrays, raw vectors and indexed
values. This PNG encoder exposes configurable internal options
enabling the user to select a speed-size tradeoff. For example,
disabling compression can speed up writing PNG by a factor of 50.
Multiple image formats are supported including raster, native rasters,
and integer and numeric arrays at color depths of 1, 2, 3 or 4. 16-bit
images are also supported. This implementation uses the 'libspng' 'C'
library which is available from
<https://github.com/randy408/libspng/>.
Author: Mike Cheng [aut, cre, cph],
Randy408 [aut, cph] ,
The PNG Reference Library Authors [aut, cph],
Cosmin Truta [cph] ,
Glenn Randers-Pehrson [cph] ,
Andreas Dilger [cph],
Guy Eric Schalnat [cph],
Mike Klein [ctb] ,
Matt Sarett [ctb] ,
James Yu [ctb] ,
[...truncated...]
Maintainer: Mike Cheng <mikefc@coolbutuseless.com>
Diff between fastpng versions 0.1.5 dated 2024-09-04 and 0.1.7 dated 2025-01-13
fastpng-0.1.5/fastpng/src/hash-color.c |only fastpng-0.1.5/fastpng/src/hash-color.h |only fastpng-0.1.7/fastpng/DESCRIPTION | 8 fastpng-0.1.7/fastpng/LICENSE | 2 fastpng-0.1.7/fastpng/MD5 | 24 - fastpng-0.1.7/fastpng/NAMESPACE | 1 fastpng-0.1.7/fastpng/NEWS.md | 9 fastpng-0.1.7/fastpng/R/write-png.R | 1 fastpng-0.1.7/fastpng/inst/doc/Overview.R | 4 fastpng-0.1.7/fastpng/inst/doc/Overview.html | 27 - fastpng-0.1.7/fastpng/src/R-get-png-info.c | 47 +- fastpng-0.1.7/fastpng/src/R-read-png.c | 173 ++++----- fastpng-0.1.7/fastpng/src/R-write-png.c | 366 ++++++-------------- fastpng-0.1.7/fastpng/vignettes/image/benchmark.png |binary 14 files changed, 272 insertions(+), 390 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Roger Bivand [ctb] ,
Michael Chirico [ctb],
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Barry Rowlingson [ctb],
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.8-5 dated 2024-12-12 and 1.8-10 dated 2025-01-13
DESCRIPTION | 26 MD5 | 324 +++--- NAMESPACE | 7 NEWS.md | 2281 +++++++++++++++++++++---------------------- R/Aclasses.R | 56 - R/Agenerics.R | 6 R/Arith_generics.R | 114 +- R/RGB.R | 24 R/RcppExports.R | 28 R/SpatRasterDataset.R | 78 - R/SpatVectorCollection.R | 34 R/Zdeprecated.R | 21 R/aggregate.R | 36 R/animate.R | 3 R/app.R | 4 R/autocor.R | 6 R/cells.R | 8 R/click.R | 17 R/coerce.R | 33 R/colors.R | 16 R/crs.R | 54 - R/dimensions.R | 34 R/distance.R | 101 + R/divide.R |only R/draw.R | 3 R/expand.R | 2 R/extent.R | 58 - R/extract.R | 51 R/extract_single.R | 4 R/focal.R | 22 R/focalMat.R | 2 R/gdal.R | 48 R/generics.R | 219 ++-- R/geom.R | 242 ++-- R/graticule.R | 24 R/init.R | 15 R/layerCor.R | 2 R/levels.R | 69 - R/lines.R | 6 R/match.R | 2 R/math.R | 30 R/merge.R | 30 R/messages.R | 15 R/names.R | 68 - R/ncdf.R | 53 R/options.R | 22 R/panel.R | 69 - R/plot.R | 29 R/plot_let.R | 1280 ++++++++++++------------ R/plot_raster.R | 48 R/plot_vector.R | 29 R/rapp.R | 6 R/rast.R | 28 R/rasterize.R | 18 R/rasterizeWin.R | 14 R/read.R | 16 R/relate.R | 90 + R/replace.R | 12 R/replace_values.R | 16 R/roll.R | 2 R/sample.R | 41 R/show.R | 32 R/spatvec.R | 528 +++++---- R/subset.R | 25 R/tags.R | 93 + R/tapp.R | 4 R/tiles.R | 39 R/time.R | 97 + R/update.R | 5 R/values.R | 86 - R/vect.R | 64 - R/watershed.R | 10 R/window.R | 6 R/wrap.R | 12 R/write.R | 21 R/xyRowColCell.R | 32 R/zonal.R | 42 R/zzz.R | 2 configure | 19 configure.ac | 19 inst/tinytest/test_extract.R | 6 inst/tinytest/test_plot.R |only man/aggregate.Rd | 6 man/as.lines.Rd | 6 man/as.points.Rd | 6 man/as.polygons.Rd | 6 man/click.Rd | 2 man/convhull.Rd | 39 man/cover.Rd | 7 man/datatype.Rd | 32 man/deprecated.Rd | 2 man/describe.Rd | 5 man/direction.Rd | 7 man/distance.Rd | 282 ++--- man/divide.Rd |only man/draw.Rd | 2 man/elongate.Rd | 86 - man/expanse.Rd | 4 man/ext.Rd | 1 man/extend.Rd | 132 +- man/extract.Rd | 3 man/factors.Rd | 8 man/gdal.Rd | 12 man/geometry.Rd | 2 man/init.Rd | 5 man/lines.Rd | 2 man/merge.Rd | 21 man/metags.Rd | 14 man/nearby.Rd | 7 man/not.na.Rd | 88 - man/nseg.Rd |only man/panel.Rd | 5 man/perim.Rd | 2 man/plot.Rd | 12 man/predict.Rd | 2 man/project.Rd | 1 man/rast.Rd | 2 man/relate.Rd | 292 ++--- man/sample.Rd | 206 +-- man/scale.Rd | 4 man/scale_linear.Rd |only man/select.Rd | 2 man/shade.Rd | 20 man/surfArea.Rd | 2 man/terra-package.Rd | 4 man/terraOptions.Rd | 124 +- man/text.Rd | 8 man/update.Rd | 6 man/viewshed.Rd | 13 man/voronoi.Rd | 3 man/vrt.Rd | 5 man/writeCDF.Rd | 2 src/RcppExports.cpp | 109 -- src/RcppFunctions.cpp | 19 src/RcppModule.cpp | 156 +- src/crs.cpp | 35 src/distRaster.cpp | 1586 +++++------------------------ src/distVector.cpp |only src/distance.cpp | 454 ++++++-- src/distance.h | 20 src/extract.cpp | 613 ++++++++--- src/gdal_algs.cpp | 43 src/gdalio.cpp | 68 - src/gdalio.h | 1 src/geos_methods.cpp | 267 ++++- src/geos_spat.h | 19 src/geosphere.cpp | 371 ++---- src/geosphere.h |only src/nearest.cpp |only src/patches.cpp | 95 + src/raster_methods.cpp | 522 ++++++++- src/rasterize.cpp | 7 src/read.cpp | 9 src/read_gdal.cpp | 317 +++++ src/read_ogr.cpp | 2 src/sample.cpp | 64 - src/spatBase.cpp | 4 src/spatBase.h | 8 src/spatRaster.cpp | 9 src/spatRaster.h | 66 - src/spatRasterMultiple.cpp | 136 ++ src/spatRasterMultiple.h | 46 src/spatVector.cpp | 17 src/spatVector.h | 37 src/vector_methods.cpp | 33 src/write_gdal.cpp | 17 src/write_ogr.cpp | 26 167 files changed, 7426 insertions(+), 6390 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran [aut],
Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 3.3.1 dated 2024-07-25 and 3.3.2 dated 2025-01-13
DESCRIPTION | 13 - MD5 | 36 +-- R/generic.predict.rfsrc.R | 2 R/rfsrc.R | 4 configure | 551 ++++++++++++++++++++++++---------------------- configure.ac | 2 data/breast.rda |binary data/follic.rda |binary data/hd.rda |binary data/housing.rda |binary data/nutrigenomic.rda |binary data/pbc.rda |binary data/peakVO2.rda |binary data/vdv.rda |binary data/veteran.rda |binary data/wihs.rda |binary data/wine.rda |binary inst/NEWS | 4 src/randomForestSRC.c | 29 ++ 19 files changed, 354 insertions(+), 287 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
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>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] ,
Saket Choudhary [ctb] ,
David Collins [ctb] ,
Charlotte Darby [ctb] ,
Jeff Farrell [ctb],
Isabella Grabski [ctb] ,
Christoph Hafemeister [ctb] ,
Yuhan Hao [ctb] ,
Austin Hartman [ctb] ,
Paul Hoffman [ctb] ,
Jaison Jain [ctb] ,
L [...truncated...]
Maintainer: Rahul Satija <seurat@nygenome.org>
Diff between Seurat versions 5.1.0 dated 2024-05-10 and 5.2.0 dated 2025-01-13
DESCRIPTION | 40 +- MD5 | 143 +++++----- NAMESPACE | 6 NEWS.md | 20 + R/clustering.R | 184 +++++++------ R/convenience.R | 107 ++++++- R/differential_expression.R | 22 + R/dimensional_reduction.R | 81 ++++- R/generics.R | 18 - R/integration.R | 43 +-- R/integration5.R | 2 R/objects.R | 40 +- R/preprocessing.R | 357 +++++++++++++++++++++----- R/sketching.R | 79 ++++- R/visualization.R | 48 ++- README.md | 1 build/Seurat.pdf |binary build/stage23.rdb |binary man/CCAIntegration.Rd | 4 man/CalculateBarcodeInflections.Rd | 2 man/ColorDimSplit.Rd | 3 man/DimPlot.Rd | 5 man/DotPlot.Rd | 2 man/FastRPCAIntegration.Rd | 2 man/FeaturePlot.Rd | 4 man/FeatureScatter.Rd | 2 man/FindAllMarkers.Rd | 4 man/FindClusters.Rd | 15 - man/FindMarkers.Rd | 2 man/FindNeighbors.Rd | 14 - man/FindSubCluster.Rd | 2 man/FindTransferAnchors.Rd | 6 man/FindVariableFeatures.Rd | 4 man/GetImage.Rd | 3 man/ISpatialDimPlot.Rd | 2 man/ISpatialFeaturePlot.Rd | 2 man/ImageDimPlot.Rd | 2 man/ImageFeaturePlot.Rd | 2 man/IntegrateData.Rd | 10 man/IntegrateEmbeddings.Rd | 4 man/JackStraw.Rd | 2 man/JointPCAIntegration.Rd | 4 man/LeverageScore.Rd | 5 man/LinkedPlots.Rd | 2 man/Load10X_Spatial.Rd | 2 man/MULTIseqDemux.Rd | 2 man/PredictAssay.Rd | 2 man/PrepSCTIntegration.Rd | 8 man/PrepareBridgeReference.Rd | 2 man/ProjectDim.Rd | 2 man/RPCAIntegration.Rd | 4 man/Radius.Rd | 2 man/Read10X_Image.Rd | 5 man/ReadXenium.Rd | 37 ++ man/RunCCA.Rd | 2 man/RunLeiden.Rd |only man/RunSLSI.Rd | 20 + man/RunSPCA.Rd | 2 man/RunUMAP.Rd | 6 man/SCTAssay-class.Rd | 6 man/SingleDimPlot.Rd | 3 man/SingleSpatialPlot.Rd | 4 man/SketchData.Rd | 8 man/SpatialPlot.Rd | 4 man/TopNeighbors.Rd | 2 man/TransferData.Rd | 4 man/VisiumV2-class.Rd | 4 man/VlnPlot.Rd | 2 man/fortify-Spatial.Rd | 6 tests/testthat/test_differential_expression.R | 17 - tests/testthat/test_find_clusters.R |only tests/testthat/test_integration5.R | 112 ++++++++ tests/testthat/test_load_10X.R | 25 + tests/testthat/test_sketching.R |only 74 files changed, 1142 insertions(+), 451 deletions(-)
Title: Causal Inference with Tree-Based Machine Learning Algorithms
Description: Estimating heterogeneous treatment effects with tree-based machine
learning algorithms and visualizing estimated results in flexible and
presentation-ready ways. For more information, see Brand, Xu, Koch,
and Geraldo (2021) <doi:10.1177/0081175021993503>. Our current package
first started as a fork of the 'causalTree' package on 'GitHub' and we
greatly appreciate the authors for their extremely useful and free package.
Author: Jiahui Xu [cre, aut],
Tanvi Shinkre [aut],
Jennie Brand [aut]
Maintainer: Jiahui Xu <jiahuixu@ucla.edu>
Diff between htetree versions 0.1.19 dated 2024-10-13 and 0.1.20 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/causalForest.R | 17 ----------------- R/causalTree.R | 15 --------------- R/honest.causalTree.R | 31 ------------------------------- R/matchinleaves.R | 2 +- man/causalForest.Rd | 17 ----------------- man/causalTree.Rd | 15 --------------- man/honest.causalTree.Rd | 31 ------------------------------- 9 files changed, 12 insertions(+), 138 deletions(-)
Title: Thematic Map Tools
Description: Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.
Author: Martijn Tennekes [aut, cre]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmaptools versions 3.1-1 dated 2021-01-19 and 3.2 dated 2025-01-13
tmaptools-3.1-1/tmaptools/NEWS |only tmaptools-3.1-1/tmaptools/R/pkg.R |only tmaptools-3.2/tmaptools/DESCRIPTION | 18 ++++++------ tmaptools-3.2/tmaptools/MD5 | 32 +++++++++++------------ tmaptools-3.2/tmaptools/NEWS.md |only tmaptools-3.2/tmaptools/R/bb.R | 4 +- tmaptools-3.2/tmaptools/R/calc_densities.R | 4 +- tmaptools-3.2/tmaptools/R/get_brewer_pal.R | 7 +++-- tmaptools-3.2/tmaptools/R/palette_explorer.R | 6 +++- tmaptools-3.2/tmaptools/R/tmaptools-package.R |only tmaptools-3.2/tmaptools/man/approx_areas.Rd | 5 ++- tmaptools-3.2/tmaptools/man/bb.Rd | 7 ++--- tmaptools-3.2/tmaptools/man/calc_densities.Rd | 28 +++++++++++--------- tmaptools-3.2/tmaptools/man/crop_shape.Rd | 6 ++-- tmaptools-3.2/tmaptools/man/get_brewer_pal.Rd | 4 +- tmaptools-3.2/tmaptools/man/map_coloring.Rd | 13 +++++---- tmaptools-3.2/tmaptools/man/palette_explorer.Rd | 5 ++- tmaptools-3.2/tmaptools/man/pipe.Rd | 2 - tmaptools-3.2/tmaptools/man/tmaptools-package.Rd | 16 +++++++++-- 19 files changed, 93 insertions(+), 64 deletions(-)
Title: Spatial Modeling of Infectious Disease with Reinfection
Description: Geographically Dependent Individual Level Models (GDILMs) within the Susceptible-Exposed-Infectious-Recovered-Susceptible (SEIRS) framework are applied to model infectious disease transmission, incorporating reinfection dynamics. This package employs a likelihood based Monte Carlo Expectation Conditional Maximization (MCECM) algorithm for estimating model parameters. It also provides tools for GDILM fitting, parameter estimation, AIC calculation on real pandemic data, and simulation studies customized to user-defined model settings.
Author: Amin Abed [aut, cre, cph] ,
Mahmoud Torabi [ths],
Zeinab Mashreghi [ths]
Maintainer: Amin Abed <abeda@myumanitoba.ca>
Diff between GDILM.SEIRS versions 0.0.2 dated 2024-12-07 and 0.0.3 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/GDILM_SEIRS_Sim_Par_Est.R | 8 ++++---- man/GDILM_SEIRS_Sim_Par_Est.Rd | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Fit Dynamic Structural Equation Models
Description: Applies dynamic structural equation models to time-series data
with generic and simplified specification for simultaneous and lagged
effects. Methods are described in Thorson et al. (2024)
"Dynamic structural equation models synthesize ecosystem dynamics
constrained by ecological mechanisms."
Author: James Thorson [aut, cre]
Maintainer: James Thorson <James.Thorson@noaa.gov>
Diff between dsem versions 1.3.0 dated 2024-07-22 and 1.4.0 dated 2025-01-13
DESCRIPTION | 13 MD5 | 61 +- NAMESPACE | 38 + NEWS.md | 13 R/cAIC.R |only R/compute_nll.R |only R/convert_equations.R |only R/data.R | 2 R/dsem.R | 139 ++++ R/dsemRTMB.R |only R/make_dsem_ram.R | 56 + R/make_matrices.R |only R/read_model.R |only R/rgmrf.R |only R/stepwise_selection.R |only R/utility.R |only build/partial.rdb |only inst/CITATION | 5 inst/doc/dynamic_factor_analysis.R | 31 - inst/doc/dynamic_factor_analysis.Rmd | 31 - inst/doc/dynamic_factor_analysis.html | 133 ++-- inst/doc/vignette.R | 93 ++- inst/doc/vignette.Rmd | 102 +++ inst/doc/vignette.html | 969 ++++++++++++++++++---------------- man/cAIC.Rd |only man/convert_equations.Rd |only man/dsem.Rd | 16 man/dsemRTMB.Rd |only man/dsem_control.Rd | 12 man/isle_royale.Rd | 2 man/logLik.dsem.Rd | 2 man/loo_residuals.Rd |only man/plot.dsem.Rd | 15 man/read_model.Rd |only man/stepwise_selection.Rd |only src/dsem.cpp | 2 tests/testthat/test-platform.R | 130 ++-- tests/testthat/test-priors.R |only vignettes/dynamic_factor_analysis.Rmd | 31 - vignettes/vignette.Rmd | 102 +++ 40 files changed, 1336 insertions(+), 662 deletions(-)
Title: Manipulate Matrix Row and Column Labels with Ease
Description: Functions to assist manipulation of matrix
row and column labels for all types of matrix mathematics
where row and column labels are to be respected.
Author: Matthew Heun [aut, cre]
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between RCLabels versions 0.1.10 dated 2024-01-29 and 0.1.11 dated 2025-01-13
DESCRIPTION | 10 ++--- LICENSE | 2 - MD5 | 24 ++++++------- NEWS.md | 46 +++++++++++++++++--------- R/extractors.R | 25 ++++++++++++++ R/utilities.R | 39 +++++++++++++++------- build/vignette.rds |binary inst/CITATION | 8 ++-- inst/doc/RCLabels.html | 8 ++-- man/get_prepositions.Rd | 26 ++++++++++++++ man/regex_funcs.Rd | 34 ++++++++++++++----- tests/testthat/test-extractors.R | 69 ++++++++++++++++++++++++++++++++++++++- tests/testthat/test-utilities.R | 24 +++++++++++++ 13 files changed, 253 insertions(+), 62 deletions(-)
Title: Interactive Maps with 'Mapbox GL JS' and 'MapLibre GL JS'
Description: Provides an interface to the 'Mapbox GL JS' (<https://docs.mapbox.com/mapbox-gl-js/guides>)
and the 'MapLibre GL JS' (<https://maplibre.org/maplibre-gl-js/docs/>) interactive mapping libraries to help users
create custom interactive maps in R. Users can create interactive globe visualizations; layer 'sf' objects to create
filled maps, circle maps, 'heatmaps', and three-dimensional graphics; and customize map styles and views. The package
also includes utilities to use 'Mapbox' and 'MapLibre' maps in 'Shiny' web applications.
Author: Kyle Walker [aut, cre]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between mapgl versions 0.1.4 dated 2024-11-01 and 0.2.0 dated 2025-01-13
DESCRIPTION | 15 MD5 | 45 +- NAMESPACE | 8 NEWS.md | 5 R/layers.R | 8 R/legends.R | 23 - R/plugins.R | 4 R/shiny.R | 49 +++ R/storymaps.R |only R/style_helpers.R | 22 + README.md | 2 inst/htmlwidgets/lib/maplibre-gl/maplibre-gl.css | 2 inst/htmlwidgets/lib/maplibre-gl/maplibre-gl.js | 8 inst/htmlwidgets/lib/pmtiles |only inst/htmlwidgets/mapboxgl.js | 332 +++++++++++++++++++--- inst/htmlwidgets/mapboxgl.yaml | 4 inst/htmlwidgets/maplibregl.js | 347 ++++++++++++++++++++--- inst/htmlwidgets/maplibregl.yaml | 7 inst/htmlwidgets/styles/filter-control.css |only man/add_symbol_layer.Rd | 6 man/mapgl-package.Rd | 1 man/on_section.Rd |only man/set_projection.Rd |only man/set_source.Rd |only man/set_tooltip.Rd |only man/story_leaflet.Rd |only man/story_map.Rd |only man/story_maplibre.Rd |only man/story_section.Rd |only 29 files changed, 763 insertions(+), 125 deletions(-)
Title: Helper Functions for Bayesian Analyses
Description: Functions to 'numericise' 'R' objects (coerce to numeric
objects), summarise 'MCMC' (Monte Carlo Markov Chain) samples and
calculate deviance residuals as well as 'R' translations of some
'BUGS' (Bayesian Using Gibbs Sampling), 'JAGS' (Just Another Gibbs
Sampler), 'STAN' and 'TMB' (Template Model Builder) functions.
Author: Nicole Hill [aut, cre] ,
Joe Thorley [aut] ,
Kirill Mueller [ctb] ,
Nadine Hussein [ctb] ,
Poisson Consulting [cph, fnd]
Maintainer: Nicole Hill <nicole@poissonconsulting.ca>
Diff between extras versions 0.7.3 dated 2024-08-27 and 0.8.0 dated 2025-01-13
extras-0.7.3/extras/tests/testthat/test-translations.R |only extras-0.8.0/extras/DESCRIPTION | 15 - extras-0.8.0/extras/MD5 | 92 +++---- extras-0.8.0/extras/NAMESPACE | 1 extras-0.8.0/extras/NEWS.md | 16 + extras-0.8.0/extras/R/dev.R | 123 +++++++--- extras-0.8.0/extras/R/extras-package.R | 1 extras-0.8.0/extras/R/ilog.R |only extras-0.8.0/extras/R/log-lik.R | 84 +++++- extras-0.8.0/extras/R/log.R | 51 ---- extras-0.8.0/extras/R/numericise.R | 7 extras-0.8.0/extras/R/ran.R | 2 extras-0.8.0/extras/R/res.R | 2 extras-0.8.0/extras/R/sens.R | 2 extras-0.8.0/extras/R/skewnorm.R | 2 extras-0.8.0/extras/R/zzz.R |only extras-0.8.0/extras/README.md | 55 +++- extras-0.8.0/extras/build/partial.rdb |binary extras-0.8.0/extras/build/vignette.rds |binary extras-0.8.0/extras/inst/WORDLIST | 4 extras-0.8.0/extras/inst/doc/beta-binomial-deviance-residuals.R | 8 extras-0.8.0/extras/inst/doc/beta-binomial-deviance-residuals.Rmd | 10 extras-0.8.0/extras/inst/doc/beta-binomial-deviance-residuals.html | 6 extras-0.8.0/extras/inst/doc/deviance-residuals.html | 2 extras-0.8.0/extras/man/dev_skewnorm.Rd | 2 extras-0.8.0/extras/man/figures/lifecycle-deprecated.svg | 22 + extras-0.8.0/extras/man/figures/lifecycle-experimental.svg | 22 + extras-0.8.0/extras/man/figures/lifecycle-stable.svg | 30 ++ extras-0.8.0/extras/man/figures/lifecycle-superseded.svg | 22 + extras-0.8.0/extras/man/figures/logo.png |binary extras-0.8.0/extras/man/ilog.Rd | 2 extras-0.8.0/extras/man/ilog10.Rd | 2 extras-0.8.0/extras/man/ilog2.Rd | 2 extras-0.8.0/extras/man/log_lik_beta_binom.Rd | 4 extras-0.8.0/extras/man/log_lik_skewnorm.Rd | 2 extras-0.8.0/extras/man/numericise.Rd | 2 extras-0.8.0/extras/man/ran_skewnorm.Rd | 2 extras-0.8.0/extras/man/res_skewnorm.Rd | 2 extras-0.8.0/extras/man/sens_skewnorm.Rd | 2 extras-0.8.0/extras/man/skewnorm.Rd | 2 extras-0.8.0/extras/tests/testthat.R | 8 extras-0.8.0/extras/tests/testthat/_snaps/dev.md |only extras-0.8.0/extras/tests/testthat/test-dev.R | 41 ++- extras-0.8.0/extras/tests/testthat/test-ilogit.R |only extras-0.8.0/extras/tests/testthat/test-log-lik.R | 40 +++ extras-0.8.0/extras/tests/testthat/test-log.R | 8 extras-0.8.0/extras/tests/testthat/test-logit.R |only extras-0.8.0/extras/tests/testthat/test-phi.R |only extras-0.8.0/extras/tests/testthat/test-pow.R |only extras-0.8.0/extras/tests/testthat/test-res.R | 6 extras-0.8.0/extras/vignettes/beta-binomial-deviance-residuals.Rmd | 10 51 files changed, 503 insertions(+), 213 deletions(-)
Title: Modeling Animal Movement with Continuous-Time Discrete-Space
Markov Chains
Description: Software to facilitates taking movement data in xyt format and pairing it with raster covariates within a continuous time Markov chain (CTMC) framework. As described in Hanks et al. (2015) <DOI:10.1214/14-AOAS803> , this allows flexible modeling of movement in response to covariates (or covariate gradients) with model fitting possible within a Poisson GLM framework.
Author: Ephraim Hanks [aut, cre]
Maintainer: Ephraim Hanks <hanks@psu.edu>
Diff between ctmcmove versions 1.2.9 dated 2018-04-20 and 1.2.10 dated 2025-01-13
DESCRIPTION | 16 +- MD5 | 26 ++-- R/ctmc2glm.R | 40 +++---- R/get.rate.matrix.R | 32 ++--- R/path2ctmc.R | 14 +- R/rast.grad.R | 12 +- man/Pctmc.Rd | 112 ++++++++++---------- man/ctmc.sim.Rd | 136 ++++++++++++------------- man/ctmc2glm.Rd | 212 +++++++++++++++++++-------------------- man/get.UD.Rd | 144 +++++++++++++------------- man/get.rate.matrix.Rd | 184 +++++++++++++++++----------------- man/mcmc.fmove.Rd | 262 ++++++++++++++++++++++++------------------------- man/path2ctmc.Rd | 216 ++++++++++++++++++++-------------------- man/rast.grad.Rd | 144 +++++++++++++------------- 14 files changed, 777 insertions(+), 773 deletions(-)
Title: Clustering via Quadratic Scoring
Description: Performs tuning of clustering models, methods and algorithms including the problem of determining an appropriate number of clusters. Validation of cluster analysis results is performed via quadratic scoring using resampling methods, as in Coraggio, L. and Coretto, P. (2023) <doi:10.1016/j.jmva.2023.105181>.
Author: Luca Coraggio [cre, aut] ,
Pietro Coretto [aut]
Maintainer: Luca Coraggio <luca.coraggio@unina.it>
Diff between qcluster versions 1.2 dated 2024-12-06 and 1.2.1 dated 2025-01-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 6 +++++- build/partial.rdb |binary inst/CITATION | 4 ++-- 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing
with meteorological data in the tidy data framework. Extends 'ggplot2'
for better plotting of scalar and vector fields and provides commonly
used analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between metR versions 0.16.0 dated 2024-10-14 and 0.17.0 dated 2025-01-13
DESCRIPTION | 6 +- MD5 | 32 +++++++-------- NEWS.md | 11 ++++- R/geom_streamline.R | 2 R/scale_longitude.R | 3 - README.md | 7 --- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Visualization-tools.html | 77 ++++++++++++++++---------------------- inst/doc/Working-with-data.html | 18 ++++---- man/discretised_scale.Rd | 6 +- man/figures/field-1.png |binary man/figures/timeseries-1.png |binary man/label_scales.Rd | 6 +- man/metR.Rd | 3 - man/scale_divergent.Rd | 6 +- man/scale_longitude.Rd | 6 -- 17 files changed, 86 insertions(+), 97 deletions(-)
Title: A GeoJson Processing Toolkit
Description: Includes functions for processing GeoJson objects <https://en.wikipedia.org/wiki/GeoJSON> relying on 'RFC 7946' <https://datatracker.ietf.org/doc/html/rfc7946>. The geojson encoding is based on 'json11', a tiny JSON library for 'C++11' <https://github.com/dropbox/json11>. Furthermore, the source code is exported in R through the 'Rcpp' and 'RcppArmadillo' packages.
Author: Lampros Mouselimis [aut, cre] ,
Dropbox Inc [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between geojsonR versions 1.1.1 dated 2023-01-12 and 1.1.2 dated 2025-01-13
DESCRIPTION | 12 MD5 | 26 NEWS.md | 8 README.md | 4 build/vignette.rds |binary inst/doc/the_geojsonR_package.R | 654 +++++++++++------------ inst/doc/the_geojsonR_package.Rmd | 6 inst/doc/the_geojsonR_package.html | 1016 +++++++++++++++++++++++-------------- src/FROM_geojson.cpp | 2 src/Makevars | 1 src/Makevars.win | 3 src/TO_geojson.cpp | 2 src/json11.cpp | 1 vignettes/the_geojsonR_package.Rmd | 6 14 files changed, 1015 insertions(+), 726 deletions(-)
Title: Estimation and Testing Classes Based on Package 'distr'
Description: Evaluation (S4-)classes based on package distr for evaluating procedures
(estimators/tests) at data/simulation in a unified way.
Author: Florian Camphausen [ctb] ,
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrTEst versions 2.8.2 dated 2024-01-31 and 2.8.3 dated 2025-01-13
DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- inst/CITATION | 4 ++-- inst/NEWS | 14 ++++++++++++++ man/0distrTEst-package.Rd | 8 ++++---- 5 files changed, 34 insertions(+), 19 deletions(-)
Title: Extensions of Package 'distr' for Teaching
Stochastics/Statistics in Secondary School
Description: Provides flexible examples of LLN and CLT for teaching purposes in secondary
school.
Author: Eleonora Feist [ctb] ,
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Anja Hueller [ctb]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrTeach versions 2.9.1 dated 2024-01-31 and 2.9.2 dated 2025-01-13
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- inst/CITATION | 4 ++-- inst/NEWS | 13 +++++++++++++ man/0distrTeach-package.Rd | 8 ++++---- 5 files changed, 29 insertions(+), 16 deletions(-)
Title: Bayesian Power Prior Design
Description: Bayesian power/type I error calculation and model fitting using
the power prior and the normalized power prior for generalized linear models.
Detailed examples of applying the package are available at <doi:10.32614/RJ-2023-016>.
Models for time-to-event outcomes are implemented in the R package 'BayesPPDSurv'.
The Bayesian clinical trial design methodology is described in Chen et al. (2011)
<doi:10.1111/j.1541-0420.2011.01561.x>, and Psioda and Ibrahim (2019)
<doi:10.1093/biostatistics/kxy009>. The normalized power prior is described in Duan et al. (2006)
<doi:10.1002/env.752> and Ibrahim et al. (2015) <doi:10.1002/sim.6728>.
Author: Yueqi Shen [aut, cre],
Matthew A. Psioda [aut],
Joseph G. Ibrahim [aut]
Maintainer: Yueqi Shen <angieshen6@gmail.com>
Diff between BayesPPD versions 1.1.2 dated 2023-11-25 and 1.1.3 dated 2025-01-13
DESCRIPTION | 15 - MD5 | 15 - NEWS.md | 10 + R/glm_fixed.R | 1 R/glm_random.R | 2 inst/CITATION |only inst/doc/bayesppd-vignette.R | 60 +++--- inst/doc/bayesppd-vignette.html | 362 ++++++++++++++++++++-------------------- src/PP_random.cpp | 83 ++++----- 9 files changed, 283 insertions(+), 265 deletions(-)
Title: File IO for Intracranial Electroencephalography
Description: Integrated toolbox supporting common file formats used for intracranial
Electroencephalography (iEEG) and deep-brain stimulation (DBS) study.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ieegio versions 0.0.2 dated 2024-10-31 and 0.0.3 dated 2025-01-13
DESCRIPTION | 15 MD5 | 76 ++-- NAMESPACE | 19 + NEWS.md | 19 + R/aaa-generics-surface.R | 136 ++++--- R/aaa-generics-volume.R | 709 ++++++++++++++++++++++++++++++++-------- R/aaa.R | 39 ++ R/as_ieegio_surface.R |only R/bci2000-cache.R | 2 R/brainvis-cache.R | 2 R/edf-cache.R | 25 - R/edf.R | 360 +++++++++++++++++--- R/hdf5-class.R | 20 - R/hdf5.R | 2 R/mat.R | 6 R/math-volume.R |only R/math.R | 14 R/mgz.R | 2 R/nifti.R | 598 ++++++++++++++++++++++++++++----- R/nsx-cache.R | 2 R/py-setup.R | 40 +- R/r3js.R |only R/rgl.R | 2 R/zzz.R | 1 inst/WORDLIST | 1 inst/doc/read-ephys.R | 43 +- inst/doc/read-ephys.Rmd | 1 inst/doc/read-imaging-data.R | 124 +++--- inst/sample_data_registry.txt | 3 man/LazyH5.Rd | 4 man/as_ieegio_surface.Rd |only man/as_ieegio_volume.Rd |only man/burn_volume.Rd |only man/imaging-surface.Rd | 3 man/imaging-volume.Rd | 30 + man/plot.ieegio_surface.Rd | 10 man/plot.ieegio_volume.Rd | 45 +- man/resample_volume.Rd |only tests/testthat.R | 2 tests/testthat/test-hdf5.R | 3 tests/testthat/test-rgbaNifti.R |only tests/testthat/test-volume.R | 10 vignettes/read-ephys.Rmd | 1 43 files changed, 1843 insertions(+), 526 deletions(-)
Title: Simulation Classes Based on Package 'distr'
Description: S4-classes for setting up a coherent framework for simulation within the distr
family of packages.
Author: Florian Camphausen [ctb] ,
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrSim versions 2.8.3 dated 2024-08-29 and 2.8.5 dated 2025-01-13
DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- inst/CITATION | 4 ++-- inst/NEWS | 18 ++++++++++++++++++ man/0distrSim-package.Rd | 6 +++--- 5 files changed, 37 insertions(+), 18 deletions(-)
Title: Distribution Classes for Distributions from Rmetrics
Description: S4-distribution classes based on package distr for distributions from packages
'fBasics' and 'fGarch'.
Author: Peter Ruckdeschel [cre, cph, aut]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrRmetrics versions 2.8.2 dated 2024-01-30 and 2.8.3 dated 2025-01-13
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- inst/CITATION | 4 ++-- inst/NEWS | 11 +++++++++++ man/0distrRmetrics-package.Rd | 6 +++--- 5 files changed, 26 insertions(+), 15 deletions(-)
Title: S4 Classes for Elliptically Contoured Distributions
Description: Distribution (S4-)classes for elliptically contoured distributions (based on
package 'distr').
Author: Peter Ruckdeschel [aut, cre, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrEllipse versions 2.8.3 dated 2024-08-29 and 2.8.4 dated 2025-01-13
DESCRIPTION | 18 +++++++++--------- MD5 | 8 ++++---- inst/CITATION | 4 ++-- inst/NEWS | 11 +++++++++++ man/0distrEllipse-package.Rd | 8 ++++---- 5 files changed, 30 insertions(+), 19 deletions(-)
Title: Split a Dataframe, Tibble, or Data.table into Training and Test
Sets
Description: Split a dataframe, tibble, or data.table into training and test sets. Return either a list, an index, or directly assign training and test sets into memory.
Author: Zhaochen He [aut, cre]
Maintainer: Zhaochen He <eastnileuc@gmail.com>
Diff between trainsplit versions 1.1 dated 2024-04-04 and 1.2 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/trainsplit.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
More information about priorityelasticnet at CRAN
Permanent link
Title: Fit Models Derived from Point Processes to Species Distributions
using 'inlabru'
Description: Integrated species distribution modeling is a rising field in quantitative ecology thanks to significant rises in the quantity of data available, increases in computational speed and the proven benefits of using such models.
Despite this, the general software to help ecologists construct such models in an easy-to-use framework is lacking.
We therefore introduce the R package 'PointedSDMs': which provides the tools to help ecologists set up integrated models and perform inference on them.
There are also functions within the package to help run spatial cross-validation for model selection, as well as generic plotting and predicting functions.
An introduction to these methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.
Author: Philip Mostert [aut, cre],
Bob O'hara [aut]
Maintainer: Philip Mostert <philip.s.mostert@ntnu.no>
Diff between PointedSDMs versions 2.1.2 dated 2024-08-21 and 2.1.3 dated 2025-01-13
DESCRIPTION | 18 - MD5 | 127 ++++++------- NAMESPACE | 2 R/blockedCV.R | 68 ++++++- R/bruSDM_predict.R | 14 - R/data.BBSColinusVirginianus.R | 2 R/data.SetophagaData.rda.R | 2 R/dataOrganize.R | 17 + R/datasetOut.R | 14 - R/fitISDM.R | 9 R/intModel.R | 22 -- R/makeLhoods.R | 21 +- R/modISDM_predict.R | 10 - R/modMarks_predict.R | 12 - R/modSpecies_predict.R | 22 +- R/nearestValue.R |only R/specifyISDM.R | 54 +++-- R/specifyMarks.R | 21 +- R/specifySpecies.R | 242 ++++++++++++++++--------- R/startISDM.R | 6 R/startMarks.R | 8 R/startSpecies.R | 8 README.md | 116 +++++------- build/vignette.rds |binary inst/doc/Marked_Point_Process.R | 17 + inst/doc/Marked_Point_Process.Rmd | 25 ++ inst/doc/Marked_Point_Process.html | 201 ++++++++++++--------- inst/doc/Setophaga.R | 141 +++++++------- inst/doc/Setophaga.Rmd | 180 +++++++++---------- inst/doc/Setophaga.html | 283 +++++++++++++++--------------- inst/doc/Solitary_tinamou.R | 59 +++--- inst/doc/Solitary_tinamou.Rmd | 71 ++++--- inst/doc/Solitary_tinamou.html | 88 +++++---- inst/doc/Spatiotemporal_example.R | 52 ++++- inst/doc/Spatiotemporal_example.Rmd | 58 ++++-- inst/doc/Spatiotemporal_example.html | 93 ++++++--- man/BBS.Rd | 2 man/BBSColinusVirginianus.Rd | 2 man/figures/README-predict_and_plot-1.png |binary man/intModel.Rd | 4 man/makeLhoods.Rd | 2 man/nearestValue.Rd |only man/predict.Rd | 2 man/specifyISDM.Rd | 106 +++++++++++ man/specifyMarks.Rd | 108 +++++++++++ man/specifySpecies.Rd | 108 +++++++++++ man/startISDM.Rd | 4 man/startMarks.Rd | 4 man/startSpecies.Rd | 4 tests/testthat/setup.R |only tests/testthat/testthat_blockedCV.R | 6 tests/testthat/testthat_dataOrganize.R | 6 tests/testthat/testthat_datasetOut.R | 7 tests/testthat/testthat_fitISDM.R | 6 tests/testthat/testthat_intModel.R | 6 tests/testthat/testthat_makeLhoods.R | 9 tests/testthat/testthat_specifyISDM.R | 8 tests/testthat/testthat_specifyMarks.R | 17 - tests/testthat/testthat_specifySpecies.R | 9 tests/testthat/testthat_startISDM.R | 13 - tests/testthat/testthat_startMarks.R | 11 - tests/testthat/testthat_startSpecies.R | 16 - vignettes/Marked_Point_Process.Rmd | 25 ++ vignettes/Setophaga.Rmd | 180 +++++++++---------- vignettes/Solitary_tinamou.Rmd | 71 ++++--- vignettes/Spatiotemporal_example.Rmd | 58 ++++-- 66 files changed, 1798 insertions(+), 1079 deletions(-)
Title: IMAGing engINEs, Tools for Application of Image Filters to Data
Matrices
Description: Provides fast application of image filters to data matrices,
using R and C++ algorithms.
Author: Wencheng Lau-Medrano [aut, cre]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
Diff between imagine versions 2.1.1 dated 2024-09-23 and 2.1.2 dated 2025-01-13
DESCRIPTION | 8 ++-- MD5 | 18 +++++----- NEWS.md | 5 +++ R/imagine-main.R | 5 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/imagine-intro.R | 64 +++++++++++++++++++-------------------- inst/doc/imagine-intro.html | 8 ++-- man/contextualMF.Rd | 5 +-- src/contextual-median-filter.cpp | 5 +-- 10 files changed, 60 insertions(+), 58 deletions(-)
More information about fastrerandomize at CRAN
Permanent link
Title: Animation of Multiple Trajectories with Uncertainty
Description: Animation of observed trajectories using spline-based interpolation (see for example, Buderman, F. E., Hooten, M. B., Ivan, J. S. and Shenk, T. M. (2016), <doi:10.1111/2041-210X.12465> "A functional model for characterizing long-distance movement behaviour". Methods Ecol Evol). Intended to be used exploratory data analysis, and perhaps for preparation of presentations.
Author: Henry Scharf [aut, cre],
Kristine Dinh [aut],
Rosales Hugo [aut],
Rivera Angelica [aut]
Maintainer: Henry Scharf <hscharf@arizona.edu>
Diff between anipaths versions 0.10.3 dated 2024-02-02 and 0.10.4 dated 2025-01-13
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS | 5 +++++ R/animate_paths.R | 8 ++++---- R/animation_expression.R | 1 + R/check_overwrite.R | 2 +- build/vignette.rds |binary inst/doc/anipaths.R | 4 ++-- inst/doc/anipaths.html | 4 ++-- inst/doc/anipaths_crawl.html | 4 ++-- inst/doc/anipaths_gam.R | 8 ++++---- man/check_overwrite.Rd | 2 +- 12 files changed, 38 insertions(+), 32 deletions(-)
Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Description: An interface (wrapper) to MPI. It also
provides interactive R manager and worker environment.
Author: Hao Yu [aut, cre]
Maintainer: Hao Yu <hyu@stats.uwo.ca>
Diff between Rmpi versions 0.7-3.1 dated 2025-01-13 and 0.7-3.3 dated 2025-01-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- configure | 9 +++++---- configure.ac | 9 +++++---- 4 files changed, 17 insertions(+), 15 deletions(-)
Title: Interface for Multiple Data Providers 'EDDS' and 'FRED'
Description: Interface for multiple data sources, such as the
`EDDS` API <https://evds2.tcmb.gov.tr/index.php?/evds/userDocs> of the
Central Bank of the Republic of Türkiye and the
`FRED` API <https://fred.stlouisfed.org/docs/api/fred/> of the Federal Reserve Bank.
Both data providers require API keys for access, which users can easily obtain
by creating accounts on their respective websites.
The package provides caching ability with the selection of periods to increase the
speed and efficiency of requests.
It combines datasets requested from different sources,
helping users when the data has common frequencies.
While combining data frames whenever possible, it also keeps all requested data
available as separate data frames to increase efficiency.
Author: Sermet Pekin [aut, cre, cph]
Maintainer: Sermet Pekin <sermet.pekin@gmail.com>
Diff between Rapi versions 1.0.5 dated 2024-04-06 and 1.0.6 dated 2025-01-13
Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/0edfb96425ca0841082054975994159b_2024_14_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/0edfb96425ca0841082054975994159b_2024_8_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/0edfb96425ca0841082054975994159b_2024_9_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/28e64743469b182c516544244dbf7bed_2024_14_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/28e64743469b182c516544244dbf7bed_2024_8_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/28e64743469b182c516544244dbf7bed_2024_9_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/3d4dc283b1b4c53f5aba5057bf787a63_2024_14_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/3d4dc283b1b4c53f5aba5057bf787a63_2024_8_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/3d4dc283b1b4c53f5aba5057bf787a63_2024_9_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/56cf7bda13139d113fde8412f5baa875_2024_14_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/56cf7bda13139d113fde8412f5baa875_2024_8_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rapi/56cf7bda13139d113fde8412f5baa875_2024_9_CACHE.RData |only Rapi-1.0.5/Rapi/tests/testthat/caches_Rsearch |only Rapi-1.0.5/Rapi/tests/testthat/caches_vyos |only Rapi-1.0.6/Rapi/DESCRIPTION | 18 +- Rapi-1.0.6/Rapi/MD5 | 68 +++------- Rapi-1.0.6/Rapi/NEWS.md | 8 + Rapi-1.0.6/Rapi/R/api_keys.R | 14 +- Rapi-1.0.6/Rapi/R/excel.R | 4 Rapi-1.0.6/Rapi/R/generics.R | 1 Rapi-1.0.6/Rapi/R/get_series_export.R | 4 Rapi-1.0.6/Rapi/R/internal_evds.R | 14 +- Rapi-1.0.6/Rapi/R/lag_df.R | 6 Rapi-1.0.6/Rapi/R/post_process_data.R | 2 Rapi-1.0.6/Rapi/R/request_funcs.R | 26 ++- Rapi-1.0.6/Rapi/R/sp_df_utils.R | 17 +- Rapi-1.0.6/Rapi/README.md | 19 +- Rapi-1.0.6/Rapi/man/excel.Rd | 4 Rapi-1.0.6/Rapi/man/get_series.Rd | 4 Rapi-1.0.6/Rapi/man/lag_df.Rd | 4 Rapi-1.0.6/Rapi/man/lag_df2.Rd | 2 Rapi-1.0.6/Rapi/man/remove_na_safe.Rd | 12 - Rapi-1.0.6/Rapi/man/set_api_key.Rd | 14 +- Rapi-1.0.6/Rapi/tests/testthat/caches_Rapi/3d4dc283b1b4c53f5aba5057bf787a63_2025_3_CACHE.RData |only Rapi-1.0.6/Rapi/tests/testthat/caches_Rapi/4fcf0e6cfe19b2219df6c66baeb0e31f_2025_3_CACHE.RData |only Rapi-1.0.6/Rapi/tests/testthat/caches_Rapi/7d9973e792dc706aa56d9dad7c226ea2_2025_3_CACHE.RData |only Rapi-1.0.6/Rapi/tests/testthat/caches_Rapi/e9343e9f8aa0c7553e699bb6a4034301_2025_3_CACHE.RData |only 37 files changed, 112 insertions(+), 129 deletions(-)
Title: Interface with Live Bikeshare Data
Description: Supplies a set of functions to interface with bikeshare data
following the General Bikeshare Feed Specification, allowing users to query
and accumulate tidy datasets for specified cities/bikeshare programs.
Author: Simon P. Couch [aut, cre],
Kaelyn Rosenberg [aut],
Mark Padgham [ctb]
Maintainer: Simon P. Couch <simonpatrickcouch@gmail.com>
Diff between gbfs versions 1.3.9 dated 2024-01-25 and 1.3.10 dated 2025-01-13
DESCRIPTION | 6 - MD5 | 8 - NEWS.md | 180 ++++++++++++++++++++++---------------------- R/utils.R | 2 tests/testthat/test-utils.R | 33 +++----- 5 files changed, 114 insertions(+), 115 deletions(-)
Title: Generic Reproducible Parallel Backend for 'foreach' Loops
Description: Provides functions to perform
reproducible parallel foreach loops, using independent
random streams as generated by L'Ecuyer's combined
multiple-recursive generator [L'Ecuyer (1999), <DOI:10.1287/opre.47.1.159>].
It enables to easily convert standard '%dopar%' loops into
fully reproducible loops, independently of the number
of workers, the task scheduling strategy, or the chosen
parallel environment and associated foreach backend.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>
Diff between doRNG versions 1.8.6 dated 2023-01-16 and 1.8.6.1 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/doRNG.Rnw | 2 +- inst/doc/doRNG.pdf |binary vignettes/doRNG.Rnw | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions).
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451>
b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>.
c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv.151 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 7.2 dated 2024-12-04 and 7.3 dated 2025-01-13
DESCRIPTION | 11 +++-- MD5 | 80 ++++++++++++++++++++++--------------------- NAMESPACE | 2 - R/acor.R | 65 ++++++++++++++++++---------------- R/acor.tune.R | 4 -- R/aeqdist.etest.R | 45 ++++++++++++++++++------ R/eqdist.etest.R |only R/hotel2T2.R | 5 +- R/james.R | 7 +-- R/scls.betest.R | 3 + R/scls2.R | 3 + man/Compositional-package.Rd | 5 +- man/acor.Rd | 5 ++ man/acor.tune.Rd | 11 +++-- man/aeqdist.etest.Rd | 13 +++++- man/alfa.pca.Rd | 2 - man/ascls.Rd | 4 +- man/atflr.Rd | 4 +- man/comp.den.Rd | 8 ++-- man/comp.test.Rd | 14 +++---- man/cv.ascls.Rd | 4 +- man/cv.atflr.Rd | 4 +- man/cv.scls.Rd | 4 +- man/cv.scrq.Rd | 16 ++------ man/cv.tflr.Rd | 4 +- man/eqdist.etest.Rd |only man/hd.meantest2.Rd | 2 - man/rcompsn.Rd | 2 - man/scls.Rd | 4 +- man/scls.betest.Rd | 4 +- man/scls.indeptest.Rd | 4 +- man/scls2.Rd | 4 +- man/scrq.Rd | 4 +- man/skewnorm.contour.Rd | 2 - man/ternary.Rd | 2 - man/ternary.coef.Rd | 2 - man/ternary.coefcr.Rd | 4 +- man/ternary.mcr.Rd | 2 - man/tflr.Rd | 4 +- man/tflr.betest.Rd | 4 +- man/tflr.indeptest.Rd | 7 ++- man/tflr2.Rd | 4 +- 42 files changed, 206 insertions(+), 172 deletions(-)
Title: Spatial Data Science Complementary Features
Description: Wrapping and supplementing commonly used functions in the R ecosystem related to spatial data science,
while serving as a basis for other packages maintained by Wenbo Lv.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between sdsfun versions 0.6.0 dated 2024-12-11 and 0.7.0 dated 2025-01-13
DESCRIPTION | 6 MD5 | 36 +-- NEWS.md | 4 R/fuzzyoverlay.R | 12 - R/linear_regression.R | 14 + R/sf_helpers.R | 422 ++++++++++++++++++++++---------------------- R/spdep_helpers.R | 430 ++++++++++++++++++++++----------------------- R/ssh_test.R | 100 +++++----- R/stratification.R | 7 R/utils.R | 1 R/vector_toolkits.R | 130 ++++++------- man/check_tbl_na.Rd | 50 ++--- man/fuzzyoverlay.Rd | 1 man/generate_subsets.Rd | 60 +++--- man/geodetector_q.Rd | 46 ++-- man/hclustgeo_disc.Rd | 4 man/sf_gk_proj_cgcs2000.Rd | 54 ++--- man/tbl_all2int.Rd | 50 ++--- src/Tbl2Mat.cpp | 10 - 19 files changed, 727 insertions(+), 710 deletions(-)
Title: Read and Write ODS Files
Description: Read ODS (OpenDocument Spreadsheet) into R as data frame. Also support writing data frame into ODS file.
Author: Gerrit-Jan Schutten [aut],
Chung-hong Chan [aut, cre] ,
Peter Brohan [aut],
Detlef Steuer [aut] ,
Thomas J. Leeper [aut] ,
John Foster [ctb],
Sergio Oller [ctb],
Jim Hester [ctb] ,
Stephen Watts [ctb],
Arthur Katossky [ctb],
Stas Malavin [ctb],
Dunca [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between readODS versions 2.3.1 dated 2024-11-05 and 2.3.2 dated 2025-01-13
readODS-2.3.1/readODS/tests/testdata/issue81.ods |only readODS-2.3.1/readODS/tests/testdata/layout_test.xls |only readODS-2.3.1/readODS/tests/testdata/layout_test.xlsx |only readODS-2.3.2/readODS/DESCRIPTION | 12 +-- readODS-2.3.2/readODS/MD5 | 20 ++--- readODS-2.3.2/readODS/NEWS.md | 6 + readODS-2.3.2/readODS/R/read_ods.R | 36 +++------- readODS-2.3.2/readODS/README.md | 4 - readODS-2.3.2/readODS/build/vignette.rds |binary readODS-2.3.2/readODS/inst/doc/overview.R | 2 readODS-2.3.2/readODS/tests/testdata/test_may_make_read_ods_crash_v2.ods |only readODS-2.3.2/readODS/tests/testthat/test_issue81.R | 4 - readODS-2.3.2/readODS/tests/testthat/test_read_ods.R | 4 + 13 files changed, 45 insertions(+), 43 deletions(-)
Title: Search Data Frames for Personally Identifiable Information
Description: Check a data frame for personal information, including names, location, disability status, and geo-coordinates.
Author: Jacob Patterson-Stein [aut, cre]
Maintainer: Jacob Patterson-Stein <jacobpstein@gmail.com>
Diff between pii versions 1.1.0 dated 2025-01-08 and 1.3.0 dated 2025-01-13
DESCRIPTION | 6 - MD5 | 8 +- NAMESPACE | 1 NEWS.md | 4 + R/check_PII.R | 196 ++++++++++++++++++++-------------------------------------- 5 files changed, 80 insertions(+), 135 deletions(-)
Title: Creates Safety Results Summary in XML to Upload to EudraCT, or
ClinicalTrials.gov
Description: The remit of the European Clinical Trials Data Base (EudraCT <https://eudract.ema.europa.eu/> ), or ClinicalTrials.gov <https://clinicaltrials.gov/>, is to provide open access to summaries of all registered clinical trial results; thus aiming to prevent non-reporting of negative results and provide open-access to results to inform future research. The amount of information required and the format of the results, however, imposes a large extra workload at the end of studies on clinical trial units. In particular, the adverse-event-reporting component requires entering: each unique combination of treatment group and safety event; for every such event above, a further 4 pieces of information (body system, number of occurrences, number of subjects, number exposed) for non-serious events, plus an extra three pieces of data for serious adverse events (numbers of causally related events, deaths, causally related deaths). This package prepares the required statistics needed by Eudr [...truncated...]
Author: Simon Bond [cre],
Beatrice Pantaleo [aut]
Maintainer: Simon Bond <simon.bond7@nhs.net>
Diff between eudract versions 1.0.2 dated 2024-11-28 and 1.0.3 dated 2025-01-13
DESCRIPTION | 8 MD5 | 160 NEWS.md | 96 R/clintrials_gov_convert.R | 140 R/clintrials_gov_upload.R | 186 R/eudract_convert.R | 72 R/incidence_table.R | 100 R/safety.R | 54 R/safety_summary.R | 572 R/simple_safety_xml.R | 120 R/soc_code.R | 28 build/vignette.rds |binary inst/doc/eudract.Rmd | 286 inst/doc/eudract.html | 15 inst/doc/standard_reporting.Rmd | 182 inst/doc/standard_reporting.html | 51 inst/extdata/1234.xml | 454 inst/extdata/ProtocolRecordSchema.xsd | 1452 +- inst/extdata/RRSUploadSchema.xsd | 1368 +- inst/extdata/adverseEvents.xsd | 570 inst/extdata/ct_safety_upload.xml | 2904 ++-- inst/extdata/find_replace.xslt | 48 inst/extdata/safety__upload.xml | 3676 ++--- inst/extdata/simple.xsd | 394 inst/extdata/simpleToCtGov.xslt | 248 inst/extdata/simpleToEudraCT.xslt | 288 inst/extdata/soc.xml | 276 man/append_xml.Rd | 24 man/clintrials_gov_convert.Rd | 134 man/clintrials_gov_upload.Rd | 170 man/create.safety_summary.Rd | 42 man/df_to_char.Rd | 30 man/dot_plot.Rd | 124 man/eudract_convert.Rd | 116 man/incidence_table.Rd | 66 man/plot.dot_plot.Rd | 32 man/print.dot_plot.Rd | 32 man/print.safety_summary.Rd | 34 man/relative_risk.Rd | 156 man/safety.Rd | 66 man/safety_summary.Rd | 134 man/simple_safety_xml.Rd | 104 man/soc_code.Rd | 48 tests/testthat.R | 10 tests/testthat/1234.xml | 454 tests/testthat/GROUP.csv | 8 tests/testthat/NONSERIOUS.csv | 164 tests/testthat/Rplots.pdf |binary tests/testthat/SERIOUS.csv | 164 tests/testthat/_snaps/dotplot/dotplot-1group.svg | 208 tests/testthat/_snaps/dotplot/dotplot-3groups.svg | 772 - tests/testthat/_snaps/dotplot/dotplot-ref-rr.svg | 488 tests/testthat/_snaps/dotplot/dotplot-ref.svg | 472 tests/testthat/_snaps/dotplot/dotplot.svg | 472 tests/testthat/bak_study_file.xml | 4030 +++--- tests/testthat/ct.xml | 3316 ++--- tests/testthat/data/all_soc.csv | 54 tests/testthat/data/all_soc_v2.csv | 56 tests/testthat/data/events.csv | 3278 ++--- tests/testthat/data/fix_ucl.R | 52 tests/testthat/data/multiple_soc.csv | 6 tests/testthat/data/no_aes.csv | 4 tests/testthat/data/no_saes.csv | 4 tests/testthat/data/output_from_ucl.xml |14114 +++++++++++----------- tests/testthat/data/repeat_occurrences.csv | 8 tests/testthat/data/socless.xml | 9846 +++++++-------- tests/testthat/data/sparse.csv | 6 tests/testthat/events.csv | 3328 ++--- tests/testthat/reference/simple.xml | 2904 ++-- tests/testthat/reference/table_ct.xml | 4016 +++--- tests/testthat/reference/table_eudract.xml | 4972 +++---- tests/testthat/simple.xml | 2904 ++-- tests/testthat/study_file.xml | 4030 +++--- tests/testthat/table_ct.xml | 4016 +++--- tests/testthat/table_eudract.xml | 3894 +++--- tests/testthat/test_append_xml.R | 36 tests/testthat/test_basic.R | 808 - tests/testthat/test_bea.R | 74 tests/testthat/test_errors.R | 566 vignettes/eudract.Rmd | 286 vignettes/standard_reporting.Rmd | 182 81 files changed, 42533 insertions(+), 42529 deletions(-)
Title: Produce Charts Following UK Government Analysis Function
Guidance
Description: Colour palettes and a 'ggplot2' theme to follow the UK Government
Analysis Function best practice guidance for producing data visualisations,
available at
<https://analysisfunction.civilservice.gov.uk/policy-store/data-visualisation-charts/>.
Includes continuous and discrete colour and fill scales, as well as a
'ggplot2' theme.
Author: Crown Copyright [cph],
Government Analysis Function [fnd],
Alice Hannah [aut],
Olivia Box Power [cre, ctb]
Maintainer: Olivia Box Power <Olivia.BoxPower@dhsc.gov.uk>
Diff between afcharts versions 0.4.0 dated 2024-11-06 and 0.4.1 dated 2025-01-13
DESCRIPTION | 10 MD5 | 75 +- NEWS.md | 8 R/af_palette.R | 6 R/afcharts-package.R | 2 R/scale_colour_continuous_af.R | 2 R/scale_colour_discrete_af.R | 1 R/scale_fill_continuous_af.R | 2 R/scale_fill_discrete_af.R | 1 R/use_afcharts.R | 16 R/utils.R | 2 README.md | 82 +- build/vignette.rds |binary inst/doc/colours.R | 17 inst/doc/colours.Rmd | 1 inst/doc/colours.html | 608 ++++++++-------- inst/doc/cookbook.R | 433 +++++++----- inst/doc/cookbook.Rmd | 1 inst/doc/cookbook.html | 1145 +++++++++++++++++--------------- inst/doc/saving.R | 11 inst/doc/saving.Rmd | 14 inst/doc/saving.html | 67 - man/figures/README-ex1-1.svg | 1077 +++++++++++++++--------------- man/figures/README-ex2-1.svg | 858 ++++++++++++----------- man/figures/README-ex3-1.svg |only man/use_afcharts.Rd | 2 tests/testthat.R | 1 tests/testthat/_snaps |only tests/testthat/helper.R |only tests/testthat/test-af_palette.R | 7 tests/testthat/test-chart-output.R |only vignettes/colours.Rmd | 1 vignettes/cookbook.Rmd | 1 vignettes/cookbook/_annotations.Rmd | 110 ++- vignettes/cookbook/_chart-types.Rmd | 170 +++- vignettes/cookbook/_colour-palettes.Rmd | 24 vignettes/cookbook/_customisations.Rmd | 143 ++- vignettes/saving.Rmd | 14 38 files changed, 2713 insertions(+), 2199 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Description: Pipeline tools coordinate the pieces of computationally
demanding analysis projects.
The 'targets' package is a 'Make'-like pipeline tool for statistics and
data science in R. The package skips costly runtime for tasks
that are already up to date,
orchestrates the necessary computation with implicit parallel computing,
and abstracts files as R objects. If all the current output matches
the current upstream code and data, then the whole pipeline is up
to date, and the results are more trustworthy than otherwise.
The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
,
Matthew T. Warkentin [ctb],
Mark Edmondson [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between targets versions 1.9.1 dated 2024-12-04 and 1.10.0 dated 2025-01-13
DESCRIPTION | 6 MD5 | 260 ++++++++++++++-------------- NAMESPACE | 6 NEWS.md | 37 +++ R/class_active.R | 57 +++--- R/class_auto.R | 27 ++ R/class_branch.R | 7 R/class_builder.R | 104 ++++++----- R/class_counter.R | 55 ++++- R/class_cue.R | 109 +++++------ R/class_database.R | 152 +++++++++++----- R/class_database_aws.R | 2 R/class_database_gcp.R | 2 R/class_database_local.R | 6 R/class_external.R | 10 - R/class_file.R | 61 ++++-- R/class_forecast.R | 11 - R/class_frames.R | 3 R/class_graph.R | 77 +++++--- R/class_junction.R | 4 R/class_lookup.R | 18 + R/class_meta.R | 62 +++--- R/class_metrics.R | 2 R/class_outdated.R | 30 +-- R/class_parallel.R | 7 R/class_pattern.R | 3 R/class_pipeline.R | 12 - R/class_progress.R | 17 + R/class_queue.R | 1 R/class_record.R | 12 - R/class_reporter.R | 16 + R/class_runtime.R | 16 - R/class_scheduler.R | 14 - R/class_sequential.R | 22 +- R/class_silent.R | 3 R/class_sitrep.R | 18 + R/class_store.R | 55 +++-- R/class_store_format_custom.R | 7 R/class_store_format_custom_methods.R | 18 + R/class_store_repository_cas.R | 2 R/class_store_repository_cas_methods.R | 43 +++- R/class_summary.R | 10 - R/class_target.R | 5 R/class_timestamp.R | 14 - R/class_vector.R | 17 + R/class_verbose.R | 17 - R/tar_built.R | 2 R/tar_config_get.R | 8 R/tar_config_set.R | 43 +++- R/tar_deduplicate.R | 4 R/tar_engine_knitr.R | 2 R/tar_format.R | 23 +- R/tar_make.R | 20 +- R/tar_make_clustermq.R | 2 R/tar_make_future.R | 2 R/tar_mermaid.R | 3 R/tar_network.R | 3 R/tar_outdated.R | 19 +- R/tar_repository_cas.R | 6 R/tar_resources_crew.R | 6 R/tar_script.R | 6 R/tar_seed.R | 4 R/tar_sitrep.R | 27 +- R/tar_started.R | 2 R/tar_target.R | 12 + R/tar_visnetwork.R | 3 R/use_targets.R | 4 R/utils_assert.R | 29 ++- R/utils_callr.R | 2 R/utils_cli.R | 7 R/utils_data.R | 15 - R/utils_files.R | 81 +++++++- R/utils_language.R | 2 inst/WORDLIST | 2 man/callr_args_default.Rd | 2 man/tar_built.Rd | 2 man/tar_config_set.Rd | 30 ++- man/tar_deduplicate.Rd | 2 man/tar_format.Rd | 10 - man/tar_make.Rd | 22 +- man/tar_make_clustermq.Rd | 22 +- man/tar_make_future.Rd | 22 +- man/tar_mermaid.Rd | 22 +- man/tar_network.Rd | 22 +- man/tar_option_set.Rd | 2 man/tar_outdated.Rd | 25 +- man/tar_resources_crew.Rd | 4 man/tar_script.Rd | 6 man/tar_seed.Rd | 2 man/tar_sitrep.Rd | 39 ++-- man/tar_started.Rd | 2 man/tar_target.Rd | 12 + man/tar_visnetwork.Rd | 22 +- man/use_targets.Rd | 4 tests/aws/test-aws_bad_args.R | 2 tests/aws/test-delete.R | 2 tests/aws/test-utils_aws.R | 68 ++++--- tests/gcp/test-class_gcp_qs.R | 10 - tests/interactive/test-class_url.R | 11 - tests/interactive/test-tar_repository_cas.R | 4 tests/testthat/test-class_auto.R | 24 ++ tests/testthat/test-class_aws.R | 12 - tests/testthat/test-class_aws_file.R | 12 - tests/testthat/test-class_counter.R | 8 tests/testthat/test-class_cue.R | 4 tests/testthat/test-class_database.R | 17 + tests/testthat/test-class_feather.R | 12 - tests/testthat/test-class_file.R | 15 + tests/testthat/test-class_fst.R | 12 - tests/testthat/test-class_fst_dt.R | 12 - tests/testthat/test-class_fst_tbl.R | 12 - tests/testthat/test-class_gcp.R | 12 - tests/testthat/test-class_gcp_file.R | 12 - tests/testthat/test-class_graph.R | 50 ++--- tests/testthat/test-class_keras.R | 12 - tests/testthat/test-class_parquet.R | 12 - tests/testthat/test-class_qs.R | 12 - tests/testthat/test-class_rds.R | 12 - tests/testthat/test-class_runtime.R | 18 - tests/testthat/test-class_sequential.R | 42 ++++ tests/testthat/test-class_store_file.R | 25 ++ tests/testthat/test-class_torch.R | 12 - tests/testthat/test-class_vector.R | 9 tests/testthat/test-tar_config_set.R | 23 ++ tests/testthat/test-tar_repository_cas.R | 13 - tests/testthat/test-tar_sitrep.R | 18 - tests/testthat/test-utils_assert.R | 8 tests/testthat/test-utils_callr.R | 21 -- tests/testthat/test-utils_data.R | 6 tests/testthat/test-utils_files.R | 113 ++++++------ tests/testthat/test-utils_oop.R | 4 131 files changed, 1769 insertions(+), 952 deletions(-)
More information about soilassessment at CRAN
Permanent link
Title: Simple Blinding Index for Randomized Controlled Trials
Description: Computes a simple blinding index for randomized controlled trials introduced in Petroff, Bacak, Dagres, Dilk, Wachter: A simple blinding index for randomized controlled trials. Contemp Clin Trials Commun. 2024 Nov 26;42:101393. <doi:10.1016/j.conctc.2024.101393>. PMID: 39686958.
Author: David Petroff [aut, cre, cph],
Miroslav Bacak [aut, cph]
Maintainer: David Petroff <david.petroff@zks.uni-leipzig.de>
Diff between SBI versions 0.1.1 dated 2024-09-11 and 0.1.2 dated 2025-01-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/sbi.R | 10 ++++------ man/BlindingIndex.Rd | 6 ++---- 4 files changed, 13 insertions(+), 17 deletions(-)
Title: Manipulate and Play 'ProTracker' Modules
Description: 'ProTracker' is a popular music tracker to sequence
music on a Commodore Amiga machine. This package offers the
opportunity to import, export, manipulate and play 'ProTracker'
module files. Even though the file format could be considered
archaic, it still remains popular to this date. This package
intends to contribute to this popularity and therewith
keeping the legacy of 'ProTracker' and the Commodore Amiga
alive.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ProTrackR versions 0.4.3 dated 2024-02-15 and 0.4.4 dated 2025-01-13
ProTrackR-0.4.3/ProTrackR/R/10ModArchiveHelpers.r |only ProTrackR-0.4.3/ProTrackR/R/11MODPlugHelpers.r |only ProTrackR-0.4.3/ProTrackR/R/12ModLandHelpers.r |only ProTrackR-0.4.3/ProTrackR/man/modArchive.Rd |only ProTrackR-0.4.3/ProTrackR/man/modLand.Rd |only ProTrackR-0.4.4/ProTrackR/DESCRIPTION | 10 ProTrackR-0.4.4/ProTrackR/MD5 | 76 ProTrackR-0.4.4/ProTrackR/NEWS.md | 472 +- ProTrackR-0.4.4/ProTrackR/R/01supporting_functions.r | 1158 +++--- ProTrackR-0.4.4/ProTrackR/R/02PTCell.r | 1490 ++++---- ProTrackR-0.4.4/ProTrackR/R/03PTTrack.r | 298 - ProTrackR-0.4.4/ProTrackR/R/04PTPattern.r | 346 - ProTrackR-0.4.4/ProTrackR/R/05PTSample.r | 2147 +++++------ ProTrackR-0.4.4/ProTrackR/R/06PTModule.r | 2682 +++++++------- ProTrackR-0.4.4/ProTrackR/R/07PTBlock.r | 314 - ProTrackR-0.4.4/ProTrackR/R/08coercion.r | 1092 ++--- ProTrackR-0.4.4/ProTrackR/R/09playing_routines.r | 3459 +++++++++---------- ProTrackR-0.4.4/ProTrackR/R/10MODPlugHelpers.r |only ProTrackR-0.4.4/ProTrackR/R/ProTrackR-package.r | 332 - ProTrackR-0.4.4/ProTrackR/R/deprecated.R |only ProTrackR-0.4.4/ProTrackR/README.md | 38 ProTrackR-0.4.4/ProTrackR/man/MODPlugToPTPattern.Rd | 4 ProTrackR-0.4.4/ProTrackR/man/PTModule-class.Rd | 2 ProTrackR-0.4.4/ProTrackR/man/PTPatternToMODPlug.Rd | 16 ProTrackR-0.4.4/ProTrackR/man/PTSample-method.Rd | 2 ProTrackR-0.4.4/ProTrackR/man/PTTrack-class.Rd | 6 ProTrackR-0.4.4/ProTrackR/man/ProTrackR-package.Rd | 8 ProTrackR-0.4.4/ProTrackR/man/fix.PTModule.Rd | 12 ProTrackR-0.4.4/ProTrackR/man/modToWave.Rd | 6 ProTrackR-0.4.4/ProTrackR/man/note.Rd | 2 ProTrackR-0.4.4/ProTrackR/man/nybble.Rd | 2 ProTrackR-0.4.4/ProTrackR/man/openmpt-deprecated.Rd |only ProTrackR-0.4.4/ProTrackR/man/patternOrder.Rd | 2 ProTrackR-0.4.4/ProTrackR/man/playMod.Rd | 10 ProTrackR-0.4.4/ProTrackR/man/playSample.Rd | 35 ProTrackR-0.4.4/ProTrackR/man/playWave.Rd | 18 ProTrackR-0.4.4/ProTrackR/man/playingtable.Rd | 6 ProTrackR-0.4.4/ProTrackR/man/plot.Rd | 2 ProTrackR-0.4.4/ProTrackR/man/rawToPTModule.Rd | 4 ProTrackR-0.4.4/ProTrackR/man/read.module.Rd | 19 ProTrackR-0.4.4/ProTrackR/man/read.sample.Rd | 7 ProTrackR-0.4.4/ProTrackR/man/write.module.Rd | 7 ProTrackR-0.4.4/ProTrackR/man/write.sample.Rd | 9 43 files changed, 6999 insertions(+), 7094 deletions(-)
Title: Reproducible Integrated Species Distribution Models Across
Norway using 'INLA'
Description: Integration of disparate datasets is needed in order to make efficient use of all available data and thereby address the issues currently threatening biodiversity.
Data integration is a powerful modeling framework which allows us to combine these datasets together into a single model, yet retain the strengths of each individual dataset.
We therefore introduce the package, 'intSDM': an R package designed to help ecologists develop a reproducible workflow of integrated species distribution models, using data both provided from the user as well as data obtained freely online.
An introduction to data integration methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.
Author: Philip Mostert [aut, cre],
Angeline Bruls [aut],
Ragnhild {Bjoerkas} [aut],
Wouter Koch [aut],
Ellen Martin [aut]
Maintainer: Philip Mostert <philip.s.mostert@ntnu.no>
Diff between intSDM versions 2.1.0 dated 2024-08-21 and 2.1.1 dated 2025-01-13
DESCRIPTION | 16 +- MD5 | 56 +++++----- NAMESPACE | 2 R/obtainCovariate.R | 15 ++ R/obtainGBIF.R | 32 ++++- R/obtainRichness.R |only R/sdmWorkflow.R | 119 ++++----------------- R/species_model.R | 107 ++++++++++++++----- R/startWorkflow.R | 2 build/vignette.rds |binary inst/doc/PennsylvaniaWarbler.R | 6 - inst/doc/PennsylvaniaWarbler.Rmd | 8 - inst/doc/PennsylvaniaWarbler.html | 29 ++--- inst/doc/RedList.R | 79 ++++++++------ inst/doc/RedList.Rmd | 135 +++++++++++++----------- inst/doc/RedList.html | 180 +++++++++++++++++---------------- inst/doc/Richness.html | 6 - man/obtainCovariate.Rd | 6 - man/obtainGBIF.Rd | 4 man/obtainRichness.Rd |only man/species_model.Rd | 18 +-- tests/testthat/setup.R |only tests/testthat/test-generateAbsences.R | 48 +++++++- tests/testthat/test-initValues.R | 6 - tests/testthat/test-obtainCovariate.R | 20 +++ tests/testthat/test-obtainGBIF.R | 22 +++- tests/testthat/test-obtainRichness.R |only tests/testthat/test-sdmWorkflow.R | 4 tests/testthat/test-species_model.R | 6 - vignettes/PennsylvaniaWarbler.Rmd | 8 - vignettes/RedList.Rmd | 135 +++++++++++++----------- 31 files changed, 598 insertions(+), 471 deletions(-)
Title: Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data. In
particular representation, manipulation, rate estimation and
simulation for multistate data - the Lexis suite of functions, which
includes interfaces to 'mstate', 'etm' and 'cmprsk' packages.
Contains functions for Age-Period-Cohort and Lee-Carter modeling and
a function for interval censored data and some useful functions for
tabulation and plotting, as well as a number of epidemiological data
sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.58 dated 2024-11-25 and 2.59 dated 2025-01-13
CHANGES | 6 DESCRIPTION | 8 - MD5 | 55 ++++---- NAMESPACE | 2 R/AaJ.Lexis.R | 2 R/ci.eta.R | 4 R/paths.Lexis.R |only inst/doc/aaflup.R | 2 inst/doc/aaflup.pdf |binary inst/doc/aaflup.rnw | 1 inst/doc/addLexis.R | 6 inst/doc/addLexis.pdf |binary inst/doc/addLexis.rnw | 6 inst/doc/crisk.R | 210 ++++++++++++++++----------------- inst/doc/crisk.pdf |binary inst/doc/crisk.rnw | 310 +++++++++++++++++++++++++------------------------ inst/doc/simLexis.R | 94 +++++++++----- inst/doc/simLexis.pdf |binary inst/doc/simLexis.rnw | 43 +++++- inst/doc/yll.R | 61 ++++++--- inst/doc/yll.pdf |binary inst/doc/yll.rnw | 47 +++++-- man/B.dk.Rd | 53 ++++---- man/paths.Lexis.Rd |only vignettes/aaflup.rnw | 1 vignettes/addLexis.rnw | 6 vignettes/crisk.rnw | 310 +++++++++++++++++++++++++------------------------ vignettes/rtall.bat |only vignettes/simLexis.rnw | 43 +++++- vignettes/yll.rnw | 47 +++++-- 30 files changed, 731 insertions(+), 586 deletions(-)
Title: Optimal Adaptive Allocation Using Deep Reinforcement Learning
Description: An implementation to compute an optimal adaptive allocation rule
using deep reinforcement learning in a dose-response study
(Matsuura et al. (2022) <doi:10.1002/sim.9247>).
The adaptive allocation rule can directly optimize a performance metric,
such as power, accuracy of the estimated target dose, or mean absolute error
over the estimated dose-response curve.
Author: Kentaro Matsuura [aut, cre, cph]
,
Koji Makiyama [aut, ctb]
Maintainer: Kentaro Matsuura <matsuurakentaro55@gmail.com>
Diff between RLoptimal versions 1.2.0 dated 2024-12-20 and 1.2.1 dated 2025-01-13
RLoptimal-1.2.0/RLoptimal/tests/testthat/test-generate_setup_code.R |only RLoptimal-1.2.1/RLoptimal/DESCRIPTION | 6 ++-- RLoptimal-1.2.1/RLoptimal/MD5 | 13 ++++------ RLoptimal-1.2.1/RLoptimal/R/rl_dnn_config.R | 1 RLoptimal-1.2.1/RLoptimal/R/simulate_one_trial.R | 2 - RLoptimal-1.2.1/RLoptimal/inst/doc/RLoptimal.html | 4 +-- RLoptimal-1.2.1/RLoptimal/man/rl_dnn_config.Rd | 1 RLoptimal-1.2.1/RLoptimal/man/simulate_one_trial.Rd | 2 - 8 files changed, 13 insertions(+), 16 deletions(-)
Title: Relationship Inference for DNA Mixtures
Description: Analysis of DNA mixtures involving relatives by computation of likelihood ratios that account for dropout and drop-in, mutations, silent alleles and population
substructure. This is useful in kinship cases, like non-invasive prenatal paternity testing, where deductions about individuals' relationships rely on DNA mixtures,
and in criminal cases where the contributors to a mixed DNA stain may be related. Relationships are represented
by pedigrees and can include kinship between more than two individuals. The main function is relMix() and its graphical user interface relMixGUI().
The implementation and method is described in Dorum et al. (2017) <doi:10.1007/s00414-016-1526-x>, Hernandis et al. (2019)
<doi:10.1016/j.fsigss.2019.09.085> and Kaur et al. (2016) <doi:10.1007/s00414-015-1276-1>.
Author: Guro Dorum [aut, cre],
Elias Hernandis [aut],
Navreet Kaur [ctb],
Thore Egeland [ctb],
Magnus Dehli Vigeland [ctb]
Maintainer: Guro Dorum <guro.dorum@gmail.com>
Diff between relMix versions 1.4 dated 2024-04-23 and 1.4.1 dated 2025-01-13
DESCRIPTION | 27 +++++++++++---------- MD5 | 32 ++++++++++++------------- NAMESPACE | 1 NEWS.md | 7 ++++- R/checkFrequenciesFile.R | 2 - R/createDatamatrix.R | 4 +-- R/relMix.R | 13 ++++++---- R/relMixGUI.R | 8 ++++-- README.md | 7 ++++- build/vignette.rds |binary inst/doc/relMix.R | 56 +++++++++++++++++++++---------------------- inst/doc/relMix.Rmd | 60 +++++++++++++++++++++++++---------------------- inst/doc/relMix.html | 42 ++++++++++++++++---------------- man/createDatamatrix.Rd | 4 +-- man/relMix.Rd | 10 ++++--- man/relMixGUI.Rd | 2 - vignettes/relMix.Rmd | 60 +++++++++++++++++++++++++---------------------- 17 files changed, 182 insertions(+), 153 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-05 1.0.2
2021-07-05 1.0.1
2020-09-23 1.0.0
Title: Snapshots for Unit Tests using the 'tinytest' Framework
Description: Snapshots for unit tests using the 'tinytest' framework for R. Includes expectations to test base R and 'ggplot2' plots as well as console output from print().
Author: Vincent Arel-Bundock [aut, cre, cph]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinysnapshot versions 0.0.6 dated 2024-08-23 and 0.0.7 dated 2025-01-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/expect_snapshot_print.R | 28 +++++++++++++++++++++++----- README.md | 20 ++++++++++++++++++++ build/partial.rdb |binary man/expect_snapshot_print.Rd | 3 +++ 7 files changed, 60 insertions(+), 15 deletions(-)
Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager
from Facebook Marketing API into R. For more details see official documents by Facebook
Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev [aut, cre]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rfacebookstat versions 2.11.0 dated 2024-07-11 and 2.12.0 dated 2025-01-13
DESCRIPTION | 6 MD5 | 26 +-- NEWS.md | 3 R/zzz.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/rfacebookstat-authorization.R | 26 +-- inst/doc/rfacebookstat-authorization.html | 8 - inst/doc/rfacebookstat-cost-data.R | 48 +++--- inst/doc/rfacebookstat-cost-data.html | 18 +- inst/doc/rfacebookstat-get-statistics.R | 232 ++++++++++++++--------------- inst/doc/rfacebookstat-get-statistics.Rmd | 2 inst/doc/rfacebookstat-get-statistics.html | 6 vignettes/rfacebookstat-get-statistics.Rmd | 2 14 files changed, 191 insertions(+), 188 deletions(-)
Title: Bayesian partial least squares regression
Description: Fits the Bayesian partial least squares regression model
introduced in Urbas et al. (2024) <doi:10.1214/24-AOAS1947>. Suitable
for univariate and multivariate regression with high-dimensional data.
Author: Szymon Urbas [aut, cre],
Pierre Lovera [ctb],
Robert Daly [ctb],
Alan O'Riordan [ctb],
Donagh Berry [ctb],
Isobel Claire Gormley [ctb]
Maintainer: Szymon Urbas <szymon.urbas@mu.ie>
Diff between bplsr versions 1.0.1 dated 2024-12-02 and 1.0.2 dated 2025-01-13
bplsr-1.0.1/bplsr/man/figures/README-pressure-1.png |only bplsr-1.0.2/bplsr/DESCRIPTION | 6 ++--- bplsr-1.0.2/bplsr/MD5 | 7 ++--- bplsr-1.0.2/bplsr/R/BPLSR.R | 24 +++----------------- bplsr-1.0.2/bplsr/man/bplsr.Rd | 2 - 5 files changed, 11 insertions(+), 28 deletions(-)
Title: Unit Testing for R
Description: Software testing is important, but, in part because it is
frustrating and boring, many of us avoid it. 'testthat' is a testing
framework for R that is easy to learn and use, and integrates with
your existing 'workflow'.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
R Core team [ctb] )
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between testthat versions 3.2.2 dated 2024-12-10 and 3.2.3 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/expect-no-condition.R | 7 ++++++- R/snapshot-reporter.R | 4 +++- tests/testthat/test-expect-no-condition.R | 10 ++++++---- 6 files changed, 30 insertions(+), 14 deletions(-)
Title: Extensions of Package 'distr'
Description: Extends package 'distr' by functionals, distances, and conditional distributions.
Author: Matthias Kohl [cre, cph],
Peter Ruckdeschel [aut, cph]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between distrEx versions 2.9.5 dated 2024-09-02 and 2.9.6 dated 2025-01-13
DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- R/sysdata.rda |binary inst/NEWS | 10 ++++++++++ man/0distrEx-package.Rd | 8 ++++---- 5 files changed, 28 insertions(+), 17 deletions(-)
Title: Fast Conversion of R Colors to Color Component Values and Native
Packed Integer Format
Description: Color values in R are often represented as strings of hexadecimal
colors or named colors. This package offers fast conversion of
these color representations to either an array of red/green/blue/alpha values
or to the packed integer format used in native raster objects. Functions
for conversion are also exported at the 'C' level for use in other packages.
This fast conversion
of colors is implemented using an order-preserving minimal perfect hash
derived from Majewski et al (1996) "A Family of Perfect Hashing Methods"
<doi:10.1093/comjnl/39.6.547>.
Author: Mike Cheng [aut, cre, cph]
Maintainer: Mike Cheng <mikefc@coolbutuseless.com>
Diff between colorfast versions 1.0.0 dated 2024-12-16 and 1.0.1 dated 2025-01-13
colorfast-1.0.0/colorfast/src/col_to_packed_int.c |only colorfast-1.0.1/colorfast/DESCRIPTION | 17 + colorfast-1.0.1/colorfast/LICENSE | 2 colorfast-1.0.1/colorfast/MD5 | 30 +- colorfast-1.0.1/colorfast/NAMESPACE | 2 colorfast-1.0.1/colorfast/NEWS.md | 9 colorfast-1.0.1/colorfast/R/col_to_rgb.R | 46 ++++ colorfast-1.0.1/colorfast/build |only colorfast-1.0.1/colorfast/inst |only colorfast-1.0.1/colorfast/man/col_to_int.Rd | 2 colorfast-1.0.1/colorfast/man/int_to_col.Rd |only colorfast-1.0.1/colorfast/man/set_alpha.Rd |only colorfast-1.0.1/colorfast/src/alpha.c |only colorfast-1.0.1/colorfast/src/col_to_int.c |only colorfast-1.0.1/colorfast/src/col_to_rgb.c | 110 +++++----- colorfast-1.0.1/colorfast/src/init.c | 24 +- colorfast-1.0.1/colorfast/src/int_to_col.c |only colorfast-1.0.1/colorfast/tests/testthat/test-named-colours.R | 23 +- colorfast-1.0.1/colorfast/vignettes |only 19 files changed, 194 insertions(+), 71 deletions(-)
Title: The R WINS Package
Description: Calculate the win statistics (win ratio, net benefit and win odds) for prioritized multiple endpoints, plot the win statistics and win proportions over study time if at least one time-to-event endpoint is analyzed, and simulate datasets with dependent endpoints. The package can handle any type of outcomes (continuous, ordinal, binary, time-to-event) and allow users to perform stratified analysis, inverse probability of censoring weighting (IPCW) and inverse probability of treatment weighting (IPTW) analysis.
Author: Ying Cui [aut, cre],
Bo Huang [aut]
Maintainer: Ying Cui <cuiyingbeicheng@gmail.com>
Diff between WINS versions 1.4.2 dated 2024-04-29 and 1.4.3 dated 2025-01-13
DESCRIPTION | 6 +++--- MD5 | 12 ++++++++---- R/iptw_covipcw.adjusted.KL.R |only R/iptw_covipcw.win.stat.R |only R/iptw_ipcw.adjusted.KL.R |only R/iptw_ipcw.win.stat.R |only R/win.stat.R | 15 +++++++++++++-- inst/doc/vignette.pdf |binary man/win.stat.Rd | 6 +++++- 9 files changed, 29 insertions(+), 10 deletions(-)
Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Description: An interface (wrapper) to MPI. It also
provides interactive R manager and worker environment.
Author: Hao Yu [aut, cre]
Maintainer: Hao Yu <hyu@stats.uwo.ca>
Diff between Rmpi versions 0.7-2.1 dated 2024-09-23 and 0.7-3.1 dated 2025-01-13
DESCRIPTION | 14 MD5 | 6 configure | 2741 +++++++++++++++++++++++++++++++---------------------------- configure.ac | 15 4 files changed, 1476 insertions(+), 1300 deletions(-)
Title: JavaScript Charts Tool
Description: Provides an R interface for using 'AmCharts' Library. Based on
'htmlwidgets', it provides a global architecture to generate 'JavaScript' source
code for charts. Most of classes in the library have their equivalent in R
with S4 classes; for those classes, not all properties have been referenced but
can easily be added in the constructors. Complex properties (e.g. 'JavaScript'
object) can be passed as named list. See examples at
<https://datastorm-open.github.io/introduction_ramcharts/>
and <https://www.amcharts.com/> for
more information about the library. The package includes the free version
of 'AmCharts' Library. Its only limitation is a small link to the web site
displayed on your charts. If you enjoy this library, do not hesitate to refer
to this page <https://www.amcharts.com/online-store/> to purchase a licence,
and thus support its creators and get a period of Priority Support. See also
<https://www.amcharts.com/about/> for more information about 'AmChart [...truncated...]
Author: Benoit Thieurmel [aut, cre],
Antanas Marcelionis [aut, cph]
Maintainer: Benoit Thieurmel <bthieurmel@gmail.com>
Diff between rAmCharts versions 2.1.15 dated 2022-09-30 and 2.1.16 dated 2025-01-13
DESCRIPTION | 8 MD5 | 74 +- NAMESPACE | 1 R/chart_amBarplot.R | 5 R/chart_amFloatingBar.R | 5 R/chart_amGauge.R | 5 R/chart_amRadar.R | 7 R/chart_amTimeSeries.R | 8 R/class_AmChart.R | 3 R/class_AmGraph.R | 2 R/class_AmObject.R | 20 R/class_AmStockChart.R | 3 R/class_DataSet.R | 2 R/shiny_modules_export.R | 10 R/shiny_modules_timeSeries.R | 20 R/union_AmCharts.R | 1 R/utils_amOptions.R | 2 inst/htmlwidgets/lib/plugins/export/README.md | 6 man/AmGraph.Rd | 2 man/DataSet-class.Rd | 2 man/amBarplot.Rd | 5 man/amFloatingBar.Rd | 5 man/amOptions.Rd | 2 man/amPlot.Rd | 8 man/amRadar.Rd | 5 man/amSolidGauge.Rd | 5 man/amTimeSeries.Rd | 18 man/getCurrentStockData.Rd | 4 man/getTransformTS.Rd | 4 man/initialize-AmChart.Rd | 3 man/listProperties-AmObject.Rd | 4 man/methods-AmObject.Rd | 14 man/rAmCharts-shinymodules-ts.Rd | 26 man/rAmCharts-shinymodules.Rd | 10 tests/testthat/test_AmStockChart_setters.R | 66 +- tests/testthat/test_amBoxplot.R | 112 ++-- tests/testthat/test_amchart_setters.R | 330 ++++++------ tests/testthat/test_getAggregateTS.R | 714 +++++++++++++------------- 38 files changed, 731 insertions(+), 790 deletions(-)
Title: Get Data from the French National Database on Water 'Hub'Eau'
Description: Collection of functions to help retrieving data from
'Hub'Eau' the free and public French National APIs on water
<https://hubeau.eaufrance.fr/>.
Author: David Dorchies [aut, cre] ,
Pascal Irz [ctb] ,
Sebastien Grall [ctb],
Philippe Amiotte Suchet [ctb]
Maintainer: David Dorchies <david.dorchies@inrae.fr>
Diff between hubeau versions 0.5.0 dated 2024-03-04 and 0.5.1 dated 2025-01-13
DESCRIPTION | 9 LICENSE | 4 MD5 | 84 +-- NEWS.md | 7 R/get_ecoulement.R | 170 +++---- R/get_hydrobio.R | 138 ++--- R/get_hydrometrie.R | 301 ++++++------ R/get_indicateurs_services.R | 200 ++++---- R/get_niveaux_nappes.R | 132 ++--- R/get_prelevements.R | 106 ++-- R/get_qualite_eau_potable.R | 122 ++--- R/get_qualite_nappes.R | 100 ++-- R/get_temperature.R | 100 ++-- R/list_apis.R | 64 +- R/list_endpoints.R | 10 R/list_params.R | 24 - README.md | 424 +++++++++--------- build/vignette.rds |binary inst/CITATION | 46 - inst/WORDLIST | 244 +++++----- inst/doc/data_extraction_naiades.R | 70 +- inst/doc/data_extraction_naiades.html | 6 inst/doc/example_ecoulement_api.R | 28 - inst/doc/example_ecoulement_api.html | 48 +- inst/doc/example_niveaux_nappes_api.R | 60 +- inst/doc/example_niveaux_nappes_api.html | 45 + man/convert_list_to_tibble.Rd | 82 +-- man/doApiQuery.Rd | 120 ++--- man/get_ecoulement.Rd | 130 ++--- man/get_hydrobio.Rd | 110 ++-- man/get_hydrometrie.Rd | 138 ++--- man/get_indicateurs_services.Rd | 144 +++--- man/get_niveaux_nappes.Rd | 110 ++-- man/get_prelevements.Rd | 90 +-- man/get_qualite_eau_potable.Rd | 114 ++-- man/get_temperature.Rd | 94 +-- man/lists.Rd | 90 +-- tests/spelling.R | 6 tests/testthat.R | 8 tests/testthat/test-convert_ellipsis_to_params.R | 10 tests/testthat/test-doApiQuery.R | 19 tests/testthat/test-get_hydrometrie_observations_tr.R | 46 - tests/testthat/test-run_all_examples.R | 56 +- 43 files changed, 1976 insertions(+), 1933 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: Hierarchical continuous (and discrete) time state space modelling, for linear
and nonlinear systems measured by continuous variables, with limited support for
binary data. The subject specific dynamic system is modelled as a stochastic
differential equation (SDE) or difference equation, measurement models are typically multivariate normal factor models.
Linear mixed effects SDE's estimated via maximum likelihood and optimization are the default.
Nonlinearities, (state dependent parameters) and random effects on all parameters
are possible, using either max likelihood / max a posteriori optimization
(with optional importance sampling) or Stan's Hamiltonian Monte Carlo sampling.
See <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf>
for details. Priors may be used. For the conceptual overview of the hierarchical Bayesian
linear SDE approach,
see <https://www.researchgate.net/publication/324093594_Hierarchical_Bayesian_Continuous_Time_Dynamic_Mod [...truncated...]
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph],
Trustees of Columbia University [cph]
Maintainer: Charles Driver <charles.driver2@uzh.ch>
Diff between ctsem versions 3.10.1 dated 2024-08-19 and 3.10.2 dated 2025-01-13
DESCRIPTION | 10 MD5 | 51 - NEWS.md | 4 R/ctACF.R | 9 R/ctCheckFit.R | 233 ++++-- R/ctDataHelp.R | 2 R/ctDiscretePars.R | 2 R/ctLOO.R | 228 +++--- R/ctStanFit.R | 5 R/ctSummarise.R | 60 + R/ctTIpredAuto.R | 99 +- R/sgd.R | 24 R/stanoptimis.R | 437 +++++------- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 2 inst/doc/hierarchicalmanual.pdf |binary inst/doc/hierarchicalmanual.rnw | 76 -- man/AnomAuth.Rd | 2 man/ctFitCovCheck.Rd |only man/ctLOO.Rd | 10 man/stanoptimis.Rd | 13 tests/testthat/test-bootstrapScoreHessian.R |only tests/testthat/test-ctLOO.R | 61 + tests/testthat/test-stantipred.R | 2 tests/testthat/test-timevarying.R | 15 vignettes/hierarchicalmanual.rnw | 76 -- vignettes/hierarchicalrefs.bib | 1004 +++++++++++++++++++--------- 28 files changed, 1502 insertions(+), 923 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-10-16 1.1-9
2021-11-18 1.1-8
2021-09-13 1.1-7
2020-12-17 1.1-6
2020-10-31 1.1-5
2020-10-06 1.1-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-06 0.7.1
2020-06-04 0.6.6
2020-02-03 0.6.0
2019-08-22 0.5.7
2019-05-14 0.5.5
2018-04-25 0.5.0
2017-07-10 0.3.4
2016-11-30 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-03 1.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-21 0.2.1
2020-06-04 0.1.9
2019-08-22 0.1.5
2018-12-02 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-29 0.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-10 1.6.0
2023-05-02 1.5.0
2020-02-19 1.4.1
2020-02-04 1.3.2