Title: Summary Plots with Adjusted Error Bars
Description: Computes standard error and confidence interval of various descriptive statistics under
various designs and sampling schemes. The main function, superb(), return a plot. It can
also be used to obtain a dataframe with the statistics and their precision intervals
so that other plotting environments (e.g., Excel)
can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109>
or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005)
<doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012)
<doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>,
Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding
<doi:10.20982/tqmp.15.1.p001> for specific references.
The documentation is available at <https://dcousin3.github.io/superb/> .
Author: Denis Cousineau [aut, cre],
Bradley Harding [ctb],
Marc-Andre Goulet [ctb],
Jesika Walker [art, pre]
Maintainer: Denis Cousineau <denis.cousineau@uottawa.ca>
Diff between superb versions 1.0.0 dated 2025-08-18 and 1.0.1 dated 2025-12-04
DESCRIPTION | 36 +- MD5 | 66 ++-- NEWS.md | 6 R/grd.R | 2 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/CustomizingSuperbPlots.R | 10 inst/doc/CustomizingSuperbPlots.Rmd | 10 inst/doc/CustomizingSuperbPlots.html | 158 +++++----- inst/doc/TheMakingOf.html | 12 inst/doc/Vignette3.html | 4 inst/doc/Vignette4.html | 4 inst/doc/Vignette5.html | 22 - inst/doc/Vignette6.html | 46 +- inst/doc/Vignette7.html | 2 inst/doc/Vignette8.html | 2 inst/doc/Vignette9.html | 12 inst/doc/VignetteA.html | 32 +- inst/doc/VignetteB.html | 4 inst/doc/VignetteC.Rmd | 6 inst/doc/VignetteC.html | 18 - inst/doc/VignetteE.html | 2 inst/doc/VignetteF.R | 4 inst/doc/VignetteF.Rmd | 4 inst/doc/VignetteF.html | 6 inst/doc/VignetteH.html | 14 inst/superbShiny/App.R | 8 inst/superbShiny/rsconnect/shinyapps.io/dcousin3/superbshiny.dcf | 2 man/GRD.Rd | 2 tests/testthat/test_GRD.R | 29 + vignettes/CustomizingSuperbPlots.Rmd | 10 vignettes/VignetteC.Rmd | 6 vignettes/VignetteF.Rmd | 4 34 files changed, 283 insertions(+), 262 deletions(-)
Title: Bayesian Additive Regression Trees with Stan-Sampled Parametric
Extensions
Description: Fits semiparametric linear and multilevel models with non-parametric additive Bayesian additive regression tree (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) components and Stan (Stan Development Team (2021) <https://mc-stan.org/>) sampled parametric ones. Multilevel models can be expressed using 'lme4' syntax (Bates, Maechler, Bolker, and Walker (2015) <doi:10.18637/jss.v067.i01>).
Author: Vincent Dorie [aut, cre] ,
Ben Goodrich [ctb] ,
Jonah Gabry [ctb] ,
Imad Ali [ctb] ,
Sam Brilleman [ctb] ,
Paul-Christian Burkner [ctb] ,
Joshua Pritikin [ctb] ,
Andrew Gelman [ctb] ,
Bob Carpenter [ctb] ,
Matt Hoffman [ctb] ,
Daniel Lee [ctb] ,
Mich [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between stan4bart versions 0.0-10 dated 2024-09-04 and 0.0-11 dated 2025-12-04
DESCRIPTION | 39 - MD5 | 8 R/lme4_functions.R | 1482 ++++++++++++++++++++++++++++++----------------------- configure | 5 configure.ac | 5 5 files changed, 871 insertions(+), 668 deletions(-)
Title: Statistical Methods for Anthropometric Data
Description: Statistical methodologies especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based on clustering, the statistical concept of data depth, statistical shape analysis and archetypal analysis. Please see Vinue (2017) <doi:10.18637/jss.v077.i06>.
Author: Guillermo Vinue [aut, cre],
Irene Epifanio [aut],
Amelia Simo [aut],
M. Victoria Ibanez [aut],
Juan Domingo [aut],
Guillermo Ayala [aut]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between Anthropometry versions 1.20 dated 2025-07-23 and 1.21 dated 2025-12-04
Anthropometry-1.20/Anthropometry/R/CCbiclustAnthropo.R |only Anthropometry-1.20/Anthropometry/R/overlapBiclustersByRows.R |only Anthropometry-1.20/Anthropometry/man/CCbiclustAnthropo.Rd |only Anthropometry-1.20/Anthropometry/man/overlapBiclustersByRows.Rd |only Anthropometry-1.21/Anthropometry/DESCRIPTION | 11 +++---- Anthropometry-1.21/Anthropometry/MD5 | 14 +++------- Anthropometry-1.21/Anthropometry/NAMESPACE | 6 ---- Anthropometry-1.21/Anthropometry/NEWS | 4 ++ Anthropometry-1.21/Anthropometry/inst/doc/Anthropometry.pdf |binary Anthropometry-1.21/Anthropometry/man/Anthropometry-package.Rd | 6 +--- 10 files changed, 16 insertions(+), 25 deletions(-)
Title: Interface for Multilevel Regression and Poststratification
Description: Dual interfaces, graphical and programmatic, designed for
intuitive applications of Multilevel Regression and Poststratification (MRP).
Users can apply the method to a variety of datasets, from electronic health records
to sample survey data, through an end-to-end Bayesian data analysis workflow.
The package provides robust tools for data cleaning, exploratory analysis,
flexible model building, and insightful result visualization. For more details, see
Si et al. (2020) <https://www150.statcan.gc.ca/n1/en/pub/12-001-x/2020002/article/00003-eng.pdf?st=iF1_Fbrh>
and Si (2025) <doi:10.1214/24-STS932>.
Author: Toan Tran [cre, aut, cph],
Jonah Gabry [aut, cph],
Yajuan Si [aut, cph]
Maintainer: Toan Tran <trannttoan97@gmail.com>
Diff between shinymrp versions 0.9.1 dated 2025-11-11 and 0.10.0 dated 2025-12-04
shinymrp-0.10.0/shinymrp/DESCRIPTION | 12 shinymrp-0.10.0/shinymrp/MD5 | 65 - shinymrp-0.10.0/shinymrp/NEWS.md | 12 shinymrp-0.10.0/shinymrp/R/fct_data.R | 7 shinymrp-0.10.0/shinymrp/R/fct_data_geo.R |only shinymrp-0.10.0/shinymrp/R/fct_model.R | 410 +++++++--- shinymrp-0.10.0/shinymrp/R/global.R | 10 shinymrp-0.10.0/shinymrp/R/mod_analyze_model.R | 42 - shinymrp-0.10.0/shinymrp/R/mod_learn_interface.R | 28 shinymrp-0.10.0/shinymrp/R/model.R | 3 shinymrp-0.10.0/shinymrp/R/shiny_model.R | 3 shinymrp-0.10.0/shinymrp/R/utils_model.R | 109 ++ shinymrp-0.10.0/shinymrp/R/utils_ui.R | 38 shinymrp-0.10.0/shinymrp/R/workflow.R | 36 shinymrp-0.10.0/shinymrp/build/vignette.rds |binary shinymrp-0.10.0/shinymrp/inst/doc/data-prep.Rmd | 1 shinymrp-0.10.0/shinymrp/inst/doc/data-prep.html | 3 shinymrp-0.10.0/shinymrp/inst/doc/spatial-prior.R |only shinymrp-0.10.0/shinymrp/inst/doc/spatial-prior.Rmd |only shinymrp-0.10.0/shinymrp/inst/doc/spatial-prior.html |only shinymrp-0.10.0/shinymrp/inst/doc/workflow.R | 6 shinymrp-0.10.0/shinymrp/inst/doc/workflow.Rmd | 8 shinymrp-0.10.0/shinymrp/inst/doc/workflow.html | 25 shinymrp-0.10.0/shinymrp/inst/scripts/utils.R | 4 shinymrp-0.10.0/shinymrp/man/MRPModel-method-summary.Rd | 3 shinymrp-0.10.0/shinymrp/man/MRPWorkflow-method-create_model.Rd | 13 shinymrp-0.10.0/shinymrp/tests/testthat/test-model-helper.R |only shinymrp-0.10.0/shinymrp/tests/testthat/test-mrp-model.R | 2 shinymrp-0.10.0/shinymrp/vignettes/data-prep.Rmd | 1 shinymrp-0.10.0/shinymrp/vignettes/data/spatial_prior |only shinymrp-0.10.0/shinymrp/vignettes/data/workflow |only shinymrp-0.10.0/shinymrp/vignettes/figures/sample_size_map.png |only shinymrp-0.10.0/shinymrp/vignettes/spatial-prior.Rmd |only shinymrp-0.10.0/shinymrp/vignettes/workflow.Rmd | 8 shinymrp-0.9.1/shinymrp/vignettes/data/loo.csv |only shinymrp-0.9.1/shinymrp/vignettes/data/model.qs2 |only shinymrp-0.9.1/shinymrp/vignettes/data/workflow.qs2 |only shinymrp-0.9.1/shinymrp/vignettes/spatial_prior.html |only 38 files changed, 607 insertions(+), 242 deletions(-)
Title: qPCR Data Analysis
Description: Various methods are employed for statistical analysis and graphical presentation of real-time PCR (quantitative PCR or qPCR) data. 'rtpcr' handles amplification efficiency calculation, statistical analysis and graphical representation of real-time PCR data based on up to two reference genes. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor), analysis of variance (ANOVA), analysis of covariance (ANCOVA) or analysis of repeated measure data to calculate the fold change (FC, Delta Delta Ct method) or relative expression (RE, Delta Ct method). The functions further provide standard errors and confidence intervals for means, a [...truncated...]
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <gh.mirzaghaderi@uok.ac.ir>
Diff between rtpcr versions 2.0.3 dated 2025-11-08 and 2.0.4 dated 2025-12-04
DESCRIPTION | 6 MD5 | 61 +++++---- R/package_data.r | 66 +++++----- R/qpcrANOVAFC.r | 6 data/Lee_etal2020qPCR.rda |binary data/Taylor_etal2019.rda |binary data/data_1factor.rda |binary data/data_2factor.rda |binary data/data_2factorBlock.rda |binary data/data_3factor.rda |binary data/data_repeated_measure_1.rda |binary data/data_repeated_measure_2.rda |binary data/data_withTechRep.rda |binary inst/CITATION |only inst/doc/vignette.html | 192 +++++++++++++++---------------- inst/extdata/Lee_etal2020qPCR.csv | 2 inst/extdata/data_1factor.csv | 2 inst/extdata/data_2factor.csv | 2 inst/extdata/data_2factorBlock.csv | 2 inst/extdata/data_3factor.csv | 2 inst/extdata/data_repeated_measure_1.csv | 2 inst/extdata/data_repeated_measure_2.csv | 2 inst/extdata/data_withTechRep.csv | 2 man/Lee_etal2020qPCR.Rd | 8 - man/data_1factor.Rd | 10 - man/data_2factor.Rd | 8 - man/data_2factorBlock.Rd | 8 - man/data_3factor.Rd | 8 - man/data_repeated_measure_1.Rd | 8 - man/data_repeated_measure_2.Rd | 8 - man/data_withTechRep.Rd | 8 - man/qpcrANOVAFC.Rd | 6 32 files changed, 209 insertions(+), 210 deletions(-)
Title: Interface to the 'nanoarrow' 'C' Library
Description: Provides an 'R' interface to the 'nanoarrow' 'C' library and the
'Apache Arrow' application binary interface. Functions to import and
export 'ArrowArray', 'ArrowSchema', and 'ArrowArrayStream' 'C' structures
to and from 'R' objects are provided alongside helpers to facilitate zero-copy
data transfer among 'R' bindings to libraries implementing the 'Arrow' 'C'
data interface.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between nanoarrow versions 0.7.0-1 dated 2025-09-24 and 0.7.0-2 dated 2025-12-04
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/convert-array.R | 2 ++ tests/testthat/test-altrep.R | 20 ++++++++++++++------ tests/testthat/test-convert-array.R | 12 ------------ 5 files changed, 23 insertions(+), 25 deletions(-)
Title: Statistical Tools for the Analysis of Psychophysical Data
Description: Tools for the analysis of psychophysical data in R. This package allows to estimate the Point of Subjective Equivalence (PSE)
and the Just Noticeable Difference (JND), either from a psychometric function or from a Generalized Linear Mixed Model (GLMM).
Additionally, the package allows plotting the fitted models and the response data, simulating psychometric functions of different shapes, and simulating data sets.
For a description of the use of GLMMs applied to psychophysical data, refer to Moscatelli et al. (2012).
Author: Alessandro Moscatelli [aut, cre] ,
Priscilla Balestrucci [aut]
Maintainer: Alessandro Moscatelli <moskante@gmail.com>
Diff between MixedPsy versions 1.2.0 dated 2025-02-18 and 1.3.0 dated 2025-12-04
DESCRIPTION | 15 ++++---- MD5 | 9 ++--- NAMESPACE | 1 NEWS.md | 5 ++ R/mix_utils.R | 90 +++++++++++++++++++++++++++++++++++++++++++++++--- man/MixInterpolate.Rd |only 6 files changed, 104 insertions(+), 16 deletions(-)
Title: Ensemble Learning Framework for Diagnostic and Prognostic
Modeling
Description: Provides a framework to build and evaluate diagnosis or
prognosis models using stacking, voting, and bagging ensemble
techniques with various base learners. The package also includes
tools for visualization and interpretation of models. The development
version of the package is available on 'GitHub' at
<https://github.com/xiaojie0519/E2E>. The methods
are based on the foundational work of Breiman (1996) <doi:10.1007/BF00058655>
on bagging and Wolpert (1992) <doi:10.1016/S0893-6080(05)80023-1>
on stacking.
Author: Shanjie Luan [aut, cre]
Maintainer: Shanjie Luan <Luan20050519@163.com>
Diff between E2E versions 0.1.1 dated 2025-11-28 and 0.1.2 dated 2025-12-04
DESCRIPTION | 12 ++--- MD5 | 40 +++++++++---------- NAMESPACE | 1 R/diagnosis.R | 21 +-------- R/prognosis.R | 35 ++++++++++------ inst/doc/advanced-features.R | 4 - inst/doc/advanced-features.Rmd | 4 - inst/doc/advanced-features.html | 8 +-- inst/doc/diagnostic-workflow.R | 16 +++---- inst/doc/diagnostic-workflow.Rmd | 16 +++---- inst/doc/diagnostic-workflow.html | 80 +++++++++++++++++++++++++++----------- inst/doc/getting-started.html | 2 inst/doc/integrated-pipeline.R | 6 +- inst/doc/integrated-pipeline.Rmd | 6 +- inst/doc/integrated-pipeline.html | 8 +-- inst/doc/prognostic-workflow.html | 2 man/imbalance_dia.Rd | 6 +- man/xb_dia.Rd | 16 ------- vignettes/advanced-features.Rmd | 4 - vignettes/diagnostic-workflow.Rmd | 16 +++---- vignettes/integrated-pipeline.Rmd | 6 +- 21 files changed, 162 insertions(+), 147 deletions(-)
Title: Hydro-Meteorological Catchments Datasets for the 'airGR'
Packages
Description: Sample of hydro-meteorological datasets extracted from the 'CAMELS-FR' French database <doi:10.57745/WH7FJR>.
It provides metadata and catchment-scale aggregated hydro-meteorological time series on a pool of French catchments for use by the 'airGR' packages.
Author: Olivier Delaigue [aut, cre] ,
Pierre Brigode [aut] ,
Guillaume Thirel [aut] ,
Benoît Genot [ctb],
Guilherme Mendoza Guimaraes [ctb]
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGRdatasets versions 0.2.2 dated 2025-11-18 and 0.2.3 dated 2025-12-04
DESCRIPTION | 8 ++++---- MD5 | 46 +++++++++++++++++++++++----------------------- NEWS.md | 9 +++++++++ README.md | 2 +- build/partial.rdb |binary data/A273011002.rda |binary data/A605102001.rda |binary data/B222001001.rda |binary data/E540031001.rda |binary data/E645651001.rda |binary data/F439000101.rda |binary data/H010002001.rda |binary data/H120101001.rda |binary data/H622101001.rda |binary data/J171171001.rda |binary data/J421191001.rda |binary data/K134181001.rda |binary data/K265401001.rda |binary data/K731261001.rda |binary data/V123521001.rda |binary data/X031001001.rda |binary data/X045401001.rda |binary data/Y643401001.rda |binary data/Y862000101.rda |binary 24 files changed, 37 insertions(+), 28 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>).
Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>) and a tutorial explains applications in survival analysis
(Siegfried et al., 2025, <DOI:10.48550/arXiv.2402.06428>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.108 [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [ctb] ,
Sandra Siegfried [aut] ,
Lucas Kook [aut] ,
Susanne Dandl [ctb] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.3-0 dated 2025-11-18 and 1.3-1 dated 2025-12-04
tram-1.3-0/tram/vignettes/COXME-margsurv-plot-1.pdf |only tram-1.3-0/tram/vignettes/HTECOX-DFS-plot-1.pdf |only tram-1.3-0/tram/vignettes/TVAR-DFS-plot-1.pdf |only tram-1.3-0/tram/vignettes/TVAR-iDFS-plot-1.pdf |only tram-1.3-1/tram/DESCRIPTION | 8 tram-1.3-1/tram/MD5 | 44 - tram-1.3-1/tram/demo/mtram.Rout.save | 48 - tram-1.3-1/tram/demo/survtram.R | 10 tram-1.3-1/tram/demo/survtram.Rout.save | 334 +++++++---- tram-1.3-1/tram/inst/NEWS.Rd | 8 tram-1.3-1/tram/inst/doc/NAMI.Rnw | 2 tram-1.3-1/tram/inst/doc/NAMI.pdf |binary tram-1.3-1/tram/inst/doc/mtram.R | 35 - tram-1.3-1/tram/inst/doc/mtram.Rnw | 43 - tram-1.3-1/tram/inst/doc/mtram.pdf |binary tram-1.3-1/tram/inst/doc/survtram.R | 36 - tram-1.3-1/tram/inst/doc/survtram.Rnw | 215 +++---- tram-1.3-1/tram/inst/doc/survtram.pdf |binary tram-1.3-1/tram/inst/doc/tram.pdf |binary tram-1.3-1/tram/vignettes/NAMI.Rnw | 2 tram-1.3-1/tram/vignettes/mtram.Rnw | 43 - tram-1.3-1/tram/vignettes/survtram-COXME-margsurv-plot-1.pdf |only tram-1.3-1/tram/vignettes/survtram-HTECOX-DFS-plot-1.pdf |only tram-1.3-1/tram/vignettes/survtram-TVAR-DFS-plot-1.pdf |only tram-1.3-1/tram/vignettes/survtram-TVAR-iDFS-plot-1.pdf |only tram-1.3-1/tram/vignettes/survtram.Rnw | 215 +++---- tram-1.3-1/tram/vignettes/survtram.bib | 15 27 files changed, 600 insertions(+), 458 deletions(-)
Title: A Universal Differential Expression Prediction Tool for
Single-Cell and Spatial Genomics Data
Description: One key exploratory analysis step in single-cell genomics data analysis
is the prediction of features with different activity levels. For example, we want
to predict differentially expressed genes (DEGs) in single-cell RNA-seq data,
spatial DEGs in spatial transcriptomics data, or differentially accessible
regions (DARs) in single-cell ATAC-seq data. 'singleCellHaystack' predicts differentially
active features in single cell omics datasets without relying on the clustering
of cells into arbitrary clusters. 'singleCellHaystack' uses Kullback-Leibler
divergence to find features (e.g., genes, genomic regions, etc) that are active
in subsets of cells that are non-randomly positioned inside an input space (such as
1D trajectories, 2D tissue sections, multi-dimensional embeddings, etc). For
the theoretical background of 'singleCellHaystack' we refer to our original paper
Vandenbon and Diez (Nature Communications, 2020) <doi:10.1038/s41467-020-17900-3>
and our update Vandenbon and Diez [...truncated...]
Author: Alexis Vandenbon [aut, cre] ,
Diego Diez [aut]
Maintainer: Alexis Vandenbon <alexis.vandenbon@gmail.com>
Diff between singleCellHaystack versions 1.0.2 dated 2024-01-11 and 1.0.3 dated 2025-12-04
DESCRIPTION | 11 LICENSE | 4 MD5 | 144 - NAMESPACE | 118 - NEWS.md | 78 - R/data.R | 28 R/debug.R | 146 - R/haystack.R | 1276 ++++++++-------- R/haystack_IO.R | 104 - R/haystack_clustering.R | 202 +- R/haystack_clustering_highD.R | 412 ++--- R/haystack_continuous.R | 1394 +++++++++--------- R/haystack_highD.R | 874 +++++------ R/haystack_visualization.R | 474 +++--- R/randomization.R | 98 - R/s3.R | 506 +++--- R/singleCellHaystack-package.R | 20 R/sparse.R | 98 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 60 inst/doc/a01_toy_example.R | 144 - inst/doc/a01_toy_example.Rmd | 240 +-- inst/doc/a01_toy_example.html | 980 ++++++------ man/dat.expression.Rd | 20 man/dat.tsne.Rd | 20 man/default_bandwidth.nrd.Rd | 34 man/extract_row_dgRMatrix.Rd | 42 man/extract_row_lgRMatrix.Rd | 42 man/get_D_KL.Rd | 46 man/get_D_KL_continuous_highD.Rd | 56 man/get_D_KL_highD.Rd | 46 man/get_density.Rd | 62 man/get_dist_two_sets.Rd | 38 man/get_euclidean_distance.Rd | 38 man/get_grid_points.Rd | 42 man/get_log_p_D_KL.Rd | 46 man/get_log_p_D_KL_continuous.Rd | 68 man/get_parameters_haystack.Rd | 42 man/get_reference.Rd | 38 man/haystack.Rd | 184 +- man/haystack_2D.Rd | 62 man/haystack_continuous_highD.Rd | 120 - man/haystack_highD.Rd | 82 - man/hclust_haystack.Rd | 102 - man/hclust_haystack_highD.Rd | 74 man/hclust_haystack_raw.Rd | 50 man/kde2d_faster.Rd | 32 man/kmeans_haystack.Rd | 56 man/kmeans_haystack_highD.Rd | 80 - man/kmeans_haystack_raw.Rd | 54 man/plot_compare_ranks.Rd | 36 man/plot_gene_haystack.Rd | 106 - man/plot_gene_haystack_raw.Rd | 80 - man/plot_gene_set_haystack.Rd | 106 - man/plot_gene_set_haystack_raw.Rd | 74 man/plot_rand_KLD.Rd | 46 man/plot_rand_fit.Rd | 38 man/read_haystack.Rd | 34 man/show_result_haystack.Rd | 114 - man/singleCellHaystack-package.Rd | 58 man/write_haystack.Rd | 32 tests/testthat.R | 8 tests/testthat/test-extract_row.R | 40 tests/testthat/test-haystack_continuous.R | 64 tests/testthat/test-haystack_sparse.R | 78 - vignettes/a01_toy_example.Rmd | 240 +-- vignettes/examples/a02_example_scRNAseq.Rmd | 288 +-- vignettes/examples/a03_example_spatial_visium.Rmd | 198 +- vignettes/examples/a04_example_spatial_slideseqV2.Rmd | 198 +- vignettes/examples/a05_moca_100k.Rmd | 182 +- vignettes/examples/a07_gene_sets.Rmd | 174 +- vignettes/examples/a08_gene_clustering.Rmd | 268 +-- 73 files changed, 5727 insertions(+), 5722 deletions(-)
More information about singleCellHaystack at CRAN
Permanent link
Title: Spectrally Deconfounded Models
Description: Screen for and analyze non-linear sparse direct effects in the presence of unobserved confounding using the spectral deconfounding techniques (Ćevid, Bühlmann, and Meinshausen (2020)<jmlr.org/papers/v21/19-545.html>, Guo, Ćevid, and Bühlmann (2022) <doi:10.1214/21-AOS2152>). These methods have been shown to be a good estimate for the true direct effect if we observe many covariates, e.g., high-dimensional settings, and we have fairly dense confounding. Even if the assumptions are violated, it seems like there is not much to lose, and the deconfounded models will, in general, estimate a function closer to the true one than classical least squares optimization. 'SDModels' provides functions SDAM() for Spectrally Deconfounded Additive Models (Scheidegger, Guo, and Bühlmann (2025) <doi:10.1145/3711116>) and SDForest() for Spectrally Deconfounded Random Forests (Ulmer, Scheidegger, and Bühlmann (2025) <doi:10.48550/arXiv.2502.03969>).
Author: Markus Ulmer [aut, cre, cph] ,
Cyrill Scheidegger [aut]
Maintainer: Markus Ulmer <markus.ulmer@stat.math.ethz.ch>
Diff between SDModels versions 1.0.13 dated 2025-06-05 and 2.0.0 dated 2025-12-04
SDModels-1.0.13/SDModels/R/List.R |only SDModels-1.0.13/SDModels/R/copy.R |only SDModels-1.0.13/SDModels/man/copy.SDForest.Rd |only SDModels-1.0.13/SDModels/man/copy.SDTree.Rd |only SDModels-1.0.13/SDModels/man/fromList.SDForest.Rd |only SDModels-1.0.13/SDModels/man/fromList.SDTree.Rd |only SDModels-1.0.13/SDModels/man/print.SDTree.Rd |only SDModels-1.0.13/SDModels/man/toList.SDForest.Rd |only SDModels-1.0.13/SDModels/man/toList.SDTree.Rd |only SDModels-2.0.0/SDModels/DESCRIPTION | 16 - SDModels-2.0.0/SDModels/MD5 | 88 ++---- SDModels-2.0.0/SDModels/NAMESPACE | 12 SDModels-2.0.0/SDModels/NEWS.md | 9 SDModels-2.0.0/SDModels/R/SDAM.R | 2 SDModels-2.0.0/SDModels/R/SDForest.R | 122 +++----- SDModels-2.0.0/SDModels/R/SDTree.R | 176 ++++-------- SDModels-2.0.0/SDModels/R/cvSDTree.R | 56 +-- SDModels-2.0.0/SDModels/R/get_cp_seq.R | 4 SDModels-2.0.0/SDModels/R/paths.R | 14 SDModels-2.0.0/SDModels/R/plot.R | 66 +++- SDModels-2.0.0/SDModels/R/predict.R | 50 ++- SDModels-2.0.0/SDModels/R/print.R | 24 - SDModels-2.0.0/SDModels/R/prune.R | 22 - SDModels-2.0.0/SDModels/R/simData.R | 80 +++-- SDModels-2.0.0/SDModels/R/transformations.R | 20 - SDModels-2.0.0/SDModels/R/utility.R | 93 ++---- SDModels-2.0.0/SDModels/R/varImp.R | 18 - SDModels-2.0.0/SDModels/README.md | 26 - SDModels-2.0.0/SDModels/build/partial.rdb |binary SDModels-2.0.0/SDModels/build/vignette.rds |binary SDModels-2.0.0/SDModels/inst/CITATION | 10 SDModels-2.0.0/SDModels/inst/REFERENCES.bib | 17 - SDModels-2.0.0/SDModels/inst/doc/Runtime.R | 5 SDModels-2.0.0/SDModels/inst/doc/Runtime.Rmd | 9 SDModels-2.0.0/SDModels/inst/doc/Runtime.html | 36 -- SDModels-2.0.0/SDModels/man/SDForest.Rd | 9 SDModels-2.0.0/SDModels/man/SDTree.Rd | 13 SDModels-2.0.0/SDModels/man/cvSDTree.Rd | 9 SDModels-2.0.0/SDModels/man/figures/README-SDTree-1.png |binary SDModels-2.0.0/SDModels/man/figures/README-SDTreeplot-1.png |only SDModels-2.0.0/SDModels/man/get_Q.Rd | 5 SDModels-2.0.0/SDModels/man/get_W.Rd | 5 SDModels-2.0.0/SDModels/man/plot.SDTree.Rd | 17 - SDModels-2.0.0/SDModels/man/prune.SDForest.Rd | 4 SDModels-2.0.0/SDModels/man/prune.SDTree.Rd | 5 SDModels-2.0.0/SDModels/man/regPath.SDForest.Rd | 6 SDModels-2.0.0/SDModels/man/simulate_data_step.Rd | 19 - SDModels-2.0.0/SDModels/tests/testthat/test-parallel.R | 4 SDModels-2.0.0/SDModels/tests/testthat/test-tree.R | 7 SDModels-2.0.0/SDModels/vignettes/Runtime.Rmd | 9 50 files changed, 488 insertions(+), 599 deletions(-)
Title: Bridging the Gap Between Qualitative Data and Quantitative
Analysis
Description: Automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse
including frequency counts of sentence types, words, sentences, turns of talk, syllables and other assorted
analysis tasks. The package provides parsing tools for preparing transcript data. Many functions enable the user
to aggregate data by any number of grouping variables, providing analysis and seamless integration with other R
packages that undertake higher level analysis and visualization of text. This affords the user a more efficient
and targeted analysis. 'qdap' is designed for transcript analysis, however, many functions are applicable to other
areas of Text Mining/ Natural Language Processing.
Author: Tyler Rinker [aut, cre],
Bryan Goodrich [ctb],
Dason Kurkiewicz [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdap versions 2.4.6 dated 2023-05-11 and 2.4.6.1 dated 2025-12-04
DESCRIPTION | 8 +-- MD5 | 73 +++++++++++++++++----------------- R/check_text.R | 2 R/lexical_classification.R | 2 R/new_project.R | 18 ++++---- R/qdap-package.R | 2 R/trans_venn.R | 2 R/word_stats.R | 2 build |only data/DATA.SPLIT.rda |binary data/DATA.rda |binary data/DATA2.rda |binary data/env.syl.rda |binary data/hamlet.rda |binary data/mraja1.rda |binary data/mraja1spl.rda |binary data/pres_debate_raw2012.rda |binary data/pres_debates2012.rda |binary data/raj.act.1.rda |binary data/raj.act.1POS.rda |binary data/raj.act.2.rda |binary data/raj.act.3.rda |binary data/raj.act.4.rda |binary data/raj.act.5.rda |binary data/raj.demographics.rda |binary data/raj.rda |binary data/rajPOS.rda |binary data/rajSPLIT.rda |binary data/raw.time.span.rda |binary data/sample.time.span.rda |binary man/check_text.Rd | 2 man/env.syl.Rd | 2 man/new_project.Rd | 16 +++---- man/plot.lexical.Rd | 2 man/qdap.Rd | 19 ++++++++ man/trans_venn.Rd | 2 man/word_stats.Rd | 2 tests/testthat/test-dispersion_plot.R | 2 38 files changed, 88 insertions(+), 68 deletions(-)
Title: Policy Learning
Description: Package for learning and evaluating (subgroup) policies via doubly robust loss functions. Policy learning methods include doubly robust blip/conditional average treatment effect learning and sequential policy tree learning. Methods for (subgroup) policy evaluation include doubly robust cross-fitting and online estimation/sequential validation. See Nordland and Holst (2022) <doi:10.48550/arXiv.2212.02335> for documentation and references.
Author: Andreas Nordland [aut, cre],
Klaus Holst [aut]
Maintainer: Andreas Nordland <andreasnordland@gmail.com>
Diff between polle versions 1.6.1 dated 2025-12-01 and 1.6.2 dated 2025-12-04
DESCRIPTION | 6 +-- MD5 | 22 +++++------ R/g_models.R | 52 ++++++++++++++++----------- R/q_models.R | 55 ++++++++++++++++------------ inst/doc/policy_data.html | 6 +-- inst/doc/policy_eval.html | 6 +-- inst/doc/policy_learn.html | 6 +-- man/g_model.Rd | 14 +++---- man/q_model.Rd | 14 +++---- tests/testthat/test-g_xgboost.R | 77 +++++++++++++++++++++------------------- tests/testthat/test-q_sl.R | 3 + tests/testthat/test-q_xgboost.R | 31 ++++++++++------ 12 files changed, 162 insertions(+), 130 deletions(-)
Title: Download and Manipulate Data from Istat
Description: Download data from ISTAT (Italian Institute of Statistics) database, both old and new provider (respectively, <http://dati.istat.it/> and <https://esploradati.istat.it/databrowser/>). Additional functions for manipulating data are provided. Moreover, a 'shiny' application called 'shinyIstat' can be used to search, download and filter datasets in an easier way.
Author: Elena Gradi [aut, cre],
Alissa Lelli [aut],
Daniela Ichim [aut]
Maintainer: Elena Gradi <elenaagradi@gmail.com>
This is a re-admission after prior archival of version 1.0 dated 2024-09-10
Diff between istat versions 1.0 dated 2024-09-10 and 1.1.1 dated 2025-12-04
DESCRIPTION | 12 MD5 | 54 - NAMESPACE | 178 +-- R/filter_istat.R | 118 +- R/filter_istat_interactive.R | 178 +-- R/get_i_stat.R | 233 ++-- R/get_istatdata.R | 218 ++-- R/list_i_stat.R | 97 + R/list_istatdata.R | 479 ++++----- R/plot_interactive.R | 196 +-- R/search_i_stat.R | 181 +-- R/search_istatdata.R | 566 +++++----- R/shinyIstat.R | 704 ++++++++----- build/vignette.rds |binary inst/doc/Get_started_with_istat_package.R | 18 inst/doc/Get_started_with_istat_package.Rmd | 646 +++++------- inst/doc/Get_started_with_istat_package.html | 1407 +++++++++++++-------------- man/filter_istat.Rd | 64 - man/filter_istat_interactive.Rd | 50 man/get_i_stat.Rd | 104 + man/get_istatdata.Rd | 104 + man/list_i_stat.Rd | 40 man/list_istatdata.Rd | 40 man/plot_interactive.Rd | 50 man/search_i_stat.Rd | 54 - man/search_istatdata.Rd | 54 - man/shinyIstat.Rd | 44 vignettes/Get_started_with_istat_package.Rmd | 646 +++++------- 28 files changed, 3400 insertions(+), 3135 deletions(-)
Title: Object-Oriented Implementation of Dose Escalation Designs
Description: Implements a wide range of dose escalation
designs. The focus is on model-based designs, ranging from classical and
modern continual reassessment methods (CRMs) based on dose-limiting toxicity
endpoints to dual-endpoint designs taking into account a biomarker/efficacy
outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy
to setup a new design with custom JAGS code. However, it is also possible to
implement 3+3 designs for comparison or models with non-Bayesian estimation.
The whole package is written in a modular form in the S4 class system, making it
very flexible for adaptation to new models, escalation or stopping rules.
Further details are presented in
Sabanes Bove et al. (2019) <doi:10.18637/jss.v089.i10>.
Author: Daniel Sabanes Bove [aut, cre],
Wai Yin Yeung [aut],
Burak Kuersad Guenhan [aut],
Giuseppe Palermo [aut],
Thomas Jaki [aut],
Jiawen Zhu [aut],
Ziwei Liao [aut],
Dimitris Kontos [aut],
Marlene Schulte-Goebel [aut],
Doug Kelkhoff [aut] ,
Oliver Boix [a [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between crmPack versions 2.0.0 dated 2025-11-29 and 2.0.1 dated 2025-12-04
DESCRIPTION | 6 MD5 | 48 +-- NEWS.md | 6 R/Model-validity.R | 2 build/partial.rdb |binary inst/doc/ordinal-crm.html | 88 +++--- inst/doc/tidy_method.html | 28 +- inst/doc/trial_analysis.html | 348 +++++++++++++-------------- inst/doc/trial_definition.html | 2 inst/doc/upgrading_from_the_old_crmPack.html | 15 - man/nextBest.Rd | 29 +- man/stopTrial.Rd | 57 +--- tests/testthat/helper-testthat.R | 23 + tests/testthat/test-Design-methods.R | 50 +-- tests/testthat/test-Model-class.R | 156 ++++++------ tests/testthat/test-Model-methods.R | 4 tests/testthat/test-Model-validity.R | 30 +- tests/testthat/test-Rules-methods.R | 62 ++-- tests/testthat/test-Samples-methods.R | 50 +-- tests/testthat/test-Simulations-methods.R | 32 +- tests/testthat/test-fromQuantiles.R | 8 tests/testthat/test-helpers_jags.R | 4 tests/testthat/test-helpers_knitr.R | 16 - tests/testthat/test-sas-results-part-1.R | 8 tests/testthat/test-sas-results-part-2.R | 8 25 files changed, 547 insertions(+), 533 deletions(-)
Title: General Utility Functions for Analysis of Clinical Data
Description: Utility functions to facilitate the import,
the reporting and analysis of clinical data.
Example datasets in 'SDTM' and 'ADaM' format, containing a subset of patients/domains
from the 'CDISC Pilot 01 study' are also available as R datasets to demonstrate
the package functionalities.
Author: Laure Cougnaud [aut, cre],
Michela Pasetto [aut],
Arne De Roeck [rev] ,
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between clinUtils versions 0.2.1 dated 2025-09-03 and 0.2.2 dated 2025-12-04
DESCRIPTION | 10 ++-- MD5 | 14 +++--- build/vignette.rds |binary data/dataADaMCDISCP01.RData |binary data/dataSDTMCDISCP01.RData |binary inst/NEWS | 2 inst/doc/clinUtils-vignette.html | 81 +++++++++++++++++++-------------------- tests/testthat/test_getClinDT.R | 6 +- 8 files changed, 58 insertions(+), 55 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-10 1.21
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-17 0.3.3
2022-06-20 0.3.1
2020-06-10 0.3.0
2020-01-08 0.2.3
2019-06-05 0.2.2
2019-01-02 0.2.1
2018-04-20 0.1.4
2018-04-20 0.1.5
2017-11-18 0.1.3
2017-09-10 0.1.2
2017-06-09 0.1.1
2016-10-05 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-19 2.1.0
2024-11-22 2.0.1
2024-09-12 2.0.0
2024-01-09 1.2.1
2023-09-12 1.2.0
2023-04-15 1.1.0
2023-01-23 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-25 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-08 1.2.3
2021-03-18 1.2.2
2020-10-07 1.2.1
2020-09-22 1.2.0
2020-06-04 1.1.0
2020-05-18 1.0.0
Title: Next Eigenvalue Sufficiency Test
Description: Determine the number of dimensions to retain in exploratory factor analysis. The main function, nest(), returns the solution and the plot(nest()) returns a plot.
Author: P.-O. Caron [aut, cre, cph]
Maintainer: P.-O. Caron <pocaron19@gmail.com>
Diff between Rnest versions 1.2 dated 2025-06-19 and 1.3 dated 2025-12-04
DESCRIPTION | 10 +++++----- MD5 | 14 ++++++++------ NAMESPACE | 2 +- R/cor_nest.R | 17 ++++++++++------- R/fareg.R |only R/nest.R | 5 ++--- man/cov_nest.Rd | 6 +++--- man/fareg.Rd |only man/nest.Rd | 2 +- 9 files changed, 30 insertions(+), 26 deletions(-)
Title: Presenting Statistical Results Effectively
Description: Includes functions and data used in the book "Presenting Statistical Results Effectively", Andersen and Armstrong (2022, ISBN: 978-1446269800). Several functions aid in data visualization - creating compact letter displays for simple slopes, kernel density estimates with normal density overlay. Other functions aid in post-model evaluation heatmap fit statistics for binary predictors, several variable importance measures, compact letter displays and simple-slope calculation. Finally, the package makes available the example datasets used in the book.
Author: Dave Armstrong [aut, cre],
Robert Andersen [aut],
Justin Esarey [cph],
John Fox [cph],
Michael Friendly [cph],
Adrian Bowman [cph],
Adelchi Azzalini [cph]
Maintainer: Dave Armstrong <davearmstrong.ps@gmail.com>
Diff between psre versions 0.2 dated 2025-11-24 and 0.3 dated 2025-12-04
DESCRIPTION | 12 ++-- MD5 | 6 +- NAMESPACE | 4 + R/effective_functions.r | 139 +++++++++++++++++++++++++++++++++++++++++++++++- 4 files changed, 150 insertions(+), 11 deletions(-)
Title: Header-Only 'C++' and 'R' Interface
Description: Provides a header only, 'C++' interface to 'R' with enhancements over 'cpp11'. Enforces copy-on-write
semantics consistent with 'R' behavior. Offers native support for ALTREP objects, 'UTF-8' string handling, modern
'C++11' features and idioms, and reduced memory requirements. Allows for vendoring, making it useful for restricted
environments. Compared to 'cpp11', it adds support for converting 'C++' maps to 'R' lists, 'Roxygen' documentation
directly in 'C++' code, proper handling of matrix attributes, support for nullable external pointers, bidirectional
copy of complex number types, flexibility in type conversions, use of nullable pointers, and various performance
optimizations.
Author: Mauricio Vargas Sepulveda [aut, cre] ,
Posit Software, PBC [aut]
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
Diff between cpp4r versions 0.3.0 dated 2025-10-16 and 0.4.0 dated 2025-12-04
cpp4r-0.3.0/cpp4r/README.md |only cpp4r-0.3.0/cpp4r/inst/include/fmt |only cpp4r-0.4.0/cpp4r/DESCRIPTION | 13 cpp4r-0.4.0/cpp4r/MD5 | 82 cpp4r-0.4.0/cpp4r/NEWS.md | 10 cpp4r-0.4.0/cpp4r/R/register.R | 142 cpp4r-0.4.0/cpp4r/R/template.R | 8 cpp4r-0.4.0/cpp4r/R/unvendor.R | 32 cpp4r-0.4.0/cpp4r/R/vendor.R | 13 cpp4r-0.4.0/cpp4r/inst/WORDLIST | 3 cpp4r-0.4.0/cpp4r/inst/extdata/pkgtemplate/README.md | 14 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/R.hpp | 88 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/as.hpp | 136 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/attribute_proxy.hpp | 34 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/complexes.hpp | 252 - cpp4r-0.4.0/cpp4r/inst/include/cpp4r/cpp_version.hpp |only cpp4r-0.4.0/cpp4r/inst/include/cpp4r/data_frame.hpp | 63 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/doubles.hpp | 161 - cpp4r-0.4.0/cpp4r/inst/include/cpp4r/environment.hpp | 122 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/external_pointer.hpp | 79 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/function.hpp | 44 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/integers.hpp | 217 - cpp4r-0.4.0/cpp4r/inst/include/cpp4r/list.hpp | 61 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/list_of.hpp | 47 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/logicals.hpp | 281 - cpp4r-0.4.0/cpp4r/inst/include/cpp4r/matrix.hpp | 292 - cpp4r-0.4.0/cpp4r/inst/include/cpp4r/named_arg.hpp | 59 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/protect.hpp | 192 - cpp4r-0.4.0/cpp4r/inst/include/cpp4r/r_bool.hpp | 64 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/r_complex.hpp | 124 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/r_string.hpp | 52 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/r_vector.hpp | 1561 ---------- cpp4r-0.4.0/cpp4r/inst/include/cpp4r/r_vector_fwd.hpp |only cpp4r-0.4.0/cpp4r/inst/include/cpp4r/r_vector_impl.hpp |only cpp4r-0.4.0/cpp4r/inst/include/cpp4r/r_vector_writable_impl.hpp |only cpp4r-0.4.0/cpp4r/inst/include/cpp4r/raws.hpp | 297 - cpp4r-0.4.0/cpp4r/inst/include/cpp4r/sexp.hpp | 134 cpp4r-0.4.0/cpp4r/inst/include/cpp4r/strings.hpp | 333 -- cpp4r-0.4.0/cpp4r/man/pkg_template.Rd | 4 cpp4r-0.4.0/cpp4r/man/register.Rd | 6 cpp4r-0.4.0/cpp4r/man/unvendor.Rd | 4 cpp4r-0.4.0/cpp4r/man/vendor.Rd | 12 cpp4r-0.4.0/cpp4r/tests/testthat/_snaps/register.md | 14 cpp4r-0.4.0/cpp4r/tests/testthat/test-register.R | 42 44 files changed, 1109 insertions(+), 3983 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-16 0.3.1
2024-07-03 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-07 0.5.0
2022-12-11 0.4.5
2022-12-10 0.4.0
2022-06-27 0.3.0
2022-05-29 0.2.0
2022-04-05 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-12 0.9.6-1
2018-04-06 0.9.6
2017-06-08 0.9.5-3
2017-01-19 0.9.5-2
2017-01-18 0.9.5
2016-05-04 0.9.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-17 2.4.1
2020-04-29 2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-12 1.0.3
2020-11-14 0.9.2
2020-07-18 0.9.1
2020-06-09 0.8.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-17 0.1.3
2020-06-04 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-30 0.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-08 0.0.7
2020-03-28 0.0.6
2019-03-14 0.0.5
2018-09-20 0.0.4
2018-07-15 0.0.3
2018-06-20 0.0.2
2018-04-26 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-10 2.2
2021-07-25 2.1
2021-07-12 2.0
2021-07-11 1.1
2021-05-26 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-24 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-05-14 0.0.41
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-20 0.1.4
2022-05-30 0.1.3
2022-05-27 0.1.2
2020-11-08 0.1.1
2020-03-28 0.1.0
2019-09-23 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-11-23 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-04 0.0.0.3
2023-11-14 0.0.0.2
2023-11-02 0.0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-25 2.0.0
2024-06-15 1.0.2
2024-04-09 1.0.1
2024-03-21 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-01 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-25 2.1.2
2022-01-14 2.1.1
2015-10-28 2.1.0
2015-06-18 2.0.0
2013-04-22 1.2.1
2013-03-21 1.2.0
2013-01-30 1.1.0
2012-10-10 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-10 2.2.2
2020-12-06 2.2.1
2020-02-16 2.1.4
2020-01-31 2.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-24 2.5
2025-01-14 2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-27 0.3.0
2022-05-19 0.1.3
Title: Survival Data Analysis using Average Hazard
Description: Performs two-sample comparisons based on average hazard with survival weight (AHSW) or general censoring-free incidence rate (CFIR) proposed by Uno and Horiguchi (2023) <doi:10.1002/sim.9651>.
Author: Hajime Uno [aut] ,
Miki Horiguchi [aut, cre] ,
Zihan Qian [aut]
Maintainer: Miki Horiguchi <horiguchimiki@gmail.com>
Diff between survAH versions 1.0.0 dated 2023-01-17 and 1.2.0 dated 2025-12-04
DESCRIPTION | 20 - MD5 | 43 +- NAMESPACE | 9 NEWS.md | 41 ++ R/ah1.R | 134 +++++--- R/ah1_var4strata.R |only R/ah2.R | 299 +++++++------------ R/ah2_core1.R |only R/ah2_strata.R |only R/ahreg.R |only R/ahreg.sample.data.R |only R/cox1.R |only R/kmcens2.R |only R/print.ah2.R | 81 ++++- R/print.ahreg.R |only R/survAH-package.R | 19 - R/vtm.R |only README.md | 22 + build/vignette.rds |binary inst/doc/vignette-survAH.R | 120 +++++++ inst/doc/vignette-survAH.Rmd | 330 ++++++++++++++++++++- inst/doc/vignette-survAH.html | 635 +++++++++++++++++++++++++++++++++++------- man/ah1.Rd |only man/ah2.Rd | 72 +++- man/ahreg.Rd |only man/ahreg.sample.data.Rd |only man/print.ahreg.Rd |only man/survAH-package.Rd | 8 vignettes/vignette-survAH.Rmd | 330 ++++++++++++++++++++- 29 files changed, 1706 insertions(+), 457 deletions(-)
Title: Client for 'mapshaper' for 'Geospatial' Operations
Description: Edit and simplify 'geojson', 'Spatial', and 'sf'
objects. This is wrapper around the 'mapshaper' 'JavaScript' library
by Matthew Bloch <https://github.com/mbloch/mapshaper/> to perform
topologically-aware polygon simplification, as well as other
operations such as clipping, erasing, dissolving, and converting
'multi-part' to 'single-part' geometries.
Author: Andy Teucher [aut, cre] ,
Kenton Russell [aut] ,
Matthew Bloch [cph]
Maintainer: Andy Teucher <andy.teucher@gmail.com>
Diff between rmapshaper versions 0.5.0 dated 2023-04-10 and 0.6.0 dated 2025-12-04
rmapshaper-0.5.0/rmapshaper/R/rmapshaper.R |only rmapshaper-0.5.0/rmapshaper/inst/mapshaper/LICENSE-d3-dsv |only rmapshaper-0.5.0/rmapshaper/inst/mapshaper/LICENSE-minimist |only rmapshaper-0.5.0/rmapshaper/inst/mapshaper/LICENSE-open |only rmapshaper-0.5.0/rmapshaper/inst/mapshaper/LICENSE-optimist |only rmapshaper-0.5.0/rmapshaper/inst/mapshaper/LICENSE-rbush |only rmapshaper-0.5.0/rmapshaper/inst/mapshaper/LICENSE-wordwrap |only rmapshaper-0.5.0/rmapshaper/inst/mapshaper/mapshaper-browserify.js |only rmapshaper-0.5.0/rmapshaper/man/rmapshaper.Rd |only rmapshaper-0.5.0/rmapshaper/tools |only rmapshaper-0.6.0/rmapshaper/DESCRIPTION | 20 rmapshaper-0.6.0/rmapshaper/MD5 | 161 +- rmapshaper-0.6.0/rmapshaper/NAMESPACE | 3 rmapshaper-0.6.0/rmapshaper/NEWS.md | 19 rmapshaper-0.6.0/rmapshaper/R/as_spatial_methods.R | 8 rmapshaper-0.6.0/rmapshaper/R/clip_erase.R | 575 +++++++--- rmapshaper-0.6.0/rmapshaper/R/dissolve.R | 221 +++ rmapshaper-0.6.0/rmapshaper/R/explode.R | 5 rmapshaper-0.6.0/rmapshaper/R/filter_fields.R | 3 rmapshaper-0.6.0/rmapshaper/R/filter_islands.R | 111 + rmapshaper-0.6.0/rmapshaper/R/inner_lines.R | 8 rmapshaper-0.6.0/rmapshaper/R/lines.R | 14 rmapshaper-0.6.0/rmapshaper/R/points.R | 32 rmapshaper-0.6.0/rmapshaper/R/rmapshaper-package.R |only rmapshaper-0.6.0/rmapshaper/R/simplify.R | 313 ++++- rmapshaper-0.6.0/rmapshaper/R/utils.R | 400 ++++-- rmapshaper-0.6.0/rmapshaper/R/zzz.R | 19 rmapshaper-0.6.0/rmapshaper/README.md | 37 rmapshaper-0.6.0/rmapshaper/build/vignette.rds |binary rmapshaper-0.6.0/rmapshaper/inst/doc/rmapshaper.R | 2 rmapshaper-0.6.0/rmapshaper/inst/doc/rmapshaper.Rmd | 2 rmapshaper-0.6.0/rmapshaper/inst/doc/rmapshaper.html | 23 rmapshaper-0.6.0/rmapshaper/inst/issue-tests |only rmapshaper-0.6.0/rmapshaper/inst/mapshaper/LICENSE-flatbush |only rmapshaper-0.6.0/rmapshaper/inst/mapshaper/LICENSE-iconv-lite | 5 rmapshaper-0.6.0/rmapshaper/inst/mapshaper/LICENSE-idb-keyval |only rmapshaper-0.6.0/rmapshaper/inst/mapshaper/LICENSE-kdbush |only rmapshaper-0.6.0/rmapshaper/inst/mapshaper/LICENSE-mproj |only rmapshaper-0.6.0/rmapshaper/inst/mapshaper/LICENSE-rw | 3 rmapshaper-0.6.0/rmapshaper/inst/mapshaper/LICENSE-sync-request |only rmapshaper-0.6.0/rmapshaper/inst/mapshaper/LICENSE-togeojson |only rmapshaper-0.6.0/rmapshaper/inst/mapshaper/LICENSE-tokml |only rmapshaper-0.6.0/rmapshaper/inst/mapshaper/README.md | 107 + rmapshaper-0.6.0/rmapshaper/inst/mapshaper/mapshaper-browserify.min.js | 8 rmapshaper-0.6.0/rmapshaper/inst/mapshaper/node_packages.csv | 23 rmapshaper-0.6.0/rmapshaper/inst/mapshaper/update_licenses.R |only rmapshaper-0.6.0/rmapshaper/inst/sticker |only rmapshaper-0.6.0/rmapshaper/man/apply_mapshaper_commands.Rd | 43 rmapshaper-0.6.0/rmapshaper/man/figures |only rmapshaper-0.6.0/rmapshaper/man/ms_clip.Rd | 33 rmapshaper-0.6.0/rmapshaper/man/ms_dissolve.Rd | 31 rmapshaper-0.6.0/rmapshaper/man/ms_erase.Rd | 33 rmapshaper-0.6.0/rmapshaper/man/ms_explode.Rd | 31 rmapshaper-0.6.0/rmapshaper/man/ms_filter_fields.Rd | 17 rmapshaper-0.6.0/rmapshaper/man/ms_filter_islands.Rd | 31 rmapshaper-0.6.0/rmapshaper/man/ms_innerlines.Rd | 31 rmapshaper-0.6.0/rmapshaper/man/ms_lines.Rd | 31 rmapshaper-0.6.0/rmapshaper/man/ms_points.Rd | 31 rmapshaper-0.6.0/rmapshaper/man/ms_simplify.Rd | 33 rmapshaper-0.6.0/rmapshaper/man/rmapshaper-package.Rd |only rmapshaper-0.6.0/rmapshaper/tests/testthat/_snaps/clip_erase.md | 58 - rmapshaper-0.6.0/rmapshaper/tests/testthat/_snaps/dissolve.md | 12 rmapshaper-0.6.0/rmapshaper/tests/testthat/_snaps/drop_null_geometries.md | 2 rmapshaper-0.6.0/rmapshaper/tests/testthat/_snaps/explode.md | 8 rmapshaper-0.6.0/rmapshaper/tests/testthat/_snaps/filter_islands.md | 8 rmapshaper-0.6.0/rmapshaper/tests/testthat/_snaps/innerlines.md | 4 rmapshaper-0.6.0/rmapshaper/tests/testthat/_snaps/lines.md | 6 rmapshaper-0.6.0/rmapshaper/tests/testthat/_snaps/points.md | 10 rmapshaper-0.6.0/rmapshaper/tests/testthat/_snaps/simplify.md | 104 + rmapshaper-0.6.0/rmapshaper/tests/testthat/helpers.R | 2 rmapshaper-0.6.0/rmapshaper/tests/testthat/setup.R | 55 rmapshaper-0.6.0/rmapshaper/tests/testthat/test-apply_mapshaper_commands.R | 1 rmapshaper-0.6.0/rmapshaper/tests/testthat/test-clip_erase.R | 213 ++- rmapshaper-0.6.0/rmapshaper/tests/testthat/test-dissolve.R | 42 rmapshaper-0.6.0/rmapshaper/tests/testthat/test-drop_null_geometries.R | 10 rmapshaper-0.6.0/rmapshaper/tests/testthat/test-explode.R | 10 rmapshaper-0.6.0/rmapshaper/tests/testthat/test-filter_fields.R | 40 rmapshaper-0.6.0/rmapshaper/tests/testthat/test-filter_islands.R | 148 ++ rmapshaper-0.6.0/rmapshaper/tests/testthat/test-innerlines.R | 34 rmapshaper-0.6.0/rmapshaper/tests/testthat/test-lines.R | 50 rmapshaper-0.6.0/rmapshaper/tests/testthat/test-points.R | 70 - rmapshaper-0.6.0/rmapshaper/tests/testthat/test-simplify.R | 200 +++ rmapshaper-0.6.0/rmapshaper/tests/testthat/test-utils.R | 59 - rmapshaper-0.6.0/rmapshaper/tests/testthat/test-zzz.R |only rmapshaper-0.6.0/rmapshaper/vignettes/rmapshaper.Rmd | 2 85 files changed, 2522 insertions(+), 1093 deletions(-)
Title: Predict with 'tidymodels' Workflows in Databases
Description: Turn 'tidymodels' workflows into objects containing the
sufficient sequential equations to perform predictions. These smaller
objects allow for low dependency prediction locally or directly in
databases.
Author: Emil Hvitfeldt [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between orbital versions 0.3.1 dated 2025-08-29 and 0.4.0 dated 2025-12-04
DESCRIPTION | 13 - MD5 | 71 +++++---- NAMESPACE | 7 NEWS.md | 12 + R/adjust_equivocal_zone.R |only R/adjust_numeric_range.R |only R/adjust_predictions_custom.R |only R/adjust_probability_threshold.R |only R/orbital.R | 2 R/show_query.R |only R/tailor.R |only R/workflows.R | 15 +- README.md | 13 + build/vignette.rds |binary inst/doc/supported-models.R | 2 inst/doc/supported-models.Rmd | 12 + inst/doc/supported-models.html | 131 +++++++++--------- man/augment.orbital_class.Rd | 2 man/orbital.Rd | 2 man/orbital_dt.Rd | 2 man/orbital_inline.Rd | 2 man/orbital_json_read.Rd | 2 man/orbital_json_write.Rd | 2 man/orbital_r_fun.Rd | 2 man/orbital_sql.Rd | 2 man/predict.orbital_class.Rd | 2 tests/testthat/_snaps/adjust_equivocal_zone.md |only tests/testthat/_snaps/adjust_probability_threshold.md |only tests/testthat/_snaps/orbital.md | 8 - tests/testthat/_snaps/show_query.md |only tests/testthat/derby.log | 10 - tests/testthat/test-adjust_equivocal_zone.R |only tests/testthat/test-adjust_numeric_range.R |only tests/testthat/test-adjust_predictions_custom.R |only tests/testthat/test-adjust_probability_threshold.R |only tests/testthat/test-orbital.R | 19 -- tests/testthat/test-show_query.R |only tests/testthat/test-step_impute_mode.R | 44 ++++-- tests/testthat/test-step_novel.R | 12 - tests/testthat/test-step_other.R | 12 - tests/testthat/test-step_select.R | 20 -- tests/testthat/test-step_unknown.R | 32 +++- tests/testthat/test-tailor.R |only vignettes/supported-models.Rmd | 12 + 44 files changed, 268 insertions(+), 197 deletions(-)
Title: Lightweight Framework for Orchestrating Multi-Agent Large
Language Models
Description: Provides tools for creating agents with persistent state using
R6 classes <https://cran.r-project.org/package=R6> and the 'ellmer'
package <https://cran.r-project.org/package=ellmer>. Tracks prompts,
messages, and agent metadata for reproducible, multi-turn large language
model sessions.
Author: Mohamed El Fodil Ihaddaden [aut, cre]
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between mini007 versions 0.2.1 dated 2025-11-03 and 0.2.2 dated 2025-12-04
DESCRIPTION | 10 MD5 | 17 - NAMESPACE | 5 NEWS.md | 18 + R/Agent.R | 470 ++++++++++++++++++++++++---- README.md | 328 +++++++++++-------- man/Agent.Rd | 279 +++++++++++++--- man/LeadAgent.Rd | 2 man/figures/README-unnamed-chunk-23-1.png |only tests/testthat/test-agent.R | 502 ++++++++++++++++++++++++------ 10 files changed, 1264 insertions(+), 367 deletions(-)
Title: Constrained Regression for Survey Data
Description: Domain mean estimation with monotonicity or block monotone constraints. See Xu X, Meyer MC and Opsomer JD (2021)<doi:10.1016/j.jspi.2021.02.004> for more details.
Author: Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>
Diff between csurvey versions 1.12 dated 2025-05-23 and 1.14 dated 2025-12-04
DESCRIPTION | 12 +++++++----- MD5 | 16 ++++++++++++---- R/plot.csvy.R | 18 ++++++++++-------- build |only inst |only man/csvy.Rd | 15 +++------------ man/plot_csvy_control.Rd | 18 ++++++++++-------- tests |only vignettes |only 9 files changed, 42 insertions(+), 37 deletions(-)
Title: Generation of Different Animated Christmas Cards
Description: Generation of different Christmas cards, most of them being
animated. Most of the cards can be generated in three languages (English,
Catalan and Spanish). The collection started in 2009.
Author: Jose Barrera-Gomez [aut, cre]
Maintainer: Jose Barrera-Gomez <jose.barrera@uab.cat>
Diff between christmas versions 1.4.0 dated 2024-12-10 and 1.4.1 dated 2025-12-04
christmas-1.4.0/christmas/NEWS |only christmas-1.4.1/christmas/DESCRIPTION | 13 ++++----- christmas-1.4.1/christmas/MD5 | 16 ++++++----- christmas-1.4.1/christmas/NAMESPACE | 1 christmas-1.4.1/christmas/NEWS.md |only christmas-1.4.1/christmas/R/auxiliarFunctions.R | 33 +++++++++++++++++++++++ christmas-1.4.1/christmas/R/xmasfractaltree.R | 10 ++---- christmas-1.4.1/christmas/R/xmaspeace.R |only christmas-1.4.1/christmas/README.md | 23 ++++++++++------ christmas-1.4.1/christmas/man/xmasfractaltree.Rd | 5 ++- christmas-1.4.1/christmas/man/xmaspeace.Rd |only 11 files changed, 72 insertions(+), 29 deletions(-)
Title: 'shiny' Application for Biological Dosimetry
Description: A tool to perform all different statistical tests and calculations
needed by Biological dosimetry Laboratories. Detailed documentation is
available in <https://biodosetools-team.github.io/documentation/>.
Author: Alfredo Hernandez [aut] ,
Anna Frances-Abellan [aut, cre] ,
David Endesfelder [aut],
Pere Puig [aut]
Maintainer: Anna Frances-Abellan <anna.frances@uab.cat>
Diff between biodosetools versions 3.7.1 dated 2025-10-22 and 3.7.1.2 dated 2025-12-04
DESCRIPTION | 6 MD5 | 22 - NEWS.md | 2 R/calcs_estimation.R | 4 R/calcs_interlab.R | 451 ++++++++++++++++++----------------- R/mod_interlab_server.R | 23 + R/utils_estimation.R | 4 R/utils_fitting.R | 2 R/utils_interlab.R | 82 +++--- R/utils_mixed.R | 2 inst/doc/interlab.html | 12 tests/testthat/test-golem_utils_ui.R | 313 +++++++++++------------- 12 files changed, 472 insertions(+), 451 deletions(-)
Title: The SHAPBoost Feature Selection Algorithm
Description: The implementation of SHAPBoost, a boosting-based feature selection technique that ranks features iteratively based on Shapley values.
Author: Oemer Tarik Oezyilmaz [aut, cre, cph] ,
Tamas Szili-Toeroek [aut, cph]
Maintainer: Oemer Tarik Oezyilmaz <o.t.ozyilmaz@umcg.nl>
Diff between SHAPBoost versions 1.0.0 dated 2025-09-29 and 1.0.1 dated 2025-12-04
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/shapboost_estimator.R | 6 +++++- R/shapboost_regressor.R | 30 +++++++++++++++++++----------- R/shapboost_survival.R | 43 ++++++++++++++++++++++++++----------------- README.md | 2 +- 7 files changed, 67 insertions(+), 40 deletions(-)
Title: Local Political Actor Network Diachronic Analysis Tools
Description: Provides functions to prepare, visualize, and analyse diachronic
network data on local political actors, with a particular focus on
the development of local party systems and identification of actor groups.
Formalizes and automates a continuity diagram method that has been previously
applied in research on Czech local politics, e.g. Bubenicek and Kubalek (2010,
ISSN:1803-8220), Kubalek and Bubenicek (2012, ISSN:1803-8220), and Cmejrek,
Bubenicek, and Copik (2010, ISBN:978-80-247-3061-5). The package also
includes several example datasets derived from Czech municipal
elections, compiled from official election results, field research, and
previously published case studies on Czech local politics.
Author: Vaclav Bubenicek [aut, cre, cph] )
Maintainer: Vaclav Bubenicek <bubenicek@pef.czu.cz>
Diff between lpanda versions 0.2.0 dated 2025-11-29 and 0.2.1 dated 2025-12-04
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/text_conversion.R | 11 ++++++++--- README.md | 6 +++--- inst/CITATION | 8 ++------ man/figures/README-basic_continuity_diagram-1.png |binary man/figures/README-continuity_snapshots-1.png |binary man/figures/README-continuity_use-1.png |binary man/figures/README-continuity_use-2.png |binary tests/testthat/test-text_conversion.R | 16 ++++++++-------- 11 files changed, 40 insertions(+), 33 deletions(-)
Title: Tools for HTML
Description: Tools for HTML generation and output.
Author: Joe Cheng [aut],
Carson Sievert [aut, cre] ,
Barret Schloerke [aut] ,
Winston Chang [aut] ,
Yihui Xie [aut],
Jeff Allen [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Carson Sievert <carson@posit.co>
Diff between htmltools versions 0.5.8.1 dated 2024-04-04 and 0.5.9 dated 2025-12-04
DESCRIPTION | 15 ++++++++------- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/tags.R | 2 +- man/capturePlot.Rd | 2 +- man/plotTag.Rd | 2 +- man/tagList.Rd | 2 +- src/template.c | 6 ++---- tests/testthat/test-tag-query.R | 5 +++-- 9 files changed, 29 insertions(+), 25 deletions(-)
Title: Convert Statistical Objects into Tidy Tibbles
Description: Summarizes key information about statistical objects in tidy
tibbles. This makes it easy to report results, create plots and
consistently work with large numbers of models at once. Broom
provides three verbs that each provide different types of information
about a model. tidy() summarizes information about model components
such as coefficients of a regression. glance() reports information
about an entire model, such as goodness of fit measures like AIC and
BIC. augment() adds information about individual observations to a
dataset, such as fitted values or influence measures.
Author: David Robinson [aut],
Alex Hayes [aut] ,
Simon Couch [aut] ,
Emil Hvitfeldt [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Indrajeet Patil [ctb] ,
Derek Chiu [ctb],
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Dieter Menne [ctb],
Benjamin Nutter [ctb], [...truncated...]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between broom versions 1.0.10 dated 2025-09-13 and 1.0.11 dated 2025-12-04
broom-1.0.10/broom/tests/test-all.R |only broom-1.0.11/broom/DESCRIPTION | 16 ++++++---- broom-1.0.11/broom/MD5 | 31 ++++++++++----------- broom-1.0.11/broom/NEWS.md | 6 +++- broom-1.0.11/broom/R/hmisc.R | 2 - broom-1.0.11/broom/R/mediation.R | 2 - broom-1.0.11/broom/README.md | 2 - broom-1.0.11/broom/build/vignette.rds |binary broom-1.0.11/broom/inst/doc/adding-tidiers.html | 4 +- broom-1.0.11/broom/inst/doc/available-methods.html | 4 +- broom-1.0.11/broom/inst/doc/bootstrapping.html | 4 +- broom-1.0.11/broom/inst/doc/broom.html | 4 +- broom-1.0.11/broom/inst/doc/broom_and_dplyr.html | 4 +- broom-1.0.11/broom/man/broom.Rd | 3 +- broom-1.0.11/broom/man/figures/logo.png |binary broom-1.0.11/broom/man/tidy.mediate.Rd | 2 - broom-1.0.11/broom/man/tidy.rcorr.Rd | 2 - 17 files changed, 47 insertions(+), 39 deletions(-)
Title: Medulloblastoma Subgroups Prediction
Description: Utilizing a combination of machine learning models (Random Forest, Naive Bayes, K-Nearest Neighbor, Support Vector Machines, Extreme Gradient Boosting, and Linear Discriminant Analysis) and a deep Artificial Neural Network model, 'MBMethPred' can predict medulloblastoma subgroups, including wingless (WNT), sonic hedgehog (SHH), Group 3, and Group 4 from DNA methylation beta values. See Sharif Rahmani E, Lawarde A, Lingasamy P, Moreno SV, Salumets A and Modhukur V (2023), MBMethPred: a computational framework for the accurate classification of childhood medulloblastoma subgroups using data integration and AI-based approaches. Front. Genet. 14:1233657. <doi: 10.3389/fgene.2023.1233657> for more details.
Author: Edris Sharif Rahmani [aut, ctb, cre] ,
Ankita Sunil Lawarde [aut, ctb] ,
Vijayachitra Modhukur [aut, ctb]
Maintainer: Edris Sharif Rahmani <rahmani.biotech@gmail.com>
Diff between MBMethPred versions 0.1.4.3 dated 2025-06-17 and 0.1.4.4 dated 2025-12-04
DESCRIPTION | 8 MD5 | 8 R/XGBoostModel.r | 94 +++++-- build/vignette.rds |binary inst/doc/MBMethPred_introduction.html | 404 ++++++++++------------------------ 5 files changed, 194 insertions(+), 320 deletions(-)
Title: Interface to the 'PubChem' Database for Chemical Data Retrieval
Description: Provides an interface to the 'PubChem' database via the PUG REST <https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest> and
PUG View <https://pubchem.ncbi.nlm.nih.gov/docs/pug-view> services. This package allows users to automatically
access chemical and biological data from 'PubChem', including compounds, substances, assays, and various other data types.
Functions are available to retrieve data in different formats, perform searches, and access detailed annotations.
Author: Selcuk Korkmaz [aut, cre] ,
Bilge Eren Yamasan [aut] ,
Dincer Goksuluk [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between PubChemR versions 2.1.7 dated 2025-11-05 and 2.1.8 dated 2025-12-04
PubChemR-2.1.7/PubChemR/tests |only PubChemR-2.1.8/PubChemR/DESCRIPTION | 9 ++++----- PubChemR-2.1.8/PubChemR/MD5 | 21 +++------------------ PubChemR-2.1.8/PubChemR/NAMESPACE | 1 - PubChemR-2.1.8/PubChemR/R/00_globals.R | 1 - 5 files changed, 7 insertions(+), 25 deletions(-)
Title: Wrapper for the 'Official Hacker News' API
Description: Use the Official Hacker News API through R. Retrieve
posts, articles and other items in form of convenient R objects.
Author: Ryszard Szymanski [aut, cre],
Piotr Janus [aut],
Zuzanna Magierska [aut],
Rafal Muszynski [aut],
Andrzej Nowikowski [aut]
Maintainer: Ryszard Szymanski <ryszard.szymanski@outlook.com>
Diff between hackeRnews versions 0.2.1 dated 2025-04-08 and 0.2.2 dated 2025-12-04
DESCRIPTION | 8 MD5 | 16 NEWS.md | 4 build/vignette.rds |binary inst/doc/hackeRnews-specs.R | 46 inst/doc/hackeRnews-specs.Rmd | 18 inst/doc/hackeRnews-specs.html | 60 - tests/testthat/_snaps/api.md | 2222 ++++++++++++++++++++--------------------- vignettes/hackeRnews-specs.Rmd | 18 9 files changed, 1175 insertions(+), 1217 deletions(-)
Title: Create, and Refine Data Nuggets
Description: Creating, and refining data nuggets.
Data nuggets reduce a large dataset into a small collection of nuggets of
data, each containing a center (location), weight (importance), and scale
(variability) parameter. Data nugget centers are created by choosing
observations in the dataset which are as equally spaced apart as possible.
Data nugget weights are created by counting the number observations
closest to a given data nugget center. We then say the data nugget
'contains' these observations and the data nugget center is recalculated
as the mean of these observations. Data nugget scales are created by
calculating the trace of the covariance matrix of the observations
contained within a data nugget divided by the dimension of the dataset.
Data nuggets are refined by 'splitting' data nuggets which have scales or
shapes (defined as the ratio of the two largest eigenvalues of the
covariance matrix of the observations contained within the data nugget)
Reference paper: [1] Beavers, T. E., Cheng [...truncated...]
Author: Rituparna Dey [aut, cre],
Yajie Duan [aut],
Traymon Beavers [aut],
Javier Cabrera [aut],
Ge Cheng [aut],
Kunting Qi [aut],
Mariusz Lubomirski [aut]
Maintainer: Rituparna Dey <rituparnadey525@gmail.com>
Diff between datanugget versions 1.3.1 dated 2024-09-14 and 1.4.0 dated 2025-12-04
datanugget-1.3.1/datanugget/R/createDNcenters.R |only datanugget-1.4.0/datanugget/DESCRIPTION | 20 datanugget-1.4.0/datanugget/MD5 | 16 datanugget-1.4.0/datanugget/R/create.DNcenters.R |only datanugget-1.4.0/datanugget/R/createDN.R | 1090 +++++++------------- datanugget-1.4.0/datanugget/R/create_refine.DN.R | 26 datanugget-1.4.0/datanugget/R/getDN.means.R |only datanugget-1.4.0/datanugget/man/create.DN.Rd | 26 datanugget-1.4.0/datanugget/man/create.DNcenters.Rd | 18 datanugget-1.4.0/datanugget/man/create_refine.DN.Rd | 6 datanugget-1.4.0/datanugget/man/getDN.means.Rd |only 11 files changed, 464 insertions(+), 738 deletions(-)
Title: Estimate Survival from Common Data Model Cohorts
Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
Author: Kim Lopez-Gueell [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut] ,
Xintong Li [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut]
Maintainer: Kim Lopez-Gueell <kim.lopez@spc.ox.ac.uk>
Diff between CohortSurvival versions 1.0.3 dated 2025-08-18 and 1.1.0 dated 2025-12-04
CohortSurvival-1.0.3/CohortSurvival/R/utils-pipe.R |only CohortSurvival-1.0.3/CohortSurvival/R/utils-tidy-eval.R |only CohortSurvival-1.0.3/CohortSurvival/man/pipe.Rd |only CohortSurvival-1.0.3/CohortSurvival/man/tidyeval.Rd |only CohortSurvival-1.1.0/CohortSurvival/DESCRIPTION | 22 CohortSurvival-1.1.0/CohortSurvival/MD5 | 87 CohortSurvival-1.1.0/CohortSurvival/NAMESPACE | 14 CohortSurvival-1.1.0/CohortSurvival/NEWS.md | 24 CohortSurvival-1.1.0/CohortSurvival/R/CohortSurvival-package.R | 1 CohortSurvival-1.1.0/CohortSurvival/R/addCohortSurvival.R | 90 CohortSurvival-1.1.0/CohortSurvival/R/asSurvivalResult.R | 597 ++ CohortSurvival-1.1.0/CohortSurvival/R/estimateSurvival.R | 726 +-- CohortSurvival-1.1.0/CohortSurvival/R/inputValidation.R | 10 CohortSurvival-1.1.0/CohortSurvival/R/mockMGUS2cdm.R | 86 CohortSurvival-1.1.0/CohortSurvival/R/plotSurvival.R | 161 CohortSurvival-1.1.0/CohortSurvival/R/tableSurvival.R | 534 +- CohortSurvival-1.1.0/CohortSurvival/README.md | 10 CohortSurvival-1.1.0/CohortSurvival/build/vignette.rds |binary CohortSurvival-1.1.0/CohortSurvival/inst/doc/a01_Single_event_of_interest.R | 22 CohortSurvival-1.1.0/CohortSurvival/inst/doc/a01_Single_event_of_interest.Rmd | 22 CohortSurvival-1.1.0/CohortSurvival/inst/doc/a01_Single_event_of_interest.html | 2222 ++++------ CohortSurvival-1.1.0/CohortSurvival/inst/doc/a02_Competing_risk_survival.R | 12 CohortSurvival-1.1.0/CohortSurvival/inst/doc/a02_Competing_risk_survival.Rmd | 12 CohortSurvival-1.1.0/CohortSurvival/inst/doc/a02_Competing_risk_survival.html | 404 - CohortSurvival-1.1.0/CohortSurvival/inst/doc/a03_Further_survival_analyses.R | 32 CohortSurvival-1.1.0/CohortSurvival/inst/doc/a03_Further_survival_analyses.Rmd | 32 CohortSurvival-1.1.0/CohortSurvival/inst/doc/a03_Further_survival_analyses.html | 38 CohortSurvival-1.1.0/CohortSurvival/man/CohortSurvival-package.Rd | 2 CohortSurvival-1.1.0/CohortSurvival/man/addCohortSurvival.Rd | 8 CohortSurvival-1.1.0/CohortSurvival/man/asSummarisedResult.Rd |only CohortSurvival-1.1.0/CohortSurvival/man/asSurvivalResult.Rd | 4 CohortSurvival-1.1.0/CohortSurvival/man/plotSurvival.Rd | 9 CohortSurvival-1.1.0/CohortSurvival/man/riskTable.Rd | 59 CohortSurvival-1.1.0/CohortSurvival/man/tableDoc.Rd |only CohortSurvival-1.1.0/CohortSurvival/man/tableSurvival.Rd | 65 CohortSurvival-1.1.0/CohortSurvival/man/tableSurvivalAttrition.Rd |only CohortSurvival-1.1.0/CohortSurvival/man/tableSurvivalEvents.Rd |only CohortSurvival-1.1.0/CohortSurvival/tests/testthat/setup.R |only CohortSurvival-1.1.0/CohortSurvival/tests/testthat/test-addCohortSurvival.R | 319 - CohortSurvival-1.1.0/CohortSurvival/tests/testthat/test-asSurvivalResult.R |only CohortSurvival-1.1.0/CohortSurvival/tests/testthat/test-estimateSurvival.R | 844 ++- CohortSurvival-1.1.0/CohortSurvival/tests/testthat/test-mockMGUS2cdm.R | 8 CohortSurvival-1.1.0/CohortSurvival/tests/testthat/test-plotSurvival.R | 20 CohortSurvival-1.1.0/CohortSurvival/tests/testthat/test-reexports-omopgenerics.R | 22 CohortSurvival-1.1.0/CohortSurvival/tests/testthat/test-riskTable.R | 14 CohortSurvival-1.1.0/CohortSurvival/tests/testthat/test-tableSurvival.R | 68 CohortSurvival-1.1.0/CohortSurvival/tests/testthat/test-tableSurvivalAttrition.R |only CohortSurvival-1.1.0/CohortSurvival/vignettes/a01_Single_event_of_interest.Rmd | 22 CohortSurvival-1.1.0/CohortSurvival/vignettes/a02_Competing_risk_survival.Rmd | 12 CohortSurvival-1.1.0/CohortSurvival/vignettes/a03_Further_survival_analyses.Rmd | 32 50 files changed, 3871 insertions(+), 2795 deletions(-)
More information about CohortSurvival at CRAN
Permanent link
Title: Categorical Data
Description: This R-package contains examples from the book "Regression for Categorical Data", Tutz 2012, Cambridge University Press. The names of the examples refer to the chapter and the data set that is used.
Author: Gunther Schauberger [aut, cre],
Gerhard Tutz [aut]
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between catdata versions 1.2.4 dated 2024-01-25 and 1.2.5 dated 2025-12-04
DESCRIPTION | 18 MD5 | 166 +++---- build/vignette.rds |binary data/birth.rda |binary inst/doc/altbin-teratology.pdf |binary inst/doc/binary-unemployment.R | 80 +-- inst/doc/binary-unemployment.pdf |binary inst/doc/binary-vaso.pdf |binary inst/doc/count-children.pdf |binary inst/doc/count-encephalitis.pdf |binary inst/doc/count-insolvency.pdf |binary inst/doc/count-medcare.pdf |binary inst/doc/loglinear-birth.R | 178 ++++---- inst/doc/loglinear-birth.pdf |binary inst/doc/loglinear-leukoplakia.R | 22 - inst/doc/loglinear-leukoplakia.pdf |binary inst/doc/modbin-dust.R | 26 - inst/doc/modbin-dust.pdf |binary inst/doc/modbin-foodstamp.R | 12 inst/doc/modbin-foodstamp.pdf |binary inst/doc/modbin-unemployment1.R | 42 +- inst/doc/modbin-unemployment1.pdf |binary inst/doc/modbin-unemployment2.R | 188 ++++---- inst/doc/modbin-unemployment2.pdf |binary inst/doc/multinomial-addiction1.R | 110 ++--- inst/doc/multinomial-addiction1.pdf |binary inst/doc/multinomial-addiction2.R | 40 - inst/doc/multinomial-addiction2.pdf |binary inst/doc/multinomial-party1.R | 72 +-- inst/doc/multinomial-party1.pdf |binary inst/doc/multinomial-party2.R | 80 +-- inst/doc/multinomial-party2.pdf |binary inst/doc/multinomial-travel.R | 80 +-- inst/doc/multinomial-travel.pdf |binary inst/doc/multivariate-birth1.R | 38 - inst/doc/multivariate-birth1.pdf |binary inst/doc/multivariate-birth2.R | 168 ++++---- inst/doc/multivariate-birth2.pdf |binary inst/doc/multivariate-knee.R | 106 ++--- inst/doc/multivariate-knee.pdf |binary inst/doc/ordinal-arthritis.R | 20 inst/doc/ordinal-arthritis.Rnw | 2 inst/doc/ordinal-arthritis.pdf |binary inst/doc/ordinal-knee1.R | 70 +-- inst/doc/ordinal-knee1.Rnw | 2 inst/doc/ordinal-knee1.pdf |binary inst/doc/ordinal-knee2.R | 78 +-- inst/doc/ordinal-knee2.Rnw | 16 inst/doc/ordinal-knee2.pdf |binary inst/doc/ordinal-retinopathy1.R | 7 inst/doc/ordinal-retinopathy1.Rnw | 7 inst/doc/ordinal-retinopathy1.pdf |binary inst/doc/ordinal-retinopathy2.R | 10 inst/doc/ordinal-retinopathy2.Rnw | 10 inst/doc/ordinal-retinopathy2.pdf |binary inst/doc/prediction-medcare.R | 650 +++++++++++++++---------------- inst/doc/prediction-medcare.pdf |binary inst/doc/random-aids.R | 22 - inst/doc/random-aids.pdf |binary inst/doc/random-betablocker.R | 76 +-- inst/doc/random-betablocker.pdf |binary inst/doc/random-knee1.R | 46 +- inst/doc/random-knee1.pdf |binary inst/doc/random-knee2.R | 52 +- inst/doc/random-knee2.pdf |binary inst/doc/random-knee3.R | 54 +- inst/doc/random-knee3.pdf |binary inst/doc/semiparametric-addiction.R | 120 ++--- inst/doc/semiparametric-addiction.pdf |binary inst/doc/semiparametric-children.R | 24 - inst/doc/semiparametric-children.pdf |binary inst/doc/semiparametric-dust.R | 24 - inst/doc/semiparametric-dust.pdf |binary inst/doc/semiparametric-unemployment.R | 100 ++-- inst/doc/semiparametric-unemployment.pdf |binary inst/doc/tree-dust.R | 144 +++--- inst/doc/tree-dust.pdf |binary inst/doc/tree-unemployment.R | 76 +-- inst/doc/tree-unemployment.pdf |binary vignettes/ordinal-arthritis.Rnw | 2 vignettes/ordinal-knee1.Rnw | 2 vignettes/ordinal-knee2.Rnw | 16 vignettes/ordinal-retinopathy1.Rnw | 7 vignettes/ordinal-retinopathy2.Rnw | 10 84 files changed, 1542 insertions(+), 1531 deletions(-)
Title: A Generator of Multidimensional Noise
Description: Generation of natural looking noise has many application
within simulation, procedural generation, and art, to name a few. The
'ambient' package provides an interface to the 'FastNoise' C++ library
and allows for efficient generation of perlin, simplex, worley, cubic,
value, and white noise with optional perturbation in either 2, 3, or 4
(in case of simplex and white noise) dimensions.
Author: Thomas Lin Pedersen [cre, aut] ,
Jordan Peck [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between ambient versions 1.0.2 dated 2022-09-08 and 1.0.3 dated 2025-12-04
ambient-1.0.2/ambient/src/Makevars |only ambient-1.0.3/ambient/DESCRIPTION | 55 +--- ambient-1.0.3/ambient/LICENSE | 4 ambient-1.0.3/ambient/MD5 | 45 +-- ambient-1.0.3/ambient/NEWS.md | 20 - ambient-1.0.3/ambient/R/aaa.R | 74 ++++- ambient-1.0.3/ambient/R/curl.R | 135 ++++++++-- ambient-1.0.3/ambient/R/dplyr.R | 10 ambient-1.0.3/ambient/R/fracture.R | 29 +- ambient-1.0.3/ambient/R/gradient.R | 39 ++ ambient-1.0.3/ambient/R/import-standalone-obj-type.R |only ambient-1.0.3/ambient/R/import-standalone-types-check.R |only ambient-1.0.3/ambient/R/long_grid.R | 32 +- ambient-1.0.3/ambient/R/noise-blue.R | 11 ambient-1.0.3/ambient/R/noise-cubic.R | 56 +++- ambient-1.0.3/ambient/R/noise-perlin.R | 74 ++++- ambient-1.0.3/ambient/R/noise-simplex.R | 93 +++++- ambient-1.0.3/ambient/R/noise-value.R | 74 ++++- ambient-1.0.3/ambient/R/noise-white.R | 72 ++++- ambient-1.0.3/ambient/R/noise-worley.R | 119 ++++++-- ambient-1.0.3/ambient/R/pattern-checkerboard.R | 9 ambient-1.0.3/ambient/R/trans_affine.R | 8 ambient-1.0.3/ambient/R/zzz.R | 8 ambient-1.0.3/ambient/README.md | 13 ambient-1.0.3/ambient/man/figures/README-unnamed-chunk-3-1.png |binary 25 files changed, 725 insertions(+), 255 deletions(-)
Title: Advanced 'tryCatch()' and 'try()' Functions
Description: Advanced tryCatch() and try() functions for better error handling
(logging, stack trace with source code references and support for post-mortem analysis via dump files).
Author: Juergen Altfeld [aut, cre, cph],
Charles Epaillard [ctb],
Brandon Bertelsen [ctb],
Valerian Wrobel [ctb],
Duccio Aiazzi [ctb]
Maintainer: Juergen Altfeld <jaltfeld@altfeld-im.de>
Diff between tryCatchLog versions 1.3.1 dated 2021-10-25 and 1.3.3 dated 2025-12-04
DESCRIPTION | 23 MD5 | 55 NAMESPACE | 2 NEWS.md | 22 R/get_pretty_tryCatchLog_options.R | 19 R/is_package_available.R | 4 R/limited_Labels_Compact.R | 4 R/log2console.R | 20 R/set_logging_functions.R | 26 R/set_logging_package.R |only R/zzz.R | 38 build/vignette.rds |binary inst/doc/90_appendix.Rmd_child | 4 inst/doc/tryCatchLog-intro.R | 386 ++--- inst/doc/tryCatchLog-intro.html | 1009 ++++++++------ man/build.log.output.Rd | 3 man/is.package.available.Rd | 2 man/limitedLabelsCompact.Rd | 4 man/set.logging.functions.Rd | 14 man/set.logging.package.Rd |only man/tryCatchLog.Rd | 3 man/tryLog.Rd | 3 tests/testthat/init_unit_test.R | 10 tests/testthat/test_build_log_output.R | 17 tests/testthat/test_is_windows.R | 10 tests/testthat/test_namespace_hooks.R | 63 tests/testthat/test_platform_functions.R | 22 tests/testthat/test_set_logging_package.R |only tests/testthat/test_zzz_call_without_attaching_issue_41.R | 29 vignettes/90_appendix.Rmd_child | 4 30 files changed, 1068 insertions(+), 728 deletions(-)
Title: Troubles Solver for 'lme4'
Description: The main function of the package aims to update 'lmer()'/'glmer()' models depending on their warnings, so trying to avoid convergence and singularity problems.
Author: Iago Gine-Vazquez [aut, cre]
Maintainer: Iago Gine-Vazquez <iago.gin-vaz@protonmail.com>
Diff between trouBBlme4SolveR versions 0.1.3 dated 2025-11-29 and 0.1.4 dated 2025-12-04
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- NEWS.md | 9 +++++ R/trouBBlme4SolveR.r | 8 ++--- inst/doc/introduction.R | 70 +++++++++++++++++++++++---------------------- inst/doc/introduction.Rnw | 37 ++++++++++++----------- inst/doc/introduction.pdf |binary vignettes/introduction.Rnw | 37 ++++++++++++----------- 8 files changed, 98 insertions(+), 85 deletions(-)
More information about trouBBlme4SolveR at CRAN
Permanent link
Title: Vowel Covariation Tools
Description: Tools to support research on vowel covariation. Methods are provided to
support Principal Component Analysis workflows (as in Brand et al. (2021)
<doi:10.1016/j.wocn.2021.101096> and Wilson Black et al. (2023)
<doi:10.1515/lingvan-2022-0086>).
Author: Joshua Wilson Black [aut, cre, cph] ,
James Brand [aut]
Maintainer: Joshua Wilson Black <joshua.black@canterbury.ac.nz>
This is a re-admission after prior archival of version 0.4.1 dated 2025-05-06
Diff between nzilbb.vowels versions 0.4.1 dated 2025-05-06 and 0.4.2 dated 2025-12-04
DESCRIPTION | 15 ++-- MD5 | 25 +++--- NAMESPACE | 1 NEWS.md | 10 ++ R/correlation_plots.R | 2 R/pca_rotate_procrustes.R | 36 ++++------ R/plot_pc_vs.R | 8 +- build/partial.rdb |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-2-2.png |binary man/figures/README-unnamed-chunk-2-3.png |binary man/nzilbb.vowels-package.Rd | 2 tests/testthat/_snaps/correlation_plots/plot-correlation-counts.svg | 10 +- tests/testthat/test-pca_rotate_procrustes.R |only 14 files changed, 59 insertions(+), 50 deletions(-)
Title: Tool for Diagnosis of Tables Joins and Complementary Join
Features
Description: Tool for diagnosing table joins. It combines the speed of `collapse`
and `data.table`, the flexibility of `dplyr`, and the diagnosis and features
of the `merge` command in `Stata`.
Author: R.Andres Castaneda [aut, cre],
Zander Prinsloo [aut],
Rossana Tatulli [aut]
Maintainer: R.Andres Castaneda <acastanedaa@worldbank.org>
Diff between joyn versions 0.2.4 dated 2024-12-13 and 0.3.0 dated 2025-12-04
DESCRIPTION | 13 MD5 | 49 +- NEWS.md | 228 ++++++----- R/checks.R | 339 +++++++++++----- R/dplyr-joins.R | 5 R/fix_by_vars.R | 67 ++- R/joyn-merge.R | 19 R/joyn-package.R | 8 R/merge-data.table.R | 14 R/possible_ids.R | 341 ++++++++++------- R/utils.R | 6 R/zzz.R | 2 README.md | 3 build/vignette.rds |binary inst/doc/adv-functionalities.html | 20 inst/doc/aux-functions.html | 76 +-- inst/doc/dplyr-joins.html | 3 inst/doc/main-functionalities.html | 3 inst/doc/merge-wrapper.html | 3 inst/doc/messages.html | 15 man/check_var_class.Rd |only man/filter_vars.Rd |only man/possible_ids.Rd | 2 tests/testthat/helper-testdata.R |only tests/testthat/test-checks.R | 741 ++++++++++++++++++++----------------- tests/testthat/test-joyn.R | 27 + tests/testthat/test-possible_ids.R | 651 ++++++++++++++------------------ 27 files changed, 1476 insertions(+), 1159 deletions(-)
Title: Visualize Function Call Dependencies in R Source Code
Description: Provides tools to analyze R source code and detect function definitions
and their internal dependencies across multiple files. Creates interactive network
visualizations using 'visNetwork' to display function call relationships, with
detailed tooltips showing function arguments, return values, and documentation.
Supports both individual files and directory-based analysis with automatic file
detection. Useful for understanding code structure, identifying dependencies,
and documenting R projects.
Author: Chathura Jayalath [aut, cre]
Maintainer: Chathura Jayalath <acj.chathura@gmail.com>
Diff between funviewR versions 0.1.0 dated 2025-11-09 and 0.1.1 dated 2025-12-04
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 14 ++++++++++++++ R/graph.R | 26 +++++++++++++++++++++----- README.md | 3 +++ 5 files changed, 45 insertions(+), 12 deletions(-)
Title: Graphical Modelling and Ordination using Copulas
Description: Creates 'graphs' of species associations (interactions) and ordination biplots from
co-occurrence data by fitting discrete gaussian copula graphical models. Methods described in
Popovic, GC., Hui, FKC., Warton, DI., (2018) <doi:10.1016/j.jmva.2017.12.002>.
Author: Gordana Popovic [aut],
David Warton [ctb, cre],
Francis K.C. Hui [ctb],
Michelle Lim [ctb]
Maintainer: David Warton <david.warton@unsw.edu.au>
Diff between ecoCopula versions 1.0.2 dated 2022-03-01 and 1.0.6 dated 2025-12-04
ecoCopula-1.0.2/ecoCopula/inst/doc/the_basics.R |only ecoCopula-1.0.2/ecoCopula/inst/doc/the_basics.Rmd |only ecoCopula-1.0.2/ecoCopula/inst/doc/the_basics.html |only ecoCopula-1.0.2/ecoCopula/tests |only ecoCopula-1.0.2/ecoCopula/vignettes/the_basics.Rmd |only ecoCopula-1.0.6/ecoCopula/DESCRIPTION | 24 ecoCopula-1.0.6/ecoCopula/MD5 | 84 +- ecoCopula-1.0.6/ecoCopula/NAMESPACE | 83 +- ecoCopula-1.0.6/ecoCopula/NEWS.md | 11 ecoCopula-1.0.6/ecoCopula/R/cgr.R | 640 ++++++++--------- ecoCopula-1.0.6/ecoCopula/R/cgr_s3.R | 282 +++---- ecoCopula-1.0.6/ecoCopula/R/cord.R | 369 ++++----- ecoCopula-1.0.6/ecoCopula/R/cord_s3.R | 468 ++++++------ ecoCopula-1.0.6/ecoCopula/R/data.R | 88 +- ecoCopula-1.0.6/ecoCopula/R/stackedsdm.R | 368 ++++----- ecoCopula-1.0.6/ecoCopula/R/stackedsdm_s3.R | 492 ++++++------- ecoCopula-1.0.6/ecoCopula/R/test-helpers.R |only ecoCopula-1.0.6/ecoCopula/R/utils.R | 464 ++++++------ ecoCopula-1.0.6/ecoCopula/R/utils_stackedsdm.R | 174 ++-- ecoCopula-1.0.6/ecoCopula/README.md | 59 - ecoCopula-1.0.6/ecoCopula/build/vignette.rds |binary ecoCopula-1.0.6/ecoCopula/inst/CITATION | 32 ecoCopula-1.0.6/ecoCopula/inst/doc/ecoCopula.Rmd |only ecoCopula-1.0.6/ecoCopula/inst/doc/ecoCopula.html |only ecoCopula-1.0.6/ecoCopula/man/cgr.Rd | 146 +-- ecoCopula-1.0.6/ecoCopula/man/cord.Rd | 116 +-- ecoCopula-1.0.6/ecoCopula/man/figure |only ecoCopula-1.0.6/ecoCopula/man/figures |only ecoCopula-1.0.6/ecoCopula/man/fitted.stackedsdm.Rd | 98 +- ecoCopula-1.0.6/ecoCopula/man/plot.cgr.Rd | 150 ++- ecoCopula-1.0.6/ecoCopula/man/plot.cord.Rd | 130 +-- ecoCopula-1.0.6/ecoCopula/man/plot.stackedsdm.Rd | 42 - ecoCopula-1.0.6/ecoCopula/man/predict.stackedsdm.Rd | 130 +-- ecoCopula-1.0.6/ecoCopula/man/print.cgr.Rd | 52 - ecoCopula-1.0.6/ecoCopula/man/print.cord.Rd | 50 - ecoCopula-1.0.6/ecoCopula/man/reexports.Rd | 32 ecoCopula-1.0.6/ecoCopula/man/residuals.stackedsdm.Rd | 102 +- ecoCopula-1.0.6/ecoCopula/man/save_png.Rd |only ecoCopula-1.0.6/ecoCopula/man/simulate.cord.Rd | 100 +- ecoCopula-1.0.6/ecoCopula/man/spider.Rd | 116 +-- ecoCopula-1.0.6/ecoCopula/man/stackedsdm.Rd | 142 +-- ecoCopula-1.0.6/ecoCopula/man/summary.cgr.Rd | 52 - ecoCopula-1.0.6/ecoCopula/man/summary.cord.Rd | 50 - ecoCopula-1.0.6/ecoCopula/vignettes/ecoCopula.Rmd |only ecoCopula-1.0.6/ecoCopula/vignettes/ecoCopula.Rmd.orig |only 45 files changed, 2593 insertions(+), 2553 deletions(-)
Title: R6-Based ML Learners for 'mlexperiments'
Description: Enhances 'mlexperiments'
<https://CRAN.R-project.org/package=mlexperiments> with additional
machine learning ('ML') learners. The package provides R6-based
learners for the following algorithms: 'glmnet'
<https://CRAN.R-project.org/package=glmnet>, 'ranger'
<https://CRAN.R-project.org/package=ranger>, 'xgboost'
<https://CRAN.R-project.org/package=xgboost>, and 'lightgbm'
<https://CRAN.R-project.org/package=lightgbm>. These can be used
directly with the 'mlexperiments' R package.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mllrnrs versions 0.0.6 dated 2025-09-08 and 0.0.7 dated 2025-12-04
DESCRIPTION | 12 - MD5 | 58 ++--- NAMESPACE | 20 - R/learner_lightgbm.R | 89 +++++-- R/learner_xgboost.R | 139 ++++++++---- R/zzz.R | 58 ++--- build/vignette.rds |binary inst/doc/mllrnrs_glmnet_binary.html | 180 ++++++++++++--- inst/doc/mllrnrs_glmnet_multiclass.html | 180 ++++++++++++--- inst/doc/mllrnrs_glmnet_regression.html | 180 ++++++++++++--- inst/doc/mllrnrs_lightgbm_binary.html | 180 ++++++++++++--- inst/doc/mllrnrs_lightgbm_multiclass.html | 180 ++++++++++++--- inst/doc/mllrnrs_lightgbm_regression.html | 180 ++++++++++++--- inst/doc/mllrnrs_ranger_binary.html | 180 ++++++++++++--- inst/doc/mllrnrs_ranger_multiclass.html | 180 ++++++++++++--- inst/doc/mllrnrs_ranger_regression.html | 180 ++++++++++++--- inst/doc/mllrnrs_xgboost_binary.html | 180 ++++++++++++--- inst/doc/mllrnrs_xgboost_multiclass.R | 52 ++-- inst/doc/mllrnrs_xgboost_multiclass.html | 234 +++++++++++++++----- inst/doc/mllrnrs_xgboost_multiclass.qmd | 56 ++-- inst/doc/mllrnrs_xgboost_regression.html | 180 ++++++++++++--- man/LearnerGlmnet.Rd | 296 ++++++++++++------------- man/LearnerLightgbm.Rd | 342 ++++++++++++++--------------- man/LearnerRanger.Rd | 298 ++++++++++++------------- man/LearnerXgboost.Rd | 344 +++++++++++++++--------------- tests/testthat.R | 30 +- tests/testthat/test-binary.R | 1 tests/testthat/test-lints.R | 26 +- tests/testthat/test-multiclass.R | 2 vignettes/mllrnrs_xgboost_multiclass.qmd | 56 ++-- 30 files changed, 2746 insertions(+), 1347 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-31 0.2.0
2019-11-18 0.1.8
2019-08-05 0.1.6
2019-06-28 0.1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-28 0.1.7
2025-09-24 0.1.6
2025-07-14 0.1.5
2025-06-09 0.1.4
2025-04-24 0.1.3
2025-04-16 0.1.2
2025-03-05 0.1.0
Title: Optimal Confidence Intervals for Visual Testing
Description: Identifies the optimal confidence level to represent the results of a set of pairwise tests as suggested by Armstrong and Poirier (2025) <doi:10.1017/pan.2024.24>.
Author: Dave Armstrong [aut, cre] ,
William Poirier [aut]
Maintainer: Dave Armstrong <davearmstrong.ps@gmail.com>
Diff between VizTest versions 0.5 dated 2025-08-29 and 0.6 dated 2025-12-04
VizTest-0.5/VizTest/inst/doc/viztest_intro.R |only VizTest-0.5/VizTest/inst/doc/viztest_intro.Rmd |only VizTest-0.5/VizTest/inst/doc/viztest_intro.html |only VizTest-0.5/VizTest/vignettes/viztest_intro.Rmd |only VizTest-0.6/VizTest/DESCRIPTION | 16 VizTest-0.6/VizTest/MD5 | 56 +- VizTest-0.6/VizTest/NAMESPACE | 20 VizTest-0.6/VizTest/R/functions.R | 389 +++++++++++++- VizTest-0.6/VizTest/README.md |only VizTest-0.6/VizTest/build/vignette.rds |binary VizTest-0.6/VizTest/inst/doc/compact_letter_displays.R |only VizTest-0.6/VizTest/inst/doc/compact_letter_displays.Rmd |only VizTest-0.6/VizTest/inst/doc/compact_letter_displays.html |only VizTest-0.6/VizTest/inst/doc/heatmaps.R |only VizTest-0.6/VizTest/inst/doc/heatmaps.Rmd |only VizTest-0.6/VizTest/inst/doc/heatmaps.html |only VizTest-0.6/VizTest/inst/doc/sig_diffs_explanation.R |only VizTest-0.6/VizTest/inst/doc/sig_diffs_explanation.Rmd |only VizTest-0.6/VizTest/inst/doc/sig_diffs_explanation.html |only VizTest-0.6/VizTest/inst/doc/significance_brackets.R |only VizTest-0.6/VizTest/inst/doc/significance_brackets.Rmd |only VizTest-0.6/VizTest/inst/doc/significance_brackets.html |only VizTest-0.6/VizTest/inst/doc/viztest_intro_v2.R |only VizTest-0.6/VizTest/inst/doc/viztest_intro_v2.Rmd |only VizTest-0.6/VizTest/inst/doc/viztest_intro_v2.html |only VizTest-0.6/VizTest/man/get_letters.Rd |only VizTest-0.6/VizTest/man/make_annotations.Rd |only VizTest-0.6/VizTest/man/make_vt_data.Rd | 15 VizTest-0.6/VizTest/man/plot.viztest.Rd | 34 + VizTest-0.6/VizTest/man/viztest.Rd | 4 VizTest-0.6/VizTest/tests |only VizTest-0.6/VizTest/vignettes/RJreferences.bib | 64 ++ VizTest-0.6/VizTest/vignettes/compact_letter_displays.Rmd |only VizTest-0.6/VizTest/vignettes/heatmaps.Rmd |only VizTest-0.6/VizTest/vignettes/sig_diffs_explanation.Rmd |only VizTest-0.6/VizTest/vignettes/significance_brackets.Rmd |only VizTest-0.6/VizTest/vignettes/viztest_intro_v2.Rmd |only 37 files changed, 556 insertions(+), 42 deletions(-)
Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of
statistical regression models. The central algorithm is
Fisher scoring and iterative reweighted least squares.
At the heart of this package are the vector generalized linear
and additive model (VGLM/VGAM) classes. VGLMs can be loosely
thought of as multivariate GLMs. VGAMs are data-driven
VGLMs that use smoothing. The book "Vector Generalized
Linear and Additive Models: With an Implementation in R"
(Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of
the statistical framework and the package. Currently only
fixed-effects models are implemented. Many (100+) models and
distributions are estimated by maximum likelihood estimation
(MLE) or penalized MLE. The other classes are RR-VGLMs
(reduced-rank VGLMs), quadratic RR-VGLMs, doubly constrained
RR-VGLMs, quadratic RR-VGLMs, reduced-rank VGAMs,
RCIMs (row-column interaction models)---these classes perform
constrained and unconstrained quadratic ordination (CQO/UQO)
models in ecolog [...truncated...]
Author: Thomas Yee [aut, cre] ,
Cleve Moler [ctb]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAM versions 1.1-13 dated 2025-02-12 and 1.1-14 dated 2025-12-04
VGAM-1.1-13/VGAM/R/Linksold.R |only VGAM-1.1-13/VGAM/data/flourbeetle.rda |only VGAM-1.1-13/VGAM/man/flourbeetle.Rd |only VGAM-1.1-14/VGAM/DESCRIPTION | 10 VGAM-1.1-14/VGAM/MD5 | 196 ++--- VGAM-1.1-14/VGAM/NAMESPACE | 48 + VGAM-1.1-14/VGAM/NEWS | 63 + VGAM-1.1-14/VGAM/R/family.aunivariate.R | 9 VGAM-1.1-14/VGAM/R/family.basics.R | 201 +++-- VGAM-1.1-14/VGAM/R/family.binomial.R | 270 ++++--- VGAM-1.1-14/VGAM/R/family.categorical.R | 312 ++++++-- VGAM-1.1-14/VGAM/R/family.circular.R | 897 ++++++++++++++++--------- VGAM-1.1-14/VGAM/R/family.functions.R | 127 ++- VGAM-1.1-14/VGAM/R/family.gaitd.R | 15 VGAM-1.1-14/VGAM/R/family.glmgam.R | 229 ++++-- VGAM-1.1-14/VGAM/R/family.loglin.R | 932 ++++++++++++++++++++++++-- VGAM-1.1-14/VGAM/R/family.positive.R | 76 ++ VGAM-1.1-14/VGAM/R/family.rrr.R | 93 +- VGAM-1.1-14/VGAM/R/family.univariate.R | 273 ++++--- VGAM-1.1-14/VGAM/R/family.zeroinf.R | 31 VGAM-1.1-14/VGAM/R/hdeff.R | 492 +++++++++++-- VGAM-1.1-14/VGAM/R/links.q | 145 ++-- VGAM-1.1-14/VGAM/R/logLik.vlm.q | 56 - VGAM-1.1-14/VGAM/R/model.matrix.vglm.q | 68 + VGAM-1.1-14/VGAM/R/summary.vgam.q | 2 VGAM-1.1-14/VGAM/R/summary.vglm.q | 359 +++++++++- VGAM-1.1-14/VGAM/R/vcov.pvgam.R | 1 VGAM-1.1-14/VGAM/R/vglm.control.q | 96 +- VGAM-1.1-14/VGAM/R/vglm.fit.q | 69 + VGAM-1.1-14/VGAM/build/partial.rdb |binary VGAM-1.1-14/VGAM/data/Huggins89.t1.rda |binary VGAM-1.1-14/VGAM/data/Huggins89table1.rda |binary VGAM-1.1-14/VGAM/data/alclevels.rda |binary VGAM-1.1-14/VGAM/data/alcoff.rda |binary VGAM-1.1-14/VGAM/data/auuc.rda |binary VGAM-1.1-14/VGAM/data/backPain.rda |binary VGAM-1.1-14/VGAM/data/backPain2.rda |binary VGAM-1.1-14/VGAM/data/beggs.rda |binary VGAM-1.1-14/VGAM/data/budworm.rda |binary VGAM-1.1-14/VGAM/data/car.all.rda |binary VGAM-1.1-14/VGAM/data/cfibrosis.rda |binary VGAM-1.1-14/VGAM/data/corbet.rda |binary VGAM-1.1-14/VGAM/data/crashbc.rda |binary VGAM-1.1-14/VGAM/data/crashf.rda |binary VGAM-1.1-14/VGAM/data/crashi.rda |binary VGAM-1.1-14/VGAM/data/crashmc.rda |binary VGAM-1.1-14/VGAM/data/crashp.rda |binary VGAM-1.1-14/VGAM/data/crashtr.rda |binary VGAM-1.1-14/VGAM/data/deermice.rda |binary VGAM-1.1-14/VGAM/data/ducklings.rda |binary VGAM-1.1-14/VGAM/data/eyed.rda |only VGAM-1.1-14/VGAM/data/fbeetle.rda |only VGAM-1.1-14/VGAM/data/finney44.rda |binary VGAM-1.1-14/VGAM/data/hspider.rda |binary VGAM-1.1-14/VGAM/data/lakeO.rda |binary VGAM-1.1-14/VGAM/data/leukemia.rda |binary VGAM-1.1-14/VGAM/data/lpossums.rda |binary VGAM-1.1-14/VGAM/data/marital.nz.rda |binary VGAM-1.1-14/VGAM/data/melbmaxtemp.rda |binary VGAM-1.1-14/VGAM/data/pneumo.rda |binary VGAM-1.1-14/VGAM/data/prinia.rda |binary VGAM-1.1-14/VGAM/data/ruge.rda |binary VGAM-1.1-14/VGAM/data/toxop.rda |binary VGAM-1.1-14/VGAM/data/venice.rda |binary VGAM-1.1-14/VGAM/data/venice90.rda |binary VGAM-1.1-14/VGAM/data/wine.rda |binary VGAM-1.1-14/VGAM/inst/CITATION | 27 VGAM-1.1-14/VGAM/man/CM.equid.Rd | 41 - VGAM-1.1-14/VGAM/man/CommonVGAMffArguments.Rd | 87 ++ VGAM-1.1-14/VGAM/man/VGAM-package.Rd | 9 VGAM-1.1-14/VGAM/man/acat.Rd | 5 VGAM-1.1-14/VGAM/man/binom2.or.Rd | 7 VGAM-1.1-14/VGAM/man/binomialff.Rd | 7 VGAM-1.1-14/VGAM/man/binormalUC.Rd | 10 VGAM-1.1-14/VGAM/man/cardUC.Rd | 109 +-- VGAM-1.1-14/VGAM/man/cardioid.Rd | 139 +++ VGAM-1.1-14/VGAM/man/cops.Rd | 221 ++++-- VGAM-1.1-14/VGAM/man/cops3.Rd |only VGAM-1.1-14/VGAM/man/copsd.Rd |only VGAM-1.1-14/VGAM/man/copsd3.Rd |only VGAM-1.1-14/VGAM/man/cratio.Rd | 4 VGAM-1.1-14/VGAM/man/cumulative.Rd | 110 ++- VGAM-1.1-14/VGAM/man/depvar.Rd | 60 + VGAM-1.1-14/VGAM/man/dgaitdplot.Rd | 5 VGAM-1.1-14/VGAM/man/eyed.Rd |only VGAM-1.1-14/VGAM/man/fbeetle.Rd |only VGAM-1.1-14/VGAM/man/genpoisson1.Rd | 2 VGAM-1.1-14/VGAM/man/loglinb3.Rd | 137 ++- VGAM-1.1-14/VGAM/man/loglinb4.Rd |only VGAM-1.1-14/VGAM/man/model.framevlm.Rd | 10 VGAM-1.1-14/VGAM/man/multilogitlink.Rd | 24 VGAM-1.1-14/VGAM/man/multinomial.Rd | 211 +++-- VGAM-1.1-14/VGAM/man/negbinomial.Rd | 6 VGAM-1.1-14/VGAM/man/notdocumentedyet.Rd | 30 VGAM-1.1-14/VGAM/man/poissonff.Rd | 17 VGAM-1.1-14/VGAM/man/posbernoulli.t.Rd | 7 VGAM-1.1-14/VGAM/man/propodds.Rd | 5 VGAM-1.1-14/VGAM/man/sratio.Rd | 4 VGAM-1.1-14/VGAM/man/summaryvglm.Rd | 17 VGAM-1.1-14/VGAM/man/trplot.qrrvglm.Rd | 9 VGAM-1.1-14/VGAM/man/undocumented-methods.Rd | 3 VGAM-1.1-14/VGAM/man/vglm.control.Rd | 64 + VGAM-1.1-14/VGAM/man/vonmises.Rd | 2 VGAM-1.1-14/VGAM/man/wsdm.Rd | 56 - VGAM-1.1-14/VGAM/man/wsdm3.Rd |only 105 files changed, 4839 insertions(+), 1676 deletions(-)
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Hippocampal
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12' preprocessed
datasets and 'HippUnfold' hippocampal segmentation outputs for a given
sample by restructuring the data values into a single file. The single
file can then be used by the package for analyses independently from
its base dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.4.3 dated 2025-10-21 and 1.4.4 dated 2025-12-04
DESCRIPTION | 11 ++- MD5 | 31 +++++------ NAMESPACE | 4 + NEWS.md | 13 ++++ R/RFT_vertex_analysis.R | 39 ++++++++----- R/TFCE_vertex_analysis.R | 92 +++++++++++++++++++++++---------- R/TFCE_vertex_analysis_mixed.R | 59 +++++++++------------ R/VWRfirstrun.R | 2 R/other_functions.R | 20 +++++-- R/plot_surf.R | 22 ++++++- R/plot_surf3d.R | 92 ++++++++++++++++++++++++--------- inst/python/brainstat.stats.SLM_VWR.py | 81 +++++++++++++++++++++++++---- man/RFT_vertex_analysis.Rd | 5 + man/TFCE_vertex_analysis.Rd | 5 + man/TFCE_vertex_analysis_mixed.Rd | 5 + man/plot_surf3d.Rd | 10 ++- vignettes/SPRENG_tstatmaps.png |only 17 files changed, 350 insertions(+), 141 deletions(-)
Title: Pipeline for Explainable Machine Learning with Functional Data
Description: Implements the Variable importance Explainable Elastic Shape Analysis pipeline for explainable machine learning with functional data inputs. Converts training and testing data functional inputs to elastic shape analysis principal components that account for vertical and/or horizontal variability. Computes feature importance to identify important principal components and visualizes variability captured by functional principal components. See Goode et al. (2025) <doi:10.48550/arXiv.2501.07602> for technical details about the methodology.
Author: Katherine Goode [cre, aut],
J. Derek Tucker [aut],
Sandia National Laboratories [cph, fnd]
Maintainer: Katherine Goode <kjgoode@sandia.gov>
Diff between veesa versions 0.1.6 dated 2025-01-17 and 0.1.7 dated 2025-12-04
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NAMESPACE | 1 + NEWS.md | 13 +++++++++++++ R/plot_pc_diffs.R |only README.md | 2 ++ man/plot_pc_diffs.Rd |only 7 files changed, 26 insertions(+), 8 deletions(-)
Title: VA CVD Risk Score
Description: Estimates the predicted 10-year cardiovascular (CVD) risk score (in probability) for civilian women, women military service
members and veterans by inputting patient profiles. The proposed women CVD risk score improves the accuracy of the
existing American College of Cardiology/American Heart Association CVD risk assessment
tool in predicting long‐term CVD risk for VA women, particularly in young and racial/ethnic
minority women. See the reference: Jeon‐Slaughter, H., Chen, X., Tsai, S., Ramanan, B., & Ebrahimi, R.
(2021) <doi:10.1161/JAHA.120.019217>.
Author: Xiaofei Chen [aut, cre],
Haekyung Jeon-Slaughter [aut]
Maintainer: Xiaofei Chen <bill.nj08873@gmail.com>
Diff between vaRiskScore versions 1.1.0 dated 2023-05-31 and 2.0.0 dated 2025-12-04
DESCRIPTION | 10 +- MD5 | 8 +- NAMESPACE | 4 - R/vaScore.R | 193 +++++++++++++++++++++++++++++++++++++++++++++++++++++---- man/vaScore.Rd | 18 +++-- 5 files changed, 205 insertions(+), 28 deletions(-)
Title: Time Series with Matrix Profile
Description: A toolkit implementing the Matrix Profile concept
that was created by CS-UCR
<http://www.cs.ucr.edu/~eamonn/MatrixProfile.html>.
Author: Francisco Bischoff [aut, cre] ,
Michael Yeh [res, ccp, ctb] ,
Diego Silva [res, ccp, ctb] ,
Yan Zhu [res, ccp, ctb] ,
Hoang Dau [res, ccp, ctb] ,
Michele Linardi [res, ccp, ctb]
Maintainer: Francisco Bischoff <fbischoff@med.up.pt>
Diff between tsmp versions 0.4.15 dated 2022-08-20 and 0.4.16 dated 2025-12-04
DESCRIPTION | 27 ++-- MD5 | 37 ++--- NEWS | 250 +++++++++++++++++++------------------ NEWS.md | 252 +++++++++++++++++++------------------- README.md | 122 +++++++++--------- build/vignette.rds |binary inst/API-v0.4.16 |only inst/doc/press.R | 4 inst/doc/press.html | 122 +++++++++--------- inst/schemaorg.json | 4 man/figures/dependency_plot-1.png |binary man/floss.Rd | 4 man/floss_cac.Rd | 6 man/floss_extract.Rd | 6 man/fluss.Rd | 2 man/fluss_cac.Rd | 6 man/fluss_extract.Rd | 6 man/fluss_score.Rd | 6 src/Makevars | 2 src/Makevars.win | 2 20 files changed, 438 insertions(+), 420 deletions(-)
Title: Manipulation of Microsoft Word and PowerPoint Documents
Description: Access and manipulate 'Microsoft Word', 'RTF' and 'Microsoft
PowerPoint' documents from R. The package focuses on tabular and
graphical reporting from R; it also provides two functions that let
users get document content into data objects. A set of functions lets
add and remove images, tables and paragraphs of text in new or
existing documents. The package does not require any installation of
Microsoft products to be able to write Microsoft files.
Author: David Gohel [aut, cre],
Stefan Moog [aut],
Mark Heckmann [aut] ,
ArData [cph],
Frank Hangler [ctb] ,
Liz Sander [ctb] ,
Anton Victorson [ctb] ,
Jon Calder [ctb] ,
John Harrold [ctb] ,
John Muschelli [ctb] ,
Bill Denney [ctb] ,
Nikolai Beck [ctb] ,
Gr [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between officer versions 0.7.1 dated 2025-11-14 and 0.7.2 dated 2025-12-04
DESCRIPTION | 6 MD5 | 36 +++-- NAMESPACE | 5 NEWS.md | 15 ++ R/dev-utils.R | 265 +++++++++++++++++++++++++++++++++++++------ R/formatting_properties.R | 3 R/fortify_docx.R | 20 +-- R/officer.R | 28 ++++ R/ooxml_block_objects.R | 23 ++- R/post-proc.R | 16 ++ R/rtf.R | 5 R/utils.R | 4 man/as_base64.Rd |only man/base64_to_image.Rd |only man/docx_summary.Rd | 3 man/from_base64.Rd |only man/image_to_base64.Rd | 4 man/officer.Rd | 31 +++++ man/plot_in_png.Rd |only man/unordered_list.Rd | 23 ++- tests/testthat/test-images.R | 176 ++++++++++++++++++++++++++++ 21 files changed, 571 insertions(+), 92 deletions(-)
Title: Legends for Maps
Description: Create legends for maps and other graphics. Thematic maps need to
be accompanied by legible legends to be fully comprehensible. This package
offers a wide range of legends useful for cartography, some of which may
also be useful for other types of graphics.
Author: Timothee Giraud [cre, aut]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between maplegend versions 0.3.0 dated 2025-06-30 and 0.4.0 dated 2025-12-04
DESCRIPTION | 8 MD5 | 51 ++- NAMESPACE | 2 NEWS.md | 11 R/leg.R | 81 +++--- R/leg_comp.R | 16 - R/leg_draw.R | 36 +- R/leg_histo.R |only R/lg_choro.R | 268 +++++++++----------- R/lg_choro_horiz.R | 282 ++++++++-------------- R/lg_cont.R | 14 - R/lg_cont_horiz.R | 17 - R/lg_grad_line.R | 208 +++++++--------- R/lg_prop.R | 438 +++++++++------------------------- R/lg_prop_horiz.R | 232 ++++++++---------- R/lg_prop_line.R | 204 ++++++--------- R/lg_symb.R | 279 +++++++++------------ R/lg_typo.R | 248 ++++++++----------- R/lg_utils.R | 485 ++++++++++++++------------------------ README.md | 21 + inst/tinytest/test_comp.R | 27 ++ inst/tinytest/test_coords.R | 31 +- inst/tinytest/tests.R | 74 +++++ man/figures/README-example-1.png |binary man/figures/README-example2-1.png |binary man/leg.Rd | 59 +++- man/leg_comp.Rd | 17 - 27 files changed, 1373 insertions(+), 1736 deletions(-)
Title: Political Science Academic Research Gears
Description: Using these tools to simplify the research process of political science and other social sciences. The current version can create folder system for academic project in political science, calculate psychological trait scores, visualize experimental and spatial data, and set up color-blind palette, functions used in academic research of political psychology or political science in general.
Author: Yue Hu [aut, cre],
Qian Qiu [ctb],
Wen Deng [ctb]
Maintainer: Yue Hu <yuehu@tsinghua.edu.cn>
Diff between drhutools versions 1.0.0 dated 2024-12-05 and 1.0.1 dated 2025-12-04
DESCRIPTION | 16 +- MD5 | 22 +-- NAMESPACE | 1 NEWS.md | 6 R/goodmap.R | 332 ++++++++++++++++++------------------------------ R/sysdata.rda |only R/traits.R | 33 +++- R/utils.R |only build/vignette.rds |binary inst/doc/drhutools.Rmd | 1 inst/doc/drhutools.html | 43 +++--- man/goodmap.Rd | 8 - vignettes/drhutools.Rmd | 1 13 files changed, 209 insertions(+), 254 deletions(-)
Title: Doubly Robust Difference-in-Differences Estimators
Description: Implements the locally efficient doubly robust difference-in-differences (DiD)
estimators for the average treatment effect proposed by Sant'Anna and Zhao (2020)
<doi:10.1016/j.jeconom.2020.06.003>. The estimator combines inverse probability weighting and outcome
regression estimators (also implemented in the package) to form estimators with
more attractive statistical properties. Two different estimation methods can be used
to estimate the nuisance functions.
Author: Pedro H. C. Sant'Anna [aut, cre, cph],
Jun Zhao [aut]
Maintainer: Pedro H. C. Sant'Anna <pedrohcgs@gmail.com>
Diff between DRDID versions 1.2.2 dated 2025-05-30 and 1.2.3 dated 2025-12-04
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 5 ++++- R/drdid_imp_panel.R | 2 +- R/drdid_imp_rc.R | 12 ++++++------ R/drdid_imp_rc1.R | 2 +- R/drdid_panel.R | 2 +- R/drdid_rc.R | 2 +- R/drdid_rc1.R | 2 +- R/ipw_did_panel.R | 6 +++--- R/ipw_did_rc.R | 12 ++++++------ R/reg_did_panel.R | 2 +- R/reg_did_rc.R | 2 +- R/std_ipw_did_panel.R | 2 +- R/std_ipw_did_rc.R | 2 +- 15 files changed, 46 insertions(+), 43 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.15 [...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 7.9 dated 2025-11-18 and 8.0 dated 2025-12-04
DESCRIPTION | 14 +++++++------- MD5 | 30 +++++++++++++++++------------- NAMESPACE | 1 + R/diria0.est.R |only R/pyramid.R |only R/tflr.R | 13 +++++++------ R/tflr.betest.R | 6 +++--- R/tflr.indeptest.R | 6 +++--- R/tflr.irls.R | 2 +- R/tflr2.R | 4 ++-- man/Compositional-package.Rd | 4 ++-- man/diria0.est.Rd |only man/pyramid.Rd |only man/ternary.Rd | 2 +- man/tflr.Rd | 14 ++++++++------ man/tflr.betest.Rd | 5 ++++- man/tflr.indeptest.Rd | 7 +++++-- man/tflr2.Rd | 5 ++++- 18 files changed, 65 insertions(+), 48 deletions(-)
Title: Extra Analysis Results Data Utilities
Description: Create extra Analysis Results Data (ARD) summary objects.
The package supplements the simple ARD functions from the 'cards'
package, exporting functions to put statistical results in the ARD
format. These objects are used and re-used to construct summary
tables, visualizations, and written reports.
Author: Daniel D. Sjoberg [aut, cre] ,
Abinaya Yogasekaram [aut],
Emily de la Rua [aut],
Malcolm Barrett [ctb] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cardx versions 0.3.0 dated 2025-08-27 and 0.3.1 dated 2025-12-04
cardx-0.3.0/cardx/R/ard_emmeans_mean_difference.R |only cardx-0.3.0/cardx/man/ard_emmeans_mean_difference.Rd |only cardx-0.3.0/cardx/tests/testthat/_snaps/ard_emmeans_mean_difference.md |only cardx-0.3.0/cardx/tests/testthat/test-ard_emmeans_mean_difference.R |only cardx-0.3.1/cardx/DESCRIPTION | 8 cardx-0.3.1/cardx/MD5 | 221 +++++----- cardx-0.3.1/cardx/NAMESPACE | 2 cardx-0.3.1/cardx/NEWS.md | 8 cardx-0.3.1/cardx/R/ard_categorical_ci.R | 8 cardx-0.3.1/cardx/R/ard_emmeans_contrast.R |only cardx-0.3.1/cardx/R/ard_emmeans_emmeans.R |only cardx-0.3.1/cardx/R/ard_incidence_rate.R | 2 cardx-0.3.1/cardx/R/ard_stats_mantelhaen_test.R | 2 cardx-0.3.1/cardx/R/ard_tabulate_abnormal.R | 2 cardx-0.3.1/cardx/R/deprecated.R | 12 cardx-0.3.1/cardx/R/import-standalone-check_pkg_installed.R | 95 +--- cardx-0.3.1/cardx/R/import-standalone-cli_call_env.R | 7 cardx-0.3.1/cardx/README.md | 2 cardx-0.3.1/cardx/man/ard_aod_wald_test.Rd | 2 cardx-0.3.1/cardx/man/ard_attributes.Rd | 2 cardx-0.3.1/cardx/man/ard_car_anova.Rd | 2 cardx-0.3.1/cardx/man/ard_car_vif.Rd | 2 cardx-0.3.1/cardx/man/ard_categorical_ci.Rd | 2 cardx-0.3.1/cardx/man/ard_categorical_ci.survey.design.Rd | 2 cardx-0.3.1/cardx/man/ard_continuous_ci.Rd | 2 cardx-0.3.1/cardx/man/ard_continuous_ci.survey.design.Rd | 2 cardx-0.3.1/cardx/man/ard_effectsize_cohens_d.Rd | 2 cardx-0.3.1/cardx/man/ard_effectsize_hedges_g.Rd | 2 cardx-0.3.1/cardx/man/ard_emmeans.Rd |only cardx-0.3.1/cardx/man/ard_missing.survey.design.Rd | 2 cardx-0.3.1/cardx/man/ard_regression.Rd | 2 cardx-0.3.1/cardx/man/ard_regression_basic.Rd | 2 cardx-0.3.1/cardx/man/ard_smd_smd.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_anova.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_aov.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_chisq_test.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_fisher_test.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_kruskal_test.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_mantelhaen_test.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_mcnemar_test.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_mood_test.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_oneway_test.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_poisson_test.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_prop_test.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_t_test.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_t_test_onesample.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_wilcox_test.Rd | 2 cardx-0.3.1/cardx/man/ard_stats_wilcox_test_onesample.Rd | 2 cardx-0.3.1/cardx/man/ard_summary.survey.design.Rd | 2 cardx-0.3.1/cardx/man/ard_survey_svychisq.Rd | 2 cardx-0.3.1/cardx/man/ard_survey_svyranktest.Rd | 2 cardx-0.3.1/cardx/man/ard_survey_svyttest.Rd | 2 cardx-0.3.1/cardx/man/ard_survival_survdiff.Rd | 2 cardx-0.3.1/cardx/man/ard_survival_survfit.Rd | 2 cardx-0.3.1/cardx/man/ard_survival_survfit_diff.Rd | 2 cardx-0.3.1/cardx/man/ard_tabulate.survey.design.Rd | 2 cardx-0.3.1/cardx/man/ard_tabulate_value.survey.design.Rd | 2 cardx-0.3.1/cardx/man/ard_total_n.survey.design.Rd | 2 cardx-0.3.1/cardx/man/construction_helpers.Rd | 2 cardx-0.3.1/cardx/man/deprecated.Rd | 3 cardx-0.3.1/cardx/man/dot-format_cohens_d_results.Rd | 2 cardx-0.3.1/cardx/man/dot-format_hedges_g_results.Rd | 2 cardx-0.3.1/cardx/man/dot-format_mcnemartest_results.Rd | 2 cardx-0.3.1/cardx/man/dot-format_moodtest_results.Rd | 2 cardx-0.3.1/cardx/man/dot-format_poissontest_results.Rd | 2 cardx-0.3.1/cardx/man/dot-format_survfit_results.Rd | 2 cardx-0.3.1/cardx/man/dot-format_ttest_results.Rd | 2 cardx-0.3.1/cardx/man/dot-format_wilcoxtest_results.Rd | 2 cardx-0.3.1/cardx/man/dot-process_survfit_probs.Rd | 2 cardx-0.3.1/cardx/man/dot-process_survfit_time.Rd | 2 cardx-0.3.1/cardx/man/proportion_ci.Rd | 2 cardx-0.3.1/cardx/tests/testthat/_snaps/ard_emmeans_contrast.md |only cardx-0.3.1/cardx/tests/testthat/_snaps/ard_emmeans_emmeans.md |only cardx-0.3.1/cardx/tests/testthat/test-ard_aod_wald_test.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_attributes.survey.design.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_car_anova.R | 4 cardx-0.3.1/cardx/tests/testthat/test-ard_car_vif.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_categorical_ci.data.frame.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_categorical_ci.survey.design.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_continuous_ci.data.frame.R | 7 cardx-0.3.1/cardx/tests/testthat/test-ard_continuous_ci.survey.design.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_effectsize_cohens_d.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_effectsize_hedges_g.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_emmeans_contrast.R |only cardx-0.3.1/cardx/tests/testthat/test-ard_emmeans_emmeans.R |only cardx-0.3.1/cardx/tests/testthat/test-ard_missing.survey.design.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_proportion_ci.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_regression.R | 7 cardx-0.3.1/cardx/tests/testthat/test-ard_regression_basic.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_smd_smd.R | 4 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_anova.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_aov.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_chisq_test.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_fisher_test.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_kruskal_test.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_mantelhaen_test.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_mcnemar_test.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_mood_test.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_oneway_test.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_poisson_test.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_prop_test.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_t_test.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_t_test_onesample.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_wilcox_test.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_stats_wilcox_test_onesample.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_summary.survey.design.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_survey_svychisq.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_survey_svyranktest.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_survey_svyttest.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_survival_survdiff.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_survival_survfit.R | 4 cardx-0.3.1/cardx/tests/testthat/test-ard_survival_survfit_diff.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_tabulate.survey.design.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_tabulate_value.survey.design.R | 2 cardx-0.3.1/cardx/tests/testthat/test-ard_total_n.survey.design.R | 2 cardx-0.3.1/cardx/tests/testthat/test-construction_helpers.R | 2 cardx-0.3.1/cardx/tests/testthat/test-proportion_ci.R | 2 117 files changed, 292 insertions(+), 282 deletions(-)