Title: R Interface for Apache Sedona
Description: R interface for 'Apache Sedona' based on 'sparklyr'
(<https://sedona.apache.org>).
Author: Apache Sedona [aut, cre],
Jia Yu [ctb, cph],
Yitao Li [aut, cph] ,
The Apache Software Foundation [cph],
RStudio [cph]
Maintainer: Apache Sedona <private@sedona.apache.org>
Diff between apache.sedona versions 1.7.2 dated 2025-06-08 and 1.8.0 dated 2025-09-12
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/dependencies.R | 4 ++-- README.md | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Discontinuous Hamiltonian Monte Carlo with Varying Trajectory
Length
Description: Hamiltonian Monte Carlo for both continuous and discontinuous posterior
distributions with a customizable trajectory length termination criterion.
See Nishimura et al. (2020) <doi:10.1093/biomet/asz083> for the original
Discontinuous Hamiltonian Monte Carlo; Hoffman et al. (2014)
<doi:10.48550/arXiv.1111.4246> and Betancourt (2016) <doi:10.48550/arXiv.1601.00225>
for the definition of possible Hamiltonian Monte Carlo termination criteria.
Author: Paolo Manildo [aut, cre]
Maintainer: Paolo Manildo <paolo.manildo@phd.unipd.it>
Diff between XDNUTS versions 1.6.3 dated 2025-09-07 and 1.6.4 dated 2025-09-12
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/partial.rdb |binary inst/doc/Tutorial_for_main_functions.R | 1 + inst/doc/Tutorial_for_main_functions.Rmd | 1 + inst/doc/Tutorial_for_main_functions.html | 6 +++--- vignettes/Tutorial_for_main_functions.Rmd | 1 + 7 files changed, 16 insertions(+), 13 deletions(-)
Title: Object Oriented Solution for Robust Factor Analysis
Description: Outliers virtually exist in any datasets of any application field.
To avoid the impact of outliers, we need to use robust estimators.
Classical estimators of multivariate mean and covariance matrix are
the sample mean and the sample covariance matrix. Outliers will
affect the sample mean and the sample covariance matrix, and thus
they will affect the classical factor analysis which depends on
the classical estimators (Pison, G., Rousseeuw, P.J., Filzmoser,
P. and Croux, C. (2003) <doi:10.1016/S0047-259X(02)00007-6>).
So it is necessary to use the robust estimators of the sample
mean and the sample covariance matrix. There are several robust
estimators in the literature: Minimum Covariance Determinant estimator,
Orthogonalized Gnanadesikan-Kettenring, Minimum Volume Ellipsoid,
M, S, and Stahel-Donoho.
The most direct way to make multivariate analysis more robust is to replace
the sample mean and the sample covariance matrix of the classical estimators
to robust estimators (Maronna [...truncated...]
Author: Frederic Bertrand [cre] ,
Ying-Ying Zhang [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between robustfa versions 1.1-0 dated 2023-04-16 and 1.2-0 dated 2025-09-12
DESCRIPTION | 23 ++++-- MD5 | 30 ++++++--- NAMESPACE | 8 +- NEWS.md | 27 ++++++-- R/Z_accessors.R |only build/partial.rdb |binary build/vignette.rds |binary inst/_pkgdown.yml |only inst/doc/robustfa-knitr.pdf |binary inst/helper |only man/FaCov.Rd | 10 +-- man/figures |only man/myplotDD.Rd | 146 ++++++++++++++++++++++---------------------- tests |only 14 files changed, 138 insertions(+), 106 deletions(-)
Title: Statistical Modelling in Action with R
Description: Datasets and functions for the book "Modélisation statistique par la pratique avec R", F. Bertrand, E. Claeys and M. Maumy-Bertrand (2019, ISBN:9782100793525, Dunod, Paris). The first chapter of the book is dedicated to an introduction to the R statistical software. The second chapter deals with correlation analysis: Pearson, Spearman and Kendall simple, multiple and partial correlation coefficients. New wrapper functions for permutation tests or bootstrap of matrices of correlation are provided with the package. The third chapter is dedicated to data exploration with factorial analyses (PCA, CA, MCA, MDA) and clustering. The fourth chapter is dedicated to regression analysis: fitting and model diagnostics are detailed. The exercises focus on covariance analysis, logistic regression, Poisson regression, two-way analysis of variance for fixed or random factors. Various example datasets are shipped with the package: for instance on pokemon, world of warcraft, house tasks or food nutritio [...truncated...]
Author: Frederic Bertrand [cre, aut] ,
Emmanuelle Claeys [aut],
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between ModStatR versions 1.4.0 dated 2025-08-27 and 1.4.1 dated 2025-09-12
DESCRIPTION | 29 ++++++++++++++--------------- MD5 | 8 ++++---- NEWS.md | 5 +++++ inst/CITATION | 5 +++-- man/ModStatR-package.Rd | 4 ++-- 5 files changed, 28 insertions(+), 23 deletions(-)
Title: Prioritize Variables with Joint Variable Importance Plot in
Observational Study Design
Description: In the observational study design stage, matching/weighting methods are
conducted. However, when many background variables are present, the decision as to
which variables to prioritize for matching/weighting is not trivial. Thus, the
joint treatment-outcome variable importance plots are created to guide variable
selection. The joint variable importance plots enhance variable comparisons via
unadjusted bias curves derived under the omitted variable bias framework. The
plots translate variable importance into recommended values for tuning parameters
in existing methods. Post-matching and/or weighting plots can also be used to
visualize and assess the quality of the observational study design. The method
motivation and derivation is presented in "Prioritizing Variables for Observational
Study Design using the Joint Variable Importance Plot" by Liao et al. (2024)
<doi:10.1080/00031305.2024.2303419>. See the package paper by Liao and Pimentel
(2024) <doi:10.21105/joss.06093> for [...truncated...]
Author: Lauren D. Liao [aut, cre] ,
Samuel D. Pimentel [aut]
Maintainer: Lauren D. Liao <ldliao@berkeley.edu>
Diff between jointVIP versions 1.0.0 dated 2024-11-21 and 1.0.1 dated 2025-09-12
DESCRIPTION | 12 +- MD5 | 14 +- NEWS.md | 4 inst/doc/additional_options.html | 6 - inst/doc/jointVIP.R | 3 inst/doc/jointVIP.Rmd | 3 inst/doc/jointVIP.html | 208 +++++++++++++++++++-------------------- vignettes/jointVIP.Rmd | 3 8 files changed, 128 insertions(+), 125 deletions(-)
Title: Read and Write 'jamovi' Files ('.omv')
Description: The free and open a statistical spreadsheet 'jamovi'
(<https://www.jamovi.org>) aims to make statistical analyses easy and
intuitive. 'jamovi' produces syntax that can directly be used in R (in
connection with the R-package 'jmv'). Having import / export routines for
the data files 'jamovi' produces ('.omv') permits an easy transfer of
data and analyses between 'jamovi' and R.
Author: Sebastian Jentschke [aut, cre, cph]
Maintainer: Sebastian Jentschke <sebastian.jentschke@uib.no>
Diff between jmvReadWrite versions 0.4.11 dated 2025-06-15 and 0.4.12 dated 2025-09-12
DESCRIPTION | 8 - MD5 | 93 ++++++++++----------- NAMESPACE | 1 NEWS.md | 11 ++ R/aggregate_omv.R |only R/arrange_cols_omv.R | 3 R/combine_cols_omv.R | 3 R/convert_to_omv.R | 3 R/describe_omv.R | 5 - R/distances_omv.R | 2 R/globals.R | 7 - R/label_vars_omv.R | 3 R/long2wide_omv.R | 3 R/merge_cols_omv.R | 3 R/merge_rows_omv.R | 3 R/read_omv.R | 29 ++++++ R/search_omv.R | 3 R/sort_omv.R | 3 R/transform_vars_omv.R | 2 R/transpose_omv.R | 3 R/wide2long_omv.R | 93 +++++++++++++-------- R/write_omv.R | 3 README.md | 4 build/vignette.rds |binary inst/CITATION | 2 inst/doc/jmvReadWrite.Rmd | 4 inst/doc/jmvReadWrite.html | 7 + man/aggregate_omv.Rd |only man/arrange_cols_omv.Rd | 3 man/combine_cols_omv.Rd | 3 man/convert_to_omv.Rd | 3 man/describe_omv.Rd | 5 - man/distances_omv.Rd | 2 man/label_vars_omv.Rd | 3 man/long2wide_omv.Rd | 3 man/merge_cols_omv.Rd | 3 man/merge_rows_omv.Rd | 3 man/read_omv.Rd | 29 ++++++ man/search_omv.Rd | 3 man/sort_omv.Rd | 3 man/transform_vars_omv.Rd | 2 man/transpose_omv.Rd | 3 man/wide2long_omv.Rd | 3 man/write_omv.Rd | 3 tests/testthat/test-aggregate_omv.R |only tests/testthat/test-combine_cols_omv.R | 2 tests/testthat/test-globals.R | 4 tests/testthat/test-wide2long_omv.R | 146 ++++++++++++++++++++++++++++----- vignettes/jmvReadWrite.Rmd | 4 49 files changed, 356 insertions(+), 175 deletions(-)
Title: Visualizing Pedigrees with 'ggplot2' and 'plotly'
Description: Provides plotting functions for visualizing pedigrees in behavior genetics and kinship research. The package complements 'BGmisc' [Garrison et al. (2024) <doi:10.21105/joss.06203>] by rendering pedigrees using the 'ggplot2' framework and offers a modern alternative to the base-graphics pedigree plot in 'kinship2' [Sinnwell et al. (2014) <doi:10.1159/000363105>]. Features include support for duplicated individuals, complex mating structures, integration with simulated pedigrees, and layout customization.
Author: S. Mason Garrison [aut, cre, cph]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>
Diff between ggpedigree versions 0.8.0 dated 2025-07-04 and 0.9.0 dated 2025-09-12
ggpedigree-0.8.0/ggpedigree/man/makeSymmetricKey.Rd |only ggpedigree-0.8.0/ggpedigree/man/tooltip_fmt.Rd |only ggpedigree-0.9.0/ggpedigree/DESCRIPTION | 8 ggpedigree-0.9.0/ggpedigree/MD5 | 99 - ggpedigree-0.9.0/ggpedigree/NEWS.md | 25 ggpedigree-0.9.0/ggpedigree/R/calcConnections.R | 27 ggpedigree-0.9.0/ggpedigree/R/calcConnectionsHelpers.R | 12 ggpedigree-0.9.0/ggpedigree/R/calcCoordinates.R | 309 ++- ggpedigree-0.9.0/ggpedigree/R/defaultPlotConfig.R | 163 + ggpedigree-0.9.0/ggpedigree/R/documentData.R | 19 ggpedigree-0.9.0/ggpedigree/R/ggPedigreeInteractive.R | 163 + ggpedigree-0.9.0/ggpedigree/R/ggPhenotypeByDegree.R | 39 ggpedigree-0.9.0/ggpedigree/R/ggpedigree.R | 938 ++++++---- ggpedigree-0.9.0/ggpedigree/R/ggpedigreeHelpers.R | 91 ggpedigree-0.9.0/ggpedigree/R/plotPedigree.R | 64 ggpedigree-0.9.0/ggpedigree/R/processExtras.R | 8 ggpedigree-0.9.0/ggpedigree/README.md | 7 ggpedigree-0.9.0/ggpedigree/build/partial.rdb |binary ggpedigree-0.9.0/ggpedigree/build/vignette.rds |binary ggpedigree-0.9.0/ggpedigree/inst/doc/v00_plots.R | 29 ggpedigree-0.9.0/ggpedigree/inst/doc/v00_plots.Rmd | 33 ggpedigree-0.9.0/ggpedigree/inst/doc/v00_plots.html | 111 - ggpedigree-0.9.0/ggpedigree/inst/doc/v10_interactiveplots.html | 30 ggpedigree-0.9.0/ggpedigree/inst/doc/v20_matrix.html | 15 ggpedigree-0.9.0/ggpedigree/man/ASOIAF.Rd | 71 ggpedigree-0.9.0/ggpedigree/man/addFocalFillColumn.Rd |only ggpedigree-0.9.0/ggpedigree/man/addTwins.Rd |only ggpedigree-0.9.0/ggpedigree/man/alignPedigreeWithHints.Rd |only ggpedigree-0.9.0/ggpedigree/man/alignPedigreeWithRelations.Rd |only ggpedigree-0.9.0/ggpedigree/man/dot-addAnnotate.Rd | 3 ggpedigree-0.9.0/ggpedigree/man/dot-addLabels.Rd | 7 ggpedigree-0.9.0/ggpedigree/man/dot-addNodes.Rd | 7 ggpedigree-0.9.0/ggpedigree/man/dot-addOverlay.Rd | 13 ggpedigree-0.9.0/ggpedigree/man/dot-addScales.Rd | 7 ggpedigree-0.9.0/ggpedigree/man/dot-addSelfSegment.Rd | 7 ggpedigree-0.9.0/ggpedigree/man/dot-adjustSpacing.Rd | 73 ggpedigree-0.9.0/ggpedigree/man/dot-computeCurvedMidpoint.Rd | 89 ggpedigree-0.9.0/ggpedigree/man/dot-makeSymmetricKey.Rd |only ggpedigree-0.9.0/ggpedigree/man/dot-preparePhenotypeByDegreeData.Rd | 11 ggpedigree-0.9.0/ggpedigree/man/dot-restoreNames.Rd | 85 ggpedigree-0.9.0/ggpedigree/man/figures/README-basic-usage-1.png |binary ggpedigree-0.9.0/ggpedigree/man/figures/hex.png |binary ggpedigree-0.9.0/ggpedigree/man/formatTooltip.Rd |only ggpedigree-0.9.0/ggpedigree/man/getDefaultPlotConfig.Rd | 125 - ggpedigree-0.9.0/ggpedigree/man/ggPedigreeInteractive.Rd | 13 ggpedigree-0.9.0/ggpedigree/man/optimizePedigree.Rd |only ggpedigree-0.9.0/ggpedigree/man/optimizePlotlyPedigree.Rd |only ggpedigree-0.9.0/ggpedigree/man/optimizeStaticPedigree.Rd |only ggpedigree-0.9.0/ggpedigree/man/preparePedigreeData.Rd |only ggpedigree-0.9.0/ggpedigree/man/transformPed.Rd |only ggpedigree-0.9.0/ggpedigree/tests/testthat/Rplots.pdf |binary ggpedigree-0.9.0/ggpedigree/tests/testthat/test-calcConnectionsHelpers.R | 52 ggpedigree-0.9.0/ggpedigree/tests/testthat/test-defaultPlotConfig.R | 21 ggpedigree-0.9.0/ggpedigree/tests/testthat/test-ggPedigree.R | 107 + ggpedigree-0.9.0/ggpedigree/tests/testthat/test-ggPedigreeInteractive.R | 24 ggpedigree-0.9.0/ggpedigree/tests/testthat/test-plotPedigree.R | 4 ggpedigree-0.9.0/ggpedigree/vignettes/v00_plots.Rmd | 33 57 files changed, 1934 insertions(+), 1008 deletions(-)
Title: Creates Analysis Results Datasets
Description: Contains functions to help create an Analysis Results Dataset.
The dataset follows industry recommended structure. The dataset can be
created in multiple passes, using different data frames as input. Analysis
Results Datasets are used in the pharmaceutical and biotech industries
to capture analysis in a common tabular data structure.
Author: David Bosak [aut, cre],
Kevin Kramer [ctb],
Jack Fuller [ctb],
Matt Baldwin [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between ards versions 0.1.1 dated 2023-03-21 and 0.1.2 dated 2025-09-12
DESCRIPTION | 8 MD5 | 33 +-- NEWS.md | 5 R/ards.R | 8 README.md | 4 build/vignette.rds |binary inst/doc/ards.R | 2 inst/doc/ards.Rmd | 2 inst/doc/ards.html | 489 ++++++++++++++++++++++----------------------- man/ards.Rd | 20 + man/images/ards.png |only man/images/ards14.png |only man/images/ards15.png |only man/images/ards25.png |only man/images/ards3.png |only man/images/ards30.png |only man/images/ards4.png |only man/images/ards46.png |only man/images/logo.png |only man/init_ards.Rd | 2 tests/testthat/test-ards.R | 37 +++ vignettes/ards.Rmd | 2 22 files changed, 341 insertions(+), 271 deletions(-)
Title: Tutorials for "R for Data Science"
Description: When assigned "R for Data Science" (Wickham, Çetinkaya-Rundel,
and Grolemund (2023, ISBN: 1492097402)), students should read the book and
type in all the associated R commands themselves. Sadly, that never happens.
These tutorials allow students to demonstrate (and their instructors
to be sure) that all work has been completed. See Kane (2023)
<https://ppbds.github.io/tutorial.helpers/articles/instructions.html> from
the 'tutorial.helpers' package for a background discussion.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Diff between r4ds.tutorials versions 0.3.2 dated 2025-06-05 and 0.3.3 dated 2025-09-12
r4ds.tutorials-0.3.2/r4ds.tutorials/inst/tutorials/00-introduction |only r4ds.tutorials-0.3.2/r4ds.tutorials/inst/tutorials/02a-rstudio-and-code |only r4ds.tutorials-0.3.2/r4ds.tutorials/inst/tutorials/02b-rstudio-and-quarto |only r4ds.tutorials-0.3.2/r4ds.tutorials/inst/tutorials/04a-rstudio-and-github-introduction |only r4ds.tutorials-0.3.2/r4ds.tutorials/inst/tutorials/04b-rstudio-and-github-advanced |only r4ds.tutorials-0.3.2/r4ds.tutorials/inst/tutorials/06-terminal |only r4ds.tutorials-0.3.2/r4ds.tutorials/inst/tutorials/28-quarto-websites-introduction |only r4ds.tutorials-0.3.2/r4ds.tutorials/inst/tutorials/29-quarto-websites-advanced |only r4ds.tutorials-0.3.3/r4ds.tutorials/DESCRIPTION | 18 - r4ds.tutorials-0.3.3/r4ds.tutorials/MD5 | 120 ++-------- r4ds.tutorials-0.3.3/r4ds.tutorials/NEWS.md | 6 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/01-data-visualization/tutorial.Rmd | 4 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/03-data-transformation/tutorial.Rmd | 9 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/05-data-tidying/tutorial.Rmd | 4 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/07-data-import/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/08-getting-help/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/09-layers/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/10-exploratory-data-analysis/tutorial.Rmd | 4 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/11-communication/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/12-logical-vectors/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/13-numbers/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/14-strings/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/15-regular-expressions/tutorial.Rmd | 10 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/16-factors/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/17-dates-and-times/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/18-missing-values/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/19-joins/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/20-spreadsheets/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/21-databases/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/22-arrow/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/23-hierarchical-data/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/24-web-scraping/tutorial.Rmd | 17 - r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/25-functions/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/26-iteration/tutorial.Rmd | 2 r4ds.tutorials-0.3.3/r4ds.tutorials/inst/tutorials/27-a-field-guide-to-base-R/tutorial.Rmd | 2 35 files changed, 80 insertions(+), 148 deletions(-)
More information about r4ds.tutorials at CRAN
Permanent link
Title: Isotonic Inference for Circular Data
Description: A bunch of functions to deal with circular data under order restrictions.
Author: Sandra Barragan [aut, cre],
Miguel A. Fernandez [aut],
Cristina Rueda. [aut]
Maintainer: Sandra Barragan <sandra.barragan@gmail.com>
Diff between isocir versions 2.0-7.1 dated 2023-08-17 and 2.1 dated 2025-09-12
DESCRIPTION | 22 +- MD5 | 20 +- NEWS | 470 ++++++++++++++++++++++++---------------------------- R/plot.isocir.R | 354 +++++++++++++++++++-------------------- build/vignette.rds |binary inst/CITATION | 45 ++-- inst/COPYRIGHTS | 34 +-- inst/doc/isocir.pdf |binary man/CLM.Rd | 2 man/mrl.Rd | 2 man/plot.isocir.Rd | 2 11 files changed, 472 insertions(+), 479 deletions(-)
Title: Flexible Bayesian Model Selection and Model Averaging
Description: Implements the Mode Jumping Markov Chain Monte Carlo algorithm described in <doi:10.1016/j.csda.2018.05.020> and its Genetically Modified counterpart described in <doi:10.1613/jair.1.13047> as well as the sub-sampling versions described in <doi:10.1016/j.ijar.2022.08.018> for flexible Bayesian model selection and model averaging.
Author: Jon Lachmann [cre, aut],
Aliaksandr Hubin [aut]
Maintainer: Jon Lachmann <jon@lachmann.nu>
Diff between FBMS versions 1.1 dated 2025-02-26 and 1.2 dated 2025-09-12
FBMS-1.1/FBMS/data/exoplanet.RData |only FBMS-1.1/FBMS/man/gauss.Rd |only FBMS-1.1/FBMS/man/linear.g.prior.loglik.Rd |only FBMS-1.1/FBMS/man/to23.Rd |only FBMS-1.1/FBMS/man/to25.Rd |only FBMS-1.1/FBMS/man/to35.Rd |only FBMS-1.1/FBMS/man/to72.Rd |only FBMS-1.2/FBMS/DESCRIPTION | 14 FBMS-1.2/FBMS/MD5 | 136 - FBMS-1.2/FBMS/NAMESPACE | 34 FBMS-1.2/FBMS/R/alpha_generation.R | 8 FBMS-1.2/FBMS/R/arguments.R | 30 FBMS-1.2/FBMS/R/diagnostics.R | 81 FBMS-1.2/FBMS/R/exa-data.R | 21 FBMS-1.2/FBMS/R/fbms.R | 363 +++- FBMS-1.2/FBMS/R/feature.R | 14 FBMS-1.2/FBMS/R/feature_generation.R | 22 FBMS-1.2/FBMS/R/gmjmcmc.R | 134 - FBMS-1.2/FBMS/R/gmjmcmc_support.R | 70 FBMS-1.2/FBMS/R/likelihoods.R | 701 +++++++- FBMS-1.2/FBMS/R/local_optim.R | 14 FBMS-1.2/FBMS/R/mjmcmc.R | 98 - FBMS-1.2/FBMS/R/nonlinear_functions.R | 55 FBMS-1.2/FBMS/R/parallel.R | 51 FBMS-1.2/FBMS/R/predict.R | 325 ++- FBMS-1.2/FBMS/R/results.R | 234 ++ FBMS-1.2/FBMS/R/summary.R | 65 FBMS-1.2/FBMS/build/partial.rdb |binary FBMS-1.2/FBMS/build/vignette.rds |binary FBMS-1.2/FBMS/data/exoplanet.rda |only FBMS-1.2/FBMS/inst/doc/FBMS-guide.R | 407 ++++ FBMS-1.2/FBMS/inst/doc/FBMS-guide.Rmd | 794 +++++++++ FBMS-1.2/FBMS/inst/doc/FBMS-guide.html | 1811 +++++++++++++++------- FBMS-1.2/FBMS/man/arcsinh.Rd |only FBMS-1.2/FBMS/man/compute_effects.Rd | 8 FBMS-1.2/FBMS/man/diagn_plot.Rd | 25 FBMS-1.2/FBMS/man/exoplanet.Rd | 21 FBMS-1.2/FBMS/man/fbms.Rd | 46 FBMS-1.2/FBMS/man/fbms.mlik.master.Rd |only FBMS-1.2/FBMS/man/gaussian.loglik.Rd | 10 FBMS-1.2/FBMS/man/gaussian.loglik.g.Rd |only FBMS-1.2/FBMS/man/gaussian_tcch_log_likelihood.Rd |only FBMS-1.2/FBMS/man/gen.params.gmjmcmc.Rd | 6 FBMS-1.2/FBMS/man/gen.params.mjmcmc.Rd | 4 FBMS-1.2/FBMS/man/get.best.model.Rd | 4 FBMS-1.2/FBMS/man/glm.loglik.Rd |only FBMS-1.2/FBMS/man/glm.loglik.g.Rd |only FBMS-1.2/FBMS/man/glm.logpost.bas.Rd |only FBMS-1.2/FBMS/man/gmjmcmc.Rd | 64 FBMS-1.2/FBMS/man/gmjmcmc.parallel.Rd | 44 FBMS-1.2/FBMS/man/lm.logpost.bas.Rd |only FBMS-1.2/FBMS/man/log_prior.Rd | 6 FBMS-1.2/FBMS/man/logistic.loglik.Rd | 8 FBMS-1.2/FBMS/man/logistic.loglik.ala.Rd | 4 FBMS-1.2/FBMS/man/marginal.probs.Rd | 5 FBMS-1.2/FBMS/man/merge_results.Rd | 7 FBMS-1.2/FBMS/man/mjmcmc.Rd | 45 FBMS-1.2/FBMS/man/mjmcmc.parallel.Rd | 6 FBMS-1.2/FBMS/man/model.string.Rd | 4 FBMS-1.2/FBMS/man/plot.gmjmcmc.Rd | 5 FBMS-1.2/FBMS/man/plot.gmjmcmc_merged.Rd | 8 FBMS-1.2/FBMS/man/plot.mjmcmc.Rd | 5 FBMS-1.2/FBMS/man/plot.mjmcmc_parallel.Rd | 6 FBMS-1.2/FBMS/man/predict.bgnlm_model.Rd | 3 FBMS-1.2/FBMS/man/predict.gmjmcmc.Rd | 10 FBMS-1.2/FBMS/man/predict.gmjmcmc_merged.Rd | 11 FBMS-1.2/FBMS/man/predict.gmjmcmc_parallel.Rd | 21 FBMS-1.2/FBMS/man/predict.mjmcmc.Rd | 18 FBMS-1.2/FBMS/man/predict.mjmcmc_parallel.Rd | 19 FBMS-1.2/FBMS/man/print.feature.Rd | 17 FBMS-1.2/FBMS/man/string.population.Rd | 5 FBMS-1.2/FBMS/man/string.population.models.Rd | 5 FBMS-1.2/FBMS/man/summary.gmjmcmc.Rd | 5 FBMS-1.2/FBMS/man/summary.gmjmcmc_merged.Rd | 8 FBMS-1.2/FBMS/man/summary.mjmcmc.Rd | 4 FBMS-1.2/FBMS/man/summary.mjmcmc_parallel.Rd | 6 FBMS-1.2/FBMS/vignettes/FBMS-guide.Rmd | 794 +++++++++ 77 files changed, 5312 insertions(+), 1437 deletions(-)
Title: Recursive Non-Additive Emulator for Multi-Fidelity Data
Description: Performs RNA emulation and active learning proposed by Heo and Sung (2025) <doi:10.1080/00401706.2024.2376173> for multi-fidelity computer experiments. The RNA emulator is particularly useful when the simulations with different fidelity level are nonlinearly correlated. The hyperparameters in the model are estimated by maximum likelihood estimation.
Author: Junoh Heo [aut, cre],
Chih-Li Sung [aut]
Maintainer: Junoh Heo <heojunoh@msu.edu>
Diff between RNAmf versions 1.1.1 dated 2025-06-07 and 1.1.2 dated 2025-09-12
RNAmf-1.1.1/RNAmf/LICENSE |only RNAmf-1.1.2/RNAmf/DESCRIPTION | 8 RNAmf-1.1.2/RNAmf/MD5 | 21 RNAmf-1.1.2/RNAmf/R/ALC.R | 1272 ++++++++++++++++++------------------ RNAmf-1.1.2/RNAmf/R/ALMC.R | 67 - RNAmf-1.1.2/RNAmf/R/GP.R | 2 RNAmf-1.1.2/RNAmf/R/NestedX.R | 24 RNAmf-1.1.2/RNAmf/R/RNAmf.R | 10 RNAmf-1.1.2/RNAmf/R/functions.R | 28 RNAmf-1.1.2/RNAmf/man/ALC_RNAmf.Rd | 4 RNAmf-1.1.2/RNAmf/man/ALMC_RNAmf.Rd | 6 RNAmf-1.1.2/RNAmf/man/NestedX.Rd | 1 12 files changed, 731 insertions(+), 712 deletions(-)
Title: Calculating Bilateral and Multilateral Price Indexes
Description: Preparing a scanner data set for price dynamics calculations (data selecting, data classification, data matching, data filtering). Computing bilateral and multilateral indexes. For details on these methods see: Diewert and Fox (2020)
<doi:10.1080/07350015.2020.1816176>, Białek (2019) <doi:10.2478/jos-2019-0014> or Białek (2020) <doi:10.2478/jos-2020-0037>.
Author: Jacek Bialek [aut, cre]
Maintainer: Jacek Bialek <jacek.bialek@uni.lodz.pl>
Diff between PriceIndices versions 0.2.3 dated 2025-01-24 and 0.2.4 dated 2025-09-12
PriceIndices-0.2.3/PriceIndices/man/figures/README-unnamed-chunk-34-1.png |only PriceIndices-0.2.3/PriceIndices/man/figures/README-unnamed-chunk-37-1.png |only PriceIndices-0.2.3/PriceIndices/man/figures/README-unnamed-chunk-43-1.png |only PriceIndices-0.2.3/PriceIndices/man/figures/README-unnamed-chunk-47-1.png |only PriceIndices-0.2.3/PriceIndices/man/figures/README-unnamed-chunk-49-1.png |only PriceIndices-0.2.3/PriceIndices/man/figures/README-unnamed-chunk-63-1.png |only PriceIndices-0.2.3/PriceIndices/man/figures/README-unnamed-chunk-65-1.png |only PriceIndices-0.2.3/PriceIndices/man/figures/README-unnamed-chunk-70-1.png |only PriceIndices-0.2.4/PriceIndices/DESCRIPTION | 9 PriceIndices-0.2.4/PriceIndices/MD5 | 112 PriceIndices-0.2.4/PriceIndices/NAMESPACE | 1 PriceIndices-0.2.4/PriceIndices/NEWS.md | 14 PriceIndices-0.2.4/PriceIndices/R/PriceIndices.R | 4 PriceIndices-0.2.4/PriceIndices/R/dataMARS.R |only PriceIndices-0.2.4/PriceIndices/R/f_data_processing.R | 372 +- PriceIndices-0.2.4/PriceIndices/R/f_extensions_multilateral_indices.R | 39 PriceIndices-0.2.4/PriceIndices/R/f_full_multilateral_indices.R | 151 PriceIndices-0.2.4/PriceIndices/R/f_internal.R | 133 PriceIndices-0.2.4/PriceIndices/README.md | 1250 +++++-- PriceIndices-0.2.4/PriceIndices/data/dataMARS.rda |only PriceIndices-0.2.4/PriceIndices/inst/doc/PriceIndices.R | 11 PriceIndices-0.2.4/PriceIndices/inst/doc/PriceIndices.Rmd | 23 PriceIndices-0.2.4/PriceIndices/inst/doc/PriceIndices.html | 1740 +++++++--- PriceIndices-0.2.4/PriceIndices/man/MARS.Rd |only PriceIndices-0.2.4/PriceIndices/man/PriceIndices.Rd | 6 PriceIndices-0.2.4/PriceIndices/man/dataMARS.Rd |only PriceIndices-0.2.4/PriceIndices/man/data_aggregating.Rd | 6 PriceIndices-0.2.4/PriceIndices/man/data_filtering.Rd | 4 PriceIndices-0.2.4/PriceIndices/man/data_imputing.Rd | 41 PriceIndices-0.2.4/PriceIndices/man/data_preparing.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/figures/README-unnamed-chunk-19-1.png |binary PriceIndices-0.2.4/PriceIndices/man/figures/README-unnamed-chunk-20-1.png |binary PriceIndices-0.2.4/PriceIndices/man/figures/README-unnamed-chunk-35-1.png |only PriceIndices-0.2.4/PriceIndices/man/figures/README-unnamed-chunk-38-1.png |binary PriceIndices-0.2.4/PriceIndices/man/figures/README-unnamed-chunk-39-1.png |only PriceIndices-0.2.4/PriceIndices/man/figures/README-unnamed-chunk-44-1.png |binary PriceIndices-0.2.4/PriceIndices/man/figures/README-unnamed-chunk-45-1.png |binary PriceIndices-0.2.4/PriceIndices/man/figures/README-unnamed-chunk-46-1.png |only PriceIndices-0.2.4/PriceIndices/man/figures/README-unnamed-chunk-48-1.png |only PriceIndices-0.2.4/PriceIndices/man/figures/README-unnamed-chunk-50-1.png |only PriceIndices-0.2.4/PriceIndices/man/figures/README-unnamed-chunk-64-1.png |only PriceIndices-0.2.4/PriceIndices/man/figures/README-unnamed-chunk-66-1.png |only PriceIndices-0.2.4/PriceIndices/man/figures/README-unnamed-chunk-71-1.png |binary PriceIndices-0.2.4/PriceIndices/man/figures/README-unnamed-chunk-72-1.png |only PriceIndices-0.2.4/PriceIndices/man/geksaqi_fbew.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/geksaqi_fbmw.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/geksaqi_splice.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/geksgaqi.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/geksgaqi_fbew.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/geksgaqi_fbmw.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/geksgaqi_splice.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/geksgl.Rd | 4 PriceIndices-0.2.4/PriceIndices/man/geksl.Rd | 4 PriceIndices-0.2.4/PriceIndices/man/gekslm_fbew.Rd | 4 PriceIndices-0.2.4/PriceIndices/man/gekslm_fbmw.Rd | 4 PriceIndices-0.2.4/PriceIndices/man/gekslm_splice.Rd | 4 PriceIndices-0.2.4/PriceIndices/man/m_decomposition.Rd | 4 PriceIndices-0.2.4/PriceIndices/man/wgeksaqi_fbew.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/wgeksaqi_fbmw.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/wgeksaqi_splice.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/wgeksgaqi.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/wgeksgaqi_fbew.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/wgeksgaqi_fbmw.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/wgeksgaqi_splice.Rd | 2 PriceIndices-0.2.4/PriceIndices/man/wgeksgl.Rd | 4 PriceIndices-0.2.4/PriceIndices/man/wgeksl.Rd | 4 PriceIndices-0.2.4/PriceIndices/vignettes/PriceIndices.Rmd | 23 67 files changed, 3098 insertions(+), 903 deletions(-)
Title: Statistical Framework to Define Subgroups in Complex Datasets
Description: High-dimensional datasets that do not exhibit a clear intrinsic clustered structure pose a challenge to conventional clustering algorithms. For this reason, we developed an unsupervised framework that helps scientists to better subgroup their datasets based on visual cues, please see Gao S, Mutter S, Casey A, Makinen V-P (2019) Numero: a statistical framework to define multivariable subgroups in complex population-based datasets, Int J Epidemiology, 48:369-37, <doi:10.1093/ije/dyy113>. The framework includes the necessary functions to construct a self-organizing map of the data, to evaluate the statistical significance of the observed data patterns, and to visualize the results.
Author: Song Gao [aut],
Stefan Mutter [aut],
Aaron E. Casey [aut],
Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine@gmail.com>
Diff between Numero versions 1.9.10 dated 2025-08-31 and 1.10.1 dated 2025-09-12
DESCRIPTION | 8 +- MD5 | 28 ++++---- R/numero.create.R | 1 R/numero.evaluate.R | 1 R/numero.quality.R | 3 R/numero.summary.R | 5 - inst/doc/intro.R | 52 +++++++++++---- inst/doc/intro.html | 163 +++++++++++++++++++++++++++++++++---------------- inst/doc/intro.rmd | 84 +++++++++++++++++++------ man/numero.evaluate.Rd | 2 man/numero.plot.Rd | 2 man/numero.quality.Rd | 6 - man/numero.subrgoup.Rd | 2 man/numero.summary.Rd | 4 - vignettes/intro.rmd | 84 +++++++++++++++++++------ 15 files changed, 306 insertions(+), 139 deletions(-)
Title: Fast, Easy, and Visual Bayesian Inference
Description: Accelerate Bayesian analytics workflows in 'R' through interactive modelling,
visualization, and inference. Define probabilistic graphical models using directed
acyclic graphs (DAGs) as a unifying language for business stakeholders, statisticians,
and programmers. This package relies on interfacing with the 'numpyro' python package.
Author: Adam Fleischhacker [aut, cre, cph],
Daniela Dapena [ctb],
Rose Nguyen [ctb],
Jared Sharpe [ctb]
Maintainer: Adam Fleischhacker <ajf@udel.edu>
Diff between causact versions 0.5.8 dated 2025-08-22 and 0.6.0 dated 2025-09-12
DESCRIPTION | 8 LICENSE | 4 MD5 | 42 +- NEWS.md | 17 R/dag_numpyro.R | 627 ++++++++++++------------------- R/dagp_plot.R | 109 +++-- R/install_causact_deps.R | 12 README.md | 83 ++-- man/causact-package.Rd | 62 +-- man/check_r_causact_env.Rd | 22 - man/chimpanzeesDF.Rd | 60 +- man/dag_greta.Rd | 114 ++--- man/dag_numpyro.Rd | 86 +--- man/distributions.Rd | 416 ++++++++++---------- man/figures/chimpsGraphPost-1.png |binary man/figures/gretaPost-1.png |binary man/install_causact_deps.Rd | 60 +- man/meaningfulLabels.Rd | 38 - man/schoolsDF.Rd | 42 +- tests/testthat.R | 8 vignettes/gretaCardPlot-1.svg | 622 +++++++++++++++--------------- vignettes/postCardPlatePlot-1.svg | 766 +++++++++++++++++++------------------- 22 files changed, 1546 insertions(+), 1652 deletions(-)
Title: Synthesize Bio API Wrapper
Description: Access Synthesize Bio models from their API <https://app.synthesize.bio/> using
this wrapper that provides a convenient interface to the Synthesize Bio API, allowing users
to generate realistic gene expression data based on specified biological conditions. This package
enables researchers to easily access AI-generated transcriptomic data for various
modalities including bulk RNA-seq, single-cell RNA-seq, microarray data, and more.
Author: Candace Savonen [aut, cre]
Maintainer: Candace Savonen <cansav09@gmail.com>
Diff between rsynthbio versions 2.0.0 dated 2025-06-04 and 2.2.1 dated 2025-09-12
DESCRIPTION | 6 MD5 | 37 +++-- NAMESPACE | 1 NEWS.md | 8 - R/call_model_api.R | 40 +++--- R/key-handlers.R | 8 - R/utils.R | 21 ++- README.md | 32 ++--- build/vignette.rds |binary inst/doc/getting-started.R | 16 -- inst/doc/getting-started.Rmd | 92 +++++++++----- inst/doc/getting-started.html | 224 +++++++++++++++++++++++------------- man/figures |only man/get_valid_modalities.Rd | 5 man/get_valid_query.Rd | 4 man/predict_query.Rd | 11 + man/validate_modality.Rd | 2 man/validate_query.Rd | 2 tests/testthat/test-data-handlers.R | 2 vignettes/getting-started.Rmd | 92 +++++++++----- 20 files changed, 371 insertions(+), 232 deletions(-)
Title: Interpretable Machine Learning and Statistical Inference with
Accumulated Local Effects (ALE)
Description: Accumulated Local Effects (ALE) were initially developed as a model-agnostic approach for global explanations of the results of black-box machine learning algorithms. ALE has a key advantage over other approaches like partial dependency plots (PDP) and SHapley Additive exPlanations (SHAP): its values represent a clean functional decomposition of the model. As such, ALE values are not affected by the presence or absence of interactions among variables in a mode. Moreover, its computation is relatively rapid. This package reimplements the algorithms for calculating ALE data and develops highly interpretable visualizations for plotting these ALE values. It also extends the original ALE concept to add bootstrap-based confidence intervals and ALE-based statistics that can be used for statistical inference. For more details, see Okoli, Chitu. 2023. “Statistical Inference Using Machine Learning and Classical Techniques Based on Accumulated Local Effects (ALE).” arXiv. <doi:10.48550/arXiv.2 [...truncated...]
Author: Chitu Okoli [aut, cre]
Maintainer: Chitu Okoli <Chitu.Okoli@skema.edu>
Diff between ale versions 0.5.2 dated 2025-08-29 and 0.5.3 dated 2025-09-12
ale-0.5.2/ale/man/ale.Rd |only ale-0.5.3/ale/DESCRIPTION | 10 ale-0.5.3/ale/MD5 | 59 - ale-0.5.3/ale/NAMESPACE | 1 ale-0.5.3/ale/NEWS.md | 402 ++++++----- ale-0.5.3/ale/R/ALE.R | 105 +-- ale-0.5.3/ale/R/ALEpDist.R | 96 +- ale-0.5.3/ale/R/ModelBoot.R | 36 - ale-0.5.3/ale/R/unpackaged_utils.R | 637 +++++++++++-------- ale-0.5.3/ale/README.md | 73 +- ale-0.5.3/ale/inst/doc/ale-intro.R | 67 + ale-0.5.3/ale/inst/doc/ale-intro.Rmd | 67 + ale-0.5.3/ale/inst/doc/ale-intro.html | 81 +- ale-0.5.3/ale/inst/doc/ale-small-datasets.R | 106 +-- ale-0.5.3/ale/inst/doc/ale-small-datasets.Rmd | 106 +-- ale-0.5.3/ale/inst/doc/ale-small-datasets.html | 185 +++-- ale-0.5.3/ale/inst/doc/ale-statistics.R | 85 +- ale-0.5.3/ale/inst/doc/ale-statistics.Rmd | 85 +- ale-0.5.3/ale/inst/doc/ale-statistics.html | 97 +- ale-0.5.3/ale/inst/doc/ale-x-datatypes.R | 65 + ale-0.5.3/ale/inst/doc/ale-x-datatypes.Rmd | 65 + ale-0.5.3/ale/inst/doc/ale-x-datatypes.html | 101 +-- ale-0.5.3/ale/man/ALE.Rd |only ale-0.5.3/ale/man/ALEpDist.Rd | 96 +- ale-0.5.3/ale/man/ModelBoot.Rd | 36 - ale-0.5.3/ale/man/retrieve_rds.Rd |only ale-0.5.3/ale/tests/testthat/Rplots.pdf |binary ale-0.5.3/ale/tests/testthat/test-unpackaged_utils.R | 77 ++ ale-0.5.3/ale/vignettes/ale-intro.Rmd | 67 + ale-0.5.3/ale/vignettes/ale-small-datasets.Rmd | 106 +-- ale-0.5.3/ale/vignettes/ale-statistics.Rmd | 85 +- ale-0.5.3/ale/vignettes/ale-x-datatypes.Rmd | 65 + 32 files changed, 1808 insertions(+), 1253 deletions(-)
Title: Probability Distributions as S3 Objects
Description: Tools to create and manipulate probability distributions
using S3. Generics pdf(), cdf(), quantile(), and random() provide
replacements for base R's d/p/q/r style functions. Functions and
arguments have been named carefully to minimize confusion for students
in intro stats courses. The documentation for each distribution
contains detailed mathematical notes.
Author: Alex Hayes [aut, cre] ,
Ralph Moller-Trane [aut],
Emil Hvitfeldt [ctb] ,
Daniel Jordan [aut],
Paul Northrop [aut],
Moritz N. Lang [aut] ,
Achim Zeileis [aut] ,
Bruna Wundervald [ctb],
Alessandro Gasparini [ctb]
Maintainer: Alex Hayes <alexpghayes@gmail.com>
Diff between distributions3 versions 0.2.2 dated 2024-09-16 and 0.2.3 dated 2025-09-12
DESCRIPTION | 16 +++++------ MD5 | 36 ++++++++++++------------- NEWS.md | 8 ++++- R/FIFA2018.R | 8 ++--- R/plot.R | 6 ++-- README.md | 2 - inst/doc/intro-to-hypothesis-testing.html | 2 - inst/doc/one-sample-sign-tests.html | 5 ++- inst/doc/one-sample-t-confidence-interval.html | 3 +- inst/doc/one-sample-t-test.html | 5 ++- inst/doc/one-sample-z-confidence-interval.html | 3 +- inst/doc/one-sample-z-test-for-proportion.html | 3 +- inst/doc/one-sample-z-test.html | 5 ++- inst/doc/paired-tests.html | 25 +++++++++-------- inst/doc/poisson.html | 7 ++-- inst/doc/two-sample-z-test.html | 9 +++--- man/FIFA2018.Rd | 2 - man/geom_auc.Rd | 8 +++-- tests/testthat/test-plot.R | 22 ++++++++------- 19 files changed, 96 insertions(+), 79 deletions(-)
More information about distributions3 at CRAN
Permanent link
Title: Population Assignment using Genetic, Non-Genetic or Integrated
Data in a Machine Learning Framework
Description: Use Monte-Carlo and K-fold cross-validation coupled with machine-
learning classification algorithms to perform population assignment, with
functionalities of evaluating discriminatory power of independent training
samples, identifying informative loci, reducing data dimensionality for genomic
data, integrating genetic and non-genetic data, and visualizing results.
Author: Kuan-Yu Chen [aut, cre],
Elizabeth A. Marschall [aut],
Michael G. Sovic [aut],
Anthony C. Fries [aut],
H. Lisle Gibbs [aut],
Stuart A. Ludsin [aut]
Maintainer: Kuan-Yu (Alex) Chen <alexkychen@gmail.com>
Diff between assignPOP versions 1.3.0 dated 2024-03-13 and 1.3.1 dated 2025-09-12
DESCRIPTION | 23 ++++++++++++++++------- MD5 | 12 ++++++------ R/accuracy.MC.R | 2 +- man/accuracy.MC.Rd | 2 +- tests/testthat.R | 1 + tests/testthat/test_accuracy.R | 4 ++-- tests/testthat/test_membership.R | 2 +- 7 files changed, 28 insertions(+), 18 deletions(-)
Title: Scatter Pie Plot
Description: Creates scatterpie plots, especially useful for plotting pies on a map.
Author: Guangchuang Yu [aut, cre] ,
Shuangbin Xu [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between scatterpie versions 0.2.5 dated 2025-06-21 and 0.2.6 dated 2025-09-12
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/geom_scatterpie.R | 19 ++++++++++--------- R/geom_scatterpie_legend.R | 7 ++++--- build/vignette.rds |binary inst/doc/scatterpie.html | 36 ++++++++++++++++++++---------------- 8 files changed, 51 insertions(+), 39 deletions(-)
Title: Rasch Model Parameters by Pairwise Algorithm
Description: Performs the explicit calculation
-- not estimation! -- of the Rasch item parameters for dichotomous and
polytomous item responses, using a pairwise comparison approach. Person
parameters (WLE) are calculated according to Warm's weighted likelihood
approach.
Author: Joerg-Henrik Heine [aut, cre],
Christian Grebe [ctb]
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>
Diff between pairwise versions 0.6.1-0 dated 2023-04-17 and 0.6.2-0 dated 2025-09-12
pairwise-0.6.1-0/pairwise/R/i.str.pattern.R |only pairwise-0.6.1-0/pairwise/man/pairwise-package.Rd |only pairwise-0.6.2-0/pairwise/DESCRIPTION | 24 pairwise-0.6.2-0/pairwise/MD5 | 135 +- pairwise-0.6.2-0/pairwise/NAMESPACE | 4 pairwise-0.6.2-0/pairwise/NEWS | 455 +++++----- pairwise-0.6.2-0/pairwise/R/Q.R | 1 pairwise-0.6.2-0/pairwise/R/Qtest.R |only pairwise-0.6.2-0/pairwise/R/andersentest.pers.R | 13 pairwise-0.6.2-0/pairwise/R/catprob.R | 1 pairwise-0.6.2-0/pairwise/R/deltapar.R | 1 pairwise-0.6.2-0/pairwise/R/esc.R | 6 pairwise-0.6.2-0/pairwise/R/ftab.R | 1 pairwise-0.6.2-0/pairwise/R/gif.R | 1 pairwise-0.6.2-0/pairwise/R/grm.R | 1 pairwise-0.6.2-0/pairwise/R/iff.R | 1 pairwise-0.6.2-0/pairwise/R/logLik.pers.R | 12 pairwise-0.6.2-0/pairwise/R/lrtest.pers.R | 3 pairwise-0.6.2-0/pairwise/R/make.incidenz.R | 1 pairwise-0.6.2-0/pairwise/R/pair.R | 1 pairwise-0.6.2-0/pairwise/R/pairSE.R | 1 pairwise-0.6.2-0/pairwise/R/pairwise-package.R | 7 pairwise-0.6.2-0/pairwise/R/pairwise.S.R | 1 pairwise-0.6.2-0/pairwise/R/pairwise.SepRel.R | 91 +- pairwise-0.6.2-0/pairwise/R/pairwise.item.fit.R | 1 pairwise-0.6.2-0/pairwise/R/pairwise.person.fit.R | 1 pairwise-0.6.2-0/pairwise/R/pers.R | 1 pairwise-0.6.2-0/pairwise/R/ptbis.R | 1 pairwise-0.6.2-0/pairwise/R/q3.R | 1 pairwise-0.6.2-0/pairwise/R/residuals.pers.R | 1 pairwise-0.6.2-0/pairwise/R/rfa.R | 1 pairwise-0.6.2-0/pairwise/R/simra.R | 1 pairwise-0.6.2-0/pairwise/R/tff.R | 1 pairwise-0.6.2-0/pairwise/build/vignette.rds |binary pairwise-0.6.2-0/pairwise/data/DEU_PISA2012.RData |binary pairwise-0.6.2-0/pairwise/data/KCT.RData |binary pairwise-0.6.2-0/pairwise/data/Neoffi5.RData |binary pairwise-0.6.2-0/pairwise/data/bfiN.RData |binary pairwise-0.6.2-0/pairwise/data/bfiN_miss.RData |binary pairwise-0.6.2-0/pairwise/data/bfi_cov.RData |binary pairwise-0.6.2-0/pairwise/data/cog.RData |binary pairwise-0.6.2-0/pairwise/data/cogBOOKLET.RData |binary pairwise-0.6.2-0/pairwise/data/kft5.RData |binary pairwise-0.6.2-0/pairwise/data/sim200x3.RData |binary pairwise-0.6.2-0/pairwise/inst/doc/DEU_PISA2012_description.pdf |binary pairwise-0.6.2-0/pairwise/man/Q.Rd | 2 pairwise-0.6.2-0/pairwise/man/Qtest.Rd |only pairwise-0.6.2-0/pairwise/man/andersentest.pers.Rd | 2 pairwise-0.6.2-0/pairwise/man/catprob.Rd | 2 pairwise-0.6.2-0/pairwise/man/deltapar.Rd | 1 pairwise-0.6.2-0/pairwise/man/esc.Rd | 2 pairwise-0.6.2-0/pairwise/man/ftab.Rd | 1 pairwise-0.6.2-0/pairwise/man/gif.Rd | 2 pairwise-0.6.2-0/pairwise/man/grm.Rd | 2 pairwise-0.6.2-0/pairwise/man/iff.Rd | 2 pairwise-0.6.2-0/pairwise/man/lrtest.pers.Rd | 2 pairwise-0.6.2-0/pairwise/man/make.incidenz.Rd | 1 pairwise-0.6.2-0/pairwise/man/pair.Rd | 2 pairwise-0.6.2-0/pairwise/man/pairSE.Rd | 2 pairwise-0.6.2-0/pairwise/man/pairwise.S.Rd | 2 pairwise-0.6.2-0/pairwise/man/pairwise.SepRel.Rd | 2 pairwise-0.6.2-0/pairwise/man/pairwise.item.fit.Rd | 2 pairwise-0.6.2-0/pairwise/man/pairwise.person.fit.Rd | 2 pairwise-0.6.2-0/pairwise/man/pairwise_PACKAGE.Rd |only pairwise-0.6.2-0/pairwise/man/pers.Rd | 2 pairwise-0.6.2-0/pairwise/man/ptbis.Rd | 1 pairwise-0.6.2-0/pairwise/man/q3.Rd | 2 pairwise-0.6.2-0/pairwise/man/rfa.Rd | 2 pairwise-0.6.2-0/pairwise/man/sim200x3.Rd | 4 pairwise-0.6.2-0/pairwise/man/simra.Rd | 1 pairwise-0.6.2-0/pairwise/man/tff.Rd | 2 71 files changed, 452 insertions(+), 363 deletions(-)
Title: Many Ways to Make, Modify, Mark, and Measure Myriad Networks
Description: Many tools for making, modifying, marking, measuring,
and motifs and memberships of many different types of networks.
All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
on directed, multiplex, multimodal, signed, and other networks.
The package includes functions for importing and exporting, creating and generating networks,
modifying networks and node and tie attributes,
and describing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Christian Steglich [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manynet versions 1.6.0 dated 2025-08-22 and 1.6.1 dated 2025-09-12
manynet-1.6.0/manynet/inst/tutorials/tutorial2 |only manynet-1.6.1/manynet/DESCRIPTION | 13 - manynet-1.6.1/manynet/MD5 | 28 +- manynet-1.6.1/manynet/NAMESPACE | 3 manynet-1.6.1/manynet/NEWS.md | 32 +++ manynet-1.6.1/manynet/R/class_networks.R | 10 manynet-1.6.1/manynet/R/data_ison.R | 70 ++++++ manynet-1.6.1/manynet/R/make_create.R | 155 +++++++++++++++ manynet-1.6.1/manynet/R/manynet-tutorials.R | 13 - manynet-1.6.1/manynet/R/mark_net.R | 3 manynet-1.6.1/manynet/data/irps_nuclear_discourse.rda |only manynet-1.6.1/manynet/data/ison_judo_moves.rda |only manynet-1.6.1/manynet/inst/CITATION |only manynet-1.6.1/manynet/man/irps_nuclear_discourse.Rd |only manynet-1.6.1/manynet/man/ison_judo_moves.Rd |only manynet-1.6.1/manynet/man/make_create.Rd | 12 + manynet-1.6.1/manynet/tests/testthat/test-manip_format.R | 2 17 files changed, 314 insertions(+), 27 deletions(-)
Title: Configural Frequencies Analysis Using Log-Linear Modeling
Description: Offers several functions for Configural Frequencies Analysis (CFA), which is a useful statistical tool for the analysis of multiway contingency tables. CFA was introduced by G. A. Lienert as 'Konfigurations Frequenz Analyse - KFA'. Lienert, G. A. (1971). Die Konfigurationsfrequenzanalyse: I. Ein neuer Weg zu Typen und Syndromen. Zeitschrift für Klinische Psychologie und Psychotherapie, 19(2), 99–115.
Author: Joerg-Henrik Heine [aut, cre, com],
Rainer W. Alexandrowicz [aut, com],
Mark Stemmler [rev, com]
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>
Diff between confreq versions 1.6.1-1 dated 2022-11-13 and 1.6.1-3 dated 2025-09-12
confreq-1.6.1-1/confreq/man/confreq-package.Rd |only confreq-1.6.1-3/confreq/DESCRIPTION | 23 - confreq-1.6.1-3/confreq/MD5 | 22 - confreq-1.6.1-3/confreq/NEWS | 8 confreq-1.6.1-3/confreq/R/CFA.R | 436 ++++++++++++------------- confreq-1.6.1-3/confreq/R/S2CFA.R | 2 confreq-1.6.1-3/confreq/R/confreq-package.R | 152 ++++---- confreq-1.6.1-3/confreq/R/dat2fre.R | 261 +++++++------- confreq-1.6.1-3/confreq/R/fre2dat.R | 6 confreq-1.6.1-3/confreq/R/plot.CFA.R | 196 +++++------ confreq-1.6.1-3/confreq/man/CFA.Rd | 14 confreq-1.6.1-3/confreq/man/confreq_PACKAGE.Rd |only confreq-1.6.1-3/confreq/man/fre2dat.Rd | 6 13 files changed, 578 insertions(+), 548 deletions(-)
Title: Constrained Iteratively Reweighted Least Squares
Description: Fitting and inference functions for generalized linear models with constrained coefficients.
Author: Pierre Masselot [aut, cre, cph] ,
Antonio Gasparrini [aut]
Maintainer: Pierre Masselot <pierre.masselot@lshtm.ac.uk>
Diff between cirls versions 0.3.1 dated 2024-09-12 and 0.4.0 dated 2025-09-12
cirls-0.3.1/cirls/R/check_cmat.R |only cirls-0.3.1/cirls/R/clist2cmat.R |only cirls-0.3.1/cirls/R/coef_simu.R |only cirls-0.3.1/cirls/man/check_cmat.Rd |only cirls-0.3.1/cirls/man/confint.cirls.Rd |only cirls-0.3.1/cirls/man/examples/check_cmat.R |only cirls-0.3.1/cirls/tests/testthat/test-check_Cmat.R |only cirls-0.3.1/cirls/tests/testthat/test-clist2cmat.R |only cirls-0.4.0/cirls/DESCRIPTION | 22 - cirls-0.4.0/cirls/MD5 | 83 +++-- cirls-0.4.0/cirls/NAMESPACE | 16 cirls-0.4.0/cirls/NEWS.md | 102 ++++-- cirls-0.4.0/cirls/R/buildCmat.R |only cirls-0.4.0/cirls/R/checkCmat.R |only cirls-0.4.0/cirls/R/chkshp.R |only cirls-0.4.0/cirls/R/cirls.control.R | 74 +--- cirls-0.4.0/cirls/R/cirls.fit.R | 274 +++++++++++------ cirls-0.4.0/cirls/R/coneproj.fit.R | 24 - cirls-0.4.0/cirls/R/confint.cirls.R | 79 ---- cirls-0.4.0/cirls/R/constr2Clist.R |only cirls-0.4.0/cirls/R/dm.R |only cirls-0.4.0/cirls/R/dmat.R |only cirls-0.4.0/cirls/R/edf.R |only cirls-0.4.0/cirls/R/logLik.cirls.R |only cirls-0.4.0/cirls/R/mkDmat.R |only cirls-0.4.0/cirls/R/mkShpCmat.R |only cirls-0.4.0/cirls/R/osqp.def.R | 25 - cirls-0.4.0/cirls/R/quadprog.fit.R | 90 +++-- cirls-0.4.0/cirls/R/shapeConstr.R |only cirls-0.4.0/cirls/R/shapeConstr.bs.R |only cirls-0.4.0/cirls/R/shapeConstr.default.R |only cirls-0.4.0/cirls/R/shapeConstr.factor.R |only cirls-0.4.0/cirls/R/shapeConstr.ns.R |only cirls-0.4.0/cirls/R/shapeConstr.onebasis.R |only cirls-0.4.0/cirls/R/shapeConstr.ps.R |only cirls-0.4.0/cirls/R/simulCoef.R |only cirls-0.4.0/cirls/R/uncons.R |only cirls-0.4.0/cirls/R/vcov.cirls.R | 44 +- cirls-0.4.0/cirls/R/zerosumConstr.R |only cirls-0.4.0/cirls/README.md | 16 cirls-0.4.0/cirls/build/partial.rdb |binary cirls-0.4.0/cirls/man/buildCmat.Rd |only cirls-0.4.0/cirls/man/checkCmat.Rd |only cirls-0.4.0/cirls/man/cirls.control.Rd | 17 - cirls-0.4.0/cirls/man/cirls.fit.Rd | 26 - cirls-0.4.0/cirls/man/dmat.Rd |only cirls-0.4.0/cirls/man/edf.Rd |only cirls-0.4.0/cirls/man/examples/checkCmat_ex.R |only cirls-0.4.0/cirls/man/examples/edf_ex.R |only cirls-0.4.0/cirls/man/examples/logLik_ex.R |only cirls-0.4.0/cirls/man/examples/new_methods.R | 8 cirls-0.4.0/cirls/man/logLik.cirls.Rd |only cirls-0.4.0/cirls/man/shapeConstr.Rd |only cirls-0.4.0/cirls/man/simulCoef.Rd |only cirls-0.4.0/cirls/man/uncons.Rd |only cirls-0.4.0/cirls/man/zerosumConstr.Rd |only cirls-0.4.0/cirls/tests/other |only cirls-0.4.0/cirls/tests/testthat/test-aliased.R | 68 ++-- cirls-0.4.0/cirls/tests/testthat/test-checkCmat.R |only cirls-0.4.0/cirls/tests/testthat/test-cirls_call.R |only cirls-0.4.0/cirls/tests/testthat/test-cirls_results.R | 52 ++- cirls-0.4.0/cirls/tests/testthat/test-constraintSpec.R |only cirls-0.4.0/cirls/tests/testthat/test-inference.R | 261 ++++++++-------- cirls-0.4.0/cirls/tests/testthat/test-shapeConstr.R |only cirls-0.4.0/cirls/tests/testthat/test-simulations.R |only 65 files changed, 719 insertions(+), 562 deletions(-)
Title: Projection Pursuit Based on Gaussian Mixtures and Evolutionary
Algorithms
Description: Projection Pursuit (PP) algorithm for dimension reduction based on Gaussian Mixture Models (GMMs) for density estimation using Genetic Algorithms (GAs) to maximise an approximated negentropy index. For more details see Scrucca and Serafini (2019) <doi:10.1080/10618600.2019.1598871>.
Author: Alessio Serafini [aut] ,
Luca Scrucca [aut, cre]
Maintainer: Luca Scrucca <luca.scrucca@unibo.it>
Diff between ppgmmga versions 1.3 dated 2023-11-17 and 1.3.1 dated 2025-09-12
DESCRIPTION | 17 ++++---- MD5 | 24 ++++++------ build/vignette.rds |binary inst/doc/ppgmmga.R | 10 ++--- inst/doc/ppgmmga.html | 94 ++++++++++++++++++++++++------------------------- man/nclass.numpy.Rd | 2 - man/plot.ppgmmga.Rd | 4 +- man/ppgmmga-class.Rd | 2 - man/ppgmmga-package.Rd | 2 - man/ppgmmga.Rd | 10 ++--- man/ppgmmga.options.Rd | 8 ++-- man/summary.ppgmmga.Rd | 2 - src/Makevars | 2 - 13 files changed, 89 insertions(+), 88 deletions(-)
Title: A Heatmap-Like Visualization Tool
Description: A data visualization design that provides comparison between
two (Double) data sources (usually on a par with each other) on one
reformed heatmap, while inheriting 'ggplot2' features.
Author: Youzhi Yu [aut, cre],
Trent Buskirk [aut, ths]
Maintainer: Youzhi Yu <yuyouzhi666@icloud.com>
Diff between ggDoubleHeat versions 0.1.2 dated 2023-08-24 and 0.1.3 dated 2025-09-12
ggDoubleHeat-0.1.2/ggDoubleHeat/R/ggDoubleHeat.R |only ggDoubleHeat-0.1.2/ggDoubleHeat/man/ggDoubleHeat.Rd |only ggDoubleHeat-0.1.3/ggDoubleHeat/DESCRIPTION | 8 +++--- ggDoubleHeat-0.1.3/ggDoubleHeat/MD5 | 14 +++++----- ggDoubleHeat-0.1.3/ggDoubleHeat/NEWS.md | 3 ++ ggDoubleHeat-0.1.3/ggDoubleHeat/R/geom-heat-circle.R | 16 ++++++++---- ggDoubleHeat-0.1.3/ggDoubleHeat/R/geom-heat-grid.R | 11 ++++---- ggDoubleHeat-0.1.3/ggDoubleHeat/R/geom-heat-tri.R | 10 ++++--- ggDoubleHeat-0.1.3/ggDoubleHeat/R/ggDoubleHeat-package.R |only ggDoubleHeat-0.1.3/ggDoubleHeat/man/ggDoubleHeat-package.Rd |only 10 files changed, 37 insertions(+), 25 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <DOI:10.1111/2041-210X.12283>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped.
Author: Michael Krabbe Borregaard [aut, cre]
Maintainer: Michael Krabbe Borregaard <mkborregaard@sund.ku.dk>
Diff between nodiv versions 1.4.2 dated 2023-08-21 and 1.4.3 dated 2025-09-12
DESCRIPTION | 11 ++++++----- MD5 | 4 ++-- man/phyplot.Rd | 2 +- 3 files changed, 9 insertions(+), 8 deletions(-)
Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions used in
'mlr3' and its companion packages. Comes with helper functions for
functional programming, for printing, to work with 'data.table', as
well as some generally useful 'R6' classes. This package also
supersedes the package 'BBmisc'.
Author: Marc Becker [cre, aut] ,
Michel Lang [aut] ,
Patrick Schratz [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3misc versions 0.18.0 dated 2025-05-26 and 0.19.0 dated 2025-09-12
DESCRIPTION | 10 +- MD5 | 23 +++--- NAMESPACE | 12 +++ NEWS.md | 5 + R/conditions.R |only R/encapsulate.R | 140 ++++++++++++++++++++++++++++---------- R/printf.R | 20 +---- R/topo_sort.R | 21 ++--- man/encapsulate.Rd | 7 + man/mlr_conditions.Rd |only tests/testthat/_snaps |only tests/testthat/test_conditions.R |only tests/testthat/test_encapsulate.R | 41 ++++++++++- tests/testthat/test_printf.R | 23 +----- 14 files changed, 201 insertions(+), 101 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Pre-made models that can be rapidly tailored to various chemicals
and species using chemical-specific in vitro data and physiological
information. These tools allow incorporation of chemical
toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE")
into bioinformatics, as described by Pearce et al. (2017)
(<doi:10.18637/jss.v079.i04>). Chemical-specific
in vitro data characterizing toxicokinetics have been obtained
from relatively high-throughput experiments. The
chemical-independent ("generic") physiologically-based ("PBTK") and empirical
(for example, one compartment) "TK" models included here can be
parameterized with in vitro data or in silico predictions which are
provided for thousands of chemicals, multiple exposure routes,
and various species. High throughput toxicokinetics ("HTTK") is the
combination of in vitro data and generic models. We establish the
expected accuracy of HTTK for chemicals without in vivo data
through statistical evaluation of HTTK predicti [...truncated...]
Author: John Wambaugh [aut, cre] ,
Sarah Davidson-Fritz [aut] ,
Robert Pearce [aut] ,
Caroline Ring [aut] ,
Greg Honda [aut] ,
Mark Sfeir [aut],
Matt Linakis [aut] ,
Dustin Kapraun [aut] ,
Kimberly Truong [aut] ,
Colin Thomson [aut] ,
Meredith Scherer [aut] [...truncated...]
Maintainer: John Wambaugh <wambaugh.research@gmail.com>
Diff between httk versions 2.7.2 dated 2025-08-29 and 2.7.3 dated 2025-09-12
DESCRIPTION | 12 MD5 | 50 NEWS.md | 7 R/add_chemtable.R | 16 R/load_dawson2021.R | 3 R/load_honda2023.R | 3 R/load_pradeep2020.R | 3 R/load_sipes2017.R | 3 R/modelinfo_1comppfas.R | 10 build/partial.rdb |binary inst/doc/V1_IntroToHTTK.html | 10 inst/doc/Va_Pearce2017.html | 16 inst/doc/Vb_Ring2017.html | 4 inst/doc/Ve_Truong2025.html | 4 inst/doc/Vf_WambaughSubmitted.R | 73 - inst/doc/Vf_WambaughSubmitted.Rmd | 74 - inst/doc/Vf_WambaughSubmitted.html | 2429 ++++++++++++++++++------------------- inst/doc/Vg_MeadeSubmitted.html | 6 inst/doc/Vh_SchererSubmitted.html | 4 man/add_chemtable.Rd | 5 man/augment.table.Rd | 5 man/httk-package.Rd | 2 man/parameterize_steadystate.Rd | 4 src/dermal.c | 5 src/model_gas_pbtk.c | 83 + vignettes/Vf_WambaughSubmitted.Rmd | 74 - 26 files changed, 1584 insertions(+), 1321 deletions(-)
Title: Hierarchical Risk Clustering Portfolio Allocation Strategies
Description: Machine learning hierarchical risk clustering portfolio allocation strategies.
The implemented methods are:
Hierarchical risk parity (De Prado, 2016) <DOI: 10.3905/jpm.2016.42.4.059>.
Hierarchical clustering-based asset allocation (Raffinot, 2017)
<DOI: 10.3905/jpm.2018.44.2.089>.
Hierarchical equal risk contribution portfolio (Raffinot, 2018)
<DOI: 10.2139/ssrn.3237540>.
A Constrained Hierarchical Risk Parity Algorithm with Cluster-based Capital Allocation (Pfitzingera and Katzke, 2019)
<https://www.ekon.sun.ac.za/wpapers/2019/wp142019/wp142019.pdf>.
Author: Carlos Trucios [aut, cre] ,
Moon Jun Kwon [aut],
Sao Paulo Research Foundation , grant 2022/09122-0 [fnd],
Programa de Incentivo a Novos Docentes da UNICAMP , grant 2525/23
[fnd]
Maintainer: Carlos Trucios <ctrucios@unicamp.br>
Diff between HierPortfolios versions 1.0.1 dated 2024-08-18 and 1.0.2 dated 2025-09-12
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- R/DHRP_Portfolio.R | 2 +- R/HCAA_Portfolio.R | 2 +- R/HERC_Portfolio.R | 2 +- 5 files changed, 14 insertions(+), 13 deletions(-)
More information about HierPortfolios at CRAN
Permanent link
Title: Dot Density Maps
Description: Generate point data for representing people within spatial data. This
collects a suite of tools for creating simple dot density maps. Several functions
from different spatial packages are standardized to take the same arguments so
that they can be easily substituted for each other.
Author: Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
Diff between dots versions 0.0.2 dated 2022-07-15 and 0.0.3 dated 2025-09-12
dots-0.0.2/dots/R/utils-pipe.R |only dots-0.0.2/dots/man/pipe.Rd |only dots-0.0.3/dots/DESCRIPTION | 21 - dots-0.0.3/dots/LICENSE | 4 dots-0.0.3/dots/MD5 | 74 ++-- dots-0.0.3/dots/NAMESPACE | 2 dots-0.0.3/dots/NEWS.md | 4 dots-0.0.3/dots/R/clip_water.R | 60 +-- dots-0.0.3/dots/R/data.R | 48 +- dots-0.0.3/dots/R/dots-package.R | 6 dots-0.0.3/dots/R/dots.R | 112 +++--- dots-0.0.3/dots/R/engine.R | 19 - dots-0.0.3/dots/R/filter_pts.R | 34 +- dots-0.0.3/dots/README.md | 27 + dots-0.0.3/dots/build/vignette.rds |binary dots-0.0.3/dots/inst/doc/making_dot_density_maps.R | 8 dots-0.0.3/dots/inst/doc/making_dot_density_maps.Rmd | 244 +++++++-------- dots-0.0.3/dots/inst/doc/making_dot_density_maps.html | 207 ++++++------ dots-0.0.3/dots/man/boston_water.Rd | 36 +- dots-0.0.3/dots/man/clip_water.Rd | 64 +-- dots-0.0.3/dots/man/dots.Rd | 72 ++-- dots-0.0.3/dots/man/dots_points.Rd | 72 ++-- dots-0.0.3/dots/man/engine_sf_hexagonal.Rd | 52 +-- dots-0.0.3/dots/man/engine_sf_random.Rd | 50 +-- dots-0.0.3/dots/man/engine_sf_regular.Rd | 52 +-- dots-0.0.3/dots/man/engine_sp_clustered.Rd | 54 +-- dots-0.0.3/dots/man/engine_sp_hexagonal.Rd | 54 +-- dots-0.0.3/dots/man/engine_sp_nonaligned.Rd | 54 +-- dots-0.0.3/dots/man/engine_sp_random.Rd | 54 +-- dots-0.0.3/dots/man/engine_sp_regular.Rd | 54 +-- dots-0.0.3/dots/man/engine_sp_stratified.Rd | 54 +-- dots-0.0.3/dots/man/engine_terra.Rd | 50 +-- dots-0.0.3/dots/man/figures/README-example-1.png |only dots-0.0.3/dots/man/figures/README-unnamed-chunk-2-1.png |only dots-0.0.3/dots/man/filter_pts.Rd | 52 +-- dots-0.0.3/dots/man/suffolk.Rd | 36 +- dots-0.0.3/dots/tests/testthat.R | 24 - dots-0.0.3/dots/tests/testthat/setup.R | 4 dots-0.0.3/dots/tests/testthat/test-dots.R | 8 dots-0.0.3/dots/vignettes/making_dot_density_maps.Rmd | 244 +++++++-------- 40 files changed, 1018 insertions(+), 992 deletions(-)
Title: Common Plots for Analysis
Description: Select data analysis plots, under a standardized calling interface implemented on top of 'ggplot2' and 'plotly'.
Plots of interest include: 'ROC', gain curve, scatter plot with marginal distributions,
conditioned scatter plot with marginal densities,
box and stem with matching theoretical distribution, and density with matching theoretical distribution.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between WVPlots versions 1.3.8 dated 2024-04-22 and 1.3.9 dated 2025-09-12
DESCRIPTION | 12 ++-- MD5 | 18 +++---- NAMESPACE | 1 R/LogLogPlot.R | 2 R/ScatterHist.R | 10 +++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/WVPlots_concept.html | 22 ++++---- inst/doc/WVPlots_examples.html | 104 ++++++++++++++++++++--------------------- man/LogLogPlot.Rd | 2 10 files changed, 91 insertions(+), 80 deletions(-)
Title: Filter Based Feature Selection for 'mlr3'
Description: Extends 'mlr3' with filter methods for feature selection.
Besides standalone filter methods built-in methods of any
machine-learning algorithm are supported. Partial scoring of
multivariate filter methods is supported.
Author: Marc Becker [cre, aut] ,
Patrick Schratz [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3filters versions 0.8.1 dated 2024-11-08 and 0.9.0 dated 2025-09-12
DESCRIPTION | 22 ++++++++++----------- MD5 | 22 ++++++++++----------- NAMESPACE | 1 NEWS.md | 8 +++++++ R/Filter.R | 37 ++++++++++++++++++++++-------------- R/FilterBoruta.R | 2 - R/FilterPerformance.R | 8 +++++-- R/FilterPermutation.R | 4 +-- R/zzz.R | 1 build/partial.rdb |binary man/Filter.Rd | 6 ++--- tests/testthat/test_filter_boruta.R | 7 ++++++ 12 files changed, 74 insertions(+), 44 deletions(-)
Title: Analysis and Visualization of Multi-Omics Data
Description: A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10. [...truncated...]
Author: Dongyue Yu [aut, cre, cph]
Maintainer: Dongyue Yu <yudongyue@mail.nankai.edu.cn>
Diff between TransProR versions 1.0.6 dated 2025-08-26 and 1.0.7 dated 2025-09-12
TransProR-1.0.6/TransProR/R/HighlightByNode.R |only TransProR-1.0.6/TransProR/man/add_new_tile_layer.Rd |only TransProR-1.0.6/TransProR/man/circos_fruits.Rd |only TransProR-1.0.6/TransProR/man/highlight_by_node.Rd |only TransProR-1.0.7/TransProR/DESCRIPTION | 6 TransProR-1.0.7/TransProR/MD5 | 12 - TransProR-1.0.7/TransProR/NAMESPACE | 4 TransProR-1.0.7/TransProR/R/CircosFruits.R | 205 -------------------- TransProR-1.0.7/TransProR/inst/doc/TransProR.html | 4 9 files changed, 9 insertions(+), 222 deletions(-)
Title: A User-Friendly R 'shiny' Application for Multi-Omics Data
Integration and Analysis
Description: A 'shiny' application, which allows you to perform single- and
multi-omics analyses using your own omics datasets. After the upload
of the omics datasets and a metadata file, single-omics is performed
for feature selection and dataset reduction. These datasets are used
for pairwise- and multi-omics analyses, where automatic tuning is
done to identify correlations between the datasets - the end goal
of the recommended 'Holomics' workflow.
Methods used in the package were implemented in the package 'mixomics'
by Florian Rohart,Benoît Gautier,Amrit Singh,Kim-Anh Lê Cao (2017) <doi:10.1371/journal.pcbi.1005752>
and are described there in further detail.
Author: Katharina Munk [aut, cre],
Eva M. Molin [aut, ctb],
Guenter Brader [ctb],
Lisa Ziemba [ctb],
AIT Austrian Institute of Technology GmbH [cph]
Maintainer: Katharina Munk <katharinamunk@yahoo.de>
Diff between Holomics versions 1.1.1 dated 2024-06-07 and 1.2.0 dated 2025-09-12
DESCRIPTION | 13 +- MD5 | 46 ++++---- NEWS.md | 44 ++++---- R/mod_DIABLO.R | 39 +++++-- R/mod_PCA.R | 23 +++- R/mod_PLSDA.R | 70 +++++++++--- R/mod_Upload.R | 171 ++++++++++++++++--------------- R/mod_sPLS.R | 66 ++++++++---- R/utils_Upload.R | 16 ++ R/utils_server.R | 50 +++++++-- R/utils_ui.R | 15 ++ README.md | 48 ++++---- build/vignette.rds |binary inst/app/www/01-home.md | 2 inst/app/www/css/custom.css | 6 - inst/app/www/css/theme.css | 12 ++ inst/app/www/help-plots.html | 14 +- inst/app/www/help-plots.md | 14 +- inst/app/www/help-tuning.md | 8 - inst/doc/Holomics.Rmd | 142 +++++++++++++++++++------ inst/doc/Holomics.html | 214 ++++++++++++++++++++++++++------------- vignettes/Holomics.Rmd | 142 +++++++++++++++++++------ vignettes/bibliography.bib | 2 vignettes/images/Upload_data.png |binary 24 files changed, 776 insertions(+), 381 deletions(-)
Title: Spatiotemporal Resampling Methods for 'mlr3'
Description: Extends the mlr3 machine learning framework with
spatio-temporal resampling methods to account for the presence of
spatiotemporal autocorrelation (STAC) in predictor variables. STAC may
cause highly biased performance estimates in cross-validation if
ignored. A JSS article is available at <doi:10.18637/jss.v111.i07>.
Author: Patrick Schratz [aut, cre] ,
Marc Becker [aut] ,
Jannes Muenchow [ctb] ,
Michel Lang [ctb]
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
This is a re-admission after prior archival of version 2.3.3 dated 2025-07-10
Diff between mlr3spatiotempcv versions 2.3.3 dated 2025-07-10 and 2.3.4 dated 2025-09-12
DESCRIPTION | 8 ++--- MD5 | 14 ++++----- NEWS.md | 7 ++++ R/ResamplingRepeatedSpCVknndm.R | 41 ++++++++++++++--------------- README.md | 2 - man/mlr_resamplings_repeated_spcv_knndm.Rd | 40 ++++++++++++++-------------- tests/testthat/data/cookfarm_subset.rds |binary tests/testthat/test-2-autoplot.R | 14 ++++++--- 8 files changed, 70 insertions(+), 56 deletions(-)
More information about mlr3spatiotempcv at CRAN
Permanent link
Title: Iterative Bias Reduction
Description: Multivariate smoothing using iterative bias reduction with kernel, thin plate splines, Duchon splines or low rank splines.
Author: Pierre-Andre Cornillon [aut, cre],
Nicolas Hengartner [aut],
Eric Matzner-Lober [aut]
Maintainer: Pierre-Andre Cornillon <pierre-andre.cornillon@univ-rennes2.fr>
Diff between ibr versions 2.0-4 dated 2023-09-13 and 2.0-5 dated 2025-09-12
DESCRIPTION | 18 ++++++++++++------ MD5 | 44 ++++++++++++++++++++++---------------------- R/bwchoice.R | 2 +- R/ibr.fit.R | 2 +- R/iterchoiceA.R | 4 ++-- R/iterchoiceAcv.R | 4 ++-- R/iterchoiceS1.R | 4 ++-- R/iterchoiceS1cv.R | 4 ++-- R/iterchoiceS1lrcv.R | 4 ++-- R/lambdachoice.R | 2 +- R/lambdachoicelr.R | 4 ++-- R/lrsmoother.R | 2 +- man/betaS1lr.Rd | 2 +- man/departnoyau.Rd | 2 +- man/forward.Rd | 6 +++--- man/ibr.Rd | 10 +++++----- man/ibr.fit.Rd | 10 +++++----- man/iterchoiceA.Rd | 4 ++-- man/iterchoiceAcv.Rd | 2 +- man/iterchoiceS1.Rd | 4 ++-- man/iterchoiceS1cv.Rd | 2 +- man/iterchoiceS1lrcv.Rd | 2 +- man/lrsmoother.Rd | 2 +- 23 files changed, 73 insertions(+), 67 deletions(-)
Title: Statistics for Holland's Theory of Vocational Choice
Description: Offers a convenient way to compute parameters in the framework of the theory of vocational choice introduced by J.L. Holland, (1997). A comprehensive summary to this theory of vocational choice is given in Holland, J.L. (1997). Making vocational choices. A theory of vocational personalities and work environments. Lutz, FL: Psychological Assessment.
Author: Joerg-Henrik Heine [aut, cre, com],
Florian Hartmann [aut, com],
Bernhard Ertl [rev, com],
Christian Tarnai [com, ths]
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>
Diff between holland versions 0.1.2-3 dated 2025-04-17 and 0.1.2-4 dated 2025-09-12
DESCRIPTION | 26 +++++++------------------- MD5 | 14 +++++++------- NAMESPACE | 2 -- NEWS | 3 +++ R/Circ_pro.R | 2 +- R/Mplus_fit.R | 2 +- R/holland-package.R | 2 -- man/Circ_pro.Rd | 2 +- 8 files changed, 20 insertions(+), 33 deletions(-)
Title: Data Science for Psychologists
Description: All datasets and functions required for the examples and exercises of the book "Data Science for Psychologists" (by Hansjoerg Neth, Konstanz University, 2025), freely available at <https://bookdown.org/hneth/ds4psy/>. The book and corresponding courses introduce principles and methods of data science to students of psychology and other biological or social sciences. The 'ds4psy' package primarily provides datasets, but also functions for data generation and manipulation (e.g., of text and time data) and graphics that are used in the book and its exercises. All functions included in 'ds4psy' are designed to be explicit and instructive, rather than efficient or elegant.
Author: Hansjoerg Neth [aut, cre]
Maintainer: Hansjoerg Neth <h.neth@uni.kn>
Diff between ds4psy versions 1.0.0 dated 2023-09-15 and 1.1.0 dated 2025-09-12
DESCRIPTION | 17 - MD5 | 228 ++++++++--------- NAMESPACE | 4 NEWS.md | 73 ++++- R/color_fun.R | 4 R/data.R | 577 +++++++++++++++++++++++++++++++++++++++----- R/data_fun.R | 48 ++- R/num_fun.R | 177 +++++++++++-- R/num_util_fun.R | 43 +-- R/plot_fun.R | 223 ++++++++++++++++- R/start.R | 2 R/text_fun.R | 47 +-- R/theme_fun.R | 28 +- R/time_fun.R | 10 R/util_fun.R | 15 + README.md | 180 ++++++++----- build/partial.rdb |binary build/vignette.rds |binary data/exp_num_dt.rda |binary data/i2ds_survey.rda |only data/tb.rda |binary inst/CITATION | 8 inst/WORDLIST | 36 ++ inst/doc/ds4psy.R | 32 +- inst/doc/ds4psy.Rmd | 70 +++-- inst/doc/ds4psy.html | 94 ++++--- inst/images/i2ds_logo_1.png |only inst/images/i2ds_logo_2.png |only inst/images/logo.png |binary inst/images/logo_OLD.png |only man/Bushisms.Rd | 9 man/Trumpisms.Rd | 15 - man/Umlaut.Rd | 2 man/base2dec.Rd | 5 man/capitalize.Rd | 11 man/caseflip.Rd | 4 man/cclass.Rd | 2 man/change_time.Rd | 2 man/chars_to_text.Rd | 2 man/coin.Rd | 4 man/collapse_chars.Rd | 2 man/count_chars.Rd | 2 man/count_chars_words.Rd | 2 man/count_words.Rd | 4 man/countries.Rd | 5 man/cur_date.Rd | 2 man/cur_time.Rd | 2 man/data_1.Rd | 3 man/data_2.Rd | 3 man/data_t1.Rd | 1 man/data_t1_de.Rd | 3 man/data_t1_tab.Rd | 3 man/data_t2.Rd | 3 man/data_t3.Rd | 3 man/data_t4.Rd | 3 man/dec2base.Rd | 8 man/dice.Rd | 2 man/dice_2.Rd | 2 man/dt_10.Rd | 5 man/exp_num_dt.Rd | 33 +- man/exp_wide.Rd | 3 man/falsePosPsy_all.Rd | 7 man/fame.Rd | 5 man/flowery.Rd | 5 man/fruits.Rd | 5 man/get_set.Rd | 2 man/i2ds_survey.Rd |only man/invert_rules.Rd | 2 man/is_equal.Rd | 16 - man/is_wholenumber.Rd | 2 man/l33t_rul35.Rd | 5 man/map_text_chars.Rd | 2 man/map_text_coord.Rd | 2 man/map_text_regex.Rd | 4 man/metachar.Rd | 2 man/num_as_char.Rd | 2 man/num_as_ordinal.Rd | 2 man/num_equal.Rd | 10 man/outliers.Rd | 3 man/pal_n_sq.Rd | 2 man/pi_100k.Rd | 3 man/plot_charmap.Rd | 3 man/plot_chars.Rd | 6 man/plot_circ_points.Rd |only man/plot_fn.Rd | 3 man/plot_fun.Rd | 5 man/plot_n.Rd | 3 man/plot_text.Rd | 6 man/plot_tiles.Rd | 1 man/posPsy_AHI_CESD.Rd | 9 man/posPsy_long.Rd | 7 man/posPsy_p_info.Rd | 9 man/posPsy_wide.Rd | 7 man/read_ascii.Rd | 4 man/sample_char.Rd | 5 man/sample_date.Rd | 2 man/sample_time.Rd | 2 man/t3.Rd | 5 man/t4.Rd | 5 man/t_1.Rd | 5 man/t_2.Rd | 5 man/t_3.Rd | 5 man/t_4.Rd | 5 man/table6.Rd | 5 man/table7.Rd | 5 man/table8.Rd | 5 man/table9.Rd | 3 man/tb.Rd | 7 man/text_to_chars.Rd | 2 man/text_to_sentences.Rd | 2 man/text_to_words.Rd | 2 man/theme_clean.Rd | 9 man/theme_ds4psy.Rd | 9 man/theme_empty.Rd | 11 man/transl33t.Rd | 4 man/words_to_text.Rd | 2 man/zodiac.Rd | 4 vignettes/ds4psy.Rmd | 70 +++-- 118 files changed, 1740 insertions(+), 649 deletions(-)
Title: Inferential Methods for Multimodal and Other Networks
Description: A set of tools for testing networks.
It includes functions for univariate and multivariate
conditional uniform graph and quadratic assignment procedure testing,
and network regression.
The package is a complement to
'Multimodal Political Networks' (2021, ISBN:9781108985000),
and includes various datasets used in the book.
Built on the 'manynet' package, all functions operate with matrices,
edge lists, and 'igraph', 'network', and 'tidygraph' objects,
and on one-mode and two-mode (bipartite) networks.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Jael Tan [ctb] ,
Bernhard Bieri [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between migraph versions 1.5.0 dated 2025-06-20 and 1.5.2 dated 2025-09-12
DESCRIPTION | 12 +++++------ MD5 | 28 ++++++++++++------------- NAMESPACE | 3 +- NEWS.md | 36 +++++++++++++++++++++++++++++++++ R/data_mpn.R | 2 - R/measure_over.R | 14 +++++++++++- R/migraph-package.R | 12 ++++++++++- R/model_diffusion.R | 4 +-- R/model_regression.R | 7 ++---- R/reexports_classes.R | 2 - inst/CITATION | 1 man/make_play.Rd | 2 - man/mpn_elite_usa.Rd | 2 - man/regression.Rd | 2 - tests/testthat/test-model_regression.R | 11 ++++++++++ 15 files changed, 103 insertions(+), 35 deletions(-)
Title: Markov Chain Monte Carlo Small Area Estimation
Description: Fit multi-level models with possibly correlated
random effects using Markov Chain Monte Carlo simulation.
Such models allow smoothing over space and time and are useful in,
for example, small area estimation.
Author: Harm Jan Boonstra [aut, cre],
Grzegorz Baltissen [ctb]
Maintainer: Harm Jan Boonstra <hjboonstra@gmail.com>
Diff between mcmcsae versions 0.7.9 dated 2025-06-04 and 0.8.0 dated 2025-09-12
DESCRIPTION | 22 ++--- MD5 | 123 +++++++++++++++++---------------- NAMESPACE | 4 + NEWS | 10 ++ R/AR1_sampler.R | 8 +- R/GMRF_extension.R | 14 +-- R/MCMCsim.R | 8 +- R/MatrixUtils.R | 38 +++++++++- R/TMVN_sampler.R | 76 ++++++++++---------- R/aux_closures.R | 12 +-- R/cMVN_sampler.R | 30 ++++---- R/cholesky.R | 2 R/conjugate_gradients.R | 13 +-- R/f_binomial.R | 10 +- R/f_gaussian.R | 13 --- R/f_multinomial.R | 6 - R/f_negbinomial.R | 8 +- R/f_poisson.R | 8 +- R/formulas.R | 3 R/kronprod.R | 15 +--- R/mc_bart.R | 25 ++++-- R/mc_block.R | 99 ++++++++++++-------------- R/mc_gen.R | 155 ++++++++++++++++++++++++++---------------- R/mc_gl.R | 2 R/mc_mec.R | 111 +++++++++++++++++++++--------- R/mc_offset.R | 11 ++ R/mc_reg.R | 87 ++++++++++++++++++----- R/mc_s.R |only R/mc_vfac.R | 33 ++++---- R/mc_vreg.R | 20 +++-- R/mcmcsae.R | 12 +-- R/model_eval.R | 28 +++++-- R/modelmatrix.R | 4 - R/models.R | 91 +++++++++++++----------- R/parallel.R | 18 ++-- R/plots.R | 4 - R/prediction.R | 4 - R/priors.R | 16 ++-- R/projection.R | 18 ++-- R/samplers.R | 132 ++++++++++++++--------------------- R/sbc.R | 4 - R/set_constraints.R | 8 +- R/sparse_template.R | 42 ++++++----- R/tabMatrix.R | 10 +- build/vignette.rds |binary inst/doc/area_level.html | 70 +++++++++--------- man/MCMC-object-conversion.Rd | 2 man/brt.Rd | 4 - man/correlation.Rd | 2 man/gen.Rd | 4 - man/mc_offset.Rd | 4 - man/mec.Rd | 4 - man/reg.Rd | 7 - man/s.Rd |only man/vfac.Rd | 4 - man/vreg.Rd | 4 - tests/testthat/test_gen.R | 26 +++++++ tests/testthat/test_linalg.R | 32 ++++++++ tests/testthat/test_linreg.R | 17 ++++ tests/testthat/test_mat_sum.R | 4 - tests/testthat/test_mec.R |only tests/testthat/test_sim.R | 11 ++ tests/testthat/test_spatial.R | 4 - tests/testthat/test_varmod.R | 13 ++- 64 files changed, 918 insertions(+), 651 deletions(-)
Title: Post-Process 'ggplot2' Plots with 'TikZ' Code Using Plot
Coordinates
Description: Annotation of 'ggplot2' plots with arbitrary 'TikZ' code, using absolute data or relative plot coordinates.
Author: Oliver Thomas [aut, cre]
Maintainer: Oliver Thomas <ost.dev@posteo.net>
Diff between ggtikz versions 0.1.3 dated 2024-06-16 and 0.1.4 dated 2025-09-12
DESCRIPTION | 10 +++++----- MD5 | 27 +++++++++++++++------------ NAMESPACE | 1 + R/ggtikz-package.R |only R/ggtikzCanvas.R | 31 +++++++++++++++++++++++++++---- R/padding.R | 4 ++-- build/vignette.rds |binary inst/doc/examples.R | 2 ++ inst/doc/examples.pdf |binary man/dense_rank.Rd |only man/ggtikz-package.Rd |only tests/testthat/helpers.R | 2 -- tests/testthat/test-ggtikz.R | 5 ----- tests/testthat/test-ggtikzAnnotation.R | 2 -- tests/testthat/test-ggtikzCanvas.R | 20 +++++++++----------- tests/testthat/test-ggtikzTransform.R | 2 -- 16 files changed, 61 insertions(+), 45 deletions(-)
Title: Model Transport of Environmental DNA in River Networks
Description: Runs the eDITH (environmental DNA Integrating Transport
and Hydrology) model, which implements a mass balance of environmental DNA (eDNA)
transport at a river network scale coupled with a species distribution model
to obtain maps of species distribution. eDITH can work with both eDNA concentration
(e.g., obtained via quantitative polymerase chain reaction) or metabarcoding
(read count) data. Parameter estimation can be performed via Bayesian techniques
(via the 'BayesianTools' package) or optimization algorithms. An interface to the
'DHARMa' package for posterior predictive checks is provided. See Carraro and
Altermatt (2024) <doi:10.1111/2041-210X.14317> for a package introduction;
Carraro et al. (2018) <doi:10.1073/pnas.1813843115> and Carraro et al. (2020)
<doi:10.1038/s41467-020-17337-8> for methodological details.
Author: Luca Carraro [cre, aut],
Florian Altermatt [aut],
University of Zurich [cph, fnd]
Maintainer: Luca Carraro <luca.carraro@hotmail.it>
Diff between eDITH versions 1.0.0 dated 2024-05-24 and 1.1.0 dated 2025-09-12
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- NEWS.md | 10 ++++++++++ R/eval_posterior_eDITH.R | 3 +++ R/run_eDITH_optim.R | 1 + R/run_eDITH_optim_joint.R | 1 + man/eval_posterior_eDITH.Rd | 4 +++- man/posterior_pred_sim_eDITH.Rd | 4 ++-- man/run_eDITH_BT.Rd | 22 +++++++++++----------- man/run_eDITH_BT_joint.Rd | 22 +++++++++++----------- man/run_eDITH_optim.Rd | 4 ++-- man/run_eDITH_optim_joint.Rd | 4 ++-- man/run_eDITH_single.Rd | 2 +- man/sampling_strategy_direct.Rd | 2 +- man/sampling_strategy_eDNA.Rd | 2 +- man/wigger.Rd | 2 +- 16 files changed, 68 insertions(+), 51 deletions(-)
Title: Tools for Managing SSH and Git Credentials
Description: Setup and retrieve HTTPS and SSH credentials for use with 'git' and
other services. For HTTPS remotes the package interfaces the 'git-credential'
utility which 'git' uses to store HTTP usernames and passwords. For SSH
remotes we provide convenient functions to find or generate appropriate SSH
keys. The package both helps the user to setup a local git installation, and
also provides a back-end for git/ssh client libraries to authenticate with
existing user credentials.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between credentials versions 2.0.2 dated 2024-10-04 and 2.0.3 dated 2025-09-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 3 +++ R/onattach.R | 2 +- build/vignette.rds |binary inst/doc/intro.html | 5 +++-- 6 files changed, 16 insertions(+), 12 deletions(-)
Title: QTL EM Algorithm Mapping and Hotspots Detection
Description: For QTL mapping, this package comprises several functions designed to execute diverse
tasks, such as simulating or analyzing data, calculating significance thresholds, and
visualizing QTL mapping results. The single-QTL or multiple-QTL method, which enables
the fitting and comparison of various statistical models, is employed to analyze the
data for estimating QTL parameters. The models encompass linear regression, permutation
tests, normal mixture models, and truncated normal mixture models. The Gaussian stochastic
process is utilized to compute significance thresholds for QTL detection on a genetic
linkage map within experimental populations. Two types of data, complete genotyping, and
selective genotyping data from various experimental populations, including backcross, F2,
recombinant inbred (RI) populations, and advanced intercrossed (AI) populations, are
considered in the QTL mapping analysis. For QTL hotspot detection, statistical methods can
be developed based on either utilizin [...truncated...]
Author: Ping-Yuan Chung [cre],
Chen-Hung Kao [aut],
Y.-T. Guo [aut],
H.-N. Ho [aut],
H.-I. Lee [aut],
P.-Y. Wu [aut],
M.-H. Yang [aut],
M.-H. Zeng [aut]
Maintainer: Ping-Yuan Chung <pychung@webmail.stat.sinica.edu.tw>
Diff between QTLEMM versions 3.0.1 dated 2025-03-11 and 3.1.0 dated 2025-09-12
DESCRIPTION | 6 +- MD5 | 46 ++++++++-------- R/EM.MIM.R | 14 +++- R/EM.MIMv.R | 25 ++++---- R/EQF.permu.R | 26 ++++----- R/IM.search.R | 2 R/LOD.QTLdetect.R | 2 R/LRTthre.R | 2 R/MIM.points.R | 14 +++- R/MIM.search.R | 14 +++- R/Qhot.EQF.R | 110 +++++++++++++++++++-------------------- R/Qhot.R | 2 inst/extdata/gramene.QTL.RDATA |only inst/extdata/gramene.chr.RDATA |only inst/extdata/gramene.trait.RDATA |only inst/extdata/yeast.process.RDATA |only man/EM.MIM.Rd | 2 man/EM.MIMv.Rd | 2 man/EQF.permu.Rd | 8 +- man/IM.search.Rd | 2 man/LOD.QTLdetect.Rd | 2 man/LRTthre.Rd | 2 man/MIM.points.Rd | 9 ++- man/MIM.search.Rd | 9 ++- man/Qhot.EQF.Rd | 24 ++++---- man/Qhot.Rd | 9 ++- 26 files changed, 184 insertions(+), 148 deletions(-)
Title: Optimal Channel Networks
Description: Generate and analyze Optimal Channel Networks (OCNs):
oriented spanning trees reproducing all scaling features characteristic
of real, natural river networks. As such, they can be used in a variety
of numerical experiments in the fields of hydrology, ecology and
epidemiology. See Carraro et al. (2020) <doi:10.1002/ece3.6479>
for a presentation of the package; Rinaldo et al. (2014)
<doi:10.1073/pnas.1322700111> for a theoretical overview on the OCN
concept; Furrer and Sain (2010) <doi:10.18637/jss.v036.i10> for the
construct used.
Author: Luca Carraro [aut, cre],
Florian Altermatt [ctb],
Emanuel A. Fronhofer [ctb],
Reinhard Furrer [ctb],
Isabelle Gounand [ctb],
Andrea Rinaldo [ctb],
Enrico Bertuzzo [aut]
Maintainer: Luca Carraro <luca.carraro@hotmail.it>
Diff between OCNet versions 1.2.2 dated 2024-04-16 and 1.2.3 dated 2025-09-12
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- NEWS.md | 6 ++++++ R/draw_thematic_OCN.R | 2 +- inst/doc/OCNet.html | 4 ++-- man/OCN_to_AEM.Rd | 6 +++--- man/aggregate_OCN.Rd | 6 +++--- man/create_OCN.Rd | 2 +- man/draw_elev2D_OCN.Rd | 4 ++-- man/draw_elev3D_OCN.Rd | 2 +- man/draw_elev3Drgl_OCN.Rd | 9 +++++---- man/draw_subcatchments_OCN.Rd | 2 +- man/draw_thematic_OCN.Rd | 8 ++++---- man/landscape_OCN.Rd | 2 +- man/paths_OCN.Rd | 4 ++-- man/plot.Rd | 2 +- 16 files changed, 51 insertions(+), 44 deletions(-)
Title: A Toolbox for Conditional Inference Trees and Random Forests
Description: Additions to 'party' and 'partykit' packages : tools for the interpretation of forests (surrogate trees, prototypes, etc.), feature selection (see Gregorutti et al (2017) <doi:10.48550/arXiv.1310.5726>, Hapfelmeier and Ulm (2013) <doi:10.1016/j.csda.2012.09.020>, Altmann et al (2010) <doi:10.1093/bioinformatics/btq134>) and parallelized versions of conditional forest and variable importance functions. Also modules and a shiny app for conditional inference trees.
Author: Nicolas Robette [aut, cre]
Maintainer: Nicolas Robette <nicolas.robette@uvsq.fr>
Diff between moreparty versions 0.4 dated 2023-11-22 and 0.4.2 dated 2025-09-12
moreparty-0.4.2/moreparty/DESCRIPTION | 21 +-- moreparty-0.4.2/moreparty/MD5 | 30 +--- moreparty-0.4.2/moreparty/NEWS.md | 16 ++ moreparty-0.4.2/moreparty/R/NiceTreePlot.R | 25 +++ moreparty-0.4.2/moreparty/R/NodeTreePlot.R | 107 +++++++++++++++- moreparty-0.4.2/moreparty/R/NodesInfo.R | 42 +++++- moreparty-0.4.2/moreparty/README.md | 19 ++ moreparty-0.4.2/moreparty/inst/CITATION |only moreparty-0.4.2/moreparty/man/GetAleData.Rd | 8 - moreparty-0.4.2/moreparty/man/GetInteractionStrength.Rd | 4 moreparty-0.4.2/moreparty/man/GetPartialData.Rd | 10 - moreparty-0.4.2/moreparty/man/fastcforest.Rd | 14 +- moreparty-0.4.2/moreparty/man/fastvarImp.Rd | 8 - moreparty-0.4.2/moreparty/man/ggVarImp.Rd | 2 moreparty-0.4/moreparty/build |only moreparty-0.4/moreparty/inst/doc |only moreparty-0.4/moreparty/vignettes |only 17 files changed, 238 insertions(+), 68 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description: Contains functions for multiple imputation which
complements existing functionality in R.
In particular, several imputation methods for the
mice package (van Buuren & Groothuis-Oudshoorn, 2011,
<doi:10.18637/jss.v045.i03>) are implemented.
Main features of the miceadds package include
plausible value imputation (Mislevy, 1991,
<doi:10.1007/BF02294457>), multilevel imputation for
variables at any level or with any number of hierarchical
and non-hierarchical levels (Grund, Luedtke & Robitzsch,
2018, <doi:10.1177/1094428117703686>; van Buuren, 2018,
Ch.7, <doi:10.1201/9780429492259>), imputation using
partial least squares (PLS) for high dimensional
predictors (Robitzsch, Pham & Yanagida, 2016),
nested multiple imputation (Rubin, 2003,
<doi:10.1111/1467-9574.00217>), substantive model
compatible imputation (Bartlett et al., 2015,
<doi:10.1177/0962280214521348>), and features
for the generation of synthetic datasets
(Reiter, 2005, <doi:10. [...truncated...]
Author: Alexander Robitzsch [aut, cre] ,
Simon Grund [aut] ,
Thorsten Henke [ctb]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 3.17-44 dated 2024-01-09 and 3.18-36 dated 2025-09-12
DESCRIPTION | 29 ++++- MD5 | 126 ++++++++++++------------ R/ANSI_create_table.R | 45 ++++---- R/RcppExports.R | 2 R/VariableNames2String.R | 8 - R/adj_groupmean.R |only R/complete.miceadds.R | 6 - R/covTest.R | 13 +- R/crlrem.R | 8 - R/cronbach_alpha.R | 4 R/cxxfunction.copy.R | 12 +- R/datalist2mids.R | 38 +++---- R/datlist_create.R | 32 +++--- R/fast.groupmean.R | 7 - R/fast.groupsum.R | 7 - R/filename_split.R | 9 - R/files_move.R | 18 +-- R/include.2l.predictors_v1.R | 4 R/mice.impute.2l.groupmean.R | 4 R/mice.impute.2l.groupmean.elim.R | 10 - R/mice.impute.2l.plausible.values.R | 7 - R/mice.impute.2l.pls.R | 7 - R/mice.impute.bygroup.R | 18 +-- R/mice.impute.catpmm.R | 20 +-- R/mice.impute.tricube.pmm2.R | 7 - R/mice.nmi.R | 34 +++--- R/mice_imputation_2l_lmer.R | 42 ++++---- R/mice_imputation_args_include_wy.R | 4 R/mice_imputation_bygroup_modify_arguments.R | 4 R/mice_imputation_create_contextual_variables.R | 8 - R/mice_impute_catpmm_create_dummies_y.R | 4 R/mice_multilevel_add_groupmeans.R | 4 R/mice_multilevel_create_formula.R | 10 - R/mice_multilevel_imputation_pmm5.R | 14 +- R/mice_multilevel_impute_groupmean.R | 6 - R/miceadds_call_internal.R | 4 R/miceadds_ginv.R | 4 R/miceadds_import_CDM_CDM_rmvnorm.R | 4 R/miceadds_weighted_centering.R | 4 R/miceadds_weighted_scaling_y.R | 4 R/pca.covridge.R | 4 R/plausible.value.imputation.R | 30 ++--- R/scale_datlist.R | 6 - R/scan0.R | 4 R/source.Rcpp.all.R | 24 ++-- R/string_find_first.R | 4 R/summary.mira.nmi.R | 28 ++--- R/sumpreserving.rounding.R | 10 - R/syn_da.R | 30 +++-- R/syn_da_extend_list.R |only R/syn_da_synthesize_lm.R | 13 +- R/tw.mcmc.imputation.R | 13 +- R/visitSequence.determine.R | 4 R/with.datlist.R | 8 - R/within.NestedImputationList.R | 6 - R/zzz.R | 13 -- build/partial.rdb |binary inst/NEWS | 12 ++ man/lm.cluster.Rd | 11 -- man/mice.impute.catpmm.Rd | 4 man/syn_da.Rd | 48 ++++++++- man/write.pspp.Rd | 12 +- src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 2 65 files changed, 472 insertions(+), 409 deletions(-)
Title: Semi-Supervised Algorithm for Document Scaling
Description: A word embeddings-based semi-supervised model for document scaling Watanabe (2020) <doi:10.1080/19312458.2020.1832976>.
LSS allows users to analyze large and complex corpora on arbitrary dimensions with seed words exploiting efficiency of word embeddings (SVD, Glove).
It can generate word vectors on a users-provided corpus or incorporate a pre-trained word vectors.
Author: Kohei Watanabe [aut, cre, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between LSX versions 1.4.5 dated 2025-06-19 and 1.5.0 dated 2025-09-12
LSX-1.4.5/LSX/R/textmodel.R |only LSX-1.4.5/LSX/tests/testthat/test-textmodel.R |only LSX-1.5.0/LSX/DESCRIPTION | 6 LSX-1.5.0/LSX/MD5 | 32 ++-- LSX-1.5.0/LSX/NAMESPACE | 1 LSX-1.5.0/LSX/NEWS.md | 5 LSX-1.5.0/LSX/R/as.textmodel.R | 138 ++++++++++----------- LSX-1.5.0/LSX/R/textmodel_lss.R |only LSX-1.5.0/LSX/R/textmodel_lss2.R |only LSX-1.5.0/LSX/R/textplot.R | 2 LSX-1.5.0/LSX/inst/WORDLIST | 1 LSX-1.5.0/LSX/man/as.textmodel_lss.Rd | 50 ++++++- LSX-1.5.0/LSX/man/coef.textmodel_lss.Rd | 2 LSX-1.5.0/LSX/man/textmodel_lss.Rd | 66 +++++++--- LSX-1.5.0/LSX/man/weight_seeds.Rd | 2 LSX-1.5.0/LSX/tests/testthat/Rplots.pdf |binary LSX-1.5.0/LSX/tests/testthat/test-as.textmodel.R | 9 + LSX-1.5.0/LSX/tests/testthat/test-textmodel_lss.R |only LSX-1.5.0/LSX/tests/testthat/test-textmodel_lss2.R |only LSX-1.5.0/LSX/tests/testthat/test-textplot.R | 1 20 files changed, 203 insertions(+), 112 deletions(-)
Title: GCC Estimation of the Multilevel Factor Model
Description: Provides methods for model selection, estimation, inference, and simulation for the
multilevel factor model, based on the principal component estimation and generalised
canonical correlation approach. Details can be found in "Generalised Canonical Correlation
Estimation of the Multilevel Factor Model." Lin and Shin (2025) <doi:10.2139/ssrn.4295429>.
Author: Rui Lin [aut, cre],
Yongcheol Shin [aut]
Maintainer: Rui Lin <ruilin1081@gmail.com>
Diff between GCCfactor versions 1.1.0 dated 2025-06-27 and 1.1.1 dated 2025-09-12
DESCRIPTION | 10 +- MD5 | 11 +- NAMESPACE | 5 + R/utility_functions.R | 4 - R/vcov_functions.R | 163 +++++++++++++++++++++++++------------------- man/summary.multi_result.Rd | 1 man/vcov_POET.Rd |only 7 files changed, 110 insertions(+), 84 deletions(-)
Title: Tables of Descriptive Statistics in HTML
Description: Create HTML tables of descriptive statistics, as one would expect
to see as the first table (i.e. "Table 1") in a medical/epidemiological journal
article.
Author: Benjamin Rich [aut, cre, cph]
Maintainer: Benjamin Rich <mail@benjaminrich.net>
Diff between table1 versions 1.4.3 dated 2023-01-06 and 1.5.0 dated 2025-09-12
table1-1.4.3/table1/man/render.strat.default.Rd |only table1-1.5.0/table1/DESCRIPTION | 15 table1-1.5.0/table1/MD5 | 92 table1-1.5.0/table1/NAMESPACE | 114 table1-1.5.0/table1/NEWS.md | 301 table1-1.5.0/table1/R/eqcut.R | 310 table1-1.5.0/table1/R/t1read.R | 208 table1-1.5.0/table1/R/table1.R | 3377 ++++--- table1-1.5.0/table1/README.md | 142 table1-1.5.0/table1/build/vignette.rds |binary table1-1.5.0/table1/inst/doc/table1-examples.R | 420 table1-1.5.0/table1/inst/doc/table1-examples.Rmd | 1046 +- table1-1.5.0/table1/inst/doc/table1-examples.html | 4500 ++++------ table1-1.5.0/table1/inst/doc/table1-latex.R | 106 table1-1.5.0/table1/inst/doc/table1-latex.Rmd | 367 table1-1.5.0/table1/inst/doc/table1-latex.pdf |binary table1-1.5.0/table1/inst/doc/table1-weighted.R |only table1-1.5.0/table1/inst/doc/table1-weighted.Rmd |only table1-1.5.0/table1/inst/doc/table1-weighted.html |only table1-1.5.0/table1/inst/table1_defaults_1.0/table1_defaults.css | 204 table1-1.5.0/table1/man/as.data.frame.table1.Rd | 38 table1-1.5.0/table1/man/eqcut.Rd | 218 table1-1.5.0/table1/man/factorp.Rd |only table1-1.5.0/table1/man/indexed.Rd |only table1-1.5.0/table1/man/indices.Rd |only table1-1.5.0/table1/man/knit_print.table1.Rd | 40 table1-1.5.0/table1/man/label.Rd | 84 table1-1.5.0/table1/man/parse.abbrev.render.code.Rd | 108 table1-1.5.0/table1/man/print.table1.Rd | 46 table1-1.5.0/table1/man/render.categorical.default.Rd | 66 table1-1.5.0/table1/man/render.continuous.default.Rd | 60 table1-1.5.0/table1/man/render.default.Rd | 140 table1-1.5.0/table1/man/render.missing.default.Rd | 58 table1-1.5.0/table1/man/render.strat.Rd |only table1-1.5.0/table1/man/render.varlabel.Rd | 11 table1-1.5.0/table1/man/signif_pad.Rd | 136 table1-1.5.0/table1/man/stats.apply.rounding.Rd | 132 table1-1.5.0/table1/man/stats.default.Rd | 140 table1-1.5.0/table1/man/subsetp.Rd | 56 table1-1.5.0/table1/man/t1flex.Rd | 50 table1-1.5.0/table1/man/t1kable.Rd | 57 table1-1.5.0/table1/man/t1read.Rd | 164 table1-1.5.0/table1/man/table.rows.Rd | 142 table1-1.5.0/table1/man/table1.Rd | 409 table1-1.5.0/table1/man/units.Rd | 72 table1-1.5.0/table1/man/update_html.Rd | 38 table1-1.5.0/table1/man/weighted.Rd |only table1-1.5.0/table1/vignettes/style.css | 44 table1-1.5.0/table1/vignettes/table1-examples.Rmd | 1046 +- table1-1.5.0/table1/vignettes/table1-latex.Rmd | 367 table1-1.5.0/table1/vignettes/table1-weighted.Rmd |only table1-1.5.0/table1/vignettes/vignette.css | 416 52 files changed, 7759 insertions(+), 7581 deletions(-)
Title: Web Application for the SSD Module of the MOSAIC Platform
Description: Web application using 'shiny' for the SSD (Species
Sensitivity Distribution) module of the MOSAIC (MOdeling and
StAtistical tools for ecotoxICology) platform. It estimates the
Hazardous Concentration for x% of the species (HCx) from toxicity
values that can be censored and provides various plotting options for
a better understanding of the results. See our companion paper
Kon Kam King et al. (2014) <doi:10.48550/arXiv.1311.5772>.
Author: Aurelie Siberchicot [cre, aut] ,
Milena Kaag [aut],
Sandrine Charles [aut] ,
UMR5558 LBBE MEPS [cph, fnd],
rhandsontable contributors [ctb, cph]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ssd4mosaic versions 1.0.3 dated 2025-03-11 and 1.0.4-2 dated 2025-09-12
DESCRIPTION | 12 - MD5 | 16 +- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 30 ++- inst/doc/R_functions.html | 241 +++++++++++++++----------------- inst/doc/ssd4mosaic.html | 159 +++++++++------------ tests/testthat/test-fct_ci_plots.R | 4 tests/testthat/test-fct_options_plots.R | 2 9 files changed, 222 insertions(+), 242 deletions(-)
Title: Partial Least Squares Regression for Generalized Linear Models
Description: Provides (weighted) Partial least squares Regression for generalized linear models and repeated k-fold cross-validation of such models using various criteria <doi:10.48550/arXiv.1810.01005>. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between plsRglm versions 1.5.1 dated 2023-03-14 and 1.6.0 dated 2025-09-12
DESCRIPTION | 28 +- MD5 | 288 +++++++++++++++--------------- NEWS.md | 14 + R/AICpls.R | 2 R/PLS_glm_wvc.R | 4 R/PLS_lm_wvc.R | 4 R/aic.dof.R | 2 R/bootpls.R | 2 R/bootplsglm.R | 2 R/boxplots.bootpls.R | 2 R/coef.plsRglmmodel.R | 2 R/coef.plsRmodel.R | 2 R/coefs.plsR.R | 2 R/coefs.plsR.raw.R | 2 R/coefs.plsRglm.R | 2 R/coefs.plsRglm.raw.R | 2 R/coefs.plsRglmnp.R | 2 R/coefs.plsRnp.r | 2 R/confints.bootpls.R | 2 R/cv.plsR.R | 4 R/cv.plsRglm.R | 2 R/cvtable.R | 4 R/datasets.R | 2 R/dicho.R | 2 R/infcrit.dof.R | 2 R/kfolds2CVinfos_glm.R | 4 R/kfolds2CVinfos_lm.R | 4 R/kfolds2Chisq.R | 4 R/kfolds2Chisqind.R | 4 R/kfolds2Mclassed.R | 4 R/kfolds2Mclassedind.R | 4 R/kfolds2Press.R | 4 R/kfolds2Pressind.R | 4 R/kfolds2coeff.R | 4 R/loglikpls.R | 2 R/permcoefs.plsR.R | 2 R/permcoefs.plsR.raw.R | 2 R/permcoefs.plsRglm.R | 2 R/permcoefs.plsRglm.raw.R | 2 R/permcoefs.plsRglmnp.R | 2 R/permcoefs.plsRnp.R | 2 R/plot.table.summary.cv.plsRglmmodel.R | 4 R/plot.table.summary.cv.plsRmodel.R | 4 R/plots.confints.bootpls.R | 2 R/plsR.R | 4 R/plsR.dof.R | 2 R/plsRglm-package.R | 22 +- R/plsRglm.R | 4 R/predict.plsRglmmodel.R | 4 R/predict.plsRmodel.R | 4 R/print.coef.plsRglmmodel.R | 4 R/print.coef.plsRmodel.R | 4 R/print.cv.plsRglmmodel.R | 4 R/print.cv.plsRmodel.R | 4 R/print.plsRglmmodel.R | 4 R/print.plsRmodel.R | 4 R/print.summary.plsRglmmodel.R | 4 R/print.summary.plsRmodel.R | 4 R/signpred.R | 4 R/simul_data_UniYX.R | 2 R/simul_data_UniYX_binom.R | 2 R/simul_data_YX.R | 2 R/simul_data_complete.R | 2 R/summary.cv.plsRglmmodel.R | 4 R/summary.cv.plsRmodel.R | 4 R/summary.plsRglmmodel.R | 4 R/summary.plsRmodel.R | 4 R/tilt.bootpls.R | 2 R/tilt.bootplsglm.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/_pkgdown.yml | 5 man/AICpls.Rd | 2 man/CorMat.Rd | 2 man/PLS_glm_wvc.Rd | 4 man/PLS_lm_wvc.Rd | 4 man/aic.dof.Rd | 2 man/bootpls.Rd | 2 man/bootplsglm.Rd | 2 man/boxplots.bootpls.Rd | 2 man/coef.plsRglmmodel.Rd | 2 man/coef.plsRmodel.Rd | 2 man/coefs.plsR.Rd | 2 man/coefs.plsR.raw.Rd | 2 man/coefs.plsRglm.Rd | 2 man/coefs.plsRglm.raw.Rd | 2 man/coefs.plsRglmnp.Rd | 2 man/coefs.plsRnp.Rd | 2 man/confints.bootpls.Rd | 2 man/cv.plsR.Rd | 4 man/cv.plsRglm.Rd | 2 man/cvtable.Rd | 4 man/dicho.Rd | 2 man/infcrit.dof.Rd | 2 man/kfolds2CVinfos_glm.Rd | 4 man/kfolds2CVinfos_lm.Rd | 4 man/kfolds2Chisq.Rd | 4 man/kfolds2Chisqind.Rd | 4 man/kfolds2Mclassed.Rd | 4 man/kfolds2Mclassedind.Rd | 4 man/kfolds2Press.Rd | 4 man/kfolds2Pressind.Rd | 4 man/kfolds2coeff.Rd | 4 man/loglikpls.Rd | 2 man/permcoefs.plsR.Rd | 2 man/permcoefs.plsR.raw.Rd | 2 man/permcoefs.plsRglm.Rd | 2 man/permcoefs.plsRglm.raw.Rd | 2 man/permcoefs.plsRglmnp.Rd | 2 man/permcoefs.plsRnp.Rd | 2 man/plot.table.summary.cv.plsRglmmodel.Rd | 4 man/plot.table.summary.cv.plsRmodel.Rd | 4 man/plots.confints.bootpls.Rd | 2 man/plsR.Rd | 4 man/plsR.dof.Rd | 2 man/plsRglm-package.Rd | 25 ++ man/plsRglm.Rd | 4 man/predict.plsRglmmodel.Rd | 4 man/predict.plsRmodel.Rd | 4 man/print.coef.plsRglmmodel.Rd | 4 man/print.coef.plsRmodel.Rd | 4 man/print.cv.plsRglmmodel.Rd | 4 man/print.cv.plsRmodel.Rd | 4 man/print.plsRglmmodel.Rd | 4 man/print.plsRmodel.Rd | 4 man/print.summary.plsRglmmodel.Rd | 4 man/print.summary.plsRmodel.Rd | 4 man/signpred.Rd | 4 man/simul_data_UniYX.Rd | 2 man/simul_data_UniYX_binom.Rd | 2 man/simul_data_YX.Rd | 2 man/simul_data_complete.Rd | 2 man/summary.cv.plsRglmmodel.Rd | 4 man/summary.cv.plsRmodel.Rd | 4 man/summary.plsRglmmodel.Rd | 4 man/summary.plsRmodel.Rd | 4 man/tilt.bootpls.Rd | 2 man/tilt.bootplsglm.Rd | 2 tests |only 140 files changed, 413 insertions(+), 359 deletions(-)
Title: Combined Visualisation of Phylogenetic and Epidemiological Data
Description: A collection of utilities and 'ggplot2' extensions to assist with
visualisations in genomic epidemiology. This includes the 'phylepic' chart,
a visual combination of a phylogenetic tree and a matched epidemic curve.
The included 'ggplot2' extensions such as date axes binned by week are
relevant for other applications in epidemiology and beyond. The approach is
described in Suster et al. (2024) <doi:10.1101/2024.04.02.24305229>.
Author: Carl Suster [aut, cre] ,
Western Sydney Local Health District, NSW Health [cph]
Maintainer: Carl Suster <carl.suster@sydney.edu.au>
Diff between phylepic versions 0.2.0 dated 2024-05-31 and 0.3.0 dated 2025-09-12
phylepic-0.2.0/phylepic/R/bin.R |only phylepic-0.2.0/phylepic/R/stat_week.R |only phylepic-0.2.0/phylepic/R/stat_week_2d.R |only phylepic-0.2.0/phylepic/man/stat_week.Rd |only phylepic-0.2.0/phylepic/man/stat_week_2d.Rd |only phylepic-0.3.0/phylepic/DESCRIPTION | 22 +- phylepic-0.3.0/phylepic/LICENSE | 4 phylepic-0.3.0/phylepic/MD5 | 75 +++--- phylepic-0.3.0/phylepic/NAMESPACE | 15 + phylepic-0.3.0/phylepic/NEWS.md | 12 + phylepic-0.3.0/phylepic/R/breaks_cached.R |only phylepic-0.3.0/phylepic/R/geom_calendar.R | 89 +++----- phylepic-0.3.0/phylepic/R/helpers_ggplot.R | 87 +++++--- phylepic-0.3.0/phylepic/R/phylepic-package.R | 1 phylepic-0.3.0/phylepic/R/plot.phylepic.R | 26 +- phylepic-0.3.0/phylepic/R/plot_bars.R | 11 - phylepic-0.3.0/phylepic/R/plot_calendar.R | 108 +++++----- phylepic-0.3.0/phylepic/R/plot_epicurve.R | 90 ++++---- phylepic-0.3.0/phylepic/R/plot_tree.R | 38 +-- phylepic-0.3.0/phylepic/R/scale_week.R | 10 phylepic-0.3.0/phylepic/R/stat_bin_2d_auto.R |only phylepic-0.3.0/phylepic/R/stat_bin_auto.R |only phylepic-0.3.0/phylepic/R/stat_bin_location.R |only phylepic-0.3.0/phylepic/R/vnd_ggplot2_bin.R |only phylepic-0.3.0/phylepic/R/vnd_ggplot2_utils.R |only phylepic-0.3.0/phylepic/R/week.R | 4 phylepic-0.3.0/phylepic/README.md | 9 phylepic-0.3.0/phylepic/build/partial.rdb |binary phylepic-0.3.0/phylepic/build/vignette.rds |binary phylepic-0.3.0/phylepic/inst/CITATION | 9 phylepic-0.3.0/phylepic/inst/COPYRIGHTS | 7 phylepic-0.3.0/phylepic/inst/doc/phylepic.R | 44 ++-- phylepic-0.3.0/phylepic/inst/doc/phylepic.Rmd | 24 +- phylepic-0.3.0/phylepic/inst/doc/phylepic.html | 79 ++++--- phylepic-0.3.0/phylepic/inst/enteric_metadata.csv | 34 +-- phylepic-0.3.0/phylepic/man/breaks_cached.Rd |only phylepic-0.3.0/phylepic/man/geom_calendar.Rd | 43 ++- phylepic-0.3.0/phylepic/man/phylepic-package.Rd | 4 phylepic-0.3.0/phylepic/man/plot_calendar.Rd | 15 - phylepic-0.3.0/phylepic/man/plot_epicurve.Rd | 17 - phylepic-0.3.0/phylepic/man/scale_x_week.Rd | 2 phylepic-0.3.0/phylepic/man/stat_bin_2d_auto.Rd |only phylepic-0.3.0/phylepic/man/stat_bin_auto.Rd |only phylepic-0.3.0/phylepic/man/stat_bin_location.Rd |only phylepic-0.3.0/phylepic/tests/testthat/test-breaks_cached.R |only phylepic-0.3.0/phylepic/tests/testthat/test-stat_bin_location.R |only phylepic-0.3.0/phylepic/vignettes/phylepic.Rmd | 24 +- 47 files changed, 498 insertions(+), 405 deletions(-)
Title: A Forward-Pipe Operator for R
Description: Provides a mechanism for chaining commands with a new
forward-pipe operator, %>%. This operator will forward a value, or the
result of an expression, into the next function call/expression.
There is flexible support for the type of right-hand side expressions.
For more information, see package vignette. To quote Rene Magritte,
"Ceci n'est pas un pipe."
Author: Stefan Milton Bache [aut, cph] ,
Hadley Wickham [aut],
Lionel Henry [cre],
Posit Software, PBC [cph, fnd]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between magrittr versions 2.0.3 dated 2022-03-30 and 2.0.4 dated 2025-09-12
DESCRIPTION | 19 LICENSE | 4 MD5 | 29 - NEWS.md | 5 README.md | 43 - build/vignette.rds |binary inst/doc/magrittr.R | 36 - inst/doc/magrittr.html | 582 ++++++++++++++++++------- inst/doc/tradeoffs.R | 292 ++++++------ inst/doc/tradeoffs.html | 963 +++++++++++++++++++++++++++--------------- man/magrittr-package.Rd | 6 src/pipe.c | 8 src/utils.c | 2 src/utils.h | 25 - tests/testthat/Rplots.pdf |only tests/testthat/_snaps/pipe.md | 4 16 files changed, 1323 insertions(+), 695 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-23 1.0.1
2021-05-07 1.0.0
Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are cumulative probability
distributions which are fitted to toxicity concentrations for
different species as described by Posthuma et al.(2001)
<isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to
fit distributions such as the gamma, log-logistic, log-normal and
log-normal log-normal mixture. Multiple distributions can be averaged
using Akaike Information Criteria. Confidence intervals on hazard
concentrations and proportions are produced by bootstrapping.
Author: Joe Thorley [aut, cre] ,
Rebecca Fisher [aut],
David Fox [aut],
Carl Schwarz [aut],
Angeline Tillmanns [ctb],
Seb Dalgarno [ctb] ,
Kathleen McTavish [ctb],
Heather Thompson [ctb],
Doug Spry [ctb],
Rick van Dam [ctb],
Graham Batley [ctb],
Ali Azizishi [...truncated...]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between ssdtools versions 2.3.0 dated 2025-02-20 and 2.4.0 dated 2025-09-12
ssdtools-2.3.0/ssdtools/R/test-helpers.R |only ssdtools-2.3.0/ssdtools/tests/testthat/_snaps/fit/tidy_stable_computable.csv |only ssdtools-2.3.0/ssdtools/tests/testthat/_snaps/hc-root.md |only ssdtools-2.3.0/ssdtools/tests/testthat/_snaps/hc/hc_cis_chloride50.csv |only ssdtools-2.3.0/ssdtools/tests/testthat/_snaps/hc/hc_err_avg.csv |only ssdtools-2.3.0/ssdtools/tests/testthat/_snaps/hc/hc_err_two.csv |only ssdtools-2.3.0/ssdtools/tests/testthat/_snaps/hc/hcici_multi.csv |only ssdtools-2.3.0/ssdtools/tests/testthat/_snaps/hp/hp_err_avg.csv |only ssdtools-2.3.0/ssdtools/tests/testthat/_snaps/hp/hp_err_two.csv |only ssdtools-2.4.0/ssdtools/DESCRIPTION | 31 ssdtools-2.4.0/ssdtools/MD5 | 613 ++--- ssdtools-2.4.0/ssdtools/NAMESPACE | 10 ssdtools-2.4.0/ssdtools/NEWS.md | 47 ssdtools-2.4.0/ssdtools/R/at-boundary.R |only ssdtools-2.4.0/ssdtools/R/bcanz.R | 62 ssdtools-2.4.0/ssdtools/R/boot.R | 11 ssdtools-2.4.0/ssdtools/R/burrrIII3.R | 6 ssdtools-2.4.0/ssdtools/R/censored.R | 1 ssdtools-2.4.0/ssdtools/R/chk.R | 12 ssdtools-2.4.0/ssdtools/R/ci-methods.R |only ssdtools-2.4.0/ssdtools/R/cis.R | 10 ssdtools-2.4.0/ssdtools/R/computable.R |only ssdtools-2.4.0/ssdtools/R/data.R | 12 ssdtools-2.4.0/ssdtools/R/dists.R | 12 ssdtools-2.4.0/ssdtools/R/est-methods.R |only ssdtools-2.4.0/ssdtools/R/estimates.R | 2 ssdtools-2.4.0/ssdtools/R/exposure.R | 14 ssdtools-2.4.0/ssdtools/R/fit-burrlioz.R | 8 ssdtools-2.4.0/ssdtools/R/fit.R | 57 ssdtools-2.4.0/ssdtools/R/gamma.R | 6 ssdtools-2.4.0/ssdtools/R/ggplot.R | 2 ssdtools-2.4.0/ssdtools/R/glance.R | 20 ssdtools-2.4.0/ssdtools/R/gof.R | 55 ssdtools-2.4.0/ssdtools/R/gompertz.R | 10 ssdtools-2.4.0/ssdtools/R/hc-burrlioz.R | 1 ssdtools-2.4.0/ssdtools/R/hc.R | 63 ssdtools-2.4.0/ssdtools/R/hcp-average.R |only ssdtools-2.4.0/ssdtools/R/hcp-ind.R |only ssdtools-2.4.0/ssdtools/R/hcp-ma.R |only ssdtools-2.4.0/ssdtools/R/hcp-multi.R |only ssdtools-2.4.0/ssdtools/R/hcp-samples.R |only ssdtools-2.4.0/ssdtools/R/hcp-tmbfit.R |only ssdtools-2.4.0/ssdtools/R/hcp-weighted.R |only ssdtools-2.4.0/ssdtools/R/hcp.R | 460 --- ssdtools-2.4.0/ssdtools/R/helpers.R | 41 ssdtools-2.4.0/ssdtools/R/hp.R | 77 ssdtools-2.4.0/ssdtools/R/internal.R | 5 ssdtools-2.4.0/ssdtools/R/invpareto.R | 6 ssdtools-2.4.0/ssdtools/R/lgumbel.R | 10 ssdtools-2.4.0/ssdtools/R/licensing.R | 2 ssdtools-2.4.0/ssdtools/R/llogis-llogis.R | 6 ssdtools-2.4.0/ssdtools/R/llogis.R | 6 ssdtools-2.4.0/ssdtools/R/lnorm-lnorm.R | 6 ssdtools-2.4.0/ssdtools/R/lnorm.R | 6 ssdtools-2.4.0/ssdtools/R/match-moments.R | 3 ssdtools-2.4.0/ssdtools/R/multi.R | 7 ssdtools-2.4.0/ssdtools/R/operators.R |only ssdtools-2.4.0/ssdtools/R/params.R | 36 ssdtools-2.4.0/ssdtools/R/plot-cf.R | 1 ssdtools-2.4.0/ssdtools/R/pqr.R | 1 ssdtools-2.4.0/ssdtools/R/predict.R | 13 ssdtools-2.4.0/ssdtools/R/scales.R | 4 ssdtools-2.4.0/ssdtools/R/subset.R | 13 ssdtools-2.4.0/ssdtools/R/sysdata.rda |only ssdtools-2.4.0/ssdtools/R/tidy.R | 2 ssdtools-2.4.0/ssdtools/R/utils.R | 14 ssdtools-2.4.0/ssdtools/R/weibull.R | 6 ssdtools-2.4.0/ssdtools/R/wqg.R | 6 ssdtools-2.4.0/ssdtools/README.md | 45 ssdtools-2.4.0/ssdtools/build/vignette.rds |binary ssdtools-2.4.0/ssdtools/data/boron_pred.rda |binary ssdtools-2.4.0/ssdtools/data/dist_data.rda |binary ssdtools-2.4.0/ssdtools/inst/doc/faqs.Rmd | 1 ssdtools-2.4.0/ssdtools/inst/doc/faqs.html | 10 ssdtools-2.4.0/ssdtools/inst/doc/ssdtools.R | 21 ssdtools-2.4.0/ssdtools/inst/doc/ssdtools.Rmd | 26 ssdtools-2.4.0/ssdtools/inst/doc/ssdtools.html | 139 - ssdtools-2.4.0/ssdtools/man/boron_pred.Rd | 9 ssdtools-2.4.0/ssdtools/man/comma_signif.Rd | 1 ssdtools-2.4.0/ssdtools/man/dgompertz.Rd | 1 ssdtools-2.4.0/ssdtools/man/dist_data.Rd | 5 ssdtools-2.4.0/ssdtools/man/dlgumbel.Rd | 1 ssdtools-2.4.0/ssdtools/man/figures/README-unnamed-chunk-4-1.png |binary ssdtools-2.4.0/ssdtools/man/geom_ssd.Rd | 1 ssdtools-2.4.0/ssdtools/man/glance.fitdists.Rd | 6 ssdtools-2.4.0/ssdtools/man/is_censored.Rd | 1 ssdtools-2.4.0/ssdtools/man/params.Rd | 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ssdtools-2.4.0/ssdtools/man/ssd_hc_bcanz.Rd | 4 ssdtools-2.4.0/ssdtools/man/ssd_hc_burrlioz.Rd | 1 ssdtools-2.4.0/ssdtools/man/ssd_hp.Rd | 50 ssdtools-2.4.0/ssdtools/man/ssd_hp_bcanz.Rd | 13 ssdtools-2.4.0/ssdtools/man/ssd_match_moments.Rd | 3 ssdtools-2.4.0/ssdtools/man/ssd_plot_cf.Rd | 1 ssdtools-2.4.0/ssdtools/man/ssd_r.Rd | 85 ssdtools-2.4.0/ssdtools/man/ssd_wqg_bc.Rd | 1 ssdtools-2.4.0/ssdtools/man/ssd_wqg_burrlioz.Rd | 1 ssdtools-2.4.0/ssdtools/man/ssdtools-package.Rd | 1 ssdtools-2.4.0/ssdtools/man/stat_ssd.Rd | 1 ssdtools-2.4.0/ssdtools/man/subset.fitdists.Rd | 6 ssdtools-2.4.0/ssdtools/src/Makevars | 3 ssdtools-2.4.0/ssdtools/src/Makevars.win | 2 ssdtools-2.4.0/ssdtools/src/TMB/ll_burrIII3.hpp | 4 ssdtools-2.4.0/ssdtools/src/TMB/ll_gamma.hpp | 89 ssdtools-2.4.0/ssdtools/src/TMB/ll_gompertz.hpp | 4 ssdtools-2.4.0/ssdtools/src/TMB/ll_invpareto.hpp | 3 ssdtools-2.4.0/ssdtools/src/TMB/ll_lgumbel.hpp | 8 ssdtools-2.4.0/ssdtools/src/TMB/ll_llogis.hpp | 4 ssdtools-2.4.0/ssdtools/src/TMB/ll_llogis_llogis.hpp | 6 ssdtools-2.4.0/ssdtools/src/TMB/ll_lnorm.hpp | 4 ssdtools-2.4.0/ssdtools/src/TMB/ll_lnorm_lnorm.hpp | 6 ssdtools-2.4.0/ssdtools/src/TMB/ll_weibull.hpp | 89 ssdtools-2.4.0/ssdtools/tests/testthat/_snaps/at-boundary |only ssdtools-2.4.0/ssdtools/tests/testthat/_snaps/bcanz/hc_chloride.csv | 10 ssdtools-2.4.0/ssdtools/tests/testthat/_snaps/bcanz/hp_chloride.csv | 4 ssdtools-2.4.0/ssdtools/tests/testthat/_snaps/bcanz/hp_chloride_proportion.csv |only ssdtools-2.4.0/ssdtools/tests/testthat/_snaps/burrIII3.md |only ssdtools-2.4.0/ssdtools/tests/testthat/_snaps/burrIII3/hc_chloride.csv | 4 ssdtools-2.4.0/ssdtools/tests/testthat/_snaps/burrIII3/hc_uranium.csv | 4 ssdtools-2.4.0/ssdtools/tests/testthat/_snaps/censoring |only ssdtools-2.4.0/ssdtools/tests/testthat/_snaps/ci-methods.md |only ssdtools-2.4.0/ssdtools/tests/testthat/_snaps/data/dist_data.csv | 22 ssdtools-2.4.0/ssdtools/tests/testthat/_snaps/est-methods.md |only 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ssdtools-2.4.0/ssdtools/tests/testthat/test-subset.R | 3 ssdtools-2.4.0/ssdtools/tests/testthat/test-summary.R | 27 ssdtools-2.4.0/ssdtools/tests/testthat/test-utils.R | 16 ssdtools-2.4.0/ssdtools/tests/testthat/test-weibull.R | 30 ssdtools-2.4.0/ssdtools/tests/testthat/test-weighted.R | 6 ssdtools-2.4.0/ssdtools/vignettes/faqs.Rmd | 1 ssdtools-2.4.0/ssdtools/vignettes/ssdtools.Rmd | 26 337 files changed, 4070 insertions(+), 3608 deletions(-)
Title: Tools at the Intersection of 'purrr' and 'dplyr'
Description: Some functions at the intersection of 'dplyr' and
'purrr' that formerly lived in 'purrr'.
Author: Lionel Henry [aut, cre],
Hadley Wickham [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between purrrlyr versions 0.0.8 dated 2022-03-29 and 0.0.10 dated 2025-09-12
DESCRIPTION | 22 ++++++++++---------- MD5 | 18 ++++++++-------- NEWS.md | 10 +++++++++ R/dmap.R | 2 - R/rows.R | 4 +-- README.md | 1 man/by_row.Rd | 4 +-- man/dmap.Rd | 58 ++++++++++++++++++++++++++++++++---------------------- src/fast-copy.cpp | 14 ++++++++----- src/utils.h | 3 ++ 10 files changed, 82 insertions(+), 54 deletions(-)
Title: Miscellaneous Functions for the Analysis of Educational
Assessments
Description: Miscellaneous functions for data cleaning and data analysis of educational assessments. Includes functions for descriptive
analyses, character vector manipulations and weighted statistics. Mainly a lightweight dependency for the packages 'eatRep',
'eatGADS', 'eatPrep' and 'eatModel' (which will be subsequently submitted to 'CRAN').
The function for defining (weighted) contrasts in weighted effect coding refers to
te Grotenhuis et al. (2017) <doi:10.1007/s00038-016-0901-1>.
Functions for weighted statistics refer to
Wolter (2007) <doi:10.1007/978-0-387-35099-8>.
Author: Sebastian Weirich [aut, cre],
Martin Hecht [aut],
Karoline Sachse [aut],
Benjamin Becker [aut],
Nicole Mahler [aut],
Edna Grewers [ctb]
Maintainer: Sebastian Weirich <sebastian.weirich@iqb.hu-berlin.de>
Diff between eatTools versions 0.7.8 dated 2024-12-18 and 0.7.9 dated 2025-09-12
DESCRIPTION | 10 ++-- MD5 | 24 ++++++----- NAMESPACE | 1 NEWS.md | 6 ++ R/cleanifyString.r | 4 - R/existsBackgroundVariables.r | 25 +++++++++++ R/mergeAttr.r | 54 +++++++++++++++---------- data |only inst |only man/checkBackgroundVariables.Rd |only man/data.timss1.rd |only man/existsBackgroundVariables.Rd | 3 - tests/testthat/helper_badString.rds |only tests/testthat/test_checkBackgroundVariables.R |only tests/testthat/test_cleanifyString.R | 11 +++++ tests/testthat/test_mergeAttr.R | 28 ++++++------ 16 files changed, 113 insertions(+), 53 deletions(-)
Title: China Map Data from AutoNavi Map
Description: According to the code or the name of the administrative division at the county level and above provided by the Ministry of Civil Affairs of the People's Republic of China in 2022, get the map file online from the website of AutoNavi Map (<http://datav.aliyun.com/portal/school/atlas/area_selector>).
Author: Panfeng Zhang [aut, cre]
Maintainer: Panfeng Zhang <zhangpf08@163.com>
Diff between cnmap versions 0.1.0 dated 2024-04-02 and 0.1.1 dated 2025-09-12
DESCRIPTION | 19 - MD5 | 21 - NEWS.md |only R/data.R | 2 R/getMap.R | 6 build/vignette.rds |binary data/ad.rda |binary inst/doc/Introduction.R | 20 - inst/doc/Introduction.Rmd | 27 - inst/doc/Introduction.html | 644 +++++++++++++++++++++------------------------ man/getMap.Rd | 104 +++---- vignettes/Introduction.Rmd | 27 - 12 files changed, 413 insertions(+), 457 deletions(-)
Title: Decorate a 'ggplot' with Associated Information
Description: For many times, we are not just aligning plots as what 'cowplot' and 'patchwork' did. Users would like to align associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. Inspired by the 'Method 2' in 'ggtree' (G Yu (2018) <doi:10.1093/molbev/msy194>), 'aplot' provides utilities to aligns associated subplots to a main plot at different sides (left, right, top and bottom) with axes exactly matched.
Author: Guangchuang Yu [aut, cre] ,
Shuangbin Xu [ctb] ,
Thomas Hackl [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between aplot versions 0.2.8 dated 2025-07-02 and 0.2.9 dated 2025-09-12
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/aplot.R | 2 +- R/utilities.R | 2 +- build/partial.rdb |binary 6 files changed, 15 insertions(+), 10 deletions(-)