Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is
the core database application for biobanks. Participant data, once
collected from any data source, must be integrated and stored in a central
data repository under a uniform model. 'Opal' is such a central repository.
It can import, process, validate, query, analyze, report, and export data.
'Opal' is typically used in a research center to analyze the data acquired at
assessment centres. Its ultimate purpose is to achieve seamless
data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal'
web services and to perform operations on the R server side. 'DataSHIELD'
administration tools are also provided.
Author: Yannick Marcon [aut, cre] ,
Amadou Gaye [ctb] ,
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between opalr versions 3.5.1 dated 2025-11-16 and 3.5.2 dated 2025-12-09
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/opal.file.R | 8 +++++--- R/opal.sql.R | 1 + build/vignette.rds |binary inst/doc/datashield-admin.html | 4 ++-- inst/doc/opal-files.html | 4 ++-- inst/doc/opal-projects.html | 4 ++-- inst/doc/opal-rsession.html | 4 ++-- 9 files changed, 25 insertions(+), 22 deletions(-)
Title: Meta-Analytic Effect Size Calculation for Pre-Post Designs with
Correlation Imputation
Description: Tools for the calculation of effect sizes (standardised mean difference) and mean difference in pre-post controlled studies, including robust imputation of missing variances (standard deviation of changes) and correlations (Pearson correlation coefficient). The main function 'metacor_dual()' implements several methods for imputing missing standard deviation of changes or Pearson correlation coefficient, and generates transparent imputation reports. Designed for meta-analyses with incomplete summary statistics. For details on the methods, see Higgins et al. (2023) and Fu et al. (2013).
Author: Iker J. Bautista [aut, cre],
Saul M. Rodriguez [ctb]
Maintainer: Iker J. Bautista <ikerugr@gmail.com>
Diff between metacor versions 1.2.0 dated 2025-09-26 and 1.2.1 dated 2025-12-09
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NAMESPACE | 1 + R/check_metacor_consistency.R |only inst/doc/introduccion.html | 16 ++++++++-------- man/check_metacor_consistency.Rd |only 6 files changed, 17 insertions(+), 14 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.7.0 dated 2025-10-31 and 0.7.1 dated 2025-12-09
DESCRIPTION | 8 +-- MD5 | 22 ++++---- NEWS.md | 6 ++ R/MaestroPipeline.R | 27 ++++++---- R/MaestroPipelineList.R | 41 ++++++++++++++++ build/vignette.rds |binary inst/doc/maestro-1-quick-start.html | 8 +-- inst/doc/maestro-3-advanced-scheduling.html | 12 ++-- inst/doc/maestro-4-directed-acyclic-graphs.html | 20 ++++---- inst/doc/maestro-5-logging.html | 60 ++++++++++++------------ inst/doc/maestro-8-conditionals.html | 42 ++++++++-------- man/MaestroPipelineList.Rd | 21 ++++++++ 12 files changed, 171 insertions(+), 96 deletions(-)
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with
details from statistical tests included in the plots themselves. It
provides an easier syntax to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports the most common types of
statistical approaches and tests: parametric, nonparametric, robust,
and Bayesian versions of t-test/ANOVA, correlation analyses,
contingency table analysis, meta-analysis, and regression analyses.
References: Patil (2021) <doi:10.21105/joss.03236>.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 0.13.3 dated 2025-10-05 and 0.13.4 dated 2025-12-09
DESCRIPTION | 47 +++++++++++++-------------------- MD5 | 34 +++++++++++------------ NEWS.md | 14 +++++++-- R/ggbarstats.R | 11 ++++--- R/ggbetweenstats.R | 3 +- R/ggcoefstats.R | 18 +++++++----- R/ggdotplotstats.R | 11 ++++--- R/ggpiestats.R | 7 ++++ R/ggwithinstats.R | 3 +- README.md | 2 - man/ggstatsplot-package.Rd | 5 --- man/grouped_ggbarstats.Rd | 11 ++++--- man/grouped_ggbetweenstats.Rd | 3 +- man/grouped_ggdotplotstats.Rd | 11 ++++--- man/grouped_ggpiestats.Rd | 7 ++++ man/grouped_ggwithinstats.Rd | 3 +- tests/testthat/_snaps/extract-stats.md | 11 +++++++ tests/testthat/test-extract-stats.R | 1 18 files changed, 115 insertions(+), 87 deletions(-)
More information about AdaptiveBoxplot at CRAN
Permanent link
Title: Metrics of R Packages
Description: Static code analyses for R packages using the external code-tagging
libraries 'ctags' and 'gtags'. Static analyses enable packages to be
analysed very quickly, generally a couple of seconds at most. The package
also provides access to a database generating by applying the main function
to the full 'CRAN' archive, enabling the statistical properties of any package
to be compared with all other 'CRAN' packages.
Author: Mark Padgham [aut, cre] ,
Michael Sumner [ctb] ,
Jeffrey Hollister [ctb] ,
Egor Kotov [ctb]
Maintainer: Mark Padgham <mark.padgham@email.com>
This is a re-admission after prior archival of version 0.1.1 dated 2022-06-21
Diff between pkgstats versions 0.1.1 dated 2022-06-21 and 0.2.1 dated 2025-12-09
pkgstats-0.1.1/pkgstats/R/archive-trawl.R |only pkgstats-0.1.1/pkgstats/R/extract_tarball.R |only pkgstats-0.1.1/pkgstats/R/pkgstats.R |only pkgstats-0.1.1/pkgstats/configure |only pkgstats-0.1.1/pkgstats/inst/CITATION |only pkgstats-0.1.1/pkgstats/src/Makevars.win |only pkgstats-0.1.1/pkgstats/tools |only pkgstats-0.1.1/pkgstats/vignettes/installation.md |only pkgstats-0.1.1/pkgstats/vignettes/pkgstats.md |only pkgstats-0.2.1/pkgstats/DESCRIPTION | 41 +- pkgstats-0.2.1/pkgstats/MD5 | 125 ++++---- pkgstats-0.2.1/pkgstats/NAMESPACE | 4 pkgstats-0.2.1/pkgstats/NEWS.md |only pkgstats-0.2.1/pkgstats/R/cran-data-archive.R |only pkgstats-0.2.1/pkgstats/R/cran-data-current.R |only pkgstats-0.2.1/pkgstats/R/cran-data-fn-names.R |only pkgstats-0.2.1/pkgstats/R/cran-data-update.R |only pkgstats-0.2.1/pkgstats/R/ctags-install.R | 104 +++++-- pkgstats-0.2.1/pkgstats/R/ctags-test.R | 73 +++-- pkgstats-0.2.1/pkgstats/R/desc-stats.R | 22 + pkgstats-0.2.1/pkgstats/R/external-calls.R | 44 +-- pkgstats-0.2.1/pkgstats/R/extra-stats.R | 51 +-- pkgstats-0.2.1/pkgstats/R/extract-tarball.R |only pkgstats-0.2.1/pkgstats/R/function-names.R | 68 ++-- pkgstats-0.2.1/pkgstats/R/gtags-install.R | 13 pkgstats-0.2.1/pkgstats/R/loc.R | 14 pkgstats-0.2.1/pkgstats/R/onload.R | 18 - pkgstats-0.2.1/pkgstats/R/pkgstats-data-download.R | 6 pkgstats-0.2.1/pkgstats/R/pkgstats-function.R |only pkgstats-0.2.1/pkgstats/R/pkgstats-package.R | 1 pkgstats-0.2.1/pkgstats/R/pkgstats-summary.R | 34 +- pkgstats-0.2.1/pkgstats/R/plot.R | 32 -- pkgstats-0.2.1/pkgstats/R/rd-stats.R | 42 ++ pkgstats-0.2.1/pkgstats/R/roxygen-blocks.R |only pkgstats-0.2.1/pkgstats/R/tag-data-call-graph.R | 9 pkgstats-0.2.1/pkgstats/R/tag-data-ctags.R | 43 +-- pkgstats-0.2.1/pkgstats/R/tag-data-gtags.R | 38 +- pkgstats-0.2.1/pkgstats/R/tag-data.R | 61 ++-- pkgstats-0.2.1/pkgstats/R/utils.R | 62 +++- pkgstats-0.2.1/pkgstats/R/zzz.R |only pkgstats-0.2.1/pkgstats/README.md |only pkgstats-0.2.1/pkgstats/build/vignette.rds |binary pkgstats-0.2.1/pkgstats/inst/doc/installation.R | 20 - pkgstats-0.2.1/pkgstats/inst/doc/installation.Rmd | 18 - pkgstats-0.2.1/pkgstats/inst/doc/installation.html | 143 +++++----- pkgstats-0.2.1/pkgstats/inst/doc/pkgstats.R | 10 pkgstats-0.2.1/pkgstats/inst/doc/pkgstats.Rmd | 6 pkgstats-0.2.1/pkgstats/inst/doc/pkgstats.html | 131 ++++----- pkgstats-0.2.1/pkgstats/man/ctags_install.Rd | 6 pkgstats-0.2.1/pkgstats/man/ctags_test.Rd | 15 - pkgstats-0.2.1/pkgstats/man/desc_stats.Rd | 2 pkgstats-0.2.1/pkgstats/man/dl_pkgstats_data.Rd | 5 pkgstats-0.2.1/pkgstats/man/extract_tarball.Rd | 2 pkgstats-0.2.1/pkgstats/man/loc_stats.Rd | 2 pkgstats-0.2.1/pkgstats/man/pkgstats-package.Rd | 10 pkgstats-0.2.1/pkgstats/man/pkgstats.Rd | 32 +- pkgstats-0.2.1/pkgstats/man/pkgstats_cran_current_from_full.Rd |only pkgstats-0.2.1/pkgstats/man/pkgstats_fns_from_archive.Rd | 16 - pkgstats-0.2.1/pkgstats/man/pkgstats_fns_update.Rd |only pkgstats-0.2.1/pkgstats/man/pkgstats_from_archive.Rd | 23 - pkgstats-0.2.1/pkgstats/man/pkgstats_summary.Rd | 4 pkgstats-0.2.1/pkgstats/man/pkgstats_update.Rd |only pkgstats-0.2.1/pkgstats/man/plot_network.Rd | 2 pkgstats-0.2.1/pkgstats/man/rd_stats.Rd | 4 pkgstats-0.2.1/pkgstats/man/tags_data.Rd | 4 pkgstats-0.2.1/pkgstats/tests/testthat/helper-archive-trawl.R |only pkgstats-0.2.1/pkgstats/tests/testthat/test-archive-trawl.R | 104 +++++-- pkgstats-0.2.1/pkgstats/tests/testthat/test-cran-update.R |only pkgstats-0.2.1/pkgstats/tests/testthat/test-ctags.R | 5 pkgstats-0.2.1/pkgstats/tests/testthat/test-desc-stats.R | 7 pkgstats-0.2.1/pkgstats/tests/testthat/test-fn-names.R |only pkgstats-0.2.1/pkgstats/tests/testthat/test-pkgstats.R | 40 ++ pkgstats-0.2.1/pkgstats/tests/testthat/test-plot-network.R | 9 pkgstats-0.2.1/pkgstats/tests/testthat/test-summary.R | 7 pkgstats-0.2.1/pkgstats/vignettes/installation.Rmd | 18 - pkgstats-0.2.1/pkgstats/vignettes/pkgstats.Rmd | 6 76 files changed, 948 insertions(+), 608 deletions(-)
Title: Mixed Models for Repeated Measures
Description: Mixed models for repeated measures (MMRM) are a popular
choice for analyzing longitudinal continuous outcomes in randomized
clinical trials and beyond; see Cnaan, Laird and Slasor (1997)
<doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E>
for a tutorial and Mallinckrodt, Lane, Schnell, Peng and Mancuso
(2008) <doi:10.1177/009286150804200402> for a review. This package
implements MMRM based on the marginal linear model without random
effects using Template Model Builder ('TMB') which enables fast and
robust model fitting. Users can specify a variety of covariance
matrices, weight observations, fit models with restricted or standard
maximum likelihood inference, perform hypothesis testing with
Satterthwaite or Kenward-Roger adjustment, and extract least square
means estimates by using 'emmeans'.
Author: Daniel Sabanes Bove [aut, cre] ,
Liming Li [aut] ,
Julia Dedic [aut],
Doug Kelkhoff [aut],
Kevin Kunzmann [aut],
Brian Matthew Lang [aut],
Christian Stock [aut],
Ya Wang [aut],
Craig Gower-Page [ctb],
Dan James [aut],
Jonathan Sidi [aut],
Daniel Leib [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between mmrm versions 0.3.15 dated 2025-06-10 and 0.3.16 dated 2025-12-09
mmrm-0.3.15/mmrm/man/h_first_contain_categorical.Rd |only mmrm-0.3.15/mmrm/man/h_get_contrast.Rd |only mmrm-0.3.15/mmrm/tests/testthat/_snaps/car.md |only mmrm-0.3.15/mmrm/tests/testthat/test-car.R |only mmrm-0.3.16/mmrm/DESCRIPTION | 24 mmrm-0.3.16/mmrm/MD5 | 160 - mmrm-0.3.16/mmrm/NAMESPACE | 1 mmrm-0.3.16/mmrm/NEWS.md | 21 mmrm-0.3.16/mmrm/R/between-within.R | 12 mmrm-0.3.16/mmrm/R/component.R | 115 - mmrm-0.3.16/mmrm/R/cov_struct.R | 24 mmrm-0.3.16/mmrm/R/fit.R | 84 mmrm-0.3.16/mmrm/R/interop-car.R | 345 ++- mmrm-0.3.16/mmrm/R/interop-emmeans.R | 42 mmrm-0.3.16/mmrm/R/kenwardroger.R | 48 mmrm-0.3.16/mmrm/R/mmrm-methods.R | 335 ++- mmrm-0.3.16/mmrm/R/residual.R | 7 mmrm-0.3.16/mmrm/R/satterthwaite.R | 3 mmrm-0.3.16/mmrm/R/testing.R | 118 - mmrm-0.3.16/mmrm/R/tidiers.R | 45 mmrm-0.3.16/mmrm/R/tmb-methods.R | 333 ++- mmrm-0.3.16/mmrm/R/tmb.R | 299 +- mmrm-0.3.16/mmrm/R/utils-formula.R | 10 mmrm-0.3.16/mmrm/R/utils-nse.R | 9 mmrm-0.3.16/mmrm/R/utils.R | 692 ++++++ mmrm-0.3.16/mmrm/R/zzz.R | 40 mmrm-0.3.16/mmrm/build/partial.rdb |binary mmrm-0.3.16/mmrm/build/vignette.rds |binary mmrm-0.3.16/mmrm/inst/WORDLIST | 13 mmrm-0.3.16/mmrm/inst/doc/covariance.Rmd | 20 mmrm-0.3.16/mmrm/inst/doc/covariance.html | 23 mmrm-0.3.16/mmrm/inst/doc/hypothesis_testing.Rmd | 94 mmrm-0.3.16/mmrm/inst/doc/hypothesis_testing.html | 166 - mmrm-0.3.16/mmrm/inst/doc/introduction.R | 2 mmrm-0.3.16/mmrm/inst/doc/introduction.html | 200 + mmrm-0.3.16/mmrm/inst/doc/mmrm_review_methods.html | 74 mmrm-0.3.16/mmrm/man/Anova.mmrm.Rd | 22 mmrm-0.3.16/mmrm/man/component.Rd | 5 mmrm-0.3.16/mmrm/man/df_md.Rd | 2 mmrm-0.3.16/mmrm/man/emp_start.Rd | 21 mmrm-0.3.16/mmrm/man/h_anova_single_mmrm_model.Rd |only mmrm-0.3.16/mmrm/man/h_assert_lrt_suitability.Rd |only mmrm-0.3.16/mmrm/man/h_assert_nested_models.Rd |only mmrm-0.3.16/mmrm/man/h_check_columns_nested.Rd |only mmrm-0.3.16/mmrm/man/h_check_cov_struct_nesting.Rd |only mmrm-0.3.16/mmrm/man/h_check_covar_nesting.Rd |only mmrm-0.3.16/mmrm/man/h_check_fits_all_data_same.Rd |only mmrm-0.3.16/mmrm/man/h_construct_model_frame_inputs.Rd | 13 mmrm-0.3.16/mmrm/man/h_contr_sum_type3_contrasts.Rd |only mmrm-0.3.16/mmrm/man/h_dataset_sort_all.Rd |only mmrm-0.3.16/mmrm/man/h_first_term_containing_categ.Rd |only mmrm-0.3.16/mmrm/man/h_fits_common_data.Rd |only mmrm-0.3.16/mmrm/man/h_generate_new_name.Rd |only mmrm-0.3.16/mmrm/man/h_get_minimal_fit_data.Rd |only mmrm-0.3.16/mmrm/man/h_mmrm_tmb_fit.Rd | 12 mmrm-0.3.16/mmrm/man/h_mmrm_tmb_formula_parts.Rd | 1 mmrm-0.3.16/mmrm/man/h_refit_mmrm.Rd |only mmrm-0.3.16/mmrm/man/h_test_md.Rd | 21 mmrm-0.3.16/mmrm/man/h_type2_contrast.Rd |only mmrm-0.3.16/mmrm/man/h_type3_contrasts.Rd |only mmrm-0.3.16/mmrm/man/mmrm_control.Rd | 14 mmrm-0.3.16/mmrm/man/mmrm_tmb_methods.Rd | 41 mmrm-0.3.16/mmrm/man/stats_anova.Rd |only mmrm-0.3.16/mmrm/src/covariance.h | 11 mmrm-0.3.16/mmrm/src/test-covariance.cpp | 68 mmrm-0.3.16/mmrm/src/utils.h | 7 mmrm-0.3.16/mmrm/tests/additional.R |only mmrm-0.3.16/mmrm/tests/testthat/_snaps/interop-car.md |only mmrm-0.3.16/mmrm/tests/testthat/_snaps/kenwardroger.md | 416 +-- mmrm-0.3.16/mmrm/tests/testthat/_snaps/testing.md | 4 mmrm-0.3.16/mmrm/tests/testthat/_snaps/tmb-methods.md | 838 +++---- mmrm-0.3.16/mmrm/tests/testthat/helper-examples.R | 148 + mmrm-0.3.16/mmrm/tests/testthat/test-between-within.R | 31 mmrm-0.3.16/mmrm/tests/testthat/test-component.R | 100 mmrm-0.3.16/mmrm/tests/testthat/test-cov-struct.R | 4 mmrm-0.3.16/mmrm/tests/testthat/test-cpp-covariance.R | 206 + mmrm-0.3.16/mmrm/tests/testthat/test-cpp-utils.R | 92 mmrm-0.3.16/mmrm/tests/testthat/test-emmeans.R | 149 + mmrm-0.3.16/mmrm/tests/testthat/test-empirical.R | 250 +- mmrm-0.3.16/mmrm/tests/testthat/test-fit.R | 108 - mmrm-0.3.16/mmrm/tests/testthat/test-interop-car.R |only mmrm-0.3.16/mmrm/tests/testthat/test-interop-parsnip.R | 25 mmrm-0.3.16/mmrm/tests/testthat/test-interop.R | 16 mmrm-0.3.16/mmrm/tests/testthat/test-kenwardroger.R | 241 +- mmrm-0.3.16/mmrm/tests/testthat/test-mmrm-methods.R | 427 +++ mmrm-0.3.16/mmrm/tests/testthat/test-testing.R | 20 mmrm-0.3.16/mmrm/tests/testthat/test-tidiers.R | 27 mmrm-0.3.16/mmrm/tests/testthat/test-tmb-methods.R | 616 ++++- mmrm-0.3.16/mmrm/tests/testthat/test-tmb.R | 1073 ++++++++-- mmrm-0.3.16/mmrm/tests/testthat/test-utils.R | 58 mmrm-0.3.16/mmrm/vignettes/covariance.Rmd | 20 mmrm-0.3.16/mmrm/vignettes/hypothesis_testing.Rmd | 94 mmrm-0.3.16/mmrm/vignettes/subsections/_intro-hypothesis_testing.Rmd | 33 93 files changed, 6452 insertions(+), 2141 deletions(-)
Title: Robust Methods for High-Dimensional Data
Description: Robust methods for high-dimensional data, in particular linear
model selection techniques based on least angle regression and sparse
regression. Specifically, the package implements robust least angle
regression (Khan, Van Aelst & Zamar, 2007; <doi:10.1198/016214507000000950>),
(robust) groupwise least angle regression (Alfons, Croux & Gelper, 2016;
<doi:10.1016/j.csda.2015.02.007>), and sparse least trimmed squares
regression (Alfons, Croux & Gelper, 2013; <doi:10.1214/12-AOAS575>).
Author: Andreas Alfons [aut, cre] ,
Dirk Eddelbuettel [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robustHD versions 0.8.2 dated 2025-10-02 and 0.8.3 dated 2025-12-09
DESCRIPTION | 11 MD5 | 56 +- NAMESPACE | 1 NEWS | 488 ++++++++++---------- R/TopGear.R | 160 +++--- R/coef.R | 254 +++++----- R/corHuber.R | 280 +++++------ R/fitted.R | 204 ++++---- R/grouplars.R | 652 +++++++++++++-------------- R/grplars.R | 752 +++++++++++++++---------------- R/lambda0.R | 228 ++++----- R/plot.R | 32 - R/predict.R | 470 +++++++++---------- R/residuals.R | 262 +++++----- R/rlars.R | 704 ++++++++++++++--------------- R/rstandard.R | 334 ++++++------- R/setupCritPlot.R | 5 R/setupDiagnosticPlot.R | 952 +++++++++++++++++++-------------------- R/sparseLTS.R | 1106 +++++++++++++++++++++++----------------------- R/tslars.R | 644 +++++++++++++------------- R/tslarsP.R | 610 ++++++++++++------------- R/winsorize.R | 386 ++++++++-------- build/partial.rdb |binary data/datalist | 4 inst/CITATION | 22 man/TopGear.Rd | 158 +++--- man/rstandard.seqModel.Rd | 226 ++++----- src/corHuber.cpp | 1 src/fastRlars.cpp | 1 29 files changed, 4508 insertions(+), 4495 deletions(-)
Title: Comparing and Visualizing Differences Between Surveys
Description: Easily analyze and visualize differences between samples (e.g., benchmark comparisons, nonresponse comparisons in surveys) on three levels. The comparisons can be univariate, bivariate or multivariate. On univariate level the variables of interest of a survey and a comparison survey (i.e. benchmark) are compared, by calculating one of several difference measures (e.g., relative difference in mean), and an average difference between the surveys. On bivariate level a function can calculate significant differences in correlations for the surveys. And on multivariate levels a function can calculate significant differences in model coefficients between the surveys of comparison. All of those differences can be easily plotted and outputted as a table. For more detailed information on the methods and example use see Rohr, B., Silber, H., & Felderer, B. (2024). Comparing the Accuracy of Univariate, Bivariate, and Multivariate Estimates across Probability and Nonprobability Surveys with Po [...truncated...]
Author: Bjoern Rohr [aut, cre, cph],
Barbara Felderer [aut]
Maintainer: Bjoern Rohr <bjoern.rohr@gesis.org>
Diff between sampcompR versions 0.3.1.2 dated 2025-07-04 and 0.3.2 dated 2025-12-09
sampcompR-0.3.1.2/sampcompR/data/card.RData |only sampcompR-0.3.2/sampcompR/DESCRIPTION | 6 sampcompR-0.3.2/sampcompR/MD5 | 44 +-- sampcompR-0.3.2/sampcompR/NAMESPACE | 1 sampcompR-0.3.2/sampcompR/NEWS.md | 4 sampcompR-0.3.2/sampcompR/R/Bivdiff.R | 7 sampcompR-0.3.2/sampcompR/R/Bivdiff_Plot.R | 4 sampcompR-0.3.2/sampcompR/R/Output_Tables.R | 35 +- sampcompR-0.3.2/sampcompR/R/Unidiff_Plot.R | 129 +++++++++- sampcompR-0.3.2/sampcompR/R/card.R | 12 sampcompR-0.3.2/sampcompR/data/card.rda |only sampcompR-0.3.2/sampcompR/man/R_indicator.Rd | 15 + sampcompR-0.3.2/sampcompR/man/biv_bias_per_variable.Rd | 3 sampcompR-0.3.2/sampcompR/man/biv_compare.Rd | 3 sampcompR-0.3.2/sampcompR/man/biv_compare_table.Rd | 3 sampcompR-0.3.2/sampcompR/man/biv_per_variable.Rd | 3 sampcompR-0.3.2/sampcompR/man/card.Rd | 2 sampcompR-0.3.2/sampcompR/man/heatmap_biv_compare.Rd | 2 sampcompR-0.3.2/sampcompR/man/plot_biv_compare.Rd | 2 sampcompR-0.3.2/sampcompR/man/plot_uni_compare.Rd | 5 sampcompR-0.3.2/sampcompR/tests/testthat/helper_biv_compare.R | 55 ++-- sampcompR-0.3.2/sampcompR/tests/testthat/helper_uni_compare.R | 46 +-- sampcompR-0.3.2/sampcompR/tests/testthat/test-biv_compare_table.R | 28 +- sampcompR-0.3.2/sampcompR/tests/testthat/test-uni_compare_table.R | 14 - 24 files changed, 289 insertions(+), 134 deletions(-)
Title: Temporal Trends in Ecological Niche Models
Description: Computes temporal trends in environmental suitability obtained from ecological niche models, based on a set of species presence point coordinates and predictor variables.
Author: A. Marcia Barbosa [aut, cre],
Joao Alirio [aut],
Nuno Garcia [aut],
Joao Campos [aut],
Ana Claudia Teodoro [aut],
Lia Barbara Duarte [aut],
Isabel Pocas [aut],
Salvador Arenas-Castro [aut],
Neftali Sillero [aut]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between ecotrends versions 1.1 dated 2025-07-07 and 1.2 dated 2025-12-09
ecotrends |only 1 file changed
Title: Estimate the Four Parameters of Stable Laws using Different
Methods
Description: Estimate the four parameters of stable laws using maximum
likelihood method, generalised method of moments with
finite and continuum number of points, iterative
Koutrouvelis regression and Kogon-McCulloch method. The
asymptotic properties of the estimators (covariance
matrix, confidence intervals) are also provided.
Author: Tarak Kharrat [aut] ,
Georgi N. Boshnakov [aut, cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between StableEstim versions 2.3 dated 2024-10-24 and 2.4 dated 2025-12-09
DESCRIPTION | 26 MD5 | 28 NAMESPACE | 12 NEWS.md | 16 R/GMMParamsEstim.R | 40 R/InitialGuess.R | 2 R/OutputFileManip.R | 12 R/ToolsFct.R | 15 R/WeightingMatrix.R | 2 README.md | 3 build/partial.rdb |binary inst/REFERENCES.bib | 2114 ++++++++++++++++++++-------------------- man/GMMParametersEstim.Rd | 11 man/McCullochParametersEstim.Rd | 5 man/expect_almost_equal.Rd | 3 15 files changed, 1159 insertions(+), 1130 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 5.0.0 dated 2025-11-28 and 5.0.1 dated 2025-12-09
DESCRIPTION | 6 MD5 | 101 +++-- NAMESPACE | 4 NEWS.md | 18 + R/RcppExports.R | 16 R/dfIni.R | 6 R/rxRaw.R |only R/rxode-options.R | 4 R/rxode2.R | 12 R/rxode2_md5.R | 2 R/rxrandom.R | 24 + R/utils.R | 2 data/rxReservedKeywords.rda |binary data/rxResidualError.rda |binary data/rxSyntaxFunctions.rda |binary inst/doc/rxode2-syntax.html | 26 - inst/include/rxode2.h | 4 inst/include/rxode2_model_shared.c | 50 +- inst/include/rxode2_model_shared.h | 92 ++--- inst/include/rxode2parseVer.h | 4 man/rxDeserialize.Rd |only man/rxGetSerialType_.Rd |only man/rxNumLoaded.Rd |only man/rxRawToC.Rd |only man/rxSerialize.Rd |only man/rxUnloadAll.Rd | 2 man/rxbeta.Rd | 2 man/rxbinom.Rd | 1 man/rxcauchy.Rd | 1 man/rxchisq.Rd | 2 man/rxexp.Rd | 2 man/rxf.Rd | 1 man/rxgamma.Rd | 2 man/rxgeom.Rd | 2 man/rxnbinom.Rd | 4 man/rxpois.Rd | 2 man/rxt.Rd | 1 man/rxunif.Rd | 2 man/rxweibull.Rd | 2 src/RcppExports.cpp | 19 - src/approx.cpp | 2 src/codegen.c | 27 - src/codegen.h | 38 -- src/codegen2.h | 30 - src/dlsoda.f | 7 src/init.c | 9 src/par_solve.cpp | 9 src/parseFunsRandom.h | 75 ++-- src/qs.cpp | 83 ++++ src/rxData.cpp | 7 src/rxthreefry.cpp | 660 +++++++++++++++++++++---------------- src/rxthreefry.h | 69 +-- tests/testthat.R | 8 tests/testthat/test-random.R | 28 + tests/testthat/test-raw.R |only 55 files changed, 884 insertions(+), 584 deletions(-)
Title: Version-Control for CRAN, GitHub, and GitLab Packages
Description: Make R scripts reproducible, by ensuring that
every time a given script is run, the same version of the used packages are
loaded (instead of whichever version the user running the script happens to
have installed). This is achieved by using the command
groundhog.library() instead of the base command library(), and including a
date in the call. The date is used to call on the same version of the
package every time (the most recent version available at that date).
Load packages from CRAN, GitHub, or Gitlab.
Author: Uri Simonsohn [aut, cre] ,
Hugo Gruson [ctb, aut]
Maintainer: Uri Simonsohn <urisohn@gmail.com>
Diff between groundhog versions 3.2.3 dated 2025-05-12 and 3.3.0 dated 2025-12-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/get.dependencies.R | 2 -- R/get.snowball.R | 12 +++++++++++- R/groundhog.library.R | 26 ++++++++++++++++++++++++++ R/update_cran.toc_if.needed.R | 29 +++++++++++++++++++++++++++-- R/zzz.R | 2 +- 7 files changed, 75 insertions(+), 16 deletions(-)
Title: Building and Managing Local Databases from 'Google Earth Engine'
Description: Simplifies the creation, management, and updating of local databases using data extracted from 'Google Earth Engine' ('GEE'). It integrates with 'GEE' to store, aggregate, and process spatio-temporal data, leveraging 'SQLite' for efficient, serverless storage. The 'geeLite' package provides utilities for data transformation and supports real-time monitoring and analysis of geospatial features, making it suitable for researchers and practitioners in geospatial science. For details, see Kurbucz and Andrée (2025) "Building and Managing Local Databases from Google Earth Engine with the geeLite R Package" <https://hdl.handle.net/10986/43165>.
Author: Marcell T. Kurbucz [aut, cre],
Bo Pieter Johannes Andree [aut]
Maintainer: Marcell T. Kurbucz <m.kurbucz@ucl.ac.uk>
Diff between geeLite versions 1.0.4 dated 2025-12-01 and 1.0.5 dated 2025-12-09
DESCRIPTION | 12 MD5 | 35 NAMESPACE | 3 R/access_db.R | 1540 +++++++++++++++++++++--------------------- R/gee_install.R | 16 R/run_geelite.R | 416 +++++++---- R/set_config.R | 192 ++--- R/utils.R | 51 - README.md | 352 ++++----- man/check_rgee_ready.Rd | 21 man/drive_auth_ready.Rd |only man/ensure_sessioninfo.Rd |only man/gee_install.Rd | 6 man/read_db.Rd | 7 man/set_config.Rd | 4 man/set_depend.Rd | 12 man/update_grid_stats.Rd | 2 tests/testthat.R | 35 tests/testthat/setup.R |only tests/testthat/test-geelite.R | 264 +++---- 20 files changed, 1563 insertions(+), 1405 deletions(-)
Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly
web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>,
<https://www.euroleaguebasketball.net/eurocup/> and <https://www.acb.com/>, following the instructions
of their respectives robots.txt files, when available. Box score data are available for the three leagues.
Play-by-play and spatial shooting data are also available for the Spanish league. Methods for analysis include a
population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats,
team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games,
maps of nationalities, combinations of lineups, possessions-related variables, timeouts,
performance by periods, personal fouls, offensive rebounds and different types of shooting charts.
Please see Vinue [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between BAwiR versions 1.4.2 dated 2025-11-20 and 1.4.3 dated 2025-12-09
BAwiR-1.4.2/BAwiR/R/get_barplot_monthly_stats.R |only BAwiR-1.4.2/BAwiR/man/get_barplot_monthly_stats.Rd |only BAwiR-1.4.3/BAwiR/DESCRIPTION | 8 - BAwiR-1.4.3/BAwiR/MD5 | 34 ++--- BAwiR-1.4.3/BAwiR/NAMESPACE | 2 BAwiR-1.4.3/BAwiR/NEWS | 7 + BAwiR-1.4.3/BAwiR/R/do_possession.R | 107 ++++++++++++++++- BAwiR-1.4.3/BAwiR/R/do_usage.R | 132 +++++++++++---------- BAwiR-1.4.3/BAwiR/R/get_donut_usage_action.R | 7 - BAwiR-1.4.3/BAwiR/R/get_plot_monthly_stats.R |only BAwiR-1.4.3/BAwiR/R/get_sticker.R | 101 +++++++++------- BAwiR-1.4.3/BAwiR/inst/doc/BAwiR.R | 3 BAwiR-1.4.3/BAwiR/inst/doc/BAwiR.Rmd | 3 BAwiR-1.4.3/BAwiR/inst/doc/BAwiR.html | 9 - BAwiR-1.4.3/BAwiR/inst/doc/BAwiR_pbp.html | 4 BAwiR-1.4.3/BAwiR/inst/doc/BAwiR_sc.html | 4 BAwiR-1.4.3/BAwiR/man/get_donut_usage_action.Rd | 4 BAwiR-1.4.3/BAwiR/man/get_plot_monthly_stats.Rd |only BAwiR-1.4.3/BAwiR/man/get_sticker.Rd | 39 +++--- BAwiR-1.4.3/BAwiR/vignettes/BAwiR.Rmd | 3 20 files changed, 312 insertions(+), 155 deletions(-)
Title: A Bootstrap-Based Power Estimation Tool for Spatial
Transcriptomics
Description: Power estimation and sample size calculation for 10X Visium Spatial Transcriptomics data to detect differential expressed genes between two conditions based on bootstrap resampling. See Shui et al. (2025) <doi:10.1371/journal.pcbi.1013293> for method details.
Author: Lan Shui [aut, cre]
Maintainer: Lan Shui <Lan.Shui@uth.tmc.edu>
Diff between PoweREST versions 0.1.1 dated 2025-08-24 and 0.1.2 dated 2025-12-09
DESCRIPTION | 18 ++++++------ MD5 | 31 ++++++++++----------- NAMESPACE | 2 - R/PoweREST.R | 55 +++++++++++++------------------------ R/PoweREST_gene.R | 72 +++++++++++++++++++------------------------------ R/PoweREST_subset.R | 57 ++++++++++++-------------------------- R/fit_XGBoost.R | 25 ++++++++--------- R/plotly_powerest.R | 14 +++++++-- R/pred_XGBoost.R | 10 +++--- R/utils.R |only R/vis_XGBoost.R | 15 ++++++++-- inst/doc/PoweREST.R | 4 +- inst/doc/PoweREST.Rmd | 4 +- inst/doc/PoweREST.html | 4 +- man/fit_XGBoost.Rd | 8 ++--- man/plotly_powerest.Rd | 1 vignettes/PoweREST.Rmd | 4 +- 17 files changed, 146 insertions(+), 178 deletions(-)
Title: Automated Classification of Mass Spectra
Description: Functions to classify mass spectra in known categories and to determine discriminant mass-to-charge values (m/z). Includes easy-to-use preprocessing pipelines for Matrix Assisted Laser Desorption Ionisation - Time Of Flight Mass Spectrometry (MALDI-TOF) mass spectra, methods to select discriminant m/z from labelled libraries, and tools to predict categories (species, phenotypes, etc.) from selected features. Also provides utilities to build design matrices from peak intensities and labels. While this package was developed with the aim of identifying very similar species or phenotypes of bacteria from MALDI-TOF MS, the functions of this package can also be used to classify other categories associated to mass spectra; or from mass spectra obtained with other mass spectrometry techniques. Parallelized processing and optional C++-accelerated functions are available (notably to deal with large datasets) from version 0.5.0. If you use this package in your research, please cite the associat [...truncated...]
Author: Alexandre Godmer [aut, cre],
Quentin Giai Gianetto [aut],
Karen Druart [aut]
Maintainer: Alexandre Godmer <alexandre.godmer@aphp.fr>
Diff between MSclassifR versions 0.4.0 dated 2025-07-02 and 0.5.0 dated 2025-12-09
DESCRIPTION | 32 + MD5 | 67 ++- NAMESPACE | 64 +-- R/LogReg.R | 607 +++++++++++++++++----------------- R/LogReg_rf_fast.R |only R/PeakDetection.R | 224 ++++++++++-- R/PlotSpectra.R | 220 ++++++++---- R/PredictFastClass.R | 350 +++++++++---------- R/PredictLogReg.R | 530 +++++++++++++++++++---------- R/RcppExports.R |only R/SelectionVar.R | 728 +++++++++++++++++------------------------ R/SelectionVarStat.R | 317 ++++++++++++++--- R/SignalProcessing.R | 130 ++----- R/SignalProcessingUltra.R |only R/alignSpectra_landmark_cpp.R |only R/build_XY_from_peaks.R |only R/build_X_from_peaks_fast.R |only R/cpp-helpers.R |only R/fast_cvpvi.R |only R/fast_mda.R |only R/internal-docs.R |only R/smote_classif.R | 322 +++++++----------- R/utils-core.R |only R/utils-parallel.R |only build/partial.rdb |binary man/LogReg.Rd | 367 ++++++-------------- man/LogReg_rf_fast.Rd |only man/MSclassifR-cpp-helpers.Rd |only man/PeakDetection.Rd | 238 ++++++++----- man/PlotSpectra.Rd | 129 ++++--- man/PredictFastClass.Rd | 228 +++++++----- man/PredictLogReg.Rd | 379 +++++++++------------ man/SelectionVar.Rd | 4 man/SelectionVarStat.Rd | 176 +++++---- man/SignalProcessing.Rd | 190 +++------- man/SignalProcessingUltra.Rd |only man/build_XY_from_peaks.Rd |only man/build_X_from_peaks_fast.Rd |only man/dot-safe_n_workers.Rd |only man/fast_cvpvi.Rd |only man/fast_mda.Rd |only man/msclassifr-internal.Rd |only man/smote_classif.Rd | 141 +++---- src |only 44 files changed, 2879 insertions(+), 2564 deletions(-)
Title: Generalized Synthetic Control Method
Description: Conducts causal inference with interactive fixed-effect models. It imputes counterfactuals for each treated unit using control group information based on a linear interactive fixed effects model that incorporates unit-specific intercepts interacted with time-varying coefficients. This method generalizes the synthetic control method to the case of multiple treated units and variable treatment periods, and improves efficiency and interpretability.
Author: Yiqing Xu [aut, cre] ,
Licheng Liu [aut],
Ziyi Liu [aut],
Shiyun Hu [aut]
Maintainer: Yiqing Xu <yiqingxu@stanford.edu>
Diff between gsynth versions 1.2.1 dated 2021-08-06 and 1.3.1 dated 2025-12-09
gsynth-1.2.1/gsynth/R/RcppExports.R |only gsynth-1.2.1/gsynth/R/core.R |only gsynth-1.2.1/gsynth/R/cumu.R |only gsynth-1.2.1/gsynth/R/interFE.R |only gsynth-1.2.1/gsynth/README.md |only gsynth-1.2.1/gsynth/man/cumuEff.rd |only gsynth-1.2.1/gsynth/man/interFE.Rd |only gsynth-1.2.1/gsynth/man/print.interFE.Rd |only gsynth-1.2.1/gsynth/src |only gsynth-1.3.1/gsynth/DESCRIPTION | 34 gsynth-1.3.1/gsynth/MD5 | 39 gsynth-1.3.1/gsynth/NAMESPACE | 38 gsynth-1.3.1/gsynth/NEWS.md |only gsynth-1.3.1/gsynth/R/default.R | 909 ----------------- gsynth-1.3.1/gsynth/R/effect.R |only gsynth-1.3.1/gsynth/R/plot.R | 1494 +---------------------------- gsynth-1.3.1/gsynth/R/zzz.r | 2 gsynth-1.3.1/gsynth/man/effect.Rd |only gsynth-1.3.1/gsynth/man/gsynth-internal.Rd | 10 gsynth-1.3.1/gsynth/man/gsynth-package.Rd | 7 gsynth-1.3.1/gsynth/man/gsynth.Rd | 91 - gsynth-1.3.1/gsynth/man/plot.gsynth.Rd | 24 gsynth-1.3.1/gsynth/man/print.gsynth.Rd | 10 gsynth-1.3.1/gsynth/man/simdata.Rd | 6 gsynth-1.3.1/gsynth/man/turnout.Rd | 8 25 files changed, 218 insertions(+), 2454 deletions(-)
Title: Graph Visualisation Engine Widget for R and 'shiny' Apps
Description: Create stunning network experiences powered by the 'G6' graph visualisation engine
'JavaScript' library <https://g6.antv.antgroup.com/en>. In 'shiny' mode, modify your
graph directly from the server function to dynamically interact with nodes and edges.
Select your favorite layout among 20 choices. 15 behaviors are available such as
interactive edge creation, collapse-expand and brush select.
17 plugins designed to improve the user experience such as a mini-map,
toolbars and grid lines. Customise the look and feel of your graph with comprehensive
options for nodes, edges and more.
Author: David Granjon [aut, cre],
David Schoch [aut],
cynkra GmbH [fnd],
Bristol Myers Squibb [fnd]
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between g6R versions 0.1.0 dated 2025-07-10 and 0.5.0 dated 2025-12-09
g6R-0.1.0/g6R/man/g6_focus_elements.Rd |only g6R-0.5.0/g6R/DESCRIPTION | 8 g6R-0.5.0/g6R/MD5 | 116 ++-- g6R-0.5.0/g6R/NAMESPACE | 58 ++ g6R-0.5.0/g6R/NEWS.md | 50 + g6R-0.5.0/g6R/R/behaviors.R | 218 +++++++- g6R-0.5.0/g6R/R/elements.R |only g6R-0.5.0/g6R/R/g6.R | 58 +- g6R-0.5.0/g6R/R/igraph.R | 26 - g6R-0.5.0/g6R/R/options.R | 14 g6R-0.5.0/g6R/R/plugins.R | 63 ++ g6R-0.5.0/g6R/R/proxy.R | 597 +++++++++++++++++++++-- g6R-0.5.0/g6R/R/utils.R | 19 g6R-0.5.0/g6R/R/zzz.R |only g6R-0.5.0/g6R/README.md | 7 g6R-0.5.0/g6R/data/lesmis.rda |binary g6R-0.5.0/g6R/data/tree.rda |binary g6R-0.5.0/g6R/inst/doc/g6R.R | 32 + g6R-0.5.0/g6R/inst/doc/g6R.html | 375 ++++++++++---- g6R-0.5.0/g6R/inst/doc/g6R.qmd | 45 + g6R-0.5.0/g6R/inst/examples/dataframe/app.R | 20 g6R-0.5.0/g6R/inst/examples/demo/app.R | 8 g6R-0.5.0/g6R/inst/examples/html/app.R | 1 g6R-0.5.0/g6R/inst/examples/list/app.R | 41 + g6R-0.5.0/g6R/inst/examples/update-plugin/app.R | 9 g6R-0.5.0/g6R/inst/htmlwidgets/g6.js | 2 g6R-0.5.0/g6R/man/as_g6_element.Rd |only g6R-0.5.0/g6R/man/as_g6_elements.Rd |only g6R-0.5.0/g6R/man/brush_select.Rd | 9 g6R-0.5.0/g6R/man/bubble_sets.Rd | 4 g6R-0.5.0/g6R/man/click_select.Rd | 44 + g6R-0.5.0/g6R/man/context_menu.Rd | 32 + g6R-0.5.0/g6R/man/create_edge.Rd | 89 +++ g6R-0.5.0/g6R/man/figures/g6-layers.png |binary g6R-0.5.0/g6R/man/g6-add.Rd | 48 + g6R-0.5.0/g6R/man/g6-element-toggle.Rd | 18 g6R-0.5.0/g6R/man/g6-focus.Rd |only g6R-0.5.0/g6R/man/g6-get.Rd | 2 g6R-0.5.0/g6R/man/g6-remove.Rd | 38 + g6R-0.5.0/g6R/man/g6-set.Rd | 80 +++ g6R-0.5.0/g6R/man/g6-update.Rd | 47 + g6R-0.5.0/g6R/man/g6_data.Rd |only g6R-0.5.0/g6R/man/g6_element.Rd |only g6R-0.5.0/g6R/man/g6_elements.Rd |only g6R-0.5.0/g6R/man/g6_options.Rd | 3 g6R-0.5.0/g6R/man/g6_set_theme.Rd | 152 +++++ g6R-0.5.0/g6R/man/g6_update_behavior.Rd | 37 + g6R-0.5.0/g6R/man/g6_update_layout.Rd |only g6R-0.5.0/g6R/man/g6_update_plugin.Rd | 57 ++ g6R-0.5.0/g6R/man/hull.Rd | 2 g6R-0.5.0/g6R/man/is_g6_data.Rd |only g6R-0.5.0/g6R/man/is_g6_element.Rd |only g6R-0.5.0/g6R/man/is_g6_elements.Rd |only g6R-0.5.0/g6R/man/lasso_select.Rd | 7 g6R-0.5.0/g6R/tests/testthat/_snaps/behaviors.md | 197 ++++--- g6R-0.5.0/g6R/tests/testthat/_snaps/elements.md |only g6R-0.5.0/g6R/tests/testthat/_snaps/layouts.md | 130 +++-- g6R-0.5.0/g6R/tests/testthat/_snaps/plugins.md | 184 ++++--- g6R-0.5.0/g6R/tests/testthat/_snaps/proxy.md | 6 g6R-0.5.0/g6R/tests/testthat/test-elements.R |only g6R-0.5.0/g6R/tests/testthat/test-g6.R | 7 g6R-0.5.0/g6R/tests/testthat/test-igraph.R | 10 g6R-0.5.0/g6R/tests/testthat/test-layouts.R | 347 +++++++++++++ g6R-0.5.0/g6R/tests/testthat/test-plugins.R | 3 g6R-0.5.0/g6R/tests/testthat/test-proxy.R | 157 ++---- g6R-0.5.0/g6R/tests/testthat/test-zzz.R |only g6R-0.5.0/g6R/vignettes/g6R.qmd | 45 + 67 files changed, 2925 insertions(+), 597 deletions(-)
Title: User Friendly Data Visualization
Description: A comprehensive visualization toolkit built with coders of all
skill levels and color-vision impaired audiences in mind. It allows creation
of finely-tuned, publication-quality figures from single function calls.
Visualizations include scatter plots, compositional bar plots, violin, box,
and ridge plots, and more. Customization ranges from size and title
adjustments to discrete-group circling and labeling, hidden data overlay
upon cursor hovering via ggplotly() conversion, and many more, all with
simple, discrete inputs. Color blindness friendliness is powered by legend
adjustments (enlarged keys), and by allowing the use of shapes or
letter-overlay in addition to the carefully selected dittoColors().
Author: Daniel Bunis [aut, cre]
Maintainer: Daniel Bunis <daniel.bunis@ucsf.edu>
Diff between dittoViz versions 1.0.4 dated 2025-07-22 and 1.0.5 dated 2025-12-09
DESCRIPTION | 8 +++---- MD5 | 34 ++++++++++++++--------------- NEWS.md | 7 ++++++ R/dittoColors.R | 2 - R/scatterPlot.R | 16 +++++++------- R/utils.R | 16 ++++++++++++++ R/utils_data_gather.R | 4 +-- R/utils_plot_mods.R | 4 +-- R/yPlot.R | 4 +-- man/barPlot.Rd | 4 +-- man/dittoColors.Rd | 2 - man/freqPlot.Rd | 4 +-- man/scatterHex.Rd | 15 ++++++------- man/scatterPlot.Rd | 15 ++++++------- man/yPlot.Rd | 4 +-- tests/testthat/test-hover.R | 11 +++++++++ tests/testthat/test-scatter.R | 16 ++++++++++++++ tests/testthat/test-utils.R | 48 ++++++++++++++++++++++++++++++++++++++++++ 18 files changed, 155 insertions(+), 59 deletions(-)
Title: Calibration Performance
Description: Plots calibration curves and computes statistics for assessing calibration performance. See Lasai et al. (2025) <doi:10.48550/arXiv.2503.08389>, De Cock Campo (2023) <doi:10.48550/arXiv.2309.08559> and Van Calster et al. (2016) <doi:10.1016/j.jclinepi.2015.12.005>.
Author: De Cock Bavo [aut, cre],
Barrenada Lasai [aut],
Nieboer Daan [aut],
Van Calster Ben [aut],
Steyerberg Ewout [aut],
Vergouwe Yvonne [aut]
Maintainer: De Cock Bavo <bavo.decock@kuleuven.be>
Diff between CalibrationCurves versions 2.0.7 dated 2025-07-07 and 3.0.0 dated 2025-12-09
DESCRIPTION | 17 MD5 | 53 +- NAMESPACE | 17 R/CGC.R |only R/MAC2.R |only R/MIXC.R |only R/globals.R |only R/helperFunctions.R | 85 ++++ R/printFunction.R | 30 + R/rcspline.plot.noprint.R | 2 R/val.prob.ci.2.R | 33 + R/valProbCluster.R |only R/valProbSurvival.R | 3 R/valProbggplot.R | 23 - README.md | 12 build/vignette.rds |binary data/clustertestdata.rda |only data/clustertraindata.rda |only inst/CITATION | 17 inst/doc/CalibrationCurves.R | 51 ++ inst/doc/CalibrationCurves.Rmd | 333 +++++++++++++++++ inst/doc/CalibrationCurves.html | 409 ++++++++++++++++++-- man/CGC.Rd |only man/CalibrationCurves.Rd | 5 man/MAC2.Rd |only man/MIXC.Rd |only man/clustertraindata.Rd |only man/print.ClusteredCalibrationCurve.Rd |only man/val.prob.ci.2.Rd | 2 man/valProbCluster.Rd |only man/valProbSurvival.Rd | 3 man/valProbggplot.Rd | 646 ++++++++++++++++----------------- vignettes/CalibrationCurves.Rmd | 333 +++++++++++++++++ vignettes/references.bib | 8 34 files changed, 1665 insertions(+), 417 deletions(-)
More information about CalibrationCurves at CRAN
Permanent link
Title: 'SciViews::R' - Standard Dialog Boxes for Windows, MacOS and
Linuxes
Description: Quickly construct standard dialog boxes for your GUI, including
message boxes, input boxes, list, file or directory selection, ... In case R
cannot display GUI dialog boxes, a simpler command line version of these
interactive elements is also provided as fallback solution.
Author: Philippe Grosjean [aut, cre] ,
Paul Hibbins [ctb]
Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
Diff between svDialogs versions 1.1.1 dated 2025-08-26 and 1.1.2 dated 2025-12-09
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/dlg_dir.R | 13 ++++++++++--- R/dlg_input.R | 10 ++++++++-- R/dlg_open.R | 13 ++++++++++--- R/dlg_save.R | 12 ++++++++++-- R/svDialogs-internal.R | 6 ++++++ inst/CITATION | 4 ++-- inst/doc/svDialogs.html | 4 ++-- 10 files changed, 64 insertions(+), 26 deletions(-)
Title: Easily Downloads a Gene Expression Dataset from a GEO Code and
Retrieves the Gene Symbols of Its Probesets
Description: A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, <doi:10.1007/978-1-0716-1839-4_12>.
Author: Davide Chicco [aut, cre]
Maintainer: Davide Chicco <davidechicco@davidechicco.it>
Diff between geneExpressionFromGEO versions 1.2 dated 2025-04-11 and 1.3 dated 2025-12-09
DESCRIPTION | 11 ++--- MD5 | 9 ++-- NAMESPACE | 2 R/geneExpressionFromGEO.r | 77 ++++++++++++++++++++++++++++++++--- man/getDatasetFeaturesFromGEOcode.Rd |only man/getGeneExpressionFromGEO.Rd | 3 - 6 files changed, 86 insertions(+), 16 deletions(-)
More information about geneExpressionFromGEO at CRAN
Permanent link
Title: High Dimensional Categorical Data Visualization
Description: Easy visualization for datasets with more than two categorical variables and additional continuous variables. The package is particularly useful for exploring complex categorical data in the context of pathway analysis across multiple conditions. This package is now in maintenance-only mode and kept for legacy compatibility; for new projects and active development, please use the successor package 'ggdiceplot' (see <https://github.com/maflot/ggdiceplot> and <https://dice-and-domino-plot.readthedocs.io/en/latest/>).
Author: Matthias Flotho [aut, cre]
Maintainer: Matthias Flotho <matthias.flotho@ccb.uni-saarland.de>
Diff between diceplot versions 0.2.1 dated 2025-08-18 and 0.2.2 dated 2025-12-09
DESCRIPTION | 10 +++++----- MD5 | 3 ++- R/zzz.R |only 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Linters for 'box' Modules
Description: Static code analysis of 'box' modules.
The package enhances code quality by providing linters that check for common issues,
enforce best practices, and ensure consistent coding standards.
Author: Ricardo Rodrigo Basa [aut, cre],
Jakub Nowicki [aut],
Mateusz Kolomanski [ctb],
Guilherme Vituri [ctb],
Appsilon Sp. z o.o. [cph]
Maintainer: Ricardo Rodrigo Basa <opensource+rodrigo@appsilon.com>
Diff between box.linters versions 0.10.6 dated 2025-06-26 and 0.10.7 dated 2025-12-09
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/box_func_import_count_linter.R | 2 +- R/get_box_module_exports.R | 6 +++++- R/zzz.R | 6 ++++-- inst/WORDLIST | 2 +- man/box_default_linters.Rd | 2 +- man/rhino_default_linters.Rd | 2 +- 9 files changed, 30 insertions(+), 18 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-19 0.1.2
2021-05-12 0.1.0
2021-05-12 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-09 0.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-08 0.1.1
2020-03-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-17 1.14.4
2019-10-28 1.14.3
2019-03-15 1.12.1
2018-01-19 1.9.0
2017-10-24 1.8.0
2017-06-14 1.7.0
2016-12-20 1.5.0
2016-07-23 1.2.0
2016-05-22 1.0
Title: Word and Document Vector Models
Description: Create dense vector representation of words and documents using 'quanteda'. Currently implements Word2vec (Mikolov et al., 2013) <doi:10.48550/arXiv.1310.4546> and Latent Semantic Analysis (Deerwester et al., 1990) <doi:10.1002/(SICI)1097-4571(199009)41:6%3C391::AID-ASI1%3E3.0.CO;2-9>.
Author: Kohei Watanabe [aut, cre, cph] ,
Jan Wijffels [aut] ,
BNOSAC [cph] ,
Max Fomichev [ctb, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between wordvector versions 0.5.1 dated 2025-06-20 and 0.6.0 dated 2025-12-09
wordvector-0.5.1/wordvector/man/as.matrix.textmodel_wordvector.Rd |only wordvector-0.5.1/wordvector/man/print.textmodel_docvector.Rd |only wordvector-0.5.1/wordvector/man/print.textmodel_wordvector.Rd |only wordvector-0.6.0/wordvector/DESCRIPTION | 8 wordvector-0.6.0/wordvector/MD5 | 69 +- wordvector-0.6.0/wordvector/NAMESPACE | 8 wordvector-0.6.0/wordvector/NEWS.md | 7 wordvector-0.6.0/wordvector/R/RcppExports.R | 4 wordvector-0.6.0/wordvector/R/as.doc2vec.R |only wordvector-0.6.0/wordvector/R/doc2vec.R | 128 +--- wordvector-0.6.0/wordvector/R/lsa.R | 21 wordvector-0.6.0/wordvector/R/utils.R | 189 ++++-- wordvector-0.6.0/wordvector/R/word2vec.R | 169 +++-- wordvector-0.6.0/wordvector/inst/WORDLIST | 4 wordvector-0.6.0/wordvector/man/as.matrix.Rd |only wordvector-0.6.0/wordvector/man/as.textmodel_doc2vec.Rd |only wordvector-0.6.0/wordvector/man/perplexity.Rd |only wordvector-0.6.0/wordvector/man/print.textmodel_doc2vec.Rd |only wordvector-0.6.0/wordvector/man/print.textmodel_word2vec.Rd |only wordvector-0.6.0/wordvector/man/probability.Rd | 19 wordvector-0.6.0/wordvector/man/similarity.Rd | 20 wordvector-0.6.0/wordvector/man/textmodel_doc2vec.Rd | 72 +- wordvector-0.6.0/wordvector/man/textmodel_word2vec.Rd | 27 wordvector-0.6.0/wordvector/src/RcppExports.cpp | 13 wordvector-0.6.0/wordvector/src/dev.h |only wordvector-0.6.0/wordvector/src/word2vec/trainThread.cpp | 155 ++++- wordvector-0.6.0/wordvector/src/word2vec/trainThread.hpp | 31 - wordvector-0.6.0/wordvector/src/word2vec/word2vec.cpp | 19 wordvector-0.6.0/wordvector/src/word2vec/word2vec.hpp | 41 - wordvector-0.6.0/wordvector/src/wordvector.cpp | 157 +++-- wordvector-0.6.0/wordvector/tests/data |only wordvector-0.6.0/wordvector/tests/misc/compare_doc2vec.R |only wordvector-0.6.0/wordvector/tests/misc/probability.R |only wordvector-0.6.0/wordvector/tests/misc/test_large.R | 30 wordvector-0.6.0/wordvector/tests/misc/test_small.R | 80 ++ wordvector-0.6.0/wordvector/tests/testthat/test-as.doc2vec.R |only wordvector-0.6.0/wordvector/tests/testthat/test-doc2vec.R | 197 ++++-- wordvector-0.6.0/wordvector/tests/testthat/test-lsa.R | 46 - wordvector-0.6.0/wordvector/tests/testthat/test-model.R | 96 ++- wordvector-0.6.0/wordvector/tests/testthat/test-pre06.R |only wordvector-0.6.0/wordvector/tests/testthat/test-utils.R | 302 ++++++++-- wordvector-0.6.0/wordvector/tests/testthat/test-word2vec.R | 268 +++++++- 42 files changed, 1610 insertions(+), 570 deletions(-)
Title: Variable Length Markov Chains ('VLMC') Models
Description: Functions, Classes & Methods for estimation, prediction, and
simulation (bootstrap) of Variable Length Markov Chain ('VLMC') Models.
Author: Martin Maechler [aut, cre]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between VLMC versions 1.4-4 dated 2024-08-19 and 1.4-5 dated 2025-12-09
ChangeLog | 10 ++++++++++ DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- man/predict.vlmc.Rd | 6 +++--- man/residuals.vlmc.Rd | 4 ++-- src/vlmc.h | 4 ++-- 6 files changed, 29 insertions(+), 18 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive prebuilt widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut] ,
Joe Cheng [aut],
JJ Allaire [aut],
Carson Sievert [aut, cre] ,
Barret Schloerke [aut] ,
Garrick Aden-Buie [aut] ,
Yihui Xie [aut],
Jeff Allen [aut],
Jonathan McPherson [aut],
Alan Dipert [aut],
Barbara Borges [aut],
Posit Softwa [...truncated...]
Maintainer: Carson Sievert <carson@posit.co>
Diff between shiny versions 1.12.0 dated 2025-12-03 and 1.12.1 dated 2025-12-09
DESCRIPTION | 12 MD5 | 55 +-- NAMESPACE | 2 NEWS.md | 24 + R/bind-cache.R | 2 R/bind-event.R | 4 R/extended-task.R | 31 +- R/otel-attr-srcref.R | 16 - R/otel-collect.R | 7 R/otel-with.R |only R/reactives.R | 18 - R/shiny-options.R | 22 + R/shinywrappers.R | 4 inst/www/shared/busy-indicators/busy-indicators.css | 2 inst/www/shared/shiny-autoreload.js | 2 inst/www/shared/shiny-showcase.css | 2 inst/www/shared/shiny-showcase.js | 2 inst/www/shared/shiny-testmode.js | 2 inst/www/shared/shiny.js | 4 inst/www/shared/shiny.min.js | 4 man/ExtendedTask.Rd | 23 + man/shinyOptions.Rd | 21 - man/withOtelCollect.Rd |only tests/testthat/helper-otel.R |only tests/testthat/test-otel-attr-srcref.R | 306 +++++++++++++------- tests/testthat/test-otel-extended-task.R |only tests/testthat/test-otel-label.R | 21 - tests/testthat/test-otel-mock.R | 95 ++++-- tests/testthat/test-otel-shiny.R | 32 -- tests/testthat/test-otel-with.R |only tests/testthat/test-timer.R | 14 31 files changed, 480 insertions(+), 247 deletions(-)
Title: Reliability Growth Analysis
Description: Modeling and plotting functions for Reliability Growth Analysis (RGA). Models include the Duane (1962) <doi:10.1109/TA.1964.4319640>, Non-Homogeneous Poisson Process (NHPP) by Crow (1975) (No. AMSAATR138), Piecewise Weibull NHPP by Guo et al. (2010) <doi:10.1109/RAMS.2010.5448029>, and Piecewise Weibull NHPP with Change Point Detection based on the 'segmented' package by Muggeo (2024) <https://cran.r-project.org/package=segmented>.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
This is a re-admission after prior archival of version 0.3.1 dated 2025-11-21
Diff between ReliaGrowR versions 0.3.1 dated 2025-11-21 and 0.3.2 dated 2025-12-09
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/duane.R | 6 +++--- R/rga.R | 8 ++++---- inst/doc/RGA.Rmd | 8 ++++---- inst/doc/RGA.html | 8 ++++---- man/ReliaGrowR-package.Rd | 2 +- man/duane.Rd | 6 +++--- man/rga.Rd | 8 ++++---- tests/testthat/Rplots.pdf |binary tests/testthat/test-srr-duane.R | 9 +++++++++ tests/testthat/test-srr-rga.R | 24 +++++++++++++++++++++--- vignettes/RGA.Rmd | 8 ++++---- 13 files changed, 73 insertions(+), 46 deletions(-)
Title: Interface to 'REDCap'
Description: Access data stored in 'REDCap' databases using the Application
Programming Interface (API). 'REDCap' (Research Electronic Data CAPture;
<https://projectredcap.org>, Harris, et al. (2009) <doi:10.1016/j.jbi.2008.08.010>,
Harris, et al. (2019) <doi:10.1016/j.jbi.2019.103208>) is
a web application for building and managing online surveys and databases
developed at Vanderbilt University. The API allows users to access data
and project meta data (such as the data dictionary) from the web
programmatically. The 'redcapAPI' package facilitates the process of
accessing data with options to prepare an analysis-ready data set
consistent with the definitions in a database's data dictionary.
Author: Benjamin Nutter [ctb, aut],
Shawn Garbett [cre, ctb] ,
Savannah Obregon [ctb],
Thomas Obadia [ctb],
Marcus Lehr [ctb],
Brian High [ctb],
Stephen Lane [ctb],
Will Beasley [ctb],
Will Gray [ctb],
Nick Kennedy [ctb],
Tan Hsi-Nien [ctb],
Jeffrey Horner [ [...truncated...]
Maintainer: Shawn Garbett <shawn.garbett@vumc.org>
Diff between redcapAPI versions 2.11.4 dated 2025-10-29 and 2.11.5 dated 2025-12-09
DESCRIPTION | 6 MD5 | 52 - NEWS.md | 10 R/docsUserMethods.R | 6 R/exportRecordsTyped.R | 22 R/exportUsers.R | 167 ++--- R/importUsers.R | 66 +- R/makeApiCall.R | 42 - R/prepUserImportData.R | 310 ++++------ R/redcapDataStructure.R | 3 R/unlockREDCap.R | 1 build/vignette.rds |binary inst/doc/redcapAPI-best-practices.pdf |binary inst/doc/redcapAPI-casting-data.pdf |binary inst/doc/redcapAPI-data-validation.pdf |binary inst/doc/redcapAPI-faq.pdf |binary inst/doc/redcapAPI-getting-started-connecting.pdf |binary inst/doc/redcapAPI-missing-data-detection.pdf |binary inst/doc/redcapAPI-offline-connection.pdf |binary man/makeApiCall.Rd | 5 man/prepUserImportData.Rd | 28 man/recordsTypedMethods.Rd | 2 man/userMethods.Rd | 6 tests/testthat/test-020-redcapConnection-ArgumentValidation.R | 8 tests/testthat/test-101-userMethods-Functionality.R | 21 tests/testthat/test-103-userRoleAssignmentMethods-Functionality.R | 7 tests/testthat/test-361-userStructureVersion.R | 54 + 27 files changed, 458 insertions(+), 358 deletions(-)
Title: Analysis of Diffusion and Contagion Processes on Networks
Description: Empirical statistical analysis, visualization and simulation of
diffusion and contagion processes on networks. The package implements algorithms
for calculating network diffusion statistics such as transmission rate, hazard
rates, exposure models, network threshold levels, infectiousness (contagion),
and susceptibility. The package is inspired by work published in Valente,
et al., (2015) <DOI:10.1016/j.socscimed.2015.10.001>; Valente (1995) <ISBN:
9781881303213>, Myers (2000) <DOI:10.1086/303110>, Iyengar and others (2011)
<DOI:10.1287/mksc.1100.0566>, Burt (1987) <DOI:10.1086/228667>; among others.
Author: George Vega Yon [aut, cre] ,
Thomas Valente [aut, cph] ,
Anibal Olivera Morales [aut, ctb] ,
Stephanie Dyal [ctb] ,
Timothy Hayes [ctb]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
This is a re-admission after prior archival of version 1.23.0 dated 2025-06-12
Diff between netdiffuseR versions 1.23.0 dated 2025-06-12 and 1.24.0 dated 2025-12-09
DESCRIPTION | 25 - MD5 | 55 ++- NAMESPACE | 2 NEWS.md | 8 R/degree_adoption_diagnostic.R |only README.md | 346 ++++++++++------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/analyzing-medical-innovation-data.html | 20 - inst/doc/introduction-to-netdiffuser.html | 4 man/bass.Rd | 1 man/classify_adopters.Rd | 1 man/cumulative_adopt_count.Rd | 1 man/degree_adoption_diagnostic.Rd |only man/dgr.Rd | 1 man/ego_variance.Rd | 1 man/exposure.Rd | 1 man/figures/README-Adopters-1.png |only man/figures/README-BoringThreshold-1.png |only man/figures/README-Hazard-1.png |only man/figures/README-NiceThreshold-1.png |only man/figures/README-mosaic-1.png |only man/figures/README-plot_diffnet-1.png |only man/figures/README-plot_diffnet2-1.png |only man/figures/README-plot_diffnet2-withmap-1.png |only man/figures/README-plot_infectsuscept-1.png |only man/figures/README-plot_infectsuscept-2.png |only man/hazard_rate.Rd | 1 man/infection.Rd | 1 man/moran.Rd | 1 man/struct_equiv.Rd | 1 man/threshold.Rd | 1 man/vertex_covariate_dist.Rd | 1 src/infection.cpp | 5 tests/testthat/test-degree-adoption-diagnostic.R |only 35 files changed, 241 insertions(+), 236 deletions(-)
Title: Use Foreach to Parallelize via the Future Framework
Description: The 'future' package provides a unifying parallelization framework for R that supports many parallel and distributed backends <doi:10.32614/RJ-2021-048>. The 'foreach' package provides a powerful API for iterating over an R expression in parallel. The 'doFuture' package brings the best of the two together. There are two alternative ways to use this package. The recommended approach is to use 'y <- foreach(...) %dofuture% { ... }', which does not require using 'registerDoFuture()' and has many advantages over '%dopar%'. The alternative is the traditional 'foreach' approach by registering the 'foreach' adapter 'registerDoFuture()' and so that 'y <- foreach(...) %dopar% { ... }' runs in parallelizes with the 'future' framework.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between doFuture versions 1.1.2 dated 2025-07-14 and 1.1.3 dated 2025-12-09
DESCRIPTION | 8 +-- MD5 | 66 +++++++++++++------------- NEWS.md | 8 +++ R/doFuture2.R | 7 -- R/options.R | 26 +++++----- build/vignette.rds |binary inst/doc/doFuture-1-overview.html | 4 - inst/doc/doFuture-2-dopar.html | 4 - inst/doc/doFuture-3-dofuture.html | 4 - inst/testme/deploy.R | 2 inst/testme/test-foreach_dofuture,globals.R | 50 ++++++++++++++++++- man/doFuture.options.Rd | 16 +++--- tests/test-foreach_dofuture,errors.R | 1 tests/test-foreach_dofuture,globals.R | 1 tests/test-foreach_dofuture,nested_colon.R | 1 tests/test-foreach_dofuture,nested_dofuture.R | 1 tests/test-foreach_dofuture,rng.R | 1 tests/test-foreach_dofuture.R | 1 tests/test-foreach_dopar,doRNG,dopar.R | 1 tests/test-foreach_dopar,doRNG,dorng.R | 1 tests/test-foreach_dopar,errors.R | 1 tests/test-foreach_dopar,flavor_dofuture.R | 1 tests/test-foreach_dopar,globals.R | 1 tests/test-foreach_dopar,nested_colon.R | 1 tests/test-foreach_dopar,nested_dopar.R | 1 tests/test-foreach_dopar,options-for-export.R | 1 tests/test-foreach_dopar.R | 1 tests/test-makeChunks.R | 1 tests/test-options,nested.R | 1 tests/test-registerDoFuture.R | 1 tests/test-times.R | 1 tests/test-utils.R | 1 tests/test-with.DoPar.R | 1 tests/test-withDoRNG.R | 1 34 files changed, 144 insertions(+), 73 deletions(-)
Title: Estimate Graph Dimension using Cross-Validated Eigenvalues
Description: Cross-validated eigenvalues are estimated by
splitting a graph into two parts, the training and the test graph.
The training graph is used to estimate eigenvectors, and
the test graph is used to evaluate the correlation between the training
eigenvectors and the eigenvectors of the test graph.
The correlations follow a simple central limit theorem that can
be used to estimate graph dimension via hypothesis testing, see
Chen et al. (2021) <doi:10.48550/arXiv.2108.03336> for details.
Author: Fan Chen [aut] ,
Alex Hayes [cre, aut, cph] ,
Karl Rohe [aut]
Maintainer: Alex Hayes <alexpghayes@gmail.com>
Diff between gdim versions 0.1.0 dated 2023-09-05 and 0.1.1 dated 2025-12-09
gdim-0.1.0/gdim/man/pipe.Rd |only gdim-0.1.1/gdim/DESCRIPTION | 20 +-- gdim-0.1.1/gdim/MD5 | 28 ++-- gdim-0.1.1/gdim/NAMESPACE | 2 gdim-0.1.1/gdim/NEWS.md | 4 gdim-0.1.1/gdim/R/eigcv.R | 89 +++++++++------ gdim-0.1.1/gdim/R/utils.R | 15 -- gdim-0.1.1/gdim/README.md | 21 +-- gdim-0.1.1/gdim/build |only gdim-0.1.1/gdim/man/eigcv.Rd | 7 - gdim-0.1.1/gdim/man/figures/README-unnamed-chunk-3-1.png |binary gdim-0.1.1/gdim/man/gdim-package.Rd | 2 gdim-0.1.1/gdim/man/plot.eigcv.Rd | 7 - gdim-0.1.1/gdim/man/print.eigcv.Rd | 7 - gdim-0.1.1/gdim/tests/testthat/test-eigcv.R | 11 - gdim-0.1.1/gdim/tests/testthat/test-split_graph.R | 1 16 files changed, 107 insertions(+), 107 deletions(-)
Title: Location and Visualization of Clustered Somatic Mutations
Description: Identification and visualization of groups of closely spaced mutations in the DNA sequence of cancer genome. The extremely mutated zones are searched in the symmetric dissimilarity matrix using the anti-Robinson matrix properties. Different data sets are obtained to describe and plot the clustered mutations information.
Author: David Lora [aut, cre]
Maintainer: David Lora <dalora@ucm.es>
This is a re-admission after prior archival of version 1.0.1 dated 2016-04-29
Diff between ClusteredMutations versions 1.0.1 dated 2016-04-29 and 1.0.2 dated 2025-12-09
DESCRIPTION | 21 +- MD5 | 23 +- NAMESPACE | 3 build/partial.rdb |only build/vignette.rds |binary inst/doc/vignetteClustered.R | 218 ++++++++++++------------- inst/doc/vignetteClustered.Rnw | 345 ++++++++++++++++++++-------------------- inst/doc/vignetteClustered.pdf |binary man/PD4107a.Rd | 24 +- man/dissmutmatrix.Rd | 160 +++++++++--------- man/imd.Rd | 161 +++++++++--------- man/showers.Rd | 12 - vignettes/vignetteClustered.Rnw | 345 ++++++++++++++++++++-------------------- 13 files changed, 664 insertions(+), 648 deletions(-)
More information about ClusteredMutations at CRAN
Permanent link
Title: Broadly Useful Convenient and Efficient R Functions
Description: Broadly useful convenient and efficient R functions
that bring users concise and elegant R data analyses.
This package includes easy-to-use functions for
(1) basic R programming
(e.g., set working directory to the path of currently opened file;
import/export data from/to files in any format;
print tables to Microsoft Word);
(2) multivariate computation
(e.g., compute scale sums/means/... with reverse scoring);
(3) reliability analyses and factor analyses;
(4) descriptive statistics and correlation analyses;
(5) t-test, multi-factor analysis of variance (ANOVA),
simple-effect analysis, and post-hoc multiple comparison;
(6) tidy report of statistical models
(to R Console and Microsoft Word);
(7) mediation and moderation analyses (PROCESS);
and (8) additional toolbox for statistics and graphics.
Author: Han Wu Shuang Bao [aut, cre]
Maintainer: Han Wu Shuang Bao <baohws@foxmail.com>
Diff between bruceR versions 2025.8 dated 2025-08-20 and 2025.11 dated 2025-12-09
DESCRIPTION | 10 ++--- MD5 | 30 +++++++-------- NEWS.md | 8 +++- R/bruceR-stats_1_basic.R | 14 +++---- R/bruceR-stats_5_advance.R | 4 +- R/bruceR-stats_6_plot.R | 84 ++++++++++++++++++++++---------------------- R/bruceR.R | 12 +++--- R/bruceR_utils.R | 24 ++++++------ man/PROCESS.Rd | 2 - man/bruceR-package.Rd | 12 +++--- man/grapes-allin-grapes.Rd | 6 +-- man/grapes-anyin-grapes.Rd | 6 +-- man/grapes-nonein-grapes.Rd | 6 +-- man/grapes-partin-grapes.Rd | 6 +-- man/med_summary.Rd | 2 - man/theme_bruce.Rd | 4 +- 16 files changed, 117 insertions(+), 113 deletions(-)
More information about resizableSplitLayout at CRAN
Permanent link
Title: Apply Function to Elements in Parallel using Futures
Description: Implementations of apply(), by(), eapply(), lapply(), Map(), .mapply(), mapply(), replicate(), sapply(), tapply(), and vapply() that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster. These future_*apply() functions come with the same pros and cons as the corresponding base-R *apply() functions but with the additional feature of being able to be processed via the future framework <doi:10.32614/RJ-2021-048>.
Author: Henrik Bengtsson [aut, cre, cph] ,
R Core Team [cph, ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.apply versions 1.20.0 dated 2025-06-06 and 1.20.1 dated 2025-12-09
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 9 +++++++++ R/future_apply.R | 2 ++ R/future_lapply.R | 24 +++++++++++++++++++++++- R/future_xapply.R | 2 +- build/vignette.rds |binary inst/doc/future.apply-1-overview.html | 4 ++-- man/future_lapply.Rd | 27 +++++++++++++++++++++++++-- 9 files changed, 74 insertions(+), 18 deletions(-)
More information about decompositionLE at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-19 1.2.7
2024-05-25 1.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-09 3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-07 1.1.8
2024-11-04 1.1.7
2024-05-15 1.1.6
2023-09-21 1.1.5
2023-03-21 1.1.4
2022-03-27 1.1.3
2022-02-18 1.1.2
2021-12-19 1.1.0
2021-09-27 1.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-02-19 1.0.0
2024-02-02 0.5.1
Title: Inline Asynchronous Generator Results into Documents
Description: Given a 'coro' asynchronous generator instance that produces text,
write that text into a document selection in 'RStudio' and 'Positron'. This
is particularly helpful for streaming large language model responses into
the user's editor.
Author: Simon Couch [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between streamy versions 0.2.0 dated 2025-05-21 and 0.2.1 dated 2025-12-09
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/stream.R | 2 +- R/utils.R | 4 ++++ tests/testthat/test-stream.R | 2 ++ 6 files changed, 19 insertions(+), 9 deletions(-)
Title: Sparse Vectors for Use in Data Frames
Description: Provides sparse vectors powered by ALTREP (Alternative
Representations for R Objects) that behave like regular vectors, and
can thus be used in data frames. Also provides tools to convert
between sparse matrices and data frames with sparse columns and
functions to interact with sparse vectors.
Author: Emil Hvitfeldt [aut, cre] ,
Davis Vaughan [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between sparsevctrs versions 0.3.4 dated 2025-05-25 and 0.3.5 dated 2025-12-09
DESCRIPTION | 8 ++-- MD5 | 52 +++++++++++++++--------------- NEWS.md | 4 ++ R/sparse_character.R | 4 ++ R/sparse_double.R | 4 ++ R/sparse_integer.R | 4 ++ R/sparse_logical.R | 4 ++ build/vignette.rds |binary man/coerce_to_sparse_data_frame.Rd | 2 - man/coerce_to_sparse_matrix.Rd | 2 - man/coerce_to_sparse_tibble.Rd | 2 - man/has_sparse_elements.Rd | 2 - man/sparsevctrs-package.Rd | 2 - src/altrep-sparse-double.c | 14 ++++++-- src/altrep-sparse-integer.c | 14 ++++++-- src/altrep-sparse-logical.c | 14 ++++++-- src/altrep-sparse-string.c | 17 ++++++++- src/init.c | 16 +++++++++ src/sparse-utils.h | 6 ++- tests/testthat/_snaps/sparse_character.md | 14 ++++---- tests/testthat/_snaps/sparse_double.md | 14 ++++---- tests/testthat/_snaps/sparse_integer.md | 14 ++++---- tests/testthat/_snaps/sparse_logical.md | 14 ++++---- tests/testthat/test-sparse_character.R | 10 ++--- tests/testthat/test-sparse_double.R | 10 ++--- tests/testthat/test-sparse_integer.R | 10 ++--- tests/testthat/test-sparse_logical.R | 10 ++--- 27 files changed, 174 insertions(+), 93 deletions(-)
Title: (Robust) Mediation Analysis
Description: Perform mediation analysis via the fast-and-robust bootstrap test ROBMED (Alfons, Ates & Groenen, 2022a; <doi:10.1177/1094428121999096>), as well as various other methods. Details on the implementation and code examples can be found in Alfons, Ates, and Groenen (2022b) <doi:10.18637/jss.v103.i13>. Further discussion on robust mediation analysis can be found in Alfons & Schley (2025) <doi:10.1002/wics.70051>.
Author: Andreas Alfons [aut, cre] ,
Nufer Y. Ates [dtc]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robmed versions 1.2.2 dated 2025-09-08 and 1.3.0 dated 2025-12-09
DESCRIPTION | 10 +-- MD5 | 48 +++++++-------- NEWS | 7 ++ R/BSG2014.R | 127 +++++++++++++++++++++++------------------- R/fit_mediation.R | 23 ++----- R/robmed-package.R | 6 - R/setup_weight_plot.R | 6 - R/summary.R | 24 ++----- R/test_mediation.R | 24 ++----- R/weight_plot.R | 6 - build/partial.rdb |binary data/BSG2014.RData |binary inst/CITATION | 9 +- inst/doc/robmed-intro.R | 18 ++--- inst/doc/robmed-intro.Rnw | 23 +++---- inst/doc/robmed-intro.pdf |binary man/BSG2014.Rd | 127 +++++++++++++++++++++++------------------- man/fit_mediation.Rd | 23 ++----- man/robmed-package.Rd | 6 - man/setup_weight_plot.Rd | 6 - man/summary.test_mediation.Rd | 24 ++----- man/test_mediation.Rd | 24 ++----- man/weight_plot.Rd | 6 - vignettes/robmed-intro.Rnw | 23 +++---- vignettes/robmed.bib | 4 - 25 files changed, 277 insertions(+), 297 deletions(-)
Title: Map Pages of Memory
Description: R interface to POSIX mmap and Window's MapViewOfFile.
Author: Jeffrey A. Ryan [aut, cre]
Maintainer: Jeffrey A. Ryan <jeff.a.ryan@gmail.com>
Diff between mmap versions 0.6-22 dated 2023-12-08 and 0.6-23 dated 2025-12-09
DESCRIPTION | 15 ++++++++++----- MD5 | 6 +++--- inst/doc/mmap.pdf |binary src/mmap.c | 10 ++-------- 4 files changed, 15 insertions(+), 16 deletions(-)
Title: A Modular, Integrated Approach to Maximum Entropy Distribution
Modeling
Description: Tools for training, selecting, and evaluating maximum entropy
(and standard logistic regression) distribution models. This package
provides tools for user-controlled transformation of explanatory variables,
selection of variables by nested model comparison, and flexible model
evaluation and projection. It follows principles based on the maximum-
likelihood interpretation of maximum entropy modeling, and uses infinitely-
weighted logistic regression for model fitting. The package is described in
Vollering et al. (2019; <doi:10.1002/ece3.5654>).
Author: Julien Vollering [aut, cre],
Sabrina Mazzoni [aut],
Rune Halvorsen [aut],
Steven Phillips [cph],
Michael Bedward [ctb]
Maintainer: Julien Vollering <julienvollering@gmail.com>
Diff between MIAmaxent versions 1.4.0 dated 2025-10-18 and 1.4.1 dated 2025-12-09
DESCRIPTION | 6 LICENSE | 2 MD5 | 148 - NAMESPACE | 32 NEWS.md | 168 - R/MIAmaxent-package.R | 96 - R/calculateRVA.R | 108 - R/chooseModel.R | 160 - R/compare.R | 176 - R/data.R | 146 - R/deriveVars.R | 300 +-- R/dvsfromev.R | 266 +- R/modelFromLambdas.R | 144 - R/parsdvs.R | 116 - R/parsevs.R | 360 +-- R/plotFOP.R | 328 +-- R/plotResp.R | 216 +- R/plotResp2.R | 162 - R/projectModel.R | 346 +-- R/readData.R | 310 +-- R/runIWLR.R | 162 - R/runLR.R | 68 R/selectDVforEV.R | 276 +- R/selectEV.R | 286 +-- R/splselect.R | 58 R/testAUC.R | 226 +- R/transfclosures.R | 218 +- R/utils.R | 590 +++--- README.md | 172 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 22 inst/doc/NCEAS.R | 108 - inst/doc/NCEAS.Rmd | 1168 ++++++------ inst/doc/NCEAS.html | 2 inst/doc/a-modeling-example.Rmd | 964 +++++----- inst/doc/a-modeling-example.html | 12 inst/extdata/EV_categorical/geoberg.asc | 414 ++-- inst/extdata/EV_categorical/geolmja1.asc | 414 ++-- inst/extdata/EV_categorical/lcucor1.asc | 414 ++-- inst/extdata/EV_categorical/lcutilt4.asc | 414 ++-- inst/extdata/EV_categorical/terslpps15.asc | 414 ++-- inst/extdata/EV_continuous/pca1.asc | 414 ++-- inst/extdata/EV_continuous/prbygall.asc | 414 ++-- inst/extdata/EV_continuous/prtilany.asc | 414 ++-- inst/extdata/EV_continuous/teraspif.asc | 414 ++-- inst/extdata/EV_continuous/terdem.asc | 414 ++-- inst/extdata/EV_continuous/terslpdg.asc | 414 ++-- inst/extdata/EV_continuous/tersolrade.asc | 414 ++-- inst/extdata/EV_continuous/tertpi09.asc | 414 ++-- inst/extdata/occurrence_PA.csv | 246 +- inst/extdata/occurrence_PO.csv | 2120 +++++++++++------------ inst/extdata/sommerfeltia/1.lambdas | 22 inst/extdata/sommerfeltia/EV_continuous/EV11.asc | 26 inst/extdata/sommerfeltia/EV_continuous/EV12.asc | 26 inst/extdata/sommerfeltia/EV_continuous/EV13.asc | 26 inst/extdata/sommerfeltia/EV_continuous/EV14.asc | 26 inst/extdata/sommerfeltia/Sp1.csv | 22 man/MIAmaxent-package.Rd | 2 man/chooseModel.Rd | 92 man/deriveVars.Rd | 252 +- man/modelFromLambdas.Rd | 68 man/plotFOP.Rd | 212 +- man/plotResp.Rd | 116 - man/projectModel.Rd | 212 +- man/readData.Rd | 222 +- man/selectDVforEV.Rd | 212 +- man/selectEV.Rd | 248 +- man/testAUC.Rd | 114 - man/toydata_dvs.Rd | 60 man/toydata_seldvs.Rd | 62 man/toydata_selevs.Rd | 64 man/toydata_sp1po.Rd | 58 vignettes/NCEAS.Rmd | 1168 ++++++------ vignettes/a-modeling-example.Rmd | 964 +++++----- 75 files changed, 9975 insertions(+), 9969 deletions(-)
Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing with
meteorological data in the tidy data framework. Extends 'ggplot2' for
better plotting of scalar and vector fields and provides commonly used
analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between metR versions 0.18.2 dated 2025-09-05 and 0.18.3 dated 2025-12-09
DESCRIPTION | 8 - MD5 | 54 ++++---- NEWS.md | 6 R/ReadNetCDF.R | 9 - README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Visualization-tools.html | 236 ++++++++++++++++---------------------- inst/doc/Working-with-data.html | 225 +++++++++++++++--------------------- man/MakeBreaks.Rd | 2 man/MaskLand.Rd | 2 man/ReadNetCDF.Rd | 2 man/Smooth2D.Rd | 2 man/discretised_scale.Rd | 17 +- man/geom_arrow.Rd | 8 - man/geom_contour2.Rd | 10 - man/geom_contour_fill.Rd | 10 - man/geom_contour_tanaka.Rd | 10 - man/geom_relief.Rd | 8 - man/geom_streamline.Rd | 8 - man/geom_text_contour.Rd | 19 +-- man/guide_colourstrip.Rd | 8 - man/label_scales.Rd | 10 - man/scale_divergent.Rd | 15 +- man/scale_longitude.Rd | 4 man/stat_na.Rd | 8 - man/stat_subset.Rd | 8 - tests/testthat/test-ReadNetCDF.R | 9 + 28 files changed, 345 insertions(+), 357 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 2.7.3 dated 2025-09-12 and 2.7.4 dated 2025-12-09
httk-2.7.3/httk/data/Frank2018.RData |only httk-2.7.3/httk/data/Kapraun2022Vignette.RData |only httk-2.7.3/httk/data/Linakis2020.RData |only httk-2.7.3/httk/data/Scherer2025Vignette.RData |only httk-2.7.3/httk/data/Truong2025Vignette.RData |only httk-2.7.3/httk/data/vignettes.RData |only httk-2.7.3/httk/data/wambaugh2019.RData |only httk-2.7.3/httk/inst/doc/V2_IntrotoIVIVE.R |only httk-2.7.3/httk/inst/doc/V2_IntrotoIVIVE.Rmd |only httk-2.7.3/httk/inst/doc/V2_IntrotoIVIVE.html |only httk-2.7.3/httk/inst/doc/Va_Pearce2017.R |only httk-2.7.3/httk/inst/doc/Va_Pearce2017.Rmd |only httk-2.7.3/httk/inst/doc/Va_Pearce2017.html |only httk-2.7.3/httk/inst/doc/Vb_Ring2017.R |only httk-2.7.3/httk/inst/doc/Vb_Ring2017.Rmd |only httk-2.7.3/httk/inst/doc/Vb_Ring2017.html |only httk-2.7.3/httk/inst/doc/Vc_Pearce2017.R |only httk-2.7.3/httk/inst/doc/Vc_Pearce2017.Rmd |only httk-2.7.3/httk/inst/doc/Vc_Pearce2017.html |only httk-2.7.3/httk/inst/doc/Vd_Frank2019.R |only httk-2.7.3/httk/inst/doc/Vd_Frank2019.Rmd |only httk-2.7.3/httk/inst/doc/Vd_Frank2019.html |only httk-2.7.3/httk/inst/doc/Ve_Truong2025.R |only httk-2.7.3/httk/inst/doc/Ve_Truong2025.Rmd |only httk-2.7.3/httk/inst/doc/Ve_Truong2025.html |only httk-2.7.3/httk/inst/doc/Vf_WambaughSubmitted.R |only httk-2.7.3/httk/inst/doc/Vf_WambaughSubmitted.Rmd |only httk-2.7.3/httk/inst/doc/Vf_WambaughSubmitted.html |only httk-2.7.3/httk/inst/doc/Vg_MeadeSubmitted.R |only httk-2.7.3/httk/inst/doc/Vg_MeadeSubmitted.Rmd |only httk-2.7.3/httk/inst/doc/Vg_MeadeSubmitted.html |only httk-2.7.3/httk/inst/doc/Vh_SchererSubmitted.R |only httk-2.7.3/httk/inst/doc/Vh_SchererSubmitted.Rmd |only httk-2.7.3/httk/inst/doc/Vh_SchererSubmitted.html |only httk-2.7.3/httk/man/Dimitrijevic.IVD.Rd |only httk-2.7.3/httk/man/Frank2018invivo.Rd |only httk-2.7.3/httk/man/Obach2008.Rd |only httk-2.7.3/httk/man/Scherer2025.IVD.Rd |only httk-2.7.3/httk/man/Wetmore2012.Rd |only httk-2.7.3/httk/man/aylward2014.Rd |only httk-2.7.3/httk/man/concentration_data_Linakis2020.Rd |only httk-2.7.3/httk/man/fetalpcs.Rd |only httk-2.7.3/httk/man/howgate.Rd |only httk-2.7.3/httk/man/johnson.Rd |only httk-2.7.3/httk/man/metabolism_data_Linakis2020.Rd |only httk-2.7.3/httk/man/onlyp.Rd |only httk-2.7.3/httk/man/pc.data.Rd |only httk-2.7.3/httk/man/pharma.Rd |only httk-2.7.3/httk/man/pksim.pcs.Rd |only httk-2.7.3/httk/man/pregnonpregaucs.Rd |only httk-2.7.3/httk/man/supptab1_Linakis2020.Rd |only httk-2.7.3/httk/man/supptab2_Linakis2020.Rd |only httk-2.7.3/httk/man/thyroid.ac50s.Rd |only httk-2.7.3/httk/man/truong25.seem3.Rd |only httk-2.7.3/httk/man/wambaugh2019.Rd |only httk-2.7.3/httk/man/wambaugh2019.nhanes.Rd |only httk-2.7.3/httk/man/wambaugh2019.raw.Rd |only httk-2.7.3/httk/man/wambaugh2019.seem3.Rd |only httk-2.7.3/httk/man/wambaugh2019.tox21.Rd |only httk-2.7.3/httk/man/wang2018.Rd |only httk-2.7.3/httk/vignettes/V2_IntrotoIVIVE.Rmd |only httk-2.7.3/httk/vignettes/Va_Pearce2017.Rmd |only httk-2.7.3/httk/vignettes/Vb_Ring2017.Rmd |only httk-2.7.3/httk/vignettes/Vc_Pearce2017.Rmd |only httk-2.7.3/httk/vignettes/Vd_Frank2019.Rmd |only httk-2.7.3/httk/vignettes/Ve_Truong2025.Rmd |only httk-2.7.3/httk/vignettes/Vf_WambaughSubmitted.Rmd |only httk-2.7.3/httk/vignettes/Vg_MeadeSubmitted.Rmd |only httk-2.7.3/httk/vignettes/Vh_SchererSubmitted.Rmd |only httk-2.7.4/httk/DESCRIPTION | 15 httk-2.7.4/httk/MD5 | 187 +--- httk-2.7.4/httk/NAMESPACE | 10 httk-2.7.4/httk/NEWS.md | 17 httk-2.7.4/httk/R/calc_mc_css.R | 2 httk-2.7.4/httk/R/calc_mc_oral_equiv.R | 10 httk-2.7.4/httk/R/convert_units.R | 8 httk-2.7.4/httk/R/data.R | 718 +----------------- httk-2.7.4/httk/R/do_initial_dose_pbtk.R |only httk-2.7.4/httk/R/httk_vignettes.R |only httk-2.7.4/httk/R/in.list.R | 103 +- httk-2.7.4/httk/R/invitro_mc.R | 10 httk-2.7.4/httk/R/modelinfo_dermal_1subcomp.R | 3 httk-2.7.4/httk/R/parameterize_pfas1comp.R | 17 httk-2.7.4/httk/R/solve_1comp.R | 2 httk-2.7.4/httk/R/solve_1comp_lifestage.R | 4 httk-2.7.4/httk/R/solve_3comp.R | 12 httk-2.7.4/httk/R/solve_3comp2.R | 12 httk-2.7.4/httk/R/solve_3comp_lifestage.R | 12 httk-2.7.4/httk/R/solve_dermal_pbtk.R | 9 httk-2.7.4/httk/R/solve_gas_pbtk.R | 24 httk-2.7.4/httk/R/solve_model.R | 53 - httk-2.7.4/httk/R/solve_pbtk.R | 8 httk-2.7.4/httk/R/solve_pbtk_lifestage.R | 8 httk-2.7.4/httk/R/sysdata.rda |binary httk-2.7.4/httk/README.md | 36 httk-2.7.4/httk/build/partial.rdb |binary httk-2.7.4/httk/build/vignette.rds |binary httk-2.7.4/httk/data/Tables.RData |binary httk-2.7.4/httk/inst/CITATION | 2 httk-2.7.4/httk/inst/REFERENCES.bib | 47 - httk-2.7.4/httk/inst/doc/V1_IntroToHTTK.Rmd | 2 httk-2.7.4/httk/inst/doc/V1_IntroToHTTK.html | 141 +-- httk-2.7.4/httk/inst/doc/V2_IntroToIVIVE.R |only httk-2.7.4/httk/inst/doc/V2_IntroToIVIVE.Rmd |only httk-2.7.4/httk/inst/doc/V2_IntroToIVIVE.html |only httk-2.7.4/httk/man/calc_mc_css.Rd | 2 httk-2.7.4/httk/man/calc_mc_oral_equiv.Rd | 10 httk-2.7.4/httk/man/example.seem.Rd | 46 - httk-2.7.4/httk/man/example.toxcast.Rd | 58 - httk-2.7.4/httk/man/figures/httk.png |binary httk-2.7.4/httk/man/httk-package.Rd | 1 httk-2.7.4/httk/man/httk_vignettes.Rd |only httk-2.7.4/httk/man/in.list.Rd | 78 + httk-2.7.4/httk/man/is.httk.Rd | 12 httk-2.7.4/httk/man/mcnally_dt.Rd | 9 httk-2.7.4/httk/man/parameterize_pfas1comp.Rd | 17 httk-2.7.4/httk/man/solve_1comp.Rd | 2 httk-2.7.4/httk/man/solve_1comp_lifestage.Rd | 4 httk-2.7.4/httk/man/solve_3comp.Rd | 12 httk-2.7.4/httk/man/solve_3comp2.Rd | 12 httk-2.7.4/httk/man/solve_3comp_lifestage.Rd | 12 httk-2.7.4/httk/man/solve_dermal_pbtk.Rd | 3 httk-2.7.4/httk/man/solve_gas_pbtk.Rd | 15 httk-2.7.4/httk/man/solve_model.Rd | 6 httk-2.7.4/httk/man/solve_pbtk.Rd | 8 httk-2.7.4/httk/man/solve_pbtk_lifestage.Rd | 8 httk-2.7.4/httk/src/init.c | 17 httk-2.7.4/httk/src/model_aerosol_pbtk.c |only httk-2.7.4/httk/src/model_gas_pbtk.c | 10 httk-2.7.4/httk/tests/cheminfo_test.Rout.save | 506 ++++++------ httk-2.7.4/httk/tests/solve_dermal_test.Rout.save | 132 +-- httk-2.7.4/httk/vignettes/V1_IntroToHTTK.Rmd | 2 httk-2.7.4/httk/vignettes/V2_IntroToIVIVE.Rmd |only 133 files changed, 936 insertions(+), 1518 deletions(-)
Title: Hierarchical Optimal Matching and Machine Learning Toolbox
Description: Various functions and algorithms are provided here for solving optimal matching
tasks in the context of preclinical cancer studies. Further, various helper and plotting
functions are provided for unsupervised and supervised machine learning as well as longitudinal
mixed-effects modeling of tumor growth response patterns.
Author: Teemu Daniel Laajala [aut, cre]
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Diff between hamlet versions 0.9.6 dated 2018-05-26 and 0.9.8 dated 2025-12-09
DESCRIPTION | 19 +++++++++++++------ MD5 | 32 ++++++++++++++++---------------- NEWS | 1 + R/matchtools.R | 18 +++++++++--------- R/memtools.R | 16 ++++++++-------- R/plottools.R | 26 ++++++++++++++++---------- build/vignette.rds |binary inst/doc/introduction.R | 2 +- inst/doc/introduction.Rnw | 2 +- inst/doc/introduction.pdf |binary man/hamlet-package.Rd | 10 ---------- man/hmap.Rd | 13 +++++++------ man/hmap.key.Rd | 5 ++++- man/match.ga.Rd | 16 ++++++++-------- man/mix.binary.Rd | 2 +- man/mixplot.Rd | 7 ++++--- vignettes/introduction.Rnw | 2 +- 17 files changed, 90 insertions(+), 81 deletions(-)
Title: Model Butcher
Description: Provides a set of S3 generics to axe components of fitted
model objects and help reduce the size of model objects saved to disk.
Author: Joyce Cahoon [aut] ,
Davis Vaughan [aut],
Max Kuhn [cre, aut] ,
Alex Hayes [aut],
Julia Silge [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between butcher versions 0.3.6 dated 2025-08-18 and 0.4.0 dated 2025-12-09
DESCRIPTION | 41 ++--- MD5 | 240 +++++++++++++++++--------------- NAMESPACE | 16 ++ NEWS.md | 13 + R/axe-generics.R | 97 ++++++++++++- R/butcher-package.R | 13 + R/c5.R | 8 - R/docs.R | 26 +-- R/earth.R | 4 R/elnet.R | 5 R/flexsurvreg.R | 8 - R/function.R | 1 R/glmnet.R | 5 R/kknn.R | 4 R/ksvm.R | 5 R/lm.R | 5 R/locate.R | 18 -- R/mass.R | 14 + R/model_fit.R | 16 -- R/multnet.R | 4 R/new.R | 63 +++++--- R/nnet.R | 5 R/randomForest.R | 4 R/ranger.R | 4 R/recipe.R | 12 - R/rpart.R | 22 -- R/rsample-data.R |only R/rsample-indicators.R |only R/spark.R | 2 R/survreg.R | 4 R/survreg.penal.R | 4 R/tabnet_fit.R |only R/train.recipe.R | 8 - R/ui.R | 8 - R/utilities.R | 15 +- R/weigh.R | 28 +++ R/xgb.R | 51 ++++-- R/xrf.R | 4 README.md | 2 build/stage23.rdb |binary build/vignette.rds |binary inst/doc/available-axe-methods.R | 12 - inst/doc/available-axe-methods.Rmd | 12 - inst/doc/available-axe-methods.html | 46 ++++-- inst/doc/butcher.R | 8 - inst/doc/butcher.Rmd | 8 - inst/doc/butcher.html | 10 - inst/extdata |only man/axe-C5.0.Rd | 10 - man/axe-KMeansCluster.Rd | 2 man/axe-NaiveBayes.Rd | 2 man/axe-bart.Rd | 2 man/axe-coxph.Rd | 2 man/axe-earth.Rd | 6 man/axe-elnet.Rd | 6 man/axe-flexsurvreg.Rd | 8 - man/axe-function.Rd | 2 man/axe-gam.Rd | 2 man/axe-gausspr.Rd | 2 man/axe-glmnet.Rd | 6 man/axe-ipred.Rd | 2 man/axe-kknn.Rd | 6 man/axe-kproto.Rd | 2 man/axe-ksvm.Rd | 6 man/axe-lm.Rd | 6 man/axe-mass.Rd | 15 +- man/axe-mda.Rd | 2 man/axe-model_fit.Rd | 14 - man/axe-multnet.Rd | 6 man/axe-nnet.Rd | 6 man/axe-pls.Rd | 2 man/axe-randomForest.Rd | 6 man/axe-ranger.Rd | 6 man/axe-rda.Rd | 2 man/axe-recipe.Rd | 14 - man/axe-rpart.Rd | 22 -- man/axe-rsample-data.Rd |only man/axe-rsample-indicators.Rd |only man/axe-sclass.Rd | 2 man/axe-spark.Rd | 4 man/axe-survreg.Rd | 6 man/axe-survreg.penal.Rd | 6 man/axe-tabnet_fit.Rd |only man/axe-terms.Rd | 2 man/axe-train.Rd | 2 man/axe-train.recipe.Rd | 10 - man/axe-xgb.Booster.Rd | 33 ++-- man/axe-xrf.Rd | 2 man/butcher-package.Rd | 6 man/new_model_butcher.Rd | 11 + tests/testthat/_snaps/new.md |only tests/testthat/_snaps/rsample.md |only tests/testthat/helper-objects.R | 6 tests/testthat/test-bart.R | 18 +- tests/testthat/test-earth.R | 12 - tests/testthat/test-elnet.R | 7 tests/testthat/test-flexsurvreg.R | 29 ++- tests/testthat/test-gam.R | 6 tests/testthat/test-gausspr.R | 17 -- tests/testthat/test-glmnet.R | 4 tests/testthat/test-ipred.R | 100 ++++++++++--- tests/testthat/test-klaR.R | 8 - tests/testthat/test-kproto.R | 3 tests/testthat/test-ksvm.R | 8 - tests/testthat/test-lm.R | 9 - tests/testthat/test-mass.R | 40 ++++- tests/testthat/test-mda.R | 32 ++-- tests/testthat/test-mixOmics.R | 27 ++- tests/testthat/test-multnet.R | 17 +- tests/testthat/test-new.R |only tests/testthat/test-nnet.R | 6 tests/testthat/test-randomForest.R | 30 ++-- tests/testthat/test-ranger.R | 40 +++-- tests/testthat/test-recipe.R | 266 ++++++++++++++++++++---------------- tests/testthat/test-rpart.R | 19 +- tests/testthat/test-rsample.R |only tests/testthat/test-sclass.R | 5 tests/testthat/test-spark.R | 74 +++++----- tests/testthat/test-survreg.R | 15 +- tests/testthat/test-tabnet_fit.R |only tests/testthat/test-train.R | 48 +++--- tests/testthat/test-train.recipe.R | 24 ++- tests/testthat/test-ui.R | 13 - tests/testthat/test-xgb.R | 104 +++++++++----- tests/testthat/test-xrf.R | 41 ++++- vignettes/available-axe-methods.Rmd | 12 - vignettes/butcher.Rmd | 8 - 127 files changed, 1340 insertions(+), 834 deletions(-)