Title: High-Level Functions for Tabulating, Charting and Reporting
Survey Data
Description: Craft polished tables and plots in Markdown reports.
Simply choose whether to treat your data as counts or metrics,
and the package will automatically generate well-designed default tables and plots for you.
Boiled down to the basics, with labeling features and simple interactive reports.
All functions are 'tidyverse' compatible.
Author: Jakob Juenger [aut, cre, cph] ,
Henrieke Kotthoff [aut, ctb],
Chantal Gaertner [ctb]
Maintainer: Jakob Juenger <jakob.juenger@uni-muenster.de>
Diff between volker versions 3.1.0 dated 2025-04-05 and 3.2.0 dated 2025-10-10
volker-3.1.0/volker/man/dot-density_mode.Rd |only volker-3.1.0/volker/man/dot-effect_npmi.Rd |only volker-3.2.0/volker/DESCRIPTION | 15 volker-3.2.0/volker/MD5 | 192 + volker-3.2.0/volker/NAMESPACE | 11 volker-3.2.0/volker/NEWS.md | 103 - volker-3.2.0/volker/R/agree.R |only volker-3.2.0/volker/R/checks.R | 53 volker-3.2.0/volker/R/clean.R | 149 + volker-3.2.0/volker/R/cluster.R | 7 volker-3.2.0/volker/R/config.R | 14 volker-3.2.0/volker/R/data.R | 15 volker-3.2.0/volker/R/effects.R | 772 +++++-- volker-3.2.0/volker/R/labels.R | 48 volker-3.2.0/volker/R/model.R | 383 +++ volker-3.2.0/volker/R/plots.R | 680 ++++-- volker-3.2.0/volker/R/report.R | 99 - volker-3.2.0/volker/R/skim.R | 2 volker-3.2.0/volker/R/tables.R | 175 + volker-3.2.0/volker/R/utils.R | 21 volker-3.2.0/volker/README.md | 214 +- volker-3.2.0/volker/data/chatgpt.rda |binary volker-3.2.0/volker/inst/doc/introduction.R | 286 +- volker-3.2.0/volker/inst/doc/introduction.Rmd | 1032 ++++++---- volker-3.2.0/volker/inst/doc/introduction.html | 721 +++---- volker-3.2.0/volker/man/VLKR_NA_OMIT.Rd |only volker-3.2.0/volker/man/VLKR_PLOT_LABELWRAP.Rd | 2 volker-3.2.0/volker/man/add_model.Rd |only volker-3.2.0/volker/man/adjust_p.Rd |only volker-3.2.0/volker/man/agree_tab.Rd |only volker-3.2.0/volker/man/chatgpt.Rd | 15 volker-3.2.0/volker/man/check_is_param.Rd | 1 volker-3.2.0/volker/man/check_nonequal_columns.Rd |only volker-3.2.0/volker/man/data_onehot.Rd |only volker-3.2.0/volker/man/data_rm_missings.Rd | 6 volker-3.2.0/volker/man/data_round.Rd |only volker-3.2.0/volker/man/diagnostics_cooksd.Rd |only volker-3.2.0/volker/man/diagnostics_qq.Rd |only volker-3.2.0/volker/man/diagnostics_resid_fitted.Rd |only volker-3.2.0/volker/man/diagnostics_scale_location.Rd |only volker-3.2.0/volker/man/dot-agree_classification.Rd |only volker-3.2.0/volker/man/dot-agree_confusion.Rd |only volker-3.2.0/volker/man/dot-agree_items.Rd |only volker-3.2.0/volker/man/dot-agree_reliability.Rd |only volker-3.2.0/volker/man/dot-attr_setcolumn.Rd |only volker-3.2.0/volker/man/dot-effect_correlations.Rd | 33 volker-3.2.0/volker/man/dot-get_density_mode.Rd |only volker-3.2.0/volker/man/dot-get_plot_limits.Rd |only volker-3.2.0/volker/man/dot-knit_shorten.Rd |only volker-3.2.0/volker/man/dot-knit_table.Rd | 13 volker-3.2.0/volker/man/dot-pair_agreement.Rd |only volker-3.2.0/volker/man/dot-pair_disagreement.Rd |only volker-3.2.0/volker/man/dot-plot_bars.Rd | 8 volker-3.2.0/volker/man/dot-plot_heatmap.Rd |only volker-3.2.0/volker/man/dot-report_agr.Rd |only volker-3.2.0/volker/man/dot-report_mdl.Rd |only volker-3.2.0/volker/man/dot-to_vlkr_plot.Rd | 4 volker-3.2.0/volker/man/effect_counts_items.Rd | 14 volker-3.2.0/volker/man/effect_counts_items_grouped.Rd | 31 volker-3.2.0/volker/man/effect_counts_items_grouped_items.Rd | 34 volker-3.2.0/volker/man/effect_counts_one_grouped.Rd | 28 volker-3.2.0/volker/man/effect_metrics_items.Rd | 14 volker-3.2.0/volker/man/effect_metrics_items_cor.Rd | 6 volker-3.2.0/volker/man/effect_metrics_items_cor_items.Rd | 6 volker-3.2.0/volker/man/effect_metrics_items_grouped.Rd | 6 volker-3.2.0/volker/man/effect_metrics_one_cor.Rd | 6 volker-3.2.0/volker/man/effect_metrics_one_grouped.Rd | 6 volker-3.2.0/volker/man/figures/youtube.png |only volker-3.2.0/volker/man/get_baseline.Rd | 23 volker-3.2.0/volker/man/get_betas.Rd |only volker-3.2.0/volker/man/get_correlation.Rd |only volker-3.2.0/volker/man/get_npmi.Rd |only volker-3.2.0/volker/man/get_prefix.Rd | 15 volker-3.2.0/volker/man/get_title.Rd | 2 volker-3.2.0/volker/man/labs_prefix.Rd |only volker-3.2.0/volker/man/map_label.Rd |only volker-3.2.0/volker/man/model_metrics_plot.Rd | 7 volker-3.2.0/volker/man/model_metrics_tab.Rd | 22 volker-3.2.0/volker/man/plot_counts_items_grouped.Rd | 5 volker-3.2.0/volker/man/plot_counts_items_grouped_items.Rd | 22 volker-3.2.0/volker/man/plot_counts_one_grouped.Rd | 9 volker-3.2.0/volker/man/plot_metrics_items_cor_items.Rd | 3 volker-3.2.0/volker/man/plot_metrics_one_cor.Rd | 3 volker-3.2.0/volker/man/report_counts.Rd | 10 volker-3.2.0/volker/man/report_metrics.Rd | 16 volker-3.2.0/volker/man/tab_counts_items_cor.Rd | 2 volker-3.2.0/volker/man/tab_counts_items_grouped.Rd | 2 volker-3.2.0/volker/man/tab_counts_items_grouped_items.Rd | 12 volker-3.2.0/volker/man/tab_metrics_items_grouped_items.Rd | 4 volker-3.2.0/volker/man/vlkr_colors_contrast.Rd |only volker-3.2.0/volker/man/vlkr_colors_discrete.Rd | 4 volker-3.2.0/volker/man/vlkr_colors_polarized.Rd | 4 volker-3.2.0/volker/man/vlkr_colors_sequential.Rd | 4 volker-3.2.0/volker/tests/testthat/_markdown/plots.Rmd | 169 + volker-3.2.0/volker/tests/testthat/_markdown/tables.Rmd | 7 volker-3.2.0/volker/tests/testthat/_snaps/clean.md | 221 +- volker-3.2.0/volker/tests/testthat/_snaps/clusters.md | 57 volker-3.2.0/volker/tests/testthat/_snaps/effects.md | 751 +++++-- volker-3.2.0/volker/tests/testthat/_snaps/factors.md | 135 - volker-3.2.0/volker/tests/testthat/_snaps/idx.md | 195 + volker-3.2.0/volker/tests/testthat/_snaps/labels.md | 411 ++-- volker-3.2.0/volker/tests/testthat/_snaps/skim.md | 94 volker-3.2.0/volker/tests/testthat/_snaps/tables.md | 1079 ++++++----- volker-3.2.0/volker/tests/testthat/test-checks.R | 15 volker-3.2.0/volker/tests/testthat/test-clean.R | 11 volker-3.2.0/volker/tests/testthat/test-clusters.R | 32 volker-3.2.0/volker/tests/testthat/test-effects.R | 240 ++ volker-3.2.0/volker/tests/testthat/test-factors.R | 21 volker-3.2.0/volker/tests/testthat/test-idx.R | 13 volker-3.2.0/volker/tests/testthat/test-labels.R | 3 volker-3.2.0/volker/tests/testthat/test-plots.R | 229 +- volker-3.2.0/volker/tests/testthat/test-tables.R | 328 ++- volker-3.2.0/volker/tests/testthat/test-theme.R | 104 - volker-3.2.0/volker/vignettes/introduction.Rmd | 1032 ++++++---- 114 files changed, 7191 insertions(+), 3350 deletions(-)
Title: Variable Selection for Clustering and Classification
Description: Performs variable selection/feature reduction under a clustering or
classification framework. In particular, it can be used in an automated fashion
using mixture model-based methods ('teigen' and 'mclust' are currently supported).
Can account for mixtures of non-Gaussian distributions via Manly transform (via 'ManlyMix').
See Andrews and McNicholas (2014) <doi:10.1007/s00357-013-9139-2> and Neal and McNicholas (2023)
<doi:10.48550/arXiv.2305.16464>.
Author: Jeffrey L. Andrews [aut],
Mackenzie R. Neal [aut, cre],
Paul D. McNicholas [aut]
Maintainer: Mackenzie R. Neal <nealm6@mcmaster.ca>
Diff between vscc versions 0.7 dated 2023-10-17 and 0.8 dated 2025-10-10
ChangeLog | 5 +++++ DESCRIPTION | 19 ++++++++++--------- MD5 | 14 +++++++------- R/vsccmanly.R | 2 +- inst/CITATION | 6 +++--- man/vscc-package.Rd | 6 +++--- man/vscc.Rd | 2 +- man/vsccmanly.Rd | 2 +- 8 files changed, 31 insertions(+), 25 deletions(-)
Title: Data from all Seasons of Survivor (US) TV Series in Tidy Format
Description: Datasets detailing the results, castaways, and events of each
season of Survivor for the US, Australia, South Africa, New Zealand, and the
UK. This includes details on the cast, voting history, immunity and reward
challenges, jury votes, boot order, advantage details, and episode ratings.
Use this for analysis of trends and statistics of the game.
Author: Daniel Oehm [aut, cre],
Carly Levitz [ctb]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between survivoR versions 2.3.7 dated 2025-09-09 and 2.3.8 dated 2025-10-10
DESCRIPTION | 6 MD5 | 58 ++-- NEWS.md | 6 R/datasets.R | 5 README.md | 464 ++++++++++++++++++++++++++++----------- data/advantage_details.rda |binary data/advantage_movement.rda |binary data/auction_details.rda |binary data/boot_mapping.rda |binary data/boot_order.rda |binary data/castaway_details.rda |binary data/castaway_scores.rda |binary data/castaways.rda |binary data/challenge_description.rda |binary data/challenge_results.rda |binary data/challenge_summary.rda |binary data/confessionals.rda |binary data/episodes.rda |binary data/journeys.rda |binary data/jury_votes.rda |binary data/season_summary.rda |binary data/survivor_auction.rda |binary data/tribe_colours.rda |binary data/tribe_mapping.rda |binary data/viewers.rda |binary data/vote_history.rda |binary man/castaway_scores.Rd | 3 man/journeys.Rd | 2 tests/testthat/tests-functions.R | 1 tests/testthat/tests.R | 27 +- 30 files changed, 413 insertions(+), 159 deletions(-)
Title: 'RStudio' Package Manager
Description: Enables binary package installations on Linux distributions.
Provides access to 'RStudio' public repositories at
<https://packagemanager.posit.co>, and transparent management of
system requirements without administrative privileges. Currently supported
distributions are 'CentOS' / 'RHEL', and several 'RHEL' derivatives
('Rocky Linux', 'AlmaLinux', 'Oracle Linux', and 'Amazon Linux'),
'openSUSE' / 'SLES', 'Debian', and 'Ubuntu' LTS.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between rspm versions 0.6.1 dated 2024-10-29 and 0.7.0 dated 2025-10-10
rspm-0.6.1/rspm/R/userdir.R |only rspm-0.6.1/rspm/inst/COPYRIGHTS |only rspm-0.7.0/rspm/DESCRIPTION | 23 +++++++++++------------ rspm-0.7.0/rspm/LICENSE | 2 +- rspm-0.7.0/rspm/MD5 | 16 +++++++--------- rspm-0.7.0/rspm/NEWS.md | 6 ++++++ rspm-0.7.0/rspm/R/rspm.R | 4 ++-- rspm-0.7.0/rspm/R/utils.R | 8 ++------ rspm-0.7.0/rspm/README.md | 10 +++++----- rspm-0.7.0/rspm/man/rspm-package.Rd | 4 ++-- 10 files changed, 36 insertions(+), 37 deletions(-)
Title: Fast Library for Number Theory
Description: An R interface to 'FLINT' <https://flintlib.org/>, a C library for
number theory. 'FLINT' extends GNU 'MPFR' <https://www.mpfr.org/>
and GNU 'MP' <https://gmplib.org/> with support for operations on
standard rings (the integers, the integers modulo n, finite
fields, the rational, p-adic, real, and complex numbers) as well
as matrices and polynomials over rings. 'FLINT' implements
midpoint-radius interval arithmetic, also known as ball
arithmetic, in the real and complex numbers, enabling computation
in arbitrary precision with rigorous propagation of rounding and
other errors; see Johansson (2017) <doi:10.1109/TC.2017.2690633>.
Finally, 'FLINT' provides ball arithmetic implementations of many
special mathematical functions, with high coverage of reference
works such as the NIST Digital Library of Mathematical Functions
<https://dlmf.nist.gov/>. The R interface defines S4 classes,
generic functions, and methods for representation and basic
operations as [...truncated...]
Author: Mikael Jagan [aut, cre] ,
Martin Maechler [ctb]
Maintainer: Mikael Jagan <jaganmn@mcmaster.ca>
Diff between flint versions 0.1.1 dated 2025-10-08 and 0.1.2 dated 2025-10-10
DESCRIPTION | 8 ++--- MD5 | 15 +++++---- NAMESPACE | 2 - R/flint.R | 32 ++++++++++++++++++-- R/foreign.R |only R/zzz.R | 91 ----------------------------------------------------------- configure | 18 +++++------ configure.ac | 2 - inst/NEWS.Rd | 12 +++++++ 9 files changed, 65 insertions(+), 115 deletions(-)
More information about WeibullModiAMR at CRAN
Permanent link
Title: Reversal Association Pattern Analysis for Categorical Data
Description: Implements reversal association pattern analysis for categorical data. Detects sub-tables exhibiting reversal associations in contingency tables, provides visualization tools, and supports simulation-based validation for complex I × J tables.
Author: Subbiah M [aut, cre]
Maintainer: Subbiah M <sisufive@gmail.com>
This is a re-admission after prior archival of version 1.1 dated 2013-05-02
Diff between RAP versions 1.1 dated 2013-05-02 and 1.2.2 dated 2025-10-10
RAP-1.1/RAP/man/RAP-package.Rd |only RAP-1.2.2/RAP/DESCRIPTION | 24 +++-- RAP-1.2.2/RAP/MD5 | 9 -- RAP-1.2.2/RAP/NAMESPACE | 10 +- RAP-1.2.2/RAP/R/fnRAP.R | 166 +++++++++++++++++++++++------------------ RAP-1.2.2/RAP/man/fnRAP.Rd | 54 +++++++------ 6 files changed, 146 insertions(+), 117 deletions(-)
Title: 'shiny' Application for Biological Dosimetry
Description: A tool to perform all different statistical tests and calculations
needed by Biological dosimetry Laboratories. Detailed documentation is
available in <https://biodosetools-team.github.io/documentation/>.
Author: Alfredo Hernandez [aut] ,
Anna Frances-Abellan [aut, cre] ,
David Endesfelder [aut],
Pere Puig [aut]
Maintainer: Anna Frances-Abellan <anna.frances@uab.cat>
This is a re-admission after prior archival of version 3.6.1 dated 2022-11-16
Diff between biodosetools versions 3.6.1 dated 2022-11-16 and 3.6.2 dated 2025-10-10
biodosetools-3.6.1/biodosetools/man/biodosetools.Rd |only biodosetools-3.6.1/biodosetools/vignettes/figures/screenshot-translocations-fit-02.png |only biodosetools-3.6.1/biodosetools/vignettes/figures/screenshot-translocations-fit-03.png |only biodosetools-3.6.2/biodosetools/DESCRIPTION | 39 biodosetools-3.6.2/biodosetools/MD5 | 369 - biodosetools-3.6.2/biodosetools/NAMESPACE | 113 biodosetools-3.6.2/biodosetools/NEWS.md | 1250 +-- biodosetools-3.6.2/biodosetools/R/app_config.R | 72 biodosetools-3.6.2/biodosetools/R/app_server.R | 120 biodosetools-3.6.2/biodosetools/R/app_ui.R | 500 - biodosetools-3.6.2/biodosetools/R/biodosetools-package.R | 38 biodosetools-3.6.2/biodosetools/R/calcs_aberrations.R | 439 - biodosetools-3.6.2/biodosetools/R/calcs_characteristic_limits.R |only biodosetools-3.6.2/biodosetools/R/calcs_estimation.R | 1612 ++-- biodosetools-3.6.2/biodosetools/R/calcs_fitting.R | 1348 ++-- biodosetools-3.6.2/biodosetools/R/calcs_interlab.R |only biodosetools-3.6.2/biodosetools/R/calcs_mixed.R |only biodosetools-3.6.2/biodosetools/R/calcs_translocations.R | 239 biodosetools-3.6.2/biodosetools/R/mod_estimation_dicent_ui.R | 1405 ++-- biodosetools-3.6.2/biodosetools/R/mod_estimation_micro_ui.R | 1311 ++- biodosetools-3.6.2/biodosetools/R/mod_estimation_server.R | 3347 +++++----- biodosetools-3.6.2/biodosetools/R/mod_estimation_trans_ui.R | 1889 ++--- biodosetools-3.6.2/biodosetools/R/mod_fitting_dicent_ui.R | 914 +- biodosetools-3.6.2/biodosetools/R/mod_fitting_micro_ui.R | 914 +- biodosetools-3.6.2/biodosetools/R/mod_fitting_server.R | 1086 +-- biodosetools-3.6.2/biodosetools/R/mod_fitting_trans_ui.R | 1208 +-- biodosetools-3.6.2/biodosetools/R/mod_interlab_server.R |only biodosetools-3.6.2/biodosetools/R/mod_interlab_ui.R |only biodosetools-3.6.2/biodosetools/R/mod_limits_dicent_ui.R |only biodosetools-3.6.2/biodosetools/R/mod_limits_server.R |only biodosetools-3.6.2/biodosetools/R/mod_mixed_server.R |only biodosetools-3.6.2/biodosetools/R/mod_mixed_ui.R |only biodosetools-3.6.2/biodosetools/R/mod_trans_server.R | 278 biodosetools-3.6.2/biodosetools/R/run_app.R | 34 biodosetools-3.6.2/biodosetools/R/utils_estimation.R | 1011 +-- biodosetools-3.6.2/biodosetools/R/utils_fitting.R | 176 biodosetools-3.6.2/biodosetools/R/utils_interlab.R |only biodosetools-3.6.2/biodosetools/R/utils_limits.R |only biodosetools-3.6.2/biodosetools/R/utils_mixed.R |only biodosetools-3.6.2/biodosetools/README.md | 182 biodosetools-3.6.2/biodosetools/build/partial.rdb |binary biodosetools-3.6.2/biodosetools/build/vignette.rds |binary biodosetools-3.6.2/biodosetools/inst/CITATION | 36 biodosetools-3.6.2/biodosetools/inst/app/help/estimation/dose_assessment.md | 12 biodosetools-3.6.2/biodosetools/inst/app/help/interlab |only biodosetools-3.6.2/biodosetools/inst/app/help/limits |only biodosetools-3.6.2/biodosetools/inst/app/help/mixed |only biodosetools-3.6.2/biodosetools/inst/app/help/save/estimation_data_save_report.md | 29 biodosetools-3.6.2/biodosetools/inst/app/reports/estimation-report-docx.Rmd | 777 +- biodosetools-3.6.2/biodosetools/inst/app/reports/estimation-report-pdf.Rmd | 814 +- biodosetools-3.6.2/biodosetools/inst/app/reports/fitting-report-pdf.Rmd | 445 - biodosetools-3.6.2/biodosetools/inst/app/reports/interlab-report-pdf.Rmd |only biodosetools-3.6.2/biodosetools/inst/app/reports/mx-report-docx.Rmd |only biodosetools-3.6.2/biodosetools/inst/app/reports/mx-report-pdf.Rmd |only biodosetools-3.6.2/biodosetools/inst/app/www/about_body.md | 46 biodosetools-3.6.2/biodosetools/inst/doc/dicent-estimation.R | 179 biodosetools-3.6.2/biodosetools/inst/doc/dicent-estimation.Rmd | 268 biodosetools-3.6.2/biodosetools/inst/doc/dicent-estimation.html | 1018 +-- biodosetools-3.6.2/biodosetools/inst/doc/dicent-fitting.R | 100 biodosetools-3.6.2/biodosetools/inst/doc/dicent-fitting.Rmd | 196 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biodosetools-3.6.2/biodosetools/vignettes/trans-estimation.Rmd | 306 biodosetools-3.6.2/biodosetools/vignettes/trans-fitting.Rmd | 226 221 files changed, 17650 insertions(+), 15569 deletions(-)
Title: Dyad Ratios Algorithm
Description: Estimates the Dyad Ratios Algorithm for pooling and smoothing poll estimates. The Dyad Ratios Algorithm smooths both forward and backward in time over polling results allowing differences in both question type and polling house. The result is an estimate of a single latent variable that describes the systematic trend over time in the (noisy) polling results. See James A. Stimson (2018) <doi:10.1177/0759106318761614> and the package's vignette for more details.
Author: Dave Armstrong [cre],
James Stimson [aut]
Maintainer: Dave Armstrong <davearmstrong.ps@gmail.com>
Diff between DyadRatios versions 1.2 dated 2025-09-30 and 1.3 dated 2025-10-10
DESCRIPTION | 12 - MD5 | 20 - NAMESPACE | 8 R/boot_dr.R |only R/extract.R | 455 ++++++++++++++++++++++++++++++++++++++++- inst/doc/extract-vignette.R | 62 +++++ inst/doc/extract-vignette.Rmd | 95 ++++++++ inst/doc/extract-vignette.html | 396 +++++++++++++++++++++++------------ man/boot_dr.Rd |only man/extract.Rd | 9 man/summary.extract.Rd | 2 vignettes/extract-vignette.Rmd | 95 ++++++++ 12 files changed, 974 insertions(+), 180 deletions(-)
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 13. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood est [...truncated...]
Author: Anthony Hammond [aut, cre],
Environment Agency [ctb],
JBA Consulting [ctb]
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 1.0.1 dated 2025-10-08 and 1.0.2 dated 2025-10-10
DESCRIPTION | 6 MD5 | 4 tests/testthat/test-All.R |10996 ++++++++++++++++++++++------------------------ 3 files changed, 5501 insertions(+), 5505 deletions(-)
Title: Analysis of Spatial Stratified Heterogeneity
Description: Detecting spatial associations via spatial stratified heterogeneity, accounting for spatial dependencies, interpretability, complex interactions, and robust stratification. In addition, it supports the spatial stratified heterogeneity family described in Lv et al. (2025)<doi:10.1111/tgis.70032>.
Author: Wenbo Lv [aut, cre, cph] ,
Yangyang Lei [aut] ,
Fangmei Liu [aut] ,
Jianwu Yan [aut] ,
Yongze Song [aut] ,
Wufan Zhao [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between gdverse versions 1.3-3 dated 2025-04-02 and 1.5 dated 2025-10-10
gdverse-1.3-3/gdverse/vignettes/precompile.R |only gdverse-1.5/gdverse/DESCRIPTION | 25 gdverse-1.5/gdverse/MD5 | 76 - gdverse-1.5/gdverse/NEWS.md | 8 gdverse-1.5/gdverse/R/geodetector.R | 4 gdverse-1.5/gdverse/R/idsa.R | 2 gdverse-1.5/gdverse/R/r_interact_py.R | 36 gdverse-1.5/gdverse/R/rgd.R | 5 gdverse-1.5/gdverse/R/rid.R | 5 gdverse-1.5/gdverse/R/robustdisc.R | 6 gdverse-1.5/gdverse/R/zzz.R | 2 gdverse-1.5/gdverse/README.md | 2 gdverse-1.5/gdverse/build/vignette.rds |binary gdverse-1.5/gdverse/inst/CITATION | 2 gdverse-1.5/gdverse/inst/doc/gd.Rmd | 862 +++++++++--------- gdverse-1.5/gdverse/inst/doc/gd.html | 2 gdverse-1.5/gdverse/inst/doc/idsa.Rmd | 200 ++-- gdverse-1.5/gdverse/inst/doc/opgd.Rmd | 2 gdverse-1.5/gdverse/inst/doc/opgd.html | 2 gdverse-1.5/gdverse/inst/doc/rgdrid.Rmd | 34 gdverse-1.5/gdverse/inst/doc/rgdrid.html | 47 gdverse-1.5/gdverse/inst/doc/shegd.Rmd | 34 gdverse-1.5/gdverse/inst/doc/shegd.html | 34 gdverse-1.5/gdverse/inst/doc/spade.Rmd | 47 gdverse-1.5/gdverse/inst/doc/spade.html | 49 - gdverse-1.5/gdverse/inst/python/__pycache__ |only gdverse-1.5/gdverse/inst/python/cpd_disc.py | 80 - gdverse-1.5/gdverse/man/figures/gd/NTDs_map-1.png |binary gdverse-1.5/gdverse/man/figures/rgdrid/rgd_id-1.png |binary gdverse-1.5/gdverse/man/figures/rgdrid/rid_plot-1.png |binary gdverse-1.5/gdverse/man/rgd.Rd | 6 gdverse-1.5/gdverse/man/rid.Rd | 6 gdverse-1.5/gdverse/man/robust_disc.Rd | 6 gdverse-1.5/gdverse/vignettes/gd.Rmd | 862 +++++++++--------- gdverse-1.5/gdverse/vignettes/idsa.Rmd | 200 ++-- gdverse-1.5/gdverse/vignettes/opgd.Rmd | 2 gdverse-1.5/gdverse/vignettes/rgdrid.Rmd | 34 gdverse-1.5/gdverse/vignettes/rgdrid.Rmd.orig | 26 gdverse-1.5/gdverse/vignettes/shegd.Rmd | 34 gdverse-1.5/gdverse/vignettes/spade.Rmd | 47 40 files changed, 1313 insertions(+), 1476 deletions(-)
Title: An Interface Between the 'FSKX' Standard and 'R'
Description: Functions for importing, creating, editing and
exporting 'FSK' files <https://foodrisklabs.bfr.bund.de/fskx-food-safety-knowledge-exchange-format/>
using the 'R' programming environment. Furthermore, it enables users
to run simulations contained in the 'FSK' files and visualize the results.
Author: Alberto Garre [aut, cre],
Miguel de Alba Aparicio [aut],
Thomas Schueler [aut],
Pablo S. Fernandez [aut],
Matthias Filter [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between FSK2R versions 0.1.3 dated 2022-02-25 and 0.2.0 dated 2025-10-10
DESCRIPTION | 16 MD5 | 53 NAMESPACE | 40 NEWS.md | 46 R/create_fsk.R | 38 R/export_fsk.R | 390 ++++- R/getters.R | 88 - R/io_utils.R |only R/metadata_classes.R |only R/open_fsk.R | 217 ++- R/simulations.R | 484 +++++- build/vignette.rds |binary inst/CITATION | 21 inst/doc/basic_FSK2R.R | 240 +-- inst/doc/basic_FSK2R.Rmd | 29 inst/doc/basic_FSK2R.html | 2177 ++++++++++++++++--------------- man/FSKAuthor.Rd |only man/FSKDataBackground.Rd |only man/FSKGeneralInformation.Rd |only man/FSKMetadata.Rd |only man/FSKModelCategory.Rd |only man/FSKModelMath.Rd |only man/FSKParameter.Rd |only man/FSKReference.Rd |only man/FSKScope.Rd |only man/clean_empty_values.Rd |only man/clean_json_string.Rd |only man/create_fsk.Rd | 5 man/export_workspace.Rd |only man/extract_script_filenames_from_rdf.Rd |only man/get_simulations.Rd | 7 man/read_other_files.Rd | 4 man/run_all_simulations.Rd | 21 man/run_simulation.Rd | 29 vignettes/basic_FSK2R.Rmd | 29 35 files changed, 2443 insertions(+), 1491 deletions(-)
Title: Estimating Aboveground Biomass and Its Uncertainty in Tropical
Forests
Description: Contains functions for estimating above-ground biomass/carbon and its uncertainty in tropical forests. These functions allow to (1) retrieve and correct taxonomy, (2) estimate wood density and its uncertainty, (3) build height-diameter models, (4) manage tree and plot coordinates, (5) estimate above-ground biomass/carbon at stand level with associated uncertainty. To cite ‘BIOMASS’, please use citation(‘BIOMASS’). For more information, see Réjou-Méchain et al. (2017) <doi:10.1111/2041-210X.12753>.
Author: Maxime Rejou-Mechain [aut, dtc],
Guillaume Cornu [aut] ,
Dominique Lamonica [aut, cre],
Arthur Bailly [aut],
Arthur Pere [aut],
Ariane Tanguy [aut],
Jerome Chave [dtc],
Ted Feldpausch [dtc],
Philippe Verley [ctb],
Camille Piponiot [aut],
Bruno Heraul [...truncated...]
Maintainer: Dominique Lamonica <dominique.lamonica@ird.fr>
Diff between BIOMASS versions 2.2.4 dated 2025-05-19 and 2.2.4-1 dated 2025-10-10
BIOMASS-2.2.4-1/BIOMASS/DESCRIPTION | 8 BIOMASS-2.2.4-1/BIOMASS/MD5 | 42 BIOMASS-2.2.4-1/BIOMASS/build/partial.rdb |binary BIOMASS-2.2.4-1/BIOMASS/build/vignette.rds |binary BIOMASS-2.2.4-1/BIOMASS/inst/doc/Vignette_BIOMASS.R | 124 - BIOMASS-2.2.4-1/BIOMASS/inst/doc/Vignette_BIOMASS.html | 724 +++++---- BIOMASS-2.2.4-1/BIOMASS/inst/doc/Vignette_spatialized_trees_and_forest_stand_metrics.R | 16 BIOMASS-2.2.4-1/BIOMASS/inst/doc/Vignette_spatialized_trees_and_forest_stand_metrics.html | 759 +++++----- BIOMASS-2.2.4-1/BIOMASS/tests/testthat/_snaps/subplot_summary/subplot-summary-multiple-metrics-204.svg | 1 BIOMASS-2.2.4-1/BIOMASS/tests/testthat/_snaps/subplot_summary/subplot-summary-multiple-plot-201.svg | 1 BIOMASS-2.2.4-1/BIOMASS/tests/testthat/_snaps/subplot_summary/subplot-summary-multiple-plot-204.svg | 1 BIOMASS-2.2.4-1/BIOMASS/tests/testthat/_snaps/subplot_summary/subplot-summary-proj-coords.svg | 1 BIOMASS-2.2.4-1/BIOMASS/tests/testthat/_snaps/subplot_summary/subplot-summary-quantile.svg | 1 BIOMASS-2.2.4-1/BIOMASS/tests/testthat/_snaps/subplot_summary/subplot-summary-rel-coords.svg | 1 BIOMASS-2.2.4-1/BIOMASS/tests/testthat/test-check_coord_plot.R | 4 BIOMASS-2.2.4-1/BIOMASS/tests/testthat/test-modelHD.R | 3 BIOMASS-2.2.4-1/BIOMASS/tests/testthat/test-small_function.R | 10 BIOMASS-2.2.4-1/BIOMASS/tests/testthat/test-subplot_summary.R | 2 BIOMASS-2.2.4-1/BIOMASS/tests/testthat/test-summaryByPlot.R | 2 BIOMASS-2.2.4/BIOMASS/tests/testthat/_snaps/check_coord_plot |only BIOMASS-2.2.4/BIOMASS/tests/testthat/_snaps/modelHD |only 21 files changed, 992 insertions(+), 708 deletions(-)
Title: Generate Optimal Designs of Accelerated Life Test using
PSO-Based Algorithm
Description: A computationally efficient solution for generating optimal experimental designs in Accelerated Life Testing (ALT). Leveraging a Particle Swarm Optimization (PSO)-based hybrid algorithm, the package identifies optimal test plans that minimize estimation variance under specified failure models and stress profiles. For more detailed, see Lee et al. (2025), Optimal Robust Strategies for Accelerated Life Tests and Fatigue Testing of Polymer Composite Materials, submitted to Annals of Applied Statistics, <https://imstat.org/journals-and-publications/annals-of-applied-statistics/annals-of-applied-statistics-next-issues/>, and Hoang (2025), Model-Robust Minimax Design of Accelerated Life Tests via PSO-based Hybrid Algorithm, Master' Thesis, Unpublished.
Author: Hoai-Linh Hoang [aut, cre],
I-Chen Lee [aut],
Ping-Yang Chen [aut],
Ray-Bing Chen [aut],
Weng Kee Wong [aut]
Maintainer: Hoai-Linh Hoang <hoailinh.hoang17@gmail.com>
Diff between minimaxALT versions 1.0.1 dated 2025-09-15 and 1.0.2 dated 2025-10-10
minimaxALT-1.0.1/minimaxALT/tests/testthat/test_local_design.R |only minimaxALT-1.0.2/minimaxALT/DESCRIPTION | 8 - minimaxALT-1.0.2/minimaxALT/MD5 | 21 ++- minimaxALT-1.0.2/minimaxALT/NEWS.md |only minimaxALT-1.0.2/minimaxALT/R/common.R | 64 ++++++---- minimaxALT-1.0.2/minimaxALT/R/equivalence_theorem.R | 27 +++- minimaxALT-1.0.2/minimaxALT/R/minimaxALT-package.R | 26 ++-- minimaxALT-1.0.2/minimaxALT/inst |only minimaxALT-1.0.2/minimaxALT/man/check_equivalence_theorem.Rd | 11 + minimaxALT-1.0.2/minimaxALT/tests/testthat/test-check-equivalence-theorem.R |only minimaxALT-1.0.2/minimaxALT/tests/testthat/test-locally-optimal-design-1factor.R |only minimaxALT-1.0.2/minimaxALT/tests/testthat/test-locally-optimal-design-2factor.R |only 12 files changed, 104 insertions(+), 53 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column and row wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. References: a) Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>. b) Tsagris M. and Papadakis M. (2018). Forward regression in R: from the extreme slow to the extreme fast. Journal of Data Science, 16(4): 771--780. <doi:10.6339/JDS.201810_16(4).00006>. c) Chatzipantsiou C., Dimitriadis M., Papadakis M. and Tsagris M. (2020). Extremely Efficient Permutation and Bootstrap Hypothesis Tests Using Hypothesis Tests Using R. Journal of Modern Applied Statistical Methods, 18(2), eP2898. <doi:10.48550/arXiv.1806.10947>. d) Tsagris M., Papadakis M., Alenazi A. and Alzeley O. (2024). Computationally Efficient Outlier Detection for High-Dimensional Data Using the [...truncated...]
Author: Manos Papadakis [aut, cre, cph],
Michail Tsagris [aut],
Marios Dimitriadis [aut],
Stefanos Fafalios [aut],
Matteo Fasiolo [aut],
Morgan Jacob [ctb],
Giorgos Borboudakis [aut],
John Burkardt [aut],
Changliang Zou [aut]
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast versions 2.1.5.1 dated 2025-03-13 and 2.1.5.2 dated 2025-10-10
DESCRIPTION | 8 - MD5 | 42 ++++---- NEWS.md | 13 ++ R/regression_models.R | 2 R/variable_selection.R | 52 +++++++--- build/partial.rdb |binary inst/include/Rfast/Dist.h | 6 + inst/include/Rfast/assertions.hpp | 2 man/bic.corfsreg.Rd | 5 man/dcov.Rd | 3 src/Diag.cpp | 1 src/Makevars | 4 src/Makevars.win | 2 src/Sort.cpp | 1 src/cholesky.cpp | 1 src/col_statistical.cpp | 5 src/cts.cpp | 4 src/dista.cpp | 191 ++++++++++++++++++++------------------ src/gamma.cpp | 1 src/odds_helper.cpp | 1 src/spat_med.cpp | 2 src/system_files.h | 1 22 files changed, 198 insertions(+), 149 deletions(-)
Title: Import, Process, Analyse, and Calculate Rates from Respirometry
Data
Description: Provides a structural, reproducible workflow for the
processing and analysis of respirometry data. It contains analytical
functions and utilities for working with oxygen time-series to determine
respiration or oxygen production rates, and to make it easier to report and
share analyses. See Harianto et al. 2019 <doi:10.1111/2041-210X.13162>.
Author: Nicholas Carey [aut, cre],
Januar Harianto [aut]
Maintainer: Nicholas Carey <nicholascarey@gmail.com>
Diff between respR versions 2.3.3 dated 2024-05-10 and 2.3.4 dated 2025-10-10
DESCRIPTION | 12 +++--- MD5 | 64 +++++++++++++++++----------------- NEWS.md | 15 +++++-- R/auto_rate.R | 2 - R/format_time.R | 5 -- R/inspect.R | 15 +++---- README.md | 8 +--- man/format_time.Rd | 6 --- man/inspect.Rd | 13 ++---- tests/testthat/test-adjust_rate.R | 2 - tests/testthat/test-adjust_rate.ft.R | 2 - tests/testthat/test-auto_rate.R | 2 - tests/testthat/test-auto_rate.int.R | 10 ++--- tests/testthat/test-calc_rate.R | 2 - tests/testthat/test-calc_rate.bg.R | 2 - tests/testthat/test-calc_rate.ft.R | 2 - tests/testthat/test-calc_rate.int.R | 2 - tests/testthat/test-convert_DO.R | 2 - tests/testthat/test-convert_MR.R | 2 - tests/testthat/test-convert_rate.R | 2 - tests/testthat/test-convert_rate.ft.R | 2 - tests/testthat/test-convert_val.R | 2 - tests/testthat/test-format_time.R | 2 - tests/testthat/test-inspect.R | 2 - tests/testthat/test-inspect.ft.R | 2 - tests/testthat/test-oxy_crit.R | 2 - tests/testthat/test-select_rate.R | 2 - tests/testthat/test-select_rate.ft.R | 2 - tests/testthat/test-subsample.R | 2 - tests/testthat/test-subset_data.R | 2 - tests/testthat/test-unit_args.R | 2 - tests/testthat/test-utils.R | 2 - tests/testthat/test-various.R | 2 - 33 files changed, 94 insertions(+), 102 deletions(-)
Title: Nonparametric Estimation of Regression Models with
Factor-by-Curve Interactions
Description: A method for obtaining nonparametric estimates of regression models
with or without factor-by-curve interactions using local polynomial kernel
smoothers or splines. Additionally, a parametric model (allometric model) can be
estimated.
Author: Marta Sestelo [aut, cre] ,
Nora M. Villanueva [aut],
Javier Roca-Pardinas [aut]
Maintainer: Marta Sestelo <sestelo@uvigo.es>
Diff between npregfast versions 1.5.2 dated 2022-09-02 and 1.6.0 dated 2025-10-10
DESCRIPTION | 13 +++++++------ MD5 | 11 ++++++----- NEWS | 15 ++++++++++++++- R/npregfast-package.R | 1 + README.md | 8 ++++---- man/npregfast.Rd |only src/program2.f90 | 42 ++++++++++++++++++++++++++++++++++++++---- 7 files changed, 70 insertions(+), 20 deletions(-)
Title: Dose-Response Network Meta-Analysis in a Frequentist Way
Description: A set of functions providing the implementation of the network meta-analysis model with dose-response relationships, predicted values of the fitted model and dose-response plots in a frequentist way.
Author: Maria Petropoulou [aut, cre] ,
Guido Schwarzer [aut]
Maintainer: Maria Petropoulou <m.petropoulou.a@gmail.com>
Diff between netdose versions 0.6-0 dated 2025-04-17 and 0.7-2 dated 2025-10-10
netdose-0.6-0/netdose/NEWS |only netdose-0.7-2/netdose/DESCRIPTION | 21 - netdose-0.7-2/netdose/MD5 | 52 +- netdose-0.7-2/netdose/NAMESPACE | 36 + netdose-0.7-2/netdose/NEWS.md |only netdose-0.7-2/netdose/R/anesthesia.R | 120 +++-- netdose-0.7-2/netdose/R/antidepressants.R | 46 +- netdose-0.7-2/netdose/R/dotplot.R |only netdose-0.7-2/netdose/R/meta-chk.R | 15 netdose-0.7-2/netdose/R/multiarm.R | 12 netdose-0.7-2/netdose/R/netdose-internal.R | 193 ++++----- netdose-0.7-2/netdose/R/netdose-package.R | 41 + netdose-0.7-2/netdose/R/netdose.R | 501 ++++++++++++------------ netdose-0.7-2/netdose/R/nma_dose.R | 77 +-- netdose-0.7-2/netdose/R/plot.netdose.R | 443 ++++++++++----------- netdose-0.7-2/netdose/R/predict.netdose.R | 145 +++--- netdose-0.7-2/netdose/R/prepare.R | 120 ----- netdose-0.7-2/netdose/R/print.netdose.R | 452 ++++++++++----------- netdose-0.7-2/netdose/R/print.predict.netdose.R | 13 netdose-0.7-2/netdose/R/setref.R | 2 netdose-0.7-2/netdose/R/setseq.R | 2 netdose-0.7-2/netdose/man/anesthesia.Rd | 118 +++-- netdose-0.7-2/netdose/man/antidepressants.Rd | 44 +- netdose-0.7-2/netdose/man/dotplot.Rd |only netdose-0.7-2/netdose/man/netdose-package.Rd | 24 - netdose-0.7-2/netdose/man/netdose.Rd | 169 ++++---- netdose-0.7-2/netdose/man/plot.netdose.Rd | 102 ++-- netdose-0.7-2/netdose/man/predict.netdose.Rd | 49 +- netdose-0.7-2/netdose/man/print.netdose.Rd | 14 29 files changed, 1422 insertions(+), 1389 deletions(-)
Title: Laplace Factor Model Analysis and Evaluation
Description: Enables the generation of Laplace factor models across diverse Laplace distributions and facilitates the application of Sparse Online Principal Component (SOPC), Incremental Principal Component (IPC), Perturbation Principal Component (PPC), Stochastic Approximation Principal Component (SAPC), Sparse Principal Component (SPC) and other PC methods and Farm Test methods to these models. Evaluates the efficacy of these methods within the context of Laplace factor models by scrutinizing parameter estimation accuracy, mean square error, and the degree of sparsity.
Author: Guangbao Guo [aut, cre],
Siqi Liu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between LFM versions 0.3.1 dated 2025-06-11 and 0.3.2 dated 2025-10-10
LFM-0.3.1/LFM/R/FanPC_LFM.R |only LFM-0.3.1/LFM/R/Ftest_LFM.R |only LFM-0.3.1/LFM/R/GulPC_LFM.R |only LFM-0.3.1/LFM/R/IPC_LFM.R |only LFM-0.3.1/LFM/R/OPC_LFM.R |only LFM-0.3.1/LFM/R/PC1_LFM.R |only LFM-0.3.1/LFM/R/PC2_LFM.R |only LFM-0.3.1/LFM/R/PPC1_LFM.R |only LFM-0.3.1/LFM/R/PPC2_LFM.R |only LFM-0.3.1/LFM/R/SAPC_LFM.R |only LFM-0.3.1/LFM/R/SOPC_LFM.R |only LFM-0.3.1/LFM/R/SPC_LFM.R |only LFM-0.3.1/LFM/man/FanPC_LFM.Rd |only LFM-0.3.1/LFM/man/Ftest_LFM.Rd |only LFM-0.3.1/LFM/man/GulPC_LFM.Rd |only LFM-0.3.1/LFM/man/IPC_LFM.Rd |only LFM-0.3.1/LFM/man/OPC_LFM.Rd |only LFM-0.3.1/LFM/man/PC1_LFM.Rd |only LFM-0.3.1/LFM/man/PC2_LFM.Rd |only LFM-0.3.1/LFM/man/PPC1_LFM.Rd |only LFM-0.3.1/LFM/man/PPC2_LFM.Rd |only LFM-0.3.1/LFM/man/SAPC_LFM.Rd |only LFM-0.3.1/LFM/man/SOPC_LFM.Rd |only LFM-0.3.1/LFM/man/SPC_LFM.Rd |only LFM-0.3.2/LFM/DESCRIPTION | 12 ++++----- LFM-0.3.2/LFM/MD5 | 52 ++++++++++++++++++++--------------------- LFM-0.3.2/LFM/NAMESPACE | 31 ++++++++++-------------- LFM-0.3.2/LFM/R/FanPC.R |only LFM-0.3.2/LFM/R/Ftest.R |only LFM-0.3.2/LFM/R/GulPC.R |only LFM-0.3.2/LFM/R/IPC.R |only LFM-0.3.2/LFM/R/OPC.R |only LFM-0.3.2/LFM/R/PC1.R |only LFM-0.3.2/LFM/R/PC2.R |only LFM-0.3.2/LFM/R/PPC1.R |only LFM-0.3.2/LFM/R/PPC2.R |only LFM-0.3.2/LFM/R/SAPC.R |only LFM-0.3.2/LFM/R/SOPC.R |only LFM-0.3.2/LFM/R/SPC.R |only LFM-0.3.2/LFM/man/FanPC.Rd |only LFM-0.3.2/LFM/man/Ftest.Rd |only LFM-0.3.2/LFM/man/GulPC.Rd |only LFM-0.3.2/LFM/man/IPC.Rd |only LFM-0.3.2/LFM/man/OPC.Rd |only LFM-0.3.2/LFM/man/PC1.Rd |only LFM-0.3.2/LFM/man/PC2.Rd |only LFM-0.3.2/LFM/man/PPC1.Rd |only LFM-0.3.2/LFM/man/PPC2.Rd |only LFM-0.3.2/LFM/man/SAPC.Rd |only LFM-0.3.2/LFM/man/SOPC.Rd |only LFM-0.3.2/LFM/man/SPC.Rd |only 51 files changed, 45 insertions(+), 50 deletions(-)
Title: Implementation of the 3D Alpha-Shape for the Reconstruction of
3D Sets from a Point Cloud
Description: Implementation in R of the alpha-shape of a finite set of points in the three-dimensional space. The alpha-shape generalizes the convex hull and allows to recover the shape of non-convex and even non-connected sets in 3D, given a random sample of points taken into it. Besides the computation of the alpha-shape, this package provides users with functions to compute the volume of the alpha-shape, identify the connected components and facilitate the three-dimensional graphical visualization of the estimated set.
Author: Beatriz Pateiro-Lopez [aut, cre],
Thomas Lafarge [aut]
Maintainer: Beatriz Pateiro-Lopez <beatriz.pateiro@usc.es>
Diff between alphashape3d versions 1.3.2 dated 2023-01-24 and 1.3.3 dated 2025-10-10
alphashape3d-1.3.2/alphashape3d/README.md |only alphashape3d-1.3.3/alphashape3d/DESCRIPTION | 17 ++++++++----- alphashape3d-1.3.3/alphashape3d/MD5 | 13 ++++----- alphashape3d-1.3.3/alphashape3d/man/components_ashape3d.Rd | 4 +-- alphashape3d-1.3.3/alphashape3d/man/inashape3d.Rd | 4 +-- alphashape3d-1.3.3/alphashape3d/man/plot.ashape3d.Rd | 10 +++---- alphashape3d-1.3.3/alphashape3d/man/surfaceNormals.Rd | 6 ++-- alphashape3d-1.3.3/alphashape3d/man/volume_ashape3d.Rd | 4 +-- 8 files changed, 31 insertions(+), 27 deletions(-)
Title: Customizable China Map Visualizations
Description: A 'ggplot2' extension for visualizing China’s map, offering customizable projections, boundary styles, and buffer zones for thematic maps.
Suitable for spatial data analysis and enhancing map visualization with flexible styling options.
Author: Liang Ren [aut, cre]
Maintainer: Liang Ren <rl23@mails.tsinghua.edu.cn>
Diff between ggmapcn versions 0.1.2 dated 2025-01-14 and 0.2.0 dated 2025-10-10
DESCRIPTION | 15 - MD5 | 29 +- NAMESPACE | 39 +++ NEWS.md |only R/annotation_compass.R |only R/annotation_scalebar.R |only R/check_geodata.R | 374 ++++++++++++++++++++++++++------------ R/compass_styles.R |only R/geom_boundary_cn.R | 224 +++++++++++++--------- R/geom_mapcn.R | 193 +++++++++++-------- R/ggmapcn-package.R |only inst/doc/Adding_Basic_Map.html | 18 - inst/doc/Adding_Spatial_Data.html | 18 - man/annotation_compass.Rd |only man/annotation_scalebar.Rd |only man/check_geodata.Rd | 85 +++++++- man/compass-styles.Rd |only man/geom_boundary_cn.Rd | 115 +++++++---- man/geom_mapcn.Rd | 72 ++++--- man/ggmapcn-package.Rd |only 20 files changed, 756 insertions(+), 426 deletions(-)
Title: Spatial Point Patterns Analysis
Description: Perform first- and second-order multi-scale analyses derived from Ripley K-function (Ripley B. D. (1977) <doi:10.1111/j.2517-6161.1977.tb01615.x>), for univariate,
multivariate and marked mapped data in rectangular, circular or irregular shaped sampling windows, with tests of
statistical significance based on Monte Carlo simulations.
Author: Raphael Pelissier [aut],
Francois Goreaud [aut],
Philippe Verley [ctb],
Dominique Lamonica [cre]
Maintainer: Dominique Lamonica <dominique.lamonica@ird.fr>
Diff between ads versions 1.5-10 dated 2023-12-11 and 1.5-11 dated 2025-10-10
DESCRIPTION | 31 ++++++++++++++++++++----------- MD5 | 12 ++++++------ R/fads.R | 4 ++-- inst/CITATION | 36 ++++++++++++++++++++---------------- man/kdfun.Rd | 8 ++++---- man/kmfun.Rd | 4 ++-- man/krfun.Rd | 4 ++-- 7 files changed, 56 insertions(+), 43 deletions(-)
Title: Embedded JavaScript and WebAssembly Engine for R
Description: An R interface to V8 <https://v8.dev>: Google's open source JavaScript
and WebAssembly engine. This package can be compiled either with V8 or NodeJS
when built as a shared library.
Author: Jeroen Ooms [aut, cre] ,
George Stagg [ctb] ,
Jan Marvin Garbuszus [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between V8 versions 8.0.0 dated 2025-09-26 and 8.0.1 dated 2025-10-10
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS | 4 ++++ build/partial.rdb |binary inst/doc/npm.html | 4 ++-- inst/doc/v8_intro.html | 6 +++--- src/Makevars.win | 2 +- src/bindings.cpp | 3 +++ tools/winlibs.R | 6 +++--- 9 files changed, 29 insertions(+), 22 deletions(-)
Title: Cleans and Normalizes FLUOstar DBF and DAT Files from 'Liposome'
Flux Assays
Description: Cleans and Normalizes FLUOstar DBF and DAT Files obtained from liposome flux assays. Users should verify extended usage of the package on files from other assay types.
Author: Tingwei Adeck [aut, cre, cph] ,
Tesla Adeck [cph],
Amina Adeck [cph]
Maintainer: Tingwei Adeck <awesome.tingwei@outlook.com>
Diff between normfluodbf versions 2.0.0 dated 2024-09-27 and 2.0.3 dated 2025-10-10
normfluodbf-2.0.0/normfluodbf/man/demo.Rd |only normfluodbf-2.0.3/normfluodbf/DESCRIPTION | 23 - normfluodbf-2.0.3/normfluodbf/MD5 | 100 +++- normfluodbf-2.0.3/normfluodbf/NAMESPACE | 15 normfluodbf-2.0.3/normfluodbf/NEWS.md | 14 normfluodbf-2.0.3/normfluodbf/R/main.R | 174 ++++++-- normfluodbf-2.0.3/normfluodbf/R/normfluodbf-package.R | 2 normfluodbf-2.0.3/normfluodbf/R/normfluodbf_utils.R | 209 +++++++++- normfluodbf-2.0.3/normfluodbf/R/plate.R | 11 normfluodbf-2.0.3/normfluodbf/R/plate_data.R | 9 normfluodbf-2.0.3/normfluodbf/R/plot.R | 5 normfluodbf-2.0.3/normfluodbf/R/shiny.R | 33 + normfluodbf-2.0.3/normfluodbf/R/shiny_utils.R |only normfluodbf-2.0.3/normfluodbf/R/subset.R | 1 normfluodbf-2.0.3/normfluodbf/README.md | 12 normfluodbf-2.0.3/normfluodbf/inst/doc/normfluodbf.html | 6 normfluodbf-2.0.3/normfluodbf/inst/doc/test_file.html | 16 normfluodbf-2.0.3/normfluodbf/inst/shiny |only normfluodbf-2.0.3/normfluodbf/man/figures/2uM_Cs.png |only normfluodbf-2.0.3/normfluodbf/man/figures/2uM_K.png |only normfluodbf-2.0.3/normfluodbf/man/figures/ACMA_Var.png |only normfluodbf-2.0.3/normfluodbf/man/figures/ACMA_Var_1.png |only normfluodbf-2.0.3/normfluodbf/man/figures/Lipo_NavAb_1.jpg |only normfluodbf-2.0.3/normfluodbf/man/figures/NavAb_Protocol_NC.jpeg |only normfluodbf-2.0.3/normfluodbf/man/figures/NavAb_Protocol_PC.jpeg |only normfluodbf-2.0.3/normfluodbf/man/figures/NavAb_Protocol_T.jpeg |only normfluodbf-2.0.3/normfluodbf/man/figures/lipsum.png |only normfluodbf-2.0.3/normfluodbf/man/figures/lipsum.svg |only normfluodbf-2.0.3/normfluodbf/man/figures/nfd_plot.png |only normfluodbf-2.0.3/normfluodbf/man/figures/noise.png |only normfluodbf-2.0.3/normfluodbf/man/figures/qc_demo-1.png |only normfluodbf-2.0.3/normfluodbf/man/figures/visualization_demo-1.png |only normfluodbf-2.0.3/normfluodbf/man/find_random_port.Rd |only normfluodbf-2.0.3/normfluodbf/man/fluorthresholdcheck.Rd | 5 normfluodbf-2.0.3/normfluodbf/man/normalize_liposome_fluor_dats.Rd | 4 normfluodbf-2.0.3/normfluodbf/man/normfluodbf_utils.Rd | 30 + normfluodbf-2.0.3/normfluodbf/man/run_demo.Rd |only normfluodbf-2.0.3/normfluodbf/man/run_demo_bg.Rd |only normfluodbf-2.0.3/normfluodbf/man/run_demo_in_background.Rd |only normfluodbf-2.0.3/normfluodbf/man/run_demo_script.Rd |only normfluodbf-2.0.3/normfluodbf/man/shiny_random_port.Rd |only normfluodbf-2.0.3/normfluodbf/man/viewerpane_background_normfluodbf.Rd |only normfluodbf-2.0.3/normfluodbf/man/wait_for_bg_shinyapp.Rd |only normfluodbf-2.0.3/normfluodbf/tests/testthat/Rplots.pdf |only normfluodbf-2.0.3/normfluodbf/tests/testthat/test_new_utils.R |only normfluodbf-2.0.3/normfluodbf/tests/testthat/test_normfluodat.R | 7 normfluodbf-2.0.3/normfluodbf/tests/testthat/test_pipeline.R | 8 normfluodbf-2.0.3/normfluodbf/tests/testthat/test_plot.R | 58 +- normfluodbf-2.0.3/normfluodbf/tests/testthat/test_plot_dev.R | 29 - 49 files changed, 621 insertions(+), 150 deletions(-)
Title: Multivariate Normality Tests
Description: A comprehensive suite for assessing multivariate normality using six statistical tests
(Mardia, Henze–Zirkler, Henze–Wagner, Royston, Doornik–Hansen, Energy).
Also includes univariate diagnostics, bivariate density visualization, robust outlier
detection, power transformations (e.g., Box–Cox, Yeo–Johnson), and imputation strategies
("mean", "median", "mice") for handling missing data. Bootstrap resampling is supported
for selected tests to improve p-value accuracy in small samples.
Diagnostic plots are available via both 'ggplot2' and interactive 'plotly' visualizations. See Korkmaz et al. (2014) <https://journal.r-project.org/archive/2014-2/korkmaz-goksuluk-zararsiz.pdf>.
Author: Selcuk Korkmaz [aut, cre] ,
Dincer Goksuluk [aut],
Gokmen Zararsiz [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between MVN versions 6.1 dated 2025-06-10 and 6.2 dated 2025-10-10
DESCRIPTION | 10 ++++++---- MD5 | 19 ++++++++++++++++--- NAMESPACE | 1 + R/run_mvn_app.R |only README.md | 6 ++++++ inst/mvn-shiny-app |only man/run_mvn_app.Rd |only 7 files changed, 29 insertions(+), 7 deletions(-)
Title: A Grammar of Interactive Graphics
Description: Provides a bridge between the 'loon' and 'ggplot2' packages. Extends the grammar of ggplot to add clauses to create interactive 'loon' plots. Existing ggplot(s) can be turned into interactive 'loon' plots and 'loon' plots into static ggplot(s); the function 'loon.ggplot()' is the bridge from one plot structure to the other.
Author: Zehao Xu [aut, cre],
R. Wayne Oldford [aut]
Maintainer: Zehao Xu <z267xu@gmail.com>
Diff between loon.ggplot versions 1.3.4 dated 2024-04-01 and 1.3.5 dated 2025-10-10
DESCRIPTION | 12 +- MD5 | 94 ++++++++++----------- R/CartesianGuides.R | 2 R/deprecated_functions.R | 22 ++-- R/g_getLocations-deprecated.R | 2 R/g_getPlots-deprecated.R | 2 R/get_activeGeomLayers.R | 2 R/ggCompound.R | 2 R/ggplot2loon-ggmatrix.R | 2 R/ggplot2loon-ggplot.R | 2 R/ggplot2loon-patchwork.R | 2 R/interactive-ggproto.R | 26 ++--- R/l_ggplot.R | 7 - R/l_histogram.R | 1 R/loon2ggplot-l_layer_histogram.R | 4 R/loon2ggplot-l_serialaxes.R | 2 R/loon2ggplot.R | 20 ++-- R/polarGuides.R | 2 R/scale_multi.R | 11 +- R/size.R | 6 - R/unexportedFunctions.R | 30 ++++++ inst/doc/ggplot2loon.R | 2 inst/doc/ggplot2loon.Rmd | 2 inst/doc/ggplot2loon.html | 10 +- inst/doc/grammarOfInteractiveGraphics.Rmd | 2 inst/doc/grammarOfInteractiveGraphics.html | 26 +++-- inst/doc/linking.html | 10 +- inst/doc/loon2ggplot.html | 4 inst/doc/pipes.html | 4 inst/doc/thereAndBackAgain.html | 70 +++++++-------- man/g_getLocations.Rd | 2 man/g_getPlots.Rd | 2 man/geom_imageGlyph-deprecated.Rd | 77 +++++++++++++---- man/geom_pointrangeGlyph-deprecated.Rd | 75 ++++++++++++---- man/geom_serialAxesGlyph-deprecated.Rd | 75 ++++++++++++---- man/geom_textGlyph-deprecated.Rd | 74 ++++++++++++---- man/ggSerialAxes-deprecated.Rd | 2 man/interactivity.Rd | 2 man/l_ggplot.Rd | 4 man/linking.Rd | 2 man/scaleBox.Rd | 2 man/selection.Rd | 4 man/zoom.Rd | 14 +-- tests/testthat/test_ggplot2loon_geometricObjects.R | 10 +- tests/testthat/test_loon2ggplot.R | 34 +++---- tests/testthat/test_loon2ggplot_facets.R | 2 vignettes/ggplot2loon.Rmd | 2 vignettes/grammarOfInteractiveGraphics.Rmd | 2 48 files changed, 483 insertions(+), 285 deletions(-)
Title: Broadcasted Array Operations Like 'NumPy'
Description: Implements efficient 'NumPy'-like broadcasted operations for atomic and recursive arrays.
In the context of operations involving 2 (or more) arrays,
“broadcasting” refers to efficiently recycling array dimensions without allocating additional memory.
Besides linking to 'Rcpp',
'broadcast' does not use any external libraries in any way;
'broadcast' was essentially made from scratch and can be installed out-of-the-box.
The implementations available in 'broadcast' include, but are not limited to, the following.
1) Broadcasted element-wise operations on any 2 arrays;
they support a large set of
relational, arithmetic, Boolean, string, and bit-wise operations.
2) A faster, more memory efficient, and broadcasted abind-like function,
for binding arrays along an arbitrary dimension.
3) Broadcasted ifelse-like, and apply-like functions.
4) Casting functions,
that cast subset-groups of an array to a new dimension, cast nested lists to dimensional lists, and vice-versa.
5) A few linear algebra fu [...truncated...]
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tony_a_wilkes@outlook.com>
Diff between broadcast versions 0.1.5.1 dated 2025-10-04 and 0.1.5.3 dated 2025-10-10
broadcast-0.1.5.1/broadcast/inst/tinytest/internal/test-set_vind.R |only broadcast-0.1.5.1/broadcast/src/rcpp_set_vind.cpp |only broadcast-0.1.5.3/broadcast/DESCRIPTION | 6 broadcast-0.1.5.3/broadcast/MD5 | 112 broadcast-0.1.5.3/broadcast/NEWS.md | 10 broadcast-0.1.5.3/broadcast/R/RcppExports.R | 170 - broadcast-0.1.5.3/broadcast/R/bc_b.R | 75 broadcast-0.1.5.3/broadcast/R/bc_bit.R | 60 broadcast-0.1.5.3/broadcast/R/bc_cplx.R | 8 broadcast-0.1.5.3/broadcast/R/bc_d.R | 86 broadcast-0.1.5.3/broadcast/R/bc_i.R | 77 broadcast-0.1.5.3/broadcast/R/bc_ifelse.R | 2 broadcast-0.1.5.3/broadcast/R/bc_list.R | 5 broadcast-0.1.5.3/broadcast/R/bc_raw.R | 4 broadcast-0.1.5.3/broadcast/R/bc_str.R | 12 broadcast-0.1.5.3/broadcast/R/bcapply.R | 4 broadcast-0.1.5.3/broadcast/R/broadcastWrappers.R | 25 broadcast-0.1.5.3/broadcast/R/internal_binary.R | 15 broadcast-0.1.5.3/broadcast/R/internal_bind.R | 26 broadcast-0.1.5.3/broadcast/R/internal_bind_names.R | 2 broadcast-0.1.5.3/broadcast/R/internal_functions.R | 8 broadcast-0.1.5.3/broadcast/R/internal_opfuns.R | 21 broadcast-0.1.5.3/broadcast/R/ndim.R | 1 broadcast-0.1.5.3/broadcast/R/overload_ops_andor.R | 8 broadcast-0.1.5.3/broadcast/R/overload_ops_math.R | 4 broadcast-0.1.5.3/broadcast/R/overload_relops.R | 20 broadcast-0.1.5.3/broadcast/inst/examples/broadcast_cast.R | 35 broadcast-0.1.5.3/broadcast/inst/examples/dropnests.R | 3 broadcast-0.1.5.3/broadcast/inst/examples/ndim.R | 16 broadcast-0.1.5.3/broadcast/inst/tinytest/bc_num/test-bc_d_rel.R | 7 broadcast-0.1.5.3/broadcast/inst/tinytest/bc_num/test-relop_precision.R | 7 broadcast-0.1.5.3/broadcast/inst/tinytest/internal/test-orthogonal.R | 8 broadcast-0.1.5.3/broadcast/inst/tinytest/test-S4error-callerenv.R | 2 broadcast-0.1.5.3/broadcast/inst/tinytest/test-ndim.R | 13 broadcast-0.1.5.3/broadcast/man/aaa02_broadcast_casting.Rd | 35 broadcast-0.1.5.3/broadcast/man/bc.b.Rd | 5 broadcast-0.1.5.3/broadcast/man/bc.bit.Rd | 2 broadcast-0.1.5.3/broadcast/man/bc.d.Rd | 2 broadcast-0.1.5.3/broadcast/man/bc.i.Rd | 5 broadcast-0.1.5.3/broadcast/man/dropnests.Rd | 3 broadcast-0.1.5.3/broadcast/man/ndim.Rd | 16 broadcast-0.1.5.3/broadcast/src/C_bindhelper_max_type.c |only broadcast-0.1.5.3/broadcast/src/C_bindhelper_sum_along.c |only broadcast-0.1.5.3/broadcast/src/C_bindhelper_vdims.c |only broadcast-0.1.5.3/broadcast/src/C_chunkify_dims.c |only broadcast-0.1.5.3/broadcast/src/RcppExports.cpp | 458 +-- broadcast-0.1.5.3/broadcast/src/broadcast.h | 1362 ++-------- broadcast-0.1.5.3/broadcast/src/rcpp_acast.cpp | 11 broadcast-0.1.5.3/broadcast/src/rcpp_bcDist_dec.cpp |only broadcast-0.1.5.3/broadcast/src/rcpp_bcFact_int.cpp |only broadcast-0.1.5.3/broadcast/src/rcpp_bcRel_b.cpp |only broadcast-0.1.5.3/broadcast/src/rcpp_bcRel_bit.cpp |only broadcast-0.1.5.3/broadcast/src/rcpp_bcRel_dec.cpp | 9 broadcast-0.1.5.3/broadcast/src/rcpp_bc_b.cpp | 23 broadcast-0.1.5.3/broadcast/src/rcpp_bc_bind.cpp | 8 broadcast-0.1.5.3/broadcast/src/rcpp_bc_bit.cpp | 29 broadcast-0.1.5.3/broadcast/src/rcpp_bc_int.cpp | 91 broadcast-0.1.5.3/broadcast/src/rcpp_bc_str.cpp | 5 broadcast-0.1.5.3/broadcast/src/rcpp_bindhelpers.cpp | 91 broadcast-0.1.5.3/broadcast/src/rcpp_classes.cpp | 17 broadcast-0.1.5.3/broadcast/src/rcpp_mergedims.cpp | 11 broadcast-0.1.5.3/broadcast/src/rcpp_normalize_dims.cpp | 5 62 files changed, 1190 insertions(+), 1850 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 1.6.0 dated 2025-06-03 and 1.7.0 dated 2025-10-10
bbotk-1.6.0/bbotk/tests/testthat/_snaps/OptimizerCmaes.md |only bbotk-1.6.0/bbotk/tests/testthat/_snaps/OptimizerDesignPoints.md |only bbotk-1.6.0/bbotk/tests/testthat/_snaps/OptimizerFocusSearch.md |only bbotk-1.6.0/bbotk/tests/testthat/_snaps/OptimizerGenSA.md |only bbotk-1.6.0/bbotk/tests/testthat/_snaps/OptimizerGridSearch.md |only bbotk-1.6.0/bbotk/tests/testthat/_snaps/OptimizerLocalSearch.md |only bbotk-1.6.0/bbotk/tests/testthat/_snaps/OptimizerNLoptr.md |only bbotk-1.6.0/bbotk/tests/testthat/_snaps/OptimizerRandomSearch.md |only bbotk-1.6.0/bbotk/tests/testthat/test_OptimizerChain.R |only bbotk-1.6.0/bbotk/tests/testthat/test_OptimizerCmaes.R |only bbotk-1.6.0/bbotk/tests/testthat/test_OptimizerDesignPoints.R |only bbotk-1.6.0/bbotk/tests/testthat/test_OptimizerFocusSearch.R |only bbotk-1.6.0/bbotk/tests/testthat/test_OptimizerGenSA.R |only bbotk-1.6.0/bbotk/tests/testthat/test_OptimizerGridSearch.R |only bbotk-1.6.0/bbotk/tests/testthat/test_OptimizerIrace.R |only bbotk-1.6.0/bbotk/tests/testthat/test_OptimizerLocalSearch.R |only bbotk-1.6.0/bbotk/tests/testthat/test_OptimizerNLoptr.R |only bbotk-1.6.0/bbotk/tests/testthat/test_OptimizerRandomSearch.R |only bbotk-1.7.0/bbotk/DESCRIPTION | 15 bbotk-1.7.0/bbotk/MD5 | 122 +++--- bbotk-1.7.0/bbotk/NAMESPACE | 6 bbotk-1.7.0/bbotk/NEWS.md | 19 + bbotk-1.7.0/bbotk/R/ContextAsync.R | 4 bbotk-1.7.0/bbotk/R/Objective.R | 5 bbotk-1.7.0/bbotk/R/OptimInstanceAsync.R | 2 bbotk-1.7.0/bbotk/R/OptimizerAsync.R | 99 +++++ bbotk-1.7.0/bbotk/R/OptimizerBatchChain.R | 83 ++-- bbotk-1.7.0/bbotk/R/OptimizerBatchFocusSearch.R | 12 bbotk-1.7.0/bbotk/R/OptimizerBatchGenSA.R | 135 ++++--- bbotk-1.7.0/bbotk/R/OptimizerBatchIrace.R | 84 ++-- bbotk-1.7.0/bbotk/R/OptimizerBatchLocalSearch.R | 178 +--------- bbotk-1.7.0/bbotk/R/OptimizerBatchNLoptr.R | 159 +++++--- bbotk-1.7.0/bbotk/R/OptimizerBatchRandomSearch.R | 5 bbotk-1.7.0/bbotk/R/local_search.R |only bbotk-1.7.0/bbotk/R/zzz.R | 5 bbotk-1.7.0/bbotk/build/partial.rdb |binary bbotk-1.7.0/bbotk/man/ContextAsync.Rd | 3 bbotk-1.7.0/bbotk/man/Objective.Rd | 6 bbotk-1.7.0/bbotk/man/bbotk-package.Rd | 9 bbotk-1.7.0/bbotk/man/local_search.Rd |only bbotk-1.7.0/bbotk/man/local_search_control.Rd |only bbotk-1.7.0/bbotk/man/mlr_optimizers_chain.Rd | 32 - bbotk-1.7.0/bbotk/man/mlr_optimizers_focus_search.Rd | 8 bbotk-1.7.0/bbotk/man/mlr_optimizers_gensa.Rd | 102 +++-- bbotk-1.7.0/bbotk/man/mlr_optimizers_irace.Rd | 76 +++- bbotk-1.7.0/bbotk/man/mlr_optimizers_local_search.Rd | 74 ---- bbotk-1.7.0/bbotk/man/mlr_optimizers_nloptr.Rd | 72 ++-- bbotk-1.7.0/bbotk/man/tiny_logging.Rd |only bbotk-1.7.0/bbotk/man/tiny_result.Rd |only bbotk-1.7.0/bbotk/src/init.c | 29 + bbotk-1.7.0/bbotk/src/local_search.c |only bbotk-1.7.0/bbotk/src/local_search.h |only bbotk-1.7.0/bbotk/src/rc_helpers.c |only bbotk-1.7.0/bbotk/src/rc_helpers.h |only bbotk-1.7.0/bbotk/src/test_local_search.c |only bbotk-1.7.0/bbotk/src/test_local_search.h |only bbotk-1.7.0/bbotk/tests/testthat/_snaps/OptimizerBatchCmaes.md |only bbotk-1.7.0/bbotk/tests/testthat/_snaps/OptimizerBatchDesignPoints.md |only bbotk-1.7.0/bbotk/tests/testthat/_snaps/OptimizerBatchFocusSearch.md |only bbotk-1.7.0/bbotk/tests/testthat/_snaps/OptimizerBatchGenSA.md |only bbotk-1.7.0/bbotk/tests/testthat/_snaps/OptimizerBatchGridSearch.md |only bbotk-1.7.0/bbotk/tests/testthat/_snaps/OptimizerBatchNLoptr.md |only bbotk-1.7.0/bbotk/tests/testthat/_snaps/OptimizerBatchRandomSearch.md |only bbotk-1.7.0/bbotk/tests/testthat/helper.R | 15 bbotk-1.7.0/bbotk/tests/testthat/setup.R | 2 bbotk-1.7.0/bbotk/tests/testthat/test_ArchiveAsync.R | 3 bbotk-1.7.0/bbotk/tests/testthat/test_ArchiveAsyncFrozen.R | 4 bbotk-1.7.0/bbotk/tests/testthat/test_CallbackAsync.R | 44 +- bbotk-1.7.0/bbotk/tests/testthat/test_OptimInstanceAsyncSingleCrit.R | 36 +- bbotk-1.7.0/bbotk/tests/testthat/test_OptimizerAsynDesignPoints.R | 3 bbotk-1.7.0/bbotk/tests/testthat/test_OptimizerAsynGridSearch.R | 3 bbotk-1.7.0/bbotk/tests/testthat/test_OptimizerAsync.R | 43 +- bbotk-1.7.0/bbotk/tests/testthat/test_OptimizerAsyncRandomSearch.R | 5 bbotk-1.7.0/bbotk/tests/testthat/test_OptimizerBatchChain.R |only bbotk-1.7.0/bbotk/tests/testthat/test_OptimizerBatchCmaes.R |only bbotk-1.7.0/bbotk/tests/testthat/test_OptimizerBatchDesignPoints.R |only bbotk-1.7.0/bbotk/tests/testthat/test_OptimizerBatchFocusSearch.R |only bbotk-1.7.0/bbotk/tests/testthat/test_OptimizerBatchGenSA.R |only bbotk-1.7.0/bbotk/tests/testthat/test_OptimizerBatchGridSearch.R |only bbotk-1.7.0/bbotk/tests/testthat/test_OptimizerBatchIrace.R |only bbotk-1.7.0/bbotk/tests/testthat/test_OptimizerBatchLocalSearch.R |only bbotk-1.7.0/bbotk/tests/testthat/test_OptimizerBatchNLoptr.R |only bbotk-1.7.0/bbotk/tests/testthat/test_OptimizerBatchRandomSearch.R |only bbotk-1.7.0/bbotk/tests/testthat/test_c_functions.R |only bbotk-1.7.0/bbotk/tests/testthat/test_local_search.R |only bbotk-1.7.0/bbotk/tests/testthat/test_mlr_callbacks.R | 8 86 files changed, 878 insertions(+), 632 deletions(-)
Title: Evaluation of Failure Time Surrogate Endpoints in Individual
Patient Data Meta-Analyses
Description: Provides functions for the evaluation of
surrogate endpoints when both the surrogate and the true endpoint are failure
time variables. The approaches implemented are:
(1) the two-step approach (Burzykowski et al, 2001) <DOI:10.1111/1467-9876.00244> with a copula model (Clayton, Plackett, Hougaard) at
the first step and either a linear regression of log-hazard ratios at the second
step (either adjusted or not for measurement error);
(2) mixed proportional hazard models estimated via mixed Poisson GLM
(Rotolo et al, 2017 <DOI:10.1177/0962280217718582>).
Author: Federico Rotolo [aut] ,
Xavier Paoletti [ctb],
Marc Buyse [ctb],
Tomasz Burzykowski [ctb],
Stefan Michiels [ctb] ,
Dan Chaltiel [cre]
Maintainer: Dan Chaltiel <dan.chaltiel@gustaveroussy.fr>
Diff between surrosurv versions 1.1.26 dated 2023-04-14 and 1.1.27 dated 2025-10-10
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ README.md | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/surrosurv.pdf |binary man/surrosurv.Rd | 4 ++-- 7 files changed, 15 insertions(+), 15 deletions(-)
Title: Analysis of Single-Cell Chromatin Data
Description: A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
Author: Tim Stuart [aut, cre] ,
Avi Srivastava [aut] ,
Paul Hoffman [ctb] ,
Rahul Satija [ctb]
Maintainer: Tim Stuart <stuartt@a-star.edu.sg>
Diff between Signac versions 1.15.0 dated 2025-08-18 and 1.16.0 dated 2025-10-10
DESCRIPTION | 12 +++++------ MD5 | 32 ++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 16 ++++++++++++++ R/genomeinfodb-methods.R | 6 ++--- R/links.R | 29 +++++++++++++-------------- R/objects.R | 15 ++++++-------- R/peaks.R | 3 +- R/quantification.R | 2 - R/utilities.R | 47 +++++++++++++++++++++++++++++++++----------- man/ChromatinAssay-class.Rd | 2 - man/CreateChromatinAssay.Rd | 2 - man/GenomeBinMatrix.Rd | 2 - man/Signac-package.Rd | 4 +-- man/as.ChromatinAssay.Rd | 2 - man/seqinfo-methods.Rd | 6 ++--- src/group.cpp | 3 ++ 17 files changed, 113 insertions(+), 71 deletions(-)
Title: Proportional Apportionment
Description: Calculate seat apportionment for legislative bodies with
various methods. The algorithms include divisor or highest averages methods
(e.g. Jefferson, Webster or Adams), largest remainder methods and
biproportional apportionment.
Gaffke, N. & Pukelsheim, F. (2008) <doi:10.1016/j.mathsocsci.2008.01.004>
Oelbermann, K. F. (2016) <doi:10.1016/j.mathsocsci.2016.02.003>.
Author: Flavio Poletti [aut, cre, cph]
Maintainer: Flavio Poletti <flavio.poletti@hotmail.ch>
Diff between proporz versions 1.5.1 dated 2025-03-10 and 1.5.2 dated 2025-10-10
proporz-1.5.1/proporz/inst/bazi.R |only proporz-1.5.1/proporz/inst/test-bazi_biproportional_examples.R |only proporz-1.5.1/proporz/inst/test-read_bazi_data.R |only proporz-1.5.1/proporz/inst/test-read_bazi_data_coverage.R |only proporz-1.5.1/proporz/man/weight_list_votes.Rd |only proporz-1.5.2/proporz/DESCRIPTION | 8 proporz-1.5.2/proporz/MD5 | 90 ++-- proporz-1.5.2/proporz/NAMESPACE | 1 proporz-1.5.2/proporz/NEWS.md | 7 proporz-1.5.2/proporz/R/S3.R | 10 proporz-1.5.2/proporz/R/biproportional-check.R | 37 + proporz-1.5.2/proporz/R/biproportional-divisors.R | 2 proporz-1.5.2/proporz/R/biproportional-lower.R | 4 proporz-1.5.2/proporz/R/biproportional-upper.R | 60 +-- proporz-1.5.2/proporz/R/biproportional-wto.R | 20 - proporz-1.5.2/proporz/R/biproportional.R | 71 ++- proporz-1.5.2/proporz/R/proporz.R | 10 proporz-1.5.2/proporz/R/quorum.R | 6 proporz-1.5.2/proporz/R/quota_methods.R | 2 proporz-1.5.2/proporz/R/shinyapp.R | 10 proporz-1.5.2/proporz/R/utils.R | 11 proporz-1.5.2/proporz/README.md | 43 +- proporz-1.5.2/proporz/build/vignette.rds |binary proporz-1.5.2/proporz/inst/bazi |only proporz-1.5.2/proporz/inst/doc/apportionment_scenarios.R | 54 +- proporz-1.5.2/proporz/inst/doc/apportionment_scenarios.Rmd | 57 +- proporz-1.5.2/proporz/inst/doc/apportionment_scenarios.html | 75 ++- proporz-1.5.2/proporz/inst/doc/modifying_biproporz.R | 149 +++---- proporz-1.5.2/proporz/inst/doc/modifying_biproporz.Rmd | 166 ++++---- proporz-1.5.2/proporz/inst/doc/modifying_biproporz.html | 192 +++++----- proporz-1.5.2/proporz/man/biproporz.Rd | 17 proporz-1.5.2/proporz/man/figures/shinyapp-example.gif |binary proporz-1.5.2/proporz/man/largest_remainder_method.Rd | 2 proporz-1.5.2/proporz/man/pukelsheim.Rd | 37 + proporz-1.5.2/proporz/man/quorum_functions.Rd | 2 proporz-1.5.2/proporz/man/reached_quorum_total.Rd | 2 proporz-1.5.2/proporz/man/upper_apportionment.Rd | 12 proporz-1.5.2/proporz/man/weight_votes_matrix.Rd |only proporz-1.5.2/proporz/tests/testthat/test-biproportional-data.R | 2 proporz-1.5.2/proporz/tests/testthat/test-biproportional-errors.R | 46 +- proporz-1.5.2/proporz/tests/testthat/test-biproportional-wto.R | 5 proporz-1.5.2/proporz/tests/testthat/test-biproportional.R | 98 ++++- proporz-1.5.2/proporz/tests/testthat/test-proporz.R | 6 proporz-1.5.2/proporz/tests/testthat/test-quorum.R | 10 proporz-1.5.2/proporz/tests/testthat/test-round.R | 58 +-- proporz-1.5.2/proporz/tests/testthat/test-utils.R | 4 proporz-1.5.2/proporz/vignettes/apportionment_scenarios.Rmd | 57 +- proporz-1.5.2/proporz/vignettes/modifying_biproporz.Rmd | 166 ++++---- 48 files changed, 913 insertions(+), 696 deletions(-)
Title: Simulate Data from State Space Models
Description: Provides a streamlined and user-friendly framework
for simulating data in state space models,
particularly when the number of subjects/units (n) exceeds one,
a scenario commonly encountered in social and behavioral sciences.
This package was designed to generate data for the simulations
performed in Pesigan, Russell, and Chow (2025) <doi:10.1037/met0000779>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph] ,
Michael A. Russell [ctb] ,
Sy-Miin Chow [ctb]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between simStateSpace versions 1.2.11 dated 2025-09-26 and 1.2.12 dated 2025-10-10
DESCRIPTION | 35 ++++++++++++++++++-------- MD5 | 24 +++++++++--------- NEWS.md | 6 ++++ R/RcppExports.R | 42 ++++++++++++++++++++++++------- inst/CITATION | 38 ++++++++++++++++++---------- man/SimBetaN.Rd | 4 +++ man/SimPhiN.Rd | 11 ++++++++ man/TestPhi.Rd | 11 +++++++- man/TestStability.Rd | 7 ++++- man/TestStationarity.Rd | 5 +++ man/simStateSpace-package.Rd | 8 +++++- src/RcppExports.cpp | 47 ++++++++++++++++++++--------------- src/source.cpp | 57 ++++++++++++++++++++++++++++++------------- 13 files changed, 209 insertions(+), 86 deletions(-)
Title: Time-Series Models to the Crop Phenology
Description: Fit a time-series model
to a crop phenology data, such as time-series rice canopy height.
This package returns the model parameters as the summary statistics of crop phenology,
and these parameters will be useful to characterize the growth pattern of each cultivar and
predict manually-measured traits, such as days to heading and biomass.
Please see Taniguchi et al. (2022) <doi:10.3389/fpls.2022.998803> and
Taniguchi et al. (2025) <doi: 10.3389/frai.2024.1477637> for detail.
This package has been designed for scientific use.
Use for commercial purposes shall not be allowed.
Author: Shoji Taniguchi [aut, cre],
The National Agriculture and Food Research Organization [cph]
Maintainer: Shoji Taniguchi <taniguchi.shoji938@naro.go.jp>
Diff between phenolocrop versions 0.0.2 dated 2023-07-13 and 0.0.4 dated 2025-10-10
DESCRIPTION | 15 +-- MD5 | 31 ++++--- NAMESPACE | 1 R/doubleLogis.R |only R/logisLateDicrease.R | 2 R/phenololine.R | 22 ++++- R/riceCIg_eg.R |only README.md | 6 + build/vignette.rds |binary data/riceCIg_eg.rda |only inst/doc/doubleLogis.R |only inst/doc/doubleLogis.Rmd |only inst/doc/doubleLogis.html |only inst/doc/logisLateDicr.R | 2 inst/doc/logisLateDicr.html | 191 ++++++++++++++++++++++---------------------- man/doubleLogis.Rd |only man/logisLateDicr.Rd | 110 ++++++++++++------------- man/phenololine.Rd | 67 +++++++-------- man/riceCH_eg.Rd | 42 ++++----- man/riceCIg_eg.Rd |only vignettes/doubleLogis.Rmd |only 21 files changed, 264 insertions(+), 225 deletions(-)
Title: Conduct Sensitivity Analysis with Continuous Exposures and
Binary or Continuous Outcomes
Description: Performs sensitivity analysis for the sharp null, attributable effects, and weak nulls in matched studies with continuous exposures and binary or continuous outcomes as described in Zhang, Small, Heng (2024) <doi:10.48550/arXiv.2401.06909> and Zhang, Heng (2024) <doi:10.48550/arXiv.2409.12848>. Two of the functions require installation of the 'Gurobi' optimizer. Please see <https://docs.gurobi.com/current/#refman/ins_the_r_package.html> for guidance.
Author: Jeffrey Zhang [aut, cre]
Maintainer: Jeffrey Zhang <jeffreyzhang1226@gmail.com>
Diff between doseSens versions 0.1.0 dated 2024-01-17 and 1.0.0 dated 2025-10-10
doseSens-0.1.0/doseSens/data/treat_out_match.rda |only doseSens-0.1.0/doseSens/man/treat_out_match.Rd |only doseSens-1.0.0/doseSens/DESCRIPTION | 18 +-- doseSens-1.0.0/doseSens/MD5 | 50 +++++++--- doseSens-1.0.0/doseSens/NAMESPACE | 19 +++ doseSens-1.0.0/doseSens/R/AE.R | 31 ++++-- doseSens-1.0.0/doseSens/R/data.R | 31 ++++-- doseSens-1.0.0/doseSens/R/opti_helpers.R |only doseSens-1.0.0/doseSens/R/sharp.R | 15 +-- doseSens-1.0.0/doseSens/R/stat_helpers.R |only doseSens-1.0.0/doseSens/R/test_stats.R |only doseSens-1.0.0/doseSens/data/lead_bmd.rda |only doseSens-1.0.0/doseSens/data/lead_crime.rda |only doseSens-1.0.0/doseSens/man/apply_permutation_to_matrix.Rd |only doseSens-1.0.0/doseSens/man/binary_thresh_attribute.Rd | 4 doseSens-1.0.0/doseSens/man/constant_effects_test.Rd |only doseSens-1.0.0/doseSens/man/dev_TV.Rd | 6 - doseSens-1.0.0/doseSens/man/dose_attributable_general.Rd | 12 +- doseSens-1.0.0/doseSens/man/dose_sensitivity_mc_gen.Rd | 4 doseSens-1.0.0/doseSens/man/dose_thresh_attributable_one_sided.Rd | 13 +- doseSens-1.0.0/doseSens/man/extract_OLS.Rd |only doseSens-1.0.0/doseSens/man/extract_above_threshold_vs_baseline.Rd |only doseSens-1.0.0/doseSens/man/extract_below_threshold_vs_baseline.Rd |only doseSens-1.0.0/doseSens/man/extract_max_vs_baseline.Rd |only doseSens-1.0.0/doseSens/man/extract_min_vs_baseline.Rd |only doseSens-1.0.0/doseSens/man/extract_stochastic_intervention.Rd |only doseSens-1.0.0/doseSens/man/extract_threshold_effect.Rd |only doseSens-1.0.0/doseSens/man/extract_threshold_effect_function.Rd |only doseSens-1.0.0/doseSens/man/lead_bmd.Rd |only doseSens-1.0.0/doseSens/man/lead_crime.Rd |only doseSens-1.0.0/doseSens/man/max_expectation.Rd |only doseSens-1.0.0/doseSens/man/max_ratio.Rd |only doseSens-1.0.0/doseSens/man/max_ratio_new.Rd |only doseSens-1.0.0/doseSens/man/max_ratios_summary.Rd |only doseSens-1.0.0/doseSens/man/normal_test_gen.Rd | 4 doseSens-1.0.0/doseSens/man/prob_bounds.Rd |only doseSens-1.0.0/doseSens/man/sharp_double_statistic.Rd |only doseSens-1.0.0/doseSens/man/sharp_null_double_test.Rd |only doseSens-1.0.0/doseSens/man/var_est.Rd |only doseSens-1.0.0/doseSens/man/weak_null_test.Rd |only 40 files changed, 142 insertions(+), 65 deletions(-)
Title: Bayesian Methods for Image Segmentation using a Potts Model
Description: Various algorithms for segmentation of 2D and 3D images, such
as computed tomography and satellite remote sensing. This package implements
Bayesian image analysis using the hidden Potts model with external field
prior of Moores et al. (2015) <doi:10.1016/j.csda.2014.12.001>.
Latent labels are sampled using chequerboard updating or Swendsen-Wang.
Algorithms for the smoothing parameter include pseudolikelihood, path sampling,
the exchange algorithm, approximate Bayesian computation (ABC-MCMC and ABC-SMC),
and the parametric functional approximate Bayesian (PFAB) algorithm. Refer to
Moores, Pettitt & Mengersen (2020) <doi:10.1007/978-3-030-42553-1_6> for an overview
and also to <doi:10.1007/s11222-014-9525-6> and <doi:10.1214/18-BA1130> for
further details of specific algorithms.
Author: Matt Moores [aut, cre, cph] ,
Dai Feng [ctb],
Kerrie Mengersen [aut, ths]
Maintainer: Matt Moores <mmoores@gmail.com>
Diff between bayesImageS versions 0.6-1 dated 2021-04-11 and 0.7-0 dated 2025-10-10
bayesImageS-0.6-1/bayesImageS/inst/doc/swNoData.R |only bayesImageS-0.6-1/bayesImageS/inst/doc/swNoData.Rmd |only bayesImageS-0.6-1/bayesImageS/inst/doc/swNoData.html |only bayesImageS-0.6-1/bayesImageS/vignettes/swNoData.Rmd |only bayesImageS-0.7-0/bayesImageS/DESCRIPTION | 28 bayesImageS-0.7-0/bayesImageS/MD5 | 44 bayesImageS-0.7-0/bayesImageS/NEWS.md | 188 +- bayesImageS-0.7-0/bayesImageS/R/bayesImageS.R | 70 bayesImageS-0.7-0/bayesImageS/README.md | 317 +-- bayesImageS-0.7-0/bayesImageS/build/partial.rdb |binary bayesImageS-0.7-0/bayesImageS/build/vignette.rds |binary bayesImageS-0.7-0/bayesImageS/inst/CITATION | 186 -- bayesImageS-0.7-0/bayesImageS/inst/doc/Background.html | 606 +++++-- bayesImageS-0.7-0/bayesImageS/inst/doc/mcmcPotts.R | 206 +- bayesImageS-0.7-0/bayesImageS/inst/doc/mcmcPotts.html | 741 +++++--- bayesImageS-0.7-0/bayesImageS/inst/doc/mcmcPottsNoData.R | 182 +- bayesImageS-0.7-0/bayesImageS/inst/doc/mcmcPottsNoData.html | 827 ++++++---- bayesImageS-0.7-0/bayesImageS/inst/image/README-unnamed-chunk-5-1.png |binary bayesImageS-0.7-0/bayesImageS/inst/image/README-unnamed-chunk-6-1.png |binary bayesImageS-0.7-0/bayesImageS/inst/image/README-unnamed-chunk-7-1.png |binary bayesImageS-0.7-0/bayesImageS/inst/image/README-unnamed-chunk-8-1.png |binary bayesImageS-0.7-0/bayesImageS/man/bayesImageS.Rd | 4 bayesImageS-0.7-0/bayesImageS/src/PottsUtil.cpp | 2 bayesImageS-0.7-0/bayesImageS/src/mcmcPotts.cpp | 18 bayesImageS-0.7-0/bayesImageS/src/smcPotts.cpp | 14 25 files changed, 2115 insertions(+), 1318 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-18 0.2.0
2016-11-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-20 2.3
2022-11-23 2.2
2022-09-17 2.1
2022-09-14 2.0
2018-07-19 1.2
2018-02-02 1.1
2017-11-10 1.0
Title: Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text
Shaping
Description: Provides access to the text shaping functionality in the
'HarfBuzz' library and the bidirectional algorithm in the 'Fribidi'
library. 'textshaping' is a low-level utility package mainly for
graphic devices that expands upon the font tool-set provided by the
'systemfonts' package.
Author: Thomas Lin Pedersen [cre, aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between textshaping versions 1.0.3 dated 2025-09-02 and 1.0.4 dated 2025-10-10
DESCRIPTION | 10 ++-- MD5 | 12 ++--- NEWS.md | 5 ++ build/vignette.rds |binary man/get_font_features.Rd | 2 src/string_shape.cpp | 100 +++++++++++++++++++++++++++++++++++++++-------- src/string_shape.h | 19 ++++++++ 7 files changed, 120 insertions(+), 28 deletions(-)
Title: Flexible Bayesian Optimization
Description: A modern and flexible approach to Bayesian Optimization / Model
Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox
providing both ready-to-use optimization algorithms as well as their fundamental
building blocks allowing for straightforward implementation of custom
algorithms. Single- and multi-objective optimization is supported as well as
mixed continuous, categorical and conditional search spaces. Moreover, using
'mlr3mbo' for hyperparameter optimization of machine learning models within the
'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use
optimization algorithms include Efficient Global Optimization by Jones et al.
(1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006)
<doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008)
<doi:10.1007/978-3-540-87700-4_78>.
Author: Marc Becker [cre, aut] ,
Lennart Schneider [aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Florian Pfisterer [aut] ,
Martin Binder [aut],
Sebastian Fischer [aut] ,
Michael H. Buselli [cph],
Wessel Dankers [cph],
Carlos Fonseca [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3mbo versions 0.3.2 dated 2025-10-02 and 0.3.3 dated 2025-10-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/AcqFunction.R | 4 +++- 4 files changed, 13 insertions(+), 7 deletions(-)
Title: Robust Estimation in the Presence of Cellwise and Casewise
Contamination and Missing Data
Description: Robust Estimation of Multivariate Location and Scatter in the
Presence of Cellwise and Casewise Contamination and Missing Data.
Author: Andy Leung [aut],
Mike Danilov [aut],
Victor Yohai [aut],
Ruben Zamar [aut],
Claudio Agostinelli [cre]
Maintainer: Claudio Agostinelli <claudio.agostinelli@unitn.it>
Diff between GSE versions 4.2-1 dated 2022-12-13 and 4.2-3 dated 2025-10-10
DESCRIPTION | 32 ++++++++++++++++++++++++++------ MD5 | 18 +++++++++--------- R/simulation-utils.R | 27 ++++++++++++++++++++++++++- man/boston.Rd | 4 ++-- man/calcium.Rd | 4 ++-- src/cov-em.h | 3 ++- src/emve.cpp | 10 ++++++---- src/emve.h | 3 ++- src/gse-rocke.h | 3 ++- src/gse.h | 3 ++- 10 files changed, 79 insertions(+), 28 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-24 3.0
2023-02-21 1.4.1
2023-01-16 1.4
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.6.2 dated 2025-08-27 and 1.6.3 dated 2025-10-10
DESCRIPTION | 8 MD5 | 64 R/GPModel.R | 31 configure.ac | 2 demo/GPBoost_algorithm.R | 3 demo/generalized_linear_Gaussian_process_mixed_effects_models.R | 6 man/GPModel.Rd | 12 man/GPModel_shared_params.Rd | 19 man/fit.GPModel.Rd | 7 man/fit.Rd | 7 man/fitGPModel.Rd | 19 man/set_optim_params.GPModel.Rd | 7 man/set_optim_params.Rd | 7 src/CG_utils.cpp | 184 src/Vecchia_utils.cpp | 12 src/c_api.cpp | 8 src/gpboost_R.cpp | 10 src/gpboost_R.h | 6 src/include/GPBoost/CG_utils.h | 56 src/include/GPBoost/cov_fcts.h | 112 src/include/GPBoost/likelihoods.h | 1903 +++++++--- src/include/GPBoost/optim_utils.h | 6 src/include/GPBoost/re_comp.h | 2 src/include/GPBoost/re_model.h | 10 src/include/GPBoost/re_model_template.h | 672 +-- src/include/GPBoost/utils.h | 44 src/include/LightGBM/c_api.h | 6 src/re_model.cpp | 34 tests/testthat/test_GPModel_gaussian_process.R | 219 - tests/testthat/test_GPModel_grouped_random_effects.R | 12 tests/testthat/test_GPModel_non_Gaussian_data.R | 230 + tests/testthat/test_z_GPBoost_algorithm.R | 49 tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data.R | 139 33 files changed, 2749 insertions(+), 1157 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran [aut],
Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 3.4.2 dated 2025-09-30 and 3.4.3 dated 2025-10-10
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/generic.predict.rfsrc.R | 2 +- R/rfsrc.R | 4 ++-- configure | 18 +++++++++--------- configure.ac | 2 +- inst/NEWS | 10 ++++++++-- src/importance.c | 7 +------ src/trace.c | 6 +++--- src/trace.h | 6 +++--- 10 files changed, 41 insertions(+), 40 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Fast, Sensitive, and Accurate Integration of Single Cell Data
Description: Implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al <doi:10.1038/s41592-019-0619-0>. Package includes a standalone Harmony function and interfaces to external frameworks.
Author: Ilya Korsunsky [cre, aut] ,
Martin Hemberg [aut] ,
Nikolaos Patikas [aut, ctb] ,
Hongcheng Yao [aut, ctb] ,
Nghia Millard [aut] ,
Jean Fan [aut, ctb] ,
Kamil Slowikowski [aut, ctb] ,
Miles Smith [ctb],
Soumya Raychaudhuri [aut]
Maintainer: Ilya Korsunsky <ilya.korsunsky@gmail.com>
Diff between harmony versions 1.2.3 dated 2024-11-27 and 1.2.4 dated 2025-10-10
DESCRIPTION | 27 ++++++++++++++++----------- MD5 | 16 ++++++++-------- inst/doc/Seurat.html | 26 +++++++++++++------------- inst/doc/detailedWalkthrough.R | 2 +- inst/doc/detailedWalkthrough.Rmd | 2 +- inst/doc/detailedWalkthrough.html | 8 ++++---- inst/doc/quickstart.html | 4 ++-- src/Makevars | 1 + vignettes/detailedWalkthrough.Rmd | 2 +- 9 files changed, 47 insertions(+), 41 deletions(-)
Title: Extending 'gt' for Beautiful HTML Tables
Description: Provides additional functions for creating beautiful tables
with 'gt'. The functions are generally wrappers around boilerplate or
adding opinionated niche capabilities and helpers functions.
Author: Thomas Mock [aut, cre, cph],
Daniel D. Sjoberg [ctb]
Maintainer: Thomas Mock <j.thomasmock@gmail.com>
Diff between gtExtras versions 0.6.0 dated 2025-05-29 and 0.6.1 dated 2025-10-10
DESCRIPTION | 6 - MD5 | 13 +- NEWS.md | 158 +++++++++++++++++----------------- R/gt_plt_conf_int.R | 62 +++++++------ tests/testthat/test-gt_pct_bar.R | 13 ++ tests/testthat/test-gt_plt_bar.R | 6 - tests/testthat/test-gt_plt_conf_int.R | 2 tests/testthat/test_test-gt_pct_bar.R |only 8 files changed, 144 insertions(+), 116 deletions(-)
Title: Solve the Empirical Bayes Normal Means Problem
Description: Provides simple, fast, and stable functions to fit the normal
means model using empirical Bayes. For available models and details, see
function ebnm(). Our JSS article,
Willwerscheid, Carbonetto, and Stephens (2025) <doi:10.18637/jss.v114.i03>,
provides a detailed introduction to the package.
Author: Jason Willwerscheid [aut],
Matthew Stephens [aut],
Peter Carbonetto [aut, cre],
Andrew Goldstein [ctb],
Yusha Liu [ctb]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between ebnm versions 1.1-38 dated 2025-09-05 and 1.1-42 dated 2025-10-10
DESCRIPTION | 15 +++---- MD5 | 22 +++++----- NAMESPACE | 3 - R/horseshoe.R | 9 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/baseball.html | 55 +++++++++++++-------------- inst/doc/extending_ebnm.html | 37 ++++++++---------- inst/doc/shrink_intro.html | 43 ++++++++++----------- tests/testthat/test_horseshoe.R | 1 tests/testthat/test_optmethod.R | 12 +++-- tests/testthat/test_prior_family_inference.R | 3 - 12 files changed, 101 insertions(+), 99 deletions(-)
Title: A Flexible Container to Transport and Manipulate Data and
Associated Resources
Description: Provides a flexible container to transport and manipulate complex
sets of data. These data may consist of multiple data files and associated
meta data and ancillary files. Individual data objects have associated system
level meta data, and data files are linked together using the OAI-ORE standard
resource map which describes the relationships between the files. The OAI-
ORE standard is described at <https://www.openarchives.org/ore/>. Data packages
can be serialized and transported as structured files that have been created
following the BagIt specification. The BagIt specification is described at
<https://datatracker.ietf.org/doc/html/draft-kunze-bagit-08>.
Author: Matthew B. Jones [aut, cre] ,
Peter Slaughter [aut] ,
Jeanette Clark [ctb] ,
Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between datapack versions 1.4.1 dated 2022-06-10 and 1.4.2 dated 2025-10-10
datapack-1.4.1/datapack/NEWS |only datapack-1.4.2/datapack/DESCRIPTION | 26 - datapack-1.4.2/datapack/MD5 | 86 +-- datapack-1.4.2/datapack/NEWS.md |only datapack-1.4.2/datapack/R/DataObject.R | 6 datapack-1.4.2/datapack/R/DataPackage.R | 27 - datapack-1.4.2/datapack/R/ResourceMap.R | 16 datapack-1.4.2/datapack/R/SystemMetadata.R | 18 datapack-1.4.2/datapack/R/datapack-package.r | 8 datapack-1.4.2/datapack/R/dmsg.R | 2 datapack-1.4.2/datapack/R/zzz.R | 2 datapack-1.4.2/datapack/README.md | 4 datapack-1.4.2/datapack/build/vignette.rds |binary datapack-1.4.2/datapack/inst/doc/datapack-overview.R | 62 +- datapack-1.4.2/datapack/inst/doc/datapack-overview.Rmd | 2 datapack-1.4.2/datapack/inst/doc/datapack-overview.html | 339 +++++++-------- datapack-1.4.2/datapack/man/DataObject-class.Rd | 2 datapack-1.4.2/datapack/man/DataPackage-class.Rd | 4 datapack-1.4.2/datapack/man/DataPackage-initialize.Rd | 4 datapack-1.4.2/datapack/man/ResourceMap-class.Rd | 4 datapack-1.4.2/datapack/man/ResourceMap-initialize.Rd | 2 datapack-1.4.2/datapack/man/SystemMetadata-class.Rd | 4 datapack-1.4.2/datapack/man/SystemMetadata-initialize.Rd | 2 datapack-1.4.2/datapack/man/addAccessRule.Rd | 6 datapack-1.4.2/datapack/man/canRead.Rd | 2 datapack-1.4.2/datapack/man/clearAccessPolicy.Rd | 2 datapack-1.4.2/datapack/man/createFromTriples.Rd | 2 datapack-1.4.2/datapack/man/datapack-deprecated.Rd | 2 datapack-1.4.2/datapack/man/datapack.Rd | 13 datapack-1.4.2/datapack/man/describeWorkflow.Rd | 8 datapack-1.4.2/datapack/man/dmsg.Rd | 4 datapack-1.4.2/datapack/man/freeResourceMap.Rd | 2 datapack-1.4.2/datapack/man/getTriples.Rd | 2 datapack-1.4.2/datapack/man/getValue.Rd | 2 datapack-1.4.2/datapack/man/parseRDF.Rd | 2 datapack-1.4.2/datapack/man/removeAccessRule.Rd | 4 datapack-1.4.2/datapack/man/serializePackage.Rd | 4 datapack-1.4.2/datapack/man/serializeRDF.Rd | 6 datapack-1.4.2/datapack/man/serializeToBagIt.Rd | 2 datapack-1.4.2/datapack/man/setPublicAccess.Rd | 2 datapack-1.4.2/datapack/man/setValue.Rd | 2 datapack-1.4.2/datapack/man/updateMetadata.Rd | 2 datapack-1.4.2/datapack/man/updateRelationships.Rd | 2 datapack-1.4.2/datapack/man/validate.Rd | 2 datapack-1.4.2/datapack/vignettes/datapack-overview.Rmd | 2 45 files changed, 360 insertions(+), 335 deletions(-)
Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to
graphics (mostly for base graphics), permutation tests, running
mean/median, and general utilities.
Author: Karl W Broman [aut, cre] ,
Aimee Teo Broman [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between broman versions 0.88 dated 2025-09-03 and 0.90 dated 2025-10-10
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/brocolors.R | 34 ++++++++++++++++++---------------- tests/testthat/test-crayons.R | 12 ++++++++++++ 5 files changed, 44 insertions(+), 25 deletions(-)
Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve models. References: Merkle & Rosseel (2018) <doi:10.18637/jss.v085.i04>; Merkle et al. (2021) <doi:10.18637/jss.v100.i06>.
Author: Edgar Merkle [aut, cre] ,
Yves Rosseel [aut],
Ben Goodrich [aut],
Mauricio Garnier-Villarreal [ctb] ,
Terrence D. Jorgensen [ctb] ,
Huub Hoofs [ctb] ,
Rens van de Schoot [ctb] ,
Andrew Johnson [ctb] ,
Matthew Emery [ctb]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between blavaan versions 0.5-8 dated 2025-01-08 and 0.5-9 dated 2025-10-10
DESCRIPTION | 20 +- MD5 | 30 +-- NAMESPACE | 6 NEWS.md | 13 + R/blav_adapt_quad.R | 16 +- R/blav_model_loglik.R | 4 R/blav_predict.R | 22 ++ R/blav_utils.R | 83 ++++------ R/blavaan.R | 38 +--- R/lav_export_stanmarg.R | 368 +++++++++++++++++++++++++--------------------- R/postpred.R | 2 R/set_inits.R | 2 R/stanmarg_data.R | 157 ++++++++++++------- README.md | 2 inst/stan/stanmarg.stan | 345 +++++++++++++++++++++++++++++++++++-------- inst/testdata/sysdata.rda |binary 16 files changed, 715 insertions(+), 393 deletions(-)