Title: Scalable Joint Species Distribution Modeling
Description: A scalable and fast method for estimating joint Species Distribution Models (jSDMs) for big community data, including eDNA data. The package estimates a full (i.e. non-latent) jSDM with different response distributions (including the traditional multivariate probit model). The package allows to perform variation partitioning (VP) / ANOVA on the fitted models to separate the contribution of environmental, spatial, and biotic associations. In addition, the total R-squared can be further partitioned per species and site to reveal the internal metacommunity structure, see Leibold et al., <doi:10.1111/oik.08618>. The internal structure can then be regressed against environmental and spatial distinctiveness, richness, and traits to analyze metacommunity assembly processes. The package includes support for accounting for spatial autocorrelation and the option to fit responses using deep neural networks instead of a standard linear predictor. As described in Pichler & Hartig (2021) [...truncated...]
Author: Maximilian Pichler [aut, cre] ,
Florian Hartig [aut] ,
Wang Cai [ctb]
Maintainer: Maximilian Pichler <maximilian.pichler@biologie.uni-regensburg.de>
Diff between sjSDM versions 1.0.6 dated 2024-08-19 and 1.0.7 dated 2025-09-17
DESCRIPTION | 15 MD5 | 40 - NEWS.md | 9 R/anova.R | 24 - R/importance.R | 101 ++-- R/installation_help.R | 8 R/internalStructure.R | 231 ++++++++--- R/sjSDM.R | 4 R/sjSDM_cv.R | 5 build/stage23.rdb |binary build/vignette.rds |binary inst/doc/sjSDM_Introduction.Rmd | 8 inst/doc/sjSDM_Introduction.html | 24 - inst/python/sjSDM_py/__pycache__/dist_mvp.cpython-310.pyc |binary inst/python/sjSDM_py/__pycache__/model_sjSDM.cpython-310.pyc |binary inst/python/sjSDM_py/dist_mvp.py | 4 inst/python/sjSDM_py/model_sjSDM.py | 35 + man/installation_help.Rd | 8 tests/testthat/test-5-importance.R | 218 +++++----- vignettes/sjSDM_Introduction.Rmd | 8 vignettes/sjSDM_Introduction.orig | 8 21 files changed, 458 insertions(+), 292 deletions(-)
Title: Bootstrapping Helpers for Structural Equation Modelling
Description: A collection of helper functions for forming
bootstrapping confidence intervals and examining bootstrap
estimates in structural equation modelling. Currently
supports models fitted by the 'lavaan' package by
Rosseel (2012) <doi: 10.18637/jss.v048.i02>.
Author: Wendie Yang [aut, cre] ,
Shu Fai Cheung [aut]
Maintainer: Wendie Yang <1581075494q@gmail.com>
Diff between semboottools versions 0.1.0 dated 2025-04-01 and 0.1.1 dated 2025-09-17
DESCRIPTION | 12 MD5 | 8 NEWS.md | 78 +++++- README.md | 13 - man/hist_qq_boot.Rd | 662 ++++++++++++++++++++++++++-------------------------- 5 files changed, 424 insertions(+), 349 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.21.0 dated 2025-04-24 and 1.22.0 dated 2025-09-17
broom.helpers-1.21.0/broom.helpers/R/select_utilities.R |only broom.helpers-1.21.0/broom.helpers/man/dot-formula_list_to_named_list.Rd |only broom.helpers-1.21.0/broom.helpers/man/dot-generic_selector.Rd |only broom.helpers-1.21.0/broom.helpers/man/dot-select_to_varnames.Rd |only broom.helpers-1.22.0/broom.helpers/DESCRIPTION | 20 broom.helpers-1.22.0/broom.helpers/MD5 | 96 +- broom.helpers-1.22.0/broom.helpers/NAMESPACE | 8 broom.helpers-1.22.0/broom.helpers/NEWS.md | 17 broom.helpers-1.22.0/broom.helpers/R/broom.helpers-package.R | 2 broom.helpers-1.22.0/broom.helpers/R/custom_tidiers.R | 43 - broom.helpers-1.22.0/broom.helpers/R/model_get_assign.R | 13 broom.helpers-1.22.0/broom.helpers/R/model_get_contrasts.R | 10 broom.helpers-1.22.0/broom.helpers/R/model_get_model_frame.R | 9 broom.helpers-1.22.0/broom.helpers/R/model_get_model_matrix.R | 14 broom.helpers-1.22.0/broom.helpers/R/model_get_weights.R | 10 broom.helpers-1.22.0/broom.helpers/build/vignette.rds |binary broom.helpers-1.22.0/broom.helpers/data/supported_models.rda |binary broom.helpers-1.22.0/broom.helpers/inst/doc/broom-helpers.R | 2 broom.helpers-1.22.0/broom.helpers/inst/doc/broom-helpers.Rmd | 2 broom.helpers-1.22.0/broom.helpers/inst/doc/broom-helpers.html | 394 +++++----- broom.helpers-1.22.0/broom.helpers/man/model_get_assign.Rd | 3 broom.helpers-1.22.0/broom.helpers/man/model_get_contrasts.Rd | 3 broom.helpers-1.22.0/broom.helpers/man/model_get_model_matrix.Rd | 7 broom.helpers-1.22.0/broom.helpers/man/model_get_pairwise_contrasts.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/model_get_weights.Rd | 3 broom.helpers-1.22.0/broom.helpers/man/model_list_variables.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/select_helpers.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/supported_models.Rd | 1 broom.helpers-1.22.0/broom.helpers/man/tidy_add_estimate_to_reference_rows.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_add_header_rows.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_add_pairwise_contrasts.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_add_reference_rows.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_all_effects.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_avg_comparisons.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_avg_slopes.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_broom.Rd | 4 broom.helpers-1.22.0/broom.helpers/man/tidy_ggpredict.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_group_by.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_marginal_contrasts.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_marginal_predictions.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_margins.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_multgee.Rd | 6 broom.helpers-1.22.0/broom.helpers/man/tidy_parameters.Rd | 10 broom.helpers-1.22.0/broom.helpers/man/tidy_plus_plus.Rd | 2 broom.helpers-1.22.0/broom.helpers/man/tidy_svy_vglm.Rd | 6 broom.helpers-1.22.0/broom.helpers/man/tidy_vgam.Rd | 6 broom.helpers-1.22.0/broom.helpers/man/tidy_with_broom_or_parameters.Rd | 9 broom.helpers-1.22.0/broom.helpers/man/tidy_zeroinfl.Rd | 6 broom.helpers-1.22.0/broom.helpers/tests/testthat/test-model_get_n.R | 25 broom.helpers-1.22.0/broom.helpers/tests/testthat/test-tidy_plus_plus.R | 36 broom.helpers-1.22.0/broom.helpers/vignettes/broom-helpers.Rmd | 2 51 files changed, 466 insertions(+), 333 deletions(-)
Title: R Interface to the A/B Street Transport System Simulation
Software
Description: Provides functions to convert origin-destination data,
represented as straight 'desire lines' in the 'sf' Simple Features
class system, into JSON files that can be directly imported into
A/B Street <https://www.abstreet.org>, a free and open source tool
for simulating urban transport systems and scenarios of change
<doi:10.1007/s10109-020-00342-2>.
Author: Robin Lovelace [aut, cre] ,
Nathanael Sheehan [aut] ,
Trevor Nederlof [aut],
Lucas Dias [ctb],
Dustin Carlino [aut]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between abstr versions 0.4.1 dated 2021-11-30 and 0.4.2 dated 2025-09-17
DESCRIPTION | 29 MD5 | 90 +- NAMESPACE | 18 NEWS.md | 57 + R/ab_scenario.R | 680 +++++++++++----------- R/data.R | 12 R/montlake_buildings.R | 54 - R/montlake_od.R | 38 - R/montlake_zones.R | 32 - R/sao_paulo_activity_df_20.R | 124 ++-- R/utils-pipe.R | 38 - README.md | 538 +++++++++-------- build/vignette.rds |binary inst/doc/abstr.R | 96 +-- inst/doc/abstr.Rmd | 352 +++++------ inst/doc/abstr.html | 841 ++++++++++++++++++--------- inst/doc/activity.R | 234 +++---- inst/doc/activity.Rmd | 496 ++++++++-------- inst/doc/activity.html | 1002 ++++++++++++++++++++------------- inst/doc/montlake.R | 254 ++++---- inst/doc/montlake.Rmd | 452 +++++++------- inst/doc/montlake.html | 921 +++++++++++++++++++----------- inst/doc/pct_to_abstr.R | 404 ++++++------- inst/doc/pct_to_abstr.Rmd | 679 +++++++++++----------- inst/doc/pct_to_abstr.html | 1087 ++++++++++++++++++++++-------------- inst/extdata/activity_leeds.json | 188 +++--- inst/extdata/minimal_scenario.json | 86 +- inst/extdata/minimal_scenario2.json | 162 ++--- man/ab_json.Rd | 132 ++-- man/ab_save.Rd | 38 - man/ab_scenario.Rd | 180 ++--- man/ab_sf.Rd | 76 +- man/ab_time_normal.Rd | 64 +- man/figures/README-input-1.png |binary man/figures/README-outputplot-1.png |binary man/leeds_site_area.Rd | 26 man/montlake_buildings.Rd | 70 +- man/montlake_od.Rd | 60 - man/montlake_zones.Rd | 54 - man/pipe.Rd | 40 - man/sao_paulo_activity_df_20.Rd | 86 +- man/sao_paulo_activity_sf_20.Rd | 84 +- vignettes/abstr.Rmd | 352 +++++------ vignettes/activity.Rmd | 496 ++++++++-------- vignettes/montlake.Rmd | 452 +++++++------- vignettes/pct_to_abstr.Rmd | 679 +++++++++++----------- 46 files changed, 6443 insertions(+), 5410 deletions(-)
Title: Steve's Toy Data for Teaching About a Variety of Methodological,
Social, and Political Topics
Description: This is a collection of various kinds of data with broad uses for teaching.
My students, and academics like me who teach the same topics I teach, should find
this useful if their teaching workflow is also built around the R programming
language. The applications are multiple but mostly cluster on topics of statistical
methodology, international relations, and political economy.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steve@svmiller.com>
Diff between stevedata versions 1.6.0 dated 2025-07-18 and 1.7.0 dated 2025-09-17
DESCRIPTION | 6 ++-- MD5 | 57 ++++++++++++++++++++++++++------------------- NEWS.md | 15 +++++++++++ R/rd-GHR04.R | 16 ++++++++---- R/rd-Lipset59.R | 11 +++++--- R/rd-Weede84.R |only R/rd-mmb_war.R |only R/rd-stevesteps.R |only build/partial.rdb |binary data/DJIA.rda |binary data/ESS10NO.rda |binary data/GHR04.rda |binary data/PPGE.rda |binary data/USFAHR.rda |binary data/Weede84.rda |only data/chile88.rda |binary data/china_peace.rda |binary data/coffee_imports.rda |binary data/country_isocodes.rda |binary data/eu_ua_fta24.rda |binary data/mmb_war.rda |only data/rok_unga.rda |binary data/scb_regions.rda |binary data/states_war.rda |binary data/stevesteps.rda |only data/thatcher_approval.rda |binary data/turnips.rda |binary data/wb_groups.rda |binary data/wbd_example.rda |binary man/GHR04.Rd | 16 ++++++++---- man/Lipset59.Rd | 11 +++++--- man/Weede84.Rd |only man/mmb_war.Rd |only man/stevesteps.Rd |only 34 files changed, 87 insertions(+), 45 deletions(-)
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Alejandro Szmulewicz [aut] ,
Tom Palmer [aut] ,
Miguel Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryanodea@hsph.harvard.edu>
Diff between SEQTaRget versions 0.13.1 dated 2025-09-15 and 1.0.0 dated 2025-09-17
DESCRIPTION | 18 +++++++++++++----- MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + R/SEQopts.R | 3 ++- R/SEQuential.R | 4 ++-- R/class_definitions.R | 2 +- README.md | 37 +++++++++++++++++++------------------ inst/doc/ITT.html | 2 +- inst/doc/SEQuential.html | 2 +- inst/doc/censoring.html | 2 +- inst/doc/doseresponse.html | 2 +- man/SEQopts.Rd | 2 +- man/SEQuential.Rd | 4 ++-- 13 files changed, 57 insertions(+), 46 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.3.5 dated 2025-08-18 and 2.3.6 dated 2025-09-17
GitStats-2.3.5/GitStats/inst/cache_workflow.R |only GitStats-2.3.5/GitStats/inst/example_workflow.R |only GitStats-2.3.5/GitStats/inst/get_commits_workflow.R |only GitStats-2.3.5/GitStats/inst/get_files_workflow.R |only GitStats-2.3.5/GitStats/inst/get_issues_workflow.R |only GitStats-2.3.5/GitStats/inst/get_orgs_workflow.R |only GitStats-2.3.5/GitStats/inst/get_repos_for_individual_users.R |only GitStats-2.3.5/GitStats/inst/get_repos_tree_workflow.R |only GitStats-2.3.5/GitStats/inst/get_repos_urls_workflow.R |only GitStats-2.3.5/GitStats/inst/get_storage_workflow.R |only GitStats-2.3.5/GitStats/inst/set_hosts.R |only GitStats-2.3.5/GitStats/inst/set_many_repos.R |only GitStats-2.3.5/GitStats/inst/set_tokens.R |only GitStats-2.3.5/GitStats/inst/verbose_workflow.R |only GitStats-2.3.5/GitStats/tests/testthat/_snaps/00-api-requests.md |only GitStats-2.3.6/GitStats/DESCRIPTION | 6 GitStats-2.3.6/GitStats/MD5 | 93 +--- GitStats-2.3.6/GitStats/NEWS.md | 13 GitStats-2.3.6/GitStats/R/EngineGraphQL.R | 58 +- GitStats-2.3.6/GitStats/R/EngineGraphQLGitHub.R | 231 +++++----- GitStats-2.3.6/GitStats/R/EngineGraphQLGitLab.R | 156 ++++-- GitStats-2.3.6/GitStats/R/EngineRest.R | 31 - GitStats-2.3.6/GitStats/R/EngineRestGitHub.R | 106 ++-- GitStats-2.3.6/GitStats/R/EngineRestGitLab.R | 129 +++-- GitStats-2.3.6/GitStats/R/GQLQueryGitHub.R | 17 GitStats-2.3.6/GitStats/R/GQLQueryGitLab.R | 17 GitStats-2.3.6/GitStats/R/GitHost.R | 124 +++-- GitStats-2.3.6/GitStats/R/GitHostGitHub.R | 7 GitStats-2.3.6/GitStats/R/GitHostGitLab.R | 32 - GitStats-2.3.6/GitStats/R/GitStats.R | 67 +- GitStats-2.3.6/GitStats/R/get_repos.R | 4 GitStats-2.3.6/GitStats/man/get_repos.Rd | 4 GitStats-2.3.6/GitStats/tests/testthat/_snaps/00-get_orgs-GitLab.md | 8 GitStats-2.3.6/GitStats/tests/testthat/_snaps/01-get_repos-GitHub.md | 30 - GitStats-2.3.6/GitStats/tests/testthat/_snaps/01-get_repos-GitLab.md | 6 GitStats-2.3.6/GitStats/tests/testthat/_snaps/02-get_commits-GitHub.md | 8 GitStats-2.3.6/GitStats/tests/testthat/_snaps/03-get_files_structure-GitLab.md | 2 GitStats-2.3.6/GitStats/tests/testthat/_snaps/04-get_files_content-GitHub.md | 2 GitStats-2.3.6/GitStats/tests/testthat/_snaps/04-get_files_content-GitLab.md | 4 GitStats-2.3.6/GitStats/tests/testthat/_snaps/helpers.md | 2 GitStats-2.3.6/GitStats/tests/testthat/helper-error-fixtures.R | 16 GitStats-2.3.6/GitStats/tests/testthat/helper-expect-responses.R | 10 GitStats-2.3.6/GitStats/tests/testthat/helper-expect-tables.R | 21 GitStats-2.3.6/GitStats/tests/testthat/helper-fixtures.R | 100 +++- GitStats-2.3.6/GitStats/tests/testthat/test-00-api-requests.R | 29 - GitStats-2.3.6/GitStats/tests/testthat/test-00-get_orgs-GitHub.R | 19 GitStats-2.3.6/GitStats/tests/testthat/test-00-get_orgs-GitLab.R | 20 GitStats-2.3.6/GitStats/tests/testthat/test-00-graphql_errors.R | 11 GitStats-2.3.6/GitStats/tests/testthat/test-01-get_repos-GitHub.R | 170 ++++--- GitStats-2.3.6/GitStats/tests/testthat/test-01-get_repos-GitLab.R | 17 GitStats-2.3.6/GitStats/tests/testthat/test-01-get_repos-GitStats.R | 2 GitStats-2.3.6/GitStats/tests/testthat/test-02-get_commits-GitHub.R | 41 + GitStats-2.3.6/GitStats/tests/testthat/test-03-get_files_structure-GitLab.R | 4 GitStats-2.3.6/GitStats/tests/testthat/test-04-get_files-REST-GitHub.R |only GitStats-2.3.6/GitStats/tests/testthat/test-04-get_files-REST-GitLab.R |only GitStats-2.3.6/GitStats/tests/testthat/test-06-get_issues-GitHub.R | 19 56 files changed, 1000 insertions(+), 636 deletions(-)
Title: Flexible, Extensible, & Reproducible Pupillometry Preprocessing
Description: Pupillometry offers a non-invasive window into the mind and has been used extensively as a psychophysiological readout of arousal signals linked with cognitive processes like attention, stress, and emotional states [Clewett et al. (2020) <doi:10.1038/s41467-020-17851-9>; Kret & Sjak-Shie (2018) <doi:10.3758/s13428-018-1075-y>; Strauch (2024) <doi:10.1016/j.tins.2024.06.002>]. Yet, despite decades of pupillometry research, many established packages and workflows to date lack design patterns based on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles [see Wilkinson et al. (2016) <doi:10.1038/sdata.2016.18>]. 'eyeris' provides a modular, performant, and extensible preprocessing framework for pupillometry data with BIDS-like organization and interactive output reports [Esteban et al. (2019) <doi:10.1038/s41592-018-0235-4>; Gorgolewski et al. (2016) <doi:10.1038/sdata.2016.44>]. Development was supported, in part, by the S [...truncated...]
Author: Shawn Schwartz [aut, cre] ,
Mingjian He [ctb],
Haopei Yang [ctb],
Alice Xue [ctb],
Gustavo Santiago-Reyes [ctb]
Maintainer: Shawn Schwartz <shawn.t.schwartz@gmail.com>
Diff between eyeris versions 2.1.1 dated 2025-07-26 and 3.0.0 dated 2025-09-17
eyeris-2.1.1/eyeris/R/utils-alert.R |only eyeris-2.1.1/eyeris/man/alert.Rd |only eyeris-3.0.0/eyeris/DESCRIPTION | 16 eyeris-3.0.0/eyeris/MD5 | 254 eyeris-3.0.0/eyeris/NAMESPACE | 15 eyeris-3.0.0/eyeris/NEWS.md | 141 eyeris-3.0.0/eyeris/R/constants.R | 10 eyeris-3.0.0/eyeris/R/core-logging.R |only eyeris-3.0.0/eyeris/R/eyeris-package.R | 3 eyeris-3.0.0/eyeris/R/pipeline-bidsify.R | 2881 ++++------ eyeris-3.0.0/eyeris/R/pipeline-bin.R | 36 eyeris-3.0.0/eyeris/R/pipeline-confounds.R | 243 eyeris-3.0.0/eyeris/R/pipeline-deblink.R | 29 eyeris-3.0.0/eyeris/R/pipeline-detransient.R | 10 eyeris-3.0.0/eyeris/R/pipeline-detrend.R | 9 eyeris-3.0.0/eyeris/R/pipeline-downsample.R | 48 eyeris-3.0.0/eyeris/R/pipeline-epoch.R | 266 eyeris-3.0.0/eyeris/R/pipeline-glassbox.R | 504 - eyeris-3.0.0/eyeris/R/pipeline-handler.R | 74 eyeris-3.0.0/eyeris/R/pipeline-interpolate.R | 23 eyeris-3.0.0/eyeris/R/pipeline-loadasc.R | 79 eyeris-3.0.0/eyeris/R/pipeline-lpfilt.R | 25 eyeris-3.0.0/eyeris/R/pipeline-zscore.R | 46 eyeris-3.0.0/eyeris/R/plot.eyeris.R | 287 eyeris-3.0.0/eyeris/R/utils-baseline.R | 51 eyeris-3.0.0/eyeris/R/utils-checks.R | 128 eyeris-3.0.0/eyeris/R/utils-database.R |only eyeris-3.0.0/eyeris/R/utils-epoch.R | 110 eyeris-3.0.0/eyeris/R/utils-error_handler.R | 2 eyeris-3.0.0/eyeris/R/utils-eyelogger.R | 6 eyeris-3.0.0/eyeris/R/utils-gallery.R | 350 + eyeris-3.0.0/eyeris/R/utils-parquet-split.R |only eyeris-3.0.0/eyeris/R/utils-parsers.R | 32 eyeris-3.0.0/eyeris/R/utils-progress_bar.R | 9 eyeris-3.0.0/eyeris/R/utils-render_report.R | 160 eyeris-3.0.0/eyeris/R/utils-zip-cleanup.R |only eyeris-3.0.0/eyeris/R/utils-zip-gallery.R |only eyeris-3.0.0/eyeris/R/zzz.R | 35 eyeris-3.0.0/eyeris/README.md | 267 eyeris-3.0.0/eyeris/build/vignette.rds |binary eyeris-3.0.0/eyeris/inst/WORDLIST | 42 eyeris-3.0.0/eyeris/inst/doc/anatomy.html | 5 eyeris-3.0.0/eyeris/inst/doc/chunked-database-export.R |only 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Title: Canonical Correlations and Tests of Independence
Description: A simple interface for multivariate correlation analysis that unifies various classical
statistical procedures including t-tests, tests in univariate and multivariate linear models,
parametric and nonparametric tests for correlation, Kruskal-Wallis tests, common approximate
versions of Wilcoxon rank-sum and signed rank tests, chi-squared tests of independence, score
tests of particular hypotheses in generalized linear models, canonical correlation analysis and
linear discriminant analysis.
Author: Robert Schlicht [aut, cre]
Maintainer: Robert Schlicht <robert.schlicht@tu-dresden.de>
Diff between cctest versions 2.1.0 dated 2025-05-07 and 2.2.0 dated 2025-09-17
DESCRIPTION | 6 +- MD5 | 8 +-- R/cctest.R | 126 ++++++++++++++++++++++++++---------------------------- build/partial.rdb |binary man/cctest.Rd | 114 ++++++++++++++++++++++++++---------------------- 5 files changed, 130 insertions(+), 124 deletions(-)
Title: Beta Kernel Process Modeling
Description: Implements the Beta Kernel Process (BKP) for nonparametric modeling of spatially varying binomial probabilities, together with its extension, the Dirichlet Kernel Process (DKP), for categorical or multinomial data.
The package provides functions for model fitting, predictive inference with uncertainty quantification, posterior simulation, and visualization in one-and two-dimensional input spaces.
Multiple kernel functions (Gaussian, Matern 5/2, and Matern 3/2) are supported, with hyperparameters optimized through multi-start gradient-based search.
For more details, see Zhao, Qing, and Xu (2025) <doi:10.48550/arXiv.2508.10447>.
Author: Jiangyan Zhao [cre, aut],
Kunhai Qing [aut],
Jin Xu [aut]
Maintainer: Jiangyan Zhao <zhaojy2017@126.com>
Diff between BKP versions 0.2.0 dated 2025-09-16 and 0.2.1 dated 2025-09-17
DESCRIPTION | 6 ++-- MD5 | 16 ++++++------- NEWS.md | 6 ++++ README.md | 2 - inst/CITATION | 2 - inst/doc/vignettes.R | 6 ++++ inst/doc/vignettes.Rmd | 58 ++++++++++++++++++++++++++---------------------- inst/doc/vignettes.pdf |binary vignettes/vignettes.Rmd | 58 ++++++++++++++++++++++++++---------------------- 9 files changed, 88 insertions(+), 66 deletions(-)
Title: Develop a 'Telegram Bot' with R
Description: Provides a pure interface for the 'Telegram Bot API'
<http://core.telegram.org/bots/api>. In addition to the pure API
implementation, it features a number of tools to make the development of
'Telegram' bots with R easy and straightforward, providing an easy-to-use
interface that takes some work off the programmer.
Author: Ernest Benedito [aut, cre],
Chris Stefano [ctb]
Maintainer: Ernest Benedito <ebeneditos@gmail.com>
Diff between telegram.bot versions 3.0.0 dated 2022-09-07 and 3.0.1 dated 2025-09-17
DESCRIPTION | 8 MD5 | 226 - NAMESPACE | 104 NEWS.md | 190 - R/base.R | 216 - R/basefilter.R | 157 - R/bot.R | 3585 +++++++++++------------- R/callbackqueryhandler.R | 121 R/commandhandler.R | 257 - R/dispatcher.R | 329 +- R/errorhandler.R | 97 R/filters.R | 121 R/handler.R | 283 - R/inlinequeryresult.R | 101 R/messagehandler.R | 165 - R/replymarkup.R | 713 ++-- R/telegram.bot-package.R | 107 R/update.R | 427 +- R/updater.R | 481 +-- R/utils.R | 171 - R/webhook.R | 872 ++--- README.md | 424 +- build/vignette.rds |binary inst/doc/telegrambot-advanced-filters.R | 85 inst/doc/telegrambot-advanced-filters.Rmd | 213 - inst/doc/telegrambot-advanced-filters.html | 896 +++-- inst/doc/telegrambot-basic-functionalities.R | 96 inst/doc/telegrambot-basic-functionalities.Rmd | 210 - inst/doc/telegrambot-basic-functionalities.html | 925 +++--- inst/doc/telegrambot-building-a-bot.R | 68 inst/doc/telegrambot-building-a-bot.Rmd | 208 - inst/doc/telegrambot-building-a-bot.html | 901 +++--- inst/doc/telegrambot-introduction.R | 160 - inst/doc/telegrambot-introduction.Rmd | 360 +- inst/doc/telegrambot-introduction.html | 1113 +++---- inst/doc/telegrambot-set-a-proxy.R | 24 inst/doc/telegrambot-set-a-proxy.Rmd | 62 inst/doc/telegrambot-set-a-proxy.html | 743 ++-- inst/doc/telegrambot-the-add-operator.R | 108 inst/doc/telegrambot-the-add-operator.Rmd | 198 - inst/doc/telegrambot-the-add-operator.html | 845 ++--- man/BaseFilter.Rd | 86 man/Bot.Rd | 186 - man/CallbackQueryHandler.Rd | 44 man/CommandHandler.Rd | 116 man/Dispatcher.Rd | 64 man/ErrorHandler.Rd | 78 man/ForceReply.Rd | 66 man/Handler.Rd | 180 - man/InlineKeyboardButton.Rd | 104 man/InlineKeyboardMarkup.Rd | 124 man/InlineQueryResult.Rd | 88 man/KeyboardButton.Rd | 70 man/MessageFilters.Rd | 98 man/MessageHandler.Rd | 70 man/ReplyKeyboardMarkup.Rd | 116 man/ReplyKeyboardRemove.Rd | 110 man/TelegramObject-add.Rd | 126 man/TelegramObject.Rd | 86 man/Update.Rd | 76 man/Updater.Rd | 184 - man/Webhook.Rd | 298 - man/add_error_handler.Rd | 70 man/add_handler.Rd | 66 man/answerCallbackQuery.Rd | 76 man/answerInlineQuery.Rd | 130 man/bot_token.Rd | 54 man/check_update.Rd | 32 man/clean_updates.Rd | 24 man/deleteMessage.Rd | 54 man/deleteWebhook.Rd | 30 man/editMessageCaption.Rd | 94 man/editMessageReplyMarkup.Rd | 78 man/editMessageText.Rd | 102 man/effective_chat.Rd | 28 man/effective_message.Rd | 28 man/effective_user.Rd | 24 man/filtersLogic.Rd | 68 man/forwardMessage.Rd | 52 man/from_chat_id.Rd | 22 man/from_user_id.Rd | 22 man/getFile.Rd | 82 man/getMe.Rd | 28 man/getUpdates.Rd | 106 man/getUserProfilePhotos.Rd | 66 man/getWebhookInfo.Rd | 34 man/handle_update.Rd | 44 man/leaveChat.Rd | 36 man/running.Rd | 22 man/sendAnimation.Rd | 146 man/sendAudio.Rd | 152 - man/sendChatAction.Rd | 92 man/sendDocument.Rd | 138 man/sendLocation.Rd | 110 man/sendMessage.Rd | 124 man/sendPhoto.Rd | 130 man/sendSticker.Rd | 110 man/sendVideo.Rd | 154 - man/sendVideoNote.Rd | 122 man/sendVoice.Rd | 138 man/setWebhook.Rd | 132 man/set_token.Rd | 28 man/start_polling.Rd | 96 man/start_server.Rd | 98 man/stop_polling.Rd | 60 man/stop_server.Rd | 56 man/telegram.bot.Rd | 132 man/user_id.Rd | 54 vignettes/telegrambot-advanced-filters.Rmd | 213 - vignettes/telegrambot-basic-functionalities.Rmd | 210 - vignettes/telegrambot-building-a-bot.Rmd | 208 - vignettes/telegrambot-introduction.Rmd | 360 +- vignettes/telegrambot-set-a-proxy.Rmd | 62 vignettes/telegrambot-the-add-operator.Rmd | 198 - 114 files changed, 11819 insertions(+), 11716 deletions(-)
Title: Data Science Labs
Description: Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops. 26 datasets are available for case studies in data visualization, statistical inference, modeling, linear regression, data wrangling and machine learning.
Author: Rafael A. Irizarry [aut, cre],
Amy Gill [aut]
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>
Diff between dslabs versions 0.8.0 dated 2024-03-01 and 0.9.0 dated 2025-09-17
DESCRIPTION | 23 ++++++++++----- MD5 | 16 +++++++--- NAMESPACE | 1 R/fit_recommender_model.R |only R/results_us_election_2012.R |only build/partial.rdb |binary data/polls_us_election_2016.rda |binary data/results_us_election_2012.rda |only inst/script/make-polls_us_election_2016.R | 41 +++++++++++++++------------- inst/script/make-results_us_election_2012.R |only man/fit_recommender_model.Rd |only man/results_us_election_2012.Rd |only 12 files changed, 51 insertions(+), 30 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions).
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis. <doi:10.48550/arXiv.1106.1451>.
b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534. <doi:10.6339/JDS.201407_12(3).0008>.
c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444. <doi:10.48550/arXiv.15 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 7.7 dated 2025-08-18 and 7.8 dated 2025-09-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 +- R/mkde.R | 26 ++++++++++++++++---------- man/Compositional-package.Rd | 4 ++-- man/mkde.Rd | 5 ++++- 6 files changed, 32 insertions(+), 23 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilD [...truncated...]
Author: Dylan Beaudette [aut, cre],
Pierre Roudier [aut, ctb],
Andrew Brown [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between aqp versions 2.2 dated 2025-02-15 and 2.2-1 dated 2025-09-17
aqp-2.2-1/aqp/DESCRIPTION | 11 aqp-2.2-1/aqp/MD5 | 109 +++----- aqp-2.2-1/aqp/NAMESPACE | 3 aqp-2.2-1/aqp/NEWS.md | 12 aqp-2.2-1/aqp/R/NCSP.R | 100 ++++--- aqp-2.2-1/aqp/R/SoilProfileCollection-metadata.R | 3 aqp-2.2-1/aqp/R/accumulateDepths.R | 22 + aqp-2.2-1/aqp/R/aqp-package.R | 2 aqp-2.2-1/aqp/R/col2Munsell.R | 8 aqp-2.2-1/aqp/R/colorChart.R | 6 aqp-2.2-1/aqp/R/data-documentation.R | 6 aqp-2.2-1/aqp/R/evalMissingData.R | 10 aqp-2.2-1/aqp/R/fragmentClasses.R | 2 aqp-2.2-1/aqp/R/hzTransitionProbabilities.R | 2 aqp-2.2-1/aqp/R/mixMunsell.R | 4 aqp-2.2-1/aqp/R/mostLikelyHzSequence.R | 2 aqp-2.2-1/aqp/R/munsell2rgb.R | 14 - aqp-2.2-1/aqp/R/particleSizeClasses.R |only aqp-2.2-1/aqp/R/random_profile.R | 57 ++++ aqp-2.2-1/aqp/build/partial.rdb |binary aqp-2.2-1/aqp/build/vignette.rds |binary aqp-2.2-1/aqp/data/munsell.spectra.rda |binary aqp-2.2-1/aqp/data/munsell.spectra.wide.rda |binary aqp-2.2-1/aqp/data/munsellHuePosition.rda |binary aqp-2.2-1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.R | 2 aqp-2.2-1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.Rmd | 2 aqp-2.2-1/aqp/inst/doc/Introduction-to-SoilProfileCollection-Objects.html | 136 +++++----- aqp-2.2-1/aqp/inst/doc/Munsell-color-conversion.R | 2 aqp-2.2-1/aqp/inst/doc/Munsell-color-conversion.Rmd | 2 aqp-2.2-1/aqp/inst/doc/Munsell-color-conversion.html | 4 aqp-2.2-1/aqp/inst/doc/NCSP.R | 4 aqp-2.2-1/aqp/inst/doc/NCSP.Rmd | 4 aqp-2.2-1/aqp/inst/doc/NCSP.html | 12 aqp-2.2-1/aqp/inst/doc/label-placement.R | 19 - aqp-2.2-1/aqp/inst/doc/label-placement.Rmd | 20 - aqp-2.2-1/aqp/inst/doc/label-placement.html | 134 +++++---- aqp-2.2-1/aqp/man/NCSP.Rd | 28 -- aqp-2.2-1/aqp/man/accumulateDepths.Rd | 6 aqp-2.2-1/aqp/man/col2Munsell.Rd | 10 aqp-2.2-1/aqp/man/colorChart.Rd | 2 aqp-2.2-1/aqp/man/mixMunsell.Rd | 4 aqp-2.2-1/aqp/man/munsell.spectra.Rd | 4 aqp-2.2-1/aqp/man/munsell2rgb.Rd | 6 aqp-2.2-1/aqp/man/random_profile.Rd | 5 aqp-2.2-1/aqp/man/rgb2munsell.Rd | 10 aqp-2.2-1/aqp/man/rp.Rd |only aqp-2.2-1/aqp/tests/testthat/Rplots.pdf |binary aqp-2.2-1/aqp/tests/testthat/test-NCSP.R | 37 ++ aqp-2.2-1/aqp/tests/testthat/test-spec2Munsell.R | 42 +++ aqp-2.2-1/aqp/vignettes/Introduction-to-SoilProfileCollection-Objects.Rmd | 2 aqp-2.2-1/aqp/vignettes/Munsell-color-conversion.Rmd | 2 aqp-2.2-1/aqp/vignettes/NCSP.Rmd | 4 aqp-2.2-1/aqp/vignettes/label-placement.Rmd | 20 - aqp-2.2/aqp/R/unroll.R |only aqp-2.2/aqp/inst/_pkgdown.yml |only aqp-2.2/aqp/inst/doc/missing-data.R |only aqp-2.2/aqp/inst/doc/missing-data.Rmd |only aqp-2.2/aqp/inst/doc/missing-data.html |only aqp-2.2/aqp/man/unroll.Rd |only aqp-2.2/aqp/vignettes/missing-data.Rmd |only 60 files changed, 540 insertions(+), 356 deletions(-)
Title: 'Arrow' Database Connectivity ('ADBC') Driver Manager
Description: Provides a developer-facing interface to 'Arrow' Database
Connectivity ('ADBC') for the purposes of driver development, driver
testing, and building high-level database interfaces for users. 'ADBC'
<https://arrow.apache.org/adbc/> is an API standard for database access
libraries that uses 'Arrow' for result sets and query parameters.
Author: Dewey Dunnington [aut, cre] ,
Apache Arrow [aut, cph],
Apache Software Foundation [cph]
Maintainer: Dewey Dunnington <dewey@dunnington.ca>
Diff between adbcdrivermanager versions 0.19.0-1 dated 2025-07-20 and 0.20.0 dated 2025-09-17
DESCRIPTION | 6 MD5 | 38 - R/driver_void.R | 15 man/adbc_driver_load.Rd | 6 man/adbc_load_flags.Rd | 11 src/Makevars | 3 src/Makevars.win | 3 src/c/driver/postgresql/postgres_type.h | 18 src/c/driver/sqlite/sqlite.cc | 17 src/c/driver/sqlite/statement_reader.c | 56 ++ src/c/driver/sqlite/statement_reader.h | 6 src/c/driver_manager/adbc_driver_manager.cc | 522 ++++++++++++++++++++----- src/c/driver_manager/current_arch.h | 53 ++ src/c/include/arrow-adbc/adbc_driver_manager.h | 33 + src/c/vendor/nanoarrow/nanoarrow.c | 251 +++++++++++- src/c/vendor/nanoarrow/nanoarrow.h | 447 ++++++++++++++------- src/c/vendor/nanoarrow/nanoarrow.hpp | 473 +++++++++++++++------- src/init.c | 5 src/radbc.cc | 9 tests/testthat/test-driver_void.R | 5 20 files changed, 1508 insertions(+), 469 deletions(-)
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Title: Price Index Aggregation
Description: Most price indexes are made with a two-step procedure, where
period-over-period elementary indexes are first calculated for a collection
of elementary aggregates at each point in time, and then aggregated according
to a price index aggregation structure. These indexes can then be chained
together to form a time series that gives the evolution of prices with
respect to a fixed base period. This package contains a collection of
functions that revolve around this work flow, making it easy to build
standard price indexes, and implement the methods described by
Balk (2008, <doi:10.1017/CBO9780511720758>), von der Lippe (2007,
<doi:10.3726/978-3-653-01120-3>), and the CPI manual (2020,
<doi:10.5089/9781484354841.069>) for bilateral price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between piar versions 0.8.2 dated 2025-03-19 and 0.8.3 dated 2025-09-17
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