Title: A Toolkit for Omics Data Visualization
Description: Provides a suite of tools for the comprehensive visualization of multi-omics data, including genomics, transcriptomics, and proteomics. Offers user-friendly functions to generate publication-quality plots, thereby facilitating the exploration and interpretation of complex biological datasets. Supports seamless integration with popular R visualization frameworks and is well-suited for both exploratory data analysis and the presentation of final results. Key formats and methods are presented in Huang, S., et al. (2024) "The Born in Guangzhou Cohort Study enables generational genetic discoveries" <doi:10.1038/s41586-023-06988-4>.
Author: Zhen Lu [aut, cre]
Maintainer: Zhen Lu <luzh29@mail2.sysu.edu.cn>
Diff between omixVizR versions 1.1.3 dated 2025-07-20 and 1.4.0 dated 2025-10-11
DESCRIPTION | 12 +++++++----- LICENSE | 4 ++-- MD5 | 28 ++++++++++++++++++---------- NAMESPACE | 23 +++++++++++++++++++++++ NEWS.md | 24 ++++++++++++++++++++++++ R/MR_2SLS.R |only R/gwas_power.R | 36 ++++++++++++++++++++++++++---------- R/gwas_qqman.R | 32 ++++++++++++++++++++++---------- R/omixVizR-package.R | 3 ++- R/plot_forest.R |only R/plot_heatmap.R |only inst/WORDLIST | 27 ++++++++++++++++++++++++++- man/MR_2SLS.Rd |only man/plot_forest.Rd |only man/plot_gwas_power.Rd | 10 ++++------ man/plot_heatmap.Rd |only man/plot_qqman.Rd | 15 ++++++++------- tests/testthat/test-MR_2SLS.R |only tests/testthat/test-plot_forest.R |only 19 files changed, 162 insertions(+), 52 deletions(-)
Title: Statistical Depth Functions for Multivariate Analysis
Description: Data depth concept offers a variety of powerful and user friendly
tools for robust exploration and inference for multivariate data. The offered
techniques may be successfully used in cases of lack of our knowledge on
parametric models generating data due to their nature. The
package consist of among others implementations of several data depth techniques
involving multivariate quantile-quantile plots, multivariate scatter estimators,
multivariate Wilcoxon tests and robust regressions.
Author: Zygmunt Zawadzki [aut, cre],
Daniel Kosiorowski [aut],
Krzysztof Slomczynski [ctb],
Mateusz Bocian [ctb],
Anna Wegrzynkiewicz [ctb]
Maintainer: Zygmunt Zawadzki <zygmunt@zstat.pl>
Diff between DepthProc versions 2.1.5 dated 2022-02-03 and 2.1.6 dated 2025-10-11
DESCRIPTION | 9 ++++----- MD5 | 32 ++++++++++++++++---------------- R/DepthBasedTests.R | 8 +++++++- R/asymmetrycurve.R | 8 +++++++- R/functional_boxplot.R | 10 +++++----- README.md | 12 +++--------- build/partial.rdb |binary inst/CITATION | 12 +++++++----- man/asymmetryCurve.Rd | 8 +++++++- man/figures/README-contour-1.png |binary man/figures/README-fncBox-1.png |binary man/figures/README-persp-1.png |binary man/fncBoxPlot.Rd | 6 +++--- man/mWilcoxonTest.Rd | 8 +++++++- src/Depth.cpp | 2 +- src/Makevars | 1 - src/Makevars.win | 1 - 17 files changed, 67 insertions(+), 50 deletions(-)
Title: An Import Mechanism for R
Description: Alternative mechanism for importing objects from packages
and R modules. The syntax allows for importing multiple objects with a single
command in an expressive way. The import package bridges some of the gap
between using library (or require) and direct (single-object) imports.
Furthermore the imported objects are not placed in the current environment.
Author: Stefan Milton Bache [aut],
Magnus Thor Torfason [aut, cre]
Maintainer: Magnus Thor Torfason <m@zulutime.net>
Diff between import versions 1.3.2 dated 2024-01-21 and 1.3.3 dated 2025-10-11
import-1.3.2/import/vignettes/import.png |only import-1.3.3/import/DESCRIPTION | 11 import-1.3.3/import/MD5 | 32 - import-1.3.3/import/NEWS.md | 12 import-1.3.3/import/R/from.R | 6 import-1.3.3/import/R/import.R | 6 import-1.3.3/import/R/safe_assign.R | 3 import-1.3.3/import/build/build_and_release_process.R | 4 import-1.3.3/import/build/vignette.rds |binary import-1.3.3/import/inst/WORDLIST | 3 import-1.3.3/import/inst/doc/import.R | 416 +++++++++--------- import-1.3.3/import/inst/doc/import.Rmd | 5 import-1.3.3/import/inst/doc/import.html | 10 import-1.3.3/import/man/figures/logo.png |only import-1.3.3/import/man/import.Rd | 8 import-1.3.3/import/man/importfunctions.Rd | 6 import-1.3.3/import/tests/test_import/test_from.R | 8 import-1.3.3/import/vignettes/import.Rmd | 5 18 files changed, 280 insertions(+), 255 deletions(-)
Title: Easy Data Wrangling and Statistical Transformations
Description: A lightweight package to assist in key steps involved in any data
analysis workflow: (1) wrangling the raw data to get it in the needed form,
(2) applying preprocessing steps and statistical transformations, and
(3) compute statistical summaries of data properties and distributions.
It is also the data wrangling backend for packages in 'easystats' ecosystem.
References: Patil et al. (2022) <doi:10.21105/joss.04684>.
Author: Indrajeet Patil [aut] ,
Etienne Bacher [aut, cre] ,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Brenton M. Wiernik [aut] ,
Remi Theriault [ctb] ,
Thomas J. Faulkenberry [rev],
Robert Garrett [rev]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between datawizard versions 1.2.0 dated 2025-07-17 and 1.3.0 dated 2025-10-11
DESCRIPTION | 13 LICENSE | 4 MD5 | 487 ++--- NAMESPACE | 4 NEWS.md | 2108 ++++++++++++------------ R/adjust.R | 434 ++-- R/assign_labels.R | 335 ++- R/categorize.R | 927 +++++----- R/center.R | 659 ++++--- R/contrs.R | 198 +- R/convert_na_to.R | 420 ++-- R/convert_to_na.R | 420 ++-- R/data.R | 42 R/data_addprefix.R | 136 - R/data_arrange.R | 272 +-- R/data_codebook.R | 1074 ++++++------ R/data_duplicated.R | 201 +- R/data_extract.R | 301 +-- R/data_group.R | 158 - R/data_match.R | 764 ++++---- R/data_merge.R | 817 ++++----- R/data_modify.R | 1276 +++++++------- R/data_partition.R | 319 +-- R/data_peek.R | 281 +-- R/data_read.R | 983 +++++------ R/data_relocate.R | 340 ++- R/data_remove.R | 74 R/data_rename.R | 568 +++--- R/data_replicate.R | 246 +- R/data_rescale.R | 696 ++++--- R/data_restoretype.R | 100 - R/data_reverse.R | 612 +++--- R/data_rotate.R | 192 +- R/data_seek.R | 358 ++-- R/data_select.R | 84 R/data_separate.R | 833 ++++----- R/data_summary.R | 482 ++--- R/data_tabulate.R | 490 ++++- R/data_to_long.R | 748 ++++---- R/data_to_wide.R | 892 +++++----- R/data_unique.R | 295 +-- R/data_unite.R | 230 +- R/data_write.R | 658 +++---- R/data_xtabulate.R | 260 ++ R/datawizard-package.R | 42 R/demean.R | 1115 ++++++------ R/describe_distribution.R | 1513 +++++++++-------- R/descriptives.R | 382 ++-- R/extract_column_names.R | 358 ++-- R/format.R | 192 +- R/labels_to_levels.R | 211 +- R/makepredictcall.R | 163 - R/mean_sd.R | 171 + R/means_by_group.R | 621 +++---- R/normalize.R | 613 +++--- R/ranktransform.R | 397 ++-- R/recode_into.R | 592 +++--- R/recode_values.R | 1096 ++++++------ R/remove_empty.R | 249 +- R/replace_nan_inf.R | 124 - R/rescale_weights.R | 876 +++++---- R/reshape_ci.R | 265 +-- R/row_count.R | 257 +- R/row_means.R | 411 ++-- R/select_nse.R | 1399 ++++++++------- R/skewness_kurtosis.R | 948 +++++----- R/slide.R | 207 +- R/smoothness.R | 262 +- R/standardize.R | 830 ++++----- R/standardize.models.R | 1092 ++++++------ R/text_format.R | 300 +-- R/to_factor.R | 276 +-- R/to_numeric.R | 637 +++---- R/unnormalize.R | 319 +-- R/unstandardize.R | 615 +++---- R/utils-cols.R | 183 +- R/utils-rows.R | 290 +-- R/utils.R | 53 R/utils_labels.R | 173 + R/utils_standardize_center.R | 958 ++++++---- R/visualisation_recipe.R | 177 +- R/weighted_mean_median_sd_mad.R | 301 +-- R/winsorize.R | 295 +-- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 24 inst/WORDLIST | 20 inst/doc/overview_of_vignettes.R | 22 inst/doc/overview_of_vignettes.Rmd | 74 inst/doc/overview_of_vignettes.html | 566 +++--- man/adjust.Rd | 2 man/as.prop.table.Rd |only man/assign_labels.Rd | 296 +-- man/categorize.Rd | 528 +++--- man/center.Rd | 400 ++-- man/coef_var.Rd | 186 +- man/coerce_to_numeric.Rd | 44 man/colnames.Rd | 100 - man/contr.deviation.Rd | 2 man/convert_na_to.Rd | 344 +-- man/convert_to_na.Rd | 252 +- man/data_arrange.Rd | 70 man/data_codebook.Rd | 18 man/data_duplicated.Rd | 218 +- man/data_extract.Rd | 294 +-- man/data_group.Rd | 2 man/data_merge.Rd | 412 ++-- man/data_partition.Rd | 168 - man/data_peek.Rd | 210 +- man/data_prefix_suffix.Rd | 214 +- man/data_relocate.Rd | 310 +-- man/data_replicate.Rd | 200 +- man/data_restoretype.Rd | 70 man/data_rotate.Rd | 136 - man/data_seek.Rd | 136 - man/data_separate.Rd | 454 ++--- man/data_summary.Rd | 134 - man/data_tabulate.Rd | 80 man/data_to_long.Rd | 2 man/data_to_wide.Rd | 64 man/data_unique.Rd | 214 +- man/data_unite.Rd | 232 +- man/datawizard-package.Rd | 102 - man/describe_distribution.Rd | 7 man/distribution_mode.Rd | 60 man/dot-is_deprecated.Rd | 38 man/efc.Rd | 24 man/extract_column_names.Rd | 398 ++-- man/labels_to_levels.Rd | 240 +- man/makepredictcall.dw_transformer.Rd | 106 - man/mean_sd.Rd | 98 - man/means_by_group.Rd | 264 +-- man/nhanes_sample.Rd | 28 man/normalize.Rd | 372 ++-- man/ranktransform.Rd | 288 +-- man/recode_into.Rd | 252 +- man/recode_values.Rd | 598 +++--- man/replace_nan_inf.Rd | 64 man/rescale.Rd | 390 ++-- man/rescale_weights.Rd | 2 man/reshape_ci.Rd | 76 man/reverse.Rd | 300 +-- man/row_count.Rd | 274 +-- man/row_means.Rd | 336 +-- man/rownames.Rd | 110 - man/skewness.Rd | 296 +-- man/slide.Rd | 288 +-- man/smoothness.Rd | 74 man/standardize.Rd | 584 +++--- man/standardize.default.Rd | 200 +- man/text_format.Rd | 162 - man/to_factor.Rd | 268 +-- man/to_numeric.Rd | 290 +-- man/visualisation_recipe.Rd | 60 man/weighted_mean.Rd | 112 - man/winsorize.Rd | 196 +- tests/testthat.R | 8 tests/testthat/_snaps/data_codebook.md | 1488 +++++++++------- tests/testthat/_snaps/data_read.md | 240 +- tests/testthat/_snaps/data_tabulate.md | 354 ++-- tests/testthat/_snaps/describe_distribution.md | 258 +- tests/testthat/_snaps/windows/means_by_group.md | 68 tests/testthat/helper-state.R | 173 + tests/testthat/helper.R | 6 tests/testthat/test-adjust.R | 90 - tests/testthat/test-assign_labels.R | 124 - tests/testthat/test-attributes-grouped-df.R | 132 - tests/testthat/test-attributes.R | 360 ++-- tests/testthat/test-categorize.R | 945 +++++++--- tests/testthat/test-center.R | 392 ++-- tests/testthat/test-coef_var.R | 77 tests/testthat/test-contr.deviation.R | 64 tests/testthat/test-convert_na_to.R | 903 +++++----- tests/testthat/test-convert_to_na.R | 329 ++- tests/testthat/test-data_addprefix.R | 96 - tests/testthat/test-data_arrange.R | 293 +-- tests/testthat/test-data_codebook.R | 475 ++--- tests/testthat/test-data_duplicated.R | 224 +- tests/testthat/test-data_extract.R | 328 +-- tests/testthat/test-data_group.R | 190 +- tests/testthat/test-data_match.R | 721 ++++---- tests/testthat/test-data_merge.R | 602 +++--- tests/testthat/test-data_modify.R | 1908 +++++++++++---------- tests/testthat/test-data_partition.R | 271 +-- tests/testthat/test-data_peek.R | 70 tests/testthat/test-data_read.R | 1159 +++++++------ tests/testthat/test-data_recode.R | 809 +++++---- tests/testthat/test-data_relocate.R | 263 +- tests/testthat/test-data_remove.R | 261 +- tests/testthat/test-data_rename.R | 459 ++--- tests/testthat/test-data_reorder.R | 58 tests/testthat/test-data_replicate.R | 159 + tests/testthat/test-data_rescale.R | 416 ++-- tests/testthat/test-data_restoretype.R | 68 tests/testthat/test-data_reverse.R | 1026 ++++++----- tests/testthat/test-data_rotate.R | 182 +- tests/testthat/test-data_seek.R | 170 + tests/testthat/test-data_select.R | 865 ++++----- tests/testthat/test-data_separate.R | 753 ++++---- tests/testthat/test-data_shift.R | 78 tests/testthat/test-data_summary.R | 567 +++--- tests/testthat/test-data_tabulate.R | 676 ++++++- tests/testthat/test-data_to_factor.R | 381 ++-- tests/testthat/test-data_to_long.R | 1051 ++++++----- tests/testthat/test-data_to_numeric.R | 486 +++-- tests/testthat/test-data_to_wide.R | 1203 +++++++------ tests/testthat/test-data_unique.R | 338 +-- tests/testthat/test-data_unite.R | 368 ++-- tests/testthat/test-data_write.R | 312 +-- tests/testthat/test-demean.R | 610 ++++-- tests/testthat/test-describe_distribution.R | 939 ++++++---- tests/testthat/test-distributions.R | 24 tests/testthat/test-empty-dataframe.R | 148 - tests/testthat/test-extract_column_names.R | 384 ++-- tests/testthat/test-labelled_data.R | 775 ++++---- tests/testthat/test-labels_to_levels.R | 302 +-- tests/testthat/test-makepredictcall.R | 134 - tests/testthat/test-mean_sd.R | 47 tests/testthat/test-means_by_group.R | 58 tests/testthat/test-normalize.R | 481 ++--- tests/testthat/test-print.dw_transformer.R | 14 tests/testthat/test-ranktransform.R | 284 +-- tests/testthat/test-recode_into.R | 762 +++++--- tests/testthat/test-replace_nan_inf.R | 78 tests/testthat/test-rescale_weights.R | 311 +-- tests/testthat/test-reshape_ci.R | 54 tests/testthat/test-row_count.R | 156 + tests/testthat/test-row_means.R | 115 - tests/testthat/test-select_nse.R | 334 +-- tests/testthat/test-skewness-kurtosis.R | 180 +- tests/testthat/test-smoothness.R | 66 tests/testthat/test-standardize-data.R | 778 ++++---- tests/testthat/test-standardize_datagrid.R | 35 tests/testthat/test-standardize_models.R | 834 +++++---- tests/testthat/test-std_center.R | 392 ++-- tests/testthat/test-std_center_scale_args.R | 126 - tests/testthat/test-text_format.R | 170 - tests/testthat/test-unnormalize.R | 284 +-- tests/testthat/test-utils.R | 92 - tests/testthat/test-utils_cols.R | 232 +- tests/testthat/test-utils_rows.R | 447 ++--- tests/testthat/test-weighted-stats.R | 86 tests/testthat/test-winsorization.R | 99 - vignettes/bibliography.bib | 358 ++-- vignettes/overview_of_vignettes.Rmd | 74 245 files changed, 46446 insertions(+), 40323 deletions(-)
Title: Cumulative History Analysis for Bistable Perception Time Series
Description: Estimates cumulative history for time-series for continuously
viewed bistable perceptual rivalry displays. Computes cumulative history
via a homogeneous first order differential process. I.e., it assumes
exponential growth/decay of the history as a function time and perceptually
dominant state, Pastukhov & Braun (2011) <doi:10.1167/11.10.12>.
Supports Gamma, log normal, and normal distribution families.
Provides a method to compute history directly and example of using the
computation on a custom Stan code.
Author: Alexander Pastukhov [aut, cre]
Maintainer: Alexander Pastukhov <pastukhov.alexander@gmail.com>
Diff between bistablehistory versions 1.1.2 dated 2023-09-13 and 1.1.3 dated 2025-10-11
DESCRIPTION | 12 MD5 | 24 build/partial.rdb |binary build/vignette.rds |binary inst/doc/cumulative-history.html | 13 inst/doc/usage-examples.R | 56 inst/doc/usage-examples.html | 10 inst/doc/writing-stan-code.R | 66 inst/doc/writing-stan-code.html | 1 man/bistablehistory-package.Rd | 1 man/waic.cumhist.Rd | 2 src/stanExports_historylm.cc | 34 src/stanExports_historylm.h | 3510 +++++++++++++++++++-------------------- 13 files changed, 1902 insertions(+), 1827 deletions(-)
More information about bistablehistory at CRAN
Permanent link
Title: Point Process Models with LASSO-Type Penalties
Description: Toolkit for fitting point process models with sequences of LASSO penalties ("regularisation paths"), as described in Renner, I.W. and Warton, D.I. (2013) <doi:10.1111/j.1541-0420.2012.01824.x>. Regularisation paths of Poisson point process models or area-interaction models can be fitted with LASSO, adaptive LASSO or elastic net penalties. A number of criteria are available to judge the bias-variance tradeoff.
Author: Ian Renner [aut, cre]
Maintainer: Ian Renner <Ian.Renner@newcastle.edu.au>
Diff between ppmlasso versions 1.4 dated 2024-01-31 and 1.5 dated 2025-10-11
ppmlasso-1.4/ppmlasso/R/ppmlasso |only ppmlasso-1.5/ppmlasso/DESCRIPTION | 16 ++++-- ppmlasso-1.5/ppmlasso/MD5 | 58 +++---------------------- ppmlasso-1.5/ppmlasso/NAMESPACE | 12 ++--- ppmlasso-1.5/ppmlasso/R/ppmlasso_functions.R | 2 ppmlasso-1.5/ppmlasso/data/BlueMountains.RData |binary ppmlasso-1.5/ppmlasso/inst/NEWS | 4 - ppmlasso-1.5/ppmlasso/man/envelope-methods.Rd | 2 ppmlasso-1.5/ppmlasso/man/ppmlasso.Rd | 4 - 9 files changed, 29 insertions(+), 69 deletions(-)
Title: Additional Tools for Developing Spatially Explicit Discrete
Event Simulation (SpaDES) Models
Description: Provides GIS and map utilities, plus additional modeling
tools for developing cellular automata, dynamic raster models, and
agent based models in 'SpaDES'. Included are various methods for
spatial spreading, spatial agents, GIS operations, random map
generation, and others. See '?SpaDES.tools' for an categorized
overview of these additional tools. The suggested package 'NLMR' can
be installed from the following repository:
(<https://PredictiveEcology.r-universe.dev>).
Author: Eliot J B McIntire [aut] ,
Alex M Chubaty [aut, cre] ,
Yong Luo [ctb],
Ceres Barros [ctb] ,
Steve Cumming [ctb],
Jean Marchal [ctb],
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <achubaty@for-cast.ca>
Diff between SpaDES.tools versions 2.0.7 dated 2024-05-15 and 2.0.8 dated 2025-10-11
DESCRIPTION | 65 +-- MD5 | 19 NEWS.md | 13 R/distanceFromEachPoint.R | 42 + R/reexports.R |only R/spread.R | 76 +-- R/spread2.R | 13 inst/WORDLIST | 16 man/spread.Rd | 2 man/spread2.Rd | 12 tests/testthat/test-spread.R | 917 +++++++++++++++++++++++++++++++------------ 11 files changed, 815 insertions(+), 360 deletions(-)
Title: The 'HighFive' 'C++' Interface to 'HDF5'
Description: A modern idiomatic header-only 'C++'' interface for 'libhdf5'. Original software can be found at <https://github.com/highfive-devs/highfive/>.
Author: Andrew Robbins [aut, cre] ,
Luc Grosheintz [aut] ,
Blue Brain Project/EPFL [aut]
Maintainer: Andrew Robbins <robbiand@umich.edu>
Diff between HighFive versions 3.1.0 dated 2025-07-22 and 3.2.0 dated 2025-10-11
DESCRIPTION | 10 ++++++---- MD5 | 12 ++++++------ NEWS.md | 5 +++++ inst/include/highfive/H5DataType.hpp | 22 ++++++++++++++++++++++ inst/include/highfive/H5Version.hpp | 6 +++--- inst/include/highfive/bits/H5DataType_misc.hpp | 12 ++++++++++++ inst/include/highfive/bits/h5t_wrapper.hpp | 8 ++++++++ 7 files changed, 62 insertions(+), 13 deletions(-)
Title: Health Economic Simulation Modeling and Decision Analysis
Description: A modular and computationally efficient R package for
parameterizing, simulating, and analyzing health economic simulation
models. The package supports cohort discrete time state transition models
(Briggs et al. 1998) <doi:10.2165/00019053-199813040-00003>,
N-state partitioned survival models (Glasziou et al. 1990)
<doi:10.1002/sim.4780091106>, and individual-level continuous
time state transition models (Siebert et al. 2012) <doi:10.1016/j.jval.2012.06.014>,
encompassing both Markov (time-homogeneous and time-inhomogeneous) and
semi-Markov processes. Decision uncertainty from a cost-effectiveness analysis is
quantified with standard graphical and tabular summaries of a probabilistic
sensitivity analysis (Claxton et al. 2005, Barton et al. 2008) <doi:10.1002/hec.985>,
<doi:10.1111/j.1524-4733.2008.00358.x>. Use of C++ and data.table
make individual-patient simulation, probabilistic sensitivity analysis,
and incorporation of patient heterogeneity fast.
Author: Devin Incerti [aut, cre],
Jeroen P. Jansen [aut],
Mark Clements [aut],
R Core Team [ctb]
Maintainer: Devin Incerti <devin.incerti@gmail.com>
Diff between hesim versions 0.5.6 dated 2025-09-28 and 0.5.7 dated 2025-10-11
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Title: A Future API for Parallel Processing using 'callr'
Description: Implementation of the Future API <doi:10.32614/RJ-2021-048> on top of the 'callr' package. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, on your local (Linux, macOS, Windows, ...) machine. Contrary to backends relying on the 'parallel' package (e.g. 'future::multisession') and socket connections, the 'callr' backend provided here can run more than 125 parallel R processes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.callr versions 0.10.1 dated 2025-07-10 and 0.10.2 dated 2025-10-11
DESCRIPTION | 8 ++-- MD5 | 50 ++++++++++++++-------------- NEWS.md | 15 ++++++++ R/CallrFutureBackend-class.R | 17 ++++++++- R/package.R | 6 ++- inst/WORDLIST | 1 inst/doc/future.callr.html | 10 ++--- inst/doc/future.callr.md.rsp | 8 ++-- inst/testme/test-callr,launch-failure.R | 4 +- inst/testme/test-callr,worker-termination.R | 4 +- inst/testme/test-demo.R | 4 +- inst/testme/test-dotdotdot.R | 1 inst/testme/test-future,labels.R | 1 inst/testme/test-future,lazy.R | 1 inst/testme/test-globals,formulas.R | 8 ++-- inst/testme/test-globals,manual.R | 4 +- inst/testme/test-globals,subassignment.R | 4 +- inst/testme/test-globals,tricky.R | 4 +- inst/testme/test-nbrOfWorkers.R | 4 +- inst/testme/test-plan.R | 7 ++- inst/testme/test-rng.R | 4 +- inst/testme/test-stdout.R | 4 +- inst/testme/test-zzz,future_lapply.R | 1 man/CallrFutureBackend.Rd | 2 - man/future.callr.Rd | 6 ++- vignettes/future.callr.md.rsp | 8 ++-- 26 files changed, 112 insertions(+), 74 deletions(-)
Title: Primal or Dual Cone Projections with Routines for Constrained
Regression
Description: Routines doing cone projection and quadratic programming, as well as doing estimation and inference for constrained parametric regression and shape-restricted regression problems. See Mary C. Meyer (2013)<doi:10.1080/03610918.2012.659820> for more details.
Author: Mary C. Meyer [aut],
Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>
Diff between coneproj versions 1.20 dated 2025-02-19 and 1.21 dated 2025-10-11
ChangeLog | 8 DESCRIPTION | 12 - MD5 | 10 - NAMESPACE | 2 R/coneproj.R | 8 src/coneproj.cpp | 441 ++++++++++++++++++++++++++++++------------------------- 6 files changed, 266 insertions(+), 215 deletions(-)
Title: ACSS, Corresponding INSS, and GLP Algorithms
Description: Allow user to run the Adaptive Correlated Spike and Slab (ACSS) algorithm, corresponding INdependent Spike and Slab (INSS) algorithm, and Giannone, Lenza and Primiceri (GLP) algorithm with adaptive burn-in.
All of the three algorithms are used to fit high dimensional data set with either sparse structure, or dense structure with smaller contributions from all predictors.
The state-of-the-art GLP algorithm is in Giannone, D., Lenza, M., & Primiceri, G. E. (2021, ISBN:978-92-899-4542-4)
"Economic predictions with big data: The illusion of sparsity".
The two new algorithms, ACSS algorithm and INSS algorithm, and the discussion on their performance can be seen in
Yang, Z., Khare, K., & Michailidis, G. (2024, submitted to Journal of Business & Economic Statistics) "Bayesian methodology for adaptive sparsity and shrinkage in regression".
Author: Ziqian Yang [cre, aut],
Kshitij Khare [aut],
George Michailidis [aut]
Maintainer: Ziqian Yang <zi.yang@ufl.edu>
Diff between ACSSpack versions 0.0.1.4 dated 2024-07-04 and 1.0.0.2 dated 2025-10-11
ACSSpack-0.0.1.4/ACSSpack/R/E1.R |only ACSSpack-1.0.0.2/ACSSpack/DESCRIPTION | 14 ++-- ACSSpack-1.0.0.2/ACSSpack/MD5 | 12 +-- ACSSpack-1.0.0.2/ACSSpack/R/E3.R |only ACSSpack-1.0.0.2/ACSSpack/R/main_fun.R | 97 +++++++++++++++++++++++-------- ACSSpack-1.0.0.2/ACSSpack/man/ACSS_gs.Rd | 26 ++++++-- ACSSpack-1.0.0.2/ACSSpack/man/GLP_gs.Rd | 13 ++-- ACSSpack-1.0.0.2/ACSSpack/man/INSS_gs.Rd | 26 ++++++-- 8 files changed, 132 insertions(+), 56 deletions(-)
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(-)
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
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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 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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(-)
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(-)
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(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut] ,
Yoonkyoung Jeon [aut],
Jaewoong Heo [aut],
Youngsun Park [aut] ,
Hyungwoo Jo [aut],
Jeongmin Seo [aut],
Hojun LEE [aut],
Sungho Choi [aut],
Yeji Ka [...truncated...]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.6.13 dated 2025-08-19 and 1.6.15 dated 2025-10-09
DESCRIPTION | 8 - MD5 | 24 ++--- NAMESPACE | 2 NEWS.md | 5 + R/DataManager.R | 13 +- R/bar.R | 64 ++++++++++++++ R/box.R | 149 +++++++++++++++++++++++++++++---- R/jsBasicGadget.R | 2 R/scatter.R | 109 +++++++++++++++++++++++- inst/doc/jsmodule.html | 4 inst/doc/jsmodule_subgroup_cmprsk.html | 4 man/scatterServer.Rd | 1 man/scatterUI.Rd | 1 13 files changed, 341 insertions(+), 45 deletions(-)
Title: Basic Pipe and Open Channel Hydraulics
Description: Functions for basic hydraulic calculations related to
water flow in circular pipes both flowing full (under pressure), and
partially full (gravity flow), and trapezoidal open channels. For
pressure flow this includes friction loss calculations by solving
the Darcy-Weisbach equation for head loss, flow or diameter,
plotting a Moody diagram, matching a pump characteristic curve to a system
curve, and solving for flows in a pipe network using the Hardy-Cross method.
The Darcy-Weisbach friction factor is calculated using the Colebrook
(or Colebrook-White equation), the basis of the Moody diagram, the original
citation being Colebrook (1939) <doi:10.1680/ijoti.1939.13150>. For gravity
flow, the Manning equation is used, again solving for missing parameters.
The derivation of and solutions using the Darcy-Weisbach equation and the
Manning equation are outlined in many fluid mechanics texts such as
Finnemore and Maurer (2024, ISBN:978-1-264-78729-6). Some gradually- and
rapidly-varied f [...truncated...]
Author: Ed Maurer [aut, cre],
Irucka Embry [aut, ctb]
Maintainer: Ed Maurer <emaurer@scu.edu>
Diff between hydraulics versions 0.7.1 dated 2024-11-17 and 0.7.2 dated 2025-10-09
DESCRIPTION | 8 +-- MD5 | 16 +++---- NEWS.md | 4 + R/moody.R | 19 ++++++-- README.md | 69 +++++++++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/hydraulics_vignette.html | 35 ++++++++-------- man/figures/README-moody-diagram-1.png |binary man/figures/README-xc-plot-circle-1.png |binary 9 files changed, 114 insertions(+), 37 deletions(-)
Title: Probabilistic Regression Trees
Description: Implementation of Probabilistic Regression Trees (PRTree),
providing functions for model fitting and prediction, with specific adaptations
to handle missing values. The main computations are implemented in 'Fortran'
for high efficiency. The package is based on the PRTree methodology described in
Alkhoury et al. (2020), "Smooth and Consistent Probabilistic Regression Trees"
<https://proceedings.neurips.cc/paper_files/paper/2020/file/8289889263db4a40463e3f358bb7c7a1-Paper.pdf>.
Details on the treatment of missing data and implementation aspects are presented in
Prass, T.S.; Neimaier, A.S.; Pumi, G. (2025), "Handling Missing Data in Probabilistic Regression Trees:
Methods and Implementation in R" <doi:10.48550/arXiv.2510.03634>.
Author: Alisson Silva Neimaier [aut] ,
Taiane Schaedler Prass [aut, ths, cre]
Maintainer: Taiane Schaedler Prass <taianeprass@gmail.com>
Diff between PRTree versions 0.1.3 dated 2025-05-22 and 1.0.0 dated 2025-10-09
PRTree-0.1.3/PRTree/R/pr_tree_predict.R |only PRTree-0.1.3/PRTree/src/base.f90 |only PRTree-1.0.0/PRTree/DESCRIPTION | 39 ++-- PRTree-1.0.0/PRTree/MD5 | 32 +-- PRTree-1.0.0/PRTree/NAMESPACE | 3 PRTree-1.0.0/PRTree/R/misc.R |only PRTree-1.0.0/PRTree/R/prtree.R | 21 +- PRTree-1.0.0/PRTree/R/prtree_control.R |only PRTree-1.0.0/PRTree/R/prtree_main.R | 282 +++++++++++++++++++---------- PRTree-1.0.0/PRTree/R/prtree_predict.R |only PRTree-1.0.0/PRTree/inst/news.md | 98 ++++++++-- PRTree-1.0.0/PRTree/man/PRTree.Package.Rd | 13 - PRTree-1.0.0/PRTree/man/pr_tree.Rd | 77 ++++--- PRTree-1.0.0/PRTree/man/pr_tree_control.Rd |only PRTree-1.0.0/PRTree/man/predict.prtree.Rd | 27 +- PRTree-1.0.0/PRTree/src/Makevars | 13 + PRTree-1.0.0/PRTree/src/Makevars.win | 13 + PRTree-1.0.0/PRTree/src/PRTree_init.c | 80 ++++++-- PRTree-1.0.0/PRTree/src/Rcalls.f90 |only PRTree-1.0.0/PRTree/src/prtree.f90 |only PRTree-1.0.0/PRTree/src/prtree_misc.f90 |only PRTree-1.0.0/PRTree/src/prtree_types.f90 |only 22 files changed, 497 insertions(+), 201 deletions(-)
Title: Synthesise and Correlate Likert Scale and Rating-Scale Data
Based on Summary Statistics
Description: Generate and correlate synthetic Likert and rating-scale data
with predefined means, standard deviations, Cronbach's Alpha, Factor
Loading table, and other summary statistics.
Worked examples and documentation are available in the package
articles, accessible via
<https://winzarh.github.io/LikertMakeR/>.
Author: Hume Winzar [cre, aut]
Maintainer: Hume Winzar <winzar@gmail.com>
Diff between LikertMakeR versions 1.1.0 dated 2025-05-30 and 1.2.0 dated 2025-10-09
LikertMakeR-1.1.0/LikertMakeR/inst/doc/makeCorrLoadings_validate.R |only LikertMakeR-1.1.0/LikertMakeR/inst/doc/makeCorrLoadings_validate.Rmd |only LikertMakeR-1.1.0/LikertMakeR/inst/doc/makeCorrLoadings_validate.html |only LikertMakeR-1.1.0/LikertMakeR/vignettes/LikertMakeR_3.png |only LikertMakeR-1.1.0/LikertMakeR/vignettes/data |only LikertMakeR-1.1.0/LikertMakeR/vignettes/makeCorrLoadings_validate.Rmd |only LikertMakeR-1.1.0/LikertMakeR/vignettes/skew_chart.png |only LikertMakeR-1.2.0/LikertMakeR/.Rinstignore |only LikertMakeR-1.2.0/LikertMakeR/DESCRIPTION | 17 LikertMakeR-1.2.0/LikertMakeR/LICENSE | 4 LikertMakeR-1.2.0/LikertMakeR/MD5 | 104 LikertMakeR-1.2.0/LikertMakeR/NAMESPACE | 4 LikertMakeR-1.2.0/LikertMakeR/NEWS.md | 30 LikertMakeR-1.2.0/LikertMakeR/R/alpha.R | 134 LikertMakeR-1.2.0/LikertMakeR/R/correlateScales.R | 484 - LikertMakeR-1.2.0/LikertMakeR/R/eigenvalues.R | 122 LikertMakeR-1.2.0/LikertMakeR/R/lcor.R | 137 LikertMakeR-1.2.0/LikertMakeR/R/lexact.R | 102 LikertMakeR-1.2.0/LikertMakeR/R/lfast.R | 255 LikertMakeR-1.2.0/LikertMakeR/R/makeCorrAlpha.R | 26 LikertMakeR-1.2.0/LikertMakeR/R/makeCorrLoadings.R | 447 - LikertMakeR-1.2.0/LikertMakeR/R/makeItems.R | 284 LikertMakeR-1.2.0/LikertMakeR/R/makeItemsScale.R | 25 LikertMakeR-1.2.0/LikertMakeR/R/makePaired.R | 50 LikertMakeR-1.2.0/LikertMakeR/R/makeRepeated.R |only LikertMakeR-1.2.0/LikertMakeR/README.md | 233 LikertMakeR-1.2.0/LikertMakeR/build/vignette.rds |binary LikertMakeR-1.2.0/LikertMakeR/inst/WORDLIST |only LikertMakeR-1.2.0/LikertMakeR/inst/doc/LikertMakeR_vignette.R | 90 LikertMakeR-1.2.0/LikertMakeR/inst/doc/LikertMakeR_vignette.Rmd | 3180 +++++----- LikertMakeR-1.2.0/LikertMakeR/inst/doc/LikertMakeR_vignette.html | 2652 ++++---- LikertMakeR-1.2.0/LikertMakeR/inst/logo.png |only LikertMakeR-1.2.0/LikertMakeR/man/alpha.Rd | 2 LikertMakeR-1.2.0/LikertMakeR/man/correlateScales.Rd | 5 LikertMakeR-1.2.0/LikertMakeR/man/eigenvalues.Rd | 2 LikertMakeR-1.2.0/LikertMakeR/man/figures |only LikertMakeR-1.2.0/LikertMakeR/man/lcor.Rd | 129 LikertMakeR-1.2.0/LikertMakeR/man/lexact.Rd | 4 LikertMakeR-1.2.0/LikertMakeR/man/lfast.Rd | 18 LikertMakeR-1.2.0/LikertMakeR/man/makeCorrAlpha.Rd | 10 LikertMakeR-1.2.0/LikertMakeR/man/makeCorrLoadings.Rd | 117 LikertMakeR-1.2.0/LikertMakeR/man/makeItems.Rd | 4 LikertMakeR-1.2.0/LikertMakeR/man/makeItemsScale.Rd | 5 LikertMakeR-1.2.0/LikertMakeR/man/makePaired.Rd | 221 LikertMakeR-1.2.0/LikertMakeR/man/makeRepeated.Rd |only LikertMakeR-1.2.0/LikertMakeR/tests/testthat/test-alpha.R | 60 LikertMakeR-1.2.0/LikertMakeR/tests/testthat/test-eigenvalues.R | 44 LikertMakeR-1.2.0/LikertMakeR/tests/testthat/test-lcor.R | 126 LikertMakeR-1.2.0/LikertMakeR/tests/testthat/test-lfast.R | 79 LikertMakeR-1.2.0/LikertMakeR/tests/testthat/test-makeCorrAlpha.R | 30 LikertMakeR-1.2.0/LikertMakeR/tests/testthat/test-makeCorrLoadings.R | 25 LikertMakeR-1.2.0/LikertMakeR/tests/testthat/test-makeItems.R | 64 LikertMakeR-1.2.0/LikertMakeR/tests/testthat/test-makeItemsScale.R | 40 LikertMakeR-1.2.0/LikertMakeR/tests/testthat/test-makePaired.R | 76 LikertMakeR-1.2.0/LikertMakeR/tests/testthat/test_makeRepeated.R |only LikertMakeR-1.2.0/LikertMakeR/vignettes/LikertMakeR_vignette.Rmd | 3180 +++++----- LikertMakeR-1.2.0/LikertMakeR/vignettes/img |only LikertMakeR-1.2.0/LikertMakeR/vignettes/references.bib | 395 + 58 files changed, 7044 insertions(+), 5972 deletions(-)
Title: Artificial Neural Networks for Anomaly Detection
Description: Training of neural networks for classification and regression tasks
using mini-batch gradient descent. Special features include a function for
training autoencoders, which can be used to detect anomalies, and some
related plotting functions. Multiple activation functions are supported,
including tanh, relu, step and ramp. For the use of the step and ramp
activation functions in detecting anomalies using autoencoders, see
Hawkins et al. (2002) <doi:10.1007/3-540-46145-0_17>. Furthermore,
several loss functions are supported, including robust ones such as Huber
and pseudo-Huber loss, as well as L1 and L2 regularization. The possible
options for optimization algorithms are RMSprop, Adam and SGD with momentum.
The package contains a vectorized C++ implementation that facilitates
fast training through mini-batch learning.
Author: Bart Lammers [aut, cre]
Maintainer: Bart Lammers <bart.f.lammers@gmail.com>
Diff between ANN2 versions 2.3.4 dated 2020-12-01 and 2.4.0 dated 2025-10-09
DESCRIPTION | 23 +++--- MD5 | 30 ++++---- NAMESPACE | 2 R/plotting.R | 16 ++-- README.md | 138 +++++++++++++++++++++++++++++++++++++++-- inst/cereal/types/memory.hpp | 2 src/ANN.cpp | 1 src/Activations.cpp | 20 +++-- src/Activations.h | 30 ++++---- src/Loss.h | 20 ++--- src/Makevars | 7 -- src/Optimizer.h | 12 +-- src/RcppExports.cpp | 5 + tests/testthat.R | 5 - tests/testthat/test-gradient.R | 8 +- tests/testthat/test-plotting.R | 42 +++++++----- 16 files changed, 250 insertions(+), 111 deletions(-)
Title: Dependency Logo
Description: Plots dependency logos from a set of aligned input sequences.
Author: Jan Grau [aut, cre],
Jens Keilwagen [aut],
Martin Nettling [aut]
Maintainer: Jan Grau <grau@informatik.uni-halle.de>
Diff between DepLogo versions 1.2.1 dated 2024-02-15 and 1.2.2 dated 2025-10-09
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/DepLogo.html | 14 ++++++-------- tests/testthat/test-Partitioning.R | 2 +- 5 files changed, 14 insertions(+), 16 deletions(-)
Title: Simulate Stock-Flow Consistent Models
Description: Routines to write, simulate, and validate stock-flow consistent (SFC) models. The accounting structure of SFC models are described in Godley and Lavoie (2007, ISBN:978-1-137-08599-3). The algorithms implemented to solve the models (Gauss-Seidel and Broyden) are described in Kinsella and O'Shea (2010) <doi:10.2139/ssrn.1729205> and Peressini and Sullivan (1988, ISBN:0-387-96614-5).
Author: Joao Macalos [aut, cre]
Maintainer: Joao Macalos <joaomacalos@gmail.com>
Diff between sfcr versions 0.2.1 dated 2021-10-11 and 0.2.3 dated 2025-10-09
DESCRIPTION | 9 MD5 | 48 +- NEWS.md | 17 R/sfcr_baseline.R | 740 +++++++++++++++++----------------- R/sfcr_find_order.R | 284 ++++++------- R/sfcr_sankey.R | 222 +++++----- R/sfcr_scenario.R | 604 +++++++++++++-------------- R/sfcr_set.R | 298 ++++++------- R/sfcr_shock.R | 86 +-- R/sfcr_validate.R | 734 ++++++++++++++++----------------- R/utils-solvers.R | 408 +++++++++--------- README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/sfcr_multis.R | 2 inst/doc/sfcr_multis.Rmd | 292 ++++++------- inst/doc/sfcr_multis.html | 547 ++++++++++++++++++------- man/dot-check_external_consistency.Rd | 58 +- man/sfcr_random.Rd | 60 +- src/Makevars | 1 src/Makevars.win | 1 tests/testthat/test-sfcr_baseline.R | 220 +++++----- tests/testthat/test-sfcr_random.R | 6 tests/testthat/test-sfcr_scenario.R | 404 +++++++++--------- vignettes/sfcr_multis.Rmd | 292 ++++++------- 25 files changed, 2798 insertions(+), 2539 deletions(-)
Title: Bayesian Estimation of Naloxone Kit Number Under-Reporting
Description: Bayesian model and associated tools for generating estimates of
total naloxone kit numbers distributed and used from naloxone kit orders
data. Provides functions for generating simulated data of naloxone kit use
and functions for generating samples from the posterior.
Author: Mike Irvine [aut, cre, cph] ,
Samantha Bardwell [ctb],
Andrew Johnson [ctb]
Maintainer: Mike Irvine <mike.irvine@bccdc.ca>
Diff between bennu versions 0.3.1 dated 2025-07-25 and 0.3.2 dated 2025-10-09
DESCRIPTION | 10 MD5 | 33 NEWS.md | 5 R/est_naloxone.R | 580 +++--- README.md | 197 +- build/vignette.rds |binary configure | 2 configure.win | 11 inst/doc/Introduction.R | 268 +- inst/doc/Introduction.html | 1397 +++++++-------- inst/doc/simulation_validation_experiments.R | 344 +-- inst/doc/simulation_validation_experiments.html | 1130 ++++++------ man/figures/README-example-1.png |binary src/Makevars |only src/stanExports_distribution_covariate_model.cc | 34 src/stanExports_distribution_covariate_model.h | 2155 +++++++++++------------- tests/testthat/test-kit_summary_table.R | 60 tests/testthat/test-plot_kit_use.R | 72 18 files changed, 3113 insertions(+), 3185 deletions(-)
Title: Bayesian Statistics for 2D/3D Transformations
Description: Fits 2D and 3D geometric transformations via 'Stan' probabilistic programming engine (
Stan Development Team (2021) <https://mc-stan.org>). Returns posterior distribution for individual
parameters of the fitted distribution. Allows for computation of LOO and WAIC information criteria
(Vehtari A, Gelman A, Gabry J (2017) <doi:10.1007/s11222-016-9696-4>) as well as Bayesian R-squared
(Gelman A, Goodrich B, Gabry J, and Vehtari A (2018) <doi:10.1080/00031305.2018.1549100>).
Author: Alexander Pastukhov [aut, cre] ,
Claus-Christian Carbon [aut]
Maintainer: Alexander (Sasha) Pastukhov <pastukhov.alexander@gmail.com>
Diff between TriDimRegression versions 1.0.2 dated 2023-09-13 and 1.0.3 dated 2025-10-09
DESCRIPTION | 15 MD5 | 38 NEWS.md | 11 R/TriDimRegression-package.R | 2 R/coef.R | 4 R/predict.R | 4 R/variable_summary.R | 4 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/calibration.html | 19 inst/doc/comparing_faces.html | 7 inst/doc/transformation_matrices.html | 6 man/TriDimRegression-package.Rd | 3 man/coef.tridim_transformation.Rd | 4 man/predict.tridim_transformation.Rd | 4 man/variable_summary.Rd | 4 man/waic.tridim_transformation.Rd | 2 src/stanExports_tridim_transformation.cc | 34 src/stanExports_tridim_transformation.h | 2393 ++++++++++++++++++------------- 20 files changed, 1549 insertions(+), 1007 deletions(-)
More information about TriDimRegression at CRAN
Permanent link
Title: Geostatistical Modeling of Spatially Referenced Data
Description: Geostatistical analysis of continuous and count data.
Implements stationary Gaussian processes with Matérn correlation for spatial prediction,
as described in Diggle and Giorgi (2019, ISBN: 978-1-138-06102-7).
Author: Emanuele Giorgi [aut, cre] ,
Claudio Fronterre [ctb]
Maintainer: Emanuele Giorgi <e.giorgi@bham.ac.uk>
Diff between RiskMap versions 0.1.0 dated 2024-06-25 and 1.0.0 dated 2025-10-09
DESCRIPTION | 32 MD5 | 61 NAMESPACE | 59 R/abund_sma.R |only R/auxiliary.R | 1077 +++++++++++++-- R/globals.R |only R/infect_sma.R |only R/mda_modelling.R |only R/package-imports.R |only R/parameter_estimation.R | 1814 +++++++++++++++---------- R/spatial_prediction.R | 2264 +++++++++++++++++++++++++++++--- R/tz_covariates.R |only R/tz_malaria.R |only README.md | 96 - build |only data/abund_sma.rdata |only data/infect_sma.rdata |only data/tz_covariates.rdata |only data/tz_malaria.rdata |only man/Laplace_sampling_MCMC.Rd | 101 + man/abund_sma.Rd |only man/assess_pp.Rd |only man/assess_sim.Rd |only man/check_mcmc.Rd |only man/compute_ID_coords.Rd |only man/convex_hull_sf.Rd |only man/dast.Rd |only man/figures |only man/glgpm.Rd | 8 man/glgpm_sim.Rd | 8 man/infect_sma.Rd |only man/maxim.integrand.Rd | 5 man/plot_AnPIT.Rd |only man/plot_mda.Rd |only man/plot_score.Rd |only man/plot_sim_surf.Rd |only man/pred_over_grid.Rd | 2 man/pred_target_grid.Rd | 11 man/pred_target_shp.Rd | 94 - man/print.summary.RiskMap.sim.res.Rd |only man/print.summary.RiskMap.spatial.cv.Rd |only man/summary.RiskMap.sim.res.Rd |only man/summary.RiskMap.spatial.cv.Rd |only man/surf_sim.Rd |only man/to_table.Rd | 29 man/tz_covariates.Rd |only man/tz_malaria.Rd |only man/update_predictors.Rd |only 48 files changed, 4397 insertions(+), 1264 deletions(-)
Title: Transfer 'REDCap' Data to Database
Description: Transfer 'REDCap' (Research Electronic Data Capture) data to a database,
specifically optimized for 'DuckDB'.
Processes data in chunks to handle large datasets without exceeding available memory.
Features include data labeling, coded value conversion, and hearing a "quack" sound on success.
Author: Dylan Pieper [aut, cre]
Maintainer: Dylan Pieper <dylanpieper@gmail.com>
Diff between redquack versions 0.2.0 dated 2025-05-14 and 0.3.0 dated 2025-10-09
redquack-0.2.0/redquack/man/figures/redquack-hex.png |only redquack-0.2.0/redquack/tests/testthat/helper-redcap.R |only redquack-0.2.0/redquack/tests/testthat/test-redcap_to_duckdb.R |only redquack-0.3.0/redquack/DESCRIPTION | 21 redquack-0.3.0/redquack/MD5 | 36 redquack-0.3.0/redquack/NAMESPACE | 41 redquack-0.3.0/redquack/NEWS.md | 30 redquack-0.3.0/redquack/R/collect_labeled.R |only redquack-0.3.0/redquack/R/collect_list.R |only redquack-0.3.0/redquack/R/helpers.R | 462 +++++++ redquack-0.3.0/redquack/R/optimize_data_types.R | 34 redquack-0.3.0/redquack/R/redcap_to_db.R | 653 +++++++--- redquack-0.3.0/redquack/README.md | 243 ++- redquack-0.3.0/redquack/man/close_duckdb.Rd |only redquack-0.3.0/redquack/man/collect_labeled.Rd |only redquack-0.3.0/redquack/man/collect_list.Rd |only redquack-0.3.0/redquack/man/figures/redquack.png |only redquack-0.3.0/redquack/man/inspect.Rd |only redquack-0.3.0/redquack/man/list_to_env.Rd |only redquack-0.3.0/redquack/man/metadata.Rd |only redquack-0.3.0/redquack/man/redcap_log.Rd |only redquack-0.3.0/redquack/man/redcap_to_db.Rd | 93 - redquack-0.3.0/redquack/man/remove_duckdb.Rd |only redquack-0.3.0/redquack/man/save_parquet.Rd |only redquack-0.3.0/redquack/man/tbl_redcap.Rd |only redquack-0.3.0/redquack/man/transfer_log.Rd |only redquack-0.3.0/redquack/man/use_duckdb.Rd |only redquack-0.3.0/redquack/tests/testthat/helpers.R |only redquack-0.3.0/redquack/tests/testthat/test-redcap_to_db.R |only 29 files changed, 1293 insertions(+), 320 deletions(-)
Title: Extreme Risk Measures
Description: A set of procedures for estimating risks related to extreme events via risk measures such as Expectile, Value-at-Risk, etc. is provided. Estimation methods for univariate independent observations and temporal dependent observations are available. The methodology is extended to the case of independent multidimensional observations. The statistical inference is performed through parametric and non-parametric estimators. Inferential procedures such as confidence intervals, confidence regions and hypothesis testing are obtained by exploiting the asymptotic theory. Adapts the methodologies derived in Padoan and Stupfler (2022) <doi:10.3150/21-BEJ1375>, Davison et al. (2023) <doi:10.1080/07350015.2022.2078332>, Daouia et al. (2018) <doi:10.1111/rssb.12254>, Drees (2000) <doi:10.1214/aoap/1019487617>, Drees (2003) <doi:10.3150/bj/1066223272>, de Haan and Ferreira (2006) <doi:10.1007/0-387-34471-3>, de Haan et al. (2016) <doi:10.1007/s00780-015-0287-6> [...truncated...]
Author: Simone Padoan [cre, aut],
Gilles Stupfler [aut],
Carlotta Pacifici [aut]
Maintainer: Simone Padoan <simone.padoan@unibocconi.it>
Diff between ExtremeRisks versions 0.0.4-1 dated 2025-04-26 and 0.0.5 dated 2025-10-09
ExtremeRisks-0.0.4-1/ExtremeRisks/R/Estimation.r |only ExtremeRisks-0.0.4-1/ExtremeRisks/R/Expectiles.r |only ExtremeRisks-0.0.4-1/ExtremeRisks/R/MultiEstimation.r |only ExtremeRisks-0.0.4-1/ExtremeRisks/R/Simulation.r |only ExtremeRisks-0.0.4-1/ExtremeRisks/R/UniEstimation.r |only ExtremeRisks-0.0.5/ExtremeRisks/DESCRIPTION | 23 +++---- ExtremeRisks-0.0.5/ExtremeRisks/MD5 | 41 +++++++++---- ExtremeRisks-0.0.5/ExtremeRisks/NAMESPACE | 16 +++-- ExtremeRisks-0.0.5/ExtremeRisks/R/Estimation.R |only ExtremeRisks-0.0.5/ExtremeRisks/R/Expectiles.R |only ExtremeRisks-0.0.5/ExtremeRisks/R/MultiEstimation.R |only ExtremeRisks-0.0.5/ExtremeRisks/R/Prediction.R |only ExtremeRisks-0.0.5/ExtremeRisks/R/Simulation.R |only ExtremeRisks-0.0.5/ExtremeRisks/R/UniEstimation.R |only ExtremeRisks-0.0.5/ExtremeRisks/inst |only ExtremeRisks-0.0.5/ExtremeRisks/man/Bqgpd_c.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/Bqgpd_d.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/MultiHTailIndex.Rd | 2 ExtremeRisks-0.0.5/ExtremeRisks/man/cpost_stat.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/estMultiExpectiles.Rd | 2 ExtremeRisks-0.0.5/ExtremeRisks/man/estPOT.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/expectiles.Rd | 2 ExtremeRisks-0.0.5/ExtremeRisks/man/extBQuant.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/extBQuantx.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/extMultiQuantile.Rd | 2 ExtremeRisks-0.0.5/ExtremeRisks/man/fitdGPD.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/plotBayes.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/predDens.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/predDensx.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/predMultiExpectiles.Rd | 2 ExtremeRisks-0.0.5/ExtremeRisks/man/predQuant.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/quantF.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/scedastic.test.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/schedastic.test.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/testTailHomo.Rd |only 35 files changed, 54 insertions(+), 36 deletions(-)
Title: 'KorAP' Web Service Client Package
Description: A client package that makes the 'KorAP' web service API accessible from R. The corpus analysis platform 'KorAP' has been developed as a scientific tool to make potentially large, stratified and multiply annotated corpora, such as the 'German Reference Corpus DeReKo' or the 'Corpus of the Contemporary Romanian Language CoRoLa', accessible for linguists to let them verify hypotheses and to find interesting patterns in real language use. The 'RKorAPClient' package provides access to 'KorAP' and the corpora behind it for user-created R code, as a programmatic alternative to the 'KorAP' web user-interface. You can learn more about 'KorAP' and use it directly on 'DeReKo' at <https://korap.ids-mannheim.de/>.
Author: Marc Kupietz [aut, cre],
Nils Diewald [ctb],
Leibniz Institute for the German Language [cph, fnd]
Maintainer: Marc Kupietz <kupietz@ids-mannheim.de>
Diff between RKorAPClient versions 1.2.0 dated 2025-09-10 and 1.2.1 dated 2025-10-09
DESCRIPTION | 8 MD5 | 10 NEWS.md | 6 R/KorAPQuery.R | 480 +++++++++++--------------------- tests/testthat/test-fetchAnnotations.R | 28 + tests/testthat/test-parse-annotations.R | 47 ++- 6 files changed, 264 insertions(+), 315 deletions(-)
Title: Query 'R' Versions, Including 'r-release' and 'r-oldrel'
Description: Query the main 'R' 'SVN' repository to find the
versions 'r-release' and 'r-oldrel' refer to, and also all previous
'R' versions and their release dates.
Author: Gabor Csardi [aut, cre],
Jeroen Ooms [ctb],
R Consortium [fnd],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between rversions versions 2.1.2 dated 2022-08-31 and 3.0.0 dated 2025-10-09
rversions-2.1.2/rversions/R/keep-head.R |only rversions-2.1.2/rversions/R/nicks.R |only rversions-2.1.2/rversions/R/urls.R |only rversions-3.0.0/rversions/DESCRIPTION | 20 rversions-3.0.0/rversions/MD5 | 213 ++++++ rversions-3.0.0/rversions/NAMESPACE | 14 rversions-3.0.0/rversions/NEWS.md | 18 rversions-3.0.0/rversions/R/api.R |only rversions-3.0.0/rversions/R/available.R |only rversions-3.0.0/rversions/R/compat-vctrs.R |only rversions-3.0.0/rversions/R/current-os.R |only rversions-3.0.0/rversions/R/iso-date.R |only rversions-3.0.0/rversions/R/json.R |only rversions-3.0.0/rversions/R/linux-distros.R |only rversions-3.0.0/rversions/R/macos.R | 25 rversions-3.0.0/rversions/R/platform.R |only rversions-3.0.0/rversions/R/rematch2.R |only rversions-3.0.0/rversions/R/resolve.R |only rversions-3.0.0/rversions/R/rtools-versions.R |only rversions-3.0.0/rversions/R/rversions.R | 90 -- rversions-3.0.0/rversions/R/tarball.R | 14 rversions-3.0.0/rversions/R/utils.R | 27 rversions-3.0.0/rversions/R/win.R | 14 rversions-3.0.0/rversions/README.md | 319 +++++----- rversions-3.0.0/rversions/man/available.Rd |only rversions-3.0.0/rversions/man/current_r_platform.Rd |only rversions-3.0.0/rversions/man/linux_distros.Rd |only rversions-3.0.0/rversions/man/r_oldrel.Rd | 21 rversions-3.0.0/rversions/man/r_release.Rd | 21 rversions-3.0.0/rversions/man/r_release_macos.Rd | 27 rversions-3.0.0/rversions/man/r_release_tarball.Rd | 21 rversions-3.0.0/rversions/man/r_release_win.Rd | 21 rversions-3.0.0/rversions/man/r_versions.Rd | 2 rversions-3.0.0/rversions/man/resolve.Rd |only rversions-3.0.0/rversions/man/rtools_versions.Rd |only rversions-3.0.0/rversions/man/rversions-package.Rd | 1 rversions-3.0.0/rversions/tests/testthat.R | 4 rversions-3.0.0/rversions/tests/testthat/_snaps |only rversions-3.0.0/rversions/tests/testthat/fixtures |only rversions-3.0.0/rversions/tests/testthat/helper-mock.R |only rversions-3.0.0/rversions/tests/testthat/helper-proxy.R |only rversions-3.0.0/rversions/tests/testthat/helper.R |only rversions-3.0.0/rversions/tests/testthat/test-api.R |only rversions-3.0.0/rversions/tests/testthat/test-available.R |only rversions-3.0.0/rversions/tests/testthat/test-linux-distros.R |only rversions-3.0.0/rversions/tests/testthat/test-macos.R |only rversions-3.0.0/rversions/tests/testthat/test-platform.R |only rversions-3.0.0/rversions/tests/testthat/test-resolve.R |only rversions-3.0.0/rversions/tests/testthat/test-rtools-versions.R |only rversions-3.0.0/rversions/tests/testthat/test-rversions.R | 39 - rversions-3.0.0/rversions/tests/testthat/test-tarball.R |only rversions-3.0.0/rversions/tests/testthat/test-utils.R |only rversions-3.0.0/rversions/tests/testthat/test-win.R |only 53 files changed, 614 insertions(+), 297 deletions(-)
Title: Scans R Projects for Vulnerable Third Party Dependencies
Description: Collects a list of your third party R packages, and scans
them with the 'OSS' Index provided by 'Sonatype', reporting back on
any vulnerabilities that are found in the third party packages you
use.
Author: Jeffry Hesse [aut],
Brittany Belle [aut],
Colin Gillespie [aut, cre] ,
Dan Rollo [aut],
Josiah Parry [aut] ,
Sonatype [cph]
Maintainer: Colin Gillespie <csgillespie@gmail.com>
Diff between oysteR versions 0.1.1 dated 2021-01-10 and 0.1.4 dated 2025-10-09
oysteR-0.1.1/oysteR/R/deprecated.R |only oysteR-0.1.1/oysteR/man/audit_deps.Rd |only oysteR-0.1.1/oysteR/tests/testthat/test-get_vulnerabilities.R |only oysteR-0.1.4/oysteR/DESCRIPTION | 57 +--- oysteR-0.1.4/oysteR/MD5 | 44 ++- oysteR-0.1.4/oysteR/NAMESPACE | 5 oysteR-0.1.4/oysteR/NEWS.md | 20 + oysteR-0.1.4/oysteR/R/audit.R | 33 +- oysteR-0.1.4/oysteR/R/cache.R | 24 + oysteR-0.1.4/oysteR/R/call_os_index.R | 123 ++++------ oysteR-0.1.4/oysteR/R/expect_secure.R | 11 oysteR-0.1.4/oysteR/R/file_audits.R | 72 +++++ oysteR-0.1.4/oysteR/R/get_token.R |only oysteR-0.1.4/oysteR/R/get_vulnerabilities.R | 47 ++- oysteR-0.1.4/oysteR/R/print.R | 10 oysteR-0.1.4/oysteR/R/utils.R | 37 ++- oysteR-0.1.4/oysteR/build |only oysteR-0.1.4/oysteR/inst/doc |only oysteR-0.1.4/oysteR/man/audit.Rd | 5 oysteR-0.1.4/oysteR/man/audit_conda.Rd |only oysteR-0.1.4/oysteR/man/audit_installed_r_pkgs.Rd | 5 oysteR-0.1.4/oysteR/tests/testthat/environment.yml |only oysteR-0.1.4/oysteR/tests/testthat/test-audit.R | 10 oysteR-0.1.4/oysteR/tests/testthat/test-audit_pkg.R | 4 oysteR-0.1.4/oysteR/tests/testthat/test-cache.R | 5 oysteR-0.1.4/oysteR/tests/testthat/test-env-yml.R |only oysteR-0.1.4/oysteR/tests/testthat/test-get_token.R |only oysteR-0.1.4/oysteR/vignettes |only 28 files changed, 313 insertions(+), 199 deletions(-)
Title: Generalized Linear Mixed Models using Template Model Builder
Description: Fit linear and generalized linear mixed models with various
extensions, including zero-inflation. The models are fitted using maximum
likelihood estimation via 'TMB' (Template Model Builder). Random effects are
assumed to be Gaussian on the scale of the linear predictor and are integrated
out using the Laplace approximation. Gradients are calculated using automatic
differentiation.
Author: Mollie Brooks [aut, cre] ,
Ben Bolker [aut] ,
Kasper Kristensen [aut],
Martin Maechler [aut] ,
Arni Magnusson [aut] ,
Maeve McGillycuddy [ctb],
Hans Skaug [aut] ,
Anders Nielsen [aut] ,
Casper Berg [aut] ,
Koen van Bentham [aut],
Nafis Sadat [ctb] ,
[...truncated...]
Maintainer: Mollie Brooks <mollieebrooks@gmail.com>
Diff between glmmTMB versions 1.1.12 dated 2025-08-18 and 1.1.13 dated 2025-10-09
DESCRIPTION | 12 +-- MD5 | 70 ++++++++++---------- NAMESPACE | 3 R/denom_df.R |only R/emmeans.R | 66 +++++++++++++++--- R/enum.R | 3 R/family.R | 16 +++- R/glmmTMB.R | 83 ++++++++++++++++++----- R/methods.R | 112 ++++++++++++++++++-------------- inst/NEWS.Rd | 36 +++++++++- inst/doc/covstruct.R | 1 inst/doc/covstruct.html | 37 ++++++---- inst/doc/covstruct.rmd | 6 - inst/doc/glmmTMB.pdf |binary inst/doc/hacking.html | 4 - inst/doc/mcmc.html | 8 +- inst/doc/miscEx.html | 4 - inst/doc/model_evaluation.pdf |binary inst/doc/parallel.html | 4 - inst/doc/priors.R | 7 +- inst/doc/priors.html | 11 +-- inst/doc/priors.rmd | 7 +- inst/doc/sim.html | 6 - inst/doc/troubleshooting.html | 4 - inst/vignette_data/model_evaluation.rda |binary man/dof_KR.Rd |only man/getME.glmmTMB.Rd | 2 man/glmmTMB.Rd | 4 - man/residuals.glmmTMB.Rd | 1 man/summary.glmmTMB.Rd |only src/glmmTMB.cpp | 35 ++++++---- tests/testthat/test-basics.R | 9 +- tests/testthat/test-ddf.R |only tests/testthat/test-downstream.R | 4 - tests/testthat/test-predict.R | 93 ++++++++++++++++++++++++++ tests/testthat/test-varstruc.R | 32 +++++++++ vignettes/covstruct.rmd | 6 - vignettes/priors.rmd | 7 +- 38 files changed, 495 insertions(+), 198 deletions(-)
Title: The P-Model and BiomeE Modelling Framework
Description: Implements the Simulating Optimal FUNctioning framework for
site-scale simulations of ecosystem processes, including model
calibration. It contains 'Fortran 90' modules for the P-model (Stocker
et al. (2020) <doi:10.5194/gmd-13-1545-2020>), SPLASH
(Davis et al. (2017) <doi:10.5194/gmd-10-689-2017>)
and BiomeE (Weng et al. (2015)
<doi:10.5194/bg-12-2655-2015>).
Author: Benjamin Stocker [aut, cre] ,
Koen Hufkens [aut] ,
Josefa Aran Paredes [aut] ,
Laura Marques [ctb] ,
Mayeul Marcadella [ctb] ,
Ensheng Weng [ctb] ,
Fabian Bernhard [aut] ,
Geocomputation and Earth Observation, University of Bern [cph, fnd]
Maintainer: Benjamin Stocker <benjamin.stocker@gmail.com>
Diff between rsofun versions 5.0.0 dated 2024-11-28 and 5.1.0 dated 2025-10-09
rsofun-5.0.0/rsofun/R/init_dates_dataframe.R |only rsofun-5.0.0/rsofun/R/zzz.R |only rsofun-5.0.0/rsofun/src/classdefs.mod.f90 |only rsofun-5.0.0/rsofun/src/datatypes.mod.f90 |only rsofun-5.0.0/rsofun/src/interface_biosphere_biomee.mod.f90 |only rsofun-5.0.0/rsofun/src/params_siml_biomee.mod.f90 |only rsofun-5.0.0/rsofun/src/sofun_r.f90 |only rsofun-5.0.0/rsofun/src/vegetation_biomee.mod.f90 |only rsofun-5.0.0/rsofun/tests/testthat/test-ancillary-functions.R |only rsofun-5.0.0/rsofun/vignettes/files/biomee_use.Rmd__biomee_gs_leuning_output___out.RDS |only rsofun-5.0.0/rsofun/vignettes/files/biomee_use.Rmd__biomee_p_model_output___calibrated_out.RDS |only rsofun-5.0.0/rsofun/vignettes/files/biomee_use.Rmd__biomee_p_model_output___out.RDS |only rsofun-5.1.0/rsofun/DESCRIPTION | 30 rsofun-5.1.0/rsofun/MD5 | 205 - rsofun-5.1.0/rsofun/NAMESPACE | 4 rsofun-5.1.0/rsofun/R/calib_sofun.R | 64 rsofun-5.1.0/rsofun/R/cost_likelihood_biomee.R | 32 rsofun-5.1.0/rsofun/R/cost_likelihood_pmodel.R | 16 rsofun-5.1.0/rsofun/R/cost_rmse_biomee.R | 4 rsofun-5.1.0/rsofun/R/data.R | 211 + rsofun-5.1.0/rsofun/R/luluc.R |only rsofun-5.1.0/rsofun/R/run_biomee_f_bysite.R | 1233 ++++++---- rsofun-5.1.0/rsofun/R/run_pmodel_f_bysite.R | 493 ++- rsofun-5.1.0/rsofun/R/run_pmodel_onestep_f_bysite.R |only rsofun-5.1.0/rsofun/R/runread_biomee_f.R | 141 - 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Title: Supporting Functions Maintained by Zhen Lu
Description: Miscellaneous functions commonly used by LuLab. This package aims to help more researchers on epidemiology to perform data management and visualization more efficiently.
Author: Zhen Lu [aut, cre]
Maintainer: Zhen Lu <luzh29@mail2.sysu.edu.cn>
Diff between lulab.utils versions 0.0.4 dated 2024-10-07 and 1.0.0 dated 2025-10-09
lulab.utils-0.0.4/lulab.utils/man/Table1.Rd |only lulab.utils-1.0.0/lulab.utils/DESCRIPTION | 20 lulab.utils-1.0.0/lulab.utils/LICENSE |only lulab.utils-1.0.0/lulab.utils/MD5 | 51 - lulab.utils-1.0.0/lulab.utils/NAMESPACE | 5 lulab.utils-1.0.0/lulab.utils/NEWS.md | 8 lulab.utils-1.0.0/lulab.utils/R/SCI_TFL.R | 411 ++++---- lulab.utils-1.0.0/lulab.utils/R/lulab.utils-package.R | 16 lulab.utils-1.0.0/lulab.utils/R/regression_utilities.R |only lulab.utils-1.0.0/lulab.utils/R/utilities.R | 491 +++++----- lulab.utils-1.0.0/lulab.utils/README.md | 42 lulab.utils-1.0.0/lulab.utils/build/vignette.rds |binary lulab.utils-1.0.0/lulab.utils/inst/WORDLIST |only lulab.utils-1.0.0/lulab.utils/inst/doc/lulab_utils.Rmd | 44 lulab.utils-1.0.0/lulab.utils/inst/doc/lulab_utils.html | 3 lulab.utils-1.0.0/lulab.utils/man/check_cha.Rd | 72 - lulab.utils-1.0.0/lulab.utils/man/check_wget.Rd | 50 - lulab.utils-1.0.0/lulab.utils/man/extract_logistic_model.Rd |only lulab.utils-1.0.0/lulab.utils/man/lulab.utils-package.Rd | 2 lulab.utils-1.0.0/lulab.utils/man/round2.Rd |only lulab.utils-1.0.0/lulab.utils/man/test_mirror.Rd | 60 - lulab.utils-1.0.0/lulab.utils/man/use_wget.Rd | 66 - lulab.utils-1.0.0/lulab.utils/tests/spelling.R |only lulab.utils-1.0.0/lulab.utils/tests/testthat.R | 24 lulab.utils-1.0.0/lulab.utils/tests/testthat/test-Table1.R | 51 - lulab.utils-1.0.0/lulab.utils/tests/testthat/test-check_cha.R | 18 lulab.utils-1.0.0/lulab.utils/tests/testthat/test-check_wget.R | 16 lulab.utils-1.0.0/lulab.utils/tests/testthat/test-test_mirror.R | 22 lulab.utils-1.0.0/lulab.utils/tests/testthat/test-use_wget.R | 50 - lulab.utils-1.0.0/lulab.utils/vignettes/lulab_utils.Rmd | 44 30 files changed, 800 insertions(+), 766 deletions(-)
Title: Graphs and Tables for OMOP Results
Description: Provides methods to transform omop_result objects into
formatted tables and figures, facilitating the visualisation of study
results working with the Observational Medical Outcomes Partnership
(OMOP) Common Data Model.
Author: Marti Catala [aut] ,
Nuria Mercade-Besora [aut, cre] ,
Yuchen Guo [ctb] ,
Elin Rowlands [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Edward Burn [ctb]
Maintainer: Nuria Mercade-Besora <nuria.mercadebesora@ndorms.ox.ac.uk>
Diff between visOmopResults versions 1.3.0 dated 2025-10-05 and 1.3.1 dated 2025-10-09
DESCRIPTION | 6 MD5 | 32 - R/plottingThemes.R | 306 +++++++--------- data/data.rda |binary inst/createMockReportData.R | 6 inst/doc/a01_tables.html | 558 ++++++++++++++--------------- inst/doc/a02_plots.R | 2 inst/doc/a02_plots.Rmd | 594 +++++++++++++++---------------- inst/doc/a02_plots.html | 42 +- inst/doc/a03_quarto_reports.R | 3 inst/doc/a03_quarto_reports.Rmd | 541 ++++++++++++++-------------- inst/doc/a03_quarto_reports.html | 12 inst/doc/a04_shiny_apps.Rmd | 738 +++++++++++++++++++-------------------- inst/doc/a04_shiny_apps.html | 29 - vignettes/a02_plots.Rmd | 594 +++++++++++++++---------------- vignettes/a03_quarto_reports.Rmd | 541 ++++++++++++++-------------- vignettes/a04_shiny_apps.Rmd | 738 +++++++++++++++++++-------------------- 17 files changed, 2359 insertions(+), 2383 deletions(-)
More information about visOmopResults at CRAN
Permanent link
Title: Manipulation of Matched Phylogenies and Data using 'data.table'
Description: An implementation that combines trait data and a phylogenetic tree (or trees) into a
single object of class 'treedata.table'. The resulting object can be easily
manipulated to simultaneously change the trait- and tree-level sampling.
Currently implemented functions allow users to use a 'data.table' syntax when
performing operations on the trait dataset within the 'treedata.table' object.
For more details see Roman-Palacios et al. (2021) <doi:10.7717/peerj.12450>.
Author: Josef Uyeda [aut] ,
Cristian Roman-Palacios [aut, cre] ,
April Wright [aut] ,
Luke Harmon [ctb],
Hugo Gruson [rev],
Kari Norman [rev]
Maintainer: Cristian Roman-Palacios <cromanpa@arizona.edu>
This is a re-admission after prior archival of version 0.1.0 dated 2020-09-30
Diff between treedata.table versions 0.1.0 dated 2020-09-30 and 0.1.1 dated 2025-10-09
treedata.table-0.1.0/treedata.table/inst/doc/E_Preprint.R |only treedata.table-0.1.0/treedata.table/inst/doc/E_Preprint.Rmd |only treedata.table-0.1.0/treedata.table/inst/doc/E_Preprint.html |only treedata.table-0.1.0/treedata.table/vignettes/E_Preprint.Rmd |only treedata.table-0.1.0/treedata.table/vignettes/media |only treedata.table-0.1.1/treedata.table/DESCRIPTION | 37 - treedata.table-0.1.1/treedata.table/MD5 | 66 - treedata.table-0.1.1/treedata.table/R/as.treedata.table.R | 30 treedata.table-0.1.1/treedata.table/R/droptreedata.table.R | 6 treedata.table-0.1.1/treedata.table/R/extractVector.R | 4 treedata.table-0.1.1/treedata.table/R/init.R |only treedata.table-0.1.1/treedata.table/R/pulltreedata.table.R | 2 treedata.table-0.1.1/treedata.table/R/tdt.R | 2 treedata.table-0.1.1/treedata.table/R/tdt_methods.R | 4 treedata.table-0.1.1/treedata.table/R/treedata.table.R | 10 treedata.table-0.1.1/treedata.table/build/vignette.rds |binary treedata.table-0.1.1/treedata.table/inst/doc/AA_treedata.table_intro_english.Rmd | 18 treedata.table-0.1.1/treedata.table/inst/doc/AA_treedata.table_intro_english.html | 338 ++++++--- treedata.table-0.1.1/treedata.table/inst/doc/AB_treedata.table_intro_spanish.Rmd | 14 treedata.table-0.1.1/treedata.table/inst/doc/AB_treedata.table_intro_spanish.html | 340 ++++++---- treedata.table-0.1.1/treedata.table/inst/doc/B_multiphylo_treedata.table.Rmd | 10 treedata.table-0.1.1/treedata.table/inst/doc/B_multiphylo_treedata.table.html | 238 ++++--- treedata.table-0.1.1/treedata.table/inst/doc/C_PartialMatching.Rmd | 2 treedata.table-0.1.1/treedata.table/inst/doc/C_PartialMatching.html | 253 ++++--- treedata.table-0.1.1/treedata.table/inst/doc/D_AdditionalFunctions_treedata.table.Rmd | 2 treedata.table-0.1.1/treedata.table/inst/doc/D_AdditionalFunctions_treedata.table.html | 234 ++++-- treedata.table-0.1.1/treedata.table/man/head.treedata.table.Rd | 3 treedata.table-0.1.1/treedata.table/man/sub-.treedata.table.Rd | 7 treedata.table-0.1.1/treedata.table/man/sub-sub-.treedata.table.Rd | 3 treedata.table-0.1.1/treedata.table/man/tail.treedata.table.Rd | 3 treedata.table-0.1.1/treedata.table/tests/testthat/test.treedata.table.R | 12 treedata.table-0.1.1/treedata.table/vignettes/AA_treedata.table_intro_english.Rmd | 18 treedata.table-0.1.1/treedata.table/vignettes/AB_treedata.table_intro_spanish.Rmd | 14 treedata.table-0.1.1/treedata.table/vignettes/B_multiphylo_treedata.table.Rmd | 10 treedata.table-0.1.1/treedata.table/vignettes/C_PartialMatching.Rmd | 2 treedata.table-0.1.1/treedata.table/vignettes/D_AdditionalFunctions_treedata.table.Rmd | 2 36 files changed, 1014 insertions(+), 670 deletions(-)
More information about treedata.table at CRAN
Permanent link
Title: A Unified Data Layer for Large-Scale Single-Cell, Spatial and
Bulk Immunomics
Description: Provides a unified data layer for single-cell, spatial and bulk
T-cell and B-cell immune receptor repertoire data. Think AnnData or SeuratObject,
but for AIRR data, a.k.a. Adaptive Immune Receptor Repertoire, VDJ-seq, RepSeq, or
VDJ sequencing data.
Author: Vadim I. Nazarov [aut, cre]
Maintainer: Vadim I. Nazarov <support@immunomind.com>
Diff between immundata versions 0.0.3 dated 2025-09-04 and 0.0.5 dated 2025-10-09
DESCRIPTION | 17 - MD5 | 33 +- NAMESPACE | 2 R/core_immundata.R | 14 R/io_immundata_write.R | 9 R/operations_external_annotate_seurat.R |only R/operations_utils.R | 2 R/test_utils.R | 9 README.md | 165 +++------- inst/extdata/single_cell/immundata-lb6.csv/annotations.parquet |binary inst/extdata/single_cell/immundata-lb6.csv/metadata.json | 2 inst/extdata/single_cell/immundata-lt6.csv/annotations.parquet |binary inst/extdata/single_cell/immundata-lt6.csv/metadata.json | 2 man/ImmunData.Rd | 4 man/annotate_seurat.Rd |only man/get_test_idata.Rd | 1 man/get_test_immundata.Rd |only man/immundata-package.Rd | 5 man/write_immundata.Rd | 7 19 files changed, 136 insertions(+), 136 deletions(-)
Title: Goodness-of-Fit Testing for Structural Equation Models
Description: Supports eigenvalue block-averaging p-values (Foldnes, Grønneberg, 2018) <doi:10.1080/10705511.2017.1373021>,
penalized eigenvalue block-averaging p-values (Foldnes, Moss, Grønneberg, 2024) <doi:10.1080/10705511.2024.2372028>, penalized
regression p-values (Foldnes, Moss, Grønneberg, 2024) <doi:10.1080/10705511.2024.2372028>, as well as traditional p-values such as Satorra-Bentler. All p-values can
be calculated using unbiased or biased gamma estimates (Du, Bentler, 2022) <doi:10.1080/10705511.2022.2063870>
and two choices of chi square statistics.
Author: Jonas Moss [aut, cre] ,
Njal Foldnes [ctb] ,
Steffen Groenneberg [ctb]
Maintainer: Jonas Moss <jonas.moss.statistics@gmail.com>
This is a re-admission after prior archival of version 0.5.0 dated 2024-01-18
Diff between semTests versions 0.5.0 dated 2024-01-18 and 0.7.1 dated 2025-10-09
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Title: Collinearity Detection using Redefined Variance Inflation Factor
and Graphical Methods
Description: The detection of troubling approximate collinearity in a multiple linear regression model is a classical problem in Econometrics. This package is focused on determining whether or not the degree of approximate multicollinearity in a multiple linear regression model is of concern, meaning that it affects the statistical analysis (i.e. individual significance tests) of the model. This objective is achieved by using the variance inflation factor redefined and the scatterplot between the variance inflation factor and the coefficient of variation. For more details see Salmerón R., García C.B. and García J. (2018) <doi:10.1080/00949655.2018.1463376>, Salmerón, R., Rodríguez, A. and García C. (2020) <doi:10.1007/s00180-019-00922-x>, Salmerón, R., García, C.B, Rodríguez, A. and García, C. (2022) <doi:10.32614/RJ-2023-010>, Salmerón, R., García, C.B. and García, J. (2025) <doi:10.1007/s10614-024-10575-8> and Salmerón, R., García, C.B, García J. (2023, working paper) < [...truncated...]
Author: R. Salmeron [aut, cre],
C.B. Garcia [aut]
Maintainer: R. Salmeron <romansg@ugr.es>
Diff between rvif versions 3.1 dated 2025-09-05 and 3.2 dated 2025-10-09
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Title: Knock Errors Off Nice Guesses
Description: Miscellaneous functions and data used in psychological research and teaching. Keng
currently has a built-in dataset depress, and could (1) scale a vector; (2) compute the cut-off
values of Pearson's r with known sample size; (3) test the significance and compute the post-hoc
power for Pearson's r with known sample size; (4) conduct a priori power analysis and plan the
sample size for Pearson's r; (5) compare lm()'s fitted outputs using R-squared, f_squared,
post-hoc power, and PRE (Proportional Reduction in Error, also called partial R-squared or
partial Eta-squared); (6) calculate PRE from partial correlation, Cohen's f, or f_squared;
(7) conduct a priori power analysis and plan the sample size for one or a set of predictors in
regression analysis; (8) conduct post-hoc power analysis for one or a set of predictors in
regression analysis with known sample size; (9) randomly pick numbers for Chinese Super Lotto
and Double Color Balls; (10) assess course objective achievement in Outcome- [...truncated...]
Author: Qingyao Zhang [aut, cre]
Maintainer: Qingyao Zhang <qingyaozhang@outlook.com>
Diff between Keng versions 2025.9.1 dated 2025-08-31 and 2025.10.8 dated 2025-10-09
DESCRIPTION | 8 - MD5 | 56 ++++++----- NAMESPACE | 2 NEWS.md | 5 + R/assess_coa.R | 71 +++++++++++--- R/pick_sl.R | 120 ++++++++++++------------ R/power_lm.R | 125 ++++++++----------------- R/power_r.R | 118 +++++++---------------- R/powered_lm.R |only R/powered_r.R |only R/print.Keng_power.R | 8 - README.md | 195 ++++++++++++++++++++------------------- inst/doc/PRE.html | 5 - inst/doc/assessCOA.R | 12 +- inst/doc/assessCOA.Rmd | 6 - inst/doc/assessCOA.html | 121 ++++++++++++------------ inst/doc/commonSampleSizes.html | 23 ---- inst/doc/partialRegression.html | 5 - inst/doc/planSampleSize.html | 14 +- man/assess_coa.Rd | 21 +++- man/pick_sl.Rd | 2 man/power_lm.Rd | 15 --- man/power_r.Rd | 12 -- man/powered_lm.Rd |only man/powered_r.Rd |only tests/testthat/test-assess_coa.R | 26 +++-- tests/testthat/test-power_lm.R | 4 tests/testthat/test-power_r.R | 7 - tests/testthat/test-powered_lm.R |only tests/testthat/test-powered_r.R |only tests/testthat/test-test_r.R | 8 - vignettes/assessCOA.Rmd | 6 - 32 files changed, 471 insertions(+), 524 deletions(-)
Title: Measurement Units for R Vectors
Description: Support for measurement units in R vectors, matrices
and arrays: automatic propagation, conversion, derivation
and simplification of units; raising errors in case of unit
incompatibility. Compatible with the POSIXct, Date and difftime
classes. Uses the UNIDATA udunits library and unit database for
unit compatibility checking and conversion.
Documentation about 'units' is provided in the paper by Pebesma, Mailund &
Hiebert (2016, <doi:10.32614/RJ-2016-061>), included in this package as a
vignette; see 'citation("units")' for details.
Author: Edzer Pebesma [aut, cre] ,
Thomas Mailund [aut],
Tomasz Kalinowski [aut],
James Hiebert [ctb],
Inaki Ucar [aut] ,
Thomas Lin Pedersen [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between units versions 0.8-7 dated 2025-03-11 and 1.0-0 dated 2025-10-09
DESCRIPTION | 15 - MD5 | 77 ++--- NAMESPACE | 9 NEWS.md | 26 + R/RcppExports.R | 4 R/arith.R | 54 +-- R/conversion.R | 6 R/init.R | 2 R/make_units.R | 250 +++++------------ R/options.R | 12 R/scale_units.R | 120 +++++--- R/symbolic_units.R | 106 +++++-- R/tidyverse.R | 4 R/udunits.R | 19 - build/vignette.rds |binary configure | 18 - inst/doc/measurement_units_in_R.html | 17 - inst/doc/units.R | 1 inst/doc/units.Rmd | 1 inst/doc/units.html | 126 ++++---- man/convert_to_base.Rd |only man/matrixOps.units.Rd |only man/scale_units.Rd | 48 ++- man/udunits2.Rd | 12 man/units.Rd | 64 +--- man/units_options.Rd | 6 src/RcppExports.cpp | 38 -- src/tokenizer.cpp |only src/udunits.cpp | 50 +-- tests/testthat/_snaps/plot/ggplot2-other-alpha.svg |only tests/testthat/_snaps/plot/ggplot2-other-color.svg |only tests/testthat/_snaps/plot/ggplot2-other-fill.svg |only tests/testthat/_snaps/plot/ggplot2-other-linewidth.svg |only tests/testthat/_snaps/plot/ggplot2-other-radius.svg |only tests/testthat/_snaps/plot/ggplot2-other-size-area.svg |only tests/testthat/_snaps/plot/ggplot2-other-size.svg |only tests/testthat/_snaps/plot/ggplot2-range.svg |only tests/testthat/_snaps/tidyverse.md | 11 tests/testthat/test_arith.R | 11 tests/testthat/test_plot.R | 57 +++ tests/testthat/test_symbolic_units.R | 29 + tests/testthat/test_tidyverse.R | 4 tests/testthat/test_udunits.R | 8 tests/testthat/test_unit_creation.R | 87 ++--- vignettes/units.Rmd | 1 45 files changed, 715 insertions(+), 578 deletions(-)
Title: Minimization Methods for Ill-Conditioned Problems
Description: Implementation of methods for minimizing ill-conditioned problems. Currently only includes regularized (quasi-)newton optimization (Kanzow and Steck et al. (2023), <doi:10.1007/s12532-023-00238-4>).
Author: Bert van der Veen [aut, cre]
Maintainer: Bert van der Veen <bert_van_der_veen@hotmail.com>
Diff between minic versions 1.0.2 dated 2025-06-05 and 1.0.3 dated 2025-10-09
DESCRIPTION | 8 +-- MD5 | 8 +-- NEWS.md | 8 +++ README.md | 2 src/minic.cpp | 148 +++++++++++++++++++++++++++++++++++----------------------- 5 files changed, 107 insertions(+), 67 deletions(-)
Title: Tidy and Streamlined Metabolomics Data Workflows
Description: Facilitate tasks typically encountered during metabolomics data analysis including data import, filtering, missing value imputation (Stacklies et al. (2007) <doi:10.1093/bioinformatics/btm069>, Stekhoven et al. (2012) <doi:10.1093/bioinformatics/btr597>, Tibshirani et al. (2017) <doi:10.18129/B9.BIOC.IMPUTE>, Troyanskaya et al. (2001) <doi:10.1093/bioinformatics/17.6.520>), normalization (Bolstad et al. (2003) <doi:10.1093/bioinformatics/19.2.185>, Dieterle et al. (2006) <doi:10.1021/ac051632c>, Zhao et al. (2020) <doi:10.1038/s41598-020-72664-6>) transformation, centering and scaling (Van Den Berg et al. (2006) <doi:10.1186/1471-2164-7-142>) as well as statistical tests and plotting. 'metamorphr' introduces a tidy (Wickham et al. (2019) <doi:10.21105/joss.01686>) format for metabolomics data and is designed to make it easier to build elaborate analysis workflows and to integrate them with 'tidyverse' packages including 'dplyr' and [...truncated...]
Author: Yannik Schermer [aut, cre, cph]
Maintainer: Yannik Schermer <yannik.schermer@chem.rptu.de>
Diff between metamorphr versions 0.1.1 dated 2025-09-01 and 0.2.0 dated 2025-10-09
DESCRIPTION | 8 MD5 | 35 ++-- NAMESPACE | 4 NEWS.md | 10 + R/data.R | 24 ++ R/internal_functions.R | 45 +++++ R/misc.R | 194 ++++++++++++++++++++++++ R/sysdata.rda |binary README.md | 6 data/atoms.rda |only inst/doc/conjugate-screening.html | 4 man/atoms.Rd |only man/calc_km.Rd |only man/calc_kmd.Rd |only man/calc_nominal_km.Rd |only man/figures/functions.svg | 2 man/figures/logo.png |only man/formula_to_mass.Rd |only man/metamorphr-package.Rd | 4 tests/testthat/test-calc_kmd.R |only tests/testthat/test-formula_to_mass.R |only tests/testthat/test-impute_knn.R | 2 tests/testthat/test-normalize_quantile_smooth.R | 4 23 files changed, 319 insertions(+), 23 deletions(-)
Title: Matrix Functions for Teaching and Learning Linear Algebra and
Multivariate Statistics
Description: A collection of matrix functions for teaching and learning matrix
linear algebra as used in multivariate statistical methods. Many of these functions are
designed for tutorial purposes in learning matrix algebra ideas using R. In some
cases, functions are provided for concepts available elsewhere in R, but where
the function call or name is not obvious. In other cases, functions are provided
to show or demonstrate an algorithm. In addition, a collection of functions are
provided for drawing vector diagrams in 2D and 3D and for rendering matrix
expressions and equations in LaTeX.
Author: Michael Friendly [aut, cre] ,
John Fox [aut] ,
Phil Chalmers [aut] ,
Georges Monette [ctb] ,
Gaston Sanchez [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between matlib versions 1.0.0 dated 2024-10-02 and 1.0.1 dated 2025-10-09
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Title: Client for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@lamin.ai>
Diff between laminr versions 1.1.1 dated 2025-05-15 and 1.2.0 dated 2025-10-09
laminr-1.1.1/laminr/man/lamin_connect.Rd |only laminr-1.1.1/laminr/man/lamin_delete.Rd |only laminr-1.1.1/laminr/man/lamin_disconnect.Rd |only laminr-1.1.1/laminr/man/lamin_init.Rd |only laminr-1.1.1/laminr/man/lamin_login.Rd |only laminr-1.1.1/laminr/man/lamin_logout.Rd |only laminr-1.1.1/laminr/man/lamin_save.Rd |only laminr-1.2.0/laminr/DESCRIPTION | 18 laminr-1.2.0/laminr/MD5 | 61 - laminr-1.2.0/laminr/NAMESPACE | 9 laminr-1.2.0/laminr/R/Registry.R | 22 laminr-1.2.0/laminr/R/checks.R | 19 laminr-1.2.0/laminr/R/file_loaders.R | 18 laminr-1.2.0/laminr/R/file_openers.R | 8 laminr-1.2.0/laminr/R/import.R | 27 laminr-1.2.0/laminr/R/lamin_cli.R | 428 +++++++---- laminr-1.2.0/laminr/R/lamindb.R | 108 +- laminr-1.2.0/laminr/R/laminr-package.R | 4 laminr-1.2.0/laminr/R/packages.R | 96 +- laminr-1.2.0/laminr/R/require.R | 115 ++ laminr-1.2.0/laminr/R/reticulate-utils.R | 46 + laminr-1.2.0/laminr/R/status.R |only laminr-1.2.0/laminr/R/temporary-instance.R |only laminr-1.2.0/laminr/R/ui.R | 16 laminr-1.2.0/laminr/R/utils.R | 136 ++- laminr-1.2.0/laminr/R/zzz.R | 2 laminr-1.2.0/laminr/build/vignette.rds |binary laminr-1.2.0/laminr/man/get_current_lamin_instance.Rd | 2 laminr-1.2.0/laminr/man/get_current_lamin_settings.Rd |only laminr-1.2.0/laminr/man/get_current_lamin_user.Rd | 2 laminr-1.2.0/laminr/man/import_module.Rd | 4 laminr-1.2.0/laminr/man/lamin_cli.Rd |only laminr-1.2.0/laminr/man/laminr_status.Rd |only laminr-1.2.0/laminr/man/require_module.Rd | 7 laminr-1.2.0/laminr/man/use_temporary_instance.Rd |only laminr-1.2.0/laminr/tests/testthat/setup.R | 33 laminr-1.2.0/laminr/tests/testthat/test-file_loaders.R | 29 laminr-1.2.0/laminr/tests/testthat/test-status.R |only laminr-1.2.0/laminr/tests/testthat/test-temporary-instance.R |only 39 files changed, 884 insertions(+), 326 deletions(-)
Title: Check Color Palettes for Problems with Color Vision Deficiency
Description: Compare color palettes with simulations of color vision deficiencies - deuteranopia, protanopia, and tritanopia.
It includes calculation of distances between colors, and creating summaries of differences between a color palette and simulations of color vision deficiencies.
This work was inspired by the blog post at <https://www.datawrapper.de/blog/colorblind-check>.
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between colorblindcheck versions 1.0.2 dated 2023-05-13 and 1.0.4 dated 2025-10-09
DESCRIPTION | 13 +++--- MD5 | 32 +++++++++------- NAMESPACE | 1 R/palette_plot.R | 44 ++++++++++++++++++---- README.md | 16 ++------ build/vignette.rds |binary inst/doc/intro-to-colorblindcheck.R | 4 +- inst/doc/intro-to-colorblindcheck.Rmd | 2 - inst/doc/intro-to-colorblindcheck.html | 62 +++++++++++++++---------------- man/colorblindcheck-package.Rd | 4 +- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/logo.png |only man/palette_bivariate_plot.Rd | 8 +++- man/palette_plot.Rd | 5 ++ tests/testthat/_snaps |only tests/testthat/test-plot.R | 7 +++ vignettes/intro-to-colorblindcheck.Rmd | 2 - 17 files changed, 123 insertions(+), 77 deletions(-)
More information about colorblindcheck at CRAN
Permanent link
Title: 'StreamCatTools'
Description: Tools for using the 'StreamCat' and 'LakeCat' API and
interacting with the 'StreamCat' and 'LakeCat' database.
Convenience functions in the package wrap the API for 'StreamCat'
on <https://api.epa.gov/StreamCat/streams/metrics>.
Author: Marc Weber [aut, cre],
Ryan Hill [ctb],
Travis Hudson [ctb],
Allen Brookes [ctb],
David Rebhuhn [ctb],
Michael Dumelle [ctb],
Zachary Smith [ctb]
Maintainer: Marc Weber <weber.marc@epa.gov>
Diff between StreamCatTools versions 0.7.0 dated 2025-09-15 and 0.8.0 dated 2025-10-09
DESCRIPTION | 13 ++- MD5 | 60 +++++++++-------- NAMESPACE | 2 NEWS.md | 9 ++ R/lc_get_comid.R | 2 R/lc_get_data.R | 22 ++++-- R/lc_get_params.R | 117 +++++++++++++++++++++++++++++++-- R/sc_get_comid.R | 9 +- R/sc_get_data.R | 24 +++++- R/sc_get_params.R | 124 +++++++++++++++++++++++++++++++++--- README.md | 3 inst/doc/Applications.html | 4 - inst/doc/Introduction.R | 2 inst/doc/Introduction.Rmd | 2 inst/doc/Introduction.html | 2 inst/doc/LakeCat.R | 2 inst/doc/LakeCat.Rmd | 2 inst/doc/LakeCat.html | 14 ++-- man/lc_get_comid.Rd | 2 man/lc_get_data.Rd | 2 man/lc_get_metric_names.Rd |only man/lc_get_params.Rd | 8 +- man/lc_nlcd.Rd | 2 man/sc_get_comid.Rd | 5 - man/sc_get_data.Rd | 2 man/sc_get_metric_names.Rd |only man/sc_get_params.Rd | 9 +- man/sc_nlcd.Rd | 2 tests/testthat/test-lc_get_params.R | 24 +++--- tests/testthat/test-sc_get_params.R | 33 +++++++++ vignettes/Introduction.Rmd | 2 vignettes/LakeCat.Rmd | 2 32 files changed, 393 insertions(+), 113 deletions(-)
More information about StreamCatTools at CRAN
Permanent link
Title: Work with Open Road Traffic Casualty Data from Great Britain
Description: Work with and download road traffic casualty data from Great
Britain. Enables access to the UK's official road safety statistics,
'STATS19'. Enables users to specify a download directory for the data,
which can be set permanently by adding `STATS19_DOWNLOAD_DIRECTORY=/path/to/a/dir`
to your `.Renviron` file, which can be opened with `usethis::edit_r_environ()`.
The data is provided as a series of `.csv` files.
This package downloads, reads-in and formats the data, making it suitable
for analysis. See the stats19 vignette for details. Data available from
1979 to 2024. See the official data series at
<https://www.data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-accidents-safety-data>.
The package is described in a paper in the Journal of Open Source Software
(Lovelace et al. 2019) <doi:10.21105/joss.01181>.
See
Gilardi et al. (2022) <doi:10.1111/rssa.12823>,
Vidal-Tortosa et al. (2021) <doi:10.1016/j.jth.2021.101291>,
Tait et al. (2023) <doi:10.101 [...truncated...]
Author: Robin Lovelace [aut, cre] ,
Malcolm Morgan [aut] ,
Layik Hama [aut] ,
Mark Padgham [aut] ,
David Ranzolin [rev],
Adam Sparks [rev, ctb] ,
Ivo Wengraf [ctb],
RAC Foundation [fnd],
Blaise Kelly [aut]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stats19 versions 3.3.1 dated 2025-01-15 and 3.4.0 dated 2025-10-09
DESCRIPTION | 61 MD5 | 62 NAMESPACE | 1 NEWS.md | 12 R/adjustments.R | 7 R/dl.R | 35 R/format.R | 2 R/get.R | 24 R/read.R | 12 R/utils.R | 71 build/vignette.rds |binary data/file_names.rda |binary data/stats19_schema.rda |binary data/stats19_variables.rda |binary inst/doc/blog.html | 8 inst/doc/factsheet.R |only inst/doc/factsheet.Rmd |only inst/doc/factsheet.html |only inst/doc/stats19-training-setup.html | 4 inst/doc/stats19-training.html | 23 inst/doc/stats19-vehicles.html | 4 inst/doc/stats19.R | 25 inst/doc/stats19.Rmd | 35 inst/doc/stats19.html |10145 +++++++++++++++++++++++++++++++++-- man/dl_stats19.Rd | 13 man/find_file_name.Rd | 1 man/get_data_directory.Rd | 7 man/get_stats19.Rd | 19 man/get_stats19_adjustments.Rd | 2 man/get_url.Rd | 2 man/read_collisions.Rd | 8 man/read_vehicles.Rd | 4 vignettes/factsheet.Rmd |only vignettes/stats19.Rmd | 35 34 files changed, 9983 insertions(+), 639 deletions(-)
Title: Statistical Modeling
Description: A collection of algorithms and functions to aid statistical modeling. Includes limiting dilution analysis (aka ELDA), growth curve comparisons, mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Also includes advanced generalized linear model functions including Tweedie and Digamma distributional families, secure convergence and exact distributional calculations for unit deviances.
Author: Gordon Smyth [cre, aut],
Lizhong Chen [aut],
Yifang Hu [ctb],
Peter Dunn [ctb],
Belinda Phipson [ctb],
Yunshun Chen [ctb]
Maintainer: Gordon Smyth <smyth@wehi.edu.au>
Diff between statmod versions 1.5.0 dated 2023-01-06 and 1.5.1 dated 2025-10-09
DESCRIPTION | 34 +++++++-- MD5 | 12 +-- build/partial.rdb |binary inst/CITATION | 180 ++++++++++++++++++++++++++---------------------- inst/NEWS | 6 + man/expectedDeviance.Rd | 19 ++++- man/glmscoretest.Rd | 2 7 files changed, 160 insertions(+), 93 deletions(-)
Title: Sparsity by Worst-Case Quadratic Penalties
Description: Fits classical sparse regression models with
efficient active set algorithms by solving quadratic problems as described by
Grandvalet, Chiquet and Ambroise (2017) <doi:10.48550/arXiv.1210.2077>. Also provides a few
methods for model selection purpose (cross-validation, stability selection).
Author: Julien Chiquet [aut, cre]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between quadrupen versions 0.2-12 dated 2024-06-25 and 0.2-13 dated 2025-10-09
DESCRIPTION | 13 +-- MD5 | 34 ++++---- NEWS.md | 6 + R/crossval-class.R | 12 +-- R/crossval.R | 4 - R/init.R | 2 R/quadrupen-class.R | 4 - R/stability-class.R | 8 +- R/stability.R | 4 - build/partial.rdb |binary demo/quad_breg.R | 2 inst/WORDLIST | 8 -- man/crossval.Rd | 4 - man/stability.Rd | 4 - src/Makevars | 4 - src/Makevars.win | 6 - src/elastic_net.cpp | 208 ++++++++++++++++++++++++++-------------------------- src/quadratic.cpp | 6 - 18 files changed, 168 insertions(+), 161 deletions(-)
Title: Lightweight Reproducible Reporting
Description: Distributed reproducible computing framework, adopting
ideas from git, docker and other software. By defining a
lightweight interface around the inputs and outputs of an
analysis, a lot of the repetitive work for reproducible research
can be automated. We define a simple format for organising and
describing work that facilitates collaborative reproducible
research and acknowledges that all analyses are run multiple times
over their lifespans.
Author: Rich FitzJohn [aut, cre],
Robert Ashton [aut],
Martin Eden [aut],
Alex Hill [aut],
Wes Hinsley [aut],
Mantra Kusumgar [aut],
Paul Lietar [aut],
James Thompson [aut],
Katy Gaythorpe [aut],
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between orderly versions 1.4.3 dated 2021-09-22 and 2.0.0 dated 2025-10-09
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Title: Genome Polarization via Diagnostic Index Expectation
Maximization
Description: Implements a likelihood-based method for genome polarization, identifying
which alleles of SNV markers belong to either side of a barrier to gene flow. The
approach co-estimates individual assignment, barrier strength, and divergence between
sides, with direct application to studies of hybridization. Includes VCF-to-diem
conversion and input checks, support for mixed ploidy and parallelization, and tools
for visualization and diagnostic outputs. Based on diagnostic index expectation
maximization as described in Baird et al. (2023) <doi:10.1111/2041-210X.14010>.
Author: Natalia Martinkova [aut, cre] ,
Stuart Baird [aut]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Diff between diemr versions 1.5 dated 2025-09-11 and 1.5.1 dated 2025-10-09
DESCRIPTION | 24 +- MD5 | 50 +++-- NAMESPACE | 1 NEWS.md | 10 + R/ModelOfDiagnostic.r | 3 R/diem.r | 26 +- R/emPolarise.r | 6 R/extdata.r | 29 +-- R/hybridIndex.r |only R/importPolarized.r | 54 +++--- R/pHetErrOnStateCount.r | 7 R/plotDeFinetti.r | 24 +- R/plotMarkerAxis.r | 40 ++-- R/plotPolarized.r | 14 - R/rank2map.r | 6 R/smoothPolarizedGenotypes.r | 5 R/variantSites.r | 20 +- R/vcf2diem.r | 87 ++++++---- README.md |only inst/doc/Importing-data-for-genome-polarisation.html | 4 inst/doc/Understanding-genome-polarisation-output-files.html | 4 inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.html | 4 man/hybridIndex.Rd |only man/rank2map.Rd | 2 man/smoothPolarizedGenotypes.Rd | 7 man/variantSites.Rd | 6 man/vcf2diem.Rd | 29 ++- tests/testthat/test_hybridIndex.r |only 28 files changed, 259 insertions(+), 203 deletions(-)
Title: Bootstrap for State Space Models
Description: Provides a streamlined and user-friendly framework for
bootstrapping in state space models, particularly when the number of
subjects/units (n) exceeds one, a scenario commonly encountered in
social and behavioral sciences. The parametric bootstrap implemented
here was developed and applied 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 bootStateSpace versions 1.0.2 dated 2025-02-14 and 1.0.3 dated 2025-10-09
DESCRIPTION | 43 ++++++++++++++++++++++----------- MD5 | 12 ++++----- NEWS.md | 6 ++++ R/bootStateSpace-methods.R | 54 +++++++++++++++++++++++------------------- build/partial.rdb |binary inst/CITATION | 38 ++++++++++++++++++----------- man/bootStateSpace-package.Rd | 8 +++++- 7 files changed, 102 insertions(+), 59 deletions(-)
More information about bootStateSpace at CRAN
Permanent link
Title: Weibull Analysis for Reliability Engineering
Description: Life data analysis in the graphical tradition of Waloddi Weibull. Methods derived from Robert B. Abernethy (2008, ISBN 0-965306-3-2), Wayne Nelson (1982, ISBN: 9780471094586), William Q. Meeker and Lois A. Escobar (1998, ISBN: 1-471-14328-6), John I. McCool, (2012, ISBN: 9781118217986).
Author: David Silkworth [aut],
Jurgen Symynck [aut],
Jacob Ormerod [cre],
OpenReliability.org [cph]
Maintainer: Jacob Ormerod <jake@openreliability.org>
Diff between WeibullR versions 1.2.1 dated 2022-06-25 and 1.2.4 dated 2025-10-09
WeibullR-1.2.1/WeibullR/README.md |only WeibullR-1.2.4/WeibullR/DESCRIPTION | 9 ++---- WeibullR-1.2.4/WeibullR/MD5 | 13 ++++----- WeibullR-1.2.4/WeibullR/R/plot.wblr.R | 18 ++++++------ WeibullR-1.2.4/WeibullR/man/options.wblr.Rd | 22 +++++++-------- WeibullR-1.2.4/WeibullR/man/wblr.Rd | 40 ++++++++++++++++------------ WeibullR-1.2.4/WeibullR/man/wblr.conf.Rd | 16 +++++------ WeibullR-1.2.4/WeibullR/src/Makevars | 1 8 files changed, 61 insertions(+), 58 deletions(-)
Title: 'Rcpp' Integration for 'CGAL'
Description: Creates a header only package to link to the 'CGAL'
(Computational Geometry Algorithms Library)
header files in 'Rcpp'. There are a variety of potential uses for
the software such as Hilbert sorting, K-D Tree nearest neighbors,
and convex hull algorithms. For more information about how to use the header files,
see the 'CGAL' documentation at <https://www.cgal.org>. Currently
downloads version 6.1 of the 'CGAL' header files.
Author: Eric Dunipace [aut, cre] ,
Tyler Morgan-Wall [ctb],
The CGAL Project [cph]
Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>
Diff between RcppCGAL versions 6.0.1 dated 2025-01-08 and 6.1 dated 2025-10-09
DESCRIPTION | 19 +-- MD5 | 18 +- NEWS.md | 4 R/zzz.R | 2 build/vignette.rds |binary inst/AUTHORS | 225 ++++++++++++++++++++---------------- inst/doc/Installation.html | 9 - inst/include/CGAL_zip.tar.xz |binary man/RcppCGAL-package.Rd | 2 tools/config/downloader_functions.R | 113 +++++++++++++++++- 10 files changed, 269 insertions(+), 123 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 4.1.0 dated 2025-08-29 and 4.1.1 dated 2025-10-09
DESCRIPTION | 8 MD5 | 72 ++++---- NAMESPACE | 14 + NEWS.md | 30 +++ R/addCwres.R | 2 R/augPred.R | 6 R/broom.R | 18 +- R/cov.R | 2 R/focei.R | 5 R/foceiControl.R | 20 ++ R/iov.R | 329 +++++++++++++++++++++++++++++++++++++-- R/mix.R |only R/nlmixr2Keywords.R | 1 R/nlmixr2_md5.R | 2 R/nmObjGet.R | 37 +++- R/nmObjGetEtaMat.R |only R/ofv.R | 2 R/preProcessZeroOmega.R | 77 +++++++++ R/print.R | 22 ++ R/saem.R | 2 R/saemControl.R | 5 R/simulate.R | 20 +- R/vpc.R | 17 +- R/zzz.R | 14 + data/nlmixr2Keywords.rda |binary man/dot-downgradeEtas.Rd |only man/dot-iniS3.Rd |only man/foceiControl.Rd | 16 + man/nlmixr2.Rd | 87 +++++----- man/nlmixr2Keywords.Rd | 1 man/nlmixr2iovLogvarCv.Rd |only man/rmEta.Rd |only man/rmdhunks/nlmixr2Keywords.Rmd | 3 man/saemControl.Rd | 16 + src/Makevars.in | 2 src/inner.cpp | 10 - src/scale.h | 7 tests/testthat/test-augpred.R | 33 +++ tests/testthat/test-iov.R | 58 ++++++ tests/testthat/test-mix.R |only tests/testthat/test-piping.R |only 41 files changed, 804 insertions(+), 134 deletions(-)
Title: Estimation and Prediction Methods for High-Dimensional Mixed
Frequency Time Series Data
Description: The 'midasml' package implements estimation and prediction methods for high-dimensional mixed-frequency (MIDAS) time-series and panel data regression models. The regularized MIDAS models are estimated using orthogonal (e.g. Legendre) polynomials and sparse-group LASSO (sg-LASSO) estimator. For more information on the 'midasml' approach see Babii, Ghysels, and Striaukas (2021, JBES forthcoming) <doi:10.1080/07350015.2021.1899933>. The package is equipped with the fast implementation of the sg-LASSO estimator by means of proximal block coordinate descent. High-dimensional mixed frequency time-series data can also be easily manipulated with functions provided in the package.
Author: Jonas Striaukas [cre, aut],
Andrii Babii [aut],
Jad Beyhum [aut],
Eric Ghysels [aut],
Alex Kostrov [ctb]
Maintainer: Jonas Striaukas <jonas.striaukas@gmail.com>
Diff between midasml versions 0.1.10 dated 2022-04-29 and 0.1.11 dated 2025-10-09
DESCRIPTION | 11 +++++++---- MD5 | 10 +++++++--- NAMESPACE | 7 ++++--- R/fa.sglfit.R |only R/predict.fa.sglfit.R |only man/fa.sglfit.Rd |only man/midasml-package.Rd | 7 +++++++ man/predict.fa.sglfit.Rd |only 8 files changed, 25 insertions(+), 10 deletions(-)
Title: Generalized Random Forests
Description: Forest-based statistical estimation and inference.
GRF provides non-parametric methods for heterogeneous treatment effects estimation
(optionally using right-censored outcomes, multiple treatment arms or outcomes, or instrumental variables),
as well as least-squares regression, quantile regression, and survival regression,
all with support for missing covariates.
Author: Julie Tibshirani [aut],
Susan Athey [aut],
Rina Friedberg [ctb],
Vitor Hadad [ctb],
David Hirshberg [ctb],
Luke Miner [ctb],
Erik Sverdrup [aut, cre],
Stefan Wager [aut],
Marvin Wright [ctb]
Maintainer: Erik Sverdrup <erik.sverdrup@monash.edu>
Diff between grf versions 2.4.0 dated 2024-11-15 and 2.5.0 dated 2025-10-09
DESCRIPTION | 8 - MD5 | 68 +++++----- R/RcppExports.R | 4 R/causal_survival_forest.R | 4 R/lm_forest.R | 28 +--- R/rank_average_treatment.R | 2 R/survival_forest.R | 10 + man/causal_survival_forest.Rd | 4 man/lm_forest.Rd | 14 -- man/predict.lm_forest.Rd | 14 -- man/rank_average_treatment_effect.Rd | 2 man/survival_forest.Rd | 9 + src/RcppExports.cpp | 9 - src/SurvivalForestBindings.cpp | 3 src/src/forest/ForestTrainers.cpp | 4 src/src/forest/ForestTrainers.h | 2 src/src/splitting/AcceleratedSurvivalSplittingRule.cpp |only src/src/splitting/AcceleratedSurvivalSplittingRule.h |only src/src/splitting/SurvivalSplittingRule.cpp | 10 - src/src/splitting/SurvivalSplittingRule.h | 4 src/src/splitting/factory/CausalSurvivalSplittingRuleFactory.cpp | 3 src/src/splitting/factory/CausalSurvivalSplittingRuleFactory.h | 1 src/src/splitting/factory/InstrumentalSplittingRuleFactory.cpp | 1 src/src/splitting/factory/InstrumentalSplittingRuleFactory.h | 1 src/src/splitting/factory/MultiCausalSplittingRuleFactory.cpp | 1 src/src/splitting/factory/MultiCausalSplittingRuleFactory.h | 1 src/src/splitting/factory/MultiRegressionSplittingRuleFactory.cpp | 1 src/src/splitting/factory/MultiRegressionSplittingRuleFactory.h | 1 src/src/splitting/factory/ProbabilitySplittingRuleFactory.cpp | 1 src/src/splitting/factory/ProbabilitySplittingRuleFactory.h | 1 src/src/splitting/factory/RegressionSplittingRuleFactory.cpp | 1 src/src/splitting/factory/RegressionSplittingRuleFactory.h | 1 src/src/splitting/factory/SplittingRuleFactory.h | 1 src/src/splitting/factory/SurvivalSplittingRuleFactory.cpp | 10 + src/src/splitting/factory/SurvivalSplittingRuleFactory.h | 7 - src/src/tree/TreeTrainer.cpp | 2 36 files changed, 132 insertions(+), 101 deletions(-)
Title: Generate Fully-Sequential Space-Filling Designs Inside a Unit
Hypercube
Description: Provides three methods to generate fully-sequential space-filling designs inside a unit hypercube. A 'fully-sequential space-filling design' means a sequence of nested designs (as the design size varies from one point up to some maximum number of points) with the design points added one at a time and such that the design at each size has good space-filling properties. Two methods target the minimum pairwise distance criterion and generate maximin designs, among which one method is more efficient when design size is large. One method targets the maximum hole size criterion and uses a heuristic to generate what is closer to a minimax design.
Author: Boyang Shang [aut, cre],
Daniel W. Apley [aut]
Maintainer: Boyang Shang <boyangshang2015@u.northwestern.edu>
Diff between FSSF versions 0.1.1 dated 2020-02-05 and 0.1.2 dated 2025-10-09
DESCRIPTION | 21 ++++++++++++++------- MD5 | 12 ++++++------ man/FSSF_b.Rd | 2 +- src/Makevars | 2 -- src/Makevars.win | 2 -- src/RcppExports.cpp | 5 +++++ src/kd_split.cpp | 6 +++--- 7 files changed, 29 insertions(+), 21 deletions(-)
Title: Data Analysis and Graphics Data and Functions
Description: Functions and data sets used in examples and exercises in the
text Maindonald, J.H. and Braun, W.J. (2003, 2007, 2010) "Data
Analysis and Graphics Using R", and in an upcoming Maindonald,
Braun, and Andrews text that builds on this earlier text.
Author: John H Maindonald [aut],
W. John Braun [aut, cre]
Maintainer: W. John Braun <john.braun@ubc.ca>
Diff between DAAG versions 1.25.6 dated 2024-05-26 and 1.25.7 dated 2025-10-09
DESCRIPTION | 19 +++++-- MD5 | 26 +++++----- build/vignette.rds |binary inst/doc/simulate-regdiags.R | 42 ++++++++-------- inst/doc/simulate-regdiags.html | 101 ++++++++++++++++++++++----------------- inst/doc/simulate-varselect.R | 12 ++-- inst/doc/simulate-varselect.html | 65 +++++++++++++++---------- man/DAAGtheme.Rd | 11 ++-- man/greatLakes.Rd | 4 - man/hotspots.Rd | 2 man/hurricNamed.Rd | 4 - man/nassCDS.Rd | 1 man/nasshead.Rd | 1 man/zzDAAGxdb.Rd | 2 14 files changed, 164 insertions(+), 126 deletions(-)
Title: Cluster Analysis via Random Partition Distributions
Description: Cluster analysis is performed using pairwise distance information and a random partition distribution. The method is
implemented for two random partition distributions. It draws samples and then obtains and plots clustering estimates.
An implementation of a selection algorithm is provided for the mass parameter of the partition distribution. Since
pairwise distances are the principal input to this procedure, it is most comparable to the hierarchical and k-medoids
clustering methods. The method is Dahl, Andros, Carter (2022+) <doi:10.1002/sam.11602>.
Author: David B. Dahl [aut, cre] ,
R. Jacob Andros [aut] ,
J. Brandon Carter [aut] ,
Alex Crichton [ctb] ,
Brendan Zabarauskas [ctb] ,
David B. Dahl [ctb] ,
David Tolnay [ctb] ,
Jim Turner [ctb] ,
Jorge Aparicio [ctb] ,
Josh Stone [ctb] ,
Mikhail Vorotilov [ [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between caviarpd versions 0.3.20 dated 2025-06-02 and 0.3.21 dated 2025-10-09
DESCRIPTION | 10 ++--- MD5 | 22 +++++------ NEWS | 4 ++ src/rust/epa/src/clust.rs | 4 +- src/rust/epa/src/epa.rs | 2 - src/rust/rbindings/src/lib.rs | 5 ++ src/rust/roxido/Cargo.lock | 8 ++-- src/rust/roxido/src/lib.rs | 78 ++++++++++++++++++++++++++++++++++++--- src/rust/roxido_macro/Cargo.lock | 8 ++-- src/rust/roxido_macro/src/lib.rs | 4 +- src/rust/vendor.tar.gz |binary tools/build_rust_library.R | 3 + 12 files changed, 112 insertions(+), 36 deletions(-)
Title: Variational Multivariate Spatial Small Area Estimation
Description: Variational Autoencoded Multivariate Spatial Fay-Herriot models are designed to efficiently estimate population parameters in small area estimation. This package implements the variational generalized multivariate spatial Fay-Herriot model (VGMSFH) using 'NumPyro' and 'PyTorch' backends, as demonstrated by Wang, Parker, and Holan (2025) <doi:10.48550/arXiv.2503.14710>. The 'vmsae' package provides utility functions to load weights of the pretrained variational autoencoders (VAEs) as well as tools to train custom VAEs tailored to users specific applications.
Author: Zhenhua Wang [aut, cre],
Paul A. Parker [aut, res],
Scott H. Holan [aut, res]
Maintainer: Zhenhua Wang <zhenhua.wang@missouri.edu>
Diff between vmsae versions 0.1.1 dated 2025-06-20 and 0.1.2 dated 2025-10-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/py/vgmsfh.py | 34 +++++++++++++++++----------------- 3 files changed, 22 insertions(+), 22 deletions(-)
Title: Command Line Optional and Positional Argument Parser
Description: A command line parser to
be used with 'Rscript' to write "#!" shebang scripts that gracefully
accept positional and optional arguments and automatically generate usage.
Author: Trevor L. Davis [aut, cre] ,
Allen Day [ctb] ,
Python Software Foundation [ctb] ,
Paul Newell [ctb]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between argparse versions 2.2.5 dated 2024-12-20 and 2.3.1 dated 2025-10-08
DESCRIPTION | 11 MD5 | 16 NEWS.md | 37 +- R/argparse.R | 733 +++++++++++++++++++++++------------------ build/vignette.rds |binary exec/display_file.R | 49 +- exec/example.R | 98 +++-- inst/doc/argparse.html | 227 ++++++------ tests/testthat/test-argparse.R | 689 +++++++++++++++++++++----------------- 9 files changed, 1054 insertions(+), 806 deletions(-)
Title: Manipulating External Pointers
Description: There is limited native support for external pointers in the R interface.
This package provides some basic tools to verify, create and modify 'externalptr' objects.
Author: Randy Lai [aut],
Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
This is a re-admission after prior archival of version 1.1.3 dated 2020-04-03
Diff between xptr versions 1.1.3 dated 2020-04-03 and 1.2.0 dated 2025-10-08
ChangeLog |only DESCRIPTION | 30 ++++++------- LICENSE | 4 - MD5 | 41 ++++++++++-------- NAMESPACE | 2 R/xptr.R | 92 +++++++++++++++++++++-------------------- README.md | 52 +++++++++++++++++++---- cleanup |only inst |only man/is_null_xptr.Rd | 4 - man/is_xptr.Rd | 4 - man/new_xptr.Rd | 6 +- man/register_xptr_finalizer.Rd | 11 +++- man/set_xptr_address.Rd | 7 ++- man/set_xptr_protected.Rd | 11 +++- man/set_xptr_tag.Rd | 11 +++- man/xptr.Rd | 9 ++-- man/xptr_address.Rd | 9 ++-- man/xptr_clear.Rd | 5 +- man/xptr_protected.Rd | 4 - man/xptr_tag.Rd | 4 - src/xptr.c | 32 ++++++++------ tests |only 23 files changed, 206 insertions(+), 132 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 0.4.0 dated 2025-02-09 and 1.0.1 dated 2025-10-08
UKFE-0.4.0/UKFE/data/AMSP.csv |only UKFE-0.4.0/UKFE/data/NRFAData.csv |only UKFE-0.4.0/UKFE/data/QMEDData.csv |only UKFE-0.4.0/UKFE/data/ThamesPQ.csv |only UKFE-0.4.0/UKFE/data/UKOutline.csv |only UKFE-1.0.1/UKFE/DESCRIPTION | 25 UKFE-1.0.1/UKFE/MD5 | 289 UKFE-1.0.1/UKFE/NAMESPACE | 16 UKFE-1.0.1/UKFE/NEWS.md |only UKFE-1.0.1/UKFE/R/AMSP.R | 26 UKFE-1.0.1/UKFE/R/All.R |12991 +++++++++++++++++-------------- UKFE-1.0.1/UKFE/R/FlowAnalysis.R | 589 - UKFE-1.0.1/UKFE/R/GISfuncs.R | 209 UKFE-1.0.1/UKFE/R/GetData.R | 1620 ++- UKFE-1.0.1/UKFE/R/NRFAData.R | 18 UKFE-1.0.1/UKFE/R/QMEDData.R | 18 UKFE-1.0.1/UKFE/R/RainfallAnalysis.R | 220 UKFE-1.0.1/UKFE/R/ThamesPQ.R | 28 UKFE-1.0.1/UKFE/R/UKOutline.R | 22 UKFE-1.0.1/UKFE/README.md |only UKFE-1.0.1/UKFE/build |only UKFE-1.0.1/UKFE/data/AMSP.rda |binary UKFE-1.0.1/UKFE/data/NRFAData.rda |binary UKFE-1.0.1/UKFE/data/QMEDData.rda |binary UKFE-1.0.1/UKFE/data/ThamesPQ.rda |binary UKFE-1.0.1/UKFE/data/UKOutline.rda |binary UKFE-1.0.1/UKFE/inst |only UKFE-1.0.1/UKFE/man/AMImport.Rd | 13 UKFE-1.0.1/UKFE/man/AMSP.Rd | 4 UKFE-1.0.1/UKFE/man/AMplot.Rd | 3 UKFE-1.0.1/UKFE/man/ARF.Rd | 3 UKFE-1.0.1/UKFE/man/AddGauge.Rd | 28 UKFE-1.0.1/UKFE/man/AggDayHour.Rd | 26 UKFE-1.0.1/UKFE/man/AnnualStat.Rd | 21 UKFE-1.0.1/UKFE/man/BFI.Rd | 9 UKFE-1.0.1/UKFE/man/Bootstrap.Rd | 21 UKFE-1.0.1/UKFE/man/CDsXML.Rd | 17 UKFE-1.0.1/UKFE/man/ConvertGridRef.Rd | 6 UKFE-1.0.1/UKFE/man/DDF.Rd | 16 UKFE-1.0.1/UKFE/man/DDF99.Rd | 14 UKFE-1.0.1/UKFE/man/DDF99Pars.Rd | 19 UKFE-1.0.1/UKFE/man/DDFExtract.Rd | 16 UKFE-1.0.1/UKFE/man/DDFImport.Rd | 19 UKFE-1.0.1/UKFE/man/DeTrend.Rd | 12 UKFE-1.0.1/UKFE/man/DesHydro.Rd | 9 UKFE-1.0.1/UKFE/man/DiagPlots.Rd | 14 UKFE-1.0.1/UKFE/man/DonAdj.Rd | 19 UKFE-1.0.1/UKFE/man/ERPlot.Rd | 27 UKFE-1.0.1/UKFE/man/EVPlot.Rd | 7 UKFE-1.0.1/UKFE/man/EVPlotAdd.Rd | 39 UKFE-1.0.1/UKFE/man/EVPool.Rd | 42 UKFE-1.0.1/UKFE/man/EncProb.Rd | 10 UKFE-1.0.1/UKFE/man/FlowDurationCurve.Rd | 30 UKFE-1.0.1/UKFE/man/FlowSplit.Rd | 45 UKFE-1.0.1/UKFE/man/GEVAM.Rd | 16 UKFE-1.0.1/UKFE/man/GEVEst.Rd | 24 UKFE-1.0.1/UKFE/man/GEVGF.Rd | 3 UKFE-1.0.1/UKFE/man/GEVPars.Rd | 30 UKFE-1.0.1/UKFE/man/GenLogAM.Rd | 16 UKFE-1.0.1/UKFE/man/GenLogEst.Rd | 23 UKFE-1.0.1/UKFE/man/GenLogGF.Rd | 3 UKFE-1.0.1/UKFE/man/GenLogPars.Rd | 28 UKFE-1.0.1/UKFE/man/GenParetoEst.Rd | 26 UKFE-1.0.1/UKFE/man/GenParetoGF.Rd | 16 UKFE-1.0.1/UKFE/man/GenParetoPOT.Rd | 18 UKFE-1.0.1/UKFE/man/GenParetoPars.Rd | 29 UKFE-1.0.1/UKFE/man/GetAM.Rd | 8 UKFE-1.0.1/UKFE/man/GetCDs.Rd | 7 UKFE-1.0.1/UKFE/man/GetDataEA_QH.Rd | 38 UKFE-1.0.1/UKFE/man/GetDataEA_Rain.Rd | 33 UKFE-1.0.1/UKFE/man/GetDataMetOffice.Rd | 16 UKFE-1.0.1/UKFE/man/GetDataNRFA.Rd | 16 UKFE-1.0.1/UKFE/man/GetDataSEPA_QH.Rd | 33 UKFE-1.0.1/UKFE/man/GetDataSEPA_Rain.Rd | 27 UKFE-1.0.1/UKFE/man/GetQMED.Rd | 5 UKFE-1.0.1/UKFE/man/GoFCompare.Rd | 7 UKFE-1.0.1/UKFE/man/GoFComparePool.Rd | 7 UKFE-1.0.1/UKFE/man/GumbelAM.Rd | 16 UKFE-1.0.1/UKFE/man/GumbelEst.Rd | 16 UKFE-1.0.1/UKFE/man/GumbelGF.Rd | 3 UKFE-1.0.1/UKFE/man/GumbelPars.Rd | 23 UKFE-1.0.1/UKFE/man/H2.Rd | 11 UKFE-1.0.1/UKFE/man/HydroPlot.Rd | 11 UKFE-1.0.1/UKFE/man/Kappa3AM.Rd | 16 UKFE-1.0.1/UKFE/man/Kappa3Est.Rd | 24 UKFE-1.0.1/UKFE/man/Kappa3GF.Rd | 10 UKFE-1.0.1/UKFE/man/Kappa3Pars.Rd | 20 UKFE-1.0.1/UKFE/man/LKurt.Rd | 7 UKFE-1.0.1/UKFE/man/LMoments.Rd | 7 UKFE-1.0.1/UKFE/man/LRatioChange.Rd | 16 UKFE-1.0.1/UKFE/man/LSkew.Rd | 7 UKFE-1.0.1/UKFE/man/LSkewUrb.Rd | 22 UKFE-1.0.1/UKFE/man/Lcv.Rd | 7 UKFE-1.0.1/UKFE/man/LcvUrb.Rd | 20 UKFE-1.0.1/UKFE/man/MonthlyStats.Rd | 14 UKFE-1.0.1/UKFE/man/NGRDist.Rd | 16 UKFE-1.0.1/UKFE/man/NRFAData.Rd | 4 UKFE-1.0.1/UKFE/man/NonFloodAdj.Rd | 13 UKFE-1.0.1/UKFE/man/NonFloodAdjPool.Rd | 18 UKFE-1.0.1/UKFE/man/OptimPars.Rd | 7 UKFE-1.0.1/UKFE/man/POTextract.Rd | 29 UKFE-1.0.1/UKFE/man/POTt.Rd | 18 UKFE-1.0.1/UKFE/man/Pool.Rd | 41 UKFE-1.0.1/UKFE/man/PoolEst.Rd | 26 UKFE-1.0.1/UKFE/man/PoolSmall.Rd | 25 UKFE-1.0.1/UKFE/man/QMED.Rd | 28 UKFE-1.0.1/UKFE/man/QMEDData.Rd | 4 UKFE-1.0.1/UKFE/man/QMEDDonEq.Rd | 35 UKFE-1.0.1/UKFE/man/QMEDLink.Rd | 5 UKFE-1.0.1/UKFE/man/QMEDPOT.Rd | 7 UKFE-1.0.1/UKFE/man/QMEDfseSS.Rd | 7 UKFE-1.0.1/UKFE/man/QuickResults.Rd | 24 UKFE-1.0.1/UKFE/man/Rating.Rd | 23 UKFE-1.0.1/UKFE/man/ReFH.Rd | 19 UKFE-1.0.1/UKFE/man/SCF.Rd | 5 UKFE-1.0.1/UKFE/man/SimData.Rd | 8 UKFE-1.0.1/UKFE/man/TrendTest.Rd | 20 UKFE-1.0.1/UKFE/man/UAF.Rd | 13 UKFE-1.0.1/UKFE/man/UEF.Rd | 3 UKFE-1.0.1/UKFE/man/Uncertainty.Rd | 38 UKFE-1.0.1/UKFE/man/WGaugLSkew.Rd | 9 UKFE-1.0.1/UKFE/man/WGaugLcv.Rd | 9 UKFE-1.0.1/UKFE/man/WeightsGLSkew.Rd | 9 UKFE-1.0.1/UKFE/man/WeightsGLcv.Rd | 9 UKFE-1.0.1/UKFE/man/WeightsUnLSkew.Rd | 9 UKFE-1.0.1/UKFE/man/WeightsUnLcv.Rd | 9 UKFE-1.0.1/UKFE/man/WungLSkew.Rd | 9 UKFE-1.0.1/UKFE/man/WungLcv.Rd | 9 UKFE-1.0.1/UKFE/man/Zdists.Rd | 13 UKFE-1.0.1/UKFE/tests |only UKFE-1.0.1/UKFE/vignettes |only 131 files changed, 10149 insertions(+), 7611 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 0.1.0 dated 2025-09-21 and 0.1.1 dated 2025-10-08
flint-0.1.0/flint/tests/hypgeom.R |only flint-0.1.1/flint/DESCRIPTION | 38 - flint-0.1.1/flint/MD5 | 58 +- flint-0.1.1/flint/NAMESPACE | 12 flint-0.1.1/flint/R/S3.R | 4 flint-0.1.1/flint/R/flint.R | 112 ++++- flint-0.1.1/flint/R/utils.R | 8 flint-0.1.1/flint/R/zzz.R | 90 ++++ flint-0.1.1/flint/configure | 18 flint-0.1.1/flint/configure.ac | 2 flint-0.1.1/flint/inst/NEWS.Rd | 78 +++ flint-0.1.1/flint/man/arb_hypgeom_bessel_j.Rd | 2 flint-0.1.1/flint/man/flint-class.Rd | 41 +- flint-0.1.1/flint/man/flint-package.Rd | 29 + flint-0.1.1/flint/src/acb.c | 7 flint-0.1.1/flint/src/acf.c | 7 flint-0.1.1/flint/src/arb.c | 7 flint-0.1.1/flint/src/arf.c | 7 flint-0.1.1/flint/src/flint.c | 525 +++++++++++++++++++++----- flint-0.1.1/flint/src/flint.h | 14 flint-0.1.1/flint/src/fmpq.c | 7 flint-0.1.1/flint/src/fmpz.c | 7 flint-0.1.1/flint/src/foreign.c |only flint-0.1.1/flint/src/init.c | 23 + flint-0.1.1/flint/src/mag.c | 7 flint-0.1.1/flint/src/slong.c | 6 flint-0.1.1/flint/src/ulong.c | 6 flint-0.1.1/flint/tests/ambiguity.R | 7 flint-0.1.1/flint/tests/foreign.R |only flint-0.1.1/flint/tests/match.R | 2 flint-0.1.1/flint/tests/reg-tests.R | 45 ++ flint-0.1.1/flint/tests/special.R |only 32 files changed, 955 insertions(+), 214 deletions(-)
Title: Geolocalização De Endereços Brasileiros (Geocoding Brazilian
Addresses)
Description: Método simples e eficiente de geolocalizar dados no Brasil. O
pacote é baseado em conjuntos de dados espaciais abertos de endereços
brasileiros, utilizando como fonte principal o Cadastro Nacional de Endereços
para Fins Estatísticos (CNEFE). O CNEFE é publicado pelo Instituto Brasileiro
de Geografia e Estatística (IBGE), órgão oficial de estatísticas e geografia
do Brasil. (A simple and efficient method for geolocating data in Brazil. The
package is based on open spatial datasets of Brazilian addresses, primarily
using the Cadastro Nacional de Endereços para Fins Estatísticos (CNEFE),
published by the Instituto Brasileiro de Geografia e Estatística (IBGE),
Brazil's official statistics and geography agency.)
Author: Rafael H. M. Pereira [aut, cre] ,
Daniel Herszenhut [aut] ,
Arthur Bazolli [ctb],
Ipea - Instituto de Pesquisa Economica Aplicada [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between geocodebr versions 0.2.1 dated 2025-07-07 and 0.3.0 dated 2025-10-08
geocodebr-0.2.1/geocodebr/tests/tests_rafa/arrow_distinct.R |only geocodebr-0.2.1/geocodebr/tests/tests_rafa/busca_por_cep_alternativas.R |only geocodebr-0.2.1/geocodebr/tests/tests_rafa/calculate_precision.R |only geocodebr-0.2.1/geocodebr/tests/tests_rafa/geocoding_en.Rmd |only geocodebr-0.2.1/geocodebr/tests/tests_rafa/geocoding_pt.Rmd |only geocodebr-0.3.0/geocodebr/DESCRIPTION | 8 geocodebr-0.3.0/geocodebr/MD5 | 114 +- geocodebr-0.3.0/geocodebr/NEWS.md | 28 geocodebr-0.3.0/geocodebr/R/busca_por_cep.R | 35 geocodebr-0.3.0/geocodebr/R/cache.R | 77 + geocodebr-0.3.0/geocodebr/R/create_geocodebr_db.R | 3 geocodebr-0.3.0/geocodebr/R/download_cnefe.R | 27 geocodebr-0.3.0/geocodebr/R/geocode.R | 40 geocodebr-0.3.0/geocodebr/R/geocode_duckdb.R |only geocodebr-0.3.0/geocodebr/R/geocode_reverso.R | 20 geocodebr-0.3.0/geocodebr/R/match_cases.R | 41 geocodebr-0.3.0/geocodebr/R/match_cases_probabilistic.R | 221 ----- geocodebr-0.3.0/geocodebr/R/match_weighted_cases.R | 67 - geocodebr-0.3.0/geocodebr/R/match_weighted_cases_probabilistic.R | 156 +-- geocodebr-0.3.0/geocodebr/R/trata_empates_geocode.R | 1 geocodebr-0.3.0/geocodebr/R/trata_empates_geocode_duckdb.R |only geocodebr-0.3.0/geocodebr/R/trata_empates_geocode_duckdb2.R |only geocodebr-0.3.0/geocodebr/R/utils.R | 4 geocodebr-0.3.0/geocodebr/README.md | 29 geocodebr-0.3.0/geocodebr/build/vignette.rds |binary geocodebr-0.3.0/geocodebr/inst/doc/geocode.R | 51 - geocodebr-0.3.0/geocodebr/inst/doc/geocode.Rmd | 72 + geocodebr-0.3.0/geocodebr/inst/doc/geocode.html | 146 +-- geocodebr-0.3.0/geocodebr/inst/doc/geocode_reverso.R | 38 geocodebr-0.3.0/geocodebr/inst/doc/geocode_reverso.html | 56 - geocodebr-0.3.0/geocodebr/inst/doc/geocodebr.R | 114 +- geocodebr-0.3.0/geocodebr/inst/doc/geocodebr.Rmd | 12 geocodebr-0.3.0/geocodebr/inst/doc/geocodebr.html | 49 - geocodebr-0.3.0/geocodebr/man/apaga_data_release_antigo.Rd |only geocodebr-0.3.0/geocodebr/man/busca_por_cep.Rd | 108 +- geocodebr-0.3.0/geocodebr/man/create_index.Rd | 24 geocodebr-0.3.0/geocodebr/man/definir_pasta_cache.Rd | 6 geocodebr-0.3.0/geocodebr/man/figures/logo.svg | 412 +++++----- geocodebr-0.3.0/geocodebr/man/geocode.Rd | 68 + geocodebr-0.3.0/geocodebr/man/geocode_reverso.Rd | 132 +-- geocodebr-0.3.0/geocodebr/man/roxygen/templates/h3_res.R |only geocodebr-0.3.0/geocodebr/man/roxygen/templates/precision_section.R | 40 geocodebr-0.3.0/geocodebr/man/roxygen/templates/resultado_sf.R |only geocodebr-0.3.0/geocodebr/man/update_input_db.Rd | 44 - geocodebr-0.3.0/geocodebr/tests/tests_pedro |only geocodebr-0.3.0/geocodebr/tests/tests_rafa/benchmark_LIKE.R | 40 geocodebr-0.3.0/geocodebr/tests/tests_rafa/benchmark_reg_adm.R | 62 + geocodebr-0.3.0/geocodebr/tests/tests_rafa/empate_duck.R |only geocodebr-0.3.0/geocodebr/tests/tests_rafa/meta.R | 2 geocodebr-0.3.0/geocodebr/tests/tests_rafa/munis_bbox.R | 2 geocodebr-0.3.0/geocodebr/tests/tests_rafa/release_v2_v3.R |only geocodebr-0.3.0/geocodebr/tests/tests_rafa/states_bbox.R | 2 geocodebr-0.3.0/geocodebr/tests/tests_rafa/test_rafa.R | 67 - geocodebr-0.3.0/geocodebr/tests/testthat/_snaps/cache.md | 60 - geocodebr-0.3.0/geocodebr/tests/testthat/_snaps/definir_campos.md | 16 geocodebr-0.3.0/geocodebr/tests/testthat/_snaps/download_cnefe.md | 18 geocodebr-0.3.0/geocodebr/tests/testthat/_snaps/error.md | 18 geocodebr-0.3.0/geocodebr/tests/testthat/_snaps/message.md | 14 geocodebr-0.3.0/geocodebr/tests/testthat/test-busca_por_cep.R | 6 geocodebr-0.3.0/geocodebr/tests/testthat/test-download_cnefe.R | 12 geocodebr-0.3.0/geocodebr/tests/testthat/test-geocode.R | 13 geocodebr-0.3.0/geocodebr/tests/testthat/test-geocode_duckdb.R |only geocodebr-0.3.0/geocodebr/tests/testthat/test-geocode_reverso.R | 2 geocodebr-0.3.0/geocodebr/vignettes/geocode.Rmd | 72 + geocodebr-0.3.0/geocodebr/vignettes/geocodebr.Rmd | 12 65 files changed, 1383 insertions(+), 1278 deletions(-)
Title: Maps Bone Densities from CT Scans to Surface Models
Description: Allows local bone density estimates to be derived from CT data and mapped to 3D bone models in a reproducible manner. Processing can be performed at the individual bone or group level. Also includes tools for visualizing the bone density estimates. Example methods are described in Telfer et al., (2021) <doi:10.1002/jor.24792>, Telfer et al., (2021) <doi:10.1016/j.jse.2021.05.011>.
Author: Scott Telfer [aut, cre, cph] ,
Lucas Lacambra [aut]
Maintainer: Scott Telfer <scott.telfer@gmail.com>
Diff between BoneDensityMapping versions 0.1.3 dated 2025-08-26 and 0.1.4 dated 2025-10-08
DESCRIPTION | 6 MD5 | 18 +- NEWS.md | 4 R/BoneDensityFunctions.R | 4 build/vignette.rds |binary inst/doc/example-workflow-vignette.R | 43 +++-- inst/doc/example-workflow-vignette.Rmd | 47 +++--- inst/doc/example-workflow-vignette.html | 245 +++++++++++++++----------------- man/plot_mesh.Rd | 4 vignettes/example-workflow-vignette.Rmd | 47 +++--- 10 files changed, 220 insertions(+), 198 deletions(-)
More information about BoneDensityMapping at CRAN
Permanent link
Title: Agricultural Datasets
Description: Datasets from books, papers, and websites related to
agriculture. Example graphics and analyses are included. Data come
from small-plot trials, multi-environment trials, uniformity trials,
yield monitors, and more.
Author: Kevin Wright [aut, cre, cph]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between agridat versions 1.24 dated 2024-10-27 and 1.25 dated 2025-10-08
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agridat-1.25/agridat/man/wiedemann.safflower.uniformity.Rd | 4 agridat-1.25/agridat/vignettes/agridat_data.Rmd | 5 agridat-1.25/agridat/vignettes/agridat_uniformity_data.Rmd | 626 +++++--- 87 files changed, 2350 insertions(+), 1183 deletions(-)
Title: Interpretable Neural Network Based on Generalized Additive
Models
Description: Neural Additive Model framework based on Generalized Additive Models from Hastie & Tibshirani (1990, ISBN:9780412343902), which trains a different neural network to estimate the contribution of each feature to the response variable. The networks are trained independently leveraging the local scoring and backfitting algorithms to ensure that the Generalized Additive Model converges and it is additive. The resultant Neural Network is a highly accurate and interpretable deep learning model, which can be used for high-risk AI practices where decision-making should be based on accountable and interpretable algorithms.
Author: Ines Ortega-Fernandez [aut, cre, cph] ,
Marta Sestelo [aut, cph]
Maintainer: Ines Ortega-Fernandez <iortega@gradiant.org>
Diff between neuralGAM versions 1.1.1 dated 2024-04-19 and 2.0.0 dated 2025-10-08
neuralGAM-1.1.1/neuralGAM/man/neuralGAM.Rd |only neuralGAM-1.1.1/neuralGAM/man/plot.neuralGAM.Rd |only neuralGAM-1.1.1/neuralGAM/man/predict.neuralGAM.Rd |only neuralGAM-1.1.1/neuralGAM/man/print.neuralGAM.Rd |only neuralGAM-1.1.1/neuralGAM/man/summary.neuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/DESCRIPTION | 22 neuralGAM-2.0.0/neuralGAM/MD5 | 110 +- neuralGAM-2.0.0/neuralGAM/NAMESPACE | 41 neuralGAM-2.0.0/neuralGAM/NEWS.md | 18 neuralGAM-2.0.0/neuralGAM/R/NeuralGAM.R | 517 ++++++---- neuralGAM-2.0.0/neuralGAM/R/autoplot.neuralGAM.R | 337 ++++-- neuralGAM-2.0.0/neuralGAM/R/build_feature_NN.R | 294 ++++- neuralGAM-2.0.0/neuralGAM/R/dev.R | 82 + neuralGAM-2.0.0/neuralGAM/R/diagnose.R |only neuralGAM-2.0.0/neuralGAM/R/diriv.R | 9 neuralGAM-2.0.0/neuralGAM/R/formula.R | 292 ++++- neuralGAM-2.0.0/neuralGAM/R/install.R | 59 + neuralGAM-2.0.0/neuralGAM/R/inv_link.R | 19 neuralGAM-2.0.0/neuralGAM/R/link.R | 20 neuralGAM-2.0.0/neuralGAM/R/mu_eta.R |only neuralGAM-2.0.0/neuralGAM/R/neuralGAM-package.R | 1 neuralGAM-2.0.0/neuralGAM/R/plot.NeuralGAM.R | 184 +-- neuralGAM-2.0.0/neuralGAM/R/plot_history.NeuralGAM.R |only neuralGAM-2.0.0/neuralGAM/R/predict.NeuralGAM.R | 475 ++++++--- neuralGAM-2.0.0/neuralGAM/R/print.NeuralGAM.R | 106 -- neuralGAM-2.0.0/neuralGAM/R/sim_neuralGAM_data.R |only neuralGAM-2.0.0/neuralGAM/R/summary.NeuralGAM.R | 330 +++++- neuralGAM-2.0.0/neuralGAM/R/uncertainty_estimation.R |only neuralGAM-2.0.0/neuralGAM/R/weight.R | 16 neuralGAM-2.0.0/neuralGAM/README.md | 223 +++- neuralGAM-2.0.0/neuralGAM/man/NeuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/man/autoplot.neuralGAM.Rd | 118 +- neuralGAM-2.0.0/neuralGAM/man/build_feature_NN.Rd | 129 +- neuralGAM-2.0.0/neuralGAM/man/dev.Rd | 6 neuralGAM-2.0.0/neuralGAM/man/diagnose.Rd |only neuralGAM-2.0.0/neuralGAM/man/diriv.Rd | 2 neuralGAM-2.0.0/neuralGAM/man/dot-combine_uncertainties_sampling.Rd |only neuralGAM-2.0.0/neuralGAM/man/dot-combine_uncertainties_variance.Rd |only neuralGAM-2.0.0/neuralGAM/man/dot-compute_uncertainty.Rd |only neuralGAM-2.0.0/neuralGAM/man/dot-joint_pi_both_variance.Rd |only neuralGAM-2.0.0/neuralGAM/man/dot-joint_se_eta_mcdropout.Rd |only neuralGAM-2.0.0/neuralGAM/man/dot-mc_dropout_forward.Rd |only neuralGAM-2.0.0/neuralGAM/man/get_formula_elements.Rd | 80 + neuralGAM-2.0.0/neuralGAM/man/inv_link.Rd | 2 neuralGAM-2.0.0/neuralGAM/man/link.Rd | 4 neuralGAM-2.0.0/neuralGAM/man/mu_eta.Rd |only neuralGAM-2.0.0/neuralGAM/man/neuralGAM-package.Rd | 3 neuralGAM-2.0.0/neuralGAM/man/plot.NeuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/man/plot_history.Rd |only neuralGAM-2.0.0/neuralGAM/man/predict.NeuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/man/print.NeuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/man/sim_neuralGAM_data.Rd |only neuralGAM-2.0.0/neuralGAM/man/summary.NeuralGAM.Rd |only neuralGAM-2.0.0/neuralGAM/man/validate_activation.Rd |only neuralGAM-2.0.0/neuralGAM/man/validate_loss.Rd |only neuralGAM-2.0.0/neuralGAM/man/weight.Rd | 4 neuralGAM-2.0.0/neuralGAM/tests/testthat/setup.R | 1 neuralGAM-2.0.0/neuralGAM/tests/testthat/test-NeuralGAM.R | 486 ++++++++- neuralGAM-2.0.0/neuralGAM/tests/testthat/test-autoplot.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-build_feature_NN.R | 183 +++ neuralGAM-2.0.0/neuralGAM/tests/testthat/test-dev.R | 142 +- neuralGAM-2.0.0/neuralGAM/tests/testthat/test-diagnose.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-diriv.R | 2 neuralGAM-2.0.0/neuralGAM/tests/testthat/test-epistemic-pi.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-formula.R | 152 ++ neuralGAM-2.0.0/neuralGAM/tests/testthat/test-inv_link.R | 32 neuralGAM-2.0.0/neuralGAM/tests/testthat/test-link.R | 49 neuralGAM-2.0.0/neuralGAM/tests/testthat/test-mu_eta.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-plot.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-plot_history.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-predict.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-print.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-summary.R |only neuralGAM-2.0.0/neuralGAM/tests/testthat/test-weight.R | 16 74 files changed, 3399 insertions(+), 1167 deletions(-)
Title: Constrained Multivariate Least Squares
Description: Solves multivariate least squares (MLS) problems subject to constraints on the coefficients, e.g., non-negativity, orthogonality, equality, inequality, monotonicity, unimodality, smoothness, etc. Includes flexible functions for solving MLS problems subject to user-specified equality and/or inequality constraints, as well as a wrapper function that implements 24 common constraint options. Also does k-fold or generalized cross-validation to tune constraint options for MLS problems. See ten Berge (1993, ISBN:9789066950832) for an overview of MLS problems, and see Goldfarb and Idnani (1983) <doi:10.1007/BF02591962> for a discussion of the underlying quadratic programming algorithm.
Author: Nathaniel E. Helwig [aut, cre]
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between CMLS versions 1.0-1 dated 2023-03-31 and 1.1 dated 2025-10-08
ChangeLog | 10 ++++++++++ DESCRIPTION | 16 ++++++++++------ MD5 | 10 +++++----- build/partial.rdb |binary man/mlsei.Rd | 2 +- man/mlsun.Rd | 2 +- 6 files changed, 27 insertions(+), 13 deletions(-)
Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen [aut, cre],
Gavin L. Simpson [aut],
F. Guillaume Blanchet [aut],
Roeland Kindt [aut],
Pierre Legendre [aut],
Peter R. Minchin [aut],
R.B. O'Hara [aut],
Peter Solymos [aut],
M. Henry H. Stevens [aut],
Eduard Szoecs [aut],
Helene Wagner [a [...truncated...]
Maintainer: Jari Oksanen <jhoksane@gmail.com>
Diff between vegan versions 2.7-1 dated 2025-06-05 and 2.7-2 dated 2025-10-08
vegan-2.7-1/vegan/inst/doc/FAQ-vegan.R |only vegan-2.7-2/vegan/DESCRIPTION | 6 vegan-2.7-2/vegan/MD5 | 163 +++--- vegan-2.7-2/vegan/NEWS.md | 67 ++ vegan-2.7-2/vegan/R/CCorA.R | 4 vegan-2.7-2/vegan/R/MDSaddpoints.R | 3 vegan-2.7-2/vegan/R/add1.cca.R | 18 vegan-2.7-2/vegan/R/anova.ccabyterm.R | 21 vegan-2.7-2/vegan/R/beals.R | 4 vegan-2.7-2/vegan/R/biplot.rda.R | 54 -- vegan-2.7-2/vegan/R/capscale.R | 3 vegan-2.7-2/vegan/R/cca.default.R | 2 vegan-2.7-2/vegan/R/cca.formula.R | 3 vegan-2.7-2/vegan/R/dbrda.R | 3 vegan-2.7-2/vegan/R/decorana.R | 4 vegan-2.7-2/vegan/R/decostand.R | 23 vegan-2.7-2/vegan/R/designdist.R | 10 vegan-2.7-2/vegan/R/distconnected.R | 2 vegan-2.7-2/vegan/R/diversity.R | 2 vegan-2.7-2/vegan/R/downweight.R | 2 vegan-2.7-2/vegan/R/factorfit.R | 6 vegan-2.7-2/vegan/R/fisher.alpha.R | 4 vegan-2.7-2/vegan/R/influence.cca.R | 5 vegan-2.7-2/vegan/R/make.commsim.R | 32 - vegan-2.7-2/vegan/R/mantel.R | 19 vegan-2.7-2/vegan/R/mantel.partial.R | 27 - vegan-2.7-2/vegan/R/monoMDS.R | 2 vegan-2.7-2/vegan/R/no.shared.R | 4 vegan-2.7-2/vegan/R/nullmodel.R | 2 vegan-2.7-2/vegan/R/ordConstrained.R | 2 vegan-2.7-2/vegan/R/orderingKM.R | 20 vegan-2.7-2/vegan/R/ordiParseFormula.R | 16 vegan-2.7-2/vegan/R/ordilabel.R | 19 vegan-2.7-2/vegan/R/ordipointlabel.R | 2 vegan-2.7-2/vegan/R/ordisurf.R | 3 vegan-2.7-2/vegan/R/permatfull.R | 2 vegan-2.7-2/vegan/R/permatswap.R | 2 vegan-2.7-2/vegan/R/permustats.R | 8 vegan-2.7-2/vegan/R/permutest.cca.R | 5 vegan-2.7-2/vegan/R/plot.varpart234.R | 6 vegan-2.7-2/vegan/R/poolaccum.R | 2 vegan-2.7-2/vegan/R/predict.cca.R | 5 vegan-2.7-2/vegan/R/predict.rda.R | 5 vegan-2.7-2/vegan/R/print.monoMDS.R | 3 vegan-2.7-2/vegan/R/rarecurve.R | 2 vegan-2.7-2/vegan/R/rarefy.R | 2 vegan-2.7-2/vegan/R/raupcrick.R | 2 vegan-2.7-2/vegan/R/rda.default.R | 2 vegan-2.7-2/vegan/R/rda.formula.R | 3 vegan-2.7-2/vegan/R/rrarefy.R | 4 vegan-2.7-2/vegan/R/scores.default.R | 4 vegan-2.7-2/vegan/R/simpleRDA2.R | 2 vegan-2.7-2/vegan/R/spantree.R | 2 vegan-2.7-2/vegan/R/specaccum.R | 3 vegan-2.7-2/vegan/R/stepacross.R | 5 vegan-2.7-2/vegan/R/taxondive.R | 2 vegan-2.7-2/vegan/R/treedist.R | 2 vegan-2.7-2/vegan/R/treedive.R | 2 vegan-2.7-2/vegan/R/vectorfit.R | 6 vegan-2.7-2/vegan/R/vegdist.R | 4 vegan-2.7-2/vegan/R/wascores.R | 4 vegan-2.7-2/vegan/R/wcmdscale.R | 4 vegan-2.7-2/vegan/build/partial.rdb |binary vegan-2.7-2/vegan/build/vignette.rds |binary vegan-2.7-2/vegan/inst/doc/FAQ-vegan.Rmd | 356 +++++--------- vegan-2.7-2/vegan/inst/doc/FAQ-vegan.html | 323 ++++--------- vegan-2.7-2/vegan/inst/doc/decision-vegan.pdf |binary vegan-2.7-2/vegan/inst/doc/diversity-vegan.pdf |binary vegan-2.7-2/vegan/inst/doc/intro-vegan.R | 86 +-- vegan-2.7-2/vegan/inst/doc/intro-vegan.Rnw | 203 ++++---- vegan-2.7-2/vegan/inst/doc/intro-vegan.pdf |binary vegan-2.7-2/vegan/inst/doc/partitioning.Rnw | 4 vegan-2.7-2/vegan/inst/doc/partitioning.pdf |binary vegan-2.7-2/vegan/man/biplot.rda.Rd | 20 vegan-2.7-2/vegan/man/cascadeKM.Rd | 8 vegan-2.7-2/vegan/man/mantel.Rd | 15 vegan-2.7-2/vegan/man/ordilabel.Rd | 4 vegan-2.7-2/vegan/src/getF.c | 55 +- vegan-2.7-2/vegan/tests/cca-object-tests.Rout.save | 502 +++++++++------------ vegan-2.7-2/vegan/tests/vegan-tests.Rout.save | 64 +- vegan-2.7-2/vegan/vignettes/FAQ-vegan.Rmd | 356 +++++--------- vegan-2.7-2/vegan/vignettes/intro-vegan.Rnw | 203 ++++---- vegan-2.7-2/vegan/vignettes/partitioning.Rnw | 4 83 files changed, 1286 insertions(+), 1567 deletions(-)
Title: Time Series Analysis Tools
Description: A system contains easy-to-use tools as a support for time series analysis courses. In particular, it incorporates a technique called Generalized Method of Wavelet Moments (GMWM) as well as its robust implementation for fast and robust parameter estimation of time series models which is described, for example, in Guerrier et al. (2013) <doi: 10.1080/01621459.2013.799920>. More details can also be found in the paper linked to via the URL below.
Author: Stephane Guerrier [aut, cre, cph],
James Balamuta [aut, cph],
Roberto Molinari [aut, cph],
Justin Lee [aut],
Lionel Voirol [aut],
Yuming Zhang [aut],
Wenchao Yang [ctb],
Nathanael Claussen [ctb],
Yunxiang Zhang [ctb],
Christian Gunning [cph],
Romain [...truncated...]
Maintainer: Stephane Guerrier <stef.guerrier@gmail.com>
Diff between simts versions 0.2.2 dated 2023-08-31 and 0.2.3 dated 2025-10-08
DESCRIPTION | 9 +-- MD5 | 100 ++++++++++++++++++++++---------------------- NAMESPACE | 1 NEWS.md | 5 ++ R/RcppExports.R | 58 ------------------------- R/gmwm.r | 8 --- R/model_selection.R | 2 R/ts.model.R | 2 README.md | 47 ++++++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/vignettes.R | 52 +++++++++++----------- inst/doc/vignettes.html | 62 ++++++++++++++------------- man/batch_modwt_wvar_cpp.Rd | 2 man/bl14_filter.Rd | 2 man/bl20_filter.Rd | 2 man/ci_eta3.Rd | 2 man/ci_eta3_robust.Rd | 2 man/ci_wave_variance.Rd | 2 man/d16_filter.Rd | 2 man/d4_filter.Rd | 2 man/d6_filter.Rd | 2 man/d8_filter.Rd | 2 man/fk14_filter.Rd | 2 man/fk22_filter.Rd | 2 man/fk4_filter.Rd | 2 man/fk6_filter.Rd | 2 man/fk8_filter.Rd | 2 man/gmwm_engine.Rd | 4 - man/gmwm_imu.Rd | 2 man/haar_filter.Rd | 2 man/la16_filter.Rd | 2 man/la20_filter.Rd | 2 man/la8_filter.Rd | 2 man/mb16_filter.Rd | 2 man/mb24_filter.Rd | 2 man/mb4_filter.Rd | 2 man/mb8_filter.Rd | 2 man/modwt_wvar_cpp.Rd | 2 man/plus-.ts.model.Rd | 2 man/predict.gmwm.Rd | 2 man/select_filter.Rd | 2 man/simts-package.Rd | 1 man/summary.gmwm.Rd | 2 man/update.gmwm.Rd | 2 man/w4_filter.Rd | 2 man/wvar_cpp.Rd | 2 src/gmwm_logic.cpp | 4 - src/rtoarmadillo.cpp | 4 - src/wave_variance.cpp | 12 ----- src/wv_filters.cpp | 42 ------------------ 51 files changed, 156 insertions(+), 321 deletions(-)
Title: R Interface to the Pushbullet Messaging Service
Description: An R interface to the Pushbullet messaging service which
provides fast and efficient notifications (and file transfer) between
computers, phones and tablets. An account has to be registered at the
site <https://www.pushbullet.com> site to obtain a (free) API key.
Author: Dirk Eddelbuettel [aut, cre] ,
Bill Evans [ctb],
Mike Birdgeneau [ctb],
Henrik Bengtsson [ctb],
Seth Wenchel [ctb],
Colin Gillespie [ctb],
Chan-Yub Park [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RPushbullet versions 0.3.4 dated 2021-03-01 and 0.3.5 dated 2025-10-08
ChangeLog | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 31 ++++++++++++++++++++++------- MD5 | 12 +++++------ R/isValid.R | 10 ++++----- R/pushes.R | 2 - README.md | 8 +++---- inst/NEWS.Rd | 13 ++++++++++++ 7 files changed, 115 insertions(+), 23 deletions(-)
Title: PX-Web Data by API
Description: Function to read PX-Web data into R via API. The example code reads data from the three national statistical institutes, Statistics Norway, Statistics Sweden and Statistics Finland.
Author: Oeyvind Langsrud [aut, cre],
Jan Bruusgaard [aut],
Solveig Bjoerkholt [ctb],
Susie Jentoft [ctb]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between PxWebApiData versions 1.0.0 dated 2024-11-01 and 1.1.0 dated 2025-10-08
DESCRIPTION | 10 - MD5 | 25 ++-- NAMESPACE | 1 NEWS.md | 10 + R/ApiData.R | 61 ++++++---- build/vignette.rds |binary inst/doc/Introduction.R | 17 ++ inst/doc/Introduction.Rmd | 43 +++++-- inst/doc/Introduction.html | 246 ++++++++++++++++++++++++------------------ man/ApiData.Rd | 25 +++- man/MakeUrl.Rd | 6 - man/figures |only tests/testthat/test-ApiData.R | 25 ---- vignettes/Introduction.Rmd | 43 +++++-- 14 files changed, 310 insertions(+), 202 deletions(-)
Title: Converting Transport Data from GTFS Format to GPS-Like Records
Description: Convert general transit feed specification (GTFS) data to global positioning system (GPS) records in 'data.table' format. It also has some functions to subset GTFS data in time and space and to convert both representations to simple feature format.
Author: Rafael H. M. Pereira [aut] ,
Pedro R. Andrade [aut, cre] ,
Joao Bazzo [aut] ,
Daniel Herszenhut [ctb] ,
Marcin Stepniak [ctb],
Marcus Saraiva [ctb] ,
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Pedro R. Andrade <pedro.andrade@inpe.br>
Diff between gtfs2gps versions 2.1-2 dated 2024-10-08 and 2.1-3 dated 2025-10-08
DESCRIPTION | 23 +++++----- MD5 | 25 ++++++++--- R/zzz.R | 4 - build/vignette.rds |binary inst/doc/intro_to_gtfs2gps.R | 2 inst/doc/intro_to_gtfs2gps.html | 71 +++++++++++++++----------------- tests/testthat/agency.txt |only tests/testthat/calendar.txt |only tests/testthat/poa.zip |only tests/testthat/routes.txt |only tests/testthat/shapes.txt |only tests/testthat/stop_times.txt |only tests/testthat/stops.txt |only tests/testthat/test_gtfs2gps.R | 2 tests/testthat/test_simplify_shapes.R | 5 -- tests/testthat/trips.txt |only vignettes/poa_small.zip |only vignettes/sao_small-DESKTOP-V07AVEN.zip |only vignettes/sao_small.zip |only 19 files changed, 71 insertions(+), 61 deletions(-)
Title: Power Calculation for Two-Way Factorial Designs
Description: The basic use of this package is with 3 sequential functions. One to generate expected cell means and standard deviations, along with correlation and covariance matrices in the case of repeated measurements. This is followed by experiment simulation i number of times. Finally, power is calculated from the simulated data. Features that may be considered in the model are interaction, measure correlation and non-normal distributions.
Author: Louis Macias [aut, cre, cph] ,
Silke Szymczak [aut]
Maintainer: Louis Macias <louis.macias@uni-luebeck.de>
Diff between extraSuperpower versions 1.5.4 dated 2025-08-25 and 1.5.5 dated 2025-10-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/repeated_twoway_generation.R | 2 +- inst/doc/eSp_balanced_design_powertest.html | 8 ++++---- 5 files changed, 17 insertions(+), 13 deletions(-)
More information about extraSuperpower at CRAN
Permanent link
Title: Electric Vehicle Charging Sessions Simulation
Description: Simulation of Electric Vehicles charging sessions using Gaussian models, together with time-series power demand calculations.
Author: Marc Canigueral [aut, cre, cph]
Maintainer: Marc Canigueral <marccanyigueral@gmail.com>
Diff between evsim versions 1.6.1 dated 2025-05-07 and 1.7.0 dated 2025-10-08
evsim-1.6.1/evsim/R/parallel-processing.R |only evsim-1.6.1/evsim/man/mclapply.windows.Rd |only evsim-1.7.0/evsim/DESCRIPTION | 12 evsim-1.7.0/evsim/MD5 | 24 - evsim-1.7.0/evsim/NAMESPACE | 6 evsim-1.7.0/evsim/NEWS.md | 7 evsim-1.7.0/evsim/R/charging_infrastructure.R | 9 evsim-1.7.0/evsim/R/demand.R | 197 ++++------ evsim-1.7.0/evsim/R/simulation.R | 31 + evsim-1.7.0/evsim/man/adapt_charging_features.Rd | 9 evsim-1.7.0/evsim/man/get_demand.Rd | 11 evsim-1.7.0/evsim/man/get_occupancy.Rd | 11 evsim-1.7.0/evsim/man/plot_occupancy_duration_curve.Rd | 6 evsim-1.7.0/evsim/tests/testthat/test-charging_infrastructure.R | 2 14 files changed, 166 insertions(+), 159 deletions(-)
Title: A Modular Approach to Dose-Finding Clinical Trials
Description: Methods for working with dose-finding clinical trials. We provide
implementations of many dose-finding clinical trial designs, including the
continual reassessment method (CRM) by O'Quigley et al. (1990)
<doi:10.2307/2531628>, the toxicity probability interval (TPI) design by Ji
et al. (2007) <doi:10.1177/1740774507079442>, the modified TPI (mTPI) design
by Ji et al. (2010) <doi:10.1177/1740774510382799>, the Bayesian optimal
interval design (BOIN) by Liu & Yuan (2015) <doi:10.1111/rssc.12089>, EffTox
by Thall & Cook (2004) <doi:10.1111/j.0006-341X.2004.00218.x>; the design of
Wages & Tait (2015) <doi:10.1080/10543406.2014.920873>, and the 3+3
described by Korn et al. (1994) <doi:10.1002/sim.4780131802>. All designs
are implemented with a common interface. We also offer optional additional
classes to tailor the behaviour of all designs, including avoiding skipping
doses, stopping after n patients have been treated at the recommended [...truncated...]
Author: Kristian Brock [aut, cre] ,
Daniel Slade [aut] ,
Michael Sweeting [aut] ,
Conor Norris [ctb] ,
Bharat Bhushan [ctb]
Maintainer: Kristian Brock <kristian.brock@gmail.com>
Diff between escalation versions 0.1.10 dated 2024-06-27 and 0.2.3 dated 2025-10-08
DESCRIPTION | 32 MD5 | 271 +- NAMESPACE | 77 NEWS.md | 20 R/boin12_rds.R |only R/boin_comb_selector.R |only R/boin_selector.R | 44 R/check_simulations_consistency.R |only R/combo_selector.R |only R/combo_selector_factory.R |only R/convergence_plot.R | 25 R/demand_n_at_dose.R | 41 R/derived_dose_selector.R | 36 R/dfcrm_selector.R | 36 R/dont_skip_doses.R | 3 R/dose_escalation_table.R |only R/dose_selector_summary_methods.R | 120 - R/escalation-package.R | 4 R/expand_last_dose_to_cohort.R |only R/follow_path.R | 53 R/helpers.R | 146 + R/interface.R | 22 R/mtpi2_selector.R | 28 R/mtpi_selector.R | 37 R/outcomes_to_arrays.R |only R/parse_phase1_2_outcomes.R | 44 R/parse_phase1_outcomes.R | 42 R/phase1_2_comb_sim.R |only R/phase1_2_dose_paths.R | 12 R/phase1_2_outcomes_to_cohorts.R | 24 R/phase1_2_sim.R | 6 R/phase1_dose_paths.R | 12 R/phase1_outcomes_to_cohorts.R | 30 R/phase1_sim.R | 4 R/phase1_tite_sim.R | 45 R/select_boin12_obd.R | 39 R/select_boin_comb_mtd.R |only R/select_boin_mtd.R | 30 R/select_dose_by_cibp.R | 1 R/select_mtpi2_mtd.R | 94 R/select_mtpi_mtd.R | 75 R/select_tpi_mtd.R | 86 R/selector.R | 57 R/simulations.R | 396 ++- R/stack_sims_vert.R | 46 R/stick_on_num_tox.R |only R/stop_when_n_at_dose_selector.R | 31 R/stop_when_too_toxic.R | 66 R/stop_when_tox_ci_covered.R | 50 R/tpi_selector.R | 17 R/try_rescue_dose.R | 53 R/unadmit_untested.R |only README.md | 46 build/vignette.rds |binary inst/doc/A100-DoseSelectors.R | 5 inst/doc/A100-DoseSelectors.Rmd | 11 inst/doc/A100-DoseSelectors.html | 197 - inst/doc/A205-CRM.R | 8 inst/doc/A205-CRM.Rmd | 4 inst/doc/A205-CRM.html | 76 inst/doc/A207-NBG.R | 6 inst/doc/A207-NBG.Rmd | 4 inst/doc/A207-NBG.html | 77 inst/doc/A210-TPI.R | 15 inst/doc/A210-TPI.Rmd | 22 inst/doc/A210-TPI.html | 183 - inst/doc/A220-mTPI.R | 15 inst/doc/A220-mTPI.Rmd | 22 inst/doc/A220-mTPI.html | 184 - inst/doc/A230-BOIN.R | 12 inst/doc/A230-BOIN.Rmd | 22 inst/doc/A230-BOIN.html | 89 inst/doc/A280-TITE.R |only inst/doc/A280-TITE.Rmd |only inst/doc/A280-TITE.html |only inst/doc/A310-EfficacyToxicity.R |only inst/doc/A310-EfficacyToxicity.Rmd |only inst/doc/A310-EfficacyToxicity.html |only inst/doc/A360-Combinations.R |only inst/doc/A360-Combinations.Rmd |only inst/doc/A360-Combinations.html |only inst/doc/A600-DosePaths.R | 20 inst/doc/A600-DosePaths.html | 60 inst/doc/A700-Simulation.R | 16 inst/doc/A700-Simulation.html | 6 inst/doc/A710-SimulationComparison.R | 6 inst/doc/A710-SimulationComparison.html | 8 man/boin12_rds.Rd |only man/check_simulations_consistency.Rd |only man/combo_selector.Rd |only man/convergence_plot.Rd | 25 man/dose_escalation_table.Rd |only man/dose_string_to_vector.Rd |only man/dose_strings.Rd |only man/dose_vector_to_string.Rd |only man/doses_given.Rd | 15 man/escalation-package.Rd | 26 man/expand_last_dose_to_cohort.Rd |only man/get_boin.Rd | 19 man/get_boin_comb.Rd |only man/get_dose_combo_indices.Rd |only man/get_mtpi.Rd | 8 man/get_mtpi2.Rd | 8 man/get_tpi.Rd | 8 man/median_prob_tox.Rd | 11 man/prob_tox_exceeds.Rd | 11 man/prob_tox_quantile.Rd | 11 man/recommended_dose.Rd | 11 man/select_boin12_obd.Rd | 32 man/select_boin_comb_mtd.Rd |only man/select_boin_mtd.Rd | 28 man/select_mtpi2_mtd.Rd | 39 man/select_mtpi_mtd.Rd | 40 man/select_tpi_mtd.Rd | 42 man/selector.Rd | 2 man/simulations.Rd | 3 man/stick_on_num_tox.Rd |only man/try_rescue_dose.Rd | 2 man/unadmit_untested.Rd |only tests/testthat/test_boin.R | 54 tests/testthat/test_boin12_rds.R |only tests/testthat/test_boin_comb.R |only tests/testthat/test_demand_n_at_dose.R | 8 tests/testthat/test_dfcrm.R | 8 tests/testthat/test_dont_skip_doses.R | 8 tests/testthat/test_expand_last_dose_to_cohort.R |only tests/testthat/test_follow_path.R | 15 tests/testthat/test_helpers.R |only tests/testthat/test_mtpi.R | 2700 +++++++++++------------ tests/testthat/test_mtpi2.R | 716 +++--- tests/testthat/test_outcomes_to_arrays.R |only tests/testthat/test_select_boin_mtd.R | 24 tests/testthat/test_select_dose_by_cibp.R | 11 tests/testthat/test_select_mtpi2_mtd.R | 24 tests/testthat/test_select_mtpi_mtd.R | 24 tests/testthat/test_select_tpi_mtd.R | 24 tests/testthat/test_simulate_trials.R | 39 tests/testthat/test_spruce_outcomes_df.R |only tests/testthat/test_stick_on_num_tox.R |only tests/testthat/test_stop_at_n.R | 8 tests/testthat/test_stop_when_n_at_dose.R | 8 tests/testthat/test_stop_when_too_toxic.R | 8 tests/testthat/test_stop_when_tox_ci_covered.R | 8 tests/testthat/test_three_plus_three.R | 16 tests/testthat/test_tpi.R | 835 +++---- tests/testthat/test_trialr_crm.R | 24 tests/testthat/test_trialr_nbg.R | 8 tests/testthat/test_try_rescue_dose.R | 8 tests/testthat/test_unadmit_untested.R |only vignettes/A100-DoseSelectors.Rmd | 11 vignettes/A205-CRM.Rmd | 4 vignettes/A207-NBG.Rmd | 4 vignettes/A210-TPI.Rmd | 22 vignettes/A220-mTPI.Rmd | 22 vignettes/A230-BOIN.Rmd | 22 vignettes/A280-TITE.Rmd |only vignettes/A310-EfficacyToxicity.Rmd |only vignettes/A360-Combinations.Rmd |only vignettes/library.bib | 54 159 files changed, 5159 insertions(+), 3268 deletions(-)
Title: Forest Estimations and Dendrometric Computations
Description: Computation of dendrometric and structural parameters from forest inventory data. The objective is to provide a user-friendly R package for researchers, ecologists, foresters, statisticians, loggers and other persons who deal with forest inventory data. The package includes advanced distribution fitting capabilities with multiple estimation methods (Maximum Likelihood, Maximum Product Spacing with ties correction methods following Cheng & Amin (1983), and Method of Moments) for probability distributions commonly used in forestry. Visualization tools with confidence bands using delta method and parametric bootstrap are provided for three-parameter Weibull distribution fitting to diameter data. Useful conversion of angle value from degree to radian, conversion from angle to slope (in percentage) and their reciprocals as well as principal angle determination are also included. Position and dispersion parameters usually found in forest studies are implemented. The package contains Fibo [...truncated...]
Author: Narcisse Yehouenou [aut, cre],
Information and Communication Technology for you ONG [fnd]
Maintainer: Narcisse Yehouenou <narcisstar211@gmail.com>
Diff between dendrometry versions 0.0.3 dated 2025-04-24 and 0.0.4 dated 2025-10-08
dendrometry-0.0.3/dendrometry/man/adjWeibull.Rd |only dendrometry-0.0.3/dendrometry/man/param_i.Rd |only dendrometry-0.0.4/dendrometry/DESCRIPTION | 27 dendrometry-0.0.4/dendrometry/MD5 | 63 dendrometry-0.0.4/dendrometry/NAMESPACE | 17 dendrometry-0.0.4/dendrometry/NEWS.md | 26 dendrometry-0.0.4/dendrometry/R/dendrometry.R | 1308 ++++++++++----- dendrometry-0.0.4/dendrometry/R/fit_distributions.R |only dendrometry-0.0.4/dendrometry/build/partial.rdb |binary dendrometry-0.0.4/dendrometry/build/vignette.rds |binary dendrometry-0.0.4/dendrometry/inst/doc/dendrometry.R | 4 dendrometry-0.0.4/dendrometry/inst/doc/dendrometry.Rmd | 155 + dendrometry-0.0.4/dendrometry/inst/doc/dendrometry.html | 17 dendrometry-0.0.4/dendrometry/man/AIC.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/BIC.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/Tree.Rd | 6 dendrometry-0.0.4/dendrometry/man/basal.Rd | 15 dendrometry-0.0.4/dendrometry/man/basal_i.Rd | 2 dendrometry-0.0.4/dendrometry/man/baseFunction.Rd |only dendrometry-0.0.4/dendrometry/man/ci_bands_bootstrap.Rd |only dendrometry-0.0.4/dendrometry/man/ci_bands_delta.Rd |only dendrometry-0.0.4/dendrometry/man/coef.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/confint.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/create_objective.Rd |only dendrometry-0.0.4/dendrometry/man/dendrometry-package.Rd | 9 dendrometry-0.0.4/dendrometry/man/densityRegen.Rd | 7 dendrometry-0.0.4/dendrometry/man/dweibull3.Rd |only dendrometry-0.0.4/dendrometry/man/fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/fit_lmoments.Rd |only dendrometry-0.0.4/dendrometry/man/fit_moments.Rd |only dendrometry-0.0.4/dendrometry/man/fit_optimization.Rd |only dendrometry-0.0.4/dendrometry/man/fit_weibull_plot.Rd |only dendrometry-0.0.4/dendrometry/man/format_ci.Rd |only dendrometry-0.0.4/dendrometry/man/format_ci_inline.Rd |only dendrometry-0.0.4/dendrometry/man/get_cdf.Rd |only dendrometry-0.0.4/dendrometry/man/get_default_bounds.Rd |only dendrometry-0.0.4/dendrometry/man/get_param_names.Rd |only dendrometry-0.0.4/dendrometry/man/get_pdf.Rd |only dendrometry-0.0.4/dendrometry/man/get_start_values.Rd |only dendrometry-0.0.4/dendrometry/man/logLik.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/makedata.Rd | 39 dendrometry-0.0.4/dendrometry/man/nestedFunBuilder.Rd |only dendrometry-0.0.4/dendrometry/man/optimize_params.Rd |only dendrometry-0.0.4/dendrometry/man/param.Rd |only dendrometry-0.0.4/dendrometry/man/print.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/summary.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/man/vcov.fit_dist.Rd |only dendrometry-0.0.4/dendrometry/vignettes/dendrometry.Rmd | 155 + 48 files changed, 1252 insertions(+), 598 deletions(-)
Title: Utilities for Interacting with the 'CTX' APIs
Description: Access chemical, hazard, bioactivity, and exposure data from the
Computational Toxicology and Exposure ('CTX') APIs
<https://www.epa.gov/comptox-tools/computational-toxicology-and-exposure-apis>.
'ctxR' was developed to streamline the process of accessing the information
available through the 'CTX' APIs without requiring prior knowledge of how to
use APIs. Most data is also available on the CompTox Chemical Dashboard
('CCD') <https://comptox.epa.gov/dashboard/> and other resources found at the
EPA Computational Toxicology and Exposure Online Resources
<https://www.epa.gov/comptox-tools>.
Author: Paul Kruse [aut] ,
Caroline Ring [aut] ,
Madison Feshuk [ctb, cre] ,
Brianna Dirks [ctb] ,
Carter Thunes [ctb],
Jason Brown [ctb]
Maintainer: Madison Feshuk <feshuk.madison@epa.gov>
Diff between ctxR versions 1.1.2 dated 2025-04-07 and 1.1.3 dated 2025-10-08
ctxR-1.1.2/ctxR/inst/doc/Bioactivity.R |only ctxR-1.1.2/ctxR/inst/doc/Bioactivity.Rmd |only ctxR-1.1.2/ctxR/inst/doc/Bioactivity.html |only ctxR-1.1.2/ctxR/inst/doc/Chemical.R |only ctxR-1.1.2/ctxR/inst/doc/Chemical.Rmd |only ctxR-1.1.2/ctxR/inst/doc/Chemical.html |only ctxR-1.1.2/ctxR/inst/doc/Exposure.R |only ctxR-1.1.2/ctxR/inst/doc/Exposure.Rmd |only ctxR-1.1.2/ctxR/inst/doc/Exposure.html |only ctxR-1.1.2/ctxR/inst/doc/Hazard.R |only ctxR-1.1.2/ctxR/inst/doc/Hazard.Rmd |only ctxR-1.1.2/ctxR/inst/doc/Hazard.html |only ctxR-1.1.2/ctxR/inst/doc/Introduction.R |only ctxR-1.1.2/ctxR/inst/doc/Introduction.Rmd |only ctxR-1.1.2/ctxR/inst/doc/Introduction.html |only ctxR-1.1.2/ctxR/tests/testthat/chemical/chemical |only ctxR-1.1.2/ctxR/tests/testthat/exposure-batch/expo-demo |only ctxR-1.1.2/ctxR/tests/testthat/exposure-batch/expo-gen |only ctxR-1.1.2/ctxR/tests/testthat/exposure-batch/exposure |only ctxR-1.1.2/ctxR/tests/testthat/exposure/expo-demo |only ctxR-1.1.2/ctxR/tests/testthat/exposure/expo-gen |only ctxR-1.1.2/ctxR/tests/testthat/exposure/exposure |only ctxR-1.1.2/ctxR/vignettes/1/0/chemical |only ctxR-1.1.2/ctxR/vignettes/1/0/hazard |only ctxR-1.1.2/ctxR/vignettes/5/0/expo-demo |only ctxR-1.1.2/ctxR/vignettes/5/0/expo-gen |only ctxR-1.1.2/ctxR/vignettes/5/0/exposure |only ctxR-1.1.2/ctxR/vignettes/Bioactivity.Rmd |only ctxR-1.1.2/ctxR/vignettes/Chemical.Rmd |only ctxR-1.1.2/ctxR/vignettes/Exposure.Rmd |only ctxR-1.1.2/ctxR/vignettes/Hazard.Rmd |only ctxR-1.1.2/ctxR/vignettes/Introduction.Rmd |only ctxR-1.1.3/ctxR/DESCRIPTION | 42 ctxR-1.1.3/ctxR/MD5 | 641 +++++--- ctxR-1.1.3/ctxR/NAMESPACE | 27 ctxR-1.1.3/ctxR/NEWS.md | 27 ctxR-1.1.3/ctxR/R/chemical-APIs-batch.R | 329 +++- ctxR-1.1.3/ctxR/R/chemical-APIs.R | 295 +++- ctxR-1.1.3/ctxR/R/exposure-APIs-batch.R | 722 ++++++++++ ctxR-1.1.3/ctxR/R/exposure-APIs.R | 515 +++++++ ctxR-1.1.3/ctxR/R/hazard-APIs-batch.R | 31 ctxR-1.1.3/ctxR/R/hazard-APIs.R | 34 ctxR-1.1.3/ctxR/README.md | 33 ctxR-1.1.3/ctxR/build/vignette.rds |binary ctxR-1.1.3/ctxR/data/bioactivity_api_server.rda |binary ctxR-1.1.3/ctxR/data/chemical_api_server.rda |binary ctxR-1.1.3/ctxR/data/exposure_api_server.rda |binary ctxR-1.1.3/ctxR/data/hazard_api_server.rda |binary ctxR-1.1.3/ctxR/inst/CITATION |only ctxR-1.1.3/ctxR/inst/doc/ctxR_01_Introduction.R |only ctxR-1.1.3/ctxR/inst/doc/ctxR_01_Introduction.Rmd |only ctxR-1.1.3/ctxR/inst/doc/ctxR_01_Introduction.html |only ctxR-1.1.3/ctxR/inst/doc/ctxR_02_Chemical.R |only ctxR-1.1.3/ctxR/inst/doc/ctxR_02_Chemical.Rmd |only ctxR-1.1.3/ctxR/inst/doc/ctxR_02_Chemical.html |only ctxR-1.1.3/ctxR/inst/doc/ctxR_03_Bioactivity.R |only ctxR-1.1.3/ctxR/inst/doc/ctxR_03_Bioactivity.Rmd |only ctxR-1.1.3/ctxR/inst/doc/ctxR_03_Bioactivity.html |only ctxR-1.1.3/ctxR/inst/doc/ctxR_04_Exposure.R |only ctxR-1.1.3/ctxR/inst/doc/ctxR_04_Exposure.Rmd |only ctxR-1.1.3/ctxR/inst/doc/ctxR_04_Exposure.html |only ctxR-1.1.3/ctxR/inst/doc/ctxR_05_Hazard.R |only ctxR-1.1.3/ctxR/inst/doc/ctxR_05_Hazard.Rmd |only ctxR-1.1.3/ctxR/inst/doc/ctxR_05_Hazard.html |only ctxR-1.1.3/ctxR/inst/httptest/request.R | 8 ctxR-1.1.3/ctxR/man/check_existence_by_dtxsid.Rd | 2 ctxR-1.1.3/ctxR/man/check_existence_by_dtxsid_batch.Rd | 2 ctxR-1.1.3/ctxR/man/chemical_contains.Rd | 6 ctxR-1.1.3/ctxR/man/chemical_contains_batch.Rd | 2 ctxR-1.1.3/ctxR/man/chemical_equal.Rd | 6 ctxR-1.1.3/ctxR/man/chemical_equal_batch.Rd | 2 ctxR-1.1.3/ctxR/man/chemical_starts_with.Rd | 6 ctxR-1.1.3/ctxR/man/chemical_starts_with_batch.Rd | 2 ctxR-1.1.3/ctxR/man/create_hazard_data.table.Rd | 2 ctxR-1.1.3/ctxR/man/ctxR_options.Rd | 6 ctxR-1.1.3/ctxR/man/get_aggregate_records_by_dtxsid.Rd |only ctxR-1.1.3/ctxR/man/get_aggregate_records_by_dtxsid_batch.Rd |only ctxR-1.1.3/ctxR/man/get_aggregate_records_by_medium.Rd |only ctxR-1.1.3/ctxR/man/get_aggregate_records_by_medium_batch.Rd |only ctxR-1.1.3/ctxR/man/get_all_assays.Rd | 2 ctxR-1.1.3/ctxR/man/get_all_list_types.Rd | 2 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Title: Draw Venn Diagram by 'ggplot2'
Description: An easy-to-use way to draw pretty Venn diagrams using 'ggplot2'.
This package provides functions to create Venn diagrams with customizable
colors, labels, and styling options.
Author: Linlin Yan [aut, cre]
Maintainer: Linlin Yan <yanlinlin82@gmail.com>
Diff between ggvenn versions 0.1.18 dated 2025-10-08 and 0.1.19 dated 2025-10-08
DESCRIPTION | 6 - MD5 | 30 +++--- NEWS.md | 69 +++++++------ R/data_preparation.R | 2 R/geom_venn.R | 21 ++-- R/ggvenn.R | 2 README.md | 164 +++++++++++++++++++++++---------- man/geom_venn.Rd | 2 man/ggvenn.Rd | 2 tests/testthat/_snaps/color_size.md | 8 - tests/testthat/_snaps/geom_venn.md | 32 +++--- tests/testthat/_snaps/ggvenn.md | 70 +++++++------- tests/testthat/_snaps/percentages.md | 24 ++-- tests/testthat/_snaps/set-totals.md | 56 +++++------ tests/testthat/_snaps/show_elements.md | 16 +-- tests/testthat/_snaps/stats.md | 126 ++++++++++++------------- 16 files changed, 352 insertions(+), 278 deletions(-)
Title: Interaction Between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap
API. REDCap (Research Electronic Data CAPture) is a web application for
building and managing online surveys and databases developed at Vanderbilt
University. The Application Programming Interface (API) offers an avenue
to access and modify data programmatically, improving the capacity for
literate and reproducible programming.
Author: Will Beasley [aut, cre] ,
David Bard [ctb] ,
Thomas Wilson [ctb],
John J Aponte [ctb],
Rollie Parrish [ctb] ,
Benjamin Nutter [ctb],
Andrew Peters [ctb] ,
Hao Zhu [ctb] ,
Janosch Linkersdoerfer [ctb] ,
Jonathan Mang [ctb] ,
Felix Torres [ctb],
Philip [...truncated...]
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between REDCapR versions 1.5.0 dated 2025-07-28 and 1.6.0 dated 2025-10-08
DESCRIPTION | 10 LICENSE | 4 MD5 | 770 +- NAMESPACE | 110 NEWS.md | 70 R/REDCapR-package.R | 132 R/constant.R | 462 - R/create-batch-glossary.R | 208 R/helpers-testing.R | 264 R/kernel-api.R | 239 R/metadata-utilities.R | 270 R/project-dag-write.R | 364 - R/project-delete-multiple-arm.R | 220 R/project-delete-single-arm.R | 224 R/project-simple.R | 332 - R/redcap-arm-export.R | 372 - R/redcap-column-sanitize.R | 128 R/redcap-dag-read.R | 335 - R/redcap-delete.R | 432 - R/redcap-event-instruments.R | 366 - R/redcap-event-read.R | 368 - R/redcap-file-download-oneshot.R | 521 - R/redcap-file-repo-list.R | 389 - R/redcap-file-upload-oneshot.R | 401 - R/redcap-instrument-download.R | 465 - R/redcap-instruments.R | 333 - R/redcap-log-read.R | 446 - R/redcap-metadata-coltypes.R | 1014 +-- R/redcap-metadata-read.R | 438 - R/redcap-metadata-write.R | 316 - R/redcap-next-free-record-name.R | 288 R/redcap-project-info-read.R | 604 - R/redcap-project.R | 267 R/redcap-read-eav-oneshot.R | 708 +- R/redcap-read-oneshot-eav.R | 818 +- R/redcap-read-oneshot.R | 808 +- R/redcap-read.R | 1232 ++-- R/redcap-report.R | 499 - R/redcap-survey-link-export-oneshot.R | 343 - R/redcap-users-export.R | 451 - R/redcap-variables.R | 347 - R/redcap-version.R | 221 R/redcap-write-oneshot.R | 406 - R/redcap-write.R | 424 - R/retrieve-credential.R | 794 +- R/sanitize-token.R | 196 R/skippers.R | 38 R/utilities.R | 236 R/validate.R | 830 +- README.md | 190 build/vignette.rds |binary inst/WORDLIST | 316 - inst/doc/BasicREDCapROperations.R | 186 inst/doc/BasicREDCapROperations.Rmd | 344 - inst/doc/BasicREDCapROperations.html | 1044 +-- inst/doc/SecurityDatabase.Rmd | 694 +- inst/doc/SecurityDatabase.html | 1438 ++-- inst/doc/TroubleshootingApiCalls.R | 38 inst/doc/TroubleshootingApiCalls.Rmd | 1068 +-- inst/doc/TroubleshootingApiCalls.html | 2114 +++--- inst/doc/advanced-redcapr-operations.R | 282 inst/doc/advanced-redcapr-operations.Rmd | 540 - inst/doc/advanced-redcapr-operations.html | 1192 +-- inst/doc/longitudinal-and-repeating.R | 254 inst/doc/longitudinal-and-repeating.Rmd | 852 +- inst/doc/longitudinal-and-repeating.html | 3080 +++++----- inst/doc/workflow-read.R | 212 inst/doc/workflow-read.Rmd | 866 +- inst/doc/workflow-read.html | 1422 ++-- inst/doc/workflow-write.R | 34 inst/doc/workflow-write.Rmd | 838 +- inst/doc/workflow-write.html | 1512 ++-- inst/misc/bad.credentials | 16 inst/misc/conflicting-rows.credentials | 16 inst/misc/coph.credentials | 77 inst/misc/dev-2.credentials | 77 inst/misc/example.credentials | 77 inst/misc/out-of-order.credentials | 16 inst/misc/plugin-redirection.yml | 46 inst/misc/project-redirection.yml | 206 inst/misc/skeleton.credentials | 38 inst/misc/validation-transformation.yml | 280 inst/misc/vignette.css | 72 inst/misc/zero-rows.credentials | 12 inst/test-data/project-color-boxes/Readme.md | 106 inst/test-data/project-color-boxes/data.csv | 8 inst/test-data/project-color-boxes/dictionary.csv | 6 inst/test-data/projects/README.md | 54 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inst/test-data/projects/blank-for-gray-status/dictionary.csv | 36 inst/test-data/projects/checkboxes-1/data.csv | 10 inst/test-data/projects/checkboxes-1/dictionary.csv | 10 inst/test-data/projects/clinical-trial-1/README.md | 12 inst/test-data/projects/dag-write/README.md | 24 inst/test-data/projects/dag-write/data.csv | 8 inst/test-data/projects/dag-write/dictionary.csv | 32 inst/test-data/projects/dag/README.md | 16 inst/test-data/projects/decimal-comma-and-dot/data.csv | 10 inst/test-data/projects/decimal-comma-and-dot/dictionary.csv | 18 inst/test-data/projects/decimal-comma-and-dot/metadata.csv | 18 inst/test-data/projects/decimal-comma-and-dot/redcapr-specific/default-mismatched.R | 12 inst/test-data/projects/decimal-comma/data.csv | 10 inst/test-data/projects/decimal-comma/dictionay.csv | 12 inst/test-data/projects/decimal-comma/redcapr-specific/default-mismatched.R | 12 inst/test-data/projects/decimal-comma/redcapr-specific/set-locale.R | 10 inst/test-data/projects/decimal-dot/data.csv | 10 inst/test-data/projects/decimal-dot/dictionary.csv | 12 inst/test-data/projects/decimal-dot/redcapr-specific/set-locale.R | 10 inst/test-data/projects/file-repo/README.md | 32 inst/test-data/projects/file-repo/data.csv | 6 inst/test-data/projects/file-repo/dictionary.csv | 12 inst/test-data/projects/longitudinal/arm.csv | 4 inst/test-data/projects/longitudinal/data.csv | 38 inst/test-data/projects/longitudinal/dictionary.csv | 192 inst/test-data/projects/longitudinal/event.csv | 26 inst/test-data/projects/longitudinal/expected/default.R | 398 - inst/test-data/projects/longitudinal/expected/dummy.R | 4 inst/test-data/projects/longitudinal/expected/filter-character.R | 68 inst/test-data/projects/longitudinal/expected/filter-numeric.R | 98 inst/test-data/projects/longitudinal/expected/so-example-data-frame-retrieval.R | 4 inst/test-data/projects/metadata-write/data.csv | 12 inst/test-data/projects/metadata-write/dictionary.csv | 34 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vignettes/SecurityDatabase.Rmd | 694 +- vignettes/TroubleshootingApiCalls.Rmd | 1068 +-- vignettes/advanced-redcapr-operations.Rmd | 540 - vignettes/longitudinal-and-repeating.Rmd | 852 +- vignettes/workflow-read.Rmd | 866 +- vignettes/workflow-write.Rmd | 838 +- 386 files changed, 42136 insertions(+), 42114 deletions(-)
Title: Machine Learning-Assisted, Marker-Based Tool for Single-Cell and
Spatial Transcriptomics Annotation
Description: Annotates single-cell and spatial-transcriptomic (ST) data using marker datasets. Supports unified markers list ('Markers_list') creation from built-in databases (e.g., 'Cellmarker2', 'PanglaoDB', 'scIBD', 'TCellSI'), Seurat objects, or user-supplied Excel files. SlimR can predict calculate parameters by machine learning algorithms (e.g., 'Random Forest', 'Gradient Boosting', 'Support Vector Machine', 'Ensemble Learning'), and based on Markers_list, calculate gene expression of different cell types and predict annotation information and calculate corresponding AUC and annotate it, then verify it. At the same time, it can calculate gene expression corresponding to the cell type to generate a reference map for manual annotation (e.g., 'Heat Map', 'Feature Plots', 'Combined Plots'). For more details see Kabacoff (2020, ISBN:9787115420572).
Author: Zhaoqing Wang [aut, cre]
Maintainer: Zhaoqing Wang <zhaoqingwang@mail.sdu.edu.cn>
Diff between SlimR versions 1.0.7 dated 2025-08-18 and 1.0.8 dated 2025-10-08
DESCRIPTION | 32 +++--- MD5 | 118 ++++++++++++----------- NAMESPACE | 6 + NEWS.md | 8 + R/Celltype_Annotation.R | 2 R/Celltype_Annotation_Combined.R | 4 R/Celltype_Annotation_Features.R | 6 - R/Celltype_Annotation_Heatmap.R | 2 R/Celltype_Calculate.R | 11 +- R/Celltype_Verification.R | 6 - R/Celltype_annotation_Cellmarker2.R | 8 - R/Celltype_annotation_Excel.R | 8 - R/Celltype_annotation_PanglaoDB.R | 8 - R/Celltype_annotation_Seurat.R | 10 +- R/Database_Cellmarker2.R | 2 R/Database_Cellmarker2_raw.R | 2 R/Database_Cellmarker2_table.R | 2 R/Database_Markers_list_TCellSI.R | 2 R/Database_Markers_list_scIBD.R | 6 - R/Database_PanglaoDB.R | 2 R/Database_PanglaoDB_raw.R | 2 R/Database_PanglaoDB_table.R | 2 R/Expression_calculate.R | 2 R/Markers_filter_Cellmarker2.R | 2 R/Markers_filter_PanglaoDB.R | 2 R/Probability_calculate.R | 2 R/Probability_parameter.R |only R/Read_excel_markers.R | 2 R/Read_seurat_markers.R | 14 +- R/onattach.R | 12 +- README.md | 164 ++++++++++++++++++++------------- data/Markers_list_scIBD.rda |binary man/Cellmarker2.Rd | 4 man/Cellmarker2_raw.Rd | 4 man/Cellmarker2_table.Rd | 4 man/Celltype_Annotation.Rd | 7 - man/Celltype_Annotation_Combined.Rd | 6 - man/Celltype_Annotation_Features.Rd | 8 - man/Celltype_Annotation_Heatmap.Rd | 4 man/Celltype_Calculate.Rd | 7 - man/Celltype_Verification.Rd | 9 + man/Celltype_annotation_Cellmarker2.Rd | 8 - man/Celltype_annotation_Excel.Rd | 8 - man/Celltype_annotation_PanglaoDB.Rd | 8 - man/Celltype_annotation_Seurat.Rd | 8 - man/Markers_filter_Cellmarker2.Rd | 4 man/Markers_filter_PanglaoDB.Rd | 4 man/Markers_list_TCellSI.Rd | 4 man/Markers_list_scIBD.Rd | 8 + man/PanglaoDB.Rd | 4 man/PanglaoDB_raw.Rd | 4 man/PanglaoDB_table.Rd | 4 man/Parameter_Calculate.Rd |only man/Read_excel_markers.Rd | 4 man/Read_seurat_markers.Rd | 10 +- man/calculate_cluster_variability.Rd |only man/calculate_expression.Rd | 14 ++ man/calculate_expression_skewness.Rd |only man/calculate_probability.Rd | 14 ++ man/estimate_batch_effect.Rd |only man/extract_dataset_features.Rd |only man/generate_training_data.Rd |only man/postprocess_parameters.Rd |only man/predict_optimal_parameters.Rd |only man/train_parameter_model.Rd |only 65 files changed, 355 insertions(+), 253 deletions(-)
Title: Rapid Asynchronous and Distributed Computing
Description: Package to tackle large-scale problems asynchronously across
a distributed network. Employing a database centric model, rush
enables workers to communicate tasks and their results over a shared
'Redis' database. Key features include low task overhead, efficient
caching, and robust error handling. The package powers the
asynchronous optimization algorithms in the 'bbotk' and 'mlr3tuning'
packages.
Author: Marc Becker [cre, aut, cph]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between rush versions 0.3.1 dated 2025-09-16 and 0.4.0 dated 2025-10-08
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------ NEWS.md | 7 ++++++ R/Rush.R | 44 ++++++++++++++++++++++++++++++++++++--- man/Rush.Rd | 28 +++++++++++++++++++++++- man/RushWorker.Rd | 1 tests/testthat/test-Rush.R | 32 ++++++++++++++++++++++++++++ tests/testthat/test-RushWorker.R | 38 +++++++++++++++++++++++++++++++++ 8 files changed, 155 insertions(+), 15 deletions(-)
Title: Patient-Reported Outcome Data Analysis with Stan
Description: Algorithms and subroutines for patient-reported outcome data analysis.
Author: Bin Wang [aut, cre]
Maintainer: Bin Wang <bwang831@gmail.com>
Diff between prome versions 2.0.1.4 dated 2025-10-02 and 2.0.1.9 dated 2025-10-08
DESCRIPTION | 13 ++++++------- MD5 | 6 +++--- R/blindinglogit.R | 5 +++-- man/lslogit.Rd | 6 +++--- 4 files changed, 15 insertions(+), 15 deletions(-)
Title: Acquiring and Processing Data from Japan Institute for Health
Security
Description: Download and post process the infectious disease case data
from Japan Institute for Health Security. Also the package included
ready-to-analyse datasets. See the data source website for further details
<https://id-info.jihs.go.jp/>.
Author: Tomonori Hoshi [aut, cre],
Erina Ishigaki [aut],
Satoshi Kaneko [aut]
Maintainer: Tomonori Hoshi <tomonori.hoshi.japan@gmail.com>
Diff between jpinfect versions 0.1.4 dated 2025-10-07 and 0.1.5 dated 2025-10-08
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/jpinfect_read_confirmed.R | 8 ++++++-- inst/doc/jpinfect.html | 4 ++-- 4 files changed, 17 insertions(+), 13 deletions(-)
Title: Simplify Survival Data Analysis and Model Fitting
Description: Inspect survival data, plot Kaplan-Meier curves, assess the
proportional hazards assumption, fit parametric survival models,
predict and plot survival and hazards, and export the outputs to
'Excel'. A simple interface for fitting survival models using
flexsurv::flexsurvreg(), flexsurv::flexsurvspline(),
flexsurvcure::flexsurvcure(), and survival::survreg().
Author: Niall Davison [aut, cre] ,
Brad Kievit [aut],
Maple Health Group, LLC [cph, fnd]
Maintainer: Niall Davison <niall.davison@maplehealthgroup.com>
Diff between easysurv versions 2.0.1 dated 2024-06-21 and 2.0.2 dated 2025-10-08
DESCRIPTION | 23 - MD5 | 38 - NEWS.md | 19 R/plot.R | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/easysurv.R | 126 +++--- inst/doc/easysurv.html | 741 +++++++++++++++++++------------------- man/easy_bc.Rd | 54 +- man/easy_lung.Rd | 68 +-- man/easysurv-package.Rd | 2 man/figures/fit-models-a-dark.svg | 2 man/figures/fit-models-a.svg | 2 man/figures/get-KM-r-1.png |binary man/figures/plot-models-r-1.png |binary man/figures/plot-models-r-2.png |binary man/figures/plot-models-r-3.png |binary man/figures/plot-models-r-4.png |binary man/figures/test-PH-r-1.png |binary man/figures/test-PH-r-2.png |binary 20 files changed, 543 insertions(+), 538 deletions(-)
Title: Double Machine Learning for Static Panel Models with Fixed
Effects
Description: The 'xtdml' package implements partially linear panel regression (PLPR) models with high-dimensional confounding variables and an exogenous treatment variable within the double machine learning framework. The package is used to estimate the structural parameter (treatment effect) in static panel data models with fixed effects using the approaches established in Clarke and Polselli (2025) <doi:10.1093/ectj/utaf011>. 'xtdml' is built on the object-oriented package 'DoubleML' (Bach et al., 2024) <doi:10.18637/jss.v108.i03> using the 'mlr3' ecosystem.
Author: Annalivia Polselli [aut, cre]
Maintainer: Annalivia Polselli <apolselli.econ@gmail.com>
Diff between xtdml versions 0.1.5 dated 2025-09-08 and 0.1.6 dated 2025-10-08
DESCRIPTION | 10 MD5 | 10 R/xtdml_data.R | 852 +++++++++++++++++++++++++++---------------------------- R/xtdml_plr.R | 2 README.md | 20 + man/xtdml_plr.Rd | 4 6 files changed, 461 insertions(+), 437 deletions(-)
Title: Automatically Retrieve Multidimensional Distributed Data Sets
Description: Automatically fetch, transform and arrange subsets of
multidimensional data sets (collections of files) stored in local and/or
remote file systems or servers, using multicore capabilities where possible.
This tool provides an interface to perceive a collection of data sets as a single
large multidimensional data array, and enables the user to request for automatic
retrieval, processing and arrangement of subsets of the large array. Wrapper
functions to add support for custom file formats can be plugged in/out, making
the tool suitable for any research field where large multidimensional data sets
are involved.
Author: Nicolau Manubens [aut],
An-Chi Ho [aut] ,
Nuria Perez-Zanon [aut] ,
Victoria Agudetse [cre, ctb],
Eva Rifa [ctb],
Bruno de Paula Kinoshita [ctb],
Javier Vegas [ctb],
Pierre-Antoine Bretonniere [ctb],
Roberto Serrano [ctb],
BSC-CNS [aut, cph]
Maintainer: Victoria Agudetse <victoria.agudetse@bsc.es>
This is a re-admission after prior archival of version 2.4.0 dated 2024-09-19
Diff between startR versions 2.4.0 dated 2024-09-19 and 3.0.0 dated 2025-10-08
DESCRIPTION | 25 ++-- MD5 | 30 ++-- NAMESPACE | 3 NEWS.md | 21 +++ R/ByChunks_autosubmit.R | 159 +++++++++++++++++++------- R/ByChunks_ecflow.R | 67 +++++++++- R/Collect.R | 41 +++++- R/Compute.R | 6 R/NcDataReader.R | 11 - R/SelectorChecker.R | 3 R/Start.R | 17 ++ R/Utils.R | 52 +++++++- inst/chunking/Autosubmit/autosubmit.yml | 2 inst/chunking/Autosubmit/platforms.yml | 29 ++++ inst/chunking/Autosubmit/startR_autosubmit.sh | 3 inst/chunking/ecFlow/Chunk.ecf | 1 16 files changed, 365 insertions(+), 105 deletions(-)
Title: Optimal Stratification of Sampling Frames for Multipurpose
Sampling Surveys
Description: Tools for the optimization of stratified sampling design. It determines a stratification of a sampling frame that minimizes sample cost while satisfying precision constraints in a multivariate and multidomain context. The approach relies on a genetic algorithm; each candidate partition of the frame is an individual whose fitness is evaluated via the Bethel-Chromy allocation to meet target precisions. Functions support analysis of optimization results, labeling of the frame with new strata, and drawing a sample according to the optimal allocation. Algorithmic components adapt code from the 'genalg' package. See M. Ballin and G. Barcaroli (2020) "R package SamplingStrata: new developments and extension to Spatial Sampling" <doi:10.48550/arXiv.2004.09366>.
Author: Giulio Barcaroli [aut, cre],
Marco Ballin [aut],
Hanjo Odendaal [aut],
Daniela Pagliuca [aut],
Egon Willighagen [aut],
Diego Zardetto [aut]
Maintainer: Giulio Barcaroli <gbarcaroli@gmail.com>
Diff between SamplingStrata versions 1.5-4 dated 2022-11-15 and 1.5-5 dated 2025-10-08
DESCRIPTION | 33 ++- MD5 | 25 +- NEWS | 4 R/optimizeStrata.R | 2 R/optimizeStrata2.R | 3 R/optimizeStrataSpatial.R | 3 build/vignette.rds |binary inst/CITATION | 69 ++++--- inst/doc/SamplingStrata.html | 209 +++++++++++------------ inst/doc/models.R | 26 +- inst/doc/models.html | 4 inst/doc/spatial.R | 24 +- inst/doc/spatial.html | 4 vignettes/spatial_figures/unnamed-chunk-10-1.jpg |only 14 files changed, 219 insertions(+), 187 deletions(-)
More information about SamplingStrata at CRAN
Permanent link
Title: Factor-Augmented Regression Scenarios
Description: Provides a comprehensive framework in R for modeling and forecasting economic scenarios based on multi-level dynamic factor model. The package enables users to: (i) extract global and group-specific factors using a flexible multi-level factor structure; (ii) compute asymptotically valid confidence regions for the estimated factors, accounting for uncertainty in the factor loadings; (iii) obtain estimates of the parameters of the factor-augmented quantile regressions together with their standard deviations; (iv) recover full predictive conditional densities from estimated quantiles; (v) obtain risk measures based on extreme quantiles of the conditional densities; (vi) estimate the conditional density and the corresponding extreme quantiles when the factors are stressed.
Author: Gian Pietro Bellocca [aut, cre],
Ignacio Garron [aut],
Vladimir Rodriguez-Caballero [aut],
Esther Ruiz [aut]
Maintainer: Gian Pietro Bellocca <gbellocc@est-econ.uc3m.es>
Diff between FARS versions 0.6.0 dated 2025-10-07 and 0.6.1 dated 2025-10-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/plot.R | 3 ++- inst/doc/Factor_Augmented_Regression_Scenarios_in_R.pdf |binary 4 files changed, 8 insertions(+), 7 deletions(-)
Title: Dynamic Mode Decomposition Forecasting with Conformal Predictive
Sampling
Description: The DYMO package provides tools for multi-feature time-series forecasting using a Dynamic Mode Decomposition (DMD) model combined with conformal predictive sampling for uncertainty quantification.
Author: Giancarlo Vercellino [aut, cre, cph]
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between dymo versions 1.1.0 dated 2022-05-05 and 2.0.0 dated 2025-10-08
DESCRIPTION | 24 - MD5 | 12 NAMESPACE | 35 +- NEWS.md | 17 + R/main.R | 860 ++++++++++++++++++++++++++++++++++++------------------------ man/dymo.Rd | 79 +++-- tests |only 7 files changed, 628 insertions(+), 399 deletions(-)
Title: Visualising and Interpreting Statistical Models Fit to
Compositional Data
Description: Statistical models fit to compositional data are often difficult to interpret due to the sum to 1 constraint on data variables. 'DImodelsVis' provides novel visualisations tools to aid with the interpretation of models fit to compositional data. All visualisations in the package are created using the 'ggplot2' plotting framework and can be extended like every other 'ggplot' object.
Author: Rishabh Vishwakarma [aut, cre] ,
Caroline Brophy [aut],
Laura Byrne [aut],
Catherine Hurley [aut]
Maintainer: Rishabh Vishwakarma <vishwakr@tcd.ie>
Diff between DImodelsVis versions 1.0.3 dated 2025-08-23 and 1.0.4 dated 2025-10-08
DImodelsVis-1.0.3/DImodelsVis/man/add_ID_terms.Rd |only DImodelsVis-1.0.3/DImodelsVis/man/add_interaction_terms.Rd |only DImodelsVis-1.0.4/DImodelsVis/DESCRIPTION | 11 DImodelsVis-1.0.4/DImodelsVis/MD5 | 127 - DImodelsVis-1.0.4/DImodelsVis/NAMESPACE | 1 DImodelsVis-1.0.4/DImodelsVis/NEWS.md | 6 DImodelsVis-1.0.4/DImodelsVis/R/ConditionalTernary.R | 4 DImodelsVis-1.0.4/DImodelsVis/R/GradientChange.R | 6 DImodelsVis-1.0.4/DImodelsVis/R/GroupedTernary.R | 6 DImodelsVis-1.0.4/DImodelsVis/R/ModelDiagnostics.R | 6 DImodelsVis-1.0.4/DImodelsVis/R/ModelSelection.R | 3 DImodelsVis-1.0.4/DImodelsVis/R/PredictionContributions.R | 22 DImodelsVis-1.0.4/DImodelsVis/R/SanityChecks.R | 9 DImodelsVis-1.0.4/DImodelsVis/R/SimplexPath.R | 11 DImodelsVis-1.0.4/DImodelsVis/R/Ternary.R | 2 DImodelsVis-1.0.4/DImodelsVis/R/VisualiseEffects.R | 9 DImodelsVis-1.0.4/DImodelsVis/R/utilities.R | 175 -- DImodelsVis-1.0.4/DImodelsVis/build/vignette.rds |binary DImodelsVis-1.0.4/DImodelsVis/inst/WORDLIST | 5 DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-DImodelsMulti-models.Rmd | 6 DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-DImodelsMulti-models.html | 12 DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-black-box-models.R |only DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-black-box-models.Rmd |only DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-black-box-models.html |only DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-complex-models.R | 2 DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-complex-models.Rmd | 14 DImodelsVis-1.0.4/DImodelsVis/inst/doc/DImodelsVis-with-complex-models.html | 49 DImodelsVis-1.0.4/DImodelsVis/man/DI_ID_and_ints.Rd |only DImodelsVis-1.0.4/DImodelsVis/man/add_add_var.Rd | 4 DImodelsVis-1.0.4/DImodelsVis/man/add_prediction.Rd | 3 DImodelsVis-1.0.4/DImodelsVis/man/conditional_ternary.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/conditional_ternary_data.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/custom_filter.Rd | 158 - DImodelsVis-1.0.4/DImodelsVis/man/get_colours.Rd | 70 DImodelsVis-1.0.4/DImodelsVis/man/get_shades.Rd | 58 DImodelsVis-1.0.4/DImodelsVis/man/gradient_change.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/gradient_change_data.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/gradient_change_plot.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/grouped_ternary.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/grouped_ternary_data.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/grouped_ternary_plot.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/model_diagnostics.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/model_diagnostics_data.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/model_diagnostics_plot.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/model_selection.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/prediction_contributions.Rd | 9 DImodelsVis-1.0.4/DImodelsVis/man/prediction_contributions_plot.Rd | 6 DImodelsVis-1.0.4/DImodelsVis/man/simplex_path.Rd | 3 DImodelsVis-1.0.4/DImodelsVis/man/simplex_path_data.Rd | 3 DImodelsVis-1.0.4/DImodelsVis/man/simplex_path_plot.Rd | 3 DImodelsVis-1.0.4/DImodelsVis/man/visualise_effects.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/man/visualise_effects_data.Rd | 4 DImodelsVis-1.0.4/DImodelsVis/man/visualise_effects_plot.Rd | 2 DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/ConditionalTernary/ct-dimodels-data-manual.svg | 16 DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/GroupedTernary/gt-with-dimodels-data-manual.svg | 9 DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/PredictionContributions/pc-basic-dimodels-and-custom-data.svg | 140 - DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/PredictionContributions/pc-with-add-var-in-dimodels.svg | 840 +++++----- DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/PredictionContributions/pc-with-add-var-single-and-custom-data.svg | 300 +-- DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/PredictionContributions/pc-with-basic-dimodels.svg | 84 - DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/PredictionContributions/pc-with-data-manually-prepared.svg | 120 - DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/PredictionContributions/pc-with-pie-data.svg | 474 ++--- DImodelsVis-1.0.4/DImodelsVis/tests/testthat/_snaps/Ternary/ternary-with-add-var-and-aes.svg | 34 DImodelsVis-1.0.4/DImodelsVis/tests/testthat/test-ConditionalTernary.R | 3 DImodelsVis-1.0.4/DImodelsVis/tests/testthat/test-GroupedTernary.R | 3 DImodelsVis-1.0.4/DImodelsVis/tests/testthat/test-SanityChecks.R | 7 DImodelsVis-1.0.4/DImodelsVis/vignettes/DImodelsVis-with-DImodelsMulti-models.Rmd | 6 DImodelsVis-1.0.4/DImodelsVis/vignettes/DImodelsVis-with-black-box-models.Rmd |only DImodelsVis-1.0.4/DImodelsVis/vignettes/DImodelsVis-with-complex-models.Rmd | 14 68 files changed, 1436 insertions(+), 1449 deletions(-)
Title: Threshold Selection and Uncertainty for Extreme Value Analysis
Description: Provides functions for the selection of thresholds for use in
extreme value models, based mainly on the methodology in
Northrop, Attalides and Jonathan (2017) <doi:10.1111/rssc.12159>.
It also performs predictive inferences about future extreme values,
based either on a single threshold or on a weighted average of inferences
from multiple thresholds, using the 'revdbayes' package
<https://cran.r-project.org/package=revdbayes>.
At the moment only the case where the data can be treated as
independent identically distributed observations is considered.
Author: Paul J. Northrop [aut, cre, cph],
Nicolas Attalides [aut]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between threshr versions 1.0.6 dated 2024-07-17 and 1.0.7 dated 2025-10-08
DESCRIPTION | 10 +++---- MD5 | 16 ++++++------ NEWS.md | 7 +++++ R/ithresh.R | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/threshr-vignette.html | 44 +++++++++++++++++---------------- man/ithresh.Rd | 2 - tests/testthat/test-plot_and_summary.R | 3 -- 9 files changed, 46 insertions(+), 38 deletions(-)
Title: Multiblock Exploratory and Predictive Data Analysis
Description: Exploratory and predictive methods for the analysis of several blocks of variables measured on the same individuals.
Author: Benjamin Mahieu [aut, cre],
Essomanda Tchandao Mangamana [aut],
Evelyne Vigneau [aut],
Veronique Cariou [aut]
Maintainer: Benjamin Mahieu <benjamin.mahieu@oniris-nantes.fr>
Diff between MBAnalysis versions 2.1.0 dated 2025-07-10 and 2.1.1 dated 2025-10-08
DESCRIPTION | 6 MD5 | 104 +++--- R/ComDim.R | 598 ++++++++++++++++++------------------- R/MBPCA.R | 584 ++++++++++++++++++------------------ R/MBPLS.R | 756 +++++++++++++++++++++++------------------------ R/MBValidation.R | 418 ++++++++++++------------- R/MBWCov.R | 804 +++++++++++++++++++++++++------------------------- R/MBplotBlocks.R | 392 ++++++++++++------------ R/MBplotScores.R | 280 ++++++++--------- R/MBplotVars.R | 444 +++++++++++++-------------- R/coef.MBPLS.R | 78 ++-- R/coef.MBWCov.R | 72 ++-- R/ham-data.R | 2 R/plot.ComDim.R | 2 R/plot.MBPCA.R | 2 R/plot.MBPLS.R | 2 R/plot.MBWCov.R | 2 R/predict.MBPLS.R | 2 R/predict.MBWCov.R | 100 +++--- R/print.ComDim.R | 120 +++---- R/print.MBPCA.R | 120 +++---- R/print.MBPLS.R | 142 ++++---- R/print.MBWCov.R | 142 ++++---- R/summary.ComDim.R | 7 R/summary.MBPCA.R | 7 R/summary.MBPLS.R | 7 R/summary.MBWCov.R | 7 build/partial.rdb |binary man/ComDim.Rd | 2 man/MBPCA.Rd | 2 man/MBPLS.Rd | 2 man/MBValidation.Rd | 2 man/MBWCov.Rd | 2 man/MBplotBlocks.Rd | 2 man/MBplotScores.Rd | 2 man/MBplotVars.Rd | 2 man/coef.MBPLS.Rd | 2 man/coef.MBWCov.Rd | 2 man/ham.Rd | 2 man/plot.ComDim.Rd | 2 man/plot.MBPCA.Rd | 2 man/plot.MBPLS.Rd | 2 man/plot.MBWCov.Rd | 2 man/predict.MBPLS.Rd | 2 man/predict.MBWCov.Rd | 2 man/print.ComDim.Rd | 4 man/print.MBPCA.Rd | 4 man/print.MBPLS.Rd | 4 man/print.MBWCov.Rd | 4 man/summary.ComDim.Rd | 2 man/summary.MBPCA.Rd | 2 man/summary.MBPLS.Rd | 2 man/summary.MBWCov.Rd | 2 53 files changed, 2635 insertions(+), 2623 deletions(-)
Title: Count Transformation Models
Description: Count transformation models featuring
parameters interpretable as discrete hazard ratios, odds ratios,
reverse-time discrete hazard ratios, or transformed expectations.
An appropriate data transformation for a count outcome and
regression coefficients are simultaneously estimated by maximising
the exact discrete log-likelihood using the computational framework
provided in package 'mlt', technical details are given in
Siegfried & Hothorn (2020) <DOI:10.1111/2041-210X.13383>.
The package also contains an experimental implementation of
multivariate count transformation models with an application
to multi-species distribution models <DOI:10.48550/arXiv.2201.13095>.
Author: Sandra Siegfried [aut, cre] ,
Luisa Barbanti [aut] ,
Torsten Hothorn [aut]
Maintainer: Sandra Siegfried <sandra.siegfried@alumni.uzh.ch>
Diff between cotram versions 0.5-2 dated 2024-09-18 and 0.5-3 dated 2025-10-08
cotram-0.5-2/cotram/tests/confband-Ex.Rout.save |only cotram-0.5-3/cotram/DESCRIPTION | 15 ++++++++------- cotram-0.5-3/cotram/MD5 | 13 ++++++------- cotram-0.5-3/cotram/R/predict.R | 10 ++++------ cotram-0.5-3/cotram/build/partial.rdb |binary cotram-0.5-3/cotram/build/vignette.rds |binary cotram-0.5-3/cotram/inst/NEWS.Rd | 6 ++++++ cotram-0.5-3/cotram/inst/doc/cotram.pdf |binary 8 files changed, 24 insertions(+), 20 deletions(-)
Title: Wavelet Variance
Description: Provides a series of tools to compute and plot quantities related to classical and robust wavelet variance for time series and regular lattices. More details can be found, for example, in Serroukh, A., Walden, A.T., & Percival, D.B. (2000) <doi:10.2307/2669537> and Guerrier, S. & Molinari, R. (2016) <doi:10.48550/arXiv.1607.05858>.
Author: Stephane Guerrier [aut, cre],
James Balamuta [aut],
Justin Lee [aut],
Roberto Molinari [aut],
Yuming Zhang [aut],
Mucyo Karemera [aut],
Nathanael Claussen [ctb],
Haotian Xu [ctb],
Lionel Voirol [ctb]
Maintainer: Stephane Guerrier <stef.guerrier@gmail.com>
Diff between wv versions 0.1.2 dated 2023-08-31 and 0.1.3 dated 2025-10-08
DESCRIPTION | 11 ++++------ MD5 | 32 ++++++++++++++--------------- NEWS.md | 5 ++++ R/RcppExports.R | 34 ++++++++++--------------------- README.md | 16 ++++++-------- man/batch_modwt_wvar_cpp.Rd | 8 ++----- man/ci_eta3.Rd | 10 +++------ man/ci_eta3_robust.Rd | 4 --- man/ci_wave_variance.Rd | 4 --- man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/modwt_wvar_cpp.Rd | 4 --- man/wv.Rd | 2 - man/wvar_cpp.Rd | 4 --- src/rtoarmadillo.cpp | 4 +-- src/wave_variance.cpp | 34 ++++++++++--------------------- 17 files changed, 69 insertions(+), 103 deletions(-)
Title: Transformation Boosting Machines
Description: Boosting the likelihood of conditional and shift transformation models as introduced in <DOI:10.1007/s11222-019-09870-4>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tbm versions 0.3-7 dated 2025-04-09 and 0.3-8 dated 2025-10-08
tbm-0.3-7/tbm/tests/bodyfat.Rout.save |only tbm-0.3-8/tbm/DESCRIPTION | 11 ++++++----- tbm-0.3-8/tbm/MD5 | 9 ++++----- tbm-0.3-8/tbm/build/vignette.rds |binary tbm-0.3-8/tbm/inst/NEWS.Rd | 6 ++++++ tbm-0.3-8/tbm/inst/doc/tbm_supplement.pdf |binary 6 files changed, 16 insertions(+), 10 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.1-10 dated 2024-11-19 and 1.1-11 dated 2025-10-08
mlt.docreg-1.1-10/mlt.docreg/tests/AFT-Ex.Rout.save |only mlt.docreg-1.1-10/mlt.docreg/tests/KM-Ex.Rout.save |only mlt.docreg-1.1-10/mlt.docreg/tests/faithful.Rout.save |only mlt.docreg-1.1-10/mlt.docreg/tests/orm-Ex.Rout.save |only mlt.docreg-1.1-10/mlt.docreg/tests/timedep_covar.Rout.save |only mlt.docreg-1.1-10/mlt.docreg/tests/truncreg-Ex.Rout.save |only mlt.docreg-1.1-11/mlt.docreg/DESCRIPTION | 11 +++---- mlt.docreg-1.1-11/mlt.docreg/MD5 | 20 ++++--------- mlt.docreg-1.1-11/mlt.docreg/build/vignette.rds |binary mlt.docreg-1.1-11/mlt.docreg/inst/NEWS.Rd | 8 ++++- mlt.docreg-1.1-11/mlt.docreg/inst/doc/mlt.pdf |binary mlt.docreg-1.1-11/mlt.docreg/tests/AFT-Ex.R | 1 mlt.docreg-1.1-11/mlt.docreg/tests/orm-Ex.R | 3 - mlt.docreg-1.1-11/mlt.docreg/vignettes/mlt.bib | 9 +++-- 14 files changed, 28 insertions(+), 24 deletions(-)
Title: Hierarchical Partitioning of Marginal R2 for Generalized
Mixed-Effect Models
Description: Conducts hierarchical partitioning to calculate individual contributions of each predictor (fixed effects) towards marginal R2 for generalized linear mixed-effect model (including lm, glm and glmm) based on output of r.squaredGLMM() in 'MuMIn', applying the algorithm of Lai J.,Zou Y., Zhang S.,Zhang X.,Mao L.(2022)glmm.hp: an R package for computing individual effect of predictors in generalized linear mixed models.Journal of Plant Ecology,15(6)1302-1307<doi:10.1093/jpe/rtac096>.
Author: Jiangshan Lai [aut, cre] ,
Kim Nimon [aut],
Yao Liu [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between glmm.hp versions 0.1-8 dated 2025-03-24 and 1.0-0 dated 2025-10-08
DESCRIPTION | 11 ++++++----- MD5 | 6 ++++-- NAMESPACE | 2 ++ R/detect_glm_family.r |only man/detect_glm_family.Rd |only 5 files changed, 12 insertions(+), 7 deletions(-)
Title: High Dimensional Data Visualization
Description: It provides materials (i.e. 'serial axes' objects, Andrew's plot, various glyphs for scatter plot) to visualize high dimensional data.
Author: Zehao Xu [aut, cre],
R. Wayne Oldford [aut],
Teun van den Brand [ctb]
Maintainer: Zehao Xu <z267xu@gmail.com>
Diff between ggmulti versions 1.0.7 dated 2024-04-09 and 1.0.8 dated 2025-10-08
DESCRIPTION | 16 ++--- MD5 | 88 +++++++++++++-------------- NAMESPACE | 4 - R/coord-serialaxes.R | 9 ++ R/geom-density-.R | 2 R/geom-hist-.R | 2 R/geom-image-glyph.R | 4 - R/geom-polygon-glyph.R | 5 - R/geom-quantiles.R | 2 R/geom-serialaxes-density.R | 4 - R/geom-serialaxes-glyph.R | 4 - R/geom-serialaxes-hist.R | 4 - R/geom-serialaxes-quantile.R | 15 ++-- R/geom-serialaxes.R | 8 +- R/position-dodge-.R | 10 +-- R/position-identity-.R | 4 - R/position-stack-.R | 14 ++-- R/stat-hist-.R | 6 - R/stat-serialaxes-hist.R | 3 R/stat-serialaxes.R | 4 - R/unexported_ggplot2_functions.R | 1 R/utils-geom.R | 2 inst/doc/glyph.R | 4 - inst/doc/glyph.Rmd | 4 - inst/doc/glyph.html | 24 +++---- inst/doc/highDim.html | 12 +-- inst/doc/histogram-density-.Rmd | 2 inst/doc/histogram-density-.html | 12 +-- man/geom_density_.Rd | 64 +++++++++++++++----- man/geom_hist_.Rd | 53 +++++++++++----- man/geom_image_glyph.Rd | 73 ++++++++++++++++++----- man/geom_polygon_glyph.Rd | 73 ++++++++++++++++++----- man/geom_quantiles.Rd | 55 +++++++++++++---- man/geom_serialaxes.Rd | 88 +++++++++++++++++++++------ man/geom_serialaxes_density.Rd | 91 ++++++++++++++++++++++------ man/geom_serialaxes_glyph.Rd | 73 ++++++++++++++++++----- man/geom_serialaxes_hist.Rd | 101 +++++++++++++++++++++++--------- man/geom_serialaxes_quantile.Rd | 88 +++++++++++++++++++++------ man/ggmulti-package.Rd | 7 +- man/position_dodge_.Rd | 26 +++++++- man/position_stack_.Rd | 4 - tests/testthat/test_generalized_geoms.R | 2 tests/testthat/test_glyphs.R | 4 - vignettes/glyph.Rmd | 4 - vignettes/histogram-density-.Rmd | 2 45 files changed, 755 insertions(+), 322 deletions(-)
Title: Penalized Transformation Models
Description: Partially penalized versions of specific transformation models
implemented in package 'mlt'. Available models include a fully parametric version
of the Cox model, other parametric survival models (Weibull, etc.), models for
binary and ordered categorical variables, normal and transformed-normal (Box-Cox type)
linear models, and continuous outcome logistic regression. Hyperparameter tuning
is facilitated through model-based optimization functionalities from package 'mlrMBO'.
The accompanying vignette describes the methodology used in 'tramnet' in detail.
Transformation models and model-based optimization are described in
Hothorn et al. (2019) <doi:10.1111/sjos.12291> and
Bischl et al. (2016) <doi:10.48550/arXiv.1703.03373>, respectively.
Author: Lucas Kook [cre, aut],
Balint Tamasi [ctb],
Sandra Siegfried [ctb],
Samuel Pawel [ctb],
Torsten Hothorn [ctb]
Maintainer: Lucas Kook <lucasheinrich.kook@gmail.com>
Diff between tramnet versions 0.0-8 dated 2023-03-10 and 0.0-9 dated 2025-10-08
tramnet-0.0-8/tramnet/tests/Colr-pen.Rout.save |only tramnet-0.0-9/tramnet/DESCRIPTION | 12 ++++++------ tramnet-0.0-9/tramnet/MD5 | 7 +++---- tramnet-0.0-9/tramnet/build/vignette.rds |binary tramnet-0.0-9/tramnet/inst/doc/tramnet.pdf |binary 5 files changed, 9 insertions(+), 10 deletions(-)
Title: Track 'ggplot2' Calls
Description: Provides a way to log 'ggplot' component calls, which can be
useful for debugging and understanding how 'ggplot' objects are created.
The logged calls can be printed, saved, and re-executed to reproduce the
original 'ggplot' object.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between gglogger versions 0.1.6 dated 2025-06-19 and 0.1.7 dated 2025-10-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/gglogger.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Draw Venn Diagram by 'ggplot2'
Description: An easy-to-use way to draw pretty Venn diagrams using 'ggplot2'.
This package provides functions to create Venn diagrams with customizable
colors, labels, and styling options.
Author: Linlin Yan [aut, cre]
Maintainer: Linlin Yan <yanlinlin82@gmail.com>
Diff between ggvenn versions 0.1.10 dated 2023-03-30 and 0.1.18 dated 2025-10-08
ggvenn-0.1.10/ggvenn/R/data_frame_to_list.R |only ggvenn-0.1.10/ggvenn/R/list_to_data_frame.R |only ggvenn-0.1.10/ggvenn/man/data_frame_to_list.Rd |only ggvenn-0.1.10/ggvenn/man/figures |only ggvenn-0.1.10/ggvenn/man/list_to_data_frame.Rd |only ggvenn-0.1.18/ggvenn/DESCRIPTION | 22 ggvenn-0.1.18/ggvenn/MD5 | 47 + ggvenn-0.1.18/ggvenn/NAMESPACE | 11 ggvenn-0.1.18/ggvenn/NEWS.md |only ggvenn-0.1.18/ggvenn/R/data_preparation.R |only ggvenn-0.1.18/ggvenn/R/geom_venn.R | 396 +++++++++----- ggvenn-0.1.18/ggvenn/R/ggvenn-package.R |only ggvenn-0.1.18/ggvenn/R/ggvenn.R | 676 +++++++------------------ ggvenn-0.1.18/ggvenn/R/globals.R | 31 - ggvenn-0.1.18/ggvenn/R/venn_geometry.R |only ggvenn-0.1.18/ggvenn/README.md | 11 ggvenn-0.1.18/ggvenn/man/data_preparation.Rd |only ggvenn-0.1.18/ggvenn/man/geom_venn.Rd | 118 +++- ggvenn-0.1.18/ggvenn/man/get_venn_table.Rd |only ggvenn-0.1.18/ggvenn/man/ggvenn-package.Rd |only ggvenn-0.1.18/ggvenn/man/ggvenn.Rd | 75 +- ggvenn-0.1.18/ggvenn/tests |only 22 files changed, 676 insertions(+), 711 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>).
Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.1080/00031305.2023.2203177>) can be fitted as well. The package contains an implementation of
a doubly robust score test, [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [ctb] ,
Sandra Siegfried [aut] ,
Lucas Kook [aut] ,
Susanne Dandl [ctb] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.2-4 dated 2025-09-23 and 1.2-5 dated 2025-10-08
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- R/methods.R | 8 ++++++-- cleanup |only inst/NEWS.Rd | 6 ++++++ inst/doc/NAMI.pdf |binary inst/doc/mtram.pdf |binary inst/doc/survtram.pdf |binary inst/doc/tram.pdf |binary 9 files changed, 24 insertions(+), 13 deletions(-)
Title: Tools for Creating, Updating, and Analyzing Survey Replicate
Weights
Description: Provides tools for creating and working with survey replicate weights,
extending functionality of the 'survey' package from Lumley (2004) <doi:10.18637/jss.v009.i08>.
Implements bootstrap methods for complex surveys, including the generalized survey bootstrap
as described by Beaumont and Patak (2012) <doi:10.1111/j.1751-5823.2011.00166.x>.
Methods are provided for applying nonresponse adjustments to
both full-sample and replicate weights as described by
Rust and Rao (1996) <doi:10.1177/096228029600500305>.
Implements methods for sample-based calibration described by Opsomer and Erciulescu (2021)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2021002/article/00006-eng.htm>.
Diagnostic functions are included to compare weights and weighted estimates
from different sets of replicate weights.
Author: Ben Schneider [aut, cre]
Maintainer: Ben Schneider <benjamin.julius.schneider@gmail.com>
Diff between svrep versions 0.9.0 dated 2025-09-20 and 0.9.1 dated 2025-10-08
DESCRIPTION | 6 MD5 | 20 NEWS.md | 418 +-- R/bootstrap_helpers.R | 7 README.md | 2 inst/CITATION | 4 man/estimate_boot_sim_cv.Rd | 4 tests/testthat/test-add_inactive_replicates.R | 294 +- tests/testthat/test-bootstrap-helpers.R | 19 tests/testthat/test-fays-generalized-replication.R | 1134 +++++----- tests/testthat/test-quadratic_forms_of_survey_design_objects.R | 544 ++-- 11 files changed, 1222 insertions(+), 1230 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 4.1.0 dated 2025-08-29 and 4.1.1 dated 2025-10-08
DESCRIPTION | 8 - MD5 | 51 +++++------ NAMESPACE | 2 NEWS.md | 19 ++++ R/err.R | 15 +++ R/mu-cov-downgrade.R | 2 R/mu.R | 8 + R/rxShiny.R | 4 R/rxStack.R | 36 ++++++- R/rxUiGet.R | 2 R/rxode2_md5.R | 2 R/rxsolve.R | 8 - R/symengine.R | 6 - inst/doc/rxode2-syntax.html | 28 +++--- inst/include/rxode2_model_shared.h | 9 + inst/include/rxode2parseVer.h | 4 man/dot-getErrDist.Rd |only man/rxStack.Rd | 6 + src/etTran.cpp | 18 ++- src/par_solve.cpp | 6 - src/parseVars.h | 3 src/tran.c | 4 tests/testthat/test-etTrans.R | 167 ++++++++++++++++++++++++++++++++++++- tests/testthat/test-mix.R | 9 + tests/testthat/test-occ.R | 34 +++++++ tests/testthat/test-ui-assert.R | 10 -- tests/testthat/test-ui-props.R | 43 +++++++++ 27 files changed, 422 insertions(+), 82 deletions(-)
Title: Render Sequence Plots using 'ggplot2'
Description: A set of wrapper functions that mainly re-produces most of the
sequence plots rendered with TraMineR::seqplot(). Whereas 'TraMineR' uses base
R to produce the plots this library draws on 'ggplot2'.
The plots are produced on the basis of a sequence object defined
with TraMineR::seqdef(). The package automates the reshaping and plotting
of sequence data. Resulting plots are of class 'ggplot', i.e. components
can be added and tweaked using '+' and regular 'ggplot2' functions.
Author: Marcel Raab [aut, cre]
Maintainer: Marcel Raab <marcel.raab@gmail.com>
Diff between ggseqplot versions 0.8.7 dated 2025-06-30 and 0.8.8 dated 2025-10-08
ggseqplot-0.8.7/ggseqplot/tests/testthat/test-internal_helper.R |only ggseqplot-0.8.8/ggseqplot/DESCRIPTION | 13 ggseqplot-0.8.8/ggseqplot/MD5 | 41 ggseqplot-0.8.8/ggseqplot/NAMESPACE | 1 ggseqplot-0.8.8/ggseqplot/NEWS.md | 142 - ggseqplot-0.8.8/ggseqplot/R/ggseqdplot.R | 752 ++--- ggseqplot-0.8.8/ggseqplot/R/ggseqeplot.R | 8 ggseqplot-0.8.8/ggseqplot/R/ggseqfplot.R | 17 ggseqplot-0.8.8/ggseqplot/R/ggseqiplot.R | 38 ggseqplot-0.8.8/ggseqplot/R/ggseqmsplot.R | 23 ggseqplot-0.8.8/ggseqplot/R/ggseqmtplot.R | 23 ggseqplot-0.8.8/ggseqplot/R/ggseqrfplot.R | 81 ggseqplot-0.8.8/ggseqplot/R/ggseqrplot.R | 52 ggseqplot-0.8.8/ggseqplot/R/ggseqtrplot.R | 15 ggseqplot-0.8.8/ggseqplot/R/internal_helpers.R | 20 ggseqplot-0.8.8/ggseqplot/build/partial.rdb |binary ggseqplot-0.8.8/ggseqplot/build/vignette.rds |binary ggseqplot-0.8.8/ggseqplot/inst/CITATION | 20 ggseqplot-0.8.8/ggseqplot/inst/doc/ggseqplot.R | 37 ggseqplot-0.8.8/ggseqplot/inst/doc/ggseqplot.Rmd | 1293 +++++----- ggseqplot-0.8.8/ggseqplot/inst/doc/ggseqplot.html | 120 ggseqplot-0.8.8/ggseqplot/vignettes/ggseqplot.Rmd | 1293 +++++----- 22 files changed, 2018 insertions(+), 1971 deletions(-)
Title: Kernel Ridge Regression using 'RcppArmadillo'
Description: Provides core computational operations in C++ via 'RcppArmadillo', enabling faster performance than pure R, improved numerical stability, and parallel execution with OpenMP where available. On systems without OpenMP support, the package automatically falls back to single-threaded execution with no user configuration required. For efficient model selection, it integrates with 'CVST' to provide sequential-testing cross-validation that identifies competitive hyperparameters without exhaustive grid search. The package offers a unified interface for exact kernel ridge regression and three scalable approximations—Nyström, Pivoted Cholesky, and Random Fourier Features—allowing analyses with substantially larger sample sizes than are feasible with exact KRR. It also integrates with the 'tidymodels' ecosystem via the 'parsnip' model specification 'krr_reg', and the S3 method tunable.krr_reg(). To understand the theoretical background, one can refer to Wainwright (2019) <doi:10.1017/978110862 [...truncated...]
Author: Gyeongmin Kim [aut] ,
Seyoung Lee [aut] ,
Miyoung Jang [aut] ,
Kwan-Young Bak [aut, cre, cph]
Maintainer: Kwan-Young Bak <kybak@sungshin.ac.kr>
Diff between FastKRR versions 0.1.0 dated 2025-09-22 and 0.1.1 dated 2025-10-08
FastKRR-0.1.0/FastKRR/R/make_Z.R |only FastKRR-0.1.0/FastKRR/man/fit_krr.Rd |only FastKRR-0.1.0/FastKRR/man/make_Z.Rd |only FastKRR-0.1.0/FastKRR/man/pred_krr.Rd |only FastKRR-0.1.0/FastKRR/man/rff_random.Rd |only FastKRR-0.1.1/FastKRR/DESCRIPTION | 10 FastKRR-0.1.1/FastKRR/MD5 | 49 - FastKRR-0.1.1/FastKRR/NAMESPACE | 12 FastKRR-0.1.1/FastKRR/R/CVST_linkfunction.R | 295 +++++----- FastKRR-0.1.1/FastKRR/R/FastKRR-package.R | 4 FastKRR-0.1.1/FastKRR/R/RcppExports.R | 4 FastKRR-0.1.1/FastKRR/R/approx_kernel.R | 188 +++--- FastKRR-0.1.1/FastKRR/R/link2tidymodels.R | 137 ---- FastKRR-0.1.1/FastKRR/R/make_kernel.R | 25 FastKRR-0.1.1/FastKRR/R/print.R |only FastKRR-0.1.1/FastKRR/R/rff_random.R | 49 - FastKRR-0.1.1/FastKRR/README.md | 79 +- FastKRR-0.1.1/FastKRR/man/FastKRR-package.Rd | 2 FastKRR-0.1.1/FastKRR/man/approx_kernel.Rd | 128 ++-- FastKRR-0.1.1/FastKRR/man/fastkrr.Rd | 75 +- FastKRR-0.1.1/FastKRR/man/figures/README-unnamed-chunk-4-1.png |only FastKRR-0.1.1/FastKRR/man/krr_reg.Rd | 4 FastKRR-0.1.1/FastKRR/man/make_kernel.Rd | 23 FastKRR-0.1.1/FastKRR/man/predict.krr.Rd |only FastKRR-0.1.1/FastKRR/man/print.approx_kernel.Rd |only FastKRR-0.1.1/FastKRR/man/print.kernel_matrix.Rd |only FastKRR-0.1.1/FastKRR/man/print.krr.Rd |only FastKRR-0.1.1/FastKRR/src/RcppExports.cpp | 15 FastKRR-0.1.1/FastKRR/src/kernel.cpp | 8 FastKRR-0.1.1/FastKRR/src/pchol.cpp | 3 FastKRR-0.1.1/FastKRR/src/rff.cpp | 12 31 files changed, 526 insertions(+), 596 deletions(-)
Title: Water Quality Analysis Tools for the Brazilian Context
Description: Tools to import, clean, validate, and analyze freshwater quality data in Brazil.
Implements water quality indices including the Water Quality Index (WQI/IQA),
the Trophic State Index (TSI/IET) after Carlson (1977) <doi:10.4319/lo.1977.22.2.0361>
and Lamparelli (2004) <https://www.teses.usp.br/teses/disponiveis/41/41134/tde-20032006-075813/publico/TeseLamparelli2004.pdf>,
and the National Sanitation Foundation Water Quality Index (NSF WQI)
<doi:10.1007/s11157-023-09650-7>. The package also checks
compliance with Brazilian standard CONAMA Resolution 357/2005
<https://conama.mma.gov.br/?id=450&option=com_sisconama&task=arquivo.download>
and generates reproducible reports for routine monitoring workflows.
Author: Vinicius Saraiva Santos [aut, cre]
Maintainer: Vinicius Saraiva Santos <vinisaraiva@gmail.com>
Diff between tikatuwq versions 0.5.1 dated 2025-10-01 and 0.6.2 dated 2025-10-07
DESCRIPTION | 6 - MD5 | 18 +++-- NAMESPACE | 11 +++ NEWS.md | 23 +++++++ R/analysis_text.R | 57 +++++++++++------- R/plot_trend.R |only R/trend_param.R |only README.md | 117 ++++++++++++++++++++++++-------------- man/generate_analysis.Rd | 25 ++++---- man/plot_trend.Rd |only man/trend_param.Rd |only tests/testthat/test-plot_trend.R |only tests/testthat/test-trend_param.R |only 13 files changed, 174 insertions(+), 83 deletions(-)
Title: Satellite Image Time Series Analysis for Earth Observation Data
Cubes
Description: An end-to-end toolkit for land use and land cover classification
using big Earth observation data. Builds satellite image data cubes from cloud collections.
Supports visualization methods for images and time series and
smoothing filters for dealing with noisy time series.
Enables merging of multi-source imagery (SAR, optical, DEM).
Includes functions for quality assessment of training samples using self-organized maps and
to reduce training samples imbalance. Provides machine learning algorithms including support vector machines,
random forests, extreme gradient boosting, multi-layer perceptrons,
temporal convolution neural networks, and temporal attention encoders.
Performs efficient classification of big Earth observation data cubes and includes
functions for post-classification smoothing based on Bayesian inference.
Enables best practices for estimating area and assessing accuracy of land change.
Includes object-based spatio-temporal segmentation for space-time OBIA.
Minimum recomme [...truncated...]
Author: Rolf Simoes [aut],
Gilberto Camara [aut, cre, ths],
Felipe Souza [aut],
Felipe Carlos [aut],
Lorena Santos [ctb],
Charlotte Pelletier [ctb],
Estefania Pizarro [ctb],
Karine Ferreira [ctb, ths],
Alber Sanchez [ctb],
Alexandre Assuncao [ctb],
Daniel Fa [...truncated...]
Maintainer: Gilberto Camara <gilberto.camara.inpe@gmail.com>
Diff between sits versions 1.5.3-1 dated 2025-09-03 and 1.5.3-2 dated 2025-10-07
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- R/sits_lstm_fcn.R | 1 + src/smooth.cpp | 4 ++-- tests/testthat/Rplots.pdf |only tests/testthat/test-ml.R | 2 -- 6 files changed, 12 insertions(+), 12 deletions(-)
Title: Incremental Calculation of Dynamic Time Warping
Description: The Dynamic Time Warping (DTW) distance measure for time series allows non-linear alignments of time series to match similar patterns in time series of different lengths and or different speeds. IncDTW is characterized by (1) the incremental calculation of DTW (reduces runtime complexity to a linear level for updating the DTW distance) - especially for life data streams or subsequence matching, (2) the vector based implementation of DTW which is faster because no matrices are allocated (reduces the space complexity from a quadratic to a linear level in the number of observations) - for all runtime intensive DTW computations, (3) the subsequence matching algorithm runDTW, that efficiently finds the k-NN to a query pattern in a long time series, and (4) C++ in the heart. For details about DTW see the original paper "Dynamic programming algorithm optimization for spoken word recognition" by Sakoe and Chiba (1978) <DOI:10.1109/TASSP.1978.1163055>. For details about this package, Dyn [...truncated...]
Author: Maximilian Leodolter [aut, cre]
Maintainer: Maximilian Leodolter <maximilian.leodolter@gmail.com>
Diff between IncDTW versions 1.1.4.4 dated 2022-03-16 and 1.1.4.5 dated 2025-10-07
DESCRIPTION | 12 +- MD5 | 12 +- NEWS.md | 288 ++++++++++++++++++++++++++--------------------------- build/partial.rdb |binary man/drink_glass.Rd | 96 ++++++++--------- src/Makevars | 2 src/Makevars.win | 2 7 files changed, 207 insertions(+), 205 deletions(-)
Title: Makes 'R' Easier for Everyone
Description: A meta-package that aims to make 'R' easier for everyone,
especially programmers who have a background in 'SAS®' software.
This set of packages brings many useful concepts to 'R', including
data libraries, data dictionaries, formats
and format catalogs, a data step, and a traceable log. The system
also includes a package that replicates several commonly-used 'SAS®' procedures,
like 'PROC FREQ', 'PROC MEANS', and 'PROC REG'.
Author: David Bosak [aut, cre]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between sassy versions 1.2.8 dated 2025-09-10 and 1.2.9 dated 2025-10-07
DESCRIPTION | 6 +- MD5 | 116 +++++++++++++++++++++---------------------- NEWS.md | 5 + R/oq.R | 4 - README.md | 3 - build/vignette.rds |binary inst/doc/sassy-ae.Rmd | 6 +- inst/doc/sassy-ae.html | 11 ++-- inst/doc/sassy-ae2.Rmd | 2 inst/doc/sassy-ae2.html | 7 +- inst/doc/sassy-chgbase.Rmd | 2 inst/doc/sassy-chgbase.html | 7 +- inst/doc/sassy-dm.Rmd | 2 inst/doc/sassy-dm.html | 7 +- inst/doc/sassy-ds.Rmd | 2 inst/doc/sassy-ds.html | 7 +- inst/doc/sassy-figure.Rmd | 6 +- inst/doc/sassy-figure.html | 11 ++-- inst/doc/sassy-figureby.Rmd | 6 +- inst/doc/sassy-figureby.html | 11 ++-- inst/doc/sassy-forest.Rmd | 2 inst/doc/sassy-forest.html | 7 +- inst/doc/sassy-intext.Rmd | 8 +- inst/doc/sassy-intext.html | 13 ++-- inst/doc/sassy-listing.Rmd | 2 inst/doc/sassy-listing.html | 7 +- inst/doc/sassy-pfigure.Rmd | 2 inst/doc/sassy-pfigure.html | 7 +- inst/doc/sassy-plisting.Rmd | 2 inst/doc/sassy-plisting.html | 7 +- inst/doc/sassy-profile.Rmd | 2 inst/doc/sassy-profile.html | 7 +- inst/doc/sassy-shift.Rmd | 2 inst/doc/sassy-shift.html | 7 +- inst/doc/sassy-survival.Rmd | 4 - inst/doc/sassy-survival.html | 9 +-- inst/doc/sassy-vs.Rmd | 2 inst/doc/sassy-vs.html | 7 +- inst/doc/sassy.Rmd | 34 ++++++------ inst/doc/sassy.html | 54 ++++++++++++-------- man/run_oq.Rd | 4 - tests/testthat/test-oq.R | 15 ++--- vignettes/sassy-ae.Rmd | 6 +- vignettes/sassy-ae2.Rmd | 2 vignettes/sassy-chgbase.Rmd | 2 vignettes/sassy-dm.Rmd | 2 vignettes/sassy-ds.Rmd | 2 vignettes/sassy-figure.Rmd | 6 +- vignettes/sassy-figureby.Rmd | 6 +- vignettes/sassy-forest.Rmd | 2 vignettes/sassy-intext.Rmd | 8 +- vignettes/sassy-listing.Rmd | 2 vignettes/sassy-pfigure.Rmd | 2 vignettes/sassy-plisting.Rmd | 2 vignettes/sassy-profile.Rmd | 2 vignettes/sassy-shift.Rmd | 2 vignettes/sassy-survival.Rmd | 4 - vignettes/sassy-vs.Rmd | 2 vignettes/sassy.Rmd | 34 ++++++------ 59 files changed, 272 insertions(+), 239 deletions(-)
Title: Link Interactive Plots and Tables in 'shiny' Applications
Description: Build powerful, linked-view dashboards in 'shiny' applications. With a
declarative, one-line setup, you can create bidirectional links between
interactive components. When a user interacts with one element (e.g., clicking
a map marker), all linked components (such as 'DT' tables or other charts)
instantly update. Supports 'leaflet' maps, 'DT' tables, 'plotly' charts, and spatial data
via 'sf' objects out-of-the-box, with an extensible API for custom components.
Author: Jake Wagoner [aut, cre] ,
Centers for Disease Control and Prevention's Center for Forecasting and
Outbreak Analytics [fnd]
Maintainer: Jake Wagoner <jakew@sci.utah.edu>
Diff between linkeR versions 0.1.2 dated 2025-09-21 and 0.1.3 dated 2025-10-07
DESCRIPTION | 8 - MD5 | 51 ++++-- NAMESPACE | 3 NEWS.md | 9 + R/dt.R | 4 R/plotly.R |only R/registry.R | 19 ++ R/simple_api.R | 25 +++ README.md | 20 ++ build/vignette.rds |binary inst/doc/getting-started.Rmd | 5 inst/doc/getting-started.html | 8 - inst/doc/multiple-components.R | 67 +------- inst/doc/multiple-components.Rmd | 72 +-------- inst/doc/multiple-components.html | 235 ++++++++++++------------------- inst/doc/using-plotly.R |only inst/doc/using-plotly.Rmd |only inst/doc/using-plotly.html |only inst/examples/automatic_plotly_linking.R |only inst/examples/complex_linking_app.R | 29 +-- inst/examples/sf_app.R | 4 inst/examples/vignette-test.R |only man/apply_default_plotly_behavior.Rd |only man/extract_plotly_id.Rd |only man/link_plots.Rd | 5 man/prepare_plotly_linking.Rd |only man/register_plotly.Rd |only man/setup_plotly_observers.Rd |only man/smart_coordinate_lookup.Rd |only man/update_plotly_selection.Rd |only tests/testthat/test-plotly.R |only vignettes/getting-started.Rmd | 5 vignettes/multiple-components.Rmd | 72 +-------- vignettes/using-plotly.Rmd |only 34 files changed, 271 insertions(+), 370 deletions(-)
Title: Exploratory Data Analysis, Group Comparison Tools, and Other
Procedures
Description: Provides a comprehensive set of tools for descriptive statistics,
graphical data exploration, outlier detection, homoscedasticity testing, and
multiple comparison procedures. Includes manual implementations of Levene's test,
Bartlett's test, and the Fligner-Killeen test, as well as post hoc comparison
methods such as Tukey, Scheffé, Games-Howell, Brunner-Munzel, and others.
This version introduces two new procedures: the Jonckheere-Terpstra trend test
and the Jarque-Bera test with Glinskiy's (2024) correction. Designed for use in
teaching, applied statistical analysis, and reproducible research.
Additionally you can find a post hoc Test Planner, which helps you to make a
decision on which procedure is most suitable.
Author: Carlos Jimenez-Gallardo [aut, cre]
Maintainer: Carlos Jimenez-Gallardo <carlos.jimenez@ufrontera.cl>
Diff between Analitica versions 2.0.0 dated 2025-09-26 and 2.1.2 dated 2025-10-07
DESCRIPTION | 14 + MD5 | 22 +-- NAMESPACE | 14 + R/LeveneTest.R | 290 +++++++++++++++++++++++++++++----------- R/MauchlyTest.R |only R/plot_comparations.R | 2 R/posthoc_planner.R | 290 ++++++++++++++++++++++------------------ R/summary_homocedasticidad.R | 88 ++++++++++-- inst/doc/Analitica-intro.html | 156 ++++++++++++--------- man/Levene.Test.Rd | 41 ++++- man/MauchlyTest.Rd |only man/Posthoc_planner.Rd | 86 ++++------- man/summary.homocedasticidad.Rd | 11 - 13 files changed, 647 insertions(+), 367 deletions(-)
Title: Provides a 'PySpark' Back-End for the 'sparklyr' Package
Description: It enables 'sparklyr' to integrate with 'Spark Connect', and
'Databricks Connect' by providing a wrapper over the 'PySpark' 'python'
library.
Author: Edgar Ruiz [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Edgar Ruiz <edgar@posit.co>
Diff between pysparklyr versions 0.1.8 dated 2025-05-19 and 0.1.9 dated 2025-10-07
DESCRIPTION | 12 ++--- MD5 | 20 ++++---- NAMESPACE | 3 + NEWS.md | 14 ++++++ R/data-write.R | 18 +++++++ R/package.R | 3 - R/python-import-check.R | 67 +++++++++++++++++----------- R/sparklyr-spark-connect.R | 5 ++ R/start-stop-service.R | 18 +++++-- inst/rstudio/shinycon/app.R | 86 +++++++++++++++++++++++++++---------- man/spark_connect_service_start.Rd | 6 +- 11 files changed, 180 insertions(+), 72 deletions(-)
Title: 'Stata' Markdown
Description: Settings and functions to extend the 'knitr' 'Stata' engine.
Author: Doug Hemken [aut, cre] ),
Tom Palmer [ctb] ,
Philipp Lepert [ctb]
Maintainer: Doug Hemken <d_hemken@yahoo.com>
Diff between Statamarkdown versions 0.9.4 dated 2025-08-23 and 0.9.6 dated 2025-10-07
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/find_stata.r | 16 +++++++++++----- 3 files changed, 17 insertions(+), 11 deletions(-)
Title: Factor-Augmented Regression Scenarios
Description: Provides a comprehensive framework in R for modeling and forecasting economic scenarios based on multi-level dynamic factor model. The package enables users to: (i) extract global and group-specific factors using a flexible multi-level factor structure; (ii) compute asymptotically valid confidence regions for the estimated factors, accounting for uncertainty in the factor loadings; (iii) obtain estimates of the parameters of the factor-augmented quantile regressions together with their standard deviations; (iv) recover full predictive conditional densities from estimated quantiles; (v) obtain risk measures based on extreme quantiles of the conditional densities; (vi) estimate the conditional density and the corresponding extreme quantiles when the factors are stressed.
Author: Gian Pietro Bellocca [aut, cre],
Ignacio Garron [aut],
Vladimir Rodriguez-Caballero [aut],
Esther Ruiz [aut]
Maintainer: Gian Pietro Bellocca <gbellocc@est-econ.uc3m.es>
Diff between FARS versions 0.5.0 dated 2025-07-16 and 0.6.0 dated 2025-10-07
FARS-0.5.0/FARS/R/compute_gamma_FPR.R |only FARS-0.5.0/FARS/R/compute_lambda.R |only FARS-0.5.0/FARS/R/plot.fars.R |only FARS-0.5.0/FARS/R/plot.mldfm.R |only FARS-0.5.0/FARS/R/plot_factors.mldfm.R |only FARS-0.5.0/FARS/R/plot_fars_density.R |only FARS-0.5.0/FARS/R/plot_loadings.mldfm.R |only FARS-0.5.0/FARS/R/plot_residuals_mldfm.R |only FARS-0.5.0/FARS/R/print.fars.R |only FARS-0.5.0/FARS/R/print.fars_density.R |only FARS-0.5.0/FARS/R/print.mldfm.R |only FARS-0.5.0/FARS/R/summary.fars.R |only FARS-0.5.0/FARS/R/summary.fars_density.R |only FARS-0.5.0/FARS/R/summary.mldfm.R |only FARS-0.5.0/FARS/inst/doc/Factor_Augmented_Regression_Scenarios_in_R.Rmd |only FARS-0.5.0/FARS/inst/doc/Factor_Augmented_Regression_Scenarios_in_R.html |only FARS-0.5.0/FARS/inst/extdata/DataBase.xlsx |only FARS-0.5.0/FARS/inst/extdata/Data_IMF.xlsx |only FARS-0.5.0/FARS/man/compute_gamma_FPR.Rd |only FARS-0.5.0/FARS/man/compute_lambda.Rd |only FARS-0.5.0/FARS/vignettes/Factor_Augmented_Regression_Scenarios_in_R.Rmd |only FARS-0.5.0/FARS/vignettes/pdf |only FARS-0.6.0/FARS/DESCRIPTION | 18 FARS-0.6.0/FARS/MD5 | 204 +++++----- FARS-0.6.0/FARS/NAMESPACE | 58 ++ FARS-0.6.0/FARS/R/apply_identifications.R | 115 +++-- FARS-0.6.0/FARS/R/beta_ols.R |only FARS-0.6.0/FARS/R/build_factor_structure.R | 24 - FARS-0.6.0/FARS/R/canonical_correlation_analysis.R | 17 FARS-0.6.0/FARS/R/compute_density.R | 50 +- FARS-0.6.0/FARS/R/compute_fars.R | 106 ++--- FARS-0.6.0/FARS/R/compute_fpr_gamma.R |only FARS-0.6.0/FARS/R/compute_initial_factors.R | 72 ++- FARS-0.6.0/FARS/R/compute_loadings.R |only FARS-0.6.0/FARS/R/compute_optimal_delta.R | 7 FARS-0.6.0/FARS/R/compute_stressed_factors.R | 20 FARS-0.6.0/FARS/R/compute_subsample.R | 16 FARS-0.6.0/FARS/R/correct_outliers.R | 4 FARS-0.6.0/FARS/R/create_scenario.R | 179 ++++---- FARS-0.6.0/FARS/R/data_doc.R |only FARS-0.6.0/FARS/R/eigen_sorted.R | 13 FARS-0.6.0/FARS/R/get_distribution.R |only FARS-0.6.0/FARS/R/get_ellipsoids.R |only FARS-0.6.0/FARS/R/get_factors.R | 45 +- FARS-0.6.0/FARS/R/get_level_factors.R |only FARS-0.6.0/FARS/R/get_loadings.R |only FARS-0.6.0/FARS/R/get_mldfm_list.R |only FARS-0.6.0/FARS/R/get_mldfm_model.R |only FARS-0.6.0/FARS/R/get_quantile_levels.R |only FARS-0.6.0/FARS/R/get_quantiles.R |only FARS-0.6.0/FARS/R/get_residuals.R |only FARS-0.6.0/FARS/R/get_sigma_list.R |only FARS-0.6.0/FARS/R/get_stressed_factors.R |only FARS-0.6.0/FARS/R/l_density.R | 37 + FARS-0.6.0/FARS/R/mldfm.R | 52 +- FARS-0.6.0/FARS/R/mldfm_subsampling.R | 31 + FARS-0.6.0/FARS/R/multiple_blocks.R | 144 +++---- FARS-0.6.0/FARS/R/nl_density.R | 37 + FARS-0.6.0/FARS/R/orthogonalize_factors.R | 2 FARS-0.6.0/FARS/R/plot.R |only FARS-0.6.0/FARS/R/print.R |only FARS-0.6.0/FARS/R/q_reg.R | 37 + FARS-0.6.0/FARS/R/quantile_risk.R | 24 - FARS-0.6.0/FARS/R/single_block.R | 73 ++- FARS-0.6.0/FARS/R/summary.R |only FARS-0.6.0/FARS/R/update_factor_list.R | 20 FARS-0.6.0/FARS/README.md | 19 FARS-0.6.0/FARS/build/vignette.rds |binary FARS-0.6.0/FARS/data |only FARS-0.6.0/FARS/inst/doc/Factor_Augmented_Regression_Scenarios_in_R.pdf |only FARS-0.6.0/FARS/inst/doc/Factor_Augmented_Regression_Scenarios_in_R.pdf.asis |only FARS-0.6.0/FARS/inst/extdata/Inflation.xlsx |only FARS-0.6.0/FARS/man/apply_identifications.Rd | 33 + FARS-0.6.0/FARS/man/beta_ols.Rd | 15 FARS-0.6.0/FARS/man/build_factor_structure.Rd | 17 FARS-0.6.0/FARS/man/canonical_correlation_analysis.Rd | 42 -- FARS-0.6.0/FARS/man/compute_density.Rd | 27 - FARS-0.6.0/FARS/man/compute_fars.Rd | 45 +- FARS-0.6.0/FARS/man/compute_fpr_gamma.Rd |only FARS-0.6.0/FARS/man/compute_initial_factors.Rd | 28 + FARS-0.6.0/FARS/man/compute_loadings.Rd |only FARS-0.6.0/FARS/man/compute_optimal_delta.Rd | 8 FARS-0.6.0/FARS/man/compute_stressed_factors.Rd | 20 FARS-0.6.0/FARS/man/compute_subsample.Rd | 22 - FARS-0.6.0/FARS/man/correct_outliers.Rd | 2 FARS-0.6.0/FARS/man/create_scenario.Rd | 23 - FARS-0.6.0/FARS/man/dep_variable.Rd |only FARS-0.6.0/FARS/man/eigen_sorted.Rd | 14 FARS-0.6.0/FARS/man/get_distribution.Rd |only FARS-0.6.0/FARS/man/get_distribution.fars_density.Rd |only FARS-0.6.0/FARS/man/get_ellipsoids.Rd |only FARS-0.6.0/FARS/man/get_ellipsoids.fars_scenario.Rd |only FARS-0.6.0/FARS/man/get_factors.Rd | 15 FARS-0.6.0/FARS/man/get_factors.mldfm.Rd |only FARS-0.6.0/FARS/man/get_level_factors.Rd |only FARS-0.6.0/FARS/man/get_loadings.Rd |only FARS-0.6.0/FARS/man/get_loadings.mldfm.Rd |only FARS-0.6.0/FARS/man/get_mldfm_list.Rd |only FARS-0.6.0/FARS/man/get_mldfm_list.mldfm_subsample.Rd |only FARS-0.6.0/FARS/man/get_mldfm_model.Rd |only FARS-0.6.0/FARS/man/get_mldfm_model.mldfm_subsample.Rd |only FARS-0.6.0/FARS/man/get_quantile_levels.Rd |only FARS-0.6.0/FARS/man/get_quantile_levels.fars.Rd |only FARS-0.6.0/FARS/man/get_quantiles.Rd |only FARS-0.6.0/FARS/man/get_quantiles.fars.Rd |only FARS-0.6.0/FARS/man/get_residuals.Rd |only FARS-0.6.0/FARS/man/get_residuals.mldfm.Rd |only FARS-0.6.0/FARS/man/get_sigma_list.Rd |only FARS-0.6.0/FARS/man/get_stressed_factors.Rd |only FARS-0.6.0/FARS/man/get_stressed_factors.fars.Rd |only FARS-0.6.0/FARS/man/inflation_data.Rd |only FARS-0.6.0/FARS/man/l_density.Rd | 26 + FARS-0.6.0/FARS/man/mf_data.Rd |only FARS-0.6.0/FARS/man/mldfm.Rd | 30 - FARS-0.6.0/FARS/man/mldfm_subsampling.Rd | 13 FARS-0.6.0/FARS/man/multiple_blocks.Rd |only FARS-0.6.0/FARS/man/nl_density.Rd | 26 + FARS-0.6.0/FARS/man/orthogonalize_factors.Rd | 4 FARS-0.6.0/FARS/man/plot.fars.Rd | 8 FARS-0.6.0/FARS/man/plot.fars_density.Rd | 9 FARS-0.6.0/FARS/man/plot.fars_scenario.Rd |only FARS-0.6.0/FARS/man/plot.mldfm.Rd | 20 FARS-0.6.0/FARS/man/plot.mldfm_subsample.Rd |only FARS-0.6.0/FARS/man/plot_factors.mldfm.Rd | 19 FARS-0.6.0/FARS/man/plot_loadings.mldfm.Rd | 17 FARS-0.6.0/FARS/man/plot_residuals.mldfm.Rd | 13 FARS-0.6.0/FARS/man/print.fars.Rd | 10 FARS-0.6.0/FARS/man/print.fars_density.Rd | 8 FARS-0.6.0/FARS/man/print.fars_scenario.Rd |only FARS-0.6.0/FARS/man/print.mldfm.Rd | 8 FARS-0.6.0/FARS/man/print.mldfm_subsample.Rd |only FARS-0.6.0/FARS/man/q_reg.Rd | 26 + FARS-0.6.0/FARS/man/quantile_risk.Rd | 17 FARS-0.6.0/FARS/man/single_block.Rd | 20 FARS-0.6.0/FARS/man/summary.fars.Rd | 11 FARS-0.6.0/FARS/man/summary.fars_density.Rd | 11 FARS-0.6.0/FARS/man/summary.fars_scenario.Rd |only FARS-0.6.0/FARS/man/summary.mldfm.Rd | 8 FARS-0.6.0/FARS/man/summary.mldfm_subsample.Rd |only FARS-0.6.0/FARS/man/update_factor_list.Rd | 16 FARS-0.6.0/FARS/vignettes/Factor_Augmented_Regression_Scenarios_in_R.pdf.asis |only 141 files changed, 1258 insertions(+), 797 deletions(-)
Title: Animation of Multiple Trajectories with Uncertainty
Description: Animation of observed trajectories using spline-based interpolation (see for example, Buderman, F. E., Hooten, M. B., Ivan, J. S. and Shenk, T. M. (2016), <doi:10.1111/2041-210X.12465> "A functional model for characterizing long-distance movement behaviour". Methods Ecol Evol). Intended to be used exploratory data analysis, and perhaps for preparation of presentations.
Author: Henry Scharf [aut, cre],
Kristine Dinh [aut],
Rosales Hugo [aut],
Rivera Angelica [aut]
Maintainer: Henry Scharf <hscharf@arizona.edu>
Diff between anipaths versions 0.10.5 dated 2025-03-01 and 0.10.6 dated 2025-10-07
DESCRIPTION | 8 - MD5 | 32 ++--- NEWS | 11 +- R/animate_paths.R | 17 ++- R/animation_expression.R | 21 ++- R/check_overwrite.R | 6 - R/mapping.R | 30 +---- build/vignette.rds |binary inst/doc/anipaths.R | 236 +++++++++++++++++++++---------------------- inst/doc/anipaths.html | 8 - inst/doc/anipaths_crawl.R | 110 ++++++++++---------- inst/doc/anipaths_crawl.html | 8 - inst/doc/anipaths_gam.R | 64 +++++------ inst/doc/anipaths_gam.html | 8 - man/animate_paths.Rd | 12 +- man/animation_expression.Rd | 6 + man/check_overwrite.Rd | 4 17 files changed, 301 insertions(+), 280 deletions(-)
Title: Make 'ggplot2' Graphics Interactive
Description: Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Author: David Gohel [aut, cre],
Panagiotis Skintzos [aut],
Mike Bostock [cph] ,
Speros Kokenes [cph] ,
Eric Shull [cph] ,
Lee Thomason [cph] ,
Vladimir Agafonkin [cph] ,
Eric Book [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between ggiraph versions 0.9.1 dated 2025-09-16 and 0.9.2 dated 2025-10-07
ggiraph-0.9.1/ggiraph/inst/htmlwidgets/lib |only ggiraph-0.9.1/ggiraph/man/font_family_exists.Rd |only ggiraph-0.9.2/ggiraph/DESCRIPTION | 36 +- ggiraph-0.9.2/ggiraph/MD5 | 71 ++-- ggiraph-0.9.2/ggiraph/NAMESPACE | 14 ggiraph-0.9.2/ggiraph/NEWS.md | 29 + ggiraph-0.9.2/ggiraph/R/dsvg.R | 1 ggiraph-0.9.2/ggiraph/R/fonts.R | 157 ++++++++-- ggiraph-0.9.2/ggiraph/R/geom_boxplot_interactive.R | 4 ggiraph-0.9.2/ggiraph/R/geom_path_interactive.R | 1 ggiraph-0.9.2/ggiraph/R/geom_quasirandom_interactive.R |only ggiraph-0.9.2/ggiraph/R/geom_ribbon_interactive.R | 130 +------- ggiraph-0.9.2/ggiraph/R/girafe.R | 103 +++--- ggiraph-0.9.2/ggiraph/R/girafe_options.R | 73 +++- ggiraph-0.9.2/ggiraph/R/ipar.R | 12 ggiraph-0.9.2/ggiraph/R/utils.R | 2 ggiraph-0.9.2/ggiraph/R/utils_data.r |only ggiraph-0.9.2/ggiraph/R/utils_ggplot2.R | 32 -- ggiraph-0.9.2/ggiraph/inst/htmlwidgets/girafe.css |only ggiraph-0.9.2/ggiraph/inst/htmlwidgets/girafe.js | 6 ggiraph-0.9.2/ggiraph/inst/htmlwidgets/girafe.yaml | 25 - ggiraph-0.9.2/ggiraph/inst/tinytest/test-dsvg_text.R | 2 ggiraph-0.9.2/ggiraph/inst/tinytest/test-fonts.R | 4 ggiraph-0.9.2/ggiraph/inst/tinytest/test-geom_point_interactive.R | 2 ggiraph-0.9.2/ggiraph/inst/tinytest/test-geom_ribbon_interactive.R | 32 ++ ggiraph-0.9.2/ggiraph/inst/tinytest/test-interactive_text_grob.R | 2 ggiraph-0.9.2/ggiraph/man/annotate_interactive.Rd | 20 + ggiraph-0.9.2/ggiraph/man/element_interactive.Rd | 12 ggiraph-0.9.2/ggiraph/man/geom_bar_interactive.Rd | 31 + ggiraph-0.9.2/ggiraph/man/geom_point_interactive.Rd | 12 ggiraph-0.9.2/ggiraph/man/geom_quasirandom_interactive.Rd |only ggiraph-0.9.2/ggiraph/man/geom_text_interactive.Rd | 38 +- ggiraph-0.9.2/ggiraph/man/girafe.Rd | 61 +++ ggiraph-0.9.2/ggiraph/man/match_family.Rd | 1 ggiraph-0.9.2/ggiraph/man/opts_toolbar.Rd | 64 +++- ggiraph-0.9.2/ggiraph/man/opts_zoom.Rd | 6 ggiraph-0.9.2/ggiraph/man/validated_fonts.Rd | 1 37 files changed, 618 insertions(+), 366 deletions(-)
Title: Truncated Multivariate Normal and t Distribution Simulation
Description: Simulation of random vectors from truncated multivariate normal
and t distributions based on the algorithms proposed by Yifang Li and Sujit K. Ghosh (2015) <doi:10.1080/15598608.2014.996690>.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between tmvtnsim versions 0.1.3 dated 2022-10-09 and 0.1.4 dated 2025-10-07
DESCRIPTION | 14 ++++++++------ MD5 | 12 ++++++------ R/tmvtnsim-package.R | 2 -- build/partial.rdb |binary man/tmvtnsim-package.Rd | 1 - src/Makevars | 2 -- src/Makevars.win | 2 -- 7 files changed, 14 insertions(+), 19 deletions(-)
Title: Optimal Dose Escalation Using Deep Reinforcement Learning
Description: An implementation to compute an optimal dose escalation rule
using deep reinforcement learning in phase I oncology trials
(Matsuura et al. (2023) <doi:10.1080/10543406.2023.2170402>).
The dose escalation rule can directly optimize the percentages of correct
selection (PCS) of the maximum tolerated dose (MTD).
Author: Kentaro Matsuura [aut, cre, cph]
Maintainer: Kentaro Matsuura <matsuurakentaro55@gmail.com>
Diff between RLescalation versions 1.0.2 dated 2025-02-07 and 1.0.3 dated 2025-10-07
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- NAMESPACE | 2 ++ R/compute_rl_scenarios.R | 1 + R/escalation_rule.R | 4 +++- build/vignette.rds |binary inst/doc/RLescalation.Rmd | 2 +- inst/doc/RLescalation.html | 7 +++---- vignettes/RLescalation.Rmd | 2 +- 9 files changed, 25 insertions(+), 21 deletions(-)
Title: Run Once and Save Result
Description: Package 'runonce' helps automating the saving of long-running code
to help running the same code multiple times. If you run some long-running
code once, it saves the result in a file on disk. Then, if the result
already exists, i.e. if the code has already been run and its output has
already been saved, it just reads the result from the stored file instead
of running the code again.
Author: Florian Prive [aut, cre]
Maintainer: Florian Prive <florian.prive.21@gmail.com>
Diff between runonce versions 0.3.2 dated 2025-07-30 and 0.3.3 dated 2025-10-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/download-file.R | 5 +++-- man/download_file.Rd | 11 ++++++----- 4 files changed, 16 insertions(+), 14 deletions(-)
Title: Add Ipea Editorial Standards to 'ggplot2' Graphics
Description: Convenient functions to create 'ggplot2' graphics following the
editorial guidelines of the Institute for Applied Economic
Research (Ipea).
Author: Pedro Ferreira [aut, cre],
Pedro Jorge [aut],
Daniel Lima [aut],
Gustavo Coelho [aut],
Rafael H. M. Pereira [aut],
Lucas Mation [aut],
Fabio Vaz [ctb],
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Pedro Ferreira <pedro.ferreira2@ipea.gov.br>
Diff between ipeaplot versions 0.4.1 dated 2025-02-26 and 0.5.0 dated 2025-10-07
ipeaplot-0.4.1/ipeaplot/R/save_eps.R |only ipeaplot-0.4.1/ipeaplot/R/save_pdf.R |only ipeaplot-0.4.1/ipeaplot/man/save_eps.Rd |only ipeaplot-0.4.1/ipeaplot/man/save_pdf.Rd |only ipeaplot-0.5.0/ipeaplot/DESCRIPTION | 10 ipeaplot-0.5.0/ipeaplot/MD5 | 30 ipeaplot-0.5.0/ipeaplot/NAMESPACE | 5 ipeaplot-0.5.0/ipeaplot/NEWS.md | 41 ipeaplot-0.5.0/ipeaplot/R/save_ipeaplot.R |only ipeaplot-0.5.0/ipeaplot/README.md | 19 ipeaplot-0.5.0/ipeaplot/build/vignette.rds |binary ipeaplot-0.5.0/ipeaplot/inst/doc/cookbook.R | 598 ++++++------- ipeaplot-0.5.0/ipeaplot/inst/doc/cookbook.html | 4 ipeaplot-0.5.0/ipeaplot/inst/doc/intro_ipeaplot.R | 177 ++- ipeaplot-0.5.0/ipeaplot/inst/doc/intro_ipeaplot.Rmd | 63 + ipeaplot-0.5.0/ipeaplot/inst/doc/intro_ipeaplot.html | 108 +- ipeaplot-0.5.0/ipeaplot/man/save_ipeaplot.Rd |only ipeaplot-0.5.0/ipeaplot/tests/tests_pedro_alves/exemplos.R | 42 ipeaplot-0.5.0/ipeaplot/vignettes/intro_ipeaplot.Rmd | 63 + 19 files changed, 689 insertions(+), 471 deletions(-)
Title: Visualising Bipartite Networks and Calculating Some (Ecological)
Indices
Description: Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.
Author: Carsten F. Dormann [aut, cre] ,
Jochen Fruend [aut] ,
Bernd Gruber [aut] ,
Tobias Bauer [ctb] ,
Stephen Beckett [ctb] ,
Mariano Devoto [ctb] ,
Gabriel M.F. Felix [ctb] ,
Jose M. Iriondo [ctb] ,
Tore Opsahl [ctb] ,
Rafael B.P. Pinheiro [ctb] ,
Rouven [...truncated...]
Maintainer: Carsten F. Dormann <carsten.dormann@biom.uni-freiburg.de>
Diff between bipartite versions 2.22 dated 2025-09-08 and 2.23 dated 2025-10-07
bipartite-2.22/bipartite/src/bmn5.cc |only bipartite-2.22/bipartite/vignettes/Intro2bipartite-concordance.tex |only bipartite-2.22/bipartite/vignettes/figures/motten1982_plotweb_old.pdf |only bipartite-2.23/bipartite/DESCRIPTION | 8 - bipartite-2.23/bipartite/MD5 | 27 ++--- bipartite-2.23/bipartite/R/plotweb.R | 28 +++++ bipartite-2.23/bipartite/inst/doc/Intro2bipartite.R | 54 ++++------ bipartite-2.23/bipartite/inst/doc/Intro2bipartite.Rnw | 20 +-- bipartite-2.23/bipartite/inst/doc/Intro2bipartite.pdf |binary bipartite-2.23/bipartite/inst/doc/PlottingWithBipartite.html | 4 bipartite-2.23/bipartite/inst/extdata |only bipartite-2.23/bipartite/man/bipartite-package.Rd | 7 + bipartite-2.23/bipartite/man/plotweb.Rd | 2 bipartite-2.23/bipartite/vignettes/Intro2bipartite.Rnw | 20 +-- bipartite-2.23/bipartite/vignettes/figures/motten1982_plotweb.pdf |binary bipartite-2.23/bipartite/vignettes/figures/twocolumn-betweenPlot-1.pdf |binary 16 files changed, 95 insertions(+), 75 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via 'modsem' it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8.3."
Klein, A., & Moosb [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre] ,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.12 dated 2025-08-27 and 1.0.13 dated 2025-10-07
modsem-1.0.12/modsem/tests/testthat/test_higher_order.R |only modsem-1.0.13/modsem/DESCRIPTION | 6 modsem-1.0.13/modsem/MD5 | 113 +- modsem-1.0.13/modsem/NAMESPACE | 1 modsem-1.0.13/modsem/R/bootstrap.R | 54 - modsem-1.0.13/modsem/R/check_model_da.R | 63 + modsem-1.0.13/modsem/R/construct_matrices_da.R | 41 modsem-1.0.13/modsem/R/generics_lavaan.R | 4 modsem-1.0.13/modsem/R/generics_modsem_da.R | 16 modsem-1.0.13/modsem/R/generics_modsem_pi.R | 4 modsem-1.0.13/modsem/R/labelled_params_da.R | 21 modsem-1.0.13/modsem/R/lavaan_labels.R | 25 modsem-1.0.13/modsem/R/model_da.R | 49 - modsem-1.0.13/modsem/R/model_parameters_da.R | 4 modsem-1.0.13/modsem/R/modsem_da.R | 26 modsem-1.0.13/modsem/R/modsem_mplus.R | 182 +++ modsem-1.0.13/modsem/R/optimize_da.R | 189 +++ modsem-1.0.13/modsem/R/parser.R | 9 modsem-1.0.13/modsem/R/plot_interaction.R | 237 +++- modsem-1.0.13/modsem/R/reliablity_single_item.R | 190 +++ modsem-1.0.13/modsem/R/scale_correction_ordered.R | 486 +++++++++- modsem-1.0.13/modsem/R/simple_slopes.R | 96 + modsem-1.0.13/modsem/R/standardized_solution.R | 40 modsem-1.0.13/modsem/R/tokenizer.R | 3 modsem-1.0.13/modsem/R/twostep.R | 2 modsem-1.0.13/modsem/R/utils.R | 106 +- modsem-1.0.13/modsem/R/utils_da.R | 195 +++- modsem-1.0.13/modsem/R/utils_pi.R | 7 modsem-1.0.13/modsem/README.md | 11 modsem-1.0.13/modsem/inst/doc/customizing.html | 2 modsem-1.0.13/modsem/inst/doc/higher_order_interactions.R | 58 - modsem-1.0.13/modsem/inst/doc/higher_order_interactions.Rmd | 102 +- modsem-1.0.13/modsem/inst/doc/higher_order_interactions.html | 127 +- modsem-1.0.13/modsem/inst/doc/observed_lms_qml.html | 38 modsem-1.0.13/modsem/inst/doc/plot_interactions.R | 85 + modsem-1.0.13/modsem/inst/doc/plot_interactions.Rmd | 105 ++ modsem-1.0.13/modsem/inst/doc/plot_interactions.html | 120 ++ modsem-1.0.13/modsem/man/bootstrap_modsem.Rd | 5 modsem-1.0.13/modsem/man/modsem_da.Rd | 18 modsem-1.0.13/modsem/man/modsem_mplus.Rd | 6 modsem-1.0.13/modsem/man/parameter_estimates.Rd | 10 modsem-1.0.13/modsem/man/plot_interaction.Rd | 22 modsem-1.0.13/modsem/man/plot_jn.Rd | 6 modsem-1.0.13/modsem/man/plot_surface.Rd | 65 + modsem-1.0.13/modsem/man/simple_slopes.Rd | 12 modsem-1.0.13/modsem/src/Makevars | 5 modsem-1.0.13/modsem/src/equations_lms.cpp | 268 +++-- modsem-1.0.13/modsem/tests/testthat/test_bootstrap.R | 3 modsem-1.0.13/modsem/tests/testthat/test_higher_order_da.R |only modsem-1.0.13/modsem/tests/testthat/test_higher_order_pi.R |only modsem-1.0.13/modsem/tests/testthat/test_linear_da.R | 7 modsem-1.0.13/modsem/tests/testthat/test_lms.R | 2 modsem-1.0.13/modsem/tests/testthat/test_mplus.R | 31 modsem-1.0.13/modsem/tests/testthat/test_ordered_da.R | 3 modsem-1.0.13/modsem/tests/testthat/test_sam.R | 29 modsem-1.0.13/modsem/tests/testthat/test_simple_slopes.R | 59 + modsem-1.0.13/modsem/tests/testthat/test_zero_variance_indicator_lms.R | 2 modsem-1.0.13/modsem/vignettes/higher_order_interactions.Rmd | 102 +- modsem-1.0.13/modsem/vignettes/plot_interactions.Rmd | 105 ++ 59 files changed, 2920 insertions(+), 657 deletions(-)
Title: Hierarchical Partitioning of Adjusted R2 and Explained Deviance
for Generalized Additive Models
Description: Conducts hierarchical partitioning to calculate individual contributions of each predictor towards adjusted R2 and explained deviance for generalized additive models based on output of 'gam()' and 'bam()' in 'mgcv' package, applying the algorithm in this paper: Lai(2024) <doi:10.1016/j.pld.2024.06.002>.
Author: Jiangshan Lai [aut, cre] ,
Jing Tang [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between gam.hp versions 0.0-3 dated 2024-12-15 and 0.0-4 dated 2025-10-07
DESCRIPTION | 13 - MD5 | 6 R/gam.hp.r | 746 ++++++++++++++++++++++++++++++---------------------------- man/gam.hp.Rd | 75 ++++- 4 files changed, 448 insertions(+), 392 deletions(-)
Title: Conventional and Fuzzy Data Envelopment Analysis
Description: Set of functions for Data Envelopment Analysis. It runs both classic and fuzzy DEA models. See: Banker, R.; Charnes, A.; Cooper, W.W. (1984). <doi:10.1287/mnsc.30.9.1078>, Charnes, A.; Cooper, W.W.; Rhodes, E. (1978). <doi:10.1016/0377-2217(78)90138-8> and Charnes, A.; Cooper, W.W.; Rhodes, E. (1981). <doi:10.1287/mnsc.27.6.668>.
Author: Vicente Bolos [aut, cre],
Vicente Coll-Serrano [aut],
Rafael Benitez Suarez [aut]
Maintainer: Vicente Bolos <vicente.bolos@uv.es>
Diff between deaR versions 1.5 dated 2025-06-13 and 1.5.1 dated 2025-10-07
DESCRIPTION | 20 - MD5 | 192 ++++++++--------- R/bootstrap_basic.R | 9 R/cross_efficiency.R | 6 R/cross_efficiency_fuzzy.R | 4 R/eff_dmus.R | 2 R/efficiencies.R | 43 ++- R/efficiencies.dea.R | 150 ++++++------- R/efficiencies.dea_fuzzy.R | 439 ++++++++++++++++++++-------------------- R/extreme_efficient.R | 2 R/is.dea.R | 3 R/is.dea_fuzzy.R | 2 R/is.deadata.R | 3 R/is.deadata_fuzzy.R | 3 R/is.friends.R | 2 R/lambdas.R | 2 R/make_deadata.R | 2 R/make_deadata_fuzzy.R | 3 R/make_malmquist.R | 2 R/malmquist_index.R | 4 R/maximal_friends.R | 2 R/model_additive.R | 9 R/model_addmin.R | 9 R/model_addsupereff.R | 8 R/model_basic.R | 8 R/model_deaps.R | 8 R/model_dir.R | 7 R/model_fdh.R | 6 R/model_lgo.R | 21 + R/model_multiplier.R | 7 R/model_nonradial.R | 8 R/model_profit.R | 5 R/model_qgo.R | 23 +- R/model_rdm.R | 8 R/model_sbmeff.R | 9 R/model_sbmsupereff.R | 7 R/model_supereff.R | 7 R/modelfuzzy_guotanaka.R | 7 R/modelfuzzy_kaoliu.R | 21 + R/modelfuzzy_possibilistic.R | 7 R/multipliers.R | 2 R/plot.dea.R | 2 R/plot.dea_fuzzy.R | 2 R/read_data.R | 2 R/read_data_fuzzy.R | 3 R/read_malmquist.R | 2 R/references.R | 4 R/rts.R | 7 R/slacks.R | 2 R/summary.dea.R | 6 R/summary.dea_fuzzy.R | 6 R/targets.R | 83 +++++-- R/undesirable_basic.R | 2 man/bootstrap_basic.Rd | 6 man/cross_efficiency.Rd | 7 man/cross_efficiency_fuzzy.Rd | 5 man/efficiencies.Rd | 4 man/efficiencies.dea.Rd | 3 man/efficiencies.dea_fuzzy.Rd | 4 man/is.dea.Rd | 2 man/is.dea_fuzzy.Rd | 2 man/is.deadata.Rd | 2 man/is.deadata_fuzzy.Rd | 2 man/lambdas.Rd | 3 man/make_deadata.Rd | 2 man/make_deadata_fuzzy.Rd | 3 man/make_malmquist.Rd | 2 man/malmquist_index.Rd | 4 man/model_additive.Rd | 10 man/model_addmin.Rd | 10 man/model_addsupereff.Rd | 9 man/model_basic.Rd | 9 man/model_deaps.Rd | 9 man/model_dir.Rd | 8 man/model_fdh.Rd | 7 man/model_lgo.Rd | 8 man/model_multiplier.Rd | 8 man/model_nonradial.Rd | 9 man/model_profit.Rd | 6 man/model_qgo.Rd | 10 man/model_rdm.Rd | 9 man/model_sbmeff.Rd | 10 man/model_sbmsupereff.Rd | 10 man/model_supereff.Rd | 8 man/modelfuzzy_guotanaka.Rd | 7 man/modelfuzzy_kaoliu.Rd | 15 + man/modelfuzzy_possibilistic.Rd | 7 man/multipliers.Rd | 3 man/read_data.Rd | 3 man/read_data_fuzzy.Rd | 4 man/read_malmquist.Rd | 3 man/references.Rd | 5 man/rts.Rd | 4 man/slacks.Rd | 3 man/summary.dea.Rd | 6 man/summary.dea_fuzzy.Rd | 6 man/targets.Rd | 5 97 files changed, 938 insertions(+), 527 deletions(-)
Title: Fast Tidy Tools for Date and Date-Time Manipulation
Description: A set of fast tidy functions for wrangling, completing and
summarising date and date-time data. It combines 'tidyverse' syntax
with the efficiency of 'data.table' and speed of 'collapse'.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between timeplyr versions 1.1.0 dated 2025-03-17 and 1.1.1 dated 2025-10-07
timeplyr-1.1.0/timeplyr/R/dt_utils.R |only timeplyr-1.1.0/timeplyr/R/timeplyr.R |only timeplyr-1.1.0/timeplyr/R/utils-pipe.R |only timeplyr-1.1.0/timeplyr/man/pipe.Rd |only timeplyr-1.1.0/timeplyr/tests/testthat/test-age_years.R |only timeplyr-1.1.1/timeplyr/DESCRIPTION | 22 - timeplyr-1.1.1/timeplyr/MD5 | 145 +++----- timeplyr-1.1.1/timeplyr/NAMESPACE | 10 timeplyr-1.1.1/timeplyr/NEWS.md | 11 timeplyr-1.1.1/timeplyr/R/abc.R | 178 +++++----- timeplyr-1.1.1/timeplyr/R/age_years.R | 14 timeplyr-1.1.1/timeplyr/R/calendar.R | 23 + timeplyr-1.1.1/timeplyr/R/collapse_utils.R | 25 - timeplyr-1.1.1/timeplyr/R/df_utils.R | 69 ++- timeplyr-1.1.1/timeplyr/R/fast_stats.R | 2 timeplyr-1.1.1/timeplyr/R/get_time_delay.R | 51 +- timeplyr-1.1.1/timeplyr/R/growth.R | 2 timeplyr-1.1.1/timeplyr/R/gsum.R | 107 ------ timeplyr-1.1.1/timeplyr/R/is_whole_number.R | 4 timeplyr-1.1.1/timeplyr/R/iso_week.R | 2 timeplyr-1.1.1/timeplyr/R/resolution.R | 15 timeplyr-1.1.1/timeplyr/R/roll.R | 14 timeplyr-1.1.1/timeplyr/R/roll_na_fill.R | 4 timeplyr-1.1.1/timeplyr/R/roll_utils.R | 22 - timeplyr-1.1.1/timeplyr/R/scales.R | 2 timeplyr-1.1.1/timeplyr/R/time_arithmetic.R | 66 ++- timeplyr-1.1.1/timeplyr/R/time_by.R | 66 ++- timeplyr-1.1.1/timeplyr/R/time_core.R | 10 timeplyr-1.1.1/timeplyr/R/time_cut.R | 154 ++++++-- timeplyr-1.1.1/timeplyr/R/time_diff.R | 36 +- timeplyr-1.1.1/timeplyr/R/time_elapsed.R | 2 timeplyr-1.1.1/timeplyr/R/time_episodes.R | 136 ++++++- timeplyr-1.1.1/timeplyr/R/time_expand.R | 55 +-- timeplyr-1.1.1/timeplyr/R/time_gaps.R | 6 timeplyr-1.1.1/timeplyr/R/time_ggplot.R | 54 +-- timeplyr-1.1.1/timeplyr/R/time_id.R | 4 timeplyr-1.1.1/timeplyr/R/time_interval.R | 48 +- timeplyr-1.1.1/timeplyr/R/time_is_regular.R | 4 timeplyr-1.1.1/timeplyr/R/time_roll.R | 26 - timeplyr-1.1.1/timeplyr/R/time_seq.R | 6 timeplyr-1.1.1/timeplyr/R/time_seq_fill.R | 2 timeplyr-1.1.1/timeplyr/R/time_seq_id.R | 28 - timeplyr-1.1.1/timeplyr/R/time_units.R | 5 timeplyr-1.1.1/timeplyr/R/time_utils.R | 47 -- timeplyr-1.1.1/timeplyr/R/timeplyr-package.R | 3 timeplyr-1.1.1/timeplyr/R/timespan.R | 10 timeplyr-1.1.1/timeplyr/R/ts_as_tbl.R | 30 - timeplyr-1.1.1/timeplyr/R/year_month.R | 25 - timeplyr-1.1.1/timeplyr/man/age_years.Rd | 2 timeplyr-1.1.1/timeplyr/man/get_time_delay.Rd | 6 timeplyr-1.1.1/timeplyr/man/is_whole_number.Rd | 4 timeplyr-1.1.1/timeplyr/man/time_add.Rd | 8 timeplyr-1.1.1/timeplyr/man/time_by.Rd | 14 timeplyr-1.1.1/timeplyr/man/time_cut.Rd | 79 ++-- timeplyr-1.1.1/timeplyr/man/time_diff.Rd | 60 +-- timeplyr-1.1.1/timeplyr/man/time_episodes.Rd | 16 timeplyr-1.1.1/timeplyr/man/time_expand.Rd | 12 timeplyr-1.1.1/timeplyr/man/time_gaps.Rd | 4 timeplyr-1.1.1/timeplyr/man/time_ggplot.Rd | 20 - timeplyr-1.1.1/timeplyr/man/time_is_regular.Rd | 2 timeplyr-1.1.1/timeplyr/man/time_roll.Rd | 6 timeplyr-1.1.1/timeplyr/man/timeplyr-package.Rd | 22 - timeplyr-1.1.1/timeplyr/man/ts_as_tbl.Rd | 4 timeplyr-1.1.1/timeplyr/tests/testthat.R | 2 timeplyr-1.1.1/timeplyr/tests/testthat/_snaps/time_by.md | 30 + timeplyr-1.1.1/timeplyr/tests/testthat/_snaps/time_episodes.md | 39 +- timeplyr-1.1.1/timeplyr/tests/testthat/test-calendar.R | 4 timeplyr-1.1.1/timeplyr/tests/testthat/test-get_time_delay.R | 76 ++-- timeplyr-1.1.1/timeplyr/tests/testthat/test-roll_mean.R | 38 +- timeplyr-1.1.1/timeplyr/tests/testthat/test-time_by.R | 27 - timeplyr-1.1.1/timeplyr/tests/testthat/test-time_core.R | 8 timeplyr-1.1.1/timeplyr/tests/testthat/test-time_diff.R | 4 timeplyr-1.1.1/timeplyr/tests/testthat/test-time_elapsed.R | 24 - timeplyr-1.1.1/timeplyr/tests/testthat/test-time_episodes.R | 176 ++++----- timeplyr-1.1.1/timeplyr/tests/testthat/test-time_expand.R | 145 ++++---- timeplyr-1.1.1/timeplyr/tests/testthat/test-time_roll.R | 8 76 files changed, 1267 insertions(+), 1118 deletions(-)
Title: 'R' 'SDK' and Exporters for 'OpenTelemetry'
Description: 'OpenTelemetry' is a collection of tools,
'APIs', and 'SDKs' used to instrument, generate, collect, and export
telemetry data (metrics, logs, and traces) for analysis in order to
understand your software's performance and behavior.
This package contains the 'OpenTelemetry' 'SDK', and exporters.
Use this package to export traces, metrics, logs from instrumented
'R' code. Use the 'otel' package to instrument your 'R' code for
'OpenTelemetry'.
Author: Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd] ,
opentelemetry-cpp authors [ctb]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between otelsdk versions 0.2.1 dated 2025-09-23 and 0.2.2 dated 2025-10-07
DESCRIPTION | 6 +-- MD5 | 16 +++++----- NEWS.md | 4 ++ configure | 10 +++--- src/span.c | 3 - src/vendor/opentelemetry-cpp.patch | 57 +++++++++++++++++++++++++++++++++++-- tests/testthat.R | 26 ++++++---------- tests/testthat/test-meter.R | 1 tests/testthat/test-print.R | 2 + 9 files changed, 89 insertions(+), 36 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 3.0.0 dated 2025-09-17 and 3.0.1 dated 2025-10-07
DESCRIPTION | 12 +- MD5 | 19 +-- NEWS.md | 14 ++ R/utils-checks.R | 50 +++++++++ R/zzz.R | 9 - README.md | 159 +++++++++++++++++++++++++++---- inst/WORDLIST | 5 inst/doc/complete-pipeline.html | 56 +++++----- inst/doc/epoching-bids-reports.html | 50 ++++----- man/check_arrow.Rd |only man/figures/README-unnamed-chunk-3-1.png |binary 11 files changed, 281 insertions(+), 93 deletions(-)
Title: Bayesian Estimation and Forecasting of Age-Specific Rates
Description: Fast Bayesian estimation and forecasting of age-specific
rates, probabilities, and means, based on 'Template Model Builder'.
Author: John Bryant [aut, cre],
Junni Zhang [aut],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between bage versions 0.9.6 dated 2025-10-01 and 0.9.7 dated 2025-10-07
DESCRIPTION | 10 MD5 | 90 +-- R/bage_mod-methods.R | 28 - R/fit.R | 31 - R/make-outputs.R | 35 - R/sim.R | 2 R/util.R | 222 +++++++- inst/doc/vig01_intro.R | 1 inst/doc/vig01_intro.Rmd | 1 inst/doc/vig01_intro.html | 144 ++--- inst/doc/vig04_svd.R | 1 inst/doc/vig04_svd.Rmd | 1 inst/doc/vig04_svd.html | 2 inst/doc/vig05_bdef.R | 1 inst/doc/vig05_bdef.Rmd | 1 inst/doc/vig05_bdef.html | 78 +- inst/doc/vig06_mortality.R | 1 inst/doc/vig06_mortality.Rmd | 26 inst/doc/vig06_mortality.html | 105 +-- inst/doc/vig07_simulation.R | 26 inst/doc/vig07_simulation.Rmd | 37 - inst/doc/vig07_simulation.html | 790 +++--------------------------- inst/doc/vig09_covariates.R | 1 inst/doc/vig09_covariates.Rmd | 1 inst/doc/vig09_covariates.html | 38 - inst/doc/vig10_datamod.R | 1 inst/doc/vig10_datamod.Rmd | 1 inst/doc/vig10_datamod.html | 86 +-- man/fit.bage_mod.Rd | 28 - src/Makevars | 1 tests/testthat/_snaps/bage_mod-methods.md | 4 tests/testthat/test-all-models.R | 2 tests/testthat/test-bage_mod-methods.R | 131 ++-- tests/testthat/test-bage_prior-methods.R | 2 tests/testthat/test-fit.R | 59 +- tests/testthat/test-make-inputs.R | 2 tests/testthat/test-make-outputs.R | 83 ++- tests/testthat/test-sim.R | 34 - tests/testthat/test-util.R | 255 +++++++++ vignettes/vig01_intro.Rmd | 1 vignettes/vig04_svd.Rmd | 1 vignettes/vig05_bdef.Rmd | 1 vignettes/vig06_mortality.Rmd | 26 vignettes/vig07_simulation.Rmd | 37 - vignettes/vig09_covariates.Rmd | 1 vignettes/vig10_datamod.Rmd | 1 46 files changed, 1223 insertions(+), 1207 deletions(-)
Title: Acquiring and Processing Data from Japan Institute for Health
Security
Description: Download and post process the infectious disease case data
from Japan Institute for Health Security. Also the package included
ready-to-analyse datasets. See the data source website for further details
<https://id-info.jihs.go.jp/>.
Author: Tomonori Hoshi [aut, cre],
Erina Ishigaki [aut],
Satoshi Kaneko [aut]
Maintainer: Tomonori Hoshi <tomonori.hoshi.japan@gmail.com>
Diff between jpinfect versions 0.1.3 dated 2025-09-11 and 0.1.4 dated 2025-10-07
DESCRIPTION | 6 MD5 | 18 +- R/jpinfect_get_bullet.R | 7 R/jpinfect_get_confirmed.R | 106 +++++++++++-- R/jpinfect_read_confirmed.R | 27 +++ data/bullet.rda |binary inst/doc/jpinfect.html | 204 +++++++++++++------------- inst/extdata/1999_Syu_11.xls |binary man/jpinfect_get_confirmed.Rd | 4 tests/testthat/test-jpinfect_read_confirmed.R | 5 10 files changed, 242 insertions(+), 135 deletions(-)
Title: Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data. In
particular representation, manipulation, rate estimation and
simulation for multistate data - the Lexis suite of functions, which
includes interfaces to 'mstate', 'etm' and 'cmprsk' packages.
Contains functions for Age-Period-Cohort and Lee-Carter modeling and
a function for interval censored data. Has functions for extracting
and manipulating parameter estimates and predicted values (ci.lin
and its cousins), as well as a number of epidemiological data sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.60 dated 2025-07-08 and 2.61 dated 2025-10-07
CHANGES | 10 +++ DESCRIPTION | 14 ++-- MD5 | 126 ++++++++++++++++++++------------------ NAMESPACE | 3 R/paths.Lexis.R | 2 R/xcutLexis.R |only inst/doc/01flup.R | 80 ++++++++++++------------ inst/doc/01flup.pdf |binary inst/doc/02addLexis.pdf |binary inst/doc/03crisk.pdf |binary inst/doc/04simLexis.pdf |binary inst/doc/05yll.pdf |binary man/cutLexis.Rd | 18 +++-- man/paths.Lexis.Rd | 9 +- man/xcutLexis.Rd |only vignettes/01flup-Ieff.pdf |binary vignettes/01flup-IeffR.pdf |binary vignettes/01flup-box1.pdf |binary vignettes/01flup-box4.pdf |binary vignettes/01flup-dmL1.pdf |binary vignettes/01flup-dmL2.pdf |binary vignettes/01flup-dur-int-RR.pdf |binary vignettes/01flup-dur-int.pdf |binary vignettes/01flup-ins-time.pdf |binary vignettes/01flup-mbox.pdf |binary vignettes/01flup-mboxr.pdf |binary vignettes/01flup-pr-a.pdf |binary vignettes/01flup-sep-HR.pdf |binary vignettes/01flup-sep-mort.pdf |binary vignettes/01flup.R |only vignettes/01flup.pdf |only vignettes/01flup.rnw | 38 ++++++----- vignettes/01flup.tex | 116 ++++++++++++++++++---------------- vignettes/02addLexis.R |only vignettes/02addLexis.pdf |only vignettes/02addLexis.tex | 16 ++-- vignettes/03crisk-Sr1.pdf |binary vignettes/03crisk-Sr2.pdf |binary vignettes/03crisk-boxes.pdf |binary vignettes/03crisk-boxes4.pdf |binary vignettes/03crisk-boxes5.pdf |binary vignettes/03crisk-cR.pdf |binary vignettes/03crisk-crates.pdf |binary vignettes/03crisk-difrat.pdf |binary vignettes/03crisk-difratx.pdf |binary vignettes/03crisk-rates-ci.pdf |binary vignettes/03crisk-rates-l.pdf |binary vignettes/03crisk-rates.pdf |binary vignettes/03crisk-stack-ci.pdf |binary vignettes/03crisk-stack.pdf |binary vignettes/03crisk.R |only vignettes/03crisk.pdf |only vignettes/03crisk.tex | 8 +- vignettes/04simLexis-boxes.pdf |binary vignettes/04simLexis-comp-0.pdf |binary vignettes/04simLexis-mort-int.pdf |binary vignettes/04simLexis-pstate0.pdf |binary vignettes/04simLexis-pstatex.pdf |binary vignettes/04simLexis-pstatey.pdf |binary vignettes/04simLexis.R |only vignettes/04simLexis.pdf |only vignettes/04simLexis.tex | 18 ++--- vignettes/05yll-imm.pdf |binary vignettes/05yll-states.pdf |binary vignettes/05yll-sus.pdf |binary vignettes/05yll-tot.pdf |binary vignettes/05yll.R |only vignettes/05yll.pdf |only vignettes/05yll.tex | 10 +-- vignettes/fixall.bat | 22 +++--- 70 files changed, 266 insertions(+), 224 deletions(-)
Title: A Robust Interface to ArcGIS 'Geocoding Services'
Description: A very fast and robust interface to ArcGIS 'Geocoding
Services'. Provides capabilities for reverse geocoding, finding
address candidates, character-by-character search autosuggestion, and
batch geocoding. The public 'ArcGIS World Geocoder' is accessible for
free use via 'arcgisgeocode' for all services except batch geocoding.
'arcgisgeocode' also integrates with 'arcgisutils' to provide access
to custom locators or private 'ArcGIS World Geocoder' hosted on
'ArcGIS Enterprise'. Learn more in the 'Geocode service' API reference
<https://developers.arcgis.com/rest/geocode/api-reference/overview-world-geocoding-service.htm>.
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcgisgeocode versions 0.3.0 dated 2025-07-28 and 0.4.0 dated 2025-10-07
arcgisgeocode-0.3.0/arcgisgeocode/R/sysdata.rda |only arcgisgeocode-0.3.0/arcgisgeocode/README.md |only arcgisgeocode-0.3.0/arcgisgeocode/data/world_geocoder.rda |only arcgisgeocode-0.3.0/arcgisgeocode/man/world_geocoder.Rd |only arcgisgeocode-0.4.0/arcgisgeocode/DESCRIPTION | 8 arcgisgeocode-0.4.0/arcgisgeocode/MD5 | 28 +- arcgisgeocode-0.4.0/arcgisgeocode/NAMESPACE | 1 arcgisgeocode-0.4.0/arcgisgeocode/NEWS.md | 5 arcgisgeocode-0.4.0/arcgisgeocode/R/core-batch-geocode.R | 120 ++++++---- arcgisgeocode-0.4.0/arcgisgeocode/R/doc-data.R | 13 - arcgisgeocode-0.4.0/arcgisgeocode/R/list-geocoders.R | 22 + arcgisgeocode-0.4.0/arcgisgeocode/R/utils-geocoder-obj.R | 16 - arcgisgeocode-0.4.0/arcgisgeocode/data/esri_wkids.rda |binary arcgisgeocode-0.4.0/arcgisgeocode/man/list_geocoders.Rd | 11 arcgisgeocode-0.4.0/arcgisgeocode/src/rust/src/batch_geocode.rs | 18 - arcgisgeocode-0.4.0/arcgisgeocode/src/rust/src/find_candidates.rs | 3 arcgisgeocode-0.4.0/arcgisgeocode/tests/testthat/_snaps |only arcgisgeocode-0.4.0/arcgisgeocode/tests/testthat/test-geocode-addresses.R |only 18 files changed, 155 insertions(+), 90 deletions(-)
Title: Ecometric Models of Trait–Environment Relationships at the
Community Level
Description: Provides a framework for modeling relationships between functional traits and both quantitative and qualitative environmental variables at the community level. It includes tools for trait binning, likelihood-based environmental estimation, model evaluation, fossil projection into modern ecometric space, and result visualization. For more details see Vermillion et al. (2018) <doi:10.1007/978-3-319-94265-0_17>, Polly et al. (2011) <doi:10.1098/rspb.2010.2233> and Polly and Head (2015) <doi:10.1017/S1089332600002953>.
Author: Maria A. Hurtado-Materon [cre, aut],
Leila Siciliano-Martina [aut],
A. Michelle Lawing [cph, aut]
Maintainer: Maria A. Hurtado-Materon <maria.h.m_1995@tamu.edu>
Diff between commecometrics versions 1.0.0 dated 2025-07-22 and 1.0.1 dated 2025-10-07
DESCRIPTION | 6 ++--- MD5 | 42 +++++++++++++++++++-------------------- NEWS.md | 5 ++++ R/data.R | 4 +-- R/ecometric_model.R | 11 ++++------ R/ecometric_model_qual.R | 12 +++++------ R/ecometric_space_qual.R | 16 +++----------- R/optimal_bins.R | 2 - R/reconstruct_env.R | 4 +-- R/reconstruct_env_qual.R | 16 +++++++------- R/sensitivity_analysis.R | 8 +++---- R/sensitivity_analysis_qual.R | 8 +++---- build/vignette.rds |binary man/ecometric_model.Rd | 11 ++++------ man/ecometric_model_qual.Rd | 12 +++++------ man/ecometric_space_qual.Rd | 7 +----- man/fossils.Rd | 4 +-- man/optimal_bins.Rd | 2 - man/reconstruct_env.Rd | 4 +-- man/reconstruct_env_qual.Rd | 10 ++++----- man/sensitivity_analysis.Rd | 8 +++---- man/sensitivity_analysis_qual.Rd | 8 +++---- 22 files changed, 96 insertions(+), 104 deletions(-)
More information about commecometrics at CRAN
Permanent link
Title: Assemble 'SSN' Objects
Description: Import, create and assemble data needed to fit spatial-statistical stream-network models using the 'SSN2' package for 'R'. Streams, observations, and prediction locations are represented as simple features and specific tools provided to define topological relationships between features; calculate the hydrologic distances (with flow-direction preserved) and the spatial additive function used to weight converging stream segments; and export the topological, spatial, and attribute information to an `SSN` (spatial stream network) object, which can be efficiently stored, accessed and analysed in 'R'. A detailed description of methods used to calculate and format the spatial data can be found in Peterson, E.E. and Ver Hoef, J.M., (2014) <doi:10.18637/jss.v056.i02>.
Author: Erin Peterson [aut, cre] ,
Michael Dumelle [aut] ,
Alan Pearse [aut] ,
Dan Teleki [ctb],
Jay M. Ver Hoef [ctb]
Maintainer: Erin Peterson <erin@peterson-consulting.com>
Diff between SSNbler versions 1.1.0 dated 2025-03-25 and 1.1.1 dated 2025-10-06
SSNbler-1.1.0/SSNbler/R/lines_to_lsn_temp.R |only SSNbler-1.1.0/SSNbler/man/lines_to_lsn_temp.Rd |only SSNbler-1.1.0/SSNbler/tests/testthat/test-workflow.R |only SSNbler-1.1.1/SSNbler/DESCRIPTION | 15 + SSNbler-1.1.1/SSNbler/MD5 | 41 +++-- SSNbler-1.1.1/SSNbler/NAMESPACE | 1 SSNbler-1.1.1/SSNbler/NEWS.md | 11 + SSNbler-1.1.1/SSNbler/R/afv_edges.R | 4 SSNbler-1.1.1/SSNbler/R/get_pdist_nodes.R | 13 + SSNbler-1.1.1/SSNbler/R/lines_to_lsn.R | 83 +++++++---- SSNbler-1.1.1/SSNbler/R/pdist_node_coords.R | 18 +- SSNbler-1.1.1/SSNbler/README.md | 4 SSNbler-1.1.1/SSNbler/build/partial.rdb |binary SSNbler-1.1.1/SSNbler/build/vignette.rds |binary SSNbler-1.1.1/SSNbler/inst/CITATION | 4 SSNbler-1.1.1/SSNbler/inst/doc/introduction.html | 10 - SSNbler-1.1.1/SSNbler/man/lines_to_lsn.Rd | 8 - SSNbler-1.1.1/SSNbler/tests/testthat/helper.R |only SSNbler-1.1.1/SSNbler/tests/testthat/test-accum_edges.R |only SSNbler-1.1.1/SSNbler/tests/testthat/test-afv_edges.R |only SSNbler-1.1.1/SSNbler/tests/testthat/test-afv_sites.R |only SSNbler-1.1.1/SSNbler/tests/testthat/test-copy_lsn_to_temp.R |only SSNbler-1.1.1/SSNbler/tests/testthat/test-data.R |only SSNbler-1.1.1/SSNbler/tests/testthat/test-lines_to_lsn.R |only SSNbler-1.1.1/SSNbler/tests/testthat/test-sites_to_lsn.R |only SSNbler-1.1.1/SSNbler/tests/testthat/test-ssn_assemble.R |only SSNbler-1.1.1/SSNbler/tests/testthat/test-ssn_check.R |only SSNbler-1.1.1/SSNbler/tests/testthat/test-updist_edges.R |only SSNbler-1.1.1/SSNbler/tests/testthat/test-updist_sites.R |only 29 files changed, 136 insertions(+), 76 deletions(-)
Title: Animal Movement Modelling using Hidden Markov Models
Description: Provides tools for animal movement modelling using hidden Markov
models. These include processing of tracking data, fitting hidden Markov models
to movement data, visualization of data and fitted model, decoding of the state
process, etc. <doi:10.1111/2041-210X.12578>.
Author: Theo Michelot [aut, cre],
Roland Langrock [aut, ctb],
Toby Patterson [aut, ctb],
Brett McClintock [ctb],
Eric Rexstad [ctb]
Maintainer: Theo Michelot <theo.michelot@dal.ca>
Diff between moveHMM versions 1.11 dated 2025-06-23 and 1.12 dated 2025-10-06
DESCRIPTION | 10 +- MD5 | 24 ++--- NEWS.md | 8 + R/prepData.R | 11 +- inst/doc/moveHMM-custom-plots.pdf |binary inst/doc/moveHMM-example.pdf |binary inst/doc/moveHMM-guide.R | 162 +++++++++++++++++------------------ inst/doc/moveHMM-guide.pdf |binary inst/doc/moveHMM-starting-values.R | 94 ++++++++++---------- inst/doc/moveHMM-starting-values.pdf |binary man/prepData.Rd | 5 - src/densities.h | 12 +- src/nLogLike.cpp | 2 13 files changed, 168 insertions(+), 160 deletions(-)
Title: Use Data from the Czech Public Finance Database
Description: Get programmatic access to data from the Czech public
budgeting and accounting database, Státní pokladna
<https://monitor.statnipokladna.gov.cz/>.
Author: Petr Bouchal [aut, cre]
Maintainer: Petr Bouchal <pbouchal@gmail.com>
Diff between statnipokladna versions 0.7.4 dated 2024-08-21 and 0.7.7 dated 2025-10-06
statnipokladna-0.7.4/statnipokladna/man/add_codelist.Rd |only statnipokladna-0.7.4/statnipokladna/man/get_codelist.Rd |only statnipokladna-0.7.4/statnipokladna/man/get_dataset.Rd |only statnipokladna-0.7.4/statnipokladna/man/get_dataset_doc.Rd |only statnipokladna-0.7.4/statnipokladna/man/get_table.Rd |only statnipokladna-0.7.7/statnipokladna/DESCRIPTION | 15 +- statnipokladna-0.7.7/statnipokladna/MD5 | 63 ++++------ statnipokladna-0.7.7/statnipokladna/NAMESPACE | 5 statnipokladna-0.7.7/statnipokladna/NEWS.md | 18 ++ statnipokladna-0.7.7/statnipokladna/R/codelists.R | 47 ------- statnipokladna-0.7.7/statnipokladna/R/datasets.R | 41 ------ statnipokladna-0.7.7/statnipokladna/R/shared.R | 2 statnipokladna-0.7.7/statnipokladna/R/tables.R | 29 +--- statnipokladna-0.7.7/statnipokladna/R/utils.R | 6 statnipokladna-0.7.7/statnipokladna/README.md | 8 - statnipokladna-0.7.7/statnipokladna/build/vignette.rds |binary statnipokladna-0.7.7/statnipokladna/inst/doc/how-the-data-works-cz.Rmd | 14 +- statnipokladna-0.7.7/statnipokladna/inst/doc/how-the-data-works-cz.html | 17 +- statnipokladna-0.7.7/statnipokladna/inst/doc/statnipokladna.Rmd | 10 - statnipokladna-0.7.7/statnipokladna/inst/doc/statnipokladna.html | 14 +- statnipokladna-0.7.7/statnipokladna/inst/doc/workflow.Rmd | 2 statnipokladna-0.7.7/statnipokladna/inst/doc/workflow.html | 11 - statnipokladna-0.7.7/statnipokladna/man/sp_add_codelist.Rd | 2 statnipokladna-0.7.7/statnipokladna/man/sp_codelists.Rd | 4 statnipokladna-0.7.7/statnipokladna/man/sp_datasets.Rd | 2 statnipokladna-0.7.7/statnipokladna/man/sp_get_codelist.Rd | 2 statnipokladna-0.7.7/statnipokladna/man/sp_get_codelist_viewer.Rd | 2 statnipokladna-0.7.7/statnipokladna/man/sp_get_dataset.Rd | 2 statnipokladna-0.7.7/statnipokladna/man/sp_get_table.Rd | 4 statnipokladna-0.7.7/statnipokladna/man/sp_tables.Rd | 2 statnipokladna-0.7.7/statnipokladna/tests/testthat/test-datasets.R | 1 statnipokladna-0.7.7/statnipokladna/tests/testthat/test-tables.R | 1 statnipokladna-0.7.7/statnipokladna/vignettes/how-the-data-works-cz.Rmd | 14 +- statnipokladna-0.7.7/statnipokladna/vignettes/statnipokladna.Rmd | 10 - statnipokladna-0.7.7/statnipokladna/vignettes/workflow.Rmd | 2 35 files changed, 131 insertions(+), 219 deletions(-)
More information about statnipokladna at CRAN
Permanent link
Title: Shrinkage Covariance Matrix Estimators
Description: Provides nonparametric Steinian shrinkage estimators of the covariance matrix that are suitable in high dimensional settings, that is when the number of variables is larger than the sample size.
Author: Anestis Touloumis [aut, cre]
Maintainer: Anestis Touloumis <A.Touloumis@brighton.ac.uk>
Diff between ShrinkCovMat versions 1.4.0 dated 2019-07-30 and 2.1.0 dated 2025-10-06
ShrinkCovMat-1.4.0/ShrinkCovMat/inst/NEWS |only ShrinkCovMat-1.4.0/ShrinkCovMat/man/shrinkcovmat.equal.Rd |only ShrinkCovMat-1.4.0/ShrinkCovMat/man/shrinkcovmat.identity.Rd |only ShrinkCovMat-1.4.0/ShrinkCovMat/man/shrinkcovmat.unequal.Rd |only ShrinkCovMat-1.4.0/ShrinkCovMat/src/Makevars.win |only ShrinkCovMat-1.4.0/ShrinkCovMat/tests/testthat/test_shrinkage_equal.R |only ShrinkCovMat-1.4.0/ShrinkCovMat/tests/testthat/test_shrinkage_unequal.R |only ShrinkCovMat-2.1.0/ShrinkCovMat/DESCRIPTION | 28 ++- ShrinkCovMat-2.1.0/ShrinkCovMat/MD5 | 64 ++++---- ShrinkCovMat-2.1.0/ShrinkCovMat/NAMESPACE | 1 ShrinkCovMat-2.1.0/ShrinkCovMat/R/ShrinkCovMat-deprecated.R |only ShrinkCovMat-2.1.0/ShrinkCovMat/R/ShrinkCovMat-package.R | 29 ++- ShrinkCovMat-2.1.0/ShrinkCovMat/R/ShrinkCovMat_data.R | 12 - ShrinkCovMat-2.1.0/ShrinkCovMat/R/ShrinkCovMat_internals.R |only ShrinkCovMat-2.1.0/ShrinkCovMat/R/print.targetsel.R | 8 - ShrinkCovMat-2.1.0/ShrinkCovMat/R/shrinkcovmat.R |only ShrinkCovMat-2.1.0/ShrinkCovMat/R/shrinkcovmat.equal.R | 19 +- ShrinkCovMat-2.1.0/ShrinkCovMat/R/shrinkcovmat.identity.R | 21 +- ShrinkCovMat-2.1.0/ShrinkCovMat/R/shrinkcovmat.unequal.R | 22 +- ShrinkCovMat-2.1.0/ShrinkCovMat/R/targetsel.default.R | 8 - ShrinkCovMat-2.1.0/ShrinkCovMat/R/targetselection.R | 75 ++++------ ShrinkCovMat-2.1.0/ShrinkCovMat/build |only ShrinkCovMat-2.1.0/ShrinkCovMat/data/colon.rda |binary ShrinkCovMat-2.1.0/ShrinkCovMat/inst/CITATION | 21 -- ShrinkCovMat-2.1.0/ShrinkCovMat/inst/NEWS.Rd |only ShrinkCovMat-2.1.0/ShrinkCovMat/inst/doc |only ShrinkCovMat-2.1.0/ShrinkCovMat/man/ShrinkCovMat-deprecated.Rd |only ShrinkCovMat-2.1.0/ShrinkCovMat/man/ShrinkCovMat-package.Rd | 33 ++-- ShrinkCovMat-2.1.0/ShrinkCovMat/man/colon.Rd | 13 + ShrinkCovMat-2.1.0/ShrinkCovMat/man/shrinkcovmat.Rd |only ShrinkCovMat-2.1.0/ShrinkCovMat/man/shrinkcovmat.equal-deprecated.Rd |only ShrinkCovMat-2.1.0/ShrinkCovMat/man/shrinkcovmat.identity-deprecated.Rd |only ShrinkCovMat-2.1.0/ShrinkCovMat/man/shrinkcovmat.unequal-deprecated.Rd |only ShrinkCovMat-2.1.0/ShrinkCovMat/man/targetselection.Rd | 16 +- ShrinkCovMat-2.1.0/ShrinkCovMat/src/Makevars | 14 - ShrinkCovMat-2.1.0/ShrinkCovMat/src/RcppExports.cpp | 5 ShrinkCovMat-2.1.0/ShrinkCovMat/tests/testthat/test_internals.R |only ShrinkCovMat-2.1.0/ShrinkCovMat/tests/testthat/test_misc.R | 11 + ShrinkCovMat-2.1.0/ShrinkCovMat/tests/testthat/test_shrinkage_diagonal.R |only ShrinkCovMat-2.1.0/ShrinkCovMat/tests/testthat/test_shrinkage_identity.R | 26 +-- ShrinkCovMat-2.1.0/ShrinkCovMat/tests/testthat/test_shrinkage_spherical.R |only ShrinkCovMat-2.1.0/ShrinkCovMat/tests/testthat/test_targetselection.R | 28 +-- ShrinkCovMat-2.1.0/ShrinkCovMat/vignettes |only 43 files changed, 235 insertions(+), 219 deletions(-)
Title: Use Open Data from the Czech Statistical Office in R
Description: Get programmatic access to the open data provided by the
Czech Statistical Office (CZSO, <https://csu.gov.cz>).
Author: Petr Bouchal [aut, cre] ,
Jindra Lacko [ctb]
Maintainer: Petr Bouchal <pbouchal@gmail.com>
Diff between czso versions 0.4.3 dated 2025-09-09 and 0.4.4 dated 2025-10-06
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/catalogue.R | 2 ++ man/czso_filter_catalogue.Rd | 2 ++ tests/testthat/test-catalogue.R | 1 + tests/testthat/test-workflow-utilities.R | 2 ++ 7 files changed, 20 insertions(+), 9 deletions(-)
Title: Penalized Meta-Analysis
Description: Conduct penalized meta-analysis, see Van Lissa, Van Erp, & Clapper
(2023) <doi:10.31234/osf.io/6phs5>. In meta-analysis, there are
often between-study differences. These can be coded as moderator variables,
and controlled for using meta-regression. However, if the number of
moderators is large relative to the number of studies, such an analysis may
be overfit. Penalized meta-regression is useful in these cases, because
it shrinks the regression slopes of irrelevant moderators towards zero.
Author: Caspar J van Lissa [aut, cre] ,
Sara J van Erp [aut]
Maintainer: Caspar J van Lissa <c.j.vanlissa@tilburguniversity.edu>
This is a re-admission after prior archival of version 0.1.4 dated 2025-03-30
Diff between pema versions 0.1.4 dated 2025-03-30 and 0.1.5 dated 2025-10-06
DESCRIPTION | 9 MD5 | 21 R/brma.R | 932 +++++++++++++++++------------------ R/check_workshop_data.R | 7 build/partial.rdb |binary build/vignette.rds |binary inst/doc/meta-analysis_tutorial.R | 500 +++++++++--------- inst/doc/meta-analysis_tutorial.Rmd | 294 +++++------ inst/doc/meta-analysis_tutorial.html | 924 ++++------------------------------ man/check_workshop_data.Rd | 4 vignettes/meta-analysis_tutorial.Rmd | 294 +++++------ vignettes/tutorial_funnel.png |only 12 files changed, 1182 insertions(+), 1803 deletions(-)
Title: Supervised Feature Selection
Description: Interfaces for choosing important predictors in supervised
regression, classification, and censored regression models. Permuted
importance scores (Biecek and Burzykowski (2021)
<doi:10.1201/9780429027192>) can be computed for 'tidymodels' model
fits.
Author: Max Kuhn [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between important versions 0.2.0 dated 2025-09-05 and 0.2.1 dated 2025-10-06
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 6 ++++-- build/partial.rdb |binary inst/WORDLIST | 3 ++- man/important-package.Rd | 2 +- tests/testthat/test-plots.R | 30 ++++++++++-------------------- 7 files changed, 27 insertions(+), 34 deletions(-)
Title: German Election Database (GERDA)
Description: Provides tools to download comprehensive datasets of local,
state, and federal election results in Germany from 1990 to 2025. The package
facilitates access to data on turnout, vote shares for major parties, and
demographic information across different levels of government (municipal, state,
and federal). It offers access to geographically harmonized datasets
that account for changes in municipal boundaries over time and incorporate
mail-in voting districts. Users can easily retrieve, clean, and standardize
German electoral data, making it ready for analysis. Data is sourced from
<https://github.com/awiedem/german_election_data>.
Author: Hanno Hilbig [aut, cre]
Maintainer: Hanno Hilbig <hhilbig@ucdavis.edu>
Diff between gerda versions 0.2.0 dated 2025-08-19 and 0.2.1 dated 2025-10-06
DESCRIPTION | 6 +- MD5 | 10 ++-- NEWS.md | 11 +++++ R/load_gerda_web.R | 12 +++++ inst/doc/gerda.R | 22 +++++----- tests/testthat/test-load_gerda_web.R | 77 +++++++++++++++++++++++++++++++++++ 6 files changed, 119 insertions(+), 19 deletions(-)
Title: Fairness Evaluation Metrics with Confidence Intervals for Binary
Protected Attributes
Description: A collection of functions for computing fairness metrics for machine learning and statistical models, including confidence intervals for each metric. The package supports the evaluation of group-level fairness criterion commonly used in fairness research, particularly in healthcare for binary protected attributes. It is based on the overview of fairness in machine learning written by Gao et al (2024) <doi:10.48550/arXiv.2406.09307>.
Author: Jianhui Gao [aut] ,
Benjamin Smith [aut, cre] ,
Benson Chou [aut] ,
Jessica Gronsbell [aut]
Maintainer: Benjamin Smith <benyamin.smith@mail.utoronto.ca>
Diff between fairmetrics versions 1.0.6 dated 2025-09-11 and 1.0.7 dated 2025-10-06
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/CITATION | 38 +++++++++++++++++++++----------------- 3 files changed, 26 insertions(+), 22 deletions(-)
Title: Extracts the Backbone from Networks
Description: An implementation of methods for extracting a sparse unweighted network (i.e. a backbone)
from an unweighted network (e.g., Hamann et al., 2016 <doi:10.1007/s13278-016-0332-2>), a weighted network
(e.g., Serrano et al., 2009 <doi:10.1073/pnas.0808904106>), or a weighted projection (e.g., Neal et al., 2021
<doi:10.1038/s41598-021-03238-3>).
Author: Zachary Neal [aut, cre] ,
Rachel Domagalski [ctb],
Bruce Sagan [ctb],
Karl Godard [ctb]
Maintainer: Zachary Neal <zpneal@msu.edu>
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Title: Explore Socrata Data with Ease
Description: Provides an interface to search, read, query, and retrieve metadata for
datasets hosted on 'Socrata' open data portals. Supports all 'Socrata' data types,
including spatial data returned as 'sf' objects.
Author: Ryan Zomorrodi [aut, cre]
Maintainer: Ryan Zomorrodi <rzomor2@uic.edu>
Diff between socratadata versions 0.1.0 dated 2025-07-29 and 0.1.1 dated 2025-10-06
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Title: Visualizing and Quantifying Decision Uncertainty
Description: A suite of tools to help modelers and decision-makers effectively
interpret and communicate decision risk when evaluating multiple policy options.
It uses model outputs from uncertainty analysis for baseline scenarios and policy
alternatives to generate visual representations of uncertainty and quantitative
measures for assessing associated risks. For more details see
Wiggins and colleagues (2025) <doi:10.1371/journal.pone.0332522> and <https://dut.ihe.ca/>.
Author: Megan Wiggins [aut, cre] ,
Marie Betsy Varughese [aut] ,
Ellen Rafferty [aut] ,
Sasha van Katwyk [aut] ,
Christopher McCabe [aut] ,
Jeff Round [aut] ,
Erin Kirwin [aut] ,
Institute of Health Economics [cph, aut],
Canadian Network for Modelling Infect [...truncated...]
Maintainer: Megan Wiggins <mwiggins@ihe.ca>
Diff between DUToolkit versions 1.0.1 dated 2025-09-16 and 1.0.2 dated 2025-10-06
DESCRIPTION | 9 - MD5 | 30 ++--- NEWS.md | 11 + README.md | 198 ++++++++++++++++++++++++++------- inst/doc/Calculating_Risk.html | 5 inst/doc/DUToolkit.Rmd | 2 inst/doc/DUToolkit.html | 8 - inst/doc/Fan_Plots.html | 5 inst/doc/density_plots.html | 5 inst/doc/rain_plot.html | 5 inst/doc/temporal_plot.html | 5 man/figures/README-density-1.png |binary man/figures/README-fan-1.png |binary man/figures/README-plot_temporal-1.png |binary man/figures/README-rain-1.png |binary vignettes/DUToolkit.Rmd | 2 16 files changed, 214 insertions(+), 71 deletions(-)
Title: Fetch United States Congressional Records (1995-Present)
Description: Fetch United States Congressional Records from their API <https://api.govinfo.gov/docs/> such as congressional
speeches, speaker names, and metadata about congressional sessions, and detailed granule records.
Optional parameters allow users to specify congressional sessions,
and the maximum number of speeches to retrieve. Data is parsed, cleaned, and
returned in a structured dataframe for analysis.
Author: Steph Buongiorno [aut, cre]
Maintainer: Steph Buongiorno <steph.buon@proton.me>
Diff between uscongress versions 1.0.0 dated 2025-05-12 and 1.0.2 dated 2025-10-06
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/zzz_helpers.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Tools for Tidy Vowel Normalization
Description: An implementation of tidy speaker vowel normalization.
This includes generic functions for defining new normalization methods for
points, formant tracks, and Discrete Cosine Transform coefficients, as well
as convenience functions implementing established normalization methods.
References for the implemented methods are:
Johnson, Keith (2020) <doi:10.5334/labphon.196>
Lobanov, Boris (1971) <doi:10.1121/1.1912396>
Nearey, Terrance M. (1978) <https://sites.ualberta.ca/~tnearey/Nearey1978_compressed.pdf>
Syrdal, Ann K., and Gopal, H. S. (1986) <doi:10.1121/1.393381>
Watt, Dominic, and Fabricius, Anne (2002) <https://www.latl.leeds.ac.uk/article/evaluation-of-a-technique-for-improving-the-mapping-of-multiple-speakers-vowel-spaces-in-the-f1-f2-plane/>.
Author: Josef Fruehwald [cre, aut, cph]
Maintainer: Josef Fruehwald <JoFrhwld@gmail.com>
Diff between tidynorm versions 0.3.0 dated 2025-06-16 and 0.3.1 dated 2025-10-06
tidynorm-0.3.0/tidynorm/man/figures/logo.svg |only tidynorm-0.3.1/tidynorm/DESCRIPTION | 10 tidynorm-0.3.1/tidynorm/MD5 | 45 ++-- tidynorm-0.3.1/tidynorm/NAMESPACE | 1 tidynorm-0.3.1/tidynorm/NEWS.md | 5 tidynorm-0.3.1/tidynorm/R/dct.R | 13 + tidynorm-0.3.1/tidynorm/R/dct_norm.R | 18 + tidynorm-0.3.1/tidynorm/R/norm.R | 62 +++--- tidynorm-0.3.1/tidynorm/R/ops.R |only tidynorm-0.3.1/tidynorm/R/tidynorm-package.R | 1 tidynorm-0.3.1/tidynorm/R/track_norm.R | 101 +++++++--- tidynorm-0.3.1/tidynorm/R/utils.R | 62 ++++++ tidynorm-0.3.1/tidynorm/README.md | 4 tidynorm-0.3.1/tidynorm/inst/doc/dct.html | 10 tidynorm-0.3.1/tidynorm/inst/doc/norm-methods.html | 41 ++-- tidynorm-0.3.1/tidynorm/inst/doc/normalization-overview.html | 10 tidynorm-0.3.1/tidynorm/inst/doc/normalizing_formant_tracks.html | 2 tidynorm-0.3.1/tidynorm/man/figures/README-norm-1.png |binary tidynorm-0.3.1/tidynorm/man/figures/README-rnorm-1.png |binary tidynorm-0.3.1/tidynorm/man/figures/README-unnorm-1.png |binary tidynorm-0.3.1/tidynorm/man/figures/logo.png |binary tidynorm-0.3.1/tidynorm/man/figures/logo_design.svg |only tidynorm-0.3.1/tidynorm/src/dct.cpp | 3 tidynorm-0.3.1/tidynorm/tests/testthat/test-formant-ops.R |only tidynorm-0.3.1/tidynorm/tests/testthat/test-transforms.R |only tidynorm-0.3.1/tidynorm/tests/testthat/test_barkz_errors.R |only tidynorm-0.3.1/tidynorm/tests/testthat/test_reloc.R |only 27 files changed, 278 insertions(+), 110 deletions(-)
Title: SOM Bound to Realize Euclidean and Relational Outputs
Description: The stochastic (also called on-line) version of the Self-Organising
Map (SOM) algorithm is provided. Different versions of the
algorithm are implemented, for numeric and relational data and for
contingency tables as described, respectively, in Kohonen (2001)
<isbn:3-540-67921-9>, Olteanu & Villa-Vialaneix (2005)
<doi:10.1016/j.neucom.2013.11.047> and Cottrell et al (2004)
<doi:10.1016/j.neunet.2004.07.010>. The package also contains many
plotting features (to help the user interpret the results), can
handle (and impute) missing values and is delivered with a
graphical user interface based on 'shiny'.
Author: Nathalie Vialaneix [aut, cre] ,
Elise Maigne [aut],
Jerome Mariette [aut],
Madalina Olteanu [aut],
Fabrice Rossi [aut],
Laura Bendhaiba [ctb],
Julien Boelaert [ctb]
Maintainer: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Diff between SOMbrero versions 1.4.4 dated 2025-08-18 and 1.5.0 dated 2025-10-06
DESCRIPTION | 11 - MD5 | 42 ++++- NEWS.md | 8 R/superclasses.R | 292 ++++++++++++++++++++--------------- inst/doc/a-doc-SOMbrero-package.html | 12 - man/superClass.Rd | 11 + vignettes/c-doc-numericSOM_files |only 7 files changed, 233 insertions(+), 143 deletions(-)
Title: Estimate Gaussian and Student's t Mixture Vector Autoregressive
Models
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive, Student's t mixture vector autoregressive, and Gaussian and Student's t
mixture vector autoregressive models, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function and generalized
forecast error variance decomposition.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (2025) <doi:10.1080/07350015.2024.2322090>,
Savi Virolainen (in press) <doi:10.1016/j.ecosta.2025.09.003>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 2.2.0 dated 2025-06-19 and 2.2.1 dated 2025-10-06
DESCRIPTION | 8 +-- MD5 | 106 ++++++++++++++++++++-------------------- NEWS.md | 5 + R/GIRFandGFEVD.R | 6 +- R/GSMVARconstruction.R | 29 ++++------ R/MAINest.R | 7 +- R/data.R | 15 ++--- R/generateParams.R | 9 +-- R/geneticAlgorithm.R | 7 +- R/linearIRF.R | 2 R/loglikelihood.R | 7 +- R/parameterReforms.R | 9 +-- R/uncondMoments.R | 9 +-- README.md | 15 ++--- inst/doc/gmvarkit-vignette.Rnw | 1 inst/doc/gmvarkit-vignette.pdf |binary man/GAfit.Rd | 7 +- man/GFEVD.Rd | 6 +- man/GSMVAR.Rd | 7 +- man/Pearson_residuals.Rd | 7 +- man/add_data.Rd | 7 +- man/alt_gsmvar.Rd | 7 +- man/cond_moment_plot.Rd | 7 +- man/cond_moments.Rd | 7 +- man/diagnostic_plot.Rd | 7 +- man/estimate_sgsmvar.Rd | 7 +- man/euromone.Rd | 9 +-- man/fitGSMVAR.Rd | 7 +- man/get_Sigmas.Rd | 9 +-- man/get_regime_autocovs.Rd | 7 +- man/get_regime_autocovs_int.Rd | 7 +- man/get_test_Omega.Rd | 7 +- man/gsmvar_to_sgsmvar.Rd | 7 +- man/iterate_more.Rd | 7 +- man/linear_IRF.Rd | 2 man/loglikelihood.Rd | 7 +- man/loglikelihood_int.Rd | 7 +- man/print_std_errors.Rd | 7 +- man/profile_logliks.Rd | 7 +- man/quantile_residual_tests.Rd | 7 +- man/quantile_residuals.Rd | 7 +- man/quantile_residuals_int.Rd | 7 +- man/random_ind2.Rd | 9 +-- man/simulate.gsmvar.Rd | 7 +- man/simulate_gsmvar_int.Rd | 7 +- man/sort_W_and_lambdas.Rd | 9 +-- man/stmvar_to_gstmvar.Rd | 8 +-- man/swap_parametrization.Rd | 7 +- man/uncond_moments.Rd | 7 +- man/uncond_moments_int.Rd | 7 +- man/usamon.Rd | 2 man/usamone.Rd | 4 - vignettes/gmvarkit-vignette.Rnw | 1 vignettes/refs.bib | 29 ++++++---- 54 files changed, 239 insertions(+), 273 deletions(-)
Title: Exponential-Family Random Network Models
Description: Estimation of fully and partially observed Exponential-Family Random Network Models (ERNM). Exponential-family Random Graph Models (ERGM) and Gibbs Fields are special cases of ERNMs and can also be estimated with the package. Please cite Fellows and Handcock (2012), "Exponential-family Random Network Models" available at <doi:10.48550/arXiv.1208.0121>.
Author: Ian Fellows [aut],
Duncan Clark [aut, cre]
Maintainer: Duncan Clark <dac6@williams.edu>
Diff between ernm versions 1.0.2 dated 2025-07-28 and 1.0.3 dated 2025-10-06
ernm-1.0.2/ernm/man/as.BinaryNet.Rd |only ernm-1.0.2/ernm/man/as.network.DirectedNet.Rd |only ernm-1.0.2/ernm/man/as.network.Rcpp_DirectedNet.Rd |only ernm-1.0.2/ernm/man/as.network.Rcpp_UndirectedNet.Rd |only ernm-1.0.2/ernm/man/as.network.UndirectedNet.Rd |only ernm-1.0.2/ernm/man/plot.Rcpp_DirectedNet.Rd |only ernm-1.0.2/ernm/man/plot.Rcpp_UndirectedNet.Rd |only ernm-1.0.3/ernm/DESCRIPTION | 8 ernm-1.0.3/ernm/MD5 | 108 +++--- ernm-1.0.3/ernm/NAMESPACE | 6 ernm-1.0.3/ernm/R/00-classes.R | 6 ernm-1.0.3/ernm/R/BinaryNet.R | 152 +++++++-- ernm-1.0.3/ernm/R/ernm-fit.R | 44 +- ernm-1.0.3/ernm/R/ernm-gof.R | 104 ++++-- ernm-1.0.3/ernm/R/ernm-methods.R | 296 +++++-------------- ernm-1.0.3/ernm/R/ernm-models.R | 78 ++--- ernm-1.0.3/ernm/R/ernm.R | 189 ++++++++++-- ernm-1.0.3/ernm/R/likelihoods.R | 108 ++++-- ernm-1.0.3/ernm/R/method_registration.R | 1 ernm-1.0.3/ernm/R/roxygen.R | 240 ++++++++++++++- ernm-1.0.3/ernm/R/util.R | 17 - ernm-1.0.3/ernm/README.md | 189 +++++++++++- ernm-1.0.3/ernm/inst/include/BinaryNet.h | 6 ernm-1.0.3/ernm/inst/include/Constraints.h | 2 ernm-1.0.3/ernm/inst/include/DyadToggles.h | 3 ernm-1.0.3/ernm/man/BinaryNet.Rd | 112 ++++++- ernm-1.0.3/ernm/man/DirectedNet-class.Rd | 2 ernm-1.0.3/ernm/man/ErnmModels.Rd | 5 ernm-1.0.3/ernm/man/ErnmSamplers.Rd | 5 ernm-1.0.3/ernm/man/Figures |only ernm-1.0.3/ernm/man/MissingErnmModel.Rd | 8 ernm-1.0.3/ernm/man/UndirectedNet-class.Rd | 2 ernm-1.0.3/ernm/man/calculateStatistics.Rd | 18 - ernm-1.0.3/ernm/man/call-symbols.Rd | 3 ernm-1.0.3/ernm/man/createCppModel.Rd | 24 + ernm-1.0.3/ernm/man/createCppSampler.Rd | 65 +++- ernm-1.0.3/ernm/man/ernm-formula.Rd |only ernm-1.0.3/ernm/man/ernm-terms.Rd |only ernm-1.0.3/ernm/man/ernm.Rd | 43 ++ ernm-1.0.3/ernm/man/ernmFit.Rd | 26 - ernm-1.0.3/ernm/man/ernmPackageSkeleton.Rd | 2 ernm-1.0.3/ernm/man/ernm_gof.Rd | 56 ++- ernm-1.0.3/ernm/man/extract-methods.Rd | 41 ++ ernm-1.0.3/ernm/man/fullErnmLikelihood.Rd | 12 ernm-1.0.3/ernm/man/logLik.ernm.Rd |only ernm-1.0.3/ernm/man/marErnmLikelihood.Rd | 8 ernm-1.0.3/ernm/man/mcmcEss.Rd | 6 ernm-1.0.3/ernm/man/mcmcse.Rd | 6 ernm-1.0.3/ernm/man/plot.ernm.Rd | 2 ernm-1.0.3/ernm/man/print.ErnmSummary.Rd |only ernm-1.0.3/ernm/man/print.ernm.Rd | 4 ernm-1.0.3/ernm/man/registerDirectedStatistic.Rd | 5 ernm-1.0.3/ernm/man/register_rcpp_net_methods.Rd | 1 ernm-1.0.3/ernm/man/runErnmCppTests.Rd | 7 ernm-1.0.3/ernm/man/simulateStatistics.Rd | 21 + ernm-1.0.3/ernm/man/summary.ernm.Rd | 6 ernm-1.0.3/ernm/man/taperedErnmLikelihood.Rd | 8 ernm-1.0.3/ernm/src/VarAttrib.cpp | 3 ernm-1.0.3/ernm/src/test_TaperedModel.cpp | 4 ernm-1.0.3/ernm/tests/testthat/test-BinaryNet.R | 1 60 files changed, 1447 insertions(+), 616 deletions(-)
Title: Non-Crossing Additive Regression Quantiles and Non-Parametric
Growth Charts
Description: Fits non-crossing regression quantiles as a function of linear covariates and multiple smooth terms, including varying coefficients, via B-splines with L1-norm difference penalties.
Random intercepts and variable selection are allowed via the lasso penalties.
The smoothing parameters are estimated as part of the model fitting, see Muggeo and others (2021) <doi:10.1177/1471082X20929802>. Monotonicity and concavity
constraints on the fitted curves are allowed, see Muggeo and others (2013) <doi:10.1007/s10651-012-0232-1>,
and also <doi:10.13140/RG.2.2.12924.85122> or <doi:10.13140/RG.2.2.29306.21445> some code examples.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between quantregGrowth versions 1.7-1 dated 2024-05-20 and 1.7-2 dated 2025-10-06
DESCRIPTION | 11 - MD5 | 30 +-- NEWS | 44 ---- R/gcrq.r | 45 +++-- R/ncross.rq.fitX.R | 345 ++++++++++++++++++++++++-------------- R/ncross.rq.fitXB.r | 375 ++++++++++++++++++++++++++---------------- R/ncross.rq.fitXBsparse.r | 25 +- build/vignette.rds |binary inst/doc/quantregGrowth.R | 30 ++- inst/doc/quantregGrowth.Rmd | 16 + inst/doc/quantregGrowth.html | 256 ++++++++++++---------------- man/gcrq.Rd | 24 +- man/logLik.gcrq.Rd | 4 man/ncross.rq.fitXB.Rd | 12 + man/quantregGrowth-package.Rd | 4 vignettes/quantregGrowth.Rmd | 16 + 16 files changed, 711 insertions(+), 526 deletions(-)
More information about quantregGrowth at CRAN
Permanent link
Title: Do 16s Data Analysis and Generate Figures
Description: Provides functions to enhance the available
statistical analysis procedures in R by providing simple functions to
analysis and visualize the 16S rRNA data.Here we present a tutorial
with minimum working examples to demonstrate usage and dependencies.
Author: Kai Guo [aut, cre],
Pan Gao [aut]
Maintainer: Kai Guo <guokai8@gmail.com>
Diff between microbial versions 0.0.21 dated 2024-05-15 and 0.0.22 dated 2025-10-06
DESCRIPTION | 8 - MD5 | 16 +-- R/Functions.R | 18 +-- build/vignette.rds |binary inst/doc/microbial.R | 24 ++-- inst/doc/microbial.Rmd | 4 inst/doc/microbial.html | 252 +++++++++++++++++++++++------------------------- man/preRef.Rd | 5 vignettes/microbial.Rmd | 4 9 files changed, 156 insertions(+), 175 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.6.2 dated 2025-08-20 and 0.6.3 dated 2025-10-06
DESCRIPTION | 6 MD5 | 26 +-- NEWS.md | 6 R/MaestroPipeline.R | 5 inst/doc/maestro-1-quick-start.html | 6 inst/doc/maestro-2-motivation-concepts.html | 141 +++++++++++++++++ inst/doc/maestro-3-advanced-scheduling.html | 157 ++++++++++++++++++- inst/doc/maestro-3-advanced-scheduling.qmd | 2 inst/doc/maestro-4-directed-acyclic-graphs.html | 18 +- inst/doc/maestro-5-logging.html | 191 ++++++++++++++++++++---- inst/doc/maestro-6-deployment.html | 141 +++++++++++++++++ inst/doc/maestro-7-tag-reference.html | 141 +++++++++++++++++ man/figures/README-/unnamed-chunk-3.svg | 2 vignettes/maestro-3-advanced-scheduling.qmd | 2 14 files changed, 772 insertions(+), 72 deletions(-)
Title: A Very Fast 2D Concave Hull Algorithm
Description: The concaveman function ports the 'concaveman' (<https://github.com/mapbox/concaveman>) library from 'mapbox'. It computes the concave polygon(s) for one or several set of points.
Author: Joel Gombin [cre, aut],
Ramnath Vaidyanathan [aut],
Vladimir Agafonkin [aut],
Mapbox [cph]
Maintainer: Joel Gombin <joel.gombin@gmail.com>
Diff between concaveman versions 1.1.0 dated 2020-05-11 and 1.2.0 dated 2025-10-06
DESCRIPTION | 14 +++++++------- MD5 | 15 ++++++++------- NAMESPACE | 2 +- NEWS.md | 3 +++ R/concaveman-pkg.R | 9 ++------- R/concaveman.R | 39 ++++++++++++++++++++++++++++++--------- man/concaveman-package.Rd |only man/concaveman.Rd | 10 +++++----- tests/testthat/test_concaveman.R | 16 ++++++++++++++++ 9 files changed, 72 insertions(+), 36 deletions(-)
Title: Nominal Data Mining Analysis
Description: Functions for nominal data mining based on bipartite graphs, which build a pipeline for analysis and missing values imputation. Methods are mainly from the paper: Jafari, Mohieddin, et al. (2021) <doi:10.1101/2021.03.18.436040>, some new ones are also included.
Author: Mohieddin Jafari [aut, cre],
Cheng Chen [aut],
Zangene Ehsan [aut]
Maintainer: Mohieddin Jafari <mohieddin.jafari@helsinki.fi>
Diff between NIMAA versions 0.2.1 dated 2022-04-11 and 0.2.2 dated 2025-10-06
NIMAA-0.2.1/NIMAA/man/NIMAA.Rd |only NIMAA-0.2.2/NIMAA/DESCRIPTION | 17 NIMAA-0.2.2/NIMAA/MD5 | 26 - NIMAA-0.2.2/NIMAA/NEWS.md | 4 NIMAA-0.2.2/NIMAA/R/NIMAA-package.R | 4 NIMAA-0.2.2/NIMAA/R/data.R | 2 NIMAA-0.2.2/NIMAA/R/plot-incidence-matrix.R | 2 NIMAA-0.2.2/NIMAA/README.md | 4 NIMAA-0.2.2/NIMAA/build/vignette.rds |binary NIMAA-0.2.2/NIMAA/inst/doc/NIMAA-vignette.R | 38 - NIMAA-0.2.2/NIMAA/inst/doc/NIMAA-vignette.html | 540 ++++++++++++------------- NIMAA-0.2.2/NIMAA/man/NIMAA-package.Rd |only NIMAA-0.2.2/NIMAA/man/beatAML.Rd | 2 NIMAA-0.2.2/NIMAA/man/figures/logo.png |binary NIMAA-0.2.2/NIMAA/man/plotIncMatrix.Rd | 2 15 files changed, 330 insertions(+), 311 deletions(-)