Title: A Lightweight Interface Between 'igraph' and 'ggplot2' Graphics
Description: An interface for rendering 'igraph' objects as 'ggplot2' graphics
within a normalized coordinate space. 'RGraphSpace' implements new
geometries that treat a graph as a single coherent object, synchronizing
node and edge layers under standard aesthetic mappings. Node features are
resolved on demand, supporting high-dimensional data without expanding
node tables. Spatial alignment is available at the pixel level,
with node coordinates anchored to pixel centers through a half-pixel
offset, enabling precise node positioning over external reference frames
such as images and maps.
Author: Sysbiolab Team [aut],
Flavio Kessler [ctb],
Jonathan Back [ctb],
Lana Querne [ctb],
Victor Apolonio [ctb],
Vinicius Chagas [ctb],
Mauro Castro [cre]
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
Diff between RGraphSpace versions 1.4.1 dated 2026-06-24 and 1.5.0 dated 2026-07-23
RGraphSpace-1.4.1/RGraphSpace/R/gspace-supplements.R |only RGraphSpace-1.4.1/RGraphSpace/man/GeomGraphSpace.Rd |only RGraphSpace-1.5.0/RGraphSpace/DESCRIPTION | 31 RGraphSpace-1.5.0/RGraphSpace/MD5 | 93 - RGraphSpace-1.5.0/RGraphSpace/NAMESPACE | 11 RGraphSpace-1.5.0/RGraphSpace/R/annotation-gspace.R | 69 RGraphSpace-1.5.0/RGraphSpace/R/geom-edgespace.R | 750 ++++++++-- RGraphSpace-1.5.0/RGraphSpace/R/geom-graphspace.R | 483 ------ RGraphSpace-1.5.0/RGraphSpace/R/geom-nodespace.R | 209 +- RGraphSpace-1.5.0/RGraphSpace/R/gspace-addition.R |only RGraphSpace-1.5.0/RGraphSpace/R/gspace-checks.R | 5 RGraphSpace-1.5.0/RGraphSpace/R/gspace-classes.R | 242 ++- RGraphSpace-1.5.0/RGraphSpace/R/gspace-coercion.R | 33 RGraphSpace-1.5.0/RGraphSpace/R/gspace-constructor.R | 184 ++ RGraphSpace-1.5.0/RGraphSpace/R/gspace-generics.R | 22 RGraphSpace-1.5.0/RGraphSpace/R/gspace-ggplot-constructor.R | 31 RGraphSpace-1.5.0/RGraphSpace/R/gspace-methods.R | 330 ++-- RGraphSpace-1.5.0/RGraphSpace/R/gspace-misc.R | 23 RGraphSpace-1.5.0/RGraphSpace/R/gspace-normalize.R | 135 - RGraphSpace-1.5.0/RGraphSpace/R/gspace-subscript.R |only RGraphSpace-1.5.0/RGraphSpace/R/gspace-subset.R |only RGraphSpace-1.5.0/RGraphSpace/R/gspace-themes.R | 117 - RGraphSpace-1.5.0/RGraphSpace/R/gspace-validation.R | 116 + RGraphSpace-1.5.0/RGraphSpace/build/vignette.rds |binary RGraphSpace-1.5.0/RGraphSpace/data/datalist | 3 RGraphSpace-1.5.0/RGraphSpace/data/gs_image_toy.RData |only RGraphSpace-1.5.0/RGraphSpace/data/gtoy1.RData |binary RGraphSpace-1.5.0/RGraphSpace/inst/NEWS.Rd | 9 RGraphSpace-1.5.0/RGraphSpace/inst/doc/RGraphSpace.R | 91 - RGraphSpace-1.5.0/RGraphSpace/inst/doc/RGraphSpace.Rmd | 120 - RGraphSpace-1.5.0/RGraphSpace/inst/doc/RGraphSpace.html | 250 ++- RGraphSpace-1.5.0/RGraphSpace/man/GraphSpace-accessors.Rd | 14 RGraphSpace-1.5.0/RGraphSpace/man/GraphSpace-class.Rd | 12 RGraphSpace-1.5.0/RGraphSpace/man/GraphSpace-methods.Rd | 14 RGraphSpace-1.5.0/RGraphSpace/man/GraphSpace-subscript.Rd |only RGraphSpace-1.5.0/RGraphSpace/man/RGraphSpace-package.Rd | 4 RGraphSpace-1.5.0/RGraphSpace/man/StatEdgeSpace.Rd | 2 RGraphSpace-1.5.0/RGraphSpace/man/annotation_gspace_image.Rd | 23 RGraphSpace-1.5.0/RGraphSpace/man/geom_edgespace.Rd | 112 + RGraphSpace-1.5.0/RGraphSpace/man/geom_graphspace.Rd | 213 -- RGraphSpace-1.5.0/RGraphSpace/man/geom_nodespace.Rd | 77 - RGraphSpace-1.5.0/RGraphSpace/man/getGraphSpace-methods.Rd | 3 RGraphSpace-1.5.0/RGraphSpace/man/gs_add_edges.Rd |only RGraphSpace-1.5.0/RGraphSpace/man/gs_add_nodes.Rd |only RGraphSpace-1.5.0/RGraphSpace/man/gs_image_toy.Rd |only RGraphSpace-1.5.0/RGraphSpace/man/gs_subset.Rd |only RGraphSpace-1.5.0/RGraphSpace/man/normalizeGraphSpace-methods.Rd | 14 RGraphSpace-1.5.0/RGraphSpace/man/plotGraphSpace-methods.Rd | 40 RGraphSpace-1.5.0/RGraphSpace/man/summary-GraphSpace-method.Rd |only RGraphSpace-1.5.0/RGraphSpace/man/theme_gspace.Rd | 2 RGraphSpace-1.5.0/RGraphSpace/vignettes/RGraphSpace.Rmd | 120 - RGraphSpace-1.5.0/RGraphSpace/vignettes/bibliography.bib | 19 RGraphSpace-1.5.0/RGraphSpace/vignettes/clipboard.js |only RGraphSpace-1.5.0/RGraphSpace/vignettes/custom.css | 42 54 files changed, 2405 insertions(+), 1663 deletions(-)
Title: Main Path Analysis for Citation and Directed Networks
Description: Implements Main Path Analysis (MPA) as introduced by Hummon and
Doreian (1989) <doi:10.1016/0378-8733(89)90017-8>. Given a directed acyclic
graph (DAG) representing a citation or precedence network, the package
computes traversal weights (SPC, SPLC, SPNP) for each edge and extracts
the global, local, and key-route main paths. Also provides tools for DAG
validation, node role classification (source/terminal/user), per-component
path extraction for disconnected networks, and scale-free network testing.
Accepts 'igraph' objects or edge-list data frames as input. Includes
readers for 'Pajek' (.net) and 'Gephi' export (.gexf, .graphml) files.
Author: Paulo H Resende [aut, cre]
Maintainer: Paulo H Resende <paulo.resende@ttu.edu>
Diff between mpaR versions 0.4.0 dated 2026-06-26 and 0.5.0 dated 2026-07-23
DESCRIPTION | 8 MD5 | 62 +- NAMESPACE | 35 - NEWS.md | 25 + R/build_citation_network.R |only R/component_paths.R | 4 R/fetch_openalex.R |only R/mainpath.R | 731 +++++++++++++++++----------------- R/mpa.R | 173 ++++---- R/node_edge_weights.R | 247 +++++------ R/plot.R | 439 ++++++++++---------- R/read_pajek.R | 476 +++++++++++----------- R/utils.R | 348 ++++++++++------ inst/extdata/sample_network_pajek.net | 258 ++++++------ man/build_citation_network.Rd |only man/check_dag.Rd | 104 ++-- man/check_scale_free.Rd | 134 +++--- man/classify_nodes.Rd | 170 +++---- man/component_paths.Rd | 4 man/edge_weights.Rd | 91 ++-- man/fetch_openalex.Rd |only man/key_route_sweep.Rd |only man/main_path.Rd | 292 +++++++------ man/mpa.Rd | 179 ++++---- man/mpaR-package.Rd | 56 +- man/node_weights.Rd | 110 ++--- man/plot_mpa.Rd | 287 +++++++------ man/read_gephi_export.Rd | 94 ++-- man/read_pajek.Rd | 106 ++-- man/traversal_weights.Rd | 136 +++--- tests/testthat/setup.R | 14 tests/testthat/test-keyroute-sweep.R |only tests/testthat/test-mainpath.R | 1 tests/testthat/test-read_pajek.R | 240 +++++------ tests/testthat/test-weights.R | 31 - 35 files changed, 2547 insertions(+), 2308 deletions(-)
Title: Standardized Moderation Effect and Its Confidence Interval
Description: Functions for computing a standardized moderation effect
in moderated regression and forming its confidence interval
by nonparametric bootstrapping as proposed in
Cheung, Cheung, Lau, Hui, and Vong (2022)
<doi:10.1037/hea0001188>. Also includes simple-to-use
functions for computing conditional effects (unstandardized
or standardized) and plotting moderation effects.
Author: Shu Fai Cheung [aut, cre] ,
David Weng Ngai Vong [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between stdmod versions 0.2.13 dated 2026-05-04 and 0.2.14 dated 2026-07-23
DESCRIPTION | 8 MD5 | 74 ++-- NEWS.md | 11 R/condeff.R | 18 + R/plotmod.R | 19 + R/std_selected.R | 14 R/stdmod_lavaan.R | 13 README.md | 79 ++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/cond_effect.Rmd | 543 ++++++++++++++++++----------------- inst/doc/cond_effect.html | 28 + inst/doc/moderation.Rmd | 35 +- inst/doc/moderation.html | 40 +- inst/doc/plotmod.Rmd | 8 inst/doc/plotmod.html | 12 inst/doc/std_selected.Rmd | 16 - inst/doc/std_selected.html | 20 + inst/doc/stdmod.Rmd | 16 - inst/doc/stdmod.html | 20 + inst/doc/stdmod_lavaan.Rmd | 16 - inst/doc/stdmod_lavaan.html | 21 + man/cond_effect.Rd | 16 + man/plotmod.Rd | 18 + man/std_selected.Rd | 15 man/stdmod-package.Rd | 5 man/stdmod_lavaan.Rd | 13 vignettes/cond_effect.Rmd | 543 ++++++++++++++++++----------------- vignettes/cond_effect.Rmd.original | 21 + vignettes/moderation.Rmd | 35 +- vignettes/moderation.Rmd.original | 13 vignettes/plotmod.Rmd | 8 vignettes/std_selected.Rmd | 16 - vignettes/std_selected.Rmd.original | 14 vignettes/stdmod.Rmd | 16 - vignettes/stdmod.Rmd.original | 14 vignettes/stdmod_lavaan.Rmd | 16 - vignettes/stdmod_lavaan.Rmd.original | 10 38 files changed, 1155 insertions(+), 629 deletions(-)
Title: Pipe-Friendly Framework for Basic Statistical Tests
Description: Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy,
for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses.
The output of each test is automatically transformed into a tidy data frame to facilitate visualization.
Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix.
Functions are also included to facilitate the analysis of factorial experiments, including purely 'within-Ss' designs
(repeated measures), purely 'between-Ss' designs, and mixed 'within-and-between-Ss' designs.
It's also possible to compute several effect size metrics, including "eta squared" for ANOVA, "Cohen's d" for t-test and
'Cramer V' for the association between categorical variables.
The package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between rstatix versions 1.0.0 dated 2026-07-03 and 1.1.0 dated 2026-07-23
rstatix-1.0.0/rstatix/R/get_manova_table.R |only rstatix-1.0.0/rstatix/tools |only rstatix-1.1.0/rstatix/DESCRIPTION | 27 rstatix-1.1.0/rstatix/MD5 | 285 +++++---- rstatix-1.1.0/rstatix/NAMESPACE | 10 rstatix-1.1.0/rstatix/NEWS.md | 53 + rstatix-1.1.0/rstatix/R/anova_summary.R | 10 rstatix-1.1.0/rstatix/R/anova_test.R | 14 rstatix-1.1.0/rstatix/R/as_cor_mat.R | 5 rstatix-1.1.0/rstatix/R/box_m.R | 5 rstatix-1.1.0/rstatix/R/check_test_assumptions.R |only rstatix-1.1.0/rstatix/R/chisq_test.R | 5 rstatix-1.1.0/rstatix/R/cliff_delta.R |only rstatix-1.1.0/rstatix/R/cochran_qtest.R | 5 rstatix-1.1.0/rstatix/R/cohens_d.R | 176 +++++- rstatix-1.1.0/rstatix/R/conover_test.R | 12 rstatix-1.1.0/rstatix/R/cor_as_symbols.R | 5 rstatix-1.1.0/rstatix/R/cor_mark_significant.R | 5 rstatix-1.1.0/rstatix/R/cor_mat.R | 5 rstatix-1.1.0/rstatix/R/cor_plot.R | 5 rstatix-1.1.0/rstatix/R/cor_reorder.R | 5 rstatix-1.1.0/rstatix/R/cor_reshape.R | 5 rstatix-1.1.0/rstatix/R/cor_select.R | 8 rstatix-1.1.0/rstatix/R/cor_test.R | 5 rstatix-1.1.0/rstatix/R/cramer_v.R | 137 ++++ rstatix-1.1.0/rstatix/R/dunn_test.R | 34 + rstatix-1.1.0/rstatix/R/dunnett_test.R | 9 rstatix-1.1.0/rstatix/R/emmeans_test.R | 9 rstatix-1.1.0/rstatix/R/eta_squared.R | 89 ++- rstatix-1.1.0/rstatix/R/fisher_test.R | 5 rstatix-1.1.0/rstatix/R/fligner_test.R | 5 rstatix-1.1.0/rstatix/R/friedman_conover_test.R | 15 rstatix-1.1.0/rstatix/R/friedman_effsize.R | 26 rstatix-1.1.0/rstatix/R/friedman_nemenyi_test.R | 10 rstatix-1.1.0/rstatix/R/friedman_test.R | 9 rstatix-1.1.0/rstatix/R/games_howell_test.R | 30 - rstatix-1.1.0/rstatix/R/get_pvalue_position.R | 15 rstatix-1.1.0/rstatix/R/get_summary_stats.R | 5 rstatix-1.1.0/rstatix/R/get_test_label.R | 276 +++++++++ rstatix-1.1.0/rstatix/R/kruskal_effesize.R | 66 +- rstatix-1.1.0/rstatix/R/kruskal_test.R | 5 rstatix-1.1.0/rstatix/R/ks_test.R | 5 rstatix-1.1.0/rstatix/R/levene_test.R | 5 rstatix-1.1.0/rstatix/R/mahalanobis_distance.R | 5 rstatix-1.1.0/rstatix/R/mcnemar_test.R | 5 rstatix-1.1.0/rstatix/R/omega_squared.R |only rstatix-1.1.0/rstatix/R/outliers.R | 5 rstatix-1.1.0/rstatix/R/posthoc_test.R |only rstatix-1.1.0/rstatix/R/prop_test.R | 5 rstatix-1.1.0/rstatix/R/prop_trend_test.R | 5 rstatix-1.1.0/rstatix/R/reexports.R | 3 rstatix-1.1.0/rstatix/R/rstatix-references.R |only rstatix-1.1.0/rstatix/R/shapiro_test.R | 9 rstatix-1.1.0/rstatix/R/sign_test.R | 17 rstatix-1.1.0/rstatix/R/t_test.R | 94 +++ rstatix-1.1.0/rstatix/R/tidy_glance.R |only rstatix-1.1.0/rstatix/R/tukey_hsd.R | 5 rstatix-1.1.0/rstatix/R/utilities.R | 80 ++ rstatix-1.1.0/rstatix/R/utilities_two_sample_test.R | 24 rstatix-1.1.0/rstatix/R/utils-manova.R | 3 rstatix-1.1.0/rstatix/R/welch_anova_test.R | 5 rstatix-1.1.0/rstatix/R/wilcox_effsize.R | 91 ++- rstatix-1.1.0/rstatix/R/wilcox_test.R | 165 +++++ rstatix-1.1.0/rstatix/README.md | 286 ++++++---- rstatix-1.1.0/rstatix/build |only rstatix-1.1.0/rstatix/inst/WORDLIST | 151 ++--- rstatix-1.1.0/rstatix/inst/doc |only rstatix-1.1.0/rstatix/man/Manova.Rd | 5 rstatix-1.1.0/rstatix/man/anova_summary.Rd | 5 rstatix-1.1.0/rstatix/man/anova_test.Rd | 14 rstatix-1.1.0/rstatix/man/as_cor_mat.Rd | 5 rstatix-1.1.0/rstatix/man/box_m.Rd | 7 rstatix-1.1.0/rstatix/man/check_test_assumptions.Rd |only rstatix-1.1.0/rstatix/man/chisq_test.Rd | 7 rstatix-1.1.0/rstatix/man/cliff_delta.Rd |only rstatix-1.1.0/rstatix/man/cochran_qtest.Rd | 7 rstatix-1.1.0/rstatix/man/cohens_d.Rd | 62 ++ rstatix-1.1.0/rstatix/man/conover_test.Rd | 12 rstatix-1.1.0/rstatix/man/cor_as_symbols.Rd | 5 rstatix-1.1.0/rstatix/man/cor_mark_significant.Rd | 7 rstatix-1.1.0/rstatix/man/cor_mat.Rd | 5 rstatix-1.1.0/rstatix/man/cor_plot.Rd | 5 rstatix-1.1.0/rstatix/man/cor_reorder.Rd | 5 rstatix-1.1.0/rstatix/man/cor_reshape.Rd | 5 rstatix-1.1.0/rstatix/man/cor_select.Rd | 8 rstatix-1.1.0/rstatix/man/cor_test.Rd | 5 rstatix-1.1.0/rstatix/man/cramer_v.Rd | 95 +++ rstatix-1.1.0/rstatix/man/dunn_test.Rd | 16 rstatix-1.1.0/rstatix/man/dunnett_test.Rd | 9 rstatix-1.1.0/rstatix/man/emmeans_test.Rd | 11 rstatix-1.1.0/rstatix/man/eta_squared.Rd | 39 + rstatix-1.1.0/rstatix/man/figures |only rstatix-1.1.0/rstatix/man/fisher_test.Rd | 7 rstatix-1.1.0/rstatix/man/fligner_test.Rd | 5 rstatix-1.1.0/rstatix/man/friedman_conover_test.Rd | 15 rstatix-1.1.0/rstatix/man/friedman_effsize.Rd | 23 rstatix-1.1.0/rstatix/man/friedman_nemenyi_test.Rd | 10 rstatix-1.1.0/rstatix/man/friedman_test.Rd | 11 rstatix-1.1.0/rstatix/man/games_howell_test.Rd | 21 rstatix-1.1.0/rstatix/man/get_pvalue_position.Rd | 17 rstatix-1.1.0/rstatix/man/get_summary_stats.Rd | 5 rstatix-1.1.0/rstatix/man/get_test_label.Rd | 42 + rstatix-1.1.0/rstatix/man/kruskal_effsize.Rd | 30 + rstatix-1.1.0/rstatix/man/kruskal_test.Rd | 7 rstatix-1.1.0/rstatix/man/ks_test.Rd | 5 rstatix-1.1.0/rstatix/man/levene_test.Rd | 7 rstatix-1.1.0/rstatix/man/mahalanobis_distance.Rd | 7 rstatix-1.1.0/rstatix/man/mcnemar_test.Rd | 7 rstatix-1.1.0/rstatix/man/omega_squared.Rd |only rstatix-1.1.0/rstatix/man/outliers.Rd | 7 rstatix-1.1.0/rstatix/man/posthoc_test.Rd |only rstatix-1.1.0/rstatix/man/prop_test.Rd | 7 rstatix-1.1.0/rstatix/man/prop_trend_test.Rd | 7 rstatix-1.1.0/rstatix/man/reexports.Rd | 11 rstatix-1.1.0/rstatix/man/rstatix-references.Rd |only rstatix-1.1.0/rstatix/man/shapiro_test.Rd | 11 rstatix-1.1.0/rstatix/man/sign_test.Rd | 21 rstatix-1.1.0/rstatix/man/t_test.Rd | 21 rstatix-1.1.0/rstatix/man/tidy.rstatix_test.Rd |only rstatix-1.1.0/rstatix/man/tukey_hsd.Rd | 7 rstatix-1.1.0/rstatix/man/welch_anova_test.Rd | 7 rstatix-1.1.0/rstatix/man/wilcox_effsize.Rd | 48 + rstatix-1.1.0/rstatix/man/wilcox_test.Rd | 33 - rstatix-1.1.0/rstatix/tests/testthat/test-anova_test-ci.R | 25 rstatix-1.1.0/rstatix/tests/testthat/test-apa-label.R |only rstatix-1.1.0/rstatix/tests/testthat/test-bootstrap_ci.R |only rstatix-1.1.0/rstatix/tests/testthat/test-check_test_assumptions.R |only rstatix-1.1.0/rstatix/tests/testthat/test-cliff_delta.R |only rstatix-1.1.0/rstatix/tests/testthat/test-cohens_d-analytic-ci.R |only rstatix-1.1.0/rstatix/tests/testthat/test-cohens_d.R | 15 rstatix-1.1.0/rstatix/tests/testthat/test-conover_test.R | 8 rstatix-1.1.0/rstatix/tests/testthat/test-cramer_v.R |only rstatix-1.1.0/rstatix/tests/testthat/test-dunnett_test.R | 43 + rstatix-1.1.0/rstatix/tests/testthat/test-effect_size_column.R |only rstatix-1.1.0/rstatix/tests/testthat/test-emmeans_test.R | 1 rstatix-1.1.0/rstatix/tests/testthat/test-eta_squared.R |only rstatix-1.1.0/rstatix/tests/testthat/test-friedman_conover_test.R | 7 rstatix-1.1.0/rstatix/tests/testthat/test-friedman_nemenyi_test.R | 21 rstatix-1.1.0/rstatix/tests/testthat/test-kruskal_effsize.R | 22 rstatix-1.1.0/rstatix/tests/testthat/test-omega_squared.R |only rstatix-1.1.0/rstatix/tests/testthat/test-paired_effect_sizes.R |only rstatix-1.1.0/rstatix/tests/testthat/test-posthoc_test.R |only rstatix-1.1.0/rstatix/tests/testthat/test-rank_effsize_methods.R |only rstatix-1.1.0/rstatix/tests/testthat/test-references-hygiene.R |only rstatix-1.1.0/rstatix/tests/testthat/test-sign_test.R |only rstatix-1.1.0/rstatix/tests/testthat/test-tidy_glance.R |only rstatix-1.1.0/rstatix/tests/testthat/test-tidyselect-deprecations.R | 2 rstatix-1.1.0/rstatix/vignettes |only 148 files changed, 2735 insertions(+), 510 deletions(-)
Title: Most Probable Number and Other Microbial Enumeration Techniques
Description: Calculates the Most Probable Number (MPN) to quantify the
concentration (density) of microbes in serial dilutions of a laboratory
sample (described in Jarvis, 2010 <doi:10.1111/j.1365-2672.2010.04792.x>).
Also calculates the Aerobic Plate Count (APC) for similar microbial
enumeration experiments.
Author: Martine Ferguson [aut] ,
John Ihrie [cre, aut]
Maintainer: John Ihrie <John.Ihrie@fda.hhs.gov>
Diff between MPN versions 0.4.0 dated 2024-10-22 and 0.5.0 dated 2026-07-23
DESCRIPTION | 11 ++-- MD5 | 36 ++++++------- NEWS.md | 23 ++------ R/MPN.R | 8 +- R/f_apc.R | 40 ++++---------- R/f_mpn.R | 67 ++++++++++++------------ R/helpers_APC.R | 76 +++++++++++++++------------ R/helpers_MPN.R | 88 ++++++++++++++++---------------- build/vignette.rds |binary inst/doc/a_mpn-vignette.Rmd | 19 +++--- inst/doc/a_mpn-vignette.html | 74 +++++++++++++------------- inst/doc/b_apc-vignette.Rmd | 11 ++-- inst/doc/b_apc-vignette.html | 29 +++++----- man/MPN-package.Rd | 9 +-- man/apc.Rd | 25 ++------- man/mpn.Rd | 33 ++++++------ tests/testthat/test_apc.R | 118 +++++++++++++++++++++++++++---------------- vignettes/a_mpn-vignette.Rmd | 19 +++--- vignettes/b_apc-vignette.Rmd | 11 ++-- 19 files changed, 353 insertions(+), 344 deletions(-)
Title: Dirichlet Random Forest
Description: Implementation of the Dirichlet Random Forest algorithm
for compositional response data. Trees are grown using a Dirichlet
log-likelihood splitting criterion, with maximum likelihood ('MLE') and
method-of-moments ('MOM') parameter estimation. Provides averaging-based
predictions (average of responses within terminal nodes), parameter-based
predictions (expected value derived from the estimated Dirichlet
parameters within terminal nodes), and distributional predictions
represented as a weighted distribution over the training responses.
Out-of-bag estimation and impurity- and permutation-based variable
importance are also supported. For more details see Masoumifard, van der
Westhuizen, and Gardner-Lubbe (2026, ISBN:9781032903910).
Author: Khaled Masoumifard [aut, cre] ,
Stephan van der Westhuizen [aut] ,
Sugnet Lubbe [aut]
Maintainer: Khaled Masoumifard <masoumifardk@yahoo.com>
Diff between DirichletRF versions 0.1.0 dated 2026-03-23 and 0.2.0 dated 2026-07-23
DirichletRF-0.1.0/DirichletRF/R/parallel_utils.R |only DirichletRF-0.1.0/DirichletRF/man/predict.dirichlet_forest.Rd |only DirichletRF-0.1.0/DirichletRF/man/print.dirichlet_forest.Rd |only DirichletRF-0.2.0/DirichletRF/DESCRIPTION | 25 DirichletRF-0.2.0/DirichletRF/MD5 | 24 DirichletRF-0.2.0/DirichletRF/NAMESPACE | 9 DirichletRF-0.2.0/DirichletRF/NEWS.md |only DirichletRF-0.2.0/DirichletRF/R/RcppExports.R | 20 DirichletRF-0.2.0/DirichletRF/R/dirichlet_forest.R | 825 ++++++++-- DirichletRF-0.2.0/DirichletRF/man/DirichletRF.Rd | 265 ++- DirichletRF-0.2.0/DirichletRF/man/importance.DirichletRF.Rd |only DirichletRF-0.2.0/DirichletRF/man/permutation_importance.Rd |only DirichletRF-0.2.0/DirichletRF/man/predict.DirichletRF.Rd |only DirichletRF-0.2.0/DirichletRF/man/predict_weights.Rd |only DirichletRF-0.2.0/DirichletRF/man/print.DirichletRF.Rd |only DirichletRF-0.2.0/DirichletRF/man/sample_conditional.Rd |only DirichletRF-0.2.0/DirichletRF/src/RcppExports.cpp | 65 DirichletRF-0.2.0/DirichletRF/src/dirichlet_forest.cpp | 521 +++++- 18 files changed, 1537 insertions(+), 217 deletions(-)
Title: Robust Distance-Based Visualization and Analysis of Mixed-Type
Data
Description: Robust distance-based methods applied to matrices and data frames, producing distance matrices that can be used as input for various visualization techniques such as graphs, heatmaps, or multidimensional scaling configurations. See Boj and Grané (2024) <doi:10.1016/j.seps.2024.101992>.
Author: Marcos Alvarez [aut],
Eva Boj [aut, cre],
Aurea Grane [aut]
Maintainer: Eva Boj <evaboj@ub.edu>
Diff between dbrobust versions 1.0.0 dated 2025-09-22 and 1.1.0 dated 2026-07-23
dbrobust-1.0.0/dbrobust/R/dist_mixed.R |only dbrobust-1.0.0/dbrobust/man/convert_to_dist.Rd |only dbrobust-1.0.0/dbrobust/man/dist_binary.Rd |only dbrobust-1.0.0/dbrobust/man/dist_categorical.Rd |only dbrobust-1.0.0/dbrobust/man/dist_continuous.Rd |only dbrobust-1.0.0/dbrobust/man/dist_mixed.Rd |only dbrobust-1.0.0/dbrobust/man/format_output.Rd |only dbrobust-1.0.0/dbrobust/man/get_custom_palette.Rd |only dbrobust-1.0.0/dbrobust/man/plot_heatmap.Rd |only dbrobust-1.0.0/dbrobust/man/plot_mds.Rd |only dbrobust-1.0.0/dbrobust/man/plot_qgraph.Rd |only dbrobust-1.0.0/dbrobust/man/robust_RelMS.Rd |only dbrobust-1.0.0/dbrobust/man/robust_covariance_gv.Rd |only dbrobust-1.0.0/dbrobust/man/robust_ggower.Rd |only dbrobust-1.0.0/dbrobust/tests/testthat/test-test-visualize_distances.R |only dbrobust-1.1.0/dbrobust/DESCRIPTION | 18 dbrobust-1.1.0/dbrobust/MD5 | 84 +- dbrobust-1.1.0/dbrobust/NAMESPACE | 17 dbrobust-1.1.0/dbrobust/NEWS.md |only dbrobust-1.1.0/dbrobust/R/RcppExports.R |only dbrobust-1.1.0/dbrobust/R/calculate_distances.R | 152 +++-- dbrobust-1.1.0/dbrobust/R/convert_to_dist.R | 1 dbrobust-1.1.0/dbrobust/R/cramerdistw_impl.R |only dbrobust-1.1.0/dbrobust/R/dbrobust-package.R |only dbrobust-1.1.0/dbrobust/R/devlin_cramer.R |only dbrobust-1.1.0/dbrobust/R/dist_binary.R | 99 ++- dbrobust-1.1.0/dbrobust/R/dist_categorical.R | 120 ++-- dbrobust-1.1.0/dbrobust/R/dist_continuous.R | 34 - dbrobust-1.1.0/dbrobust/R/format_output.R | 1 dbrobust-1.1.0/dbrobust/R/get_custom_palette.R | 1 dbrobust-1.1.0/dbrobust/R/make_euclidean.R | 169 +++-- dbrobust-1.1.0/dbrobust/R/merge_distances.R |only dbrobust-1.1.0/dbrobust/R/non2euclidw_cramer.R |only dbrobust-1.1.0/dbrobust/R/plot_heatmap.R | 58 +- dbrobust-1.1.0/dbrobust/R/plot_mds.R | 92 +-- dbrobust-1.1.0/dbrobust/R/plot_qgraph.R | 122 ++-- dbrobust-1.1.0/dbrobust/R/robust_RelMS.R | 282 +++++----- dbrobust-1.1.0/dbrobust/R/robust_covariance_gv.R | 30 - dbrobust-1.1.0/dbrobust/R/robust_covariance_mcd.R |only dbrobust-1.1.0/dbrobust/R/robust_distances.R | 165 ++++- dbrobust-1.1.0/dbrobust/R/robust_ggower.R | 169 +++-- dbrobust-1.1.0/dbrobust/R/validate_colors.R |only dbrobust-1.1.0/dbrobust/R/visualize_distances.R | 15 dbrobust-1.1.0/dbrobust/build/partial.rdb |binary dbrobust-1.1.0/dbrobust/inst/REFERENCES.bib | 108 ++- dbrobust-1.1.0/dbrobust/man/calculate_distances.Rd | 165 +++-- dbrobust-1.1.0/dbrobust/man/make_euclidean.Rd | 86 +-- dbrobust-1.1.0/dbrobust/man/merge_distances.Rd |only dbrobust-1.1.0/dbrobust/man/robust_distances.Rd | 102 ++- dbrobust-1.1.0/dbrobust/man/visualize_distances.Rd | 8 dbrobust-1.1.0/dbrobust/src |only dbrobust-1.1.0/dbrobust/tests/testthat/test-calculate_distances.R | 113 ++-- dbrobust-1.1.0/dbrobust/tests/testthat/test-make_euclidean.R | 139 +++- dbrobust-1.1.0/dbrobust/tests/testthat/test-merge_distances.R |only dbrobust-1.1.0/dbrobust/tests/testthat/test-robust_distances.R | 107 ++- dbrobust-1.1.0/dbrobust/tests/testthat/test-visualize_distances.R |only 56 files changed, 1469 insertions(+), 988 deletions(-)
Title: An Interface to IBGE's SIDRA API
Description: Provides a flexible interface to the aggregate data available
from the Brazilian Institute of Geography and Statistics (IBGE) through
its SIDRA application programming interfaces. SIDRA is IBGE's system for
retrieving aggregate statistical data.
Author: Renato Prado Siqueira [aut, cre]
Maintainer: Renato Prado Siqueira <rpradosiqueira@gmail.com>
Diff between sidrar versions 0.2.9 dated 2022-07-12 and 0.3.0 dated 2026-07-23
sidrar-0.2.9/sidrar/vignettes/fig1.png |only sidrar-0.2.9/sidrar/vignettes/fig2.png |only sidrar-0.3.0/sidrar/DESCRIPTION | 25 sidrar-0.3.0/sidrar/MD5 | 42 sidrar-0.3.0/sidrar/NAMESPACE | 1 sidrar-0.3.0/sidrar/NEWS.md | 35 sidrar-0.3.0/sidrar/R/get_sidra.R | 631 ++++----------- sidrar-0.3.0/sidrar/R/info_sidra.R | 322 +++---- sidrar-0.3.0/sidrar/R/query.R |only sidrar-0.3.0/sidrar/R/search_sidra.R | 123 ++ sidrar-0.3.0/sidrar/R/utils.R |only sidrar-0.3.0/sidrar/README.md | 156 ++- sidrar-0.3.0/sidrar/build/vignette.rds |binary sidrar-0.3.0/sidrar/inst/doc/Introduction_to_sidrar.R | 156 +-- sidrar-0.3.0/sidrar/inst/doc/Introduction_to_sidrar.Rmd | 347 ++++---- sidrar-0.3.0/sidrar/inst/doc/Introduction_to_sidrar.html | 535 +++++++++--- sidrar-0.3.0/sidrar/man/get_sidra.Rd | 145 +-- sidrar-0.3.0/sidrar/man/info_sidra.Rd | 21 sidrar-0.3.0/sidrar/man/search_sidra.Rd | 13 sidrar-0.3.0/sidrar/tests |only sidrar-0.3.0/sidrar/vignettes/Introduction_to_sidrar.Rmd | 347 ++++---- 21 files changed, 1531 insertions(+), 1368 deletions(-)
Title: Generation of ENVIREM Variables
Description: Generation of bioclimatic rasters that are complementary to the typical 19 bioclim variables.
Author: Pascal O. Title [aut],
Jordan B. Bemmels [aut],
Pascal Title [cre]
Maintainer: Pascal Title <pascal.title@stonybrook.edu>
Diff between envirem versions 3.1 dated 2025-05-15 and 3.2 dated 2026-07-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/ETsolradRasters.R | 2 +- R/envirem-package.R | 2 +- man/envirem.Rd | 1 + 5 files changed, 11 insertions(+), 10 deletions(-)
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format):
MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>),
Dia-NN (Demichev et al 2020 <doi:10.1038/s41592-019-0638-x>),
Fragpipe (da Veiga et al 2020 <doi:10.1038/s41592-020-0912-y>),
ionbot (Degroeve et al 2021 <doi:10.1101/2021.07.02.450686>),
MassChroq (Valot et al 2011 <doi:10.1002/pmic.201100120>),
OpenMS (Strauss et al 2021 <doi:10.1038/nmeth.3959>),
ProteomeDiscoverer (Orsburn 2021 <doi:10.3390/proteomes9010015>),
Proline (Bouyssie et a [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 2.0.2 dated 2026-04-29 and 2.1.0 dated 2026-07-23
DESCRIPTION | 22 MD5 | 186 +- NAMESPACE | 1 NEWS.md |only R/AucRoc.R | 2 R/VolcanoPlotW2.R | 4 R/cleanListCoNames.R | 2 R/combineMultFilterNAimput.R | 8 R/convAASeq2mass.R | 3 R/corColumnOrder.R | 4 R/countNoOfCommonPeptides.R | 2 R/exportAsWombatP.R | 2 R/exportSdrfDraft.R | 3 R/extrSpeciesAnnot.R | 2 R/extractTestingResults.R | 292 ++-- R/foldChangeArrow2.R | 74 - R/fuseProteomicsProjects.R | 6 R/getUPS1acc.R | 2 R/inspectSpeciesIndic.R | 5 R/isolNAneighb.R | 9 R/massDeFormula.R | 6 R/matrixNAinspect.R | 26 R/matrixNAneighbourImpute.R | 10 R/plotROC.R | 13 R/razorNoFilter.R | 10 R/readAlphaPeptFile.R | 9 R/readDiaNNFile.R | 134 - R/readDiaNNPeptides.R | 10 R/readFasta2.R | 2 R/readFragpipeFile.R | 12 R/readIonbotPeptides.R | 17 R/readMassChroQFile.R | 8 R/readMaxQuantFile.R | 11 R/readMaxQuantPeptides.R | 7 R/readOpenMSFile.R | 10 R/readProlineFile.R | 17 R/readProtDiscovFile.R | 363 ----- R/readProteomeDiscovererFile.R | 84 - R/readProteomeDiscovererPeptides.R | 18 R/readSampleMetaData.R | 2294 +++++++++++++++++----------------- R/readSdrf.R | 12 R/readUCSCtable.R | 14 R/readUniProtExport.R | 16 R/readWombatNormFile.R | 7 R/removeSampleInList.R | 5 R/replMissingProtNames.R | 7 R/shortSoftwName.R | 7 R/summarizeForROC.R | 16 R/test2grp.R | 6 R/testRobustToNAimputation.R | 116 - build/vignette.rds |binary inst/doc/wrProteoVignette1.Rmd | 4 inst/doc/wrProteoVignette1.html | 410 +++--- inst/doc/wrProteoVignetteUPS1.R | 9 inst/doc/wrProteoVignetteUPS1.Rmd | 9 inst/doc/wrProteoVignetteUPS1.html | 1674 ++++++++++++------------ man/VolcanoPlotW2.Rd | 2 man/combineMultFilterNAimput.Rd | 6 man/dot-getSpeciesFromEntryName.Rd |only man/dot-plotQuantDistr.Rd | 3 man/extractTestingResults.Rd | 38 man/foldChangeArrow2.Rd | 7 man/fuseProteomicsProjects.Rd | 2 man/isolNAneighb.Rd | 2 man/massDeFormula.Rd | 3 man/matrixNAinspect.Rd | 10 man/matrixNAneighbourImpute.Rd | 4 man/plotROC.Rd | 11 man/razorNoFilter.Rd | 8 man/readAlphaPeptFile.Rd | 2 man/readDiaNNFile.Rd | 8 man/readDiaNNPeptides.Rd | 6 man/readFragpipeFile.Rd | 6 man/readIonbotPeptides.Rd | 12 man/readMassChroQFile.Rd | 6 man/readMaxQuantFile.Rd | 2 man/readMaxQuantPeptides.Rd | 4 man/readOpenMSFile.Rd | 6 man/readProlineFile.Rd | 17 man/readProtDiscovFile.Rd | 20 man/readProteomeDiscovererFile.Rd | 14 man/readProteomeDiscovererPeptides.Rd | 12 man/readSampleMetaData.Rd | 4 man/readSdrf.Rd | 2 man/readUCSCtable.Rd | 6 man/readUniProtExport.Rd | 7 man/readWombatNormFile.Rd | 2 man/removeSampleInList.Rd | 2 man/replMissingProtNames.Rd | 2 man/shortSoftwName.Rd | 4 man/summarizeForROC.Rd | 2 man/test2grp.Rd | 4 man/testRobustToNAimputation.Rd | 2 vignettes/wrProteoVignette1.Rmd | 4 vignettes/wrProteoVignetteUPS1.Rmd | 9 95 files changed, 3051 insertions(+), 3212 deletions(-)
Title: Bivariate Within- and Between-Cluster Correlations
Description: Separates supplied variables into within- and
between-cluster components and calculates bivariate correlations for
each level separately. For Pearson correlations, the centered-score
decomposition corresponds to commonly used between- and within-cluster
correlations reviewed by Tu et al. (2025) <doi:10.1002/sim.10326>.
The package's descriptive Spearman option is distinct from the clustered
rank parameters introduced in that paper. The package is also
motivated by the distinction between within- and between-person
variation described by Curran and Bauer (2011)
<doi:10.1146/annurev.psych.093008.100356> and by Hamaker (2024)
<doi:10.1080/00273171.2022.2155930>.
The package is intended for longitudinal or otherwise clustered data
where researchers need transparent correlation matrices before fitting
more complex multilevel models.
Author: Pascal Kueng [aut, cre, cph]
Maintainer: Pascal Kueng <pascal.kueng@psychologie.uzh.ch>
Diff between wbCorr versions 0.3.1 dated 2026-06-09 and 0.3.2 dated 2026-07-23
wbCorr-0.3.1/wbCorr/tests/testthat/Create_Tests.R |only wbCorr-0.3.1/wbCorr/tests/testthat/Rplots.pdf |only wbCorr-0.3.1/wbCorr/tests/testthat/testdata |only wbCorr-0.3.2/wbCorr/DESCRIPTION | 23 wbCorr-0.3.2/wbCorr/MD5 | 105 +- wbCorr-0.3.2/wbCorr/NAMESPACE | 3 wbCorr-0.3.2/wbCorr/NEWS.md |only wbCorr-0.3.2/wbCorr/R/01_pre_00_input_validation_and_prep.R | 178 ++++ wbCorr-0.3.2/wbCorr/R/01_pre_01_centering_wb.R | 6 wbCorr-0.3.2/wbCorr/R/01_pre_02_assumption_checks.R | 55 + wbCorr-0.3.2/wbCorr/R/02_cor_01_main_base.R | 395 ++++++++-- wbCorr-0.3.2/wbCorr/R/02_cor_02_initializing.R | 19 wbCorr-0.3.2/wbCorr/R/02_cor_03_calculating_statistics.R | 13 wbCorr-0.3.2/wbCorr/R/02_cor_04_method_01_pearson.R | 105 +- wbCorr-0.3.2/wbCorr/R/02_cor_04_method_02_spearman.R | 52 - wbCorr-0.3.2/wbCorr/R/03_ICC_compute_ICC1.R | 78 +- wbCorr-0.3.2/wbCorr/R/04_post_00_matrix_diagnostics.R |only wbCorr-0.3.2/wbCorr/R/04_post_01_formatting_results_table.R | 18 wbCorr-0.3.2/wbCorr/R/04_post_01_formatting_summarizing.R | 7 wbCorr-0.3.2/wbCorr/R/04_post_02_accessor_functions.R | 142 +++ wbCorr-0.3.2/wbCorr/R/05_viz_00_apply_types.R | 59 + wbCorr-0.3.2/wbCorr/R/05_viz_01_plot_lower_panel.R | 59 - wbCorr-0.3.2/wbCorr/R/05_viz_01_plot_upper_panel.R | 67 - wbCorr-0.3.2/wbCorr/R/05_viz_02_plot_all.R | 401 ++++++++--- wbCorr-0.3.2/wbCorr/R/06_export_to_excel.R | 91 +- wbCorr-0.3.2/wbCorr/R/simdat_intensive_longitudinal.R | 7 wbCorr-0.3.2/wbCorr/R/wbCorr.R | 394 ++++++++-- wbCorr-0.3.2/wbCorr/README.md | 188 ++--- wbCorr-0.3.2/wbCorr/build |only wbCorr-0.3.2/wbCorr/inst/CITATION | 23 wbCorr-0.3.2/wbCorr/inst/WORDLIST | 40 - wbCorr-0.3.2/wbCorr/inst/doc |only wbCorr-0.3.2/wbCorr/man/get_ICC.Rd | 28 wbCorr-0.3.2/wbCorr/man/get_matrix.Rd | 38 - wbCorr-0.3.2/wbCorr/man/get_matrix_diagnostics.Rd |only wbCorr-0.3.2/wbCorr/man/get_table.Rd | 5 wbCorr-0.3.2/wbCorr/man/plot-wbCorr-method.Rd | 18 wbCorr-0.3.2/wbCorr/man/simdat_intensive_longitudinal.Rd | 7 wbCorr-0.3.2/wbCorr/man/to_excel.Rd | 24 wbCorr-0.3.2/wbCorr/man/wbCorr.Rd | 193 ++++- wbCorr-0.3.2/wbCorr/tests/testthat/test-estimands.R | 2 wbCorr-0.3.2/wbCorr/tests/testthat/test-excel-export.R |only wbCorr-0.3.2/wbCorr/tests/testthat/test-icc-pearson.R |only wbCorr-0.3.2/wbCorr/tests/testthat/test-input-validation.R |only wbCorr-0.3.2/wbCorr/tests/testthat/test-matrix-diagnostics.R |only wbCorr-0.3.2/wbCorr/tests/testthat/test-numeric-accessors.R |only wbCorr-0.3.2/wbCorr/tests/testthat/test-pair-diagnostics.R |only wbCorr-0.3.2/wbCorr/tests/testthat/test-plot-parity.R |only wbCorr-0.3.2/wbCorr/tests/testthat/test-print.R |only wbCorr-0.3.2/wbCorr/tests/testthat/test-spearman.R |only wbCorr-0.3.2/wbCorr/tests/testthat/test-statsby.R |only wbCorr-0.3.2/wbCorr/tests/testthat/test-wbCorr.R | 17 wbCorr-0.3.2/wbCorr/vignettes |only 53 files changed, 2058 insertions(+), 802 deletions(-)
Title: Conservation Indicators Using Spatial Information
Description: Supports the assessment of the degree of conservation of taxa
in conservation systems, both in ex situ (in genebanks,
botanical gardens, and other repositories), and in situ
(in protected natural areas). Methods are described in
Carver et al. (2021) <doi:10.1111/ecog.05430>, building on
Khoury et al. (2020) <doi:10.1073/pnas.2007029117>,
Khoury et al. (2019) <doi:10.1016/j.ecolind.2018.11.016>,
Khoury et al. (2019) <doi:10.1111/DDI.13008>,
Castaneda-Alvarez et al. (2016) <doi:10.1038/nplants.2016.22>,
and Ramirez-Villegas et al. (2010) <doi:10.1371/journal.pone.0013497>.
Author: Dan Carver [aut, cre, cph] ,
Sarah Gore [aut, cph] ,
Chrystian Sosa [aut, cph] ,
Colin Khoury [aut, cph] ,
Julian Ramirez-Villegas [aut, cph] ,
Valentin Stefan [ctb],
Harold Achicanoy [ctb, cph],
Maria Victoria Diaz [ctb, cph],
Steven Sotelo [ctb, cp [...truncated...]
Maintainer: Dan Carver <carver.dan1@gmail.com>
Diff between GapAnalysis versions 2.0.2 dated 2026-05-12 and 2.1.0 dated 2026-07-23
DESCRIPTION | 11 + MD5 | 50 ++++---- NEWS.md | 7 + R/ERSex.R | 31 +++-- R/ERSin.R | 75 +++++++++---- R/SRSex.R | 2 R/SRSin.R | 2 R/checkOccurrences.R | 2 R/generateCounts.R | 2 R/generateEcoSelection.R | 2 R/generateGBuffers.R | 5 build/partial.rdb |binary build/vignette.rds |binary inst/doc/multipleSpecies_vignette.R | 6 - inst/doc/multipleSpecies_vignette.Rmd | 6 - inst/doc/multipleSpecies_vignette.html | 185 ++++++++++++++++----------------- man/ERSex.Rd | 24 +++- man/ERSin.Rd | 20 +++ man/SRSex.Rd | 2 man/SRSin.Rd | 2 man/checkOccurrences.Rd | 2 man/generateCounts.Rd | 2 man/generateEcoSelection.Rd | 2 man/generateGBuffers.Rd | 2 tests |only vignettes/multipleSpecies_vignette.Rmd | 6 - 26 files changed, 265 insertions(+), 183 deletions(-)
Title: Retrieve, Transform and Analyze the Barcode of Life Data Systems
Data
Description: Facilitates retrieval, transformation and analysis of the data
from the Barcode of Life Data Systems (BOLD) database <https://boldsystems.org/>.
This package allows both public and private user data to be easily downloaded into the R
environment using a variety of inputs such as: IDs (processid, sampleid), BINs, dataset codes,
project codes, taxonomy, geography etc. It provides frictionless data conversion
into formats compatible with other R-packages and third-party tools,
as well as functions for sequence alignment & clustering, biodiversity analysis and spatial mapping.
Author: Sameer Padhye [aut, cre],
Liliana Ballesteros-Mejia [aut],
Timothy Agda [aut],
Jireh Agda [aut],
Sujeevan Ratnasingham [aut]
Maintainer: Sameer Padhye <spadhye@uoguelph.ca>
Diff between BOLDconnectR versions 1.0.0 dated 2025-09-17 and 1.0.1 dated 2026-07-23
DESCRIPTION | 23 LICENSE | 4 MD5 | 110 ++-- NAMESPACE | 227 ++++----- NEWS.md |only R/external.bold.analyze.align.R | 225 ++++----- R/external.bold.analyze.diversity.R | 613 +++++++++++--------------- R/external.bold.analyze.map.R | 213 ++++----- R/external.bold.analyze.tree.R | 260 ++++------- R/external.bold.apikey.R | 16 R/external.bold.data.summarize.R | 251 ++++------ R/external.bold.export.R | 298 +++++------- R/external.bold.fetch.R | 334 +++++--------- R/external.bold.fields.info.R | 85 +-- R/external.bold.full.search.R | 461 +++++++------------ R/external.bold.public.search.R | 244 ++++------ R/globals.R | 3 R/helper.align.msa.gen_ape_obj.R | 131 ++--- R/helper.column_presets.R | 426 ++++++++---------- R/helper.diversity.gencommmat.R | 527 ++++++++++------------ R/helper.fetch.bold.data.allids.R | 137 +---- R/helper.fetch.filters.R | 603 ++++++++++--------------- R/helper.fetch.functions.4.datawrangling.R | 210 +++----- R/helper.fetch.get.bin_project_dataset.pids.R | 218 +++------ R/helper.fetch.json_data_download_&_json2df.R | 122 +---- R/helper.functions.4.bold.analyze.diversity.R | 214 ++++----- R/helper.functions.4.bold.data.summarize.R | 501 ++++++++++----------- R/helper.functions.4.bold.public.search.R | 587 +++++++++++------------- R/test.data2.R |only README.md | 508 +++++++++++++-------- build |only data/test.data2.rda |only inst |only man/bold.analyze.align.Rd | 145 +++--- man/bold.analyze.diversity.Rd | 350 +++++++------- man/bold.analyze.map.Rd | 127 ++--- man/bold.analyze.tree.Rd | 204 ++++---- man/bold.apikey.Rd | 6 man/bold.data.summarize.Rd | 218 ++++----- man/bold.export.Rd | 185 ++++--- man/bold.fetch.Rd | 52 +- man/bold.fields.info.Rd | 52 +- man/bold.full.search.Rd | 52 +- man/bold.public.search.Rd | 133 ++--- man/figures/lifecycle-archived.svg | 42 - man/figures/lifecycle-defunct.svg | 42 - man/figures/lifecycle-deprecated.svg | 42 - man/figures/lifecycle-experimental.svg | 42 - man/figures/lifecycle-maturing.svg | 42 - man/figures/lifecycle-questioning.svg | 42 - man/figures/lifecycle-soft-deprecated.svg | 42 - man/figures/lifecycle-stable.svg | 58 +- man/figures/lifecycle-superseded.svg | 42 - man/id.files.Rd | 24 - man/post.api.res.fetch.Rd | 24 - man/test.data.Rd | 52 +- man/test.data2.Rd |only vignettes |only 58 files changed, 4451 insertions(+), 5118 deletions(-)
Title: Conditional Inference Trees with Stacked Multiple Imputation
Description: Implements the stacked-imputation workflow for conditional
inference trees ('ctree') described in Sherlock et al. (2026)
<doi:10.1080/00273171.2026.2661244>. When data contain missing values,
multiply imputed datasets (e.g., from 'mice') are stacked vertically
and a single 'ctree' is fit on the combined data. To correct for the
artificially inflated sample size introduced by stacking, the pruning
significance threshold is divided by the number of imputations M
(the Stack/M correction), producing a conservative but interpretable
single tree that incorporates imputation uncertainty without requiring
pooling of structurally different trees. Also exports
stack_imputations() and rescale_alpha() as standalone utilities. The
underlying 'ctree' algorithm is provided by 'partykit'
(Hothorn & Zeileis, 2015; Hothorn, Hornik & Zeileis, 2006
<doi:10.1198/106186006X133933>).
Author: Phillip Sherlock [aut, cre]
Maintainer: Phillip Sherlock <phillip.sherlock@ufl.edu>
Diff between ctreeMI versions 0.1.0 dated 2026-07-10 and 0.2.0 dated 2026-07-23
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++++---- NAMESPACE | 6 ++++++ NEWS.md | 9 +++++++++ R/node_table.R |only build/partial.rdb |binary man/node_table.Rd |only man/report_ctreeMI.Rd |only tests/testthat.R |only tests/testthat/test-node-table.R |only 10 files changed, 28 insertions(+), 8 deletions(-)
Title: More Flexible Form of Boolean Verbose
Description: R functions are not supposed to print text without giving
the user the option to turn the printing off or on using a Boolean
'verbose' in a construct like 'if(verbose) print(...)'. But this black/white
approach is rather rigid, and an approach with shades of gray might be more
appropriate in many circumstances.
Author: Barry Zeeberg [aut, cre]
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Diff between vprint versions 1.2 dated 2025-06-04 and 1.3 dated 2026-07-23
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/vprint.R | 14 +++++++++++--- build/vignette.rds |binary inst/doc/vprint.html | 4 ++-- man/vprint.Rd | 6 ++++-- 6 files changed, 27 insertions(+), 17 deletions(-)
Title: Modeling Species Distributions in Three Dimensions
Description: Facilitates modeling species' ecological niches and
geographic distributions based on occurrences and environments that
have a vertical as well as horizontal component, and projecting models
into three-dimensional geographic space. Working in three dimensions is
useful in an aquatic context when the organisms one wishes to model can
be found across a wide range of depths in the water column. The package
also contains functions to automatically generate marine training
model training regions using machine learning, and interpolate and smooth
patchily sampled environmental rasters using thin plate splines.
Davis Rabosky AR, Cox CL, Rabosky DL, Title PO, Holmes IA, Feldman A, McGuire JA (2016) <doi:10.1038/ncomms11484>.
Nychka D, Furrer R, Paige J, Sain S (2021) <doi:10.5065/D6W957CT>.
Pateiro-Lopez B, Rodriguez-Casal A (2022) <https://CRAN.R-project.org/package=alphahull>.
Author: Hannah L. Owens [aut, cre, cph] ,
Emmaline Sheahan [aut] ,
Carsten Rahbek [aut]
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
Diff between voluModel versions 0.2.4 dated 2026-05-23 and 0.2.5 dated 2026-07-23
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/visualizations.R | 25 ++++++++++++------------- inst/doc/a_Introduction.html | 18 +++++++++--------- inst/doc/b_RasterProcessing.html | 12 ++++++------ inst/doc/c_DataSampling.html | 14 +++++++------- inst/doc/d_Visualization.html | 14 +++++++------- inst/doc/e_GLMWorkflow.html | 28 ++++++++++++++-------------- 9 files changed, 70 insertions(+), 67 deletions(-)
Title: Render Tables, Listings, and Figures for Clinical Submissions
Description: Render clinical submission tables, listings, and figures to
'RTF', 'LaTeX', 'Typst', 'HTML', 'PDF', and 'DOCX' from pre-summarised
data frames, with no external 'Java' or 'SAS' dependency. Features include
decimal alignment via font metrics, multi-level column headers with
passthrough leaves, predicate-targeted cell styling, footnotes,
group-aware pagination, and figures that wrap a plot or image in the
same page chrome as a table. Built for Clinical Data Interchange Standards
Consortium (CDISC) Analysis Data Model (ADaM) workflows and
regulatory submissions to agencies such as the Food and Drug
Administration (FDA), European Medicines Agency (EMA), and
Pharmaceuticals and Medical Devices Agency (PMDA).
Author: Vignesh Thanikachalam [aut, cre, cph]
Maintainer: Vignesh Thanikachalam <about.vignesh@gmail.com>
Diff between tabular versions 0.3.1 dated 2026-07-20 and 0.3.2 dated 2026-07-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ tests/testthat/test-backend_pdf.R | 6 ++++++ 4 files changed, 18 insertions(+), 6 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 1.4.0 dated 2026-06-17 and 1.4.1 dated 2026-07-23
DESCRIPTION | 9 MD5 | 60 + NAMESPACE | 1 NEWS.md | 11 R/classAchillesTable.R | 4 R/classCdmReference.R | 66 +- R/classCdmSource.R | 3 R/classCodelist.R | 8 R/classCohortTable.R | 2 R/classOmopTable.R | 4 R/classSummarisedResult.R | 22 R/data.R |only R/importConceptSetExpression.R | 17 R/logger.R | 14 R/methodBind.R | 8 R/sysdata.rda |binary R/utilities.R | 8 data |only inst/doc/logging.html | 52 - inst/doc/summarised_result.html | 886 ++++++++++++++-------------- man/bind.summarised_result.Rd | 8 man/guessCdmVersion.Rd |only man/logMessage.Rd | 9 man/newCdmReference.Rd | 7 man/newCohortTable.Rd | 2 man/newSummarisedResult.Rd | 9 man/omopgenerics-package.Rd | 1 man/reexports.Rd | 4 man/supportedCdmVersions.Rd |only tests/testthat/test-classCdmReference.R | 54 + tests/testthat/test-classSummarisedResult.R | 34 + tests/testthat/test-logger.R | 30 tests/testthat/test-methodBind.R | 36 + 33 files changed, 826 insertions(+), 543 deletions(-)
Title: Infrastructure for Mediation Model Fitting and Extraction
Description: Provides S7-based infrastructure for fitting mediation models,
extracting path coefficients, and performing bootstrap inference. Designed
as a foundation package for the mediation analysis ecosystem, supporting
'probmed', 'RMediation', and 'medrobust' packages. Implements unified interfaces
for model fitting across different engines (currently generalized linear models,
with future support for mixed models and Bayesian methods), standardized
extraction of mediation paths from various model types, and robust bootstrap
inference methods. Mediation methods are described in MacKinnon, Lockwood and
Williams (2004) <doi:10.1207/s15327906mbr3901_4>, Preacher and Hayes (2008)
<doi:10.3758/brm.40.3.879>, Tofighi and MacKinnon (2011)
<doi:10.3758/s13428-011-0076-x>, and VanderWeele (2014)
<doi:10.1097/EDE.0000000000000121>.
Author: Davood Tofighi [aut, cre, cph]
Maintainer: Davood Tofighi <dtofighi@gmail.com>
Diff between medfit versions 0.2.1 dated 2026-06-18 and 0.3.2 dated 2026-07-23
.aspell |only DESCRIPTION | 24 MD5 | 58 +- NAMESPACE | 3 R/classes.R | 448 ++++++++++++++++ R/extract-lavaan.R | 545 +++++++++++++++++++ R/extract-lm.R | 584 +++++++++++++++++++-- R/fit-glm.R | 99 ++- R/generics-effects.R | 146 +++++ R/methods-base.R | 277 +++++++++ R/zzz.R | 45 + inst/CITATION | 29 + inst/WORDLIST | 24 man/BootstrapResult.Rd | 13 man/InteractionMediationData.Rd |only man/MediationData.Rd | 14 man/ParallelMediationData.Rd |only man/SerialMediationData.Rd | 6 man/decompose.Rd |only man/dot-classify_multimediator_structure.Rd |only man/dot-classify_multimediator_structure_lavaan.Rd |only man/dot-extract_interaction_mediation_lavaan.Rd |only man/dot-extract_interaction_mediation_lm.Rd |only man/dot-extract_mediation_lm_impl.Rd | 6 man/dot-extract_parallel_mediation_lavaan.Rd |only man/dot-extract_parallel_mediation_lm.Rd |only man/dot-find_interaction_term.Rd |only man/dot-find_interaction_term_lavaan.Rd |only man/extract_mediation_lavaan.Rd | 15 man/fit_mediation.Rd | 16 man/medfit-package.Rd | 7 tests/testthat/helper-test-data.R | 14 tests/testthat/test-extract-interaction-lavaan.R |only tests/testthat/test-extract-interaction-lm.R |only tests/testthat/test-extract-parallel-lavaan.R |only tests/testthat/test-extract-parallel.R |only tests/testthat/test-family-slot.R |only tests/testthat/test-fit-glm.R | 92 +++ tests/testthat/test-interaction-class.R |only tests/testthat/test-parallel-mediation.R |only 40 files changed, 2336 insertions(+), 129 deletions(-)
Title: Distance-Based Learning for Mixed-Type Data
Description: Provides tools for constructing, computing, and using distance
measures for numerical, categorical, and mixed-type data. The package
implements a flexible framework in which continuous and categorical
components can be combined under additive, commensurable, and
association-aware specifications. Supported methods include classical
distances such as Gower, Euclidean, Manhattan, and Mahalanobis-type
distances; categorical dissimilarities such as simple matching,
occurrence-frequency, and association-based measures; and mixed-type
presets designed to reduce biases due to variable type, scale,
distribution, redundancy, and number of categories. The package also
provides scaling options, supervised and unsupervised distance
constructions, leave-one-variable-out tools for distance-based variable
importance, and integration with distance-based learning workflows such
as nearest-neighbour prediction, partitioning around medoids, and
spectral clustering. Methods are motivated by van de Velden,
[...truncated...]
Author: Alfonso Iodice D'Enza [aut, cre],
Angelos Markos [aut],
Michel van de Velden [aut],
Carlo Cavicchia [aut]
Maintainer: Alfonso Iodice D'Enza <iodicede@unina.it>
Diff between manydist versions 0.5.0 dated 2026-06-09 and 0.5.1 dated 2026-07-23
manydist-0.5.0/manydist/R/all_dist_methods_specs.R |only manydist-0.5.0/manydist/R/commensurable_weight.R |only manydist-0.5.0/manydist/R/cont_delta_single_attr.R |only manydist-0.5.0/manydist/R/daisy_gower_dist.R |only manydist-0.5.0/manydist/R/delta_knn_ba.R |only manydist-0.5.0/manydist/R/mix_delta.R |only manydist-0.5.0/manydist/R/sysdata.rda |only manydist-0.5.1/manydist/DESCRIPTION | 13 manydist-0.5.1/manydist/MD5 | 46 - manydist-0.5.1/manydist/NAMESPACE | 7 manydist-0.5.1/manydist/NEWS.md | 41 + manydist-0.5.1/manydist/R/all_dist_method_specs.R |only manydist-0.5.1/manydist/R/benchmark_mdist.R | 629 ++++++++++++++++- manydist-0.5.1/manydist/R/data-wdi_2022.R |only manydist-0.5.1/manydist/R/dist_methods_tbl.R | 62 + manydist-0.5.1/manydist/R/mdist.R | 73 + manydist-0.5.1/manydist/R/pam_dist_functions.R | 20 manydist-0.5.1/manydist/R/step_mdist_functions.R | 152 +++- manydist-0.5.1/manydist/README.md |only manydist-0.5.1/manydist/data/wdi_2022.rda |only manydist-0.5.1/manydist/inst/CITATION | 32 manydist-0.5.1/manydist/inst/NOTICE |only manydist-0.5.1/manydist/man/all_dist_method_specs.Rd |only manydist-0.5.1/manydist/man/autoplot.MDistBenchmark.Rd |only manydist-0.5.1/manydist/man/benchmark_comparisons.Rd |only manydist-0.5.1/manydist/man/benchmark_mdist.Rd |only manydist-0.5.1/manydist/man/dist_methods_tbl.Rd |only manydist-0.5.1/manydist/man/dist_methods_tbl_cat.Rd |only manydist-0.5.1/manydist/man/figures |only manydist-0.5.1/manydist/man/mdist.Rd | 33 manydist-0.5.1/manydist/man/response_aware_methods.Rd |only manydist-0.5.1/manydist/man/step_mdist.Rd | 38 - manydist-0.5.1/manydist/man/wdi_2022.Rd |only manydist-0.5.1/manydist/tests |only 34 files changed, 1032 insertions(+), 114 deletions(-)
Title: Utilities and Helpers for Single Case Experimental Design (SCED)
using 'ggplot2'
Description: Provides specialized visualization tools for Single-Case Experimental Design (SCED)
research using 'ggplot2'. SCED studies are a crucial methodology in behavioral and
educational research where individual participants serve as their own controls through
carefully designed experimental phases. This package extends 'ggplot2' to create
publication-ready graphics with professional phase change lines, support for multiple
baseline designs, and styling functions that follow SCED visualization conventions.
Key functions include adding phase change demarcation lines to existing plots and
formatting axes with broken axis appearance commonly used in single-case research.
Author: Shawn Gilroy [aut, cre, cph]
Maintainer: Shawn Gilroy <sgilroy1@lsu.edu>
Diff between ggsced versions 0.1.7 dated 2026-07-20 and 0.1.9 dated 2026-07-23
DESCRIPTION | 10 MD5 | 93 NAMESPACE | 32 R/data.R | 86 R/ggsced.R | 490 ++-- R/ggsced_grobs.R | 274 +- R/ggsced_helpers.R | 589 +++- R/ggsced_reporting.R | 54 R/ggsced_theme.R | 112 R/ggsced_utils.R | 186 - README.md | 706 ++--- build/vignette.rds |binary data/LozyEtAl2020Data.RData |only demo/00Index | 5 demo/demo_gilroy_2015.R | 189 - demo/demo_gilroy_2021.R | 250 +- demo/demo_lozy_2020.R |only inst/doc/ggsced-vignette.R | 1232 +++++----- inst/doc/ggsced-vignette.Rmd | 1584 +++++++------ inst/doc/ggsced-vignette.html | 2553 +++++++++++---------- man/Gilroyetal2015.Rd | 60 man/Gilroyetal2021.Rd | 56 man/LozyEtAl2020Data.Rd |only man/ggsced.Rd | 50 man/ggsced_condition_labels.Rd | 40 man/ggsced_extract_domain.Rd | 34 man/ggsced_facet_labels.Rd | 44 man/ggsced_get_panels.Rd | 34 man/ggsced_internal_x_axis.Rd | 46 man/ggsced_internal_y_axis.Rd | 46 man/ggsced_name_dogleg.Rd | 42 man/ggsced_name_dogleg_lateral.Rd | 42 man/ggsced_output_console.Rd | 32 man/ggsced_prep_labels.Rd |only man/ggsced_prep_lines.Rd |only man/ggsced_scale_units.Rd | 38 man/ggsced_style_x.Rd | 42 man/ggsced_style_y.Rd | 42 man/sced_phase_change_complex_lateral_grob.Rd | 42 man/sced_phase_change_complex_lateral_post_grob.Rd | 38 man/sced_phase_change_complex_lateral_pre_grob.Rd | 38 man/sced_phase_change_main_panel_grob.Rd | 38 man/sced_phase_change_simple_lateral_grob.Rd | 42 tests/testthat.R | 24 tests/testthat/Rplots.pdf |binary tests/testthat/test-ggsced.R | 122 - tests/testthat/test-ggsced_helpers.R | 467 +++ tests/testthat/test-ggsced_scale_units.R | 14 tests/testthat/test-ggsced_theme.R | 8 vignettes/ggsced-vignette.Rmd | 1584 +++++++------ 50 files changed, 6354 insertions(+), 5156 deletions(-)
Title: Access Open Data from the Finnish 'Finlex' Legislative Database
Description: Provides functions to retrieve and structure Finnish
legislative data made available through the 'Finlex' Open Data API
(<https://www.finlex.fi/en/open-data>). Functions cover retrieval of
statute catalogues, statute titles, structured statute metadata, and
cross-references between amending and amended statutes, returned as
tidy tibbles for further analysis.
Author: Kristian Vepsaelaeinen [aut, cre]
Maintainer: Kristian Vepsaelaeinen <kristian.vepsalainen@proton.me>
Diff between finlex versions 0.1.0 dated 2026-07-22 and 0.2.0 dated 2026-07-23
DESCRIPTION | 12 +++++++----- MD5 | 25 ++++++++++++++++++++----- NAMESPACE | 3 +++ NEWS.md | 12 ++++++++++++ R/get_consolidated_text.R |only R/get_doc.R |only R/get_text.R |only README.md | 6 +++++- build |only inst/CITATION |only inst/WORDLIST | 3 +-- inst/doc |only man/figures |only man/flx_get_consolidated_text.Rd |only man/flx_get_doc.Rd |only man/flx_get_text.Rd |only tests/testthat/test-get_consolidated_text.R |only tests/testthat/test-get_doc.R |only tests/testthat/test-get_text.R |only vignettes |only 20 files changed, 48 insertions(+), 13 deletions(-)
Title: Bayesian Simultaneous Credible Bands for Polynomial Regression
Description: Provides functions to construct two-sided Bayesian simultaneous
credible bands (BSCBs) for the regression curve in univariate polynomial
regression over a finite covariate interval. Six methods are implemented,
including Normal-Gamma conjugate priors (with empirical Bayes,
unit-information, and g-prior hyperparameter specifications), non-conjugate
priors fitted via Hamiltonian Monte Carlo (HMC) using 'cmdstanr', and
a non-informative independent Jeffreys prior approach. Also includes
functions for computing the empirical simultaneous coverage rate (ESCR) and
posterior simultaneous coverage probability (PSCP), enabling performance
comparison across methods. The methodology is described in:
Yang et al. (2026). "Bayesian simultaneous credible bands for polynomial
regression" <doi:10.48550/arXiv.2606.28015>.
Author: Fei Yang [aut, cre, cph] ,
Yang Han [aut, cph] ,
Wei Liu [aut, cph] ,
Ian Hall [aut, cph]
Maintainer: Fei Yang <fei.yang@manchester.ac.uk>
Diff between BSCB versions 1.0.1 dated 2026-07-13 and 1.0.2 dated 2026-07-23
BSCB-1.0.1/BSCB/inst/BSCB_1.0.1.pdf |only BSCB-1.0.2/BSCB/DESCRIPTION | 50 +++++++++++++++++----------- BSCB-1.0.2/BSCB/MD5 | 8 ++-- BSCB-1.0.2/BSCB/NEWS.md | 8 +++- BSCB-1.0.2/BSCB/inst/BSCB_1.0.2.pdf |only BSCB-1.0.2/BSCB/inst/doc/BSCB-vignette.html | 8 ++-- 6 files changed, 46 insertions(+), 28 deletions(-)
Title: Tweedie Distribution
Description: Provides density, distribution function, quantile function, and random
generation for the Tweedie distribution under the compound Poisson-Gamma
parameterisation with power parameter in (1, 2). The density is evaluated
using the series expansion of Dunn and Smyth (2005) <doi:10.1007/s11222-005-4070-y>,
implemented in C++ via 'Rcpp' and 'RcppArmadillo' for performance. A constructor
compatible with the 'distributional' package is also provided for use in tidy
modelling workflows.
Author: Stefano Damato [aut, cre]
Maintainer: Stefano Damato <stefanodamato128@gmail.com>
Diff between tweedieDistr versions 0.1.0 dated 2026-07-15 and 0.1.1 dated 2026-07-23
DESCRIPTION | 10 +++++----- MD5 | 10 ++++++---- NEWS.md |only README.md | 5 +++-- man/tweedieDistr-package.Rd | 2 +- src/Makevars |only src/dtweedie.cpp | 18 ++++++++++++++---- 7 files changed, 29 insertions(+), 16 deletions(-)
Title: Spatial Early Warning Signals of Ecosystem Degradation
Description: Tools to compute and assess significance of early-warnings signals (EWS) of ecosystem degradation. EWS are spatial metrics derived from raster data -- e.g. spatial autocorrelation -- that increase before an ecosystem undergoes a non-linear transition (Genin et al. (2018) <doi:10.1111/2041-210X.13058>).
Author: Alain Danet [aut],
Alexandre Genin [aut, cre] ,
Vishwesha Guttal [aut],
Sonia Kefi [aut],
Sabiha Majumder [aut],
Sumithra Sankaran [aut],
Florian Schneider [aut]
Maintainer: Alexandre Genin <alexandre.genin@inrae.fr>
Diff between spatialwarnings versions 3.1.1 dated 2025-08-18 and 3.1.2 dated 2026-07-23
DESCRIPTION | 12 ++-- MD5 | 19 +++--- NEWS | 15 +++++ R/clustering.R | 12 +++- R/lsw_sews.R | 2 src/RcppExports.cpp | 22 +++---- src/clustering.cpp | 17 +++--- src/norm_constants.cpp | 33 +++++++---- tests/testthat/buggy_matrix_for_pairs.rds |only tests/testthat/test-clustering.R | 84 ++++++++++++++++++++++++++---- tests/testthat/test-psdfit.R | 2 11 files changed, 157 insertions(+), 61 deletions(-)
More information about spatialwarnings at CRAN
Permanent link
Title: Riemannian Methods for Principal Component Analysis, Regression
and Visualization
Description: Provides tools for statistical analysis on Riemannian
manifolds using local geometry derived from Uniform Manifold Approximation
and Projection (UMAP), Isometric Mapping (Isomap), and Density-Based
Spatial Clustering of Applications with Noise (DBSCAN). The package
supports dimensionality reduction, visualization, Riemannian principal
component analysis, and Riemannian linear regression for multivariate data
analysis. Methods based on Uniform Manifold Approximation and Projection
follow McInnes et al. (2018) <doi:10.21105/joss.00861>.
Author: Oldemar Rodriguez Rojas [aut, cre],
Jennifer Lobo Vasquez [aut]
Maintainer: Oldemar Rodriguez Rojas <oldemar.rodriguez@ucr.ac.cr>
Diff between riemannianStats versions 0.1.1 dated 2026-07-17 and 0.2.0 dated 2026-07-23
riemannianStats-0.1.1/riemannianStats/inst/doc/Data10d250_example.R |only riemannianStats-0.1.1/riemannianStats/inst/doc/Data10d250_example.Rmd |only riemannianStats-0.1.1/riemannianStats/inst/doc/Data10d250_example.html |only riemannianStats-0.1.1/riemannianStats/inst/doc/students_example.R |only riemannianStats-0.1.1/riemannianStats/inst/doc/students_example.Rmd |only riemannianStats-0.1.1/riemannianStats/inst/doc/students_example.html |only riemannianStats-0.1.1/riemannianStats/man/riem.plot.3d.Rd |only riemannianStats-0.1.1/riemannianStats/vignettes/Data10d250_example.Rmd |only riemannianStats-0.1.1/riemannianStats/vignettes/students_example.Rmd |only riemannianStats-0.2.0/riemannianStats/DESCRIPTION | 24 riemannianStats-0.2.0/riemannianStats/MD5 | 71 riemannianStats-0.2.0/riemannianStats/NAMESPACE | 18 riemannianStats-0.2.0/riemannianStats/R/correlation.R | 143 + riemannianStats-0.2.0/riemannianStats/R/distances.R | 12 riemannianStats-0.2.0/riemannianStats/R/pca.R | 567 +++++- riemannianStats-0.2.0/riemannianStats/R/regression.R |only riemannianStats-0.2.0/riemannianStats/R/riemannian-analysis.R | 1 riemannianStats-0.2.0/riemannianStats/R/similarities.R | 815 +++++++++- riemannianStats-0.2.0/riemannianStats/R/visualization.R | 720 +++++--- riemannianStats-0.2.0/riemannianStats/build/vignette.rds |binary riemannianStats-0.2.0/riemannianStats/inst/doc/data10d250-pca-umap-step-by-step.R |only riemannianStats-0.2.0/riemannianStats/inst/doc/data10d250-pca-umap-step-by-step.Rmd |only riemannianStats-0.2.0/riemannianStats/inst/doc/data10d250-pca-umap-step-by-step.html |only riemannianStats-0.2.0/riemannianStats/inst/doc/riemannian-regression-umap-dbscan-isomap.R |only riemannianStats-0.2.0/riemannianStats/inst/doc/riemannian-regression-umap-dbscan-isomap.Rmd |only riemannianStats-0.2.0/riemannianStats/inst/doc/riemannian-regression-umap-dbscan-isomap.html |only riemannianStats-0.2.0/riemannianStats/inst/doc/student-pca-umap-complete-workflow.Rmd.R |only riemannianStats-0.2.0/riemannianStats/inst/doc/student-pca-umap-complete-workflow.Rmd.Rmd |only riemannianStats-0.2.0/riemannianStats/inst/doc/student-pca-umap-complete-workflow.Rmd.html |only riemannianStats-0.2.0/riemannianStats/inst/doc/student-pca-umap-step-by-step.R |only riemannianStats-0.2.0/riemannianStats/inst/doc/student-pca-umap-step-by-step.Rmd |only riemannianStats-0.2.0/riemannianStats/inst/doc/student-pca-umap-step-by-step.html |only riemannianStats-0.2.0/riemannianStats/man/coef.riem.lm.Rd |only riemannianStats-0.2.0/riemannianStats/man/fitted.riem.lm.Rd |only riemannianStats-0.2.0/riemannianStats/man/print.riem.lm.Rd |only riemannianStats-0.2.0/riemannianStats/man/print.riem.pca.Rd |only riemannianStats-0.2.0/riemannianStats/man/print.summary.riem.lm.Rd |only riemannianStats-0.2.0/riemannianStats/man/residuals.riem.lm.Rd |only riemannianStats-0.2.0/riemannianStats/man/riem.biplot.Rd | 106 - riemannianStats-0.2.0/riemannianStats/man/riem.biplot.default.Rd |only riemannianStats-0.2.0/riemannianStats/man/riem.biplot.riem.pca.Rd |only riemannianStats-0.2.0/riemannianStats/man/riem.dist.Rd | 2 riemannianStats-0.2.0/riemannianStats/man/riem.ind.coord.Rd | 2 riemannianStats-0.2.0/riemannianStats/man/riem.lm.Rd |only riemannianStats-0.2.0/riemannianStats/man/riem.original.scale.Rd |only riemannianStats-0.2.0/riemannianStats/man/riem.pca.Rd |only riemannianStats-0.2.0/riemannianStats/man/riem.plot.Rd | 59 riemannianStats-0.2.0/riemannianStats/man/riem.plot.default.Rd |only riemannianStats-0.2.0/riemannianStats/man/riem.plot.riem.pca.Rd |only riemannianStats-0.2.0/riemannianStats/man/riem.plot3d.Rd |only riemannianStats-0.2.0/riemannianStats/man/riem.similarities.dbscan.Rd |only riemannianStats-0.2.0/riemannianStats/man/riem.similarities.isomap.Rd |only riemannianStats-0.2.0/riemannianStats/man/riem.similarities.umap.Rd | 39 riemannianStats-0.2.0/riemannianStats/man/summary.riem.lm.Rd |only riemannianStats-0.2.0/riemannianStats/vignettes/data10d250-pca-umap-step-by-step.Rmd |only riemannianStats-0.2.0/riemannianStats/vignettes/riemannian-regression-umap-dbscan-isomap.Rmd |only riemannianStats-0.2.0/riemannianStats/vignettes/student-pca-umap-complete-workflow.Rmd.Rmd |only riemannianStats-0.2.0/riemannianStats/vignettes/student-pca-umap-step-by-step.Rmd |only 58 files changed, 1948 insertions(+), 631 deletions(-)
More information about riemannianStats at CRAN
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Title: Download and Display Map Tiles
Description: To create maps from tiles, 'maptiles' downloads, composes and
displays tiles from a large number of providers (e.g. 'OpenStreetMap',
'Stadia', 'Esri', 'CARTO', or 'Thunderforest').
Author: Timothee Giraud [cre, aut] ,
Diego Hernangomez [ctb] ,
Robert J. Hijmans [ctb] ,
Hugh A. Graham [ctb],
Miles McBain [cph]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between maptiles versions 0.11.0 dated 2025-12-12 and 0.12.0 dated 2026-07-23
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 7 +++++++ R/create_provider.R | 3 ++- R/get_tiles.R | 2 +- R/slippymath.R | 2 +- R/utils.R | 9 ++++++++- README.md | 20 +++++++------------- inst/tinytest/test_maptiles.R | 6 +++++- man/create_provider.Rd | 3 ++- man/figures/README-example-1.png |binary man/figures/README-example2-1.png |binary man/maptiles.Rd | 5 +++++ 13 files changed, 54 insertions(+), 35 deletions(-)
Title: Lilliefors-Corrected Kolmogorov-Smirnov Goodness-of-Fit Tests
Description: Implements the Lilliefors-corrected Kolmogorov-Smirnov test for use
in goodness-of-fit tests, suitable when population parameters are unknown and
must be estimated by sample statistics. P-values are estimated by simulation.
Can be used with a variety of continuous distributions, including normal,
lognormal, univariate mixtures of normals, uniform, loguniform, exponential,
gamma, and Weibull distributions. Functions to generate random numbers and
calculate density, distribution, and quantile functions are provided for use
with the log uniform and mixture distributions.
Author: Phil Novack-Gottshall [aut, cre],
Steve C. Wang [aut]
Maintainer: Phil Novack-Gottshall <pnovack-gottshall@ben.edu>
Diff between KScorrect versions 1.4.0 dated 2019-07-03 and 1.4.2 dated 2026-07-23
DESCRIPTION | 21 ++++++++++++--------- MD5 | 20 ++++++++++---------- NEWS.md | 20 +++++++++++++++----- R/KScorrect.R | 5 +---- R/LcKS.R | 2 +- R/ks_test_stat.R | 9 +++++---- R/qmixnorm.R | 2 +- README.md | 9 +++++---- man/KScorrect-package.Rd | 10 +++++++++- man/LcKS.Rd | 13 ++++++++++--- man/ks_test_stat.Rd | 9 +++++---- 11 files changed, 74 insertions(+), 46 deletions(-)
Title: 'JDemetra+' Quality Report Generator
Description: Tool for generating quality reports from cruncher outputs
(and calculating series scores). The latest version of the cruncher
can be downloaded here:
<https://github.com/jdemetra/jwsacruncher/releases>.
Author: Tanguy Barthelemy [aut, cre, art],
Eulalie Delaune [aut],
Alain Quartier-la-Tente [aut] ,
Institut national de la statistique et des etudes economiques [cph]
,
Anna Smyk [aut]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between JDCruncheR versions 0.4.0 dated 2026-06-12 and 0.4.1 dated 2026-07-23
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JDCruncheR-0.4.1/JDCruncheR/R/deprecated.R | 30 JDCruncheR-0.4.1/JDCruncheR/R/export.R | 258 JDCruncheR-0.4.1/JDCruncheR/R/extractQR.R | 20 JDCruncheR-0.4.1/JDCruncheR/R/extract_JVS.R | 262 JDCruncheR-0.4.1/JDCruncheR/R/extraction.R | 184 JDCruncheR-0.4.1/JDCruncheR/R/print.R |only JDCruncheR-0.4.1/JDCruncheR/R/reading.R | 26 JDCruncheR-0.4.1/JDCruncheR/R/thresholds.R | 88 JDCruncheR-0.4.1/JDCruncheR/R/zzz.R | 1 JDCruncheR-0.4.1/JDCruncheR/README.md | 10 JDCruncheR-0.4.1/JDCruncheR/build/vignette.rds |binary JDCruncheR-0.4.1/JDCruncheR/inst/doc/Plug_in_JVS-EN.R |only JDCruncheR-0.4.1/JDCruncheR/inst/doc/Plug_in_JVS-EN.Rmd |only JDCruncheR-0.4.1/JDCruncheR/inst/doc/Plug_in_JVS-EN.html |only JDCruncheR-0.4.1/JDCruncheR/inst/doc/Plug_in_JVS-FR.R |only JDCruncheR-0.4.1/JDCruncheR/inst/doc/Plug_in_JVS-FR.Rmd |only JDCruncheR-0.4.1/JDCruncheR/inst/doc/Plug_in_JVS-FR.html |only JDCruncheR-0.4.1/JDCruncheR/inst/extdata/WS/WS_world/Output/SAProcessing-1/demetra_m.csv | 14 JDCruncheR-0.4.1/JDCruncheR/inst/extdata/WS/WS_world/Output/SAProcessing-1/series_decomposition_s_cmp.csv |only JDCruncheR-0.4.1/JDCruncheR/inst/extdata/WS/WS_world/Output/SAProcessing-1/series_decomposition_sa_cmp.csv |only JDCruncheR-0.4.1/JDCruncheR/inst/extdata/WS/WS_world/Output/SAProcessing-1/series_decomposition_t_cmp.csv |only JDCruncheR-0.4.1/JDCruncheR/inst/extdata/WS/WS_world/Output/SAProcessing-1/series_decomposition_y_cmp.csv |only JDCruncheR-0.4.1/JDCruncheR/inst/extdata/WS/WS_world/SAProcessing/SAProcessing-1.xml | 2817 +++++++++- JDCruncheR-0.4.1/JDCruncheR/man/JDCruncheR-package.Rd | 6 JDCruncheR-0.4.1/JDCruncheR/man/JVS_matrix.Rd | 46 JDCruncheR-0.4.1/JDCruncheR/man/QR_matrix.Rd | 52 JDCruncheR-0.4.1/JDCruncheR/man/QR_var_manipulation.Rd | 100 JDCruncheR-0.4.1/JDCruncheR/man/deprecated-JDCruncheR.Rd | 36 JDCruncheR-0.4.1/JDCruncheR/man/extract_JVS.Rd | 86 JDCruncheR-0.4.1/JDCruncheR/man/extract_QR.Rd | 4 JDCruncheR-0.4.1/JDCruncheR/man/figures/logo.svg | 2 JDCruncheR-0.4.1/JDCruncheR/man/fr-JVS_matrix.Rd |only JDCruncheR-0.4.1/JDCruncheR/man/fr-QR_matrix.Rd | 6 JDCruncheR-0.4.1/JDCruncheR/man/fr-QR_var_manipulation.Rd |only JDCruncheR-0.4.1/JDCruncheR/man/fr-compute_score.Rd | 2 JDCruncheR-0.4.1/JDCruncheR/man/fr-extract_JVS.Rd |only JDCruncheR-0.4.1/JDCruncheR/man/fr-extract_QR.Rd | 17 JDCruncheR-0.4.1/JDCruncheR/man/fr-get_thresholds.Rd |only JDCruncheR-0.4.1/JDCruncheR/man/fr-print.QR_matrix.Rd | 2 JDCruncheR-0.4.1/JDCruncheR/man/fr-recode_indicator_num.Rd | 20 JDCruncheR-0.4.1/JDCruncheR/man/fr-set_thresholds.Rd |only JDCruncheR-0.4.1/JDCruncheR/man/fr-write.JVS_matrix.Rd |only JDCruncheR-0.4.1/JDCruncheR/man/fr-write.QR_matrix.Rd | 22 JDCruncheR-0.4.1/JDCruncheR/man/fr-write.Rd |only JDCruncheR-0.4.1/JDCruncheR/man/fr-write.mQR_matrix.Rd | 27 JDCruncheR-0.4.1/JDCruncheR/man/get_thresholds.Rd | 8 JDCruncheR-0.4.1/JDCruncheR/man/print.QR_matrix.Rd | 12 JDCruncheR-0.4.1/JDCruncheR/man/rbind.QR_matrix.Rd | 4 JDCruncheR-0.4.1/JDCruncheR/man/recode_indicator_num.Rd | 42 JDCruncheR-0.4.1/JDCruncheR/man/set_thresholds.Rd | 8 JDCruncheR-0.4.1/JDCruncheR/man/sort.Rd | 4 JDCruncheR-0.4.1/JDCruncheR/man/weighted_score.Rd | 13 JDCruncheR-0.4.1/JDCruncheR/man/write.JVS_matrix.Rd | 38 JDCruncheR-0.4.1/JDCruncheR/man/write.QR_matrix.Rd | 28 JDCruncheR-0.4.1/JDCruncheR/man/write.Rd | 27 JDCruncheR-0.4.1/JDCruncheR/man/write.mQR_matrix.Rd | 43 JDCruncheR-0.4.1/JDCruncheR/tests/testthat/data/JVS |only JDCruncheR-0.4.1/JDCruncheR/tests/testthat/helper.R |only JDCruncheR-0.4.1/JDCruncheR/tests/testthat/test-extractJVS.R |only JDCruncheR-0.4.1/JDCruncheR/vignettes/Plug_in_JVS-EN.Rmd |only JDCruncheR-0.4.1/JDCruncheR/vignettes/Plug_in_JVS-FR.Rmd |only 82 files changed, 4494 insertions(+), 1155 deletions(-)
Title: Tidy Integration of Large Language Models
Description: A tidy interface for integrating large language model (LLM) APIs such as 'Claude', 'OpenAI', 'Gemini', 'Mistral', and local models via 'Ollama' into R workflows. The package supports text, image, audio, video, and document interactions; a unified media interface for attaching inline files or uploading to provider file stores; batch request APIs for cost-efficient large-scale processing; and a pipeline-oriented interface for seamless integration into data workflows. Web services are available at <https://www.anthropic.com>, <https://openai.com>, <https://aistudio.google.com/>, <https://mistral.ai/> and <https://ollama.com>.
Author: Eduard Bruell [aut, cre],
Jia Zhang [ctb]
Maintainer: Eduard Bruell <eduard.bruell@zew.de>
Diff between tidyllm versions 0.5.0 dated 2026-04-30 and 0.5.1 dated 2026-07-23
DESCRIPTION | 6 LICENSE | 4 MD5 | 55 +- NEWS.md | 24 R/api_chat_completions.R | 10 R/api_claude.R | 278 ++++++++--- R/api_gemini.R | 10 R/api_ollama.R | 8 R/api_openai.R | 6 R/api_openrouter.R | 4 inst/doc/tidyllm.R | 8 inst/doc/tidyllm.Rmd | 10 inst/doc/tidyllm.html | 10 man/claude_chat.Rd | 37 + man/claude_websearch.Rd | 21 man/gemini_chat.Rd | 4 man/gemini_embedding.Rd | 4 man/ollama_chat.Rd | 4 man/openai_chat.Rd | 4 man/openrouter_chat.Rd | 4 man/send_claude_batch.Rd | 26 - man/send_gemini_batch.Rd | 2 man/send_ollama_batch.Rd | 4 man/send_openai_batch.Rd | 4 tests/testthat/ollama/localhost-11434/api/chat-6c3e3d-POST.R |only tests/testthat/test_api_gemini.R | 4 tests/testthat/test_api_ollama.R | 4 tests/testthat/test_api_openai.R | 7 vignettes/tidyllm.Rmd | 10 29 files changed, 396 insertions(+), 176 deletions(-)
Title: Standardized Economic Reporting and Automated Dynamic Writing /
Synthèse d'Écrits Avec des Règles Automatisées et Dynamiques
Description: Provides tools for generating dynamic and standardized
economic narratives in R Markdown documents. The package is primarily
designed for French-language statistical and economic publications.
It includes functions to describe changes in levels, percentages,
trends, accelerations and short-term economic developments using
consistent linguistic rules. The package supports automated reporting
workflows and reproducible economic writing.
Fournit des outils permettant de générer des textes économiques
dynamiques et standardisés dans des documents R Markdown. Le package
est principalement conçu pour les publications statistiques et
économiques en français. Il propose des fonctions permettant de
décrire les évolutions de niveaux, de pourcentages, de tendances,
d'accélérations et les évolutions conjoncturelles à l'aide de règles
linguistiques homogènes. Le package facilite l'automatisation de la
rédaction et la reproductibilité des publications économiques.
Author: Alexandre Cazenave-Lacroutz [aut] ,
Jules Lejas [cre],
Direction de l'animation de la recherche, des etudes et des
statistiques [cph]
Maintainer: Jules Lejas <jules.lejas@gmail.com>
Diff between serad versions 0.2.2 dated 2026-07-01 and 0.2.3 dated 2026-07-23
DESCRIPTION | 6 +- MD5 | 42 +++++++++---------- R/g_nom.R | 8 ++- R/g_nom_taux.R | 57 ++++++++++++++++++++++---- R/g_verbe.R | 12 ++++- R/g_verbe_taux.R | 72 +++++++++++++++++++++++----------- R/init_serad_en.R | 32 ++++++--------- R/init_serad_fr.R | 40 ++++++++---------- inst/doc/exemple.html | 4 - inst/doc/serad.html | 22 +++++----- man/g_nom.Rd | 8 ++- man/g_nom_taux.Rd | 23 ++++++++-- man/g_verbe.Rd | 12 ++++- man/g_verbe_taux.Rd | 15 +++++-- tests/testthat/test-gETa_nom.R | 4 - tests/testthat/test-gETa_nom_taux.R | 4 - tests/testthat/test-gETa_verbe.R | 10 ++-- tests/testthat/test-gETa_verbe_taux.R | 8 +-- tests/testthat/test-g_nom.R | 11 ++--- tests/testthat/test-g_nom_taux.R | 13 ++---- tests/testthat/test-g_verbe.R | 30 ++++---------- tests/testthat/test-g_verbe_taux.R | 24 ++--------- 22 files changed, 264 insertions(+), 193 deletions(-)
Title: Multiple Checks on MEDITS Trawl Survey Data
Description: Provides quality checks for MEDITS (International Bottom Trawl Survey in the Mediterranean) trawl survey exchange data tables (TA (Haul data), TB (Catch data), TC (Biological data), TE (Biological individual data), TL (Litter data)). The main function RoME() calls all check functions in a defined sequence to perform a complete quality control of TX (Generic exchange data) data, including header validation, controlled-vocabulary checks, cross-table consistency tests, and biological plausibility checks. No automatic correction is applied: the package detects errors, warns the user, and specifies the type of error to ease data correction. Checks can be run simultaneously on multi-year datasets. An embedded 'shiny' application is also provided via run_RoME_app(). References describing the methods: MEDITS Working Group (2017).
Author: Walter Zupa [aut, cre],
Isabella Bitetto [aut],
Maria Teresa Spedicato [aut],
Loredana Casciaro [rev],
Cosmidano Neglia [rev]
Maintainer: Walter Zupa <zupa@fondazionecoispa.org>
Diff between RoME versions 0.2.3 dated 2026-04-23 and 0.2.4 dated 2026-07-23
DESCRIPTION | 8 - MD5 | 240 +++++++++++++++++----------------- NEWS.md | 5 R/checkHeader.R | 198 +++++++++++++--------------- R/check_0_fieldsTA.r | 86 +++++------- R/check_TE_TC.r | 123 ++++++++--------- R/check_area.r | 218 +++++++++++++++--------------- R/check_associations_category_TL.r | 103 ++++++-------- R/check_bridles_length.r | 88 +++++------- R/check_class.r | 8 - R/check_date_haul.r | 120 ++++++++--------- R/check_dictionary_new.r | 22 +-- R/check_dm.r | 103 +++++++------- R/check_haul_species_TCTB.r | 102 ++++++-------- R/check_hauls_TATB.r | 89 ++++++------ R/check_hauls_TATL.r | 99 ++++++-------- R/check_hauls_TBTA.r | 71 ++++------ R/check_hauls_TLTA.r | 94 ++++++------- R/check_identical_records.r | 24 +-- R/check_individual_weightTC.r | 145 +++++++++----------- R/check_individual_weightTE.r | 20 +- R/check_length_NEW.r | 42 +++-- R/check_length_class_codeTC.r | 95 ++++++------- R/check_mat_stages.r | 106 ++++++--------- R/check_nb_TE.r | 120 ++++++++--------- R/check_nb_per_sexTC.r | 146 ++++++++++---------- R/check_nbtotTB.r | 69 ++++----- R/check_nm_TB.r | 12 - R/check_no_empty_fields.r | 123 ++++++++--------- R/check_numeric_range.R | 91 +++++------- R/check_position_in_Med.r | 106 +++++++-------- R/check_raising_NEW.r | 116 ++++++++++------ R/check_rubincode.r | 135 ++++++++----------- R/check_smallest_mature.r | 28 +-- R/check_spawning_period.r | 58 +++----- R/check_step_length_distr.r | 91 +++++------- R/check_swept_area.r | 50 +++---- R/check_type.r | 73 ++++------ R/check_unique_valid_haul.r | 83 +++++------ R/check_weight.r | 40 ++--- R/check_weight_tot_nb.r | 18 +- R/check_year.r | 192 +++++++++++++-------------- inst/CITATION | 9 - inst/doc/RoME_vignettes.Rmd | 3 inst/doc/RoME_vignettes.html | 11 - man/RoME.Rd | 2 man/RoMEBScc.Rd | 2 man/RoMEcc.Rd | 2 man/Rsufi_files.Rd | 2 man/TM_list.Rd | 2 man/assTL.Rd | 4 man/checkHeader.Rd | 2 man/check_0_fieldsTA.Rd | 2 man/check_G1_G2.Rd | 2 man/check_TE_TC.Rd | 2 man/check_area.Rd | 2 man/check_associations_category_TL.Rd | 2 man/check_bridles_length.Rd | 2 man/check_class.Rd | 2 man/check_consistencyTA_distance.Rd | 2 man/check_consistencyTA_duration.Rd | 2 man/check_date_haul.Rd | 2 man/check_depth.Rd | 2 man/check_dictionary.Rd | 2 man/check_distance.Rd | 3 man/check_dm.Rd | 2 man/check_haul_species_TCTB.Rd | 2 man/check_hauls_TATB.Rd | 2 man/check_hauls_TATL.Rd | 2 man/check_hauls_TBTA.Rd | 2 man/check_hauls_TLTA.Rd | 2 man/check_identical_records.Rd | 2 man/check_individual_weightTC.Rd | 2 man/check_individual_weightTE.Rd | 2 man/check_length.Rd | 2 man/check_length_class_codeTC.Rd | 2 man/check_mat_stages.Rd | 2 man/check_nb_TE.Rd | 2 man/check_nb_per_sexTC.Rd | 2 man/check_nbtotTB.Rd | 2 man/check_nm_TB.Rd | 2 man/check_no_empty_fields.Rd | 2 man/check_numeric_range.Rd | 2 man/check_position.Rd | 2 man/check_position_in_Med.Rd | 2 man/check_quadrant.Rd | 2 man/check_quasiidentical_records.Rd | 2 man/check_rubincode.Rd | 2 man/check_smallest_mature.Rd | 2 man/check_spawning_period.Rd | 2 man/check_species_TBTC.Rd | 2 man/check_step_length_distr.Rd | 2 man/check_stratum.Rd | 2 man/check_stratum_code.Rd | 2 man/check_subsampling.Rd | 2 man/check_temperature.Rd | 2 man/check_type.Rd | 2 man/check_unique_valid_haul.Rd | 2 man/check_weight.Rd | 2 man/check_weight_tot_nb.Rd | 2 man/check_year.Rd | 2 man/classes.Rd | 2 man/create_catch.Rd | 2 man/create_haul.Rd | 2 man/create_length.Rd | 2 man/create_strata.Rd | 2 man/error.table.Rd | 2 man/graphs_TA.Rd | 2 man/haul_at_sea.Rd | 2 man/list_g1_g2.Rd | 4 man/mat_stages.Rd | 4 man/printError.Rd | 2 man/printError_cc.Rd | 2 man/scheme_individual_data.Rd | 2 man/templateTA.Rd | 2 man/templateTB.Rd | 2 man/templateTC.Rd | 2 man/templateTE.Rd | 2 man/templateTL.Rd | 2 man/time.Rd | 4 vignettes/RoME_vignettes.Rmd | 3 121 files changed, 1921 insertions(+), 2024 deletions(-)
Title: Precision Profile Weighted Deming Regression
Description: Weighted Deming regression, also known as 'errors-in-variable'
regression, is applied with suitable weights. Weights are modeled via a
precision profile; thus the methods implemented here are referred to as
precision profile weighted Deming (PWD) regression. The package covers
two settings – one where the precision profiles are known either from
external studies or from adequate replication of the X and Y readings,
and one in which there is a plausible functional form for the precision
profiles but the exact (unknown) function must be estimated from the
(generally singlicate) readings.
The function set includes tools for: estimated standard errors (via
jackknifing); standardized-residual analysis function with regression
diagnostic tools for normality, linearity and constant variance; and an
outlier analysis identifying significant outliers for closer investigation.
The following reference provides further information on mathematical
derivations and applications.
Hawkins, D.M., and J.J [...truncated...]
Author: Douglas M. Hawkins [aut, cph],
Jessica J. Kraker [aut, cre]
Maintainer: Jessica J. Kraker <krakerjj@uwec.edu>
Diff between ppwdeming versions 2.1.0 dated 2026-03-15 and 3.0.2 dated 2026-07-23
DESCRIPTION | 18 ++- MD5 | 56 ++++++--- NAMESPACE | 11 + NEWS.md | 37 ++++++ R/PWD_RL.r | 8 - R/PWD_get_gh.r | 260 ++++++++++++++++++++++++++++++---------------- R/PWD_inference.r | 194 ++++++++++++++++++++++++---------- R/PWD_known.r | 74 ++++++++----- R/PWD_outlier.r | 109 ++++++++++++++----- R/PWD_resi.r | 45 ++++--- R/WD_General.r | 8 - R/WD_Linnet.r | 7 - R/multi_PWD.r |only R/multi_PWD_inf.r |only R/multi_PWD_inner.r |only R/multi_PWD_out.r |only R/summary_PWD_get_gh.R |only R/summary_PWD_inference.R |only R/summary_PWD_known.R |only R/summary_PWD_outlier.R |only R/summary_PWD_resi.R |only man/PWD_RL.Rd | 8 - man/PWD_get_gh.Rd | 64 ++++++----- man/PWD_inference.Rd | 70 ++++++++---- man/PWD_known.Rd | 22 ++- man/PWD_outlier.Rd | 35 ++++-- man/PWD_resi.Rd | 17 +-- man/WD_General.Rd | 8 - man/WD_Linnet.Rd | 7 - man/multi_PWD.Rd |only man/multi_PWD_inf.Rd |only man/multi_PWD_inner.Rd |only man/multi_PWD_out.Rd |only man/summary.pwdgetgh.Rd |only man/summary.pwdinf.Rd |only man/summary.pwdknown.Rd |only man/summary.pwdout.Rd |only man/summary.pwdresi.Rd |only 38 files changed, 724 insertions(+), 334 deletions(-)
Title: Visualization of Viral Protein Sequence Diversity Dynamics
Description: To ease the visualization of outputs from Diversity Motif Analyser ('DiMA';
<https://github.com/BVU-BILSAB/DiMA>). 'vDiveR' allows visualization of the diversity
motifs (index and its variants – major, minor and unique) for elucidation of
the underlying inherent dynamics. Please refer <https://vdiver-manual.readthedocs.io/en/latest/>
for more information.
Author: Pendy Tok [aut, cre],
Li Chuin Chong [aut],
Evgenia Chikina [aut],
Yin Cheng Chen [aut],
Mohammad Asif Khan [aut]
Maintainer: Pendy Tok <pendytok0518@gmail.com>
Diff between vDiveR versions 2.2.0 dated 2026-05-11 and 2.2.1 dated 2026-07-23
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS.md | 6 ++---- R/plot_conservation_level.R | 21 ++++++++------------- tests/testthat/test-plot-conservation-level.R |only 5 files changed, 17 insertions(+), 23 deletions(-)
More information about scShardSplitRef at CRAN
Permanent link
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'.
For example, the 'parallelFor()' function can be used to convert the work of
a standard serial "for" loop into a parallel one and the 'parallelReduce()'
function can be used for accumulating aggregate or other values.
Author: Kevin Ushey [aut, cre] ,
JJ Allaire [aut],
Romain Francois [aut, cph],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] ,
Hamada S. Badr [ctb] ,
Dirk Eddelbuettel [aut] ,
Intel [aut, cph] ,
UXL Foundation [aut, cph] ,
Microsoft [cph],
Posit, PB [...truncated...]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between RcppParallel versions 5.1.11-2 dated 2026-03-05 and 6.0.0 dated 2026-07-23
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RcppParallel-6.0.0/RcppParallel/src/tbb/SECURITY.md |only RcppParallel-6.0.0/RcppParallel/src/tbb/SUPPORT.md |only RcppParallel-6.0.0/RcppParallel/src/tbb/SYSTEM_REQUIREMENTS.md |only RcppParallel-6.0.0/RcppParallel/src/tbb/WASM_Support.md |only RcppParallel-6.0.0/RcppParallel/src/tbb/cmake/README.md |only RcppParallel-6.0.0/RcppParallel/src/tbb/cmake/android |only RcppParallel-6.0.0/RcppParallel/src/tbb/cmake/compilers |only RcppParallel-6.0.0/RcppParallel/src/tbb/cmake/config_generation.cmake |only RcppParallel-6.0.0/RcppParallel/src/tbb/cmake/hwloc_detection.cmake |only RcppParallel-6.0.0/RcppParallel/src/tbb/cmake/memcheck.cmake |only RcppParallel-6.0.0/RcppParallel/src/tbb/cmake/packaging.cmake |only RcppParallel-6.0.0/RcppParallel/src/tbb/cmake/post_install |only RcppParallel-6.0.0/RcppParallel/src/tbb/cmake/python |only RcppParallel-6.0.0/RcppParallel/src/tbb/cmake/resumable_tasks.cmake |only RcppParallel-6.0.0/RcppParallel/src/tbb/cmake/sanitize.cmake |only 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RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/collaborative_call_once.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/combinable.h | 68 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/concurrent_hash_map.h | 1621 ---- RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/concurrent_lru_cache.h | 270 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/concurrent_map.h | 370 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/concurrent_priority_queue.h | 533 - RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/concurrent_queue.h | 460 - RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/concurrent_set.h | 284 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/concurrent_unordered_map.h | 473 - RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/concurrent_unordered_set.h | 429 - RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/concurrent_vector.h | 1368 --- RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/enumerable_thread_specific.h | 1122 -- RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/flow_graph.h | 3971 ---------- RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/flow_graph_abstractions.h | 40 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/global_control.h | 65 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/info.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/memory_pool.h | 262 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/mutex.h | 216 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/null_mutex.h | 37 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/null_rw_mutex.h | 39 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/parallel_for.h | 406 - RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/parallel_for_each.h | 120 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/parallel_invoke.h | 441 - RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/parallel_pipeline.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/parallel_reduce.h | 638 - RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/parallel_scan.h | 397 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/parallel_sort.h | 238 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/partitioner.h | 661 - RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/profiling.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/queuing_mutex.h | 94 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/queuing_rw_mutex.h | 135 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/rw_mutex.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/scalable_allocator.h | 375 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/spin_mutex.h | 195 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/spin_rw_mutex.h | 239 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/task.h | 1094 -- RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/task_arena.h | 420 - RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/task_group.h | 244 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/task_scheduler_observer.h | 147 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/tbb.h | 74 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/tbb_allocator.h | 190 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/tbbmalloc_proxy.h | 52 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/tick_count.h | 123 RcppParallel-6.0.0/RcppParallel/src/tbb/include/tbb/version.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/integration |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/CMakeLists.txt |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/address_waiter.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/allocator.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/arena.cpp | 1636 +--- RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/arena.h | 679 - RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/arena_slot.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/arena_slot.h |only 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RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/intrusive_list.h | 155 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/itt_notify.cpp | 48 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/itt_notify.h | 102 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/mailbox.h | 161 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/main.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/main.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/market.cpp | 888 -- RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/market.h | 373 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/market_concurrent_monitor.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/misc.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/misc.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/misc_ex.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/observer_proxy.cpp | 354 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/observer_proxy.h | 89 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/parallel_pipeline.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/permit_manager.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/pm_client.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/private_server.cpp | 276 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/profiling.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/queuing_rw_mutex.cpp | 917 +- RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/rml_base.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/rml_tbb.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/rml_tbb.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/rml_thread_monitor.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/rtm_mutex.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/rtm_rw_mutex.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/scheduler_common.h | 830 +- RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/semaphore.cpp | 20 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RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/thread_dispatcher.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/thread_dispatcher.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/thread_dispatcher_client.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/thread_request_serializer.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/thread_request_serializer.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/threading_control.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/threading_control.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/threading_control_client.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/tls.h | 69 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/tools_api/disable_warnings.h | 6 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/tools_api/ittnotify.h | 1300 ++- RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/tools_api/ittnotify_config.h | 321 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/tools_api/ittnotify_static.c | 902 ++ RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/tools_api/ittnotify_static.h | 78 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/tools_api/ittnotify_types.h | 42 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/tools_api/legacy/ittnotify.h | 77 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/version.cpp |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbb/waiters.h |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbbind |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/CMakeLists.txt |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/Customize.h | 95 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/MapMemory.h | 38 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/Statistics.h | 4 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/Synchronize.h | 93 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/TypeDefinitions.h | 4 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/backend.cpp | 302 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/backend.h | 67 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/backref.cpp | 262 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/def |only RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/frontend.cpp | 656 - RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/large_objects.cpp | 226 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/large_objects.h | 66 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/shared_utils.h | 9 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/tbbmalloc.cpp | 44 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/tbbmalloc.rc | 61 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/tbbmalloc_internal.h | 196 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc/tbbmalloc_internal_api.h | 2 RcppParallel-6.0.0/RcppParallel/src/tbb/src/tbbmalloc_proxy |only 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Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly
web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>,
<https://www.euroleaguebasketball.net/eurocup/> and <https://www.acb.com/>, following the instructions
of their respectives robots.txt files, when available. Box score data are available for the three leagues.
Play-by-play and spatial shooting data are also available for the Spanish league. Methods for analysis include a
population pyramid, 2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats,
team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games,
maps of nationalities, combinations of lineups, possessions-related variables, timeouts,
performance by periods, personal fouls, offensive rebounds and different types of shooting charts.
Please see Vinue [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between BAwiR versions 1.5.2 dated 2026-06-11 and 1.5.3 dated 2026-07-23
DESCRIPTION | 10 +++---- MD5 | 24 ++++++++-------- NEWS | 7 ++++ R/do_viz_shots_gradient.R | 40 +++++++++++++++++++++------- R/do_viz_shots_scatter.R | 60 ++++++++++++++++++++++++++++++++---------- R/get_heatmap_bb.R | 3 +- R/get_sticker.R | 4 +- inst/doc/BAwiR.html | 10 +++---- inst/doc/BAwiR_pbp.html | 10 +++---- inst/doc/BAwiR_sc.html | 10 +++---- man/acb_shooting_data_2425.Rd | 36 ++++++++++++++++++++++++- man/do_viz_shots_gradient.Rd | 6 +++- man/do_viz_shots_scatter.Rd | 23 +++++++++++++++- 13 files changed, 182 insertions(+), 61 deletions(-)
Title: Analyzing Randomized Experiments Using Multi-Arm Bandits
Description: Simulates response-adaptive experimental trials using
Multi-Arm Bandits. Adaptive robust estimators defined in Hadad et al.
(2021) <doi:10.1073/pnas.2014602118> and Offer-Westort et al. (2021)
<doi:10.1111/ajps.12597> are used to robustly estimate conditional
expectations and treatment effects. Provides significant simulation
customization options for imperfect information, non-stationary
bandits, and increased exploration strategies for assignments.
Author: Noah Ochital [aut, cre, cph] ,
Ryan T. Moore [ctb, cph]
Maintainer: Noah Ochital <no9857a@american.edu>
Diff between whatifbandit versions 0.3.0 dated 2025-11-03 and 1.0.2 dated 2026-07-23
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Title: Workflows for Health Technology Assessments in R using Discrete
EveNts
Description: Toolkit to support and perform discrete event simulations with and without
resource constraints in the context of health technology assessments (HTA).
The package focuses on cost-effectiveness modelling and aims to be submission-ready
to relevant HTA bodies in alignment with 'NICE TSD 15'
<https://sheffield.ac.uk/nice-dsu/tsds/patient-level-simulation>.
More details an examples can be found in the package website <https://jsanchezalv.github.io/WARDEN/>.
Author: Javier Sanchez Alvarez [aut, cre],
Gabriel Lemyre [ctb],
Valerie Aponte Ribero [ctb]
Maintainer: Javier Sanchez Alvarez <javiersanchezeco@gmail.com>
Diff between WARDEN versions 2.0.3 dated 2026-05-27 and 2.0.6 dated 2026-07-23
DESCRIPTION | 6 MD5 | 95 NAMESPACE | 14 NEWS.md | 38 R/RcppExports.R | 56 R/calculator_f.R | 148 R/input_f.R | 5592 ++++++++++++----------- R/results_summary_f.R | 1204 ++-- R/run_engine.R | 19 R/run_engine_constrained.R | 20 R/run_sim.R | 19 R/run_sim_parallel.R | 28 R/utilities.R |only R/validate.R |only build/vignette.rds |binary inst/doc/example_ssd.html | 332 - man/add_item.Rd | 2 man/adj_val.Rd | 9 man/ast_as_list.Rd | 126 man/draw_categorical.Rd |only man/input_block.Rd | 266 - man/print.warden_results.Rd |only man/qcategorical.Rd |only man/qgamma_mse.Rd | 54 man/qtimecov.Rd | 340 - man/random_stream.Rd | 5 man/release.Rd |only man/release_all.Rd |only man/release_all_if_using.Rd |only man/release_if_using.Rd |only man/resource_discrete.Rd | 121 man/run_sim.Rd | 2 man/run_sim_parallel.Rd | 2 man/scale_remaining_time.Rd |only man/seize.Rd |only man/seize_all.Rd |only man/shared_decr.Rd |only man/shared_incr.Rd |only man/shared_input.Rd | 2 man/summary_results_det.Rd | 25 man/summary_results_sim.Rd | 15 man/validate_model.Rd |only man/waning_hr.Rd |only man/with_write_flags_lang.Rd | 122 src/RcppExports.cpp | 179 src/evt_queue.cpp | 8 src/resource_constrained.cpp | 912 ++- tests/testthat/test-input_f.R | 40 tests/testthat/test-model_runs.R | 119 tests/testthat/test-queues.R | 25 tests/testthat/test-regression_eBC.R | 386 - tests/testthat/test-regression_inputs_selector.R | 656 +- tests/testthat/test-regression_ssd.R | 310 - tests/testthat/test-regression_ssd_constrained.R | 464 - tests/testthat/test-resource_discrete.R | 823 +++ tests/testthat/test-resource_helpers.R |only tests/testthat/test-utilities.R |only tests/testthat/test-validate.R |only 58 files changed, 7450 insertions(+), 5134 deletions(-)
Title: Threshold-Sweep QCA
Description: Provides threshold sweep methods for Qualitative Comparative
Analysis (QCA). Implements Condition Threshold Sweep-Single (CTS-S),
Condition Threshold Sweep-Multiple (CTS-M), Outcome Threshold Sweep (OTS),
and Dual Threshold Sweep (DTS) for systematic exploration of threshold
calibration effects on crisp-set QCA results. These methods extend
traditional robustness approaches by treating threshold variation as an
exploratory tool for discovering causal structures. Also provides Fiss
(2011) <doi:10.5465/amj.2011.60263120> core/peripheral condition
classification via compute_fiss_core() and generate_fiss_chart(), enabling
four-symbol configuration charts that distinguish core conditions (present
in both parsimonious and intermediate solutions) from peripheral conditions
(intermediate only). Built on top of the 'QCA' package by Dusa (2019)
<doi:10.1007/978-3-319-75668-4>, with function arguments following 'QCA'
conventions. Based on set-theoretic methods by Ragin (2008)
<doi: [...truncated...]
Author: Yuki Toyoda [aut, cre],
Japan Society for the Promotion of Science [fnd]
Maintainer: Yuki Toyoda <yuki.toyoda.ds@hosei.ac.jp>
Diff between ThSQCA versions 2.0.4 dated 2026-07-22 and 2.0.5 dated 2026-07-23
DESCRIPTION | 8 +- MD5 | 19 +++-- NEWS.md | 47 ++++++++++++++ R/tsqca_config_chart.R | 43 ++++++++++--- R/tsqca_core.R | 73 +++++++++++++++++----- R/tsqca_fiss_core.R | 111 ++++++++++++++++++++++++++++------ inst/doc/ThSQCA_Reproducible_EN.html | 2 inst/doc/ThSQCA_Tutorial_EN.html | 2 man/build_parsim_status_map.Rd |only man/extract_sol_terms_by_model.Rd |only tests/testthat/test-endtoend-cyclic.R | 56 +++++++++++++++++ tests/testthat/test-fiss-polarity.R |only 12 files changed, 305 insertions(+), 56 deletions(-)
Title: Offline Taxonomic Name Matching Against Darwin Core Backbones
Description: Match taxonomic names against locally stored Darwin Core backbone
databases ('WFO', 'COL', 'GBIF', 'ITIS', 'NCBI Taxonomy', 'Open Tree of Life',
'WoRMS', 'Euro+Med', 'Species Fungorum', 'AlgaeBase', 'FishBase',
'SeaLifeBase', 'Reptile Database', 'LCVP', 'WCVP'). Provides offline fuzzy and exact
matching with synonym resolution, hybrid name detection, and a unified output
schema across all sources. All heavy computation runs in the 'vectra' C11
columnar engine.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between taxify versions 0.3.4 dated 2026-07-09 and 0.4.0 dated 2026-07-23
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| 50 taxify-0.4.0/taxify/tests/testthat/test-fuzzy-boundary.R |only taxify-0.4.0/taxify/tests/testthat/test-gap-verbs.R |only taxify-0.4.0/taxify/tests/testthat/test-gbif.R | 97 taxify-0.4.0/taxify/tests/testthat/test-gidias.R |only taxify-0.4.0/taxify/tests/testthat/test-hybrid-traits.R |only taxify-0.4.0/taxify/tests/testthat/test-hybrid.R | 31 taxify-0.4.0/taxify/tests/testthat/test-inspect.R | 915 taxify-0.4.0/taxify/tests/testthat/test-invacost.R |only taxify-0.4.0/taxify/tests/testthat/test-itis.R |only taxify-0.4.0/taxify/tests/testthat/test-manifest.R | 33 taxify-0.4.0/taxify/tests/testthat/test-match.R | 56 taxify-0.4.0/taxify/tests/testthat/test-meta.R | 192 taxify-0.4.0/taxify/tests/testthat/test-multi-backend.R | 362 taxify-0.4.0/taxify/tests/testthat/test-ncbi.R | 50 taxify-0.4.0/taxify/tests/testthat/test-new-enrichments.R |only taxify-0.4.0/taxify/tests/testthat/test-new-verbs.R |only taxify-0.4.0/taxify/tests/testthat/test-ott.R | 50 taxify-0.4.0/taxify/tests/testthat/test-phylacine.R |only taxify-0.4.0/taxify/tests/testthat/test-region-marine.R |only taxify-0.4.0/taxify/tests/testthat/test-region.R | 463 taxify-0.4.0/taxify/tests/testthat/test-register.R | 305 taxify-0.4.0/taxify/tests/testthat/test-reptiledb.R | 144 taxify-0.4.0/taxify/tests/testthat/test-taxify-long.R | 185 taxify-0.4.0/taxify/tests/testthat/test-taxify.R | 141 taxify-0.4.0/taxify/tests/testthat/test-trait-genus-join.R | 2 taxify-0.4.0/taxify/tests/testthat/test-trait-registry.R | 248 taxify-0.4.0/taxify/tests/testthat/test-untested-verbs.R |only taxify-0.4.0/taxify/tests/testthat/test-worms.R | 50 taxify-0.4.0/taxify/vignettes/articles |only taxify-0.4.0/taxify/vignettes/backbones.Rmd |only taxify-0.4.0/taxify/vignettes/custom-data.Rmd | 8 taxify-0.4.0/taxify/vignettes/enrichments.Rmd | 145 taxify-0.4.0/taxify/vignettes/fuzzy-matching.Rmd | 2 taxify-0.4.0/taxify/vignettes/hybrids-and-aggregates.Rmd |only taxify-0.4.0/taxify/vignettes/inspecting-names.Rmd | 546 taxify-0.4.0/taxify/vignettes/large-scale.Rmd | 255 taxify-0.4.0/taxify/vignettes/migration.Rmd | 115 taxify-0.4.0/taxify/vignettes/quickstart.Rmd | 40 taxify-0.4.0/taxify/vignettes/regions.Rmd | 468 395 files changed, 29719 insertions(+), 25156 deletions(-)
Title: Build, Import, and Export GEXF Graph Files
Description: Create, read, and write 'GEXF' (Graph Exchange 'XML' Format) graph files (used in 'Gephi' and others). Using the 'XML' package, rgexf allows reading and writing GEXF files, including attributes, 'GEXF' visual attributes (such as color, size, and position), network dynamics (for both edges and nodes), and edges' weights. Users can build/handle graphs element-by-element or massively through data frames, visualize the graph on a web browser through 'gexf-js' (a 'javascript' library), and interact with the 'igraph' package.
Author: George Vega Yon [aut, cre] ,
Jorge Fabrega Lacoa [ctb],
Joshua Kunst [ctb],
Raphael Velt [cph] ,
Gephi Consortium [cph] ,
Cornelius Fritz [rev] ,
Jonathan Cardoso Silva [rev]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
This is a re-admission after prior archival of version 0.16.3 dated 2024-07-01
Diff between rgexf versions 0.16.3 dated 2024-07-01 and 0.17.0 dated 2026-07-23
rgexf-0.16.3/rgexf/inst/NEWS |only rgexf-0.16.3/rgexf/inst/doc/rgexf.R |only rgexf-0.16.3/rgexf/inst/doc/rgexf.Rmd |only rgexf-0.16.3/rgexf/inst/doc/rgexf.html |only rgexf-0.16.3/rgexf/inst/gexf-graphs/lesmiserables.png |only rgexf-0.16.3/rgexf/inst/tinytest/rundemos.R.old |only rgexf-0.16.3/rgexf/vignettes/rgexf.Rmd |only rgexf-0.17.0/rgexf/DESCRIPTION | 19 rgexf-0.17.0/rgexf/MD5 | 114 ++++- rgexf-0.17.0/rgexf/NAMESPACE | 8 rgexf-0.17.0/rgexf/NEWS.md | 47 ++ rgexf-0.17.0/rgexf/R/bugs.R | 2 rgexf-0.17.0/rgexf/R/gexf.R | 2 rgexf-0.17.0/rgexf/R/manipulation.R | 6 rgexf-0.17.0/rgexf/R/methods.R | 4 rgexf-0.17.0/rgexf/R/plot.R | 343 ++++++++++++++---- rgexf-0.17.0/rgexf/R/read.gexf.R | 2 rgexf-0.17.0/rgexf/R/rgexf-package.R | 8 rgexf-0.17.0/rgexf/README.md | 187 +++------ rgexf-0.17.0/rgexf/build/vignette.rds |binary rgexf-0.17.0/rgexf/inst/CITATION | 3 rgexf-0.17.0/rgexf/inst/WORDLIST | 3 rgexf-0.17.0/rgexf/inst/doc/getting-started.R |only rgexf-0.17.0/rgexf/inst/doc/getting-started.Rmd |only rgexf-0.17.0/rgexf/inst/doc/getting-started.html |only rgexf-0.17.0/rgexf/inst/doc/sigmajs.R |only rgexf-0.17.0/rgexf/inst/doc/sigmajs.Rmd |only rgexf-0.17.0/rgexf/inst/doc/sigmajs.html |only rgexf-0.17.0/rgexf/inst/htmlwidgets |only rgexf-0.17.0/rgexf/inst/tinytest/test-widgets.r |only rgexf-0.17.0/rgexf/man/add.gexf.node.Rd | 2 rgexf-0.17.0/rgexf/man/check.dpl.edges.Rd | 4 rgexf-0.17.0/rgexf/man/figures/igraph-1.png |binary rgexf-0.17.0/rgexf/man/figures/lesmiserables.png |only rgexf-0.17.0/rgexf/man/gexf-class.Rd | 2 rgexf-0.17.0/rgexf/man/gexf-methods.Rd | 6 rgexf-0.17.0/rgexf/man/gexfjs.Rd |only rgexf-0.17.0/rgexf/man/new.gexf.graph.Rd | 2 rgexf-0.17.0/rgexf/man/plot.gexf.Rd | 142 ------- rgexf-0.17.0/rgexf/man/plot_gexfjs.Rd |only rgexf-0.17.0/rgexf/man/read.gexf.Rd | 2 rgexf-0.17.0/rgexf/man/rgexf-package.Rd | 9 rgexf-0.17.0/rgexf/man/sigmajs.Rd |only rgexf-0.17.0/rgexf/man/switch.edges.Rd | 4 rgexf-0.17.0/rgexf/vignettes/getting-started.Rmd |only rgexf-0.17.0/rgexf/vignettes/lesmiserables.png |only rgexf-0.17.0/rgexf/vignettes/sigmajs.Rmd |only 47 files changed, 550 insertions(+), 371 deletions(-)
Title: Assortative Mating Simulation and Multivariate Bernoulli
Variates
Description: Simulation of phenotype / genotype data under assortative and
disassortative mating. Includes functions for generating Bahadur order-2
multivariate Bernoulli variables with general and diagonal-plus-low-rank
correlation structures, and for writing simulated genotypes to disk as
binary int8 or PLINK bed files. Further details are provided in:
Border and Malik (2023) <doi:10.1186/s12859-023-05442-6>.
Author: Richard Border [aut, cre] ,
Osman Malik [aut]
Maintainer: Richard Border <border.richard@gmail.com>
Diff between rBahadur versions 1.0.0 dated 2023-08-25 and 1.1.0 dated 2026-07-23
DESCRIPTION | 32 +++-- MD5 | 62 +++++++-- NAMESPACE | 8 + NEWS.md | 130 ++++++++++++++++++++ R/am_covariance_structure.R | 99 +++++++++++++-- R/am_equilibrium_parameters.R | 43 +++++- R/am_simulate.R | 244 +++++++++++++++++++++++++++++++++------ R/am_stream.R |only R/cli.R |only R/genotype_io.R |only R/mosaic.R |only R/rb_dplr.R | 136 ++++++++++++++++----- R/rb_unstr.R | 57 +++++---- R/reference.R |only README.md | 170 ++++++++++++++++++++++++++- build |only exec |only inst/CITATION | 4 inst/doc |only inst/extdata |only man/am_covariance_structure.Rd | 47 ++++++- man/am_equilibrium_parameters.Rd | 8 - man/am_mosaic.Rd |only man/am_simulate.Rd | 80 ++++++++++-- man/download_1kg_panel.Rd |only man/kg_reference.Rd |only man/rb_dplr.Rd | 25 +++ man/rb_unstr.Rd | 8 - man/rbahadur_cli_path.Rd |only man/rbahadur_main.Rd |only man/read_genotypes.Rd |only man/vcf_to_panel.Rd |only man/write_genotypes.Rd |only tests |only vignettes |only 35 files changed, 978 insertions(+), 175 deletions(-)
Title: Quantile Treatment Effects
Description: Provides several methods for computing the Quantile Treatment
Effect (QTE) and Quantile Treatment Effect on the Treated (QTT). The main
cases covered are (i) treatment is randomly assigned, (ii) treatment is as
good as randomly assigned after conditioning on covariates (selection on
observables) using the methods of Firpo (2007)
<doi:10.1111/j.1468-0262.2007.00738.x>, and (iii) identification is based
on a Difference in Differences assumption, with support for several
varieties including Athey and Imbens (2006)
<doi:10.1111/j.1468-0262.2006.00668.x>, Callaway and Li (2019)
<doi:10.3982/QE935>, and Callaway, Li, and Oka (2018)
<doi:10.1016/j.jeconom.2018.06.008>. Version 2.0 adds a unified staggered
treatment adoption API (built on 'ptetools') for all DiD-based estimators,
as well as a new lagged-outcome unconfoundedness estimator ('lou_qtt').
Author: Brantly Callaway [aut, cre]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>
This is a re-admission after prior archival of version 1.3.1 dated 2022-09-01
Diff between qte versions 1.3.1 dated 2022-09-01 and 2.0.0 dated 2026-07-23
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qte-2.0.0/qte/man/lalonde.Rd | 2 qte-2.0.0/qte/man/lalonde.exp.Rd | 2 qte-2.0.0/qte/man/lalonde.exp.panel.Rd | 2 qte-2.0.0/qte/man/lalonde.psid.Rd | 2 qte-2.0.0/qte/man/lalonde.psid.panel.Rd | 4 qte-2.0.0/qte/man/lou_gt.Rd |only qte-2.0.0/qte/man/lou_qtt.Rd |only qte-2.0.0/qte/man/mdid.Rd |only qte-2.0.0/qte/man/mdid_gt.Rd |only qte-2.0.0/qte/man/panel.checks.Rd | 14 - qte-2.0.0/qte/man/panel.qtet.Rd | 64 +++-- qte-2.0.0/qte/man/panel_qtt.Rd |only qte-2.0.0/qte/man/panel_qtt_gt.Rd |only qte-2.0.0/qte/man/panel_qtt_long_agg.Rd |only qte-2.0.0/qte/man/panelize.data.Rd | 1 qte-2.0.0/qte/man/plot.QTE.Rd | 57 ---- qte-2.0.0/qte/man/print.summary.QTE.Rd | 13 - qte-2.0.0/qte/man/qdid.Rd |only qte-2.0.0/qte/man/qdid_gt.Rd |only qte-2.0.0/qte/man/qte-package.Rd |only qte-2.0.0/qte/man/setupData.Rd | 13 - qte-2.0.0/qte/man/summary.QTE.Rd | 14 - qte-2.0.0/qte/man/three_period_subset.Rd |only qte-2.0.0/qte/man/unc_qte.Rd |only qte-2.0.0/qte/man/wquant.Rd |only qte-2.0.0/qte/tests |only qte-2.0.0/qte/vignettes/intro.qmd |only qte-2.0.0/qte/vignettes/panel-estimators.qmd |only qte-2.0.0/qte/vignettes/precomputed |only qte-2.0.0/qte/vignettes/staggered-adoption.qmd |only 131 files changed, 1200 insertions(+), 850 deletions(-)
Title: Pólya Tree Type Models
Description: Fits Bayesian nonparametric models based on Pólya tree
processes, including adaptive Pólya trees, Markov adaptive Pólya trees,
optional Pólya trees, and their conditional-density counterparts.
Methods are described in Ma (2017) <doi:10.1214/16-BA1021>, Ma (2017)
<doi:10.1214/17-EJS1254>, and Wong and Ma (2010)
<doi:10.1214/09-AOS755>.
Author: Li Ma [aut, cre]
Maintainer: Li Ma <mastatlab@gmail.com>
Diff between PTT versions 1.0 dated 2026-07-22 and 1.0.1 dated 2026-07-23
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NEWS.md | 17 +++++++++++++++++ R/apt.R | 6 ++++-- R/cond_apt.R | 4 +++- R/utils.R | 14 ++++++++++++++ man/apt.Rd | 3 ++- man/cond.apt.Rd | 3 ++- src/cgbt.cpp | 11 +++++++++-- src/gbt.cpp | 2 +- src/gbt.h | 2 +- src/helpers.h | 2 +- src/main.cpp | 32 ++++++++++++++++++++++++++++++++ tests/api.R | 31 +++++++++++++++++++++++++++++++ 14 files changed, 133 insertions(+), 26 deletions(-)
Title: Implementation of the Potential Model
Description: Provides functions to compute the potential model as defined by
Stewart (1941) <doi:10.1126/science.93.2404.89>. Several options are available
to customize the model, such as the possibility to fine-tune the distance
friction functions or to use custom distance matrices. Some computations are
parallelized to improve their efficiency.
Author: Timothee Giraud [cre, aut] ,
Hadrien Commenges [aut]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between potential versions 0.2.0 dated 2022-07-04 and 0.3.0 dated 2026-07-23
DESCRIPTION | 19 - MD5 | 53 ++-- NEWS.md | 9 R/create_grid.R | 17 - R/create_matrix.R | 15 - R/equipotential.R | 10 R/mcpotential.R | 6 R/package.R | 2 R/potential.R | 4 R/utils.R |only README.md | 12 build/partial.rdb |binary build/vignette.rds |binary inst/doc/potential.R | 77 +++--- inst/doc/potential.Rmd | 27 -- inst/doc/potential.html | 494 ++++++++++++++++++++++++----------------- inst/tinytest/test_curv.R | 13 + man/create_grid.Rd | 2 man/create_matrix.Rd | 6 man/equipotential.Rd | 2 man/figures/demo-1.png |binary man/figures/demox-1.png |binary man/mcpotential.Rd | 2 man/potential-package.Rd | 19 + man/potential.Rd | 2 vignettes/potential.Rmd | 27 -- vignettes/references.bib | 4 vignettes/web_only/exemple.Rmd | 83 +++--- 28 files changed, 529 insertions(+), 376 deletions(-)
Title: Beautiful Graph Drawing
Description: A graph visualization engine that emphasizes on
aesthetics at the same time providing default parameters that yield
out-of-the-box-nice visualizations. The package is built on top of
'The Grid Graphics Package' and seamlessly work with 'igraph' and
'network' objects.
Author: George Vega Yon [aut, cre] ,
Porter Bischoff [aut]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between netplot versions 0.3-0 dated 2024-06-30 and 0.4-0 dated 2026-07-23
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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 1.7.1 dated 2026-07-22 and 1.7.1.1 dated 2026-07-23
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ configure.ac | 2 +- src/include/GPBoost/likelihoods.h | 20 ++++++++++---------- src/include/GPBoost/re_comp.h | 11 +++++++++-- tests/testthat/test_GPModel_egpd.R | 4 ++++ tests/testthat/test_GPModel_tweedie.R | 4 ++++ 7 files changed, 38 insertions(+), 23 deletions(-)
Title: Fast and Flexible Implementations of Exploratory Factor Analysis
Tools
Description: Provides a complete workflow for exploratory factor analysis
(EFA). It covers data screening and factorability checks, a suite of
factor retention criteria for choosing the number of factors, and factor
extraction by principal axis factoring, maximum likelihood, unweighted
least squares, or diagonally weighted least squares from Pearson,
Spearman, Kendall, polychoric, tetrachoric, or two-stage
full-information maximum likelihood correlations. A built-in rotation
engine offers a range of orthogonal and oblique rotations, and standard
errors for loadings and related quantities can be obtained by analytic,
robust, or bootstrap methods. Further tools support model averaging
across analytic choices, multigroup EFA with factor congruence, EFA on
multiply imputed data, Schmid-Leiman transformation, reliability
coefficients (including McDonald's omegas), factor score estimation,
data simulation, and power analysis. Computationally intensive
procedures are implemented in 'C++' for speed.
Author: Markus Steiner [aut, cre] ,
Silvia Steiner [aut] ,
William Revelle [ctb],
Max Auerswald [ctb],
Morten Moshagen [ctb],
John Ruscio [ctb],
Brendan Roche [ctb],
Urbano Lorenzo-Seva [ctb],
David Navarro-Gonzalez [ctb],
Johan Braeken [ctb],
Andreas Soteri [...truncated...]
Maintainer: Markus Steiner <markus.d.steiner@gmail.com>
Diff between EFAtools versions 0.8.0 dated 2026-07-07 and 1.0.0 dated 2026-07-23
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EFAtools-1.0.0/EFAtools/src/paf_iter.cpp | 7 EFAtools-1.0.0/EFAtools/src/parallel.cpp | 4 EFAtools-1.0.0/EFAtools/src/polychoric.cpp | 33 EFAtools-1.0.0/EFAtools/src/rotate.cpp | 136 EFAtools-1.0.0/EFAtools/src/sim.cpp | 6 EFAtools-1.0.0/EFAtools/tests/testthat/_snaps/EFA.md | 79 EFAtools-1.0.0/EFAtools/tests/testthat/_snaps/control.md |only EFAtools-1.0.0/EFAtools/tests/testthat/_snaps/efa_average.md |only EFAtools-1.0.0/EFAtools/tests/testthat/_snaps/efa_bartlett.md |only EFAtools-1.0.0/EFAtools/tests/testthat/_snaps/efa_compare.md |only EFAtools-1.0.0/EFAtools/tests/testthat/_snaps/efa_group.md | 4 EFAtools-1.0.0/EFAtools/tests/testthat/_snaps/efa_group/efa-group-congruence-plot.svg | 10 EFAtools-1.0.0/EFAtools/tests/testthat/_snaps/efa_group/efa-group-differences-plot.svg | 312 - EFAtools-1.0.0/EFAtools/tests/testthat/_snaps/efa_kmo.md |only EFAtools-1.0.0/EFAtools/tests/testthat/_snaps/efa_mi.md |only EFAtools-1.0.0/EFAtools/tests/testthat/_snaps/efa_power.md | 7 EFAtools-1.0.0/EFAtools/tests/testthat/_snaps/efa_schmid_leiman.md |only EFAtools-1.0.0/EFAtools/tests/testthat/_snaps/format-loadings.md | 15 EFAtools-1.0.0/EFAtools/tests/testthat/_snaps/snapshots.md | 10 EFAtools-1.0.0/EFAtools/tests/testthat/helper-slow.R | 2 EFAtools-1.0.0/EFAtools/tests/testthat/helper-snapshot.R | 2 EFAtools-1.0.0/EFAtools/tests/testthat/test-EFA-boot.R | 74 EFAtools-1.0.0/EFAtools/tests/testthat/test-EFA-fields.R | 353 - EFAtools-1.0.0/EFAtools/tests/testthat/test-EFA-fiml.R | 1320 ++--- EFAtools-1.0.0/EFAtools/tests/testthat/test-EFA-vcov-slot.R | 39 EFAtools-1.0.0/EFAtools/tests/testthat/test-EFA.R | 1466 +++--- EFAtools-1.0.0/EFAtools/tests/testthat/test-EFA_POOLED-mi2s.R | 112 EFAtools-1.0.0/EFAtools/tests/testthat/test-EFA_POOLED-routing.R | 8 EFAtools-1.0.0/EFAtools/tests/testthat/test-EFA_POOLED-rubin-rotated.R | 839 +-- EFAtools-1.0.0/EFAtools/tests/testthat/test-OMEGA.R | 6 EFAtools-1.0.0/EFAtools/tests/testthat/test-ROTATE_OBLQ.R | 60 EFAtools-1.0.0/EFAtools/tests/testthat/test-ROTATE_ORTH.R | 17 EFAtools-1.0.0/EFAtools/tests/testthat/test-ULS.R | 2 EFAtools-1.0.0/EFAtools/tests/testthat/test-arg-aliases.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-control.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-cor-method-poly.R | 76 EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_average-fiml.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_average-grid.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_average.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_bartlett.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_cd.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_compare.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_ekc.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_group.R | 1700 ++++--- EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_hull.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_kgc.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_kmo.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_map.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_mi.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_nest.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_parallel.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_power.R | 38 EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_procrustes.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_reliability.R | 38 EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_retain.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_schmid_leiman.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_scree.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_screen.R | 40 EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_simulate.R | 120 EFAtools-1.0.0/EFAtools/tests/testthat/test-efa_smt.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-fiml-moments.R | 5 EFAtools-1.0.0/EFAtools/tests/testthat/test-format-loadings.R | 556 +- EFAtools-1.0.0/EFAtools/tests/testthat/test-helper.R | 89 EFAtools-1.0.0/EFAtools/tests/testthat/test-match-arg-ci.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-polychoric.R | 94 EFAtools-1.0.0/EFAtools/tests/testthat/test-prepare_cor_input.R | 51 EFAtools-1.0.0/EFAtools/tests/testthat/test-procrustes-consensus.R | 2 EFAtools-1.0.0/EFAtools/tests/testthat/test-regression-rotations.R | 28 EFAtools-1.0.0/EFAtools/tests/testthat/test-reliability_adapters.R | 40 EFAtools-1.0.0/EFAtools/tests/testthat/test-reliability_core.R | 2 EFAtools-1.0.0/EFAtools/tests/testthat/test-reliability_result.R | 2 EFAtools-1.0.0/EFAtools/tests/testthat/test-retention-controls.R |only EFAtools-1.0.0/EFAtools/tests/testthat/test-se-information.R | 1214 +++-- EFAtools-1.0.0/EFAtools/tests/testthat/test-se-sandwich.R | 1186 ++--- EFAtools-1.0.0/EFAtools/tests/testthat/test-snapshots.R | 8 EFAtools-1.0.0/EFAtools/tests/testthat/test-superseded.R |only EFAtools-1.0.0/EFAtools/vignettes/EFAtools.Rmd | 397 + EFAtools-1.0.0/EFAtools/vignettes/Migrating_to_efa.Rmd |only EFAtools-1.0.0/EFAtools/vignettes/Ordinal_and_missing_data.Rmd |only 334 files changed, 11969 insertions(+), 11237 deletions(-)
Title: Prepare Electronic Prescription Record Data to Estimate Drug
Exposure
Description: Prepare prescription data (such as from the Clinical Practice Research Datalink) into an analysis-ready format, with start and stop dates for each patient's prescriptions. Based on Pye et al (2018) <doi:10.1002/pds.4440>.
Author: Belay Birlie Yimer [aut] ,
David Selby [aut, cre, cph] ,
Meghna Jani [aut],
Goran Nenadic [aut],
Mark Lunt [aut],
William G. Dixon [aut]
Maintainer: David Selby <David.Selby@dfki.de>
This is a re-admission after prior archival of version 0.0.4 dated 2021-11-09
Diff between drugprepr versions 0.0.4 dated 2021-11-09 and 0.0.7 dated 2026-07-23
drugprepr-0.0.4/drugprepr/data/dataset1.rda |only drugprepr-0.0.4/drugprepr/man/dataset1.Rd |only drugprepr-0.0.7/drugprepr/DESCRIPTION | 28 - drugprepr-0.0.7/drugprepr/LICENSE | 4 drugprepr-0.0.7/drugprepr/MD5 | 90 +-- drugprepr-0.0.7/drugprepr/NAMESPACE | 50 - drugprepr-0.0.7/drugprepr/NEWS.md | 16 drugprepr-0.0.7/drugprepr/R/data.R | 18 drugprepr-0.0.7/drugprepr/R/ndd.R | 110 ++-- drugprepr-0.0.7/drugprepr/R/utils.R | 56 +- drugprepr-0.0.7/drugprepr/README.md | 56 +- drugprepr-0.0.7/drugprepr/build/vignette.rds |binary drugprepr-0.0.7/drugprepr/data/cprd.rda |only drugprepr-0.0.7/drugprepr/inst/doc/introduction.R | 110 ++-- drugprepr-0.0.7/drugprepr/inst/doc/introduction.Rmd | 378 +++++++-------- drugprepr-0.0.7/drugprepr/inst/doc/introduction.pdf |binary drugprepr-0.0.7/drugprepr/man/clean_duration.Rd | 84 +-- drugprepr-0.0.7/drugprepr/man/close_small_gaps.Rd | 70 +- drugprepr-0.0.7/drugprepr/man/compute_ndd.Rd | 88 +-- drugprepr-0.0.7/drugprepr/man/cprd.Rd |only drugprepr-0.0.7/drugprepr/man/decision_1.Rd | 104 ++-- drugprepr-0.0.7/drugprepr/man/decision_10.Rd | 82 +-- drugprepr-0.0.7/drugprepr/man/decision_2.Rd | 102 ++-- drugprepr-0.0.7/drugprepr/man/decision_3.Rd | 104 ++-- drugprepr-0.0.7/drugprepr/man/decision_4.Rd | 102 ++-- drugprepr-0.0.7/drugprepr/man/decision_5.Rd | 78 +-- drugprepr-0.0.7/drugprepr/man/decision_6.Rd | 84 +-- drugprepr-0.0.7/drugprepr/man/decision_7.Rd | 72 +- drugprepr-0.0.7/drugprepr/man/decision_8.Rd | 78 +-- drugprepr-0.0.7/drugprepr/man/decision_9.Rd | 84 +-- drugprepr-0.0.7/drugprepr/man/drug_prep.Rd | 102 ++-- drugprepr-0.0.7/drugprepr/man/example_therapy.Rd | 37 - drugprepr-0.0.7/drugprepr/man/get_mode.Rd | 32 - drugprepr-0.0.7/drugprepr/man/impute.Rd | 118 ++-- drugprepr-0.0.7/drugprepr/man/impute_duration.Rd | 84 +-- drugprepr-0.0.7/drugprepr/man/impute_ndd.Rd | 58 +- drugprepr-0.0.7/drugprepr/man/impute_qty.Rd | 62 +- drugprepr-0.0.7/drugprepr/man/isolate_overlaps.Rd | 108 ++-- drugprepr-0.0.7/drugprepr/man/make_decisions.Rd | 154 +++--- drugprepr-0.0.7/drugprepr/man/min_max_dat.Rd | 55 +- drugprepr-0.0.7/drugprepr/man/outside_range.Rd | 46 - drugprepr-0.0.7/drugprepr/man/shift_interval.Rd | 36 - drugprepr-0.0.7/drugprepr/tests/testthat.R | 8 drugprepr-0.0.7/drugprepr/tests/testthat/test-drugprep.R | 60 +- drugprepr-0.0.7/drugprepr/tests/testthat/test-impute.R | 188 +++---- drugprepr-0.0.7/drugprepr/tests/testthat/test-ndd.R | 28 - drugprepr-0.0.7/drugprepr/tests/testthat/test-utils.R | 44 - drugprepr-0.0.7/drugprepr/vignettes/introduction.Rmd | 378 +++++++-------- 48 files changed, 1849 insertions(+), 1797 deletions(-)
Title: Data Bank for Statistical Analysis and Visualization
Description: Contains data organized by topics: categorical data, regression model,
means comparisons, independent and repeated measures ANOVA, mixed ANOVA and ANCOVA.
The package code is under GPL-2; the data sets are covered by the terms in
the 'LICENSE.note' file (the author's data sets under CC0 1.0, and the
'heartdisease' data under CC BY 4.0, see the 'heartdisease' help page).
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between datarium versions 0.1.0 dated 2019-05-21 and 0.2.0 dated 2026-07-23
DESCRIPTION | 16 ++++--- LICENSE.note |only MD5 | 101 +++++++++++++++++++++++++++++------------------ NEWS.md |only R/AirPassengersDf.R |only R/antismoking.R |only R/anxiety.R | 29 ++++++++++++- R/datarium-package.R |only R/depression.R | 37 ++++++++++++++--- R/genderweight.R | 24 +++++++++-- R/headache.R | 33 ++++++++++----- R/heartattack.R | 27 +++++++++--- R/heartdisease.R |only R/housetasks.raw.R | 27 ++++++++++++ R/infections.R |only R/jobsatisfaction.R | 23 +++++++++- R/marketing.R | 24 +++++++++-- R/mice.R | 20 ++++++++- R/mice2.R | 21 ++++++++- R/performance.R | 26 +++++++++++- R/properties.R | 21 ++++++++- R/renalstone.R |only R/selfesteem.R | 28 ++++++++++++- R/selfesteem2.R | 31 +++++++++++++- R/stress.R | 24 ++++++++++- R/taskachievment.R |only R/titanic.raw.R | 20 +++++++-- R/weightloss.R | 34 ++++++++++++++- README.md | 95 +++++++++++++++++++++++++++++--------------- build |only data/AirPassengersDf.rda |only data/antismoking.rda |only data/heartdisease.rda |only data/infections.rda |only data/renalstone.rda |only data/stress.rda |binary data/taskachievment.rda |only inst/data.R |only man/AirPassengersDf.Rd |only man/antismoking.Rd |only man/anxiety.Rd | 34 ++++++++++++++- man/datarium.Rd |only man/depression.Rd | 42 ++++++++++++++++--- man/figures |only man/genderweight.Rd | 29 +++++++++++-- man/headache.Rd | 38 ++++++++++++----- man/heartattack.Rd | 32 +++++++++++--- man/heartdisease.Rd |only man/housetasks.raw.Rd | 32 ++++++++++++++ man/infections.Rd |only man/jobsatisfaction.Rd | 28 ++++++++++++- man/marketing.Rd | 31 ++++++++++++-- man/mice.Rd | 25 ++++++++++- man/mice2.Rd | 26 +++++++++++- man/performance.Rd | 31 +++++++++++++- man/properties.Rd | 26 +++++++++++- man/renalstone.Rd |only man/selfesteem.Rd | 33 ++++++++++++++- man/selfesteem2.Rd | 36 +++++++++++++++- man/stress.Rd | 29 ++++++++++++- man/taskachievment.Rd |only man/titanic.raw.Rd | 27 ++++++++++-- man/weightloss.Rd | 39 ++++++++++++++++-- tests |only 64 files changed, 1010 insertions(+), 189 deletions(-)
Title: MCMC Algorithms for the Coalescent
Description: Flexible framework for coalescent analyses in R. It includes a main function running the MCMC algorithm, auxiliary functions for tree rearrangement, and some functions to compute population genetic parameters. Extended description can be found in Paradis (2020) <doi:10.1201/9780429466700>. For details on the MCMC algorithm, see Kuhner et al. (1995) <doi:10.1093/genetics/140.4.1421> and Drummond et al. (2002) <doi:10.1093/genetics/161.3.1307>.
Author: Emmanuel Paradis [aut, cre, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between coalescentMCMC versions 0.4-4 dated 2022-04-22 and 0.5 dated 2026-07-23
DESCRIPTION | 13 +++++++------ MD5 | 22 +++++++++++----------- NAMESPACE | 7 +++---- NEWS | 4 +++- build/vignette.rds |binary inst/CITATION | 18 +++++++----------- inst/doc/CoalescentModels.R | 2 -- inst/doc/CoalescentModels.pdf |binary inst/doc/Running_coalescentMCMC.R | 2 -- inst/doc/Running_coalescentMCMC.pdf |binary man/plotTHETA.Rd | 2 +- vignettes/coalescentMCMC.bib | 9 +++++++++ 12 files changed, 41 insertions(+), 38 deletions(-)
More information about coalescentMCMC at CRAN
Permanent link
Title: Biological Indicators and Indices for MEDITS Survey Data
Description: Supports the standardized analysis of Mediterranean
International Bottom Trawl Survey (MEDITS) data and the calculation
of biological indicators for selected species and population
components. The package provides functions to estimate abundance
and biomass indices, analyse size structure and length frequency
distributions, derive sex ratio and maturity related metrics,
explore spatial patterns, and assess temporal trends across
surveys. Developed for integration within the Regional Database
for Fisheries (RDBFIS) framework, it is intended to work on
quality checked input data and to produce reproducible outputs
that can support monitoring, comparative analyses among
Geographical Sub-Areas (GSAs) and countries, and fishery management.
Author: Walter Zupa [aut, cre],
Loredana Casciaro [rev],
Cosmidano Neglia [rev],
Isabella Bitetto [rev],
Maria Teresa Spedicato [aut]
Maintainer: Walter Zupa <zupa@fondazionecoispa.org>
Diff between BioIndex versions 0.6.4 dated 2026-05-29 and 0.6.5 dated 2026-07-23
DESCRIPTION | 8 MD5 | 16 - NEWS.md | 186 +++++++++--------- R/merge_TATB.r | 448 ++++++++++++++++++++++++++++---------------- R/merge_TATBTC.r | 521 +++++++++++++++++++++++++--------------------------- R/merge_TATC.r | 123 ++++++++---- man/merge_TATB.Rd | 106 +++++----- man/merge_TATBTC.Rd | 57 +++-- man/merge_TATC.Rd | 46 +++- 9 files changed, 850 insertions(+), 661 deletions(-)
Title: A Stable Isotope Mixing Model
Description: Fits Stable Isotope Mixing Models (SIMMs) and is meant as a longer term replacement to the previous widely-used package SIAR. SIMMs are used to infer dietary proportions of organisms consuming various food sources from observations on the stable isotope values taken from the organisms' tissue samples. However SIMMs can also be used in other scenarios, such as in sediment mixing or the composition of fatty acids. The main functions are simmr_load() and simmr_mcmc(). The two vignettes contain a quick start and a full listing of all the features. The methods used are detailed in the papers Parnell et al 2010 <doi:10.1371/journal.pone.0009672>, and Parnell et al 2013 <doi:10.1002/env.2221>.
Author: Emma Govan [aut],
Andrew Parnell [cre, aut]
Maintainer: Andrew Parnell <andrew.parnell1@ucd.ie>
Diff between simmr versions 0.5.2 dated 2026-05-11 and 0.5.3 dated 2026-07-23
DESCRIPTION | 8 +- MD5 | 16 ++-- NEWS.md | 4 + R/posterior_predictive.simmr_output.R | 2 inst/doc/advanced_plotting.html | 12 +-- inst/doc/quick_start.html | 56 +++++++-------- inst/doc/simmr.html | 106 ++++++++++++++--------------- tests/testthat/Rplots.pdf |binary tests/testthat/test_simmr_misc_functions.R | 69 ++++++++++++++++++ 9 files changed, 173 insertions(+), 100 deletions(-)
Title: Online Changepoint Detection in Univariate and Multivariate Data
Streams
Description: Provides high-performance online changepoint detection in univariate and multivariate data
streams. Implements efficient 'C++' backends for the 'focus', 'md-focus' and 'np-focus'
algorithms, with an 'R' interface for real-time monitoring and offline analysis.
The package bundles code from 'Qhull' <http://www.qhull.org/>, by C. B. Barber and
The Geometry Center. See 'inst/COPYRIGHTS' for details.
Author: Gaetano Romano [aut, cre, trl],
Kes Ward [aut],
Yuntang Fan [aut],
Guillem Rigaill [aut],
Vincent Runge [aut],
Idris A. Eckley [aut],
Paul Fearnhead [aut],
C. B. Barber [ctb, cph] ,
The Geometry Center [cph]
Maintainer: Gaetano Romano <g.romano@lancaster.ac.uk>
Diff between focus versions 0.1.8 dated 2026-06-25 and 0.1.9 dated 2026-07-23
focus-0.1.8/focus/man/detector_pieces_len.Rd |only focus-0.1.9/focus/DESCRIPTION | 16 focus-0.1.9/focus/MD5 | 21 focus-0.1.9/focus/R/RcppExports.R | 4 focus-0.1.9/focus/README.md | 58 focus-0.1.9/focus/inst/CITATION |only focus-0.1.9/focus/man/detector_cands_len.Rd |only focus-0.1.9/focus/man/focus-package.Rd | 2 focus-0.1.9/focus/src/ARpInfo.h | 6 focus-0.1.9/focus/src/RcppExports.cpp | 10 focus-0.1.9/focus/src/focus_ARp.cpp | 1721 +++++++----------------- focus-0.1.9/focus/src/focus_rcpp_module.cpp | 6 focus-0.1.9/focus/tests/testthat/test-generic.R | 14 13 files changed, 605 insertions(+), 1253 deletions(-)
Title: Time Series Analysis Toolkit Based on Symbolic Aggregate
Discretization, i.e. SAX
Description: Implements time series z-normalization, SAX, HOT-SAX, VSM, SAX-VSM, RePair, and RRA
algorithms for time series discord (anomaly) discovery, grammatical compression, and
interpretable time series classification.
Author: Pavel Senin [aut, cre]
Maintainer: Pavel Senin <seninp@gmail.com>
Diff between jmotif versions 1.3.1 dated 2026-07-08 and 1.3.2 dated 2026-07-23
DESCRIPTION | 12 ++++---- MD5 | 49 +++++++++++++++++------------------ NEWS.md |only R/RcppExports.R | 4 +- R/jmotif.R | 33 +++++++++++++---------- README.md | 40 ++++++++++++++++++++-------- man/cosine_dist.Rd | 8 ++--- man/cosine_sim.Rd | 12 ++++++++ man/find_discords_brute_force.Rd | 14 +++++++--- man/find_discords_hotsax.Rd | 18 +++++++++--- man/find_discords_rra.Rd | 12 ++++---- man/is_equal_mindist.Rd | 4 +- man/manyseries_to_wordbag.Rd | 5 +++ man/sax_via_window.Rd | 4 ++ man/series_to_wordbag.Rd | 5 +++ src/paa.cpp | 4 ++ src/rra.cpp | 4 ++ src/sax-vsm.cpp | 27 ++++++++++++++++++- src/sax.cpp | 3 ++ src/string.cpp | 7 +++-- tests/testthat/test_PAA.R | 1 tests/testthat/test_cosine_sim.R | 12 ++++++++ tests/testthat/test_cosines.R | 16 +++++++++++ tests/testthat/test_discord_rra.R | 22 +++++++++++++++ tests/testthat/test_min_dist_equal.R | 2 + tests/testthat/test_str.R | 2 + 26 files changed, 238 insertions(+), 82 deletions(-)
Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut],
Timo Bechger [aut],
Jesse Koops [aut, cre],
Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>
Diff between dexter versions 1.7.2 dated 2026-01-21 and 1.8.0 dated 2026-07-23
DESCRIPTION | 11 MD5 | 117 +++--- NAMESPACE | 5 NEWS.md | 12 R/RcppExports.R | 24 - R/ability.R | 30 - R/database.R | 11 R/dexter.R | 265 +++++--------- R/dif.R | 9 R/equating.R | 67 +-- R/fit_enorm.R | 74 ++-- R/individual_differences.R | 4 R/interaction_model.R | 13 R/latent_cor.R | 59 +-- R/misc.R | 62 ++- R/misc_anon.R | 370 ++++++++++++-------- R/oplike.R | 13 R/param.R | 161 +++++++- R/plausible_scores.R | 162 +------- R/plausible_values.R | 93 ++--- R/predicates.R | 3 R/resp_data.R | 3 R/suf_stats.R | 4 R/theta_functions.R | 17 build/vignette.rds |binary inst/doc/DIF_vignette.html | 10 inst/doc/Equating.Rmd | 2 inst/doc/Equating.html | 18 inst/doc/Plausible_Values.Rmd | 4 inst/doc/Plausible_Values.html | 16 inst/doc/Test_Individual_differences.html | 14 inst/doc/dexter.html | 123 +++--- inst/doc/profile-plots.html | 20 - inst/extdata/dexter_sqlite.sql | 2 inst/extdata/dexter_standard.sql | 2 man/add_item_properties.Rd | 2 man/add_person_properties.Rd | 2 man/coef.enorm.Rd | 21 - man/dexter-package.Rd | 12 man/latent_cor.Rd | 3 man/plausible_scores.Rd | 4 man/plausible_values.Rd | 11 man/start_new_project.Rd | 5 src/RcppExports.cpp | 119 ++++-- src/ability.cpp | 33 - src/enrmBayes.cpp | 2 src/progress.cpp |only src/progress.h | 79 ---- src/pv.cpp | 545 +++++++++++++++++++++--------- src/shared.cpp | 7 src/shared.h | 1 src/simulation.cpp | 180 +++++++-- tests/testthat/setup.R | 2 tests/testthat/test_ability.R | 11 tests/testthat/test_data_selection.R | 3 tests/testthat/test_p2p.R | 2 tests/testthat/test_plausible_scores.R | 9 tests/testthat/test_plausible_values.R | 29 + vignettes/Equating.Rmd | 2 vignettes/Plausible_Values.Rmd | 4 60 files changed, 1643 insertions(+), 1245 deletions(-)
Title: Easy Access for South Korea Census Data and Boundaries
Description: Census and administrative data in South Korea are a basic source of
quantitative and mixed-methods research for social and urban scientists.
This package provides a 'sf' (Pebesma et al., 2024 <doi:10.32614/CRAN.package.sf>)
based standardized workflow based on direct open API access to the major census and
administrative data sources and pre-generated files in South Korea.
Author: Insang Song [aut, cre] ,
Sohyun Park [aut, ctb] ,
Hyesop Shin [aut, ctb]
Maintainer: Insang Song <geoissong@snu.ac.kr>
Diff between tidycensuskr versions 0.2.8 dated 2026-05-04 and 0.3.0 dated 2026-07-23
DESCRIPTION | 8 LICENSE | 2 MD5 | 60 ++-- NEWS.md | 8 R/anycensus.R | 452 +++++++++++++++++++++++++++++----- R/datasets.R | 19 - R/load_districts.R | 12 R/utility.R | 2 README.md | 29 +- build/vignette.rds |binary data/censuskor.rda |binary inst/CITATION |only inst/doc/v01_intro.R | 45 +++ inst/doc/v01_intro.Rmd | 90 ++++++ inst/doc/v01_intro.html | 185 +++++++++++-- inst/doc/v02_regional_analysis.R | 13 inst/doc/v02_regional_analysis.Rmd | 13 inst/doc/v02_regional_analysis.html | 143 +++++----- inst/doc/v03_gallery.html | 29 +- inst/doc/v04_data_cleaning_kosis.html | 6 inst/doc/v05_contributors_guide.html | 18 - inst/extdata/kogl_type1.jpg |only man/adm2_sf_2020.Rd | 2 man/anycensus.Rd | 93 ++++++ man/censuskor.Rd | 13 man/figures/README-final_map-1.png |binary man/figures/README-mapmaking-1.png |binary man/figures/README-seoul_map-1.png |binary man/kr_grid_adm2_sgis_2020.Rd | 4 man/load_districts.Rd | 4 vignettes/v01_intro.Rmd | 90 ++++++ vignettes/v02_regional_analysis.Rmd | 13 32 files changed, 1055 insertions(+), 298 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-07-09 0.0.1
Title: Explore Fitted Linear and Generalised Linear Models with 'shiny'
Description: Provides a 'shiny' application that helps learners connect
regression tables to fitted generalised linear models. Users
construct models via drag-and-drop controls, obtain fitted
equations and plain-language explanations generated by a large
language model, and can view plots of the fitted model in
settings with a single continuous covariate.
Author: James Curran [aut, cre]
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between WMFM versions 1.0.4 dated 2026-07-04 and 1.1.4 dated 2026-07-23
DESCRIPTION | 33 MD5 | 169 ++- NAMESPACE | 6 NEWS.md | 380 ++++++ R/analysis-recipe-build.R |only R/analysis-recipe-download.R |only R/analysis-recipe-dynamic.R |only R/analysis-recipe-render-analysis.R |only R/analysis-recipe-render-core.R |only R/api-runModel.R | 79 + R/app-comparableObservation-ui.R |only R/app-observationResidual-ui.R |only R/app-plot-uiHelpers.R | 19 R/app-server-analysis-download.R |only R/app-server-explanation.R | 9 R/app-server-fit-model.R | 64 + R/app-server-plot.R | 1 R/app-server-reactive-state.R | 1 R/app-server-state-helpers.R | 1 R/app-server.R | 5 R/app-ui.R | 15 R/class-analysisRecipe.R |only R/evaluation-suite.R |only R/examples-run.R | 35 R/model-ci-data.R | 62 + R/model-confidence-intervals.R |only R/model-factor-coercion.R |only R/model-lm-explanation.R | 19 R/model-question-classifier.R | 97 + R/model-question-comparable-observations.R |only R/model-question-conditional-quantile.R |only R/model-question-followup-answer.R | 367 ++++++ R/model-question-observation-residual.R |only R/model-question-prediction-lm.R | 543 +++++++++- R/model-question-research-prediction.R | 18 R/model-question-route.R |only R/plot-model.R | 12 R/plot-utils.R | 34 R/prompt-explain.R | 101 + R/prompt-followup-controls.R | 39 inst/extdata/examples/AlternativeQuestionGuidance |only inst/extdata/examples/AnalysisPurpose |only inst/extdata/examples/AnalysisUsefulness |only inst/extdata/examples/CausalProof |only inst/extdata/examples/CoursePrediction1 |only inst/extdata/examples/CoursePrediction2 |only inst/extdata/examples/CoursePrediction3 |only inst/extdata/examples/DiamondsII/DiamondsII.spec.yml | 1 inst/extdata/examples/DiamondsIII/DiamondsIII.spec.yml | 1 inst/extdata/examples/DiamondsIV/DiamondsIV.spec.yml | 1 inst/extdata/examples/DiamondsPrediction1 |only inst/extdata/examples/DiamondsPrediction2 |only inst/extdata/examples/DiamondsPrediction3 |only inst/extdata/examples/DifferentModel |only inst/extdata/examples/ModelCapability |only inst/extdata/examples/ModelQuality |only inst/extdata/examples/OystersPrediction1 |only inst/extdata/examples/OystersPrediction2 |only inst/extdata/examples/OystersPrediction3 |only inst/extdata/examples/PassChanceUndefined |only inst/extdata/examples/PredictionPurpose |only inst/extdata/examples/QuakesPrediction1 |only inst/extdata/examples/QuakesPrediction2 |only inst/extdata/examples/QuakesPrediction3 |only inst/extdata/examples/QuestionNotUnderstood |only inst/extdata/examples/ResultMeaning |only inst/extdata/examples/UncertainQuestion |only inst/extdata/examples/developer/observation-questions |only inst/extdata/examples/example-metadata.yml | 108 + man/analysisRecipeDownloadExtension.Rd |only man/buildAnalysisRecipeFromFit.Rd |only man/drawModelPlot.Rd | 4 man/encodeAnalysisRecipeString.Rd |only man/isAnalysisRecipe.Rd |only man/listWMFMEvaluationExamples.Rd |only man/makeFactorOnlyPlot.Rd | 10 man/modelConfidenceIntervals.Rd |only man/newAnalysisRecipe.Rd |only man/plotCiControlsUi.Rd | 6 man/registerAnalysisDownloadObserver.Rd |only man/renderAnalysisRecipeAnalysisQuarto.Rd |only man/renderAnalysisRecipeAnovaChunk.Rd |only man/renderAnalysisRecipeCodeChunk.Rd |only man/renderAnalysisRecipeConfidenceIntervalChunk.Rd |only man/renderAnalysisRecipeCoreQuarto.Rd |only man/renderAnalysisRecipeDataChunk.Rd |only man/renderAnalysisRecipeDiagnosticChunk.Rd |only man/renderAnalysisRecipeModelChunk.Rd |only man/renderAnalysisRecipeModelPlotChunk.Rd |only man/renderAnalysisRecipePackageChunk.Rd |only man/renderAnalysisRecipePreparationChunk.Rd |only man/renderAnalysisRecipePreparationSection.Rd |only man/renderAnalysisRecipeSummaryChunk.Rd |only man/restoreTransformedPredictorSources.Rd |only man/runModel.Rd | 4 man/runWMFMEvaluationSuite.Rd |only man/updateAnalysisRecipeSection.Rd |only man/validateAnalysisRecipe.Rd |only man/writeAnalysisRecipeDownload.Rd |only man/writeAnalysisRecipeQuarto.Rd |only tests/testthat/test-analysis-recipe-analysis-rendering.R |only tests/testthat/test-analysis-recipe-core-rendering.R |only tests/testthat/test-analysis-recipe-download.R |only tests/testthat/test-analysis-recipe-dynamic-rendering.R |only tests/testthat/test-analysis-recipe.R |only tests/testthat/test-app-comparableObservation-ui.R |only tests/testthat/test-app-observationResidual-ui.R |only tests/testthat/test-course-followup-example.R | 4 tests/testthat/test-evaluation-suite.R |only tests/testthat/test-explanation-prompt-diagnostics.R | 4 tests/testthat/test-factor-only-plot-style.R |only tests/testthat/test-followup-prompt-controls.R | 43 tests/testthat/test-intelligent-question-handling.R |only tests/testthat/test-log-log-models.R | 9 tests/testthat/test-model-factor-coercion.R |only tests/testthat/test-model-question-classifier.R | 14 tests/testthat/test-model-question-comparable-observations.R |only tests/testthat/test-model-question-conditional-quantile.R |only tests/testthat/test-model-question-observation-residual.R |only tests/testthat/test-model-question-prediction-glm.R | 27 tests/testthat/test-model-question-prediction-lm.R | 40 tests/testthat/test-model-question-route.R |only tests/testthat/test-natural-prediction-questions.R |only tests/testthat/test-observation-question-development-examples.R |only tests/testthat/test-prediction-example-availability.R |only tests/testthat/test-transformed-prediction-inputs.R |only tests/testthat/test-transformed-predictor-prediction.R |only 127 files changed, 2177 insertions(+), 208 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement
complex random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
an efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [...truncated...]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.9.22 dated 2026-07-21 and 1.9.23 dated 2026-07-23
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/ichol.cpp | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Simple Features for R
Description: Support for simple feature access, a standardized way to
encode and analyze spatial vector data. Binds to 'GDAL'
<doi:10.5281/zenodo.5884351> for reading and writing data, to 'GEOS'
<doi:10.5281/zenodo.11396894> for geometrical operations,
and to 'PROJ' <doi:10.5281/zenodo.5884394> for projection
conversions and datum transformations. Uses by default the 's2'
package for geometry operations on geodetic (long/lat degree)
coordinates.
Author: Edzer Pebesma [aut, cre] ,
Roger Bivand [ctb] ,
Etienne Racine [ctb],
Michael Sumner [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb] ,
Kirill Mueller [ctb],
Thomas Lin Pedersen [ctb],
Dan Baston [c [...truncated...]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 1.1-1 dated 2026-05-06 and 1.1-2 dated 2026-07-23
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/sf1.html | 6 +++--- inst/doc/sf2.html | 6 +++--- inst/doc/sf4.html | 2 +- inst/doc/sf7.html | 10 +++++----- man/st_cast.Rd | 4 ++-- tests/stars.R | 10 ++++++---- tests/stars.Rout.save | 20 ++++++++++---------- 12 files changed, 48 insertions(+), 42 deletions(-)
Title: Generate Sample Censoring
Description: Provides functions to generate censored samples of type I, II and III, from any random sample generator. It also supplies the option to create left and right censorship. Along with this, the generation of samples with interval censoring is in the testing phase, with two options of fixed length intervals and random lengths. Additional functions generate complex inspection, delayed-entry, hybrid, progressive, covariate-dependent, frailty-dependent, and competing-risk observation structures while retaining a consistent and verifiable data object.
Author: Daniel Saavedra [aut, cre, cph] ,
Pedro L Ramos [aut]
Maintainer: Daniel Saavedra <dlsaavedra@uc.cl>
Diff between rcens versions 0.1.1 dated 2024-03-19 and 0.2.2 dated 2026-07-23
DESCRIPTION | 17 ++-- MD5 | 76 ++++++++++++++++++--- NAMESPACE | 29 +++++++- NEWS.md |only R/rcensI.R | 2 R/rcenscomp-calibration.R |only R/rcenscomp-class.R |only R/rcenscomp-dependent.R |only R/rcenscomp-hybrid.R |only R/rcenscomp-inspection.R |only R/rcenscomp-progressive.R |only R/rcenscomp-utils.R |only R/rcenscomp-weibull.R |only R/rcenscomp.R |only R/rcurefT3.R | 2 README.md | 38 ++++++++++ build |only inst |only man/examples/rcensIfix.R | 2 man/rcens-package.Rd |only man/rcensI.Rd | 2 man/rcensIfix.Rd | 2 man/rcensT3.Rd | 2 man/rcenscomp-methods.Rd |only man/rcenscomp.Rd |only man/rcenscomp_adaptive_progressive_type2.Rd |only man/rcenscomp_calibrate_progressive_hybrid_time.Rd |only man/rcenscomp_calibrate_time.Rd |only man/rcenscomp_competing_risks.Rd |only man/rcenscomp_covariate_censoring.Rd |only man/rcenscomp_current_status.Rd |only man/rcenscomp_delayed_entry.Rd |only man/rcenscomp_generalized_hybrid.Rd |only man/rcenscomp_hybrid_type1.Rd |only man/rcenscomp_hybrid_type2.Rd |only man/rcenscomp_informative_frailty.Rd |only man/rcenscomp_interval.Rd |only man/rcenscomp_progressive_hybrid.Rd |only man/rcenscomp_progressive_type1.Rd |only man/rcenscomp_progressive_type2.Rd |only man/rcenscomp_rweibull_censor_ph.Rd |only man/rcenscomp_rweibull_ph.Rd |only man/rcenscomp_rweibull_ph_frailty.Rd |only man/rcenscomp_rweibull_rate.Rd |only man/rcurefT3.Rd | 2 tests |only vignettes |only 47 files changed, 149 insertions(+), 25 deletions(-)
Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre] ,
Andreas Rappold [ctb]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between Deriv versions 4.2.0 dated 2025-06-20 and 4.3.0 dated 2026-07-23
Deriv-4.2.0/Deriv/NEWS |only Deriv-4.3.0/Deriv/DESCRIPTION | 14 ++++++++------ Deriv-4.3.0/Deriv/MD5 | 23 ++++++++++++++--------- Deriv-4.3.0/Deriv/NAMESPACE | 3 +++ Deriv-4.3.0/Deriv/NEWS.md |only Deriv-4.3.0/Deriv/R/Deriv.R | 1 + Deriv-4.3.0/Deriv/R/RcppExports.R |only Deriv-4.3.0/Deriv/R/Simplify.R | 6 ++---- Deriv-4.3.0/Deriv/inst/CITATION | 2 +- Deriv-4.3.0/Deriv/man/Deriv-package.Rd | 2 +- Deriv-4.3.0/Deriv/man/Deriv.Rd | 3 +++ Deriv-4.3.0/Deriv/man/Deriv_cpp.Rd |only Deriv-4.3.0/Deriv/man/Simplify_cpp.Rd |only Deriv-4.3.0/Deriv/src |only Deriv-4.3.0/Deriv/tests/testthat/test_Simplify.R | 10 ++++++++++ 15 files changed, 43 insertions(+), 21 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-17 0.2.6.2
2019-06-18 0.2.4
2018-05-18 0.2.2
2018-04-16 0.2.0
2017-07-31 0.1.9
2017-07-17 0.1.8
2016-12-01 0.1.5
2015-10-07 0.1.4
2015-06-23 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-22 0.1.1
2017-11-13 0.1.0