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(-)
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(-)
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(-)
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 2.0.2 dated 2026-07-15 and 2.0.4 dated 2026-07-22
DESCRIPTION | 9 - MD5 | 26 ++-- NEWS.md | 77 ++++++++++++ R/tsqca_config_chart.R | 79 ++++++------- R/tsqca_core.R | 126 +++++++++++---------- R/tsqca_helpers.R | 89 +++++++------- R/tsqca_report.R | 23 +++ README.md | 6 - inst/doc/ThSQCA_Reproducible_EN.html | 2 inst/doc/ThSQCA_Tutorial_EN.html | 2 tests/testthat/helper-fixtures.R |only tests/testthat/test-edge-inputs.R |only tests/testthat/test-endtoend-cyclic.R |only tests/testthat/test-extractor-consistency-stress.R |only tests/testthat/test-generate-report-e2e.R |only tests/testthat/test-intermediate-covS.R |only tests/testthat/test-multisolution-covS.R |only tests/testthat/test-report-chart-extractors.R |only 18 files changed, 282 insertions(+), 157 deletions(-)
Title: Nonparametric Item Response Theory
Description: Fits nonparametric item and option characteristic curves using kernel smoothing. It allows for optimal selection of the smoothing bandwidth using cross-validation and a variety of exploratory plotting tools. The kernel smoothing is based on methods described in Silverman, B.W. (1986). Density Estimation for Statistics and Data Analysis. Chapman & Hall, London.
Author: Angelo Mazza [aut],
Antonio Punzo [aut],
Brian McGuire [aut, cre]
Maintainer: Brian McGuire <mcguirebc@gmail.com>
Diff between KernSmoothIRT versions 6.4 dated 2020-02-17 and 6.6 dated 2026-07-22
KernSmoothIRT-6.4/KernSmoothIRT/src/Makevars |only KernSmoothIRT-6.4/KernSmoothIRT/src/Makevars.win |only KernSmoothIRT-6.6/KernSmoothIRT/DESCRIPTION | 20 +++++++---- KernSmoothIRT-6.6/KernSmoothIRT/MD5 | 17 ++++----- KernSmoothIRT-6.6/KernSmoothIRT/NAMESPACE | 2 - KernSmoothIRT-6.6/KernSmoothIRT/inst/CITATION | 16 ++++---- KernSmoothIRT-6.6/KernSmoothIRT/man/KernSmoothIRT-package.Rd | 4 +- KernSmoothIRT-6.6/KernSmoothIRT/man/ksIRT.Rd | 2 - KernSmoothIRT-6.6/KernSmoothIRT/man/plot.ksIRT.Rd | 2 - KernSmoothIRT-6.6/KernSmoothIRT/man/subjOCCDIF.Rd | 2 - KernSmoothIRT-6.6/KernSmoothIRT/src/init.c |only 11 files changed, 36 insertions(+), 29 deletions(-)
Title: Process Command Line Arguments
Description: Process command line arguments, allowing scripts to
behave like functions, with well-defined inputs and outputs.
Helps make data analysis workflows more modular,
and therefore more transparent, flexible, and reliable.
Author: John Bryant [aut, cre],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between command versions 0.1.3 dated 2025-11-22 and 0.2.0 dated 2026-07-22
DESCRIPTION | 21 ++---- MD5 | 53 ++++++++------- NAMESPACE | 1 NEWS.md | 35 ++++++++++ R/check-functions.R | 14 ++-- R/cmd_assign.R | 3 R/command-package.R | 13 ++- R/extract_make.R | 5 - R/extract_shell.R | 5 - R/helper-functions.R | 107 ++++++++++++++++++++++++++++--- R/makefile.R | 9 +- R/shell_script.R | 9 +- R/use_renv.R |only man/cmd_assign.Rd | 3 man/command-package.Rd | 17 +++-- man/extract_make.Rd | 3 man/extract_shell.Rd | 3 man/makefile.Rd | 5 - man/shell_script.Rd | 5 - man/use_renv.Rd |only tests/testthat/helper.R | 26 +++++++ tests/testthat/test-check-functions.R | 12 +-- tests/testthat/test-cmd_assign.R | 61 ++++++++++++++++++ tests/testthat/test-extract_make.R | 11 +-- tests/testthat/test-extract_shell.R | 12 +-- tests/testthat/test-helper-functions.R | 111 +++++++++++++++++++++++++++++++++ tests/testthat/test-makefile.R | 17 ++--- tests/testthat/test-shell_script.R | 13 --- tests/testthat/test-use_renv.R |only 29 files changed, 447 insertions(+), 127 deletions(-)
Title: Lossless CDISC-Native Input and Output for Clinical Datasets
Description: Reads and writes clinical-trial datasets losslessly across
'SAS' XPORT (XPT), Clinical Data Interchange Standards Consortium
(CDISC) Dataset-JSON, and 'Apache Parquet', applying a specification to
produce submission-ready Study Data Tabulation Model (SDTM) and
Analysis Data Model (ADaM) datasets. A single canonical metadata model
carries labels, CDISC data types, lengths, 'SAS' display formats,
controlled-terminology references, and sort keys identically across
every format, so conversion between any two formats is lossless by
construction. Pure 'R' and lightweight, with no external 'SAS' or
'Java' runtime. Implements the published format specifications for
CDISC Dataset-JSON
(<https://cdisc-org.github.io/DataExchange-DatasetJson/doc/dataset-json1-1.html>)
and 'SAS' XPORT
(<https://www.loc.gov/preservation/digital/formats/fdd/fdd000466.shtml>).
Author: Vignesh Thanikachalam [aut, cre, cph]
Maintainer: Vignesh Thanikachalam <about.vignesh@gmail.com>
Diff between artoo versions 0.1.2 dated 2026-07-01 and 0.1.3 dated 2026-07-22
DESCRIPTION | 6 MD5 | 46 +++--- NEWS.md | 34 ++++ R/check_spec.R | 25 +++ R/checks.R | 7 R/codec_json.R | 7 R/codec_ndjson.R | 6 R/codec_parquet.R | 6 R/codec_xpt.R | 45 +++++ R/encoding.R | 279 +++++++++++++++++++++++++++++++++---- inst/WORDLIST | 111 ++++++++------ inst/spec_rules.json | 11 + man/artoo_checks.Rd | 6 man/write_json.Rd | 7 man/write_ndjson.Rd | 6 man/write_parquet.Rd | 6 man/write_xpt.Rd | 28 ++- tests/testthat/_snaps/checks.md | 2 tests/testthat/_snaps/codec_xpt.md | 10 + tests/testthat/_snaps/encoding.md | 20 ++ tests/testthat/test-check_spec.R | 43 +++++ tests/testthat/test-codec_xpt.R | 42 +++++ tests/testthat/test-encoding.R | 200 ++++++++++++++++++++++++++ tests/testthat/test-members.R | 4 24 files changed, 831 insertions(+), 126 deletions(-)
Title: Reference Based Multiple Imputation
Description: Implements standard and reference based multiple imputation methods for continuous
longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular,
this package supports deterministic conditional mean imputation and jackknifing as described
in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described
in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum
likelihood imputation as described in von Hippel and Bartlett (2021) <doi:10.1214/20-STS793>.
Author: Lukas A. Widmer [aut, cre] ,
Craig Gower-Page [aut],
Isaac Gravestock [aut] ,
Alessandro Noci [aut],
Marcel Wolbers [aut] ,
Daniel Sabanes Bove [aut] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Lukas A. Widmer <lukas_andreas.widmer@novartis.com>
Diff between rbmi versions 1.6.0 dated 2026-01-23 and 1.6.1 dated 2026-07-22
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Title: Moments and Distributions of Ratios of Quadratic Forms Using
Recursion
Description: Evaluates moments of ratios (and products) of quadratic forms
in normal variables, specifically using recursive algorithms developed by
Bao and Kan (2013) <doi:10.1016/j.jmva.2013.03.002> and Hillier et al.
(2014) <doi:10.1017/S0266466613000364>. Also provides distribution,
quantile, and probability density functions of simple ratios of quadratic
forms in normal variables with several algorithms. Originally developed as
a supplement to Watanabe (2023) <doi:10.1007/s00285-023-01930-8> for
evaluating average evolvability measures in evolutionary quantitative
genetics, but can be used for a broader class of statistics. Generating
functions for these moments are also closely related to the top-order zonal
and invariant polynomials of matrix arguments.
Author: Junya Watanabe [aut, cre, cph] ,
Patrick Alken [cph] ,
Brian Gough [cph] ,
Pavel Holoborodko [cph] ,
Gerard Jungman [cph] ,
Reid Priedhorsky [cph] ,
Free Software Foundation, Inc. [cph]
Maintainer: Junya Watanabe <Junya.Watanabe@vetmeduni.ac.at>
Diff between qfratio versions 1.1.1 dated 2024-02-08 and 1.1.2 dated 2026-07-22
DESCRIPTION | 19 MD5 | 240 ++++----- NAMESPACE | 1 NEWS.md | 8 R/dist_funs.R | 836 +++++++++++++++++++------------ R/dk_funs.R | 248 ++++----- R/hgs_funs.R | 16 R/qfratio-package.R | 8 R/ratio_fun.R | 421 ++++++--------- R/rqf_funs.R | 116 ++-- R/utils.R | 82 ++- README.md | 22 build/partial.rdb |binary build/vignette.rds |binary configure | 692 ++++++++++++++------------ configure.ac | 27 - inst/doc/qfratio.R | 12 inst/doc/qfratio.Rmd | 58 +- inst/doc/qfratio.html | 423 ++++++++------- inst/doc/qfratio_distr.R | 161 +++--- inst/doc/qfratio_distr.Rmd | 125 +++- inst/doc/qfratio_distr.html | 894 +++++++++++++++++---------------- man/dot-run_check_conv.Rd |only man/pqfr.Rd | 325 ++---------- man/pqfr_int.Rd |only man/qfmrm.Rd | 20 man/qfpm.Rd | 7 man/qfratio-package.Rd | 26 man/qfrm.Rd | 31 - man/rqfr.Rd | 131 +++- src/config.h.in | 11 src/gsl/build.h |only src/gsl/err/error.c | 2 src/gsl/err/gsl_errno.h | 2 src/gsl/err/strerror.c | 2 src/gsl/gsl_inline.h | 2 src/gsl/gsl_machine.h | 2 src/gsl/gsl_math.h | 2 src/gsl/gsl_minmax.h | 2 src/gsl/gsl_mode.h | 2 src/gsl/gsl_nan.h | 2 src/gsl/gsl_pow_int.h | 2 src/gsl/gsl_precision.h | 2 src/gsl/gsl_types.h | 2 src/gsl/integration/err.c | 2 src/gsl/integration/gsl_integration.h | 21 src/gsl/integration/initialise.c | 2 src/gsl/integration/positivity.c | 2 src/gsl/integration/qags.c | 2 src/gsl/integration/qelg.c | 2 src/gsl/integration/qk.c | 2 src/gsl/integration/qk15.c | 2 src/gsl/integration/qpsrt.c | 2 src/gsl/integration/qpsrt2.c | 2 src/gsl/integration/reset.c | 2 src/gsl/integration/set_initial.c | 2 src/gsl/integration/util.c | 2 src/gsl/integration/workspace.c | 2 src/gsl/poly/eval.c |only src/gsl/poly/gsl_poly.h | 2 src/gsl/roots/brent.c | 2 src/gsl/roots/convergence.c | 2 src/gsl/roots/fsolver.c | 2 src/gsl/roots/gsl_roots.h | 2 src/gsl/roots/roots.h | 2 src/gsl/specfunc/bessel.c | 2 src/gsl/specfunc/bessel.h | 2 src/gsl/specfunc/bessel_I0.c | 2 src/gsl/specfunc/bessel_I1.c | 2 src/gsl/specfunc/bessel_In.c | 2 src/gsl/specfunc/bessel_Inu.c | 2 src/gsl/specfunc/bessel_J1.c | 2 src/gsl/specfunc/bessel_K0.c | 2 src/gsl/specfunc/bessel_Knu.c | 2 src/gsl/specfunc/bessel_amp_phase.c | 2 src/gsl/specfunc/bessel_amp_phase.h | 2 src/gsl/specfunc/bessel_temme.c | 2 src/gsl/specfunc/bessel_temme.h | 2 src/gsl/specfunc/beta.c | 2 src/gsl/specfunc/cheb_eval.c | 2 src/gsl/specfunc/chebyshev.h | 2 src/gsl/specfunc/check.h | 2 src/gsl/specfunc/elementary.c | 2 src/gsl/specfunc/error.h | 2 src/gsl/specfunc/eval.h | 2 src/gsl/specfunc/exp.c | 5 src/gsl/specfunc/gamma.c | 4 src/gsl/specfunc/gsl_sf_bessel.h | 2 src/gsl/specfunc/gsl_sf_elementary.h | 2 src/gsl/specfunc/gsl_sf_exp.h | 2 src/gsl/specfunc/gsl_sf_gamma.h | 2 src/gsl/specfunc/gsl_sf_hyperg.h | 2 src/gsl/specfunc/gsl_sf_laguerre.h | 2 src/gsl/specfunc/gsl_sf_log.h | 2 src/gsl/specfunc/gsl_sf_pow_int.h | 2 src/gsl/specfunc/gsl_sf_psi.h | 2 src/gsl/specfunc/gsl_sf_result.h | 2 src/gsl/specfunc/gsl_sf_trig.h | 2 src/gsl/specfunc/gsl_sf_zeta.h | 2 src/gsl/specfunc/hyperg.c | 2 src/gsl/specfunc/hyperg.h | 2 src/gsl/specfunc/hyperg_1F1.c | 18 src/gsl/specfunc/hyperg_2F1.c | 2 src/gsl/specfunc/hyperg_U.c | 25 src/gsl/specfunc/laguerre.c | 2 src/gsl/specfunc/log.c | 2 src/gsl/specfunc/poch.c | 7 src/gsl/specfunc/pow_int.c | 2 src/gsl/specfunc/psi.c | 2 src/gsl/specfunc/result.c | 2 src/gsl/specfunc/trig.c | 2 src/gsl/specfunc/zeta.c | 2 src/gsl/sys/coerce.c | 2 src/gsl/sys/fdiv.c | 2 src/gsl/sys/gsl_sys.h | 2 src/gsl/sys/infnan.c | 2 src/hgs_funs.cpp | 26 src/scripts/SOURCES_GSL.mkf | 1 tests/testthat/test_distr.R | 20 tools/config.guess | 33 - tools/config.sub | 901 +++++++++++++++++++++++++--------- vignettes/qfratio.Rmd | 58 +- vignettes/qfratio_distr.Rmd | 125 +++- 123 files changed, 3683 insertions(+), 2675 deletions(-)
Title: Testing DBI Backends
Description: A helper that tests DBI back ends for conformity to the
interface.
Author: Kirill Mueller [aut, cre] ,
RStudio [cph],
R Consortium [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between DBItest versions 1.8.2 dated 2024-12-07 and 1.8.3 dated 2026-07-22
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| 13 DBItest-1.8.3/DBItest/man/spec_transaction_begin_commit_rollback.Rd | 3 DBItest-1.8.3/DBItest/man/spec_transaction_with_transaction.Rd | 9 DBItest-1.8.3/DBItest/man/test_all.Rd | 6 DBItest-1.8.3/DBItest/man/test_arrow.Rd | 26 - DBItest-1.8.3/DBItest/man/test_compliance.Rd | 26 - DBItest-1.8.3/DBItest/man/test_connection.Rd | 26 - DBItest-1.8.3/DBItest/man/test_data_type.Rd | 2 DBItest-1.8.3/DBItest/man/test_driver.Rd | 26 - DBItest-1.8.3/DBItest/man/test_getting_started.Rd | 26 - DBItest-1.8.3/DBItest/man/test_meta.Rd | 26 - DBItest-1.8.3/DBItest/man/test_result.Rd | 26 - DBItest-1.8.3/DBItest/man/test_sql.Rd | 26 - DBItest-1.8.3/DBItest/man/test_stress.Rd | 26 - DBItest-1.8.3/DBItest/man/test_transaction.Rd | 26 - DBItest-1.8.3/DBItest/man/tweaks.Rd | 14 DBItest-1.8.3/DBItest/tests/testthat/test-tweaks.R | 2 126 files changed, 971 insertions(+), 903 deletions(-)
Title: 'SAS Studio'-Style Interactive Dataset Viewer
Description: An interactive dataset viewer that renders a fast, scrollable
grid with a column-selection panel, per-column property metadata, and
a names-versus-labels header toggle, modelled on the 'SAS Studio' table
viewer. Runs from one codebase in interactive 'Shiny' apps and in static
HTML documents, with a free-text row filter, header sort, and CSV
export, and handles large datasets without row sampling by querying
them in the browser with 'DuckDB-WASM'.
Author: Vignesh Thanikachalam [aut, cre, cph]
Maintainer: Vignesh Thanikachalam <about.vignesh@gmail.com>
Diff between datasetviewer versions 0.1.1 dated 2026-07-09 and 0.2.0 dated 2026-07-22
DESCRIPTION | 6 - MD5 | 12 +- NEWS.md | 10 ++ README.md | 2 inst/doc/datasetviewer.html | 174 ++++++++++++++++++------------------- inst/htmlwidgets/datasetviewer.css | 2 inst/htmlwidgets/datasetviewer.js | 164 +++++++++++++++++----------------- 7 files changed, 191 insertions(+), 179 deletions(-)
Title: Beta Product Confidence Procedure for Right Censored Data
Description: Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data, and for medians [Fay and Brittain <DOI:10.1002/sim.6905>]. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time, and differences in medians [Fay, Proschan, and Brittain <DOI:10.1111/biom.12231>]. Basically, the package gives exact inference methods for one- and two-sample exact inferences for Kaplan-Meier curves (e.g., generalizing Fisher's exact test to allow for right censoring), which are especially important for latter parts of the survival curve, small sample sizes or heavily censored data. Includes mid-p options.
Author: Michael P. Fay [aut, cre],
Allyson Mateja [ctb],
Megan Grieco [ctb]
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between bpcp versions 1.5.4 dated 2026-07-21 and 1.5.5 dated 2026-07-22
DESCRIPTION | 8 +- MD5 | 12 +-- NAMESPACE | 2 NEWS | 3 R/delta2samp.R | 170 +++++++++++++++++++++++++++++++--------------- inst/doc/discreteBPCP.pdf |binary man/bpcp-internal.Rd | 16 ++-- 7 files changed, 139 insertions(+), 72 deletions(-)
Title: Biomonitoring and Bioassessment Calculations
Description: An aid for manipulating data associated with biomonitoring and bioassessment. Calculations include metric calculation, marking of excluded taxa,
subsampling, and multimetric index calculation. Targeted communities are benthic macroinvertebrates, fish, periphyton, and coral. As described in the Revised Rapid Bioassessment Protocols (Barbour et al. 1999) <https://archive.epa.gov/water/archive/web/html/index-14.html>.
Author: Erik W. Leppo [aut, cre] ,
Jen Stamp [ctb],
John van Sickles [ctb],
Ben Block [ctb]
Maintainer: Erik W. Leppo <Erik.Leppo@tetratech.com>
Diff between BioMonTools versions 1.2.4 dated 2025-10-09 and 1.3.1 dated 2026-07-22
DESCRIPTION | 13 MD5 | 116 +-- NAMESPACE | 6 NEWS | 243 ++++++ NEWS.md | 243 ++++++ R/BioMonTools.R |only R/MapTaxaObs.R | 6 R/assign_indexclass.R | 8 R/data.R | 80 ++ R/markExcluded.R | 9 R/metric_stats.R | 61 - R/metric_stats2.R | 20 R/metric_values.R | 1178 ++++++++++++++++++++++++++----- R/qc_taxa.R | 272 ------- R/qc_taxa_match_official.R |only R/qc_taxa_names_proof.R |only R/qc_taxa_phylo.R |only R/qc_taxa_values_character.R |only R/qc_taxa_values_logical.R |only R/qc_taxa_values_numeric.R |only R/rarify.R | 5 R/taxa_translate.R | 2 README.md | 30 build/vignette.rds |binary data/data_algae_names_official.rda |only data/data_algae_names_user.rda |only data/data_benthos_MBSS.rda |binary data/data_benthos_PacNW.rda |binary data/data_diatom_mmi_dev.rda |binary data/data_mmi_dev_small.rda |binary data/data_taxa_names_issues.rda |only inst/doc/vignette_BioMonTools.R | 9 inst/doc/vignette_BioMonTools.Rmd | 11 inst/doc/vignette_BioMonTools.html | 157 ++-- inst/doc/vignette_MapTaxaObs.html | 4 inst/doc/vignette_NewIndex.Rmd | 2 inst/doc/vignette_NewIndex.html | 4 inst/extdata/MetricNames.xlsx |binary inst/extdata/MetricScoring.xlsx |binary man/BioMonTools-package.Rd |only man/MapTaxaObs.Rd | 3 man/data_algae_names_official.Rd |only man/data_algae_names_user.Rd |only man/data_benthos_MBSS.Rd | 2 man/data_benthos_PacNW.Rd | 2 man/data_coral_bcg_metric_qc.Rd | 3 man/data_diatom_mmi_dev.Rd | 13 man/data_mmi_dev_small.Rd | 4 man/data_taxa_names_issues.Rd |only man/markExcluded.Rd | 3 man/metric.stats2.Rd | 8 man/metric.values.Rd | 4 man/metric.values.algae.Rd | 3 man/qc_taxa.Rd | 76 -- man/qc_taxa_match_official.Rd |only man/qc_taxa_names_proof.Rd |only man/qc_taxa_phylo.Rd |only man/qc_taxa_values_character.Rd |only man/qc_taxa_values_logical.Rd |only man/qc_taxa_values_numeric.Rd |only man/rarify.Rd | 2 man/taxa_translate.Rd | 2 tests/testthat/test_markExcluded.R | 5 tests/testthat/test_metric_calc.R | 1107 ++++++++++++++++++++++++++++- tests/testthat/test_metric_names.R | 13 tests/testthat/test_metric_stats.R | 36 tests/testthat/test_metric_values.R |only tests/testthat/test_qc_taxa_values_foo.R |only vignettes/vignette_BioMonTools.Rmd | 11 vignettes/vignette_NewIndex.Rmd | 2 70 files changed, 2984 insertions(+), 794 deletions(-)
Title: Interactive Fixed Effects Estimator for Panel Data
Description: Implements the interactive fixed effects ('IFE') panel estimator of
Bai (2009) <doi:10.3982/ECTA6135> for balanced and unbalanced panels, with
optional additive unit and/or time fixed effects. Provides analytical
standard errors ('homoskedastic', 'HC1' heteroskedasticity-robust,
cluster-robust by unit, and heteroskedasticity- and autocorrelation-
consistent), together with asymptotic incidental-parameter bias correction
for large panels, including a dynamic extension for predetermined
(lagged-dependent) regressors following Moon and Weidner (2017)
<doi:10.1017/S0266466615000328>. The number of factors is chosen by
information criteria (Bai and Ng 2002 <doi:10.1111/1468-0262.00273>) or by
singular value thresholding. Unbalanced panels are handled by an
expectation-maximisation algorithm with nuclear-norm-regularised
initialisation, with estimation, analytical inference, and bias correction
following Su, Wang and Wang (2025) <doi:10.2139/ssrn.5177283> and building [...truncated...]
Author: Binzhi Chen [aut, cre]
Maintainer: Binzhi Chen <Binzhi.Chen9@gmail.com>
Diff between xtife versions 0.1.3 dated 2026-04-21 and 0.1.4 dated 2026-07-22
DESCRIPTION | 33 MD5 | 32 NAMESPACE | 3 R/ife.R | 256 +++-- R/ife_unbalanced.R |only README.md | 213 +++- build/vignette.rds |binary inst/CITATION |only inst/doc/xtife-introduction.R | 218 +++- inst/doc/xtife-introduction.Rmd | 821 +++++++++++++++--- inst/doc/xtife-introduction.html | 1135 ++++++++++++++++++++----- man/dot-bias_correct.Rd | 5 man/dot-bias_correct_mw.Rd | 8 man/ife.Rd | 10 man/ife_select_r_unb.Rd |only man/ife_unbalanced.Rd |only tests/testthat/test-ife-unbalanced-inference.R |only tests/testthat/test-ife-unbalanced.R |only tests/testthat/test-ife.R | 57 + vignettes/xtife-introduction.Rmd | 821 +++++++++++++++--- 20 files changed, 2874 insertions(+), 738 deletions(-)
Title: Classification Models with Copula Functions
Description: Provides several classifiers based on probabilistic models. These classifiers allow to model the dependence structure of continuous features through bivariate copula functions and graphical models, see Salinas-Gutiérrez et al. (2014) <doi:10.1007/s00180-013-0457-y>.
Author: Rogelio Salinas Gutierrez [aut, cre, cph] ,
Angelica Hernandez Quintero [aut, cph] ,
Pedro Abraham Montoya Calzada [aut, cph] ,
Carlos Alberto Lopez Hernandez [aut, cph] ,
Juan Manuel Marquez Romero [aut, cph]
Maintainer: Rogelio Salinas Gutierrez <rogelio.salinas@edu.uaa.mx>
This is a re-admission after prior archival of version 1.1.0 dated 2025-09-19
Diff between MLCOPULA versions 1.1.0 dated 2025-09-19 and 1.1.1 dated 2026-07-22
DESCRIPTION | 10 +++---- MD5 | 10 +++---- NAMESPACE | 2 - R/classification_report.R | 62 +++++++++++++++++++++++++++++++++++++--------- R/norm_test.R | 10 ++++++- build/partial.rdb |binary 6 files changed, 71 insertions(+), 23 deletions(-)
Title: Fuzzy Rule-Based Systems for Classification and Regression Tasks
Description: An implementation of various learning algorithms based on fuzzy rule-based systems (FRBSs) for dealing with classification and regression tasks. Moreover, it allows to construct an FRBS model defined by human experts.
FRBSs are based on the concept of fuzzy sets, proposed by Zadeh in 1965, which aims at
representing the reasoning of human experts in a set of IF-THEN rules, to
handle real-life problems in, e.g., control, prediction and inference, data
mining, bioinformatics data processing, and robotics. FRBSs are also known
as fuzzy inference systems and fuzzy models. During the modeling of an
FRBS, there are two important steps that need to be conducted: structure
identification and parameter estimation. Nowadays, there exists a wide
variety of algorithms to generate fuzzy IF-THEN rules automatically from
numerical data, covering both steps. Approaches that have been used in the
past are, e.g., heuristic procedures, neuro-fuzzy techniques, clustering
methods, genetic algorithms, squar [...truncated...]
Author: Lala Septem Riza [aut],
Christoph Bergmeir [aut, cre],
Francisco Herrera [aut],
Jose Manuel Benitez [aut]
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>
Diff between frbs versions 3.2-0 dated 2019-12-15 and 3.3-0 dated 2026-07-22
DESCRIPTION | 29 ++++++++++++++++++++++------- MD5 | 33 +++++++++++++++++---------------- NAMESPACE | 1 + NEWS.md |only R/FRBS.MainFunction.R | 3 ++- build/vignette.rds |binary inst/CITATION | 16 ++++++++-------- inst/doc/lala2015frbs.ltx | 6 +++--- inst/doc/lala2015frbs.pdf |binary inst/doc/lala2015pmml.R | 1 - inst/doc/lala2015pmml.Rtex | 10 +++++----- inst/doc/lala2015pmml.pdf |binary man/frbs-package.Rd | 4 ++-- man/summary.frbs.Rd | 4 ++-- vignettes/lala2015frbs.bib | 43 +++++++++++++++++++++++++++++++------------ vignettes/lala2015frbs.ltx | 6 +++--- vignettes/lala2015pmml.Rtex | 10 +++++----- vignettes/lala2015pmml.bib | 4 ++-- 18 files changed, 103 insertions(+), 67 deletions(-)
Title: Your Go-to Motif Accountant
Description: Provides the 'C++' header-only library 'barry' for use in R packages.
'barry' is a 'C++' template library for counting sufficient statistics on binary
arrays and building discrete exponential-family models. It provides tools for
sparse arrays, user-defined count statistics, support set constraints,
power set generation, and includes modules for Discrete Exponential Family Models
(DEFMs) and network statistics. By placing these headers in this package, we
offer an efficient distribution system for CRAN as replication of this code in
the sources of other packages is avoided. This package follows the same
approach as the 'BH' package which provides 'Boost' headers for R packages.
Author: George Vega Yon [aut, cre] ,
U.S. Army Medical Research Acquisition Activity [fnd] ,
National Cancer Institute [fnd]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between barry versions 0.2.1 dated 2025-12-01 and 0.2.2 dated 2026-07-22
DESCRIPTION | 17 ++- MD5 | 18 +-- NEWS.md | 14 +++ README.md | 102 +++++++++++++--------- inst/include/barry/barry.hpp | 2 inst/include/barry/freqtable.hpp | 122 ++++++++++++++++++++++----- inst/include/barry/model-meat.hpp | 74 +++++----------- inst/include/barry/models/defm/defm-meat.hpp | 9 + inst/include/barry/typedefs.hpp | 35 ++++++- man/barry-package.Rd | 6 + 10 files changed, 266 insertions(+), 133 deletions(-)
Title: Declarative API for Staged Survey Weights
Description: Builds survey weights from design base weights by chaining
hierarchical adjustments (unknown eligibility, nonresponse and calibration)
through a declarative, pipeable, 'tidymodels'-style API. Calibration follows
Deville and Sarndal (1992) <doi:10.2307/2290268>. Variances are obtained with
a bootstrap that resamples primary sampling units and re-applies the whole
recipe on each replicate, following the rescaling bootstrap of Rao and Wu
(1988) <doi:10.1080/01621459.1988.10478591>, so the replicate weights carry
the variability of every adjustment. The weights also bridge to the 'survey'
and 'srvyr' packages for design-based inference.
Author: Juan Pablo Ferreira [aut, cre]
Maintainer: Juan Pablo Ferreira <juanpablo.ferreira@fcea.edu.uy>
Diff between weightflow versions 0.1.0 dated 2026-06-30 and 0.2.0 dated 2026-07-22
DESCRIPTION | 11 MD5 | 135 +++- NAMESPACE | 5 NEWS.md | 168 ++++- R/adjustments.R | 777 ++++++++++++++++++++++-- R/data.R | 3 R/plots.R | 3 R/prep.R | 102 +++ R/print.R | 6 R/r-indicators.R |only R/report.R | 202 +++++- R/spec.R | 438 +++++++++++-- R/variance.R | 218 ++++++ README.md | 289 ++++++++ build/vignette.rds |binary data/sample_one.rda |binary inst/WORDLIST | 87 ++ inst/doc/advanced-methods.R |only inst/doc/advanced-methods.Rmd |only inst/doc/advanced-methods.html |only inst/doc/calibration-totals.R |only inst/doc/calibration-totals.Rmd |only inst/doc/calibration-totals.html |only inst/doc/calibration.R |only inst/doc/calibration.Rmd |only inst/doc/calibration.html |only inst/doc/model-calibration.R |only inst/doc/model-calibration.Rmd |only inst/doc/model-calibration.html |only inst/doc/nonresponse-propensities.R |only inst/doc/nonresponse-propensities.Rmd |only inst/doc/nonresponse-propensities.html |only inst/doc/preparing-the-sample.R |only inst/doc/preparing-the-sample.Rmd |only inst/doc/preparing-the-sample.html |only inst/doc/quickstart.R |only inst/doc/quickstart.Rmd |only inst/doc/quickstart.html |only inst/doc/validation-against-survey.R |only inst/doc/validation-against-survey.Rmd |only inst/doc/validation-against-survey.html |only inst/doc/variance-estimation.R | 12 inst/doc/variance-estimation.Rmd | 72 +- inst/doc/variance-estimation.html | 188 +++-- inst/doc/weightflow.R |only inst/doc/weightflow.Rmd |only inst/doc/weightflow.html |only man/as_svydesign.Rd | 16 man/collect_replicate_weights.Rd | 2 man/figures |only man/jackknife_estimate.Rd |only man/jackknife_weights.Rd |only man/plot.prepped_weighting_spec.Rd | 3 man/prep.Rd | 15 man/report_weighting.Rd | 9 man/sample_one.Rd | 3 man/step_assert.Rd | 4 man/step_calibrate.Rd | 158 ++++ man/step_drop_ineligible.Rd | 3 man/step_model_calibration.Rd | 76 ++ man/step_nonresponse.Rd | 56 + man/step_rescale.Rd | 3 man/step_round.Rd | 3 man/step_select_within.Rd | 21 man/step_trim.Rd | 3 man/step_trim_weights.Rd | 32 man/step_unknown_eligibility.Rd | 3 man/y_model.Rd | 7 tests/testthat/_snaps |only tests/testthat/test-advanced-methods.R |only tests/testthat/test-alerts.R |only tests/testthat/test-calibrate-by-domain.R |only tests/testthat/test-calibrate-totals.R |only tests/testthat/test-calibrate-vs-survey.R |only tests/testthat/test-coverage-branches.R |only tests/testthat/test-engines.R |only tests/testthat/test-guardrails.R |only tests/testthat/test-invariants.R |only tests/testthat/test-jackknife.R |only tests/testthat/test-model-calibration-cluster.R |only tests/testthat/test-model-calibration-xtotals.R |only tests/testthat/test-r-indicator.R |only tests/testthat/test-report-convergence.R |only tests/testthat/test-report-plots.R |only tests/testthat/test-scale.R |only tests/testthat/test-select-within-nselected.R |only tests/testthat/test-snapshot.R |only tests/testthat/test-survey-validation.R |only vignettes/advanced-methods.Rmd |only vignettes/calibration-totals.Rmd |only vignettes/calibration.Rmd |only vignettes/model-calibration.Rmd |only vignettes/nonresponse-propensities.Rmd |only vignettes/preparing-the-sample.Rmd |only vignettes/quickstart.Rmd |only vignettes/validation-against-survey.Rmd |only vignettes/variance-estimation.Rmd | 72 +- vignettes/weightflow.Rmd |only 98 files changed, 2782 insertions(+), 423 deletions(-)
Title: Seamless AWS Cloud Bursting for Parallel R Workloads
Description: A 'future' backend that enables seamless execution of parallel R
workloads on 'Amazon Web Services' ('AWS', <https://aws.amazon.com>),
including 'EC2' and 'Fargate'. 'staRburst' handles environment
synchronization, data transfer, quota management, and worker orchestration
automatically, allowing users to scale from local execution to 100+ cloud
workers with a single line of code change.
Author: Scott Friedman [aut, cre]
Maintainer: Scott Friedman <help@starburst.ing>
Diff between starburst versions 0.3.8 dated 2026-03-19 and 0.3.9 dated 2026-07-22
DESCRIPTION | 12 MD5 | 269 ++-- NEWS.md | 141 ++ R/aws-clients.R |only R/cost.R |only R/ec2-pool.R | 35 R/errors.R | 2 R/future-starburst.R | 4 R/images.R |only R/network.R |only R/plan-starburst.R | 34 R/s3-io.R |only R/session-api.R | 95 + R/setup.R | 122 +- R/starburst-estimate.R | 22 R/starburst-map.R | 75 - R/task-definition.R |only R/task-registry.R |only R/utils.R | 1650 ----------------------------- README.md | 171 +-- build/vignette.rds |binary inst/doc/detached-sessions.R | 45 inst/doc/detached-sessions.Rmd | 56 inst/doc/detached-sessions.html | 70 - inst/doc/example-api-calls.R | 26 inst/doc/example-api-calls.Rmd | 82 - inst/doc/example-api-calls.html | 140 -- inst/doc/example-bootstrap.R | 6 inst/doc/example-bootstrap.Rmd | 55 inst/doc/example-bootstrap.html | 56 inst/doc/example-feature-engineering.R | 4 inst/doc/example-feature-engineering.Rmd | 50 inst/doc/example-feature-engineering.html | 53 inst/doc/example-geospatial.R | 4 inst/doc/example-geospatial.Rmd | 60 - inst/doc/example-geospatial.html | 98 + inst/doc/example-grid-search.R | 16 inst/doc/example-grid-search.Rmd | 63 - inst/doc/example-grid-search.html | 109 - inst/doc/example-monte-carlo.R | 8 inst/doc/example-monte-carlo.Rmd | 75 - inst/doc/example-monte-carlo.html | 121 -- inst/doc/example-reports.R | 2 inst/doc/example-reports.Rmd | 49 inst/doc/example-reports.html | 86 - inst/doc/example-risk-modeling.R | 17 inst/doc/example-risk-modeling.Rmd | 57 - inst/doc/example-risk-modeling.html | 103 - inst/doc/getting-started.R | 242 +--- inst/doc/getting-started.Rmd | 396 +++--- inst/doc/getting-started.html | 697 ++++++------ inst/doc/performance.R |only inst/doc/performance.Rmd |only inst/doc/performance.html |only inst/doc/troubleshooting.Rmd | 7 inst/doc/troubleshooting.html | 9 inst/doc/workload-shapes.R |only inst/doc/workload-shapes.Rmd |only inst/doc/workload-shapes.html |only inst/templates/Dockerfile.base | 6 man/StarburstFuture.Rd | 2 man/aws-clients.Rd |only man/build_base_image.Rd | 2 man/build_environment_image.Rd | 2 man/build_initial_environment.Rd | 2 man/calculate_task_cost.Rd | 2 man/calculate_total_cost.Rd | 2 man/check_aws_credentials.Rd | 2 man/check_ecr_image_age.Rd | 2 man/check_ecr_image_exists.Rd | 2 man/cleanup_s3_files.Rd | 2 man/compute_env_hash.Rd | 2 man/cost.Rd |only man/create_ecr_lifecycle_policy.Rd | 2 man/create_task.Rd | 2 man/dot-static_ec2_prices.Rd |only man/ensure_base_image.Rd | 2 man/ensure_buildx_builder.Rd |only man/ensure_environment.Rd | 2 man/ensure_log_group.Rd | 2 man/estimate_cost.Rd | 16 man/extract_region_from_key.Rd | 2 man/figures/logo.png |binary man/get_aws_account_id.Rd | 2 man/get_base_image_source.Rd | 2 man/get_base_image_uri.Rd | 2 man/get_ec2_client.Rd | 8 man/get_ec2_instance_price.Rd | 13 man/get_ec2_ondemand_price.Rd |only man/get_ec2_spot_price.Rd |only man/get_ecr_client.Rd | 2 man/get_ecs_client.Rd | 2 man/get_execution_role_arn.Rd | 2 man/get_instance_vcpus.Rd | 2 man/get_or_create_security_group.Rd | 2 man/get_or_create_subnets.Rd | 2 man/get_or_create_task_definition.Rd | 2 man/get_s3_client.Rd | 2 man/get_service_quotas_client.Rd | 2 man/get_starburst_bucket.Rd | 2 man/get_starburst_security_groups.Rd | 2 man/get_starburst_subnets.Rd | 2 man/get_task_arn.Rd | 2 man/get_task_registry.Rd | 2 man/get_task_role_arn.Rd | 2 man/get_vpc_config.Rd | 2 man/images.Rd |only man/list_active_clusters.Rd | 2 man/list_task_arns.Rd | 2 man/network.Rd |only man/poll_for_result.Rd | 2 man/public_base_image_exists.Rd |only man/result_exists.Rd | 2 man/run.StarburstFuture.Rd | 2 man/s3-io.Rd |only man/serialize_and_upload.Rd | 2 man/should_cleanup_s3.Rd |only man/starburst-package.Rd | 5 man/starburst_cluster.Rd | 23 man/starburst_config.Rd | 42 man/starburst_map.Rd | 24 man/starburst_session.Rd | 61 - man/starburst_setup.Rd | 22 man/stop_running_tasks.Rd | 2 man/store_task_arn.Rd | 2 man/task-definition.Rd |only man/task-registry.Rd |only man/utils.Rd | 6 tests/testthat/helper-aws.R | 14 tests/testthat/test-cost.R | 90 + tests/testthat/test-detached-sessions.R | 69 + tests/testthat/test-docker.R | 140 ++ tests/testthat/test-ec2-pool.R |only tests/testthat/test-integration-examples.R | 9 tests/testthat/test-plan.R | 35 tests/testthat/test-security.R | 52 tests/testthat/test-setup.R |only tools |only vignettes/detached-sessions.Rmd | 56 vignettes/example-api-calls.Rmd | 82 - vignettes/example-bootstrap.Rmd | 55 vignettes/example-feature-engineering.Rmd | 50 vignettes/example-geospatial.Rmd | 60 - vignettes/example-grid-search.Rmd | 63 - vignettes/example-monte-carlo.Rmd | 75 - vignettes/example-reports.Rmd | 49 vignettes/example-risk-modeling.Rmd | 57 - vignettes/getting-started.Rmd | 396 +++--- vignettes/performance.Rmd |only vignettes/troubleshooting.Rmd | 7 vignettes/workload-shapes.Rmd |only 151 files changed, 3212 insertions(+), 3955 deletions(-)
Title: Quadratic Inference Function
Description: Developed to perform the estimation and inference for regression
coefficient parameters in longitudinal marginal models using the method of
quadratic inference functions. Like generalized estimating equations, this
method is also a quasi-likelihood inference method. It has been showed that
the method gives consistent estimators of the regression coefficients even if
the correlation structure is misspecified, and it is more efficient than GEE
when the correlation structure is misspecified. Based on Qu, A., Lindsay,
B.G. and Li, B. (2000) <doi:10.1093/biomet/87.4.823>.
Author: Zhichang Jiang [aut],
Peter Song [aut],
Michael Kleinsasser [cre]
Maintainer: Michael Kleinsasser <biostat-cran-manager@umich.edu>
Diff between qif versions 1.5 dated 2019-07-20 and 1.5.1 dated 2026-07-22
DESCRIPTION | 14 MD5 | 22 NAMESPACE | 28 R/data.R | 68 +- R/qif.r | 1564 +++++++++++++++++++++++------------------------ README.md | 218 +++--- man/epil.Rd | 70 +- man/exacerb.Rd | 42 - man/print.qif.Rd | 67 -- man/print.summary.qif.Rd | 71 +- man/qif.Rd | 282 ++++---- man/summary.qif.Rd | 56 - 12 files changed, 1256 insertions(+), 1246 deletions(-)
Title: Viewing Observational Health Data Sciences and Informatics
Results via 'shiny' Modules
Description: Users can build a single 'shiny' app for exploring population characterization, population-level causal effect estimation, and patient-level prediction results generated via the R analyses packages in 'HADES' (see <https://ohdsi.github.io/Hades/>). Learn more about 'OhdsiShinyAppBuilder' at <https://ohdsi.github.io/OhdsiShinyAppBuilder/>.
Author: Jenna Reps [aut, cre],
Nathan Hall [aut],
Josh Ide [aut],
Jamie Gibert [aut]
Maintainer: Jenna Reps <jreps@its.jnj.com>
Diff between OhdsiShinyAppBuilder versions 1.0.0 dated 2024-12-10 and 1.1.0 dated 2026-07-22
DESCRIPTION | 18 +- MD5 | 70 ++++----- R/AddConfig.R | 6 R/CreateConfig.R | 29 ++- R/ViewShiny.R | 21 +- R/createResultDatabaseSettings.R | 3 R/saveLoadConfig.R | 6 R/ui.R | 111 ++++++++++++--- build/vignette.rds |binary inst/doc/shinyAppModules.R | 2 inst/doc/shinyAppModules.Rmd | 2 inst/doc/shinyAppModules.html | 207 ++++++++++++---------------- man/OhdsiShinyAppBuilder.Rd | 1 man/addModuleConfig.Rd | 7 man/createDefaultAboutConfig.Rd | 17 ++ man/createDefaultCharacterizationConfig.Rd | 17 ++ man/createDefaultCohortDiagnosticsConfig.Rd | 17 ++ man/createDefaultCohortGeneratorConfig.Rd | 17 ++ man/createDefaultCohortMethodConfig.Rd | 17 ++ man/createDefaultDatasourcesConfig.Rd | 17 ++ man/createDefaultEstimationConfig.Rd | 17 ++ man/createDefaultEvidenceSynthesisConfig.Rd | 17 ++ man/createDefaultHomeConfig.Rd | 17 ++ man/createDefaultPhevaluatorConfig.Rd | 17 ++ man/createDefaultPredictionConfig.Rd | 17 ++ man/createDefaultReportConfig.Rd | 17 ++ man/createDefaultResultDatabaseSettings.Rd | 1 man/createDefaultSccsConfig.Rd | 17 ++ man/createModuleConfig.Rd | 17 ++ man/createShinyApp.Rd | 8 + man/initializeModuleConfig.Rd | 7 man/loadConfig.Rd | 7 man/saveConfig.Rd | 7 man/viewShiny.Rd | 10 + tests/testthat/test-addConfig.R | 8 - vignettes/shinyAppModules.Rmd | 2 36 files changed, 557 insertions(+), 214 deletions(-)
More information about OhdsiShinyAppBuilder at CRAN
Permanent link
Title: 'Rcpp' Integration for the 'mlpack' Library
Description: A fast, flexible machine learning library, written in C++, that
aims to provide fast, extensible implementations of cutting-edge
machine learning algorithms. See also Curtin et al. (2023)
<doi:10.21105/joss.05026>.
Author: Yashwant Singh Parihar [aut, ctb, cph],
Ryan Curtin [aut, ctb, cph, cre],
Dirk Eddelbuettel [aut, ctb, cph],
James Balamuta [aut, ctb, cph],
Bill March [ctb, cph],
Dongryeol Lee [ctb, cph],
Nishant Mehta [ctb, cph],
Parikshit Ram [ctb, cph],
James Cl [...truncated...]
Maintainer: Ryan Curtin <ryan@ratml.org>
Diff between mlpack versions 4.8.0 dated 2026-07-16 and 4.8.0-1 dated 2026-07-22
DESCRIPTION | 8 +- MD5 | 32 +++++----- inst/include/mlpack.h | 16 +++++ inst/include/mlpack/config.hpp | 19 +++++ inst/include/mlpack/core/audio/audio.hpp | 4 + inst/include/mlpack/core/data/image_letterbox.hpp | 19 +++++ inst/include/mlpack/core/data/image_resize_crop.hpp | 26 ++++++++ inst/include/mlpack/core/data/imputation_methods/mean_imputation.hpp | 4 - inst/include/mlpack/core/data/imputation_methods/median_imputation.hpp | 4 - inst/include/mlpack/core/data/load_audio.hpp | 19 +++++ inst/include/mlpack/core/data/load_image.hpp | 17 +++++ inst/include/mlpack/core/data/save_audio.hpp | 17 +++++ inst/include/mlpack/core/data/save_image.hpp | 12 +++ inst/include/mlpack/core/stb/stb.hpp | 4 + inst/include/mlpack/methods/ann/models/yolov3/yolov3_impl.hpp | 1 inst/include/mlpack/methods/ann/models/yolov3/yolov3_tiny_impl.hpp | 2 src/rcpp_mlpack.h | 24 +++++-- 17 files changed, 196 insertions(+), 32 deletions(-)
Title: API Wrapper for 'Ipeadata'
Description: Provides direct access to the macroeconomic, financial,
and regional database maintained by the Institute for
Applied Economic Research (Ipea) via the Ipeadata API.
For more information, see <https://www.ipeadata.gov.br/>.
Author: Luiz Eduardo Gomes [aut, cre] ,
Daniel Herszenhut [ctb] ,
Instituto de Pesquisa Economica Aplicada [cph, fnd]
Maintainer: Luiz Eduardo Gomes <luiz.gomes@ipea.gov.br>
Diff between ipeadatar versions 0.2.0 dated 2026-05-28 and 0.2.1 dated 2026-07-22
ipeadatar-0.2.0/ipeadatar/man/figures/README-pressure-1.png |only ipeadatar-0.2.1/ipeadatar/DESCRIPTION | 6 ipeadatar-0.2.1/ipeadatar/MD5 | 33 +-- ipeadatar-0.2.1/ipeadatar/NEWS.md | 26 ++ ipeadatar-0.2.1/ipeadatar/R/available_series.R | 60 +++++- ipeadatar-0.2.1/ipeadatar/R/available_subjects.R | 47 +++- ipeadatar-0.2.1/ipeadatar/R/available_territories.R | 49 ++++ ipeadatar-0.2.1/ipeadatar/R/ipeadata.R | 118 +++++++++--- ipeadatar-0.2.1/ipeadatar/R/metadata.R | 107 ++++++++-- ipeadatar-0.2.1/ipeadatar/R/search_series.R | 12 - ipeadatar-0.2.1/ipeadatar/inst/WORDLIST | 4 ipeadatar-0.2.1/ipeadatar/inst/doc/ipeadatar.R | 2 ipeadatar-0.2.1/ipeadatar/inst/doc/ipeadatar.Rmd | 4 ipeadatar-0.2.1/ipeadatar/inst/doc/ipeadatar.html | 6 ipeadatar-0.2.1/ipeadatar/man/ipeadata.Rd | 8 ipeadatar-0.2.1/ipeadatar/man/metadata.Rd | 5 ipeadatar-0.2.1/ipeadatar/man/search_series.Rd | 5 ipeadatar-0.2.1/ipeadatar/vignettes/ipeadatar.Rmd | 4 18 files changed, 381 insertions(+), 115 deletions(-)
Title: Tools for Scoring and Evaluating Hubverse Model Outputs
Description: Provides tools for scoring and evaluating 'hubverse' model outputs
against observed data, wrapping scoring workflows from the
'scoringutils' package and bridging hubverse model output formats
to 'scoringutils' forecast classes.
Author: Anna Krystalli [aut, cre] ,
Nicholas Reich [aut] ,
Evan Ray [aut],
Nikos Bosse [aut] ,
Kimberlyn Roosa [aut],
Zhian Kamvar [ctb] ,
Li Shandross [ctb] ,
Becky Sweger [ctb],
Lucie Contamin [ctb],
Consortium of Infectious Disease Modeling Hubs [cph]
Maintainer: Anna Krystalli <annakrystalli@googlemail.com>
Diff between hubEvals versions 0.3.1 dated 2026-07-17 and 0.4.0 dated 2026-07-22
hubEvals-0.3.1/hubEvals/tests/testthat/helper-suppress_wilcox_ties.R |only hubEvals-0.4.0/hubEvals/DESCRIPTION | 6 hubEvals-0.4.0/hubEvals/MD5 | 13 hubEvals-0.4.0/hubEvals/NEWS.md | 6 hubEvals-0.4.0/hubEvals/R/score_model_out.R | 53 ++ hubEvals-0.4.0/hubEvals/man/score_model_out.Rd | 5 hubEvals-0.4.0/hubEvals/tests/testthat/test-score_model_out.R | 219 ++++++++++ hubEvals-0.4.0/hubEvals/tests/testthat/test-score_model_out_rel_metrics.R | 133 ++---- 8 files changed, 347 insertions(+), 88 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.7.0.1 dated 2026-07-13 and 1.7.1 dated 2026-07-22
DESCRIPTION | 8 MD5 | 52 R/GPModel.R | 237 R/gpb.Booster.R | 22 R/gpb.Dataset.R | 28 R/gpb.train.R | 16 configure.ac | 2 demo/generalized_linear_Gaussian_process_mixed_effects_models.R | 10 man/GPModel.Rd | 83 man/GPModel_shared_params.Rd | 102 man/fitGPModel.Rd | 83 src/Vecchia_utils.cpp | 148 src/include/GPBoost/CG_utils.h | 4 src/include/GPBoost/Vecchia_utils.h | 6 src/include/GPBoost/cov_fcts.h | 421 + src/include/GPBoost/egpd_utils.h |only src/include/GPBoost/likelihoods.h | 3267 +++++++++- src/include/GPBoost/re_comp.h | 143 src/include/GPBoost/re_model.h | 2 src/include/GPBoost/re_model_template.h | 98 src/include/GPBoost/tweedie_utils.h |only src/objective/regression_objective.hpp | 2 src/re_model.cpp | 11 tests/testthat/Rplots.pdf |binary tests/testthat/test_GPModel_ar1_multifidelity.R |only tests/testthat/test_GPModel_egpd.R |only tests/testthat/test_GPModel_non_Gaussian_data.R | 204 tests/testthat/test_GPModel_tweedie.R |only tests/testthat/test_GPModel_zero_inflated_hurdle.R |only tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data.R | 12 30 files changed, 4368 insertions(+), 593 deletions(-)
Title: Memory-Efficient Storage of Large Data on Disk and Fast Access
Functions
Description: The ff package provides data structures that are stored on
disk but behave (almost) as if they were in RAM by transparently
mapping only a section (pagesize) in main memory - the effective
virtual memory consumption per ff object. ff supports R's standard
atomic data types 'double', 'logical', 'raw' and 'integer' and
non-standard atomic types boolean (1 bit), quad (2 bit unsigned),
nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte
unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned),
single (4 byte float with NAs). For example 'quad' allows efficient
storage of genomic data as an 'A','T','G','C' factor. The unsigned
types support 'circular' arithmetic. There is also support for
close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and
custom close-to-atomic types.
ff not only has native C-support for vectors, matrices and arrays
with flexible dimorder (major column-order, major row-order and
generalizations for arrays). There is also a ffdf cla [...truncated...]
Author: Daniel Adler [aut],
Christian Glaeser [ctb],
Oleg Nenadic [ctb],
Jens Oehlschlaegel [aut, cre],
Martijn Schuemie [ctb],
Walter Zucchini [ctb]
Maintainer: Jens Oehlschlaegel <Jens.Oehlschlaegel@truecluster.com>
Diff between ff versions 4.5.2 dated 2025-01-12 and 4.5.3 dated 2026-07-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/array.R | 2 +- R/ffbit.R | 8 ++++++-- R/hi.R | 4 ++-- R/zzz.R | 6 +++++- tests/testthat/test-zero_lengths.R | 10 +++++----- 7 files changed, 29 insertions(+), 21 deletions(-)
Title: Sparse Functional Data Analysis Methods
Description: Provides algorithms to fit linear regression models under several popular penalization techniques and functional linear regression models based on Majorizing-Minimizing (MM) and Alternating Direction Method of Multipliers (ADMM) techniques.
See Boyd et al (2010) <doi:10.1561/2200000016> for complete introduction to the method.
Author: Mauro Bernardi [aut, cre],
Marco Stefanucci [aut],
Antonio Canale [ctb]
Maintainer: Mauro Bernardi <mauro.bernardi@unipd.it>
Diff between fdaSP versions 1.1.2 dated 2026-04-27 and 1.1.3 dated 2026-07-22
DESCRIPTION | 10 - MD5 | 13 + NEWS.md |only R/dof_utils.R | 147 ++++++++++----------- R/f2sreg.R | 366 +++++++++++++++++++++++++++++++++--------------------- build/partial.rdb |binary man/f2sSP.Rd | 104 ++++++++++----- man/f2sSP_cv.Rd | 82 +++++++----- 8 files changed, 433 insertions(+), 289 deletions(-)
Title: General Bivariate Copula Theory and Many Utility Functions
Description: Extensive functions for bivariate copula (bicopula) computations and related operations
for bicopula theory. The lower, upper, product, and select other bicopula are implemented along
with operations including the diagonal, survival copula, dual of a copula, co-copula, and
numerical bicopula density. Level sets, horizontal and vertical sections are supported. Numerical
derivatives and inverses of a bicopula are provided through which simulation is implemented.
Bicopula composition, convex combination, asymmetry extension, and products also are provided.
Support extends to the Kendall Function as well as the Lmoments thereof. Kendall Tau,
Spearman Rho and Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer-
Wolff Sigma, tail dependency, tail order, skewness, and bivariate Lmoments are implemented, and
positive/negative quadrant dependency, left (right) increasing (decreasing) are available.
Other features include Kullback-Leibler Divergence, Vuong Procedure, spectral measure, [...truncated...]
Author: William Asquith [aut, cre]
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between copBasic versions 2.2.14 dated 2026-05-22 and 2.2.15 dated 2026-07-22
DESCRIPTION | 8 +- MD5 | 35 ++++++---- NAMESPACE | 3 NEWS | 16 ++++ R/EuvCOP.R | 2 R/EvuCOP.R | 2 R/LMRuvCOP.R |only R/LMRvuCOP.R |only R/TRIcop.R |only R/wolfCOPtest.R | 131 ++++++++++++++++++++++++++++++------- inst/LMRvuDEMO.R |only man/EMPIRgrid_fast.Rd | 6 - man/EuvCOP.Rd | 4 - man/EvuCOP.Rd | 4 - man/LMRuvCOP.Rd |only man/LMRvuCOP.Rd |only man/TRIcop.Rd |only man/copBasic-package.Rd | 16 +++- man/prod2COP.Rd | 2 man/wolfCOP.Rd | 13 ++- man/wolfCOPtest.Rd | 142 +++++++++++++++++++++++++++++++++++++---- man/wolfCOPtest_data_smlsam.Rd | 2 22 files changed, 310 insertions(+), 76 deletions(-)
Title: Zero-Modified Complex 'Tri-Parametric' Pearson Distribution for
Overdispersed Count Data
Description: Implements zero-modified versions of the Complex 'Tri-Parametric'
Pearson distribution for overdispersed count data. The package addresses
limitations of existing implementations when the parameter b approaches
zero. It provides distribution functions, maximum likelihood estimation,
and diagnostic tools for modeling count data with excess zeros. The
methodology is based on 'Rodriguez-Avi' and coauthors (2003)
<doi:10.1007/s00362-002-0134-7>.
Author: Rasheedat Oladoja [aut, cre]
Maintainer: Rasheedat Oladoja <roladoja@ttu.edu>
Diff between zmctp versions 0.1.1 dated 2026-07-09 and 0.1.2 dated 2026-07-22
DESCRIPTION | 6 +- MD5 | 21 +++++---- NEWS.md |only R/ctp_fit.R | 8 +++ R/moments.R | 78 ++++++++++++++++++++++++++--------- R/zictp_fit.R | 7 ++- inst/WORDLIST | 48 ++++++++++----------- inst/doc/introduction.html | 6 +- man/mean_ctp.Rd | 16 +------ man/mean_zictp.Rd | 9 +--- man/mode_ctp.Rd |only man/mode_zictp.Rd |only tests/testthat/test-moments.R | 92 ++++++++++++++++++++++++++++++++++++++++++ 13 files changed, 213 insertions(+), 78 deletions(-)
Title: Extract Drug Dosages from Free-Text Prescriptions
Description: Utilities for converting unstructured electronic prescribing instructions into structured medication data. Extracts drug dose, units, daily dosing frequency and intervals from English-language prescriptions. Based on Karystianis et al. (2015) <doi:10.1186/s12911-016-0255-x>.
Author: David Selby [aut, cre] ,
Belay Birlie Yimer [ctb],
Ben Marwick [ctb]
Maintainer: David Selby <david_antony.selby@dfki.de>
This is a re-admission after prior archival of version 0.1.2 dated 2021-07-19
Diff between doseminer versions 0.1.2 dated 2021-07-19 and 0.2.1 dated 2026-07-22
DESCRIPTION | 16 LICENSE | 4 MD5 | 66 +- NEWS.md | 30 - R/data.R | 184 +++--- R/doseminer-package.R | 16 R/extract.R | 386 ++++++------ R/numbers.R | 662 +++++++++++----------- R/units.R | 160 ++--- README.md | 296 +++++---- build/partial.rdb |only build/vignette.rds |binary inst/doc/case_study.R | 78 +- inst/doc/case_study.Rmd | 198 +++--- inst/doc/case_study.html | 830 ++++++++++++++------------- inst/doc/introduction.R | 76 +- inst/doc/introduction.Rmd | 238 +++---- inst/doc/introduction.html | 1170 +++++++++++++++++++-------------------- man/doseminer-package.Rd | 61 +- man/drug_units.Rd | 39 - man/example_cprd.Rd | 5 man/example_prescriptions.Rd | 5 man/extract_from_prescription.Rd | 74 +- man/hourly_to_daily.Rd | 34 - man/latin_medical_terms.Rd | 5 man/multiply_dose.Rd | 42 - man/numb_replacements.Rd | 9 man/regex_numbers.Rd | 7 man/weekly_to_daily.Rd | 34 - tests/testthat.R | 8 tests/testthat/test-examples.R |only tests/testthat/test-numbers.R | 78 +- tests/testthat/test-utils.R | 94 +-- vignettes/case_study.Rmd | 198 +++--- vignettes/introduction.Rmd | 238 +++---- 35 files changed, 2701 insertions(+), 2640 deletions(-)
Title: Systematic Comparison of Trip Distribution Laws and Models
Description: The main purpose of this package is to propose a rigorous framework to fairly compare trip distribution laws and models as described in Lenormand et al. (2016) <doi:10.1016/j.jtrangeo.2015.12.008>.
Author: Maxime Lenormand [aut, cre]
Maintainer: Maxime Lenormand <maxime.lenormand@inrae.fr>
Diff between TDLM versions 1.1.3 dated 2025-10-03 and 1.1.4 dated 2026-07-22
TDLM-1.1.3/TDLM/man/figures/GravVsOpp.png |only TDLM-1.1.3/TDLM/man/figures/Inputs.png |only TDLM-1.1.3/TDLM/man/figures/Models.png |only TDLM-1.1.3/TDLM/man/figures/OD.png |only TDLM-1.1.3/TDLM/man/figures/Proba.png |only TDLM-1.1.4/TDLM/DESCRIPTION | 8 TDLM-1.1.4/TDLM/MD5 | 51 ++-- TDLM-1.1.4/TDLM/NEWS.md | 32 ++ TDLM-1.1.4/TDLM/R/run_law.R | 5 TDLM-1.1.4/TDLM/R/run_law_model.R | 21 + TDLM-1.1.4/TDLM/R/run_model.R | 33 +- TDLM-1.1.4/TDLM/README.md | 4 TDLM-1.1.4/TDLM/build/vignette.rds |binary TDLM-1.1.4/TDLM/inst/doc/TDLM.Rmd | 40 ++- TDLM-1.1.4/TDLM/inst/doc/TDLM.html | 258 ++++++++++----------- TDLM-1.1.4/TDLM/inst/java/Sij.jar |binary TDLM-1.1.4/TDLM/inst/java/TDLM.class |binary TDLM-1.1.4/TDLM/inst/java/TDLM.jar |binary TDLM-1.1.4/TDLM/inst/java/TDM.class |binary TDLM-1.1.4/TDLM/inst/java/TDM.jar |binary TDLM-1.1.4/TDLM/java/TDLM.java | 24 + TDLM-1.1.4/TDLM/java/TDM.java | 21 - TDLM-1.1.4/TDLM/man/extract_spatial_information.Rd | 2 TDLM-1.1.4/TDLM/man/figures/Fig1.png |only TDLM-1.1.4/TDLM/man/figures/Fig2.png |only TDLM-1.1.4/TDLM/man/figures/Fig3.png |only TDLM-1.1.4/TDLM/man/figures/Fig4.png |only TDLM-1.1.4/TDLM/man/figures/Fig5.png |only TDLM-1.1.4/TDLM/man/figures/Fig6.png |only TDLM-1.1.4/TDLM/man/run_law_model.Rd | 12 TDLM-1.1.4/TDLM/man/run_model.Rd | 28 +- TDLM-1.1.4/TDLM/vignettes/TDLM.Rmd | 40 ++- 32 files changed, 339 insertions(+), 240 deletions(-)
Title: Adaptive Machine Learning-Powered, Context-Matching Tool for
Single-Cell and Spatial Transcriptomics Annotation
Description: Annotates single-cell and spatial-transcriptomic (ST) data using context-matching marker datasets. It creates a unified marker list (`Markers_list`) from multiple sources: built-in curated databases ('Cellmarker2', 'PanglaoDB', 'ScType', 'scIBD', 'TCellSI', 'PCTIT', 'PCTAM'), Seurat objects with cell labels, or user-provided Excel tables. SlimR first uses adaptive machine learning for parameter optimization, and then offers two automated annotation approaches: 'cluster-based' and 'per-cell'. Cluster-based annotation assigns one label per cluster, expression-based probability calculation, and AUC validation. Per-cell annotation assigns labels to individual cells using three scoring methods with adaptive thresholds and ratio-based confidence filtering, plus optional UMAP spatial smoothing, making it ideal for heterogeneous clusters and rare cell types. The package also supports semi-automated workflows with heatmaps, feature plots, and combined visualizations for manual annotation. For m [...truncated...]
Author: Zhaoqing Wang [aut, cre]
Maintainer: Zhaoqing Wang <zhaoqingwang@mail.sdu.edu.cn>
Diff between SlimR versions 1.1.6 dated 2026-06-30 and 1.1.7 dated 2026-07-22
SlimR-1.1.6/SlimR/R/plot_pheatmap.R |only SlimR-1.1.7/SlimR/DESCRIPTION | 12 - SlimR-1.1.7/SlimR/MD5 | 33 +- SlimR-1.1.7/SlimR/NAMESPACE | 16 + SlimR-1.1.7/SlimR/NEWS.md | 13 + SlimR-1.1.7/SlimR/R/Compute_Gene_AUC_ROC.R | 2 SlimR-1.1.7/SlimR/R/Plot_Hierarchy_Proportion.R |only SlimR-1.1.7/SlimR/R/Plot_Voronoi_Diagram.R |only SlimR-1.1.7/SlimR/R/Plot_pheatmap.R |only SlimR-1.1.7/SlimR/R/paletteDiscrete.R |only SlimR-1.1.7/SlimR/README.md | 173 ++++++++++++++- SlimR-1.1.7/SlimR/man/ArchRPalettes.Rd |only SlimR-1.1.7/SlimR/man/Celltype_Compare.Rd | 5 SlimR-1.1.7/SlimR/man/Celltype_annotation_Cellmarker2.Rd | 5 SlimR-1.1.7/SlimR/man/Celltype_annotation_Excel.Rd | 5 SlimR-1.1.7/SlimR/man/Celltype_annotation_PanglaoDB.Rd | 5 SlimR-1.1.7/SlimR/man/Celltype_annotation_Seurat.Rd | 5 SlimR-1.1.7/SlimR/man/Compute_Gene_AUC_ROC.Rd | 7 SlimR-1.1.7/SlimR/man/Plot_Hierarchy_Proportion.Rd |only SlimR-1.1.7/SlimR/man/Plot_Voronoi_diagram.Rd |only SlimR-1.1.7/SlimR/man/paletteDiscrete.Rd |only SlimR-1.1.7/SlimR/man/plot.pheatmap.Rd | 2 22 files changed, 254 insertions(+), 29 deletions(-)
Title: R Client for the BIODATACR Biodiversity Data Platform of Costa
Rica
Description: Provides functions to query occurrence records, species
information, and datasets from BIODATACR
<https://biodiversidad.go.cr>, the national biodiversity information
platform of Costa Rica managed by the Technical Office of CONAGEBIO.
Built on the Atlas of Living Australia (ALA) API infrastructure.
Author: Manuel Spinola [aut, cre]
Maintainer: Manuel Spinola <mspinola10@gmail.com>
Diff between rbiodatacr versions 0.1.1 dated 2026-05-05 and 0.1.2 dated 2026-07-22
DESCRIPTION | 10 ++--- MD5 | 12 +++--- NEWS.md | 14 +++++++ R/bdcr_occurrences.R | 75 ++++++++++++++++++++++++++++++++++++------ R/bdcr_occurrences_batch.R | 34 ++++++++++++++----- man/bdcr_occurrences.Rd | 18 ++++++++-- man/bdcr_occurrences_batch.Rd | 14 ++++++- 7 files changed, 142 insertions(+), 35 deletions(-)
Title: Another Approach to Package Installation
Description: The goal of 'pak' is to make package installation faster and
more reliable. In particular, it performs all HTTP operations in
parallel, so metadata resolution and package downloads are fast.
Metadata and package files are cached on the local disk as well. 'pak'
has a dependency solver, so it finds version conflicts before
performing the installation. This version of 'pak' supports CRAN,
'Bioconductor' and 'GitHub' packages as well.
Author: Gabor Csardi [aut, cre],
Jim Hester [aut],
Posit Software, PBC [cph, fnd] ,
Winston Chang [ctb] ,
Ascent Digital Services [cph, fnd] ,
Hadley Wickham [ctb, cph] ,
Jeroen Ooms [ctb] ,
Maelle Salmon [ctb] ,
Duncan Temple Lang [ctb] ,
Lloyd Hilaiel [cph [...truncated...]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pak versions 0.11.0 dated 2026-07-15 and 0.11.1 dated 2026-07-22
DESCRIPTION | 6 MD5 | 97 +++++----- NEWS.md | 8 man/chunks/install.Rmd | 16 - man/install.Rd | 16 - src/library/pkgdepends/DESCRIPTION | 2 src/library/pkgdepends/R/dep-utils.R | 16 + src/library/pkgdepends/R/gh-app.R | 72 +++++-- src/library/pkgdepends/R/install-plan.R | 101 +++++++++-- src/library/pkgdepends/R/pkg-plan.R | 1 src/library/pkgdepends/R/solve.R | 1 src/library/pkgdepends/R/sysreqs2.R | 4 src/library/pkgdepends/R/tojson.R | 3 src/library/pkgdepends/R/type-github.R | 37 +++- src/library/pkgdepends/R/zzz-pkgdepends-config.R | 8 src/library/pkgdepends/inst/WORDLIST | 1 src/library/pkgdepends/inst/docs/pak-config-docs.rds |binary src/library/pkgdepends/inst/sysreqs/HEAD | 2 src/library/pkgdepends/inst/sysreqs/rules/Abseil.json | 30 --- src/library/pkgdepends/inst/sysreqs/rules/blosc.json | 19 +- src/library/pkgdepends/inst/sysreqs/rules/chrome.json | 27 -- src/library/pkgdepends/inst/sysreqs/rules/cln.json | 18 + src/library/pkgdepends/inst/sysreqs/rules/dotnet10.json |only src/library/pkgdepends/inst/sysreqs/rules/dotnet8.json |only src/library/pkgdepends/inst/sysreqs/rules/dotnet9.json |only src/library/pkgdepends/inst/sysreqs/rules/exiftool.json | 30 --- src/library/pkgdepends/inst/sysreqs/rules/faiss.json |only src/library/pkgdepends/inst/sysreqs/rules/fluidsynth.json | 15 + src/library/pkgdepends/inst/sysreqs/rules/ginac.json | 5 src/library/pkgdepends/inst/sysreqs/rules/grpcpp.json | 10 - src/library/pkgdepends/inst/sysreqs/rules/gtkmm2.json |only src/library/pkgdepends/inst/sysreqs/rules/haveged.json | 17 - src/library/pkgdepends/inst/sysreqs/rules/hdf5.json | 15 - src/library/pkgdepends/inst/sysreqs/rules/hiredis.json | 30 --- src/library/pkgdepends/inst/sysreqs/rules/imagemagick.json | 30 --- src/library/pkgdepends/inst/sysreqs/rules/libavif.json |only src/library/pkgdepends/inst/sysreqs/rules/libbsd.json | 17 - src/library/pkgdepends/inst/sysreqs/rules/libgit2.json | 17 - src/library/pkgdepends/inst/sysreqs/rules/libmecab.json | 42 ---- src/library/pkgdepends/inst/sysreqs/rules/libsodium.json | 30 --- src/library/pkgdepends/inst/sysreqs/rules/libssh.json | 15 - src/library/pkgdepends/inst/sysreqs/rules/libssh2.json | 15 - src/library/pkgdepends/inst/sysreqs/rules/ncurses.json |only src/library/pkgdepends/inst/sysreqs/rules/netcdf4.json | 15 - src/library/pkgdepends/inst/sysreqs/rules/openbabel.json | 15 - src/library/pkgdepends/inst/sysreqs/rules/opencv.json | 20 -- src/library/pkgdepends/inst/sysreqs/rules/openmpt.json | 15 + src/library/pkgdepends/inst/sysreqs/rules/protobuf-grpc.json | 20 -- src/library/pkgdepends/inst/sysreqs/rules/redland.json | 3 src/library/pkgdepends/inst/sysreqs/rules/sdl2.json | 20 ++ src/library/pkgdepends/inst/sysreqs/rules/udunits2.json | 46 ++--- src/library/pkgdepends/inst/sysreqs/rules/v8.json | 2 src/library/pkgdepends/inst/sysreqs/rules/zeromq.json | 30 --- 53 files changed, 433 insertions(+), 526 deletions(-)
Title: Multi-Resolution Scanning for Cross-Sample and Cross-Group
Differences
Description: Implements the multi-resolution scanning (MRS) method for
cross-sample distribution comparisons, as described in Soriano and Ma (2017)
<doi:10.1111/rssb.12180>, and the analysis of distributional variation
(ANDOVA) method for cross-group comparisons introduced in Ma and Soriano
(2018) <doi:10.1080/10618600.2017.1402774>. Both methods use nonparametric
models on multi-resolution partition trees to detect and characterize
differences among distributions, with tools for visualizing the results.
Author: Jacopo Soriano [aut],
Li Ma [aut, cre]
Maintainer: Li Ma <mastatlab@gmail.com>
This is a re-admission after prior archival of version 1.2.6 dated 2023-12-11
Diff between MRS versions 1.2.6 dated 2023-12-11 and 1.3.2 dated 2026-07-22
DESCRIPTION | 43 ++- MD5 | 63 ++-- NAMESPACE | 8 NEWS.md |only R/RcppExports.R | 8 R/andova.R | 225 ++++++++--------- R/bFDR.R |only R/mrs.R | 158 ++++------- R/plot1D.R | 167 +++++++----- R/plot1DSigWindows.R |only R/plot2D.R | 217 +++++++++------- R/plotTree.R | 280 +++++++++++++++------ R/print.summary.mrs.R | 38 +- R/summary.mrs.R | 84 +++--- R/utils.R |only README.md |only build/partial.rdb |binary demo |only man/andova.Rd | 49 ++- man/mrs.Rd | 34 +- man/plot1D.Rd | 31 +- man/plot1DSigWindows.Rd |only man/plot2D.Rd | 33 +- man/plotTree.Rd | 31 +- man/print.summary.mrs.Rd | 18 - man/summary.mrs.Rd | 10 src/RcppExports.cpp | 27 +- src/helpers.cpp | 41 +-- src/helpers.h | 2 src/main.cpp | 113 ++++++++ src/recursion.cpp | 619 +++++++++++++++++++++++++++++++++++++++++++---- src/recursion.h | 57 +++- tests |only 33 files changed, 1649 insertions(+), 707 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc] ,
Christoph Burow [aut, trl, dtc] ,
Michael Dietze [aut] ,
Margret C. Fuchs [aut] ,
Christoph Schmidt [aut] ,
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] ,
Norbert Mercier [aut] ,
Rachel K. Smedley [ct [...truncated...]
Maintainer: Sebastian Kreutzer <maintainer_luminescence@r-luminescence.org>
Diff between Luminescence versions 1.2.1 dated 2026-03-25 and 1.3.0 dated 2026-07-22
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Luminescence-1.3.0/Luminescence/R/analyse_SAR.CWOSL.R | 1060 ++++------ Luminescence-1.3.0/Luminescence/R/analyse_SAR.NCF.R |only Luminescence-1.3.0/Luminescence/R/analyse_SAR.TL.R | 41 Luminescence-1.3.0/Luminescence/R/analyse_baSAR.R | 741 ++---- Luminescence-1.3.0/Luminescence/R/analyse_pIRIRSequence.R | 75 Luminescence-1.3.0/Luminescence/R/analyse_portableOSL.R | 22 Luminescence-1.3.0/Luminescence/R/apply_EfficiencyCorrection.R | 59 Luminescence-1.3.0/Luminescence/R/calc_AliquotSize.R | 29 Luminescence-1.3.0/Luminescence/R/calc_FastRatio.R | 15 Luminescence-1.3.0/Luminescence/R/calc_Huntley2006.R | 128 - Luminescence-1.3.0/Luminescence/R/calc_IEU.R | 8 Luminescence-1.3.0/Luminescence/R/calc_Lamothe2003.R | 2 Luminescence-1.3.0/Luminescence/R/calc_MinDose.R | 161 - Luminescence-1.3.0/Luminescence/R/calc_OSLLxTxRatio.R | 247 +- Luminescence-1.3.0/Luminescence/R/calc_SourceDoseRate.R | 54 Luminescence-1.3.0/Luminescence/R/calc_Statistics.R | 191 - 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Luminescence-1.3.0/Luminescence/man/calc_FadingCorr.Rd | 12 Luminescence-1.3.0/Luminescence/man/calc_FastRatio.Rd | 12 Luminescence-1.3.0/Luminescence/man/calc_FiniteMixture.Rd | 6 Luminescence-1.3.0/Luminescence/man/calc_FuchsLang2001.Rd | 8 Luminescence-1.3.0/Luminescence/man/calc_HomogeneityTest.Rd | 8 Luminescence-1.3.0/Luminescence/man/calc_Huntley2006.Rd | 14 Luminescence-1.3.0/Luminescence/man/calc_IEU.Rd | 8 Luminescence-1.3.0/Luminescence/man/calc_Lamothe2003.Rd | 10 Luminescence-1.3.0/Luminescence/man/calc_MaxDose.Rd | 18 Luminescence-1.3.0/Luminescence/man/calc_MinDose.Rd | 34 Luminescence-1.3.0/Luminescence/man/calc_MoransI.Rd | 4 Luminescence-1.3.0/Luminescence/man/calc_OSLLxTxDecomposed.Rd | 6 Luminescence-1.3.0/Luminescence/man/calc_OSLLxTxRatio.Rd | 148 - Luminescence-1.3.0/Luminescence/man/calc_SourceDoseRate.Rd | 40 Luminescence-1.3.0/Luminescence/man/calc_Statistics.Rd | 12 Luminescence-1.3.0/Luminescence/man/calc_TLLxTxRatio.Rd | 14 Luminescence-1.3.0/Luminescence/man/calc_ThermalLifetime.Rd | 4 Luminescence-1.3.0/Luminescence/man/calc_WodaFuchs2008.Rd | 4 Luminescence-1.3.0/Luminescence/man/calc_gSGC.Rd | 6 Luminescence-1.3.0/Luminescence/man/calc_gSGC_feldspar.Rd | 6 Luminescence-1.3.0/Luminescence/man/combine_De_Dr.Rd | 8 Luminescence-1.3.0/Luminescence/man/convert_Activity2Concentration.Rd | 4 Luminescence-1.3.0/Luminescence/man/convert_BIN2CSV.Rd | 4 Luminescence-1.3.0/Luminescence/man/convert_CW2pHMi.Rd | 8 Luminescence-1.3.0/Luminescence/man/convert_CW2pLM.Rd | 10 Luminescence-1.3.0/Luminescence/man/convert_CW2pLMi.Rd | 8 Luminescence-1.3.0/Luminescence/man/convert_CW2pPMi.Rd | 8 Luminescence-1.3.0/Luminescence/man/convert_Concentration2DoseRate.Rd | 4 Luminescence-1.3.0/Luminescence/man/convert_Daybreak2CSV.Rd | 4 Luminescence-1.3.0/Luminescence/man/convert_PSL2CSV.Rd | 4 Luminescence-1.3.0/Luminescence/man/convert_PSL2Risoe.BINfileData.Rd | 20 Luminescence-1.3.0/Luminescence/man/convert_RLum2Risoe.BINfileData.Rd | 18 Luminescence-1.3.0/Luminescence/man/convert_SG2MG.Rd | 10 Luminescence-1.3.0/Luminescence/man/convert_Second2Gray.Rd | 15 Luminescence-1.3.0/Luminescence/man/convert_Wavelength2Energy.Rd | 8 Luminescence-1.3.0/Luminescence/man/convert_XSYG2CSV.Rd | 4 Luminescence-1.3.0/Luminescence/man/correct_PMTLinearity.Rd | 4 Luminescence-1.3.0/Luminescence/man/dot-as.latex.table.Rd | 2 Luminescence-1.3.0/Luminescence/man/extract_IrradiationTimes.Rd | 30 Luminescence-1.3.0/Luminescence/man/extract_ROI.Rd | 10 Luminescence-1.3.0/Luminescence/man/fit_CWCurve.Rd | 10 Luminescence-1.3.0/Luminescence/man/fit_DoseResponseCurve.Rd | 158 - Luminescence-1.3.0/Luminescence/man/fit_EmissionSpectra.Rd | 8 Luminescence-1.3.0/Luminescence/man/fit_LMCurve.Rd | 6 Luminescence-1.3.0/Luminescence/man/fit_OSLLifeTimes.Rd | 8 Luminescence-1.3.0/Luminescence/man/fit_SurfaceExposure.Rd | 2 Luminescence-1.3.0/Luminescence/man/fit_ThermalQuenching.Rd | 2 Luminescence-1.3.0/Luminescence/man/get_Layout.Rd | 2 Luminescence-1.3.0/Luminescence/man/get_RLum.Rd | 46 Luminescence-1.3.0/Luminescence/man/get_rightAnswer.Rd | 2 Luminescence-1.3.0/Luminescence/man/import_Data.Rd | 6 Luminescence-1.3.0/Luminescence/man/length_RLum.Rd | 16 Luminescence-1.3.0/Luminescence/man/melt_RLum.Rd | 12 Luminescence-1.3.0/Luminescence/man/merge_RLum.Analysis.Rd | 32 Luminescence-1.3.0/Luminescence/man/merge_RLum.Data.Curve.Rd | 10 Luminescence-1.3.0/Luminescence/man/merge_RLum.Data.Spectrum.Rd | 12 Luminescence-1.3.0/Luminescence/man/merge_RLum.Rd | 24 Luminescence-1.3.0/Luminescence/man/merge_RLum.Results.Rd | 13 Luminescence-1.3.0/Luminescence/man/merge_Risoe.BINfileData.Rd | 14 Luminescence-1.3.0/Luminescence/man/metadata.Rd | 32 Luminescence-1.3.0/Luminescence/man/methods_RLum.Rd | 14 Luminescence-1.3.0/Luminescence/man/names_RLum.Rd | 16 Luminescence-1.3.0/Luminescence/man/normalise_RLum.Rd | 20 Luminescence-1.3.0/Luminescence/man/plot_AbanicoPlot.Rd | 28 Luminescence-1.3.0/Luminescence/man/plot_DRCSummary.Rd | 14 Luminescence-1.3.0/Luminescence/man/plot_DRTResults.Rd | 14 Luminescence-1.3.0/Luminescence/man/plot_DetPlot.Rd | 59 Luminescence-1.3.0/Luminescence/man/plot_DoseResponseCurve.Rd | 14 Luminescence-1.3.0/Luminescence/man/plot_FilterCombinations.Rd | 6 Luminescence-1.3.0/Luminescence/man/plot_GrowthCurve.Rd | 41 Luminescence-1.3.0/Luminescence/man/plot_Histogram.Rd | 22 Luminescence-1.3.0/Luminescence/man/plot_KDE.Rd | 6 Luminescence-1.3.0/Luminescence/man/plot_MoranScatterplot.Rd | 4 Luminescence-1.3.0/Luminescence/man/plot_NRt.Rd | 10 Luminescence-1.3.0/Luminescence/man/plot_OSLAgeSummary.Rd | 8 Luminescence-1.3.0/Luminescence/man/plot_RLum.Analysis.Rd | 10 Luminescence-1.3.0/Luminescence/man/plot_RLum.Data.Curve.Rd | 8 Luminescence-1.3.0/Luminescence/man/plot_RLum.Data.Image.Rd | 10 Luminescence-1.3.0/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 22 Luminescence-1.3.0/Luminescence/man/plot_RLum.Rd | 18 Luminescence-1.3.0/Luminescence/man/plot_RLum.Results.Rd | 18 Luminescence-1.3.0/Luminescence/man/plot_ROI.Rd | 8 Luminescence-1.3.0/Luminescence/man/plot_RadialPlot.Rd | 27 Luminescence-1.3.0/Luminescence/man/plot_Risoe.BINfileData.Rd | 10 Luminescence-1.3.0/Luminescence/man/plot_SingleGrainDisc.Rd | 4 Luminescence-1.3.0/Luminescence/man/plot_ViolinPlot.Rd | 4 Luminescence-1.3.0/Luminescence/man/read_BIN2R.Rd | 14 Luminescence-1.3.0/Luminescence/man/read_BINXLOG2R.Rd | 8 Luminescence-1.3.0/Luminescence/man/read_Daybreak2R.Rd | 8 Luminescence-1.3.0/Luminescence/man/read_HeliosOSL2R.Rd | 8 Luminescence-1.3.0/Luminescence/man/read_PSL2R.Rd | 12 Luminescence-1.3.0/Luminescence/man/read_RF2R.Rd | 10 Luminescence-1.3.0/Luminescence/man/read_SPE2R.Rd | 18 Luminescence-1.3.0/Luminescence/man/read_TIFF2R.Rd | 6 Luminescence-1.3.0/Luminescence/man/read_XSYG2R.Rd | 10 Luminescence-1.3.0/Luminescence/man/remove_RLum.Rd | 18 Luminescence-1.3.0/Luminescence/man/remove_SignalBackground.Rd | 16 Luminescence-1.3.0/Luminescence/man/replicate_RLum.Rd | 12 Luminescence-1.3.0/Luminescence/man/report_RLum.Rd | 2 Luminescence-1.3.0/Luminescence/man/sTeve.Rd | 2 Luminescence-1.3.0/Luminescence/man/scale_GammaDose.Rd | 2 Luminescence-1.3.0/Luminescence/man/set_RLum.Rd | 28 Luminescence-1.3.0/Luminescence/man/set_Risoe.BINfileData.Rd | 10 Luminescence-1.3.0/Luminescence/man/show.Rd | 2 Luminescence-1.3.0/Luminescence/man/smooth_RLum.Rd | 12 Luminescence-1.3.0/Luminescence/man/sort_RLum.Rd | 16 Luminescence-1.3.0/Luminescence/man/structure_RLum.Rd | 16 Luminescence-1.3.0/Luminescence/man/subset_SingleGrainData.Rd | 8 Luminescence-1.3.0/Luminescence/man/template_DRAC.Rd | 2 Luminescence-1.3.0/Luminescence/man/trim_RLum.Data.Rd | 12 Luminescence-1.3.0/Luminescence/man/tune_Data.Rd | 12 Luminescence-1.3.0/Luminescence/man/use_DRAC.Rd | 4 Luminescence-1.3.0/Luminescence/man/verify_SingleGrainData.Rd | 22 Luminescence-1.3.0/Luminescence/man/view.Rd | 10 Luminescence-1.3.0/Luminescence/man/write_R2BIN.Rd | 10 Luminescence-1.3.0/Luminescence/man/write_R2TIFF.Rd | 10 Luminescence-1.3.0/Luminescence/man/write_RLum2CSV.Rd | 12 Luminescence-1.3.0/Luminescence/src/Makevars | 2 Luminescence-1.3.0/Luminescence/src/Makevars.win | 2 Luminescence-1.3.0/Luminescence/src/RcppExports.cpp | 59 Luminescence-1.3.0/Luminescence/src/src_EED_Calc_Overall_StatUncertainty.cpp | 13 Luminescence-1.3.0/Luminescence/src/src_fit_functions.cpp | 37 Luminescence-1.3.0/Luminescence/tests/testthat/_data/LxTx_Bluszcz.rds |only Luminescence-1.3.0/Luminescence/tests/testthat/setup.R | 9 Luminescence-1.3.0/Luminescence/tests/testthat/test_RLum.Analysis-class.R | 16 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_Al2O3C_CrossTalk.R | 4 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_Al2O3C_ITC.R | 8 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_Al2O3C_Measurement.R | 2 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_FadingMeasurement.R | 10 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_IRSAR.RF.R | 14 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_SAR.CWOSL.R | 174 + Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_SAR.NCF.R |only Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_SAR.TL.R | 6 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_baSAR.R | 40 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_pIRIRSequence.R | 37 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_portableOSL.R | 4 Luminescence-1.3.0/Luminescence/tests/testthat/test_apply_EfficiencyCorrection.R | 19 Luminescence-1.3.0/Luminescence/tests/testthat/test_as_latex_table.R | 6 Luminescence-1.3.0/Luminescence/tests/testthat/test_calc_Huntley2006.R | 89 Luminescence-1.3.0/Luminescence/tests/testthat/test_calc_IEU.R | 8 Luminescence-1.3.0/Luminescence/tests/testthat/test_calc_MinDose.R | 31 Luminescence-1.3.0/Luminescence/tests/testthat/test_calc_OSLLxTxRatio.R | 100 Luminescence-1.3.0/Luminescence/tests/testthat/test_calc_SourceDoseRate.R | 69 Luminescence-1.3.0/Luminescence/tests/testthat/test_calc_Statistics.R | 8 Luminescence-1.3.0/Luminescence/tests/testthat/test_calc_TLLxTxRatio.R | 2 Luminescence-1.3.0/Luminescence/tests/testthat/test_convert_CW2pX.R | 2 Luminescence-1.3.0/Luminescence/tests/testthat/test_convert_Second2Gray.R | 5 Luminescence-1.3.0/Luminescence/tests/testthat/test_extract_IrradiationTimes.R | 7 Luminescence-1.3.0/Luminescence/tests/testthat/test_fit_DoseResponseCurve.R | 305 ++ Luminescence-1.3.0/Luminescence/tests/testthat/test_fit_EmissionSpectra.R | 29 Luminescence-1.3.0/Luminescence/tests/testthat/test_fit_OSLLifeTimes.R | 2 Luminescence-1.3.0/Luminescence/tests/testthat/test_get_RLum.R | 4 Luminescence-1.3.0/Luminescence/tests/testthat/test_internals.R | 22 Luminescence-1.3.0/Luminescence/tests/testthat/test_merge_RLum.Results.R | 6 Luminescence-1.3.0/Luminescence/tests/testthat/test_methods_S3.R | 3 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_AbanicoPlot.R | 24 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_DRCSummary.R | 2 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_DRTResults.R | 6 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_DetPlot.R | 20 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_DoseResponseCurve.R | 41 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_GrowthCurve.R | 26 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_Histogram.R | 4 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_KDE.R | 11 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_NRt.R | 6 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_RLum.Analysis.R | 2 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_RLum.Data.Spectrum.R | 59 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_RLum.Results.R | 7 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_RadialPlot.R | 36 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_ViolinPlot.R | 7 Luminescence-1.3.0/Luminescence/tests/testthat/test_read_Daybreak2R.R | 8 Luminescence-1.3.0/Luminescence/tests/testthat/test_read_XSYG2R.R | 6 Luminescence-1.3.0/Luminescence/tests/testthat/test_set_RLum.R | 25 Luminescence-1.3.0/Luminescence/tests/testthat/test_verify_SingleGrainData.R | 40 Luminescence-1.3.0/Luminescence/tests/testthat/test_zzz.R | 21 288 files changed, 5955 insertions(+), 5506 deletions(-)
Title: Geolocalização De Endereços Brasileiros (Geocoding Brazilian
Addresses)
Description: Método simples e eficiente de geolocalizar dados no Brasil. O
pacote é baseado em conjuntos de dados espaciais abertos de endereços
brasileiros, utilizando como fonte principal o Cadastro Nacional de Endereços
para Fins Estatísticos (CNEFE). O CNEFE é publicado pelo Instituto Brasileiro
de Geografia e Estatística (IBGE), órgão oficial de estatísticas e geografia
do Brasil. (A simple and efficient method for geolocating data in Brazil. The
package is based on open spatial datasets of Brazilian addresses, primarily
using the Cadastro Nacional de Endereços para Fins Estatísticos (CNEFE),
published by the Instituto Brasileiro de Geografia e Estatística (IBGE),
Brazil's official statistics and geography agency.)
Author: Rafael H. M. Pereira [aut, cre] ,
Daniel Herszenhut [aut] ,
Gabriel Garcia de Almeida [aut] ,
Arthur Bazolli [ctb],
Pedro Milreu Cunha [ctb],
ITpS - Instituto Todos pela Saude [fnd],
Ipea - Instituto de Pesquisa Economica Aplicada [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between geocodebr versions 0.6.3 dated 2026-05-24 and 0.6.4 dated 2026-07-22
DESCRIPTION | 6 - MD5 | 26 +++---- NEWS.md | 11 ++- R/geocode.R | 2 build/vignette.rds |binary inst/doc/geocode.R | 52 +++++++------- inst/doc/geocode.html | 41 ----------- inst/doc/geocode_reverso.R | 38 +++++----- inst/doc/geocode_reverso.html | 50 ++++--------- inst/doc/geocodebr.R | 116 ++++++++++++++++---------------- inst/doc/geocodebr.html | 24 +----- tests/testthat/_snaps/cache.md | 60 ++++++++-------- tests/testthat/_snaps/definir_campos.md | 16 ++-- tests/testthat/_snaps/message.md | 14 +-- 14 files changed, 201 insertions(+), 255 deletions(-)
Title: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
Description: Toolbox to process raw data from closed loop flux chamber (or tent)
setups into ecosystem gas fluxes usable for analysis. It goes from a
data frame of gas concentration over time (which can contain several
measurements) and a meta data file indicating which measurement was done
when, to a data frame of ecosystem gas fluxes including quality diagnostics.
Organized with one function per step, maximizing user flexibility and backwards
compatibility. Different models to estimate the fluxes from the raw data are
available: exponential as described in
Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, exponential as described in
Hutchinson and Mosier (1981) <doi:10.2136/sssaj1981.03615995004500020017x>,
quadratic, and linear. Other functions include quality assessment,
plotting for visual check, calculation of fluxes based on the setup
specific parameters (chamber size, plot area, ...), gross primary production
and transpiration rate calculation, and light response curves.
Author: Joseph Gaudard [aut, cre] ,
Richard James Telford [aut]
Maintainer: Joseph Gaudard <joseph.gaudard@pm.me>
Diff between fluxible versions 1.3.6 dated 2026-02-05 and 1.4.0 dated 2026-07-22
DESCRIPTION | 10 MD5 | 160 +++--- NAMESPACE | 7 NEWS.md | 11 R/check_bare_col.R |only R/flux_calc.R | 101 ++- R/flux_calc_frac.R |only R/flux_calc_vol.R |only R/flux_conc.R |only R/flux_diff.R | 10 R/flux_drygas.R | 22 R/flux_fitting.R | 31 - R/flux_fitting_exptz.R | 3 R/flux_fitting_hm.R | 3 R/flux_fitting_lm.R | 3 R/flux_fitting_quadratic.R | 3 R/flux_fitting_zhao18.R | 3 R/flux_flag_count.R | 30 - R/flux_fortify.R | 13 R/flux_gep.R | 3 R/flux_gpp.R | 14 R/flux_lrc.R | 17 R/flux_match.R | 65 -- R/flux_plot.R | 27 - R/flux_quality.R | 82 ++- R/flux_units.R | 12 R/stupeflux.R | 18 README.md | 49 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/data-prep.Rmd | 1 inst/doc/data-prep.html | 5 inst/doc/fluxible.R | 4 inst/doc/fluxible.Rmd | 6 inst/doc/fluxible.html | 82 +-- inst/doc/li7500.html | 16 inst/doc/two-gases.html | 2 inst/doc/vol_conc.R |only inst/doc/vol_conc.Rmd |only inst/doc/vol_conc.html |only man/check_bare_col.Rd |only man/figures/README-short-example-1.png |binary man/flux_calc.Rd | 37 + man/flux_calc_frac.Rd |only man/flux_calc_vol.Rd |only man/flux_conc.Rd |only man/flux_diff.Rd | 4 man/flux_drygas.Rd | 11 man/flux_fitting.Rd | 17 man/flux_flag_count.Rd | 14 man/flux_fortify.Rd | 3 man/flux_gpp.Rd | 7 man/flux_lrc.Rd | 10 man/flux_match.Rd | 28 - man/flux_plot.Rd | 15 man/flux_quality.Rd | 78 +-- man/flux_units.Rd | 3 man/fluxible-package.Rd | 1 man/stupeflux.Rd | 12 tests/testthat/_snaps/flux_calc.md | 31 - tests/testthat/_snaps/flux_conc.md |only tests/testthat/_snaps/flux_fitting.md | 52 +- tests/testthat/_snaps/flux_flag_count.md | 46 - tests/testthat/_snaps/flux_plot.md | 256 ---------- tests/testthat/_snaps/flux_plot/facet-ordering.svg |only tests/testthat/_snaps/flux_plot/flux-diff-and-lm.svg | 26 - tests/testthat/_snaps/flux_plot/ggssave-and-print.svg | 58 +- tests/testthat/_snaps/flux_plot/plot-as-an-object.svg | 58 +- tests/testthat/_snaps/flux_plot/plot-for-exp-hm-fit.svg | 72 +- tests/testthat/_snaps/flux_plot/plot-for-exp-tz-fit-with-mid-missing-data.svg | 32 - tests/testthat/_snaps/flux_plot/plot-for-exp-tz-fit.svg | 32 - tests/testthat/_snaps/flux_plot/plot-for-kappamax-fit.svg | 94 +-- tests/testthat/_snaps/flux_plot/plot-for-linear-fit.svg | 58 +- tests/testthat/_snaps/flux_plot/plot-for-quadratic-fit-with-mid-missing-data.svg | 44 - tests/testthat/_snaps/flux_plot/plot-with-custom-facet-id.svg | 58 +- tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-exp-hm.svg | 10 tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-exp-tz.svg | 12 tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-quadratic.svg | 10 tests/testthat/test-flux_calc.R | 38 + tests/testthat/test-flux_conc.R |only tests/testthat/test-flux_fitting.R | 16 tests/testthat/test-flux_match.R | 64 -- tests/testthat/test-flux_plot.R | 81 +-- tests/testthat/test-flux_quality.R | 8 tests/testthat/test-flux_units.R | 9 vignettes/data-prep.Rmd | 1 vignettes/ex_data/sample_vol_conc.csv |only vignettes/fluxible.Rmd | 6 vignettes/vol_conc.Rmd |only 89 files changed, 1092 insertions(+), 1133 deletions(-)
Title: Estimation of Life Expectancies Using Multi-State Models
Description: Functions to compute state-specific and marginal life expectancies. The computation is based on a fitted continuous-time multi-state model that includes an absorbing death state; see Van den Hout (2017, ISBN:9781466568402). The fitted multi-state model model should be estimated using the 'msm' package using age as the time-scale.
Author: Ardo van den Hout [aut, cre],
Mei Sum Chan [aut]
Maintainer: Ardo van den Hout <ardo.vandenhout@ucl.ac.uk>
Diff between elect versions 1.2 dated 2019-04-03 and 1.2.1 dated 2026-07-22
DESCRIPTION | 18 +++++++++++++----- MD5 | 8 ++++---- NEWS | 5 +++++ man/electData.Rd | 4 ++-- man/summary.elect.Rd | 2 +- 5 files changed, 25 insertions(+), 12 deletions(-)
Title: Goodness-of-Fit and Calibration Tests for Logistic Regression
Description: Provides a unified battery of goodness-of-fit and calibration tests
for binary logistic regression, runnable in a single call via
'run.all.gof()'. The package introduces the author's own tests aimed at
sparse data --- the omnibus Ebrahim-Farrington (EF) test, the Directed EF
('EDGE') test that targets smooth calibration-shape departures, and a
Cauchy-combination ensemble --- and aggregates a wide range of classical and
modern tests for comparison, including Hosmer-Lemeshow, McCullagh,
Osius-Rojek, le Cessie-van Houwelingen, Stute-Zhu, the binary-adaptive
'BAGofT' test, and the 'GiViTI' calibration test (each obtained from its own
package, where installed, and attributed to its authors). The tools are
particularly suited to sparse data, where the Hosmer-Lemeshow test loses
power. For more details see Hosmer (1980) <doi:10.1080/03610928008827941> and
Farrington (1996) <doi:10.1111/j.2517-6161.1996.tb02086.x>.
Author: Ebrahim Khaled Ebrahim [aut, cre]
Maintainer: Ebrahim Khaled Ebrahim <ebrahimkhaled@alexu.edu.eg>
Diff between ebrahim.gof versions 2.1.0 dated 2026-06-17 and 2.4.0 dated 2026-07-22
DESCRIPTION | 40 +- MD5 | 42 ++- NAMESPACE | 3 NEWS.md | 106 +++++++ R/data.R |only R/def_ensemble_gof.R | 29 ++ R/def_gof.R | 5 R/ebrahim.gof-package.R |only R/edge_gof.R |only R/install_suggests.R |only R/run_all_gof.R | 442 ++++++++++++++++++++++++++++----- R/zzz.R |only README.md | 149 ++++++++++- build/partial.rdb |only build/vignette.rds |binary data |only inst/CITATION |only inst/doc/ebrahim-farrington-intro.html | 99 +++---- inst/doc/ebrahim-gof-toolbox.R |only inst/doc/ebrahim-gof-toolbox.Rmd |only inst/doc/ebrahim-gof-toolbox.html |only man/def.gof.Rd | 5 man/ebrahim.gof-package.Rd |only man/edge.gof.Rd |only man/edges.gof.Rd |only man/gof_demo.Rd |only man/gof_demo_grouped.Rd |only man/gof_install_suggests.Rd |only man/run.all.gof.Rd | 134 +++++++++- tests/testthat/test-parallel.R |only vignettes/ebrahim-gof-toolbox.Rmd |only 31 files changed, 891 insertions(+), 163 deletions(-)
Title: Conway-Maxwell Poisson (COM-Poisson) Regression
Description: Fit Conway-Maxwell Poisson (COM-Poisson or CMP) regression models
to count data (Sellers & Shmueli, 2010) <doi:10.1214/09-AOAS306>. The
package provides functions for model estimation, dispersion testing, and
diagnostics. Zero-inflated CMP regression (Sellers & Raim, 2016)
<doi:10.1016/j.csda.2016.01.007> is also supported.
Author: Kimberly Sellers [aut],
Thomas Lotze [aut],
Andrew Raim [cre, aut]
Maintainer: Andrew Raim <andrew.raim@gmail.com>
Diff between COMPoissonReg versions 0.8.1 dated 2023-11-29 and 0.8.2 dated 2026-07-22
COMPoissonReg-0.8.1/COMPoissonReg/inst/doc/vignette.R |only COMPoissonReg-0.8.1/COMPoissonReg/inst/doc/vignette.Rmd |only COMPoissonReg-0.8.1/COMPoissonReg/inst/doc/vignette.pdf |only COMPoissonReg-0.8.1/COMPoissonReg/man/COMPoissonReg-options.Rd |only COMPoissonReg-0.8.1/COMPoissonReg/vignettes/vignette.Rmd |only COMPoissonReg-0.8.1/COMPoissonReg/vignettes/vignette_files |only COMPoissonReg-0.8.2/COMPoissonReg/DESCRIPTION | 33 +++- COMPoissonReg-0.8.2/COMPoissonReg/MD5 | 72 +++------- COMPoissonReg-0.8.2/COMPoissonReg/NEWS.md |only COMPoissonReg-0.8.2/COMPoissonReg/R/S3methods.R | 2 COMPoissonReg-0.8.2/COMPoissonReg/R/cmp-reg.R | 38 ++--- COMPoissonReg-0.8.2/COMPoissonReg/R/cmp.R | 6 COMPoissonReg-0.8.2/COMPoissonReg/R/glm.R | 39 ++--- COMPoissonReg-0.8.2/COMPoissonReg/R/helpers.R | 65 +++++---- COMPoissonReg-0.8.2/COMPoissonReg/R/package.R | 31 ---- COMPoissonReg-0.8.2/COMPoissonReg/R/util.R | 2 COMPoissonReg-0.8.2/COMPoissonReg/R/zicmp-reg.R | 41 ++--- COMPoissonReg-0.8.2/COMPoissonReg/R/zicmp.R | 4 COMPoissonReg-0.8.2/COMPoissonReg/R/zip.R | 2 COMPoissonReg-0.8.2/COMPoissonReg/build/vignette.rds |binary COMPoissonReg-0.8.2/COMPoissonReg/inst/doc/COMPoissonReg.R |only COMPoissonReg-0.8.2/COMPoissonReg/inst/doc/COMPoissonReg.pdf |only COMPoissonReg-0.8.2/COMPoissonReg/inst/doc/COMPoissonReg.qmd |only COMPoissonReg-0.8.2/COMPoissonReg/man/CMP-Distribution.Rd | 4 COMPoissonReg-0.8.2/COMPoissonReg/man/COMPoissonReg-package.Rd | 14 + COMPoissonReg-0.8.2/COMPoissonReg/man/ZICMP-Distribution.Rd | 4 COMPoissonReg-0.8.2/COMPoissonReg/man/get.control.Rd | 14 + COMPoissonReg-0.8.2/COMPoissonReg/man/glm.cmp-CMP-support.Rd | 24 +-- COMPoissonReg-0.8.2/COMPoissonReg/man/glm.cmp-ZICMP-support.Rd | 17 +- COMPoissonReg-0.8.2/COMPoissonReg/man/glm.cmp-raw.Rd | 6 COMPoissonReg-0.8.2/COMPoissonReg/man/glm.cmp.Rd | 2 COMPoissonReg-0.8.2/COMPoissonReg/src/cmp.cpp | 4 COMPoissonReg-0.8.2/COMPoissonReg/vignettes/COMPoissonReg.qmd |only COMPoissonReg-0.8.2/COMPoissonReg/vignettes/common.sty | 58 ++++++-- 34 files changed, 259 insertions(+), 223 deletions(-)
Title: Extensible Framework for Data Pattern Exploration
Description: A framework for systematic exploration of
association rules (Agrawal et al., 1994, <https://www.vldb.org/conf/1994/P487.PDF>),
contrast patterns (Chen, 2022, <doi:10.48550/arXiv.2209.13556>),
emerging patterns (Dong et al., 1999, <doi:10.1145/312129.312191>),
subgroup discovery (Atzmueller, 2015, <doi:10.1002/widm.1144>),
and conditional correlations (Hájek, 1978, <doi:10.1007/978-3-642-66943-9>).
User-defined functions may also be supplied to guide custom pattern searches.
Supports both crisp (Boolean) and fuzzy data. Generates candidate conditions
expressed as elementary conjunctions, evaluates them on a dataset, and
inspects the induced sub-data for statistical, logical, or structural
properties such as associations, correlations, or contrasts. Includes methods
for visualization of logical structures and supports interactive exploration
through integrated Shiny applications.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between nuggets versions 2.2.1 dated 2026-06-10 and 2.2.2 dated 2026-07-22
nuggets-2.2.1/nuggets/src/dig/TautologyTree.h |only nuggets-2.2.1/nuggets/src/test-dig-TautologyTree.cpp |only nuggets-2.2.2/nuggets/DESCRIPTION | 12 nuggets-2.2.2/nuggets/MD5 | 101 nuggets-2.2.2/nuggets/NAMESPACE | 1 nuggets-2.2.2/nuggets/NEWS.md | 144 - nuggets-2.2.2/nuggets/R/cluster_associations.R | 4 nuggets-2.2.2/nuggets/R/dig.R | 22 nuggets-2.2.2/nuggets/R/dig_associations.R | 19 nuggets-2.2.2/nuggets/R/dig_baseline_contrasts.R | 12 nuggets-2.2.2/nuggets/R/dig_complement_contrasts.R | 12 nuggets-2.2.2/nuggets/R/dig_correlations.R | 12 nuggets-2.2.2/nuggets/R/dig_grid.R | 12 nuggets-2.2.2/nuggets/R/dig_paired_baseline_contrasts.R | 12 nuggets-2.2.2/nuggets/R/dig_tautologies.R | 45 nuggets-2.2.2/nuggets/R/helper-format_percent.R |only nuggets-2.2.2/nuggets/R/nuggets-package.R | 1 nuggets-2.2.2/nuggets/R/parse_condition.R | 5 nuggets-2.2.2/nuggets/R/partition.R | 11 nuggets-2.2.2/nuggets/R/ui-associationsClusterModule.R | 138 + nuggets-2.2.2/nuggets/R/ui-exploreApp.R | 20 nuggets-2.2.2/nuggets/R/ui-numericFilterModule.R | 2 nuggets-2.2.2/nuggets/R/ui-variableFilterModule.R | 2 nuggets-2.2.2/nuggets/build/partial.rdb |binary nuggets-2.2.2/nuggets/build/vignette.rds |binary nuggets-2.2.2/nuggets/inst/doc/association-rules.R |only nuggets-2.2.2/nuggets/inst/doc/association-rules.Rmd |only nuggets-2.2.2/nuggets/inst/doc/association-rules.html |only nuggets-2.2.2/nuggets/inst/doc/data-preparation.R | 51 nuggets-2.2.2/nuggets/inst/doc/data-preparation.Rmd | 218 + nuggets-2.2.2/nuggets/inst/doc/data-preparation.html | 1471 +++++++----- nuggets-2.2.2/nuggets/inst/doc/nuggets.Rmd | 4 nuggets-2.2.2/nuggets/inst/doc/nuggets.html | 7 nuggets-2.2.2/nuggets/man/dig.Rd | 22 nuggets-2.2.2/nuggets/man/dig_associations.Rd | 19 nuggets-2.2.2/nuggets/man/dig_baseline_contrasts.Rd | 12 nuggets-2.2.2/nuggets/man/dig_complement_contrasts.Rd | 12 nuggets-2.2.2/nuggets/man/dig_correlations.Rd | 12 nuggets-2.2.2/nuggets/man/dig_grid.Rd | 12 nuggets-2.2.2/nuggets/man/dig_paired_baseline_contrasts.Rd | 12 nuggets-2.2.2/nuggets/man/dig_tautologies.Rd | 24 nuggets-2.2.2/nuggets/man/nuggets-package.Rd | 4 nuggets-2.2.2/nuggets/src/Makevars | 3 nuggets-2.2.2/nuggets/src/dig.cpp | 123 - nuggets-2.2.2/nuggets/src/dig/BaseChain.h | 33 nuggets-2.2.2/nuggets/src/dig/Clause.h | 9 nuggets-2.2.2/nuggets/src/dig/DeductionEngine.h |only nuggets-2.2.2/nuggets/src/dig/Digger.h | 70 nuggets-2.2.2/nuggets/src/dig/SparseBitChain.h |only nuggets-2.2.2/nuggets/src/test-dig-DeductionEngine.cpp |only nuggets-2.2.2/nuggets/src/test-dig-SparseBitChain.cpp |only nuggets-2.2.2/nuggets/tests/testthat/test-dig.R | 91 nuggets-2.2.2/nuggets/tests/testthat/test-parse_condition.R | 2 nuggets-2.2.2/nuggets/tests/testthat/test-partition.R | 320 +- nuggets-2.2.2/nuggets/vignettes/association-rules.Rmd |only nuggets-2.2.2/nuggets/vignettes/data-preparation.Rmd | 218 + nuggets-2.2.2/nuggets/vignettes/nuggets.Rmd | 4 57 files changed, 2207 insertions(+), 1133 deletions(-)
Title: Langa-Weir Classification of Cognitive Function for 2022 HRS
Data
Description: Generates the Langa-Weir classification of cognitive function for
the 2022 Health and Retirement Study (HRS) cognition data. It is
particularly useful for researchers studying cognitive aging who wish to
work with the most recent release of HRS data. The package provides
user-friendly functions for data preprocessing, scoring, and classification
allowing users to easily apply the Langa-Weir classification system.
For details regarding the;
HRS <https://hrsdata.isr.umich.edu/> and
Langa-Weir classifications <https://hrsdata.isr.umich.edu/data-products/langa-weir-classification-cognitive-function-1995-2022>.
Author: Cormac Monaghan [cph, aut, cre] ,
Rafael de Andrade Moral [aut] ,
Joanna McHugh Power [aut]
Maintainer: Cormac Monaghan <cormacmonaghan@protonmail.com>
Diff between lwc2022 versions 1.0.0 dated 2024-11-20 and 1.0.1 dated 2026-07-22
DESCRIPTION | 32 ++--- LICENSE | 4 MD5 | 52 ++++---- NAMESPACE | 28 ++-- R/classify.R | 146 ++++++++++++---------- R/data.R | 169 +++++++++++++------------- R/extract.R | 95 +++++++------- R/globals.R | 42 +++--- R/score.R | 175 +++++++++++++++------------ R/score_recall.R | 56 ++++---- R/score_subtraction.R | 68 +++++----- build/vignette.rds |binary inst/doc/example_data.R | 18 +- inst/doc/example_data.Rmd | 287 ++++++++++++++++++++++----------------------- inst/doc/example_data.html | 27 ++-- inst/doc/lwc2022.R | 7 - inst/doc/lwc2022.Rmd | 186 ++++++++++++++--------------- inst/doc/lwc2022.html | 90 +++++++------- man/classify.Rd | 80 ++++++------ man/cog_data.Rd | 136 ++++++++++----------- man/cog_data_score.Rd | 70 +++++----- man/extract.Rd | 80 ++++++------ man/score.Rd | 78 ++++++------ man/score_recall.Rd | 68 +++++----- man/score_subtraction.Rd | 80 ++++++------ vignettes/example_data.Rmd | 287 ++++++++++++++++++++++----------------------- vignettes/lwc2022.Rmd | 186 ++++++++++++++--------------- 27 files changed, 1299 insertions(+), 1248 deletions(-)
Title: Fast Library for Number Theory
Description: An R interface to 'FLINT' <https://flintlib.org/>, a C library for
number theory. 'FLINT' extends GNU 'MPFR' <https://www.mpfr.org/>
and GNU 'MP' <https://gmplib.org/> with support for operations on
standard rings (the integers, the integers modulo n, finite
fields, the rational, p-adic, real, and complex numbers) as well
as matrices and polynomials over rings. 'FLINT' implements
midpoint-radius interval arithmetic, also known as ball
arithmetic, in the real and complex numbers, enabling computation
in arbitrary precision with rigorous propagation of rounding and
other errors; see Johansson (2017) <doi:10.1109/TC.2017.2690633>.
Finally, 'FLINT' provides ball arithmetic implementations of many
special mathematical functions, with high coverage of reference
works such as the NIST Digital Library of Mathematical Functions
<https://dlmf.nist.gov/>. The R interface defines S4 classes,
generic functions, and methods for representation and basic
operations as [...truncated...]
Author: Mikael Jagan [aut, cre] ,
Martin Maechler [ctb]
Maintainer: Mikael Jagan <jaganmn2@gmail.com>
Diff between flint versions 0.1.4 dated 2025-12-19 and 0.1.5 dated 2026-07-22
DESCRIPTION | 12 ++++++------ MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- R/acb_special.R | 16 ++++++++-------- R/flint.R | 38 ++++++++++++++++++++++++++++++++++---- build/partial.rdb |binary configure | 34 +++++++++++++++++----------------- configure.ac | 6 +++--- inst/NEWS.Rd | 33 ++++++++++++++++++++++++++++----- man/flint-class.Rd | 13 +++++++++++-- src/flint.h | 3 +++ src/utils.c | 33 ++++++++++++++++++++++++++------- tests/reg-tests.R | 6 ++++++ 13 files changed, 155 insertions(+), 65 deletions(-)
Title: Co-Occurrence Network Construction and Manipulation
Description: Constructs co-occurrence networks from several types of input
data, such as delimited fields, long/bipartite tables, binary
matrices, or wide sequences. Returns tidy edge data frames and
supports optional scaling, splitting into several networks,
thresholding, and subsetting. Provides eight similarity measures,
including Jaccard, cosine, and association strength. Supports export
to several network and file formats. Network construction and
analysis methods follow Saqr, Lopez-Pernas, Conde, and
Hernandez-Garcia (2024, <doi:10.1007/978-3-031-54464-4_15>).
Author: Mohammed Saqr [aut, cre, cph],
Sonsoles Lopez-Pernas [aut, cph],
Kamila Misiejuk [aut, cph]
Maintainer: Mohammed Saqr <saqr@saqr.me>
Diff between cooccure versions 0.1.1 dated 2026-04-24 and 0.4.0 dated 2026-07-22
DESCRIPTION | 6 MD5 | 41 - NAMESPACE | 2 NEWS.md | 137 +++ R/converters.R | 29 R/cooccurrence.R | 824 +++++++++++++++++++++-- R/data.R | 19 R/methods.R | 409 ++++++++++- data/demo.rda |binary inst/WORDLIST | 11 inst/doc/imdb-tutorial.R | 6 inst/doc/imdb-tutorial.Rmd | 11 inst/doc/imdb-tutorial.html | 967 +++++++++++++++------------ man/as.data.frame.summary.cooccurrence.Rd |only man/cooccurrence.Rd | 150 ++++ man/demo.Rd | 19 man/plot.cooccurrence.Rd | 11 man/print.cooccurrence.Rd | 2 man/print.summary.cooccurrence.Rd |only man/summary.cooccurrence.Rd | 18 tests/testthat/test-cooccurrence.R | 974 +++++++++++++++++++++++++++- tests/testthat/test-nestimate-equivalence.R |only vignettes/imdb-tutorial.Rmd | 11 23 files changed, 3034 insertions(+), 613 deletions(-)
Title: Comparison of Variance - Covariance Patterns
Description: Comparison of variance - covariance patterns using relative principal component analysis (relative eigenanalysis), as described in Le Maitre and Mitteroecker (2019) <doi:10.1111/2041-210X.13253>. Also provides functions to compute group covariance matrices, distance matrices, and perform proportionality tests. A worked sample on the body shape of cichlid fishes is included, based on the dataset from Kerschbaumer et al. (2013) <doi:10.5061/dryad.fc02f>.
Author: Anne Le Maitre [aut, cre] ,
Philipp Mitteroecker [aut]
Maintainer: Anne Le Maitre <anne.le.maitre@univie.ac.at>
Diff between vcvComp versions 1.0.2 dated 2020-12-17 and 1.0.3 dated 2026-07-22
vcvComp-1.0.2/vcvComp/NEWS |only vcvComp-1.0.3/vcvComp/DESCRIPTION | 22 vcvComp-1.0.3/vcvComp/MD5 | 23 vcvComp-1.0.3/vcvComp/NEWS.md |only vcvComp-1.0.3/vcvComp/R/Tropheus-IK-coord-dataset.R | 20 vcvComp-1.0.3/vcvComp/R/Tropheus-dataset.R | 22 vcvComp-1.0.3/vcvComp/R/relative.eigen.R | 2 vcvComp-1.0.3/vcvComp/build/partial.rdb |only vcvComp-1.0.3/vcvComp/build/vignette.rds |binary vcvComp-1.0.3/vcvComp/inst/CITATION | 4 vcvComp-1.0.3/vcvComp/inst/doc/vcvComp-worked-example.html | 1128 +++++++++---- vcvComp-1.0.3/vcvComp/man/Tropheus.IK.coord.Rd | 20 vcvComp-1.0.3/vcvComp/man/Tropheus.Rd | 22 vcvComp-1.0.3/vcvComp/man/relative.eigen.Rd | 2 14 files changed, 859 insertions(+), 406 deletions(-)
Title: Distributions Compatible with Automatic Differentiation by
'RTMB'
Description: Extends the functionality of the 'RTMB' <https://kaskr.r-universe.dev/RTMB> package by providing a collection of non-standard probability distributions compatible with automatic differentiation (AD). While 'RTMB' enables flexible and efficient modelling, including random effects, its built-in support is limited to standard distributions. The package adds additional AD-compatible distributions, broadening the range of models that can be implemented and estimated using 'RTMB'. Automatic differentiation and Laplace approximation are described in Kristensen et al. (2016) <doi:10.18637/jss.v070.i05>.
Author: Jan-Ole Fischer [aut, cre]
Maintainer: Jan-Ole Fischer <jan-ole.fischer@mailbox.org>
This is a re-admission after prior archival of version 1.0.4 dated 2026-04-09
Diff between RTMBdist versions 1.0.4 dated 2026-04-09 and 1.0.5 dated 2026-07-22
RTMBdist-1.0.4/RTMBdist/tests/testthat/test-myfunction.R |only RTMBdist-1.0.5/RTMBdist/DESCRIPTION | 8 RTMBdist-1.0.5/RTMBdist/MD5 | 306 ++++++---- RTMBdist-1.0.5/RTMBdist/NAMESPACE | 14 RTMBdist-1.0.5/RTMBdist/R/aaa_utils.R | 22 RTMBdist-1.0.5/RTMBdist/R/bccg.R | 16 RTMBdist-1.0.5/RTMBdist/R/bcpe.R | 34 - RTMBdist-1.0.5/RTMBdist/R/bct.R | 14 RTMBdist-1.0.5/RTMBdist/R/beta2.R | 8 RTMBdist-1.0.5/RTMBdist/R/betabinom.R | 2 RTMBdist-1.0.5/RTMBdist/R/betaprime.R | 2 RTMBdist-1.0.5/RTMBdist/R/dirichlet.R | 5 RTMBdist-1.0.5/RTMBdist/R/dirmult.R | 3 RTMBdist-1.0.5/RTMBdist/R/exgauss.R | 12 RTMBdist-1.0.5/RTMBdist/R/foldnorm.R | 2 RTMBdist-1.0.5/RTMBdist/R/gamma2.R | 3 RTMBdist-1.0.5/RTMBdist/R/gengamma.R | 4 RTMBdist-1.0.5/RTMBdist/R/genpois.R | 2 RTMBdist-1.0.5/RTMBdist/R/gmrf.R | 14 RTMBdist-1.0.5/RTMBdist/R/gompertz.R |only RTMBdist-1.0.5/RTMBdist/R/gumbel.R | 2 RTMBdist-1.0.5/RTMBdist/R/invchisq.R | 6 RTMBdist-1.0.5/RTMBdist/R/invgamma.R | 5 RTMBdist-1.0.5/RTMBdist/R/invgauss.R | 1 RTMBdist-1.0.5/RTMBdist/R/kumar.R | 15 RTMBdist-1.0.5/RTMBdist/R/laplace.R | 2 RTMBdist-1.0.5/RTMBdist/R/llogis.R |only RTMBdist-1.0.5/RTMBdist/R/mcreport.R | 14 RTMBdist-1.0.5/RTMBdist/R/mvt.R | 3 RTMBdist-1.0.5/RTMBdist/R/nbinom2.R | 36 - RTMBdist-1.0.5/RTMBdist/R/oibeta.R | 8 RTMBdist-1.0.5/RTMBdist/R/oibeta2.R | 5 RTMBdist-1.0.5/RTMBdist/R/pareto.R | 6 RTMBdist-1.0.5/RTMBdist/R/pgweibull.R | 6 RTMBdist-1.0.5/RTMBdist/R/powerexp.R | 14 RTMBdist-1.0.5/RTMBdist/R/skewnorm.R | 20 RTMBdist-1.0.5/RTMBdist/R/skewnorm2.R | 16 RTMBdist-1.0.5/RTMBdist/R/skewt.R | 18 RTMBdist-1.0.5/RTMBdist/R/skewt2.R | 4 RTMBdist-1.0.5/RTMBdist/R/t2.R | 18 RTMBdist-1.0.5/RTMBdist/R/truncnorm.R | 6 RTMBdist-1.0.5/RTMBdist/R/trunct.R | 3 RTMBdist-1.0.5/RTMBdist/R/trunct2.R | 2 RTMBdist-1.0.5/RTMBdist/R/vm.R | 13 RTMBdist-1.0.5/RTMBdist/R/vmf.R | 7 RTMBdist-1.0.5/RTMBdist/R/vmf2.R | 6 RTMBdist-1.0.5/RTMBdist/R/wishart.R | 4 RTMBdist-1.0.5/RTMBdist/R/wrpcauchy.R | 2 RTMBdist-1.0.5/RTMBdist/R/zibeta.R | 5 RTMBdist-1.0.5/RTMBdist/R/zibeta2.R | 3 RTMBdist-1.0.5/RTMBdist/R/zibinom.R | 3 RTMBdist-1.0.5/RTMBdist/R/zigamma.R | 3 RTMBdist-1.0.5/RTMBdist/R/zigamma2.R | 13 RTMBdist-1.0.5/RTMBdist/R/ziinvgauss.R | 6 RTMBdist-1.0.5/RTMBdist/R/zilnorm.R | 3 RTMBdist-1.0.5/RTMBdist/R/zinbinom.R | 5 RTMBdist-1.0.5/RTMBdist/R/zinbinom2.R | 3 RTMBdist-1.0.5/RTMBdist/R/zipois.R | 3 RTMBdist-1.0.5/RTMBdist/R/ziweibull.R | 3 RTMBdist-1.0.5/RTMBdist/R/zoibeta.R | 8 RTMBdist-1.0.5/RTMBdist/R/zoibeta2.R | 4 RTMBdist-1.0.5/RTMBdist/README.md | 5 RTMBdist-1.0.5/RTMBdist/build/vignette.rds |binary RTMBdist-1.0.5/RTMBdist/inst/doc/Examples.R | 63 +- RTMBdist-1.0.5/RTMBdist/inst/doc/Examples.Rmd | 71 +- RTMBdist-1.0.5/RTMBdist/inst/doc/Examples.html | 134 ++-- RTMBdist-1.0.5/RTMBdist/inst/doc/adding-a-distribution.R |only RTMBdist-1.0.5/RTMBdist/inst/doc/adding-a-distribution.Rmd |only RTMBdist-1.0.5/RTMBdist/inst/doc/adding-a-distribution.html |only RTMBdist-1.0.5/RTMBdist/inst/doc/distlist.Rmd | 4 RTMBdist-1.0.5/RTMBdist/inst/doc/distlist.html | 6 RTMBdist-1.0.5/RTMBdist/man/bccg.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/bcpe.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/bct.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/beta2.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/betabinom.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/betaprime.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/dirichlet.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/dirmult.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/exgauss.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/figures/README-sim_residuals-1.png |binary RTMBdist-1.0.5/RTMBdist/man/foldnorm.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/gamma2.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/gengamma.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/genpois.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/gompertz.Rd |only RTMBdist-1.0.5/RTMBdist/man/gumbel.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/invchisq.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/invgamma.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/invgauss.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/kumar.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/laplace.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/llogis.Rd |only RTMBdist-1.0.5/RTMBdist/man/mcreport.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/mvt.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/nbinom2.Rd | 8 RTMBdist-1.0.5/RTMBdist/man/oibeta.Rd | 5 RTMBdist-1.0.5/RTMBdist/man/oibeta2.Rd | 5 RTMBdist-1.0.5/RTMBdist/man/pareto.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/pgweibull.Rd | 9 RTMBdist-1.0.5/RTMBdist/man/powerexp.Rd | 7 RTMBdist-1.0.5/RTMBdist/man/skewnorm.Rd | 11 RTMBdist-1.0.5/RTMBdist/man/skewnorm2.Rd | 12 RTMBdist-1.0.5/RTMBdist/man/skewt.Rd | 5 RTMBdist-1.0.5/RTMBdist/man/skewt2.Rd | 12 RTMBdist-1.0.5/RTMBdist/man/t2.Rd | 11 RTMBdist-1.0.5/RTMBdist/man/truncnorm.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/trunct.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/trunct2.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/vm.Rd | 17 RTMBdist-1.0.5/RTMBdist/man/vmf.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/wishart.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/wrpcauchy.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/zibeta.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zibeta2.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zibinom.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zigamma.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zigamma2.Rd | 11 RTMBdist-1.0.5/RTMBdist/man/ziinvgauss.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zilnorm.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zinbinom.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zinbinom2.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zipois.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/ziweibull.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zoibeta.Rd | 5 RTMBdist-1.0.5/RTMBdist/man/zoibeta2.Rd | 4 RTMBdist-1.0.5/RTMBdist/tests/testthat/helper-distcheck.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-bccg.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-bcpe.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-bct.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-beta2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-betabinom.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-betaprime.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-dirichlet.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-dirmult.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-exgauss.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-foldnorm.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-gamma2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-gengamma.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-genpois.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-gmrf.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-gompertz.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-gumbel.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-invchisq.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-invgamma.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-invgauss.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-kumar.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-laplace.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-llogis.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-mvt.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-nbinom2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-oibeta.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-oibeta2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-pgweibull.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-powerexp.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-skellam.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-skewnorm.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-skewnorm2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-skewt.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-skewt2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-t2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-truncnorm.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-trunct.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-trunct2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-vm.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-vmf.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-vmf2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-wishart.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-wrpcauchy.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zibeta.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zibinom.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zigamma.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zigamma2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-ziinvgauss.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zilnorm.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zinbinom.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zinbinom2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zipois.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-ziweibull.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zoibeta.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zoibeta2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-ztbinom.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-ztnbinom.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-ztnbinom2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-ztpois.R |only RTMBdist-1.0.5/RTMBdist/vignettes/Examples.Rmd | 71 +- RTMBdist-1.0.5/RTMBdist/vignettes/adding-a-distribution.Rmd |only RTMBdist-1.0.5/RTMBdist/vignettes/distlist.Rmd | 4 188 files changed, 940 insertions(+), 426 deletions(-)
Title: Nonparametric Hazard Rate Estimation
Description: Provides functions and examples for histogram, kernel (classical, variable bandwidth and transformations based, see e.g. Bagkavos (2008), <doi:10.1080/10485250802440184>, discrete and semiparametric hazard rate estimators.
Author: Dimitrios Bagkavos [aut, cre]
Maintainer: Dimitrios Bagkavos <dimitrios.bagkavos@gmail.com>
Diff between NPHazardRate versions 0.1 dated 2018-11-02 and 0.3 dated 2026-07-22
DESCRIPTION | 12 ++-- MD5 | 18 +++--- man/DefVarBandRule.Rd | 10 --- man/DiscHazRateAuxFunctions.Rd | 19 +----- man/NP.M.Estimate.Rd | 2 man/SimpsonInt.Rd | 2 man/TransHazRateEst.Rd | 17 +---- man/TutzPritscher.Rd | 121 ++++++++++++++++++----------------------- man/VarBandHazEst.Rd | 9 +-- man/WeibHazFunctionals.Rd | 2 10 files changed, 87 insertions(+), 125 deletions(-)
Title: Numerical Tools for 'Rcpp' and Lambda Functions
Description: Provides a 'C++' API for routinely used numerical tools such as integration,
root-finding, and optimization, where function arguments are given as
lambdas. This facilitates 'Rcpp' programming, enabling the development of
'R'-like code in 'C++' where functions can be defined on the fly and use
variables in the surrounding environment.
Author: Andrew M. Raim [aut, cre]
Maintainer: Andrew M. Raim <andrew.raim@gmail.com>
Diff between fntl versions 0.1.2 dated 2024-11-12 and 0.1.3 dated 2026-07-22
DESCRIPTION | 14 MD5 | 111 NAMESPACE | 2 NEWS.md | 6 R/RcppExports.R | 37 build/vignette.rds |binary inst/doc/examples |only inst/doc/fntl.R | 74 inst/doc/fntl.pdf |binary inst/doc/fntl.qmd | 714 +++--- inst/include/args.h | 6 inst/include/findroot-bisect.h | 6 inst/include/findroot-brent.h | 6 inst/include/goldensection.h | 2 inst/include/gradient.h | 4 inst/include/integrate.h | 2 inst/include/jacobian.h | 4 inst/include/log-sum-exp.h | 4 inst/include/optimize-brent.h | 2 inst/include/outer.h | 61 inst/include/result.h | 43 inst/include/trunc.h | 69 inst/include/typedefs-rcpp.h | 1 inst/include/util.h | 30 inst/tinytest/test-outer.R |only man/fntl-package.Rd | 5 man/outer.Rd | 32 src/RcppExports.cpp | 29 src/rcpp-interface.cpp | 39 src/rcpp-interface.h | 38 vignettes/.install_extras |only vignettes/common.sty | 2 vignettes/examples/arma.cpp |only vignettes/examples/first.cpp | 2 vignettes/examples/logger.cpp |only vignettes/examples/outer-sp.cpp |only vignettes/examples/outer.cpp | 11 vignettes/fntl.html | 4444 +++++++++++++++++++++++++++++++++++----- vignettes/fntl.html.md |only vignettes/fntl.qmd | 714 +++--- vignettes/references.bib | 66 41 files changed, 5323 insertions(+), 1257 deletions(-)
Title: VCG Sampling using Energy-Based Covariate Balancing
Description: Provides a principled framework for sampling Virtual Control Group (VCG) using energy distance-based covariate balancing. The package offers visualization tools to assess covariate balance and includes a permutation test to evaluate the statistical significance of observed deviations.
Author: Andreas Schulz [aut, cre] ,
Sanofi [cph, fnd]
Maintainer: Andreas Schulz <andreas.schulz2@sanofi.com>
Diff between eVCGsampler versions 1.1.0 dated 2026-07-06 and 1.1.2 dated 2026-07-22
DESCRIPTION | 6 +-- MD5 | 19 +++++----- NEWS.md |only R/VCG_sampler.R | 59 +++++++++++++++++++++++++++++--- R/combine_variables.R | 4 +- R/energy_distance.R | 2 - R/find_outliers.R | 4 +- R/robust_scale.R | 19 ++++++---- inst/doc/eVCGsampler_user_guide.html | 56 +++++++++++++++--------------- man/robust_scale.Rd | 5 +- tests/testthat/test-combine_variables.R | 2 - 11 files changed, 117 insertions(+), 59 deletions(-)
Title: Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as
calculating spectral indexes, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [aut] ,
Ned Horning [aut],
Jakob Schwalb-Willmann [aut] ,
Robert J. Hijmans [ctb] ,
Konstantin Mueller [aut, cre]
Maintainer: Konstantin Mueller <konstantinfinn.mueller@gmx.de>
Diff between RStoolbox versions 1.0.2.2 dated 2025-10-02 and 1.0.2.3 dated 2026-07-22
DESCRIPTION | 12 +++++------ MD5 | 21 ++++++++++--------- NEWS.md | 6 +++++ R/mesma.R | 39 ++++++++++++++++++++++++------------- README.md | 19 ++++++++---------- man/mesma.Rd | 5 ++-- man/rescaleImage.Rd | 2 - man/spectralIndices.Rd | 26 ------------------------ tests/testthat/Rplots.pdf |only tests/testthat/test-mesma.R | 14 ++++++------- tests/testthat/test-oneHotEncode.R | 6 +++-- tests/testthat/test-superClass.R | 4 +++ 12 files changed, 77 insertions(+), 77 deletions(-)
Title: 'GGML' Tensor Operations for Machine Learning
Description: Provides 'R' bindings to the 'GGML' tensor library for machine
learning, optimized for 'Vulkan' GPU acceleration with a transparent CPU
fallback. The package features a 'Keras'-like sequential API and a
'PyTorch'-style 'autograd' engine for building, training, and deploying
neural networks. Key capabilities include high-performance 5D tensor
operations, 'f16' precision, and efficient quantization. It supports
native 'ONNX' model import (50+ operators) and 'GGUF' weight loading
from the 'llama.cpp' and 'Hugging Face' ecosystems. Designed for
zero-overhead inference via dedicated weight buffering, it integrates
seamlessly as a 'parsnip' engine for 'tidymodels' and provides
first-class learners for the 'mlr3' framework.
See <https://github.com/ggml-org/ggml> for more information about the
underlying library.
Author: Yuri Baramykov [aut, cre] ,
Georgi Gerganov [ctb, cph] ,
Jeffrey Quesnelle [ctb, cph] ,
Bowen Peng [ctb, cph] ,
Mozilla Foundation [ctb, cph]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Diff between ggmlR versions 0.8.1 dated 2026-07-13 and 0.8.2 dated 2026-07-22
DESCRIPTION | 6 +-- MD5 | 19 ++++++------ NEWS.md | 4 ++ R/gpu_linalg.R | 16 ++++++++++ R/sc_contracts.R | 10 ++++++ R/sc_umap.R | 6 +++ README.md | 10 ++++++ inst/examples/profile_tests.R |only tests/testthat.R | 3 + tests/testthat/test-mlr3-autograd.R | 55 ++++++++++++++++++++++++++++++++---- tests/testthat/test-sc-umap.R | 19 +++++------- 11 files changed, 119 insertions(+), 29 deletions(-)
Title: Hasse Diagram of the Layout Structure and Restricted Layout
Structure
Description: Returns a Hasse diagram of the layout structure (Bate and Chatfield (2016)) <doi:10.1080/00224065.2016.11918173> or the restricted layout structure (Bate and Chatfield (2016)) <doi:10.1080/00224065.2016.11918174> of an experimental design.
Author: Damianos Michaelides [aut, cre],
Simon Bate [aut],
Marion Chatfield [aut]
Maintainer: Damianos Michaelides <dm3g15@soton.ac.uk>
Diff between hassediagrams versions 2.0 dated 2026-01-17 and 2.1 dated 2026-07-22
DESCRIPTION | 8 +++---- MD5 | 6 ++--- R/internal.R | 13 +++++++++-- inst/doc/Introduction_to_hassediagrams.html | 32 ++++++++++++---------------- 4 files changed, 32 insertions(+), 27 deletions(-)
Title: Additional Layout Algorithms for Network Visualizations
Description: Several new layout algorithms to visualize networks are provided which are not part of 'igraph'.
Most are based on the concept of stress majorization by Gansner et al. (2004) <doi:10.1007/978-3-540-31843-9_25>.
Some more specific algorithms allow the user to emphasize hidden group structures in networks or focus on specific nodes.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between graphlayouts versions 1.2.4 dated 2026-06-19 and 1.2.5 dated 2026-07-22
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++++-------- NAMESPACE | 2 ++ NEWS.md | 4 ++++ R/RcppExports.R | 8 ++++++++ R/graphlayouts.R | 1 + R/layout_tree.R |only R/layouts.R | 25 +++++++++++++++++++++++++ man/graphlayouts-package.Rd | 6 ++++++ man/layout_tree_unrooted.Rd |only src/RcppExports.cpp | 32 ++++++++++++++++++++++++++++++++ src/unrooted_tree.cpp |only tests/testthat/test-layout_tree.R |only 13 files changed, 93 insertions(+), 11 deletions(-)
Title: Discrete-Time Multistate Models
Description: Discrete-time multistate models with a user-friendly workflow. The package provides tools for processing data, several ways of estimating parametric and nonparametric multistate models, and an extensive set of Markov chain methods which use transition probabilities derived from the multistate model. Some of the implemented methods are described in Schneider et al. (2024) <doi:10.1080/00324728.2023.2176535>, Dudel (2021) <doi:10.1177/0049124118782541>, Dudel & Myrskylä (2020) <doi:10.1186/s12963-020-00217-0>, van den Hout (2017) <doi:10.1201/9781315374321>.
Author: Christian Dudel [aut, cre]
Maintainer: Christian Dudel <dudel@demogr.mpg.de>
Diff between dtms versions 0.4.2 dated 2026-02-25 and 0.5.0 dated 2026-07-22
DESCRIPTION | 8 LICENSE | 4 MD5 | 37 ++-- NAMESPACE | 1 NEWS.md | 13 + R/dtms.R | 3 R/dtms_censoring.R | 6 R/dtms_expectancy.R | 2 R/dtms_impute.R |only R/dtms_matrix.R | 2 R/dtms_transitions.R | 26 ++- README.md | 249 ++++++++++++++++++----------- man/dtms.Rd | 93 +++++----- man/dtms_aggregate.Rd | 106 ++++++------ man/dtms_duration.Rd | 134 +++++++-------- man/dtms_expectancy.Rd | 2 man/dtms_impute.Rd |only man/dtms_matrix.Rd | 2 man/dtms_occurrence.Rd | 140 ++++++++-------- man/dtms_survivor.Rd | 140 ++++++++-------- man/figures/README-regressionpredict-1.png |only 21 files changed, 537 insertions(+), 431 deletions(-)
Title: Alternative and Fast ROC Analysis
Description: Alternative and fast algorithms for the analysis of receiver operating
characteristics curves (ROC curves) as described in Thomas et al. (2017)
<doi:10.1186/s41512-017-0017-y> and Thomas et al. (2023) <doi:10.1016/j.ajogmf.2023.101110>.
Author: Gregoire Thomas [aut, cre] ,
Robin Tuytten [ctb] ,
Jef Moerman [ctb],
Xavier Robin [cph] ,
Stefan Siegert [cph]
Maintainer: Gregoire Thomas <gregoire.thomas@SQU4RE.com>
Diff between alternativeROC versions 1.0.4 dated 2025-11-24 and 1.0.5 dated 2026-07-22
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS | 5 +++++ R/alternativeROC-common-args.R | 4 +++- R/rocperf.R | 20 +++++++++++--------- build/partial.rdb |binary man/alternativeROC-common-args.Rd | 4 ++++ man/alternativeROC-package.Rd | 5 +++++ man/rocperf.Rd | 3 +++ tests/testthat/test_rocperf.R | 10 ++++++++++ 10 files changed, 55 insertions(+), 24 deletions(-)
More information about alternativeROC at CRAN
Permanent link
Title: Uniform Data Model and 'Zarr' Interchange for Single-Cell Omics
Description: A lightweight interchange layer for single-cell and spatial omics
data, built on the L-star model of labelled axes and typed fields over them,
serialized to the 'Zarr' format. Provides bidirectional converters
("profiles") for 'Seurat', 'SingleCellExperiment', 'Conos', and 'pagoda2'
objects, including collections of heterogeneous samples, via a shared C++
core ('libstar') so the same store is readable from R, 'Python', and C++.
Author: Peter Kharchenko [aut, cre]
Maintainer: Peter Kharchenko <pk.restricted@gmail.com>
Diff between lstar versions 0.1.0 dated 2026-06-22 and 0.2.1 dated 2026-07-22
lstar-0.1.0/lstar/man/write_pagoda2.Rd |only lstar-0.2.1/lstar/DESCRIPTION | 14 lstar-0.2.1/lstar/MD5 | 63 - lstar-0.2.1/lstar/NAMESPACE | 6 lstar-0.2.1/lstar/NEWS.md | 131 ++ lstar-0.2.1/lstar/R/backed.R | 8 lstar-0.2.1/lstar/R/cpp11.R | 16 lstar-0.2.1/lstar/R/lstar.R | 28 lstar-0.2.1/lstar/R/profile_pagoda2.R | 134 +- lstar-0.2.1/lstar/R/profile_sce.R | 1 lstar-0.2.1/lstar/R/profile_seurat.R | 91 + lstar-0.2.1/lstar/R/view.R |only lstar-0.2.1/lstar/R/viewer.R |only lstar-0.2.1/lstar/inst/include/libzarr |only lstar-0.2.1/lstar/inst/include/lstar/lstar.hpp | 845 +++++++++++++----- lstar-0.2.1/lstar/man/dot-lstar_drop_cache.Rd |only lstar-0.2.1/lstar/man/extend_for_viewer.Rd |only lstar-0.2.1/lstar/man/lstar_read.Rd | 2 lstar-0.2.1/lstar/man/lstar_write.Rd | 16 lstar-0.2.1/lstar/man/lstar_write_viewer.Rd |only lstar-0.2.1/lstar/man/read_pagoda2.Rd |only lstar-0.2.1/lstar/man/view.Rd |only lstar-0.2.1/lstar/man/viewer_extend.Rd |only lstar-0.2.1/lstar/man/write_seurat.Rd | 11 lstar-0.2.1/lstar/src/Makevars | 24 lstar-0.2.1/lstar/src/cpp11.cpp | 32 lstar-0.2.1/lstar/src/lstar_cpp.cpp | 88 + lstar-0.2.1/lstar/tests/testthat/test-pagoda2.R | 20 lstar-0.2.1/lstar/tests/testthat/test-roundtrip.R | 12 lstar-0.2.1/lstar/tests/testthat/test-view.R |only lstar-0.2.1/lstar/tests/testthat/test-viewer-export.R |only 31 files changed, 1177 insertions(+), 365 deletions(-)
Title: Make Symmetric and Asymmetric ARDL Estimations
Description: Implements estimation procedures for Autoregressive Distributed Lag (ARDL)
and Nonlinear ARDL (NARDL) models, which allow researchers to investigate both
short- and long-run relationships in time series data under mixed orders of integration.
The package supports simultaneous modeling of symmetric and asymmetric regressors,
flexible treatment of short-run and long-run asymmetries, and automated equation handling.
It includes several cointegration testing approaches such as the Pesaran-Shin-Smith F
and t bounds tests, and narayan test.
Methodological foundations are provided in Pesaran, Shin, and Smith (2001)
<doi:10.1016/S0304-4076(01)00049-5> and Shin, Yu, and Greenwood-Nimmo (2014, ISBN:9780123855079).
Author: Huseyin karamelikli [aut, cre] ,
Huseyin Utku Demir [aut]
Maintainer: Huseyin karamelikli <hakperest@gmail.com>
Diff between kardl versions 2.0.4 dated 2026-07-17 and 2.0.5 dated 2026-07-22
DESCRIPTION | 6 MD5 | 32 ++-- R/multipliers.R | 8 - R/print.R | 229 ++++++++++++++------------------ R/tests.R | 11 - inst/doc/intro.R | 6 inst/doc/intro.Rmd | 6 inst/doc/intro.html | 253 +++++++++++++++++------------------- man/bootstrap.Rd | 20 ++ man/ecm.Rd | 16 -- man/kardl.Rd | 16 -- man/mplier.Rd | 5 tests/testthat/Rplots.pdf |binary tests/testthat/test-print-summary.R | 6 tests/testthat/test-print.R | 2 tests/testthat/test-tests.R | 7 vignettes/intro.Rmd | 6 17 files changed, 298 insertions(+), 331 deletions(-)
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' <https://libgit2.org> with
support for SSH and HTTPS remotes. All functions in 'gert' use basic R data
types (such as vectors and data-frames) for their arguments and return values.
User credentials are shared with command line 'git' through the git-credential
store and ssh keys stored on disk or ssh-agent.
Author: Jeroen Ooms [aut, cre] ,
Maelle Salmon [aut] ,
Jennifer Bryan [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between gert versions 2.3.1 dated 2026-01-11 and 2.4.0 dated 2026-07-22
gert-2.3.1/gert/NEWS |only gert-2.4.0/gert/DESCRIPTION | 13 + gert-2.4.0/gert/MD5 | 142 +++++++++++---------- gert-2.4.0/gert/NAMESPACE | 15 ++ gert-2.4.0/gert/NEWS.md |only gert-2.4.0/gert/R/archive.R | 3 gert-2.4.0/gert/R/branch.R | 71 ++++++++++ gert-2.4.0/gert/R/commit.R | 172 ++++++++++++++++++++++---- gert-2.4.0/gert/R/config.R | 131 ++++++++++++++----- gert-2.4.0/gert/R/diff.R | 10 + gert-2.4.0/gert/R/errors.R | 4 gert-2.4.0/gert/R/fetch.R | 68 ++++++++-- gert-2.4.0/gert/R/gert-package.R | 39 +++++ gert-2.4.0/gert/R/ignore.R | 2 gert-2.4.0/gert/R/init.R | 10 - gert-2.4.0/gert/R/merge.R | 36 +++-- gert-2.4.0/gert/R/open.R | 4 gert-2.4.0/gert/R/pr.R | 12 + gert-2.4.0/gert/R/rebase.R | 46 ++++-- gert-2.4.0/gert/R/remotes.R | 47 +++++-- gert-2.4.0/gert/R/repository.R | 24 ++- gert-2.4.0/gert/R/restore.R |only gert-2.4.0/gert/R/roxygen2.R |only gert-2.4.0/gert/R/signature.R | 5 gert-2.4.0/gert/R/stash.R | 1 gert-2.4.0/gert/R/submodules.R | 9 - gert-2.4.0/gert/R/tag.R | 3 gert-2.4.0/gert/R/utils-sha.R |only gert-2.4.0/gert/R/worktree.R | 1 gert-2.4.0/gert/build/vignette.rds |binary gert-2.4.0/gert/cleanup | 1 gert-2.4.0/gert/configure | 4 gert-2.4.0/gert/inst/doc/gert.html | 13 + gert-2.4.0/gert/man/gert-package.Rd | 5 gert-2.4.0/gert/man/git_archive.Rd | 25 ++- gert-2.4.0/gert/man/git_branch.Rd | 88 +++++++++++-- gert-2.4.0/gert/man/git_commit.Rd | 80 ++++-------- gert-2.4.0/gert/man/git_config.Rd | 92 ++++++++++--- gert-2.4.0/gert/man/git_diff.Rd | 35 +++-- gert-2.4.0/gert/man/git_fetch.Rd | 40 ++++-- gert-2.4.0/gert/man/git_history.Rd |only gert-2.4.0/gert/man/git_ignore.Rd | 29 ++-- gert-2.4.0/gert/man/git_merge.Rd | 61 +++++---- gert-2.4.0/gert/man/git_open.Rd | 4 gert-2.4.0/gert/man/git_rebase.Rd | 51 ++++--- gert-2.4.0/gert/man/git_remote.Rd | 32 +++- gert-2.4.0/gert/man/git_repo.Rd | 59 ++++++-- gert-2.4.0/gert/man/git_reset.Rd | 25 ++- gert-2.4.0/gert/man/git_restore.Rd |only gert-2.4.0/gert/man/git_revert.Rd |only gert-2.4.0/gert/man/git_signature.Rd | 25 ++- gert-2.4.0/gert/man/git_stash.Rd | 27 ++-- gert-2.4.0/gert/man/git_submodule.Rd | 9 - gert-2.4.0/gert/man/git_tag.Rd | 29 ++-- gert-2.4.0/gert/man/git_worktree.Rd | 27 ++-- gert-2.4.0/gert/man/github.Rd | 6 gert-2.4.0/gert/man/user_is_configured.Rd | 2 gert-2.4.0/gert/src/branch.c | 14 -- gert-2.4.0/gert/src/clone.c | 28 ++-- gert-2.4.0/gert/src/commit.c | 85 ++++++++---- gert-2.4.0/gert/src/config.c | 64 ++++++--- gert-2.4.0/gert/src/files.c | 32 +++- gert-2.4.0/gert/src/init.c | 20 +-- gert-2.4.0/gert/src/utils.c | 11 + gert-2.4.0/gert/src/utils.h | 3 gert-2.4.0/gert/tests/spelling.R | 10 + gert-2.4.0/gert/tests/testthat/test-auth.R | 68 ++++++++-- gert-2.4.0/gert/tests/testthat/test-branch.R |only gert-2.4.0/gert/tests/testthat/test-clone.R | 53 +++++++- gert-2.4.0/gert/tests/testthat/test-commit.R | 113 ++++++++++++++++- gert-2.4.0/gert/tests/testthat/test-config.R | 53 +++++++- gert-2.4.0/gert/tests/testthat/test-ignore.R | 21 +-- gert-2.4.0/gert/tests/testthat/test-merge.R | 5 gert-2.4.0/gert/tests/testthat/test-rebase.R | 88 ++++++++++--- gert-2.4.0/gert/tests/testthat/test-remotes.R | 99 +++++++++++++- gert-2.4.0/gert/tests/testthat/test-restore.R |only gert-2.4.0/gert/tools/winlibs.R | 10 - 77 files changed, 1769 insertions(+), 645 deletions(-)
Title: Prediction and Interpretation in Decision Trees for
Classification and Regression
Description: Optimization of conditional inference trees from the package 'party'
for classification and regression.
For optimization, the model space is searched for the best tree on the full sample by
means of repeated subsampling. Restrictions are allowed so that only trees are accepted
which do not include pre-specified uninterpretable split results (cf. Weihs & Buschfeld, 2021a).
The function PrInDT() represents the basic resampling loop for 2-class classification (cf. Weihs
& Buschfeld, 2021a). The function RePrInDT() (repeated PrInDT()) allows for repeated
applications of PrInDT() for different percentages of the observations of the large and the
small classes (cf. Weihs & Buschfeld, 2021c). The function NesPrInDT() (nested PrInDT())
allows for an extra layer of subsampling for a specific factor variable (cf. Weihs & Buschfeld,
2021b). The functions PrInDTMulev() and PrInDTMulab() deal with multilevel and multilabel
classification. In addition to these PrInDT() variants for c [...truncated...]
Author: Claus Weihs [aut, cre],
Sarah Buschfeld [aut],
Niklas Nitsch [ctb]
Maintainer: Claus Weihs <claus.weihs@tu-dortmund.de>
Diff between PrInDT versions 2.0.2 dated 2025-09-11 and 2.0.3 dated 2026-07-22
DESCRIPTION | 14 +++++++------- MD5 | 6 +++--- R/SimMixPrInDT.R | 2 +- man/SimMixPrInDT.Rd | 2 +- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: NWS Hydrology Models: SAC-SMA, SNOW17, UH, CONSUSE, CHANLOSS
Description: Interface to the National Weather Service operational
hydrology models, Sacramento Soil Moisture Accounting (SAC-SMA),
Snow Accumulation and Ablation (SNOW17). Also provides an
interface to the unit hydrograph routing model (UH), consumptive use (CONSUSE)
and channel loss/gain modules (CHANLOSS). The Fortran code used in this package
is considered "legacy" and is not supported officially by NWS,
but it should not have any significant differences from current
operational models.
Author: Cameron Bracken [aut, cre] ,
Geoffrey Walters [aut] ,
Eric Anderson [ctb] ),
George F. Smith [ctb] ),
Janice M. Lewis [ctb] ),
John E. Pask [ctb] ; see
inst/COPYRIGHTS),
Ondrej Certik [ctb] ,
John Burkardt [ctb] ,
National Oceanic and Atmospheric Adm [...truncated...]
Maintainer: Cameron Bracken <cameron.bracken@pnnl.gov>
Diff between nwsrfsr versions 1.0.2 dated 2026-07-17 and 1.0.3 dated 2026-07-22
nwsrfsr-1.0.2/nwsrfsr/src/Makevars |only nwsrfsr-1.0.3/nwsrfsr/DESCRIPTION | 12 ++--- nwsrfsr-1.0.3/nwsrfsr/MD5 | 28 +++++++------ nwsrfsr-1.0.3/nwsrfsr/NEWS.md | 35 ++++++++++++++++ nwsrfsr-1.0.3/nwsrfsr/R/sac-snow-uh.R | 70 ++++++++++++++++++++++++++++----- nwsrfsr-1.0.3/nwsrfsr/cleanup |only nwsrfsr-1.0.3/nwsrfsr/configure |only nwsrfsr-1.0.3/nwsrfsr/man/nwsrfsr.Rd | 2 nwsrfsr-1.0.3/nwsrfsr/man/rsnwelev.Rd | 32 ++++++++++++--- nwsrfsr-1.0.3/nwsrfsr/src/Makevars.in |only nwsrfsr-1.0.3/nwsrfsr/src/Makevars.win | 24 +++++++---- nwsrfsr-1.0.3/nwsrfsr/src/aesc19.f | 6 ++ nwsrfsr-1.0.3/nwsrfsr/src/fka7.f | 5 ++ nwsrfsr-1.0.3/nwsrfsr/src/flag7.f | 11 ++++- nwsrfsr-1.0.3/nwsrfsr/src/pin7.f | 5 ++ nwsrfsr-1.0.3/nwsrfsr/src/umemst.f | 7 ++- nwsrfsr-1.0.3/nwsrfsr/src/zero19.f | 9 +++- 17 files changed, 199 insertions(+), 47 deletions(-)
Title: Toolkit for HLA Immunogenomics
Description: A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods. Tran et al., (2025) <doi:10.1111/iji.70013>.
Author: Livia Tran [aut],
Ryan Nickens [aut],
Leamon Crooms IV [aut],
Derek Pappas [aut],
Vinh Luu [ctb],
Josh Bredeweg [ctb],
Steven Mack [aut, cre]
Maintainer: Steven Mack <Steven.Mack@ucsf.edu>
Diff between HLAtools versions 1.6.3 dated 2025-07-21 and 1.11.0 dated 2026-07-22
DESCRIPTION | 10 MD5 | 64 + NAMESPACE | 2 NEWS.md | 47 + R/SearchandBuildAlignments.R | 2 R/UpdateAll.R | 28 R/VersionValidation.R | 18 R/atlasMaker.R | 1321 +++++++++++++++++++-------------------- R/buildAlignments.R | 177 ++--- R/buildGazetteer.R | 20 R/compareSequences.R | 91 +- R/data.R | 32 R/extractGenomicReferenceGenes.R |only R/globals.R | 3 R/locusValidator.R | 18 README.md | 37 - build/vignette.rds |binary data/HLAatlas.rda |binary data/HLAgazetteer.rda |binary data/IMGTGenomicReferences.rda |only data/IMGTHLAGeneTypes.rda |binary data/fragmentFeatureNames.rda |binary inst/doc/HLAtools.Rmd | 31 inst/doc/HLAtools.html | 56 + man/HLAatlas.Rd | 2 man/HLAgazetteer.Rd | 11 man/IMGTGenomicReferences.Rd |only man/buildAlignments.Rd | 6 man/buildGazetteer.Rd | 13 man/buildGenomicReferences.Rd |only man/compareSequences.Rd | 17 man/getLatestVersion.Rd | 2 man/multiLocusValidation.Rd | 4 man/updateAll.Rd | 4 vignettes/HLAtools.Rmd | 31 35 files changed, 1163 insertions(+), 884 deletions(-)
Title: Modelling Structured Dynamical Systems in 'greta'
Description: A 'greta' extension for analysing transition matrices and
ordinary differential equations representing dynamical systems. Provides
functions for analysing transition matrices by iteration, and solving
ordinary differential equations. This is an extension to the 'greta'
software, Golding (2019) <doi:10.21105/joss.01601>.
Author: Nick Golding [aut, cph] ,
Nicholas Tierney [aut, cre]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
This is a re-admission after prior archival of version 0.2.2 dated 2024-11-13
Diff between greta.dynamics versions 0.2.2 dated 2024-11-13 and 0.2.3 dated 2026-07-22
DESCRIPTION | 17 +++-- MD5 | 28 ++++---- NEWS.md | 21 ++++++ R/greta.dynamics-package.R | 2 R/iterate_dynamic_function.R | 22 ++++++ R/iterate_dynamic_matrix.R | 30 +++++++++ R/iterate_matrix.R | 4 - README.md | 2 build/vignette.rds |binary inst/doc/iterate-matrix-example.html | 112 +++++++++++++++++------------------ inst/doc/ode-solve-example.html | 20 +++--- man/greta.dynamics.Rd | 3 man/iterate_dynamic_function.Rd | 23 ++++++- man/iterate_dynamic_matrix.Rd | 31 +++++++++ man/iterate_matrix.Rd | 4 - 15 files changed, 223 insertions(+), 96 deletions(-)
More information about greta.dynamics at CRAN
Permanent link
Title: GeoServer REST API R Interface
Description: Provides an R interface to the GeoServer REST API, allowing to upload
and publish data in a GeoServer web-application and expose data to OGC Web-Services.
The package currently supports all CRUD (Create,Read,Update,Delete) operations
on GeoServer workspaces, namespaces, datastores (stores of vector data), featuretypes,
layers, styles, as well as vector data upload operations. For more information about
the GeoServer REST API, see <https://docs.geoserver.org/main/en/user/rest/>.
Author: Emmanuel Blondel [aut, cre]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geosapi versions 0.8 dated 2026-01-12 and 0.8-1 dated 2026-07-22
DESCRIPTION | 10 +- MD5 | 36 ++++----- NEWS.md | 14 ++- R/GSAccessControlListManager.R | 116 ++++++++++++++++++++++++----- R/GSCoverageStoreManager.R | 2 R/GSLayerRule.R | 2 R/GSRestRule.R | 10 -- R/GSRule.R | 6 - R/GSServiceRule.R | 2 R/geosapi.R | 2 README.md | 2 inst/doc/geosapi.Rmd | 16 ++-- inst/doc/geosapi.html | 16 ++-- man/GSAccessControlListManager.Rd | 152 +++++++++++++++++++++++++++++++++++--- man/GSCoverageStoreManager.Rd | 2 man/GSRestRule.Rd | 10 -- man/GSRule.Rd | 4 - man/geosapi.Rd | 2 vignettes/geosapi.Rmd | 16 ++-- 19 files changed, 308 insertions(+), 112 deletions(-)
Title: The Environmental Costs of Flow Regulation
Description: An application to calculate the daily environmental costs of river
flow regulation by dams based on García de Jalón et al. (2017)
<doi:10.1007/s11269-017-1663-0>.
Author: Silvestre Garcia de Jalon [aut],
Javier Martinez-Lopez [aut, cre],
Marta Gonzalez del Tanago [aut],
Carlos Alonso [aut],
Diego Garcia de Jalon [aut]
Maintainer: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>
Diff between FlowRegEnvCost versions 0.1.1 dated 2017-10-18 and 0.1.2 dated 2026-07-22
DESCRIPTION | 35 +++++++++++++++++++++++++++++------ MD5 | 10 ++++++---- NEWS.md |only R/data.R | 6 +++--- build |only inst/CITATION | 41 +++++++++++++++++++++-------------------- man/flowdata.Rd | 6 +++--- 7 files changed, 62 insertions(+), 36 deletions(-)
More information about FlowRegEnvCost at CRAN
Permanent link
Title: Data Sets to Accompany Designing Experiments and Analyzing Data:
A Model Comparison Perspective (Maxwell, Delaney, and Kelley,
2027, 4th Edition)
Description: Data sets that accompany the book "Designing experiments and
analyzing data: A model comparison perspective" (4th ed.) by
Maxwell, Delaney, and Kelley (2027; ISBN 978-1-041-25384-6; Routledge).
Contains all of the data sets in the book's chapters and end-of-chapter
exercises. Beginning with version 2.0, the package is tailored to the 4th
edition of the book; for the data as distributed with the 3rd edition
(2018), install the archived version 1.0.2 from CRAN. We recommend the
'DMAR' package as the companion for carrying out the book's analyses; these
analyses are illustrated in the book itself using the 'MBESS' package, which
may be used as well. The book's companion website is available at
<https://designingexperiments.com/> and its publisher page at
<https://www.routledge.com/Designing-Experiments-and-Analyzing-Data-A-Model-Comparison-Perspective/Maxwell-Delaney-Kelley/p/book/9781041253846>.
Author: Scott E. Maxwell [aut],
Harold D. Delaney [aut],
Ken Kelley [aut, cre]
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between AMCP versions 1.0.2 dated 2024-06-07 and 2.0.0 dated 2026-07-22
AMCP-1.0.2/AMCP/data/C12T21.rda |only AMCP-1.0.2/AMCP/data/C13T12.rda |only AMCP-1.0.2/AMCP/data/C13T14.rda |only AMCP-1.0.2/AMCP/data/C4T7.rda |only AMCP-1.0.2/AMCP/data/C7T15.rda |only AMCP-1.0.2/AMCP/data/C7T23.rda |only AMCP-1.0.2/AMCP/data/C9T11.rda |only AMCP-1.0.2/AMCP/data/chapter_12_table_21.rda |only AMCP-1.0.2/AMCP/data/chapter_13_table_12.rda |only AMCP-1.0.2/AMCP/data/chapter_13_table_14.rda |only AMCP-1.0.2/AMCP/data/chapter_4_table_7.rda |only AMCP-1.0.2/AMCP/data/chapter_7_table_15.rda |only AMCP-1.0.2/AMCP/data/chapter_7_table_23.rda |only AMCP-1.0.2/AMCP/data/chapter_9_table_11.rda |only AMCP-1.0.2/AMCP/man/chapter_12_table_21.Rd |only AMCP-1.0.2/AMCP/man/chapter_13_table_12.Rd |only AMCP-1.0.2/AMCP/man/chapter_13_table_14.Rd |only AMCP-1.0.2/AMCP/man/chapter_4_table_7.Rd |only AMCP-1.0.2/AMCP/man/chapter_7_table_15.Rd |only AMCP-1.0.2/AMCP/man/chapter_7_table_23.Rd |only AMCP-1.0.2/AMCP/man/chapter_9_table_11.Rd |only AMCP-2.0.0/AMCP/DESCRIPTION | 49 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Title: Fit 'TabNet' Models for Classification and Regression
Description: Implements the 'TabNet' model by Sercan O. Arik et al. (2019)
<doi:10.48550/arXiv.1908.07442> with 'Coherent Hierarchical
Multi-label Classification Networks' by Giunchiglia et al.
<doi:10.48550/arXiv.2010.10151> and provides a consistent interface
for fitting and creating predictions. It's also fully compatible with
the 'tidymodels' ecosystem.
Author: Daniel Falbel [aut],
RStudio [cph],
Christophe Regouby [cre, ctb],
Egill Fridgeirsson [ctb],
Philipp Haarmeyer [ctb],
Sven Verweij [ctb]
Maintainer: Christophe Regouby <christophe.regouby@free.fr>
Diff between tabnet versions 0.9.0 dated 2026-06-12 and 0.9.1 dated 2026-07-22
tabnet-0.9.0/tabnet/build/partial.rdb |only tabnet-0.9.0/tabnet/man/tabnet-package.Rd |only tabnet-0.9.1/tabnet/DESCRIPTION | 18 ++- tabnet-0.9.1/tabnet/MD5 | 46 ++++------ tabnet-0.9.1/tabnet/NEWS.md | 4 tabnet-0.9.1/tabnet/R/hardhat.R | 1 tabnet-0.9.1/tabnet/README.md | 8 - tabnet-0.9.1/tabnet/build/vignette.rds |binary tabnet-0.9.1/tabnet/inst/WORDLIST | 3 tabnet-0.9.1/tabnet/inst/doc/Hierarchical_classification.R | 1 tabnet-0.9.1/tabnet/inst/doc/Hierarchical_classification.Rmd | 1 tabnet-0.9.1/tabnet/inst/doc/Missing_data_predictors.R | 3 tabnet-0.9.1/tabnet/inst/doc/Missing_data_predictors.Rmd | 3 tabnet-0.9.1/tabnet/inst/doc/Missing_data_predictors.html | 6 - tabnet-0.9.1/tabnet/inst/doc/interpretation.R | 1 tabnet-0.9.1/tabnet/inst/doc/interpretation.Rmd | 1 tabnet-0.9.1/tabnet/man/figures/README-model-explain-1.png |binary tabnet-0.9.1/tabnet/man/figures/README-model-fit-1.png |binary tabnet-0.9.1/tabnet/man/figures/README-step-explain-1.png |binary tabnet-0.9.1/tabnet/man/figures/README-step-pretrain-1.png |binary tabnet-0.9.1/tabnet/tests/testthat/Rplots.pdf |binary tabnet-0.9.1/tabnet/tests/testthat/test-parsnip.R | 5 - tabnet-0.9.1/tabnet/vignettes/Hierarchical_classification.Rmd | 1 tabnet-0.9.1/tabnet/vignettes/Missing_data_predictors.Rmd | 3 tabnet-0.9.1/tabnet/vignettes/interpretation.Rmd | 1 25 files changed, 62 insertions(+), 44 deletions(-)
Title: Create Interactive Web Graphics via 'plotly.js'
Description: Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.
Author: Carson Sievert [aut, cre] ,
Chris Parmer [aut],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut] ,
Pedro Despouy [aut],
Salim Brueggemann [ctb] ,
Plotly Technologies Inc. [cph]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 4.12.0 dated 2026-01-24 and 4.12.1 dated 2026-07-22
DESCRIPTION | 10 +- MD5 | 40 ++++----- NAMESPACE | 5 - NEWS.md | 16 +++ R/ggplotly.R | 23 ++++- R/imports.R | 1 R/kaleido.R | 52 ++++++++++-- R/layout.R | 4 R/plotly.R | 3 R/plotly_build.R | 3 R/utils.R | 2 README.md | 2 man/config.Rd | 4 man/figures/README-volcano-surface.png |only man/plot_ly.Rd | 3 tests/testthat/_snaps/ggplot-size/size-global-scaling.svg | 2 tests/testthat/_snaps/ggplot-theme/theme-marker-default.svg | 2 tests/testthat/test-ggplot-facets.R | 6 - tests/testthat/test-ggplot-legend.R | 12 +- tests/testthat/test-group2NA.R | 2 tests/testthat/test-kaleido.R |only tests/testthat/test-plotly.R | 6 + 22 files changed, 139 insertions(+), 59 deletions(-)
Title: Test of No Main and/or Interaction Effects in Functional Data
Description: Distribution free heteroscedastic tests for functional data.
The following tests are included in this package: test of no main treatment or contrast
effect and no simple treatment effect given in
Wang, Higgins, and Blasi (2010) <doi:10.1016/j.spl.2009.11.016>,
no main time effect, and no interaction effect based on
original observations given in Wang and Akritas (2010a)
<doi:10.1080/10485250903171621>
and tests based on ranks given in Wang and Akritas (2010b)
<doi:10.1016/j.jmva.2010.03.012>.
Author: Haiyan Wang [aut, cre],
Michael Akritas [aut],
James Higgins [aut],
Dale Blasi [aut]
Maintainer: Haiyan Wang <hwang@ksu.edu>
Diff between HeterFunctionalData versions 0.1.0 dated 2020-08-20 and 1.0 dated 2026-07-22
HeterFunctionalData-0.1.0/HeterFunctionalData/man/fun.sigijj12.Rd |only HeterFunctionalData-1.0/HeterFunctionalData/DESCRIPTION | 22 +- HeterFunctionalData-1.0/HeterFunctionalData/MD5 | 22 +- HeterFunctionalData-1.0/HeterFunctionalData/NAMESPACE | 22 +- HeterFunctionalData-1.0/HeterFunctionalData/R/functions.R | 102 +++++++--- HeterFunctionalData-1.0/HeterFunctionalData/man/eu.Rd | 6 HeterFunctionalData-1.0/HeterFunctionalData/man/fun.sigijj12R.Rd |only HeterFunctionalData-1.0/HeterFunctionalData/man/sigijj12C.Rd |only HeterFunctionalData-1.0/HeterFunctionalData/man/sigma4.Rd | 21 +- HeterFunctionalData-1.0/HeterFunctionalData/man/sigma4R.Rd |only HeterFunctionalData-1.0/HeterFunctionalData/man/sigma4bootstrap.Rd | 4 HeterFunctionalData-1.0/HeterFunctionalData/man/sigma4jackknife.Rd | 4 HeterFunctionalData-1.0/HeterFunctionalData/man/taufun.Rd | 2 HeterFunctionalData-1.0/HeterFunctionalData/src |only 14 files changed, 141 insertions(+), 64 deletions(-)
More information about HeterFunctionalData at CRAN
Permanent link
Title: Generalized Elastic Nets
Description: Implements several extensions of the elastic net regularization
scheme. These extensions include individual feature penalties for the L1 term,
feature-feature penalties for the L2 term, as well as translation coefficients
for the latter.
Author: Artem Sokolov [aut, cre]
Maintainer: Artem Sokolov <artem.sokolov@gmail.com>
Diff between gelnet versions 1.2.1 dated 2016-04-05 and 1.2.2 dated 2026-07-22
CHANGES | 8 DESCRIPTION | 15 MD5 | 37 +- NAMESPACE | 3 R/gelnet.R | 5 build/vignette.rds |binary inst/doc/basics.R | 20 - inst/doc/basics.Rmd | 2 inst/doc/basics.html | 822 ++++++++++++++++++++++++++------------------- man/L1.ceiling.Rd | 13 man/adj2lapl.Rd | 1 man/adj2nlapl.Rd | 1 man/gelnet.Rd | 24 + man/gelnet.cv.Rd | 23 - man/gelnet.ker.Rd | 17 man/gelnet.lin.obj.Rd | 15 man/gelnet.logreg.obj.Rd | 17 man/gelnet.oneclass.obj.Rd | 12 src/init.c |only vignettes/basics.Rmd | 2 20 files changed, 625 insertions(+), 412 deletions(-)
Title: Relationship Matrices for Diploid and Autopolyploid Species
Description: Fast computation of A (pedigree), G (genomic-base), and H (A corrected
by G) relationship matrices for diploid and autopolyploid species. Several methods
are implemented considering additive and non-additive models.
Author: Rodrigo Amadeu [aut, cre],
Luis Ferrao [aut, ctb],
Thiago Oliveira [aut, ctb],
Catherine Cellon [ctb],
Leticia Lara [ctb],
Marcio Resende [ctb],
Ivone Oliveira [ctb],
Patricio Munoz [ctb],
Augusto Garcia [ctb]
Maintainer: Rodrigo Amadeu <rramadeu@gmail.com>
Diff between AGHmatrix versions 2.1.4 dated 2023-10-03 and 3.0.1 dated 2026-07-22
DESCRIPTION | 51 - MD5 | 120 +- NAMESPACE | 34 R/Amatrix.R | 524 ++++------ R/AmatrixPolyCross.R | 379 +++---- R/Gmatrix.R | 786 +++++++-------- R/Hmatrix.R | 451 +++++--- R/Mcheck.R | 326 +++--- R/RcppExports.R |only R/datatreat.R | 392 ++----- R/expandAmatrix.R | 162 +-- R/filterpedigree.R | 114 +- R/formatmatrix.R | 180 +-- R/missingdata.R | 182 +-- R/ped.mrode-data.R | 38 R/ped.sol-data.R | 38 R/snp.pine-data.R | 38 R/snp.sol-data.R | 38 README.md | 712 +++++++------- build/vignette.rds |binary data/datalist | 8 inst/CITATION | 32 inst/doc/Tutorial_AGHmatrix.R | 472 ++++----- inst/doc/Tutorial_AGHmatrix.Rmd | 820 ++++++++-------- inst/doc/Tutorial_AGHmatrix.html | 1974 +++++++++++++++++++-------------------- inst/misc/ISSUE | 4 inst/misc/Tutorial_AGHmatrix.R | 380 +++---- inst/misc/Tutorial_AGHmatrix.Rmd | 640 ++++++------ inst/misc/converttofrequency.R | 224 ++-- inst/misc/explorematrix.R | 122 +- inst/misc/misc.R | 180 +-- man/Amatrix.Rd | 201 ++- man/AmatrixPolyCross.Rd | 110 +- man/Gmatrix.Rd | 283 +++-- man/H_martini_blocks.Rd |only man/Hmatrix.Rd | 182 +-- man/Mcheck.Rd | 6 man/asciitonumber.Rd |only man/datatreat.Rd | 65 - man/expandAmatrix.Rd | 76 - man/filterpedigree.Rd | 54 - man/formatmatrix.Rd | 110 +- man/missingdata.Rd | 54 - man/munoz_var_mean_by_Aclass.Rd |only man/ped.mrode.Rd | 46 man/ped.sol.Rd | 48 man/snp.pine.Rd | 48 man/snp.sol.Rd | 48 src |only tests |only vignettes/Tutorial_AGHmatrix.Rmd | 820 ++++++++-------- 51 files changed, 5820 insertions(+), 5752 deletions(-)
Title: Anomaly Detection in Temporal Networks
Description: Anomaly detection in dynamic, temporal networks. The package
'oddnet' uses a feature-based method to identify anomalies. First, it computes
many features for each network. Then it models the features using time series
methods. Using time series residuals it detects anomalies. This way, the
temporal dependencies are accounted for when identifying anomalies
(Kandanaarachchi, Sanderson, Hyndman 2024) <doi:10.1109/ISCMI63661.2024.10851659>.
Author: Sevvandi Kandanaarachchi [aut, cre] ,
Rob Hyndman [aut]
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>
Diff between oddnet versions 0.1.1 dated 2024-02-11 and 0.1.2 dated 2026-07-22
DESCRIPTION | 22 ++++++++-------- MD5 | 21 ++++++++------- R/anomaly_detection.R | 17 +++++++++--- R/features.R | 7 +++-- R/laplacian_eigenvalue_method.R | 6 ++-- build/partial.rdb |only build/vignette.rds |binary inst/doc/oddnet.html | 53 ++++++++++++++++++++++++++-------------- man/anomalous_networks.Rd | 11 +++++--- man/compute_features.Rd | 2 - man/lad.Rd | 6 ++-- man/oddnet-package.Rd | 4 ++- 12 files changed, 92 insertions(+), 57 deletions(-)
Title: Multistate Model Bias-Corrected Robust Variance
Description: Computes robust and bias-corrected sandwich variance estimators for multi-state Cox models with clustered time-to-event data. Also provides Wald tests for heterogeneity, generalized least-squares linear trends, and order-restricted trends among transition-specific coefficients. The methodology extends the marginal Cox model bias-correction framework of Wang et al. (2023) <doi:10.1002/bimj.202200113> to the multi-state setting.
Author: Can Meng [aut, cre],
Denise Esserman [aut],
Fan Li [aut],
Erich Greene [aut]
Maintainer: Can Meng <can.meng@yale.edu>
Diff between mmbcv versions 0.3.0 dated 2026-03-31 and 1.0.0 dated 2026-07-22
DESCRIPTION | 10 MD5 | 23 NAMESPACE | 3 NEWS.md |only R/dissipation-tests-helper.R |only R/heterogeneity-test.R |only R/linear-trend-test.R |only R/order-restricted-test.R |only inst/doc/mmbcv-intro.R | 120 ++ inst/doc/mmbcv-intro.Rmd | 1394 ++++++++++++++++++++++---------- inst/doc/mmbcv-intro.html | 1321 +++++++++++++++++++++++------- man/heterogeneity_test.Rd |only man/linear_trend_test.Rd |only man/order_restricted_test.Rd |only tests/testthat/test-dissipation-tests.R |only vignettes/mmbcv-intro.Rmd | 1394 ++++++++++++++++++++++---------- vignettes/references.bib | 129 ++ 17 files changed, 3253 insertions(+), 1141 deletions(-)
Title: Calculate Generalized Eigenvalues, the Generalized Schur
Decomposition and the Generalized Singular Value Decomposition
of a Matrix Pair with Lapack
Description: Functions to compute generalized eigenvalues and eigenvectors,
the generalized Schur decomposition and
the generalized Singular Value Decomposition of a matrix pair,
using Lapack routines.
Author: Berend Hasselman [aut],
Jonathan M. Lees [cre],
Lapack authors [aut, cph]
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between geigen versions 2.3 dated 2019-05-30 and 2.4 dated 2026-07-22
DESCRIPTION | 24 +++++++++++++++--------- MD5 | 14 +++++++------- build/partial.rdb |binary man/geigen.Rd | 6 +++--- man/gevalues.Rd | 2 +- man/gqz.Rd | 8 ++++---- man/gsvd.Rd | 14 +++++++------- src/zggsvdall.f | 12 ++++++------ 8 files changed, 43 insertions(+), 37 deletions(-)
Title: Recursive Two-Stage Models to Address Endogeneity
Description: Various recursive two-stage models to address the endogeneity issue of treatment variables in observational study or mediators in experiments. The details of the models are discussed in Peng (2023) <doi:10.1287/isre.2022.1113>.
Author: Jing Peng [aut, cre]
Maintainer: Jing Peng <jing.peng@uconn.edu>
Diff between endogeneity versions 2.1.5 dated 2025-10-12 and 2.1.6 dated 2026-07-22
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- R/pln.R | 10 +++++++++- R/probit_linearRE.R | 7 ++++--- build/vignette.rds |binary inst/doc/vignette.html | 6 +++--- man/bilinear.Rd | 22 +++++++++++----------- man/biprobit.Rd | 22 +++++++++++----------- man/biprobit_latent.Rd | 22 +++++++++++----------- man/biprobit_partial.Rd | 22 +++++++++++----------- man/linear_probit.Rd | 22 +++++++++++----------- man/pln.Rd | 5 +++++ man/pln_linear.Rd | 22 +++++++++++----------- man/pln_probit.Rd | 22 +++++++++++----------- man/probit_linear.Rd | 22 +++++++++++----------- man/probit_linearRE.Rd | 27 +++++++++++++++------------ man/probit_linear_latent.Rd | 22 +++++++++++----------- man/probit_linear_partial.Rd | 22 +++++++++++----------- 18 files changed, 167 insertions(+), 150 deletions(-)
Title: Probability Distributions as S3 Objects
Description: Tools to create and manipulate probability distributions
using S3. Generics pdf(), cdf(), quantile(), and random() provide
replacements for base R's d/p/q/r style functions. Functions and
arguments have been named carefully to minimize confusion for students
in intro stats courses. The documentation for each distribution
contains detailed mathematical notes.
Author: Alex Hayes [aut] ,
Ralph Moller-Trane [aut] ,
Daniel Jordan [aut],
Paul Northrop [aut] ,
Moritz N. Lang [aut] ,
Achim Zeileis [aut, cre] ,
Emil Hvitfeldt [ctb] ,
Bruna Wundervald [ctb] ,
Alessandro Gasparini [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between distributions3 versions 0.2.3 dated 2025-09-12 and 0.2.4 dated 2026-07-22
DESCRIPTION | 55 +++--- LICENSE | 2 MD5 | 234 ++++++++++++++-------------- NEWS.md | 10 + R/Bernoulli.R | 2 R/Binomial.R | 2 R/Cauchy.R | 2 R/ChiSquare.R | 2 R/Exponential.R | 4 R/FisherF.R | 2 R/Frechet.R | 2 R/Gamma.R | 2 R/GeneralisedExtremeValue.R | 4 R/GeneralisedPareto.R | 2 R/Geometric.R | 4 R/Gumbel.R | 2 R/HurdleNegativeBinomial.R | 2 R/HurdlePoisson.R | 2 R/HyperGeometric.R | 6 R/LogNormal.R | 2 R/Logistic.R | 2 R/Multinomial.R | 2 R/NegativeBinomial.R | 4 R/Normal.R | 2 R/Poisson.R | 2 R/PoissonBinomial.R | 2 R/ReversedWeibull.R | 2 R/StudentsT.R | 2 R/Tukey.R | 2 R/Weibull.R | 16 - R/ZINegativeBinomial.R | 2 R/ZIPoisson.R | 2 R/ZTNegativeBinomial.R | 2 R/ZTPoisson.R | 2 README.md | 13 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/intro-to-hypothesis-testing.html | 2 inst/doc/one-sample-sign-tests.html | 2 inst/doc/one-sample-t-test.html | 2 inst/doc/one-sample-z-test-for-proportion.R | 12 - inst/doc/one-sample-z-test.html | 2 inst/doc/paired-tests.html | 22 +- inst/doc/poisson.html | 27 +-- inst/doc/two-sample-z-test.html | 6 man/Bernoulli.Rd | 32 +-- man/Beta.Rd | 38 ++-- man/Binomial.Rd | 32 +-- man/Categorical.Rd | 30 +-- man/Cauchy.Rd | 40 ++-- man/ChiSquare.Rd | 40 ++-- man/Erlang.Rd | 38 ++-- man/Exponential.Rd | 40 ++-- man/FisherF.Rd | 40 ++-- man/Frechet.Rd | 40 ++-- man/GEV.Rd | 40 ++-- man/GP.Rd | 40 ++-- man/Gamma.Rd | 40 ++-- man/Geometric.Rd | 32 +-- man/Gumbel.Rd | 40 ++-- man/HurdleNegativeBinomial.Rd | 32 +-- man/HurdlePoisson.Rd | 32 +-- man/HyperGeometric.Rd | 32 +-- man/LogNormal.Rd | 40 ++-- man/Logistic.Rd | 40 ++-- man/Multinomial.Rd | 32 +-- man/NegativeBinomial.Rd | 32 +-- man/Normal.Rd | 40 ++-- man/Poisson.Rd | 32 +-- man/PoissonBinomial.Rd | 32 +-- man/RevWeibull.Rd | 40 ++-- man/StudentsT.Rd | 40 ++-- man/Tukey.Rd | 40 ++-- man/Uniform.Rd | 38 ++-- man/Weibull.Rd | 42 ++--- man/ZINegativeBinomial.Rd | 32 +-- man/ZIPoisson.Rd | 32 +-- man/ZTNegativeBinomial.Rd | 32 +-- man/ZTPoisson.Rd | 32 +-- man/cdf.Geometric.Rd | 8 man/cdf.HyperGeometric.Rd | 8 man/cdf.LogNormal.Rd | 10 - man/cdf.Logistic.Rd | 8 man/cdf.NegativeBinomial.Rd | 8 man/cdf.Normal.Rd | 8 man/cdf.StudentsT.Rd | 8 man/cdf.Tukey.Rd | 4 man/cdf.Weibull.Rd | 8 man/distributions3-package.Rd | 11 - man/fit_mle.LogNormal.Rd | 10 - man/fit_mle.Normal.Rd | 8 man/geom_auc.Rd | 2 man/pdf.Geometric.Rd | 8 man/pdf.HyperGeometric.Rd | 8 man/pdf.LogNormal.Rd | 10 - man/pdf.Logistic.Rd | 8 man/pdf.Multinomial.Rd | 4 man/pdf.NegativeBinomial.Rd | 8 man/pdf.Normal.Rd | 8 man/pdf.StudentsT.Rd | 8 man/pdf.Weibull.Rd | 8 man/quantile.Geometric.Rd | 8 man/quantile.HyperGeometric.Rd | 8 man/quantile.LogNormal.Rd | 10 - man/quantile.Logistic.Rd | 8 man/quantile.NegativeBinomial.Rd | 8 man/quantile.Normal.Rd | 8 man/quantile.StudentsT.Rd | 8 man/quantile.Tukey.Rd | 4 man/quantile.Weibull.Rd | 8 man/random.Geometric.Rd | 8 man/random.HyperGeometric.Rd | 8 man/random.LogNormal.Rd | 10 - man/random.Logistic.Rd | 8 man/random.Multinomial.Rd | 4 man/random.NegativeBinomial.Rd | 8 man/random.StudentsT.Rd | 8 man/random.Weibull.Rd | 8 118 files changed, 1009 insertions(+), 1003 deletions(-)
More information about distributions3 at CRAN
Permanent link
Title: Color Schemes for Dichromats
Description: Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness
based on the work of Françoise Viénot and co-authors, especially <doi:10.1038/376127a0> and <doi:10.1364/josaa.14.002647>.
More recent functions for simulating color vision deficiency are provided in the 'colorspace' package.
Author: Thomas Lumley [aut] ,
Achim Zeileis [aut, cre] ,
Kenneth Knoblauch [ctb] ,
Scott Waichler [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between dichromat versions 2.0-0.1 dated 2022-05-02 and 2.0-1 dated 2026-07-22
DESCRIPTION | 44 ++++++++++++++++++++++++-------------------- MD5 | 18 +++++++++++------- NAMESPACE | 4 ++-- NEWS.md |only R/sysdata.rda |binary R/zzz.R |only README.md |only build |only data/dalton.rda |binary man/colorschemes.Rd | 5 +---- man/dalton.Rd | 20 +++++++++++--------- man/dichromat.Rd | 15 +++++++++------ 12 files changed, 58 insertions(+), 48 deletions(-)
Title: Reparameterized Regression Models
Description: Provides estimation and data generation tools for several new regression models,
including the gamma, beta, inverse gamma, beta prime, log-normal and log-logistic
distributions. These models can be parameterized based on the mean, median, mode,
geometric mean and harmonic mean, except for the log-logistic model which is based
on alternative parametrizations.
For details, see Bourguignon and Gallardo (2025a) <doi:10.1016/j.chemolab.2025.105382> and
Bourguignon and Gallardo (2025b) <doi:10.1111/stan.70007>.
The package also implements higher-order likelihood inference through Skovgaard-adjusted
likelihood ratio statistics and predictive shrinkage estimators reparameterized
beta regression models.
Author: Diego Gallardo [aut, cre],
Marcelo Bourguignon [aut],
Marcia Brandao [aut],
Tiago Magalhaes [ctb],
Rafael Izbicki [ctb]
Maintainer: Diego Gallardo <dgallardo@ubiobio.cl>
Diff between rregm versions 1.2 dated 2026-06-08 and 1.3 dated 2026-07-21
DESCRIPTION | 19 ++-- INDEX | 1 MD5 | 146 ++++++++++++++++++++++++++++---- NAMESPACE | 32 +++++-- NEWS.md | 4 R/BEGM.R | 85 +++++++++++-------- R/BPAM.R |only R/BPGM.R |only R/BPHM.R |only R/BPMD.R |only R/BPMO.R |only R/GAM.R |only R/GGM.R |only R/GHM.R |only R/GMD.R |only R/GMO.R |only R/LL.R |only R/LL2.R |only R/LL3.R |only R/LL4.R |only R/LL5.R |only R/LNAM.R |only R/LNGM.R |only R/LNHM.R |only R/LNMD.R |only R/LNMO.R |only R/dBPAM.R |only R/dBPGM.R |only R/dBPHM.R |only R/dBPMD.R |only R/dBPMO.R |only R/dGAM.R |only R/dGGM.R |only R/dGHM.R |only R/dGMD.R |only R/dGMO.R |only R/dLL.R |only R/dLL2.R |only R/dLL3.R |only R/dLL4.R |only R/dLL5.R |only R/dLL6.R |only R/dLNAM.R |only R/dLNGM.R |only R/dLNHM.R |only R/dLNMD.R |only R/dLNMO.R |only R/dRLL.R |only R/fit.RBE.R | 102 ++++++++++++++++------- R/fit.RBP.R | 235 +++++++++++++++++++++++++++++++---------------------- R/fit.RGA.R | 134 ++++++++++++++++++------------ R/fit.RIG.R | 84 ++++++++++++++---- R/fit.RLL.R |only R/fit.RLN.R | 48 ++++++++-- R/pBPAM.R |only R/pBPGM.R |only R/pBPHM.R |only R/pBPMD.R |only R/pBPMO.R |only R/pGAM.R |only R/pGGM.R |only R/pGHM.R |only R/pGMD.R |only R/pGMO.R |only R/pLL.R |only R/pLL2.R |only R/pLL3.R |only R/pLL4.R |only R/pLL5.R |only R/pLL6.R |only R/pLNAM.R |only R/pLNGM.R |only R/pLNHM.R |only R/pLNMD.R |only R/pLNMO.R |only R/pRLL.R |only R/qBPAM.R |only R/qBPGM.R |only R/qBPHM.R |only R/qBPMD.R |only R/qBPMO.R |only R/qGAM.R |only R/qGGM.R |only R/qGHM.R |only R/qGMD.R |only R/qGMO.R |only R/qLL.R |only R/qLL2.R |only R/qLL3.R |only R/qLL4.R |only R/qLL5.R |only R/qLL6.R |only R/qLNAM.R |only R/qLNGM.R |only R/qLNHM.R |only R/qLNMD.R |only R/qLNMO.R |only R/qRLL.R |only R/rBPAM.R |only R/rBPGM.R |only R/rBPHM.R |only R/rBPMD.R |only R/rBPMO.R |only R/rGAM.R |only R/rGGM.R |only R/rGHM.R |only R/rGMD.R |only R/rGMO.R |only R/rLL.R |only R/rLL2.R |only R/rLL3.R |only R/rLL4.R |only R/rLL5.R |only R/rLL6.R |only R/rLNAM.R |only R/rLNGM.R |only R/rLNHM.R |only R/rLNMD.R |only R/rLNMO.R |only R/rRLL.R |only R/summary.rregm.R | 15 +-- man/RBE.Rd | 10 +- man/RBE.skov.Rd | 2 man/RBP.Rd | 77 +++++++++++++++-- man/RGA.Rd | 75 +++++++++++++++- man/RIG.Rd | 15 ++- man/RLL.Rd |only man/RLN.Rd | 70 ++++++++++++++- man/tools.rregm.Rd | 1 129 files changed, 854 insertions(+), 301 deletions(-)
Title: Mediation Analysis Confidence Intervals
Description: Computes confidence intervals for nonlinear functions of model
parameters (e.g., product of k coefficients) in single-level and multilevel
structural equation
models. Methods include the distribution of the product,
Monte Carlo simulation, and bootstrap methods. It also performs the Model-Based
Constrained Optimization (MBCO) procedure for hypothesis testing of indirect
effects.
References:
Tofighi, D., and MacKinnon, D. P. (2011). RMediation: An R package for mediation
analysis confidence intervals. Behavior Research Methods, 43, 692-700.
<doi:10.3758/s13428-011-0076-x>;
Tofighi, D., and Kelley, K. (2020). Improved inference in mediation analysis: Introducing the model-based constrained optimization procedure.
Psychological Methods, 25(4), 496-515. <doi:10.1037/met0000259>;
Tofighi, D. (2020). Bootstrap Model-Based Constrained Optimization Tests of
Indirect Effects. Frontiers in Psychology, 10, 2989.
<doi:10.3389/fpsyg.2019.02989>.
Author: Davood Tofighi [aut, cre]
Maintainer: Davood Tofighi <dtofighi@gmail.com>
Diff between RMediation versions 1.5.0 dated 2026-06-19 and 1.6.1 dated 2026-07-21
RMediation-1.5.0/RMediation/man/ProductNormal_from_lavaan.Rd |only RMediation-1.5.0/RMediation/man/is_valid_for_computation.Rd |only RMediation-1.5.0/RMediation/man/utils_validation.Rd |only RMediation-1.5.0/RMediation/man/validate_ProductNormal.Rd |only RMediation-1.6.1/RMediation/DESCRIPTION | 16 RMediation-1.6.1/RMediation/MD5 | 141 +++---- RMediation-1.6.1/RMediation/NAMESPACE | 5 RMediation-1.6.1/RMediation/NEWS.md | 48 ++ RMediation-1.6.1/RMediation/R/00_classes.R | 185 ++++++--- RMediation-1.6.1/RMediation/R/MBCOResult_methods.R | 6 RMediation-1.6.1/RMediation/R/ProductNormal3_methods.R |only RMediation-1.6.1/RMediation/R/ProductNormal_methods.R | 31 + RMediation-1.6.1/RMediation/R/RMediation.R | 4 RMediation-1.6.1/RMediation/R/ci.R | 6 RMediation-1.6.1/RMediation/R/ci_medfit.R | 65 +-- RMediation-1.6.1/RMediation/R/confintAsymp.R | 8 RMediation-1.6.1/RMediation/R/confintMC.R | 4 RMediation-1.6.1/RMediation/R/external_methods.R | 53 +- RMediation-1.6.1/RMediation/R/internal_s7_compute.R | 16 RMediation-1.6.1/RMediation/R/mbco.R | 5 RMediation-1.6.1/RMediation/R/mbco_semi.R | 4 RMediation-1.6.1/RMediation/R/medci.R | 6 RMediation-1.6.1/RMediation/R/medci_legacy_backup.R | 6 RMediation-1.6.1/RMediation/R/medci_prototype.R | 12 RMediation-1.6.1/RMediation/R/pprodnormal.R | 2 RMediation-1.6.1/RMediation/R/prod3_core.R |only RMediation-1.6.1/RMediation/R/qprodnormal.R | 2 RMediation-1.6.1/RMediation/R/utils_stats.R | 27 - RMediation-1.6.1/RMediation/R/utils_validation.R | 96 ++--- RMediation-1.6.1/RMediation/R/zzz.R | 1 RMediation-1.6.1/RMediation/README.md | 35 + RMediation-1.6.1/RMediation/build/partial.rdb |binary RMediation-1.6.1/RMediation/build/vignette.rds |binary RMediation-1.6.1/RMediation/inst/WORDLIST | 98 +++-- RMediation-1.6.1/RMediation/inst/doc/getting-started.R | 60 +-- RMediation-1.6.1/RMediation/inst/doc/getting-started.Rmd | 66 ++- RMediation-1.6.1/RMediation/inst/doc/getting-started.html | 186 +++++----- RMediation-1.6.1/RMediation/inst/doc/methods-comparison.R | 26 - RMediation-1.6.1/RMediation/inst/doc/methods-comparison.Rmd | 34 - RMediation-1.6.1/RMediation/inst/doc/methods-comparison.html | 58 +-- RMediation-1.6.1/RMediation/inst/doc/serial-mediation-with-medfit.R | 19 - RMediation-1.6.1/RMediation/inst/doc/serial-mediation-with-medfit.Rmd | 21 - RMediation-1.6.1/RMediation/inst/doc/serial-mediation-with-medfit.html | 33 - RMediation-1.6.1/RMediation/man/MBCOResult.Rd | 3 RMediation-1.6.1/RMediation/man/ProductNormal.Rd | 3 RMediation-1.6.1/RMediation/man/ProductNormal2.Rd | 3 RMediation-1.6.1/RMediation/man/ProductNormal3.Rd |only RMediation-1.6.1/RMediation/man/RMediation-package.Rd | 5 RMediation-1.6.1/RMediation/man/cdf.Rd | 8 RMediation-1.6.1/RMediation/man/ci.Rd | 12 RMediation-1.6.1/RMediation/man/ci_mediation_data.Rd | 12 RMediation-1.6.1/RMediation/man/dist_quantile.Rd | 8 RMediation-1.6.1/RMediation/man/dot-ci_core.Rd | 4 RMediation-1.6.1/RMediation/man/mbco.Rd | 108 ++--- RMediation-1.6.1/RMediation/man/medci.Rd | 15 RMediation-1.6.1/RMediation/man/medci_prototype.Rd | 9 RMediation-1.6.1/RMediation/man/pprodnormal.Rd | 2 RMediation-1.6.1/RMediation/man/pprodnormal3.Rd |only RMediation-1.6.1/RMediation/man/qprodnormal.Rd | 2 RMediation-1.6.1/RMediation/man/tidy.Rd | 5 RMediation-1.6.1/RMediation/tests/testthat/test-ci-medfit-covariance.R | 82 ++-- RMediation-1.6.1/RMediation/tests/testthat/test-ci.R | 52 +- RMediation-1.6.1/RMediation/tests/testthat/test-legacy-compat.R | 12 RMediation-1.6.1/RMediation/tests/testthat/test-mbco-legacy.R | 14 RMediation-1.6.1/RMediation/tests/testthat/test-medci.R | 4 RMediation-1.6.1/RMediation/tests/testthat/test-product-distributions.R | 6 RMediation-1.6.1/RMediation/tests/testthat/test-product-normal3.R |only RMediation-1.6.1/RMediation/tests/testthat/test-s7-display.R | 16 RMediation-1.6.1/RMediation/tests/testthat/test-s7-integration.R | 44 +- RMediation-1.6.1/RMediation/tests/testthat/test-s7-mbco.R | 22 - RMediation-1.6.1/RMediation/tests/testthat/test-s7-productnormal.R | 12 RMediation-1.6.1/RMediation/tests/testthat/test-s7-prototype.R | 27 - RMediation-1.6.1/RMediation/tests/testthat/test-serial-medfit-integration.R | 24 - RMediation-1.6.1/RMediation/vignettes/getting-started.Rmd | 66 ++- RMediation-1.6.1/RMediation/vignettes/methods-comparison.Rmd | 34 - RMediation-1.6.1/RMediation/vignettes/serial-mediation-with-medfit.Rmd | 21 - 76 files changed, 1211 insertions(+), 809 deletions(-)
Title: Generating Cluster Masks for Single-Cell Dimensional Reduction
Plots
Description: Implements a procedure to automatically generate 2D masks
for clusters on dimensional reduction plots from methods like
t-SNE (t-distributed stochastic neighbor embedding) or
UMAP (uniform manifold approximation and projection),
with a focus on single-cell RNA-sequencing data.
Author: Alexey Sergushichev [aut, cre]
Maintainer: Alexey Sergushichev <alsergbox@gmail.com>
Diff between mascarade versions 0.3.5 dated 2026-07-08 and 0.4.1 dated 2026-07-21
mascarade-0.3.5/mascarade/R/ggforce_points_to_path.R |only mascarade-0.4.1/mascarade/DESCRIPTION | 19 mascarade-0.4.1/mascarade/MD5 | 70 - mascarade-0.4.1/mascarade/NAMESPACE | 5 mascarade-0.4.1/mascarade/NEWS.md | 4 mascarade-0.4.1/mascarade/R/RcppExports.R |only mascarade-0.4.1/mascarade/R/fancyMask.R | 75 + mascarade-0.4.1/mascarade/R/generateMask.R | 2 mascarade-0.4.1/mascarade/R/ggforce_mark_label.R | 284 ++--- mascarade-0.4.1/mascarade/R/mark_label.R | 529 +++++++--- mascarade-0.4.1/mascarade/R/mark_shape.R | 198 ++- mascarade-0.4.1/mascarade/R/mascarade-package.R | 4 mascarade-0.4.1/mascarade/R/placeLabels.R |only mascarade-0.4.1/mascarade/R/zzz.R | 3 mascarade-0.4.1/mascarade/inst/doc/mascarade-gallery.R | 47 mascarade-0.4.1/mascarade/inst/doc/mascarade-gallery.Rmd | 62 + mascarade-0.4.1/mascarade/inst/doc/mascarade-gallery.html | 175 ++- mascarade-0.4.1/mascarade/inst/doc/mascarade-tutorial.R | 5 mascarade-0.4.1/mascarade/inst/doc/mascarade-tutorial.Rmd | 5 mascarade-0.4.1/mascarade/inst/doc/mascarade-tutorial.html | 122 +- mascarade-0.4.1/mascarade/man/buildBoxFit.Rd |only mascarade-0.4.1/mascarade/man/effectiveLength.Rd |only mascarade-0.4.1/mascarade/man/fancyMask.Rd | 41 mascarade-0.4.1/mascarade/man/firstLeaderHit.Rd |only mascarade-0.4.1/mascarade/man/forcePolish.Rd |only mascarade-0.4.1/mascarade/man/geom_mark_shape.Rd | 75 + mascarade-0.4.1/mascarade/man/hungarian.Rd |only mascarade-0.4.1/mascarade/man/my_make_label.Rd |only mascarade-0.4.1/mascarade/man/my_place_labels.Rd |only mascarade-0.4.1/mascarade/man/oneMoveSweepKernel.Rd |only mascarade-0.4.1/mascarade/man/radialCandidates.Rd |only mascarade-0.4.1/mascarade/man/simplify_outer.Rd |only mascarade-0.4.1/mascarade/man/twoMoveSweepKernel.Rd |only mascarade-0.4.1/mascarade/src |only mascarade-0.4.1/mascarade/tests/testthat/fixtures |only mascarade-0.4.1/mascarade/tests/testthat/helper-score.R |only mascarade-0.4.1/mascarade/tests/testthat/test-balance_wrap.R |only mascarade-0.4.1/mascarade/tests/testthat/test-geom_mark_shape.R | 58 + mascarade-0.4.1/mascarade/tests/testthat/test-placement.R |only mascarade-0.4.1/mascarade/vignettes/mascarade-gallery.Rmd | 62 + mascarade-0.4.1/mascarade/vignettes/mascarade-tutorial.Rmd | 5 41 files changed, 1286 insertions(+), 564 deletions(-)
Title: Connector to 'CouchDB'
Description: Provides an interface to the 'NoSQL' database 'CouchDB'
(<https://couchdb.apache.org/>). Methods are provided for managing
databases within 'CouchDB', including creating/deleting/updating/transferring,
and managing documents within databases. One can connect with a local
'CouchDB' instance, or a remote 'CouchDB' database such as 'IBM Cloudant'.
Documents can be inserted directly from vectors, lists, data.frames,
and 'JSON'. Targeted at 'CouchDB' v2 or greater.
Author: Yaoxiang Li [aut, cre] ,
Eduard Szoecs [aut] ,
Scott Chamberlain [aut] ,
rOpenSci [fnd]
Maintainer: Yaoxiang Li <liyaoxiang@outlook.com>
Diff between sofa versions 0.4.0 dated 2020-06-26 and 0.4.2 dated 2026-07-21
DESCRIPTION | 36 LICENSE | 4 MD5 | 236 - NAMESPACE | 112 NEWS.md | 169 - R/active_tasks.R | 41 R/attach.r | 323 +- R/cushion.R | 371 +- R/databases.r | 28 R/db_alldocs.R | 140 - R/db_bulk_create.R | 274 +- R/db_bulk_get.R | 80 R/db_bulk_update.R | 146 - R/db_changes.R | 150 - R/db_compact.R | 70 R/db_create.r | 55 R/db_delete.r | 54 R/db_explain.R | 137 - R/db_index.R | 160 - R/db_info.r | 49 R/db_list.r | 45 R/db_query.R | 173 - R/db_replicate.r | 129 R/design.R | 305 +- R/design_search.R | 440 +-- R/doc_create.r | 325 +- R/doc_delete.r | 68 R/doc_get.r | 102 R/doc_head.r | 64 R/doc_update.r | 78 R/doc_upsert.R | 93 R/documents.r | 42 R/getattach.r | 18 R/membership.R | 41 R/parse_df.R | 110 R/ping.r | 40 R/restart.R | 35 R/revisions.r | 85 R/session.R | 41 R/sofa-package.r | 102 R/uuids.r | 43 R/zzz.r | 347 +- README.md | 227 - build/vignette.rds |binary inst/doc/query_tutorial.R | 16 inst/doc/query_tutorial.Rmd | 82 inst/doc/query_tutorial.html | 3394 +++++++++++++------------- inst/doc/sofa.Rmd | 876 +++--- inst/doc/sofa.html | 3888 ++++++++++++++---------------- inst/examples/omdb.json | 222 - inst/ignore/db_updates.R | 86 inst/ignore/sofa_alldocs.R | 30 inst/ignore/sofa_createdb.R | 28 inst/ignore/sofa_dbinfo.R | 36 inst/ignore/sofa_deldoc.R | 48 inst/ignore/sofa_deletedb.R | 42 inst/ignore/sofa_getdoc.R | 40 inst/ignore/sofa_head.R | 48 inst/ignore/sofa_listdbs.R | 12 man/Cushion.Rd | 506 +-- man/active_tasks.Rd | 66 man/attach_get-defunct.Rd | 30 man/attachments.Rd | 250 - man/databases.Rd | 36 man/db_alldocs.Rd | 172 - man/db_bulk_create.Rd | 224 - man/db_bulk_get.Rd | 104 man/db_bulk_update.Rd | 142 - man/db_changes.Rd | 204 - man/db_compact.Rd | 104 man/db_create.Rd | 84 man/db_delete.Rd | 82 man/db_explain.Rd | 182 - man/db_index.Rd | 168 - man/db_info.Rd | 78 man/db_list.Rd | 70 man/db_query.Rd | 346 +- man/db_replicate.Rd | 151 - man/db_revisions.Rd | 100 man/design.Rd | 262 +- man/design_search.Rd | 392 +-- man/doc_create.Rd | 248 - man/doc_delete.Rd | 94 man/doc_get.Rd | 158 - man/doc_head.Rd | 88 man/doc_update.Rd | 108 man/doc_upsert.Rd | 108 man/documents.Rd | 54 man/figures |only man/membership.Rd | 66 man/parse_df.Rd | 70 man/ping.Rd | 70 man/restart.Rd | 62 man/session.Rd | 66 man/sofa-package.Rd | 135 - man/uuids.Rd | 70 tests/test-all.R | 6 tests/testthat/helper-sofa.R | 483 +++ tests/testthat/test-attachments.R |only tests/testthat/test-cushion.R |only tests/testthat/test-db_alldocs.R | 77 tests/testthat/test-db_bulk_create.R | 68 tests/testthat/test-db_bulk_get.R | 76 tests/testthat/test-db_bulk_update.R | 126 tests/testthat/test-db_changes.R | 104 tests/testthat/test-db_create.R | 94 tests/testthat/test-db_delete.R | 76 tests/testthat/test-db_explain.R | 78 tests/testthat/test-db_info.R | 58 tests/testthat/test-db_list.R | 21 tests/testthat/test-db_query.R | 254 + tests/testthat/test-design.R |only tests/testthat/test-design_search.R | 126 tests/testthat/test-design_search_many.R | 116 tests/testthat/test-doc_create.R | 139 - tests/testthat/test-doc_delete.R |only tests/testthat/test-doc_upsert.R | 164 - tests/testthat/test-helper-fake-couchdb.R |only tests/testthat/test-internal_helpers.R |only tests/testthat/test-parse_df.R |only tests/testthat/test-revisions.R |only tests/testthat/test-server_api.R |only vignettes/query_tutorial.Rmd | 82 vignettes/sofa.Rmd | 876 +++--- 124 files changed, 11690 insertions(+), 10920 deletions(-)
Title: Simulate and Visualize the Gaussian Puff Forward Atmospheric
Model
Description: Simulate and run the Gaussian puff forward atmospheric
model in sensor (specific sensor coordinates) or grid (across the
grid of a full oil and gas operations site) modes, following Jia, M.,
Fish, R., Daniels, W., Sprinkle, B. and Hammerling, D. (2024)
<doi:10.26434/chemrxiv-2023-hc95q-v3>. Numerous visualization options,
including static and animated, 2D and 3D, and a site map generator
based on sensor and source coordinates.
Author: Teagan Ward [aut],
Philip Waggoner [aut],
Will Daniels [aut],
Meng Jia [aut],
Dorit Hammerling [aut, ths],
Callan Okenberg [cre]
Maintainer: Callan Okenberg <cal_okenberg@mines.edu>
Diff between puff versions 0.1.0 dated 2025-04-10 and 0.1.1 dated 2026-07-21
DESCRIPTION | 18 LICENSE | 4 MD5 | 54 R/globals.R | 12 R/helpers.R | 546 ++++----- R/plots.R | 2154 +++++++++++++++++++------------------- R/simulate_grid_mode.R | 426 +++---- R/simulate_sensor_mode.R | 432 +++---- build/vignette.rds |binary inst/doc/getting-started.R | 218 +-- inst/doc/getting-started.Rmd | 316 ++--- inst/doc/getting-started.html | 1026 +++++++++--------- man/compute_sigma_vals.Rd | 44 man/faceted_time_series_plot2.Rd | 128 +- man/get_stab_class.Rd | 46 man/gpuff.Rd | 88 - man/interpolate_wind_data.Rd | 62 - man/is_day.Rd | 40 man/plot_2d_animated.Rd | 180 +-- man/plot_3d_animated.Rd | 172 +-- man/simulate_grid_mode.Rd | 196 +-- man/simulate_sensor_mode.Rd | 194 +-- man/wind_vector_convert.Rd | 46 tests/testthat.R | 8 tests/testthat/test_grid_mode.R | 122 +- tests/testthat/test_plots.R | 716 ++++++------ tests/testthat/test_sensor_mode.R | 184 +-- vignettes/getting-started.Rmd | 316 ++--- 28 files changed, 3875 insertions(+), 3873 deletions(-)
Title: Handling Missing Data in Stochastic Block Models
Description: When a network is partially observed (here, NAs in the adjacency matrix rather than 1 or 0
due to missing information between node pairs), it is possible to account for the underlying process
that generates those NAs. 'missSBM', presented in 'Barbillon, Chiquet and Tabouy' (2022) <doi:10.18637/jss.v101.i12>,
adjusts the popular stochastic block model from network data sampled under various missing data conditions,
as described in 'Tabouy, Barbillon and Chiquet' (2019) <doi:10.1080/01621459.2018.1562934>.
Author: Julien Chiquet [aut, cre] ,
Pierre Barbillon [aut] ,
Timothee Tabouy [aut],
Jean-Benoist Leger [ctb] ,
Francois Gindraud [ctb] ,
grossBM team [ctb]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between missSBM versions 1.0.5 dated 2025-03-13 and 1.1.0 dated 2026-07-21
missSBM-1.0.5/missSBM/src/nlopt_wrapper.cpp |only missSBM-1.0.5/missSBM/src/nlopt_wrapper.h |only missSBM-1.0.5/missSBM/src/packing.cpp |only missSBM-1.0.5/missSBM/src/packing.h |only missSBM-1.0.5/missSBM/src/utils.h |only missSBM-1.1.0/missSBM/DESCRIPTION | 19 missSBM-1.1.0/missSBM/MD5 | 141 ++-- missSBM-1.1.0/missSBM/NAMESPACE | 3 missSBM-1.1.0/missSBM/NEWS.md | 63 + missSBM-1.1.0/missSBM/R/R6Class-missSBM_collection.R | 320 +++++---- missSBM-1.1.0/missSBM/R/R6Class-missSBM_fit.R | 322 +++++++-- missSBM-1.1.0/missSBM/R/R6Class-networkSampling_fit.R | 31 missSBM-1.1.0/missSBM/R/R6Class-partlyObservedNetwork.R | 47 - missSBM-1.1.0/missSBM/R/R6Class-simpleSBM_fit.R | 169 ++-- missSBM-1.1.0/missSBM/R/RcppExports.R | 12 missSBM-1.1.0/missSBM/R/estimateMissSBM.R | 163 +++- missSBM-1.1.0/missSBM/R/kmeans.R | 12 missSBM-1.1.0/missSBM/R/missSBM-package.R | 5 missSBM-1.1.0/missSBM/R/observeNetwork.R | 12 missSBM-1.1.0/missSBM/R/utils_missSBM.R | 150 +++- missSBM-1.1.0/missSBM/build/partial.rdb |binary missSBM-1.1.0/missSBM/build/vignette.rds |binary missSBM-1.1.0/missSBM/inst/WORDLIST | 22 missSBM-1.1.0/missSBM/inst/doc/case_study_war_networks.R | 51 - missSBM-1.1.0/missSBM/inst/doc/case_study_war_networks.Rmd | 79 +- missSBM-1.1.0/missSBM/inst/doc/case_study_war_networks.html | 135 ++- missSBM-1.1.0/missSBM/man/SimpleSBM_fit.Rd | 203 +++-- missSBM-1.1.0/missSBM/man/SimpleSBM_fit_MNAR.Rd | 199 +++-- missSBM-1.1.0/missSBM/man/SimpleSBM_fit_noCov.Rd | 168 ++-- missSBM-1.1.0/missSBM/man/SimpleSBM_fit_withCov.Rd | 172 ++--- missSBM-1.1.0/missSBM/man/blockDyadSampler.Rd | 101 +- missSBM-1.1.0/missSBM/man/blockDyadSampling_fit.Rd | 128 +-- missSBM-1.1.0/missSBM/man/blockNodeSampler.Rd | 91 +- missSBM-1.1.0/missSBM/man/blockNodeSampling_fit.Rd | 128 +-- missSBM-1.1.0/missSBM/man/covarDyadSampling_fit.Rd | 95 +- missSBM-1.1.0/missSBM/man/covarNodeSampling_fit.Rd | 95 +- missSBM-1.1.0/missSBM/man/degreeSampler.Rd | 86 +- missSBM-1.1.0/missSBM/man/degreeSampling_fit.Rd | 156 ++-- missSBM-1.1.0/missSBM/man/doubleStandardSampler.Rd | 86 +- missSBM-1.1.0/missSBM/man/doubleStandardSampling_fit.Rd | 150 ++-- missSBM-1.1.0/missSBM/man/dyadSampler.Rd | 89 +- missSBM-1.1.0/missSBM/man/dyadSampling_fit.Rd | 95 +- missSBM-1.1.0/missSBM/man/estimateMissSBM.Rd | 27 missSBM-1.1.0/missSBM/man/figures |only missSBM-1.1.0/missSBM/man/l1_similarity.Rd | 3 missSBM-1.1.0/missSBM/man/missSBM-package.Rd | 4 missSBM-1.1.0/missSBM/man/missSBM_collection.Rd | 273 +++++--- missSBM-1.1.0/missSBM/man/missSBM_fit.Rd | 339 +++++++--- missSBM-1.1.0/missSBM/man/missSBM_param.Rd |only missSBM-1.1.0/missSBM/man/networkSampler.Rd | 114 +-- missSBM-1.1.0/missSBM/man/networkSampling.Rd | 136 ++-- missSBM-1.1.0/missSBM/man/networkSamplingDyads_fit.Rd | 165 ++-- missSBM-1.1.0/missSBM/man/networkSamplingNodes_fit.Rd | 165 ++-- missSBM-1.1.0/missSBM/man/nodeSampler.Rd | 50 - missSBM-1.1.0/missSBM/man/nodeSampling_fit.Rd | 95 +- missSBM-1.1.0/missSBM/man/observeNetwork.Rd | 26 missSBM-1.1.0/missSBM/man/partlyObservedNetwork.Rd | 166 ++-- missSBM-1.1.0/missSBM/man/simpleDyadSampler.Rd | 94 +- missSBM-1.1.0/missSBM/man/simpleNodeSampler.Rd | 94 +- missSBM-1.1.0/missSBM/man/snowballSampler.Rd | 86 +- missSBM-1.1.0/missSBM/src/Makevars |only missSBM-1.1.0/missSBM/src/RcppExports.cpp | 33 missSBM-1.1.0/missSBM/src/SBM_bernoulli.cpp | 201 ++++- missSBM-1.1.0/missSBM/src/kmeans.cpp | 23 missSBM-1.1.0/missSBM/tests/testthat/test-M-step-newton-covariates.R |only missSBM-1.1.0/missSBM/tests/testthat/test-MISSSBM_collection.R | 11 missSBM-1.1.0/missSBM/tests/testthat/test-SAMPLING-fit-without-covariate.R | 40 - missSBM-1.1.0/missSBM/tests/testthat/test-TOP-LEVEL-consistency.R | 4 missSBM-1.1.0/missSBM/tests/testthat/test-TOP-LEVEL-estimate.R | 8 missSBM-1.1.0/missSBM/tests/testthat/test-consistency-on-fully-observed-network.R | 2 missSBM-1.1.0/missSBM/tests/testthat/test-explore-block-count.R |only missSBM-1.1.0/missSBM/tests/testthat/test-missSBM_collection-degenerate.R |only missSBM-1.1.0/missSBM/tests/testthat/test-missSBM_collection-estimate_chain.R |only missSBM-1.1.0/missSBM/tests/testthat/test-missSBM_fit-polish.R |only missSBM-1.1.0/missSBM/tests/testthat/test-missSBM_fit-split-merge.R |only missSBM-1.1.0/missSBM/tests/testthat/test-missSBM_param.R |only missSBM-1.1.0/missSBM/tests/testthat/test-repair-empty-classes.R |only missSBM-1.1.0/missSBM/vignettes/case_study_war_networks.Rmd | 79 +- 78 files changed, 3560 insertions(+), 2476 deletions(-)
Title: Approximate Bayesian Latent Variable Analysis
Description: Implements approximate Bayesian inference for Structural
Equation Models (SEM) using a custom adaptation of the Integrated
Nested Laplace Approximation (Rue et al., 2009)
<doi:10.1111/j.1467-9868.2008.00700.x> as described in Jamil and Rue
(2026a) <doi:10.48550/arXiv.2603.25690>. Provides a computationally
efficient alternative to Markov Chain Monte Carlo (MCMC) for Bayesian
estimation, allowing users to fit latent variable models using the
'lavaan' syntax. See also the companion paper on implementation and
workflows, Jamil and Rue (2026b) <doi:10.48550/arXiv.2604.00671>.
Author: Haziq Jamil [aut, cre, cph] ,
Havard Rue [ctb] ,
Alvin Bong [ctb]
Maintainer: Haziq Jamil <haziq.jamil@gmail.com>
Diff between INLAvaan versions 0.3.0 dated 2026-07-11 and 0.3.1 dated 2026-07-21
DESCRIPTION | 6 - MD5 | 46 +++---- NEWS.md | 7 + R/create_lav_from_inlavaan_internal.R | 2 R/inlavaan.R | 4 R/method-fitmeasures.R | 24 +++- R/utils.R | 5 README.md | 33 ++--- inst/doc/INLAvaan.html | 166 ++++++++++++++-------------- inst/doc/mediation.html | 8 - man/figures/README-fig-compare-poldem-1.png |binary man/fitmeasures.Rd | 26 +++- man/standardisedsolution.Rd | 6 - tests/testthat/test-binary.R | 3 tests/testthat/test-cfa.R | 6 + tests/testthat/test-equality_constraints.R | 6 + tests/testthat/test-growth.R | 6 + tests/testthat/test-loo-missing-2l.R | 11 + tests/testthat/test-loo-missing.R | 3 tests/testthat/test-mediation.R | 3 tests/testthat/test-multigroup.R | 13 +- tests/testthat/test-multilevel.R | 3 tests/testthat/test-optim_method.R | 7 + tests/testthat/test-sem.R | 6 + 24 files changed, 250 insertions(+), 150 deletions(-)
Title: Headers and Static Libraries for 'HDF5'
Description: Provides a self-contained, static build of the 'HDF5'
(Hierarchical Data Format 5) 'C' library (release 2.1.1) for R
package developers. Designed for use in the 'LinkingTo' field,
it enables zero-dependency integration by building the library
entirely from source during installation. Additionally, it compiles
and internally links a comprehensive suite of advanced compression
filters and their 'HDF5' plugins (Zstd, LZ4, Blosc/Blosc2, Snappy,
ZFP, Bzip2, LZF, Bitshuffle, szip, and gzip). These plugins are
integrated out-of-the-box, allowing downstream packages to utilize
high-performance compression directly through the standard 'HDF5'
API while keeping the underlying third-party headers fully
encapsulated. 'HDF5' is developed by The HDF Group
<https://www.hdfgroup.org/>.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd],
The HDF Group [ctb, cph] ,
The Board of Trustees of the University of Illinois [cph] ,
Jean-loup Gailly [ctb, cph] ,
Mark Adler [ctb, cph] ,
Kiyoshi Masui [...truncated...]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between hdf5lib versions 2.1.1.1 dated 2026-05-15 and 2.1.1.2 dated 2026-07-21
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS.md | 6 ++++++ src/filters/c-blosc2-2.23.1.tar.gz |binary src/patches/c-blosc2-2.23.1/09-const-warnings.patch |only 5 files changed, 13 insertions(+), 6 deletions(-)
Title: Bivariate Copula Functions Based on Regular Grid
Description: Estimates grid type bivariate copula functions, calculates some association measures and provides several copula graphics.
Author: Rogelio Salinas Gutierrez [aut, cre, cph] ,
Angelica Hernandez Quintero [aut, cph] ,
Pedro Abraham Montoya Calzada [aut, cph]
Maintainer: Rogelio Salinas Gutierrez <rogelio.salinas@edu.uaa.mx>
This is a re-admission after prior archival of version 1.1.1 dated 2026-05-06
Diff between GRIDCOPULA versions 1.1.1 dated 2026-05-06 and 1.1.2 dated 2026-07-21
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: All Hierarchical or Graphical Generalized Linear Models
Description: Find all hierarchical models of specified generalized linear
model with information criterion (AIC, BIC, or AICc) within specified
cutoff of minimum value. Alternatively, find all such graphical models.
Use branch and bound algorithm so we do not have to fit all models.
Author: Charles J. Geyer [aut, cre]
Maintainer: Charles J. Geyer <geyer@umn.edu>
Diff between glmbb versions 0.5-1 dated 2020-11-21 and 0.6 dated 2026-07-21
ChangeLog | 2 ++ DESCRIPTION | 23 +++++++++++++---------- MD5 | 14 ++++++++------ R/glmbb.R | 18 +++++++++--------- inst/NEWS.Rd | 27 ++++++++++++++++++++++++--- man/crabs.Rd | 2 +- man/glmbb.Rd | 2 +- tests/catrec.txt |only tests/sports.txt |only 9 files changed, 58 insertions(+), 30 deletions(-)
Title: Methods for Calculating Gradient Surface Metrics
Description: Methods for calculating gradient surface metrics for
continuous analysis of landscape features.
Author: Annie C. Smith [aut],
Phoebe Zarnetske [aut],
Kyla Dahlin [aut, cre],
Adam Wilson [aut],
Andrew Latimer [aut],
Kelly Kapsar [aut]
Maintainer: Kyla Dahlin <kdahlin@msu.edu>
Diff between geodiv versions 1.1.0 dated 2023-10-05 and 1.1.1 dated 2026-07-21
DESCRIPTION | 38 + LICENSE | 4 MD5 | 170 ++--- NAMESPACE | 206 +++--- NEWS.md | 114 +-- R/RcppExports.R | 60 +- R/aacf.R | 704 +++++++++++------------ R/basics.R | 522 ++++++++--------- R/bearingarea.R | 958 ++++++++++++++++---------------- R/bestfit.R | 240 ++++---- R/data.R | 138 ++-- R/fftshift.R | 138 ++-- R/focalmetrics.R | 486 ++++++++-------- R/fourier.R | 840 ++++++++++++++-------------- R/geodiv-package.R | 18 R/localsurface.R | 626 ++++++++++---------- R/movingwindow.R | 762 ++++++++++++------------- R/sdq.R | 200 +++--- R/sfd.R | 90 +-- R/simpsons.R | 260 ++++---- R/surfacearea.R | 404 ++++++------- R/utilities.R | 360 ++++++------ R/zshift.R | 292 ++++----- README.md | 118 +-- build/vignette.rds |binary inst/doc/geodiv_Examples.pdf.asis | 12 man/aacf.Rd | 64 +- man/area_above.Rd | 102 +-- man/bearing_area.Rd | 66 +- man/bestfitplane.Rd | 66 +- man/dot-calculate_met_focal.Rd | 136 ++-- man/dot-deg2rad.Rd | 34 - man/dot-maxdist.Rd | 66 +- man/dot-mindist.Rd | 66 +- man/dot-rad2deg.Rd | 34 - man/fftshift.Rd | 88 +- man/find_flat.Rd | 78 +- man/findpeaks.Rd | 68 +- man/findvalleys.Rd | 74 +- man/fitplane.Rd | 70 +- man/flatsa.Rd | 68 +- man/focal_metrics.Rd | 164 ++--- man/height_ba.Rd | 60 +- man/normforest.Rd | 74 +- man/orelevation.Rd | 60 +- man/orforest.Rd | 66 +- man/pad_edges.Rd | 60 +- man/plot_ba_curve.Rd | 74 +- man/remove_plane.Rd | 66 +- man/rotate.Rd | 34 - man/s10z.Rd | 52 - man/sa.Rd | 58 - man/sbi.Rd | 54 - man/sci.Rd | 58 - man/scl.Rd | 76 +- man/sdc.Rd | 72 +- man/sdq.Rd | 66 +- man/sdq6.Rd | 66 +- man/sdr.Rd | 64 +- man/sds.Rd | 52 - man/sfd.Rd | 72 +- man/sfd_.Rd | 72 +- man/simpsons.Rd | 90 +-- man/sk.Rd | 60 +- man/sku.Rd | 68 +- man/slopecalc.Rd | 72 +- man/slopemeans.Rd | 82 +- man/smean.Rd | 54 - man/sph.Rd | 54 - man/spk.Rd | 60 +- man/sq.Rd | 60 +- man/srw.Rd | 80 +- man/ssc.Rd | 56 - man/ssk.Rd | 64 +- man/std.Rd | 78 +- man/stxr.Rd | 78 +- man/surface_area.Rd | 70 +- man/sv.Rd | 54 - man/svi.Rd | 58 - man/svk.Rd | 60 +- man/texture_image.Rd | 206 +++--- man/window_metric.Rd | 146 ++-- man/zshift.Rd | 102 +-- tests/testthat.R | 10 tests/testthat/test_inputs_spatRaster.R | 302 +++++----- vignettes/geodiv_Examples.pdf.asis | 12 86 files changed, 6133 insertions(+), 6103 deletions(-)
Title: Exploratory Factor Analysis Functions for Assessing
Dimensionality
Description: Functions for an assortment of factor analysis-related
procedures, including eleven procedures for determining the number of
factors; for factor analysis with multiple options for methods of extraction
and rotation; for bifactor analysis; for extension factor analysis;
options for running the analyses using either raw data
or correlation matrices as input and with options
for conducting the analyses using Pearson correlations,
Kendall correlations, Spearman correlations, gamma correlations, or polychoric
correlations; wrapper 'lavaan'-based functions for factorial invariance
and exploratory structural equation modeling;
functions for the factorability of a correlation matrix,
for the congruences between factors from different datasets, for the
assessment of local independence, for the assessment of factor solution
complexity, for internal consistency, and for correcting Pearson correlation
coefficients for attenuation due to unreliability.
Auerswald & Moshagen (2019, ISSN:1939-1463 [...truncated...]
Author: Brian P. O'Connor [aut, cre]
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between EFA.dimensions versions 0.1.8.6 dated 2026-02-04 and 0.1.8.8 dated 2026-07-21
DESCRIPTION | 40 - MD5 | 100 ++-- NAMESPACE | 19 R/BIFACTOR.R |only R/COMPLEXITY.R | 25 - R/CONGRUENCE.R | 16 R/CORRECTED_CORRELS.R | 44 + R/DIMTESTS.R | 120 ++++- R/EFA.R | 295 ++++++------- R/EFA_SCORES.R | 39 - R/EMPKC.R | 8 R/ESEM.R |only R/EXTENSION_FA.R | 58 +- R/FACTORABILITY.R | 48 +- R/Factorial_Invariance.R |only R/INTERNAL.CONSISTENCY.R | 206 +++------ R/LOCALDEP.R | 24 - R/MAP.R | 26 - R/MISSING_INFO.R | 8 R/NEVALSGT1.R | 18 R/OMEGA.R |only R/PARALLEL.R | 20 R/PCA.R | 106 ++-- R/POLYCHORIC_R.R | 14 R/PROCRUSTES.R | 20 R/RAWPAR.R | 40 - R/ROOTFIT.R | 20 R/SALIENT.R | 45 + R/SCREE_PLOT.R | 11 R/SESCREE.R | 11 R/SMT.R | 18 R/utilities_bifactor.R |only R/utilities_boc.R | 953 +++++++++++++++++++++++------------------- build |only data/data_RSE.rda |binary data/data_RSE_not_recoded.rda |only data/data_RSE_sex.rda |only inst |only man/BIFACTOR.Rd |only man/DIMTESTS.Rd | 55 -- man/EFA.Rd | 173 ++++--- man/EFA.dimensions-package.Rd | 44 + man/ESEM.Rd |only man/Factorial_Invariance.Rd |only man/INTERNAL_CONSISTENCY.Rd | 136 ----- man/OMEGA.Rd |only man/PCA.Rd | 122 ++++- man/RAWPAR.Rd | 6 man/RECODE.Rd | 12 man/SALIENT.Rd | 7 man/data_RSE.Rd | 16 man/data_RSE_not_recoded.Rd |only man/data_RSE_sex.Rd |only vignettes |only 54 files changed, 1537 insertions(+), 1386 deletions(-)
More information about EFA.dimensions at CRAN
Permanent link
Title: Dynamic Shrinkage Process and Change Point Detection
Description: Provides efficient Markov chain Monte Carlo (MCMC) algorithms for
dynamic shrinkage processes, which extend global-local shrinkage priors to
the time series setting by allowing shrinkage to depend on its own past.
These priors yield locally adaptive estimates, useful for time series and
regression functions with irregular features. The package includes full MCMC
implementations for trend filtering using dynamic shrinkage on signal differences,
producing locally constant or linear fits with adaptive credible bands.
Also included are models with static shrinkage and normal-inverse-Gamma priors for comparison.
Additional tools cover dynamic regression with time-varying coefficients and
B-spline models with shrinkage on basis differences, allowing for flexible
curve-fitting with unequally spaced data. Some support for heteroscedastic errors,
outlier detection, and change point estimation.
Methods in this package are described in Kowal et al. (2019) <doi:10.1111/rssb.12325>,
Wu et al. [...truncated...]
Author: Daniel R. Kowal [aut, cph],
Haoxuan Wu [aut],
Toryn Schafer [aut, cre] ,
Jason B. Cho [aut],
David S. Matteson [aut]
Maintainer: Toryn Schafer <toryn27@gmail.com>
Diff between dsp versions 1.5.1 dated 2026-07-16 and 1.6.0 dated 2026-07-21
DESCRIPTION | 6 ++-- MD5 | 22 ++++++++-------- NEWS.md | 12 ++++++++ R/component_samplers.R | 59 +++++++++++++++++++++++++++++++++++-------- R/dsp-package.R | 7 +++++ R/dsp_model.R | 53 ++++++++++++++++++++++++++++++++++++++- R/nb_btf.R | 66 +++++++++++++++++++++++++++++++++++++------------ R/plotmethods.R | 12 +++++++- R/print.R | 6 ++-- man/btf_nb.Rd | 35 ++++++++++++++++++------- man/dsp_fit.Rd | 5 +++ src/mat_dec.cpp | 12 ++++++++ 12 files changed, 240 insertions(+), 55 deletions(-)
Title: Drug Response Prediction from Differential Multi-Omics Networks
Description: While it has been well established that drugs affect and help
patients differently, personalized drug response predictions remain
challenging. Solutions based on single omics measurements have been proposed,
and networks provide means to incorporate molecular interactions into reasoning.
However, how to integrate the wealth of information contained in multiple omics
layers still poses a complex problem.
We present a novel network analysis pipeline, DrDimont, Drug response prediction
from Differential analysis of multi-omics networks. It allows for comparative
conclusions between two conditions and translates them into differential drug
response predictions. DrDimont focuses on molecular interactions. It establishes
condition-specific networks from correlation within an omics layer that are
then reduced and combined into heterogeneous, multi-omics molecular networks.
A novel semi-local, path-based integration step ensures integrative conclusions.
Differential predictions are derived fro [...truncated...]
Author: Katharina Baum [cre] ,
Pauline Hiort [aut] ,
Julian Hugo [aut] ,
Spoorthi Kashyap [aut] ,
Nataniel Mueller [aut] ,
Justus Zeinert [aut]
Maintainer: Katharina Baum <katharina.baum@fu-berlin.de>
This is a re-admission after prior archival of version 0.1.6 dated 2025-11-08
Diff between DrDimont versions 0.1.6 dated 2025-11-08 and 0.1.7 dated 2026-07-21
DESCRIPTION | 11 ++-- LICENSE | 2 MD5 | 57 ++++++++++++------------ R/interaction_score.R | 23 ++++------ R/network_generation.R | 4 - R/pipeline_functions.R | 10 ++-- R/settings.R | 10 ++-- README.md |only build/vignette.rds |binary data/combined_graphs_example.rda |binary data/correlation_matrices_example.rda |binary data/differential_graph_example.rda |binary data/drug_gene_interactions.rda |binary data/drug_response_scores_example.rda |binary data/drug_target_edges_example.rda |binary data/individual_graphs_example.rda |binary data/interaction_score_graphs_example.rda |binary data/layers_example.rda |binary data/metabolite_data.rda |binary data/metabolite_protein_interactions.rda |binary data/mrna_data.rda |binary data/phosphosite_data.rda |binary data/protein_data.rda |binary inst/doc/DrDimont_Vignette.R | 18 ++----- inst/doc/DrDimont_Vignette.Rmd | 24 +++------- inst/doc/DrDimont_Vignette.html | 69 +++++++++++++----------------- inst/python_igraph_interaction_score.py | 11 ++++ man/generate_interaction_score_graphs.Rd | 2 man/run_pipeline.Rd | 2 vignettes/DrDimont_Vignette.Rmd | 24 +++------- 30 files changed, 126 insertions(+), 141 deletions(-)
Title: Ranking Methods for Competition Results
Description: Compute ranking and rating based on competition
results. Methods of different nature are implemented: with fixed
Head-to-Head structure, with variable Head-to-Head structure and with
iterative nature. All algorithms are taken from the book 'Who’s #1?:
The science of rating and ranking' by Amy N. Langville and Carl D.
Meyer (2012, ISBN:978-0-691-15422-0).
Author: Evgeni Chasnovski [aut, cre]
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>
Diff between comperank versions 0.1.1 dated 2020-03-03 and 0.1.2 dated 2026-07-21
DESCRIPTION | 14 MD5 | 42 - NEWS.md | 4 R/colley.R | 2 R/comperank-package.R | 2 R/data.R | 6 R/iterative.R | 10 R/keener.R | 2 R/utils.R | 2 README.md | 274 +++++------ build/vignette.rds |binary inst/doc/methods-overview.Rmd | 6 inst/doc/methods-overview.html | 973 ++++++++++++++++++++++++----------------- man/colley.Rd | 2 man/comperank-package.Rd | 9 man/elo.Rd | 4 man/keener.Rd | 6 man/snooker_events.Rd | 8 man/snooker_matches.Rd | 8 man/snooker_players.Rd | 8 src/RcppExports.cpp | 5 vignettes/methods-overview.Rmd | 6 22 files changed, 784 insertions(+), 609 deletions(-)
Title: Self Calibrating Quantile-Quantile Plots for Visual Testing
Description: Provides the function qqtest which incorporates uncertainty in its
qqplot display(s) so that the user might have a better sense of the
evidence against the specified distributional hypothesis. qqtest draws a
quantile quantile plot for visually assessing whether the data come from a
test distribution that has been defined in one of many ways. The vertical
axis plots the data quantiles, the horizontal those of a test distribution.
The default behaviour generates 1000 samples from the test distribution and
overlays the plot with shaded pointwise interval estimates for the ordered
quantiles from the test distribution. A small number of independently
generated exemplar quantile plots can also be overlaid. Both the interval
estimates and the exemplars provide different comparative information to
assess the evidence provided by the qqplot for or against the hypothesis
that the data come from the test distribution (default is normal or
gaussian). Finally, a visual test of significance (a [...truncated...]
Author: Wayne Oldford [aut, cre]
Maintainer: Wayne Oldford <rwoldford@uwaterloo.ca>
Diff between qqtest versions 1.2.0 dated 2020-03-16 and 1.2.1 dated 2026-07-21
DESCRIPTION | 13 - MD5 | 33 ++-- NEWS.md | 6 R/hideLocation.R | 7 - R/qqtest.R | 2 build/partial.rdb |only build/vignette.rds |binary inst/doc/K-distribution.R | 14 +- inst/doc/K-distribution.html | 289 +++++++++++++++++++++++++++---------------- man/WachusettReservoir.Rd | 6 man/bacteria.Rd | 6 man/hideLocation.Rd | 6 man/penicillin.Rd | 6 man/primer.Rd | 6 man/pullstrength.Rd | 6 man/qqtest.Rd | 2 man/sittingHeights.Rd | 6 man/stacklossDistances.Rd | 6 18 files changed, 262 insertions(+), 152 deletions(-)
Title: Semi-Parametric Joint Modeling of Longitudinal and Survival Data
Description: Implements scalable joint models for large-scale competing risks time-to-event data with one or multiple longitudinal biomarkers using the efficient algorithms developed by Li et al. (2022) <doi:10.1155/2022/1362913> and <doi:10.48550/arXiv.2506.12741>.
The time-to-event process is modeled using a cause-specific Cox proportional hazards model
with time-fixed covariates, while longitudinal biomarkers are modeled
using linear mixed-effects models. The association between the longitudinal
and survival processes is captured through shared random effects. The
package enables analysis of large-scale biomedical data to model biomarker
trajectories, estimate their effects on event risks, and perform dynamic
prediction of future events based on patients' longitudinal histories.
Functions for simulating survival and longitudinal data for multiple
biomarkers are included, along with built-in example datasets. The package
also supports modeling a single biomarker with heterogeneous wit [...truncated...]
Author: Shanpeng Li [aut, cre],
Ace Mejia-Sanchez [ctb],
Emily Ouyang [ctb],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between FastJM versions 1.6.0 dated 2026-03-28 and 1.7.0 dated 2026-07-21
FastJM-1.6.0/FastJM/R/AUCJMMLSM.R |only FastJM-1.6.0/FastJM/R/ConcordanceJMMLSM.R |only FastJM-1.6.0/FastJM/R/Concordancejmcs.R |only FastJM-1.6.0/FastJM/R/DynPredAccjmcs.R |only FastJM-1.6.0/FastJM/R/MAEQJMMLSM.R |only FastJM-1.6.0/FastJM/R/PEJMMLSM.R |only FastJM-1.6.0/FastJM/R/Pkmv.us.R |only FastJM-1.6.0/FastJM/R/Pkmv.us_SF.R |only FastJM-1.6.0/FastJM/R/anova.jmcs.R |only FastJM-1.6.0/FastJM/R/summary.AUCJMMLSM.R |only FastJM-1.6.0/FastJM/R/summary.ConcordanceJMMLSM.R |only FastJM-1.6.0/FastJM/R/summary.Concordancejmcs.R |only FastJM-1.6.0/FastJM/R/summary.DynPredAccjmcs.R |only FastJM-1.6.0/FastJM/R/summary.MAEQJMMLSM.R |only FastJM-1.6.0/FastJM/R/summary.PEJMMLSM.R |only FastJM-1.6.0/FastJM/build |only FastJM-1.6.0/FastJM/inst/doc |only FastJM-1.6.0/FastJM/man/AUCJMMLSM.Rd |only FastJM-1.6.0/FastJM/man/ConcordanceJMMLSM.Rd |only FastJM-1.6.0/FastJM/man/Concordancejmcs.Rd |only FastJM-1.6.0/FastJM/man/DynPredAccjmcs.Rd |only FastJM-1.6.0/FastJM/man/MAEQJMMLSM.Rd |only FastJM-1.6.0/FastJM/man/PEJMMLSM.Rd |only FastJM-1.6.0/FastJM/man/anova.Rd |only FastJM-1.6.0/FastJM/man/plot.survfitJMMLSM.Rd |only FastJM-1.6.0/FastJM/man/residuals.Rd |only FastJM-1.6.0/FastJM/vignettes |only FastJM-1.7.0/FastJM/DESCRIPTION | 17 FastJM-1.7.0/FastJM/MD5 | 185 +-- FastJM-1.7.0/FastJM/NAMESPACE | 41 FastJM-1.7.0/FastJM/NEWS.md | 4 FastJM-1.7.0/FastJM/R/Concordance.JMMLSM.R |only FastJM-1.7.0/FastJM/R/Concordance.R |only FastJM-1.7.0/FastJM/R/Concordance.jmcs.R |only FastJM-1.7.0/FastJM/R/Concordance.mvjmcs.R |only FastJM-1.7.0/FastJM/R/DynPredAcc.JMMLSM.R |only FastJM-1.7.0/FastJM/R/DynPredAcc.R |only FastJM-1.7.0/FastJM/R/DynPredAcc.jmcs.R |only FastJM-1.7.0/FastJM/R/DynPredAcc.mvjmcs.R |only FastJM-1.7.0/FastJM/R/FastJM.R | 8 FastJM-1.7.0/FastJM/R/GetBayes.R | 121 ++ FastJM-1.7.0/FastJM/R/Getmvinit.R | 373 +++++- FastJM-1.7.0/FastJM/R/JMMLSM.R | 130 +- FastJM-1.7.0/FastJM/R/JMMLSM_control.R |only FastJM-1.7.0/FastJM/R/P.us.R | 21 FastJM-1.7.0/FastJM/R/Pk.us.R | 37 FastJM-1.7.0/FastJM/R/RcppExports.R | 16 FastJM-1.7.0/FastJM/R/combine_biomarkers.R |only FastJM-1.7.0/FastJM/R/estepMV_worker.R | 18 FastJM-1.7.0/FastJM/R/estepMV_workerSF.R | 15 FastJM-1.7.0/FastJM/R/fixef.R | 20 FastJM-1.7.0/FastJM/R/getbSig.R | 59 - FastJM-1.7.0/FastJM/R/getbSig_grad.R | 123 +- FastJM-1.7.0/FastJM/R/getbSig_gradSF.R | 74 - FastJM-1.7.0/FastJM/R/getbsigSF.R | 32 FastJM-1.7.0/FastJM/R/jmcs.R | 103 + FastJM-1.7.0/FastJM/R/jmcs_control.R |only FastJM-1.7.0/FastJM/R/logLik.R | 103 + FastJM-1.7.0/FastJM/R/logLikCR.R | 116 ++ FastJM-1.7.0/FastJM/R/mvjmcs.R | 529 ++++++--- FastJM-1.7.0/FastJM/R/mvjmcs_control.R |only FastJM-1.7.0/FastJM/R/plot.jmcs.R | 166 ++ FastJM-1.7.0/FastJM/R/plot.survfitJMMLSM.R | 30 FastJM-1.7.0/FastJM/R/plot.survfitjmcs.R |only FastJM-1.7.0/FastJM/R/plot.survfitmvjmcs.R |only FastJM-1.7.0/FastJM/R/print.mvjmcs.R | 221 +++ FastJM-1.7.0/FastJM/R/print.survfitJMMLSM.R | 2 FastJM-1.7.0/FastJM/R/print.survfitjmcs.R | 2 FastJM-1.7.0/FastJM/R/ranef.R | 28 FastJM-1.7.0/FastJM/R/residuals.jmcs.R | 3 FastJM-1.7.0/FastJM/R/simJMWSVdata.R |only FastJM-1.7.0/FastJM/R/simJMdata.R |only FastJM-1.7.0/FastJM/R/simmvJMdata.R | 48 FastJM-1.7.0/FastJM/R/simmvJMdatalm.R |only FastJM-1.7.0/FastJM/R/summary.Concordance.R |only FastJM-1.7.0/FastJM/R/summary.DynPredAcc.R |only FastJM-1.7.0/FastJM/R/summary.JMMLSM.R | 4 FastJM-1.7.0/FastJM/R/supporting_timeplot.R |only FastJM-1.7.0/FastJM/R/survfitJM.JMMLSM.R |only FastJM-1.7.0/FastJM/R/survfitJM.R |only FastJM-1.7.0/FastJM/R/survfitJM.jmcs.R |only FastJM-1.7.0/FastJM/R/survfitJM.mvjmcs.R |only FastJM-1.7.0/FastJM/R/survfitJMMLSM.R | 9 FastJM-1.7.0/FastJM/R/survfitjmcs.R | 8 FastJM-1.7.0/FastJM/R/survfitmvjmcs.R | 19 FastJM-1.7.0/FastJM/R/timeplot.R |only FastJM-1.7.0/FastJM/R/vcov.jmcs.R | 90 - FastJM-1.7.0/FastJM/R/vcov.mvjmcs.R |only FastJM-1.7.0/FastJM/README.md | 559 ++++++---- FastJM-1.7.0/FastJM/inst/WORDLIST | 11 FastJM-1.7.0/FastJM/man/Concordance.Rd |only FastJM-1.7.0/FastJM/man/DynPredAcc.Rd |only FastJM-1.7.0/FastJM/man/JMMLSM.Rd | 94 - FastJM-1.7.0/FastJM/man/JMMLSM_control.Rd |only FastJM-1.7.0/FastJM/man/combine_biomarkers.Rd |only FastJM-1.7.0/FastJM/man/figures/README-unnamed-chunk-11-1.png |only FastJM-1.7.0/FastJM/man/figures/README-unnamed-chunk-12-1.png |only FastJM-1.7.0/FastJM/man/figures/README-unnamed-chunk-14-1.png |only FastJM-1.7.0/FastJM/man/figures/README-unnamed-chunk-15-1.png |only FastJM-1.7.0/FastJM/man/figures/README-unnamed-chunk-17-1.png |only FastJM-1.7.0/FastJM/man/figures/README-unnamed-chunk-3-1.png |only FastJM-1.7.0/FastJM/man/figures/README-unnamed-chunk-4-1.png |binary FastJM-1.7.0/FastJM/man/figures/README-unnamed-chunk-5-1.png |only FastJM-1.7.0/FastJM/man/figures/README-unnamed-chunk-8-1.png |only FastJM-1.7.0/FastJM/man/fixef.Rd | 2 FastJM-1.7.0/FastJM/man/jmcs.Rd | 102 - FastJM-1.7.0/FastJM/man/jmcs_control.Rd |only FastJM-1.7.0/FastJM/man/mvjmcs.Rd | 197 ++- FastJM-1.7.0/FastJM/man/mvjmcs_control.Rd |only FastJM-1.7.0/FastJM/man/plot.Rd |only FastJM-1.7.0/FastJM/man/plot.jmcs.Rd | 2 FastJM-1.7.0/FastJM/man/ranef.Rd | 4 FastJM-1.7.0/FastJM/man/residuals.jmcs.Rd |only FastJM-1.7.0/FastJM/man/simJMWSVdata.Rd |only FastJM-1.7.0/FastJM/man/simJMdata.Rd |only FastJM-1.7.0/FastJM/man/simmvJMdata.Rd | 6 FastJM-1.7.0/FastJM/man/simmvJMdatalm.Rd |only FastJM-1.7.0/FastJM/man/summary.Concordance.Rd |only FastJM-1.7.0/FastJM/man/summary.Rd | 60 - FastJM-1.7.0/FastJM/man/survfitJM.Rd |only FastJM-1.7.0/FastJM/man/survfitJMMLSM.Rd | 8 FastJM-1.7.0/FastJM/man/survfitjmcs.Rd | 7 FastJM-1.7.0/FastJM/man/survfitmvjmcs.Rd | 7 FastJM-1.7.0/FastJM/man/timeplot.Rd |only FastJM-1.7.0/FastJM/man/vcov.Rd | 13 FastJM-1.7.0/FastJM/src/RcppExports.cpp | 135 ++ FastJM-1.7.0/FastJM/src/getmvCov.cpp | 3 FastJM-1.7.0/FastJM/src/getmvCovSF.cpp | 1 FastJM-1.7.0/FastJM/src/getmvCov_lm.cpp |only FastJM-1.7.0/FastJM/src/getmvCov_lmSF.cpp |only FastJM-1.7.0/FastJM/src/normalapprox_lm.cpp |only FastJM-1.7.0/FastJM/src/normalapprox_lmSF.cpp |only 132 files changed, 2866 insertions(+), 1120 deletions(-)
Title: Asymmetry Measures for Probability Density Functions
Description: Provides functions and examples for the weak and strong density asymmetry measures in the articles: "A measure of asymmetry", Patil, Patil and Bagkavos (2012) <doi:10.1007/s00362-011-0401-6> and "A measure of asymmetry based on a new necessary and sufficient condition for symmetry", Patil, Bagkavos and Wood (2014) <doi:10.1007/s13171-013-0034-z>. The measures provided here are useful for quantifying the asymmetry of the shape of a density of a random variable. The package facilitates implementation of the measures which are applicable in a variety of fields including e.g. probability theory, statistics and economics.
Author: Dimitrios Bagkavos [aut, cre],
Lucia Gamez [aut]
Maintainer: Dimitrios Bagkavos <dimitrios.bagkavos@gmail.com>
Diff between asymmetry.measures versions 0.2 dated 2020-07-22 and 0.3 dated 2026-07-21
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ man/GDP.Per.head.dist.1995.Rd | 2 +- man/GDP.Per.head.dist.2005.Rd | 2 +- man/d.sample.Rd | 2 +- man/edf.Rd | 2 +- man/p.sample.Rd | 4 ++-- man/pdfsq.Rd | 2 +- man/pdfsqcdf.Rd | 2 +- man/pdfsqcdfstar.Rd | 4 ++-- man/pdfthird.Rd | 4 ++-- man/q.sample.Rd | 2 +- man/r.sample.Rd | 2 +- 13 files changed, 30 insertions(+), 30 deletions(-)
More information about asymmetry.measures at CRAN
Permanent link
Title: Extracts Risk Neutral Densities of Prices, Money Market Rates
and Government Bond Yields from Interest Rates Futures Options
Prices
Description: Provides with parametric Risk Neutral Densities (RNDs) and cumulative densities of futures prices on fixed-income products. It relies on options on Short Term Interest Rate futures or options on government bond futures. It models the futures price as a mixture of lognormal densities. It also provides with the RNDs and cumulative densities of the money market rate or the government bond yield inferred from the futures price, using the RND of the futures price. The package also provides with the probability attached to each bond in the delivery basket of a government bond futures to be the cheapest at maturity, and also the non parametric distribution of the spread between two bond yields, using two RNDs based on options on bond futures of the same maturity. The package leverages on the works of Melick, W. R. and Thomas, C. P. (1997) <doi:10.2307/2331318> and B. Bahra (1998) <doi:10.2139/ssrn.77429>.
Author: William Arrata [aut, cre]
Maintainer: William Arrata <william.arrata@gmail.com>
Diff between yrnd versions 0.1.4 dated 2026-06-14 and 0.1.5 dated 2026-07-21
yrnd-0.1.4/yrnd/inst/doc/yrnd_functions.R |only yrnd-0.1.4/yrnd/inst/doc/yrnd_functions.Rmd |only yrnd-0.1.4/yrnd/inst/doc/yrnd_functions.html |only yrnd-0.1.4/yrnd/vignettes/yrnd_functions.Rmd |only yrnd-0.1.5/yrnd/DESCRIPTION | 12 +++--- yrnd-0.1.5/yrnd/MD5 | 50 ++++++++++++++------------ yrnd-0.1.5/yrnd/NAMESPACE | 5 ++ yrnd-0.1.5/yrnd/R/bond_future_charac_bbg.R | 2 - yrnd-0.1.5/yrnd/R/bond_future_price.R | 33 ++++++++--------- yrnd-0.1.5/yrnd/R/bond_yield_spread.R |only yrnd-0.1.5/yrnd/R/ctd_bond_yield.R | 45 +++++++++++------------ yrnd-0.1.5/yrnd/R/deliv_bonds_charac_bbg.R | 2 - yrnd-0.1.5/yrnd/R/globals.R | 3 + yrnd-0.1.5/yrnd/R/option_prices_bbg.R | 4 +- yrnd-0.1.5/yrnd/R/proba_ctd.R | 17 ++------ yrnd-0.1.5/yrnd/R/proba_ctd_opt.R |only yrnd-0.1.5/yrnd/R/stir_future_charac_bbg.R | 2 - yrnd-0.1.5/yrnd/R/stir_future_price.R | 31 +++++++--------- yrnd-0.1.5/yrnd/R/stir_rate.R | 32 ++++++++-------- yrnd-0.1.5/yrnd/build/vignette.rds |binary yrnd-0.1.5/yrnd/inst/doc/yrnd-functions.R |only yrnd-0.1.5/yrnd/inst/doc/yrnd-functions.Rmd |only yrnd-0.1.5/yrnd/inst/doc/yrnd-functions.html |only yrnd-0.1.5/yrnd/man/bond_future_price.Rd | 20 +++++----- yrnd-0.1.5/yrnd/man/bond_yield_spread.Rd |only yrnd-0.1.5/yrnd/man/ctd_bond_yield.Rd | 22 +++++------ yrnd-0.1.5/yrnd/man/deliv_bonds_charac_bbg.Rd | 2 - yrnd-0.1.5/yrnd/man/option_prices_bbg.Rd | 2 - yrnd-0.1.5/yrnd/man/proba_ctd_opt.Rd |only yrnd-0.1.5/yrnd/man/stir_future_price.Rd | 18 ++++----- yrnd-0.1.5/yrnd/man/stir_rate.Rd | 18 ++++----- yrnd-0.1.5/yrnd/vignettes/yrnd-functions.Rmd |only 32 files changed, 162 insertions(+), 158 deletions(-)
Title: Native 'LaTeX' Math Rendering for Grid Graphics
Description: Renders 'LaTeX' math equations as native R grid graphics objects
(grobs) using the 'MicroTeX' 'C++' library as the layout engine. Produces
resolution-independent vector output that works on any R graphics device,
with no external 'LaTeX' installation required.
Author: Alim Dayim [aut, cre] ,
Nano Michael [cph] ,
Bundled math font authors [cph]
Maintainer: Alim Dayim <ad938@cam.ac.uk>
Diff between gridmicrotex versions 0.0.4 dated 2026-06-01 and 0.0.5 dated 2026-07-21
DESCRIPTION | 8 +- MD5 | 48 +++++++-------- NEWS.md | 14 +++- R/cache.R | 17 +++-- R/fonts.R | 4 - R/ggplot2-integration.R | 11 +++ R/grid-builder.R | 3 R/latex-grob.R | 108 ++++++++++++++++++++--------------- R/options.R | 16 ++--- R/text-font-auto.R | 17 ----- inst/doc/getting-started.html | 6 - man/build_latex_children.Rd | 3 man/dot-make_text_measurer.Rd | 5 - man/element_latex.Rd | 12 +-- man/geom_latex.Rd | 14 +--- man/gridmicrotex-package.Rd | 5 + man/grobMark.Rd | 4 - man/latex_dims.Rd | 14 ++-- man/latex_grob.Rd | 30 +++++---- man/latex_options.Rd | 16 ++--- man/latex_tree.Rd | 14 ++-- src/otf_math_reader.cpp | 28 +++++---- tests/testthat/Rplots.pdf |binary tests/testthat/test-ggplot2.R | 18 +++++ tests/testthat/test-marks-and-just.R | 90 +++++++++++++++++++++++++++++ 25 files changed, 333 insertions(+), 172 deletions(-)
Title: Complex-Valued Wavelet Lifting for Signal Denoising
Description: Implementations of recent complex-valued wavelet shrinkage procedures for smoothing irregularly sampled signals, see Hamilton et al (2018) <doi:10.1080/00401706.2017.1281846>.
Author: Matt Nunes [aut, cre],
Marina Knight [aut],
Jean Hamilton [ctb],
Piotr Fryzlewicz [ctb]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>
Diff between CNLTreg versions 0.1-2 dated 2018-07-18 and 0.1-3 dated 2026-07-21
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- build/partial.rdb |binary man/cnlt.reg.Rd | 4 ++-- man/fwtnppermC.Rd | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: 'Constrained Quantile Regression with B-Splines'
Description: Quantile regression with B-splines under shape constraints.
The initial version with cubic splines is now augmented with splines
of degree 1 to 4. Constraints for degrees 3 (monotone) and 4
(monotone and convex) use the Karlin-Studden SOCP characterization
for the sign of the polynomial, while other constraints applied
at the knots are added as linear problems. The method for cubic
splines is described in Abbes (2026) <doi:10.5281/zenodo.17427913>.
Other formulations are simple consequences of the other given
references. This R implementation is intended for demonstration
and prototyping. All B-spline and polynomial functions have been
rewritten for consistency. An equivalent Python package is available
at <https://pypi.org/project/BsplineQuantRegpy/>.
Author: Alexandre Abbes [aut, cre]
Maintainer: Alexandre Abbes <alexandre.abbes@proton.me>
Diff between BsplineQuantReg versions 0.1.0 dated 2026-06-23 and 0.2.0 dated 2026-07-21
BsplineQuantReg-0.1.0/BsplineQuantReg/R/zzz.R |only BsplineQuantReg-0.1.0/BsplineQuantReg/man/Spline_der_knots.Rd |only BsplineQuantReg-0.1.0/BsplineQuantReg/man/apply_karlin_constraints.Rd |only BsplineQuantReg-0.1.0/BsplineQuantReg/man/bspline_to_deriv_coeffs_pp.Rd |only BsplineQuantReg-0.1.0/BsplineQuantReg/man/is_beta.Rd |only BsplineQuantReg-0.1.0/BsplineQuantReg/man/package_version.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/DESCRIPTION | 33 BsplineQuantReg-0.2.0/BsplineQuantReg/MD5 | 108 +- BsplineQuantReg-0.2.0/BsplineQuantReg/NAMESPACE | 75 - BsplineQuantReg-0.2.0/BsplineQuantReg/NEWS |only BsplineQuantReg-0.2.0/BsplineQuantReg/R/bspline-base.R | 339 +++--- BsplineQuantReg-0.2.0/BsplineQuantReg/R/bspline-eval.R | 489 ++++++---- BsplineQuantReg-0.2.0/BsplineQuantReg/R/constraints.R |only BsplineQuantReg-0.2.0/BsplineQuantReg/R/cubic-regression.R |only BsplineQuantReg-0.2.0/BsplineQuantReg/R/deriv-coeffs.R |only BsplineQuantReg-0.2.0/BsplineQuantReg/R/imports.R | 9 BsplineQuantReg-0.2.0/BsplineQuantReg/R/linear-regression.R |only BsplineQuantReg-0.2.0/BsplineQuantReg/R/onLoad.R | 42 BsplineQuantReg-0.2.0/BsplineQuantReg/R/polynomial-utils.R | 360 +++---- BsplineQuantReg-0.2.0/BsplineQuantReg/R/quadratic-regression.R |only BsplineQuantReg-0.2.0/BsplineQuantReg/R/quantile-regression.R | 416 ++------ BsplineQuantReg-0.2.0/BsplineQuantReg/R/quartic-regression.R |only BsplineQuantReg-0.2.0/BsplineQuantReg/R/test_bsqr.R | 195 ++- BsplineQuantReg-0.2.0/BsplineQuantReg/README.md | 232 +++- BsplineQuantReg-0.2.0/BsplineQuantReg/build/partial.rdb |binary BsplineQuantReg-0.2.0/BsplineQuantReg/demo/00Index | 14 BsplineQuantReg-0.2.0/BsplineQuantReg/demo/comprehensive.R | 332 +++--- BsplineQuantReg-0.2.0/BsplineQuantReg/demo/convexity.R | 242 ++-- BsplineQuantReg-0.2.0/BsplineQuantReg/demo/degrees_comparison.R |only BsplineQuantReg-0.2.0/BsplineQuantReg/demo/demo_der3.R |only BsplineQuantReg-0.2.0/BsplineQuantReg/demo/logistic.R | 403 ++++---- BsplineQuantReg-0.2.0/BsplineQuantReg/demo/monotonicity.R | 133 +- BsplineQuantReg-0.2.0/BsplineQuantReg/demo/temperature.R | 421 ++++---- BsplineQuantReg-0.2.0/BsplineQuantReg/demo/temperature2.R | 487 +++++---- BsplineQuantReg-0.2.0/BsplineQuantReg/inst/CITATION | 97 + BsplineQuantReg-0.2.0/BsplineQuantReg/inst/References.bib | 82 - BsplineQuantReg-0.2.0/BsplineQuantReg/man/Bspline_base.Rd | 104 +- BsplineQuantReg-0.2.0/BsplineQuantReg/man/Bspline_deriv.Rd | 42 BsplineQuantReg-0.2.0/BsplineQuantReg/man/Omega.Rd | 48 BsplineQuantReg-0.2.0/BsplineQuantReg/man/SplineConstQuantRegBs1.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/SplineConstQuantRegBs2.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/SplineConstQuantRegBs3.Rd | 145 +- BsplineQuantReg-0.2.0/BsplineQuantReg/man/SplineConstQuantRegBs4.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/SplineCubicQuant.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/SplineLinearQuant.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/SplineQuadraticQuant.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/SplineQuarticQuant.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/Spline_der_knot.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/apply_karlin_cubic.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/apply_karlin_quadratic.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/apply_linear_constraint.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/bs_direct.Rd | 38 BsplineQuantReg-0.2.0/BsplineQuantReg/man/bspline_to_deriv_coeffs_cubic.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/bspline_to_deriv_coeffs_lin.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/bspline_to_deriv_coeffs_quad.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/bspline_to_deriv_coeffs_quart.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/change_polynomial_base_taylor.Rd | 48 BsplineQuantReg-0.2.0/BsplineQuantReg/man/dot-onAttach.Rd | 32 BsplineQuantReg-0.2.0/BsplineQuantReg/man/evalpp.Rd | 40 BsplineQuantReg-0.2.0/BsplineQuantReg/man/make_spline.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/makpp.Rd | 40 BsplineQuantReg-0.2.0/BsplineQuantReg/man/poly_eval.Rd | 46 BsplineQuantReg-0.2.0/BsplineQuantReg/man/polyadd.Rd | 48 BsplineQuantReg-0.2.0/BsplineQuantReg/man/polyderiv.Rd | 50 - BsplineQuantReg-0.2.0/BsplineQuantReg/man/polymul.Rd | 54 - BsplineQuantReg-0.2.0/BsplineQuantReg/man/print.callable_spline.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/print.quantile_spline.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/quantile_spline.Rd |only BsplineQuantReg-0.2.0/BsplineQuantReg/man/reduce_pol.Rd | 44 BsplineQuantReg-0.2.0/BsplineQuantReg/man/spline_eval.Rd | 64 - BsplineQuantReg-0.2.0/BsplineQuantReg/man/test_karlin_simple.Rd | 48 BsplineQuantReg-0.2.0/BsplineQuantReg/man/view_basis.Rd | 38 72 files changed, 2779 insertions(+), 2659 deletions(-)
More information about BsplineQuantReg at CRAN
Permanent link
Title: Weighted and Standard Elo Rates
Description: Estimates the standard and weighted Elo (WElo, Angelini et al., 2022 <doi:10.1016/j.ejor.2021.04.011>) rates. The current version provides Elo and WElo rates for tennis, according to different systems of weights (games or sets) and scale factors (constant, proportional to the number of matches, with more weight on Grand Slam matches or matches played on a specific surface). Moreover, the package gives the possibility of estimating the (bootstrap) standard errors for the rates. Finally, the package includes betting functions that automatically select the matches on which place a bet.
Author: Vincenzo Candila [aut, cre]
Maintainer: Vincenzo Candila <vcandila@unisa.it>
Diff between welo versions 0.1.4 dated 2024-03-19 and 0.1.5 dated 2026-07-21
DESCRIPTION | 8 +- MD5 | 10 +-- NEWS.md | 11 ++-- R/functions.R | 145 +++++++++++++++++++++++++++++++++++++++++++++-------- build/partial.rdb |binary man/tennis_data.Rd | 23 ++++++-- 6 files changed, 158 insertions(+), 39 deletions(-)
Title: Analysis of Two-Way Tables
Description: Carries out analyses of two-way tables with one observation per cell, together with graphical displays
for an additive fit and
a diagnostic plot for removable 'non-additivity' via a power transformation of the response.
It implements methods from Tukey's Exploratory Data Analysis (1973) <ISBN: 978-0201076165>, including a
1-degree-of-freedom test for row*column 'non-additivity', linear in the row and column effects.
Author: Michael Friendly [aut, cre] ,
Richard M. Heiberger [aut],
John Fox [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between twoway versions 0.6.3 dated 2020-06-26 and 0.7.0 dated 2026-07-21
DESCRIPTION | 18 +++++++++------ MD5 | 53 ++++++++++++++++++++++++++------------------- NAMESPACE | 3 ++ NEWS.md | 14 +++++++++++ R/anova.twoway.R | 12 +++++++--- R/as.data.frame.twoway.R | 3 +- R/data.R | 55 +++++++++++++++++++++++++++++++++++++++++++++-- R/plot.twoway.R | 2 + R/twoway.R | 2 - R/twoway.formula.R | 4 ++- data/Rubber.RData |only data/VermontPop.RData |only data/sentRT.RData |binary man/Arizona.Rd | 8 ++++-- man/Rubber.Rd |only man/VermontPop.Rd |only man/as.twoway.Rd | 11 +++++---- man/drugs.Rd | 5 +++- man/figures |only man/hstart.Rd | 5 +++- man/insectCounts.Rd | 4 ++- man/meanfit.Rd | 3 +- man/plot.twoway.Rd | 24 +++++++++++--------- man/print.twoway.Rd | 3 -- man/taskRT.Rd | 6 +++-- man/to_long.Rd | 11 +++++---- man/twoway.Rd | 14 ++++++++--- man/twoway.formula.Rd | 4 ++- 28 files changed, 193 insertions(+), 71 deletions(-)
Title: Rearrangement Distances Between Phylogenetic Trees
Description: Fast calculation of tree rearrangement distances.
For unrooted trees: Subtree Prune and Regraft (SPR), Tree Bisection and
Reconnection (TBR), and Replug distances, using the algorithms of Whidden
and Matsen (2017) <doi:10.48550/arXiv.1511.07529>.
For rooted trees: rooted SPR (rSPR) distance, using the fixed-parameter
algorithms of Whidden, Beiko, and Zeh (2013) <doi:10.1137/110845045>.
Author: Martin R. Smith [aut, cre, cph] ,
Chris Whidden [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TBRDist versions 2.0.0 dated 2026-03-30 and 2.0.1 dated 2026-07-21
DESCRIPTION | 6 MD5 | 186 +++--- NAMESPACE | 40 - NEWS.md | 4 R/RcppExports.R | 64 +- R/rspr.R | 246 ++++---- R/uspr.R | 734 ++++++++++++------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/TBRDist.html | 4 man/RSPRDist.Rd | 194 +++--- man/dot-CheckRooted.Rd | 38 - man/rspr_dist.Rd | 52 - src/rspr/R/rspR.r | 116 +-- src/rspr/R/rspR_examples.r | 52 - src/rspr/gen_rooted_trees.pl | 284 ++++----- src/rspr/multi_test.sh | 302 +++++----- src/rspr/rspr.h | 4 src/rspr/test_trees/big_test | 4 src/rspr/test_trees/big_test2 | 4 src/rspr/test_trees/bigtest_mult.txt | 2 src/rspr/test_trees/cluster_1.txt | 4 src/rspr/test_trees/cluster_10.txt | 2 src/rspr/test_trees/cluster_11.txt | 2 src/rspr/test_trees/cluster_12.txt | 2 src/rspr/test_trees/cluster_13.txt | 6 src/rspr/test_trees/cluster_14.txt | 4 src/rspr/test_trees/cluster_15.txt | 4 src/rspr/test_trees/cluster_16.txt | 2 src/rspr/test_trees/cluster_17.txt | 2 src/rspr/test_trees/cluster_18.txt | 2 src/rspr/test_trees/cluster_19.txt | 4 src/rspr/test_trees/cluster_2.txt | 4 src/rspr/test_trees/cluster_3.txt | 4 src/rspr/test_trees/cluster_4.txt | 4 src/rspr/test_trees/cluster_5.txt | 2 src/rspr/test_trees/cluster_6.txt | 2 src/rspr/test_trees/cluster_7.txt | 2 src/rspr/test_trees/cluster_8.txt | 2 src/rspr/test_trees/cluster_9.txt | 2 src/rspr/test_trees/cluster_a.txt | 2 src/rspr/test_trees/cluster_b.txt | 2 src/rspr/test_trees/cluster_c.txt | 2 src/rspr/test_trees/cluster_d.txt | 2 src/rspr/test_trees/cluster_e.txt | 2 src/rspr/test_trees/cluster_f.txt | 2 src/rspr/test_trees/cluster_test | 4 src/rspr/test_trees/mult_big_test | 2 src/rspr/test_trees/multi_cluster_test | 2 src/rspr/test_trees/multi_cluster_test_b.txt | 2 src/rspr/test_trees/multi_tree_7.1_test_00.txt | 2 src/rspr/test_trees/multi_tree_7.3_test_00.txt | 2 src/rspr/test_trees/multi_tree_7.4_test_00.txt | 2 src/rspr/test_trees/multi_tree_8.2_test_00.txt | 2 src/rspr/test_trees/multi_tree_8.4_test_00.txt | 2 src/rspr/test_trees/multi_tree_8.4_test_01.txt | 2 src/rspr/test_trees/multi_tree_8.5_test_00.txt | 2 src/rspr/test_trees/multi_tree_8.6_test_00.txt | 2 src/rspr/test_trees/multi_tree_8.7_test_00.txt | 2 src/rspr/test_trees/multi_tree_8.7_test_01.txt | 2 src/rspr/test_trees/multi_tree_basic.txt | 6 src/rspr/test_trees/multi_tree_basic_2.txt | 4 src/rspr/test_trees/multi_tree_basic_5.txt | 6 src/rspr/test_trees/multi_tree_test_00.txt | 2 src/rspr/test_trees/rand_mult_.txt | 2 src/rspr/test_trees/rand_mult_10.txt | 2 src/rspr/test_trees/rand_mult_15.txt | 2 src/rspr/test_trees/rand_mult_xx.txt | 2 src/rspr/test_trees/rho_test.txt | 2 src/rspr/test_trees/rho_test2.txt | 4 src/rspr/test_trees/show_moves_test.txt | 4 src/rspr/test_trees/show_moves_test_1.txt | 2 src/rspr/test_trees/show_moves_test_2.txt | 4 src/rspr/test_trees/single_cut_test_00.txt | 2 src/rspr/test_trees/single_cut_test_01.txt | 2 src/rspr/test_trees/trees2.txt | 4 src/rspr/test_trees/trees3.txt | 4 src/rspr/test_trees/trees4.txt | 4 src/rspr/test_trees/trees5.txt | 4 src/rspr/test_trees/trees6.txt | 4 src/rspr/test_trees/trees7.txt | 4 src/rspr/test_trees/trees_100_17.txt | 4 src/rspr/test_trees/trees_100_17_a.txt | 4 src/rspr/test_trees/trees_100_17_mult.txt | 4 src/rspr/test_trees/trees_100_24.txt | 4 src/rspr/test_trees/trees_100_24_a.txt | 4 src/rspr/test_trees/trees_100_24_mult.txt | 4 src/rspr/test_trees/trees_100_9.txt | 4 src/rspr/test_trees/trees_100_9_a.txt | 4 src/rspr/test_trees/trees_a.txt | 4 src/rspr/tests/pairwise | 8 src/uspr/tbr.h | 4 src/uspr/uspr.h | 10 tests/testthat/test-rspr.R | 396 ++++++------- 94 files changed, 1490 insertions(+), 1468 deletions(-)
Title: Interpretation of Point Forecasts as State-Dependent Quantiles
and Expectiles
Description: Estimate specification models for the state-dependent level of an optimal quantile/expectile forecast.
Wald Tests and the test of overidentifying restrictions are implemented. Plotting of the estimated specification model is possible.
The package contains two data sets with forecasts and realizations: the daily accumulated precipitation at London, UK from the high-resolution model of the
European Centre for Medium-Range Weather Forecasts (ECMWF, <https://www.ecmwf.int/>) and GDP growth Greenbook data by the US Federal Reserve.
See Schmidt, Katzfuss and Gneiting (2015) <doi:10.48550/arXiv.1506.01917> for more details on the identification and estimation of a directive behind a point forecast.
Author: Patrick Schmidt [aut, cre]
Maintainer: Patrick Schmidt <pschmidte@gmail.com>
Diff between PointFore versions 0.2.0 dated 2019-02-22 and 0.2.1 dated 2026-07-21
DESCRIPTION | 14 MD5 | 63 +- NEWS.md |only R/data.R | 6 R/estimate_functional.R | 7 README.md | 68 +- build/vignette.rds |binary data/GDP.rda |binary inst/doc/GDP.R | 42 - inst/doc/GDP.Rmd | 45 - inst/doc/GDP.html | 1066 +++++++++++++++++++++++++++----------------- inst/doc/Precipitation.R | 12 inst/doc/Precipitation.Rmd | 2 inst/doc/Precipitation.html | 526 ++++++++++++++++----- inst/doc/Tutorial.R | 28 - inst/doc/Tutorial.html | 843 +++++++++++++++++++++++----------- man/GDP.Rd | 11 man/PointFore.Rd | 1 man/constant.Rd | 10 man/estimate.functional.Rd | 23 man/expectiles.Rd | 3 man/logistic_linear.Rd | 10 man/plot.pointfore.Rd | 11 man/precipitation.Rd | 6 man/probit_break.Rd | 11 man/probit_linear.Rd | 10 man/probit_spline2.Rd | 10 man/probit_spline3.Rd | 12 man/quantiles.Rd | 3 man/summary.pointfore.Rd | 2 tests/testthat/testGDP.R | 2 vignettes/GDP.Rmd | 45 - vignettes/Precipitation.Rmd | 2 33 files changed, 1851 insertions(+), 1043 deletions(-)
Title: Descriptive Analysis and Visualization for Panel Data
Description: Provides a comprehensive set of tools for describing and visualizing panel data structures,
as well as for summarizing and visualizing variables within a panel data context.
Author: Dmitrii Tereshchenko [aut, cre]
Maintainer: Dmitrii Tereshchenko <dtereshch@gmail.com>
Diff between paneldesc versions 0.1.1 dated 2026-03-23 and 0.2.0 dated 2026-07-21
DESCRIPTION | 9 - MD5 | 100 ++++++++------ NAMESPACE | 13 + NEWS.md | 15 ++ R/add_means.R |only R/decompose_factor.R | 8 - R/decompose_numeric.R | 6 R/describe_balance.R | 8 - R/describe_dimensions.R | 6 R/describe_incomplete.R | 27 +++ R/describe_patterns.R | 11 + R/describe_periods.R | 9 - R/make_balanced.R |only R/make_demeaned.R |only R/make_long.R |only R/make_panel.R | 208 ++++-------------------------- R/make_wide.R |only R/plot_demeaned.R |only R/plot_heterogeneity.R | 11 - R/plot_missing.R | 29 ++-- R/plot_patterns.R | 14 +- R/plot_periods.R | 11 + R/production.R | 4 R/summarize_missing.R | 6 R/summarize_numeric.R | 8 - R/summarize_transition.R | 6 README.md | 9 + build/vignette.rds |binary data/production.rda |binary inst/doc/data-processing.R |only inst/doc/data-processing.Rmd |only inst/doc/data-processing.html |only inst/doc/getting-started.R | 16 +- inst/doc/getting-started.Rmd | 25 ++- inst/doc/getting-started.html | 287 ++++++++++++++++++++++-------------------- man/add_means.Rd |only man/decompose_factor.Rd | 7 - man/decompose_numeric.Rd | 5 man/describe_balance.Rd | 7 - man/describe_dimensions.Rd | 5 man/describe_incomplete.Rd | 5 man/describe_patterns.Rd | 12 + man/describe_periods.Rd | 10 - man/make_balanced.Rd |only man/make_demeaned.Rd |only man/make_long.Rd |only man/make_panel.Rd | 46 ++---- man/make_wide.Rd |only man/plot_demeaned.Rd |only man/plot_heterogeneity.Rd | 11 - man/plot_missing.Rd | 14 +- man/plot_patterns.Rd | 15 +- man/plot_periods.Rd | 10 - man/production.Rd | 4 man/summarize_missing.Rd | 5 man/summarize_numeric.Rd | 8 - man/summarize_transition.Rd | 5 vignettes/data-processing.Rmd |only vignettes/getting-started.Rmd | 25 ++- 59 files changed, 538 insertions(+), 502 deletions(-)
Title: Latent Variable Gaussian Process Modeling with Qualitative and
Quantitative Input Variables
Description: Fit response surfaces for datasets with latent-variable Gaussian
process modeling, predict responses for new inputs, and plot latent
variables locations in the latent space (only 1D or 2D). The input
variables of the datasets can be quantitative, qualitative/categorical or
mixed. The output variable of the datasets is a scalar (quantitative). The
optimization of the likelihood function is done using a successive
approximation/relaxation algorithm similar to another GP modeling package
"GPM". The modeling method is published in "A Latent Variable Approach to
Gaussian Process Modeling with Qualitative and Quantitative Factors" by
Yichi Zhang, Siyu Tao, Wei Chen, and Daniel W. Apley (2018)
<doi:10.48550/arXiv.1806.07504>. The package is developed in IDEAL of
Northwestern University.
Author: Siyu Tao [aut, cre],
Yichi Zhang [aut],
Daniel W. Apley [aut],
Wei Chen [aut]
Maintainer: Siyu Tao <siyutao2020@u.northwestern.edu>
Diff between LVGP versions 2.1.5 dated 2019-01-11 and 2.1.6 dated 2026-07-21
DESCRIPTION | 39 +++++++++++++++++++++++++++------------ MD5 | 15 ++++++++------- NEWS |only R/LVGP_fit.R | 16 ++++++++-------- R/LVGP_predict.R | 8 ++++---- R/example-data.R | 2 +- man/LVGP_fit.Rd | 16 ++++++++-------- man/LVGP_predict.Rd | 6 +++--- man/math_example.Rd | 2 +- 9 files changed, 60 insertions(+), 44 deletions(-)
Title: Apply-Style Dispatch for High-Performance Computing
Description: Provides apply-style functions using the Message Passing Interface ('MPI')
to improve the High-Performance Computing ('HPC') environment in R.
The package supports long vectors and efficient handling of large datasets for
MPI-based parallel computations.
Author: Ei-ji Nakama [aut, cre],
Junji NAKANO [aut]
Maintainer: Ei-ji Nakama <nakama@ki.rim.or.jp>
This is a re-admission after prior archival of version 0.21-247 dated 2021-09-04
Diff between Rhpc versions 0.21-247 dated 2021-09-04 and 0.26.4 dated 2026-07-21
Rhpc-0.21-247/Rhpc/README |only Rhpc-0.21-247/Rhpc/src/RhpcSerialize.c |only Rhpc-0.21-247/Rhpc/src/common/Rhpc_ms.h |only Rhpc-0.21-247/Rhpc/src/registerDynamicSymbol.c |only Rhpc-0.21-247/Rhpc/src/worker/RhpcWorkerSerialize.c |only Rhpc-0.26.4/Rhpc/ChangeLog | 8 Rhpc-0.26.4/Rhpc/DESCRIPTION | 37 Rhpc-0.26.4/Rhpc/MD5 | 93 Rhpc-0.26.4/Rhpc/NAMESPACE | 11 Rhpc-0.26.4/Rhpc/R/Rhpc.R | 10 Rhpc-0.26.4/Rhpc/R/RhpcRNG.R | 29 Rhpc-0.26.4/Rhpc/README.md |only Rhpc-0.26.4/Rhpc/build |only Rhpc-0.26.4/Rhpc/cleanup | 15 Rhpc-0.26.4/Rhpc/configure | 2792 ++++++++++---------- Rhpc-0.26.4/Rhpc/configure.ac | 31 Rhpc-0.26.4/Rhpc/inst |only Rhpc-0.26.4/Rhpc/man/Rhpc-package.Rd | 162 - Rhpc-0.26.4/Rhpc/man/Rhpc_EvalQ.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_Export.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_apply.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_enquote.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_finalize.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_getHandle.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_initialize.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_lapply.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_lapplyLB.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_numberOfWorker.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_sapply.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_sapplyLB.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_serialize.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_setupRNG.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_splitList.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_worker_call.Rd |only Rhpc-0.26.4/Rhpc/man/Rhpc_worker_noback.Rd |only Rhpc-0.26.4/Rhpc/src/Makevars.in | 10 Rhpc-0.26.4/Rhpc/src/Makevars.win | 41 Rhpc-0.26.4/Rhpc/src/RhpcMPI.c | 257 - Rhpc-0.26.4/Rhpc/src/RhpcMPIWorkerCall.c |only Rhpc-0.26.4/Rhpc/src/RhpcMPIWorkerCall.h | 198 - Rhpc-0.26.4/Rhpc/src/RhpcMPIlapplyLB.c |only Rhpc-0.26.4/Rhpc/src/RhpcMPIlapplyLB.h | 292 -- Rhpc-0.26.4/Rhpc/src/RhpcMPIlapplyseq.c |only Rhpc-0.26.4/Rhpc/src/RhpcMPIlapplyseq.h | 279 - Rhpc-0.26.4/Rhpc/src/Rhpc_init.c |only Rhpc-0.26.4/Rhpc/src/common/Makefile.in |only Rhpc-0.26.4/Rhpc/src/common/Makefile.win |only Rhpc-0.26.4/Rhpc/src/common/Rhpc.h | 122 Rhpc-0.26.4/Rhpc/src/common/RhpcMS.c |only Rhpc-0.26.4/Rhpc/src/common/RhpcSerialize.c |only Rhpc-0.26.4/Rhpc/src/common/fakemaster.h | 6 Rhpc-0.26.4/Rhpc/src/msmpi64.def |only Rhpc-0.26.4/Rhpc/src/worker/Makefile.in | 17 Rhpc-0.26.4/Rhpc/src/worker/Makefile.win | 35 Rhpc-0.26.4/Rhpc/src/worker/RhpcSpawnWin64.cmd |only Rhpc-0.26.4/Rhpc/src/worker/RhpcWorker.c | 70 Rhpc-0.26.4/Rhpc/src/worker/RhpcWorker_LapplyLB.c |only Rhpc-0.26.4/Rhpc/src/worker/RhpcWorker_LapplyLB.h | 254 - Rhpc-0.26.4/Rhpc/src/worker/RhpcWorker_Lapplyseq.c |only Rhpc-0.26.4/Rhpc/src/worker/RhpcWorker_Lapplyseq.h | 288 -- Rhpc-0.26.4/Rhpc/src/worker/RhpcWorker_WorkerCall.c |only Rhpc-0.26.4/Rhpc/src/worker/RhpcWorker_WorkerCall.h | 162 - Rhpc-0.26.4/Rhpc/src/worker/fakemaster.c | 11 Rhpc-0.26.4/Rhpc/vignettes |only 64 files changed, 1928 insertions(+), 3302 deletions(-)
Title: Electrical Properties of Resistor Networks
Description: Electrical properties of resistor networks using matrix methods.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between ResistorArray versions 1.0-32 dated 2019-01-29 and 1.0-33 dated 2026-07-21
DESCRIPTION | 14 +++++++------- MD5 | 29 +++++++++++++++++------------ NAMESPACE | 2 +- R/ResistorArray.R | 12 +++++------- README.md |only build/partial.rdb |binary build/vignette.rds |binary data/SquaredSquare.rda |binary inst/CITATION | 11 +++-------- inst/ResistorArray_icon.png |only inst/ResistorArray_icon.svg |only inst/ResistorArray_stickermaker.R |only inst/doc/ResistorArray.R | 2 -- inst/doc/ResistorArray.pdf |binary man/cube.Rd | 2 +- man/figures |only man/resistance.Rd | 4 ++-- vignettes/resistors.bib | 5 +---- 18 files changed, 37 insertions(+), 44 deletions(-)
Title: A Lightweight Interface to NYC Open Data APIs
Description: Provides a unified set of helper functions to access datasets
from the NYC Open Data platform <https://opendata.cityofnewyork.us/>.
Functions return results as tidy tibbles and support optional filtering,
sorting, and row limits via the Socrata API. The package includes endpoints
for 311 service requests, DOB job applications, juvenile justice metrics,
school safety, environmental data, event permitting, and additional citywide datasets.
Author: Christian Martinez [aut, cre] ,
Crystal Adote [ctb] ,
Jonah Dratfield [ctb] ,
Joyce Escatel-Flores [ctb] ,
Rob Hutto [ctb] ,
Isley Jean-Pierre [ctb] ,
Shannon Joyce [ctb] ,
Laura Rose-Werner [ctb] ,
Emma Tupone [ctb] ,
Xinru Wang [ctb]
Maintainer: Christian Martinez <c.martinez0@outlook.com>
Diff between nycOpenData versions 0.2.2 dated 2026-06-18 and 0.2.3 dated 2026-07-21
DESCRIPTION | 12 ++++---- MD5 | 14 +++++----- NEWS.md | 57 +++++------------------------------------- README.md | 22 +++++++++++----- inst/CITATION | 4 +- inst/doc/getting-started.Rmd | 2 - inst/doc/getting-started.html | 6 ++-- vignettes/getting-started.Rmd | 2 - 8 files changed, 43 insertions(+), 76 deletions(-)
Title: Merger Simulation and Calibration
Description: Analyze mergers between firms. Models of competition include
differentiated Bertrand price-setting, Nash bargaining, and second score
auctions, as implemented in Panhans and Taragin (2023)
<doi:10.1016/j.ijindorg.2023.102986>. Calibrates demand systems including
standard logit, nested logit, and generalized nested logit as
implemented in Panhans and Wiemer (2026) <doi:10.1093/joclec/nhaf037>.
Author: Matthew T Panhans [aut, cre]
Maintainer: Matthew T Panhans <mpanhans@gmail.com>
Diff between mergersim versions 0.1.0 dated 2026-07-02 and 0.2.0 dated 2026-07-21
DESCRIPTION | 6 MD5 | 44 +++--- NEWS.md | 4 R/bargain_calibrate.R | 15 +- R/bargain_foc.R | 2 R/bertrand_calibrate.R | 69 ++++----- R/bertrand_calibrate_gnl.R | 202 +++++----------------------- R/ssa_calibrate.R | 19 +- R/ssbargain_calibrate.R | 15 +- inst/doc/calibrating-gnl-demand.R | 18 -- inst/doc/calibrating-gnl-demand.Rmd | 21 -- inst/doc/calibrating-gnl-demand.html | 108 +++++++------- inst/doc/horizontal-merger-simulations.R | 27 +-- inst/doc/horizontal-merger-simulations.Rmd | 31 ++-- inst/doc/horizontal-merger-simulations.html | 34 ++-- man/bargain_calibrate.Rd | 8 - man/bargain_foc.Rd | 2 man/bertrand_calibrate.Rd | 8 - man/bertrand_calibrate_gnl.Rd | 33 ---- man/ssa_calibrate.Rd | 8 - man/ssbargain_calibrate.Rd | 8 - vignettes/calibrating-gnl-demand.Rmd | 21 -- vignettes/horizontal-merger-simulations.Rmd | 31 ++-- 23 files changed, 295 insertions(+), 439 deletions(-)
Title: 3D Plotting with 'ggplot2'
Description: A 'ggplot2' extension for creating 3D figures.
Provides 3D geoms, stats, and a coord_3d() coordinate
system supporting rotation, perspective, and lighting.
Author: Matthew Kling [aut, cre, cph]
Maintainer: Matthew Kling <mattkling@berkeley.edu>
Diff between ggcube versions 0.1.0 dated 2026-05-27 and 0.2.0 dated 2026-07-21
DESCRIPTION | 16 ++- MD5 | 111 ++++++++++++++---------- NAMESPACE | 3 NEWS.md | 6 + R/animate-3d.R | 94 ++++++++++++++++----- R/geom-hull-3d.R | 11 -- R/geom-path-3d.R | 2 R/geom-point-3d.R | 2 R/geom-segment-3d.R | 2 R/grid-gen.R | 4 R/guide_3d.R | 151 ++++++++++++++++++++++++++++------ R/label-rendering.R | 72 +++++++++++----- R/light.R | 45 ++++++---- R/orbit-3d.R |only R/panel-rendering.R | 23 ++++- R/shared-docs.R | 72 +++++++++------- R/theme.R | 75 +++++++--------- R/zzz.R | 11 +- README.md | 109 +++++++++++++++++------- build/vignette.rds |binary inst/doc/ggcube.R | 5 - inst/doc/ggcube.Rmd | 29 ++++-- inst/doc/ggcube.html | 62 +++++++------ inst/htmlwidgets |only man/anim_save_3d.Rd | 2 man/animate_3d.Rd | 12 +- man/cube_theming.Rd | 12 +- man/element_rect.Rd | 56 +++++------- man/figures/README-anim-1.gif |only man/figures/README-bar-1.png |binary man/figures/README-contour-1.png |only man/figures/README-contour_anim-1.gif |binary man/figures/README-functions-1.png |binary man/figures/README-smooth-1.png |binary man/figures/README-text-1.png |binary man/geom_col_3d.Rd | 2 man/geom_contour_3d.Rd | 2 man/geom_hull_3d.Rd | 4 man/geom_path_3d.Rd | 19 ---- man/geom_point_3d.Rd | 19 ---- man/geom_segment_3d.Rd | 19 ---- man/ggcube.Rd | 5 + man/grid_generation.Rd | 30 +++--- man/guide_3d.Rd | 2 man/orbit_3d-shiny.Rd |only man/orbit_3d.Rd |only man/position_on_face.Rd | 2 man/renderers_3d.Rd | 2 man/scale_z_continuous.Rd | 8 - man/scale_z_discrete.Rd | 6 - man/sort_params.Rd |only man/sorting_methods.Rd | 30 +++--- man/stat_density_3d.Rd | 2 man/stat_distributions_3d.Rd | 8 - man/zlim.Rd | 6 - tests/testthat/Rplots.pdf |only tests/testthat/test-guide_3d.R |only tests/testthat/test-label-rendering.R |only tests/testthat/test-light.R |only tests/testthat/test-orbit-3d.R |only tests/testthat/test-theme.R |only vignettes/ggcube.Rmd | 29 ++++-- 62 files changed, 726 insertions(+), 456 deletions(-)
Title: Difference-in-Differences with a Continuous Treatment
Description: Provides methods for difference-in-differences with a continuous treatment and staggered treatment adoption. Includes estimation of treatment effects and causal responses as a function of the dose, event studies indexed by length of exposure to the treatment, and aggregation into overall average effects. Uniform inference procedures are included, along with both parametric and nonparametric models for treatment effects. The methods are based on Callaway, Goodman-Bacon, and Sant'Anna (2025) <doi:10.48550/arXiv.2107.02637>.
Author: Brantly Callaway [aut, cre],
Andrew Goodman-Bacon [aut],
Pedro H. C. Sant'Anna [aut]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>
This is a re-admission after prior archival of version 0.1.0 dated 2025-07-03
Diff between contdid versions 0.1.0 dated 2025-07-03 and 0.1.1 dated 2026-07-21
DESCRIPTION | 12 ++-- MD5 | 26 +++++----- NEWS.md | 9 +++ R/ggcont_did.R | 4 - README.md | 65 ++++++++++++++----------- inst/CITATION | 2 man/cont_did.Rd | 79 +++++++++++++++++++++---------- man/contdid-package.Rd | 1 man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-5-2.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/setup_pte_cont.Rd | 2 14 files changed, 123 insertions(+), 77 deletions(-)
Title: Automatic Plotting and Theming of Many Graphs
Description: Visual exploration and presentation of networks should not be difficult.
This package includes functions for plotting networks and network-related metrics with sensible and pretty defaults.
It includes 'ggplot2'-based plot methods for many popular network package classes.
It also includes some novel layout algorithms, and options for straightforward, consistent themes.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between autograph versions 1.0.3 dated 2026-05-01 and 1.1.1 dated 2026-07-21
autograph-1.0.3/autograph/inst/tutorials/tutorial2 |only autograph-1.1.1/autograph/DESCRIPTION | 19 autograph-1.1.1/autograph/MD5 | 67 autograph-1.1.1/autograph/NAMESPACE | 21 autograph-1.1.1/autograph/NEWS.md | 106 + autograph-1.1.1/autograph/R/autograph_utilities.R | 4 autograph-1.1.1/autograph/R/graph_aes.R |only autograph-1.1.1/autograph/R/graph_edges.R | 211 -- autograph-1.1.1/autograph/R/graph_labels.R | 105 - autograph-1.1.1/autograph/R/graph_nodes.R | 70 autograph-1.1.1/autograph/R/graphr.R | 59 autograph-1.1.1/autograph/R/graphs.R | 51 autograph-1.1.1/autograph/R/grapht.R | 978 ++++++---- autograph-1.1.1/autograph/R/layout_layered.R | 17 autograph-1.1.1/autograph/R/plot_analysis.R | 44 autograph-1.1.1/autograph/R/plot_convergence.R | 2 autograph-1.1.1/autograph/R/theme_palettes.R | 3 autograph-1.1.1/autograph/README.md | 4 autograph-1.1.1/autograph/build/partial.rdb |binary autograph-1.1.1/autograph/inst/tutorials/autograph1 |only autograph-1.1.1/autograph/man/layout_configuration.Rd | 2 autograph-1.1.1/autograph/man/layout_partition.Rd | 4 autograph-1.1.1/autograph/man/plot_convergence.Rd | 4 autograph-1.1.1/autograph/man/plot_gof.Rd | 6 autograph-1.1.1/autograph/man/plot_graphr.Rd | 43 autograph-1.1.1/autograph/man/plot_graphs.Rd | 15 autograph-1.1.1/autograph/man/plot_grapht.Rd | 120 - autograph-1.1.1/autograph/man/plot_interp.Rd | 5 autograph-1.1.1/autograph/man/reexports.Rd | 4 autograph-1.1.1/autograph/tests/testthat/Rplots.pdf |only autograph-1.1.1/autograph/tests/testthat/helper-functional.R |only autograph-1.1.1/autograph/tests/testthat/helper-tutorials.R |only autograph-1.1.1/autograph/tests/testthat/test-functional_aes.R |only autograph-1.1.1/autograph/tests/testthat/test-functional_layouts.R |only autograph-1.1.1/autograph/tests/testthat/test-functional_plots.R |only autograph-1.1.1/autograph/tests/testthat/test-functional_themes.R |only autograph-1.1.1/autograph/tests/testthat/test-graphr.R | 142 + autograph-1.1.1/autograph/tests/testthat/test-grapht.R |only autograph-1.1.1/autograph/tests/testthat/test-tutorials_autograph.R |only 39 files changed, 1403 insertions(+), 703 deletions(-)
Title: Metrics of R Packages
Description: Static code analyses for R packages using the external code-tagging
libraries 'ctags' and 'gtags'. Static analyses enable packages to be
analysed very quickly, generally a couple of seconds at most. The package
also provides access to a database generating by applying the main function
to the full 'CRAN' archive, enabling the statistical properties of any package
to be compared with all other 'CRAN' packages.
Author: Mark Padgham [aut, cre] ,
Michael Sumner [ctb] ,
Jeffrey Hollister [ctb] ,
Egor Kotov [ctb]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between pkgstats versions 0.2.3 dated 2026-06-01 and 0.2.4 dated 2026-07-21
DESCRIPTION | 10 +-- MD5 | 26 +++++---- NEWS.md | 16 ++++- R/ctags-test.R | 46 ++++++++++------ R/plot.R | 104 +++++++++++++++++++++++++++--------- R/zzz.R | 35 +++++++++--- README.md | 105 +++++++++++++++---------------------- build/vignette.rds |binary inst/doc/installation.html | 4 - inst/doc/pkgstats.html | 8 +- inst/js |only man/plot_network.Rd | 22 ++++--- tests/testthat/test-plot-network.R | 13 +++- 13 files changed, 244 insertions(+), 145 deletions(-)
Title: GDP - Workflow Management
Description: Tools, methods and processes for the management
of analysis workflows. These lightweight solutions facilitate
structuring R&D activities. These solutions were developed to comply
with Good Documentation Practice (GDP),
with ALCOA+ principles as proposed by the U.S. FDA, and
with FAIR principles as discussed by Jacobsen et al. (2017) <doi:10.1162/dint_r_00024>.
Author: Gregoire Thomas [aut, cre, cph] ,
Metabolomic Diagnostics Ltd. [fnd]
Maintainer: Gregoire Thomas <gregoire.thomas@SQU4RE.com>
Diff between D4TAlink.light versions 2.1.21 dated 2025-09-10 and 2.1.22 dated 2026-07-21
DESCRIPTION | 27 +++++++------- MD5 | 72 +++++++++++++++++++------------------- NEWS | 6 +++ R/D4TAlink-common-args-doc.R | 15 ++++--- build/vignette.rds |binary inst/doc/D4TAlink_basics.html | 9 ++-- inst/doc/D4TAlink_quickstart.html | 9 ++-- man/D4TAlink-common-args.Rd | 24 +++++++++++- man/binaryFn.Rd | 2 - man/catReport.Rd | 2 - man/docFn.Rd | 2 - man/getTaskFilepath.Rd | 2 - man/jpegReport.Rd | 5 ++ man/jpegReportFn.Rd | 2 - man/pdfReport.Rd | 2 - man/pdfReportFn.Rd | 2 - man/pngReport.Rd | 6 +++ man/pngReportFn.Rd | 2 - man/querySQLite.Rd | 2 - man/readBinary.Rd | 2 - man/readFeather.Rd | 2 - man/readPickle.Rd | 2 - man/readReportJSON.Rd | 2 - man/readReportTable.Rd | 2 - man/readSQLite.Rd | 2 - man/reportFn.Rd | 2 - man/reportXlsFn.Rd | 2 - man/saveBinary.Rd | 2 - man/saveBinaryE.Rd | 2 - man/saveFeather.Rd | 2 - man/savePickle.Rd | 2 - man/saveReportJSON.Rd | 2 - man/saveReportTable.Rd | 2 - man/saveReportXls.Rd | 2 - man/saveSQLite.Rd | 2 - man/scanReport.Rd | 2 - tests/testthat/test01.R | 28 +++++++++----- 37 files changed, 150 insertions(+), 103 deletions(-)
More information about D4TAlink.light at CRAN
Permanent link
Title: Continuous-Time Mediation
Description: Computes effect sizes, standard errors, and confidence intervals
for total, direct, and indirect effects in continuous-time mediation models
as described in Pesigan, Russell, and Chow (2025) <doi:10.1037/met0000779>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph] ,
Michael A. Russell [ctb] ,
Sy-Miin Chow [ctb]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between cTMed versions 1.0.9 dated 2026-02-05 and 1.0.10 dated 2026-07-21
cTMed-1.0.10/cTMed/DESCRIPTION | 10 cTMed-1.0.10/cTMed/MD5 | 349 +++-- cTMed-1.0.10/cTMed/NAMESPACE | 22 cTMed-1.0.10/cTMed/NEWS.md | 17 cTMed-1.0.10/cTMed/R/RcppExports.R | 64 cTMed-1.0.10/cTMed/R/cTMed-boot-beta-std.R | 22 cTMed-1.0.10/cTMed/R/cTMed-boot-beta.R | 19 cTMed-1.0.10/cTMed/R/cTMed-boot-central-dot.R | 10 cTMed-1.0.10/cTMed/R/cTMed-boot-central-std-dot.R |only cTMed-1.0.10/cTMed/R/cTMed-boot-direct-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-boot-direct-central.R |only cTMed-1.0.10/cTMed/R/cTMed-boot-indirect-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-boot-indirect-central.R | 27 cTMed-1.0.10/cTMed/R/cTMed-boot-med-std.R | 42 cTMed-1.0.10/cTMed/R/cTMed-boot-med.R | 35 cTMed-1.0.10/cTMed/R/cTMed-boot-total-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-boot-total-central.R | 27 cTMed-1.0.10/cTMed/R/cTMed-delta-beta-std-dot.R | 27 cTMed-1.0.10/cTMed/R/cTMed-delta-beta-std.R | 31 cTMed-1.0.10/cTMed/R/cTMed-delta-beta.R | 20 cTMed-1.0.10/cTMed/R/cTMed-delta-central-dot.R | 10 cTMed-1.0.10/cTMed/R/cTMed-delta-central-std-dot.R |only cTMed-1.0.10/cTMed/R/cTMed-delta-direct-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-delta-direct-central.R |only cTMed-1.0.10/cTMed/R/cTMed-delta-indirect-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-delta-indirect-central.R | 32 cTMed-1.0.10/cTMed/R/cTMed-delta-med-std-dot.R | 27 cTMed-1.0.10/cTMed/R/cTMed-delta-med-std.R | 51 cTMed-1.0.10/cTMed/R/cTMed-delta-med.R | 36 cTMed-1.0.10/cTMed/R/cTMed-delta-total-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-delta-total-central.R | 32 cTMed-1.0.10/cTMed/R/cTMed-direct-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-direct-central.R |only cTMed-1.0.10/cTMed/R/cTMed-direct-std.R | 3 cTMed-1.0.10/cTMed/R/cTMed-direct.R | 4 cTMed-1.0.10/cTMed/R/cTMed-indirect-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-indirect-central.R | 17 cTMed-1.0.10/cTMed/R/cTMed-indirect-std.R | 3 cTMed-1.0.10/cTMed/R/cTMed-indirect.R | 4 cTMed-1.0.10/cTMed/R/cTMed-mc-beta-std-dot.R | 25 cTMed-1.0.10/cTMed/R/cTMed-mc-beta-std.R | 27 cTMed-1.0.10/cTMed/R/cTMed-mc-beta.R | 20 cTMed-1.0.10/cTMed/R/cTMed-mc-central-dot.R | 10 cTMed-1.0.10/cTMed/R/cTMed-mc-central-std-dot.R |only cTMed-1.0.10/cTMed/R/cTMed-mc-direct-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-mc-direct-central.R |only cTMed-1.0.10/cTMed/R/cTMed-mc-indirect-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-mc-indirect-central.R | 26 cTMed-1.0.10/cTMed/R/cTMed-mc-med-std-dot.R | 25 cTMed-1.0.10/cTMed/R/cTMed-mc-med-std.R | 46 cTMed-1.0.10/cTMed/R/cTMed-mc-med.R | 39 cTMed-1.0.10/cTMed/R/cTMed-mc-phi-sigma.R | 38 cTMed-1.0.10/cTMed/R/cTMed-mc-phi.R | 4 cTMed-1.0.10/cTMed/R/cTMed-mc-total-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-mc-total-central.R | 26 cTMed-1.0.10/cTMed/R/cTMed-med-std.R | 31 cTMed-1.0.10/cTMed/R/cTMed-med.R | 29 cTMed-1.0.10/cTMed/R/cTMed-methods-ctmedboot.R | 25 cTMed-1.0.10/cTMed/R/cTMed-methods-ctmeddelta.R | 16 cTMed-1.0.10/cTMed/R/cTMed-methods-ctmedmc.R | 39 cTMed-1.0.10/cTMed/R/cTMed-methods-ctmedmed.R | 16 cTMed-1.0.10/cTMed/R/cTMed-plot-beta-ci-dot.R | 11 cTMed-1.0.10/cTMed/R/cTMed-plot-central-ci-dot.R | 32 cTMed-1.0.10/cTMed/R/cTMed-plot-central-dot.R | 14 cTMed-1.0.10/cTMed/R/cTMed-plot-med-ci-dot.R | 6 cTMed-1.0.10/cTMed/R/cTMed-plot-med-dot.R | 4 cTMed-1.0.10/cTMed/R/cTMed-plot-trajectory-dot.R | 4 cTMed-1.0.10/cTMed/R/cTMed-posterior-beta-std-dot.R |only cTMed-1.0.10/cTMed/R/cTMed-posterior-beta-std.R |only cTMed-1.0.10/cTMed/R/cTMed-posterior-beta.R | 20 cTMed-1.0.10/cTMed/R/cTMed-posterior-central-dot.R | 10 cTMed-1.0.10/cTMed/R/cTMed-posterior-central-std-dot.R |only cTMed-1.0.10/cTMed/R/cTMed-posterior-direct-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-posterior-direct-central.R |only cTMed-1.0.10/cTMed/R/cTMed-posterior-indirect-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-posterior-indirect-central.R | 32 cTMed-1.0.10/cTMed/R/cTMed-posterior-med-std.R |only cTMed-1.0.10/cTMed/R/cTMed-posterior-med.R | 34 cTMed-1.0.10/cTMed/R/cTMed-posterior-total-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-posterior-total-central.R | 28 cTMed-1.0.10/cTMed/R/cTMed-total-central-std.R |only cTMed-1.0.10/cTMed/R/cTMed-total-central.R | 17 cTMed-1.0.10/cTMed/R/cTMed-total-std.R | 7 cTMed-1.0.10/cTMed/R/cTMed-total.R | 6 cTMed-1.0.10/cTMed/R/cTMed-trajectory.R | 7 cTMed-1.0.10/cTMed/build/partial.rdb |binary cTMed-1.0.10/cTMed/man/BootBeta.Rd | 95 - cTMed-1.0.10/cTMed/man/BootBetaStd.Rd | 106 + cTMed-1.0.10/cTMed/man/BootDirectCentral.Rd |only cTMed-1.0.10/cTMed/man/BootDirectCentralStd.Rd |only cTMed-1.0.10/cTMed/man/BootIndirectCentral.Rd | 97 - cTMed-1.0.10/cTMed/man/BootIndirectCentralStd.Rd |only cTMed-1.0.10/cTMed/man/BootMed.Rd | 95 - cTMed-1.0.10/cTMed/man/BootMedStd.Rd | 98 - cTMed-1.0.10/cTMed/man/BootTotalCentral.Rd | 97 - cTMed-1.0.10/cTMed/man/BootTotalCentralStd.Rd |only cTMed-1.0.10/cTMed/man/DeltaBeta.Rd | 96 - cTMed-1.0.10/cTMed/man/DeltaBetaStd.Rd | 112 + cTMed-1.0.10/cTMed/man/DeltaDirectCentral.Rd |only cTMed-1.0.10/cTMed/man/DeltaDirectCentralStd.Rd |only cTMed-1.0.10/cTMed/man/DeltaIndirectCentral.Rd | 98 - cTMed-1.0.10/cTMed/man/DeltaIndirectCentralStd.Rd |only cTMed-1.0.10/cTMed/man/DeltaMed.Rd | 96 - cTMed-1.0.10/cTMed/man/DeltaMedStd.Rd | 105 - cTMed-1.0.10/cTMed/man/DeltaTotalCentral.Rd | 98 - cTMed-1.0.10/cTMed/man/DeltaTotalCentralStd.Rd |only cTMed-1.0.10/cTMed/man/Direct.Rd | 91 - cTMed-1.0.10/cTMed/man/DirectCentral.Rd |only cTMed-1.0.10/cTMed/man/DirectCentralStd.Rd |only cTMed-1.0.10/cTMed/man/DirectStd.Rd | 91 - cTMed-1.0.10/cTMed/man/Indirect.Rd | 91 - cTMed-1.0.10/cTMed/man/IndirectCentral.Rd | 93 - cTMed-1.0.10/cTMed/man/IndirectCentralStd.Rd |only cTMed-1.0.10/cTMed/man/IndirectStd.Rd | 91 - cTMed-1.0.10/cTMed/man/MCBeta.Rd | 96 - cTMed-1.0.10/cTMed/man/MCBetaStd.Rd | 105 - cTMed-1.0.10/cTMed/man/MCDirectCentral.Rd |only cTMed-1.0.10/cTMed/man/MCDirectCentralStd.Rd |only cTMed-1.0.10/cTMed/man/MCIndirectCentral.Rd | 96 - cTMed-1.0.10/cTMed/man/MCIndirectCentralStd.Rd |only cTMed-1.0.10/cTMed/man/MCMed.Rd | 95 - cTMed-1.0.10/cTMed/man/MCMedStd.Rd | 104 - cTMed-1.0.10/cTMed/man/MCPhi.Rd | 95 - cTMed-1.0.10/cTMed/man/MCPhiSigma.Rd | 104 - cTMed-1.0.10/cTMed/man/MCTotalCentral.Rd | 96 - cTMed-1.0.10/cTMed/man/MCTotalCentralStd.Rd |only cTMed-1.0.10/cTMed/man/Med.Rd | 93 - cTMed-1.0.10/cTMed/man/MedStd.Rd | 93 - cTMed-1.0.10/cTMed/man/PosteriorBeta.Rd | 96 - cTMed-1.0.10/cTMed/man/PosteriorBetaStd.Rd |only cTMed-1.0.10/cTMed/man/PosteriorDirectCentral.Rd |only cTMed-1.0.10/cTMed/man/PosteriorDirectCentralStd.Rd |only cTMed-1.0.10/cTMed/man/PosteriorIndirectCentral.Rd | 102 - cTMed-1.0.10/cTMed/man/PosteriorIndirectCentralStd.Rd |only cTMed-1.0.10/cTMed/man/PosteriorMed.Rd | 96 - cTMed-1.0.10/cTMed/man/PosteriorMedStd.Rd |only cTMed-1.0.10/cTMed/man/PosteriorTotalCentral.Rd | 98 - cTMed-1.0.10/cTMed/man/PosteriorTotalCentralStd.Rd |only cTMed-1.0.10/cTMed/man/Total.Rd | 91 - cTMed-1.0.10/cTMed/man/TotalCentral.Rd | 93 - cTMed-1.0.10/cTMed/man/TotalCentralStd.Rd |only cTMed-1.0.10/cTMed/man/TotalStd.Rd | 91 - cTMed-1.0.10/cTMed/man/Trajectory.Rd | 98 - cTMed-1.0.10/cTMed/man/cTMed-package.Rd | 5 cTMed-1.0.10/cTMed/man/confint.ctmedboot.Rd | 2 cTMed-1.0.10/cTMed/man/plot.ctmedboot.Rd | 2 cTMed-1.0.10/cTMed/man/print.ctmedboot.Rd | 2 cTMed-1.0.10/cTMed/man/summary.ctmedboot.Rd | 2 cTMed-1.0.10/cTMed/src/RcppExports.cpp | 201 ++ cTMed-1.0.10/cTMed/src/source.cpp | 673 +++++++++- cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-boot-beta-std.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-boot-beta.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-boot-direct-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-boot-direct-central.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-boot-indirect-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-boot-indirect-central.R | 13 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-boot-med-std.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-boot-med.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-boot-total-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-boot-total-central.R | 13 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-delta-beta-std-diag.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-delta-beta-std.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-delta-beta.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-delta-direct-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-delta-direct-central.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-delta-indirect-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-delta-indirect-central.R | 15 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-delta-med-std-diag.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-delta-med-std.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-delta-med.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-delta-total-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-delta-total-central.R | 15 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-direct-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-direct-central.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-direct-std.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-direct.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-indirect-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-indirect-central.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-indirect-std.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-indirect.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-beta-std-diag.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-beta-std.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-beta.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-direct-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-direct-central.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-indirect-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-indirect-central.R | 15 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-med-std-diag.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-med-std.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-med.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-phi-sigma-diag.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-phi-sigma.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-phi.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-total-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-mc-total-central.R | 15 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-posterior-beta-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-posterior-beta.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-posterior-direct-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-posterior-direct-central.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-posterior-indirect-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-posterior-indirect-central.R | 15 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-posterior-med-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-posterior-med.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-posterior-total-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-posterior-total-central.R | 15 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-test-stable.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-total-central-std.R |only cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-total-central.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-total-std.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-total.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-trajectory.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-wald-ci-dot.R | 7 cTMed-1.0.10/cTMed/tests/testthat/test-cTMed-wald-probs-of-alpha-dot.R | 7 cTMed-1.0.9/cTMed/tests/testthat/test-cTMed.R |only 214 files changed, 4144 insertions(+), 2062 deletions(-)
Title: Open Trade Statistics API Wrapper and Utility Program
Description: Access 'Open Trade Statistics' API from R to download
international trade data.
Author: Mauricio Vargas [aut, cre, cph] ,
Joshua Kunst [ctb] ,
Alexey Kravchenko [ctb] ,
Emma Mendelsohn [ctb] ,
Daniela de los Santos [ctb] ,
Emily Riederer [rev] ,
Mark Padgham [rev] ,
Amanda Dobbyn [rev] ,
Jorge Cimentada [rev] ,
UN Comtrade [dtc],
The Wo [...truncated...]
Maintainer: Mauricio Vargas <m.vargas.sepulveda@gmail.com>
Diff between tradestatistics versions 7.0.0 dated 2026-07-07 and 7.1.0 dated 2026-07-21
DESCRIPTION | 6 +-- MD5 | 10 ++--- NEWS.md | 5 ++ R/ots_create_tidy_data.R | 6 ++- data/ots_countries.rda |binary inst/doc/basic-usage.html | 79 +++++++++++++++++++++++++++------------------- 6 files changed, 66 insertions(+), 40 deletions(-)
More information about tradestatistics at CRAN
Permanent link
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 1.9.21 dated 2026-03-23 and 1.9.22 dated 2026-07-21
DESCRIPTION | 8 - MD5 | 32 ++-- NEWS | 12 + R/TMB.R | 200 ++++++++++++++++++++++++++++-- inst/include/TMBad/TMBad.cpp | 6 inst/include/TMBad/graph_transform.hpp | 3 inst/include/convert.hpp | 3 inst/include/distributions_R.hpp | 42 ++++++ inst/include/tiny_ad/atomic.hpp | 12 + inst/include/tiny_ad/compois/combinom.hpp |only inst/include/tiny_ad/tiny_ad/tiny_ad.hpp | 10 - inst/include/tmbutils/R_inla.hpp | 2 inst/include/tmbutils/density.hpp | 18 +- man/runSymbolicAnalysis.Rd | 23 +++ src/Makevars | 4 src/ichol.cpp |only src/init.c | 17 ++ src/utils.c | 23 --- 18 files changed, 349 insertions(+), 66 deletions(-)
Title: Steve's R Markdown Templates
Description: These are my collection of 'R Markdown' templates, mostly for compilation to PDF.
These are useful for all things academic and professional, if you are using 'R Markdown'
for things like your CV or your articles and manuscripts.
Author: Steven Miller [aut, cre]
Maintainer: Steven Miller <steve@svmiller.com>
Diff between stevetemplates versions 1.3.0 dated 2026-05-29 and 1.4.0 dated 2026-07-21
DESCRIPTION | 6 MD5 | 18 +- NEWS.md | 8 + R/article2.R | 11 + R/article3.R | 11 + inst/rmarkdown/templates/article2/resources/template.tex | 104 +++++++-------- inst/rmarkdown/templates/article2/skeleton/skeleton.Rmd | 7 - inst/rmarkdown/templates/article3/resources/template.tex | 69 ++++----- man/article2.Rd | 10 + man/article3.Rd | 11 + 10 files changed, 142 insertions(+), 113 deletions(-)
More information about stevetemplates at CRAN
Permanent link
Title: Quantitative Trait Locus Mapping in Experimental Crosses
Description: Provides a set of tools to perform quantitative
trait locus (QTL) analysis in experimental crosses. It is a
reimplementation of the 'R/qtl' package to better handle
high-dimensional data and complex cross designs.
Broman et al. (2019) <doi:10.1534/genetics.118.301595>.
Author: Karl W Broman [aut, cre] ,
R Core Team [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2 versions 0.44 dated 2026-07-06 and 0.46 dated 2026-07-21
DESCRIPTION | 8 - MD5 | 65 ++++++------- NEWS.md | 14 ++ R/chr_lengths.R | 13 ++ R/cluster_util.R | 2 R/qtl2-package.R | 1 R/scan1gen.R | 2 R/scan1perm.R | 3 README.md | 1 man/chr_lengths.Rd | 3 man/qtl2-package.Rd | 1 man/scan1gen.Rd | 2 man/scan1perm.Rd | 2 tests/testthat/_snaps/plot_genes/plot-genes-2.svg |only tests/testthat/test-calc_geno_freq.R | 49 +++------- tests/testthat/test-calc_hotspots.R | 2 tests/testthat/test-calcerrorlod.R | 39 +++----- tests/testthat/test-chr_lengths.R | 17 +++ tests/testthat/test-compare_geno.R | 14 +- tests/testthat/test-compare_maps.R | 1 tests/testthat/test-control_files.R | 61 ++++-------- tests/testthat/test-count_xo.R | 8 - tests/testthat/test-create_gene_query_func.R | 14 +- tests/testthat/test-create_variant_query_func.R | 3 tests/testthat/test-est_herit.R | 2 tests/testthat/test-find_index_snp.R | 1 tests/testthat/test-find_peaks.R | 11 -- tests/testthat/test-io.R | 23 ++-- tests/testthat/test-n_missing.R | 20 +--- tests/testthat/test-plot_genes.R | 2 tests/testthat/test-reduce_markers.R | 107 ++++++++++------------ tests/testthat/test-scan1_pg.R | 34 +++--- tests/testthat/test-scan1snps.R | 14 +- tests/testthat/test-simgeno.R | 8 - 34 files changed, 271 insertions(+), 276 deletions(-)
Title: Mutation Testing
Description: Measure quality of your tests.
'muttest' introduces small changes (mutations) to your code
and runs your tests to check if they catch the changes.
If they do, your tests are good.
If not, your assertions are not specific enough.
'muttest' gives you percent score of how often your tests catch the changes.
Author: Jakub Sobolewski [aut, cre]
Maintainer: Jakub Sobolewski <jakupsob@gmail.com>
Diff between muttest versions 0.2.1 dated 2026-06-24 and 0.3.0 dated 2026-07-21
DESCRIPTION | 17 +-- MD5 | 114 +++++++++++++----------- NAMESPACE | 5 + NEWS.md | 11 ++ R/mutator-operator.R | 65 ------------- R/mutator-statement.R | 2 R/mutator.R | 82 ++++++++++++++++- R/muttest.R | 72 ++++++++++----- R/project_copy_strategy.R | 55 ++++++++--- R/report-html.R |only R/reporter-json.R |only R/reporter-multi.R |only R/reporter-progress.R | 81 +++++++++-------- R/reporter.R | 30 ++++-- R/test_strategy.R | 12 ++ README.md | 17 +-- build/vignette.rds |binary inst/doc/ci-integration.html | 3 inst/doc/getting-started.Rmd | 5 - inst/doc/getting-started.html | 39 +++++--- inst/doc/interpreting-results.Rmd | 17 +++ inst/doc/interpreting-results.html | 101 ++++++++++++--------- inst/doc/mutation-testing-101.Rmd | 15 +-- inst/doc/mutation-testing-101.html | 19 ++-- inst/doc/mutators.html | 52 +++++----- inst/examples/shipping/R/discount.R |only inst/report |only inst/schema |only man/JSONMutationReporter.Rd |only man/MultiReporter.Rd |only man/MutationReporter.Rd | 23 +--- man/Mutator.Rd | 6 - man/PackageCopyStrategy.Rd | 26 +++++ man/ProgressMutationReporter.Rd | 21 +--- man/default_reporter.Rd | 2 man/muttest.Rd | 8 - man/muttest_plan.Rd | 4 man/report.Rd |only tests/acceptance/test_package.feature | 20 ++-- tests/testthat/_snaps/muttest.md | 19 +++- tests/testthat/_snaps/report-html |only tests/testthat/_snaps/reporter-json |only tests/testthat/_snaps/test_reporter-progress.md | 22 ++-- tests/testthat/setup-expect.R | 9 + tests/testthat/test-mutator-boolean.R | 4 tests/testthat/test-mutator-call.R | 4 tests/testthat/test-mutator-condition.R | 14 +- tests/testthat/test-mutator-index.R | 6 - tests/testthat/test-mutator-na.R | 6 - tests/testthat/test-mutator-numeric.R | 6 - tests/testthat/test-mutator-operator.R | 11 -- tests/testthat/test-mutator-return.R | 4 tests/testthat/test-mutator-statement.R | 6 - tests/testthat/test-mutator-string.R | 6 - tests/testthat/test-mutator-unary.R | 4 tests/testthat/test-muttest.R | 31 +++++- tests/testthat/test-project_copy_strategy.R | 42 ++++++++ tests/testthat/test-report-html.R |only tests/testthat/test-reporter-json.R |only tests/testthat/test-reporter-multi.R |only tests/testthat/test-test_strategy.R | 44 +++++++++ vignettes/getting-started.Rmd | 5 - vignettes/interpreting-results.Rmd | 17 +++ vignettes/mutation-testing-101.Rmd | 15 +-- 64 files changed, 766 insertions(+), 433 deletions(-)
Title: Generation and Analysis of 3-Level, 4-Level and 5-Level
Factorial Block Designs
Description: Provides tools to generate and analyze 3-level, 4-level and
5-level linear factorial block designs, including complete factorial layouts,
fractional factorial layouts, confounded factorial layouts, and
design-characteristic summaries. The package includes utilities for
recursive construction, defining-contrast identification, alias and
confounding summaries, incidence matrix construction, and selected
design-characteristic diagnostics. The methodological framework follows
foundational work on factorial block designs, including Gupta (1983)
<doi:10.1111/j.2517-6161.1983.tb01253.x>.
Author: Vankudoth Kumar [aut],
Sukanta Dash [aut, cre],
Med Ram Verma [aut]
Maintainer: Sukanta Dash <sukanta.iasri@gmail.com>
Diff between lfebd3 versions 0.2.0 dated 2026-05-07 and 0.3.0 dated 2026-07-21
lfebd3-0.2.0/lfebd3/man/build_triplet.Rd |only lfebd3-0.2.0/lfebd3/man/canonical_effect.Rd |only lfebd3-0.2.0/lfebd3/man/defining_subgroup.Rd |only lfebd3-0.2.0/lfebd3/man/direct_aliases_from_dc.Rd |only lfebd3-0.2.0/lfebd3/man/effect_aliases_low_order.Rd |only lfebd3-0.2.0/lfebd3/man/effect_label.Rd |only lfebd3-0.2.0/lfebd3/man/effect_order.Rd |only lfebd3-0.2.0/lfebd3/man/find_defining_contrasts.Rd |only lfebd3-0.2.0/lfebd3/man/fractional_confounding_summary.Rd |only lfebd3-0.2.0/lfebd3/man/generate_effect_catalog.Rd |only lfebd3-0.2.0/lfebd3/man/is_independent_mod3.Rd |only lfebd3-0.2.0/lfebd3/man/low_order_aliases_from_subgroup.Rd |only lfebd3-0.2.0/lfebd3/man/rank_mod3.Rd |only lfebd3-0.2.0/lfebd3/man/reduce_once.Rd |only lfebd3-0.2.0/lfebd3/man/reduce_repeated.Rd |only lfebd3-0.3.0/lfebd3/DESCRIPTION | 14 lfebd3-0.3.0/lfebd3/MD5 | 80 lfebd3-0.3.0/lfebd3/NAMESPACE | 13 lfebd3-0.3.0/lfebd3/NEWS.md | 67 lfebd3-0.3.0/lfebd3/R/lfebd.R | 8235 +++++----- lfebd3-0.3.0/lfebd3/man/FactChar.Rd | 8 lfebd3-0.3.0/lfebd3/man/T_design.Rd |only lfebd3-0.3.0/lfebd3/man/generate_Tn_full.Rd | 70 lfebd3-0.3.0/lfebd3/man/get_Tn_square.Rd | 14 lfebd3-0.3.0/lfebd3/man/lfebd.defining.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd.independent.confound.effects.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd3-package.Rd | 15 lfebd3-0.3.0/lfebd3/man/lfebd3.Rd | 21 lfebd3-0.3.0/lfebd3/man/lfebd3.cf.Rd | 32 lfebd3-0.3.0/lfebd3/man/lfebd3.cf.full.Rd | 36 lfebd3-0.3.0/lfebd3/man/lfebd3.ff.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd3.fr.Rd | 40 lfebd3-0.3.0/lfebd3/man/lfebd3_T_design.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd3_analyze.Rd | 69 lfebd3-0.3.0/lfebd3/man/lfebd3_factor_relations.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd3_gf3_nullspace.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd3_gf3_rref.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd3_mod3.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd3_normalize_defining_vector.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd3_order_from_vector.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd3_select_rows.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd3_select_rows_CF_first.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd3_to_run_table.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd3_word_from_vector.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd4.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd4.cf.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd4.cf.full.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd4.ff.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd4.fr.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd4_Tstep.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd4_add4.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd4_analyze.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd4_defining.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd4_independent_confound_effects.Rd |only lfebd3-0.3.0/lfebd3/man/lfebd4_to_run_table.Rd |only lfebd3-0.3.0/lfebd3/man/print.lfebd3_analyze_result.Rd | 18 lfebd3-0.3.0/lfebd3/man/print.lfebd3_cf_design.Rd |only lfebd3-0.3.0/lfebd3/man/print.lfebd3_cf_principal.Rd |only lfebd3-0.3.0/lfebd3/man/print.lfebd3_fr.Rd | 14 lfebd3-0.3.0/lfebd3/man/print.lfebd4_analyze_result.Rd |only lfebd3-0.3.0/lfebd3/man/print.lfebd4_cf_design.Rd |only lfebd3-0.3.0/lfebd3/man/print.lfebd4_cf_principal.Rd |only lfebd3-0.3.0/lfebd3/man/print.lfebd4_fr_design.Rd |only lfebd3-0.3.0/lfebd3/tests |only 64 files changed, 4757 insertions(+), 3989 deletions(-)
Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version
of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now
maintained separately just for the calendaring subset). See the included file 'AUTHORS'
for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel [aut, cre] ,
QuantLib Authors [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.1.2 dated 2026-07-14 and 0.1.3 dated 2026-07-21
ChangeLog | 12 ++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/partial.rdb |binary inst/NEWS.Rd | 12 ++++++++++-- src/Makevars.in | 2 +- src/ql/time/calendars/islamicholidays.cpp | 1 + tools/configure.R | 8 ++++++++ 8 files changed, 43 insertions(+), 14 deletions(-)
Title: Compute and Visualize Profile Extrema Functions
Description: Computes profile extrema functions for arbitrary functions. If the function is expensive-to-evaluate it computes profile extrema by emulating the function with a Gaussian process (using package 'DiceKriging'). In this case uncertainty quantification on the profile extrema can also be computed. The different plotting functions for profile extrema give the user a tool to better locate excursion sets.
Author: Dario Azzimonti [aut, cre, cph]
Maintainer: Dario Azzimonti <dario.azzimonti@gmail.com>
Diff between profExtrema versions 0.2.1 dated 2020-03-21 and 0.2.2 dated 2026-07-21
profExtrema-0.2.1/profExtrema/R/help.R |only profExtrema-0.2.2/profExtrema/DESCRIPTION | 16 - profExtrema-0.2.2/profExtrema/MD5 | 85 ++++---- profExtrema-0.2.2/profExtrema/NEWS.md | 6 profExtrema-0.2.2/profExtrema/R/bound_functions.R | 4 profExtrema-0.2.2/profExtrema/R/cleanProfiles.R | 8 profExtrema-0.2.2/profExtrema/R/coordProf_UQ.R | 34 +-- profExtrema-0.2.2/profExtrema/R/coordinateProfiles.R | 16 - profExtrema-0.2.2/profExtrema/R/data.R | 2 profExtrema-0.2.2/profExtrema/R/getMaxNumOpt.R | 64 +++--- profExtrema-0.2.2/profExtrema/R/getProfiles_optim.R | 12 - profExtrema-0.2.2/profExtrema/R/gradKm.R | 6 profExtrema-0.2.2/profExtrema/R/graphicsFuns.R | 4 profExtrema-0.2.2/profExtrema/R/obliqueProf_UQ.R | 34 +-- profExtrema-0.2.2/profExtrema/R/obliqueProfiles.R | 16 - profExtrema-0.2.2/profExtrema/R/plot_univariate_profiles_UQ.R | 44 ++-- profExtrema-0.2.2/profExtrema/R/profExtrema-package.R |only profExtrema-0.2.2/profExtrema/R/profExtremaNumOpt.R | 36 +-- profExtrema-0.2.2/profExtrema/README.md | 97 +++++++--- profExtrema-0.2.2/profExtrema/man/approxMaxMin.Rd | 28 +- profExtrema-0.2.2/profExtrema/man/approxProfileExtrema.Rd | 26 +- profExtrema-0.2.2/profExtrema/man/bound_profiles.Rd | 16 + profExtrema-0.2.2/profExtrema/man/cleanProfileResults.Rd | 8 profExtrema-0.2.2/profExtrema/man/coastal_flooding.Rd | 8 profExtrema-0.2.2/profExtrema/man/coordProf_UQ.Rd | 52 +++-- profExtrema-0.2.2/profExtrema/man/coordinateProfiles.Rd | 31 ++- profExtrema-0.2.2/profExtrema/man/getAllMaxMin.Rd | 10 - profExtrema-0.2.2/profExtrema/man/getChangePoints.Rd | 4 profExtrema-0.2.2/profExtrema/man/getMax.Rd | 8 profExtrema-0.2.2/profExtrema/man/getMaxMinMC.Rd | 10 - profExtrema-0.2.2/profExtrema/man/getMin.Rd | 8 profExtrema-0.2.2/profExtrema/man/getProfileExtrema.Rd | 10 - profExtrema-0.2.2/profExtrema/man/getProfileInf_optim.Rd | 6 profExtrema-0.2.2/profExtrema/man/getProfileSup_optim.Rd | 6 profExtrema-0.2.2/profExtrema/man/gradKm_dnewdata.Rd | 16 + profExtrema-0.2.2/profExtrema/man/obliqueProf_UQ.Rd | 53 +++-- profExtrema-0.2.2/profExtrema/man/obliqueProfiles.Rd | 32 ++- profExtrema-0.2.2/profExtrema/man/plotBivariateProfiles.Rd | 11 - profExtrema-0.2.2/profExtrema/man/plotMaxMin.Rd | 10 - profExtrema-0.2.2/profExtrema/man/plotOneBivProfile.Rd | 11 - profExtrema-0.2.2/profExtrema/man/plot_univariate_profiles_UQ.Rd | 19 + profExtrema-0.2.2/profExtrema/man/profExtrema-package.Rd |only profExtrema-0.2.2/profExtrema/man/profExtrema.Rd | 6 profExtrema-0.2.2/profExtrema/man/prof_mean_var_Delta.Rd | 12 - profExtrema-0.2.2/profExtrema/man/setPlotOptions.Rd | 38 +-- 45 files changed, 526 insertions(+), 397 deletions(-)
Title: Multivariate Methods Based on the Oja Median and Related
Concepts
Description: Calculating the Oja median, Oja signs and ranks and methods based upon them. For details, see the the corresponding publication Fischer, Mosler, et al. (2020) <doi:10.18637/jss.v092.i08>.
Author: Daniel Fischer [aut, cre] ,
Juho Eagling [aut] ,
Karl Mosler [aut] ,
Jyrki Moettoenen [aut] ,
Klaus Nordhausen [aut] ,
Oleksii Pokotylo [aut] ,
Daniel Vogel [aut],
Tommi Ronkainen [ctb] ,
Makoto Matsumoto [ctb, cph] ,
Takuji Nishimura [ctb, cph] ,
Shaw [...truncated...]
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
This is a re-admission after prior archival of version 1.0-0 dated 2020-02-23
Diff between OjaNP versions 1.0-0 dated 2020-02-23 and 2.0 dated 2026-07-21
DESCRIPTION | 91 +++++++++++++++++++++++++++++--- MD5 | 62 ++++++++++++---------- R/createHyperplaneSample.R | 80 +++++++++++++++++++--------- R/ojaMedian.control.R | 2 demo/00Index | 3 - demo/ojaMedianDemo.R | 2 demo/paper-section-4.2.R |only inst/ChangeLog | 5 + man/OjaNP-package.Rd | 6 +- man/ojaMedianControl.Rd | 6 +- man/ojaRCM.Rd | 8 +- man/ojaRank.Rd | 8 -- man/ojaSCM.Rd | 2 man/ojaSign.Rd | 2 src/MersenneTwister.h | 8 +- src/algorithms.cpp | 85 +++++++++--------------------- src/bounded_search.cpp | 6 -- src/det.c | 4 + src/global.h | 16 +++-- src/index.cpp | 7 +- src/interface.cpp | 20 +++---- src/interface.h | 6 +- src/lattice.h | 2 src/matrix.h | 2 src/oja_geometry.cpp | 4 - src/ojasr.c | 125 +++++++++++++++++++++++---------------------- src/random.cpp | 18 +----- src/vkm.cpp | 9 ++- tests |only 29 files changed, 337 insertions(+), 252 deletions(-)
Title: Analysis of Antimicrobial Minimum Inhibitory Concentration Data
Description: Analyse, plot, and tabulate antimicrobial minimum inhibitory concentration (MIC) data.
Validate the results of an MIC experiment by comparing observed MIC values to
a gold standard assay, in line with standards from the International Organization for
Standardization (2021) <https://www.iso.org/standard/79377.html>.
Author: Alessandro Gerada [aut, cre, cph]
Maintainer: Alessandro Gerada <alessandro.gerada2@liverpool.ac.uk>
Diff between MIC versions 2.0.0 dated 2025-12-04 and 2.0.1 dated 2026-07-21
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NEWS.md | 4 ++++ man/MIC-package.Rd | 7 ++++++- 4 files changed, 19 insertions(+), 10 deletions(-)
Title: Beta Product Confidence Procedure for Right Censored Data
Description: Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data, and for medians [Fay and Brittain <DOI:10.1002/sim.6905>]. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time, and differences in medians [Fay, Proschan, and Brittain <DOI:10.1111/biom.12231>]. Basically, the package gives exact inference methods for one- and two-sample exact inferences for Kaplan-Meier curves (e.g., generalizing Fisher's exact test to allow for right censoring), which are especially important for latter parts of the survival curve, small sample sizes or heavily censored data. Includes mid-p options.
Author: Michael P. Fay [aut, cre],
Allyson Mateja [ctb],
Megan Grieco [ctb]
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between bpcp versions 1.5.1 dated 2026-02-19 and 1.5.4 dated 2026-07-21
bpcp-1.5.1/bpcp/demo/Simulation2025_cancerdata.R |only bpcp-1.5.1/bpcp/demo/Simulation2025_discrete.R |only bpcp-1.5.1/bpcp/demo/Simulation2025_discrete_difference.R |only bpcp-1.5.1/bpcp/demo/Simulation2025_discrete_summary.R |only bpcp-1.5.4/bpcp/DESCRIPTION | 8 +- bpcp-1.5.4/bpcp/MD5 | 42 +++++++------ bpcp-1.5.4/bpcp/NEWS | 14 ++++ bpcp-1.5.4/bpcp/R/bpcp2sample.R | 7 +- bpcp-1.5.4/bpcp/R/delta2samp.R | 30 ++++++--- bpcp-1.5.4/bpcp/build/vignette.rds |binary bpcp-1.5.4/bpcp/demo/00Index | 16 ++--- bpcp-1.5.4/bpcp/demo/Calculation2025_no_censoring.R | 33 +++++----- bpcp-1.5.4/bpcp/demo/Calculation2026_no_censoring.R |only bpcp-1.5.4/bpcp/demo/PlottingTransformationFigures.R | 44 -------------- bpcp-1.5.4/bpcp/demo/Sim2026_functions.R |only bpcp-1.5.4/bpcp/demo/Simulation2026_discrete_functions.R |only bpcp-1.5.4/bpcp/demo/Simulation2026_discrete_summary.R |only bpcp-1.5.4/bpcp/demo/sim2026_plotResults.R |only bpcp-1.5.4/bpcp/demo/sim2026_runCode.R |only bpcp-1.5.4/bpcp/inst/doc/discreteBPCP.R | 2 bpcp-1.5.4/bpcp/inst/doc/discreteBPCP.pdf |binary bpcp-1.5.4/bpcp/man/kmci.object.Rd | 2 bpcp-1.5.4/bpcp/man/kmciLR.object.Rd | 2 bpcp-1.5.4/bpcp/man/kmciLRgroup.object.Rd | 2 bpcp-1.5.4/bpcp/man/kmciLRtidy.object.Rd | 2 bpcp-1.5.4/bpcp/man/twosamp.object.Rd | 2 bpcp-1.5.4/bpcp/tests/testthat/test-bpcp2sample.R | 2 27 files changed, 98 insertions(+), 110 deletions(-)
Title: Biochar Characterisation and Adsorption Data Analysis
Description: A toolkit for analysing biochar characterisation and batch
adsorption experiments. Provides functions to parse structured sample
identifiers encoding pyrolysis conditions, read raw FTIR and XRD
instrument output, compute adsorption capacity and removal efficiency,
fit adsorption isotherms following Langmuir (1918)
<doi:10.1021/ja02242a004> and Sips (1948) <doi:10.1063/1.1746922>
among other models, fit adsorption kinetics following Ho and McKay
(1999) <doi:10.1016/S0032-9592(98)00112-5> and Chien and Clayton
(1980) <doi:10.2136/sssaj1980.03615995004400020013x> among other
models, fit batches of samples at once, compute van't Hoff
thermodynamic parameters, baseline-correct and pick peaks in FTIR
spectra, deconvolve XRD patterns into a crystallinity index, compute
BET surface area following Brunauer, Emmett, and Teller (1938)
<doi:10.1021/ja01269a023>, compute proximate and ultimate analysis
summaries including directly from a thermogravimetric analysis (TGA [...truncated...]
Author: Sukamal Sarkar [aut, cre]
Maintainer: Sukamal Sarkar <sukamal.sarkar@gm.rkmvu.ac.in>
Diff between biocharkit versions 0.2.0 dated 2026-07-21 and 0.3.0 dated 2026-07-21
DESCRIPTION | 16 ++++-- MD5 | 34 +++++++++---- NAMESPACE | 10 ++++ NEWS.md | 35 ++++++++++++++ R/biocharkit-package.R | 2 R/plotting.R | 49 +++++++++++++++++++ R/tga.R |only inst/WORDLIST | 14 +++++ inst/doc/biocharkit-intro.R | 24 +++++++++ inst/doc/biocharkit-intro.Rmd | 42 ++++++++++++++++- inst/doc/biocharkit-intro.html | 91 +++++++++++++++++++++++++++++-------- man/assign_dtg_peaks.Rd |only man/biocharkit-package.Rd | 2 man/find_dtg_peaks.Rd |only man/plot_tga.Rd |only man/read_tga_txt.Rd |only man/tga_decomposition_reference.Rd |only man/tga_dtg.Rd |only man/tga_kinetics_kissinger.Rd |only man/tga_normalize.Rd |only man/tga_stages.Rd |only man/tga_stages_batch.Rd |only tests/testthat/test-tga.R |only vignettes/biocharkit-intro.Rmd | 42 ++++++++++++++++- 24 files changed, 323 insertions(+), 38 deletions(-)
Title: Plot FTIR Spectra
Description: The goal of 'PlotFTIR' is to easily and quickly kick-start the production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using 'ggplot2'. The produced plots can be published directly or further modified by 'ggplot2' functions.
L'objectif de 'PlotFTIR' est de démarrer facilement et rapidement la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de 'ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions 'ggplot2'.
Author: Philip Bulsink [aut, cre] ,
Ulrich Makanda [trl] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources [cph]
Maintainer: Philip Bulsink <philip.bulsink@nrcan-rncan.gc.ca>
Diff between PlotFTIR versions 1.2.1 dated 2025-08-25 and 1.3.0 dated 2026-07-21
DESCRIPTION | 10 MD5 | 137 NAMESPACE | 59 NEWS.md | 6 R/PlotFTIR-package.R | 14 R/aaa-shared_params.R |only R/data.R | 194 R/io.R | 1894 +- R/manipulations.R | 1770 +- R/maths.R | 1883 +- R/plot_ftir.R | 688 R/utils.R | 398 R/zzz.R | 58 README.md |20553 ++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/plotting_ftir_spectra.R | 445 inst/doc/plotting_ftir_spectra.Rmd | 944 - inst/doc/plotting_ftir_spectra.html | 1890 +- man/PlotFTIR-package.Rd | 63 man/add_band.Rd | 140 man/add_subtract_scalar.Rd | 104 man/add_wavenumber_marker.Rd | 206 man/average_spectra.Rd | 91 man/biodiesel.Rd | 128 man/check_ftir_data.Rd | 76 man/chemospec_to_plotftir.Rd | 68 man/compress_low_energy.Rd | 106 man/compress_trans.Rd | 46 man/conversion.Rd | 139 man/dot-ggplot.Rd | 70 man/dot-shared-params.Rd |only man/figures/README-basic_plot_en-1.png |binary man/figures/README-basic_plot_fr-1.png |binary man/figures/README-biodiesel_compress_en-1.png |binary man/figures/README-biodiesel_compress_fr-1.png |binary man/figures/README-biodiesel_labelled_en-1.png |binary man/figures/README-biodiesel_labelled_fr-1.png |binary man/figures/README-biodiesel_rename_en-1.png |binary man/figures/README-biodiesel_rename_fr-1.png |binary man/figures/README-biodiesel_zoom_en-1.png |binary man/figures/README-biodiesel_zoom_fr-1.png |binary man/figures/README-stack_plot_en-1.png |binary man/figures/README-stack_plot_fr-1.png |binary man/figures/README-tidy_en-1.png |binary man/figures/README-tidy_fr-1.png |binary man/get_plot_sample_ids.Rd | 76 man/highlight_sample.Rd | 86 man/intensity_type.Rd | 47 man/ir_to_plotftir.Rd | 74 man/move_plot_legend.Rd | 158 man/normalize_spectra.Rd | 123 man/plot_ftir.Rd | 147 man/plot_ftir_core.Rd | 167 man/plot_ftir_stacked.Rd | 201 man/plotftir_to_chemospec.Rd | 110 man/plotftir_to_ir.Rd | 88 man/print.PlotFTIR_data.Rd |only man/read_ftir.Rd | 96 man/read_ftir_directory.Rd | 104 man/recalculate_baseline.Rd | 239 man/rename_plot_sample_ids.Rd | 104 man/sample_spectra.Rd | 100 man/save_plot.Rd | 72 man/zoom_in_on_range.Rd | 88 tests/testthat.R | 24 tests/testthat/test-io.R | 1263 - tests/testthat/test-manipulations.R | 1136 - tests/testthat/test-maths.R | 3244 +-- tests/testthat/test-plot_ftir.R | 342 tests/testthat/test-utils.R | 117 vignettes/plotting_ftir_spectra.Rmd | 944 - 71 files changed, 30391 insertions(+), 10939 deletions(-)
Title: Flexible Bayesian Optimization
Description: A modern and flexible approach to Bayesian Optimization / Model
Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox
providing both ready-to-use optimization algorithms as well as their fundamental
building blocks allowing for straightforward implementation of custom
algorithms. Single- and multi-objective optimization is supported as well as
mixed continuous, categorical and conditional search spaces. Moreover, using
'mlr3mbo' for hyperparameter optimization of machine learning models within the
'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use
optimization algorithms include Efficient Global Optimization by Jones et al.
(1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006)
<doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008)
<doi:10.1007/978-3-540-87700-4_78>.
Author: Marc Becker [cre, aut] ,
Lennart Schneider [aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Florian Pfisterer [aut] ,
Martin Binder [aut],
Sebastian Fischer [aut] ,
Michael H. Buselli [cph],
Wessel Dankers [cph],
Carlos Fonseca [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3mbo versions 1.1.1 dated 2026-04-24 and 1.2.0 dated 2026-07-21
mlr3mbo-1.1.1/mlr3mbo/R/AcqOptimzerRandomSearch.R |only mlr3mbo-1.2.0/mlr3mbo/DESCRIPTION | 20 mlr3mbo-1.2.0/mlr3mbo/MD5 | 271 ++++----- mlr3mbo-1.2.0/mlr3mbo/NEWS.md | 56 ++ mlr3mbo-1.2.0/mlr3mbo/R/AcqFunction.R | 2 mlr3mbo-1.2.0/mlr3mbo/R/AcqFunctionAEI.R | 10 mlr3mbo-1.2.0/mlr3mbo/R/AcqFunctionEHVI.R | 3 mlr3mbo-1.2.0/mlr3mbo/R/AcqFunctionEHVIGH.R | 16 mlr3mbo-1.2.0/mlr3mbo/R/AcqFunctionEI.R | 3 mlr3mbo-1.2.0/mlr3mbo/R/AcqFunctionEILog.R | 3 mlr3mbo-1.2.0/mlr3mbo/R/AcqFunctionEIPS.R | 3 mlr3mbo-1.2.0/mlr3mbo/R/AcqFunctionMulti.R | 17 mlr3mbo-1.2.0/mlr3mbo/R/AcqFunctionPI.R | 3 mlr3mbo-1.2.0/mlr3mbo/R/AcqFunctionSmsEgo.R | 13 mlr3mbo-1.2.0/mlr3mbo/R/AcqFunctionStochasticCB.R | 4 mlr3mbo-1.2.0/mlr3mbo/R/AcqFunctionStochasticEI.R | 3 mlr3mbo-1.2.0/mlr3mbo/R/AcqOptimizer.R | 28 - mlr3mbo-1.2.0/mlr3mbo/R/AcqOptimizerDirect.R | 164 ++--- mlr3mbo-1.2.0/mlr3mbo/R/AcqOptimizerLbfgsb.R | 94 ++- mlr3mbo-1.2.0/mlr3mbo/R/AcqOptimizerLocalSearch.R | 46 + mlr3mbo-1.2.0/mlr3mbo/R/AcqOptimizerRandomSearch.R |only mlr3mbo-1.2.0/mlr3mbo/R/InputTrafoUnitcube.R | 23 mlr3mbo-1.2.0/mlr3mbo/R/OptimizerADBO.R | 1 mlr3mbo-1.2.0/mlr3mbo/R/OptimizerAsyncMbo.R | 72 +- mlr3mbo-1.2.0/mlr3mbo/R/OptimizerMbo.R | 34 - mlr3mbo-1.2.0/mlr3mbo/R/OutputTrafo.R | 14 mlr3mbo-1.2.0/mlr3mbo/R/OutputTrafoLog.R | 30 - mlr3mbo-1.2.0/mlr3mbo/R/OutputTrafoStandardize.R | 14 mlr3mbo-1.2.0/mlr3mbo/R/ResultAssignerSurrogate.R | 10 mlr3mbo-1.2.0/mlr3mbo/R/Surrogate.R | 37 + mlr3mbo-1.2.0/mlr3mbo/R/SurrogateLearner.R | 77 +- mlr3mbo-1.2.0/mlr3mbo/R/SurrogateLearnerCollection.R | 74 +- mlr3mbo-1.2.0/mlr3mbo/R/TunerADBO.R | 6 mlr3mbo-1.2.0/mlr3mbo/R/TunerAsyncMbo.R | 17 mlr3mbo-1.2.0/mlr3mbo/R/TunerMbo.R | 7 mlr3mbo-1.2.0/mlr3mbo/R/bayesopt_ego.R | 7 mlr3mbo-1.2.0/mlr3mbo/R/bayesopt_emo.R | 3 mlr3mbo-1.2.0/mlr3mbo/R/bayesopt_mpcl.R | 24 mlr3mbo-1.2.0/mlr3mbo/R/bayesopt_parego.R | 21 mlr3mbo-1.2.0/mlr3mbo/R/bayesopt_smsego.R | 3 mlr3mbo-1.2.0/mlr3mbo/R/helper.R | 30 - mlr3mbo-1.2.0/mlr3mbo/R/mbo_defaults.R | 27 mlr3mbo-1.2.0/mlr3mbo/R/mlr_loop_functions.R | 19 mlr3mbo-1.2.0/mlr3mbo/R/sugar.R | 59 +- mlr3mbo-1.2.0/mlr3mbo/README.md | 48 + mlr3mbo-1.2.0/mlr3mbo/build/partial.rdb |binary mlr3mbo-1.2.0/mlr3mbo/inst |only mlr3mbo-1.2.0/mlr3mbo/man/AcqFunction.Rd | 270 ++++----- mlr3mbo-1.2.0/mlr3mbo/man/AcqOptimizer.Rd | 186 +++--- mlr3mbo-1.2.0/mlr3mbo/man/AcqOptimizerDirect.Rd | 171 +++--- mlr3mbo-1.2.0/mlr3mbo/man/AcqOptimizerLbfgsb.Rd | 163 +++-- mlr3mbo-1.2.0/mlr3mbo/man/AcqOptimizerLocalSearch.Rd | 144 ++--- mlr3mbo-1.2.0/mlr3mbo/man/AcqOptimizerRandomSearch.Rd | 122 ++-- mlr3mbo-1.2.0/mlr3mbo/man/InputTrafo.Rd | 201 +++---- mlr3mbo-1.2.0/mlr3mbo/man/InputTrafoUnitcube.Rd | 140 ++--- mlr3mbo-1.2.0/mlr3mbo/man/OutputTrafo.Rd | 280 +++++----- mlr3mbo-1.2.0/mlr3mbo/man/OutputTrafoLog.Rd | 228 ++++---- mlr3mbo-1.2.0/mlr3mbo/man/OutputTrafoStandardize.Rd | 228 ++++---- mlr3mbo-1.2.0/mlr3mbo/man/ResultAssigner.Rd | 155 ++--- mlr3mbo-1.2.0/mlr3mbo/man/Surrogate.Rd | 247 ++++---- mlr3mbo-1.2.0/mlr3mbo/man/SurrogateLearner.Rd | 172 ++---- mlr3mbo-1.2.0/mlr3mbo/man/SurrogateLearnerCollection.Rd | 175 +++--- mlr3mbo-1.2.0/mlr3mbo/man/default_acqfunction.Rd | 14 mlr3mbo-1.2.0/mlr3mbo/man/default_acqoptimizer.Rd | 14 mlr3mbo-1.2.0/mlr3mbo/man/default_gp.Rd | 18 mlr3mbo-1.2.0/mlr3mbo/man/default_loop_function.Rd | 14 mlr3mbo-1.2.0/mlr3mbo/man/default_result_assigner.Rd | 14 mlr3mbo-1.2.0/mlr3mbo/man/default_rf.Rd | 22 mlr3mbo-1.2.0/mlr3mbo/man/default_surrogate.Rd | 17 mlr3mbo-1.2.0/mlr3mbo/man/loop_function.Rd | 2 mlr3mbo-1.2.0/mlr3mbo/man/mbo_defaults.Rd | 36 - mlr3mbo-1.2.0/mlr3mbo/man/mlr3mbo-package.Rd | 1 mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions.Rd | 6 mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions_aei.Rd | 119 ++-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions_cb.Rd | 95 +-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions_ehvi.Rd | 118 ++-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions_ehvigh.Rd | 126 ++-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions_ei.Rd | 117 ++-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions_ei_log.Rd | 117 ++-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions_eips.Rd | 126 ++-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions_mean.Rd | 92 +-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions_multi.Rd | 121 ++-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions_pi.Rd | 114 ++-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions_sd.Rd | 92 +-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions_smsego.Rd | 140 ++--- mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions_stochastic_cb.Rd | 138 ++-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqfunctions_stochastic_ei.Rd | 137 ++-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_acqoptimizers.Rd | 4 mlr3mbo-1.2.0/mlr3mbo/man/mlr_input_trafos.Rd | 6 mlr3mbo-1.2.0/mlr3mbo/man/mlr_loop_functions.Rd | 18 mlr3mbo-1.2.0/mlr3mbo/man/mlr_loop_functions_ego.Rd | 4 mlr3mbo-1.2.0/mlr3mbo/man/mlr_loop_functions_emo.Rd | 2 mlr3mbo-1.2.0/mlr3mbo/man/mlr_loop_functions_mpcl.Rd | 2 mlr3mbo-1.2.0/mlr3mbo/man/mlr_loop_functions_parego.Rd | 2 mlr3mbo-1.2.0/mlr3mbo/man/mlr_loop_functions_smsego.Rd | 4 mlr3mbo-1.2.0/mlr3mbo/man/mlr_optimizers_adbo.Rd | 100 +-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_optimizers_async_mbo.Rd | 199 +++---- mlr3mbo-1.2.0/mlr3mbo/man/mlr_optimizers_mbo.Rd | 197 +++---- mlr3mbo-1.2.0/mlr3mbo/man/mlr_output_trafos.Rd | 6 mlr3mbo-1.2.0/mlr3mbo/man/mlr_result_assigners.Rd | 6 mlr3mbo-1.2.0/mlr3mbo/man/mlr_result_assigners_archive.Rd | 104 +-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_result_assigners_surrogate.Rd | 122 ++-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_tuners_adbo.Rd | 124 ++-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_tuners_async_mbo.Rd | 157 +++-- mlr3mbo-1.2.0/mlr3mbo/man/mlr_tuners_mbo.Rd | 164 +++-- mlr3mbo-1.2.0/mlr3mbo/src/infill.c | 6 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/helper.R | 2 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_AcqFunctionAEI.R | 16 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_AcqFunctionEHVI.R | 28 + mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_AcqFunctionEHVIGH.R | 55 + mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_AcqFunctionEI.R | 16 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_AcqFunctionEIPS.R | 12 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_AcqFunctionMulti.R | 33 + mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_AcqFunctionSmsEgo.R | 38 + mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_AcqFunctionStochasticCB.R | 13 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_AcqOptimizer.R | 80 ++ mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_AcqOptimizerDirect.R | 52 + mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_AcqOptimizerLbfgsb.R | 107 +++ mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_AcqOptimizerLocalSearch.R | 12 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_AcqOptimizerRandomSearch.R | 6 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_InputTrafoUnitcube.R | 16 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_OptimizerAsyncMbo.R | 26 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_OptimizerMbo.R | 39 + mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_OutputTrafo.R | 26 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_OutputTrafoLog.R | 54 + mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_OutputTrafoStandardize.R | 31 + mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_ResultAssignerSurrogate.R | 15 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_SurrogateLearner.R | 65 ++ mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_SurrogateLearnerCollection.R | 33 + mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_TunerAsyncMbo.R | 5 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_bayesopt_ego.R | 16 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_bayesopt_emo.R | 2 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_bayesopt_mpcl.R | 19 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_bayesopt_parego.R | 67 ++ mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_conditions.R | 4 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_mbo_defaults.R | 6 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_mlr_loop_functions.R | 4 mlr3mbo-1.2.0/mlr3mbo/tests/testthat/test_sugar.R | 24 138 files changed, 4869 insertions(+), 3388 deletions(-)
Title: Header-Only 'C++' and 'R' Interface
Description: Provides a header only, 'C++' interface to 'R' with enhancements
over 'cpp11'. Enforces copy-on-write semantics consistent with 'R'
behavior. Offers native support for ALTREP objects, 'UTF-8' string
handling, modern 'C++' features and idioms, and reduced memory
requirements. Allows for vendoring, making it useful for restricted
environments. Compared to 'cpp11', it adds support for converting 'C++'
maps to 'R' lists, 'Roxygen' documentation directly in 'C++' code, proper
handling of matrix attributes, support for nullable external pointers,
bidirectional copy of complex number types, flexibility in type
conversions, use of nullable pointers, and various performance
optimizations.
Author: Mauricio Vargas Sepulveda [aut, cre] ,
Posit Software, PBC [aut]
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
Diff between cpp4r versions 1.0.0 dated 2026-06-12 and 1.1.0 dated 2026-07-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 21 ++++++++++++++++++--- inst/include/cpp4r/function.hpp | 8 ++++---- inst/include/cpp4r/r_vector_fwd.hpp | 2 +- 5 files changed, 30 insertions(+), 15 deletions(-)
Title: Kernel Ridge Regression using 'RcppArmadillo'
Description: Provides core computational operations in C++ via 'RcppArmadillo', enabling faster performance than pure R, improved numerical stability, and parallel execution with OpenMP where available. On systems without OpenMP support, the package automatically falls back to single-threaded execution with no user configuration required. For efficient model selection, it integrates with 'CVST' to provide sequential-testing cross-validation and additionally supports restricted maximum likelihood (REML) for continuous optimization of the regularization parameter. The package offers a unified interface for exact kernel ridge regression and three scalable approximations—Nyström, Pivoted Cholesky, and Random Fourier Features—allowing analyses with substantially larger sample sizes than are feasible with exact KRR. It also integrates with the 'tidymodels' ecosystem via the 'parsnip' model specification 'krr_reg', and the S3 method tunable.krr_reg(). To understand the theoretical background, one can refe [...truncated...]
Author: Gyeongmin Kim [aut] ,
Seyoung Lee [aut] ,
Miyoung Jang [aut] ,
Kwan-Young Bak [aut, cre, cph]
Maintainer: Kwan-Young Bak <kybak@sungshin.ac.kr>
Diff between FastKRR versions 0.1.2 dated 2025-11-15 and 0.2.1 dated 2026-07-21
FastKRR-0.1.2/FastKRR/man/error.Rd |only FastKRR-0.1.2/FastKRR/man/print.kernel_matrix.Rd |only FastKRR-0.2.1/FastKRR/DESCRIPTION | 13 FastKRR-0.2.1/FastKRR/MD5 | 91 FastKRR-0.2.1/FastKRR/NAMESPACE | 91 FastKRR-0.2.1/FastKRR/R/CVST_linkfunction.R | 1173 +++++----- FastKRR-0.2.1/FastKRR/R/FastKRR-package.R | 46 FastKRR-0.2.1/FastKRR/R/RcppExports.R | 94 FastKRR-0.2.1/FastKRR/R/approx_kernel.R | 486 ++-- FastKRR-0.2.1/FastKRR/R/coef.R | 92 FastKRR-0.2.1/FastKRR/R/error.R | 160 - FastKRR-0.2.1/FastKRR/R/link2tidymodels.R | 746 +++--- FastKRR-0.2.1/FastKRR/R/make_kernel.R | 118 - FastKRR-0.2.1/FastKRR/R/param.R | 191 - FastKRR-0.2.1/FastKRR/R/plot.R | 157 - FastKRR-0.2.1/FastKRR/R/print.R | 284 -- FastKRR-0.2.1/FastKRR/R/rff_random.R | 120 - FastKRR-0.2.1/FastKRR/R/summary.R | 117 FastKRR-0.2.1/FastKRR/README.md | 482 ++-- FastKRR-0.2.1/FastKRR/man/FastKRR-package.Rd | 72 FastKRR-0.2.1/FastKRR/man/approx_kernel.Rd | 302 +- FastKRR-0.2.1/FastKRR/man/coef.krr.Rd | 92 FastKRR-0.2.1/FastKRR/man/error.krr.Rd | 120 - FastKRR-0.2.1/FastKRR/man/fastkrr.Rd | 423 +-- FastKRR-0.2.1/FastKRR/man/fastkrr_fit_wrapper.Rd |only FastKRR-0.2.1/FastKRR/man/figures/README-unnamed-chunk-4-1.png |binary FastKRR-0.2.1/FastKRR/man/krr_reg.Rd | 286 +- FastKRR-0.2.1/FastKRR/man/make_kernel.Rd | 130 - FastKRR-0.2.1/FastKRR/man/param.Rd | 47 FastKRR-0.2.1/FastKRR/man/param.krr.Rd | 118 - FastKRR-0.2.1/FastKRR/man/plot.krr.Rd | 96 FastKRR-0.2.1/FastKRR/man/predict.krr.Rd | 100 FastKRR-0.2.1/FastKRR/man/print.approx_kernel.Rd | 86 FastKRR-0.2.1/FastKRR/man/print.krr.Rd | 87 FastKRR-0.2.1/FastKRR/man/summary.krr.Rd | 90 FastKRR-0.2.1/FastKRR/man/tunable.krr_reg.Rd | 42 FastKRR-0.2.1/FastKRR/src/RcppExports.cpp | 118 - FastKRR-0.2.1/FastKRR/src/kernel.cpp | 44 FastKRR-0.2.1/FastKRR/src/nystorm.cpp | 102 FastKRR-0.2.1/FastKRR/src/pchol.cpp | 287 -- FastKRR-0.2.1/FastKRR/src/reml.cpp |only FastKRR-0.2.1/FastKRR/src/rff.cpp | 75 FastKRR-0.2.1/FastKRR/src/solve_chol.cpp | 12 FastKRR-0.2.1/FastKRR/tests |only 44 files changed, 3680 insertions(+), 3510 deletions(-)
Title: Univariate Time Series Forecasting
Description: An engine for univariate time series forecasting using
different regression models in an autoregressive way. The engine
provides an uniform interface for applying the different models.
Furthermore, it is extensible so that users can easily apply their
own regression models to univariate time series forecasting and
benefit from all the features of the engine, such as preprocessings
or estimation of forecast accuracy.
Author: Maria Pilar Frias-Bustamante [aut] ,
Francisco Martinez [aut, cre, cph]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between utsf versions 1.3.3 dated 2026-04-22 and 1.3.4 dated 2026-07-21
DESCRIPTION | 8 MD5 | 26 - NEWS.md | 5 R/estimate_accuracy.R | 3 README.md | 26 - build/vignette.rds |binary inst/doc/utsf.R | 31 + inst/doc/utsf.Rmd | 245 ++++++----- inst/doc/utsf.html | 862 ++++++++++++++++++++------------------- man/create_model.Rd | 4 man/figures/README-example-1.png |binary man/reexports.Rd | 2 man/utsf-package.Rd | 1 vignettes/utsf.Rmd | 245 ++++++----- 14 files changed, 836 insertions(+), 622 deletions(-)
Title: Quasi-Periodic Time Series Characteristics
Description: Calculate Characteristics of Quasi-Periodic Time Series, e.g. Estuarine Water Levels.
Author: Tom Cox [aut, cre],
Lennert Schepers [aut]
Maintainer: Tom Cox <tom.cox@uantwerp.be>
Diff between Tides versions 2.1 dated 2018-08-03 and 2.1.1 dated 2026-07-21
ChangeLog | 3 +++ DESCRIPTION | 18 +++++++++++++----- MD5 | 22 +++++++++++----------- R/Summary.R | 4 ++-- R/Tides.R | 18 +++++++++++------- build/vignette.rds |binary data/example.RData |binary inst/doc/Tides.pdf |binary man/IT.Rd | 2 -- man/TidalCharacteristics.Rd | 16 +++++++++++----- man/Tides.Rd | 2 +- man/summary.Tides.Rd | 2 -- 12 files changed, 52 insertions(+), 35 deletions(-)
Title: Methods for Computing Spatial, Temporal, and Spatiotemporal
Statistics
Description: Methods for computing spatial, temporal, and spatiotemporal
statistics as described in Gouhier and Guichard (2014)
<doi:10.1111/2041-210X.12188>. These methods include
empirical univariate, bivariate and multivariate
variograms; fitting variogram models; phase locking and synchrony analysis;
generating autocorrelated and cross-correlated matrices.
Author: Tarik C. Gouhier [aut, cre]
Maintainer: Tarik C. Gouhier <tarik.gouhier@gmail.com>
Diff between synchrony versions 0.3.8 dated 2019-12-05 and 0.3.9 dated 2026-07-21
DESCRIPTION | 18 +++++++++++------- MD5 | 8 ++++---- R/plot.synchrony.R | 2 +- inst/NEWS.Rd | 8 ++++++++ man/coord2dist.Rd | 2 +- 5 files changed, 25 insertions(+), 13 deletions(-)
Title: Projection Pursuit Oblique Decision Trees and Random Forests
Description: Builds decision trees by splitting on linear combinations of
randomly chosen variables. Projection pursuit is used to choose a
projection of the variables that best separates the groups. Using linear
combinations of variables to separate groups takes the correlation between
variables into account, which allows the model to outperform a traditional
decision tree when the separation between groups occurs in combinations of
variables. Single trees can be assembled into random forests for improved
accuracy. Implements projection pursuit classification trees (Lee, Cook,
Park and Lee (2013) <doi:10.1214/13-EJS810>) and projection
pursuit forests (da Silva, Cook and Lee (2021)
<doi:10.1080/10618600.2020.1870480>), following the earlier 'PPforest'
package.
Author: Andres Vidal [aut, cre, cph],
Natalia da Silva [aut]
Maintainer: Andres Vidal <andres@andresvidal.dev>
Diff between ppforest2 versions 0.1.1 dated 2026-07-19 and 0.1.2 dated 2026-07-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 6 ++++++ inst/include/nlohmann/json.hpp | 9 +++++++++ 4 files changed, 22 insertions(+), 7 deletions(-)
Title: Odds Ratio Tools for Logistic Regression
Description: Produces odds ratio analyses with comprehensive reporting tools. Generates
plots, summary tables, and diagnostic checks for logistic regression models
fitted with 'glm()' using binomial family. Provides visualisation methods,
formatted reporting tables via 'gt', and tools to assess logistic regression
model assumptions.
Author: Craig Parylo [aut, cre, cph]
Maintainer: Craig Parylo <craig.parylo2@nhs.net>
Diff between plotor versions 1.0.0 dated 2026-02-14 and 1.1.0 dated 2026-07-21
plotor-1.0.0/plotor/inst/doc/using_plotor.R |only plotor-1.0.0/plotor/inst/doc/using_plotor.Rmd |only plotor-1.0.0/plotor/inst/doc/using_plotor.html |only plotor-1.0.0/plotor/vignettes/using_plotor.Rmd |only plotor-1.1.0/plotor/DESCRIPTION | 15 plotor-1.1.0/plotor/LICENSE | 4 plotor-1.1.0/plotor/MD5 | 69 plotor-1.1.0/plotor/NAMESPACE | 14 plotor-1.1.0/plotor/NEWS.md | 556 plotor-1.1.0/plotor/R/plot_or.R | 7556 +++++----- plotor-1.1.0/plotor/R/plotor-package.R | 16 plotor-1.1.0/plotor/README.md | 298 plotor-1.1.0/plotor/build/vignette.rds |binary plotor-1.1.0/plotor/inst/doc/check_or.R |only plotor-1.1.0/plotor/inst/doc/check_or.html |only plotor-1.1.0/plotor/inst/doc/check_or.qmd |only plotor-1.1.0/plotor/inst/doc/plot_or.R |only plotor-1.1.0/plotor/inst/doc/plot_or.html |only plotor-1.1.0/plotor/inst/doc/plot_or.qmd |only plotor-1.1.0/plotor/inst/doc/table_or.R |only plotor-1.1.0/plotor/inst/doc/table_or.html |only plotor-1.1.0/plotor/inst/doc/table_or.qmd |only plotor-1.1.0/plotor/inst/doc/using_plotor_quickstart.R |only plotor-1.1.0/plotor/inst/doc/using_plotor_quickstart.html |only plotor-1.1.0/plotor/inst/doc/using_plotor_quickstart.qmd |only plotor-1.1.0/plotor/man/check_or.Rd | 84 plotor-1.1.0/plotor/man/figures/readme_check_or.html | 96 plotor-1.1.0/plotor/man/figures/readme_table_or.html | 1238 - plotor-1.1.0/plotor/man/plot_or.Rd | 130 plotor-1.1.0/plotor/man/plotor-package.Rd | 52 plotor-1.1.0/plotor/man/table_or.Rd | 182 plotor-1.1.0/plotor/tests/testthat.R | 24 plotor-1.1.0/plotor/tests/testthat/helper_generate_data.R | 1526 +- plotor-1.1.0/plotor/tests/testthat/test-assumptions.R |only plotor-1.1.0/plotor/tests/testthat/test-confidence-intervals.R |only plotor-1.1.0/plotor/tests/testthat/test-plot_or.R | 510 plotor-1.1.0/plotor/tests/testthat/test-runtime-estimation.R |only plotor-1.1.0/plotor/tests/testthat/test-table_or.R |only plotor-1.1.0/plotor/tests/testthat/test-validation.R |only plotor-1.1.0/plotor/tests/testthat/test_data/make_test_data.R | 1614 +- plotor-1.1.0/plotor/tools/generate_readme_figures.R | 202 plotor-1.1.0/plotor/vignettes/check_or.qmd |only plotor-1.1.0/plotor/vignettes/images |only plotor-1.1.0/plotor/vignettes/plot_or.qmd |only plotor-1.1.0/plotor/vignettes/table_or.qmd |only plotor-1.1.0/plotor/vignettes/using_plotor_quickstart.qmd |only 46 files changed, 6938 insertions(+), 7248 deletions(-)
Title: Cell Type Annotation Using Large Language Models
Description: Automated cell type annotation for single-cell RNA sequencing data
using consensus predictions from multiple large language models. Integrates
with Seurat objects and provides uncertainty quantification for annotations.
Supports various LLM providers including OpenAI, Anthropic, and Google.
For details see Yang et al. (2026) <doi:10.1038/s42003-026-10420-8>.
Author: Chen Yang [aut, cre, cph]
Maintainer: Chen Yang <cafferychen777@tamu.edu>
This is a re-admission after prior archival of version 2.0.5 dated 2026-05-11
Diff between mLLMCelltype versions 2.0.5 dated 2026-05-11 and 2.0.7 dated 2026-07-21
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Title: Optimal Multilevel Matching using a Network Algorithm
Description: Performs multilevel matches for data with cluster-
level treatments and individual-level outcomes using a network
optimization algorithm. Functions for checking balance at the
cluster and individual levels are also provided, as are methods
for permutation-inference-based outcome analysis. Details in
Pimentel et al. (2018) <doi:10.1214/17-AOAS1118>. The optmatch
package, which is useful for running many of the provided
functions, may be downloaded from Github at
<https://github.com/markmfredrickson/optmatch> if not available on
CRAN.
Author: Luke Keele [aut],
Luke Miratrix [aut],
Sam Pimentel [aut, cre],
Paul Rosenbaum [ctb]
Maintainer: Sam Pimentel <spi@berkeley.edu>
Diff between matchMulti versions 1.1.14 dated 2025-04-18 and 1.1.15 dated 2026-07-21
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/multiMatch_vignette.Rnw | 4 ++-- inst/doc/multiMatch_vignette.pdf |binary vignettes/keele_revised2.bib | 22 ++++++++++++++++++++++ vignettes/multiMatch_vignette.Rnw | 4 ++-- 7 files changed, 36 insertions(+), 14 deletions(-)
Title: Leave One Out Kernel Density Estimates for Outlier Detection
Description: Outlier detection using leave-one-out kernel density estimates and
extreme value theory. The bandwidth for kernel density estimates is computed
using persistent homology, a technique in topological data analysis. Using
peak-over-threshold method, a generalized Pareto distribution is fitted to
the log of leave-one-out kde values to identify outliers.
Author: Sevvandi Kandanaarachchi [aut, cre] ,
Rob Hyndman [aut] ,
Chris Fraley [ctb]
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>
Diff between lookout versions 2.0.1 dated 2026-03-26 and 2.0.2 dated 2026-07-21
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- NAMESPACE | 3 +++ R/bandwidth.R | 13 ++++++------- R/bickel_doksum.R |only R/lookoutliers.R | 3 ++- R/outlier_persistence.R | 15 ++++++--------- man/lookout-package.Rd | 1 + man/mvscale.Rd | 2 +- man/reexports.Rd | 2 +- 10 files changed, 33 insertions(+), 31 deletions(-)
Title: Deep Learning Models for Image Segmentation
Description: A general-purpose workflow for image segmentation using TensorFlow models based on the U-Net architecture by Ronneberger et al. (2015) <doi:10.48550/arXiv.1505.04597> and the U-Net++ architecture by Zhou et al. (2018) <doi:10.48550/arXiv.1807.10165>. We provide pre-trained models for assessing canopy density and understory vegetation density from vegetation photos. In addition, the package provides a workflow for easily creating model input and model architectures for general-purpose image segmentation based on grayscale or color images, both for binary and multi-class image segmentation.
Author: Juergen Niedballa [aut, cre] ,
Jan Axtner [aut] ,
Leibniz Institute for Zoo and Wildlife Research [cph]
Maintainer: Juergen Niedballa <camtrapr@gmail.com>
Diff between imageseg versions 0.5.0 dated 2022-05-29 and 0.5.2 dated 2026-07-21
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Title: Gaussian Process Modelling in 'greta'
Description: Provides a syntax to create and combine Gaussian process kernels
in 'greta'. You can then use these kernels to define either full rank or
sparse Gaussian processes, and project a fitted process to new coordinates.
This lets you include Gaussian process components in the statistical models
you write with 'greta'. This is an extension to the 'greta' software, Golding
(2019) <doi:10.21105/joss.01601>.
Author: Nick Golding [aut, cph] ,
Jian Yen [ctb],
Nicholas Tierney [aut, cre]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
This is a re-admission after prior archival of version 0.2.2 dated 2024-11-13
Diff between greta.gp versions 0.2.2 dated 2024-11-13 and 0.2.3 dated 2026-07-21
DESCRIPTION | 27 ++++++++++++++++----------- MD5 | 18 +++++++++--------- NEWS.md | 12 ++++++++++++ R/gp.R | 6 +++--- README.md | 8 ++++---- build/vignette.rds |binary inst/doc/getting-started.html | 13 +++++++------ man/figures/README-plotting-1.png |binary man/gp.Rd | 6 +++--- man/greta.gp.Rd | 1 + 10 files changed, 55 insertions(+), 36 deletions(-)