Title: MASCOTNUM / RT-UQ Algorithms Template Tools
Description: Helper functions for MASCOTNUM / RT-UQ <https://uq.math.cnrs.fr/> algorithm template, for design of numerical experiments practice:
algorithm template parser to support MASCOTNUM specification <https://github.com/MASCOTNUM/algorithms>,
'ask & tell' decoupling injection (inspired by <https://search.r-project.org/CRAN/refmans/sensitivity/html/decoupling.html>)
to use "crimped" algorithms (like uniroot(), optim(), ...) from outside R,
basic template examples: Brent algorithm for 1 dim root finding and L-BFGS-B from base optim().
Author: Yann Richet [aut, cre]
Maintainer: Yann Richet <yann.richet@asnr.fr>
Diff between templr versions 0.2-1 dated 2025-07-26 and 0.2-2 dated 2026-01-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/algorithm.R | 8 ++++---- R/import.R | 2 +- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Optimize and Compress Image Files with 'reSmush.it'
Description: Compress local and online images using the 'reSmush.it' API
service <https://resmush.it/>.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between resmush versions 0.2.1 dated 2024-12-18 and 0.2.2 dated 2026-01-12
resmush-0.2.1/resmush/vignettes/jpg_example_compress.jpg |only resmush-0.2.1/resmush/vignettes/jpg_example_compress_low.jpg |only resmush-0.2.2/resmush/DESCRIPTION | 14 resmush-0.2.2/resmush/MD5 | 78 resmush-0.2.2/resmush/NAMESPACE | 16 resmush-0.2.2/resmush/NEWS.md | 6 resmush-0.2.2/resmush/R/resmush-package.R | 14 resmush-0.2.2/resmush/R/resmush_clean_dir.R | 3 resmush-0.2.2/resmush/R/resmush_dir.R | 210 - resmush-0.2.2/resmush/R/resmush_file.R | 528 ++-- resmush-0.2.2/resmush/R/resmush_url.R | 556 ++-- resmush-0.2.2/resmush/R/show_report.R | 219 - resmush-0.2.2/resmush/R/sysdata.rda |binary resmush-0.2.2/resmush/R/utils.R | 31 resmush-0.2.2/resmush/README.md | 469 +-- resmush-0.2.2/resmush/build/vignette.rds |binary resmush-0.2.2/resmush/inst/CITATION | 42 resmush-0.2.2/resmush/inst/REFERENCES.bib | 14 resmush-0.2.2/resmush/inst/WORDLIST | 51 resmush-0.2.2/resmush/inst/doc/resmush.Rmd | 314 +- resmush-0.2.2/resmush/inst/doc/resmush.html | 1260 +++++----- resmush-0.2.2/resmush/inst/schemaorg.json | 90 resmush-0.2.2/resmush/man/figures/logo.png |binary resmush-0.2.2/resmush/man/resmush-package.Rd | 52 resmush-0.2.2/resmush/man/resmush_clean_dir.Rd | 126 - resmush-0.2.2/resmush/man/resmush_dir.Rd | 214 - resmush-0.2.2/resmush/man/resmush_file.Rd | 213 - resmush-0.2.2/resmush/man/resmush_url.Rd | 200 - resmush-0.2.2/resmush/man/roxygen/meta.R | 12 resmush-0.2.2/resmush/tests/testthat.R | 24 resmush-0.2.2/resmush/tests/testthat/_snaps/remush_url.md | 8 resmush-0.2.2/resmush/tests/testthat/test-formats-local.R | 189 - resmush-0.2.2/resmush/tests/testthat/test-formats.R | 268 +- resmush-0.2.2/resmush/tests/testthat/test-remush_url.R | 51 resmush-0.2.2/resmush/tests/testthat/test-resmuh_dir.R | 472 +-- resmush-0.2.2/resmush/tests/testthat/test-resmush_clean_dir.R | 15 resmush-0.2.2/resmush/tests/testthat/test-resmush_file.R | 803 +++--- resmush-0.2.2/resmush/tests/testthat/test-show_report.R | 3 resmush-0.2.2/resmush/tests/testthat/test-utils.R | 18 resmush-0.2.2/resmush/vignettes/REFERENCES.bib | 14 resmush-0.2.2/resmush/vignettes/resmush.Rmd | 314 +- 41 files changed, 3551 insertions(+), 3360 deletions(-)
Title: Business Analytics using R and Shiny
Description: A platform-independent browser-based interface for business
analytics in R, based on the shiny package. The application combines the
functionality of 'radiant.data', 'radiant.design', 'radiant.basics',
'radiant.model', and 'radiant.multivariate'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
This is a re-admission after prior archival of version 1.6.6 dated 2024-05-21
Diff between radiant versions 1.6.6 dated 2024-05-21 and 1.6.7 dated 2026-01-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- README.md | 2 +- build/vignette.rds |binary inst/doc/programming.R | 6 +++--- inst/doc/programming.html | 29 +++++++++++++++-------------- 6 files changed, 28 insertions(+), 27 deletions(-)
Title: Genetic Linkage Maps in Autopolyploids
Description: Constructs genetic linkage maps in autopolyploid full-sib populations.
Uses pairwise recombination fraction estimation as the first
source of information to sequentially position allelic variants
in specific homologous chromosomes. For situations where pairwise
analysis has limited power, the algorithm relies on the multilocus
likelihood obtained through a hidden Markov model (HMM).
Methods are described in Mollinari and Garcia (2019)
<doi:10.1534/g3.119.400378> and Mollinari et al. (2020)
<doi:10.1534/g3.119.400620>.
Author: Marcelo Mollinari [aut, cre] ,
Gabriel Gesteira [aut] ,
Cristiane Taniguti [aut] ,
Jeekin Lau [aut] ,
Oscar Riera-Lizarazu [ctb] ,
Guilherme Pereira [ctb] ,
Augusto Garcia [ctb] ,
Zhao-Bang Zeng [ctb] ,
Katharine Preedy [ctb, cph] ,
Robert Gentleman [...truncated...]
Maintainer: Marcelo Mollinari <marcelo.mollinari@proton.me>
This is a re-admission after prior archival of version 0.4.1 dated 2024-03-06
Diff between mappoly versions 0.4.1 dated 2024-03-06 and 0.4.2 dated 2026-01-12
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mappoly-0.4.2/mappoly/R/prior_dist_hmm.R | 84 mappoly-0.4.2/mappoly/R/read_fitpoly.R | 596 +- mappoly-0.4.2/mappoly/R/read_mappoly.R | 770 +- mappoly-0.4.2/mappoly/R/read_mappoly_csv.R | 400 - mappoly-0.4.2/mappoly/R/read_mappoly_prob.R | 624 +- mappoly-0.4.2/mappoly/R/read_mappoly_vcf.R | 720 +- mappoly-0.4.2/mappoly/R/reest_map_error.R | 674 +- mappoly-0.4.2/mappoly/R/reestimate_map.R | 290 mappoly-0.4.2/mappoly/R/rf_list_to_matrix.R | 640 +- mappoly-0.4.2/mappoly/R/segreg_poly.R | 114 mappoly-0.4.2/mappoly/R/sim_homologous.R | 210 mappoly-0.4.2/mappoly/R/simulation_utils.R | 310 - mappoly-0.4.2/mappoly/R/single_map_hmm.R | 124 mappoly-0.4.2/mappoly/R/single_paprent_single_phase_hmm.R | 140 mappoly-0.4.2/mappoly/R/split_and_rephase.R | 300 - mappoly-0.4.2/mappoly/R/utils.R | 2960 +++++----- mappoly-0.4.2/mappoly/R/zzz.R | 26 mappoly-0.4.2/mappoly/README.md | 330 - mappoly-0.4.2/mappoly/build/partial.rdb |binary mappoly-0.4.2/mappoly/build/vignette.rds |binary 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mappoly-0.4.2/mappoly/man/check_data_dist_sanity.Rd | 24 mappoly-0.4.2/mappoly/man/check_data_dose_sanity.Rd | 24 mappoly-0.4.2/mappoly/man/check_data_sanity.Rd | 64 mappoly-0.4.2/mappoly/man/check_if_rf_is_possible.Rd | 32 mappoly-0.4.2/mappoly/man/check_ls_phase.Rd | 28 mappoly-0.4.2/mappoly/man/check_pairwise.Rd | 48 mappoly-0.4.2/mappoly/man/compare_haplotypes.Rd | 50 mappoly-0.4.2/mappoly/man/compare_maps.Rd | 38 mappoly-0.4.2/mappoly/man/concatenate_new_marker.Rd | 60 mappoly-0.4.2/mappoly/man/concatenate_ph_list.Rd | 24 mappoly-0.4.2/mappoly/man/create_map.Rd | 24 mappoly-0.4.2/mappoly/man/cross_simulate.Rd | 166 mappoly-0.4.2/mappoly/man/detect_info_par.Rd | 28 mappoly-0.4.2/mappoly/man/dist_prob_to_class.Rd | 64 mappoly-0.4.2/mappoly/man/draw_cross.Rd | 44 mappoly-0.4.2/mappoly/man/draw_phases.Rd | 44 mappoly-0.4.2/mappoly/man/drop_marker.Rd | 68 mappoly-0.4.2/mappoly/man/edit_order.Rd | 92 mappoly-0.4.2/mappoly/man/elim_conf_using_two_pts.Rd | 48 mappoly-0.4.2/mappoly/man/elim_equiv.Rd | 46 mappoly-0.4.2/mappoly/man/elim_redundant.Rd | 82 mappoly-0.4.2/mappoly/man/est_full_hmm_with_global_error.Rd | 184 mappoly-0.4.2/mappoly/man/est_full_hmm_with_prior_prob.Rd | 172 mappoly-0.4.2/mappoly/man/est_haplo_hmm.Rd | 46 mappoly-0.4.2/mappoly/man/est_map_haplo_given_genoprob.Rd | 28 mappoly-0.4.2/mappoly/man/est_pairwise_rf.Rd | 194 mappoly-0.4.2/mappoly/man/est_pairwise_rf2.Rd | 116 mappoly-0.4.2/mappoly/man/est_rf_hmm.Rd | 337 - mappoly-0.4.2/mappoly/man/est_rf_hmm_sequential.Rd | 336 - mappoly-0.4.2/mappoly/man/est_rf_hmm_single_phase.Rd | 48 mappoly-0.4.2/mappoly/man/est_rf_hmm_single_phase_single_parent.Rd | 44 mappoly-0.4.2/mappoly/man/export_data_to_polymapR.Rd | 40 mappoly-0.4.2/mappoly/man/export_map_list.Rd | 64 mappoly-0.4.2/mappoly/man/export_qtlpoly.Rd | 76 mappoly-0.4.2/mappoly/man/extract_map.Rd | 44 mappoly-0.4.2/mappoly/man/filter_aneuploid.Rd | 82 mappoly-0.4.2/mappoly/man/filter_individuals.Rd | 78 mappoly-0.4.2/mappoly/man/filter_map_at_hmm_thres.Rd | 46 mappoly-0.4.2/mappoly/man/filter_missing.Rd | 88 mappoly-0.4.2/mappoly/man/filter_missing_ind.Rd | 38 mappoly-0.4.2/mappoly/man/filter_missing_mrk.Rd | 38 mappoly-0.4.2/mappoly/man/filter_non_conforming_classes.Rd | 24 mappoly-0.4.2/mappoly/man/filter_segregation.Rd | 80 mappoly-0.4.2/mappoly/man/find_blocks.Rd | 208 mappoly-0.4.2/mappoly/man/format_rf.Rd | 24 mappoly-0.4.2/mappoly/man/framework_map.Rd | 148 mappoly-0.4.2/mappoly/man/generate_all_link_phase_elim_equivalent.Rd | 70 mappoly-0.4.2/mappoly/man/generate_all_link_phases_elim_equivalent_haplo.Rd | 74 mappoly-0.4.2/mappoly/man/genetic-mapping-functions.Rd | 108 mappoly-0.4.2/mappoly/man/genotyping_global_error.Rd | 40 mappoly-0.4.2/mappoly/man/get_LOD.Rd | 42 mappoly-0.4.2/mappoly/man/get_cache_two_pts_from_web.Rd | 34 mappoly-0.4.2/mappoly/man/get_counts.Rd | 42 mappoly-0.4.2/mappoly/man/get_counts_all_phases.Rd | 46 mappoly-0.4.2/mappoly/man/get_counts_single_parent.Rd | 68 mappoly-0.4.2/mappoly/man/get_counts_two_parents.Rd | 42 mappoly-0.4.2/mappoly/man/get_dosage_type.Rd | 54 mappoly-0.4.2/mappoly/man/get_full_info_tail.Rd | 28 mappoly-0.4.2/mappoly/man/get_genomic_order.Rd | 74 mappoly-0.4.2/mappoly/man/get_ij.Rd | 40 mappoly-0.4.2/mappoly/man/get_indices_from_selected_phases.Rd | 50 mappoly-0.4.2/mappoly/man/get_ols_map.Rd | 24 mappoly-0.4.2/mappoly/man/get_ph_conf_ret_sh.Rd | 44 mappoly-0.4.2/mappoly/man/get_ph_list_subset.Rd | 24 mappoly-0.4.2/mappoly/man/get_rf_from_list.Rd | 74 mappoly-0.4.2/mappoly/man/get_rf_from_mat.Rd | 24 mappoly-0.4.2/mappoly/man/get_states_and_emission_single_parent.Rd | 24 mappoly-0.4.2/mappoly/man/get_submap.Rd | 186 mappoly-0.4.2/mappoly/man/get_tab_mrks.Rd | 34 mappoly-0.4.2/mappoly/man/get_w_m.Rd | 24 mappoly-0.4.2/mappoly/man/gg_color_hue.Rd | 24 mappoly-0.4.2/mappoly/man/group_mappoly.Rd | 170 mappoly-0.4.2/mappoly/man/hexafake.Rd | 84 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mappoly-0.4.2/mappoly/man/paralell_pairwise_discrete_rcpp.Rd | 50 mappoly-0.4.2/mappoly/man/paralell_pairwise_probability.Rd | 82 mappoly-0.4.2/mappoly/man/parallel_block.Rd | 46 mappoly-0.4.2/mappoly/man/perm_pars.Rd | 24 mappoly-0.4.2/mappoly/man/perm_tot.Rd | 24 mappoly-0.4.2/mappoly/man/ph_list_to_matrix.Rd | 44 mappoly-0.4.2/mappoly/man/ph_matrix_to_list.Rd | 40 mappoly-0.4.2/mappoly/man/plot.mappoly.homoprob.Rd | 82 mappoly-0.4.2/mappoly/man/plot.mappoly.prefpair.profiles.Rd | 80 mappoly-0.4.2/mappoly/man/plot_GIC.Rd | 54 mappoly-0.4.2/mappoly/man/plot_compare_haplotypes.Rd | 88 mappoly-0.4.2/mappoly/man/plot_genome_vs_map.Rd | 98 mappoly-0.4.2/mappoly/man/plot_map_list.Rd | 102 mappoly-0.4.2/mappoly/man/plot_mappoly.map2.Rd | 28 mappoly-0.4.2/mappoly/man/plot_mrk_info.Rd | 52 mappoly-0.4.2/mappoly/man/plot_one_map.Rd | 24 mappoly-0.4.2/mappoly/man/plot_progeny_dosage_change.Rd | 115 mappoly-0.4.2/mappoly/man/poly_hmm_est.Rd | 52 mappoly-0.4.2/mappoly/man/prepare_map.Rd | 24 mappoly-0.4.2/mappoly/man/print_ph.Rd | 24 mappoly-0.4.2/mappoly/man/read_fitpoly.Rd | 232 mappoly-0.4.2/mappoly/man/read_geno.Rd | 250 mappoly-0.4.2/mappoly/man/read_geno_csv.Rd | 206 mappoly-0.4.2/mappoly/man/read_geno_prob.Rd | 262 mappoly-0.4.2/mappoly/man/read_vcf.Rd | 264 mappoly-0.4.2/mappoly/man/reest_rf.Rd | 132 mappoly-0.4.2/mappoly/man/rev_map.Rd | 42 mappoly-0.4.2/mappoly/man/rf_list_to_matrix.Rd | 216 mappoly-0.4.2/mappoly/man/rf_snp_filter.Rd | 186 mappoly-0.4.2/mappoly/man/sample_data.Rd | 74 mappoly-0.4.2/mappoly/man/segreg_poly.Rd | 92 mappoly-0.4.2/mappoly/man/select_rf.Rd | 24 mappoly-0.4.2/mappoly/man/sim_cross_one_informative_parent.Rd | 46 mappoly-0.4.2/mappoly/man/sim_cross_two_informative_parents.Rd | 44 mappoly-0.4.2/mappoly/man/sim_homologous.Rd | 114 mappoly-0.4.2/mappoly/man/solcap.dose.map.Rd | 34 mappoly-0.4.2/mappoly/man/solcap.err.map.Rd | 34 mappoly-0.4.2/mappoly/man/solcap.mds.map.Rd | 34 mappoly-0.4.2/mappoly/man/solcap.prior.map.Rd | 34 mappoly-0.4.2/mappoly/man/split_and_rephase.Rd | 162 mappoly-0.4.2/mappoly/man/split_mappoly.Rd | 38 mappoly-0.4.2/mappoly/man/summary_maps.Rd | 54 mappoly-0.4.2/mappoly/man/table_to_mappoly.Rd | 36 mappoly-0.4.2/mappoly/man/tetra.solcap.Rd | 94 mappoly-0.4.2/mappoly/man/tetra.solcap.geno.dist.Rd | 112 mappoly-0.4.2/mappoly/man/update_framework_map.Rd | 114 mappoly-0.4.2/mappoly/man/update_map.Rd | 62 mappoly-0.4.2/mappoly/man/update_missing.Rd | 24 mappoly-0.4.2/mappoly/man/update_ph_list_at_hmm_thres.Rd | 28 mappoly-0.4.2/mappoly/man/v_2_m.Rd | 24 mappoly-0.4.2/mappoly/src/calc_genoprob.cpp | 2 mappoly-0.4.2/mappoly/src/calc_genoprob_based_on_phased_marker_blocks.cpp | 2 mappoly-0.4.2/mappoly/src/calc_genoprob_based_on_phased_marker_blocks.h | 2 mappoly-0.4.2/mappoly/src/calc_loglike_given_map.cpp | 2 mappoly-0.4.2/mappoly/src/calc_loglike_given_map.h | 2 mappoly-0.4.2/mappoly/src/combinatorial.cpp | 2 mappoly-0.4.2/mappoly/src/est_hmm_map_based_on_phased_mrk_blocks.cpp | 2 mappoly-0.4.2/mappoly/src/est_hmm_map_based_on_phased_mrk_blocks.h | 2 mappoly-0.4.2/mappoly/src/est_map_hmm_given_dose.cpp | 2 mappoly-0.4.2/mappoly/src/est_map_hmm_given_dose.h | 2 mappoly-0.4.2/mappoly/src/hmm_elements.cpp | 2 mappoly-0.4.2/mappoly/src/hmm_single_parent.cpp | 2 mappoly-0.4.2/mappoly/src/pairwise_estimation.cpp | 2 mappoly-0.4.2/mappoly/src/pairwise_estimation_rcppparallel.cpp | 2 mappoly-0.4.2/mappoly/src/read_mappoly_vcf.cpp | 2 mappoly-0.4.2/mappoly/vignettes/mappoly_startguide.Rmd | 490 - 238 files changed, 21947 insertions(+), 21912 deletions(-)
Title: Formal Concept Analysis
Description: Provides tools to perform fuzzy formal concept analysis, presented in Wille (1982) <doi:10.1007/978-3-642-01815-2_23> and in Ganter and Obiedkov (2016) <doi:10.1007/978-3-662-49291-8>. It provides functions to load and save a formal context, extract its concept lattice and implications. In addition, one can use the implications to compute semantic closures of fuzzy sets and, thus, build recommendation systems. Matrix factorization is provided by the GreConD+ algorithm (Belohlavek and Trneckova, 2024 <doi:10.1109/TFUZZ.2023.3330760>).
Author: Domingo Lopez Rodriguez [aut, cre] ,
Angel Mora [aut],
Jesus Dominguez [aut],
Ana Villalon [aut]
Maintainer: Domingo Lopez Rodriguez <dominlopez78@gmail.com>
Diff between fcaR versions 1.2.2 dated 2023-11-30 and 1.3.0 dated 2026-01-12
fcaR-1.2.2/fcaR/src/subsetting.cpp |only fcaR-1.3.0/fcaR/DESCRIPTION | 48 fcaR-1.3.0/fcaR/MD5 | 203 ++- fcaR-1.3.0/fcaR/NAMESPACE | 37 fcaR-1.3.0/fcaR/NEWS.md | 29 fcaR-1.3.0/fcaR/R/RcppExports.R | 156 ++ fcaR-1.3.0/fcaR/R/check_properties.R |only fcaR-1.3.0/fcaR/R/compute_closure.R | 149 +- fcaR-1.3.0/fcaR/R/compute_closure_fuzzy.R |only fcaR-1.3.0/fcaR/R/concept_lattice.R | 628 +++++++---- fcaR-1.3.0/fcaR/R/concept_miners_registry.R |only fcaR-1.3.0/fcaR/R/concept_set.R | 184 +-- fcaR-1.3.0/fcaR/R/formal_context.R | 799 ++++++--------- fcaR-1.3.0/fcaR/R/imp_to_basis.R | 63 - fcaR-1.3.0/fcaR/R/implication_set.R | 588 +++++------ fcaR-1.3.0/fcaR/R/labeling.R |only fcaR-1.3.0/fcaR/R/latex_exporter.R |only fcaR-1.3.0/fcaR/R/lattice_plot.R | 482 +++------ fcaR-1.3.0/fcaR/R/logics.R |only fcaR-1.3.0/fcaR/R/match_attributes.R | 46 fcaR-1.3.0/fcaR/R/metrics.R |only fcaR-1.3.0/fcaR/R/plot_auxiliary.R |only fcaR-1.3.0/fcaR/R/plot_context.R | 2 fcaR-1.3.0/fcaR/R/random_contexts.R |only fcaR-1.3.0/fcaR/R/reduce_transitivity.R | 17 fcaR-1.3.0/fcaR/R/repository.R |only fcaR-1.3.0/fcaR/R/scaling.R | 25 fcaR-1.3.0/fcaR/R/simplification.R | 57 - fcaR-1.3.0/fcaR/R/stability.R |only fcaR-1.3.0/fcaR/R/subsets.R | 156 ++ fcaR-1.3.0/fcaR/R/to_fraction.R | 2 fcaR-1.3.0/fcaR/R/utils.R |only fcaR-1.3.0/fcaR/R/zzz.R | 84 + fcaR-1.3.0/fcaR/README.md | 135 ++ fcaR-1.3.0/fcaR/build/vignette.rds |binary fcaR-1.3.0/fcaR/inst/doc/advanced_lattice_metrics.R |only fcaR-1.3.0/fcaR/inst/doc/advanced_lattice_metrics.Rmd |only fcaR-1.3.0/fcaR/inst/doc/advanced_lattice_metrics.html |only fcaR-1.3.0/fcaR/inst/doc/arules.R | 4 fcaR-1.3.0/fcaR/inst/doc/arules.Rmd | 2 fcaR-1.3.0/fcaR/inst/doc/arules.html | 81 - fcaR-1.3.0/fcaR/inst/doc/concept_lattice.R | 36 fcaR-1.3.0/fcaR/inst/doc/concept_lattice.Rmd | 30 fcaR-1.3.0/fcaR/inst/doc/concept_lattice.html | 615 +++++------ fcaR-1.3.0/fcaR/inst/doc/conceptual-scaling.R | 286 +++-- fcaR-1.3.0/fcaR/inst/doc/conceptual-scaling.Rmd | 246 ++-- fcaR-1.3.0/fcaR/inst/doc/conceptual-scaling.html | 447 ++++---- fcaR-1.3.0/fcaR/inst/doc/creating_contexts.R |only fcaR-1.3.0/fcaR/inst/doc/creating_contexts.Rmd |only fcaR-1.3.0/fcaR/inst/doc/creating_contexts.html |only fcaR-1.3.0/fcaR/inst/doc/extending_equivalence.R | 61 - fcaR-1.3.0/fcaR/inst/doc/extending_equivalence.Rmd | 42 fcaR-1.3.0/fcaR/inst/doc/extending_equivalence.html | 171 +-- fcaR-1.3.0/fcaR/inst/doc/fuzzy_fca.R |only fcaR-1.3.0/fcaR/inst/doc/fuzzy_fca.Rmd |only fcaR-1.3.0/fcaR/inst/doc/fuzzy_fca.html |only fcaR-1.3.0/fcaR/inst/doc/implications.R | 32 fcaR-1.3.0/fcaR/inst/doc/implications.Rmd | 32 fcaR-1.3.0/fcaR/inst/doc/implications.html | 327 +++--- fcaR-1.3.0/fcaR/inst/doc/lattice_properties.R |only fcaR-1.3.0/fcaR/inst/doc/lattice_properties.Rmd |only fcaR-1.3.0/fcaR/inst/doc/lattice_properties.html |only fcaR-1.3.0/fcaR/inst/doc/lattice_visualization.R |only fcaR-1.3.0/fcaR/inst/doc/lattice_visualization.Rmd |only fcaR-1.3.0/fcaR/inst/doc/lattice_visualization.html |only fcaR-1.3.0/fcaR/inst/doc/matrix_factorization.R |only fcaR-1.3.0/fcaR/inst/doc/matrix_factorization.Rmd |only fcaR-1.3.0/fcaR/inst/doc/matrix_factorization.html |only fcaR-1.3.0/fcaR/inst/doc/random_contexts.R |only fcaR-1.3.0/fcaR/inst/doc/random_contexts.Rmd |only fcaR-1.3.0/fcaR/inst/doc/random_contexts.html |only fcaR-1.3.0/fcaR/inst/rstudio |only fcaR-1.3.0/fcaR/man/ConceptLattice.Rd | 149 ++ fcaR-1.3.0/fcaR/man/ConceptSet.Rd | 15 fcaR-1.3.0/fcaR/man/FormalContext.Rd | 39 fcaR-1.3.0/fcaR/man/ImplicationSet.Rd | 96 + fcaR-1.3.0/fcaR/man/RandomContext.Rd |only fcaR-1.3.0/fcaR/man/RandomDistributiveContext.Rd |only fcaR-1.3.0/fcaR/man/calculate_density.Rd |only fcaR-1.3.0/fcaR/man/calculate_grades.Rd |only fcaR-1.3.0/fcaR/man/calculate_separation.Rd |only fcaR-1.3.0/fcaR/man/calculate_stability.Rd |only fcaR-1.3.0/fcaR/man/compute_labels_and_colors.Rd |only fcaR-1.3.0/fcaR/man/conceptRegistry.Rd |only fcaR-1.3.0/fcaR/man/export_to_tikz.Rd |only fcaR-1.3.0/fcaR/man/fcaR-package.Rd | 6 fcaR-1.3.0/fcaR/man/fetch_context.Rd |only fcaR-1.3.0/fcaR/man/figures/README-unnamed-chunk-4-1.png |binary fcaR-1.3.0/fcaR/man/get_fcarepository_contexts.Rd |only fcaR-1.3.0/fcaR/man/lattice_plot.Rd |only fcaR-1.3.0/fcaR/man/print_repo_details.Rd |only fcaR-1.3.0/fcaR/man/randomize_context.Rd |only fcaR-1.3.0/fcaR/man/save_tikz.Rd |only fcaR-1.3.0/fcaR/man/select_repository_context.Rd |only fcaR-1.3.0/fcaR/src/LatticeMeetJoin.cpp |only fcaR-1.3.0/fcaR/src/LatticeProperties.cpp |only fcaR-1.3.0/fcaR/src/Logics.cpp | 83 - fcaR-1.3.0/fcaR/src/MatrixFactorization.cpp |only fcaR-1.3.0/fcaR/src/Randomize.cpp |only fcaR-1.3.0/fcaR/src/RcppExports.cpp | 580 ++++++++++ fcaR-1.3.0/fcaR/src/Transitivity.cpp |only fcaR-1.3.0/fcaR/src/aux_functions.cpp | 113 +- fcaR-1.3.0/fcaR/src/aux_functions.h | 13 fcaR-1.3.0/fcaR/src/binary_next_closure.cpp |only fcaR-1.3.0/fcaR/src/binary_operations.cpp |only fcaR-1.3.0/fcaR/src/binary_operations.h |only fcaR-1.3.0/fcaR/src/fastcbo-binary.cpp |only fcaR-1.3.0/fcaR/src/fastcbo.cpp |only fcaR-1.3.0/fcaR/src/formatting.cpp |only fcaR-1.3.0/fcaR/src/fuzzy_do.cpp |only fcaR-1.3.0/fcaR/src/implication_tree.cpp | 45 fcaR-1.3.0/fcaR/src/inclose.cpp |only fcaR-1.3.0/fcaR/src/inclose_binary_final.cpp |only fcaR-1.3.0/fcaR/src/inclose_binary_old.cpp |only fcaR-1.3.0/fcaR/src/inclose_binary_old.h |only fcaR-1.3.0/fcaR/src/lattice_algorithms.cpp |only fcaR-1.3.0/fcaR/src/metrics.cpp |only fcaR-1.3.0/fcaR/src/metrics_advanced.cpp |only fcaR-1.3.0/fcaR/src/my_tests.cpp |only fcaR-1.3.0/fcaR/src/nextclosure.cpp | 414 ++++--- fcaR-1.3.0/fcaR/src/set_operations_galois.cpp | 798 ++++++-------- fcaR-1.3.0/fcaR/src/set_operations_galois.h | 133 +- fcaR-1.3.0/fcaR/src/subsetting_dispatcher.cpp |only fcaR-1.3.0/fcaR/src/subsetting_legacy.cpp |only fcaR-1.3.0/fcaR/src/vector_operations.cpp | 24 fcaR-1.3.0/fcaR/src/vector_operations.h | 19 fcaR-1.3.0/fcaR/tests/testthat/Rplots.pdf |binary fcaR-1.3.0/fcaR/tests/testthat/test-concept_lattice.R | 63 - fcaR-1.3.0/fcaR/tests/testthat/test-imp_to_basis_new.R |only fcaR-1.3.0/fcaR/tests/testthat/test-metrics.R |only fcaR-1.3.0/fcaR/tests/testthat/test-random_contexts.R |only fcaR-1.3.0/fcaR/tests/testthat/test-test_metrics.R |only fcaR-1.3.0/fcaR/tests/testthat/test-visualization.R |only fcaR-1.3.0/fcaR/vignettes/advanced_lattice_metrics.Rmd |only fcaR-1.3.0/fcaR/vignettes/arules.Rmd | 2 fcaR-1.3.0/fcaR/vignettes/concept_lattice.Rmd | 30 fcaR-1.3.0/fcaR/vignettes/conceptual-scaling.Rmd | 246 ++-- fcaR-1.3.0/fcaR/vignettes/creating_contexts.Rmd |only fcaR-1.3.0/fcaR/vignettes/extending_equivalence.Rmd | 42 fcaR-1.3.0/fcaR/vignettes/fuzzy_fca.Rmd |only fcaR-1.3.0/fcaR/vignettes/implications.Rmd | 32 fcaR-1.3.0/fcaR/vignettes/lattice_properties.Rmd |only fcaR-1.3.0/fcaR/vignettes/lattice_visualization.Rmd |only fcaR-1.3.0/fcaR/vignettes/matrix_factorization.Rmd |only fcaR-1.3.0/fcaR/vignettes/random_contexts.Rmd |only 145 files changed, 5550 insertions(+), 3694 deletions(-)
Title: Bayesian Hierarchical Analysis of Cognitive Models of Choice
Description: Fit Bayesian (hierarchical) cognitive models
using a linear modeling language interface using particle Metropolis Markov
chain Monte Carlo sampling with Gibbs steps. The diffusion decision model (DDM),
linear ballistic accumulator model (LBA), racing diffusion model (RDM), and the lognormal
race model (LNR) are supported. Additionally, users can specify their own likelihood
function and/or choose for non-hierarchical
estimation, as well as for a diagonal, blocked or full multivariate normal
group-level distribution to test individual differences. Prior specification
is facilitated through methods that visualize the (implied) prior.
A wide range of plotting functions assist in assessing model convergence and
posterior inference. Models can be easily evaluated using functions
that plot posterior predictions or using relative model comparison metrics
such as information criteria or Bayes factors.
References: Stevenson et al. (2024) <doi:10.31234/osf.io/2e4dq>.
Author: Niek Stevenson [aut, cre] ,
Michelle Donzallaz [aut],
Andrew Heathcote [aut],
Steven Miletic [aut],
Luke Strickland [ctb],
Frank Hezemans [ctb],
Raphael Hartmann [ctb],
Karl C. Klauer [ctb],
Steven G. Johnson [ctb],
Jean M. Linhart [ctb],
Brian Gough [...truncated...]
Maintainer: Niek Stevenson <niek.stevenson@gmail.com>
Diff between EMC2 versions 3.3.0 dated 2025-12-02 and 3.4.1 dated 2026-01-12
EMC2-3.3.0/EMC2/man/plot_ss_if.Rd |only EMC2-3.3.0/EMC2/man/plot_ss_srrt.Rd |only EMC2-3.4.1/EMC2/DESCRIPTION | 14 EMC2-3.4.1/EMC2/MD5 | 90 EMC2-3.4.1/EMC2/NAMESPACE | 9 EMC2-3.4.1/EMC2/NEWS.md | 101 EMC2-3.4.1/EMC2/R/EMC2-package.R | 1 EMC2-3.4.1/EMC2/R/RcppExports.R | 8 EMC2-3.4.1/EMC2/R/SBC.R | 107 EMC2-3.4.1/EMC2/R/design.R | 50 EMC2-3.4.1/EMC2/R/fitting.R | 1 EMC2-3.4.1/EMC2/R/map.R | 28 EMC2-3.4.1/EMC2/R/model_DDM.R | 4 EMC2-3.4.1/EMC2/R/model_SS.R | 1188 ++++++----- EMC2-3.4.1/EMC2/R/new_map.R | 20 EMC2-3.4.1/EMC2/R/plotting.R | 296 ++ EMC2-3.4.1/EMC2/R/plotting_ss.R | 221 +- EMC2-3.4.1/EMC2/R/s3_funcs.R | 12 EMC2-3.4.1/EMC2/R/sampling.R | 2 EMC2-3.4.1/EMC2/R/trend.R | 763 ++++++- EMC2-3.4.1/EMC2/R/utils.R | 10 EMC2-3.4.1/EMC2/inst/doc/Simulation-based-Calibration.R | 2 EMC2-3.4.1/EMC2/inst/doc/Simulation-based-Calibration.Rmd | 2 EMC2-3.4.1/EMC2/inst/doc/Simulation-based-Calibration.html | 18 EMC2-3.4.1/EMC2/inst/doc/trends.R | 4 EMC2-3.4.1/EMC2/inst/doc/trends.Rmd | 24 EMC2-3.4.1/EMC2/inst/doc/trends.html | 45 EMC2-3.4.1/EMC2/man/EMC2-package.Rd | 4 EMC2-3.4.1/EMC2/man/apply_kernel.Rd |only EMC2-3.4.1/EMC2/man/design.Rd | 3 EMC2-3.4.1/EMC2/man/fix_custom_kernel_pointers.Rd |only EMC2-3.4.1/EMC2/man/get_custom_kernel_pointers.Rd |only EMC2-3.4.1/EMC2/man/get_power_spectra.Rd |only EMC2-3.4.1/EMC2/man/make_trend.Rd | 142 + EMC2-3.4.1/EMC2/man/plot_sbc_ecdf.Rd | 12 EMC2-3.4.1/EMC2/man/plot_spectrum.Rd |only EMC2-3.4.1/EMC2/man/set_custom_kernel_pointers.Rd |only EMC2-3.4.1/EMC2/src/Makevars | 1 EMC2-3.4.1/EMC2/src/Makevars.win | 1 EMC2-3.4.1/EMC2/src/RcppExports.cpp | 37 EMC2-3.4.1/EMC2/src/particle_ll.cpp | 54 EMC2-3.4.1/EMC2/src/trend.h | 408 ++- EMC2-3.4.1/EMC2/tests/testthat/_snaps/Darwin/fMRI.md | 56 EMC2-3.4.1/EMC2/tests/testthat/_snaps/Darwin/fit.md | 60 EMC2-3.4.1/EMC2/tests/testthat/_snaps/Darwin/variant_funs.md | 190 - EMC2-3.4.1/EMC2/tests/testthat/_snaps/kernels.md |only EMC2-3.4.1/EMC2/tests/testthat/_snaps/trend.md | 141 + EMC2-3.4.1/EMC2/tests/testthat/test-kernels.R |only EMC2-3.4.1/EMC2/tests/testthat/test-trend.R | 147 + EMC2-3.4.1/EMC2/vignettes/Simulation-based-Calibration.Rmd | 2 EMC2-3.4.1/EMC2/vignettes/trends.Rmd | 24 51 files changed, 3057 insertions(+), 1245 deletions(-)
Title: An R Package for Evaluating Scholarly Expertise Indices for
Institutional Research Assessment
Description: Institutional performance assessment remains a key challenge to a multitude of stakeholders. Existing indicators such as h-type indicators, g-type indicators, and many others do not reflect expertise of institutions that defines their research portfolio. The package offers functionality to compute and visualise two novel indices: the x-index and the xd-index. The x-index evaluates an institution's scholarly expertise within a specific discipline or field, while the xd-index provides a broader assessment of overall scholarly expertise considering an institution's publication pattern and strengths across coarse thematic areas. These indices offer a nuanced understanding of institutional research capabilities, aiding stakeholders in research management and resource allocation decisions. Lathabai, H.H., Nandy, A., and Singh, V.K. (2021) <doi:10.1007/s11192-021-04188-3>. Nandy, A., Lathabai, H.H., and Singh, V.K. (2023) <doi:10.5281/zenodo.8305585>. This package provides the h-, [...truncated...]
Author: Nilabhra Rohan Das [cre, aut] ,
Abhirup Nandy [aut]
Maintainer: Nilabhra Rohan Das <nr.das@yahoo.com>
Diff between xxdi versions 1.2.4 dated 2025-06-16 and 1.3.1 dated 2026-01-12
DESCRIPTION | 16 +- MD5 | 29 +++-- NAMESPACE | 5 NEWS.md | 13 ++ R/data.R |only R/g_index.R | 80 +++++++------- R/h_index.R | 73 ++++++------- R/ivw_xd_index.R |only R/x_index.R | 121 ++++++++++++--------- R/xc_index.R |only R/xd_index.R | 287 +++++++++++++++++++++++++++++++++++----------------- data |only man/WoSdata.Rd |only man/g_index.Rd | 63 +++++------ man/h_index.Rd | 65 +++++------ man/ivw_xd_index.Rd |only man/x_index.Rd | 85 +++++++-------- man/xc_index.Rd |only man/xd_index.Rd | 115 +++++++++++++------- 19 files changed, 562 insertions(+), 390 deletions(-)
Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an efficient implementation
of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.
This package is its R interface. The package includes efficient linear
model solver and tree learning algorithms. The package can automatically
do parallel computation on a single machine which could be more than 10
times faster than existing gradient boosting packages. It supports
various objective functions, including regression, classification and ranking.
The package is made to be extensible, so that users are also allowed to define
their own objectives easily.
Author: Tianqi Chen [aut],
Tong He [aut],
Michael Benesty [aut],
Vadim Khotilovich [aut],
Yuan Tang [aut] ,
Hyunsu Cho [aut],
Kailong Chen [aut],
Rory Mitchell [aut],
Ignacio Cano [aut],
Tianyi Zhou [aut],
Mu Li [aut],
Junyuan Xie [aut],
Min Lin [aut],
Yifen [...truncated...]
Maintainer: Jiaming Yuan <jm.yuan@outlook.com>
Diff between xgboost versions 3.1.2.1 dated 2025-12-03 and 3.1.3.1 dated 2026-01-12
DESCRIPTION | 8 +- MD5 | 36 ++++++------ R/xgb.train.R | 30 +++++----- configure | 18 +++--- configure.ac | 2 inst/doc/xgboost_introduction.Rmd | 2 inst/doc/xgboost_introduction.html | 21 +++---- man/xgb.params.Rd | 26 ++++----- man/xgboost.Rd | 18 +++--- src/config.h | 4 - src/include/xgboost/version_config.h | 2 src/include/xgboost/windefs.h | 4 + src/src/collective/tracker.cc | 2 src/src/common/deterministic.cuh | 8 +- src/src/tree/gpu_hist/histogram.cu | 12 ++-- src/src/tree/param.h | 8 +- src/xgboost_R.cc | 4 - tests/testthat/test_basic.R | 97 +++++++++++++++++++++++++++++++++++ vignettes/xgboost_introduction.Rmd | 2 19 files changed, 202 insertions(+), 102 deletions(-)
Title: Timing, Anatomical, Therapeutic and Chemical Based Medication
Clustering
Description: Agglomerative hierarchical clustering with a bespoke distance
measure based on medication similarities in the Anatomical Therapeutic
Chemical Classification System, medication timing and
medication amount or dosage. Tools for summarizing, illustrating and
manipulating the cluster objects are also available.
Author: Anna Laksafoss [aut, cre]
Maintainer: Anna Laksafoss <adls@ssi.dk>
Diff between tame versions 0.2.0 dated 2025-04-02 and 0.2.1 dated 2026-01-12
tame-0.2.0/tame/tests/testthat/test-ismedic.R |only tame-0.2.1/tame/DESCRIPTION | 18 - tame-0.2.1/tame/MD5 | 42 ++-- tame-0.2.1/tame/NAMESPACE | 1 tame-0.2.1/tame/R/RcppExports.R | 12 - tame-0.2.1/tame/R/crop.R | 42 ++-- tame-0.2.1/tame/R/employ.R | 156 ++++++++------- tame-0.2.1/tame/R/enrich.R | 2 tame-0.2.1/tame/R/extractors.R | 28 +- tame-0.2.1/tame/R/medic-utils.R | 226 ++++++++-------------- tame-0.2.1/tame/R/medic.R | 65 +++--- tame-0.2.1/tame/R/plot-utils.R | 3 tame-0.2.1/tame/R/plot.R | 5 tame-0.2.1/tame/R/refactor.R | 16 - tame-0.2.1/tame/R/summary-utils.R | 28 ++ tame-0.2.1/tame/R/summary.R | 24 +- tame-0.2.1/tame/R/tame_package.R | 1 tame-0.2.1/tame/man/construct_plot_data.Rd | 3 tame-0.2.1/tame/man/plot_summary.Rd | 3 tame-0.2.1/tame/man/regex_inner_join.Rd |only tame-0.2.1/tame/tests/testthat/test-employ.R | 42 +++- tame-0.2.1/tame/tests/testthat/test-medic-utils.R | 188 +++++++++++++++++- tame-0.2.1/tame/tests/testthat/test-medic.R | 73 ++++++- 23 files changed, 622 insertions(+), 356 deletions(-)
Title: Demographic Analysis and Data Manipulation
Description: Perform tasks commonly encountered when
preparing and analysing demographic data.
Some functions are intended for end users, and
others for developers. Includes functions for
working with life tables.
Author: John Bryant [aut, cre],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between poputils versions 0.4.2 dated 2025-07-12 and 0.5.0 dated 2026-01-12
poputils-0.4.2/poputils/data/iran_fertility.rda |only poputils-0.4.2/poputils/data/nzmort.rda |only poputils-0.4.2/poputils/data/nzmort_rvec.rda |only poputils-0.4.2/poputils/man/iran_fertility.Rd |only poputils-0.4.2/poputils/man/nzmort.Rd |only poputils-0.4.2/poputils/man/nzmort_rvec.Rd |only poputils-0.5.0/poputils/DESCRIPTION | 8 poputils-0.5.0/poputils/MD5 | 91 ++-- poputils-0.5.0/poputils/NAMESPACE | 3 poputils-0.5.0/poputils/NEWS.md | 20 + poputils-0.5.0/poputils/R/age-helpers.R | 28 + poputils-0.5.0/poputils/R/check-functions.R | 195 +++++++--- poputils-0.5.0/poputils/R/cpp11.R | 4 poputils-0.5.0/poputils/R/datasets.R | 71 ++- poputils-0.5.0/poputils/R/ex_to_lifetab.R | 28 - poputils-0.5.0/poputils/R/intrinsic_growth_rate.R |only poputils-0.5.0/poputils/R/lifetab.R | 5 poputils-0.5.0/poputils/R/logit.R | 2 poputils-0.5.0/poputils/R/poputils-package.R | 18 poputils-0.5.0/poputils/R/tfr.R | 16 poputils-0.5.0/poputils/R/tfr_to_asfr.R |only poputils-0.5.0/poputils/R/to_matrix.R | 3 poputils-0.5.0/poputils/R/util.R | 25 + poputils-0.5.0/poputils/README.md | 29 - poputils-0.5.0/poputils/build/vignette.rds |binary poputils-0.5.0/poputils/data/booth_standard.rda |only poputils-0.5.0/poputils/data/irn_fert.rda |only poputils-0.5.0/poputils/data/nzl_mort.rda |only poputils-0.5.0/poputils/data/nzl_mort_rvec.rda |only poputils-0.5.0/poputils/data/west_lifetab.rda |binary poputils-0.5.0/poputils/inst/doc/poputils.R | 18 poputils-0.5.0/poputils/inst/doc/poputils.Rmd | 22 - poputils-0.5.0/poputils/inst/doc/poputils.html | 67 +-- poputils-0.5.0/poputils/man/booth_standard.Rd |only poputils-0.5.0/poputils/man/dot-intrinsic_growth_rate.Rd |only poputils-0.5.0/poputils/man/ex_to_lifetab_brass.Rd | 16 poputils-0.5.0/poputils/man/figures/sticker |only poputils-0.5.0/poputils/man/irn_fert.Rd |only poputils-0.5.0/poputils/man/logit.Rd | 2 poputils-0.5.0/poputils/man/nzl_mort.Rd |only poputils-0.5.0/poputils/man/nzl_mort_rvec.Rd |only poputils-0.5.0/poputils/man/poputils-package.Rd | 17 poputils-0.5.0/poputils/man/tfr.Rd | 12 poputils-0.5.0/poputils/man/tfr_to_asfr_scale.Rd |only poputils-0.5.0/poputils/man/west_lifetab.Rd | 20 - poputils-0.5.0/poputils/src/cpp11.cpp | 36 + poputils-0.5.0/poputils/src/intrinsic_growth_rate.cpp |only poputils-0.5.0/poputils/tests/testthat/test-check-functions.R | 189 +++++++-- poputils-0.5.0/poputils/tests/testthat/test-ex_to_lifetab.R | 14 poputils-0.5.0/poputils/tests/testthat/test-intrinsic_growth_rate-src.R |only poputils-0.5.0/poputils/tests/testthat/test-intrinsic_growth_rate.R |only poputils-0.5.0/poputils/tests/testthat/test-lifetab.R | 41 +- poputils-0.5.0/poputils/tests/testthat/test-tfr.R | 12 poputils-0.5.0/poputils/tests/testthat/test-tfr_to_asfr.R |only poputils-0.5.0/poputils/tests/testthat/test-to_matrix.R | 42 ++ poputils-0.5.0/poputils/tests/testthat/test-util.R | 46 ++ poputils-0.5.0/poputils/vignettes/poputils.Rmd | 22 - 57 files changed, 797 insertions(+), 325 deletions(-)
Title: A Lightweight and Flexible Web Framework
Description: A very flexible framework for building server side logic in
R. The framework is unopinionated when it comes to how HTTP requests
and WebSocket messages are handled and supports all levels of app
complexity; from serving static content to full-blown dynamic
web-apps. Fiery does not hold your hand as much as e.g. the shiny
package does, but instead sets you free to create your web app the way
you want.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between fiery versions 1.4.1 dated 2025-11-18 and 1.5.0 dated 2026-01-12
DESCRIPTION | 8 MD5 | 38 ++-- NAMESPACE | 3 NEWS.md | 14 + R/Fire.R | 310 ++++++++++++++++++++++--------------- R/HandlerStack.R | 105 +++++------- R/PromiseStack.R | 259 +++++++++++++++++------------- R/aaa.R | 10 - R/loggers.R | 109 +++++++------ R/request_store.R | 3 README.md | 3 man/Fire.Rd | 2 man/loggers.Rd | 25 +- man/random_port.Rd | 2 tests/testthat/_snaps/Fire.md | 20 -- tests/testthat/_snaps/loggers.md | 24 +- tests/testthat/test-Fire.R | 10 - tests/testthat/test-HandlerStack.R | 8 tests/testthat/test-PromiseStack.R | 4 tests/testthat/test-loggers.R | 8 20 files changed, 535 insertions(+), 430 deletions(-)
Title: Lightweight One-Line Resolving Microbial Ecology Program
Description: Provides a robust collection of functions tailored for microbial ecology analysis, encompassing both data analysis and visualization. It introduces an encapsulation feature that streamlines the process into a summary object. With the initial configuration of this summary object, users can execute a wide range of analyses with a single line of code, requiring only two essential parameters for setup. The package delivers comprehensive outputs including analysis objects, statistical outcomes, and visualization-ready data, enhancing the efficiency of research workflows. Designed with user-friendliness in mind, it caters to both novices and seasoned researchers, offering an intuitive interface coupled with adaptable customization options to meet diverse analytical needs.
Author: Ningqi Wang [aut, cre, cph],
Yaozhong Zhang [aut],
Gaofei Jiang [aut]
Maintainer: Ningqi Wang <2434066068@qq.com>
Diff between LorMe versions 2.0.1 dated 2025-11-17 and 2.0.2 dated 2026-01-12
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/0.LorMe_define.R | 2 -- R/LorMe_pipeline.R | 23 ++++++++++++++++++----- R/compare_plot.R | 4 ++-- R/indicator_analysis.R | 2 +- R/sub_tax_summary.R | 20 +++++++++++++------- man/LorMe_pipeline.Rd | 3 +++ 8 files changed, 47 insertions(+), 27 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started.
Author: Robert J. Hijmans [cre, aut] ,
Marcia Barbosa [ctb] ,
Roger Bivand [ctb] ,
Andrew Brown [ctb] ,
Michael Chirico [ctb] ,
Emanuele Cordano [ctb] ,
Krzysztof Dyba [ctb] ,
Edzer Pebesma [ctb] ,
Barry Rowlingson [ctb] ,
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.8-86 dated 2025-11-28 and 1.8-93 dated 2026-01-12
terra-1.8-86/terra/R/clip.R |only terra-1.8-86/terra/R/polygons.R |only terra-1.8-93/terra/DESCRIPTION | 8 - terra-1.8-93/terra/MD5 | 105 ++++++++-------- terra-1.8-93/terra/NAMESPACE | 4 terra-1.8-93/terra/NEWS.md | 38 +++++ terra-1.8-93/terra/R/Agenerics.R | 4 terra-1.8-93/terra/R/Arith_generics.R | 68 ++++++---- terra-1.8-93/terra/R/RcppExports.R | 8 - terra-1.8-93/terra/R/aggregate.R | 2 terra-1.8-93/terra/R/app.R | 2 terra-1.8-93/terra/R/distance.R | 2 terra-1.8-93/terra/R/extract.R | 41 ++++-- terra-1.8-93/terra/R/extract_single.R | 2 terra-1.8-93/terra/R/gdal.R | 39 +++++- terra-1.8-93/terra/R/geom.R | 18 ++ terra-1.8-93/terra/R/lines.R | 2 terra-1.8-93/terra/R/plot_axes.R | 2 terra-1.8-93/terra/R/plot_cartogram.R | 27 ++-- terra-1.8-93/terra/R/plot_clip.R |only terra-1.8-93/terra/R/plot_let.R | 172 +++++++++++++++------------ terra-1.8-93/terra/R/plot_raster.R | 55 ++++---- terra-1.8-93/terra/R/plot_vector.R | 22 ++- terra-1.8-93/terra/R/sample.R | 26 ++-- terra-1.8-93/terra/R/show.R | 12 + terra-1.8-93/terra/R/vect.R | 114 +++++++++++++---- terra-1.8-93/terra/R/zonal.R | 2 terra-1.8-93/terra/R/zzz.R | 23 ++- terra-1.8-93/terra/man/aggregate.Rd | 2 terra-1.8-93/terra/man/app.Rd | 2 terra-1.8-93/terra/man/cartogram.Rd | 4 terra-1.8-93/terra/man/compare-generics.Rd | 2 terra-1.8-93/terra/man/datatype.Rd | 14 +- terra-1.8-93/terra/man/focal.Rd | 6 terra-1.8-93/terra/man/gdal.Rd | 30 ++++ terra-1.8-93/terra/man/plet.Rd | 36 +++-- terra-1.8-93/terra/man/rasterize.Rd | 6 terra-1.8-93/terra/man/sample.Rd | 5 terra-1.8-93/terra/man/split.Rd | 2 terra-1.8-93/terra/man/summarize-generics.Rd | 7 - terra-1.8-93/terra/man/tapp.Rd | 2 terra-1.8-93/terra/man/terrain.Rd | 2 terra-1.8-93/terra/man/vect.Rd | 11 + terra-1.8-93/terra/man/width.Rd | 4 terra-1.8-93/terra/src/Makevars.in | 2 terra-1.8-93/terra/src/Makevars.ucrt | 19 +- terra-1.8-93/terra/src/RcppExports.cpp | 24 ++- terra-1.8-93/terra/src/RcppFunctions.cpp | 66 +++++++--- terra-1.8-93/terra/src/RcppModule.cpp | 9 + terra-1.8-93/terra/src/arith.cpp | 31 ++++ terra-1.8-93/terra/src/read_ogr.cpp | 14 +- terra-1.8-93/terra/src/spatRaster.h | 8 - terra-1.8-93/terra/src/vecmath.cpp | 10 + terra-1.8-93/terra/src/vecmath.h | 35 +++++ terra-1.8-93/terra/src/vecmathse.cpp | 29 ++++ 55 files changed, 803 insertions(+), 377 deletions(-)
Title: Targeted Inference
Description: Various methods for targeted and semiparametric inference including
augmented inverse probability weighted (AIPW) estimators for missing data and
causal inference (Bang and Robins (2005) <doi:10.1111/j.1541-0420.2005.00377.x>),
variable importance and conditional average treatment effects (CATE)
(van der Laan (2006) <doi:10.2202/1557-4679.1008>),
estimators for risk differences and relative risks (Richardson et al. (2017)
<doi:10.1080/01621459.2016.1192546>), assumption lean inference for generalized
linear model parameters (Vansteelandt et al. (2022) <doi:10.1111/rssb.12504>).
Author: Klaus K. Holst [aut, cre],
Benedikt Sommer [aut],
Andreas Nordland [aut],
Christian B. Pipper [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between targeted versions 0.7 dated 2025-12-10 and 0.7.1 dated 2026-01-12
DESCRIPTION | 9 +-- MD5 | 21 ++++--- NAMESPACE | 1 NEWS.md | 4 + R/superlearner.R | 13 +++- inst/doc/predictionclass.html | 26 ++++----- inst/doc/riskregression.html | 32 +++++------ inst/slowtest/test_cate.R |only inst/slowtest/test_sl.R | 8 ++ inst/tinytest/test_cate.R | 96 ----------------------------------- inst/tinytest/test_learner_xgboost.R | 22 +++++--- man/superlearner.Rd | 1 12 files changed, 81 insertions(+), 152 deletions(-)
Title: R Optimization Infrastructure
Description: The R Optimization Infrastructure ('ROI') <doi:10.18637/jss.v094.i15>
is a sophisticated framework for handling optimization problems in R.
Additional information can be found on the 'ROI' homepage <https://roi.r-forge.r-project.org/>.
Author: Kurt Hornik [aut] ,
David Meyer [aut],
Florian Schwendinger [aut] ,
Stefan Theussl [aut, cre] ,
Diethelm Wuertz [ctb]
Maintainer: Stefan Theussl <Stefan.Theussl@R-Project.org>
Diff between ROI versions 1.0-1 dated 2023-04-20 and 1.0-2 dated 2026-01-12
DESCRIPTION | 16 +++++++++------- MD5 | 22 +++++++++++----------- R/bounds.R | 20 +++++++++++++++++--- R/constraints.R | 21 +++++++++++++++++---- R/plugin.R | 4 ++-- R/roi.R | 4 ++-- R/types.R | 4 ++++ man/ROI_bound.Rd | 6 +++--- man/ROI_constraint.Rd | 4 ++-- man/ROI_plugin_build_equality_constraints.Rd | 2 +- man/ROI_plugin_build_inequality_constraints.Rd | 2 +- man/ROI_solve.Rd | 4 ++-- 12 files changed, 71 insertions(+), 38 deletions(-)
Title: Derivative-Free Optimization in R using C++
Description: Perform derivative-free optimization algorithms in R using C++.
A wrapper interface is provided to call C function of the 'bobyqa' implementation
(See <https://github.com/emmt/Algorithms/tree/master/bobyqa>).
Author: Sam Watson [aut, cre],
Yi Pan [aut],
Eric Thiebaut [aut],
Mike Powell [aut]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between rminqa versions 0.2.2 dated 2023-01-08 and 0.3.1 dated 2026-01-12
rminqa-0.2.2/rminqa/R/zzz.R |only rminqa-0.2.2/rminqa/man/rminqa.Rd |only rminqa-0.3.1/rminqa/DESCRIPTION | 24 +++++------ rminqa-0.3.1/rminqa/MD5 | 22 ++++++---- rminqa-0.3.1/rminqa/NAMESPACE | 5 +- rminqa-0.3.1/rminqa/R/RcppExports.R | 51 +++++++++++++++++++++++- rminqa-0.3.1/rminqa/inst/include/newuoa.h |only rminqa-0.3.1/rminqa/inst/include/newuoa_impl.h |only rminqa-0.3.1/rminqa/inst/include/optim.h |only rminqa-0.3.1/rminqa/man/bobyqa_rosen_test1.Rd |only rminqa-0.3.1/rminqa/man/bobyqa_rosen_test2.Rd |only rminqa-0.3.1/rminqa/src/Makevars | 2 rminqa-0.3.1/rminqa/src/Makevars.win | 2 rminqa-0.3.1/rminqa/src/RcppExports.cpp | 23 ++++++++++ rminqa-0.3.1/rminqa/src/rbobyqa_example.cpp | 4 + rminqa-0.3.1/rminqa/src/rbobyqa_example_new.cpp |only 16 files changed, 106 insertions(+), 27 deletions(-)
Title: A Glimpse at the Diversity of Peru's Endemic Plants
Description: Introducing a novel and updated database showcasing Peru's endemic plants. This meticulously compiled and revised botanical collection encompasses a remarkable assemblage of over 7,898 distinct species. The data for this resource was sourced from the work of Govaerts, R., Nic Lughadha, E., Black, N. et al., titled 'The World Checklist of Vascular Plants: A continuously updated resource for exploring global plant diversity', published in Sci Data 8, 215 (2021) <doi:10.1038/s41597-021-00997-6>.
Author: Paul E. Santos Andrade [aut, cre] ,
Lucely L. Vilca Bustamante [aut]
Maintainer: Paul E. Santos Andrade <paulefrens@gmail.com>
Diff between ppendemic versions 0.1.9 dated 2025-06-09 and 0.2.0 dated 2026-01-12
DESCRIPTION | 12 +-- MD5 | 14 ++- R/matching_ppendemic.R | 2 R/ppendemic_data.R | 109 +++++++++++++++++++++++++++++++ R/zzz.R | 97 ++++++++++++++++++--------- README.md | 14 +-- data/ppendemic_tab15.rda |only man/figures/README-unnamed-chunk-2-1.png |binary man/ppendemic_tab15.Rd |only 9 files changed, 196 insertions(+), 52 deletions(-)
Title: Download and Process Public Domain Works from Project Gutenberg
Description: Download and process public domain works in the Project
Gutenberg collection <https://www.gutenberg.org/>. Includes metadata
for all Project Gutenberg works, so that they can be searched and
retrieved.
Author: Jordan Bradford [aut, cre] ,
Jon Harmon [aut] ,
Myfanwy Johnston [aut],
David Robinson [aut, cph]
Maintainer: Jordan Bradford <jrdnbradford@gmail.com>
Diff between gutenbergr versions 0.3.1 dated 2025-12-14 and 0.4.0 dated 2026-01-12
DESCRIPTION | 25 MD5 | 127 NAMESPACE | 27 NEWS.md | 9 R/data.R | 417 R/globals.R | 33 R/gutenberg_cache.R |only R/gutenberg_download.R | 355 R/gutenberg_mirrors.R | 250 R/gutenberg_strip.R | 155 R/gutenberg_works.R | 241 R/gutenbergr-package.R | 20 R/utils.R | 165 R/zzz.R |only README.md | 518 build/vignette.rds |binary data/gutenberg_authors.rda |binary data/gutenberg_languages.rda |binary data/gutenberg_metadata.rda |binary data/gutenberg_subjects.rda |binary inst/WORDLIST | 70 inst/doc/gutenbergr.R | 154 inst/doc/gutenbergr.Rmd | 308 inst/doc/gutenbergr.html | 1352 - man/flatten_gutenberg_id.Rd | 2 man/gutenberg_add_metadata.Rd | 2 man/gutenberg_authors.Rd | 6 man/gutenberg_cache_clear_all.Rd |only man/gutenberg_cache_dir.Rd |only man/gutenberg_cache_files.Rd |only man/gutenberg_cache_list.Rd |only man/gutenberg_cache_remove_ids.Rd |only man/gutenberg_cache_set.Rd |only man/gutenberg_download.Rd | 135 man/gutenberg_ensure_cache_dir.Rd |only man/gutenberg_get_all_mirrors.Rd | 68 man/gutenberg_get_mirror.Rd | 50 man/gutenberg_languages.Rd | 6 man/gutenberg_metadata.Rd | 159 man/gutenberg_strip.Rd | 86 man/gutenberg_subjects.Rd | 138 man/gutenberg_url.Rd | 4 man/gutenberg_works.Rd | 172 man/gutenbergr-package.Rd | 63 man/is_working_gutenberg_mirror.Rd | 5 man/read_next.Rd | 4 man/sample_books.Rd | 4 man/try_gutenberg_download.Rd | 2 tests/README.md |only tests/testthat.R | 16 tests/testthat/fixtures/105-0-zip |17480 ++++++++++++------------ tests/testthat/fixtures/109-to-strip.txt | 802 - tests/testthat/fixtures/109-zip | 3252 ++-- tests/testthat/fixtures/2-zip | 528 tests/testthat/fixtures/MIRRORS-ALL | 42 tests/testthat/fixtures/README | 96 tests/testthat/fixtures/create_fixtures.R | 40 tests/testthat/fixtures/harvest-filetypes---txt | 424 tests/testthat/fixtures/pg68283-txt | 3208 ++-- tests/testthat/helper-cache.R |only tests/testthat/helper-integration-tests.R |only tests/testthat/helper-mocks.R | 28 tests/testthat/test-data.R | 128 tests/testthat/test-gutenberg_cache.R |only tests/testthat/test-gutenberg_download.R | 110 tests/testthat/test-gutenberg_mirrors.R | 194 tests/testthat/test-gutenberg_strip.R | 18 tests/testthat/test-gutenberg_works.R | 114 tests/testthat/test-integration-gutenberg_api.R |only tests/testthat/test-utils.R | 112 tests/testthat/test-zzz.R |only vignettes/gutenbergr.Rmd | 308 72 files changed, 16076 insertions(+), 15956 deletions(-)
Title: Descriptive Statistics, Transition Plots, and More
Description: Utilities for common medical-statistics graphics
and tables, including automatic creation of publication-ready "Table 1"
summaries; transition (Sankey) plots; flow-chart helpers that extend the
grid package; Bézier lines and arrows; and a singular-value-decomposition-
based variable-selection method.
Author: Max Gordon [aut, cre]
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 3.0.4 dated 2025-08-19 and 3.1.0 dated 2026-01-12
DESCRIPTION | 12 MD5 | 117 +- NAMESPACE | 25 NEWS.md | 919 +++++++-------- R/bezierArrowGradient.R | 10 R/bezierArrowSmpl.R | 2 R/boxGrob_prConvert2Coords.R | 117 +- R/boxGrob_spread_npc_norm_helpers.R |only R/boxGrobs_S3_fns.R | 1 R/boxGrobs_align.R | 212 ++- R/boxGrobs_boxGrob.R | 44 R/boxGrobs_boxPropGrob.R | 60 - R/boxGrobs_boxShapes.R |only R/boxGrobs_connect.R | 308 ++--- R/boxGrobs_connect_pr_helpers.R |only R/boxGrobs_connect_pr_many_to_one_boxes.R |only R/boxGrobs_connect_pr_many_to_one_fan_in_on_top_boxes.R |only R/boxGrobs_connect_pr_one_to_many_boxes.R |only R/boxGrobs_connect_pr_single_boxes.R |only R/boxGrobs_distance.R | 3 R/boxGrobs_labelConnector.R |only R/boxGrobs_move.R | 181 ++- R/boxGrobs_print.Gmisc_list_of_boxes.R | 15 R/boxGrobs_spread.R | 394 ++++-- R/transitionPlot.R | 4 build/vignette.rds |binary inst/doc/Descriptives.Rmd | 1 inst/doc/Descriptives.html | 9 inst/doc/Grid-based_flowcharts.R | 241 ++-- inst/doc/Grid-based_flowcharts.Rmd | 301 +++-- inst/doc/Grid-based_flowcharts.html | 930 ++++++++-------- inst/doc/Transition-class.Rmd | 1 inst/doc/Transition-class.html | 9 inst/doc/transitionPlot.Rmd | 1 inst/doc/transitionPlot.html | 9 inst/examples/alignBox_ex.R | 49 inst/examples/connectGrob_example.R | 39 inst/examples/moveBox_ex.R | 46 inst/examples/spreadBox_ex.R | 43 man/align.Rd | 63 - man/bezierArrowGradient.Rd | 2 man/bezierArrowSmpl.Rd | 2 man/box.Rd | 12 man/boxPropGrob.Rd | 3 man/boxShapes.Rd |only man/connect.Rd | 169 ++ man/coords.Rd | 1 man/distance.Rd | 1 man/labelConnector.Rd |only man/moveBox.Rd | 56 man/prConvert2Coords.Rd | 19 man/prGetBoxAxisDefaults.Rd |only man/print.Gmisc_connector_label.Rd |only man/setConnectorLabels.Rd |only man/spread.Rd | 103 + man/transitionPlot.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test-align_pipe.R |only tests/testthat/test-boxGrob_move.R | 31 tests/testthat/test-boxShapes.R |only tests/testthat/test-connectGrob_N_centered.R |only tests/testthat/test-connectGrob_fan_in_top.R |only tests/testthat/test-getDescriptionStats_tidyselect.R | 102 - tests/testthat/test-labelConnector.R |only tests/testthat/test-setConnectorLabels.R |only vignettes/Descriptives.Rmd | 1 vignettes/Grid-based_flowcharts.Rmd | 301 +++-- vignettes/Transition-class.Rmd | 1 vignettes/transitionPlot.Rmd | 1 69 files changed, 3084 insertions(+), 1891 deletions(-)
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/stable/en/user/rest/>.
Author: Emmanuel Blondel [aut, cre]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geosapi versions 0.7-2 dated 2025-09-01 and 0.8 dated 2026-01-12
DESCRIPTION | 10 - MD5 | 28 ++- NAMESPACE | 5 NEWS.md | 10 + R/GSAccessControlListManager.R |only R/GSLayerRule.R |only R/GSManager.R | 8 R/GSRESTResource.R | 10 + R/GSRestRule.R |only R/GSRule.R |only R/GSServiceRule.R |only README.md | 2 build/vignette.rds |binary inst/doc/geosapi.html | 329 +++++++++++++++++--------------------- man/GSAccessControlListManager.Rd |only man/GSLayerRule.Rd |only man/GSRESTResource.Rd | 2 man/GSRestRule.Rd |only man/GSRule.Rd |only man/GSServiceRule.Rd |only 20 files changed, 204 insertions(+), 200 deletions(-)
Title: Ditwah Storm Data and Tools for Storm Monitoring and Early
Warning November 2025, Sri Lanka
Description: The Ditwah storm began impacting Sri Lanka on 25 November 2025. Ditwah provides a collection of tidy, well-structured datasets to
support storm data management, monitoring, and early warning applications in Sri Lanka.
The publicly available data were converted to tidy data format for easy analysis.
The package processes weather data, flood data and situation report data (families affected, etc.).
The package also includes functions for analyzing river level progression and load dashboard visualizations to enhance situational awareness. This is also developed for educational purposes to support learning in data wrangling, visualization, and disaster analytics.
Author: Thiyanga S. Talagala [aut, cre]
Maintainer: Thiyanga S. Talagala <ttalagala@sjp.ac.lk>
Diff between Ditwah versions 1.0.0 dated 2025-12-05 and 1.0.1 dated 2026-01-12
DESCRIPTION | 6 +++--- MD5 | 4 ++-- data/realtime_waterlevel_kelani_ganga.rda |binary 3 files changed, 5 insertions(+), 5 deletions(-)
Title: Performs Tests for Cluster Tendency of a Data Set
Description: Test for cluster tendency (clusterability) of a data set.
The methods implemented - reducing the data set to a single dimension using principal component analysis or computing
pairwise distances, and performing a multimodality test like the Dip Test or Silverman's Critical Bandwidth Test -
are described in Adolfsson, Ackerman, and Brownstein (2019) <doi:10.1016/j.patcog.2018.10.026>. Such methods can inform whether clustering algorithms
are appropriate for a data set.
Author: Zachariah Neville [aut, cre],
Naomi Brownstein [aut],
Maya Ackerman [aut],
Andreas Adolfsson [aut]
Maintainer: Zachariah Neville <zachariahneville@outlook.com>
Diff between clusterability versions 0.2.1.0 dated 2025-09-29 and 0.2.2.0 dated 2026-01-12
clusterability-0.2.1.0/clusterability/R/dipsilverman.R |only clusterability-0.2.1.0/clusterability/R/paramchecks.R |only clusterability-0.2.1.0/clusterability/R/reducestandardize.R |only clusterability-0.2.1.0/clusterability/inst/doc/Rplots.R |only clusterability-0.2.1.0/clusterability/inst/doc/clusterability_timings.R |only clusterability-0.2.1.0/clusterability/tests/testthat/test_printsummary.R |only clusterability-0.2.1.0/clusterability/tests/testthat/test_reducestandardize.R |only clusterability-0.2.1.0/clusterability/tests/testthat/test_validateparams.R |only clusterability-0.2.2.0/clusterability/DESCRIPTION | 8 clusterability-0.2.2.0/clusterability/MD5 | 55 + clusterability-0.2.2.0/clusterability/NEWS.md | 3 clusterability-0.2.2.0/clusterability/R/clusterability.R | 117 ++-- clusterability-0.2.2.0/clusterability/R/clusterabilitytest.R | 288 +++++----- clusterability-0.2.2.0/clusterability/R/data_standardization.R |only clusterability-0.2.2.0/clusterability/R/dimension_reduction.R |only clusterability-0.2.2.0/clusterability/R/hypothesis_tests.R |only clusterability-0.2.2.0/clusterability/R/input_validation.R |only clusterability-0.2.2.0/clusterability/R/normals1.R | 11 clusterability-0.2.2.0/clusterability/R/normals2.R | 11 clusterability-0.2.2.0/clusterability/R/normals3.R | 11 clusterability-0.2.2.0/clusterability/R/normals4.R | 11 clusterability-0.2.2.0/clusterability/R/normals5.R | 11 clusterability-0.2.2.0/clusterability/README.md | 14 clusterability-0.2.2.0/clusterability/inst/doc/SupplementalFiles.md |only clusterability-0.2.2.0/clusterability/inst/doc/examples.R | 18 clusterability-0.2.2.0/clusterability/inst/doc/examples_performance_testing.R |only clusterability-0.2.2.0/clusterability/inst/doc/examples_plots.R |only clusterability-0.2.2.0/clusterability/man/clusterability.Rd | 105 ++- clusterability-0.2.2.0/clusterability/man/clusterabilitytest.Rd | 39 - clusterability-0.2.2.0/clusterability/man/normals1.Rd | 3 clusterability-0.2.2.0/clusterability/man/normals2.Rd | 13 clusterability-0.2.2.0/clusterability/man/normals3.Rd | 15 clusterability-0.2.2.0/clusterability/man/normals4.Rd | 13 clusterability-0.2.2.0/clusterability/man/normals5.Rd | 15 clusterability-0.2.2.0/clusterability/tests/testthat/test_clusterabilitytest.R |only clusterability-0.2.2.0/clusterability/tests/testthat/test_data_standardization.R |only clusterability-0.2.2.0/clusterability/tests/testthat/test_dimension_reduction.R |only clusterability-0.2.2.0/clusterability/tests/testthat/test_input_validation.R |only 38 files changed, 425 insertions(+), 336 deletions(-)
More information about clusterability at CRAN
Permanent link
Title: Generate Citation File Format ('cff') Metadata for R Packages
Description: The Citation File Format version 1.2.0
<doi:10.5281/zenodo.5171937> is a human and machine readable file
format which provides citation metadata for software. This package
provides core utilities to generate and validate this metadata.
Author: Diego Hernangomez [aut, cre, cph] ,
Joao Martins [rev] ,
Scott Chamberlain [rev]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between cffr versions 1.2.0 dated 2025-01-25 and 1.2.1 dated 2026-01-12
cffr-1.2.0/cffr/inst/doc/bibtex_cff.R |only cffr-1.2.0/cffr/inst/doc/bibtex_cff.Rmd |only cffr-1.2.0/cffr/inst/doc/bibtex_cff.html |only cffr-1.2.0/cffr/inst/doc/crosswalk.R |only cffr-1.2.0/cffr/inst/doc/crosswalk.Rmd |only cffr-1.2.0/cffr/inst/doc/crosswalk.html |only cffr-1.2.0/cffr/inst/doc/paper.Rmd |only cffr-1.2.0/cffr/inst/doc/paper.html |only cffr-1.2.0/cffr/man/chunks/cffclass.html |only cffr-1.2.0/cffr/vignettes/bibtex_cff.Rmd |only cffr-1.2.0/cffr/vignettes/crosswalk.Rmd |only cffr-1.2.0/cffr/vignettes/paper.Rmd |only cffr-1.2.1/cffr/DESCRIPTION | 17 cffr-1.2.1/cffr/MD5 | 163 - cffr-1.2.1/cffr/NEWS.md | 9 cffr-1.2.1/cffr/R/as_bibentry.R | 828 +++-- cffr-1.2.1/cffr/R/as_cff.R | 30 cffr-1.2.1/cffr/R/as_cff_person.R | 46 cffr-1.2.1/cffr/R/as_cff_reference.R | 8 cffr-1.2.1/cffr/R/assertions.R | 27 cffr-1.2.1/cffr/R/cff.R | 10 cffr-1.2.1/cffr/R/cff_create.R | 39 cffr-1.2.1/cffr/R/cff_gha_update.R | 154 - cffr-1.2.1/cffr/R/cff_git_hook.R | 4 cffr-1.2.1/cffr/R/cff_read.R | 583 ++-- cffr-1.2.1/cffr/R/cff_validate.R | 269 - cffr-1.2.1/cffr/R/cff_write.R | 52 cffr-1.2.1/cffr/R/cff_write_misc.R | 277 + cffr-1.2.1/cffr/R/deprecated.R | 67 cffr-1.2.1/cffr/R/encoded_utf_to_latex.R | 5 cffr-1.2.1/cffr/R/methods.R | 76 cffr-1.2.1/cffr/R/utils-alerts.R | 177 - cffr-1.2.1/cffr/R/utils-bib.R | 21 cffr-1.2.1/cffr/R/utils-cff_read.R | 766 ++--- cffr-1.2.1/cffr/R/utils-cff_ref.R | 48 cffr-1.2.1/cffr/R/utils-create.R | 443 +-- cffr-1.2.1/cffr/R/utils-methods.R | 17 cffr-1.2.1/cffr/R/utils-persons.R | 236 + cffr-1.2.1/cffr/R/utils-schema.R | 5 cffr-1.2.1/cffr/R/utils.R | 38 cffr-1.2.1/cffr/R/zzz.R | 2 cffr-1.2.1/cffr/README.md | 166 - cffr-1.2.1/cffr/build/partial.rdb |binary cffr-1.2.1/cffr/build/vignette.rds |binary cffr-1.2.1/cffr/data/cran_to_spdx.rda |binary cffr-1.2.1/cffr/inst/WORDLIST | 5 cffr-1.2.1/cffr/inst/doc/bibtex-cff.R |only cffr-1.2.1/cffr/inst/doc/bibtex-cff.Rmd |only cffr-1.2.1/cffr/inst/doc/bibtex-cff.html |only cffr-1.2.1/cffr/inst/doc/cffr.html | 29 cffr-1.2.1/cffr/inst/doc/joss-paper.Rmd |only cffr-1.2.1/cffr/inst/doc/joss-paper.html |only cffr-1.2.1/cffr/inst/doc/r-cff.R |only cffr-1.2.1/cffr/inst/doc/r-cff.Rmd |only cffr-1.2.1/cffr/inst/doc/r-cff.html |only cffr-1.2.1/cffr/inst/extdata/cran_licenses.csv | 314 +- cffr-1.2.1/cffr/inst/schemaorg.json | 4 cffr-1.2.1/cffr/inst/yaml/update-citation-cff.yaml | 6 cffr-1.2.1/cffr/man/as_bibentry.Rd | 2 cffr-1.2.1/cffr/man/as_cff_person.Rd | 2 cffr-1.2.1/cffr/man/cff_class.Rd | 51 cffr-1.2.1/cffr/man/cff_read.Rd | 2 cffr-1.2.1/cffr/man/chunks/cffclass.Rmd | 2 cffr-1.2.1/cffr/man/cran_to_spdx.Rd | 2 cffr-1.2.1/cffr/man/figures/logo.png |binary cffr-1.2.1/cffr/tests/testthat/_snaps/as_cff_person.md | 1 cffr-1.2.1/cffr/tests/testthat/_snaps/cff_create.md | 2 cffr-1.2.1/cffr/tests/testthat/_snaps/methods.md | 4 cffr-1.2.1/cffr/tests/testthat/_snaps/utils-create.md | 4 cffr-1.2.1/cffr/tests/testthat/test-as_bibentry.R | 10 cffr-1.2.1/cffr/tests/testthat/test-as_cff.R | 331 +- cffr-1.2.1/cffr/tests/testthat/test-as_cff_person.R | 35 cffr-1.2.1/cffr/tests/testthat/test-as_cff_reference.R | 1550 +++++------ cffr-1.2.1/cffr/tests/testthat/test-cff.R | 76 cffr-1.2.1/cffr/tests/testthat/test-cff_create.R | 147 - cffr-1.2.1/cffr/tests/testthat/test-cff_gha_update.R | 5 cffr-1.2.1/cffr/tests/testthat/test-cff_modify.R | 16 cffr-1.2.1/cffr/tests/testthat/test-cff_read.R | 38 cffr-1.2.1/cffr/tests/testthat/test-cff_validate.R | 20 cffr-1.2.1/cffr/tests/testthat/test-cff_write.R | 20 cffr-1.2.1/cffr/tests/testthat/test-cff_write_misc.R | 285 -- cffr-1.2.1/cffr/tests/testthat/test-deprecated.R | 10 cffr-1.2.1/cffr/tests/testthat/test-methods.R | 29 cffr-1.2.1/cffr/tests/testthat/test-mock-package.R | 25 cffr-1.2.1/cffr/tests/testthat/test-utils-alerts.R | 5 cffr-1.2.1/cffr/tests/testthat/test-utils-cff_create.R | 42 cffr-1.2.1/cffr/tests/testthat/test-utils-create.R | 13 cffr-1.2.1/cffr/tests/testthat/test-utils-persons.R | 1 cffr-1.2.1/cffr/tests/testthat/test-utils.R | 1 cffr-1.2.1/cffr/tests/testthat/test-xtra-check-bibtex-ruby.R | 55 cffr-1.2.1/cffr/vignettes/bibtex-cff.Rmd |only cffr-1.2.1/cffr/vignettes/joss-paper.Rmd |only cffr-1.2.1/cffr/vignettes/r-cff.Rmd |only cffr-1.2.1/cffr/vignettes/tweet-1.png |binary 94 files changed, 3891 insertions(+), 3836 deletions(-)
Title: Slide Automation for Tables, Listings and Figures
Description: The normal process of creating clinical study slides is that
a statistician manually type in the numbers from outputs and a
separate statistician to double check the typed in numbers. This
process is time consuming, resource intensive, and error prone.
Automatic slide generation is a solution to address these issues. It
reduces the amount of work and the required time when creating slides,
and reduces the risk of errors from manually typing or copying numbers
from the output to slides. It also helps users to avoid unnecessary
stress when creating large amounts of slide decks in a short time
window.
Author: Joe Zhu [cre, aut] ,
Heng Wang [aut],
Yinqi Zhao [aut],
Bo Ci [aut],
Liming Li [aut],
Laura Wang [ctb],
Xiaoli Duan [aut],
Stefan Pascal Thoma [aut],
Thomas Neitmann [ctb],
Miles Almond [aut],
Mahdi About [ctb],
Kai Lim [ctb],
Nolan Steed [ctb],
Daol [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between autoslider.core versions 0.3.1 dated 2025-09-25 and 0.3.2 dated 2026-01-12
DESCRIPTION | 24 +- MD5 | 24 +- NAMESPACE | 340 +++++++++++++++--------------- NEWS.md | 186 ++++++++-------- R/package.R | 115 +++++----- inst/doc/adding_templates.html | 4 inst/doc/autoslideR.html | 8 inst/doc/generate_placeholder_slides.html | 4 inst/doc/tlg_templates.html | 4 inst/doc/use_LLM.html | 4 inst/doc/using_formats.html | 4 tests/testthat/test-srep_outputs.R | 102 ++++----- tests/testthat/test_ai.R | 4 13 files changed, 415 insertions(+), 408 deletions(-)
More information about autoslider.core at CRAN
Permanent link
Title: Extract Circadian Rhythms Metrics from Actigraphy Data
Description: Circadian rhythms are rhythms that oscillate about every 24 h, which has been observed in multiple physiological processes including core body temperature, hormone secretion, heart rate, blood pressure, and many others. Measuring circadian rhythm with wearables is based on a principle that there is increased movement during wake periods and reduced movement during sleep periods, and has been shown to be reliable and valid. This package can be used to extract nonparametric circadian metrics like intradaily variability (IV), interdaily stability (IS), and relative amplitude (RA); and parametric cosinor model and extended cosinor model coefficient. Details can be found in Junrui Di et al (2019) <doi:10.1007/s12561-019-09236-4>.
Author: Junrui Di [aut, cre],
Vadim zipunnikov [aut],
Vincent van Hees [ctb]
Maintainer: Junrui Di <dijunrui@gmail.com>
Diff between ActCR versions 0.3.0 dated 2022-05-11 and 0.4.0 dated 2026-01-12
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 1 + NEWS.md | 26 +++++++++++++++++++------- R/ActCosinor.R | 13 ++++++++++--- R/ActCosinor_long.R | 11 ++++++----- man/ActCosinor.Rd | 2 ++ man/ActCosinor_long.Rd | 3 ++- 8 files changed, 52 insertions(+), 28 deletions(-)
Title: Individual Conditional Expectation Plot Toolbox
Description: Implements Individual Conditional Expectation (ICE) plots, a tool for visualizing the model estimated by any supervised learning algorithm. ICE plots refine Friedman's partial dependence plot by graphing the functional relationship between the predicted response and a covariate of interest for individual observations. Specifically, ICE plots highlight the variation in the fitted values across the range of a covariate of interest, suggesting where and to what extent they may exist.
Author: Alex Goldstein [aut],
Adam Kapelner [aut, cre] ,
Justin Bleich [aut]
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between ICEbox versions 1.1.5 dated 2022-08-22 and 1.2 dated 2026-01-12
CHANGELOG | 98 +++-- DESCRIPTION | 35 + MD5 | 74 ++-- NAMESPACE | 53 ++ R/RcppExports.R |only R/WhiteWine.R |only R/additivityLineup.R |only R/backfitter.R |only R/clusterICE.R | 334 +++++++++++------- R/dice.R | 250 +++++++++++-- R/ice.R | 693 ++++++++++++++++++++++++-------------- R/plot.dice.R | 586 +++++++++++++++++++------------- R/plot.ice.R | 722 ++++++++++++++++++++++++---------------- R/print.dice.R | 18 R/print.ice.R | 18 R/summary.dice.R | 16 R/summary.ice.R | 16 R/zzz.R |only inst/CITATION | 39 +- man/WhiteWine.Rd | 44 +- man/additivityLineup.Rd |only man/backfitter.Rd |only man/clusterICE.Rd | 186 +++++----- man/colSds_cpp.Rd |only man/derivative_cpp.Rd |only man/dice.Rd | 225 ++++++------ man/ice.Rd | 298 +++++++--------- man/melt_ice_curves_cpp.Rd |only man/plot.dice.Rd | 187 +++++----- man/plot.ice.Rd | 279 +++++++-------- man/print.dice.Rd | 36 - man/print.ice.Rd | 36 - man/rowCenter_cpp.Rd |only man/sg_smooth_cpp.Rd |only man/summary.dice.Rd | 37 -- man/summary.ice.Rd | 36 - man/transform_ice_curves_cpp.Rd |only src |only tests |only 39 files changed, 2556 insertions(+), 1760 deletions(-)
Title: The Fill-Mask Association Test
Description: The Fill-Mask Association Test ('FMAT')
<doi:10.1037/pspa0000396>
is an integrative, probability-based social computing method
using Masked Language Models to measure conceptual associations
(e.g., attitudes, biases, stereotypes, social norms, cultural values)
as propositional semantic representations in natural language.
Supported language models include 'BERT'
<doi:10.48550/arXiv.1810.04805> and its variants available at 'Hugging Face'
<https://huggingface.co/models?pipeline_tag=fill-mask>.
Methodological references and installation guidance are provided at
<https://psychbruce.github.io/FMAT/>.
Author: Han Wu Shuang Bao [aut, cre]
Maintainer: Han Wu Shuang Bao <baohws@foxmail.com>
Diff between FMAT versions 2025.12 dated 2025-12-15 and 2026.1 dated 2026-01-12
DESCRIPTION | 14 - MD5 | 24 +-- NAMESPACE | 2 NEWS.md | 13 + R/FMAT.R | 369 +++++++++++++++++++++++++++++++++++-------------- README.md | 90 ++++++----- man/BERT_vocab.Rd | 21 ++ man/FMAT-package.Rd | 2 man/FMAT_run.Rd | 40 +++-- man/ICC_models.Rd | 6 man/LPR_reliability.Rd | 2 man/fill_mask.Rd | 3 man/special_case.Rd |only man/weight_decay.Rd |only 14 files changed, 396 insertions(+), 190 deletions(-)