Title: Correlated Meta-Analysis
Description: Performs Correlated Meta-Analysis ('corrmeta') across multiple OMIC
scans, accounting for hidden non-independencies between elements of the
scans due to overlapping samples, related samples, or other information.
For more information about the method, refer to the paper
Province MA. (2013) <doi:10.1142/9789814447973_0023>.
Author: Woo Seok Jung [aut, cre],
Michael Province [aut, cph]
Maintainer: Woo Seok Jung <jungw@wustl.edu>
Diff between corrmeta versions 1.0.0 dated 2024-03-08 and 1.0.1 dated 2025-10-24
DESCRIPTION | 8 +++--- LICENSE | 4 +-- MD5 | 20 ++++++++-------- R/polycorr.R | 2 - R/tetracorr.R | 2 - README.md | 24 ++++++++------------ build/vignette.rds |binary inst/doc/vignette.R | 4 +-- inst/doc/vignette.html | 58 ++++++++++++++++++++++--------------------------- man/polycorr.Rd | 2 - man/tetracorr.Rd | 6 ++--- 11 files changed, 61 insertions(+), 69 deletions(-)
Title: Boundary Regression Discontinuity Designs
Description: Provides estimation and inference procedures for boundary regression discontinuity (RD) designs
using local polynomial methods, based on either bivariate coordinates or distance-based approaches.
Methods are developed in Cattaneo, Titiunik, and Yu (2025)
<https://mdcattaneo.github.io/papers/Cattaneo-Titiunik-Yu_2025_BoundaryRD.pdf>.
Author: Matias D. Cattaneo [aut],
Rocio Titiunik [aut],
Ruiqi Rae Yu [aut, cre]
Maintainer: Ruiqi Rae Yu <rae.yu@princeton.edu>
Diff between rd2d versions 0.0.2 dated 2025-06-10 and 0.0.3 dated 2025-10-24
DESCRIPTION | 6 +- MD5 | 22 ++++---- R/rd2d.R | 104 +++++++++++++++++++++++++++------------- R/rd2d_dist.R | 121 +++++++++++++++++++++++++++++++++-------------- R/rd2d_dist_fn.R | 6 +- R/rd2d_fn_v2.R | 2 R/rdbw2d_dist.R | 2 man/rd2d.Rd | 8 +-- man/rd2d.dist.Rd | 8 +-- man/rdbw2d.dist.Rd | 2 man/summary.rd2d.Rd | 5 + man/summary.rd2d.dist.Rd | 3 + 12 files changed, 191 insertions(+), 98 deletions(-)
Title: Non-Parametric Bayesian Analyses of Animal Movement
Description: Methods for assessing animal movement from telemetry and biologging
data using non-parametric Bayesian methods. This includes features for pre-
processing and analysis of data, as well as the visualization of results
from the models. This framework does not rely on standard parametric density
functions, which provides flexibility during model fitting. Further details
regarding part of this framework can be found in Cullen et al. (2022) <doi:10.1111/2041-210X.13745>.
Author: Joshua Cullen [aut, cre, cph] ,
Denis Valle [aut, cph]
Maintainer: Joshua Cullen <joshcullen10@gmail.com>
Diff between bayesmove versions 0.2.1 dated 2021-10-22 and 0.2.3 dated 2025-10-24
bayesmove-0.2.1/bayesmove/man/get_MAP_internal.Rd |only bayesmove-0.2.3/bayesmove/DESCRIPTION | 19 bayesmove-0.2.3/bayesmove/MD5 | 29 - bayesmove-0.2.3/bayesmove/NAMESPACE | 1 bayesmove-0.2.3/bayesmove/NEWS.md | 11 bayesmove-0.2.3/bayesmove/R/LDA_helper_functions.R | 46 +- bayesmove-0.2.3/bayesmove/R/segmentation_helper_functions.R | 49 -- bayesmove-0.2.3/bayesmove/R/shinyapp.R | 192 +++++----- bayesmove-0.2.3/bayesmove/README.md | 52 +- bayesmove-0.2.3/bayesmove/inst/CITATION | 59 ++- bayesmove-0.2.3/bayesmove/inst/WORDLIST | 4 bayesmove-0.2.3/bayesmove/man/assign_behavior.Rd | 8 bayesmove-0.2.3/bayesmove/man/insert_NAs.Rd | 2 bayesmove-0.2.3/bayesmove/man/shiny_tracks.Rd | 2 bayesmove-0.2.3/bayesmove/src/RcppExports.cpp | 5 bayesmove-0.2.3/bayesmove/tests/testthat/test-assign_behavior.R | 3 16 files changed, 265 insertions(+), 217 deletions(-)
Title: Estimate the Effective Reproductive Number with Trend Filtering
Description: Use trend filtering, a type of regularized nonparametric
regression, to estimate the instantaneous reproduction number, also
called Rt. This value roughly says how many new infections will result
from each new infection today. Values larger than 1 indicate that an
epidemic is growing while those less than 1 indicate decline. For more
details about this methodology, see Liu, Cai, Gustafson, and McDonald (2024)
<doi:10.1371/journal.pcbi.1012324>.
Author: Daniel J. McDonald [aut, cre, cph],
Jiaping Liu [aut],
Zhenglun Cai [ctb]
Maintainer: Daniel J. McDonald <daniel@stat.ubc.ca>
Diff between rtestim versions 1.0.0 dated 2025-07-05 and 1.0.1 dated 2025-10-24
DESCRIPTION | 6 MD5 | 38 ++-- NEWS.md | 8 R/discretize_gamma.R | 6 R/estimate_rt.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/delay-distributions.R | 20 +- inst/doc/delay-distributions.Rmd | 41 ++-- inst/doc/delay-distributions.html | 293 ++++++++++++++++----------------- inst/doc/rtestim.R | 6 inst/doc/rtestim.Rmd | 8 inst/doc/rtestim.html | 52 +++-- man/figures/README-cv-estimate-1.png |binary man/figures/README-full-fit-1.png |binary src/rtestim_path.cpp | 23 +- tests/testthat/test-delay_calculator.R | 7 tests/testthat/test-fast_convolve.R | 2 vignettes/delay-distributions.Rmd | 41 ++-- vignettes/rtestim.Rmd | 8 20 files changed, 290 insertions(+), 272 deletions(-)
Title: Lightweight Interface to TIGER/Line Shapefiles
Description: Download geographic shapes from the United States Census Bureau
TIGER/Line Shapefiles <https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html>.
Functions support downloading and reading in geographic boundary data.
All downloads can be set up with a cache to avoid multiple downloads.
Data is available back to 2000 for most geographies.
Author: Christopher T. Kenny [aut, cre] ,
Cory McCartan [aut]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
Diff between tinytiger versions 0.0.10 dated 2025-04-29 and 0.0.11 dated 2025-10-24
DESCRIPTION | 14 - LICENSE | 4 MD5 | 223 +++++++++++------------ NEWS.md | 54 +++-- R/address_ranges.R | 12 - R/ai_an_nh_areas.R | 6 R/anrc.R | 6 R/area_landmarks.R | 10 - R/area_water.R | 12 - R/block_groups.R | 10 - R/blocks.R | 10 - R/cache.R | 108 +++++------ R/cbsa.R | 4 R/coastline.R | 8 R/congressional_districts.R | 12 - R/consolidated_cities.R | 8 R/counties.R | 8 R/county_subdivisions.R | 8 R/csa.R | 64 +++--- R/data.R | 36 +-- R/elementary_school_districts.R | 8 R/estates.R | 8 R/linear_water.R | 12 - R/lookup.R | 244 +++++++++++++------------- R/metropolitan_divisions.R | 4 R/military.R | 8 R/new_england_city.R | 8 R/new_england_city_divisions.R | 4 R/new_england_combined_areas.R | 4 R/places.R | 8 R/point_landmarks.R | 10 - R/polygon_edges.R | 12 - R/polygon_faces.R | 12 - R/primary_roads.R | 8 R/primary_secondary_roads.R | 10 - R/puma.R | 12 - R/rails.R | 8 R/roads.R | 12 - R/secondary_school_districts.R | 8 R/state_leg_lower.R | 8 R/state_leg_upper.R | 8 R/states.R | 6 R/subbarrio.R | 8 R/tinytiger-package.R | 34 +-- R/tract.R | 10 - R/tribal_block_groups.R | 8 R/tribal_subdivisions.R | 8 R/tribal_tracts.R | 8 R/uac.R | 10 - R/unified_school_districts.R | 8 R/utils.R | 2 R/voting_districts.R | 10 - R/zcta.R | 8 R/zzroxygen.R |only R/zzz.R | 12 - build/vignette.rds |binary inst/doc/tinytiger.html | 49 ++--- inst/templates/test-tinytiger.R | 8 man/tt_address_ranges.Rd | 4 man/tt_ai_an_nh_areas.Rd | 4 man/tt_anrc.Rd | 4 man/tt_area_landmarks.Rd | 4 man/tt_area_water.Rd | 4 man/tt_block_groups.Rd | 4 man/tt_blocks.Rd | 4 man/tt_cbsa.Rd | 2 man/tt_coastline.Rd | 4 man/tt_congressional_districts.Rd | 4 man/tt_consolidated_cities.Rd | 4 man/tt_counties.Rd | 4 man/tt_county_subdivisions.Rd | 4 man/tt_csa.Rd | 2 man/tt_elementary_school_districts.Rd | 4 man/tt_estates.Rd | 4 man/tt_linear_water.Rd | 4 man/tt_metropolitan_divisions.Rd | 2 man/tt_military.Rd | 4 man/tt_new_england_cities.Rd | 4 man/tt_new_england_city_divisions.Rd | 2 man/tt_new_england_combined_areas.Rd | 2 man/tt_places.Rd | 4 man/tt_point_landmarks.Rd | 4 man/tt_polygon_edges.Rd | 4 man/tt_polygon_faces.Rd | 4 man/tt_primary_roads.Rd | 4 man/tt_primary_secondary_roads.Rd | 4 man/tt_puma.Rd | 4 man/tt_rails.Rd | 4 man/tt_roads.Rd | 4 man/tt_secondary_school_districts.Rd | 4 man/tt_state_leg_lower.Rd | 4 man/tt_state_leg_upper.Rd | 4 man/tt_states.Rd | 4 man/tt_subbarrios.Rd | 4 man/tt_tracts.Rd | 4 man/tt_tribal_block_groups.Rd | 4 man/tt_tribal_subdivisions.Rd | 4 man/tt_tribal_tracts.Rd | 4 man/tt_uac.Rd | 4 man/tt_unified_school_districts.Rd | 4 man/tt_voting_districts.Rd | 4 man/tt_zcta.Rd | 4 tests/testthat/setup.R | 3 tests/testthat/test-ai_an_nh_areas.R | 8 tests/testthat/test-anrc.R | 8 tests/testthat/test-area_landmarks.R | 8 tests/testthat/test-area_water.R | 8 tests/testthat/test-cbsa.R | 8 tests/testthat/test-congressional_districts.R | 8 tests/testthat/test-counties.R | 8 tests/testthat/test-roads.R | 8 tests/testthat/test-state_leg_upper.R | 8 tests/testthat/test-tract.R | 8 113 files changed, 739 insertions(+), 732 deletions(-)
Title: Tidy Population Genetics
Description: We provide a tidy grammar of population genetics, facilitating
the manipulation and analysis of data on biallelic single nucleotide
polymorphisms (SNPs). 'tidypopgen' scales to very large genetic datasets
by storing genotypes on disk, and performing operations on them in
chunks, without ever loading all data in memory. The full
functionalities of the package are described in Carter et al. (2025)
<doi:10.1101/2025.06.06.658325>.
Author: Evie Carter [aut],
Eirlys Tysall [aut],
Andrea Manica [aut, cre, cph] ,
Chang Christopher [ctb] ),
Shaun Purcell [ctb] ),
Bengtsson Henrik [ctb] )
Maintainer: Andrea Manica <am315@cam.ac.uk>
Diff between tidypopgen versions 0.3.2 dated 2025-08-27 and 0.4.0 dated 2025-10-24
tidypopgen-0.3.2/tidypopgen/R/utils.R |only tidypopgen-0.4.0/tidypopgen/DESCRIPTION | 8 tidypopgen-0.4.0/tidypopgen/MD5 | 317 +-- tidypopgen-0.4.0/tidypopgen/NAMESPACE | 1 tidypopgen-0.4.0/tidypopgen/NEWS.md | 8 tidypopgen-0.4.0/tidypopgen/R/gen_tibble.R | 475 +---- tidypopgen-0.4.0/tidypopgen/R/gen_tibble_bed.R |only tidypopgen-0.4.0/tidypopgen/R/gen_tibble_fbm.R |only tidypopgen-0.4.0/tidypopgen/R/gen_tibble_packedancestry.R | 79 tidypopgen-0.4.0/tidypopgen/R/gen_tibble_ped.R | 16 tidypopgen-0.4.0/tidypopgen/R/gen_tibble_vcf.R | 28 tidypopgen-0.4.0/tidypopgen/R/gt_add_sf.R | 7 tidypopgen-0.4.0/tidypopgen/R/gt_admixture.R | 7 tidypopgen-0.4.0/tidypopgen/R/gt_as_geno_lea.R | 1 tidypopgen-0.4.0/tidypopgen/R/gt_as_hierfstat.R | 2 tidypopgen-0.4.0/tidypopgen/R/gt_as_plink.R | 114 - tidypopgen-0.4.0/tidypopgen/R/gt_as_vcf.R | 2 tidypopgen-0.4.0/tidypopgen/R/gt_cluster_pca.R | 4 tidypopgen-0.4.0/tidypopgen/R/gt_dapc.R | 29 tidypopgen-0.4.0/tidypopgen/R/gt_extract_f2.R | 26 tidypopgen-0.4.0/tidypopgen/R/gt_from_genlight.R |only tidypopgen-0.4.0/tidypopgen/R/gt_has_imputed.R | 8 tidypopgen-0.4.0/tidypopgen/R/gt_helper_functions.R | 69 tidypopgen-0.4.0/tidypopgen/R/gt_impute_simple.R | 15 tidypopgen-0.4.0/tidypopgen/R/gt_impute_xgboost.R | 26 tidypopgen-0.4.0/tidypopgen/R/gt_load.R | 43 tidypopgen-0.4.0/tidypopgen/R/gt_order_loci.R | 3 tidypopgen-0.4.0/tidypopgen/R/gt_pca_autoSVD.R | 29 tidypopgen-0.4.0/tidypopgen/R/gt_pca_partialSVD.R | 9 tidypopgen-0.4.0/tidypopgen/R/gt_pca_randomSVD.R | 18 tidypopgen-0.4.0/tidypopgen/R/gt_pcadapt.R | 10 tidypopgen-0.4.0/tidypopgen/R/gt_pseudohaploid.R | 8 tidypopgen-0.4.0/tidypopgen/R/gt_save.R | 40 tidypopgen-0.4.0/tidypopgen/R/gt_snmf.R | 11 tidypopgen-0.4.0/tidypopgen/R/gt_update_backingfile.R | 61 tidypopgen-0.4.0/tidypopgen/R/indiv_het_obs.R | 2 tidypopgen-0.4.0/tidypopgen/R/indiv_inbreeding.R | 4 tidypopgen-0.4.0/tidypopgen/R/indiv_missingness.R | 5 tidypopgen-0.4.0/tidypopgen/R/indiv_ploidy.R | 9 tidypopgen-0.4.0/tidypopgen/R/is_loci_table_ordered.R | 30 tidypopgen-0.4.0/tidypopgen/R/local_reimplementations.R |only tidypopgen-0.4.0/tidypopgen/R/loci_alt_freq.R | 22 tidypopgen-0.4.0/tidypopgen/R/loci_hwe.R | 6 tidypopgen-0.4.0/tidypopgen/R/loci_ld_clump.R | 43 tidypopgen-0.4.0/tidypopgen/R/loci_missingness.R | 11 tidypopgen-0.4.0/tidypopgen/R/loci_pi.R | 10 tidypopgen-0.4.0/tidypopgen/R/loci_transitions.R | 2 tidypopgen-0.4.0/tidypopgen/R/loci_transversions.R | 2 tidypopgen-0.4.0/tidypopgen/R/pairwise_allele_sharing.R | 9 tidypopgen-0.4.0/tidypopgen/R/pairwise_grm.R | 3 tidypopgen-0.4.0/tidypopgen/R/pairwise_ibs.R | 4 tidypopgen-0.4.0/tidypopgen/R/pairwise_king.R | 13 tidypopgen-0.4.0/tidypopgen/R/pairwise_pop_fst.R | 12 tidypopgen-0.4.0/tidypopgen/R/pop_fis.R | 11 tidypopgen-0.4.0/tidypopgen/R/pop_fst.R | 1 tidypopgen-0.4.0/tidypopgen/R/pop_global_stats.R | 7 tidypopgen-0.4.0/tidypopgen/R/pop_het_exp.R | 6 tidypopgen-0.4.0/tidypopgen/R/pop_het_obs.R | 6 tidypopgen-0.4.0/tidypopgen/R/pop_tajimas_d.R | 6 tidypopgen-0.4.0/tidypopgen/R/predict_gt_pca.R | 21 tidypopgen-0.4.0/tidypopgen/R/rbind_dry_run.R | 14 tidypopgen-0.4.0/tidypopgen/R/rbind_gen_tibble.R | 102 - tidypopgen-0.4.0/tidypopgen/R/scale_fill_distruct.R | 1 tidypopgen-0.4.0/tidypopgen/R/select_loci.R | 8 tidypopgen-0.4.0/tidypopgen/R/select_loci_if.R | 3 tidypopgen-0.4.0/tidypopgen/R/show_genotypes.R | 2 tidypopgen-0.4.0/tidypopgen/R/show_loci.R | 2 tidypopgen-0.4.0/tidypopgen/R/show_ploidy.R | 1 tidypopgen-0.4.0/tidypopgen/R/snp_allele_sharing.R | 19 tidypopgen-0.4.0/tidypopgen/R/snp_ibs.R | 28 tidypopgen-0.4.0/tidypopgen/R/snp_king.R | 21 tidypopgen-0.4.0/tidypopgen/R/subset_bigSNP.R | 66 tidypopgen-0.4.0/tidypopgen/R/tidypopgen-package.R | 7 tidypopgen-0.4.0/tidypopgen/R/vcf_to_fbm_cpp_fast.R | 86 tidypopgen-0.4.0/tidypopgen/R/vcf_to_fbm_vcfR.R | 139 - tidypopgen-0.4.0/tidypopgen/R/windows_indiv_roh.R | 29 tidypopgen-0.4.0/tidypopgen/README.md | 3 tidypopgen-0.4.0/tidypopgen/inst/WORDLIST | 16 tidypopgen-0.4.0/tidypopgen/inst/doc/a01_overview.R | 8 tidypopgen-0.4.0/tidypopgen/inst/doc/a01_overview.Rmd | 31 tidypopgen-0.4.0/tidypopgen/inst/doc/a01_overview.html | 306 +-- tidypopgen-0.4.0/tidypopgen/inst/doc/a02_qc.R | 6 tidypopgen-0.4.0/tidypopgen/inst/doc/a02_qc.Rmd | 14 tidypopgen-0.4.0/tidypopgen/inst/doc/a02_qc.html | 235 +- tidypopgen-0.4.0/tidypopgen/inst/doc/a03_example_clustering_and_dapc.R | 3 tidypopgen-0.4.0/tidypopgen/inst/doc/a03_example_clustering_and_dapc.Rmd | 9 tidypopgen-0.4.0/tidypopgen/inst/doc/a03_example_clustering_and_dapc.html | 390 ++-- tidypopgen-0.4.0/tidypopgen/inst/doc/a99_plink_cheatsheet.html | 41 tidypopgen-0.4.0/tidypopgen/inst/doc/tidypopgen.Rmd | 8 tidypopgen-0.4.0/tidypopgen/inst/doc/tidypopgen.html | 32 tidypopgen-0.4.0/tidypopgen/inst/extdata/bigsnp_obj_gt |only tidypopgen-0.4.0/tidypopgen/man/find_duplicated_loci.Rd | 12 tidypopgen-0.4.0/tidypopgen/man/gen_tibble.Rd | 13 tidypopgen-0.4.0/tidypopgen/man/gt_admixture.Rd | 6 tidypopgen-0.4.0/tidypopgen/man/gt_as_genind.Rd | 2 tidypopgen-0.4.0/tidypopgen/man/gt_as_genlight.Rd | 2 tidypopgen-0.4.0/tidypopgen/man/gt_as_geno_lea.Rd | 5 tidypopgen-0.4.0/tidypopgen/man/gt_as_hierfstat.Rd | 2 tidypopgen-0.4.0/tidypopgen/man/gt_cluster_pca.Rd | 5 tidypopgen-0.4.0/tidypopgen/man/gt_dapc.Rd | 19 tidypopgen-0.4.0/tidypopgen/man/gt_extract_f2.Rd | 24 tidypopgen-0.4.0/tidypopgen/man/gt_from_genlight.Rd |only tidypopgen-0.4.0/tidypopgen/man/gt_impute_simple.Rd | 5 tidypopgen-0.4.0/tidypopgen/man/gt_impute_xgboost.Rd | 5 tidypopgen-0.4.0/tidypopgen/man/gt_pca_autoSVD.Rd | 8 tidypopgen-0.4.0/tidypopgen/man/gt_pca_partialSVD.Rd | 3 tidypopgen-0.4.0/tidypopgen/man/gt_pca_randomSVD.Rd | 9 tidypopgen-0.4.0/tidypopgen/man/gt_pcadapt.Rd | 5 tidypopgen-0.4.0/tidypopgen/man/gt_snmf.Rd | 7 tidypopgen-0.4.0/tidypopgen/man/gt_update_backingfile.Rd | 1 tidypopgen-0.4.0/tidypopgen/man/indiv_inbreeding.Rd | 6 tidypopgen-0.4.0/tidypopgen/man/indiv_missingness.Rd | 2 tidypopgen-0.4.0/tidypopgen/man/loci_ld_clump.Rd | 12 tidypopgen-0.4.0/tidypopgen/man/loci_missingness.Rd | 6 tidypopgen-0.4.0/tidypopgen/man/loci_pi.Rd | 2 tidypopgen-0.4.0/tidypopgen/man/pairwise_allele_sharing.Rd | 3 tidypopgen-0.4.0/tidypopgen/man/pairwise_grm.Rd | 5 tidypopgen-0.4.0/tidypopgen/man/pairwise_king.Rd | 17 tidypopgen-0.4.0/tidypopgen/man/pairwise_pop_fst.Rd | 5 tidypopgen-0.4.0/tidypopgen/man/pop_fis.Rd | 7 tidypopgen-0.4.0/tidypopgen/man/pop_fst.Rd | 3 tidypopgen-0.4.0/tidypopgen/man/pop_global_stats.Rd | 5 tidypopgen-0.4.0/tidypopgen/man/pop_het_exp.Rd | 2 tidypopgen-0.4.0/tidypopgen/man/pop_het_obs.Rd | 2 tidypopgen-0.4.0/tidypopgen/man/pop_tajimas_d.Rd | 2 tidypopgen-0.4.0/tidypopgen/man/predict_gt_pca.Rd | 2 tidypopgen-0.4.0/tidypopgen/man/scale_fill_distruct.Rd | 3 tidypopgen-0.4.0/tidypopgen/man/select_loci.Rd | 8 tidypopgen-0.4.0/tidypopgen/man/select_loci_if.Rd | 5 tidypopgen-0.4.0/tidypopgen/man/show_ploidy.Rd | 3 tidypopgen-0.4.0/tidypopgen/man/snp_allele_sharing.Rd | 15 tidypopgen-0.4.0/tidypopgen/man/snp_ibs.Rd | 18 tidypopgen-0.4.0/tidypopgen/man/snp_king.Rd | 16 tidypopgen-0.4.0/tidypopgen/man/windows_indiv_roh.Rd | 7 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_filter_high_relatedness.R | 2 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_gen_tibble.R | 944 +--------- tidypopgen-0.4.0/tidypopgen/tests/testthat/test_gen_tibble_save_load.R | 106 + tidypopgen-0.4.0/tidypopgen/tests/testthat/test_gen_tibble_vcf.R |only tidypopgen-0.4.0/tidypopgen/tests/testthat/test_gt_add_sf.R | 4 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_gt_as_plink.R | 191 +- tidypopgen-0.4.0/tidypopgen/tests/testthat/test_gt_as_vcf.R | 6 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_gt_extract_f2.R | 4 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_gt_from_genlight.R |only tidypopgen-0.4.0/tidypopgen/tests/testthat/test_gt_impute_xgboost.R | 13 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_gt_order_loci.R | 55 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_loci_freq.R | 30 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_loci_ld_clump.R | 23 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_loci_missingness.R | 32 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_pairwise_allele_sharing.R | 2 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_ploidy_vcf.R | 1 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_qc_report_indiv.R | 3 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_rbind_gen_tibble.R | 133 + tidypopgen-0.4.0/tidypopgen/tests/testthat/test_show_loci.R | 55 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_show_ploidy.R | 2 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_snp_ibs.R | 4 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_snp_king.R | 6 tidypopgen-0.4.0/tidypopgen/tests/testthat/test_window_indiv_roh.R | 57 tidypopgen-0.4.0/tidypopgen/tests/testthat/testdata/plink_doubleNA |only tidypopgen-0.4.0/tidypopgen/vignettes/a01_overview.Rmd | 31 tidypopgen-0.4.0/tidypopgen/vignettes/a02_qc.Rmd | 14 tidypopgen-0.4.0/tidypopgen/vignettes/a03_example_clustering_and_dapc.Rmd | 9 tidypopgen-0.4.0/tidypopgen/vignettes/img |only tidypopgen-0.4.0/tidypopgen/vignettes/tidypopgen.Rmd | 8 163 files changed, 2846 insertions(+), 2527 deletions(-)
Title: Irregularly Observed Autoregressive Models
Description: Data sets, functions and scripts with examples to implement autoregressive models for irregularly observed time series. The models available in this package are the irregular autoregressive model (Eyheramendy et al.(2018) <doi:10.1093/mnras/sty2487>), the complex irregular autoregressive model (Elorrieta et al.(2019) <doi:10.1051/0004-6361/201935560>) and the bivariate irregular autoregressive model (Elorrieta et al.(2021) <doi:10.1093/mnras/stab1216>).
Author: Elorrieta Felipe [aut, cre],
Ojeda Cesar [aut],
Eyheramendy Susana [aut],
Palma Wilfredo [aut]
Maintainer: Elorrieta Felipe <felipe.elorrieta@usach.cl>
Diff between iAR versions 1.3.1 dated 2025-07-03 and 1.3.2 dated 2025-10-24
iAR-1.3.1/iAR/R/foldlc.R |only iAR-1.3.1/iAR/R/harmonicfit.R |only iAR-1.3.1/iAR/man/foldlc.Rd |only iAR-1.3.1/iAR/man/iARPermutation.Rd |only iAR-1.3.1/iAR/man/iARTest.Rd |only iAR-1.3.2/iAR/DESCRIPTION | 8 ++-- iAR-1.3.2/iAR/MD5 | 72 +++++++++++++++++------------------- iAR-1.3.2/iAR/NAMESPACE | 4 -- iAR-1.3.2/iAR/R/00_utilities.R | 14 +++++++ iAR-1.3.2/iAR/R/01_BiARclass.R | 8 +++- iAR-1.3.2/iAR/R/01_CiARclass.R | 7 ++- iAR-1.3.2/iAR/R/04_kalman.R | 10 +++-- iAR-1.3.2/iAR/R/05_fit.R | 6 +-- iAR-1.3.2/iAR/R/08_plot.R | 3 + iAR-1.3.2/iAR/R/08_summary.R | 26 ++++++++++++- iAR-1.3.2/iAR/R/09_harmonicfit.R |only iAR-1.3.2/iAR/R/09_pairingits.R | 28 +++++++------- iAR-1.3.2/iAR/R/09_phase.R |only iAR-1.3.2/iAR/R/BiARkalman.R | 2 - iAR-1.3.2/iAR/R/CiARkalman.R | 3 + iAR-1.3.2/iAR/R/clcep.R | 4 +- iAR-1.3.2/iAR/R/dmcep.R | 4 +- iAR-1.3.2/iAR/R/dscut.R | 4 +- iAR-1.3.2/iAR/R/eb.R | 4 +- iAR-1.3.2/iAR/R/iARPermutation.R | 5 ++ iAR-1.3.2/iAR/R/iARkalman.R | 1 iAR-1.3.2/iAR/R/iARloglik.R | 1 iAR-1.3.2/iAR/R/iARtest.R | 5 ++ iAR-1.3.2/iAR/build/partial.rdb |binary iAR-1.3.2/iAR/man/BiAR.Rd | 8 +++- iAR-1.3.2/iAR/man/CiAR.Rd | 8 +++- iAR-1.3.2/iAR/man/clcep.Rd | 4 +- iAR-1.3.2/iAR/man/dmcep.Rd | 4 +- iAR-1.3.2/iAR/man/dscut.Rd | 4 +- iAR-1.3.2/iAR/man/eb.Rd | 4 +- iAR-1.3.2/iAR/man/harmonicfit.Rd | 50 ++++++++++++------------- iAR-1.3.2/iAR/man/pairingits.Rd | 6 +-- iAR-1.3.2/iAR/man/phase.Rd |only iAR-1.3.2/iAR/man/utilities.Rd | 21 ++++++++++ iAR-1.3.2/iAR/src/BiARfit.cpp | 5 +- iAR-1.3.2/iAR/src/BiARphikalman.cpp | 1 41 files changed, 219 insertions(+), 115 deletions(-)
Title: Utility Functions for Davidian Curves
Description: A Davidian curve defines a seminonparametric density, whose shape and flexibility can be tuned by
easy to estimate parameters. Since a special case of a Davidian curve is the standard normal density,
Davidian curves can be used for relaxing normality assumption in statistical applications (Zhang & Davidian, 2001)
<doi:10.1111/j.0006-341X.2001.00795.x>. This package provides the density function, the gradient of
the loglikelihood and a random generator for Davidian curves.
Author: Ozan Oegreden [aut, cre]
Maintainer: Ozan Oegreden <oguzhanogreden@protonmail.com>
Diff between dcurver versions 0.9.2 dated 2020-11-04 and 0.9.3 dated 2025-10-24
DESCRIPTION | 19 ++++++++++++------- MD5 | 12 ++++++------ NEWS.md | 4 ++++ build/partial.rdb |binary src/Makevars | 12 +----------- src/Makevars.win | 13 +------------ src/RcppExports.cpp | 5 +++++ 7 files changed, 29 insertions(+), 36 deletions(-)
Title: Vincent van Gogh Colour Palette Generator
Description: Provides 'ggplot2'-compatible colour palettes inspired by Vincent van Gogh's paintings. Each palette contains five colours, manually selected by hexadecimal values. Includes tools for assessing colour vision deficiency (CVD) accessibility.
Author: Cheryl Isabella Lim [aut, cre]
Maintainer: Cheryl Isabella Lim <cheryl.academic@gmail.com>
Diff between vangogh versions 0.1.2 dated 2025-08-21 and 0.1.3 dated 2025-10-24
DESCRIPTION | 25 ++- MD5 | 35 +++-- NAMESPACE | 9 + NEWS.md | 83 ++++++++---- R/check_vangogh_cvd.R |only R/cvd_palette_scores.R |only R/palette_accessibility.R | 181 +++++++++++++++++++++++--- README.md | 238 +++++------------------------------ data |only inst/extdata |only man/check_all_vangogh_cvd.Rd |only man/check_palette.Rd | 2 man/check_vangogh_cvd.Rd |only man/generate_cvd_scores_data.Rd |only man/get_cvd_safe_palettes.Rd |only man/plot_cvd_simulation.Rd |only man/print_cvd_badge.Rd |only man/summarize_cvd_accessibility.Rd |only man/vangogh.Rd | 2 man/vangogh_cvd_scores.Rd |only man/vangogh_export.Rd | 56 ++++---- man/vangogh_palette_info_with_cvd.Rd |only man/vangogh_suggest.Rd | 32 ++-- tests |only 24 files changed, 348 insertions(+), 315 deletions(-)
Title: Transcription Elongation Profiling
Description: The general principle relies on calculating the cumulative signal of nascent
RNA sequencing over the gene body of any given gene or transcription unit.
'tepr' can identify transcription attenuation sites by comparing profile to
a null model which assumes uniform read density over the entirety of the
transcription unit. It can also identify increased or diminished
transcription attenuation by comparing two conditions. Besides rigorous
statistical testing and high sensitivity, a major feature of 'tepr' is its
ability to provide the elongation pattern of each individual gene, including
the position of the main attenuation point when such a phenomenon occurs.
Using 'tepr', users can visualize and refine genome-wide aggregated analyses
of elongation patterns to robustly identify effects specific to subsets of
genes. These metrics are suitable for internal comparisons (between genes in
each condition) and for studying elongation of the same gene in different
conditions or comparing it to a p [...truncated...]
Author: Nicolas Descostes [cre],
Victor Billon [aut],
Gael Cristofari [aut]
Maintainer: Nicolas Descostes <nicolas.descostes@gmail.com>
Diff between tepr versions 1.1.10 dated 2025-09-03 and 1.1.11 dated 2025-10-24
DESCRIPTION | 6 MD5 | 15 NEWS | 4 R/meandifference.R | 6 inst/doc/tepr.R | 3 inst/doc/tepr.Rmd | 3 inst/doc/tepr.html | 1151 ++++++++++++++++++++++++++---------------- inst/extdata/chromtabtest.rds |only vignettes/tepr.Rmd | 3 9 files changed, 745 insertions(+), 446 deletions(-)
Title: Many Ways to Make, Modify, Mark, and Measure Myriad Networks
Description: Many tools for making, modifying, marking, measuring,
and motifs and memberships of many different types of networks.
All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
on directed, multiplex, multimodal, signed, and other networks.
The package includes functions for importing and exporting, creating and generating networks,
modifying networks and node and tie attributes,
and describing networks with sensible defaults.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Christian Steglich [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between manynet versions 1.6.1 dated 2025-09-12 and 1.6.5 dated 2025-10-24
manynet-1.6.1/manynet/data/irps_nuclear_discourse.rda |only manynet-1.6.1/manynet/man/irps_nuclear_discourse.Rd |only manynet-1.6.1/manynet/tests/testthat/test-print_class.R |only manynet-1.6.5/manynet/DESCRIPTION | 8 manynet-1.6.5/manynet/MD5 | 195 - manynet-1.6.5/manynet/NAMESPACE | 17 manynet-1.6.5/manynet/NEWS.md | 90 manynet-1.6.5/manynet/R/class_measures.R | 6 manynet-1.6.5/manynet/R/class_networks.R | 85 manynet-1.6.5/manynet/R/data_fict.R |only manynet-1.6.5/manynet/R/data_irps.R |only manynet-1.6.5/manynet/R/data_ison.R | 473 --- manynet-1.6.5/manynet/R/make_generate.R | 43 manynet-1.6.5/manynet/R/make_read.R | 566 ++++ manynet-1.6.5/manynet/R/manip_correlation.R | 2 manynet-1.6.5/manynet/R/manip_nodes.R | 4 manynet-1.6.5/manynet/R/manip_reformed.R | 14 manynet-1.6.5/manynet/R/manynet-defunct.R | 2 manynet-1.6.5/manynet/R/manynet-glossary.R |only manynet-1.6.5/manynet/R/manynet-tutorials.R | 138 - manynet-1.6.5/manynet/R/manynet-utils.R | 4 manynet-1.6.5/manynet/R/mark_nodes.R | 12 manynet-1.6.5/manynet/R/mark_ties.R | 28 manynet-1.6.5/manynet/R/measure_centrality.R | 184 + manynet-1.6.5/manynet/R/measure_closure.R | 14 manynet-1.6.5/manynet/R/measure_cohesion.R | 18 manynet-1.6.5/manynet/R/measure_diffusion.R | 2 manynet-1.6.5/manynet/R/measure_features.R | 26 manynet-1.6.5/manynet/R/measure_heterogeneity.R | 18 manynet-1.6.5/manynet/R/measure_hierarchy.R | 17 manynet-1.6.5/manynet/R/measure_holes.R | 16 manynet-1.6.5/manynet/R/member_cliques.R | 2 manynet-1.6.5/manynet/R/member_community.R | 24 manynet-1.6.5/manynet/R/member_components.R | 26 manynet-1.6.5/manynet/R/member_core.R | 89 manynet-1.6.5/manynet/R/member_equivalence.R | 8 manynet-1.6.5/manynet/R/model_cluster.R | 7 manynet-1.6.5/manynet/R/motif_brokerage.R |only manynet-1.6.5/manynet/R/motif_census.R | 204 - manynet-1.6.5/manynet/R/reexports_classes.R | 4 manynet-1.6.5/manynet/R/zzz.R | 2 manynet-1.6.5/manynet/data/fict_actually.rda |only manynet-1.6.5/manynet/data/irps_nuclear.rda |only manynet-1.6.5/manynet/data/ison_emotions.rda |only manynet-1.6.5/manynet/inst/tutorials/tutorial0/tutorial0.Rmd | 10 manynet-1.6.5/manynet/inst/tutorials/tutorial1/data.Rmd | 158 - manynet-1.6.5/manynet/inst/tutorials/tutorial3/centrality.Rmd | 93 manynet-1.6.5/manynet/inst/tutorials/tutorial3/centrality.html | 336 +- manynet-1.6.5/manynet/inst/tutorials/tutorial4/community.Rmd | 92 manynet-1.6.5/manynet/inst/tutorials/tutorial4/community.html | 1344 ++++++++-- manynet-1.6.5/manynet/inst/tutorials/tutorial5/position.Rmd | 109 manynet-1.6.5/manynet/inst/tutorials/tutorial5/position.html | 885 +++++- manynet-1.6.5/manynet/inst/tutorials/tutorial6/topology.Rmd | 135 - manynet-1.6.5/manynet/inst/tutorials/tutorial6/topology.html | 712 ++++- manynet-1.6.5/manynet/man/fict_actually.Rd |only manynet-1.6.5/manynet/man/fict_friends.Rd | 2 manynet-1.6.5/manynet/man/fict_greys.Rd | 2 manynet-1.6.5/manynet/man/fict_lotr.Rd | 2 manynet-1.6.5/manynet/man/fict_potter.Rd | 2 manynet-1.6.5/manynet/man/fict_starwars.Rd | 10 manynet-1.6.5/manynet/man/fict_thrones.Rd | 2 manynet-1.6.5/manynet/man/glossary.Rd | 2 manynet-1.6.5/manynet/man/irps_911.Rd | 2 manynet-1.6.5/manynet/man/irps_blogs.Rd | 2 manynet-1.6.5/manynet/man/irps_books.Rd | 2 manynet-1.6.5/manynet/man/irps_nuclear.Rd |only manynet-1.6.5/manynet/man/irps_revere.Rd | 2 manynet-1.6.5/manynet/man/irps_usgeo.Rd | 2 manynet-1.6.5/manynet/man/irps_wwi.Rd | 2 manynet-1.6.5/manynet/man/ison_adolescents.Rd | 3 manynet-1.6.5/manynet/man/ison_algebra.Rd | 4 manynet-1.6.5/manynet/man/ison_emotions.Rd |only manynet-1.6.5/manynet/man/ison_hightech.Rd | 4 manynet-1.6.5/manynet/man/ison_lawfirm.Rd | 4 manynet-1.6.5/manynet/man/ison_marvel.Rd | 4 manynet-1.6.5/manynet/man/ison_monks.Rd | 2 manynet-1.6.5/manynet/man/ison_physicians.Rd | 16 manynet-1.6.5/manynet/man/make_cran.Rd | 45 manynet-1.6.5/manynet/man/make_mnet.Rd | 17 manynet-1.6.5/manynet/man/make_read.Rd | 11 manynet-1.6.5/manynet/man/mark_core.Rd | 55 manynet-1.6.5/manynet/man/measure_central_close.Rd | 34 manynet-1.6.5/manynet/man/measure_central_degree.Rd | 2 manynet-1.6.5/manynet/man/measure_central_eigen.Rd | 37 manynet-1.6.5/manynet/man/measure_heterogeneity.Rd | 2 manynet-1.6.5/manynet/man/measure_hierarchy.Rd | 3 manynet-1.6.5/manynet/man/member_brokerage.Rd | 2 manynet-1.6.5/manynet/man/member_components.Rd | 13 manynet-1.6.5/manynet/man/model_cluster.Rd | 5 manynet-1.6.5/manynet/man/motif_brokerage.Rd | 2 manynet-1.6.5/manynet/tests/testthat/test-make_create.R | 20 manynet-1.6.5/manynet/tests/testthat/test-manip_as.R | 9 manynet-1.6.5/manynet/tests/testthat/test-manynet-glossary.R |only manynet-1.6.5/manynet/tests/testthat/test-mark_nodes.R | 28 manynet-1.6.5/manynet/tests/testthat/test-mark_ties.R | 17 manynet-1.6.5/manynet/tests/testthat/test-measure_centrality.R | 19 manynet-1.6.5/manynet/tests/testthat/test-measure_closure.R | 6 manynet-1.6.5/manynet/tests/testthat/test-measure_cohesion.R | 15 manynet-1.6.5/manynet/tests/testthat/test-measure_features.R | 23 manynet-1.6.5/manynet/tests/testthat/test-measure_heterogeneity.R | 9 manynet-1.6.5/manynet/tests/testthat/test-measure_hierarchy.R |only manynet-1.6.5/manynet/tests/testthat/test-measure_holes.R | 20 manynet-1.6.5/manynet/tests/testthat/test-measure_properties.R |only manynet-1.6.5/manynet/tests/testthat/test-member_cliques.R |only manynet-1.6.5/manynet/tests/testthat/test-member_components.R |only manynet-1.6.5/manynet/tests/testthat/test-member_core.R |only manynet-1.6.5/manynet/tests/testthat/test-model_cluster.R |only manynet-1.6.5/manynet/tests/testthat/test-motif_brokerage.R |only manynet-1.6.5/manynet/tests/testthat/test-motif_census.R | 57 109 files changed, 4706 insertions(+), 2038 deletions(-)
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
developed by the research group around Cornelia Dowling through
querying experts.
Author: Cord Hockemeyer [aut, cre],
Peter Steiner [ctb],
Wai Wong [ctb]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 1.3-0 dated 2025-09-30 and 2.0-0 dated 2025-10-24
kstMatrix-1.3-0/kstMatrix/R/kmSRdiagram.R |only kstMatrix-1.3-0/kstMatrix/R/kmbasisdiagram.R |only kstMatrix-1.3-0/kstMatrix/R/kmhasse.R |only kstMatrix-1.3-0/kstMatrix/man/kmSRdiagram.Rd |only kstMatrix-1.3-0/kstMatrix/man/kmbasisdiagram.Rd |only kstMatrix-1.3-0/kstMatrix/man/kmhasse.Rd |only kstMatrix-1.3-0/kstMatrix/man/kmsassess.Rd |only kstMatrix-2.0-0/kstMatrix/Changelog | 11 kstMatrix-2.0-0/kstMatrix/DESCRIPTION | 20 kstMatrix-2.0-0/kstMatrix/MD5 | 115 +-- kstMatrix-2.0-0/kstMatrix/NAMESPACE | 24 kstMatrix-2.0-0/kstMatrix/R/kmSR2basis.R |only kstMatrix-2.0-0/kstMatrix/R/kmassess.R | 448 +++++++------ kstMatrix-2.0-0/kstMatrix/R/kmbasis.R | 48 - kstMatrix-2.0-0/kstMatrix/R/kmbasis.kmsurmiserelation.R |only kstMatrix-2.0-0/kstMatrix/R/kmbasis.matrix.R |only kstMatrix-2.0-0/kstMatrix/R/kmcolors.R | 5 kstMatrix-2.0-0/kstMatrix/R/kmeqreduction.R | 10 kstMatrix-2.0-0/kstMatrix/R/kmfamset.R |only kstMatrix-2.0-0/kstMatrix/R/kmgenerate.R | 5 kstMatrix-2.0-0/kstMatrix/R/kmiita2SR.R |only kstMatrix-2.0-0/kstMatrix/R/kmiswellgraded.R | 92 +- kstMatrix-2.0-0/kstMatrix/R/kmneighbourhood.R | 14 kstMatrix-2.0-0/kstMatrix/R/kmnotions.R | 4 kstMatrix-2.0-0/kstMatrix/R/kmnotions2.R |only kstMatrix-2.0-0/kstMatrix/R/kmsassess.R | 19 kstMatrix-2.0-0/kstMatrix/R/kmsf2basis.R | 4 kstMatrix-2.0-0/kstMatrix/R/kmsimulate.R | 125 +-- kstMatrix-2.0-0/kstMatrix/R/kmspace.R |only kstMatrix-2.0-0/kstMatrix/R/kmstructure.R |only kstMatrix-2.0-0/kstMatrix/R/kmsurmisefunction.R | 9 kstMatrix-2.0-0/kstMatrix/R/kmsurmiserelation.R | 5 kstMatrix-2.0-0/kstMatrix/R/kmtrivial.R | 8 kstMatrix-2.0-0/kstMatrix/R/kmunionclosure.R | 97 +- kstMatrix-2.0-0/kstMatrix/R/plot.R |only kstMatrix-2.0-0/kstMatrix/data/cad.rda |binary kstMatrix-2.0-0/kstMatrix/data/fractions.rda |binary kstMatrix-2.0-0/kstMatrix/data/readwrite.rda |binary kstMatrix-2.0-0/kstMatrix/data/xpl.rda |binary kstMatrix-2.0-0/kstMatrix/inst/doc/kstMatrix.R | 10 kstMatrix-2.0-0/kstMatrix/inst/doc/kstMatrix.Rmd | 18 kstMatrix-2.0-0/kstMatrix/inst/doc/kstMatrix.html | 284 ++++---- kstMatrix-2.0-0/kstMatrix/man/kmSR2basis.Rd |only kstMatrix-2.0-0/kstMatrix/man/kmassess.Rd | 80 +- kstMatrix-2.0-0/kstMatrix/man/kmassessbayesian.Rd | 3 kstMatrix-2.0-0/kstMatrix/man/kmassesshalfsplit.Rd | 3 kstMatrix-2.0-0/kstMatrix/man/kmassessinformative.Rd | 3 kstMatrix-2.0-0/kstMatrix/man/kmassessmentsimulation.Rd | 3 kstMatrix-2.0-0/kstMatrix/man/kmassessmultiplicative.Rd | 3 kstMatrix-2.0-0/kstMatrix/man/kmbasis.Rd | 27 kstMatrix-2.0-0/kstMatrix/man/kmbasis.kmsurmiserelation.Rd |only kstMatrix-2.0-0/kstMatrix/man/kmbasis.matrix.Rd |only kstMatrix-2.0-0/kstMatrix/man/kmcolors.Rd | 6 kstMatrix-2.0-0/kstMatrix/man/kmeqreduction.Rd | 3 kstMatrix-2.0-0/kstMatrix/man/kmfamset.Rd |only kstMatrix-2.0-0/kstMatrix/man/kmfringe.Rd | 3 kstMatrix-2.0-0/kstMatrix/man/kmgenerate.Rd | 6 kstMatrix-2.0-0/kstMatrix/man/kmiita2SR.Rd |only kstMatrix-2.0-0/kstMatrix/man/kmiswellgraded.Rd | 3 kstMatrix-2.0-0/kstMatrix/man/kmneighbourhood.Rd | 8 kstMatrix-2.0-0/kstMatrix/man/kmnneighbourhood.Rd | 12 kstMatrix-2.0-0/kstMatrix/man/kmnotions.Rd | 3 kstMatrix-2.0-0/kstMatrix/man/kmnotions2.Rd |only kstMatrix-2.0-0/kstMatrix/man/kmsf2basis.Rd | 4 kstMatrix-2.0-0/kstMatrix/man/kmspace.Rd |only kstMatrix-2.0-0/kstMatrix/man/kmstructure.Rd |only kstMatrix-2.0-0/kstMatrix/man/kmsurmisefunction.Rd | 4 kstMatrix-2.0-0/kstMatrix/man/kmsurmiserelation.Rd | 4 kstMatrix-2.0-0/kstMatrix/man/kmunionclosure.Rd | 4 kstMatrix-2.0-0/kstMatrix/man/plot.Rd |only kstMatrix-2.0-0/kstMatrix/vignettes/kstMatrix.Rmd | 18 71 files changed, 839 insertions(+), 736 deletions(-)
Title: Power Calculation for Two-Way Factorial Designs
Description: The basic use of this package is with 3 sequential functions. One to generate expected cell means and standard deviations, along with correlation and covariance matrices in the case of repeated measurements. This is followed by experiment simulation i number of times. Finally, power is calculated from the simulated data. Features that may be considered in the model are interaction, measure correlation and non-normal distributions.
Author: Louis Macias [aut, cre, cph] ,
Silke Szymczak [aut]
Maintainer: Louis Macias <louis.macias@uni-luebeck.de>
Diff between extraSuperpower versions 1.5.5 dated 2025-10-08 and 1.6.0 dated 2025-10-24
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 4 R/plot_powercurves.R | 11 - R/repeated_twoway_generation.R | 28 ++- R/twoway_simultesting.R | 53 ++--- inst/doc/eSp_balanced_design_powertest.html | 8 tests/testthat/test-twoway_simulation_testing.R | 215 +++++++++++++----------- 8 files changed, 197 insertions(+), 142 deletions(-)
More information about extraSuperpower at CRAN
Permanent link
Title: Quantifying (Animal) Sound Degradation
Description: Intended to facilitate acoustic analysis of (animal) sound propagation experiments, which typically aim to quantify changes in signal structure when transmitted in a given habitat by broadcasting and re-recording animal sounds at increasing distances. The package offers a workflow with functions to prepare the data set for analysis as well as to calculate and visualize several degradation metrics, including blur ratio, signal-to-noise ratio, excess attenuation and envelope correlation among others (Dabelsteen et al 1993 <doi:10.1121/1.406682>).
Author: Marcelo Araya-Salas [aut, cre] ,
Michael Mahoney [rev] ,
Dena Clink [rev]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
This is a re-admission after prior archival of version 2.1.5 dated 2025-07-17
Diff between baRulho versions 2.1.5 dated 2025-07-17 and 2.1.6 dated 2025-10-24
DESCRIPTION | 6 +-- MD5 | 20 +++++------ NEWS.md | 7 +++ R/master_sound_file.R | 2 - README.md | 20 +++++------ inst/doc/align_test_sounds.R | 2 - inst/doc/align_test_sounds.Rmd | 2 - inst/doc/align_test_sounds.html | 50 ++++++++++++++-------------- inst/doc/quantify_degradation.html | 65 ++++++++++++++++++------------------- man/master_sound_file.Rd | 2 - vignettes/align_test_sounds.Rmd | 2 - 11 files changed, 92 insertions(+), 86 deletions(-)
Title: Foundations Toolkit and Datasets for Data Science
Description: Provides a collection of helper functions and illustrative datasets to support learning and teaching of data science with R. The package is designed as a companion to the book <https://book-data-science-r.netlify.app>, making key data science techniques accessible to individuals with minimal coding experience. Functions include tools for data partitioning, performance evaluation, and data transformations (e.g., z-score and min-max scaling). The included datasets are curated to highlight practical applications in data exploration, modeling, and multivariate analysis. An early inspiration for the package came from an ancient Persian idiom about "eating the liver," symbolizing deep and immersive engagement with knowledge.
Author: Reza Mohammadi [aut, cre] ,
Kevin Burke [aut]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between liver versions 1.23 dated 2025-10-05 and 1.24 dated 2025-10-24
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ data/adult.RData |binary inst/doc/liver-example.R | 2 +- inst/doc/liver-example.Rmd | 2 +- inst/doc/liver-example.html | 10 ++-------- man/churn.Rd | 2 +- man/churnCredit.Rd | 2 +- man/churnTel.Rd | 2 +- man/figures/logo.png |binary vignettes/liver-example.Rmd | 2 +- 12 files changed, 26 insertions(+), 28 deletions(-)
Title: Assurance Methods for Clinical Trials with a Delayed Treatment
Effect
Description: Provides functions for planning clinical trials subject to a delayed
treatment effect using assurance-based methods. Includes two 'shiny'
applications for interactive exploration, simulation, and visualisation of
trial designs and outcomes. The methodology is described in:
Salsbury JA, Oakley JE, Julious SA, Hampson LV (2024)
"Assurance methods for designing a clinical trial with a delayed treatment
effect" <doi:10.1002/sim.10136>,
Salsbury JA, Oakley JE, Julious SA, Hampson LV (2024)
"Adaptive clinical trial design with delayed treatment effects using
elicited prior distributions" <doi:10.48550/arXiv.2509.07602>.
Author: James Salsbury [aut, cre]
Maintainer: James Salsbury <jsalsbury1@sheffield.ac.uk>
Diff between DTEAssurance versions 1.0.0 dated 2025-10-14 and 1.0.1 dated 2025-10-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/main.R | 38 +++++++++++++++++++++++++++++++++++--- R/utils.R | 6 +++++- 5 files changed, 52 insertions(+), 11 deletions(-)
Title: Stepwise Regression Analysis
Description: Stepwise regression is a statistical technique used for model selection. This package streamlines stepwise regression analysis by supporting multiple regression types(linear, Cox, logistic, Poisson, Gamma, and negative binomial), incorporating popular selection strategies(forward, backward, bidirectional, and subset), and offering essential metrics. It enables users to apply multiple selection strategies and metrics in a single function call, visualize variable selection processes, and export results in various formats. StepReg offers a data-splitting option to address potential issues with invalid statistical inference and a randomized forward selection option to avoid overfitting. We validated StepReg's accuracy using public datasets within the SAS software environment. For an interactive web interface, users can install the companion 'StepRegShiny' package.
Author: Junhui Li [cre] ,
Junhui Li [aut],
Kai Hu [aut],
Xiaohuan Lu [aut],
Sushmita N Nayak [ctb],
Cesar Bautista Sotelo [ctb],
Michael A Lodato [ctb],
Wenxin Liu [aut],
Lihua Julie Zhu [aut]
Maintainer: Junhui Li <junhui.li11@umassmed.edu>
Diff between StepReg versions 1.6.0 dated 2025-09-30 and 1.6.1 dated 2025-10-24
StepReg-1.6.0/StepReg/R/StepRegShinyApp.R |only StepReg-1.6.0/StepReg/inst/shiny |only StepReg-1.6.0/StepReg/man/StepRegShinyApp.Rd |only StepReg-1.6.1/StepReg/DESCRIPTION | 16 -- StepReg-1.6.1/StepReg/MD5 | 36 +--- StepReg-1.6.1/StepReg/NAMESPACE | 28 --- StepReg-1.6.1/StepReg/NEWS.md | 24 +++ StepReg-1.6.1/StepReg/R/plot.StepReg.R | 18 +- StepReg-1.6.1/StepReg/R/report.R | 8 - StepReg-1.6.1/StepReg/R/stepwise.R | 4 StepReg-1.6.1/StepReg/R/stepwiseUtils.R | 25 +-- StepReg-1.6.1/StepReg/inst/doc/StepReg.R | 4 StepReg-1.6.1/StepReg/inst/doc/StepReg.Rmd | 6 StepReg-1.6.1/StepReg/inst/doc/StepReg.html | 149 +++++++++---------- StepReg-1.6.1/StepReg/man/StepReg-package.Rd | 2 StepReg-1.6.1/StepReg/tests/testthat.R | 2 StepReg-1.6.1/StepReg/tests/testthat/test_stepwise.R | 4 StepReg-1.6.1/StepReg/vignettes/StepReg.Rmd | 6 18 files changed, 153 insertions(+), 179 deletions(-)
Title: Hierarchical Partitioning of Adjusted R2 and Explained Deviance
for Generalized Additive Models
Description: Conducts hierarchical partitioning to calculate individual contributions of each predictor towards adjusted R2 and explained deviance for generalized additive models based on output of 'gam()' and 'bam()' in 'mgcv' package, applying the algorithm in this paper: Lai(2024) <doi:10.1016/j.pld.2024.06.002>.
Author: Jiangshan Lai [aut, cre] ,
Jing Tang [aut]
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Diff between gam.hp versions 0.0-4 dated 2025-10-07 and 0.0-5 dated 2025-10-24
DESCRIPTION | 8 MD5 | 6 R/gam.hp.r | 746 +++++++++++++++++++++++++++------------------------------- man/gam.hp.Rd | 75 +---- 4 files changed, 390 insertions(+), 445 deletions(-)
Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks <doi:10.18637/jss.v098.i08>.
Author: Matteo Magnani [aut, cre],
Luca Rossi [aut] ,
Davide Vega [aut] ,
Obaida Hanteer [ctb]
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>
Diff between multinet versions 4.3.1 dated 2025-09-23 and 4.3.2 dated 2025-10-24
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 4 ++++ R/functions.R | 6 +++--- R/igraph.R | 2 +- 5 files changed, 16 insertions(+), 12 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 1.7.0 dated 2025-10-10 and 1.7.1 dated 2025-10-24
DESCRIPTION | 6 MD5 | 212 ++++++++++++------------ NEWS.md | 5 R/Archive.R | 3 R/ArchiveAsync.R | 55 ++++++ R/ArchiveAsyncFrozen.R | 55 ++++++ R/ArchiveBatch.R | 45 +++++ R/CallbackAsync.R | 2 R/CallbackBatch.R | 2 R/ContextAsync.R | 1 R/ContextBatch.R | 1 R/Objective.R | 2 R/ObjectiveRFun.R | 25 ++ R/ObjectiveRFunDt.R | 38 ++++ R/ObjectiveRFunMany.R | 23 ++ R/OptimInstance.R | 2 R/OptimInstanceAsync.R | 1 R/OptimInstanceAsyncMultiCrit.R | 41 ++++ R/OptimInstanceAsyncSingleCrit.R | 38 ++++ R/OptimInstanceBatch.R | 1 R/OptimInstanceBatchMultiCrit.R | 33 +++ R/OptimInstanceBatchSingleCrit.R | 30 +++ R/OptimInstanceMultiCrit.R | 1 R/OptimInstanceSingleCrit.R | 1 R/Optimizer.R | 2 R/OptimizerAsync.R | 5 R/OptimizerAsyncDesignPoints.R | 54 ++++++ R/OptimizerAsyncGridSearch.R | 53 ++++++ R/OptimizerAsyncRandomSearch.R | 53 ++++++ R/OptimizerBatch.R | 1 R/OptimizerBatchChain.R | 57 +++--- R/OptimizerBatchCmaes.R | 70 ++++--- R/OptimizerBatchDesignPoints.R | 49 +++-- R/OptimizerBatchFocusSearch.R | 43 ++++ R/OptimizerBatchGenSA.R | 49 +++-- R/OptimizerBatchGridSearch.R | 43 ++++ R/OptimizerBatchIrace.R | 24 +- R/OptimizerBatchLocalSearch.R | 42 ++++ R/OptimizerBatchNLoptr.R | 70 ++++--- R/OptimizerBatchRandomSearch.R | 43 ++++ R/Progressor.R | 3 R/as_terminator.R | 1 R/assertions.R | 1 R/helper.R | 10 - R/sugar.R | 69 +++++++ R/worker_loops.R | 2 README.md | 56 +++--- man/Archive.Rd | 5 man/ArchiveAsync.Rd | 55 ++++++ man/ArchiveAsyncFrozen.Rd | 58 ++++++ man/ArchiveBatch.Rd | 45 +++++ man/CallbackAsync.Rd | 3 man/CallbackBatch.Rd | 3 man/ContextAsync.Rd | 3 man/ContextBatch.Rd | 3 man/Objective.Rd | 6 man/ObjectiveRFun.Rd | 28 ++- man/ObjectiveRFunDt.Rd | 41 ++++ man/ObjectiveRFunMany.Rd | 26 ++ man/OptimInstance.Rd | 3 man/OptimInstanceAsync.Rd | 3 man/OptimInstanceAsyncMultiCrit.Rd | 42 ++++ man/OptimInstanceAsyncSingleCrit.Rd | 39 ++++ man/OptimInstanceBatch.Rd | 3 man/OptimInstanceBatchMultiCrit.Rd | 34 +++ man/OptimInstanceBatchSingleCrit.Rd | 31 +++ man/OptimInstanceMultiCrit.Rd | 3 man/OptimInstanceSingleCrit.Rd | 3 man/Optimizer.Rd | 3 man/OptimizerAsync.Rd | 3 man/OptimizerBatch.Rd | 3 man/Progressor.Rd | 4 man/as_terminator.Rd | 3 man/assign_result_default.Rd | 3 man/bbotk_assertions.Rd | 3 man/callback_async.Rd | 3 man/callback_batch.Rd | 3 man/is_dominated.Rd | 3 man/mlr_optimizers_async_design_points.Rd | 55 ++++++ man/mlr_optimizers_async_grid_search.Rd | 54 ++++++ man/mlr_optimizers_async_random_search.Rd | 54 ++++++ man/mlr_optimizers_chain.Rd | 58 +++--- man/mlr_optimizers_cmaes.Rd | 70 ++++--- man/mlr_optimizers_design_points.Rd | 49 +++-- man/mlr_optimizers_focus_search.Rd | 54 +++--- man/mlr_optimizers_gensa.Rd | 50 +++-- man/mlr_optimizers_grid_search.Rd | 54 +++--- man/mlr_optimizers_irace.Rd | 25 +- man/mlr_optimizers_local_search.Rd | 43 ++++ man/mlr_optimizers_nloptr.Rd | 71 ++++---- man/mlr_optimizers_random_search.Rd | 54 +++--- man/oi.Rd | 31 +++ man/oi_async.Rd | 39 ++++ man/search_start.Rd | 2 man/terminated_error.Rd | 3 man/tiny_logging.Rd | 3 man/tiny_result.Rd | 3 man/trafo_xs.Rd | 3 man/transform_xdt_to_xss.Rd | 2 src/local_search.c | 64 +++---- src/local_search.h | 6 src/rc_helpers.c | 8 src/rc_helpers.h | 4 src/test_local_search.c | 69 +++---- src/test_local_search.h | 10 - tests/testthat/test_OptimizerAsync.R | 59 ++++++ tests/testthat/test_OptimizerBatchLocalSearch.R | 2 107 files changed, 2303 insertions(+), 587 deletions(-)
Title: Visualization of Spline Effects in GAM and GLM Models
Description: Creates 'ggplot2'-based visualizations of smooth effects from GAM (Generalized Additive Models)
fitted with 'mgcv' and spline effects from GLM (Generalized Linear Models). Supports interaction terms
and provides hazard ratio plots with histograms for survival analysis.
Wood (2017, ISBN:9781498728331) provides comprehensive methodology for generalized additive models.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between splineplot versions 0.1.1 dated 2025-09-30 and 0.2.0 dated 2025-10-24
DESCRIPTION | 6 MD5 | 10 - NEWS.md | 20 +++ R/splineplot.R | 262 ++++++++++++++++++++---------------------- README.md | 44 ------- inst/doc/getting-started.html | 148 ++++++++--------------- 6 files changed, 213 insertions(+), 277 deletions(-)
Title: Statistical Shape Analysis
Description: Routines for the statistical analysis of landmark
shapes, including Procrustes analysis, graphical displays, principal
components analysis, permutation and bootstrap tests, thin-plate
spline transformation grids and comparing covariance matrices.
See Dryden, I.L. and Mardia, K.V. (2016). Statistical shape analysis,
with Applications in R (2nd Edition), John Wiley and Sons.
Author: Ian Dryden [aut, cre]
Maintainer: Ian Dryden <ian.dryden@nottingham.ac.uk>
Diff between shapes versions 1.2.7 dated 2023-02-03 and 1.2.8 dated 2025-10-24
DESCRIPTION | 22 + MD5 | 78 +++--- NAMESPACE | 8 NEWS.md | 16 + R/shapes.R | 516 +++++++++++++++++++++++++++++++++++++++++++-- README.md | 4 data/T1mice.rda |only data/apes.rda |binary data/brains.rda |binary data/cortical.rda |binary data/digit3.dat.rda |binary data/dna.dat.rda |binary data/gels.rda |binary data/gorf.dat.rda |binary data/gorm.dat.rda |binary data/humanmove.rda |binary data/macaques.rda |binary data/macf.dat.rda |binary data/macm.dat.rda |binary data/mice.rda |binary data/nsa.rda |binary data/panf.dat.rda |binary data/panm.dat.rda |binary data/pongof.dat.rda |binary data/pongom.dat.rda |binary data/protein.rda |binary data/qcet2.dat.rda |binary data/qlet2.dat.rda |binary data/qset2.dat.rda |binary data/rats.rda |binary data/sand.rda |binary data/schizophrenia.dat.rda |binary data/schizophrenia.rda |binary data/shells.rda |binary data/sooty.dat.rda |binary data/sooty.rda |binary data/steroids.rda |binary man/T1mice.Rd |only man/pns.Rd | 27 ++ man/pnss3d.Rd | 11 man/shapes-internal.Rd | 6 41 files changed, 610 insertions(+), 78 deletions(-)
Title: Classifications and Codelists for Statistics Norway
Description: Functions to search, retrieve, apply and update classifications
and codelists using Statistics Norway's API <https://www.ssb.no/klass>
from the system 'KLASS'. Retrieves classifications by date with options
to choose language, hierarchical level and formatting.
Author: Susie Jentoft [aut, cre],
Diana-Cristina Iancu [aut],
Lisa Li [aut],
Oeyvind I. Berntsen [aut],
Statistics Norway [cph]
Maintainer: Susie Jentoft <susie.jentoft@ssb.no>
Diff between klassR versions 1.0.2 dated 2025-02-07 and 1.0.3 dated 2025-10-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 9 +++------ R/UpdateKlass-graph-build.R | 19 ++++++++++--------- 4 files changed, 19 insertions(+), 21 deletions(-)
Title: Multi-Omic Differentially Expressed Gene-Gene Pairs
Description: Performs multi-omic differential network
analysis by revealing differential interactions between molecular entities
(genes, proteins, transcription factors, or other biomolecules) across the
omic datasets provided.
For each omic dataset, a differential network is constructed where
links represent statistically significant differential interactions between
entities. These networks are then integrated into a comprehensive visualization
using distinct colors to distinguish interactions from different omic layers.
This unified display allows interactive exploration of cross-omic
patterns, such as differential interactions present at both transcript and
protein levels. For each link, users can access differential statistical
significance metrics (p values or adjusted p values, calculated via robust or
traditional linear regression with interaction term) and differential regression
plots.
The methods implemented in this package are described in Sciacca et al. (2023)
<doi:10.1093/bioinform [...truncated...]
Author: Elisabetta Sciacca [aut, cre, cph] ,
Myles Lewis [ctb]
Maintainer: Elisabetta Sciacca <e.sciacca@qmul.ac.uk>
This is a re-admission after prior archival of version 1.1.0 dated 2025-07-29
Diff between multiDEGGs versions 1.1.0 dated 2025-07-29 and 1.1.1 dated 2025-10-24
DESCRIPTION | 8 +-- MD5 | 16 +++---- NEWS.md | 3 + R/feature_selection_for_ML.R | 2 inst/doc/multiDEGGs_vignette.R | 3 - inst/doc/multiDEGGs_vignette.Rmd | 5 -- inst/doc/multiDEGGs_vignette.html | 82 ++++++-------------------------------- man/cat_parallel.Rd | 2 vignettes/multiDEGGs_vignette.Rmd | 5 -- 9 files changed, 31 insertions(+), 95 deletions(-)
Title: Bias-Corrected GEE for Cluster Randomized Trials
Description: Population-averaged models have been increasingly used in the design and analysis of
cluster randomized trials (CRTs). To facilitate the applications of population-averaged
models in CRTs, the package implements the generalized estimating equations (GEE) and
matrix-adjusted estimating equations (MAEE) approaches to jointly estimate the marginal
mean models correlation models both for general CRTs and stepped wedge CRTs. Despite the
general GEE/MAEE approach, the package also implements a fast cluster-period GEE method by
Li et al. (2022) <doi:10.1093/biostatistics/kxaa056>
specifically for stepped wedge CRTs with large and variable cluster-period sizes and gives
a simple and efficient estimating equations approach based on the cluster-period means to
estimate the intervention effects as well as correlation parameters. In addition, the package
also provides functions for generating correlated binary data with specific mean vector and
correlation matrix based on the multivariate pr [...truncated...]
Author: Hengshi Yu [aut, cre],
Fan Li [aut],
Paul Rathouz [aut],
Elizabeth L. Turner [aut],
John Preisser [aut]
Maintainer: Hengshi Yu <hengshi@umich.edu>
Diff between geeCRT versions 1.1.4 dated 2025-06-23 and 1.1.5 dated 2025-10-24
DESCRIPTION | 8 +++---- MD5 | 11 +++++---- NEWS.md | 6 ++--- R/binMAEE.R | 43 +++++++++++++++++++++++++++++++++++--- R/contMAEE.R | 57 ++++++++++++++++++++++++++++++++++++++++++++++++--- README.md |only inst/doc/geeCRT.html | 6 ++--- 7 files changed, 110 insertions(+), 21 deletions(-)
Title: DSM and LiDAR Downloader
Description: A collection of functions to search and download
Digital Surface Model (DSM) and Light Detection and Ranging (LiDAR) data via APIs,
including 'OpenTopography' <https://portal.opentopography.org/apidocs/> and
'TNMAccess' <https://apps.nationalmap.gov/tnmaccess/#/>, and canopy tree height data.
Author: Xiaohao Yang [aut, cre, cph],
Nathan Fox [aut],
Derek Van Berkel [aut],
Mark Lindquist [aut]
Maintainer: Xiaohao Yang <xiaohaoy@umich.edu>
This is a re-admission after prior archival of version 1.2.1 dated 2025-06-05
Diff between dsmSearch versions 1.2.1 dated 2025-06-05 and 1.2.2 dated 2025-10-24
DESCRIPTION | 20 +- MD5 | 23 +- NAMESPACE | 4 R/get_dsm_30.R | 8 R/get_lidar.R | 21 +- R/lidar_search.R | 2 R/sysdata.rda |only R/utils.R | 375 ++++++++++++++++++++++++++++++++++++++++ build/vignette.rds |binary inst/doc/dsmSearch.R | 46 ++-- inst/doc/dsmSearch.html | 313 ++++++++++++++++++++++++++------- man/get_lidar.Rd | 27 +- tests/testthat/test-get_lidar.R | 9 13 files changed, 712 insertions(+), 136 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-22 5.1.4
2025-10-21 5.1.2
2025-10-21 5.1.3
2025-07-21 5.1.1
2025-04-02 5.1
2025-02-28 5.0.6
2024-12-11 5.0.5
2024-07-26 5.0.4
2024-07-07 5.0.2
2024-06-27 5.0.0
2023-05-20 4.0.2
2023-05-15 4.0.1
2023-05-04 4.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-31 1.4.0
2022-10-29 1.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-29 1.0.0
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Yoonkyoung Jeon [aut],
Jaehun Shon [aut],
Hyojong Myung [aut],
Hyungwoo Jo [aut],
Sungho Choi [aut],
Jaewoong Heo [aut],
Mingu Jee [aut],
Yujeong Yoon [aut],
Minhyuk Kim [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.3.18 dated 2025-10-01 and 1.3.19 dated 2025-10-24
DESCRIPTION | 14 - MD5 | 14 - NEWS.md | 4 R/cox2.R | 341 +++++++++++++++++++++----- inst/doc/jstable.html | 28 +- inst/doc/jstable_competing_risk_analysis.html | 4 inst/doc/jstable_options.html | 4 man/cox2.display.Rd | 4 8 files changed, 322 insertions(+), 91 deletions(-)
Title: Read 'Blackrock-Microsystems' Files ('NEV', 'NSx')
Description: Loads 'Blackrock' <https://blackrockneurotech.com> neural signal
data files into the memory, provides utility tools to extract the data into
common formats such as plain-text 'tsv' and 'HDF5'.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between readNSx versions 0.0.5 dated 2024-09-03 and 0.0.6 dated 2025-10-24
DESCRIPTION | 10 +- MD5 | 15 ++-- NEWS.md | 4 + R/hdf5-alternative.R |only R/hdf5.R | 147 ++++++++++++++++++++++++++-------------- R/nsx.R | 6 - build/vignette.rds |binary inst/doc/read-nev-nsx-data.html | 1 tests/testthat/test-rawToSEXP.R | 6 + 9 files changed, 123 insertions(+), 66 deletions(-)
Title: File IO for Intracranial Electroencephalography
Description: Integrated toolbox supporting common file formats used for intracranial
Electroencephalography (iEEG) and deep-brain stimulation (DBS) study.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ieegio versions 0.0.5 dated 2025-07-22 and 0.0.6 dated 2025-10-24
DESCRIPTION | 6 MD5 | 18 - NAMESPACE | 2 NEWS.md | 6 R/edf.R | 606 ++++++++++++++++++++++++++++++++++++++++-- R/hdf5-class.R | 22 + R/hdf5.R | 6 README.md | 6 inst/sample_data_registry.txt | 2 man/write_edf.Rd |only tests/testthat/test-edf.R |only 11 files changed, 625 insertions(+), 49 deletions(-)
Title: Modeling Earthquake Data Using 'ETAS' Model
Description: Fits the space-time Epidemic Type Aftershock Sequence
('ETAS') model to earthquake catalogs using a stochastic 'declustering'
approach. The 'ETAS' model is a 'spatio-temporal' marked point process
model and a special case of the 'Hawkes' process. The package is based
on a Fortran program by 'Jiancang Zhuang'
(available at <https://bemlar.ism.ac.jp/zhuang/software.html>),
which is modified and translated into C++ and C such that it
can be called from R. Parallel computing with 'OpenMP' is possible
on supported platforms.
Author: Abdollah Jalilian [aut, cre] ,
Jiancang Zhuang [ctb]
Maintainer: Abdollah Jalilian <stat4aj@gmail.com>
Diff between ETAS versions 0.6.1.1 dated 2024-09-23 and 0.7.2 dated 2025-10-24
DESCRIPTION | 18 - MD5 | 59 ++-- NAMESPACE | 2 R/catalog.R | 7 R/search.isc.R | 8 R/simetas.R |only README.md | 44 ++- build/partial.rdb |binary build/vignette.rds |binary cleanup | 9 configure | 559 ++++++++++++++++++++++-------------------- configure.ac | 42 ++- inst/doc/usingETASWeapper.pdf |binary man/ETAS-internal.Rd | 5 man/catalog.Rd | 2 man/date2day.Rd | 2 man/etas.Rd | 8 man/etas.object.Rd | 8 man/italy.quakes.Rd | 4 man/japan.quakes.Rd | 2 man/lambda.Rd | 4 man/rates.Rd | 2 man/resid.etas.Rd | 2 man/search.isc.Rd | 12 src/Makevars.in | 1 src/Makevars.win | 2 src/RcppExports.cpp | 6 src/declust.c | 4 src/fitMP.cpp | 6 src/funcs.h | 16 - src/lambda.c | 8 31 files changed, 479 insertions(+), 363 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A large C/C++-based package for advanced data transformation and
statistical computing in R that is extremely fast, class-agnostic, robust, and
programmer friendly. Core functionality includes a rich set of S3 generic grouped
and weighted statistical functions for vectors, matrices and data frames, which
provide efficient low-level vectorizations, OpenMP multithreading, and skip missing
values by default. These are integrated with fast grouping and ordering algorithms
(also callable from C), and efficient data manipulation functions. The package also
provides a flexible and rigorous approach to time series and panel data in R, fast
functions for data transformation and common statistical procedures, detailed
(grouped, weighted) summary statistics, powerful tools to work with nested data,
fast data object conversions, functions for memory efficient R programming, and
helpers to effectively deal with variable labels, attributes, and missing data. It
seamlessly supports base R objects/cla [...truncated...]
Author: Sebastian Krantz [aut, cre] ,
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Morgan Jacob [ctb],
Dirk Eddelbuettel [ctb],
Laurent Berge [ctb],
Kevin Tappe [ctb],
Alina Cherkas [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999- [...truncated...]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 2.1.3 dated 2025-08-18 and 2.1.4 dated 2025-10-24
collapse-2.1.3/collapse/tests/testthat/test-fHDbetween-fHDwithin-HDB-HDW.R |only collapse-2.1.4/collapse/DESCRIPTION | 8 collapse-2.1.4/collapse/MD5 | 63 +++--- collapse-2.1.4/collapse/NEWS.md | 6 collapse-2.1.4/collapse/R/BY.R | 16 - collapse-2.1.4/collapse/R/GRP.R | 4 collapse-2.1.4/collapse/R/collap.R | 6 collapse-2.1.4/collapse/R/descr.R | 6 collapse-2.1.4/collapse/R/dot.R |only collapse-2.1.4/collapse/R/fsubset_ftransform_fmutate.R | 20 +- collapse-2.1.4/collapse/R/fsummarise.R | 4 collapse-2.1.4/collapse/R/pivot.R | 2 collapse-2.1.4/collapse/inst/doc/collapse_documentation.Rmd | 3 collapse-2.1.4/collapse/inst/doc/collapse_documentation.html | 8 collapse-2.1.4/collapse/inst/doc/collapse_for_tidyverse_users.Rmd | 2 collapse-2.1.4/collapse/inst/doc/collapse_for_tidyverse_users.html | 30 --- collapse-2.1.4/collapse/inst/doc/collapse_object_handling.Rmd | 4 collapse-2.1.4/collapse/inst/doc/collapse_object_handling.html | 80 ++------ collapse-2.1.4/collapse/man/GRP.Rd | 18 - collapse-2.1.4/collapse/man/collapse-documentation.Rd | 30 +-- collapse-2.1.4/collapse/man/collapse-options.Rd | 50 ++--- collapse-2.1.4/collapse/man/pad.Rd | 4 collapse-2.1.4/collapse/man/pivot.Rd | 16 - collapse-2.1.4/collapse/man/qsu.Rd | 6 collapse-2.1.4/collapse/man/summary-statistics.Rd | 2 collapse-2.1.4/collapse/src/ExportSymbols.c | 1 collapse-2.1.4/collapse/src/collapse_c.h | 1 collapse-2.1.4/collapse/src/fmean.c | 5 collapse-2.1.4/collapse/src/fsum.c | 5 collapse-2.1.4/collapse/src/small_helper.c | 94 ++++++++++ collapse-2.1.4/collapse/tests/testthat/test-fhdbetween-fhdwithin-HDB-HDW.R |only collapse-2.1.4/collapse/vignettes/collapse_documentation.Rmd | 3 collapse-2.1.4/collapse/vignettes/collapse_for_tidyverse_users.Rmd | 2 collapse-2.1.4/collapse/vignettes/collapse_object_handling.Rmd | 4 34 files changed, 278 insertions(+), 225 deletions(-)