Title: 'PLINK' 2 Binary (.pgen) Reader
Description: A thin wrapper over 'PLINK' 2's core libraries which provides an R
interface for reading .pgen files. A minimal .pvar loader is also
included. Chang et al. (2015) <doi:10.1186/s13742-015-0047-8>.
Author: Christopher Chang [aut, cre],
Eric Biggers [ctb, cph] ,
Yann Collet [ctb] ,
Meta Platforms, Inc. [cph] ,
Evan Nemerson [ctb, cph] ,
Przemyslaw Skibinski [ctb] ,
Nick Terrell [ctb]
Maintainer: Christopher Chang <chrchang@alumni.caltech.edu>
Diff between pgenlibr versions 0.6.1 dated 2026-03-28 and 0.6.2 dated 2026-06-05
DESCRIPTION | 8 MD5 | 49 NEWS.md | 5 configure | 18 configure.ac | 2 src/Makevars.in | 11 src/Makevars.win | 2 src/pgenlibr.cpp | 16 tools/include/include/pgenlib_ffi_support.cc | 9 tools/include/include/pgenlib_ffi_support.h | 14 tools/include/include/pgenlib_misc.h | 36 tools/include/include/pgenlib_read.cc | 14 tools/include/include/plink2_base.cc | 364 --- tools/include/include/plink2_base.h | 2335 +------------------- tools/include/include/plink2_bgzf.h | 1 tools/include/include/plink2_bits.h | 1 tools/include/include/plink2_float.cc | 9 tools/include/include/plink2_float.h | 82 tools/include/include/plink2_memory.h | 1 tools/include/include/plink2_simd.cc |only tools/include/include/plink2_simd.h |only tools/include/include/plink2_string.h | 1 tools/include/include/plink2_text.cc | 2 tools/include/include/plink2_thread.h | 3 tools/include/include/pvar_ffi_support.cc | 3 tools/include/libdeflate/lib/arm/arm_cpu_features.c | 4 tools/include/zstd/lib/compress/zstd_preSplit.c |only 27 files changed, 420 insertions(+), 2570 deletions(-)
Title: Extensible Data Structures for Multivariate Analysis
Description: Provides a set of basic and extensible data structures and functions for multivariate analysis, including dimensionality reduction techniques, projection methods, and preprocessing functions. The aim of this package is to offer a flexible and user-friendly framework for multivariate analysis that can be easily extended for custom requirements and specific data analysis tasks.
Author: Bradley Buchsbaum [aut, cre]
Maintainer: Bradley Buchsbaum <brad.buchsbaum@gmail.com>
Diff between multivarious versions 0.3.0 dated 2026-01-21 and 0.3.2 dated 2026-06-05
DESCRIPTION | 18 +- MD5 | 153 +++++++++++++---------- NAMESPACE | 41 +++--- NEWS.md | 40 ++++++ R/all_generic.R | 18 +- R/bi_projector.R | 8 - R/bootstrap.R | 9 + R/cPCA.R | 17 +- R/cca.R |only R/classifier.R | 16 -- R/cv.R | 3 R/discriminant_projector.R | 1 R/effect_operator.R |only R/geneig.R | 60 --------- R/mixed_bootstrap.R |only R/mixed_permutation.R |only R/mixed_regress.R |only R/mixed_row_engine.R |only R/mixed_utils.R |only R/multiblock.R | 36 +---- R/nystrom_embedding.R | 6 R/pca.R | 78 +++++------ R/plsc.R | 8 - R/plsc_inference.R | 6 R/pre_process.R | 111 +++++++++------- R/projector.R | 29 +--- R/regress.R | 28 ++-- R/svd.R | 5 R/twoway_projector.R | 22 +-- R/utils.R | 8 + README.md | 58 ++++++++ build/vignette.rds |binary inst/doc/CPCAplus.Rmd | 2 inst/doc/CPCAplus.html | 4 inst/doc/Classifier.R | 4 inst/doc/Classifier.Rmd | 4 inst/doc/Classifier.html | 14 +- inst/doc/Extending.R | 95 ++++---------- inst/doc/Extending.Rmd | 115 ++++++----------- inst/doc/Extending.html | 179 ++++++++++----------------- inst/doc/Introduction.R | 37 +++++ inst/doc/Introduction.Rmd | 57 ++++++++ inst/doc/Introduction.html | 97 ++++++++++++-- inst/doc/Mixed_Regress.R |only inst/doc/Mixed_Regress.Rmd |only inst/doc/Mixed_Regress.html |only inst/doc/Multiblock.html | 61 ++++----- inst/doc/Nystrom.html | 6 inst/doc/Partial_Projection.html | 65 ++++----- inst/doc/PermutationTesting.R | 36 +++++ inst/doc/PermutationTesting.Rmd | 52 +++++++ inst/doc/PermutationTesting.html | 123 +++++++++++++----- inst/doc/PreProcessing.html | 45 +++--- inst/doc/SVD_PCA.html | 50 +++---- man/apply_rotation.Rd | 2 man/bootstrap.effect_operator.Rd |only man/cPCAplus.Rd | 13 + man/cca.Rd |only man/concat_pre_processors.Rd | 4 man/effect.Rd |only man/effect_operator.Rd |only man/geneig.Rd | 14 -- man/identity_basis.Rd |only man/mixed_regress.Rd |only man/partial_project.Rd | 11 + man/partial_project.cross_projector.Rd | 4 man/perm_test.effect_operator.Rd |only man/print.pre_processor.Rd | 2 man/print.prepper.Rd | 2 man/project_block.multiblock_projector.Rd | 4 man/scores.cca.Rd |only man/shared_pca.Rd |only man/supplied_basis.Rd |only tests/testthat/test_cca.R |only tests/testthat/test_cpca.R | 2 tests/testthat/test_cross_projector.R | 19 +- tests/testthat/test_discriminant_projector.R | 25 +-- tests/testthat/test_effect_operator.R |only tests/testthat/test_geneig.R | 9 - tests/testthat/test_geneig_methods.R | 6 tests/testthat/test_mixed_correctness.R |only tests/testthat/test_mixed_regress.R |only tests/testthat/test_preprocess.R | 106 +++++++++++---- tests/testthat/test_projector.R | 24 +-- vignettes/CPCAplus.Rmd | 2 vignettes/Classifier.Rmd | 4 vignettes/Extending.Rmd | 115 ++++++----------- vignettes/Introduction.Rmd | 57 ++++++++ vignettes/Mixed_Regress.Rmd |only vignettes/PermutationTesting.Rmd | 52 +++++++ 90 files changed, 1344 insertions(+), 958 deletions(-)
Title: Automated Routing Engine for Longitudinal Missing Data
Description: Provides an automated routing engine for longitudinal missing
data. It utilizes a Lagrange-constrained Random Forest based on sample
size, missingness rate, and skew to preserve structural variance.
Author: Xiyuan Guo [aut, cre]
Maintainer: Xiyuan Guo <tommyguo039@gmail.com>
Diff between smriti versions 0.1.0 dated 2026-05-21 and 0.2.0 dated 2026-06-05
smriti-0.1.0/smriti/tests/simulation_study.R |only smriti-0.2.0/smriti/DESCRIPTION | 17 - smriti-0.2.0/smriti/MD5 | 44 ++- smriti-0.2.0/smriti/NAMESPACE | 5 smriti-0.2.0/smriti/R/RcppExports.R | 4 smriti-0.2.0/smriti/R/router.R | 321 ++++++++++++++++++++--- smriti-0.2.0/smriti/R/smriti_fiml.R |only smriti-0.2.0/smriti/R/smriti_mi.R |only smriti-0.2.0/smriti/R/wrappers.R |only smriti-0.2.0/smriti/README.md | 2 smriti-0.2.0/smriti/build/vignette.rds |binary smriti-0.2.0/smriti/inst/doc/introduction.R | 8 smriti-0.2.0/smriti/inst/doc/introduction.Rmd | 58 +++- smriti-0.2.0/smriti/inst/doc/introduction.html | 55 ++- smriti-0.2.0/smriti/inst/doc/outlier-robust.R |only smriti-0.2.0/smriti/inst/doc/outlier-robust.Rmd |only smriti-0.2.0/smriti/inst/doc/outlier-robust.html |only smriti-0.2.0/smriti/man/smriti_fiml.Rd |only smriti-0.2.0/smriti/man/smriti_forest.Rd |only smriti-0.2.0/smriti/man/smriti_impute.Rd | 68 ++++ smriti-0.2.0/smriti/man/smriti_mi.Rd |only smriti-0.2.0/smriti/man/smriti_mice.Rd |only smriti-0.2.0/smriti/man/smriti_ranger.Rd |only smriti-0.2.0/smriti/src/Makevars | 1 smriti-0.2.0/smriti/src/Makevars.win | 1 smriti-0.2.0/smriti/src/RcppExports.cpp | 14 - smriti-0.2.0/smriti/src/lagrange.cpp | 126 ++++++--- smriti-0.2.0/smriti/tests/test_imputation.R |only smriti-0.2.0/smriti/vignettes/introduction.Rmd | 58 +++- smriti-0.2.0/smriti/vignettes/outlier-robust.Rmd |only 30 files changed, 609 insertions(+), 173 deletions(-)
Title: Tabulate Descriptive Statistics in Multiple Formats
Description: Creates a table of descriptive statistics
for factor and numeric columns in a data frame. Displays
these by groups, if any. Highly customizable, with support
for 'html' and 'pdf' provided by 'kableExtra'. Respects
original column order, column labels, and factor level order.
See ?tablet.data.frame and vignettes.
Author: Tim Bergsma [aut, cre]
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between tablet versions 0.7.1 dated 2026-01-09 and 0.8.1 dated 2026-06-05
DESCRIPTION | 6 - MD5 | 32 +++--- NAMESPACE | 12 +- R/io_tablet.R |only R/tablet.R | 168 ++++++++++++++++++++------------- R/tablette.R | 24 +--- inst/doc/tablet-introduction-html.html | 4 inst/doc/tablet-introduction-pdf.pdf |binary man/as_kable.tablet.Rd | 10 - man/escape_latex.Rd | 31 +++++- man/escape_latex.default.Rd | 6 - man/escape_latex.latex.Rd | 12 +- man/io_csv.tablet.Rd |only man/io_tablet.Rd |only man/io_tablet.character.Rd |only man/io_tablet.data.frame.Rd |only man/io_tablet.tablet.Rd |only man/tablet.data.frame.Rd | 14 -- man/tablet.tablette.Rd | 4 tests/testthat/test-tablet.R | 97 +++++++++---------- 20 files changed, 240 insertions(+), 180 deletions(-)
Title: Import Brazilian Real Estate Data into R
Description: Provides access to Brazilian real estate market data from multiple
official sources: the Central Bank of Brazil (BCB), the Brazilian
Association of Real Estate Developers (ABRAINC), the Brazilian Association
of Real Estate Credit and Savings Entities (ABECIP), the Getulio Vargas
Foundation (FGV), and the Bank for International Settlements (BIS).
Author: Vinicius Oike Reginatto [aut, cre, cph]
Maintainer: Vinicius Oike Reginatto <viniciusoike@gmail.com>
This is a re-admission after prior archival of version 1.0.0 dated 2026-05-27
Diff between realestatebr versions 1.0.0 dated 2026-05-27 and 1.0.1 dated 2026-06-05
realestatebr-1.0.0/realestatebr/R/cache-github.R |only realestatebr-1.0.0/realestatebr/R/cache-user.R |only realestatebr-1.0.0/realestatebr/R/get-dataset.R |only realestatebr-1.0.0/realestatebr/R/helpers-dataset.R |only realestatebr-1.0.0/realestatebr/R/helpers-download.R |only realestatebr-1.0.0/realestatebr/R/list-datasets.R |only realestatebr-1.0.0/realestatebr/R/realestatebr-package.R |only realestatebr-1.0.0/realestatebr/R/rppi-helpers.R |only realestatebr-1.0.0/realestatebr/R/utils-encoding.R |only realestatebr-1.0.0/realestatebr/R/utils-globals.R |only realestatebr-1.0.0/realestatebr/man/check_cache_status.Rd |only realestatebr-1.0.0/realestatebr/man/check_github_available.Rd |only realestatebr-1.0.0/realestatebr/man/clear_user_cache.Rd |only realestatebr-1.0.0/realestatebr/man/download_from_github_release.Rd |only realestatebr-1.0.0/realestatebr/man/encoding-utils.Rd |only realestatebr-1.0.0/realestatebr/man/ensure_cache_dir.Rd |only realestatebr-1.0.0/realestatebr/man/get_cache_age.Rd |only realestatebr-1.0.0/realestatebr/man/get_cache_metadata.Rd |only realestatebr-1.0.0/realestatebr/man/get_cache_release_tag.Rd |only realestatebr-1.0.0/realestatebr/man/get_cached_file_path.Rd |only realestatebr-1.0.0/realestatebr/man/get_from_local_cache.Rd |only realestatebr-1.0.0/realestatebr/man/get_github_repo.Rd |only realestatebr-1.0.0/realestatebr/man/get_user_cache_dir.Rd |only realestatebr-1.0.0/realestatebr/man/handle_dataset_cache.Rd |only realestatebr-1.0.0/realestatebr/man/has_piggyback.Rd |only realestatebr-1.0.0/realestatebr/man/is_cache_stale.Rd |only realestatebr-1.0.0/realestatebr/man/is_cache_up_to_date.Rd |only realestatebr-1.0.0/realestatebr/man/is_cached.Rd |only realestatebr-1.0.0/realestatebr/man/list_cached_files.Rd |only realestatebr-1.0.0/realestatebr/man/list_github_assets.Rd |only realestatebr-1.0.0/realestatebr/man/load_from_user_cache.Rd |only realestatebr-1.0.0/realestatebr/man/rppi-helpers.Rd |only realestatebr-1.0.0/realestatebr/man/save_cache_metadata.Rd |only realestatebr-1.0.0/realestatebr/man/save_to_user_cache.Rd |only realestatebr-1.0.0/realestatebr/man/update_cache_from_github.Rd |only realestatebr-1.0.0/realestatebr/tests/testthat/test-cache-user.R |only realestatebr-1.0.1/realestatebr/DESCRIPTION | 29 realestatebr-1.0.1/realestatebr/MD5 | 178 +-- realestatebr-1.0.1/realestatebr/NAMESPACE | 5 realestatebr-1.0.1/realestatebr/NEWS.md | 55 realestatebr-1.0.1/realestatebr/R/cache_github.R |only realestatebr-1.0.1/realestatebr/R/get_abecip_indicators.R | 27 realestatebr-1.0.1/realestatebr/R/get_abrainc_indicators.R | 25 realestatebr-1.0.1/realestatebr/R/get_bcb_realestate.R | 69 - realestatebr-1.0.1/realestatebr/R/get_bcb_series.R | 32 realestatebr-1.0.1/realestatebr/R/get_dataset.R |only realestatebr-1.0.1/realestatebr/R/get_fgv_ibre.R | 47 realestatebr-1.0.1/realestatebr/R/get_rppi.R | 132 -- realestatebr-1.0.1/realestatebr/R/get_rppi_bis.R | 22 realestatebr-1.0.1/realestatebr/R/get_secovi.R | 27 realestatebr-1.0.1/realestatebr/R/helpers_dataset.R |only realestatebr-1.0.1/realestatebr/R/helpers_download.R |only realestatebr-1.0.1/realestatebr/R/list_datasets.R |only realestatebr-1.0.1/realestatebr/R/realestatebr_package.R |only realestatebr-1.0.1/realestatebr/R/rppi_helpers.R |only realestatebr-1.0.1/realestatebr/R/utils_encoding.R |only realestatebr-1.0.1/realestatebr/R/utils_globals.R |only realestatebr-1.0.1/realestatebr/README.md | 12 realestatebr-1.0.1/realestatebr/inst/doc/getting-started.R | 307 ++--- realestatebr-1.0.1/realestatebr/inst/doc/getting-started.Rmd | 14 realestatebr-1.0.1/realestatebr/inst/doc/getting-started.html | 456 ------- realestatebr-1.0.1/realestatebr/inst/doc/working-with-rppi.R | 578 +++++----- realestatebr-1.0.1/realestatebr/inst/doc/working-with-rppi.Rmd | 2 realestatebr-1.0.1/realestatebr/inst/doc/working-with-rppi.html | 91 - realestatebr-1.0.1/realestatebr/man/apply_table_filtering.Rd | 15 realestatebr-1.0.1/realestatebr/man/attach_dataset_metadata.Rd | 8 realestatebr-1.0.1/realestatebr/man/clear_session_cache.Rd |only realestatebr-1.0.1/realestatebr/man/dot-ENCODING_MAP.Rd | 2 realestatebr-1.0.1/realestatebr/man/download_csv.Rd | 2 realestatebr-1.0.1/realestatebr/man/download_excel.Rd | 2 realestatebr-1.0.1/realestatebr/man/download_with_retry.Rd | 2 realestatebr-1.0.1/realestatebr/man/download_zip.Rd | 2 realestatebr-1.0.1/realestatebr/man/encoding_utils.Rd |only realestatebr-1.0.1/realestatebr/man/fallback_to_github_cache.Rd | 16 realestatebr-1.0.1/realestatebr/man/fetch_github_release_asset.Rd |only realestatebr-1.0.1/realestatebr/man/get_abecip_indicators.Rd | 14 realestatebr-1.0.1/realestatebr/man/get_abrainc_indicators.Rd | 14 realestatebr-1.0.1/realestatebr/man/get_available_tables.Rd | 10 realestatebr-1.0.1/realestatebr/man/get_bcb_realestate.Rd | 11 realestatebr-1.0.1/realestatebr/man/get_bcb_series.Rd | 5 realestatebr-1.0.1/realestatebr/man/get_cached_name.Rd | 7 realestatebr-1.0.1/realestatebr/man/get_dataset.Rd | 26 realestatebr-1.0.1/realestatebr/man/get_dataset_from_source.Rd | 22 realestatebr-1.0.1/realestatebr/man/get_dataset_info.Rd | 2 realestatebr-1.0.1/realestatebr/man/get_dataset_with_fallback.Rd | 33 realestatebr-1.0.1/realestatebr/man/get_fgv_ibre.Rd | 8 realestatebr-1.0.1/realestatebr/man/get_from_github_cache.Rd | 7 realestatebr-1.0.1/realestatebr/man/get_from_internal_function.Rd | 6 realestatebr-1.0.1/realestatebr/man/get_rppi.Rd | 4 realestatebr-1.0.1/realestatebr/man/get_rppi_bis.Rd | 11 realestatebr-1.0.1/realestatebr/man/get_rppi_fipezap.Rd | 4 realestatebr-1.0.1/realestatebr/man/get_rppi_igmi.Rd | 4 realestatebr-1.0.1/realestatebr/man/get_rppi_iqa.Rd | 4 realestatebr-1.0.1/realestatebr/man/get_rppi_iqaiw.Rd | 4 realestatebr-1.0.1/realestatebr/man/get_rppi_ivar.Rd | 10 realestatebr-1.0.1/realestatebr/man/get_rppi_ivgr.Rd | 4 realestatebr-1.0.1/realestatebr/man/get_rppi_secovi_sp.Rd | 4 realestatebr-1.0.1/realestatebr/man/get_secovi.Rd | 7 realestatebr-1.0.1/realestatebr/man/list_datasets.Rd | 2 realestatebr-1.0.1/realestatebr/man/load_dataset_registry.Rd | 2 realestatebr-1.0.1/realestatebr/man/memo_key.Rd |only realestatebr-1.0.1/realestatebr/man/realestatebr-package.Rd | 4 realestatebr-1.0.1/realestatebr/man/registry_to_tibble.Rd | 2 realestatebr-1.0.1/realestatebr/man/rppi_helpers.Rd |only realestatebr-1.0.1/realestatebr/man/show_import_message.Rd | 9 realestatebr-1.0.1/realestatebr/man/supports_table_all.Rd | 2 realestatebr-1.0.1/realestatebr/man/test_encoding_patterns.Rd | 2 realestatebr-1.0.1/realestatebr/man/validate_and_resolve_table.Rd | 14 realestatebr-1.0.1/realestatebr/man/validate_dataset.Rd | 2 realestatebr-1.0.1/realestatebr/man/validate_dataset_params.Rd | 17 realestatebr-1.0.1/realestatebr/tests/testthat/test-helpers-dataset.R | 154 -- realestatebr-1.0.1/realestatebr/tests/testthat/test-integration-get_dataset.R | 107 - realestatebr-1.0.1/realestatebr/tests/testthat/test-internal-functions.R | 54 realestatebr-1.0.1/realestatebr/vignettes/getting-started.Rmd | 14 realestatebr-1.0.1/realestatebr/vignettes/working-with-rppi.Rmd | 2 115 files changed, 885 insertions(+), 1880 deletions(-)
Title: Translates R Help Documentation using Large Language Models
Description: Translates R help documentation on the fly by using a Large
Language model of your choice. If you are using 'RStudio' or
'Positron' the translated help will appear in the help pane.
Author: Edgar Ruiz [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Edgar Ruiz <edgar@posit.co>
Diff between lang versions 0.1.0 dated 2025-10-30 and 0.1.1 dated 2026-06-05
DESCRIPTION | 36 +- MD5 | 47 +- NAMESPACE | 2 NEWS.md |only R/help-shims.R | 28 + R/import-standalone-obj-type.R |only R/import-standalone-purrr.R |only R/import-standalone-types-check.R |only R/lang-help.R | 61 ++- R/lang-package.R |only R/lang-use.R | 79 +++-- R/lang.R | 3 R/rd-parse.R |only R/rd-translate.R | 519 ++++++++++++++++++++------------- README.md | 235 ++++++++------ man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/help.Rd | 7 man/lang-package.Rd |only man/lang_help.Rd | 18 - man/lang_use.Rd | 27 + tests/testthat/_snaps/help-shims.md | 8 tests/testthat/_snaps/lang-help.md | 32 +- tests/testthat/_snaps/lang-use.md | 9 tests/testthat/test-help-shims.R | 23 + tests/testthat/test-lang-help.R | 20 - tests/testthat/test-lang-use.R | 10 tests/testthat/test-rd-translate.R | 113 ++++++- 30 files changed, 844 insertions(+), 433 deletions(-)
Title: Make 'PICRUSt2' Output Analysis and Visualization Easier
Description: Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) <doi:10.1093/bioinformatics/btad470>.
Author: Chen Yang [aut, cre],
Liangliang Zhang [aut]
Maintainer: Chen Yang <cafferychen7850@gmail.com>
Diff between ggpicrust2 versions 2.5.16 dated 2026-05-20 and 2.5.17 dated 2026-06-05
DESCRIPTION | 6 +-- MD5 | 28 +++++++------- NEWS.md | 55 ++++++++++++++++++++++++--- R/legend_annotation_utils.R | 22 +++++++---- R/pathway_annotation.R | 4 +- R/pathway_daa.R | 2 - R/pathway_errorbar.R | 87 +++++++++++++++++++++----------------------- R/pathway_gsea.R | 18 +++------ R/pathway_heatmap.R | 10 +---- R/pathway_pca.R | 2 - R/pathway_ridgeplot.R | 7 ++- R/pathway_volcano.R | 4 ++ R/visualize_gsea.R | 13 ++---- man/pathway_errorbar.Rd | 4 +- man/run_fgsea.Rd | 2 - 15 files changed, 152 insertions(+), 112 deletions(-)
Title: Dunn's Test of Multiple Comparisons Using Rank Sums
Description: Computes Dunn's test (1964) for stochastic superiority and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic superiority among k groups (Kruskal and Wallis, 1952). 'dunn.test' makes k(k-1)/2 multiple pairwise comparisons based on Dunn's z-test-statistic approximations to the actual rank statistics. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. 'dunn.test' accounts for tied ranks.
Author: Alexis Dinno [aut, cre, cph]
Maintainer: Alexis Dinno <alexis.dinno@pdx.edu>
Diff between dunn.test versions 1.4.0 dated 2026-05-28 and 1.4.1 dated 2026-06-05
DESCRIPTION | 8 ++--- MD5 | 6 +-- R/dunn.test.R | 84 +++++++++++++++++++++++++------------------------------ R/kwallis.test.R | 33 +++------------------ 4 files changed, 51 insertions(+), 80 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>).
Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Barbanti and Hothorn, 2022,
<DOI:10.1093/biostatistics/kxac048>) and a tutorial explains applications in survival analysis
(Siegfried et al., 2025, <DOI:10.48550/arXiv.2402.06428>). Multivariate conditional transformation models
(Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023,
<DOI:10.108 [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Luisa Barbanti [ctb] ,
Sandra Siegfried [aut] ,
Lucas Kook [aut] ,
Susanne Dandl [ctb] ,
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 1.4-2 dated 2026-05-09 and 1.4-3 dated 2026-06-05
tram-1.4-2/tram/inst/npnsimulations |only tram-1.4-3/tram/DESCRIPTION | 8 +-- tram-1.4-3/tram/MD5 | 83 +++++++++++++++++++-------------- tram-1.4-3/tram/build/partial.rdb |binary tram-1.4-3/tram/inst/NEWS.Rd | 6 ++ tram-1.4-3/tram/inst/doc/NAMI.R | 11 ++++ tram-1.4-3/tram/inst/doc/NAMI.Rnw | 13 ++++- tram-1.4-3/tram/inst/doc/NAMI.pdf |binary tram-1.4-3/tram/inst/doc/mtram.R | 11 ++++ tram-1.4-3/tram/inst/doc/mtram.Rnw | 13 ++++- tram-1.4-3/tram/inst/doc/mtram.pdf |binary tram-1.4-3/tram/inst/doc/survtram.R | 11 ++++ tram-1.4-3/tram/inst/doc/survtram.Rnw | 15 +++++ tram-1.4-3/tram/inst/doc/survtram.pdf |binary tram-1.4-3/tram/inst/doc/tram.R | 11 ++++ tram-1.4-3/tram/inst/doc/tram.Rnw | 13 ++++- tram-1.4-3/tram/inst/doc/tram.pdf |binary tram-1.4-3/tram/inst/npn_empeval/TDA.R | 15 ++--- tram-1.4-3/tram/inst/npn_simulations |only tram-1.4-3/tram/man/Compris.Rd | 29 +++++------ tram-1.4-3/tram/vignettes/NAMI.Rnw | 13 ++++- tram-1.4-3/tram/vignettes/mtram.Rnw | 13 ++++- tram-1.4-3/tram/vignettes/survtram.Rnw | 15 +++++ tram-1.4-3/tram/vignettes/tram.Rnw | 13 ++++- 24 files changed, 224 insertions(+), 69 deletions(-)
Title: Flexibly Tune Families of Probability Distributions
Description: Fits probability distributions to data and plugs into the
'probaverse' suite of R packages so distribution objects are ready for
further manipulation and evaluation. Supports methods such as maximum
likelihood and L-moments, and provides diagnostics including empirical
ranking and quantile score.
Author: Vincenzo Coia [aut, cre, cph]
Maintainer: Vincenzo Coia <vincenzo.coia@gmail.com>
Diff between famish versions 0.2.0 dated 2025-12-08 and 0.2.1 dated 2026-06-05
DESCRIPTION | 6 +++--- MD5 | 13 +++++++------ NEWS.md | 5 +++++ R/fit_dst.R | 23 ++++++++--------------- build/vignette.rds |binary inst/doc/fitting.html | 4 ++-- man/fit_dst.Rd | 4 +++- tests/testthat/test-lmom-lp3.R |only 8 files changed, 28 insertions(+), 27 deletions(-)
Title: Flexible, Extensible, & Reproducible Pupillometry Preprocessing
Description: Pupillometry offers a non-invasive window into the mind and has been used extensively as a psychophysiological readout of arousal signals linked with cognitive processes like attention, stress, and emotional states [Clewett et al. (2020) <doi:10.1038/s41467-020-17851-9>; Kret & Sjak-Shie (2018) <doi:10.3758/s13428-018-1075-y>; Strauch (2024) <doi:10.1016/j.tins.2024.06.002>]. Yet, despite decades of pupillometry research, many established packages and workflows to date lack design patterns based on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles [see Wilkinson et al. (2016) <doi:10.1038/sdata.2016.18>]. 'eyeris' provides a modular, performant, and extensible preprocessing framework for pupillometry data with BIDS-like organization and interactive output reports [Esteban et al. (2019) <doi:10.1038/s41592-018-0235-4>; Gorgolewski et al. (2016) <doi:10.1038/sdata.2016.44>]. Development was supported, in part, by the S [...truncated...]
Author: Shawn Schwartz [aut, cre] ,
Mingjian He [ctb],
Haopei Yang [ctb],
Alice Xue [ctb],
Gustavo Santiago-Reyes [ctb]
Maintainer: Shawn Schwartz <shawn.t.schwartz@gmail.com>
Diff between eyeris versions 3.0.1 dated 2025-10-07 and 3.1.0 dated 2026-06-05
DESCRIPTION | 10 +- MD5 | 65 +++++++++--------- NEWS.md | 20 +++++ R/pipeline-epoch.R | 8 ++ R/pipeline-glassbox.R | 13 +++ R/utils-parsers.R | 107 +++++++++++++++++++++++-------- R/utils-render_report.R | 100 +++++++++++++++++++++++++--- README.md | 61 +++++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 4 + inst/doc/complete-pipeline.html | 62 ++++++++--------- inst/doc/database-guide.R | 6 - inst/doc/database-guide.Rmd | 6 - inst/doc/database-guide.html | 44 ++++++------ inst/doc/epoching-bids-reports.html | 50 +++++++------- inst/doc/reports.html | 4 - inst/figures |only man/bidsify.Rd | 2 man/epoch.Rd | 2 man/eyeris-package.Rd | 5 + man/figures/README-timeseries-plot-1.png |binary man/figures/README-timeseries-plot-2.png |binary man/figures/README-timeseries-plot-3.png |binary man/figures/README-timeseries-plot-4.png |binary man/figures/README-timeseries-plot-5.png |binary man/figures/README-timeseries-plot-6.png |binary man/figures/README-timeseries-plot-7.png |binary man/figures/README-timeseries-plot-8.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/glassbox.Rd | 2 man/plot.eyeris.Rd | 4 - man/should_omit_parameter.Rd |only tests/testthat/test-format_call_stack.R |only vignettes/database-guide.Rmd | 6 - 35 files changed, 385 insertions(+), 196 deletions(-)
Title: Statistical Transformations
Description: Performs various statistical transformations; Box-Cox and Log (Box and Cox, 1964) <doi:10.1111/j.2517-6161.1964.tb00553.x>, Glog (Durbin et al., 2002) <doi:10.1093/bioinformatics/18.suppl_1.S105>, Neglog (Whittaker et al., 2005) <doi:10.1111/j.1467-9876.2005.00520.x>, Reciprocal (Tukey, 1957), Log Shift (Feng et al., 2016) <doi:10.1002/sta4.104>, Bickel-Docksum (Bickel and Doksum, 1981) <doi:10.1080/01621459.1981.10477649>, Yeo-Johnson (Yeo and Johnson, 2000) <doi:10.1093/biomet/87.4.954>, Square Root (Medina et al., 2019), Manly (Manly, 1976) <doi:10.2307/2988129>, Modulus (John and Draper, 1980) <doi:10.2307/2986305>, Dual (Yang, 2006) <doi:10.1016/j.econlet.2006.01.011>, Gpower (Kelmansky et al., 2013) <doi:10.1515/sagmb-2012-0030>. It also performs graphical approaches, assesses the success of the transformation via tests and plots.
Author: Muge Coskun Yildirim [aut],
Osman Dag [aut, cre]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between Transform versions 1.0 dated 2023-06-08 and 1.1 dated 2026-06-05
DESCRIPTION | 9 +++++---- MD5 | 34 ++++++++++++++++++---------------- NAMESPACE | 2 +- R/selectTransform.R |only man/Transform.Rd | 6 +----- man/bcTransform.Rd | 3 +-- man/bdTransform.Rd | 4 +--- man/dlTransform.Rd | 5 +---- man/glTransform.Rd | 4 +--- man/gpTransform.Rd | 6 +----- man/lgTransform.Rd | 6 +----- man/lsTransform.Rd | 5 +---- man/mdTransform.Rd | 6 +----- man/mnTransform.Rd | 5 +---- man/nlTransform.Rd | 5 +---- man/rpTransform.Rd | 5 +---- man/selectTransform.Rd |only man/ssTransform.Rd | 5 +---- man/yjTransform.Rd | 6 +----- 19 files changed, 38 insertions(+), 78 deletions(-)
Title: An Analyzer of International Large Scale Assessments in
Education
Description: An easy way to analyze international large-scale assessments and surveys in education or any other dataset that includes replicated weights (Balanced Repeated Replication (BRR) weights, Jackknife replicate weights,...) while also allowing for analysis with multiply imputed variables (plausible values). It supports the estimation of univariate statistics (e.g. mean, variance, standard deviation, quantiles), frequencies, correlation, linear regression and any other model already implemented in R that takes a data frame and weights as parameters. It also includes options to prepare the results for publication, following the table formatting standards of the Organization for Economic Cooperation and Development (OECD).
Author: Rodolfo Ilizaliturri [aut, cre],
Francesco Avvisati [aut],
Francois Keslair [aut]
Maintainer: Rodolfo Ilizaliturri <rodolfo.ilizaliturri@oecd.org>
Diff between Rrepest versions 1.6.12 dated 2026-04-03 and 1.6.13 dated 2026-06-05
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/rrepest.R | 9 ++++++++- R/rrepest_base.R | 1 + 4 files changed, 15 insertions(+), 7 deletions(-)
Title: Sparse and Group Sparse Linear Models
Description: Fits the solution paths of classical sparse regression models with efficient active set algorithms by solving small sub-problems. Include LASSO, SCAD, MCP, (Sparse) Group-LASSO, Cooperative-LASSO, (Group) LAVA, (Generalized) Fused-Lasso and (Generalized) Elastic-Net. Also provides methods for model selection purpose (information criteria, cross-validation, stability selection).
Author: Julien Chiquet [aut, cre]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between quadrupen versions 0.2-13 dated 2025-10-09 and 1.0-0 dated 2026-06-05
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quadrupen-0.2-13/quadrupen/tests/testthat/test-senet.R |only quadrupen-0.2-13/quadrupen/tests/testthat/test-sparse.R |only quadrupen-0.2-13/quadrupen/tests/testthat/test-warm.R |only quadrupen-1.0-0/quadrupen/DESCRIPTION | 53 - quadrupen-1.0-0/quadrupen/MD5 | 263 ++++- quadrupen-1.0-0/quadrupen/NAMESPACE | 75 + quadrupen-1.0-0/quadrupen/NEWS.md | 120 +- quadrupen-1.0-0/quadrupen/R/CrossValidation-R6Class.R |only quadrupen-1.0-0/quadrupen/R/DataModel-R6Class.R |only quadrupen-1.0-0/quadrupen/R/InformationCriteria-R6Class.R |only quadrupen-1.0-0/quadrupen/R/QuadrupenFit-R6Class.R |only quadrupen-1.0-0/quadrupen/R/RcppExports.R |only quadrupen-1.0-0/quadrupen/R/Regularizers-R6Class.R |only quadrupen-1.0-0/quadrupen/R/StabilityPath-R6Class.R |only quadrupen-1.0-0/quadrupen/R/bounded-reg.R |only quadrupen-1.0-0/quadrupen/R/fused-lasso.R |only quadrupen-1.0-0/quadrupen/R/group-lava.R |only quadrupen-1.0-0/quadrupen/R/group_sparse_lm.R |only 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Title: Nonlinear Nonparametric Statistics
Description: NNS (Nonlinear Nonparametric Statistics) leverages partial moments – the fundamental elements of variance that asymptotically approximate the area under f(x) – to provide a robust foundation for nonlinear analysis while maintaining linear equivalences. Designed for real-world data that violates symmetry, linearity, or distributional assumptions, NNS delivers a comprehensive suite of advanced statistical techniques, including: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic superiority / dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995, Second edition: <https://ovvo-financial.github.io/NNS/book/>).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.open.source@gmail.com>
Diff between NNS versions 12.0 dated 2026-04-10 and 12.1 dated 2026-06-05
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More information about nlmixr2targets at CRAN
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More information about NeutroIBDAnalysis at CRAN
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Title: Fitting Discrete Distribution Models to Count Data
Description: Provides functions for fitting discrete distribution models to count data.
Included are the Poisson, the negative binomial, the Poisson-inverse gaussian and, most importantly,
a new implementation of the Poisson-beta distribution (density, distribution and quantile
functions, and random number generator) together with a needed new implementation of
Kummer's function (also: confluent hypergeometric function of the first kind). Three
different implementations of the Gillespie algorithm allow data simulation based on the
basic, switching or bursting mRNA generating processes. Moreover, likelihood functions for
four variants of each of the three aforementioned distributions are also available.
The variants include one population and two population mixtures, both with and without
zero-inflation. The package depends on the 'MPFR' libraries (<https://www.mpfr.org/>) which need to be installed separately
(see description at <https://github.com/fuchslab/scModels>).
This package is s [...truncated...]
Author: Lisa Amrhein [aut] ,
Kumar Harsha [aut, cre] ,
Christiane Fuchs [aut] ,
Pavel Holoborodko [ctb]
Maintainer: Kumar Harsha <kumarharsha.0292@gmail.com>
This is a re-admission after prior archival of version 1.0.4 dated 2023-01-24
Diff between scModels versions 1.0.4 dated 2023-01-24 and 1.0.5 dated 2026-06-05
DESCRIPTION | 25 MD5 | 48 NAMESPACE | 104 - NEWS.md | 55 R/RcppExports.R | 116 - R/gillespie.R | 280 ++-- R/log_likelihood.R | 1580 ++++++++++++------------- R/par_est_fns.R | 766 ++++++------ R/pb.R | 168 +- man/Inverse-Gaussian.Rd | 48 man/Poisson-beta.Rd | 114 - man/chf_1F1.Rd | 52 man/fit_params.Rd | 64 - man/gmRNA.Rd | 126 - man/nlogL.Rd | 356 ++--- src/Makevars | 2 src/Makevars.win | 2 src/gillespie.cpp | 2 tests/testthat.R | 8 tests/testthat/test-NAs.R | 56 tests/testthat/test-chf_1F1.R | 10 tests/testthat/test-discrete-sum.R | 14 tests/testthat/test-discrete.R | 28 tests/testthat/test-inappropriate-parameters.R | 54 tests/testthat/test-likelihood.R | 64 - 25 files changed, 2071 insertions(+), 2071 deletions(-)
Title: Functions and Data for the Book, a Primer of Ecology with R
Description: Provides data and functions for "A Primer of Ecology with R" by M. Henry H. Stevens (2009) <doi:10.1007/978-0-387-89882-7>.
Author: M. Henry H. Stevens [aut, cre]
Maintainer: M. Henry H. Stevens <hank.stevens@miamioh.edu>
This is a re-admission after prior archival of version 1.2.0 dated 2021-01-06
Diff between primer versions 1.2.0 dated 2021-01-06 and 1.2.1 dated 2026-06-05
DESCRIPTION | 26 +++++++++++++++----------- MD5 | 30 +++++++++++++++--------------- R/alogistic.R | 2 +- R/clogistic.R | 3 +-- R/one_over_f.R | 2 +- R/plot_f.R | 21 +++++++++++++-------- R/primer-package.R | 23 ++--------------------- R/spec_mimic.R | 16 ++++++++++------ data/ClostExp.rda |binary inst/CITATION | 28 +++++++++++++++------------- man/alogistic.Rd | 2 +- man/clogistic.Rd | 3 +-- man/one_over_f.Rd | 2 +- man/plot_f.Rd | 13 +++++++------ man/primer-package.Rd | 18 ++++-------------- man/spec_mimic.Rd | 13 ++++++++----- 16 files changed, 95 insertions(+), 107 deletions(-)
Title: Weighted Meta-Analysis with Pseudo-Populations
Description: Implementation of integrative weighting approaches for multiple observational studies and causal inferences. The package features three weighting approaches, each representing a special case of the unified weighting framework, introduced by Guha and Li (2024) <doi:10.1093/biomtc/ujae070>, which includes an extension of inverse probability weights for data integration settings.
Author: Subharup Guha [aut, cre],
Mengqi Xu [aut],
Chayce Reed [aut],
Kashish Priyam [aut],
Yi Li [aut]
Maintainer: Subharup Guha <Subharup.Guha@dartmouth.edu>
Diff between WMAP versions 1.2.0 dated 2025-06-17 and 1.3.0 dated 2026-06-05
DESCRIPTION | 21 MD5 | 76 +- NAMESPACE | 7 R/data.R | 55 + R/diagnostics.R |only R/other-functions.R | 1256 +++++++++++++++++++++++++++------------ R/plot.R | 108 ++- R/stage-1-functions.R | 238 +++++-- R/stage-1.R | 114 ++- R/stage-2-functions.R | 454 +++++++++++--- R/stage-2.R | 176 ++++- R/summary.R | 202 +++++- R/utils.R | 43 + build |only inst |only man/Stage1.Rd |only man/balancing.weights.Rd | 30 man/bootStrap.Rd |only man/causal.estimate.Rd | 85 +- man/check.factor.Rd |only man/checkSample.Rd |only man/demo.Rd | 40 + man/fn.ESS_FLEXOR.Rd |only man/fn.Estimate_mgPS.Rd |only man/fn.FLEXOR.Rd |only man/fn.IC.Rd |only man/fn.Omnibus.Rd |only man/fn.PMF_quantile.Rd |only man/fn.RF_ZFirst.Rd |only man/fn.RF_crossfit_once.Rd |only man/fn.RF_fit_single.Rd |only man/fn.RF_tune_nodesize.Rd |only man/fn.SVD.Rd |only man/fn.Stage2.Rd |only man/fn.Weights.Rd |only man/fn.check_ess.Rd |only man/fn.check_extreme_weights.Rd |only man/fn.check_positivity.Rd |only man/fn.clip.Rd |only man/fn.createListData.Rd |only man/fn.fit_outcome_model.Rd |only man/fn.loop.Rd |only man/fn.rdirichlet.Rd |only man/fn.run_diagnostics.Rd |only man/fn.userInputChecks_1.Rd |only man/fn.userInputChecks_2.Rd |only man/fn.userInputChecks_3.Rd |only man/global_variables.Rd |only man/grapes-or-or-grapes.Rd |only man/is.natural.Rd |only man/is.probvector.Rd |only man/plot.causal_estimates.Rd | 22 man/preStage1.Rd |only man/summary.balancing_weights.Rd | 24 man/summary.causal_estimates.Rd | 26 man/write_res.Rd |only man/write_sigma_ratio.Rd |only vignettes |only 58 files changed, 2231 insertions(+), 746 deletions(-)
Title: Numerical Calibration of Proxy-Climate Relationships
Description: Bootstrapped response and correlation functions,
seasonal correlations and evaluation of reconstruction
skills for use in dendroclimatology and dendroecology,
see Zang and Biondi (2015) <doi:10.1111/ecog.01335>.
Author: Christian Zang [aut, cre, cph, trl],
Franco Biondi [ctb, cph]
Maintainer: Christian Zang <christian.zang@hswt.de>
Diff between treeclim versions 2.0.7.1 dated 2024-12-16 and 2.0.8.0 dated 2026-06-05
DESCRIPTION | 16 ++++++++-------- MD5 | 19 ++++++++++--------- NEWS.md |only R/dcc.R | 8 +++++++- man/dcc.Rd | 2 +- src/Makevars | 3 +-- src/Makevars.win | 4 +--- src/corfun_exact.cpp | 8 ++++---- src/pcor.cpp | 14 ++++++++------ src/respo_exact.cpp | 8 ++++---- tests/testthat/test_dcc.R | 8 +++----- 11 files changed, 47 insertions(+), 43 deletions(-)
Title: Clustering via Quadratic Scoring
Description: Performs tuning of clustering models, methods and algorithms including the problem of determining an appropriate number of clusters. Validation of cluster analysis results is performed via quadratic scoring using resampling methods, as in Coraggio, L. and Coretto, P. (2023) <doi:10.1016/j.jmva.2023.105181>.
Author: Luca Coraggio [cre, aut] ,
Pietro Coretto [aut]
Maintainer: Luca Coraggio <luca.coraggio@unina.it>
Diff between qcluster versions 2.0.0 dated 2026-04-13 and 2.0.1 dated 2026-06-05
DESCRIPTION | 8 ++--- MD5 | 8 ++--- NEWS | 5 +++ src/ecm.c | 53 +++++++++++++++++++++------------- tests/testthat/test-gmix-clustering.R | 42 ++++++++++++++++++++------ 5 files changed, 78 insertions(+), 38 deletions(-)
Title: Advice on R Package Building
Description: Give advice about good practices when building R packages.
Advice includes functions and syntax to avoid, package structure, code
complexity, code formatting, etc.
Author: Mark Padgham [aut, cre] ,
Ascent Digital Services UK Limited [cph] ,
Karina Marks [aut] ,
Daniel de Bortoli [aut] ,
Gabor Csardi [aut],
Hannah Frick [aut],
Owen Jones [aut] ,
Hannah Alexander [aut],
Ana Simmons [ctb] ,
Fabian Scheipl [ctb] ,
Athanasi [...truncated...]
Maintainer: Mark Padgham <mark@ropensci.org>
Diff between goodpractice versions 1.0.5 dated 2024-06-04 and 1.1.0 dated 2026-06-05
goodpractice-1.0.5/goodpractice/R/chk_tnf.R |only goodpractice-1.0.5/goodpractice/R/my_linters.R |only goodpractice-1.0.5/goodpractice/R/prep_expressions.R |only goodpractice-1.0.5/goodpractice/man/default_r_file_pattern.Rd |only goodpractice-1.0.5/goodpractice/man/get_marker.Rd |only goodpractice-1.0.5/goodpractice/man/make_rcmd_check.Rd |only goodpractice-1.0.5/goodpractice/man/package_collate.Rd |only goodpractice-1.0.5/goodpractice/man/prep_expressions.Rd |only goodpractice-1.0.5/goodpractice/man/r_package_files.Rd |only goodpractice-1.0.5/goodpractice/man/seq_linter.Rd |only goodpractice-1.0.5/goodpractice/tests/testthat/test-tf.R |only goodpractice-1.1.0/goodpractice/DESCRIPTION | 66 goodpractice-1.1.0/goodpractice/MD5 | 226 +- goodpractice-1.1.0/goodpractice/NAMESPACE | 23 goodpractice-1.1.0/goodpractice/NEWS.md | 100 + goodpractice-1.1.0/goodpractice/R/api.R | 39 goodpractice-1.1.0/goodpractice/R/chk_avoided_packages.R |only goodpractice-1.1.0/goodpractice/R/chk_code_structure.R |only goodpractice-1.1.0/goodpractice/R/chk_covr.R | 22 goodpractice-1.1.0/goodpractice/R/chk_cyclocomp.R | 25 goodpractice-1.1.0/goodpractice/R/chk_description.R | 244 ++ goodpractice-1.1.0/goodpractice/R/chk_generic.R |only goodpractice-1.1.0/goodpractice/R/chk_lintr.R | 531 +++++ goodpractice-1.1.0/goodpractice/R/chk_namespace.R | 15 goodpractice-1.1.0/goodpractice/R/chk_rcmdcheck.R | 12 goodpractice-1.1.0/goodpractice/R/chk_rd.R |only goodpractice-1.1.0/goodpractice/R/chk_revdep.R |only goodpractice-1.1.0/goodpractice/R/chk_roxygen2.R |only goodpractice-1.1.0/goodpractice/R/chk_spelling.R |only goodpractice-1.1.0/goodpractice/R/chk_tidyverse.R |only goodpractice-1.1.0/goodpractice/R/chk_urlchecker.R |only goodpractice-1.1.0/goodpractice/R/chk_vignette.R |only goodpractice-1.1.0/goodpractice/R/customization.R | 2 goodpractice-1.1.0/goodpractice/R/gp.R | 211 ++ goodpractice-1.1.0/goodpractice/R/lists.R | 192 ++ goodpractice-1.1.0/goodpractice/R/prep_covr.R | 26 goodpractice-1.1.0/goodpractice/R/prep_cyclocomp.R | 10 goodpractice-1.1.0/goodpractice/R/prep_description.R | 15 goodpractice-1.1.0/goodpractice/R/prep_lintr.R | 111 - goodpractice-1.1.0/goodpractice/R/prep_namespace.R | 13 goodpractice-1.1.0/goodpractice/R/prep_rcmdcheck.R | 10 goodpractice-1.1.0/goodpractice/R/prep_rd.R |only goodpractice-1.1.0/goodpractice/R/prep_revdep.R |only goodpractice-1.1.0/goodpractice/R/prep_roxygen2.R |only goodpractice-1.1.0/goodpractice/R/prep_source.R |only goodpractice-1.1.0/goodpractice/R/prep_spelling.R |only goodpractice-1.1.0/goodpractice/R/prep_tidyverse.R |only goodpractice-1.1.0/goodpractice/R/prep_urlchecker.R |only goodpractice-1.1.0/goodpractice/R/prep_utils.R |only goodpractice-1.1.0/goodpractice/R/prep_vignette.R |only goodpractice-1.1.0/goodpractice/R/print.R | 155 - goodpractice-1.1.0/goodpractice/R/rstudio_markers.R | 2 goodpractice-1.1.0/goodpractice/R/treesitter.R |only goodpractice-1.1.0/goodpractice/R/utils.R | 100 + goodpractice-1.1.0/goodpractice/README.md | 540 +++++ goodpractice-1.1.0/goodpractice/build/vignette.rds |binary goodpractice-1.1.0/goodpractice/inst/bad1/R/bad_extension.r |only goodpractice-1.1.0/goodpractice/inst/doc/custom_checks.R | 2 goodpractice-1.1.0/goodpractice/inst/doc/custom_checks.Rmd | 4 goodpractice-1.1.0/goodpractice/inst/doc/custom_checks.html | 58 goodpractice-1.1.0/goodpractice/inst/doc/goodpractice.R | 101 - goodpractice-1.1.0/goodpractice/inst/doc/goodpractice.Rmd | 280 ++ goodpractice-1.1.0/goodpractice/inst/doc/goodpractice.html | 943 ++++++++-- goodpractice-1.1.0/goodpractice/man/all_check_groups.Rd |only goodpractice-1.1.0/goodpractice/man/all_checks.Rd | 3 goodpractice-1.1.0/goodpractice/man/checks.Rd | 13 goodpractice-1.1.0/goodpractice/man/checks_by_group.Rd |only goodpractice-1.1.0/goodpractice/man/customization.Rd | 4 goodpractice-1.1.0/goodpractice/man/default_checks.Rd |only goodpractice-1.1.0/goodpractice/man/describe_check.Rd |only goodpractice-1.1.0/goodpractice/man/describe_check_groups.Rd |only goodpractice-1.1.0/goodpractice/man/export_json.Rd | 10 goodpractice-1.1.0/goodpractice/man/failed_checks.Rd | 11 goodpractice-1.1.0/goodpractice/man/failed_positions.Rd | 5 goodpractice-1.1.0/goodpractice/man/goodpractice-package.Rd | 16 goodpractice-1.1.0/goodpractice/man/gp.Rd | 70 goodpractice-1.1.0/goodpractice/man/print.goodPractice.Rd | 5 goodpractice-1.1.0/goodpractice/man/results.Rd | 15 goodpractice-1.1.0/goodpractice/man/tidyverse_checks.Rd |only goodpractice-1.1.0/goodpractice/tests/testthat/_snaps/describe-check.md |only goodpractice-1.1.0/goodpractice/tests/testthat/_snaps/print.md | 63 goodpractice-1.1.0/goodpractice/tests/testthat/bad2/R/attach.R | 8 goodpractice-1.1.0/goodpractice/tests/testthat/bad2/tests |only goodpractice-1.1.0/goodpractice/tests/testthat/bad_data_load |only goodpractice-1.1.0/goodpractice/tests/testthat/bad_export_order |only goodpractice-1.1.0/goodpractice/tests/testthat/bad_missing |only goodpractice-1.1.0/goodpractice/tests/testthat/bad_print |only goodpractice-1.1.0/goodpractice/tests/testthat/bad_r_ext |only goodpractice-1.1.0/goodpractice/tests/testthat/bad_rd |only goodpractice-1.1.0/goodpractice/tests/testthat/bad_roxygen |only goodpractice-1.1.0/goodpractice/tests/testthat/bad_spelling |only goodpractice-1.1.0/goodpractice/tests/testthat/bad_tidyverse |only goodpractice-1.1.0/goodpractice/tests/testthat/bad_vignettes |only goodpractice-1.1.0/goodpractice/tests/testthat/good/inst |only goodpractice-1.1.0/goodpractice/tests/testthat/good/man/func1.Rd | 7 goodpractice-1.1.0/goodpractice/tests/testthat/good_print |only goodpractice-1.1.0/goodpractice/tests/testthat/good_tidyverse |only goodpractice-1.1.0/goodpractice/tests/testthat/no_roxygen |only goodpractice-1.1.0/goodpractice/tests/testthat/setup.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-api.R | 64 goodpractice-1.1.0/goodpractice/tests/testthat/test-avoided-packages.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-check-selection.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-complexity.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-coverage.R | 32 goodpractice-1.1.0/goodpractice/tests/testthat/test-custom.R | 8 goodpractice-1.1.0/goodpractice/tests/testthat/test-cyclocomp.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-describe-check.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-description.R | 278 ++ goodpractice-1.1.0/goodpractice/tests/testthat/test-documentation.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-duplicate-docs.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-exclude-path.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-gp.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-integrity.R | 4 goodpractice-1.1.0/goodpractice/tests/testthat/test-lintr.R | 110 - goodpractice-1.1.0/goodpractice/tests/testthat/test-namespace.R | 50 goodpractice-1.1.0/goodpractice/tests/testthat/test-on-exit.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-prep-expressions.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-print-return.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-print.R | 134 + goodpractice-1.1.0/goodpractice/tests/testthat/test-r-file-extension.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-rcmdcheck-checks.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-rcmdcheck.R | 4 goodpractice-1.1.0/goodpractice/tests/testthat/test-rd-checks.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-revdep.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-roxygen2.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-rstudio-markers.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-spelling.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-tidyverse.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-treesitter.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-urlchecker.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-utils.R |only goodpractice-1.1.0/goodpractice/tests/testthat/test-vignette.R |only goodpractice-1.1.0/goodpractice/vignettes/custom_checks.Rmd | 4 goodpractice-1.1.0/goodpractice/vignettes/goodpractice.Rmd | 280 ++ 134 files changed, 4421 insertions(+), 855 deletions(-)
Title: Publication-Ready Forest Plots with 'ggplot2'
Description: Transform model coefficients into flexible forest
plots using 'ggplot2'. Provides helpers to standardize
coefficient data from a range of modelling workflows and render
publication-ready forest plots with a consistent interface.
Author: Carson Richardson [aut, cre, cph]
Maintainer: Carson Richardson <carson.richardson@outlook.com>
Diff between ggforestplotR versions 0.2.1 dated 2026-05-29 and 0.2.2 dated 2026-06-05
ggforestplotR-0.2.1/ggforestplotR/tests/testthat/Rplots.pdf |only ggforestplotR-0.2.2/ggforestplotR/DESCRIPTION | 6 ggforestplotR-0.2.2/ggforestplotR/MD5 | 20 ggforestplotR-0.2.2/ggforestplotR/NAMESPACE | 1 ggforestplotR-0.2.2/ggforestplotR/NEWS.md | 9 ggforestplotR-0.2.2/ggforestplotR/R/as_forest_data.R | 34 + ggforestplotR-0.2.2/ggforestplotR/R/ggforestplot.R | 4 ggforestplotR-0.2.2/ggforestplotR/R/ggplot_add_scales.R |only ggforestplotR-0.2.2/ggforestplotR/R/utils.R | 203 ++++++---- ggforestplotR-0.2.2/ggforestplotR/README.md | 176 ++++---- ggforestplotR-0.2.2/ggforestplotR/man/ggforestplot.Rd | 2 ggforestplotR-0.2.2/ggforestplotR/tests/testthat/test-ggforestplot.R | 64 ++- 12 files changed, 339 insertions(+), 180 deletions(-)
Title: Clustering with Compositional Data
Description: Cluster analysis with compositional data using the alpha--transformation. Relevant papers include: Tsagris M. and Kontemeniotis N. (2025). Lobachevskii Journal of Mathematics <doi:10.1134/S1995080225613700>. Tsagris M.T., Preston S. and Wood A.T.A. (2011), <doi:10.48550/arXiv.1106.1451>. Garcia-Escudero Luis A., Gordaliza Alfonso, Matran Carlos, Mayo-Iscar Agustin. (2008), <doi:10.1214/07-AOS515>.
Author: Michail Tsagris [aut, cre],
Nikolaos Kontemeniotis [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between CompositionalClust versions 1.2 dated 2025-11-03 and 1.3 dated 2026-06-05
DESCRIPTION | 14 +++++++------- MD5 | 16 ++++++++-------- NAMESPACE | 4 +--- man/CompositionalClust-package.Rd | 8 +++++--- man/alfa.cikmeans.Rd | 4 +++- man/alfa.kmeans.Rd | 4 +++- man/alfa.mix.norm.Rd | 4 +++- man/bic.alfamixnorm.Rd | 4 +++- man/clust.plot.Rd | 4 +++- 9 files changed, 36 insertions(+), 26 deletions(-)
More information about CompositionalClust at CRAN
Permanent link
Title: Call R from R
Description: It is sometimes useful to perform a computation in a separate
R process, without affecting the current R process at all. This
packages does exactly that.
Author: Gabor Csardi [aut, cre, cph] ,
Winston Chang [aut],
Posit Software, PBC [cph, fnd] ,
Ascent Digital Services [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between callr versions 3.7.6 dated 2024-03-25 and 3.8.0 dated 2026-06-05
DESCRIPTION | 24 - LICENSE | 4 MD5 | 161 ++++---- NAMESPACE | 2 NEWS.md | 34 + R/aaa-rstudio-detect.R | 79 ++- R/callr-package.R | 3 R/check.R | 90 ++-- R/error.R | 56 +- R/eval-bg.R | 48 +- R/eval.R | 63 ++- R/hook.R | 145 +++++-- R/load-client.R | 47 +- R/options.R | 11 R/package.R | 37 + R/presets.R | 61 ++- R/processx-forward.R | 1 R/r-process.R | 66 ++- R/r-session.R | 549 ++++++++++++++++++--------- R/rcmd-bg.R | 24 - R/rcmd-process.R | 40 +- R/rcmd.R | 57 ++ R/result.R | 23 - R/rscript.R | 92 +++- R/run.R | 48 +- R/script.R | 171 +++++--- R/setup.R | 270 +++++++++---- R/standalone-errors.R | 430 ++++++++++++++------- R/test-helpers.R | 13 R/utils.R | 55 ++ R/x-client.R | 1 README.md | 43 +- inst/WORDLIST | 24 + man/callr-package.Rd | 125 +++--- man/r.Rd | 36 + man/r_bg.Rd | 45 +- man/r_copycat.Rd | 11 man/r_process.Rd | 228 ++++++----- man/r_session.Rd | 575 +++++++++++++++-------------- man/r_session_options.Rd | 5 man/r_vanilla.Rd | 13 man/rcmd.Rd | 13 man/rcmd_bg.Rd | 11 man/rcmd_copycat.Rd | 11 man/rcmd_process.Rd | 207 +++++----- man/reexports.Rd | 2 man/rscript.Rd | 5 man/rscript_process.Rd | 202 +++++----- tests/testthat/_snaps/error.md | 59 ++ tests/testthat/_snaps/eval.md |only tests/testthat/_snaps/load-client.md |only tests/testthat/_snaps/options.md |only tests/testthat/_snaps/r-bg.md |only tests/testthat/_snaps/r-session.md |only tests/testthat/fixtures/csomag/R/libpath.R | 1 tests/testthat/fixtures/script.R | 1 tests/testthat/helper-mock.R |only tests/testthat/helper.R | 80 ++-- tests/testthat/test-archs.R | 36 + tests/testthat/test-bugs.R | 1 tests/testthat/test-callback.R | 2 tests/testthat/test-clean-subprocess.R | 19 tests/testthat/test-error.R | 32 + tests/testthat/test-eval.R | 52 +- tests/testthat/test-function-env.R | 32 + tests/testthat/test-hook.R | 3 tests/testthat/test-libpath.R | 115 ++++- tests/testthat/test-load-client.R | 22 - tests/testthat/test-messages.R | 13 tests/testthat/test-options.R | 23 - tests/testthat/test-otel.R |only tests/testthat/test-package.R | 1 tests/testthat/test-presets.R | 5 tests/testthat/test-quit.R | 12 tests/testthat/test-r-bg.R | 23 - tests/testthat/test-r-process.R | 1 tests/testthat/test-r-session-messages.R | 31 + tests/testthat/test-r-session.R | 108 +++-- tests/testthat/test-rcmd-bg.R | 1 tests/testthat/test-rcmd-process.R | 2 tests/testthat/test-rcmd.R | 13 tests/testthat/test-rscript.R | 99 ++++ tests/testthat/test-spelling.R | 4 tests/testthat/test-timeout.R | 1 tests/testthat/test-utils.R | 92 +++- 85 files changed, 3332 insertions(+), 1813 deletions(-)
Title: Agentic Item Generation, Review, and Analysis
Description: Provides tools for validating, generating, reviewing, reporting,
and visualising assessment item generation workflows. The package supports
tabular item-bank templates, item-bank validation, 'Python'-backed agentic
generation workflows, multimodal diagram generation, quality summaries, and
'HTML' reporting. External artificial intelligence services and related
'API' calls require user-supplied credentials and are not called during
package checks. The workflow is informed by automatic item generation
methods described by Gierl and Haladyna (2013, ISBN:9780415897518) and
evidence-centered assessment design described by Mislevy et al. (2003)
<doi:10.1002/j.2333-8504.2003.tb01908.x>.
Author: Moses O. Omopekunola [aut, cre]
Maintainer: Moses O. Omopekunola <omopekunola.m@hse.ru>
Diff between AIGRA versions 0.1.1 dated 2026-06-03 and 0.1.2 dated 2026-06-05
DESCRIPTION | 6 +-- MD5 | 17 +++++---- NAMESPACE | 2 + R/aigra-user-api.R |only man/aigra_backend_help.Rd |only man/aigra_generate_items.Rd | 74 +++++++++++++++++++++--------------------- man/aigra_print_summary.Rd | 8 ---- man/aigra_print_validation.Rd | 10 ----- man/aigra_python_info.Rd | 4 -- man/aigra_set_api_keys.Rd |only man/aigra_write_admin_html.Rd | 20 ----------- 11 files changed, 52 insertions(+), 89 deletions(-)
Title: Embedding and Clustering with Alignment for Spatial Omics
Datasets
Description: An efficient data integration method is provided for multiple spatial transcriptomics data with non-cluster-relevant effects such as the complex batch effects. It unifies spatial factor analysis simultaneously with spatial clustering and embedding alignment, requiring only partially shared cell/domain clusters across datasets. More details can be referred to Wei Liu, et al. (2023) <doi:10.1038/s41467-023-35947-w>.
Author: Wei Liu [aut, cre],
Yi Yang [aut],
Jin Liu [aut]
Maintainer: Wei Liu <liuweideng@gmail.com>
Diff between PRECAST versions 1.8 dated 2025-12-15 and 1.9 dated 2026-06-05
PRECAST-1.8/PRECAST/man/sp_means_Rcpp.Rd |only PRECAST-1.8/PRECAST/man/sp_sums_Rcpp.Rd |only PRECAST-1.9/PRECAST/DESCRIPTION | 14 PRECAST-1.9/PRECAST/MD5 | 30 - PRECAST-1.9/PRECAST/NAMESPACE | 2 PRECAST-1.9/PRECAST/R/main.R | 46 ++ PRECAST-1.9/PRECAST/README.md | 5 PRECAST-1.9/PRECAST/build/vignette.rds |binary PRECAST-1.9/PRECAST/inst/doc/PRECAST.BreastCancer.R | 288 ++++++++--------- PRECAST-1.9/PRECAST/inst/doc/PRECAST.BreastCancer.html | 23 - PRECAST-1.9/PRECAST/inst/doc/PRECAST.DLPFC.R | 136 ++++---- PRECAST-1.9/PRECAST/inst/doc/PRECAST.DLPFC.html | 23 - PRECAST-1.9/PRECAST/inst/doc/PRECAST.DLPFC4.R | 272 ++++++++-------- PRECAST-1.9/PRECAST/inst/doc/PRECAST.DLPFC4.html | 23 - PRECAST-1.9/PRECAST/inst/doc/PRECAST.Simu.R | 258 +++++++-------- PRECAST-1.9/PRECAST/inst/doc/PRECAST.Simu.html | 172 ++++------ PRECAST-1.9/PRECAST/inst/doc/PRECAST.html | 3 17 files changed, 668 insertions(+), 627 deletions(-)
Title: p-Value Aggregation Methods
Description: Contains functionality for performing the following methods of p-value aggregation: Fisher's method [Fisher, RA (1932, ISBN: 9780028447308)], the Lancaster method (weighted Fisher's method) [Lancaster, HO (1961, <doi:10.1111/j.1467-842X.1961.tb00058.x>)], and Sidak correction [Sidak, Z (1967, <doi:10.1080/01621459.1967.10482935>)]. Please cite Yi et al., the manuscript corresponding to this package [Yi, L et al., (2017), <doi:10.1101/190199>].
Author: Lynn Yi [aut],
Lior Pachter [aut],
Elise Maigne [cre]
Maintainer: Elise Maigne <elise.maigne@inrae.fr>
Diff between aggregation versions 1.0.1 dated 2018-01-25 and 1.0.2 dated 2026-06-05
DESCRIPTION | 28 +++++++++++++++++++++------- MD5 | 9 +++++---- NAMESPACE | 6 ++++-- NEWS.md |only R/fisher.R | 1 + R/lancaster.R | 1 + 6 files changed, 32 insertions(+), 13 deletions(-)
Title: Make Data Based on Different Geographies Comparable
Description: Several functions to allow comparisons of data across different geographies, in particular for Canadian census data from different censuses.
Author: Jens von Bergmann [aut, cre]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between tongfen versions 0.3.6 dated 2025-05-01 and 0.3.7 dated 2026-06-05
DESCRIPTION | 11 +- MD5 | 28 ++++--- NEWS.md | 6 + R/helpers.R | 90 ++++++++++++++++++----- R/tongfen.R | 146 +++++++++++++++++++++++--------------- README.md | 10 +- build/stage23.rdb |binary build/vignette.rds |binary inst/doc/polling_districts.html | 15 ++- inst/doc/tongfen-ca-estimate.html | 7 + inst/doc/tongfen.html | 13 +-- inst/doc/tongfen_ca.html | 13 +-- inst/doc/tongfen_us.html | 7 + tests |only 14 files changed, 223 insertions(+), 123 deletions(-)
Title: Fitting Semi-Parametric Generalized log-Gamma Regression Models
Description: Set of tools to fit a linear multiple or semi-parametric regression
models with the possibility of non-informative random right or left censoring.
Under this setup, the localization parameter of the response variable distribution is modeled by using linear multiple regression
or semi-parametric functions, whose non-parametric components may be approximated
by natural cubic spline or P-splines. The supported distribution for the model error is a generalized log-gamma distribution which includes
the generalized extreme value and standard normal distributions as important special cases. Inference is based on likelihood, penalized likelihood and bootstrap methods.
Lastly, some numerical and graphical devices for diagnostic of the fitted models are offered.
Author: Carlos Alberto Cardozo Delgado [aut, cre, cph] ,
Gilberto Paula [aut],
Luis Vanegas [aut]
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between sglg versions 0.2.6 dated 2026-01-14 and 0.2.7 dated 2026-06-05
sglg-0.2.6/sglg/R/plot.npc.R |only sglg-0.2.7/sglg/DESCRIPTION | 6 +- sglg-0.2.7/sglg/MD5 | 12 ++-- sglg-0.2.7/sglg/R/influence.sglg.R | 9 +-- sglg-0.2.7/sglg/R/plotnpc.R |only sglg-0.2.7/sglg/R/response_scheme.R | 9 +-- sglg-0.2.7/sglg/R/summary.sglg.R | 10 +-- sglg-0.2.7/sglg/man/plotnpc.Rd | 101 ++++++++++++++++++------------------ 8 files changed, 75 insertions(+), 72 deletions(-)
Title: Kernel-Based Regularized Least Squares
Description: Implements Kernel-based Regularized Least Squares (KRLS), a
machine learning method to fit multidimensional functions y = f(x) for
regression and classification problems without relying on linearity or
additivity assumptions. KRLS finds the best fitting function by
minimizing the squared loss of a Tikhonov regularization problem,
using Gaussian kernels as radial basis functions. For further details
see Hainmueller and Hazlett (2014, <doi:10.1093/pan/mpt019>).
Author: Jens Hainmueller [aut, cre],
Chad Hazlett [aut]
Maintainer: Jens Hainmueller <jhain@stanford.edu>
Diff between KRLS versions 1.1-0 dated 2026-04-30 and 1.7-0 dated 2026-06-05
DESCRIPTION | 12 MD5 | 59 ++-- NAMESPACE | 18 + NEWS.md | 351 +++++++++++++++++++++++++ R/autoplot.R |only R/bandwidth.R |only R/broom_methods.R |only R/categorical.R |only R/fdskrls.r | 103 +++---- R/get_landmarks.R |only R/krls.R | 441 ++++++++++++++++++++++++++------ R/lambdasearch.r | 81 ++++- R/nystrom.R |only R/predict.krls.R | 149 ++++++---- R/solveforc.R | 4 R/summary.krls.R | 177 ++++++++---- build |only inst/doc |only man/b_maxvarK.Rd |only man/fdskrls.Rd | 2 man/gausskernel.Rd | 2 man/get_landmarks.Rd |only man/krls.Rd | 163 ++++++++++- man/lambdasearch.Rd | 13 man/looloss.Rd | 2 man/plot.krls.Rd | 2 man/predict.krls.Rd | 2 man/solveforc.Rd | 2 man/summary.krls.Rd | 2 tests/testthat/test-autoplot.R |only tests/testthat/test-broom-methods.R |only tests/testthat/test-formula-interface.R |only tests/testthat/test-krls.R | 56 +++- tests/testthat/test-nystrom.R |only vignettes |only 35 files changed, 1318 insertions(+), 323 deletions(-)
Title: Tools for Exploring Animal Movement Data
Description: Provides tools for exploring animal tracking data, from raw
telemetry points to summaries, interactive maps, and home range
estimates. It is designed to be beginner-friendly and requires minimal
data wrangling.
Author: Taylor Craft [aut, cre]
Maintainer: Taylor Craft <taylor.craft.mail@gmail.com>
Diff between ezTrack versions 0.1.0 dated 2025-09-16 and 0.1.1 dated 2026-06-05
ezTrack-0.1.0/ezTrack/R/globals.R |only ezTrack-0.1.1/ezTrack/DESCRIPTION | 42 - ezTrack-0.1.1/ezTrack/MD5 | 44 - ezTrack-0.1.1/ezTrack/R/ez_home_range.R | 89 ++- ezTrack-0.1.1/ezTrack/R/ez_map.R | 18 ezTrack-0.1.1/ezTrack/R/ez_summary.R | 48 + ezTrack-0.1.1/ezTrack/R/ez_track.R | 306 ++++++++++- ezTrack-0.1.1/ezTrack/R/godwit_tracks_gambia.R |only ezTrack-0.1.1/ezTrack/R/utils-pipe.R | 10 ezTrack-0.1.1/ezTrack/R/utils.R |only ezTrack-0.1.1/ezTrack/README.md | 10 ezTrack-0.1.1/ezTrack/build/vignette.rds |binary ezTrack-0.1.1/ezTrack/data/godwit_tracks_gambia.rda |only ezTrack-0.1.1/ezTrack/inst/doc/getting-started.R | 8 ezTrack-0.1.1/ezTrack/inst/doc/getting-started.Rmd | 11 ezTrack-0.1.1/ezTrack/inst/doc/getting-started.html | 370 +++++--------- ezTrack-0.1.1/ezTrack/man/ez_summary.Rd | 17 ezTrack-0.1.1/ezTrack/man/ez_track.Rd | 7 ezTrack-0.1.1/ezTrack/man/godwit_tracks_gambia.Rd |only ezTrack-0.1.1/ezTrack/man/pipe.Rd | 13 ezTrack-0.1.1/ezTrack/tests/testthat.R |only ezTrack-0.1.1/ezTrack/tests/testthat/test-ez_home_range.R | 2 ezTrack-0.1.1/ezTrack/tests/testthat/test-ez_map.R | 19 ezTrack-0.1.1/ezTrack/tests/testthat/test-ez_summary.R | 8 ezTrack-0.1.1/ezTrack/tests/testthat/test-ez_track.R | 82 +++ ezTrack-0.1.1/ezTrack/vignettes/getting-started.Rmd | 11 26 files changed, 762 insertions(+), 353 deletions(-)
Title: Event Prediction
Description: Predicts enrollment and events at the design or analysis stage
using specified enrollment and time-to-event models through
simulations.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between eventPred versions 0.2.9 dated 2025-06-10 and 0.3.0 dated 2026-06-05
DESCRIPTION | 16 MD5 | 56 NEWS.md | 674 +++++----- R/eventPred-package.R | 378 ++--- R/fitDropout.R | 31 R/fitEnrollment.R | 20 R/fitEvent.R | 28 R/getPrediction.R | 616 ++++++--- R/predictEnrollment.R | 17 R/predictEvent.R | 71 - R/summarizeObserved.R | 18 README.md |only build/vignette.rds |binary inst/doc/event_prediction_after_enrollment_completion.html | 5 inst/doc/event_prediction_at_the_design_stage.html | 5 inst/doc/event_prediction_before_enrollment_completion.html | 5 inst/doc/event_prediction_incorporating_covariates.html | 5 inst/doc/event_prediction_incorporating_prior_information.html | 5 man/figures |only man/fitDropout.Rd | 9 man/fitEnrollment.Rd | 12 man/fitEvent.Rd | 9 man/getPrediction.Rd | 56 man/predictEnrollment.Rd | 10 man/predictEvent.Rd | 19 man/summarizeObserved.Rd | 12 tests/testthat/test-fitDropout.R | 16 tests/testthat/test-fitEvent.R | 16 tests/testthat/test-getPrediction.R | 208 +++ tests/testthat/test-predictEvent.R | 32 30 files changed, 1525 insertions(+), 824 deletions(-)
Title: Congruence Class Models for Networks
Description: Provides an implementation of Congruence Class Models (CCMs) for
generating networks. For additional details on CCMs see Goyal, Blitzstein,
and De Gruttola (2014) <doi:10.1017/nws.2014.2> and
Goyal, De Gruttola, Martin, Rennert, and Onnela <doi:10.48550/arXiv.2603.02467>.
'ccmnet' facilitates sampling networks based on specific topological properties
and attribute mixing patterns using a Markov Chain Monte Carlo framework.
The implementation builds upon code from the 'ergm' package;
see Handcock, Hunter, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i01>.
Author: Ravi Goyal [aut, cre],
Statnet Development Team [ctb, cph]
Maintainer: Ravi Goyal <ravi.j.goyal@gmail.com>
Diff between CCMnet versions 1.1.0 dated 2026-05-25 and 1.1.1 dated 2026-06-05
DESCRIPTION | 6 MD5 | 20 - R/CCMnet_Sample.R | 6 R/documentation.R | 22 - inst/doc/CCMnet_introduction.R | 2 inst/doc/CCMnet_introduction.Rmd | 39 + inst/doc/CCMnet_introduction.html | 754 ++++++++++++++++++-------------------- man/ccm_distributions.Rd | 4 man/ccm_properties.Rd | 18 man/sample_ccm.Rd | 6 vignettes/CCMnet_introduction.Rmd | 39 + 11 files changed, 453 insertions(+), 463 deletions(-)
Title: Bayesian Vector Heterogeneous Autoregressive Modeling
Description: Tools to model and forecast multivariate time series
including Bayesian Vector heterogeneous autoregressive (VHAR) model
by Kim & Baek (2023) (<doi:10.1080/00949655.2023.2281644>).
'bvhar' can model Vector Autoregressive (VAR), VHAR, Bayesian VAR (BVAR), and Bayesian VHAR (BVHAR) models.
Author: Young Geun Kim [aut, cre, cph] ,
Changryong Baek [ctb]
Maintainer: Young Geun Kim <ygeunkimstat@gmail.com>
Diff between bvhar versions 2.4.0 dated 2026-02-01 and 2.4.1 dated 2026-06-05
bvhar-2.4.0/bvhar/vignettes/forecasting.R |only bvhar-2.4.0/bvhar/vignettes/forecasting.html |only bvhar-2.4.1/bvhar/DESCRIPTION | 6 bvhar-2.4.1/bvhar/MD5 | 107 +++-- bvhar-2.4.1/bvhar/NAMESPACE | 2 bvhar-2.4.1/bvhar/NEWS.md | 22 + bvhar-2.4.1/bvhar/R/RcppExports.R | 24 + bvhar-2.4.1/bvhar/R/forecast.R | 4 bvhar-2.4.1/bvhar/R/irf.R | 187 +++++++-- bvhar-2.4.1/bvhar/R/misc-r.R | 83 +++- bvhar-2.4.1/bvhar/R/plot.R | 6 bvhar-2.4.1/bvhar/R/summary-forecast.R | 139 +++---- bvhar-2.4.1/bvhar/README.md | 2 bvhar-2.4.1/bvhar/inst/doc/bvhar.html | 120 +++--- bvhar-2.4.1/bvhar/inst/doc/shrinkage.html | 170 +++++--- bvhar-2.4.1/bvhar/inst/doc/stochastic-volatility.html | 129 +++--- bvhar-2.4.1/bvhar/inst/include/bvhar/base | 2 bvhar-2.4.1/bvhar/inst/include/bvhar/mniw | 1 bvhar-2.4.1/bvhar/inst/include/bvhar/ols | 1 bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/bayes.h | 7 bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/dfm/config.h | 2 bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/forecaster.h | 62 ++- bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/irf.h |only bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/misc/coef_helper.h | 14 bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/misc/dl_helper.h | 56 +- bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/misc/gdp_helper.h | 8 bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/misc/helper.h | 3 bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/misc/hs_helper.h | 18 bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/misc/minn_helper.h | 2 bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/misc/ng_helper.h | 44 +- bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/misc/ssvs_helper.h | 15 bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/mniw/forecaster.h | 6 bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/mniw/irf.h |only bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/mniw/minnesota.h | 17 bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/mniw/spillover.h | 8 bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/shrinkage/config.h | 89 ++++ bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/shrinkage/shrinkage.h | 114 ++++-- bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/triangular/config.h | 189 +++++++--- bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/triangular/forecaster.h | 66 ++- bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/triangular/irf.h |only bvhar-2.4.1/bvhar/inst/include/bvhar/src/bayes/triangular/triangular.h | 98 +++++ bvhar-2.4.1/bvhar/inst/include/bvhar/src/core/common.h | 98 ++++- bvhar-2.4.1/bvhar/inst/include/bvhar/src/core/commoncpp.h |only bvhar-2.4.1/bvhar/inst/include/bvhar/src/core/commondefs.h | 83 +++- bvhar-2.4.1/bvhar/inst/include/bvhar/src/core/eigen.h | 7 bvhar-2.4.1/bvhar/inst/include/bvhar/src/core/eigen_plugins.h |only bvhar-2.4.1/bvhar/inst/include/bvhar/src/core/forecaster.h | 21 - bvhar-2.4.1/bvhar/inst/include/bvhar/src/core/irf.h |only bvhar-2.4.1/bvhar/inst/include/bvhar/src/math/design.h | 61 +++ bvhar-2.4.1/bvhar/inst/include/bvhar/src/math/random.h | 29 + bvhar-2.4.1/bvhar/inst/include/bvhar/src/math/rng.h |only bvhar-2.4.1/bvhar/inst/include/bvhar/src/ols/irf.h |only bvhar-2.4.1/bvhar/inst/include/bvhar/triangular | 1 bvhar-2.4.1/bvhar/inst/tests |only bvhar-2.4.1/bvhar/man/irf.Rd | 62 ++- bvhar-2.4.1/bvhar/src/RcppExports.cpp | 68 +++ bvhar-2.4.1/bvhar/src/ols.cpp | 14 bvhar-2.4.1/bvhar/src/triangular.cpp | 18 58 files changed, 1658 insertions(+), 627 deletions(-)
Title: Easy and Accessible Bayesian Measurement Models Using 'brms'
Description: Fit computational and measurement models using full Bayesian
inference. The package provides a simple and accessible interface by
translating complex domain-specific models into 'brms' syntax, a
powerful and flexible framework for fitting Bayesian regression models
using 'Stan'. The package is designed so that users can easily apply
state-of-the-art models in various research fields, and so that
researchers can use it as a new model development framework.
References: Frischkorn and Popov (2025) <doi:10.3758/s13428-025-02643-0>.
Author: Vencislav Popov [aut, cre, cph] ,
Gidon T. Frischkorn [aut, cph] ,
Chenyu Li [ctb],
Paul-Christian Buerkner [cph]
Maintainer: Vencislav Popov <vencislav.popov@gmail.com>
Diff between bmm versions 1.3.0 dated 2026-03-30 and 1.3.1 dated 2026-06-05
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ R/model_ddm.R | 17 ++++++----------- inst/stan_chunks/cswald_helper_functions.stan | 2 +- man/bmm-package.Rd | 2 +- man/figures/README-unnamed-chunk-4-1.png |binary 7 files changed, 26 insertions(+), 23 deletions(-)
Title: Tipping Point Analysis for Bayesian Dynamic Borrowing
Description: Tipping point analysis for clinical trials that employ
Bayesian dynamic borrowing via robust meta-analytic predictive (MAP)
priors. Further functions facilitate expert elicitation of a primary
weight of the informative component of the robust MAP prior and
computation of operating characteristics. Intended use is the
planning, analysis and interpretation of extrapolation studies in
pediatric drug development, but applicability is generally wider.
Author: Christian Stock [aut, cre] ,
Morten Dreher [aut],
Lars Andersen [aut],
Emma Torrini [ctb],
Boehringer Ingelheim Pharma GmbH & Co. KG [cph, fnd]
Maintainer: Christian Stock <christian.stock@boehringer-ingelheim.com>
Diff between tipmap versions 1.0.0 dated 2026-05-27 and 1.0.1 dated 2026-06-05
DESCRIPTION | 6 +-- MD5 | 10 ++--- NEWS.md | 4 ++ R/get_cum_probs_1exp.R | 69 ++++++++++++++++++++++++--------------- inst/doc/expert_elicitation.html | 4 +- inst/doc/introduction.html | 4 +- 6 files changed, 59 insertions(+), 38 deletions(-)
Title: REST API Client for the 'PGS' Catalog
Description: Programmatic access to the 'PGS' Catalog.
This package provides easy access to 'PGS' Catalog data by
accessing the REST API <https://www.pgscatalog.org/rest/>.
Author: Ramiro Magno [aut, cre] ,
Isabel Duarte [aut] ,
Ana-Teresa Maia [aut] ,
Rise Health [cph, fnd],
Pattern Institute [cph, fnd] ,
Acuity Analytics [cph, fnd]
Maintainer: Ramiro Magno <ramiro.morgado@acuityanalytics.com>
This is a re-admission after prior archival of version 0.1.10 dated 2025-05-31
Diff between quincunx versions 0.1.10 dated 2025-05-31 and 0.2.0 dated 2026-06-05
DESCRIPTION | 30 MD5 | 60 NEWS.md | 5 R/class-scores.R | 2 R/class-trait_categories.R | 2 R/class-traits.R | 24 R/get_scores.R | 2 R/get_traits.R | 2 README.md | 30 build/partial.rdb |binary man/bind.Rd | 8 man/figures/logo.svg |10029 +++++++++++++++++++------------------- man/get_scores.Rd | 2 man/get_trait_categories.Rd | 2 man/get_traits.Rd | 2 man/n.Rd | 2 man/open_in_dbsnp.Rd | 2 man/open_in_pgs_catalog.Rd | 2 man/open_in_pubmed.Rd | 2 man/scores-class.Rd | 2 man/setop.Rd | 14 man/subset-cohorts.Rd | 2 man/subset-performance_metrics.Rd | 2 man/subset-publications.Rd | 2 man/subset-releases.Rd | 2 man/subset-sample_sets.Rd | 2 man/subset-scores.Rd | 2 man/subset-trait_categories.Rd | 2 man/subset-traits.Rd | 2 man/trait_categories-class.Rd | 2 man/traits-class.Rd | 24 31 files changed, 5209 insertions(+), 5057 deletions(-)
Title: Prepare American Psychological Association Journal Articles with
R Markdown
Description: Tools to create dynamic, submission-ready manuscripts, which
conform to American Psychological Association manuscript guidelines. We
provide R Markdown document formats for manuscripts (PDF and Word) and
revision letters (PDF). Helper functions facilitate reporting statistical
analyses or create publication-ready tables and plots.
Author: Frederik Aust [aut, cre] ,
Marius Barth [aut] ,
Birk Diedenhofen [ctb],
Christoph Stahl [ctb],
Joseph V. Casillas [ctb],
Rudolf Siegel [ctb]
Maintainer: Frederik Aust <frederik.aust@uni-koeln.de>
Diff between papaja versions 0.1.4 dated 2025-09-26 and 0.1.5 dated 2026-06-05
DESCRIPTION | 8 LICENSE | 2 MD5 | 44 R/add_custom_effect_sizes.R | 1 R/apa_print_emm_lsm.R | 5 R/deprecated_defunct.R | 4 R/r_refs.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.md | 21 inst/doc/extending_apa_print.html | 12 inst/doc/papaja.pdf |binary inst/rmarkdown/templates/revision_letter/resources/revision_letter.tex | 37 man/render_appendix.Rd | 2 tests/testthat/test_apa_print_anova.R | 27 tests/testthat/test_apa_print_htest.R | 24 tests/testthat/test_apa_print_merMod.R | 2 tests/testthat/test_apa_table.R | 22 tests/testthat/test_apa_table.log | 696 ++----- tests/testthat/test_apa_table.tex | 981 ---------- vignettes/papaja_files |only vignettes/references.json | 4 22 files changed, 417 insertions(+), 1477 deletions(-)
Title: Computation of the Multivariate Marine Recovery Index
Description: Computation of the multivariate marine recovery index, including functions for data visualization and ecological diagnostics of marine ecosystems. The computational details are described in the original publication. Reference: Chauvel, N., Grall, J., Thiébaut, E., Houbin, C., Pezy, J.-P., 2026. A general-purpose multivariate marine recovery index (MUMARINEX) for quantifying the influence of human activities on benthic habitat ecological status. Ecological Indicators 188, 115002.
Author: Nathan Chauvel [aut, cre]
Maintainer: Nathan Chauvel <nathan.chauvel@outlook.fr>
Diff between mumarinex versions 1.0 dated 2025-10-14 and 2.0 dated 2026-06-05
DESCRIPTION | 16 - MD5 | 38 +-- NAMESPACE | 2 NEWS.md | 22 + R/Simulated_data.R | 32 +- R/decomplot.R | 31 +- R/diagnostic_tool.R | 153 +++++++----- R/mum_GUI.R |only R/mumarinex.R | 47 ++- README.md |only build/vignette.rds |binary data/Simulated_data.rda |binary inst/doc/Using-the-MUMARINEX-Package.R | 16 - inst/doc/Using-the-MUMARINEX-Package.Rmd | 39 +-- inst/doc/Using-the-MUMARINEX-Package.html | 358 +++++++++++++++--------------- man/Simulated_data.Rd | 32 +- man/decomplot.Rd | 9 man/diagnostic_tool.Rd | 10 man/figures |only man/mum_GUI.Rd |only man/mumarinex.Rd | 18 - vignettes/Using-the-MUMARINEX-Package.Rmd | 39 +-- 22 files changed, 468 insertions(+), 394 deletions(-)
Title: Mixture-of-Experts Wishart Models for Covariance Data
Description: Methods for maximum likelihood and Bayesian estimation for the Wishart mixture model and the mixture-of-experts Wishart (MoE-Wishart) model. The package provides four inference algorithms for these models, each implemented using the expectation–maximization (EM) algorithm for maximum likelihood estimation and a fully Bayesian approach via Gibbs-within-Metropolis–Hastings sampling.
Author: The Tien Mai [aut],
Zhi Zhao [aut, cre]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between moewishart versions 1.1 dated 2026-04-21 and 1.2 dated 2026-06-05
DESCRIPTION | 8 - MD5 | 20 +-- NEWS.md | 5 README.md | 328 ++++++++++++++++++---------------------------------- build/vignette.rds |binary data/CTRP.rda |binary inst/doc/Intro.R | 2 inst/doc/Intro.Rmd | 13 +- inst/doc/Intro.html | 13 +- man/figures |only vignettes/Intro.Rmd | 13 +- 11 files changed, 164 insertions(+), 238 deletions(-)
Title: Interactive Volcano Plot
Description: Generate interactive volcano plots for exploring gene expression data. Built with 'ggplot2', the plots are rendered interactive using 'ggiraph', enabling users to hover over points to display detailed information or click to trigger custom actions.
Author: Guangchuang Yu [aut, cre, cph]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ivolcano versions 0.0.5 dated 2026-02-14 and 0.0.6 dated 2026-06-05
DESCRIPTION | 8 MD5 | 20 +- NEWS.md | 7 R/ivolcano.R | 55 +++++- build/vignette.rds |binary inst/doc/ivolcano.R | 13 + inst/doc/ivolcano.html | 407 ++++++++++++++++++++++++++++++++++++++++--------- inst/doc/ivolcano.qmd | 16 + man/ivolcano.Rd | 8 man/ivolcano_point.Rd | 10 + vignettes/ivolcano.qmd | 16 + 11 files changed, 452 insertions(+), 108 deletions(-)
Title: Cross-Validation for Model Selection
Description: Cross-validate one or multiple regression and classification models
and get relevant evaluation metrics in a tidy format. Validate the
best model on a test set and compare it to a baseline evaluation.
Alternatively, evaluate predictions from an external model. Currently
supports regression and classification (binary and multiclass).
Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R.,
& Wambugu M. (2019, ISBN: 9781838550134).
Author: Ludvig Renbo Olsen [aut, cre] ,
Hugh Benjamin Zachariae [aut],
Indrajeet Patil [ctb] ,
Daniel Luedecke [ctb]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between cvms versions 2.0.0 dated 2025-11-10 and 2.0.1 dated 2026-06-05
DESCRIPTION | 16 - MD5 | 110 +++---- NEWS.md | 8 R/confusion_matrix.R | 4 R/get_nested_model_coefficients.R | 148 +++++++++- R/helpers.R | 9 build/stage23.rdb |binary inst/doc/Creating_a_confusion_matrix.html | 29 + inst/doc/available_metrics.html | 4 inst/doc/cross_validating_custom_functions.html | 31 +- inst/doc/evaluate_by_id.html | 11 inst/doc/picking_the_number_of_folds_for_cross-validation.html | 17 - man/baseline.Rd | 8 man/baseline_binomial.Rd | 8 man/baseline_gaussian.Rd | 8 man/baseline_multinomial.Rd | 8 man/binomial_metrics.Rd | 12 man/confusion_matrix.Rd | 12 man/cross_validate.Rd | 8 man/cross_validate_fn.Rd | 8 man/dynamic_font_color_settings.Rd | 14 man/evaluate.Rd | 12 man/evaluate_residuals.Rd | 12 man/font.Rd | 14 man/gaussian_metrics.Rd | 12 man/model_functions.Rd | 8 man/multinomial_metrics.Rd | 12 man/plot_confusion_matrix.Rd | 14 man/plot_metric_density.Rd | 14 man/plot_probabilities.Rd | 14 man/plot_probabilities_ecdf.Rd | 14 man/predict_functions.Rd | 8 man/preprocess_functions.Rd | 8 man/sum_tile_settings.Rd | 14 man/update_hyperparameters.Rd | 8 man/validate.Rd | 8 man/validate_fn.Rd | 8 tests/testthat/test_cross_validate.R | 29 + tests/testthat/test_validate.R | 25 + tests/testthat/test_validate_fn.R | 70 ++++ vignettes/man/figures/vignette_conf_mat-unnamed-chunk-12-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-13-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-14-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-15-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-16-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-16-2.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-17-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-18-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-5-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-6-1.png |binary vignettes/man/figures/vignette_conf_mat-unnamed-chunk-9-1.png |binary vignettes/man/figures/vignette_cv_custom_fn-unnamed-chunk-35-1.png |binary vignettes/man/figures/vignette_pick_k-unnamed-chunk-28-1.png |binary vignettes/man/figures/vignette_pick_k-unnamed-chunk-3-1.png |binary vignettes/man/figures/vignette_pick_k-unnamed-chunk-32-1.png |binary vignettes/man/figures/vignette_pick_k-unnamed-chunk-5-1.png |binary 56 files changed, 517 insertions(+), 260 deletions(-)
Title: Visualizing Generalized Canonical Discriminant and Canonical
Correlation Analysis
Description: Functions for computing and visualizing
generalized canonical discriminant analyses and canonical correlation analysis
for a multivariate linear model.
Traditional canonical discriminant analysis is restricted to a one-way 'MANOVA'
design and is equivalent to canonical correlation analysis between a set of quantitative
response variables and a set of dummy variables coded from the factor variable.
The 'candisc' package generalizes this to higher-way 'MANOVA' designs
for all factors in a multivariate linear model,
computing canonical scores and vectors for each term. The graphic functions provide low-rank (1D, 2D, 3D)
visualizations of terms in an 'mlm' via the 'plot.candisc' and 'heplot.candisc' methods. Related plots are
now provided for canonical correlation analysis when all predictors are quantitative. Methods for
linear discriminant analysis are now included.
Author: Michael Friendly [aut, cre] ,
John Fox [aut]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between candisc versions 1.1.0 dated 2025-11-25 and 1.1.1 dated 2026-06-05
DESCRIPTION | 10 +++++----- MD5 | 42 ++++++++++++++++++++++-------------------- NAMESPACE | 4 ++++ NEWS.md | 8 ++++++++ R/cancor.R | 3 +-- R/candisc-package.R | 4 ++-- R/candisc.R | 3 +-- R/candiscList.R | 3 +-- R/confusion.R |only R/data.R | 12 +++++------- R/heplot.cancor.R | 25 ++++++++++++++++++++++++- R/heplot.candisc.R | 16 ++++++++++++---- R/heplot3d.cancor.R | 19 ++++++++++++++++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/diabetes.html | 30 +++++++++++++++--------------- man/HSB.Rd | 2 +- man/cereal.Rd | 7 ++----- man/confusion.Rd |only man/heplot.cancor.Rd | 11 +++++++++++ man/painters2.Rd | 2 +- man/plot_discrim.Rd | 4 ++-- man/vectors.Rd | 4 ++-- 23 files changed, 137 insertions(+), 72 deletions(-)
Title: Bayesian Sample Size and Precision Considerations for Risk
Prediction Models
Description: Performs Bayesian sample size, precision, and value-of-information analysis for external validation of existing multi-variable prediction models using the approach proposed by Sadatsafavi and colleagues (2026) <doi:10.1002/sim.70389>.
Author: Mohsen Sadatsafavi [aut, cre] ,
Anna Luo [ctb]
Maintainer: Mohsen Sadatsafavi <mohsen.sadatsafavi@ubc.ca>
Diff between bayespmtools versions 0.0.1 dated 2026-03-29 and 0.0.2 dated 2026-06-05
DESCRIPTION | 15 MD5 | 114 - NAMESPACE | 82 - NEWS.md | 40 R/RM.R | 128 - R/bayespmtools-package.R | 34 R/core.R | 2779 +++++++++++++++++----------------- R/evidence.R | 674 ++++---- R/isaric.R | 44 R/modelrevisionvoi.R | 154 - R/valprec.R | 902 +++++------ R/valsamp.R | 878 +++++----- README.md | 114 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/bayespmtools_tutorial.R | 304 +-- inst/doc/bayespmtools_tutorial.Rmd | 528 +++--- inst/doc/bayespmtools_tutorial.html | 1433 ++++++++--------- inst/doc/getting_started.R | 112 - inst/doc/getting_started.Rmd | 298 +-- inst/doc/getting_started.html | 989 ++++++------ man/bayespmtools-package.Rd | 53 man/bpm_valprec.Rd | 176 +- man/bpm_valsamp.Rd | 222 +- man/calc_ciw_2s.Rd | 64 man/calc_ciw_mc.Rd | 66 man/calc_ciw_sample.Rd | 60 man/calc_cstat.Rd | 42 man/calc_riley_vars.Rd | 52 man/calc_se_sp.Rd | 60 man/find_n_mean.Rd | 50 man/find_n_quantile.Rd | 46 man/infer_cal_int_from_mean.Rd | 50 man/infer_cal_int_from_oe.Rd | 50 man/infer_correlation.Rd | 54 man/inv_mean_quantile.Rd | 46 man/inv_moments.Rd | 44 man/isaric.Rd | 64 man/moments.Rd | 38 man/plot_cal_distance.Rd | 74 man/plot_cal_instability.Rd | 74 man/process_evidence.Rd | 106 - man/rbnorm.Rd | 58 man/riley_samp.Rd | 66 tests |only vignettes/bayespmtools_tutorial.Rmd | 528 +++--- vignettes/getting_started.Rmd | 298 +-- vignettes/precomputed/prec_result.rds |binary vignettes/precomputed/samp_result.rds |binary vignettes/precomputed/voi_result.rds |binary vignettes/references.bib | 62 51 files changed, 6240 insertions(+), 5885 deletions(-)