Title: Visualization of 'exametrika' Output Using 'ggplot2'
Description: Provides 'ggplot2'-based visualization functions for output objects
from the 'exametrika' package, which implements test data engineering methods
described in Shojima (2022, ISBN:978-981-16-9547-1). Supports a wide range of
psychometric models including Item Response Theory, Latent Class Analysis,
Latent Rank Analysis, Biclustering (binary, ordinal, and nominal),
Bayesian Network Models, and related network models. All plot functions
return 'ggplot2' objects that can be further customized by the user.
Author: Koji Kosugi [aut, cre] ,
Daichi Kamimura [aut]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Diff between ggExametrika versions 1.1.2 dated 2026-08-21 and 1.2.0 dated 2026-09-24
DESCRIPTION | 8 +- MD5 | 14 ++- NEWS.md | 39 +++++++++ R/arraytoLDPSR.R | 141 ++++++++++++++++++++++++++++++------ R/palette.R | 19 ++++ man/dot-extract_legend.Rd |only man/dot-gg_exametrika_sequential.Rd |only man/plotArray_gg.Rd | 12 ++- tests/testthat/test-plotArray_gg.R | 36 +++++++++ 9 files changed, 232 insertions(+), 37 deletions(-)
Title: Patterned Fills for 'ggplot2' and 'grid' Graphics
Description: Provides geometric patterns to replace solid color fills in
statistical graphics. These patterns ensure figures remain distinguishable
when viewed by colorblind readers or when printed in black and white. The
included patterns can be customized in terms of scale, rotation, color,
fill, line type, and line width. Compatible with the 'ggplot2' package as
well as 'grid' graphics.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between fillpattern versions 1.0.3 dated 2026-02-13 and 1.0.4 dated 2026-09-24
DESCRIPTION | 8 +++---- MD5 | 32 +++++++++++++++---------------- NEWS.md | 8 +++++++ R/fill_pattern.r | 10 ++++++--- R/makeContent.r | 9 ++++---- R/scale_fill_pattern.r | 6 ++--- README.md | 8 +++---- man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/fill_pattern.Rd | 10 ++++++--- man/reexports.Rd | 2 - man/scale_fill_pattern.Rd | 7 ++++-- tests/testthat/test-fill_pattern.r | 3 +- tests/testthat/test-makeContent.r | 28 ++++++++++++++++++++++++++- tests/testthat/test-scale_fill_pattern.r | 9 +++++++- 17 files changed, 97 insertions(+), 43 deletions(-)
Title: Parse StatCan PUMF Files
Description: Facilitate working with Statistics Canada (StatCan) Public Use
Microdata Files (PUMF). Enables downloading of available PUMF data,
parsing of metadata from command files or other sources to infer the layout
structure, variable labels and value labels as well as missing data values,
and returns a connection to a 'DuckDB' database with the labelled data.
Data and documentation come from Statistics Canada's Public Use Microdata
Files <https://www.statcan.gc.ca/en/microdata/pumf>, distributed under the
Statistics Canada Open Licence
<https://www.statcan.gc.ca/en/terms-conditions/open-licence>.
Author: Jens von Bergmann [aut, cre]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between canpumf versions 0.5.2 dated 2026-07-03 and 0.6.0 dated 2026-09-24
DESCRIPTION | 10 MD5 | 146 + NAMESPACE | 6 NEWS.md | 65 R/api.R | 204 +- R/borealis.R |only R/cache_mgmt.R | 72 R/helpers.R | 5 R/lfs_hist.R |only R/lfs_pipeline.R | 346 ---- R/lfs_timeline.R |only R/longitudinal.R |only R/metadata_parsers.R | 1090 ++++++++++++-- R/pdf_repair.R |only R/pipeline.R | 354 ++++ R/pumf.R | 7 R/pumf_collection.R | 113 + R/pumf_documentation.R | 37 R/registry.R | 583 +++++-- R/statcan_catalogue.R | 45 README.md | 96 + inst/doc/Census.html | 6 inst/doc/LFS.R | 75 inst/doc/LFS.Rmd | 117 + inst/doc/LFS.html | 206 ++ inst/doc/onboarding.Rmd | 4 inst/doc/onboarding.html | 6 inst/doc/pipeline.R | 15 inst/doc/pipeline.Rmd | 107 + inst/doc/pipeline.html | 128 + inst/doc/submodules.R | 2 inst/doc/submodules.Rmd | 4 inst/doc/submodules.html | 14 inst/doc/working_with_canpumf.R | 17 inst/doc/working_with_canpumf.Rmd | 29 inst/doc/working_with_canpumf.html | 294 ++- inst/extdata/lfs_hist |only inst/extdata/lfs_timeline |only man/dot-pumf_apply_pdf_repairs.Rd |only man/dot-pumf_pdf_choose_candidates.Rd |only man/dot-pumf_pdf_position_agreement.Rd |only man/dot-pumf_pdf_resolve_duplicate_blocks.Rd |only man/dot-pumf_pdf_select_blocks.Rd |only man/dot-pumf_validate_pdf_freqs.Rd |only man/get_lfs_timeline.Rd |only man/get_pumf.Rd | 32 man/list_borealis_pumf_catalogue.Rd |only man/list_borealis_pumf_files.Rd |only man/list_canpumf_collection.Rd | 6 man/list_statcan_pumf_catalogue.Rd | 3 man/parse_pdf_freq_codebook.Rd |only man/parse_sas_odesi.Rd |only man/pumf_freq_validation.Rd |only man/pumf_label_repairs.Rd |only man/pumf_parse_metadata.Rd | 3 man/pumf_registry_entry.Rd | 40 man/pumf_resolve_version.Rd | 26 tests/TEST_COVERAGE.md | 37 tests/fixtures/spss_mono/continuations.sps |only tests/testthat/helper-overrides.R | 18 tests/testthat/override_verification.csv | 2039 ++++++++++++--------------- tests/testthat/test-api.R | 63 tests/testthat/test-borealis.R |only tests/testthat/test-lfs-timeline.R |only tests/testthat/test-longitudinal.R |only tests/testthat/test-merge-metadata.R | 42 tests/testthat/test-metadata-io.R | 3 tests/testthat/test-parse-sas-cards.R | 122 + tests/testthat/test-parse-spss-mono.R | 107 + tests/testthat/test-parse-spss-split.R | 2 tests/testthat/test-pdf-repair.R |only tests/testthat/test-pipeline-census.R | 41 tests/testthat/test-pipeline-chss.R |only tests/testthat/test-pipeline-gss.R | 309 ++++ tests/testthat/test-pipeline-pals.R |only tests/testthat/test-pipeline-sgvp.R | 39 tests/testthat/test-pipeline-shs.R | 23 tests/testthat/test-pipeline-stage3.R | 228 +++ tests/testthat/test-registry.R | 32 tests/testthat/test-sentinel-labels.R |only tests/testthat/test-statcan-adapter.R | 14 vignettes/LFS.Rmd | 117 + vignettes/onboarding.Rmd | 4 vignettes/pipeline.Rmd | 107 + vignettes/submodules.Rmd | 4 vignettes/working_with_canpumf.Rmd | 29 86 files changed, 5568 insertions(+), 2125 deletions(-)
Title: Backward Joint Model for the Dynamic Prediction of Both
Time-to-Event and Longitudinal Outcomes
Description: Provides tools to fit joint models of multivariate longitudinal data and time-to-event data for dynamic prediction. It allows the joint prediction of both future time-to-event outcomes and future longitudinal outcomes conditional on survival. The models accommodate irregularly measured longitudinal data and competing risks outcomes. The use of the backward joint model enables fast and efficient computation, especially for applications with large sample sizes and many longitudinal variables.
Author: Wenhao Li [aut, cre],
Liang Li [aut]
Maintainer: Wenhao Li <wenhaoli.jlu@gmail.com>
Diff between BJM versions 0.1.0 dated 2026-07-04 and 0.2.0 dated 2026-09-24
BJM-0.1.0/BJM/R/pbc2.R |only BJM-0.1.0/BJM/data/pbc2.rda |only BJM-0.1.0/BJM/man/pbc2.Rd |only BJM-0.1.0/BJM/man/print_BJM.Rd |only BJM-0.2.0/BJM/DESCRIPTION | 13 BJM-0.2.0/BJM/MD5 | 141 +++-- BJM-0.2.0/BJM/NAMESPACE | 11 BJM-0.2.0/BJM/NEWS.md |only BJM-0.2.0/BJM/R/checkBandcountConvergence.R |only BJM-0.2.0/BJM/R/cmtPlot.R | 65 +- BJM-0.2.0/BJM/R/conditionalDT.R | 20 BJM-0.2.0/BJM/R/conditionalDesign.R |only BJM-0.2.0/BJM/R/conditionalYDT.R | 284 +++++------ BJM-0.2.0/BJM/R/conditionalYDTBio.R | 224 ++++---- BJM-0.2.0/BJM/R/conditionalYT.R | 156 +----- BJM-0.2.0/BJM/R/conditionalYTBio.R | 120 +--- BJM-0.2.0/BJM/R/dynamicPrediction.R | 246 +++++---- BJM-0.2.0/BJM/R/dynamicPredictionBio.R | 262 ++++++---- BJM-0.2.0/BJM/R/dynamicPredictionShared.R |only BJM-0.2.0/BJM/R/imports.R | 3 BJM-0.2.0/BJM/R/longitudinalSub.R | 161 ++++-- BJM-0.2.0/BJM/R/longitudinalSubVar.R | 2 BJM-0.2.0/BJM/R/marginalT.R | 18 BJM-0.2.0/BJM/R/methods.R | 170 ++---- BJM-0.2.0/BJM/R/pbc3.R | 4 BJM-0.2.0/BJM/R/predictPlot.R | 359 +++++++++----- BJM-0.2.0/BJM/R/processVariance.R | 14 BJM-0.2.0/BJM/R/riskPlot.R | 226 ++++++-- BJM-0.2.0/BJM/R/survivalSub.R | 56 +- BJM-0.2.0/BJM/R/survivalTrans.R |only BJM-0.2.0/BJM/R/validateInputs.R |only BJM-0.2.0/BJM/README.md |only BJM-0.2.0/BJM/build |only BJM-0.2.0/BJM/inst |only BJM-0.2.0/BJM/man/apply_survival_trans.Rd |only BJM-0.2.0/BJM/man/assert_all_formulas.Rd |only BJM-0.2.0/BJM/man/assert_bandcount.Rd |only BJM-0.2.0/BJM/man/assert_class.Rd |only BJM-0.2.0/BJM/man/assert_data_frame.Rd |only BJM-0.2.0/BJM/man/assert_data_list.Rd |only BJM-0.2.0/BJM/man/assert_index.Rd |only BJM-0.2.0/BJM/man/assert_positive_integer.Rd |only BJM-0.2.0/BJM/man/assert_scalar_numeric.Rd |only BJM-0.2.0/BJM/man/assert_string.Rd |only BJM-0.2.0/BJM/man/assert_survival_trans.Rd |only BJM-0.2.0/BJM/man/assert_vars_in_data.Rd |only BJM-0.2.0/BJM/man/auto_tune_bandcount.Rd |only BJM-0.2.0/BJM/man/bandcount_auto_start.Rd |only BJM-0.2.0/BJM/man/build_conditional_design.Rd |only BJM-0.2.0/BJM/man/build_longitudinal_matrix_bio.Rd |only BJM-0.2.0/BJM/man/checkBandcountConvergence.Rd |only BJM-0.2.0/BJM/man/clamp_risk_prob.Rd |only BJM-0.2.0/BJM/man/cmtPlot.Rd | 15 BJM-0.2.0/BJM/man/conditionalDT.Rd | 8 BJM-0.2.0/BJM/man/conditionalYDT.Rd | 18 BJM-0.2.0/BJM/man/conditionalYDTBio.Rd | 18 BJM-0.2.0/BJM/man/conditionalYT.Rd | 18 BJM-0.2.0/BJM/man/conditionalYTBio.Rd | 18 BJM-0.2.0/BJM/man/dynamicPrediction.Rd | 119 ++-- BJM-0.2.0/BJM/man/dynamicPredictionBio.Rd | 118 ++-- BJM-0.2.0/BJM/man/longitudinalSub.Rd | 77 ++- BJM-0.2.0/BJM/man/longitudinalSubVar.Rd | 4 BJM-0.2.0/BJM/man/marginalT.Rd | 8 BJM-0.2.0/BJM/man/max_relative_diff.Rd |only BJM-0.2.0/BJM/man/pbc3.Rd | 4 BJM-0.2.0/BJM/man/predictPlot.Rd | 117 +++- BJM-0.2.0/BJM/man/prepare_infinity_grid.Rd |only BJM-0.2.0/BJM/man/print.dynamicPrediction.BJM.Rd | 14 BJM-0.2.0/BJM/man/print.dynamicPredictionBio.BJM.Rd | 16 BJM-0.2.0/BJM/man/print.longitudinalSub.BJM.Rd | 3 BJM-0.2.0/BJM/man/print.survivalSub.BJM.Rd | 13 BJM-0.2.0/BJM/man/printBJM.Rd |only BJM-0.2.0/BJM/man/process_variance.Rd | 2 BJM-0.2.0/BJM/man/riskPlot.Rd | 71 ++ BJM-0.2.0/BJM/man/select_patient_longitudinal_data.Rd |only BJM-0.2.0/BJM/man/select_patient_longitudinal_data_bio.Rd |only BJM-0.2.0/BJM/man/subset_at_risk.Rd |only BJM-0.2.0/BJM/man/summary.dynamicPrediction.BJM.Rd | 4 BJM-0.2.0/BJM/man/summary.dynamicPredictionBio.BJM.Rd | 4 BJM-0.2.0/BJM/man/summary.survivalSub.BJM.Rd | 10 BJM-0.2.0/BJM/man/survivalSub.Rd | 27 - BJM-0.2.0/BJM/man/survivalTrans.Rd |only BJM-0.2.0/BJM/man/warn_unsafe_formula_terms.Rd |only BJM-0.2.0/BJM/tests |only BJM-0.2.0/BJM/vignettes |only 85 files changed, 1865 insertions(+), 1396 deletions(-)
Title: Test Data Engineering
Description: Implements comprehensive test data engineering methods as described in
Shojima (2022, ISBN:978-9811699856). Provides statistical techniques for
engineering and processing test data: Classical Test Theory (CTT) with
reliability coefficients for continuous ability assessment; Item Response
Theory (IRT) including Rasch, 2PL, and 3PL models with item/test information
functions; Latent Class Analysis (LCA) for nominal clustering; Latent Rank
Analysis (LRA) for ordinal clustering with automatic determination of cluster
numbers; Biclustering methods including infinite relational models for
simultaneous clustering of examinees and items without predefined cluster
numbers; and Bayesian Network Models (BNM) for visualizing inter-item
dependencies. Features local dependence analysis through LRA and biclustering,
parameter estimation, dimensionality assessment, and network structure
visualization for educational, psychological, and social science research.
Author: Koji Kosugi [aut, cre]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Diff between exametrika versions 2.0.0 dated 2026-08-20 and 2.1.0 dated 2026-09-24
DESCRIPTION | 6 MD5 | 77 +++++---- NAMESPACE | 3 NEWS.md | 142 +++++++++++++++++ R/00_EMclus.R | 96 +++++++----- R/00_exametrikaPlot.R | 2 R/00_labels.R |only R/00_plot_biclustering.R | 153 ++++++++++++------- R/00_release_bullets.R |only R/01_dataFormat.R | 15 + R/04C_ParameterEstimation.R | 1 R/05_LCA.R | 3 R/06_LRA.R | 18 +- R/07_Biclustering.R | 1 R/07_IRM.R | 1 R/08A_BNM.R | 1 R/09_LDLRA.R | 1 R/10_LDB.R | 1 R/11_BINET.R | 1 R/12_LRA_ordinal.R | 1 R/13_LRA_rated.R | 1 R/14_grm.R | 1 R/15_Biclustering_nominal.R | 1 R/16_Biclustering_ordinal.R | 6 R/17_Biclustering_nominal_IRM.R | 1 R/18_Biclustering_ordinal_IRM.R | 1 R/19_Biclustering_rated.R | 1 R/20_Biclustering_rated_IRM.R | 1 R/RcppExports.R | 4 inst/WORDLIST | 269 ++++++++++++++++++++++------------ inst/doc/biclustering.html | 6 inst/doc/getting-started.html | 4 inst/doc/guide-ja.html | 4 inst/doc/irt.html | 14 - inst/doc/network-models.html | 4 man/LRA.Rd | 17 +- src/RcppExports.cpp | 21 ++ src/som_core.cpp |only tests/testthat/test-dataFormat-edge.R | 22 +- tests/testthat/test-grm.R | 5 tests/testthat/test-labels.R |only tests/testthat/test-lra-som.R |only 42 files changed, 639 insertions(+), 267 deletions(-)
Title: Search Algorithms and Loss Functions for Bayesian Clustering
Description: The SALSO algorithm is an efficient randomized greedy search method to find a point estimate for a random partition based on a loss function and posterior Monte Carlo samples. The algorithm is implemented for many loss functions, including the Binder loss and a generalization of the variation of information loss, both of which allow for unequal weights on the two types of clustering mistakes. Efficient implementations are also provided for Monte Carlo estimation of the posterior expected loss of a given clustering estimate. See Dahl, Johnson, Müller (2022) <doi:10.1080/10618600.2022.2069779>.
Author: David B. Dahl [aut, cre] ,
Devin J. Johnson [aut] ,
Peter Mueller [aut],
Andres Felipe Barrientos [aut],
Garritt Page [aut],
David Dunson [aut],
Authors of the dependency Rust crates [ctb]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.3.78 dated 2026-04-16 and 0.3.79 dated 2026-09-24
DESCRIPTION | 10 - MD5 | 16 - NAMESPACE | 52 +++--- NEWS | 3 man/salso-package.Rd | 1 man/salso.Rd | 2 src/rust/Cargo.lock | 397 +++++-------------------------------------------- src/rust/vendor.tar.xz |binary tools/configure.R | 22 ++ 9 files changed, 112 insertions(+), 391 deletions(-)
Title: Feature Allocation Neighborhood Greedy Search Algorithm
Description: A neighborhood-based, greedy search algorithm is performed to estimate a feature allocation by minimizing the expected loss based on posterior samples from the feature allocation distribution. The method is described in Dahl, Johnson, and Andros (2023) "Comparison and Bayesian Estimation of Feature Allocations" <doi:10.1080/10618600.2023.2204136>.
Author: David B. Dahl [aut, cre] ,
R. Jacob Andros [aut] ,
Devin J. Johnson [aut] ,
Authors of the dependency Rust crates [ctb]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between fangs versions 0.2.22 dated 2026-03-07 and 0.2.25 dated 2026-09-24
fangs-0.2.22/fangs/src/abort_shim.c |only fangs-0.2.22/fangs/src/shim.c |only fangs-0.2.25/fangs/DESCRIPTION | 10 fangs-0.2.25/fangs/LICENSE | 2 fangs-0.2.25/fangs/MD5 | 48 ++-- fangs-0.2.25/fangs/NEWS | 14 + fangs-0.2.25/fangs/build/partial.rdb |binary fangs-0.2.25/fangs/src/Makevars.win.in | 12 - fangs-0.2.25/fangs/src/r_init_shim.c |only fangs-0.2.25/fangs/src/rust/Cargo.lock | 182 ++++++---------- fangs-0.2.25/fangs/src/rust/Cargo.toml | 10 fangs-0.2.25/fangs/src/rust/build.rs | 12 - fangs-0.2.25/fangs/src/rust/lapjv-rust/Cargo.lock | 169 ++++---------- fangs-0.2.25/fangs/src/rust/lapjv-rust/Cargo.toml | 5 fangs-0.2.25/fangs/src/rust/rbindings/Cargo.lock | 2 fangs-0.2.25/fangs/src/rust/rbindings/Cargo.toml | 5 fangs-0.2.25/fangs/src/rust/rbindings/src/lib.rs | 226 +++++++++----------- fangs-0.2.25/fangs/src/rust/roxido/Cargo.lock | 6 fangs-0.2.25/fangs/src/rust/roxido/Cargo.toml | 5 fangs-0.2.25/fangs/src/rust/roxido/src/lib.rs | 155 +++++++------ fangs-0.2.25/fangs/src/rust/roxido_macro/Cargo.lock | 2 fangs-0.2.25/fangs/src/rust/roxido_macro/Cargo.toml | 5 fangs-0.2.25/fangs/src/rust/roxido_macro/src/lib.rs | 4 fangs-0.2.25/fangs/src/rust/src/lib.rs | 34 --- fangs-0.2.25/fangs/src/rust/vendor.tar.xz |binary fangs-0.2.25/fangs/src/shims.c |only fangs-0.2.25/fangs/tools/configure.R | 195 +++++++++++++---- 27 files changed, 542 insertions(+), 561 deletions(-)
Title: Simulating Realistic Gene Expression and Clinical Data
Description: The Ultimate Microrray Prediction, Reality and Inference
Engine (UMPIRE) is a package to facilitate the simulation of realistic
microarray data sets with links to associated outcomes. See Zhang and
Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>. Version 2.0 adds the
ability to simulate realistic mixed-typed clinical data.
Author: Kevin R. Coombes [aut, cre],
Jiexin Zhang [aut],
Caitlin E. Coombes [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Umpire versions 2.0.11 dated 2025-02-04 and 2.0.12 dated 2026-09-24
DESCRIPTION | 10 - MD5 | 12 - build/vignette.rds |binary inst/doc/Umpire.R | 2 inst/doc/Umpire.pdf |binary inst/doc/Umpire2.html | 362 ++++++++++++++++++++------------------------------ inst/doc/surv.html | 294 ++++++++++++++++++++-------------------- 7 files changed, 306 insertions(+), 374 deletions(-)
Title: Systematic Identification of Bimodally Expressed Genes Using
RNAseq Data
Description: Provides models to identify bimodally expressed genes from
RNAseq data based on the Bimodality Index. SIBERG models the RNAseq data in
the finite mixture modeling framework and incorporates mechanisms for
dealing with RNAseq normalization. Three types of mixture models are
implemented, namely, the mixture of log normal, negative binomial, or
generalized Poisson distribution. See Tong et al. (2013)
<doi:10.1093/bioinformatics/bts713>.
Author: Pan Tong [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between SIBERG versions 2.0.4 dated 2025-04-08 and 2.0.5 dated 2026-09-24
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- build/vignette.rds |binary data/simDat.rda |binary inst/doc/SIBER.R | 2 -- inst/doc/SIBER.pdf |binary 6 files changed, 10 insertions(+), 12 deletions(-)
Title: Extending the Newman Studentized Range Statistic to
Transcriptomics
Description: Extends the classical Newman studentized range statistic
in various ways that can be applied to genome-scale transcriptomic
or other expression data.
Author: Zachary B. Abrams [aut],
Greg Gershkowitz [aut],
Anoushka Joglekar [aut],
Chao Liu [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between NewmanOmics versions 1.1.3 dated 2026-07-06 and 1.1.4 dated 2026-09-24
DESCRIPTION | 10 - MD5 | 22 +-- NAMESPACE | 38 ++--- build/vignette.rds |binary data/GSE6631.rda |binary data/LungPair.rda |binary inst/doc/newmanomics.html | 291 ++++++++++++++++++++----------------------- man/01-NewmanPaired-class.Rd | 130 +++++++++---------- man/02-pairedStat.Rd | 226 ++++++++++++++++----------------- man/03-MixOf3Beta-class.Rd | 156 +++++++++++------------ man/04-fitMix3.Rd | 168 ++++++++++++------------ man/05-bankStat.Rd | 64 ++++----- 12 files changed, 548 insertions(+), 557 deletions(-)
Title: Using Needleman-Wunsch to Match Sample Names
Description: The Needleman-Wunsch global alignment algorithm can be
used to find approximate matches between sample names in different
data sets. See Wang et al. (2010) <doi:10.4137/CIN.S5613>.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between NameNeedle versions 1.2.10 dated 2026-03-14 and 1.2.11 dated 2026-09-24
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- build/vignette.rds |binary data/cellLineNames.RData |binary inst/doc/blastName.R | 2 -- inst/doc/blastName.pdf |binary 6 files changed, 10 insertions(+), 12 deletions(-)
Title: Integrating Multiple Modalities of High Throughput Assays Using
Item Response Theory
Description: Provides a systematic framework for
integrating multiple modalities of assays profiled on the same set of
samples. The goal is to identify genes that are altered in cancer
either marginally or consistently across different assays. The
heterogeneity among different platforms and different samples are
automatically adjusted so that the overall alteration magnitude can
be accurately inferred. See Tong and Coombes (2012)
<doi:10.1093/bioinformatics/bts561>.
Author: Pan Tong [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between integIRTy versions 1.0.8 dated 2025-04-08 and 1.0.9 dated 2026-09-24
DESCRIPTION | 10 - MD5 | 50 +++--- NAMESPACE | 44 ++--- R/Ii.R | 38 ++-- R/Pi.R | 32 ++-- R/calculatePermutedScoreByGeneSampling.R | 24 +-- R/computeAbility.R | 64 ++++---- R/fitOnSinglePlat.R | 70 ++++---- R/intIRTeasyRun.R | 166 ++++++++++----------- R/intIRTeasyRunFromRaw.R | 196 ++++++++++++------------- R/simulateBinaryResponseMat.R | 38 ++-- R/thetaEst.R | 110 +++++++------- build/vignette.rds |binary data/OV.rda |binary inst/doc/integIRTy.R | 2 inst/doc/integIRTy.pdf |binary man/calculatePermutedScoreByGeneSampling.Rd | 184 +++++++++++------------ man/computeAbility.Rd | 162 ++++++++++---------- man/dichotomize.Rd | 102 ++++++------- man/dichotomizeCN.Rd | 114 +++++++------- man/dichotomizeExpr.Rd | 148 +++++++++---------- man/dichotomizeMethy.Rd | 108 ++++++------- man/fitOnSinglePlat.Rd | 166 ++++++++++----------- man/intIRTeasyRun.Rd | 168 ++++++++++----------- man/intIRTeasyRunFromRaw.Rd | 218 ++++++++++++++-------------- man/simulateBinaryResponseMat.Rd | 136 ++++++++--------- 26 files changed, 1174 insertions(+), 1176 deletions(-)
Title: Classes and Methods for Training and Using Binary Prediction
Models
Description: Defines classes and methods to learn models and use them
to predict binary outcomes. These are generic tools, but we also
include specific examples for many common classifiers.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Modeler versions 3.4.10 dated 2026-08-21 and 3.4.11 dated 2026-09-24
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- inst/doc/Modeler.pdf |binary 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Classes and Methods to Use Genetic Algorithms for Feature
Selection
Description: Defines classes and methods that can be used
to implement genetic algorithms for feature selection. The idea is
that we want to select a fixed number of features to combine into a
linear classifier that can predict a binary outcome, and can use a
genetic algorithm heuristically to select an optimal set of features.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between GenAlgo versions 2.2.1 dated 2025-04-07 and 2.2.2 dated 2026-09-24
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ build/vignette.rds |binary data/gaTourResults.rda |binary data/tourData09.rda |binary inst/doc/genalg.R | 2 -- inst/doc/genalg.pdf |binary 7 files changed, 11 insertions(+), 13 deletions(-)
Title: Classes and Methods for Cross Validation of "Class Prediction"
Algorithms
Description: Defines classes and methods to cross-validate various
binary classification algorithms used for "class prediction"
problems.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between CrossValidate versions 2.3.5 dated 2025-04-07 and 2.3.6 dated 2026-09-24
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/CrossVal.R | 2 -- inst/doc/CrossVal.pdf |binary 5 files changed, 9 insertions(+), 11 deletions(-)
Title: The Bimodality Index
Description: Defines the functions used to compute the
bimodal index as defined by Wang et al. (2009)
<https://pmc.ncbi.nlm.nih.gov/articles/PMC2730180/>,
<doi:10.4137/CIN.S2846>.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between BimodalIndex versions 1.1.11 dated 2025-04-07 and 1.1.13 dated 2026-09-24
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/bim.R | 2 -- inst/doc/bim.pdf |binary 5 files changed, 9 insertions(+), 11 deletions(-)
Title: Imports Recipe and Log Files from Angstrom Engineering Thermal
Evaporator
Description: Imports and parses recipe and log files generated by
Angstrom Engineering thermal evaporation systems. These files
contain time-series measurements and process metadata, including
chamber pressure, source activity, deposition rate, film thickness,
tooling parameters, substrate conditions, and related deposition
variables. The package provides functions to extract, organize, and
summarize process information in a compact format suitable for data
analysis, visualization, and quality control workflows.
Author: Thomas Gredig [aut, cre, cph]
Maintainer: Thomas Gredig <tgredig@csulb.edu>
Diff between angstromATE versions 0.1.3 dated 2024-10-20 and 0.2.3 dated 2026-09-24
DESCRIPTION | 28 ++++++++++------ MD5 | 24 ++++++++------ NAMESPACE | 15 ++++++--- NEWS.md | 12 ++++++- R/ATE.complete.R | 26 +++++++++++++-- R/ATE.import.R | 2 - R/ATE.readRecipe.R |only R/ATE.status.R | 6 +-- README.md | 35 ++++++++++++++++++--- inst/extdata/S1S3_Radak_SCEH_FePcH2Pc_NoHeatV2.rcp |only man/ATE.readRecipe.Rd |only tests/testthat/test-ATEcomplete.R | 2 - tests/testthat/test-Recipe.R |only tests/testthat/test-Status.R | 2 - tests/testthat/test-general.R | 2 - 15 files changed, 114 insertions(+), 40 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor
Analysis-1 (Parafac) model or Parallel Factor Analysis-2 (Parafac2) model fit to
a three-way or four-way data array. See Harshman and Lundy (1994):
<doi:10.1016/0167-9473(94)90132-5>. Classification using principal component
analysis (PCA) fit to a two-way data matrix is also supported. Uses component
weights from one mode of a Parafac, Parafac2, or PCA model as features to tune
parameters for one or more classification methods via a k-fold cross-validation
procedure. Allows for constraints on different tensor modes. Allows for
inclusion of additional features alongside features generated by the component
model. Supports penalized logistic regression, support vector machine, random
forest, feed-forward neural network, regularized discriminant analysis, and
gradient boosting machine. Supports binary and multiclass classification.
Predicts class labels or class probabilities and calculates multiple
classification performanc [...truncated...]
Author: Matthew A. Asisgress [aut, cre]
Maintainer: Matthew A. Asisgress <mattgress@protonmail.ch>
Diff between cpfa versions 1.3.2 dated 2026-08-01 and 1.3.3 dated 2026-09-24
ChangeLog | 20 +++++ DESCRIPTION | 12 +-- MD5 | 28 ++++---- R/cpfa.R | 162 +++++++++++++++++++++++++++--------------------- R/tunecpfa.R | 6 - build/vignette.rds |binary inst/doc/cpfa.pdf |binary man/cpfa.Rd | 20 ++--- man/cpm.Rd | 8 +- man/cpm.all.Rd | 6 - man/plotcpfa.Rd | 39 +++++------ man/predict.tunecpfa.Rd | 6 - man/print.tunecpfa.Rd | 6 - man/simcpfa.Rd | 4 - man/tunecpfa.Rd | 21 +----- 15 files changed, 182 insertions(+), 156 deletions(-)
Title: External Control Borrowing for Rare Disease Trials
Description: Implements causal inference methods for incorporating external
control data into randomized controlled trials (RCTs) with longitudinal
outcomes. Provides an analysis module supporting weighting-based methods
such as inverse probability weighting (IPW) and augmented inverse
probability weighting (AIPW), difference-in-differences (DID), and
synthetic control approaches for borrowing external control information,
as well as a simulation module for generating trial and external control
data, evaluating estimator performance via Monte Carlo studies, and
conducting power analyses for sample size determination. Methods are
based on Zhou et al. (2024) <doi:10.1093/jrsssa/qnae075> and
Zhou et al. (2024) <doi:10.1080/10543406.2024.2330209>.
Author: Lei Shi [aut],
Matt Secrest [cre, aut] ,
Herbert Pang [aut],
Chen Chen [aut],
Jiawen Zhu [aut],
Genentech, Inc. [cph]
Maintainer: Matt Secrest <secrmatt@gmail.com>
Diff between rdborrow versions 0.0.4.0 dated 2026-08-31 and 0.0.4.1 dated 2026-09-24
DESCRIPTION | 20 +++---- MD5 | 67 ++++++++++++------------ NAMESPACE | 3 - NEWS.md | 11 +++ R/did_ec_aipw.R | 15 ++--- R/did_ec_ipw.R | 18 ++---- R/did_ec_or.R | 4 - R/ec_aipw.R | 18 +++--- R/ec_ipw.R | 26 +++------ R/ec_weights.R |only R/method_class.R | 20 +++++-- R/package.R | 3 - R/scm.R | 4 - R/simulate_X_mixture.R | 8 +- inst/doc/OLE_analysis_workflow.Rmd | 4 - inst/doc/OLE_analysis_workflow.html | 24 ++++---- inst/doc/OLE_simulation_workflow.Rmd | 4 - inst/doc/OLE_simulation_workflow.html | 8 +- inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 6 +- inst/doc/primary_analysis_workflow.html | 4 - inst/doc/primary_simulation_workflow.html | 4 - man/did_ec_aipw.Rd | 2 man/did_ec_ipw.Rd | 2 man/did_ec_or.Rd | 2 man/ec_ipw.Rd | 3 - man/scm.Rd | 2 tests/testthat/test-full_pipeline_did_ec_aipw.R | 44 +++++++++++++++ tests/testthat/test-full_pipeline_did_ec_ipw.R | 37 +++++++++++++ tests/testthat/test-full_pipeline_scm.R | 2 tests/testthat/test-method_class.R | 30 ++++++++++ tests/testthat/test-run_analysis.R | 4 - vignettes/OLE_analysis_workflow.Rmd | 4 - vignettes/OLE_simulation_workflow.Rmd | 4 - vignettes/introduction.Rmd | 2 35 files changed, 263 insertions(+), 148 deletions(-)
Title: Data to Illustrate OOMPA Algorithms
Description: This is a data-only package to provide example data for
other packages that are part of the "Object-Oriented Microrray and
Proteomics Analysis" suite of packages. These are described in more
detail at the package URL.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between oompaData versions 3.1.5 dated 2025-04-06 and 3.1.7 dated 2026-09-24
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- data/clinical.info.rda |binary data/expression.data.rda |binary data/gene.info.rda |binary data/lungData.rda |binary 6 files changed, 10 insertions(+), 10 deletions(-)
Title: Community Detection for Evolving Multiplex Networks
Description: Multiplex temporal community detection with customizable interlayer coupling. Runs Louvain or Leiden community detection on each network layer and constructs interlayer ties using Jaccard similarity, overlap coefficient, node-strength weighted variants, or direct node identity links, and also provides a two-stage snapshot-and-match tracker that aligns independently detected per-layer communities across time with the Hungarian assignment algorithm. Supports user-specified layer connectivity via the layer_links argument, enabling adjacent-only temporal coupling that avoids the long-range pooling problem in standard multislice approaches.
Author: Jared Edgerton [aut, cre]
Maintainer: Jared Edgerton <jared.edgerton@gmail.com>
Diff between dynamicmultiplex versions 1.1.0 dated 2026-08-07 and 1.3.1 dated 2026-09-24
DESCRIPTION | 6 MD5 | 44 ++-- NAMESPACE | 2 NEWS.md | 73 +++++++ R/bootstrap_multilayer.R | 43 ++++ R/co_assignment_ci.R | 96 +++++----- R/fit_multilayer_identity_ties.R | 17 + R/fit_multilayer_jaccard.R | 16 + R/fit_multilayer_overlap.R | 16 + R/fit_multilayer_weighted_jaccard.R | 16 + R/fit_multilayer_weighted_overlap.R | 16 + R/multilayer_utils.R | 286 ++++++++++++++++++++++++------- R/partition_stability.R |only inst |only man/bootstrap_multilayer.Rd | 7 man/co_assignment_ci.Rd | 70 +++---- man/community_est.Rd | 10 - man/fit_multilayer_identity_ties.Rd | 17 + man/fit_multilayer_jaccard.Rd | 10 - man/fit_multilayer_overlap.Rd | 10 - man/fit_multilayer_weighted_jaccard.Rd | 10 - man/fit_multilayer_weighted_overlap.Rd | 10 - man/partition_stability.Rd |only tests/testthat/test-audit-verification.R | 16 + 24 files changed, 589 insertions(+), 202 deletions(-)
More information about dynamicmultiplex at CRAN
Permanent link
Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
Description: Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ/NIFTI format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surfa [...truncated...]
Author: Tim Schaefer [aut, cre] ,
Van Essen Lab [cph] .),
Montreal Neurological Institute [cph] .)
Maintainer: Tim Schaefer <ts+code@rcmd.org>
Diff between freesurferformats versions 1.0.2 dated 2026-09-08 and 1.1.0 dated 2026-09-24
DESCRIPTION | 6 MD5 | 571 ++++++++++++-- NAMESPACE | 90 ++ R/cifti.R | 349 ++++++-- R/cifti_parcels.R |only R/dti_tracks_utils.R |only R/fs_tracts.R |only R/nifti2_extensions.R |only R/nifti_common.R | 121 +++ R/nifti_to_mgh.R | 698 +++++++++++------ R/read_analyze.R |only R/read_cifti.R |only R/read_cifti_connectome.R |only R/read_cifti_header.R |only R/read_dti_tcktsf.R | 949 ++++++++++++++++++++++-- R/read_dti_trk.R | 544 +++++++++++-- R/read_dwi_gradients.R |only R/read_fs_annot.R | 2 R/read_fs_curv.R | 12 R/read_fs_surface.R | 96 -- R/read_fs_transform.R | 413 ++++++++++ R/read_fs_volume.R | 30 R/read_nifti1.R | 32 R/read_nifti2.R | 36 R/read_nrrd.R |only R/safety_checks.R | 52 + R/trackvis_affine.R |only R/transforms_common.R |only R/transforms_convert.R |only R/vtk_legacy.R |only R/write_analyze.R |only R/write_cifti.R |only R/write_cifti_axes.R |only R/write_cifti_connectome.R |only R/write_cifti_fs.R |only R/write_dti_tracks.R |only R/write_dwi_gradients.R |only R/write_fs_curv.R | 10 R/write_fs_surface.R | 429 ++++++++++ R/write_fs_transform.R |only R/write_fs_volume.R | 37 R/write_nifti1.R | 124 ++- R/write_nifti2.R | 63 + inst/extdata/analyze |only inst/extdata/cifti |only inst/extdata/nrrd |only inst/extdata/sphere_v42_binary.vtk |only inst/extdata/sphere_v51_binary.vtk |only inst/extdata/tracts_v51_binary.vtk |only man/CIFTI_EXTENSION_CODE.Rd |only man/analyze.dtype.info.Rd |only man/analyze.header.check.Rd |only man/analyze.header.to.vox2ras.Rd |only man/analyze.mat.sidecar.to.vox2ras.Rd |only man/analyze.pair.files.Rd |only man/analyze.read.char.field.Rd |only man/analyze.read.header.internal.Rd |only man/analyze.read.magic.Rd |only man/analyze.write.data.internal.Rd |only man/analyzeheader.for.data.Rd |only man/analyzeheader.template.Rd |only man/apply.affine.to.coords.Rd |only man/as.fs.tracts.Rd |only man/as.list.fs.tracts.Rd |only man/as.tsf.scalars.Rd |only man/axcodes2ornt.Rd |only man/build.mrtrix.header.Rd |only man/build.mrtrix.header.stable.Rd |only man/cifti.annot.list.Rd |only man/cifti.annot.parcels.Rd |only man/cifti.array.with.new.first.dim.Rd |only man/cifti.assign.rows.Rd |only man/cifti.axes.to.maps.Rd |only man/cifti.axis.brain.models.Rd |only man/cifti.axis.for.maps.Rd |only man/cifti.axis.from.template.Rd |only man/cifti.axis.labels.Rd |only man/cifti.axis.named.maps.Rd |only man/cifti.axis.parcels.Rd |only man/cifti.axis.parcels.from.annot.Rd |only man/cifti.axis.scalars.Rd |only man/cifti.axis.series.Rd |only man/cifti.axis.size.Rd |only man/cifti.axis.surface.sizes.Rd |only man/cifti.axis.surfaces.Rd |only man/cifti.brain.model.surface.Rd |only man/cifti.brain.model.volume.Rd |only man/cifti.brainordinate.dim.Rd |only man/cifti.brainordinate.dims.Rd |only man/cifti.check.axes.Rd |only man/cifti.check.data.for.axes.Rd |only man/cifti.check.index.list.Rd |only man/cifti.check.index.selection.Rd |only man/cifti.check.label.table.Rd |only man/cifti.check.object.Rd |only man/cifti.compute.index.ranges.Rd |only man/cifti.connectome.axes.Rd |only man/cifti.data.for.all.vertices.Rd |only man/cifti.data.for.connectome.Rd |only man/cifti.data.for.grayordinates.Rd |only man/cifti.data.object.Rd |only man/cifti.data.per.structure.Rd |only man/cifti.data.structures.Rd |only man/cifti.data.surface.size.Rd |only man/cifti.dense.structure.matrix.Rd |only man/cifti.dim.labels.Rd |only man/cifti.dim.to.front.Rd |only man/cifti.file.looks.like.cifti1.Rd |only man/cifti.file.looks.like.cifti2.Rd |only man/cifti.file.type.for.axes.Rd |only man/cifti.file.type.for.extension.Rd |only man/cifti.file.types.Rd |only man/cifti.grayordinates.Rd |only man/cifti.grayordinates.for.axes.Rd |only man/cifti.grayordinates.for.model.Rd |only man/cifti.header.from.axes.Rd |only man/cifti.header.of.Rd |only man/cifti.index.type.short.Rd |only man/cifti.index.types.Rd |only man/cifti.is.connectome.axis.Rd |only man/cifti.label.table.Rd |only man/cifti.label.table.for.writing.Rd |only man/cifti.map.for.dim.Rd |only man/cifti.map.name.Rd |only man/cifti.map.type.description.Rd |only man/cifti.matrix.dim.sizes.Rd |only man/cifti.merge.axes.Rd |only man/cifti.model.types.Rd |only man/cifti.nifti.header.for.axes.Rd |only man/cifti.other.dim.Rd |only man/cifti.parcel.Rd |only man/cifti.parcels.Rd |only man/cifti.parcels.axis.of.Rd |only man/cifti.parse.attr.Rd |only man/cifti.parse.brain.models.Rd |only man/cifti.parse.child.int.vector.Rd |only man/cifti.parse.child.voxel.indices.Rd |only man/cifti.parse.indices.map.Rd |only man/cifti.parse.int.vector.Rd |only man/cifti.parse.label.table.Rd |only man/cifti.parse.metadata.Rd |only man/cifti.parse.named.maps.Rd |only man/cifti.parse.numeric.vector.Rd |only man/cifti.parse.parcels.Rd |only man/cifti.parse.series.Rd |only man/cifti.parse.surfaces.Rd |only man/cifti.parse.volumes.Rd |only man/cifti.parse.xml.Rd |only man/cifti.prepare.surface.data.Rd |only man/cifti.read.matrix.Rd |only man/cifti.read.rows.Rd |only man/cifti.read.values.Rd |only man/cifti.region.name.without.hemisphere.Rd |only man/cifti.series.info.Rd |only man/cifti.stop.if.cifti.Rd |only man/cifti.stop.if.cifti.name.Rd |only man/cifti.structure.canonical.Rd |only man/cifti.structure.data.Rd |only man/cifti.structure.data.dim.Rd |only man/cifti.structure.data.one.Rd |only man/cifti.structure.from.specifier.Rd |only man/cifti.structure.short.Rd |only man/cifti.structures.Rd |only man/cifti.subset.dim.Rd |only man/cifti.surface.vertex.count.Rd |only man/cifti.surface.vertex.counts.Rd |only man/cifti.validate.axes.Rd |only man/cifti.validate.brain.models.Rd |only man/cifti.validate.dims.coverage.Rd |only man/cifti.validate.file.extension.Rd |only man/cifti.validate.index.range.Rd |only man/cifti.validate.indices.map.Rd |only man/cifti.validate.parcels.Rd |only man/cifti.validate.read.size.Rd |only man/cifti.volume.Rd |only man/cifti.xml.add.indices.map.Rd |only man/cifti.xml.add.metadata.Rd |only man/cifti.xml.int.vector.Rd |only man/cifti.xml.num.Rd |only man/cifti.xml.num.vector.Rd |only man/cifti.xml.version.Rd |only man/coord.bbox.Rd |only man/detect.dti.tract.format.Rd |only man/dot-canonicalize.gradient.table.Rd |only man/dot-cifti.label.table.for.users.Rd |only man/dot-dti.bzero.threshold.Rd |only man/dot-find.bval.file.Rd |only man/dot-format.gradient.values.Rd |only man/dot-format.header.size.Rd |only man/dot-name.gradient.table.columns.Rd |only man/dot-read.dti.tcktsf.Rd | 42 - man/dot-read.numeric.table.Rd |only man/dot-write.numeric.table.Rd |only man/dti.track.bbox.Rd |only man/dti.track.count.Rd |only man/dti.track.iterator.Rd |only man/fileopen.write.gz.or.not.Rd |only man/finite.rows.Rd |only man/format_bytes_human.Rd |only man/fs.tracts.Rd |only man/fs.tracts.coords.Rd |only man/fs.tracts.count.Rd |only man/fs.tracts.lengths.Rd |only man/fs.tracts.point.count.Rd |only man/fs.transform.Rd |only man/fsl.scaled.voxel.matrix.Rd |only man/get.dti.trk.endianness.Rd | 7 man/group.start.rows.Rd |only man/groups.in.bbox.Rd |only man/guess.transform.format.Rd |only man/guess.writable.transform.format.Rd |only man/infinite.rows.Rd |only man/inv.ornt.aff.Rd |only man/invert.fs.transform.Rd |only man/io.orientation.Rd |only man/is.analyze.file.Rd |only man/is.fs.tracts.Rd |only man/is.fs.transform.Rd |only man/is.gzip.file.Rd |only man/is.identity.matrix.Rd |only man/is.mrtrix.end.line.Rd |only man/itk.key.value.Rd |only man/itk.numeric.value.Rd |only man/length.fs.tracts.Rd |only man/lta.volume.info.lines.Rd |only man/merge.bbox.Rd |only man/mesh.face.normals.Rd |only man/mghheader.is.ras.valid.Rd | 18 man/mghheader.ras2vox.Rd | 18 man/mghheader.ras2vox.tkreg.Rd | 18 man/mghheader.scanner2tkreg.Rd | 18 man/mghheader.tkreg2scanner.Rd | 18 man/mghheader.vox2ras.Rd | 18 man/mghheader.vox2ras.tkreg.Rd | 18 man/mrtrix.track.iterator.Rd |only man/next.buffer.capacity.Rd |only man/ni1header.for.data.Rd | 5 man/ni1header.template.Rd | 9 man/ni2header.template.Rd | 2 man/nifti.dtype.info.Rd | 5 man/nifti.header.to.vox2ras.Rd |only man/nifti.info.from.file.Rd |only man/nifti.info.from.oro.instance.Rd |only man/nifti.resolve.filepath.Rd |only man/nifti2.extension.Rd |only man/nifti2.extension.content.Rd |only man/nifti2.extension.size.Rd |only man/nifti2.extension.text.Rd |only man/nifti2.get.extension.Rd |only man/nifti2.read.extensions.Rd |only man/nifti2.strip.nul.Rd |only man/nifti2.trailing.nul.removed.Rd |only man/nifti2.write.extensions.Rd |only man/nii1header.for.mgh.Rd | 6 man/nrrd.dwi.info.Rd |only man/nrrd.field.Rd |only man/nrrd.field.key.Rd |only man/nrrd.parse.field.value.Rd |only man/nrrd.parse.header.Rd |only man/nrrd.parse.matrix.Rd |only man/nrrd.parse.quoted.list.Rd |only man/nrrd.parse.vector.Rd |only man/nrrd.parse.vector.list.Rd |only man/nrrd.raw.to.numeric.Rd |only man/nrrd.read.data.Rd |only man/nrrd.read.header.lines.Rd |only man/nrrd.read.remainder.Rd |only man/nrrd.read.values.Rd |only man/nrrd.resolve.data.files.Rd |only man/nrrd.skip.lines.Rd |only man/nrrd.type.info.Rd |only man/nrrd.vox2ras.Rd |only man/open.maybe.gzip.Rd |only man/open.mrtrix.payload.Rd |only man/ornt.transform.Rd |only man/ornt2axcodes.Rd |only man/parse.mrtrix.count.Rd |only man/parse.mrtrix.datatype.Rd |only man/parse.mrtrix.file.entry.Rd |only man/parse.mrtrix.header.Rd |only man/parse.mrtrix.write.datatype.Rd |only man/print.dti.track.iterator.Rd |only man/print.fs.cifti.Rd |only man/print.fs.cifti.data.Rd |only man/print.fs.connectome.Rd |only man/print.fs.tracts.Rd |only man/print.fs.transform.Rd |only man/read.analyze.data.Rd |only man/read.analyze.header.Rd |only man/read.cifti.Rd |only man/read.cifti.header.Rd |only man/read.cifti.rows.Rd |only man/read.dti.bval.Rd |only man/read.dti.bvec.Rd |only man/read.dti.grad.Rd |only man/read.dti.gradients.Rd |only man/read.dti.tck.Rd | 48 + man/read.dti.tck.header.Rd |only man/read.dti.trk.Rd | 53 + man/read.dti.trk.header.Rd |only man/read.dti.tsf.Rd | 33 man/read.dti.tsf.header.Rd |only man/read.fs.connectome.cifti.Rd |only man/read.fs.gca.Rd | 2 man/read.fs.morph.Rd | 8 man/read.fs.morph.cifti.Rd | 43 - man/read.fs.parcellation.cifti.Rd | 23 man/read.fs.series.cifti.Rd | 20 man/read.fs.surface.stl.ascii.Rd | 4 man/read.fs.surface.stl.bin.Rd | 2 man/read.fs.surface.vtk.Rd | 26 man/read.fs.tracts.vtk.Rd |only man/read.fs.transform.Rd | 26 man/read.fs.transform.dat.Rd | 24 man/read.fs.transform.fslmat.Rd |only man/read.fs.transform.itk.Rd |only man/read.fs.transform.lta.Rd | 25 man/read.fs.transform.xfm.Rd | 23 man/read.fs.volume.Rd | 8 man/read.fs.volume.analyze.Rd |only man/read.fs.volume.nii.Rd | 22 man/read.fs.volume.nrrd.Rd |only man/read.matlab.v4.matrix.Rd |only man/read.mrtrix.header.Rd |only man/read.mrtrix.stream.Rd |only man/read.nifti.values.Rd |only man/read.nifti2.header.Rd | 8 man/read.nifti2.header.internal.Rd | 2 man/read.nrrd.header.Rd |only man/read.trk.records.Rd |only man/read.vtk.legacy.polydata.Rd |only man/scan.dti.tract.file.Rd |only man/scan.mrtrix.file.Rd |only man/scan.trk.file.Rd |only man/skip.connection.bytes.Rd |only man/sm0to1.Rd | 18 man/sm1to0.Rd | 18 man/split.mrtrix.chunk.Rd |only man/sub-.fs.tracts.Rd |only man/sub-sub-.fs.tracts.Rd |only man/subset.groups.Rd |only man/summary.fs.transform.Rd |only man/text.line.is.numeric.Rd |only man/trackvis.affine.to.rasmm.Rd |only man/transform.bbox.Rd |only man/transform.descriptor.path.Rd |only man/transform.file.sniff.text.Rd |only man/transform.flip.handedness.Rd |only man/transform.geometry.for.side.Rd |only man/transform.matrix.row.lines.Rd |only man/transform.value.text.Rd |only man/transform.values.text.Rd |only man/transform.world.frame.Rd |only man/transform2lps.Rd |only man/transform2ras.Rd |only man/transform2voxel.Rd |only man/transform2world.Rd |only man/trk.track.iterator.Rd |only man/validate.bbox.Rd |only man/validate.dti.gradients.Rd |only man/validate.fs.transform.Rd |only man/validate_allocation_size.Rd | 14 man/volume.descriptor.Rd |only man/volume.geometry.Rd |only man/vtk.as.indices.Rd |only man/vtk.cell.section.layout.Rd |only man/vtk.check.triangles.Rd |only man/vtk.data.type.info.Rd |only man/vtk.next.line.Rd |only man/vtk.next.section.Rd |only man/vtk.parse.cell.section.Rd |only man/vtk.parse.count.Rd |only man/vtk.peek.line.Rd |only man/vtk.read.header.Rd |only man/vtk.reader.bytes.Rd |only man/vtk.reader.close.Rd |only man/vtk.reader.fill.Rd |only man/vtk.reader.new.Rd |only man/vtk.reader.numbers.Rd |only man/vtk.reader.peek.Rd |only man/vtk.section.values.Rd |only man/vtk.section.values.ascii.Rd |only man/vtk.split.line.Rd |only man/vtk.write.surface.ascii.Rd |only man/vtk.write.surface.binary.Rd |only man/write.analyze.Rd |only man/write.analyze.char.field.Rd |only man/write.analyze.header.internal.Rd |only man/write.cifti.Rd |only man/write.dti.bval.Rd |only man/write.dti.bvec.Rd |only man/write.dti.grad.Rd |only man/write.dti.tck.Rd |only man/write.dti.trk.Rd |only man/write.dti.tsf.Rd |only man/write.fs.connectome.cifti.Rd |only man/write.fs.morph.Rd | 7 man/write.fs.morph.cifti.Rd |only man/write.fs.parcellated.cifti.Rd |only man/write.fs.parcellation.cifti.Rd |only man/write.fs.series.cifti.Rd |only man/write.fs.surface.Rd | 6 man/write.fs.surface.obj.Rd | 4 man/write.fs.surface.off.Rd | 4 man/write.fs.surface.off.ply2.Rd | 4 man/write.fs.surface.ply.Rd | 4 man/write.fs.surface.ply2.Rd | 4 man/write.fs.surface.stl.Rd |only man/write.fs.surface.vtk.Rd | 40 - man/write.fs.transform.Rd |only man/write.fs.transform.dat.Rd |only man/write.fs.transform.fslmat.Rd |only man/write.fs.transform.itk.Rd |only man/write.fs.transform.lta.Rd |only man/write.fs.transform.xfm.Rd |only man/write.fs.volume.Rd | 8 man/write.mrtrix.streamlines.Rd |only man/write.nifti1.Rd | 26 man/write.nifti1.data.internal.Rd |only man/write.nifti1.header.internal.Rd |only man/write.nifti2.Rd | 10 man/write.stl.ascii.Rd |only man/write.stl.binary.Rd |only man/write.trk.header.Rd |only tests/testthat/helper-functions-for-tests.R | 242 ++++++ tests/testthat/test-cifti-connectome-official.R |only tests/testthat/test-cifti-dispatch.R |only tests/testthat/test-cifti2.R | 90 ++ tests/testthat/test-cifti_connectome.R |only tests/testthat/test-cifti_parcels.R |only tests/testthat/test-dti-large-file-handling.R |only tests/testthat/test-dti_tracks_utils.R |only tests/testthat/test-itk_transform.R |only tests/testthat/test-nifti_read_order.R |only tests/testthat/test-nifti_to_mgh.R | 57 + tests/testthat/test-read_analyze.R |only tests/testthat/test-read_cifti.R |only tests/testthat/test-read_cifti_header.R |only tests/testthat/test-read_cifti_rows.R |only tests/testthat/test-read_dti_tcktsf.R | 307 +++++++ tests/testthat/test-read_dti_trk.R |only tests/testthat/test-read_dwi_gradients.R |only tests/testthat/test-read_nifti2_extensions.R |only tests/testthat/test-read_nrrd.R |only tests/testthat/test-transform_conversion.R |only tests/testthat/test-transforms_common.R |only tests/testthat/test-vtk.R |only tests/testthat/test-write_analyze.R |only tests/testthat/test-write_cifti.R |only tests/testthat/test-write_dwi_gradients.R |only tests/testthat/test-write_fs_surface.R | 115 ++ tests/testthat/test-write_fs_transform.R |only tests/testthat/test-write_nifti2.R | 4 tests/testthat/test-write_nifti2_extensions.R |only 454 files changed, 5338 insertions(+), 910 deletions(-)
More information about freesurferformats at CRAN
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Title: Classes and Methods for "Class Discovery" with Microarrays or
Proteomics
Description: Defines the classes used for "class discovery" problems
in the OOMPA project (<http://silicovore.com/OOMPA/index.html>). Class
discovery primarily consists of unsupervised clustering methods with
attempts to assess their statistical significance.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between ClassDiscovery versions 3.4.10 dated 2026-07-27 and 3.4.11 dated 2026-09-24
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/maha-test.pdf |binary inst/doc/oompa-cd.pdf |binary 5 files changed, 10 insertions(+), 10 deletions(-)
More information about ClassDiscovery at CRAN
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Title: Classes and Methods for "Class Comparison" Problems on
Microarrays
Description: Defines the classes used for "class comparison" problems
in the OOMPA project (<http://silicovore.com/OOMPA/index.html>). Class
comparison includes tests for differential expression; see Simon's
book for details on typical problem types.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between ClassComparison versions 3.3.5 dated 2025-02-05 and 3.3.6 dated 2026-09-24
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/oompa-cc.R | 2 -- inst/doc/oompa-cc.pdf |binary 5 files changed, 10 insertions(+), 12 deletions(-)
More information about ClassComparison at CRAN
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Title: Tiny 'shiny' Server - Lightweight Multi-App 'shiny' Proxy
Description: A lightweight, 'WebSocket'-enabled proxy server for hosting multiple
'shiny' applications with automatic health monitoring, session management,
and resource cleanup. Provides a simple entry point to run the server using
a JSON configuration file.
Author: Lars Bernhardsson [aut, cre]
Maintainer: Lars Bernhardsson <cran.sherry228@passinbox.com>
Diff between tinyshinyserver versions 0.2.0 dated 2026-09-17 and 0.2.1 dated 2026-09-24
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/utils.R | 5 ++++- tests/testthat/helper-async.R | 3 ++- tests/testthat/test-async-proxy.R | 8 ++++---- tests/testthat/test-review-regressions.R | 13 +++++++++++++ 7 files changed, 38 insertions(+), 15 deletions(-)
More information about tinyshinyserver at CRAN
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Title: Qualitative Palettes with Many Colors
Description: Tools for creating, viewing, and assessing qualitative
palettes with many (20-30 or more) colors. See Coombes and colleagues
(2019) <doi:10.18637/jss.v090.c01>.
Author: Guy Brock [aut],
Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Polychrome versions 1.6.1 dated 2026-07-06 and 1.6.2 dated 2026-09-24
DESCRIPTION | 10 MD5 | 32 +-- build/vignette.rds |binary data/Dark24.rda |binary data/Light24.rda |binary data/alphabet.rda |binary data/colorsafe.rda |binary data/glasbey.rda |binary data/iscc.rda |binary data/palette36.rda |binary data/sky-colors.rda |binary data/xkcd.rda |binary inst/doc/color-deficits.html | 340 ++++++++++++++----------------- inst/doc/colornames.html | 224 +++++++++------------ inst/doc/creatingPalettes.html | 437 ++++++++++++++++------------------------- inst/doc/polychrome.html | 235 ++++++++++------------ inst/doc/testgg.html | 259 +++++++++++------------- 17 files changed, 696 insertions(+), 841 deletions(-)
Title: Partial LeAst Squares for Multiomic Analysis
Description: Contains tools for supervised analyses of incomplete, overlapping
multiomics datasets. Applies partial least squares in multiple steps to find
models that predict survival outcomes. See Yamaguchi et al. (2023)
<doi:10.1101/2023.03.10.532096>.
Author: Kevin R. Coombes [cre, aut],
Kyoko Yamaguchi [aut],
Salma Abdelbaky [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between plasma versions 1.1.5 dated 2025-05-27 and 1.1.6 dated 2026-09-24
DESCRIPTION | 10 MD5 | 14 build/vignette.rds |binary data/mirESCA.rda |binary data/tfESCA.rda |binary inst/bib/bioinformatics.csl | 268 +++---- inst/bib/plasma.bib | 1544 ++++++++++++++++++++++---------------------- inst/doc/plasma.pdf |binary 8 files changed, 918 insertions(+), 918 deletions(-)
Title: Class Unions, Matrix Operations, and Color Schemes for OOMPA
Description: Provides the class unions that must be
preloaded in order for the basic tools in the OOMPA (Object-Oriented
Microarray and Proteomics Analysis) project to be defined and loaded.
It also includes vectorized operations for row-by-row means,
variances, and t-tests. Finally, it provides new color schemes.
Details on the packages in the OOMPA project can be found at
<http://silicovore.com/OOMPA/index.html>.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between oompaBase versions 3.2.11 dated 2026-01-11 and 3.2.12 dated 2026-09-24
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/oompa.R | 2 -- inst/doc/oompa.pdf |binary 5 files changed, 10 insertions(+), 12 deletions(-)
Title: Resampling Algorithms for 'mlr3' Framework
Description: A supervised learning algorithm inputs a train set,
and outputs a prediction function, which can be used on a test set.
If each data point belongs to a subset
(such as geographic region, year, etc), then
how do we know if subsets are similar enough so that
we can get accurate predictions on one subset,
after training on Other subsets?
And how do we know if training on All subsets would improve
prediction accuracy, relative to training on the Same subset?
SOAK, Same/Other/All K-fold cross-validation, <doi:10.1002/sam.70055>
can be used to answer these questions, by fixing a test subset,
training models on Same/Other/All subsets, and then
comparing test error rates (Same versus Other and Same versus All).
Also provides code for estimating how many train samples
are required to get accurate predictions on a test set.
Author: Toby Hocking [aut, cre] ,
Daniel Agyapong [ctb] ,
Michel Lang [ctb] ,
Bernd Bischl [ctb] ,
Jakob Richter [ctb] ,
Patrick Schratz [ctb] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [ctb],
Florian Pfisterer [ctb] ,
[...truncated...]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between mlr3resampling versions 2026.5.19 dated 2026-05-19 and 2026.9.24 dated 2026-09-24
mlr3resampling-2026.5.19/mlr3resampling/vignettes/mlr3resampling |only mlr3resampling-2026.5.19/mlr3resampling/vignettes/vignettes |only mlr3resampling-2026.9.24/mlr3resampling/DESCRIPTION | 6 mlr3resampling-2026.9.24/mlr3resampling/MD5 | 122 mlr3resampling-2026.9.24/mlr3resampling/NAMESPACE | 22 mlr3resampling-2026.9.24/mlr3resampling/NEWS | 420 - mlr3resampling-2026.9.24/mlr3resampling/R/Learners.R | 138 mlr3resampling-2026.9.24/mlr3resampling/R/RcppExports.R | 34 mlr3resampling-2026.9.24/mlr3resampling/R/ResamplingSameOtherSizesCV.R | 480 +- mlr3resampling-2026.9.24/mlr3resampling/R/proj.R | 722 +-- mlr3resampling-2026.9.24/mlr3resampling/R/pvalue.R | 586 +- mlr3resampling-2026.9.24/mlr3resampling/R/score.R | 115 mlr3resampling-2026.9.24/mlr3resampling/R/zzz.R | 40 mlr3resampling-2026.9.24/mlr3resampling/build/vignette.rds |binary mlr3resampling-2026.9.24/mlr3resampling/inst/CITATION | 32 mlr3resampling-2026.9.24/mlr3resampling/inst/doc/SOAKED.R | 276 - mlr3resampling-2026.9.24/mlr3resampling/inst/doc/SOAKED.Rmd | 480 +- mlr3resampling-2026.9.24/mlr3resampling/inst/doc/SOAKED.html | 683 +-- mlr3resampling-2026.9.24/mlr3resampling/inst/doc/proj.R | 437 - mlr3resampling-2026.9.24/mlr3resampling/inst/doc/proj.Rmd | 987 ++-- mlr3resampling-2026.9.24/mlr3resampling/inst/doc/proj.html | 2164 ++++----- mlr3resampling-2026.9.24/mlr3resampling/inst/doc/subset_group_stratum.R | 220 mlr3resampling-2026.9.24/mlr3resampling/inst/doc/subset_group_stratum.Rmd | 614 +- mlr3resampling-2026.9.24/mlr3resampling/inst/doc/subset_group_stratum.html | 1083 ++-- mlr3resampling-2026.9.24/mlr3resampling/inst/extdata/batchtools.conf.R | 14 mlr3resampling-2026.9.24/mlr3resampling/inst/extdata/slurm-afterok.tmpl | 100 mlr3resampling-2026.9.24/mlr3resampling/inst/slurm-afterok.tmpl | 100 mlr3resampling-2026.9.24/mlr3resampling/man/AZtrees.Rd | 122 mlr3resampling-2026.9.24/mlr3resampling/man/Learners.Rd | 212 mlr3resampling-2026.9.24/mlr3resampling/man/ResamplingSameOtherSizesCV.Rd | 534 +- mlr3resampling-2026.9.24/mlr3resampling/man/proj_compute.Rd | 156 mlr3resampling-2026.9.24/mlr3resampling/man/proj_grid.Rd | 204 mlr3resampling-2026.9.24/mlr3resampling/man/proj_results.Rd | 210 mlr3resampling-2026.9.24/mlr3resampling/man/proj_submit.Rd | 194 mlr3resampling-2026.9.24/mlr3resampling/man/proj_test.Rd | 180 mlr3resampling-2026.9.24/mlr3resampling/man/pvalue.Rd | 122 mlr3resampling-2026.9.24/mlr3resampling/man/pvalue_downsample.Rd | 148 mlr3resampling-2026.9.24/mlr3resampling/man/score.Rd | 128 mlr3resampling-2026.9.24/mlr3resampling/src/RcppExports.cpp | 18 mlr3resampling-2026.9.24/mlr3resampling/src/interface.cpp | 36 mlr3resampling-2026.9.24/mlr3resampling/src/stratified_group_cv.cpp | 117 mlr3resampling-2026.9.24/mlr3resampling/src/stratified_group_cv.h | 13 mlr3resampling-2026.9.24/mlr3resampling/tests/testthat.R | 4 mlr3resampling-2026.9.24/mlr3resampling/tests/testthat/test-CRAN-pvalue-downsample.R | 522 +- mlr3resampling-2026.9.24/mlr3resampling/tests/testthat/test-CRAN.R | 2210 +++++----- mlr3resampling-2026.9.24/mlr3resampling/vignettes/SOAKED.Rmd | 480 +- mlr3resampling-2026.9.24/mlr3resampling/vignettes/proj.Rmd | 987 ++-- mlr3resampling-2026.9.24/mlr3resampling/vignettes/subset_group_stratum.Rmd | 614 +- 48 files changed, 8559 insertions(+), 8527 deletions(-)
More information about mlr3resampling at CRAN
Permanent link
Title: Mapping-Based Additive Gaussian Process Models
Description: Fits mapping-based additive Gaussian process models for
experiments in which each component has both a quantitative level and a
position in an ordered sequence. Two model structures are available: a
compact two-dimensional mapping and a full mapping with one fewer
dimension than the number of components. Both models support parameter
estimation, point prediction, and plug-in predictive uncertainty. Input
checks validate the sequence data and apply consistent scaling to the
quantitative inputs. Computationally intensive covariance and gradient
calculations are implemented in C++ with 'Rcpp'. Initial-design functions
combine a space-filling Latin hypercube with sequence permutations. The
sequence portion can be generated randomly or optimized with simulated
annealing or space-filling threshold accepting. Expected improvement can
be optimized over both parts of the input, and a sequential interface
supports Bayesian optimization of an expensive user-supplied objective.
An integrated workf [...truncated...]
Author: Tony Wang [aut, cre, cph],
Qian Xiao [aut, cph],
Yaping Wang [cph],
Abhyuday Mandal [cph],
Xinwei Deng [cph]
Maintainer: Tony Wang <wangtony883@gmail.com>
Diff between magp versions 0.8.0 dated 2026-09-03 and 0.12.0 dated 2026-09-24
DESCRIPTION | 29 ++ MD5 | 73 ++++++- NAMESPACE | 15 + NEWS.md | 68 ++++++ R/RcppExports.R | 4 R/acquisition.R |only R/bayesian-optimization.R |only R/engine-rcpp.R | 249 ++++++++++++++++++++++++- R/initial-design-complete.R |only R/initial-design-quantitative.R |only R/initial-design-sequence.R |only R/initial-design-sfta.R |only R/integrated-workflow.R |only R/magp2d-package.R | 13 + R/model-methods.R | 20 ++ README.md | 254 +++++++++++++++++++++++++- build |only inst/CITATION |only inst/benchmarks |only inst/doc |only inst/examples |only man/magp-package.Rd | 22 ++ man/magp2d_fit.Rd | 21 +- man/magp_bayes_optimize.Rd |only man/magp_bayes_optimize_from_scratch.Rd |only man/magp_expected_improvement.Rd |only man/magp_initial_design.Rd |only man/magp_joint_criterion.Rd |only man/magp_next_point.Rd |only man/magp_quantitative_criterion.Rd |only man/magp_quantitative_design.Rd |only man/magp_sequence_criterion.Rd |only man/magp_sequence_design.Rd |only man/magpfull_fit.Rd | 19 + man/print.magp_bayes_opt.Rd |only man/print.magp_initial_design.Rd |only man/print.magp_next_point.Rd |only man/print.magp_quantitative_design.Rd |only man/print.magp_sequence_design.Rd |only src/RcppExports.cpp | 18 + src/sequence_sfta.cpp |only tests/testthat/test-bayesian-optimization.R |only tests/testthat/test-initial-design-complete.R |only tests/testthat/test-initial-design-sequence.R |only tests/testthat/test-initial-design-sfta.R |only tests/testthat/test-integrated-workflow.R |only tests/testthat/test-multistart-parallel.R |only tests/testthat/test-sfta-core.R |only vignettes |only 49 files changed, 764 insertions(+), 41 deletions(-)
Title: 'DataSHIELD' RO-Crate Governance Functions
Description: Tools for wrapping 'DataSHIELD' analyses into RO-Crate
(Research Object Crate) objects. Provides functions to create structured
metadata for federated data analysis projects, enabling governance
tracking of data access, project membership, analysis execution and
output validation across distributed data sources.
Author: Roberto Villegas-Diaz [aut, cre] ,
Becca Wilson [aut] ,
Olly Butters [aut] ,
Stuart Wheater [aut] ,
University of Liverpool [cph]
Maintainer: Roberto Villegas-Diaz <r.villegas-diaz@outlook.com>
Diff between dsROCrate versions 0.2.2 dated 2026-08-21 and 0.2.3 dated 2026-09-24
DESCRIPTION | 8 MD5 | 24 NEWS.md | 27 R/backend-opal.R | 2 R/safe-call-utils.R | 35 R/safe-call.R | 4 R/safe-symbol-utils.R | 4 R/safe-symbol.R | 2 R/safe_output.R | 392 ++ R/utils-safe_output.R | 2 inst/doc/getting-started.html | 5089 ++++++++++++++++++++++++++++++++++++-- tests/testthat/test-safe-call.R | 2 tests/testthat/test-safe_output.R | 129 13 files changed, 5322 insertions(+), 398 deletions(-)
Title: Cox Models by Likelihood Based Boosting for a Single Survival
Endpoint or Competing Risks
Description: Provides routines for fitting Cox models by likelihood based
boosting for single event survival data with right censoring or in the
presence of competing risks. The methodology is described in Binder
and Schumacher (2008) <doi:10.1186/1471-2105-9-14> and Binder et al.
(2009) <doi:10.1093/bioinformatics/btp088>.
Author: John Zobolas [cre, aut] ,
Harald Binder [aut]
Maintainer: John Zobolas <bblodfon@gmail.com>
Diff between CoxBoost versions 1.5.1 dated 2025-12-11 and 1.5.2 dated 2026-09-24
DESCRIPTION | 10 +- MD5 | 32 ++++---- NAMESPACE | 44 ++++++----- NEWS.md | 10 ++ R/CoxBoost.R | 118 +++++++++++++------------------ R/estimPVal.R | 13 +-- R/iCoxBoost.R | 14 +-- R/resample.CoxBoost.R | 12 +-- README.md | 17 ++-- man/CoxBoost-package.Rd | 9 ++ man/cv.CoxBoost.Rd | 16 +--- man/estimPVal.Rd | 13 +-- man/figures/README-unnamed-chunk-9-1.png |binary man/iCoxBoost.Rd | 14 +-- man/optimCoxBoostPenalty.Rd | 13 +-- man/predict.CoxBoost.Rd | 19 ++++ man/resample.CoxBoost.Rd | 9 +- 17 files changed, 189 insertions(+), 174 deletions(-)
Title: Threshold-Sweep QCA
Description: Provides threshold sweep methods for Qualitative Comparative
Analysis (QCA). Implements Condition Threshold Sweep (CTS, for one or
several conditions), Outcome Threshold Sweep (OTS), and Dual Threshold
Sweep (DTS) for systematic exploration of threshold calibration effects on
crisp-set QCA results. These methods extend traditional robustness
approaches by treating threshold variation as an explicit analytical
dimension and recording the sufficiency solution obtained at each
threshold setting. Also provides Fiss (2011)
<doi:10.5465/amj.2011.60263120> core/peripheral condition classification
via compute_fiss_core() and generate_fiss_chart(), enabling four-symbol
configuration charts that distinguish core conditions (present in both
parsimonious and intermediate solutions) from peripheral conditions
(intermediate only). Built on top of the 'QCA' package by Dusa (2019)
<doi:10.1007/978-3-319-75668-4>, with function arguments following 'QCA'
conventions. Based on set-theoretic m [...truncated...]
Author: Yuki Toyoda [aut, cre],
Japan Society for the Promotion of Science [fnd]
Maintainer: Yuki Toyoda <yuki.toyoda.ds@hosei.ac.jp>
Diff between ThSQCA versions 2.0.6 dated 2026-07-31 and 2.0.7 dated 2026-09-24
DESCRIPTION | 43 MD5 | 59 NAMESPACE | 6 NEWS.md | 2156 +++++++++++++------------- R/ThSQCA-package.R | 55 R/tsqca_core.R | 76 R/tsqca_cts.R | 40 R/tsqca_fiss_core.R | 2 R/tsqca_methods.R | 16 R/tsqca_ots_dts.R | 40 R/tsqca_report.R | 97 - README.md | 56 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 30 inst/doc/ThSQCA_Reproducible_EN.R | 16 inst/doc/ThSQCA_Reproducible_EN.Rmd | 26 inst/doc/ThSQCA_Reproducible_EN.html | 89 - inst/doc/ThSQCA_Tutorial_EN.R | 734 ++------ inst/doc/ThSQCA_Tutorial_EN.Rmd | 1622 +++++++------------ inst/doc/ThSQCA_Tutorial_EN.html | 2631 +++++++++++++------------------- man/ThSQCA-package.Rd | 2 man/ctSweepM.Rd | 9 man/ctSweepS.Rd | 9 man/dtSweep.Rd | 9 man/otSweep.Rd | 9 man/validate_pre_calibrated.Rd | 3 tests/testthat/test-s3-methods.R | 300 +-- tests/testthat/test-v207-output-fixes.R |only vignettes/ThSQCA_Reproducible_EN.Rmd | 26 vignettes/ThSQCA_Tutorial_EN.Rmd | 1622 +++++++------------ 31 files changed, 4358 insertions(+), 5425 deletions(-)
Title: Basic Functions for Pre-Processing Microarrays
Description: Provides classes to pre-process microarray gene
expression data as part of the OOMPA collection of packages
described at <http://silicovore.com/OOMPA/index.html>.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between PreProcess versions 3.1.9 dated 2025-04-06 and 3.1.10 dated 2026-09-24
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/oompa-prep.R | 2 -- inst/doc/oompa-prep.pdf |binary 5 files changed, 10 insertions(+), 12 deletions(-)
Title: J&J Innovative Medicine ADaM Test Data
Description: A set of Analysis Data Model (ADaM) datasets constructed by
modifying the ADaM datasets in the 'pharmaverseadam' package to meet J&J Innovative Medicine's
standard data structure for Clinical and Statistical Programming.
Author: David Munoz Tord [aut, cre],
Nicholas Masel [aut],
Joe Kovach [aut],
Mahesh Divakaran [ctb],
Renfei Mao [ctb],
J&J Innovative Medicine [cph, fnd]
Maintainer: David Munoz Tord <david.munoztord@mailbox.org>
Diff between pharmaverseadamjnj versions 0.0.5 dated 2026-05-08 and 0.0.6 dated 2026-09-24
DESCRIPTION | 13 - MD5 | 104 ++++++---- NAMESPACE | 6 NEWS.md | 170 +++++++++++++---- R/adae.R | 211 ++++++++++++--------- R/adaecomp.R |only R/adaeocmq.R | 221 ++++++++++++----------- R/adagocmq.R | 82 ++++---- R/adcm.R | 156 ++++++++-------- R/addili.R | 170 ++++++++--------- R/addisp.R |only R/adeg.R | 170 ++++++++--------- R/adex.R | 286 ++++++++++++++--------------- R/adexsum.R | 78 ++++---- R/adishum.R |only R/adlb.R | 337 +++++++++++++++++------------------ R/adpc.R | 288 ++++++++++++++--------------- R/adsl.R | 257 +++++++++++++------------- R/adslcomp.R |only R/adttesaf.R | 46 ++-- R/advs.R | 196 ++++++++++---------- R/pharmaverseadamjnj-package.R | 8 README.md | 137 +++++++------- data/adae.rda |binary data/adaecomp.rda |only data/adaeocmq.rda |binary data/adagocmq.rda |binary data/adcm.rda |binary data/addili.rda |binary data/addisp.rda |only data/adeg.rda |binary data/adex.rda |binary data/adexsum.rda |binary data/adishum.rda |only data/adlb.rda |binary data/adpc.rda |binary data/adsl.rda |binary data/adslcomp.rda |only data/adttesaf.rda |binary data/advs.rda |binary inst/WORDLIST | 272 ++++++++++++++++------------ man/adae.Rd | 239 +++++++++++++----------- man/adaecomp.Rd |only man/adaeocmq.Rd | 249 ++++++++++++++----------- man/adagocmq.Rd | 110 +++++------ man/adcm.Rd | 184 +++++++++---------- man/addili.Rd | 198 ++++++++++---------- man/addisp.Rd |only man/adeg.Rd | 198 ++++++++++---------- man/adex.Rd | 314 ++++++++++++++++---------------- man/adexsum.Rd | 106 +++++------ man/adishum.Rd |only man/adlb.Rd | 365 ++++++++++++++++++-------------------- man/adpc.Rd | 316 ++++++++++++++++---------------- man/adsl.Rd | 285 +++++++++++++++-------------- man/adslcomp.Rd |only man/adttesaf.Rd | 74 +++---- man/advs.Rd | 224 ++++++++++++----------- man/pharmaverseadamjnj-package.Rd | 58 +++--- 59 files changed, 3202 insertions(+), 2926 deletions(-)
More information about pharmaverseadamjnj at CRAN
Permanent link
Title: Generator of Synthetic Patient Data for the OMOP Common Data
Model
Description: Tools to generate synthetic patient-level test datasets in the
Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM).
Includes a chat-driven generator backed by large language models and an
interactive 'shiny' designer for editing CDM test sets.
Author: Cesar Barboza [aut, cre] ,
Ger Inberg [aut] ,
Adam Black [aut]
Maintainer: Cesar Barboza <c.barboza@mi-erasmusmc.nl>
Diff between PatientGenerator versions 0.2.4 dated 2026-09-15 and 0.2.5 dated 2026-09-24
DESCRIPTION | 7 MD5 | 29 NAMESPACE | 1 NEWS.md | 4 R/hecateSearch.R | 1 R/patientChat.R | 44 inst/jsonSchemas/cdm54schema-PET.json |only inst/jsonSchemas/cdm54schema-complete.json | 42 man/patientChat.Rd | 238 +- tests/testthat/test-patientChat.R | 147 + tests/testthat/test-prompts.R | 5 tests/testthat/testCases/patient-chat-test.json | 1421 +++++--------- tests/testthat/testCases/patient_chat_ovarian_stages.json | 84 tests/testthat/testCases/pregnancy_test.json | 367 +-- tests/testthat/testCases/test_diabetes_patients.json | 804 +++---- tests/testthat/testCases/test_diabetes_patients_30.json | 804 +++---- 16 files changed, 1806 insertions(+), 2192 deletions(-)
More information about PatientGenerator at CRAN
Permanent link
Title: Linear Predictive Models Based on the LIBLINEAR C/C++ Library
Description: A wrapper around the LIBLINEAR C/C++ library for machine
learning (available at
<https://www.csie.ntu.edu.tw/~cjlin/liblinear/>). LIBLINEAR is
a simple library for solving large-scale regularized linear
classification and regression. It currently supports
L2-regularized classification (such as logistic regression,
L2-loss linear SVM and L1-loss linear SVM) as well as
L1-regularized classification (such as L2-loss linear SVM and
logistic regression) and L2-regularized support vector
regression (with L1- or L2-loss). The main features of
LiblineaR include multi-class classification (one-vs-the rest,
and Crammer & Singer method), cross validation for model
selection, probability estimates (logistic regression only) or
weights for unbalanced data. The estimation of the models is
particularly fast as compared to other libraries.
Author: Thibault Helleputte [cre, aut, cph],
Jerome Paul [aut],
Pierre Gramme [aut],
Chih-Jen Lin [cph] ; see LICENSE.note)
Maintainer: Thibault Helleputte <thibault.helleputte@dnalytics.com>
Diff between LiblineaR versions 2.10-25 dated 2026-09-11 and 2.10-26 dated 2026-09-24
DESCRIPTION | 8 +- MD5 | 24 +++++--- NEWS | 10 +++ R/LiblineaR.R | 68 +++++++------------------ R/heuristicC.R | 76 ++++++++++++++++++++-------- R/internal.R |only R/predict.R | 49 +----------------- inst/doc/LiblineaR-intro.html | 20 +++---- man/LiblineaR.Rd | 15 ++--- man/heuristicC.Rd | 10 ++- tests/testthat/test-bias.R |only tests/testthat/test-class-weights.R |only tests/testthat/test-heuristicC.R |only tests/testthat/test-input-validation.R |only tests/testthat/test-liblinear-vector-data.R |only tests/testthat/test-p0-fixes.R | 14 +++++ 16 files changed, 149 insertions(+), 145 deletions(-)
Title: Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools. Melo D, Garcia G, Hubbe A, Assis A P, Marroig G. (2016) <doi:10.12688/f1000research.7082.3>.
Author: Diogo Melo [aut, cre] ,
Ana Paula Assis [aut] ,
Edgar Zanella [ctb],
Fabio Andrade Machado [aut] ,
Guilherme Garcia [aut],
Alex Hubbe [rev] ,
Gabriel Marroig [ths]
Maintainer: Diogo Melo <diogro@gmail.com>
Diff between evolqg versions 0.3-6 dated 2025-09-05 and 0.4-3 dated 2026-09-24
DESCRIPTION | 15 +- MD5 | 27 ++-- NAMESPACE | 184 ++++++++++++++++++--------------- R/EvolQG.R | 7 - R/KrzSubspaceBootstrap.R | 7 - R/MantelCor.R | 5 R/MatrixStatistics.R | 35 ++++-- build |only man/KrzSubspaceBootstrap.Rd | 10 + man/MeanMatrixStatistics.Rd | 27 ++++ man/evolqg.Rd | 3 man/ratones.Rd | 7 - tests/testthat/test.KrzSubspace.r | 16 ++ tests/testthat/test.MatrixStatistics.r | 21 ++- tests/testthat/test.TestModularity.r | 8 - 15 files changed, 237 insertions(+), 135 deletions(-)
Title: Algorithms and Tools for Tabular Statistics and Hierarchical
Computations
Description: Includes general data manipulation functions, algorithms for statistical disclosure control (Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6> and functions for hierarchical computations by sparse model matrices (Langsrud, 2023) <doi:10.32614/RJ-2023-088>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Bjoern-Helge Mevik [ctb],
Vidar Norstein Klungre [rev] ,
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between SSBtools versions 1.8.8 dated 2026-08-21 and 1.8.9 dated 2026-09-24
DESCRIPTION | 8 - MD5 | 13 +-- NAMESPACE | 2 NEWS.md | 6 + R/Extend0.R | 6 + R/Extend0rnd1.R | 183 +++++++++++++++++++++++++++++++++++++++++--- man/Extend0_n_rnd_groups.Rd |only man/Extend0rnd1.Rd | 2 8 files changed, 199 insertions(+), 21 deletions(-)
Title: Dirichlet Process Bayesian Clustering, Profile Regression
Description: Bayesian clustering using a Dirichlet process mixture model. This model is an alternative to regression models, non-parametrically linking a response vector to covariate data through cluster membership. The package allows Bernoulli, Binomial, Poisson, Normal, survival and categorical response, as well as Normal and discrete covariates. It also allows for fixed effects in the response model, where a spatial CAR (conditional autoregressive) term can be also included. Additionally, predictions may be made for the response, and missing values for the covariates are handled. Several samplers and label switching moves are implemented along with diagnostic tools to assess convergence. A number of R functions for post-processing of the output are also provided. In addition to fitting mixtures, it may additionally be of interest to determine which covariates actively drive the mixture components. This is implemented in the package as variable selection. The main reference for the package is Liv [...truncated...]
Author: David I. Hastie [aut],
Silvia Liverani [aut, cre],
Sylvia Richardson [aut],
Aurore J. Lavigne [aut],
Lucy Leigh [aut],
Lamiae Azizi [aut],
Xi Liu [aut],
Ruizhu Huang [aut],
Austin Gratton [aut],
Wei Jing [aut]
Maintainer: Silvia Liverani <liveranis@gmail.com>
Diff between PReMiuM versions 3.2.13 dated 2024-01-09 and 3.2.14 dated 2026-09-24
ChangeLog | 5 ++++ DESCRIPTION | 56 +++++++++++++++++++++++++++++++++++++++++++++++------- MD5 | 10 ++++----- NAMESPACE | 2 - R/generateData.R | 3 +- build/partial.rdb |binary 6 files changed, 62 insertions(+), 14 deletions(-)
Title: Calculate Tree Traits from Terrestrial Lidar
Description: Measuring tree architecture from terrestrial lidar data, including tree-level properties, crown characteristics, and structural attributes derived from quantitative structure models (QSMs).
Author: Jeffery B. Cannon [aut, cre]
Maintainer: Jeffery B. Cannon <jeffery.cannon@jonesctr.org>
This is a re-admission after prior archival of version 0.1.2 dated 2026-02-25
Diff between tReeTraits versions 0.1.2 dated 2026-02-25 and 0.1.3 dated 2026-09-24
DESCRIPTION | 15 ++---- MD5 | 18 ++++--- NEWS.md |only R/diagnostics.R | 11 ++-- R/pyfunctions.R | 45 ++++++------------ R/pytlidar-setup.R | 2 R/traits_from_qsm.R | 111 +++++++++++++++++++++++++++++++++++----------- README.md | 19 +++++-- man/figures/downloads.png |only man/fit_taper_Kozak.Rd | 42 ++++++++++++----- man/plot_qsm3d.Rd | 4 + 11 files changed, 171 insertions(+), 96 deletions(-)
Title: Spatial Logistic Gaussian Process for Field Density Estimation
Description: Provides tools for conditional and spatially dependent
density estimation using Spatial Logistic Gaussian Processes (SLGPs).
The approach represents probability densities through finite-rank
Gaussian process priors transformed via a spatial logistic density
transformation, enabling flexible non-parametric modeling of
heterogeneous data. Functionality includes density prediction,
quantile and moment estimation, sampling methods, and preprocessing
routines for basis functions. Applications arise in spatial statistics,
machine learning, and uncertainty quantification.
The methodology builds on the framework of Leonard (1978)
<doi:10.1111/j.2517-6161.1978.tb01655.x>, Lenk (1988) <doi:10.1080/01621459.1988.10478625>,
Tokdar (2007) <doi:10.1198/106186007X210206>, Tokdar (2010) <doi:10.1214/10-BA605>,
and is further aligned with recent developments
in Bayesian non-parametric modelling: see Gautier (2023) <https://boristheses.unibe.ch/4377/>,
and Gautier (2025) &l [...truncated...]
Author: Athenais Gautier [aut, cre]
Maintainer: Athenais Gautier <athenais.gautier@onera.fr>
Diff between SLGP versions 1.1.1 dated 2026-09-07 and 2.0.0 dated 2026-09-24
DESCRIPTION | 15 MD5 | 57 - NAMESPACE | 2 R/PredictAndSimulate.R | 1471 ++++++++++++++++----------------- R/SLGPclass.R | 126 +- R/diagnostics.R |only R/hessian.R |only R/methods.R | 481 +++++++--- R/slgp.R | 1544 ++++++++++++++++++----------------- inst/doc/IntroductionSLGP.R | 23 inst/doc/IntroductionSLGP.Rmd | 23 inst/doc/IntroductionSLGP.html | 70 + inst/doc/SLGPdiscrete.R | 12 inst/doc/SLGPdiscrete.Rmd | 12 inst/doc/SLGPdiscrete.html | 47 - inst/stan/likelihoodComposed.stan | 47 - inst/stan/likelihoodSimple.stan | 19 man/SLGP-class.Rd | 17 man/plot-SLGP-missing-method.Rd | 24 man/predict-SLGP-method.Rd | 38 man/print-SLGP-method.Rd | 20 man/retrainSLGP.Rd | 11 man/simulate-SLGP-method.Rd | 56 - man/slgp.Rd | 8 man/summary-SLGP-method.Rd | 35 man/timing.Rd |only man/update-SLGP-method.Rd | 37 src/stanExports_likelihoodComposed.h | 291 ++---- src/stanExports_likelihoodSimple.h | 189 +--- vignettes/IntroductionSLGP.Rmd | 23 vignettes/SLGPdiscrete.Rmd | 12 31 files changed, 2511 insertions(+), 2199 deletions(-)
More information about riskweightedassets at CRAN
Permanent link
Title: A Grammar of Graphics for Comparative Genomics
Description: An extension of 'ggplot2' for creating complex genomic
maps. It builds on the power of 'ggplot2' and 'tidyverse' adding new 'ggplot2'-style
geoms & positions and 'dplyr'-style verbs to manipulate the underlying data. It
implements a layout concept inspired by 'ggraph' and introduces tracks to bring
tidiness to the mess that is genomics data.
Author: Thomas Hackl [aut, cre],
Markus J. Ankenbrand [aut],
Bart van Adrichem [aut],
Kristina Haslinger [ctb, sad]
Maintainer: Thomas Hackl <t.hackl@rug.nl>
Diff between gggenomes versions 1.1.3 dated 2026-02-23 and 1.2.0 dated 2026-09-24
gggenomes-1.1.3/gggenomes/R/scale_x.R |only gggenomes-1.1.3/gggenomes/inst/doc/emales.R |only gggenomes-1.1.3/gggenomes/inst/doc/emales.Rmd |only gggenomes-1.1.3/gggenomes/inst/doc/emales.html |only gggenomes-1.1.3/gggenomes/man/GeomFeatText.Rd |only gggenomes-1.1.3/gggenomes/man/figures/emales.png |only gggenomes-1.1.3/gggenomes/man/scale_x_bp.Rd |only gggenomes-1.1.3/gggenomes/tests/testthat/test_strand.R |only gggenomes-1.1.3/gggenomes/vignettes/emales |only gggenomes-1.1.3/gggenomes/vignettes/emales.Rmd |only gggenomes-1.2.0/gggenomes/DESCRIPTION | 12 - gggenomes-1.2.0/gggenomes/MD5 | 93 +++++----- gggenomes-1.2.0/gggenomes/NAMESPACE | 8 gggenomes-1.2.0/gggenomes/NEWS.md | 5 gggenomes-1.2.0/gggenomes/R/feats.R | 21 +- gggenomes-1.2.0/gggenomes/R/focus.R | 26 +- gggenomes-1.2.0/gggenomes/R/geom_feat.R | 21 -- gggenomes-1.2.0/gggenomes/R/geom_gene_text.R | 2 gggenomes-1.2.0/gggenomes/R/geom_wiggle.R | 25 +- gggenomes-1.2.0/gggenomes/R/gggenomes.R | 43 +++- gggenomes-1.2.0/gggenomes/R/layout.R | 75 +++++++- gggenomes-1.2.0/gggenomes/R/links.R | 31 +-- gggenomes-1.2.0/gggenomes/R/position_strandpile.R | 10 - gggenomes-1.2.0/gggenomes/R/read_gff3.R | 10 - gggenomes-1.2.0/gggenomes/R/scale_x_genomic.R |only gggenomes-1.2.0/gggenomes/R/scalebar.R |only gggenomes-1.2.0/gggenomes/R/vars.R | 7 gggenomes-1.2.0/gggenomes/R/zzz.R | 29 +++ gggenomes-1.2.0/gggenomes/README.md | 2 gggenomes-1.2.0/gggenomes/build/vignette.rds |binary gggenomes-1.2.0/gggenomes/data/emale_ava.rda |binary gggenomes-1.2.0/gggenomes/data/emale_prot_ava.rda |binary gggenomes-1.2.0/gggenomes/inst/doc/flip.Rmd | 2 gggenomes-1.2.0/gggenomes/inst/doc/flip.html | 31 ++- gggenomes-1.2.0/gggenomes/inst/doc/gggenomes.html | 138 +++++++-------- gggenomes-1.2.0/gggenomes/man/axis_scalebar.Rd |only gggenomes-1.2.0/gggenomes/man/def_formats.Rd | 22 +- gggenomes-1.2.0/gggenomes/man/draw_scalebar_grob.Rd |only gggenomes-1.2.0/gggenomes/man/focus.Rd | 11 - gggenomes-1.2.0/gggenomes/man/geom_wiggle.Rd | 8 gggenomes-1.2.0/gggenomes/man/gggenomes.Rd | 17 + gggenomes-1.2.0/gggenomes/man/layout_genomes.Rd | 17 + gggenomes-1.2.0/gggenomes/man/nice_scalebar_length.Rd |only gggenomes-1.2.0/gggenomes/man/resolve_scalebar_label.Rd |only gggenomes-1.2.0/gggenomes/man/resolve_scalebar_length.Rd |only gggenomes-1.2.0/gggenomes/man/scale_x_genomic.Rd |only gggenomes-1.2.0/gggenomes/man/scalebar_style.Rd |only gggenomes-1.2.0/gggenomes/vignettes/_vignettes.qmd |only gggenomes-1.2.0/gggenomes/vignettes/emales-final.png |only gggenomes-1.2.0/gggenomes/vignettes/emales-p1.png |only gggenomes-1.2.0/gggenomes/vignettes/emales-p2.png |only gggenomes-1.2.0/gggenomes/vignettes/emales-p3.png |only gggenomes-1.2.0/gggenomes/vignettes/emales-p4a.png |only gggenomes-1.2.0/gggenomes/vignettes/emales-p4b.png |only gggenomes-1.2.0/gggenomes/vignettes/emales-p5.png |only gggenomes-1.2.0/gggenomes/vignettes/emales-p6.png |only gggenomes-1.2.0/gggenomes/vignettes/emales-p7.png |only gggenomes-1.2.0/gggenomes/vignettes/emales.qmd |only gggenomes-1.2.0/gggenomes/vignettes/flip.Rmd | 2 gggenomes-1.2.0/gggenomes/vignettes/marginal.qmd |only 60 files changed, 413 insertions(+), 255 deletions(-)
Title: Type-Faithful and Human-Readable JSON for R Values
Description: Writing an R value as JSON that a human can read, and reading
it back unchanged. The 'jsonlite' package offers either a readable but
lossy pair of functions or a faithful but verbose one; this package
emits ordinary JSON for ordinary values and annotates only what JSON
cannot express, namely the distinction between integer and double,
typed missing values, non-finite numbers, attributes, and objects from
the S3, S4 and S7 systems.
Author: Nicolas Bennett [aut, cre, cph],
YaoYuan [ctb, cph]
Maintainer: Nicolas Bennett <nicolas@cynkra.com>
Diff between typedjson versions 0.1.0 dated 2026-09-18 and 0.1.1 dated 2026-09-24
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ inst/doc/benchmarks.html | 20 ++++++++++---------- inst/doc/handles.html | 6 +++--- inst/doc/r6.html | 4 ++-- src/write.cpp | 12 +++++++----- 7 files changed, 35 insertions(+), 29 deletions(-)
Title: Statistical Tools for African National Statistics Institutes
Description: A comprehensive statistical toolbox for National Statistics
Institutes (INS) in Africa. Provides functions for survey data import
('KoboToolbox', 'ODK', 'CSPro', 'Excel', 'Stata', 'SPSS'), data
processing and validation, weighted statistical analysis (descriptive
statistics, cross-tabulations, regression, Human Development Index (HDI),
Multidimensional Poverty Index (MPI) following Alkire and Foster (2011)
<doi:10.1093/oep/gpr051>, inequalities), visualization (age pyramids,
thematic maps, official charts) and dissemination ('SDMX' export, 'DDI'
metadata, anonymization, Word/PDF reports). Designed to work in
resource-constrained environments, offline and in French.
Author: Dikers Amoko [aut, cre, ctb],
Josue Honore Dasse [ctb]
Maintainer: Dikers Amoko <diamoko@gmail.com>
Diff between statAfrikR versions 0.2.0 dated 2026-09-20 and 0.2.1 dated 2026-09-24
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ R/rapports.R | 12 +++++++++--- README.md | 10 +++++++--- inst/doc/contributeurs.Rmd | 3 ++- inst/doc/contributeurs.html | 12 +++++++++++- vignettes/contributeurs.Rmd | 3 ++- 7 files changed, 42 insertions(+), 19 deletions(-)
Title: Conformal Prediction for Spatially and Spatio-Temporally
Dependent Data
Description: Provides distribution-free, model-agnostic prediction
intervals for spatially and spatio-temporally dependent data using
localized conformal calibration. Implements locally weighted split
conformal prediction for geostatistical (point-referenced) data based on
spatial-distance kernels, and a neighbourhood-weighted conformal
procedure for areal (lattice) data based on graph adjacency structures.
Relaxes the standard exchangeability assumption using spatial proximity,
following the localized conformal framework of Mao, Martin and Reich
(2024) <doi:10.1080/01621459.2022.2147531>. Includes comprehensive
spatial diagnostic tools to audit empirical coverage, conditional
spatial strata, and boundary proximity effects.
Author: Ahmed Sattar Jabbar [aut, cre]
Maintainer: Ahmed Sattar Jabbar <ahmed.state.me@gmail.com>
Diff between spconform versions 0.1.0 dated 2026-09-12 and 0.1.1 dated 2026-09-24
DESCRIPTION | 45 MD5 | 98 + NAMESPACE | 67 - NEWS.md | 32 R/diagnose.R | 651 +++++++---- R/methods.R | 200 ++- R/scp_areal.R | 8 R/scp_geostatistical.R | 324 ++--- R/spconform-package.R |only R/utils.R | 256 ++-- README.md | 55 - build/partial.rdb |only build/vignette.rds |binary inst/benchmarks |only inst/doc/getting-help.Rmd | 9 inst/doc/getting-help.html | 14 inst/doc/spconform-intro.R | 122 -- inst/doc/spconform-intro.Rmd | 432 +++---- inst/doc/spconform-intro.html | 568 ++++------ inst/scripts/baghdad_temperature_conformal_prediction.R |only inst/scripts/code.R | 871 ++++++++++------ inst/scripts/code.Rmd |only inst/scripts/code.html |only inst/scripts/code.md |only inst/scripts/comprehensive_jss_comparisons.R |only inst/scripts/drone_sensing_outputs |only inst/scripts/drone_sensing_study.R |only inst/scripts/figures_html |only inst/scripts/nc_sids_areal_study.R |only inst/scripts/satellite_sensing_outputs |only inst/scripts/satellite_sensing_study.R |only inst/scripts/sdss_conformal_simulation_study.R |only inst/scripts/tables_jss_manuscript.tex |only inst/scripts/verify_v010_execution_time.R |only man/areal_neighbor_weights.Rd | 58 - man/as.data.frame.spconform.Rd |only man/coverage_report.Rd | 67 - man/diagnose.Rd | 93 + man/plot.spconform.Rd | 44 man/plot.spconform_diagnose.Rd |only man/predict.spconform.Rd |only man/print.spconform.Rd | 41 man/residuals.spconform.Rd |only man/scp_areal.Rd | 140 +- man/scp_geostatistical.Rd | 218 ++-- man/spatial_kernel_weights.Rd | 127 +- man/spconform-package.Rd |only man/summary.spconform.Rd | 40 tests/testthat/test-scp.R | 225 ++-- vignettes/getting-help.Rmd | 9 vignettes/spconform-intro.Rmd | 432 +++---- 51 files changed, 2778 insertions(+), 2468 deletions(-)
Title: Large Language Models and Agentic AI
Description: Unified interface for creating LLM and Agent objects, generating responses and
performing batch inference based on a type-checked and validated 'S7' backend. Features
reasoning, structured output, memory management, and tool use. Supports 'Ollama'
<https://docs.ollama.com/api>,
'OpenAI'-compatible <https://developers.openai.com/api/reference/overview>, and
'Anthropic'-compatible <https://platform.claude.com/docs/en/api/getting-started> endpoints.
Runs Apple's on-device 'Foundation Models' through the 'rtemis-afm' bridge
<https://github.com/rtemis-org/rtemis-afm>.
Author: E.D. Gennatas [aut, cre, cph]
Maintainer: E.D. Gennatas <gennatas@gmail.com>
Diff between rtemis.llm versions 0.8.1 dated 2026-05-04 and 0.8.7 dated 2026-09-24
DESCRIPTION | 17 MD5 | 100 +++-- NAMESPACE | 15 NEWS.md |only R/00_init.R | 492 ++----------------------- R/01_Schema.R | 272 ++++++++++++- R/02_Message.R | 32 + R/03_State.R | 6 R/04_Tool.R | 39 + R/05_LLMConfig.R | 292 +++++++++++--- R/06_LLM.R | 394 ++++++++++++++++---- R/07_Agent.R | 184 ++++++--- R/08_OutputValidation.R |only R/map.R | 626 ++++++++++++++++++++++++++------ R/utils_anthropic.R | 116 +++-- R/utils_apple.R |only R/utils_llm_adapter.R | 347 +++++++++++++++-- R/utils_ollama.R | 24 - R/utils_openai.R | 98 +++-- R/utils_security.R | 180 ++++++++- R/zzz.R | 3 README.md | 81 ++++ man/agentapply.Rd | 27 + man/apple_check_available.Rd |only man/apple_health.Rd |only man/config_Apple.Rd |only man/config_Ollama.Rd | 3 man/config_OpenAI.Rd | 17 man/create_Apple.Rd |only man/create_Ollama.Rd | 3 man/create_OpenAI.Rd | 9 man/create_agent.Rd | 2 man/field.Rd | 42 +- man/generate.Rd | 21 - man/llmapply.Rd | 29 + man/logprobs.Rd |only man/map.Rd | 22 + man/reasoning.Rd | 6 man/responses.Rd | 8 man/rtemis.llm-package.Rd | 5 man/token_probs.Rd |only man/tools.Rd | 2 man/validate_output.Rd |only man/validation_results.Rd |only tests/testthat/helper_apple.R |only tests/testthat/helper_envvar.R |only tests/testthat/helper_keychain.R |only tests/testthat/helper_ollama.R | 6 tests/testthat/test_LLM.R | 17 tests/testthat/test_Message.R | 11 tests/testthat/test_Schema.R | 232 +++++++++++ tests/testthat/test_anthropic.R | 14 tests/testthat/test_apple.R |only tests/testthat/test_call_options.R |only tests/testthat/test_credentials.R |only tests/testthat/test_map.R | 371 ++++++++++++++++++ tests/testthat/test_ollama.R | 155 +++++++ tests/testthat/test_openai.R | 301 ++++++++++++++- tests/testthat/test_output_validation.R |only tests/testthat/test_tools.R | 14 60 files changed, 3559 insertions(+), 1076 deletions(-)
Title: Social Network Measures using Matrices
Description: Provides measures to describe and manipulate one-mode, two-mode,
multiplex, and multilevel networks using matrix algebra. Implements
functions for network centrality, cohesive subgroups, communities,
structural holes, roles and positions, similarity measures, path distances,
signed networks, segregation, social influence, and random network
generation. Supports ego-centric and whole-network analyses, including
dyadic and triadic censuses, structural balance, bipartite projections,
measures with overlapping group memberships, Q-analysis,
neighbourhood-inclusion dominance, main path analysis of citation networks,
and permutation tests for networks.
Key references: Bonacich (1972) <doi:10.1080/0022250X.1972.9989806>,
Breiger (1974) <doi:10.2307/2576011>,
Kivela et al. (2014) <doi:10.1093/comnet/cnu016>,
Espinosa-Rada et al. (2024) <doi:10.1016/j.socnet.2023.11.008>,
Schoch and Brandes (2016) <doi:10.1017/S0956792516000401>,
Traag et al. (2019) <doi:10.1038 [...truncated...]
Author: Alejandro Espinosa-Rada [cre, aut]
Maintainer: Alejandro Espinosa-Rada <anespinosa@uc.cl>
Diff between netmem versions 1.0-3 dated 2026-04-16 and 1.1-0 dated 2026-09-24
DESCRIPTION | 29 - MD5 | 184 ++++++-- NAMESPACE | 57 ++ NEWS.md |only R/basic_stats.R | 14 R/campnet.R |only R/categories.R |only R/census.R | 292 ++++++++----- R/centrality.R |only R/cohesive_subgroups.R | 406 +++++++++++++------ R/community.R |only R/degree.R | 332 ++++++++++----- R/dominance.R |only R/dynamics.R |only R/equivalence.R |only R/homophily.R | 234 +++++++++- R/inference.R |only R/main_path.R |only R/multilayer.R |only R/path_distances.R | 279 ++++++++----- R/random_networks.R | 292 ++++++++++--- R/signed.R | 95 +--- R/similarities.R | 338 ++++++++------- R/structural_holes.R | 242 +++++++++-- R/structure.R | 425 ++++++++++++++++++- R/triad_uman.R | 67 +-- R/triad_uman_internals.R | 2 R/utilities.R | 601 ++++++++++++++-------------- README.md | 231 +++++++++- build/vignette.rds |binary data/campnet.rda |only inst/doc/distinctive.R |only inst/doc/distinctive.Rmd |only inst/doc/distinctive.html |only inst/doc/multilayer.R | 59 ++ inst/doc/multilayer.Rmd | 135 +++++- inst/doc/multilayer.html | 810 ++++++++++++++++++++------------------ inst/doc/netmem.R |only inst/doc/netmem.Rmd |only inst/doc/netmem.html |only man/aggregate_layers.Rd |only man/alter_composition.Rd |only man/alter_heterogeneity.Rd |only man/alter_homophily.Rd |only man/betweenness_centrality.Rd |only man/block_density.Rd |only man/bonacich_power.Rd |only man/brokerage_roles.Rd |only man/campnet.Rd |only man/centrality_centralization.Rd |only man/citation_decay.Rd |only man/clique_max.Rd |only man/closeness_centrality.Rd |only man/communities.Rd |only man/components_id.Rd | 33 + man/concor.Rd |only man/core_periphery.Rd |only man/cug_test.Rd |only man/dag.Rd |only man/dir_inclusion.Rd |only man/dist_sim_matrix.Rd | 11 man/dominance_layers.Rd |only man/dominance_pairs.Rd |only man/dominance_ranks.Rd |only man/dyad_triad_table.Rd | 26 - man/eb_constraint.Rd | 32 + man/edgelist_to_matrix.Rd | 31 + man/ego_net.Rd | 3 man/ei_index.Rd | 17 man/eigenvector_centrality.Rd |only man/extract_component.Rd | 4 man/fractional_approach.Rd | 86 +++- man/gen_density.Rd | 10 man/geodesics.Rd |only man/hyperevent_dominance.Rd |only man/ind_rand_matrix.Rd | 16 man/indirect_rel.Rd |only man/k_core.Rd | 8 man/katz_centrality.Rd |only man/krackhardt_index.Rd |only man/leading_eigen.Rd |only man/leiden.Rd |only man/main_path.Rd |only man/main_path_diag.Rd |only man/meta_matrix.Rd | 6 man/mix_matrix.Rd | 8 man/modularity_score.Rd |only man/multilevel_degree.Rd | 55 ++ man/multiplex_census.Rd | 31 + man/neigh_inclusion.Rd |only man/page_rank_centrality.Rd |only man/pareto_dominance.Rd |only man/partition_centrality.Rd |only man/pos_dominance.Rd |only man/pref_attachment.Rd |only man/preserved_order.Rd |only man/q_analysis.Rd | 90 +++- man/qap_cor.Rd |only man/qap_lm.Rd |only man/rege.Rd |only man/segregation.Rd |only man/set_inclusion.Rd |only man/simplicial_complexes.Rd | 55 ++ man/small_world.Rd |only man/social_influence.Rd |only man/structural_holes.Rd |only man/supra_adjacency.Rd |only man/threshold_diffusion.Rd |only man/trans_coef.Rd | 17 man/traversal_weights.Rd |only man/triad_uman.Rd | 11 man/zone_sample.Rd | 3 tests/testthat/test_audit.R |only tests/testthat/test_categories.R |only tests/testthat/test_centrality.R |only tests/testthat/test_cliques.R | 24 + tests/testthat/test_community.R |only tests/testthat/test_constraint.R |only tests/testthat/test_coverage.R |only tests/testthat/test_degree.R | 142 ++++++ tests/testthat/test_dominance.R |only tests/testthat/test_dyads.R | 22 - tests/testthat/test_dynamics.R |only tests/testthat/test_equivalence.R |only tests/testthat/test_extensions.R |only tests/testthat/test_generators.R |only tests/testthat/test_inference.R |only tests/testthat/test_macro.R |only tests/testthat/test_main_path.R |only tests/testthat/test_multilayer.R |only tests/testthat/test_paths.R |only tests/testthat/test_positional.R |only tests/testthat/test_q_analysis.R |only tests/testthat/test_segregation.R |only tests/testthat/test_simplicial.R |only tests/testthat/test_triad_uman.R |only vignettes/distinctive.Rmd |only vignettes/multilayer.Rmd | 135 +++++- vignettes/netmem.Rmd |only 139 files changed, 4263 insertions(+), 1737 deletions(-)
Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series. 'mvMORPH' also proposes high-dimensional multivariate comparative tools (linear models using Generalized Least Squares and multivariate tests) based on penalized likelihood and Empirical Bayes approaches. See
Clavel et al. (2015) <DOI:10.1111/2041-210X.12420>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, Clavel & Morlon (2020) <DOI:10.1093/sysbio/syaa010>, and Montoya et al. (2026) <DOI:10.1093/sysbio/syag051>.
Author: Julien Clavel [aut, cre],
with contributions from Aaron King [aut],
Emmanuel Paradis [aut]
Maintainer: Julien Clavel <julien.clavel@hotmail.fr>
Diff between mvMORPH versions 1.2.1 dated 2024-08-28 and 1.2.2 dated 2026-09-24
DESCRIPTION | 15 MD5 | 60 +-- NAMESPACE | 18 - NEWS.md | 7 R/classes_methods.r | 694 ++++++++++++++++++++++++++++++---------- R/fun.r | 59 +++ R/multivariate.stat.r | 288 ++++++++++------ R/mvSIM.r | 71 ++++ R/mvgls.dfa.r | 133 +++++-- R/mvgls.r | 81 +++- R/p3ca.r |only R/penalized.r | 158 +++++++-- R/plot_methods.r | 114 ++++++ R/testLRT.r | 185 ++++++++++ R/utils.r | 27 + R/zzz.r | 26 + README.md | 6 build/vignette.rds |binary inst/doc/How_to_use_mvMORPH.R | 184 +++++----- inst/doc/How_to_use_mvMORPH.pdf |binary inst/doc/tutorial_mvMORPH.R | 96 ++--- inst/doc/tutorial_mvMORPH.pdf |binary man/EIC.Rd | 2 man/LRT.Rd | 35 +- man/effectsize.Rd | 17 man/manova.gls.Rd | 9 man/mapping.asr.Rd |only man/mvgls.Rd | 32 + man/mvgls.pca.Rd | 2 man/p3ca.Rd |only man/pcLoadings.Rd |only man/pcaShape.Rd | 7 src/pic_loglik_mvmorph.c | 2 33 files changed, 1773 insertions(+), 555 deletions(-)
Title: Linear Mixed Models with Sparse Matrix Methods and Smoothing
Description: Provides tools for fitting linear mixed models using sparse matrix
methods and variance component estimation. Applications include spline-based
modeling of spatial and temporal trends using penalized splines (Boer, 2023)
<doi:10.1177/1471082X231178591>.
Author: Martin Boer [aut] ,
Bart-Jan van Rossum [aut, cre]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between LMMsolver versions 1.0.13 dated 2026-05-29 and 1.0.14 dated 2026-09-24
LMMsolver-1.0.13/LMMsolver/man/ADchol.Rd |only LMMsolver-1.0.14/LMMsolver/DESCRIPTION | 10 LMMsolver-1.0.14/LMMsolver/MD5 | 109 - LMMsolver-1.0.14/LMMsolver/NAMESPACE | 39 LMMsolver-1.0.14/LMMsolver/NEWS.md | 8 LMMsolver-1.0.14/LMMsolver/R/DifferentiationCholesky.R | 181 +- LMMsolver-1.0.14/LMMsolver/R/HarvilleODE.R | 244 +- LMMsolver-1.0.14/LMMsolver/R/LMMsolve-class.R | 2 LMMsolver-1.0.14/LMMsolver/R/RcppExports.R | 48 LMMsolver-1.0.14/LMMsolver/R/constructFixed.R | 2 LMMsolver-1.0.14/LMMsolver/R/constructRandom.R | 4 LMMsolver-1.0.14/LMMsolver/R/getHeritability.R | 143 + LMMsolver-1.0.14/LMMsolver/R/ginverse.R | 258 ++- LMMsolver-1.0.14/LMMsolver/R/mLogLik.R | 36 LMMsolver-1.0.14/LMMsolver/R/orthoModel.R | 84 LMMsolver-1.0.14/LMMsolver/R/predictFunctions.R | 31 LMMsolver-1.0.14/LMMsolver/R/sparseMixedModels.R | 49 LMMsolver-1.0.14/LMMsolver/R/splinesFunctions.R | 1 LMMsolver-1.0.14/LMMsolver/R/utils.R | 21 LMMsolver-1.0.14/LMMsolver/build/partial.rdb |binary LMMsolver-1.0.14/LMMsolver/build/vignette.rds |binary LMMsolver-1.0.14/LMMsolver/inst/doc/Solving_Linear_Mixed_Models.R | 10 LMMsolver-1.0.14/LMMsolver/inst/doc/Solving_Linear_Mixed_Models.Rmd | 10 LMMsolver-1.0.14/LMMsolver/inst/doc/Solving_Linear_Mixed_Models.html | 63 LMMsolver-1.0.14/LMMsolver/inst/tinytest/GLMMFull |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/binomial1 |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/binomial2 |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/binomial3 |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/effDim0 |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/effDims |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/gam1DFull |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/mLogLik0 |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/modCoefsSe |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/multinomial1 |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/spl1DFull |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/spl2DFull |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/spl2DFull2 |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/spl2DFull3 |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/spl3DFull |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/spl3DFull2 |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/spl3DFull3 |binary LMMsolver-1.0.14/LMMsolver/inst/tinytest/test_HarvilleODE.R | 12 LMMsolver-1.0.14/LMMsolver/inst/tinytest/test_LMMsolve.R | 7 LMMsolver-1.0.14/LMMsolver/inst/tinytest/test_LMMsolver_chol.R |only LMMsolver-1.0.14/LMMsolver/inst/tinytest/test_getHeritability.R | 4 LMMsolver-1.0.14/LMMsolver/inst/tinytest/test_ginverse.R |only LMMsolver-1.0.14/LMMsolver/inst/tinytest/test_internal_functions.R | 8 LMMsolver-1.0.14/LMMsolver/inst/tinytest/varComps |binary LMMsolver-1.0.14/LMMsolver/man/as.ginverse.Rd | 73 LMMsolver-1.0.14/LMMsolver/src/ADcholesky.cpp | 842 +++++----- LMMsolver-1.0.14/LMMsolver/src/ADcholesky.h |only LMMsolver-1.0.14/LMMsolver/src/AuxFun.cpp | 3 LMMsolver-1.0.14/LMMsolver/src/LMMsolver_chol.cpp |only LMMsolver-1.0.14/LMMsolver/src/RcppExports.cpp | 75 LMMsolver-1.0.14/LMMsolver/src/SparseMatrix.cpp | 98 + LMMsolver-1.0.14/LMMsolver/src/SparseMatrix.h | 6 LMMsolver-1.0.14/LMMsolver/src/cholesky.cpp | 527 ++++-- LMMsolver-1.0.14/LMMsolver/vignettes/Solving_Linear_Mixed_Models.Rmd | 10 58 files changed, 1875 insertions(+), 1143 deletions(-)
Title: Kolmogorov-Zurbenko Adaptive Filters
Description: Time series analysis including break detection, spectral
analysis, and Kolmogorov-Zurbenko Fourier transforms, following
Zurbenko et al. (1996) <doi:10.1175/1520-0442(1996)009%3C3548:DDITSO%3E2.0.CO;2>
and Yang and Zurbenko (2010) <doi:10.1002/wics.71>.
Author: Brian Close [aut, cre],
Igor Zurbenko [aut],
Mingzeng Sun [aut]
Maintainer: Brian Close <brian.close@gmail.com>
Diff between kza versions 4.2.0 dated 2026-09-14 and 4.2.1 dated 2026-09-24
DESCRIPTION | 13 ++++++---- MD5 | 16 +++++++----- NEWS.md | 43 ++++++++++++++++++++++++++++++++++ R/kzft.R | 18 +++++++++++--- man/kzft.Rd | 9 +++++-- man/kzp.Rd | 14 +++++++---- man/kzs.Rd | 7 +++-- man/kztp.Rd | 6 +++- tests/testthat/test-kzft-odd-window.R |only tests/testthat/test-kztp-box-index.R |only 10 files changed, 100 insertions(+), 26 deletions(-)
Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database
<https://ec.europa.eu/eurostat> together with search and manipulation
utilities.
Author: Leo Lahti [aut, cre] ,
Janne Huovari [aut],
Markus Kainu [aut],
Przemyslaw Biecek [aut],
Daniel Antal [ctb],
Daniel Loos [ctb] ,
Diego Hernangomez [ctb] ,
Joona Lehtomaki [ctb],
Francois Briatte [ctb],
Reto Stauffer [ctb],
Paul Rougieux [ctb],
Anna V [...truncated...]
Maintainer: Leo Lahti <leo.lahti@iki.fi>
Diff between eurostat versions 4.0.0 dated 2023-12-19 and 4.1.1 dated 2026-09-24
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Title: Non-Compartmental Analysis for Campsis Simulation Platform
Description: A flexible and user-friendly non-compartmental analysis (NCA)
toolkit designed to work seamlessly with simulated pharmacokinetic
data generated using the 'campsis' ecosystem. The package provides a
comprehensive framework to compute standard and custom NCA metrics,
including exposure (AUC), peak/trough concentrations, half-life and
time-above/below thresholds, with support for configurable time
windows and summary statistics. 'campsisnca' integrates tightly with
'campsis' and 'campsismod', enabling streamlined workflows from
simulation to analysis. In addition, the package provides a JSON-based
interface to define NCA analyses, metrics and options using formal
schemas, allowing analyses to be created, validated and executed
outside of R and facilitating reproducibility, automation and system
integration. The package also includes utilities for generating
formatted summary tables and exporting results in multiple formats
suitable for reporting. Trapezoidal rule implementation for AUC
ca [...truncated...]
Author: Nicolas Luyckx [aut, cre],
Calvagone [cph]
Maintainer: Nicolas Luyckx <nicolas.luyckx@lynxsoft.be>
Diff between campsisnca versions 1.7.1 dated 2026-09-15 and 1.7.2 dated 2026-09-24
DESCRIPTION | 17 ++++++++++------- MD5 | 4 ++-- NEWS.md | 3 +++ 3 files changed, 15 insertions(+), 9 deletions(-)
Title: Automated Functions for Basic Statistical Tests
Description: Provides simple and intuitive functions for basic statistical analyses.
Methods include the t-test (Student 1908 <doi:10.1093/biomet/6.1.1>),
the Mann-Whitney U test (Mann and Whitney 1947 <doi:10.1214/aoms/1177730491>),
Pearson's correlation (Pearson 1895 <doi:10.1098/rspl.1895.0041>),
and analysis of variance (Fisher 1925, <doi:10.1007/978-1-4612-4380-9_5>).
Functions are compatible with 'ggplot2' and 'dplyr'.
Author: Luiz Garcia [aut, cre]
Maintainer: Luiz Garcia <luiz.cardoso@ufpr.br>
Diff between autotestR versions 1.2.16 dated 2026-08-21 and 1.2.17 dated 2026-09-24
DESCRIPTION | 6 MD5 | 10 - R/Interaction_test.R | 415 ++++++++++++++++++++++++------------------------ R/utils_stats.R | 2 README.md | 5 man/test.interaction.Rd | 32 ++- 6 files changed, 249 insertions(+), 221 deletions(-)
Title: Tidying, Analysis, and Fast Visualization of Animal and Plant
Pedigrees
Description: Provides tools for the analysis and visualization of animal and
plant pedigrees. Analytical methods include equivalent complete generations,
generation intervals, effective population size (via inbreeding, coancestry,
and demographic approaches), founder and ancestor contributions, partial
inbreeding, genetic diversity indices, and additive (A), dominance (D), and
epistatic (AA) relationship matrices. Core algorithms — ancestry tracing,
topological sorting, inbreeding coefficients, and matrix construction — are
implemented in C++ ('Rcpp', 'RcppArmadillo') and 'data.table', scaling to
pedigrees with over one million individuals. Matrix-free pedigree
traversals apply additive relationship matrices or their inverses to
vectors and matrices without materializing dense square matrices. Pedigree
graphs are rendered via 'igraph' with support for compact full-sib family
display; relationship matrices can be visualized as heatmaps. Supports
complex mating systems, including selfing and pedigree [...truncated...]
Author: Sheng Luan [aut, cre]
Maintainer: Sheng Luan <luansheng@gmail.com>
Diff between visPedigree versions 1.9.0 dated 2026-07-15 and 1.10.1 dated 2026-09-24
visPedigree-1.10.1/visPedigree/DESCRIPTION | 7 - visPedigree-1.10.1/visPedigree/MD5 | 60 +++++----- visPedigree-1.10.1/visPedigree/NAMESPACE | 1 visPedigree-1.10.1/visPedigree/NEWS.md | 16 ++ visPedigree-1.10.1/visPedigree/R/pedexport.R |only visPedigree-1.10.1/visPedigree/README.md | 15 +- visPedigree-1.10.1/visPedigree/build/vignette.rds |binary visPedigree-1.10.1/visPedigree/inst/doc/draw-pedigree.R | 2 visPedigree-1.10.1/visPedigree/inst/doc/draw-pedigree.Rmd | 13 +- visPedigree-1.10.1/visPedigree/inst/doc/draw-pedigree.html | 49 ++++---- visPedigree-1.10.1/visPedigree/inst/doc/efficient-visPedigree-workflows.Rmd | 4 visPedigree-1.10.1/visPedigree/inst/doc/efficient-visPedigree-workflows.html | 4 visPedigree-1.10.1/visPedigree/inst/doc/pedigree-analysis.Rmd | 11 + visPedigree-1.10.1/visPedigree/inst/doc/pedigree-analysis.html | 21 +-- visPedigree-1.10.1/visPedigree/inst/doc/relationship-matrix.R | 2 visPedigree-1.10.1/visPedigree/inst/doc/relationship-matrix.Rmd | 21 ++- visPedigree-1.10.1/visPedigree/inst/doc/relationship-matrix.html | 45 ++++--- visPedigree-1.10.1/visPedigree/inst/doc/tidy-pedigree.Rmd | 4 visPedigree-1.10.1/visPedigree/inst/doc/tidy-pedigree.html | 9 - visPedigree-1.10.1/visPedigree/inst/doc/tidyped-structure.Rmd | 6 - visPedigree-1.10.1/visPedigree/inst/doc/tidyped-structure.html | 6 - visPedigree-1.10.1/visPedigree/man/dot-ensure_export_cols.Rd |only visPedigree-1.10.1/visPedigree/man/dot-pedexport_char.Rd |only visPedigree-1.10.1/visPedigree/man/dot-pedexport_num.Rd |only visPedigree-1.10.1/visPedigree/man/pedexport.Rd |only visPedigree-1.10.1/visPedigree/tests/testthat/test-as-tidyped.R | 16 ++ visPedigree-1.10.1/visPedigree/tests/testthat/test-pedexport-extra.R |only visPedigree-1.10.1/visPedigree/tests/testthat/test-pedexport.R |only visPedigree-1.10.1/visPedigree/vignettes/draw-pedigree.Rmd | 13 +- visPedigree-1.10.1/visPedigree/vignettes/efficient-visPedigree-workflows.Rmd | 4 visPedigree-1.10.1/visPedigree/vignettes/pedigree-analysis.Rmd | 11 + visPedigree-1.10.1/visPedigree/vignettes/relationship-matrix.Rmd | 21 ++- visPedigree-1.10.1/visPedigree/vignettes/tidy-pedigree.Rmd | 4 visPedigree-1.10.1/visPedigree/vignettes/tidyped-structure.Rmd | 6 - visPedigree-1.9.0/visPedigree/tests/testthat/Rplots.pdf |only 35 files changed, 234 insertions(+), 137 deletions(-)
Title: Analysis the Weather Data for Agriculture
Description: Functions are collected to analyse weather data for agriculture
purposes including to read weather records in multiple formats,
calculate extreme climate index. Demonstration data are included the
SILO daily climate data (licensed under CC BY 4.0, <https://www.longpaddock.qld.gov.au/silo/>).
Author: Bangou Zheng [aut, cre]
Maintainer: Bangou Zheng <zheng.bangyou@gmail.com>
Diff between tidyweather versions 0.3.0 dated 2026-08-20 and 0.3.2 dated 2026-09-24
DESCRIPTION | 6 ++-- MD5 | 15 +++++----- R/thermal_time.R | 42 ++++++++++++++++++++---------- R/utilities.R | 10 +++---- inst/extdata/ppd_40082.met |only man/day_length.Rd | 4 +- man/interpolate_hourly_sin_pp_adjusted.Rd | 28 +++++++++++++++----- man/thermal_time.Rd | 4 +- tests/testthat/test-thermal_time.R | 30 ++++++++++----------- 9 files changed, 85 insertions(+), 54 deletions(-)
Title: High Throughput Phenotyping (HTP) Data Analysis
Description: Phenotypic analysis of data coming from high throughput
phenotyping (HTP) platforms, including different types of outlier detection,
spatial analysis, and parameter estimation. The package is being developed
within the EPPN2020 project (<https://cordis.europa.eu/project/id/731013>).
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r/>).
Author: Emilie J Millet [aut] ,
Maria Xose Rodriguez Alvarez [aut] ,
Diana Marcela Perez Valencia [aut] ,
Isabelle Sanchez [aut],
Nadine Hilgert [aut],
Bart-Jan van Rossum [aut, cre] ,
Fred van Eeuwijk [aut] ,
Martin Boer [aut]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenHTP versions 1.0.9.4 dated 2026-07-06 and 1.0.9.5 dated 2026-09-24
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 28 +++++++++++++++++----------- NEWS.md | 4 ++++ inst/doc/Overview_HTP.html | 16 ++++++++-------- inst/tinytest/test_detectSerieOut.R | 6 ++++-- 6 files changed, 43 insertions(+), 31 deletions(-)
Title: 'Shiny' Bindings for Designsystemet Components
Description: Provides 'R' wrappers for the Designsystemet component library
<https://designsystemet.no>, enabling use of Norwegian government design system
components in 'Shiny' applications. Includes web components and CSS-based
HTML components with full 'Shiny' input binding support.
Author: Novica Nakov [aut, cre, cph]
Maintainer: Novica Nakov <nnovica@gmail.com>
Diff between shinyds versions 0.5.0 dated 2026-08-22 and 0.6.0 dated 2026-09-24
shinyds-0.5.0/shinyds/inst/www/js/ds-bindings-generated.js |only shinyds-0.6.0/shinyds/DESCRIPTION | 7 + shinyds-0.6.0/shinyds/MD5 | 31 ++++---- shinyds-0.6.0/shinyds/NEWS.md | 6 + shinyds-0.6.0/shinyds/R/ds-dependencies.R | 5 - shinyds-0.6.0/shinyds/R/ds-misc.R | 43 ++++++++++-- shinyds-0.6.0/shinyds/README.md | 2 shinyds-0.6.0/shinyds/inst/doc/getting-started.R | 6 + shinyds-0.6.0/shinyds/inst/doc/getting-started.html | 16 ++-- shinyds-0.6.0/shinyds/inst/doc/getting-started.qmd | 6 + shinyds-0.6.0/shinyds/inst/examples/showcase/app.R | 3 shinyds-0.6.0/shinyds/inst/www/css/designsystemet.min.css | 4 - shinyds-0.6.0/shinyds/inst/www/js/designsystemet-web.umd.js | 16 ++-- shinyds-0.6.0/shinyds/man/ds_avatar.Rd | 5 + shinyds-0.6.0/shinyds/man/ds_avatar_stack.Rd | 18 ++++- shinyds-0.6.0/shinyds/tests/testthat/test-showcase.R | 29 +++++++- shinyds-0.6.0/shinyds/vignettes/getting-started.qmd | 6 + 17 files changed, 144 insertions(+), 59 deletions(-)
Title: Integrated Datasets for the 'rmorie' Package
Description: Integrated open data fixtures used by the 'rmorie' package for examples,
vignettes, and tests. Contains snapshots of publicly available datasets
from open-data portals built on the Comprehensive Knowledge Archive
Network ('CKAN', <https://ckan.org/>), 'Socrata'
(<https://dev.socrata.com/>), and 'Opendatasoft'
(<https://www.huwise.com/>) (Chicago, New York City, Toronto, Vancouver,
and others), Statistics Canada Canadian Centre for Justice and Community
Safety Statistics ('CCJS') tables, a multi-agent-reviewed corpus of
Ontario Special Investigations Unit ('SIU', <https://www.siu.on.ca/>)
director's reports, and synthetic fixtures for unit tests. Also ships a
small set of analyst-facing helpers for releasing aggregate statistics
without re-identification risk: Laplace and Gaussian differential
privacy mechanisms and k-anonymity, l-diversity, and cell suppression
verifiers.
Author: Vansh Singh Ruhela [aut, cre]
Maintainer: Vansh Singh Ruhela <vsruhela@proton.me>
Diff between rmoriedata versions 0.3.2 dated 2026-09-17 and 0.3.3 dated 2026-09-24
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rmoriedata-0.3.3/rmoriedata/inst/extdata/_checksums.sig |only rmoriedata-0.3.3/rmoriedata/inst/extdata/_schema.csv |only rmoriedata-0.3.3/rmoriedata/inst/extdata/_signing_key.json |only rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/_catalog.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/arsau_2020_2022_useofforce_agrregatesummarybyyear_2020_2022.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/arsau_2020_2022_useofforce_detaileddataset_2020_2022.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/arsau_2023_uof_individual_records.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/arsau_2023_uof_main_records.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/arsau_2023_uof_probe_cycle_records.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/arsau_2023_uof_weapon_records_invaliddata.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/arsau_2024_uof_individual_records.parquet |binary 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rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/chicago_iucr_codes.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/chicago_neighborhoods.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/chicago_opendata_bulk_catalog.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/cihi_data_tables.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/cpads_pumf_synthetic.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/edmonton_opendata_bulk_catalog.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/edmonton_opendata_crime_adjacent_catalog.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/montreal_opendata_bulk_catalog.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/montreal_sim_intervention_types.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/montreal_sim_interventions_sample.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/nibrs_synthetic.parquet 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rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/otis_c03_individuals_race_by_gender_sample.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/otis_c04_individuals_race_by_region_sample.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/otis_c05_individuals_religion_by_region_sample.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/otis_c06_individuals_age_by_region_sample.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/otis_c07_individuals_alerts_sample.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/otis_c08_individuals_religion_by_gender_sample.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/otis_c09_individuals_age_by_gender_sample.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/otis_c10_aggregate_durations_by_institution_sample.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/otis_c11_aggregate_lengths_sample.parquet |binary 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rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/vancouver_opendata_catalog.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/vancouver_public_art.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/vic_lga_criminal_incidents.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/parquet/vpd_crime_sample.parquet |binary rmoriedata-0.3.3/rmoriedata/inst/extdata/vic |only rmoriedata-0.3.3/rmoriedata/man/arrest_sample.Rd | 18 rmoriedata-0.3.3/rmoriedata/man/ask.Rd | 2 rmoriedata-0.3.3/rmoriedata/man/clear_chicago_cache.Rd |only rmoriedata-0.3.3/rmoriedata/man/complaint_sample.Rd | 31 rmoriedata-0.3.3/rmoriedata/man/fetch_cihi_table.Rd | 10 rmoriedata-0.3.3/rmoriedata/man/load_chicago_data.Rd | 49 - rmoriedata-0.3.3/rmoriedata/man/load_cihi_data_tables.Rd | 12 rmoriedata-0.3.3/rmoriedata/man/load_siu_reports.Rd | 29 rmoriedata-0.3.3/rmoriedata/man/morie_cell_suppress.Rd | 39 rmoriedata-0.3.3/rmoriedata/man/morie_core.Rd | 26 rmoriedata-0.3.3/rmoriedata/man/morie_data_catalog.Rd | 26 rmoriedata-0.3.3/rmoriedata/man/morie_data_checksums.Rd | 9 rmoriedata-0.3.3/rmoriedata/man/morie_data_dictionary.Rd | 32 rmoriedata-0.3.3/rmoriedata/man/morie_data_load.Rd | 41 - rmoriedata-0.3.3/rmoriedata/man/morie_data_path.Rd |only rmoriedata-0.3.3/rmoriedata/man/morie_data_verify.Rd |only rmoriedata-0.3.3/rmoriedata/man/morie_dp_gaussian_mean.Rd | 4 rmoriedata-0.3.3/rmoriedata/man/morie_dp_laplace_count.Rd | 8 rmoriedata-0.3.3/rmoriedata/man/morie_dp_laplace_histogram.Rd | 6 rmoriedata-0.3.3/rmoriedata/man/morie_k_anonymity_verify.Rd | 26 rmoriedata-0.3.3/rmoriedata/man/morie_l_diversity_verify.Rd | 18 rmoriedata-0.3.3/rmoriedata/man/morie_read_parquet.Rd |only rmoriedata-0.3.3/rmoriedata/man/morie_write_parquet.Rd |only rmoriedata-0.3.3/rmoriedata/man/rmoriedata-package.Rd | 2 rmoriedata-0.3.3/rmoriedata/man/rmoriedata-victoria.Rd | 66 - rmoriedata-0.3.3/rmoriedata/tests/testthat/_problems |only rmoriedata-0.3.3/rmoriedata/tests/testthat/helper-chicago-cache.R |only rmoriedata-0.3.3/rmoriedata/tests/testthat/test-ask-shell.R |only rmoriedata-0.3.3/rmoriedata/tests/testthat/test-data-integrity.R |only rmoriedata-0.3.3/rmoriedata/tests/testthat/test-data-store.R |only rmoriedata-0.3.3/rmoriedata/tests/testthat/test-dp.R | 5 rmoriedata-0.3.3/rmoriedata/tests/testthat/test-load_chicago_data.R | 21 rmoriedata-0.3.3/rmoriedata/tests/testthat/test-load_siu_reports.R |only rmoriedata-0.3.3/rmoriedata/tests/testthat/test-network-guards.R |only rmoriedata-0.3.3/rmoriedata/tests/testthat/test-parquet-encoding.R |only rmoriedata-0.3.3/rmoriedata/tests/testthat/test-parquet-store.R |only rmoriedata-0.3.3/rmoriedata/tests/testthat/test-provenance-path.R |only rmoriedata-0.3.3/rmoriedata/tests/testthat/test-signing-pin.R |only rmoriedata-0.3.3/rmoriedata/tests/testthat/testthat-problems.rds |only rmoriedata-0.3.3/rmoriedata/vignettes/rmoriedata.Rmd | 8 155 files changed, 1167 insertions(+), 581 deletions(-)
Title: 'Rcpp' Bindings to 'FastAD' Auto-Differentiation
Description: The header-only 'C++' template library 'FastAD' for automatic
differentiation <https://github.com/JamesYang007/FastAD> is provided by
this package, along with a few illustrative examples that can all be called
from R.
Author: Dirk Eddelbuettel [aut, cre] ,
James Yang [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppFastAD versions 0.0.4 dated 2024-09-24 and 0.0.5 dated 2026-09-24
RcppFastAD-0.0.4/RcppFastAD/src/Makevars |only RcppFastAD-0.0.4/RcppFastAD/src/Makevars.win |only RcppFastAD-0.0.5/RcppFastAD/ChangeLog | 36 ++++++++++++++++++++++++ RcppFastAD-0.0.5/RcppFastAD/DESCRIPTION | 13 ++++---- RcppFastAD-0.0.5/RcppFastAD/MD5 | 19 +++++++----- RcppFastAD-0.0.5/RcppFastAD/README.md | 4 +- RcppFastAD-0.0.5/RcppFastAD/build/partial.rdb |binary RcppFastAD-0.0.5/RcppFastAD/cleanup | 2 - RcppFastAD-0.0.5/RcppFastAD/configure |only RcppFastAD-0.0.5/RcppFastAD/configure.win |only RcppFastAD-0.0.5/RcppFastAD/inst/NEWS.Rd | 10 ++++++ RcppFastAD-0.0.5/RcppFastAD/src/Makevars.in |only RcppFastAD-0.0.5/RcppFastAD/src/Makevars.win.in |only RcppFastAD-0.0.5/RcppFastAD/tools |only 14 files changed, 67 insertions(+), 17 deletions(-)
Title: Minimalist Async Evaluation Framework for R
Description: Evaluates R expressions asynchronously and in parallel,
locally or distributed across networks. An official parallel cluster
type for R. Built on 'nanonext' and 'NNG', its non-polling,
event-driven architecture scales from a laptop to thousands of
processes across high-performance computing clusters and cloud
platforms. Features FIFO scheduling with task cancellation and bounded
queues, promises for reactive programming, 'OpenTelemetry' distributed
tracing, and custom serialization for cross-language data types.
Author: Charlie Gao [aut, cre] ,
Joe Cheng [ctb],
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between mirai versions 2.7.2 dated 2026-07-20 and 2.7.3 dated 2026-09-24
DESCRIPTION | 10 +++++----- MD5 | 36 ++++++++++++++++++------------------ NAMESPACE | 1 + NEWS.md | 7 +++++++ R/daemon.R | 12 ++++++++++-- R/daemons.R | 8 ++++++++ R/mirai-package.R | 4 ++-- inst/doc/mirai.html | 2 +- inst/doc/v01-reference.Rmd | 2 +- inst/doc/v01-reference.html | 4 ++-- inst/doc/v02-promises.html | 2 +- inst/doc/v03-serialization.html | 2 +- inst/doc/v04-parallel.html | 2 +- inst/doc/v05-opentelemetry.html | 2 +- inst/doc/v06-packages.html | 2 +- inst/doc/v07-questions.html | 2 +- man/serial_config.Rd | 8 ++++++++ tests/tests.R | 6 ++++++ vignettes/v01-reference.Rmd | 2 +- 19 files changed, 76 insertions(+), 38 deletions(-)
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana [aut, cre] ,
Joan Salvador [ctb]
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 4.10.3 dated 2026-08-28 and 4.10.4 dated 2026-09-24
DESCRIPTION | 8 - MD5 | 12 - NEWS.md | 5 R/z[.createTable.R | 2 build/vignette.rds |binary inst/doc/compareGroups_vignette.html | 237 +++++++++++++++++------------------ man/compareGroups-package.Rd | 4 7 files changed, 136 insertions(+), 132 deletions(-)
Title: Generic PK/PD Simulation Platform Campsis
Description: A generic, easy-to-use and intuitive
pharmacokinetic/pharmacodynamic (PK/PD) simulation platform based on
the R packages 'rxode2' and 'mrgsolve'. Campsis provides an
abstraction layer over the underlying processes of defining a PK/PD
model, assembling a custom dataset and running a simulation. The
package has a strong dependency on the R package 'campsismod', which
allows models to be read from and written to files, including through
a JSON-based interface, and to be adapted further on the fly in the R
environment. In addition, 'campsis' allows users to assemble datasets
in an intuitive manner, including via a JSON-based interface to import
Campsis datasets defined using formal JSON schemas distributed with
the package. Once the dataset is ready, the package prepares the
simulation, calls 'rxode2' or 'mrgsolve' (at the user's choice), and
returns the results for the given model, dataset and desired
simulation settings. The package itself is licensed under the GPL (>=
3); the JSON sc [...truncated...]
Author: Nicolas Luyckx [aut, cre],
Calvagone [cph]
Maintainer: Nicolas Luyckx <nicolas.luyckx@lynxsoft.be>
Diff between campsis versions 1.9.1 dated 2026-09-17 and 1.9.2 dated 2026-09-24
DESCRIPTION | 19 +++++++++++-------- MD5 | 4 ++-- NEWS.md | 3 +++ 3 files changed, 16 insertions(+), 10 deletions(-)
Title: Bayesian Spatial Functional Clustering
Description: Bayesian clustering of spatial regions with similar functional shapes using
spanning trees and latent Gaussian models. The method enforces spatial contiguity
within clusters and supports a wide range of latent Gaussian models, including
non-Gaussian likelihoods, via the R-INLA framework. The algorithm is based on Zhong,
R., Chacón-Montalván, E. A., and Moraga, P. (2026) <doi:10.1002/sim.70597>,
extending the approach of Zhang, B., Sang, H., Luo, Z. T., and Huang, H. (2023)
<doi:10.1214/22-AOAS1643>. The package includes tools for model fitting, convergence
diagnostics, visualization, and summarization of clustering results.
Author: Erick A. Chacon-Montalvan [aut, cre] ,
Ruiman Zhong [aut] ,
Paula Moraga [aut]
Maintainer: Erick A. Chacon-Montalvan <erick.chaconmontalvan@wur.nl>
Diff between sfclust versions 1.1.0 dated 2026-07-28 and 1.1.1 dated 2026-09-24
DESCRIPTION | 8 - MD5 | 18 ++-- NEWS.md | 14 +++ inst/doc/vg02-advanced-features.R | 46 +--------- inst/doc/vg02-advanced-features.Rmd | 102 ++++++++-------------- inst/doc/vg02-advanced-features.html | 156 +++++++++++++++-------------------- inst/doc/vg03-data-frame.html | 56 +++++------- inst/vigdata/gaussian-mcmc1.rds |binary inst/vigdata/gaussian-mcmc2.rds |binary vignettes/vg02-advanced-features.Rmd | 102 ++++++++-------------- 10 files changed, 205 insertions(+), 297 deletions(-)
Title: Systematic Conservation Prioritization in R
Description: Systematic conservation prioritization using mixed integer linear
programming (MILP). It provides a flexible interface for building and
solving conservation planning problems. Once built, conservation planning
problems can be solved using a variety of commercial and open-source exact
algorithm solvers. By using exact algorithm solvers, solutions can be
generated that are guaranteed to be optimal (or within a pre-specified
optimality gap). Furthermore, conservation problems can be constructed to
optimize the spatial allocation of different management actions or zones,
meaning that conservation practitioners can identify solutions that benefit
multiple stakeholders. To solve large-scale or complex conservation
planning problems, users should install the Gurobi optimization software
(available from <https://www.gurobi.com/>) and the 'gurobi' R package (see
Gurobi Installation Guide vignette for details). Users can also install the
IBM CPLEX software (<https://www.ibm.com/products [...truncated...]
Author: Jeffrey O Hanson [aut] ,
Richard Schuster [aut, cre] ,
Nina Morrell [aut],
Matthew Strimas-Mackey [aut] ,
Sandra Neubert [aut] ,
Brandon P M Edwards [aut] ,
Matthew E Watts [aut],
Peter Arcese [aut] ,
Joseph R Bennett [aut] ,
Hugh P Possingham [aut]
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>
Diff between prioritizr versions 8.1.0 dated 2025-11-10 and 9.0.1 dated 2026-09-24
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608 files changed, 125718 insertions(+), 120523 deletions(-)
Title: Process Data from Wearable Light Loggers and Optical Radiation
Dosimeters
Description: Import, processing, validation, and visualization of personal light exposure measurement data from wearable devices. The package implements features such as the import of data and metadata files, conversion of common file formats, validation of light logging data, verification of crucial metadata, calculation of common parameters, and semi-automated analysis and visualization.
Author: Johannes Zauner [aut, cre] ,
Manuel Spitschan [aut] ,
Steffen Hartmeyer [aut] ,
European Partnership on Metrology [fnd]
has received funding from the European Partnership on Metrology,
co-financed by the European Union's Horizon Europe Research and
[...truncated...]
Maintainer: Johannes Zauner <johannes.zauner@tum.de>
Diff between LightLogR versions 0.10.3 dated 2026-04-28 and 0.10.6 dated 2026-09-24
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Title: Build Graphs for Landscape Genetics Analysis
Description: Build graphs for landscape genetics analysis. This set of
functions can be used to import and convert spatial and genetic data
initially in different formats, import landscape graphs created with
'Graphab' software (Foltete et al., 2021) <doi:10.1016/j.simpa.2021.100065>,
make diagnosis plots of isolation by distance relationships in order to
choose how to build genetic graphs, create graphs with a large range of
pruning methods, weight their links with several genetic distances, plot
and analyse graphs, compare them with other graphs. It uses functions from
other packages such as 'adegenet'
(Jombart, 2008) <doi:10.1093/bioinformatics/btn129> and 'igraph' (Csardi
et Nepusz, 2006) <https://igraph.org/>. It also implements methods
commonly used in landscape genetics to create graphs, described by Dyer et
Nason (2004) <doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et
Fefferman (2017) <doi:10.1111/mec.14059>, and to analyse distance data
(van Strien et a [...truncated...]
Author: Paul Savary [aut, cre] ,
Gilles Vuidel [ctb] ,
Tyler Rudolph [ctb],
Alexandrine Daniel [ctb] ,
Jong Yoon Jeon [ctb]
Maintainer: Paul Savary <psavary@protonmail.com>
Diff between graph4lg versions 1.8.0 dated 2023-01-30 and 2.0.0 dated 2026-09-24
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graph4lg-2.0.0/graph4lg/inst/doc/landscape_graph_3.R | 342 graph4lg-2.0.0/graph4lg/inst/doc/landscape_graph_3.Rmd | 1074 +- graph4lg-2.0.0/graph4lg/inst/doc/landscape_graph_3.html | 915 + graph4lg-2.0.0/graph4lg/inst/extdata/graphab_example |only graph4lg-2.0.0/graph4lg/inst/extdata/rast_simul50.tif |only graph4lg-2.0.0/graph4lg/inst/extdata/res_g.RDa |binary graph4lg-2.0.0/graph4lg/man/check_graphab_object.Rd |only graph4lg-2.0.0/graph4lg/man/check_graphab_version.Rd |only graph4lg-2.0.0/graph4lg/man/dist_max_corr.Rd | 1 graph4lg-2.0.0/graph4lg/man/genepop_to_genind.Rd | 2 graph4lg-2.0.0/graph4lg/man/genind_to_genepop.Rd | 12 graph4lg-2.0.0/graph4lg/man/get_graphab.Rd | 2 graph4lg-2.0.0/graph4lg/man/get_graphab_linkset.Rd | 10 graph4lg-2.0.0/graph4lg/man/get_graphab_linkset_cost.Rd | 13 graph4lg-2.0.0/graph4lg/man/get_graphab_metric.Rd | 49 graph4lg-2.0.0/graph4lg/man/get_graphab_raster_codes.Rd | 9 graph4lg-2.0.0/graph4lg/man/graph_to_gpkg.Rd |only graph4lg-2.0.0/graph4lg/man/graph_to_shp.Rd | 7 graph4lg-2.0.0/graph4lg/man/graphab_capacity.Rd | 43 graph4lg-2.0.0/graph4lg/man/graphab_corridor.Rd | 18 graph4lg-2.0.0/graph4lg/man/graphab_graph.Rd | 18 graph4lg-2.0.0/graph4lg/man/graphab_habitat.Rd |only graph4lg-2.0.0/graph4lg/man/graphab_interpol.Rd | 19 graph4lg-2.0.0/graph4lg/man/graphab_link.Rd | 35 graph4lg-2.0.0/graph4lg/man/graphab_merge_graph.Rd |only graph4lg-2.0.0/graph4lg/man/graphab_metapatch.Rd |only graph4lg-2.0.0/graph4lg/man/graphab_metric.Rd | 50 graph4lg-2.0.0/graph4lg/man/graphab_modul.Rd | 18 graph4lg-2.0.0/graph4lg/man/graphab_pointset.Rd | 65 graph4lg-2.0.0/graph4lg/man/graphab_project.Rd | 47 graph4lg-2.0.0/graph4lg/man/graphab_project_desc.Rd | 55 graph4lg-2.0.0/graph4lg/man/graphab_show.Rd |only graph4lg-2.0.0/graph4lg/man/graphab_to_igraph.Rd | 43 graph4lg-2.0.0/graph4lg/man/link_compar.Rd | 2 graph4lg-2.0.0/graph4lg/man/mat_cost_dist.Rd | 12 graph4lg-2.0.0/graph4lg/man/mat_gen_dist.Rd | 5 graph4lg-2.0.0/graph4lg/man/mat_geo_dist.Rd | 8 graph4lg-2.0.0/graph4lg/man/mat_pw_dps.Rd | 3 graph4lg-2.0.0/graph4lg/man/mypalette.Rd | 4 graph4lg-2.0.0/graph4lg/man/sample_raster.Rd | 7 graph4lg-2.0.0/graph4lg/vignettes/biblio_vignette.bib | 5239 +++++----- graph4lg-2.0.0/graph4lg/vignettes/genetic_graph_2.Rmd | 894 - graph4lg-2.0.0/graph4lg/vignettes/graph_comparisons_4.Rmd | 682 - graph4lg-2.0.0/graph4lg/vignettes/input_data_processing_1.Rmd | 65 graph4lg-2.0.0/graph4lg/vignettes/landscape_graph_3.Rmd | 1074 +- 108 files changed, 14622 insertions(+), 12774 deletions(-)
Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and
unified Future API for sequential and parallel processing of R
expression via futures. The simplest way to evaluate an expression
in parallel is to use `x %<-% { expression }` with `plan(multisession)`.
This package implements sequential, multicore, multisession, and
cluster futures. With these, R expressions can be evaluated on the
local machine, in parallel a set of local machines, or distributed
on a mix of local and remote machines.
Extensions to this package implement additional backends for
processing futures via compute cluster schedulers, etc.
Because of its unified API, there is no need to modify any code in order
switch from sequential on the local machine to, say, distributed
processing on a remote compute cluster.
Another strength of this package is that global variables and functions
are automatically identified and exported as needed, making it
straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.75.0 dated 2026-07-20 and 1.76.0 dated 2026-09-24
DESCRIPTION | 8 MD5 | 44 ++-- NAMESPACE | 104 ++++++----- NEWS.md | 27 ++ R/000.re-exports.R | 9 R/backend_api-11.ClusterFutureBackend-class.R | 9 R/backend_api-evalFuture.R | 10 - R/utils_api-makeClusterFuture.R | 145 +++++++++++++++- inst/doc/future-1-overview.html | 2 inst/doc/future-2-output.html | 2 inst/doc/future-2b-backend.html | 2 inst/doc/future-3-topologies.html | 2 inst/doc/future-4-issues.html | 2 inst/doc/future-4-non-exportable-objects.html | 2 inst/doc/future-5-startup.html | 2 inst/doc/future-6-future-api-backend-specification.html | 2 inst/doc/future-7-for-package-developers.html | 2 inst/doc/future-8-how-future-is-validated.html | 2 inst/testme/test-future,workdir.R |only inst/testme/test-makeClusterFuture-clusterEvalQ.R |only inst/testme/test-multisession-libpaths.R | 2 man/getGlobalsAndPackages.Rd | 3 man/makeClusterFuture.Rd | 38 +++- tests/test-future,workdir.R |only tests/test-makeClusterFuture-clusterEvalQ.R |only 25 files changed, 317 insertions(+), 102 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-01 0.1.3
2024-04-30 0.1.2
2024-04-21 0.1.1
2022-05-18 0.1.0
Title: Templated Unified Library for Posterior Approximation in
Bayesian Hierarchical Models
Description: A general-purpose engine for fitting Bayesian hierarchical models
with spatial fields, temporal effects, spatially varying coefficients, and
multiple inference backends. Scalable spatial structure includes Hilbert
space approximate Gaussian processes (HSGP; Riutort-Mayol et al. 2023
<doi:10.1007/s11222-022-10167-2>), nearest-neighbor Gaussian processes
(NNGP; Datta et al. 2016 <doi:10.1080/01621459.2015.1044091>), intrinsic
conditional autoregressive models (ICAR; Besag, York, and Mollie 1991
<doi:10.1007/BF00116466>), the reparameterized Besag-York-Mollie model
(BYM2; Riebler et al. 2016 <doi:10.1177/0962280216660421>), and stochastic
partial differential equation fields (SPDE; Lindgren, Rue, and Lindstrom
2011 <doi:10.1111/j.1467-9868.2011.00777.x>). Temporal structure covers
random walks, autoregressive processes, and Gaussian processes. Inference
is tiered by correctness guarantee: exact Hamiltonian Monte Carlo with the
No-U-Turn sampler, Laplace and n [...truncated...]
Author: Gilles Colling [aut, cre, cph] ,
Frances Y. Kuo [ctb, cph] ,
Stephen Joe [ctb, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between tulpa versions 0.5.0 dated 2026-09-21 and 0.6.0 dated 2026-09-24
DESCRIPTION | 6 MD5 | 82 +-- NEWS.md | 225 +++++++++ R/diagnostics_generic.R | 3 R/fit_st_nested.R | 14 R/fit_st_nested_auto_grid.R | 5 R/hyper_grid.R | 13 R/hyper_grid_refine.R | 197 ++++---- R/laplace_diagnostics.R | 101 ++++ R/nested_laplace.R | 56 ++ R/nested_laplace_auto_grid.R | 71 +-- R/nested_laplace_joint.R | 43 + R/nested_laplace_joint_helpers.R | 6 R/nested_laplace_joint_pareto_k.R | 8 R/nested_laplace_moments.R | 189 ++++++-- R/plot_diagnostics.R | 50 ++ R/posterior_draws_hyper.R | 289 +++++++++++- R/settings.R | 17 inst/include/tulpa/ad_scalar_math.h |only inst/include/tulpa/lkj_chol.h |only inst/include/tulpa/re_term_prior.h |only man/diagnostic_summary.Rd | 8 man/fit_st_nested.Rd | 8 man/tulpa_hyper_draws.Rd | 6 man/tulpa_hyper_grid.Rd | 7 man/tulpa_nested_laplace.Rd | 7 man/tulpa_nested_laplace_joint.Rd | 9 src/autodiff_utils.h | 186 ------- src/lkj_chol_helpers.h | 79 --- src/tulpa_priors_re.h | 98 ---- tests/testthat/helper-sparse-icar-arm.R |only tests/testthat/helper-spatial-beta-coverage.R |only tests/testthat/test-axis-sd-estimator.R | 4 tests/testthat/test-consistency-bisection.R |only tests/testthat/test-copy-alpha-resolution.R | 2 tests/testthat/test-hyper-draws.R | 446 +++++++++++++++++++ tests/testthat/test-hyper-grid.R | 6 tests/testthat/test-hyper-quadrature-refinement.R | 8 tests/testthat/test-hyper-share.R |only tests/testthat/test-inner-debias-note.R |only tests/testthat/test-joint-axis-refinable.R | 26 - tests/testthat/test-nested-laplace-joint-auto-grid.R | 30 - tests/testthat/test-outer-grid-collapse-reporting.R |only tests/testthat/test-phi-grid-placement.R | 20 tests/testthat/test-settings.R | 2 tests/testthat/test-spatial-beta-coverage.R |only tests/testthat/test-subspace-debias-backends.R | 30 + 47 files changed, 1704 insertions(+), 653 deletions(-)
Title: Estimated Glomerular Filtration Rate (eGFR) Calculators
Description: A comprehensive, vectorised toolkit for estimating glomerular
filtration rate (eGFR) and creatinine clearance from serum creatinine,
cystatin C, or both. Implements adult, paediatric, and
neonatal equations, including the Chronic Kidney Disease Epidemiology
Collaboration (CKD-EPI) equations (2009, 2012, 2021), the Modification
of Diet in Renal Disease (MDRD) Study equation, Cockcroft-Gault, the
European Kidney Function Consortium (EKFC) equations, the Full Age
Spectrum (FAS) equations, the Lund-Malmoe equations, the Berlin
Initiative Study (BIS) equations, the Schwartz bedside equation, the
Chronic Kidney Disease in Children Under 25 (CKiD U25) equations, the
Caucasian, Asian, Paediatric, and Adult (CAPA) cystatin C equation, and
a neonatal equation. Helpers for body surface area, chronic kidney
disease (CKD) staging following the Kidney Disease: Improving Global
Outcomes (KDIGO) guideline, and unit conversions are included.
Methods are described in Levey et al. (2009) <doi:10.7326/ [...truncated...]
Author: Markus Hovd [aut, cre, cph]
Maintainer: Markus Hovd <markus@hovd.io>
Diff between egfr versions 1.1.1 dated 2026-06-26 and 2.0.0 dated 2026-09-24
egfr-1.1.1/egfr/man/egfr_ckid_u25_cr_extended.Rd |only egfr-2.0.0/egfr/DESCRIPTION | 14 egfr-2.0.0/egfr/LICENSE | 4 egfr-2.0.0/egfr/MD5 | 96 - egfr-2.0.0/egfr/NAMESPACE | 51 - egfr-2.0.0/egfr/NEWS.md | 102 +- egfr-2.0.0/egfr/R/ckd-epi.R | 437 ++++---- egfr-2.0.0/egfr/R/ekfc.R | 607 ++++++----- egfr-2.0.0/egfr/R/helpers.R | 200 +-- egfr-2.0.0/egfr/R/mdrd.R | 162 +-- egfr-2.0.0/egfr/R/pediatric.R | 465 ++++----- egfr-2.0.0/egfr/R/utils.R | 206 ++-- egfr-2.0.0/egfr/README.md | 226 ++-- egfr-2.0.0/egfr/build/partial.rdb |binary egfr-2.0.0/egfr/build/vignette.rds |binary egfr-2.0.0/egfr/inst/CITATION | 31 egfr-2.0.0/egfr/inst/doc/egfr.R | 74 - egfr-2.0.0/egfr/inst/doc/egfr.Rmd | 194 +-- egfr-2.0.0/egfr/inst/doc/egfr.html | 861 ++++++++--------- egfr-2.0.0/egfr/man/bsa.Rd | 64 - egfr-2.0.0/egfr/man/ckd_stage.Rd | 50 egfr-2.0.0/egfr/man/convert_creatinine.Rd | 46 egfr-2.0.0/egfr/man/egfr-package.Rd | 76 - egfr-2.0.0/egfr/man/egfr_bis_cr.Rd | 93 - egfr-2.0.0/egfr/man/egfr_capa.Rd | 65 - egfr-2.0.0/egfr/man/egfr_ckdepi_cr_2009.Rd | 114 +- egfr-2.0.0/egfr/man/egfr_ckdepi_cr_2021.Rd | 90 - egfr-2.0.0/egfr/man/egfr_ckdepi_cr_cys_2021.Rd | 98 - egfr-2.0.0/egfr/man/egfr_ckdepi_cys_2012.Rd | 80 - egfr-2.0.0/egfr/man/egfr_ckdepi_cys_2021.Rd | 90 + egfr-2.0.0/egfr/man/egfr_ckid_u25_cr.Rd | 108 +- egfr-2.0.0/egfr/man/egfr_ckid_u25_cr_cys.Rd | 108 +- egfr-2.0.0/egfr/man/egfr_ckid_u25_cys.Rd | 76 - egfr-2.0.0/egfr/man/egfr_cockcroft_gault.Rd | 105 +- egfr-2.0.0/egfr/man/egfr_ekfc_cr.Rd | 135 +- egfr-2.0.0/egfr/man/egfr_ekfc_cr_cys.Rd | 110 +- egfr-2.0.0/egfr/man/egfr_ekfc_cys.Rd | 81 - egfr-2.0.0/egfr/man/egfr_fas_cr.Rd | 103 +- egfr-2.0.0/egfr/man/egfr_lund_malmo.Rd | 96 + egfr-2.0.0/egfr/man/egfr_mdrd.Rd | 106 +- egfr-2.0.0/egfr/man/egfr_neonatal.Rd | 85 - egfr-2.0.0/egfr/man/egfr_schwartz.Rd | 82 - egfr-2.0.0/egfr/man/gfr_bsa_adjust.Rd | 54 - egfr-2.0.0/egfr/tests/testthat.R | 8 egfr-2.0.0/egfr/tests/testthat/test-ckd-epi.R | 130 +- egfr-2.0.0/egfr/tests/testthat/test-ekfc-fas.R | 200 +-- egfr-2.0.0/egfr/tests/testthat/test-helpers.R | 46 egfr-2.0.0/egfr/tests/testthat/test-pediatric.R | 85 - egfr-2.0.0/egfr/tests/testthat/test-reference-values.R |only egfr-2.0.0/egfr/vignettes/egfr.Rmd | 194 +-- 50 files changed, 3372 insertions(+), 3136 deletions(-)
Title: Audit Statistical Fidelity of AI-Mediated Official Statistics
Description: Provides deterministic tools for auditing whether artificial
intelligence systems preserve the numerical, semantic, contextual,
temporal, geographic, unit, provenance, revision, transformation, and
uncertainty properties of official statistics. Structured reference
statistics and machine-generated claims can be compared using
non-compensatory critical-error rules, weakest-link and geometric fidelity
summaries, provenance graphs, and portable SHA-256 proof bundles. The
package provides bounded connectors for official statistical services, an
easy schema-detection and file-import layer for arbitrary official
organisations, extensible provider registries, and a search-first natural-
language verification layer that classifies statistical claims, selects
suitable official sources, retrieves candidate evidence, matches statistical
dimensions, and compares claimed values. If no reference year is stated,
verification uses the latest available matching official observation and
discloses the re [...truncated...]
Author: Hossein Hassani [aut],
Steve MacFeely [aut],
Leila Marvian Mashhad [aut, cre]
Maintainer: Leila Marvian Mashhad <leila.marveian@gmail.com>
Diff between AI4OfficialStats versions 0.1.0 dated 2026-09-22 and 0.2.0 dated 2026-09-24
DESCRIPTION | 32 ++-- MD5 | 53 ++++-- NAMESPACE | 25 +++ NEWS.md | 69 +++++++++ R/api-registry.R | 110 +++++++++++++- R/claim-verification.R |only R/easy-mode.R |only R/extract.R | 12 + R/provider-eurostat-search.R |only R/provider-reference.R | 50 +++++- R/provider-who.R |only R/providers-extra.R | 10 - R/statfidelity-package.R | 5 R/utils.R | 5 README.md | 237 +++++++++++++++++++++++++++++-- inst/CITATION | 2 inst/GSBPM_ALIGNMENT.md | 2 inst/extdata/country_aliases.csv |only man/api_extensions.Rd | 2 man/as_stat_reference.Rd | 13 + man/claim_verification.Rd |only man/easy_mode.Rd |only man/eurostat_catalogue.Rd |only man/providers.Rd | 5 man/providers_extra.Rd | 11 - man/register_official_provider.Rd |only man/search_official_stats.Rd | 13 - man/statfidelity-package.Rd | 6 man/who_connector.Rd |only tests/testthat/test-api-extension.R | 5 tests/testthat/test-claim-verification.R |only tests/testthat/test-easy-mode.R |only tests/testthat/test-providers-offline.R | 1 tests/testthat/test-who.R |only 34 files changed, 570 insertions(+), 98 deletions(-)
More information about AI4OfficialStats at CRAN
Permanent link
Title: Taxonomic Hierarchy Distances and Lineage Analysis
Description: Computes distances between taxonomic hierarchy nodes using lineage
data retrieved from The Taxonomicon <http://taxonomicon.taxonomy.nl>. For
distinct nodes, distance is defined as the reciprocal of the depth of their
most recent common ancestor; identical nodes have distance zero. This
definition yields an ultrametric within each connected hierarchy. Functions
are provided for auditable name resolution, online or user-supplied lineage
analysis, clade membership, pairwise and matrix distance calculation,
hierarchical clustering, principal coordinates analysis, portable JSON
analysis bundles, and cache management. Distance matrices are returned as
base R 'dist' objects. The distances represent classification depth rather
than evolutionary time or phylogenetic branch length.
Author: Rodrigo Fonseca Villa [aut, cre]
Maintainer: Rodrigo Fonseca Villa <rodrigo03.villa@gmail.com>
Diff between taxodist versions 0.7.0 dated 2026-08-28 and 0.8.0 dated 2026-09-24
DESCRIPTION | 22 - MD5 | 31 + NAMESPACE | 7 NEWS.md | 49 ++ R/bundle.R |only R/distance.R | 54 +- R/fetch.R | 383 +++++++++++++++++++ R/taxodist-package.R | 15 R/utils.R | 32 + inst/CITATION | 2 inst/schema |only man/distance_matrix.Rd | 8 man/print.taxodist_bundle.Rd |only man/print.taxodist_resolution.Rd |only man/read_taxodist_bundle.Rd |only man/taxo_bundle.Rd |only man/taxo_from_lineages.Rd |only man/taxo_resolve.Rd |only man/taxodist-package.Rd | 15 man/write_taxodist_bundle.Rd |only tests/testthat/test-distance.R | 758 +++++++++++++++++++++++++++++++++++++-- 21 files changed, 1294 insertions(+), 82 deletions(-)
Title: Neutrosophic Analysis Crossover Designs
Description: Provides methods for Neutrosophic Analysis of Variance (NANOVA)
and Neutrosophic Analysis of Covariance (NANCOVA) for crossover designs,
as well as NANOVA for multi-session designs with direct and residual
effects using interval-valued observations. For crisp data, users can
enter identical lower and upper values for the response and covariate
variables to obtain results equivalent to classical Analysis of
Variance (ANOVA) and Analysis of Covariance (ANCOVA), respectively.
The basic concepts of neutrosophic statistics are based on Smarandache
(2014) <https://fs.unm.edu/NeutrosophicStatistics.pdf>, while the analysis
procedures implemented in this package are newly developed.
Author: Boyina Devi Priyanka [aut, ctb],
Neethu R.S [aut, ctb],
Cini Varghese [aut, ctb],
Mohd Harun [aut, ctb],
Anindita Datta [aut, ctb],
Vinaykumar L.N. [aut, cre]
Maintainer: Vinaykumar L.N. <vinaymandya123@gmail.com>
Diff between NeutroCODsAnalysis versions 0.2.0 dated 2026-08-21 and 0.2.1 dated 2026-09-24
DESCRIPTION | 6 - MD5 | 6 - NAMESPACE | 1 R/MSDnsANOVA.R | 320 ++++++++++++++++++++++++++++++++++++++++----------------- 4 files changed, 233 insertions(+), 100 deletions(-)
More information about NeutroCODsAnalysis at CRAN
Permanent link
Title: Graphical Lasso for Longitudinal Data
Description: Estimate treatment-specific precision matrices (networks) from longitudinal
high-dimensional normal data. The corresponding random effects are also estimated.
It is motivated by the analysis of omics data in clinical trials where the longitudinal
omics data becomes increasingly common. It includes both one-stage models (without
treatment) and two-stage models (with one treatment). For details of the algorithms,
please check the materials on its GitHub repo. If you have any questions, feel free to
contact the maintainers through the email below.
Author: Jie Zhou [aut, cre, cph],
Jiang Gui [aut],
Weston Viles [aut],
Anne Hoen [aut]
Maintainer: Jie Zhou <chowstat@gmail.com>
Diff between lglasso versions 0.1.0 dated 2022-01-15 and 2.0.0 dated 2026-09-24
lglasso-0.1.0/lglasso/R/heterFunction.R |only lglasso-0.1.0/lglasso/R/homoFunction.R |only lglasso-0.1.0/lglasso/R/sample_data.R |only lglasso-0.1.0/lglasso/R/sharedFunction.R |only lglasso-0.1.0/lglasso/README.md |only lglasso-0.1.0/lglasso/data/sample_data.rda |only lglasso-0.1.0/lglasso/man/heterlongraph.Rd |only lglasso-0.1.0/lglasso/man/homolongraph.Rd |only lglasso-0.1.0/lglasso/man/iss.Rd |only lglasso-0.1.0/lglasso/man/ll_homo.Rd |only lglasso-0.1.0/lglasso/man/lli_homo.Rd |only lglasso-0.1.0/lglasso/man/logdensity.Rd |only lglasso-0.1.0/lglasso/man/mle.Rd |only lglasso-0.1.0/lglasso/man/mle_alpha.Rd |only lglasso-0.1.0/lglasso/man/mle_net.Rd |only lglasso-0.1.0/lglasso/man/mle_tau.Rd |only lglasso-0.1.0/lglasso/man/phifunction.Rd |only lglasso-0.1.0/lglasso/man/sample_data.Rd |only lglasso-2.0.0/lglasso/DESCRIPTION | 47 ++-- lglasso-2.0.0/lglasso/MD5 | 37 +-- lglasso-2.0.0/lglasso/NAMESPACE | 4 lglasso-2.0.0/lglasso/R/datalist.R |only lglasso-2.0.0/lglasso/R/functionV1.R |only lglasso-2.0.0/lglasso/R/sysdata.rda |only lglasso-2.0.0/lglasso/data/datalist.rda |only lglasso-2.0.0/lglasso/inst |only lglasso-2.0.0/lglasso/man/Simulate.Rd |only lglasso-2.0.0/lglasso/man/datalist.Rd |only lglasso-2.0.0/lglasso/man/lglasso.Rd | 290 +++++++++++++++++++---------- lglasso-2.0.0/lglasso/tests |only 30 files changed, 242 insertions(+), 136 deletions(-)
Title: Language Server Protocol
Description: An implementation of the Language Server Protocol
for R. The Language Server protocol is used by an editor client to
integrate features like auto completion. See
<https://microsoft.github.io/language-server-protocol/> for details.
Author: Randy Lai [aut, cre],
Kun Ren [ctb]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between languageserver versions 0.3.19 dated 2026-09-13 and 0.3.20 dated 2026-09-24
DESCRIPTION | 8 +- MD5 | 32 ++++---- NEWS.md | 31 +++++++ R/diagnostics.R | 40 +++++++++- R/formatting.R | 95 ++++++++++++++++++++++++ R/handlers-general.R | 1 R/handlers-langfeatures.R | 7 - R/handlers-textsync.R | 10 ++ R/handlers-workspace.R | 5 + R/languageserver.R | 11 ++ R/protocol.R | 17 ++-- src/navigation.c | 18 +++- tests/testthat.R | 8 +- tests/testthat/test-diagnostics-configuration.R |only tests/testthat/test-formatting-background.R |only tests/testthat/test-handlers-langfeatures.R | 3 tests/testthat/test-navigation-index.R | 3 tests/testthat/test-response-json.R | 15 +++ 18 files changed, 262 insertions(+), 42 deletions(-)
More information about languageserver at CRAN
Permanent link
Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression, Cox model, multiple-response Gaussian, and the grouped multinomial regression; see <doi:10.18637/jss.v033.i01> and <doi:10.18637/jss.v039.i05>. There are two new and important additions. The family argument can be a GLM family object, which opens the door to any programmed family (<doi:10.18637/jss.v106.i01>). This comes with a modest computational cost, so when the built-in families suffice, they should be used instead. The other novelty is the relax option, which refits each of the active sets in the path unpenalized. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the papers cited.
Author: Jerome Friedman [aut],
Trevor Hastie [aut, cre],
Rob Tibshirani [aut],
Balasubramanian Narasimhan [aut],
Kenneth Tay [aut],
Noah Simon [aut],
Junyang Qian [ctb],
James Yang [aut],
Jonathan Taylor [aut]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between glmnet versions 5.0 dated 2026-05-04 and 5.1 dated 2026-09-24
DESCRIPTION | 8 ++++---- MD5 | 31 ++++++++++++++++--------------- NEWS.md | 5 +++++ R/check.penalty.factor.R |only R/glmnet.R | 13 +++++++++---- R/glmnet.control.R | 39 ++++++++++++++++++++------------------- R/makeX.R | 2 +- inst/doc/Coxnet.pdf |binary inst/doc/glmnet-history.pdf |binary inst/doc/glmnet.R | 4 ++-- inst/doc/glmnet.Rmd | 4 ++-- inst/doc/glmnet.pdf |binary inst/doc/glmnetFamily.pdf |binary inst/doc/relax.pdf |binary man/glmnet.Rd | 9 +++++++-- man/na.replace.Rd | 2 +- vignettes/glmnet.Rmd | 4 ++-- 17 files changed, 69 insertions(+), 52 deletions(-)
Title: Access and Manage 'Microsoft Fabric'
Description: Access 'Microsoft Fabric' workspaces, items, and workload
endpoints through its web application programming interfaces (APIs).
Connect to data in 'OneLake', 'Lakehouse', 'Warehouse', semantic model,
and 'Eventhouse' items, with support for 'DBI', 'Arrow', 'GraphQL', and
'Spark'. Manage files, tables, refreshes, jobs, schedules, ingestion,
and long-running operations.
Author: Luka Koning [aut, cre, cph],
Kennispunt Twente [fnd]
Maintainer: Luka Koning <koningluka@gmail.com>
Diff between fabricQueryR versions 0.2.1 dated 2026-04-03 and 1.0.0 dated 2026-09-24
DESCRIPTION | 36 LICENSE | 2 MD5 | 319 + NAMESPACE | 119 NEWS.md | 156 R/auth.R |only R/connection_strings.R |only R/fabricQueryR-package.R | 59 R/fabric_arrow_conversion.R |only R/fabric_arrow_staging.R |only R/fabric_catalog.R |only R/fabric_discovery.R |only R/fabric_function_invoke.R |only R/fabric_graphql_query.R |only R/fabric_item_r6.R |only R/fabric_job_scheduler.R |only R/fabric_jobs.R |only R/fabric_json.R |only R/fabric_kql_ingestion.R |only R/fabric_kql_query.R |only R/fabric_lakehouse_tables.R |only R/fabric_livy.R | 2091 +++++++- R/fabric_livy_batch.R |only R/fabric_livy_recovery.R |only R/fabric_livy_session.R |only R/fabric_mirrored_database_tables.R |only R/fabric_numeric_format.R |only R/fabric_onelake_catalog.R |only R/fabric_onelake_files.R |only R/fabric_onelake_read_delta_table.R | 1922 ++++++-- R/fabric_onelake_shortcuts.R |only R/fabric_onelake_table_exists.R |only R/fabric_operations.R |only R/fabric_pbi_dax_query.R | 1855 +++++++ R/fabric_pbi_refresh.R |only R/fabric_sql_connect.R | 2334 +++++++++- R/fabric_sql_tables.R |only R/fabric_warehouse_tables.R |only R/httr2_helpers.R | 951 +++- R/inform.R | 136 R/zzz.R |only README.md | 438 + build |only inst/doc |only inst/examples/fabric_livy_query.R | 99 man/FabricItem.Rd |only man/FabricLivyBatch.Rd |only man/FabricLivySession.Rd |only man/FabricLivyStatement.Rd |only man/fabricQueryR-package.Rd | 67 man/fabric_catalog_search.Rd |only man/fabric_delta_config.Rd |only man/fabric_function_invoke.Rd |only man/fabric_graphql_collect.Rd |only man/fabric_graphql_cursor.Rd |only man/fabric_graphql_paginate.Rd |only man/fabric_graphql_query.Rd |only man/fabric_graphql_schema.Rd |only man/fabric_item.Rd |only man/fabric_items.Rd |only man/fabric_job_instances.Rd |only man/fabric_job_run.Rd |only man/fabric_job_schedule_config.Rd |only man/fabric_job_schedules.Rd |only man/fabric_kql_export.Rd |only man/fabric_kql_ingest.Rd |only man/fabric_kql_query.Rd |only man/fabric_kql_read_table.Rd |only man/fabric_kql_tables.Rd |only man/fabric_kql_write_table.Rd |only man/fabric_lakehouse_read_table.Rd |only man/fabric_lakehouse_tables.Rd |only man/fabric_livy_batch_submit.Rd |only man/fabric_livy_query.Rd | 300 - man/fabric_livy_session.Rd |only man/fabric_livy_sessions.Rd |only man/fabric_mirrored_database_tables.Rd |only man/fabric_onelake_catalog.Rd |only man/fabric_onelake_files.Rd |only man/fabric_onelake_object_files.Rd |only man/fabric_onelake_read_delta_table.Rd | 225 man/fabric_onelake_schema_exists.Rd |only man/fabric_onelake_shortcuts.Rd |only man/fabric_operation_status.Rd |only man/fabric_pbi_dax_query.Rd | 222 man/fabric_pbi_refresh.Rd |only man/fabric_sql_connect.Rd | 216 man/fabric_sql_connection_info.Rd |only man/fabric_sql_query.Rd | 215 man/fabric_sql_tables.Rd |only man/fabric_typed_items.Rd |only man/fabric_user_data_functions.Rd |only man/fabric_warehouse_read_table.Rd |only man/fabric_warehouse_tables.Rd |only man/fabric_warehouse_write_table.Rd |only man/fabric_workspaces.Rd |only man/figures |only man/print.fabric_graphql_rows.Rd |only man/print.fabric_job.Rd |only man/print.fabric_job_instance.Rd |only man/print.fabric_job_schedule.Rd |only man/print.fabric_kql_export_result.Rd |only man/print.fabric_kql_ingestion.Rd |only man/print.fabric_kql_ingestion_status.Rd |only man/print.fabric_kql_write_result.Rd |only man/print.fabric_pbi_refresh.Rd |only man/print.fabric_pbi_refresh_detail.Rd |only tests/README.md |only tests/fixtures |only tests/testthat.R | 22 tests/testthat/_snaps |only tests/testthat/fixtures |only tests/testthat/helper-delta-rs-oracle.R |only tests/testthat/helper-fabric-authorization.R |only tests/testthat/helper-fabric-external-shortcuts.R |only tests/testthat/helper-fabric-functions.R |only tests/testthat/helper-fabric-hc.R |only tests/testthat/helper-fabric-integration.R |only tests/testthat/helper-fabric-item-r6.R |only tests/testthat/helper-fabric-notebook.R |only tests/testthat/helper-graphql-request.R |only tests/testthat/helper-kql-export-precision.R |only tests/testthat/helper-local-integration-runner.R |only tests/testthat/helper-numeric-format.R |only tests/testthat/helper-pbi-currency.R |only tests/testthat/helper-refresh-marker.R |only tests/testthat/helper-test-fixtures.R |only tests/testthat/helper-vignettes.R |only tests/testthat/setup-progress.R |only tests/testthat/test-authorization-fixtures.R |only tests/testthat/test-backward-compatibility.R |only tests/testthat/test-ci-integration-summary.R |only tests/testthat/test-cran-policy.R |only tests/testthat/test-delta-rs-oracle.R |only tests/testthat/test-external-shortcut-fixtures.R |only tests/testthat/test-fabric-integration-helpers.R |only tests/testthat/test-fabric_arrow_conversion.R |only tests/testthat/test-fabric_arrow_null_structs.R |only tests/testthat/test-fabric_arrow_staging.R |only tests/testthat/test-fabric_catalog.R |only tests/testthat/test-fabric_discovery.R |only tests/testthat/test-fabric_function_invoke.R |only tests/testthat/test-fabric_graphql_query.R |only tests/testthat/test-fabric_item_r6.R |only tests/testthat/test-fabric_job_scheduler.R |only tests/testthat/test-fabric_jobs.R |only tests/testthat/test-fabric_json.R |only tests/testthat/test-fabric_kql_export.R |only tests/testthat/test-fabric_kql_export_precision.R |only tests/testthat/test-fabric_kql_ingestion.R |only tests/testthat/test-fabric_kql_query.R |only tests/testthat/test-fabric_kql_write_table.R |only tests/testthat/test-fabric_lakehouse_tables.R |only tests/testthat/test-fabric_livy.R |only tests/testthat/test-fabric_mirrored_database_tables.R |only tests/testthat/test-fabric_numeric_format.R |only tests/testthat/test-fabric_onelake_download_encoding.R |only tests/testthat/test-fabric_onelake_files.R |only tests/testthat/test-fabric_onelake_read_delta_table.R |only tests/testthat/test-fabric_onelake_shortcuts.R |only tests/testthat/test-fabric_onelake_table_exists.R |only tests/testthat/test-fabric_operations.R |only tests/testthat/test-fabric_pbi_dax_query.R | 1633 ++++++ tests/testthat/test-fabric_pbi_refresh.R |only tests/testthat/test-fabric_sql_connect.R |only tests/testthat/test-fabric_sql_tables.R |only tests/testthat/test-fabric_warehouse_tables.R |only tests/testthat/test-function-fixtures.R |only tests/testthat/test-helper-fabric-integration.R |only tests/testthat/test-http-auth.R |only tests/testthat/test-inform.R |only tests/testthat/test-integration-fabric-auth-discovery-authorization.R |only tests/testthat/test-integration-fabric-auth-discovery.R |only tests/testthat/test-integration-fabric-functions.R |only tests/testthat/test-integration-fabric-jobs-dependencies.R |only tests/testthat/test-integration-fabric-jobs-overrides.R |only tests/testthat/test-integration-fabric-jobs-r6-credentials.R |only tests/testthat/test-integration-fabric-jobs-schedule-workloads.R |only tests/testthat/test-integration-fabric-jobs-schedules-nonutc.R |only tests/testthat/test-integration-fabric-jobs.R |only tests/testthat/test-integration-fabric-kql-graphql-datetime.R |only tests/testthat/test-integration-fabric-kql-graphql-datetimes.R |only tests/testthat/test-integration-fabric-kql-graphql-decimal-precision.R |only tests/testthat/test-integration-fabric-kql-graphql-parameters.R |only tests/testthat/test-integration-fabric-kql-graphql-recovery.R |only tests/testthat/test-integration-fabric-kql-graphql-unsigned.R |only tests/testthat/test-integration-fabric-kql-graphql.R |only tests/testthat/test-integration-fabric-livy-cancel.R |only tests/testthat/test-integration-fabric-livy-delegated.R |only tests/testthat/test-integration-fabric-livy-dependencies.R |only tests/testthat/test-integration-fabric-livy-empty-schema.R |only tests/testthat/test-integration-fabric-livy-languages.R |only tests/testthat/test-integration-fabric-livy.R |only tests/testthat/test-integration-fabric-onelake-download-encoding.R |only tests/testthat/test-integration-fabric-onelake-endpoints.R |only tests/testthat/test-integration-fabric-onelake-guid-case.R |only tests/testthat/test-integration-fabric-onelake-null-structs.R |only tests/testthat/test-integration-fabric-onelake-shortcut-case.R |only tests/testthat/test-integration-fabric-onelake-shortcut-transforms.R |only tests/testthat/test-integration-fabric-onelake-staging-collision.R |only tests/testthat/test-integration-fabric-onelake-tables.R |only tests/testthat/test-integration-fabric-onelake-write-types.R |only tests/testthat/test-integration-fabric-onelake.R |only tests/testthat/test-integration-fabric-power-bi-refresh-outcomes.R |only tests/testthat/test-integration-fabric-power-bi.R |only tests/testthat/test-integration-fabric-runtime-compatibility.R |only tests/testthat/test-integration-fabric-sql-narrowing.R |only tests/testthat/test-integration-fabric-sql-numeric-policy.R |only tests/testthat/test-integration-fabric-sql-records.R |only tests/testthat/test-integration-fabric-sql-rollback.R |only tests/testthat/test-integration-fabric-sql.R |only tests/testthat/test-integration-feature-gates.R |only tests/testthat/test-kql-dynamic-parameters.R |only tests/testthat/test-livy-session-errors.R |only tests/testthat/test-local-integration-runner.R |only tests/testthat/test-package-metadata.R |only tests/testthat/test-r6-lifecycle-credentials.R |only tests/testthat/test-readme.R |only tests/testthat/test-sql-table-records.R |only tests/testthat/test-vignettes.R |only tests/testthat/test-warehouse-narrowing.R |only vignettes |only 222 files changed, 11710 insertions(+), 1707 deletions(-)
Title: Microbial Community Ecology Data Analysis
Description: A series of data analysis approaches for microbiome data based on the R6 class. The classes are designed for data preprocessing, niche analysis, taxonomic abundance plot, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis, functional redundancy analysis, metabolites analysis, etc.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 2.3.0 dated 2026-07-07 and 2.4.0 dated 2026-09-24
DESCRIPTION | 10 MD5 | 49 ++-- NAMESPACE | 3 R/help.R | 2 R/trans_alpha.R | 45 +++- R/trans_beta.R | 3 R/trans_classifier.R | 453 +++++++++++++++++++++++++++++++++++++------ R/trans_diff.R | 232 ++++++++++++++++++---- R/trans_env.R | 499 +++++++++++++++++++++++++++++++++++++++++++++--- R/trans_func.R | 2 R/trans_metab.R | 2 R/trans_mst.R |only R/trans_multiomics.R |only R/trans_network.R | 51 +++- R/trans_niche.R | 347 +++++++++++++++++++++++++++++++++ R/trans_rarefy.R |only R/utility.R | 4 R/zzz.R |only man/microeco.Rd | 2 man/trans_classifier.Rd | 91 +++++++- man/trans_diff.Rd | 47 +++- man/trans_env.Rd | 147 +++++++++++++- man/trans_func.Rd | 6 man/trans_metab.Rd | 6 man/trans_mst.Rd |only man/trans_multiomics.Rd |only man/trans_network.Rd | 5 man/trans_niche.Rd | 194 ++++++++++++++++++ man/trans_rarefy.Rd |only 29 files changed, 1982 insertions(+), 218 deletions(-)
Title: Dependencies for the 'jamovi' Framework
Description: A framework for creating rich interactive analyses for the jamovi
platform (see <https://www.jamovi.org> for more information).
Author: Jonathon Love [aut, cre, cph]
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvcore versions 2.7.38 dated 2026-07-18 and 28.3 dated 2026-09-24
DESCRIPTION | 15 +- MD5 | 56 ++++---- NAMESPACE | 5 R/analysis.R | 34 +++-- R/column.R | 127 +++++++++++------- R/format.R |only R/html.R | 2 R/htmlify.R |only R/i18n.R | 6 R/image.R | 8 + R/notice.R | 1 R/options.R | 179 ++++++++++++++++++++++++++ R/package.R | 50 +++++++ R/svg.R |only R/table-fold.R | 12 + R/table.R | 10 - R/text.R |only R/utils.R | 278 ----------------------------------------- R/validate.R | 2 inst/jamovi.proto | 12 + man/Analysis.Rd | 32 ---- man/Cell.BEGIN_GROUP.Rd | 3 man/NoticeType.Rd | 3 man/Options.Rd | 43 ------ man/asFormula.Rd | 3 man/jmvcore-package.Rd |only man/marshalFormula.Rd | 11 + man/reexports.Rd | 2 man/stringifyTerm.Rd | 3 tests/testthat/test-format.R |only tests/testthat/test-htmlify.R |only tests/testthat/test-i18n.R |only tests/testthat/test-validate.R | 1 33 files changed, 426 insertions(+), 472 deletions(-)
Title: Draw Network with Data
Description: Extends the 'ggplot2' plotting system to support network visualization. Inspired by the 'Method 1' in 'ggtree' (G Yu (2018) <doi:10.1093/molbev/msy194>), 'ggtangle' is designed to work with network associated data.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggtangle versions 0.1.2 dated 2026-04-22 and 0.1.3 dated 2026-09-24
DESCRIPTION | 8 MD5 | 51 +- NAMESPACE | 136 +++-- NEWS.md | 162 +++--- R/AllGenerics.r | 83 +-- R/cnet.r | 725 +++++++++++++++--------------- R/drag-network.R | 104 ++-- R/ggtangle-package.R | 6 R/graph-layout.R | 274 +++++------ R/graph.r | 565 ++++++++++++----------- R/interactive.R | 126 ++--- R/reexports.r | 88 +-- R/utilities.r | 90 +-- R/zzz.R | 10 README.md | 30 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/ggtangle.R | 352 +++++++------- inst/doc/ggtangle.html | 900 +++++++++++++++++++------------------- inst/doc/ggtangle.qmd | 454 +++++++++---------- man/cnetplot.Rd | 5 man/geom_edge_interactive.Rd | 106 ++-- man/geom_edge_text_interactive.Rd | 68 +- man/ggplot.igraph.Rd |only man/ggtangle-package.Rd | 5 man/reexports.Rd | 6 vignettes/ggtangle.qmd | 454 +++++++++---------- 27 files changed, 2439 insertions(+), 2369 deletions(-)
Title: Bayesian Gaussian Graphical Models
Description: Fit Bayesian Gaussian graphical models. The methods are separated into
two Bayesian approaches for inference: hypothesis testing and estimation. There are
extensions for confirmatory hypothesis testing, comparing Gaussian graphical models,
and node wise predictability. These methods were recently introduced in the Gaussian
graphical model literature, including
Williams (2019) <doi:10.31234/osf.io/x8dpr>,
Williams and Mulder (2019) <doi:10.31234/osf.io/ypxd8>,
Williams, Rast, Pericchi, and Mulder (2019) <doi:10.31234/osf.io/yt386>.
Author: Donald Williams [aut],
Joris Mulder [aut],
Philippe Rast [aut, cre]
Maintainer: Philippe Rast <rast.ph@gmail.com>
Diff between BGGM versions 2.1.6 dated 2025-12-02 and 2.2.0 dated 2026-09-24
DESCRIPTION | 14 MD5 | 84 +-- NAMESPACE | 3 NEWS.md | 164 ++++++ R/RcppExports.R | 36 - R/bggm_missing.R | 160 ++---- R/coef.estimate.R | 2 R/confirm.R | 31 - R/constrained_post.R | 2 R/convergence.R | 4 R/estimate.R | 36 + R/explore.default.R | 213 ++++++-- R/ggm_compare_bf.default.R | 13 R/ggm_compare_confirm.R | 49 + R/ggm_search.R | 88 ++- R/helpers.R | 88 +++ R/pcor_2_cor.BGGM.R | 13 R/plot.select.R | 94 ++- R/plot_prior.R | 5 R/posterior_predict.R | 8 R/posterior_samples.R | 12 R/predict.estimate.R | 2 R/predictability.R | 2 R/regression_summary.R | 2 R/roll_your_own.R | 2 R/select.explore.R | 761 +++++++++++++++++++++--------- R/var_estimate.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/control.html | 2 inst/doc/hyp_3_ways.html | 2 inst/doc/mcmc_diagnostics.Rmd | 4 inst/doc/mcmc_diagnostics.html | 6 inst/doc/ppc_custom.html | 12 inst/doc/test_sum.html | 2 inst/doc/var_model.html | 2 man/convergence.Rd | 2 man/explore.Rd | 51 +- man/ggm_search.Rd | 52 +- man/select.explore.Rd | 117 ++++ src/RcppExports.cpp | 114 ++-- src/bggm_fast.cpp | 1037 ++++++++++++++--------------------------- vignettes/mcmc_diagnostics.Rmd | 4 43 files changed, 1966 insertions(+), 1330 deletions(-)
Title: Species Identification using DNA Barcodes
Description: To perform species identification using DNA barcodes.
Author: Ai-bing ZHANG [aut, cre],
Meng-di HAO [aut],
Cai-qing YANG [aut],
Zhi-yong SHI [aut]
Maintainer: Ai-bing ZHANG <Zhangab2008@mail.cnu.edu.cn>
Diff between BarcodingR versions 1.0-3 dated 2020-04-14 and 1.0-4 dated 2026-09-24
DESCRIPTION | 24 +++++++++++++++++------- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 2 +- R/DNAbin2kmerFreqMatrix.R | 4 ++-- R/FMF.R | 2 +- R/FMFtheta12.R | 1 - R/TDR2.R | 2 +- R/barcodes.eval.R | 4 ++-- R/barcoding.spe.identify.R | 4 ++-- R/barcoding.spe.identify2.R | 16 ++++++++-------- R/bbsik.R | 6 +++--- R/char2NumVector.R | 2 +- R/compare2delimitations.R | 2 +- R/optimize.kmer.R | 4 ++-- R/sample.ref.R | 4 ++-- R/save.ids.R | 5 +++-- R/summarize.ref.R | 10 +++++----- man/barcoding.spe.identify2.Rd | 2 +- 18 files changed, 69 insertions(+), 59 deletions(-)
Title: Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based
Null Model Analysis
Description: To implement a general framework to quantitatively infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis, abbreviated as 'iCAMP' (Ning et al 2020) <doi:10.1038/s41467-020-18560-z>. It can quantitatively assess the relative importance of different community assembly processes, such as selection, dispersal, and drift, for both communities and each phylogenetic group ('bin'). Each bin usually consists of different taxa from a family or an order. The package also provides functions to implement some other published methods, including neutral taxa percentage (Burns et al 2016) <doi:10.1038/ismej.2015.142> based on neutral theory model and quantifying assembly processes based on entire-community null models ('QPEN', Stegen et al 2013) <doi:10.1038/ismej.2013.93>. It also includes some handy functions, particularly for big datasets, such as phylogenetic and taxonomic null model analysis at both community and bin levels, between-taxa niche differen [...truncated...]
Author: Daliang Ning [aut, cre]
Maintainer: Daliang Ning <ningdaliang@ou.edu>
Diff between iCAMP versions 1.8.6 dated 2026-08-25 and 1.9.1 dated 2026-09-24
DESCRIPTION | 6 MD5 | 24 R/RC.bin.bigc.r | 2 R/RC.bin.cm.r | 2 R/icamp.big.r | 4 R/icamp.cm.r | 1426 +++++++++++++++++++++++++-------------------------- R/icamp.cm2.r | 4 man/RC.bin.bigc.Rd | 1 man/RC.bin.cm.Rd | 1 man/iCAMP-package.Rd | 5 man/icamp.big.Rd | 4 man/icamp.cm.Rd | 4 man/icamp.cm2.Rd | 4 13 files changed, 748 insertions(+), 739 deletions(-)
Title: 'C++' Implementations of Functional Enrichment Analysis
Description: Fast implementations of functional enrichment analysis methods using 'C++' via 'Rcpp'.
Currently provides Over-Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA),
Weighted Enrichment Analysis for ORA and GSEA, Network-based Set Enrichment Analysis (NSEA),
multi-layer network-based enrichment, and multi-omics integration workflows. Additional
features include early fusion at the feature level, late fusion at the pathway level,
multi-omics contribution tracing, topology-aware explanation helpers, Bayesian term
selection, and extremely fast Random Walk with Restart (RWR) using 'RcppEigen'. The
enrichment methods build on GSEA by Subramanian et al. (2005)
<doi:10.1073/pnas.0506580102>, the multilevel strategy derived from 'fgsea'
by Korotkevich et al. (2021) <doi:10.1101/060012>, and network-based
enrichment ideas described by Glaab et al. (2012)
<doi:10.1093/bioinformatics/bts389>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between enrichit versions 0.2.4 dated 2026-09-17 and 0.2.5 dated 2026-09-24
DESCRIPTION | 6 - MD5 | 24 ++-- NAMESPACE | 4 NEWS.md | 231 ++++++++++++++++++++------------------- R/converters.R |only R/gsea.R | 9 + R/gseaScores.R | 20 ++- R/ora.R | 12 ++ R/ora_gson.R | 14 ++ R/print.R | 32 ++++- man/as_enrichResult.Rd |only man/as_gseaResult.Rd |only tests/testthat/test-converters.R |only tests/testthat/test-gsea.R | 52 ++++++++ tests/testthat/test-ora.R | 44 +++++++ 15 files changed, 308 insertions(+), 140 deletions(-)
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