Title: Test, Document, Containerise, and Deploy R Packages
Description: Reproducibility is essential to the progress of research,
yet achieving it remains elusive even in computational fields.
Continuous Integration (CI) platforms offer a powerful way to launch automated workflows
to check and document code, but often require considerable time, effort,
and technical expertise to setup. We therefore developed the rworkflows suite
to make robust CI workflows easy and freely accessible to all R package developers.
rworkflows consists of 1) a CRAN/Bioconductor-compatible R package template,
2) an R package to quickly implement a standardised workflow, and
3) a centrally maintained GitHub Action.
Author: Brian Schilder [aut, cre] ,
Alan Murphy [aut, ctb] ,
Hiranyamaya Dash [ctb] ,
Nathan Skene [aut]
Maintainer: Brian Schilder <brian_schilder@alumni.brown.edu>
Diff between rworkflows versions 1.0.6 dated 2025-01-23 and 1.0.8 dated 2026-01-08
rworkflows-1.0.6/rworkflows/inst/rworkflows_1.0.1.pdf |only rworkflows-1.0.8/rworkflows/DESCRIPTION | 25 - rworkflows-1.0.8/rworkflows/MD5 | 44 +- rworkflows-1.0.8/rworkflows/NEWS.md | 21 + rworkflows-1.0.8/rworkflows/R/fill_yaml.R | 8 rworkflows-1.0.8/rworkflows/R/use_workflow.R | 18 - rworkflows-1.0.8/rworkflows/README.md | 56 +-- rworkflows-1.0.8/rworkflows/build/vignette.rds |binary rworkflows-1.0.8/rworkflows/inst/doc/bioconductor.html | 60 +-- rworkflows-1.0.8/rworkflows/inst/doc/depgraph.html | 97 ++--- rworkflows-1.0.8/rworkflows/inst/doc/docker.html | 52 +- rworkflows-1.0.8/rworkflows/inst/doc/repos.html | 52 +- rworkflows-1.0.8/rworkflows/inst/doc/rworkflows.Rmd | 6 rworkflows-1.0.8/rworkflows/inst/doc/rworkflows.html | 176 +++++----- rworkflows-1.0.8/rworkflows/inst/rworkflows_1.0.8.pdf |only rworkflows-1.0.8/rworkflows/inst/templates/Dockerfile | 3 rworkflows-1.0.8/rworkflows/inst/templates/rworkflows_template.yml | 2 rworkflows-1.0.8/rworkflows/inst/templates/rworkflows_template_static.yml | 2 rworkflows-1.0.8/rworkflows/man/use_workflow.Rd | 16 rworkflows-1.0.8/rworkflows/tests/testthat/test-get_authors.R | 2 rworkflows-1.0.8/rworkflows/tests/testthat/test-get_description.R | 8 rworkflows-1.0.8/rworkflows/tests/testthat/test-infer_docker_org.R | 9 rworkflows-1.0.8/rworkflows/tests/testthat/test-messager.R | 5 rworkflows-1.0.8/rworkflows/vignettes/rworkflows.Rmd | 6 24 files changed, 381 insertions(+), 287 deletions(-)
Title: Monitoring and Analyzing Dedoose Qualitative Data Exports
Description: Streamlines analysis of qualitative data exported from 'Dedoose' <https://www.dedoose.com>.
Supports monitoring thematic saturation, calculating code frequencies,
organizing excerpts, generating dynamic codebooks, and producing code network maps
within 'R'.
Author: Abiraahmi Shankar [aut, cre] ,
Catalina Canizares [aut] ,
Francisco Cardozo [aut] ,
Sabrina Stockmans [aut],
Pamela Morris-Perez [aut]
Maintainer: Abiraahmi Shankar <abiraahmi.shankar@nyu.edu>
Diff between DedooseR versions 2.0.0.1 dated 2026-01-07 and 2.0.0.2 dated 2026-01-08
DedooseR-2.0.0.1/DedooseR/inst/raw_data |only DedooseR-2.0.0.2/DedooseR/DESCRIPTION | 10 +++++----- DedooseR-2.0.0.2/DedooseR/MD5 | 13 +++++-------- DedooseR-2.0.0.2/DedooseR/NEWS.md | 3 +++ DedooseR-2.0.0.2/DedooseR/inst/doc/Cooccurence.html | 2 +- DedooseR-2.0.0.2/DedooseR/inst/doc/Intro_to_DedooseR.html | 8 ++++---- DedooseR-2.0.0.2/DedooseR/inst/doc/Summarizing_Codes.html | 4 ++-- 7 files changed, 20 insertions(+), 20 deletions(-)
Title: Toolkit for Analyzing Curricular Complexity
Description: Enables educational researchers and practitioners to calculate the curricular complexity of a plan of study, visualize its prerequisite structure at scale, and conduct customizable analyses. The original tool can be found at <https://curricularanalytics.org>. Additional functions to explore curriculum complexity from the literature are also included.
Author: David Reeping [aut, cre]
Maintainer: David Reeping <reepindp@ucmail.uc.edu>
Diff between CurricularComplexity versions 1.0 dated 2025-11-04 and 1.0.1 dated 2026-01-08
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS.md |only R/admissibility_test.R | 2 +- R/deferment_factor.R | 1 + inst/doc/CurricularComplexity-demo.Rmd | 8 ++++---- inst/doc/CurricularComplexity-demo.html | 16 ++++++++-------- man/admissibility_test.Rd | 2 +- vignettes/CurricularComplexity-demo.Rmd | 8 ++++---- 9 files changed, 30 insertions(+), 28 deletions(-)
More information about CurricularComplexity at CRAN
Permanent link
Title: Selecting General Circulation Models for Species Distribution
Modeling
Description: Methods to help selecting General Circulation Models (GCMs)
in the context of projecting models to future scenarios. It is provided
clusterization algorithms, distance and correlation metrics, as well as
a tailor-made algorithm to detect the optimum subset of GCMs that recreate
the environment of all GCMs as proposed in Esser et al. (2025) <doi:10.1111/gcb.70008>.
Author: Dayani Bailly [aut] ,
Reginaldo Re [aut] ,
Marcos R. Lima [aut] ,
Luiz Esser [aut, cre, cph]
Maintainer: Luiz Esser <luizesser@gmail.com>
Diff between chooseGCM versions 1.2 dated 2025-08-23 and 1.3 dated 2026-01-08
chooseGCM-1.2/chooseGCM/man/worldclim_data.Rd |only chooseGCM-1.3/chooseGCM/DESCRIPTION | 13 chooseGCM-1.3/chooseGCM/MD5 | 88 +- chooseGCM-1.3/chooseGCM/NAMESPACE | 15 chooseGCM-1.3/chooseGCM/NEWS.md | 5 chooseGCM-1.3/chooseGCM/R/WorldClim_data.R | 303 +++++----- chooseGCM-1.3/chooseGCM/R/closestdist_gcms.R | 5 chooseGCM-1.3/chooseGCM/R/compare_gcms.R | 5 chooseGCM-1.3/chooseGCM/R/cor_gcms.R | 5 chooseGCM-1.3/chooseGCM/R/dist_gcms.R | 5 chooseGCM-1.3/chooseGCM/R/env_gcms.R | 6 chooseGCM-1.3/chooseGCM/R/flatten_gcms.R | 5 chooseGCM-1.3/chooseGCM/R/hclust_gcms.R | 5 chooseGCM-1.3/chooseGCM/R/import_gcms.R | 2 chooseGCM-1.3/chooseGCM/R/kmeans_gcms.R | 5 chooseGCM-1.3/chooseGCM/R/montecarlo_gcms.R | 5 chooseGCM-1.3/chooseGCM/R/optk_gcms.R | 5 chooseGCM-1.3/chooseGCM/R/summary_gcms.R | 5 chooseGCM-1.3/chooseGCM/R/transform_gcms.R | 5 chooseGCM-1.3/chooseGCM/README.md | 2 chooseGCM-1.3/chooseGCM/man/WorldClim_data.Rd |only chooseGCM-1.3/chooseGCM/man/closestdist_gcms.Rd | 5 chooseGCM-1.3/chooseGCM/man/compare_gcms.Rd | 5 chooseGCM-1.3/chooseGCM/man/cor_gcms.Rd | 5 chooseGCM-1.3/chooseGCM/man/dist_gcms.Rd | 5 chooseGCM-1.3/chooseGCM/man/env_gcms.Rd | 6 chooseGCM-1.3/chooseGCM/man/flatten_gcms.Rd | 5 chooseGCM-1.3/chooseGCM/man/hclust_gcms.Rd | 5 chooseGCM-1.3/chooseGCM/man/import_gcms.Rd | 2 chooseGCM-1.3/chooseGCM/man/kmeans_gcms.Rd | 5 chooseGCM-1.3/chooseGCM/man/montecarlo_gcms.Rd | 5 chooseGCM-1.3/chooseGCM/man/optk_gcms.Rd | 5 chooseGCM-1.3/chooseGCM/man/summary_gcms.Rd | 5 chooseGCM-1.3/chooseGCM/man/transform_gcms.Rd | 5 chooseGCM-1.3/chooseGCM/tests/testthat/test-closestdist_gcms.R | 2 chooseGCM-1.3/chooseGCM/tests/testthat/test-compare_gcms.R | 2 chooseGCM-1.3/chooseGCM/tests/testthat/test-cor_gcms.R | 2 chooseGCM-1.3/chooseGCM/tests/testthat/test-dist_gcms.R | 6 chooseGCM-1.3/chooseGCM/tests/testthat/test-env_gcms.R | 6 chooseGCM-1.3/chooseGCM/tests/testthat/test-flatten_gcms.R | 2 chooseGCM-1.3/chooseGCM/tests/testthat/test-hclust_gcms.R | 6 chooseGCM-1.3/chooseGCM/tests/testthat/test-kmeans_gcms.R | 2 chooseGCM-1.3/chooseGCM/tests/testthat/test-montecarlo_gcms.R | 4 chooseGCM-1.3/chooseGCM/tests/testthat/test-optk_gcms.R | 8 chooseGCM-1.3/chooseGCM/tests/testthat/test-summary-gcms.R | 8 chooseGCM-1.3/chooseGCM/tests/testthat/test-transform_gcms.R | 30 46 files changed, 362 insertions(+), 268 deletions(-)
Title: Access to the List of Birds Species of Peru
Description: Allows access to the data found in the species list featured in the renowned 'List of the Birds of Peru' Plenge, M. A. (2023) <https://sites.google.com/site/boletinunop/checklist>. This publication stands as one of Peru's most comprehensive reviews of bird diversity. The dataset incorporates detailed species accounts and has been meticulously structured for effortless utilization within the R environment.
Author: Paul E. Santos Andrade [aut, cre]
Maintainer: Paul E. Santos Andrade <paulefrens@gmail.com>
Diff between avesperu versions 0.0.6 dated 2025-07-05 and 0.0.8 dated 2026-01-08
avesperu-0.0.6/avesperu/R/aves_peru_2025_v3.R |only avesperu-0.0.6/avesperu/data/aves_peru_2025_v3.rda |only avesperu-0.0.6/avesperu/man/aves_peru_2025_v3.Rd |only avesperu-0.0.8/avesperu/DESCRIPTION | 9 avesperu-0.0.8/avesperu/MD5 | 32 avesperu-0.0.8/avesperu/NAMESPACE | 7 avesperu-0.0.8/avesperu/R/aves_peru_2025_v5.R |only avesperu-0.0.8/avesperu/R/aves_peru_data.R |only avesperu-0.0.8/avesperu/R/get_avesperu.R | 528 ++++++++-- avesperu-0.0.8/avesperu/R/internals.R | 98 + avesperu-0.0.8/avesperu/R/onload.R | 33 avesperu-0.0.8/avesperu/README.md | 425 ++++++-- avesperu-0.0.8/avesperu/data/aves_peru_2025_v4.rda |only avesperu-0.0.8/avesperu/data/aves_peru_2025_v5.rda |only avesperu-0.0.8/avesperu/inst/CITATION | 43 avesperu-0.0.8/avesperu/man/aves_peru_2025_v4.Rd |only avesperu-0.0.8/avesperu/man/aves_peru_2025_v5.Rd |only avesperu-0.0.8/avesperu/man/figures/README-unnamed-chunk-2-1.png |binary avesperu-0.0.8/avesperu/man/search_avesperu.Rd | 130 +- avesperu-0.0.8/avesperu/man/standardize_names.Rd |only avesperu-0.0.8/avesperu/man/unop_check_update.Rd | 6 avesperu-0.0.8/avesperu/tests/testthat/test-test_search_avesperu.R | 24 22 files changed, 1047 insertions(+), 288 deletions(-)
Title: Sampling Design for Spatially Explicit Capture-Recapture
Description: Tools for designing spatially explicit capture-recapture studies of animal populations. This is primarily a simulation manager for package 'secr'. Extensions in version 2.5.0 include costing and evaluation of detector spacing.
Author: Murray Efford [aut, cre] ,
Ian Durbach [ctb]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secrdesign versions 2.10.0 dated 2025-06-13 and 2.10.1 dated 2026-01-08
secrdesign-2.10.0/secrdesign/R/simOU.capthist.R |only secrdesign-2.10.0/secrdesign/man/simOU.capthist.Rd |only secrdesign-2.10.1/secrdesign/DESCRIPTION | 12 secrdesign-2.10.1/secrdesign/MD5 | 52 +- secrdesign-2.10.1/secrdesign/NAMESPACE | 2 secrdesign-2.10.1/secrdesign/NEWS | 21 + secrdesign-2.10.1/secrdesign/R/En2.R | 6 secrdesign-2.10.1/secrdesign/R/Lambda.R | 14 secrdesign-2.10.1/secrdesign/R/Qpm.R | 4 secrdesign-2.10.1/secrdesign/R/getdetectpar.R | 2 secrdesign-2.10.1/secrdesign/R/make.scenarios.R | 4 secrdesign-2.10.1/secrdesign/R/methods.R | 2 secrdesign-2.10.1/secrdesign/R/optimalSpacing.R | 109 ++++- secrdesign-2.10.1/secrdesign/R/run.scenarios.R | 276 ++++++++------- secrdesign-2.10.1/secrdesign/R/saturation.R | 2 secrdesign-2.10.1/secrdesign/R/scenarioSummary.R | 4 secrdesign-2.10.1/secrdesign/R/utility.R | 85 ---- secrdesign-2.10.1/secrdesign/build/partial.rdb |binary secrdesign-2.10.1/secrdesign/man/Lambda.Rd | 9 secrdesign-2.10.1/secrdesign/man/costing.Rd | 4 secrdesign-2.10.1/secrdesign/man/estimateSummary.Rd | 14 secrdesign-2.10.1/secrdesign/man/make.scenarios.Rd | 2 secrdesign-2.10.1/secrdesign/man/plot.optimalSpacing.Rd | 16 secrdesign-2.10.1/secrdesign/man/run.scenarios.Rd | 10 secrdesign-2.10.1/secrdesign/man/secrdesign-internal.Rd | 2 secrdesign-2.10.1/secrdesign/man/secrdesign-package.Rd | 16 secrdesign-2.10.1/secrdesign/man/validate.Rd | 17 secrdesign-2.10.1/secrdesign/tests/testthat/test-simOU.R | 2 28 files changed, 379 insertions(+), 308 deletions(-)
Title: Reptile Database Data
Description: Provides easy access to 'The Reptile Database', a comprehensive catalogue of all living reptile species and their classification. This package includes taxonomic data for over 10,000 reptile species, approximately 2,800 of which are subspecies, covering all extant reptiles. The dataset features taxonomic names, synonyms, distribution data, type specimens, and literature references, making it ready for research and analysis. Data is sourced from 'The Reptile Database' <http://www.reptile-database.org/>.
Author: Paul Efren Santos Andrade [aut, cre]
Maintainer: Paul Efren Santos Andrade <paulefrens@gmail.com>
Diff between reptiledb.data versions 0.0.0.1 dated 2025-07-05 and 0.0.0.2 dated 2026-01-08
DESCRIPTION | 10 MD5 | 22 - NAMESPACE | 8 R/chek_reptiledb_status.R | 514 ++++++++++++++++++------------------- R/internal.R |only R/reptiledb.R | 89 ++++-- data/reptiledb_092025.rda |only man/check_data_update.Rd | 56 ++-- man/check_internet_connection.Rd | 4 man/extract_date_from_name.Rd | 9 man/get_latest_reptile_download.Rd | 62 +--- man/print.reptile_update_check.Rd |only man/reptiledb_012025.Rd | 47 +-- man/reptiledb_092025.Rd |only 14 files changed, 428 insertions(+), 393 deletions(-)
More information about reptiledb.data at CRAN
Permanent link
Title: PRO-CTCAE Scoring, Analysis, and Graphical Tools
Description: A collection of tools to facilitate standardized analysis
and graphical procedures when using the National Cancer Institute’s
Patient-Reported Outcomes version of the Common Terminology Criteria for
Adverse Events (PRO-CTCAE) and other PRO measurements.
Author: Blake Langlais [aut],
Brie Noble [ctb, cre],
Mia Truman [ctb],
Molly Voss [ctb],
Amylou Dueck [aut]
Maintainer: Brie Noble <noble.brie@mayo.edu>
Diff between ProAE versions 1.0.3 dated 2024-10-21 and 1.0.4 dated 2026-01-08
DESCRIPTION | 18 ++--- MD5 | 20 +++--- R/sysdata.rda |binary README.md | 19 ++++-- data/PROCTCAE_table.rda |binary inst/doc/toxAUC.html | 4 - inst/doc/toxFigures.R | 2 inst/doc/toxFigures.Rmd | 2 inst/doc/toxFigures.html | 11 +-- inst/doc/toxTables.html | 145 ++++++++++++++++++----------------------------- vignettes/toxFigures.Rmd | 2 11 files changed, 101 insertions(+), 122 deletions(-)
Title: Statistical Methods for Microbiome Compositional Data
Description: A suite of methods for powerful and robust microbiome data analysis addressing zero-inflation, phylogenetic structure and compositional effects. Includes the LinDA method for differential abundance analysis (Zhou et al. (2022)<doi:10.1186/s13059-022-02655-5>), the BMDD (Bimodal Dirichlet Distribution) method for accurate modeling and imputation of zero-inflated microbiome sequencing data (Zhou et al. (2025)<doi:10.1371/journal.pcbi.1013124>) and compositional sparse CCA methods for microbiome multi-omics data integration (Deng et al. (2024) <doi: 10.3389/fgene.2024.1489694>).
Author: Xianyang Zhang [aut],
Jun Chen [aut, cre],
Huijuan Zhou [ctb],
Linsui Deng [ctb]
Maintainer: Jun Chen <chen.jun2@mayo.edu>
Diff between MicrobiomeStat versions 1.2 dated 2024-04-01 and 1.3 dated 2026-01-08
DESCRIPTION | 25 +++++++++++++++++-------- MD5 | 26 +++++++++++++++++++++++--- NAMESPACE | 13 +++++++++++++ R/CCA_algorithm.R |only R/RcppExports.R |only R/bmdd_R.R |only R/bmdd_nlopt.R |only R/bmdd_nlopt_check_available.R |only R/bmdd_wrapper.R |only R/data.R |only cleanup |only configure |only data/smokers.rda |binary inst |only man/DGP_OC.Rd |only man/bmdd.Rd |only man/bmdd.nlopt.Rd |only man/cscca.CV.Rd |only man/cscca.Rd |only src |only 20 files changed, 53 insertions(+), 11 deletions(-)
More information about MicrobiomeStat at CRAN
Permanent link
Title: Estimate and Simulate from Location Dependent Marked Point
Processes
Description: A suite of tools for estimating, assessing model fit, simulating from, and visualizing location dependent marked point processes characterized by regularity in the pattern.
You provide a reference marked point process, a set of raster images containing location specific covariates, and select the estimation algorithm and type of mark model.
'ldmppr' estimates the process and mark models and allows you to check the appropriateness of the model using a variety of diagnostic tools.
Once a satisfactory model fit is obtained, you can simulate from the model and visualize the results.
Documentation for the package 'ldmppr' is available in the form of a vignette.
Author: Lane Drew [aut, cre, cph] ,
Andee Kaplan [aut]
Maintainer: Lane Drew <lanetdrew@gmail.com>
Diff between ldmppr versions 1.0.4 dated 2025-02-24 and 1.1.0 dated 2026-01-08
ldmppr-1.0.4/ldmppr/R/estimate_parameters_sc.R |only ldmppr-1.0.4/ldmppr/R/estimate_parameters_sc_parallel.R |only ldmppr-1.0.4/ldmppr/man/estimate_parameters_sc.Rd |only ldmppr-1.0.4/ldmppr/man/estimate_parameters_sc_parallel.Rd |only ldmppr-1.1.0/ldmppr/DESCRIPTION | 25 ldmppr-1.1.0/ldmppr/MD5 | 84 +- ldmppr-1.1.0/ldmppr/NAMESPACE | 28 ldmppr-1.1.0/ldmppr/NEWS.md | 11 ldmppr-1.1.0/ldmppr/R/RcppExports.R | 16 ldmppr-1.1.0/ldmppr/R/check_model_fit.R | 101 +- ldmppr-1.1.0/ldmppr/R/estimate_helpers.R |only ldmppr-1.1.0/ldmppr/R/estimate_process_parameters.R |only ldmppr-1.1.0/ldmppr/R/extra.R | 5 ldmppr-1.1.0/ldmppr/R/extract_covars.R | 34 ldmppr-1.1.0/ldmppr/R/internal_helpers.R |only ldmppr-1.1.0/ldmppr/R/mark_model_s3.R |only ldmppr-1.1.0/ldmppr/R/model_check_s3.R |only ldmppr-1.1.0/ldmppr/R/plot_mpp.R | 25 ldmppr-1.1.0/ldmppr/R/power_law_mapping.R | 20 ldmppr-1.1.0/ldmppr/R/predict_marks.R | 156 ++- ldmppr-1.1.0/ldmppr/R/process_fit_s3.R |only ldmppr-1.1.0/ldmppr/R/scale_rasters.R | 1 ldmppr-1.1.0/ldmppr/R/sim_s3.R |only ldmppr-1.1.0/ldmppr/R/simulate_mpp.R | 178 ++-- ldmppr-1.1.0/ldmppr/R/simulate_sc.R | 48 - ldmppr-1.1.0/ldmppr/R/train_mark_model.R | 176 ++-- ldmppr-1.1.0/ldmppr/build/partial.rdb |binary ldmppr-1.1.0/ldmppr/build/vignette.rds |binary ldmppr-1.1.0/ldmppr/data/small_example_data.rda |binary ldmppr-1.1.0/ldmppr/inst/doc/ldmppr_howto.R | 111 +- ldmppr-1.1.0/ldmppr/inst/doc/ldmppr_howto.Rmd | 191 ++-- ldmppr-1.1.0/ldmppr/inst/doc/ldmppr_howto.html | 530 +++++++------ ldmppr-1.1.0/ldmppr/inst/extdata/example_mark_model.rds |binary ldmppr-1.1.0/ldmppr/man/check_model_fit.Rd | 15 ldmppr-1.1.0/ldmppr/man/estimate_process_parameters.Rd |only ldmppr-1.1.0/ldmppr/man/extract_covars.Rd | 7 ldmppr-1.1.0/ldmppr/man/full_sc_lhood_fast.Rd |only ldmppr-1.1.0/ldmppr/man/ldmppr-internal.Rd |only ldmppr-1.1.0/ldmppr/man/ldmppr_fit.Rd |only ldmppr-1.1.0/ldmppr/man/ldmppr_mark_model.Rd |only ldmppr-1.1.0/ldmppr/man/ldmppr_model_check.Rd |only ldmppr-1.1.0/ldmppr/man/ldmppr_sim.Rd |only ldmppr-1.1.0/ldmppr/man/plot_mpp.Rd | 2 ldmppr-1.1.0/ldmppr/man/predict_marks.Rd | 8 ldmppr-1.1.0/ldmppr/man/simulate_mpp.Rd | 21 ldmppr-1.1.0/ldmppr/man/simulate_sc.Rd | 6 ldmppr-1.1.0/ldmppr/man/train_mark_model.Rd | 9 ldmppr-1.1.0/ldmppr/src/RcppExports.cpp | 18 ldmppr-1.1.0/ldmppr/src/self_correcting_model.cpp | 488 ++++++++++- ldmppr-1.1.0/ldmppr/tests |only ldmppr-1.1.0/ldmppr/vignettes/ldmppr_howto.Rmd | 191 ++-- 51 files changed, 1686 insertions(+), 819 deletions(-)
Title: Bayesian Deep Gaussian Processes using MCMC
Description: Performs Bayesian posterior inference for deep Gaussian
processes following Sauer, Gramacy, and Higdon (2023, <doi:10.48550/arXiv.2012.08015>).
See Sauer (2023, <http://hdl.handle.net/10919/114845>) for comprehensive
methodological details and <https://bitbucket.org/gramacylab/deepgp-ex/> for
a variety of coding examples. Models are trained through MCMC including
elliptical slice sampling of latent Gaussian layers and Metropolis-Hastings
sampling of kernel hyperparameters. Gradient-enhancement and gradient
predictions are offered following Booth (2025, <doi:10.48550/arXiv.2512.18066>).
Vecchia approximation for faster
computation is implemented following Sauer, Cooper, and Gramacy
(2023, <doi:10.48550/arXiv.2204.02904>). Optional monotonic warpings are
implemented following Barnett et al. (2025, <doi:10.48550/arXiv.2408.01540>).
Downstream tasks include sequential design
through active learning Cohn/integrated mean squared error (ALC/IMSE; Sauer,
G [...truncated...]
Author: Annie S. Booth [aut, cre]
Maintainer: Annie S. Booth <annie_booth@vt.edu>
Diff between deepgp versions 1.1.3 dated 2024-08-19 and 1.2.0 dated 2026-01-08
deepgp-1.1.3/deepgp/src/approx.cpp |only deepgp-1.2.0/deepgp/DESCRIPTION | 52 - deepgp-1.2.0/deepgp/MD5 | 83 +- deepgp-1.2.0/deepgp/NAMESPACE | 12 deepgp-1.2.0/deepgp/R/ALC.R | 166 ++-- deepgp-1.2.0/deepgp/R/IMSE.R | 227 +++--- deepgp-1.2.0/deepgp/R/RcppExports.R | 28 deepgp-1.2.0/deepgp/R/checks.R | 280 ++++--- deepgp-1.2.0/deepgp/R/continue.R | 297 ++++---- deepgp-1.2.0/deepgp/R/deepgp-package.R | 29 deepgp-1.2.0/deepgp/R/fit.R | 595 ++++++++-------- deepgp-1.2.0/deepgp/R/gibbs.R | 675 ++++++++++++------ deepgp-1.2.0/deepgp/R/gibbs_vecchia.R | 673 +++++++++++------- deepgp-1.2.0/deepgp/R/krig.R |only deepgp-1.2.0/deepgp/R/mcmc.R | 460 ++++++------ deepgp-1.2.0/deepgp/R/mcmc_vecchia.R | 365 +++++---- deepgp-1.2.0/deepgp/R/misc.R | 259 +++---- deepgp-1.2.0/deepgp/R/plot.R | 288 +++---- deepgp-1.2.0/deepgp/R/predict.R | 996 +++++++++++++++++++-------- deepgp-1.2.0/deepgp/R/predict_vecchia.R | 964 ++++++++++++++++++-------- deepgp-1.2.0/deepgp/R/sample.R |only deepgp-1.2.0/deepgp/R/trim.R | 45 - deepgp-1.2.0/deepgp/R/vecchia.R | 354 +++++---- deepgp-1.2.0/deepgp/README.md | 175 +++- deepgp-1.2.0/deepgp/build/vignette.rds |binary deepgp-1.2.0/deepgp/inst/doc/deepgp.R | 262 ++++--- deepgp-1.2.0/deepgp/inst/doc/deepgp.Rmd | 347 +++++---- deepgp-1.2.0/deepgp/inst/doc/deepgp.html | 643 +++++++++-------- deepgp-1.2.0/deepgp/man/ALC.Rd | 4 deepgp-1.2.0/deepgp/man/IMSE.Rd | 4 deepgp-1.2.0/deepgp/man/continue.Rd | 34 deepgp-1.2.0/deepgp/man/deepgp-package.Rd | 21 deepgp-1.2.0/deepgp/man/fit_one_layer.Rd | 80 +- deepgp-1.2.0/deepgp/man/fit_three_layer.Rd | 104 +- deepgp-1.2.0/deepgp/man/fit_two_layer.Rd | 143 ++- deepgp-1.2.0/deepgp/man/plot.Rd | 9 deepgp-1.2.0/deepgp/man/post_sample.Rd |only deepgp-1.2.0/deepgp/man/predict.Rd | 88 +- deepgp-1.2.0/deepgp/man/to_vec.Rd |only deepgp-1.2.0/deepgp/src/RcppExports.cpp | 174 +++- deepgp-1.2.0/deepgp/src/cov.cpp | 158 +++- deepgp-1.2.0/deepgp/src/cov.h | 8 deepgp-1.2.0/deepgp/src/vecchia.cpp | 290 +++++-- deepgp-1.2.0/deepgp/vignettes/deepgp.Rmd | 347 +++++---- deepgp-1.2.0/deepgp/vignettes/references.bib | 42 - 45 files changed, 6005 insertions(+), 3776 deletions(-)
Title: Functions to Streamline Statistical Analysis and Reporting
Description: Built upon popular R packages such as 'ggstatsplot' and 'ARTool', this collection offers a wide array of tools for simplifying reproducible analyses, generating high-quality visualizations, and producing 'APA'-compliant outputs. The primary goal of this package is to significantly reduce repetitive coding efforts, allowing you to focus on interpreting results. Whether you're dealing with ANOVA assumptions, reporting effect sizes, or creating publication-ready visualizations, this package makes these tasks easier.
Author: Mark Colley [aut, cre, cph]
Maintainer: Mark Colley <mark.colley@yahoo.de>
Diff between colleyRstats versions 0.0.1 dated 2025-12-19 and 0.0.2 dated 2026-01-08
DESCRIPTION | 29 - LICENSE | 4 MD5 | 96 ++-- NAMESPACE | 149 +++---- R/globals.R | 14 R/imports.R | 32 - R/plotting.R | 207 +++++++--- R/reporting.R | 78 ++- R/setup.R | 373 +++++++++---------- R/utils.R | 214 +++++++--- README.md | 58 ++ inst |only man/add_pareto_emoa_column.Rd | 70 +-- man/checkAssumptionsForAnova.Rd | 76 +-- man/check_homogeneity_by_group.Rd | 42 +- man/check_normality_by_group.Rd | 43 +- man/colleyRstats_setup.Rd | 136 +++--- man/data-the-data-frame.Rd | 76 +-- man/debug_contr_error.Rd | 70 +-- man/generateEffectPlot.Rd | 156 +++---- man/generateMoboPlot.Rd | 126 +++--- man/generateMoboPlot2.Rd | 114 ++--- man/ggbetweenstatsWithPriorNormalityCheck.Rd | 128 +++--- man/ggbetweenstatsWithPriorNormalityCheckAsterisk.Rd | 118 +++--- man/ggwithinstatsWithPriorNormalityCheck.Rd | 128 +++--- man/ggwithinstatsWithPriorNormalityCheckAsterisk.Rd | 120 +++--- man/latexify_report.Rd | 121 +++--- man/n_fun.Rd |only man/na.zero.Rd |only man/normalize.Rd | 60 +-- man/not_empty.Rd | 38 - man/not_in.Rd |only man/pathPrep.Rd |only man/rFromNPAV.Rd | 60 +-- man/rFromWilcox.Rd | 66 +-- man/rFromWilcoxAdjusted.Rd | 74 +-- man/remove_outliers_REI.Rd | 70 +-- man/reportART.Rd | 104 ++--- man/reportDunnTest.Rd | 100 ++--- man/reportDunnTestTable.Rd | 134 +++--- man/reportMeanAndSD.Rd | 64 +-- man/reportNPAV.Rd | 78 ++- man/reportNparLD.Rd | 106 ++--- man/reportggstatsplot.Rd | 78 +-- man/reportggstatsplotPostHoc.Rd | 132 +++--- man/reshape_data.Rd | 138 +++---- man/stat_sum_df.Rd | 66 +-- tests/testthat/helper-load.R |only tests/testthat/test-plotting.R | 155 ++++++- tests/testthat/test-reporting.R |only tests/testthat/test-setup.R |only tests/testthat/test-utils.R | 291 ++++++++++++-- 52 files changed, 2571 insertions(+), 2021 deletions(-)
Title: Computing Graph Structures on WikiPathways
Description: Converts pathways from 'WikiPathways' GPML format or
'KEGG' KGML format into 'igraph' objects. Includes tools to find all
cycles in the resulting graphs and determine which ones involve
negative feedback (inhibition).
Author: Kevin R. Coombes [aut, cre],
Polina Bombina [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between WayFindR versions 0.5.0 dated 2025-11-05 and 0.7.0 dated 2026-01-08
DESCRIPTION | 13 - MD5 | 36 +-- NAMESPACE | 7 R/06-cycles.R | 74 ++++++ R/10-keggUtil.R | 15 + R/sysdata.rda |binary build/vignette.rds |binary data/edgeColors.rda |binary data/edgeTypes.rda |binary data/nodeColors.rda |binary data/nodeShapes.rda |binary inst/doc/WayFindR_getStarted.R | 2 inst/doc/WayFindR_getStarted.Rmd | 2 inst/doc/WayFindR_getStarted.html | 446 ++++++++++++++------------------------ inst/doc/WayFindR_metrics.html | 364 +++++++++++++------------------ inst/doc/WayFindR_plots.html | 290 +++++++++++------------- man/04-cycles.Rd | 17 + tests/06-testCycle.R | 2 vignettes/WayFindR_getStarted.Rmd | 2 19 files changed, 600 insertions(+), 670 deletions(-)
Title: Drugs Databases Parser
Description: This tool is for parsing public drug databases such as 'DrugBank' XML database <https://go.drugbank.com/>.
The parsed data are then returned in a proper 'R' object called 'dvobject'.
Author: Mohammed Ali [aut, cre],
Ali Ezzat [aut],
Hao Zhu [rev],
Emma Mendelsohn [rev]
Maintainer: Mohammed Ali <moh_fcis@yahoo.com>
Diff between dbparser versions 2.0.3 dated 2024-04-20 and 2.2.1 dated 2026-01-08
dbparser-2.0.3/dbparser/man/add_drugbank_info.Rd |only dbparser-2.2.1/dbparser/DESCRIPTION | 10 dbparser-2.2.1/dbparser/MD5 | 74 dbparser-2.2.1/dbparser/NAMESPACE | 18 dbparser-2.2.1/dbparser/NEWS.md | 55 dbparser-2.2.1/dbparser/R/drugbank_parser.R | 8 dbparser-2.2.1/dbparser/R/dvobject_metadata.R | 214 dbparser-2.2.1/dbparser/R/merge_helpers.R |only dbparser-2.2.1/dbparser/R/nsides_parsers.R |only dbparser-2.2.1/dbparser/R/onsides_parser.R |only dbparser-2.2.1/dbparser/R/utils.R |only dbparser-2.2.1/dbparser/README.md | 96 dbparser-2.2.1/dbparser/build/vignette.rds |binary dbparser-2.2.1/dbparser/inst/WORDLIST |only dbparser-2.2.1/dbparser/inst/doc/dbparser.R | 85 dbparser-2.2.1/dbparser/inst/doc/dbparser.Rmd | 150 dbparser-2.2.1/dbparser/inst/doc/dbparser.html | 3051 +++++----- dbparser-2.2.1/dbparser/inst/doc/dbparser_2_2.Rmd |only dbparser-2.2.1/dbparser/inst/doc/dbparser_2_2.html |only dbparser-2.2.1/dbparser/inst/doc/drugbank_nside.R |only dbparser-2.2.1/dbparser/inst/doc/drugbank_nside.Rmd |only dbparser-2.2.1/dbparser/inst/doc/drugbank_nside.html |only dbparser-2.2.1/dbparser/inst/onside.RDS |only dbparser-2.2.1/dbparser/inst/onside.zip |only dbparser-2.2.1/dbparser/inst/two_drugs.RDS |only dbparser-2.2.1/dbparser/inst/twoside_raw.zip |only dbparser-2.2.1/dbparser/man/add_database_info.Rd |only dbparser-2.2.1/dbparser/man/build_metadata.Rd |only dbparser-2.2.1/dbparser/man/cett_nodes_options.Rd | 2 dbparser-2.2.1/dbparser/man/count_top_level_lists.Rd |only dbparser-2.2.1/dbparser/man/dbparser.Rd | 2 dbparser-2.2.1/dbparser/man/drug_node_options.Rd | 2 dbparser-2.2.1/dbparser/man/find_dataframes_recursive.Rd |only dbparser-2.2.1/dbparser/man/find_second_database.Rd |only dbparser-2.2.1/dbparser/man/merge_drugbank_onsides.Rd |only dbparser-2.2.1/dbparser/man/merge_drugbank_twosides.Rd |only dbparser-2.2.1/dbparser/man/parseDrugBank.Rd | 2 dbparser-2.2.1/dbparser/man/parseOnSIDES.Rd |only dbparser-2.2.1/dbparser/man/parseTWOSIDES.Rd |only dbparser-2.2.1/dbparser/man/references_node_options.Rd | 4 dbparser-2.2.1/dbparser/man/show_dvobject_metadata.Rd | 29 dbparser-2.2.1/dbparser/man/subset_drugbank_dvobject.Rd |only dbparser-2.2.1/dbparser/man/subset_onsides_dvobject.Rd |only dbparser-2.2.1/dbparser/tests/testthat/_snaps/drugbank-parser.md | 1286 ++-- dbparser-2.2.1/dbparser/tests/testthat/_snaps/merge_functions.md |only dbparser-2.2.1/dbparser/tests/testthat/_snaps/onside_parser.md |only dbparser-2.2.1/dbparser/tests/testthat/_snaps/twoside_parser.md |only dbparser-2.2.1/dbparser/tests/testthat/_snaps/utils.md |only dbparser-2.2.1/dbparser/tests/testthat/test_dvobject_metadata.R | 12 dbparser-2.2.1/dbparser/tests/testthat/test_merge_functions.R |only dbparser-2.2.1/dbparser/tests/testthat/test_onside_parser.R |only dbparser-2.2.1/dbparser/tests/testthat/test_twoside_parser.R |only dbparser-2.2.1/dbparser/tests/testthat/test_utils.R |only dbparser-2.2.1/dbparser/vignettes/dbparser.Rmd | 150 dbparser-2.2.1/dbparser/vignettes/dbparser_2_2.Rmd |only dbparser-2.2.1/dbparser/vignettes/drugbank_nside.Rmd |only 56 files changed, 2925 insertions(+), 2325 deletions(-)
Title: Build Species Distribution Modeling using 'caret'
Description: Use machine learning algorithms and advanced geographic information system tools to
build Species Distribution Modeling in a extensible and modern fashion.
Author: Dayani Bailly [aut] ,
Edivando Couto [aut] ,
Jose Hilario Delconte Ferreira [aut] ,
Marcos R. Lima [aut] ,
Reginaldo Re [aut] ,
Valeria Batista [aut] ,
Luiz Fernando Esser [aut, cre, cph]
Maintainer: Luiz Fernando Esser <luizesser@gmail.com>
Diff between caretSDM versions 1.2.3 dated 2025-11-06 and 1.2.5 dated 2026-01-08
caretSDM-1.2.3/caretSDM/tests/testthat/_snaps/train_sdm.md |only caretSDM-1.2.5/caretSDM/DESCRIPTION | 10 caretSDM-1.2.5/caretSDM/MD5 | 45 caretSDM-1.2.5/caretSDM/NAMESPACE | 13 caretSDM-1.2.5/caretSDM/NEWS.md | 9 caretSDM-1.2.5/caretSDM/R/WorldClim_data.R | 205 ++-- caretSDM-1.2.5/caretSDM/R/add_scenarios.R | 31 caretSDM-1.2.5/caretSDM/R/buffer_sdm.R | 34 caretSDM-1.2.5/caretSDM/R/checkmate.R | 497 +++++++++- caretSDM-1.2.5/caretSDM/R/input_sdm.R | 17 caretSDM-1.2.5/caretSDM/README.md | 2 caretSDM-1.2.5/caretSDM/data/occ.rda |binary caretSDM-1.2.5/caretSDM/man/WorldClim_data.Rd | 45 caretSDM-1.2.5/caretSDM/man/buffer_sdm.Rd | 5 caretSDM-1.2.5/caretSDM/tests/testthat/_snaps/gcms_ensembles.md | 6 caretSDM-1.2.5/caretSDM/tests/testthat/_snaps/predict_sdm.md | 160 +-- caretSDM-1.2.5/caretSDM/tests/testthat/test-WorldClim_data.R | 1 caretSDM-1.2.5/caretSDM/tests/testthat/test-add_predictors.R | 1 caretSDM-1.2.5/caretSDM/tests/testthat/test-add_scenarios.R | 1 caretSDM-1.2.5/caretSDM/tests/testthat/test-buffer_sdm.R | 17 caretSDM-1.2.5/caretSDM/tests/testthat/test-data_clean.R | 6 caretSDM-1.2.5/caretSDM/tests/testthat/test-input_sdm.R | 9 caretSDM-1.2.5/caretSDM/tests/testthat/test-train_sdm.R | 43 caretSDM-1.2.5/caretSDM/tests/testthat/test-use_mem.R | 8 24 files changed, 865 insertions(+), 300 deletions(-)
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Alejandro Szmulewicz [aut] ,
Tom Palmer [aut] ,
Miguel Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryan.odea@psi.ch>
Diff between SEQTaRget versions 1.3.2 dated 2025-11-10 and 1.3.3 dated 2026-01-08
DESCRIPTION | 6 MD5 | 123 +++++----- NEWS.md |only R/SEQestimate.R | 7 R/SEQexpand.R | 10 R/SEQopts.R | 87 ++++--- R/SEQuential.R | 25 +- R/class_definitions.R | 12 - R/class_methods.R | 20 - R/class_setters.R | 22 + R/data.R | 24 +- R/internal_analysis.R | 5 R/internal_covariates.R | 32 +- R/internal_fatglmHelpers.R | 17 + R/internal_hazard.R | 2 R/internal_misc.R | 9 R/internal_models.R | 1 R/internal_multinomial.R | 6 R/internal_weights.R | 49 +++- README.md | 4 inst/doc/ITT.R | 29 +- inst/doc/ITT.Rmd | 29 +- inst/doc/ITT.html | 14 - inst/doc/SEQuential.R | 40 +-- inst/doc/SEQuential.Rmd | 8 inst/doc/SEQuential.html | 200 +++++++++++++++++ inst/doc/censoring.R | 294 +++++++++++++------------- inst/doc/censoring.Rmd | 38 ++- inst/doc/censoring.html | 354 +++++++++++++++++++++---------- inst/doc/doseresponse.R | 29 +- inst/doc/doseresponse.Rmd | 29 +- inst/doc/doseresponse.html | 14 - inst/doc/seqopts.Rmd | 117 +++++----- inst/doc/seqopts.html | 415 +++++++++++++++++++------------------ man/SEQdata.LTFU.Rd | 28 +- man/SEQdata.Rd | 24 +- man/SEQdata.multitreatment.Rd | 26 +- man/SEQestimate.Rd | 16 - man/SEQexpand.Rd | 4 man/SEQopts.Rd | 77 +++--- man/SEQuential.Rd | 18 - man/compevent.Rd | 2 man/covariates.Rd | 2 man/diagnostics.Rd | 2 man/hazard_ratio.Rd | 2 man/km_curve.Rd | 4 man/km_data.Rd | 2 man/risk_comparison.Rd | 2 man/risk_data.Rd | 2 man/show-SEQoutput-method.Rd | 2 tests/testthat/test_coefficients.R | 60 +++-- tests/testthat/test_deviation.R | 2 tests/testthat/test_hazard.R | 2 tests/testthat/test_misc.R | 2 tests/testthat/test_multinomial.R | 26 +- tests/testthat/test_parallel.R | 4 tests/testthat/test_survival.R | 6 tests/testthat/test_warnings.R | 4 vignettes/ITT.Rmd | 29 +- vignettes/SEQuential.Rmd | 8 vignettes/censoring.Rmd | 38 ++- vignettes/doseresponse.Rmd | 29 +- vignettes/seqopts.Rmd | 117 +++++----- 63 files changed, 1571 insertions(+), 1040 deletions(-)
Title: Implementation of Remez Algorithm for Polynomial and Rational
Function Approximation
Description: Implements the algorithm of Remez (1962) for polynomial minimax
approximation and of Cody et al. (1968) <doi:10.1007/BF02162506> for
rational minimax approximation.
Author: Avraham Adler [aut, cre, cph]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between minimaxApprox versions 0.4.3 dated 2024-06-20 and 0.5.0 dated 2026-01-08
DESCRIPTION | 11 ++-- MD5 | 28 +++++----- NAMESPACE | 10 ++- R/MiniMaxApprox.R | 92 +++++++++++++++++----------------- R/RemezRational.R | 10 +-- R/methods.R | 22 ++++---- R/shared.R | 2 build/partial.rdb |binary inst/CITATION | 2 inst/NEWS.Rd | 21 +++++++ inst/tinytest/test_MiniMaxApprox.R | 26 +++++++-- inst/tinytest/test_package_metadata.R | 10 ++- inst/tinytest/test_shared.R | 2 src/Chebyshev.c | 2 src/compHorner.c | 45 ++++++++++------ 15 files changed, 170 insertions(+), 113 deletions(-)
Title: R Shiny Application for Latent Structure Analysis with a
Graphical User Interface
Description: Provides an interactive Shiny-based toolkit for conducting latent structure analyses, including Latent Profile Analysis (LPA), Latent Class Analysis (LCA), Latent Trait Analysis (LTA/IRT), Exploratory Factor Analysis (EFA), Confirmatory Factor Analysis (CFA), and Structural Equation Modeling (SEM). The implementation is grounded in established methodological frameworks: LPA is supported through 'tidyLPA' (Rosenberg et al., 2018) <doi:10.21105/joss.00978>, LCA through 'poLCA' (Linzer & Lewis, 2011), LTA/IRT via 'mirt' (Chalmers, 2012) <doi:10.18637/jss.v048.i06>, and EFA via 'psych' (Revelle, 2025). SEM and CFA functionalities build upon the 'lavaan' framework (Rosseel, 2012) <doi:10.18637/jss.v048.i02>. Users can upload datasets or use built-in examples, fit models, compare fit indices, visualize results, and export outputs without programming.
Author: Hasan Djidu [aut, cre] ,
Heri Retnawati [ctb] ,
Samsul Hadi [ctb] ,
Haryanto [ctb]
Maintainer: Hasan Djidu <hasandjidu@gmail.com>
Diff between projectLSA versions 0.0.3 dated 2025-12-10 and 0.0.5 dated 2026-01-08
projectLSA-0.0.3/projectLSA/man/figures/README-pressure-1.png |only projectLSA-0.0.3/projectLSA/man/figures/lpa_example.png |only projectLSA-0.0.3/projectLSA/man/figures/lpa_example2.png |only projectLSA-0.0.5/projectLSA/DESCRIPTION | 17 projectLSA-0.0.5/projectLSA/LICENSE | 2 projectLSA-0.0.5/projectLSA/MD5 | 47 - projectLSA-0.0.5/projectLSA/NEWS.md | 11 projectLSA-0.0.5/projectLSA/R/projectLSA-package.R | 1 projectLSA-0.0.5/projectLSA/R/run_app.R | 3 projectLSA-0.0.5/projectLSA/R/zzz.R | 1 projectLSA-0.0.5/projectLSA/README.md | 48 - projectLSA-0.0.5/projectLSA/inst/app/app.R | 4 projectLSA-0.0.5/projectLSA/inst/app/homepage_ui.R | 4 projectLSA-0.0.5/projectLSA/inst/app/lca_ui.R | 21 projectLSA-0.0.5/projectLSA/inst/app/lpa_ui.R | 76 + projectLSA-0.0.5/projectLSA/inst/app/lta_ui.R | 3 projectLSA-0.0.5/projectLSA/inst/app/serverCFA.R | 8 projectLSA-0.0.5/projectLSA/inst/app/serverEFA.R | 2 projectLSA-0.0.5/projectLSA/inst/app/serverLCA.R | 234 ++++- projectLSA-0.0.5/projectLSA/inst/app/serverLPA.R | 425 +++++----- projectLSA-0.0.5/projectLSA/inst/app/serverLTA.R | 407 ++++++--- projectLSA-0.0.5/projectLSA/man/figures/CFA4.png |only projectLSA-0.0.5/projectLSA/man/figures/CFA7.png |only projectLSA-0.0.5/projectLSA/man/figures/Homepage.png |only projectLSA-0.0.5/projectLSA/man/figures/LCA2.png |only projectLSA-0.0.5/projectLSA/man/figures/LCA3.png |only projectLSA-0.0.5/projectLSA/man/figures/LPA3.png |only projectLSA-0.0.5/projectLSA/man/figures/LPA4.png |only projectLSA-0.0.5/projectLSA/man/figures/LTA3.png |only projectLSA-0.0.5/projectLSA/man/figures/LTA6.png |only projectLSA-0.0.5/projectLSA/man/figures/SEM.png |only 31 files changed, 875 insertions(+), 439 deletions(-)
Title: A Collection of Functions for Negligible Effect/Equivalence
Testing
Description: Researchers often want to evaluate whether there is a negligible
relationship among variables. The 'negligible' package provides functions that
are useful for conducting negligible effect testing (also called
equivalence testing). For example, there are functions for evaluating the
equivalence of means or the presence of a negligible association
(correlation or regression). Beribisky, N., Mara, C., & Cribbie, R. A. (2020) <doi:10.20982/tqmp.16.4.p424>.
Beribisky, N., Davidson, H., Cribbie, R. A. (2019) <doi:10.7717/peerj.6853>.
Shiskina, T., Farmus, L., & Cribbie, R. A. (2018) <doi:10.20982/tqmp.14.3.p167>.
Mara, C. & Cribbie, R. A. (2017) <doi:10.1080/00220973.2017.1301356>.
Counsell, A. & Cribbie, R. A. (2015) <doi:10.1111/bmsp.12045>.
van Wieringen, K. & Cribbie, R. A. (2014) <doi:10.1111/bmsp.12015>.
Goertzen, J. R. & Cribbie, R. A. (2010) <doi:10.1348/000711009x475853>.
Cribbie, R. A., Gruman, J. & Arpin-Cribbi [...truncated...]
Author: Robert Cribbie [aut, cre],
Udi Alter [aut],
Nataly Beribisky [aut],
Phil Chalmers [aut],
Alyssa Counsell [aut],
Linda Farmus [aut],
Naomi Martinez Gutierrez [aut],
Victoria Ng [ctb]
Maintainer: Robert Cribbie <cribbie@yorku.ca>
Diff between negligible versions 0.1.9 dated 2024-09-09 and 0.1.11 dated 2026-01-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/neg.intcat.R | 14 ++++++-------- R/neg.intcont.R | 32 ++++++++++---------------------- R/neg_normal.R | 14 +++++++++++++- README.md | 4 ++++ 6 files changed, 42 insertions(+), 40 deletions(-)
Title: Statistical Functions for the
Maxwell-Boltzmann-Bose-Einstein-Fermi-Dirac (MBBEFD) Family of
Distributions
Description: Provides probability mass, distribution, quantile, random variate
generation, and method-of-moments parameter fitting for the MBBEFD family of
distributions used in insurance modeling as described in Bernegger (1997)
<doi:10.2143/AST.27.1.563208> without any external dependencies.
Author: Avraham Adler [aut, cre, cph]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between MBBEFDLite versions 0.0.5 dated 2025-01-31 and 0.1.0 dated 2026-01-08
DESCRIPTION | 9 ++-- MD5 | 34 +++++++-------- NAMESPACE | 15 ++++-- R/mbbefd.R | 11 +--- R/mom.R | 75 +++++++++++++++++++++------------- build/partial.rdb |binary inst/CITATION | 2 inst/NEWS.Rd | 45 ++++++++++++++++++++ inst/tinytest/test_MoMmb.R | 38 +++++++++++++---- inst/tinytest/test_package_metadata.R | 2 man/MBBEFDLite-internal.Rd | 1 man/MoMmb.Rd | 23 +++++++--- man/dpqrmb.Rd | 4 - src/MBBEFDLite.h | 2 src/dmb.c | 2 src/ecmb.c | 2 src/pmb.c | 2 src/qrmb.c | 4 - 18 files changed, 188 insertions(+), 83 deletions(-)
Title: Generalized Kumaraswamy Distribution Family
Description: Implements the five-parameter Generalized Kumaraswamy ('gkw')
distribution proposed by 'Carrasco, Ferrari and Cordeiro (2010)'
<doi:10.48550/arXiv.1004.0911> and its seven nested sub-families for
modeling bounded continuous data on the unit interval (0,1). The 'gkw'
distribution extends the Kumaraswamy distribution described by Jones (2009)
<doi:10.1016/j.stamet.2008.04.001>. Provides density, distribution,
quantile, and random generation functions, along with analytical
log-likelihood, gradient, and Hessian functions implemented in 'C++' via
'RcppArmadillo' for maximum computational efficiency. Suitable for modeling
proportions, rates, percentages, and indices exhibiting complex features
such as asymmetry, or heavy tails and other shapes not adequately captured by
standard distributions like simple Beta or Kumaraswamy.
Author: Jose Evandeilton Lopes [aut, cre]
Maintainer: Jose Evandeilton Lopes <evandeilton@gmail.com>
Diff between gkwdist versions 1.1.1 dated 2025-11-27 and 1.1.2 dated 2026-01-08
DESCRIPTION | 6 MD5 | 145 +-- NEWS.md | 31 R/beta.R | 603 +++++++------- R/bkw.R | 815 ++++++++++--------- R/bpmc.R | 894 +++++++++++---------- R/ekw.R | 901 +++++++++++---------- R/gkw.R | 975 ++++++++++++----------- R/kkw.R | 779 ++++++++++-------- R/kw.R | 664 ++++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/into-gkwdist.html | 14 inst/doc/theory-gkwdist.html | 4 inst/paper |only man/dbeta_.Rd | 21 man/dbkw.Rd | 21 man/dekw.Rd | 18 man/dgkw.Rd | 13 man/dkkw.Rd | 16 man/dkw.Rd | 20 man/dmc.Rd | 18 man/grbeta.Rd | 24 man/grbkw.Rd | 52 - man/grekw.Rd | 72 - man/grgkw.Rd | 64 - man/grkkw.Rd | 29 man/grkw.Rd | 43 - man/grmc.Rd | 117 +- man/hsbeta.Rd | 72 + man/hsbkw.Rd | 113 +- man/hsekw.Rd | 108 +- man/hsgkw.Rd | 130 +-- man/hskkw.Rd | 101 +- man/hskw.Rd | 56 - man/hsmc.Rd | 115 +- man/llbeta.Rd | 82 + man/llbkw.Rd | 136 +-- man/llekw.Rd | 166 ++- man/llgkw.Rd | 222 +++-- man/llkkw.Rd | 148 ++- man/llkw.Rd | 136 +-- man/llmc.Rd | 118 +- man/pbeta_.Rd | 21 man/pbkw.Rd | 18 man/pekw.Rd | 21 man/pgkw.Rd | 24 man/pkkw.Rd | 19 man/pkw.Rd | 21 man/pmc.Rd | 21 man/qbeta_.Rd | 7 man/qbkw.Rd | 13 man/qekw.Rd | 12 man/qgkw.Rd | 12 man/qkkw.Rd | 13 man/qkw.Rd | 7 man/qmc.Rd | 10 man/rbeta_.Rd | 15 man/rbkw.Rd | 43 - man/rekw.Rd | 30 man/rgkw.Rd | 17 man/rkkw.Rd | 42 - man/rkw.Rd | 24 man/rmc.Rd | 50 - src/beta_.cpp | 391 --------- src/bkw.cpp | 1015 ------------------------ src/bpmc.cpp | 676 ---------------- src/ekw.cpp | 778 ------------------ src/gkw.cpp | 977 ----------------------- src/kkw.cpp | 1130 --------------------------- src/kw.cpp | 460 ---------- tests/testthat/test-derivatives-validation.R |only tests/testthat/test-mle-performance.R |only 73 files changed, 4804 insertions(+), 9125 deletions(-)
Title: Analysis of Sex Differences in Omics Data for Complex Diseases
Description: Tools to analyze sex differences in omics data for complex diseases. It includes functions for differential expression analysis using the 'limma' method <doi:10.1093/nar/gkv007>, interaction testing between sex and disease, pathway enrichment with 'clusterProfiler' <doi:10.1089/omi.2011.0118>, and gene regulatory network (GRN) construction and analysis using 'igraph'. The package enables a reproducible workflow from raw data processing to biological interpretation.
Author: Enrico Glaab [aut, cre],
Sophie Le Bars [aut],
Mohamed Soudy [aut],
Murodzhon Akhmedov [cph]
Maintainer: Enrico Glaab <enrico.glaab@uni.lu>
Diff between XYomics versions 0.1.2 dated 2025-12-15 and 0.1.3 dated 2026-01-08
DESCRIPTION | 12 - MD5 | 24 +- NAMESPACE | 3 R/pathway_enrichment.R | 36 +++ R/pathway_enrichment_sc.R | 334 +++++++++++++++++++------------------ inst/doc/XYomics_bulk_example.R | 2 inst/doc/XYomics_bulk_example.html | 4 inst/doc/XYomics_sc_example.R | 4 inst/doc/XYomics_sc_example.Rmd | 2 inst/doc/XYomics_sc_example.html | 178 ++++++++++--------- man/categorized_enrich_sc.Rd | 2 man/improved_pathway_enrichment.Rd | 2 vignettes/XYomics_sc_example.Rmd | 2 13 files changed, 331 insertions(+), 274 deletions(-)
Title: Compare and Verify File Contents
Description: Extendable 'R6' file comparison classes, including a 'shiny' app for combining the comparison functionality into a file comparison application. The package idea originates from pharma companies' drug development processes, where statisticians and statistical programmers need to review and compare different versions of the same outputs and datasets. The package implementation itself is not tied to any specific industry and can be used in any context for easy file comparisons between different file version sets.
Author: Juha Javanainen [aut, cre],
Tiina Kirsilae [ctb],
Anna Wiksten [ctb]
Maintainer: Juha Javanainen <ejuhjav@gmail.com>
Diff between verifyr2 versions 1.0.0 dated 2025-07-16 and 1.1.0 dated 2026-01-08
DESCRIPTION | 12 +++---- MD5 | 9 +++-- NEWS.md |only R/TxtFileComparator.R | 66 ++++++++++++++++++++++++++++++++++++++++-- README.md | 51 ++++++++++++++++++++------------ inst/shiny_examples/app/app.R | 9 ++++- 6 files changed, 114 insertions(+), 33 deletions(-)
Title: Multivariate Covariance Generalized Linear Models
Description: Fitting multivariate covariance generalized linear
models (McGLMs) to data. McGLM is a general framework for non-normal
multivariate data analysis, designed to handle multivariate response
variables, along with a wide range of temporal and spatial correlation
structures defined in terms of a covariance link function combined
with a matrix linear predictor involving known matrices.
The models take non-normality into account in the conventional way
by means of a variance function, and the mean structure is modelled
by means of a link function and a linear predictor.
The models are fitted using an efficient Newton scoring algorithm
based on quasi-likelihood and Pearson estimating functions, using
only second-moment assumptions. This provides a unified approach to
a wide variety of different types of response variables and covariance
structures, including multivariate extensions of repeated measures,
time series, longitudinal, spatial and spatio-temporal structures.
The package offers a u [...truncated...]
Author: Wagner Hugo Bonat [aut, cre]
Maintainer: Wagner Hugo Bonat <wbonat@ufpr.br>
This is a re-admission after prior archival of version 0.8.0 dated 2022-09-15
Diff between mcglm versions 0.8.0 dated 2022-09-15 and 0.9.0 dated 2026-01-08
mcglm-0.8.0/mcglm/LICENSE |only mcglm-0.8.0/mcglm/inst/CITATION |only mcglm-0.9.0/mcglm/DESCRIPTION | 18 mcglm-0.9.0/mcglm/MD5 | 302 ++--- mcglm-0.9.0/mcglm/R/fit_mcglm.R | 19 mcglm-0.9.0/mcglm/R/mc_KLIC.R | 12 mcglm-0.9.0/mcglm/R/mc_RJC.R | 51 mcglm-0.9.0/mcglm/R/mc_S3_methods.R | 1068 +++++++++++++------- mcglm-0.9.0/mcglm/R/mc_anova_disp.R | 181 +-- mcglm-0.9.0/mcglm/R/mc_auxiliar.R | 1 mcglm-0.9.0/mcglm/R/mc_bias_correct_std.R | 5 mcglm-0.9.0/mcglm/R/mc_build_C.R | 8 mcglm-0.9.0/mcglm/R/mc_build_F.R | 6 mcglm-0.9.0/mcglm/R/mc_build_bdiag.R | 3 mcglm-0.9.0/mcglm/R/mc_build_omega.R | 5 mcglm-0.9.0/mcglm/R/mc_build_sigma.R | 15 mcglm-0.9.0/mcglm/R/mc_build_sigmab.R | 3 mcglm-0.9.0/mcglm/R/mc_car.R | 13 mcglm-0.9.0/mcglm/R/mc_complete_data.R | 6 mcglm-0.9.0/mcglm/R/mc_compute_rho.R | 5 mcglm-0.9.0/mcglm/R/mc_conditional_test.R | 4 mcglm-0.9.0/mcglm/R/mc_core_cross_variability.R | 3 mcglm-0.9.0/mcglm/R/mc_core_pearson.R | 4 mcglm-0.9.0/mcglm/R/mc_correction.R | 2 mcglm-0.9.0/mcglm/R/mc_cross_sensitivity.R | 2 mcglm-0.9.0/mcglm/R/mc_cross_variability.R | 4 mcglm-0.9.0/mcglm/R/mc_derivative_C_rho.R | 4 mcglm-0.9.0/mcglm/R/mc_derivative_cholesky.R | 4 mcglm-0.9.0/mcglm/R/mc_derivative_expm.R | 3 mcglm-0.9.0/mcglm/R/mc_derivative_sigma_beta.R | 5 mcglm-0.9.0/mcglm/R/mc_dexp_gold.R | 1 mcglm-0.9.0/mcglm/R/mc_dexpm.R | 6 mcglm-0.9.0/mcglm/R/mc_dglm.R | 7 mcglm-0.9.0/mcglm/R/mc_dist.R | 10 mcglm-0.9.0/mcglm/R/mc_ess.R | 10 mcglm-0.9.0/mcglm/R/mc_getInformation.R | 14 mcglm-0.9.0/mcglm/R/mc_gof.R | 9 mcglm-0.9.0/mcglm/R/mc_gosho.R | 7 mcglm-0.9.0/mcglm/R/mc_id.R | 9 mcglm-0.9.0/mcglm/R/mc_initial_values.R | 13 mcglm-0.9.0/mcglm/R/mc_link_function.R | 10 mcglm-0.9.0/mcglm/R/mc_list2vec.R | 9 mcglm-0.9.0/mcglm/R/mc_ma.R | 39 mcglm-0.9.0/mcglm/R/mc_main_function.R | 151 +- mcglm-0.9.0/mcglm/R/mc_manova.R | 141 ++ mcglm-0.9.0/mcglm/R/mc_manova_disp.R | 138 ++ mcglm-0.9.0/mcglm/R/mc_matrix_linear_predictor.R | 56 - mcglm-0.9.0/mcglm/R/mc_mixed.R | 111 +- mcglm-0.9.0/mcglm/R/mc_ns.R | 72 - mcglm-0.9.0/mcglm/R/mc_pAIC.R | 45 mcglm-0.9.0/mcglm/R/mc_pBIC.R | 53 mcglm-0.9.0/mcglm/R/mc_pearson.R | 84 + mcglm-0.9.0/mcglm/R/mc_plogLik.R | 54 - mcglm-0.9.0/mcglm/R/mc_quasi_score.R | 56 - mcglm-0.9.0/mcglm/R/mc_remove_na.R | 42 mcglm-0.9.0/mcglm/R/mc_robust_std.R | 54 - mcglm-0.9.0/mcglm/R/mc_rw.R | 78 - mcglm-0.9.0/mcglm/R/mc_sensitivity.R | 4 mcglm-0.9.0/mcglm/R/mc_sic.R | 95 + mcglm-0.9.0/mcglm/R/mc_sic_covariance.R | 110 +- mcglm-0.9.0/mcglm/R/mc_transform_list_bdiag.R | 40 mcglm-0.9.0/mcglm/R/mc_twin.R | 106 + mcglm-0.9.0/mcglm/R/mc_updatedBeta.R | 37 mcglm-0.9.0/mcglm/R/mc_updatedCov.R | 44 mcglm-0.9.0/mcglm/R/mc_variability.R | 49 mcglm-0.9.0/mcglm/R/mc_variance_function.R | 92 - mcglm-0.9.0/mcglm/R/mcglm.R | 464 +++----- mcglm-0.9.0/mcglm/README.md |only mcglm-0.9.0/mcglm/build/vignette.rds |binary mcglm-0.9.0/mcglm/inst/doc/GLMExamples.R | 64 - mcglm-0.9.0/mcglm/inst/doc/GLMExamples.Rmd | 16 mcglm-0.9.0/mcglm/inst/doc/GLMExamples.html | 208 +-- mcglm-0.9.0/mcglm/inst/doc/UniModels.R | 52 mcglm-0.9.0/mcglm/inst/doc/UniModels.Rmd | 10 mcglm-0.9.0/mcglm/inst/doc/UniModels.html | 172 +-- mcglm-0.9.0/mcglm/man/ESS.Rd | 6 mcglm-0.9.0/mcglm/man/GOSHO.Rd | 7 mcglm-0.9.0/mcglm/man/Hunting.Rd | 84 - mcglm-0.9.0/mcglm/man/NewBorn.Rd | 113 -- mcglm-0.9.0/mcglm/man/RJC.Rd | 45 mcglm-0.9.0/mcglm/man/ahs.Rd | 103 - mcglm-0.9.0/mcglm/man/anova.mcglm.Rd | 63 - mcglm-0.9.0/mcglm/man/coef.mcglm.Rd | 36 mcglm-0.9.0/mcglm/man/confint.mcglm.Rd | 26 mcglm-0.9.0/mcglm/man/covprod.Rd | 5 mcglm-0.9.0/mcglm/man/fit_mcglm.Rd | 17 mcglm-0.9.0/mcglm/man/fitted.mcglm.Rd | 14 mcglm-0.9.0/mcglm/man/gof.Rd | 9 mcglm-0.9.0/mcglm/man/mc_anova_disp.Rd | 58 - mcglm-0.9.0/mcglm/man/mc_bias_corrected_std.Rd | 5 mcglm-0.9.0/mcglm/man/mc_build_C.Rd | 8 mcglm-0.9.0/mcglm/man/mc_build_F.Rd | 6 mcglm-0.9.0/mcglm/man/mc_build_bdiag.Rd | 3 mcglm-0.9.0/mcglm/man/mc_build_omega.Rd | 5 mcglm-0.9.0/mcglm/man/mc_build_sigma.Rd | 15 mcglm-0.9.0/mcglm/man/mc_build_sigma_between.Rd | 3 mcglm-0.9.0/mcglm/man/mc_car.Rd | 13 mcglm-0.9.0/mcglm/man/mc_complete_data.Rd | 6 mcglm-0.9.0/mcglm/man/mc_compute_rho.Rd | 5 mcglm-0.9.0/mcglm/man/mc_conditional_test.Rd | 4 mcglm-0.9.0/mcglm/man/mc_core_pearson.Rd | 4 mcglm-0.9.0/mcglm/man/mc_correction.Rd | 2 mcglm-0.9.0/mcglm/man/mc_cross_sensitivity.Rd | 2 mcglm-0.9.0/mcglm/man/mc_cross_variability.Rd | 2 mcglm-0.9.0/mcglm/man/mc_derivative_C_rho.Rd | 4 mcglm-0.9.0/mcglm/man/mc_derivative_cholesky.Rd | 4 mcglm-0.9.0/mcglm/man/mc_derivative_expm.Rd | 3 mcglm-0.9.0/mcglm/man/mc_derivative_sigma_beta.Rd | 5 mcglm-0.9.0/mcglm/man/mc_dexp_gold.Rd | 1 mcglm-0.9.0/mcglm/man/mc_dglm.Rd | 7 mcglm-0.9.0/mcglm/man/mc_dist.Rd | 5 mcglm-0.9.0/mcglm/man/mc_expm.Rd | 6 mcglm-0.9.0/mcglm/man/mc_getInformation.Rd | 14 mcglm-0.9.0/mcglm/man/mc_id.Rd | 9 mcglm-0.9.0/mcglm/man/mc_initial_values.Rd | 13 mcglm-0.9.0/mcglm/man/mc_link_function.Rd | 10 mcglm-0.9.0/mcglm/man/mc_list2vec.Rd | 9 mcglm-0.9.0/mcglm/man/mc_ma.Rd | 34 mcglm-0.9.0/mcglm/man/mc_manova.Rd | 30 mcglm-0.9.0/mcglm/man/mc_manova_disp.Rd | 38 mcglm-0.9.0/mcglm/man/mc_matrix_linear_predictor.Rd | 42 mcglm-0.9.0/mcglm/man/mc_mixed.Rd | 96 + mcglm-0.9.0/mcglm/man/mc_ns.Rd | 62 - mcglm-0.9.0/mcglm/man/mc_pearson.Rd | 86 + mcglm-0.9.0/mcglm/man/mc_quasi_score.Rd | 48 mcglm-0.9.0/mcglm/man/mc_remove_na.Rd | 39 mcglm-0.9.0/mcglm/man/mc_robust_std.Rd | 45 mcglm-0.9.0/mcglm/man/mc_rw.Rd | 60 - mcglm-0.9.0/mcglm/man/mc_sandwich.Rd | 1 mcglm-0.9.0/mcglm/man/mc_sensitivity.Rd | 4 mcglm-0.9.0/mcglm/man/mc_sic.Rd | 84 - mcglm-0.9.0/mcglm/man/mc_sic_covariance.Rd | 97 + mcglm-0.9.0/mcglm/man/mc_transform_list_bdiag.Rd | 29 mcglm-0.9.0/mcglm/man/mc_twin.Rd | 78 - mcglm-0.9.0/mcglm/man/mc_updateBeta.Rd | 26 mcglm-0.9.0/mcglm/man/mc_updateCov.Rd | 31 mcglm-0.9.0/mcglm/man/mc_variability.Rd | 35 mcglm-0.9.0/mcglm/man/mc_variance_function.Rd | 83 - mcglm-0.9.0/mcglm/man/mcglm.Rd | 123 +- mcglm-0.9.0/mcglm/man/pAIC.Rd | 38 mcglm-0.9.0/mcglm/man/pBIC.Rd | 44 mcglm-0.9.0/mcglm/man/pKLIC.Rd | 8 mcglm-0.9.0/mcglm/man/plogLik.Rd | 46 mcglm-0.9.0/mcglm/man/plot.mcglm.Rd | 69 - mcglm-0.9.0/mcglm/man/print.mcglm.Rd | 16 mcglm-0.9.0/mcglm/man/residuals.mcglm.Rd | 32 mcglm-0.9.0/mcglm/man/soil.Rd | 73 - mcglm-0.9.0/mcglm/man/soya.Rd | 55 - mcglm-0.9.0/mcglm/man/summary.mcglm.Rd | 49 mcglm-0.9.0/mcglm/man/vcov.mcglm.Rd | 19 mcglm-0.9.0/mcglm/src/Makevars.win |only mcglm-0.9.0/mcglm/tests/testthat/test_mc_build_C.R | 20 mcglm-0.9.0/mcglm/vignettes/GLMExamples.Rmd | 16 mcglm-0.9.0/mcglm/vignettes/UniModels.Rmd | 10 154 files changed, 4276 insertions(+), 2747 deletions(-)
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.8.1 dated 2025-12-19 and 0.9.0 dated 2026-01-08
DESCRIPTION | 8 +- MD5 | 68 +++++++++++++------------ NAMESPACE | 3 + NEWS.md | 22 ++++++++ R/add_interactions_by_step.R |only R/combine_answers.R | 3 - R/grouped_tbl_pivot_wider.R | 23 +++++--- R/gtsummary_themes.R | 25 ++++++++- R/long_to_periods.R | 8 +- R/long_to_seq.R |only R/periods_to_long.R | 4 - R/plot_categorical.R | 4 - R/plot_continuous.R | 4 - R/plot_means.R | 4 - R/plot_multiple_answers.R | 8 +- R/plot_proportions.R | 15 ++--- R/plot_trajectories.R | 24 ++++++-- R/proportion.R | 14 ++--- R/step_with_na.R | 39 +++++++++----- README.md | 12 ++-- man/add_interactions_by_step.Rd |only man/combine_answers.Rd | 3 - man/grouped_tbl_pivot_wider.Rd | 15 ++++- man/gtsummary_themes.Rd | 12 +++- man/long_to_periods.Rd | 8 +- man/long_to_seq.Rd |only man/periods_to_long.Rd | 4 - man/plot_categorical.Rd | 9 +-- man/plot_continuous.Rd | 9 +-- man/plot_means.Rd | 9 +-- man/plot_multiple_answers.Rd | 8 +- man/plot_proportions.Rd | 17 +++--- man/plot_trajectories.Rd | 16 +++-- man/proportion.Rd | 14 ++--- tests/testthat/test-add_interactions_by_step.R |only tests/testthat/test-gtsummary-themes.R | 17 +++++- tests/testthat/test-long_to_seq.R |only tests/testthat/test-plot_trajectories.R | 19 ++++++ 38 files changed, 295 insertions(+), 153 deletions(-)
Title: Docorate (Decorate + Output) Displays
Description: A framework for creating production outputs. Users can frame a table, listing, or figure with headers and footers and save to an output file. Stores an intermediate 'docorator' object for reproducibility and rendering to multiple output types.
Author: Becca Krouse [aut, cre],
Shannon Haughton [aut],
Seongbin Hong [aut],
Dragoș Moldovan-Gruenfeld [aut],
GlaxoSmithKline Research & Development Limited [cph, fnd]
Maintainer: Becca Krouse <becca.z.krouse@gsk.com>
Diff between docorator versions 0.5.0 dated 2025-09-30 and 0.5.1 dated 2026-01-08
DESCRIPTION | 10 MD5 | 37 +- NEWS.md | 14 R/docorate.R | 136 ++++--- R/prep_obj_tex.R | 1 R/render.R | 21 - R/scale_gt.R | 150 +++++--- R/utils.R | 27 + R/utils_gt.R | 38 +- inst/doc/display_sizing.html | 593 ++++++++++++++++------------------ man/as_docorator.Rd | 3 man/check_pkg_version.Rd |only man/doc_path.Rd | 2 man/render_pdf.Rd | 8 man/render_rtf.Rd | 5 tests/testthat/_snaps/prep_obj_tex.md | 12 tests/testthat/test-prep_obj_rtf.R | 6 tests/testthat/test-scale_gt.R | 65 +++ tests/testthat/test-utils.R | 36 ++ tests/testthat/test-utils_gt.R | 98 +++++ 20 files changed, 779 insertions(+), 483 deletions(-)
Title: Streamline Population Genomic and Genetic Analyses
Description: Estimate commonly used population genomic statistics and generate publication quality figures. 'PopGenHelpR' uses vcf, 'geno' (012), and csv files to generate output.
Author: Keaka Farleigh [aut, cph, cre] ,
Mason Murphy [aut, cph, ctb] ,
Christopher Blair [aut, cph, ctb] ,
Tereza Jezkova [aut, cph, ctb]
Maintainer: Keaka Farleigh <keakafarleigh@gmail.com>
Diff between PopGenHelpR versions 1.4.1 dated 2025-08-19 and 1.4.2 dated 2026-01-08
DESCRIPTION | 8 MD5 | 14 NEWS.md | 5 R/Differentiation.R | 1199 ++++++++++++++++++++++++------------------------- R/Heterozygosity.R | 7 README.md | 5 man/Differentiation.Rd | 6 man/Heterozygosity.Rd | 6 8 files changed, 640 insertions(+), 610 deletions(-)
More information about outlierspinner at CRAN
Permanent link
Title: Simulate Data from a (Time-Dependent) Causal DAG
Description: Simulate complex data from a given directed acyclic graph and information about each individual node.
Root nodes are simply sampled from the specified distribution. Child Nodes are simulated according to
one of many implemented regressions, such as logistic regression, linear
regression, poisson regression or any other function. Also includes a comprehensive framework for discrete-time
simulation, discrete-event simulation, and networks-based simulation which can generate even more complex longitudinal and dependent data.
For more details, see Robin Denz, Nina Timmesfeld (2025) <doi:10.48550/arXiv.2506.01498>.
Author: Robin Denz [aut, cre],
Katharina Meiszl [aut]
Maintainer: Robin Denz <robin.denz@rub.de>
Diff between simDAG versions 0.4.1 dated 2025-10-15 and 0.5.0 dated 2026-01-08
simDAG-0.4.1/simDAG/vignettes/images_v_joss/disc_time_sim.bib.sav.tmp |only simDAG-0.5.0/simDAG/DESCRIPTION | 12 simDAG-0.5.0/simDAG/MD5 | 144 ++- simDAG-0.5.0/simDAG/NAMESPACE | 11 simDAG-0.5.0/simDAG/NEWS.md | 29 simDAG-0.5.0/simDAG/R/dag.r | 39 + simDAG-0.5.0/simDAG/R/distributions.r | 24 simDAG-0.5.0/simDAG/R/do.r | 8 simDAG-0.5.0/simDAG/R/formula_interface.r | 15 simDAG-0.5.0/simDAG/R/input_checks.r | 123 +++ simDAG-0.5.0/simDAG/R/node_aalen.r |only simDAG-0.5.0/simDAG/R/node_binomial.r | 13 simDAG-0.5.0/simDAG/R/node_cox.r | 38 - simDAG-0.5.0/simDAG/R/node_gaussian.r | 14 simDAG-0.5.0/simDAG/R/node_negative_binomial.r | 2 simDAG-0.5.0/simDAG/R/node_poisson.r | 2 simDAG-0.5.0/simDAG/R/node_time_to_event.r | 10 simDAG-0.5.0/simDAG/R/sim2long.r | 6 simDAG-0.5.0/simDAG/R/sim2start_stop.r | 48 - simDAG-0.5.0/simDAG/R/sim2start_stop_collapse.r | 34 simDAG-0.5.0/simDAG/R/sim_discrete_event.r |only simDAG-0.5.0/simDAG/R/sim_discrete_time.r | 54 + simDAG-0.5.0/simDAG/R/sim_dt_helpers.r | 22 simDAG-0.5.0/simDAG/R/sim_n_datasets.r | 39 - simDAG-0.5.0/simDAG/README.md | 3 simDAG-0.5.0/simDAG/build/vignette.rds |binary simDAG-0.5.0/simDAG/inst/doc/simDAG.html | 12 simDAG-0.5.0/simDAG/inst/doc/v_cookbook.R | 28 simDAG-0.5.0/simDAG/inst/doc/v_cookbook.Rmd | 43 + simDAG-0.5.0/simDAG/inst/doc/v_cookbook.html | 376 ++++++---- simDAG-0.5.0/simDAG/inst/doc/v_covid_example.html | 2 simDAG-0.5.0/simDAG/inst/doc/v_custom_nodes.Rmd | 2 simDAG-0.5.0/simDAG/inst/doc/v_custom_nodes.html | 9 simDAG-0.5.0/simDAG/inst/doc/v_sim_discrete_event.R |only simDAG-0.5.0/simDAG/inst/doc/v_sim_discrete_event.Rmd |only simDAG-0.5.0/simDAG/inst/doc/v_sim_discrete_event.html |only simDAG-0.5.0/simDAG/inst/doc/v_sim_discrete_time.R | 12 simDAG-0.5.0/simDAG/inst/doc/v_sim_discrete_time.Rmd | 22 simDAG-0.5.0/simDAG/inst/doc/v_sim_discrete_time.html | 154 ++-- simDAG-0.5.0/simDAG/inst/doc/v_sim_from_dag.Rmd | 1 simDAG-0.5.0/simDAG/inst/doc/v_sim_from_dag.html | 23 simDAG-0.5.0/simDAG/man/as_tidy_dagitty.DAG.Rd |only simDAG-0.5.0/simDAG/man/do.Rd | 16 simDAG-0.5.0/simDAG/man/network.Rd | 2 simDAG-0.5.0/simDAG/man/node.Rd | 20 simDAG-0.5.0/simDAG/man/node_aalen.Rd |only simDAG-0.5.0/simDAG/man/node_cox.Rd | 15 simDAG-0.5.0/simDAG/man/node_next_time.Rd |only simDAG-0.5.0/simDAG/man/node_time_to_event.Rd | 16 simDAG-0.5.0/simDAG/man/plot.DAG.Rd | 4 simDAG-0.5.0/simDAG/man/rsample.Rd |only simDAG-0.5.0/simDAG/man/rtexp.Rd |only simDAG-0.5.0/simDAG/man/sim2data.Rd | 2 simDAG-0.5.0/simDAG/man/simDAG.Rd | 15 simDAG-0.5.0/simDAG/man/sim_discrete_event.Rd |only simDAG-0.5.0/simDAG/man/sim_discrete_time.Rd | 18 simDAG-0.5.0/simDAG/man/sim_from_dag.Rd | 4 simDAG-0.5.0/simDAG/man/sim_n_datasets.Rd | 12 simDAG-0.5.0/simDAG/tests/testthat.R | 1 simDAG-0.5.0/simDAG/tests/testthat/test_as_tidy_daggity.DAG.r |only simDAG-0.5.0/simDAG/tests/testthat/test_calc_linpred.r |only simDAG-0.5.0/simDAG/tests/testthat/test_do.r | 43 + simDAG-0.5.0/simDAG/tests/testthat/test_input_checks_sim_discrete_event.r |only simDAG-0.5.0/simDAG/tests/testthat/test_node_aalen.r |only simDAG-0.5.0/simDAG/tests/testthat/test_node_cox.r | 30 simDAG-0.5.0/simDAG/tests/testthat/test_node_time_to_event.r | 47 + simDAG-0.5.0/simDAG/tests/testthat/test_parse_formula.r | 6 simDAG-0.5.0/simDAG/tests/testthat/test_rsample.r |only simDAG-0.5.0/simDAG/tests/testthat/test_rtexp.r |only simDAG-0.5.0/simDAG/tests/testthat/test_set_event_centric.r |only simDAG-0.5.0/simDAG/tests/testthat/test_sim2long.last.r | 24 simDAG-0.5.0/simDAG/tests/testthat/test_sim2start_stop.all.r | 28 simDAG-0.5.0/simDAG/tests/testthat/test_sim2start_stop.last.r | 64 + simDAG-0.5.0/simDAG/tests/testthat/test_sim_discrete_event.r |only simDAG-0.5.0/simDAG/tests/testthat/test_sim_discrete_time.r | 78 ++ simDAG-0.5.0/simDAG/tests/testthat/test_sim_n_datasets.r | 53 + simDAG-0.5.0/simDAG/tests/testthat/test_supports_mixed_terms.r | 6 simDAG-0.5.0/simDAG/vignettes/images_v_joss/disc_time_sim.bib | 99 ++ simDAG-0.5.0/simDAG/vignettes/images_v_sim_discrete_event |only simDAG-0.5.0/simDAG/vignettes/v_cookbook.Rmd | 43 + simDAG-0.5.0/simDAG/vignettes/v_custom_nodes.Rmd | 2 simDAG-0.5.0/simDAG/vignettes/v_sim_discrete_event.Rmd |only simDAG-0.5.0/simDAG/vignettes/v_sim_discrete_time.Rmd | 22 simDAG-0.5.0/simDAG/vignettes/v_sim_from_dag.Rmd | 1 84 files changed, 1612 insertions(+), 433 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.6.4 dated 2025-11-07 and 1.6.5 dated 2026-01-08
gpboost-1.6.4/gpboost/tests/testthat/_snaps |only gpboost-1.6.5/gpboost/DESCRIPTION | 8 gpboost-1.6.5/gpboost/MD5 | 46 gpboost-1.6.5/gpboost/R/GPModel.R | 20 gpboost-1.6.5/gpboost/R/gpb.Booster.R | 9 gpboost-1.6.5/gpboost/R/gpb.cv.R | 20 gpboost-1.6.5/gpboost/R/gpboost.R | 9 gpboost-1.6.5/gpboost/configure.ac | 2 gpboost-1.6.5/gpboost/configure.win | 9 gpboost-1.6.5/gpboost/man/gpb.cv.Rd | 7 gpboost-1.6.5/gpboost/man/gpb.grid.search.tune.parameters.Rd | 7 gpboost-1.6.5/gpboost/man/gpb_shared_params.Rd | 7 gpboost-1.6.5/gpboost/src/CG_utils.cpp | 10 gpboost-1.6.5/gpboost/src/Makevars.win | 2 gpboost-1.6.5/gpboost/src/c_api.cpp | 16 gpboost-1.6.5/gpboost/src/gpboost_R.cpp | 20 gpboost-1.6.5/gpboost/src/gpboost_R.h | 22 gpboost-1.6.5/gpboost/src/include/GPBoost/CG_utils.h | 8 gpboost-1.6.5/gpboost/src/include/GPBoost/DF_utils.h | 126 gpboost-1.6.5/gpboost/src/include/GPBoost/likelihoods.h | 2008 +++++++++- gpboost-1.6.5/gpboost/src/include/GPBoost/re_model.h | 10 gpboost-1.6.5/gpboost/src/include/GPBoost/re_model_template.h | 56 gpboost-1.6.5/gpboost/src/include/LightGBM/c_api.h | 18 gpboost-1.6.5/gpboost/src/re_model.cpp | 24 gpboost-1.6.5/gpboost/tests/testthat/test_GPModel_non_Gaussian_data.R | 219 - 25 files changed, 2429 insertions(+), 254 deletions(-)
Title: Tidy Finance Helper Functions
Description: Helper functions for empirical research in financial
economics, addressing a variety of topics covered in Scheuch, Voigt,
and Weiss (2023) <doi:10.1201/b23237>. The package is designed to
provide shortcuts for issues extensively discussed in the book,
facilitating easier application of its concepts. For more information
and resources related to the book, visit
<https://www.tidy-finance.org/r/index.html>.
Author: Christoph Scheuch [aut, cre, cph] ,
Stefan Voigt [aut, cph] ,
Patrick Weiss [aut, cph] ,
Maximilian Muecke [ctb]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between tidyfinance versions 0.4.4 dated 2025-05-07 and 0.4.5 dated 2026-01-08
DESCRIPTION | 8 ++-- MD5 | 22 ++++++------- NEWS.md | 6 +++ R/download_data_fred.R | 10 +----- R/get_wrds_connection.R | 2 - R/global_variables.R | 3 + README.md | 2 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/dates-in-tidyfinance.html | 61 ++++++++++++++++++------------------- inst/doc/using-tidyfinance.html | 5 +-- man/get_wrds_connection.Rd | 4 +- 12 files changed, 64 insertions(+), 59 deletions(-)
Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' access to the 'CCTZ' timezone library is provided. 'CCTZ' is
a C++ library for translating between absolute and civil times using the rules
of a time zone. The 'CCTZ' source code, released under the Apache 2.0 License,
is included in this package. See <https://github.com/google/cctz> for more
details.
Author: Dirk Eddelbuettel [aut, cre] ,
Bradley White [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCCTZ versions 0.2.13 dated 2024-12-11 and 0.2.14 dated 2026-01-08
RcppCCTZ-0.2.13/RcppCCTZ/src/Makevars.ucrt |only RcppCCTZ-0.2.13/RcppCCTZ/src/time_tool.cc |only RcppCCTZ-0.2.14/RcppCCTZ/ChangeLog | 27 RcppCCTZ-0.2.14/RcppCCTZ/DESCRIPTION | 21 RcppCCTZ-0.2.14/RcppCCTZ/MD5 | 48 RcppCCTZ-0.2.14/RcppCCTZ/README.md | 6 RcppCCTZ-0.2.14/RcppCCTZ/inst/NEWS.Rd | 8 RcppCCTZ-0.2.14/RcppCCTZ/inst/include/cctz/civil_time_detail.h | 16 RcppCCTZ-0.2.14/RcppCCTZ/inst/include/cctz/time_zone.h | 3 RcppCCTZ-0.2.14/RcppCCTZ/src/Makevars | 26 RcppCCTZ-0.2.14/RcppCCTZ/src/Makevars.win | 27 RcppCCTZ-0.2.14/RcppCCTZ/src/time_zone_fixed.cc | 2 RcppCCTZ-0.2.14/RcppCCTZ/src/time_zone_format.cc | 57 RcppCCTZ-0.2.14/RcppCCTZ/src/time_zone_if.cc | 16 RcppCCTZ-0.2.14/RcppCCTZ/src/time_zone_if.h | 9 RcppCCTZ-0.2.14/RcppCCTZ/src/time_zone_impl.cc | 6 RcppCCTZ-0.2.14/RcppCCTZ/src/time_zone_impl.h | 4 RcppCCTZ-0.2.14/RcppCCTZ/src/time_zone_info.cc | 651 +++++----- RcppCCTZ-0.2.14/RcppCCTZ/src/time_zone_info.h | 25 RcppCCTZ-0.2.14/RcppCCTZ/src/time_zone_libc.cc | 86 - RcppCCTZ-0.2.14/RcppCCTZ/src/time_zone_libc.h | 9 RcppCCTZ-0.2.14/RcppCCTZ/src/time_zone_lookup.cc | 49 RcppCCTZ-0.2.14/RcppCCTZ/src/time_zone_name_win.cc |only RcppCCTZ-0.2.14/RcppCCTZ/src/time_zone_name_win.h |only RcppCCTZ-0.2.14/RcppCCTZ/src/time_zone_posix.h | 2 RcppCCTZ-0.2.14/RcppCCTZ/src/tzfile.h | 42 RcppCCTZ-0.2.14/RcppCCTZ/src/zone_info_source.cc | 2 27 files changed, 663 insertions(+), 479 deletions(-)
Title: R Interface to 'IGN' Web Services
Description: Automatic open data acquisition from resources of IGN
('Institut National de Information Geographique et forestiere')
(<https://www.ign.fr/>). Available datasets include various types of
raster and vector data, such as digital elevation models, state
borders, spatial databases, cadastral parcels, and more. 'happign' also
provide access to API Carto (<https://apicarto.ign.fr/api/doc/>).
Author: Paul Carteron [aut, cre]
Maintainer: Paul Carteron <carteronpaul@gmail.com>
Diff between happign versions 0.3.6 dated 2025-09-03 and 0.3.7 dated 2026-01-08
happign-0.3.6/happign/data/cog_2023.rda |only happign-0.3.6/happign/data/com_2024.rda |only happign-0.3.6/happign/man/cog_2023.Rd |only happign-0.3.6/happign/man/com_2024.Rd |only happign-0.3.6/happign/tests/testthat/get_loc_info |only happign-0.3.6/happign/tests/testthat/get_loc_info error |only happign-0.3.6/happign/tests/testthat/get_loc_info no data |only happign-0.3.6/happign/tests/testthat/get_loc_info no layer |only happign-0.3.6/happign/tests/testthat/get_loc_info sf |only happign-0.3.6/happign/tests/testthat/get_wfs_default_crs |only happign-0.3.6/happign/tests/testthat/get_wfs_default_geometry_name |only happign-0.3.6/happign/tests/testthat/test-get_location_info.R |only happign-0.3.6/happign/tests/testthat/wfs_ecql_filter |only happign-0.3.6/happign/tests/testthat/wfs_empty |only happign-0.3.6/happign/tests/testthat/wfs_intersect |only happign-0.3.6/happign/vignettes/get_wfs-1.jpeg |only happign-0.3.6/happign/vignettes/get_wfs2-1.jpeg |only happign-0.3.6/happign/vignettes/get_wms_raster-1.jpeg |only happign-0.3.6/happign/vignettes/get_wmts-1.jpeg |only happign-0.3.7/happign/DESCRIPTION | 18 happign-0.3.7/happign/MD5 | 95 +- happign-0.3.7/happign/NAMESPACE | 18 happign-0.3.7/happign/NEWS.md | 21 happign-0.3.7/happign/R/data.R | 30 happign-0.3.7/happign/R/get_apicarto_cadastre.R | 4 happign-0.3.7/happign/R/get_wfs.R | 427 +++------- happign-0.3.7/happign/R/get_wfs_attributes.R | 12 happign-0.3.7/happign/R/predicates.R |only happign-0.3.7/happign/R/utils.R | 51 - happign-0.3.7/happign/README.md | 2 happign-0.3.7/happign/inst/doc/getting_started.Rmd | 305 +++---- happign-0.3.7/happign/inst/doc/getting_started.html | 407 ++++----- happign-0.3.7/happign/man/bbox_cql.Rd |only happign-0.3.7/happign/man/get_wfs.Rd | 148 +-- happign-0.3.7/happign/man/get_wfs_attributes.Rd | 14 happign-0.3.7/happign/man/spatial_cql.Rd |only happign-0.3.7/happign/man/spatial_predicates.Rd |only happign-0.3.7/happign/tests/testthat.R | 8 happign-0.3.7/happign/tests/testthat/mock_get_wfs |only happign-0.3.7/happign/tests/testthat/mock_utils |only happign-0.3.7/happign/tests/testthat/test-bbox_cql.R |only happign-0.3.7/happign/tests/testthat/test-get_wfs.R | 311 ++++--- happign-0.3.7/happign/tests/testthat/test-get_wms_raster.R | 99 -- happign-0.3.7/happign/tests/testthat/test-get_wmts.R | 59 - happign-0.3.7/happign/tests/testthat/test-predicates.R |only happign-0.3.7/happign/tests/testthat/test-spatial_cql.R |only happign-0.3.7/happign/tests/testthat/test-utils.R | 76 - happign-0.3.7/happign/vignettes/getting_started.Rmd | 305 +++---- happign-0.3.7/happign/vignettes/getting_started_orig.Rmd.orig |only happign-0.3.7/happign/vignettes/plot_dem-1.png |only happign-0.3.7/happign/vignettes/plot_ortho-1.png |only happign-0.3.7/happign/vignettes/plot_roundabout-1.png |only happign-0.3.7/happign/vignettes/plot_wfs-1.png |only happign-0.3.7/happign/vignettes/precompile.R | 12 54 files changed, 1038 insertions(+), 1384 deletions(-)
Title: Interactive Structural Equation Modeling (SEM) and Multi-Group
Path Diagrams
Description: Provides an interactive workflow for visualizing structural equation modeling (SEM), multi-group path diagrams, and network diagrams in R. Users can directly manipulate nodes and edges to create publication-quality figures while maintaining statistical model integrity. Supports integration with 'lavaan', 'OpenMx', 'tidySEM', and 'blavaan' etc. Features include parameter-based aesthetic mapping, generative AI assistance, and complete reproducibility by exporting metadata for script-based workflows.
Author: Seung Hyun Min [aut, cre]
Maintainer: Seung Hyun Min <seung.min@mail.mcgill.ca>
Diff between ggsem versions 0.9.6 dated 2025-12-16 and 0.9.7 dated 2026-01-08
DESCRIPTION | 24 MD5 | 30 NAMESPACE | 21 R/create_bundle.R | 106 - R/draw_annotations.R | 14 R/draw_lines.R | 20 R/ggsem_app.R | 850 +++++---- R/ggsem_launch.R | 16 R/ggsem_silent.R | 85 R/globals.R | 4 R/reproduce_metadata.R | 72 R/utils_graph.R | 786 +++++--- R/utils_model.R | 901 +++++++-- README.md | 30 inst/shiny/app.R | 4582 ++++++++++++++++++++++++++++++++++++++----------- man/ggsem.Rd | 4 16 files changed, 5659 insertions(+), 1886 deletions(-)
Title: Ecosystem Multifunctionality: Richness, Divergence, and
Regularity
Description: Analyzes and quantifies ecosystem multifunctionality with functions to calculate multifunctionality richness (MFric), multifunctionality divergence (MFdiv), and multifunctionality regularity (MFreg). These indices help assess the relationship between biodiversity and multiple ecosystem functions. For more details, see Byrnes et al. (2014) <doi:10.1111/2041-210X.12143> and Chao et al. (2024) <doi:10.1111/ele.14336>.
Author: Yan He [aut, cre],
Rui Yang [aut],
Lingfeng Mao [aut]
Maintainer: Yan He <heyan@njfu.edu.cn>
Diff between emf versions 0.1.0 dated 2025-05-29 and 0.2.0 dated 2026-01-08
emf-0.1.0/emf/R/forestfunctions.R |only emf-0.1.0/emf/data/forestfunctions.rda |only emf-0.1.0/emf/man/forestfunctions.Rd |only emf-0.1.0/emf/tests |only emf-0.2.0/emf/DESCRIPTION | 13 +- emf-0.2.0/emf/MD5 | 31 +++--- emf-0.2.0/emf/NAMESPACE | 1 emf-0.2.0/emf/R/MFK.R |only emf-0.2.0/emf/R/MFdiv.R | 167 +++++++++++---------------------- emf-0.2.0/emf/R/MFreg.R | 138 ++++++++------------------- emf-0.2.0/emf/R/MFric.R | 122 +++++++----------------- emf-0.2.0/emf/R/functions.R |only emf-0.2.0/emf/R/site.R |only emf-0.2.0/emf/data/functions.rda |only emf-0.2.0/emf/data/site.rda |only emf-0.2.0/emf/man/MFK.Rd |only emf-0.2.0/emf/man/MFdiv.Rd | 73 ++++++++------ emf-0.2.0/emf/man/MFreg.Rd | 62 ++++++------ emf-0.2.0/emf/man/MFric.Rd | 58 ++++++----- emf-0.2.0/emf/man/functions.Rd |only emf-0.2.0/emf/man/site.Rd |only 21 files changed, 272 insertions(+), 393 deletions(-)
Title: Object-Oriented Implementation of Dose Escalation Designs
Description: Implements a wide range of dose escalation
designs. The focus is on model-based designs, ranging from classical and
modern continual reassessment methods (CRMs) based on dose-limiting toxicity
endpoints to dual-endpoint designs taking into account a biomarker/efficacy
outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy
to setup a new design with custom JAGS code. However, it is also possible to
implement 3+3 designs for comparison or models with non-Bayesian estimation.
The whole package is written in a modular form in the S4 class system, making it
very flexible for adaptation to new models, escalation or stopping rules.
Further details are presented in
Sabanes Bove et al. (2019) <doi:10.18637/jss.v089.i10>.
Author: Daniel Sabanes Bove [aut, cre],
Wai Yin Yeung [aut],
Burak Kuersad Guenhan [aut],
Giuseppe Palermo [aut],
Thomas Jaki [aut],
Jiawen Zhu [aut],
Ziwei Liao [aut],
Dimitris Kontos [aut],
Marlene Schulte-Goebel [aut],
Doug Kelkhoff [aut] ,
Oliver Boix [a [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between crmPack versions 2.0.1 dated 2025-12-04 and 2.0.2 dated 2026-01-08
DESCRIPTION | 6 MD5 | 990 NAMESPACE | 1508 - NEWS.md | 784 R/CrmPackClass-class.R | 26 R/CrmPackClass-methods.R | 104 R/Data-class.R | 1382 - R/Data-methods.R | 2076 - R/Data-validity.R | 550 R/Design-class.R | 2450 +- R/Design-methods.R | 8622 ++++---- R/Design-validity.R | 170 R/McmcOptions-class.R | 238 R/McmcOptions-methods.R | 176 R/McmcOptions-validity.R | 146 R/Model-class.R | 7040 +++--- R/Model-methods.R | 3886 +-- R/Model-validity.R | 1424 - R/ModelParams-class.R | 156 R/ModelParams-validity.R | 92 R/Rules-class.R | 7400 +++---- R/Rules-methods.R | 9058 ++++---- R/Rules-validity.R | 1656 - R/Samples-class.R | 132 R/Samples-methods.R | 4702 ++-- R/Samples-validity.R | 60 R/Simulations-class.R | 2034 - R/Simulations-methods.R | 6038 ++--- R/Simulations-validity.R | 340 R/checkmate.R | 960 R/crmPack-package.R | 268 R/fromQuantiles.R | 852 R/helpers.R | 1958 - R/helpers_broom.R | 422 R/helpers_covr.R | 178 R/helpers_data.R | 482 R/helpers_design.R | 604 R/helpers_jags.R | 520 R/helpers_knitr.R | 90 R/helpers_knitr_CohortSize.R | 560 R/helpers_knitr_Design.R | 1432 - R/helpers_knitr_GeneralData.R | 930 R/helpers_knitr_GeneralModel.R | 2806 +- R/helpers_knitr_Increments.R | 710 R/helpers_knitr_NextBest.R | 1272 - R/helpers_knitr_SafetyWindow.R | 582 R/helpers_knitr_Stopping.R | 1240 - R/helpers_model.R | 512 R/helpers_rules.R | 1810 - R/helpers_samples.R | 54 R/helpers_simulations.R | 142 R/logger.R | 128 R/mcmc.R | 1564 - R/utils-pipe.R | 28 R/utils.R | 66 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 40 inst/REFERENCES.bib | 200 inst/WORDLIST | 500 inst/doc/crmPack-jss-paper.Rmd | 1934 - inst/doc/crmPack-jss-paper.html | 2517 +- inst/doc/example.Rmd | 6422 +++--- inst/doc/example.html | 5551 ++--- inst/doc/knit_print.Rmd | 1486 - inst/doc/knit_print.html | 2425 +- inst/doc/ordinal-crm.R | 268 inst/doc/ordinal-crm.Rmd | 530 inst/doc/ordinal-crm.html | 1552 - inst/doc/parallel_computing_with_extensions.R | 712 inst/doc/parallel_computing_with_extensions.Rmd | 886 inst/doc/parallel_computing_with_extensions.html | 1811 - inst/doc/rolling-crm.Rmd | 588 inst/doc/rolling-crm.html | 1192 - inst/doc/simulations.R | 174 inst/doc/simulations.Rmd | 230 inst/doc/simulations.html | 916 inst/doc/tidy_method.R | 238 inst/doc/tidy_method.Rmd | 352 inst/doc/tidy_method.html | 1835 - inst/doc/trial_analysis.R | 912 inst/doc/trial_analysis.Rmd | 1292 - inst/doc/trial_analysis.html | 5466 ++--- inst/doc/trial_definition.R | 158 inst/doc/trial_definition.Rmd | 426 inst/doc/trial_definition.html | 1349 - inst/doc/trial_sanity_checks.Rmd | 1080 - inst/doc/trial_sanity_checks.html | 3231 +-- inst/doc/trial_simulation.R | 178 inst/doc/trial_simulation.Rmd | 212 inst/doc/trial_simulation.html | 898 inst/doc/upgrading_from_the_old_crmPack.R | 786 inst/doc/upgrading_from_the_old_crmPack.Rmd | 988 inst/doc/upgrading_from_the_old_crmPack.html | 7186 +++--- man/CohortSize-class.Rd | 54 man/CohortSizeConst-class.Rd | 70 man/CohortSizeDLT-class.Rd | 84 man/CohortSizeMax-class.Rd | 94 man/CohortSizeMin-class.Rd | 94 man/CohortSizeOrdinal-class.Rd | 82 man/CohortSizeParts-class.Rd | 76 man/CohortSizeRange-class.Rd | 86 man/CrmPackClass.Rd | 28 man/DADesign-class.Rd | 278 man/DALogisticLogNormal-class.Rd | 162 man/DASimulations-class.Rd | 72 man/DLTLikelihood.Rd | 40 man/Data-class.Rd | 194 man/DataDA-class.Rd | 140 man/DataDual-class.Rd | 100 man/DataGrouped-class.Rd | 102 man/DataMixture-class.Rd | 114 man/DataOrdinal-class.Rd | 164 man/DataParts-class.Rd | 116 man/Design-class.Rd | 220 man/DesignGrouped-class.Rd | 324 man/DesignOrdinal-class.Rd | 247 man/DualDesign-class.Rd | 206 man/DualEndpoint-class.Rd | 214 man/DualEndpointBeta-class.Rd | 198 man/DualEndpointEmax-class.Rd | 160 man/DualEndpointRW-class.Rd | 166 man/DualResponsesDesign-class.Rd | 174 man/DualResponsesSamplesDesign-class.Rd | 190 man/DualSimulations-class.Rd | 178 man/DualSimulationsSummary-class.Rd | 58 man/EffFlexi-class.Rd | 320 man/Effloglog-class.Rd | 388 man/FractionalCRM-class.Rd | 102 man/GeneralData-class.Rd | 60 man/GeneralModel-class.Rd | 138 man/GeneralSimulations-class.Rd | 110 man/GeneralSimulationsSummary-class.Rd | 108 man/Increments-class.Rd | 48 man/IncrementsDoseLevels-class.Rd | 98 man/IncrementsHSRBeta-class.Rd | 120 man/IncrementsMaxToxProb-class.Rd | 96 man/IncrementsMin-class.Rd | 118 man/IncrementsOrdinal-class.Rd | 92 man/IncrementsRelative-class.Rd | 100 man/IncrementsRelativeDLT-class.Rd | 118 man/IncrementsRelativeDLTCurrent-class.Rd | 88 man/IncrementsRelativeParts-class.Rd | 138 man/LogisticIndepBeta-class.Rd | 298 man/LogisticKadane-class.Rd | 132 man/LogisticKadaneBetaGamma-class.Rd | 198 man/LogisticLogNormal-class.Rd | 104 man/LogisticLogNormalGrouped-class.Rd | 110 man/LogisticLogNormalMixture-class.Rd | 188 man/LogisticLogNormalOrdinal-class.Rd | 78 man/LogisticLogNormalSub-class.Rd | 114 man/LogisticNormal-class.Rd | 114 man/LogisticNormalFixedMixture-class.Rd | 196 man/LogisticNormalMixture-class.Rd | 170 man/McmcOptions-class.Rd | 152 man/MinimalInformative.Rd | 198 man/ModelEff-class.Rd | 84 man/ModelLogNormal-class.Rd | 106 man/ModelParamsNormal-class.Rd | 94 man/ModelPseudo-class.Rd | 48 man/ModelTox-class.Rd | 86 man/NextBest-class.Rd | 54 man/NextBestDualEndpoint-class.Rd | 188 man/NextBestEWOC-class.Rd | 120 man/NextBestInfTheory-class.Rd | 76 man/NextBestMTD-class.Rd | 94 man/NextBestMaxGain-class.Rd | 96 man/NextBestMaxGainSamples-class.Rd | 142 man/NextBestMinDist-class.Rd | 76 man/NextBestNCRM-class.Rd | 122 man/NextBestNCRMLoss-class.Rd | 170 man/NextBestOrdinal-class.Rd | 96 man/NextBestProbMTDLTE-class.Rd | 88 man/NextBestProbMTDMinDist-class.Rd | 92 man/NextBestTD-class.Rd | 98 man/NextBestTDsamples-class.Rd | 114 man/NextBestThreePlusThree-class.Rd | 56 man/OneParExpPrior-class.Rd | 118 man/OneParLogNormalPrior-class.Rd | 110 man/ProbitLogNormal-class.Rd | 118 man/ProbitLogNormalRel-class.Rd | 108 man/PseudoDualFlexiSimulations-class.Rd | 68 man/PseudoDualSimulations-class.Rd | 144 man/PseudoDualSimulationsSummary-class.Rd | 92 man/PseudoSimulations-class.Rd | 182 man/PseudoSimulationsSummary-class.Rd | 200 man/Quantiles2LogisticNormal.Rd | 138 man/RuleDesign-class.Rd | 140 man/RuleDesignOrdinal-class.Rd | 140 man/SafetyWindow-class.Rd | 44 man/SafetyWindowConst-class.Rd | 106 man/SafetyWindowSize-class.Rd | 156 man/Samples-class.Rd | 112 man/Simulations-class.Rd | 180 man/SimulationsSummary-class.Rd | 68 man/StartingDose-class.Rd | 66 man/Stopping-class.Rd | 58 man/StoppingAll-class.Rd | 102 man/StoppingAny-class.Rd | 102 man/StoppingCohortsNearDose-class.Rd | 102 man/StoppingExternal-class.Rd | 56 man/StoppingHighestDose-class.Rd | 82 man/StoppingList-class.Rd | 112 man/StoppingLowestDoseHSRBeta-class.Rd | 162 man/StoppingMTDCV-class.Rd | 94 man/StoppingMTDdistribution-class.Rd | 126 man/StoppingMaxGainCIRatio-class.Rd | 106 man/StoppingMinCohorts-class.Rd | 78 man/StoppingMinPatients-class.Rd | 78 man/StoppingMissingDose-class.Rd | 62 man/StoppingOrdinal-class.Rd | 84 man/StoppingPatientsNearDose-class.Rd | 104 man/StoppingSpecificDose-class.Rd | 112 man/StoppingTDCIRatio-class.Rd | 110 man/StoppingTargetBiomarker-class.Rd | 120 man/StoppingTargetProb-class.Rd | 98 man/TDDesign-class.Rd | 204 man/TDsamplesDesign-class.Rd | 208 man/TITELogisticLogNormal-class.Rd | 148 man/Validate.Rd | 68 man/and-Stopping-Stopping-method.Rd | 60 man/and-Stopping-StoppingAll-method.Rd | 66 man/and-StoppingAll-Stopping-method.Rd | 66 man/approximate.Rd | 228 man/assertions.Rd | 52 man/biomarker.Rd | 224 man/check_equal.Rd | 152 man/check_format.Rd | 142 man/check_length.Rd | 98 man/check_probabilities.Rd | 202 man/check_probability.Rd | 126 man/check_probability_range.Rd | 140 man/check_range.Rd | 184 man/crmPack.Rd | 110 man/crmPackExample.Rd | 34 man/crmPackHelp.Rd | 32 man/dapply.Rd | 112 man/dinvGamma.Rd | 52 man/dose.Rd | 514 man/doseFunction.Rd | 158 man/dose_grid_range.Rd | 118 man/efficacy.Rd | 236 man/efficacyFunction.Rd | 102 man/enable_logging.Rd | 114 man/examine.Rd | 562 man/figures/crmPack-sticker-new.svg | 380 man/fit.Rd | 618 man/fitGain.Rd | 302 man/fitPEM.Rd | 252 man/gain.Rd | 304 man/get-Samples-character-method.Rd | 116 man/getEff.Rd | 88 man/get_result_list.Rd | 62 man/h_all_equivalent.Rd | 56 man/h_barplot_percentages.Rd | 46 man/h_blind_plot_data.Rd | 48 man/h_calc_report_label_percentage.Rd | 50 man/h_check_fun_formals.Rd | 62 man/h_convert_ordinal_data.Rd | 48 man/h_convert_ordinal_model.Rd | 50 man/h_convert_ordinal_samples.Rd | 50 man/h_covr_helpers.Rd | 130 man/h_default_if_empty.Rd | 52 man/h_determine_dlts.Rd | 86 man/h_find_interval.Rd | 100 man/h_format_number.Rd | 82 man/h_get_formatted_dosegrid.Rd | 56 man/h_get_min_inf_beta.Rd | 52 man/h_get_quantiles_start_values.Rd | 52 man/h_group_data.Rd | 50 man/h_in_range.Rd | 76 man/h_info_theory_dist.Rd | 52 man/h_is_positive_definite.Rd | 72 man/h_jags_add_dummy.Rd | 110 man/h_jags_extract_samples.Rd | 38 man/h_jags_get_data.Rd | 82 man/h_jags_get_model_inits.Rd | 82 man/h_jags_join_models.Rd | 58 man/h_jags_write_model.Rd | 102 man/h_knit_format_func.Rd | 24 man/h_model_dual_endpoint_beta.Rd | 108 man/h_model_dual_endpoint_rho.Rd | 76 man/h_model_dual_endpoint_sigma2betaw.Rd | 70 man/h_model_dual_endpoint_sigma2w.Rd | 72 man/h_next_best_eligible_doses.Rd | 74 man/h_next_best_mg_ci.Rd | 68 man/h_next_best_mg_doses_at_grid.Rd | 74 man/h_next_best_mg_plot.Rd | 96 man/h_next_best_mgsamples_plot.Rd | 86 man/h_next_best_ncrm_loss_plot.Rd | 94 man/h_next_best_td_plot.Rd | 78 man/h_next_best_tdsamples_plot.Rd | 80 man/h_null_if_na.Rd | 46 man/h_obtain_dose_grid_range.Rd | 34 man/h_plot_data_cohort_lines.Rd | 60 man/h_plot_data_df.Rd | 118 man/h_plot_doses_tried.Rd | 44 man/h_plot_simulation_trajectory.Rd | 48 man/h_prepare_labels.Rd | 46 man/h_prepare_units.Rd | 38 man/h_pseudo_sim_fit_summary.Rd | 52 man/h_pseudo_sim_inverse_dose.Rd | 52 man/h_quantiles_target_function.Rd | 82 man/h_rapply.Rd | 128 man/h_simulations_output_format.Rd | 36 man/h_slots.Rd | 58 man/h_summarize_add_stats.Rd | 48 man/h_test_named_numeric.Rd | 148 man/h_this_truth.Rd | 44 man/h_unpack_stopit.Rd | 38 man/h_validate_combine_results.Rd | 48 man/h_validate_common_data_slots.Rd | 34 man/knit_print.Rd | 1874 - man/logit.Rd | 46 man/match_within_tolerance.Rd | 58 man/maxDose.Rd | 624 man/maxSize.Rd | 92 man/mcmc.Rd | 688 man/minSize.Rd | 92 man/myBayesLogit.Rd | 58 man/names-Samples-method.Rd | 50 man/nextBest.Rd | 2002 - man/ngrid.Rd | 80 man/or-Stopping-Stopping.Rd | 60 man/or-Stopping-StoppingAny.Rd | 66 man/or-StoppingAny-Stopping.Rd | 66 man/pinvGamma.Rd | 54 man/pipe.Rd | 40 man/plot-Data-ModelTox-method.Rd | 118 man/plot-Data.Rd | 206 man/plot-DataDA-missing-method.Rd | 90 man/plot-DataDual-ModelEff-method.Rd | 126 man/plot-DataDual-missing-method.Rd | 86 man/plot-DualSimulations-missing-method.Rd | 500 man/plot-DualSimulationsSummary-missing-method.Rd | 318 man/plot-GeneralSimulations-missing-method.Rd | 276 man/plot-GeneralSimulationsSummary-missing-method.Rd | 86 man/plot-PseudoDualFlexiSimulations-missing-method.Rd | 280 man/plot-PseudoDualSimulations-missing-method.Rd | 314 man/plot-PseudoDualSimulationsSummary-missing-method.Rd | 504 man/plot-PseudoSimulationsSummary-missing-method.Rd | 282 man/plot-Samples-DALogisticLogNormal-method.Rd | 56 man/plot-Samples-DualEndpoint-method.Rd | 166 man/plot-Samples-GeneralModel-method.Rd | 134 man/plot-Samples-ModelEff-method.Rd | 142 man/plot-Samples-ModelTox-method.Rd | 130 man/plot-SimulationsSummary-missing-method.Rd | 260 man/plot.gtable.Rd | 52 man/plotDualResponses.Rd | 308 man/plotGain.Rd | 288 man/positive_number.Rd | 26 man/printVignette.Rd | 44 man/prob.Rd | 442 man/probFunction.Rd | 140 man/probit.Rd | 46 man/qinvGamma.Rd | 54 man/rinvGamma.Rd | 44 man/saveSample.Rd | 86 man/set_seed.Rd | 52 man/show-DualSimulationsSummary-method.Rd | 270 man/show-GeneralSimulationsSummary-method.Rd | 42 man/show-PseudoDualSimulationsSummary-method.Rd | 306 man/show-PseudoSimulationsSummary-method.Rd | 262 man/show-SimulationsSummary-method.Rd | 212 man/simulate-DADesign-method.Rd | 384 man/simulate-Design-method.Rd | 296 man/simulate-DesignGrouped-method.Rd | 278 man/simulate-DualDesign-method.Rd | 372 man/simulate-DualResponsesDesign-method.Rd | 288 man/simulate-DualResponsesSamplesDesign-method.Rd | 458 man/simulate-RuleDesign-method.Rd | 166 man/simulate-TDDesign-method.Rd | 268 man/simulate-TDsamplesDesign-method.Rd | 276 man/size.Rd | 1024 man/stopTrial.Rd | 3240 +-- man/summary-DualSimulations-method.Rd | 272 man/summary-GeneralSimulations-method.Rd | 56 man/summary-PseudoDualFlexiSimulations-method.Rd | 292 man/summary-PseudoDualSimulations-method.Rd | 342 man/summary-PseudoSimulations-method.Rd | 272 man/summary-Simulations-method.Rd | 236 man/tidy.Rd | 524 man/update-Data-method.Rd | 140 man/update-DataDA-method.Rd | 132 man/update-DataDual-method.Rd | 84 man/update-DataOrdinal-method.Rd | 142 man/update-DataParts-method.Rd | 98 man/update-ModelPseudo-method.Rd | 150 man/v_cohort_size.Rd | 104 man/v_data_objects.Rd | 166 man/v_design.Rd | 96 man/v_general_simulations.Rd | 94 man/v_increments.Rd | 150 man/v_mcmcoptions_objects.Rd | 58 man/v_model_objects.Rd | 236 man/v_model_params.Rd | 58 man/v_next_best.Rd | 202 man/v_pseudo_simulations.Rd | 90 man/v_safety_window.Rd | 68 man/v_samples_objects.Rd | 52 man/v_starting_dose.Rd | 42 man/v_stopping.Rd | 176 man/windowLength.Rd | 400 tests/test-package-load.R | 18 tests/testthat.R | 6 tests/testthat/_jags/model.bug | 50 tests/testthat/fixtures/knit_print_data_classes_template.Rmd | 78 tests/testthat/fixtures/knit_print_object_specific_template.Rmd | 40 tests/testthat/fixtures/knit_print_template.Rmd | 40 tests/testthat/fixtures/knit_print_template.html | 828 tests/testthat/fixtures/make_persistent_objects_for_mocked_constructors.R | 744 tests/testthat/helper-McmcOptions.R | 32 tests/testthat/helper-data.R | 508 tests/testthat/helper-design.R | 534 tests/testthat/helper-logger.R | 44 tests/testthat/helper-model.R | 790 tests/testthat/helper-modelparams.R | 12 tests/testthat/helper-rules.R | 320 tests/testthat/helper-samples.R | 464 tests/testthat/helper-testthat.R | 84 tests/testthat/test-CrmPackClass-class.R | 238 tests/testthat/test-CrmPackClass-methods.R | 292 tests/testthat/test-Data-class.R | 528 tests/testthat/test-Data-methods.R | 1376 - tests/testthat/test-Data-validity.R | 682 tests/testthat/test-Design-class.R | 1162 - tests/testthat/test-Design-methods.R | 3666 +-- tests/testthat/test-Design-validity.R | 172 tests/testthat/test-McmcOptions-class.R | 92 tests/testthat/test-McmcOptions-methods.R | 48 tests/testthat/test-McmcOptions-validity.R | 112 tests/testthat/test-Model-class.R | 3242 +-- tests/testthat/test-Model-methods.R | 5036 ++-- tests/testthat/test-Model-validity.R | 2364 +- tests/testthat/test-ModelParams-class.R | 72 tests/testthat/test-ModelParams-validity.R | 160 tests/testthat/test-Rules-class.R | 3104 +- tests/testthat/test-Rules-methods.R |10440 +++++----- tests/testthat/test-Rules-validity.R | 3462 +-- tests/testthat/test-Samples-class.R | 36 tests/testthat/test-Samples-methods.R | 4612 ++-- tests/testthat/test-Samples-validity.R | 118 tests/testthat/test-Simulations-class.R | 1668 - tests/testthat/test-Simulations-methods.R | 2456 +- tests/testthat/test-Simulations-validity.R | 342 tests/testthat/test-Validate-class.R | 184 tests/testthat/test-accuracy-published.R | 778 tests/testthat/test-checkmate.R | 754 tests/testthat/test-fromQuantiles.R | 470 tests/testthat/test-helpers-simulations.R | 94 tests/testthat/test-helpers.R | 1976 - tests/testthat/test-helpers_covr.R | 258 tests/testthat/test-helpers_design.R | 472 tests/testthat/test-helpers_jags.R | 554 tests/testthat/test-helpers_knitr.R | 830 tests/testthat/test-helpers_knitr_Design.R | 1134 - tests/testthat/test-helpers_knitr_NextBest.R | 936 tests/testthat/test-helpers_knitr_SafetyWindow.R | 286 tests/testthat/test-helpers_knitr_Stopping.R | 1126 - tests/testthat/test-helpers_model.R | 578 tests/testthat/test-helpers_rules.R | 1100 - tests/testthat/test-helpers_samples.R | 120 tests/testthat/test-logger.R | 116 tests/testthat/test-mcmc.R | 318 tests/testthat/test-sas-results-part-1.R | 806 tests/testthat/test-sas-results-part-2.R | 982 tests/testthat/test-utils.R | 72 tests/testthat/testdata/sc1_recdose.csv | 10 tests/testthat/testdata/sc1_sit1.csv | 18 tests/testthat/testdata/sc1_sit2.csv | 18 tests/testthat/testdata/sc1_sit3.csv | 18 tests/testthat/testdata/sc1_sit4.csv | 18 tests/testthat/testdata/sc2_recdose.csv | 10 tests/testthat/testdata/sc2_sit1.csv | 14 tests/testthat/testdata/sc2_sit2.csv | 14 tests/testthat/testdata/sc2_sit3.csv | 14 tests/testthat/testdata/sc2_sit4.csv | 14 tests/testthat/testdata/sc3_recdose.csv | 10 tests/testthat/testdata/sc3_sit1.csv | 22 tests/testthat/testdata/sc3_sit2.csv | 22 tests/testthat/testdata/sc3_sit3.csv | 22 tests/testthat/testdata/sc3_sit4.csv | 22 vignettes/crmPack-jss-paper.Rmd | 1934 - vignettes/example.Rmd | 6422 +++--- vignettes/knit_print.Rmd | 1486 - vignettes/ordinal-crm.Rmd | 530 vignettes/parallel_computing_with_extensions.Rmd | 886 vignettes/rolling-crm.Rmd | 588 vignettes/simulations.Rmd | 230 vignettes/tidy_method.Rmd | 352 vignettes/trial_analysis.Rmd | 1292 - vignettes/trial_definition.Rmd | 426 vignettes/trial_sanity_checks.Rmd | 1080 - vignettes/trial_simulation.Rmd | 212 vignettes/upgrading_from_the_old_crmPack.Rmd | 988 vignettes/vignettes.bib | 852 496 files changed, 135837 insertions(+), 135815 deletions(-)
Title: Evaluation of Presence-Absence Models
Description: Collection of functions to evaluate presence-absence models. It
comprises functions to adjust discrimination statistics for the
representativeness effect through case-weighting, along with functions for
visualizing the outcomes. Originally outlined in:
Jiménez-Valverde (2022) The uniform AUC: dealing with the
representativeness effect in presence-absence models. Methods Ecol. Evol,
13, 1224-1236.
Author: Alberto Jimenez-Valverde [aut, cre]
Maintainer: Alberto Jimenez-Valverde <alberto.jimenez.valverde@gmail.com>
Diff between vandalico versions 0.2.0 dated 2025-10-29 and 0.2.1 dated 2026-01-08
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 10 ++++++++++ R/AUCuniform.2.R | 6 +++--- R/AUCuniform.R | 4 +++- R/AUCuniform_trap.R | 3 +++ man/AUCuniform.2.Rd | 6 +++--- man/AUCuniform.Rd | 4 +++- man/AUCuniform_trap.Rd | 3 +++ 9 files changed, 40 insertions(+), 20 deletions(-)
Title: Linear Trend Segmentation
Description: Performs the detection of linear trend changes for univariate time series
by implementing the bottom-up unbalanced wavelet transformation proposed by
H. Maeng and P. Fryzlewicz (2023). The estimated number and locations of the
change-points are returned with the piecewise-linear estimator for signal.
Author: Hyeyoung Maeng [aut, cre],
Piotr Fryzlewicz [aut]
Maintainer: Hyeyoung Maeng <hyeyoung.maeng@durham.ac.uk>
Diff between trendsegmentR versions 1.3.0 dated 2023-08-24 and 1.3.1 dated 2026-01-08
DESCRIPTION | 8 +++---- MD5 | 4 +-- R/misc.R | 63 ++++++++++++++++++++++-------------------------------------- 3 files changed, 30 insertions(+), 45 deletions(-)
Title: Spectral Clustering-Based Method for Identifying B Cell Clones
Description: Provides a computational framework for identification of B cell clones from
Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data. Three main
functions are included (identicalClones, hierarchicalClones, and spectralClones)
that perform clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins)
which share the same V gene, J gene and junction length.
Nouri N and Kleinstein SH (2018) <doi: 10.1093/bioinformatics/bty235>.
Nouri N and Kleinstein SH (2019) <doi: 10.1101/788620>.
Gupta NT, et al. (2017) <doi: 10.4049/jimmunol.1601850>.
Author: Nima Nouri [aut],
Edel Aron [ctb],
Gisela Gabernet [ctb],
Cole Jensen [ctb],
Huimin Lyu [ctb],
Susanna Marquez [ctb, cre],
Jason Vander Heiden [aut],
Steven Kleinstein [aut, cph]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between scoper versions 1.3.0 dated 2023-10-06 and 1.4.0 dated 2026-01-08
DESCRIPTION | 48 +++-- MD5 | 36 ++-- NAMESPACE | 2 NEWS.md | 22 ++ R/Functions.R | 360 ++++++++++++++++++++++++++++-------------- R/Scoper.R | 4 README.md | 11 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/Scoper-Vignette.R | 17 + inst/doc/Scoper-Vignette.Rmd | 11 - inst/doc/Scoper-Vignette.pdf |binary man/hierarchicalClones.Rd | 23 +- man/identicalClones.Rd | 20 +- man/plotCloneSummary.Rd | 2 man/scoper-package.Rd | 5 man/scoper.Rd | 1 man/spectralClones.Rd | 22 +- vignettes/Scoper-Vignette.Rmd | 11 - 19 files changed, 386 insertions(+), 209 deletions(-)
Title: The Reinert Method for Textual Data Clustering
Description: An R implementation of the Reinert text clustering method. For more
details about the algorithm see the included vignettes or Reinert (1990)
<doi:10.1177/075910639002600103>.
Author: Julien Barnier [aut, cre],
Florian Prive [ctb]
Maintainer: Julien Barnier <julien.barnier@cnrs.fr>
Diff between rainette versions 0.3.1.1 dated 2023-03-28 and 0.3.2 dated 2026-01-08
DESCRIPTION | 14 - MD5 | 66 ++--- NEWS.md | 5 R/RcppExports.R | 7 R/cutree.R | 4 R/import.R | 27 +- R/plot.R | 340 +++++++++++++++++++++------- R/rainette.R | 54 ++-- R/rainette2.R | 87 ++++--- R/rainette2_explor.R | 140 ++++++++--- R/rainette_explor.R | 101 ++++++-- R/shiny.R | 449 +++++++++++++++++++------------------ R/split_segments.R | 62 +++-- R/stats.R | 32 +- R/utils.R | 56 +++- README.md | 19 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/algorithmes.Rmd | 22 - inst/doc/algorithmes.html | 313 +++++++++++++++++++------- inst/doc/algorithms_en.Rmd | 18 - inst/doc/algorithms_en.html | 252 +++++++++++++++------ inst/doc/introduction_en.R | 4 inst/doc/introduction_en.html | 416 ++++++++++++++++++++-------------- inst/doc/introduction_usage.R | 14 - inst/doc/introduction_usage.Rmd | 13 - inst/doc/introduction_usage.html | 464 +++++++++++++++++++++++---------------- man/import_corpus_iramuteq.Rd | 3 man/rainette.Rd | 2 man/rainette2.Rd | 2 man/rainette_plot.Rd | 14 + vignettes/algorithmes.Rmd | 22 - vignettes/algorithms_en.Rmd | 18 - vignettes/introduction_usage.Rmd | 13 - 34 files changed, 1943 insertions(+), 1110 deletions(-)
Title: R Client for the 'OMOPHub' Medical Vocabulary API
Description: Provides an R interface to the 'OMOPHub' API for accessing
'OHDSI ATHENA' standardized medical vocabularies. Supports concept search,
vocabulary exploration, hierarchy navigation, relationship queries, and
concept mappings with automatic pagination and rate limiting.
Author: Alex Chen [aut, cre, cph],
Observational Health Data Science and Informatics [cph]
Maintainer: Alex Chen <alex@omophub.com>
Diff between omophub versions 1.1.0 dated 2025-12-17 and 1.3.0 dated 2026-01-08
DESCRIPTION | 8 MD5 | 80 +++---- NEWS.md | 40 +++ R/concepts.R | 238 ++++++++++++++------- R/domains.R | 54 ---- R/hierarchy.R | 113 ++++++---- R/mappings.R | 89 ++----- R/relationships.R | 100 ++++---- R/search.R | 42 +-- R/vocabularies.R | 107 +++++---- README.md | 269 +++++++++++++++++------- inst/doc/getting-started.R | 4 inst/doc/getting-started.Rmd | 4 inst/doc/getting-started.html | 4 inst/examples/map_between_vocabularies.R | 57 ++--- inst/examples/navigate_hierarchy.R | 12 - inst/examples/search_concepts.R | 2 man/ConceptsResource.Rd | 152 +++++++++---- man/DomainsResource.Rd | 35 --- man/HierarchyResource.Rd | 75 ++++-- man/MappingsResource.Rd | 49 ---- man/RelationshipsResource.Rd | 60 ++--- man/SearchResource.Rd | 20 - man/VocabulariesResource.Rd | 86 +++++-- man/omophub-package.Rd | 13 - tests/testthat/test-concepts-integration.R | 15 - tests/testthat/test-concepts.R | 41 +-- tests/testthat/test-domains-integration.R | 25 -- tests/testthat/test-domains.R | 33 +- tests/testthat/test-hierarchy-integration.R | 22 + tests/testthat/test-hierarchy.R | 217 +++++++++++++++++-- tests/testthat/test-mappings-integration.R | 7 tests/testthat/test-mappings.R | 79 +------ tests/testthat/test-relationships-integration.R | 12 - tests/testthat/test-relationships.R | 58 ----- tests/testthat/test-request.R |only tests/testthat/test-search.R | 26 +- tests/testthat/test-utils.R | 216 +++++++++++++++++++ tests/testthat/test-vocabularies-integration.R | 12 - tests/testthat/test-vocabularies.R | 63 ++--- tests/testthat/test-zzz.R |only vignettes/getting-started.Rmd | 4 42 files changed, 1555 insertions(+), 988 deletions(-)
Title: Access to Spanish Meteorological Stations Services
Description: Access to different Spanish meteorological stations data services and APIs (AEMET, SMC, MG,
Meteoclimatic...).
Author: Victor Granda [aut, cre] ,
Miquel de Caceres [ctb] ,
Aitor Ameztegui [ctb] ,
Luis Franco [ctb],
Ruben Fernandez-Casal [ctb]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>
Diff between meteospain versions 0.3.0 dated 2025-11-12 and 0.3.1 dated 2026-01-08
DESCRIPTION | 6 MD5 | 37 +- NAMESPACE | 1 NEWS.md | 11 R/get_data.R | 44 ++ R/meteocat_helpers.R | 4 R/meteogalicia_helpers.R | 4 R/ria_helpers.R | 5 README.md | 71 ++-- inst/doc/aemet.html | 8 inst/doc/api_limits.html | 573 +++++++++++++++++---------------- inst/doc/compatibility.html | 101 ++--- inst/doc/meteocat.html | 2 inst/doc/meteoclimatic.html | 54 +-- inst/doc/meteogalicia.html | 8 inst/doc/ria.html | 14 man/figures/README-plot_stations-1.png |binary man/figures/README-plot_stations-2.png |binary man/get_variables_from.Rd |only tests/testthat/test-meteocat.R | 25 + 20 files changed, 542 insertions(+), 426 deletions(-)
Title: An Interface for Running 'NetLogo' Simulations
Description: An interface for 'NetLogo' <https://www.netlogo.org> that enables
programmatic setup and execution of simulations. Designed to facilitate
integrating 'NetLogo' models into reproducible workflows by creating and
running 'BehaviorSpace' experiments and retrieving their results.
Author: Daniel Vartanian [aut, cre, ccp, cph]
Maintainer: Daniel Vartanian <danielvartan@proton.me>
Diff between logolink versions 0.1.0 dated 2025-10-09 and 1.0.0 dated 2026-01-08
logolink-0.1.0/logolink/R/inspect_experiment_file.R |only logolink-0.1.0/logolink/man/figures/readme-wolf-sheep-model-plot-1.png |only logolink-0.1.0/logolink/man/inspect_experiment_file.Rd |only logolink-0.1.0/logolink/tests/testthat/test-inspect_experiment_file.R |only logolink-1.0.0/logolink/DESCRIPTION | 20 logolink-1.0.0/logolink/MD5 | 93 + logolink-1.0.0/logolink/NAMESPACE | 8 logolink-1.0.0/logolink/NEWS.md | 33 logolink-1.0.0/logolink/R/create_experiment.R | 562 +++++++-- logolink-1.0.0/logolink/R/find_netlogo_console.R |only logolink-1.0.0/logolink/R/find_netlogo_home.R |only logolink-1.0.0/logolink/R/find_netlogo_version.R |only logolink-1.0.0/logolink/R/get_netlogo_shape.R |only logolink-1.0.0/logolink/R/inspect_experiment.R |only logolink-1.0.0/logolink/R/parse_netlogo_color.R |only logolink-1.0.0/logolink/R/parse_netlogo_list.R | 173 ++- logolink-1.0.0/logolink/R/read_experiment.R |only logolink-1.0.0/logolink/R/read_experiment_lists.R |only logolink-1.0.0/logolink/R/read_experiment_metadata.R |only logolink-1.0.0/logolink/R/read_experiment_spreadsheet.R |only logolink-1.0.0/logolink/R/read_experiment_statistics.R |only logolink-1.0.0/logolink/R/read_experiment_table.R |only logolink-1.0.0/logolink/R/run_experiment.R | 563 +++++++--- logolink-1.0.0/logolink/R/utils-checks.R |only logolink-1.0.0/logolink/R/utils-imports.R |only logolink-1.0.0/logolink/R/utils-mocks.R | 19 logolink-1.0.0/logolink/README.md | 353 +++--- logolink-1.0.0/logolink/build |only logolink-1.0.0/logolink/inst/CITATION | 22 logolink-1.0.0/logolink/inst/WORDLIST | 18 logolink-1.0.0/logolink/inst/doc |only logolink-1.0.0/logolink/man/create_experiment.Rd | 406 +++++-- logolink-1.0.0/logolink/man/figures/readme-wolf-sheep-model-plot-1-1.png |only logolink-1.0.0/logolink/man/figures/vignette-spread-of-disease-model-animation-1.gif |only logolink-1.0.0/logolink/man/figures/vignette-spread-of-disease-model-plot-1.png |only logolink-1.0.0/logolink/man/figures/vignette-spread-of-disease-model-plot-2.png |only logolink-1.0.0/logolink/man/figures/vignette-wolf-sheep-model-animation-1.gif |only logolink-1.0.0/logolink/man/figures/vignette-wolf-sheep-model-plot-1.png |only logolink-1.0.0/logolink/man/find_netlogo_console.Rd |only logolink-1.0.0/logolink/man/find_netlogo_home.Rd |only logolink-1.0.0/logolink/man/find_netlogo_version.Rd |only logolink-1.0.0/logolink/man/get_netlogo_shape.Rd |only logolink-1.0.0/logolink/man/inspect_experiment.Rd |only logolink-1.0.0/logolink/man/parse_netlogo_color.Rd |only logolink-1.0.0/logolink/man/parse_netlogo_list.Rd | 73 + logolink-1.0.0/logolink/man/read_experiment.Rd |only logolink-1.0.0/logolink/man/run_experiment.Rd | 319 +++-- logolink-1.0.0/logolink/tests/testthat.R | 14 logolink-1.0.0/logolink/tests/testthat/test-create_experiment.R | 283 +++-- logolink-1.0.0/logolink/tests/testthat/test-find_netlogo_console.R |only logolink-1.0.0/logolink/tests/testthat/test-find_netlogo_home.R |only logolink-1.0.0/logolink/tests/testthat/test-find_netlogo_version.R |only logolink-1.0.0/logolink/tests/testthat/test-get_netlogo_shape.R |only logolink-1.0.0/logolink/tests/testthat/test-inspect_experiment.R |only logolink-1.0.0/logolink/tests/testthat/test-parse_netlogo_color.R |only logolink-1.0.0/logolink/tests/testthat/test-parse_netlogo_list.R | 74 + logolink-1.0.0/logolink/tests/testthat/test-read_experiment.R |only logolink-1.0.0/logolink/tests/testthat/test-read_experiment_lists.R |only logolink-1.0.0/logolink/tests/testthat/test-read_experiment_metadata.R |only logolink-1.0.0/logolink/tests/testthat/test-read_experiment_spreadsheet.R |only logolink-1.0.0/logolink/tests/testthat/test-read_experiment_statistics.R |only logolink-1.0.0/logolink/tests/testthat/test-read_experiment_table.R |only logolink-1.0.0/logolink/tests/testthat/test-run_experiment-sod.R |only logolink-1.0.0/logolink/tests/testthat/test-run_experiment-vsa.R |only logolink-1.0.0/logolink/tests/testthat/test-run_experiment-wfp.R |only logolink-1.0.0/logolink/tests/testthat/test-run_experiment.R | 441 +++++-- logolink-1.0.0/logolink/tests/testthat/test-utils-checks.R |only logolink-1.0.0/logolink/tests/testthat/test-utils-imports.R |only logolink-1.0.0/logolink/tests/testthat/test-utils-mocks.R | 41 logolink-1.0.0/logolink/vignettes |only 70 files changed, 2638 insertions(+), 877 deletions(-)
Title: The Gumbel-Hougaard Copula
Description: Provides probability functions (cumulative distribution and density functions), simulation function (Gumbel copula multivariate simulation) and estimation functions (Maximum Likelihood Estimation, Inference For Margins, Moment Based Estimation and Canonical Maximum Likelihood).
Author: Christophe Dutang [aut, cre] ,
Anne-Lise Caillat [ctb],
Veronique Larrieu [ctb],
Triet Nguyen [ctb]
Maintainer: Christophe Dutang <dutangc@gmail.com>
Diff between gumbel versions 1.10-4 dated 2025-11-28 and 1.10-5 dated 2026-01-08
gumbel-1.10-4/gumbel/inst/doc/gumbel.Rnw |only gumbel-1.10-4/gumbel/inst/doc/gumbel.pdf |only gumbel-1.10-4/gumbel/vignettes/gumbel.Rnw |only gumbel-1.10-5/gumbel/DESCRIPTION | 7 ++++--- gumbel-1.10-5/gumbel/MD5 | 13 +++++++------ gumbel-1.10-5/gumbel/README.md | 5 ++++- gumbel-1.10-5/gumbel/build/vignette.rds |binary gumbel-1.10-5/gumbel/inst/doc/GumbelDoc.R |only gumbel-1.10-5/gumbel/inst/doc/GumbelDoc.Rmd |only gumbel-1.10-5/gumbel/inst/doc/GumbelDoc.html |only gumbel-1.10-5/gumbel/vignettes/GumbelDoc.Rmd |only 11 files changed, 15 insertions(+), 10 deletions(-)
Title: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell
Transcriptomics
Description: An open, multi-algorithmic pipeline for easy, fast and efficient
analysis of cellular sub-populations and the molecular signatures that
characterize them. The pipeline consists of four successive steps: data
pre-processing, cellular clustering with pseudo-temporal ordering, defining
differential expressed genes and biomarker identification. More details on
Ghannoum et. al. (2021) <doi:10.3390/ijms22031399>. This package implements
extensions of the work published by Ghannoum et. al. (2019)
<doi:10.1101/700989>.
Author: Salim Ghannoum [aut, cph],
Alvaro Koehn-Luque [aut, ths],
Waldir Leoncio [cre, aut],
Damiano Fantini [ctb]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between DIscBIO versions 1.2.2 dated 2023-11-06 and 1.2.3 dated 2026-01-08
DESCRIPTION | 18 +++++----- MD5 | 57 +++++++++++++++++---------------- NAMESPACE | 7 +--- NEWS.md | 5 ++ R/DIscBIO-classes.R | 2 - R/DIscBIO-generic-ClustDiffGenes.R | 39 +++++----------------- R/DIscBIO-generic-Clustexp.R | 2 - R/DIscBIO-generic-DEGanalysis.R | 55 +++++-------------------------- R/DIscBIO-generic-DEGanalysis2clust.R | 50 ++++------------------------ R/DIscBIO-generic-Exprmclust.R | 10 ++--- R/DIscBIO-generic-FindOutliers.R | 8 ++-- R/DIscBIO-generic-PCAplotSymbols.R | 2 - R/DIscBIO-generic-clusteringOrder.R | 2 - R/DIscBIO-generic-plotExptSNE.R | 2 - R/DIscBIO-generic-plotOrderTsne.R | 2 - R/DIscBIO-generic-plotSymbolstSNE.R | 4 +- R/DIscBIO-generic-pseudoTimeOrdering.R | 2 - R/Jaccard.R | 2 - R/PlotMBpca.R | 2 - R/cross.val.R | 2 - R/datasets.R | 7 ++++ R/internal-functions-samr-adapted.R | 24 ++++++------- R/internal-functions.R | 26 ++++++++++++++- R/retrieve_geneList.R |only data/geneList.rda |only man/Clustexp.Rd | 2 - man/DISCBIO.Rd | 2 - man/FindOutliers.Rd | 2 - man/geneList.Rd |only man/plotSymbolstSNE.Rd | 2 - man/rankcols.Rd | 2 - 31 files changed, 144 insertions(+), 196 deletions(-)
Title: Clinical Publication
Description: Accelerate the process from clinical data to medical publication,
including clinical data cleaning, significant result screening, and the
generation of publish-ready tables and figures.
Author: Yue Niu [aut, cre, cph] ,
Keyun Wang [aut]
Maintainer: Yue Niu <niuyuesam@163.com>
Diff between clinpubr versions 1.1.1 dated 2025-12-19 and 1.2.0 dated 2026-01-08
DESCRIPTION | 26 - MD5 | 37 +- NAMESPACE | 6 NEWS.md | 10 R/combine_files.R | 11 R/data_overview.R |only R/mark_outlier.R | 167 ++++++++++- R/merge.R |only R/time_roc.R | 2 R/utils.R | 7 README.md | 89 +++++ man/combine_files.Rd | 3 man/data_overview.Rd |only man/detect_outliers.Rd |only man/mad_outlier.Rd | 40 +- man/merge_by_substring.Rd |only tests/testthat/_snaps/classif_model_compare.md | 20 - tests/testthat/_snaps/interactions.md | 54 +-- tests/testthat/_snaps/rcs_plot.md | 80 ++--- tests/testthat/_snaps/regressions.md | 372 ++++++++++++------------- tests/testthat/test-data_overview.R |only tests/testthat/test-mark_outlier.R | 115 +++++++ tests/testthat/test-merge.R |only 23 files changed, 709 insertions(+), 330 deletions(-)
Title: Cluster Gauss-Newton Method
Description: Find multiple solutions of a nonlinear least squares problem. Cluster Gauss-Newton method does not assume uniqueness of the solution of the nonlinear least squares problem and compute multiple minimizers. Please cite the following paper when this software is used in your research: Aoki et al. (2020) <doi:10.1007/s11081-020-09571-2>. Cluster Gauss–Newton method. Optimization and Engineering, 1-31. Please cite the following paper when profile likelihood plot is drawn with this software and used in your research: Aoki and Sugiyama (2024) <doi:10.1002/psp4.13055>. Cluster Gauss-Newton method for a quick approximation of profile likelihood: With application to physiologically-based pharmacokinetic models. CPT Pharmacometrics Syst Pharmacol.13(1):54-67. GPT based helper bot available at <https://chatgpt.com/g/g-684936db9e748191a2796debb00cd755-cluster-gauss-newton-method-helper-bot> .
Author: Yasunori Aoki [aut, cre]
Maintainer: Yasunori Aoki <yaoki@uwaterloo.ca>
Diff between CGNM versions 0.9.2 dated 2025-09-11 and 0.9.3 dated 2026-01-08
DESCRIPTION | 6 MD5 | 12 R/Cluster_Gauss_Newton_method.R | 6 R/PostProcess.R | 2 inst/doc/CGNM-vignette.html | 290 +++++----- inst/shinyCGNM/CodeGenerationRelatedFunctions.R | 26 inst/shinyCGNM/rsconnect/shinyapps.io/bluetreeme/shinyCGNM.dcf | 2 7 files changed, 181 insertions(+), 163 deletions(-)
Title: Analyzing Data with Cellwise Outliers
Description: Tools for detecting cellwise outliers and robust methods to analyze
data which may contain them. Contains the implementation of the algorithms described in
Rousseeuw and Van den Bossche (2018) <doi:10.1080/00401706.2017.1340909> (open access)
Hubert et al. (2019) <doi:10.1080/00401706.2018.1562989> (open access),
Raymaekers and Rousseeuw (2021) <doi:10.1080/00401706.2019.1677270> (open access),
Raymaekers and Rousseeuw (2021) <doi:10.1007/s10994-021-05960-5> (open access),
Raymaekers and Rousseeuw (2021) <doi:10.52933/jdssv.v1i3.18> (open access),
Raymaekers and Rousseeuw (2022) <doi:10.1080/01621459.2023.2267777> (open access)
Rousseeuw (2022) <doi:10.1016/j.ecosta.2023.01.007> (open access).
Examples can be found in the vignettes:
"DDC_examples", "MacroPCA_examples", "wrap_examples", "transfo_examples",
"DI_examples", "cellMCD_examples" , "Correspondence_analysis_examples",
and "cellwise_weights_examples".
Author: Jakob Raymaekers [aut, cre],
Peter Rousseeuw [aut],
Wannes Van den Bossche [ctb],
Mia Hubert [ctb]
Maintainer: Jakob Raymaekers <jakob.raymaekers@uantwerpen.be>
Diff between cellWise versions 2.5.4 dated 2025-09-23 and 2.5.5 dated 2026-01-08
cellWise-2.5.4/cellWise/src/cwcov.cpp |only cellWise-2.5.4/cellWise/src/cwcov.h |only cellWise-2.5.5/cellWise/DESCRIPTION | 12 cellWise-2.5.5/cellWise/MD5 | 38 - cellWise-2.5.5/cellWise/NAMESPACE | 1 cellWise-2.5.5/cellWise/R/RcppExports.R | 8 cellWise-2.5.5/cellWise/R/cellHandler.R | 8 cellWise-2.5.5/cellWise/inst/doc/Correspondence_analysis_examples.html | 30 cellWise-2.5.5/cellWise/inst/doc/DDC_examples.html | 2 cellWise-2.5.5/cellWise/inst/doc/DI_examples.html | 32 cellWise-2.5.5/cellWise/inst/doc/MacroPCA_examples.html | 2 cellWise-2.5.5/cellWise/inst/doc/cellMCD_examples.html | 336 ++++------ cellWise-2.5.5/cellWise/inst/doc/cellwise_weights_examples.html | 2 cellWise-2.5.5/cellWise/inst/doc/transfo_examples.html | 2 cellWise-2.5.5/cellWise/inst/doc/wrap_examples.html | 2 cellWise-2.5.5/cellWise/src/LocScaleEstimators.cpp | 5 cellWise-2.5.5/cellWise/src/Main.cpp | 109 +++ cellWise-2.5.5/cellWise/src/RcppExports.cpp | 39 + cellWise-2.5.5/cellWise/src/cellMCD.cpp | 111 +++ cellWise-2.5.5/cellWise/src/cellMCD.h | 7 cellWise-2.5.5/cellWise/src/lts.cpp |only cellWise-2.5.5/cellWise/src/lts.h |only 22 files changed, 475 insertions(+), 271 deletions(-)
Title: Sentiment Analysis for Text, Image and Video using Transformer
Models
Description: Implements sentiment analysis using huggingface <https://huggingface.co> transformer zero-shot classification model pipelines for text and image data. The default text pipeline is Cross-Encoder's DistilRoBERTa <https://huggingface.co/cross-encoder/nli-distilroberta-base> and default image/video pipeline is Open AI's CLIP <https://huggingface.co/openai/clip-vit-base-patch32>. All other zero-shot classification model pipelines can be implemented using their model name from <https://huggingface.co/models?pipeline_tag=zero-shot-classification>.
Author: Alexander Christensen [aut] ,
Hudson Golino [aut] ,
Aleksandar Tomasevic [aut, cre]
Maintainer: Aleksandar Tomasevic <atomashevic@gmail.com>
Diff between transforEmotion versions 0.1.6 dated 2025-05-15 and 0.1.7 dated 2026-01-08
transforEmotion-0.1.6/transforEmotion/man/conda_check.Rd |only transforEmotion-0.1.7/transforEmotion/DESCRIPTION | 26 transforEmotion-0.1.7/transforEmotion/MD5 | 131 transforEmotion-0.1.7/transforEmotion/NAMESPACE | 46 transforEmotion-0.1.7/transforEmotion/R/auto_device.R | 17 transforEmotion-0.1.7/transforEmotion/R/cleanup_utils.R |only transforEmotion-0.1.7/transforEmotion/R/datasets_findingemo.R |only transforEmotion-0.1.7/transforEmotion/R/delete_transformer.R | 1 transforEmotion-0.1.7/transforEmotion/R/evaluate_emotions.R |only transforEmotion-0.1.7/transforEmotion/R/global_vars.R |only transforEmotion-0.1.7/transforEmotion/R/hf_auth.R |only transforEmotion-0.1.7/transforEmotion/R/image_scores.R | 212 + transforEmotion-0.1.7/transforEmotion/R/internal_bindings.R |only transforEmotion-0.1.7/transforEmotion/R/map_discrete_to_vad.R |only transforEmotion-0.1.7/transforEmotion/R/model_management.R |only transforEmotion-0.1.7/transforEmotion/R/model_registry.R |only transforEmotion-0.1.7/transforEmotion/R/rag.R | 1660 ++++++++-- transforEmotion-0.1.7/transforEmotion/R/rag_evaluation.R |only transforEmotion-0.1.7/transforEmotion/R/rag_json.R |only transforEmotion-0.1.7/transforEmotion/R/rag_retrievers.R |only transforEmotion-0.1.7/transforEmotion/R/rag_sentemo.R |only transforEmotion-0.1.7/transforEmotion/R/reticulate_env.R |only transforEmotion-0.1.7/transforEmotion/R/sentence_similarity.R | 2 transforEmotion-0.1.7/transforEmotion/R/setup_gpu_modules.R | 77 transforEmotion-0.1.7/transforEmotion/R/setup_miniconda.R | 87 transforEmotion-0.1.7/transforEmotion/R/setup_modules.R | 237 - transforEmotion-0.1.7/transforEmotion/R/transformer_scores.R | 152 transforEmotion-0.1.7/transforEmotion/R/vad_definitions.R |only transforEmotion-0.1.7/transforEmotion/R/vad_scores.R |only transforEmotion-0.1.7/transforEmotion/R/video_scores.R | 106 transforEmotion-0.1.7/transforEmotion/R/zzz.R | 31 transforEmotion-0.1.7/transforEmotion/README.md | 146 transforEmotion-0.1.7/transforEmotion/build/partial.rdb |binary transforEmotion-0.1.7/transforEmotion/build/vignette.rds |binary transforEmotion-0.1.7/transforEmotion/data/emotions.rda |binary transforEmotion-0.1.7/transforEmotion/data/neo_ipip_extraversion.RData |binary transforEmotion-0.1.7/transforEmotion/data/stop_words.RData |binary transforEmotion-0.1.7/transforEmotion/data/tinytrolls.rda |binary transforEmotion-0.1.7/transforEmotion/inst/doc/Setup.pdf |binary transforEmotion-0.1.7/transforEmotion/inst/doc/evaluate_emotions.R |only transforEmotion-0.1.7/transforEmotion/inst/doc/evaluate_emotions.Rmd |only transforEmotion-0.1.7/transforEmotion/inst/doc/evaluate_emotions.html |only transforEmotion-0.1.7/transforEmotion/inst/extdata/trump1.jpg |only transforEmotion-0.1.7/transforEmotion/inst/extdata/trump2.jpg |only transforEmotion-0.1.7/transforEmotion/inst/python/__pycache__ |only transforEmotion-0.1.7/transforEmotion/inst/python/download_findingemo.py |only transforEmotion-0.1.7/transforEmotion/inst/python/image.py | 934 ++++- transforEmotion-0.1.7/transforEmotion/inst/python/load_findingemo_annotations.py |only transforEmotion-0.1.7/transforEmotion/inst/python/video.py | 12 transforEmotion-0.1.7/transforEmotion/man/add_vision_model.Rd |only transforEmotion-0.1.7/transforEmotion/man/as_rag_table.Rd |only transforEmotion-0.1.7/transforEmotion/man/check_findingemo_quality.Rd |only transforEmotion-0.1.7/transforEmotion/man/check_nvidia_gpu.Rd | 22 transforEmotion-0.1.7/transforEmotion/man/dot-init_builtin_models.Rd |only transforEmotion-0.1.7/transforEmotion/man/dot-vision_model_registry.Rd |only transforEmotion-0.1.7/transforEmotion/man/download_findingemo_data.Rd |only transforEmotion-0.1.7/transforEmotion/man/evaluate_emotions.Rd |only transforEmotion-0.1.7/transforEmotion/man/get_vision_model_config.Rd |only transforEmotion-0.1.7/transforEmotion/man/image_scores.Rd | 20 transforEmotion-0.1.7/transforEmotion/man/image_scores_dir.Rd |only transforEmotion-0.1.7/transforEmotion/man/is_vision_model_registered.Rd |only transforEmotion-0.1.7/transforEmotion/man/list_vision_models.Rd |only transforEmotion-0.1.7/transforEmotion/man/load_findingemo_annotations.Rd |only transforEmotion-0.1.7/transforEmotion/man/map_discrete_to_vad.Rd |only transforEmotion-0.1.7/transforEmotion/man/map_to_emo8.Rd |only transforEmotion-0.1.7/transforEmotion/man/parse_rag_json.Rd |only transforEmotion-0.1.7/transforEmotion/man/plot.emotion_evaluation.Rd |only transforEmotion-0.1.7/transforEmotion/man/prepare_findingemo_evaluation.Rd |only transforEmotion-0.1.7/transforEmotion/man/print.emotion_evaluation.Rd |only transforEmotion-0.1.7/transforEmotion/man/rag.Rd | 130 transforEmotion-0.1.7/transforEmotion/man/rag_json_utils.Rd |only transforEmotion-0.1.7/transforEmotion/man/rag_retrievers.Rd |only transforEmotion-0.1.7/transforEmotion/man/rag_sentemo.Rd |only transforEmotion-0.1.7/transforEmotion/man/register_retriever.Rd |only transforEmotion-0.1.7/transforEmotion/man/register_vision_model.Rd |only transforEmotion-0.1.7/transforEmotion/man/remove_vision_model.Rd |only transforEmotion-0.1.7/transforEmotion/man/setup_gpu_modules.Rd | 4 transforEmotion-0.1.7/transforEmotion/man/setup_miniconda.Rd | 13 transforEmotion-0.1.7/transforEmotion/man/setup_modules.Rd |only transforEmotion-0.1.7/transforEmotion/man/setup_popular_models.Rd |only transforEmotion-0.1.7/transforEmotion/man/show_vision_models.Rd |only transforEmotion-0.1.7/transforEmotion/man/summary.emotion_evaluation.Rd |only transforEmotion-0.1.7/transforEmotion/man/te_cleanup_default_venv.Rd |only transforEmotion-0.1.7/transforEmotion/man/transformer_scores.Rd | 6 transforEmotion-0.1.7/transforEmotion/man/vad_scores.Rd |only transforEmotion-0.1.7/transforEmotion/man/validate_rag_json.Rd |only transforEmotion-0.1.7/transforEmotion/man/validate_rag_predictions.Rd |only transforEmotion-0.1.7/transforEmotion/man/video_scores.Rd | 18 transforEmotion-0.1.7/transforEmotion/tests/testthat/test_evaluate_emotions.R |only transforEmotion-0.1.7/transforEmotion/tests/testthat/test_findingemo.R |only transforEmotion-0.1.7/transforEmotion/tests/testthat/test_hf_auth_wrappers.R |only transforEmotion-0.1.7/transforEmotion/tests/testthat/test_image_scores.R | 99 transforEmotion-0.1.7/transforEmotion/tests/testthat/test_map_discrete_to_vad.R |only transforEmotion-0.1.7/transforEmotion/tests/testthat/test_rag_parsers.R |only transforEmotion-0.1.7/transforEmotion/tests/testthat/test_transformer_scores.R | 42 transforEmotion-0.1.7/transforEmotion/tests/testthat/test_vad_scores.R |only transforEmotion-0.1.7/transforEmotion/tests/testthat/test_video_scores.R | 2 transforEmotion-0.1.7/transforEmotion/vignettes/evaluate_emotions.Rmd |only 98 files changed, 3245 insertions(+), 988 deletions(-)
More information about transforEmotion at CRAN
Permanent link
Title: Enhance Reproducibility of R Code
Description: A collection of high-level, machine- and OS-independent tools
for making reproducible and reusable content in R.
The two workhorse functions are 'Cache()' and 'prepInputs()'.
'Cache()' allows for nested caching, is robust to environments and objects
with environments (like functions), and deals with some classes of
file-backed R objects e.g., from 'terra' and 'raster' packages.
Both functions have been developed to be foundational components of data
retrieval and processing in continuous workflow situations. In both functions,
efforts are made to make the first and subsequent calls of functions have
the same result, but faster at subsequent times by way of checksums
and digesting. Several features are still under development, including
cloud storage of cached objects allowing for sharing between users. Several
advanced options are available, see '?reproducibleOptions()'.
Author: Eliot J B McIntire [aut, cre] ,
Alex M Chubaty [aut] ,
Tati Micheletti [ctb] ,
Ceres Barros [ctb] ,
Ian Eddy [ctb] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between reproducible versions 2.1.2 dated 2024-12-12 and 3.0.0 dated 2026-01-08
reproducible-2.1.2/reproducible/man/fastMask.Rd |only reproducible-3.0.0/reproducible/DESCRIPTION | 56 reproducible-3.0.0/reproducible/MD5 | 329 reproducible-3.0.0/reproducible/NAMESPACE | 433 - reproducible-3.0.0/reproducible/NEWS.md | 1553 +-- reproducible-3.0.0/reproducible/R/DBI.R | 2509 +++--- reproducible-3.0.0/reproducible/R/GPT2.R |only reproducible-3.0.0/reproducible/R/cache-helpers.R | 1153 +- reproducible-3.0.0/reproducible/R/cache-internals.R | 228 reproducible-3.0.0/reproducible/R/cache.R | 4158 ++++------ reproducible-3.0.0/reproducible/R/cacheGeo.R | 663 + reproducible-3.0.0/reproducible/R/checksums.R | 793 - reproducible-3.0.0/reproducible/R/cloud.R | 757 - reproducible-3.0.0/reproducible/R/convertPaths.R | 455 - reproducible-3.0.0/reproducible/R/copy.R | 475 - reproducible-3.0.0/reproducible/R/download.R | 2519 +++--- reproducible-3.0.0/reproducible/R/downloadTileAndUpload.R |only reproducible-3.0.0/reproducible/R/exportedMethods.R | 2424 +++-- reproducible-3.0.0/reproducible/R/gis.R | 108 reproducible-3.0.0/reproducible/R/helpers.R | 1412 +-- reproducible-3.0.0/reproducible/R/listNamed.R | 58 reproducible-3.0.0/reproducible/R/messages.R | 988 +- reproducible-3.0.0/reproducible/R/objectSize.R | 352 reproducible-3.0.0/reproducible/R/options.R | 636 - reproducible-3.0.0/reproducible/R/packages.R | 130 reproducible-3.0.0/reproducible/R/paths.R | 1000 +- reproducible-3.0.0/reproducible/R/postProcess.R | 1527 +-- reproducible-3.0.0/reproducible/R/postProcessTo.R | 3867 ++++----- reproducible-3.0.0/reproducible/R/preProcess.R | 3874 ++++----- reproducible-3.0.0/reproducible/R/prepInputs.R | 3467 ++++---- reproducible-3.0.0/reproducible/R/reproducible-package.R | 88 reproducible-3.0.0/reproducible/R/robustDigest.R | 1188 +- reproducible-3.0.0/reproducible/R/search.R | 114 reproducible-3.0.0/reproducible/R/showCacheEtc.R | 1725 ++-- reproducible-3.0.0/reproducible/R/spatialObjects-class.R | 18 reproducible-3.0.0/reproducible/R/terra-migration.R | 178 reproducible-3.0.0/reproducible/R/zzz.R | 135 reproducible-3.0.0/reproducible/README.md | 220 reproducible-3.0.0/reproducible/build/vignette.rds |binary reproducible-3.0.0/reproducible/inst/CITATION | 30 reproducible-3.0.0/reproducible/inst/WORDLIST | 331 reproducible-3.0.0/reproducible/inst/doc/Intro-to-Cache.R | 453 - reproducible-3.0.0/reproducible/inst/doc/Intro-to-Cache.Rmd | 684 - reproducible-3.0.0/reproducible/inst/doc/Intro-to-Cache.html | 3612 +++----- reproducible-3.0.0/reproducible/inst/examples/example_Cache.R | 244 reproducible-3.0.0/reproducible/inst/examples/example_assessDataType.R | 226 reproducible-3.0.0/reproducible/inst/examples/example_checkPath.R | 44 reproducible-3.0.0/reproducible/inst/examples/example_postProcess.R | 124 reproducible-3.0.0/reproducible/inst/examples/example_postProcessTo.R | 56 reproducible-3.0.0/reproducible/man/Cache.Rd | 1129 +- reproducible-3.0.0/reproducible/man/CacheDigest.Rd | 108 reproducible-3.0.0/reproducible/man/CacheGeo.Rd | 331 reproducible-3.0.0/reproducible/man/CacheHelpers.Rd | 450 - reproducible-3.0.0/reproducible/man/Checksums.Rd | 220 reproducible-3.0.0/reproducible/man/Copy.Rd | 210 reproducible-3.0.0/reproducible/man/Filenames.Rd | 108 reproducible-3.0.0/reproducible/man/Path-class.Rd | 124 reproducible-3.0.0/reproducible/man/addTags.Rd |only reproducible-3.0.0/reproducible/man/archiveExtractBinary.Rd | 38 reproducible-3.0.0/reproducible/man/assessDataType.Rd | 284 reproducible-3.0.0/reproducible/man/basename2.Rd | 38 reproducible-3.0.0/reproducible/man/cacheId.Rd |only reproducible-3.0.0/reproducible/man/checkAndMakeCloudFolderID.Rd | 84 reproducible-3.0.0/reproducible/man/checkPath.Rd | 130 reproducible-3.0.0/reproducible/man/checkRelative.Rd | 70 reproducible-3.0.0/reproducible/man/cloudDownload.Rd | 98 reproducible-3.0.0/reproducible/man/cloudUploadFromCache.Rd | 96 reproducible-3.0.0/reproducible/man/compareNA.Rd | 56 reproducible-3.0.0/reproducible/man/convertCallToCommonFormat.Rd |only reproducible-3.0.0/reproducible/man/convertPaths.Rd | 82 reproducible-3.0.0/reproducible/man/copyFile.Rd | 164 reproducible-3.0.0/reproducible/man/debugCache.Rd | 52 reproducible-3.0.0/reproducible/man/deprecated.Rd | 338 reproducible-3.0.0/reproducible/man/detectActiveCores.Rd |only reproducible-3.0.0/reproducible/man/determineFilename.Rd | 166 reproducible-3.0.0/reproducible/man/digest.Rd | 58 reproducible-3.0.0/reproducible/man/dlGeneric.Rd | 64 reproducible-3.0.0/reproducible/man/dlGoogle.Rd | 135 reproducible-3.0.0/reproducible/man/dot-file.move.Rd | 40 reproducible-3.0.0/reproducible/man/dot-formalsNotInCurrentDots.Rd | 52 reproducible-3.0.0/reproducible/man/dot-isMemoised.Rd | 52 reproducible-3.0.0/reproducible/man/dot-objSizeWithTry.Rd |only reproducible-3.0.0/reproducible/man/dot-removeCacheAtts.Rd | 28 reproducible-3.0.0/reproducible/man/dot-requireNamespace.Rd | 64 reproducible-3.0.0/reproducible/man/dot-whereInStack.Rd |only reproducible-3.0.0/reproducible/man/dotWrap.Rd | 316 reproducible-3.0.0/reproducible/man/downloadFile.Rd | 247 reproducible-3.0.0/reproducible/man/downloadRemote.Rd | 207 reproducible-3.0.0/reproducible/man/exportedMethods.Rd | 589 - reproducible-3.0.0/reproducible/man/extractFromArchive.Rd | 128 reproducible-3.0.0/reproducible/man/fixErrorsIn.Rd | 66 reproducible-3.0.0/reproducible/man/gdalwarpFns.Rd | 228 reproducible-3.0.0/reproducible/man/grepSysCalls.Rd | 44 reproducible-3.0.0/reproducible/man/guessAtTarget.Rd | 50 reproducible-3.0.0/reproducible/man/harmonizeCall.Rd |only reproducible-3.0.0/reproducible/man/internetExists.Rd | 48 reproducible-3.0.0/reproducible/man/isInteractive.Rd | 34 reproducible-3.0.0/reproducible/man/isSpatial.Rd |only reproducible-3.0.0/reproducible/man/isUpdated.Rd | 34 reproducible-3.0.0/reproducible/man/isWindows.Rd | 24 reproducible-3.0.0/reproducible/man/keepOrigGeom.Rd | 50 reproducible-3.0.0/reproducible/man/linkOrCopy.Rd | 185 reproducible-3.0.0/reproducible/man/listFilesInArchive.Rd | 39 reproducible-3.0.0/reproducible/man/listNamed.Rd | 54 reproducible-3.0.0/reproducible/man/loadFile.Rd | 39 reproducible-3.0.0/reproducible/man/matchCall2.Rd |only reproducible-3.0.0/reproducible/man/mergeCache.Rd | 130 reproducible-3.0.0/reproducible/man/messageColoured.Rd | 222 reproducible-3.0.0/reproducible/man/movedCache.Rd | 148 reproducible-3.0.0/reproducible/man/normPath.Rd | 152 reproducible-3.0.0/reproducible/man/numCoresToUse.Rd |only reproducible-3.0.0/reproducible/man/objSize.Rd | 153 reproducible-3.0.0/reproducible/man/paddedFloatToChar.Rd | 72 reproducible-3.0.0/reproducible/man/pkgEnv.Rd | 56 reproducible-3.0.0/reproducible/man/postProcess.Rd | 336 reproducible-3.0.0/reproducible/man/postProcessTo.Rd | 568 - reproducible-3.0.0/reproducible/man/preProcess.Rd | 282 reproducible-3.0.0/reproducible/man/prefix.Rd | 84 reproducible-3.0.0/reproducible/man/prepInputs.Rd | 728 - reproducible-3.0.0/reproducible/man/prepInputsWithTiles.Rd |only reproducible-3.0.0/reproducible/man/prepareFileBackedRaster.Rd | 97 reproducible-3.0.0/reproducible/man/purge.Rd | 139 reproducible-3.0.0/reproducible/man/purgeChecksums.Rd |only reproducible-3.0.0/reproducible/man/rasterRead.Rd | 38 reproducible-3.0.0/reproducible/man/relativePaths.Rd | 126 reproducible-3.0.0/reproducible/man/remapFilenames.Rd | 42 reproducible-3.0.0/reproducible/man/reproducible-package.Rd | 154 reproducible-3.0.0/reproducible/man/reproducibleOptions.Rd | 516 - reproducible-3.0.0/reproducible/man/retry.Rd | 98 reproducible-3.0.0/reproducible/man/robustDigest.Rd | 369 reproducible-3.0.0/reproducible/man/saveToCache.Rd | 111 reproducible-3.0.0/reproducible/man/search.Rd | 96 reproducible-3.0.0/reproducible/man/set.randomseed.Rd | 56 reproducible-3.0.0/reproducible/man/setSubAttrInList.Rd | 50 reproducible-3.0.0/reproducible/man/studyAreaName.Rd | 62 reproducible-3.0.0/reproducible/man/tempdir2.Rd | 64 reproducible-3.0.0/reproducible/man/tempfile2.Rd | 64 reproducible-3.0.0/reproducible/man/terra-migration.Rd | 84 reproducible-3.0.0/reproducible/man/testForArchiveExtract.Rd | 46 reproducible-3.0.0/reproducible/man/unrarPath.Rd | 34 reproducible-3.0.0/reproducible/man/usesPointer.Rd |only reproducible-3.0.0/reproducible/man/viewCache.Rd | 518 - reproducible-3.0.0/reproducible/man/writeFuture.Rd | 119 reproducible-3.0.0/reproducible/tests/test-all.R | 53 reproducible-3.0.0/reproducible/tests/testthat/helper-allEqual.R | 1021 +- reproducible-3.0.0/reproducible/tests/testthat/setup.R | 120 reproducible-3.0.0/reproducible/tests/testthat/test-cache.R | 3856 +++++---- reproducible-3.0.0/reproducible/tests/testthat/test-cacheGeo.R | 296 reproducible-3.0.0/reproducible/tests/testthat/test-cacheHelpers.R | 679 - reproducible-3.0.0/reproducible/tests/testthat/test-checkPath.R | 197 reproducible-3.0.0/reproducible/tests/testthat/test-checksums.R | 176 reproducible-3.0.0/reproducible/tests/testthat/test-cloud.R | 557 - reproducible-3.0.0/reproducible/tests/testthat/test-cluster.R | 158 reproducible-3.0.0/reproducible/tests/testthat/test-copy.R | 208 reproducible-3.0.0/reproducible/tests/testthat/test-devMode.R | 162 reproducible-3.0.0/reproducible/tests/testthat/test-download.R | 46 reproducible-3.0.0/reproducible/tests/testthat/test-examples.R | 109 reproducible-3.0.0/reproducible/tests/testthat/test-filesMissingExtension.R | 152 reproducible-3.0.0/reproducible/tests/testthat/test-gis.R | 124 reproducible-3.0.0/reproducible/tests/testthat/test-misc.R | 648 - reproducible-3.0.0/reproducible/tests/testthat/test-multipleCacheRepo.R | 103 reproducible-3.0.0/reproducible/tests/testthat/test-paths.R | 102 reproducible-3.0.0/reproducible/tests/testthat/test-postProcess.R | 738 - reproducible-3.0.0/reproducible/tests/testthat/test-postProcessTerra.R | 989 +- reproducible-3.0.0/reproducible/tests/testthat/test-preProcessDoesntWork.R | 386 reproducible-3.0.0/reproducible/tests/testthat/test-preProcessWorks.R | 1408 +-- reproducible-3.0.0/reproducible/tests/testthat/test-prepInputs-large-files.R | 213 reproducible-3.0.0/reproducible/tests/testthat/test-prepInputs.R | 4123 +++++---- reproducible-3.0.0/reproducible/tests/testthat/test-prepInputsInNestedArchives.R | 494 - reproducible-3.0.0/reproducible/tests/testthat/test-prepInputsUrlTiles.R |only reproducible-3.0.0/reproducible/tests/testthat/test-reproducibleVerbose.R | 54 reproducible-3.0.0/reproducible/tests/testthat/test-robustDigest.R | 96 reproducible-3.0.0/reproducible/tests/testthat/test-symlinks.R | 261 reproducible-3.0.0/reproducible/vignettes/Intro-to-Cache.Rmd | 684 - 174 files changed, 39257 insertions(+), 37415 deletions(-)
Title: A Functionally Oriented Interface for Integrating 'Julia' with R
Description: Allows to import functions and whole packages from 'Julia' in R.
Imported 'Julia' functions can directly be called as R functions.
Data structures can be translated between 'Julia' and R.
More details can also be found in the corresponding article
<doi:10.18637/jss.v101.i06>.
Author: Stefan Lenz [aut, cre] ,
Harald Binder [aut, ths] ,
Angelo D'Ambrosio [ctb] ,
June Choe [ctb]
Maintainer: Stefan Lenz <stefan-m-lenz@web.de>
Diff between JuliaConnectoR versions 1.1.4 dated 2024-10-08 and 1.1.5 dated 2026-01-08
JuliaConnectoR-1.1.4/JuliaConnectoR/inst/examples/iris-example/project_1_9 |only JuliaConnectoR-1.1.5/JuliaConnectoR/DESCRIPTION | 20 - JuliaConnectoR-1.1.5/JuliaConnectoR/MD5 | 16 - JuliaConnectoR-1.1.5/JuliaConnectoR/R/connecting.R | 111 ++++++++-- JuliaConnectoR-1.1.5/JuliaConnectoR/R/handling_dataframes.R | 8 JuliaConnectoR-1.1.5/JuliaConnectoR/inst/examples/iris-example/project_1_10 |only JuliaConnectoR-1.1.5/JuliaConnectoR/man/as.data.frame.JuliaProxy.Rd | 8 JuliaConnectoR-1.1.5/JuliaConnectoR/man/startJuliaServer.Rd | 46 +++- JuliaConnectoR-1.1.5/JuliaConnectoR/tests/testthat/test.R | 16 - 9 files changed, 169 insertions(+), 56 deletions(-)
More information about JuliaConnectoR at CRAN
Permanent link
Title: Analyzing Wildlife Data with Detection Error
Description: Models for analyzing site occupancy and count data models
with detection error, including
single-visit based models (Lele et al. 2012 <doi:10.1093/jpe/rtr042>,
Moreno et al. 2010 <doi:10.1890/09-1073.1>,
Solymos et al. 2012 <doi:10.1002/env.1149>,
Denes et al. 2016 <doi:10.1111/1365-2664.12818>),
conditional distance sampling and time-removal models (QPAD)
(Solymos et al. 2013 <doi:10.1111/2041-210X.12106>,
Solymos et al. 2018 <doi:10.1650/CONDOR-18-32.1>),
and single bin QPAD (SQPAD) models
(Lele & Solymos 2025 <doi:10.1093/ornithapp/duaf078>).
Package development was supported by the
Alberta Biodiversity Monitoring Institute
and the Boreal Avian Modelling Project.
Author: Peter Solymos [aut, cre] ,
Monica Moreno [aut],
Subhash R. Lele [aut],
Steven L. Van Wilgenburg [ctb]
Maintainer: Peter Solymos <psolymos@gmail.com>
Diff between detect versions 0.5-0 dated 2025-09-01 and 0.5-1 dated 2026-01-08
DESCRIPTION | 12 MD5 | 10 NAMESPACE | 3 R/sqpad.R | 898 +++++++++++++++++++++++++++++++++++++++++++++------------- inst/WORDLIST | 4 man/sqpad.Rd | 17 - 6 files changed, 736 insertions(+), 208 deletions(-)
Title: Dependency Management with 'roxygen'-Style Comments
Description: Manage your source code dependencies
by decorating your existing R code with special,
'roxygen'-style comments.
Author: Peter Solymos [aut, cre] ,
Analythium Solutions Inc. [cph, fnd]
Maintainer: Peter Solymos <peter@analythium.io>
Diff between deps versions 0.4.0 dated 2024-07-07 and 0.4.1 dated 2026-01-08
DESCRIPTION | 11 - MD5 | 14 +- NEWS.md | 4 R/create.R | 10 - R/install.R | 45 ++++--- R/utils.R | 254 ++++++++++++++++++++-------------------- inst/WORDLIST | 4 inst/examples/03-cli/deps-cli.R | 8 - 8 files changed, 189 insertions(+), 161 deletions(-)
Title: Fitting and Tuning Regularized Cause-Specific Cox Models with
Elastic-Net Penalty
Description: Flexible tools to fit, tune and obtain absolute risk predictions from regularized cause-specific cox models with elastic-net penalty.
Author: Shahin Roshani [aut, cre, cph]
Maintainer: Shahin Roshani <s.roshani@nki.nl>
Diff between CSCNet versions 0.1.2 dated 2022-11-08 and 0.1.3 dated 2026-01-08
DESCRIPTION | 22 +- MD5 | 24 +- NAMESPACE | 4 NEWS.md | 10 + R/tune_penCSC.R | 94 +++------ README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/CSCNet.R | 36 +-- inst/doc/CSCNet.Rmd | 36 +-- inst/doc/CSCNet.html | 499 ++++++++++++++++++++++++--------------------------- man/tune_penCSC.Rd | 36 +-- vignettes/CSCNet.Rmd | 36 +-- 13 files changed, 357 insertions(+), 444 deletions(-)
Title: Correlation-Based and Model-Based Predictor Pruning
Description: Provides functions for predictor pruning using association-based and model-based approaches. Includes corrPrune() for fast correlation-based pruning, modelPrune() for VIF-based regression pruning, and exact graph-theoretic algorithms (Eppstein–Löffler–Strash, Bron–Kerbosch) for exhaustive subset enumeration. Supports linear models, GLMs, and mixed models ('lme4', 'glmmTMB').
Author: Gilles Colling [aut, cre]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between corrselect versions 3.0.5 dated 2025-12-16 and 3.1.0 dated 2026-01-08
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corrselect-3.1.0/corrselect/vignettes/workflows_cache/html/unnamed-chunk-2_cd4898f9febd142781216c357528ab42.rdx |only corrselect-3.1.0/corrselect/vignettes/workflows_cache/html/unnamed-chunk-3_2998d1cdf75c8ae9847131903349ed16.RData |only corrselect-3.1.0/corrselect/vignettes/workflows_cache/html/unnamed-chunk-3_2998d1cdf75c8ae9847131903349ed16.rdb |only corrselect-3.1.0/corrselect/vignettes/workflows_cache/html/unnamed-chunk-3_2998d1cdf75c8ae9847131903349ed16.rdx |only corrselect-3.1.0/corrselect/vignettes/workflows_cache/html/unnamed-chunk-4_8e671d409df5c92d42553f08e2d017d6.RData |only corrselect-3.1.0/corrselect/vignettes/workflows_cache/html/unnamed-chunk-4_8e671d409df5c92d42553f08e2d017d6.rdb |only corrselect-3.1.0/corrselect/vignettes/workflows_cache/html/unnamed-chunk-4_8e671d409df5c92d42553f08e2d017d6.rdx |only corrselect-3.1.0/corrselect/vignettes/workflows_cache/html/unnamed-chunk-5_d6cb6bb3b89156ecce84fbcfe708c366.RData |only 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Title: Package Admix for Admixture (aka Contamination) Models
Description: Implements techniques to estimate the unknown quantities
related to two-component admixture models, where the two components
can belong to any distribution (note that in the case of multinomial
mixtures, the two components must belong to the same family).
Estimation methods depend on the assumptions made on the unknown
component density; see Bordes and Vandekerkhove (2010)
<doi:10.3103/S1066530710010023>, Patra and Sen (2016)
<doi:10.1111/rssb.12148>, and Milhaud, Pommeret, Salhi, Vandekerkhove
(2024) <doi:10.3150/23-BEJ1593>. In practice, one can estimate both
the mixture weight and the unknown component density in a wide variety
of frameworks. On top of that, hypothesis tests can be performed in
one and two-sample contexts to test the unknown component density (see
Milhaud, Pommeret, Salhi and Vandekerkhove (2022)
<doi:10.1016/j.jspi.2021.05.010>, and Milhaud, Pommeret, Salhi,
Vandekerkhove (2024) <doi:10.3150/23-BEJ1593>). Finally, clustering of
unknown [...truncated...]
Author: Xavier Milhaud [aut, cre],
Pierre Vandekerkhove [ctb],
Denys Pommeret [ctb],
Yahia Salhi [ctb]
Maintainer: Xavier Milhaud <xavier.milhaud.research@gmail.com>
Diff between admix versions 2.5.1 dated 2025-09-05 and 2.5.2 dated 2026-01-08
admix-2.5.1/admix/man/get_cluster_members.admix_cluster.Rd |only admix-2.5.1/admix/man/get_cluster_sizes.admix_cluster.Rd |only admix-2.5.1/admix/man/get_discrepancy_id.IBM_test.Rd |only admix-2.5.1/admix/man/get_discrepancy_id.Rd |only admix-2.5.1/admix/man/get_discrepancy_matrix.IBM_test.Rd |only admix-2.5.1/admix/man/get_discrepancy_matrix.admix_cluster.Rd |only admix-2.5.1/admix/man/get_discrepancy_rank.IBM_test.Rd |only admix-2.5.1/admix/man/get_known_component.admix_cluster.Rd |only admix-2.5.1/admix/man/get_known_component.admix_estim.Rd |only admix-2.5.1/admix/man/get_known_component.htest.Rd |only admix-2.5.1/admix/man/get_mixing_weights.admix_estim.Rd |only admix-2.5.1/admix/man/get_mixing_weights.htest.Rd |only admix-2.5.1/admix/man/get_statistic_components.IBM_test.Rd |only admix-2.5.1/admix/man/get_tabulated_dist.IBM_test.Rd |only admix-2.5.1/admix/man/reject_nullHyp.htest.Rd |only admix-2.5.1/admix/man/which_rank.htest.Rd |only admix-2.5.2/admix/DESCRIPTION | 8 admix-2.5.2/admix/MD5 | 126 +- admix-2.5.2/admix/NAMESPACE | 16 admix-2.5.2/admix/R/IBM_k_samples_test.R | 211 +--- admix-2.5.2/admix/R/admix_cluster.R | 61 - admix-2.5.2/admix/R/admix_estim.R | 52 - admix-2.5.2/admix/R/admix_model.R | 14 admix-2.5.2/admix/R/admix_test.R | 33 admix-2.5.2/admix/R/decontaminated_dist.R | 341 ++---- admix-2.5.2/admix/R/estim_BVdk.R | 26 admix-2.5.2/admix/R/estim_IBM.R | 54 - admix-2.5.2/admix/R/estim_PS.R | 13 admix-2.5.2/admix/R/extractors.R | 519 +++++----- admix-2.5.2/admix/R/gaussianity_test.R | 31 admix-2.5.2/admix/R/orthobasis_test.R | 55 - admix-2.5.2/admix/R/twoComp_mixt.R | 104 -- admix-2.5.2/admix/R/utils.R | 107 +- admix-2.5.2/admix/README.md | 4 admix-2.5.2/admix/build/partial.rdb |binary admix-2.5.2/admix/build/vignette.rds |binary admix-2.5.2/admix/inst/doc/admixture-clustering.html | 4 admix-2.5.2/admix/inst/doc/admixture-weight-estimation.R | 6 admix-2.5.2/admix/inst/doc/admixture-weight-estimation.Rmd | 6 admix-2.5.2/admix/inst/doc/admixture-weight-estimation.html | 39 admix-2.5.2/admix/inst/doc/test-hypothesis.html | 4 admix-2.5.2/admix/man/admix_estim.Rd | 14 admix-2.5.2/admix/man/admix_model.Rd | 2 admix-2.5.2/admix/man/admix_test.Rd | 13 admix-2.5.2/admix/man/decontaminated_cdf.Rd | 14 admix-2.5.2/admix/man/decontaminated_density.Rd | 94 - admix-2.5.2/admix/man/estim_IBM.Rd | 2 admix-2.5.2/admix/man/get_cluster_members.Rd | 46 admix-2.5.2/admix/man/get_cluster_sizes.Rd | 4 admix-2.5.2/admix/man/get_discrepancy_matrix.Rd | 12 admix-2.5.2/admix/man/get_discrepancy_rank.Rd | 10 admix-2.5.2/admix/man/get_known_component.Rd | 29 admix-2.5.2/admix/man/get_mixing_weights.Rd | 35 admix-2.5.2/admix/man/get_mixture_data.Rd | 19 admix-2.5.2/admix/man/get_statistic_components.Rd | 8 admix-2.5.2/admix/man/get_tabulated_dist.Rd | 32 admix-2.5.2/admix/man/is_equal_knownComp.Rd | 4 admix-2.5.2/admix/man/plot.admix_model.Rd | 4 admix-2.5.2/admix/man/plot.decontaminated_density.Rd | 112 -- admix-2.5.2/admix/man/plot.twoComp_mixt.Rd | 14 admix-2.5.2/admix/man/print.admix_estim.Rd | 6 admix-2.5.2/admix/man/print.admix_model.Rd | 4 admix-2.5.2/admix/man/print.decontaminated_density.Rd | 6 admix-2.5.2/admix/man/print.twoComp_mixt.Rd | 6 admix-2.5.2/admix/man/reject_nullHyp.Rd | 28 admix-2.5.2/admix/man/summary.admix_estim.Rd | 4 admix-2.5.2/admix/man/summary.admix_model.Rd | 4 admix-2.5.2/admix/man/summary.decontaminated_density.Rd | 6 admix-2.5.2/admix/man/summary.twoComp_mixt.Rd | 6 admix-2.5.2/admix/man/twoComp_mixt.Rd | 12 admix-2.5.2/admix/man/which_rank.Rd | 30 admix-2.5.2/admix/vignettes/admixture-weight-estimation.Rmd | 6 72 files changed, 1267 insertions(+), 1153 deletions(-)
Title: Automated Functional Annotation of Genetic Variants and Linked
Proxies
Description: To automated functional annotation of genetic variants and linked proxies. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.
Author: Alireza Ani [aut, cre],
Zoha Kamali [aut],
Ahmad Vaez [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between SNPannotator versions 1.4.3 dated 2025-11-26 and 1.4.6 dated 2026-01-08
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NAMESPACE | 2 +- R/aaa.R | 2 +- R/eqtl_funcs.R | 4 +++- R/logger_funcs.R | 44 ++++++++++++++++++++++---------------------- R/misc_files.R | 2 +- R/zzz.R | 2 +- 8 files changed, 42 insertions(+), 40 deletions(-)
Title: Makefile Generator for R Analytical Projects
Description: Creates and maintains a build process for complex analytic tasks in R.
Package allows to easily generate Makefile for the (GNU) 'make' tool, which drives the build process
by (in parallel) executing build commands in order to update results accordingly to given dependencies
on changed data or updated source files.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between rmake versions 1.2.1 dated 2025-11-12 and 1.2.2 dated 2026-01-08
rmake-1.2.1/rmake/inst/doc/rmake-intro.R |only rmake-1.2.1/rmake/inst/doc/rmake-intro.Rnw |only rmake-1.2.1/rmake/inst/doc/rmake-intro.pdf |only rmake-1.2.1/rmake/vignettes/bibl.bib |only rmake-1.2.1/rmake/vignettes/pipefig.png |only rmake-1.2.1/rmake/vignettes/rmake-intro.Rnw |only rmake-1.2.2/rmake/DESCRIPTION | 10 - rmake-1.2.2/rmake/MD5 | 58 ++++++----- rmake-1.2.2/rmake/NAMESPACE | 1 rmake-1.2.2/rmake/NEWS.md | 18 ++- rmake-1.2.2/rmake/R/hasGnuMake.R |only rmake-1.2.2/rmake/R/inShell.R | 22 +++- rmake-1.2.2/rmake/R/make.R | 5 rmake-1.2.2/rmake/R/makefile.R | 12 +- rmake-1.2.2/rmake/R/rmake.R | 1 rmake-1.2.2/rmake/build/vignette.rds |binary rmake-1.2.2/rmake/inst/doc/build-rules.R |only rmake-1.2.2/rmake/inst/doc/build-rules.Rmd |only rmake-1.2.2/rmake/inst/doc/build-rules.html |only rmake-1.2.2/rmake/inst/doc/getting-started.R |only rmake-1.2.2/rmake/inst/doc/getting-started.Rmd |only rmake-1.2.2/rmake/inst/doc/getting-started.html |only rmake-1.2.2/rmake/inst/doc/project-management.R |only rmake-1.2.2/rmake/inst/doc/project-management.Rmd |only rmake-1.2.2/rmake/inst/doc/project-management.html |only rmake-1.2.2/rmake/inst/doc/tasks-and-templates.R |only rmake-1.2.2/rmake/inst/doc/tasks-and-templates.Rmd |only rmake-1.2.2/rmake/inst/doc/tasks-and-templates.html |only rmake-1.2.2/rmake/man/hasGnuMake.Rd |only rmake-1.2.2/rmake/man/rmake-package.Rd | 2 rmake-1.2.2/rmake/tests/testthat/test-inShell.R | 18 ++- rmake-1.2.2/rmake/tests/testthat/test-makefile.R | 100 +++++++++++++------ rmake-1.2.2/rmake/tests/testthat/test-markdownRule.R | 40 ++++--- rmake-1.2.2/rmake/tests/testthat/test-offlineRule.R | 8 - rmake-1.2.2/rmake/tests/testthat/test-rRule.R | 24 ++-- rmake-1.2.2/rmake/tests/testthat/test-run-simple.R | 2 rmake-1.2.2/rmake/tests/testthat/test-run-subdir.R | 1 rmake-1.2.2/rmake/tests/testthat/test-run-tasks.R | 1 rmake-1.2.2/rmake/vignettes/build-rules.Rmd |only rmake-1.2.2/rmake/vignettes/getting-started.Rmd |only rmake-1.2.2/rmake/vignettes/project-management.Rmd |only rmake-1.2.2/rmake/vignettes/tasks-and-templates.Rmd |only 42 files changed, 216 insertions(+), 107 deletions(-)
Title: Bayesian Modeling: Estimate a Computer Model and Make Uncertain
Predictions
Description: An interface to the 'BaM' (Bayesian Modeling) engine,
a 'Fortran'-based executable aimed at estimating a model
with a Bayesian approach and using it for prediction,
with a particular focus on uncertainty quantification.
Classes are defined for the various building blocks of
'BaM' inference (model, data, error models, Markov Chain Monte Carlo (MCMC) samplers, predictions).
The typical usage is as follows:
(1) specify the model to be estimated;
(2) specify the inference setting (dataset, parameters, error models...);
(3) perform Bayesian-MCMC inference;
(4) read, analyse and use MCMC samples;
(5) perform prediction experiments.
Technical details are available (in French) in
Renard (2017) <https://hal.science/hal-02606929v1>.
Examples of applications include
Mansanarez et al. (2019) <doi:10.1029/2018WR023389>,
Le Coz et al. (2021) <doi:10.1002/hyp.14169>,
Perret et al. (2021) <doi:10.1029/2020WR027745>,
Darienzo et al. (2021) <doi:10.1029/2020WR028607> and
Pe [...truncated...]
Author: Benjamin Renard [aut, cre, cph] ,
INRAE [fnd],
Ministere de la Transition Ecologique - SCHAPI [fnd]
Maintainer: Benjamin Renard <benjamin.renard@inrae.fr>
Diff between RBaM versions 1.1.1 dated 2025-09-30 and 1.1.2 dated 2026-01-08
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/RUI.R | 4 ++-- R/utilities_private.R | 2 ++ 5 files changed, 16 insertions(+), 9 deletions(-)
Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data by Normal
and Skew-Normal distributions, considering appropriate parameterizations of
the variance-covariance matrix that takes into account the intrinsic nature of
interval data, and lead to four different possible configuration structures.
The Skew-Normal parameters can be estimated by maximum likelihood, while Normal
parameters may be estimated by maximum likelihood or robust trimmed maximum
likelihood methods.
Author: Pedro Duarte Silva [aut, cre],
Paula Brito [aut]
Maintainer: Pedro Duarte Silva <psilva@ucp.pt>
Diff between MAINT.Data versions 2.7.2 dated 2025-09-15 and 2.7.3 dated 2026-01-08
CHANGELOG | 8 +++++- DESCRIPTION | 8 +++--- MD5 | 20 ++++++++-------- NAMESPACE | 2 - R/ClasGenMetDef.R | 3 +- R/IdtOutl_methods.R | 8 ------ R/fasttle.R | 56 +++++++++++++++++++++++++++++++++------------ man/IDtOutl-class.Rd | 3 +- man/MAINT.Data-internal.Rd | 5 ++-- man/MAINT.Data-package.Rd | 4 +-- man/getIdtOutl.Rd | 10 +++++++- 11 files changed, 82 insertions(+), 45 deletions(-)
Title: Functions for Community Data and Ordinations
Description: A collection of functions useful in (vegetation) community analyses and ordinations. Includes automatic species selection for ordination diagrams, NMDS stress/scree plots, species response curves, merging of taxa as well as calculation and sorting of synoptic tables.
Author: Friedemann von Lampe [aut, cre] ,
Schellenberg Jenny [aut]
Maintainer: Friedemann von Lampe <fvonlampe@uni-goettingen.de>
Diff between goeveg versions 0.7.9 dated 2025-09-03 and 0.7.10 dated 2026-01-08
DESCRIPTION | 11 +++++---- MD5 | 20 ++++++++--------- NEWS.md | 3 ++ R/sem.r | 4 +-- R/syntable.R | 19 ++++++++++++---- R/syntable_long.R | 61 +++++++++++++++++++++++++++++++++++++++++++++++++----- R/syntable_wide.R | 30 ++++++++++++++++++++++---- README.md | 2 - build/partial.rdb |binary man/sem.Rd | 4 +-- man/syntable.Rd | 14 +++++++++--- 11 files changed, 130 insertions(+), 38 deletions(-)
Title: Genetic Algorithms
Description: Flexible general-purpose toolbox implementing genetic
algorithms (GAs) for stochastic optimisation. Binary, real-valued, and
permutation representations are available to optimize a fitness
function, i.e. a function provided by users depending on their
objective function. Several genetic operators are available and can be
combined to explore the best settings for the current task.
Furthermore, users can define new genetic operators and easily
evaluate their performances. Local search using general-purpose
optimisation algorithms can be applied stochastically to exploit
interesting regions. GAs can be run sequentially or in parallel, using
an explicit master-slave parallelisation or a coarse-grain islands
approach. For more details see Scrucca (2013)
<doi:10.18637/jss.v053.i04> and Scrucca (2017)
<doi:10.32614/RJ-2017-008>.
Author: Luca Scrucca [aut, cre]
Maintainer: Luca Scrucca <luca.scrucca@unibo.it>
Diff between GA versions 3.2.4 dated 2024-01-28 and 3.2.5 dated 2026-01-08
DESCRIPTION | 15 MD5 | 32 NEWS.md | 4 R/gade.R | 1 README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/GA.R | 290 inst/doc/GA.Rmd | 15 inst/doc/GA.html |160656 ---------------------------------------------------- man/GA-package.Rd | 2 man/de.Rd | 2 man/ga.Rd | 2 man/gaisl.Rd | 4 src/RcppExports.cpp | 2 src/genope.cpp | 41 vignettes/GA.Rmd | 15 17 files changed, 325 insertions(+), 160762 deletions(-)
Title: Manage Data from the Finance Markets
Description: A set of tools designed to perform descriptive data analysis on assets, manage asset portfolios and capital allocation, and download, organize, and maintain data from the "Tehran Stock Exchange" and "NOBITEX" platforms.
Author: Ali Saeb [aut, cre]
Maintainer: Ali Saeb <ali.saeb@gmail.com>
Diff between TSEtools versions 0.2.2 dated 2023-06-20 and 1.0.0 dated 2026-01-08
DESCRIPTION | 18 +++++++++++------- MD5 | 34 ++++++++++++++++++++++++++++++---- NAMESPACE | 4 +++- R/cancel.R |only R/depth.R |only R/getNBTX.R |only R/hello.R |only R/lastPrft.R |only R/lst.R |only R/marketInfo.R |only R/orderADD.R |only R/orderBook.R |only R/orderList.R |only R/tradeInfo.R |only R/updateStatus.R |only R/walletLST.R |only README.md | 3 +++ man/cancel.Rd |only man/depth.Rd |only man/getNBTX.Rd |only man/getTSE.Rd | 2 +- man/hello.Rd |only man/lastPrft.Rd |only man/lst.Rd |only man/marketInfo.Rd |only man/orderADD.Rd |only man/orderBook.Rd |only man/orderList.Rd |only man/tradeInfo.Rd |only man/updateStatus.Rd |only man/walletLST.Rd |only 31 files changed, 48 insertions(+), 13 deletions(-)
Title: Collection of Utility Functions for Data Analysis and Computing
Description: Provides utility functions for data analysis and scientific computing. Includes functions for logging, parallel processing, and other computational tasks to streamline workflows.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between thisutils versions 0.3.1 dated 2025-11-17 and 0.3.6 dated 2026-01-08
DESCRIPTION | 10 +-- MD5 | 25 ++++--- NAMESPACE | 1 NEWS.md | 25 +++++++ R/add_pkg_file.R | 9 ++ R/log_message.R | 152 +++++++++++++++++++++++++++++------------------ R/parallelize_fun.R | 60 ++++++++---------- R/thisutils-package.R | 5 + R/utils.R | 22 ++++++ README.md | 4 - man/get_namespace_fun.Rd |only man/log_message.Rd | 23 ++++--- man/thisutils-package.Rd | 2 man/thisutils_logo.Rd | 3 14 files changed, 220 insertions(+), 121 deletions(-)
Title: Semiparametric Spatial Filtering with Eigenvectors in
(Generalized) Linear Models
Description: Tools to decompose (transformed) spatial connectivity matrices and perform supervised or unsupervised semiparametric spatial filtering in a regression framework. The package supports unsupervised spatial filtering in standard linear as well as some generalized linear regression models.
Author: Sebastian Juhl [aut, cre]
Maintainer: Sebastian Juhl <sebastian.juhl@t-online.de>
Diff between spfilteR versions 2.1.0 dated 2025-02-21 and 2.2.0 dated 2026-01-08
DESCRIPTION | 11 +- MD5 | 32 ++++---- NEWS.md | 14 +++ R/glmFilter.R | 44 ++++++----- R/lmFilter.R | 131 +++++++++++++++++++++++++++++------ R/methods.R | 2 R/utils.R | 59 +++++++++++++++- R/vp.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/spfilteR_vignette.R | 26 ++++--- inst/doc/spfilteR_vignette.Rmd | 18 +++- inst/doc/spfilteR_vignette.html | 147 ++++++++++++++++++++-------------------- man/glmFilter.Rd | 17 ++-- man/lmFilter.Rd | 57 ++++++++++++--- tests/testthat/testing.R | 131 +++++++++++++++++++++-------------- vignettes/spfilteR_vignette.Rmd | 18 +++- 17 files changed, 479 insertions(+), 232 deletions(-)
Title: Tools for Highfrequency Data Analysis
Description: Provide functionality to manage, clean and match highfrequency
trades and quotes data, calculate various liquidity measures, estimate and
forecast volatility, detect price jumps and investigate microstructure noise and intraday
periodicity. A detailed vignette can be found in the open-access paper
"Analyzing Intraday Financial Data in R: The highfrequency Package"
by Boudt, Kleen, and Sjoerup (2022, <doi:10.18637/jss.v104.i08>).
Author: Kris Boudt [aut, cre] ,
Jonathan Cornelissen [aut],
Scott Payseur [aut],
Giang Nguyen [ctb],
Onno Kleen [aut] ,
Emil Sjoerup [aut]
Maintainer: Kris Boudt <kris.boudt@ugent.be>
Diff between highfrequency versions 1.0.2 dated 2025-12-08 and 1.0.3 dated 2026-01-08
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/dataHandling.R | 8 ++++---- R/driftBursts.R | 5 +++-- R/internal.R | 6 +++++- R/jumpTests.R | 2 +- R/realizedMeasures.R | 2 +- R/spotVolAndDrift.R | 3 ++- man/spotVol.Rd | 3 ++- tests/testthat/Rplots.pdf |binary 11 files changed, 36 insertions(+), 25 deletions(-)
Title: Integrated Interface of Bayesian Single Index Models using
'nimble'
Description: Provides tools for fitting Bayesian single index models with
flexible choices of priors for both the index and the link function.
The package implements model estimation and posterior inference using
efficient MCMC algorithms built on the 'nimble' framework, allowing
users to specify, extend, and simulate models in a unified and
reproducible manner. The following methods are implemented in the
package: Antoniadis et al. (2004)
<https://www.jstor.org/stable/24307224>, Wang (2009)
<doi:10.1016/j.csda.2008.12.010>, Choi et al. (2011)
<doi:10.1080/10485251003768019>, Dhara et al. (2019)
<doi:10.1214/19-BA1170>, McGee et al. (2023) <doi:10.1111/biom.13569>.
Author: Seowoo Jung [aut, cre],
Eun-kyung Lee [aut]
Maintainer: Seowoo Jung <jsw1347@ewha.ac.kr>
Diff between BayesSIM versions 1.0.0 dated 2025-12-18 and 1.0.1 dated 2026-01-08
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/bayesSIM.R | 51 ++++++++++++++++++++++++++++++++++++++++++++++----- R/bsFisher.R | 1 - build/partial.rdb |binary 5 files changed, 53 insertions(+), 13 deletions(-)
Title: Easy Access for South Korea Census Data and Boundaries
Description: Census and administrative data in South Korea are a basic source of
quantitative and mixed-methods research for social and urban scientists.
This package provides a 'sf' (Pebesma et al., 2024 <doi:10.32614/CRAN.package.sf>)
based standardized workflow based on direct open API access to the major census and
administrative data sources and pre-generated files in South Korea.
Author: Insang Song [aut, cre] ,
Sohyun Park [aut, ctb] ,
Hyesop Shin [aut, ctb]
Maintainer: Insang Song <geoissong@snu.ac.kr>
Diff between tidycensuskr versions 0.2.5 dated 2025-11-24 and 0.2.7 dated 2026-01-08
DESCRIPTION | 11 MD5 | 55 - NEWS.md | 2 R/anycensus.R | 5 R/datasets.R | 2 README.md | 153 ++++- data/censuskor.rda |binary inst/doc/v01_intro.R | 2 inst/doc/v01_intro.Rmd | 141 ++++ inst/doc/v01_intro.html | 965 +++++++++++++++++++++++++++++++--- inst/doc/v02_regional_analysis.R | 92 +++ inst/doc/v02_regional_analysis.Rmd | 122 ++++ inst/doc/v02_regional_analysis.html | 156 +++++ inst/doc/v03_gallery.R | 119 ++++ inst/doc/v03_gallery.Rmd | 132 ++++ inst/doc/v03_gallery.html | 148 +++++ inst/doc/v04_data_cleaning_kosis.html | 4 inst/doc/v05_contributors_guide.Rmd | 41 + inst/doc/v05_contributors_guide.html | 305 ++++++++++ inst/extdata/lookup_district_code.csv | 2 man/anycensus.Rd | 5 man/censuskor.Rd | 2 man/figures/README-final_map-1.png |only man/figures/README-mapmaking-1.png |binary man/figures/README-seoul_map-1.png |binary vignettes/v01_intro.Rmd | 141 ++++ vignettes/v02_regional_analysis.Rmd | 122 ++++ vignettes/v03_gallery.Rmd | 132 ++++ vignettes/v05_contributors_guide.Rmd | 41 + 29 files changed, 2713 insertions(+), 187 deletions(-)
Title: Analyses of Text using Transformers Models from HuggingFace,
Natural Language Processing and Machine Learning
Description: Link R with Transformers from Hugging Face to transform text variables to word embeddings; where the word embeddings are used to statistically test the mean difference between set of texts, compute semantic similarity scores between texts, predict numerical variables, and visual statistically significant words according to various dimensions etc. For more information see <https://www.r-text.org>.
Author: Oscar Kjell [aut, cre] ,
Salvatore Giorgi [aut] ,
Andrew Schwartz [aut]
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Diff between text versions 1.7.0 dated 2025-09-01 and 1.8.0 dated 2026-01-08
text-1.7.0/text/tests/testthat/test_1_1_Analyses_flow_dlatk.R |only text-1.8.0/text/DESCRIPTION | 10 text-1.8.0/text/MD5 | 103 text-1.8.0/text/NAMESPACE | 3 text-1.8.0/text/NEWS.md | 11 text-1.8.0/text/R/0_0_text_install.R | 94 text-1.8.0/text/R/0_1_globals.R | 2 text-1.8.0/text/R/1_1_textEmbed.R | 1239 +++++----- text-1.8.0/text/R/2_1_1_textTrainN.R | 2 text-1.8.0/text/R/2_2_textTrainRegression.R | 13 text-1.8.0/text/R/4_0_textPlot.R | 8 text-1.8.0/text/README.md | 149 - text-1.8.0/text/build/vignette.rds |binary text-1.8.0/text/data/raw_embeddings_1.rda |binary text-1.8.0/text/inst/doc/LBAM.R | 28 text-1.8.0/text/inst/doc/LBAM.Rmd | 2 text-1.8.0/text/inst/doc/LBAM.html | 9 text-1.8.0/text/inst/doc/ext_install_guide.R | 88 text-1.8.0/text/inst/doc/ext_install_guide.html | 5 text-1.8.0/text/inst/doc/huggingface_in_r.R | 110 text-1.8.0/text/inst/doc/huggingface_in_r.html | 116 text-1.8.0/text/inst/doc/huggingface_in_r_and_computer_capacity.R | 24 text-1.8.0/text/inst/doc/implicit_motives_tutorial.R | 54 text-1.8.0/text/inst/doc/lbam_tutorial.R | 88 text-1.8.0/text/inst/doc/psychological_methods.R | 666 ++--- text-1.8.0/text/inst/doc/removing_huggingface_transformers_cache_files.R | 18 text-1.8.0/text/inst/doc/reticulate.html | 5 text-1.8.0/text/inst/doc/text.R | 131 - text-1.8.0/text/inst/doc/text.Rmd | 41 text-1.8.0/text/inst/doc/text.html | 41 text-1.8.0/text/inst/extdata/The_L-BAM_Library.csv | 51 text-1.8.0/text/inst/python/__pycache__/transformer_embs.cpython-39.pyc |binary text-1.8.0/text/inst/python/huggingface_Interface3.py | 454 +++ text-1.8.0/text/inst/python/run_DLATKGetEmbedding_test.py | 50 text-1.8.0/text/inst/python/transformer_embs.py | 93 text-1.8.0/text/man/textEmbed.Rd | 17 text-1.8.0/text/man/textEmbedRawLayers.Rd | 11 text-1.8.0/text/man/textTokenize.Rd | 7 text-1.8.0/text/man/textTrainNPlot.Rd | 5 text-1.8.0/text/man/textTrainRegression.Rd | 2 text-1.8.0/text/tests/testthat.R | 1 text-1.8.0/text/tests/testthat/_snaps/2_9_textTrainExamples/examples-error-plot.svg | 55 text-1.8.0/text/tests/testthat/_snaps/2_9_textTrainExamples/examples-histogram-plot.svg | 55 text-1.8.0/text/tests/testthat/_snaps/2_9_textTrainExamples/examples-scatter-plot.svg | 155 - text-1.8.0/text/tests/testthat/test_1_1_Analyses_flow.R | 261 -- text-1.8.0/text/tests/testthat/test_1_2_textEmbed.R | 114 text-1.8.0/text/tests/testthat/test_2_10_lbam_models.R | 127 - text-1.8.0/text/tests/testthat/test_2_1_textTrainRegression.R | 9 text-1.8.0/text/tests/testthat/test_2_2_textTrainRandomForest.R | 2 text-1.8.0/text/tests/testthat/test_2_3_textTrain_strata.R | 20 text-1.8.0/text/tests/testthat/test_PM_tutorial.R | 16 text-1.8.0/text/vignettes/LBAM.Rmd | 2 text-1.8.0/text/vignettes/text.Rmd | 41 53 files changed, 2567 insertions(+), 2041 deletions(-)
Title: Cryptographic Hash, Extendable-Output and Binary Encoding
Functions
Description: Fast and memory-efficient streaming hash functions, binary
encoding and serialization. Hashes strings and raw vectors directly.
Stream hashes files which can be larger than memory, as well as
in-memory objects through R's serialization mechanism. Implements the
SHA-256, SHA-3 and 'Keccak' cryptographic hash functions, SHAKE256
extendable-output function (XOF), 'SipHash' pseudo-random function,
base64 and base58 encoding, and 'CBOR' serialization.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between secretbase versions 1.0.5 dated 2025-03-04 and 1.1.0 dated 2026-01-08
secretbase-1.0.5/secretbase/inst |only secretbase-1.1.0/secretbase/DESCRIPTION | 50 ++-- secretbase-1.1.0/secretbase/MD5 | 46 ++-- secretbase-1.1.0/secretbase/NAMESPACE | 4 secretbase-1.1.0/secretbase/NEWS.md | 5 secretbase-1.1.0/secretbase/R/base.R | 151 ++++++++++++++ secretbase-1.1.0/secretbase/R/secret.R | 128 +++++------- secretbase-1.1.0/secretbase/R/secretbase-package.R |only secretbase-1.1.0/secretbase/README.md | 177 ++++++++++------- secretbase-1.1.0/secretbase/build/partial.rdb |binary secretbase-1.1.0/secretbase/man/base58dec.Rd |only secretbase-1.1.0/secretbase/man/base58enc.Rd |only secretbase-1.1.0/secretbase/man/cbordec.Rd |only secretbase-1.1.0/secretbase/man/cborenc.Rd |only secretbase-1.1.0/secretbase/man/keccak.Rd | 4 secretbase-1.1.0/secretbase/man/secretbase-package.Rd | 23 +- secretbase-1.1.0/secretbase/man/sha3.Rd | 4 secretbase-1.1.0/secretbase/man/shake256.Rd | 8 secretbase-1.1.0/secretbase/man/siphash13.Rd | 2 secretbase-1.1.0/secretbase/src/base.c | 48 ++-- secretbase-1.1.0/secretbase/src/base2.c |only secretbase-1.1.0/secretbase/src/base3.c |only secretbase-1.1.0/secretbase/src/init.c | 7 secretbase-1.1.0/secretbase/src/secret.c | 4 secretbase-1.1.0/secretbase/src/secret.h | 186 +++++++++++++++++- secretbase-1.1.0/secretbase/src/secret2.c | 123 +---------- secretbase-1.1.0/secretbase/src/secret3.c | 4 secretbase-1.1.0/secretbase/tests/tests.R | 144 +++++++++++++ 28 files changed, 773 insertions(+), 345 deletions(-)
Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
This is a re-admission after prior archival of version 10.0.0 dated 2025-12-06
Diff between rswipl versions 10.0.0 dated 2025-12-06 and 10.1.1 dated 2026-01-08
rswipl-10.0.0/rswipl/src/swipl |only rswipl-10.1.1/rswipl/DESCRIPTION | 8 rswipl-10.1.1/rswipl/MD5 | 6884 ++++++++++++++++---------- rswipl-10.1.1/rswipl/NEWS.md | 12 rswipl-10.1.1/rswipl/inst/patch/02-clib.patch | 10 rswipl-10.1.1/rswipl/inst/patch/03-cpp.patch | 16 rswipl-10.1.1/rswipl/inst/patch/04-cpp.patch | 4 rswipl-10.1.1/rswipl/inst/patch/patches.sh | 3 rswipl-10.1.1/rswipl/inst/patch/unpatches.sh |only rswipl-10.1.1/rswipl/inst/swipl |only rswipl-10.1.1/rswipl/src/Makevars | 18 rswipl-10.1.1/rswipl/src/Makevars.win | 2 rswipl-10.1.1/rswipl/src/install.libs.R | 2 rswipl-10.1.1/rswipl/src/swipl-devel |only 14 files changed, 4305 insertions(+), 2654 deletions(-)
Title: Simple Functions to Save Time and Memory
Description: Fast and memory-efficient (or 'cheap') tools to facilitate
efficient programming, saving time and memory. It aims to provide
'cheaper' alternatives to common base R functions, as well as some
additional functions.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cheapr versions 1.4.0 dated 2025-11-28 and 1.5.0 dated 2026-01-08
cheapr-1.4.0/cheapr/inst/include/core.h |only cheapr-1.4.0/cheapr/src/decls.h |only cheapr-1.4.0/cheapr/src/set_math.cpp |only cheapr-1.5.0/cheapr/DESCRIPTION | 6 cheapr-1.5.0/cheapr/MD5 | 110 - cheapr-1.5.0/cheapr/NAMESPACE | 26 cheapr-1.5.0/cheapr/NEWS.md | 49 cheapr-1.5.0/cheapr/R/cpp11.R | 954 +++++----- cheapr-1.5.0/cheapr/R/lists.R | 4 cheapr-1.5.0/cheapr/R/math.R |only cheapr-1.5.0/cheapr/R/new_vector.R |only cheapr-1.5.0/cheapr/R/scalars.R | 20 cheapr-1.5.0/cheapr/R/set_math.R | 7 cheapr-1.5.0/cheapr/R/threads.R |only cheapr-1.5.0/cheapr/R/zzz.R | 14 cheapr-1.5.0/cheapr/README.md | 476 ++-- cheapr-1.5.0/cheapr/inst/include/cheapr |only cheapr-1.5.0/cheapr/inst/include/cheapr_api.h | 115 - cheapr-1.5.0/cheapr/man/figures/README-unnamed-chunk-53-1.png |only cheapr-1.5.0/cheapr/man/figures/README-unnamed-chunk-53-2.png |only cheapr-1.5.0/cheapr/man/figures/README-unnamed-chunk-60-1.png |only cheapr-1.5.0/cheapr/man/figures/README-unnamed-chunk-60-2.png |only cheapr-1.5.0/cheapr/man/math.Rd |only cheapr-1.5.0/cheapr/man/new_vector.Rd |only cheapr-1.5.0/cheapr/man/set_math.Rd | 10 cheapr-1.5.0/cheapr/man/threads.Rd |only cheapr-1.5.0/cheapr/src/altrep.cpp | 68 cheapr-1.5.0/cheapr/src/api.cpp | 166 - cheapr-1.5.0/cheapr/src/attrs.cpp | 82 cheapr-1.5.0/cheapr/src/cast.cpp | 94 cheapr-1.5.0/cheapr/src/cast.h | 642 +++--- cheapr-1.5.0/cheapr/src/cheapr.h | 10 cheapr-1.5.0/cheapr/src/combine.cpp | 748 +++---- cheapr-1.5.0/cheapr/src/conditions.cpp | 532 ++--- cheapr-1.5.0/cheapr/src/cpp11.cpp | 390 ++-- cheapr-1.5.0/cheapr/src/declarations.h |only cheapr-1.5.0/cheapr/src/gcd.cpp | 380 +-- cheapr-1.5.0/cheapr/src/groups.cpp | 28 cheapr-1.5.0/cheapr/src/int64.cpp | 125 - cheapr-1.5.0/cheapr/src/internal_helpers.h |only cheapr-1.5.0/cheapr/src/lag.cpp | 426 +--- cheapr-1.5.0/cheapr/src/lists.cpp | 646 +----- cheapr-1.5.0/cheapr/src/math.cpp |only cheapr-1.5.0/cheapr/src/nas.cpp | 470 ++-- cheapr-1.5.0/cheapr/src/replace.cpp | 107 - cheapr-1.5.0/cheapr/src/scalars.cpp | 325 +-- cheapr-1.5.0/cheapr/src/sequences.cpp | 177 - cheapr-1.5.0/cheapr/src/sset.cpp | 726 +++---- cheapr-1.5.0/cheapr/src/strings.cpp | 91 cheapr-1.5.0/cheapr/src/types.h | 5 cheapr-1.5.0/cheapr/src/utils.cpp | 579 ++---- cheapr-1.5.0/cheapr/src/variadic.h | 28 cheapr-1.5.0/cheapr/src/which.cpp | 251 -- cheapr-1.5.0/cheapr/tests/testthat.R | 2 cheapr-1.5.0/cheapr/tests/testthat/test-combine.R | 9 cheapr-1.5.0/cheapr/tests/testthat/test-data_frame.R | 2 cheapr-1.5.0/cheapr/tests/testthat/test-gcd.R | 22 cheapr-1.5.0/cheapr/tests/testthat/test-is_whole_number.R |only cheapr-1.5.0/cheapr/tests/testthat/test-math.R |only cheapr-1.5.0/cheapr/tests/testthat/test-nas.R | 5 cheapr-1.5.0/cheapr/tests/testthat/test-set_math.R | 4 cheapr-1.5.0/cheapr/tests/testthat/test-sset.R | 2 cheapr-1.5.0/cheapr/tests/testthat/test-valgrind.R |only cheapr-1.5.0/cheapr/tests/testthat/test_bin.R | 3 64 files changed, 4105 insertions(+), 4831 deletions(-)
Title: Custom Gov Style Inputs for Shiny
Description: Collection of 'shiny' application styling that are the based
on the GOV.UK Design System. See
<https://design-system.service.gov.uk/components/> for details.
Author: Ross Wyatt [aut],
Cam Race [aut, cre],
Sarah Wong [aut],
Richard Bielby [ctb],
Charlotte Foster [ctb],
Jeni Martin [ctb]
Maintainer: Cam Race <camrace8@gmail.com>
Diff between shinyGovstyle versions 0.1.0 dated 2024-09-12 and 0.1.1 dated 2026-01-08
DESCRIPTION | 26 MD5 | 253 NAMESPACE | 96 NEWS.md | 4 R/accordion.R | 256 R/attachDependency.R | 162 R/backlink_Input.R | 110 R/banner.R | 80 R/checkbox_input.R | 214 R/clean_heading_text.R | 26 R/contents_links.R | 570 - R/cookieBanner.R | 300 R/date_Input.R | 226 R/details.R | 80 R/error_off.R | 118 R/error_on.R | 128 R/error_sum_update.R | 110 R/error_summary.R | 130 R/file_Input.R | 246 R/font.R | 66 R/footer.R | 172 R/govLayouts.R | 238 R/govTable.R | 236 R/govTabs.R | 276 R/gov_button.R | 148 R/gov_layout.R | 88 R/header.R | 158 R/heading_text.R | 74 R/input_field.R | 176 R/insert_text.R | 72 R/label_hint.R | 74 R/noti_banner.R | 106 R/panel_output.R | 78 R/radio_button_input.R | 504 R/run_example.R | 868 - R/select_input.R | 94 R/summary.R | 162 R/tag.R | 84 R/text_area_input.R | 106 R/text_input.R | 220 R/utils-pipe.R | 28 R/warning_text.R | 76 R/word_count.R | 122 R/zzz.R | 22 README.md | 1332 +- inst/www/css/font.css | 68 inst/www/css/govuk-frontend-norem.css |15434 +++++++++++++++--------------- inst/www/images/favicon.svg | 2 inst/www/js/accordion.js | 206 inst/www/js/contents_link.js | 126 inst/www/js/date_input_binding.js | 110 inst/www/js/govTab.js | 36 inst/www/js/govuk-frontend-5.4.0.min.js | 2 inst/www/js/radio_button_input_binding.js | 132 man/accordion.Rd | 108 man/backlink_Input.Rd | 114 man/banner.Rd | 80 man/button_Input.Rd | 86 man/checkbox_Input.Rd | 180 man/clean_heading_text.Rd | 40 man/contents_link.Rd | 414 man/cookieBanner.Rd | 130 man/date_Input.Rd | 170 man/details.Rd | 88 man/error_off.Rd | 124 man/error_on.Rd | 130 man/error_summary.Rd | 116 man/error_summary_update.Rd | 112 man/file_Input.Rd | 184 man/font.Rd | 66 man/footer.Rd | 78 man/govTable.Rd | 138 man/govTabs.Rd | 102 man/gov_layout.Rd | 94 man/gov_summary.Rd | 114 man/header.Rd | 108 man/heading_text.Rd | 78 man/input_field.Rd | 160 man/insert_text.Rd | 84 man/label_hint.Rd | 86 man/layouts.Rd | 180 man/noti_banner.Rd | 98 man/panel_output.Rd | 86 man/pipe.Rd | 40 man/radio_button_Input.Rd | 218 man/run_example.Rd | 40 man/select_Input.Rd | 98 man/subcontents_links.Rd | 104 man/tag_Input.Rd | 80 man/text_Input.Rd | 186 man/text_area_Input.Rd | 90 man/warning_text.Rd | 78 man/word_count.Rd | 108 tests/testthat.R | 8 tests/testthat/_snaps |only tests/testthat/test-accordion.R | 36 tests/testthat/test-backlink_Input.R | 17 tests/testthat/test-banner.R | 26 tests/testthat/test-checkbox_input.R | 142 tests/testthat/test-clean_heading_text.R | 16 tests/testthat/test-contents_links.R | 56 tests/testthat/test-cookieBanner.R | 54 tests/testthat/test-date_Input.R | 120 tests/testthat/test-details.R | 30 tests/testthat/test-error_summary.R | 96 tests/testthat/test-file_Input.R | 84 tests/testthat/test-font.R | 14 tests/testthat/test-footer.R | 42 tests/testthat/test-govTable.R | 56 tests/testthat/test-govTabs.R | 52 tests/testthat/test-gov_button.R | 170 tests/testthat/test-gov_layout.R | 40 tests/testthat/test-header.R | 16 tests/testthat/test-heading_text.R | 66 tests/testthat/test-input_field.R | 58 tests/testthat/test-insert_text.R | 38 tests/testthat/test-label_hint.R | 28 tests/testthat/test-noti_banner.R | 68 tests/testthat/test-panel_output.R | 26 tests/testthat/test-radio_button_input.R | 188 tests/testthat/test-run_example.R | 24 tests/testthat/test-select_input.R | 34 tests/testthat/test-subcontents_links.R | 38 tests/testthat/test-summary.R | 42 tests/testthat/test-tag.R | 52 tests/testthat/test-text_area_input.R | 128 tests/testthat/test-text_input.R | 122 tests/testthat/test-warning_text.R | 20 128 files changed, 15716 insertions(+), 15712 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] ,
Florian De Boissieu [ctb] ,
Andrew Sanchez Meador [ctb] for
segment_snags),
Bourdon Jean-Francois [ctb] for
track_sensor),
Gatziolis Demetrios [ctb] for
track_sensor),
Leon Steinmeier [c [...truncated...]
Maintainer: Jean-Romain Roussel <info@r-lidar.com>
Diff between lidR versions 4.2.2 dated 2025-11-06 and 4.2.3 dated 2026-01-08
DESCRIPTION | 8 ++--- MD5 | 50 ++++++++++++++++++------------------ NEWS.md | 5 +++ R/Class-LAS.R | 4 +- R/add_attribute.R | 2 - R/classify.R | 2 - R/las_tools.R | 2 - R/rasterize.R | 2 - R/utils_threads.R | 2 - build/vignette.rds |binary inst/doc/lidR-LAS-class.Rmd | 6 ++-- inst/doc/lidR-LAS-class.html | 6 ++-- inst/doc/lidR-LAScatalog-class.Rmd | 2 - inst/doc/lidR-LAScatalog-class.html | 2 - inst/include/lidR/Grid3D.h | 30 ++++++++------------- man/LAS-class.Rd | 2 - man/LASheader-class.Rd | 2 - man/add_attribute.Rd | 2 - man/classify.Rd | 2 - man/las_utilities.Rd | 2 - man/rasterize.Rd | 2 - src/altrep.cpp | 17 ++++++++++-- src/knn.cpp | 2 - tests/testthat/Rplots.pdf |binary vignettes/lidR-LAS-class.Rmd | 6 ++-- vignettes/lidR-LAScatalog-class.Rmd | 2 - 26 files changed, 86 insertions(+), 76 deletions(-)
Title: Fast Functional Mixed Models using Fast Univariate Inference
Description: Implementation of the fast univariate inference approach (Cui et al. (2022) <doi:10.1080/10618600.2021.1950006>, Loewinger et al. (2024) <doi:10.7554/eLife.95802.2>, Xin et al. (2025)) for fitting functional mixed models. User guides and Python package information can be found at <https://github.com/gloewing/photometry_FLMM>.
Author: Erjia Cui [aut],
Gabriel Loewinger [aut],
Al Xin [aut, cre]
Maintainer: Al Xin <axin@andrew.cmu.edu>
Diff between fastFMM versions 0.4.0 dated 2025-03-13 and 1.0.0 dated 2026-01-08
fastFMM-0.4.0/fastFMM/R/all_crossterms.R |only fastFMM-0.4.0/fastFMM/R/cov_nnls.R |only fastFMM-0.4.0/fastFMM/R/pspline_setting.R |only fastFMM-0.4.0/fastFMM/R/select_knots.R |only fastFMM-0.4.0/fastFMM/README.md |only fastFMM-0.4.0/fastFMM/inst/doc/fastFMM-vignette.R |only fastFMM-0.4.0/fastFMM/inst/doc/fastFMM-vignette.Rmd |only fastFMM-0.4.0/fastFMM/inst/doc/fastFMM-vignette.pdf |only fastFMM-0.4.0/fastFMM/man/all_crossterms.Rd |only fastFMM-0.4.0/fastFMM/man/pspline_setting.Rd |only fastFMM-0.4.0/fastFMM/vignettes/fastFMM-vignette.Rmd |only fastFMM-0.4.0/fastFMM/vignettes/time_series.csv |only fastFMM-1.0.0/fastFMM/DESCRIPTION | 26 fastFMM-1.0.0/fastFMM/MD5 | 85 fastFMM-1.0.0/fastFMM/NAMESPACE | 91 fastFMM-1.0.0/fastFMM/NEWS.md | 54 fastFMM-1.0.0/fastFMM/R/G_estimate.R | 494 +++- fastFMM-1.0.0/fastFMM/R/G_estimate_randint.R | 111 fastFMM-1.0.0/fastFMM/R/G_generate.R | 394 ++- fastFMM-1.0.0/fastFMM/R/d2pvt-data.R |only fastFMM-1.0.0/fastFMM/R/fastFMM.R |only fastFMM-1.0.0/fastFMM/R/fui.R | 2169 ++++--------------- fastFMM-1.0.0/fastFMM/R/globals.R | 2 fastFMM-1.0.0/fastFMM/R/lick-data.R |only fastFMM-1.0.0/fastFMM/R/massmm.R |only fastFMM-1.0.0/fastFMM/R/plot_fui.R | 426 ++- fastFMM-1.0.0/fastFMM/R/unimm.R | 359 ++- fastFMM-1.0.0/fastFMM/R/utils.R |only fastFMM-1.0.0/fastFMM/R/var_analytic.R |only fastFMM-1.0.0/fastFMM/R/var_bootstrap.R |only fastFMM-1.0.0/fastFMM/R/var_parallel.R |only fastFMM-1.0.0/fastFMM/build/partial.rdb |only fastFMM-1.0.0/fastFMM/build/vignette.rds |binary fastFMM-1.0.0/fastFMM/data |only fastFMM-1.0.0/fastFMM/inst/WORDLIST | 146 - fastFMM-1.0.0/fastFMM/inst/doc/d2pvt.R |only fastFMM-1.0.0/fastFMM/inst/doc/d2pvt.Rmd |only fastFMM-1.0.0/fastFMM/inst/doc/d2pvt.html |only fastFMM-1.0.0/fastFMM/inst/doc/fastFMM.R |only fastFMM-1.0.0/fastFMM/inst/doc/fastFMM.Rmd |only fastFMM-1.0.0/fastFMM/inst/doc/fastFMM.html |only fastFMM-1.0.0/fastFMM/man/G_estimate.Rd | 52 fastFMM-1.0.0/fastFMM/man/G_estimate_randint.Rd | 15 fastFMM-1.0.0/fastFMM/man/G_generate.Rd | 26 fastFMM-1.0.0/fastFMM/man/bdiag_m.Rd |only fastFMM-1.0.0/fastFMM/man/cov_nnls.Rd | 37 fastFMM-1.0.0/fastFMM/man/cov_organize_start.Rd |only fastFMM-1.0.0/fastFMM/man/d2pvt.Rd |only fastFMM-1.0.0/fastFMM/man/fui.Rd | 339 +- fastFMM-1.0.0/fastFMM/man/lick.Rd |only fastFMM-1.0.0/fastFMM/man/massmm.Rd |only fastFMM-1.0.0/fastFMM/man/new_fastFMM.Rd |only fastFMM-1.0.0/fastFMM/man/new_fastFMMconc.Rd |only fastFMM-1.0.0/fastFMM/man/plot_fui.Rd | 158 - fastFMM-1.0.0/fastFMM/man/select_knots.Rd | 49 fastFMM-1.0.0/fastFMM/man/unimm.Rd | 31 fastFMM-1.0.0/fastFMM/man/var_analytic.Rd |only fastFMM-1.0.0/fastFMM/man/var_bootstrap.Rd |only fastFMM-1.0.0/fastFMM/man/var_parallel.Rd |only fastFMM-1.0.0/fastFMM/man/var_parallel.fastFMM.Rd |only fastFMM-1.0.0/fastFMM/tests/spelling.R | 6 fastFMM-1.0.0/fastFMM/vignettes/d2pvt.Rmd |only fastFMM-1.0.0/fastFMM/vignettes/fastFMM.Rmd |only fastFMM-1.0.0/fastFMM/vignettes/vignettes.bib |only 64 files changed, 2227 insertions(+), 2843 deletions(-)
Title: Data Quality in Epidemiological Research
Description: Data quality assessments guided by a
'data quality framework introduced by Schmidt and colleagues, 2021'
<doi:10.1186/s12874-021-01252-7> target the
data quality dimensions integrity, completeness, consistency, and
accuracy. The scope of applicable functions rests on the
availability of extensive metadata which can be provided in
spreadsheet tables. Either standardized (e.g. as 'html5' reports) or
individually tailored reports can be generated. For an introduction
into the specification of corresponding metadata, please refer to the
'package website'
<https://dataquality.qihs.uni-greifswald.de/VIN_Annotation_of_Metadata.html>.
Author: University Medicine Greifswald [cph],
Elisa Kasbohm [aut] ,
Elena Salogni [aut] ,
Joany Marino [aut] ,
Adrian Richter [aut] ,
Carsten Oliver Schmidt [aut] ,
Stephan Struckmann [aut, cre] ,
German Research Foundation [fnd],
National Research Data Inf [...truncated...]
Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>
Diff between dataquieR versions 2.8.2 dated 2025-12-22 and 2.8.7 dated 2026-01-08
DESCRIPTION | 6 - MD5 | 47 ++++++---- NAMESPACE | 2 NEWS.md | 26 +++++ R/000_exception_classes.R | 21 ++++ R/print.dataquieR_resultset2.R | 11 ++ R/reflection.R | 1 R/util_condition_constructor_factory.R | 15 +++ R/util_evaluate_calls.R | 7 - R/util_generate_pages_from_report.R | 10 +- R/zzz_globs.R | 12 +- build/vignette.rds |binary inst/menu/script.js | 3 inst/menu/style_toplevel.css | 5 - inst/report-dt-style/report-dt-style.css | 6 + inst/templates/default/iframe.html | 6 + inst/templates/default/report.html | 6 + man/dataquieR.applicability_problem.Rd |only man/dataquieR.intrinsic_applicability_problem.Rd |only man/figures |only tests/testthat/helper_no_testthat.R |only tests/testthat/test-dq_report2.R | 107 ++++++++++++++++++++--- tests/testthat/test-prep_render_pie_charts.R | 2 23 files changed, 244 insertions(+), 49 deletions(-)
Title: Clustering
Description: A tool that implements the clustering algorithms from 'mothur' (Schloss PD et al. (2009) <doi:10.1128/AEM.01541-09>). 'clustur' make use of the cluster() and make.shared() command from 'mothur'. Our cluster() function has five different algorithms implemented: 'OptiClust', 'furthest', 'nearest', 'average', and 'weighted'. 'OptiClust' is an optimized clustering method for Operational Taxonomic Units, and you can learn more here, (Westcott SL, Schloss PD (2017) <doi:10.1128/mspheredirect.00073-17>). The make.shared() command is always applied at the end of the clustering command. This functionality allows us to generate and create clustering and abundance data efficiently.
Author: Gregory Johnson [aut] ,
Sarah Westcott [aut],
Patrick Schloss [aut, cre, cph]
Maintainer: Patrick Schloss <pschloss@umich.edu>
Diff between clustur versions 0.1.3 dated 2025-04-21 and 0.1.4 dated 2026-01-08
clustur-0.1.3/clustur/src/MothurDependencies/CountTable.h |only clustur-0.1.4/clustur/DESCRIPTION | 14 - clustur-0.1.4/clustur/MD5 | 122 +++++----- clustur-0.1.4/clustur/NEWS.md | 9 clustur-0.1.4/clustur/R/cluster.R | 39 ++- clustur-0.1.4/clustur/R/cluster_data_converters.R | 2 clustur-0.1.4/clustur/R/cluster_object-getters.R | 18 - clustur-0.1.4/clustur/R/distance_object-getters.R | 8 clustur-0.1.4/clustur/README.md | 1 clustur-0.1.4/clustur/build/partial.rdb |binary clustur-0.1.4/clustur/build/vignette.rds |binary clustur-0.1.4/clustur/inst/doc/clustur.html | 10 clustur-0.1.4/clustur/src/Adapters/CountTableAdapter.h | 16 - clustur-0.1.4/clustur/src/Adapters/DistanceFileReader.h | 19 - clustur-0.1.4/clustur/src/Adapters/MatrixAdapter.h | 2 clustur-0.1.4/clustur/src/ClusterCommand.cpp | 32 +- clustur-0.1.4/clustur/src/ClusterExportTestFixture.cpp | 22 - clustur-0.1.4/clustur/src/ColumnDistanceMatrixReader.cpp | 70 +++-- clustur-0.1.4/clustur/src/ColumnReaderTestFixture.cpp | 29 +- clustur-0.1.4/clustur/src/CountTableAdapter.cpp | 34 +- clustur-0.1.4/clustur/src/CountTableAdapterTestFixture.cpp | 1 clustur-0.1.4/clustur/src/DataStructures |only clustur-0.1.4/clustur/src/DistanceFileReader.cpp | 31 +- clustur-0.1.4/clustur/src/ListVector.cpp | 2 clustur-0.1.4/clustur/src/MatrixAdapter.cpp | 52 ++-- clustur-0.1.4/clustur/src/MatrixAdapterTestFixture.cpp | 25 -- clustur-0.1.4/clustur/src/MothurDependencies/ClusterExport.h | 20 - clustur-0.1.4/clustur/src/MothurDependencies/ColumnDistanceMatrixReader.h | 5 clustur-0.1.4/clustur/src/MothurDependencies/DataVector.h | 2 clustur-0.1.4/clustur/src/MothurDependencies/ListVector.h | 2 clustur-0.1.4/clustur/src/MothurDependencies/OptiCluster.h | 4 clustur-0.1.4/clustur/src/MothurDependencies/OptiData.h | 4 clustur-0.1.4/clustur/src/MothurDependencies/RAbundVector.h | 2 clustur-0.1.4/clustur/src/MothurDependencies/ReadPhylipMatrix.h | 5 clustur-0.1.4/clustur/src/MothurDependencies/SparseDistanceMatrix.h | 1 clustur-0.1.4/clustur/src/MothurDependencies/Utils.h | 1 clustur-0.1.4/clustur/src/MothurDependencies/WeightedLinkage.h | 2 clustur-0.1.4/clustur/src/OptiCluster.cpp | 13 - clustur-0.1.4/clustur/src/OptiClusterTestFixture.cpp | 2 clustur-0.1.4/clustur/src/OptiData.cpp | 20 + clustur-0.1.4/clustur/src/OptiDataTestFixture.cpp | 1 clustur-0.1.4/clustur/src/OptimatrixAdapterTestFixture.cpp | 13 - clustur-0.1.4/clustur/src/PhylipReaderTestFixture.cpp | 25 +- clustur-0.1.4/clustur/src/RAbundVector.cpp | 4 clustur-0.1.4/clustur/src/RAbundVectorTestFixture.cpp | 5 clustur-0.1.4/clustur/src/ReadPhylipMatrix.cpp | 36 +- clustur-0.1.4/clustur/src/SharedFileBuilderTestFixture.cpp | 4 clustur-0.1.4/clustur/src/SharedFileTestFixture.cpp | 8 clustur-0.1.4/clustur/src/SparseDistanceMatrix.cpp | 5 clustur-0.1.4/clustur/src/SparseMatrixTestFixture.cpp | 4 clustur-0.1.4/clustur/src/Tests/ClusterExportTestFixture.h | 4 clustur-0.1.4/clustur/src/Tests/MatrixAdapterTestFixture.h | 5 clustur-0.1.4/clustur/src/Tests/SharedFileTestFixture.h | 1 clustur-0.1.4/clustur/src/Utils.cpp | 1 clustur-0.1.4/clustur/src/main.cpp | 39 ++- clustur-0.1.4/clustur/src/test-cluster.cpp | 42 +-- clustur-0.1.4/clustur/src/test-cluster_export.cpp | 8 clustur-0.1.4/clustur/src/test-column_reader_test_fixture.cpp | 20 + clustur-0.1.4/clustur/src/test-matrix_adapter.cpp | 34 ++ clustur-0.1.4/clustur/src/test-optimatrix-adapter.cpp | 40 ++- clustur-0.1.4/clustur/src/test-read_phylip.cpp | 5 clustur-0.1.4/clustur/src/test-utils.cpp | 1 clustur-0.1.4/clustur/tests/testthat/test-test-opticluster.R | 17 + 63 files changed, 564 insertions(+), 399 deletions(-)
Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Description: Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
Author: Guangchuang Yu [aut, cre, cph] ,
Bradley Jones [ctb],
Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between tidytree versions 0.4.6 dated 2023-12-12 and 0.4.7 dated 2026-01-08
tidytree-0.4.6/tidytree/build |only tidytree-0.4.6/tidytree/inst/doc |only tidytree-0.4.6/tidytree/vignettes |only tidytree-0.4.7/tidytree/DESCRIPTION | 20 - tidytree-0.4.7/tidytree/MD5 | 87 ++---- tidytree-0.4.7/tidytree/NAMESPACE | 4 tidytree-0.4.7/tidytree/NEWS.md | 8 tidytree-0.4.7/tidytree/R/AllClasses.R | 72 ++--- tidytree-0.4.7/tidytree/R/AllGenerics.R | 340 ++++++++++++------------ tidytree-0.4.7/tidytree/R/ancestor.R | 98 ++++-- tidytree-0.4.7/tidytree/R/ape.R | 73 ++--- tidytree-0.4.7/tidytree/R/as-tibble.R | 33 +- tidytree-0.4.7/tidytree/R/converter.R | 36 +- tidytree-0.4.7/tidytree/R/filter.R | 14 tidytree-0.4.7/tidytree/R/full-join.R | 23 + tidytree-0.4.7/tidytree/R/get-data.R | 18 - tidytree-0.4.7/tidytree/R/get-fields.R | 6 tidytree-0.4.7/tidytree/R/groupClade.R | 4 tidytree-0.4.7/tidytree/R/groupOTU.R | 12 tidytree-0.4.7/tidytree/R/isTip.R | 18 - tidytree-0.4.7/tidytree/R/method-MRCA.R | 8 tidytree-0.4.7/tidytree/R/method-accessor.R | 10 tidytree-0.4.7/tidytree/R/method-drop-tip.R | 50 +-- tidytree-0.4.7/tidytree/R/method-get-treetext.R | 10 tidytree-0.4.7/tidytree/R/method-groupClade.R | 10 tidytree-0.4.7/tidytree/R/method-groupOTU.R | 30 +- tidytree-0.4.7/tidytree/R/method-merge.R | 4 tidytree-0.4.7/tidytree/R/method-reroot.R | 98 +++--- tidytree-0.4.7/tidytree/R/mutate.R | 10 tidytree-0.4.7/tidytree/R/nodeid.R | 24 - tidytree-0.4.7/tidytree/R/offspring.R | 68 ++-- tidytree-0.4.7/tidytree/R/pull.R | 8 tidytree-0.4.7/tidytree/R/reexports.R | 72 ++--- tidytree-0.4.7/tidytree/R/rename.R | 10 tidytree-0.4.7/tidytree/R/select.R | 14 tidytree-0.4.7/tidytree/R/show.R | 36 +- tidytree-0.4.7/tidytree/R/sibling.R | 8 tidytree-0.4.7/tidytree/R/tidy-package.R |only tidytree-0.4.7/tidytree/R/tree-subset.R | 4 tidytree-0.4.7/tidytree/R/zzz.R | 66 ---- tidytree-0.4.7/tidytree/inst/CITATION | 11 tidytree-0.4.7/tidytree/man/drop.tip-methods.Rd | 4 tidytree-0.4.7/tidytree/man/groupClade.Rd | 2 tidytree-0.4.7/tidytree/man/node.label.Rd | 2 tidytree-0.4.7/tidytree/man/tidytree-package.Rd |only tidytree-0.4.7/tidytree/man/tip.label.Rd | 2 46 files changed, 715 insertions(+), 712 deletions(-)
Title: Tidy Plots for Scientific Papers
Description: The goal of 'tidyplots' is to streamline the creation of publication-ready plots for scientific papers. It allows to gradually add, remove and adjust plot components using a consistent and intuitive syntax.
Author: Jan Broder Engler [aut, cre, cph]
Maintainer: Jan Broder Engler <broder.engler@gmail.com>
Diff between tidyplots versions 0.3.1 dated 2025-07-02 and 0.4.0 dated 2026-01-08
DESCRIPTION | 14 MD5 | 572 +++++----- NEWS.md | 29 R/aaa.R | 2 R/add-annotation.R | 51 R/add-general.R | 5 R/add-heatmap.R | 2 R/add-misc.R | 4 R/add-points.R | 9 R/add-proportional.R | 15 R/add-stats.R | 22 R/adjust.R | 111 + R/colors.R | 17 R/data_levels.R | 10 R/facet-ext.R |only R/facet-grid-ext.R |only R/facet-wrap-ext.R |only R/helpers.R | 30 R/plot.R | 183 ++- R/themes.R | 159 +- README.md | 3 inst/doc/tidyplots.html | 43 man/add_annotation_text.Rd | 4 man/add_barstack_absolute.Rd | 3 man/add_count_bar.Rd | 3 man/add_data_labels.Rd | 6 man/add_data_points.Rd | 7 man/add_mean_bar.Rd | 3 man/add_median_bar.Rd | 3 man/add_sum_bar.Rd | 3 man/add_test_pvalue.Rd | 6 man/add_violin.Rd | 4 man/adjust_font.Rd | 4 man/adjust_legend_title.Rd | 2 man/adjust_size.Rd | 17 man/adjust_title.Rd | 8 man/adjust_x_axis.Rd | 4 man/common_arguments.Rd | 5 man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png 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Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra.
Differences with other sparse matrix packages are:
(1) we only support (essentially) one sparse matrix format,
(2) based on transparent and simple structure(s),
(3) tailored for MCMC calculations within G(M)RF.
(4) and it is fast and scalable (with the extension package spam64).
Documentation about 'spam' is provided by vignettes included in this package, see also Furrer and Sain (2010) <doi:10.18637/jss.v036.i10>; see 'citation("spam")' for details.
Author: Reinhard Furrer [aut, cre] ,
Florian Gerber [aut] ,
Roman Flury [aut] ,
Daniel Gerber [ctb],
Kaspar Moesinger [ctb],
Annina Cincera [ctb],
Youcef Saad [ctb] ,
Esmond G. Ng [ctb] ,
Barry W. Peyton [ctb] ,
Joseph W.H. Liu [ctb] ,
Alan D. George [ctb] , [...truncated...]
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>
Diff between spam versions 2.11-1 dated 2025-01-20 and 2.11-3 dated 2026-01-08
spam-2.11-1/spam/R/tmp.R |only spam-2.11-1/spam/inst/doc/jss15.pdf |only spam-2.11-1/spam/inst/doc/jss15.pdf.asis |only spam-2.11-1/spam/vignettes/jss15.pdf.asis |only spam-2.11-3/spam/DESCRIPTION | 15 ++-- spam-2.11-3/spam/MD5 | 51 ++++++-------- spam-2.11-3/spam/NEWS.md | 23 ++++++ spam-2.11-3/spam/R/diff.R | 11 ++- spam-2.11-3/spam/R/kronecker.R | 2 spam-2.11-3/spam/build/partial.rdb |binary spam-2.11-3/spam/build/vignette.rds |binary spam-2.11-3/spam/inst/CITATION | 6 - spam-2.11-3/spam/inst/doc/spam.R | 6 - spam-2.11-3/spam/inst/doc/spam.pdf |binary spam-2.11-3/spam/man/gmult.Rd | 8 +- spam-2.11-3/spam/man/options.Rd | 6 - spam-2.11-3/spam/man/spam-package.Rd | 2 spam-2.11-3/spam/tests/Examples |only spam-2.11-3/spam/tests/demo_cholesky.Rout.save | 8 +- spam-2.11-3/spam/tests/demo_jss10-example1.Rout.save | 8 +- spam-2.11-3/spam/tests/demo_jss10-figures-table.Rout.save | 8 +- spam-2.11-3/spam/tests/demo_jss15-BYM.Rout.save | 8 +- spam-2.11-3/spam/tests/demo_jss15-Leroux.Rout.save | 8 +- spam-2.11-3/spam/tests/demo_spam.Rout.save | 8 +- spam-2.11-3/spam/tests/demo_timing.Rout.save | 8 +- spam-2.11-3/spam/tests/jss_areal_counts.Rout.save | 8 +- spam-2.11-3/spam/tests/testthat.Rout.save | 10 +- spam-2.11-3/spam/tests/testthat/test-diff.R | 3 spam-2.11-3/spam/vignettes/spam.bib | 2 29 files changed, 119 insertions(+), 90 deletions(-)
Title: Efficient Bayesian Inference for Time-Varying Parameter Models
with Shrinkage
Description: Efficient Markov chain Monte Carlo (MCMC) algorithms for fully Bayesian estimation of time-varying parameter models with shrinkage priors, both dynamic and static. Details on the algorithms used are provided in Bitto and Frühwirth-Schnatter (2019) <doi:10.1016/j.jeconom.2018.11.006> and
Cadonna et al. (2020) <doi:10.3390/econometrics8020020> and Knaus and Frühwirth-Schnatter (2023) <doi:10.48550/arXiv.2312.10487>. For details on the package, please see Knaus et al. (2021) <doi:10.18637/jss.v100.i13>. For the multivariate extension, see the 'shrinkTVPVAR' package.
Author: Peter Knaus [aut, cre] ,
Angela Bitto-Nemling [aut],
Annalisa Cadonna [aut] ,
Sylvia Fruehwirth-Schnatter [aut] ,
Daniel Winkler [ctb],
Kemal Dingic [ctb]
Maintainer: Peter Knaus <peter.knaus@wu.ac.at>
Diff between shrinkTVP versions 3.1.0 dated 2025-06-02 and 3.1.1 dated 2026-01-08
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/shrinkTVP_methods.R | 3 +++ build/vignette.rds |binary inst/doc/shrinkTVP.ltx | 2 +- inst/doc/shrinkTVP.pdf |binary vignettes/shrinkTVP.bib | 11 +++++------ vignettes/shrinkTVP.ltx | 2 +- 9 files changed, 26 insertions(+), 19 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut],
Namita Gupta [aut],
Susanna Marquez [aut, cre],
Julian Zhou [aut],
Nima Nouri [aut],
Noah Yann Lee [aut],
Ang Cui [ctb],
Jason Vander Heiden [aut],
Gur Yaari [aut],
Steven Kleinstein [aut, cph]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between shazam versions 1.3.0 dated 2025-10-20 and 1.3.1 dated 2026-01-08
DESCRIPTION | 8 +++---- MD5 | 24 +++++++++++----------- NEWS.md | 10 +++++++++ R/MutationProfiling.R | 20 +++++++++++------- R/TargetingModels.R | 4 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Baseline-Vignette.pdf |binary inst/doc/DistToNearest-Vignette.pdf |binary inst/doc/Mutation-Vignette.pdf |binary inst/doc/Shmulate-Vignette.pdf |binary inst/doc/Targeting-Vignette.pdf |binary man/distToNearest.Rd | 38 ++++++++++++++++++++++-------------- 13 files changed, 65 insertions(+), 39 deletions(-)
Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Description: Implements spatial and spatiotemporal GLMMs (Generalized Linear
Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial
Differential Equation) Gaussian Markov random field approximation to
Gaussian random fields. One common application is for spatially explicit
species distribution models (SDMs).
See Anderson et al. (2024) <doi:10.1101/2022.03.24.485545>.
Author: Sean C. Anderson [aut, cre] ,
Eric J. Ward [aut] ,
Philina A. English [aut] ,
Lewis A. K. Barnett [aut] ,
James T. Thorson [aut, cph] ,
Joe Watson [ctb] ,
Julia Indivero [ctb] ,
Jillian C. Dunic [ctb] ,
Joseph Barss [ctb],
Cole C. Monnahan [ctb, cph] [...truncated...]
Maintainer: Sean C. Anderson <sean@seananderson.ca>
Diff between sdmTMB versions 0.8.0 dated 2025-11-26 and 0.8.1 dated 2026-01-08
DESCRIPTION | 14 +- MD5 | 33 +++--- NEWS.md | 35 +++++++ R/fit.R | 11 +- R/get-range-edge.R | 148 ++++++++++++++---------------- R/index.R | 99 ++++++++++---------- R/parsing.R | 12 -- R/predict.R | 21 +++- R/print.R | 15 +-- R/residuals.R | 53 ++++++++++ R/utils.R | 26 +++++ man/get_range_edge.Rd | 3 src/sdmTMB.cpp | 98 +++++++------------ src/utils.h | 23 ++++ tests/testthat/test-4-index-calculation.R | 5 - tests/testthat/test-extra-time.R | 32 ++++++ tests/testthat/test-index.R | 57 +++++++++++ tests/testthat/test-se-fit.R |only 18 files changed, 444 insertions(+), 241 deletions(-)
Title: Easily Access and Maintain Time-Based Versioned Data
(Slowly-Changing-Dimension)
Description: A collection of functions that enable easy access and updating of a database of data over time.
More specifically, the package facilitates type-2 history for data-warehouses and provides a number
of Quality of life improvements for working on SQL databases with R.
For reference see Ralph Kimball and Margy Ross (2013, ISBN 9781118530801).
Author: Rasmus Skytte Randloev [aut, cre, rev] ,
Marcus Munch Gruenewald [aut] ,
Lasse Engbo Christiansen [rev, ctb] ,
Sofia Myrup Otero [rev],
Kim Daniel Jacobsen [ctb],
Statens Serum Institut [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>
Diff between SCDB versions 0.5.1 dated 2025-02-27 and 0.5.2 dated 2026-01-08
DESCRIPTION | 25 +- MD5 | 82 ++++----- NEWS.md | 17 + R/0_miscellaneous.R | 3 R/Logger.R | 3 R/db_timestamp.R | 43 ++++ R/filter_keys.R | 6 R/getTableSignature.R | 68 ++++--- R/get_tables.R | 2 R/helpers.R | 2 R/update_snapshot.R | 20 +- build/vignette.rds |binary inst/doc/SCDB.html | 16 - inst/doc/benchmarks.html | 4 inst/doc/slowly-changing-dimension.R | 280 ++++++++++++++++---------------- inst/doc/slowly-changing-dimension.html | 145 ++-------------- inst/extdata/benchmarks.rds |binary man/SCDB-package.Rd | 2 man/close_connection.Rd | 2 man/create_index.Rd | 2 man/create_logs_if_missing.Rd | 2 man/create_table.Rd | 2 man/db_locks.Rd | 2 man/db_timestamp.Rd | 2 man/defer_db_cleanup.Rd | 2 man/get_connection.Rd | 2 man/get_schema.Rd | 2 man/get_table.Rd | 2 man/get_tables.Rd | 2 man/interlace.Rd | 2 man/is.historical.Rd | 2 man/joins.Rd | 2 man/nrow.Rd | 2 man/schema_exists.Rd | 2 man/slice_time.Rd | 2 man/table_exists.Rd | 2 man/unite.tbl_dbi.Rd | 2 man/update_snapshot.Rd | 2 tests/testthat/test-Logger.R | 21 +- tests/testthat/test-db_timestamp.R | 70 +++++++- tests/testthat/test-filter_keys.R | 6 tests/testthat/test-getTableSignature.R | 4 42 files changed, 462 insertions(+), 397 deletions(-)
Title: Exporting Tools for 'rtables'
Description: Designed to create and display complex tables with R, the
'rtables' R package allows cells in an 'rtables' object to contain any
high-dimensional data structure, which can then be displayed with
cell-specific formatting instructions. Additionally, the
'rtables.officer' package supports export formats related to the
Microsoft Office software suite, including Microsoft Word ('docx') and
Microsoft PowerPoint ('pptx').
Author: Gabriel Becker [ctb],
Davide Garolini [aut] ,
Emily de la Rua [aut] ,
Abinaya Yogasekaram [aut] ,
Joe Zhu [aut, cre] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between rtables.officer versions 0.1.1 dated 2025-09-23 and 0.1.2 dated 2026-01-08
DESCRIPTION | 29 MD5 | 24 NAMESPACE | 39 - NEWS.md | 4 R/as_flextable.R | 1130 +++++++++++++++++------------------ R/package.R | 25 R/theme_defaults.R | 733 +++++++++++----------- inst/doc/export_rlistings.html | 10 inst/doc/rtables.officer.html | 12 man/rtables.officer-package.Rd | 78 +- man/tt_to_flextable.Rd | 542 ++++++++-------- tests/testthat/test-as_flextable.R | 559 +++++++++-------- tests/testthat/test-export_as_docx.R | 264 ++++---- 13 files changed, 1755 insertions(+), 1694 deletions(-)
More information about rtables.officer at CRAN
Permanent link
Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart()
in the 'rpart' package.
Author: Stephen Milborrow [aut, cre]
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between rpart.plot versions 3.1.3 dated 2025-07-26 and 3.1.4 dated 2026-01-08
DESCRIPTION | 6 ++--- MD5 | 34 +++++++++++++++---------------- NEWS.md | 4 +++ inst/doc/prp.pdf |binary inst/slowtests/rpart.report.bat | 2 - inst/slowtests/test.describe.col.bat | 2 - inst/slowtests/test.imports.bat | 2 - inst/slowtests/test.na.bat | 2 - inst/slowtests/test.palette.bat | 2 - inst/slowtests/test.rpart.plot.Rout.save | 12 +++++----- inst/slowtests/test.rpart.plot.bat | 2 - inst/slowtests/test.rpart.rules.bat | 2 - inst/slowtests/test.type5.bat | 2 - inst/slowtests/usersplits.bat | 2 - inst/slowtests/vignette.bat | 2 - inst/slowtests/webpage.figs.bat | 2 - man/prp.Rd | 6 +++-- man/rpart.plot.Rd | 4 ++- 18 files changed, 48 insertions(+), 40 deletions(-)
Title: Radiocarbon Equations
Description: Provides functions for the calibration of radiocarbon dates, as well as options to calculate different radiocarbon-related timescales (cal BP, cal BC/AD, C14 age, F14C, pMC, D14C) and estimating the effects of contamination or local reservoir offsets (Reimer and Reimer 2001 <doi:10.1017/S0033822200038339>). The methods follow long-established recommendations such as Stuiver and Polach (1977) <doi:10.1017/S0033822200003672> and Reimer et al. (2004) <doi:10.1017/S0033822200033154>. This package uses the calibration curves from the data package 'rintcal'.
Author: Maarten Blaauw [aut, cre] ,
Paula Reimer [ctb] ,
Vegard Martinsen [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rice versions 1.5.0 dated 2025-12-15 and 1.6.0 dated 2026-01-08
rice-1.5.0/rice/man/calibrate.table.Rd |only rice-1.6.0/rice/DESCRIPTION | 19 + rice-1.6.0/rice/MD5 | 74 +++--- rice-1.6.0/rice/NAMESPACE | 2 rice-1.6.0/rice/NEWS.md | 9 rice-1.6.0/rice/R/calibrate.R | 163 ++++++++------ rice-1.6.0/rice/R/marine.R | 4 rice-1.6.0/rice/R/plots.R | 120 +++++----- rice-1.6.0/rice/R/rice.R | 40 ++- rice-1.6.0/rice/R/sets.R | 8 rice-1.6.0/rice/R/sources.R | 2 rice-1.6.0/rice/R/timescales.R | 31 +- rice-1.6.0/rice/build/partial.rdb |binary rice-1.6.0/rice/build/vignette.rds |binary rice-1.6.0/rice/data/shells.rda |binary rice-1.6.0/rice/inst/doc/rice.R | 10 rice-1.6.0/rice/inst/doc/rice.Rmd | 19 + rice-1.6.0/rice/inst/doc/rice.html | 322 +++++++++++++++-------------- rice-1.6.0/rice/man/age.range.Rd | 2 rice-1.6.0/rice/man/caldist.Rd | 10 rice-1.6.0/rice/man/calibratable.Rd |only rice-1.6.0/rice/man/calibrate.Rd | 14 - rice-1.6.0/rice/man/draw.ccurve.Rd | 3 rice-1.6.0/rice/man/draw.dates.Rd | 9 rice-1.6.0/rice/man/howmuchC14.Rd | 10 rice-1.6.0/rice/man/hpd.Rd | 2 rice-1.6.0/rice/man/hpd.overlap.Rd | 2 rice-1.6.0/rice/man/l.calib.Rd | 2 rice-1.6.0/rice/man/older.Rd | 3 rice-1.6.0/rice/man/overlap.Rd | 2 rice-1.6.0/rice/man/p.range.Rd | 3 rice-1.6.0/rice/man/point.estimates.Rd | 2 rice-1.6.0/rice/man/r.calib.Rd | 5 rice-1.6.0/rice/man/rice-package.Rd | 6 rice-1.6.0/rice/man/rice.Rd | 6 rice-1.6.0/rice/man/span.Rd | 4 rice-1.6.0/rice/man/younger.Rd | 3 rice-1.6.0/rice/tests/testthat/test-rice.R | 16 - rice-1.6.0/rice/vignettes/rice.Rmd | 19 + 39 files changed, 537 insertions(+), 409 deletions(-)
Title: Estimation and Validation Methods for Subgroup Identification
and Personalized Medicine
Description: Provides functions for fitting and validation of models for subgroup
identification and personalized medicine / precision medicine under the general subgroup
identification framework of Chen et al. (2017) <doi:10.1111/biom.12676>.
This package is intended for use for both randomized controlled trials and
observational studies and is described in detail in Huling and Yu (2021)
<doi:10.18637/jss.v098.i05>.
Author: Jared Huling [aut, cre] ,
Aaron Potvien [ctb],
Alexandros Karatzoglou [cph],
Alex Smola [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between personalized versions 0.2.7 dated 2022-06-27 and 0.2.8 dated 2026-01-08
DESCRIPTION | 14 MD5 | 42 - NAMESPACE | 3 R/fit_subgroup.R | 75 +- R/validate_subgroup.R | 2 R/weighted_svm.R | 2 R/xgboost_functions.R | 498 +++++++++++--- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 inst/doc/efficiency_augmentation_personalized.html | 243 +++---- inst/doc/fitting_itrs_with_xgboost.R | 18 inst/doc/fitting_itrs_with_xgboost.Rmd | 8 inst/doc/fitting_itrs_with_xgboost.html | 333 +++++---- inst/doc/multicategory_treatments_with_personalized.html | 393 +++++------ inst/doc/usage_of_the_personalized_package.R | 2 inst/doc/usage_of_the_personalized_package.html | 507 +++++++-------- man/fit.subgroup.Rd | 67 + man/validate.subgroup.Rd | 2 man/weighted.ksvm.Rd | 2 vignettes/fitting_itrs_with_xgboost.Rmd | 8 22 files changed, 1280 insertions(+), 945 deletions(-)
Title: Datasets for "Statistics: UnLocking the Power of Data"
Description: Datasets for the fourth edition of "Statistics: Unlocking the Power of Data" by Lock^5
Includes versions of datasets from earlier editions.
Author: Robin Lock [aut, cre]
Maintainer: Robin Lock <rlock@stlawu.edu>
Diff between Lock5Data versions 3.0.0 dated 2021-07-22 and 4.0.1 dated 2026-01-08
Lock5Data-3.0.0/Lock5Data/data/Flight433.rda |only Lock5Data-3.0.0/Lock5Data/data/Honeybee.rda |only Lock5Data-3.0.0/Lock5Data/man/Flight433.Rd |only Lock5Data-3.0.0/Lock5Data/man/Honeybee.Rd |only Lock5Data-3.0.0/Lock5Data/man/Lock5Data-package.Rd |only Lock5Data-4.0.1/Lock5Data/DESCRIPTION | 12 Lock5Data-4.0.1/Lock5Data/MD5 | 355 ++++++++---- Lock5Data-4.0.1/Lock5Data/NAMESPACE | 3 Lock5Data-4.0.1/Lock5Data/NEWS.md | 13 Lock5Data-4.0.1/Lock5Data/data/ACS.rda |binary Lock5Data-4.0.1/Lock5Data/data/ACS3e.rda |only Lock5Data-4.0.1/Lock5Data/data/AllCountries.rda |binary Lock5Data-4.0.1/Lock5Data/data/AllCountries3e.rda |only Lock5Data-4.0.1/Lock5Data/data/April14Temps.rda |binary Lock5Data-4.0.1/Lock5Data/data/April14Temps3e.rda |only Lock5Data-4.0.1/Lock5Data/data/BMI.rda |only Lock5Data-4.0.1/Lock5Data/data/BaseballHits2024.rda |only Lock5Data-4.0.1/Lock5Data/data/BaseballSalaries2024.rda |only Lock5Data-4.0.1/Lock5Data/data/BaseballTimes.rda |binary Lock5Data-4.0.1/Lock5Data/data/BaseballTimes1e.rda |only Lock5Data-4.0.1/Lock5Data/data/COVIDCollege.rda |only Lock5Data-4.0.1/Lock5Data/data/COVIDCollegeStacked.rda |only Lock5Data-4.0.1/Lock5Data/data/CarDepreciation.rda |binary Lock5Data-4.0.1/Lock5Data/data/CarDepreciation3e.rda |only Lock5Data-4.0.1/Lock5Data/data/CarbonDioxide.rda |binary Lock5Data-4.0.1/Lock5Data/data/CarbonDioxide3e.rda |only Lock5Data-4.0.1/Lock5Data/data/Cars2025.rda |only Lock5Data-4.0.1/Lock5Data/data/CarsEV2025.rda |only Lock5Data-4.0.1/Lock5Data/data/Celtics2024.rda |only Lock5Data-4.0.1/Lock5Data/data/CityTemps.rda |binary Lock5Data-4.0.1/Lock5Data/data/CityTemps3e.rda |only Lock5Data-4.0.1/Lock5Data/data/CollegeExperience.rda |only Lock5Data-4.0.1/Lock5Data/data/CollegeScores.rda |binary Lock5Data-4.0.1/Lock5Data/data/CollegeScores2yr.rda |binary Lock5Data-4.0.1/Lock5Data/data/CollegeScores2yr3e.rda |only Lock5Data-4.0.1/Lock5Data/data/CollegeScores3e.rda |only Lock5Data-4.0.1/Lock5Data/data/CollegeScores4yr.rda |binary Lock5Data-4.0.1/Lock5Data/data/CollegeScores4yr3e.rda |only Lock5Data-4.0.1/Lock5Data/data/DecemberFlights.rda |binary Lock5Data-4.0.1/Lock5Data/data/DecemberFlights3e.rda |only Lock5Data-4.0.1/Lock5Data/data/EducationLiteracy.rda |binary Lock5Data-4.0.1/Lock5Data/data/EducationLiteracy3e.rda |only Lock5Data-4.0.1/Lock5Data/data/ElectionMargin.rda |binary Lock5Data-4.0.1/Lock5Data/data/ElectionMargin2012.rda |only Lock5Data-4.0.1/Lock5Data/data/EmployedACS.rda |binary Lock5Data-4.0.1/Lock5Data/data/EmployedACS3e.rda |only Lock5Data-4.0.1/Lock5Data/data/Flight433_3e.rda |only Lock5Data-4.0.1/Lock5Data/data/Flight475.rda |only Lock5Data-4.0.1/Lock5Data/data/GlobalInternet2024.rda |only Lock5Data-4.0.1/Lock5Data/data/GroundhogDay.rda |only Lock5Data-4.0.1/Lock5Data/data/HappyPlanetIndex.rda |binary Lock5Data-4.0.1/Lock5Data/data/HappyPlanetIndex2010.rda |only Lock5Data-4.0.1/Lock5Data/data/HockeyPenalties2025.rda |only Lock5Data-4.0.1/Lock5Data/data/HollywoodMovies.rda |binary Lock5Data-4.0.1/Lock5Data/data/HollywoodMovies2018.rda |only Lock5Data-4.0.1/Lock5Data/data/HomesForSale.rda |binary Lock5Data-4.0.1/Lock5Data/data/HomesForSale3e.rda |only Lock5Data-4.0.1/Lock5Data/data/HomesForSaleCA.rda |binary Lock5Data-4.0.1/Lock5Data/data/HomesForSaleCA3e.rda |only Lock5Data-4.0.1/Lock5Data/data/HomesForSaleCanton.rda |binary Lock5Data-4.0.1/Lock5Data/data/HomesForSaleCanton3e.rda |only Lock5Data-4.0.1/Lock5Data/data/HomesForSaleNY.rda |binary Lock5Data-4.0.1/Lock5Data/data/HomesForSaleNY3e.rda |only Lock5Data-4.0.1/Lock5Data/data/Honeybee2012.rda |only Lock5Data-4.0.1/Lock5Data/data/Honeybee2023.rda |only Lock5Data-4.0.1/Lock5Data/data/HotDogs2024.rda |only Lock5Data-4.0.1/Lock5Data/data/HouseStarts2024.rda |only Lock5Data-4.0.1/Lock5Data/data/Hurricanes2024.rda |only Lock5Data-4.0.1/Lock5Data/data/InkjetPrinters.rda |binary Lock5Data-4.0.1/Lock5Data/data/InkjetPrinters1e.rda |only Lock5Data-4.0.1/Lock5Data/data/LifeExpectancyVehicles.rda |binary Lock5Data-4.0.1/Lock5Data/data/LifeExpectancyVehicles3e.rda |only Lock5Data-4.0.1/Lock5Data/data/ManhattanApartments.rda |binary Lock5Data-4.0.1/Lock5Data/data/ManhattanApartments2019.rda |only Lock5Data-4.0.1/Lock5Data/data/MustangPrice.rda |binary Lock5Data-4.0.1/Lock5Data/data/MustangPrice1e.rda |only Lock5Data-4.0.1/Lock5Data/data/NBAPlayers2024.rda |only Lock5Data-4.0.1/Lock5Data/data/NBAStandings2024.rda |only Lock5Data-4.0.1/Lock5Data/data/NFLContracts2024.rda |only Lock5Data-4.0.1/Lock5Data/data/NFLPreseason2024.rda |only Lock5Data-4.0.1/Lock5Data/data/NFLScores2024.rda |only Lock5Data-4.0.1/Lock5Data/data/Ninja.rda |only Lock5Data-4.0.1/Lock5Data/data/OlympicMarathon2024.rda |only Lock5Data-4.0.1/Lock5Data/data/OttawaSenators2024.rda |only Lock5Data-4.0.1/Lock5Data/data/PASeniors.rda |binary Lock5Data-4.0.1/Lock5Data/data/PASeniors2019.rda |only Lock5Data-4.0.1/Lock5Data/data/ProcessedFoods.rda |only Lock5Data-4.0.1/Lock5Data/data/PublicLibraries.rda |only Lock5Data-4.0.1/Lock5Data/data/RestaurantTips.rda |binary Lock5Data-4.0.1/Lock5Data/data/RestaurantTips1e.rda |only Lock5Data-4.0.1/Lock5Data/data/RetailSales.rda |binary Lock5Data-4.0.1/Lock5Data/data/RetailSales3e.rda |only Lock5Data-4.0.1/Lock5Data/data/RockandRoll2024.rda |only Lock5Data-4.0.1/Lock5Data/data/RollerCoasters.rda |only Lock5Data-4.0.1/Lock5Data/data/SalaryBySex.rda |only Lock5Data-4.0.1/Lock5Data/data/SampColleges.rda |binary Lock5Data-4.0.1/Lock5Data/data/SampColleges2yr.rda |binary Lock5Data-4.0.1/Lock5Data/data/SampColleges2yr3e.rda |only Lock5Data-4.0.1/Lock5Data/data/SampColleges3e.rda |only Lock5Data-4.0.1/Lock5Data/data/SampColleges4yr.rda |binary Lock5Data-4.0.1/Lock5Data/data/SampColleges4yr3e.rda |only Lock5Data-4.0.1/Lock5Data/data/SampCountries.rda |binary Lock5Data-4.0.1/Lock5Data/data/SampCountries3e.rda |only Lock5Data-4.0.1/Lock5Data/data/SandP500.rda |binary Lock5Data-4.0.1/Lock5Data/data/SandP5003e.rda |only Lock5Data-4.0.1/Lock5Data/data/Showers.rda |only Lock5Data-4.0.1/Lock5Data/data/SkateboardPrices.rda |binary Lock5Data-4.0.1/Lock5Data/data/SkateboardPrices2012.rda |only Lock5Data-4.0.1/Lock5Data/data/StockChanges.rda |binary Lock5Data-4.0.1/Lock5Data/data/StockChanges1e.rda |only Lock5Data-4.0.1/Lock5Data/data/TenCountries.rda |binary Lock5Data-4.0.1/Lock5Data/data/TenCountries3e.rda |only Lock5Data-4.0.1/Lock5Data/data/TextbookCosts.rda |binary Lock5Data-4.0.1/Lock5Data/data/TextbookCosts2011.rda |only Lock5Data-4.0.1/Lock5Data/data/USStates.rda |binary Lock5Data-4.0.1/Lock5Data/data/USStates3e.rda |only Lock5Data-4.0.1/Lock5Data/data/XylitolEffect.rda |only Lock5Data-4.0.1/Lock5Data/man/ACS.Rd | 13 Lock5Data-4.0.1/Lock5Data/man/ACS3e.Rd |only Lock5Data-4.0.1/Lock5Data/man/AllCountries.Rd | 20 Lock5Data-4.0.1/Lock5Data/man/AllCountries1e.Rd | 2 Lock5Data-4.0.1/Lock5Data/man/AllCountries2e.Rd | 2 Lock5Data-4.0.1/Lock5Data/man/AllCountries3e.Rd |only Lock5Data-4.0.1/Lock5Data/man/April14Temps.Rd | 14 Lock5Data-4.0.1/Lock5Data/man/April14Temps1e.Rd | 2 Lock5Data-4.0.1/Lock5Data/man/April14Temps3e.Rd |only Lock5Data-4.0.1/Lock5Data/man/BMI.Rd |only Lock5Data-4.0.1/Lock5Data/man/BaseballHits2019.Rd | 2 Lock5Data-4.0.1/Lock5Data/man/BaseballHits2024.Rd |only Lock5Data-4.0.1/Lock5Data/man/BaseballSalaries2024.Rd |only Lock5Data-4.0.1/Lock5Data/man/BaseballTimes.Rd | 10 Lock5Data-4.0.1/Lock5Data/man/BaseballTimes1e.Rd |only Lock5Data-4.0.1/Lock5Data/man/BodyTemp50.Rd | 2 Lock5Data-4.0.1/Lock5Data/man/COVIDCollege.Rd |only Lock5Data-4.0.1/Lock5Data/man/COVIDCollegeStacked.Rd |only Lock5Data-4.0.1/Lock5Data/man/CarDepreciation.Rd | 13 Lock5Data-4.0.1/Lock5Data/man/CarDepreciation3e.Rd |only Lock5Data-4.0.1/Lock5Data/man/CarbonDioxide.Rd | 10 Lock5Data-4.0.1/Lock5Data/man/CarbonDioxide3e.Rd |only Lock5Data-4.0.1/Lock5Data/man/Cars2015.Rd | 88 +- Lock5Data-4.0.1/Lock5Data/man/Cars2020.Rd | 2 Lock5Data-4.0.1/Lock5Data/man/Cars2025.Rd |only Lock5Data-4.0.1/Lock5Data/man/Cars2025EV.Rd |only Lock5Data-4.0.1/Lock5Data/man/Celtics2024.Rd |only Lock5Data-4.0.1/Lock5Data/man/CityTemps.Rd | 12 Lock5Data-4.0.1/Lock5Data/man/CityTemps3e.Rd |only Lock5Data-4.0.1/Lock5Data/man/CollegeExperience.Rd |only Lock5Data-4.0.1/Lock5Data/man/CollegeScores.Rd | 18 Lock5Data-4.0.1/Lock5Data/man/CollegeScores2yr.Rd | 18 Lock5Data-4.0.1/Lock5Data/man/CollegeScores2yr3e.Rd |only Lock5Data-4.0.1/Lock5Data/man/CollegeScores3e.Rd |only Lock5Data-4.0.1/Lock5Data/man/CollegeScores4yr.Rd | 18 Lock5Data-4.0.1/Lock5Data/man/CollegeScores4yr3e.Rd |only Lock5Data-4.0.1/Lock5Data/man/DecemberFlights.Rd | 6 Lock5Data-4.0.1/Lock5Data/man/DecemberFlights2e.Rd | 2 Lock5Data-4.0.1/Lock5Data/man/DecemberFlights3e.Rd |only Lock5Data-4.0.1/Lock5Data/man/EducationLiteracy.Rd | 8 Lock5Data-4.0.1/Lock5Data/man/EducationLiteracy2e.Rd | 2 Lock5Data-4.0.1/Lock5Data/man/EducationLiteracy3e.Rd |only Lock5Data-4.0.1/Lock5Data/man/ElectionMargin.Rd | 6 Lock5Data-4.0.1/Lock5Data/man/ElectionMargin2012.Rd |only Lock5Data-4.0.1/Lock5Data/man/EmployedACS.Rd | 16 Lock5Data-4.0.1/Lock5Data/man/EmployedACS2017.Rd |only Lock5Data-4.0.1/Lock5Data/man/Flight433_3e.Rd |only Lock5Data-4.0.1/Lock5Data/man/Flight475.Rd |only Lock5Data-4.0.1/Lock5Data/man/FootballBrain.Rd | 2 Lock5Data-4.0.1/Lock5Data/man/ForestFires.Rd | 4 Lock5Data-4.0.1/Lock5Data/man/GlobalInternet2019.Rd | 4 Lock5Data-4.0.1/Lock5Data/man/GlobalInternet2024.Rd |only Lock5Data-4.0.1/Lock5Data/man/GroundhogDay.Rd |only Lock5Data-4.0.1/Lock5Data/man/HappyPlanetIndex.Rd | 27 Lock5Data-4.0.1/Lock5Data/man/HappyPlanetIndex2010.Rd |only Lock5Data-4.0.1/Lock5Data/man/HockeyPenalties2025.Rd |only Lock5Data-4.0.1/Lock5Data/man/HollywoodMovies.Rd | 39 - Lock5Data-4.0.1/Lock5Data/man/HollywoodMovies2018.Rd |only Lock5Data-4.0.1/Lock5Data/man/HomesForSale.Rd | 17 Lock5Data-4.0.1/Lock5Data/man/HomesForSale3e.Rd |only 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Title: Easy Visualization of Conditional Effects from Regression Models
Description: Offers a flexible and user-friendly interface for visualizing conditional
effects from a broad range of regression models, including mixed-effects and generalized
additive (mixed) models. Compatible model types include lm(), rlm(), glm(), glm.nb(),
betareg(), and gam() (from 'mgcv'); nonlinear models via nls(); generalized least
squares via gls(); and survival models via coxph() (from 'survival').
Mixed-effects models with random intercepts and/or slopes can be fitted using lmer(),
glmer(), glmer.nb(), glmmTMB(), or gam() (from 'mgcv', via smooth terms).
Plots are rendered using base R graphics with extensive customization options.
Approximate confidence intervals for nls() and betareg() models are computed using
the delta method. Robust standard errors for rlm() are computed using the sandwich
estimator (Zeileis 2004) <doi:10.18637/jss.v011.i10>. For beta regression using
'betareg', see Cribari-Neto and Zeileis (2010) <doi:10.18637/jss.v034.i02>. For
mixed-effects models w [...truncated...]
Author: Luca Corlatti [aut, cre]
Maintainer: Luca Corlatti <lucac1980@yahoo.it>
Diff between easyViz versions 1.2.0 dated 2025-11-30 and 2.0.0 dated 2026-01-08
easyViz-1.2.0/easyViz/R/easyViz_1.2.0.R |only easyViz-2.0.0/easyViz/DESCRIPTION | 32 easyViz-2.0.0/easyViz/MD5 | 20 easyViz-2.0.0/easyViz/NAMESPACE | 7 easyViz-2.0.0/easyViz/NEWS.md | 57 + easyViz-2.0.0/easyViz/R/easyViz.R |only easyViz-2.0.0/easyViz/R/ez-backtransform.R |only easyViz-2.0.0/easyViz/R/ez-build-output.R |only easyViz-2.0.0/easyViz/R/ez-newdata.R |only easyViz-2.0.0/easyViz/R/ez-plot-categorical.R |only easyViz-2.0.0/easyViz/R/ez-plot-dispatch.R |only easyViz-2.0.0/easyViz/R/ez-plot-numeric.R |only easyViz-2.0.0/easyViz/R/ez-predictions.R |only easyViz-2.0.0/easyViz/R/ez-prepare-data.R |only easyViz-2.0.0/easyViz/R/ez-utils.R |only easyViz-2.0.0/easyViz/R/print.easyviz_pred_df.R |only easyViz-2.0.0/easyViz/man/easyViz.Rd | 770 ++++++++++++++---------- 17 files changed, 576 insertions(+), 310 deletions(-)
Title: Reinforcement Learning Tools for Two-Alternative Forced Choice
Tasks
Description: Tools for building Rescorla-Wagner Models for Two-Alternative
Forced Choice tasks, commonly employed in psychological research.
Most concepts and ideas within this R package are referenced from
Sutton and Barto (2018) <ISBN:9780262039246>.
The package allows for the intuitive definition of RL models using simple
if-else statements and three basic models built into this R package are
referenced from
Niv et al. (2012) <doi:10.1523/JNEUROSCI.5498-10.2012>.
Our approach to constructing and evaluating these computational models
is informed by the guidelines proposed in
Wilson & Collins (2019) <doi:10.7554/eLife.49547>.
Example datasets included with the package are sourced from the work of
Mason et al. (2024) <doi:10.3758/s13423-023-02415-x>.
Author: YuKi [aut, cre]
Maintainer: YuKi <hmz1969a@gmail.com>
Diff between binaryRL versions 0.9.8 dated 2025-10-28 and 0.9.9 dated 2026-01-08
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- R/2_arrange_data.R | 2 +- R/7_digits.R | 43 ++++++++++++++++++++++++------------------- R/8_output.R | 6 +++--- R/process_optimize_para.R | 10 +++++++--- R/step1_run_m.R | 4 ++-- build/partial.rdb |binary man/binaryRL-package.Rd | 2 +- man/run_m.Rd | 4 ++-- src/5_decision_making.cpp | 1 + 11 files changed, 56 insertions(+), 46 deletions(-)
Title: Manage the Life Cycle of your Package Functions
Description: Manage the life cycle of your exported functions with shared
conventions, documentation badges, and user-friendly deprecation
warnings.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between lifecycle versions 1.0.4 dated 2023-11-07 and 1.0.5 dated 2026-01-08
lifecycle-1.0.4/lifecycle/R/compat-obj-type.R |only lifecycle-1.0.4/lifecycle/R/compat-types-check.R |only lifecycle-1.0.4/lifecycle/man/lint_lifecycle.Rd |only lifecycle-1.0.4/lifecycle/man/signal_experimental.Rd |only lifecycle-1.0.5/lifecycle/DESCRIPTION | 16 lifecycle-1.0.5/lifecycle/MD5 | 82 +-- lifecycle-1.0.5/lifecycle/NAMESPACE | 1 lifecycle-1.0.5/lifecycle/NEWS.md | 20 lifecycle-1.0.5/lifecycle/R/deprecate.R | 255 ++++++----- lifecycle-1.0.5/lifecycle/R/expect.R | 2 lifecycle-1.0.5/lifecycle/R/import-standalone-obj-type.R |only lifecycle-1.0.5/lifecycle/R/import-standalone-types-check.R |only lifecycle-1.0.5/lifecycle/R/lint.R | 223 +++++++-- lifecycle-1.0.5/lifecycle/R/signal.R | 78 +-- lifecycle-1.0.5/lifecycle/R/spec.R | 10 lifecycle-1.0.5/lifecycle/R/utils.R | 17 lifecycle-1.0.5/lifecycle/R/verbosity.R | 24 - lifecycle-1.0.5/lifecycle/README.md | 2 lifecycle-1.0.5/lifecycle/build/vignette.rds |binary lifecycle-1.0.5/lifecycle/inst/doc/communicate.R | 42 - lifecycle-1.0.5/lifecycle/inst/doc/communicate.Rmd | 20 lifecycle-1.0.5/lifecycle/inst/doc/communicate.html | 224 ++++----- lifecycle-1.0.5/lifecycle/inst/doc/manage.R | 16 lifecycle-1.0.5/lifecycle/inst/doc/stages.R | 12 lifecycle-1.0.5/lifecycle/inst/doc/stages.Rmd | 6 lifecycle-1.0.5/lifecycle/inst/doc/stages.html | 6 lifecycle-1.0.5/lifecycle/inst/lintr |only lifecycle-1.0.5/lifecycle/man/deprecate_soft.Rd | 19 lifecycle-1.0.5/lifecycle/man/deprecated-signallers.Rd |only lifecycle-1.0.5/lifecycle/man/expect_deprecated.Rd | 2 lifecycle-1.0.5/lifecycle/man/lifecycle-package.Rd | 6 lifecycle-1.0.5/lifecycle/man/lifecycle_linter.Rd |only lifecycle-1.0.5/lifecycle/man/signal_stage.Rd | 23 lifecycle-1.0.5/lifecycle/man/verbosity.Rd | 2 lifecycle-1.0.5/lifecycle/tests/testthat/_snaps/deprecate.md | 24 - lifecycle-1.0.5/lifecycle/tests/testthat/_snaps/lifecycle.md |only lifecycle-1.0.5/lifecycle/tests/testthat/_snaps/signal.md | 30 - lifecycle-1.0.5/lifecycle/tests/testthat/_snaps/spec.md | 2 lifecycle-1.0.5/lifecycle/tests/testthat/_snaps/warning.md | 2 lifecycle-1.0.5/lifecycle/tests/testthat/helper-lifecycle.R | 12 lifecycle-1.0.5/lifecycle/tests/testthat/helper-zeallot.R | 8 lifecycle-1.0.5/lifecycle/tests/testthat/test-deprecate.R | 79 ++- lifecycle-1.0.5/lifecycle/tests/testthat/test-lifecycle.R | 50 +- lifecycle-1.0.5/lifecycle/tests/testthat/test-signal.R | 24 - lifecycle-1.0.5/lifecycle/tests/testthat/test-warning.R | 3 lifecycle-1.0.5/lifecycle/vignettes/communicate.Rmd | 20 lifecycle-1.0.5/lifecycle/vignettes/stages.Rmd | 6 47 files changed, 783 insertions(+), 585 deletions(-)
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' <https://libgit2.org> with
support for SSH and HTTPS remotes. All functions in 'gert' use basic R data
types (such as vectors and data-frames) for their arguments and return values.
User credentials are shared with command line 'git' through the git-credential
store and ssh keys stored on disk or ssh-agent.
Author: Jeroen Ooms [aut, cre] ,
Jennifer Bryan [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between gert versions 2.2.0 dated 2025-11-16 and 2.3.0 dated 2026-01-08
DESCRIPTION | 8 +- MD5 | 88 +++++++++++++++-------------- NAMESPACE | 21 ++++++ NEWS | 4 + R/archive.R | 18 +++-- R/branch.R | 52 +++++++++++------ R/certs.R | 24 ++++--- R/commit.R | 67 ++++++++++++---------- R/config.R | 12 +-- R/credentials.R | 59 +++++++++++-------- R/diff.R | 4 - R/errors.R | 63 ++++++++++---------- R/fetch.R | 124 +++++++++++++++++++++++++++-------------- R/init.R | 61 ++++++++++++-------- R/merge.R | 47 +++++++++------ R/open.R | 37 +++++++----- R/pr.R | 12 +-- R/rebase.R | 34 +++++------ R/remotes.R | 31 ++++------ R/repository.R | 6 - R/signature.R | 28 +++++---- R/stash.R | 24 +++++-- R/submodules.R | 68 +++++++++++++--------- R/tag.R | 8 +- R/worktree.R |only inst/doc/gert.html | 10 +-- man/git_archive.Rd | 3 man/git_branch.Rd | 3 man/git_commit.Rd | 3 man/git_config.Rd | 3 man/git_diff.Rd | 3 man/git_fetch.Rd | 3 man/git_ignore.Rd | 3 man/git_merge.Rd | 3 man/git_rebase.Rd | 3 man/git_remote.Rd | 3 man/git_repo.Rd | 3 man/git_reset.Rd | 3 man/git_signature.Rd | 3 man/git_stash.Rd | 3 man/git_tag.Rd | 3 man/git_worktree.Rd |only src/init.c | 20 ++++++ src/utils.h | 1 src/worktree.c |only tests/testthat/test-remotes.R | 2 tests/testthat/test-worktree.R |only 47 files changed, 594 insertions(+), 384 deletions(-)
Title: Automated Reporting of Results and Statistical Models
Description: The aim of the 'report' package is to bridge the gap between
R’s output and the formatted results contained in your manuscript.
This package converts statistical models and data frames into textual
reports suited for publication, ensuring standardization and quality
in results reporting.
Author: Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Indrajeet Patil [aut] ,
Remi Theriault [aut, cre] ,
Mattan S. Ben-Shachar [aut] ,
Brenton M. Wiernik [aut] ,
Rudolf Siegel [ctb] ,
Camden Bock [ctb]
Maintainer: Remi Theriault <remi.theriault@mail.mcgill.ca>
Diff between report versions 0.6.2 dated 2025-11-03 and 0.6.3 dated 2026-01-08
DESCRIPTION | 6 MD5 | 136 ++++---- NEWS.md | 6 R/cite_easystats.R | 190 ++++++++--- R/format_citation.R | 33 +- R/format_model.R | 3 R/report.MixMod.R | 12 R/report.aov.R | 126 +++++-- R/report.bayesfactor_models.R | 217 ++++++++----- R/report.character.R | 119 ++++--- R/report.compare.loo.R | 16 - R/report.compare_performance.R | 68 +++- R/report.data.frame.R | 297 ++++++++++-------- R/report.estimate_contrasts.R | 23 + R/report.factor.R | 119 +++++-- R/report.glmmTMB.R | 12 R/report.htest.R | 92 ++++- R/report.lavaan.R | 48 ++- R/report.lm.R | 7 R/report.lme.R | 12 R/report.lme4.R | 12 R/report.numeric.R | 223 +++++++++---- R/report.sessionInfo.R | 44 ++ R/report.stanreg.R | 63 +++ R/report.test_performance.R | 25 + R/report_effectsize.R | 27 + R/report_htest_chi2.R | 83 ++++- R/report_htest_cor.R | 8 R/report_htest_fisher.R | 64 +++- R/report_htest_ttest.R | 27 + R/report_htest_wilcox.R | 25 + R/report_info.R | 6 R/report_intercept.R | 16 - R/report_misc.R | 5 R/report_model.R | 1 R/report_participants.R | 399 ++++++++++++++++++------- R/report_performance.R | 44 ++ R/report_priors.R | 1 R/report_random.R | 1 R/report_s.R | 21 + R/report_sample.R | 203 ++++++++---- R/report_table.R | 35 +- R/utils_combine_tables.R | 27 + R/utils_misspelled_variables.R | 33 +- tests/testthat/_snaps/windows/report.lm.md | 96 +++--- tests/testthat/test-brms-performance-fix.R | 5 tests/testthat/test-coverage-MixMod.R | 3 tests/testthat/test-coverage-compare-loo.R | 3 tests/testthat/test-format_algorithm_formula.R | 25 + tests/testthat/test-format_citation.R | 13 tests/testthat/test-format_model.R | 44 ++ tests/testthat/test-glmmtmb-duplication-fix.R | 72 +++- tests/testthat/test-report.aov.R | 60 ++- tests/testthat/test-report.data.frame.R | 6 tests/testthat/test-report.htest-chi2.R | 8 tests/testthat/test-report.htest-fisher.R | 3 tests/testthat/test-report.htest-friedman.R | 3 tests/testthat/test-report.htest-t-test.R | 79 +++- tests/testthat/test-report.htest-wilcox.R | 43 ++ tests/testthat/test-report.ivreg.R | 3 tests/testthat/test-report.lmer.R | 5 tests/testthat/test-report.stanreg.R | 31 + tests/testthat/test-report_basic_methods.R | 71 +++- tests/testthat/test-report_info_misc_text.R | 23 + tests/testthat/test-report_participants.R | 44 ++ tests/testthat/test-report_performance.R | 23 + tests/testthat/test-report_sample.R | 55 ++- tests/testthat/test-report_table.R | 4 tests/testthat/test-utils_helpers.R | 16 - 69 files changed, 2611 insertions(+), 1062 deletions(-)
Title: Machinery for Processing Random Effect Formulas
Description: Takes formulas including random-effects components (formatted as in 'lme4', 'glmmTMB', etc.) and processes them. Includes various helper functions.
Author: Ben Bolker [aut, cre] ,
Anna Ly [ctb]
Maintainer: Ben Bolker <bolker@mcmaster.ca>
Diff between reformulas versions 0.4.3 dated 2025-12-17 and 0.4.3.1 dated 2026-01-08
DESCRIPTION | 9 +++--- MD5 | 20 +++++++------ NAMESPACE | 2 + NEWS.md | 10 +++++- R/VarCorr.R | 67 ++++++++++++++++++++++++++++++++++++--------- R/utils.R | 31 ++++++++++++++------ build/partial.rdb |binary inst/tinytest/test_utils.R | 34 +++++++++++++++++++++- man/formfuns.Rd | 2 - man/splitForm.Rd | 2 - tests/testthat |only tests/testthat.R |only 12 files changed, 136 insertions(+), 41 deletions(-)
Title: R and C++ Interfaces to 'spdlog' C++ Header Library for Logging
Description: The mature and widely-used C++ logging library 'spdlog' by Gabi Melman provides
many desirable features. This package bundles these header files for easy use by R packages
from both their R and C or C++ code. Explicit use via 'LinkingTo:' is also supported. Also
see the 'spdl' package which enhanced this package with a consistent R and C++ interface.
Author: Dirk Eddelbuettel [aut, cre] ,
Gabi Melman [aut] ,
Victor Zverovic [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSpdlog versions 0.0.23 dated 2025-10-12 and 0.0.24 dated 2026-01-08
RcppSpdlog-0.0.23/RcppSpdlog/inst/include/spdlog/fmt/bundled/locale.h |only RcppSpdlog-0.0.24/RcppSpdlog/ChangeLog | 21 RcppSpdlog-0.0.24/RcppSpdlog/DESCRIPTION | 8 RcppSpdlog-0.0.24/RcppSpdlog/MD5 | 159 +++--- RcppSpdlog-0.0.24/RcppSpdlog/build/partial.rdb |binary RcppSpdlog-0.0.24/RcppSpdlog/build/vignette.rds |binary RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/async_logger-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/async_logger.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/cfg/helpers-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/cfg/helpers.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/common-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/common.h | 188 ++++---- RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/backtracer-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/backtracer.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/file_helper-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/file_helper.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/fmt_helper.h | 14 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/log_msg-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/log_msg.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/log_msg_buffer-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/log_msg_buffer.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/mpmc_blocking_q.h | 4 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/os-inl.h | 231 ++++------ RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/os.h | 22 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/periodic_worker-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/periodic_worker.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/registry-inl.h | 22 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/registry.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/tcp_client.h | 5 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/thread_pool-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/thread_pool.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/udp_client-windows.h | 6 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/udp_client.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/details/windows_include.h | 4 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/bin_to_hex.h | 8 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/bundled/base.h | 34 + RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/bundled/chrono.h | 9 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/bundled/color.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/bundled/compile.h | 5 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/bundled/format-inl.h | 7 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/bundled/format.h | 28 - RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/bundled/os.h | 17 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/bundled/ranges.h | 19 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/bundled/std.h | 164 +++---- RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/chrono.h | 20 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/compile.h | 20 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/fmt.h | 18 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/ostr.h | 20 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/ranges.h | 20 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/std.h | 20 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/fmt/xchar.h | 20 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/logger-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/logger.h | 38 - RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/mdc.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/pattern_formatter-inl.h | 35 - RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/pattern_formatter.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/android_sink.h | 28 - RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/ansicolor_sink-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/ansicolor_sink.h | 6 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/base_sink-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/base_sink.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/basic_file_sink-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/basic_file_sink.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/msvc_sink.h | 28 - RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/qt_sinks.h | 22 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/rotating_file_sink-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/rotating_file_sink.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/sink-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/sink.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/stdout_color_sinks-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/stdout_color_sinks.h | 6 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/stdout_sinks-inl.h | 24 - RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/stdout_sinks.h | 4 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/systemd_sink.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/tcp_sink.h | 4 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/udp_sink.h | 4 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/wincolor_sink-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/sinks/wincolor_sink.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/spdlog-inl.h | 2 RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/spdlog.h | 67 +- RcppSpdlog-0.0.24/RcppSpdlog/inst/include/spdlog/version.h | 2 81 files changed, 752 insertions(+), 703 deletions(-)
Title: R Commander Miscellaneous Functions
Description: Various statistical, graphics, and data-management functions used by the Rcmdr package in the R Commander GUI for R.
Author: John Fox [aut],
Manuel Munoz-Marquez [aut, cre],
Robert Muenchen [ctb],
Dan Putler [ctb]
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between RcmdrMisc versions 2.9-2 dated 2025-07-23 and 2.10.1 dated 2026-01-08
RcmdrMisc-2.10.1/RcmdrMisc/DESCRIPTION | 22 RcmdrMisc-2.10.1/RcmdrMisc/MD5 | 134 +-- RcmdrMisc-2.10.1/RcmdrMisc/NAMESPACE | 157 ++- RcmdrMisc-2.10.1/RcmdrMisc/NEWS | 8 RcmdrMisc-2.10.1/RcmdrMisc/R/Barplot.R | 43 RcmdrMisc-2.10.1/RcmdrMisc/R/DeltaMethod.R | 59 - RcmdrMisc-2.10.1/RcmdrMisc/R/Dotplot.R | 37 RcmdrMisc-2.10.1/RcmdrMisc/R/Percents.R | 112 +- RcmdrMisc-2.10.1/RcmdrMisc/R/RcmdrMisc-package.R |only RcmdrMisc-2.10.1/RcmdrMisc/R/bin.var.R | 76 + RcmdrMisc-2.10.1/RcmdrMisc/R/binnedCounts.R | 75 + RcmdrMisc-2.10.1/RcmdrMisc/R/cluster.R | 123 ++ RcmdrMisc-2.10.1/RcmdrMisc/R/cv.R |only RcmdrMisc-2.10.1/RcmdrMisc/R/discreteCounts.R | 71 + RcmdrMisc-2.10.1/RcmdrMisc/R/discretePlot.R | 38 RcmdrMisc-2.10.1/RcmdrMisc/R/gumbel.R | 80 + RcmdrMisc-2.10.1/RcmdrMisc/R/mergeRows.R | 76 + RcmdrMisc-2.10.1/RcmdrMisc/R/normalityTest.R | 136 ++- RcmdrMisc-2.10.1/RcmdrMisc/R/numSummary.R | 57 - RcmdrMisc-2.10.1/RcmdrMisc/R/partial.cor.R | 157 ++- RcmdrMisc-2.10.1/RcmdrMisc/R/piechart.R | 44 - RcmdrMisc-2.10.1/RcmdrMisc/R/plotBoot.R | 90 +- RcmdrMisc-2.10.1/RcmdrMisc/R/plots.R | 738 ++++++++++------- RcmdrMisc-2.10.1/RcmdrMisc/R/rcorr.adjust.R | 44 - RcmdrMisc-2.10.1/RcmdrMisc/R/readSAS.R | 23 RcmdrMisc-2.10.1/RcmdrMisc/R/readSPSS.R | 54 - RcmdrMisc-2.10.1/RcmdrMisc/R/readStata.R | 25 RcmdrMisc-2.10.1/RcmdrMisc/R/readXL.R | 63 + RcmdrMisc-2.10.1/RcmdrMisc/R/reliability.R | 37 RcmdrMisc-2.10.1/RcmdrMisc/R/repeatedMeasuresPlot.R | 320 ++++--- RcmdrMisc-2.10.1/RcmdrMisc/R/reshapeL2W.R | 133 +-- RcmdrMisc-2.10.1/RcmdrMisc/R/reshapeW2L.R | 139 ++- RcmdrMisc-2.10.1/RcmdrMisc/R/stepwise.R | 82 + RcmdrMisc-2.10.1/RcmdrMisc/R/summarySandwich.R | 75 + RcmdrMisc-2.10.1/RcmdrMisc/man/Barplot.Rd | 122 +- RcmdrMisc-2.10.1/RcmdrMisc/man/DeltaMethod.Rd | 83 - RcmdrMisc-2.10.1/RcmdrMisc/man/Dotplot.Rd | 71 - RcmdrMisc-2.10.1/RcmdrMisc/man/Gumbel.Rd |only RcmdrMisc-2.10.1/RcmdrMisc/man/Hist.Rd | 74 - RcmdrMisc-2.10.1/RcmdrMisc/man/KMeans.Rd | 88 +- RcmdrMisc-2.10.1/RcmdrMisc/man/RcmdrMisc-package.Rd |only RcmdrMisc-2.10.1/RcmdrMisc/man/assignCluster.Rd | 91 +- RcmdrMisc-2.10.1/RcmdrMisc/man/bin.var.Rd | 65 - RcmdrMisc-2.10.1/RcmdrMisc/man/binVariable.Rd |only RcmdrMisc-2.10.1/RcmdrMisc/man/binnedCounts.Rd | 55 - RcmdrMisc-2.10.1/RcmdrMisc/man/colPercents.Rd | 90 +- RcmdrMisc-2.10.1/RcmdrMisc/man/cv.Rd |only RcmdrMisc-2.10.1/RcmdrMisc/man/discreteCounts.Rd | 94 -- RcmdrMisc-2.10.1/RcmdrMisc/man/discretePlot.Rd | 88 +- RcmdrMisc-2.10.1/RcmdrMisc/man/indexplot.Rd | 89 +- RcmdrMisc-2.10.1/RcmdrMisc/man/lineplot.Rd | 72 - RcmdrMisc-2.10.1/RcmdrMisc/man/mergeRows.Rd | 88 +- RcmdrMisc-2.10.1/RcmdrMisc/man/normalityTest.Rd | 83 + RcmdrMisc-2.10.1/RcmdrMisc/man/numSummary.Rd | 84 - RcmdrMisc-2.10.1/RcmdrMisc/man/partial.cor.Rd | 78 + RcmdrMisc-2.10.1/RcmdrMisc/man/piechart.Rd | 54 - RcmdrMisc-2.10.1/RcmdrMisc/man/plotBoot.Rd | 85 - RcmdrMisc-2.10.1/RcmdrMisc/man/plotDistr.Rd | 81 + RcmdrMisc-2.10.1/RcmdrMisc/man/plotMeans.Rd | 137 +-- RcmdrMisc-2.10.1/RcmdrMisc/man/rcorr.adjust.Rd | 102 +- RcmdrMisc-2.10.1/RcmdrMisc/man/readSAS.Rd | 40 RcmdrMisc-2.10.1/RcmdrMisc/man/readSPSS.Rd | 63 - RcmdrMisc-2.10.1/RcmdrMisc/man/readStata.Rd | 48 - RcmdrMisc-2.10.1/RcmdrMisc/man/readXL.Rd | 67 - RcmdrMisc-2.10.1/RcmdrMisc/man/reexports.Rd |only RcmdrMisc-2.10.1/RcmdrMisc/man/reliability.Rd | 59 - RcmdrMisc-2.10.1/RcmdrMisc/man/repeatedMeasuresPlot.Rd | 144 +-- RcmdrMisc-2.10.1/RcmdrMisc/man/reshapeL2W.Rd | 64 - RcmdrMisc-2.10.1/RcmdrMisc/man/reshapeW2L.Rd | 103 +- RcmdrMisc-2.10.1/RcmdrMisc/man/stepwise.Rd | 97 +- RcmdrMisc-2.10.1/RcmdrMisc/man/summarySandwich.Rd | 57 - RcmdrMisc-2.9-2/RcmdrMisc/man/gumbel.Rd |only 72 files changed, 3533 insertions(+), 2411 deletions(-)
Title: Pena-Yohai Initial Estimator for Robust S-Regression
Description: Deterministic Pena-Yohai initial estimator for robust S estimators
of regression. The procedure is described in detail in
Pena, D., & Yohai, V. (1999) <doi:10.2307/2670164>.
Author: David Kepplinger [aut, cre],
Matias Salibian-Barrera [aut],
Gabriela Cohen Freue [aut]
Maintainer: David Kepplinger <david.kepplinger@gmail.com>
Diff between pyinit versions 1.1.4 dated 2025-12-03 and 1.1.5 dated 2026-01-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 2 ++ src/Makevars | 2 +- src/Makevars.win | 1 - 5 files changed, 11 insertions(+), 10 deletions(-)
Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph] ,
Mike Cheng [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between parallelly versions 1.46.0 dated 2025-12-12 and 1.46.1 dated 2026-01-08
DESCRIPTION | 6 MD5 | 88 ++-- NEWS.md | 25 + R/010.cli.R | 2 R/availableCores.R | 4 R/makeClusterPSOCK.R | 2 R/makeClusterSequential.R | 20 + R/makeNodePSOCK.R | 2 R/utils.R | 26 - inst/WORDLIST | 5 inst/doc/parallelly-10-local-workers.html | 8 inst/doc/parallelly-10-local-workers.md | 8 inst/doc/parallelly-12-remote-workers.html | 32 - inst/doc/parallelly-12-remote-workers.md | 32 - inst/doc/parallelly-17-hpc-workers.html | 8 inst/doc/parallelly-17-hpc-workers.md | 8 inst/doc/parallelly-22-wine-workers.html | 12 inst/doc/parallelly-22-wine-workers.md | 12 inst/doc/parallelly-25-sandbox-workers.html | 4 inst/doc/parallelly-25-sandbox-workers.md | 4 inst/testme/_prologue/030.imports.R | 2 inst/testme/_prologue/090.options.R | 2 inst/testme/run.R | 115 +----- inst/testme/test-autoStopCluster.R | 5 inst/testme/test-availableCores.R | 523 ++++++++++++++++++++++++++++ inst/testme/test-availableWorkers.R | 14 inst/testme/test-cgroups.R | 42 ++ inst/testme/test-cli.R |only inst/testme/test-cloneNode.R | 2 inst/testme/test-freePort.R | 76 +++- inst/testme/test-isForkedChild.R | 1 inst/testme/test-isNodeAlive.R | 106 +++++ inst/testme/test-killNode.R | 17 inst/testme/test-makeClusterPSOCK.R | 55 ++ inst/testme/test-makeClusterSequential.R | 39 -- inst/testme/test-makeNodePSOCK.R | 171 +++++++++ inst/testme/test-options-and-envvars.R | 2 man/availableCores.Rd | 4 man/makeClusterPSOCK.Rd | 10 man/makeClusterSequential.Rd | 13 tests/test-cli.R |only vignettes/parallelly-10-local-workers.md | 8 vignettes/parallelly-12-remote-workers.md | 32 - vignettes/parallelly-17-hpc-workers.md | 8 vignettes/parallelly-22-wine-workers.md | 12 vignettes/parallelly-25-sandbox-workers.md | 4 46 files changed, 1276 insertions(+), 295 deletions(-)
Title: Comprehensive Collection of Color Palettes
Description: The choices of color palettes in R can be quite overwhelming
with palettes spread over many packages with many different API's.
This packages aims to collect all color palettes across the R
ecosystem under the same package with a streamlined API.
Author: See AUTHORS file. [aut],
Emil Hvitfeldt [aut, cre]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between paletteer versions 1.6.0 dated 2024-01-21 and 1.7.0 dated 2026-01-08
paletteer-1.6.0/paletteer/R/paletteer.R |only paletteer-1.7.0/paletteer/DESCRIPTION | 36 paletteer-1.7.0/paletteer/LICENSE.note | 28 paletteer-1.7.0/paletteer/MD5 | 221 paletteer-1.7.0/paletteer/NAMESPACE | 3 paletteer-1.7.0/paletteer/NEWS.md | 11 paletteer-1.7.0/paletteer/R/aaa.R | 20 paletteer-1.7.0/paletteer/R/completeme.R | 33 paletteer-1.7.0/paletteer/R/data.R | 13 paletteer-1.7.0/paletteer/R/ggplot2_scales_binned.R | 27 paletteer-1.7.0/paletteer/R/ggplot2_scales_continuous.R | 26 paletteer-1.7.0/paletteer/R/ggplot2_scales_discrete.R | 45 paletteer-1.7.0/paletteer/R/import-standalone-obj-type.R |only paletteer-1.7.0/paletteer/R/import-standalone-types-check.R |only paletteer-1.7.0/paletteer/R/paletteer-package.R | 11 paletteer-1.7.0/paletteer/R/paletteer_c.R | 9 paletteer-1.7.0/paletteer/R/paletteer_c_wrappers.R | 101 paletteer-1.7.0/paletteer/R/paletteer_d.R | 27 paletteer-1.7.0/paletteer/R/paletteer_dynamic.R | 15 paletteer-1.7.0/paletteer/R/sysdata.rda |binary paletteer-1.7.0/paletteer/README.md | 179 paletteer-1.7.0/paletteer/data/paletteer_packages.rda |binary paletteer-1.7.0/paletteer/data/palettes_c_names.rda |binary paletteer-1.7.0/paletteer/data/palettes_d.rda |binary paletteer-1.7.0/paletteer/data/palettes_d_names.rda |binary paletteer-1.7.0/paletteer/man/figures/README-unnamed-chunk-6-1.png |binary paletteer-1.7.0/paletteer/man/figures/colorPaletteFinder.gif |only paletteer-1.7.0/paletteer/man/ggplot2-scales-binned.Rd | 2 paletteer-1.7.0/paletteer/man/ggplot2-scales-continuous.Rd | 2 paletteer-1.7.0/paletteer/man/ggplot2-scales-discrete.Rd | 2 paletteer-1.7.0/paletteer/man/paleteer-c-wrapper.Rd | 1 paletteer-1.7.0/paletteer/man/paletteer-package.Rd | 16 paletteer-1.7.0/paletteer/man/paletteer_c.Rd | 9 paletteer-1.7.0/paletteer/man/paletteer_d.Rd | 13 paletteer-1.7.0/paletteer/man/paletteer_packages.Rd | 9 paletteer-1.7.0/paletteer/man/palettes_c_names.Rd | 4 paletteer-1.7.0/paletteer/man/palettes_d.Rd | 4 paletteer-1.7.0/paletteer/man/palettes_d_names.Rd | 6 paletteer-1.7.0/paletteer/man/palettes_dynamic_names.Rd | 2 paletteer-1.7.0/paletteer/tests/testthat.R | 8 paletteer-1.7.0/paletteer/tests/testthat/_snaps/ggplot2_scales_binned.md |only paletteer-1.7.0/paletteer/tests/testthat/_snaps/ggplot2_scales_continuous.md |only paletteer-1.7.0/paletteer/tests/testthat/_snaps/ggplot2_scales_discrete.md |only paletteer-1.7.0/paletteer/tests/testthat/_snaps/paletteer_c.md |only paletteer-1.7.0/paletteer/tests/testthat/_snaps/paletteer_d.md | 18 paletteer-1.7.0/paletteer/tests/testthat/_snaps/paletteer_dynamic.md |only paletteer-1.7.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/amerika.svg |only paletteer-1.7.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/awtools.svg | 82 paletteer-1.7.0/paletteer/tests/testthat/_snaps/vdiffr_palette_check/beyonce.svg | 2560 - 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Title: Unified Multiple Testing Procedures
Description: Designed to ease the application and comparison of multiple
hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are
standardized and usable by the accompanying 'mutossGUI'.
Author: MuToss Coding Team [aut] ,
Gilles Blanchard [aut],
Thorsten Dickhaus [aut],
Niklas Hack [aut],
Frank Konietschke [aut],
Kornelius Rohmeyer [aut, cre],
Jonathan Rosenblatt [aut],
Marsel Scheer [aut],
Wiebke Werft [aut]
Maintainer: Kornelius Rohmeyer <rohmeyer@small-projects.de>
Diff between mutoss versions 0.1-13 dated 2023-03-14 and 0.1-14 dated 2026-01-08
DESCRIPTION | 51 ++++++++++++++++++++++++++++++++++++++------- MD5 | 16 +++++++------- NEWS | 4 +++ build/vignette.rds |binary inst/doc/quickstart.pdf |binary inst/doc/simToolManual.pdf |binary man/Qvalue.Rd | 9 +++++-- man/pval2locfdr.Rd | 9 +++++-- man/pval2qval.Rd | 9 +++++-- 9 files changed, 74 insertions(+), 24 deletions(-)
Title: Mixed Models for Repeated Measures
Description: Mixed models for repeated measures (MMRM) are a popular
choice for analyzing longitudinal continuous outcomes in randomized
clinical trials and beyond; see Cnaan, Laird and Slasor (1997)
<doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E>
for a tutorial and Mallinckrodt, Lane, Schnell, Peng and Mancuso
(2008) <doi:10.1177/009286150804200402> for a review. This package
implements MMRM based on the marginal linear model without random
effects using Template Model Builder ('TMB') which enables fast and
robust model fitting. Users can specify a variety of covariance
matrices, weight observations, fit models with restricted or standard
maximum likelihood inference, perform hypothesis testing with
Satterthwaite or Kenward-Roger adjustment, and extract least square
means estimates by using 'emmeans'.
Author: Daniel Sabanes Bove [aut, cre] ,
Liming Li [aut] ,
Julia Dedic [aut],
Doug Kelkhoff [aut],
Kevin Kunzmann [aut],
Brian Matthew Lang [aut],
Christian Stock [aut],
Ya Wang [aut],
Craig Gower-Page [ctb],
Dan James [aut],
Jonathan Sidi [aut],
Daniel Leib [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between mmrm versions 0.3.16 dated 2025-12-09 and 0.3.17 dated 2026-01-08
DESCRIPTION | 6 MD5 | 516 - NAMESPACE | 138 NEWS.md | 446 - R/between-within.R | 278 - R/catch-routine-registration.R | 16 R/component.R | 364 - R/cov_struct.R | 942 +-- R/data.R | 136 R/empirical.R | 98 R/fit.R | 1188 ++-- R/interop-car.R | 702 +- R/interop-emmeans.R | 216 R/interop-parsnip.R | 166 R/kenwardroger.R | 438 - R/mmrm-methods.R | 1124 ++-- R/mmrm-package.R | 46 R/residual.R | 74 R/satterthwaite.R | 668 +- R/skipping.R | 62 R/testing.R | 408 - R/tidiers.R | 416 - R/tmb-methods.R | 1774 +++--- R/tmb.R | 1380 ++--- R/utils-formula.R | 200 R/utils-nse.R | 270 - R/utils.R | 2376 ++++---- R/zzz.R | 326 - build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 446 - inst/WORDLIST | 242 inst/doc/algorithm.R | 12 inst/doc/algorithm.Rmd | 708 +- inst/doc/algorithm.html | 1214 ++-- inst/doc/between_within.R | 36 inst/doc/between_within.Rmd | 250 inst/doc/between_within.html | 1192 ++-- inst/doc/coef_vcov.R | 12 inst/doc/coef_vcov.Rmd | 194 inst/doc/coef_vcov.html | 769 +- inst/doc/covariance.R | 12 inst/doc/covariance.Rmd | 508 - inst/doc/covariance.html | 1110 ++-- inst/doc/empirical_wls.Rmd | 521 - inst/doc/empirical_wls.html | 1120 ++-- inst/doc/hypothesis_testing.R | 34 inst/doc/hypothesis_testing.Rmd | 530 - inst/doc/hypothesis_testing.html | 1442 ++--- inst/doc/introduction.R | 716 +- inst/doc/introduction.Rmd | 128 inst/doc/introduction.html | 5286 +++++++++---------- inst/doc/kenward.R | 12 inst/doc/kenward.Rmd | 762 +- inst/doc/kenward.html | 1404 ++--- inst/doc/methodological_introduction.R | 12 inst/doc/methodological_introduction.Rmd | 228 inst/doc/methodological_introduction.html | 988 +-- inst/doc/mmrm_review_methods.R | 252 inst/doc/mmrm_review_methods.Rmd | 1240 ++-- inst/doc/mmrm_review_methods.html | 2271 ++++---- inst/doc/package_structure.Rmd | 391 - inst/doc/package_structure.html | 1116 ++-- inst/doc/predict.R | 14 inst/doc/predict.Rmd | 454 - inst/doc/predict.html | 1076 ++-- inst/doc/satterthwaite.R | 12 inst/doc/satterthwaite.Rmd | 480 - inst/doc/satterthwaite.html | 1048 +-- inst/jss.csl | 1166 ++-- man/Anova.mmrm.Rd | 82 man/COV_TYPES.Rd | 74 man/as.cov_struct.Rd | 140 man/bcva_data.Rd | 66 man/cached_mmrm_results.Rd | 68 man/car_add_mmrm.Rd | 36 man/check_package_version.Rd | 48 man/component.Rd | 176 man/cov_struct.Rd | 98 man/cov_type_abbr.Rd | 38 man/cov_type_name.Rd | 38 man/covariance_types.Rd | 268 man/df_1d.Rd | 64 man/df_md.Rd | 68 man/drop_elements.Rd | 42 man/emit_tidymodels_register_msg.Rd | 32 man/emmeans_support.Rd | 50 man/emp_start.Rd | 86 man/fev_data.Rd | 72 man/figures/lifecycle-archived.svg | 2 man/figures/lifecycle-defunct.svg | 2 man/figures/lifecycle-deprecated.svg | 2 man/figures/lifecycle-experimental.svg | 2 man/figures/lifecycle-maturing.svg | 2 man/figures/lifecycle-questioning.svg | 2 man/figures/lifecycle-stable.svg | 2 man/figures/lifecycle-superseded.svg | 2 man/figures/logo.svg | 712 +- man/fill_names.Rd | 38 man/fit_mmrm.Rd | 138 man/fit_single_optimizer.Rd | 138 man/flat_expr.Rd | 98 man/format.cov_struct.Rd | 38 man/format_symbols.Rd | 38 man/formula_rhs.Rd | 46 man/h_add_covariance_terms.Rd | 54 man/h_add_terms.Rd | 54 man/h_anova_single_mmrm_model.Rd | 62 man/h_assert_lrt_suitability.Rd | 60 man/h_assert_nested_models.Rd | 72 man/h_check_columns_nested.Rd | 74 man/h_check_cov_struct_nesting.Rd | 66 man/h_check_covar_nesting.Rd | 54 man/h_check_fits_all_data_same.Rd | 82 man/h_coef_table.Rd | 38 man/h_confirm_large_levels.Rd | 38 man/h_construct_model_frame_inputs.Rd | 80 man/h_contr_sum_type3_contrasts.Rd | 38 man/h_dataset_sort_all.Rd | 40 man/h_default_value.Rd | 44 man/h_df_1d_bw.Rd | 44 man/h_df_1d_kr.Rd | 46 man/h_df_1d_res.Rd | 46 man/h_df_1d_sat.Rd | 46 man/h_df_1d_sat_empirical.Rd | 44 man/h_df_bw_calc.Rd | 46 man/h_df_md_bw.Rd | 46 man/h_df_md_from_1d.Rd | 42 man/h_df_md_kr.Rd | 46 man/h_df_md_res.Rd | 46 man/h_df_md_sat.Rd | 46 man/h_df_min_bw.Rd | 44 man/h_df_to_tibble.Rd | 48 man/h_drop_covariance_terms.Rd | 46 man/h_drop_levels.Rd | 42 man/h_extra_levels.Rd | 30 man/h_extract_covariance_terms.Rd | 38 man/h_first_term_containing_categ.Rd | 48 man/h_fits_common_data.Rd | 52 man/h_generate_new_name.Rd | 50 man/h_get_cov_default.Rd | 54 man/h_get_empirical.Rd | 76 man/h_get_index.Rd | 34 man/h_get_kr_comp.Rd | 72 man/h_get_minimal_fit_data.Rd | 64 man/h_get_na_action.Rd | 24 man/h_get_optimizers.Rd | 104 man/h_get_prediction.Rd | 64 man/h_get_prediction_variance.Rd | 38 man/h_get_sim_per_subj.Rd | 38 man/h_get_theta_from_cov.Rd | 44 man/h_gradient.Rd | 48 man/h_jac_list.Rd | 48 man/h_kr_df.Rd | 58 man/h_md_denom_df.Rd | 48 man/h_mmrm_tmb_assert_start.Rd | 36 man/h_mmrm_tmb_check_conv.Rd | 42 man/h_mmrm_tmb_data.Rd | 150 man/h_mmrm_tmb_extract_cov.Rd | 54 man/h_mmrm_tmb_fit.Rd | 112 man/h_mmrm_tmb_formula_parts.Rd | 80 man/h_mmrm_tmb_parameters.Rd | 54 man/h_newdata_add_pred.Rd | 58 man/h_obtain_lvls.Rd | 42 man/h_optimizer_fun.Rd | 36 man/h_partial_fun_args.Rd | 58 man/h_print_aic_list.Rd | 34 man/h_print_call.Rd | 42 man/h_print_cov.Rd | 38 man/h_quad_form.Rd | 74 man/h_reconcile_cov_struct.Rd | 50 man/h_record_all_output.Rd | 70 man/h_refit_mmrm.Rd | 66 man/h_register_s3.Rd | 52 man/h_residuals_normalized.Rd | 36 man/h_residuals_pearson.Rd | 36 man/h_residuals_response.Rd | 36 man/h_split_control.Rd | 42 man/h_summarize_all_fits.Rd | 36 man/h_tbl_confint_terms.Rd | 40 man/h_test_1d.Rd | 50 man/h_test_md.Rd | 68 man/h_tmb_version_sufficient.Rd | 30 man/h_tmb_warn_non_deterministic.Rd | 34 man/h_tr.Rd | 36 man/h_type2_contrast.Rd | 44 man/h_type3_contrasts.Rd | 40 man/h_valid_formula.Rd | 38 man/h_var_adj.Rd | 60 man/h_warn_na_action.Rd | 24 man/h_within_or_between.Rd | 44 man/is_infix.Rd | 50 man/mmrm-package.Rd | 98 man/mmrm.Rd | 256 man/mmrm_control.Rd | 200 man/mmrm_methods.Rd | 148 man/mmrm_tidiers.Rd | 146 man/mmrm_tmb_methods.Rd | 558 +- man/parsnip_add_mmrm.Rd | 44 man/position_symbol.Rd | 54 man/print.cov_struct.Rd | 38 man/reexports.Rd | 36 man/refit_multiple_optimizers.Rd | 66 man/register_on_load.Rd | 72 man/stats_anova.Rd | 372 - man/std_start.Rd | 58 man/tmb_cov_type.Rd | 36 man/validate_cov_struct.Rd | 36 src/Makevars | 4 tests/additional.R | 340 - tests/testthat.R | 6 tests/testthat/_snaps/interop-car.md | 736 +- tests/testthat/helper-examples.R | 542 +- tests/testthat/helper-skipping.R | 18 tests/testthat/test-between-within.R | 384 - tests/testthat/test-component.R | 346 - tests/testthat/test-cov-struct.R | 308 - tests/testthat/test-cpp-covariance.R | 586 +- tests/testthat/test-cpp-utils.R | 184 tests/testthat/test-cpp.R | 2 tests/testthat/test-emmeans.R | 692 +- tests/testthat/test-empirical.R | 1338 ++-- tests/testthat/test-fit.R | 2058 +++---- tests/testthat/test-interop-car.R | 1104 ++-- tests/testthat/test-interop-parsnip.R | 208 tests/testthat/test-interop.R | 70 tests/testthat/test-kenwardroger.R | 1142 ++-- tests/testthat/test-mmrm-methods.R | 1174 ++-- tests/testthat/test-residual.R | 58 tests/testthat/test-satterthwaite.R | 564 +- tests/testthat/test-skipping.R | 72 tests/testthat/test-testing.R | 216 tests/testthat/test-tidiers.R | 530 - tests/testthat/test-tmb-methods.R | 3256 ++++++------ tests/testthat/test-tmb.R | 5380 ++++++++++---------- tests/testthat/test-utils-formula.R | 230 tests/testthat/test-utils-nse.R | 208 tests/testthat/test-utils.R | 820 +-- vignettes/algorithm.Rmd | 708 +- vignettes/between_within.Rmd | 250 vignettes/coef_vcov.Rmd | 194 vignettes/covariance.Rmd | 508 - vignettes/empirical_wls.Rmd | 521 - vignettes/hypothesis_testing.Rmd | 530 - vignettes/introduction.Rmd | 128 vignettes/kenward.Rmd | 762 +- vignettes/methodological_introduction.Rmd | 228 vignettes/mmrm_review_methods.Rmd | 1240 ++-- vignettes/mmrm_review_refs.bib | 542 +- vignettes/package_structure.Rmd | 391 - vignettes/predict.Rmd | 454 - vignettes/satterthwaite.Rmd | 480 - vignettes/subsections/_intro-acknowledgments.Rmd | 18 vignettes/subsections/_intro-customizations.Rmd | 642 +- vignettes/subsections/_intro-getting_started.Rmd | 60 vignettes/subsections/_intro-hypothesis_testing.Rmd | 284 - vignettes/subsections/_intro-lower_level.Rmd | 42 vignettes/subsections/_intro-model_features.Rmd | 256 vignettes/subsections/_intro-tidymodels.Rmd | 272 - 259 files changed, 42381 insertions(+), 42371 deletions(-)
Title: The MBESS R Package
Description: Implements methods that are useful in designing research studies and analyzing data, with
particular emphasis on methods that are developed for or used within the behavioral,
educational, and social sciences (broadly defined). That being said, many of the methods
implemented within MBESS are applicable to a wide variety of disciplines. MBESS has a
suite of functions for a variety of related topics, such as effect sizes, confidence intervals
for effect sizes (including standardized effect sizes and noncentral effect sizes), sample size
planning (from the accuracy in parameter estimation [AIPE], power analytic, equivalence, and
minimum-risk point estimation perspectives), mediation analysis, various properties of
distributions, and a variety of utility functions. MBESS (pronounced 'em-bes') was originally
an acronym for 'Methods for the Behavioral, Educational, and Social Sciences,' but MBESS became
more general and now contains methods applicable and used in a wide variety of fields and [...truncated...]
Author: Ken Kelley [aut, cre]
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between MBESS versions 4.9.41 dated 2025-07-25 and 4.9.42 dated 2026-01-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/upsilon.R | 12 ++++++------ 3 files changed, 12 insertions(+), 12 deletions(-)
Title: Mediation, Moderation and Moderated-Mediation After Model
Fitting
Description: Computes indirect effects, conditional effects, and conditional
indirect effects in a structural equation model or path model after model
fitting, with no need to define any user parameters or label any paths in
the model syntax, using the approach presented in Cheung and Cheung
(2024) <doi:10.3758/s13428-023-02224-z>. Can also form bootstrap
confidence intervals by doing bootstrapping only once and reusing the
bootstrap estimates in all subsequent computations. Supports bootstrap
confidence intervals for standardized (partially or completely) indirect
effects, conditional effects, and conditional indirect effects as described
in Cheung (2009) <doi:10.3758/BRM.41.2.425> and Cheung, Cheung, Lau, Hui,
and Vong (2022) <doi:10.1037/hea0001188>. Model fitting can be done by
structural equation modeling using lavaan() or regression using lm().
Author: Shu Fai Cheung [aut, cre] ,
Sing-Hang Cheung [aut] ,
Rong Wei Sun [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between manymome versions 0.3.2 dated 2025-12-14 and 0.3.3 dated 2026-01-08
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 11 +++++++++++ R/delta_med.R | 6 +++--- README.md | 2 +- inst/doc/mod_levels.html | 4 ++-- man/delta_med.Rd | 6 +++--- tests/testthat/test_lavaan2lm_list.R | 11 +++++++---- 8 files changed, 37 insertions(+), 23 deletions(-)
Title: Utilities for Scheduling Functions to Execute Later with Event
Loops
Description: Executes arbitrary R or C functions some time after the
current time, after the R execution stack has emptied. The functions
are scheduled in an event loop.
Author: Winston Chang [aut] ,
Joe Cheng [aut],
Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Marcus Geelnard [ctb, cph] ,
Evan Nemerson [ctb, cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between later versions 1.4.4 dated 2025-08-27 and 1.4.5 dated 2026-01-08
DESCRIPTION | 19 ++- MD5 | 36 +++---- NEWS.md | 4 R/later-package.R | 2 R/later.R | 8 - build/vignette.rds |binary inst/doc/later-cpp.html | 9 - inst/include/later.h | 7 + inst/promise_task.cpp |only man/later-package.Rd | 4 man/later_fd.Rd | 2 src/callback_registry.cpp | 166 --------------------------------- src/callback_registry.h | 7 - src/debug.cpp | 4 src/later.cpp | 25 +--- src/later_posix.cpp | 4 src/later_win32.cpp | 6 - tests/testthat/_snaps/private-loops.md | 16 +-- tests/testthat/test-promises.R |only tests/testthat/test-run_now.R | 4 20 files changed, 88 insertions(+), 235 deletions(-)
Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function
(Corless et al, 1996) <doi:10.1007/BF02124750> without the need for
installing the entire GSL.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between lamW versions 2.2.5 dated 2025-07-08 and 2.2.6 dated 2026-01-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 2 +- build/partial.rdb |binary inst/CITATION | 2 +- inst/NEWS.Rd | 8 ++++++++ inst/tinytest/test_lamW.R | 5 +++++ src/lambertW.cpp | 4 ++-- 8 files changed, 28 insertions(+), 15 deletions(-)
Title: The 'HighFive' 'C++' Interface to 'HDF5'
Description: A modern idiomatic header-only 'C++'' interface for 'libhdf5'. Original software can be found at <https://github.com/highfive-devs/highfive/>.
Author: Andrew Robbins [aut, cre] ,
Luc Grosheintz [aut] ,
Blue Brain Project/EPFL [aut]
Maintainer: Andrew Robbins <robbiand@umich.edu>
Diff between HighFive versions 3.2.0 dated 2025-10-11 and 3.3.0 dated 2026-01-08
DESCRIPTION | 10 +++++----- MD5 | 19 ++++++++++--------- NEWS.md | 8 ++++++++ inst/COPYRIGHTS | 2 ++ inst/include/highfive/H5DataSpace.hpp | 2 +- inst/include/highfive/H5Version.hpp | 6 +++--- inst/include/highfive/bits/H5DataType_misc.hpp | 11 ++++++++++- inst/include/highfive/bits/H5Dataspace_misc.hpp | 9 ++++++--- inst/include/highfive/bits/H5Slice_traits.hpp | 17 ++++++++++++++--- inst/include/highfive/bits/H5Slice_traits_misc.hpp | 8 ++++---- inst/include/highfive/mdspan.hpp |only 11 files changed, 63 insertions(+), 29 deletions(-)
Title: Use Image in 'ggplot2'
Description: Supports image files and graphic objects to be visualized in
'ggplot2' graphic system.
Author: Guangchuang Yu [aut, cre, cph] ,
Shuangbin Xu [ctb] ,
Yonghe Xia [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggimage versions 0.3.4 dated 2025-08-24 and 0.3.5 dated 2026-01-08
DESCRIPTION | 19 +- MD5 | 22 +-- NAMESPACE | 5 R/geom_image.R | 286 ++++++++++++++++++++++++++++++------------ R/geom_interactive.R | 31 ++++ R/geom_phylopic.R | 7 - R/geom_subview.R | 2 R/ggbackground.R | 2 man/geom_image.Rd | 7 + man/geom_image_interactive.Rd | 18 ++ man/geom_phylopic.Rd | 4 man/ggimage-package.Rd | 1 12 files changed, 303 insertions(+), 101 deletions(-)
Title: Fuzzy Similarity in Species Distributions
Description: Functions to compute fuzzy versions of species occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis, and prevalence-independent favourability obtained from probability of presence), as well as pair-wise fuzzy similarity (based on fuzzy logic versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model consensus and comparison (overlap and fuzzy similarity, fuzzy loss, fuzzy gain), and for data preparation, such as obtaining unique abbreviations of species names, defining the background region, cleaning and gridding (thinning) point occurrence data onto raster maps, selecting among (pseudo)absences to address survey bias, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, selecting relevant variables for models, assessing the false discovery rate, or analysing and dealing with multicollinearity. Initially desc [...truncated...]
Author: A. Marcia Barbosa [aut],
Alba Estrada [ctb],
Paul Melloy [ctb],
Jose Carlos Guerrero [fnd],
A. Marcia Barbosa [cre]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between fuzzySim versions 4.38 dated 2025-10-14 and 4.46 dated 2026-01-08
DESCRIPTION | 9 +-- MD5 | 50 +++++++++---------- NEWS.md | 115 ++++++++++++++++++++++++++++++++++++++++++++ R/cleanCoords.R | 28 +++++----- R/corSelect.R | 15 +++-- R/distMat.R | 60 +++++++++++++---------- R/distPres.R | 5 + R/getRegion.R | 123 ++++++++++++++++++++++++++++++++++-------------- R/multTSA.R | 4 - R/multicol.R | 59 ++++++++++++++--------- data/rotif.env.rda |binary data/rotifers.rda |binary man/biasLayer.Rd | 4 - man/cleanCoords.Rd | 6 +- man/corSelect.Rd | 22 ++++---- man/distMat.Rd | 16 +++--- man/distPres.Rd | 25 +++------ man/favClass.Rd | 6 +- man/fuzzySim-package.Rd | 6 +- man/getRegion.Rd | 39 ++++++++------- man/gridRecords.Rd | 37 ++++++++++---- man/multTSA.Rd | 2 man/multicol.Rd | 70 +++++++++++++++++++-------- man/partialResp.Rd | 6 +- man/selectAbsences.Rd | 2 man/simMat.Rd | 3 - 26 files changed, 484 insertions(+), 228 deletions(-)
Title: Economic Entity Identifier Standardization
Description: Provides utility functions for standardizing economic entity
(economy, aggregate, institution, etc.) name and id in economic datasets such
as those published by the International Monetary Fund and World Bank. Aims to
facilitate consistent data analysis, reporting, and joining across datasets.
Used as a foundational building block in the 'EconDataverse' family of
packages (<https://www.econdataverse.org>).
Author: L. Teal Emery [cre],
Christopher C. Smith [aut],
Christoph Scheuch [ctb],
Teal Insights [cph]
Maintainer: L. Teal Emery <lte@tealinsights.com>
Diff between econid versions 0.0.2 dated 2025-07-07 and 0.0.3 dated 2026-01-08
DESCRIPTION | 15 - MD5 | 32 +- NEWS.md | 4 R/add_entity_pattern.R | 9 R/create_entity_regex.R | 22 - R/fuzzyjoin.R | 14 - R/list_entity_patterns.R | 10 R/reset_patterns.R | 18 - R/standardize_entity.R | 229 ++++++++++++---- README.md | 15 - man/econid-package.Rd | 2 tests/testthat/helper.R | 27 + tests/testthat/test-add_entity_pattern.R | 12 tests/testthat/test-data.R | 133 +++++---- tests/testthat/test-list_entity_patterns.R | 8 tests/testthat/test-reset_patterns.R | 14 - tests/testthat/test-standardize-entity.R | 402 +++++++++++++++++++---------- 17 files changed, 649 insertions(+), 317 deletions(-)
Title: Identify Relevant Clinical Codes and Evaluate Their Use
Description: Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Author: Edward Burn [aut, cre] ,
Marta Alcalde-Herraiz [aut] ,
Marti Catala [aut] ,
Xihang Chen [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [aut] ,
Danielle Newby [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CodelistGenerator versions 4.0.0 dated 2025-12-17 and 4.0.1 dated 2026-01-08
DESCRIPTION | 6 - MD5 | 12 +- NEWS.md | 52 +++++++++++ R/benchmarkCodelistGenerator.R | 4 R/runSearch.R | 23 ---- R/summariseCodeUse.R | 5 + inst/doc/a10_CodelistGeneratorBenchmark.html | 126 +++++++++++++-------------- 7 files changed, 135 insertions(+), 93 deletions(-)
More information about CodelistGenerator at CRAN
Permanent link
Title: Set of Tools to Compute Various Climate Indices
Description: Set of tools to compute metrics and indices for climate analysis.
The package provides functions to compute extreme indices, evaluate the
agreement between models and combine theses models into an ensemble. Multi-model
time series of climate indices can be computed either after averaging the 2-D
fields from different models provided they share a common grid or by combining
time series computed on the model native grid. Indices can be assigned weights
and/or combined to construct new indices. The package makes use of some of the
methods described in:
N. Manubens et al. (2018) <doi:10.1016/j.envsoft.2018.01.018>.
Author: BSC-CNS [aut, cph],
Nuria Perez-Zanon [aut] ,
An-Chi Ho [ctb],
Victoria Agudetse [cre],
Nicolau Manubens [ctb],
Alasdair Hunter [aut],
Louis-Philippe Caron [ctb],
Eva Rifa [ctb],
Ulrich Drepper [ctb],
David Bronaugh [ctb],
James Hiebert [ctb]
Maintainer: Victoria Agudetse <victoria.agudetse@bsc.es>
Diff between ClimProjDiags versions 0.3.4 dated 2025-09-01 and 0.3.5 dated 2026-01-08
DESCRIPTION |only MD5 | 16 - NEWS.md | 7 README.md |only build |only inst/doc/anomaly_agreement.html |only inst/doc/diurnaltemp.Rmd |only inst/doc/diurnaltemp.html | 436 ++++++++++++------------------ inst/doc/extreme_indices.Rmd |only inst/doc/extreme_indices.html | 565 +++++++++++++++------------------------- inst/doc/heatcoldwaves.html | 420 +++++++++++------------------ man |only 12 files changed, 565 insertions(+), 879 deletions(-)
Title: Get Data Frame Representations of 'Elasticsearch' Results
Description: 'Elasticsearch' is an open-source, distributed, document-based datastore
(<https://www.elastic.co/products/elasticsearch>).
It provides an 'HTTP' 'API' for querying the database and extracting datasets, but that
'API' was not designed for common data science workflows like pulling large batches of
records and normalizing those documents into a data frame that can be used as a training
dataset for statistical models. 'uptasticsearch' provides an interface for 'Elasticsearch'
that is explicitly designed to make these data science workflows easy and fun.
Author: James Lamb [aut, cre],
Nick Paras [aut],
Austin Dickey [aut],
Michael Frasco [ctb],
Weiwen Gu [ctb],
Will Dearden [ctb],
Uptake Technologies Inc. [cph]
Maintainer: James Lamb <jaylamb20@gmail.com>
Diff between uptasticsearch versions 1.0.0 dated 2025-02-24 and 1.1.0 dated 2026-01-08
DESCRIPTION | 11 +- MD5 | 36 +++---- NAMESPACE | 4 R/es_search.R | 37 +++++-- R/get_fields.R | 9 + R/helperfuns.R | 23 ++-- R/logging.R | 36 ++++--- R/uptasticsearch.R | 1 inst/doc/FAQ.html | 147 +++++++++++++++++++------------ man/doc_shared.Rd | 2 man/es_search.Rd | 9 + man/get_fields.Rd | 4 tests/testthat/test-chomp_aggs.R | 13 -- tests/testthat/test-chomp_hits.R | 13 -- tests/testthat/test-es_search.R | 13 -- tests/testthat/test-get_fields.R | 13 -- tests/testthat/test-integration.R | 33 ++---- tests/testthat/test-parse_date_time.R | 12 -- tests/testthat/test-unpack_nested_data.R | 14 -- 19 files changed, 206 insertions(+), 224 deletions(-)
More information about uptasticsearch at CRAN
Permanent link
Title: qPCR Data Analysis
Description: Tools for qPCR data analysis using Delta Ct and Delta Delta Ct methods, including t-tests, ANOVA, ANCOVA, repeated-measures models, and publication-ready visualizations. The package supports multiple target, and multiple reference genes, and uses a calculation framework adopted from Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods.
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <gh.mirzaghaderi@uok.ac.ir>
Diff between rtpcr versions 2.1.0 dated 2025-12-19 and 2.1.1 dated 2026-01-08
rtpcr-2.1.0/rtpcr/R/plotOneFactor.r |only rtpcr-2.1.0/rtpcr/R/plotThreeFactor.r |only rtpcr-2.1.0/rtpcr/R/plotTwoFactor.r |only rtpcr-2.1.0/rtpcr/inst/doc/vignette.R |only rtpcr-2.1.0/rtpcr/inst/doc/vignette.Rmd |only rtpcr-2.1.0/rtpcr/inst/doc/vignette.html |only rtpcr-2.1.0/rtpcr/man/plotOneFactor.Rd |only rtpcr-2.1.0/rtpcr/man/plotThreeFactor.Rd |only rtpcr-2.1.0/rtpcr/man/plotTwoFactor.Rd |only rtpcr-2.1.0/rtpcr/vignettes/vignette.Rmd |only rtpcr-2.1.0/rtpcr/vignettes/vignette_files |only rtpcr-2.1.1/rtpcr/DESCRIPTION | 17 rtpcr-2.1.1/rtpcr/MD5 | 142 - rtpcr-2.1.1/rtpcr/NAMESPACE | 8 rtpcr-2.1.1/rtpcr/NEWS.md |only rtpcr-2.1.1/rtpcr/R/ANOVA_DCt.r | 369 +-- rtpcr-2.1.1/rtpcr/R/ANOVA_DDCt.r | 513 +---- rtpcr-2.1.1/rtpcr/R/Means_DDCt.r | 58 rtpcr-2.1.1/rtpcr/R/REPEATED_DDCt.r | 524 ++--- rtpcr-2.1.1/rtpcr/R/TTEST_DDCt.r | 245 +- rtpcr-2.1.1/rtpcr/R/efficiency.r | 8 rtpcr-2.1.1/rtpcr/R/globalVariables.r | 3 rtpcr-2.1.1/rtpcr/R/meanTech.r | 9 rtpcr-2.1.1/rtpcr/R/multiplot.r | 36 rtpcr-2.1.1/rtpcr/R/package_data.r | 32 rtpcr-2.1.1/rtpcr/R/plotFactor.r |only rtpcr-2.1.1/rtpcr/R/qpcrhlpr.r | 964 +++++++++- rtpcr-2.1.1/rtpcr/build/vignette.rds |binary rtpcr-2.1.1/rtpcr/data/data_2factor3ref.rda |binary rtpcr-2.1.1/rtpcr/data/data_repeated_measure_1.rda |binary rtpcr-2.1.1/rtpcr/data/data_repeated_measure_2.rda |binary rtpcr-2.1.1/rtpcr/inst/CITATION | 4 rtpcr-2.1.1/rtpcr/inst/doc/Manual.R |only rtpcr-2.1.1/rtpcr/inst/doc/Manual.Rmd |only rtpcr-2.1.1/rtpcr/inst/doc/Manual.html |only rtpcr-2.1.1/rtpcr/inst/doc/Method.R |only rtpcr-2.1.1/rtpcr/inst/doc/Method.Rmd |only rtpcr-2.1.1/rtpcr/inst/doc/Method.html |only rtpcr-2.1.1/rtpcr/inst/extdata/Lee_etal2020qPCR.csv | 2 rtpcr-2.1.1/rtpcr/inst/extdata/data_1factor.csv | 2 rtpcr-2.1.1/rtpcr/inst/extdata/data_1factor_Two_ref.csv | 32 rtpcr-2.1.1/rtpcr/inst/extdata/data_1factor_one_ref.csv | 2 rtpcr-2.1.1/rtpcr/inst/extdata/data_1factor_one_ref_Eff.csv | 2 rtpcr-2.1.1/rtpcr/inst/extdata/data_2factor.csv | 2 rtpcr-2.1.1/rtpcr/inst/extdata/data_2factor3ref.csv | 2 rtpcr-2.1.1/rtpcr/inst/extdata/data_2factorBlock.csv | 2 rtpcr-2.1.1/rtpcr/inst/extdata/data_2factorBlock3ref.csv | 50 rtpcr-2.1.1/rtpcr/inst/extdata/data_3factor.csv | 2 rtpcr-2.1.1/rtpcr/inst/extdata/data_repeated_measure_1.csv | 14 rtpcr-2.1.1/rtpcr/inst/extdata/data_repeated_measure_2.csv | 38 rtpcr-2.1.1/rtpcr/inst/extdata/data_repeated_measure_3bLock.csv |only rtpcr-2.1.1/rtpcr/inst/extdata/data_withTechRep.csv | 2 rtpcr-2.1.1/rtpcr/inst/extdata/farokh_et_al_2025.csv |only rtpcr-2.1.1/rtpcr/man/ANOVA_DCt.Rd | 130 - rtpcr-2.1.1/rtpcr/man/ANOVA_DDCt.Rd | 183 - rtpcr-2.1.1/rtpcr/man/Lee_etal2020qPCR.Rd | 58 rtpcr-2.1.1/rtpcr/man/Means_DDCt.Rd | 49 rtpcr-2.1.1/rtpcr/man/REPEATED_DDCt.Rd | 117 - rtpcr-2.1.1/rtpcr/man/TTEST_DDCt.Rd | 37 rtpcr-2.1.1/rtpcr/man/data_1factor.Rd | 54 rtpcr-2.1.1/rtpcr/man/data_2factor.Rd | 56 rtpcr-2.1.1/rtpcr/man/data_2factor3ref.Rd | 12 rtpcr-2.1.1/rtpcr/man/data_2factorBlock.Rd | 58 rtpcr-2.1.1/rtpcr/man/data_3factor.Rd | 58 rtpcr-2.1.1/rtpcr/man/data_efficiency.Rd | 50 rtpcr-2.1.1/rtpcr/man/data_repeated_measure_1.Rd | 10 rtpcr-2.1.1/rtpcr/man/data_repeated_measure_2.Rd | 10 rtpcr-2.1.1/rtpcr/man/data_withTechRep.Rd | 60 rtpcr-2.1.1/rtpcr/man/efficiency.Rd | 4 rtpcr-2.1.1/rtpcr/man/figures |only rtpcr-2.1.1/rtpcr/man/meanTech.Rd | 7 rtpcr-2.1.1/rtpcr/man/multiplot.Rd | 36 rtpcr-2.1.1/rtpcr/man/plotFactor.Rd |only rtpcr-2.1.1/rtpcr/vignettes/Manual.Rmd |only rtpcr-2.1.1/rtpcr/vignettes/Method.Rmd |only 75 files changed, 2199 insertions(+), 1874 deletions(-)
Title: Large Language Model (LLM) Tools for Psychological Text Analysis
Description: A collection of large language model (LLM) text analysis methods
designed with psychological data in mind. Currently, LLMing (aka "lemming")
includes a text anomaly detection method based on the angle-based subspace
approach described by Zhang, Lin, and Karim (2015) and a text generation method.
<doi:10.1016/j.ress.2015.05.025>.
Author: Lindley Slipetz [aut, cre],
Teague Henry [aut],
Siqi Sun [ctb]
Maintainer: Lindley Slipetz <ddj6tu@virginia.edu>
Diff between LLMing versions 1.0.0 dated 2025-10-21 and 1.1.0 dated 2026-01-08
DESCRIPTION | 12 ++-- MD5 | 19 ++++--- NEWS.md | 8 +-- R/embed.R | 127 ++++++++++++++++++++++++++-------------------------- R/text_datagen.R |only R/vector_SNN.R | 41 ++++++++-------- README.md | 119 ++++++++++++++++++++++++++++++++++++------------ build/partial.rdb |binary inst/python |only man/embed.Rd | 1 man/text_datagen.Rd |only man/vector_SNN.Rd | 3 - 12 files changed, 198 insertions(+), 132 deletions(-)