Title: Generate Predicted Writing Quality Scores
Description: Imports variables from 'ReaderBench' (Dascalu et al.,
2018)<doi:10.1007/978-3-319-66610-5_48>, 'Coh-Metrix' (McNamara et
al., 2014)<doi:10.1017/CBO9780511894664>, and/or 'GAMET' (Crossley et
al., 2019) <doi:10.17239/jowr-2019.11.02.01> output files; downloads
predictive scoring models described in Mercer & Cannon
(2022)<doi:10.31244/jero.2022.01.03> and Mercer et
al.(2021)<doi:10.1177/0829573520987753>; and generates predicted
writing quality and curriculum-based measurement (McMaster & Espin,
2007)<doi:10.1177/00224669070410020301> scores.
Author: Sterett H. Mercer [aut, cre]
Maintainer: Sterett H. Mercer <sterett.mercer@ubc.ca>
Diff between writeAlizer versions 1.6.4 dated 2025-09-30 and 1.7.0 dated 2025-10-21
writeAlizer-1.6.4/writeAlizer/R/internal_example_helpers.R |only writeAlizer-1.6.4/writeAlizer/R/writeAlizer-package.R |only writeAlizer-1.6.4/writeAlizer/build/partial.rdb |only writeAlizer-1.6.4/writeAlizer/man/dot-wa_rb_keep_exclude_from_sample.Rd |only writeAlizer-1.6.4/writeAlizer/man/writeAlizer.Rd |only writeAlizer-1.6.4/writeAlizer/tests/testthat/test-artifact-registry-ensure-file.R |only writeAlizer-1.6.4/writeAlizer/tests/testthat/test-artifact-registry-loaders.R |only writeAlizer-1.6.4/writeAlizer/tests/testthat/test-artifact-registry-more.R |only writeAlizer-1.7.0/writeAlizer/DESCRIPTION | 18 writeAlizer-1.7.0/writeAlizer/LICENSE |only writeAlizer-1.7.0/writeAlizer/MD5 | 88 +- writeAlizer-1.7.0/writeAlizer/NAMESPACE | 5 writeAlizer-1.7.0/writeAlizer/NEWS.md | 72 + writeAlizer-1.7.0/writeAlizer/R/artifact_registry.R | 388 ++++++---- writeAlizer-1.7.0/writeAlizer/R/cache.R | 2 writeAlizer-1.7.0/writeAlizer/R/download.R | 40 - writeAlizer-1.7.0/writeAlizer/R/file_utilities.R | 137 ++- writeAlizer-1.7.0/writeAlizer/R/model_deps.R | 23 writeAlizer-1.7.0/writeAlizer/R/predict_values.R | 118 ++- writeAlizer-1.7.0/writeAlizer/R/seed_example_helpers.R |only writeAlizer-1.7.0/writeAlizer/R/writeAlizer.R | 73 - writeAlizer-1.7.0/writeAlizer/README.md | 49 - writeAlizer-1.7.0/writeAlizer/build/vignette.rds |only writeAlizer-1.7.0/writeAlizer/inst/CITATION | 45 - writeAlizer-1.7.0/writeAlizer/inst/doc |only writeAlizer-1.7.0/writeAlizer/man/wa_cache_dir.Rd | 2 writeAlizer-1.7.0/writeAlizer/man/wa_download.Rd | 26 writeAlizer-1.7.0/writeAlizer/man/wa_seed_example_models.Rd | 83 +- writeAlizer-1.7.0/writeAlizer/man/writeAlizer-package.Rd | 57 + writeAlizer-1.7.0/writeAlizer/tests/testthat/_snaps |only writeAlizer-1.7.0/writeAlizer/tests/testthat/helper-network.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/helper-quiet.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/helper-sample-paths.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/helper-urls.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/setup-cache.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/setup-reset-options.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-artifact-registry-downloads.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-artifact-registry-paths.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-artifact-registry-registry.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-artifact-registry.R | 286 ++++++- writeAlizer-1.7.0/writeAlizer/tests/testthat/test-cache-checksum.R | 55 - writeAlizer-1.7.0/writeAlizer/tests/testthat/test-download-snapshots.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-download.R | 73 + writeAlizer-1.7.0/writeAlizer/tests/testthat/test-file-utilities-branches.R | 82 +- writeAlizer-1.7.0/writeAlizer/tests/testthat/test-file-utilities-files.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-file-utilities.R | 50 - writeAlizer-1.7.0/writeAlizer/tests/testthat/test-helper-urls.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-import-rb-namebased.R | 25 writeAlizer-1.7.0/writeAlizer/tests/testthat/test-import-validation.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-integration-predict_quality.R | 197 +++-- writeAlizer-1.7.0/writeAlizer/tests/testthat/test-model-deps.R | 125 +-- writeAlizer-1.7.0/writeAlizer/tests/testthat/test-predict-values-input.R |only writeAlizer-1.7.0/writeAlizer/tests/testthat/test-predict-values-negative.R | 71 + writeAlizer-1.7.0/writeAlizer/tests/testthat/test-preprocess-and-download.R | 123 +-- writeAlizer-1.7.0/writeAlizer/tests/testthat/test-smoke-basic.R | 4 writeAlizer-1.7.0/writeAlizer/tests/testthat/test-smoke-rb_mod3all-mocked.R | 58 - writeAlizer-1.7.0/writeAlizer/vignettes |only 57 files changed, 1665 insertions(+), 710 deletions(-)
Title: Automatic Univariate Time Series Modelling of many Kinds
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
time series models of many kinds.
Harvey AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>.
Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>.
Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>
Diff between UComp versions 5.1.2 dated 2025-10-21 and 5.1.3 dated 2025-10-21
ChangeLog | 2 +- DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/ARIMAmodel.h | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Mediterranean Forest Simulation
Description: Simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Author: Miquel De Caceres [aut, cre, cph] ,
Nicolas Martin-StPaul [aut] ,
Victor Granda [aut] ,
Antoine Cabon [aut] ,
Arsene Druel [aut] ,
Julien Ruffault [aut] ,
Jordi Martinez-Vilalta [ctb] ,
Maurizio Mencuccini [ctb] ,
Francois Pimont [ctb] ,
Herve Cochar [...truncated...]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between medfate versions 4.8.3 dated 2025-08-27 and 4.8.4 dated 2025-10-21
DESCRIPTION | 10 +- MD5 | 68 ++++++++-------- NAMESPACE | 3 R/RcppExports.R | 4 R/defaultControl.R | 9 -- R/extract.R | 33 +++++--- R/plot.spwb.R | 24 +++++ R/plot_internals.R | 83 ++++++++++++++------ R/shinyplot.R | 66 ++++++++++------ R/summary.spwb.R | 9 +- data/SpParamsDefinition.rda |binary man/defaultControl.Rd | 6 - man/extract.Rd | 2 man/plot.spwb.Rd | 13 +++ man/shinyplot.Rd | 3 man/summary.spwb.Rd | 13 ++- src/RcppExports.cpp | 9 +- src/communication_structures.cpp | 31 ++++++- src/communication_structures.h | 2 src/growth.cpp | 13 +-- src/inner_sureau.cpp | 138 +++++++++++++++++++++++++++------- src/inner_sureau.h | 2 src/modelInput.cpp | 16 ++- src/phenology.cpp | 13 ++- src/spwb.cpp | 15 ++- src/spwb_day.cpp | 94 +++++++++++------------ src/spwb_day.h | 2 src/struct_sureau.h | 1 src/transpiration_advanced.cpp | 37 +++++---- src/transpiration_basic.cpp | 8 + tests/testthat/Rplots.pdf |binary tests/testthat/test_fordyn.R | 11 ++ tests/testthat/test_growth.R | 8 + tests/testthat/test_post_processing.R | 21 +++++ tests/testthat/test_spwb.R | 45 +++++++++++ 35 files changed, 579 insertions(+), 233 deletions(-)
Title: Implementations of Semi-Supervised Learning Approaches for
Classification
Description: A collection of implementations of semi-supervised classifiers
and methods to evaluate their performance. The package includes implementations
of, among others, Implicitly Constrained Learning, Moment Constrained Learning,
the Transductive SVM, Manifold regularization, Maximum Contrastive Pessimistic
Likelihood estimation, S4VM and WellSVM.
Author: Jesse Krijthe [aut, cre]
Maintainer: Jesse Krijthe <jkrijthe@gmail.com>
Diff between RSSL versions 0.9.7 dated 2023-12-07 and 0.9.8 dated 2025-10-21
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 1 + R/svmd.R | 1 + man/RSSL-package.Rd | 2 +- src/utils.cpp | 3 +-- 6 files changed, 14 insertions(+), 13 deletions(-)
Title: Robust Functional Linear Regression
Description: Functions for implementing robust methods for functional linear regression. In the functional linear regression, we consider scalar-on-function linear regression and function-on-function linear regression.
Author: Ufuk Beyaztas [aut, cre, cph] ,
Han Lin Shang [aut]
Maintainer: Ufuk Beyaztas <ufukbeyaztas@gmail.com>
Diff between robflreg versions 1.2 dated 2024-01-23 and 1.3 dated 2025-10-21
ChangeLog | 5 +++++ DESCRIPTION | 18 ++++++++++-------- MD5 | 35 ++++++++++++++++++++++++++++++----- NAMESPACE | 13 ++++++++++++- R/BIC_fun.R |only R/BIC_fun_JAS.R |only R/calculate_percentile.R |only R/check_loss.R |only R/fpqr.R |only R/fpqr_dgp.R |only R/getAmat.R |only R/par_opt.R |only R/paramCV.R |only R/pen2SLS_est.R |only R/pqr.R |only R/predict_fpqr.R |only R/predict_sffr2SLS.R |only R/qcov.R |only R/sff_dgp.R |only R/sffr_pen2SLS.R |only R/smooth_fun.R |only R/svd_flip.R |only R/utils.R |only R/var.sel.R | 42 +++++++++++++++++++++--------------------- man/fpqr.Rd |only man/fpqr_dgp.Rd |only man/predict_fpqr.Rd |only man/predict_sffr2SLS.Rd |only man/robflreg-package.Rd | 40 +++++++++++++++++++++++++++++----------- man/sff_dgp.Rd |only man/sffr_pen2SLS.Rd |only 31 files changed, 107 insertions(+), 46 deletions(-)
Title: Loglikelihood Adjustment for Extreme Value Models
Description: Performs adjusted inferences based on model objects fitted, using
maximum likelihood estimation, by the extreme value analysis packages
'eva' <https://cran.r-project.org/package=eva>,
'evd' <https://cran.r-project.org/package=evd>,
'evir' <https://cran.r-project.org/package=evir>,
'extRemes' <https://cran.r-project.org/package=extRemes>,
'fExtremes' <https://cran.r-project.org/package=fExtremes>,
'ismev' <https://cran.r-project.org/package=ismev>,
'mev' <https://cran.r-project.org/package=mev>,
'POT' <https://cran.r-project.org/package=POT> and
'texmex' <https://cran.r-project.org/package=texmex>.
Adjusted standard errors and an adjusted loglikelihood are provided, using
the 'chandwich' package <https://cran.r-project.org/package=chandwich>
and the object-oriented features of the 'sandwich' package
<https://cran.r-project.org/package=sandwich>. The adjustment is based on a
robust sandwich estimator of the parameter covar [...truncated...]
Author: Paul J. Northrop [aut, cre, cph],
Camellia Yin [aut, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between lax versions 1.2.3 dated 2024-02-25 and 1.2.4 dated 2025-10-21
DESCRIPTION | 10 ++++---- MD5 | 44 +++++++++++++++++------------------ NAMESPACE | 1 NEWS.md | 7 +++++ R/alogLik_methods.R | 16 +++++++++++-- R/bernoulli.R | 4 +-- R/lax-internal.R | 4 +-- R/mev.R | 32 +++++++++++++++++--------- R/mev_egp.R | 13 ++++++++-- R/return_level.R | 4 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/lax-vignette.R | 16 ++++++------- inst/doc/lax-vignette.Rmd | 2 - inst/doc/lax-vignette.html | 10 ++++---- man/alogLik.Rd | 2 - man/bernoulli.Rd | 4 +-- man/lax-internal.Rd | 2 - man/logLik.logLikVec.Rd | 16 ++++++++++++- man/logLikVec.Rd | 12 +++++++++ man/return_level.Rd | 2 - tests/testthat/test-logLik-mev.R | 48 ++++++++++++++++++++++++++------------- vignettes/lax-vignette.Rmd | 2 - 23 files changed, 168 insertions(+), 83 deletions(-)
Title: List Things to Do
Description: Manage a 'GitHub' problem using R: wrangle issues, labels and
milestones. It includes functions for storing, prioritizing (sorting),
displaying, adding, deleting, and selecting (filtering) issues based
on qualitative and quantitative information. Issues (labels and
milestones) are written in lists and categorized into the S3 class to
be easily manipulated as datasets in R.
Author: Tanguy Barthelemy [aut, cre]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between IssueTrackeR versions 1.2.0 dated 2025-07-16 and 1.3.0 dated 2025-10-21
IssueTrackeR-1.2.0/IssueTrackeR/inst/data_issues/list_issues.yaml |only IssueTrackeR-1.3.0/IssueTrackeR/DESCRIPTION | 8 IssueTrackeR-1.3.0/IssueTrackeR/LICENSE | 4 IssueTrackeR-1.3.0/IssueTrackeR/MD5 | 76 IssueTrackeR-1.3.0/IssueTrackeR/NAMESPACE | 13 IssueTrackeR-1.3.0/IssueTrackeR/NEWS.md | 29 IssueTrackeR-1.3.0/IssueTrackeR/R/IssueTrackeR-package.R | 38 IssueTrackeR-1.3.0/IssueTrackeR/R/check.R |only IssueTrackeR-1.3.0/IssueTrackeR/R/comments.R |only IssueTrackeR-1.3.0/IssueTrackeR/R/finding-objects.R |only IssueTrackeR-1.3.0/IssueTrackeR/R/format.R | 66 IssueTrackeR-1.3.0/IssueTrackeR/R/print.R | 518 +++-- IssueTrackeR-1.3.0/IssueTrackeR/R/summary.R | 92 IssueTrackeR-1.3.0/IssueTrackeR/R/update_database.R | 178 - IssueTrackeR-1.3.0/IssueTrackeR/R/utils.R |only IssueTrackeR-1.3.0/IssueTrackeR/R/wrangling_dataset_issues.R | 958 +++++----- IssueTrackeR-1.3.0/IssueTrackeR/R/wrangling_dataset_labels.R | 90 IssueTrackeR-1.3.0/IssueTrackeR/R/wrangling_dataset_milestones.R | 76 IssueTrackeR-1.3.0/IssueTrackeR/R/wrangling_issues.R | 74 IssueTrackeR-1.3.0/IssueTrackeR/R/wrangling_repo.R |only IssueTrackeR-1.3.0/IssueTrackeR/R/zzz.R | 22 IssueTrackeR-1.3.0/IssueTrackeR/README.md | 58 IssueTrackeR-1.3.0/IssueTrackeR/inst/data_issues/closed_issues.yaml |only IssueTrackeR-1.3.0/IssueTrackeR/inst/data_issues/generate-files.R |only IssueTrackeR-1.3.0/IssueTrackeR/inst/data_issues/list_labels.yaml | 25 IssueTrackeR-1.3.0/IssueTrackeR/inst/data_issues/list_milestones.yaml | 3 IssueTrackeR-1.3.0/IssueTrackeR/inst/data_issues/open_issues.yaml |only IssueTrackeR-1.3.0/IssueTrackeR/man/IssueTrackeR-package.Rd | 48 IssueTrackeR-1.3.0/IssueTrackeR/man/figures/logo.svg |only IssueTrackeR-1.3.0/IssueTrackeR/man/format_labels.Rd | 74 IssueTrackeR-1.3.0/IssueTrackeR/man/format_milestones.Rd | 76 IssueTrackeR-1.3.0/IssueTrackeR/man/get.Rd | 3 IssueTrackeR-1.3.0/IssueTrackeR/man/get_all_repos.Rd |only IssueTrackeR-1.3.0/IssueTrackeR/man/new_issue.Rd | 15 IssueTrackeR-1.3.0/IssueTrackeR/man/new_issues.Rd | 8 IssueTrackeR-1.3.0/IssueTrackeR/man/print.Rd | 8 IssueTrackeR-1.3.0/IssueTrackeR/man/summary.Rd | 5 IssueTrackeR-1.3.0/IssueTrackeR/man/update_database.Rd | 114 - IssueTrackeR-1.3.0/IssueTrackeR/man/with_labels.Rd |only IssueTrackeR-1.3.0/IssueTrackeR/man/with_text.Rd |only IssueTrackeR-1.3.0/IssueTrackeR/man/write.Rd | 2 IssueTrackeR-1.3.0/IssueTrackeR/tests/spelling.R | 14 IssueTrackeR-1.3.0/IssueTrackeR/tests/testthat.R | 24 IssueTrackeR-1.3.0/IssueTrackeR/tests/testthat/helper.R | 64 IssueTrackeR-1.3.0/IssueTrackeR/tests/testthat/test-check.R |only IssueTrackeR-1.3.0/IssueTrackeR/tests/testthat/test-get_issues.R | 114 - 46 files changed, 1589 insertions(+), 1308 deletions(-)
Title: Maximum Likelihood Analysis of Animal Movement Behavior Using
Multivariate Hidden Markov Models
Description: Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, hierarchical HMMs, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, random effects, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.
Author: Brett McClintock [aut, cre],
Theo Michelot [aut]
Maintainer: Brett McClintock <brett.mcclintock@noaa.gov>
Diff between momentuHMM versions 1.5.6 dated 2025-07-21 and 1.5.7 dated 2025-10-21
momentuHMM-1.5.6/momentuHMM/vignettes/plot_buffaloExampleCT011.pdf |only momentuHMM-1.5.6/momentuHMM/vignettes/plot_buffaloResultsCT.pdf |only momentuHMM-1.5.6/momentuHMM/vignettes/plot_buffaloStatesCT.pdf |only momentuHMM-1.5.7/momentuHMM/DESCRIPTION | 10 +-- momentuHMM-1.5.7/momentuHMM/MD5 | 31 ++++------ momentuHMM-1.5.7/momentuHMM/NEWS | 7 ++ momentuHMM-1.5.7/momentuHMM/R/fitHMM.R | 12 --- momentuHMM-1.5.7/momentuHMM/R/momentuHMM_utils.R | 7 ++ momentuHMM-1.5.7/momentuHMM/R/simData.R | 4 - momentuHMM-1.5.7/momentuHMM/README.md | 2 momentuHMM-1.5.7/momentuHMM/build/partial.rdb |binary momentuHMM-1.5.7/momentuHMM/build/vignette.rds |binary momentuHMM-1.5.7/momentuHMM/inst/doc/momentuHMM.pdf |binary momentuHMM-1.5.7/momentuHMM/man/simData.Rd | 2 momentuHMM-1.5.7/momentuHMM/src/densities.h | 26 ++++---- momentuHMM-1.5.7/momentuHMM/src/nLogLike.cpp | 2 momentuHMM-1.5.7/momentuHMM/vignettes/examples/buffaloExample.R | 14 ++++ momentuHMM-1.5.7/momentuHMM/vignettes/examples/elephantExample.R | 8 -- 18 files changed, 71 insertions(+), 54 deletions(-)
More information about AgeTopicModels at CRAN
Permanent link
Title: Variable Selection Using Random Forests
Description: Three steps variable selection procedure based on random forests.
Initially developed to handle high dimensional data (for which number of
variables largely exceeds number of observations), the package is very
versatile and can treat most dimensions of data, for regression and
supervised classification problems. First step is dedicated to eliminate
irrelevant variables from the dataset. Second step aims to select all
variables related to the response for interpretation purpose. Third step
refines the selection by eliminating redundancy in the set of variables
selected by the second step, for prediction purpose.
Genuer, R. Poggi, J.-M. and Tuleau-Malot, C. (2015)
<https://journal.r-project.org/articles/RJ-2015-018/>.
Author: Robin Genuer [aut, cre],
Jean-Michel Poggi [aut],
Christine Tuleau-Malot [aut]
Maintainer: Robin Genuer <Robin.Genuer@u-bordeaux.fr>
Diff between VSURF versions 1.2.0 dated 2022-12-15 and 1.2.1 dated 2025-10-21
VSURF-1.2.0/VSURF/tests/testthat/case_win32_test_iris.R |only VSURF-1.2.0/VSURF/tests/testthat/case_win32b_test_orange.R |only VSURF-1.2.0/VSURF/tests/testthat/testthat-problems.rds |only VSURF-1.2.1/VSURF/DESCRIPTION | 13 +- VSURF-1.2.1/VSURF/MD5 | 36 ++--- VSURF-1.2.1/VSURF/NEWS | 4 VSURF-1.2.1/VSURF/R/VSURF.R | 4 VSURF-1.2.1/VSURF/R/VSURF_interp.R | 52 ++++---- VSURF-1.2.1/VSURF/R/VSURF_pred.R | 60 ++++----- VSURF-1.2.1/VSURF/R/VSURF_thres.R | 2 VSURF-1.2.1/VSURF/R/plot.VSURF.R | 2 VSURF-1.2.1/VSURF/R/predict.VSURF.R | 8 - VSURF-1.2.1/VSURF/man/VSURF.Rd | 4 VSURF-1.2.1/VSURF/man/VSURF_interp.Rd | 2 VSURF-1.2.1/VSURF/man/VSURF_pred.Rd | 2 VSURF-1.2.1/VSURF/man/VSURF_thres.Rd | 2 VSURF-1.2.1/VSURF/man/plot.VSURF.Rd | 2 VSURF-1.2.1/VSURF/man/predict.VSURF.Rd | 8 - VSURF-1.2.1/VSURF/tests/testthat/test_iris.R | 30 +--- VSURF-1.2.1/VSURF/tests/testthat/test_irisParallel.R |only VSURF-1.2.1/VSURF/tests/testthat/test_orange.R | 83 +++++++------ 21 files changed, 161 insertions(+), 153 deletions(-)
Title: An 'SVG' Graphics Device
Description: A graphics device for R that produces 'Scalable Vector
Graphics'. 'svglite' is a fork of the older 'RSvgDevice' package.
Author: Hadley Wickham [aut],
Lionel Henry [aut],
Thomas Lin Pedersen [cre, aut] ,
T Jake Luciani [aut],
Matthieu Decorde [aut],
Vaudor Lise [aut],
Tony Plate [ctb] ,
David Gohel [ctb] ,
Yixuan Qiu [ctb] ,
Hakon Malmedal [ctb] ,
Posit Software, PBC [cph, fnd [...truncated...]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between svglite versions 2.2.1 dated 2025-05-12 and 2.2.2 dated 2025-10-21
svglite-2.2.1/svglite/inst/doc/fonts.R |only svglite-2.2.1/svglite/inst/doc/fonts.Rmd |only svglite-2.2.1/svglite/inst/doc/fonts.html |only svglite-2.2.1/svglite/vignettes/fonts.Rmd |only svglite-2.2.2/svglite/DESCRIPTION | 8 +- svglite-2.2.2/svglite/MD5 | 42 ++++++--------- svglite-2.2.2/svglite/NEWS.md | 5 + svglite-2.2.2/svglite/R/SVG.R | 2 svglite-2.2.2/svglite/R/fonts.R | 2 svglite-2.2.2/svglite/R/inlineSVG.R | 2 svglite-2.2.2/svglite/README.md | 4 - svglite-2.2.2/svglite/build/vignette.rds |binary svglite-2.2.2/svglite/inst/doc/scaling.html | 9 +-- svglite-2.2.2/svglite/man/editSVG.Rd | 2 svglite-2.2.2/svglite/man/htmlSVG.Rd | 2 svglite-2.2.2/svglite/man/stringSVG.Rd | 2 svglite-2.2.2/svglite/man/svglite.Rd | 2 svglite-2.2.2/svglite/man/xmlSVG.Rd | 2 svglite-2.2.2/svglite/src/SvgStream.h | 3 - svglite-2.2.2/svglite/tests/testthat/test-clip.svg | 4 + svglite-2.2.2/svglite/tests/testthat/test-no-clip.svg | 4 + svglite-2.2.2/svglite/tests/testthat/test-scale-text.svg | 4 + svglite-2.2.2/svglite/tests/testthat/test-text.R | 12 ---- svglite-2.2.2/svglite/tests/testthat/test-text.svg | 4 + 24 files changed, 63 insertions(+), 52 deletions(-)
Title: Haplotype-Aware CNV Analysis from scRNA-Seq
Description: A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.
Author: Teng Gao [cre, aut],
Ruslan Soldatov [aut],
Hirak Sarkar [aut],
Evan Biederstedt [aut],
Peter Kharchenko [aut]
Maintainer: Teng Gao <tgaoteng@gmail.com>
Diff between numbat versions 1.4.2 dated 2024-09-20 and 1.5.1 dated 2025-10-21
DESCRIPTION | 8 +- MD5 | 28 ++++++--- NEWS.md | 8 ++ R/diagnostics.R | 90 ++++++++++++++++++++++++++++--- R/main.R | 37 +++++++----- R/vis.R | 12 ++-- README.md | 6 ++ inst/bin/get_binned_atac.R |only inst/bin/get_binned_rna.R |only inst/bin/get_gene_binned_intersections.R |only inst/bin/input_prep.R |only inst/bin/pileup_and_phase.R | 25 +++++++- inst/bin/run_numbat_multiome.R |only inst/extdata |only man/annot_consensus.Rd | 4 - man/check_gtf_input.Rd |only man/plot_phylo_heatmap.Rd | 3 + man/run_numbat.Rd | 6 ++ 18 files changed, 183 insertions(+), 44 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate
cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random
effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>.
Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray,
Ghosh-Lin, Binomial regression) with fast computation of influence functions.
Author: Klaus K. Holst [aut, cre],
Thomas Scheike [aut]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.3.7 dated 2025-08-30 and 1.3.8 dated 2025-10-21
DESCRIPTION | 10 MD5 | 97 NAMESPACE | 2 NEWS.md | 4 R/WA-estimands.R | 2 R/binomial.regression.R | 868 ++++++ R/cifreg.R | 4 R/phreg.R | 18 R/phreg_rct.R | 7 R/ratio.regression.R | 19 R/recreg.R | 3074 ++++++++++++------------ R/recurrent.marginal.R | 16 R/restricted.mean.R | 7 R/sim-pc-hazard.R | 100 build/vignette.rds |binary inst/doc/basic-dutils.html | 12 inst/doc/binomial-family.html | 12 inst/doc/binomial-twin.html | 12 inst/doc/binreg-TRS.html | 12 inst/doc/binreg-ate.R | 38 inst/doc/binreg-ate.Rmd | 45 inst/doc/binreg-ate.html | 527 ++-- inst/doc/binreg.html | 12 inst/doc/cifreg.html | 12 inst/doc/cooking-survival-data.R | 210 - inst/doc/cooking-survival-data.Rmd | 329 +- inst/doc/cooking-survival-data.html | 937 +++---- inst/doc/glm-utility.html | 12 inst/doc/haplo-discrete-ttp.html | 12 inst/doc/interval-discrete-survival.html | 12 inst/doc/marginal-cox.html | 12 inst/doc/mediation-survival.html | 12 inst/doc/phreg_rct.Rmd | 4 inst/doc/phreg_rct.html | 17 inst/doc/recurrent-events.html | 14 inst/doc/rmst-ate.html | 32 inst/doc/survival-ate.html | 172 - inst/doc/time-to-event-family-studies-arev.html | 16 inst/doc/twostage-survival.html | 12 inst/doc/while-alive.html | 12 inst/tinytest/test_cluster.R |only man/binregATE.Rd | 13 man/binregG.Rd | 3 man/binregRatio.Rd | 17 man/phreg_rct.Rd | 5 man/sim.cif.Rd | 9 man/sim.recurrent.Rd | 4 vignettes/binreg-ate.Rmd | 45 vignettes/cooking-survival-data.Rmd | 329 +- vignettes/phreg_rct.Rmd | 4 50 files changed, 3991 insertions(+), 3163 deletions(-)
Title: Tools for Nonparametric Martingale Posterior Sampling
Description: Performs Bayesian nonparametric density estimation using Martingale
posterior distributions including the Copula Resampling (CopRe) algorithm.
Also included are a Gibbs sampler for the marginal Gibbs-type mixture model and
an extension to include full uncertainty quantification via a predictive
sequence resampling (SeqRe) algorithm. The CopRe and SeqRe samplers generate
random nonparametric distributions as output, leading to complete nonparametric
inference on posterior summaries. Routines for calculating arbitrary
functionals from the sampled distributions are included as well as an important
algorithm for finding the number and location of modes, which can then be used
to estimate the clusters in the data using, for example, k-means.
Implements work developed in Moya B., Walker S. G. (2022).
<doi:10.48550/arxiv.2206.08418>, Fong, E., Holmes, C., Walker, S. G. (2021)
<doi:10.48550/arxiv.2103.15671>, and Escobar M. D., West, M. (1995)
<doi:10.1080/01621459.1995.10476550 [...truncated...]
Author: Blake Moya [cre, aut],
The University of Texas at Austin [cph, fnd]
Maintainer: Blake Moya <blakemoya@utexas.edu>
Diff between copre versions 0.2.1 dated 2024-05-21 and 0.2.2 dated 2025-10-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 14 +++++++++----- build/partial.rdb |binary src/seq_measures.cpp | 2 +- 5 files changed, 17 insertions(+), 13 deletions(-)
Title: Tools to Visualize CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<https://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsafvis' R-package provides a collection of R-operators for the analysis and
visualization of CM SAF NetCDF data.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsafvis versions 1.2.9 dated 2024-09-30 and 1.3.0 dated 2025-10-21
DESCRIPTION | 12 MD5 | 62 +-- NAMESPACE | 17 NEWS.md | 8 R/fieldmean_and_anomaly_map.R | 13 R/getColors.R | 631 +++++++++++++++++++++++++++++++++ R/helper_time_series_compare.R | 4 R/plot_abs_map.R | 43 +- R/plot_fieldmean.R | 108 ++++- R/plot_fieldmean_and_map.R | 138 ++++--- R/plot_warming_stripes.R | 491 ++++++++++++------------- R/ranking.R | 44 +- R/recalculateImageDimensions.R | 10 R/render_plot.R | 262 +++++++++++-- R/render_plot_1d.R | 11 R/render_plot_1d_advanced.R | 12 R/render_plot_hist_compare.R | 1 R/render_plot_hovmoller.R | 18 R/render_plot_side_by_side.R | 1 R/render_plot_time_series_compare.R | 12 R/render_region_plot.R | 515 +++++++++++++++----------- R/trend_plot.R | 4 inst/WORDLIST | 5 inst/extdata/quicklook_config.yml | 20 + man/render_plot.Rd | 8 man/render_plot_1d.Rd | 12 man/render_plot_1d_advanced.Rd | 12 man/render_plot_hist_compare.Rd | 3 man/render_plot_hovmoller.Rd | 6 man/render_plot_side_by_side.Rd | 3 man/render_plot_time_series_compare.Rd | 12 man/render_region_plot.Rd | 86 +--- 32 files changed, 1843 insertions(+), 741 deletions(-)
Title: Machine Learning Modelling for Everyone
Description: A minimal library specifically designed to make the estimation of
Machine Learning (ML) techniques as easy and accessible as possible,
particularly within the framework of the Knowledge Discovery in
Databases (KDD) process in data mining. The package provides
essential tools to structure and execute each stage of a predictive
or classification modeling workflow, aligning closely with the
fundamental steps of the KDD methodology, from data selection and
preparation, through model building and tuning, to the
interpretation and evaluation of results using Sensitivity Analysis.
The 'MLwrap' workflow is organized into four core steps;
preprocessing(), build_model(), fine_tuning(), and
sensitivity_analysis(). These steps correspond, respectively, to
data preparation and transformation, model construction,
hyperparameter optimization, and sensitivity analysis. The user can
access comprehensive model evaluation results including fit
assessment metrics, plots, predictions, and performance diagn [...truncated...]
Author: Javier Martinez Garcia [aut] ,
Juan Jose Montano Moreno [ctb] ,
Albert Sese [cre, ctb]
Maintainer: Albert Sese <albert.sese@uib.es>
Diff between MLwrap versions 0.2.0 dated 2025-10-11 and 0.2.1 dated 2025-10-21
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/create_xgboost.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: High-Dimensional Model Selection
Description: Model selection and averaging for regression, generalized linear models, generalized additive models, graphical models and mixtures, focusing on Bayesian model selection and information criteria (Bayesian information criterion etc.). See Rossell (2025) <doi:10.5281/zenodo.17119597> (see the URL field below for its URL) for a hands-on book describing the methods, examples and suggested citations if you use the package.
Author: David Rossell [aut, cre],
John D. Cook [ctb],
Donatello Telesca [aut],
P. Roebuck [ctb],
Oriol Abril [aut],
Miquel Torrens [aut],
Peter Mueller [ctb],
William Hallahan [ctb]
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between modelSelection versions 1.0.3 dated 2025-09-21 and 1.0.4 dated 2025-10-21
modelSelection-1.0.3/modelSelection/tests/testthat/testthat-problems.rds |only modelSelection-1.0.4/modelSelection/ChangeLog |only modelSelection-1.0.4/modelSelection/DESCRIPTION | 14 - modelSelection-1.0.4/modelSelection/MD5 | 44 ++--- modelSelection-1.0.4/modelSelection/NAMESPACE | 3 modelSelection-1.0.4/modelSelection/R/RcppExports.R | 12 - modelSelection-1.0.4/modelSelection/R/bms_ortho.R | 34 ++-- modelSelection-1.0.4/modelSelection/R/cil.R | 16 - modelSelection-1.0.4/modelSelection/R/eBayes.R | 14 - modelSelection-1.0.4/modelSelection/R/greedyGLM.R | 14 - modelSelection-1.0.4/modelSelection/R/infocriteria.R | 85 +++++++--- modelSelection-1.0.4/modelSelection/R/localnulltest.R | 26 +-- modelSelection-1.0.4/modelSelection/R/modelSelection.R | 52 +++--- modelSelection-1.0.4/modelSelection/R/modelSelectionGLM.R | 18 +- modelSelection-1.0.4/modelSelection/R/modelsearch.R | 14 - modelSelection-1.0.4/modelSelection/README.md | 4 modelSelection-1.0.4/modelSelection/man/bestBIC.Rd | 30 +++ modelSelection-1.0.4/modelSelection/man/localnulltest.Rd | 10 - modelSelection-1.0.4/modelSelection/man/modelSelection.Rd | 43 ++--- modelSelection-1.0.4/modelSelection/src/RcppExports.cpp | 24 +- modelSelection-1.0.4/modelSelection/src/modelSel_regression.cpp | 30 +-- modelSelection-1.0.4/modelSelection/src/modelSel_regression.h | 6 modelSelection-1.0.4/modelSelection/tests/testthat/test-modelSelection-enum.R | 16 - modelSelection-1.0.4/modelSelection/tests/testthat/test-modelSelection-gibbs.R | 12 - 24 files changed, 301 insertions(+), 220 deletions(-)
More information about modelSelection at CRAN
Permanent link
Title: 'Domino Data R SDK'
Description: A wrapper on top of the 'Domino Data Python SDK' library. It lets
you query and access 'Domino Data Sources' directly from your R environment.
Under the hood, 'Domino Data R SDK' leverages the API provided by the
'Domino Data Python SDK', which must be installed as a prerequisite.
'Domino' is a platform that makes it easy to run your code on scalable
hardware, with integrated version control and collaboration features
designed for analytical workflows. See
<https://docs.dominodatalab.com/en/latest/api_guide/140b48/domino-data-api>
for more information.
Author: Gabriel Haim [aut, cre]
Maintainer: Gabriel Haim <gabriel.haim@dominodatalab.com>
Diff between DominoDataR versions 0.2.3 dated 2023-08-17 and 0.3.0 dated 2025-10-21
DESCRIPTION | 10 ++-- MD5 | 39 ++++++++++++------ NAMESPACE | 9 ++++ R/client.R | 44 ++++++++++++++++++-- R/config.R | 26 +++++++++--- R/http.R | 91 ++++++++++++++++++++++++++++++++++++++++-- R/netapp_volumes.R |only R/python.R | 2 R/zzz.R | 6 ++ README.md | 17 ++++++- man/datasource_client.Rd | 11 ++++- man/encode_url_path.Rd |only man/get_file_url.Rd |only man/get_netapp_token.Rd |only man/get_volume.Rd |only man/list_files.Rd |only man/list_snapshots.Rd |only man/list_volumes.Rd |only man/load_oauth_credentials.Rd | 6 +- man/make_request.Rd |only man/netapp_volume_client.Rd |only man/put_volume_object.Rd |only man/py_select_interpreter.Rd | 2 man/query.Rd | 2 man/save_volume_object.Rd |only man/upload_volume_object.Rd |only tests/testthat/test-client.R | 14 ++++++ 27 files changed, 237 insertions(+), 42 deletions(-)
Title: Running 'MLwiN' from Within R
Description: An R command interface to the 'MLwiN' multilevel
modelling software package.
Author: Zhengzheng Zhang [aut, cre],
Chris Charlton [aut],
Richard Parker [aut],
George Leckie [aut],
William Browne [aut]
Maintainer: Zhengzheng Zhang <zhengzheng236@gmail.com>
Diff between R2MLwiN versions 0.8-9 dated 2024-01-29 and 0.8-10 dated 2025-10-21
DESCRIPTION | 24 ++-- MD5 | 38 +++--- NAMESPACE | 291 ++++++++++++++++++++++++------------------------- NEWS | 15 ++ R/Formula.translate.R | 54 +++++++++ R/R2MLwiN-package.R | 3 R/data-tutorial.R | 2 R/init.R | 4 R/mlwin2bugs.R | 97 ++++------------ R/runMLwiN.R | 197 +++++++++++++++++++++++++++++++-- R/sixway.R | 2 build/partial.rdb |binary demo/MCMCGuide07.R | 14 +- demo/MCMCGuide08.R | 7 + demo/MCMCGuide17.R | 5 man/R2MLwiN-package.Rd | 6 - man/mlwin2bugs.Rd | 52 +------- man/runMLwiN.Rd | 4 man/sixway.Rd | 2 man/tutorial.Rd | 2 20 files changed, 495 insertions(+), 324 deletions(-)
Title: A GUI for Dual and Bulk RNA-Sequencing Analysis
Description: A 'shiny' app that supports both dual and bulk RNA-seq, with the dual
RNA-seq functionality offering the flexibility to perform either a
sequential approach (where reads are mapped separately to each genome)
or a combined approach (where reads are aligned to a single merged
genome). The user-friendly interface automates the analysis process,
providing step-by-step guidance, making it easy for users to navigate
between different analysis steps, and download intermediate results
and publication-ready plots.
Author: Carmine Fruggiero [aut, cre],
Gaetano Aufiero [aut]
Maintainer: Carmine Fruggiero <fruggierocarmine3@gmail.com>
Diff between inDAGO versions 1.0.2 dated 2025-09-19 and 1.0.3 dated 2025-10-21
DESCRIPTION | 14 MD5 | 28 NAMESPACE | 4 R/BulkAlignment.R | 62 + R/CombinedAlignment.R | 41 - R/SequentialAlignment.R | 1178 ++++++++++++++++++------------------- R/app.R | 7 R/mappingBulkServerLogic.R | 505 +++++++-------- R/mappingBulkUserInterface.R | 681 ++++++++++----------- R/mappingSequentialServerLogic.R | 639 ++++++++++---------- R/mappingSequentialUserInterface.R | 742 +++++++++++------------ R/zzz.R | 8 man/BulkAlignment.Rd | 3 tests/testthat.R | 24 tests/testthat/test-inDAGO_shiny.R | 22 15 files changed, 1978 insertions(+), 1980 deletions(-)
Title: Asymptotic Timing
Description: Computing and visualizing comparative
asymptotic timings of different algorithms and code versions.
Also includes functionality for comparing empirical timings with
expected references such as linear or quadratic,
<https://en.wikipedia.org/wiki/Asymptotic_computational_complexity>
Also includes functionality for measuring asymptotic memory and other
quantities.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between atime versions 2025.5.24 dated 2025-05-27 and 2025.9.30 dated 2025-10-21
DESCRIPTION | 17 MD5 | 100 +-- NAMESPACE | 44 - NEWS | 462 +++++++------- R/atime.R | 503 ++++++---------- R/atime_grid.R |only R/predict.R | 246 +++---- R/references.R | 370 +++++------ R/test.R | 771 ++++++++++++------------ R/versions.R | 396 ++++++------ build/vignette.rds |binary inst/doc/Custom_Plots.R | 135 ++-- inst/doc/Custom_Plots.Rmd | 195 +++--- inst/doc/Custom_Plots.html | 445 +++++++------- inst/doc/Custom_References.R | 122 +-- inst/doc/Custom_References.Rmd | 279 ++++---- inst/doc/Custom_References.html | 633 ++++++++++---------- inst/doc/Custom_Units.R | 124 +-- inst/doc/Custom_Units.Rmd | 315 ++++------ inst/doc/Custom_Units.html | 609 ++++++++++--------- inst/doc/cum_median.R | 56 - inst/doc/cum_median.Rmd | 101 +-- inst/doc/cum_median.html | 344 +++++------ inst/doc/regex.R | 120 +-- inst/doc/regex.Rmd | 215 +++--- inst/doc/regex.html | 520 +++++++++------- inst/doc/sparse.R | 378 +++++------- inst/doc/sparse.Rmd | 698 +++++++++++----------- inst/doc/sparse.html | 1248 ++++++++++++++++++++++------------------ inst/example_tests.R | 82 +- inst/global_edit.R | 82 +- man/atime.Rd | 130 ++-- man/atime_grid.Rd | 200 +++--- man/atime_pkg.Rd | 238 +++---- man/atime_test.Rd | 128 ++-- man/atime_test_list.Rd | 164 ++--- man/atime_versions.Rd | 202 +++--- man/atime_versions_exprs.Rd | 180 ++--- man/atime_versions_remove.Rd | 32 - man/glob_find_replace.Rd | 38 - man/references_best.Rd | 104 +-- tests/testthat.R | 4 tests/testthat/test-CRAN.R | 1077 +++++++++++++++++----------------- vignettes/Custom_Plots.Rmd | 195 +++--- vignettes/Custom_References.Rmd | 279 ++++---- vignettes/Custom_Units.Rmd | 315 ++++------ vignettes/cum_median.Rmd | 101 +-- vignettes/data.table__files |only vignettes/git__files |only vignettes/images |only vignettes/regex.Rmd | 215 +++--- vignettes/sparse.Rmd | 698 +++++++++++----------- 52 files changed, 7046 insertions(+), 6864 deletions(-)
Title: Identifiability of Linear Structural Equation Models
Description: Provides routines to check identifiability or non-identifiability
of linear structural equation models as described in Drton, Foygel, and
Sullivant (2011) <doi:10.1214/10-AOS859>, Foygel, Draisma, and Drton (2012)
<doi:10.1214/12-AOS1012>, and other works. The routines are based on the graphical
representation of structural equation models.
Author: Rina Foygel Barber [aut],
Mathias Drton [aut],
Luca Weihs [aut],
Nils Sturma [cre, aut]
Maintainer: Nils Sturma <nils.sturma@epfl.ch>
Diff between SEMID versions 0.4.1 dated 2023-07-19 and 0.4.2 dated 2025-10-21
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- NEWS.md | 3 +++ R/FlowGraph.R | 14 ++++++-------- man/updateEdgeCapacities.Rd | 2 +- 5 files changed, 21 insertions(+), 20 deletions(-)
Title: An R Package for the Mean Measure of Divergence (MMD)
Description: Offers a graphical user interface for the calculation of the mean measure of divergence, with facilities for trait selection and graphical representations <doi:10.1002/ajpa.23336>.
Author: Frederic Santos [aut, cre]
Maintainer: Frederic Santos <frederic.santos@u-bordeaux.fr>
Diff between AnthropMMD versions 4.0.3 dated 2023-11-29 and 4.1.0 dated 2025-10-21
DESCRIPTION | 9 ++--- MD5 | 24 ++++++------- NEWS.md | 9 +++++ R/mmd.R | 15 +++----- R/small_utils.R | 1 build/vignette.rds |binary inst/doc/intro_AnthropMMD.R | 6 +-- inst/doc/intro_AnthropMMD.Rmd | 30 ++++++++++------- inst/doc/intro_AnthropMMD.html | 71 ++++++++++++++++++++++++----------------- man/mmd.Rd | 4 +- tests/testthat/test-mmd.R | 68 +++++++++++++++++++++++++-------------- vignettes/biblio.bib | 9 +++++ vignettes/intro_AnthropMMD.Rmd | 30 ++++++++++------- 13 files changed, 171 insertions(+), 105 deletions(-)
Title: Mapping Cortical Folding Patterns
Description: Visualizes sulcal morphometry data derived from 'BrainVisa' <https://brainvisa.info/> including width, depth, surface area, and length. The package enables mapping of statistical group results or subject-level values onto cortical surface maps, with options to focus on all sulci or only selected regions of interest. Users can display all four measures simultaneously or restrict plots to chosen measures, creating composite, publication-quality brain visualizations in R to support the analysis and interpretation of sulcal morphology.
Author: Mahan Shafie [aut, cre],
Fabrizio Pizzagalli [aut]
Maintainer: Mahan Shafie <mahan.shafie@unito.it>
Diff between sulcimap versions 1.0.5 dated 2025-10-14 and 1.0.6 dated 2025-10-21
DESCRIPTION | 24 +++++++++++++++--------- MD5 | 7 ++++--- NEWS.md | 4 ++++ inst/CITATION |only man/sulcimap-package.Rd | 7 ++++++- 5 files changed, 29 insertions(+), 13 deletions(-)
Title: Reading, Quality Control and Preprocessing of MBA (Multiplex
Bead Assay) Data
Description: Speeds up the process of loading raw data from MBA (Multiplex Bead Assay) examinations, performs quality control checks, and automatically normalises the data, preparing it for more advanced, downstream tasks. The main objective of the package is to create a simple environment for a user, who does not necessarily have experience with R language. The package is developed within the project 'PvSTATEM', which is an international project aiming for malaria elimination.
Author: Jakub Grzywaczewski [aut, cre],
Tymoteusz Kwiecinski [aut] ,
Mateusz Nizwantowski [aut],
Przemyslaw Biecek [ths] ,
Nuno Sepulveda [ths]
Maintainer: Jakub Grzywaczewski <jakubzgrzywaczewski@gmail.com>
Diff between SerolyzeR versions 1.3.0 dated 2025-07-18 and 1.3.1 dated 2025-10-21
SerolyzeR-1.3.0/SerolyzeR/tests/testthat/Rplots.pdf |only SerolyzeR-1.3.0/SerolyzeR/tests/testthat/normalised_data |only SerolyzeR-1.3.1/SerolyzeR/DESCRIPTION | 18 SerolyzeR-1.3.1/SerolyzeR/MD5 | 48 SerolyzeR-1.3.1/SerolyzeR/R/classes-plate.R | 2 SerolyzeR-1.3.1/SerolyzeR/R/classes-plate_builder.R | 2 SerolyzeR-1.3.1/SerolyzeR/R/get-nmfi.R | 2 SerolyzeR-1.3.1/SerolyzeR/R/helpers.R | 31 SerolyzeR-1.3.1/SerolyzeR/R/merge-plate-outputs.R | 175 - SerolyzeR-1.3.1/SerolyzeR/R/parser-xponent.R | 6 SerolyzeR-1.3.1/SerolyzeR/R/plots-standard_curve.R | 1 SerolyzeR-1.3.1/SerolyzeR/R/process-dir.R | 40 SerolyzeR-1.3.1/SerolyzeR/R/process-file.R | 19 SerolyzeR-1.3.1/SerolyzeR/build/partial.rdb |binary SerolyzeR-1.3.1/SerolyzeR/build/vignette.rds |binary SerolyzeR-1.3.1/SerolyzeR/inst/doc/example_script.R | 204 - SerolyzeR-1.3.1/SerolyzeR/inst/doc/example_script.html | 1598 +++++----- SerolyzeR-1.3.1/SerolyzeR/inst/extdata/random_blanks.csv |only SerolyzeR-1.3.1/SerolyzeR/inst/img/EU.jpg |binary SerolyzeR-1.3.1/SerolyzeR/inst/img/overview.png |binary SerolyzeR-1.3.1/SerolyzeR/man/merge_plate_outputs.Rd | 102 SerolyzeR-1.3.1/SerolyzeR/man/try_cast_as_numeric.Rd |only SerolyzeR-1.3.1/SerolyzeR/tests/testthat/test-helpers.R | 17 SerolyzeR-1.3.1/SerolyzeR/tests/testthat/test-model.R | 1 SerolyzeR-1.3.1/SerolyzeR/tests/testthat/test-parser-xponent.R | 5 SerolyzeR-1.3.1/SerolyzeR/tests/testthat/test-parser.R | 1 26 files changed, 1158 insertions(+), 1114 deletions(-)
Title: A Toolbox for Public Health and Epidemiology
Description: A toolbox for making R functions and capabilities more
accessible to students and professionals from Epidemiology and
Public Health related disciplines. Includes a function to report
coefficients and confidence intervals from models using robust
standard errors (when available), functions that expand 'ggplot2'
plots and functions relevant for introductory papers in Epidemiology
or Public Health. Please note that use of the
provided data sets is for educational purposes only.
Author: Josie Athens [aut, cre],
Frank Harell [ctb],
John Fox [ctb],
R-Core [ctb]
Maintainer: Josie Athens <josie.athens@gmail.com>
Diff between pubh versions 2.0.0 dated 2024-10-08 and 3.0.0 dated 2025-10-21
pubh-2.0.0/pubh/man/axis_labs.Rd |only pubh-2.0.0/pubh/man/box_plot.Rd |only pubh-2.0.0/pubh/man/gf_star.Rd |only pubh-2.0.0/pubh/man/hist_norm.Rd |only pubh-3.0.0/pubh/DESCRIPTION | 19 pubh-3.0.0/pubh/MD5 | 61 +- pubh-3.0.0/pubh/NAMESPACE | 25 - pubh-3.0.0/pubh/R/data.R | 23 - pubh-3.0.0/pubh/R/descriptive_functions.R | 102 ++++ pubh-3.0.0/pubh/R/epi_functions.R | 45 -- pubh-3.0.0/pubh/R/misc_functions.R | 147 ++++++- pubh-3.0.0/pubh/R/plot_functions.R | 604 ++++++++--------------------- pubh-3.0.0/pubh/build/vignette.rds |binary pubh-3.0.0/pubh/inst/doc/introduction.R | 88 +--- pubh-3.0.0/pubh/inst/doc/introduction.Rmd | 90 +--- pubh-3.0.0/pubh/inst/doc/introduction.html | 504 +++++++++++++----------- pubh-3.0.0/pubh/man/Fentress.Rd | 2 pubh-3.0.0/pubh/man/Hodgkin.Rd | 8 pubh-3.0.0/pubh/man/Kirkwood.Rd | 4 pubh-3.0.0/pubh/man/Sharples.Rd | 6 pubh-3.0.0/pubh/man/Tuzson.Rd | 3 pubh-3.0.0/pubh/man/bar_error.Rd | 34 - pubh-3.0.0/pubh/man/bland_altman.Rd | 46 -- pubh-3.0.0/pubh/man/bmj.Rd |only pubh-3.0.0/pubh/man/cosm_reg.Rd |only pubh-3.0.0/pubh/man/cosm_sum.Rd |only pubh-3.0.0/pubh/man/cross_tbl.Rd |only pubh-3.0.0/pubh/man/effect_plot.Rd |only pubh-3.0.0/pubh/man/gen_bst_df.Rd | 15 pubh-3.0.0/pubh/man/gg_star.Rd |only pubh-3.0.0/pubh/man/multiple.Rd | 13 pubh-3.0.0/pubh/man/odds_trend.Rd | 25 - pubh-3.0.0/pubh/man/predict_inv.Rd | 5 pubh-3.0.0/pubh/man/qq_plot.Rd | 28 - pubh-3.0.0/pubh/man/strip_error.Rd | 61 -- pubh-3.0.0/pubh/man/theme_pubh.Rd |only pubh-3.0.0/pubh/vignettes/introduction.Rmd | 90 +--- 37 files changed, 949 insertions(+), 1099 deletions(-)
Title: Initialization of Numerical Optimization
Description: Analysis of the initialization for numerical optimization of
real-valued functions, particularly likelihood functions of statistical
models. See <https://loelschlaeger.de/ino/> for more details.
Author: Lennart Oelschlaeger [aut, cre] ,
Marius Oetting [aut] ,
Dietmar Bauer [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between ino versions 1.1.0 dated 2025-07-05 and 1.1.1 dated 2025-10-21
DESCRIPTION | 8 MD5 | 56 NAMESPACE | 158 - NEWS.md | 4 R/autoplot.R | 672 ++--- R/ino-package.R | 232 - R/nop.R | 3140 ++++++++++++------------- README.md | 278 +- build/vignette.rds |binary inst/doc/example_hmm.R | 245 - inst/doc/example_hmm.Rmd | 82 inst/doc/example_hmm.html | 1491 +++++------ inst/doc/ino.R | 310 +- inst/doc/ino.Rmd | 922 +++---- inst/doc/ino.html | 2118 ++++++++-------- man/Nop.Rd | 1510 ++++++------ man/Nop_hmm.Rd | 40 man/autoplot.Nop.Rd | 132 - man/ino-package.Rd | 72 tests/testthat.R | 8 tests/testthat/test-nop.R | 490 +-- vignettes/example_hmm.Rmd | 82 vignettes/figures/hmm-optimization-time-1.png |binary vignettes/figures/hmm-plot-dax-data-1.png |binary vignettes/figures/ino-estimated-mixtures-1.png |binary vignettes/figures/ino-faithful-plot-1.png |binary vignettes/figures/ino-plot-seconds-1.png |binary vignettes/ino.Rmd | 922 +++---- vignettes/ref.bib | 302 +- 29 files changed, 6689 insertions(+), 6585 deletions(-)
Title: Indices and Graphics for Assess Seed Germination Process
Description: A collection of different indices and visualization techniques for evaluate the seed germination process in ecophysiological studies (Lozano-Isla et al. 2019) <doi:10.1111/1440-1703.1275>.
Author: Flavio Lozano-Isla [aut, cre] ,
Omar Benites Alfaro [aut] ,
Marcelo F. Pompelli [aut, ths] ,
Denise Garcia de Santana [aut],
Marli A. Ranal [aut],
Federal University of Pernambuco [cph] ,
Federal Rural University of Pernambuco [cph] ,
Inkaverse [ctb]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between GerminaR versions 2.1.5 dated 2025-03-05 and 2.1.6 dated 2025-10-21
DESCRIPTION | 28 - MD5 | 80 +-- NEWS.md | 15 R/fplot.R | 59 ++ R/ger_summary.R | 96 +++- R/webTable.R | 11 build/vignette.rds |binary inst/GerminaQuant/rsconnect/shinyapps.io/flavjack/germinaquant.dcf | 4 inst/GerminaQuant/server.R | 117 +++-- inst/GerminaQuant/ui.R | 11 inst/doc/GerminaR.R | 11 inst/doc/GerminaR.Rmd | 11 inst/doc/GerminaR.html | 119 ++--- inst/doc/introduction.Rmd | 19 inst/doc/introduction.html | 139 +----- man/GerminaQuant.Rd | 50 +- man/fplot.Rd | 216 +++++----- man/ger_ASG.Rd | 54 +- man/ger_CVG.Rd | 50 +- man/ger_GRP.Rd | 72 +-- man/ger_GRS.Rd | 52 +- man/ger_GSP.Rd | 50 +- man/ger_MGR.Rd | 64 +- man/ger_MGT.Rd | 70 +-- man/ger_SDG.Rd | 50 +- man/ger_SYN.Rd | 72 +-- man/ger_UNC.Rd | 70 +-- man/ger_VGT.Rd | 50 +- man/ger_boxp.Rd | 146 +++--- man/ger_intime.Rd | 104 ++-- man/ger_summary.Rd | 65 +-- man/ger_testcomp.Rd | 86 +-- man/gquant_analysis.Rd | 122 ++--- man/osmp.Rd | 54 +- man/prosopis.Rd | 56 +- man/reexports.Rd | 32 - man/rep_row.Rd | 38 - man/textcolor.Rd | 68 +-- man/webTable.Rd | 68 +-- vignettes/GerminaR.Rmd | 11 vignettes/introduction.Rmd | 19 41 files changed, 1307 insertions(+), 1202 deletions(-)
Title: Ecological Inference in 2x2 Tables
Description: Implements the Bayesian and likelihood methods proposed in Imai, Lu, and Strauss (2008 <doi:10.1093/pan/mpm017>) and (2011 <doi:10.18637/jss.v042.i05>) for ecological inference in 2 by 2 tables as well as the method of bounds introduced by Duncan and Davis (1953). The package fits both parametric and nonparametric models using either the Expectation-Maximization algorithms (for likelihood models) or the Markov chain Monte Carlo algorithms (for Bayesian models). For all models, the individual-level data can be directly incorporated into the estimation whenever such data are available. Along with in-sample and out-of-sample predictions, the package also provides a functionality which allows one to quantify the effect of data aggregation on parameter estimation and hypothesis testing under the parametric likelihood models.
Author: Kosuke Imai [aut, cre],
Ying Lu [aut],
Aaron Strauss [aut],
Hubert Jin [ctb]
Maintainer: Kosuke Imai <imai@Harvard.Edu>
This is a re-admission after prior archival of version 4.0-3 dated 2022-11-03
Diff between eco versions 4.0-3 dated 2022-11-03 and 4.0-4 dated 2025-10-21
ChangeLog | 1 DESCRIPTION | 34 +++++++++-------------------- MD5 | 62 +++++++++++++++++++++++++++--------------------------- R/Qfun.R | 1 R/eco.R | 2 - R/ecoNP.R | 7 +++--- R/emeco.R | 8 +++--- R/predict.eco.R | 2 - R/varcov.R | 1 inst/CITATION | 6 +---- man/Qfun.Rd | 3 ++ man/eco.Rd | 2 - man/ecoML.Rd | 8 +++--- man/ecoNP.Rd | 7 +++--- man/varcov.Rd | 3 ++ src/bayes.c | 4 +-- src/fintegrate.c | 30 +++++++++++++------------- src/gibbsBase.c | 2 - src/gibbsBase2C.c | 4 +-- src/gibbsBaseRC.c | 4 +-- src/gibbsDP.c | 8 +++--- src/gibbsEM.c | 25 +++++++++++++-------- src/gibbsXBase.c | 4 +-- src/gibbsXDP.c | 10 ++++---- src/gibbsZBase.c | 16 ++++++------- src/preBaseX.c | 4 +-- src/preDP.c | 4 +-- src/preDPX.c | 4 +-- src/rand.c | 6 ++--- src/sample.c | 22 +++++++++---------- src/subroutines.c | 22 +++++++++---------- src/vector.c | 15 ++++++------- 32 files changed, 168 insertions(+), 163 deletions(-)
Title: Bayesian Nonparametric Mixture Models
Description: Functions to perform Bayesian nonparametric univariate and multivariate density estimation and clustering, by means of Pitman-Yor mixtures, and dependent Dirichlet process mixtures for partially exchangeable data. See Corradin et al. (2021) <doi:10.18637/jss.v100.i15> for more details.
Author: Riccardo Corradin [aut, cre],
Antonio Canale [ctb],
Bernardo Nipoti [ctb]
Maintainer: Riccardo Corradin <riccardo.corradin@gmail.com>
Diff between BNPmix versions 1.0.2 dated 2022-07-15 and 1.1.0 dated 2025-10-21
DESCRIPTION | 26 +++++++++++++++++++------- MD5 | 19 ++++++++++--------- build/partial.rdb |only build/vignette.rds |binary data/CPP.RData |binary inst/doc/BNPmix.pdf |binary man/BNPmix-package.Rd | 12 +++++++++++- src/DdpFunctions.cpp | 17 ++++++++++++----- src/Distributions.cpp | 37 +++++++++++++++++++++++++++---------- src/Makevars | 2 +- src/Makevars.win | 2 +- 11 files changed, 81 insertions(+), 34 deletions(-)
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Hippocampal
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12' preprocessed
datasets and 'HippUnfold' hippocampal segmentation outputs for a given
sample by restructuring the data values into a single file. The single
file can then be used by the package for analyses independently from
its base dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.4.2 dated 2025-10-01 and 1.4.3 dated 2025-10-21
DESCRIPTION | 10 +- MD5 | 10 +- NEWS.md | 7 + R/VWRfirstrun.R | 133 +++++++++++++++------------ inst/doc/VertexWiseR_surface_extraction.html | 51 +++++----- vignettes/VertexWiseR_surface_extraction.Rmd | 14 +- 6 files changed, 130 insertions(+), 95 deletions(-)
Title: Stochastic Gradient Descent for Scalable Estimation
Description: A fast and flexible set of tools for large scale estimation. It
features many stochastic gradient methods, built-in models, visualization
tools, automated hyperparameter tuning, model checking, interval estimation,
and convergence diagnostics.
Author: Junhyung Lyle Kim [cre, aut],
Dustin Tran [aut],
Panos Toulis [aut],
Tian Lian [ctb],
Ye Kuang [ctb],
Edoardo Airoldi [ctb]
Maintainer: Junhyung Lyle Kim <jlylekim@gmail.com>
Diff between sgd versions 1.1.2 dated 2024-01-31 and 1.1.3 dated 2025-10-21
DESCRIPTION | 10 +++++----- MD5 | 21 +++++++++++---------- NEWS.md |only R/print.sgd.R | 2 +- README.md | 5 ++--- build/vignette.rds |binary man/print.sgd.Rd | 2 +- src/sgd/explicit_sgd.h | 2 +- src/sgd/implicit_sgd.h | 2 +- src/sgd/momentum_sgd.h | 2 +- src/sgd/nesterov_sgd.h | 2 +- src/validity-check/validity_check.h | 2 +- 12 files changed, 25 insertions(+), 25 deletions(-)
Title: Structural Equation Modeling and Twin Modeling in R
Description: Quickly create, run, and report structural equation models, and twin models.
See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS.
Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R.
Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
Author: Timothy C. Bates [aut, cre] ,
Nathan Gillespie [wit],
Hermine Maes [ctb],
Michael C. Neale [ctb],
Joshua N. Pritikin [ctb],
Luis De Araujo [ctb],
Brenton Wiernik [ctb],
Michael Zakharin [wit]
Maintainer: Timothy C. Bates <timothy.c.bates@gmail.com>
This is a re-admission after prior archival of version 4.21.0 dated 2024-11-14
Diff between umx versions 4.21.0 dated 2024-11-14 and 4.59.0 dated 2025-10-21
umx-4.21.0/umx/man/umx_set_plot_use_hrbrthemes.Rd |only umx-4.21.0/umx/man/xmu_scale_wide_data.Rd |only umx-4.59.0/umx/DESCRIPTION | 22 umx-4.59.0/umx/MD5 | 360 +- umx-4.59.0/umx/NAMESPACE | 13 umx-4.59.0/umx/NEWS.md | 40 umx-4.59.0/umx/R/build_run_modify.R | 34 umx-4.59.0/umx/R/financial_functions.R |only umx-4.59.0/umx/R/fit_and_reporting.R | 179 - umx-4.59.0/umx/R/misc_and_utility.R | 1737 +++---------- umx-4.59.0/umx/R/tmx.R | 47 umx-4.59.0/umx/R/umxCLPM.R | 86 umx-4.59.0/umx/R/umxDoC.R | 56 umx-4.59.0/umx/R/umxDoC2.R |only umx-4.59.0/umx/R/umxMRDoC.R | 1049 ++++++- umx-4.59.0/umx/R/umxMatrixFree.R | 2 umx-4.59.0/umx/R/umxPower.R | 2 umx-4.59.0/umx/R/umx_build_umxGxEbiv.R | 5 umx-4.59.0/umx/R/umx_build_umxSexLim.R | 9 umx-4.59.0/umx/R/umx_build_umxSimplex.R | 10 umx-4.59.0/umx/R/xmu.R | 393 ++ umx-4.59.0/umx/R/xmu_update_covar.R |only umx-4.59.0/umx/build/partial.rdb |binary umx-4.59.0/umx/inst/WORDLIST | 17 umx-4.59.0/umx/man/bucks.Rd | 4 umx-4.59.0/umx/man/deg2rad.Rd | 2 umx-4.59.0/umx/man/figures/umx_help_figures.graffle |binary umx-4.59.0/umx/man/fin_JustifiedPE.Rd | 4 umx-4.59.0/umx/man/fin_NI.Rd | 4 umx-4.59.0/umx/man/fin_expected.Rd |only umx-4.59.0/umx/man/fin_interest.Rd | 8 umx-4.59.0/umx/man/fin_net_present_value.Rd |only umx-4.59.0/umx/man/fin_percent.Rd | 4 umx-4.59.0/umx/man/fin_ticker.Rd | 4 umx-4.59.0/umx/man/fin_valuation.Rd | 4 umx-4.59.0/umx/man/ggAddR.Rd | 1 umx-4.59.0/umx/man/install.OpenMx.Rd | 4 umx-4.59.0/umx/man/libs.Rd | 9 umx-4.59.0/umx/man/plot.MxLISRELModel.Rd | 1 umx-4.59.0/umx/man/plot.MxModel.Rd | 1 umx-4.59.0/umx/man/plot.MxModelTwinMaker.Rd | 1 umx-4.59.0/umx/man/plot.percent.Rd | 2 umx-4.59.0/umx/man/print.percent.Rd | 2 umx-4.59.0/umx/man/prolific_anonymize.Rd | 9 umx-4.59.0/umx/man/qm.Rd | 4 umx-4.59.0/umx/man/rad2deg.Rd | 2 umx-4.59.0/umx/man/tmx_show.MxMatrix.Rd | 29 umx-4.59.0/umx/man/tmx_show.MxModel.Rd | 5 umx-4.59.0/umx/man/tmx_show.Rd | 5 umx-4.59.0/umx/man/umx.Rd | 9 umx-4.59.0/umx/man/umxBrownie.Rd | 2 umx-4.59.0/umx/man/umxCLPM.Rd | 6 umx-4.59.0/umx/man/umxDoC.Rd | 4 umx-4.59.0/umx/man/umxLav2RAM.Rd | 4 umx-4.59.0/umx/man/umxMRDoC.Rd | 39 umx-4.59.0/umx/man/umxMatrixFree.Rd | 2 umx-4.59.0/umx/man/umxModel.Rd | 3 umx-4.59.0/umx/man/umxModelNames.Rd | 4 umx-4.59.0/umx/man/umxPlot.Rd | 13 umx-4.59.0/umx/man/umxPlotACE.Rd | 1 umx-4.59.0/umx/man/umxPlotACEcov.Rd | 1 umx-4.59.0/umx/man/umxPlotACEv.Rd | 1 umx-4.59.0/umx/man/umxPlotCP.Rd | 1 umx-4.59.0/umx/man/umxPlotDoC.Rd | 3 umx-4.59.0/umx/man/umxPlotFun.Rd | 4 umx-4.59.0/umx/man/umxPlotGxE.Rd | 1 umx-4.59.0/umx/man/umxPlotGxEbiv.Rd | 1 umx-4.59.0/umx/man/umxPlotIP.Rd | 1 umx-4.59.0/umx/man/umxPlotPredict.Rd |only umx-4.59.0/umx/man/umxPlotSexLim.Rd | 1 umx-4.59.0/umx/man/umxPlotSimplex.Rd | 1 umx-4.59.0/umx/man/umxPower.Rd | 2 umx-4.59.0/umx/man/umxRAM2Lav.Rd | 4 umx-4.59.0/umx/man/umxRenameMatrix.Rd | 3 umx-4.59.0/umx/man/umxSummaryDoC.Rd | 2 umx-4.59.0/umx/man/umxVersion.Rd | 4 umx-4.59.0/umx/man/umx_APA_pval.Rd | 3 umx-4.59.0/umx/man/umx_array_shift.Rd | 4 umx-4.59.0/umx/man/umx_as_numeric.Rd | 2 umx-4.59.0/umx/man/umx_find_object.Rd | 4 umx-4.59.0/umx/man/umx_fun_mean_sd.Rd | 3 umx-4.59.0/umx/man/umx_get_alphas.Rd |only umx-4.59.0/umx/man/umx_get_bracket_addresses.Rd | 3 umx-4.59.0/umx/man/umx_get_checkpoint.Rd | 2 umx-4.59.0/umx/man/umx_get_options.Rd | 2 umx-4.59.0/umx/man/umx_long2wide.Rd | 4 umx-4.59.0/umx/man/umx_lower.tri.Rd | 4 umx-4.59.0/umx/man/umx_make.Rd | 7 umx-4.59.0/umx/man/umx_make_TwinData.Rd | 2 umx-4.59.0/umx/man/umx_make_twin_data_nice.Rd | 2 umx-4.59.0/umx/man/umx_msg.Rd | 4 umx-4.59.0/umx/man/umx_open_CRAN_page.Rd | 4 umx-4.59.0/umx/man/umx_pad.Rd | 4 umx-4.59.0/umx/man/umx_print.Rd | 4 umx-4.59.0/umx/man/umx_residualize.Rd | 2 umx-4.59.0/umx/man/umx_scale_wide_twin_data.Rd | 2 umx-4.59.0/umx/man/umx_set_auto_plot.Rd | 2 umx-4.59.0/umx/man/umx_set_auto_run.Rd | 2 umx-4.59.0/umx/man/umx_set_checkpoint.Rd | 2 umx-4.59.0/umx/man/umx_set_condensed_slots.Rd | 2 umx-4.59.0/umx/man/umx_set_cores.Rd | 2 umx-4.59.0/umx/man/umx_set_data_variance_check.Rd | 2 umx-4.59.0/umx/man/umx_set_dollar_symbol.Rd | 2 umx-4.59.0/umx/man/umx_set_optimization_options.Rd | 2 umx-4.59.0/umx/man/umx_set_optimizer.Rd | 2 umx-4.59.0/umx/man/umx_set_plot_file_suffix.Rd | 2 umx-4.59.0/umx/man/umx_set_plot_format.Rd | 2 umx-4.59.0/umx/man/umx_set_separator.Rd | 2 umx-4.59.0/umx/man/umx_set_silent.Rd | 2 umx-4.59.0/umx/man/umx_set_table_format.Rd | 2 umx-4.59.0/umx/man/umx_standardize.Rd | 3 umx-4.59.0/umx/man/umx_string_to_algebra.Rd | 3 umx-4.59.0/umx/man/umx_strings2numeric.Rd | 4 umx-4.59.0/umx/man/umx_wide2long.Rd | 96 umx-4.59.0/umx/man/umx_wide2longTwinData.Rd |only umx-4.59.0/umx/man/umx_wide4lmer.Rd |only umx-4.59.0/umx/man/xmuHasSquareBrackets.Rd | 3 umx-4.59.0/umx/man/xmuLabel_MATRIX_Model.Rd | 3 umx-4.59.0/umx/man/xmuLabel_Matrix.Rd | 3 umx-4.59.0/umx/man/xmuLabel_RAM_Model.Rd | 3 umx-4.59.0/umx/man/xmuMI.Rd | 3 umx-4.59.0/umx/man/xmuMakeDeviationThresholdsMatrices.Rd | 3 umx-4.59.0/umx/man/xmuMakeOneHeadedPathsFromPathList.Rd | 3 umx-4.59.0/umx/man/xmuMakeTwoHeadedPathsFromPathList.Rd | 3 umx-4.59.0/umx/man/xmuMaxLevels.Rd | 3 umx-4.59.0/umx/man/xmuMinLevels.Rd | 3 umx-4.59.0/umx/man/xmuPropagateLabels.Rd | 3 umx-4.59.0/umx/man/xmuRAM2Ordinal.Rd | 3 umx-4.59.0/umx/man/xmuTwinSuper_Continuous.Rd | 3 umx-4.59.0/umx/man/xmuTwinSuper_NoBinary.Rd | 3 umx-4.59.0/umx/man/xmuTwinUpgradeMeansToCovariateModel.Rd | 3 umx-4.59.0/umx/man/xmu_CI_merge.Rd | 3 umx-4.59.0/umx/man/xmu_CI_stash.Rd | 3 umx-4.59.0/umx/man/xmu_DF_to_mxData_TypeCov.Rd | 3 umx-4.59.0/umx/man/xmu_PadAndPruneForDefVars.Rd | 3 umx-4.59.0/umx/man/xmu_bracket_address2rclabel.Rd | 3 umx-4.59.0/umx/man/xmu_cell_is_on.Rd | 3 umx-4.59.0/umx/man/xmu_check_levels_identical.Rd | 3 umx-4.59.0/umx/man/xmu_check_needs_means.Rd | 3 umx-4.59.0/umx/man/xmu_check_variance.Rd | 7 umx-4.59.0/umx/man/xmu_clean_label.Rd | 3 umx-4.59.0/umx/man/xmu_data_missing.Rd | 3 umx-4.59.0/umx/man/xmu_data_swap_a_block.Rd | 5 umx-4.59.0/umx/man/xmu_describe_data_WLS.Rd | 3 umx-4.59.0/umx/man/xmu_dot_define_shapes.Rd | 2 umx-4.59.0/umx/man/xmu_dot_make_paths.Rd | 3 umx-4.59.0/umx/man/xmu_dot_make_residuals.Rd | 3 umx-4.59.0/umx/man/xmu_dot_maker.Rd | 3 umx-4.59.0/umx/man/xmu_dot_mat2dot.Rd | 2 umx-4.59.0/umx/man/xmu_dot_move_ranks.Rd | 3 umx-4.59.0/umx/man/xmu_dot_rank.Rd | 2 umx-4.59.0/umx/man/xmu_dot_rank_str.Rd | 3 umx-4.59.0/umx/man/xmu_extract_column.Rd | 3 umx-4.59.0/umx/man/xmu_get_CI.Rd | 5 umx-4.59.0/umx/man/xmu_lavaan_process_group.Rd | 3 umx-4.59.0/umx/man/xmu_make_TwinSuperModel.Rd | 3 umx-4.59.0/umx/man/xmu_make_bin_cont_pair_data.Rd | 26 umx-4.59.0/umx/man/xmu_make_mxData.Rd | 3 umx-4.59.0/umx/man/xmu_match.arg.Rd | 3 umx-4.59.0/umx/man/xmu_name_from_lavaan_str.Rd | 3 umx-4.59.0/umx/man/xmu_path2twin.Rd | 3 umx-4.59.0/umx/man/xmu_path_regex.Rd | 3 umx-4.59.0/umx/man/xmu_print_algebras.Rd | 3 umx-4.59.0/umx/man/xmu_rclabel_2_bracket_address.Rd | 3 umx-4.59.0/umx/man/xmu_relevel_factors.Rd | 3 umx-4.59.0/umx/man/xmu_safe_run_summary.Rd | 3 umx-4.59.0/umx/man/xmu_set_sep_from_suffix.Rd | 3 umx-4.59.0/umx/man/xmu_show_fit_or_comparison.Rd | 3 umx-4.59.0/umx/man/xmu_simplex_corner.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_ACE.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_ACEcov.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_ACEv.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_CP.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_IP.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_RAM.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_SexLim.Rd | 3 umx-4.59.0/umx/man/xmu_standardize_Simplex.Rd | 3 umx-4.59.0/umx/man/xmu_start_value_list.Rd | 3 umx-4.59.0/umx/man/xmu_starts.Rd | 3 umx-4.59.0/umx/man/xmu_summary_RAM_group_parameters.Rd | 3 umx-4.59.0/umx/man/xmu_twin_add_WeightMatrices.Rd | 3 umx-4.59.0/umx/man/xmu_twin_check.Rd | 3 umx-4.59.0/umx/man/xmu_twin_get_var_names.Rd | 3 umx-4.59.0/umx/man/xmu_twin_make_def_means_mats_and_alg.Rd | 3 umx-4.59.0/umx/man/xmu_twin_upgrade_selDvs2SelVars.Rd | 3 umx-4.59.0/umx/man/xmu_update_covar.Rd |only umx-4.59.0/umx/tests/testthat.R | 13 187 files changed, 2698 insertions(+), 2033 deletions(-)
Title: Getting Bibliographic Records from 'OpenAlex' Database Using
'DSL' API
Description: A set of tools to extract bibliographic content from
'OpenAlex' database using API <https://docs.openalex.org>.
Author: Massimo Aria [aut, cre, cph] ,
Corrado Cuccurullo [ctb] ,
Trang Le [aut] ,
June Choe [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between openalexR versions 2.0.1 dated 2025-05-04 and 2.0.2 dated 2025-10-21
DESCRIPTION | 8 MD5 | 44 ++-- NEWS.md | 3 R/coro.R | 24 +- R/oa2bibliometrix.R | 46 +++- R/oa2df.R | 350 ++++++++++++++++++++++++++++---------- R/oa_fetch.R | 223 +++++++++++++++--------- R/oa_ngrams.R | 58 ++++-- R/oa_snowball.R | 35 ++- R/openalexR-internal.R | 2 R/simplify.R | 42 +++- R/utils.R | 60 ++++-- README.md | 46 +++- data/concept_abbrev.rda |binary data/oa2df_coverage.rda |binary man/oa_fetch.Rd | 7 man/show_authors.Rd | 4 man/show_works.Rd | 4 tests/testthat/test-coverage.R | 5 tests/testthat/test-group_by.R | 5 tests/testthat/test-oa_fetch.R | 20 ++ tests/testthat/test-oa_snowball.R | 16 + tests/testthat/test-utils.R | 10 - 23 files changed, 701 insertions(+), 311 deletions(-)
Title: An Interface to the Reptile Database
Description: Provides tools to retrieve and summarize taxonomic information and synonymy data for reptile species using data scraped from The Reptile Database website (<https://reptile-database.reptarium.cz/>). Outputs include clean and structured data frames useful for ecological, evolutionary, and conservation research.
Author: Joao Paulo dos Santos Vieira-Alencar [aut, cre] ,
Christoph Liedtke [aut]
Maintainer: Joao Paulo dos Santos Vieira-Alencar <joaopaulo.valencar@gmail.com>
Diff between letsRept versions 1.0.1 dated 2025-08-23 and 1.1.0 dated 2025-10-21
letsRept-1.0.1/letsRept/build/partial.rdb |only letsRept-1.1.0/letsRept/DESCRIPTION | 8 letsRept-1.1.0/letsRept/MD5 | 70 - letsRept-1.1.0/letsRept/NEWS.md | 37 letsRept-1.1.0/letsRept/R/data_allReptiles.R | 2 letsRept-1.1.0/letsRept/R/data_br_snakes_atlas.r |only letsRept-1.1.0/letsRept/R/data_synonymsRef.R | 6 letsRept-1.1.0/letsRept/R/internal_functions.R | 537 +++----- letsRept-1.1.0/letsRept/R/reptAdvancedSearch.R | 5 letsRept-1.1.0/letsRept/R/reptCompare.R | 155 +- letsRept-1.1.0/letsRept/R/reptSearch.R | 12 letsRept-1.1.0/letsRept/R/reptSpecies.R | 67 - letsRept-1.1.0/letsRept/R/reptSplitCheck.R | 17 letsRept-1.1.0/letsRept/R/reptStats.R | 7 letsRept-1.1.0/letsRept/R/reptSync.R | 24 letsRept-1.1.0/letsRept/R/reptSynonyms.R | 135 -- letsRept-1.1.0/letsRept/R/reptTidySyn.R | 2 letsRept-1.1.0/letsRept/README.md | 37 letsRept-1.1.0/letsRept/build/vignette.rds |binary letsRept-1.1.0/letsRept/data/allReptiles.rda |binary letsRept-1.1.0/letsRept/data/allSynonymsRef.rda |binary letsRept-1.1.0/letsRept/data/br_snakes_atlas.rda |only letsRept-1.1.0/letsRept/inst/CITATION | 26 letsRept-1.1.0/letsRept/inst/doc/case-study.R |only letsRept-1.1.0/letsRept/inst/doc/case-study.Rmd |only letsRept-1.1.0/letsRept/inst/doc/case-study.html |only letsRept-1.1.0/letsRept/inst/doc/letsRept.R | 23 letsRept-1.1.0/letsRept/inst/doc/letsRept.Rmd | 74 - letsRept-1.1.0/letsRept/inst/doc/letsRept.html | 910 ++++++-------- letsRept-1.1.0/letsRept/man/allReptiles.Rd | 2 letsRept-1.1.0/letsRept/man/allSynonymsRef.Rd | 6 letsRept-1.1.0/letsRept/man/br_snakes_atlas.Rd |only letsRept-1.1.0/letsRept/man/reptCompare.Rd | 28 letsRept-1.1.0/letsRept/man/reptSpecies.Rd | 13 letsRept-1.1.0/letsRept/man/reptSplitCheck.Rd | 11 letsRept-1.1.0/letsRept/man/reptSync.Rd | 6 letsRept-1.1.0/letsRept/man/reptSynonyms.Rd | 24 letsRept-1.1.0/letsRept/tests/testthat/test-reptCompare.R | 4 letsRept-1.1.0/letsRept/vignettes/case-study.Rmd |only letsRept-1.1.0/letsRept/vignettes/letsRept.Rmd | 74 - 40 files changed, 1200 insertions(+), 1122 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 0.5.0 dated 2025-10-19 and 0.5.1 dated 2025-10-21
DESCRIPTION | 12 - MD5 | 12 - NAMESPACE | 1 NEWS.md | 10 + R/plot_multiple_answers.R | 185 ++++++++++++++++++++++++++-- man/plot_multiple_answers.Rd | 42 +++++- tests/testthat/test-plot_multiple_answers.R | 32 ++++ 7 files changed, 272 insertions(+), 22 deletions(-)
Title: Steve's Miscellaneous Functions
Description: These are miscellaneous functions that I find useful for my research and teaching.
The contents include themes for plots, functions for simulating
quantities of interest from regression models, functions for simulating various
forms of fake data for instructional/research purposes, and many more. All told, the functions
provided here are broadly useful for data organization, data presentation, data recoding,
and data simulation.
Author: Steve Miller [aut, cre],
Ben Bolker [ctb],
Dave Armstrong [ctb],
John Fox [ctb],
Winston Chang [ctb],
Brian Ripley [ctb],
Bill Venables [ctb],
Pascal van Kooten [ctb],
Gerko Vink [ctb],
Paul Williamson [ctb],
Andreas Beger [ctb] ,
Vincent Arel-Bundoc [...truncated...]
Maintainer: Steve Miller <steven.v.miller@gmail.com>
Diff between stevemisc versions 1.8.0 dated 2024-08-23 and 1.9.0 dated 2025-10-21
DESCRIPTION | 17 +++++----- MD5 | 35 +++++++++++----------- NAMESPACE | 3 + NEWS.md | 6 +++ R/at.R | 80 +++++++++++++++++++++++++++++++++++++++++++++++++++ R/db_lselect.R | 4 +- R/linloess_plot.R | 74 ++++++++++++++++++++++++++++++++++++----------- R/print_refs.R | 51 ++++++++++++++++++++++++-------- R/ps_btscs.R | 2 - R/rd_plot.R | 11 ++++--- R/sbtscs.R | 2 - inst |only man/at.Rd | 18 +++++++++++ man/db_lselect.Rd | 4 +- man/linloess_plot.Rd | 41 ++++++++++++++++++-------- man/print_refs.Rd | 43 +++++++++++++++++++-------- man/ps_btscs.Rd | 2 - man/rd_plot.Rd | 7 +++- man/sbtscs.Rd | 2 - 19 files changed, 309 insertions(+), 93 deletions(-)
Title: Mixed Model Association Test for GEne-Environment Interaction
Description: Use a 'glmmkin' class object (GMMAT package) from the null model to perform generalized linear mixed model-based single-variant and variant set main effect tests, gene-environment interaction tests, and joint tests for association, as proposed in Wang et al. (2020) <DOI:10.1002/gepi.22351>.
Author: Xinyu Wang [aut],
Han Chen [aut, cre],
Duy Pham [aut],
Kenneth Westerman [ctb],
Cong Pan [aut],
Eric Biggers [ctb, cph] ,
Tino Reichardt [ctb, cph] library),
Meta Platforms, Inc. and affiliates [cph] library)
Maintainer: Han Chen <hanchenphd@gmail.com>
Diff between MAGEE versions 1.4.3 dated 2025-07-12 and 1.4.4 dated 2025-10-21
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- build/vignette.rds |binary data/example.rda |binary inst/doc/MAGEE.R | 9 ++++++--- inst/doc/MAGEE.Rnw | 23 ++++++++++++++++------- inst/doc/MAGEE.pdf |binary man/MAGEE-package.Rd | 4 ++-- src/fitglmm.cpp | 4 ++-- src/fitmagee.cpp | 2 +- vignettes/MAGEE.Rnw | 23 ++++++++++++++++------- 11 files changed, 59 insertions(+), 38 deletions(-)
Title: Kriging Methods for Computer Experiments
Description: Estimation, validation and prediction of kriging models. Important functions : km, print.km, plot.km, predict.km.
Author: Olivier Roustant [aut, cre] ,
David Ginsbourger [aut] ,
Yves Deville [aut] ,
Clement Chevalier [ctb],
Yann Richet [ctb]
Maintainer: Olivier Roustant <roustant@insa-toulouse.fr>
Diff between DiceKriging versions 1.6.0 dated 2021-02-23 and 1.6.1 dated 2025-10-21
DiceKriging-1.6.0/DiceKriging/README.md |only DiceKriging-1.6.1/DiceKriging/CHANGELOG | 14 +++- DiceKriging-1.6.1/DiceKriging/DESCRIPTION | 39 +++++++++-- DiceKriging-1.6.1/DiceKriging/MD5 | 40 ++++++------ DiceKriging-1.6.1/DiceKriging/R/kmEstimate.R | 6 + DiceKriging-1.6.1/DiceKriging/R/kmStruct.R | 2 DiceKriging-1.6.1/DiceKriging/R/logLikFun.R | 4 - DiceKriging-1.6.1/DiceKriging/build |only DiceKriging-1.6.1/DiceKriging/inst/CITATION | 28 +++----- DiceKriging-1.6.1/DiceKriging/man/DiceKriging-package.Rd | 16 +--- DiceKriging-1.6.1/DiceKriging/man/covIso-class.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/covTensorProduct-class.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/covVector.dx.Rd | 4 - DiceKriging-1.6.1/DiceKriging/man/km.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/leaveOneOut.km.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/leaveOneOutFun.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/leaveOneOutGrad.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/logLik.km.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/nuggetvalue.Rd | 10 +-- DiceKriging-1.6.1/DiceKriging/man/predict.km.Rd | 2 DiceKriging-1.6.1/DiceKriging/man/update.km.Rd | 2 DiceKriging-1.6.1/DiceKriging/tests/testthat/test-km.R | 13 ++- 22 files changed, 113 insertions(+), 81 deletions(-)
Title: Automatic Univariate Time Series Modelling of many Kinds
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
time series models of many kinds.
Harvey AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Hyndman RJ, Koehler AB, Ord JK, and Snyder RD (2008) <doi:10.1007/978-3-540-71918-2>.
Gómez V, Maravall A (2000) <doi:10.1002/9781118032978>.
Pedregal DJ, Trapero JR and Holgado E (2024) <doi:10.1016/j.ijforecast.2023.09.004>.
Author: Diego J. Pedregal [aut, cre]
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>
Diff between UComp versions 5.1.1 dated 2025-07-21 and 5.1.2 dated 2025-10-21
UComp-5.1.1/UComp/src/oldBSMmodel.h |only UComp-5.1.2/UComp/ChangeLog | 3 UComp-5.1.2/UComp/DESCRIPTION | 8 UComp-5.1.2/UComp/MD5 | 41 UComp-5.1.2/UComp/R/ARIMAS3functions.R | 5 UComp-5.1.2/UComp/R/ARIMAmodel.R | 11 UComp-5.1.2/UComp/R/ETSS3functions.R | 5 UComp-5.1.2/UComp/R/ETSmodel.R | 4 UComp-5.1.2/UComp/R/ETSvalidate.R | 4 UComp-5.1.2/UComp/R/TETSS3functions.R | 5 UComp-5.1.2/UComp/R/TETSmodel.R | 4 UComp-5.1.2/UComp/R/TETSvalidate.R | 4 UComp-5.1.2/UComp/R/UCestim.R | 35 UComp-5.1.2/UComp/R/UCmodel.R | 4 UComp-5.1.2/UComp/R/tools.R | 249 - UComp-5.1.2/UComp/man/plotSlide.Rd | 84 UComp-5.1.2/UComp/man/slide.Rd | 130 UComp-5.1.2/UComp/src/ARIMAmodel.h | 34 UComp-5.1.2/UComp/src/BSMmodel.h | 6379 ++++++++++++++++----------------- UComp-5.1.2/UComp/src/ETSmodel.h | 52 UComp-5.1.2/UComp/src/SSpace.h | 14 UComp-5.1.2/UComp/src/UCompC.cpp | 33 22 files changed, 3621 insertions(+), 3487 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-20 4.1.0
2025-05-28 4.0.4
2024-11-25 4.0.3
2024-08-16 4.0.2
2024-07-10 4.0.1
2023-12-13 3.0.2
2023-05-15 3.0.1
2023-02-09 2.3.0
2022-09-02 2.2.0
2022-06-15 2.1.1
2022-04-02 2.1.0
2022-02-22 2.0.2
2022-01-06 2.0.1
2021-02-04 1.5.3
2021-01-05 1.5.2
2020-06-01 1.5.1
2020-05-29 1.5.0
2020-03-17 1.4.3
2019-10-19 1.4.2
2019-09-03 1.4.1
2019-06-06 1.4.0
Title: Spatial Modeling on Stream Networks
Description: Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance (Ver Hoef, J.M. and Peterson, E.E., (2010) <DOI:10.1198/jasa.2009.ap08248>.) Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included.
Author: Michael Dumelle [aut, cre] ,
Jay M. Ver Hoef [aut],
Erin Peterson [aut],
Alan Pearse [ctb],
Dan Isaak [ctb],
Ryan A. Hill [ctb],
Marc Weber [ctb]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between SSN2 versions 0.3.1 dated 2025-09-30 and 0.4.0 dated 2025-10-21
DESCRIPTION | 16 MD5 | 104 +-- NEWS.md | 17 R/AIC_deprecated.R | 266 ++++----- R/AICc.R | 140 ++--- R/AUROC.R | 42 - R/SSN2.R | 62 +- R/Torgegram.R | 616 +++++++++++------------ R/anova.R | 518 +++++++++---------- R/augment.R | 566 ++++++++++----------- R/checks.R | 366 ++++++------- R/cov_matrix.R | 718 +++++++++++++------------- R/cov_vector.R | 588 ++++++++++----------- R/data.R | 254 ++++----- R/emmeans.R | 108 ++-- R/get_cov_vector.R | 132 ++-- R/get_data_object_bigdata.R | 517 ++++++++++--------- R/get_data_object_bigdata_glm.R | 39 - R/get_dist_object_bigdata.R | 584 ++++++++++----------- R/get_model_stats_bigdata_glm.R | 440 ++++++++-------- R/glance.R | 126 ++-- R/glances.R | 302 +++++------ R/initial.R | 636 +++++++++++------------ R/local.R | 8 R/logLik.R | 104 +-- R/loocv_glm.R | 476 ++++++++--------- R/plot.R | 576 ++++++++++----------- R/predict.R | 4 R/predict_glm.R | 1044 +++++++++++++++++++-------------------- R/predict_terms.R | 226 ++++---- R/ssn_glm.R | 3 R/ssn_import.R | 586 ++++++++++----------- R/ssn_lm.R | 5 R/ssn_simulate.R | 234 ++++---- R/utils.R | 170 +++--- R/zzz.R | 30 - README.md | 518 +++++++++---------- inst/doc/introduction.R | 368 ++++++------- inst/doc/introduction.Rmd | 2 inst/doc/introduction.pdf |binary inst/references.bib | 1044 ++++++++++++++++++++------------------- man/SSN2-package.Rd | 2 man/predict.SSN2.Rd | 4 man/ssn_glm.Rd | 6 man/ssn_lm.Rd | 4 tests/testthat/helper-data.R | 34 - tests/testthat/test-Torgegram.R | 156 ++--- tests/testthat/test-extras.R | 608 +++++++++++----------- tests/testthat/test-local.R | 194 +++---- tests/testthat/test-ssn-object.R | 228 ++++---- tests/testthat/test-ssn_glm.R | 618 +++++++++++------------ tests/testthat/test-ssn_lm.R | 602 +++++++++++----------- vignettes/introduction.Rmd | 2 53 files changed, 7553 insertions(+), 7460 deletions(-)
Title: Smooth and Tidy Spatial Features
Description: Tools for smoothing and tidying spatial features
(i.e. lines and polygons) to make them more aesthetically pleasing.
Smooth curves, fill holes, and remove small fragments from lines and
polygons.
Author: Matthew Strimas-Mackey [aut, cre]
Maintainer: Matthew Strimas-Mackey <mstrimas@gmail.com>
Diff between smoothr versions 1.1.0 dated 2025-06-25 and 1.2.1 dated 2025-10-21
smoothr-1.1.0/smoothr/data/jagged_raster.rda |only smoothr-1.1.0/smoothr/man/jagged_raster.Rd |only smoothr-1.2.1/smoothr/DESCRIPTION | 10 +++--- smoothr-1.2.1/smoothr/MD5 | 19 +++++------- smoothr-1.2.1/smoothr/NEWS.md | 5 +++ smoothr-1.2.1/smoothr/R/data.r | 12 ------- smoothr-1.2.1/smoothr/build/vignette.rds |binary smoothr-1.2.1/smoothr/inst/doc/smoothr.R | 9 +++-- smoothr-1.2.1/smoothr/inst/doc/smoothr.Rmd | 11 +++---- smoothr-1.2.1/smoothr/inst/doc/smoothr.html | 41 ++++++++++++++------------- smoothr-1.2.1/smoothr/inst/extdata |only smoothr-1.2.1/smoothr/vignettes/smoothr.Rmd | 11 +++---- 12 files changed, 58 insertions(+), 60 deletions(-)
Title: Stock Assessment Methods Toolkit
Description: Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries.
'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting,
model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Author: Quang Huynh [aut, cre],
Tom Carruthers [aut],
Adrian Hordyk [aut]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between SAMtool versions 1.8.2 dated 2025-09-05 and 1.9.0 dated 2025-10-21
DESCRIPTION | 10 MD5 | 16 NEWS.md | 3 R/RCM_assess.R | 757 ++++++++++++++++++++++----------------------- R/define_S4_generic_RCM.R | 4 inst/include/RCM.hpp | 35 +- inst/include/ns/ns_RCM.hpp | 38 +- man/RCM.Rd | 4 man/RCM_assess.Rd | 11 9 files changed, 459 insertions(+), 419 deletions(-)
Title: Psychometric Modeling Infrastructure
Description: Infrastructure for psychometric modeling such as data classes (for
item response data and paired comparisons), basic model fitting functions (for
Bradley-Terry, Rasch, parametric logistic IRT, generalized partial credit,
rating scale, multinomial processing tree models), extractor functions for
different types of parameters (item, person, threshold, discrimination,
guessing, upper asymptotes), unified inference and visualizations, and various
datasets for illustration. Intended as a common lightweight and efficient
toolbox for psychometric modeling and a common building block for fitting
psychometric mixture models in package "psychomix" and trees based on
psychometric models in package "psychotree".
Author: Achim Zeileis [aut, cre] ,
Carolin Strobl [aut] ,
Florian Wickelmaier [aut],
Basil Komboz [aut],
Julia Kopf [aut],
Lennart Schneider [aut] ,
Rudolf Debelak [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between psychotools versions 0.7-4 dated 2024-05-11 and 0.7-5 dated 2025-10-21
DESCRIPTION | 21 MD5 | 24 NEWS.md | 9 R/nplmodel.R | 6 build/partial.rdb |binary build/vignette.rds |binary demo/MathExam14W.R | 10 demo/VerbalAggression.R | 12 demo/toolbox1.R | 2 demo/toolbox2.R | 2 inst/doc/toolbox-simulation.pdf |binary man/itemresp.Rd | 2 tests/Examples/psychotools-Ex.Rout.save | 6883 ++++++++++++++++---------------- 13 files changed, 3502 insertions(+), 3469 deletions(-)
Title: Maps of Peru
Description: Information of the centroids and geographical limits of the regions, departments, provinces and districts of Peru.
Author: Jorge L. C. Musaja [aut, cre]
Maintainer: Jorge L. C. Musaja <musajajorge@gmail.com>
Diff between mapsPERU versions 2.0.0 dated 2023-08-14 and 2.0.1 dated 2025-10-21
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/map_DEP.R | 1 + R/map_DIST.R | 36 ++++++++++++++++++------------------ R/map_PROV.R | 1 + R/map_REG.R | 1 + data/map_DEP.rda |binary data/map_DIST.rda |binary data/map_PROV.rda |binary data/map_REG.rda |binary man/map_DEP.Rd | 1 + man/map_DIST.Rd | 2 +- man/map_PROV.Rd | 1 + man/map_REG.Rd | 1 + 14 files changed, 42 insertions(+), 36 deletions(-)
Title: Create 'Makefiles' Using R
Description: A user-friendly interface for the construction of
'Makefiles'.
Author: Andreas Dominik Cullmann [aut, cre],
Kirill Mueller [aut]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between MakefileR versions 1.0 dated 2016-01-08 and 1.1.0 dated 2025-10-21
MakefileR-1.0/MakefileR/inst/doc/demo.R |only MakefileR-1.0/MakefileR/inst/doc/demo.Rmd |only MakefileR-1.0/MakefileR/inst/doc/demo.html |only MakefileR-1.0/MakefileR/inst/web |only MakefileR-1.0/MakefileR/vignettes/demo.Rmd |only MakefileR-1.1.0/MakefileR/.Rinstignore |only MakefileR-1.1.0/MakefileR/DESCRIPTION | 34 ++-- MakefileR-1.1.0/MakefileR/MD5 | 81 ++++------ MakefileR-1.1.0/MakefileR/NEWS.md | 19 ++ MakefileR-1.1.0/MakefileR/R/MakefileR-package.R |only MakefileR-1.1.0/MakefileR/R/comment.R | 2 MakefileR-1.1.0/MakefileR/R/def.R | 14 + MakefileR-1.1.0/MakefileR/R/file.R | 2 MakefileR-1.1.0/MakefileR/R/group.R | 6 MakefileR-1.1.0/MakefileR/R/rule.R | 2 MakefileR-1.1.0/MakefileR/R/text.R | 2 MakefileR-1.1.0/MakefileR/R/throw.R |only MakefileR-1.1.0/MakefileR/R/zzz-autoroxy.R |only MakefileR-1.1.0/MakefileR/README.md | 64 +++++++ MakefileR-1.1.0/MakefileR/build/vignette.rds |binary MakefileR-1.1.0/MakefileR/inst/NEWS.rd |only MakefileR-1.1.0/MakefileR/inst/doc/An_Introduction_to_MakefileR.R |only MakefileR-1.1.0/MakefileR/inst/doc/An_Introduction_to_MakefileR.Rmd |only MakefileR-1.1.0/MakefileR/inst/doc/An_Introduction_to_MakefileR.html |only MakefileR-1.1.0/MakefileR/inst/runit_tests |only MakefileR-1.1.0/MakefileR/inst/tinytest |only MakefileR-1.1.0/MakefileR/inst/vignettes_code |only MakefileR-1.1.0/MakefileR/man/Concatenation.Rd | 3 MakefileR-1.1.0/MakefileR/man/MakefileR-package.Rd |only MakefileR-1.1.0/MakefileR/man/make_comment.Rd | 12 - MakefileR-1.1.0/MakefileR/man/make_def.Rd | 17 +- MakefileR-1.1.0/MakefileR/man/make_group.Rd | 12 - MakefileR-1.1.0/MakefileR/man/make_rule.Rd | 12 - MakefileR-1.1.0/MakefileR/man/make_text.Rd | 12 - MakefileR-1.1.0/MakefileR/man/makefile.Rd | 3 MakefileR-1.1.0/MakefileR/man/throw.Rd |only MakefileR-1.1.0/MakefileR/man/write_makefile.Rd | 1 MakefileR-1.1.0/MakefileR/tests/runit.R |only MakefileR-1.1.0/MakefileR/tests/testthat.R | 2 MakefileR-1.1.0/MakefileR/tests/testthat/test-def.R | 2 MakefileR-1.1.0/MakefileR/tests/testthat/test-file.R | 6 MakefileR-1.1.0/MakefileR/tests/testthat/test-rule.R | 6 MakefileR-1.1.0/MakefileR/tests/testthat/test-throw.R |only MakefileR-1.1.0/MakefileR/tests/testthat/test-write.R |only MakefileR-1.1.0/MakefileR/tests/tinytest.R |only MakefileR-1.1.0/MakefileR/vignettes/An_Introduction_to_MakefileR.Rmd |only 46 files changed, 200 insertions(+), 114 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ctb],
Paola Sebastiani [ctb],
Peter Soly [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.87 dated 2025-09-29 and 2.0.88 dated 2025-10-21
DESCRIPTION | 8 MD5 | 68 +- NEWS | 12 R/epi.nomogram.R | 68 +- R/epi.ssdxsesp.R | 50 + R/rsu.dxtest.R | 805 +++++++++++++++++++++++++---- inst/doc/epiR_descriptive.R | 60 +- inst/doc/epiR_descriptive.Rmd | 176 ++++-- inst/doc/epiR_descriptive.html | 225 +++----- inst/doc/epiR_measures_of_association.R | 78 +- inst/doc/epiR_measures_of_association.Rmd | 137 ++-- inst/doc/epiR_measures_of_association.html | 163 ++--- inst/doc/epiR_sample_size.Rmd | 14 inst/doc/epiR_sample_size.html | 22 inst/doc/epiR_surveillance.R | 52 + inst/doc/epiR_surveillance.Rmd | 68 +- inst/doc/epiR_surveillance.html | 35 - man/epi.bohning.Rd | 2 man/epi.nomogram.Rd | 14 man/epi.ssdxsesp.Rd | 37 + man/rsu.dxtest.Rd | 104 ++- man/rsu.sssep.rs.Rd | 22 vignettes/epiR_descriptive.Rmd | 176 ++++-- vignettes/epiR_measures_of_association.Rmd | 137 ++-- vignettes/epiR_sample_size.Rmd | 14 vignettes/epiR_surveillance.Rmd | 68 +- vignettes/epidemic_curve-01.png |only vignettes/epidemic_curve-02.png |only vignettes/epidemic_curve-03.png |only vignettes/epidemic_curve-04.png |only vignettes/epidemic_curve-05.png |only vignettes/epidemic_curve-06.png |only vignettes/epidemic_curve-07.png |only vignettes/epidemic_curve-08.png |only vignettes/epidemic_curve-09.png |only vignettes/low_bw_adjusted_or.png |only vignettes/low_bw_unadjusted_or.png |only vignettes/map-01.png |only vignettes/map-02.png |only vignettes/prob_dis_freedom.png |only vignettes/ranked_error_bar-01.png |only vignettes/ranked_error_bar-02.png |only vignettes/styles.css | 15 43 files changed, 1761 insertions(+), 869 deletions(-)