Title: Bayesian Penalized Quantile Regression
Description: Bayesian regularized quantile regression utilizing two major classes of shrinkage priors
(the spike-and-slab priors and the horseshoe family of priors) leads to efficient Bayesian
shrinkage estimation, variable selection and valid statistical inference. In this package,
we have implemented robust Bayesian variable selection with spike-and-slab priors under
high-dimensional linear regression models (Fan et al. (2024) <doi:10.3390/e26090794> and
Ren et al. (2023) <doi:10.1111/biom.13670>), and regularized quantile varying
coefficient models (Zhou et al.(2023) <doi:10.1016/j.csda.2023.107808>). In particular,
valid robust Bayesian inferences under both models in the presence of heavy-tailed errors
can be validated on finite samples. Additional models with spike-and-slab priors include
robust Bayesian group LASSO and robust binary Bayesian LASSO (Fan and Wu (2025)
<doi:10.1002/sta4.70078>). Besides, robust sparse Bayesian regression with the horseshoe
family of (hor [...truncated...]
Author: Kun Fan [aut],
Cen Wu [aut, cre],
Jie Ren [aut],
Xiaoxi Li [aut],
Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>
Diff between pqrBayes versions 1.2.0 dated 2025-12-07 and 1.2.1 dated 2026-03-14
DESCRIPTION | 12 ++--- MD5 | 51 +++++++++++++------------ NEWS.md | 4 + R/NonRobust.R |only R/coverage.R | 8 +-- R/estimation.R | 6 +- R/pqrBayes-package.R | 14 +++--- R/pqrBayes.R | 36 ++++++++--------- R/pqrBayes_bin.R | 11 ++++- R/pqrBayes_g.R | 10 ++++ R/pqrBayes_lin.R | 23 ++++++++--- R/pqrBayes_vc.R | 10 ++++ R/predict.pqrBayes.R | 17 ++++---- R/predict_bin.R | 2 R/predict_lin.R | 76 +++++++++++++------------------------ R/predict_lin_nonrobust.R |only R/predict_lin_robust.R |only R/predict_vc.R | 91 ++++++++++++--------------------------------- R/predict_vc_nonrobust.R |only R/predict_vc_robust.R |only R/select.pqrBayes.R | 2 R/select_lin.R | 5 +- README.md | 34 ++++++++-------- man/coverage.Rd | 8 +-- man/estimation.pqrBayes.Rd | 6 +- man/pqrBayes-package.Rd | 14 +++--- man/pqrBayes.Rd | 38 +++++++++--------- man/predict_pqrBayes.Rd | 8 ++- man/select.pqrBayes.Rd | 2 29 files changed, 240 insertions(+), 248 deletions(-)
Title: Density Deconvolution Using Bayesian Semiparametric Methods
Description: Estimates the density of a variable in a measurement error setup, potentially with an excess of zero values. For more details see Sarkar (2021) <doi:10.1080/01621459.2020.1782220>.
Author: Blake Moya [aut],
Mainak Manna [cre, aut],
Abhra Sarkar [aut],
The University of Texas at Austin [cph, fnd]
Maintainer: Mainak Manna <mainakmanna29@utexas.edu>
Diff between BayesDecon versions 0.1.4 dated 2026-01-10 and 0.1.6 dated 2026-03-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/bdeconv.R | 27 ++++++++++++++++++--------- R/subset.R | 2 +- man/bdeconv.Rd | 15 +++++++++++---- 5 files changed, 38 insertions(+), 22 deletions(-)
Title: Threshold Sweep Extensions for Qualitative Comparative Analysis
Description: Provides threshold sweep methods for Qualitative Comparative
Analysis (QCA). Implements Condition Threshold Sweep-Single (CTS-S),
Condition Threshold Sweep-Multiple (CTS-M), Outcome Threshold Sweep (OTS),
and Dual Threshold Sweep (DTS) for systematic exploration of threshold
calibration effects on crisp-set QCA results. These methods extend
traditional robustness approaches by treating threshold variation as an
exploratory tool for discovering causal structures. Also provides Fiss
(2011) <doi:10.5465/amj.2011.60263120> core/peripheral condition
classification via compute_fiss_core() and generate_fiss_chart(), enabling
four-symbol configuration charts that distinguish core conditions (present
in both parsimonious and intermediate solutions) from peripheral conditions
(intermediate only). Built on top of the 'QCA' package by Dusa (2019)
<doi:10.1007/978-3-319-75668-4>, with function arguments following 'QCA'
conventions. Based on set-theoretic methods by Ragin (2008)
<doi: [...truncated...]
Author: Yuki Toyoda [aut, cre],
Japan Society for the Promotion of Science [fnd]
Maintainer: Yuki Toyoda <yuki.toyoda.ds@hosei.ac.jp>
Diff between TSQCA versions 1.3.0 dated 2026-02-18 and 1.3.2 dated 2026-03-14
DESCRIPTION | 22 MD5 | 59 - NAMESPACE | 3 NEWS.md | 127 +++ R/TSQCA-package.R | 466 ++++++------ R/tsqca_config_chart.R | 24 R/tsqca_cts.R | 4 R/tsqca_fiss_core.R |only R/tsqca_ots_dts.R | 8 R/tsqca_report.R | 224 ++++- inst/doc/TSQCA_Reproducible_EN.R | 56 + inst/doc/TSQCA_Reproducible_EN.Rmd | 117 ++- inst/doc/TSQCA_Reproducible_EN.html | 200 ++++- inst/doc/TSQCA_Tutorial_EN.R | 62 + inst/doc/TSQCA_Tutorial_EN.Rmd | 237 ++++-- inst/doc/TSQCA_Tutorial_EN.html | 1397 +++++++++++++++++++----------------- man/SYMBOL_SETS_FISS.Rd |only man/TSQCA-package.Rd | 2 man/build_fiss_matrix.Rd |only man/classify_term_conditions.Rd |only man/compute_fiss_core.Rd |only man/ctSweepM.Rd | 3 man/ctSweepS.Rd | 3 man/dtSweep.Rd | 3 man/extract_cond_status_map.Rd |only man/extract_sol_terms.Rd |only man/generate_fiss_chart.Rd |only man/generate_report.Rd | 215 ++--- man/otSweep.Rd | 5 man/print_fiss_summary.Rd |only man/run_parsimonious.Rd |only man/write_full_report.Rd | 3 man/write_simple_report.Rd | 3 tests/testthat/test-fiss_core.R |only vignettes/TSQCA_Reproducible_EN.Rmd | 117 ++- vignettes/TSQCA_Tutorial_EN.Rmd | 237 ++++-- 36 files changed, 2314 insertions(+), 1283 deletions(-)
Title: Descriptive Statistics and Data Management Tools
Description: Provides tools for early data exploration,
variable inspection, and quick tabulation workflows in 'R'. Summarizes
variable metadata, labels, classes, missing values, and representative
values, with support for readable frequency tables, cross-tabulations,
and APA-style reporting tables. Includes helpers for interactive
codebooks, variable label extraction, clipboard export, and row-wise
descriptive summaries. Designed to make initial data analysis faster,
clearer, and easier to work with in practice.
Author: Amal Tawfik [aut, cre, cph]
Maintainer: Amal Tawfik <amal.tawfik@hesav.ch>
Diff between spicy versions 0.4.2 dated 2026-03-05 and 0.5.0 dated 2026-03-14
DESCRIPTION | 22 - MD5 | 87 ++-- NAMESPACE | 4 NEWS.md | 30 + R/code_book.R | 30 - R/copy_clipboard.R | 70 ++- R/count_n.R | 90 +++- R/cramer_v.R | 34 + R/cross_tab.R | 292 ++++++++++----- R/freq.R | 621 +++++++++++++++++---------------- R/freq_print.R | 417 +++++++++++----------- R/globals.R | 2 R/label_from_names.R | 12 R/mean_n.R | 99 +++-- R/spicy-package.R | 3 R/sum_n.R | 99 +++-- R/table_apa.R |only R/tables_ascii.R | 654 ++++++++++++++++++----------------- R/varlist.R | 106 +++-- README.md | 76 ++-- man/build_ascii_table.Rd | 10 man/code_book.Rd | 4 man/copy_clipboard.Rd | 12 man/count_n.Rd | 22 - man/cramer_v.Rd | 5 man/cross_tab.Rd | 31 + man/figures/logo.png |binary man/figures/logo_dragon.png |only man/figures/logo_old.png |only man/freq.Rd | 3 man/mean_n.Rd | 13 man/print.spicy_freq_table.Rd | 4 man/spicy-package.Rd | 2 man/spicy_print_table.Rd | 22 - man/sum_n.Rd | 13 man/table_apa.Rd |only tests/testthat/test-code_book.R | 1 tests/testthat/test-copy_clipboard.R | 24 - tests/testthat/test-count_n.R | 92 +++- tests/testthat/test-cramer_v.R | 28 - tests/testthat/test-cross_tab.R | 198 +++++----- tests/testthat/test-freq.R | 64 +-- tests/testthat/test-mean_n.R | 36 - tests/testthat/test-sum_n.R | 36 - tests/testthat/test-table_apa.R |only tests/testthat/test-tables_ascii.R | 6 tools/benchmark_cross_tab.R | 65 +++ 47 files changed, 1987 insertions(+), 1452 deletions(-)
Title: qPCR Data Analysis
Description: Tools for qPCR data analysis using Delta Ct and Delta Delta Ct methods, including t-test, Wilcoxon-test, ANOVA 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 <mirzaghaderi@gmail.com>
Diff between rtpcr versions 2.1.5 dated 2026-02-24 and 2.1.6 dated 2026-03-14
rtpcr-2.1.5/rtpcr/inst/doc/Manual.R |only rtpcr-2.1.5/rtpcr/inst/doc/Manual.Rmd |only rtpcr-2.1.5/rtpcr/inst/doc/Manual.html |only rtpcr-2.1.5/rtpcr/inst/shinyapp/README.md |only rtpcr-2.1.5/rtpcr/inst/shinyapp/readme |only rtpcr-2.1.5/rtpcr/man/figures/signif.png |only rtpcr-2.1.5/rtpcr/vignettes/Manual.Rmd |only rtpcr-2.1.6/rtpcr/DESCRIPTION | 6 rtpcr-2.1.6/rtpcr/MD5 | 85 - rtpcr-2.1.6/rtpcr/NEWS.md | 6 rtpcr-2.1.6/rtpcr/R/ANOVA_DCt.R | 64 rtpcr-2.1.6/rtpcr/R/ANOVA_DDCt.R | 74 rtpcr-2.1.6/rtpcr/R/Means_DDCt.R | 3 rtpcr-2.1.6/rtpcr/R/TTEST_DDCt.R | 32 rtpcr-2.1.6/rtpcr/R/WILCOX_DDCt.R | 25 rtpcr-2.1.6/rtpcr/R/globalVariables.R | 2 rtpcr-2.1.6/rtpcr/R/meanTech.R | 11 rtpcr-2.1.6/rtpcr/R/plotFactor.R | 8 rtpcr-2.1.6/rtpcr/build/vignette.rds |binary rtpcr-2.1.6/rtpcr/inst/doc/Method.Rmd | 3 rtpcr-2.1.6/rtpcr/inst/doc/Method.html | 845 +++++++--- rtpcr-2.1.6/rtpcr/inst/doc/manual.R |only rtpcr-2.1.6/rtpcr/inst/doc/manual.Rmd |only rtpcr-2.1.6/rtpcr/inst/doc/manual.html |only rtpcr-2.1.6/rtpcr/inst/extdata/data_2factorBlock3ref.csv | 8 rtpcr-2.1.6/rtpcr/inst/extdata/data_3factor.csv | 6 rtpcr-2.1.6/rtpcr/inst/shinyapp/app.R | 594 ++++--- rtpcr-2.1.6/rtpcr/inst/shinyapp/exp/data_2factorBlock3ref.csv | 8 rtpcr-2.1.6/rtpcr/inst/shinyapp/exp/data_3factor.csv | 6 rtpcr-2.1.6/rtpcr/inst/shinyapp/mean |only rtpcr-2.1.6/rtpcr/inst/shinyapp/rsconnect/shinyapps.io/mirzaghaderi/rtpcr.dcf | 4 rtpcr-2.1.6/rtpcr/inst/shinyapp/www |only rtpcr-2.1.6/rtpcr/man/ANOVA_DCt.Rd | 22 rtpcr-2.1.6/rtpcr/man/ANOVA_DDCt.Rd | 13 rtpcr-2.1.6/rtpcr/man/Means_DDCt.Rd | 3 rtpcr-2.1.6/rtpcr/man/TTEST_DDCt.Rd | 4 rtpcr-2.1.6/rtpcr/man/figures/Rplot02.png |binary rtpcr-2.1.6/rtpcr/man/figures/Rplot03.png |binary rtpcr-2.1.6/rtpcr/man/figures/base.png |binary rtpcr-2.1.6/rtpcr/man/figures/dataStructure1.png |binary rtpcr-2.1.6/rtpcr/man/figures/out.png |binary rtpcr-2.1.6/rtpcr/man/figures/repeated_measure.png |binary rtpcr-2.1.6/rtpcr/man/figures/sampleData1.png |binary rtpcr-2.1.6/rtpcr/man/figures/shiny_rtpcr.png |binary rtpcr-2.1.6/rtpcr/man/figures/techrep.png |binary rtpcr-2.1.6/rtpcr/man/meanTech.Rd | 7 rtpcr-2.1.6/rtpcr/man/plotFactor.Rd | 2 rtpcr-2.1.6/rtpcr/vignettes/Method.Rmd | 3 rtpcr-2.1.6/rtpcr/vignettes/manual.Rmd |only 49 files changed, 1135 insertions(+), 709 deletions(-)
Title: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS
Tool
Description: A memory-efficient, visualize-enhanced, parallel-accelerated Genome-Wide Association Study (GWAS) tool. It can
(1) effectively process large data,
(2) rapidly evaluate population structure,
(3) efficiently estimate variance components several algorithms,
(4) implement parallel-accelerated association tests of markers three methods,
(5) globally efficient design on GWAS process computing,
(6) enhance visualization of related information.
'rMVP' contains three models GLM (Alkes Price (2006) <DOI:10.1038/ng1847>), MLM (Jianming Yu (2006) <DOI:10.1038/ng1702>)
and FarmCPU (Xiaolei Liu (2016) <doi:10.1371/journal.pgen.1005767>); variance components estimation methods EMMAX
(Hyunmin Kang (2008) <DOI:10.1534/genetics.107.080101>;), FaSTLMM (method: Christoph Lippert (2011) <DOI:10.1038/nmeth.1681>,
R implementation from 'GAPIT2': You Tang and Xiaolei Liu (2016) <DOI:10.1371/journal.pone.0107684> and
'SUPER': Qishan Wang and Feng Tian (2014) <DOI:10.1371/ [...truncated...]
Author: Lilin Yin [aut],
Haohao Zhang [aut],
Zhenshuang Tang [aut],
Jingya Xu [aut],
Dong Yin [aut],
Zhiwu Zhang [aut],
Xiaohui Yuan [aut],
Mengjin Zhu [aut],
Shuhong Zhao [aut],
Xinyun Li [aut],
Qishan Wang [ctb],
Feng Tian [ctb],
Hyunmin Kang [ctb],
Xiang [...truncated...]
Maintainer: Xiaolei Liu <xll198708@gmail.com>
This is a re-admission after prior archival of version 1.4.5 dated 2025-07-23
Diff between rMVP versions 1.4.5 dated 2025-07-23 and 1.4.6 dated 2026-03-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/MVP.Data.r | 22 +++++++++++----------- src/assoc.cpp | 12 ++++++------ src/data_converter.cpp | 10 ++++++++-- src/fit_diago.cpp | 4 ++-- 6 files changed, 36 insertions(+), 30 deletions(-)
Title: Reduced Model Space Bayesian Model Averaging
Description: Implements Bayesian model averaging for settings with many
candidate regressors relative to the available sample size, including
cases where the number of regressors exceeds the number of observations.
By restricting attention to models with at most M regressors, the package
supports reduced model space inference, thereby preserving degrees of
freedom for estimation. It provides posterior summaries, Extreme Bounds
Analysis, model selection procedures, joint inclusion measures, and
graphical tools for exploring model probabilities, model size
distributions, and coefficient distributions. The methodological
approach follows Doppelhofer and Weeks (2009) <doi:10.1002/jae.1046>.
Author: Krzysztof Beck [aut, cre]
Maintainer: Krzysztof Beck <beckkrzysztof@gmail.com>
Diff between rmsBMA versions 0.1.1 dated 2026-03-11 and 0.1.2 dated 2026-03-14
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/g_regression.R | 2 +- R/g_regression_fast.R | 2 +- R/g_regression_fast_HC.R | 2 +- inst/doc/rmsBMA.html | 4 ++-- 6 files changed, 13 insertions(+), 13 deletions(-)
Title: Read 'SurveyXact' Data
Description: Imports data from the 'SurveyXact' commercial service
<https://rambollxact.com>, adds variable labels, and converts value
labels to factors in the same order as exported from 'SurveyXact'.
Author: Stephan Daus [aut, cre]
Maintainer: Stephan Daus <stephus.daus@gmail.com>
This is a re-admission after prior archival of version 0.8.4 dated 2023-03-25
Diff between readSX versions 0.8.4 dated 2023-03-25 and 0.8.8 dated 2026-03-14
readSX-0.8.4/readSX/man/figures |only readSX-0.8.8/readSX/DESCRIPTION | 21 readSX-0.8.8/readSX/LICENSE | 4 readSX-0.8.8/readSX/MD5 | 44 - readSX-0.8.8/readSX/NAMESPACE | 32 readSX-0.8.8/readSX/NEWS.md | 43 - readSX-0.8.8/readSX/R/readSX-package.R | 8 readSX-0.8.8/readSX/R/read_surveyxact.R | 428 ++++++------- readSX-0.8.8/readSX/R/utils.R | 173 ++--- readSX-0.8.8/readSX/R/write_data_for_sx.R | 71 +- readSX-0.8.8/readSX/README.md | 8 readSX-0.8.8/readSX/inst/CITATION | 28 readSX-0.8.8/readSX/inst/WORDLIST | 3 readSX-0.8.8/readSX/man/readSX-package.Rd | 48 - readSX-0.8.8/readSX/man/read_surveyxact.Rd | 4 readSX-0.8.8/readSX/man/write_data_for_sx.Rd | 50 - readSX-0.8.8/readSX/tests/testthat.R | 16 readSX-0.8.8/readSX/tests/testthat/test-prep_data_for_sx.R | 24 readSX-0.8.8/readSX/tests/testthat/test-read_surveyxact.R | 124 +++ readSX-0.8.8/readSX/tests/testthat/test-utils.R | 70 +- 20 files changed, 669 insertions(+), 530 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data management
system with support for the Structured Query Language (SQL). This
package includes all of DuckDB and an R Database Interface (DBI)
connector.
Author: Hannes Muehleisen [aut] ,
Mark Raasveldt [aut] ,
Kirill Mueller [cre] ,
Stichting DuckDB Foundation [cph],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrocher [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckdb versions 1.4.4 dated 2026-01-28 and 1.5.0 dated 2026-03-14
DESCRIPTION | 12 MD5 | 83 +++--- NEWS.md | 21 + R/backend-dbplyr__duckdb_connection.R | 2 R/cpp11.R | 8 R/relational.R | 40 ++- R/rethrow-gen.R | 8 R/version.R | 2 inst/include/duckdb_types.hpp | 4 man/duckdb.Rd | 2 man/duckdb_connection-class.Rd | 2 man/duckdb_driver-class.Rd | 2 man/duckdb_result-class.Rd | 2 src/Makevars.duckdb | 7 src/connection.cpp | 4 src/convert.cpp | 4 src/cpp11.cpp | 16 - src/database.cpp | 6 src/duckdb.tar.xz |binary src/include/rapi.hpp | 8 src/include/reltoaltrep.hpp | 8 src/include/sources.mk | 2 src/register.cpp | 4 src/relational.cpp | 35 +- src/reltoaltrep.cpp | 160 +++++++++++-- src/rfuns.cpp | 4 src/scan.cpp | 4 src/signal.cpp | 4 src/statement.cpp | 4 src/transform.cpp | 8 src/types.cpp | 4 src/utils.cpp | 4 tests/testthat.R | 12 tests/testthat/_snaps/backend-dbplyr__duckdb_connection.md | 4 tests/testthat/_snaps/error-handling.md | 16 - tests/testthat/_snaps/relational.md | 31 +- tests/testthat/_snaps/types.md | 2 tests/testthat/test-backend-dbplyr__duckdb_connection.R | 10 tests/testthat/test-numeric.R |only tests/testthat/test-readonly.R | 2 tests/testthat/test-relational.R | 104 +++++++- tests/testthat/test-timezone.R | 8 tests/testthat/test-types.R | 1 43 files changed, 514 insertions(+), 150 deletions(-)
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut],
Jim Hester [aut],
Winston Chang [aut],
Jennifer Bryan [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between devtools versions 2.4.6 dated 2025-10-03 and 2.5.0 dated 2026-03-14
devtools-2.4.6/devtools/inst/doc/dependencies.Rmd |only devtools-2.4.6/devtools/man/devtools-deprecated.Rd |only devtools-2.4.6/devtools/man/remote-reexports.Rd |only devtools-2.4.6/devtools/tests/testthat/test-build-site.R |only devtools-2.4.6/devtools/vignettes/dependencies.Rmd |only devtools-2.5.0/devtools/DESCRIPTION | 28 devtools-2.5.0/devtools/MD5 | 390 ++--- devtools-2.5.0/devtools/NAMESPACE | 228 +- devtools-2.5.0/devtools/NEWS.md | 32 devtools-2.5.0/devtools/R/R.R | 62 devtools-2.5.0/devtools/R/active.R | 109 - devtools-2.5.0/devtools/R/bash.R | 26 devtools-2.5.0/devtools/R/build-manual.R | 61 devtools-2.5.0/devtools/R/build-readme.R | 226 ++ devtools-2.5.0/devtools/R/build-site.R | 46 devtools-2.5.0/devtools/R/check-devtools.R | 290 +-- devtools-2.5.0/devtools/R/check-doc.R | 179 +- devtools-2.5.0/devtools/R/check-git.R | 54 devtools-2.5.0/devtools/R/check-mac.R | 206 +- devtools-2.5.0/devtools/R/check-win.R | 436 +++-- devtools-2.5.0/devtools/R/check.R | 534 +++--- devtools-2.5.0/devtools/R/create.R | 30 devtools-2.5.0/devtools/R/dev-mode.R | 188 +- devtools-2.5.0/devtools/R/devtools-package.R | 46 devtools-2.5.0/devtools/R/document.R | 70 devtools-2.5.0/devtools/R/git.R | 32 devtools-2.5.0/devtools/R/has-tests.R | 24 devtools-2.5.0/devtools/R/import-standalone-obj-type.R |only devtools-2.5.0/devtools/R/import-standalone-purrr.R |only devtools-2.5.0/devtools/R/import-standalone-types-check.R |only devtools-2.5.0/devtools/R/install.R | 452 +++-- devtools-2.5.0/devtools/R/lint.R | 46 devtools-2.5.0/devtools/R/missing-s3.R | 49 devtools-2.5.0/devtools/R/package-deps.R | 14 devtools-2.5.0/devtools/R/package.R | 190 +- devtools-2.5.0/devtools/R/pkgbuild.R | 94 - devtools-2.5.0/devtools/R/pkgload.R | 67 devtools-2.5.0/devtools/R/r-hub.R | 56 devtools-2.5.0/devtools/R/release.R | 764 +++++----- devtools-2.5.0/devtools/R/reload.R | 69 devtools-2.5.0/devtools/R/remotes.R | 296 ++- devtools-2.5.0/devtools/R/revdep.R | 200 +- devtools-2.5.0/devtools/R/run-examples.R | 241 +-- devtools-2.5.0/devtools/R/run-source.R | 334 ++-- devtools-2.5.0/devtools/R/save-all.R | 26 devtools-2.5.0/devtools/R/session-info.R | 71 devtools-2.5.0/devtools/R/show-news.R | 89 - devtools-2.5.0/devtools/R/sitrep.R | 516 +++--- devtools-2.5.0/devtools/R/spell-check.R | 36 devtools-2.5.0/devtools/R/test.R | 461 +++--- devtools-2.5.0/devtools/R/uninstall.R | 59 devtools-2.5.0/devtools/R/usethis.R | 42 devtools-2.5.0/devtools/R/utils.R | 104 - devtools-2.5.0/devtools/R/vignette-r.R | 134 - devtools-2.5.0/devtools/R/vignettes.R | 274 +-- devtools-2.5.0/devtools/R/wd.R | 42 devtools-2.5.0/devtools/R/zzz.R | 56 devtools-2.5.0/devtools/README.md | 345 ++-- devtools-2.5.0/devtools/build/vignette.rds |binary devtools-2.5.0/devtools/inst/WORDLIST | 345 ++-- devtools-2.5.0/devtools/inst/doc/dependencies.html | 720 +++------ devtools-2.5.0/devtools/inst/doc/dependencies.qmd |only devtools-2.5.0/devtools/inst/rstudio/addins.dcf | 48 devtools-2.5.0/devtools/man/as.package.Rd | 42 devtools-2.5.0/devtools/man/bash.Rd | 34 devtools-2.5.0/devtools/man/build.Rd | 252 +-- devtools-2.5.0/devtools/man/build_manual.Rd | 42 devtools-2.5.0/devtools/man/build_readme.Rd |only devtools-2.5.0/devtools/man/build_rmd.Rd | 64 devtools-2.5.0/devtools/man/build_site.Rd | 36 devtools-2.5.0/devtools/man/build_vignettes.Rd | 144 - devtools-2.5.0/devtools/man/check.Rd | 296 +-- devtools-2.5.0/devtools/man/check_doc_fields.Rd |only devtools-2.5.0/devtools/man/check_mac_release.Rd | 99 - devtools-2.5.0/devtools/man/check_man.Rd | 54 devtools-2.5.0/devtools/man/check_rhub.Rd | 80 - devtools-2.5.0/devtools/man/check_win.Rd | 155 +- devtools-2.5.0/devtools/man/clean_vignettes.Rd | 34 devtools-2.5.0/devtools/man/create.Rd | 62 devtools-2.5.0/devtools/man/dev_mode.Rd | 76 devtools-2.5.0/devtools/man/dev_packages.Rd | 24 devtools-2.5.0/devtools/man/dev_sitrep.Rd | 71 devtools-2.5.0/devtools/man/devtools-defunct.Rd |only devtools-2.5.0/devtools/man/devtools-package.Rd | 100 - devtools-2.5.0/devtools/man/document.Rd | 54 devtools-2.5.0/devtools/man/git_checks.Rd | 34 devtools-2.5.0/devtools/man/has_tests.Rd | 24 devtools-2.5.0/devtools/man/install-deprecated.Rd |only devtools-2.5.0/devtools/man/install.Rd | 218 +- devtools-2.5.0/devtools/man/install_deps.Rd | 176 +- devtools-2.5.0/devtools/man/is.package.Rd | 24 devtools-2.5.0/devtools/man/lint.Rd | 52 devtools-2.5.0/devtools/man/load_all.Rd | 240 +-- devtools-2.5.0/devtools/man/loaded_packages.Rd | 32 devtools-2.5.0/devtools/man/missing_s3.Rd | 35 devtools-2.5.0/devtools/man/package_file.Rd | 48 devtools-2.5.0/devtools/man/r_env_vars.Rd | 40 devtools-2.5.0/devtools/man/reexports.Rd | 66 devtools-2.5.0/devtools/man/release.Rd | 79 - devtools-2.5.0/devtools/man/release_checks.Rd | 34 devtools-2.5.0/devtools/man/reload.Rd | 62 devtools-2.5.0/devtools/man/revdep.Rd | 110 - devtools-2.5.0/devtools/man/run_examples.Rd | 108 - devtools-2.5.0/devtools/man/save_all.Rd | 30 devtools-2.5.0/devtools/man/show_news.Rd | 44 devtools-2.5.0/devtools/man/source_gist.Rd | 112 - devtools-2.5.0/devtools/man/source_url.Rd | 86 - devtools-2.5.0/devtools/man/spell_check.Rd | 42 devtools-2.5.0/devtools/man/submit_cran.Rd | 61 devtools-2.5.0/devtools/man/test.Rd | 119 - devtools-2.5.0/devtools/man/uninstall.Rd | 64 devtools-2.5.0/devtools/man/uses_testthat.Rd | 24 devtools-2.5.0/devtools/man/wd.Rd | 40 devtools-2.5.0/devtools/tests/spelling.R | 10 devtools-2.5.0/devtools/tests/testthat.R | 24 devtools-2.5.0/devtools/tests/testthat/_snaps/active.md | 42 devtools-2.5.0/devtools/tests/testthat/_snaps/build-manual.md |only devtools-2.5.0/devtools/tests/testthat/_snaps/build-readme.md | 49 devtools-2.5.0/devtools/tests/testthat/_snaps/check-doc.md |only devtools-2.5.0/devtools/tests/testthat/_snaps/check-win.md | 43 devtools-2.5.0/devtools/tests/testthat/_snaps/check.md |only devtools-2.5.0/devtools/tests/testthat/_snaps/install.md |only devtools-2.5.0/devtools/tests/testthat/_snaps/package.md | 54 devtools-2.5.0/devtools/tests/testthat/_snaps/pkgload.md |only devtools-2.5.0/devtools/tests/testthat/_snaps/release.md |only devtools-2.5.0/devtools/tests/testthat/_snaps/remotes.md |only devtools-2.5.0/devtools/tests/testthat/_snaps/run-source.md | 102 - devtools-2.5.0/devtools/tests/testthat/_snaps/show-news.md |only devtools-2.5.0/devtools/tests/testthat/_snaps/sitrep.md | 210 ++ devtools-2.5.0/devtools/tests/testthat/_snaps/test.md |only devtools-2.5.0/devtools/tests/testthat/_snaps/vignettes.md |only devtools-2.5.0/devtools/tests/testthat/check-results-note.log | 150 - devtools-2.5.0/devtools/tests/testthat/helper.R | 34 devtools-2.5.0/devtools/tests/testthat/setup.R |only devtools-2.5.0/devtools/tests/testthat/shallowRepo/HEAD | 2 devtools-2.5.0/devtools/tests/testthat/shallowRepo/config | 12 devtools-2.5.0/devtools/tests/testthat/shallowRepo/description | 2 devtools-2.5.0/devtools/tests/testthat/shallowRepo/info/exclude | 12 devtools-2.5.0/devtools/tests/testthat/shallowRepo/packed-refs | 4 devtools-2.5.0/devtools/tests/testthat/shallowRepo/refs/tags/v1.10.0 | 2 devtools-2.5.0/devtools/tests/testthat/shallowRepo/shallow | 2 devtools-2.5.0/devtools/tests/testthat/test-active.R | 82 - devtools-2.5.0/devtools/tests/testthat/test-build-manual.R |only devtools-2.5.0/devtools/tests/testthat/test-build-readme.R | 199 +- devtools-2.5.0/devtools/tests/testthat/test-check-doc.R | 79 - devtools-2.5.0/devtools/tests/testthat/test-check-win.R | 59 devtools-2.5.0/devtools/tests/testthat/test-check.R | 29 devtools-2.5.0/devtools/tests/testthat/test-install.R | 55 devtools-2.5.0/devtools/tests/testthat/test-package.R | 24 devtools-2.5.0/devtools/tests/testthat/test-pkgload.R |only devtools-2.5.0/devtools/tests/testthat/test-release.R |only devtools-2.5.0/devtools/tests/testthat/test-reload.R | 61 devtools-2.5.0/devtools/tests/testthat/test-remotes.R |only devtools-2.5.0/devtools/tests/testthat/test-run-examples.R | 16 devtools-2.5.0/devtools/tests/testthat/test-run-source.R | 147 - devtools-2.5.0/devtools/tests/testthat/test-show-news.R |only devtools-2.5.0/devtools/tests/testthat/test-sitrep.R | 257 ++- devtools-2.5.0/devtools/tests/testthat/test-test.R | 191 +- devtools-2.5.0/devtools/tests/testthat/test-uninstall.R | 26 devtools-2.5.0/devtools/tests/testthat/test-utils.R | 13 devtools-2.5.0/devtools/tests/testthat/test-vignettes.R | 131 - devtools-2.5.0/devtools/tests/testthat/testCheckExtrafile/DESCRIPTION | 18 devtools-2.5.0/devtools/tests/testthat/testCheckExtrafile/NAMESPACE | 2 devtools-2.5.0/devtools/tests/testthat/testCheckExtrafile/R/a.R | 6 devtools-2.5.0/devtools/tests/testthat/testCheckExtrafile/an_extra_file | 2 devtools-2.5.0/devtools/tests/testthat/testCheckExtrafile/man/a.Rd | 26 devtools-2.5.0/devtools/tests/testthat/testError/DESCRIPTION | 12 devtools-2.5.0/devtools/tests/testthat/testError/R/error.R | 13 devtools-2.5.0/devtools/tests/testthat/testHelp/DESCRIPTION | 16 devtools-2.5.0/devtools/tests/testthat/testHelp/NAMESPACE | 6 devtools-2.5.0/devtools/tests/testthat/testHelp/R/foofoo.R | 18 devtools-2.5.0/devtools/tests/testthat/testHelp/man/foofoo.Rd | 30 devtools-2.5.0/devtools/tests/testthat/testMarkdownVignettes/DESCRIPTION | 18 devtools-2.5.0/devtools/tests/testthat/testMarkdownVignettes/vignettes/test.Rmd | 26 devtools-2.5.0/devtools/tests/testthat/testMissingNsObject/DESCRIPTION | 12 devtools-2.5.0/devtools/tests/testthat/testMissingNsObject/NAMESPACE | 2 devtools-2.5.0/devtools/tests/testthat/testMissingNsObject/R/a.R | 2 devtools-2.5.0/devtools/tests/testthat/testPkgdown/DESCRIPTION | 24 devtools-2.5.0/devtools/tests/testthat/testPkgdown/NAMESPACE | 6 devtools-2.5.0/devtools/tests/testthat/testPkgdown/R/pkgdown-test-test.R | 21 devtools-2.5.0/devtools/tests/testthat/testPkgdown/_pkgdown.yml | 2 devtools-2.5.0/devtools/tests/testthat/testPkgdown/man/pkgdown_test_test.Rd | 34 devtools-2.5.0/devtools/tests/testthat/testPkgdown/vignettes/test.Rmd | 28 devtools-2.5.0/devtools/tests/testthat/testTest/DESCRIPTION | 28 devtools-2.5.0/devtools/tests/testthat/testTest/NAMESPACE | 4 devtools-2.5.0/devtools/tests/testthat/testTest/R/dummy.R | 1 devtools-2.5.0/devtools/tests/testthat/testTest/tests/testthat.R | 8 devtools-2.5.0/devtools/tests/testthat/testTest/tests/testthat/test-dummy.R | 6 devtools-2.5.0/devtools/tests/testthat/testTest/tests/testthat/test-envvar.R | 6 devtools-2.5.0/devtools/tests/testthat/testTestWithDepends/DESCRIPTION | 18 devtools-2.5.0/devtools/tests/testthat/testTestWithDepends/NAMESPACE | 2 devtools-2.5.0/devtools/tests/testthat/testTestWithDepends/tests/testthat.R | 8 devtools-2.5.0/devtools/tests/testthat/testTestWithDepends/tests/testthat/test-dummy.R | 6 devtools-2.5.0/devtools/tests/testthat/testTestWithFailure/DESCRIPTION | 20 devtools-2.5.0/devtools/tests/testthat/testTestWithFailure/NAMESPACE | 4 devtools-2.5.0/devtools/tests/testthat/testTestWithFailure/R/dummy.R | 1 devtools-2.5.0/devtools/tests/testthat/testTestWithFailure/tests/testthat.R | 8 devtools-2.5.0/devtools/tests/testthat/testTestWithFailure/tests/testthat/test-fail.R | 6 devtools-2.5.0/devtools/tests/testthat/testTestWithFailure/tests/testthat/test-warn.R | 6 devtools-2.5.0/devtools/tests/testthat/testUseData/DESCRIPTION | 14 devtools-2.5.0/devtools/tests/testthat/testUseData/NAMESPACE | 2 devtools-2.5.0/devtools/tests/testthat/testUseData/R/a.R | 1 devtools-2.5.0/devtools/tests/testthat/testVignetteExtras/DESCRIPTION | 14 devtools-2.5.0/devtools/tests/testthat/testVignetteExtras/vignettes/a.R | 2 devtools-2.5.0/devtools/tests/testthat/testVignetteExtras/vignettes/new.Rnw | 8 devtools-2.5.0/devtools/tests/testthat/testVignettes/DESCRIPTION | 14 devtools-2.5.0/devtools/tests/testthat/testVignettes/vignettes/new.Rnw | 10 devtools-2.5.0/devtools/tests/testthat/testVignettesBuilt/DESCRIPTION | 14 devtools-2.5.0/devtools/tests/testthat/testVignettesBuilt/R/code.R | 6 devtools-2.5.0/devtools/tests/testthat/testVignettesBuilt/vignettes/new.Rnw | 22 devtools-2.5.0/devtools/vignettes/dependencies.qmd |only 211 files changed, 8614 insertions(+), 7332 deletions(-)
Title: Bayesian Averaging for Dynamic Panels
Description: Implements Bayesian model averaging for dynamic panels with weakly
exogenous regressors as described in the paper by
Moral-Benito (2013, <doi:10.1080/07350015.2013.818003>).
The package provides functions to estimate dynamic panel data models
and analyze the results of the estimation.
Author: Krzysztof Beck [aut],
Piotr Cukier [aut],
Marcin Dubel [aut, cre],
Mariusz Szczepanczyk [aut],
Mateusz Wyszynski [aut]
Maintainer: Marcin Dubel <marcindubel@gmail.com>
Diff between badp versions 0.4.0 dated 2026-03-11 and 0.4.0.1 dated 2026-03-14
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- README.md | 6 +++--- src/Makevars | 1 + src/Makevars.win | 1 + tests/testthat/test-model_space.R | 2 +- 6 files changed, 17 insertions(+), 15 deletions(-)
Title: Comprehensive ARDL: Panel, Bootstrap and Fourier Methods
Description: A unified framework for Autoregressive Distributed Lag (ARDL) modeling
and cointegration analysis. Implements Panel ARDL with Pooled Mean Group (PMG),
Mean Group (MG), and Dynamic Fixed Effects (DFE) estimators following
Pesaran, Shin & Smith (1999) <doi:10.1002/jae.616>.
Provides bootstrap-based bounds testing per Pesaran, Shin & Smith (2001)
<doi:10.1002/jae.616>. Includes Quantile Nonlinear ARDL (QNARDL) combining
distributional and asymmetric effects based on Shin, Yu & Greenwood-Nimmo (2014)
<doi:10.1007/978-1-4899-8008-3_9>, and Fourier ARDL for modeling smooth
structural breaks following Enders & Lee (2012) <doi:10.1016/j.econlet.2012.05.019>.
Features include Augmented ARDL (AARDL) with deferred t and F tests,
Multiple-Threshold NARDL for complex asymmetries, Rolling/Recursive ARDL
for time-varying relationships, and Panel NARDL for nonlinear panel cointegration.
All methods include comprehensive diagnostics, publication-ready outputs,
an [...truncated...]
Author: Muhammad Abdullah Alkhalaf [aut, cre] ,
Merwan Roudane [ctb]
Maintainer: Muhammad Abdullah Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between ardlverse versions 1.1.2 dated 2026-03-11 and 1.1.3 dated 2026-03-14
DESCRIPTION | 11 ++++------ MD5 | 46 ++++++++++++++++++++++----------------------- R/augmented_ardl.R | 10 ++++----- R/bootstrap_ardl.R | 4 +-- R/fourier_ardl.R | 2 - R/mtnardl.R | 20 +++++++++++++------ R/panel_ardl.R | 2 - R/panel_nardl.R | 10 ++++----- R/qnardl.R | 2 - R/rolling_ardl.R | 8 +++---- man/aardl.Rd | 10 ++++----- man/ardl_diagnostics.Rd | 2 - man/ardlverse-package.Rd | 2 - man/asymmetry_test.Rd | 2 - man/boot_ardl.Rd | 4 +-- man/dynamic_multipliers.Rd | 2 - man/fourier_ardl.Rd | 4 +-- man/fourier_bounds_test.Rd | 2 - man/hausman_test.Rd | 2 - man/mtnardl.Rd | 10 ++++----- man/panel_ardl.Rd | 4 +-- man/pnardl.Rd | 24 +++++++++++------------ man/qnardl.Rd | 4 +-- man/rardl.Rd | 8 +++---- 24 files changed, 101 insertions(+), 94 deletions(-)
Title: Spatio-Temporal DBSCAN Clustering
Description: Implements the ST-DBSCAN (spatio-temporal density-based spatial
clustering of applications with noise) clustering algorithm for detecting
spatially and temporally dense regions in point data, with a fast C++ backend
via 'Rcpp'. Birant and Kut (2007) <doi:10.1016/j.datak.2006.01.013>.
Author: Antoine Le Doeuff [aut, cre]
Maintainer: Antoine Le Doeuff <antoine.ldoeuff@gmail.com>
Diff between stdbscan versions 0.1.0 dated 2026-01-27 and 0.2.0 dated 2026-03-14
stdbscan-0.1.0/stdbscan/src/st_dbscan.cpp |only stdbscan-0.2.0/stdbscan/DESCRIPTION | 12 stdbscan-0.2.0/stdbscan/MD5 | 35 + stdbscan-0.2.0/stdbscan/NAMESPACE | 8 stdbscan-0.2.0/stdbscan/NEWS.md | 16 stdbscan-0.2.0/stdbscan/R/RcppExports.R | 8 stdbscan-0.2.0/stdbscan/R/predict.R |only stdbscan-0.2.0/stdbscan/R/stdbscan.R | 246 +++++++++--- stdbscan-0.2.0/stdbscan/R/utils.R |only stdbscan-0.2.0/stdbscan/README.md | 27 - stdbscan-0.2.0/stdbscan/inst/doc/stop-identification.R | 42 +- stdbscan-0.2.0/stdbscan/inst/doc/stop-identification.Rmd | 60 +-- stdbscan-0.2.0/stdbscan/inst/doc/stop-identification.html | 258 +++++-------- stdbscan-0.2.0/stdbscan/man/predict.stdbscan.Rd |only stdbscan-0.2.0/stdbscan/man/st_dbscan.Rd | 60 +-- stdbscan-0.2.0/stdbscan/man/st_dbscan_corepoint.Rd |only stdbscan-0.2.0/stdbscan/src/RcppExports.cpp | 31 + stdbscan-0.2.0/stdbscan/src/temporal_filter.cpp |only stdbscan-0.2.0/stdbscan/src/temporal_filter_pred.cpp |only stdbscan-0.2.0/stdbscan/tests/testthat/test-check_inputs.R |only stdbscan-0.2.0/stdbscan/tests/testthat/test-predict.R |only stdbscan-0.2.0/stdbscan/tests/testthat/test-st_dbscan.R | 210 +++------- stdbscan-0.2.0/stdbscan/vignettes/stop-identification.Rmd | 60 +-- 23 files changed, 612 insertions(+), 461 deletions(-)
Title: Superlatively Fast Fuzzy Joins
Description: Empowers users to fuzzily-merge data frames with millions or tens of millions of rows in minutes with low memory usage. The package uses the locality sensitive hashing algorithms developed by Datar, Immorlica, Indyk and Mirrokni (2004) <doi:10.1145/997817.997857>, and Broder (1998) <doi:10.1109/SEQUEN.1997.666900> to avoid having to compare every pair of records in each dataset, resulting in fuzzy-merges that finish in linear time.
Author: Beniamino Green [aut, cre, cph],
Etienne Bacher [ctb] ,
The authors of the dependency Rust crates [ctb, cph]
Maintainer: Beniamino Green <beniamino.green@yale.edu>
Diff between zoomerjoin versions 0.2.2 dated 2026-01-30 and 0.2.3 dated 2026-03-14
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- inst/doc/guided_tour.html | 18 +++++++++--------- inst/doc/matching_vectors.html | 2 +- src/rust/vendor.tar.xz |binary 5 files changed, 20 insertions(+), 20 deletions(-)
Title: Optimize and Compress Image Files with 'reSmush.it'
Description: Compress local and online images using the 'reSmush.it' API
service <https://resmush.it/>.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between resmush versions 0.2.2 dated 2026-01-12 and 1.0.0 dated 2026-03-14
resmush-0.2.2/resmush/inst/doc/resmush.Rmd |only resmush-0.2.2/resmush/vignettes/resmush.Rmd |only resmush-1.0.0/resmush/DESCRIPTION | 12 resmush-1.0.0/resmush/MD5 | 77 resmush-1.0.0/resmush/NAMESPACE | 16 resmush-1.0.0/resmush/NEWS.md | 37 resmush-1.0.0/resmush/R/resmush-package.R | 14 resmush-1.0.0/resmush/R/resmush_clean_dir.R | 158 - resmush-1.0.0/resmush/R/resmush_dir.R | 221 - resmush-1.0.0/resmush/R/resmush_file.R | 574 ++--- resmush-1.0.0/resmush/R/resmush_url.R | 598 ++--- resmush-1.0.0/resmush/R/show_report.R | 230 +- resmush-1.0.0/resmush/R/sysdata.rda |binary resmush-1.0.0/resmush/R/utils.R | 231 +- resmush-1.0.0/resmush/README.md | 491 ++-- resmush-1.0.0/resmush/build/vignette.rds |binary resmush-1.0.0/resmush/inst/CITATION | 42 resmush-1.0.0/resmush/inst/REFERENCES.bib | 14 resmush-1.0.0/resmush/inst/WORDLIST | 49 resmush-1.0.0/resmush/inst/doc/resmush.html | 1130 ++++------ resmush-1.0.0/resmush/inst/doc/resmush.qmd |only resmush-1.0.0/resmush/inst/schemaorg.json | 90 resmush-1.0.0/resmush/man/resmush-package.Rd | 52 resmush-1.0.0/resmush/man/resmush_clean_dir.Rd | 127 - resmush-1.0.0/resmush/man/resmush_dir.Rd | 215 - resmush-1.0.0/resmush/man/resmush_file.Rd | 213 - resmush-1.0.0/resmush/man/resmush_url.Rd | 201 - resmush-1.0.0/resmush/man/roxygen/meta.R | 12 resmush-1.0.0/resmush/tests/testthat.R | 24 resmush-1.0.0/resmush/tests/testthat/_snaps/formats.md | 8 resmush-1.0.0/resmush/tests/testthat/_snaps/remush_url.md | 6 resmush-1.0.0/resmush/tests/testthat/_snaps/resmush_file.md | 8 resmush-1.0.0/resmush/tests/testthat/test-formats-local.R | 187 - resmush-1.0.0/resmush/tests/testthat/test-formats.R | 258 +- resmush-1.0.0/resmush/tests/testthat/test-remush_url.R | 938 ++++---- resmush-1.0.0/resmush/tests/testthat/test-resmuh_dir.R | 471 ++-- resmush-1.0.0/resmush/tests/testthat/test-resmush_clean_dir.R | 141 - resmush-1.0.0/resmush/tests/testthat/test-resmush_file.R | 831 +++---- resmush-1.0.0/resmush/tests/testthat/test-utils.R | 82 resmush-1.0.0/resmush/vignettes/REFERENCES.bib | 14 resmush-1.0.0/resmush/vignettes/jpg_example_compress.jpg |only resmush-1.0.0/resmush/vignettes/resmush.qmd |only 42 files changed, 3829 insertions(+), 3943 deletions(-)
Title: Parsing Glycan Structure Text Representations
Description: Provides functions to parse glycan structure text representations
into 'glyrepr' glycan structures. Currently, it supports StrucGP-style,
pGlyco-style, IUPAC-condensed, IUPAC-extended, IUPAC-short, WURCS,
Linear Code, and GlycoCT format. It also provides an automatic parser
to detect the format and parse the structure string.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyparse versions 0.5.6 dated 2026-02-24 and 0.5.7 dated 2026-03-14
DESCRIPTION | 6 MD5 | 36 +- NEWS.md | 6 R/auto-parse.R | 11 R/parse-glycoct.R | 429 ++++++++++++++++++----------- R/parse-iupac-extended.R | 21 + R/parse-linear-code.R | 10 R/parse-pglyco.R | 19 + R/parse-strucgp.R | 14 R/parse-wurcs.R | 53 ++- R/utils.R | 108 ------- man/parse_iupac_extended.Rd | 8 tests/testthat/test-auto-parse.R | 11 tests/testthat/test-na-support.R | 5 tests/testthat/test-parse-glycoct.R | 8 tests/testthat/test-parse-iupac-extended.R | 32 ++ tests/testthat/test-parse-linear-code.R | 6 tests/testthat/test-parse-wurcs.R | 12 tests/testthat/test-performance.R | 16 - 19 files changed, 495 insertions(+), 316 deletions(-)
Title: Access to the 'Geospatial Data Abstraction Library' ('GDAL')
Description: Provides low-level access to 'GDAL' functionality.
'GDAL' is the 'Geospatial Data Abstraction Library' a translator for raster and vector geospatial data formats
that presents a single raster abstract data model and single vector abstract data model to the calling application
for all supported formats <https://gdal.org/>. This package is focussed on providing exactly and only what GDAL does, to enable
developing further tools.
Author: Michael Sumner [aut, cre] ,
Simon Wotherspoon [ctb] ,
Mark Padgham [ctb] ),
Edzer Pebesma [ctb] ,
Roger Bivand [ctb] ,
Jim Hester [ctb, cph] ,
Timothy Keitt [ctb] ,
Jeroen Ooms [ctb] ,
Dale Maschette [ctb] ,
Joseph Stachelek [ctb],
Even Rouault [ctb] [...truncated...]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between vapour versions 0.15.0 dated 2025-12-21 and 0.16.0 dated 2026-03-14
vapour-0.15.0/vapour/R/RcppExports.R |only vapour-0.15.0/vapour/inst/benchmarks |only vapour-0.15.0/vapour/inst/cmd |only vapour-0.15.0/vapour/inst/docker |only vapour-0.15.0/vapour/inst/include/gdalwarpmem |only vapour-0.15.0/vapour/inst/pbf |only vapour-0.15.0/vapour/inst/readwrite |only vapour-0.15.0/vapour/inst/shiny |only vapour-0.15.0/vapour/inst/stars |only vapour-0.15.0/vapour/inst/warpsandbox |only vapour-0.15.0/vapour/src/RcppExports.cpp |only vapour-0.16.0/vapour/DESCRIPTION | 12 vapour-0.16.0/vapour/MD5 | 96 vapour-0.16.0/vapour/NAMESPACE | 3 vapour-0.16.0/vapour/NEWS.md | 66 vapour-0.16.0/vapour/R/00_read_block.R | 22 vapour-0.16.0/vapour/R/00_warpgeneral.R | 24 vapour-0.16.0/vapour/R/cpp11.R |only vapour-0.16.0/vapour/R/raster-input.R | 2 vapour-0.16.0/vapour/R/vapour-gdal-library.R | 11 vapour-0.16.0/vapour/R/vapour-package.R | 3 vapour-0.16.0/vapour/R/vapour_input_attributes.R | 34 vapour-0.16.0/vapour/R/vapour_input_geometry.R | 27 vapour-0.16.0/vapour/R/vapour_vrt.R | 2 vapour-0.16.0/vapour/build/vignette.rds |binary vapour-0.16.0/vapour/inst/WORDLIST | 2 vapour-0.16.0/vapour/inst/doc/feature-access.html | 221 +- vapour-0.16.0/vapour/inst/doc/vapour.html | 841 +++---- vapour-0.16.0/vapour/inst/include/common/common_vapour.h | 14 vapour-0.16.0/vapour/inst/include/gdalapplib/gdalapplib.h | 143 - vapour-0.16.0/vapour/inst/include/gdalarrowstream/gdalvectorstream.h | 199 - vapour-0.16.0/vapour/inst/include/gdalgeometry/gdalgeometry.h | 848 ++----- vapour-0.16.0/vapour/inst/include/gdallibrary/CollectorList.h | 26 vapour-0.16.0/vapour/inst/include/gdallibrary/gdal_crs.h |only vapour-0.16.0/vapour/inst/include/gdallibrary/gdal_drivers.h |only vapour-0.16.0/vapour/inst/include/gdallibrary/gdal_field_alloc.h |only vapour-0.16.0/vapour/inst/include/gdallibrary/gdal_layer_utils.h |only vapour-0.16.0/vapour/inst/include/gdallibrary/gdallibrary.h | 999 --------- vapour-0.16.0/vapour/inst/include/gdalmiscutils/gdalmiscutils.h | 27 vapour-0.16.0/vapour/inst/include/gdalraster/gdalraster.h | 1079 ++++------ vapour-0.16.0/vapour/inst/include/gdalreadwrite/gdalreadwrite.h | 208 - vapour-0.16.0/vapour/inst/include/gdalwarpgeneral/gdalwarpgeneral.h | 259 -- vapour-0.16.0/vapour/man/vapour_read_geometry.Rd | 4 vapour-0.16.0/vapour/man/vapour_write_raster_block.Rd | 5 vapour-0.16.0/vapour/src/000-stream.cpp | 22 vapour-0.16.0/vapour/src/000-warpgeneral.cpp | 61 vapour-0.16.0/vapour/src/00_config.cpp | 22 vapour-0.16.0/vapour/src/00_gdal.cpp | 62 vapour-0.16.0/vapour/src/00_geometry.cpp | 265 +- vapour-0.16.0/vapour/src/00_raster.cpp | 92 vapour-0.16.0/vapour/src/00_raster_block_io.cpp | 229 -- vapour-0.16.0/vapour/src/00_utils.cpp | 9 vapour-0.16.0/vapour/src/00_vrt.cpp | 31 vapour-0.16.0/vapour/src/cpp11.cpp |only vapour-0.16.0/vapour/src/warp_file.cpp | 29 vapour-0.16.0/vapour/tests/testthat/test-raster_read_block.R | 4 56 files changed, 2141 insertions(+), 3862 deletions(-)
Title: Sure Independence Screening
Description: Variable selection techniques are essential tools for model
selection and estimation in high-dimensional statistical models. Through this
publicly available package, we provide a unified environment to carry out
variable selection using iterative sure independence screening (SIS) (Fan and Lv (2008)<doi:10.1111/j.1467-9868.2008.00674.x>) and all
of its variants in generalized linear models (Fan and Song (2009)<doi:10.1214/10-AOS798>) and the Cox proportional hazards
model (Fan, Feng and Wu (2010)<doi:10.1214/10-IMSCOLL606>).
Author: Yang Feng [aut, cre],
Jianqing Fan [aut],
Diego Franco Saldana [aut],
Yichao Wu [aut],
Richard Samworth [aut],
Arce Domingo Relloso [aut]
Maintainer: Yang Feng <yangfengstat@gmail.com>
Diff between SIS versions 0.8-8 dated 2020-01-27 and 1.5 dated 2026-03-14
SIS-0.8-8/SIS/data/leukemia.test.RData |only SIS-0.8-8/SIS/data/leukemia.train.RData |only SIS-0.8-8/SIS/data/prostate.test.RData |only SIS-0.8-8/SIS/data/prostate.train.RData |only SIS-1.5/SIS/DESCRIPTION | 42 +- SIS-1.5/SIS/MD5 | 58 ++- SIS-1.5/SIS/NAMESPACE | 12 SIS-1.5/SIS/R/RcppExports.R |only SIS-1.5/SIS/R/SIS.R | 576 +++++++++++++++++++------------- SIS-1.5/SIS/R/boot_sis.R |only SIS-1.5/SIS/R/coxnet_internal.R |only SIS-1.5/SIS/R/globals.R |only SIS-1.5/SIS/R/leukemia.test.R |only SIS-1.5/SIS/R/leukemia.train.R |only SIS-1.5/SIS/R/predict.SIS.R | 339 +++++++++--------- SIS-1.5/SIS/R/prostate.test.R |only SIS-1.5/SIS/R/prostate.train.R |only SIS-1.5/SIS/R/standardize.R | 50 +- SIS-1.5/SIS/R/subfuns.R | 382 +++++++++++---------- SIS-1.5/SIS/R/tune.fit.R | 304 +++++++++++----- SIS-1.5/SIS/build |only SIS-1.5/SIS/data/leukemia.test.rda |only SIS-1.5/SIS/data/leukemia.train.rda |only SIS-1.5/SIS/data/prostate.test.rda |only SIS-1.5/SIS/data/prostate.train.rda |only SIS-1.5/SIS/inst/CITATION | 2 SIS-1.5/SIS/inst/doc |only SIS-1.5/SIS/man/SIS-internal.Rd |only SIS-1.5/SIS/man/SIS.Rd | 174 ++++++--- SIS-1.5/SIS/man/boot_sis.Rd |only SIS-1.5/SIS/man/leukemia.test.Rd | 41 +- SIS-1.5/SIS/man/leukemia.train.Rd | 41 +- SIS-1.5/SIS/man/predict.SIS.Rd | 83 ++-- SIS-1.5/SIS/man/prostate.test.Rd | 41 +- SIS-1.5/SIS/man/prostate.train.Rd | 39 +- SIS-1.5/SIS/man/standardize.Rd | 30 - SIS-1.5/SIS/man/tune.fit.Rd | 44 +- SIS-1.5/SIS/src |only SIS-1.5/SIS/vignettes |only 39 files changed, 1331 insertions(+), 927 deletions(-)
Title: Using Needleman-Wunsch to Match Sample Names
Description: The Needleman-Wunsch global alignment algorithm can be
used to find approximate matches between sample names in different
data sets. See Wang et al. (2010) <doi:10.4137/CIN.S5613>.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between NameNeedle versions 1.2.8 dated 2025-04-08 and 1.2.10 dated 2026-03-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary data/cellLineNames.RData |binary inst/doc/blastName.pdf |binary man/needles.Rd | 9 +++++++-- 6 files changed, 16 insertions(+), 11 deletions(-)
Title: A Macro Language for 'R' Programs
Description: A macro language for 'R' programs, which
provides a macro facility similar to 'SAS®'. This
package contains basic macro capabilities
like defining macro variables, executing conditional
logic, and defining macro functions.
Author: David Bosak [aut, cre],
Bill Huang [ctb],
Duong Tran [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between macro versions 0.1.5 dated 2025-11-26 and 0.1.6 dated 2026-03-14
DESCRIPTION | 6 MD5 | 26 ++- NEWS.md | 8 + R/symtable.R | 2 R/utilities.R | 229 ++++++++++++++++++--------------- README.md | 8 + tests/testthat/examples/log/test12.txt | 2 tests/testthat/examples/log/test13.txt | 2 tests/testthat/programs/test28.R |only tests/testthat/programs/test28_mod.R |only tests/testthat/programs/test29.R |only tests/testthat/programs/test29_mod.R |only tests/testthat/programs/test30.R |only tests/testthat/programs/test30_mod.R |only tests/testthat/programs/test31.R |only tests/testthat/programs/test31_mod.R |only tests/testthat/test-msource.R | 65 +++++++++ tests/testthat/test-utilities.R | 42 +++++- 18 files changed, 271 insertions(+), 119 deletions(-)
Title: Geometric Morphometric Analyses of 2D and 3D Landmark Data
Description: Read and manipulate landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams [aut, cre],
Michael Collyer [aut],
Antigoni Kaliontzopoulou [aut],
Erica Baken [aut]
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 4.0.10 dated 2025-02-05 and 4.1.0 dated 2026-03-14
geomorph-4.0.10/geomorph/build |only geomorph-4.0.10/geomorph/inst/doc |only geomorph-4.0.10/geomorph/man/buildtemplate.Rd |only geomorph-4.0.10/geomorph/vignettes |only geomorph-4.1.0/geomorph/DESCRIPTION | 15 geomorph-4.1.0/geomorph/MD5 | 400 geomorph-4.1.0/geomorph/NAMESPACE | 20 geomorph-4.1.0/geomorph/NEWS.md | 17 geomorph-4.1.0/geomorph/R/arrayspecs.r | 188 geomorph-4.1.0/geomorph/R/bilat.symmetry.r | 732 - geomorph-4.1.0/geomorph/R/build.template.r | 129 geomorph-4.1.0/geomorph/R/combine.subsets.R | 576 - geomorph-4.1.0/geomorph/R/compare.CR.R | 320 geomorph-4.1.0/geomorph/R/compare.ZVrel.R | 150 geomorph-4.1.0/geomorph/R/compare.evol.rates.r | 360 geomorph-4.1.0/geomorph/R/compare.multi.evol.rates.r | 332 geomorph-4.1.0/geomorph/R/compare.physign.z.r | 232 geomorph-4.1.0/geomorph/R/compare.pls.r | 254 geomorph-4.1.0/geomorph/R/coords.subset.r | 80 geomorph-4.1.0/geomorph/R/define.links.r | 36 geomorph-4.1.0/geomorph/R/define.modules.r | 152 geomorph-4.1.0/geomorph/R/define.sliders.r | 298 geomorph-4.1.0/geomorph/R/deprecated.defunct.r | 32 geomorph-4.1.0/geomorph/R/digit.curves.r | 124 geomorph-4.1.0/geomorph/R/digit.fixed.r | 134 geomorph-4.1.0/geomorph/R/digitsurface.r | 129 geomorph-4.1.0/geomorph/R/editTemplate.r | 61 geomorph-4.1.0/geomorph/R/extended.pgls.r | 440 - geomorph-4.1.0/geomorph/R/findMeanSpec.r | 54 geomorph-4.1.0/geomorph/R/geomorph.support.code.r | 5212 ++++++------- geomorph-4.1.0/geomorph/R/geomorph.utils.r | 228 geomorph-4.1.0/geomorph/R/gm.measurement.error.R | 390 geomorph-4.1.0/geomorph/R/gm.prcomp.R | 563 - geomorph-4.1.0/geomorph/R/gpagen.r | 710 - geomorph-4.1.0/geomorph/R/gridPar.r | 2 geomorph-4.1.0/geomorph/R/interlmkdist.r | 162 geomorph-4.1.0/geomorph/R/make_ggplot.r | 294 geomorph-4.1.0/geomorph/R/modularity.test.r | 356 geomorph-4.1.0/geomorph/R/morphol.disparity.r | 692 - geomorph-4.1.0/geomorph/R/phylo.modularity.r | 290 geomorph-4.1.0/geomorph/R/physignal.eigen.R | 4 geomorph-4.1.0/geomorph/R/physignal.r | 362 geomorph-4.1.0/geomorph/R/physignal.z.r | 756 - geomorph-4.1.0/geomorph/R/picknplot.shape.r | 569 - geomorph-4.1.0/geomorph/R/plotAllSpecimens.r | 211 geomorph-4.1.0/geomorph/R/plotAllometry.r | 552 - geomorph-4.1.0/geomorph/R/plotOutliers.r | 237 geomorph-4.1.0/geomorph/R/plotRefToTarget.r | 747 - geomorph-4.1.0/geomorph/R/plotspec.r | 163 geomorph-4.1.0/geomorph/R/procD.lm.r | 840 +- geomorph-4.1.0/geomorph/R/procD.pgls.r | 350 geomorph-4.1.0/geomorph/R/read.morphologika.r | 210 geomorph-4.1.0/geomorph/R/read.ply.r | 180 geomorph-4.1.0/geomorph/R/readland.fcsv.r | 62 geomorph-4.1.0/geomorph/R/readland.nts.r | 198 geomorph-4.1.0/geomorph/R/readland.shapes.r | 156 geomorph-4.1.0/geomorph/R/readland.tps.r | 146 geomorph-4.1.0/geomorph/R/readmulti.nts.r | 100 geomorph-4.1.0/geomorph/R/readmulti.tps.R | 130 geomorph-4.1.0/geomorph/R/rotate.coords.R | 242 geomorph-4.1.0/geomorph/R/shape.predictor.r | 447 - geomorph-4.1.0/geomorph/R/shapeHulls.r | 188 geomorph-4.1.0/geomorph/R/shared.support.code.R | 1299 +-- geomorph-4.1.0/geomorph/R/two.b.pls.r | 402 - geomorph-4.1.0/geomorph/R/two.d.array.r | 78 geomorph-4.1.0/geomorph/R/warpRefMesh.r | 142 geomorph-4.1.0/geomorph/R/writeland.tps.r | 76 geomorph-4.1.0/geomorph/README.md | 2 geomorph-4.1.0/geomorph/inst/CITATION | 4 geomorph-4.1.0/geomorph/man/arrayspecs.Rd | 136 geomorph-4.1.0/geomorph/man/bilat.symmetry.Rd | 482 - geomorph-4.1.0/geomorph/man/build.template.Rd |only geomorph-4.1.0/geomorph/man/combine.subsets.Rd | 340 geomorph-4.1.0/geomorph/man/compare.CR.Rd | 198 geomorph-4.1.0/geomorph/man/compare.ZVrel.Rd | 116 geomorph-4.1.0/geomorph/man/compare.evol.rates.Rd | 212 geomorph-4.1.0/geomorph/man/compare.multi.evol.rates.Rd | 240 geomorph-4.1.0/geomorph/man/compare.physignal.z.Rd | 132 geomorph-4.1.0/geomorph/man/compare.pls.Rd | 196 geomorph-4.1.0/geomorph/man/coords.subset.Rd | 70 geomorph-4.1.0/geomorph/man/define.links.Rd | 100 geomorph-4.1.0/geomorph/man/define.modules.Rd | 95 geomorph-4.1.0/geomorph/man/define.sliders.Rd | 199 geomorph-4.1.0/geomorph/man/digit.curves.Rd | 114 geomorph-4.1.0/geomorph/man/digit.fixed.Rd | 89 geomorph-4.1.0/geomorph/man/digitize2d.Rd | 174 geomorph-4.1.0/geomorph/man/digitsurface.Rd | 104 geomorph-4.1.0/geomorph/man/editTemplate.Rd | 62 geomorph-4.1.0/geomorph/man/estimate.missing.Rd | 164 geomorph-4.1.0/geomorph/man/extended.pgls.Rd | 390 geomorph-4.1.0/geomorph/man/findMeanSpec.Rd | 64 geomorph-4.1.0/geomorph/man/fixed.angle.Rd | 168 geomorph-4.1.0/geomorph/man/geomorph-package.Rd | 40 geomorph-4.1.0/geomorph/man/geomorph.data.frame.Rd | 82 geomorph-4.1.0/geomorph/man/globalIntegration.Rd | 92 geomorph-4.1.0/geomorph/man/gm.measurement.error.Rd | 362 geomorph-4.1.0/geomorph/man/gm.prcomp.Rd | 414 - geomorph-4.1.0/geomorph/man/gpagen.Rd | 506 - geomorph-4.1.0/geomorph/man/gridPar.Rd | 252 geomorph-4.1.0/geomorph/man/hummingbirds.Rd | 36 geomorph-4.1.0/geomorph/man/integration.Vrel.Rd | 108 geomorph-4.1.0/geomorph/man/integration.test.Rd | 354 geomorph-4.1.0/geomorph/man/interlmkdist.Rd | 98 geomorph-4.1.0/geomorph/man/larvalMorph.Rd | 46 geomorph-4.1.0/geomorph/man/lizards.Rd | 46 geomorph-4.1.0/geomorph/man/make_ggplot.Rd | 146 geomorph-4.1.0/geomorph/man/modularity.test.Rd | 222 geomorph-4.1.0/geomorph/man/morphol.disparity.Rd | 444 - geomorph-4.1.0/geomorph/man/mosquito.Rd | 26 geomorph-4.1.0/geomorph/man/mshape.Rd | 82 geomorph-4.1.0/geomorph/man/na.omit.geomorph.data.frame.Rd | 60 geomorph-4.1.0/geomorph/man/phylo.integration.Rd | 342 geomorph-4.1.0/geomorph/man/phylo.modularity.Rd | 212 geomorph-4.1.0/geomorph/man/physignal.Rd | 206 geomorph-4.1.0/geomorph/man/physignal.eigen.Rd | 284 geomorph-4.1.0/geomorph/man/physignal.z.Rd | 380 geomorph-4.1.0/geomorph/man/picknplot.shape.Rd | 187 geomorph-4.1.0/geomorph/man/plethShapeFood.Rd | 38 geomorph-4.1.0/geomorph/man/plethodon.Rd | 40 geomorph-4.1.0/geomorph/man/plethspecies.Rd | 36 geomorph-4.1.0/geomorph/man/plot.CR.Rd | 42 geomorph-4.1.0/geomorph/man/plot.CR.phylo.Rd | 42 geomorph-4.1.0/geomorph/man/plot.bilat.symmetry.Rd | 50 geomorph-4.1.0/geomorph/man/plot.evolrate.Rd | 42 geomorph-4.1.0/geomorph/man/plot.gm.prcomp.Rd | 120 geomorph-4.1.0/geomorph/man/plot.gpagen.Rd | 42 geomorph-4.1.0/geomorph/man/plot.mshape.Rd | 52 geomorph-4.1.0/geomorph/man/plot.physignal.Rd | 42 geomorph-4.1.0/geomorph/man/plot.physignal.eigen.Rd | 52 geomorph-4.1.0/geomorph/man/plot.physignal.z.Rd | 42 geomorph-4.1.0/geomorph/man/plot.pls.Rd | 58 geomorph-4.1.0/geomorph/man/plot.procD.lm.Rd | 104 geomorph-4.1.0/geomorph/man/plotAllSpecimens.Rd | 99 geomorph-4.1.0/geomorph/man/plotAllometry.Rd | 408 - geomorph-4.1.0/geomorph/man/plotOutliers.Rd | 141 geomorph-4.1.0/geomorph/man/plotRefToTarget.Rd | 262 geomorph-4.1.0/geomorph/man/plotspec.Rd | 143 geomorph-4.1.0/geomorph/man/print.CR.Rd | 40 geomorph-4.1.0/geomorph/man/print.CR.phylo.Rd | 40 geomorph-4.1.0/geomorph/man/print.bilat.symmetry.Rd | 40 geomorph-4.1.0/geomorph/man/print.combined.set.Rd | 40 geomorph-4.1.0/geomorph/man/print.compare.CR.Rd | 40 geomorph-4.1.0/geomorph/man/print.compare.ZVrel.Rd | 40 geomorph-4.1.0/geomorph/man/print.compare.physignal.z.Rd | 40 geomorph-4.1.0/geomorph/man/print.compare.pls.Rd | 40 geomorph-4.1.0/geomorph/man/print.evolrate.Rd | 40 geomorph-4.1.0/geomorph/man/print.evolrate1.Rd | 40 geomorph-4.1.0/geomorph/man/print.geomorphShapes.Rd | 40 geomorph-4.1.0/geomorph/man/print.gm.prcomp.Rd | 40 geomorph-4.1.0/geomorph/man/print.gpagen.Rd | 40 geomorph-4.1.0/geomorph/man/print.morphol.disparity.Rd | 40 geomorph-4.1.0/geomorph/man/print.physignal.Rd | 40 geomorph-4.1.0/geomorph/man/print.physignal.eigen.Rd | 40 geomorph-4.1.0/geomorph/man/print.physignal.z.Rd | 40 geomorph-4.1.0/geomorph/man/print.pls.Rd | 40 geomorph-4.1.0/geomorph/man/print.procD.lm.Rd | 40 geomorph-4.1.0/geomorph/man/procD.lm.Rd | 680 - geomorph-4.1.0/geomorph/man/procD.pgls.Rd | 354 geomorph-4.1.0/geomorph/man/pupfish.Rd | 44 geomorph-4.1.0/geomorph/man/pupfish.ws.Rd | 50 geomorph-4.1.0/geomorph/man/ratland.Rd | 34 geomorph-4.1.0/geomorph/man/read.morphologika.Rd | 94 geomorph-4.1.0/geomorph/man/read.ply.Rd | 94 geomorph-4.1.0/geomorph/man/readland.fcsv.Rd | 60 geomorph-4.1.0/geomorph/man/readland.nts.Rd | 110 geomorph-4.1.0/geomorph/man/readland.shapes.Rd | 178 geomorph-4.1.0/geomorph/man/readland.tps.Rd | 142 geomorph-4.1.0/geomorph/man/readmulti.nts.Rd | 70 geomorph-4.1.0/geomorph/man/readmulti.tps.Rd | 60 geomorph-4.1.0/geomorph/man/rotate.coords.Rd | 130 geomorph-4.1.0/geomorph/man/scallopPLY.Rd | 34 geomorph-4.1.0/geomorph/man/scallops.Rd | 34 geomorph-4.1.0/geomorph/man/shape.predictor.Rd | 353 geomorph-4.1.0/geomorph/man/shapeHulls.Rd | 172 geomorph-4.1.0/geomorph/man/summary.CR.Rd | 40 geomorph-4.1.0/geomorph/man/summary.CR.phylo.Rd | 40 geomorph-4.1.0/geomorph/man/summary.bilat.symmetry.Rd | 40 geomorph-4.1.0/geomorph/man/summary.combined.set.Rd | 40 geomorph-4.1.0/geomorph/man/summary.compare.CR.Rd | 40 geomorph-4.1.0/geomorph/man/summary.compare.ZVrel.Rd | 40 geomorph-4.1.0/geomorph/man/summary.compare.physignal.z.Rd | 40 geomorph-4.1.0/geomorph/man/summary.compare.pls.Rd | 40 geomorph-4.1.0/geomorph/man/summary.evolrate.Rd | 40 geomorph-4.1.0/geomorph/man/summary.evolrate1.Rd | 40 geomorph-4.1.0/geomorph/man/summary.geomorphShapes.Rd | 40 geomorph-4.1.0/geomorph/man/summary.gm.prcomp.Rd | 40 geomorph-4.1.0/geomorph/man/summary.gpagen.Rd | 40 geomorph-4.1.0/geomorph/man/summary.morphol.disparity.Rd | 40 geomorph-4.1.0/geomorph/man/summary.physignal.Rd | 40 geomorph-4.1.0/geomorph/man/summary.physignal.eigen.Rd | 40 geomorph-4.1.0/geomorph/man/summary.physignal.z.Rd | 40 geomorph-4.1.0/geomorph/man/summary.pls.Rd | 40 geomorph-4.1.0/geomorph/man/summary.procD.lm.Rd | 40 geomorph-4.1.0/geomorph/man/two.b.pls.Rd | 268 geomorph-4.1.0/geomorph/man/two.d.array.Rd | 88 geomorph-4.1.0/geomorph/man/warpRefMesh.Rd | 125 geomorph-4.1.0/geomorph/man/warpRefOutline.Rd | 106 geomorph-4.1.0/geomorph/man/writeland.tps.Rd | 56 geomorph-4.1.0/geomorph/tests/testthat.R | 8 geomorph-4.1.0/geomorph/tests/testthat/test-geomorph.R | 2064 ++--- 200 files changed, 20014 insertions(+), 20658 deletions(-)
Title: Unified Parallel and Distributed Processing in R for Everyone
Description: The purpose of this package is to provide a lightweight and
unified Future API for sequential and parallel processing of R
expression via futures. The simplest way to evaluate an expression
in parallel is to use `x %<-% { expression }` with `plan(multisession)`.
This package implements sequential, multicore, multisession, and
cluster futures. With these, R expressions can be evaluated on the
local machine, in parallel a set of local machines, or distributed
on a mix of local and remote machines.
Extensions to this package implement additional backends for
processing futures via compute cluster schedulers, etc.
Because of its unified API, there is no need to modify any code in order
switch from sequential on the local machine to, say, distributed
processing on a remote compute cluster.
Another strength of this package is that global variables and functions
are automatically identified and exported as needed, making it
straightforward to tweak existing code to make use of futures.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future versions 1.69.0 dated 2026-01-16 and 1.70.0 dated 2026-03-14
DESCRIPTION | 8 MD5 | 146 ++-- NEWS.md | 171 +++-- R/000.re-exports.R | 16 R/backend_api-11.ClusterFutureBackend-class.R | 383 +++++++------ R/backend_api-11.MulticoreFutureBackend-class.R | 15 R/backend_api-ConstantFuture-class.R | 4 R/backend_api-Future-class.R | 35 - R/backend_api-FutureRegistry.R | 4 R/backend_api-evalFuture.R | 2 R/core_api-cancel.R | 4 R/core_api-future.R | 24 R/core_api-reset.R | 2 R/core_api-resolved.R | 2 R/core_api-value.R | 15 R/delayed_api-futureAssign.R | 18 R/delayed_api-futureOf.R | 10 R/protected_api-globals.R | 22 R/protected_api-journal.R | 5 R/protected_api-resolve.R | 10 R/protected_api-result.R | 1 R/utils-options.R | 2 R/utils-uuid.R | 2 R/utils_api-makeClusterFuture.R | 19 R/utils_api-nbrOfWorkers.R | 6 R/utils_api-plan.R | 28 build/vignette.rds |binary inst/WORDLIST | 9 inst/doc/future-1-overview.html | 120 ++-- inst/doc/future-1-overview.md.rsp | 120 ++-- inst/doc/future-2-output.html | 8 inst/doc/future-2-output.md.rsp | 8 inst/doc/future-2b-backend.html | 2 inst/doc/future-2b-backend.md.rsp | 2 inst/doc/future-3-topologies.html | 16 inst/doc/future-3-topologies.md.rsp | 16 inst/doc/future-4-issues.html | 34 - inst/doc/future-4-issues.md.rsp | 34 - inst/doc/future-4-non-exportable-objects.html | 46 - inst/doc/future-4-non-exportable-objects.md.rsp | 46 - inst/doc/future-5-startup.html | 2 inst/doc/future-5-startup.md.rsp | 2 inst/doc/future-6-future-api-backend-specification.html | 20 inst/doc/future-6-future-api-backend-specification.md.rsp | 20 inst/doc/future-7-for-package-developers.html | 20 inst/doc/future-7-for-package-developers.md.rsp | 20 inst/doc/future-8-how-future-is-validated.html | 12 inst/doc/future-8-how-future-is-validated.md.rsp | 12 inst/testme/test-globals,resolve.R | 10 inst/vignettes-static/future-1-overview.md.rsp.rsp | 58 + man/Future-class.Rd | 22 man/MultiprocessFuture-class.Rd | 2 man/UniprocessFuture-class.Rd | 2 man/cancel.Rd | 4 man/future.Rd | 32 - man/futureAssign.Rd | 32 - man/futureOf.Rd | 6 man/makeClusterFuture.Rd | 21 man/multicore.Rd | 16 man/plan.Rd | 26 man/reset.Rd | 2 man/resetWorkers.Rd | 2 man/resolved.Rd | 2 man/value.Rd | 8 vignettes/future-1-overview.md.rsp | 120 ++-- vignettes/future-2-output.md.rsp | 8 vignettes/future-2b-backend.md.rsp | 2 vignettes/future-3-topologies.md.rsp | 16 vignettes/future-4-issues.md.rsp | 34 - vignettes/future-4-non-exportable-objects.md.rsp | 46 - vignettes/future-5-startup.md.rsp | 2 vignettes/future-6-future-api-backend-specification.md.rsp | 20 vignettes/future-7-for-package-developers.md.rsp | 20 vignettes/future-8-how-future-is-validated.md.rsp | 12 74 files changed, 1116 insertions(+), 932 deletions(-)
Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files
containing spectral data from spectrometers and their associated software,
output from daylight simulation models in common use, and some spectral
data repositories. As well as functions for exchange of spectral data with
other R packages. Part of the 'r4photobiology' suite,
Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] ,
Titta K. Kotilainen [ctb] ,
Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyInOut versions 0.4.32 dated 2025-09-24 and 0.4.33 dated 2026-03-13
photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/2013-05-01.hel |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/2014-08-21_cum.hel |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/2014-08-22_cum.hel |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/LI-180-irradiance.txt |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/cr6-day.dat |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/cr6-hour.dat |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/drygrass-spectrum.txt |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/enlighten-wasatch-absorbance.csv |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/enlighten-wasatch-absorbance.json |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/enlighten-wasatch-raman.csv |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/enlighten-wasatch-scope.csv |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/enlighten-wasatch-scope.json |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/enlighten-wasatch-transmission.csv |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/garbage.txt |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/reflectance.PRN |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/reflectance.jaz |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum-avaspec.csv |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum-comma.JazIrrad |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum-comma.SSIrrad |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum-comma.jaz |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum-licor-long.PRN |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum-psi-spectrapen-SP.csv |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum-seq-dark.pi |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum-seq0.pi |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum.DTA |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum.JazIrrad |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum.OVIrrad |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum.PRN |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum.SSIrrad |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum.jaz |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/spectrum.pi |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/usrout.txt |only photobiologyInOut-0.4.32/photobiologyInOut/inst/extdata/usrout2.txt |only photobiologyInOut-0.4.33/photobiologyInOut/DESCRIPTION | 25 photobiologyInOut-0.4.33/photobiologyInOut/MD5 | 165 - photobiologyInOut-0.4.33/photobiologyInOut/NAMESPACE | 1 photobiologyInOut-0.4.33/photobiologyInOut/NEWS.md | 10 photobiologyInOut-0.4.33/photobiologyInOut/R/foreign-conversion.r | 65 photobiologyInOut-0.4.33/photobiologyInOut/R/read-asd-txt.r |only photobiologyInOut-0.4.33/photobiologyInOut/R/read-aster-file.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-avaspec-csv.r | 12 photobiologyInOut-0.4.33/photobiologyInOut/R/read-fmi-cum.R | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-licor-prn.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-licor-txt.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-macam-dta.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-oojaz-file.r | 4 photobiologyInOut-0.4.33/photobiologyInOut/R/read-ooov-file.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-oopi-file.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-ooss-file.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-psi-spectrapen-csv.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/R/read-wasatch-csv.r | 2 photobiologyInOut-0.4.33/photobiologyInOut/README.md | 60 photobiologyInOut-0.4.33/photobiologyInOut/build/partial.rdb |binary photobiologyInOut-0.4.33/photobiologyInOut/build/vignette.rds |binary photobiologyInOut-0.4.33/photobiologyInOut/inst/doc/user-guide.R | 128 - photobiologyInOut-0.4.33/photobiologyInOut/inst/doc/user-guide.Rmd | 381 ++- photobiologyInOut-0.4.33/photobiologyInOut/inst/doc/user-guide.html | 1164 ++++++---- photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/asd-Rfr-panel-50pc.tsv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/asd-Rfr-soil.tsv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/asd-e-irrad-sky.csv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/asd-e-irrad-sky.csv2 |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/asd-e-irrad-sky.tsv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/asd-raw-gravel.tsv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/aster-Rpc-drygrass.txt |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/avantes-avaspec-e-irrad.csv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/bad-input-test.txt |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/campbellsci-cr6-day.dat |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/campbellsci-cr6-hour.dat |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/fmi-al-2013-05-01.hel |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/fmi-al-2014-08-21_cum.hel |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/fmi-al-2014-08-22_cum.hel |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/licor-li180-irrad.txt |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/licor-li1800-Rfr.PRN |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/licor-li1800-q-irrad-long.PRN |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/licor-li1800-q-irrad.PRN |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/macam-e-irrad.DTA |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-reflectance.jaz |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum-comma.SSIrrad |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum-comma.jaz |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum-comma.jazIrrad |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum-seq-dark.pi |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum-seq0.pi |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum.OVIrrad |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum.SSIrrad |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum.jaz |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum.jazIrrad |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/oo-spectrum.pi |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/psi-spectrapen-SP.csv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/tuv-usrout.txt |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/tuv-usrout2.txt |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/wasatch-enlighten-absorbance.csv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/wasatch-enlighten-absorbance.json |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/wasatch-enlighten-raman.csv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/wasatch-enlighten-scope.csv |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/wasatch-enlighten-scope.json |only photobiologyInOut-0.4.33/photobiologyInOut/inst/extdata/wasatch-enlighten-transmission.csv |only photobiologyInOut-0.4.33/photobiologyInOut/man/read_ASTER_txt.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_asd_txt.Rd |only photobiologyInOut-0.4.33/photobiologyInOut/man/read_avaspec_csv.Rd | 10 photobiologyInOut-0.4.33/photobiologyInOut/man/read_fmi_cum.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_li180_txt.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_licor_prn.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_macam_dta.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_oo_jazirrad.Rd | 4 photobiologyInOut-0.4.33/photobiologyInOut/man/read_oo_ovirrad.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_oo_pidata.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_oo_ssirrad.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_spectrapen_csv.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/read_wasatch_csv.Rd | 2 photobiologyInOut-0.4.33/photobiologyInOut/man/rspec2mspct.Rd | 62 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-asd.R |only photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-aster.R | 5 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-avantes.R | 2 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-fmi.R | 14 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-licor.R | 22 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-macam.R | 2 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-oo.R | 44 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-psi.R | 4 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-tuv.R | 16 photobiologyInOut-0.4.33/photobiologyInOut/tests/testthat/test-wasatch.R | 14 photobiologyInOut-0.4.33/photobiologyInOut/vignettes/user-guide.Rmd | 381 ++- 121 files changed, 1750 insertions(+), 885 deletions(-)
More information about photobiologyInOut at CRAN
Permanent link
Title: Operations to Ease Data Analyses Specific to Nigeria
Description: A set of convenience functions as well as geographical/political
data about Nigeria, aimed at simplifying work with data and information that
are specific to the country.
Author: Victor Ordu [aut, cre] ,
Laura DeCicco [ctb],
Emily Riederer [rev],
Margaret Siple [rev],
Cagri Alican [rev]
Maintainer: Victor Ordu <victorordu@outlook.com>
Diff between naijR versions 0.6.3 dated 2025-09-01 and 0.7.0 dated 2026-03-13
DESCRIPTION | 20 MD5 | 88 +- NAMESPACE | 100 +-- NEWS.md | 255 +++----- R/disambi.R | 128 ++-- R/distances.R |only R/fct.R | 86 +- R/fixmob.R | 267 ++++---- R/fixreg.R | 512 ++++++++-------- R/fixregint.R | 498 ++++++++-------- R/helpers.R | 170 ++--- R/map.R | 580 +++++++++--------- R/mapint.R | 1239 +++++++++++++++++++--------------------- R/naijR-package.R | 36 - R/regdata.R | 93 ++- R/regions.R | 1165 ++++++++++++++++++------------------- R/regionsint.R | 302 ++++----- R/sysdata.rda |binary R/zzz.R | 22 README.md | 84 +- build/vignette.rds |binary data/ngdist.rda |only inst/doc/interactive.R | 120 +-- inst/doc/interactive.Rmd | 228 +++---- inst/doc/interactive.html | 1076 +++++++++++++++++----------------- inst/doc/nigeria-maps.R | 156 ++--- inst/doc/nigeria-maps.Rmd | 297 ++++----- inst/doc/nigeria-maps.html | 1078 +++++++++++++++++----------------- man/disambiguate_lga.Rd | 80 +- man/fix_mobile.Rd | 63 +- man/fix_region.Rd | 154 ++-- man/lgas.Rd | 192 +++--- man/lgas_nigeria.Rd | 4 man/naijR-package.Rd | 56 - man/ng_distance.Rd |only man/ngdist.Rd |only man/states_nigeria.Rd | 42 - tests/testthat.R | 24 tests/testthat/data/numbers.rds |only tests/testthat/test-asreg.R | 156 ++--- tests/testthat/test-distances.R |only tests/testthat/test-fixmob.R | 318 +++++----- tests/testthat/test-fixreg.R | 370 +++++------ tests/testthat/test-isreg.R | 314 +++++----- tests/testthat/test-map.R | 904 ++++++++++++++--------------- tests/testthat/test-regions.R | 442 +++++++------- vignettes/interactive.Rmd | 228 +++---- vignettes/nigeria-maps.Rmd | 297 ++++----- 48 files changed, 6132 insertions(+), 6112 deletions(-)
Title: Native R 'torch' Implementation of 'OpenAI' 'Whisper'
Description: Speech-to-text transcription using a native R 'torch' implementation
of 'OpenAI' 'Whisper' model <https://github.com/openai/whisper>. Supports
multiple model sizes from tiny (39M parameters) to large-v3 (1.5B parameters)
with integrated download from 'HuggingFace' <https://huggingface.co/> via the
'hfhub' package. Provides automatic speech recognition with optional language
detection and translation to English. Audio preprocessing, mel spectrogram
computation, and transformer-based encoder-decoder inference are all
implemented in R using the 'torch' package.
Author: Troy Hernandez [aut, cre],
cornball.ai [cph],
OpenAI [cph] )
Maintainer: Troy Hernandez <troy@cornball.ai>
Diff between whisper versions 0.1.0 dated 2026-02-06 and 0.3.0 dated 2026-03-13
whisper-0.1.0/whisper/man/load_added_tokens.Rd |only whisper-0.3.0/whisper/DESCRIPTION | 6 whisper-0.3.0/whisper/MD5 | 66 whisper-0.3.0/whisper/NAMESPACE | 5 whisper-0.3.0/whisper/NEWS.md | 16 whisper-0.3.0/whisper/R/alignment.R |only whisper-0.3.0/whisper/R/config.R | 128 - whisper-0.3.0/whisper/R/decoder.R | 30 whisper-0.3.0/whisper/R/encoder.R | 49 whisper-0.3.0/whisper/R/language.R |only whisper-0.3.0/whisper/R/model.R | 14 whisper-0.3.0/whisper/R/tokenizer.R | 59 whisper-0.3.0/whisper/R/transcribe.R | 1311 +++++++++++- whisper-0.3.0/whisper/README.md | 52 whisper-0.3.0/whisper/inst/tinytest/test_alignment.R |only whisper-0.3.0/whisper/inst/tinytest/test_beam_search.R |only whisper-0.3.0/whisper/inst/tinytest/test_language.R |only whisper-0.3.0/whisper/inst/tinytest/test_tokenizer.R | 25 whisper-0.3.0/whisper/inst/tinytest/test_transcribe.R | 76 whisper-0.3.0/whisper/man/apply_timestamp_rules.Rd |only whisper-0.3.0/whisper/man/beam_search_decode.Rd |only whisper-0.3.0/whisper/man/build_byte_decoder.Rd |only whisper-0.3.0/whisper/man/compression_ratio.Rd |only whisper-0.3.0/whisper/man/compute_word_timestamps.Rd |only whisper-0.3.0/whisper/man/create_mel_filterbank_fallback.Rd | 7 whisper-0.3.0/whisper/man/decode_bpe_bytes.Rd | 5 whisper-0.3.0/whisper/man/decode_with_fallback.Rd |only whisper-0.3.0/whisper/man/detect_language.Rd |only whisper-0.3.0/whisper/man/detect_language_from_mel.Rd |only whisper-0.3.0/whisper/man/detect_language_from_pipeline.Rd |only whisper-0.3.0/whisper/man/dtw_align.Rd |only whisper-0.3.0/whisper/man/expand_kv_cache.Rd |only whisper-0.3.0/whisper/man/forced_decode.Rd |only whisper-0.3.0/whisper/man/get_initial_tokens.Rd | 8 whisper-0.3.0/whisper/man/greedy_decode.Rd | 18 whisper-0.3.0/whisper/man/group_into_words.Rd |only whisper-0.3.0/whisper/man/load_whisper_model.Rd | 9 whisper-0.3.0/whisper/man/medfilt1.Rd |only whisper-0.3.0/whisper/man/pipeline_transcribe.Rd |only whisper-0.3.0/whisper/man/rearrange_kv_cache.Rd |only whisper-0.3.0/whisper/man/sample_decode.Rd |only whisper-0.3.0/whisper/man/transcribe.Rd | 58 whisper-0.3.0/whisper/man/transcribe_chunk.Rd | 37 whisper-0.3.0/whisper/man/transcribe_long.Rd | 34 whisper-0.3.0/whisper/man/whisper_lang_from_id.Rd |only whisper-0.3.0/whisper/man/whisper_language_table.Rd |only whisper-0.3.0/whisper/man/whisper_pipeline.Rd |only 47 files changed, 1703 insertions(+), 310 deletions(-)
Title: Treatment Switching
Description: Implements rank preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), marginal structural model (MSM), simple two-stage estimation (TSEsimp), and improved two-stage estimation with g-estimation (TSEgest) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between trtswitch versions 0.2.4 dated 2026-02-12 and 0.2.5 dated 2026-03-13
DESCRIPTION | 6 MD5 | 66 NAMESPACE | 6 NEWS.md | 4 R/RcppExports.R | 16 R/ipcw.R | 1 R/msm.R | 2 R/trtswitch-package.R | 7 R/utilities.R | 1 man/ipcw.Rd | 1 man/kmdiff.Rd | 2 man/lrtest.Rd | 8 man/merge_append.Rd | 1 man/msm.Rd | 2 man/rmdiff.Rd | 2 src/RcppExports.cpp | 56 src/dataframe_list.cpp | 428 ++-- src/dataframe_list.h | 329 ++- src/ipcw.cpp | 400 +-- src/ipe.cpp | 191 - src/logistic_regression.cpp | 576 ++--- src/msm.cpp | 351 +-- src/recensor_sim_rpsftm.cpp | 132 - src/rpsftm.cpp | 201 + src/splines.cpp | 304 +-- src/splines.h | 12 src/survival_analysis.cpp | 4426 ++++++++++++++++++++++---------------------- src/survival_analysis.h | 10 src/tsegest.cpp | 347 +-- src/tsegestsim.cpp | 33 src/tsesimp.cpp | 240 +- src/tssim.cpp | 95 src/utilities.cpp | 635 +++--- src/utilities.h | 299 ++ 34 files changed, 4845 insertions(+), 4345 deletions(-)
Title: Response Data for Light Sensors
Description: Spectral response data for broadband ultraviolet and visible
radiation sensors. Angular response data for broadband ultraviolet and visible
radiation sensors and diffusers used as entrance optics. Data obtained from
multiple sources were used: author-supplied data from scientific research
papers, sensor-manufacturer supplied data, and published sensor
specifications. Part of the 'r4photobiology' suite Aphalo P. J. (2015)
<doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologySensors versions 0.5.2 dated 2025-09-24 and 0.5.3 dated 2026-03-13
photobiologySensors-0.5.2/photobiologySensors/R/diffusers.r |only photobiologySensors-0.5.2/photobiologySensors/R/wavebands.r |only photobiologySensors-0.5.2/photobiologySensors/man/uv_sensors.Rd |only photobiologySensors-0.5.3/photobiologySensors/DESCRIPTION | 10 photobiologySensors-0.5.3/photobiologySensors/MD5 | 117 ++-- photobiologySensors-0.5.3/photobiologySensors/NAMESPACE | 1 photobiologySensors-0.5.3/photobiologySensors/NEWS.md | 23 photobiologySensors-0.5.3/photobiologySensors/R/Berger-sensors.r | 10 photobiologySensors-0.5.3/photobiologySensors/R/DeltaT-sensors.r | 20 photobiologySensors-0.5.3/photobiologySensors/R/Irradian-sensors.r |only photobiologySensors-0.5.3/photobiologySensors/R/KIPP-sensors.r | 15 photobiologySensors-0.5.3/photobiologySensors/R/LICOR-sensors.r | 15 photobiologySensors-0.5.3/photobiologySensors/R/Skye-sensors.r | 20 photobiologySensors-0.5.3/photobiologySensors/R/SolarLight-sensors.r | 13 photobiologySensors-0.5.3/photobiologySensors/R/Solarmeter-sensors.r | 17 photobiologySensors-0.5.3/photobiologySensors/R/Specmeters-sensors.r | 18 photobiologySensors-0.5.3/photobiologySensors/R/ThiesClima-sensors.r | 17 photobiologySensors-0.5.3/photobiologySensors/R/Vishay-sensors.r | 12 photobiologySensors-0.5.3/photobiologySensors/R/VitalTech-sensors.r | 10 photobiologySensors-0.5.3/photobiologySensors/R/all-diffusers.r |only photobiologySensors-0.5.3/photobiologySensors/R/ams-sensors.r | 30 - photobiologySensors-0.5.3/photobiologySensors/R/analytik-sensors.r | 17 photobiologySensors-0.5.3/photobiologySensors/R/angular-response..R |only photobiologySensors-0.5.3/photobiologySensors/R/apogee-sensors.r | 18 photobiologySensors-0.5.3/photobiologySensors/R/diffusers-lst.r | 23 photobiologySensors-0.5.3/photobiologySensors/R/ideal-sensors.r | 16 photobiologySensors-0.5.3/photobiologySensors/R/sensors-by-waveband.r |only photobiologySensors-0.5.3/photobiologySensors/R/sensors-mspct.r | 51 +- photobiologySensors-0.5.3/photobiologySensors/R/sglux-sensors.r | 16 photobiologySensors-0.5.3/photobiologySensors/README.md | 82 ++- photobiologySensors-0.5.3/photobiologySensors/build/partial.rdb |binary photobiologySensors-0.5.3/photobiologySensors/build/vignette.rds |binary photobiologySensors-0.5.3/photobiologySensors/data/diffusers-lst.rda |binary photobiologySensors-0.5.3/photobiologySensors/data/image-sensors-mspct.rda |only photobiologySensors-0.5.3/photobiologySensors/data/sensors.mspct.rda |binary photobiologySensors-0.5.3/photobiologySensors/inst/doc/r4p-introduction.html | 2 photobiologySensors-0.5.3/photobiologySensors/inst/doc/userguide-1.R | 19 photobiologySensors-0.5.3/photobiologySensors/inst/doc/userguide-1.Rmd | 35 + photobiologySensors-0.5.3/photobiologySensors/inst/doc/userguide-1.html | 241 +++++----- photobiologySensors-0.5.3/photobiologySensors/man/all_diffusers.Rd | 175 ++++--- photobiologySensors-0.5.3/photobiologySensors/man/ams_sensors.Rd | 139 +++-- photobiologySensors-0.5.3/photobiologySensors/man/analytik_sensors.Rd | 84 +-- photobiologySensors-0.5.3/photobiologySensors/man/angular_response.Rd |only photobiologySensors-0.5.3/photobiologySensors/man/apogee_sensors.Rd | 24 photobiologySensors-0.5.3/photobiologySensors/man/berger_sensors.Rd | 72 +- photobiologySensors-0.5.3/photobiologySensors/man/deltat_sensors.Rd | 81 +-- photobiologySensors-0.5.3/photobiologySensors/man/diffusers.lst.Rd | 89 +-- photobiologySensors-0.5.3/photobiologySensors/man/electronic_components.Rd |only photobiologySensors-0.5.3/photobiologySensors/man/figures/README-example-07-1.png |binary photobiologySensors-0.5.3/photobiologySensors/man/ideal_sensors.Rd | 62 +- photobiologySensors-0.5.3/photobiologySensors/man/image_sensors.mspct.Rd |only photobiologySensors-0.5.3/photobiologySensors/man/irradian_sensors.Rd |only photobiologySensors-0.5.3/photobiologySensors/man/kipp_sensors.Rd | 122 ++--- photobiologySensors-0.5.3/photobiologySensors/man/licor_sensors.Rd | 116 ++-- photobiologySensors-0.5.3/photobiologySensors/man/photobiologySensors-package.Rd | 182 +++---- photobiologySensors-0.5.3/photobiologySensors/man/sensors-by-waveband.Rd |only photobiologySensors-0.5.3/photobiologySensors/man/sensors.mspct.Rd | 105 ++-- photobiologySensors-0.5.3/photobiologySensors/man/sglux_sensors.Rd | 109 ++-- photobiologySensors-0.5.3/photobiologySensors/man/skye_sensors.Rd | 117 ++-- photobiologySensors-0.5.3/photobiologySensors/man/solarlight_sensors.Rd | 94 +-- photobiologySensors-0.5.3/photobiologySensors/man/solarmeter_sensors.Rd | 86 +-- photobiologySensors-0.5.3/photobiologySensors/man/specmeters_sensors.Rd | 25 - photobiologySensors-0.5.3/photobiologySensors/man/thiesclima_sensors.Rd | 91 ++- photobiologySensors-0.5.3/photobiologySensors/man/vishay_sensors.Rd | 22 photobiologySensors-0.5.3/photobiologySensors/man/vitaltech_sensors.Rd | 79 +-- photobiologySensors-0.5.3/photobiologySensors/vignettes/userguide-1.Rmd | 35 + 66 files changed, 1513 insertions(+), 1264 deletions(-)
More information about photobiologySensors at CRAN
Permanent link
Title: Calculating Bilateral and Multilateral Price Indexes
Description: Preparing a scanner data set for price dynamics calculations (data selecting, data classification, data matching, data filtering). Computing bilateral and multilateral indexes. For details on these methods see: Diewert and Fox (2020)
<doi:10.1080/07350015.2020.1816176>, Białek (2019) <doi:10.2478/jos-2019-0014> or Białek (2020) <doi:10.2478/jos-2020-0037>.
Author: Jacek Bialek [aut, cre]
Maintainer: Jacek Bialek <jacek.bialek@uni.lodz.pl>
Diff between PriceIndices versions 0.2.8 dated 2026-02-18 and 0.2.9 dated 2026-03-13
DESCRIPTION | 6 ++-- MD5 | 21 +++++++------- NAMESPACE | 1 NEWS.md | 5 +++ R/PriceIndices.R | 66 +++++++++++++++++++++++---------------------- R/f_data_processing.R | 52 +++++++++++++++++++++++++++++++++++ README.md | 51 ++++++++++++++++------------------ inst/doc/PriceIndices.Rmd | 2 - inst/doc/PriceIndices.html | 5 ++- man/PriceIndices.Rd | 52 ++++++++++++++++++----------------- man/outlet_check.Rd |only vignettes/PriceIndices.Rmd | 2 - 12 files changed, 163 insertions(+), 100 deletions(-)
Title: Kinase-Substrate Enrichment Analysis
Description: Infers relative kinase activity from phosphoproteomics data
using the method described by Casado et al. (2013) <doi:10.1126/scisignal.2003573>.
Author: Danica Wiredja [aut, cre]
Maintainer: Danica Wiredja <dwiredja@gmail.com>
Diff between KSEAapp versions 0.99.0 dated 2017-05-02 and 2.0 dated 2026-03-13
KSEAapp-0.99.0/KSEAapp/R/KSEA.Complete.R |only KSEAapp-0.99.0/KSEAapp/man/KSEA.Complete.Rd |only KSEAapp-2.0/KSEAapp/DESCRIPTION | 18 KSEAapp-2.0/KSEAapp/LICENSE | 4 KSEAapp-2.0/KSEAapp/MD5 | 50 - KSEAapp-2.0/KSEAapp/NAMESPACE | 33 KSEAapp-2.0/KSEAapp/R/KSEA.Barplot.R | 342 ++++----- KSEAapp-2.0/KSEAapp/R/KSEA.Heatmap.R | 334 ++++----- KSEAapp-2.0/KSEAapp/R/KSEA.KS_table.R | 242 +++--- KSEAapp-2.0/KSEAapp/R/KSEA.Scores.1.R | 51 - KSEAapp-2.0/KSEAapp/R/KSEA.Scores.2.R | 51 - KSEAapp-2.0/KSEAapp/R/KSEA.Scores.3.R | 51 - KSEAapp-2.0/KSEAapp/R/KSEA.Scores.R | 279 +++---- KSEAapp-2.0/KSEAapp/R/PX.R | 54 - KSEAapp-2.0/KSEAapp/build/vignette.rds |binary KSEAapp-2.0/KSEAapp/inst/doc/Overview.Rmd | 361 ++++----- KSEAapp-2.0/KSEAapp/inst/doc/Overview.html | 1018 ++++++++++++++++------------ KSEAapp-2.0/KSEAapp/man/KSData.Rd | 44 - KSEAapp-2.0/KSEAapp/man/KSEA.Barplot.Rd | 101 +- KSEAapp-2.0/KSEAapp/man/KSEA.Heatmap.Rd | 118 +-- KSEAapp-2.0/KSEAapp/man/KSEA.KS_table.Rd | 84 +- KSEAapp-2.0/KSEAapp/man/KSEA.Scores.1.Rd | 55 - KSEAapp-2.0/KSEAapp/man/KSEA.Scores.2.Rd | 55 - KSEAapp-2.0/KSEAapp/man/KSEA.Scores.3.Rd | 55 - KSEAapp-2.0/KSEAapp/man/KSEA.Scores.Rd | 82 +- KSEAapp-2.0/KSEAapp/man/PX.Rd | 60 - KSEAapp-2.0/KSEAapp/vignettes/Overview.Rmd | 361 ++++----- 27 files changed, 2026 insertions(+), 1877 deletions(-)
Title: Visualizing Pedigrees with 'ggplot2' and 'plotly'
Description: Provides plotting functions for visualizing pedigrees and family trees. The package complements a behavior genetics package 'BGmisc' [Garrison et al. (2024) <doi:10.21105/joss.06203>] by rendering pedigrees using the 'ggplot2' framework. Features include support for duplicated individuals, complex mating structures, integration with simulated pedigrees, and layout customization. Due to the impending deprecation of kinship2, version 1.0 incorporates the layout helper functions from kinship2. The pedigree alignment algorithms are adapted from 'kinship2' [Sinnwell et al. (2014) <doi:10.1159/000363105>]. We gratefully acknowledge the original authors: Jason Sinnwell, Terry Therneau, Daniel Schaid, and Elizabeth Atkinson for their foundational work.
Author: S. Mason Garrison [aut, cre, cph]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>
Diff between ggpedigree versions 1.1.0.3 dated 2026-01-11 and 1.1.1.0.0 dated 2026-03-13
ggpedigree-1.1.0.3/ggpedigree/inst/doc/v10_configuration.R |only ggpedigree-1.1.0.3/ggpedigree/inst/doc/v10_configuration.Rmd |only ggpedigree-1.1.0.3/ggpedigree/inst/doc/v10_configuration.html |only ggpedigree-1.1.0.3/ggpedigree/vignettes/v10_configuration.Rmd |only ggpedigree-1.1.1.0.0/ggpedigree/DESCRIPTION | 6 ggpedigree-1.1.1.0.0/ggpedigree/MD5 | 103 +++++----- ggpedigree-1.1.1.0.0/ggpedigree/NEWS.md | 8 ggpedigree-1.1.1.0.0/ggpedigree/R/buildPlotConfig.R | 27 ++ ggpedigree-1.1.1.0.0/ggpedigree/R/calcCoordinates.R | 9 ggpedigree-1.1.1.0.0/ggpedigree/R/defaultPlotConfig.R | 26 +- ggpedigree-1.1.1.0.0/ggpedigree/R/ggPedigreeInteractive.R | 37 +-- ggpedigree-1.1.1.0.0/ggpedigree/R/ggPhenotypeByDegree.R | 20 + ggpedigree-1.1.1.0.0/ggpedigree/R/ggRelatednessMatrix.R | 3 ggpedigree-1.1.1.0.0/ggpedigree/R/ggpedigree.R | 16 - ggpedigree-1.1.1.0.0/ggpedigree/R/ggpedigreeCore.R | 38 ++- ggpedigree-1.1.1.0.0/ggpedigree/R/ggpedigreeCoreHelpers.R | 38 ++- ggpedigree-1.1.1.0.0/ggpedigree/R/ggpedigreeHelpers.R | 11 - ggpedigree-1.1.1.0.0/ggpedigree/R/kinship2_alignped3.R | 4 ggpedigree-1.1.1.0.0/ggpedigree/R/kinship2_pedigree.R | 35 ++- ggpedigree-1.1.1.0.0/ggpedigree/R/processExtras.R | 14 - ggpedigree-1.1.1.0.0/ggpedigree/README.md | 23 +- ggpedigree-1.1.1.0.0/ggpedigree/build/partial.rdb |binary ggpedigree-1.1.1.0.0/ggpedigree/build/vignette.rds |binary ggpedigree-1.1.1.0.0/ggpedigree/inst/CITATION |only ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v00_plots.R | 6 ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v00_plots.Rmd | 6 ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v00_plots.html | 2 ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v02_configuration.R |only ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v02_configuration.Rmd |only ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v02_configuration.html |only ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v20_interactiveplots.html | 28 -- ggpedigree-1.1.1.0.0/ggpedigree/inst/doc/v30_matrix.html | 41 --- ggpedigree-1.1.1.0.0/ggpedigree/man/addFocalFillColumn.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-addLabels.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-addNodes.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-addOverlay.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-addScales.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-addSelfSegment.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-addTwins.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-adjustSpacing.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/dot-preparePhenotypeByDegreeData.Rd | 6 ggpedigree-1.1.1.0.0/ggpedigree/man/dot-restoreNames.Rd | 10 ggpedigree-1.1.1.0.0/ggpedigree/man/figures/README-basic-usage-1.png |binary ggpedigree-1.1.1.0.0/ggpedigree/man/figures/README-slightly-usage-1.png |binary ggpedigree-1.1.1.0.0/ggpedigree/man/getDefaultPlotConfig.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/ggPedigree.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/ggPedigree.core.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/ggPedigreeInteractive.Rd | 15 - ggpedigree-1.1.1.0.0/ggpedigree/man/preparePedigreeData.Rd | 17 + ggpedigree-1.1.1.0.0/ggpedigree/man/recodeMissingIDs.Rd | 12 - ggpedigree-1.1.1.0.0/ggpedigree/man/transformPed.Rd | 15 - ggpedigree-1.1.1.0.0/ggpedigree/tests/testthat/Rplots.pdf |binary ggpedigree-1.1.1.0.0/ggpedigree/tests/testthat/test-defaultPlotConfig.R | 10 ggpedigree-1.1.1.0.0/ggpedigree/tests/testthat/test-ggpedigree_datainputs.R | 95 +++++---- ggpedigree-1.1.1.0.0/ggpedigree/vignettes/v00_plots.Rmd | 6 ggpedigree-1.1.1.0.0/ggpedigree/vignettes/v02_configuration.Rmd |only ggpedigree-1.1.1.0.0/ggpedigree/vignettes/v10_configuration.R |only ggpedigree-1.1.1.0.0/ggpedigree/vignettes/v10_configuration.html |only 58 files changed, 480 insertions(+), 339 deletions(-)
Title: Scalable Causal Discovery and Model Selection on Mixed Datasets
with 'rCausalMGM'
Description: Scalable methods for learning causal graphical models from mixed data, including continuous, discrete, and censored variables. The package implements CausalMGM, which combines a convex, score-based approach for learning an initial moralized graph with a producer-consumer scheme that enables efficient parallel conditional independence testing in constraint-based causal discovery algorithms. The implementation supports high-dimensional datasets and provides individual access to core components of the workflow, including MGM and the PC-Stable and FCI-Stable causal discovery algorithms. To support practical applications, the package includes multiple model selection strategies, including information criteria based on likelihood and model complexity, cross-validation for out-of-sample likelihood estimation, and stability-based approaches that assess graph robustness across subsamples.
Author: Tyler C Lovelace [aut],
Max Dudek [aut],
Jack Fiore [aut],
Panayiotis V Benos [aut, cre]
Maintainer: Panayiotis V Benos <pbenos@ufl.edu>
Diff between rCausalMGM versions 1.0 dated 2026-03-03 and 1.0.1 dated 2026-03-13
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS |only src/CensoredVariable.cpp | 12 ++++++------ src/ContinuousVariable.cpp | 2 +- 5 files changed, 15 insertions(+), 14 deletions(-)
Title: Simple Interactive Controls for R using the 'tcltk' Package
Description: A set of functions to build simple
GUI controls for R functions. These are built on the 'tcltk' package.
Uses could include changing a parameter on a graph by animating it
with a slider or a "doublebutton", up to more sophisticated control
panels.
Some functions for specific graphical tasks, referred to as 'cartoons',
are provided.
Author: Adrian Bowman [aut, cre, cph],
Ewan Crawford [aut],
Gavin Alexander [aut],
Richard Bowman [aut]
Maintainer: Adrian Bowman <adrian.bowman@glasgow.ac.uk>
Diff between rpanel versions 1.1-6 dated 2026-03-12 and 1.1-6.1 dated 2026-03-13
ChangeLog | 2 ++ DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/rp-plot4d.r | 2 +- R/rp_drop1.R | 2 +- R/rp_sample.r | 5 +++-- R/rpanel.r | 2 +- tests/testthat/test-rp.sample.r | 15 ++++++++++++--- 8 files changed, 30 insertions(+), 18 deletions(-)
Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided as a data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98), other curves (e.g., NOTCal04 [van der Plicht et al. 2004], Arnold & Libby 1951, Stuiver & Suess 1966, Pearson & Stuiver 1986) and postbomb curves. Also provided are functions to copy the curves into memory, and to read, query and plot the data underlying the IntCal20 curves.
Author: Maarten Blaauw [aut, cre] ,
Christopher Bronk Ramsey [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rintcal versions 1.3.1 dated 2025-12-07 and 1.4.0 dated 2026-03-13
DESCRIPTION | 6 - MD5 | 26 +++--- NEWS.md | 7 + R/data.R | 187 ++++++++++++++++++++++------------------------ R/intcal_json.R | 73 ++++++++++------- R/rintcal.R | 53 +++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/rintcal.html | 23 ++--- man/ccurve.Rd | 33 +++----- man/intcal.data.Rd | 160 +++++++++++++++++++-------------------- man/intcal.plot.record.Rd | 10 +- man/intcal.write.data.Rd | 2 man/rintcal-package.Rd | 2 14 files changed, 307 insertions(+), 275 deletions(-)
Title: Empirical Bayes Methods for Pharmacovigilance
Description: A suite of empirical Bayes methods to use in pharmacovigilance. Contains various model fitting and post-processing functions. For more details see Tan et al. (2025) <doi:10.48550/arXiv.2502.09816>, <doi:10.48550/arXiv.2512.01057>; Koenker and Mizera (2014) <doi:10.1080/01621459.2013.869224>; Efron (2016) <doi:10.1093/biomet/asv068>.
Author: Yihao Tan [aut, cre] ,
Marianthi Markatou [aut] ,
Saptarshi Chakraborty [aut] ,
Raktim Mukhopadhyay [aut]
Maintainer: Yihao Tan <yihaotan@buffalo.edu>
Diff between pvEBayes versions 0.2.1 dated 2026-01-11 and 0.2.2 dated 2026-03-13
DESCRIPTION | 6 MD5 | 20 - R/pvEBayes-package.R | 3 R/pvEBayes_main_function.R | 78 ++++- README.md | 127 +++++---- inst/doc/pvEBayes-introduction.Rmd | 368 +++++++++++++++------------ inst/doc/pvEBayes-introduction.html | 80 ++++- man/dot-KM_fit.Rd | 2 man/pvEBayes-package.Rd | 3 tests/testthat/test-pvEBayes_main_function.R | 17 - vignettes/pvEBayes-introduction.Rmd | 368 +++++++++++++++------------ 11 files changed, 631 insertions(+), 441 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources ('rpart', 'RWeka', 'PMML') yielding objects that share
functionality for print()/plot()/predict() methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree()) and model-based
recursive partitioning (mob()) from the 'party' package are provided based
on the new infrastructure. A description of this package was published
by Hothorn and Zeileis (2015) <https://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] ,
Heidi Seibold [ctb] ,
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.2-26 dated 2026-03-06 and 1.2-27 dated 2026-03-13
DESCRIPTION | 8 ++-- MD5 | 39 ++++++++++---------- build/partial.rdb |binary inst/NEWS.Rd | 10 +++++ inst/doc/constparty.pdf |binary inst/doc/ctree.pdf |binary inst/doc/mob.pdf |binary inst/doc/partykit.pdf |binary tests/Rplots.pdf |only tests/bugfixes.R | 2 - tests/bugfixes.Rout.save | 16 ++++---- tests/constparty.Rout.save | 6 +-- tests/regtest-MIA.Rout.save | 6 +-- tests/regtest-cforest.Rout.save | 6 +-- tests/regtest-ctree.Rout.save | 6 +-- tests/regtest-glmtree.Rout.save | 6 +-- tests/regtest-nmax.Rout.save | 6 +-- tests/regtest-node.Rout.save | 6 +-- tests/regtest-party.Rout.save | 78 ++++++++++++++++++++-------------------- tests/regtest-split.Rout.save | 6 +-- tests/regtest-weights.Rout.save | 6 +-- 21 files changed, 109 insertions(+), 98 deletions(-)
Title: Explainable Ensemble Trees
Description: The Explainable Ensemble Trees 'e2tree' approach has been proposed by Aria et al. (2024) <doi:10.1007/s00180-022-01312-6>. It aims to explain and interpret decision tree ensemble models using a single tree-like structure. 'e2tree' is a new way of explaining an ensemble tree trained through 'randomForest' or 'xgboost' packages.
Author: Massimo Aria [aut, cre, cph] ,
Agostino Gnasso [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between e2tree versions 0.2.0 dated 2025-07-16 and 1.0.0 dated 2026-03-13
e2tree-0.2.0/e2tree/R/eComparison.R |only e2tree-0.2.0/e2tree/man/eComparison.Rd |only e2tree-0.2.0/e2tree/tests/testthat.R |only e2tree-0.2.0/e2tree/tests/testthat/Rplots.pdf |only e2tree-0.2.0/e2tree/tests/testthat/test-eComparison.R |only e2tree-1.0.0/e2tree/DESCRIPTION | 20 e2tree-1.0.0/e2tree/MD5 | 92 + e2tree-1.0.0/e2tree/NAMESPACE | 37 e2tree-1.0.0/e2tree/NEWS.md | 34 e2tree-1.0.0/e2tree/R/RcppExports.R | 16 e2tree-1.0.0/e2tree/R/aaa_utils.R |only e2tree-1.0.0/e2tree/R/createDisMatrix.R | 477 ++++++---- e2tree-1.0.0/e2tree/R/credit.R |only e2tree-1.0.0/e2tree/R/e2tree.R | 282 +++-- e2tree-1.0.0/e2tree/R/eImpurity.R | 65 - e2tree-1.0.0/e2tree/R/ePredTree.R | 160 ++- e2tree-1.0.0/e2tree/R/eStoppingRules.R | 30 e2tree-1.0.0/e2tree/R/eValidation.R |only e2tree-1.0.0/e2tree/R/goi.R |only e2tree-1.0.0/e2tree/R/plot_e2tree_click.R |only e2tree-1.0.0/e2tree/R/plot_e2tree_vis.R |only e2tree-1.0.0/e2tree/R/proximity_longer.R | 2 e2tree-1.0.0/e2tree/R/roc.R | 10 e2tree-1.0.0/e2tree/R/rpart2Tree.R | 22 e2tree-1.0.0/e2tree/R/split.R | 118 +- e2tree-1.0.0/e2tree/R/vimp.R | 78 + e2tree-1.0.0/e2tree/R/zzz.R | 22 e2tree-1.0.0/e2tree/README.md | 43 e2tree-1.0.0/e2tree/data |only e2tree-1.0.0/e2tree/inst/CITATION | 12 e2tree-1.0.0/e2tree/man/check_package.Rd |only e2tree-1.0.0/e2tree/man/createDisMatrix.Rd | 93 + e2tree-1.0.0/e2tree/man/credit.Rd |only e2tree-1.0.0/e2tree/man/e2_variance.Rd |only e2tree-1.0.0/e2tree/man/e2tree.Rd | 22 e2tree-1.0.0/e2tree/man/ePredTree.Rd | 10 e2tree-1.0.0/e2tree/man/eValidation.Rd |only e2tree-1.0.0/e2tree/man/figures/README-unnamed-chunk-10-1.png |binary e2tree-1.0.0/e2tree/man/figures/README-unnamed-chunk-15-1.png |binary e2tree-1.0.0/e2tree/man/figures/README-unnamed-chunk-15-2.png |binary e2tree-1.0.0/e2tree/man/figures/README-unnamed-chunk-18-1.png |binary e2tree-1.0.0/e2tree/man/figures/README-unnamed-chunk-19-1.png |binary e2tree-1.0.0/e2tree/man/figures/README-unnamed-chunk-19-2.png |binary e2tree-1.0.0/e2tree/man/figures/README-unnamed-chunk-19-3.png |binary e2tree-1.0.0/e2tree/man/get_ensemble_type.Rd |only e2tree-1.0.0/e2tree/man/goi.Rd |only e2tree-1.0.0/e2tree/man/goi_analysis.Rd |only e2tree-1.0.0/e2tree/man/goi_perm.Rd |only e2tree-1.0.0/e2tree/man/plot.goi_perm.Rd |only e2tree-1.0.0/e2tree/man/plot_e2tree.Rd |only e2tree-1.0.0/e2tree/man/plot_e2tree_click.Rd |only e2tree-1.0.0/e2tree/man/plot_e2tree_vis.Rd |only e2tree-1.0.0/e2tree/man/print_e2tree_summary.Rd |only e2tree-1.0.0/e2tree/man/rpart2Tree.Rd | 18 e2tree-1.0.0/e2tree/man/save_e2tree_html.Rd |only e2tree-1.0.0/e2tree/src/CoOccurrences.cpp | 365 +++++++ e2tree-1.0.0/e2tree/src/Makevars |only e2tree-1.0.0/e2tree/src/Makevars.win |only e2tree-1.0.0/e2tree/src/RcppExports.cpp | 57 + e2tree-1.0.0/e2tree/tests/testthat.zip |only e2tree-1.0.0/e2tree/tests/testthat/test-createDisMatrix.R | 4 e2tree-1.0.0/e2tree/tests/testthat/test-eValidation.R |only 62 files changed, 1437 insertions(+), 652 deletions(-)
Title: Descriptive, Reliability, and Inferential Tables for
Psychometric Scales and Demographic Data
Description: Provides functions to format and summarise already computed outputs from commonly used statistical and psychometric functions into compact, single-row tables and simple graphs, with utilities to export results to CSV, Word, and Excel formats. The package does not implement new statistical methods or estimation procedures; instead, it organises and presents results obtained from existing functions such as psych::describe(), psych::alpha(), stats::t.test(), and gtsummary::tbl_summary() to streamline reporting workflows in clinical and psychological research.
Author: Darshankumar Dharaiya [aut, cre]
Maintainer: Darshankumar Dharaiya <dharaiya.darshan@gmail.com>
Diff between scaledescr versions 0.2.1 dated 2026-03-06 and 0.2.2 dated 2026-03-13
DESCRIPTION | 8 ++--- MD5 | 14 +++++---- NAMESPACE | 3 ++ NEWS.md | 9 ++++-- R/make_demographic_table.R | 46 +++++++++++++++++++++++--------- R/make_demographic_table_to_output.R |only inst/CITATION | 2 - man/make_demographic_table.Rd | 7 ++-- man/make_demographic_table_to_output.Rd |only 9 files changed, 59 insertions(+), 30 deletions(-)
Title: Wrapper for MUMPS Library
Description: Some basic features of 'MUMPS' (Multifrontal Massively Parallel
sparse direct Solver) are wrapped in a class whose methods can be used
for sequentially solving a sparse linear system (symmetric or not)
with one or many right hand sides (dense or sparse).
There is a possibility to do separately symbolic analysis,
LU (or LDL^t) factorization and system solving.
Third part ordering libraries are included and can be used: 'PORD', 'METIS', 'SCOTCH'.
'MUMPS' method was first described in Amestoy et al. (2001) <doi:10.1137/S0895479899358194>
and Amestoy et al. (2006) <doi:10.1016/j.parco.2005.07.004>.
Author: Serguei Sokol [aut, cre],
Emmanuel Agullo [ctb],
Patrick Amestoy [ctb, cph],
Maurice Bremond [ctb],
Alfredo Buttari [ctb],
Philippe Combes [ctb],
Marie Durand [ctb],
Aurelia Fevre [ctb],
Abdou Guermouche [ctb],
Guillaume Joslin [ctb],
Jacko Koster [c [...truncated...]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.2.1-37 dated 2026-02-28 and 5.2.1-41 dated 2026-03-13
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------ NEWS | 29 ++++++++++++++++---- R/zzz.R | 2 - man/RMUMPS_PERM.Rd | 8 +++-- src/lib/MUMPS_5.2.1/include/mumps_c_types.h | 2 - src/lib/MUMPS_5.2.1/src/dmumps_ooc.F | 20 ++++++------- src/lib/MUMPS_5.2.1/src/dmumps_save_restore_files.F | 4 +- src/lib/MUMPS_5.2.1/src/dsol_bwd_aux.F | 2 - tests/testthat/test_rmumps.R | 4 +- 10 files changed, 58 insertions(+), 37 deletions(-)
Title: Simplifies Plotting Data Inside Databases
Description: Leverages 'dplyr' to process the calculations of a plot inside a database.
This package provides helper functions that abstract the work at three levels:
outputs a 'ggplot', outputs the calculations, outputs the formula
needed to calculate bins.
Author: Edgar Ruiz [aut, cre]
Maintainer: Edgar Ruiz <edgararuiz@gmail.com>
Diff between dbplot versions 0.3.3 dated 2020-02-06 and 0.4.0 dated 2026-03-13
dbplot-0.3.3/dbplot/R/utils-pipe.R |only dbplot-0.3.3/dbplot/man/pipe.Rd |only dbplot-0.4.0/dbplot/DESCRIPTION | 18 dbplot-0.4.0/dbplot/LICENSE |only dbplot-0.4.0/dbplot/MD5 | 101 +- dbplot-0.4.0/dbplot/NAMESPACE | 6 dbplot-0.4.0/dbplot/NEWS.md | 42 + dbplot-0.4.0/dbplot/R/boxplot.R | 80 +- dbplot-0.4.0/dbplot/R/dbbin.R | 46 - dbplot-0.4.0/dbplot/R/dbplot-package.R |only dbplot-0.4.0/dbplot/R/dbplot.R | 23 dbplot-0.4.0/dbplot/R/discrete.R | 72 + dbplot-0.4.0/dbplot/R/histogram.R | 61 + dbplot-0.4.0/dbplot/R/raster.R | 95 +- dbplot-0.4.0/dbplot/README.md | 379 ++++++---- dbplot-0.4.0/dbplot/inst |only dbplot-0.4.0/dbplot/man/db_bin.Rd | 29 dbplot-0.4.0/dbplot/man/db_compute_bins.Rd | 22 dbplot-0.4.0/dbplot/man/db_compute_boxplot.Rd | 30 dbplot-0.4.0/dbplot/man/db_compute_count.Rd | 25 dbplot-0.4.0/dbplot/man/db_compute_raster.Rd | 29 dbplot-0.4.0/dbplot/man/dbplot-package.Rd |only dbplot-0.4.0/dbplot/man/dbplot_bar.Rd | 24 dbplot-0.4.0/dbplot/man/dbplot_boxplot.Rd | 25 dbplot-0.4.0/dbplot/man/dbplot_histogram.Rd | 23 dbplot-0.4.0/dbplot/man/dbplot_line.Rd | 26 dbplot-0.4.0/dbplot/man/dbplot_raster.Rd | 26 dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-10-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-11-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-12-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-13-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-14-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-15-1.png |only dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-16-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-17-1.png |only dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-19-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-20-1.png |only dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-4-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-5-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-6-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-7-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-8-1.png |binary dbplot-0.4.0/dbplot/man/figures/README-unnamed-chunk-9-1.png |binary dbplot-0.4.0/dbplot/man/figures/logo.png |binary dbplot-0.4.0/dbplot/man/figures/logo.svg |only dbplot-0.4.0/dbplot/tests/testthat.R | 3 dbplot-0.4.0/dbplot/tests/testthat/_snaps |only dbplot-0.4.0/dbplot/tests/testthat/helper-snapshots.R |only dbplot-0.4.0/dbplot/tests/testthat/test-boxplots.R | 23 dbplot-0.4.0/dbplot/tests/testthat/test-dbbin.R | 2 dbplot-0.4.0/dbplot/tests/testthat/test-dbplots.R | 53 + dbplot-0.4.0/dbplot/tests/testthat/test-discrete.R | 66 + dbplot-0.4.0/dbplot/tests/testthat/test-duckdb-computations.R |only dbplot-0.4.0/dbplot/tests/testthat/test-edge-cases.R |only dbplot-0.4.0/dbplot/tests/testthat/test-input-validation.R |only dbplot-0.4.0/dbplot/tests/testthat/test-raster.R | 27 56 files changed, 996 insertions(+), 360 deletions(-)
Title: An R Package for Extended Behavior Genetics Analysis
Description: Provides functions for behavior genetics analysis,
including variance component model identification [Hunter et al. (2021) <doi:10.1007/s10519-021-10055-x>],
calculation of relatedness coefficients using path-tracing methods
[Wright (1922) <doi:10.1086/279872>; McArdle & McDonald (1984) <doi:10.1111/j.2044-8317.1984.tb00802.x>],
inference of relatedness, pedigree conversion, and simulation of multi-generational family data
[Lyu et al. (2025) <doi:10.1007/s10519-025-10225-1>]. For a full overview,
see [Garrison et al. (2024) <doi:10.21105/joss.06203>]. For a big data application see [Burt et al. (2025) <doi: 10.1016/j.ebiom.2025.105911>.
Author: S. Mason Garrison [aut, cre] ,
Michael D. Hunter [aut] ,
Xuanyu Lyu [aut] ,
Rachel N. Good [ctb],
Jonathan D. Trattner [aut] ,
S. Alexandra Burt [aut]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>
Diff between BGmisc versions 1.5.2 dated 2026-01-11 and 1.6.0.1 dated 2026-03-13
BGmisc-1.5.2/BGmisc/R/cleanPedigree.R |only BGmisc-1.5.2/BGmisc/R/helpPedigree.R |only BGmisc-1.5.2/BGmisc/R/insertEven.R |only BGmisc-1.5.2/BGmisc/man/buildBetweenGenerations.Rd |only BGmisc-1.6.0.1/BGmisc/DESCRIPTION | 12 BGmisc-1.6.0.1/BGmisc/MD5 | 146 - BGmisc-1.6.0.1/BGmisc/NAMESPACE | 7 BGmisc-1.6.0.1/BGmisc/NEWS.md | 16 BGmisc-1.6.0.1/BGmisc/R/buildComponent.R | 187 + BGmisc-1.6.0.1/BGmisc/R/buildmxPedigrees.R |only BGmisc-1.6.0.1/BGmisc/R/checkIDs.R | 23 BGmisc-1.6.0.1/BGmisc/R/checkParents.R | 22 BGmisc-1.6.0.1/BGmisc/R/constructAdjacency.R | 5 BGmisc-1.6.0.1/BGmisc/R/helpChecks.R |only BGmisc-1.6.0.1/BGmisc/R/helpInsertEven.R |only BGmisc-1.6.0.1/BGmisc/R/helpNames.R |only BGmisc-1.6.0.1/BGmisc/R/helpSimulatePedigree.R |only BGmisc-1.6.0.1/BGmisc/R/helpSimulatePedigree_beta.R |only BGmisc-1.6.0.1/BGmisc/R/helpTwins.R |only BGmisc-1.6.0.1/BGmisc/R/readGedcom.R | 42 BGmisc-1.6.0.1/BGmisc/R/segmentPedigree.R | 48 BGmisc-1.6.0.1/BGmisc/R/simulatePedigree.R | 984 +++++++--- BGmisc-1.6.0.1/BGmisc/R/simulatePedigree_within.R |only BGmisc-1.6.0.1/BGmisc/R/summarizePedigree.R | 18 BGmisc-1.6.0.1/BGmisc/R/tweakPedigree.R | 295 ++ BGmisc-1.6.0.1/BGmisc/README.md | 1 BGmisc-1.6.0.1/BGmisc/build/partial.rdb |binary BGmisc-1.6.0.1/BGmisc/build/vignette.rds |binary BGmisc-1.6.0.1/BGmisc/inst/doc/v0_network.Rmd | 2 BGmisc-1.6.0.1/BGmisc/inst/doc/v0_network.html | 6 BGmisc-1.6.0.1/BGmisc/inst/doc/v1_modelingvariancecomponents.R | 27 BGmisc-1.6.0.1/BGmisc/inst/doc/v1_modelingvariancecomponents.Rmd | 47 BGmisc-1.6.0.1/BGmisc/inst/doc/v1_modelingvariancecomponents.html | 210 +- BGmisc-1.6.0.1/BGmisc/inst/doc/v2_pedigree.Rmd | 3 BGmisc-1.6.0.1/BGmisc/inst/doc/v2_pedigree.html | 4 BGmisc-1.6.0.1/BGmisc/inst/doc/v3_analyticrelatedness.html | 4 BGmisc-1.6.0.1/BGmisc/inst/doc/v5_ASOIAF.R | 41 BGmisc-1.6.0.1/BGmisc/inst/doc/v5_ASOIAF.Rmd | 49 BGmisc-1.6.0.1/BGmisc/inst/doc/v5_ASOIAF.html | 273 +- BGmisc-1.6.0.1/BGmisc/inst/doc/v6_pedigree_model_fitting.R |only BGmisc-1.6.0.1/BGmisc/inst/doc/v6_pedigree_model_fitting.Rmd |only BGmisc-1.6.0.1/BGmisc/inst/doc/v6_pedigree_model_fitting.html |only BGmisc-1.6.0.1/BGmisc/man/BGmisc-package.Rd | 2 BGmisc-1.6.0.1/BGmisc/man/addIfAny.Rd |only BGmisc-1.6.0.1/BGmisc/man/adjustKidsPerCouple.Rd | 21 BGmisc-1.6.0.1/BGmisc/man/assignCoupleIDs.Rd | 12 BGmisc-1.6.0.1/BGmisc/man/buildBtwnGenerations.Rd |only BGmisc-1.6.0.1/BGmisc/man/buildFamilyGroups.Rd |only BGmisc-1.6.0.1/BGmisc/man/buildOneFamilyGroup.Rd |only BGmisc-1.6.0.1/BGmisc/man/buildPedigreeModelCovariance.Rd |only BGmisc-1.6.0.1/BGmisc/man/buildPedigreeMx.Rd |only BGmisc-1.6.0.1/BGmisc/man/buildWithinGenerations.Rd | 19 BGmisc-1.6.0.1/BGmisc/man/createGenDataFrame.Rd | 18 BGmisc-1.6.0.1/BGmisc/man/determineSex.Rd | 10 BGmisc-1.6.0.1/BGmisc/man/dot-adjBeta.Rd | 4 BGmisc-1.6.0.1/BGmisc/man/dropIdenticalDuplicateIDs.Rd |only BGmisc-1.6.0.1/BGmisc/man/dropLink.Rd | 5 BGmisc-1.6.0.1/BGmisc/man/findMZtwins.Rd |only BGmisc-1.6.0.1/BGmisc/man/fitPedigreeModel.Rd |only BGmisc-1.6.0.1/BGmisc/man/fuseTwins.Rd |only BGmisc-1.6.0.1/BGmisc/man/insertEven.Rd | 2 BGmisc-1.6.0.1/BGmisc/man/isTwin.Rd |only BGmisc-1.6.0.1/BGmisc/man/makeInbreeding.Rd | 5 BGmisc-1.6.0.1/BGmisc/man/makeTwins.Rd | 5 BGmisc-1.6.0.1/BGmisc/man/markPotentialChildren.Rd | 22 BGmisc-1.6.0.1/BGmisc/man/ped2add.Rd | 10 BGmisc-1.6.0.1/BGmisc/man/ped2cn.Rd | 4 BGmisc-1.6.0.1/BGmisc/man/ped2com.Rd | 15 BGmisc-1.6.0.1/BGmisc/man/ped2fam.Rd | 3 BGmisc-1.6.0.1/BGmisc/man/ped2gen.Rd | 136 - BGmisc-1.6.0.1/BGmisc/man/ped2graph.Rd | 3 BGmisc-1.6.0.1/BGmisc/man/ped2maternal.Rd | 3 BGmisc-1.6.0.1/BGmisc/man/ped2mit.Rd | 4 BGmisc-1.6.0.1/BGmisc/man/ped2paternal.Rd | 3 BGmisc-1.6.0.1/BGmisc/man/restorePedColnames.Rd |only BGmisc-1.6.0.1/BGmisc/man/simulatePedigree.Rd | 19 BGmisc-1.6.0.1/BGmisc/man/standardizeColnames.Rd | 2 BGmisc-1.6.0.1/BGmisc/tests/testthat/test-buildComponent.R | 246 ++ BGmisc-1.6.0.1/BGmisc/tests/testthat/test-buildmxPedigrees.R |only BGmisc-1.6.0.1/BGmisc/tests/testthat/test-checkSex.R | 2 BGmisc-1.6.0.1/BGmisc/tests/testthat/test-helpTwins.R |only BGmisc-1.6.0.1/BGmisc/tests/testthat/test-segmentPedigree.R | 25 BGmisc-1.6.0.1/BGmisc/tests/testthat/test-simulatePedigree.R | 294 ++ BGmisc-1.6.0.1/BGmisc/tests/testthat/test-tweakPedigree.R | 358 +++ BGmisc-1.6.0.1/BGmisc/vignettes/v0_network.Rmd | 2 BGmisc-1.6.0.1/BGmisc/vignettes/v1_modelingvariancecomponents.Rmd | 47 BGmisc-1.6.0.1/BGmisc/vignettes/v2_pedigree.Rmd | 3 BGmisc-1.6.0.1/BGmisc/vignettes/v5_ASOIAF.Rmd | 49 BGmisc-1.6.0.1/BGmisc/vignettes/v6_pedigree_model_fitting.Rmd |only 89 files changed, 2961 insertions(+), 864 deletions(-)
Title: Client for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@lamin.ai>
Diff between laminr versions 1.2.2 dated 2026-01-12 and 1.3.0 dated 2026-03-13
DESCRIPTION | 10 +-- MD5 | 56 +++++++++++---------- NAMESPACE | 1 R/BasicQuerySet.R |only R/checks.R | 44 ++++++++++++----- R/file_loaders.R | 2 R/import.R | 13 ++--- R/install.R | 2 R/lamindb.R | 61 +---------------------- R/require.R | 18 ++++--- R/status.R | 25 ++++++--- R/temporary-instance.R | 75 +++++++++++------------------ R/utils.R | 92 ++++++++++++++++++------------------ R/zzz.R | 2 build/vignette.rds |binary man/get_current_lamin_instance.Rd | 12 ++-- man/get_current_lamin_settings.Rd | 8 +-- man/get_current_lamin_user.Rd | 9 +-- man/import_module.Rd | 4 - man/install_lamindb.Rd | 2 man/require_module.Rd | 2 tests/testthat/setup.R | 8 +-- tests/testthat/test-BasicQuerySet.R |only tests/testthat/test-Registry.R | 2 tests/testthat/test-checks.R | 9 +++ tests/testthat/test-import.R | 8 +-- tests/testthat/test-install.R | 11 +++- tests/testthat/test-unwrap-python.R | 6 +- tests/testthat/test-utils.R | 8 +-- tests/testthat/test-wrap-python.R | 3 - 30 files changed, 239 insertions(+), 254 deletions(-)
Title: Bayesian Model Averaging
Description: Package for Bayesian model averaging and variable selection for linear models,
generalized linear models and survival models (cox
regression).
Author: Adrian Raftery [aut],
Jennifer Hoeting [aut],
Chris Volinsky [aut],
Ian Painter [aut],
Ka Yee Yeung [aut],
Hana Sevcikova [cre]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between BMA versions 3.18.20 dated 2025-01-11 and 3.18.21 dated 2026-03-13
ChangeLog | 5 DESCRIPTION | 8 MD5 | 16 - R/bicreg.R | 2 R/iBMA.bicreg.R | 488 ++++++++++++++++++++++++++-------------------------- R/iBMA.glm.R | 63 ------ R/iBMA.surv.R | 58 ------ R/predict.bic.glm.R | 2 man/iBMA.Rd | 2 9 files changed, 282 insertions(+), 362 deletions(-)
Title: Read-Write Support for 'NumPy' Files via 'Rcpp'
Description: The 'cnpy' library written by Carl Rogers provides read and write
facilities for files created with (or for) the 'NumPy' extension for 'Python'.
Vectors and matrices of numeric types can be read or written to and from
files as well as compressed files. Support for integer files is available if
the package has been built with as C++11 which should be the default on
all platforms since the release of R 3.3.0.
Author: Dirk Eddelbuettel [aut, cre] ,
Wush Wu [aut] ,
Carl Rogers [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCNPy versions 0.2.14 dated 2025-11-03 and 0.2.15 dated 2026-03-13
ChangeLog | 17 +++++++++++++++ DESCRIPTION | 8 +++---- MD5 | 18 ++++++++-------- build/vignette.rds |binary inst/NEWS.Rd | 9 +++++++- inst/doc/RcppCNPy-intro.pdf |binary inst/doc/UsingReticulate.pdf |binary src/cnpy.cpp | 47 +++++++++++++++++++++---------------------- src/cnpy.h | 16 ++++++-------- src/cnpyMod.cpp | 19 ++++++++--------- 10 files changed, 77 insertions(+), 57 deletions(-)
Title: Analysis of Designed High-Dimensional Data using the
Comprehensive MultANOVA Framework
Description: A comprehensive and computationally fast framework to analyze high dimensional data associated with an experimental design based on Multiple ANOVAs (MultANOVA). It includes testing the overall significance of terms in the model, post-hoc analyses of significant terms and variable selection. Details may be found in Mahieu, B., & Cariou, V. (2025). MultANOVA Followed by Post Hoc Analyses for Designed High‐Dimensional Data: A Comprehensive Framework That Outperforms ASCA, rMANOVA, and VASCA. Journal of Chemometrics, 39(7). <doi:10.1002/cem.70039>.
Author: Benjamin Mahieu [aut, cre],
Veronique Cariou [aut]
Maintainer: Benjamin Mahieu <benjamin.mahieu@oniris-nantes.fr>
Diff between MultANOVA versions 1.0.1 dated 2025-09-01 and 1.1.0 dated 2026-03-13
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/plot.DCDA.R | 2 +- build/partial.rdb |binary 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Animated Glass-Style Tabs and Multi-Select Filter for 'Shiny'
Description: Tools for creating animated glassmorphism-style tab
navigation and multi-select dropdown filters in 'shiny' applications.
The package provides a tab navigation component and a searchable
multi-select widget with multiple checkbox indicator styles,
select-all controls, and customizable colour themes. The widgets are
compatible with standard 'shiny' layouts and 'bs4Dash' dashboards.
Author: George Arthur [aut, cre]
Maintainer: George Arthur <prigasgenthian48@gmail.com>
Diff between glasstabs versions 0.1.0 dated 2026-03-11 and 0.1.1 dated 2026-03-13
glasstabs-0.1.0/glasstabs/man/glassMultiSelectServer.Rd |only glasstabs-0.1.1/glasstabs/DESCRIPTION | 9 glasstabs-0.1.1/glasstabs/LICENSE | 4 glasstabs-0.1.1/glasstabs/MD5 | 78 glasstabs-0.1.1/glasstabs/NAMESPACE | 26 glasstabs-0.1.1/glasstabs/NEWS.md | 41 glasstabs-0.1.1/glasstabs/R/dependencies.R | 66 glasstabs-0.1.1/glasstabs/R/glassSelect.R |only glasstabs-0.1.1/glasstabs/R/glass_multiselect.R | 610 ++++- glasstabs-0.1.1/glasstabs/R/glass_select_theme.R | 37 glasstabs-0.1.1/glasstabs/R/zzz.R | 50 glasstabs-0.1.1/glasstabs/README.md | 263 ++ glasstabs-0.1.1/glasstabs/build/vignette.rds |binary glasstabs-0.1.1/glasstabs/inst/WORDLIST | 7 glasstabs-0.1.1/glasstabs/inst/doc/getting-started.R | 70 glasstabs-0.1.1/glasstabs/inst/doc/getting-started.Rmd | 133 + glasstabs-0.1.1/glasstabs/inst/doc/getting-started.html | 273 +- glasstabs-0.1.1/glasstabs/inst/doc/glassSelect.R |only glasstabs-0.1.1/glasstabs/inst/doc/glassSelect.Rmd |only glasstabs-0.1.1/glasstabs/inst/doc/glassSelect.html |only glasstabs-0.1.1/glasstabs/inst/doc/multiselect.R | 65 glasstabs-0.1.1/glasstabs/inst/doc/multiselect.Rmd | 105 glasstabs-0.1.1/glasstabs/inst/doc/multiselect.html | 260 +- glasstabs-0.1.1/glasstabs/inst/doc/tabs.Rmd | 392 +-- glasstabs-0.1.1/glasstabs/inst/doc/tabs.html | 5 glasstabs-0.1.1/glasstabs/inst/www/glass.css | 891 +++++--- glasstabs-0.1.1/glasstabs/inst/www/glass.js | 1273 ++++++++---- glasstabs-0.1.1/glasstabs/man/glassFilterTags.Rd | 42 glasstabs-0.1.1/glasstabs/man/glassMultiSelect.Rd | 182 - glasstabs-0.1.1/glasstabs/man/glassMultiSelectValue.Rd |only glasstabs-0.1.1/glasstabs/man/glassSelect.Rd |only glasstabs-0.1.1/glasstabs/man/glassSelectValue.Rd |only glasstabs-0.1.1/glasstabs/man/glassTabPanel.Rd | 64 glasstabs-0.1.1/glasstabs/man/glassTabsServer.Rd | 70 glasstabs-0.1.1/glasstabs/man/glassTabsUI.Rd | 68 glasstabs-0.1.1/glasstabs/man/glass_select_theme.Rd | 66 glasstabs-0.1.1/glasstabs/man/updateGlassMultiSelect.Rd |only glasstabs-0.1.1/glasstabs/man/updateGlassSelect.Rd |only glasstabs-0.1.1/glasstabs/man/useGlassTabs.Rd | 64 glasstabs-0.1.1/glasstabs/tests/testthat.R | 24 glasstabs-0.1.1/glasstabs/tests/testthat/test-glassselect.R |only glasstabs-0.1.1/glasstabs/tests/testthat/test-multiselect.R | 260 ++ glasstabs-0.1.1/glasstabs/vignettes/getting-started.Rmd | 133 + glasstabs-0.1.1/glasstabs/vignettes/glassSelect.Rmd |only glasstabs-0.1.1/glasstabs/vignettes/multiselect.Rmd | 105 glasstabs-0.1.1/glasstabs/vignettes/tabs.Rmd | 392 +-- 46 files changed, 4172 insertions(+), 1956 deletions(-)
More information about freebsdcontribs at CRAN
Permanent link
Title: Coherent Forecast Combination for Linearly Constrained Multiple
Time Series
Description: Methods and tools designed to improve the forecast accuracy for a linearly
constrained multiple time series, while fulfilling the linear/aggregation relationships
linking the components (Girolimetto and Di Fonzo, 2024 <doi:10.48550/arXiv.2412.03429>).
'FoCo2' offers multi-task forecast combination and reconciliation
approaches leveraging input from multiple forecasting models or experts and ensuring
that the resulting forecasts satisfy specified linear constraints. In addition, linear
inequality constraints (e.g., non-negativity of the forecasts) can be imposed, if needed.
Author: Daniele Girolimetto [aut, cre] ,
Tommaso Di Fonzo [aut]
Maintainer: Daniele Girolimetto <daniele.girolimetto@unipd.it>
Diff between FoCo2 versions 0.1.2 dated 2025-06-14 and 0.1.3 dated 2026-03-13
DESCRIPTION | 23 - MD5 | 26 +- NEWS.md | 6 R/mtfc_fun.R | 296 +++++++++++++++--------- R/optimal.R | 207 ++++++++++------- R/resemble.R | 567 ++++++++++++++++++++++++++++++----------------- README.md | 10 build/partial.rdb |binary man/FoCo2-package.Rd | 10 man/csscr.Rd | 2 man/cssrc.Rd | 2 man/figures/foreco.svg | 455 ++++++++----------------------------- man/figures/logo.svg | 198 ++++++---------- tests/testthat/test-cs.R | 278 +++++++++++++++++------ 14 files changed, 1125 insertions(+), 955 deletions(-)
Title: Broken Stick Model for Irregular Longitudinal Data
Description: Data on multiple individuals through time are often sampled at
times that differ between persons. Irregular observation times can severely
complicate the statistical analysis of the data. The broken stick model
approximates each subject’s trajectory by one or more connected line segments.
The times at which segments connect (breakpoints) are identical for all
subjects and under control of the user. A well-fitting broken stick model
effectively transforms individual measurements made at irregular times into
regular trajectories with common observation times. Specification of the
model requires three variables: time, measurement and subject. The
model is a special case of the linear mixed model, with time as a linear
B-spline and subject as the grouping factor. The main assumptions are:
subjects are exchangeable, trajectories between consecutive breakpoints are
straight, random effects follow a multivariate normal distribution, and
unobserved data are missing at random. The package conta [...truncated...]
Author: Stef van Buuren [aut, cre]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
This is a re-admission after prior archival of version 2.6.0 dated 2025-03-31
Diff between brokenstick versions 2.6.0 dated 2025-03-31 and 2.7.0 dated 2026-03-13
DESCRIPTION | 8 - MD5 | 54 +++---- NAMESPACE | 1 NEWS.md | 9 + R/EB.R | 4 R/brokenstick-class.R | 44 +++-- R/brokenstick.R | 71 ++++++--- R/coef.R | 23 +-- R/get.R | 110 ++++++++------ R/import.R | 2 R/internals.R | 79 +++++++--- R/kr.R | 62 +++++--- R/model.frame.R | 4 R/plot.R | 229 ++++++++++++++++++------------ R/predict.R | 132 +++++++++++------ R/print.R | 99 ++++++++++-- R/set_control.R | 34 ++-- R/summary.R | 16 +- README.md | 7 build/vignette.rds |binary inst/doc/mainfunctions.Rmd | 2 inst/doc/mainfunctions.html | 7 inst/doc/oldfriends.html | 5 inst/doc/perfectmodel.html | 57 +++---- tests/testthat/test-brokenstick_edge.R | 110 +++++++++----- tests/testthat/test-predict.brokenstick.R | 41 ++++- tests/testthat/test-smooth_covariance.R | 39 +++-- vignettes/mainfunctions.Rmd | 2 28 files changed, 811 insertions(+), 440 deletions(-)
Title: Companion to Portfolio Construction and Risk Analysis
Description: A collection of functions and data sets that support teaching a quantitative finance MS level course on Portfolio Construction and Risk Analysis, and the writing of a textbook for such a course. The package provides several real-world data sets for problem assignments and student projects, including cross-sections of stock data from the Center for Research on Security Prices, LLC (CRSP), corresponding factor exposures from S&P Global, and several S&P 500 data sets.
Author: Doug Martin [cre, aut],
Alexios Galanos [ctb],
Kirk Li [aut, ctb],
Jon Spinney [ctb],
Thomas Philips [ctb]
Maintainer: Doug Martin <martinrd3d@gmail.com>
Diff between PCRA versions 1.2 dated 2023-08-30 and 1.2.1 dated 2026-03-13
DESCRIPTION | 43 +++++++++++++++---------------------------- MD5 | 16 ++++++++-------- R/PCRAData.R | 2 +- R/factorsSPGMI.R | 2 +- build/vignette.rds |binary inst/doc/PCRAVignette.pdf |binary man/PCRA-package.Rd | 2 +- man/factorsSPGMI.Rd | 2 +- man/getPCRAData.Rd | 2 +- 9 files changed, 28 insertions(+), 41 deletions(-)
Title: Multiblock Exploratory and Predictive Data Analysis
Description: Exploratory and predictive methods for the analysis of several blocks of variables measured on the same individuals.
Author: Benjamin Mahieu [aut, cre],
Essomanda Tchandao Mangamana [aut],
Evelyne Vigneau [aut],
Veronique Cariou [aut]
Maintainer: Benjamin Mahieu <benjamin.mahieu@oniris-nantes.fr>
Diff between MBAnalysis versions 2.1.1 dated 2025-10-08 and 2.2.0 dated 2026-03-13
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/MBplotBlocks.R | 10 +++++----- R/MBplotScores.R | 2 +- R/MBplotVars.R | 4 ++-- build/partial.rdb |binary 6 files changed, 18 insertions(+), 18 deletions(-)
Title: A Driver Discovery Tool for Cancer Whole Genomes
Description: A method for finding enrichments of somatic single nucleotide variants (SNVs) and small insertions-deletions (Indels) in functional elements in the human genome. 'ActiveDriverWGS' detects coding and noncoding cancer driver elements using whole genome sequencing data. The method is part of the publication H. Zhu et al. (2020) <doi:10.1016/j.molcel.2019.12.027> "Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks" in Molecular Cell.
Author: Juri Reimand [aut, cre],
Helen Zhu [ctb],
Kevin Cheng [ctb]
Maintainer: Juri Reimand <juri.reimand@utoronto.ca>
This is a re-admission after prior archival of version 1.2.0 dated 2022-09-03
Diff between ActiveDriverWGS versions 1.2.0 dated 2022-09-03 and 1.2.1 dated 2026-03-13
DESCRIPTION | 24 - MD5 | 32 - NEWS.md | 5 R/ADWGS_test.R | 29 - R/ActiveDriverWGS.R | 44 ++ R/format_muts.R | 13 R/prepare_elements.R | 18 - README.md | 4 build/vignette.rds |binary inst/doc/ActiveDriverWGSR.R | 13 inst/doc/ActiveDriverWGSR.Rmd | 13 inst/doc/ActiveDriverWGSR.html | 598 ++++++++++++++++++++++------------ tests/testthat/test_ADWGS_test.R | 1 tests/testthat/test_ActiveDriverWGS.R | 1 tests/testthat/test_format_muts.R | 11 tests/testthat/test_input_format.R | 33 + vignettes/ActiveDriverWGSR.Rmd | 13 17 files changed, 553 insertions(+), 299 deletions(-)
More information about ActiveDriverWGS at CRAN
Permanent link
Title: A Unified Tidy Interface to R's Machine Learning Ecosystem
Description: Provides a unified tidyverse-compatible interface to R's machine
learning packages. Wraps established implementations from 'glmnet',
'randomForest', 'xgboost', 'e1071', 'rpart', 'gbm', 'nnet', 'cluster',
'dbscan', and others - providing consistent function signatures, tidy tibble
output, and unified 'ggplot2'-based visualization. The underlying algorithms
are unchanged; 'tidylearn' simply makes them easier to use together. Access
raw model objects via the $fit slot for package-specific functionality.
Methods include random forests Breiman (2001) <doi:10.1023/A:1010933404324>,
LASSO regression Tibshirani (1996) <doi:10.1111/j.2517-6161.1996.tb02080.x>,
elastic net Zou and Hastie (2005) <doi:10.1111/j.1467-9868.2005.00503.x>,
support vector machines Cortes and Vapnik (1995) <doi:10.1007/BF00994018>,
and gradient boosting Friedman (2001) <doi:10.1214/aos/1013203451>.
Author: Cesaire Tobias [aut, cre]
Maintainer: Cesaire Tobias <cesaire@sheetsolved.com>
Diff between tidylearn versions 0.1.0 dated 2026-02-06 and 0.1.1 dated 2026-03-13
DESCRIPTION | 8 MD5 | 26 NEWS.md | 122 +- R/core.R | 867 ++++++++------- R/supervised-classification.R | 694 ++++++------ R/supervised-regression.R | 758 ++++++------- R/unsupervised-market-basket.R | 2 R/visualization.R | 2366 ++++++++++++++++++++--------------------- README.md | 2 build/vignette.rds |binary inst/doc/automl.html | 3 inst/doc/getting-started.html | 4 man/tidy_apriori.Rd | 104 - man/tl_plot_model.Rd |only man/tl_plot_unsupervised.Rd |only 15 files changed, 2527 insertions(+), 2429 deletions(-)
Title: Simulation of Bird Flight Range
Description: Functions for range estimation in birds based on Pennycuick (2008)
and Pennycuick (1975), 'Flight' program which compliments Pennycuick (2008)
requires manual entry of birds which can be tedious when there are hundreds
of birds to estimate. Implemented are two ODE methods discussed in Pennycuick (1975)
and time-marching computation methods as in Pennycuick (1998) and Pennycuick (2008).
See Pennycuick (1975, ISBN:978-0-12-249405-5), Pennycuick (1998) <doi:10.1006/jtbi.1997.0572>,
and Pennycuick (2008, ISBN:9780080557816).
Author: Brian Masinde [aut, cre],
Krzysztof Bartoszek [ctb, ths]
Maintainer: Brian Masinde <masindeb@live.com>
Diff between FlyingR versions 0.2.2 dated 2022-06-27 and 0.2.3 dated 2026-03-13
DESCRIPTION | 19 - MD5 | 35 ++- NEWS.md | 13 - R/curlew_sandpiper.R |only R/garden_wablers.R |only R/input_match.R | 10 R/lesser_whitethroats.R |only R/migrate.R | 106 +++++++-- README.md | 467 +++++++++++++++++++++++++++++++++++------- build/vignette.rds |binary data/curlew_sandpiper.rda |only data/garden_wablers.rda |only data/lesser_whitethroats.rda |only inst/doc/documentation.R | 170 +++++++++++++++ inst/doc/documentation.Rmd | 243 +++++++++++++++++++++ inst/doc/documentation.html | 362 +++++++++++++++++++++++++------- man/curlew_sandpiper.Rd |only man/figures |only man/garden_wablers.Rd |only man/lesser_whitethroats.Rd |only tests/testthat/test_migrate.R | 64 ++++- vignettes/documentation.Rmd | 243 +++++++++++++++++++++ vignettes/references.bib | 74 ++++++ 23 files changed, 1586 insertions(+), 220 deletions(-)
Title: Multiple Imputation with Denoising Autoencoders
Description: A tool for multiply imputing missing data using 'MIDAS', a deep learning method based on denoising autoencoder neural networks (see Lall and Robinson, 2022; <doi:10.1017/pan.2020.49>). This algorithm offers significant accuracy and efficiency advantages over other multiple imputation strategies, particularly when applied to large datasets with complex features. Alongside interfacing with 'Python' to run the core algorithm, this package contains functions for processing data before and after model training, running imputation model diagnostics, generating multiple completed datasets, and estimating regression models on these datasets. For more information see Lall and Robinson (2023) <doi:10.18637/jss.v107.i09>. This package is deprecated in favor of 'rMIDAS2'; it remains available for existing workflows but will receive only compatibility and documentation updates.
Author: Thomas Robinson [aut, cre, cph] ,
Ranjit Lall [aut, cph] ,
Alex Stenlake [ctb, cph],
Elviss Dvinskis [ctb]
Maintainer: Thomas Robinson <ts.robinson1994@gmail.com>
Diff between rMIDAS versions 1.0.0 dated 2023-10-11 and 1.0.1 dated 2026-03-13
rMIDAS-1.0.0/rMIDAS/inst/python/__pycache__ |only rMIDAS-1.0.1/rMIDAS/DESCRIPTION | 20 +- rMIDAS-1.0.1/rMIDAS/MD5 | 48 +++--- rMIDAS-1.0.1/rMIDAS/NEWS.md | 6 rMIDAS-1.0.1/rMIDAS/R/rMIDAS-package.R |only rMIDAS-1.0.1/rMIDAS/R/zzz.R | 33 ++++ rMIDAS-1.0.1/rMIDAS/README.md | 64 +++++--- rMIDAS-1.0.1/rMIDAS/build/partial.rdb |binary rMIDAS-1.0.1/rMIDAS/build/vignette.rds |binary rMIDAS-1.0.1/rMIDAS/inst/doc/custom_python_versions.R | 108 +++++++-------- rMIDAS-1.0.1/rMIDAS/inst/doc/custom_python_versions.Rmd | 10 + rMIDAS-1.0.1/rMIDAS/inst/doc/custom_python_versions.html | 14 + rMIDAS-1.0.1/rMIDAS/inst/doc/imputation_demo.R | 92 ++++++------ rMIDAS-1.0.1/rMIDAS/inst/doc/imputation_demo.Rmd | 8 + rMIDAS-1.0.1/rMIDAS/inst/doc/imputation_demo.html | 8 + rMIDAS-1.0.1/rMIDAS/inst/doc/migrating-to-rMIDAS2.R |only rMIDAS-1.0.1/rMIDAS/inst/doc/migrating-to-rMIDAS2.Rmd |only rMIDAS-1.0.1/rMIDAS/inst/doc/migrating-to-rMIDAS2.html |only rMIDAS-1.0.1/rMIDAS/inst/doc/use-server.R | 4 rMIDAS-1.0.1/rMIDAS/inst/doc/use-server.Rmd | 12 + rMIDAS-1.0.1/rMIDAS/inst/doc/use-server.html | 10 + rMIDAS-1.0.1/rMIDAS/man/rMIDAS-package.Rd |only rMIDAS-1.0.1/rMIDAS/tests/testthat.R | 16 ++ rMIDAS-1.0.1/rMIDAS/vignettes/custom_python_versions.Rmd | 10 + rMIDAS-1.0.1/rMIDAS/vignettes/imputation_demo.Rmd | 8 + rMIDAS-1.0.1/rMIDAS/vignettes/migrating-to-rMIDAS2.Rmd |only rMIDAS-1.0.1/rMIDAS/vignettes/use-server.Rmd | 12 + 27 files changed, 309 insertions(+), 174 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Weber et al. (2021) <doi:10.18637/jss.v100.i19>
for details on applying this package while Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> explain details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Lukas A. Widmer [ctb] ,
Daniel Sabanes Bove [ctb] ,
Trustees of Columbia Univers [...truncated...]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.8-2 dated 2025-04-25 and 1.9-0 dated 2026-03-13
RBesT-1.8-2/RBesT/R/deprecation_message.R |only RBesT-1.9-0/RBesT/DESCRIPTION | 21 RBesT-1.9-0/RBesT/MD5 | 179 +- RBesT-1.9-0/RBesT/NAMESPACE | 31 RBesT-1.9-0/RBesT/NEWS.md | 27 RBesT-1.9-0/RBesT/R/BinaryExactCI.R | 4 RBesT-1.9-0/RBesT/R/EM_bmm_ab.R | 12 RBesT-1.9-0/RBesT/R/EM_bmm_mun.R | 12 RBesT-1.9-0/RBesT/R/EM_gmm.R | 12 RBesT-1.9-0/RBesT/R/EM_mnmm.R | 27 RBesT-1.9-0/RBesT/R/EM_msmm.R | 4 RBesT-1.9-0/RBesT/R/EM_plot.R | 38 RBesT-1.9-0/RBesT/R/RBesT-package.R | 3 RBesT-1.9-0/RBesT/R/decision1S.R | 189 ++ RBesT-1.9-0/RBesT/R/decision1S_boundary.R | 197 ++ RBesT-1.9-0/RBesT/R/decision2S.R | 190 ++ RBesT-1.9-0/RBesT/R/decision2S_boundary.R | 327 ++++ RBesT-1.9-0/RBesT/R/forest_plot.R | 31 RBesT-1.9-0/RBesT/R/gMAP.R | 6 RBesT-1.9-0/RBesT/R/mix.R | 121 + RBesT-1.9-0/RBesT/R/mixbeta.R | 8 RBesT-1.9-0/RBesT/R/mixcombine.R | 8 RBesT-1.9-0/RBesT/R/mixess.R | 6 RBesT-1.9-0/RBesT/R/mixfit.R | 4 RBesT-1.9-0/RBesT/R/mixgamma.R | 8 RBesT-1.9-0/RBesT/R/mixmvnorm.R | 3 RBesT-1.9-0/RBesT/R/mixnorm.R | 4 RBesT-1.9-0/RBesT/R/mixplot.R | 28 RBesT-1.9-0/RBesT/R/mixstanvar.R | 3 RBesT-1.9-0/RBesT/R/nsamples.R |only RBesT-1.9-0/RBesT/R/oc1S.R | 130 + RBesT-1.9-0/RBesT/R/oc2S.R | 358 ++++- RBesT-1.9-0/RBesT/R/plot_gMAP.R | 15 RBesT-1.9-0/RBesT/R/pos1S.R | 112 + RBesT-1.9-0/RBesT/R/pos2S.R | 373 ++++- RBesT-1.9-0/RBesT/R/posterior.R |only RBesT-1.9-0/RBesT/R/preddist.R | 3 RBesT-1.9-0/RBesT/R/robustify.R | 3 RBesT-1.9-0/RBesT/R/support.R | 3 RBesT-1.9-0/RBesT/R/sysdata.rda |binary RBesT-1.9-0/RBesT/R/zzz.R | 8 RBesT-1.9-0/RBesT/build/vignette.rds |binary RBesT-1.9-0/RBesT/data/AS.rda |binary RBesT-1.9-0/RBesT/data/colitis.rda |binary RBesT-1.9-0/RBesT/data/crohn.rda |binary RBesT-1.9-0/RBesT/data/transplant.rda |binary RBesT-1.9-0/RBesT/demo/oc2S-tte.R | 71 - RBesT-1.9-0/RBesT/demo/robustMAP.R | 252 ++- RBesT-1.9-0/RBesT/inst/doc/RBesT.pdf |binary RBesT-1.9-0/RBesT/inst/doc/introduction.html | 129 - RBesT-1.9-0/RBesT/inst/examples/ess.R | 9 RBesT-1.9-0/RBesT/inst/examples/predict_gMAP.R | 11 RBesT-1.9-0/RBesT/inst/extra/run-oq.R | 14 RBesT-1.9-0/RBesT/inst/sbc/calibration.md5 | 6 RBesT-1.9-0/RBesT/inst/sbc/make_reference_rankhist.R | 76 - RBesT-1.9-0/RBesT/inst/sbc/sbc_report.R | 18 RBesT-1.9-0/RBesT/inst/sbc/sbc_report.html | 810 ++++++------ RBesT-1.9-0/RBesT/inst/sbc/sbc_tools.R | 96 + RBesT-1.9-0/RBesT/man/RBesT-package.Rd | 2 RBesT-1.9-0/RBesT/man/create_decision1S_1sided.Rd |only RBesT-1.9-0/RBesT/man/create_decision1S_2sided.Rd |only RBesT-1.9-0/RBesT/man/create_decision1S_atomic.Rd |only RBesT-1.9-0/RBesT/man/create_decision2S_1sided.Rd |only RBesT-1.9-0/RBesT/man/create_decision2S_2sided.Rd |only RBesT-1.9-0/RBesT/man/create_decision2S_atomic.Rd |only RBesT-1.9-0/RBesT/man/decision1S.Rd | 59 RBesT-1.9-0/RBesT/man/decision1S_boundary.Rd | 5 RBesT-1.9-0/RBesT/man/decision2S.Rd | 62 RBesT-1.9-0/RBesT/man/decision2S_boundary.Rd | 17 RBesT-1.9-0/RBesT/man/draws-RBesT.Rd |only RBesT-1.9-0/RBesT/man/ess.Rd | 9 RBesT-1.9-0/RBesT/man/forest_plot.Rd | 5 RBesT-1.9-0/RBesT/man/mixplot.Rd | 23 RBesT-1.9-0/RBesT/man/nsamples.gMAP.Rd |only RBesT-1.9-0/RBesT/man/oc1S.Rd | 20 RBesT-1.9-0/RBesT/man/oc2S.Rd | 3 RBesT-1.9-0/RBesT/man/plot.EM.Rd | 14 RBesT-1.9-0/RBesT/man/plot.gMAP.Rd | 6 RBesT-1.9-0/RBesT/man/pos1S.Rd | 2 RBesT-1.9-0/RBesT/man/pos2S.Rd | 3 RBesT-1.9-0/RBesT/man/predict.gMAP.Rd | 11 RBesT-1.9-0/RBesT/tests/testthat.R | 8 RBesT-1.9-0/RBesT/tests/testthat/_snaps |only RBesT-1.9-0/RBesT/tests/testthat/test-EM.R | 15 RBesT-1.9-0/RBesT/tests/testthat/test-decision1S.R |only RBesT-1.9-0/RBesT/tests/testthat/test-decision1S_boundary.R |only RBesT-1.9-0/RBesT/tests/testthat/test-decision2S.R |only RBesT-1.9-0/RBesT/tests/testthat/test-decision2S_boundary.R |only RBesT-1.9-0/RBesT/tests/testthat/test-gMAP.R | 28 RBesT-1.9-0/RBesT/tests/testthat/test-mixdist.R | 8 RBesT-1.9-0/RBesT/tests/testthat/test-mixjson.R | 4 RBesT-1.9-0/RBesT/tests/testthat/test-mixstanvar.R | 218 +-- RBesT-1.9-0/RBesT/tests/testthat/test-oc1S.R | 99 + RBesT-1.9-0/RBesT/tests/testthat/test-oc2S.R | 369 +++++ RBesT-1.9-0/RBesT/tests/testthat/test-pos1S.R | 100 + RBesT-1.9-0/RBesT/tests/testthat/test-pos2S.R | 114 + RBesT-1.9-0/RBesT/tests/testthat/test-posterior.R |only RBesT-1.9-0/RBesT/tests/testthat/test-preddist.R | 16 98 files changed, 3947 insertions(+), 1273 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description: Contains functions for multiple imputation which
complements existing functionality in R.
In particular, several imputation methods for the
mice package (van Buuren & Groothuis-Oudshoorn, 2011,
<doi:10.18637/jss.v045.i03>) are implemented.
Main features of the miceadds package include
plausible value imputation (Mislevy, 1991,
<doi:10.1007/BF02294457>), multilevel imputation for
variables at any level or with any number of hierarchical
and non-hierarchical levels (Grund, Luedtke & Robitzsch,
2018, <doi:10.1177/1094428117703686>; van Buuren, 2018,
Ch.7, <doi:10.1201/9780429492259>), imputation using
partial least squares (PLS) for high dimensional
predictors (Robitzsch, Pham & Yanagida, 2016),
nested multiple imputation (Rubin, 2003,
<doi:10.1111/1467-9574.00217>), substantive model
compatible imputation (Bartlett et al., 2015,
<doi:10.1177/0962280214521348>), and features
for the generation of synthetic datasets
(Reiter, 2005, <doi:10. [...truncated...]
Author: Alexander Robitzsch [aut, cre] ,
Simon Grund [aut] ,
Thorsten Henke [ctb]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 3.18-36 dated 2025-09-12 and 3.19-16 dated 2026-03-13
DESCRIPTION | 8 +-- MD5 | 52 +++++++++++------------ R/RcppExports.R | 2 R/mice.impute.pls.R | 5 -- R/mice.impute.rlm.R | 4 - R/mice.nmi.R | 4 - R/mice_imputation_prepare_2l_functions.R | 25 ++++++----- R/ml_mcmc_fit.R | 4 - R/syn.constant.R | 6 +- R/syn.formula.R | 10 ++-- R/syn.mice.R | 8 +-- R/syn_da.R | 8 +-- R/syn_da_compute_pls_factors.R | 8 +-- R/syn_da_create_formula.R | 6 +- R/syn_da_extend_list.R | 4 - R/syn_da_synthesize_lm.R | 12 ++--- R/syn_mice.R | 8 +-- R/syn_mice_catch_arguments.R | 4 - R/syn_mice_completed_datasets.R | 4 - R/syn_mice_create_design_matrix.R | 8 +-- R/systime.R | 16 +++---- build/partial.rdb |binary inst/NEWS | 11 ++++ man/write.pspp.Rd | 5 -- src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 70 +++++++++++++++---------------- 27 files changed, 154 insertions(+), 142 deletions(-)
Title: Data Sets and Code for "Meta-Analysis with R"
Description: Data sets and code supporting the second edition of "Meta-Analysis with R"; first edition: Schwarzer, Carpenter, and Rücker (2015) <DOI:10.1007/978-3-319-21416-0>.
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between metabook versions 0.1-0 dated 2026-03-04 and 0.2-0 dated 2026-03-13
metabook-0.1-0/metabook/data/Law1994.rda |only metabook-0.1-0/metabook/man/Law1994.Rd |only metabook-0.2-0/metabook/DESCRIPTION | 14 ++-- metabook-0.2-0/metabook/MD5 | 73 ++++++++++++++---------- metabook-0.2-0/metabook/NAMESPACE | 3 metabook-0.2-0/metabook/NEWS.md | 21 ++++++ metabook-0.2-0/metabook/R/metabook-package.R | 8 -- metabook-0.2-0/metabook/build |only metabook-0.2-0/metabook/data/Hamza2021.rda |only metabook-0.2-0/metabook/data/Hong2015.rda |only metabook-0.2-0/metabook/data/Jalota2011.rda |only metabook-0.2-0/metabook/data/Linde2015.rda |binary metabook-0.2-0/metabook/data/Senn2013.rda |only metabook-0.2-0/metabook/data/Senn2024.rda |only metabook-0.2-0/metabook/data/Su2018.rda |only metabook-0.2-0/metabook/data/Thompson1999.rda |only metabook-0.2-0/metabook/man/Baker2009.Rd | 49 +++++++++++----- metabook-0.2-0/metabook/man/Bassler2004.Rd | 46 ++++++++++----- metabook-0.2-0/metabook/man/Curtin2002.Rd | 47 ++++++++++----- metabook-0.2-0/metabook/man/Dogliotti2014.Rd | 42 +++++++++---- metabook-0.2-0/metabook/man/Dong2013.Rd | 15 ++-- metabook-0.2-0/metabook/man/Feng2019.Rd | 36 ++++++++--- metabook-0.2-0/metabook/man/Franchini2012.Rd | 59 +++++++++++++------ metabook-0.2-0/metabook/man/Furukawa2003.Rd | 49 +++++++++++----- metabook-0.2-0/metabook/man/Greb2008.Rd | 46 ++++++++++----- metabook-0.2-0/metabook/man/Greenland1992.Rd | 44 +++++++++----- metabook-0.2-0/metabook/man/Gurusamy2011.Rd | 66 +++++++++++++++------ metabook-0.2-0/metabook/man/Hamza2021.Rd |only metabook-0.2-0/metabook/man/Higgins2008.Rd | 56 +++++++++++------- metabook-0.2-0/metabook/man/Hong2015.Rd |only metabook-0.2-0/metabook/man/Jalota2011.Rd |only metabook-0.2-0/metabook/man/Linde2015.Rd | 17 ++--- metabook-0.2-0/metabook/man/Linde2016.Rd | 17 ++--- metabook-0.2-0/metabook/man/Lloyd2010.Rd | 13 ++-- metabook-0.2-0/metabook/man/Moore1998.Rd | 9 +- metabook-0.2-0/metabook/man/Poole2003.Rd | 13 ++-- metabook-0.2-0/metabook/man/Quan2000.Rd | 13 ++-- metabook-0.2-0/metabook/man/Senn2013.Rd |only metabook-0.2-0/metabook/man/Senn2024.Rd |only metabook-0.2-0/metabook/man/Spooner2002.Rd | 13 ++-- metabook-0.2-0/metabook/man/Steurer2006.Rd | 13 ++-- metabook-0.2-0/metabook/man/Stowe2010.Rd | 15 ++-- metabook-0.2-0/metabook/man/Su2018.Rd |only metabook-0.2-0/metabook/man/Thompson1999.Rd |only metabook-0.2-0/metabook/man/Woods2010.Rd | 38 ++++++++---- metabook-0.2-0/metabook/man/metabook-package.Rd | 2 46 files changed, 547 insertions(+), 290 deletions(-)
Title: Statistics for International Large-Scale Assessments (ILSA)
Description: Calculates point estimates and standard errors using replicate weights and plausible values for International Large-Scale Assessments (ILSA), including: means, proportions, quantiles, correlations, singlelevel regressions, and multilevel regressions.
Author: Andres Christiansen [aut, cre] ,
Andres Strello [ctb]
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>
Diff between ILSAstats versions 0.4.0 dated 2025-07-15 and 0.4.4 dated 2026-03-13
ILSAstats-0.4.0/ILSAstats/R/myfunc.R |only ILSAstats-0.4.0/ILSAstats/man/myfunc.Rd |only ILSAstats-0.4.4/ILSAstats/DESCRIPTION | 9 ILSAstats-0.4.4/ILSAstats/MD5 | 67 +- ILSAstats-0.4.4/ILSAstats/NAMESPACE | 9 ILSAstats-0.4.4/ILSAstats/NEWS.md | 19 ILSAstats-0.4.4/ILSAstats/R/argchecks.R | 103 +++ ILSAstats-0.4.4/ILSAstats/R/internal.R | 41 - ILSAstats-0.4.4/ILSAstats/R/leaguetable.R |only ILSAstats-0.4.4/ILSAstats/R/prepILSA.R |only ILSAstats-0.4.4/ILSAstats/R/proflevels.R |only ILSAstats-0.4.4/ILSAstats/R/proflevels.get.R |only ILSAstats-0.4.4/ILSAstats/R/repcreate.R | 231 ++++++-- ILSAstats-0.4.4/ILSAstats/R/replm.R | 123 +++- ILSAstats-0.4.4/ILSAstats/R/repmean.R | 161 ++++- ILSAstats-0.4.4/ILSAstats/R/repmeanCI.R |only ILSAstats-0.4.4/ILSAstats/R/repprop.R | 274 +++++++++- ILSAstats-0.4.4/ILSAstats/R/repprop.table.R |only ILSAstats-0.4.4/ILSAstats/R/repquant.R | 2 ILSAstats-0.4.4/ILSAstats/R/reprho.R | 58 +- ILSAstats-0.4.4/ILSAstats/R/repse.R | 16 ILSAstats-0.4.4/ILSAstats/R/repsetup.R | 5 ILSAstats-0.4.4/ILSAstats/R/timss99.R |only ILSAstats-0.4.4/ILSAstats/data/ILSAinfo.RData |binary ILSAstats-0.4.4/ILSAstats/data/repdata.RData |binary ILSAstats-0.4.4/ILSAstats/data/timss99.RData |only ILSAstats-0.4.4/ILSAstats/inst/examples/repmeanCI_example.R |only ILSAstats-0.4.4/ILSAstats/inst/examples/repprop.table_example.R |only ILSAstats-0.4.4/ILSAstats/man/leaguetable.Rd |only ILSAstats-0.4.4/ILSAstats/man/prepILSA.Rd |only ILSAstats-0.4.4/ILSAstats/man/proflevels.Rd |only ILSAstats-0.4.4/ILSAstats/man/proflevels.get.Rd |only ILSAstats-0.4.4/ILSAstats/man/repcreate.Rd | 6 ILSAstats-0.4.4/ILSAstats/man/repglm.Rd | 4 ILSAstats-0.4.4/ILSAstats/man/replm.Rd | 11 ILSAstats-0.4.4/ILSAstats/man/repmean.Rd | 4 ILSAstats-0.4.4/ILSAstats/man/repmeanCI.Rd |only ILSAstats-0.4.4/ILSAstats/man/repprop.Rd | 11 ILSAstats-0.4.4/ILSAstats/man/repprop.table.Rd |only ILSAstats-0.4.4/ILSAstats/man/repquant.Rd | 4 ILSAstats-0.4.4/ILSAstats/man/reprho.Rd | 4 ILSAstats-0.4.4/ILSAstats/man/repse.Rd | 4 ILSAstats-0.4.4/ILSAstats/man/repsetup.Rd | 4 ILSAstats-0.4.4/ILSAstats/man/timss99.Rd |only 44 files changed, 927 insertions(+), 243 deletions(-)
Title: Estimation of Spatial Weight Matrices
Description: Bayesian estimation of spatial weight matrices in spatial
econometric panel models. Allows for estimation of spatial
autoregressive (SAR), spatial error (SEM), spatial Durbin (SDM),
spatial error Durbin (SDEM) and spatially lagged explanatory variable
(SLX) type specifications featuring an unknown spatial weight matrix.
Methodological details are given in Krisztin and Piribauer (2022)
<doi:10.1080/17421772.2022.2095426>.
Author: Tamas Krisztin [aut, cre] ,
Philipp Piribauer [aut]
Maintainer: Tamas Krisztin <krisztin@iiasa.ac.at>
Diff between estimateW versions 0.1.0 dated 2025-05-13 and 0.2.0 dated 2026-03-13
DESCRIPTION | 7 MD5 | 42 - NAMESPACE | 2 NEWS.md | 9 R/R6_samplers.R | 12 R/data.R | 150 +++--- R/logdetPaceBarry.R | 46 ++ R/ngamma.R | 1158 ++++++++++++++++++++++++++++----------------------- R/output.R | 6 R/plotting.R | 6 R/priors.R | 5 R/sdmw.R | 4 R/semw.R | 486 ++++++++++----------- R/slxw.R | 3 data/nuts1growth.rda |binary man/logdetSpline.Rd |only man/nuts1growth.Rd | 21 man/rho_priors.Rd | 5 man/sdem.Rd | 9 man/sdemw.Rd | 9 man/sem.Rd | 11 man/semw.Rd | 9 man/slx.Rd |only 23 files changed, 1125 insertions(+), 875 deletions(-)
Title: Double Machine Learning for Static Panel Models with Fixed
Effects
Description: The 'xtdml' package implements partially linear panel regression (PLPR) models with high-dimensional confounding variables and an exogenous treatment variable within the double machine learning framework. The package is used to estimate the structural parameter (treatment effect) in static panel data models with fixed effects using the approaches established in Clarke and Polselli (2025) <doi:10.1093/ectj/utaf011>. 'xtdml' is built on the object-oriented package 'DoubleML' (Bach et al., 2024) <doi:10.18637/jss.v108.i03> using the 'mlr3' ecosystem.
Author: Annalivia Polselli [aut, cre]
Maintainer: Annalivia Polselli <apolselli.econ@gmail.com>
Diff between xtdml versions 0.1.11 dated 2025-12-11 and 0.1.12 dated 2026-03-13
DESCRIPTION | 12 MD5 | 28 NAMESPACE | 116 +-- R/dataset.R | 198 ++--- R/helper.R | 888 +++++++++++------------ R/xtdml_data.R | 1438 +++++++++++++++++++------------------- R/xtdml_main.R | 212 +++++ R/xtdml_plr.R | 1166 +++++++++++++++--------------- R/zzz.R | 40 - README.md | 138 +++ man/make_plpr_data.Rd | 122 +-- man/xtdml.Rd | 997 +++++++++++++------------- man/xtdml_data.Rd | 414 +++++----- man/xtdml_data_from_data_frame.Rd | 152 ++-- man/xtdml_plr.Rd | 655 ++++++++--------- 15 files changed, 3491 insertions(+), 3085 deletions(-)
Title: Adaptive Machine Learning-Powered, Context-Matching Tool for
Single-Cell and Spatial Transcriptomics Annotation
Description: Annotates single-cell and spatial-transcriptomic (ST) data using context-matching marker datasets. It creates a unified marker list (`Markers_list`) from multiple sources: built-in curated databases ('Cellmarker2', 'PanglaoDB', 'ScType', 'scIBD', 'TCellSI', 'PCTIT', 'PCTAM'), Seurat objects with cell labels, or user-provided Excel tables. SlimR first uses adaptive machine learning for parameter optimization, and then offers two automated annotation approaches: 'cluster-based' and 'per-cell'. Cluster-based annotation assigns one label per cluster, expression-based probability calculation, and AUC validation. Per-cell annotation assigns labels to individual cells using three scoring methods with adaptive thresholds and ratio-based confidence filtering, plus optional UMAP spatial smoothing, making it ideal for heterogeneous clusters and rare cell types. The package also supports semi-automated workflows with heatmaps, feature plots, and combined visualizations for manual annotation. For m [...truncated...]
Author: Zhaoqing Wang [aut, cre]
Maintainer: Zhaoqing Wang <zhaoqingwang@mail.sdu.edu.cn>
Diff between SlimR versions 1.1.1 dated 2026-02-05 and 1.1.2 dated 2026-03-13
DESCRIPTION | 10 MD5 | 53 +- NAMESPACE | 1 NEWS.md | 7 R/Celltype_Annotation_PerCell.R | 35 + R/Database_ScType.R |only R/Markers_filter_ScType.R |only R/onattach.R | 19 - README.md | 609 +++++++++------------------------ data/ScType.rda |only data/ScType_raw.rda |only data/ScType_table.rda |only man/Cellmarker2.Rd | 5 man/Cellmarker2_raw.Rd | 5 man/Cellmarker2_table.Rd | 5 man/Markers_filter_Cellmarker2.Rd | 1 man/Markers_filter_PanglaoDB.Rd | 1 man/Markers_filter_ScType.Rd |only man/Markers_list_PCTAM.Rd | 5 man/Markers_list_PCTIT.Rd | 5 man/Markers_list_TCellSI.Rd | 5 man/Markers_list_scIBD.Rd | 5 man/PanglaoDB.Rd | 5 man/PanglaoDB_raw.Rd | 5 man/PanglaoDB_table.Rd | 5 man/Read_excel_markers.Rd | 1 man/Read_seurat_markers.Rd | 1 man/ScType.Rd |only man/ScType_raw.Rd |only man/ScType_table.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test-marker-functions.R | 47 ++ 32 files changed, 339 insertions(+), 496 deletions(-)
Title: Conduct Response Item Network (ResIN) Analysis with Social
Response Data
Description: Contains various tools to estimate, analyze, and visualize Response Item Networks. 'ResIN' dummy-codes ordered and qualitative response choices from (survey) data, calculates pairwise associations and maps the location of each item response as a node in a force-directed network. Please refer to <https://www.resinmethod.net/> for more details.
Author: Philip Warncke [cre, aut],
Dino Carpentras [aut],
Adrian Lueders [aut]
Maintainer: Philip Warncke <philip.warncke@ul.ie>
Diff between ResIN versions 2.3.0 dated 2026-03-02 and 2.3.1 dated 2026-03-13
DESCRIPTION | 10 MD5 | 38 - NAMESPACE | 11 NEWS.md | 26 + R/BrJSocPsychol_2024.R | 1 R/ResIN.R | 866 ++++++++++++++++++++++++++++++++---------- R/ResIN_boots_execute.R | 246 ++++++++--- R/ResIN_boots_extract.R | 5 R/ResIN_boots_prepare.R | 7 R/methods-ResIN.R | 16 data/BrJSocPsychol_2024.RData |binary inst/doc/ResIN-VIGNETTE.R | 38 - inst/doc/ResIN-VIGNETTE.Rmd | 77 +-- inst/doc/ResIN-VIGNETTE.html | 132 ++---- man/ResIN.Rd | 254 ++++++------ man/ResIN_boots_execute.Rd | 20 man/ResIN_boots_extract.Rd | 5 man/ResIN_boots_prepare.Rd | 7 man/plot.ResIN.Rd | 4 vignettes/ResIN-VIGNETTE.Rmd | 77 +-- 20 files changed, 1175 insertions(+), 665 deletions(-)
Title: Sparse Additive Modelling
Description: Computationally efficient tools for high dimensional predictive
modeling (regression and classification). SAM is short for sparse
additive modeling, and adopts the computationally efficient basis
spline technique. We solve the optimization problems by various
computational algorithms including the block coordinate descent
algorithm, fast iterative soft-thresholding algorithm, and newton method.
The computation is further accelerated by warm-start and active-set tricks.
Author: Haoming Jiang [aut],
Yukun Ma [aut],
Han Liu [aut],
Kathryn Roeder [aut],
Xingguo Li [aut],
Tuo Zhao [aut, cre]
Maintainer: Tuo Zhao <tourzhao@gatech.edu>
Diff between SAM versions 1.2 dated 2026-02-19 and 1.3 dated 2026-03-13
DESCRIPTION | 6 +- MD5 | 62 ++++++++++++--------- NAMESPACE | 5 + NEWS.md |only R/aaa_sam_utils.R | 51 +++++++++++++++++ R/sam.R |only R/samEL.R | 33 ++++++++--- R/samHL.R | 21 ++++--- R/samLL.R | 32 ++++++++--- R/samQL.R | 50 ++++++++++++++--- README.md |only man/sam.Rd |only man/samEL.Rd | 22 +++++++ man/samHL.Rd | 10 +++ man/samLL.Rd | 22 +++++++ man/samQL.Rd | 37 ++++++++++++ src/amalgamation.cpp | 2 src/c_api.cpp | 16 ++--- src/c_api/c_api_utils.h |only src/c_api/grpLR.cpp | 41 +++++--------- src/c_api/grpPR.cpp | 40 +++++--------- src/c_api/grpSVM.cpp | 76 ++++++++++++++++++-------- src/c_api/grplasso.cpp | 100 ++++++++++++++++++++--------------- src/objective/GLMObjective.cpp | 64 ++++++++++++++-------- src/objective/GLMObjective.h | 7 ++ src/objective/LinearCovObjective.cpp |only src/objective/LinearCovObjective.h |only src/objective/LinearObjective.cpp | 9 +-- src/objective/objective.h | 10 +++ src/solver/actgd.cpp |only src/solver/actgd.h | 20 ++----- src/solver/actnewton.cpp | 66 ++++++++++++++++++++++- src/solver/solver_params.cpp | 5 + src/solver/solver_params.h | 19 +++++- src/utils.h | 10 +++ tests/test_poisson.R |only tests/test_svm.R |only 37 files changed, 604 insertions(+), 232 deletions(-)
Title: Generate Citation File Format ('cff') Metadata for R Packages
Description: The Citation File Format version 1.2.0
<doi:10.5281/zenodo.5171937> is a human and machine readable file
format which provides citation metadata for software. This package
provides core utilities to generate and validate this metadata.
Author: Diego Hernangomez [aut, cre, cph] ,
Joao Martins [rev] ,
Scott Chamberlain [rev]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between cffr versions 1.2.1 dated 2026-01-12 and 1.3.0 dated 2026-03-13
cffr-1.2.1/cffr/inst/doc/bibtex-cff.Rmd |only cffr-1.2.1/cffr/inst/doc/cffr.Rmd |only cffr-1.2.1/cffr/inst/doc/joss-paper.Rmd |only cffr-1.2.1/cffr/inst/doc/r-cff.Rmd |only cffr-1.2.1/cffr/vignettes/bibtex-cff.Rmd |only cffr-1.2.1/cffr/vignettes/cffr.Rmd |only cffr-1.2.1/cffr/vignettes/joss-paper.Rmd |only cffr-1.2.1/cffr/vignettes/r-cff.Rmd |only cffr-1.3.0/cffr/DESCRIPTION | 16 cffr-1.3.0/cffr/MD5 | 196 cffr-1.3.0/cffr/NEWS.md | 31 cffr-1.3.0/cffr/R/as_bibentry.R | 851 +- cffr-1.3.0/cffr/R/as_cff.R | 15 cffr-1.3.0/cffr/R/as_cff_person.R | 37 cffr-1.3.0/cffr/R/as_cff_reference.R | 2 cffr-1.3.0/cffr/R/assertions.R | 28 cffr-1.3.0/cffr/R/cff.R | 11 cffr-1.3.0/cffr/R/cff_create.R | 31 cffr-1.3.0/cffr/R/cff_gha_update.R | 154 cffr-1.3.0/cffr/R/cff_git_hook.R | 40 cffr-1.3.0/cffr/R/cff_modify.R | 16 cffr-1.3.0/cffr/R/cff_read.R | 584 - cffr-1.3.0/cffr/R/cff_read_bib_text.R | 19 cffr-1.3.0/cffr/R/cff_validate.R | 265 cffr-1.3.0/cffr/R/cff_write.R | 371 cffr-1.3.0/cffr/R/cff_write_misc.R | 290 cffr-1.3.0/cffr/R/deprecated.R | 16 cffr-1.3.0/cffr/R/encoded_utf_to_latex.R | 6 cffr-1.3.0/cffr/R/methods.R | 7 cffr-1.3.0/cffr/R/utils-alerts.R | 178 cffr-1.3.0/cffr/R/utils-bib.R | 1 cffr-1.3.0/cffr/R/utils-cff_read.R | 10 cffr-1.3.0/cffr/R/utils-cff_ref.R | 1 cffr-1.3.0/cffr/R/utils-create.R | 451 - cffr-1.3.0/cffr/R/utils-persons.R | 29 cffr-1.3.0/cffr/R/utils-schema.R | 4 cffr-1.3.0/cffr/R/utils.R | 27 cffr-1.3.0/cffr/README.md | 800 +- cffr-1.3.0/cffr/build/partial.rdb |binary cffr-1.3.0/cffr/build/vignette.rds |binary cffr-1.3.0/cffr/data/cran_to_spdx.rda |binary cffr-1.3.0/cffr/inst/REFERENCES.bib | 95 cffr-1.3.0/cffr/inst/WORDLIST | 1 cffr-1.3.0/cffr/inst/doc/bibtex-cff.R | 371 cffr-1.3.0/cffr/inst/doc/bibtex-cff.html | 4178 +++++------ cffr-1.3.0/cffr/inst/doc/bibtex-cff.qmd |only cffr-1.3.0/cffr/inst/doc/cffr.R | 63 cffr-1.3.0/cffr/inst/doc/cffr.html | 1119 +- cffr-1.3.0/cffr/inst/doc/cffr.qmd |only cffr-1.3.0/cffr/inst/doc/joss-paper.html | 377 cffr-1.3.0/cffr/inst/doc/joss-paper.qmd |only cffr-1.3.0/cffr/inst/doc/r-cff.R | 172 cffr-1.3.0/cffr/inst/doc/r-cff.html | 2964 +++---- cffr-1.3.0/cffr/inst/doc/r-cff.qmd |only cffr-1.3.0/cffr/inst/examples/CITATION_basic.cff | 2 cffr-1.3.0/cffr/inst/examples/CITATION_rmarkdown | 4 cffr-1.3.0/cffr/inst/schemaorg.json | 4 cffr-1.3.0/cffr/inst/yaml/update-citation-cff.yaml | 76 cffr-1.3.0/cffr/man/as_bibentry.Rd | 21 cffr-1.3.0/cffr/man/as_cff.Rd | 14 cffr-1.3.0/cffr/man/as_cff_person.Rd | 27 cffr-1.3.0/cffr/man/cff.Rd | 8 cffr-1.3.0/cffr/man/cff_class.Rd | 36 cffr-1.3.0/cffr/man/cff_create.Rd | 23 cffr-1.3.0/cffr/man/cff_gha_update.Rd | 12 cffr-1.3.0/cffr/man/cff_git_hook.Rd | 38 cffr-1.3.0/cffr/man/cff_modify.Rd | 13 cffr-1.3.0/cffr/man/cff_read.Rd | 18 cffr-1.3.0/cffr/man/cff_read_bib_text.Rd | 15 cffr-1.3.0/cffr/man/cff_schema.Rd | 2 cffr-1.3.0/cffr/man/cff_validate.Rd | 6 cffr-1.3.0/cffr/man/cff_write.Rd | 22 cffr-1.3.0/cffr/man/cff_write_misc.Rd | 24 cffr-1.3.0/cffr/man/chunks/cffclass.Rmd | 31 cffr-1.3.0/cffr/man/chunks/person.Rmd | 6 cffr-1.3.0/cffr/man/deprecated_cff_bibentry.Rd | 3 cffr-1.3.0/cffr/man/deprecated_cff_from_bib.Rd | 8 cffr-1.3.0/cffr/man/deprecated_cff_to_bib.Rd | 14 cffr-1.3.0/cffr/man/deprecated_write.Rd | 10 cffr-1.3.0/cffr/man/encoded_utf_to_latex.Rd | 6 cffr-1.3.0/cffr/tests/testthat/_snaps/as_cff_reference.md | 2 cffr-1.3.0/cffr/tests/testthat/_snaps/cff_gha_update.md | 46 cffr-1.3.0/cffr/tests/testthat/_snaps/utils-create.md | 2387 +++--- cffr-1.3.0/cffr/tests/testthat/test-as_bibentry.R | 1 cffr-1.3.0/cffr/tests/testthat/test-as_cff.R | 1 cffr-1.3.0/cffr/tests/testthat/test-as_cff_person.R | 1 cffr-1.3.0/cffr/tests/testthat/test-as_cff_reference.R | 1521 +--- cffr-1.3.0/cffr/tests/testthat/test-assertions.R | 1 cffr-1.3.0/cffr/tests/testthat/test-cff.R | 1 cffr-1.3.0/cffr/tests/testthat/test-cff_create.R | 1131 +- cffr-1.3.0/cffr/tests/testthat/test-cff_read.R | 505 - cffr-1.3.0/cffr/tests/testthat/test-cff_validate.R | 1 cffr-1.3.0/cffr/tests/testthat/test-cff_write.R | 401 - cffr-1.3.0/cffr/tests/testthat/test-cff_write_misc.R | 273 cffr-1.3.0/cffr/tests/testthat/test-deprecated.R | 1 cffr-1.3.0/cffr/tests/testthat/test-methods.R | 1 cffr-1.3.0/cffr/tests/testthat/test-mock-package.R | 266 cffr-1.3.0/cffr/tests/testthat/test-utils-cff_create.R | 44 cffr-1.3.0/cffr/tests/testthat/test-utils-create.R | 74 cffr-1.3.0/cffr/tests/testthat/test-utils-persons.R | 3 cffr-1.3.0/cffr/tests/testthat/test-utils.R | 84 cffr-1.3.0/cffr/tests/testthat/test-xtra-check-bibtex-ruby.R | 1 cffr-1.3.0/cffr/vignettes/REFERENCES.bib | 104 cffr-1.3.0/cffr/vignettes/bibtex-cff.qmd |only cffr-1.3.0/cffr/vignettes/cffr.qmd |only cffr-1.3.0/cffr/vignettes/joss-paper.qmd |only cffr-1.3.0/cffr/vignettes/r-cff.qmd |only 107 files changed, 10214 insertions(+), 10906 deletions(-)
Title: Calculate High Resolution Water Balance of Starch Potatoes
Description: Calculates the water balance of starch potatoes from Normalized Distance Vegetation Index (NDVI) images, German Weather Service (DWD) reference evapotranspiration, German Weather Service RADOLAN precipitation data and irrigation information. For more details see Piernicke et al. (2025) <doi:10.3390/rs17183227>.
Author: Thomas Piernicke [aut, cre]
Maintainer: Thomas Piernicke <thomasp@gfz.de>
Diff between WaterBalanceR versions 0.1.20 dated 2026-03-11 and 0.1.21 dated 2026-03-13
DESCRIPTION | 6 MD5 | 12 NEWS.md | 424 ++++++++++++++++---------------- R/DownloadSentinel2.R | 2 inst/doc/WaterBalanceR_DataSources.html | 4 inst/doc/WaterBalanceR_Workflow.html | 6 man/DownloadSentinel2.Rd | 2 7 files changed, 232 insertions(+), 224 deletions(-)
Title: Spatial Absorbing Markov Chains
Description: Implements functions for working with absorbing Markov chains. The
implementation is based on the framework described in "Toward a unified
framework for connectivity that disentangles movement and mortality in space
and time" by Fletcher et al. (2019) <doi:10.1111/ele.13333>, which applies
them to spatial ecology. This framework incorporates both resistance and
absorption with spatial absorbing Markov chains (SAMC) to provide several
short-term and long-term predictions for metrics related to connectivity in
landscapes. Despite the ecological context of the framework, this package
can be used in any application of absorbing Markov chains.
Author: Andrew Marx [aut, cre, cph] ,
Robert Fletcher [ctb] ,
Miguel Acevedo [ctb] ,
Jorge Sefair [ctb] ,
Chao Wang [ctb] ,
Hughes Josie [ctb] ,
Barrett Griffin [ctb]
Maintainer: Andrew Marx <ajm.rpackages@gmail.com>
Diff between samc versions 4.1.0 dated 2026-02-05 and 4.2.1 dated 2026-03-13
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 7 +++++++ R/internal-functions.R | 40 +++++++++++++++++++++++++++++++--------- R/internal-validation.R | 31 +++++++++++++++++++++++-------- R/pairwise.R | 36 ++++++++++++++++++++++++++---------- R/samc.R | 11 +++++++---- inst/CITATION | 2 +- inst/doc/overview.html | 4 ++-- 9 files changed, 109 insertions(+), 46 deletions(-)
Title: Import Various Northern and Southern Hemisphere Climate Indices
Description: Downloads Southern Oscillation Index, Oceanic Nino
Index, North Pacific Gyre Oscillation data, North Atlantic Oscillation
and Arctic Oscillation. Data sources are described in the help files for each function.
Author: Sam Albers [aut, cre],
Elio Campitelli [ctb]
Maintainer: Sam Albers <sam.albers@gmail.com>
Diff between rsoi versions 0.5.7 dated 2026-03-06 and 0.5.8 dated 2026-03-13
DESCRIPTION | 6 +- MD5 | 7 +-- NEWS.md | 3 + R/download-roni.R | 75 ++++++++++-------------------------- tests/testthat/test-download-roni.R |only 5 files changed, 32 insertions(+), 59 deletions(-)
Title: Polytomous Variable Latent Class Analysis Parallel
Description: A 'C++' reimplementation of 'poLCA' - latent class analysis and
latent class regression models for polytomous outcome variables, also known
as latent structure analysis. It attempts to reproduce results and be as
similar as possible to the original code, while running faster, especially
with multiple repetitions, by utilising multiple threads. Further reading is
available on the Queen Mary, University of London, IT Services Research blog
<https://blog.hpc.qmul.ac.uk/speeding_up_r_packages/>.
Author: Sherman Lo [aut, cre],
Drew Linzer [aut],
Jeffrey Lewis. [aut]
Maintainer: Sherman Lo <s.lo@qmul.ac.uk>
This is a re-admission after prior archival of version 1.2.6 dated 2026-02-19
Diff between poLCAParallel versions 1.2.6 dated 2026-02-19 and 1.2.7 dated 2026-03-13
DESCRIPTION | 9 +++--- MD5 | 28 ++++++++++---------- src/blrt.cc | 10 +++++-- src/blrt_rcpp.cc | 9 +++++- src/em_algorithm_array.cc | 10 +++++-- src/em_algorithm_rcpp.cc | 16 +++++++---- src/em_algorithm_regress.cc | 61 ++++++++++++++++++-------------------------- src/em_algorithm_regress.h | 40 +++++++++++++++++++++++----- src/goodness_fit_rcpp.cc | 7 +++-- src/polca_rcpp.cc | 14 +++++----- src/regularised_error.cc | 6 ++-- src/standard_error_rcpp.cc | 14 ++++++---- src/util.cc | 7 +++++ src/util.h | 5 +++ src/util_rcpp.cc |only src/util_rcpp.h |only 16 files changed, 146 insertions(+), 90 deletions(-)
Title: Generalized Network-Based Dimensionality Reduction and Analysis
Description: Non-parametric dimensionality reduction function. Reduction with and without feature selection. Plot functions. Automated feature selections. Kosztyan et. al. (2024) <doi:10.1016/j.eswa.2023.121779>.
Author: Zsolt T. Kosztyan [aut, cre],
Marcell T. Kurbucz [aut],
Attila I. Katona [aut],
Zahid Khan [aut]
Maintainer: Zsolt T. Kosztyan <kosztyan.zsolt@gtk.uni-pannon.hu>
Diff between nda versions 0.2.4 dated 2025-02-16 and 0.2.5 dated 2026-03-13
DESCRIPTION | 6 MD5 | 8 R/ndrlm.R | 1224 +++++++++++++++++++++++++++++------------------------------ inst/NEWS | 222 +++++----- man/ndrlm.Rd | 354 ++++++++--------- 5 files changed, 911 insertions(+), 903 deletions(-)
Title: Missing Morphometric Data Simulation and Estimation
Description: Functions for simulating missing morphometric
data randomly, with taxonomic bias and with anatomical bias. LOST also
includes functions for estimating linear and geometric morphometric data.
Author: J. Arbour [aut, cre],
C. Brown [aut]
Maintainer: J. Arbour <jessica.arbour@mtsu.edu>
Diff between LOST versions 2.1.2 dated 2025-01-27 and 2.1.3 dated 2026-03-13
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/align.missing.R | 6 +++++- 3 files changed, 11 insertions(+), 7 deletions(-)
Title: An R Interface for Downloading, Reading, and Handling IPUMS Data
Description: An easy way to work with census, survey, and geographic data
provided by IPUMS in R. Generate and download data through the IPUMS
API and load IPUMS files into R with their associated metadata to
make analysis easier. IPUMS data describing 1.4 billion individuals
drawn from over 750 censuses and surveys is available free of charge
from the IPUMS website <https://www.ipums.org>.
Author: Greg Freedman Ellis [aut],
Derek Burk [aut, cre],
Finn Roberts [aut],
Joe Grover [ctb],
Dan Ehrlich [ctb],
Renae Rodgers [ctb],
Institute for Social Research and Data Innovation [cph]
Maintainer: Derek Burk <ipums+cran@umn.edu>
Diff between ipumsr versions 0.9.0 dated 2025-06-04 and 0.10.0 dated 2026-03-13
DESCRIPTION | 10 MD5 | 100 NEWS.md | 22 R/api_define_extract.R | 6993 +++++++++++++++----------------- R/api_helpers.R | 15 R/api_metadata.R | 4 R/ddi_read.R | 2363 +++++----- R/micro_read.R | 738 +-- R/micro_read_chunked.R | 734 +-- R/micro_read_yield.R | 668 +-- R/proj_config.R | 1 README.md | 896 ++-- build/vignette.rds |binary inst/doc/ipums-api-agg.R | 438 +- inst/doc/ipums-api-agg.html | 1639 +++---- inst/doc/ipums-api-micro.R | 440 +- inst/doc/ipums-api-micro.Rmd | 2 inst/doc/ipums-api-micro.html | 1807 ++++---- inst/doc/ipums-api.R | 548 +- inst/doc/ipums-api.Rmd | 1 inst/doc/ipums-api.html | 1686 +++---- inst/doc/ipums-bigdata.R | 558 +- inst/doc/ipums-bigdata.Rmd | 1331 +++--- inst/doc/ipums-bigdata.html | 2123 ++++----- inst/doc/ipums-read.R | 274 - inst/doc/ipums-read.html | 1823 ++++---- inst/doc/ipums.R | 172 inst/doc/ipums.Rmd | 1 inst/doc/ipums.html | 1350 +++--- inst/doc/value-labels.R | 348 - inst/doc/value-labels.html | 1891 ++++---- man/define_extract_micro.Rd | 1 man/get_sample_info.Rd | 1 man/ipums_data_collections.Rd | 1 man/ipums_ddi-class.Rd | 2 man/ipums_shape_join.Rd | 2 man/read_ipums_ddi.Rd | 3 man/read_ipums_micro.Rd | 2 man/read_ipums_micro_chunked.Rd | 2 man/read_ipums_micro_yield.Rd | 2 man/read_ipums_sf.Rd | 2 man/set_ipums_api_key.Rd | 15 tests/fixtures/cps_00111.xml |only tests/fixtures/ipumsi_00987.xml |only tests/testthat/helper_api.R | 13 tests/testthat/test_api_helpers.R | 2 tests/testthat/test_read_ddi.R | 25 vignettes/fixtures/wait-for-extract.yml | 166 vignettes/ipums-api-micro.Rmd | 2 vignettes/ipums-api.Rmd | 1 vignettes/ipums-bigdata.Rmd | 1331 +++--- vignettes/ipums.Rmd | 1 52 files changed, 15398 insertions(+), 15152 deletions(-)
Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Description: Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.
Author: Schaid Daniel [aut],
Jason P. Sinnwell [aut, cre]
Maintainer: Jason P. Sinnwell <sinnwell.jason@mayo.edu>
Diff between haplo.stats versions 1.9.8.2 dated 2026-02-13 and 1.9.8.3 dated 2026-03-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/haplostats.R | 4 ++++ inst/doc/haplostats.Rmd | 4 ++++ vignettes/haplostats.Rmd | 4 ++++ 5 files changed, 20 insertions(+), 8 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown" or "free") objects in R expressions
by code inspection using various strategies (ordered, liberal,
conservative, or deep-first search). The objective of this package is to
make it as simple as possible to identify global objects for the purpose
of exporting them in parallel, distributed compute environments.
Author: Henrik Bengtsson [aut, cre, cph],
Davis Vaughan [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.19.0 dated 2026-02-02 and 0.19.1 dated 2026-03-13
DESCRIPTION | 6 MD5 | 34 ++-- NEWS.md | 11 + R/Globals-class.R | 9 + R/call_find_globals_with_dotdotdot.R | 2 R/findGlobalsDFS.R | 3 R/find_globals_ordered.R | 59 ------- R/globalsByName.R | 2 R/utils-debug.R | 2 R/where.R | 2 inst/testme/test-Globals.R | 73 ++++++++- inst/testme/test-cleanup.R | 63 +++++++ inst/testme/test-dotdotdot.R | 18 ++ inst/testme/test-findGlobals,dfs.R | 52 ++++++ inst/testme/test-findGlobals.R | 126 +++++++++++++++ inst/testme/test-globalsByName.R | 19 ++ inst/testme/test-globalsOf.R | 102 ++++++++++++ inst/testme/test-utils.R | 281 +++++++++++++++++++++++++++++++++++ 18 files changed, 776 insertions(+), 88 deletions(-)
Title: Faster Generation of Quantile Quantile Plots with Large Samples
Description: New and faster implementations for quantile quantile plots.
The package also includes a function to prune data for quantile quantile
plots. This can drastically reduce the running time for large samples,
for 100 million samples, you can expect a factor 80X speedup.
Author: Gudmundur Einarsson [aut, cre],
Hafsteinn Einarsson [aut]
Maintainer: Gudmundur Einarsson <gudmundur.einarsson.phd@gmail.com>
Diff between fastqq versions 0.1.3 dated 2022-10-25 and 0.1.4 dated 2026-03-13
DESCRIPTION | 10 +- MD5 | 37 +++++--- NAMESPACE | 2 NEWS.md | 12 ++ R/RcppExports.R | 10 ++ R/qq.R | 129 ++++++++++++++++++++++++++++- README.md | 132 +++++++++++++++++++++++------- man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-ggplot-1.png |binary man/figures/README-qqchisq1_ex-1.png |only man/figures/README-qqchisq1_extreme-1.png |only man/figures/README-qqlog_ex-1.png |only man/figures/README-qqnorm_ex-1.png |binary man/figures/README-qqplot_ex-1.png |binary man/figures/README-zero_action_ex-1.png |only man/qq.Rd | 12 ++ man/qqchisq1.Rd |only man/qqlog.Rd |only src/RcppExports.cpp | 26 +++++ src/code.cpp | 115 ++++++++++++++++++++++++++ tests |only 22 files changed, 434 insertions(+), 51 deletions(-)
Title: Tools for Choice Model Estimation and Application
Description: Choice models are a widely used technique across numerous scientific disciplines. The Apollo package is a very flexible tool for the estimation and application
of choice models in R. Users are able to write their own
model functions or use a mix of already available ones. Random heterogeneity,
both continuous and discrete and at the level of individuals and
choices, can be incorporated for all models. There is support for both standalone
models and hybrid model structures. Both classical
and Bayesian estimation is available, and multiple discrete
continuous models are covered in addition to discrete choice.
Multi-threading processing is supported for estimation and a large
number of pre and post-estimation routines, including for computing posterior
(individual-level) distributions are available.
For examples, a manual, and a support forum, visit
<https://www.ApolloChoiceModelling.com>. For more information on choice
models see Train, K. (2009) <isbn:978-0-521-74738-7> and [...truncated...]
Author: Stephane Hess [aut, cre],
David Palma [aut],
Thomas Hancock [ctb]
Maintainer: Stephane Hess <S.Hess@leeds.ac.uk>
Diff between apollo versions 0.3.6 dated 2025-09-19 and 0.3.7 dated 2026-03-13
DESCRIPTION | 8 MD5 | 72 ++-- NAMESPACE | 3 R/apollo_classAlloc.R | 3 R/apollo_cnl.R | 3 R/apollo_cnl2.R | 3 R/apollo_deltaMethod.R | 4 R/apollo_el.R | 3 R/apollo_estimate.R | 31 +- R/apollo_estimateHB.R | 62 ++-- R/apollo_firstRow.R | 10 R/apollo_fmnl.R | 3 R/apollo_fnl.R | 3 R/apollo_initialise.R | 2 R/apollo_lcEM.R | 1 R/apollo_lcEM_new.R | 21 - R/apollo_makeCluster.R | 2 R/apollo_mnl.R | 8 R/apollo_modelOutput.R | 31 +- R/apollo_modifyUserDefFunc.R | 19 + R/apollo_nl.R | 3 R/apollo_prediction.R | 4 R/apollo_rrm.R | 1 R/apollo_saveOutput.R | 16 - R/apollo_searchStart.R | 6 R/apollo_speedTest.R | 15 - R/apollo_validateControl.R | 11 R/apollo_validateInputs.R | 4 R/onAttach.R | 5 inst/doc/apollofirstexample.html | 565 +++++++++++++++++++-------------------- man/apollo_estimate.Rd | 2 man/apollo_modelOutput.Rd | 1 man/apollo_prediction.Rd | 1 man/apollo_rrm.Rd | 1 man/apollo_saveOutput.Rd | 2 man/apollo_speedTest.Rd | 2 man/apollo_validateInputs.Rd | 4 37 files changed, 523 insertions(+), 412 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-03-06 1.0.4
2024-02-26 1.0.2
2024-02-26 1.0.3
2022-01-18 1.0.1
2021-11-19 1.0.0
2020-12-14 0.1.1
2020-09-29 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-03-08 1.0.14
2025-08-18 1.0.13
2024-02-26 1.0.12
2023-08-08 1.0.11
2022-04-19 1.0.10
2022-03-02 1.0.9
2021-12-12 1.0.8
2021-11-15 1.0.7
2021-10-06 1.0.6
2021-08-11 1.0.5
2021-06-29 1.0.4
2021-05-03 1.0.3
2021-03-04 1.0.2
2021-02-23 1.0.1
2021-01-28 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-26 1.5.2
2024-01-23 1.5.1
2022-10-17 1.5.0
2022-09-30 1.4.9
2022-09-26 1.4.8
2022-09-04 1.4.7
2022-04-11 1.4.6
2022-01-21 1.4.5
2021-11-08 1.4.4
2021-08-07 1.4.3
2021-06-29 1.4.2
2021-05-15 1.4.1
2021-02-23 1.4.0
Title: Predict with 'tidymodels' Workflows in Databases
Description: Turn 'tidymodels' workflows into objects containing the
sufficient sequential equations to perform predictions. These smaller
objects allow for low dependency prediction locally or directly in
databases.
Author: Emil Hvitfeldt [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between orbital versions 0.5.0 dated 2026-02-27 and 0.5.1 dated 2026-03-13
DESCRIPTION | 17 +- MD5 | 152 ++++++++++----------- NAMESPACE | 50 ++++++ NEWS.md | 10 + R/adjust_equivocal_zone.R | 8 - R/adjust_numeric_range.R | 23 +++ R/adjust_predictions_custom.R | 10 + R/adjust_probability_threshold.R | 8 - R/estimate-size.R |only R/model-xgboost.R | 17 ++ R/parsnip.R | 34 +++- R/step_adasyn.R | 5 R/step_bsmote.R | 5 R/step_center.R | 10 + R/step_corr.R | 5 R/step_downsample.R | 5 R/step_dummy.R | 14 + R/step_filter_missing.R | 5 R/step_impute_mean.R | 10 + R/step_impute_median.R | 10 + R/step_indicate_na.R | 12 + R/step_lincomb.R | 5 R/step_log.R | 11 + R/step_mutate.R | 6 R/step_nearmiss.R | 5 R/step_normalize.R | 10 + R/step_nzv.R | 5 R/step_pca.R | 10 + R/step_range.R | 10 + R/step_rm.R | 5 R/step_rose.R | 5 R/step_scale.R | 10 + R/step_select.R | 5 R/step_smote.R | 5 R/step_smotenc.R | 5 R/step_sqrt.R | 10 + R/step_tomek.R | 5 R/step_upsample.R | 5 R/step_zv.R | 5 inst/doc/supported-models.html | 110 +++++++-------- man/estimate_orbital_size.Rd |only tests/testthat/_snaps/estimate-size.md |only tests/testthat/_snaps/sql.md | 29 ---- tests/testthat/derby.log | 6 tests/testthat/test-adjust_equivocal_zone.R | 30 ++++ tests/testthat/test-adjust_numeric_range.R | 53 +++++++ tests/testthat/test-adjust_predictions_custom.R | 38 +++++ tests/testthat/test-adjust_probability_threshold.R | 26 +++ tests/testthat/test-estimate-size.R |only tests/testthat/test-model-xgboost.R | 22 +++ tests/testthat/test-sql.R | 12 - tests/testthat/test-step_adasyn.R | 15 ++ tests/testthat/test-step_bsmote.R | 15 ++ tests/testthat/test-step_center.R | 23 +++ tests/testthat/test-step_corr.R | 11 + tests/testthat/test-step_downsample.R | 15 ++ tests/testthat/test-step_dummy.R | 27 +++ tests/testthat/test-step_filter_missing.R | 11 + tests/testthat/test-step_impute_mean.R | 23 +++ tests/testthat/test-step_impute_median.R | 23 +++ tests/testthat/test-step_indicate_na.R | 23 +++ tests/testthat/test-step_lincomb.R | 11 + tests/testthat/test-step_log.R | 23 +++ tests/testthat/test-step_mutate.R | 23 +++ tests/testthat/test-step_nearmiss.R | 15 ++ tests/testthat/test-step_normalize.R | 23 +++ tests/testthat/test-step_nzv.R | 11 + tests/testthat/test-step_pca.R | 15 ++ tests/testthat/test-step_range.R | 23 +++ tests/testthat/test-step_rm.R | 11 + tests/testthat/test-step_rose.R | 15 ++ tests/testthat/test-step_scale.R | 23 +++ tests/testthat/test-step_select.R | 11 + tests/testthat/test-step_smote.R | 15 ++ tests/testthat/test-step_smotenc.R | 15 ++ tests/testthat/test-step_sqrt.R | 23 +++ tests/testthat/test-step_tomek.R | 15 ++ tests/testthat/test-step_upsample.R | 15 ++ tests/testthat/test-step_zv.R | 11 + 79 files changed, 1152 insertions(+), 190 deletions(-)
Title: Multilevel Functions
Description: Tools used by organizational researchers for the analysis of multilevel data. Includes four broad sets of tools. First, functions for estimating within-group agreement and reliability indices. Second, functions for manipulating multilevel and longitudinal (panel) data. Third, simulations for estimating power and generating multilevel data. Fourth, miscellaneous functions for estimating reliability and performing simple calculations and data transformations.
Author: Paul Bliese [aut, cre],
Gilad Chen [ctb],
Patrick Downes [ctb],
Patrick Flynn [ctb],
Jonas Lang [ctb],
Donald Schepker [ctb]
Maintainer: Paul Bliese <pdbliese@gmail.com>
Diff between multilevel versions 2.7.1 dated 2025-09-08 and 2.8 dated 2026-03-13
DESCRIPTION | 18 ++++++++++-------- MD5 | 13 ++++++++----- R/multilevel.R | 32 +++++++++++++++++++++++++------- data/banddat.rda |only man/banddat.Rd |only man/correct.gcor.Rd |only man/paneldat.Rd | 27 ++++++++++++++++----------- man/rwg.j.Rd | 12 ++++++++---- man/rwg.j.lindell.Rd | 22 +++++++++++++--------- 9 files changed, 80 insertions(+), 44 deletions(-)
Title: Intergovernmental Organizations Database
Description: Tools to extract information from the Intergovernmental
Organizations ('IGO') Database (v3), provided by the Correlates of War
Project <https://correlatesofwar.org/>. See also Pevehouse, J. C. et
al. (2020) <doi:10.1177/0022343319881175>.
Author: Diego Hernangomez [aut, cre, cph] ,
The Correlates of War Project [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between igoR versions 1.0.0 dated 2026-01-17 and 1.0.1 dated 2026-03-13
igoR-1.0.0/igoR/inst/doc/igoR.Rmd |only igoR-1.0.0/igoR/inst/doc/mapping.Rmd |only igoR-1.0.0/igoR/vignettes/AustShared-1.png |only igoR-1.0.0/igoR/vignettes/NAShared-1.png |only igoR-1.0.0/igoR/vignettes/UNMaps-1.png |only igoR-1.0.0/igoR/vignettes/igoR.Rmd |only igoR-1.0.0/igoR/vignettes/mapping.Rmd |only igoR-1.0.1/igoR/DESCRIPTION | 14 igoR-1.0.1/igoR/MD5 | 50 - igoR-1.0.1/igoR/NEWS.md | 5 igoR-1.0.1/igoR/R/sysdata.rda |binary igoR-1.0.1/igoR/README.md | 53 - igoR-1.0.1/igoR/build/partial.rdb |binary igoR-1.0.1/igoR/build/vignette.rds |binary igoR-1.0.1/igoR/data/igo_year_format3.rda |binary igoR-1.0.1/igoR/data/state_year_format3.rda |binary igoR-1.0.1/igoR/data/states2016.rda |binary igoR-1.0.1/igoR/inst/CITATION | 73 - igoR-1.0.1/igoR/inst/COPYRIGHTS | 22 igoR-1.0.1/igoR/inst/REFERENCES.bib | 86 - igoR-1.0.1/igoR/inst/WORDLIST | 1 igoR-1.0.1/igoR/inst/doc/igoR.R | 494 ++++++++-- igoR-1.0.1/igoR/inst/doc/igoR.html | 1235 ++++++++++++++----------- igoR-1.0.1/igoR/inst/doc/igoR.qmd |only igoR-1.0.1/igoR/inst/doc/mapping.html | 553 +++-------- igoR-1.0.1/igoR/inst/doc/mapping.qmd |only igoR-1.0.1/igoR/inst/schemaorg.json | 4 igoR-1.0.1/igoR/vignettes/REFERENCES.bib | 86 - igoR-1.0.1/igoR/vignettes/fig-AustShared-1.png |only igoR-1.0.1/igoR/vignettes/fig-NAShared-1.png |only igoR-1.0.1/igoR/vignettes/fig-UNMaps-1.png |only igoR-1.0.1/igoR/vignettes/igoR.qmd |only igoR-1.0.1/igoR/vignettes/mapping.qmd |only 33 files changed, 1524 insertions(+), 1152 deletions(-)
Title: Gaussian and Student-t Copula Models for Count Time Series
Description: Provides likelihood-based inference for Gaussian and Student-t
copula models for univariate count time series. Supports Poisson,
negative binomial, binomial, beta-binomial, and zero-inflated
marginals with ARMA dependence structures. Includes simulation,
maximum-likelihood estimation, residual diagnostics, and predictive
inference. Implements Time Series Minimax Exponential Tilting (TMET)
<doi:10.1016/j.csda.2026.108344>, an adaptation of minimax exponential
tilting of Botev (2017) <doi:10.1111/rssb.12162>. Also provides a
linear-cost implementation of the Geweke–Hajivassiliou–Keane (GHK)
simulator following Masarotto and Varin (2012) <doi:10.1214/12-EJS721>,
and the Continuous Extension (CE) approximation of Nguyen and
De Oliveira (2025) <doi:10.1080/02664763.2025.2498502>. The package
follows the S3 design philosophy of 'gcmr' but is developed independently.
Author: Quynh Nguyen [aut, cre],
Victor De Oliveira [aut]
Maintainer: Quynh Nguyen <nqnhu2209@gmail.com>
Diff between gctsc versions 0.1.3 dated 2025-12-17 and 0.2.0 dated 2026-03-13
gctsc-0.1.3/gctsc/R/copula-utils.R |only gctsc-0.1.3/gctsc/R/core_utils.R |only gctsc-0.1.3/gctsc/R/loglik_vmet.R |only gctsc-0.1.3/gctsc/data/campyl.csv |only gctsc-0.1.3/gctsc/inst/CITATION |only gctsc-0.1.3/gctsc/inst/examples |only gctsc-0.1.3/gctsc/man/pmvn_ce.Rd |only gctsc-0.1.3/gctsc/man/pmvn_ghk.Rd |only gctsc-0.1.3/gctsc/man/pmvn_tmet.Rd |only gctsc-0.1.3/gctsc/src/gctsc_dummy.cpp |only gctsc-0.1.3/gctsc/src/lnNpr.cpp |only gctsc-0.1.3/gctsc/src/mvnkernel.cpp |only gctsc-0.1.3/gctsc/src/predmvn.cpp |only gctsc-0.2.0/gctsc/DESCRIPTION | 34 - gctsc-0.2.0/gctsc/LICENSE | 2 gctsc-0.2.0/gctsc/MD5 | 154 ++-- gctsc-0.2.0/gctsc/NAMESPACE | 11 gctsc-0.2.0/gctsc/R/RcppExports.R | 46 + gctsc-0.2.0/gctsc/R/arma-helpers.R | 187 +++-- gctsc-0.2.0/gctsc/R/cond_mv.R |only gctsc-0.2.0/gctsc/R/cormat.R | 46 + gctsc-0.2.0/gctsc/R/data.R | 9 gctsc-0.2.0/gctsc/R/grad_jac_prod.R |only gctsc-0.2.0/gctsc/R/import.R | 7 gctsc-0.2.0/gctsc/R/loglik_ce.R | 273 +++++--- gctsc-0.2.0/gctsc/R/loglik_factory.R | 70 +- gctsc-0.2.0/gctsc/R/loglik_ghk.R | 315 ++++++---- gctsc-0.2.0/gctsc/R/loglik_tmet.R | 500 ++++++++------- gctsc-0.2.0/gctsc/R/main.R | 330 ++++++---- gctsc-0.2.0/gctsc/R/marg_utils.R | 17 gctsc-0.2.0/gctsc/R/marginals.R | 32 - gctsc-0.2.0/gctsc/R/methods-print.R | 36 - gctsc-0.2.0/gctsc/R/prediction.R | 317 ++++++---- gctsc-0.2.0/gctsc/R/residuals.R | 308 ++++++--- gctsc-0.2.0/gctsc/R/sample_utils.R |only gctsc-0.2.0/gctsc/R/sim-utils.R | 142 +++- gctsc-0.2.0/gctsc/R/simulate-gctsc.R | 272 ++++---- gctsc-0.2.0/gctsc/R/tmet_t_solver.R |only gctsc-0.2.0/gctsc/R/validate-utils.R | 75 +- gctsc-0.2.0/gctsc/README.md | 117 +++ gctsc-0.2.0/gctsc/build/vignette.rds |binary gctsc-0.2.0/gctsc/data/KCWC.rda |binary gctsc-0.2.0/gctsc/data/campyl.rda |binary gctsc-0.2.0/gctsc/data/datalist | 1 gctsc-0.2.0/gctsc/data/rota.csv |only gctsc-0.2.0/gctsc/data/rota.rda |only gctsc-0.2.0/gctsc/inst/Gaussian_copula_examples |only gctsc-0.2.0/gctsc/inst/doc/gctsc_vignette.R | 104 ++- gctsc-0.2.0/gctsc/inst/doc/gctsc_vignette.Rmd | 201 ++++-- gctsc-0.2.0/gctsc/inst/doc/gctsc_vignette.html | 755 +++++++++++++----------- gctsc-0.2.0/gctsc/inst/t_copula_examples |only gctsc-0.2.0/gctsc/man/KCWC.Rd | 32 - gctsc-0.2.0/gctsc/man/arma.cormat.Rd | 41 - gctsc-0.2.0/gctsc/man/coef.gctsc.Rd | 39 - gctsc-0.2.0/gctsc/man/gctsc.Rd | 309 +++++---- gctsc-0.2.0/gctsc/man/gctsc.opts.Rd | 54 - gctsc-0.2.0/gctsc/man/marginal.gctsc.Rd | 156 ++-- gctsc-0.2.0/gctsc/man/plot.gctsc.Rd | 156 ++-- gctsc-0.2.0/gctsc/man/pmv_ce.Rd |only gctsc-0.2.0/gctsc/man/pmv_ghk.Rd |only gctsc-0.2.0/gctsc/man/pmv_tmet.Rd |only gctsc-0.2.0/gctsc/man/predict.gctsc.Rd | 137 +++- gctsc-0.2.0/gctsc/man/print.gctsc.Rd | 40 - gctsc-0.2.0/gctsc/man/print.summary.gctsc.Rd | 40 - gctsc-0.2.0/gctsc/man/residuals.gctsc.Rd | 122 ++- gctsc-0.2.0/gctsc/man/rota.Rd |only gctsc-0.2.0/gctsc/man/sim_gctsc.Rd | 314 ++++++--- gctsc-0.2.0/gctsc/man/summary.gctsc.Rd | 46 - gctsc-0.2.0/gctsc/src/RcppExports.cpp | 120 +++ gctsc-0.2.0/gctsc/src/cond_var.cpp | 5 gctsc-0.2.0/gctsc/src/gauss_utils.cpp | 12 gctsc-0.2.0/gctsc/src/gauss_utils.h | 13 gctsc-0.2.0/gctsc/src/kernel_mvn.cpp |only gctsc-0.2.0/gctsc/src/kernel_mvt.cpp |only gctsc-0.2.0/gctsc/src/lnNpr.h | 9 gctsc-0.2.0/gctsc/src/lnTpr.h |only gctsc-0.2.0/gctsc/src/loglik_ce.cpp | 147 ++++ gctsc-0.2.0/gctsc/src/pred_mvn.cpp |only gctsc-0.2.0/gctsc/src/pred_mvt.cpp |only gctsc-0.2.0/gctsc/src/res_mvn.cpp |only gctsc-0.2.0/gctsc/src/res_mvt.cpp |only gctsc-0.2.0/gctsc/src/sampling_utils.h | 2 gctsc-0.2.0/gctsc/src/t_utils.cpp |only gctsc-0.2.0/gctsc/src/t_utils.h |only gctsc-0.2.0/gctsc/vignettes/gctsc_vignette.Rmd | 201 ++++-- 85 files changed, 4033 insertions(+), 2323 deletions(-)
Title: Efficient Inference on High-Dimensional Linear Model with
Missing Outcomes
Description: A statistically and computationally efficient debiasing method for conducting valid inference on the high-dimensional linear regression function with missing outcomes.
The reference paper is Zhang, Giessing, and Chen (2023) <doi:10.48550/arXiv.2309.06429>.
Author: Yikun Zhang [aut, cre] ,
Alexander Giessing [aut] ,
Yen-Chi Chen [aut]
Maintainer: Yikun Zhang <yikunzhang@foxmail.com>
Diff between DebiasInfer versions 0.2 dated 2023-10-09 and 0.2.1 dated 2026-03-13
DESCRIPTION | 17 +++++++------- MD5 | 12 +++++----- R/DebiasProg.R | 61 ++++++++++++++++++++++++++++++++-------------------- R/DebiasProgCV.R | 22 +++++++++++++++--- build/partial.rdb |binary man/DebiasProg.Rd | 5 ++-- man/DebiasProgCV.Rd | 5 ++-- 7 files changed, 77 insertions(+), 45 deletions(-)
More information about SigBridgeRUtils at CRAN
Permanent link
Title: Risk Regression Models and Prediction Scores for Survival
Analysis with Competing Risks
Description: Implementation of the following methods for event history analysis.
Risk regression models for survival endpoints also in the presence of competing
risks are fitted using binomial regression based on a time sequence of binary
event status variables. A formula interface for the Fine-Gray regression model
and an interface for the combination of cause-specific Cox regression models.
A toolbox for assessing and comparing performance of risk predictions (risk
markers and risk prediction models). Prediction performance is measured by the
Brier score and the area under the ROC curve for binary possibly time-dependent
outcome. Inverse probability of censoring weighting and pseudo values are used
to deal with right censored data. Lists of risk markers and lists of risk models
are assessed simultaneously. Cross-validation repeatedly splits the data, trains
the risk prediction models on one part of each split and then summarizes and
compares the performance across splits.
Author: Thomas Alexander Gerds [aut, cre],
Johan Sebastian Ohlendorff [aut],
Paul Blanche [ctb],
Rikke Mortensen [ctb],
Marvin Wright [ctb],
Nikolaj Tollenaar [ctb],
John Muschelli [ctb],
Ulla Brasch Mogensen [ctb],
Asbjoern Risom [ctb],
Brice Ozenne [aut]
Maintainer: Thomas Alexander Gerds <tag@biostat.ku.dk>
Diff between riskRegression versions 2026.02.13 dated 2026-02-16 and 2026.03.11 dated 2026-03-12
riskRegression-2026.02.13/riskRegression/tests/testthat/test-phreg.R |only riskRegression-2026.03.11/riskRegression/DESCRIPTION | 12 riskRegression-2026.03.11/riskRegression/MD5 | 29 riskRegression-2026.03.11/riskRegression/R/AUC.binary.R | 6 riskRegression-2026.03.11/riskRegression/R/CSC.R | 125 +++- riskRegression-2026.03.11/riskRegression/R/GLMnet.R | 307 +++++----- riskRegression-2026.03.11/riskRegression/R/coxLP.R | 31 - riskRegression-2026.03.11/riskRegression/R/coxStrata.R | 21 riskRegression-2026.03.11/riskRegression/R/plotCalibration.R | 8 riskRegression-2026.03.11/riskRegression/R/predict.CauseSpecificCox.R | 5 riskRegression-2026.03.11/riskRegression/R/predictRisk.R | 88 +- riskRegression-2026.03.11/riskRegression/R/print.CauseSpecificCox.R | 9 riskRegression-2026.03.11/riskRegression/man/CSC.Rd | 35 - riskRegression-2026.03.11/riskRegression/man/GLMnet.Rd | 79 +- riskRegression-2026.03.11/riskRegression/src/Makevars | 2 riskRegression-2026.03.11/riskRegression/src/Makevars.win | 1 16 files changed, 466 insertions(+), 292 deletions(-)
More information about riskRegression at CRAN
Permanent link
Title: Computes Statistics for Relational Event History Data
Description: Computes a variety of statistics for relational event models. Relational event models enable researchers to investigate both exogenous and endogenous factors influencing the evolution of a time-ordered sequence of events. These models are categorized into tie-oriented models (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>), where the probability of a dyad interacting next is modeled in a single step, and actor-oriented models (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>), which first model the probability of a sender initiating an interaction and subsequently the probability of the sender's choice of receiver. The package is designed to compute a variety of statistics that summarize exogenous and endogenous influences on the event stream for both types of models.
Author: Marlyne Meijerink-Bosman [aut],
Giuseppe Arena [ctb],
Diana Karimova [ctb],
Rumana Lakdawala [ctb],
Mahdi Shafiee Kamalabad [ctb],
Fabio Generoso Vieira [ctb],
Roger Leenders [ctb],
Joris Mulder [aut, cre]
Maintainer: Joris Mulder <j.mulder3@tilburguniversity.edu>
Diff between remstats versions 3.2.4 dated 2025-01-29 and 3.2.5 dated 2026-03-12
DESCRIPTION | 41 ++++++++++++++++++----------------------- LICENSE | 2 +- MD5 | 10 +++++----- build/partial.rdb |binary build/vignette.rds |binary src/RcppExports.cpp | 12 ++++++------ 6 files changed, 30 insertions(+), 35 deletions(-)
Title: Highly Optimized Protocol Buffer Serializers
Description: Pure C++ implementations for reading and writing several common data
formats based on Google protocol-buffers. Currently supports 'rexp.proto' for
serialized R objects, 'geobuf.proto' for binary geojson, and 'mvt.proto' for
vector tiles. This package uses the auto-generated C++ code by protobuf-compiler,
hence the entire serialization is optimized at compile time. The 'RProtoBuf'
package on the other hand uses the protobuf runtime library to provide a general-
purpose toolkit for reading and writing arbitrary protocol-buffer data in R.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between protolite versions 2.3.1 dated 2024-10-04 and 2.4.0 dated 2026-03-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars.win | 35 ++++++++++++++++++++++++++--------- 4 files changed, 36 insertions(+), 16 deletions(-)
Title: Interpolate Munsell Renotation Data from Hue Value/Chroma to
CIE/RGB
Description: Methods for interpolating data in the Munsell color system following the ASTM D-1535 standard. Hues and chromas with decimal values can be interpolated and converted to/from the Munsell color system and CIE xyY, CIE XYZ, CIE Lab, CIE Luv, or RGB. Includes ISCC-NBS color block lookup. Based on the work by Paul Centore, "The Munsell and Kubelka-Munk Toolbox".
Author: Jose Gama [aut, trl],
Paul Centore [aut, cph],
Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between munsellinterpol versions 3.2-0 dated 2025-06-18 and 3.3-2 dated 2026-03-12
DESCRIPTION | 8 +- MD5 | 78 ++++++++++---------- NEWS.md | 14 +++ R/ISCC-NBS.R | 15 ++- R/round.R | 33 ++++---- R/sysdata.rda |binary build/vignette.rds |binary data/munsellinterpol.rda |binary inst/doc/dental.html | 12 +-- inst/doc/lightness.pdf |binary inst/doc/lightness.rnw | 2 inst/doc/lociHC.pdf |binary inst/doc/lociHC.rnw | 2 inst/doc/munsellinterpol-guide.html | 24 +++--- inst/doc/soil.R | 23 ++--- inst/doc/soil.Rmd | 53 +++++++++---- inst/doc/soil.html | 132 +++++++++++++++++++--------------- inst/extdata/PantoneCoY.txt | 2 inst/extdata/Supplement1_3.6.2024.csv | 2 inst/extdata/glossybook-Centore.txt |only inst/extdata/mattebook-Joensuu.txt |only man/LabtoMunsell.Rd | 2 man/LuvtoMunsell.Rd | 2 man/MunsellBooks.Rd |only man/MunsellToLab.Rd | 2 man/MunsellToLuv.Rd | 2 man/MunsellToRGB.Rd | 2 man/MunsellToXYZ.Rd | 2 man/MunsellTosRGB.Rd | 2 man/MunsellToxyY.Rd | 4 - man/RGBtoMunsell.Rd | 2 man/XYZtoMunsell.Rd | 2 man/macros/macros.Rd | 2 man/round.Rd | 96 ++++++------------------ man/sRGBtoMunsell.Rd | 2 man/xyYtoMunsell.Rd | 4 - tests/test-rounding.R | 5 - tools/books.R |only tools/datasets.R | 94 +++++++++--------------- vignettes/lightness.rnw | 2 vignettes/lociHC.rnw | 2 vignettes/soil.Rmd | 53 +++++++++---- 42 files changed, 353 insertions(+), 329 deletions(-)
More information about munsellinterpol at CRAN
Permanent link
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc] ,
Christoph Burow [aut, trl, dtc] ,
Michael Dietze [aut] ,
Margret C. Fuchs [aut] ,
Christoph Schmidt [aut] ,
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] ,
Norbert Mercier [aut] ,
Rachel K. Smedley [ct [...truncated...]
Maintainer: Sebastian Kreutzer <maintainer_luminescence@r-luminescence.org>
Diff between Luminescence versions 1.1.2 dated 2025-12-12 and 1.2.0 dated 2026-03-12
Luminescence-1.1.2/Luminescence/R/github.R |only Luminescence-1.1.2/Luminescence/R/install_DevelopmentVersion.R |only Luminescence-1.1.2/Luminescence/inst/include |only Luminescence-1.1.2/Luminescence/man/GitHub-API.Rd |only Luminescence-1.1.2/Luminescence/man/install_DevelopmentVersion.Rd |only Luminescence-1.1.2/Luminescence/tests/testthat/test_github.R |only Luminescence-1.1.2/Luminescence/tests/testthat/test_install_DevelopmentVersion.R |only Luminescence-1.2.0/Luminescence/DESCRIPTION | 14 Luminescence-1.2.0/Luminescence/MD5 | 838 ++++---- Luminescence-1.2.0/Luminescence/NAMESPACE | 14 Luminescence-1.2.0/Luminescence/NEWS.md | 696 +++++++ Luminescence-1.2.0/Luminescence/R/Luminescence-generics.R | 276 ++ Luminescence-1.2.0/Luminescence/R/Luminescence-package.R | 129 - Luminescence-1.2.0/Luminescence/R/RLum-class.R | 29 Luminescence-1.2.0/Luminescence/R/RLum.Analysis-class.R | 121 - Luminescence-1.2.0/Luminescence/R/RLum.Data-class.R | 14 Luminescence-1.2.0/Luminescence/R/RLum.Data.Curve-class.R | 69 Luminescence-1.2.0/Luminescence/R/RLum.Data.Image-class.R | 60 Luminescence-1.2.0/Luminescence/R/RLum.Data.Spectrum-class.R | 37 Luminescence-1.2.0/Luminescence/R/RLum.Results-class.R | 22 Luminescence-1.2.0/Luminescence/R/Risoe.BINfileData-class.R | 26 Luminescence-1.2.0/Luminescence/R/Risoe.BINfileData2RLum.Analysis.R | 25 Luminescence-1.2.0/Luminescence/R/Risoe.BINfileData2RLum.Data.Curve.R | 30 Luminescence-1.2.0/Luminescence/R/addins_RLum.R | 13 Luminescence-1.2.0/Luminescence/R/analyse_Al2O3C_CrossTalk.R | 44 Luminescence-1.2.0/Luminescence/R/analyse_Al2O3C_ITC.R | 53 Luminescence-1.2.0/Luminescence/R/analyse_Al2O3C_Measurement.R | 48 Luminescence-1.2.0/Luminescence/R/analyse_FadingMeasurement.R | 97 - Luminescence-1.2.0/Luminescence/R/analyse_IRSAR.RF.R | 30 Luminescence-1.2.0/Luminescence/R/analyse_SAR.CWOSL.R | 934 +++++----- Luminescence-1.2.0/Luminescence/R/analyse_SAR.TL.R | 94 - Luminescence-1.2.0/Luminescence/R/analyse_ThermochronometryData.R | 14 Luminescence-1.2.0/Luminescence/R/analyse_baSAR.R | 604 ++---- Luminescence-1.2.0/Luminescence/R/analyse_pIRIRSequence.R | 164 - Luminescence-1.2.0/Luminescence/R/analyse_portableOSL.R | 108 - Luminescence-1.2.0/Luminescence/R/apply_CosmicRayRemoval.R | 34 Luminescence-1.2.0/Luminescence/R/apply_Crosstalk.R | 19 Luminescence-1.2.0/Luminescence/R/apply_EfficiencyCorrection.R | 55 Luminescence-1.2.0/Luminescence/R/calc_AliquotSize.R | 4 Luminescence-1.2.0/Luminescence/R/calc_AverageDose.R | 73 Luminescence-1.2.0/Luminescence/R/calc_CentralDose.R | 30 Luminescence-1.2.0/Luminescence/R/calc_CobbleDoseRate.R | 101 - Luminescence-1.2.0/Luminescence/R/calc_CommonDose.R | 39 Luminescence-1.2.0/Luminescence/R/calc_CosmicDoseRate.R | 15 Luminescence-1.2.0/Luminescence/R/calc_EED_Model.R | 16 Luminescence-1.2.0/Luminescence/R/calc_FadingCorr.R | 15 Luminescence-1.2.0/Luminescence/R/calc_FastRatio.R | 20 Luminescence-1.2.0/Luminescence/R/calc_FiniteMixture.R | 17 Luminescence-1.2.0/Luminescence/R/calc_FuchsLang2001.R | 14 Luminescence-1.2.0/Luminescence/R/calc_HomogeneityTest.R | 18 Luminescence-1.2.0/Luminescence/R/calc_Huntley2006.R | 21 Luminescence-1.2.0/Luminescence/R/calc_IEU.R | 15 Luminescence-1.2.0/Luminescence/R/calc_Lamothe2003.R | 64 Luminescence-1.2.0/Luminescence/R/calc_MaxDose.R | 42 Luminescence-1.2.0/Luminescence/R/calc_MinDose.R | 521 +++-- Luminescence-1.2.0/Luminescence/R/calc_MoransI.R | 32 Luminescence-1.2.0/Luminescence/R/calc_OSLLxTxDecomposed.R | 34 Luminescence-1.2.0/Luminescence/R/calc_OSLLxTxRatio.R | 412 ++-- Luminescence-1.2.0/Luminescence/R/calc_SourceDoseRate.R | 32 Luminescence-1.2.0/Luminescence/R/calc_Statistics.R | 6 Luminescence-1.2.0/Luminescence/R/calc_TLLxTxRatio.R | 76 Luminescence-1.2.0/Luminescence/R/calc_ThermalLifetime.R | 17 Luminescence-1.2.0/Luminescence/R/calc_WodaFuchs2008.R | 11 Luminescence-1.2.0/Luminescence/R/calc_gSGC.R | 11 Luminescence-1.2.0/Luminescence/R/calc_gSGC_feldspar.R | 8 Luminescence-1.2.0/Luminescence/R/combine_De_Dr.R | 67 Luminescence-1.2.0/Luminescence/R/convert_Activity2Concentration.R | 20 Luminescence-1.2.0/Luminescence/R/convert_BIN2CSV.R | 16 Luminescence-1.2.0/Luminescence/R/convert_CW2pHMi.R | 137 - Luminescence-1.2.0/Luminescence/R/convert_CW2pLM.R | 58 Luminescence-1.2.0/Luminescence/R/convert_CW2pLMi.R | 220 +- Luminescence-1.2.0/Luminescence/R/convert_CW2pPMi.R | 110 - Luminescence-1.2.0/Luminescence/R/convert_Concentration2DoseRate.R | 118 - Luminescence-1.2.0/Luminescence/R/convert_Daybreak2CSV.R | 21 Luminescence-1.2.0/Luminescence/R/convert_PSL2CSV.R | 25 Luminescence-1.2.0/Luminescence/R/convert_PSL2Risoe.BINfileData.R | 24 Luminescence-1.2.0/Luminescence/R/convert_RLum2Risoe.BINfileData.R | 20 Luminescence-1.2.0/Luminescence/R/convert_SG2MG.R | 65 Luminescence-1.2.0/Luminescence/R/convert_Second2Gray.R | 13 Luminescence-1.2.0/Luminescence/R/convert_Wavelength2Energy.R | 8 Luminescence-1.2.0/Luminescence/R/convert_XSYG2CSV.R | 17 Luminescence-1.2.0/Luminescence/R/correct_PMTLinearity.R | 19 Luminescence-1.2.0/Luminescence/R/extract_IrradiationTimes.R | 95 - Luminescence-1.2.0/Luminescence/R/extract_ROI.R | 14 Luminescence-1.2.0/Luminescence/R/fit_CWCurve.R | 44 Luminescence-1.2.0/Luminescence/R/fit_DoseResponseCurve.R | 146 - Luminescence-1.2.0/Luminescence/R/fit_EmissionSpectra.R | 19 Luminescence-1.2.0/Luminescence/R/fit_IsothermalHolding.R | 16 Luminescence-1.2.0/Luminescence/R/fit_LMCurve.R | 103 - Luminescence-1.2.0/Luminescence/R/fit_OSLLifeTimes.R | 13 Luminescence-1.2.0/Luminescence/R/fit_SurfaceExposure.R | 25 Luminescence-1.2.0/Luminescence/R/fit_ThermalQuenching.R | 2 Luminescence-1.2.0/Luminescence/R/import_Data.R | 16 Luminescence-1.2.0/Luminescence/R/internal_as.latex.table.R | 12 Luminescence-1.2.0/Luminescence/R/internals_RLum.R | 529 ++++- Luminescence-1.2.0/Luminescence/R/internals_Thermochronometry.R | 20 Luminescence-1.2.0/Luminescence/R/merge_RLum.Analysis.R | 30 Luminescence-1.2.0/Luminescence/R/merge_RLum.Data.Curve.R | 13 Luminescence-1.2.0/Luminescence/R/merge_RLum.Data.Spectrum.R | 23 Luminescence-1.2.0/Luminescence/R/merge_RLum.R | 23 Luminescence-1.2.0/Luminescence/R/merge_RLum.Results.R | 49 Luminescence-1.2.0/Luminescence/R/merge_Risoe.BINfileData.R | 70 Luminescence-1.2.0/Luminescence/R/methods_RLum.R | 71 Luminescence-1.2.0/Luminescence/R/plot_AbanicoPlot.R | 260 +- Luminescence-1.2.0/Luminescence/R/plot_DRCSummary.R | 49 Luminescence-1.2.0/Luminescence/R/plot_DRTResults.R | 308 +-- Luminescence-1.2.0/Luminescence/R/plot_DetPlot.R | 139 - Luminescence-1.2.0/Luminescence/R/plot_DoseResponseCurve.R | 39 Luminescence-1.2.0/Luminescence/R/plot_FilterCombinations.R | 60 Luminescence-1.2.0/Luminescence/R/plot_GrowthCurve.R | 68 Luminescence-1.2.0/Luminescence/R/plot_Histogram.R | 7 Luminescence-1.2.0/Luminescence/R/plot_KDE.R | 30 Luminescence-1.2.0/Luminescence/R/plot_MoranScatterplot.R | 41 Luminescence-1.2.0/Luminescence/R/plot_NRt.R | 27 Luminescence-1.2.0/Luminescence/R/plot_OSLAgeSummary.R | 19 Luminescence-1.2.0/Luminescence/R/plot_RLum.Analysis.R | 106 - Luminescence-1.2.0/Luminescence/R/plot_RLum.Data.Curve.R | 39 Luminescence-1.2.0/Luminescence/R/plot_RLum.Data.Image.R | 13 Luminescence-1.2.0/Luminescence/R/plot_RLum.Data.Spectrum.R | 78 Luminescence-1.2.0/Luminescence/R/plot_RLum.R | 166 - Luminescence-1.2.0/Luminescence/R/plot_RLum.Results.R | 39 Luminescence-1.2.0/Luminescence/R/plot_ROI.R | 62 Luminescence-1.2.0/Luminescence/R/plot_RadialPlot.R | 76 Luminescence-1.2.0/Luminescence/R/plot_Risoe.BINfileData.R | 22 Luminescence-1.2.0/Luminescence/R/plot_SingleGrainDisc.R | 37 Luminescence-1.2.0/Luminescence/R/plot_ViolinPlot.R | 18 Luminescence-1.2.0/Luminescence/R/read_BIN2R.R | 119 - Luminescence-1.2.0/Luminescence/R/read_BINXLOG2R.R |only Luminescence-1.2.0/Luminescence/R/read_Daybreak2R.R | 296 +-- Luminescence-1.2.0/Luminescence/R/read_HeliosOSL2R.R | 53 Luminescence-1.2.0/Luminescence/R/read_PSL2R.R | 44 Luminescence-1.2.0/Luminescence/R/read_RF2R.R | 59 Luminescence-1.2.0/Luminescence/R/read_SPE2R.R | 84 Luminescence-1.2.0/Luminescence/R/read_TIFF2R.R | 42 Luminescence-1.2.0/Luminescence/R/read_XSYG2R.R | 111 - Luminescence-1.2.0/Luminescence/R/remove_SignalBackground.R | 21 Luminescence-1.2.0/Luminescence/R/report_RLum.R | 12 Luminescence-1.2.0/Luminescence/R/scale_GammaDose.R | 18 Luminescence-1.2.0/Luminescence/R/subset_SingleGrainData.R | 31 Luminescence-1.2.0/Luminescence/R/template_DRAC.R | 21 Luminescence-1.2.0/Luminescence/R/trim_RLum.Data.R | 12 Luminescence-1.2.0/Luminescence/R/tune_Data.R | 2 Luminescence-1.2.0/Luminescence/R/use_DRAC.R | 25 Luminescence-1.2.0/Luminescence/R/verify_SingleGrainData.R | 30 Luminescence-1.2.0/Luminescence/R/write_R2BIN.R | 12 Luminescence-1.2.0/Luminescence/R/write_R2TIFF.R | 11 Luminescence-1.2.0/Luminescence/R/write_RLum2CSV.R | 12 Luminescence-1.2.0/Luminescence/R/zzz.R | 4 Luminescence-1.2.0/Luminescence/README.md | 73 Luminescence-1.2.0/Luminescence/build/partial.rdb |binary Luminescence-1.2.0/Luminescence/build/vignette.rds |binary Luminescence-1.2.0/Luminescence/data/ExampleData.RLum.Analysis.rda |binary Luminescence-1.2.0/Luminescence/data/ExampleData.XSYG.rda |binary Luminescence-1.2.0/Luminescence/data/ExampleData.portableOSL.rda |binary Luminescence-1.2.0/Luminescence/inst/WORDLIST | 89 Luminescence-1.2.0/Luminescence/inst/doc/crosstalk.html | 60 Luminescence-1.2.0/Luminescence/inst/extdata/BINX_IRSL_LOG.TXT |only Luminescence-1.2.0/Luminescence/inst/extdata/BINX_IRSL_LOG_BROKEN.TXT |only Luminescence-1.2.0/Luminescence/inst/extdata/BINX_OSL_LOG.TXT |only Luminescence-1.2.0/Luminescence/man/BaseDataSet.CosmicDoseRate.Rd | 6 Luminescence-1.2.0/Luminescence/man/BaseDataSet.Rd | 4 Luminescence-1.2.0/Luminescence/man/ExampleData.Al2O3C.Rd | 6 Luminescence-1.2.0/Luminescence/man/ExampleData.CW_OSL_Curve.Rd | 4 Luminescence-1.2.0/Luminescence/man/ExampleData.FittingLM.Rd | 2 Luminescence-1.2.0/Luminescence/man/ExampleData.XSYG.Rd | 3 Luminescence-1.2.0/Luminescence/man/Luminescence-package.Rd | 21 Luminescence-1.2.0/Luminescence/man/RLum-class.Rd | 7 Luminescence-1.2.0/Luminescence/man/RLum.Analysis-class.Rd | 4 Luminescence-1.2.0/Luminescence/man/RLum.Data-class.Rd | 2 Luminescence-1.2.0/Luminescence/man/RLum.Data.Curve-class.Rd | 7 Luminescence-1.2.0/Luminescence/man/RLum.Data.Image-class.Rd | 5 Luminescence-1.2.0/Luminescence/man/RLum.Data.Spectrum-class.Rd | 2 Luminescence-1.2.0/Luminescence/man/RLum.Results-class.Rd | 4 Luminescence-1.2.0/Luminescence/man/Risoe.BINfileData-class.Rd | 9 Luminescence-1.2.0/Luminescence/man/Risoe.BINfileData2RLum.Analysis.Rd | 9 Luminescence-1.2.0/Luminescence/man/analyse_Al2O3C_CrossTalk.Rd | 12 Luminescence-1.2.0/Luminescence/man/analyse_Al2O3C_ITC.Rd | 16 Luminescence-1.2.0/Luminescence/man/analyse_Al2O3C_Measurement.Rd | 19 Luminescence-1.2.0/Luminescence/man/analyse_FadingMeasurement.Rd | 35 Luminescence-1.2.0/Luminescence/man/analyse_IRSAR.RF.Rd | 12 Luminescence-1.2.0/Luminescence/man/analyse_SAR.CWOSL.Rd | 172 + Luminescence-1.2.0/Luminescence/man/analyse_SAR.TL.Rd | 30 Luminescence-1.2.0/Luminescence/man/analyse_baSAR.Rd | 110 - Luminescence-1.2.0/Luminescence/man/analyse_pIRIRSequence.Rd | 61 Luminescence-1.2.0/Luminescence/man/analyse_portableOSL.Rd | 47 Luminescence-1.2.0/Luminescence/man/apply_CosmicRayRemoval.Rd | 20 Luminescence-1.2.0/Luminescence/man/apply_Crosstalk.Rd | 17 Luminescence-1.2.0/Luminescence/man/apply_EfficiencyCorrection.Rd | 25 Luminescence-1.2.0/Luminescence/man/bin_RLum.Data.Rd | 4 Luminescence-1.2.0/Luminescence/man/calc_AliquotSize.Rd | 2 Luminescence-1.2.0/Luminescence/man/calc_AverageDose.Rd | 65 Luminescence-1.2.0/Luminescence/man/calc_CentralDose.Rd | 6 Luminescence-1.2.0/Luminescence/man/calc_CobbleDoseRate.Rd | 25 Luminescence-1.2.0/Luminescence/man/calc_CommonDose.Rd | 8 Luminescence-1.2.0/Luminescence/man/calc_CosmicDoseRate.Rd | 5 Luminescence-1.2.0/Luminescence/man/calc_EED_Model.Rd | 10 Luminescence-1.2.0/Luminescence/man/calc_FadingCorr.Rd | 7 Luminescence-1.2.0/Luminescence/man/calc_FastRatio.Rd | 2 Luminescence-1.2.0/Luminescence/man/calc_FiniteMixture.Rd | 6 Luminescence-1.2.0/Luminescence/man/calc_FuchsLang2001.Rd | 8 Luminescence-1.2.0/Luminescence/man/calc_HomogeneityTest.Rd | 6 Luminescence-1.2.0/Luminescence/man/calc_Huntley2006.Rd | 13 Luminescence-1.2.0/Luminescence/man/calc_IEU.Rd | 6 Luminescence-1.2.0/Luminescence/man/calc_Lamothe2003.Rd | 23 Luminescence-1.2.0/Luminescence/man/calc_MaxDose.Rd | 25 Luminescence-1.2.0/Luminescence/man/calc_MinDose.Rd | 83 Luminescence-1.2.0/Luminescence/man/calc_MoransI.Rd | 13 Luminescence-1.2.0/Luminescence/man/calc_OSLLxTxDecomposed.Rd | 12 Luminescence-1.2.0/Luminescence/man/calc_OSLLxTxRatio.Rd | 88 Luminescence-1.2.0/Luminescence/man/calc_SourceDoseRate.Rd | 22 Luminescence-1.2.0/Luminescence/man/calc_Statistics.Rd | 4 Luminescence-1.2.0/Luminescence/man/calc_TLLxTxRatio.Rd | 37 Luminescence-1.2.0/Luminescence/man/calc_ThermalLifetime.Rd | 4 Luminescence-1.2.0/Luminescence/man/calc_WodaFuchs2008.Rd | 4 Luminescence-1.2.0/Luminescence/man/calc_gSGC.Rd | 6 Luminescence-1.2.0/Luminescence/man/calc_gSGC_feldspar.Rd | 4 Luminescence-1.2.0/Luminescence/man/combine_De_Dr.Rd | 42 Luminescence-1.2.0/Luminescence/man/convert_Activity2Concentration.Rd | 18 Luminescence-1.2.0/Luminescence/man/convert_BIN2CSV.Rd | 4 Luminescence-1.2.0/Luminescence/man/convert_CW2pHMi.Rd | 38 Luminescence-1.2.0/Luminescence/man/convert_CW2pLM.Rd | 23 Luminescence-1.2.0/Luminescence/man/convert_CW2pLMi.Rd | 33 Luminescence-1.2.0/Luminescence/man/convert_CW2pPMi.Rd | 34 Luminescence-1.2.0/Luminescence/man/convert_Concentration2DoseRate.Rd | 38 Luminescence-1.2.0/Luminescence/man/convert_Daybreak2CSV.Rd | 7 Luminescence-1.2.0/Luminescence/man/convert_PSL2CSV.Rd | 10 Luminescence-1.2.0/Luminescence/man/convert_PSL2Risoe.BINfileData.Rd | 8 Luminescence-1.2.0/Luminescence/man/convert_RLum2Risoe.BINfileData.Rd | 4 Luminescence-1.2.0/Luminescence/man/convert_SG2MG.Rd | 27 Luminescence-1.2.0/Luminescence/man/convert_Second2Gray.Rd | 12 Luminescence-1.2.0/Luminescence/man/convert_Wavelength2Energy.Rd | 4 Luminescence-1.2.0/Luminescence/man/convert_XSYG2CSV.Rd | 6 Luminescence-1.2.0/Luminescence/man/correct_PMTLinearity.Rd | 10 Luminescence-1.2.0/Luminescence/man/dot-as.latex.table.Rd | 4 Luminescence-1.2.0/Luminescence/man/extract_IrradiationTimes.Rd | 9 Luminescence-1.2.0/Luminescence/man/extract_ROI.Rd | 11 Luminescence-1.2.0/Luminescence/man/fit_CWCurve.Rd | 18 Luminescence-1.2.0/Luminescence/man/fit_DoseResponseCurve.Rd | 80 Luminescence-1.2.0/Luminescence/man/fit_EmissionSpectra.Rd | 12 Luminescence-1.2.0/Luminescence/man/fit_LMCurve.Rd | 40 Luminescence-1.2.0/Luminescence/man/fit_OSLLifeTimes.Rd | 4 Luminescence-1.2.0/Luminescence/man/fit_SurfaceExposure.Rd | 10 Luminescence-1.2.0/Luminescence/man/fit_ThermalQuenching.Rd | 4 Luminescence-1.2.0/Luminescence/man/get_Layout.Rd | 2 Luminescence-1.2.0/Luminescence/man/get_RLum.Rd | 13 Luminescence-1.2.0/Luminescence/man/get_rightAnswer.Rd | 2 Luminescence-1.2.0/Luminescence/man/import_Data.Rd | 8 Luminescence-1.2.0/Luminescence/man/length_RLum.Rd | 9 Luminescence-1.2.0/Luminescence/man/melt_RLum.Rd | 4 Luminescence-1.2.0/Luminescence/man/merge_RLum.Analysis.Rd | 10 Luminescence-1.2.0/Luminescence/man/merge_RLum.Data.Curve.Rd | 11 Luminescence-1.2.0/Luminescence/man/merge_RLum.Data.Spectrum.Rd | 7 Luminescence-1.2.0/Luminescence/man/merge_RLum.Rd | 7 Luminescence-1.2.0/Luminescence/man/merge_RLum.Results.Rd | 6 Luminescence-1.2.0/Luminescence/man/merge_Risoe.BINfileData.Rd | 15 Luminescence-1.2.0/Luminescence/man/metadata.Rd | 8 Luminescence-1.2.0/Luminescence/man/methods_RLum.Rd | 28 Luminescence-1.2.0/Luminescence/man/names_RLum.Rd | 7 Luminescence-1.2.0/Luminescence/man/normalise_RLum.Rd |only Luminescence-1.2.0/Luminescence/man/plot_AbanicoPlot.Rd | 67 Luminescence-1.2.0/Luminescence/man/plot_DRCSummary.Rd | 20 Luminescence-1.2.0/Luminescence/man/plot_DRTResults.Rd | 38 Luminescence-1.2.0/Luminescence/man/plot_DetPlot.Rd | 41 Luminescence-1.2.0/Luminescence/man/plot_DoseResponseCurve.Rd | 13 Luminescence-1.2.0/Luminescence/man/plot_FilterCombinations.Rd | 9 Luminescence-1.2.0/Luminescence/man/plot_GrowthCurve.Rd | 45 Luminescence-1.2.0/Luminescence/man/plot_Histogram.Rd | 5 Luminescence-1.2.0/Luminescence/man/plot_KDE.Rd | 16 Luminescence-1.2.0/Luminescence/man/plot_MoranScatterplot.Rd | 31 Luminescence-1.2.0/Luminescence/man/plot_NRt.Rd | 9 Luminescence-1.2.0/Luminescence/man/plot_OSLAgeSummary.Rd | 10 Luminescence-1.2.0/Luminescence/man/plot_RLum.Analysis.Rd | 6 Luminescence-1.2.0/Luminescence/man/plot_RLum.Data.Curve.Rd | 17 Luminescence-1.2.0/Luminescence/man/plot_RLum.Data.Image.Rd | 11 Luminescence-1.2.0/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 21 Luminescence-1.2.0/Luminescence/man/plot_RLum.Rd | 61 Luminescence-1.2.0/Luminescence/man/plot_RLum.Results.Rd | 4 Luminescence-1.2.0/Luminescence/man/plot_ROI.Rd | 52 Luminescence-1.2.0/Luminescence/man/plot_RadialPlot.Rd | 22 Luminescence-1.2.0/Luminescence/man/plot_Risoe.BINfileData.Rd | 11 Luminescence-1.2.0/Luminescence/man/plot_SingleGrainDisc.Rd | 17 Luminescence-1.2.0/Luminescence/man/plot_ViolinPlot.Rd | 14 Luminescence-1.2.0/Luminescence/man/read_BIN2R.Rd | 28 Luminescence-1.2.0/Luminescence/man/read_BINXLOG2R.Rd |only Luminescence-1.2.0/Luminescence/man/read_Daybreak2R.Rd | 24 Luminescence-1.2.0/Luminescence/man/read_HeliosOSL2R.Rd | 24 Luminescence-1.2.0/Luminescence/man/read_PSL2R.Rd | 24 Luminescence-1.2.0/Luminescence/man/read_RF2R.Rd | 23 Luminescence-1.2.0/Luminescence/man/read_SPE2R.Rd | 28 Luminescence-1.2.0/Luminescence/man/read_TIFF2R.Rd | 21 Luminescence-1.2.0/Luminescence/man/read_XSYG2R.Rd | 18 Luminescence-1.2.0/Luminescence/man/remove_RLum.Rd | 4 Luminescence-1.2.0/Luminescence/man/remove_SignalBackground.Rd | 7 Luminescence-1.2.0/Luminescence/man/replicate_RLum.Rd | 4 Luminescence-1.2.0/Luminescence/man/report_RLum.Rd | 6 Luminescence-1.2.0/Luminescence/man/sTeve.Rd | 2 Luminescence-1.2.0/Luminescence/man/scale_GammaDose.Rd | 13 Luminescence-1.2.0/Luminescence/man/set_RLum.Rd | 7 Luminescence-1.2.0/Luminescence/man/set_Risoe.BINfileData.Rd | 4 Luminescence-1.2.0/Luminescence/man/smooth_RLum.Rd | 17 Luminescence-1.2.0/Luminescence/man/sort_RLum.Rd | 5 Luminescence-1.2.0/Luminescence/man/structure_RLum.Rd | 7 Luminescence-1.2.0/Luminescence/man/subset_SingleGrainData.Rd | 22 Luminescence-1.2.0/Luminescence/man/template_DRAC.Rd | 18 Luminescence-1.2.0/Luminescence/man/trim_RLum.Data.Rd | 4 Luminescence-1.2.0/Luminescence/man/tune_Data.Rd | 4 Luminescence-1.2.0/Luminescence/man/use_DRAC.Rd | 8 Luminescence-1.2.0/Luminescence/man/verify_SingleGrainData.Rd | 14 Luminescence-1.2.0/Luminescence/man/view.Rd | 4 Luminescence-1.2.0/Luminescence/man/write_R2BIN.Rd | 6 Luminescence-1.2.0/Luminescence/man/write_R2TIFF.Rd | 7 Luminescence-1.2.0/Luminescence/man/write_RLum2CSV.Rd | 4 Luminescence-1.2.0/Luminescence/src/Makevars | 1 Luminescence-1.2.0/Luminescence/src/Makevars.win | 1 Luminescence-1.2.0/Luminescence/src/RcppExports.cpp | 9 Luminescence-1.2.0/Luminescence/src/create_UID.cpp | 3 Luminescence-1.2.0/Luminescence/src/src_ThermoChronometry.cpp | 3 Luminescence-1.2.0/Luminescence/src/src_analyse_IRSARRF_SRS.cpp | 44 Luminescence-1.2.0/Luminescence/src/src_fit_functions.cpp | 8 Luminescence-1.2.0/Luminescence/tests/testthat/_data/OSLdecomposed_1.2.0.rds |only Luminescence-1.2.0/Luminescence/tests/testthat/_data/daybreak-tests |only Luminescence-1.2.0/Luminescence/tests/testthat/setup.R | 17 Luminescence-1.2.0/Luminescence/tests/testthat/test_RLum.Analysis-class.R | 26 Luminescence-1.2.0/Luminescence/tests/testthat/test_RLum.Data.Curve.R | 22 Luminescence-1.2.0/Luminescence/tests/testthat/test_RLum.Data.Image.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_RLum.Data.Spectrum.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_RLum.Results-class.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_Risoe.BINfileData-class.R | 12 Luminescence-1.2.0/Luminescence/tests/testthat/test_Risoe.BINfileData2RLum.Analysis.R | 10 Luminescence-1.2.0/Luminescence/tests/testthat/test_Risoe.BINfileData2RLum.Data.Curve.R | 14 Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_Al2O3C_CrossTalk.R | 35 Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_Al2O3C_ITC.R | 25 Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_Al2O3C_Measurement.R | 19 Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_FadingMeasurement.R | 118 - Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_IRSAR.RF.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_SAR.CWOSL.R | 688 +++++-- Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_SAR.TL.R | 72 Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_ThermochronometryData.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_baSAR.R | 320 ++- Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_pIRIRSequence.R | 191 -- Luminescence-1.2.0/Luminescence/tests/testthat/test_analyse_portableOSL.R | 84 Luminescence-1.2.0/Luminescence/tests/testthat/test_apply_EfficiencyCorrection.R | 59 Luminescence-1.2.0/Luminescence/tests/testthat/test_as_latex_table.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_bin_RLumData.R | 17 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_AverageDose.R | 28 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_CentralDose.R | 10 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_CobbleDoseRate.R | 27 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_CommonDose.R | 14 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_CosmicDoseRate.R | 10 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_EED_Model.R | 14 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_FastRatio.R | 7 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_FiniteMixture.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_FuchsLang2001.R | 8 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_HomogeneityTest.R | 7 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_Lamothe2003.R | 6 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_MaxDose.R | 16 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_MinDose.R | 84 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_MoransI.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_OSLLxTxDecomposed.R | 23 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_OSLLxTxRatio.R | 369 ++- Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_TLLxTxRatio.R | 89 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_ThermalLifetime.R | 6 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_WodaFuchs2008.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_gSGC.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_calc_gSGC_feldspar.R | 3 Luminescence-1.2.0/Luminescence/tests/testthat/test_combine_De_Dr.R | 16 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_Activity2Concentration.R | 3 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_CW2pX.R | 101 - Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_Concentration2DoseRate.R | 36 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_Daybreak2CSV.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_PSL2CSV.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_PSL2RisoeBINfiledata.R | 16 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_RLum2Risoe.BINfileData.R | 23 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_SG2MG.R | 44 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_Second2Gray.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_convert_XSYG2CSV.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_correct_PMTLinearity.R | 64 Luminescence-1.2.0/Luminescence/tests/testthat/test_extract_IrradiationTimes.R | 29 Luminescence-1.2.0/Luminescence/tests/testthat/test_fit_CWCurve.R | 17 Luminescence-1.2.0/Luminescence/tests/testthat/test_fit_DoseResponseCurve.R | 7 Luminescence-1.2.0/Luminescence/tests/testthat/test_fit_IsothermalHolding.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_fit_LMCurve.R | 54 Luminescence-1.2.0/Luminescence/tests/testthat/test_fit_OSLLifeTimes.R | 6 Luminescence-1.2.0/Luminescence/tests/testthat/test_fit_SurfaceExposure.R | 14 Luminescence-1.2.0/Luminescence/tests/testthat/test_internals.R | 263 ++ Luminescence-1.2.0/Luminescence/tests/testthat/test_internals_Thermochronometry.R | 8 Luminescence-1.2.0/Luminescence/tests/testthat/test_merge_RLum.Data.Spectrum.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_merge_RLum.Results.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_merge_Risoe.BINfileData.R | 16 Luminescence-1.2.0/Luminescence/tests/testthat/test_methods_S3.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_names_RLum.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_normalise_RLum.R |only Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_AbanicoPlot.R | 25 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_DRCSummary.R | 22 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_DRTResults.R | 29 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_DetPlot.R | 146 + Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_DoseResponseCurve.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_GrowthCurve.R | 17 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_Histogram.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_KDE.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_NRt.R | 14 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_RLum.Analysis.R | 6 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_RLum.Data.Curve.R | 6 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_RLum.Data.Spectrum.R | 37 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_RLum.R | 43 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_RLum.Results.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_RadialPlot.R | 16 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_Risoe.BINfileData.R | 11 Luminescence-1.2.0/Luminescence/tests/testthat/test_plot_ViolinPlot.R | 4 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_BIN2R.R | 39 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_BINXLOG2R.R |only Luminescence-1.2.0/Luminescence/tests/testthat/test_read_Daybreak2R.R | 48 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_HeliosOSL2R.R | 11 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_PSL2R.R | 57 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_RF2R.R | 10 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_SPE2R.R | 37 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_TIFF2R.R | 14 Luminescence-1.2.0/Luminescence/tests/testthat/test_read_XSYG2R.R | 29 Luminescence-1.2.0/Luminescence/tests/testthat/test_remove_SignalBackground.R | 23 Luminescence-1.2.0/Luminescence/tests/testthat/test_report_RLum.R | 12 Luminescence-1.2.0/Luminescence/tests/testthat/test_subset_RLum.R | 44 Luminescence-1.2.0/Luminescence/tests/testthat/test_subset_SingleGrainData.R | 25 Luminescence-1.2.0/Luminescence/tests/testthat/test_trim_RLum.Data.R | 2 Luminescence-1.2.0/Luminescence/tests/testthat/test_use_DRAC.R | 7 Luminescence-1.2.0/Luminescence/tests/testthat/test_write_R2TIFF.R | 5 Luminescence-1.2.0/Luminescence/tests/testthat/test_write_RLum2CSV.R | 7 Luminescence-1.2.0/Luminescence/tests/testthat/test_zzz.R | 1 427 files changed, 10871 insertions(+), 7497 deletions(-)
Title: Read Hierarchical Fixed Width Files
Description: Read hierarchical fixed width files like those commonly used by
many census data providers. Also allows for reading of data in chunks,
and reading 'gzipped' files without storing the full file in memory.
Author: Greg Freedman Ellis [aut],
Derek Burk [aut, cre],
Joe Grover [ctb],
Mark Padgham [ctb],
Hadley Wickham [ctb] ,
Jim Hester [ctb] ,
Romain Francois [ctb] ,
R Core Team [ctb] ,
RStudio [cph, fnd] ,
Jukka Jylaenki [ctb, cph] ,
Mikkel Joergensen [ctb, cph] [...truncated...]
Maintainer: Derek Burk <ipums+cran@umn.edu>
Diff between hipread versions 0.2.5 dated 2025-06-19 and 0.2.6 dated 2026-03-12
DESCRIPTION | 8 - MD5 | 10 +- NEWS.md | 4 R/col_specs.R | 242 +++++++++++++++++++++++++++++----------------------------- man/hip_rt.Rd | 2 src/iconv.cpp | 2 6 files changed, 136 insertions(+), 132 deletions(-)
Title: Design and Analysis of Hierarchical Composite Endpoints
Description: Simulate and analyze hierarchical composite endpoints. Includes implementation for the kidney hierarchical composite endpoint as defined in Heerspink HL et al (2023) “Development and validation of a new hierarchical composite end point for clinical trials of kidney disease progression” (Journal of the American Society of Nephrology 34 (2): 2025–2038, <doi:10.1681/ASN.0000000000000243>). Win odds, also called Wilcoxon-Mann-Whitney or success odds, is the main analysis method. Other win statistics (win probability, win ratio, net benefit) are also implemented in the univariate case, provided there is no censoring. The win probability analysis is based on the Brunner-Munzel test and uses the DeLong-DeLong-Clarke-Pearson variance estimator, as described by Brunner and Konietschke (2025) in “An unbiased rank-based estimator of the Mann–Whitney variance including the case of ties” (Statistical Papers 66 (1): 20, <doi:10.1007/s00362-024-01635-0>). Includes implementation of a new [...truncated...]
Author: Samvel B. Gasparyan [aut, cre]
Maintainer: Samvel B. Gasparyan <gasparyan.co@gmail.com>
Diff between hce versions 0.9.0 dated 2026-01-29 and 0.9.1 dated 2026-03-12
DESCRIPTION | 8 - MD5 | 28 ++-- NEWS.md | 21 +++ R/simKHCE.R | 66 +++++----- R/simTTE.R | 7 - inst/doc/Introduction.html | 2 inst/doc/Wins.Rmd | 6 inst/doc/Wins.html | 18 ++ inst/doc/hce.R | 39 ++++- inst/doc/hce.Rmd | 142 ++++++++++++++++----- inst/doc/hce.html | 297 +++++++++++++++++++++++++++++++-------------- inst/doc/maraca.html | 2 man/simKHCE.Rd | 23 +-- vignettes/Wins.Rmd | 6 vignettes/hce.Rmd | 142 ++++++++++++++++----- 15 files changed, 575 insertions(+), 232 deletions(-)
Title: Fast Agent-Based Epi Models
Description: A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.
Author: George Vega Yon [aut, cre] ,
Derek Meyer [aut] ,
Andrew Pulsipher [aut] ,
Susan Holmes [rev] ,
Abinash Satapathy [rev] ,
Carinogurjao [rev],
Centers for Disease Control and Prevention [fnd]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between epiworldR versions 0.12.0.0 dated 2026-02-21 and 0.13.0.0 dated 2026-03-12
DESCRIPTION | 6 MD5 | 126 +++--- NEWS.md | 13 R/agents-methods.R | 6 build/vignette.rds |binary inst/doc/advanced-modeling.html | 28 - inst/doc/getting-started.html | 60 +- inst/doc/likelihood-free-mcmc.html | 26 - inst/doc/mixing.html | 40 - inst/doc/run-multiple.html | 20 inst/include/epiworld/adjlist-meat.hpp | 8 inst/include/epiworld/agent-bones.hpp | 69 +-- inst/include/epiworld/agent-events-meat.hpp | 32 - inst/include/epiworld/agent-meat-state.hpp | 12 inst/include/epiworld/agent-meat-virus-sampling.hpp | 34 - inst/include/epiworld/agent-meat.hpp | 222 ++++------- inst/include/epiworld/agentssample-bones.hpp | 4 inst/include/epiworld/config.hpp | 9 inst/include/epiworld/entity-bones.hpp | 22 - inst/include/epiworld/entity-distribute-meat.hpp | 10 inst/include/epiworld/entity-meat.hpp | 50 -- inst/include/epiworld/epiworld.hpp | 45 ++ inst/include/epiworld/globalevent-bones.hpp | 4 inst/include/epiworld/globalevent-meat.hpp | 6 inst/include/epiworld/math/lfmcmc/lfmcmc-bones.hpp | 9 inst/include/epiworld/math/lfmcmc/lfmcmc-meat.hpp | 8 inst/include/epiworld/model-bones.hpp | 63 +-- inst/include/epiworld/model-meat-print.hpp | 6 inst/include/epiworld/model-meat.hpp | 171 +++++--- inst/include/epiworld/models/diffnet.hpp | 25 - inst/include/epiworld/models/globalevents.hpp | 8 inst/include/epiworld/models/init-functions.hpp | 30 - inst/include/epiworld/models/measlesmixing.hpp | 137 +++--- inst/include/epiworld/models/measlesmixingriskquarantine.hpp | 115 ++--- inst/include/epiworld/models/measlesschool.hpp | 107 ++--- inst/include/epiworld/models/seir.hpp | 24 - inst/include/epiworld/models/seirconnected.hpp | 51 +- inst/include/epiworld/models/seird.hpp | 28 - inst/include/epiworld/models/seirdconnected.hpp | 56 +- inst/include/epiworld/models/seirmixing.hpp | 64 +-- inst/include/epiworld/models/seirmixingquarantine.hpp | 122 ++---- inst/include/epiworld/models/sir.hpp | 10 inst/include/epiworld/models/sirconnected.hpp | 46 +- inst/include/epiworld/models/sird.hpp | 10 inst/include/epiworld/models/sirdconnected.hpp | 52 +- inst/include/epiworld/models/sirlogit.hpp | 42 -- inst/include/epiworld/models/sirmixing.hpp | 50 +- inst/include/epiworld/models/sis.hpp | 10 inst/include/epiworld/models/sisd.hpp | 10 inst/include/epiworld/models/surveillance.hpp | 59 +- inst/include/epiworld/randgraph.hpp | 16 inst/include/epiworld/random_graph.hpp | 12 inst/include/epiworld/rng-utils.hpp |only inst/include/epiworld/tool-bones.hpp | 41 +- inst/include/epiworld/tool-distribute-meat.hpp | 9 inst/include/epiworld/tool-meat.hpp | 10 inst/include/epiworld/tools |only inst/include/epiworld/virus-bones.hpp | 2 inst/include/epiworld/virus-distribute-meat.hpp | 9 inst/include/epiworld/virus-meat.hpp | 14 inst/tinytest/test-lfmcmc.R | 21 - inst/tinytest/test-sird.R | 7 src/agents.cpp | 14 src/entities.cpp | 6 src/lfmcmc.cpp | 2 65 files changed, 1177 insertions(+), 1151 deletions(-)
Title: Linear Programming Discriminant Analysis
Description: Classification method obtained through linear programming.
It is advantageous with respect to the classical developments when the distribution of the variables
involved is unknown or when the number of variables is much greater than the number of individuals.
Mathematical details behind the method are published in Nueda, et al. (2022) "LPDA: A new classification method based on linear programming".
<doi:10.1371/journal.pone.0270403>.
Author: Maria Jose Nueda [aut, cre]
Maintainer: Maria Jose Nueda <mj.nueda@ua.es>
Diff between lpda versions 1.2.2 dated 2025-10-27 and 1.2.3 dated 2026-03-12
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/lpda.R | 2 +- build/vignette.rds |binary inst/doc/lpdaUsersGuide.html | 24 ++++++++++++------------ 6 files changed, 25 insertions(+), 21 deletions(-)
Title: Time-Varying Coefficient for Single and Multi-Equation
Regressions
Description: Fitting time-varying coefficient models for single and multi-equation regressions, using kernel smoothing techniques.
Author: Isabel Casas [aut, cre],
Ruben Fernandez-Casal [aut]
Maintainer: Isabel Casas <casasis@gmail.com>
Diff between tvReg versions 0.5.9 dated 2023-09-01 and 0.5.10 dated 2026-03-12
tvReg-0.5.10/tvReg/DESCRIPTION | 10 tvReg-0.5.10/tvReg/MD5 | 67 - tvReg-0.5.10/tvReg/NEWS.md | 208 ++-- tvReg-0.5.10/tvReg/R/bw.R | 178 +-- tvReg-0.5.10/tvReg/R/forecast_tvreg.R |only tvReg-0.5.10/tvReg/R/plot_tvReg.R | 6 tvReg-0.5.10/tvReg/R/tvBOOT.R | 329 +++--- tvReg-0.5.10/tvReg/R/tvIRF.R | 29 tvReg-0.5.10/tvReg/R/tvLM.R | 274 ++--- tvReg-0.5.10/tvReg/R/tvPsi.R | 25 tvReg-0.5.10/tvReg/R/tvReg-package.R | 11 tvReg-0.5.10/tvReg/R/tvSURE.R | 688 +++++++------- tvReg-0.5.10/tvReg/R/tvVAR.R | 286 ++--- tvReg-0.5.10/tvReg/README.md |only tvReg-0.5.10/tvReg/build/vignette.rds |binary tvReg-0.5.10/tvReg/inst/CITATION | 10 tvReg-0.5.10/tvReg/inst/doc/tvReg.R | 34 tvReg-0.5.10/tvReg/inst/doc/tvReg.Rmd | 19 tvReg-0.5.10/tvReg/inst/doc/tvReg.html | 1432 +++++++++++++++++++++--------- tvReg-0.5.10/tvReg/man/CEES.Rd | 1 tvReg-0.5.10/tvReg/man/FF5F.Rd | 1 tvReg-0.5.10/tvReg/man/OECD.Rd | 1 tvReg-0.5.10/tvReg/man/RV.Rd | 1 tvReg-0.5.10/tvReg/man/bw.Rd | 23 tvReg-0.5.10/tvReg/man/bwCov.Rd | 7 tvReg-0.5.10/tvReg/man/forecast-tvReg.Rd | 2 tvReg-0.5.10/tvReg/man/tvCor.Rd | 2 tvReg-0.5.10/tvReg/man/tvCov.Rd | 4 tvReg-0.5.10/tvReg/man/tvIRF.Rd | 16 tvReg-0.5.10/tvReg/man/tvPsi.Rd | 12 tvReg-0.5.10/tvReg/man/tvReg-internals.Rd | 3 tvReg-0.5.10/tvReg/man/tvReg-package.Rd | 7 tvReg-0.5.10/tvReg/man/tvSURE.Rd | 8 tvReg-0.5.10/tvReg/man/tvVAR.Rd | 6 tvReg-0.5.10/tvReg/vignettes/tvReg.Rmd | 19 tvReg-0.5.9/tvReg/R/forecast_tvReg.R |only 36 files changed, 2180 insertions(+), 1539 deletions(-)
Title: Optimum Sample Allocation in Stratified Sampling
Description: Provides exact analytical algorithms for computing optimum sample
allocations in stratified sampling.
Supports classical Neyman-Tschuprow allocation, minimum-cost allocation under
a variance constraint, and multi-domain allocation with controlled precision.
Handles lower and upper bounds, cost constraints, and multiple domains.
Includes helper functions for variance computation, allocation summaries,
rounding, and example datasets for testing and benchmarking.
Author: Wojciech Wojciak [aut, cre],
Jacek Wesolowski [sad],
Robert Wieczorkowski [ctb]
Maintainer: Wojciech Wojciak <wojciech.wojciak@gmail.com>
Diff between stratallo versions 3.0.0 dated 2026-03-12 and 3.0.1 dated 2026-03-12
DESCRIPTION | 6 ++-- MD5 | 16 ++++++------ build/partial.rdb |binary inst/doc/stratallo.html | 4 +-- tests/testthat/test-alg_dca.R | 50 +++++++++++++++++++-------------------- tests/testthat/test-alg_rdca.R | 26 +++++++++----------- tests/testthat/test-alg_rna.R | 6 ++-- tests/testthat/test-alg_rnabox.R | 4 +-- tests/testthat/test-dopt.R | 5 +-- 9 files changed, 57 insertions(+), 60 deletions(-)
Title: Progression Models for Repeated Measures
Description: A progression model for repeated measures (PMRM)
is a continuous-time nonlinear mixed-effects model for
longitudinal clinical trials in progressive diseases.
Unlike mixed models for repeated measures (MMRMs),
which estimate treatment effects as linear combinations
of additive effects on the outcome scale,
PMRMs characterize treatment effects
in terms of the underlying disease trajectory.
This framing yields clinically interpretable quantities
such as average time saved
and percent reduction in decline due to treatment.
This package implements frequentist PMRMs by
Raket (2022) <doi:10.1002/sim.9581> using
'RTMB' by Kristensen (2016) <doi:10.18637/jss.v070.i05>.
Author: William Michael Landau [aut, cre] ,
Lars Lau Raket [aut] ,
Kasper Kristensen [aut] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between pmrm versions 0.0.2 dated 2026-01-30 and 0.0.3 dated 2026-03-12
DESCRIPTION | 6 +- MD5 | 36 +++++++------- NEWS.md | 6 ++ R/pmrm_data.R | 46 +++++++++++++----- R/predict.R | 75 +++++++++++++++++++++++------- README.md | 5 +- inst/CITATION | 1 inst/doc/models.html | 17 ++---- inst/doc/usage.html | 27 +++++----- inst/doc/validation.html | 5 +- man/pmrm_data.Rd | 20 +++++++- man/pmrm_model.Rd | 5 +- man/pmrm_model_decline_nonproportional.Rd | 5 +- man/pmrm_model_decline_proportional.Rd | 5 +- man/pmrm_model_slowing_nonproportional.Rd | 5 +- man/pmrm_model_slowing_proportional.Rd | 5 +- tests/testthat/test-predict.R | 2 vignettes/validation/coverage.png |binary vignettes/validation/version.csv | 2 19 files changed, 189 insertions(+), 84 deletions(-)
Title: Signal Component Analysis for Optically Stimulated Luminescence
Description: Function library for the identification and separation of exponentially
decaying signal components in continuous-wave optically stimulated luminescence measurements.
A special emphasis is laid on luminescence dating with quartz, which is known for
systematic errors due to signal components with unequal physical behaviour.
Also, this package enables an easy to use signal decomposition of
data sets imported and analysed with the R package 'Luminescence'.
This includes the optional automatic creation of HTML reports. Further information and tutorials
can be found at <https://luminescence.de>.
Author: Dirk Mittelstrass [aut, cre] ,
Sebastian Kreutzer [aut] ,
Christoph Schmidt [aut] ,
Marco Colombo [aut] ,
Jan Beyer [ths] ,
Johannes Heitmann [ths],
Arno Straessner [ths]
Maintainer: Dirk Mittelstrass <dirk.mittelstrass@luminescence.de>
Diff between OSLdecomposition versions 1.1.0 dated 2025-08-31 and 1.2 dated 2026-03-12
DESCRIPTION | 17 - MD5 | 66 +++--- NAMESPACE | 1 NEWS.md | 76 +++++++ R/OSLdecomposition-package.R | 3 R/RLum.OSL_correction.R | 206 +++++++++++++------ R/RLum.OSL_decomposition.R | 174 +++++++++++----- R/RLum.OSL_global_fitting.R | 80 ++++--- R/check_RLum.Data.R |only R/decompose_OSLcurve.R | 5 R/fit_OSLcurve.R | 93 ++++----- R/optimise_OSLintervals.R | 5 R/plot_MultiExponential.R | 8 R/plot_OSLcurve.R | 10 R/plot_PhotoCrosssections.R | 5 R/simulate_OSLcomponents.R | 5 R/sum_OSLcurves.R | 372 +++++++++++++++++++++--------------- README.md | 6 inst/examples/example_CW.OSL.Data.R | 6 inst/examples/example_FB.R | 10 inst/rmd/report_Step2.Rmd | 37 ++- man/OSLdecomposition-package.Rd | 4 man/RLum.OSL_correction.Rd | 46 ++-- man/RLum.OSL_decomposition.Rd | 23 +- man/RLum.OSL_global_fitting.Rd | 19 + man/check_RLum.Data.Rd |only man/decompose_OSLcurve.Rd | 5 man/fit_OSLcurve.Rd | 13 - man/optimise_OSLintervals.Rd | 5 man/plot_MultiExponential.Rd | 312 ++++++++++++++---------------- man/plot_OSLcurve.Rd | 7 man/plot_PhotoCrosssections.Rd | 5 man/simulate_OSLcomponents.Rd | 5 man/sum_OSLcurves.Rd | 50 ++-- tests |only 35 files changed, 988 insertions(+), 691 deletions(-)
More information about OSLdecomposition at CRAN
Permanent link
Title: An R Package of Minorization-Maximization Algorithm via the
Assembly--Decomposition Technology
Description: The minorization-maximization (MM) algorithm is a powerful tool for maximizing nonconcave target function. However, for most existing MM algorithms, the surrogate function in the minorization step is constructed in a case-specific manner and requires manual programming. To address this limitation, we develop the R package MMAD, which systematically integrates the assembly--decomposition technology in the MM framework. This new package provides a comprehensive computational toolkit for one-stop inference of complex target functions, including function construction, evaluation, minorization and optimization via MM algorithm. By representing the target function through a hierarchical composition of assembly functions, we design a hierarchical algorithmic structure that supports both bottom-up operations (construction, evaluation) and top-down operation (minorization).
Author: Xifen Huang [aut],
Jinfeng Xu [aut],
Jiaqi Gu [aut, cre]
Maintainer: Jiaqi Gu <jiaqigu@usf.edu>
Diff between MMAD versions 2.0 dated 2025-11-26 and 2.0.1 dated 2026-03-12
DESCRIPTION | 12 +++++++----- MD5 | 2 +- 2 files changed, 8 insertions(+), 6 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.4.4 dated 2026-02-26 and 0.4.5 dated 2026-03-12
DESCRIPTION | 6 +-- MD5 | 64 ++++++++++++++++++---------------- NEWS.md | 14 +++++++ R/cms_download_native.R | 6 +-- R/cms_download_subset.r | 72 +++++++++++++++++++++++++-------------- R/cms_product_details.r | 70 +++++++++++++++++++------------------ R/cms_product_metadata.r | 63 +++++++++++++++++----------------- R/cms_product_services.r | 1 R/cms_products_list.r | 3 + R/generics.r | 9 ++-- R/init.R | 10 ++--- README.md | 5 ++ build/vignette.rds |binary inst/doc/product-info.R |only inst/doc/product-info.Rmd |only inst/doc/product-info.html |only inst/doc/proxy.R | 13 +++++-- inst/doc/proxy.Rmd | 18 +++++++-- inst/doc/proxy.html | 68 +++++++++++++++++------------------- inst/doc/translate.R | 2 - inst/doc/translate.Rmd | 2 - inst/doc/translate.html | 6 ++- man/cms_download_subset.Rd | 16 +++----- man/cms_product_details.Rd | 3 + man/cms_product_metadata.Rd | 3 + man/cms_product_services.Rd | 3 + man/cms_products_list.Rd | 5 ++ man/cms_wmts.Rd | 2 - man/cms_zarr_proxy.Rd | 2 - man/figures/README-leaflet-1.png |binary tests/testthat/test_native.r | 13 +++++++ tests/testthat/test_subset.r | 33 +++++++++++++++++ vignettes/product-info.Rmd |only vignettes/proxy.Rmd | 18 +++++++-- vignettes/translate.Rmd | 2 - 35 files changed, 331 insertions(+), 201 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Title: Estimation Statistics with Confidence Intervals
Description: A collection of functions and 'jamovi' module for the estimation approach to inferential statistics, the approach which emphasizes effect sizes, interval estimates, and meta-analysis. Nearly all functions are based on 'statpsych' and 'metafor'. This package is still under active development, and breaking changes are likely, especially with the plot and hypothesis test functions. Data sets are included for all examples from Cumming & Calin-Jageman (2024) <ISBN:9780367531508>.
Author: Robert Calin-Jageman [aut, cre, cph]
Maintainer: Robert Calin-Jageman <rcalinjageman@dom.edu>
Diff between esci versions 1.0.9 dated 2026-01-16 and 1.0.10 dated 2026-03-12
DESCRIPTION | 6 +-- MD5 | 72 ++++++++++++++++++++++---------------------- NEWS.md | 9 ++++- R/jamovi_meta_functions.R | 4 +- R/jamovimetamdiff.b.R | 1 R/jamovimetamdiff.h.R | 15 +++++++++ R/jamovimetamean.b.R | 1 R/jamovimetamean.h.R | 15 +++++++++ R/jamovimetapdiff.b.R | 1 R/jamovimetapdiff.h.R | 15 +++++++++ R/jamovimetaproportion.b.R | 1 R/jamovimetaproportion.h.R | 15 +++++++++ R/jamovimetar.b.R | 2 - R/jamovimetar.h.R | 15 +++++++++ R/meta_any.R | 12 +++++-- R/meta_d1.R | 6 +++ R/meta_d2.R | 5 +++ R/meta_mdiff_two.R | 5 +++ R/meta_mean.R | 5 +++ R/meta_pdiff_two.R | 5 +++ R/meta_proportion.R | 5 +++ R/meta_r.R | 5 +++ build/stage23.rdb |binary man/geom_meta_diamond_h.Rd | 8 +++- man/jamovimetamdiff.Rd | 3 + man/jamovimetamean.Rd | 3 + man/jamovimetapdiff.Rd | 3 + man/jamovimetaproportion.Rd | 3 + man/jamovimetar.Rd | 3 + man/meta_any.Rd | 4 ++ man/meta_d1.Rd | 4 ++ man/meta_d2.Rd | 4 ++ man/meta_mdiff_two.Rd | 4 ++ man/meta_mean.Rd | 4 ++ man/meta_pdiff_two.Rd | 4 ++ man/meta_proportion.Rd | 4 ++ man/meta_r.Rd | 4 ++ 37 files changed, 225 insertions(+), 50 deletions(-)
Title: A Graphical User Interface for the 'yuima' Package
Description: Provides a graphical user interface for the 'yuima' package.
Author: YUIMA Project Team [aut],
Emanuele Guidotti [cre]
Maintainer: Emanuele Guidotti <emanuele.guidotti@usi.ch>
Diff between yuimaGUI versions 1.3.1 dated 2022-08-11 and 1.4.0 dated 2026-03-12
yuimaGUI-1.3.1/yuimaGUI/inst/yuimaGUI/ui/load_data/yourData.R |only yuimaGUI-1.4.0/yuimaGUI/DESCRIPTION | 19 yuimaGUI-1.4.0/yuimaGUI/MD5 | 55 yuimaGUI-1.4.0/yuimaGUI/R/sourceCodeYuimaGUI.R | 2 yuimaGUI-1.4.0/yuimaGUI/README.md |only yuimaGUI-1.4.0/yuimaGUI/inst/CITATION | 110 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/global.R | 170 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/rsconnect |only yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/eda/changepoint_non_parametric.R | 315 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/eda/changepoint_parametric.R | 1065 +-- yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/eda/clustering.R | 448 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/eda/llag_and_corr.R | 522 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/finance/profit_and_loss.R | 550 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/functions.R | 3436 +++++----- yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/load_data/finance.R | 184 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/load_data/your_file.R | 274 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/modeling/multivariate_results.R | 663 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/modeling/multivariate_start_estimation.R | 1162 +-- yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/modeling/univariate_results.R | 650 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/modeling/univariate_start_estimation.R | 1205 +-- yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/simulation/multivariate_estimated.R | 676 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/simulation/multivariate_non_estimated.R | 334 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/simulation/multivariate_results.R | 494 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/simulation/univariate_estimated.R | 652 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/simulation/univariate_non_estimated.R | 318 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/server/simulation/univariate_results.R | 310 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/ui.R | 138 yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/ui/eda/changepoint.R | 422 - yuimaGUI-1.4.0/yuimaGUI/inst/yuimaGUI/ui/load_data/finData.R | 94 yuimaGUI-1.4.0/yuimaGUI/man/yuimaGUI.Rd | 2 30 files changed, 7220 insertions(+), 7050 deletions(-)
Title: Sparse Learning with Convex and Concave Penalties
Description: Fast tools for fitting sparse generalized linear models with convex
penalties (lasso) and concave penalties (smoothly clipped absolute
deviation and minimax concave penalty). Computation uses multi-stage convex
relaxation and pathwise coordinate optimization with warm starts,
active-set updates, and screening rules. Core solvers are implemented in
C++, and coefficient paths are stored as sparse matrices for memory
efficiency.
Author: Jason Ge [aut],
Xingguo Li [aut],
Haoming Jiang [aut],
Mengdi Wang [aut],
Tong Zhang [aut],
Han Liu [aut],
Tuo Zhao [aut, cre],
Gael Guennebaud [ctb] ,
Benoit Jacob [ctb] ,
Eigen Library Authors [cph]
Maintainer: Tuo Zhao <tourzhao@gatech.edu>
Diff between picasso versions 1.4.1 dated 2026-03-10 and 1.5 dated 2026-03-12
picasso-1.4.1/picasso/src/src |only picasso-1.5/picasso/DESCRIPTION | 6 picasso-1.5/picasso/MD5 | 56 - picasso-1.5/picasso/R/gaussian_solver.R | 30 - picasso-1.5/picasso/R/logit_solver.R | 52 - picasso-1.5/picasso/R/picasso.R | 36 - picasso-1.5/picasso/R/picasso.gaussian.R | 84 +- picasso-1.5/picasso/R/picasso.logit.R | 27 picasso-1.5/picasso/R/picasso.poisson.R | 30 - picasso-1.5/picasso/R/picasso.sqrtlasso.R | 28 picasso-1.5/picasso/R/picasso_utils.R | 19 picasso-1.5/picasso/R/poisson_solver.R | 49 - picasso-1.5/picasso/R/sqrtlasso_solver.R | 49 - picasso-1.5/picasso/inst/doc/vignette.pdf |binary picasso-1.5/picasso/man/picasso.Rd | 26 picasso-1.5/picasso/src/c_api |only picasso-1.5/picasso/src/include/picasso/actgd.hpp | 3 picasso-1.5/picasso/src/include/picasso/actnewton.hpp | 3 picasso-1.5/picasso/src/include/picasso/c_api.hpp | 10 picasso-1.5/picasso/src/include/picasso/objective.hpp | 52 + picasso-1.5/picasso/src/include/picasso/solver_params.hpp | 14 picasso-1.5/picasso/src/objective |only picasso-1.5/picasso/src/picasso-all0.cpp | 15 picasso-1.5/picasso/src/picasso_R.cpp | 411 ++++++++------ picasso-1.5/picasso/src/solver |only 25 files changed, 586 insertions(+), 414 deletions(-)
Title: Forecast Reconciliation
Description: Classical (bottom-up and top-down), optimal combination and heuristic
point (Di Fonzo and Girolimetto, 2023 <doi:10.1016/j.ijforecast.2021.08.004>) and
probabilistic (Girolimetto et al. 2024 <doi:10.1016/j.ijforecast.2023.10.003>)
forecast reconciliation procedures for linearly constrained time series
(e.g., hierarchical or grouped time series) in cross-sectional, temporal,
or cross-temporal frameworks.
Author: Daniele Girolimetto [aut, cre] ,
Tommaso Di Fonzo [aut] ,
Yangzhuoran Fin Yang [ctb]
Maintainer: Daniele Girolimetto <daniele.girolimetto@unipd.it>
Diff between FoReco versions 1.1.0 dated 2025-06-07 and 1.2.0 dated 2026-03-12
DESCRIPTION | 30 MD5 | 160 ++--- NAMESPACE | 19 NEWS.md | 163 +++-- R/FoReco-package.R | 2 R/boot.R | 179 +++-- R/bottomup.R | 225 ++++--- R/cov_cs.R | 193 ++++-- R/cov_ct.R | 813 +++++++++++++++++++-------- R/cov_te.R | 394 +++++++++---- R/data.R | 66 +- R/foreco_info.R |only R/fun.R | 22 R/fun_export.R | 747 +++++++++++++----------- R/fun_residuals.R | 71 +- R/matrix_layout.R |only R/middleout.R | 281 ++++++--- R/reco_fun.R | 1264 +++++++++++++++++++++++++++--------------- R/reco_gauss.R |only R/reco_heu.R | 617 ++++++++++++-------- R/reco_lcc.R | 559 ++++++++++++------ R/reco_opt.R | 995 ++++++++++++++++++++------------- R/reco_sample.R |only R/topdown.R | 194 ++++-- README.md | 20 build/partial.rdb |binary inst/CITATION | 84 +- man/FoReco-package.Rd | 10 man/FoReco2matrix.Rd | 33 - man/aggts.Rd | 24 man/balance_hierarchy.Rd | 39 - man/commat.Rd | 4 man/csboot.Rd | 12 man/csbu.Rd | 44 - man/cscov.Rd | 80 +- man/cslcc.Rd | 158 +++-- man/csmo.Rd | 21 man/csmvn.Rd |only man/csprojmat.Rd | 41 - man/csrec.Rd | 233 ++++--- man/cssmp.Rd |only man/cstd.Rd | 15 man/cstools.Rd | 24 man/ctboot.Rd | 21 man/ctbu.Rd | 65 +- man/ctcov.Rd | 116 ++- man/ctlcc.Rd | 193 +++--- man/ctmatrix_layouts.Rd |only man/ctmo.Rd | 41 - man/ctmvn.Rd |only man/ctprojmat.Rd | 58 + man/ctrec.Rd | 263 +++++--- man/ctsmp.Rd |only man/cttd.Rd | 29 man/cttools.Rd | 42 - man/df2aggmat.Rd | 27 man/figures/logo.svg | 455 +++------------ man/heuristic-reco.Rd | 29 man/itagdp.Rd | 30 man/iterec.Rd | 29 man/lcmat.Rd | 4 man/new_foreco_info.Rd |only man/recoinfo.Rd | 25 man/residuals.Rd | 46 - man/roxygen/meta.R | 1 man/set_bounds.Rd | 30 man/shrink_estim.Rd | 18 man/shrink_oasd.Rd | 24 man/teboot.Rd | 16 man/tebu.Rd | 56 + man/tecov.Rd | 82 +- man/telcc.Rd | 175 +++-- man/tematrix_layouts.Rd |only man/temo.Rd | 27 man/temvn.Rd |only man/teprojmat.Rd | 37 - man/terec.Rd | 198 ++++-- man/tesmp.Rd |only man/tetd.Rd | 21 man/tetools.Rd | 20 man/unbalance_hierarchy.Rd | 31 - man/vndata.Rd | 36 - tests/testthat/test-cs.R | 476 ++++++++++++--- tests/testthat/test-csprob.R |only tests/testthat/test-ct.R | 605 +++++++++++++++----- tests/testthat/test-fun_exp.R | 2 tests/testthat/test-fun_res.R | 22 tests/testthat/test-te.R | 309 ++++++++-- 88 files changed, 7283 insertions(+), 4212 deletions(-)
Title: Wrapper for the Computational Morphometry Toolkit ('CMTK')
Library
Description: Provides R bindings for selected components of the
Computational Morphometry Toolkit ('CMTK') for image registration and
point transformation. A subset of the 'C++' source code required for point
transforms is bundled with 'cmtkr'. This allows direct calls into the 'CMTK'
library, avoiding command-line invocations and providing
order-of-magnitude speed improvements. Additional 'CMTK' functionality may
be wrapped in future releases. 'CMTK' is described in Rohlfing T and
Maurer CR (2003) <doi:10.1109/titb.2003.808506>.
Author: Gregory Jefferis [aut, cre] ,
Torsten Rohlfing [aut] ),
SRI International [cph] ,
Google, Inc. [cph]
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between cmtkr versions 0.2.2 dated 2026-03-08 and 0.2.3 dated 2026-03-12
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------ NEWS.md | 7 ++++ README.md | 34 ------------------------ src/Makevars.win | 3 ++ src/cmtk/Base/cmtkImageOperationReplace.h | 3 +- src/cmtk/Base/cmtkMathUtil.h | 3 +- src/cmtk/Base/cmtkSincInterpolator.h | 5 ++- src/cmtk/Base/cmtkTemplateArray.txx | 9 +++--- src/cmtk/Base/cmtkUniformVolumeInterpolator.txx | 6 ++-- 10 files changed, 38 insertions(+), 56 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, 'HippUnfold' hippocampal outputs and 'SubCortexMesh'
subcortical 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 1.4.5 dated 2025-12-15 and 1.5.0 dated 2026-03-12
VertexWiseR-1.4.5/VertexWiseR/R/zzz.R |only VertexWiseR-1.4.5/VertexWiseR/data/MNImap_hip.rdata |only VertexWiseR-1.4.5/VertexWiseR/inst/extdata/hip_points_cells.pkl |only VertexWiseR-1.4.5/VertexWiseR/man/MNImap_hip.Rd |only VertexWiseR-1.4.5/VertexWiseR/man/figures/sexdiff.png |only VertexWiseR-1.4.5/VertexWiseR/man/figures/sigcluster.png |only VertexWiseR-1.4.5/VertexWiseR/vignettes/SPRENG_tstatmaps.png |only VertexWiseR-1.4.5/VertexWiseR/vignettes/VertexWiseR_plot_overlay.asis |only VertexWiseR-1.4.5/VertexWiseR/vignettes/VertexWiseR_plot_overlay.html |only VertexWiseR-1.5.0/VertexWiseR/DESCRIPTION | 20 VertexWiseR-1.5.0/VertexWiseR/MD5 | 109 - VertexWiseR-1.5.0/VertexWiseR/NAMESPACE | 3 VertexWiseR-1.5.0/VertexWiseR/NEWS.md | 15 VertexWiseR-1.5.0/VertexWiseR/R/ASEGvextract.R |only VertexWiseR-1.5.0/VertexWiseR/R/DTSERIESvextract.R | 6 VertexWiseR-1.5.0/VertexWiseR/R/FSLRvextract.R | 15 VertexWiseR-1.5.0/VertexWiseR/R/HIPvextract.R | 2 VertexWiseR-1.5.0/VertexWiseR/R/RFT_vertex_analysis.R | 16 VertexWiseR-1.5.0/VertexWiseR/R/SURFvextract.R | 2 VertexWiseR-1.5.0/VertexWiseR/R/TFCE_vertex_analysis.R | 33 VertexWiseR-1.5.0/VertexWiseR/R/TFCE_vertex_analysis_mixed.R | 8 VertexWiseR-1.5.0/VertexWiseR/R/VWRfirstrun.R | 14 VertexWiseR-1.5.0/VertexWiseR/R/classes.r | 12 VertexWiseR-1.5.0/VertexWiseR/R/data.R | 15 VertexWiseR-1.5.0/VertexWiseR/R/getting_started.r | 34 VertexWiseR-1.5.0/VertexWiseR/R/other_functions.R | 282 +++ VertexWiseR-1.5.0/VertexWiseR/R/plot_overlay_surf.r | 715 +++++++--- VertexWiseR-1.5.0/VertexWiseR/R/plot_surf.R | 136 + VertexWiseR-1.5.0/VertexWiseR/R/plot_surf3d.R | 644 ++++++--- VertexWiseR-1.5.0/VertexWiseR/R/smooth_surf.R | 13 VertexWiseR-1.5.0/VertexWiseR/README.md | 8 VertexWiseR-1.5.0/VertexWiseR/build/vignette.rds |binary VertexWiseR-1.5.0/VertexWiseR/inst/doc/Python_troubleshooting.html | 135 + VertexWiseR-1.5.0/VertexWiseR/inst/doc/VertexWiseR_Example_1.html | 8 VertexWiseR-1.5.0/VertexWiseR/inst/doc/VertexWiseR_Example_2.html | 37 VertexWiseR-1.5.0/VertexWiseR/inst/doc/VertexWiseR_Example_3.html |only VertexWiseR-1.5.0/VertexWiseR/inst/doc/VertexWiseR_Example_3.html.asis |only VertexWiseR-1.5.0/VertexWiseR/inst/doc/VertexWiseR_plot_overlay.html |only VertexWiseR-1.5.0/VertexWiseR/inst/doc/VertexWiseR_plot_overlay.html.asis |only VertexWiseR-1.5.0/VertexWiseR/inst/doc/VertexWiseR_surface_extraction.html | 271 ++- VertexWiseR-1.5.0/VertexWiseR/inst/extdata/hip_points_cells.rds |only VertexWiseR-1.5.0/VertexWiseR/inst/python/hipp_plot.py | 2 VertexWiseR-1.5.0/VertexWiseR/inst/python/surfplot_subcortical.py |only VertexWiseR-1.5.0/VertexWiseR/man/ASEGvextract.Rd |only VertexWiseR-1.5.0/VertexWiseR/man/DTSERIESvextract.Rd | 6 VertexWiseR-1.5.0/VertexWiseR/man/FSLRvextract.Rd | 12 VertexWiseR-1.5.0/VertexWiseR/man/MNIsurface-class.Rd | 2 VertexWiseR-1.5.0/VertexWiseR/man/ROImap-class.Rd | 2 VertexWiseR-1.5.0/VertexWiseR/man/edgelist-class.Rd | 2 VertexWiseR-1.5.0/VertexWiseR/man/figures/Flowchart.JPG |binary VertexWiseR-1.5.0/VertexWiseR/man/figures/sexdiff.jpg |only VertexWiseR-1.5.0/VertexWiseR/man/figures/sigcluster.jpg |only VertexWiseR-1.5.0/VertexWiseR/man/hip_points_cells.Rd | 4 VertexWiseR-1.5.0/VertexWiseR/man/plot_overlay_surf.Rd | 17 VertexWiseR-1.5.0/VertexWiseR/man/plot_surf.Rd | 11 VertexWiseR-1.5.0/VertexWiseR/man/plot_surf3d.Rd | 17 VertexWiseR-1.5.0/VertexWiseR/vignettes/Python_troubleshooting.Rmd | 55 VertexWiseR-1.5.0/VertexWiseR/vignettes/VertexWiseR_Example_1.Rmd | 18 VertexWiseR-1.5.0/VertexWiseR/vignettes/VertexWiseR_Example_2.Rmd | 34 VertexWiseR-1.5.0/VertexWiseR/vignettes/VertexWiseR_Example_3.Rmd |only VertexWiseR-1.5.0/VertexWiseR/vignettes/VertexWiseR_Example_3.html.asis |only VertexWiseR-1.5.0/VertexWiseR/vignettes/VertexWiseR_plot_overlay.Rmd | 125 + VertexWiseR-1.5.0/VertexWiseR/vignettes/VertexWiseR_plot_overlay.html.asis |only VertexWiseR-1.5.0/VertexWiseR/vignettes/VertexWiseR_surface_extraction.Rmd | 119 + VertexWiseR-1.5.0/VertexWiseR/vignettes/allaseg_plotsurf3d.jpg |only VertexWiseR-1.5.0/VertexWiseR/vignettes/references.bib | 48 VertexWiseR-1.5.0/VertexWiseR/vignettes/surfextract.jpg |binary 67 files changed, 2216 insertions(+), 811 deletions(-)
Title: Easily Scrape and Process AFL Data
Description: An easy package for scraping and processing Australia Rules Football (AFL)
data. 'fitzRoy' provides a range of functions for accessing publicly available data
from 'AFL Tables' <https://afltables.com/afl/afl_index.html>, 'Footy Wire' <https://www.footywire.com> and
'The Squiggle' <https://squiggle.com.au>. Further functions allow for easy processing,
cleaning and transformation of this data into formats that can be used for analysis.
Author: James Day [cre, aut],
Robert Nguyen [aut],
Matthew Erbs [ctb],
Oscar Lane [aut],
Jason Zivkovic [ctb],
Jacob Holden [ctb]
Maintainer: James Day <jamesthomasday@gmail.com>
Diff between fitzRoy versions 1.6.0 dated 2024-12-10 and 1.7.0 dated 2026-03-12
DESCRIPTION | 6 - MD5 | 69 ++++++++----- NAMESPACE | 10 + R/fetch-outofcontract.R |only R/fetch-player-details.R | 82 +++++++++++----- R/fetch-player-stats.R | 32 ++++-- R/fetch_awards.R |only R/fetch_supercoach_dreamteam.R |only R/fetch_team_stats.R |only R/helpers-afl.R | 97 ++++++++++++++----- R/helpers-afltables-playerstats.R | 6 - R/helpers-afltables.R | 1 R/helpers-footywire.R | 117 +++++++++-------------- R/helpers-general.R | 116 ++++++++++++++++++++++ R/plot-score-worm.R | 12 +- inst/WORDLIST | 11 +- inst/doc/elo-ratings-example.html | 4 inst/doc/main-fetch-functions.Rmd | 1 inst/doc/main-fetch-functions.html | 2 man/fetch_awards.Rd |only man/fetch_awards_allaustralian.Rd |only man/fetch_awards_brownlow.Rd |only man/fetch_fantasy_scores.Rd |only man/fetch_outofcontract.Rd |only man/fetch_outofcontract_footywire.Rd |only man/fetch_player_details.Rd | 17 ++- man/fetch_player_stats.Rd | 9 + man/fetch_rising_star.Rd |only man/fetch_scores.Rd |only man/fetch_supercoach_scores.Rd |only man/fetch_team_stats.Rd |only man/fetch_team_stats_afltables.Rd |only man/fetch_team_stats_footywire.Rd |only man/fetch_team_stats_vflstats.Rd |only man/fitzRoy-package.Rd | 2 man/plot_score_worm.Rd | 2 man/plot_score_worm_totals.Rd | 2 man/team_abr_afl.Rd | 4 tests/testthat/test-fetch-awards.R |only tests/testthat/test-fetch-outofcontract.R |only tests/testthat/test-fetch-player-details.R | 14 ++ tests/testthat/test-fetch-player-stats.R | 8 - tests/testthat/test-fetch_supercoach_dreamteam.R |only tests/testthat/test-fetch_team_stats.R |only tests/testthat/test-team_colour_palettes.R | 14 +- vignettes/main-fetch-functions.Rmd | 1 46 files changed, 454 insertions(+), 185 deletions(-)
Title: Shape Constrained Additive Models
Description: Generalized additive models under shape
constraints on the component functions of the linear predictor.
Models can include multiple shape-constrained (univariate
and bivariate) and unconstrained terms. Routines of the
package 'mgcv' are used to set up the model matrix, print,
and plot the results. Multiple smoothing parameter
estimation by the Generalized Cross Validation or similar.
See Pya and Wood (2015) <doi:10.1007/s11222-013-9448-7>
for an overview. A broad selection of shape-constrained
smoothers, linear functionals of smooths with shape constraints,
and Gaussian models with AR1 residuals.
Author: Natalya Pya [aut, cre]
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-21 dated 2026-01-22 and 1.2-22 dated 2026-03-12
scam-1.2-21/scam/R/derivative.smooth.R |only scam-1.2-21/scam/R/uni.smooth.const-with-po.r |only scam-1.2-22/scam/ChangeLog | 8 ++++++++ scam-1.2-22/scam/DESCRIPTION | 8 ++++---- scam-1.2-22/scam/MD5 | 11 +++++------ scam-1.2-22/scam/R/bfgs.r | 7 ++++--- scam-1.2-22/scam/R/uni.smooth.const.r |only scam-1.2-22/scam/build/partial.rdb |binary 8 files changed, 21 insertions(+), 13 deletions(-)
Title: 'Rcpp' Bindings for the Boost Date_Time Library
Description: Access to Boost Date_Time functionality for dates,
durations (both for days and date time objects), time zones, and
posix time ('ptime') is provided by using 'Rcpp modules'. The
posix time implementation can support high-resolution of up to
nano-second precision by using 96 bits (instead of 64 with R)
to present a 'ptime' object (but this needs recompilation with
a #define set).
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppBDT versions 0.2.7 dated 2025-01-25 and 0.2.8 dated 2026-03-12
ChangeLog | 20 ++++++++++++++++++++ DESCRIPTION | 13 +++++++------ MD5 | 14 +++++++------- README.md | 2 +- inst/NEWS.Rd | 7 +++++++ inst/include/RcppBDTtz.h | 9 ++++----- src/RcppBDTdt.cpp | 15 +++++++-------- src/RcppBDTpt.cpp | 7 +++---- 8 files changed, 56 insertions(+), 31 deletions(-)
Title: Non-Ordered Vectors
Description: Functionality for manipulating values of associative
maps. The package is a dependency for mvp-type
packages that use the STL map class: it traps
plausible idiom that is ill-defined (implementation-specific) and
returns an informative error, rather than returning a possibly
incorrect result. To cite the package in publications please use
Hankin (2022) <doi:10.48550/ARXIV.2210.03856>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between disordR versions 0.9-8-5 dated 2025-11-03 and 0.9-8-6 dated 2026-03-12
DESCRIPTION | 6 ++--- MD5 | 12 +++++----- NAMESPACE | 2 - R/disordR.R | 6 ++--- build/vignette.rds |binary inst/doc/disindex.html | 12 +++++----- inst/doc/disordR.html | 57 +++++++++++++++++++++++++++---------------------- 7 files changed, 51 insertions(+), 44 deletions(-)
Title: Log-Linear Modelling of Triad Genotype Data
Description: Triad Log-Linear modelling of Imprinting
Environmental interactions, and Maternal effects (TriLLIEM).
This is an implementation of the log-linear model described in a series of
papers, see for example Ainsworth et al. (2010) <doi:10.1002/gepi.20547>.
Author: Kevin Heda Zhao [aut, cre],
Kelly Burkett [aut]
Maintainer: Kevin Heda Zhao <trilliemmaintainer@gmail.com>
Diff between TriLLIEM versions 0.1.0 dated 2026-03-05 and 0.1.1 dated 2026-03-12
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/partial.rdb |binary tests/testthat/test-TriLLIEM.R | 4 +++- tests/testthat/test-anova.TriLLIEM.R | 4 +++- tests/testthat/test-fullview.R | 8 +++++--- tests/testthat/test-simulate.R | 10 ++++++---- tests/testthat/test-summary.TriLLIEM.R | 6 ++++-- 8 files changed, 32 insertions(+), 22 deletions(-)
Title: Optimum Sample Allocation in Stratified Sampling
Description: Provides exact analytical algorithms for computing optimum sample
allocations in stratified sampling.
Supports classical Neyman-Tschuprow allocation, minimum-cost allocation under
a variance constraint, and multi-domain allocation with controlled precision.
Handles lower and upper bounds, cost constraints, and multiple domains.
Includes helper functions for variance computation, allocation summaries,
rounding, and example datasets for testing and benchmarking.
Author: Wojciech Wojciak [aut, cre],
Jacek Wesolowski [sad],
Robert Wieczorkowski [ctb]
Maintainer: Wojciech Wojciak <wojciech.wojciak@gmail.com>
Diff between stratallo versions 2.2.1 dated 2023-11-26 and 3.0.0 dated 2026-03-12
stratallo-2.2.1/stratallo/R/algorithms_1sided.R |only stratallo-2.2.1/stratallo/R/algorithms_2sided.R |only stratallo-2.2.1/stratallo/R/algorithms_of_other_authors.R |only stratallo-2.2.1/stratallo/R/helpers.R |only stratallo-2.2.1/stratallo/data/pop10_mM.rda |only stratallo-2.2.1/stratallo/data/pop507.rda |only stratallo-2.2.1/stratallo/data/pop969.rda |only stratallo-2.2.1/stratallo/man/CapacityScaling.Rd |only stratallo-2.2.1/stratallo/man/SimpleGreedy.Rd |only stratallo-2.2.1/stratallo/man/asummary.Rd |only stratallo-2.2.1/stratallo/man/opt_1sided.Rd |only stratallo-2.2.1/stratallo/man/pop10_mM.Rd |only stratallo-2.2.1/stratallo/man/pop507.Rd |only stratallo-2.2.1/stratallo/man/pop969.Rd |only stratallo-2.2.1/stratallo/man/ran_round.Rd |only stratallo-2.2.1/stratallo/man/rna_prior.Rd |only stratallo-2.2.1/stratallo/man/rna_rec.Rd |only stratallo-2.2.1/stratallo/man/round_oric.Rd |only stratallo-2.2.1/stratallo/man/stratallo-package.Rd |only stratallo-2.2.1/stratallo/tests/testthat/_snaps/algorithms_coma.md |only stratallo-2.2.1/stratallo/tests/testthat/_snaps/algorithms_rna.md |only stratallo-2.2.1/stratallo/tests/testthat/_snaps/algorithms_rna_rec.md |only stratallo-2.2.1/stratallo/tests/testthat/_snaps/algorithms_rnabox.md |only stratallo-2.2.1/stratallo/tests/testthat/_snaps/algorithms_sga.md |only stratallo-2.2.1/stratallo/tests/testthat/_snaps/algorithms_sgaplus.md |only stratallo-2.2.1/stratallo/tests/testthat/helper-dataobjects.R |only stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_coma.R |only stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_rna.R |only stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_rna_rec.R |only stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_rnabox.R |only stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_sga.R |only stratallo-2.2.1/stratallo/tests/testthat/test-algorithms_sgaplus.R |only stratallo-2.2.1/stratallo/tests/testthat/test-helpers.R |only stratallo-3.0.0/stratallo/DESCRIPTION | 57 stratallo-3.0.0/stratallo/MD5 | 136 + stratallo-3.0.0/stratallo/NAMESPACE | 14 stratallo-3.0.0/stratallo/NEWS.md | 14 stratallo-3.0.0/stratallo/R/alg_dca.R |only stratallo-3.0.0/stratallo/R/alg_other_authors.R |only stratallo-3.0.0/stratallo/R/alg_rdca.R |only stratallo-3.0.0/stratallo/R/alg_rna-sga-coma.R |only stratallo-3.0.0/stratallo/R/alg_rnabox.R |only stratallo-3.0.0/stratallo/R/alloc_summary.R |only stratallo-3.0.0/stratallo/R/check_rdca.R |only stratallo-3.0.0/stratallo/R/data.R | 92 - stratallo-3.0.0/stratallo/R/dopt.R |only stratallo-3.0.0/stratallo/R/helpers_dca_rdca.R |only stratallo-3.0.0/stratallo/R/opt.R | 213 +- stratallo-3.0.0/stratallo/R/rounding.R |only stratallo-3.0.0/stratallo/R/stratallo-package.R | 54 stratallo-3.0.0/stratallo/R/utils.R |only stratallo-3.0.0/stratallo/R/var.R |only stratallo-3.0.0/stratallo/README.md | 239 --- stratallo-3.0.0/stratallo/build/partial.rdb |binary stratallo-3.0.0/stratallo/build/vignette.rds |binary stratallo-3.0.0/stratallo/data/pop10s_bounds_ucost.rda |only stratallo-3.0.0/stratallo/data/pop2d4s.rda |only stratallo-3.0.0/stratallo/data/pop507s_ucost.rda |only stratallo-3.0.0/stratallo/data/pop969s_ucost.rda |only stratallo-3.0.0/stratallo/data/pop9d278s.rda |only stratallo-3.0.0/stratallo/inst/REFERENCES.bib |only stratallo-3.0.0/stratallo/inst/WORDLIST | 66 stratallo-3.0.0/stratallo/inst/doc/stratallo.R | 123 - stratallo-3.0.0/stratallo/inst/doc/stratallo.Rmd | 602 ++++---- stratallo-3.0.0/stratallo/inst/doc/stratallo.html | 744 +++++----- stratallo-3.0.0/stratallo/man/alg_1sided.Rd |only stratallo-3.0.0/stratallo/man/alloc_summary.Rd |only stratallo-3.0.0/stratallo/man/check_rdca.Rd |only stratallo-3.0.0/stratallo/man/data.Rd |only stratallo-3.0.0/stratallo/man/dca.Rd |only stratallo-3.0.0/stratallo/man/dca_M.Rd |only stratallo-3.0.0/stratallo/man/dopt.Rd |only stratallo-3.0.0/stratallo/man/fpia.Rd | 79 - stratallo-3.0.0/stratallo/man/has_mixed_signs.Rd |only stratallo-3.0.0/stratallo/man/helpers_dca_rdca.Rd |only stratallo-3.0.0/stratallo/man/is_equal.Rd |only stratallo-3.0.0/stratallo/man/obj_emptiness.Rd |only stratallo-3.0.0/stratallo/man/opt.Rd | 153 +- stratallo-3.0.0/stratallo/man/optcost.Rd | 90 - stratallo-3.0.0/stratallo/man/rdca.Rd |only stratallo-3.0.0/stratallo/man/rdca_iter.Rd |only stratallo-3.0.0/stratallo/man/rna_experimental.Rd |only stratallo-3.0.0/stratallo/man/rnabox.Rd | 173 +- stratallo-3.0.0/stratallo/man/rounding.Rd |only stratallo-3.0.0/stratallo/man/simplegreedy-capacityscaling.Rd |only stratallo-3.0.0/stratallo/man/stratallo.Rd |only stratallo-3.0.0/stratallo/man/var_st.Rd | 64 stratallo-3.0.0/stratallo/tests/spelling.R | 9 stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_coma.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_dca.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_dca0.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_rdca.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_rna.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_rna_rec.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_rnabox.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_sga.md |only stratallo-3.0.0/stratallo/tests/testthat/_snaps/alg_sgaplus.md |only stratallo-3.0.0/stratallo/tests/testthat/helper-data.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_coma.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_dca.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_dca0.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_rdca.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_rna.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_rna_rec.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_rnabox.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_sga.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alg_sgaplus.R |only stratallo-3.0.0/stratallo/tests/testthat/test-alloc_summary.R |only stratallo-3.0.0/stratallo/tests/testthat/test-check_rdca.R |only stratallo-3.0.0/stratallo/tests/testthat/test-dopt.R |only stratallo-3.0.0/stratallo/tests/testthat/test-helpers_dca_rdca.R |only stratallo-3.0.0/stratallo/tests/testthat/test-opt.R | 4 stratallo-3.0.0/stratallo/tests/testthat/test-rounding.R |only stratallo-3.0.0/stratallo/tests/testthat/test-utils.R |only stratallo-3.0.0/stratallo/tests/testthat/test-var.R |only stratallo-3.0.0/stratallo/vignettes/stratallo.Rmd | 602 ++++---- 116 files changed, 1819 insertions(+), 1709 deletions(-)
Title: Squared Extrapolation Methods for Accelerating EM-Like Monotone
Algorithms
Description: Algorithms for accelerating the convergence of slow, monotone
sequences from smooth, contraction mappings such as the EM algorithm.
It can be used to accelerate any smooth, linearly convergent scheme.
A tutorial-style introduction is available in vignette("SQUAREM").
See also: Varadhan & Roland (2008) <doi:10.18637/jss.v092.i07>.
Author: Ravi Varadhan [aut, cre]
Maintainer: Ravi Varadhan <ravi.varadhan@jhu.edu>
Diff between SQUAREM versions 2021.1 dated 2021-01-13 and 2026.1 dated 2026-03-12
DESCRIPTION | 34 ++++++------- MD5 | 6 +- man/fpiter.Rd | 32 ++++++------ man/squarem.Rd | 148 +++++++++++++++++++++++++++++---------------------------- 4 files changed, 113 insertions(+), 107 deletions(-)
Title: Accessing and Validating Marine Environmental Data from 'SHARK'
and Related Databases
Description: Provides functions to retrieve, process, analyze, and
quality-control marine physical, chemical, and biological data. The
main focus is on Swedish monitoring data available through the 'SHARK'
database <https://shark.smhi.se/en/>, with additional API support for 'Nordic
Microalgae' <https://nordicmicroalgae.org/>, 'Dyntaxa'
<https://artfakta.se/>, World Register of Marine Species ('WoRMS') <https://www.marinespecies.org>,
'AlgaeBase' <https://www.algaebase.org>, OBIS 'xylookup' web service
<https://iobis.github.io/xylookup/> and Intergovernmental Oceanographic Commission (IOC) -
UNESCO databases on harmful algae <https://www.marinespecies.org/hab/> and toxins
<https://toxins.hais.ioc-unesco.org/>.
Author: Markus Lindh [aut] ,
Anders Torstensson [aut, cre] ,
Mikael Hedblom [ctb] ,
Bengt Karlson [ctb] ,
SHARK [cph],
SBDI [fnd]
Maintainer: Anders Torstensson <anders.torstensson@smhi.se>
Diff between SHARK4R versions 1.1.0 dated 2026-03-09 and 1.1.1 dated 2026-03-12
DESCRIPTION | 6 MD5 | 50 ++-- NEWS.md | 9 inst/CITATION | 4 inst/doc/quality_control.R | 171 +++++++++++--- inst/doc/quality_control.Rmd | 139 ++++++++++- inst/doc/quality_control.html | 79 +++--- inst/doc/retrieve_hab_data.R | 50 +++- inst/doc/retrieve_hab_data.Rmd | 36 ++- inst/doc/retrieve_hab_data.html | 8 inst/doc/retrieve_nordic_microalgae_data.R | 156 +++++++++---- inst/doc/retrieve_nordic_microalgae_data.Rmd | 105 ++++++++ inst/doc/retrieve_nordic_microalgae_data.html | 54 ++-- inst/doc/retrieve_shark_data.R | 84 ++++--- inst/doc/retrieve_shark_data.Rmd | 46 +++ inst/doc/retrieve_shark_data.html | 44 +-- inst/doc/retrieve_worms_data.R | 307 ++++++++++++++++++-------- inst/doc/retrieve_worms_data.Rmd | 166 +++++++++++++- inst/doc/retrieve_worms_data.html | 259 +++++++++++---------- tests/testthat/test-worms_api_functions.R | 2 tests/testthat/test-xylookup.R | 1 vignettes/quality_control.Rmd | 139 ++++++++++- vignettes/retrieve_hab_data.Rmd | 36 ++- vignettes/retrieve_nordic_microalgae_data.Rmd | 105 ++++++++ vignettes/retrieve_shark_data.Rmd | 46 +++ vignettes/retrieve_worms_data.Rmd | 166 +++++++++++++- 26 files changed, 1746 insertions(+), 522 deletions(-)
Title: A Two-Step Approach to Testing Overall Effect of
Gene-Environment Interaction for Multiple Phenotypes
Description: Interaction between a genetic variant (e.g., a single nucleotide polymorphism) and an environmental variable (e.g., physical activity) can have a shared effect on multiple phenotypes (e.g., blood lipids). We implement a two-step method to test for an overall interaction effect on multiple phenotypes. In first step, the method tests for an overall marginal genetic association between the genetic variant and the multivariate phenotype. The genetic variants which show an evidence of marginal overall genetic effect in the first step are prioritized while testing for an overall gene-environment interaction effect in the second step. Methodology is available from: A Majumdar, KS Burch, T Haldar, S Sankararaman, B Pasaniuc, WJ Gauderman, JS Witte (2020) <doi:10.1093/bioinformatics/btaa1083>.
Author: Arunabha Majumdar [aut, cre],
Tanushree Haldar [aut]
Maintainer: Arunabha Majumdar <statgen.arunabha@gmail.com>
Diff between MPGE versions 1.0.0 dated 2020-10-23 and 1.0.1 dated 2026-03-12
DESCRIPTION | 18 - MD5 | 50 ++-- NEWS.md | 6 R/MPGE.R | 8 R/data.R | 4 R/mv_G_GE_P.R | 4 R/mv_G_GE_P_base.R | 2 R/sst.R | 4 R/whmt.R | 4 README.md | 50 ++-- build/vignette.rds |binary inst/WORDLIST |only inst/doc/mpge.R | 4 inst/doc/mpge.Rmd | 4 inst/doc/mpge.html | 441 +++++++++++++++++++++--------------------- man/MPGE.Rd | 22 +- man/SST.Rd | 4 man/WHT.Rd | 4 man/genotype_data.Rd | 4 man/mv_G_GE.Rd | 4 man/phenotype_data.Rd | 2 tests/spelling.R |only tests/testthat.R | 8 tests/testthat/test-mv_G_GE.R | 2 tests/testthat/test-sst.R | 2 tests/testthat/test-whmt.R | 2 vignettes/mpge.Rmd | 4 27 files changed, 350 insertions(+), 307 deletions(-)
More information about INCVCommunityDetection at CRAN
Permanent link
Title: Quantifying and Monetizing Health Impacts Attributable to
Exposure
Description: This R package has been developed with a focus on air pollution and noise but can be applied to other exposures. The initial development has been funded by the European Union project BEST-COST. Disclaimer: It is work in progress and the developers are not liable for any calculation errors or inaccuracies resulting from the use of this package.
Selection of relevant references (in chronological order):
WHO (2003) <https://www.who.int/publications/i/item/9241546204>,
Murray et al. (2003) <doi:10.1186/1478-7954-1-1>,
Miller & Hurley (2003) <doi:10.1136/jech.57.3.200>,
Steenland & Armstrong (2006) <doi:10.1097/01.ede.0000229155.05644.43>,
WHO (2011) <https://iris.who.int/items/723ab97c-5c33-4e3b-8df1-744aa5bc1c27>,
GBD 2019 Risk Factors Collaborators (2020) <doi:10.1016/S0140-6736(20)30752-2>.
Author: Alberto Castro [cre, aut] ,
Axel Luyten [aut] ,
Arno Pauwels [ctb] ,
Liliana Vazquez Fernandez [ctb] ,
Gianni Ardielli [ctb] ,
Iracy Pimenta [ctb] ,
Susanne Breitner [ctb] ,
Carl Baravelli [ctb] ,
Vanessa Gorasso [ctb] ,
Maria Lepnurm [ctb] ,
Andreia [...truncated...]
Maintainer: Alberto Castro <alberto.castrofernandez@swisstph.ch>
Diff between healthiar versions 0.2.3 dated 2026-02-19 and 0.2.4 dated 2026-03-12
DESCRIPTION | 8 +-- MD5 | 82 +++++++++++++++---------------- NEWS.md | 20 ++++++- R/attribute_health.R | 2 R/cba.R | 17 ++++-- R/compare.R | 6 +- R/data.R | 7 +- R/discount.R | 27 +++++----- R/get_discount_factor.R | 34 ++---------- R/get_inflation_factor.R | 13 ++++ R/get_paf.R | 2 R/monetize.R | 103 ++++++++++++++++++++++++++------------- R/socialize.R | 2 R/summarize_uncertainty.R | 7 +- R/zzz_global_variables.R | 2 README.md | 2 build/partial.rdb |binary data/exdat_cantons.rda |binary data/exdat_lifetable.rda |binary data/exdat_noise.rda |binary data/exdat_ozone.rda |binary data/exdat_pm.rda |binary data/exdat_socialize.rda |binary inst/CITATION | 3 - inst/REFERENCES.bib | 24 +++++++-- inst/doc/intro_to_healthiar.Rmd | 52 +++++++++++++------ inst/doc/intro_to_healthiar.html | 87 +++++++++++++++++++++----------- man/attribute_health.Rd | 2 man/cba.Rd | 14 ++++- man/compare.Rd | 6 +- man/discount.Rd | 28 +++++----- man/exdat_pm.Rd | 7 +- man/get_discount_factor.Rd | 13 +--- man/get_inflation_factor.Rd | 11 +++- man/get_paf.Rd | 2 man/healthiar-package.Rd | 2 man/monetize.Rd | 26 ++++++++- man/socialize.Rd | 2 man/summarize_uncertainty.Rd | 7 +- tests/testthat/test-cba.R | 36 ++++++++++--- tests/testthat/test-monetize.R | 101 +++++++++++++++++++++++++++++++++----- vignettes/intro_to_healthiar.Rmd | 52 +++++++++++++------ 42 files changed, 540 insertions(+), 269 deletions(-)
Title: Analysing 'SNP' and 'Silicodart' Data - Basic Functions
Description: Facilitates the import and analysis of 'SNP' (single nucleotide 'polymorphism')
and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT'
(Diversity Arrays Technology), however, data from other sequencing platforms can be used
once 'SNP' or related fragment presence/absence data from any source is imported. Genetic
datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for
a very compact storage of data and metadata. Functions are available for
importing and exporting of 'SNP' and 'silicodart' data, for reporting on and
filtering on various criteria (e.g. 'callrate', 'heterozygosity', 'reproducibility',
maximum allele frequency). Additional functions are available for visualization
(e.g. Principle Coordinate Analysis) and creating a spatial representation
using maps. 'dartR.base' is the 'base' package of the 'dartRverse' suits of packages.
To install the other packages, we recommend to install the 'dartRverse' package, that
su [...truncated...]
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Diana Robledo-Ruiz [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb],
Lindsay V. Clark [ctb],
Emily Stringer [ctb],
Floriaan Devloo-Delva [ctb],
Eric Archer [c [...truncated...]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartR.base versions 1.0.7 dated 2025-10-01 and 1.2.2 dated 2026-03-12
DESCRIPTION | 25 MD5 | 613 ++++++++-------- NAMESPACE | 39 - R/gi2gl.R | 1 R/gl.He.r | 4 R/gl.Ho.r | 4 R/gl.add.indmetrics.r | 4 R/gl.alf.r | 6 R/gl.allele.freq.r | 2 R/gl.amova.r | 6 R/gl.define.pop.r | 1 R/gl.diagnostics.hwe.r | 45 - R/gl.dist.ind.r | 548 +++++++------- R/gl.dist.phylo.r | 317 +++++--- R/gl.dist.pop.r | 1 R/gl.document.R |only R/gl.drop.ind.r | 1 R/gl.drop.loc.r | 5 R/gl.drop.pop.r | 17 R/gl.drop.sexlinked.r |only R/gl.edit.recode.ind.r | 1 R/gl.edit.recode.pop.r | 1 R/gl.fbm2gen.r |only R/gl.fdsim.r | 1 R/gl.filter.allna.r | 1 R/gl.filter.callrate.r | 21 R/gl.filter.excess.het.r | 1 R/gl.filter.factorloadings.r | 1 R/gl.filter.hamming.r | 498 ++++++------- R/gl.filter.heterozygosity.r | 1 R/gl.filter.hwe.r | 1 R/gl.filter.ld.r | 30 R/gl.filter.locmetric.r | 1 R/gl.filter.maf.r | 25 R/gl.filter.monomorphs.r | 1 R/gl.filter.overshoot.r | 62 - R/gl.filter.pa.r | 1 R/gl.filter.rdepth.r | 9 R/gl.filter.replicates.r |only R/gl.filter.reproducibility.r | 5 R/gl.filter.secondaries.r | 5 R/gl.filter.sexlinked.r |only R/gl.filter.taglength.r | 1 R/gl.fixed.diff.r | 1 R/gl.fst.pop.r | 6 R/gl.gen2fbm.r |only R/gl.hwe.pop.r | 1 R/gl.impute.r | 262 +++++-- R/gl.join.r | 837 +++++++++++----------- R/gl.keep.ind.r | 1 R/gl.keep.loc.r | 1 R/gl.keep.pop.r | 34 R/gl.load.r | 10 R/gl.make.recode.ind.r | 1 R/gl.make.recode.pop.r | 1 R/gl.map.interactive.r | 41 - R/gl.merge.pop.r | 1 R/gl.pcoa.plot.r | 3 R/gl.pcoa.r | 40 - R/gl.plot.heatmap.r | 302 ++++++-- R/gl.plot.snp.density.r |only R/gl.print.history.r | 1 R/gl.propShared.r | 5 R/gl.random.snp.r | 1 R/gl.randomize.snps.r | 1 R/gl.read.PLINK.r | 524 +++++++------- R/gl.read.csv.r | 54 - R/gl.read.dart.r | 22 R/gl.read.fasta.r | 33 R/gl.read.silicodart.r | 25 R/gl.read.vcf.r | 21 R/gl.reassign.ind.r |only R/gl.reassign.pop.r | 3 R/gl.recalc.metrics.r | 1 R/gl.recode.ind.r | 1 R/gl.recode.pop.r | 3 R/gl.rename.pop.r | 1 R/gl.report.allelerich.r | 740 +++++++++++++++---- R/gl.report.allna.r | 1 R/gl.report.bases.r | 1 R/gl.report.basics.r | 1 R/gl.report.callrate.r | 1 R/gl.report.diversity.r | 6 R/gl.report.excess.het.r | 1 R/gl.report.factorloadings.r | 1 R/gl.report.fstat.r | 9 R/gl.report.hamming.r | 7 R/gl.report.heterozygosity.r | 30 R/gl.report.hwe.r | 22 R/gl.report.ld.map.r | 1 R/gl.report.locmetric.r | 1 R/gl.report.maf.r | 1 R/gl.report.monomorphs.r | 3 R/gl.report.overshoot.r | 17 R/gl.report.pa.r | 1 R/gl.report.polyploid_heterozygosity.r | 6 R/gl.report.rdepth.r | 1 R/gl.report.replicates.r | 369 +++++---- R/gl.report.reproducibility.r | 3 R/gl.report.secondaries.r | 1 R/gl.report.sexlinked.r |only R/gl.report.shannon.r | 3 R/gl.report.taglength.r | 1 R/gl.sample.r | 1 R/gl.save.r | 7 R/gl.select.colors.r | 7 R/gl.select.shapes.r | 1 R/gl.smearplot.r | 85 ++ R/gl.sort.r | 56 + R/gl.subsample.ind.r | 8 R/gl.subsample.loc.r | 1 R/gl.subsample.loci.r | 1 R/gl.test.heterozygosity.r | 25 R/gl.tree.fitch.r | 1 R/gl.tree.nj.r | 3 R/gl.write.csv.r | 1 R/gl2bayesAss.R | 1 R/gl2bayescan.r | 1 R/gl2bpp.r | 5 R/gl2demerelate.r | 1 R/gl2eigenstrat.r | 1 R/gl2fasta.r | 17 R/gl2gapit.r | 5 R/gl2gds.r | 1 R/gl2genalex.r | 1 R/gl2genepop.r | 7 R/gl2gi.r | 3 R/gl2hapmap.r | 257 +++++- R/gl2hiphop.r | 1 R/gl2paup.parsimony.r | 1 R/gl2paup.svdquartets.r | 1 R/gl2phylip.r | 1 R/gl2plink.r | 18 R/gl2related.r | 3 R/gl2sa.r | 150 +--- R/gl2snapper.r | 7 R/gl2structure.r | 1 R/gl2treemix.r | 1 R/gl2vcf.r | 334 ++++---- R/theme_dartR.r | 6 R/utils.allelic.richness.r |only R/utils.basic.stats.r | 1 R/utils.check.datatype.R | 1 R/utils.collapse.matrix.r | 1 R/utils.dart2genlight.r | 32 R/utils.dartR.class.def.r | 1120 ++++++++++++++++++++++++------ R/utils.dist.binary.r | 178 +++- R/utils.dist.ind.snp.r | 322 ++++++-- R/utils.heatmap.r |only R/utils.het.report.r | 2 R/utils.plink.run.r | 2 R/utils.recalc.callrate.r | 2 R/utils.recalc.maf.r | 3 R/utils.stats.r | 2 R/zzz.r | 13 man/cbind.dartR.Rd | 18 man/gl.He.Rd | 45 - man/gl.Ho.Rd | 45 - man/gl.add.indmetrics.Rd | 4 man/gl.alf.Rd | 6 man/gl.allele.freq.Rd | 3 man/gl.amova.Rd | 1 man/gl.define.pop.Rd | 2 man/gl.diagnostics.hwe.Rd | 13 man/gl.dist.ind.Rd | 20 man/gl.dist.phylo.Rd | 163 ++-- man/gl.dist.pop.Rd | 1 man/gl.document.Rd |only man/gl.drop.ind.Rd | 2 man/gl.drop.loc.Rd | 2 man/gl.drop.pop.Rd | 2 man/gl.drop.sexlinked.Rd |only man/gl.edit.recode.ind.Rd | 1 man/gl.edit.recode.pop.Rd | 2 man/gl.fbm2gen.Rd |only man/gl.fdsim.Rd | 1 man/gl.filter.allna.Rd | 1 man/gl.filter.callrate.Rd | 10 man/gl.filter.excess.het.Rd | 1 man/gl.filter.factorloadings.Rd | 1 man/gl.filter.hamming.Rd | 110 +- man/gl.filter.heterozygosity.Rd | 1 man/gl.filter.hwe.Rd | 1 man/gl.filter.ld.Rd | 16 man/gl.filter.locmetric.Rd | 2 man/gl.filter.maf.Rd | 2 man/gl.filter.monomorphs.Rd | 2 man/gl.filter.overshoot.Rd | 2 man/gl.filter.pa.Rd | 2 man/gl.filter.rdepth.Rd | 1 man/gl.filter.replicates.Rd |only man/gl.filter.reproducibility.Rd | 1 man/gl.filter.secondaries.Rd | 8 man/gl.filter.sexlinked.Rd |only man/gl.filter.taglength.Rd | 1 man/gl.fixed.diff.Rd | 1 man/gl.fst.pop.Rd | 1 man/gl.gen2fbm.Rd |only man/gl.hwe.pop.Rd | 1 man/gl.impute.Rd | 48 + man/gl.join.Rd | 55 - man/gl.keep.ind.Rd | 2 man/gl.keep.loc.Rd | 2 man/gl.keep.pop.Rd | 2 man/gl.load.Rd | 5 man/gl.make.recode.ind.Rd | 2 man/gl.make.recode.pop.Rd | 1 man/gl.map.interactive.Rd | 5 man/gl.merge.pop.Rd | 2 man/gl.pcoa.Rd | 5 man/gl.pcoa.plot.Rd | 3 man/gl.plot.heatmap.Rd | 118 +++ man/gl.plot.snp.density.Rd |only man/gl.print.history.Rd | 1 man/gl.prop.shared.Rd | 1 man/gl.randomize.snps.Rd | 2 man/gl.read.PLINK.Rd | 22 man/gl.read.csv.Rd | 15 man/gl.read.dart.Rd | 12 man/gl.read.fasta.Rd | 25 man/gl.read.vcf.Rd | 19 man/gl.reassign.ind.Rd |only man/gl.reassign.pop.Rd | 4 man/gl.recalc.metrics.Rd | 1 man/gl.recode.ind.Rd | 2 man/gl.recode.pop.Rd | 4 man/gl.rename.pop.Rd | 2 man/gl.report.allelerich.Rd | 257 ++++++ man/gl.report.allna.Rd | 1 man/gl.report.bases.Rd | 1 man/gl.report.basics.Rd | 2 man/gl.report.callrate.Rd | 1 man/gl.report.diversity.Rd | 2 man/gl.report.excess.het.Rd | 2 man/gl.report.factorloadings.Rd | 1 man/gl.report.fstat.Rd | 9 man/gl.report.hamming.Rd | 3 man/gl.report.heterozygosity.Rd | 8 man/gl.report.ld.map.Rd | 1 man/gl.report.locmetric.Rd | 1 man/gl.report.maf.Rd | 1 man/gl.report.monomorphs.Rd | 1 man/gl.report.overshoot.Rd | 1 man/gl.report.pa.Rd | 1 man/gl.report.polyploid_heterozygosity.Rd | 7 man/gl.report.rdepth.Rd | 1 man/gl.report.replicates.Rd | 75 +- man/gl.report.reproducibility.Rd | 3 man/gl.report.secondaries.Rd | 1 man/gl.report.sexlinked.Rd |only man/gl.report.shannon.Rd | 3 man/gl.report.taglength.Rd | 1 man/gl.sample.Rd | 2 man/gl.select.colors.Rd | 7 man/gl.select.shapes.Rd | 1 man/gl.sim.genotypes.Rd | 1 man/gl.smearplot.Rd | 18 man/gl.sort.Rd | 44 - man/gl.subsample.ind.Rd | 3 man/gl.subsample.loc.Rd | 2 man/gl.subsample.loci.Rd | 1 man/gl.test.heterozygosity.Rd | 1 man/gl.tree.fitch.Rd | 1 man/gl.tree.nj.Rd | 3 man/gl.write.csv.Rd | 1 man/gl2bayesAss.Rd | 3 man/gl2bayescan.Rd | 3 man/gl2bpp.Rd | 7 man/gl2demerelate.Rd | 3 man/gl2eigenstrat.Rd | 3 man/gl2fasta.Rd | 10 man/gl2faststructure.Rd | 2 man/gl2gds.Rd | 3 man/gl2genalex.Rd | 3 man/gl2genepop.Rd | 4 man/gl2geno.Rd | 5 man/gl2gi.Rd | 8 man/gl2hapmap.Rd |only man/gl2hiphop.Rd | 3 man/gl2paup.parsimony.Rd | 1 man/gl2paup.svdquartets.Rd | 1 man/gl2phylip.Rd | 3 man/gl2plink.Rd | 13 man/gl2related.Rd | 5 man/gl2sa.Rd | 32 man/gl2snapper.Rd | 32 man/gl2structure.Rd | 3 man/gl2treemix.Rd | 3 man/gl2vcf.Rd | 19 man/glMean.Rd |only man/glSum.Rd |only man/rbind.dartR.Rd | 20 man/sub-dartR-ANY-ANY-ANY-method.Rd | 3 man/utils.allelic.richness.Rd |only man/utils.basic.stats.Rd | 1 man/utils.check.datatype.Rd | 2 man/utils.collapse.matrix.Rd | 1 man/utils.dart2genlight.Rd | 1 man/utils.dist.binary.Rd | 1 man/utils.dist.ind.snp.Rd | 15 man/utils.flag.start.Rd | 1 man/utils.hamming.Rd | 1 man/utils.heatmap.Rd |only man/utils.het.pop.Rd | 1 man/utils.impute.Rd | 1 man/utils.is.fixed.Rd | 1 man/utils.jackknife.Rd | 1 man/utils.n.var.invariant.Rd | 1 man/utils.plot.save.Rd | 1 man/utils.read.fasta.Rd | 1 man/utils.read.ped.Rd | 1 man/utils.recalc.avgpic.Rd | 1 man/utils.recalc.callrate.Rd | 1 man/utils.recalc.freqhets.Rd | 1 man/utils.recalc.freqhomref.Rd | 1 man/utils.recalc.freqhomsnp.Rd | 1 man/utils.recalc.maf.Rd | 1 man/utils.reset.flags.Rd | 1 man/utils.transpose.Rd | 1 man/utils.vcfr2genlight.polyploid.Rd | 1 320 files changed, 6734 insertions(+), 3295 deletions(-)
Title: Modelling Continuous Report Visual Short-Term Memory Studies
Description: A set of utility functions for analysing and modelling data from
continuous report short-term memory experiments using either the 2-component
mixture model of Zhang and Luck (2008) <doi:10.1038/nature06860> or the
3-component mixture model of Bays et al. (2009) <doi:10.1167/9.10.7>. Users
are also able to simulate from these models.
Author: Jim Grange [aut, cre] ,
Stuart B. Moore [aut] ,
Ed D. J. Berry [ctb],
Vencislav Popov [ctb]
Maintainer: Jim Grange <grange.jim@gmail.com>
Diff between mixtur versions 1.2.2 dated 2025-07-21 and 1.2.3 dated 2026-03-12
DESCRIPTION | 10 ++-- MD5 | 10 ++-- NAMESPACE | 1 NEWS.md | 5 +- R/plotting.R | 140 ++++++++++++++++++++++++++++++++++++----------------------- README.md | 4 - 6 files changed, 104 insertions(+), 66 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>
Diff between rswipl versions 10.1.4 dated 2026-02-23 and 10.1.5 dated 2026-03-12
rswipl-10.1.4/rswipl/src/swipl-devel/cmake/TestSignalType.c |only rswipl-10.1.4/rswipl/src/swipl-devel/cmake/TestSignalType.cmake |only rswipl-10.1.4/rswipl/src/swipl-devel/src/pl-trie.c.save |only rswipl-10.1.5/rswipl/DESCRIPTION | 10 rswipl-10.1.5/rswipl/MD5 | 127 +- rswipl-10.1.5/rswipl/NEWS.md | 6 rswipl-10.1.5/rswipl/inst/patch/03-cpp.patch | 2 rswipl-10.1.5/rswipl/inst/patch/04-cpp.patch | 4 rswipl-10.1.5/rswipl/src/install.libs.R | 2 rswipl-10.1.5/rswipl/src/swipl-devel/VERSION | 2 rswipl-10.1.5/rswipl/src/swipl-devel/boot/init.pl | 3 rswipl-10.1.5/rswipl/src/swipl-devel/boot/messages.pl | 60 - rswipl-10.1.5/rswipl/src/swipl-devel/boot/toplevel.pl | 11 rswipl-10.1.5/rswipl/src/swipl-devel/cmake/BuildType.cmake | 22 rswipl-10.1.5/rswipl/src/swipl-devel/cmake/PGO.cmake | 29 rswipl-10.1.5/rswipl/src/swipl-devel/library/console_input.pl | 94 + rswipl-10.1.5/rswipl/src/swipl-devel/library/csv.pl | 53 rswipl-10.1.5/rswipl/src/swipl-devel/library/dialect/swi/syspred_options.pl | 1 rswipl-10.1.5/rswipl/src/swipl-devel/library/prolog_code.pl | 2 rswipl-10.1.5/rswipl/src/swipl-devel/library/prolog_debug.pl | 41 rswipl-10.1.5/rswipl/src/swipl-devel/library/tableutil.pl |only rswipl-10.1.5/rswipl/src/swipl-devel/library/threadutil.pl | 249 ++-- rswipl-10.1.5/rswipl/src/swipl-devel/packages/clib/process.c.rej |only rswipl-10.1.5/rswipl/src/swipl-devel/packages/cpp/test_cpp.cpp.rej |only rswipl-10.1.5/rswipl/src/swipl-devel/packages/cpp/test_cpp.pl.rej |only rswipl-10.1.5/rswipl/src/swipl-devel/packages/http/thread_httpd.pl | 13 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/config.h.cmake | 1 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/prolog/lib/emacs/prolog_mode.pl | 11 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/prolog/lib/epilog.pl | 37 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/prolog/lib/gui_tracer.pl | 23 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/prolog/lib/prolog_predicate.pl | 28 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/prolog/lib/swi/thread_monitor.pl | 162 ++ rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/prolog/lib/trace/trace.pl | 9 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/src/evt/event.c | 21 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/src/ker/conversion.c | 4 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/src/md/md-windows.h | 3 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/src/sdl/sdlevent.c | 24 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/src/sdl/sdlimage.c | 2 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/src/txt/editor.c | 43 rswipl-10.1.5/rswipl/src/swipl-devel/packages/xpce/swipl/swipl-rc | 1 rswipl-10.1.5/rswipl/src/swipl-devel/scripts/make-distribution | 9 rswipl-10.1.5/rswipl/src/swipl-devel/scripts/make-ppa | 8 rswipl-10.1.5/rswipl/src/swipl-devel/src/ATOMS | 2 rswipl-10.1.5/rswipl/src/swipl-devel/src/CMakeLists.txt | 3 rswipl-10.1.5/rswipl/src/swipl-devel/src/SWI-Prolog.h | 19 rswipl-10.1.5/rswipl/src/swipl-devel/src/config.h.cmake | 2 rswipl-10.1.5/rswipl/src/swipl-devel/src/config/wincfg.h | 9 rswipl-10.1.5/rswipl/src/swipl-devel/src/libbf/bf_gmp.c | 21 rswipl-10.1.5/rswipl/src/swipl-devel/src/os/pl-prologflag.c | 592 +++++----- rswipl-10.1.5/rswipl/src/swipl-devel/src/os/pl-prologflag.h | 17 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-arith.c | 41 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-arith.h | 5 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-fli.c | 4 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-global.h | 1 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-gmp.c | 11 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-incl.h | 16 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-init.c | 14 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-init.h | 7 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-pro.c | 10 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-qlf.c | 33 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-thread.c | 243 +++- rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-thread.h | 8 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-trace.c | 96 - rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-trace.h | 6 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-vmi.c | 6 rswipl-10.1.5/rswipl/src/swipl-devel/src/pl-wam.c | 49 rswipl-10.1.5/rswipl/src/swipl-devel/tests/core/test_bips.pl | 193 +-- rswipl-10.1.5/rswipl/src/swipl-devel/tests/core/test_prolog_flag.pl | 88 + 68 files changed, 1712 insertions(+), 901 deletions(-)
Title: Simple Interactive Controls for R using the 'tcltk' Package
Description: A set of functions to build simple
GUI controls for R functions. These are built on the 'tcltk' package.
Uses could include changing a parameter on a graph by animating it
with a slider or a "doublebutton", up to more sophisticated control
panels.
Some functions for specific graphical tasks, referred to as 'cartoons',
are provided.
Author: Adrian Bowman [aut, cre, cph],
Ewan Crawford [aut],
Gavin Alexander [aut],
Richard Bowman [aut]
Maintainer: Adrian Bowman <adrian.bowman@glasgow.ac.uk>
Diff between rpanel versions 1.1-5.2 dated 2023-02-07 and 1.1-6 dated 2026-03-12
rpanel-1.1-5.2/rpanel/R/rp-ancova.r |only rpanel-1.1-5.2/rpanel/R/rp-anova.R |only rpanel-1.1-5.2/rpanel/R/rp-ci.r |only rpanel-1.1-5.2/rpanel/R/rp-geosim.r |only rpanel-1.1-5.2/rpanel/R/rp-gulls.r |only rpanel-1.1-5.2/rpanel/R/rp-mururoa.r |only rpanel-1.1-5.2/rpanel/R/rp-power.r |only rpanel-1.1-5.2/rpanel/R/rp-regression.r |only rpanel-1.1-5.2/rpanel/R/rp-sample.r |only rpanel-1.1-5.2/rpanel/R/rp-tables.r |only rpanel-1.1-6/rpanel/ChangeLog | 2 rpanel-1.1-6/rpanel/DESCRIPTION | 38 + rpanel-1.1-6/rpanel/MD5 | 188 ++++--- rpanel-1.1-6/rpanel/NAMESPACE | 99 ++- rpanel-1.1-6/rpanel/NEWS.md | 6 rpanel-1.1-6/rpanel/R/image.r | 257 +++++----- rpanel-1.1-6/rpanel/R/rp-colour-key.r | 4 rpanel-1.1-6/rpanel/R/rp-firth.r | 32 - rpanel-1.1-6/rpanel/R/rp-likelihood.r | 296 +++++------ rpanel-1.1-6/rpanel/R/rp-logistic.r | 68 +- rpanel-1.1-6/rpanel/R/rp-normal.r | 24 rpanel-1.1-6/rpanel/R/rp-plot3d.r | 250 +++++----- rpanel-1.1-6/rpanel/R/rp-plot4d.r | 300 +++++++----- rpanel-1.1-6/rpanel/R/rp-rmplot.r | 570 +++++++++++------------ rpanel-1.1-6/rpanel/R/rp-surface.r | 1 rpanel-1.1-6/rpanel/R/rp_ancova.R |only rpanel-1.1-6/rpanel/R/rp_anova.R |only rpanel-1.1-6/rpanel/R/rp_ci.r |only rpanel-1.1-6/rpanel/R/rp_coefficients.R |only rpanel-1.1-6/rpanel/R/rp_colours.R |only rpanel-1.1-6/rpanel/R/rp_contingency.R |only rpanel-1.1-6/rpanel/R/rp_datalink.R |only rpanel-1.1-6/rpanel/R/rp_drop1.R |only rpanel-1.1-6/rpanel/R/rp_geosim.r |only rpanel-1.1-6/rpanel/R/rp_gulls.r |only rpanel-1.1-6/rpanel/R/rp_lm.R |only rpanel-1.1-6/rpanel/R/rp_mururoa.r |only rpanel-1.1-6/rpanel/R/rp_power.r |only rpanel-1.1-6/rpanel/R/rp_regression.r |only rpanel-1.1-6/rpanel/R/rp_regression2.r |only rpanel-1.1-6/rpanel/R/rp_regression2_lm.r |only rpanel-1.1-6/rpanel/R/rp_sample.r |only rpanel-1.1-6/rpanel/R/rp_sample_old.r |only rpanel-1.1-6/rpanel/R/rp_t_test.R |only rpanel-1.1-6/rpanel/R/rp_tables.r |only rpanel-1.1-6/rpanel/R/rp_wrangle.R |only rpanel-1.1-6/rpanel/R/rpanel.r | 7 rpanel-1.1-6/rpanel/R/sysdata.rda |binary rpanel-1.1-6/rpanel/R/tkrplot.r | 264 ++++++---- rpanel-1.1-6/rpanel/R/window.r | 44 - rpanel-1.1-6/rpanel/data/Astrand.rda |only rpanel-1.1-6/rpanel/data/Clyde.rda |binary rpanel-1.1-6/rpanel/data/CofE.rda |binary rpanel-1.1-6/rpanel/data/Hyde.rda |only rpanel-1.1-6/rpanel/data/Loch_Leven.rda |only rpanel-1.1-6/rpanel/data/SO2.rda |binary rpanel-1.1-6/rpanel/data/Scottish_referendum.rda |only rpanel-1.1-6/rpanel/data/aircond.rda |binary rpanel-1.1-6/rpanel/data/cholesterol.rda |only rpanel-1.1-6/rpanel/data/doctors_smoking.rda |only rpanel-1.1-6/rpanel/data/flour_beetles.rda |only rpanel-1.1-6/rpanel/data/gullweight.rda |binary rpanel-1.1-6/rpanel/data/luthor.rda |binary rpanel-1.1-6/rpanel/data/mammal_speed.rda |only rpanel-1.1-6/rpanel/data/poisons.rda |binary rpanel-1.1-6/rpanel/data/river.rda |binary rpanel-1.1-6/rpanel/data/rodent.rda |binary rpanel-1.1-6/rpanel/data/vasoconstriction.rda |only rpanel-1.1-6/rpanel/data/worldbank.rda |binary rpanel-1.1-6/rpanel/demo/rp.image.r | 21 rpanel-1.1-6/rpanel/inst/CITATION | 55 -- rpanel-1.1-6/rpanel/inst/extdata |only rpanel-1.1-6/rpanel/inst/history.txt | 1 rpanel-1.1-6/rpanel/man/Astrand.Rd |only rpanel-1.1-6/rpanel/man/Clyde.Rd | 38 - rpanel-1.1-6/rpanel/man/Hyde.Rd |only rpanel-1.1-6/rpanel/man/Loch_Leven.Rd |only rpanel-1.1-6/rpanel/man/Scottish_referendum.Rd |only rpanel-1.1-6/rpanel/man/cholesterol.Rd |only rpanel-1.1-6/rpanel/man/doctors_smoking.Rd |only rpanel-1.1-6/rpanel/man/flour_beetles.Rd |only rpanel-1.1-6/rpanel/man/gullweight.Rd | 38 - rpanel-1.1-6/rpanel/man/mammal_speed.Rd |only rpanel-1.1-6/rpanel/man/poisons.Rd | 42 - rpanel-1.1-6/rpanel/man/rodent.Rd | 33 - rpanel-1.1-6/rpanel/man/rp.ancova.Rd | 98 ++- rpanel-1.1-6/rpanel/man/rp.anova.Rd | 98 +-- rpanel-1.1-6/rpanel/man/rp.block.Rd | 2 rpanel-1.1-6/rpanel/man/rp.button.Rd | 136 ++--- rpanel-1.1-6/rpanel/man/rp.ci.Rd | 61 +- rpanel-1.1-6/rpanel/man/rp.coefficients.Rd |only rpanel-1.1-6/rpanel/man/rp.colour.key.Rd | 4 rpanel-1.1-6/rpanel/man/rp.colours.Rd |only rpanel-1.1-6/rpanel/man/rp.contingency.Rd |only rpanel-1.1-6/rpanel/man/rp.datalink.Rd |only rpanel-1.1-6/rpanel/man/rp.drop1.Rd |only rpanel-1.1-6/rpanel/man/rp.firth.Rd | 71 +- rpanel-1.1-6/rpanel/man/rp.geosim.Rd | 36 - rpanel-1.1-6/rpanel/man/rp.gulls.Rd | 82 +-- rpanel-1.1-6/rpanel/man/rp.likelihood.Rd | 4 rpanel-1.1-6/rpanel/man/rp.lm.Rd |only rpanel-1.1-6/rpanel/man/rp.logistic.Rd | 80 +-- rpanel-1.1-6/rpanel/man/rp.menu.Rd | 154 +++--- rpanel-1.1-6/rpanel/man/rp.mururoa.Rd | 75 +-- rpanel-1.1-6/rpanel/man/rp.normal.Rd | 74 +- rpanel-1.1-6/rpanel/man/rp.plot3d.Rd | 116 ++-- rpanel-1.1-6/rpanel/man/rp.plot4d.Rd | 92 +-- rpanel-1.1-6/rpanel/man/rp.pos.Rd | 87 +-- rpanel-1.1-6/rpanel/man/rp.power.Rd | 11 rpanel-1.1-6/rpanel/man/rp.regression.Rd | 75 +-- rpanel-1.1-6/rpanel/man/rp.rmplot.Rd | 4 rpanel-1.1-6/rpanel/man/rp.sample.Rd | 50 +- rpanel-1.1-6/rpanel/man/rp.t_test.Rd |only rpanel-1.1-6/rpanel/man/rp.tables.Rd | 14 rpanel-1.1-6/rpanel/man/rp.tkrplot.Rd | 164 +++--- rpanel-1.1-6/rpanel/man/rp.wrangle.Rd |only rpanel-1.1-6/rpanel/man/rpanel.package.Rd | 49 - rpanel-1.1-6/rpanel/man/vasoconstriction.Rd |only rpanel-1.1-6/rpanel/tests |only 119 files changed, 2272 insertions(+), 2043 deletions(-)
Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
Description: Provides the 'Molecular Signatures Database' (MSigDB) gene
sets typically used with the 'Gene Set Enrichment Analysis' (GSEA)
software (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>,
Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>, Castanza et al.
2023 <doi:10.1038/s41592-023-02014-7>) as an R data frame. The package
includes the human genes as listed in MSigDB as well as the
corresponding symbols and IDs for frequently studied model organisms
such as mouse, rat, pig, fly, and yeast.
Author: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>
Diff between msigdbr versions 25.1.1 dated 2025-07-21 and 26.1.0 dated 2026-03-12
DESCRIPTION | 8 - MD5 | 22 ++-- NAMESPACE | 2 NEWS.md | 9 + R/msigdbr-collections.R | 41 ++++---- R/msigdbr.R | 50 ++++------ R/utils.R | 149 +++++++++++++++++++----------- build/partial.rdb |binary man/msigdbr.Rd | 2 man/msigdbr_collections.Rd | 2 tests/testthat/test-msigdbr-collections.R | 3 tests/testthat/test-msigdbr.R | 15 ++- 12 files changed, 186 insertions(+), 117 deletions(-)
Title: Leveraging Experiment Lines to Data Analytics
Description: The natural increase in the complexity of current research experiments and data demands better tools to enhance productivity in Data Analytics. The package is a framework designed to address the modern challenges in data analytics workflows. The package is inspired by Experiment Line concepts. It aims to provide seamless support for users in developing their data mining workflows by offering a uniform data model and method API. It enables the integration of various data mining activities, including data preprocessing, classification, regression, clustering, and time series prediction. It also offers options for hyper-parameter tuning and supports integration with existing libraries and languages. Overall, the package provides researchers with a comprehensive set of functionalities for data science, promoting ease of use, extensibility, and integration with various tools and libraries. Information on Experiment Line is based on Ogasawara et al. (2009) <doi:10.1007/978-3-642-02279-1_2 [...truncated...]
Author: Eduardo Ogasawara [aut, ths, cre] ,
Ana Carolina Sá [aut],
Antonio Castro [aut],
Caio Santos [aut],
Diego Carvalho [ctb],
Diego Salles [aut],
Eduardo Bezerra [ctb],
Esther Pacitti [ctb],
Fabio Porto [ctb],
Janio Lima [aut],
Lucas Tavares [aut],
Ra [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between daltoolbox versions 1.3.717 dated 2026-02-10 and 1.3.727 dated 2026-03-12
DESCRIPTION | 14 +++++----- MD5 | 46 ++++++++++++++++++++++------------ NAMESPACE | 22 ++++++++++++++++ R/cla_xgboost.R | 2 - R/graphics_plot_boxplot.R | 21 ++++++++------- R/graphics_plot_boxplot_class.R | 19 +++++++------- R/pat_apriori.R | 8 ++--- R/pat_cspade.R | 8 ++--- R/pat_eclat.R | 8 ++--- R/pat_pattern_miner.R | 24 +++++++++++++++++ R/trans_feature_selection_corr.R | 41 +++++++++++++++++++++++++++--- R/trans_feature_selection_fss.R |only R/trans_feature_selection_info_gain.R |only R/trans_feature_selection_lasso.R |only R/trans_feature_selection_relief.R |only R/trans_feature_selection_stepwise.R |only R/trans_sample_oversampling.R |only R/trans_sample_subsampling.R |only README.md | 6 +++- man/bal_oversampling.Rd |only man/bal_subsampling.Rd |only man/cla_xgboost.Rd | 2 - man/feature_selection_corr.Rd | 7 ++++- man/feature_selection_fss.Rd |only man/feature_selection_info_gain.Rd |only man/feature_selection_lasso.Rd |only man/feature_selection_relief.Rd |only man/feature_selection_stepwise.Rd |only man/pat_apriori.Rd | 2 - man/pat_cspade.Rd | 2 - man/pat_eclat.Rd | 2 - 31 files changed, 168 insertions(+), 66 deletions(-)
Title: Programmatic Interface to 'Orthanc' DICOM Servers
Description: An R Interface to 'Orthanc' DICOM servers for medical imaging workflows.
'Orthanc' is a lightweight, open-source DICOM server that exposes a comprehensive
REST API for managing, querying, retrieving, and modifying DICOM resources
(<https://www.orthanc-server.com>). The goal of this package is to provide
comprehensive and user-friendly access to the 'Orthanc' REST API, designed to
align with idiomatic R workflows while preserving the structure and semantics
of DICOM resources.
Author: Matthew T. Warkentin [aut, cre, cph]
Maintainer: Matthew T. Warkentin <matthew.warkentin@ucalgary.ca>
Diff between orthanc versions 0.1.0 dated 2026-03-03 and 0.2.0 dated 2026-03-11
orthanc-0.1.0/orthanc/R/retrieve.R |only orthanc-0.1.0/orthanc/inst/Orthanc/Orthanc_endpoints_1_12_10.csv |only orthanc-0.1.0/orthanc/inst/Orthanc/Orthanc_roxygen_1_12_10.csv |only orthanc-0.1.0/orthanc/inst/Orthanc/get_Orthanc_endpoints.R |only orthanc-0.1.0/orthanc/inst/Orthanc/orthanc-openapi.json |only orthanc-0.2.0/orthanc/DESCRIPTION | 11 orthanc-0.2.0/orthanc/MD5 | 64 +- orthanc-0.2.0/orthanc/NAMESPACE | 4 orthanc-0.2.0/orthanc/NEWS.md | 68 ++ orthanc-0.2.0/orthanc/R/Instance.R | 275 ++++++++-- orthanc-0.2.0/orthanc/R/Job.R | 2 orthanc-0.2.0/orthanc/R/Modality.R | 2 orthanc-0.2.0/orthanc/R/Orthanc.R | 2 orthanc-0.2.0/orthanc/R/OrthancAsync.R | 9 orthanc-0.2.0/orthanc/R/Patient.R | 179 ++++-- orthanc-0.2.0/orthanc/R/Resource.R | 62 +- orthanc-0.2.0/orthanc/R/Series.R | 158 ++++- orthanc-0.2.0/orthanc/R/Study.R | 141 +++-- orthanc-0.2.0/orthanc/R/filtering.R | 91 ++- orthanc-0.2.0/orthanc/R/retrieve-dicom.R |only orthanc-0.2.0/orthanc/R/retrieve-others.R |only orthanc-0.2.0/orthanc/R/utils-checks.R | 38 + orthanc-0.2.0/orthanc/R/utils-other.R | 10 orthanc-0.2.0/orthanc/README.md | 17 orthanc-0.2.0/orthanc/inst/benchmark_downloads.R |only orthanc-0.2.0/orthanc/inst/paper/paper.pdf |only orthanc-0.2.0/orthanc/man/Instance.Rd | 152 ++++- orthanc-0.2.0/orthanc/man/Job.Rd | 18 orthanc-0.2.0/orthanc/man/Modality.Rd | 18 orthanc-0.2.0/orthanc/man/Orthanc.Rd | 2 orthanc-0.2.0/orthanc/man/OrthancAsync.Rd | 2 orthanc-0.2.0/orthanc/man/Patient.Rd | 82 ++ orthanc-0.2.0/orthanc/man/Resource.Rd | 20 orthanc-0.2.0/orthanc/man/Series.Rd | 96 ++- orthanc-0.2.0/orthanc/man/Study.Rd | 76 ++ orthanc-0.2.0/orthanc/man/find_and_filter_patients.Rd | 11 orthanc-0.2.0/orthanc/man/retrieve_and_write_nifti.Rd |only orthanc-0.2.0/orthanc/man/retrieve_and_write_patients.Rd | 15 38 files changed, 1236 insertions(+), 389 deletions(-)
Title: Basic Sequence Processing Tool for Biological Data
Description: Primarily created as an easy and understanding way to do basic sequences surrounding the central dogma of molecular biology.
Author: Ambu Vijayan [aut, cre] ,
J. Sreekumar [aut]
Maintainer: Ambu Vijayan <ambuvjyn@gmail.com>
Diff between baseq versions 0.1.4 dated 2023-05-03 and 0.2.0 dated 2026-03-11
baseq-0.1.4/baseq/R/clean_DNA.R |only baseq-0.1.4/baseq/R/clean_DNA_sequence.R |only baseq-0.1.4/baseq/R/clean_RNA.R |only baseq-0.1.4/baseq/R/clean_RNA_sequence.R |only baseq-0.1.4/baseq/R/clean_sequence.R |only baseq-0.1.4/baseq/R/count_bases.R |only baseq-0.1.4/baseq/R/count_seq_pattern.R |only baseq-0.1.4/baseq/R/dna_to_protein.R |only baseq-0.1.4/baseq/R/dna_to_rna.R |only baseq-0.1.4/baseq/R/fastq_to_fasta.R |only baseq-0.1.4/baseq/R/gc_content.R |only baseq-0.1.4/baseq/R/gc_content_file.R |only baseq-0.1.4/baseq/R/read_fasta_df.R |only baseq-0.1.4/baseq/R/read_fasta_list.R |only baseq-0.1.4/baseq/R/read_fastq_df.R |only baseq-0.1.4/baseq/R/read_fastq_list.R |only baseq-0.1.4/baseq/R/reverse_complement.R |only baseq-0.1.4/baseq/R/rna_reverse_complement.R |only baseq-0.1.4/baseq/R/rna_to_dna.R |only baseq-0.1.4/baseq/R/rna_to_protein.R |only baseq-0.1.4/baseq/R/write_df_to_fasta.R |only baseq-0.1.4/baseq/R/write_df_to_fastq.R |only baseq-0.1.4/baseq/R/write_dna_to_rna.R |only baseq-0.1.4/baseq/R/write_list_to_fasta.R |only baseq-0.1.4/baseq/R/write_list_to_fastq.R |only baseq-0.1.4/baseq/R/write_rna_to_dna.R |only baseq-0.1.4/baseq/man/clean_DNA_file.Rd |only baseq-0.1.4/baseq/man/clean_DNA_sequence.Rd |only baseq-0.1.4/baseq/man/clean_RNA_file.Rd |only baseq-0.1.4/baseq/man/clean_RNA_sequence.Rd |only baseq-0.1.4/baseq/man/clean_sequence.Rd |only baseq-0.1.4/baseq/man/count_seq_pattern.Rd |only baseq-0.1.4/baseq/man/gc_content_file.Rd |only baseq-0.1.4/baseq/man/read.fasta_to_df.Rd |only baseq-0.1.4/baseq/man/read.fasta_to_list.Rd |only baseq-0.1.4/baseq/man/read.fastq_to_df.Rd |only baseq-0.1.4/baseq/man/read.fastq_to_list.Rd |only baseq-0.1.4/baseq/man/reverse_complement.Rd |only baseq-0.1.4/baseq/man/rna_reverse_complement.Rd |only baseq-0.1.4/baseq/man/write.df_to_fasta.Rd |only baseq-0.1.4/baseq/man/write.df_to_fastq.Rd |only baseq-0.1.4/baseq/man/write.dna_to_rna.Rd |only baseq-0.1.4/baseq/man/write.list_to_fasta.Rd |only baseq-0.1.4/baseq/man/write.list_to_fastq.Rd |only baseq-0.1.4/baseq/man/write.rna_to_dna.Rd |only baseq-0.2.0/baseq/DESCRIPTION | 21 +- baseq-0.2.0/baseq/MD5 | 124 +++++++------ baseq-0.2.0/baseq/NAMESPACE | 60 ++++-- baseq-0.2.0/baseq/NEWS.md | 24 +- baseq-0.2.0/baseq/R/analysis.R |only baseq-0.2.0/baseq/R/classes.R |only baseq-0.2.0/baseq/R/conversions.R |only baseq-0.2.0/baseq/R/data.R |only baseq-0.2.0/baseq/R/discovery.R |only baseq-0.2.0/baseq/R/io.R |only baseq-0.2.0/baseq/R/plots.R |only baseq-0.2.0/baseq/R/processing.R |only baseq-0.2.0/baseq/R/utils.R |only baseq-0.2.0/baseq/R/wetlab.R |only baseq-0.2.0/baseq/README.md | 205 ++++------------------ baseq-0.2.0/baseq/build |only baseq-0.2.0/baseq/data |only baseq-0.2.0/baseq/inst/doc |only baseq-0.2.0/baseq/man/as_Biostrings.Rd |only baseq-0.2.0/baseq/man/as_baseq_dna.Rd |only baseq-0.2.0/baseq/man/as_baseq_rna.Rd |only baseq-0.2.0/baseq/man/calculate_assembly_stats.Rd |only baseq-0.2.0/baseq/man/calculate_charge.Rd |only baseq-0.2.0/baseq/man/calculate_codon_usage.Rd |only baseq-0.2.0/baseq/man/calculate_identity.Rd |only baseq-0.2.0/baseq/man/calculate_mw.Rd |only baseq-0.2.0/baseq/man/calculate_pi.Rd |only baseq-0.2.0/baseq/man/calculate_tm.Rd |only baseq-0.2.0/baseq/man/clean_file.Rd |only baseq-0.2.0/baseq/man/clean_seq.Rd |only baseq-0.2.0/baseq/man/count_bases.Rd | 20 -- baseq-0.2.0/baseq/man/count_kmers.Rd |only baseq-0.2.0/baseq/man/count_pattern.Rd |only baseq-0.2.0/baseq/man/dna_to_protein.Rd | 36 --- baseq-0.2.0/baseq/man/dna_to_rna.Rd | 17 - baseq-0.2.0/baseq/man/fastq_to_fasta.Rd | 22 -- baseq-0.2.0/baseq/man/filter_fastq_quality.Rd |only baseq-0.2.0/baseq/man/find_cpg_islands.Rd |only baseq-0.2.0/baseq/man/find_longest_orf.Rd |only baseq-0.2.0/baseq/man/gc_content.Rd | 17 - baseq-0.2.0/baseq/man/get_genetic_code.Rd |only baseq-0.2.0/baseq/man/plot_aa_composition.Rd |only baseq-0.2.0/baseq/man/plot_dotplot.Rd |only baseq-0.2.0/baseq/man/plot_gc_skew.Rd |only baseq-0.2.0/baseq/man/plot_hydrophobicity.Rd |only baseq-0.2.0/baseq/man/read_seq.Rd |only baseq-0.2.0/baseq/man/rev_comp.Rd |only baseq-0.2.0/baseq/man/reverse_translate.Rd |only baseq-0.2.0/baseq/man/rna_to_dna.Rd | 17 - baseq-0.2.0/baseq/man/rna_to_protein.Rd | 36 --- baseq-0.2.0/baseq/man/sars_fragment.Rd |only baseq-0.2.0/baseq/man/search_motif.Rd |only baseq-0.2.0/baseq/man/shuffle_sequence.Rd |only baseq-0.2.0/baseq/man/simulate_digestion.Rd |only baseq-0.2.0/baseq/man/simulate_fasta.Rd |only baseq-0.2.0/baseq/man/simulate_fastq.Rd |only baseq-0.2.0/baseq/man/simulate_pcr.Rd |only baseq-0.2.0/baseq/man/simulate_sequence.Rd |only baseq-0.2.0/baseq/man/summarize_fasta.Rd |only baseq-0.2.0/baseq/man/translate.Rd |only baseq-0.2.0/baseq/man/write_seq.Rd |only baseq-0.2.0/baseq/tests |only baseq-0.2.0/baseq/vignettes |only 108 files changed, 231 insertions(+), 368 deletions(-)
Title: Framework for Tick Population and Infection Modeling
Description: Code to specify, run, and then visualize and analyze the results of
Ixodidae (hard-bodied ticks) population and infection dynamics models. Such
models exist in the literature, but the source code to run them is not
always available. 'IxPopDyMod' provides an easy way for these models to be
written and shared.
Author: Myles Stokowski [aut, cre],
David Allen [aut]
Maintainer: Myles Stokowski <mylesstokowski@gmail.com>
Diff between IxPopDyMod versions 0.3.0 dated 2023-10-23 and 0.4.0 dated 2026-03-11
DESCRIPTION | 22 +- MD5 | 24 +- NAMESPACE | 2 NEWS.md | 4 R/life_cycle.R | 16 - R/parameters.R | 2 R/predictors.R | 5 R/run.R | 288 ++++++++++++++++------------- R/transition.R | 6 build/partial.rdb |binary tests/testthat/_snaps/run.md | 422 ++++++++++++++++++------------------------- tests/testthat/helper.R | 2 tests/testthat/test-run.R | 19 - 13 files changed, 394 insertions(+), 418 deletions(-)
Title: Extra Twitter Bootstrap Components for Shiny
Description: Adds easy access to additional Twitter Bootstrap components to Shiny.
Author: Eric Bailey [aut],
Federico Marini [cre, ctb] ,
Jesse Koops [ctb]
Maintainer: Federico Marini <marinif@uni-mainz.de>
Diff between shinyBS versions 0.63.0 dated 2025-12-17 and 0.64.0 dated 2026-03-11
DESCRIPTION | 10 +++++----- MD5 | 5 +++-- NEWS.md |only inst/www/shinyBS.js | 4 ++-- 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Common Argument Checks for 'r-dcm' Packages
Description: Many packages in the 'r-dcm' family take similar arguments,
which are checked for expected structures and values. Rather than
duplicating code across several packages, commonly used check
functions are included here. This package can then be imported to
access the check functions in other packages.
Author: W. Jake Thompson [aut, cre] ,
University of Kansas [cph],
Institute of Education Sciences [fnd],
Accessible Teaching, Learning, and Assessment Systems [fnd]
Maintainer: W. Jake Thompson <wjakethompson@gmail.com>
Diff between rdcmchecks versions 0.1.0 dated 2025-09-15 and 0.1.1 dated 2026-03-11
DESCRIPTION | 10 ++-- MD5 | 19 ++++--- NAMESPACE | 1 NEWS.md | 8 +++ R/check-data.R | 6 +- R/check-missing.R |only R/utils.R |only inst/WORDLIST | 4 - man/check_missing.Rd |only man/rdcmchecks-package.Rd | 2 tests/testthat/test-check-data.R | 89 ++++++++++++++++++++++++++++++++++++ tests/testthat/test-check-missing.R |only tests/testthat/test-utils.R |only 13 files changed, 122 insertions(+), 17 deletions(-)
Title: Product-Limit Estimation for Censored Event History Analysis
Description: Fast and user friendly implementation of nonparametric estimators
for censored event history (survival) analysis. Kaplan-Meier and
Aalen-Johansen method.
Author: Thomas A. Gerds [aut, cre]
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between prodlim versions 2025.04.28 dated 2025-04-28 and 2026.03.11 dated 2026-03-11
DESCRIPTION | 10 MD5 | 34 +- NAMESPACE | 2 R/EventHistory.frame.R | 76 ++-- R/GeomProdlim.R |only R/StatProdlim.R |only R/geom_prodlim.R |only R/ggprodlim.R | 704 +++++++++++++++++++++++++++++++++--------- R/model.design.R | 14 R/parseFormula.R |only R/parseSpecialNames.R | 1 R/predict.prodlim.R | 1 R/prodlim-package.R | 7 R/stat_prodlim.R |only R/strip.terms.R | 4 README.md |only man/EventHistory.frame.Rd | 11 man/geom_prodlim.Rd |only man/ggprodlim.Rd | 160 ++++++--- man/model.design.Rd | 3 man/parseFormula.Rd |only tests/testthat/test-prodlim.R | 46 -- 22 files changed, 766 insertions(+), 307 deletions(-)
Title: Seasonal Adjustment with TRAMO-SEATS in 'JDemetra+' 3.x
Description: Interface to 'JDemetra+' 3.x (<https://github.com/jdemetra>)
time series analysis software. It offers full access to options and
outputs of 'TRAMO-SEATS' (Time series Regression with ARIMA noise,
Missing values and Outliers - Signal Extraction in ARIMA Time Series),
including 'TRAMO' modelling (ARIMA model with outlier detection and
trading days adjustment). ARIMA = AutoRegressive Integrated Moving Average.
Author: Jean Palate [aut],
Alain Quartier-la-Tente [aut] ,
Tanguy Barthelemy [aut, cre, art],
Anna Smyk [aut]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between rjd3tramoseats versions 3.6.0 dated 2026-01-27 and 3.7.1 dated 2026-03-11
rjd3tramoseats-3.6.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-api-3.6.0.jar |only rjd3tramoseats-3.6.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-core-3.6.0.jar |only rjd3tramoseats-3.6.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-protobuf-3.6.0.jar |only rjd3tramoseats-3.6.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-r-3.6.0.jar |only rjd3tramoseats-3.6.0/rjd3tramoseats/man/java_version.Rd |only rjd3tramoseats-3.7.1/rjd3tramoseats/DESCRIPTION | 10 - rjd3tramoseats-3.7.1/rjd3tramoseats/MD5 | 53 ++++------ rjd3tramoseats-3.7.1/rjd3tramoseats/NAMESPACE | 11 +- rjd3tramoseats-3.7.1/rjd3tramoseats/NEWS.md | 6 + rjd3tramoseats-3.7.1/rjd3tramoseats/R/revisions.R | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/R/seats.R | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/R/seats_spec.R | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/R/tramo_outliers.R | 3 rjd3tramoseats-3.7.1/rjd3tramoseats/R/tramoseats.R | 12 +- rjd3tramoseats-3.7.1/rjd3tramoseats/R/tramoseats_spec.R | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/R/zzz.R | 30 +---- rjd3tramoseats-3.7.1/rjd3tramoseats/README.md | 24 +--- rjd3tramoseats-3.7.1/rjd3tramoseats/inst/java/jdplus-tramoseats-base-api-3.7.1.jar |only rjd3tramoseats-3.7.1/rjd3tramoseats/inst/java/jdplus-tramoseats-base-core-3.7.1.jar |only rjd3tramoseats-3.7.1/rjd3tramoseats/inst/java/jdplus-tramoseats-base-protobuf-3.7.1.jar |only rjd3tramoseats-3.7.1/rjd3tramoseats/inst/java/jdplus-tramoseats-base-r-3.7.1.jar |only rjd3tramoseats-3.7.1/rjd3tramoseats/man/refresh.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/seats_decompose.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/set_seats.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/terror.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/tramo.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/tramo_forecast.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/tramo_outliers.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/tramoseats.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/tramoseats_dictionary.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/tramoseats_revisions.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/tramoseats_spec.Rd | 2 32 files changed, 82 insertions(+), 97 deletions(-)
More information about rjd3tramoseats at CRAN
Permanent link
Title: Extensible Framework for Data Pattern Exploration
Description: A framework for systematic exploration of
association rules (Agrawal et al., 1994, <https://www.vldb.org/conf/1994/P487.PDF>),
contrast patterns (Chen, 2022, <doi:10.48550/arXiv.2209.13556>),
emerging patterns (Dong et al., 1999, <doi:10.1145/312129.312191>),
subgroup discovery (Atzmueller, 2015, <doi:10.1002/widm.1144>),
and conditional correlations (Hájek, 1978, <doi:10.1007/978-3-642-66943-9>).
User-defined functions may also be supplied to guide custom pattern searches.
Supports both crisp (Boolean) and fuzzy data. Generates candidate conditions
expressed as elementary conjunctions, evaluates them on a dataset, and
inspects the induced sub-data for statistical, logical, or structural
properties such as associations, correlations, or contrasts. Includes methods
for visualization of logical structures and supports interactive exploration
through integrated Shiny applications.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between nuggets versions 2.1.2 dated 2026-02-05 and 2.2.0 dated 2026-03-11
nuggets-2.1.2/nuggets/R/msg.R |only nuggets-2.1.2/nuggets/man/explore.Rd |only nuggets-2.2.0/nuggets/DESCRIPTION | 8 nuggets-2.2.0/nuggets/MD5 | 140 +++-- nuggets-2.2.0/nuggets/NAMESPACE | 12 nuggets-2.2.0/nuggets/NEWS.md | 15 nuggets-2.2.0/nuggets/R/add_interest-associations.R | 4 nuggets-2.2.0/nuggets/R/association_matrix.R | 6 nuggets-2.2.0/nuggets/R/cluster_associations.R | 8 nuggets-2.2.0/nuggets/R/dig.R | 25 - nuggets-2.2.0/nuggets/R/dig_ancestors-associations.R |only nuggets-2.2.0/nuggets/R/dig_ancestors.R |only nuggets-2.2.0/nuggets/R/dig_associations.R | 2 nuggets-2.2.0/nuggets/R/dig_complement_contrasts.R | 7 nuggets-2.2.0/nuggets/R/dig_correlations.R | 2 nuggets-2.2.0/nuggets/R/dig_grid.R | 6 nuggets-2.2.0/nuggets/R/explore-associations.R | 39 - nuggets-2.2.0/nuggets/R/explore-baseline_contrasts.R |only nuggets-2.2.0/nuggets/R/explore-complement_contrasts.R |only nuggets-2.2.0/nuggets/R/explore-correlations.R |only nuggets-2.2.0/nuggets/R/explore-paired_baseline_contrasts.R |only nuggets-2.2.0/nuggets/R/extract_cols.R | 2 nuggets-2.2.0/nuggets/R/fire.R | 4 nuggets-2.2.0/nuggets/R/geom_diamond.R | 82 ++- nuggets-2.2.0/nuggets/R/helper-msg.R |only nuggets-2.2.0/nuggets/R/nuggets-package.R | 3 nuggets-2.2.0/nuggets/R/parse_condition.R | 2 nuggets-2.2.0/nuggets/R/partition.R | 70 +- nuggets-2.2.0/nuggets/R/plot_contingency-data.frame.R |only nuggets-2.2.0/nuggets/R/plot_contingency-default.R |only nuggets-2.2.0/nuggets/R/plot_contingency.R |only nuggets-2.2.0/nuggets/R/remove_almost_constant.R | 7 nuggets-2.2.0/nuggets/R/shorten_condition.R | 5 nuggets-2.2.0/nuggets/R/t_test.R | 2 nuggets-2.2.0/nuggets/R/testers.R | 62 ++ nuggets-2.2.0/nuggets/R/ui-associationsDetailModule.R | 175 ++++--- nuggets-2.2.0/nuggets/R/ui-conditionFilterModule.R | 60 +- nuggets-2.2.0/nuggets/R/ui-datatable2.R | 44 + nuggets-2.2.0/nuggets/R/ui-exploreApp.R | 17 nuggets-2.2.0/nuggets/R/ui-numericFilterModule.R | 197 ++++--- nuggets-2.2.0/nuggets/R/ui-rulebaseTable.R | 26 - nuggets-2.2.0/nuggets/R/ui-scatterFilterModule.R | 2 nuggets-2.2.0/nuggets/R/ui-variableFilterModule.R |only nuggets-2.2.0/nuggets/R/var_grid.R | 6 nuggets-2.2.0/nuggets/R/var_test.R | 2 nuggets-2.2.0/nuggets/R/wilcox_test.R | 2 nuggets-2.2.0/nuggets/README.md | 30 + nuggets-2.2.0/nuggets/inst/doc/data-preparation.html | 29 - nuggets-2.2.0/nuggets/inst/doc/nuggets.html | 4 nuggets-2.2.0/nuggets/man/dig_ancestors.Rd |only nuggets-2.2.0/nuggets/man/dig_complement_contrasts.Rd | 7 nuggets-2.2.0/nuggets/man/explore.associations.Rd |only nuggets-2.2.0/nuggets/man/explore.baseline_contrasts.Rd |only nuggets-2.2.0/nuggets/man/explore.complement_contrasts.Rd |only nuggets-2.2.0/nuggets/man/explore.correlations.Rd |only nuggets-2.2.0/nuggets/man/explore.paired_baseline_contrasts.Rd |only nuggets-2.2.0/nuggets/man/geom_diamond.Rd | 11 nuggets-2.2.0/nuggets/man/plot_contingency.Rd |only nuggets-2.2.0/nuggets/tests/testthat/test-add_interest-associations.R | 8 nuggets-2.2.0/nuggets/tests/testthat/test-association_matrix.R |only nuggets-2.2.0/nuggets/tests/testthat/test-dig.R | 5 nuggets-2.2.0/nuggets/tests/testthat/test-dig_ancestors-associations.R |only nuggets-2.2.0/nuggets/tests/testthat/test-dig_baseline_contrasts.R | 6 nuggets-2.2.0/nuggets/tests/testthat/test-dig_complement_contrasts.R | 5 nuggets-2.2.0/nuggets/tests/testthat/test-dig_correlations.R | 13 nuggets-2.2.0/nuggets/tests/testthat/test-dig_grid.R | 5 nuggets-2.2.0/nuggets/tests/testthat/test-dig_paired_baseline_contrasts.R | 5 nuggets-2.2.0/nuggets/tests/testthat/test-explore-associations.R |only nuggets-2.2.0/nuggets/tests/testthat/test-explore-baseline_contrasts.R |only nuggets-2.2.0/nuggets/tests/testthat/test-explore-complement_contrasts.R |only nuggets-2.2.0/nuggets/tests/testthat/test-explore-correlations.R |only nuggets-2.2.0/nuggets/tests/testthat/test-explore-paired_baseline_contrasts.R |only nuggets-2.2.0/nuggets/tests/testthat/test-geom_diamond.R | 247 +++++++++- nuggets-2.2.0/nuggets/tests/testthat/test-helper-msg.R |only nuggets-2.2.0/nuggets/tests/testthat/test-partition.R | 103 ++++ nuggets-2.2.0/nuggets/tests/testthat/test-plot_contingency.R |only nuggets-2.2.0/nuggets/tests/testthat/test-remove_almost_constant.R | 41 + nuggets-2.2.0/nuggets/tests/testthat/test-shorten_condition.R | 21 nuggets-2.2.0/nuggets/tests/testthat/test-t_test.R | 2 nuggets-2.2.0/nuggets/tests/testthat/test-testers.R | 224 ++++----- nuggets-2.2.0/nuggets/tests/testthat/test-ui-conditionFilterModule.R | 18 nuggets-2.2.0/nuggets/tests/testthat/test-ui-numericFilterModule.R | 128 +++++ nuggets-2.2.0/nuggets/tests/testthat/test-ui-rulebaseTable.R | 36 + nuggets-2.2.0/nuggets/tests/testthat/test-ui-variableFilterModule.R |only nuggets-2.2.0/nuggets/tests/testthat/test-var_test.R | 2 nuggets-2.2.0/nuggets/tests/testthat/test-wilcox_test.R | 2 86 files changed, 1451 insertions(+), 545 deletions(-)
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles, random deviates,
and densities. Log-likelihoods for multivariate Gaussian models and Gaussian copulae
parameterised by Cholesky factors of covariance or precision matrices are implemented
for interval-censored and exact data, or a mix thereof. Score functions for these
log-likelihoods are available. A class representing multiple lower triangular matrices
and corresponding methods are part of this package.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb] ,
Martin Maechler [ctb] ,
Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.3-3 dated 2025-01-10 and 1.3-5 dated 2026-03-11
mvtnorm-1.3-3/mvtnorm/inst/litdb.bib |only mvtnorm-1.3-3/mvtnorm/vignettes/litdb.bib |only mvtnorm-1.3-5/mvtnorm/DESCRIPTION | 17 mvtnorm-1.3-5/mvtnorm/MD5 | 59 mvtnorm-1.3-5/mvtnorm/NAMESPACE | 6 mvtnorm-1.3-5/mvtnorm/R/interface.R | 93 mvtnorm-1.3-5/mvtnorm/R/lpmvnorm.R | 4 mvtnorm-1.3-5/mvtnorm/R/ltMatrices.R | 35 mvtnorm-1.3-5/mvtnorm/build/partial.rdb |binary mvtnorm-1.3-5/mvtnorm/build/vignette.rds |binary mvtnorm-1.3-5/mvtnorm/inst/NEWS.Rd | 31 mvtnorm-1.3-5/mvtnorm/inst/REFERENCES.bib |only mvtnorm-1.3-5/mvtnorm/inst/doc/MVT_Rnews.Rnw | 8 mvtnorm-1.3-5/mvtnorm/inst/doc/MVT_Rnews.pdf |binary mvtnorm-1.3-5/mvtnorm/inst/doc/lmvnorm_src.R | 545 +++- mvtnorm-1.3-5/mvtnorm/inst/doc/lmvnorm_src.Rnw | 1985 +++++++++++------- mvtnorm-1.3-5/mvtnorm/inst/doc/lmvnorm_src.pdf |binary mvtnorm-1.3-5/mvtnorm/man/Mvt.Rd | 26 mvtnorm-1.3-5/mvtnorm/man/algorithms.Rd | 38 mvtnorm-1.3-5/mvtnorm/man/interface.Rd | 9 mvtnorm-1.3-5/mvtnorm/man/lpRR.Rd | 19 mvtnorm-1.3-5/mvtnorm/man/lpmvnorm.Rd | 18 mvtnorm-1.3-5/mvtnorm/man/ltMatrices.Rd | 10 mvtnorm-1.3-5/mvtnorm/man/mvtnorm-package.Rd | 6 mvtnorm-1.3-5/mvtnorm/man/pmvnorm.Rd | 40 mvtnorm-1.3-5/mvtnorm/man/pmvt.Rd | 44 mvtnorm-1.3-5/mvtnorm/man/qmvnorm.Rd | 9 mvtnorm-1.3-5/mvtnorm/man/qmvt.Rd | 22 mvtnorm-1.3-5/mvtnorm/tests/slpmvnorm.R | 87 mvtnorm-1.3-5/mvtnorm/vignettes/MVT_Rnews.Rnw | 8 mvtnorm-1.3-5/mvtnorm/vignettes/lmvnorm_src.Rnw | 1985 +++++++++++------- mvtnorm-1.3-5/mvtnorm/vignettes/lmvnorm_src.Rout.save | 577 +++-- 32 files changed, 3630 insertions(+), 2051 deletions(-)
Title: Estimate the Effective Reproductive Number with Trend Filtering
Description: Use trend filtering, a type of regularized nonparametric
regression, to estimate the instantaneous reproduction number, also
called Rt. This value roughly says how many new infections will result
from each new infection today. Values larger than 1 indicate that an
epidemic is growing while those less than 1 indicate decline. For more
details about this methodology, see Liu, Cai, Gustafson, and McDonald (2024)
<doi:10.1371/journal.pcbi.1012324>.
Author: Daniel J. McDonald [aut, cre, cph],
Jiaping Liu [aut],
Zhenglun Cai [ctb]
Maintainer: Daniel J. McDonald <daniel@stat.ubc.ca>
Diff between rtestim versions 1.0.1 dated 2025-10-24 and 1.0.2 dated 2026-03-11
rtestim-1.0.1/rtestim/inst/doc/delay-distributions.R |only rtestim-1.0.1/rtestim/inst/doc/delay-distributions.Rmd |only rtestim-1.0.1/rtestim/inst/doc/delay-distributions.html |only rtestim-1.0.1/rtestim/vignettes/backer.csv |only rtestim-1.0.1/rtestim/vignettes/delay-distns-byvar.rds |only rtestim-1.0.1/rtestim/vignettes/delay-distributions.Rmd |only rtestim-1.0.1/rtestim/vignettes/duotang-counts.rds |only rtestim-1.0.1/rtestim/vignettes/xu-etal-DATA_RAW.xlsx |only rtestim-1.0.2/rtestim/DESCRIPTION | 9 +++--- rtestim-1.0.2/rtestim/MD5 | 22 +++++----------- rtestim-1.0.2/rtestim/NEWS.md | 6 ++++ rtestim-1.0.2/rtestim/build/partial.rdb |binary rtestim-1.0.2/rtestim/build/vignette.rds |binary rtestim-1.0.2/rtestim/inst/doc/rtestim.html | 5 ++- rtestim-1.0.2/rtestim/man/figures/README-full-fit-1.png |binary rtestim-1.0.2/rtestim/src/RcppExports.cpp | 4 +- 16 files changed, 23 insertions(+), 23 deletions(-)
Title: Inference on Predicted Data
Description: Performs valid statistical inference on predicted data (IPD) using recent methods, where for a subset of the data, the outcomes have been predicted by an algorithm. Provides a wrapper function with specified defaults for the type of model and method to be used for estimation and inference. Further provides methods for tidying and summarizing results. Salerno et al., (2025) <doi:10.1093/bioinformatics/btaf055>.
Author: Stephen Salerno [aut, cre, cph] ,
Jiacheng Miao [aut],
Awan Afiaz [aut],
Kentaro Hoffman [aut],
Jesse Gronsbell [aut],
Jianhui Gao [aut],
David Cheng [aut],
Anna Neufeld [aut],
Qiongshi Lu [aut],
Tyler H McCormick [aut],
Jeffrey T Leek [aut]
Maintainer: Stephen Salerno <ssalerno@fredhutch.org>
Diff between ipd versions 0.4.0 dated 2026-03-06 and 0.4.1 dated 2026-03-11
DESCRIPTION | 10 ++-- MD5 | 12 ++--- NAMESPACE | 1 NEWS.md | 123 +++++++++++++++++++++++++++--------------------------- R/ipd-package.R | 2 README.md | 6 +- inst/doc/ipd.html | 45 +++++++++---------- 7 files changed, 98 insertions(+), 101 deletions(-)
Title: Bayesian Analyses for One- and Two-Sample Inference and
Regression Methods
Description: Perform fundamental analyses using Bayesian parametric and non-parametric inference (regression, anova, 1 and 2 sample inference, non-parametric tests, etc.). (Practically) no Markov chain Monte Carlo (MCMC) is used; all exact finite sample inference is completed via closed form solutions or else through posterior sampling automated to ensure precision in interval estimate bounds. Diagnostic plots for model assessment, and key inferential quantities (point and interval estimates, probability of direction, region of practical equivalence, and Bayes factors) and model visualizations are provided. Bayes factors are computed either by the Savage Dickey ratio given in Dickey (1971) <doi:10.1214/aoms/1177693507> or by Chib's method as given in xxx. Interpretations are from Kass and Raftery (1995) <doi:10.1080/01621459.1995.10476572>. ROPE bounds are based on discussions in Kruschke (2018) <doi:10.1177/2515245918771304>. Methods for determining the number of posterior samp [...truncated...]
Author: Daniel K. Sewell [aut, cre, cph] ,
Alan Arakkal [aut]
Maintainer: Daniel K. Sewell <daniel-sewell@uiowa.edu>
Diff between bayesics versions 2.1.0 dated 2026-02-20 and 2.1.1 dated 2026-03-11
DESCRIPTION | 6 MD5 | 14 - NAMESPACE | 384 ++++++++++++++++++++++----------------------- NEWS.md | 6 R/frac_bayes_factors.R | 3 R/lm_b.R | 20 +- man/lm_b.Rd | 8 tests/testthat/test-lm_b.R | 73 ++++++++ 8 files changed, 303 insertions(+), 211 deletions(-)
Title: A Deep Dynamic Experimental Self-Organizing Neural Network
Framework
Description: Provides a fully native R deep learning framework for
constructing, training, evaluating, and inspecting Deep Dynamic Ensemble
Self Organizing Neural Networks at research scale. The core engine is an
object oriented R6 class-based implementation with explicit control over
layer layout, dimensional flow, forward propagation, back propagation, and
transparent optimizer state updates. The framework does not rely on external
deep learning back ends, enabling direct inspection of model state,
reproducible numerical behavior, and fine grained architectural control
without requiring compiled dependencies or graphics processing unit specific
run times. Users can define dimension agnostic single layer or deep
multi-layer networks without hard coded architecture limits, with per layer
configuration vectors for activation functions, derivatives, dropout
behavior, and initialization strategies automatically aligned to network
depth through controlled replication or truncation. Reproducible workflo [...truncated...]
Author: Mathew William Armitage Fok [aut, cre]
Maintainer: Mathew William Armitage Fok <quiksilver67213@yahoo.com>
Diff between DDESONN versions 7.1.9 dated 2026-03-03 and 7.1.11 dated 2026-03-11
DDESONN-7.1.11/DDESONN/DESCRIPTION | 6 DDESONN-7.1.11/DDESONN/MD5 | 31 - DDESONN-7.1.11/DDESONN/README.md | 60 ++- DDESONN-7.1.11/DDESONN/build/partial.rdb |only DDESONN-7.1.11/DDESONN/build/vignette.rds |binary DDESONN-7.1.11/DDESONN/inst/doc/DDESONNvsKeras_1000Seeds.R |only DDESONN-7.1.11/DDESONN/inst/doc/DDESONNvsKeras_1000Seeds.Rmd |only DDESONN-7.1.11/DDESONN/inst/doc/DDESONNvsKeras_1000Seeds.html |only DDESONN-7.1.11/DDESONN/inst/doc/logs_main-change-movement_ensemble_runs_scenarioD.R | 2 DDESONN-7.1.11/DDESONN/inst/doc/logs_main-change-movement_ensemble_runs_scenarioD.Rmd | 2 DDESONN-7.1.11/DDESONN/inst/doc/logs_main-change-movement_ensemble_runs_scenarioD.html | 184 +++++----- DDESONN-7.1.11/DDESONN/inst/doc/plot-controls_scenario1-2_single-run_scenarioA.html | 24 - DDESONN-7.1.11/DDESONN/man/DDESONN-package.Rd | 2 DDESONN-7.1.11/DDESONN/man/ddesonn_artifacts_root.Rd | 6 DDESONN-7.1.11/DDESONN/man/ddesonn_plots_dir.Rd |only DDESONN-7.1.11/DDESONN/vignettes/DDESONNvsKeras_1000Seeds.Rmd |only DDESONN-7.1.11/DDESONN/vignettes/logs_main-change-movement_ensemble_runs_scenarioD.Rmd | 2 DDESONN-7.1.9/DDESONN/inst/doc/DDESONNvKeras_1000Seeds.R |only DDESONN-7.1.9/DDESONN/inst/doc/DDESONNvKeras_1000Seeds.Rmd |only DDESONN-7.1.9/DDESONN/inst/doc/DDESONNvKeras_1000Seeds.html |only DDESONN-7.1.9/DDESONN/man/DDESONN_plots_dir.Rd |only DDESONN-7.1.9/DDESONN/vignettes/DDESONNvKeras_1000Seeds.Rmd |only 22 files changed, 184 insertions(+), 135 deletions(-)
Title: Connectome Predictive Modelling in R
Description: Connectome Predictive Modelling (CPM) (Shen et al. (2017)
<doi:10.1038/nprot.2016.178>) is a method to predict individual
differences in behaviour from brain functional connectivity. 'cpmr'
provides a simple yet efficient implementation of this method.
Author: Liang Zhang [aut, cre]
Maintainer: Liang Zhang <psychelzh@outlook.com>
Diff between cpmr versions 0.1.0 dated 2024-10-06 and 0.1.1 dated 2026-03-11
cpmr-0.1.0/cpmr/tests/testthat/test-check_names.R |only cpmr-0.1.1/cpmr/DESCRIPTION | 8 cpmr-0.1.1/cpmr/LICENSE | 4 cpmr-0.1.1/cpmr/MD5 | 34 cpmr-0.1.1/cpmr/NAMESPACE | 1 cpmr-0.1.1/cpmr/NEWS.md | 131 + cpmr-0.1.1/cpmr/R/constants.R | 4 cpmr-0.1.1/cpmr/R/cpm.R | 671 ++++----- cpmr-0.1.1/cpmr/R/cpmr-package.R | 1 cpmr-0.1.1/cpmr/R/summary.R | 144 +- cpmr-0.1.1/cpmr/R/tidy.R | 3 cpmr-0.1.1/cpmr/R/utils.R |only cpmr-0.1.1/cpmr/build/partial.rdb |binary cpmr-0.1.1/cpmr/man/cpm.Rd | 6 cpmr-0.1.1/cpmr/tests/testthat.R | 24 cpmr-0.1.1/cpmr/tests/testthat/_snaps/cpm.md | 1362 ++++++++++---------- cpmr-0.1.1/cpmr/tests/testthat/_snaps/tidy.md | 294 ++-- cpmr-0.1.1/cpmr/tests/testthat/test-cpm-internals.R |only cpmr-0.1.1/cpmr/tests/testthat/test-cpm.R | 309 ++-- cpmr-0.1.1/cpmr/tests/testthat/test-utils.R |only 20 files changed, 1510 insertions(+), 1486 deletions(-)
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format):
MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), Dia-NN (Demichev et al 2020 <doi:10.1038/s41592-019-0638-x>),
Fragpipe (da Veiga et al 2020 <doi:10.1038/s41592-020-0912-y>), ionbot (Degroeve et al 2021 <doi:10.1101/2021.07.02.450686>),
MassChroq (Valot et al 2011 <doi:10.1002/pmic.201100120>),
OpenMS (Strauss et al 2021 <doi:10.1038/nmeth.3959>), ProteomeDiscoverer (Orsburn 2021 <doi:10.3390/proteomes9010015>),
Proline (Bouyssie et a [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 1.13.3 dated 2025-08-22 and 2.0.0.2 dated 2026-03-11
wrProteo-1.13.3/wrProteo/R/readProtDiscovPeptides.R |only wrProteo-1.13.3/wrProteo/man/readProtDiscovPeptides.Rd |only wrProteo-2.0.0.2/wrProteo/DESCRIPTION | 12 wrProteo-2.0.0.2/wrProteo/MD5 | 129 wrProteo-2.0.0.2/wrProteo/NAMESPACE | 2 wrProteo-2.0.0.2/wrProteo/R/combineMultFilterNAimput.R | 102 wrProteo-2.0.0.2/wrProteo/R/corColumnOrder.R | 2 wrProteo-2.0.0.2/wrProteo/R/exportSdrfDraft.R | 2 wrProteo-2.0.0.2/wrProteo/R/extractTestingResults.R | 83 wrProteo-2.0.0.2/wrProteo/R/fuseProteomicsProjects.R | 4 wrProteo-2.0.0.2/wrProteo/R/getUPS1acc.R | 47 wrProteo-2.0.0.2/wrProteo/R/matrixNAinspect.R | 18 wrProteo-2.0.0.2/wrProteo/R/matrixNAneighbourImpute.R | 32 wrProteo-2.0.0.2/wrProteo/R/readAlphaPeptFile.R | 11 wrProteo-2.0.0.2/wrProteo/R/readDiaNNFile.R | 13 wrProteo-2.0.0.2/wrProteo/R/readDiaNNPeptides.R | 11 wrProteo-2.0.0.2/wrProteo/R/readFasta2.R | 320 - wrProteo-2.0.0.2/wrProteo/R/readFragpipeFile.R | 8 wrProteo-2.0.0.2/wrProteo/R/readIonbotPeptides.R | 20 wrProteo-2.0.0.2/wrProteo/R/readMassChroQFile.R | 19 wrProteo-2.0.0.2/wrProteo/R/readMaxQuantFile.R | 46 wrProteo-2.0.0.2/wrProteo/R/readMaxQuantPeptides.R | 19 wrProteo-2.0.0.2/wrProteo/R/readOpenMSFile.R | 18 wrProteo-2.0.0.2/wrProteo/R/readProlineFile.R | 36 wrProteo-2.0.0.2/wrProteo/R/readProteomeDiscovererFile.R | 171 wrProteo-2.0.0.2/wrProteo/R/readProteomeDiscovererPeptides.R | 33 wrProteo-2.0.0.2/wrProteo/R/readSampleMetaData.R | 741 +- wrProteo-2.0.0.2/wrProteo/R/readSdrf.R | 23 wrProteo-2.0.0.2/wrProteo/R/readWombatNormFile.R | 11 wrProteo-2.0.0.2/wrProteo/R/removeSampleInList.R | 115 wrProteo-2.0.0.2/wrProteo/R/replMissingProtNames.R | 14 wrProteo-2.0.0.2/wrProteo/R/summarizeForROC.R | 2 wrProteo-2.0.0.2/wrProteo/R/testRobustToNAimputation.R | 346 + wrProteo-2.0.0.2/wrProteo/R/writeFasta2.R | 64 wrProteo-2.0.0.2/wrProteo/build/vignette.rds |binary wrProteo-2.0.0.2/wrProteo/inst/doc/wrProteoVignette1.R | 52 wrProteo-2.0.0.2/wrProteo/inst/doc/wrProteoVignette1.Rmd | 93 wrProteo-2.0.0.2/wrProteo/inst/doc/wrProteoVignette1.html | 769 ++ wrProteo-2.0.0.2/wrProteo/inst/doc/wrProteoVignetteUPS1.R | 35 wrProteo-2.0.0.2/wrProteo/inst/doc/wrProteoVignetteUPS1.Rmd | 42 wrProteo-2.0.0.2/wrProteo/inst/doc/wrProteoVignetteUPS1.html | 2566 +++++----- wrProteo-2.0.0.2/wrProteo/inst/extdata/conta1.fasta.gz |binary wrProteo-2.0.0.2/wrProteo/man/combineMultFilterNAimput.Rd | 23 wrProteo-2.0.0.2/wrProteo/man/corColumnOrder.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/dot-checkSetupGroups.Rd | 3 wrProteo-2.0.0.2/wrProteo/man/dot-commonSpecies.Rd | 4 wrProteo-2.0.0.2/wrProteo/man/dot-parseFastaHeader.Rd |only wrProteo-2.0.0.2/wrProteo/man/exportSdrfDraft.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/extractTestingResults.Rd | 16 wrProteo-2.0.0.2/wrProteo/man/matrixNAinspect.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/matrixNAneighbourImpute.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/readFasta2.Rd | 21 wrProteo-2.0.0.2/wrProteo/man/readIonbotPeptides.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/readMaxQuantFile.Rd | 4 wrProteo-2.0.0.2/wrProteo/man/readMaxQuantPeptides.Rd | 4 wrProteo-2.0.0.2/wrProteo/man/readProlineFile.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/readProtDiscovererPeptides.Rd | 4 wrProteo-2.0.0.2/wrProteo/man/readProteomeDiscovererFile.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/readProteomeDiscovererPeptides.Rd | 4 wrProteo-2.0.0.2/wrProteo/man/readSampleMetaData.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/removeSampleInList.Rd | 4 wrProteo-2.0.0.2/wrProteo/man/replMissingProtNames.Rd | 4 wrProteo-2.0.0.2/wrProteo/man/summarizeForROC.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/testRobustToNAimputation.Rd | 54 wrProteo-2.0.0.2/wrProteo/man/writeFasta2.Rd | 26 wrProteo-2.0.0.2/wrProteo/vignettes/wrProteoVignette1.Rmd | 93 wrProteo-2.0.0.2/wrProteo/vignettes/wrProteoVignetteUPS1.Rmd | 42 67 files changed, 3786 insertions(+), 2569 deletions(-)
Title: Wearable Accelerometer Data File Readers
Description: Reads data collected from wearable acceleratometers as used in sleep and physical activity research. Currently supports file formats: binary data from 'GENEActiv' <https://activinsights.com/>, .bin-format from GENEA devices (not for sale), and .cwa-format from 'Axivity' <https://axivity.com>. Further, it has functions for reading text files with epoch level aggregates from 'Actical', 'Fitbit', 'Actiwatch', 'ActiGraph', and 'PhilipsHealthBand'. Primarily designed to complement R package GGIR <https://CRAN.R-project.org/package=GGIR>.
Author: Vincent T van Hees [aut, cre],
Patrick Bos [aut] ,
Lena Kushleyeva [ctb],
Jing Hua Zhao [ctb],
Evgeny Mirkes [ctb],
Dan Jackson [ctb],
Jairo H Migueles [ctb],
Medical Research Council UK [cph, fnd],
Accelting [cph, fnd]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIRread versions 1.0.7 dated 2025-11-26 and 1.0.8 dated 2026-03-11
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 8 ++++++-- R/readActiwatchCount.R | 2 +- README.md | 2 +- man/GGIRread-package.Rd | 4 ++-- man/readParmayMatrix.Rd | 2 +- tests/testthat/test_readActiwatchCount.R | 8 +++++--- 8 files changed, 27 insertions(+), 21 deletions(-)
Title: Various Blocking Methods for Entity Resolution
Description: The goal of 'blocking' is to provide blocking methods for record linkage and deduplication using approximate nearest neighbour (ANN) algorithms and graph techniques. It supports multiple ANN implementations via 'rnndescent', 'RcppHNSW', 'RcppAnnoy', and 'mlpack' packages, and provides integration with the 'reclin2' package. The package generates shingles from character strings and similarity vectors for record comparison, and includes evaluation metrics for assessing blocking performance including false positive rate (FPR) and false negative rate (FNR) estimates. For details see: Papadakis et al. (2020) <doi:10.1145/3377455>, Steorts et al. (2014) <doi:10.1007/978-3-319-11257-2_20>, Dasylva and Goussanou (2021) <https://www150.statcan.gc.ca/n1/en/catalogue/12-001-X202100200002>, Dasylva and Goussanou (2022) <doi:10.1007/s42081-022-00153-3>.
Author: Maciej Beresewicz [aut, cre] ,
Adam Struzik [aut, ctr]
Maintainer: Maciej Beresewicz <maciej.beresewicz@ue.poznan.pl>
Diff between blocking versions 1.0.1 dated 2025-06-18 and 1.0.2 dated 2026-03-11
DESCRIPTION | 8 +- MD5 | 58 +++++++++--------- NAMESPACE | 2 NEWS.md | 10 ++- R/blocking.R | 57 ++++++++++-------- R/est_block_error.R | 127 ++++++++++++++++++++++++++++++++++------- R/methods.R | 26 +++++++- build/partial.rdb |binary build/vignette.rds |binary data/RLdata500.rda |binary data/census.rda |binary data/cis.rda |binary data/foreigners.rda |binary inst/doc/v1-deduplication.R | 8 ++ inst/doc/v1-deduplication.Rmd | 15 +++- inst/doc/v1-deduplication.html | 18 +++-- inst/doc/v2-reclin.R | 3 inst/doc/v2-reclin.Rmd | 3 inst/doc/v2-reclin.html | 15 ++-- inst/doc/v3-integration.R | 4 + inst/doc/v3-integration.Rmd | 4 + inst/doc/v3-integration.html | 14 ++-- inst/tinytest/test_annoy.R | 2 inst/tinytest/test_hnsw.R | 2 inst/tinytest/test_mlpack.R | 2 man/blocking.Rd | 9 +- man/est_block_error.Rd | 71 +++++++++++++++++++--- vignettes/v1-deduplication.Rmd | 15 +++- vignettes/v2-reclin.Rmd | 3 vignettes/v3-integration.Rmd | 4 + 30 files changed, 351 insertions(+), 129 deletions(-)
Title: Accrual Plots and Predictions for Clinical Trials
Description: Tracking accrual in clinical trials is important for trial success.
If accrual is too slow, the trial will take too long and be too expensive. If
accrual is much faster than expected, time sensitive tasks such as the writing
of statistical analysis plans might need to be rushed. 'accrualPlot' provides
functions to aid the tracking of accrual and predict when a trial will reach
it's intended sample size.
Author: Lukas Buetikofer [cre, aut],
Alan G. Haynes [aut]
Maintainer: Lukas Buetikofer <lukas.buetikofer@unibe.ch>
Diff between accrualPlot versions 1.0.7 dated 2022-08-16 and 1.0.10 dated 2026-03-11
accrualPlot-1.0.10/accrualPlot/DESCRIPTION | 20 accrualPlot-1.0.10/accrualPlot/MD5 | 72 - accrualPlot-1.0.10/accrualPlot/NEWS.md | 15 accrualPlot-1.0.10/accrualPlot/R/accrual_create_df.R | 10 accrualPlot-1.0.10/accrualPlot/R/gg_accrual_plots.R | 6 accrualPlot-1.0.10/accrualPlot/build/vignette.rds |binary accrualPlot-1.0.10/accrualPlot/inst/doc/accrualPlot.R | 16 accrualPlot-1.0.10/accrualPlot/inst/doc/accrualPlot.html | 597 +++++----- accrualPlot-1.0.10/accrualPlot/man/accrual_create_df.Rd | 2 accrualPlot-1.0.10/accrualPlot/man/accrual_plot_abs.Rd | 2 accrualPlot-1.0.10/accrualPlot/man/accrual_plot_predict.Rd | 2 accrualPlot-1.0.10/accrualPlot/tests/testthat/Rplots.pdf |only accrualPlot-1.0.10/accrualPlot/tests/testthat/_snaps |only accrualPlot-1.0.10/accrualPlot/tests/testthat/test-accrual_plots.R | 4 accrualPlot-1.0.7/accrualPlot/tests/figs |only 15 files changed, 411 insertions(+), 335 deletions(-)
Title: Calculate High Resolution Water Balance of Starch Potatoes
Description: Calculates the water balance of starch potatoes from Normalized Distance Vegetation Index (NDVI) images, German Weather Service (DWD) reference evapotranspiration, German Weather Service RADOLAN precipitation data and irrigation information. For more details see Piernicke et al. (2025) <doi:10.3390/rs17183227>.
Author: Thomas Piernicke [aut, cre]
Maintainer: Thomas Piernicke <thomasp@gfz.de>
Diff between WaterBalanceR versions 0.1.19 dated 2025-12-19 and 0.1.20 dated 2026-03-11
DESCRIPTION | 8 +- MD5 | 15 ++- NEWS.md | 9 ++ R/calcWB.R | 20 ++--- README.md | 122 ++++++++++++++------------------ inst/CITATION | 2 inst/UserGuide.md |only inst/doc/WaterBalanceR_DataSources.html | 4 - inst/doc/WaterBalanceR_Workflow.html | 6 - 9 files changed, 94 insertions(+), 92 deletions(-)
Title: Measurement Units for R Vectors
Description: Support for measurement units in R vectors, matrices
and arrays: automatic propagation, conversion, derivation
and simplification of units; raising errors in case of unit
incompatibility. Compatible with the POSIXct, Date and difftime
classes. Uses the UNIDATA udunits library and unit database for
unit compatibility checking and conversion.
Documentation about 'units' is provided in the paper by Pebesma, Mailund &
Hiebert (2016, <doi:10.32614/RJ-2016-061>), included in this package as a
vignette; see 'citation("units")' for details.
Author: Edzer Pebesma [aut, cre] ,
Thomas Mailund [aut],
Tomasz Kalinowski [aut],
James Hiebert [ctb],
Inaki Ucar [aut] ,
Thomas Lin Pedersen [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between units versions 1.0-0 dated 2025-10-09 and 1.0-1 dated 2026-03-11
units-1.0-0/units/tests/testthat/_snaps/plot/ggplot2-range.svg |only units-1.0-1/units/DESCRIPTION | 8 units-1.0-1/units/MD5 | 50 +-- units-1.0-1/units/NEWS.md | 16 + units-1.0-1/units/R/RcppExports.R | 8 units-1.0-1/units/R/mixed.R | 1 units-1.0-1/units/R/summaries.R | 12 units-1.0-1/units/R/udunits.R | 6 units-1.0-1/units/build/vignette.rds |binary units-1.0-1/units/configure | 134 ++++++++ units-1.0-1/units/configure.ac | 34 ++ units-1.0-1/units/inst/doc/measurement_units_in_R.Rmd | 2 units-1.0-1/units/inst/doc/measurement_units_in_R.html | 2 units-1.0-1/units/inst/doc/units.Rmd | 4 units-1.0-1/units/inst/doc/units.html | 104 +++--- units-1.0-1/units/src/RcppExports.cpp | 73 ++-- units-1.0-1/units/src/udunits.cpp | 150 +++------- units-1.0-1/units/src/units_types.h |only units-1.0-1/units/tests/testthat/_snaps/plot/ggplot2-range-0.svg |only units-1.0-1/units/tests/testthat/_snaps/plot/ggplot2-range-1.svg |only units-1.0-1/units/tests/testthat/_snaps/plot/ggplot2-range-2.svg |only units-1.0-1/units/tests/testthat/_snaps/plot/ggplot2-range-3.svg |only units-1.0-1/units/tests/testthat/test_conversion.R | 2 units-1.0-1/units/tests/testthat/test_mixed.R | 4 units-1.0-1/units/tests/testthat/test_plot.R | 8 units-1.0-1/units/tests/testthat/test_summaries.R | 5 units-1.0-1/units/tests/testthat/test_udunits.R | 1 units-1.0-1/units/vignettes/measurement_units_in_R.Rmd | 2 units-1.0-1/units/vignettes/units.Rmd | 4 29 files changed, 385 insertions(+), 245 deletions(-)
Title: Sumerian Cuneiform Text Analysis
Description: Provides functions for converting transliterated Sumerian texts to sign names and cuneiform characters,
creating and querying dictionaries, analyzing the structure of
Sumerian words, and creating translations. Includes a built-in dictionary and supports both
forward lookup (Sumerian to English) and reverse lookup (English to
Sumerian).
Author: Robin Wellmann [aut, cre]
Maintainer: Robin Wellmann <ro.wellmann@gmail.com>
Diff between sumer versions 1.2.0 dated 2026-02-28 and 1.3.0 dated 2026-03-11
DESCRIPTION | 7 - MD5 | 54 +++++---- NAMESPACE | 6 + R/add_brackets.R |only R/apply_translation_rules.R |only R/as.cuneiform.R | 6 - R/as.sign_name.R | 4 R/compose_skeleton_entry.R |only R/eval_operator.R |only R/extract_skeleton_entries.R | 14 ++ R/grammatical_structure.R |only R/guess_substr_info.R | 2 R/info.R | 2 R/look_up.R | 2 R/mark_ngrams.R | 2 R/mark_skeleton_entries.R | 33 +++++- R/ngram_frequencies.R | 4 R/plot_sign_grammar.R | 2 R/sign_grammar.R | 4 R/skeleton.R | 163 ++++++++++++++---------------- R/standardize_signs.R | 10 + R/translate.R | 140 +++++++++++++++++++------ inst/doc/getting-started.html | 48 ++++---- inst/doc/translating-texts.html | 2 inst/extdata/enki_and_the_world_order.txt | 2 man/add_brackets.Rd |only man/apply_translation_rules.Rd |only man/compose_skeleton_entry.Rd |only man/eval_operator.Rd |only man/extract_skeleton_entries.Rd | 90 ++++++++-------- man/grammatical_structure.Rd |only man/mark_skeleton_entries.Rd | 102 +++++++++--------- man/translate.Rd | 36 ++++-- 33 files changed, 428 insertions(+), 307 deletions(-)
Title: Seasonal Adjustment with 'X-13' in 'JDemetra+' 3.x
Description: R Interface to 'JDemetra+' 3.x
(<https://github.com/jdemetra>) time series analysis software. It
offers full access to options and outputs of 'X-13', including Reg-ARIMA
modelling (automatic AutoRegressive Integrated Moving Average (ARIMA) model
with outlier detection and trading days adjustment) and X-11 decomposition.
Author: Jean Palate [aut],
Alain Quartier-la-Tente [aut] ,
Tanguy Barthelemy [aut, cre, art],
Anna Smyk [aut]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between rjd3x13 versions 3.6.0 dated 2026-01-27 and 3.7.1 dated 2026-03-11
rjd3x13-3.6.0/rjd3x13/inst/java/jdplus-x13-base-api-3.6.0.jar |only rjd3x13-3.6.0/rjd3x13/inst/java/jdplus-x13-base-core-3.6.0.jar |only rjd3x13-3.6.0/rjd3x13/inst/java/jdplus-x13-base-protobuf-3.6.0.jar |only rjd3x13-3.6.0/rjd3x13/inst/java/jdplus-x13-base-r-3.6.0.jar |only rjd3x13-3.6.0/rjd3x13/man/java_version.Rd |only rjd3x13-3.7.1/rjd3x13/DESCRIPTION | 14 +- rjd3x13-3.7.1/rjd3x13/MD5 | 49 ++++------ rjd3x13-3.7.1/rjd3x13/NAMESPACE | 7 - rjd3x13-3.7.1/rjd3x13/NEWS.md | 6 + rjd3x13-3.7.1/rjd3x13/R/regarima_outliers.R | 2 rjd3x13-3.7.1/rjd3x13/R/revisions.R | 2 rjd3x13-3.7.1/rjd3x13/R/set_x11_spec.R | 2 rjd3x13-3.7.1/rjd3x13/R/utils.R | 1 rjd3x13-3.7.1/rjd3x13/R/x13.R | 10 +- rjd3x13-3.7.1/rjd3x13/R/x13_spec.R | 2 rjd3x13-3.7.1/rjd3x13/R/zzz.R | 26 +---- rjd3x13-3.7.1/rjd3x13/README.md | 28 +---- rjd3x13-3.7.1/rjd3x13/inst/java/jdplus-x13-base-api-3.7.1.jar |only rjd3x13-3.7.1/rjd3x13/inst/java/jdplus-x13-base-core-3.7.1.jar |only rjd3x13-3.7.1/rjd3x13/inst/java/jdplus-x13-base-protobuf-3.7.1.jar |only rjd3x13-3.7.1/rjd3x13/inst/java/jdplus-x13-base-r-3.7.1.jar |only rjd3x13-3.7.1/rjd3x13/man/refresh.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/regarima.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/regarima_outliers.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/x11.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/x11_spec.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/x13.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/x13_dictionary.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/x13_revisions.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/x13_spec.Rd | 2 30 files changed, 69 insertions(+), 98 deletions(-)
Title: Interface to 'JDemetra+' 3.x Time Series Analysis Software
Description: Interface to 'JDemetra+' 3.x (<https://github.com/jdemetra>)
time series analysis software. It offers full access to txt, csv, xml
and spreadsheets files which are meant to be read by 'JDemetra+'
Graphical User Interface.
Author: Jean Palate [aut],
Alessandro Piovani [aut, cre],
Tanguy Barthelemy [ctb, art]
Maintainer: Alessandro Piovani <alessandro.piovani@istat.it>
Diff between rjd3providers versions 3.6.0 dated 2026-02-20 and 3.7.1 dated 2026-03-11
rjd3providers-3.6.0/rjd3providers/inst/java/jdplus-spreadsheet-base-api-3.6.0.jar |only rjd3providers-3.6.0/rjd3providers/inst/java/jdplus-spreadsheet-base-r-3.6.0.jar |only rjd3providers-3.6.0/rjd3providers/inst/java/jdplus-text-base-api-3.6.0.jar |only rjd3providers-3.6.0/rjd3providers/inst/java/jdplus-text-base-r-3.6.0.jar |only rjd3providers-3.6.0/rjd3providers/inst/java/jdplus-toolkit-base-tsp-3.6.0.jar |only rjd3providers-3.6.0/rjd3providers/inst/java/jdplus-toolkit-base-xml-3.6.0.jar |only rjd3providers-3.6.0/rjd3providers/man/java_version.Rd |only rjd3providers-3.7.1/rjd3providers/DESCRIPTION | 10 rjd3providers-3.7.1/rjd3providers/MD5 | 91 - rjd3providers-3.7.1/rjd3providers/NAMESPACE | 4 rjd3providers-3.7.1/rjd3providers/NEWS.md | 9 rjd3providers-3.7.1/rjd3providers/R/deprecated.R | 344 ++-- rjd3providers-3.7.1/rjd3providers/R/jd3spreadsheet.R | 676 ++++---- rjd3providers-3.7.1/rjd3providers/R/jd3txt.R | 780 +++++----- rjd3providers-3.7.1/rjd3providers/R/jd3xml.R | 522 +++--- rjd3providers-3.7.1/rjd3providers/R/providers.R | 120 - rjd3providers-3.7.1/rjd3providers/R/zzz.R | 70 rjd3providers-3.7.1/rjd3providers/README.md | 2 rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-spreadsheet-base-api-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-spreadsheet-base-r-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-text-base-api-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-text-base-r-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-toolkit-base-tsp-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-toolkit-base-xml-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/man/dot-obs_format.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/dot-obs_gathering.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/dot-spreadsheet_moniker.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/dot-txt_moniker.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/dot-xml_moniker.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/set_spreadsheet_paths.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/set_txt_paths.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/set_xml_paths.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/spreadsheet_change_file.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/spreadsheet_content.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/spreadsheet_data.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/spreadsheet_id_to_properties.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/spreadsheet_name.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/spreadsheet_properties_to_id.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/spreadsheet_series.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/txt_change_file.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/txt_content.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/txt_data.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/txt_id_to_properties.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/txt_name.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/txt_properties_to_id.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/txt_series.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/xml_change_file.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/xml_content.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/xml_data.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/xml_id_to_properties.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/xml_name.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/xml_properties_to_id.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/xml_series.Rd | 2 53 files changed, 1330 insertions(+), 1356 deletions(-)
Title: Wrangle Large Simulation Studies
Description: An 'R6' class to set up, run, monitor, collate, and debug large simulation studies comprising many small independent replications and treatment configurations. Parallel processing, reproducibility, fault- and error-tolerance, and ability to resume an interrupted or timed-out simulation study are built in.
Author: Pavel N. Krivitsky [aut, cre]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
This is a re-admission after prior archival of version 0.1.0 dated 2025-09-22
Diff between piecemeal versions 0.1.0 dated 2025-09-22 and 0.2.0 dated 2026-03-11
DESCRIPTION | 15 MD5 | 28 - NAMESPACE | 10 NEWS |only NEWS.md | 21 + R/Piecemeal.R | 192 ++++++++--- R/consolidate.R |only R/piecemeal-package.R | 2 build/stage23.rdb |only inst/doc/piecemeal.R | 4 inst/doc/piecemeal.Rmd | 2 inst/doc/piecemeal.html | 617 +++++++++++++++++++----------------- man/Piecemeal.Rd | 18 + man/piecemeal-package.Rd | 7 tests/testthat/test-consolidation.R |only tests/testthat/test-vignette.R | 6 vignettes/piecemeal.Rmd | 2 17 files changed, 561 insertions(+), 363 deletions(-)
Title: Simulation for Factorial Designs
Description: Create datasets with factorial structure through simulation by specifying variable parameters. Extended documentation at <https://www.scienceverse.org/faux/>. Described in DeBruine (2020) <doi:10.5281/zenodo.2669586>.
Author: Lisa DeBruine [aut, cre, cph] ,
Anna Krystalli [ctb] ,
Andrew Heiss [ctb]
Maintainer: Lisa DeBruine <debruine@gmail.com>
This is a re-admission after prior archival of version 1.2.3 dated 2025-10-01
Diff between faux versions 1.2.3 dated 2025-10-01 and 1.2.4 dated 2026-03-11
DESCRIPTION | 12 +++++------ MD5 | 51 +++++++++++++++++++++++------------------------ NEWS.md | 4 ++- R/check_design.R | 2 - R/codebook.R | 2 - R/faceratings.R | 4 +-- R/plot_design.R | 2 - R/rnorm_multi.R | 2 - R/sim_design.R | 2 - R/sim_df.R | 2 - R/sim_mixed_cc.R | 2 - R/zzz.R | 2 - README.md | 4 +-- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 2 - inst/doc/sim_design.html | 40 +++++++++++++++++++----------------- man/check_design.Rd | 2 - man/codebook.Rd | 2 - man/faceratings.Rd | 2 - man/faux.Rd | 2 - man/fr4.Rd | 2 - man/plot_design.Rd | 2 - man/rnorm_multi.Rd | 2 - man/sim_design.Rd | 2 - man/sim_df.Rd | 2 - man/sim_mixed_cc.Rd | 2 - 27 files changed, 79 insertions(+), 74 deletions(-)
Title: Climate Services' Indicators Based on Sub-Seasonal to Decadal
Predictions
Description: Set of generalised tools for the flexible computation of climate
related indicators defined by the user. Each method represents a specific
mathematical approach which is combined with the possibility to select an
arbitrary time period to define the indicator. This enables a wide range of
possibilities to tailor the most suitable indicator for each particular climate
service application (agriculture, food security, energy, water management, health...).
This package is intended for sub-seasonal, seasonal and decadal climate
predictions, but its methods are also applicable to other time-scales,
provided the dimensional structure of the input is maintained. Additionally,
the outputs of the functions in this package are compatible with 'CSTools'.
This package is described in Pérez-Zanón et al. (2023)
<doi:10.1016/j.cliser.2023.100393> and was developed in the context of the
H2020 projects MED-GOLD (776467) and S2S4E (776787) projects, as well as the
Horizon Europe project MEDEWSA (101 [...truncated...]
Author: Nuria Perez-Zanon [aut] ,
Chou Chihchung [aut],
Llorenc Lledo [aut],
Victoria Agudetse [ctb, cre],
Eva Rifa [ctb],
Gonzalez-Reviriego Nube [ctb],
Marcos Rauel [ctb],
Palma Lluis [ctb],
An-Chi Ho [ctb],
Javier Corvillo [ctb],
Alberto Bojaly [ctb],
Thee [...truncated...]
Maintainer: Victoria Agudetse <victoria.agudetse@bsc.es>
Diff between CSIndicators versions 1.1.3 dated 2025-11-24 and 1.2.0 dated 2026-03-11
DESCRIPTION | 32 +++++++++++--------- MD5 | 37 ++++++++++++++++++------ NAMESPACE | 10 ++++++ NEWS.md | 19 ++++++++++++ R/AccumulationExceedingThreshold.R | 17 +++++++---- R/DayLength.R |only R/HeatIndex.R |only R/MaxSpellTimeExceedingThreshold.R |only R/MultiVarExceedingThreshold.R |only R/Threshold.R | 11 +++++-- build/vignette.rds |binary inst/doc/AgriculturalIndicators.html | 2 - inst/doc/EnergyIndicators.html | 2 - inst/doc/HeatIndexIndicator.Rmd |only inst/doc/HeatIndexIndicator.html |only man/CST_DayLength.Rd |only man/CST_HeatIndex.Rd |only man/CST_MaxSpellTimeExceedingThreshold.Rd |only man/CST_MultiVarExceedingThreshold.Rd |only man/DayLength.Rd |only man/HeatIndex.Rd |only man/MaxSpellTimeExceedingThreshold.Rd |only man/MultiVarExceedingThreshold.Rd |only vignettes/Figures/HI_ANO_OBS.png |only vignettes/Figures/HI_BIAS.png |only vignettes/Figures/HI_TimeSpellThreshold_exp.png |only vignettes/Figures/HI_TimeSpellThreshold_obs.png |only vignettes/Figures/Spatial_rh.png |only vignettes/Figures/Spatial_temp.png |only vignettes/HeatIndexIndicator.Rmd |only 30 files changed, 98 insertions(+), 32 deletions(-)
Title: Cyclomatic Complexity of R Code
Description: Cyclomatic complexity is a software metric (measurement),
used to indicate the complexity of a program. It is a quantitative
measure of the number of linearly independent paths through a
program's source code. It was developed by Thomas J. McCabe, Sr. in
1976.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between cyclocomp versions 1.1.1 dated 2023-08-30 and 1.1.2 dated 2026-03-11
DESCRIPTION | 22 ++++++----- MD5 | 50 +++++++++++++------------ NEWS.md | 4 ++ R/cyclocomp.R | 5 +- R/flowgraph.R | 37 ++++++------------ R/package_dir.R | 25 +++++++----- R/post-process.R | 10 ++--- R/utils.R | 2 - README.md | 2 + man/cyclocomp.Rd | 6 +-- man/cyclocomp_package.Rd | 4 +- man/cyclocomp_package_dir.Rd | 8 ++-- tests/testthat.R | 8 ++++ tests/testthat/_snaps |only tests/testthat/test-andor.R | 15 +++---- tests/testthat/test-break.R | 28 +++++++++----- tests/testthat/test-calls.R | 5 -- tests/testthat/test-cyclocomp-package.R | 3 - tests/testthat/test-cyclocomp_q.R | 41 +++++++++++++++----- tests/testthat/test-formatting.R |only tests/testthat/test-function.R | 4 -- tests/testthat/test-if.R | 63 +++++++++++++++++++++----------- tests/testthat/test-next.R | 49 +++++++++++++++++++----- tests/testthat/test-repeat.R | 6 --- tests/testthat/test-return.R | 9 ++-- tests/testthat/test-seq.R | 29 +++++++++----- tests/testthat/test-stress.R | 4 -- 27 files changed, 255 insertions(+), 184 deletions(-)
Title: Fits Psychometric Functions for Multiple Groups
Description: Quickly fits and plots psychometric functions (normal, logistic,
Weibull or any or any function defined by the user) for multiple groups.
Author: Linares Daniel [aut, cre],
L<U+00F3>pez-Moliner Joan [aut]
Maintainer: Linares Daniel <danilinares@gmail.com>
Diff between quickpsy versions 0.1.5.1 dated 2019-10-02 and 0.1.5.2 dated 2026-03-11
DESCRIPTION | 10 +++--- MD5 | 63 +++++++++++++++++++++---------------------- R/curvesbootstrap.R | 4 +- R/devianceboot.R | 13 ++++---- R/deviancep.R | 3 +- R/fitpsy.R | 6 ++-- R/logliksboot.R | 26 ++++++++++------- R/logliksbootsaturated.R | 4 +- R/one_parcomparisons.R | 4 +- R/one_thresholdcomparisons.R | 4 +- R/parbootstrap.R | 4 +- R/parci.R | 3 +- R/parcomparisons.R | 3 +- R/quickreadfiles.R | 4 +- R/thresholds.R | 1 R/thresholdsbootstrap.R | 4 +- R/thresholdsci.R | 2 - inst/CITATION | 8 ++--- man/dot-.Rd |only man/fitpsy.Rd | 21 ++++++++++++-- man/one_parameters.Rd | 16 +++++++++- man/parameters.Rd | 16 +++++++++- man/parn.Rd | 4 ++ man/plotcurves.Rd | 13 +++++++- man/plotcurves_.Rd | 14 +++++++-- man/plotpar.Rd | 12 ++++++-- man/plotpar_.Rd | 12 ++++++-- man/plotthresholds.Rd | 13 +++++++- man/plotthresholds_.Rd | 14 +++++++-- man/qpdat.Rd | 4 ++ man/quickpsy.Rd | 27 +++++++++++++++--- man/quickpsy_.Rd | 27 +++++++++++++++--- man/thresholds.Rd | 3 -- 33 files changed, 249 insertions(+), 113 deletions(-)
Title: A Simple Way to Specify Symmetric, Block Diagonal Matrices
Description: Provides a simple mechanism to specify a symmetric block
diagonal matrices (often used for covariance matrices). This is based
on the domain specific language implemented in 'nlmixr2' but expanded
to create matrices in R generally instead of specifying parts of
matrices to estimate. It has expanded to include some matrix manipulation
functions that are generally useful for 'rxode2' and 'nlmixr2'.
Author: Matthew L. Fidler [aut, cre] ,
Mauricio Vargas Sepulveda [ctb] ,
Bill Denney [ctb]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between lotri versions 1.0.2 dated 2025-08-29 and 1.0.3 dated 2026-03-11
DESCRIPTION | 18 + MD5 | 12 - NEWS.md | 4 build/vignette.rds |binary inst/doc/lotri-motivation.html | 410 +++++++++++++++++++++-------------------- src/nearPD.cpp | 4 src/rcm.cpp | 12 - 7 files changed, 240 insertions(+), 220 deletions(-)
Title: Merge and Download International Large-Scale Assessments (ILSA)
Data
Description: Merges and downloads 'SPSS' data from different International Large-Scale Assessments (ILSA), including: Trends in International Mathematics and Science Study (TIMSS), Progress in International Reading Literacy Study (PIRLS), and others.
Author: Andres Christiansen [aut, cre] ,
Andres Strello [ctb]
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>
Diff between ILSAmerge versions 1.3.8 dated 2025-04-10 and 1.4.0 dated 2026-03-11
DESCRIPTION | 12 - MD5 | 52 +++--- NEWS.md | 11 + R/ILSAdownload.R | 4 R/ILSAmerge.R | 2 R/ILSAready.R | 4 R/ILSArename.R | 2 R/availableILSA.R | 17 +- R/justload.R | 2 R/sysdata.rda |binary build/vignette.rds |binary inst/doc/Download.R | 14 - inst/doc/Download.html | 51 +++--- inst/doc/IdentifyILSAfiles.html | 16 - inst/doc/Load.html | 102 ++++++------ inst/doc/Merge.R | 6 inst/doc/Merge.html | 174 ++++++++++----------- inst/doc/Onestep.html | 124 +++++++-------- inst/doc/Rename.html | 28 +-- inst/extdata/ilsainfo/ILSAcou.csv | 202 ++++++++++++------------ inst/extdata/ilsainfo/ILSAlinks.csv | 2 inst/extdata/ilsainfo/ILSApops.csv | 296 ++++++++++++++++++------------------ man/ILSAdownload.Rd | 2 man/ILSAmerge.Rd | 2 man/ILSAready.Rd | 6 man/ILSArename.Rd | 2 man/justload.Rd | 2 27 files changed, 581 insertions(+), 554 deletions(-)
Title: High-Dimensional Undirected Graph Estimation
Description: Provides a general framework for
high-dimensional undirected graph estimation. It integrates
data preprocessing, neighborhood screening, graph estimation,
and model selection techniques into a pipeline. In
preprocessing stage, the nonparanormal(npn) transformation is
applied to help relax the normality assumption. In the graph
estimation stage, the graph structure is estimated by
Meinshausen-Buhlmann graph estimation, the graphical lasso,
or the TIGER (tuning-insensitive graph estimation and
regression) method, and the first two can be further
accelerated by the lossy screening rule preselecting the
neighborhood of each variable by correlation thresholding. We
target on high-dimensional data analysis usually d >> n, and
the computation is memory-optimized using the sparse matrix
output. We also provide a computationally efficient approach,
correlation thresholding graph estimation. Three
regularization/thresholding parameter selection methods are
included in this package: (1)stab [...truncated...]
Author: Haoming Jiang [aut],
Xinyu Fei [aut],
Han Liu [aut],
Kathryn Roeder [aut],
John Lafferty [aut],
Larry Wasserman [aut],
Xingguo Li [aut],
Tuo Zhao [aut, cre]
Maintainer: Tuo Zhao <tourzhao@gatech.edu>
Diff between huge versions 1.4 dated 2026-02-19 and 1.5 dated 2026-03-11
huge-1.4/huge/inst/doc/vignette.Rnw |only huge-1.4/huge/inst/doc/vignette.pdf |only huge-1.4/huge/vignettes/huge.pdf |only huge-1.4/huge/vignettes/vignette.Rnw |only huge-1.5/huge/DESCRIPTION | 30 +- huge-1.5/huge/MD5 | 80 ++++-- huge-1.5/huge/NAMESPACE | 4 huge-1.5/huge/NEWS.md |only huge-1.5/huge/R/RcppExports.R | 13 - huge-1.5/huge/R/huge-internal.R |only huge-1.5/huge/R/huge-package.R | 27 -- huge-1.5/huge/R/huge.R | 77 +----- huge-1.5/huge/R/huge.ct.R | 28 -- huge-1.5/huge/R/huge.generator.R | 60 +---- huge-1.5/huge/R/huge.glasso.R | 18 - huge-1.5/huge/R/huge.mb.R | 40 --- huge-1.5/huge/R/huge.npn.R | 17 - huge-1.5/huge/R/huge.plot.R | 12 - huge-1.5/huge/R/huge.roc.R | 15 - huge-1.5/huge/R/huge.select.R | 24 -- huge-1.5/huge/R/huge.tiger.R | 40 --- huge-1.5/huge/build/vignette.rds |binary huge-1.5/huge/configure | 18 - huge-1.5/huge/configure.ac | 2 huge-1.5/huge/inst/doc/huge-content.pdf |only huge-1.5/huge/inst/doc/huge.Rnw |only huge-1.5/huge/inst/doc/huge.pdf |only huge-1.5/huge/man/huge-package.Rd | 26 -- huge-1.5/huge/man/huge.Rd | 4 huge-1.5/huge/man/huge.select.Rd | 4 huge-1.5/huge/src/Makevars.in | 2 huge-1.5/huge/src/Makevars.win | 2 huge-1.5/huge/src/RIC.cpp | 42 --- huge-1.5/huge/src/RcppExports.cpp | 22 + huge-1.5/huge/src/SFGen.cpp | 61 +---- huge-1.5/huge/src/SPMBgraph.cpp | 344 +++-------------------------- huge-1.5/huge/src/SPMBgraphsqrt.cpp | 313 +++----------------------- huge-1.5/huge/src/huge |only huge-1.5/huge/src/huge_core.cpp |only huge-1.5/huge/src/hugeglasso.cpp | 363 ++++--------------------------- huge-1.5/huge/tests/testthat |only huge-1.5/huge/tests/testthat.R |only huge-1.5/huge/vignettes/huge-content.pdf |only huge-1.5/huge/vignettes/huge.Rnw |only 44 files changed, 351 insertions(+), 1337 deletions(-)
Title: Applied Statistical Time Series Analysis
Description: Contains data sets and scripts for analyzing time series in both the frequency and time domains including state space modeling as well as supporting the texts Time Series Analysis and Its Applications: With R Examples (5th ed), by R.H. Shumway and D.S. Stoffer. Springer Texts in Statistics, 2025, <DOI:10.1007/978-3-031-70584-7>, and Time Series: A Data Analysis Approach Using R (2nd ed). Chapman-Hall, 2026, <https://www.routledge.com/Time-Series-A-Data-Analysis-Approach-Using-R/Shumway-Stoffer/p/book/9781041031642>. Most scripts are designed to require minimal input to produce aesthetically pleasing output for ease of use in live demonstrations and course work.
Author: David Stoffer [aut, cre],
Nicky Poison [ctb, mus, spy]
Maintainer: David Stoffer <stoffer@pitt.edu>
Diff between astsa versions 2.4 dated 2025-12-15 and 2.5 dated 2026-03-11
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NEWS.md |only R/EM.R | 12 ++++++------ R/sarima.R | 6 +++--- build/partial.rdb |binary man/astsa-package.Rd | 4 ++-- 7 files changed, 21 insertions(+), 20 deletions(-)
Title: Tidy Intensive Longitudinal Data Analysis
Description: A reproducible, tidyverse-style framework for intensive longitudinal
data analysis in R, with built-in methodological safeguards, provenance
tracking, and reporting tools. Encodes time structure, enforces
within-between decomposition, provides spacing-aware lags, and integrates
diagnostics and visualization. Use ild_prepare(), ild_center(), ild_lag(),
and related functions for a unified pipeline from raw EMA/diary data to
interpretable models.
Author: Alex Litovchenko [aut, cre]
Maintainer: Alex Litovchenko <al4877@columbia.edu>
Diff between tidyILD versions 0.2.0 dated 2026-03-05 and 0.3.0 dated 2026-03-11
DESCRIPTION | 32 ++++++----- MD5 | 80 +++++++++++++++++++--------- NAMESPACE | 13 ++++ NEWS.md | 49 +++++++++++++++-- R/ild-class.R | 8 ++ R/ild_align.R | 7 ++ R/ild_center.R | 10 +++ R/ild_compare_pipelines.R |only R/ild_crosslag.R | 13 ++++ R/ild_diagnostics.R | 5 + R/ild_ipw_refit.R |only R/ild_ipw_weights.R |only R/ild_lag.R | 9 ++- R/ild_lme.R | 13 ++++ R/ild_methods.R |only R/ild_missing_model.R |only R/ild_model_tidiers.R | 77 +++++++++++++++++++------- R/ild_power.R | 10 +++ R/ild_prepare.R | 11 +++ R/ild_provenance.R |only R/ild_robust_se.R |only R/ild_tvem.R |only R/ild_tvem_plot.R |only R/package.R | 31 +++++++--- README.md | 7 +- build/vignette.rds |binary inst/doc/ild-analysis-report.R | 11 +++ inst/doc/ild-analysis-report.Rmd | 19 ++++++ inst/doc/ild-analysis-report.html | 80 ++++++++++++++++++---------- inst/doc/ild-decomposition-and-spacing.html | 4 - inst/doc/ild-glossary-and-quickstart.html | 4 - inst/doc/ild-provenance.R |only inst/doc/ild-provenance.Rmd |only inst/doc/ild-provenance.html |only inst/doc/tidyILD-workflow.html | 4 - man/ild_compare_pipelines.Rd |only man/ild_export_provenance.Rd |only man/ild_history.Rd |only man/ild_ipw_refit.Rd |only man/ild_ipw_weights.Rd |only man/ild_methods.Rd |only man/ild_missing_model.Rd |only man/ild_provenance.Rd |only man/ild_report.Rd |only man/ild_robust_se.Rd |only man/ild_tvem.Rd |only man/ild_tvem_plot.Rd |only man/tidyILD-package.Rd | 31 +++++++--- man/tidy_ild_model.Rd | 26 ++++++++- tests/testthat/test-ild_methods.R |only tests/testthat/test-ild_missing_model_ipw.R |only tests/testthat/test-ild_provenance.R |only tests/testthat/test-ild_robust_se.R |only tests/testthat/test-ild_tvem.R |only vignettes/ild-analysis-report.Rmd | 19 ++++++ vignettes/ild-provenance.Rmd |only 56 files changed, 444 insertions(+), 129 deletions(-)
Title: Interactive Tabular Matrix Problems via Pseudoinverse Estimation
Description: Provides an interactive wrapper for the 'tmpinv()' function from
the 'rtmpinv' package with options extending its functionality to pre-
and post-estimation processing and streamlined incorporation of prior cell
information. The Tabular Matrix Problems via Pseudoinverse Estimation
(TMPinv) is a two-stage estimation method that reformulates structured
table-based systems - such as allocation problems, transaction matrices,
and input-output tables - as structured least-squares problems. Based
on the Convex Least Squares Programming (CLSP) framework, TMPinv solves
systems with row and column constraints, block structure, and optionally
reduced dimensionality by (1) constructing a canonical constraint form
and applying a pseudoinverse-based projection, followed by (2) a
convex-programming refinement stage to improve fit, coherence, and
regularization (e.g., via Lasso, Ridge, or Elastic Net).
Author: Ilya Bolotov [aut, cre]
Maintainer: Ilya Bolotov <ilya.bolotov@vse.cz>
Diff between rtmpinvi versions 0.1.0 dated 2026-02-25 and 0.2.0 dated 2026-03-11
DESCRIPTION | 8 ++++---- MD5 | 3 ++- NEWS.md |only 3 files changed, 6 insertions(+), 5 deletions(-)
Title: Low-Level R to Java Interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
Author: Simon Urbanek [aut, cre, cph]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between rJava versions 1.0-14 dated 2026-01-20 and 1.0-15 dated 2026-03-11
rJava-1.0-14/rJava/jri |only rJava-1.0-15/rJava/DESCRIPTION | 6 rJava-1.0-15/rJava/MD5 | 276 +- rJava-1.0-15/rJava/NEWS | 6 rJava-1.0-15/rJava/configure | 3365 +++++++++++++++--------------- rJava-1.0-15/rJava/configure.ac | 2 rJava-1.0-15/rJava/inst/jri/JRIEngine.jar |binary rJava-1.0-15/rJava/inst/jri/REngine.jar |binary rJava-1.0-15/rJava/src/Makevars.in | 10 rJava-1.0-15/rJava/src/config.h.in | 19 rJava-1.0-15/rJava/src/java/Makefile | 5 rJava-1.0-15/rJava/src/jri |only rJava-1.0-15/rJava/src/rJava.h | 2 13 files changed, 1945 insertions(+), 1746 deletions(-)
Title: Create Randomization Lists
Description: Randomization lists are an integral component of randomized clinical trials. 'randotools' provides tools to easily create such lists.
Author: Alan G Haynes [aut, cre]
Maintainer: Alan G Haynes <alan.haynes@unibe.ch>
Diff between randotools versions 0.2.4 dated 2025-12-03 and 0.2.6 dated 2026-03-11
DESCRIPTION | 12 +++--- MD5 | 10 ++--- NEWS.md | 80 +++++++++++++++++++++++++--------------------- README.md | 14 ++++---- man/figures/imbseq-1.png |binary man/figures/imbtest-1.png |binary 6 files changed, 63 insertions(+), 53 deletions(-)
Title: Precision Based Sample Size Calculation
Description: Bland (2009) <doi:10.1136/bmj.b3985> recommended to
base study sizes on the width of the confidence interval rather the power of
a statistical test. The goal of 'presize' is to provide functions for such
precision based sample size calculations. For a given sample size, the
functions will return the precision (width of the confidence interval), and
vice versa.
Author: Armando Lenz [aut],
Alan G. Haynes [cre, aut],
Andreas Limacher [aut],
Odile Stalder [ctb],
Marie Roumet [ctb]
Maintainer: Alan G. Haynes <alan.haynes@unibe.ch>
Diff between presize versions 0.3.9 dated 2025-11-18 and 0.3.11 dated 2026-03-11
DESCRIPTION | 12 ++-- MD5 | 8 +- NEWS.md | 4 + inst/doc/presize.html | 131 ++++++++++++++++++++++++------------------------- man/presize-package.Rd | 6 +- 5 files changed, 83 insertions(+), 78 deletions(-)
Title: 'PLINK' 2 Binary (.pgen) Reader
Description: A thin wrapper over 'PLINK' 2's core libraries which provides an R
interface for reading .pgen files. A minimal .pvar loader is also
included. Chang et al. (2015) <doi:10.1186/s13742-015-0047-8>.
Author: Christopher Chang [aut, cre],
Eric Biggers [ctb, cph] ,
Yann Collet [ctb] ,
Meta Platforms, Inc. [cph] ,
Evan Nemerson [ctb, cph] ,
Przemyslaw Skibinski [ctb] ,
Nick Terrell [ctb]
Maintainer: Christopher Chang <chrchang@alumni.caltech.edu>
This is a re-admission after prior archival of version 0.5.4 dated 2026-01-17
Diff between pgenlibr versions 0.5.4 dated 2026-01-17 and 0.5.5 dated 2026-03-11
pgenlibr-0.5.4/pgenlibr/inst/include/include/SFMT.c |only pgenlibr-0.5.4/pgenlibr/inst/include/include/SFMT.h |only pgenlibr-0.5.4/pgenlibr/inst/include/include/pgenlib_write.cc |only pgenlibr-0.5.4/pgenlibr/inst/include/include/pgenlib_write.h |only pgenlibr-0.5.4/pgenlibr/inst/include/include/plink2_bitmap.cc |only pgenlibr-0.5.4/pgenlibr/inst/include/include/plink2_bitmap.h |only pgenlibr-0.5.4/pgenlibr/inst/include/include/plink2_fmath.cc |only pgenlibr-0.5.4/pgenlibr/inst/include/include/plink2_fmath.h |only pgenlibr-0.5.4/pgenlibr/inst/include/include/plink2_stats.cc |only pgenlibr-0.5.4/pgenlibr/inst/include/include/plink2_stats.h |only pgenlibr-0.5.5/pgenlibr/DESCRIPTION | 14 - pgenlibr-0.5.5/pgenlibr/MD5 | 32 +- pgenlibr-0.5.5/pgenlibr/configure | 18 - pgenlibr-0.5.5/pgenlibr/configure.ac | 2 pgenlibr-0.5.5/pgenlibr/inst/include/include/pgenlib_read.h | 1 pgenlibr-0.5.5/pgenlibr/inst/include/include/plink2_base.cc | 10 pgenlibr-0.5.5/pgenlibr/inst/include/include/plink2_base.h | 40 +++ pgenlibr-0.5.5/pgenlibr/inst/include/include/plink2_float.cc |only pgenlibr-0.5.5/pgenlibr/inst/include/include/plink2_float.h |only pgenlibr-0.5.5/pgenlibr/inst/include/include/plink2_string.cc | 8 pgenlibr-0.5.5/pgenlibr/inst/include/include/plink2_string.h | 113 ---------- pgenlibr-0.5.5/pgenlibr/src/Makevars.in | 2 pgenlibr-0.5.5/pgenlibr/src/Makevars.win | 2 23 files changed, 92 insertions(+), 150 deletions(-)
Title: Visualizing Panel Data
Description: Visualizes panel data. It has three main functionalities: (1) it plots the treatment status and missing values in a panel dataset; (2) it visualizes the temporal dynamics of a main variable of interest; (3) it depicts the bivariate relationships between a treatment variable and an outcome variable either by unit or in aggregate. For details, see <doi:10.18637/jss.v107.i07>.
Author: Hongyu Mou [aut],
Licheng Liu [aut],
Yiqing Xu [aut, cre]
Maintainer: Yiqing Xu <yiqingxu@stanford.edu>
Diff between panelView versions 1.1.18 dated 2024-06-17 and 1.2.0 dated 2026-03-11
DESCRIPTION | 14 MD5 | 11 R/panelView.R | 1771 ----------------------------------------------------- R/plot-bivariate.R |only R/plot-outcome.R |only R/plot-treat.R |only R/zzz.r | 2 tests |only 8 files changed, 37 insertions(+), 1761 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: NNS (Nonlinear Nonparametric Statistics) leverages partial moments – the fundamental elements of variance that asymptotically approximate the area under f(x) – to provide a robust foundation for nonlinear analysis while maintaining linear equivalences. NNS delivers a comprehensive suite of advanced statistical techniques, including: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.open.source@gmail.com>
Diff between NNS versions 11.6.4 dated 2026-01-10 and 11.6.5 dated 2026-03-11
DESCRIPTION | 8 MD5 | 85 ++-- R/ANOVA.R | 92 ++--- R/Boost.R | 43 +- R/FSD.R | 17 R/NNS_meboot.R | 8 R/Normalization.R | 3 R/Partial_Moments.R | 80 ++++ R/RcppExports.R | 50 -- R/SSD.R | 49 +- R/Stack.R | 7 R/TSD.R | 49 +- R/Uni_SD_Routines.R | 90 +++-- README.md | 6 build/vignette.rds |binary inst/doc/NNSvignette_Clustering_and_Regression.R | 18 - inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 18 - inst/doc/NNSvignette_Clustering_and_Regression.html | 18 - inst/doc/NNSvignette_Normalization_and_Rescaling.R |only inst/doc/NNSvignette_Normalization_and_Rescaling.Rmd |only inst/doc/NNSvignette_Normalization_and_Rescaling.html |only inst/doc/NNSvignette_Overview.R | 32 + inst/doc/NNSvignette_Overview.Rmd | 135 +++++-- inst/doc/NNSvignette_Overview.html | 311 ++++++++++-------- inst/doc/NNSvignette_Partial_Moments.Rmd | 6 inst/doc/NNSvignette_Partial_Moments.html | 8 inst/doc/NNSvignette_Sampling.R | 4 inst/doc/NNSvignette_Sampling.Rmd | 4 inst/doc/NNSvignette_Sampling.html | 4 man/Co.LPM.Rd | 9 man/Co.UPM.Rd | 9 man/PM.matrix.Rd | 24 + src/RcppExports.cpp | 26 - src/internal_functions.cpp | 39 +- src/nns_rcpp.cpp |only src/partial_moments.cpp | 86 ++-- src/partial_moments.h | 8 src/partial_moments_rcpp.cpp | 66 --- src/partial_moments_rcpp.h | 6 tests/testthat/Rplots.pdf |binary tests/testthat/test_Partial_Moments.R | 14 vignettes/NNSvignette_Clustering_and_Regression.Rmd | 18 - vignettes/NNSvignette_Normalization_and_Rescaling.Rmd |only vignettes/NNSvignette_Overview.Rmd | 135 +++++-- vignettes/NNSvignette_Partial_Moments.Rmd | 6 vignettes/NNSvignette_Sampling.Rmd | 4 46 files changed, 952 insertions(+), 643 deletions(-)