Title: Complex Partial Least Squares Structural Equation Modeling
Description: Estimate complex Structural Equation Models (SEMs) by fitting Partial
Least Squares Structural Equation Modeling (PLS-SEM) and Partial Least
Squares consistent Structural Equation Modeling (PLSc-SEM) specifications
that handle categorical data, non-linear relations, and multilevel
structures. The implementation follows Lohmöller (1989) for the classic PLS-SEM
algorithm, Dijkstra and Henseler (2015) for consistent PLSc-SEM, Dijkstra et al.,
(2014) for nonlinear PLSc-SEM, and Schuberth, Henseler, Dijkstra (2018)
for ordinal PLS-SEM and PLSc-SEM. Additional extensions are under development.
The MC-OrdPLSc algorithm, used to handle ordinal interaction models is detailed
in Slupphaug et al., (2026).
References:
Lohmöller, J.-B. (1989, ISBN:9783790803002).
"Latent Variable Path Modeling with Partial Least Squares."
Dijkstra, T. K., & Henseler, J. (2015).
<doi:10.1016/j.jmva.2015.06.002>.
"Consistent partial least squares path modeling."
Dijkstra, T. K., & Schermelleh-Engel, K. [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between plssem versions 0.1.2 dated 2026-06-01 and 0.1.3 dated 2026-07-03
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Title: Exact Matching and Matching-Adjusted Indirect Comparison (MAIC)
Description: The current version (0.3.0) streamlines the underlying code, adds a feasibility check to 'maicWt' and 'maxessWt', extends 'exmWt.2ipd' with options 'target.ipd' and 'method' for one-sided MAIC weighting between two IPDs, and adds 'wtTrtDiff' for the weighted treatment-effect difference with a Wald confidence interval based on Section 5 of Glimm & Yau (2026). The second version (0.2.0) contains implementation for exact matching which is an alternative to propensity score matching (see Glimm & Yau (2026) <doi:10.1080/19466315.2025.2507378>). The initial version (0.1.2) contains a collection of easy-to-implement tools for checking whether a MAIC can be conducted, as well as an alternative way of calculating weights (see Glimm & Yau (2022) <doi:10.1002/pst.2210>.)
Author: Lillian Yau [aut, cre],
Ekkehard Glimm [aut],
Xinlei Deng [aut]
Maintainer: Lillian Yau <maicChecks@gmail.com>
Diff between maicChecks versions 0.2.0 dated 2025-03-03 and 0.3.0 dated 2026-07-03
DESCRIPTION | 14 - MD5 | 68 +++---- NAMESPACE | 25 +- R/eAD.R | 56 +++-- R/eIPD.R | 54 +++-- R/exmLP.2ipd.R | 445 ++++++++++++++++++++-------------------------- R/exmWt.2ipd.R | 371 ++++++++++++++++++++++++-------------- R/maicChecks-package.R | 18 - R/maicLP.R | 100 +++++----- R/maicMD.R | 175 +++++++----------- R/maicPCA.R | 216 +++++++++++----------- R/maicT2Test.R | 88 ++++----- R/maicWt.R | 125 ++++++------ R/maxessWt.R | 130 +++++++------ R/sim110.R | 50 ++--- R/wtTrtDiff.R |only README.md | 40 ++-- build/partial.rdb |binary data/eAD.RData |binary data/eAD.txt | 8 data/eIPD.RData |binary data/eIPD.txt | 86 ++++---- data/sim110.rda |binary man/eAD.Rd | 64 +++--- man/eIPD.Rd | 60 +++--- man/exmLP.2ipd.Rd | 95 +++++---- man/exmWt.2ipd.Rd | 143 +++++++++----- man/maicChecks-package.Rd | 42 ++-- man/maicLP.Rd | 65 +++--- man/maicMD.Rd | 75 +++---- man/maicPCA.Rd | 81 ++++---- man/maicT2Test.Rd | 67 +++--- man/maicWt.Rd | 68 +++---- man/maxessWt.Rd | 64 +++--- man/sim110.Rd | 58 +++-- man/wtTrtDiff.Rd |only 36 files changed, 1564 insertions(+), 1387 deletions(-)
Title: Simplify Access to Data from the Amazon Region
Description: Provides tools for downloading and processing data on the
Brazilian Amazon region from a variety of official sources. Covers
environmental, agricultural, economic, and social indicators, including
deforestation and land use, greenhouse gas emissions, climate,
agricultural and livestock production, mining, energy, and foreign
trade, from providers such as the Brazilian Institute of Geography and
Statistics (IBGE), the National Institute for Space Research (INPE),
and MapBiomas. Data are cleaned and standardized for analysis at the
municipality, state, and regional levels.
Author: Laura Tavares Regadas [aut, cre],
DataZoom [fnd],
Gustavo Gonzaga [aut],
Igor Rigolon Veiga [aut],
Guilherme Jardim [aut],
Daniel AC Barbosa [aut],
Bruno Alcantara Duarte [aut],
Fredie Didier [aut],
Tito Bruni [aut],
Luiz Guilherme Lopes Moussatche [...truncated...]
Maintainer: Laura Tavares Regadas <lauratregadas@gmail.com>
Diff between datazoom.amazonia versions 1.1.0 dated 2023-12-12 and 1.2.0 dated 2026-07-03
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datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_censoagro.Rd | 22 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_climate.Rd | 23 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_datasus.Rd | 58 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_degrad.Rd | 12 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_deter.Rd | 16 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_epe.Rd | 33 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_ibama.Rd | 19 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_iema.Rd | 13 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_imazon.Rd | 13 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_ips.Rd | 23 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_mapbiomas.Rd | 22 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_pam.Rd | 6 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_pevs.Rd | 15 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_pibmunic.Rd | 8 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_population.Rd | 15 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_ppm.Rd | 16 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_prodes.Rd | 47 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_seeg.Rd | 52 datazoom.amazonia-1.2.0/datazoom.amazonia/man/load_sigmine.Rd | 9 datazoom.amazonia-1.2.0/datazoom.amazonia/man/municipalities_biomes.Rd | 2 datazoom.amazonia-1.2.0/datazoom.amazonia/man/pipe.Rd |only datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/ANEEL.Rmd | 30 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/BACI.Rmd | 161 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/CEMPRE.Rmd | 89 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/CENSOAGRO.Rmd | 261 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/COMEX.Rmd | 198 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/DEGRAD.Rmd | 185 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/DETER.Rmd | 166 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/EPE.Rmd | 95 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/IBAMA.Rmd | 114 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/IEMA.Rmd | 81 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/IMAZON.Rmd | 136 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/IPS.Rmd | 209 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/MAPBIOMAS.Rmd | 174 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/PAM.Rmd | 110 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/PEVS.Rmd | 248 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/PIBMUNIC.Rmd | 184 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/POPULATION.Rmd | 198 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/PPM.Rmd | 282 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/PRODES.Rmd | 289 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/SEEG.Rmd | 342 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/SIGMINE.Rmd | 164 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/TERRACLIMATE.Rmd | 260 datazoom.amazonia-1.2.0/datazoom.amazonia/vignettes/municipalities.Rmd | 258 165 files changed, 18744 insertions(+), 5325 deletions(-)
More information about datazoom.amazonia at CRAN
Permanent link
Title: A Versatile Toolkit for Copy Number Variation Relationship Data
Analysis and Visualization
Description: Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.
Author: James Dalgleish [aut, cre] ,
Yonghong Wang [aut],
Jack Zhu [aut],
Paul Meltzer [aut, sad]
Maintainer: James Dalgleish <jamesdalg@gmail.com>
Diff between CNVScope versions 3.7.2 dated 2022-03-30 and 3.7.5 dated 2026-07-03
DESCRIPTION | 29 MD5 | 54 NAMESPACE | 126 - NEWS.md | 326 ++-- R/CNVScopeserver.R | 2677 ++++++++++++++++----------------- R/calcVecLMs.R | 116 - R/createChromosomalMatrixSet.R | 104 - R/divisors.R | 252 +-- R/getAsymmetricBlockIndices.R | 17 R/importBreakpointBed.R | 60 R/rebinGenomicInteractions.R | 2 R/runCNVScopeShiny.R | 419 ++--- R/writeAsymmetricMeltedMatrixToDisk.R | 388 ++-- R/writeMeltedChromosomalMatrixToDisk.R | 366 ++-- build/vignette.rds |binary inst/doc/additonal_examples.R | 442 ++--- inst/doc/additonal_examples.Rmd | 22 inst/doc/additonal_examples.html | 1153 ++++++++------ inst/doc/create_input_matrix.R | 96 - inst/doc/create_input_matrix.Rmd | 2 inst/doc/create_input_matrix.html | 804 ++++++--- inst/doc/create_output_matrix.R | 160 - inst/doc/create_output_matrix.html | 729 ++++++-- inst/doc/power_analysis.R | 50 inst/doc/power_analysis.html | 715 +++++--- man/getAsymmetricBlockIndices.Rd | 2 vignettes/additonal_examples.Rmd | 22 vignettes/create_input_matrix.Rmd | 2 28 files changed, 5057 insertions(+), 4078 deletions(-)
Title: Search Download and Handle Data from the Copernicus Data Space
Ecosystem
Description: The Copernicus Data Space Ecosystem, is an open
ecosystem that provides free instant access to a wide range
of data and services from the Copernicus Sentinel missions and
more on our planet’s land, oceans and atmosphere. This package
provides entry points to several APIs allowing users to access
the data directly in R.
Author: Pepijn de Vries [aut, cre] ,
Alicia Hamer [rtm] ,
LVVN
[fnd] ,
WMR [ctr]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusDataspace versions 0.0.1 dated 2026-05-21 and 0.0.3 dated 2026-07-03
DESCRIPTION | 10 - MD5 | 42 ++-- NAMESPACE | 149 ++++++++--------- NEWS.md | 6 R/account.R | 154 +++++++++--------- R/login.R | 6 R/odata_products.R | 4 R/s3.R | 73 +++----- R/stac.R | 11 + README.md | 23 ++ inst/WORDLIST | 6 inst/doc/Authentication.Rmd | 5 inst/doc/Authentication.html | 9 - inst/doc/OData.Rmd | 348 ++++++++++++++++++++--------------------- inst/doc/OData.html | 24 +- inst/doc/STAC.html | 16 - man/dse_s3.Rd | 282 +++++++++++++++++---------------- man/dse_set_gdal_token.Rd | 2 man/dse_stac_search_request.Rd | 4 man/dse_usage.Rd | 126 +++++++------- vignettes/Authentication.Rmd | 5 vignettes/OData.Rmd | 348 ++++++++++++++++++++--------------------- 22 files changed, 851 insertions(+), 802 deletions(-)
More information about CopernicusDataspace at CRAN
Permanent link
Title: Pipe-Friendly Framework for Basic Statistical Tests
Description: Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy,
for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses.
The output of each test is automatically transformed into a tidy data frame to facilitate visualization.
Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix.
Functions are also included to facilitate the analysis of factorial experiments, including purely 'within-Ss' designs
(repeated measures), purely 'between-Ss' designs, and mixed 'within-and-between-Ss' designs.
It's also possible to compute several effect size metrics, including "eta squared" for ANOVA, "Cohen's d" for t-test and
'Cramer V' for the association between categorical variables.
The package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between rstatix versions 0.7.3 dated 2025-10-18 and 1.0.0 dated 2026-07-03
DESCRIPTION | 45 +++--- MD5 | 176 ++++++++++++++++---------- NAMESPACE | 10 + NEWS.md | 72 ++++++++++ R/add_cld.R |only R/adjust_pvalue.R | 20 ++ R/anova_summary.R | 86 ++++++++++-- R/anova_test.R | 117 +++++++++++++---- R/binom_test.R | 10 - R/chisq_test.R | 135 +++++++++++++++++++ R/cochran_qtest.R | 4 R/cohens_d.R | 24 ++- R/conover_test.R |only R/cor_test.R | 32 ++++ R/df.R | 2 R/doo.R | 12 + R/dunn_test.R | 70 +++++++++- R/dunnett_test.R |only R/emmeans_test.R | 42 +++++- R/factorial_design.R | 37 ++++- R/factors.R | 2 R/fisher_test.R | 9 - R/fligner_test.R |only R/freq_table.R | 16 +- R/friedman_conover_test.R |only R/friedman_nemenyi_test.R |only R/friedman_test.R | 4 R/games_howell_test.R | 62 +++++++-- R/get_pvalue_position.R | 106 +++++++++++++-- R/get_summary_stats.R | 76 ++++++++++- R/get_test_label.R | 34 +++-- R/kruskal_effesize.R | 15 ++ R/kruskal_test.R | 10 + R/ks_test.R |only R/levene_test.R | 8 - R/mcnemar_test.R | 30 +++- R/multinom_test.R | 2 R/p_value.R | 12 + R/prop_test.R | 14 -- R/prop_trend_test.R | 2 R/rstatix-programming.R |only R/shapiro_test.R | 8 - R/t_test.R | 54 ++++++- R/tukey_hsd.R | 5 R/utilities.R | 123 ++++++++++++++++-- R/utilities_two_sample_test.R | 136 +++++++++++++++++--- R/wilcox_effsize.R | 37 ++++- R/wilcox_test.R | 40 +++++ README.md | 21 ++- inst/WORDLIST | 37 +++++ man/add_cld.Rd |only man/adjust_pvalue.Rd | 22 +++ man/anova_summary.Rd | 13 + man/anova_test.Rd | 89 ++++++++++--- man/chisq_test.Rd | 30 ++++ man/cohens_d.Rd | 5 man/conover_test.Rd |only man/cor_test.Rd | 14 +- man/dunn_test.Rd | 28 +++- man/dunnett_test.Rd |only man/emmeans_test.Rd | 33 ++++ man/fligner_test.Rd |only man/freq_table.Rd | 3 man/friedman_conover_test.Rd |only man/friedman_nemenyi_test.Rd |only man/games_howell_test.Rd | 5 man/get_pvalue_position.Rd | 32 +++- man/get_summary_stats.Rd | 29 +++- man/kruskal_effsize.Rd | 5 man/ks_test.Rd |only man/mcnemar_test.Rd | 5 man/rstatix-programming.Rd |only man/t_test.Rd | 49 ++++++- man/wilcox_effsize.Rd | 25 +++ man/wilcox_test.Rd | 34 ++++- tests/testthat/test-add_cld.R |only tests/testthat/test-add_x_position.R | 30 ++++ tests/testthat/test-anova_test-ci.R |only tests/testthat/test-anova_test.R | 101 ++++++++++++++ tests/testthat/test-binom_test.R |only tests/testthat/test-chisq_test.R |only tests/testthat/test-cohens_d.R |only tests/testthat/test-conover_test.R |only tests/testthat/test-cor_test-weights.R |only tests/testthat/test-cor_test.R |only tests/testthat/test-doo.R |only tests/testthat/test-dunn_test.R |only tests/testthat/test-dunnett_test.R |only tests/testthat/test-emmeans_test.R | 27 +++ tests/testthat/test-error-as-na.R |only tests/testthat/test-facet-x-position.R |only tests/testthat/test-fligner_test.R |only tests/testthat/test-freq_table.R |only tests/testthat/test-friedman_conover_test.R |only tests/testthat/test-friedman_nemenyi_test.R |only tests/testthat/test-games_howell_test.R |only tests/testthat/test-get_pvalue_position.R |only tests/testthat/test-get_summary_stats.R | 62 +++++++++ tests/testthat/test-get_test_label.R |only tests/testthat/test-kruskal_effsize.R |only tests/testthat/test-kruskal_test.R |only tests/testthat/test-ks_test.R |only tests/testthat/test-mcnemar_test.R |only tests/testthat/test-p_format.R |only tests/testthat/test-p_mark_significance.R | 31 ++++ tests/testthat/test-p_value_precision.R |only tests/testthat/test-paired-id.R |only tests/testthat/test-ref-group-missing.R |only tests/testthat/test-t_test.R |only tests/testthat/test-tidyselect-deprecations.R |only tests/testthat/test-tukey_hsd.R |only tests/testthat/test-wilcox_effsize.R |only tests/testthat/test-wilcox_test.R | 86 +++++++++++- 113 files changed, 2139 insertions(+), 376 deletions(-)
Title: Compute Soil Carbon Fluxes for the National Ecological
Observatory Network Sites
Description: Acquires and synthesizes soil carbon fluxes at sites located in the National Ecological Observatory Network (NEON). Provides flux estimates and associated uncertainty as well as key environmental measurements (soil water, temperature, CO2 concentration) that are used to compute soil fluxes.
Author: John Zobitz [aut, cre] ,
Edward Ayres [aut] ,
Katie O'Rourke [ctb] ,
Zoey Werbin [ctb],
Lajntxiag Lee [ctb],
Ridwan Abdi [ctb] ,
Dijone Mehmeti [ctb] ,
Ly Xiong [ctb]
Maintainer: John Zobitz <zobitz@augsburg.edu>
Diff between neonSoilFlux versions 4.0.0 dated 2026-06-30 and 4.0.1 dated 2026-07-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 3 +++ R/compute_neon_flux.R | 12 +++++++++--- man/compute_neon_flux.Rd | 12 +++++++++--- 5 files changed, 28 insertions(+), 13 deletions(-)
Title: Fine-Scale Population Analysis (Rewrite for
Gene-Trait-Environment Interaction Analysis)
Description: Statistical tool set for population genetics. The package provides following functions: 1) estimators of genetic differentiation (FST), 2) regression analysis of environmental effects on genetic differentiation using generalized least squares (GLS) method, 3) interfaces to read and manipulate 'GENEPOP' format data files). For more information, see Kitada, Nakamichi and Kishino (2020) <doi:10.1101/2020.01.30.927186>.
Author: Reiichiro Nakamichi [aut, cre],
Shuichi Kitada [aut],
Hirohisa Kishino [aut]
Maintainer: Reiichiro Nakamichi <nakamichi_reiichiro33@fra.go.jp>
This is a re-admission after prior archival of version 0.4 dated 2020-02-28
Diff between FinePop2 versions 0.4 dated 2020-02-28 and 0.6 dated 2026-07-03
DESCRIPTION | 24 ++++++++++++++++++------ MD5 | 9 +++++---- build/partial.rdb |binary data/herring.rda |binary data/jsmackerel.rda |binary inst |only 6 files changed, 23 insertions(+), 10 deletions(-)
Title: R Interface to COVID-19 Data Hub
Description: Provides a daily summary of COVID-19 cases, deaths, recovered, tests,
vaccinations, and hospitalizations for 230+ countries, 760+ regions,
and 12000+ administrative divisions of lower level.
Includes policy measures, mobility data, and geospatial identifiers.
Data source: COVID-19 Data Hub <https://covid19datahub.io>.
Author: Emanuele Guidotti [aut, cre] ,
David Ardia [ctb]
Maintainer: Emanuele Guidotti <emanuele.guidotti@usi.ch>
Diff between COVID19 versions 3.0.3 dated 2023-02-28 and 3.0.4 dated 2026-07-03
DESCRIPTION | 17 +++++++++-------- MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 11 insertions(+), 10 deletions(-)
Title: Calculating Optimal and D-Augmented Designs for Single- and
Multi-Factor Models
Description: Calculates D-, Ds-, A-, I- and L-optimal designs, weighted combinations of these via a Compound criterion, and KL-optimal designs for model discrimination, for non-linear single- and multi-factor models, via an implementation of the cocktail algorithm (Yu, 2011, <doi:10.1007/s11222-010-9183-2>). Multi-factor models use design variables x1, x2, … with a named-list design space; single-factor models remain backward compatible. Compares designs via their efficiency, augments any design with a controlled efficiency loss, and provides efficient rounding functions to convert approximate designs to exact ones.
Author: Carlos de la Calle-Arroyo [aut, cre] ,
Jesus Lopez-Fidalgo [aut] ,
Licesio J. Rodriguez-Aragon [aut]
Maintainer: Carlos de la Calle-Arroyo <carlos.calle.arroyo@gmail.com>
Diff between optedr versions 3.0.0 dated 2026-06-23 and 3.0.1 dated 2026-07-03
DESCRIPTION | 6 - MD5 | 14 +- NEWS.md | 14 ++ R/wf_mult.R | 28 ++++ build/vignette.rds |binary inst/doc/optedr-augment.html | 163 +++++++++++++-------------- inst/doc/optedr-intro.html | 255 +++++++++++++++++-------------------------- inst/doc/optedr-kl.html | 232 ++++++++++++++++----------------------- 8 files changed, 328 insertions(+), 384 deletions(-)
Title: Generic Machine Learning Inference
Description: Generic Machine Learning Inference on heterogeneous treatment effects in randomized experiments as proposed in Chernozhukov, Demirer, Duflo and Fernández-Val (2020) <doi:10.48550/arXiv.1712.04802>. This package's workhorse is the 'mlr3' framework of Lang et al. (2019) <doi:10.21105/joss.01903>, which enables the specification of a wide variety of machine learners. The main functionality, GenericML(), runs Algorithm 1 in Chernozhukov, Demirer, Duflo and Fernández-Val (2020) <doi:10.48550/arXiv.1712.04802> for a suite of user-specified machine learners. All steps in the algorithm are customizable via setup functions. Methods for printing and plotting are available for objects returned by GenericML(). Parallel computing is supported.
Author: Max Welz [aut, cre] ,
Andreas Alfons [aut] ,
Mert Demirer [aut],
Victor Chernozhukov [aut]
Maintainer: Max Welz <max.welz@uzh.ch>
Diff between GenericML versions 0.2.2 dated 2022-06-18 and 0.2.3 dated 2026-07-03
DESCRIPTION | 23 ++-- MD5 | 40 +++---- R/GenericML.R | 15 ++ R/across-learners.R | 16 ++ R/blp.R | 26 ++++ R/clan.R | 62 +++++++---- R/gates.R | 74 ++++++++++++- R/helpers.R | 44 ++++++-- R/input-checks.R | 57 +++++++--- R/misc.R | 148 ++++++++++++++++++++------- R/plot.R | 7 - R/print.R | 4 build/partial.rdb |binary inst/CITATION | 68 +++++++----- man/BLP.Rd | 3 man/CLAN.Rd | 5 man/GATES.Rd | 7 + man/GenericML.Rd | 10 + man/GenericML_single.Rd | 10 + man/Med.Rd | 2 tests/testthat/test_GenericML-input-checks.R | 2 21 files changed, 462 insertions(+), 161 deletions(-)
Title: Get Data from the Swiss Federal Statistical Office
Description: Search and download data from the Swiss Federal Statistical Office (BFS) APIs <https://www.bfs.admin.ch/>.
Author: Felix Luginbuhl [aut, cre, cph] ,
Marius Hodel [ctb] ,
Janosch Brenzel-Weiss [ctb],
Joao Martins [ctb],
Philipp Baumann [ctb]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between BFS versions 0.7.1 dated 2026-02-05 and 0.7.2 dated 2026-07-03
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/bfs_get_sse_data.R | 10 ++++++---- R/bfs_get_sse_metadata.R | 5 ++++- man/bfs_get_sse_data.Rd | 8 +++++--- man/bfs_get_sse_metadata.Rd | 2 ++ 7 files changed, 32 insertions(+), 18 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 3.3-2 dated 2026-03-12 and 3.4-0 dated 2026-07-03
DESCRIPTION | 8 - MD5 | 54 +++++----- NEWS.md | 7 + R/MunsellToxyY.R | 7 + R/VandY.R | 70 ++++++------- R/conversions.R | 184 ++++++++++++++++++++++++------------ R/utils.R | 35 ++++++ R/xyYtoMunsell.R | 32 +++--- build/vignette.rds |binary inst/doc/dental.html | 20 +-- inst/doc/lightness.pdf |binary inst/doc/lociHC.pdf |binary inst/doc/munsellinterpol-guide.html | 63 +++++++----- inst/doc/soil.R | 14 +- inst/doc/soil.Rmd | 23 ++-- inst/doc/soil.html | 108 +++++++++++---------- man/LabtoMunsell.Rd | 3 man/LuvtoMunsell.Rd | 4 man/Munsell2xy.Rd | 5 man/MunsellBooks.Rd | 2 man/MunsellToLab.Rd | 3 man/MunsellToLuv.Rd | 6 - man/MunsellToXYZ.Rd | 55 +++++++++- man/MunsellToxyY.Rd | 21 +++- man/XYZtoMunsell.Rd | 98 ++++++++++++++++--- man/xyYtoMunsell.Rd | 33 +++++- tests/test-VandY.R | 73 +++++++------- vignettes/soil.Rmd | 23 ++-- 28 files changed, 619 insertions(+), 332 deletions(-)
More information about munsellinterpol at CRAN
Permanent link
Title: Interactive Interfaces for Results Exploration
Description: Shiny interfaces and graphical functions for multivariate analysis results exploration.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@cnrs.fr>
Diff between explor versions 0.3.10 dated 2023-04-29 and 0.3.11 dated 2026-07-03
DESCRIPTION | 12 MD5 | 36 - NEWS.md | 60 +-- R/CA_plots.R | 5 R/MCA_plots.R | 73 +-- R/PCA_plots.R | 39 -- R/explor_multi.R | 104 ++--- R/explor_multi_CA.R | 8 R/explor_multi_MCA.R | 5 R/explor_multi_PCA.R | 8 R/plots.R | 60 +-- R/prepare_results_CA.R | 1 R/prepare_results_dudi_coa.R | 1 README.md | 51 +- build/vignette.rds |binary inst/doc/introduction_en.html | 449 +++++++++++++---------- inst/doc/introduction_fr.html | 476 ++++++++++++++----------- tests/testthat/test_prepare_results_CA.R | 7 tests/testthat/test_prepare_results_dudi.coa.R | 7 19 files changed, 776 insertions(+), 626 deletions(-)
Title: Caught by the Fuzz! - A Minimalistic Fuzz-Test Runner
Description: A simple runner for fuzz-testing functions in an R package's
public interface. Fuzz testing helps identify functions lacking sufficient
argument validation, and uncovers problematic inputs that, while valid by
function signature, may cause issues within the function body.
Author: Marco Colombo [aut, cre]
Maintainer: Marco Colombo <mar.colombo13@gmail.com>
Diff between CBTF versions 0.6.0 dated 2026-02-13 and 0.7.0 dated 2026-07-03
DESCRIPTION | 10 ++-- MD5 | 42 +++++++++--------- NEWS.md | 21 +++++++++ R/CBTF-package.R | 6 +- R/fuzz.R | 55 ++++++++++++------------ R/inputs.R | 32 +++++++++++--- R/misc.R | 33 ++++++++------ R/queue.R | 14 +++--- R/summary.R | 58 ++++++++++++++++++++----- README.md | 42 +++++++++++------- man/CBTF-package.Rd | 9 +++ man/fuzz.Rd | 45 ++++++++++--------- man/get_exported_functions.Rd | 6 +- man/length.cbtf.Rd | 3 - man/print.cbtf.Rd | 14 ++++-- man/sub-sub-.cbtf.Rd | 3 - man/test_inputs.Rd | 9 ++- tests/testthat/_snaps/summary.md | 88 ++++++++++++++++++++++++++++++++++++--- tests/testthat/test_fuzz.R | 35 +++++++++++++++ tests/testthat/test_inputs.R | 12 +++-- tests/testthat/test_misc.R | 4 + tests/testthat/test_summary.R | 10 +++- 22 files changed, 392 insertions(+), 159 deletions(-)
Title: Dataset Dependency Graphs for Leakage-Aware Evaluation
Description: Represent biomedical dataset structure as typed dependency
graphs so that sample provenance, repeated-measure structure, study
design, batch effects, and temporal relationships are explicit and
inspectable. Validates dataset structure, detects sample-level overlap,
derives deterministic split constraints, and produces a tool-agnostic
split specification for leakage-aware evaluation workflows.
Author: Selcuk Korkmaz [aut, cre]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between splitGraph versions 0.2.0 dated 2026-04-29 and 0.3.0 dated 2026-07-03
DESCRIPTION | 11 MD5 | 90 - NAMESPACE | 11 NEWS.md | 132 + R/constraints.R | 201 ++ R/constructors.R | 18 R/graph-build-auto.R | 5 R/methods.R | 28 R/pairwise.R |only R/query.R | 23 R/schema-validate.R |only R/serialization.R | 98 - R/split-spec.R | 161 + R/splitGraph-package.R | 123 + README.md | 95 - build/vignette.rds |binary inst/doc/adapter-cookbook.R | 47 inst/doc/adapter-cookbook.Rmd | 132 + inst/doc/adapter-cookbook.html | 2021 ++++------------------- inst/doc/cross-language-handoff.R |only inst/doc/cross-language-handoff.Rmd |only inst/doc/cross-language-handoff.html |only inst/doc/leakage-aware-workflow.R | 98 + inst/doc/leakage-aware-workflow.Rmd | 245 ++ inst/doc/leakage-aware-workflow.html | 2676 +++++++++---------------------- inst/doc/modeling-structure.R |only inst/doc/modeling-structure.Rmd |only inst/doc/modeling-structure.html |only inst/python |only inst/schema |only man/derive_split_constraints.Rd | 35 man/graph_node_set.Rd | 13 man/migrate_json.Rd |only man/pairwise_edges.Rd |only man/splitGraph-package.Rd | 32 man/validate_json.Rd |only man/write_dependency_graph.Rd | 13 man/write_split_spec.Rd | 3 tests/testthat/test-bioleak-contract.R |only tests/testthat/test-constraints.R | 27 tests/testthat/test-json-schema.R |only tests/testthat/test-methods.R | 6 tests/testthat/test-pairwise-relations.R |only tests/testthat/test-platform-relation.R |only tests/testthat/test-python-conformance.R |only tests/testthat/test-query-paths-cap.R | 46 tests/testthat/test-region-relation.R |only tests/testthat/test-schema-version.R | 2 tests/testthat/test-serialization.R | 37 tests/testthat/test-site-relation.R |only tests/testthat/test-split-spec.R | 105 + vignettes/adapter-cookbook.Rmd | 132 + vignettes/cross-language-handoff.Rmd |only vignettes/leakage-aware-workflow.Rmd | 245 ++ vignettes/modeling-structure.Rmd |only 55 files changed, 3194 insertions(+), 3717 deletions(-)
Title: Access Data from Brazilian Central Bank: IFdata, Active
Institutions, Balance Sheets and Normative Acts
Description: Provides functions to query, retrieve, and tidy economic and
financial data from Brazilian Central Bank web services for use in R
analyses and workflows. Active institutions information, balance sheets and normative acts.
Author: Ricardo Theodoro [aut, cre]
Maintainer: Ricardo Theodoro <rtheodoro@usp.br>
Diff between bacenR versions 0.4.3 dated 2026-06-23 and 0.4.4 dated 2026-07-03
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 1 - NEWS.md | 4 ++++ R/tidy_ifdata_reports.R | 23 +++++------------------ README.md | 2 +- build/vignette.rds |binary inst/CITATION | 2 +- man/tidy_ifdata_reports.Rd | 15 +++------------ 9 files changed, 26 insertions(+), 45 deletions(-)
Title: Handling Single-Level and Hierarchically Structured Risk Factors
using Credibility and Random Effects Models
Description: Fits random effects models for multi-level/high-cardinality factors using credibility theory (Buhlmann-Straub for single-level, Jewell for hierarchical structures), GLM extensions following Ohlsson (2008) <doi:10.1080/03461230701878612>, or Tweedie generalized linear mixed models. Provides functions for model fitting, visualization, and prediction. See Campo, B.D.C. and Antonio, K. (2023) <doi:10.1080/03461238.2022.2161413>.
Author: Campo Bavo D.C. [aut, cre]
Maintainer: Campo Bavo D.C. <bavo.decock@kuleuven.be>
Diff between actuaRE versions 1.0.0 dated 2026-02-27 and 1.0.1 dated 2026-07-03
DESCRIPTION | 6 - MD5 | 48 ++++----- R/GLMC.R | 8 - R/hierCredGLM.R | 6 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/actuaRE.html | 15 +- man/BalanceProperty.Rd | 60 +++++------ man/NrUnique.Rd | 48 ++++----- man/adjustIntercept.Rd | 74 +++++++------- man/buhlmannStraub.Rd | 172 +++++++++++++++++----------------- man/buhlmannStraubGLM.Rd | 4 man/buhlmannStraubTweedie.Rd | 4 man/dataCar.Rd | 4 man/dot-addREs.Rd | 32 +++--- man/hierCredGLM.Rd | 4 man/hierCredTweedie-class.Rd | 124 ++++++++++++------------ man/hierCredTweedie.Rd | 206 ++++++++++++++++++++--------------------- man/hierCredibility-class.Rd | 130 ++++++++++++------------- man/hierCredibility.Rd | 176 +++++++++++++++++------------------ man/is.formula.Rd | 42 ++++---- man/predict.hierCredGLM.Rd | 54 +++++----- man/predict.hierCredTweedie.Rd | 54 +++++----- man/predict.hierCredibility.Rd | 48 ++++----- man/print.BalanceProperty.Rd | 46 ++++----- 25 files changed, 683 insertions(+), 682 deletions(-)
Title: Phasing, Pedigree Reconstruction, Sire Imputation and
Recombination Events Identification of Half-sib Families Using
SNP Data
Description: Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data.
Author: Mohammad Ferdosi [aut, cre],
Cedric Gondro [aut]
Maintainer: Mohammad Ferdosi <mhferdosi@yahoo.com>
Diff between hsphase versions 3.0.0 dated 2026-02-17 and 3.0.1 dated 2026-07-03
DESCRIPTION | 9 +++-- MD5 | 16 +++++----- build/vignette.rds |binary inst/doc/hsphase.pdf |binary man/addSwitch.Rd | 3 + man/fixSW.Rd | 3 + man/switchDetector.Rd | 4 ++ src/Makevars.win | 5 +-- src/SwitchAdd.cpp | 76 ++++++++++++++++++++++++++++---------------------- 9 files changed, 68 insertions(+), 48 deletions(-)
Title: External jars for 'rjdverse' R Packages
Description: It provides external jars required for the 'rjdverse' (as 'rjd3toolkit', 'rjd3x13' and 'rjd3tramoseats').
Author: Tanguy Barthelemy [aut, cre]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between rjd3jars versions 0.0.3 dated 2026-03-10 and 0.0.4 dated 2026-07-03
rjd3jars-0.0.3/rjd3jars/inst/java/protobuf-java-4.34.0.jar |only rjd3jars-0.0.3/rjd3jars/man/jd3_utilities.Rd |only rjd3jars-0.0.4/rjd3jars/DESCRIPTION | 10 rjd3jars-0.0.4/rjd3jars/MD5 | 26 - rjd3jars-0.0.4/rjd3jars/NAMESPACE | 18 rjd3jars-0.0.4/rjd3jars/NEWS.md | 96 ++-- rjd3jars-0.0.4/rjd3jars/R/utils.R |only rjd3jars-0.0.4/rjd3jars/R/zzz.R | 82 ++-- rjd3jars-0.0.4/rjd3jars/README.md | 82 ++-- rjd3jars-0.0.4/rjd3jars/inst/WORDLIST | 202 +++++----- rjd3jars-0.0.4/rjd3jars/inst/java/jdplus-sa-base-api-3.8.0.jar |only rjd3jars-0.0.4/rjd3jars/inst/java/jdplus-sa-base-core-3.8.0.jar |only rjd3jars-0.0.4/rjd3jars/inst/java/jdplus-toolkit-base-api-3.8.0.jar |only rjd3jars-0.0.4/rjd3jars/inst/java/jdplus-toolkit-base-core-3.8.0.jar |only rjd3jars-0.0.4/rjd3jars/inst/java/protobuf-java-4.35.1.jar |only rjd3jars-0.0.4/rjd3jars/java/README | 12 rjd3jars-0.0.4/rjd3jars/man/java-version.Rd |only rjd3jars-0.0.4/rjd3jars/man/reload_dictionaries.Rd |only rjd3jars-0.0.4/rjd3jars/man/reload_safactories.Rd |only rjd3jars-0.0.4/rjd3jars/man/reload_tsproviders.Rd |only 20 files changed, 289 insertions(+), 239 deletions(-)
Title: Import Air Quality Monitoring Data in a Fast and Easy Way
Description: A collection of tools to access prepared air quality monitoring
data files from web servers with ease and speed. Air quality data are
sourced from open and publicly accessible repositories and can be found in
these locations:
<https://www.eea.europa.eu/data-and-maps/data/airbase-the-european-air-quality-database-8>
and <https://discomap.eea.europa.eu/map/fme/AirQualityExportAirbase.htm>.
The web server space has been provided by Ricardo Energy & Environment.
Author: Stuart K. Grange [cre, aut]
Maintainer: Stuart K. Grange <stuart.grange@unibe.ch>
Diff between saqgetr versions 0.2.21 dated 2021-01-12 and 0.2.24 dated 2026-07-03
saqgetr-0.2.21/saqgetr/NEWS.md |only saqgetr-0.2.24/saqgetr/DESCRIPTION | 22 ++++++++++---------- saqgetr-0.2.24/saqgetr/MD5 | 13 ++++++----- saqgetr-0.2.24/saqgetr/R/dplyr_re_exports.R | 6 ++--- saqgetr-0.2.24/saqgetr/R/get_saq_simple_summaries.R | 4 +-- saqgetr-0.2.24/saqgetr/R/zzz.R | 2 + saqgetr-0.2.24/saqgetr/inst/CITATION | 2 - saqgetr-0.2.24/saqgetr/man/dplyr-functions.Rd |only saqgetr-0.2.24/saqgetr/man/zzz.Rd |only 9 files changed, 26 insertions(+), 23 deletions(-)
Title: Statistical Data Visualization, the 'seaborn' Way
Description: An 'R' port of the 'Python' 'seaborn' library. 'reaborn' mirrors the
'seaborn' public function API (identical function names, argument names, and
defaults) and renders visually indistinguishable plots using 'ggplot2'.
Because every 'reaborn' plot is a 'ggplot' object, it can be extended with the
full 'ggplot2' grammar of graphics.
Author: Shawn Schwartz [aut, cre]
Maintainer: Shawn Schwartz <shawn.t.schwartz@gmail.com>
Diff between reaborn versions 1.0.0 dated 2026-06-30 and 1.0.1 dated 2026-07-03
DESCRIPTION | 6 MD5 | 96 +++++----- NEWS.md | 118 ++++++++----- R/axisgrid.R | 25 ++ R/categorical-complex.R | 12 + R/categorical.R | 49 +++++ R/core-density.R | 6 R/datasets.R | 11 + R/distributions.R | 326 +++++++++++++++++++++++++++++++++++- R/matrix.R | 12 + R/miscplot.R | 5 R/palettes.R | 7 R/regression.R | 18 + R/relational.R | 56 ++++++ README.md | 3 man/FacetGrid.Rd | 7 man/barplot.Rd | 5 man/boxenplot.Rd | 5 man/boxplot.Rd | 5 man/catplot.Rd | 7 man/clustermap.Rd | 8 man/color_palette.Rd | 8 man/countplot.Rd | 8 man/displot.Rd | 8 man/dogplot.Rd | 3 man/ecdfplot.Rd | 7 man/figures/compare-line.png |binary man/figures/compare-reg.png |binary man/figures/compare-relplot.png |binary man/figures/hero-collage.png |binary man/heatmap.Rd | 8 man/histplot.Rd | 27 ++ man/jointplot.Rd | 7 man/kdeplot.Rd | 5 man/lineplot.Rd | 10 + man/lmplot.Rd | 7 man/pairplot.Rd | 18 + man/palplot.Rd | 4 man/pointplot.Rd | 10 + man/regplot.Rd | 7 man/relplot.Rd | 10 + man/residplot.Rd | 7 man/rugplot.Rd | 7 man/scatterplot.Rd | 14 + man/stripplot.Rd | 7 man/swarmplot.Rd | 7 man/violinplot.Rd | 5 tests/testthat/test-categorical.R | 38 ++++ tests/testthat/test-distributions.R | 218 ++++++++++++++++++++++++ 49 files changed, 1135 insertions(+), 102 deletions(-)
Title: Mixed-Effects Ordinal Regression Analysis
Description: Provides the function 'mixor' for fitting a mixed-effects ordinal and binary response models and associated methods for printing, summarizing, extracting estimated coefficients and variance-covariance matrix, and estimating contrasts for the fitted models.
Author: Kellie J. Archer [aut, cre] ,
Donald Hedeker [aut],
Rachel Nordgren [aut],
Robert D. Gibbons [aut]
Maintainer: Kellie J. Archer <archer.43@osu.edu>
This is a re-admission after prior archival of version 1.0.4 dated 2018-06-14
Diff between mixor versions 1.0.4 dated 2018-06-14 and 1.0.7 dated 2026-07-03
DESCRIPTION | 21 MD5 | 40 - NAMESPACE | 34 - R/AIC.mixor.R | 2 R/BIC.mixor.R | 2 R/mixor.R | 4 R/summary.mixor.R | 4 build/partial.rdb |binary build/vignette.rds |binary data/SmokeOnset.rda |binary data/SmokingPrevention.rda |binary data/concen.rda |binary data/irt.data.rda |binary data/norcag.rda |binary data/schizophrenia.rda |binary inst/doc/mixor.R | 394 ++++++++--------- inst/doc/mixor.pdf |binary man/schizophrenia.Rd | 98 ++-- src/mixor_init.c | 1 src/mixord_dll.f90 | 994 ++++++++++++++++++++++++++++----------------- vignettes/mixor.bib | 6 21 files changed, 945 insertions(+), 655 deletions(-)
Title: Linguistic Fuzzy Logic
Description: Various algorithms related to linguistic fuzzy logic: mining for
linguistic fuzzy association rules, composition of fuzzy relations,
performing Mamdani, implicative, and perception-based logical deduction
(PbLD), and forecasting time-series using fuzzy rule-based ensemble (FRBE).
The package also contains basic fuzzy-related algebraic functions capable of
handling missing values in different styles (Bochvar, Sobocinski, Kleene
etc.), computation of Sugeno integrals and the fuzzy transform.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between lfl versions 2.3.1 dated 2025-12-16 and 2.4.0 dated 2026-07-03
DESCRIPTION | 22 ++++++------ MD5 | 44 +++++++++++++----------- NAMESPACE | 2 + NEWS.md | 7 +++ R/aggregateConsequents.R | 2 - R/algebraNA.R | 53 +++++++++++++++++++++++++++++ R/defuzz.R | 2 - R/fire.R | 2 - R/infer.R |only R/lcut.R | 24 +++++++------ R/pbld.R | 2 - build/vignette.rds |binary man/aggregateConsequents.Rd | 2 - man/algebraNA.Rd | 3 + man/defaultHedgeParams.Rd | 5 -- man/defuzz.Rd | 2 - man/fire.Rd | 2 - man/frbe.Rd | 2 - man/infer.Rd |only man/lfl-package.Rd | 5 ++ man/lingexpr.Rd | 5 -- man/pbld.Rd | 2 - tests/testthat/test-algebraNA-upperBound.R |only tests/testthat/test-infer.R |only tests/testthat/test-lcut.R | 13 +++++++ 25 files changed, 141 insertions(+), 60 deletions(-)
Title: Simulating Admixed Genotypes Without Replacement
Description: A genomic simulation approach for creating biologically
informed individual genotypes from empirical data that 1) samples alleles
from populations without replacement, 2) segregates alleles based on species-specific
recombination rates. 'gscramble' is a flexible simulation approach that allows users
to create pedigrees of varying complexity in order to simulate admixed genotypes.
Furthermore, it allows users to track haplotype blocks from the source populations
through the pedigrees.
Author: Eric C. Anderson [aut, cre] ,
Rachael M. Giglio [aut] ,
Matt G. DeSaix [aut] ,
Timothy J. Smyser [aut]
Maintainer: Eric C. Anderson <eriq@rams.colostate.edu>
Diff between gscramble versions 1.0.1 dated 2024-02-28 and 1.0.2 dated 2026-07-03
DESCRIPTION | 23 MD5 | 24 NEWS.md | 8 README.md | 2 build/vignette.rds |binary inst/doc/about-createGSP.R | 30 inst/doc/about-createGSP.html | 3485 -------------------------------------- inst/doc/gscramble-tutorial.R | 36 inst/doc/gscramble-tutorial.Rmd | 2 inst/doc/gscramble-tutorial.html | 525 ----- inst/doc/permutation-options.R | 4 inst/doc/permutation-options.html | 2 vignettes/gscramble-tutorial.Rmd | 2 13 files changed, 121 insertions(+), 4022 deletions(-)
Title: Get and Manipulate the GESLA Dataset
Description: Promote access to the GESLA
<https://gesla787883612.wordpress.com> (Global Extreme Sea Level
Analysis) dataset, a higher-frequency sea-level record data from all
over the world. It provides functions to download it entirely, or
query subsets directly into R, without the need of downloading the
full dataset. Also, it provides a built-in web-application, so that
users can apply basic filters to select the data of interest,
generating informative plots, and showing the selected sites.
Author: Fernando Mayer [aut, cre] ,
Niamh Cahill [aut]
Maintainer: Fernando Mayer <fernando.mayer@ufpr.br>
Diff between geslaR versions 1.0-1 dated 2023-10-09 and 1.0-3 dated 2026-07-03
DESCRIPTION | 17 +++++++++-------- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 1 + NEWS.md | 17 +++++++++++++++++ R/download_gesla.R | 4 ++-- R/query_gesla.R | 9 ++++----- R/read_gesla.R | 14 ++++++-------- R/run_gesla_app.R | 12 ++---------- R/write_gesla.R | 4 ++-- README.md | 35 +++++++++++++++++++++++++++-------- build/vignette.rds |binary inst/doc/intro-to-arrow.html | 5 +++-- inst/doc/intro-to-geslaR.html | 11 ++++++----- man/download_gesla.Rd | 4 ++-- man/query_gesla.Rd | 9 ++++----- man/read_gesla.Rd | 13 +++++-------- man/run_gesla_app.Rd | 12 ++---------- man/write_gesla.Rd | 4 ++-- 18 files changed, 111 insertions(+), 94 deletions(-)
Title: Differential Gene Expression Analysis with R
Description: Analyses gene expression data derived from microarray experiments
to detect differentially expressed genes (DEGs) by employing majority voting
across five statistical models: Welch t-test, one-way ANOVA, Dunnett's test,
Half's modified t-test, and the Wilcoxon-Mann-Whitney U-test. Combined
p-values are computed with Fisher's method. Gene annotation is optional:
users may supply a GEO SOFT annotation table or rely on row names directly.
Boyer, R.S., Moore, J.S. (1991) <doi:10.1007/978-94-011-3488-0_5>.
Author: Koushik Bardhan [aut, cre, ctb] ,
Chiranjib Sarkar [aut, ths]
Maintainer: Koushik Bardhan <koushikbardhan2000@gmail.com>
Diff between DGEAR versions 0.1.4 dated 2024-06-26 and 0.2.1 dated 2026-07-03
DGEAR-0.1.4/DGEAR/R/read_and_preprocess_data.R |only DGEAR-0.1.4/DGEAR/man/read_and_preprocess_data.Rd |only DGEAR-0.2.1/DGEAR/DESCRIPTION | 39 +- DGEAR-0.2.1/DGEAR/LICENSE | 4 DGEAR-0.2.1/DGEAR/MD5 | 42 +- DGEAR-0.2.1/DGEAR/NAMESPACE | 5 DGEAR-0.2.1/DGEAR/NEWS.md | 119 ++++++-- DGEAR-0.2.1/DGEAR/R/D-Test.R | 92 ++++-- DGEAR-0.2.1/DGEAR/R/DGEAR.R | 310 ++++++++++++---------- DGEAR-0.2.1/DGEAR/R/H-Test.R | 70 ++-- DGEAR-0.2.1/DGEAR/R/One-Way-ANOVA-Test.R | 72 ++--- DGEAR-0.2.1/DGEAR/R/T-Test.R | 81 +++-- DGEAR-0.2.1/DGEAR/R/U-Test.R | 72 ++--- DGEAR-0.2.1/DGEAR/R/utils.R |only DGEAR-0.2.1/DGEAR/README.md | 172 ++++++++++-- DGEAR-0.2.1/DGEAR/build |only DGEAR-0.2.1/DGEAR/inst/WORDLIST | 2 DGEAR-0.2.1/DGEAR/man/DGEAR.Rd | 99 ++++++- DGEAR-0.2.1/DGEAR/man/dot-prepare_data.Rd |only DGEAR-0.2.1/DGEAR/man/dot-resolve_symbols.Rd |only DGEAR-0.2.1/DGEAR/man/perform_anova.Rd | 41 ++ DGEAR-0.2.1/DGEAR/man/perform_dunnett_test.Rd | 89 ++++-- DGEAR-0.2.1/DGEAR/man/perform_h_test.Rd | 49 ++- DGEAR-0.2.1/DGEAR/man/perform_t_test.Rd | 86 ++++-- DGEAR-0.2.1/DGEAR/man/perform_wilcox_test.Rd | 49 ++- 25 files changed, 1031 insertions(+), 462 deletions(-)
Title: Data Source Agnostic Filtering Tools
Description: Common API for filtering data stored in different data models.
Provides multiple filter types and reproducible R code.
Works standalone or with 'shinyCohortBuilder' as the GUI for interactive Shiny apps.
Author: Krystian Igras [cre, aut],
Adam Forys [ctb]
Maintainer: Krystian Igras <krystian8207@gmail.com>
Diff between cohortBuilder versions 0.4.0 dated 2026-02-24 and 1.0.0 dated 2026-07-03
cohortBuilder-0.4.0/cohortBuilder/man/creating-filters.Rd |only cohortBuilder-0.4.0/cohortBuilder/man/dot-as_constructor.Rd |only cohortBuilder-0.4.0/cohortBuilder/man/filter-source-types.Rd |only cohortBuilder-0.4.0/cohortBuilder/man/filter-types.Rd |only cohortBuilder-1.0.0/cohortBuilder/DESCRIPTION | 26 cohortBuilder-1.0.0/cohortBuilder/MD5 | 192 - cohortBuilder-1.0.0/cohortBuilder/NAMESPACE | 80 cohortBuilder-1.0.0/cohortBuilder/NEWS.md | 69 cohortBuilder-1.0.0/cohortBuilder/R/ai_tools.R |only cohortBuilder-1.0.0/cohortBuilder/R/attrition.R | 43 cohortBuilder-1.0.0/cohortBuilder/R/cohortBuilder-package.R | 39 cohortBuilder-1.0.0/cohortBuilder/R/cohort_methods.R | 695 ++- cohortBuilder-1.0.0/cohortBuilder/R/filter.R | 1186 ++++-- cohortBuilder-1.0.0/cohortBuilder/R/hooks.R | 26 cohortBuilder-1.0.0/cohortBuilder/R/list_operators.R | 57 cohortBuilder-1.0.0/cohortBuilder/R/repro_code_utils.R | 249 - cohortBuilder-1.0.0/cohortBuilder/R/source_methods.R | 206 + cohortBuilder-1.0.0/cohortBuilder/R/source_tblist.R | 1919 ++++++---- cohortBuilder-1.0.0/cohortBuilder/R/step.R | 148 cohortBuilder-1.0.0/cohortBuilder/README.md | 10 cohortBuilder-1.0.0/cohortBuilder/build/vignette.rds |binary cohortBuilder-1.0.0/cohortBuilder/data/librarian.rda |binary cohortBuilder-1.0.0/cohortBuilder/inst/WORDLIST |only cohortBuilder-1.0.0/cohortBuilder/inst/doc/binding-keys.R | 9 cohortBuilder-1.0.0/cohortBuilder/inst/doc/binding-keys.Rmd | 9 cohortBuilder-1.0.0/cohortBuilder/inst/doc/binding-keys.html | 8 cohortBuilder-1.0.0/cohortBuilder/inst/doc/cohort-configuration.R | 25 cohortBuilder-1.0.0/cohortBuilder/inst/doc/cohort-configuration.Rmd | 25 cohortBuilder-1.0.0/cohortBuilder/inst/doc/cohort-configuration.html | 92 cohortBuilder-1.0.0/cohortBuilder/inst/doc/cohortBuilder.R | 21 cohortBuilder-1.0.0/cohortBuilder/inst/doc/cohortBuilder.Rmd | 27 cohortBuilder-1.0.0/cohortBuilder/inst/doc/cohortBuilder.html | 385 +- cohortBuilder-1.0.0/cohortBuilder/inst/doc/custom-extensions.R | 39 cohortBuilder-1.0.0/cohortBuilder/inst/doc/custom-extensions.Rmd | 39 cohortBuilder-1.0.0/cohortBuilder/inst/doc/custom-extensions.html | 38 cohortBuilder-1.0.0/cohortBuilder/inst/doc/custom-filters.R | 244 - cohortBuilder-1.0.0/cohortBuilder/inst/doc/custom-filters.Rmd | 423 +- cohortBuilder-1.0.0/cohortBuilder/inst/doc/custom-filters.html | 629 +-- cohortBuilder-1.0.0/cohortBuilder/inst/doc/managing-cohort.R | 60 cohortBuilder-1.0.0/cohortBuilder/inst/doc/managing-cohort.Rmd | 92 cohortBuilder-1.0.0/cohortBuilder/inst/doc/managing-cohort.html | 545 +- cohortBuilder-1.0.0/cohortBuilder/inst/doc/source-intelligence.R |only cohortBuilder-1.0.0/cohortBuilder/inst/doc/source-intelligence.Rmd |only cohortBuilder-1.0.0/cohortBuilder/inst/doc/source-intelligence.html |only cohortBuilder-1.0.0/cohortBuilder/man/CbFilter.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/CbFilterDateRange.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/CbFilterDatetimeRange.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/CbFilterDiscrete.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/CbFilterDiscreteText.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/CbFilterMultiDiscrete.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/CbFilterQuery.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/CbFilterRange.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/Cohort.Rd | 278 + cohortBuilder-1.0.0/cohortBuilder/man/Source.Rd | 32 cohortBuilder-1.0.0/cohortBuilder/man/add_filter.Rd | 13 cohortBuilder-1.0.0/cohortBuilder/man/autofilter.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_domain_from_data.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_domain_from_stats.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_filter_data.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_filter_to_expr.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_get_filter_data.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_get_filter_defaults.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_get_filter_stats.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_intersect_domain.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_intersect_domain_values.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_plot_filter_data.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_register_tool.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_tool.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_tool_add_filters.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_tool_apply_filters.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_tool_clear_filters.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_tool_describe_state.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_tool_filters_meta.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_tool_get_code.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_tool_get_data_summary.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_tool_remove_filters.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_tool_remove_step.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_tool_run.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_tool_set_filter_values.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/cb_tool_toggle_filters.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/create-cohort.Rd | 11 cohortBuilder-1.0.0/cohortBuilder/man/describe.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/dot-default_filter_id.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/dot-default_filter_name.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/dot-filter_registry.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/dot-print_filter.Rd | 8 cohortBuilder-1.0.0/cohortBuilder/man/dot-propagate_domains.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/figures/README-attrition-1.png |binary cohortBuilder-1.0.0/cohortBuilder/man/filter.Rd | 12 cohortBuilder-1.0.0/cohortBuilder/man/filter_domain.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/filter_effective_value.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/filter_variables.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/get_filter_params.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/get_state.Rd | 6 cohortBuilder-1.0.0/cohortBuilder/man/grapes-greater-than-grapes.Rd | 2 cohortBuilder-1.0.0/cohortBuilder/man/register_filter_type.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/rm_filter.Rd | 13 cohortBuilder-1.0.0/cohortBuilder/man/set_source.Rd | 13 cohortBuilder-1.0.0/cohortBuilder/man/shape.Rd |only cohortBuilder-1.0.0/cohortBuilder/man/source-layer.Rd | 2 cohortBuilder-1.0.0/cohortBuilder/man/step.Rd | 13 cohortBuilder-1.0.0/cohortBuilder/man/sum_up.Rd | 8 cohortBuilder-1.0.0/cohortBuilder/man/tblist_class.Rd |only cohortBuilder-1.0.0/cohortBuilder/tests/testthat/_snaps/source_tblist/date-range-breaks-argument-is-passed-properly.svg | 4 cohortBuilder-1.0.0/cohortBuilder/tests/testthat/_snaps/source_tblist/date-range-extra-args-work.svg | 4 cohortBuilder-1.0.0/cohortBuilder/tests/testthat/_snaps/source_tblist/datetime-range-breaks-arg-works.svg | 4 cohortBuilder-1.0.0/cohortBuilder/tests/testthat/_snaps/source_tblist/datetime-range-default-breaks-work.svg | 4 cohortBuilder-1.0.0/cohortBuilder/tests/testthat/_snaps/source_tblist/datetime-range-extra-args-work.svg | 4 cohortBuilder-1.0.0/cohortBuilder/tests/testthat/_snaps/source_tblist/range-breaks-argument-is-passed-properly.svg | 4 cohortBuilder-1.0.0/cohortBuilder/tests/testthat/_snaps/source_tblist/range-extra-args-work.svg | 4 cohortBuilder-1.0.0/cohortBuilder/tests/testthat/test-ai_tools.R |only cohortBuilder-1.0.0/cohortBuilder/tests/testthat/test-cohort_methods.R | 1169 +++++- cohortBuilder-1.0.0/cohortBuilder/tests/testthat/test-data_time_filter.R | 39 cohortBuilder-1.0.0/cohortBuilder/tests/testthat/test-filter.R | 628 +++ cohortBuilder-1.0.0/cohortBuilder/tests/testthat/test-reproducible_code_utils.R | 207 - cohortBuilder-1.0.0/cohortBuilder/tests/testthat/test-source_methods.R | 50 cohortBuilder-1.0.0/cohortBuilder/tests/testthat/test-source_tblist.R | 629 ++- cohortBuilder-1.0.0/cohortBuilder/tests/testthat/test-step.R | 22 cohortBuilder-1.0.0/cohortBuilder/vignettes/binding-keys.Rmd | 9 cohortBuilder-1.0.0/cohortBuilder/vignettes/cohort-configuration.Rmd | 25 cohortBuilder-1.0.0/cohortBuilder/vignettes/cohortBuilder.Rmd | 27 cohortBuilder-1.0.0/cohortBuilder/vignettes/custom-extensions.Rmd | 39 cohortBuilder-1.0.0/cohortBuilder/vignettes/custom-filters.Rmd | 423 +- cohortBuilder-1.0.0/cohortBuilder/vignettes/managing-cohort.Rmd | 92 cohortBuilder-1.0.0/cohortBuilder/vignettes/source-intelligence.Rmd |only 125 files changed, 8277 insertions(+), 3176 deletions(-)
Title: Genome-Wide Robust Analysis for Biobank Data (GRAB)
Description: Provides a comprehensive suite of genome-wide association study (GWAS) methods
specifically designed for biobank-scale data, including but not limited to, robust approaches
for time-to-event traits (Li et al., 2025 <doi:10.1038/s43588-025-00864-z>) and ordinal
categorical traits (Bi et al., 2021 <doi:10.1016/j.ajhg.2021.03.019>). The package also offers
general frameworks for GWAS of any trait type (Bi et al., 2020 <doi:10.1016/j.ajhg.2020.06.003>),
while accounting for sample relatedness (Xu et al., 2025 <doi:10.1038/s41467-025-56669-1>) or
population structure (Ma et al., 2025 <doi:10.1186/s13059-025-03827-9>). By accurately
approximating score statistic distributions using saddlepoint approximation (SPA), these
methods can effectively control type I error rates for rare variants and in the presence of
unbalanced phenotype distributions. Additionally, the package includes functions for simulating
genotype and phenotype data to support research and method [...truncated...]
Author: Wenjian Bi [aut],
Wei Zhou [aut],
Rounak Dey [aut],
Zhangchen Zhao [aut],
Seunggeun Lee [aut],
Woody Miao [cre]
Maintainer: Woody Miao <miaolin@pku.edu.cn>
Diff between GRAB versions 0.2.4 dated 2025-12-05 and 0.2.5 dated 2026-07-03
DESCRIPTION | 12 +- MD5 | 84 +++++++++--------- NAMESPACE | 1 R/GRAB_Null_Model.R | 27 ++++- R/GRAB_Region.R | 31 +++++- R/GRM_IBD.R | 27 ++++- R/Geno.R | 12 +- R/POLMM.R | 8 + R/RcppExports.R | 182 +++++++++++++++++++-------------------- R/SAGELD.R | 67 ++++++++++---- R/SPACox.R | 2 R/SPAGRM.R | 15 ++- R/SPAmix.R | 6 + R/WtCoxG.R | 8 + build/partial.rdb |binary man/CCT.Rd | 14 +-- man/GRAB.Marker.Rd | 84 +++++++++--------- man/GRAB.NullModel.Rd | 42 ++++----- man/GRAB.POLMM.Rd | 108 +++++++++++------------ man/GRAB.POLMM.Region.Rd | 106 +++++++++++----------- man/GRAB.ReadGeno.Rd | 50 +++++----- man/GRAB.Region.Rd | 48 +++++----- man/GRAB.SAGELD.Rd | 29 ++++++ man/GRAB.SPACox.Rd | 38 ++++---- man/GRAB.SPAGRM.Rd | 30 +++--- man/GRAB.SPAmix.Rd | 46 ++++----- man/GRAB.SimuGMat.Rd | 10 +- man/GRAB.SimuGMatFromGenoFile.Rd | 24 ++--- man/GRAB.SimuPheno.Rd | 26 ++--- man/GRAB.SimubVec.Rd | 4 man/GRAB.WtCoxG.Rd | 52 +++++------ man/GRAB.getGenoInfo.Rd | 36 +++---- man/GRAB.makePlink.Rd | 20 +--- man/SAGELD.NullModel.Rd | 87 +++++++++--------- man/SPAGRM.NullModel.Rd | 26 ++--- man/fitNullModel.POLMM.Rd | 4 man/fitNullModel.SPACox.Rd | 18 +-- man/fitNullModel.SPAmix.Rd | 20 ++-- man/fitNullModel.WtCoxG.Rd | 24 ++--- man/getSparseGRM.Rd | 32 +++--- man/getTempFilesFullGRM.Rd | 14 +-- src/SPACox.h | 28 +++++- src/SPAmix.h | 25 ++++- 43 files changed, 851 insertions(+), 676 deletions(-)
Title: Lightweight Extension of the Base R Graphics System
Description: Lightweight extension of the base R graphics system, with support
for automatic legends, facets, themes, and various other enhancements.
Author: Grant McDermott [aut, cre] ,
Vincent Arel-Bundock [aut] ,
Achim Zeileis [aut] ,
Etienne Bacher [ctb]
Maintainer: Grant McDermott <contact@grantmcdermott.com>
Diff between tinyplot versions 0.6.1 dated 2026-03-28 and 0.7.0 dated 2026-07-03
DESCRIPTION | 10 MD5 | 143 +++--- NAMESPACE | 16 NEWS.md | 356 ++++++++++++++++ R/assertions.R | 9 R/by_aesthetics.R | 546 ++++++++++++++++--------- R/environment.R | 3 R/facet.R | 228 +++++++--- R/flip.R | 1 R/legend.R | 208 ++++++++- R/legend_gradient.R | 2 R/legend_multi.R | 28 + R/lim.R | 68 +++ R/repel.R |only R/sanitize_datapoints.R | 6 R/sanitize_type.R | 17 R/tinyformula.R | 2 R/tinylabel.R | 64 ++- R/tinyplot.R | 524 ++++++++++++++++++++++-- R/tinyplot.data.frame.R |only R/tinyplot.matrix.R |only R/tinyplot.ts.R |only R/tinyplot_add.R | 30 + R/tinytheme.R | 636 ++++++++++++++++++++++++------ R/title.R | 106 ++++- R/tpar.R | 54 ++ R/type_abline.R | 2 R/type_barplot.R | 244 ++++++++++- R/type_boxplot.R | 42 + R/type_chull.R |only R/type_density.R | 7 R/type_ellipse.R |only R/type_glm.R | 23 - R/type_histogram.R | 30 + R/type_lines.R | 24 + R/type_lm.R | 26 + R/type_loess.R | 20 R/type_polygon.R | 2 R/type_ridge.R | 117 +++-- R/type_spineplot.R | 170 ++++---- R/type_spline.R | 3 R/type_text.R | 130 +++++- R/type_violin.R | 61 +- R/utils.R | 157 ++++++- R/zzz.R | 7 man/build_legend_env.Rd | 5 man/draw_legend.Rd | 20 man/facet.Rd | 11 man/figures/README-quickstart2-1.png |binary man/figures/README-quickstart3-1.png |binary man/figures/README-quickstart4-1.png |binary man/figures/README-quickstart5-1.png |binary man/figures/README-quickstart_theme-1.png |binary man/repel_text.Rd |only man/tinyplot-package.Rd | 1 man/tinyplot.Rd | 133 +++++- man/tinyplot.data.frame.Rd |only man/tinyplot.matrix.Rd |only man/tinyplot.ts.Rd |only man/tinyplot_add.Rd | 9 man/tinytheme.Rd | 143 +++++- man/tinytheme_register.Rd |only man/tpar.Rd | 12 man/type_abline.Rd | 2 man/type_barplot.Rd | 108 ++++- man/type_boxplot.Rd | 33 + man/type_chull.Rd |only man/type_density.Rd | 16 man/type_ellipse.Rd |only man/type_glm.Rd | 14 man/type_jitter.Rd | 31 - man/type_lines.Rd | 20 man/type_lm.Rd | 16 man/type_loess.Rd | 18 man/type_ridge.Rd | 29 - man/type_spineplot.Rd | 69 ++- man/type_spline.Rd | 26 - man/type_text.Rd | 94 +++- man/type_violin.Rd | 65 +-- 79 files changed, 3946 insertions(+), 1051 deletions(-)
Title: Discrete Transmuted Generalized Inverse Weibull Distribution
Description: The Discrete Transmuted Generalized Inverse Weibull (DTGIW) distribution is a new distribution for count data analysis.
The DTGIW is a discrete distribution based on Atchanut and Sirinapa (2021). <DOI: 10.14456/sjst-psu.2021.149>.
In addition, a function for maximum likelihood estimation of the DTGIW distribution is provided.
Author: Atchanut Rattanalertnusorn [cre, aut],
Sirinapa Aryuyuen [aut]
Maintainer: Atchanut Rattanalertnusorn <atchanut_r@rmutt.ac.th>
Diff between dtgiw versions 1.0.0 dated 2022-03-31 and 1.1.0 dated 2026-07-03
DESCRIPTION | 12 +++++++----- MD5 | 9 ++++++--- NAMESPACE | 2 ++ R/mleDTGIW.R |only man/mleDTGIW.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test-mleDTGIW.R |only 7 files changed, 15 insertions(+), 8 deletions(-)
Title: Estimate Survival from Common Data Model Cohorts
Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
Author: Kim Lopez-Gueell [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut] ,
Xintong Li [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut]
Maintainer: Kim Lopez-Gueell <kim.lopez@spc.ox.ac.uk>
Diff between CohortSurvival versions 1.1.1 dated 2026-05-13 and 1.1.2 dated 2026-07-03
DESCRIPTION | 15 MD5 | 80 - NEWS.md | 11 R/addCohortSurvival.R | 54 R/asSurvivalResult.R | 18 R/estimateSurvival.R | 414 +++++- R/mockCohortSurvival.R | 5 R/mockMGUS2cdm.R | 5 R/plotSurvival.R | 41 R/tableSurvival.R | 66 - build/vignette.rds |binary inst/doc/a00_Creating_cohorts_for_survival.R |only inst/doc/a00_Creating_cohorts_for_survival.Rmd |only inst/doc/a00_Creating_cohorts_for_survival.html |only inst/doc/a01_Single_event_of_interest.Rmd | 19 inst/doc/a01_Single_event_of_interest.html | 1467 ++++++++++++------------ inst/doc/a02_Competing_risk_survival.Rmd | 12 inst/doc/a02_Competing_risk_survival.html | 346 +++-- inst/doc/a03_Further_survival_analyses.R | 2 inst/doc/a03_Further_survival_analyses.Rmd | 10 inst/doc/a03_Further_survival_analyses.html | 149 +- man/CohortSurvival-package.Rd | 1 man/addCohortSurvival.Rd | 54 man/asSurvivalResult.Rd | 19 man/estimateCompetingRiskSurvival.Rd | 106 + man/estimateSingleEventSurvival.Rd | 87 - man/plotSurvival.Rd | 40 man/reexports.Rd | 2 man/riskTable.Rd | 5 man/tableDoc.Rd | 2 man/tableSurvival.Rd | 29 man/tableSurvivalAttrition.Rd | 2 man/tableSurvivalEvents.Rd | 6 tests/testthat/test-addCohortSurvival.R | 244 +-- tests/testthat/test-asSurvivalResult.R | 6 tests/testthat/test-competing-risk-guard.R | 10 tests/testthat/test-estimateSurvival.R | 472 ++++--- tests/testthat/test-riskTable.R | 4 tests/testthat/test-tableSurvival.R | 49 vignettes/a00_Creating_cohorts_for_survival.Rmd |only vignettes/a01_Single_event_of_interest.Rmd | 19 vignettes/a02_Competing_risk_survival.Rmd | 12 vignettes/a03_Further_survival_analyses.Rmd | 10 43 files changed, 2277 insertions(+), 1616 deletions(-)
More information about CohortSurvival at CRAN
Permanent link
Title: Semantic Factor Analysis of Language Model Embeddings
Description: Performs exploratory factor analysis on language model embeddings
of psychological scale items. Embeds item text with sentence transformers
or other language models, transforms the embeddings into item-by-item
similarity matrices, and extracts latent factor structure via standard
exploratory factor analysis. Supports embedding-adapted parallel analysis,
several similarity transforms (atomic reversed, SQuID centering,
mean-centered Pearson), and fit diagnostics tailored to embedding matrices
(TEFI, RMSR, CAF, McDonald's omega). The underlying methods are documented
with full citations in the corresponding function help pages. Returns
objects compatible with 'psych' and 'EFAtools' workflows.
Author: Devon Yanitski [aut, cre] ,
Chris Westbury [aut]
Maintainer: Devon Yanitski <dyanitsk@ualberta.ca>
Diff between semanticfa versions 0.1.0 dated 2026-06-15 and 0.1.1 dated 2026-07-03
DESCRIPTION | 14 +-- MD5 | 76 +++++++++---------- NEWS.md | 36 +++++++++ R/anchor.R | 25 ++++-- R/congruence.R | 26 ++++++ R/data.R | 18 ++-- R/dimselect.R | 11 +- R/embed.R | 11 +- R/itemfit.R | 41 +++++++--- R/itemplot.R | 7 + R/jinglejangle.R | 5 + R/nli.R | 54 +++++++++++++- R/project.R | 8 +- R/redundancy.R | 6 + R/retention.R | 47 ++++++++++-- R/sfa.R | 12 ++- R/similarity.R | 15 ++- R/simplify.R | 2 README.md | 159 ++++++++++++++++++++++++++++++++--------- data/big5.rda |binary inst/CITATION | 2 inst/doc/introduction.Rmd | 10 +- inst/doc/introduction.html | 172 ++++++++++++++++++++++----------------------- man/big5.Rd | 18 ++-- man/sfa.Rd | 10 ++ man/sfa_anchor.Rd | 18 ++-- man/sfa_congruence.Rd | 10 ++ man/sfa_dimselect.Rd | 11 +- man/sfa_item_fit.Rd | 29 +++++-- man/sfa_jinglejangle.Rd | 5 + man/sfa_nfactors.Rd | 4 - man/sfa_nli_matrix.Rd | 6 + man/sfa_parallel.Rd | 24 +++++- man/sfa_project.Rd | 4 - man/sfa_redundancy.Rd | 6 + man/sfa_similarity.Rd | 15 ++- man/sfa_simplify.Rd | 2 tests/testthat/test-load.R | 2 vignettes/introduction.Rmd | 10 +- 39 files changed, 647 insertions(+), 284 deletions(-)
Title: Linear Model Evaluation with Randomized Residuals in a
Permutation Procedure
Description: Linear model calculations are made for many random versions of data.
Using residual randomization in a permutation procedure, sums of squares are
calculated over many permutations to generate empirical probability distributions
for evaluating model effects. Additionally, coefficients, statistics, fitted values, and residuals generated over many
permutations can be used for various procedures including pairwise tests, prediction, classification, and
model comparison. This package should provide most tools one could need for the analysis of
high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.
Author: Michael Collyer [aut, cre] ,
Dean Adams [aut]
Maintainer: Michael Collyer <mlcollyer@gmail.com>
Diff between RRPP versions 2.1.2 dated 2025-02-18 and 2.2.0 dated 2026-07-03
DESCRIPTION | 27 - MD5 | 113 ++++--- NAMESPACE | 16 + NEWS.md | 71 +++- R/ICCstats.r | 6 R/QRforX.r | 160 ++++------- R/RRPP.data.r |only R/RRPP.support.code.r | 605 +++++++++++++++++++++++++----------------- R/RRPP.utils.r | 250 +++++++++++++---- R/anova.lm.rrpp.r | 33 ++ R/base_lm.rrpp.r | 120 ++++++-- R/betaTest.r | 7 R/coef.lm.rrpp.r | 70 ++++ R/effects.r |only R/lmm.rrpp.r |only R/logLik.lm.rrpp.r | 209 +++++++++++++- R/looCV.r | 168 ++++++++++- R/mahal_dist.R | 3 R/measurement.error.r | 10 R/model.comparison.r | 75 +++-- R/ordinate.r | 14 R/pairwise.model.Z.r | 6 R/pairwise.r | 34 -- R/predict.lm.rrpp.r | 12 R/shared.support.code.r | 195 +------------ README.md | 4 build/vignette.rds |binary data/PlethCinHoff.rda |only data/PupfishMR.rda |only data/ReptAbund.rda |only data/flower.rda |only data/mammalHR.rda |only data/mammalHRphy.rda |only data/phytoplankton.rda |only data/podarcis.rda |only data/snakeHS.rda |only inst/CITATION | 2 inst/doc/ANOVA.vs.MANOVA.html | 79 ++--- inst/doc/Using.RRPP.html | 280 +++++++++++-------- man/PlethCinHoff.Rd |only man/PlethMorph.Rd | 2 man/Pupfish.Rd | 2 man/PupfishHeads.Rd | 2 man/PupfishMR.Rd |only man/QRforX.Rd | 20 - man/RRPP-package.Rd | 3 man/ReptAbund.Rd |only man/anova.lm.rrpp.Rd | 6 man/coef.lm.rrpp.Rd | 8 man/coef.lmm.rrpp.Rd |only man/effect.size.Rd | 10 man/fishy.Rd | 6 man/fixef.lmm.rrpp.Rd |only man/flower.Rd |only man/lmm.rrpp.Rd |only man/logLik.lm.rrpp.Rd | 7 man/looCV.Rd | 50 ++- man/looCV_table.Rd |only man/mahal_dist.Rd | 3 man/mammalHR.Rd |only man/mammalHRphy.Rd |only man/model.comparison.Rd | 9 man/motionpaths.Rd | 2 man/pairwise.model.Z.Rd | 2 man/phytoplankton.Rd |only man/podarcis.Rd |only man/powerTrans.Rd |only man/pval.Rd | 6 man/ranef.lmm.rrpp.Rd |only man/snakeHS.Rd |only tests/testthat/test-RRPP.R | 88 ++++++ 71 files changed, 1809 insertions(+), 986 deletions(-)
Title: Global Envelopes
Description: Implementation of global envelopes for a set of general d-dimensional vectors T
in various applications. A 100(1-alpha)% global envelope is a band bounded by two
vectors such that the probability that T falls outside this envelope in any of the d
points is equal to alpha. Global means that the probability is controlled simultaneously
for all the d elements of the vectors. The global envelopes can be used for graphical
Monte Carlo and permutation tests where the test statistic is a multivariate vector or
function (e.g. goodness-of-fit testing for point patterns and random sets, functional
analysis of variance, functional general linear model, n-sample test of correspondence
of distribution functions), for central regions of functional or multivariate data (e.g.
outlier detection, functional boxplot) and for global confidence and prediction bands
(e.g. confidence band in polynomial regression, Bayesian posterior prediction). See
Myllymäki and Mrkvička (2024) <doi:10.18637/jss.v111.i03 [...truncated...]
Author: Mari Myllymaeki [aut, cre] ,
Tomas Mrkvicka [aut],
Mikko Kuronen [ctb],
Jiri Dvorak [ctb],
Pavel Grabarnik [ctb],
Ute Hahn [ctb],
Michael Rost [ctb],
Henri Seijo [ctb]
Maintainer: Mari Myllymaeki <mari.myllymaki@luke.fi>
Diff between GET versions 1.0-7 dated 2025-05-19 and 1.0-8 dated 2026-07-02
GET-1.0-7/GET/R/appl_hotspots.r |only GET-1.0-7/GET/R/roadcrash.r |only GET-1.0-7/GET/data/roadcrash.RData |only GET-1.0-7/GET/inst/doc/HotSpots.pdf |only GET-1.0-7/GET/inst/doc/HotSpots.tex.rsp |only GET-1.0-7/GET/man/MatClust.lppm.Rd |only GET-1.0-7/GET/man/hotspots.MatClustlpp.Rd |only GET-1.0-7/GET/man/hotspots.poislpp.Rd |only GET-1.0-7/GET/man/pois.lppm.Rd |only GET-1.0-7/GET/man/rMatClustlpp.Rd |only GET-1.0-7/GET/man/roadcrash.Rd |only GET-1.0-7/GET/vignettes/HotSpots-data_MatClust_param.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_MatClust_param_obs.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_MatClust_param_sim.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_MatClust_sim.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_covariates.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_covariates_subwin.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_crashes.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_crashes_thin.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_density.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_poisson_EIP.pdf |only GET-1.0-7/GET/vignettes/HotSpots-data_poisson_K.pdf |only GET-1.0-7/GET/vignettes/HotSpots-fdrenvelope.pdf |only GET-1.0-7/GET/vignettes/HotSpots-fdrenvelope_cset.pdf |only GET-1.0-7/GET/vignettes/HotSpots.Rnw.orig |only GET-1.0-7/GET/vignettes/HotSpots.tex.rsp |only GET-1.0-8/GET/DESCRIPTION | 20 +- GET-1.0-8/GET/MD5 | 108 ++++------- GET-1.0-8/GET/NAMESPACE | 13 - GET-1.0-8/GET/NEWS | 6 GET-1.0-8/GET/R/appl_variogram.r | 8 GET-1.0-8/GET/R/curve-set.r | 6 GET-1.0-8/GET/R/fclustering.r | 10 - GET-1.0-8/GET/R/fdr.r | 12 + GET-1.0-8/GET/R/glm.R | 73 ++++--- GET-1.0-8/GET/R/plot_envelope_helper.R | 35 +-- GET-1.0-8/GET/build/vignette.rds |binary GET-1.0-8/GET/data/GDP.RData |binary GET-1.0-8/GET/data/GDPtax.RData |binary GET-1.0-8/GET/data/abide_9002_23.RData |binary GET-1.0-8/GET/data/adult_trees.RData |binary GET-1.0-8/GET/data/cgec.RData |binary GET-1.0-8/GET/data/datalist | 1 GET-1.0-8/GET/data/fallen_trees.RData |binary GET-1.0-8/GET/data/imageset3.RData |binary GET-1.0-8/GET/data/naturalness.RData |binary GET-1.0-8/GET/data/popgrowthmillion.RData |binary GET-1.0-8/GET/data/rimov.RData |binary GET-1.0-8/GET/data/saplings.RData |binary GET-1.0-8/GET/inst/doc/FDRenvelopes.pdf |binary GET-1.0-8/GET/inst/doc/FDRenvelopes.tex.rsp | 2 GET-1.0-8/GET/inst/doc/GET.pdf |binary GET-1.0-8/GET/inst/doc/GET.tex.rsp | 6 GET-1.0-8/GET/inst/doc/QuantileRegression.pdf |binary GET-1.0-8/GET/inst/doc/QuantileRegression.tex.rsp | 4 GET-1.0-8/GET/inst/doc/pointpatterns.pdf |binary GET-1.0-8/GET/inst/doc/pointpatterns.tex.rsp | 2 GET-1.0-8/GET/man/GET.variogram.Rd | 4 GET-1.0-8/GET/man/geom_central_region.Rd | 8 GET-1.0-8/GET/man/graph.flm.Rd | 3 GET-1.0-8/GET/vignettes/FDRenvelopes.Rnw.orig | 6 GET-1.0-8/GET/vignettes/FDRenvelopes.tex.rsp | 2 GET-1.0-8/GET/vignettes/GET.Rnw.orig | 4 GET-1.0-8/GET/vignettes/GET.tex.rsp | 6 GET-1.0-8/GET/vignettes/QuantileRegression.Rnw.orig | 4 GET-1.0-8/GET/vignettes/QuantileRegression.tex.rsp | 4 GET-1.0-8/GET/vignettes/pointpatterns.Rnw.orig | 2 GET-1.0-8/GET/vignettes/pointpatterns.tex.rsp | 2 68 files changed, 179 insertions(+), 172 deletions(-)
Title: Simulation of Discrete Random Variables with Marginal
Distributions and Correlation Matrix and via a Gaussian or
Student's t Copula
Description: A Gaussian or Student's t copula-based procedure for generating samples from discrete random variables with prescribed correlation matrix and marginal distributions.
Author: Alessandro Barbiero [aut, cre],
Pier Alda Ferrari [aut]
Maintainer: Alessandro Barbiero <alessandro.barbiero@unimi.it>
Diff between GenOrd versions 2.0.0 dated 2025-09-22 and 2.1.0 dated 2026-07-02
DESCRIPTION | 12 ++-- MD5 | 39 ++++++++------- NAMESPACE | 49 ++++++++++-------- R/contord.R | 129 +++++++++++++++++++++++++++++--------------------- R/estcontord.R | 31 ++++++------ R/logL.R | 14 ----- R/logLfull.R | 52 +++++++++++--------- R/logLfullz.R |only R/p_rect_t.R |only R/pmvt.alt.R | 14 ++--- README.md |only man/GenOrd-package.Rd | 14 +++-- man/contord.Rd | 44 +++++++++++++---- man/corrcheck.Rd | 6 +- man/estcontord.Rd | 52 ++++++++++++++------ man/logL.Rd | 16 +++--- man/logL_mle2.Rd | 11 ++-- man/logLfull.Rd | 17 +++--- man/logLfullz.Rd |only man/ordcont.Rd | 38 ++++++++++++-- man/ordsample.Rd | 26 +++++----- man/p_rect_t.Rd |only man/pmvt.alt.Rd | 29 ++++++----- 23 files changed, 362 insertions(+), 231 deletions(-)
Title: Parse Front Matter from Documents
Description: Extracts and parses structured metadata ('YAML' or 'TOML')
from the beginning of text documents. Front matter is a common pattern
in 'Quarto' documents, 'R Markdown' documents, static site generators,
documentation systems, content management tools and even 'Python' and
'R' scripts where metadata is placed at the top of a document,
separated from the main content by delimiter fences.
Author: Garrick Aden-Buie [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Garrick Aden-Buie <garrick@posit.co>
Diff between frontmatter versions 0.2.0 dated 2026-02-09 and 0.3.0 dated 2026-07-02
DESCRIPTION | 8 MD5 | 25 +- NEWS.md | 23 ++ R/frontmatter-package.R | 1 R/parse_front_matter.R | 4 R/write_front_matter.R | 145 +++++++++++-- README.md | 61 +++++ man/format_front_matter.Rd | 66 ++++-- man/frontmatter-package.Rd | 6 man/parse_front_matter.Rd | 6 src/extract_front_matter.cpp | 338 ++++++++++++++++++++++++++----- tests/testthat/_snaps/sql-formats.md |only tests/testthat/test-shebang.R |only tests/testthat/test-sql-formats.R |only tests/testthat/test-write_front_matter.R | 109 +++++++++ 15 files changed, 685 insertions(+), 107 deletions(-)
Title: General Purpose Client for 'ERDDAP™' Servers
Description: General purpose R client for 'ERDDAP™' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP™' information:
<https://upwell.pfeg.noaa.gov/erddap/information.html>.
Author: Scott Chamberlain [aut],
Ben Tupper [ctb],
Salvador Jesus Fernandez Bejarano [ctb],
Roy Mendelssohn [cre, ctb]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between rerddap versions 1.2.3 dated 2026-02-26 and 1.3.0 dated 2026-07-02
DESCRIPTION | 10 MD5 | 36 - NAMESPACE | 1 NEWS.md | 7 R/estimate_griddap_size.R |only R/grid.R | 144 ++++ R/zzz.r | 31 build/vignette.rds |binary inst/doc/Using_rerddap.R | 43 + inst/doc/Using_rerddap.Rmd | 235 ++++--- inst/doc/Using_rerddap.html | 1366 ++++++++++++++++++++++--------------------- man/cache_delete.Rd | 8 man/cache_details.Rd | 8 man/cache_list.Rd | 8 man/cache_setup.Rd | 8 man/disk.Rd | 4 man/estimate_griddap_size.Rd |only man/eurl.Rd | 4 man/griddap.Rd | 12 vignettes/Using_rerddap.Rmd | 235 ++++--- 20 files changed, 1285 insertions(+), 875 deletions(-)
Title: Select and Download Climate Data from 'DWD' (German Weather
Service)
Description: Handle climate data from the 'DWD' ('Deutscher Wetterdienst', see
<https://www.dwd.de/EN/climate_environment/cdc/cdc_node_en.html> for more information).
Choose observational time series from meteorological stations with 'selectDWD()'.
Find raster data from radar and interpolation according to <https://brry.github.io/rdwd/raster-data.html>.
Download (multiple) data sets with progress bars and no re-downloads through 'dataDWD()'.
Read both tabular observational data and binary gridded datasets with 'readDWD()'.
Author: Berry Boessenkool [aut, cre]
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between rdwd versions 1.9.8 dated 2025-12-21 and 1.9.17 dated 2026-07-02
DESCRIPTION | 10 - MD5 | 72 +++++----- NEWS.md | 13 + R/checkUpdates.R | 4 R/dataDWD.R | 43 +++++ R/indexFTP.R | 1 R/locdir.R | 2 R/plotRadar.R | 6 R/readDWD.R | 34 ++-- R/runLocalTests.R | 4 R/updateIndexes.R | 11 + README.md | 11 - build/vignette.rds |binary data/fileIndex.rda |binary data/formatIndex.rda |binary data/geoIndex.rda |binary data/gridIndex.rda |binary data/metaIndex.rda |binary inst/shinyapps/compare_years/app.R | 6 inst/shinyapps/compare_years/rsconnect/shinyapps.io/brry/wetter.dcf | 2 man/checkUpdates.Rd | 4 man/dataDWD.Rd | 17 ++ man/dwdbase.Rd | 5 man/dwdparams.Rd | 4 man/locdir.Rd | 4 man/plotDWD.Rd | 4 man/plotRadar.Rd | 2 man/projectRasterDWD.Rd | 10 - man/readDWD.Rd | 4 man/readDWD.deriv.Rd | 2 man/readDWD.grib2.Rd | 2 man/readDWD.hyras.Rd | 7 man/readDWD.nc.Rd | 9 - man/readDWD.radar.Rd | 10 - man/readDWD.raster.Rd | 2 man/updateIndexes.Rd | 6 man/validFileTypes.Rd | 5 37 files changed, 203 insertions(+), 113 deletions(-)
Title: Quantile Regression Forests
Description: Quantile Regression Forests is a tree-based ensemble
method for estimation of conditional quantiles. It is
particularly well suited for high-dimensional data. Predictor
variables of mixed classes can be handled. The package is
dependent on the package 'randomForest', written by Andy Liaw.
Author: Nicolai Meinshausen [aut, cre],
Loris Michel [aut]
Maintainer: Nicolai Meinshausen <meinshausen@gmail.com>
Diff between quantregForest versions 1.3-7.1 dated 2024-10-07 and 1.4-0 dated 2026-07-02
quantregForest-1.3-7.1/quantregForest/R/MDSplot.R |only quantregForest-1.3-7.1/quantregForest/R/classCenter.R |only quantregForest-1.3-7.1/quantregForest/R/combine.R |only quantregForest-1.3-7.1/quantregForest/R/convert.R |only quantregForest-1.3-7.1/quantregForest/R/getTree.R |only quantregForest-1.3-7.1/quantregForest/R/grow.R |only quantregForest-1.3-7.1/quantregForest/R/importance.R |only quantregForest-1.3-7.1/quantregForest/R/margin.R |only quantregForest-1.3-7.1/quantregForest/R/na.roughfix.R |only quantregForest-1.3-7.1/quantregForest/R/outlier.R |only quantregForest-1.3-7.1/quantregForest/R/partialPlot.R |only quantregForest-1.3-7.1/quantregForest/R/rfImpute.R |only quantregForest-1.3-7.1/quantregForest/R/rfcv.R |only quantregForest-1.3-7.1/quantregForest/R/treesize.R |only quantregForest-1.3-7.1/quantregForest/R/tuneRF.R |only quantregForest-1.3-7.1/quantregForest/R/varImpPlot.R |only quantregForest-1.3-7.1/quantregForest/R/varUsed.R |only quantregForest-1.3-7.1/quantregForest/R/zzz.R |only quantregForest-1.3-7.1/quantregForest/src |only quantregForest-1.4-0/quantregForest/DESCRIPTION | 25 quantregForest-1.4-0/quantregForest/MD5 | 37 quantregForest-1.4-0/quantregForest/NAMESPACE | 10 quantregForest-1.4-0/quantregForest/NEWS |only quantregForest-1.4-0/quantregForest/R/parallelRandomForest.R | 514 ---------- quantregForest-1.4-0/quantregForest/R/predict.quantregForest.R | 103 +- quantregForest-1.4-0/quantregForest/R/quantregForest.R | 59 - 26 files changed, 133 insertions(+), 615 deletions(-)
More information about quantregForest at CRAN
Permanent link
Title: Getting Bibliographic Records from 'OpenAlex' Database Using
'DSL' API
Description: A set of tools to extract bibliographic content from
'OpenAlex' database using API <https://developers.openalex.org/>.
Author: Massimo Aria [aut, cre, cph] ,
Corrado Cuccurullo [ctb] ,
Trang Le [aut] ,
June Choe [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between openalexR versions 3.0.1 dated 2026-01-14 and 3.1.0 dated 2026-07-02
DESCRIPTION | 10 MD5 | 82 +++---- NAMESPACE | 1 NEWS.md | 17 + R/data.R | 8 R/oa2bibliometrix.R | 2 R/oa2df.R | 426 ++++++++++++++------------------------- R/oa_fetch.R | 130 +++++++---- R/oa_ngrams.R | 6 R/oa_options.R |only R/oa_snowball.R | 4 R/simplify.R | 4 R/utils.R | 2 README.md | 145 +++++++++---- data/oa2df_coverage.rda |binary man/authors2df.Rd | 4 man/concepts2df.Rd | 4 man/countrycode.Rd | 4 man/funders2df.Rd | 4 man/institutions2df.Rd | 4 man/keywords2df.Rd | 2 man/oa2bibliometrix.Rd | 2 man/oa2df.Rd | 32 -- man/oa2df_coverage.Rd | 4 man/oa_fetch.Rd | 62 ++--- man/oa_ngrams.Rd | 6 man/oa_options.Rd |only man/oa_query.Rd | 36 +-- man/oa_request.Rd | 6 man/oa_snowball.Rd | 4 man/openalexR-package.Rd | 3 man/process_paper_authors.Rd | 2 man/publishers2df.Rd | 4 man/show_authors.Rd | 2 man/show_works.Rd | 2 man/sources2df.Rd | 4 man/topics2df.Rd | 4 man/works2df.Rd | 4 tests/testthat/fixtures |only tests/testthat/test-coverage.R | 2 tests/testthat/test-oa2df.R | 56 +++++ tests/testthat/test-oa_fetch.R | 178 +++++++++++++++- tests/testthat/test-oa_options.R |only tests/testthat/test-oa_query.R | 15 + 44 files changed, 730 insertions(+), 557 deletions(-)
Title: Latent Interaction (and Moderation) Analysis in Structural
Equation Models (SEM)
Description: Estimation of interaction (i.e., moderation) effects between latent variables
in structural equation models (SEM).
The supported methods are:
The constrained approach (Algina & Moulder, 2001).
The unconstrained approach (Marsh et al., 2004).
The residual centering approach (Little et al., 2006).
The double centering approach (Lin et al., 2010).
The latent moderated structural equations (LMS) approach (Klein & Moosbrugger, 2000).
The quasi-maximum likelihood (QML) approach (Klein & Muthén, 2007)
The constrained- unconstrained, residual- and double centering- approaches
are estimated via 'lavaan' (Rosseel, 2012), whilst the LMS- and QML- approaches
are estimated via 'modsem' it self. Alternatively model can be
estimated via 'Mplus' (Muthén & Muthén, 1998-2017).
References:
Algina, J., & Moulder, B. C. (2001).
<doi:10.1207/S15328007SEM0801_3>.
"A note on estimating the Jöreskog-Yang model for latent variable interaction using 'LISREL' 8.3."
Klein, A., & Moosb [...truncated...]
Author: Kjell Solem Slupphaug [aut, cre] ,
Mehmet Mehmetoglu [ctb] ,
Matthias Mittner [ctb]
Maintainer: Kjell Solem Slupphaug <slupphaugkjell@gmail.com>
Diff between modsem versions 1.0.20 dated 2026-06-01 and 1.0.21 dated 2026-07-02
DESCRIPTION | 15 +- MD5 | 66 +++++----- R/check_model_da.R | 2 R/construct_matrices_da.R | 7 - R/equations_lms.R | 45 +++++-- R/equations_qml.R | 4 R/generics_modsem_da.R | 8 - R/lav_syntax_functions.R | 18 ++ R/lexer.R | 6 R/mod_msg.R | 15 ++ R/model_da.R | 1 R/modsem_da.R | 32 +++-- R/modsem_data_da.R | 30 +++- R/modsem_mplus.R | 82 +++++++++++- R/ordered_mc_correction.R | 192 ++++++++++++++++++++++++++---- R/parser.R | 69 +++++++--- R/print_partable.R | 12 - R/simple_slopes.R | 44 ++---- R/summarize_partable.R | 8 - R/tokenizer.R | 39 ++++-- R/utils.R | 13 +- R/utils_da.R | 12 + R/zzz.R | 65 ++++++++++ README.md | 4 inst/doc/customize_plot_interactions.html | 2 inst/doc/observed_lms_qml.html | 6 inst/doc/plot_interactions.html | 8 - man/modsem-package.Rd | 5 man/modsem_da.Rd | 31 +++- man/modsem_mplus.Rd | 5 src/equations_lms.cpp | 86 ++----------- tests/testthat/test_composites_da.R | 3 tests/testthat/test_intchecks.R | 20 +++ tests/testthat/test_missing.R | 36 +++++ 34 files changed, 690 insertions(+), 301 deletions(-)
Title: Group Sequential Design
Description: Derives group sequential clinical trial designs and describes
their properties. Particular focus on time-to-event, binary, and
continuous outcomes. Largely based on methods described in
Jennison, Christopher and Turnbull, Bruce W., 2000,
"Group Sequential Methods with Applications to Clinical Trials"
ISBN: 0-8493-0316-8.
Author: Keaven Anderson [aut, cre],
Merck & Co., Inc., Rahway, NJ, USA and its affiliates [cph]
Maintainer: Keaven Anderson <keaven_anderson@merck.com>
Diff between gsDesign versions 3.9.0 dated 2026-02-15 and 3.10.0 dated 2026-07-02
DESCRIPTION | 10 MD5 | 677 NAMESPACE | 358 NEWS.md | 1065 - R/as_gt.R | 164 R/as_rtf.R | 504 R/as_table.R | 120 R/binomialExactPValues.R |only R/binomialPowerTable.R | 316 R/globals.R | 20 R/gsBinomial.R | 910 - R/gsBinomialExact.R | 921 - R/gsCP.R | 1061 - R/gsDesign-package.R | 8 R/gsDesign.R | 3498 ++-- R/gsMethods.R | 2147 +- R/gsNormalGrid.R | 260 R/gsSimulate.R | 242 R/gsSpending.R | 3672 ++-- R/gsSurv-eEvents.R | 668 R/gsSurv-interim.R | 90 R/gsSurv-method.R | 1098 - R/gsSurv-nSurv.R | 1378 - R/gsSurv-utils.R | 95 R/gsSurv-xtable.R | 162 R/gsSurv.R | 714 R/gsSurvCalendar.R | 436 R/gsSurvPower.R |only R/gsSurvival.R | 620 R/gsUtilities.R | 654 R/gsWTPT.R | 234 R/gsqplot.R | 2382 +- R/nBinomial1Sample.R | 82 R/nEvents.R | 118 R/nNormal.R | 284 R/sequentialPValue.R | 225 R/sfXG.R | 406 R/simBinomialSeasonalExact.R |only R/ssrCP.R | 1352 - R/toBinomialExact.R | 498 R/toInteger.R | 523 R/varBinomial.R | 640 R/xtable.R | 254 README.md | 87 build/vignette.rds |binary inst/doc/ConditionalErrorSpending.R | 420 inst/doc/ConditionalErrorSpending.Rmd | 790 inst/doc/ConditionalErrorSpending.html | 4770 ++--- inst/doc/ConditionalPowerPlot.R | 188 inst/doc/ConditionalPowerPlot.Rmd | 364 inst/doc/ConditionalPowerPlot.html | 1186 - inst/doc/GentleIntroductionToGSD.R | 206 inst/doc/GentleIntroductionToGSD.Rmd | 560 inst/doc/GentleIntroductionToGSD.html | 1416 - inst/doc/GraphicalMultiplicity.Rmd | 22 inst/doc/GraphicalMultiplicity.html | 524 inst/doc/HarmBound.R |only inst/doc/HarmBound.Rmd |only inst/doc/HarmBound.html |only inst/doc/MultiSeasonRareEvents.R |only inst/doc/MultiSeasonRareEvents.Rmd |only inst/doc/MultiSeasonRareEvents.html |only inst/doc/PoissonMixtureModel.R | 438 inst/doc/PoissonMixtureModel.Rmd | 708 inst/doc/PoissonMixtureModel.html | 2374 +- inst/doc/SelectiveBoundTesting.R |only inst/doc/SelectiveBoundTesting.Rmd |only inst/doc/SelectiveBoundTesting.html |only inst/doc/SeqDesignSurvival.R |only inst/doc/SeqDesignSurvival.Rmd |only inst/doc/SeqDesignSurvival.html |only inst/doc/SpendingFunctionOverview.R | 22 inst/doc/SpendingFunctionOverview.Rmd | 112 inst/doc/SpendingFunctionOverview.html | 646 inst/doc/SurvivalOverview.R | 388 inst/doc/SurvivalOverview.Rmd | 864 - inst/doc/SurvivalOverview.html | 2141 +- inst/doc/VaccineEfficacy.R | 562 inst/doc/VaccineEfficacy.Rmd | 929 - inst/doc/VaccineEfficacy.html | 5306 +++--- inst/doc/binomialSPRTExample.R | 122 inst/doc/binomialSPRTExample.Rmd | 312 inst/doc/binomialSPRTExample.html | 2912 +-- inst/doc/binomialTwoSample.R | 454 inst/doc/binomialTwoSample.Rmd | 782 inst/doc/binomialTwoSample.html | 8480 +++++----- inst/doc/gsDesignPackageOverview.R | 38 inst/doc/gsDesignPackageOverview.Rmd | 142 inst/doc/gsDesignPackageOverview.html | 910 - inst/doc/gsSurvBasicExamples.R | 508 inst/doc/gsSurvBasicExamples.Rmd | 848 - inst/doc/gsSurvBasicExamples.html | 4491 ++--- inst/doc/gsSurvPower.R |only inst/doc/gsSurvPower.Rmd |only inst/doc/gsSurvPower.html |only inst/doc/hGraph.Rmd | 22 inst/doc/hGraph.html | 522 inst/doc/nNormal.R | 162 inst/doc/nNormal.Rmd | 420 inst/doc/nNormal.html | 1428 - inst/doc/toInteger.R | 296 inst/doc/toInteger.Rmd | 523 inst/doc/toInteger.html | 1306 - inst/slides |only man/as_gt.Rd | 156 man/as_rtf.Rd | 292 man/as_table.Rd | 84 man/binomialPowerTable.Rd | 198 man/checkScalar.Rd | 270 man/eEvents.Rd | 270 man/gsBinomialExact.Rd | 612 man/gsBound.Rd | 284 man/gsBoundCP.Rd | 150 man/gsBoundSummary.Rd | 704 man/gsCP.Rd | 528 man/gsDensity.Rd | 242 man/gsDesign-package.Rd | 65 man/gsDesign.Rd | 828 man/gsProbability.Rd | 276 man/gsSurvCalendar.Rd | 455 man/gsSurvPower.Rd |only man/nNormal.Rd | 238 man/nSurv.Rd | 1364 - man/nSurvival.Rd | 570 man/normalGrid.Rd | 230 man/plot.gsDesign.Rd | 336 man/repeatedPValueBinomialExact.Rd |only man/sequentiaPValue.Rd | 170 man/sequentialPValueBinomialExact.Rd |only man/sfDistribution.Rd | 340 man/sfExponential.Rd | 222 man/sfHSD.Rd | 180 man/sfLDOF.Rd | 250 man/sfLinear.Rd | 298 man/sfPoints.Rd | 198 man/sfPower.Rd | 186 man/sfSpecial.Rd | 324 man/sfTDist.Rd | 238 man/sfXG.Rd | 282 man/simBinomialSeasonalExact.Rd |only man/spendingFunction.Rd | 276 man/ssrCP.Rd | 760 man/toBinomialExact.Rd | 171 man/toInteger.Rd | 198 man/varBinomial.Rd | 680 man/xtable.Rd | 22 src/gsbound.c | 2 src/gsbound1.c | 2 tests/testthat.R | 8 tests/testthat/Rplots.pdf |only tests/testthat/_snaps/independent-test-as_gt.md | 52 tests/testthat/_snaps/independent-test-as_rtf/gsBinomialExact-safety.rtf | 248 tests/testthat/_snaps/independent-test-as_rtf/gsBinomialExact.rtf | 268 tests/testthat/_snaps/independent-test-as_rtf/gsBoundSummary-footnote.rtf | 398 tests/testthat/_snaps/independent-test-as_rtf/gsBoundSummary-gsDesign.rtf | 418 tests/testthat/_snaps/independent-test-as_rtf/gsBoundSummary-gsSurv.rtf | 418 tests/testthat/_snaps/independent-test-gsBoundSummary.md | 348 tests/testthat/_snaps/independent-test-plot.binomialSPRT/binomial-sprt-plottype-1.svg | 222 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Title: Plotting Tool for Brain Atlases
Description: Provides a 'ggplot2' geom and position for visualizing brain
region data on cortical, subcortical, and white matter tract atlases.
Brain atlas geometries are stored as polygon data, enabling
seamless integration with the 'ggplot2' ecosystem including faceting,
custom scales, and themes. Mowinckel & Vidal-Piñeiro (2020)
<doi:10.1177/2515245920928009>.
Author: Athanasia Mo Mowinckel [aut, cre] ,
Didac Vidal-Pineiro [aut] ,
Ramiro Magno [ctb] ,
Center for Lifespan Changes in Brain and Cognition, University of Oslo,
Norway [cph]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between ggseg versions 2.2.0 dated 2026-06-22 and 2.2.1 dated 2026-07-02
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ inst/doc/external-data.html | 2 +- inst/doc/ggseg.html | 12 ++++++------ inst/doc/positioning-views.html | 4 ++-- tests/testthat/Rplots.pdf |binary tests/testthat/helpers.R | 14 ++++++++++++++ tests/testthat/test-coords.R | 7 ++++--- tests/testthat/test-geom-brain-polygon.R | 5 +---- tests/testthat/test-geom-brain.R | 3 +-- 11 files changed, 48 insertions(+), 31 deletions(-)
Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the
OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped
to the Observational Medical Outcomes Partnership (OMOP) common data model.
New users and prevalent users cohorts can be generated and their
characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] ,
Mike Du [ctb] ,
Yuchen Guo [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Xintong Li [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Nuria Mercade-Besora [aut] ,
Xihang Chen [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between DrugUtilisation versions 1.2.0 dated 2026-06-18 and 1.2.1 dated 2026-07-02
DESCRIPTION | 6 MD5 | 20 NEWS.md | 6 R/erafyCohort.R | 30 R/plots.R | 18 R/summariseDiscontinuationAsSurvival.R | 8 R/summariseDrugUtilisation.R | 3 R/tables.R | 2 inst/doc/create_cohorts.html | 220 inst/doc/drug_utilisation.html | 4296 ++++++++--------- tests/testthat/test-generateDrugUtilisationCohortSet.R | 5 11 files changed, 2317 insertions(+), 2297 deletions(-)
More information about DrugUtilisation at CRAN
Permanent link
Title: Access Colombian Data via APIs and Curated Datasets
Description: Provides a comprehensive interface to access diverse public data about
Colombia through multiple APIs and curated datasets. The package integrates
three different APIs: 'API-Colombia' for Colombian-specific data including
geography, culture, tourism, and government information; 'World Bank API'
for economic and demographic indicators; and 'Nager.Date' for public holidays.
The package enables users to explore various aspects of Colombia such as
geographic locations, cultural attractions, economic indicators, demographic
data, and public holidays. Additionally, 'ColombiAPI' includes curated
datasets covering Bogota air stations, business and holiday dates, public
schools, Colombian coffee exports, cannabis licenses, Medellin rainfall,
malls in Bogota, as well as datasets on indigenous languages, student
admissions and school statistics, forest liana mortality, municipal and
regional data, connectivity and digital infrastructure, program graduates,
vehicle counts, international visitors, [...truncated...]
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between ColombiAPI versions 0.3.2 dated 2026-05-06 and 0.4.0 dated 2026-07-02
ColombiAPI-0.3.2/ColombiAPI/R/get_country_info_co.R |only ColombiAPI-0.3.2/ColombiAPI/man/get_country_info_co.Rd |only ColombiAPI-0.3.2/ColombiAPI/tests/testthat/test-get_country_info_co.R |only ColombiAPI-0.4.0/ColombiAPI/DESCRIPTION | 40 +- ColombiAPI-0.4.0/ColombiAPI/MD5 | 163 ++++------ ColombiAPI-0.4.0/ColombiAPI/NAMESPACE | 1 ColombiAPI-0.4.0/ColombiAPI/NEWS.md | 21 + ColombiAPI-0.4.0/ColombiAPI/R/colombiapi-package.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/data-documentation.R | 5 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_airports.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_attractions.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_child_mortality.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_cities.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_cpi.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_departments.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_energy_use.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_gdp.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_holidays.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_hospital_beds.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_invasive_species.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_life_expectancy.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_literacy_rate.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_native_communities.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_natural_areas.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_population.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_presidents.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_radios.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_regions.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_typical_dishes.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/get_colombia_unemployment.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/utils.R | 2 ColombiAPI-0.4.0/ColombiAPI/R/view_datasets_ColombiAPI.R | 2 ColombiAPI-0.4.0/ColombiAPI/README.md | 12 ColombiAPI-0.4.0/ColombiAPI/build/vignette.rds |binary ColombiAPI-0.4.0/ColombiAPI/inst/CITATION | 2 ColombiAPI-0.4.0/ColombiAPI/inst/doc/colombiAPI_vignette.Rmd | 11 ColombiAPI-0.4.0/ColombiAPI/inst/doc/colombiAPI_vignette.html | 25 - ColombiAPI-0.4.0/ColombiAPI/inst/licenses/LICENSE | 4 ColombiAPI-0.4.0/ColombiAPI/inst/licenses/LICENSE.md | 51 +-- ColombiAPI-0.4.0/ColombiAPI/inst/licenses/LICENSES_DETAILS.md | 3 ColombiAPI-0.4.0/ColombiAPI/man/Cartagena_wifi_tbl_df.Rd | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Bogota_airstations_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Bogota_business_Date.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Bogota_holidays_Date.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Bogota_malls_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Bucaramanga_wifi_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Cannabis_Licenses_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Cartagena_wifi_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Colombia_coffee_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Medellin_rain_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-Tulua_Public_Schools_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-admitted_students_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-dead_lianas_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-digital_centers_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-digital_graduates_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-foreign_visitors_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-gdp_departments_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_airports.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_attractions.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_child_mortality.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_cities.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_cpi.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_departments.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_energy_use.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_gdp.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_holidays.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_hospital_beds.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_invasive_species.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_life_expectancy.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_literacy_rate.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_native_communities.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_natural_areas.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_population.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_presidents.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_radios.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_regions.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_typical_dishes.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-get_colombia_unemployment.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-indigenous_vocabulary_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-municipalities_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-school_levels_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-vehicle_count_tbl_df.R | 2 ColombiAPI-0.4.0/ColombiAPI/tests/testthat/test-view_datasets_ColombiAPI.R | 2 ColombiAPI-0.4.0/ColombiAPI/vignettes/colombiAPI_vignette.Rmd | 11 84 files changed, 240 insertions(+), 243 deletions(-)
Title: Access Chilean Data via APIs and Curated Datasets
Description: Provides functions to access data from public RESTful APIs including
'FINDIC API', 'World Bank API', and 'Nager.Date',
retrieving real-time or historical data related to Chile such as financial indicators,
holidays, and more.
Additionally, the package includes curated datasets related to Chile, covering topics
such as human rights violations during the Pinochet regime, electoral data, census samples,
health surveys, seismic events, territorial codes, and environmental measurements.
The package supports research and analysis focused on Chile by integrating open APIs with
high-quality datasets from multiple domains. For more information on the APIs, see:
'FINDIC' <https://findic.cl/>,
'World Bank API' <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392>,
and 'Nager.Date' <https://date.nager.at/Api>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between ChileDataAPI versions 0.2.0 dated 2025-09-11 and 0.3.0 dated 2026-07-02
ChileDataAPI-0.2.0/ChileDataAPI/R/get_country_info_cl.R |only ChileDataAPI-0.2.0/ChileDataAPI/man/get_country_info_cl.Rd |only ChileDataAPI-0.2.0/ChileDataAPI/tests/testthat/test-get_country_info_cl.R |only ChileDataAPI-0.3.0/ChileDataAPI/DESCRIPTION | 13 ChileDataAPI-0.3.0/ChileDataAPI/MD5 | 125 ++++----- ChileDataAPI-0.3.0/ChileDataAPI/NAMESPACE | 2 ChileDataAPI-0.3.0/ChileDataAPI/NEWS.md | 22 + ChileDataAPI-0.3.0/ChileDataAPI/R/chiledataapi-package.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/data-documentation.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_bitcoin.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_child_mortality.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_copper_pound.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_cpi.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_dollar.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_energy_use.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_euro.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_gdp.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_holidays.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_hospital_beds.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_ipsa.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_life_expectancy.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_literacy_rate.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_population.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_uf.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_unemployment.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_utm.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/get_chile_yen.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/utils.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/R/view_datasets_ChileDataAPI.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/README.md | 10 ChileDataAPI-0.3.0/ChileDataAPI/build/vignette.rds |binary ChileDataAPI-0.3.0/ChileDataAPI/inst/CITATION | 4 ChileDataAPI-0.3.0/ChileDataAPI/inst/doc/ChileDataAPI_vignette.Rmd | 30 -- ChileDataAPI-0.3.0/ChileDataAPI/inst/doc/ChileDataAPI_vignette.html | 132 ++++------ ChileDataAPI-0.3.0/ChileDataAPI/inst/licenses/LICENSE | 4 ChileDataAPI-0.3.0/ChileDataAPI/inst/licenses/LICENSE.md | 34 -- ChileDataAPI-0.3.0/ChileDataAPI/inst/licenses/LICENSES_DETAILS.md | 5 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-census_chile_2017_df.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-chile_earthquakes_tbl_df.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-chile_election_2021_df.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-chile_health_survey_df.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-chile_plebiscite_df.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_bitcoin.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_child_mortality.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_copper_pound.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_cpi.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_dollar.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_energy_use.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_euro.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_gdp.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_holidays.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_hospital_beds.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_ipsa.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_life_expectancy.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_literacy_rate.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_population.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_uf.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_unemployment.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_utm.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-get_chile_yen.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-malleco_tree_rings_ts.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-pinochet_regime_df.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-territorial_codes_tbl_df.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/tests/testthat/test-view_datasets_ChileDataAPI.R | 4 ChileDataAPI-0.3.0/ChileDataAPI/vignettes/ChileDataAPI_vignette.Rmd | 30 -- 65 files changed, 297 insertions(+), 310 deletions(-)
Title: 'teal' Modules for Standard Clinical Outputs
Description: Provides user-friendly tools for creating and customizing
clinical trial reports. By leveraging the 'teal' framework, this
package provides 'teal' modules to easily create an interactive panel
that allows for seamless adjustments to data presentation, thereby
streamlining the creation of detailed and accurate reports.
Author: Dony Unardi [aut, cre],
Joe Zhu [aut] ,
Jana Stoilova [aut],
Davide Garolini [aut],
Emily de la Rua [aut],
Abinaya Yogasekaram [aut],
Mahmoud Hallal [aut],
Dawid Kaledkowski [aut],
Rosemary Li [aut],
Heng Wang [aut],
Pawel Rucki [aut],
Nikolas Burkof [...truncated...]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal.modules.clinical versions 0.12.0 dated 2025-12-03 and 0.13.0 dated 2026-07-02
teal.modules.clinical-0.12.0/teal.modules.clinical/man/select_decorators.Rd |only teal.modules.clinical-0.12.0/teal.modules.clinical/man/srv_decorate_teal_data.Rd |only teal.modules.clinical-0.13.0/teal.modules.clinical/DESCRIPTION | 24 - teal.modules.clinical-0.13.0/teal.modules.clinical/MD5 | 218 ++++------ teal.modules.clinical-0.13.0/teal.modules.clinical/NEWS.md | 11 teal.modules.clinical-0.13.0/teal.modules.clinical/R/argument_convention.R | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/R/arm_ref_comp.R | 3 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_a_gee.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_a_mmrm.R | 30 - teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_barchart_simple.R | 12 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_ci.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_forest_rsp.R | 11 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_forest_tte.R | 11 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_ipp.R | 22 - teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_km.R | 12 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_lineplot.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_pp_adverse_events.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_pp_patient_timeline.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_pp_therapy.R | 12 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_g_pp_vitals.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_abnormality.R | 64 +- teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_abnormality_by_worst_grade.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_ancova.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_binary_outcome.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_coxreg.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_events.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_events_by_grade.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_events_patyear.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_events_summary.R | 14 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_exposure.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_glm_counts.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_logistic.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_mult_events.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_pp_medical_history.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_shift_by_arm.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_shift_by_arm_by_worst.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_shift_by_grade.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_smq.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_summary.R | 45 +- teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_summary_by.R | 47 +- teal.modules.clinical-0.13.0/teal.modules.clinical/R/tm_t_tte.R | 10 teal.modules.clinical-0.13.0/teal.modules.clinical/R/utils.R | 132 ------ teal.modules.clinical-0.13.0/teal.modules.clinical/README.md | 14 teal.modules.clinical-0.13.0/teal.modules.clinical/inst/WORDLIST | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/inst/doc/decorate-module-output.html | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/inst/doc/generate_tmc_test_data.R | 8 teal.modules.clinical-0.13.0/teal.modules.clinical/inst/doc/generate_tmc_test_data.Rmd | 8 teal.modules.clinical-0.13.0/teal.modules.clinical/inst/doc/generate_tmc_test_data.html | 12 teal.modules.clinical-0.13.0/teal.modules.clinical/inst/doc/quickstart_substitute.html | 17 teal.modules.clinical-0.13.0/teal.modules.clinical/inst/doc/teal-modules-clinical.html | 4 teal.modules.clinical-0.13.0/teal.modules.clinical/man/module_arguments.Rd | 5 teal.modules.clinical-0.13.0/teal.modules.clinical/man/split_choices.Rd | 6 teal.modules.clinical-0.13.0/teal.modules.clinical/man/teal.modules.clinical-package.Rd | 4 teal.modules.clinical-0.13.0/teal.modules.clinical/man/template_abnormality.Rd | 3 teal.modules.clinical-0.13.0/teal.modules.clinical/man/template_arguments.Rd | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/man/template_g_km.Rd | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/man/template_summary.Rd | 4 teal.modules.clinical-0.13.0/teal.modules.clinical/man/template_tte.Rd | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/man/tm_t_binary_outcome.Rd | 6 teal.modules.clinical-0.13.0/teal.modules.clinical/man/tm_t_summary.Rd | 11 teal.modules.clinical-0.13.0/teal.modules.clinical/man/tm_t_summary_by.Rd | 4 teal.modules.clinical-0.13.0/teal.modules.clinical/man/tm_t_tte.Rd | 6 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/_snaps/tm_g_ipp.md | 4 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/_snaps/tm_t_abnormality.md | 51 ++ teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/_snaps/tm_t_summary.md | 17 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/helper-TealAppDriver.R | 19 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/helper-testing-depth.R | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/setup-options.R | 2 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-examples.R | 29 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_a_gee.R | 62 +- teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_a_mmrm.R | 61 +- teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_barchart_simple.R | 69 +-- teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_ci.R | 32 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_forest_rsp.R | 34 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_forest_tte.R | 32 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_ipp.R | 32 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_km.R | 78 +-- teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_lineplot.R | 63 +- teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_pp_adverse_events.R | 38 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_pp_patient_timeline.R | 111 +---- teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_pp_therapy.R | 27 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_g_pp_vitals.R | 29 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_abnormality.R | 23 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_abnormality_by_worst_grade.R | 22 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_ancova.R | 34 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_binary_outcome.R | 32 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_coxreg.R | 24 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_events.R | 17 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_events_by_grade.R | 22 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_events_patyear.R | 22 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_events_summary.R | 17 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_exposure.R | 28 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_logistic.R | 26 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_mult_events.R | 21 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_pp_basic_info.R | 34 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_pp_laboratory.R | 143 +++--- teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_pp_medical_history.R | 30 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_pp_prior_medication.R | 36 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_shift_by_arm.R | 25 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_shift_by_arm_by_worst.R | 36 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_shift_by_grade.R | 26 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_smq.R | 32 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_summary.R | 19 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_summary_by.R | 27 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-shinytest2-tm_t_tte.R | 22 - teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-tm_t_abnormality.R | 20 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-tm_t_glm_counts.R | 4 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-tm_t_summary.R | 3 teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-tm_t_summary_by.R | 75 +++ teal.modules.clinical-0.13.0/teal.modules.clinical/tests/testthat/test-utils.R | 152 ++++++ teal.modules.clinical-0.13.0/teal.modules.clinical/vignettes/generate_tmc_test_data.Rmd | 8 111 files changed, 1403 insertions(+), 1391 deletions(-)
More information about teal.modules.clinical at CRAN
Permanent link
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.27 dated 2026-05-25 and 1.28 dated 2026-07-02
DESCRIPTION | 8 MD5 | 90 ++--- NEWS.md | 31 + R/class-color.R | 10 R/class-workbook-utils.R | 60 +++ R/class-workbook-wrappers.R | 3 R/class-workbook.R | 55 ++- R/get-named-regions.R | 19 - R/helper-functions.R | 3 R/openxlsx2-package.R | 14 R/standardize.R | 2 R/utils.R | 2 R/wb_load.R | 43 ++ README.md | 20 - build/vignette.rds |binary inst/AUTHORS | 1 inst/WORDLIST | 3 inst/doc/openxlsx2.R | 4 inst/doc/openxlsx2.Rmd | 5 inst/doc/openxlsx2_charts_manual.R | 2 inst/doc/openxlsx2_charts_manual.Rmd | 2 inst/doc/openxlsx2_charts_manual.html | 10 inst/include/pugixml/pugiconfig.hpp | 15 inst/include/pugixml/pugixml.cpp | 459 ++++++++++++++++++++------- inst/include/pugixml/pugixml.hpp | 107 +++--- man/named_region-wb.Rd | 5 man/openxlsx2-package.Rd | 8 man/wbWorkbook.Rd | 6 man/wb_add_data_table.Rd | 3 man/wb_dims.Rd | 2 src/helper_functions.cpp | 53 ++- src/openxlsx2.h | 5 src/write_file.cpp | 12 tests/testthat/test-class-workbook.R | 65 +++ tests/testthat/test-conditional_formatting.R | 2 tests/testthat/test-helper-functions.R | 35 ++ tests/testthat/test-loading_workbook.R | 62 +++ tests/testthat/test-named_regions.R | 2 tests/testthat/test-read_sources.R | 19 + tests/testthat/test-standardize.R | 28 + tests/testthat/test-tables.R | 26 + tests/testthat/test-utils.R | 5 tests/testthat/test-wb_styles.R | 24 + tests/testthat/test-write.R | 7 vignettes/openxlsx2.Rmd | 5 vignettes/openxlsx2_charts_manual.Rmd | 2 46 files changed, 1031 insertions(+), 313 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb],
Christine Laney [aut, ctb],
Nathan Mietkiewicz [aut, ctb],
Eric Sokol [aut, ctb],
Kaelin Cawley [aut, ctb],
NEON [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 4.0.0 dated 2026-06-19 and 4.0.1 dated 2026-07-02
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/byTileAOP.R | 5 +++-- 3 files changed, 9 insertions(+), 8 deletions(-)
Title: Providing Fast and Flexible Functions for Distance Correlation
Analysis
Description: Provides methods for distance covariance and distance correlation (Szekely, et al. (2007) <doi:10.1214/009053607000000505>), generalized version thereof (Sejdinovic, et al. (2013) <doi:10.1214/13-AOS1140>) and corresponding tests (Berschneider, Bottcher (2018) <doi:10.48550/arXiv.1808.07280>. Distance standard deviation methods (Edelmann, et al. (2020) <doi:10.1214/19-AOS1935>) and distance correlation methods for survival endpoints (Edelmann, et al. (2021) <doi:10.1111/biom.13470>) are also included.
Author: Dominic Edelmann [aut, cre],
Jochen Fiedler [aut]
Maintainer: Dominic Edelmann <dominic.edelmann@dkfz-heidelberg.de>
Diff between dcortools versions 0.1.7 dated 2025-12-09 and 0.2.0 dated 2026-07-02
DESCRIPTION | 11 - MD5 | 16 +- NEWS.md | 10 + R/auxiliary_functions.R | 2 R/distcov_test2.R | 360 ++++++++++++++++++++++++++++++++++++++---------- R/methods_test.R | 14 + R/perm_algorithms2.R | 279 ++++++++++++++++++------------------- build/partial.rdb |binary man/distcov.test.Rd | 16 +- 9 files changed, 475 insertions(+), 233 deletions(-)
Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Description: Phylogenetic trees contain components such as nodes, edges,
branches, and associated data. As the core data manipulation tool in the
'ggtree' ecosystem, 'tidytree' provides tools for converting tree objects
to tidy data frames and tidy interfaces for manipulating, analyzing, and
visualizing tree data.
Author: Guangchuang Yu [aut, cre, cph] ,
Bradley Jones [ctb],
Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between tidytree versions 0.4.7 dated 2026-01-08 and 0.4.8 dated 2026-07-02
DESCRIPTION | 14 +++-- MD5 | 25 +++++----- NEWS.md | 13 +++++ R/AllClasses.R | 3 - R/as-tibble.R | 14 +++-- R/full-join.R | 2 R/left-join.R | 16 ++++++ R/method-as-ultrametric.R | 51 ++++++++++++--------- R/offspring.R | 91 ++++++++++++++++++++++++++++++-------- R/tree-subset.R | 53 +++++++++++----------- man/reexports.Rd | 12 ++--- man/tidytree-package.Rd | 63 ++++++++++++++------------ tests/testthat/test-innerjoin.R | 2 tests/testthat/test-tree-subset.R |only 14 files changed, 233 insertions(+), 126 deletions(-)
Title: Filter Module for 'teal' Applications
Description: Data filtering module for 'teal' applications. Allows for
interactive filtering of data stored in 'data.frame' and
'MultiAssayExperiment' objects. Also displays filtered and unfiltered
observation counts.
Author: Dawid Kaledkowski [aut] ,
Pawel Rucki [aut],
Aleksander Chlebowski [aut] ,
Andre Verissimo [aut] ,
Lluis Revilla Sancho [aut] ,
Dony Unardi [rev, cre],
Kartikeya Kirar [aut],
Marcin Kosinski [aut],
Chendi Liao [aut],
Andrew Bates [aut],
Mahmoud Halla [...truncated...]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal.slice versions 0.8.0 dated 2026-06-04 and 0.8.1 dated 2026-07-02
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 6 ++++++ R/teal_slice.R | 4 ++-- 4 files changed, 15 insertions(+), 9 deletions(-)
Title: Model Context Protocol Servers and Clients
Description: Implements the Model Context Protocol (MCP). Users can start
'R'-based servers, serving functions as tools for large language
models to call before responding to the user in MCP-compatible apps
like 'Claude Desktop' and 'Claude Code', with options to run those
tools inside of interactive 'R' sessions. On the other end, when 'R'
is the client via the 'ellmer' package, users can register tools from
third-party MCP servers to integrate additional context into chats.
Author: Simon Couch [aut, cre] ,
Winston Chang [aut] ,
Charlie Gao [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between mcptools versions 0.2.1 dated 2026-03-17 and 1.0.0 dated 2026-07-02
DESCRIPTION | 12 MD5 | 57 + NEWS.md | 68 ++ R/aaa.R | 3 R/client-auth.R |only R/client-http.R |only R/client.R | 1019 +++++++++++++++++++++++++++++---- R/connect.R |only R/protocol-version.R | 6 R/server.R | 376 ++++++++++-- R/session.R | 202 ++++++ R/tools.R | 18 R/utils.R | 68 ++ README.md | 29 build/vignette.rds |binary inst/doc/server.Rmd | 37 + inst/doc/server.html | 33 + inst/example-config-remote.json | 7 man/client.Rd | 71 +- man/mcptools-package.Rd | 1 man/server.Rd | 27 tests/testthat/fixtures |only tests/testthat/helper.R | 122 +++ tests/testthat/test-client-auth.R |only tests/testthat/test-client-http.R |only tests/testthat/test-client.R | 237 +++++++ tests/testthat/test-connect.R |only tests/testthat/test-protocol-version.R | 31 + tests/testthat/test-server.R | 420 +++++++++++++ tests/testthat/test-session.R | 182 +++++ tests/testthat/test-tools.R | 139 ++++ tests/testthat/test-utils.R | 33 + vignettes/server.Rmd | 37 + 33 files changed, 2987 insertions(+), 248 deletions(-)
Title: Grammar Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Geometries: geom_table(), geom_plot() and geom_grob() add insets to
plots using native data coordinates, while geom_table_npc(), geom_plot_npc()
and geom_grob_npc() do the same using "npc" coordinates through new
aesthetics "npcx" and "npcy". Statistics: select observations based on 2D
density. Positions: radial nudging away from a center point and nudging away
from a line or curve; combined stacking and nudging; combined dodging and
nudging.
Author: Pedro J. Aphalo [aut, cre] ,
Kamil Slowikowski [ctb] ,
Michal Krassowski [ctb] ,
Daniel Sabanes Bove [ctb] ,
Stella Banjo [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpp versions 0.6.0 dated 2026-01-18 and 0.6.1 dated 2026-07-02
DESCRIPTION | 16 MD5 | 86 +-- NEWS.md | 5 R/geom-label-pairwise.r | 236 ++++++---- R/geom-text-pairwise.R | 187 +++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/grammar-extensions.Rmd | 2 inst/doc/grammar-extensions.html | 6 man/birch.df.Rd | 2 man/geom_plot.Rd | 4 man/geom_quadrant_lines.Rd | 6 man/geom_table.Rd | 4 man/geom_text_pairwise.Rd | 25 + man/geom_x_margin_arrow.Rd | 6 man/geom_x_margin_grob.Rd | 6 man/geom_x_margin_point.Rd | 6 man/ggpp-ggproto.Rd | 2 man/ggpp-package.Rd | 5 man/ivy.df.Rd | 72 +-- man/position_dodgenudge.Rd | 18 man/position_dodgenudge_to.Rd | 18 man/position_jitternudge.Rd | 18 man/position_nudge_center.Rd | 18 man/position_nudge_keep.Rd | 18 man/position_nudge_line.Rd | 18 man/position_nudge_to.Rd | 18 man/position_stacknudge.Rd | 18 man/position_stacknudge_to.Rd | 18 man/quadrant_example.df.Rd | 2 man/stat_dens1d_filter.Rd | 8 man/stat_dens1d_labels.Rd | 8 man/stat_dens2d_filter.Rd | 8 man/stat_dens2d_labels.Rd | 8 man/stat_panel_counts.Rd | 6 man/stat_quadrant_counts.Rd | 6 man/volcano_example.df.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/geom-label/geom-label-npc4.svg | 2 tests/testthat/_snaps/geom-table/geom-table-parsed-all.svg | 104 ++-- tests/testthat/_snaps/geom-table/geom-table-parsed-partial-dark.svg | 102 ++-- tests/testthat/_snaps/geom-table/geom-table-parsed-partial.svg | 102 ++-- tests/testthat/_snaps/geom-text/geom-text-npc4.svg | 2 vignettes/grammar-extensions.Rmd | 2 44 files changed, 705 insertions(+), 495 deletions(-)
Title: Miscellaneous Functions for 'ggplot2'
Description: Provides a collection of 'ggplot2' extensions and utilities
for creating geometric layers, applying themes, working with legends,
and modifying plot objects.
Author: Guangchuang Yu [aut, cre, cph] ,
Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggfun versions 0.2.0 dated 2025-07-15 and 0.2.1 dated 2026-07-02
ggfun-0.2.0/ggfun/inst/doc/ggfun.Rmd |only ggfun-0.2.0/ggfun/vignettes/ggfun.Rmd |only ggfun-0.2.1/ggfun/DESCRIPTION | 29 - ggfun-0.2.1/ggfun/MD5 | 44 + ggfun-0.2.1/ggfun/NAMESPACE | 4 ggfun-0.2.1/ggfun/NEWS.md | 9 ggfun-0.2.1/ggfun/R/geom-hist.r |only ggfun-0.2.1/ggfun/R/geom_segment_c.R | 176 +++---- ggfun-0.2.1/ggfun/R/ggelement.R | 35 - ggfun-0.2.1/ggfun/R/operator.R | 24 - ggfun-0.2.1/ggfun/R/set_font.R | 19 ggfun-0.2.1/ggfun/R/utilities.R | 4 ggfun-0.2.1/ggfun/README.md |only ggfun-0.2.1/ggfun/build/vignette.rds |binary ggfun-0.2.1/ggfun/inst/doc/ggfun.R | 248 ++++++++-- ggfun-0.2.1/ggfun/inst/doc/ggfun.html | 694 ++++++++++++++++++++--------- ggfun-0.2.1/ggfun/inst/doc/ggfun.qmd |only ggfun-0.2.1/ggfun/man/element_roundrect.Rd | 6 ggfun-0.2.1/ggfun/man/geom_hist.Rd |only ggfun-0.2.1/ggfun/man/geom_segment_c.Rd | 3 ggfun-0.2.1/ggfun/man/geom_xspline.Rd | 308 ++++++------ ggfun-0.2.1/ggfun/man/ggfun-package.Rd | 57 +- ggfun-0.2.1/ggfun/man/reexports.Rd | 4 ggfun-0.2.1/ggfun/tests |only ggfun-0.2.1/ggfun/vignettes/ggfun.qmd |only 25 files changed, 1075 insertions(+), 589 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).
Author: Francois Husson [aut, cre] ,
Julie Josse [aut],
Sebastien Le [aut],
Jeremy Mazet [aut]
Maintainer: Francois Husson <francois.husson@institut-agro.fr>
Diff between FactoMineR versions 2.15 dated 2026-06-11 and 2.16 dated 2026-07-02
FactoMineR-2.15/FactoMineR/NEWS |only FactoMineR-2.15/FactoMineR/README |only FactoMineR-2.16/FactoMineR/DESCRIPTION | 8 - FactoMineR-2.16/FactoMineR/MD5 | 71 ++++----- FactoMineR-2.16/FactoMineR/NAMESPACE | 29 ++- FactoMineR-2.16/FactoMineR/NEWS.md |only FactoMineR-2.16/FactoMineR/R/CA.R | 7 FactoMineR-2.16/FactoMineR/R/FAMD.R | 12 - FactoMineR-2.16/FactoMineR/R/HCPC.R | 10 - FactoMineR-2.16/FactoMineR/R/MCA.R | 10 - FactoMineR-2.16/FactoMineR/R/MFA.R | 17 +- FactoMineR-2.16/FactoMineR/R/PCA.R | 6 FactoMineR-2.16/FactoMineR/R/catdes.r | 12 + FactoMineR-2.16/FactoMineR/R/ellipseCA.R | 21 ++ FactoMineR-2.16/FactoMineR/R/meansComp.R | 2 FactoMineR-2.16/FactoMineR/R/plot.CA.R | 29 ++- FactoMineR-2.16/FactoMineR/R/plot.FAMD.R | 15 +- FactoMineR-2.16/FactoMineR/R/plot.MCA.R | 29 ++- FactoMineR-2.16/FactoMineR/R/plot.MFA.R | 40 +++-- FactoMineR-2.16/FactoMineR/R/plot.PCA.R | 41 +++-- FactoMineR-2.16/FactoMineR/R/plot.catdes.R | 154 +++++++++++---------- FactoMineR-2.16/FactoMineR/R/plot.meansComp.R | 26 ++- FactoMineR-2.16/FactoMineR/R/svd.triplet.R | 2 FactoMineR-2.16/FactoMineR/R/theme_factominer.R |only FactoMineR-2.16/FactoMineR/man/CA.Rd | 5 FactoMineR-2.16/FactoMineR/man/FAMD.Rd | 3 FactoMineR-2.16/FactoMineR/man/MCA.Rd | 3 FactoMineR-2.16/FactoMineR/man/MFA.Rd | 3 FactoMineR-2.16/FactoMineR/man/PCA.Rd | 3 FactoMineR-2.16/FactoMineR/man/catdes.Rd | 5 FactoMineR-2.16/FactoMineR/man/ellipseCA.Rd | 2 FactoMineR-2.16/FactoMineR/man/plot.CA.Rd | 12 - FactoMineR-2.16/FactoMineR/man/plot.FAMD.Rd | 4 FactoMineR-2.16/FactoMineR/man/plot.MCA.Rd | 12 - FactoMineR-2.16/FactoMineR/man/plot.MFA.Rd | 4 FactoMineR-2.16/FactoMineR/man/plot.PCA.Rd | 13 - FactoMineR-2.16/FactoMineR/man/plot.catdes.Rd | 7 FactoMineR-2.16/FactoMineR/man/plot.meansComp.Rd | 3 FactoMineR-2.16/FactoMineR/man/theme_factominer.Rd |only 39 files changed, 364 insertions(+), 256 deletions(-)
Title: Structural Data for Norway
Description: Datasets relating to population in municipalities, municipality/county matching, and how different municipalities have merged/redistricted over time from 2006 to 2024.
Author: Richard Aubrey White [aut, cre] ,
Chi Zhang [aut]
Maintainer: Richard Aubrey White <hello@rwhite.no>
Diff between csdata versions 2026.3.30 dated 2026-03-31 and 2026.7.2 dated 2026-07-02
DESCRIPTION | 9 LICENSE | 2 MD5 | 70 NAMESPACE | 1 NEWS.md | 8 R/add_variable_to_data_set.R | 33 R/config_aa_environments.r | 43 R/location_code_to.R | 45 R/nor_locations_hierarchy.R | 308 ++- R/nor_locations_names.R | 57 R/nor_locations_redistricting.R | 53 R/nor_population_by_age_cats.R | 140 + R/nor_population_by_sex_age_cats.R |only R/sysdata.rda |binary build/vignette.rds |binary inst/doc/csdata.Rmd | 18 inst/doc/csdata.html | 2574 ++++++++++++++++-------------- inst/doc/locations_norway.Rmd | 4 inst/doc/locations_norway.html | 877 +++++----- inst/doc/population_norway.Rmd | 8 inst/doc/population_norway.html | 2680 +++++++++++++++++--------------- man/add_granularity_geo_to_data_set.Rd | 20 man/add_iso3_to_data_set.Rd | 13 man/config.Rd | 16 man/location_code_to_granularity_geo.Rd | 25 man/location_code_to_iso3.Rd | 18 man/nb.Rd | 10 man/nor_locations_hierarchy_from_to.Rd | 42 man/nor_locations_names.Rd | 39 man/nor_locations_redistricting.Rd | 36 man/nor_population_by_age_cats.Rd | 57 man/nor_population_by_sex_age_cats.Rd |only man/se.Rd | 10 man/set_config.Rd | 17 vignettes/csdata.Rmd | 18 vignettes/locations_norway.Rmd | 4 vignettes/population_norway.Rmd | 8 37 files changed, 3985 insertions(+), 3278 deletions(-)
Title: Composite Indicators Functions
Description: A collection of functions to calculate Composite Indicators methods, focusing, in particular, on the normalisation and weighting-aggregation steps, as described in OECD Handbook on constructing composite indicators: methodology and user guide, 2008, 'Vidoli' and 'Fusco' and 'Mazziotta' <doi:10.1007/s11205-014-0710-y>, 'Mazziotta' and 'Pareto' (2016) <doi:10.1007/s11205-015-0998-2>, 'Van Puyenbroeck and 'Rogge' <doi:10.1016/j.ejor.2016.07.038> and other authors.
Author: Francesco Vidoli [aut, cre],
Elisa Fusco [aut]
Maintainer: Francesco Vidoli <fvidoli@gmail.com>
Diff between Compind versions 3.4 dated 2025-05-16 and 3.5 dated 2026-07-02
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++++------ NAMESPACE | 1 + NEWS | 35 +++++++++++++---------------------- R/ci_bod_time_decomp.R |only data/desktop.ini |only desktop.ini |only inst/desktop.ini |only inst/doc/Compind_vignette.pdf |binary man/ci_bod_constr_bad.Rd | 20 ++++++++++---------- man/ci_bod_time_decomp.Rd |only man/ci_rbod_constr_bad_Q.Rd | 30 +++++++++++++++--------------- vignettes/desktop.ini |only 13 files changed, 55 insertions(+), 57 deletions(-)
Title: Analysis and Visualization of Circular Data
Description: Circumplex models, which organize constructs in a circle around two
underlying dimensions, are popular for studying interpersonal functioning,
mood/affect, and vocational preferences/environments. This package provides
tools for analyzing and visualizing circular data, including scoring
functions for relevant instruments and a generalization of the bootstrapped
structural summary method from Zimmermann & Wright (2017)
<doi:10.1177/1073191115621795> and functions for creating publication-ready
tables and figures from the results.
Author: Jeffrey Girard [aut, cre] ,
Johannes Zimmermann [aut] ,
Aidan Wright [aut]
Maintainer: Jeffrey Girard <me@jmgirard.com>
Diff between circumplex versions 1.1.0 dated 2026-05-24 and 1.2.0 dated 2026-07-02
DESCRIPTION | 6 MD5 | 86 NEWS.md | 57 R/instrument_oop.R | 4 R/ssm_analysis.R | 88 R/ssm_bootstrap.R | 40 R/ssm_oop.R | 20 R/ssm_plot.R | 1064 +++++----- R/ssm_table.R | 2 R/tidying_functions.R | 49 R/utils.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/intermediate-ssm-analysis.Rmd | 2 inst/doc/intermediate-ssm-analysis.html | 67 inst/doc/introduction-to-ssm-analysis.Rmd | 6 inst/doc/introduction-to-ssm-analysis.html | 19 inst/doc/using-instruments.html | 2 man/norm_standardize.Rd | 5 man/score.Rd | 3 man/ssm_analyze.Rd | 34 man/ssm_parameters.Rd | 8 man/ssm_plot_circle.Rd | 2 man/ssm_plot_contrast.Rd | 2 man/ssm_plot_curve.Rd | 4 man/ssm_score.Rd | 3 src/parameters.cpp | 30 tests/testthat/_snaps/instrument_oop.md | 2 tests/testthat/_snaps/ssm_plot/group-constrast-correlation-ssm.svg | 165 - tests/testthat/_snaps/ssm_plot/many-circle-plots.svg | 8 tests/testthat/_snaps/ssm_plot/many-circle-repel.svg | 14 tests/testthat/_snaps/ssm_plot/measure-contrast-circle-ssm.svg | 4 tests/testthat/_snaps/ssm_plot/measure-contrast-ssm.svg | 294 +- tests/testthat/_snaps/ssm_plot/single-group-correlation-ssm.svg | 2 tests/testthat/_snaps/ssm_plot/single-group-mean-ssm-no-palette.svg | 2 tests/testthat/_snaps/ssm_plot/single-group-mean-ssm.svg | 2 tests/testthat/test-ssm_analysis.R | 209 + tests/testthat/test-ssm_bootstrap.R | 60 tests/testthat/test-ssm_oop.R | 50 tests/testthat/test-ssm_plot.R | 28 tests/testthat/test-tidying_functions.R | 58 tests/testthat/test-utils.R | 14 vignettes/intermediate-ssm-analysis.Rmd | 2 vignettes/introduction-to-ssm-analysis.Rmd | 6 44 files changed, 1607 insertions(+), 918 deletions(-)
Title: Bayesian Synthetic Likelihood
Description: Bayesian synthetic likelihood (BSL, Price et al. (2018) <doi:10.1080/10618600.2017.1302882>)
is an alternative to standard, non-parametric approximate Bayesian
computation (ABC). BSL assumes a multivariate normal distribution
for the summary statistic likelihood and it is suitable when the
distribution of the model summary statistics is sufficiently regular.
This package provides a Metropolis Hastings Markov chain Monte Carlo
implementation of four methods (BSL, uBSL, semiBSL and BSLmisspec) and two
shrinkage estimators (graphical lasso and Warton's estimator).
uBSL (Price et al. (2018) <doi:10.1080/10618600.2017.1302882>) uses
an unbiased estimator to the normal density. A semi-parametric version
of BSL (semiBSL, An et al. (2020) <doi:10.1007/s11222-019-09904-x>) is more robust
to non-normal summary statistics. BSLmisspec (Frazier et al. 2021
<doi:10.1080/10618600.2021.1875839>) estimates the Gaussian synthetic likelihood whilst
acknowledging that there may be [...truncated...]
Author: Ziwen An [aut] ,
Leah F. South [aut, cre] ,
Christopher C. Drovandi [aut]
Maintainer: Leah F. South <l1.south@qut.edu.au>
This is a re-admission after prior archival of version 3.2.5 dated 2022-11-03
Diff between BSL versions 3.2.5 dated 2022-11-03 and 3.2.6 dated 2026-07-02
DESCRIPTION | 24 +++++++++++++----------- MD5 | 22 +++++++++++----------- NAMESPACE | 2 ++ NEWS.md | 11 +++++++++++ R/s4-MODEL.R | 19 ++++++++++++------- build/partial.rdb |binary inst/REFERENCES.bib | 39 ++++++++++++++++++++++++--------------- man/MODEL-class.Rd | 19 ++++++++++++------- man/cell.Rd | 8 ++++---- man/ma2.Rd | 10 +++++----- man/toad.Rd | 8 ++++---- src/Makevars.win | 5 +---- 12 files changed, 99 insertions(+), 68 deletions(-)
Title: Access Brazilian Data via APIs and Curated Datasets
Description: Provides functions to access data from the 'BrasilAPI', 'Nager.Date API',
and 'World Bank API', related to Brazil's postal codes, banks, holidays,
company registrations, and economic development data. Additionally, the package includes
curated datasets related to Brazil, covering topics such as demographic data (males and
females by state and year), river levels, environmental emission factors, film festivals,
and yellow fever outbreak records. The package supports research and analysis focused on
Brazil by integrating open APIs with high-quality datasets from multiple domains. For more
information on the APIs, see:
'BrasilAPI' <https://brasilapi.com.br/>,
'Nager.Date' <https://date.nager.at/Api>,
'World Bank API' <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between BrazilDataAPI versions 0.2.0 dated 2025-09-15 and 0.3.0 dated 2026-07-02
BrazilDataAPI-0.2.0/BrazilDataAPI/R/get_brazil_vehicle_brands.R |only BrazilDataAPI-0.2.0/BrazilDataAPI/R/get_country_info_br.R |only BrazilDataAPI-0.2.0/BrazilDataAPI/man/get_brazil_vehicle_brands.Rd |only BrazilDataAPI-0.2.0/BrazilDataAPI/man/get_country_info_br.Rd |only BrazilDataAPI-0.2.0/BrazilDataAPI/tests/testthat/test-get_brazil_vehicle_brands.R |only BrazilDataAPI-0.2.0/BrazilDataAPI/tests/testthat/test-get_country_info_br.R |only BrazilDataAPI-0.3.0/BrazilDataAPI/DESCRIPTION | 27 - BrazilDataAPI-0.3.0/BrazilDataAPI/MD5 | 118 ++---- BrazilDataAPI-0.3.0/BrazilDataAPI/NAMESPACE | 3 BrazilDataAPI-0.3.0/BrazilDataAPI/NEWS.md | 18 BrazilDataAPI-0.3.0/BrazilDataAPI/R/brazildataapi-package.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/data-documentation.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_banks.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_cep.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_child_mortality.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_cnpj.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_cpi.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_energy_use.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_gdp.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_holidays.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_hospital_beds.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_life_expectancy.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_literacy_rate.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_municipalities.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_population.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_rate_name.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_rates.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/get_brazil_unemployment.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/utils.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/R/view_datasets_BrazilDataAPI.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/README.md | 10 BrazilDataAPI-0.3.0/BrazilDataAPI/build/vignette.rds |binary BrazilDataAPI-0.3.0/BrazilDataAPI/inst/CITATION | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/inst/doc/BrazilDataAPI_vignette.R | 9 BrazilDataAPI-0.3.0/BrazilDataAPI/inst/doc/BrazilDataAPI_vignette.Rmd | 24 - BrazilDataAPI-0.3.0/BrazilDataAPI/inst/doc/BrazilDataAPI_vignette.html | 190 ++++------ BrazilDataAPI-0.3.0/BrazilDataAPI/inst/licenses/LICENSE | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/inst/licenses/LICENSE.md | 37 - BrazilDataAPI-0.3.0/BrazilDataAPI/inst/licenses/LICENSES_DETAILS.md | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-Brasil_females_df.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-Brasil_males_df.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-Brazil_films_df.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-Yellow_Fever_list.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_banks.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_cep.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_child_mortality.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_cnpj.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_cpi.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_energy_use.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_gdp.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_holidays.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_hospital_beds.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_life_expectancy.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_literacy_rate.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_municipalities.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_population.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_rate_name.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_rates.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-get_brazil_unemployment.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-manaus_ts.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-sp_emission_factors_df.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/tests/testthat/test-view_datasets_BrazilDataAPI.R | 4 BrazilDataAPI-0.3.0/BrazilDataAPI/vignettes/BrazilDataAPI_vignette.Rmd | 24 - 63 files changed, 285 insertions(+), 359 deletions(-)
Title: An Arsenal of 'R' Functions for Large-Scale Statistical
Summaries
Description: An Arsenal of 'R' functions for large-scale statistical summaries,
which are streamlined to work within the latest reporting tools in 'R' and
'RStudio' and which use formulas and versatile summary statistics for summary
tables and models. The primary functions include tableby(), a Table-1-like
summary of multiple variable types 'by' the levels of one or more categorical
variables; paired(), a Table-1-like summary of multiple variable types paired across
two time points; modelsum(), which performs simple model fits on one or more endpoints
for many variables (univariate or adjusted for covariates);
freqlist(), a powerful frequency table across many categorical variables;
comparedf(), a function for comparing data.frames; and
write2(), a function to output tables to a document.
Author: Ethan Heinzen [aut, cre],
Jason Sinnwell [aut],
Elizabeth Atkinson [aut],
Tina Gunderson [aut],
Gregory Dougherty [aut],
Patrick Votruba [ctb],
Ryan Lennon [ctb],
Andrew Hanson [ctb],
Krista Goergen [ctb],
Emily Lundt [ctb],
Brendan Broderick [ctb],
[...truncated...]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>
Diff between arsenal versions 3.6.3 dated 2021-06-04 and 3.7.1 dated 2026-07-02
arsenal-3.6.3/arsenal/man/arsenal.Rd |only arsenal-3.7.1/arsenal/DESCRIPTION | 14 arsenal-3.7.1/arsenal/MD5 | 114 arsenal-3.7.1/arsenal/NAMESPACE | 14 arsenal-3.7.1/arsenal/NEWS.md | 60 arsenal-3.7.1/arsenal/R/arsenal.R | 4 arsenal-3.7.1/arsenal/R/arsenal_table.R | 46 arsenal-3.7.1/arsenal/R/formulize.R | 11 arsenal-3.7.1/arsenal/R/modelsum.R | 2 arsenal-3.7.1/arsenal/R/paired.R | 20 arsenal-3.7.1/arsenal/R/paired.control.R | 6 arsenal-3.7.1/arsenal/R/paired.stat.tests.R | 2 arsenal-3.7.1/arsenal/R/summary.tableby.R | 25 arsenal-3.7.1/arsenal/R/tableby.R | 19 arsenal-3.7.1/arsenal/R/tableby.control.R | 11 arsenal-3.7.1/arsenal/R/tableby.internal.R | 85 arsenal-3.7.1/arsenal/R/tableby.stat.tests.R | 28 arsenal-3.7.1/arsenal/R/tableby.stats.R | 291 + arsenal-3.7.1/arsenal/README.md | 1 arsenal-3.7.1/arsenal/build/vignette.rds |binary arsenal-3.7.1/arsenal/inst/doc/comparedf.R | 12 arsenal-3.7.1/arsenal/inst/doc/comparedf.html | 844 +++- arsenal-3.7.1/arsenal/inst/doc/freqlist.R | 8 arsenal-3.7.1/arsenal/inst/doc/freqlist.Rmd | 2 arsenal-3.7.1/arsenal/inst/doc/freqlist.html | 784 +++- arsenal-3.7.1/arsenal/inst/doc/labels.html | 517 ++ arsenal-3.7.1/arsenal/inst/doc/modelsum.R | 84 arsenal-3.7.1/arsenal/inst/doc/modelsum.Rmd | 2 arsenal-3.7.1/arsenal/inst/doc/modelsum.html | 2777 +++++++++------ arsenal-3.7.1/arsenal/inst/doc/paired.R | 2 arsenal-3.7.1/arsenal/inst/doc/paired.Rmd | 2 arsenal-3.7.1/arsenal/inst/doc/paired.html | 436 +- arsenal-3.7.1/arsenal/inst/doc/tableby.R | 191 - arsenal-3.7.1/arsenal/inst/doc/tableby.Rmd | 91 arsenal-3.7.1/arsenal/inst/doc/tableby.html | 2269 +++++++++--- arsenal-3.7.1/arsenal/inst/doc/write2.R | 290 - arsenal-3.7.1/arsenal/inst/doc/write2.html | 842 +++- arsenal-3.7.1/arsenal/man/arsenal-package.Rd |only arsenal-3.7.1/arsenal/man/arsenal_table.Rd | 3 arsenal-3.7.1/arsenal/man/formulize.Rd | 2 arsenal-3.7.1/arsenal/man/internal.functions.Rd | 6 arsenal-3.7.1/arsenal/man/padjust.Rd | 3 arsenal-3.7.1/arsenal/man/paired.Rd | 2 arsenal-3.7.1/arsenal/man/paired.control.Rd | 6 arsenal-3.7.1/arsenal/man/summary.modelsum.Rd | 4 arsenal-3.7.1/arsenal/man/summary.tableby.Rd | 4 arsenal-3.7.1/arsenal/man/tableby.control.Rd | 5 arsenal-3.7.1/arsenal/man/tableby.stats.Rd | 50 arsenal-3.7.1/arsenal/man/tableby.stats.internal.Rd | 40 arsenal-3.7.1/arsenal/tests/testthat/test_formulize.R | 10 arsenal-3.7.1/arsenal/tests/testthat/test_paired.R | 28 arsenal-3.7.1/arsenal/tests/testthat/test_tableby.R | 195 + arsenal-3.7.1/arsenal/tests/testthat/test_write2.R | 3 arsenal-3.7.1/arsenal/tests/testthat/write2.lm.pdf.Rmd | 8 arsenal-3.7.1/arsenal/tests/testthat/write2.yaml.pdf.Rmd | 8 arsenal-3.7.1/arsenal/vignettes/freqlist.Rmd | 2 arsenal-3.7.1/arsenal/vignettes/modelsum.Rmd | 2 arsenal-3.7.1/arsenal/vignettes/paired.Rmd | 2 arsenal-3.7.1/arsenal/vignettes/tableby.Rmd | 91 59 files changed, 7219 insertions(+), 3161 deletions(-)
Title: Sequential Change Point Detection for High-Dimensional VAR
Models
Description: Implements the algorithm introduced in Tian, Y., and Safikhani, A. (2024)
<doi:10.5705/ss.202024.0182>, "Sequential Change Point Detection in High-dimensional
Vector Auto-regressive Models". This package provides tools for detecting change points
in the transition matrices of VAR models, effectively identifying shifts in temporal
and cross-correlations within high-dimensional time series data.
Author: Yuhan Tian [aut, cre],
Abolfazl Safikhani [aut]
Maintainer: Yuhan Tian <tyh9293@gmail.com>
Diff between VARcpDetectOnline versions 0.2.0 dated 2025-02-13 and 0.2.1 dated 2026-07-02
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 12 insertions(+), 8 deletions(-)
More information about VARcpDetectOnline at CRAN
Permanent link
Title: Parse 'User-Agent' Strings
Description: Parses HTTP user agent strings and returns user agent, device and OS information. This is a 'V8'-backed package
based on the 'ua-parser' project <https://github.com/ua-parser>.
Author: Bob Rudis [aut, cph],
Greg Hunt [aut, cre, cph],
Lindsey Simon [aut] ,
Tobie Langel [aut] ,
Colman Humphrey [ctb],
Jim Vine [ctb]
Maintainer: Greg Hunt <greg@firmansyah.com>
Diff between uaparserjs versions 0.3.8 dated 2026-05-09 and 0.4.0 dated 2026-07-02
uaparserjs-0.3.8/uaparserjs/R/uaparserjs-package.R |only uaparserjs-0.3.8/uaparserjs/R/utils-mappers.R |only uaparserjs-0.4.0/uaparserjs/DESCRIPTION | 24 - uaparserjs-0.4.0/uaparserjs/MD5 | 28 - uaparserjs-0.4.0/uaparserjs/NAMESPACE | 4 uaparserjs-0.4.0/uaparserjs/NEWS.md | 6 uaparserjs-0.4.0/uaparserjs/R/uaparser.R | 144 +++++--- uaparserjs-0.4.0/uaparserjs/R/utils.R |only uaparserjs-0.4.0/uaparserjs/R/zzz.r | 4 uaparserjs-0.4.0/uaparserjs/README.md | 14 uaparserjs-0.4.0/uaparserjs/inst/js/bundle.js | 2 uaparserjs-0.4.0/uaparserjs/inst/tinytest/test_exhaustive.R | 178 +++++++++-- uaparserjs-0.4.0/uaparserjs/inst/tinytest/test_multirow.R |only uaparserjs-0.4.0/uaparserjs/inst/tinytest/test_uaparserjs.R | 119 +++++++ uaparserjs-0.4.0/uaparserjs/inst/tinytest/tests/test_ua.yaml | 6 uaparserjs-0.4.0/uaparserjs/man/ua_parse.Rd | 33 +- uaparserjs-0.4.0/uaparserjs/man/uaparserjs.Rd | 12 17 files changed, 441 insertions(+), 133 deletions(-)
Title: Simple Colour Manipulation
Description: Functions for easily manipulating colours, creating colour scales and calculating colour distances.
Author: Jon Clayden [cre, aut]
Maintainer: Jon Clayden <code@clayden.org>
Diff between shades versions 1.4.0 dated 2019-08-02 and 1.5.0 dated 2026-07-02
shades-1.4.0/shades/tests/testthat |only shades-1.4.0/shades/tests/testthat.R |only shades-1.5.0/shades/DESCRIPTION | 21 - shades-1.5.0/shades/MD5 | 90 ++--- shades-1.5.0/shades/NAMESPACE | 5 shades-1.5.0/shades/NEWS | 27 + shades-1.5.0/shades/R/adaptation.R | 2 shades-1.5.0/shades/R/distance.R | 34 +- shades-1.5.0/shades/R/properties.R | 67 ++- shades-1.5.0/shades/R/scales.R | 14 shades-1.5.0/shades/R/shade.R | 161 +++++++-- shades-1.5.0/shades/R/swatch.R | 57 ++- shades-1.5.0/shades/R/tinytest.R |only shades-1.5.0/shades/R/zzz.R | 6 shades-1.5.0/shades/README.md | 86 +++-- shades-1.5.0/shades/inst |only shades-1.5.0/shades/man/coords.Rd | 4 shades-1.5.0/shades/man/dichromat.Rd | 11 shades-1.5.0/shades/man/distance.Rd | 30 + shades-1.5.0/shades/man/gradient.Rd | 8 shades-1.5.0/shades/man/mixtures.Rd | 2 shades-1.5.0/shades/man/properties.Rd | 24 - shades-1.5.0/shades/man/shade.Rd | 43 +- shades-1.5.0/shades/man/space.Rd | 2 shades-1.5.0/shades/man/swatch.Rd | 17 - shades-1.5.0/shades/man/tinytest.Rd |only shades-1.5.0/shades/man/warp.Rd | 22 - shades-1.5.0/shades/tests/tinytest.R |only shades-1.5.0/shades/tools/figures/addmix-1.svg | 46 ++ shades-1.5.0/shades/tools/figures/dichromat-1.svg | 51 ++- shades-1.5.0/shades/tools/figures/dichromat-2.svg | 51 ++- shades-1.5.0/shades/tools/figures/ggplot-1.svg | 355 ++++++--------------- shades-1.5.0/shades/tools/figures/gradients-1.svg | 45 ++ shades-1.5.0/shades/tools/figures/gradients-2.svg | 45 ++ shades-1.5.0/shades/tools/figures/missing-1.svg | 45 ++ shades-1.5.0/shades/tools/figures/saturation-1.svg | 59 ++- shades-1.5.0/shades/tools/figures/scales-1.svg | 355 ++++++--------------- shades-1.5.0/shades/tools/figures/scales-2.svg | 355 ++++++--------------- shades-1.5.0/shades/tools/figures/submix-1.svg | 46 ++ shades-1.5.0/shades/tools/figures/tinyplot-1.svg |only shades-1.5.0/shades/tools/figures/tinyplot-2.svg |only 41 files changed, 1139 insertions(+), 1047 deletions(-)
Title: D3 JavaScript Scatterplot from R
Description: Creates 'D3' 'JavaScript' scatterplots from 'R' with interactive
features : panning, zooming, tooltips, etc.
Author: Julien Barnier [aut, cre],
Kent Russell [aut, ctb],
Mike Bostock [aut, cph] ,
Susie Lu [aut, cph] ,
Speros Kokenes [aut, cph] ,
Evan Wang [aut, cph]
Maintainer: Julien Barnier <julien.barnier@cnrs.fr>
Diff between scatterD3 versions 1.0.1 dated 2021-10-06 and 1.0.2 dated 2026-07-02
DESCRIPTION | 10 MD5 | 22 NEWS.md | 201 +++---- R/scatterD3.R | 9 README.md | 17 build/vignette.rds |binary inst/doc/introduction.R | 44 - inst/doc/introduction.Rmd | 8 inst/doc/introduction.html | 1181 ++++++++++++++++++++++++------------------ inst/htmlwidgets/scatterD3.js | 2 man/scatterD3.Rd | 6 vignettes/introduction.Rmd | 8 12 files changed, 858 insertions(+), 650 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 1.9-0 dated 2026-03-13 and 1.10-0 dated 2026-07-02
RBesT-1.10-0/RBesT/DESCRIPTION | 16 RBesT-1.10-0/RBesT/MD5 | 229 +++- RBesT-1.10-0/RBesT/NAMESPACE | 11 RBesT-1.10-0/RBesT/NEWS.md | 43 RBesT-1.10-0/RBesT/R/RBesT-package.R | 13 RBesT-1.10-0/RBesT/R/asthma.R |only RBesT-1.10-0/RBesT/R/decision1S_boundary.R | 90 + RBesT-1.10-0/RBesT/R/decision2S_boundary.R | 154 ++- RBesT-1.10-0/RBesT/R/forest_plot.R | 19 RBesT-1.10-0/RBesT/R/gMAP.R | 352 +++++-- RBesT-1.10-0/RBesT/R/gMAP_draws.R |only RBesT-1.10-0/RBesT/R/integrate_gauss_quadrature.R |only RBesT-1.10-0/RBesT/R/integrate_logit_log.R | 85 + RBesT-1.10-0/RBesT/R/mixdiff.R | 18 RBesT-1.10-0/RBesT/R/mixess.R | 22 RBesT-1.10-0/RBesT/R/mixfit.R | 18 RBesT-1.10-0/RBesT/R/mixstanvar.R | 5 RBesT-1.10-0/RBesT/R/nsamples.R | 5 RBesT-1.10-0/RBesT/R/oc1S.R | 89 + RBesT-1.10-0/RBesT/R/oc2S.R | 93 + RBesT-1.10-0/RBesT/R/plot_gMAP.R | 18 RBesT-1.10-0/RBesT/R/pos1S.R | 113 +- RBesT-1.10-0/RBesT/R/pos2S.R | 90 + RBesT-1.10-0/RBesT/R/posterior.R | 114 +- RBesT-1.10-0/RBesT/R/postmix.R | 7 RBesT-1.10-0/RBesT/R/predict_gMAP.R | 72 - RBesT-1.10-0/RBesT/R/sigma_from_family.R |only RBesT-1.10-0/RBesT/R/sysdata.rda |binary RBesT-1.10-0/RBesT/build/vignette.rds |binary RBesT-1.10-0/RBesT/data/AS.rda |binary RBesT-1.10-0/RBesT/data/asthma.rda |only RBesT-1.10-0/RBesT/data/colitis.rda |binary RBesT-1.10-0/RBesT/data/crohn.rda |binary RBesT-1.10-0/RBesT/data/transplant.rda |binary RBesT-1.10-0/RBesT/demo/00Index | 1 RBesT-1.10-0/RBesT/demo/oc2S_interim.R |only RBesT-1.10-0/RBesT/inst/doc/RBesT.pdf |binary RBesT-1.10-0/RBesT/inst/doc/introduction.html | 81 - RBesT-1.10-0/RBesT/inst/extra/oc2S_interim.R |only RBesT-1.10-0/RBesT/inst/sbc/sbc_report.html | 36 RBesT-1.10-0/RBesT/man/RBesT-package.Rd | 18 RBesT-1.10-0/RBesT/man/asthma.Rd |only RBesT-1.10-0/RBesT/man/decision1S.Rd | 8 RBesT-1.10-0/RBesT/man/decision1S_boundary.Rd | 47 RBesT-1.10-0/RBesT/man/decision2S.Rd | 8 RBesT-1.10-0/RBesT/man/decision2S_boundary.Rd | 30 RBesT-1.10-0/RBesT/man/dot-gmap_all_diag_df.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_all_draws.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_diag_df.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_divergence_count.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_draws_array.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_empty_diag_draws_array.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_empty_draws_array.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_empty_draws_summary.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_extract_diag_draws_array.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_extract_draws_array.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_mcmc_metadata.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_sampler_summary.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_summary.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_thin_draws.Rd |only RBesT-1.10-0/RBesT/man/dot-gmap_warn_no_samples.Rd |only RBesT-1.10-0/RBesT/man/draws-RBesT.Rd | 5 RBesT-1.10-0/RBesT/man/ess.Rd | 4 RBesT-1.10-0/RBesT/man/gMAP.Rd | 13 RBesT-1.10-0/RBesT/man/integrate_density.Rd |only RBesT-1.10-0/RBesT/man/integrate_density_log.Rd | 57 - RBesT-1.10-0/RBesT/man/integrate_gauss_quadrature.Rd |only RBesT-1.10-0/RBesT/man/mix.Rd | 12 RBesT-1.10-0/RBesT/man/mixbeta.Rd | 10 RBesT-1.10-0/RBesT/man/mixcombine.Rd | 10 RBesT-1.10-0/RBesT/man/mixfit.Rd | 4 RBesT-1.10-0/RBesT/man/mixgamma.Rd | 10 RBesT-1.10-0/RBesT/man/mixjson.Rd | 16 RBesT-1.10-0/RBesT/man/mixmvnorm.Rd | 10 RBesT-1.10-0/RBesT/man/mixnorm.Rd | 10 RBesT-1.10-0/RBesT/man/mixplot.Rd | 12 RBesT-1.10-0/RBesT/man/mixstanvar.Rd | 2 RBesT-1.10-0/RBesT/man/oc1S.Rd | 38 RBesT-1.10-0/RBesT/man/oc2S.Rd | 30 RBesT-1.10-0/RBesT/man/plot.EM.Rd | 4 RBesT-1.10-0/RBesT/man/pos1S.Rd | 38 RBesT-1.10-0/RBesT/man/pos2S.Rd | 30 RBesT-1.10-0/RBesT/man/resolve_sigma_family.Rd |only RBesT-1.10-0/RBesT/man/sigma_from_family.Rd |only RBesT-1.10-0/RBesT/tests/testthat/fixtures-compact |only RBesT-1.10-0/RBesT/tests/testthat/fixtures-compact-src |only RBesT-1.10-0/RBesT/tests/testthat/fixtures-mcmc-src |only RBesT-1.10-0/RBesT/tests/testthat/helper-compressed-fixtures.R |only RBesT-1.10-0/RBesT/tests/testthat/helper-fixtures.R |only RBesT-1.10-0/RBesT/tests/testthat/helper-mixstanvar.R |only RBesT-1.10-0/RBesT/tests/testthat/helper-utils.R | 14 RBesT-1.10-0/RBesT/tests/testthat/test-EM.R | 290 +++--- RBesT-1.10-0/RBesT/tests/testthat/test-design1S-family.R |only RBesT-1.10-0/RBesT/tests/testthat/test-design2S-family.R |only RBesT-1.10-0/RBesT/tests/testthat/test-gMAP-compact-fixtures.R |only RBesT-1.10-0/RBesT/tests/testthat/test-gMAP.R | 314 ------ RBesT-1.10-0/RBesT/tests/testthat/test-integrate-GQ.R |only RBesT-1.10-0/RBesT/tests/testthat/test-mixdiff.R | 143 +-- RBesT-1.10-0/RBesT/tests/testthat/test-mixdist.R | 146 +-- RBesT-1.10-0/RBesT/tests/testthat/test-mixstanvar-sampling.R |only RBesT-1.10-0/RBesT/tests/testthat/test-mixstanvar.R | 473 ---------- RBesT-1.10-0/RBesT/tests/testthat/test-oc1S.R | 191 ++-- RBesT-1.10-0/RBesT/tests/testthat/test-oc2S.R | 359 +++---- RBesT-1.10-0/RBesT/tests/testthat/test-pos1S.R | 100 +- RBesT-1.10-0/RBesT/tests/testthat/test-pos2S.R | 226 +++- RBesT-1.10-0/RBesT/tests/testthat/test-posterior.R | 117 +- RBesT-1.10-0/RBesT/tests/testthat/test-postmix.R | 7 RBesT-1.10-0/RBesT/tests/testthat/test-preddist.R | 69 - RBesT-1.10-0/RBesT/tests/testthat/test-utils.R | 251 ++--- RBesT-1.9-0/RBesT/R/SimSum.R |only RBesT-1.9-0/RBesT/man/SimSum.Rd |only 111 files changed, 2621 insertions(+), 2299 deletions(-)
Title: Confidence Intervals and Tests for Comparisons of Binomial
Proportions or Poisson Rates
Description: Computes confidence intervals for binomial or Poisson rates
and their differences or ratios. Including the rate (or risk)
difference ('RD') or rate ratio (or relative risk, 'RR') for binomial
proportions or Poisson rates, and odds ratio ('OR', binomial only).
Also confidence intervals for RD, RR or OR for paired binomial data,
and estimation of a proportion from clustered binomial data. Includes
skewness-corrected asymptotic score ('SCAS') methods, which have been
developed in Laud (2017) <doi:10.1002/pst.1813> from Miettinen and
Nurminen (1985) <doi:10.1002/sim.4780040211> and Gart and Nam (1988)
<doi:10.2307/2531848>, and in Laud (2026, under review) for paired
proportions. In each case, the same score produces hypothesis tests that are
improved versions of the non-inferiority test for binomial RD and RR
by Farrington and Manning (1990) <doi:10.1002/sim.4780091208>, or a
generalisation of the McNemar test for paired data. The package also
includes MOVER metho [...truncated...]
Author: Pete Laud [aut, cre]
Maintainer: Pete Laud <pete@sheffstat.co.uk>
Diff between ratesci versions 1.0.0 dated 2025-06-20 and 1.1.0 dated 2026-07-02
ratesci-1.0.0/ratesci/vignettes/bmj.csl |only ratesci-1.1.0/ratesci/DESCRIPTION | 62 ratesci-1.1.0/ratesci/MD5 | 127 ratesci-1.1.0/ratesci/NAMESPACE | 69 ratesci-1.1.0/ratesci/NEWS.md | 414 +- ratesci-1.1.0/ratesci/R/clusterpci.R | 198 - ratesci-1.1.0/ratesci/R/data.R | 100 ratesci-1.1.0/ratesci/R/moverci.R | 902 ++-- ratesci-1.1.0/ratesci/R/moverpairci.R |only ratesci-1.1.0/ratesci/R/orci.R |only ratesci-1.1.0/ratesci/R/orpairci.R |only ratesci-1.1.0/ratesci/R/pairbinci.R | 2353 ++++++----- ratesci-1.1.0/ratesci/R/rateci.R | 819 ++-- ratesci-1.1.0/ratesci/R/ratesci-package.R | 182 ratesci-1.1.0/ratesci/R/rdci.R |only ratesci-1.1.0/ratesci/R/rdpairci.R |only ratesci-1.1.0/ratesci/R/rrci.R |only ratesci-1.1.0/ratesci/R/rrpairci.R |only ratesci-1.1.0/ratesci/R/scoreci.R | 3728 +++++++++---------- ratesci-1.1.0/ratesci/R/scorepairci.R |only ratesci-1.1.0/ratesci/R/utils.R | 566 +- ratesci-1.1.0/ratesci/build/partial.rdb |binary ratesci-1.1.0/ratesci/build/vignette.rds |binary ratesci-1.1.0/ratesci/inst/doc/basic_contrasts.R | 170 ratesci-1.1.0/ratesci/inst/doc/basic_contrasts.Rmd | 393 +- ratesci-1.1.0/ratesci/inst/doc/basic_contrasts.html | 1485 ++++--- ratesci-1.1.0/ratesci/inst/doc/paired_contrasts.R | 94 ratesci-1.1.0/ratesci/inst/doc/paired_contrasts.Rmd | 233 - ratesci-1.1.0/ratesci/inst/doc/paired_contrasts.html | 1210 +++--- ratesci-1.1.0/ratesci/inst/doc/single_rate.R | 183 ratesci-1.1.0/ratesci/inst/doc/single_rate.Rmd | 365 - ratesci-1.1.0/ratesci/inst/doc/single_rate.html | 1401 +++---- ratesci-1.1.0/ratesci/inst/doc/stratified.R | 106 ratesci-1.1.0/ratesci/inst/doc/stratified.Rmd | 188 ratesci-1.1.0/ratesci/inst/doc/stratified.html | 1055 ++--- ratesci-1.1.0/ratesci/inst/doc/tests.R | 178 ratesci-1.1.0/ratesci/inst/doc/tests.Rmd | 356 + ratesci-1.1.0/ratesci/inst/doc/tests.html | 1403 +++---- ratesci-1.1.0/ratesci/man/cisapride.Rd | 54 ratesci-1.1.0/ratesci/man/clusterpci.Rd | 150 ratesci-1.1.0/ratesci/man/compress.Rd | 56 ratesci-1.1.0/ratesci/man/crash.Rd | 58 ratesci-1.1.0/ratesci/man/jeffreysci.Rd | 150 ratesci-1.1.0/ratesci/man/moverbci.Rd | 146 ratesci-1.1.0/ratesci/man/moverci.Rd | 244 - ratesci-1.1.0/ratesci/man/moverpairci.Rd |only ratesci-1.1.0/ratesci/man/orci.Rd |only ratesci-1.1.0/ratesci/man/orpairci.Rd |only ratesci-1.1.0/ratesci/man/pairbinci.Rd | 454 +- ratesci-1.1.0/ratesci/man/rateci.Rd | 179 ratesci-1.1.0/ratesci/man/ratesci-package.Rd | 229 - ratesci-1.1.0/ratesci/man/rdci.Rd |only ratesci-1.1.0/ratesci/man/rdpairci.Rd |only ratesci-1.1.0/ratesci/man/rrci.Rd |only ratesci-1.1.0/ratesci/man/rrpairci.Rd |only ratesci-1.1.0/ratesci/man/scasci.Rd | 336 - ratesci-1.1.0/ratesci/man/scaspci.Rd | 138 ratesci-1.1.0/ratesci/man/scoreci.Rd | 718 +-- ratesci-1.1.0/ratesci/man/scorepairci.Rd |only ratesci-1.1.0/ratesci/man/tdasci.Rd | 342 - ratesci-1.1.0/ratesci/tests/testthat.R | 24 ratesci-1.1.0/ratesci/tests/testthat/Table2x.Rdata |only ratesci-1.1.0/ratesci/tests/testthat/Table3x.Rdata |only ratesci-1.1.0/ratesci/tests/testthat/test1.R | 759 +-- ratesci-1.1.0/ratesci/tests/testthat/test2.R | 400 +- ratesci-1.1.0/ratesci/tests/testthat/test3.R | 1398 +++---- ratesci-1.1.0/ratesci/tests/testthat/test4.R | 866 ++-- ratesci-1.1.0/ratesci/tests/testthat/test5.R | 72 ratesci-1.1.0/ratesci/vignettes/REFERENCES.bib | 808 ++-- ratesci-1.1.0/ratesci/vignettes/basic_contrasts.Rmd | 393 +- ratesci-1.1.0/ratesci/vignettes/paired_contrasts.Rmd | 233 - ratesci-1.1.0/ratesci/vignettes/single_rate.Rmd | 365 - ratesci-1.1.0/ratesci/vignettes/stratified.Rmd | 188 ratesci-1.1.0/ratesci/vignettes/tests.Rmd | 356 + 74 files changed, 14583 insertions(+), 12873 deletions(-)
Title: Open Knowledge Format (OKF) Ingestion
Description: Read, validate, and load Open Knowledge Format (OKF) bundles (a
directory of markdown files with YAML frontmatter) into a portable DuckDB
catalog, build the concept graph, render to HTML, and optionally embed
concept bodies for semantic search. Deterministic and agent-free: the same
bundle always yields the same catalog, graph, and render, with no LLM calls
in the core. Conformant and permissive per the OKF v0.1 specification.
Author: Travis Jakel [aut, cre]
Maintainer: Travis Jakel <travis.s.jakel@gmail.com>
Diff between okf versions 0.5.2 dated 2026-06-30 and 0.7.0 dated 2026-07-02
DESCRIPTION | 6 +-- MD5 | 14 +++++--- NAMESPACE | 2 + NEWS.md |only R/okf.R | 74 ++++++++++++++++++++++++++++++++++++++++--- R/okf_diff.R |only man/okf_diff.Rd |only man/okf_extract_wikilinks.Rd |only man/okf_links.Rd | 3 + tests/testthat/test-core.R | 49 ++++++++++++++++++++++++++++ 10 files changed, 134 insertions(+), 14 deletions(-)
Title: Aggregate Data Modelling
Description: Fit pharmacokinetic/pharmacodynamic (PK/PD) models to aggregate-level data (mean vector
and covariance matrix per study) rather than individual-level data. Integrates
with the 'nlmixr2'/'rxode2' ecosystem via four estimation methods: a First-Order ('FO')
analytical estimator, a Monte Carlo (MC) estimator, a Gauss-Hermite quadrature ('GH')
estimator, and an Iterative Reweighting Monte Carlo ('IRMC') estimator. Methods are
based on Välitalo (2021) <doi:10.1007/s10928-021-09760-1>; software described in
van de Beek et al. (2025) <doi:10.1007/s10928-025-10011-w>.
Author: H. van de Beek [aut, cre],
P.A.J. Vaelitalo [aut],
L.B. Zwep [aut],
J.G.C. van Hasselt [aut]
Maintainer: H. van de Beek <h.van.de.beek@lacdr.leidenuniv.nl>
Diff between admixr2 versions 0.1.0 dated 2026-06-02 and 0.2.0 dated 2026-07-02
DESCRIPTION | 20 MD5 | 93 - NAMESPACE | 3 NEWS.md | 66 R/adfo.R | 1902 ++++++++++++------------- R/adgh.R |only R/adirmc.R | 173 +- R/admc.R | 428 +++-- R/datagen.R | 559 ++++--- R/model.R | 277 ++- R/parse.R | 49 R/plot.R | 203 ++ R/simulate.R | 148 - R/utils.R | 94 + R/zzz.R | 32 README.md | 321 ++-- inst/doc/admixr2.Rmd | 390 ++--- inst/doc/admixr2.html | 65 man/adfoControl.Rd | 321 ++-- man/adghControl.Rd |only man/adirmcControl.Rd | 458 +++--- man/admClearCache.Rd |only man/admControl.Rd | 416 ++--- man/admData.Rd | 40 man/datagen.Rd | 229 +-- man/datagenControl.Rd | 111 - man/nlmixr2Est.adgh.Rd |only man/plot.admFit.Rd | 194 +- src/nll.cpp | 27 tests/manual |only tests/testthat/helper-integration.R | 1253 +++++++++++----- tests/testthat/setup.R |only tests/testthat/test-adgh-nodes.R |only tests/testthat/test-control-adfo.R | 346 ++-- tests/testthat/test-control-objects.R | 364 ++++ tests/testthat/test-datagen.R |only tests/testthat/test-fo-nll.R | 952 ++++++------ tests/testthat/test-grad-analytic.R | 386 ++--- tests/testthat/test-grad-kernels.R | 6 tests/testthat/test-integration-adfo.R | 243 +-- tests/testthat/test-integration-adgh.R |only tests/testthat/test-integration-cold-session.R |only tests/testthat/test-integration-cov.R | 283 ++- tests/testthat/test-integration-grad.R | 403 ++--- tests/testthat/test-integration-irmc.R | 150 + tests/testthat/test-integration-parallel.R |only tests/testthat/test-integration-pipeline.R |only tests/testthat/test-model.R |only tests/testthat/test-nll-kernels.R | 16 tests/testthat/test-parse.R | 117 + tests/testthat/test-progress-formatting.R | 54 tests/testthat/test-restart-output-var.R |only tests/testthat/test-traceplot.R |only tests/testthat/test-utils.R | 161 ++ vignettes/admixr2.Rmd | 390 ++--- 55 files changed, 6936 insertions(+), 4807 deletions(-)
Title: A Toolkit for Connecting R and Large Language Models
Description: A complete toolkit for connecting 'R' environments with Large
Language Models (LLMs). Provides utilities for describing 'R' objects,
package documentation, and workspace state in plain text formats
optimized for LLM consumption. Supports multiple workflows:
interactive copy-paste to external chat interfaces, programmatic tool
registration with 'ellmer' chat clients, batteries-included chat
applications via 'shinychat', and exposure to external coding agents
through the Model Context Protocol. Project configuration files enable
stable, repeatable conversations with project-specific context and
preferred LLM settings.
Author: Garrick Aden-Buie [aut, cre] ,
Simon Couch [aut] ,
Joe Cheng [aut],
Posit Software, PBC [cph, fnd],
Google [cph] ,
Microsoft [cph] ,
Jamie Perkins [cph]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between btw versions 1.2.1 dated 2026-03-23 and 1.3.0 dated 2026-07-02
btw-1.2.1/btw/tests/testthat/_snaps/cli.md |only btw-1.3.0/btw/DESCRIPTION | 24 btw-1.3.0/btw/MD5 | 161 +- btw-1.3.0/btw/NAMESPACE | 4 btw-1.3.0/btw/NEWS.md | 28 btw-1.3.0/btw/R/btw_client_app.R | 360 ++++- btw-1.3.0/btw/R/btw_this.R | 8 btw-1.3.0/btw/R/mcp.R | 32 btw-1.3.0/btw/R/task_create_readme.R | 4 btw-1.3.0/btw/R/tool-agent-subagent.R | 19 btw-1.3.0/btw/R/tool-docs.R | 4 btw-1.3.0/btw/R/tool-env-df.R | 4 btw-1.3.0/btw/R/tool-env.R | 2 btw-1.3.0/btw/R/tool-files-patch.R |only btw-1.3.0/btw/R/tool-sessioninfo.R | 2 btw-1.3.0/btw/R/tool-skills.R | 301 +++- btw-1.3.0/btw/R/tools.R | 9 btw-1.3.0/btw/R/utils-ellmer.R | 220 +++ btw-1.3.0/btw/R/utils-r.R | 5 btw-1.3.0/btw/R/zzz.R | 12 btw-1.3.0/btw/exec/btw.R | 643 +++++++++- btw-1.3.0/btw/inst/cli-skill/r-btw-cli/SKILL.md | 60 btw-1.3.0/btw/inst/icons/ink-eraser.svg |only btw-1.3.0/btw/inst/js/app/btw_app.css | 55 btw-1.3.0/btw/inst/js/app/btw_app.js | 84 + btw-1.3.0/btw/inst/js/run-r/btw-run-r.css | 53 btw-1.3.0/btw/inst/js/run-r/btw-run-r.js | 58 btw-1.3.0/btw/man/btw-package.Rd | 1 btw-1.3.0/btw/man/btw.Rd | 2 btw-1.3.0/btw/man/btw_agent_tool.Rd | 2 btw-1.3.0/btw/man/btw_client.Rd | 20 btw-1.3.0/btw/man/btw_skill_install_github.Rd | 7 btw-1.3.0/btw/man/btw_skill_install_package.Rd | 7 btw-1.3.0/btw/man/btw_skill_install_project.Rd |only btw-1.3.0/btw/man/btw_task.Rd | 8 btw-1.3.0/btw/man/btw_task_create_btw_md.Rd | 10 btw-1.3.0/btw/man/btw_task_create_readme.Rd | 10 btw-1.3.0/btw/man/btw_task_create_skill.Rd | 10 btw-1.3.0/btw/man/btw_this.Rd | 8 btw-1.3.0/btw/man/btw_this.character.Rd | 10 btw-1.3.0/btw/man/btw_this.data.frame.Rd | 13 btw-1.3.0/btw/man/btw_this.environment.Rd | 8 btw-1.3.0/btw/man/btw_tool_cran_package.Rd | 4 btw-1.3.0/btw/man/btw_tool_cran_search.Rd | 4 btw-1.3.0/btw/man/btw_tool_docs_package_news.Rd | 2 btw-1.3.0/btw/man/btw_tool_env_describe_data_frame.Rd | 4 btw-1.3.0/btw/man/btw_tool_env_describe_environment.Rd | 4 btw-1.3.0/btw/man/btw_tool_files_edit.Rd | 13 btw-1.3.0/btw/man/btw_tool_files_list.Rd | 15 btw-1.3.0/btw/man/btw_tool_files_patch.Rd |only btw-1.3.0/btw/man/btw_tool_files_read.Rd | 13 btw-1.3.0/btw/man/btw_tool_files_replace.Rd | 13 btw-1.3.0/btw/man/btw_tool_files_search.Rd | 13 btw-1.3.0/btw/man/btw_tool_files_write.Rd | 13 btw-1.3.0/btw/man/btw_tool_git_branch_checkout.Rd | 16 btw-1.3.0/btw/man/btw_tool_git_branch_create.Rd | 16 btw-1.3.0/btw/man/btw_tool_git_branch_list.Rd | 16 btw-1.3.0/btw/man/btw_tool_git_commit.Rd | 16 btw-1.3.0/btw/man/btw_tool_git_diff.Rd | 16 btw-1.3.0/btw/man/btw_tool_git_log.Rd | 16 btw-1.3.0/btw/man/btw_tool_git_status.Rd | 16 btw-1.3.0/btw/man/btw_tool_package_docs.Rd | 4 btw-1.3.0/btw/man/btw_tool_pkg_check.Rd | 10 btw-1.3.0/btw/man/btw_tool_pkg_coverage.Rd | 10 btw-1.3.0/btw/man/btw_tool_pkg_document.Rd | 10 btw-1.3.0/btw/man/btw_tool_pkg_load_all.Rd | 10 btw-1.3.0/btw/man/btw_tool_pkg_test.Rd | 10 btw-1.3.0/btw/man/btw_tool_sessioninfo_is_package_installed.Rd | 6 btw-1.3.0/btw/man/btw_tool_sessioninfo_package.Rd | 6 btw-1.3.0/btw/man/btw_tool_sessioninfo_platform.Rd | 6 btw-1.3.0/btw/man/btw_tool_skill.Rd | 26 btw-1.3.0/btw/man/btw_tool_web_read_url.Rd | 2 btw-1.3.0/btw/man/btw_tools.Rd | 10 btw-1.3.0/btw/man/mcp.Rd | 38 btw-1.3.0/btw/man/use_btw_md.Rd | 2 btw-1.3.0/btw/tests/testthat/_snaps/tool-docs.md | 68 - btw-1.3.0/btw/tests/testthat/_snaps/tool-files-patch.md |only btw-1.3.0/btw/tests/testthat/helpers.R | 19 btw-1.3.0/btw/tests/testthat/test-btw_client.R | 217 +++ btw-1.3.0/btw/tests/testthat/test-btw_task.R | 1 btw-1.3.0/btw/tests/testthat/test-cli.R | 207 +-- btw-1.3.0/btw/tests/testthat/test-tool-agent-subagent.R | 41 btw-1.3.0/btw/tests/testthat/test-tool-files-patch.R |only btw-1.3.0/btw/tests/testthat/test-tool-session-package-installed.R | 3 btw-1.3.0/btw/tests/testthat/test-tool_skills.R | 220 +++ 85 files changed, 2692 insertions(+), 712 deletions(-)
Title: Interactive 3D Brain Atlas Visualization
Description: Plot brain atlases as interactive 3D meshes using 'Three.js'
via 'htmlwidgets', or render publication-quality static images through
'rgl' and 'rayshader'. A pipe-friendly API lets you map data onto
brain regions, control camera angles, toggle region edges, overlay
glass brains, and snapshot or ray-trace the result. Additional
atlases are available through the 'ggsegverse' r-universe. Mowinckel
& Vidal-Piñeiro (2020) <doi:10.1177/2515245920928009>.
Author: Athanasia Mo Mowinckel [aut, cre] ,
Didac Vidal-Pineiro [aut] ,
Center for Lifespan Changes in Brain and Cognition , University
of Oslo [cph],
three.js authors [ctb, cph]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between ggseg3d versions 2.1.1 dated 2026-04-22 and 2.1.2 dated 2026-07-02
ggseg3d-2.1.1/ggseg3d/tests/testthat/test-data_merge.R |only ggseg3d-2.1.2/ggseg3d/DESCRIPTION | 6 ggseg3d-2.1.2/ggseg3d/MD5 | 12 ggseg3d-2.1.2/ggseg3d/NEWS.md | 5 ggseg3d-2.1.2/ggseg3d/tests/testthat/helper-atlas-fixtures.R |only ggseg3d-2.1.2/ggseg3d/tests/testthat/helper-visual.R | 43 -- ggseg3d-2.1.2/ggseg3d/tests/testthat/test-brain-mesh.R | 37 - ggseg3d-2.1.2/ggseg3d/tests/testthat/test-ggseg3d.R | 227 ++++------- 8 files changed, 123 insertions(+), 207 deletions(-)
Title: Splitting-Coalescence-Estimation Method
Description: We introduce improved methods for statistically assessing birth seasonality and intra-annual variation. The first method we propose is a new idea that uses a nonparametric clustering procedure to group individuals with similar time series data and estimate birth seasonality based on the clusters. One can use the function SCEM() to implement this method. The second method estimates input parameters for use with a previously-developed parametric approach (Tornero et al., 2013). The relevant code for this approach is makeFits_OLS(), while makeFits_initial() is the code to implement the same method but with given initial conditions for two parameters. The latter can be used to show the disadvantage of the existing approach. One can use the function makeFits() to generate parametric birth seasonality estimates using either initialization. Detailed description can be found here: Chazin Hannah, Soudeep Deb, Joshua Falk, and Arun Srinivasan (2019) <doi:10.1111/arcm.12432> "New Statistica [...truncated...]
Author: Hannah Chazin [aut, cre],
Soudeep Deb [aut],
Joshua Falk [aut],
Arun Srinivasan [aut],
Kyung Serk Cho [aut]
Maintainer: Hannah Chazin <h.chazin@columbia.edu>
This is a re-admission after prior archival of version 1.1.0 dated 2021-09-02
Diff between SCEM versions 1.1.0 dated 2021-09-02 and 1.2.0 dated 2026-07-02
SCEM-1.1.0/SCEM/README.md |only SCEM-1.1.0/SCEM/build/SCEM.pdf |only SCEM-1.2.0/SCEM/DESCRIPTION | 30 - SCEM-1.2.0/SCEM/MD5 | 81 +- SCEM-1.2.0/SCEM/NAMESPACE | 35 - SCEM-1.2.0/SCEM/R/EBIC.R | 124 ++-- SCEM-1.2.0/SCEM/R/EstTrend.R | 100 +-- SCEM-1.2.0/SCEM/R/SCEM.R | 196 +++--- SCEM-1.2.0/SCEM/R/SCalgo.R | 92 +-- SCEM-1.2.0/SCEM/R/calculateRSS.R | 134 ++-- SCEM-1.2.0/SCEM/R/convertParameters.R | 110 +-- SCEM-1.2.0/SCEM/R/iteration.R | 142 ++-- SCEM-1.2.0/SCEM/R/kernel.R | 46 - SCEM-1.2.0/SCEM/R/makeFits.R | 90 +-- SCEM-1.2.0/SCEM/R/makeFits_OLS.R | 124 ++-- SCEM-1.2.0/SCEM/R/makeFits_initial.R | 136 ++-- SCEM-1.2.0/SCEM/R/sineFit.R | 92 +-- SCEM-1.2.0/SCEM/R/sine_OLS.R | 102 +-- SCEM-1.2.0/SCEM/R/sine_initial.R | 122 ++-- SCEM-1.2.0/SCEM/build/stage23.rdb |only SCEM-1.2.0/SCEM/build/vignette.rds |binary SCEM-1.2.0/SCEM/inst/CITATION | 32 - SCEM-1.2.0/SCEM/inst/doc/SCEM_example.R | 186 +++--- SCEM-1.2.0/SCEM/inst/doc/SCEM_example.Rmd | 240 ++++---- SCEM-1.2.0/SCEM/inst/doc/SCEM_example.html | 723 +++++++++++++++---------- SCEM-1.2.0/SCEM/man/EBIC.Rd | 88 +-- SCEM-1.2.0/SCEM/man/EstTrend.Rd | 64 +- SCEM-1.2.0/SCEM/man/SCEM.Rd | 102 +-- SCEM-1.2.0/SCEM/man/SCalgo.Rd | 58 +- SCEM-1.2.0/SCEM/man/calculateRSS.Rd | 82 +- SCEM-1.2.0/SCEM/man/convertParameters.Rd | 58 +- SCEM-1.2.0/SCEM/man/data-armenia.Rd | 60 +- SCEM-1.2.0/SCEM/man/iteration.Rd | 70 +- SCEM-1.2.0/SCEM/man/kernel.Rd | 50 - SCEM-1.2.0/SCEM/man/makeFits.Rd | 96 +-- SCEM-1.2.0/SCEM/man/makeFits_OLS.Rd | 74 +- SCEM-1.2.0/SCEM/man/makeFits_initial.Rd | 86 +- SCEM-1.2.0/SCEM/man/sineFit.Rd | 82 +- SCEM-1.2.0/SCEM/man/sine_OLS.Rd | 66 +- SCEM-1.2.0/SCEM/man/sine_initial.Rd | 80 +- SCEM-1.2.0/SCEM/tests/testthat.R | 8 SCEM-1.2.0/SCEM/tests/testthat/test-makeFits.R | 6 SCEM-1.2.0/SCEM/vignettes/SCEM_example.Rmd | 240 ++++---- 43 files changed, 2255 insertions(+), 2052 deletions(-)
Title: Example Metabolomics Data Sets
Description: Data sets from a variety of biological sample matrices,
analysed using a number of mass spectrometry based metabolomic analytical techniques.
The example data sets are stored remotely using GitHub releases
<https://github.com/aberHRML/metaboData/releases> which can be accessed from R using the package.
The package also includes the 'abr1' FIE-MS data set from the 'FIEmspro' package <https://github.com/aberHRML/FIEmspro> <doi:10.1038/nprot.2007.511>.
Author: Jasen Finch [aut, cre] ,
Manfred Beckmann [ctb],
David Enot [ctb],
Wanchang Lin [ctb]
Maintainer: Jasen Finch <jsnfnch4@gmail.com>
Diff between metaboData versions 0.6.3 dated 2022-02-15 and 0.6.4 dated 2026-07-02
DESCRIPTION | 16 ++-- MD5 | 17 ++-- NEWS.md | 8 ++ R/reexports.R | 7 + build/vignette.rds |binary inst/doc/metaboData.R | 34 ++++---- inst/doc/metaboData.html | 174 ++++++++++++++++++++++++++------------------- man/reexports.Rd | 17 +--- vignettes/metaboData_files |only 9 files changed, 157 insertions(+), 116 deletions(-)
Title: Computing Key Indicators of the Spatial Distribution of Economic
Activities
Description: Computes a series of indices commonly used in the fields of economic geography, economic complexity, and evolutionary economics to describe the location, distribution, spatial organization, structure, and complexity of economic activities. Functions include basic spatial indicators such as the location quotient, the Krugman specialization index, the Herfindahl or the Shannon entropy indices but also more advanced functions to compute different forms of normalized relatedness between economic activities or network-based measures of economic complexity. Most of the functions use matrix calculus and are based on bipartite (incidence) matrices consisting of region - industry pairs. These are described in Balland (2017) <http://econ.geo.uu.nl/peeg/peeg1709.pdf>.
Author: Pierre-Alexandre Balland [aut, cre, cph]
Maintainer: Pierre-Alexandre Balland <pierre.alex.balland@gmail.com>
Diff between EconGeo versions 2.0 dated 2023-06-26 and 2.1 dated 2026-07-02
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: Tidy Finance Helper Functions
Description: Helper functions for empirical research in financial
economics, addressing a variety of topics covered in Scheuch, Voigt,
and Weiss (2023) <doi:10.1201/b23237>. The package is designed to
provide shortcuts for issues extensively discussed in the book,
facilitating easier application of its concepts. For more information
and resources related to the book, visit
<https://www.tidy-finance.org/index.html>.
Author: Christoph Scheuch [aut, cre, cph] ,
Stefan Voigt [aut, cph] ,
Patrick Weiss [aut, cph] ,
Maximilian Muecke [ctb]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between tidyfinance versions 0.7.0 dated 2026-06-25 and 0.8.0 dated 2026-07-02
DESCRIPTION | 11 - MD5 | 101 ++++++----- NAMESPACE | 6 NEWS.md | 55 ++++++ R/download_data.R | 42 ++++ R/download_data_huggingface.R | 18 +- R/download_data_jkp.R |only R/download_data_osap.R | 25 ++ R/download_data_pastor_stambaugh.R |only R/download_data_stambaugh_yuan.R |only R/list_supported_datasets.R | 9 + R/tidyfinance-package.R | 2 R/validate.R | 1 README.md | 161 ++++++++++++++++--- build/vignette.rds |only inst/CITATION | 2 inst/doc |only man/create_summary_statistics.Rd | 1 man/download_data.Rd | 14 + man/download_data_constituents.Rd | 3 man/download_data_factors_ff.Rd | 3 man/download_data_factors_q.Rd | 3 man/download_data_fred.Rd | 3 man/download_data_huggingface.Rd | 3 man/download_data_jkp.Rd |only man/download_data_macro_predictors.Rd | 3 man/download_data_osap.Rd | 22 ++ man/download_data_pastor_stambaugh.Rd |only man/download_data_risk_free.Rd | 3 man/download_data_stambaugh_yuan.Rd |only man/download_data_stock_prices.Rd | 3 man/download_factor_library_grid.Rd | 3 man/download_factor_library_ids.Rd | 3 man/get_available_huggingface_files.Rd | 1 man/list_supported_datasets.Rd | 1 man/list_supported_datasets_ff.Rd | 1 man/list_supported_datasets_ff_legacy.Rd | 1 man/list_supported_datasets_macro_predictors.Rd | 1 man/list_supported_datasets_other.Rd | 1 man/list_supported_datasets_pseudo.Rd | 1 man/list_supported_datasets_wrds.Rd | 1 man/list_supported_indexes.Rd | 1 man/list_supported_jkp_factors.Rd |only man/list_tidy_finance_chapters.Rd | 1 man/open_tidy_finance_website.Rd | 1 man/tidyfinance-package.Rd | 2 man/trim.Rd | 1 man/validate_dates.Rd | 1 man/winsorize.Rd | 1 tests/testthat/_snaps/list_supported_datasets.md | 25 +- tests/testthat/test-download_data.R | 46 +++++ tests/testthat/test-download_data_huggingface.R | 42 ++++ tests/testthat/test-download_data_jkp.R |only tests/testthat/test-download_data_osap.R | 9 - tests/testthat/test-download_data_pastor_stambaugh.R |only tests/testthat/test-download_data_stambaugh_yuan.R |only vignettes |only 57 files changed, 521 insertions(+), 117 deletions(-)
Title: Visually Exploring Random Forests
Description: Graphic elements for exploring Random Forests using the
'randomForest' or 'randomForestSRC' package for survival, regression
and classification forests and 'ggplot2' package plotting. Implements
visualisations of the methods described in Breiman (2001)
<doi:10.1023/A:1010933404324> and Ishwaran, Kogalur, Blackstone, and
Lauer (2008) <doi:10.1214/08-AOAS169>.
Author: John Ehrlinger [aut, cre]
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between ggRandomForests versions 3.2.0 dated 2026-06-23 and 3.4.0 dated 2026-07-02
ggRandomForests-3.2.0/ggRandomForests/tests/testthat/Rplots.pdf |only ggRandomForests-3.4.0/ggRandomForests/DESCRIPTION | 8 ggRandomForests-3.4.0/ggRandomForests/MD5 | 88 +- ggRandomForests-3.4.0/ggRandomForests/NAMESPACE | 18 ggRandomForests-3.4.0/ggRandomForests/NEWS.md | 72 + ggRandomForests-3.4.0/ggRandomForests/R/gg_beta_uvarpro.R |only ggRandomForests-3.4.0/ggRandomForests/R/gg_beta_varpro.R | 12 ggRandomForests-3.4.0/ggRandomForests/R/gg_isopro.R | 12 ggRandomForests-3.4.0/ggRandomForests/R/gg_ivarpro.R | 13 ggRandomForests-3.4.0/ggRandomForests/R/gg_partial_rfsrc.R | 36 ggRandomForests-3.4.0/ggRandomForests/R/gg_partial_varpro.R | 247 +++++- ggRandomForests-3.4.0/ggRandomForests/R/gg_partialpro.R | 4 ggRandomForests-3.4.0/ggRandomForests/R/gg_sdependent.R |only ggRandomForests-3.4.0/ggRandomForests/R/plot.gg_beta_uvarpro.R |only ggRandomForests-3.4.0/ggRandomForests/R/plot.gg_partial_varpro.R | 106 ++ ggRandomForests-3.4.0/ggRandomForests/R/plot.gg_sdependent.R |only ggRandomForests-3.4.0/ggRandomForests/README.md | 22 ggRandomForests-3.4.0/ggRandomForests/build/vignette.rds |binary ggRandomForests-3.4.0/ggRandomForests/inst/doc/ggRandomForests-regression.html | 36 ggRandomForests-3.4.0/ggRandomForests/inst/doc/ggRandomForests-regression.qmd | 2 ggRandomForests-3.4.0/ggRandomForests/inst/doc/ggRandomForests-survival.html | 44 - ggRandomForests-3.4.0/ggRandomForests/inst/doc/ggRandomForests-survival.qmd | 11 ggRandomForests-3.4.0/ggRandomForests/inst/doc/ggRandomForests.html | 4 ggRandomForests-3.4.0/ggRandomForests/inst/doc/ggRandomForests.qmd | 2 ggRandomForests-3.4.0/ggRandomForests/inst/doc/uvarpro.R |only ggRandomForests-3.4.0/ggRandomForests/inst/doc/uvarpro.html |only ggRandomForests-3.4.0/ggRandomForests/inst/doc/uvarpro.qmd |only ggRandomForests-3.4.0/ggRandomForests/inst/doc/varpro.R | 13 ggRandomForests-3.4.0/ggRandomForests/inst/doc/varpro.html | 386 ++++++---- ggRandomForests-3.4.0/ggRandomForests/inst/doc/varpro.qmd | 150 +-- ggRandomForests-3.4.0/ggRandomForests/man/gg_beta_uvarpro.Rd |only ggRandomForests-3.4.0/ggRandomForests/man/gg_partial_rfsrc.Rd | 3 ggRandomForests-3.4.0/ggRandomForests/man/gg_partial_varpro.Rd | 40 - ggRandomForests-3.4.0/ggRandomForests/man/gg_sdependent.Rd |only ggRandomForests-3.4.0/ggRandomForests/man/plot.gg_beta_uvarpro.Rd |only ggRandomForests-3.4.0/ggRandomForests/man/plot.gg_partial_varpro.Rd | 64 + ggRandomForests-3.4.0/ggRandomForests/man/plot.gg_sdependent.Rd |only ggRandomForests-3.4.0/ggRandomForests/man/print.gg.Rd | 11 ggRandomForests-3.4.0/ggRandomForests/man/summary.gg.Rd | 15 ggRandomForests-3.4.0/ggRandomForests/tests/testthat/test_gg_beta_uvarpro.R |only ggRandomForests-3.4.0/ggRandomForests/tests/testthat/test_gg_beta_varpro.R | 7 ggRandomForests-3.4.0/ggRandomForests/tests/testthat/test_gg_isopro.R | 9 ggRandomForests-3.4.0/ggRandomForests/tests/testthat/test_gg_ivarpro.R | 9 ggRandomForests-3.4.0/ggRandomForests/tests/testthat/test_gg_partial_rfsrc.R |only ggRandomForests-3.4.0/ggRandomForests/tests/testthat/test_gg_partial_varpro.R | 180 ++++ ggRandomForests-3.4.0/ggRandomForests/tests/testthat/test_gg_sdependent.R |only ggRandomForests-3.4.0/ggRandomForests/vignettes/ggRandomForests-regression.qmd | 2 ggRandomForests-3.4.0/ggRandomForests/vignettes/ggRandomForests-survival.qmd | 11 ggRandomForests-3.4.0/ggRandomForests/vignettes/ggRandomForests.qmd | 2 ggRandomForests-3.4.0/ggRandomForests/vignettes/precompute_varpro.R | 9 ggRandomForests-3.4.0/ggRandomForests/vignettes/uvarpro.qmd |only ggRandomForests-3.4.0/ggRandomForests/vignettes/varpro.qmd | 150 +-- ggRandomForests-3.4.0/ggRandomForests/vignettes/varpro_precomputed.rds |binary 53 files changed, 1274 insertions(+), 524 deletions(-)
More information about ggRandomForests at CRAN
Permanent link
Title: R Library for 'Harmony'
Description: 'Harmony' is a tool using AI which allows you to compare items from questionnaires and identify similar content. You can try 'Harmony' at <https://harmonydata.ac.uk/app/> and you can read our blog at <https://harmonydata.ac.uk/blog/> or at <https://fastdatascience.com/how-does-harmony-work/>. Documentation at <https://harmonydata.ac.uk/harmony-r-released/>.
Author: Omar Hassoun [aut, cre],
Thomas Wood [ctb],
Alex, Nikic [ctb],
Ulster University [cph]
Maintainer: Omar Hassoun <omtarful@gmail.com>
Diff between harmonydata versions 0.3.1 dated 2025-04-20 and 0.3.2 dated 2026-07-02
DESCRIPTION | 8 +++--- MD5 | 11 +++++--- NEWS.md | 29 ++++++++++++++++------- R/match_instruments.R | 58 ++++++++++++++++++++++++++++++++++++++++++++++- man/match_instruments.Rd | 24 ++++++++++++++++++- tests |only 6 files changed, 111 insertions(+), 19 deletions(-)
Title: Coverage Correlation Coefficient and Testing for Independence
Description: Computes the coverage correlation coefficient introduced in <doi:10.48550/arXiv.2508.06402> , a statistical measure that quantifies dependence between two random vectors by computing the union volume of data-centered hypercubes in a uniform space.
Author: Tengyao Wang [aut, cre],
Mona Azadkia [aut, ctb],
Xuzhi Yang [aut, ctb]
Maintainer: Tengyao Wang <t.wang59@lse.ac.uk>
Diff between covercorr versions 1.0.0 dated 2025-08-25 and 1.1.0 dated 2026-07-02
DESCRIPTION | 13 MD5 | 28 + NAMESPACE | 10 NEWS.md |only R/Visualise_density.R |only R/covercorr-methods.R |only R/covercorr.R | 765 ++++++++++++++++++++++++++++++++++++- inst/doc/coverage_correlation.R | 95 ++++ inst/doc/coverage_correlation.Rmd | 273 +++++++++++-- inst/doc/coverage_correlation.html | 352 +++++++++++++---- man/coverage_correlation_K.Rd |only man/coverage_correlation_K_grid.Rd |only man/coverage_correlation_grid.Rd |only man/covercorr.Rd |only man/visualise_density.Rd |only tests |only vignettes/coverage_correlation.Rmd | 273 +++++++++++-- 17 files changed, 1628 insertions(+), 181 deletions(-)
Title: Extending 'mlr3' to Functional Data Analysis
Description: Extends the 'mlr3' ecosystem to functional analysis by adding
support for irregular and regular functional data as defined in the
'tf' package. The package provides 'PipeOps' for preprocessing
functional columns and for extracting scalar features, thereby
allowing standard machine learning algorithms to be applied
afterwards. Available operations include simple functional features
such as the mean or maximum, smoothing, interpolation, flattening, and
functional 'PCA'.
Author: Maximilian Muecke [aut, cre] ,
Sebastian Fischer [aut] ,
Fabian Scheipl [ctb] ,
Bernd Bischl [ctb]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between mlr3fda versions 0.6.0 dated 2026-06-01 and 0.7.0 dated 2026-07-02
DESCRIPTION | 17 ++++---- MD5 | 59 +++++++++++++++++-------------- NAMESPACE | 2 + NEWS.md | 8 ++++ R/PipeOpFDABsignal.R | 4 +- R/PipeOpFDACatch22.R |only R/PipeOpFDAFlatten.R | 6 --- R/PipeOpFDAIntegrate.R |only R/PipeOpFDARandomEffect.R | 2 - R/PipeOpFDAScaleRange.R | 12 ++---- R/PipeOpFDATsfeatures.R | 2 - R/PipeOpFDAWavelets.R | 5 +- R/PipeOpFDAZoom.R | 6 +-- R/PipeOpFPCA.R | 4 -- R/bibentries.R | 8 ++-- R/hash_input.R | 6 --- R/zzz.R | 10 +---- README.md | 2 + build/partial.rdb |binary man/mlr_pipeops_fda.bsignal.Rd | 2 + man/mlr_pipeops_fda.catch22.Rd |only man/mlr_pipeops_fda.fourier.Rd | 2 - man/mlr_pipeops_fda.integrate.Rd |only man/mlr_pipeops_fda.random_effect.Rd | 2 + man/mlr_pipeops_fda.tsfeats.Rd | 2 + man/mlr_pipeops_fda.wavelets.Rd | 2 + man/mlr_tasks_dti.Rd | 2 - man/mlr_tasks_fuel.Rd | 2 - man/mlr_tasks_phoneme.Rd | 2 - tests/testthat/helper.R | 2 - tests/testthat/test_PipeOpFDACatch22.R |only tests/testthat/test_PipeOpFDAIntegrate.R |only tests/testthat/test_PipeOpFDAWavelets.R | 6 +-- tests/testthat/test_zzz.R |only 34 files changed, 93 insertions(+), 84 deletions(-)
Title: Interface with the 'ClinicalOmicsDB' API, Allowing for Easy Data
Downloading and Importing
Description: Provides an interface to the 'ClinicalOmicsDB' API, allowing for easy data downloading and importing. 'ClinicalOmicsDB' is a database of clinical and 'omics' data from cancer patients. The database is accessible at <http://trials.linkedomics.org>.
Author: John Elizarraras [aut, ctb],
Zhiao Shi [cre]
Maintainer: Zhiao Shi <zhiao.shi@gmail.com>
Diff between clinicalomicsdbR versions 1.0.5 dated 2024-06-26 and 1.0.6 dated 2026-07-02
DESCRIPTION | 16 +++++++++------- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 15 insertions(+), 9 deletions(-)
More information about clinicalomicsdbR at CRAN
Permanent link
Title: Beta Kernel Process Modeling
Description: Implements the Beta Kernel Process (BKP) for nonparametric modeling of
covariate-dependent binomial probabilities, and the Dirichlet Kernel Process (DKP) for
categorical or multinomial response data. Scalable global-local approximations
are provided through TwinBKP and TwinDKP, using twinning-selected global subsets
and local nearest-neighbour updates.
Functions are included for model fitting, predictive inference with
uncertainty quantification, posterior simulation,
and visualization in one- and two-dimensional input spaces.
Gaussian, Matern 5/2, Matern 3/2, and Wendland kernels are supported,
with hyperparameters selected by multi-start derivative-free optimization.
For more details, see Zhao, Qing, and Xu (2025) <doi:10.48550/arXiv.2508.10447>.
Author: Jiangyan Zhao [cre, aut],
Kunhai Qing [aut],
Jin Xu [aut]
Maintainer: Jiangyan Zhao <zhaojy2017@126.com>
Diff between BKP versions 0.2.3 dated 2025-09-22 and 0.3.0 dated 2026-07-02
BKP-0.2.3/BKP/tests/testthat/Rplots.pdf |only BKP-0.2.3/BKP/tests/testthat/test-simualte_DKP.R |only BKP-0.3.0/BKP/DESCRIPTION | 27 BKP-0.3.0/BKP/MD5 | 201 ++-- BKP-0.3.0/BKP/NAMESPACE | 57 + BKP-0.3.0/BKP/NEWS.md | 32 BKP-0.3.0/BKP/R/BKP-package.R | 111 +- BKP-0.3.0/BKP/R/RcppExports.R |only BKP-0.3.0/BKP/R/fit_BKP.R | 686 +++++++++----- BKP-0.3.0/BKP/R/fit_DKP.R | 684 +++++++++----- BKP-0.3.0/BKP/R/fit_TwinBKP.R |only BKP-0.3.0/BKP/R/fit_TwinDKP.R |only BKP-0.3.0/BKP/R/fitted_BKP.R | 159 ++- BKP-0.3.0/BKP/R/fitted_DKP.R | 106 +- BKP-0.3.0/BKP/R/fitted_TwinBKP.R |only BKP-0.3.0/BKP/R/fitted_TwinDKP.R |only BKP-0.3.0/BKP/R/get_prior.R | 302 ++++-- BKP-0.3.0/BKP/R/kernel_matrix.R | 209 ++-- BKP-0.3.0/BKP/R/loss_fun.R | 362 ++++--- BKP-0.3.0/BKP/R/parameter_BKP.R | 164 ++- BKP-0.3.0/BKP/R/parameter_DKP.R | 98 +- BKP-0.3.0/BKP/R/parameter_TwinBKP.R |only BKP-0.3.0/BKP/R/parameter_TwinDKP.R |only BKP-0.3.0/BKP/R/plot_BKP.R | 709 +++++++++------ BKP-0.3.0/BKP/R/plot_DKP.R | 660 ++++++++------ BKP-0.3.0/BKP/R/plot_TwinBKP.R |only BKP-0.3.0/BKP/R/plot_TwinDKP.R |only BKP-0.3.0/BKP/R/predict_BKP.R | 613 ++++++++----- BKP-0.3.0/BKP/R/predict_DKP.R | 448 ++++++--- BKP-0.3.0/BKP/R/predict_TwinBKP.R |only BKP-0.3.0/BKP/R/predict_TwinDKP.R |only BKP-0.3.0/BKP/R/print_BKP.R | 671 +++++++------- BKP-0.3.0/BKP/R/print_DKP.R | 665 +++++++------- BKP-0.3.0/BKP/R/print_TwinBKP.R |only BKP-0.3.0/BKP/R/print_TwinDKP.R |only BKP-0.3.0/BKP/R/quantile_BKP.R | 207 ++-- BKP-0.3.0/BKP/R/quantile_DKP.R | 166 ++- BKP-0.3.0/BKP/R/quantile_TwinBKP.R |only BKP-0.3.0/BKP/R/quantile_TwinDKP.R |only BKP-0.3.0/BKP/R/simulate_BKP.R | 434 +++++---- BKP-0.3.0/BKP/R/simulate_DKP.R | 289 +++--- BKP-0.3.0/BKP/R/simulate_TwinBKP.R |only BKP-0.3.0/BKP/R/simulate_TwinDKP.R |only BKP-0.3.0/BKP/R/summary_BKP.R | 240 ++--- BKP-0.3.0/BKP/R/summary_DKP.R | 184 +--- BKP-0.3.0/BKP/R/summary_TwinBKP.R |only BKP-0.3.0/BKP/R/summary_TwinDKP.R |only BKP-0.3.0/BKP/R/utils.R | 827 ++++++++++++++++-- BKP-0.3.0/BKP/README.md | 103 +- BKP-0.3.0/BKP/inst/CITATION | 23 BKP-0.3.0/BKP/inst/COPYRIGHTS |only BKP-0.3.0/BKP/inst/WORDLIST |only BKP-0.3.0/BKP/inst/include |only BKP-0.3.0/BKP/man/BKP-package.Rd | 102 +- BKP-0.3.0/BKP/man/bkp_check_unique_locations.Rd |only BKP-0.3.0/BKP/man/bkp_compute_posterior.Rd |only BKP-0.3.0/BKP/man/bkp_ess_calibration.Rd |only BKP-0.3.0/BKP/man/bkp_ess_none_info.Rd |only BKP-0.3.0/BKP/man/bkp_shepard_m.Rd |only BKP-0.3.0/BKP/man/bkp_shepard_m_loo.Rd |only BKP-0.3.0/BKP/man/dkp_compute_posterior.Rd |only BKP-0.3.0/BKP/man/fit_BKP.Rd | 376 ++++---- BKP-0.3.0/BKP/man/fit_DKP.Rd | 385 +++++--- BKP-0.3.0/BKP/man/fit_TwinBKP.Rd |only BKP-0.3.0/BKP/man/fit_TwinDKP.Rd |only BKP-0.3.0/BKP/man/fitted.Rd | 241 +++-- BKP-0.3.0/BKP/man/get_prior.Rd | 125 +- BKP-0.3.0/BKP/man/kernel_matrix.Rd | 105 +- BKP-0.3.0/BKP/man/loss_fun.Rd | 87 + BKP-0.3.0/BKP/man/make_plot_grid.Rd |only BKP-0.3.0/BKP/man/my_2D_plot_fun.Rd |only BKP-0.3.0/BKP/man/my_2D_plot_fun_class.Rd |only BKP-0.3.0/BKP/man/my_2D_plot_fun_class_ggplot.Rd |only BKP-0.3.0/BKP/man/my_2D_plot_fun_ggplot.Rd |only BKP-0.3.0/BKP/man/parameter.Rd | 247 +++-- BKP-0.3.0/BKP/man/plot.Rd | 200 +++- BKP-0.3.0/BKP/man/posterior_summary.Rd |only BKP-0.3.0/BKP/man/predict.Rd | 321 ++++-- BKP-0.3.0/BKP/man/print.Rd | 203 ++-- BKP-0.3.0/BKP/man/quantile.Rd | 257 +++-- BKP-0.3.0/BKP/man/simulate.Rd | 183 ++- BKP-0.3.0/BKP/man/summary.Rd | 177 +-- BKP-0.3.0/BKP/src |only BKP-0.3.0/BKP/tests/testthat.R | 4 BKP-0.3.0/BKP/tests/testthat/helper-BKP.R |only BKP-0.3.0/BKP/tests/testthat/helper-DKP.R |only BKP-0.3.0/BKP/tests/testthat/helper-TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/helper-TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-fit_BKP.R | 371 +++++--- BKP-0.3.0/BKP/tests/testthat/test-fit_DKP.R | 451 ++++++--- BKP-0.3.0/BKP/tests/testthat/test-fit_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-fit_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-fitted_BKP.R | 323 ++++--- BKP-0.3.0/BKP/tests/testthat/test-fitted_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-fitted_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-get_prior.R | 130 ++ BKP-0.3.0/BKP/tests/testthat/test-kernel_matrix.R | 288 ++++++ BKP-0.3.0/BKP/tests/testthat/test-loss_fun.R | 130 ++ BKP-0.3.0/BKP/tests/testthat/test-parameter_BKP.R | 128 +- BKP-0.3.0/BKP/tests/testthat/test-parameter_DKP.R | 132 +- BKP-0.3.0/BKP/tests/testthat/test-parameter_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-parameter_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-plot_BKP.R | 195 ++-- BKP-0.3.0/BKP/tests/testthat/test-plot_DKP.R | 238 +++-- BKP-0.3.0/BKP/tests/testthat/test-plot_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-plot_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-predict_BKP.R | 192 ++-- BKP-0.3.0/BKP/tests/testthat/test-predict_DKP.R | 220 ++-- BKP-0.3.0/BKP/tests/testthat/test-predict_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-predict_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-print_BKP.R | 103 +- BKP-0.3.0/BKP/tests/testthat/test-print_DKP.R | 105 +- BKP-0.3.0/BKP/tests/testthat/test-print_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-print_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-quantile_BKP.R | 158 +-- BKP-0.3.0/BKP/tests/testthat/test-quantile_DKP.R | 232 ++--- BKP-0.3.0/BKP/tests/testthat/test-quantile_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-quantile_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-simulate_BKP.R | 232 ++--- BKP-0.3.0/BKP/tests/testthat/test-simulate_DKP.R | 201 +++- BKP-0.3.0/BKP/tests/testthat/test-simulate_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-simulate_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-summary_BKP.R | 169 +-- BKP-0.3.0/BKP/tests/testthat/test-summary_DKP.R | 187 ++-- BKP-0.3.0/BKP/tests/testthat/test-summary_TwinBKP.R |only BKP-0.3.0/BKP/tests/testthat/test-summary_TwinDKP.R |only BKP-0.3.0/BKP/tests/testthat/test-utils.R | 214 ++-- 127 files changed, 10501 insertions(+), 6348 deletions(-)
Title: 'Serpstat' API Wrapper
Description: The primary goal of 'Serpstat' API <https://api-docs.serpstat.com/docs/serpstat-public-api/jenasqbwtxdlr-introduction-to-serpstat-api>
is to reduce manual SEO (search engine optimization) and PPC (pay-per-click)
tasks. You can automate your keywords research or competitors analysis
with this API wrapper.
Author: Alex Danilin [aut, cre]
Maintainer: Alex Danilin <alexnikdanilin@gmail.com>
Diff between serpstatr versions 0.4.2 dated 2026-06-09 and 0.4.3 dated 2026-07-02
DESCRIPTION | 6 +++--- MD5 | 14 +++++++++----- NAMESPACE | 2 ++ NEWS.md | 6 ++++++ R/serp_crawling.R |only R/utility_functions.R | 13 +++++++++++-- README.md | 14 ++++++++++++++ man/sst_sc_add_task.Rd |only man/sst_sc_get_task_result.Rd |only tests/testthat/test_serp_crawling.R |only 10 files changed, 45 insertions(+), 10 deletions(-)
Title: Phenotypic Index Measures for Oak Decline Severity
Description: Oak declines are complex disease syndromes and consist of many visual indicators that include aspects of tree size, crown condition and trunk condition. This can cause difficulty in the manual classification of symptomatic and non-symptomatic trees from what is in reality a broad spectrum of oak tree health condition. Two phenotypic oak decline indexes have been developed to quantitatively describe and differentiate oak decline syndromes in Quercus robur. This package provides a toolkit to generate these decline indexes from phenotypic descriptors using the machine learning algorithm random forest. The methodology for generating these indexes is outlined in Finch et al. (2021) <doi:10.1016/j.foreco.2021.118948>.
Author: Jasen Finch [aut, cre]
Maintainer: Jasen Finch <jsnfnch4@gmail.com>
Diff between pdi versions 0.4.2 dated 2021-02-09 and 0.4.3 dated 2026-07-02
DESCRIPTION | 19 - MD5 | 26 - NAMESPACE | 1 NEWS.md | 12 R/reexports.R | 9 R/siteAdjustment.R | 62 ++- R/siteAdjustmentFactors.R | 46 +- README.md | 6 build/vignette.rds |binary inst/doc/pdi-example.R | 4 inst/doc/pdi-example.html | 695 ++++++++++++++++++++++++++++++------------- man/reexports.Rd | 21 - man/siteAdjustment.Rd | 9 man/siteAdjustmentFactors.Rd | 7 14 files changed, 617 insertions(+), 300 deletions(-)
Title: A Set of Color Palettes Inspired by OK Go Music Videos for
'ggplot2' in R
Description: A collection of aesthetically appealing color palettes for effective data visualization with 'ggplot2'. Palettes support both discrete and continuous data.
Author: Nelson de O. Quesado Filho [aut, cre],
Ana Flavia Teles Silveira [aut]
Maintainer: Nelson de O. Quesado Filho <nquesado@gmail.com>
Diff between okcolors versions 0.1.0 dated 2025-05-14 and 0.1.2 dated 2026-07-02
DESCRIPTION | 9 ++--- MD5 | 26 +++++++------- NAMESPACE | 1 NEWS.md | 11 ++++++ R/palettes.R | 46 ++++++++----------------- R/scales.R | 73 +++++++++++++++++++++-------------------- R/utils.R | 64 +++++++++++++++++++++++++++++++++++ README.md |only man/okcolors.Rd | 28 ++++++--------- man/scale_color_okcolors.Rd | 35 +++++++++---------- man/scale_fill_okcolors.Rd | 34 +++++++++---------- man/valid_palettes.Rd |only tests/testthat/test-okcolors.R | 35 ++++++++----------- tests/testthat/test-palettes.R | 12 +++++- tests/testthat/test-scales.R | 14 ++++++- 15 files changed, 231 insertions(+), 157 deletions(-)
Title: Interface to 'NetMHCIIpan'
Description: The field of immunology benefits from software that can
predict which peptide sequences trigger an immune response.
'NetMHCIIpan' is a such a tool: it predicts the
binding strength of a short peptide to a Major Histocompatibility
Complex class II (MHC-II) molecule.
'NetMHCIIpan' can be used from a web server at
<https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.2/>
or from the command-line, using a local installation. This package
allows to call 'NetMHCIIpan' from R.
Author: Richel J.C. Bilderbeek [aut, cre] ,
Lue Ping Zhao [ctb],
Byungkuk Min [ctb]
Maintainer: Richel J.C. Bilderbeek <rjcbilderbeek@gmail.com>
Diff between netmhc2pan versions 1.3.2 dated 2023-11-08 and 1.3.3 dated 2026-07-02
netmhc2pan-1.3.2/netmhc2pan/R/netmhc2pan.R |only netmhc2pan-1.3.2/netmhc2pan/man/figures/TravisCI.png |only netmhc2pan-1.3.3/netmhc2pan/DESCRIPTION | 16 ++++++++-------- netmhc2pan-1.3.3/netmhc2pan/MD5 | 11 +++++------ netmhc2pan-1.3.3/netmhc2pan/R/netmhc2pan-package.R |only netmhc2pan-1.3.3/netmhc2pan/R/netmhc2pan_report.R | 2 +- netmhc2pan-1.3.3/netmhc2pan/build/vignette.rds |binary netmhc2pan-1.3.3/netmhc2pan/inst/doc/demo.html | 6 +++--- 8 files changed, 17 insertions(+), 18 deletions(-)
Title: Create Data with Identical Statistics
Description: Creates data with identical statistics (metamers) using an iterative
algorithm proposed by Matejka & Fitzmaurice (2017) <DOI:10.1145/3025453.3025912>.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between metamer versions 0.3.0 dated 2022-06-23 and 0.3.1 dated 2026-07-02
DESCRIPTION | 18 ++++++++++-------- MD5 | 30 +++++++++++++++--------------- NEWS.md | 4 ++++ README.md | 18 +++++++----------- build/partial.rdb |binary man/delayed_with.Rd | 16 ++++++++-------- man/densify.Rd | 16 ++++++++-------- man/draw_data.Rd | 16 ++++++++-------- man/figures/README-unnamed-chunk-6-1.gif |binary man/figures/README-unnamed-chunk-8-1.gif |binary man/mean_dist_to.Rd | 16 ++++++++-------- man/mean_dist_to_sf.Rd | 16 ++++++++-------- man/mean_self_proximity.Rd | 16 ++++++++-------- man/metamer-package.Rd | 8 +++++++- man/moments_n.Rd | 16 ++++++++-------- man/rounding.Rd | 25 ++++++++----------------- 16 files changed, 107 insertions(+), 108 deletions(-)
Title: Brain Atlas Data Structures for the 'ggsegverse' Ecosystem
Description: Provides the 'ggseg_atlas' S3 class used across the 'ggsegverse'
ecosystem for 2D and 3D brain visualisation. Ships four bundled atlases
('Desikan-Killiany', 'FreeSurfer' 'aseg', 'TRACULA', 'SUIT') and functions
for querying, subsetting, renaming, and enriching atlas objects. Also
includes readers for 'FreeSurfer' statistics files.
Author: Athanasia Mo Mowinckel [aut, cre] ,
Center for Lifespan Changes in Brain and Cognition , University
of Oslo [cph]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between ggseg.formats versions 0.0.3 dated 2026-06-18 and 0.0.4 dated 2026-07-02
DESCRIPTION | 6 MD5 | 57 ++-- NEWS.md | 225 ++++++++-------- R/atlas_accessors.R | 13 R/atlas_convert.R | 4 R/atlas_polygons.R | 4 R/compat_dataframe.R | 52 +++ R/ggseg_atlas.R | 29 +- R/ggseg_atlas_data.R | 20 - R/read_freesurfer.R | 2 R/sysdata.rda |binary inst/WORDLIST | 6 inst/doc/atlas-manipulation.html | 6 inst/doc/ggseg.formats.html | 344 ++++--------------------- tests/testthat/_snaps |only tests/testthat/helper-polygons.R | 7 tests/testthat/test-atlas_accessors.R | 19 + tests/testthat/test-atlas_convert.R | 17 - tests/testthat/test-atlas_polygon_converters.R | 3 tests/testthat/test-atlas_polygon_ops.R | 5 tests/testthat/test-atlas_polygons.R | 39 +- tests/testthat/test-atlas_utils.R | 16 - tests/testthat/test-atlases.R | 12 tests/testthat/test-compat_dataframe.R | 39 ++ tests/testthat/test-ggseg-atlas-plots.R | 30 ++ tests/testthat/test-ggseg_atlas.R | 22 - tests/testthat/test-ggseg_atlas_data.R | 18 - tests/testthat/test-migrate_atlas_files.R | 15 - 28 files changed, 483 insertions(+), 527 deletions(-)
Title: Easy Plotting of Periodic Data with 'ggplot2'
Description: Implements methods to plot periodic data in any arbitrary range on the fly.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between ggperiodic versions 1.0.3 dated 2023-03-22 and 1.0.4 dated 2026-07-02
DESCRIPTION | 15 ++-- MD5 | 24 +++---- NEWS.md | 4 + R/fortify.R | 35 ----------- R/periodic.R | 1 R/unperiodic.R | 12 +-- README.md | 13 ---- build/vignette.rds |binary inst/doc/wraping-around-ggplot2.html | 95 +++++++++++++++---------------- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/ggperiodic.Rd | 9 ++ man/reexports.Rd | 2 13 files changed, 89 insertions(+), 121 deletions(-)
Title: Open-Access Computational Biology Datasets
Description: Efficiently access the 'Bedrock Bio' library of open-access
computational biology datasets. Lazily query datasets backed by 'DuckDB'
and 'Apache Iceberg', with support for predicate pushdown and column
projection to the cloud storage backend. This enables quick, iterative
access to otherwise massive, unwieldy datasets without downloading them
in full. See <https://bedrock.bio> for available datasets and
documentation.
Author: Liam Abbott [aut, cre, cph]
Maintainer: Liam Abbott <liam@bedrock.bio>
Diff between bedrockbio versions 1.4.0 dated 2026-05-28 and 2.0.0 dated 2026-07-02
DESCRIPTION | 15 +- MD5 | 46 +++--- NEWS.md | 23 +++ R/describe_namespace.R | 15 -- R/describe_table.R | 32 +--- R/list_namespaces.R | 7 R/list_tables.R | 25 ++- R/load_table.R | 19 +- R/utils.R | 105 ++++---------- R/zzz.R | 12 + README.md | 22 +-- man/bedrockbio-package.Rd | 4 man/describe_namespace.Rd | 15 -- man/describe_table.Rd | 15 +- man/list_namespaces.Rd | 6 man/list_tables.Rd | 14 + man/load_table.Rd | 9 - tests/testthat/helper-v2.R |only tests/testthat/test-describe_namespace.R | 37 ++--- tests/testthat/test-describe_table.R | 62 ++++---- tests/testthat/test-env.R |only tests/testthat/test-list_namespaces.R | 2 tests/testthat/test-list_tables.R | 35 ++++ tests/testthat/test-load_table.R | 39 ++++- tests/testthat/test-utils.R | 225 +++++++++---------------------- 25 files changed, 387 insertions(+), 397 deletions(-)
Title: 'Material UI' for 'shiny' Apps and 'Quarto'
Description: Wraps the 'Material UI' React components <https://mui.com/> for use in R, 'shiny'
applications and 'quarto' documents, including inputs, layouts, navigation, and
surfaces. All inputs come with R usage examples.
Author: Felix Luginbuhl [aut, cre, cph] ,
MUI [cph] ,
Emotion team [cph] ,
Meta Platforms, Inc. and affiliates [cph]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between muiMaterial versions 0.2.1 dated 2026-06-28 and 0.2.2 dated 2026-07-02
DESCRIPTION | 6 - MD5 | 10 +- NEWS.md | 10 ++ README.md | 4 inst/www/muiMaterial/mui-material.js | 113 +++++++++++++---------- inst/www/muiMaterial/mui-material.js.LICENSE.txt | 12 +- 6 files changed, 94 insertions(+), 61 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 1.1.1 dated 2026-05-20 and 1.2.0 dated 2026-07-02
maestro-1.1.1/maestro/R/show_network.R |only maestro-1.1.1/maestro/man/show_network.Rd |only maestro-1.1.1/maestro/tests/testthat/test-show_network.R |only maestro-1.2.0/maestro/DESCRIPTION | 10 maestro-1.2.0/maestro/MD5 | 85 +- maestro-1.2.0/maestro/NAMESPACE | 4 maestro-1.2.0/maestro/NEWS.md | 23 maestro-1.2.0/maestro/R/MaestroPipeline.R | 155 ++++ maestro-1.2.0/maestro/R/MaestroPipelineList.R | 340 +++++++++- maestro-1.2.0/maestro/R/MaestroSchedule.R | 45 - maestro-1.2.0/maestro/R/build_schedule.R | 39 - maestro-1.2.0/maestro/R/build_schedule_entry.R | 84 +- maestro-1.2.0/maestro/R/get_labels.R |only maestro-1.2.0/maestro/R/get_network.R | 1 maestro-1.2.0/maestro/R/maestro_tags.R | 66 + maestro-1.2.0/maestro/R/roxy_maestro.R | 41 + maestro-1.2.0/maestro/build/vignette.rds |binary maestro-1.2.0/maestro/inst/doc/maestro-1-quick-start.html | 2 maestro-1.2.0/maestro/inst/doc/maestro-3-advanced-scheduling.html | 6 maestro-1.2.0/maestro/inst/doc/maestro-4-directed-acyclic-graphs.R | 3 maestro-1.2.0/maestro/inst/doc/maestro-4-directed-acyclic-graphs.Rmd | 5 maestro-1.2.0/maestro/inst/doc/maestro-4-directed-acyclic-graphs.html | 84 +- maestro-1.2.0/maestro/inst/doc/maestro-4b-directed-acyclic-graphs.R |only maestro-1.2.0/maestro/inst/doc/maestro-4b-directed-acyclic-graphs.Rmd |only maestro-1.2.0/maestro/inst/doc/maestro-4b-directed-acyclic-graphs.html |only maestro-1.2.0/maestro/inst/doc/maestro-5-logging.html | 56 - maestro-1.2.0/maestro/inst/doc/maestro-7-tag-reference.html | 30 maestro-1.2.0/maestro/inst/doc/maestro-7-tag-reference.qmd | 42 + maestro-1.2.0/maestro/inst/doc/maestro-8-conditionals.html | 34 - maestro-1.2.0/maestro/man/MaestroPipeline.Rd | 169 ++++ maestro-1.2.0/maestro/man/MaestroPipelineList.Rd | 42 + maestro-1.2.0/maestro/man/MaestroSchedule.Rd | 14 maestro-1.2.0/maestro/man/build_schedule.Rd | 6 maestro-1.2.0/maestro/man/get_labels.Rd |only maestro-1.2.0/maestro/man/get_network.Rd | 3 maestro-1.2.0/maestro/man/maestro_tags.Rd | 70 ++ maestro-1.2.0/maestro/tests/testthat/_snaps/fan-in-collect.md |only maestro-1.2.0/maestro/tests/testthat/_snaps/fanout.md |only maestro-1.2.0/maestro/tests/testthat/_snaps/labels.md |only maestro-1.2.0/maestro/tests/testthat/_snaps/multicore.md | 42 + maestro-1.2.0/maestro/tests/testthat/test-build_schedule_entry.R | 52 + maestro-1.2.0/maestro/tests/testthat/test-fan-in-collect.R |only maestro-1.2.0/maestro/tests/testthat/test-fanout.R |only maestro-1.2.0/maestro/tests/testthat/test-labels.R |only maestro-1.2.0/maestro/tests/testthat/test-multicore.R | 87 ++ maestro-1.2.0/maestro/tests/testthat/test-roclets.R | 4 maestro-1.2.0/maestro/tests/testthat/test_pipelines_fan_in |only maestro-1.2.0/maestro/tests/testthat/test_pipelines_fan_in_chained |only maestro-1.2.0/maestro/tests/testthat/test_pipelines_fan_out |only maestro-1.2.0/maestro/tests/testthat/test_pipelines_fan_out_collect |only maestro-1.2.0/maestro/vignettes/maestro-4-directed-acyclic-graphs.Rmd | 5 maestro-1.2.0/maestro/vignettes/maestro-4b-directed-acyclic-graphs.Rmd |only maestro-1.2.0/maestro/vignettes/maestro-7-tag-reference.qmd | 42 + 53 files changed, 1434 insertions(+), 257 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph] ,
Finnish Biodiversity Information Facility [cph] ,
William K. Morris [aut, cre]
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.9.14 dated 2026-04-17 and 0.10.0 dated 2026-07-02
finbif-0.10.0/finbif/DESCRIPTION | 11 finbif-0.10.0/finbif/MD5 | 159 finbif-0.10.0/finbif/NAMESPACE | 12 finbif-0.10.0/finbif/NEWS.md | 598 - finbif-0.10.0/finbif/R/api_get.R | 40 finbif-0.10.0/finbif/R/dates.R | 2 finbif-0.10.0/finbif/R/finbif_check_taxa.R | 8 finbif-0.10.0/finbif/R/finbif_clear_cache.R | 4 finbif-0.10.0/finbif/R/finbif_collections.R | 103 finbif-0.10.0/finbif/R/finbif_informal_groups.R | 15 finbif-0.10.0/finbif/R/finbif_metadata.R | 15 finbif-0.10.0/finbif/R/finbif_occurrence.R | 98 finbif-0.10.0/finbif/R/finbif_occurrence_load.R | 99 finbif-0.10.0/finbif/R/finbif_records.R | 31 finbif-0.10.0/finbif/R/finbif_request_token.R | 4 finbif-0.10.0/finbif/R/finbif_taxa.R | 3 finbif-0.10.0/finbif/R/finbif_update_cache.R | 4 finbif-0.10.0/finbif/R/methods.R | 4 finbif-0.10.0/finbif/R/sysdata.R | 60 finbif-0.10.0/finbif/R/sysdata.rda |binary finbif-0.10.0/finbif/R/utils.R | 43 finbif-0.10.0/finbif/R/variables.R | 217 finbif-0.10.0/finbif/R/zzz.R | 30 finbif-0.10.0/finbif/README.md | 2 finbif-0.10.0/finbif/build/vignette.rds |binary finbif-0.10.0/finbif/inst/doc/finbif.Rmd | 209 finbif-0.10.0/finbif/inst/doc/finbif.html | 271 finbif-0.10.0/finbif/inst/doc/v02_occurrence_data.Rmd | 352 finbif-0.10.0/finbif/inst/doc/v02_occurrence_data.html | 336 finbif-0.10.0/finbif/inst/doc/v03_selecting_variables.Rmd | 210 finbif-0.10.0/finbif/inst/doc/v03_selecting_variables.html | 202 finbif-0.10.0/finbif/inst/doc/v04_metadata.Rmd | 253 finbif-0.10.0/finbif/inst/doc/v04_metadata.html | 255 finbif-0.10.0/finbif/inst/doc/v05_filtering.Rmd | 449 - finbif-0.10.0/finbif/inst/doc/v05_filtering.html | 413 finbif-0.10.0/finbif/man/finbif-package.Rd | 5 finbif-0.10.0/finbif/man/finbif_clear_cache.Rd | 3 finbif-0.10.0/finbif/man/finbif_update_cache.Rd | 3 finbif-0.10.0/finbif/man/variables.Rd | 217 finbif-0.10.0/finbif/tests/fixtures/finbif_cache_db_timeout.yml | 28 finbif-0.10.0/finbif/tests/fixtures/finbif_cache_file_timeout.yml | 28 finbif-0.10.0/finbif/tests/fixtures/finbif_cache_timeout.yml | 28 finbif-0.10.0/finbif/tests/fixtures/finbif_check_taxa.yml | 8 finbif-0.10.0/finbif/tests/fixtures/finbif_collections.yml | 3238 +++++-- finbif-0.10.0/finbif/tests/fixtures/finbif_informal_groups.yml | 4 finbif-0.10.0/finbif/tests/fixtures/finbif_last_mod1.yml | 6 finbif-0.10.0/finbif/tests/fixtures/finbif_last_mod2.yml | 6 finbif-0.10.0/finbif/tests/fixtures/finbif_last_mod3.yml | 6 finbif-0.10.0/finbif/tests/fixtures/finbif_metadata.yml | 840 +- finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence.yml | 4183 ++++++---- finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence_aggregate.yml | 3321 +++++-- finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence_api_error.yml | 4 finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence_compute_var_from_id_zero_rows.yml | 3264 +++++-- finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence_dates.yml | 3298 +++++-- finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence_load.yml | 370 finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence_print.yml | 18 finbif-0.10.0/finbif/tests/fixtures/finbif_occurrence_select_local_area.yml | 6 finbif-0.10.0/finbif/tests/fixtures/finbif_taxa.yml | 8 finbif-0.10.0/finbif/tests/testthat/_snaps/caching.md | 93 finbif-0.10.0/finbif/tests/testthat/_snaps/finbif_collections.md | 98 finbif-0.10.0/finbif/tests/testthat/_snaps/finbif_metadata.md | 29 finbif-0.10.0/finbif/tests/testthat/_snaps/finbif_occurrence.md | 160 finbif-0.10.0/finbif/tests/testthat/_snaps/finbif_occurrence_load.md | 500 - finbif-0.10.0/finbif/tests/testthat/laji-data-new-col.tsv | 2 finbif-0.10.0/finbif/tests/testthat/laji-data-pap.tsv | 2 finbif-0.10.0/finbif/tests/testthat/laji-data.tsv | 2 finbif-0.10.0/finbif/tests/testthat/test-finbif_check_taxa.R | 17 finbif-0.10.0/finbif/tests/testthat/test-finbif_collections.R | 2 finbif-0.10.0/finbif/tests/testthat/test-finbif_informal_groups.R | 4 finbif-0.10.0/finbif/tests/testthat/test-finbif_metadata.R | 4 finbif-0.10.0/finbif/tests/testthat/test-finbif_occurrence.R | 63 finbif-0.10.0/finbif/tests/testthat/test-finbif_occurrence_load.R | 13 finbif-0.10.0/finbif/tests/testthat/test-finbif_request_token.R | 11 finbif-0.10.0/finbif/tests/testthat/test-finbif_taxa.R | 13 finbif-0.10.0/finbif/tests/testthat/test-to_dwc.R | 6 finbif-0.10.0/finbif/vignettes/finbif.Rmd | 209 finbif-0.10.0/finbif/vignettes/v02_occurrence_data.Rmd | 352 finbif-0.10.0/finbif/vignettes/v03_selecting_variables.Rmd | 210 finbif-0.10.0/finbif/vignettes/v04_metadata.Rmd | 253 finbif-0.10.0/finbif/vignettes/v05_filtering.Rmd | 449 - finbif-0.9.14/finbif/tests/testthat/test-zzz.R |only 81 files changed, 16168 insertions(+), 9728 deletions(-)
Title: Explore Catálogo Taxônomico da Fauna do Brasil Database
Description: A collection of functions designed to retrieve, filter and spatialize data from the Catálogo Taxônomico da Fauna do Brasil. For more information about the dataset, please visit <https://fauna.jbrj.gov.br/fauna/listaBrasil/>.
Author: Weverton Trindade [aut, cre]
Maintainer: Weverton Trindade <wevertonf1993@gmail.com>
Diff between faunabr versions 1.0.1 dated 2026-04-19 and 1.1.0 dated 2026-07-02
DESCRIPTION | 6 MD5 | 25 - NAMESPACE | 7 NEWS.md | 6 R/data.R | 2 R/fauna_discrepancies.R | 87 +++- R/get_faunabr.R | 2 R/globals.R |only R/helpers.R | 786 +++++++++++++++++++++++++++------------------ R/load_faunabr.R | 8 R/merge_data.R |only man/fauna_discrepancies.Rd | 1 man/load_faunabr.Rd | 6 man/merge_data.Rd |only man/occurrences.Rd | 2 15 files changed, 570 insertions(+), 368 deletions(-)
Title: R Interface to 'DuckDB' Database with Spatial Extension
Description: Fast and memory-efficient functions to analyze and manipulate large
spatial datasets. It leverages the fast analytical
capabilities of ‘DuckDB’ and its spatial extension (see
<https://duckdb.org/docs/stable/core_extensions/spatial/overview>)
while maintaining compatibility with R’s spatial data ecosystem to
work with spatial vector data.
Author: Adrian Cidre Gonzalez [aut, cre] ,
Egor Kotov [aut] ,
Rafael H. M. Pereira [aut]
Maintainer: Adrian Cidre Gonzalez <adrian.cidre@gmail.com>
Diff between duckspatial versions 1.1.2 dated 2026-06-22 and 1.2.0 dated 2026-07-02
DESCRIPTION | 21 - MD5 | 82 ++++--- NAMESPACE | 14 + NEWS.md | 40 +++ R/db_extension.R | 184 +++++++++++----- R/ddbs_geom_conversion.R | 314 +++++++++++++++++++++++++++- R/ddbs_mvt.R |only R/ddbs_ops_unary.R | 176 +++++++++++++++ R/ddbs_ops_unary_line.R | 55 ++++ R/ddbs_queries.R | 36 +++ R/ddbs_templates.R | 150 +++++++++++++ R/ddbs_union.R | 152 +++++++++++++ R/utils_not_exported.R | 75 ++++++ R/zzz.R | 2 inst/doc/aw_interpolation.R | 10 inst/doc/aw_interpolation.html | 4 inst/doc/aw_interpolation.qmd | 10 inst/doc/benchmark.html | 4 inst/doc/duckspatial.R | 10 inst/doc/duckspatial.html | 12 - inst/doc/duckspatial.qmd | 10 inst/doc/spatial_joins.R | 10 inst/doc/spatial_joins.html | 4 inst/doc/spatial_joins.qmd | 10 man/ddbs_as_format.Rd | 26 ++ man/ddbs_as_mvt_geom.Rd |only man/ddbs_extension_info.Rd |only man/ddbs_geom_from.Rd |only man/ddbs_get_npoints.Rd | 20 + man/ddbs_install.Rd | 20 + man/ddbs_intersection_agg.Rd |only man/ddbs_line_node.Rd |only man/ddbs_normalize.Rd |only man/ddbs_reduce_precision.Rd |only man/ddbs_reverse.Rd |only man/ddbs_write_mbtiles.Rd |only man/duckspatial-package.Rd | 2 tests/testthat/test-db_extension.R | 66 +++++ tests/testthat/test-ddbs_geom_conversion.R | 245 +++++++++++++++++++++ tests/testthat/test-ddbs_intersection_agg.R |only tests/testthat/test-ddbs_macros.R | 70 ++++-- tests/testthat/test-ddbs_mvt.R |only tests/testthat/test-ddbs_ops_unary.R | 226 ++++++++++++++++++++ tests/testthat/test-ddbs_ops_unary_line.R | 81 +++++++ tests/testthat/test-ddbs_queries.R | 238 +++++++++++++++++++++ vignettes/aw_interpolation.qmd | 10 vignettes/duckspatial.qmd | 10 vignettes/spatial_joins.qmd | 10 48 files changed, 2258 insertions(+), 151 deletions(-)
Title: High-Level Modeling Functions with 'torch'
Description: Provides high-level modeling functions to define and train
models using the 'torch' R package. Models include linear, logistic,
and multinomial regression as well as multilayer perceptrons.
Author: Max Kuhn [aut, cre] ,
Daniel Falbel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between brulee versions 1.0.0 dated 2026-06-17 and 1.1.0 dated 2026-07-02
DESCRIPTION | 10 MD5 | 228 +++++++++----- NAMESPACE | 11 NEWS.md | 19 + R/0_utils.R | 6 R/aaa.R | 46 ++ R/autoint-fit.R | 190 +++++++++--- R/autoint-predict.R | 4 R/autoplot.R | 4 R/brulee-package.R | 1 R/checks.R | 18 - R/chronos2-fit.R | 34 +- R/chronos2-misc.R | 4 R/chronos2-predict.R | 257 ++++++---------- R/coef.R | 11 R/linear_reg-fit.R | 40 +- R/linear_reg-predict.R | 8 R/logistic_reg-fit.R | 46 +- R/logistic_reg-predict.R | 8 R/mlp-fit.R | 58 +-- R/mlp-predict.R | 15 R/multinomial_reg-fit.R | 44 +- R/multinomial_reg-predict.R | 8 R/outcome_processing.R | 6 R/resnet-fit.R | 27 + R/resnet-predict.R | 6 R/rln-fit.R | 29 + R/rln-predict.R | 6 R/saint-fit.R | 233 ++++++++++---- R/saint-predict.R | 4 R/summary.R | 28 + R/tabicl-attention.R |only R/tabicl-download.R |only R/tabicl-embedding.R |only R/tabicl-ensemble.R |only R/tabicl-fit.R |only R/tabicl-interaction.R |only R/tabicl-layers.R |only R/tabicl-learning.R |only R/tabicl-load.R |only R/tabicl-model.R |only R/tabicl-predict.R |only R/tabicl-preprocess.R |only R/tabicl-quantile.R |only R/tabicl-rope.R |only R/training_loop.R | 164 +++++++--- R/validation.R | 22 - README.md | 89 ++--- inst/WORDLIST | 14 inst/check_stages.R |only man/brulee-autoplot.Rd | 4 man/brulee-coefs.Rd | 4 man/brulee_auto_int.Rd | 26 + man/brulee_chronos.Rd | 20 - man/brulee_linear_reg.Rd | 17 - man/brulee_logistic_reg.Rd | 17 - man/brulee_mlp.Rd | 19 - man/brulee_multinomial_reg.Rd | 15 man/brulee_resnet.Rd | 17 - man/brulee_rln.Rd | 15 man/brulee_saint.Rd | 40 +- man/brulee_tab_icl.Rd |only man/predict.brulee_auto_int.Rd | 2 man/predict.brulee_chronos.Rd | 54 +-- man/predict.brulee_linear_reg.Rd | 4 man/predict.brulee_logistic_reg.Rd | 4 man/predict.brulee_mlp.Rd | 4 man/predict.brulee_multinomial_reg.Rd | 4 man/predict.brulee_resnet.Rd | 4 man/predict.brulee_rln.Rd | 4 man/predict.brulee_saint.Rd | 2 man/predict.brulee_tab_icl.Rd |only man/summary.brulee.Rd | 2 man/tab_icl_download_weights.Rd |only tests/testthat/_snaps/autoint.md | 16 + tests/testthat/_snaps/chronos2-predict.md | 64 ---- tests/testthat/_snaps/mlp-binary.md |only tests/testthat/_snaps/saint.md | 26 + tests/testthat/_snaps/tabicl-download.md |only tests/testthat/_snaps/tabicl-fit.md |only tests/testthat/_snaps/tabicl-load.md |only tests/testthat/_snaps/tabicl-preprocess.md |only tests/testthat/fixtures |only tests/testthat/helper-chronos2.R | 6 tests/testthat/helper-tabicl.R |only tests/testthat/setup.R |only tests/testthat/test-autoint.R | 75 ++++ tests/testthat/test-chronos2-fit.R | 5 tests/testthat/test-chronos2-predict.R | 456 +++++++++-------------------- tests/testthat/test-device-support.R | 2 tests/testthat/test-linear_reg-fit.R | 87 +++++ tests/testthat/test-logistic_reg-fit.R | 32 -- tests/testthat/test-mlp-binary.R | 72 +++- tests/testthat/test-mlp-multinomial.R | 28 - tests/testthat/test-mlp-regression.R | 54 ++- tests/testthat/test-multinomial_reg-fit.R | 40 +- tests/testthat/test-penalty-integration.R | 16 - tests/testthat/test-penalty.R | 10 tests/testthat/test-saint.R | 75 ++++ tests/testthat/test-schedulers.R | 2 tests/testthat/test-tabicl-attention.R |only tests/testthat/test-tabicl-download.R |only tests/testthat/test-tabicl-embedding.R |only tests/testthat/test-tabicl-ensemble.R |only tests/testthat/test-tabicl-fit.R |only tests/testthat/test-tabicl-interaction.R |only tests/testthat/test-tabicl-learning.R |only tests/testthat/test-tabicl-load.R |only tests/testthat/test-tabicl-preprocess.R |only tests/testthat/test-tabicl-quantile.R |only tests/testthat/test-tabicl-rope.R |only 111 files changed, 1840 insertions(+), 1202 deletions(-)
Title: A 'C++20' API for R
Description: A header-only 'C++20' API for manipulating R data structures
from 'C++'. Provides 'C++20' concepts specific to R, custom scalar and
vector classes with built-in NA handling, automatic object protection,
'SIMD' (single-instruction-multiple-data), parallelisation, and a
streamlined system for registering 'C++' functions, including
templates, to R. Full API reference and documentation are available at
<https://nicchr.github.io/cppally/>.
Author: Nick Christofides [aut, cre, cph] ,
Martin Leitner-Ankerl [cph] ,
Malte Skarupke [cph] ,
Posit Software, PBC [cph]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cppally versions 0.1.0 dated 2026-04-28 and 1.0.0 dated 2026-07-02
cppally-0.1.0/cppally/inst/include/cppally/r_coerce_impl.h |only cppally-0.1.0/cppally/inst/include/cppally/r_scalar_methods.h |only cppally-0.1.0/cppally/inst/include/cppally/sugar/r_copy.h |only cppally-0.1.0/cppally/inst/include/cppally/sugar/r_identical.h |only cppally-0.1.0/cppally/inst/include/cppally/sugar/r_vec_methods.h |only cppally-1.0.0/cppally/DESCRIPTION | 8 cppally-1.0.0/cppally/MD5 | 159 - cppally-1.0.0/cppally/NAMESPACE | 3 cppally-1.0.0/cppally/NEWS.md | 126 - cppally-1.0.0/cppally/R/cpp_source.R | 763 +++--- cppally-1.0.0/cppally/R/register.R | 81 cppally-1.0.0/cppally/R/use_check_data_frames.R |only cppally-1.0.0/cppally/R/use_check_factors.R |only cppally-1.0.0/cppally/R/use_copy_on_modify.R |only cppally-1.0.0/cppally/R/use_cppally.R | 221 - cppally-1.0.0/cppally/README.md | 221 + cppally-1.0.0/cppally/build/vignette.rds |binary cppally-1.0.0/cppally/inst/COPYRIGHTS | 32 cppally-1.0.0/cppally/inst/doc/cppally.R | 480 +++ cppally-1.0.0/cppally/inst/doc/cppally.Rmd | 918 +++++-- cppally-1.0.0/cppally/inst/doc/cppally.html | 1252 ++++++---- cppally-1.0.0/cppally/inst/doc/functionals.R |only cppally-1.0.0/cppally/inst/doc/functionals.Rmd |only cppally-1.0.0/cppally/inst/doc/functionals.html |only cppally-1.0.0/cppally/inst/doc/protection.R | 8 cppally-1.0.0/cppally/inst/doc/protection.Rmd | 793 +++--- cppally-1.0.0/cppally/inst/doc/protection.html | 64 cppally-1.0.0/cppally/inst/doc/vector_name_hashing.R |only cppally-1.0.0/cppally/inst/doc/vector_name_hashing.Rmd |only cppally-1.0.0/cppally/inst/doc/vector_name_hashing.html |only cppally-1.0.0/cppally/inst/include/cppally.hpp | 22 cppally-1.0.0/cppally/inst/include/cppally/r_attrs.h | 99 cppally-1.0.0/cppally/inst/include/cppally/r_coerce.h | 416 +-- cppally-1.0.0/cppally/inst/include/cppally/r_coerce_scalars.h |only cppally-1.0.0/cppally/inst/include/cppally/r_concepts.h | 239 + cppally-1.0.0/cppally/inst/include/cppally/r_copy.h |only cppally-1.0.0/cppally/inst/include/cppally/r_cplx.h | 12 cppally-1.0.0/cppally/inst/include/cppally/r_date.h | 4 cppally-1.0.0/cppally/inst/include/cppally/r_dbl.h | 6 cppally-1.0.0/cppally/inst/include/cppally/r_df.h | 288 +- cppally-1.0.0/cppally/inst/include/cppally/r_df_methods.h |only cppally-1.0.0/cppally/inst/include/cppally/r_dispatch.h | 28 cppally-1.0.0/cppally/inst/include/cppally/r_factor.h | 434 ++- cppally-1.0.0/cppally/inst/include/cppally/r_hash_names.h |only cppally-1.0.0/cppally/inst/include/cppally/r_identical.h |only cppally-1.0.0/cppally/inst/include/cppally/r_int.h | 6 cppally-1.0.0/cppally/inst/include/cppally/r_int64.h | 6 cppally-1.0.0/cppally/inst/include/cppally/r_length.h |only cppally-1.0.0/cppally/inst/include/cppally/r_lgl.h | 17 cppally-1.0.0/cppally/inst/include/cppally/r_list_helpers.h | 50 cppally-1.0.0/cppally/inst/include/cppally/r_nas.h | 101 cppally-1.0.0/cppally/inst/include/cppally/r_pmap.h |only cppally-1.0.0/cppally/inst/include/cppally/r_protect.h | 13 cppally-1.0.0/cppally/inst/include/cppally/r_psxct.h | 8 cppally-1.0.0/cppally/inst/include/cppally/r_raw.h | 6 cppally-1.0.0/cppally/inst/include/cppally/r_scalar_ops.h |only cppally-1.0.0/cppally/inst/include/cppally/r_setup.h | 9 cppally-1.0.0/cppally/inst/include/cppally/r_sexp.h | 60 cppally-1.0.0/cppally/inst/include/cppally/r_sexp_types.h | 9 cppally-1.0.0/cppally/inst/include/cppally/r_str.h | 30 cppally-1.0.0/cppally/inst/include/cppally/r_sym.h | 12 cppally-1.0.0/cppally/inst/include/cppally/r_types.h | 50 cppally-1.0.0/cppally/inst/include/cppally/r_utils.h | 18 cppally-1.0.0/cppally/inst/include/cppally/r_vec.h | 760 ++++-- cppally-1.0.0/cppally/inst/include/cppally/r_vec_ops.h |only cppally-1.0.0/cppally/inst/include/cppally/r_vec_utils.h | 70 cppally-1.0.0/cppally/inst/include/cppally/r_visit.h | 369 ++ cppally-1.0.0/cppally/inst/include/cppally/sugar/r_combine.h |only cppally-1.0.0/cppally/inst/include/cppally/sugar/r_equal.h |only cppally-1.0.0/cppally/inst/include/cppally/sugar/r_groups.h | 221 + cppally-1.0.0/cppally/inst/include/cppally/sugar/r_hash.h | 53 cppally-1.0.0/cppally/inst/include/cppally/sugar/r_list_pmap.h |only cppally-1.0.0/cppally/inst/include/cppally/sugar/r_make_vec.h | 15 cppally-1.0.0/cppally/inst/include/cppally/sugar/r_match.h | 144 + cppally-1.0.0/cppally/inst/include/cppally/sugar/r_math.h | 310 +- cppally-1.0.0/cppally/inst/include/cppally/sugar/r_n_unique.h | 55 cppally-1.0.0/cppally/inst/include/cppally/sugar/r_paste.h |only cppally-1.0.0/cppally/inst/include/cppally/sugar/r_recycle.h | 3 cppally-1.0.0/cppally/inst/include/cppally/sugar/r_rep.h |only cppally-1.0.0/cppally/inst/include/cppally/sugar/r_replace_at.h |only cppally-1.0.0/cppally/inst/include/cppally/sugar/r_seq.h | 133 - cppally-1.0.0/cppally/inst/include/cppally/sugar/r_sexp_methods.h |only cppally-1.0.0/cppally/inst/include/cppally/sugar/r_sort.h | 350 +- cppally-1.0.0/cppally/inst/include/cppally/sugar/r_stats.h | 302 -- cppally-1.0.0/cppally/inst/include/cppally/sugar/r_subset.h | 257 -- cppally-1.0.0/cppally/inst/include/cppally/sugar/r_unique.h | 50 cppally-1.0.0/cppally/inst/include/cppally_light.hpp | 5 cppally-1.0.0/cppally/inst/include/ska_sort/ska_sort.hpp | 123 cppally-1.0.0/cppally/man/cpp_register.Rd | 3 cppally-1.0.0/cppally/man/cpp_source.Rd | 70 cppally-1.0.0/cppally/man/cppally-package.Rd | 5 cppally-1.0.0/cppally/man/use_check_data_frames.Rd |only cppally-1.0.0/cppally/man/use_check_factors.Rd |only cppally-1.0.0/cppally/man/use_copy_on_modify.Rd |only cppally-1.0.0/cppally/vignettes/cppally.Rmd | 918 +++++-- cppally-1.0.0/cppally/vignettes/functionals.Rmd |only cppally-1.0.0/cppally/vignettes/protection.Rmd | 793 +++--- cppally-1.0.0/cppally/vignettes/vector_name_hashing.Rmd |only 98 files changed, 7644 insertions(+), 4437 deletions(-)
Title: High-Dimensional Methods via Generalised Singular Decomposition
Description: Construct a Canonical Variate Analysis Biplot via the Generalised Singular Value Decomposition, for cases when the number of samples is less than the number of variables. For more information on these biplots, see Ganey, R., & Gardner-Lubbe, S. (2026) <doi:10.1007/s10260-025-00831-y>.
Author: Raeesa Ganey [aut, cre]
Maintainer: Raeesa Ganey <Raeesa.ganey@wits.ac.za>
Diff between wideRhino versions 1.0.2 dated 2025-06-11 and 1.2.0 dated 2026-07-02
wideRhino-1.0.2/wideRhino/R/CVAbiplot.R |only wideRhino-1.2.0/wideRhino/DESCRIPTION | 11 wideRhino-1.2.0/wideRhino/MD5 | 24 - wideRhino-1.2.0/wideRhino/NEWS.md | 5 wideRhino-1.2.0/wideRhino/R/CVAgsvd.R |only wideRhino-1.2.0/wideRhino/R/axes_coordinates.R | 9 wideRhino-1.2.0/wideRhino/R/globals.R | 3 wideRhino-1.2.0/wideRhino/R/gsvd.R | 196 +++++++++++- wideRhino-1.2.0/wideRhino/R/plot.R | 96 ++--- wideRhino-1.2.0/wideRhino/README.md | 12 wideRhino-1.2.0/wideRhino/man/CVAbiplot.Rd | 14 wideRhino-1.2.0/wideRhino/man/CVAgsvd.Rd | 8 wideRhino-1.2.0/wideRhino/man/figures/README-example1-1.png |binary wideRhino-1.2.0/wideRhino/man/figures/README-example2-1.png |binary 14 files changed, 278 insertions(+), 100 deletions(-)
Title: Robust Generalized Linear Models (GLM) using Mixtures
Description: Robust generalized linear models (GLM) using a mixture method, as described in Beath (2018) <doi:10.1080/02664763.2017.1414164>. This assumes that the data are a mixture of standard observations, being a generalised linear model, and outlier observations from an overdispersed generalized linear model. The overdispersed linear model is obtained by including a normally distributed random effect in the linear predictor of the generalized linear model.
Author: Ken Beath [aut, cre]
Maintainer: Ken Beath <ken@kjbeath.id.au>
Diff between robmixglm versions 1.2-5 dated 2025-10-31 and 1.2-8 dated 2026-07-02
DESCRIPTION | 11 - MD5 | 32 +-- NAMESPACE | 10 - R/RcppExports.R | 38 ++-- R/binomial.fit.robmixglm.R | 372 ++++++++++++++++++++--------------------- R/gamma.fit.robmixglm.R | 166 +++++++++--------- R/gaussian.fit.robmixglm.R | 188 ++++++++++---------- R/nbinom.fit.robmixglm.R | 324 +++++++++++++++++------------------ R/outlierTest.robmixglm.R | 10 - R/poisson.fit.robmixglm.R | 244 +++++++++++++++----------- R/robmixglm.R | 12 - R/truncpoisson.fit.robmixglm.R | 255 ++++++++++++++-------------- build/vignette.rds |binary inst/NEWS | 14 + inst/doc/robmixglm-package.pdf |binary man/outlierTest.robmixglm.Rd | 6 man/robmixglm.Rd | 6 17 files changed, 888 insertions(+), 800 deletions(-)
Title: Bayesian Power Analysis Using 'brms' and 'INLA'
Description: Provides tools for Bayesian power analysis and assurance calculations using the statistical frameworks of 'brms' and 'INLA'. Includes simulation-based approaches, support for multiple decision rules (direction, threshold, ROPE), sequential designs, and visualisation helpers. Methods are based on Kruschke (2014, ISBN:9780124058880) "Doing Bayesian Data Analysis: A Tutorial with R, JAGS, and Stan", O'Hagan & Stevens (2001) <doi:10.1177/0272989X0102100307> "Bayesian Assessment of Sample Size for Clinical Trials of Cost-Effectiveness", Kruschke (2018) <doi:10.1177/2515245918771304> "Rejecting or Accepting Parameter Values in Bayesian Estimation", Rue et al. (2009) <doi:10.1111/j.1467-9868.2008.00700.x> "Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations", and Bürkner (2017) <doi:10.18637/jss.v080.i01> "brms: An R Package for Bayesian Multilevel Models using Stan".
Author: Tony Myers [aut, cre]
Maintainer: Tony Myers <admyers@aol.com>
Diff between powerbrmsINLA versions 1.2.0 dated 2026-06-02 and 1.3.0 dated 2026-07-02
powerbrmsINLA-1.2.0/powerbrmsINLA/R/plotting-helpers.R |only powerbrmsINLA-1.2.0/powerbrmsINLA/tests/testthat/sequencial-test.R |only powerbrmsINLA-1.2.0/powerbrmsINLA/tests/testthat/set-up.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/DESCRIPTION | 10 powerbrmsINLA-1.3.0/powerbrmsINLA/MD5 | 67 ++-- powerbrmsINLA-1.3.0/powerbrmsINLA/NAMESPACE | 8 powerbrmsINLA-1.3.0/powerbrmsINLA/NEWS.md | 86 +++++ powerbrmsINLA-1.3.0/powerbrmsINLA/R/compute-assurance.R | 2 powerbrmsINLA-1.3.0/powerbrmsINLA/R/decision-helpers.R | 23 + powerbrmsINLA-1.3.0/powerbrmsINLA/R/engine-main.R | 50 ++- powerbrmsINLA-1.3.0/powerbrmsINLA/R/engine-sequential-trial.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/R/engine-sequential.R | 37 +- powerbrmsINLA-1.3.0/powerbrmsINLA/R/engine-two-stage.R | 9 powerbrmsINLA-1.3.0/powerbrmsINLA/R/globals.R | 2 powerbrmsINLA-1.3.0/powerbrmsINLA/R/plotting-power.R | 6 powerbrmsINLA-1.3.0/powerbrmsINLA/R/sequential-analysis.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/R/utils-helpers.R | 6 powerbrmsINLA-1.3.0/powerbrmsINLA/README.md | 154 +++++++-- powerbrmsINLA-1.3.0/powerbrmsINLA/build/partial.rdb |binary powerbrmsINLA-1.3.0/powerbrmsINLA/build/vignette.rds |binary powerbrmsINLA-1.3.0/powerbrmsINLA/inst/doc/validation.R | 164 +++++----- powerbrmsINLA-1.3.0/powerbrmsINLA/inst/doc/validation.html | 3 powerbrmsINLA-1.3.0/powerbrmsINLA/man/brms_inla_power_sequential.Rd | 10 powerbrmsINLA-1.3.0/powerbrmsINLA/man/brms_inla_power_two_stage.Rd | 4 powerbrmsINLA-1.3.0/powerbrmsINLA/man/brms_inla_sequential_trial.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/dot-add_contour_lines.Rd | 21 - powerbrmsINLA-1.3.0/powerbrmsINLA/man/dot-geom_line_lw.Rd | 10 powerbrmsINLA-1.3.0/powerbrmsINLA/man/dot-geom_point_lw.Rd | 10 powerbrmsINLA-1.3.0/powerbrmsINLA/man/dot-gg_line_arg.Rd | 14 powerbrmsINLA-1.3.0/powerbrmsINLA/man/dot-plot_decision_assurance_curve_from_summary.Rd | 5 powerbrmsINLA-1.3.0/powerbrmsINLA/man/dot-sample_design_prior.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/dot-seq_design_fingerprint.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/plot_sequential_monitor.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/print.powerbrmsINLA_seq_design.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/print.powerbrmsINLA_seq_monitor.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/print.powerbrmsINLA_seq_trial.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/sequential_analysis.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/man/sequential_design.Rd |only powerbrmsINLA-1.3.0/powerbrmsINLA/tests/testthat/setup.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/tests/testthat/test-regression-effectname-decide.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/tests/testthat/test-sequential-analysis.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/tests/testthat/test-sequential-stopping.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/tests/testthat/test-sequential-trial.R |only powerbrmsINLA-1.3.0/powerbrmsINLA/tests/testthat/test-validation-bayesassurance.R | 104 ------ 44 files changed, 479 insertions(+), 326 deletions(-)
Title: Calculate the Open Bodem Index (OBI) Score
Description: The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in The Netherlands and the sustainability of the current agricultural practices.
The OBI score is based on four main criteria: chemical, physical, biological and management, which consist of more than 21 indicators.
By providing results of a soil analysis and management info the 'OBIC' package can be use to calculate he scores, indicators and derivatives that are used by the OBI.
More information about the Open Bodem Index can be found at <https://openbodemindex.nl/>.
Author: Sven Verweij [aut, cre] ,
Gerard Ros [aut] ,
Yuki Fujita [aut] ,
Wilbrand Hendrik Riechelman [aut] ,
Kees van den Dool [aut] ,
Job de Pater [ctb],
Nutrienten Managment Instituut [cph]
Maintainer: Sven Verweij <sven.verweij@nmi-agro.nl>
Diff between OBIC versions 4.2.3 dated 2026-02-11 and 4.3.0 dated 2026-07-02
DESCRIPTION | 8 +- MD5 | 22 +++--- NEWS.md | 15 ++++ R/nretention.r | 2 build/vignette.rds |binary data/crops.obic.rda |binary inst/doc/description-of-the-columns.html | 4 - inst/doc/obic_introduction.html | 100 +++++++++++++------------------ inst/doc/obic_score_aggregation.html | 24 +++---- inst/doc/obic_water_functions.html | 35 +++++----- inst/doc/obic_workability.html | 11 +-- man/crops.obic.Rd | 2 12 files changed, 111 insertions(+), 112 deletions(-)
Title: Designing Stated Preference Experiments
Description: Contemporary software commonly used to design stated preference experiments are expensive and the code is closed source. This is a free software package with an easy to use interface to make flexible stated preference experimental designs using state-of-the-art methods. For an overview of stated choice experimental design theory, see e.g., Rose, J. M. & Bliemer, M. C. J. (2014) in Hess S. & Daly. A. <doi:10.4337/9781781003152>. The package website can be accessed at <https://spdesign.edsandorf.me>. We acknowledge funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant INSPiRE (Grant agreement ID: 793163). The package features in Mariel et al. (2025) Environmental Valuation with Discrete Choice Experiments in R. (<doi:10.1007/978-3-031-89338-4>).
Author: Erlend Dancke Sandorf [aut, cre],
Danny Campbell [aut]
Maintainer: Erlend Dancke Sandorf <erlend.dancke.sandorf@nmbu.no>
Diff between spdesign versions 0.0.5 dated 2024-10-18 and 0.0.6 dated 2026-07-02
DESCRIPTION | 12 MD5 | 99 - NEWS.md | 10 R/DEPRECATED-set-defaults.R | 2 R/assertions.R | 39 R/block.R | 26 R/derive.R | 26 R/design.R | 194 ++- R/draws.R | 20 R/efficiency-criteria.R | 41 R/evaluate.R | 57 R/exclusions-and-conditions.R | 2 R/extract.R | 7 R/federov.R | 173 +- R/level-balance.R | 8 R/methods.R | 16 R/parsing.R | 96 + R/print.R | 7 R/priors.R | 27 R/probabilities.R | 4 R/random.R | 93 + R/remove.R | 2 R/rsc.R | 110 + R/xj.R | 23 R/zzz.R | 33 build/partial.rdb |binary build/vignette.rds |binary inst/doc/examples.R | 604 +++++----- inst/doc/examples.html | 243 ++-- inst/doc/syntax.Rmd | 8 inst/doc/syntax.html | 30 man/federov.Rd | 3 man/generate_design.Rd | 5 man/level_occurrences_specified.Rd |only man/random.Rd | 3 man/reexports.Rd | 2 man/rsc.Rd | 3 man/spdesign-package.Rd | 5 tests/testthat/test-assertions.R | 30 vignettes/examples/mnl-c-efficiency.R | 23 vignettes/examples/mnl-design-advanced.R | 17 vignettes/examples/mnl-design-bayesian-priors.R | 17 vignettes/examples/mnl-design-dummy-coding.R | 11 vignettes/examples/mnl-design-random-with-specified-level-occurrence.R | 11 vignettes/examples/mnl-design-with-alternative-specific-attributres.R | 23 vignettes/examples/mnl-design-with-exclusions.R | 19 vignettes/examples/mnl-design-with-interactions.R | 13 vignettes/examples/mnl-design-with-multiway-interactions.R | 13 vignettes/examples/mnl-design-with-sq-and-names.R | 21 vignettes/examples/mnl-design-with-supplied-candidate-set.R | 25 vignettes/syntax.Rmd | 8 51 files changed, 1402 insertions(+), 862 deletions(-)
Title: Statistical Pattern Recognition and daTing using Archaeological
Artefacts assemblageS
Description: Statistical pattern recognition and dating using archaeological artefacts assemblages.
Package of statistical tools for archaeology.
hclustcompro()/perioclust(): Bellanger Lise, Coulon Arthur, Husi Philippe (2021, ISBN:978-3-030-60103-4).
mapclust(): Bellanger Lise, Coulon Arthur, Husi Philippe (2021) <doi:10.1016/j.jas.2021.105431>.
seriograph(): Desachy Bruno (2004) <doi:10.3406/pica.2004.2396>.
cerardat(): Bellanger Lise, Husi Philippe (2012) <doi:10.1016/j.jas.2011.06.031>.
Author: Arthur Coulon [aut, cre],
Lise Bellanger [aut],
Philippe Husi [aut],
Bruno Desachy [ctb],
Benjamin Martineau [ctb]
Maintainer: Arthur Coulon <arthur-coulon@outlook.fr>
Diff between SPARTAAS versions 1.2.5 dated 2026-03-26 and 1.2.6 dated 2026-07-02
DESCRIPTION | 19 MD5 | 33 - NAMESPACE | 4 R/cerardat.R | 402 ++++++++++--- R/mapclust.R | 4 R/perioclust.R | 6 R/util.R | 13 R/zzz.R | 2 build/partial.rdb |binary inst/shiny-examples/hclustcompro.app/server.R | 216 ++++--- inst/shiny-examples/hclustcompro.app/ui.R | 777 +++++++++++++------------- inst/shiny-examples/map.app/server.R | 38 - man/arrangePlot.Rd |only man/cerardat.Rd | 92 +-- man/cerardat_estim_nf.Rd | 44 + man/extract_results.Rd | 15 man/plot.cerardat_obj.Rd | 81 +- man/seriograph.Rd | 45 + 18 files changed, 1062 insertions(+), 729 deletions(-)
Title: Optimize and Compress Image Files with 'reSmush.it'
Description: Optimize and compress local and online image files with the
'reSmush.it' 'API' <https://resmush.it/api/>. Process individual files
or entire directories. The 'API' is free for personal use, accepts
files smaller than 5 'MB' and supports 'PNG', 'JPEG', 'GIF', 'BMP' and
'TIFF' files.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between resmush versions 1.0.1 dated 2026-05-29 and 1.0.2 dated 2026-07-02
DESCRIPTION | 16 ++- MD5 | 70 +++++++-------- NAMESPACE | 16 +-- NEWS.md | 28 +++--- R/resmush-package.R | 12 ++ R/resmush_clean_dir.R | 40 ++++---- R/resmush_dir.R | 50 ++++++----- R/resmush_file.R | 71 +++++++-------- R/resmush_url.R | 70 +++++++-------- R/show_report.R | 18 ++-- R/sysdata.rda |binary R/utils.R | 87 ++++++++++++++----- README.md | 143 +++++++++++++++++--------------- build/vignette.rds |binary inst/REFERENCES.bib | 30 +++--- inst/WORDLIST | 55 ++++++------ inst/doc/resmush.html | 96 ++++++++++----------- inst/doc/resmush.qmd | 128 +++++++++++++++------------- inst/schemaorg.json | 6 - man/resmush-package.Rd | 17 ++- man/resmush_clean_dir.Rd | 27 ++---- man/resmush_dir.Rd | 59 +++++++------ man/resmush_file.Rd | 54 ++++++------ man/resmush_url.Rd | 61 +++++++------ man/roxygen/meta.R | 4 tests/testthat/_snaps/formats.md | 4 tests/testthat/_snaps/remush_url.md | 26 +++-- tests/testthat/_snaps/resmuh_dir.md | 2 tests/testthat/_snaps/resmush_file.md | 11 ++ tests/testthat/_snaps/show_report.md | 32 +++---- tests/testthat/test-formats.R | 2 tests/testthat/test-remush_url.R | 84 ++++++++++++------ tests/testthat/test-resmush_clean_dir.R | 2 tests/testthat/test-resmush_file.R | 84 +++++++++++------- vignettes/REFERENCES.bib | 30 +++--- vignettes/resmush.qmd | 128 +++++++++++++++------------- 36 files changed, 880 insertions(+), 683 deletions(-)
Title: Multilevel Analysis of Individual Heterogeneity and
Discriminatory Accuracy
Description: Tools for Multilevel Analysis of Individual Heterogeneity and
Discriminatory Accuracy (MAIHDA) for intersectional inequality research.
Methods are described in Merlo (2018) <doi:10.1016/j.socscimed.2017.12.026>
and Evans et al. (2018) <doi:10.1016/j.socscimed.2017.11.011>. The package
creates intersectional strata, fits multilevel MAIHDA models, estimates
variance partition coefficients, proportional change in variance, stratum
effects, and discriminatory-accuracy summaries, and provides diagnostic and
presentation plots.
Author: Hamid Bulut [aut, cre]
Maintainer: Hamid Bulut <me@hamidbulut.com>
Diff between MAIHDA versions 0.1.11 dated 2026-06-18 and 0.2.0 dated 2026-07-02
MAIHDA-0.1.11/MAIHDA/R/maihda_ternary.R |only MAIHDA-0.1.11/MAIHDA/man/compute_maihda_ternary_data.Rd |only MAIHDA-0.1.11/MAIHDA/man/maihda_ternary_plot.Rd |only MAIHDA-0.1.11/MAIHDA/man/plot.maihda_ternary.Rd |only MAIHDA-0.1.11/MAIHDA/man/plot_maihda_ternary.Rd |only MAIHDA-0.1.11/MAIHDA/man/plot_risk_vs_effect.Rd |only MAIHDA-0.1.11/MAIHDA/tests/testthat/test-maihda-ternary.R |only MAIHDA-0.2.0/MAIHDA/DESCRIPTION | 28 MAIHDA-0.2.0/MAIHDA/MD5 | 206 MAIHDA-0.2.0/MAIHDA/NAMESPACE | 15 MAIHDA-0.2.0/MAIHDA/NEWS.md | 46 MAIHDA-0.2.0/MAIHDA/R/app_modules.R | 24 MAIHDA-0.2.0/MAIHDA/R/calculate_pvc.R | 73 MAIHDA-0.2.0/MAIHDA/R/compare_maihda.R | 271 MAIHDA-0.2.0/MAIHDA/R/decompose_maihda.R | 40 MAIHDA-0.2.0/MAIHDA/R/design_weights.R | 75 MAIHDA-0.2.0/MAIHDA/R/discriminatory_accuracy.R | 164 MAIHDA-0.2.0/MAIHDA/R/fit_maihda.R | 106 MAIHDA-0.2.0/MAIHDA/R/information_criteria.R | 25 MAIHDA-0.2.0/MAIHDA/R/interactions.R | 342 - MAIHDA-0.2.0/MAIHDA/R/longitudinal.R | 22 MAIHDA-0.2.0/MAIHDA/R/maihda_table.R | 81 MAIHDA-0.2.0/MAIHDA/R/maihda_workflow.R | 364 - MAIHDA-0.2.0/MAIHDA/R/make_strata.R | 17 MAIHDA-0.2.0/MAIHDA/R/ordinal_engine.R | 96 MAIHDA-0.2.0/MAIHDA/R/plot_maihda.R | 3029 +++++----- MAIHDA-0.2.0/MAIHDA/R/plot_prediction_deviation_panels.R | 59 MAIHDA-0.2.0/MAIHDA/R/predict_maihda.R | 181 MAIHDA-0.2.0/MAIHDA/R/print_style.R |only MAIHDA-0.2.0/MAIHDA/R/run_app.R | 54 MAIHDA-0.2.0/MAIHDA/R/summary_maihda.R | 66 MAIHDA-0.2.0/MAIHDA/R/theme_maihda.R |only MAIHDA-0.2.0/MAIHDA/R/utils_maihda.R | 572 + MAIHDA-0.2.0/MAIHDA/R/vpc_response.R | 21 MAIHDA-0.2.0/MAIHDA/README.md | 60 MAIHDA-0.2.0/MAIHDA/build/vignette.rds |binary MAIHDA-0.2.0/MAIHDA/inst/doc/bayesian_sparse_maihda.html | 4 MAIHDA-0.2.0/MAIHDA/inst/doc/binary_outcomes.html | 10 MAIHDA-0.2.0/MAIHDA/inst/doc/case_study_brfss.R |only MAIHDA-0.2.0/MAIHDA/inst/doc/case_study_brfss.Rmd |only MAIHDA-0.2.0/MAIHDA/inst/doc/case_study_brfss.html |only MAIHDA-0.2.0/MAIHDA/inst/doc/cross_classified.R | 3 MAIHDA-0.2.0/MAIHDA/inst/doc/cross_classified.Rmd | 124 MAIHDA-0.2.0/MAIHDA/inst/doc/cross_classified.html | 243 MAIHDA-0.2.0/MAIHDA/inst/doc/finding_interactions.R | 7 MAIHDA-0.2.0/MAIHDA/inst/doc/finding_interactions.Rmd | 31 MAIHDA-0.2.0/MAIHDA/inst/doc/finding_interactions.html | 75 MAIHDA-0.2.0/MAIHDA/inst/doc/group_comparison.html | 63 MAIHDA-0.2.0/MAIHDA/inst/doc/interactive_app.html | 4 MAIHDA-0.2.0/MAIHDA/inst/doc/interpreting_plots.R | 5 MAIHDA-0.2.0/MAIHDA/inst/doc/interpreting_plots.Rmd | 21 MAIHDA-0.2.0/MAIHDA/inst/doc/interpreting_plots.html | 58 MAIHDA-0.2.0/MAIHDA/inst/doc/introduction.R | 19 MAIHDA-0.2.0/MAIHDA/inst/doc/introduction.Rmd | 50 MAIHDA-0.2.0/MAIHDA/inst/doc/introduction.html | 268 MAIHDA-0.2.0/MAIHDA/inst/doc/longitudinal.html | 10 MAIHDA-0.2.0/MAIHDA/inst/doc/planning_a_study.html | 4 MAIHDA-0.2.0/MAIHDA/inst/doc/reporting_results.html | 106 MAIHDA-0.2.0/MAIHDA/inst/shiny/app.R | 19 MAIHDA-0.2.0/MAIHDA/man/MAIHDA-package.Rd | 2 MAIHDA-0.2.0/MAIHDA/man/compare_maihda.Rd | 7 MAIHDA-0.2.0/MAIHDA/man/compare_maihda_groups.Rd | 22 MAIHDA-0.2.0/MAIHDA/man/fit_maihda.Rd | 29 MAIHDA-0.2.0/MAIHDA/man/maihda.Rd | 37 MAIHDA-0.2.0/MAIHDA/man/maihda_brms_ordinal_thresholds.Rd |only MAIHDA-0.2.0/MAIHDA/man/maihda_clmm_linpred.Rd | 12 MAIHDA-0.2.0/MAIHDA/man/maihda_discriminatory_accuracy.Rd | 17 MAIHDA-0.2.0/MAIHDA/man/maihda_interactions.Rd | 75 MAIHDA-0.2.0/MAIHDA/man/maihda_prepare_brms_sampling_weights.Rd | 6 MAIHDA-0.2.0/MAIHDA/man/maihda_table.Rd | 29 MAIHDA-0.2.0/MAIHDA/man/maihda_upset_size.Rd |only MAIHDA-0.2.0/MAIHDA/man/maihda_vpc_response.Rd | 2 MAIHDA-0.2.0/MAIHDA/man/maihda_wemix_linpred.Rd | 8 MAIHDA-0.2.0/MAIHDA/man/make_strata.Rd | 7 MAIHDA-0.2.0/MAIHDA/man/plot.maihda_analysis.Rd | 58 MAIHDA-0.2.0/MAIHDA/man/plot.maihda_model.Rd | 80 MAIHDA-0.2.0/MAIHDA/man/plot_group_comparison.Rd | 3 MAIHDA-0.2.0/MAIHDA/man/plot_obs_vs_shrunken.Rd | 16 MAIHDA-0.2.0/MAIHDA/man/plot_predicted_strata.Rd | 19 MAIHDA-0.2.0/MAIHDA/man/plot_stratum_trajectories.Rd | 16 MAIHDA-0.2.0/MAIHDA/man/plot_upset_strata.Rd |only MAIHDA-0.2.0/MAIHDA/man/predict_maihda.Rd | 27 MAIHDA-0.2.0/MAIHDA/man/stepwise_pcv.Rd | 5 MAIHDA-0.2.0/MAIHDA/man/sub-.maihda_group_comparison.Rd |only MAIHDA-0.2.0/MAIHDA/man/summary.maihda_model.Rd | 13 MAIHDA-0.2.0/MAIHDA/man/theme_maihda.Rd |only MAIHDA-0.2.0/MAIHDA/tests/testthat/test-auto_detect_family.R | 48 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-calculate_pvc.R | 9 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-compare_maihda_groups.R | 146 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-contextual.R | 30 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-correctness-regressions.R | 311 - MAIHDA-0.2.0/MAIHDA/tests/testthat/test-cross-classified.R | 32 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-design-weights.R | 281 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-discriminatory-accuracy.R | 165 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-information_criteria.R | 54 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-interactions.R | 519 + MAIHDA-0.2.0/MAIHDA/tests/testthat/test-longitudinal.R | 224 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-maihda-workflow.R | 117 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-maihda_table.R | 43 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-make_strata.R | 42 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-negbinomial.R | 1 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-ordinal-engine.R | 175 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-plot_predicted.R | 52 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-plot_upset.R |only MAIHDA-0.2.0/MAIHDA/tests/testthat/test-run_app.R | 22 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-vpc-response.R | 7 MAIHDA-0.2.0/MAIHDA/tests/testthat/test-weighted-count-vpc.R |only MAIHDA-0.2.0/MAIHDA/vignettes/brfss_precomputed.rds |only MAIHDA-0.2.0/MAIHDA/vignettes/case_study_brfss.Rmd |only MAIHDA-0.2.0/MAIHDA/vignettes/cross_classified.Rmd | 124 MAIHDA-0.2.0/MAIHDA/vignettes/figures/brfss_effect_decomp.png |only MAIHDA-0.2.0/MAIHDA/vignettes/figures/brfss_upset.png |only MAIHDA-0.2.0/MAIHDA/vignettes/figures/brfss_vpc.png |only MAIHDA-0.2.0/MAIHDA/vignettes/finding_interactions.Rmd | 31 MAIHDA-0.2.0/MAIHDA/vignettes/interpreting_plots.Rmd | 21 MAIHDA-0.2.0/MAIHDA/vignettes/introduction.Rmd | 50 116 files changed, 7111 insertions(+), 3044 deletions(-)
Title: Tree-Spatial Scan Statistic for Cluster Detection
Description: Implements the tree-spatial scan statistic for detecting clusters
that combine both spatial and hierarchical structures, as proposed by
Cancado et al. (2025) <doi:10.1007/s10651-025-00670-w>. The method extends
Kulldorff (1997) <doi:10.1080/03610929708831995> circular spatial scan
statistic and the tree-based scan statistic of Kulldorff et al. (2003)
<doi:10.1111/1541-0420.00039> by searching for anomalies in both
geographic regions and branches of hierarchical trees simultaneously. The
package also provides standalone implementations of Kulldorff's circular
spatial scan statistic and the tree-based scan statistic. Statistical
significance is assessed via Monte Carlo simulation under a Poisson or
binomial model, with optional 'OpenMP' parallelization.
Author: Allan Quadros [aut, cre] ,
Andre L. F. Cancado [aut] ,
Geiziane S. Oliveira [aut],
Luiz H. Duczmal [aut]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between treeSS versions 0.1.50 dated 2026-05-29 and 0.2.4 dated 2026-07-02
DESCRIPTION | 6 MD5 | 110 ++++++++-------- NEWS.md | 150 ++++++++++++++++++++++ R/aggregate_tree.R | 44 ++++-- R/circular_scan.R | 54 +++++--- R/data.R | 86 ++++++++++--- R/filter_clusters.R | 13 + R/generate_example_data.R | 17 +- R/get_cluster_regions.R | 13 + R/sequential_scan.R | 155 ++++++++++++++++------- R/tree_scan.R | 88 +++++++++---- R/treespatial_scan.R | 81 ++++++++---- R/vector_inputs.R | 43 ++++++ README.md | 38 +++-- data/rj_map.rda |only inst/doc/florida.R | 26 ++- inst/doc/florida.Rmd | 42 +++--- inst/doc/florida.html | 71 +++++----- inst/doc/introduction.R | 43 +++--- inst/doc/introduction.Rmd | 51 +++---- inst/doc/introduction.html | 116 ++++++++--------- inst/examples/example_brazil_rj.R | 40 +++--- inst/examples/example_chicago.R | 74 ++++++----- inst/examples/example_florida.R | 30 ++-- inst/examples/example_london.R | 26 ++- man/aggregate_tree.Rd | 31 ++-- man/chicago_map.Rd | 17 +- man/circular_scan.Rd | 39 +++-- man/filter_clusters.Rd | 76 ++++++----- man/fl_deaths.Rd | 46 +++++-- man/generate_example_data.Rd | 17 +- man/get_cluster_regions.Rd | 17 +- man/london_boroughs_map.Rd | 31 +++- man/print.circular_scan.Rd | 19 +- man/print.sequential_scan.Rd | 17 +- man/print.tree_scan.Rd | 19 +- man/print.treespatial_scan.Rd | 19 +- man/rj_map.Rd |only man/rj_mortality.Rd | 5 man/sequential_scan.Rd | 58 +++++--- man/summary.circular_scan.Rd | 15 +- man/summary.sequential_scan.Rd | 10 - man/summary.tree_scan.Rd | 15 +- man/summary.treespatial_scan.Rd | 17 +- man/treeSS-package.Rd | 2 man/tree_scan.Rd | 54 +++++--- man/treespatial_scan.Rd | 69 ++++++---- src/treescan_core.cpp | 197 ++++-------------------------- tests/testthat/test-binomial.R | 61 ++++----- tests/testthat/test-build-aggregate.R | 33 ++--- tests/testthat/test-circular-scan.R | 45 +++--- tests/testthat/test-get-cluster-regions.R | 30 +--- tests/testthat/test-sequential-scan.R | 102 ++++++--------- tests/testthat/test-tree-scan.R | 31 +++- tests/testthat/test-treespatial-scan.R | 78 +++++++---- vignettes/florida.Rmd | 42 +++--- vignettes/introduction.Rmd | 51 +++---- 57 files changed, 1554 insertions(+), 1126 deletions(-)
Title: Temporally Explicit Species Distribution Modelling
Description: Increases the ease of implementing a temporally-explicit modeling
methodology when building ecological niche and species distribution models.
Provides functions to assist with three major steps of temporally-explicit
models: (i) preprocessing species and environmental data and generating
suitable background or pseudoabsence data, (ii) building a niche model and
generating temporally-explicit predictions from that model, and (iii) model
postprocessing to explore spatiotemporal trends in model predictions.
Methodological and theoretical foundations are described in Ingenloff and
Peterson (2021) <doi:10.1111/2041-210X.13564>, Franklin (2010, ISBN:9780521700023),
Peterson et al. (2011, ISBN:9780691136882), Blonder (2018) <doi:10.1111/ecog.03187>,
Senay et al. (2013) <doi:10.1371/journal.pone.0071218>, and Li and Zhang (2024) <doi:10.48550/arXiv.2404.05933>.
Author: Connor Hughes [aut, cre] ,
Mariana Castaneda-Guzman [aut] ,
Luis E. Escobar [aut]
Maintainer: Connor Hughes <connorhughes926@gmail.com>
Diff between TemporalModelR versions 0.2.0 dated 2026-06-30 and 0.3.0 dated 2026-07-02
DESCRIPTION | 6 MD5 | 55 + NEWS.md | 14 R/analyze_temporal_patterns.R | 154 +++-- R/data_documentation.R | 24 R/generate_absences.R | 651 +++++++++++++++-------- R/helper_functions.R | 510 +++++++++--------- R/plot_model_assessment.R | 83 +- R/spatiotemporal_partition.R | 21 README.md | 13 data/tmr_absences.rda |binary data/tmr_absences_annual.rda |binary data/tmr_absences_user.rda |only data/tmr_partition.rda |binary data/tmr_partition_annual.rda |binary data/tmr_partition_small.rda |binary inst/doc/V2_Preprocessing.R | 57 +- inst/doc/V2_Preprocessing.Rmd | 77 ++ inst/doc/V2_Preprocessing.html | 207 +++++-- inst/doc/V3a_GLM.html | 6 inst/doc/V3b_GAM.html | 6 inst/doc/V3c_RF.html | 6 inst/doc/V3d_HV.html | 6 inst/doc/V4_Postprocessing.html | 26 inst/extdata/points/synthetic_user_presences.csv |only man/analyze_temporal_patterns.Rd | 80 +- man/extdata.Rd | 7 man/generate_absences.Rd | 53 + man/tmr_absences_user.Rd |only vignettes/V2_Preprocessing.Rmd | 77 ++ 30 files changed, 1404 insertions(+), 735 deletions(-)
More information about TemporalModelR at CRAN
Permanent link
Title: Simplified Statistical Analysis with Plain-English
Interpretation
Description: A toolkit for common statistical analyses including descriptive statistics, Student's t-tests (one-sample, independent, and paired), one-way and two-way Analysis of Variance (ANOVA), Multivariate Analysis of Variance (MANOVA), chi-square tests, Fisher's Exact Test, McNemar's Test, correlation analysis, simple and multiple linear regression, logistic regression, Friedman Test, and non-parametric tests (Mann-Whitney U, Wilcoxon Signed Rank, and Kruskal-Wallis). Additional tools include statistical power analysis and automated assumption checking. Each function automatically interprets results in plain English, reporting effect sizes, confidence intervals, and p-value interpretations. Post-hoc tests are automatically applied following significant results. A master function automatically detects the appropriate test based on the structure of the input data. Methods are based on Cohen, J. (1988) <doi:10.4324/9780203771587>, Tukey, J. W. (1949) <doi:10.2307/3001913>, and Shapiro [...truncated...]
Author: Uwakmfon Paul [aut, cre, cph]
Maintainer: Uwakmfon Paul <uwakmfon31@gmail.com>
Diff between statease versions 1.2.1 dated 2026-06-07 and 1.3.0 dated 2026-07-02
DESCRIPTION | 14 +- MD5 | 48 ++++++-- NAMESPACE | 17 +++ NEWS.md | 2 R/analyze.R | 177 +++++++++++++++++--------------- R/check_assumptions.R |only R/fisher_interpret.R |only R/friedman_interpret.R |only R/mcnemar_interpret.R |only R/nonparam_interpret.R | 10 + R/power_interpret.R |only R/run_app.R |only R/statease-package.R | 2 README.md | 55 +++++----- inst/doc/statease.R | 45 ++++++++ inst/doc/statease.Rmd | 87 ++++++++++++++++ inst/doc/statease.html | 249 ++++++++++++++++++++++++++++++++++++++++++++-- inst/shiny |only man/analyze.Rd | 76 +++++--------- man/check_assumptions.Rd |only man/fisher_interpret.Rd |only man/friedman_interpret.Rd |only man/mcnemar_interpret.Rd |only man/power_interpret.Rd |only man/run_app.Rd |only tests |only vignettes/statease.Rmd | 87 ++++++++++++++++ 27 files changed, 686 insertions(+), 183 deletions(-)
Title: Digitally Sign and Verify PDF Documents
Description: Digitally sign PDF documents with a 'PKCS#12' keystore and verify
their signatures. Signing produces a detached 'PKCS#7' / 'CMS' signature
('adbe.pkcs7.detached') over the document and is applied as an incremental
update, so existing signatures remain valid. The cryptography and PDF
manipulation are performed by a bundled, pure-'Rust' backend (the
'pdf_signer' crate); no Java runtime, 'OpenSSL', or external command-line
tools are required. Visible signature appearances with custom text are
supported.
Author: Andre Leite [aut, cre],
Hugo Vasconcelos [aut],
Diogo Bezerra [aut],
Authors of the vendored Rust crates [ctb, cph]
Maintainer: Andre Leite <leite@castlab.org>
Diff between pdfsigner versions 0.2.4 dated 2026-06-26 and 0.2.5 dated 2026-07-02
pdfsigner-0.2.4/pdfsigner/src/rust/pdf_signer |only pdfsigner-0.2.5/pdfsigner/DESCRIPTION | 6 +++--- pdfsigner-0.2.5/pdfsigner/MD5 | 22 ++++------------------ pdfsigner-0.2.5/pdfsigner/src/rust/Cargo.lock | 22 ++++++++++++++-------- pdfsigner-0.2.5/pdfsigner/src/rust/Cargo.toml | 2 +- pdfsigner-0.2.5/pdfsigner/src/rust/vendor.tar.xz |binary 6 files changed, 22 insertions(+), 30 deletions(-)
Title: Translate R Expressions to 'MathML' and 'LaTeX'/'MathJax'
Description: Translate R expressions to 'MathML' or 'MathJax'/'LaTeX' so that
they can be rendered in R markdown documents and shiny apps.
Author: Matthias Gondan [aut, cre, cph] ,
Irene Alfarone [aut] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
This is a re-admission after prior archival of version 1.8 dated 2026-05-22
Diff between mathml versions 1.8 dated 2026-05-22 and 1.9 dated 2026-07-02
DESCRIPTION | 15 ++++++--------- MD5 | 10 +++++----- NEWS.md | 4 ++++ build/vignette.rds |binary inst/doc/mathml.html | 7 +++---- vignettes/bibliography.bibtex | 2 +- 6 files changed, 19 insertions(+), 19 deletions(-)
Title: May All Data be Reproducible and Transparent (MADRaT) *
Description: Provides a framework which should improve reproducibility and
transparency in data processing. It provides functionality such as
automatic meta data creation and management, rudimentary quality
management, data caching, work-flow management and data aggregation.
* The title is a wish not a promise. By no means we expect this
package to deliver everything what is needed to achieve full
reproducibility and transparency, but we believe that it supports
efforts in this direction.
Author: Jan Philipp Dietrich [aut, cre] ,
Pascal Sauer [aut] ,
Lavinia Baumstark [aut] ,
Stephen Wirth [aut] ,
Anastasis Giannousakis [aut],
Renato Rodrigues [aut] ,
Benjamin Leon Bodirsky [aut] ,
Debbora Leip [aut] ,
Michael Crawford [aut] ,
Ulrich Kreidenw [...truncated...]
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
Diff between madrat versions 3.15.6 dated 2024-12-19 and 3.37.1 dated 2026-07-02
madrat-3.15.6/madrat/R/madapply.R |only madrat-3.15.6/madrat/R/madlapply.R |only madrat-3.15.6/madrat/man/madapply.Rd |only madrat-3.15.6/madrat/man/madlapply.Rd |only madrat-3.37.1/madrat/DESCRIPTION | 68 - madrat-3.37.1/madrat/MD5 | 374 ++--- madrat-3.37.1/madrat/NAMESPACE | 21 madrat-3.37.1/madrat/R/addMapping.R | 61 madrat-3.37.1/madrat/R/cacheArgumentsHash.R | 32 madrat-3.37.1/madrat/R/cacheCleanup.R | 1 madrat-3.37.1/madrat/R/cacheCopy.R | 3 madrat-3.37.1/madrat/R/cacheGet.R | 45 madrat-3.37.1/madrat/R/cacheName.R | 115 - madrat-3.37.1/madrat/R/cachePut.R | 70 - madrat-3.37.1/madrat/R/calcOutput.R | 185 ++ madrat-3.37.1/madrat/R/checkBidirectional.R | 4 madrat-3.37.1/madrat/R/cleanComment.R | 1 madrat-3.37.1/madrat/R/compareData.R | 85 - madrat-3.37.1/madrat/R/compareMadratOutputs.R | 4 madrat-3.37.1/madrat/R/downloadSource.R | 13 madrat-3.37.1/madrat/R/findBottlenecks.R | 71 - madrat-3.37.1/madrat/R/fingerprint.R | 190 +- madrat-3.37.1/madrat/R/functionCallString.R | 3 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madrat-3.37.1/madrat/man/fingerprint.Rd | 18 madrat-3.37.1/madrat/man/functionCallString.Rd | 1 madrat-3.37.1/madrat/man/getCalculations.Rd | 6 madrat-3.37.1/madrat/man/getCode.Rd | 1 madrat-3.37.1/madrat/man/getConfig.Rd | 5 madrat-3.37.1/madrat/man/getDependencies.Rd | 6 madrat-3.37.1/madrat/man/getFlags.Rd | 1 madrat-3.37.1/madrat/man/getFromComment.Rd | 1 madrat-3.37.1/madrat/man/getISOlist.Rd | 7 madrat-3.37.1/madrat/man/getLinkFunction.Rd | 5 madrat-3.37.1/madrat/man/getLocation.Rd | 6 madrat-3.37.1/madrat/man/getMadratGraph.Rd | 6 madrat-3.37.1/madrat/man/getMadratInfo.Rd | 6 madrat-3.37.1/madrat/man/getMadratMessage.Rd | 6 madrat-3.37.1/madrat/man/getMainfolder.Rd | 1 madrat-3.37.1/madrat/man/getNonDefaultArguments.Rd | 14 madrat-3.37.1/madrat/man/getSourceFolder.Rd | 1 madrat-3.37.1/madrat/man/getSources.Rd | 6 madrat-3.37.1/madrat/man/initializeConfig.Rd | 1 madrat-3.37.1/madrat/man/installedMadratUniverse.Rd | 6 madrat-3.37.1/madrat/man/isWrapperActive.Rd | 1 madrat-3.37.1/madrat/man/madTempDir.Rd | 1 madrat-3.37.1/madrat/man/madrat-package.Rd | 23 madrat-3.37.1/madrat/man/madratAttach.Rd | 5 madrat-3.37.1/madrat/man/metadataGFZ.Rd | 4 madrat-3.37.1/madrat/man/prepComment.Rd | 1 madrat-3.37.1/madrat/man/prepExtendedComment.Rd | 1 madrat-3.37.1/madrat/man/prepFunctionName.Rd | 1 madrat-3.37.1/madrat/man/pucAggregate.Rd | 4 madrat-3.37.1/madrat/man/putMadratMessage.Rd | 6 madrat-3.37.1/madrat/man/readSource.Rd | 25 madrat-3.37.1/madrat/man/redirect.Rd | 16 madrat-3.37.1/madrat/man/redirectSource.Rd | 36 madrat-3.37.1/madrat/man/regionscode.Rd | 5 madrat-3.37.1/madrat/man/resetMadratMessages.Rd | 6 madrat-3.37.1/madrat/man/retrieveData.Rd | 7 madrat-3.37.1/madrat/man/returnCalcOutput.Rd |only madrat-3.37.1/madrat/man/robustOrder.Rd | 1 madrat-3.37.1/madrat/man/setConfig.Rd | 13 madrat-3.37.1/madrat/man/toolAggregate.Rd | 20 madrat-3.37.1/madrat/man/toolCodeLabels.Rd | 4 madrat-3.37.1/madrat/man/toolCompareStatusLogs.Rd |only 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Title: Interface for Large Language Models via 'llama.cpp'
Description: Provides R bindings to 'llama.cpp' for running large language
models locally, with optional GPU acceleration via 'ggmlR'. Supports text
generation, embeddings, chat-based workflows, tool calling, and multimodal
(vision) inference. Includes 'OpenAI'- and 'Anthropic'-compatible HTTP
servers for serving local models, along with device selection and
multi-GPU support.
Author: Yuri Baramykov [aut, cre] ,
Georgi Gerganov [cph]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Diff between llamaR versions 0.2.4 dated 2026-05-27 and 0.2.5 dated 2026-07-02
llamaR-0.2.4/llamaR/src/Makevars.win |only llamaR-0.2.4/llamaR/src/models/cohere2-iswa.cpp |only llamaR-0.2.4/llamaR/src/models/gemma2-iswa.cpp |only llamaR-0.2.4/llamaR/src/models/gemma3n-iswa.cpp |only llamaR-0.2.4/llamaR/src/models/graph-context-mamba.cpp |only llamaR-0.2.4/llamaR/src/models/llama-iswa.cpp |only llamaR-0.2.4/llamaR/src/models/mimo2-iswa.cpp |only llamaR-0.2.4/llamaR/src/models/openai-moe-iswa.cpp |only llamaR-0.2.4/llamaR/src/models/pangu-embedded.cpp |only llamaR-0.2.4/llamaR/src/models/qwen3vl-moe.cpp |only llamaR-0.2.4/llamaR/src/models/t5-dec.cpp |only llamaR-0.2.4/llamaR/src/models/t5-enc.cpp |only llamaR-0.2.5/llamaR/DESCRIPTION | 22 llamaR-0.2.5/llamaR/MD5 | 463 llamaR-0.2.5/llamaR/NAMESPACE | 11 llamaR-0.2.5/llamaR/NEWS.md | 25 llamaR-0.2.5/llamaR/R/llama.R | 151 llamaR-0.2.5/llamaR/R/mtmd.R |only llamaR-0.2.5/llamaR/R/serve_anthropic.R |only llamaR-0.2.5/llamaR/README.md | 203 llamaR-0.2.5/llamaR/cleanup | 11 llamaR-0.2.5/llamaR/cleanup.win |only llamaR-0.2.5/llamaR/configure.win | 8 llamaR-0.2.5/llamaR/inst/doc/chat-and-agents.Rmd | 107 llamaR-0.2.5/llamaR/inst/doc/chat-and-agents.html | 107 llamaR-0.2.5/llamaR/inst/examples/chat_tools_ministral.R |only llamaR-0.2.5/llamaR/inst/examples/chat_tools_test.R |only llamaR-0.2.5/llamaR/inst/examples/claude_code_launcher.sh |only llamaR-0.2.5/llamaR/inst/examples/diag_qwen35.R |only llamaR-0.2.5/llamaR/inst/examples/dialog_grammar_test.R |only llamaR-0.2.5/llamaR/inst/examples/mcp_web_search.R |only llamaR-0.2.5/llamaR/inst/examples/serve_anthropic_test.sh |only llamaR-0.2.5/llamaR/inst/examples/serve_anthropic_vision.R |only llamaR-0.2.5/llamaR/inst/examples/smoke_chat_tools.R |only llamaR-0.2.5/llamaR/man/llamaR-package.Rd | 2 llamaR-0.2.5/llamaR/man/llama_chat_build.Rd |only llamaR-0.2.5/llamaR/man/llama_chat_parse.Rd |only llamaR-0.2.5/llamaR/man/llama_gen_begin.Rd | 13 llamaR-0.2.5/llamaR/man/llama_gen_begin_at.Rd |only llamaR-0.2.5/llamaR/man/llama_generate.Rd | 13 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llamaR-0.2.5/llamaR/src/common-unicode.h |only llamaR-0.2.5/llamaR/src/common.h |only llamaR-0.2.5/llamaR/src/common_chat_support.cpp |only llamaR-0.2.5/llamaR/src/jinja |only llamaR-0.2.5/llamaR/src/json-partial.cpp |only llamaR-0.2.5/llamaR/src/json-partial.h |only llamaR-0.2.5/llamaR/src/json-schema-to-grammar.cpp |only llamaR-0.2.5/llamaR/src/json-schema-to-grammar.h |only llamaR-0.2.5/llamaR/src/llama-adapter.cpp | 17 llamaR-0.2.5/llamaR/src/llama-adapter.h | 7 llamaR-0.2.5/llamaR/src/llama-arch.cpp | 1987 -- llamaR-0.2.5/llamaR/src/llama-arch.h | 62 llamaR-0.2.5/llamaR/src/llama-batch.cpp | 4 llamaR-0.2.5/llamaR/src/llama-batch.h | 2 llamaR-0.2.5/llamaR/src/llama-chat.cpp | 53 llamaR-0.2.5/llamaR/src/llama-chat.h | 5 llamaR-0.2.5/llamaR/src/llama-context.cpp | 1241 - llamaR-0.2.5/llamaR/src/llama-context.h | 77 llamaR-0.2.5/llamaR/src/llama-cparams.h | 3 llamaR-0.2.5/llamaR/src/llama-ext.h |only llamaR-0.2.5/llamaR/src/llama-grammar.cpp | 84 llamaR-0.2.5/llamaR/src/llama-graph.cpp | 642 llamaR-0.2.5/llamaR/src/llama-graph.h | 86 llamaR-0.2.5/llamaR/src/llama-hparams.cpp | 46 llamaR-0.2.5/llamaR/src/llama-hparams.h | 42 llamaR-0.2.5/llamaR/src/llama-impl.cpp | 10 llamaR-0.2.5/llamaR/src/llama-impl.h | 14 llamaR-0.2.5/llamaR/src/llama-io.cpp | 9 llamaR-0.2.5/llamaR/src/llama-io.h | 6 llamaR-0.2.5/llamaR/src/llama-kv-cache.cpp | 332 llamaR-0.2.5/llamaR/src/llama-kv-cache.h | 36 llamaR-0.2.5/llamaR/src/llama-memory-recurrent.cpp | 56 llamaR-0.2.5/llamaR/src/llama-mmap.cpp | 55 llamaR-0.2.5/llamaR/src/llama-mmap.h | 1 llamaR-0.2.5/llamaR/src/llama-model-loader.cpp | 692 llamaR-0.2.5/llamaR/src/llama-model-loader.h | 41 llamaR-0.2.5/llamaR/src/llama-model-saver.cpp | 218 llamaR-0.2.5/llamaR/src/llama-model-saver.h | 11 llamaR-0.2.5/llamaR/src/llama-model.cpp | 8029 +--------- llamaR-0.2.5/llamaR/src/llama-model.h | 236 llamaR-0.2.5/llamaR/src/llama-quant.cpp | 1074 - llamaR-0.2.5/llamaR/src/llama-vocab.cpp | 266 llamaR-0.2.5/llamaR/src/llama-vocab.h | 6 llamaR-0.2.5/llamaR/src/llama.cpp | 1092 - llamaR-0.2.5/llamaR/src/llama.h | 81 llamaR-0.2.5/llamaR/src/log.cpp |only llamaR-0.2.5/llamaR/src/log.h |only llamaR-0.2.5/llamaR/src/models/afmoe.cpp | 132 llamaR-0.2.5/llamaR/src/models/apertus.cpp | 78 llamaR-0.2.5/llamaR/src/models/arcee.cpp | 80 llamaR-0.2.5/llamaR/src/models/arctic.cpp | 78 llamaR-0.2.5/llamaR/src/models/arwkv7.cpp | 118 llamaR-0.2.5/llamaR/src/models/baichuan.cpp | 67 llamaR-0.2.5/llamaR/src/models/bailingmoe.cpp | 90 llamaR-0.2.5/llamaR/src/models/bailingmoe2.cpp | 114 llamaR-0.2.5/llamaR/src/models/bert.cpp | 133 llamaR-0.2.5/llamaR/src/models/bitnet.cpp | 114 llamaR-0.2.5/llamaR/src/models/bloom.cpp | 90 llamaR-0.2.5/llamaR/src/models/chameleon.cpp | 86 llamaR-0.2.5/llamaR/src/models/chatglm.cpp | 104 llamaR-0.2.5/llamaR/src/models/codeshell.cpp | 71 llamaR-0.2.5/llamaR/src/models/cogvlm.cpp | 67 llamaR-0.2.5/llamaR/src/models/cohere2.cpp |only llamaR-0.2.5/llamaR/src/models/command-r.cpp | 71 llamaR-0.2.5/llamaR/src/models/dbrx.cpp | 71 llamaR-0.2.5/llamaR/src/models/deci.cpp | 107 llamaR-0.2.5/llamaR/src/models/deepseek.cpp | 104 llamaR-0.2.5/llamaR/src/models/deepseek2.cpp | 202 llamaR-0.2.5/llamaR/src/models/deepseek2ocr.cpp |only llamaR-0.2.5/llamaR/src/models/delta-net-base.cpp |only llamaR-0.2.5/llamaR/src/models/dots1.cpp | 94 llamaR-0.2.5/llamaR/src/models/dream.cpp | 76 llamaR-0.2.5/llamaR/src/models/ernie4-5-moe.cpp | 39 llamaR-0.2.5/llamaR/src/models/ernie4-5.cpp | 106 llamaR-0.2.5/llamaR/src/models/eurobert.cpp |only llamaR-0.2.5/llamaR/src/models/exaone-moe.cpp | 136 llamaR-0.2.5/llamaR/src/models/exaone.cpp | 74 llamaR-0.2.5/llamaR/src/models/exaone4.cpp | 91 llamaR-0.2.5/llamaR/src/models/falcon-h1.cpp | 134 llamaR-0.2.5/llamaR/src/models/falcon.cpp | 65 llamaR-0.2.5/llamaR/src/models/gemma-embedding.cpp | 94 llamaR-0.2.5/llamaR/src/models/gemma.cpp | 57 llamaR-0.2.5/llamaR/src/models/gemma2.cpp |only llamaR-0.2.5/llamaR/src/models/gemma3.cpp | 106 llamaR-0.2.5/llamaR/src/models/gemma3n.cpp |only llamaR-0.2.5/llamaR/src/models/gemma4.cpp |only llamaR-0.2.5/llamaR/src/models/glm-dsa.cpp |only llamaR-0.2.5/llamaR/src/models/glm4-moe.cpp | 166 llamaR-0.2.5/llamaR/src/models/glm4.cpp | 132 llamaR-0.2.5/llamaR/src/models/gpt2.cpp | 78 llamaR-0.2.5/llamaR/src/models/gptneox.cpp | 102 llamaR-0.2.5/llamaR/src/models/granite-hybrid.cpp | 172 llamaR-0.2.5/llamaR/src/models/granite-moe.cpp |only llamaR-0.2.5/llamaR/src/models/granite.cpp | 129 llamaR-0.2.5/llamaR/src/models/grok.cpp | 118 llamaR-0.2.5/llamaR/src/models/grovemoe.cpp | 90 llamaR-0.2.5/llamaR/src/models/hunyuan-dense.cpp | 132 llamaR-0.2.5/llamaR/src/models/hunyuan-moe.cpp | 89 llamaR-0.2.5/llamaR/src/models/hunyuan-vl.cpp |only llamaR-0.2.5/llamaR/src/models/internlm2.cpp | 70 llamaR-0.2.5/llamaR/src/models/jais.cpp | 86 llamaR-0.2.5/llamaR/src/models/jais2.cpp |only llamaR-0.2.5/llamaR/src/models/jamba.cpp | 130 llamaR-0.2.5/llamaR/src/models/jina-bert-v2.cpp |only llamaR-0.2.5/llamaR/src/models/jina-bert-v3.cpp |only llamaR-0.2.5/llamaR/src/models/kimi-linear.cpp |only llamaR-0.2.5/llamaR/src/models/lfm2.cpp | 348 llamaR-0.2.5/llamaR/src/models/lfm2moe.cpp |only llamaR-0.2.5/llamaR/src/models/llada-moe.cpp | 76 llamaR-0.2.5/llamaR/src/models/llada.cpp | 89 llamaR-0.2.5/llamaR/src/models/llama-embed.cpp |only llamaR-0.2.5/llamaR/src/models/llama.cpp | 146 llamaR-0.2.5/llamaR/src/models/llama4.cpp |only llamaR-0.2.5/llamaR/src/models/maincoder.cpp | 67 llamaR-0.2.5/llamaR/src/models/mamba-base.cpp |only llamaR-0.2.5/llamaR/src/models/mamba.cpp | 86 llamaR-0.2.5/llamaR/src/models/mamba2.cpp |only llamaR-0.2.5/llamaR/src/models/mimo2.cpp |only llamaR-0.2.5/llamaR/src/models/minicpm.cpp |only llamaR-0.2.5/llamaR/src/models/minicpm3.cpp | 90 llamaR-0.2.5/llamaR/src/models/minimax-m2.cpp | 57 llamaR-0.2.5/llamaR/src/models/mistral3.cpp | 125 llamaR-0.2.5/llamaR/src/models/mistral4.cpp |only llamaR-0.2.5/llamaR/src/models/models.h | 1903 +- llamaR-0.2.5/llamaR/src/models/modern-bert.cpp | 93 llamaR-0.2.5/llamaR/src/models/mpt.cpp | 92 llamaR-0.2.5/llamaR/src/models/nemotron-h-moe.cpp |only llamaR-0.2.5/llamaR/src/models/nemotron-h.cpp | 204 llamaR-0.2.5/llamaR/src/models/nemotron.cpp | 79 llamaR-0.2.5/llamaR/src/models/neo-bert.cpp | 62 llamaR-0.2.5/llamaR/src/models/nomic-bert-moe.cpp |only llamaR-0.2.5/llamaR/src/models/nomic-bert.cpp |only llamaR-0.2.5/llamaR/src/models/olmo.cpp | 73 llamaR-0.2.5/llamaR/src/models/olmo2.cpp | 75 llamaR-0.2.5/llamaR/src/models/olmoe.cpp | 61 llamaR-0.2.5/llamaR/src/models/openai-moe.cpp |only llamaR-0.2.5/llamaR/src/models/openelm.cpp | 57 llamaR-0.2.5/llamaR/src/models/orion.cpp | 76 llamaR-0.2.5/llamaR/src/models/paddleocr.cpp |only llamaR-0.2.5/llamaR/src/models/pangu-embed.cpp |only llamaR-0.2.5/llamaR/src/models/phi2.cpp | 77 llamaR-0.2.5/llamaR/src/models/phi3.cpp | 102 llamaR-0.2.5/llamaR/src/models/phimoe.cpp |only llamaR-0.2.5/llamaR/src/models/plamo.cpp | 60 llamaR-0.2.5/llamaR/src/models/plamo2.cpp | 124 llamaR-0.2.5/llamaR/src/models/plamo3.cpp | 81 llamaR-0.2.5/llamaR/src/models/plm.cpp | 76 llamaR-0.2.5/llamaR/src/models/qwen.cpp | 58 llamaR-0.2.5/llamaR/src/models/qwen2.cpp | 85 llamaR-0.2.5/llamaR/src/models/qwen2moe.cpp | 96 llamaR-0.2.5/llamaR/src/models/qwen2vl.cpp | 66 llamaR-0.2.5/llamaR/src/models/qwen3.cpp | 79 llamaR-0.2.5/llamaR/src/models/qwen35.cpp |only llamaR-0.2.5/llamaR/src/models/qwen35moe.cpp |only llamaR-0.2.5/llamaR/src/models/qwen3moe.cpp | 91 llamaR-0.2.5/llamaR/src/models/qwen3next.cpp | 656 llamaR-0.2.5/llamaR/src/models/qwen3vl.cpp | 74 llamaR-0.2.5/llamaR/src/models/qwen3vlmoe.cpp |only llamaR-0.2.5/llamaR/src/models/refact.cpp | 97 llamaR-0.2.5/llamaR/src/models/rnd1.cpp | 86 llamaR-0.2.5/llamaR/src/models/rwkv6-base.cpp | 2 llamaR-0.2.5/llamaR/src/models/rwkv6.cpp | 95 llamaR-0.2.5/llamaR/src/models/rwkv6qwen2.cpp | 83 llamaR-0.2.5/llamaR/src/models/rwkv7-base.cpp | 2 llamaR-0.2.5/llamaR/src/models/rwkv7.cpp | 125 llamaR-0.2.5/llamaR/src/models/seed-oss.cpp | 78 llamaR-0.2.5/llamaR/src/models/smallthinker.cpp | 104 llamaR-0.2.5/llamaR/src/models/smollm3.cpp | 76 llamaR-0.2.5/llamaR/src/models/stablelm.cpp | 82 llamaR-0.2.5/llamaR/src/models/starcoder.cpp | 80 llamaR-0.2.5/llamaR/src/models/starcoder2.cpp | 88 llamaR-0.2.5/llamaR/src/models/step35.cpp |only llamaR-0.2.5/llamaR/src/models/t5.cpp |only llamaR-0.2.5/llamaR/src/models/t5encoder.cpp |only llamaR-0.2.5/llamaR/src/models/wavtokenizer-dec.cpp | 119 llamaR-0.2.5/llamaR/src/models/xverse.cpp | 61 llamaR-0.2.5/llamaR/src/mtmd |only llamaR-0.2.5/llamaR/src/nlohmann |only llamaR-0.2.5/llamaR/src/peg-parser.cpp |only llamaR-0.2.5/llamaR/src/peg-parser.h |only llamaR-0.2.5/llamaR/src/r_chat_interface.cpp |only llamaR-0.2.5/llamaR/src/r_llama_compat.h | 26 llamaR-0.2.5/llamaR/src/r_llama_interface.cpp | 254 llamaR-0.2.5/llamaR/src/r_mtmd_interface.cpp |only llamaR-0.2.5/llamaR/src/regex-partial.cpp |only llamaR-0.2.5/llamaR/src/regex-partial.h |only llamaR-0.2.5/llamaR/src/unicode.cpp | 290 llamaR-0.2.5/llamaR/src/unicode.h | 2 llamaR-0.2.5/llamaR/src/vendor |only llamaR-0.2.5/llamaR/tests/testthat.R | 28 llamaR-0.2.5/llamaR/tests/testthat/test-chat-build-roundtrip.R |only llamaR-0.2.5/llamaR/tests/testthat/test-chat-build.R |only llamaR-0.2.5/llamaR/tests/testthat/test-core-extra.R |only llamaR-0.2.5/llamaR/tests/testthat/test-hf.R | 12 llamaR-0.2.5/llamaR/tests/testthat/test-lora-multi.R |only llamaR-0.2.5/llamaR/tests/testthat/test-mtmd.R |only llamaR-0.2.5/llamaR/tests/testthat/test-serve-anthropic-e2e.R |only llamaR-0.2.5/llamaR/tests/testthat/test-serve-anthropic.R |only llamaR-0.2.5/llamaR/vignettes/chat-and-agents.Rmd | 107 259 files changed, 15564 insertions(+), 14350 deletions(-)
Title: Time-to-Event Landmark Analysis using an Array of Longitudinal
and Survival Sub-Models
Description: Provides a modular end-to-end framework for dynamic risk prediction
based on time-to-event and longitudinal data. This allows flexible specifications
for the longitudinal and survival sub-models. The 'landmaRk' package enables
reproducible benchmarks of different model choices, including cross-validation
to assess out-of-sample predictive performance. Methods are described in
Velasco-Pardo, Constantine-Cooke, Lees and Vallejos (2026, manuscript under
preparation) 'Landmarking with Latent Class Mixed Models for Dynamic Prediction
of Time-to-event Data with Heterogeneous Biomarker Trajectories'.
Author: Victor Velasco-Pardo [aut, cre] ,
Nathan Constantine-Cooke [aut] ,
Charlie Lees [aut] ,
Catalina Vallejos [aut]
Maintainer: Victor Velasco-Pardo <vvelasco@ed.ac.uk>
Diff between landmaRk versions 0.1.2 dated 2026-06-26 and 0.1.3 dated 2026-07-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NEWS.md | 8 +++++++- 3 files changed, 12 insertions(+), 6 deletions(-)
Title: Asymmetric Smoothed-Association Matrices via GAM Fits
Description: Render a pairwise, asymmetric smoothed-association matrix
of continuous variables. Each cell shows the fitted spline from an
'mgcv' generalised additive model, with the upper triangle
displaying 'gam(x_j ~ s(x_i))' and the lower triangle
'gam(x_i ~ s(x_j))'. Unlike Pearson's correlation matrix, the
visualisation is intentionally asymmetric, revealing
heteroscedasticity, leverage, and directional non-linearity that
a single scalar correlation hides. An asymmetry index and a
24-category shape taxonomy quantify the directional difference
and qualitative form of each fitted smooth.
Author: Max Moldovan [aut, cre, cph]
Maintainer: Max Moldovan <max.moldovan@adelaide.edu.au>
Diff between janusplot versions 0.1.0 dated 2026-04-28 and 0.1.1 dated 2026-07-02
DESCRIPTION | 7 MD5 | 48 +-- NEWS.md | 180 ++++++++++++- R/internal-assemble.R | 18 + R/internal-cell.R | 361 ++++++++++++++++++++++++-- R/internal-fit.R | 347 +++++++++++++++++++++++++ R/janusplot.R | 382 +++++++++++++++++++++++++--- R/shape-metrics.R | 2 README.md | 13 inst/CITATION | 13 inst/doc/janusplot.Rmd | 2 inst/doc/janusplot.html | 67 ++-- inst/doc/shape-recognition-sensitivity.html | 10 man/janusplot.Rd | 171 ++++++++++++ man/janusplot_data.Rd | 69 ++++- tests/testthat/test-axes.R |only tests/testthat/test-compact.R |only tests/testthat/test-derivatives.R | 30 ++ tests/testthat/test-engine.R |only tests/testthat/test-focus.R |only tests/testthat/test-integration.R | 2 tests/testthat/test-k-check.R |only tests/testthat/test-shape-sensitivity.R | 2 tests/testthat/test-validate.R | 46 +++ tests/testthat/test-validation-linear.R | 2 tests/testthat/test-vdiffr.R | 19 + vignettes/janusplot.Rmd | 2 vignettes/mathjax-config.html |only 28 files changed, 1624 insertions(+), 169 deletions(-)
Title: Recursive Partitioning for Graded Response Models
Description: Provides methods for recursive partitioning based on the
'Graded Response Model' ('GRM'), extending the 'MOB' algorithm from the
'partykit' package. The package allows for fitting
'GRM' trees that partition the population into homogeneous
subgroups based on item response patterns and covariates.
Includes specialized plotting functions for visualizing 'GRM' trees
with different terminal node displays (threshold regions,
parameter profiles, and factor score distributions). The package also implements the Longitudinal GRMTree for detecting response shift in PROMs measured at two time points, embedding a constrained two-factor longitudinal GRM within recursive partitioning, with post-hoc characterization of recalibration and reprioritization.
For more details on the methods, see Samejima (1969) <doi:10.1002/J.2333-8504.1968.TB00153.X>, Komboz et al. (2018) <doi:10.1177/0013164416664394> and Arimoro et al. (2025) <doi:10.1007/s11136-025-04018-6>.
Author: Olayinka I. Arimoro [aut, cre] ,
Tolulope T. Sajobi [aut],
Lisa M. Lix [aut],
Matthew T. James [ctb],
Maria Santana [ctb],
Emmanuel Ugochukwu [ctb]
Maintainer: Olayinka I. Arimoro <olayinka.arimoro@ucalgary.ca>
Diff between grmtree versions 0.1.0 dated 2026-01-14 and 0.2.0 dated 2026-07-02
DESCRIPTION | 17 +- MD5 | 61 ++++++++-- NAMESPACE | 24 +++- NEWS.md | 63 ++++++++-- R/generate_nodescores_dataset.R |only R/grmtree-control.R | 73 +++++++++--- R/grmtree-fscores.R | 124 --------------------- R/grmtree_long_data.R |only R/long-grmtree-discrpar.R |only R/long-grmtree-fscores.R |only R/long-grmtree-itempar.R |only R/long-grmtree-latentpar.R |only R/long-grmtree-plot.R |only R/long-grmtree-threshpar.R |only R/longitudinal_grmtree.R |only R/rs_characterize.R |only R/rs_characterize_plots.R |only README.md | 58 ++++++++- build/partial.rdb |only build/vignette.rds |binary data/grmtree_long_data.rda |only inst/doc/getting-started-with-grmtree-package.html | 4 inst/doc/longitudinal-grmtree.R |only inst/doc/longitudinal-grmtree.Rmd |only inst/doc/longitudinal-grmtree.html |only man/discrpar_longitudinal_grmtree.Rd |only man/fscores_longitudinal_grmtree.Rd |only man/generate_node_scores_dataset.Rd | 69 ++++++++--- man/grmforest.Rd | 2 man/grmtree_long_data.Rd |only man/itempar_longitudinal_grmtree.Rd |only man/latentpar_longitudinal_grmtree.Rd |only man/longitudinal_grmfit.Rd |only man/longitudinal_grmtree.Rd |only man/node_regionplot_longitudinal.Rd |only man/plot.longitudinal_grmtree.Rd |only man/plot_rs_heatmap.Rd |only man/plot_rs_tree.Rd |only man/prepare_longitudinal_data.Rd |only man/print.rs_characterization.Rd |only man/rs_characterize.Rd |only man/threshpar_longitudinal_grmtree.Rd |only tests/testthat/helper-longitudinal.R |only tests/testthat/test-all-long-grmtree.R |only tests/testthat/test-extraction-functions.R |only tests/testthat/test-fscores.R | 84 -------------- tests/testthat/test-generate_node_scores_dataset.R |only tests/testthat/test-long-grmtree.R |only tests/testthat/test-prep_long_data.R |only tests/testthat/test-rs-characterize.R |only vignettes/longitudinal-grmtree.Rmd |only 51 files changed, 288 insertions(+), 291 deletions(-)
Title: Geographic and Taxonomic Occurrence R-Based Scrubbing
Description: Streamlines downloading and cleaning biodiversity data from Integrated Digitized Biocollections (iDigBio) and the Global Biodiversity Information Facility (GBIF).
Author: Natalie N. Patten [aut] ,
Michelle L. Gaynor [aut, cre] ,
Douglas E. Soltis [ctb] ,
Pamela S. Soltis [ctb]
Maintainer: Michelle L. Gaynor <shellyleegaynor@gmail.com>
Diff between gatoRs versions 1.0.2 dated 2024-05-17 and 2.0.0 dated 2026-07-02
gatoRs-1.0.2/gatoRs/R/get_idigbio.R |only gatoRs-1.0.2/gatoRs/man/get_idigbio.Rd |only gatoRs-2.0.0/gatoRs/DESCRIPTION | 33 gatoRs-2.0.0/gatoRs/MD5 | 140 ++-- gatoRs-2.0.0/gatoRs/NAMESPACE | 129 +-- gatoRs-2.0.0/gatoRs/R/basic_locality_clean.R | 158 ++-- gatoRs-2.0.0/gatoRs/R/basis_clean.R | 126 +-- gatoRs-2.0.0/gatoRs/R/citation_bellow.R | 64 - gatoRs-2.0.0/gatoRs/R/correct_class.R | 180 ++--- gatoRs-2.0.0/gatoRs/R/data.R | 10 gatoRs-2.0.0/gatoRs/R/data_chomp.R | 66 - gatoRs-2.0.0/gatoRs/R/filter_fix_names.R | 130 +-- gatoRs-2.0.0/gatoRs/R/fixAfterPeriod.R | 58 - gatoRs-2.0.0/gatoRs/R/fix_columns.R | 122 +-- gatoRs-2.0.0/gatoRs/R/fix_names.R | 260 +++---- gatoRs-2.0.0/gatoRs/R/full_clean.R | 204 ++--- gatoRs-2.0.0/gatoRs/R/gators_download.R | 329 +++++---- gatoRs-2.0.0/gatoRs/R/gators_merge.R | 70 +- gatoRs-2.0.0/gatoRs/R/get_gbif.R | 404 +++++------ gatoRs-2.0.0/gatoRs/R/get_idigbio_arc.R |only gatoRs-2.0.0/gatoRs/R/global_vars.R | 2 gatoRs-2.0.0/gatoRs/R/matchColClasses.R | 36 - gatoRs-2.0.0/gatoRs/R/need_to_georeference.R | 72 +- gatoRs-2.0.0/gatoRs/R/needed_records.R | 52 - gatoRs-2.0.0/gatoRs/R/one_point_per_pixel.R | 110 +-- gatoRs-2.0.0/gatoRs/R/process_flagged.R | 460 ++++++------- gatoRs-2.0.0/gatoRs/R/remove_duplicates.R | 318 ++++----- gatoRs-2.0.0/gatoRs/R/remove_missing.R | 90 +- gatoRs-2.0.0/gatoRs/R/remove_skewed.R | 48 - gatoRs-2.0.0/gatoRs/R/removed_redacted.R | 50 - gatoRs-2.0.0/gatoRs/R/setupduckDB.R |only gatoRs-2.0.0/gatoRs/R/suppress_output.R | 40 - gatoRs-2.0.0/gatoRs/R/taxa_clean.R | 178 ++--- gatoRs-2.0.0/gatoRs/R/thin_points.R | 96 +- gatoRs-2.0.0/gatoRs/R/utils-pipe.R | 28 gatoRs-2.0.0/gatoRs/README.md | 116 +-- gatoRs-2.0.0/gatoRs/build/vignette.rds |binary gatoRs-2.0.0/gatoRs/inst/CITATION | 38 - gatoRs-2.0.0/gatoRs/inst/doc/Introduction.R | 12 gatoRs-2.0.0/gatoRs/inst/doc/Introduction.Rmd | 546 +++++++-------- gatoRs-2.0.0/gatoRs/inst/doc/Introduction.html | 837 ++++++++++++++++-------- gatoRs-2.0.0/gatoRs/inst/doc/ManyDownloads.Rmd | 170 ++-- gatoRs-2.0.0/gatoRs/inst/doc/ManyDownloads.html | 461 +++++++++---- gatoRs-2.0.0/gatoRs/man/basic_locality_clean.Rd | 110 +-- gatoRs-2.0.0/gatoRs/man/basis_clean.Rd | 64 - gatoRs-2.0.0/gatoRs/man/citation_bellow.Rd | 64 - gatoRs-2.0.0/gatoRs/man/correct_class.Rd | 190 ++--- gatoRs-2.0.0/gatoRs/man/data.Rd | 36 - gatoRs-2.0.0/gatoRs/man/data_chomp.Rd | 74 +- gatoRs-2.0.0/gatoRs/man/filter_fix_names.Rd | 88 +- gatoRs-2.0.0/gatoRs/man/fixAfterPeriod.Rd | 42 - gatoRs-2.0.0/gatoRs/man/fix_columns.Rd | 80 +- gatoRs-2.0.0/gatoRs/man/fix_names.Rd | 54 - gatoRs-2.0.0/gatoRs/man/full_clean.Rd | 246 +++---- gatoRs-2.0.0/gatoRs/man/gators_download.Rd | 198 +++-- gatoRs-2.0.0/gatoRs/man/gators_merge.Rd | 64 - gatoRs-2.0.0/gatoRs/man/get_gbif.Rd | 70 +- gatoRs-2.0.0/gatoRs/man/get_idigbio_arc.Rd |only gatoRs-2.0.0/gatoRs/man/matchColClasses.Rd | 44 - gatoRs-2.0.0/gatoRs/man/need_to_georeference.Rd | 74 +- gatoRs-2.0.0/gatoRs/man/needed_records.Rd | 58 - gatoRs-2.0.0/gatoRs/man/one_point_per_pixel.Rd | 92 +- gatoRs-2.0.0/gatoRs/man/pipe.Rd | 40 - gatoRs-2.0.0/gatoRs/man/process_flagged.Rd | 100 +- gatoRs-2.0.0/gatoRs/man/remove_duplicates.Rd | 162 ++-- gatoRs-2.0.0/gatoRs/man/remove_missing.Rd | 98 +- gatoRs-2.0.0/gatoRs/man/remove_redacted.Rd | 56 - gatoRs-2.0.0/gatoRs/man/remove_skewed.Rd | 52 - gatoRs-2.0.0/gatoRs/man/setupduckDB.Rd |only gatoRs-2.0.0/gatoRs/man/suppress_output.Rd | 44 - gatoRs-2.0.0/gatoRs/man/taxa_clean.Rd | 98 +- gatoRs-2.0.0/gatoRs/man/thin_points.Rd | 92 +- gatoRs-2.0.0/gatoRs/vignettes/Introduction.Rmd | 546 +++++++-------- gatoRs-2.0.0/gatoRs/vignettes/ManyDownloads.Rmd | 170 ++-- 74 files changed, 4957 insertions(+), 4392 deletions(-)
Title: Retrieval and Processing of the Spanish National Forest
Inventory
Description: Fetches, harmonizes, and analyses data from the Spanish National
Forest Inventory for reproducible, design-aware forest inventory workflows.
Computes tree- and stand-level metrics, applies sampling-based expansion
factors, estimates volume, and supports extensible processing for external
inventory designs with custom sampling schemes and volume equations. Spatial
extensions can attach plot geometries, preserve geometry sidecars through
metric workflows, and return georeferenced sf outputs for mapping and
remote-sensing integration.
Author: Wilson Lara [aut, cre] ,
Cristobal Ordonez [aut] ,
Aitor Vazquez-Veloso [aut] ,
Felipe Bravo [aut]
Maintainer: Wilson Lara <wilarhen@gmail.com>
Diff between basifoR versions 0.7.7 dated 2026-04-09 and 0.7.8 dated 2026-07-02
basifoR-0.7.7/basifoR/man/get_snfi_iavc.Rd |only basifoR-0.7.7/basifoR/man/get_snfi_vcc.Rd |only basifoR-0.7.7/basifoR/man/get_snfi_vle.Rd |only basifoR-0.7.7/basifoR/man/get_snfi_vsc.Rd |only basifoR-0.7.8/basifoR/DESCRIPTION | 17 basifoR-0.7.8/basifoR/MD5 | 150 + basifoR-0.7.8/basifoR/NAMESPACE | 52 basifoR-0.7.8/basifoR/NEWS | 74 basifoR-0.7.8/basifoR/R/dbhMetric.R | 6 basifoR-0.7.8/basifoR/R/default_snfi_volume_equations.R | 868 ----------- basifoR-0.7.8/basifoR/R/dendroMetrics.R | 171 +- basifoR-0.7.8/basifoR/R/dominant_height_method_registry.R |only basifoR-0.7.8/basifoR/R/externalMetrics.R | 156 + basifoR-0.7.8/basifoR/R/externalMetrics2Vol.R | 50 basifoR-0.7.8/basifoR/R/external_dendroMetrics.R | 101 - basifoR-0.7.8/basifoR/R/external_volume_method_registry.R | 58 basifoR-0.7.8/basifoR/R/internal.R | 506 ------ basifoR-0.7.8/basifoR/R/inventoryMetrics.R | 292 ++- basifoR-0.7.8/basifoR/R/inventoryMetrics_spatial.R |only basifoR-0.7.8/basifoR/R/listNFI_tables.R |only basifoR-0.7.8/basifoR/R/metrics2Vol.R | 119 + basifoR-0.7.8/basifoR/R/metrics2Vol_spatial.R |only basifoR-0.7.8/basifoR/R/new_concentric_design.R | 20 basifoR-0.7.8/basifoR/R/new_external_schema.R | 24 basifoR-0.7.8/basifoR/R/new_inventory_design.R | 24 basifoR-0.7.8/basifoR/R/new_volume_method.R | 6 basifoR-0.7.8/basifoR/R/nfiMetrics.R | 183 +- basifoR-0.7.8/basifoR/R/nfiMetrics_spatial.R |only basifoR-0.7.8/basifoR/R/plotNFI_spatial.R |only basifoR-0.7.8/basifoR/R/print.concentric_design.R | 4 basifoR-0.7.8/basifoR/R/print.inventory_design.R | 2 basifoR-0.7.8/basifoR/R/readNFI.R | 5 basifoR-0.7.8/basifoR/R/readNFI_spatial.R |only basifoR-0.7.8/basifoR/R/readNFIsf.R |only basifoR-0.7.8/basifoR/R/snfi_volume_equations.R | 110 - basifoR-0.7.8/basifoR/R/snfi_volume_method_registry.R | 34 basifoR-0.7.8/basifoR/R/sysdata.rda |binary basifoR-0.7.8/basifoR/R/trees_per_ha.R | 13 basifoR-0.7.8/basifoR/R/update.external_dendroMetrics.R | 25 basifoR-0.7.8/basifoR/man/addNFIcoords.Rd |only basifoR-0.7.8/basifoR/man/addNFIsf.Rd |only basifoR-0.7.8/basifoR/man/asNFI_spatial_sf.Rd |only basifoR-0.7.8/basifoR/man/copyNFIboundary_spatial.Rd |only basifoR-0.7.8/basifoR/man/copyNFIgeometry_spatial.Rd |only basifoR-0.7.8/basifoR/man/copyNFIspatial_sidecars.Rd |only basifoR-0.7.8/basifoR/man/dbhMetric.Rd | 9 basifoR-0.7.8/basifoR/man/default_dominant_height_methods.Rd |only basifoR-0.7.8/basifoR/man/default_external_volume_methods.Rd | 7 basifoR-0.7.8/basifoR/man/default_snfi_volume_equations.Rd | 26 basifoR-0.7.8/basifoR/man/dendroMetrics.Rd | 52 basifoR-0.7.8/basifoR/man/dominant_height_method_registry.Rd |only basifoR-0.7.8/basifoR/man/externalMetrics.Rd | 46 basifoR-0.7.8/basifoR/man/externalMetrics2Vol.Rd | 22 basifoR-0.7.8/basifoR/man/external_dendroMetrics.Rd | 47 basifoR-0.7.8/basifoR/man/external_volume_method_registry.Rd | 55 basifoR-0.7.8/basifoR/man/fetchNFI.Rd | 8 basifoR-0.7.8/basifoR/man/filter_gadm_province_spatial.Rd |only basifoR-0.7.8/basifoR/man/gadm_spatial.Rd |only basifoR-0.7.8/basifoR/man/getNFI.Rd | 7 basifoR-0.7.8/basifoR/man/getNFIboundary_spatial.Rd |only basifoR-0.7.8/basifoR/man/getNFIgeometry_spatial.Rd |only basifoR-0.7.8/basifoR/man/hasNFIboundary_spatial.Rd |only basifoR-0.7.8/basifoR/man/hasNFIgeometry_spatial.Rd |only basifoR-0.7.8/basifoR/man/inventoryMetrics.Rd | 136 - basifoR-0.7.8/basifoR/man/inventoryMetrics_spatial.Rd |only basifoR-0.7.8/basifoR/man/listNFI_tables.Rd |only basifoR-0.7.8/basifoR/man/metrics2Vol.Rd | 105 + basifoR-0.7.8/basifoR/man/metrics2Vol_spatial.Rd |only basifoR-0.7.8/basifoR/man/new_concentric_design.Rd | 27 basifoR-0.7.8/basifoR/man/new_dominant_height_method.Rd |only basifoR-0.7.8/basifoR/man/new_external_schema.Rd | 20 basifoR-0.7.8/basifoR/man/new_inventory_design.Rd | 42 basifoR-0.7.8/basifoR/man/new_volume_method.Rd | 18 basifoR-0.7.8/basifoR/man/nfiMetrics.Rd | 100 - basifoR-0.7.8/basifoR/man/nfiMetrics_spatial.Rd |only basifoR-0.7.8/basifoR/man/plot.inventoryMetrics_spatial.Rd |only basifoR-0.7.8/basifoR/man/plot.metrics2Vol_spatial.Rd |only basifoR-0.7.8/basifoR/man/plot.nfiMetrics_spatial.Rd |only basifoR-0.7.8/basifoR/man/plot.readNFI_spatial.Rd |only basifoR-0.7.8/basifoR/man/print.concentric_design.Rd | 15 basifoR-0.7.8/basifoR/man/print.external_schema.Rd | 18 basifoR-0.7.8/basifoR/man/print.inventory_design.Rd | 14 basifoR-0.7.8/basifoR/man/readNFI.Rd | 38 basifoR-0.7.8/basifoR/man/readNFI_spatial.Rd |only basifoR-0.7.8/basifoR/man/readNFIcoords.Rd |only basifoR-0.7.8/basifoR/man/readNFIsf.Rd |only basifoR-0.7.8/basifoR/man/snfi_design.Rd | 7 basifoR-0.7.8/basifoR/man/snfi_volume_method_registry.Rd | 50 basifoR-0.7.8/basifoR/man/trees_per_ha.Rd | 14 basifoR-0.7.8/basifoR/man/trees_per_ha.concentric_design.Rd | 17 basifoR-0.7.8/basifoR/man/trees_per_ha.inventory_design.Rd | 17 basifoR-0.7.8/basifoR/man/update.dendroMetrics.Rd | 7 basifoR-0.7.8/basifoR/man/update.external_dendroMetrics.Rd | 32 basifoR-0.7.8/basifoR/man/update.inventoryMetrics.Rd | 20 basifoR-0.7.8/basifoR/man/update.list.Rd | 10 95 files changed, 1760 insertions(+), 2296 deletions(-)
Title: Estimate Survival Data with Data Integration
Description: Provides flexible and efficient tools for integrating external risk scores into Cox proportional hazards models while accounting for population heterogeneity. Enables robust estimation, improved predictive accuracy, and user-friendly workflows for modern survival analysis. For more information, see Wang et al. (2023) <doi:10.48550/arXiv.2302.11123>.
Author: Yubo Shao [aut, cre],
Lingfeng Luo [aut],
Xiaohan Liu [aut],
Junyi Qiu [aut],
Di Wang [aut],
Kevin He [aut]
Maintainer: Yubo Shao <ybshao@umich.edu>
Diff between survkl versions 1.0.0 dated 2026-04-21 and 1.0.2 dated 2026-07-02
DESCRIPTION | 8 MD5 | 22 - R/plot.R | 8 inst/doc/Methods.Rmd | 202 ++++++++++ inst/doc/Methods.html | 192 +++++++++ inst/doc/survkl.Rmd | 914 +++++++++++++++++++++++------------------------ man/plot.coxkl_enet.Rd | 4 src/Makevars | 16 src/Makevars.win | 19 vignettes/Methods.Rmd | 202 ++++++++++ vignettes/references.bib | 12 vignettes/survkl.Rmd | 914 +++++++++++++++++++++++------------------------ 12 files changed, 1537 insertions(+), 976 deletions(-)
Title: ROBust INference for Covariate Adjustment in Randomized Clinical
Trials
Description: Performs robust estimation and inference when using covariate adjustment
and/or covariate-adaptive randomization in randomized controlled trials.
This package is trimmed to reduce the dependencies and validated to be used across industry.
See "FDA's final guidance on covariate adjustment"<https://www.regulations.gov/docket/FDA-2019-D-0934>, Tsiatis (2008) <doi:10.1002/sim.3113>,
Bugni et al. (2018) <doi:10.1080/01621459.2017.1375934>, Ye, Shao, Yi, and Zhao (2023)<doi:10.1080/01621459.2022.2049278>,
Ye, Shao, and Yi (2022)<doi:10.1093/biomet/asab015>, Rosenblum and van der Laan (2010)<doi:10.2202/1557-4679.1138>,
Wang et al. (2021)<doi:10.1080/01621459.2021.1981338>, Ye, Bannick, Yi, and Shao (2023)<doi:10.1080/24754269.2023.2205802>,
and Bannick, Shao, Liu, Du, Yi, and Ye (2024)<doi:10.48550/arXiv.2306.10213>.
Author: Liming Li [aut, cre] ,
Marlena Bannick [aut] ,
Daniel Sabanes Bove [aut] ,
Dong Xi [aut],
Ting Ye [aut],
Yanyao Yi [aut],
Gregory Chen [ctb],
Gilead Sciences, Inc. [cph, fnd],
F. Hoffmann-La Roche AG [cph, fnd],
Merck Sharp & Dohme, Inc. [cph, fnd],
[...truncated...]
Maintainer: Liming Li <liming.li1@astrazeneca.com>
Diff between RobinCar2 versions 0.2.2 dated 2026-01-09 and 0.2.3 dated 2026-07-02
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 10 ++++++++++ R/predict_couterfactual.R | 2 +- inst/WORDLIST | 23 +++++++++++++++++++++++ inst/doc/intro.html | 14 +++++++------- tests/testthat/test-predict_counterfactual.R | 13 +++++++++++++ 7 files changed, 64 insertions(+), 18 deletions(-)
Title: Higher-Level Interface of 'torch' Package to Auto-Train Neural
Networks
Description: Provides a higher-level interface to the 'torch' package for defining,
training, and fine-tuning neural networks through code generation.
The package supports several architectures, including feedforward
(multi-layer perceptron) and recurrent neural networks (RNN, LSTM,
GRU), while reducing boilerplate 'torch' code. Model training
methods also bridge to machine learning frameworks in R,
particularly the 'tidymodels' ecosystem, including 'parsnip' model
specifications, workflows, recipes, and tuning tools.
Author: Joshua Marie [aut, cre],
Antoine Soetewey [aut]
Maintainer: Joshua Marie <joshua.marie.k@gmail.com>
Diff between kindling versions 0.3.0 dated 2026-03-03 and 0.3.1 dated 2026-07-02
DESCRIPTION | 26 MD5 | 40 - NAMESPACE | 8 NEWS.md | 20 R/generalized-nn-fit.R | 1014 +++++++++++++++++++------------------ R/kindling-package.R | 17 R/plot.R |only R/utils.R | 8 R/variable-imp.R | 18 R/zzz.R | 1 README.md | 45 - inst/doc/custom-act-fn.html | 5 inst/doc/kindling.html | 5 inst/doc/special-cases.html | 5 inst/doc/tuning-capabilities.html | 5 man/autoplot.nn_fit.Rd |only man/autoplot_diagnostics.Rd |only man/kindling-varimp.Rd | 14 man/kindling.Rd | 15 man/reexports.Rd | 3 tests/testthat/test-plot.R |only tests/testthat/test-train-nn.R | 38 - tests/testthat/test-variable-imp.R | 6 23 files changed, 677 insertions(+), 616 deletions(-)
Title: Data Science Infrastructure for Global Health
Description: Supports global health data analysis, including a
publication-ready 'ggplot2' theme, a 'flextable' defaults helper,
a thin pie chart wrapper, built-in regional country-code datasets
with a WHO region lookup helper, a geometric mean function for
indicator aggregation, an average annual rate of reduction function
for indicator progress tracking, and convenience clients for the World
Health Organization Global Health Observatory (GHO) OData API
<https://ghoapi.azureedge.net/api/> and the United Nations
Sustainable Development Goals (SDG) API
<https://unstats.un.org/SDGAPI/swagger/>.
Author: Shanlong Ding [aut, cre]
Maintainer: Shanlong Ding <dings@who.int>
Diff between DSIR versions 0.7.1 dated 2026-05-23 and 0.8.0 dated 2026-07-02
DESCRIPTION | 11 ++-- MD5 | 42 ++++++++++------- NAMESPACE | 1 NEWS.md | 46 +++++++++++++++++++ R/aarr.R |only R/gho.R | 76 ++++++++++++++++++++++++++++---- README.md | 25 ++++++++++ build/vignette.rds |binary inst/WORDLIST | 3 + inst/doc/DSIR.html | 67 ++++++++++++++-------------- inst/doc/visualizing-indicators.R |only inst/doc/visualizing-indicators.Rmd |only inst/doc/visualizing-indicators.html |only man/aarr.Rd |only man/gho_count.Rd | 15 +++++- man/gho_coverage.Rd | 15 +++++- man/gho_data.Rd | 18 +++++++ man/gho_dimensions.Rd | 11 ++++ man/gho_has_data.Rd | 15 +++++- tests/testthat/test-aarr.R |only tests/testthat/test-gho-availability.R | 19 ++++++++ tests/testthat/test-gho-catalog-cache.R |only tests/testthat/test-gho-dimensions.R | 23 +++++++++ tests/testthat/test-gho-get-mock.R | 48 ++++++++++++++++++++ tests/testthat/test-gho.R | 34 ++++++++++++++ vignettes/visualizing-indicators.Rmd |only 26 files changed, 401 insertions(+), 68 deletions(-)
Title: Access Chinese Data via Public APIs and Curated Datasets
Description: Provides functions to access data from public RESTful APIs including 'Nager.Date'
and 'World Bank API', retrieving real-time or historical data related to China, such
as holidays and economic indicators. Additionally, the package includes one of the
largest curated collections of open datasets focused on China and Hong Kong, covering
topics such as air quality, demographics, input-output tables, epidemiology, political
structure, names, and social indicators. The package supports reproducible research
and teaching by integrating reliable international APIs and structured datasets from
public, academic, and government sources.
For more information on the APIs, see:
'Nager.Date' <https://date.nager.at/Api>,
'World Bank API' <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between ChinAPIs versions 0.1.1 dated 2026-02-12 and 0.2.0 dated 2026-07-02
ChinAPIs-0.1.1/ChinAPIs/R/get_country_info_cn.R |only ChinAPIs-0.1.1/ChinAPIs/man/get_country_info_cn.Rd |only ChinAPIs-0.1.1/ChinAPIs/tests/testthat/test-get_country_info_cn.R |only ChinAPIs-0.2.0/ChinAPIs/DESCRIPTION | 22 - ChinAPIs-0.2.0/ChinAPIs/MD5 | 143 ++++------ ChinAPIs-0.2.0/ChinAPIs/NAMESPACE | 2 ChinAPIs-0.2.0/ChinAPIs/NEWS.md | 17 + ChinAPIs-0.2.0/ChinAPIs/R/chinapis-package.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/data-documentation.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_child_mortality.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_cpi.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_energy_use.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_gdp.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_holidays.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_hospital_beds.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_life_expectancy.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_literacy_rate.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_population.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/get_china_unemployment.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/utils.R | 4 ChinAPIs-0.2.0/ChinAPIs/R/view_datasets_ChinAPIs.R | 4 ChinAPIs-0.2.0/ChinAPIs/README.md | 11 ChinAPIs-0.2.0/ChinAPIs/build/vignette.rds |binary ChinAPIs-0.2.0/ChinAPIs/inst/CITATION | 2 ChinAPIs-0.2.0/ChinAPIs/inst/doc/ChinAPIs_vignette.Rmd | 10 ChinAPIs-0.2.0/ChinAPIs/inst/doc/ChinAPIs_vignette.html | 18 - ChinAPIs-0.2.0/ChinAPIs/inst/licenses/LICENSE-APIs.txt | 9 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-COVID19_HongKong_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-bj_air_quality_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_admin_divisions_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_cars_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_corruption_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2002_122_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2005_42_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2007_135_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2010_41_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2012_139_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2015_42_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2017_149_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2017_42_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2018_153_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2018_42_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2020_153_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-china_io_2020_42_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-chinese_cities_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-chinese_dams_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-family_name_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_child_mortality.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_cpi.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_energy_use.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_gdp.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_holidays.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_hospital_beds.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_life_expectancy.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_literacy_rate.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_population.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-get_china_unemployment.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-given_name_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-health_family_life_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-hk_councillors_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-hk_districts_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-hk_population_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-hk_street_names_tbl_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-panda_locations_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-population_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-sars_hong_kong_list.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-shanghai_factories_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-shanghai_pm25_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-top1000name_prov_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-top100name_year_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-top50char_year_df.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-view_datasets_ChinAPIs.R | 4 ChinAPIs-0.2.0/ChinAPIs/tests/testthat/test-wenchuan_ptsd_matrix.R | 4 ChinAPIs-0.2.0/ChinAPIs/vignettes/ChinAPIs_vignette.Rmd | 10 74 files changed, 239 insertions(+), 245 deletions(-)
Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Tools for fitting self-validated ensemble models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) in small-sample design-of-experiments and related workflows, using elastic net and relaxed elastic net regression via 'glmnet' (Friedman et al. (2010) <doi:10.18637/jss.v033.i01>). Fractional random-weight bootstraps with anti-correlated validation copies are used to tune penalty paths by validation-weighted AIC/BIC. Supports Gaussian and binomial responses, deterministic expansion helpers for shared factor spaces, prediction with bootstrap uncertainty, and a random-search optimizer that respects mixture constraints and combines multiple responses via desirability functions. Also includes a permutation-based whole-model test for Gaussian SVEM fits (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). The package and its workflows are described in Karl (2026) <doi:10.1016/j.chemolab.2026.105660>. Package code was drafted with assistance from generative [...truncated...]
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 3.2.1 dated 2026-06-02 and 3.2.3 dated 2026-07-02
DESCRIPTION | 10 - MD5 | 52 +++---- NEWS | 43 ++++- R/SVEMnet.R | 143 ++++++++++++++++++- R/bigexp.R | 51 ++++++- R/coef.R | 4 R/export_candidates_csv.R | 9 - R/glmnet_compat.R | 40 +++++ R/glmnet_with_cv.R | 223 +++++++++++++++---------------- R/select_candidates.R | 6 R/svem_random_table_multi.R | 26 ++- R/svem_score_random.R | 56 ++++++- R/svem_select_score_from_table.R | 28 +++ R/svem_significance_test_parallel.R | 79 +++++++++- inst/CITATION | 20 ++ man/SVEMnet-package.Rd | 4 man/SVEMnet.Rd | 66 ++++++++- man/bigexp_terms.Rd | 9 - man/glmnet_with_cv.Rd | 41 +++-- man/lipid_screen.Rd | 4 man/svem_nonzero.Rd | 4 man/svem_random_table_multi.Rd | 2 man/svem_score_random.Rd | 27 +++ man/svem_select_from_score_table.Rd | 22 ++- man/svem_significance_test_parallel.Rd | 21 +- tests/testthat/test-audit-fixes.R |only tests/testthat/test-complexity-edf.R |only tests/testthat/test-significance-tests.R | 50 +++++- 28 files changed, 779 insertions(+), 261 deletions(-)
Title: Univariate and Multivariate Damped Random Walk Processes
Description: Provides tools for fitting and simulating univariate and multivariate damped random walk processes, also known as Ornstein-Uhlenbeck processes or first-order continuous-time autoregressive models, CAR(1) or CARMA(1, 0). The package supports irregularly spaced observation times, heteroscedastic measurement errors, missing measurements across multivariate time series, and polynomial mean trends in normalized time. The current implementation models up to ten time series jointly. Kalman filtering is used to evaluate the likelihood efficiently for maximum likelihood estimation and Bayesian posterior sampling. Users should preserve sufficient numerical precision when loading astronomical observation times; see the manual for details. Also see Hu and Tak (2020) <doi:10.48550/arXiv.2005.08049>.
Author: Zhirui Hu [aut],
Hyungsuk Tak [aut, cre]
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between Rdrw versions 1.0.2 dated 2020-09-08 and 1.0.3 dated 2026-07-02
DESCRIPTION | 20 - MD5 | 14 NAMESPACE | 4 R/drw.R | 961 +++++++++++++++++++++++---------------------------- man/Rdrw-internal.Rd | 2 man/Rdrw-package.Rd | 8 man/drw.Rd | 201 +++------- man/drw.sim.Rd | 49 +- 8 files changed, 544 insertions(+), 715 deletions(-)
Title: Degree-Day Phenology Calculator ('shiny' Application)
Description: Provides a 'shiny' application to compute daily and cumulative degree-days from minimum and maximum temperatures using average, single triangle, and single sine methods, with optional upper temperature thresholds. The application maps cumulative thermal accumulation to user-defined developmental stage thresholds and supports exporting tabular and graphical outputs. The degree-day approach follows assumptions described by Higley et al. (1986) <doi:10.1093/ee/15.5.999>.
Author: Victor Manuel Almaraz Valle [aut, cre] ,
J. Concepcion Rodriguez Maciel [aut],
Gustavo Ramirez Valverde [aut],
Jaime Alfredo Urzua Gutierrez [aut],
Manuel Alejandro Tejeda Reyes [aut]
Maintainer: Victor Manuel Almaraz Valle <almarazkrae@gmail.com>
Diff between DegreeDayCalc versions 0.1.0 dated 2026-02-17 and 0.1.1 dated 2026-07-02
DESCRIPTION | 10 - MD5 | 16 +- NAMESPACE | 1 R/degree_days.R | 171 +++++++++++------------ R/zzz.R | 7 README.md | 16 -- inst/CITATION | 69 ++++----- inst/app/app.R | 245 +++++++++++++++++++++++---------- tests/testthat/test-degree-days-core.R | 32 ++++ 9 files changed, 350 insertions(+), 217 deletions(-)
Title: Store and Transfer Amplicon Sequence Data
Description: Stores the data associated with your amplicon sequence analysis. This includes nucleotide sequences, abundance, sample and treatment assignments, taxonomic classifications, asv, otu and phylotype clusters, metadata, trees and various reports. It is designed to facilitate data analysis across multiple R packages with utility functions to read / write from 'mothur', 'qiime2', 'dada2', and 'phyloseq'.
Author: Sarah Westcott [aut] ,
Gregory Johnson [aut] ,
Pat Schloss [cph, cre]
Maintainer: Pat Schloss <pschloss@umich.edu>
Diff between strollur versions 0.1.2 dated 2026-06-24 and 0.1.3 dated 2026-07-02
DESCRIPTION | 8 MD5 | 106 +-- NAMESPACE | 1 NEWS.md | 13 R/RcppExports.R | 18 R/add.R | 40 - R/error_messages.R | 10 R/import_dataset.R | 20 R/load_dataset.R | 6 R/r6_strollur.R | 58 - R/read_mothur_oligos.R |only R/read_phyloseq.R | 2 R/read_qiime2.R | 6 R/report.R | 4 R/utils.R | 24 R/write_mothur.R | 13 README.md | 5 inst/doc/Accessing_Dataset.html | 17 inst/doc/Data_Transfers.html | 232 +++---- inst/doc/Example_Analysis_Across_Software_Tools.R | 2 inst/doc/Example_Analysis_Across_Software_Tools.Rmd | 2 inst/doc/Example_Analysis_Across_Software_Tools.html | 6 inst/doc/Functions_for_Package_Developers.html | 556 +++++++++---------- inst/doc/General_Importing.R | 3 inst/doc/General_Importing.Rmd | 5 inst/doc/General_Importing.html | 20 inst/doc/Importing_from_phyloseq.html | 8 inst/doc/Importing_from_qiime2.R | 2 inst/doc/Importing_from_qiime2.Rmd | 2 inst/doc/Importing_from_qiime2.html | 10 inst/extdata/miseq_sop.010.rds |only inst/extdata/miseq_sop.rds |binary inst/extdata/miseq_sop_table.010.rds |only inst/extdata/paired_read.oligos |only inst/include/strollur.h | 6 man/add.Rd | 11 man/read_mothur_oligos.Rd |only man/report.Rd | 4 man/strollur.Rd | 12 man/xdev_add_report.Rd | 13 man/xdev_report.Rd | 4 src/bintable.cpp | 2 src/dataset.cpp | 38 - src/rcpp_xint_xdev_functions.cpp | 55 + src/rcpp_xint_xdev_functions.h | 20 tests/testthat/_snaps/r6_strollur.md | 6 tests/testthat/test-import.R | 17 tests/testthat/test-is_equal.R | 2 tests/testthat/test-names.R | 2 tests/testthat/test-r6_strollur.R | 6 tests/testthat/test-read_mothur_oligos.R |only tests/testthat/test-save_load.R | 20 tests/testthat/test-write_mothur.R | 2 tests/testthat/test-xint-xdev.R | 2 vignettes/Example_Analysis_Across_Software_Tools.Rmd | 2 vignettes/General_Importing.Rmd | 5 vignettes/Importing_from_qiime2.Rmd | 2 57 files changed, 720 insertions(+), 710 deletions(-)
Title: 'shiny' Application for Life Table and Fertility Analysis
Description: Provides a 'shiny' application to construct age-specific life tables and fertility schedules from individual female daily egg records. The application computes age-specific survival and fertility functions and estimates key demographic parameters including the net reproductive rate, mean generation time, intrinsic rate of increase, finite rate of increase and doubling time. Optional confidence intervals can be obtained using percentile bootstrap or delete-1 jackknife resampling at the female level. Methods and definitions follow Stevens (2009) <doi:10.1007/978-0-387-89882-7> and Rossini et al. (2024) <doi:10.1371/journal.pone.0299598>.
Author: Victor Manuel Almaraz Valle [aut, cre]
Maintainer: Victor Manuel Almaraz Valle <almarazkrae@gmail.com>
Diff between LifeTableFertility versions 0.1.0 dated 2026-02-17 and 0.1.1 dated 2026-07-02
DESCRIPTION | 12 +-- MD5 | 9 +- NAMESPACE | 3 R/imports.R |only inst/CITATION | 35 +++++------ inst/app/app.R | 181 +++++++++++++++++++++++++++------------------------------ 6 files changed, 116 insertions(+), 124 deletions(-)
More information about LifeTableFertility at CRAN
Permanent link
Title: Interactive 'shiny' Application for Constructing Life Tables
Description: Provides an interactive 'shiny' application to construct stage-structured life tables from tabular input data. The application includes input validation, demographic calculations, visualization tools, and export of tables and figures to support reproducible workflows in ecological and entomological studies. Methods for life table construction follow classical demographic approaches described in Martinez (2015) <doi:10.13140/RG.2.2.21333.65760>.
Author: Victor Manuel Almaraz Valle [aut, cre],
J. Concepcion Rodriguez Maciel [aut],
Gustavo Ramirez Valverde [aut],
Carlos Eduardo Aguilar Castillo [aut],
Alejandro Perez Panduro [aut]
Maintainer: Victor Manuel Almaraz Valle <almarazkrae@gmail.com>
Diff between LifeTableBuilder versions 0.1.2 dated 2026-02-20 and 0.1.3 dated 2026-07-02
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- README.md | 2 +- inst/CITATION | 17 +++++++++-------- inst/shiny/app.R | 17 +++++++++++------ 5 files changed, 32 insertions(+), 26 deletions(-)
More information about LifeTableBuilder at CRAN
Permanent link
Title: Forest Many-Objective Robust Decision Making ('FoRDM')
Description: Forest Many-Objective Robust Decision Making ('FoRDM') is a R toolkit for supporting robust forest management under deep uncertainty.
It provides a forestry-focused application of Many-Objective Robust Decision Making ('MORDM') to forest simulation outputs,
enabling users to evaluate robustness using regret- and 'satisficing'-based measures. 'FoRDM' identifies robust solutions,
generates Pareto fronts, and offers interactive 2D, 3D, and parallel-coordinate visualizations.
Author: Marc Djahangard [aut, cre],
Rasoul Yousefpour [aut]
Maintainer: Marc Djahangard <marc.djahangard@ife.uni-freiburg.de>
Diff between FoRDM versions 1.0.2 dated 2026-04-07 and 1.0.3 dated 2026-07-02
DESCRIPTION | 10 ++++++---- MD5 | 12 ++++++------ NAMESPACE | 2 +- NEWS | 8 +++----- R/FoRDM.R | 35 ++++++++++++++++++----------------- README.md | 2 +- inst/CITATION | 23 +++++++++++++++-------- 7 files changed, 50 insertions(+), 42 deletions(-)
Title: Standardized Economic Reporting and Automated Dynamic Writing /
Synthèse d'Écrits Avec des Règles Automatisées et Dynamiques
Description: Provides tools for generating dynamic and standardized
economic narratives in R Markdown documents. The package is primarily
designed for French-language statistical and economic publications.
It includes functions to describe changes in levels, percentages,
trends, accelerations and short-term economic developments using
consistent linguistic rules. The package supports automated reporting
workflows and reproducible economic writing.
Fournit des outils permettant de générer des textes économiques
dynamiques et standardisés dans des documents R Markdown. Le package
est principalement conçu pour les publications statistiques et
économiques en français. Il propose des fonctions permettant de
décrire les évolutions de niveaux, de pourcentages, de tendances,
d'accélérations et les évolutions conjoncturelles à l'aide de règles
linguistiques homogènes. Le package facilite l'automatisation de la
rédaction et la reproductibilité des publications économiques.
Author: Alexandre Cazenave-Lacroutz [aut] ,
Jules Lejas [cre],
Direction de l'animation de la recherche, des etudes et des
statistiques [cph]
Maintainer: Jules Lejas <jules.lejas@gmail.com>
Diff between serad versions 0.2.1 dated 2026-06-17 and 0.2.2 dated 2026-07-01
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/init_serad_en.R | 18 +++++++++--------- R/init_serad_fr.R | 18 +++++++++--------- 4 files changed, 24 insertions(+), 24 deletions(-)
Title: Pathways Longitudinal and Differential Analysis in Metabolomics
Description: Perform a differential analysis at pathway level based on
metabolite quantifications and information on pathway metabolite
composition. The method, described in Guilmineau et al (2025)
<doi:10.1186/s12859-025-06118-z> is based on a Principal Component
Analysis step and on a linear mixed model.
Automatic query of metabolic pathways is also implemented.
Author: Camille Guilmineau [aut],
Remi Servien [aut, cre] ,
Nathalie Vialaneix [aut]
Maintainer: Remi Servien <remi.servien@inrae.fr>
Diff between phoenics versions 0.6 dated 2025-08-19 and 0.6.1 dated 2026-07-01
DESCRIPTION | 10 ++-- MD5 | 16 +++---- R/pathway_search.R | 2 R/test_pathway.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction.html | 100 ++++++++++++++++++++++----------------------- man/pathway_search.Rd | 2 man/test_pathway.Rd | 2 9 files changed, 68 insertions(+), 66 deletions(-)
Title: Centering and Scaling of Numeric Data
Description: Provides simple methods for centering and scaling of numeric data.
Columns or rows can be ignored when normalizing or be normalized jointly.
Author: Lennart Oelschlaeger [aut, cre]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between normalize versions 0.1.2 dated 2025-06-10 and 0.1.3 dated 2026-07-01
DESCRIPTION | 8 MD5 | 20 NAMESPACE | 18 NEWS.md | 34 - R/normalize-package.R | 16 R/normalize.R | 821 +++++++++++++++++++++++++++------------- README.md | 242 +++++------ man/normalize-package.Rd | 53 +- man/normalize.Rd | 191 ++++----- tests/testthat.R | 24 - tests/testthat/test-normalize.R | 780 +++++++++++++++++++++++--------------- 11 files changed, 1347 insertions(+), 860 deletions(-)
Title: Visualizing and Quantifying Space Use Data for Groups of Animals
Description: Offers an easy and automated way to scale up individual-level space use analysis to
that of groups. Contains functions from the 'move' package to calculate either a dynamic Brownian
bridge movement model or dynamic Bivariate Gaussian bridges from movement data for individual animals, as well as functions to
visualize and quantify space use for individuals aggregated in groups. Originally written with
passive acoustic telemetry in mind, this package also provides functionality to account for
unbalanced acoustic receiver array designs, and satellite tag data.
Author: Simon Dedman [aut, cre] ,
Maurits van Zinnicq Bergmann [aut] ,
Vital Heim [aut]
Maintainer: Simon Dedman <simondedman@gmail.com>
Diff between movegroup versions 2024.03.05 dated 2024-03-07 and 2026.07.01 dated 2026-07-01
DESCRIPTION | 23 LICENSE | 4 MD5 | 78 - NAMESPACE | 163 +-- NEWS.md | 32 R/alignraster.R | 288 ++--- R/data.R | 102 - R/globals.R |only R/moveLocErrorCalc.R | 204 +-- R/movegroup-package.R | 14 R/movegroup.R | 1571 ++++++++++++++++++------------ R/plotraster.R | 1491 +++++++++++++++------------- R/scaleraster.R | 693 ++++++------- R/stitchraster.R |only R/utils.R | 8 R/zzz.R |only README.md | 960 +++++++++--------- build/vignette.rds |binary inst/CITATION | 24 inst/Misc/RunScriptExample.R | 274 ++--- inst/doc/Using-the-movegroup-package.R | 18 inst/doc/Using-the-movegroup-package.Rmd | 4 inst/doc/Using-the-movegroup-package.html | 1456 +++++++++++++-------------- man/TracksCleaned.Rd | 64 - man/alignraster.Rd | 184 +-- man/argosFiltered.Rd | 76 - man/figures/lifecycle-archived.svg | 42 man/figures/lifecycle-defunct.svg | 42 man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-maturing.svg | 42 man/figures/lifecycle-questioning.svg | 42 man/figures/lifecycle-soft-deprecated.svg | 42 man/figures/lifecycle-stable.svg | 58 - man/figures/lifecycle-superseded.svg | 42 man/moveLocErrorCalc.Rd | 124 +- man/movegroup-package.Rd | 43 man/movegroup.Rd | 522 +++++---- man/plotraster.Rd | 608 ++++++----- man/scaleraster.Rd | 272 ++--- man/stitchraster.Rd |only vignettes/Using-the-movegroup-package.Rmd | 4 42 files changed, 5160 insertions(+), 4538 deletions(-)
Title: Access Mexican Data via APIs and Curated Datasets
Description: Provides functions to access data from public RESTful APIs including
'World Bank API', and 'Nager.Date API', covering Mexico's economic
indicators, population statistics, literacy rates, and official public
holidays. The package also includes curated datasets related to Mexico
such as air quality monitoring stations, pollution zones, income surveys,
postal abbreviations, election studies, forest productivity and
demographic data by state. It supports research and analysis focused on
Mexico by integrating reliable global APIs with structured national
datasets drawn from open and academic sources.
For more information on the APIs, see:
'World Bank API' <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392>,
and 'Nager.Date API' <https://date.nager.at/Api>.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between MexicoDataAPI versions 0.2.0 dated 2025-09-13 and 0.3.0 dated 2026-07-01
MexicoDataAPI-0.2.0/MexicoDataAPI/R/get_country_info_mx.R |only MexicoDataAPI-0.2.0/MexicoDataAPI/man/get_country_info_mx.Rd |only MexicoDataAPI-0.2.0/MexicoDataAPI/tests/testthat/test-get_country_info_mx.R |only MexicoDataAPI-0.3.0/MexicoDataAPI/DESCRIPTION | 23 +- MexicoDataAPI-0.3.0/MexicoDataAPI/MD5 | 83 ++++------ MexicoDataAPI-0.3.0/MexicoDataAPI/NAMESPACE | 2 MexicoDataAPI-0.3.0/MexicoDataAPI/NEWS.md | 12 + MexicoDataAPI-0.3.0/MexicoDataAPI/R/data-documentation.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/get_mexico_cpi.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/get_mexico_gdp.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/get_mexico_holidays.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/get_mexico_life_expectancy.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/get_mexico_literacy_rate.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/get_mexico_population.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/get_mexico_unemployment.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/mexicodataapi-package.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/utils.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/R/view_datasets_MexicoDataAPI.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/README.md | 8 MexicoDataAPI-0.3.0/MexicoDataAPI/build/vignette.rds |binary MexicoDataAPI-0.3.0/MexicoDataAPI/inst/CITATION | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/inst/doc/MexicoDataAPI_vignette.Rmd | 10 - MexicoDataAPI-0.3.0/MexicoDataAPI/inst/doc/MexicoDataAPI_vignette.html | 54 +++--- MexicoDataAPI-0.3.0/MexicoDataAPI/inst/licenses/LICENSE | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/inst/licenses/LICENSE.md | 14 - MexicoDataAPI-0.3.0/MexicoDataAPI/inst/licenses/LICENSES_DETAILS.md | 2 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-chiapas_dry_forests_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-get_mexico_cpi.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-get_mexico_gdp.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-get_mexico_holidays.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-get_mexico_life_expectancy.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-get_mexico_literacy_rate.R | 21 +- MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-get_mexico_population.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-get_mexico_unemployment.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-mex_income_2008_tbl_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-mex_income_2016_tbl_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-mexico_abb_chr.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-mexico_elections_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-mexico_states_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-pollution_stations_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-pollution_zones_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-stations_sinaica_df.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/tests/testthat/test-view_datasets_MexicoDataAPI.R | 4 MexicoDataAPI-0.3.0/MexicoDataAPI/vignettes/MexicoDataAPI_vignette.Rmd | 10 - 44 files changed, 171 insertions(+), 184 deletions(-)
Title: Diagnostic Tools for Asymptotic Theory
Description: Leveraging Monte Carlo simulations, this package provides
tools for diagnosing regression models. It implements a parametric
bootstrap framework to compute statistics, generates diagnostic
envelopes to assess goodness-of-fit, and evaluates type I error
control for Wald tests. By simulating data under the assumption that
the model is true, it helps to identify model mis-specifications and
enhances the reliability of the model inferences.
Author: Alvaro Kothe [aut, cre, cph] ,
Alexandre Patriota [aut]
Maintainer: Alvaro Kothe <kothe65@gmail.com>
Diff between asympDiag versions 0.3.2 dated 2026-02-15 and 0.3.3 dated 2026-07-01
DESCRIPTION | 6 ++--- MD5 | 12 +++++------ tests/testthat/Rplots.pdf |binary tests/testthat/test-concat.R | 7 ++++-- tests/testthat/test-envelope.R | 14 +++++++++++-- tests/testthat/test-get_refit.R | 2 + tests/testthat/test-simulate_wald_pvalues.R | 29 +++++++++++++++++++--------- 7 files changed, 48 insertions(+), 22 deletions(-)
Title: Lossless CDISC-Native Input and Output for Clinical Datasets
Description: Reads and writes clinical-trial datasets losslessly across
'SAS' XPORT (XPT), Clinical Data Interchange Standards Consortium
(CDISC) Dataset-JSON, and 'Apache Parquet', applying a specification to
produce submission-ready Study Data Tabulation Model (SDTM) and
Analysis Data Model (ADaM) datasets. A single canonical metadata model
carries labels, CDISC data types, lengths, 'SAS' display formats,
controlled-terminology references, and sort keys identically across
every format, so conversion between any two formats is lossless by
construction. Pure 'R' and lightweight, with no external 'SAS' or
'Java' runtime. Implements the published format specifications for
CDISC Dataset-JSON
(<https://cdisc-org.github.io/DataExchange-DatasetJson/doc/dataset-json1-1.html>)
and 'SAS' XPORT
(<https://www.loc.gov/preservation/digital/formats/fdd/fdd000466.shtml>).
Author: Vignesh Thanikachalam [aut, cre, cph]
Maintainer: Vignesh Thanikachalam <about.vignesh@gmail.com>
Diff between artoo versions 0.1.1 dated 2026-06-24 and 0.1.2 dated 2026-07-01
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ man/artoo-package.Rd | 2 +- tests/testthat/test-codec_json.R | 15 +++++++++++++-- 5 files changed, 27 insertions(+), 10 deletions(-)
Title: AI Screening Tools in R for Systematic Reviewing
Description: Provides functions to conduct title and abstract screening in systematic reviews using large language models, such as the Generative Pre-trained Transformer (GPT) models from 'OpenAI' <https://developers.openai.com/>. These functions can enhance the quality of title and abstract screenings while reducing the total screening time significantly. In addition, the package includes tools for quality assessment of title and abstract screenings, as described in Vembye, Christensen, Mølgaard, and Schytt (2025) <DOI:10.1037/met0000769>.
Author: Mikkel H. Vembye [aut, cre] ,
Thomas Olsen [aut]
Maintainer: Mikkel H. Vembye <mikkel.vembye@gmail.com>
Diff between AIscreenR versions 0.3.2 dated 2026-04-20 and 0.4.0 dated 2026-07-01
DESCRIPTION | 8 MD5 | 102 +- NAMESPACE | 7 NEWS.md | 144 ++- R/api_key_functions.R | 149 +++ R/claude_engine.r |only R/data.R | 41 + R/function-calling.R | 170 ++++ R/gemini_engine.r |only R/groq_engine.r | 40 - R/misc.func.hidden.price.R | 36 R/misc.func.hidden.tabscreen.R | 384 +++++++++- R/misc.helpers.R | 53 + R/ollama_engine.r | 59 - R/rate_limits.R | 73 + R/save_functions.r | 35 R/screen_analyzer.R | 2 R/screen_errors.R | 2 R/screen_errors.gpt.R | 2 R/tabscreen_claude.R |only R/tabscreen_gemini.R |only R/tabscreen_gpt.R | 41 - R/tabscreen_gpt.original.R | 8 R/tabscreen_gpt.tools.R |only R/tabscreen_mistral.R |only R/tabscreen_ollama.r | 33 build/partial.rdb |binary build/vignette.rds |binary data/claude_model_prizes.rda |only data/gemini_model_prizes.rda |only data/groq_model_prizes.rda |binary data/mistral_model_prizes.rda |only data/model_prizes.rda |binary inst/doc/Using-GPT-API-Models-For-Screening.html | 8 inst/doc/Using-GPT-API-Models-For-Screening.qmd | 2 inst/extdata/comparison-results/results_4omini_5mini_51_ministral_comparison.csv |only man/AIscreenR-package.Rd | 1 man/claude_model_prizes.Rd |only man/figures/AIscreenR_hex_light.png |only man/gemini_model_prizes.Rd |only man/get_api_key.Rd | 2 man/get_api_key_anthropic.Rd |only man/get_api_key_gemini.Rd |only man/get_api_key_groq.Rd | 2 man/get_api_key_mistral.Rd |only man/mistral_model_prizes.Rd |only man/rate_limits_per_minute.Rd | 16 man/screen_errors.gpt.Rd | 6 man/set_api_key.Rd | 2 man/tabscreen_claude.Rd |only man/tabscreen_gemini.Rd |only man/tabscreen_gpt.original.Rd | 4 man/tabscreen_gpt.tools.Rd | 26 man/tabscreen_gpt.tools_responses.Rd |only man/tabscreen_mistral.Rd |only man/tabscreen_ollama.Rd | 21 tests/testthat/test-save_functions.r | 4 tests/testthat/test-tabscreen_claude.R |only tests/testthat/test-tabscreen_gemini.R |only tests/testthat/test-tabscreen_gpt.R | 130 +-- tests/testthat/test-tabscreen_groq.R | 8 tests/testthat/test-tabscreen_mistral.R |only tests/testthat/test-tabscreen_ollama.r | 8 vignettes/Using-GPT-API-Models-For-Screening.qmd | 2 64 files changed, 1259 insertions(+), 372 deletions(-)
Title: 'A5' Discrete Global Grid System
Description: Bindings for the "A5 geospatial index"
<https://a5geo.org/>. 'A5' partitions the Earth's surface into
pentagonal cells across 31 resolution levels using an equal-area
projection onto a dodecahedron. Provides functions for indexing
coordinates to cells, traversing the cell hierarchy, computing cell
boundaries, and compacting/uncompacting cell sets. Powered by the
'A5' 'Rust' crate via 'extendr'.
Author: Hugh Graham [aut, cre],
belian.earth [cph]
Maintainer: Hugh Graham <hugh@belian.earth>
Diff between a5R versions 0.4.0 dated 2026-05-14 and 0.5.0 dated 2026-07-01
a5R-0.4.0/a5R/R/grid.R |only a5R-0.4.0/a5R/man/a5_grid.Rd |only a5R-0.4.0/a5R/src/rust/src/grid.rs |only a5R-0.4.0/a5R/tests/testthat/test-grid.R |only a5R-0.5.0/a5R/DESCRIPTION | 9 a5R-0.5.0/a5R/MD5 | 30 +- a5R-0.5.0/a5R/NAMESPACE | 1 a5R-0.5.0/a5R/NEWS.md | 23 + a5R-0.5.0/a5R/R/extendr-wrappers.R | 28 -- a5R-0.5.0/a5R/R/regions.R | 42 --- a5R-0.5.0/a5R/man/a5_polygon_to_cells.Rd | 12 a5R-0.5.0/a5R/src/rust/Cargo.lock | 336 --------------------------- a5R-0.5.0/a5R/src/rust/Cargo.toml | 5 a5R-0.5.0/a5R/src/rust/src/distance.rs | 61 ++++ a5R-0.5.0/a5R/src/rust/src/lib.rs | 2 a5R-0.5.0/a5R/src/rust/src/regions.rs | 84 ++++-- a5R-0.5.0/a5R/src/rust/vendor.tar.xz |binary a5R-0.5.0/a5R/tests/testthat/test-distance.R | 81 ++++++ 18 files changed, 249 insertions(+), 465 deletions(-)
Title: Fast and Scalable Cellwise-Robust Ensemble
Description: Functions to perform robust variable selection and regression using the Fast and Scalable
Cellwise-Robust Ensemble (FSCRE) algorithm. The approach establishes a robust foundation
using the Detect Deviating Cells (DDC) algorithm and robust correlation estimates. It then
employs a competitive ensemble architecture where a robust Least Angle Regression (LARS)
engine proposes candidate variables and cross-validation arbitrates their assignment. A final
robust MM-estimator is applied to the selected predictors.
Author: Anthony Christidis [aut, cre],
Gabriela Cohen-Freue [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between srlars versions 3.0.0 dated 2026-06-12 and 3.0.1 dated 2026-07-01
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 ++++- R/srlars.R | 6 +++--- man/srlars.Rd | 6 +++--- 5 files changed, 18 insertions(+), 15 deletions(-)
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <https://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey [aut],
Cory Nathe [cre]
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 3.4.6 dated 2026-02-21 and 3.5.0 dated 2026-07-01
DESCRIPTION | 10 +++--- MD5 | 70 +++++++++++++++++++++---------------------- NEWS | 5 +++ R/ifcookie.R | 2 - R/labkey.defaults.R | 2 - R/labkey.deleteRows.R | 2 - R/labkey.domain.R | 2 - R/labkey.executeSql.R | 2 - R/labkey.experiment.R | 2 - R/labkey.getFolders.R | 2 - R/labkey.getQueryInfo.R | 2 - R/labkey.getQueryLists.R | 2 - R/labkey.getSchemas.R | 2 - R/labkey.importRows.R | 2 - R/labkey.insertRows.R | 2 - R/labkey.moduleProperty.R | 2 - R/labkey.moveRows.R | 2 - R/labkey.pipeline.R | 2 - R/labkey.provenance.R | 2 - R/labkey.query.import.R | 2 - R/labkey.rstudio.R | 2 - R/labkey.saveBatch.R | 2 - R/labkey.security.R | 2 - R/labkey.selectRows.R | 2 - R/labkey.setCurlOptions.R | 2 - R/labkey.storage.R | 9 +++-- R/labkey.transform.R | 2 - R/labkey.updateRows.R | 2 - R/labkey.webdav.R | 2 - R/makeDF.R | 17 ++++++++-- R/makeFilter.R | 2 - R/parseHeader.R | 2 - R/schemaObjects.R | 2 - man/Rlabkey-package.Rd | 4 +- man/labkey.storage.delete.Rd | 13 +++++++ man/labkey.storage.update.Rd | 15 ++++++++- 36 files changed, 121 insertions(+), 78 deletions(-)
Title: Lightweight Toolkit for Messaging, Concurrency and the Web
Description: R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ.
A toolkit for messaging, concurrency and the web. High-performance
socket messaging over in-process, IPC, TCP, WebSocket and secure TLS
transports implements 'Scalability Protocols', a standard for common
communications patterns including publish/subscribe, request/reply and
survey. A threaded concurrency framework with intuitive 'aio' objects
that resolve automatically upon completion of asynchronous operations,
and synchronisation primitives that allow R to wait on events
signalled by concurrent threads. A unified HTTP server hosting REST
endpoints, WebSocket connections and streaming on a single port, with
a built-in HTTP client.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph],
Staysail Systems, Inc. [cph] ,
Capitar IT Group BV [cph] ,
The Mbed TLS Contributors [cph] ,
Pierre L'Ecuyer [cph] ,
sakura authors [cph] ,
R Consortium [fnd]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between nanonext versions 1.9.1 dated 2026-06-01 and 1.10.0 dated 2026-07-01
nanonext-1.10.0/nanonext/DESCRIPTION | 11 nanonext-1.10.0/nanonext/MD5 | 343 ++--- nanonext-1.10.0/nanonext/NAMESPACE | 1 nanonext-1.10.0/nanonext/NEWS.md | 17 nanonext-1.10.0/nanonext/R/aio.R | 47 nanonext-1.10.0/nanonext/R/nano.R | 64 - nanonext-1.10.0/nanonext/R/ncurl.R | 17 nanonext-1.10.0/nanonext/README.md | 10 nanonext-1.10.0/nanonext/build/vignette.rds |binary nanonext-1.10.0/nanonext/cleanup | 6 nanonext-1.10.0/nanonext/cleanup.win | 7 nanonext-1.10.0/nanonext/configure | 396 +++++- nanonext-1.10.0/nanonext/inst/doc/nanonext.html | 2 nanonext-1.10.0/nanonext/inst/doc/v01-messaging.html | 2 nanonext-1.10.0/nanonext/inst/doc/v02-protocols.Rmd | 47 nanonext-1.10.0/nanonext/inst/doc/v02-protocols.html | 39 nanonext-1.10.0/nanonext/inst/doc/v03-configuration.html | 2 nanonext-1.10.0/nanonext/inst/doc/v04-web.html | 2 nanonext-1.10.0/nanonext/man/device_aio.Rd |only nanonext-1.10.0/nanonext/man/ncurl.Rd | 17 nanonext-1.10.0/nanonext/man/ncurl_aio.Rd | 17 nanonext-1.10.0/nanonext/man/ncurl_session.Rd | 17 nanonext-1.10.0/nanonext/src/Makevars.in | 337 +++++ nanonext-1.10.0/nanonext/src/Makevars.ucrt | 310 ++++ nanonext-1.10.0/nanonext/src/Makevars.win | 310 ++++ nanonext-1.10.0/nanonext/src/aio.c | 54 nanonext-1.10.0/nanonext/src/comms.c | 22 nanonext-1.10.0/nanonext/src/core.c | 68 - nanonext-1.10.0/nanonext/src/dispatcher.c | 4 nanonext-1.10.0/nanonext/src/init.c | 1 nanonext-1.10.0/nanonext/src/mbedtls/include/mbedtls/mbedtls_config.h | 16 nanonext-1.10.0/nanonext/src/mbedtls/library/aes.c | 10 nanonext-1.10.0/nanonext/src/mbedtls/library/asn1parse.c | 2 nanonext-1.10.0/nanonext/src/mbedtls/library/asn1write.c | 4 nanonext-1.10.0/nanonext/src/mbedtls/library/bignum.c | 10 nanonext-1.10.0/nanonext/src/mbedtls/library/ccm.c | 2 nanonext-1.10.0/nanonext/src/mbedtls/library/constant_time.c | 4 nanonext-1.10.0/nanonext/src/mbedtls/library/ctr_drbg.c | 2 nanonext-1.10.0/nanonext/src/mbedtls/library/ecp.c | 10 nanonext-1.10.0/nanonext/src/mbedtls/library/gcm.c | 2 nanonext-1.10.0/nanonext/src/mbedtls/library/ssl_msg.c | 10 nanonext-1.10.0/nanonext/src/mbedtls/library/ssl_tls.c | 20 nanonext-1.10.0/nanonext/src/mbedtls/library/ssl_tls12_server.c | 2 nanonext-1.10.0/nanonext/src/mbedtls/library/x509.c | 4 nanonext-1.10.0/nanonext/src/mbedtls/library/x509_create.c | 6 nanonext-1.10.0/nanonext/src/mbedtls/library/x509write.c | 2 nanonext-1.10.0/nanonext/src/nanonext.h | 11 nanonext-1.10.0/nanonext/src/ncurl.c | 96 - nanonext-1.10.0/nanonext/src/nng/include/nng/nng.h | 286 ++++ nanonext-1.10.0/nanonext/src/nng/include/nng/protocol/pubsub0/sub.h | 7 nanonext-1.10.0/nanonext/src/nng/include/nng/supplemental/tls/engine.h | 8 nanonext-1.10.0/nanonext/src/nng/include/nng/supplemental/tls/tls.h | 7 nanonext-1.10.0/nanonext/src/nng/include/nng/supplemental/util/platform.h | 54 nanonext-1.10.0/nanonext/src/nng/src/core/aio.c | 23 nanonext-1.10.0/nanonext/src/nng/src/core/aio.h | 3 nanonext-1.10.0/nanonext/src/nng/src/core/dialer.c | 18 nanonext-1.10.0/nanonext/src/nng/src/core/dialer.h | 3 nanonext-1.10.0/nanonext/src/nng/src/core/idhash.c | 23 nanonext-1.10.0/nanonext/src/nng/src/core/idhash.h | 3 nanonext-1.10.0/nanonext/src/nng/src/core/init.c | 16 nanonext-1.10.0/nanonext/src/nng/src/core/listener.c | 42 nanonext-1.10.0/nanonext/src/nng/src/core/listener.h | 3 nanonext-1.10.0/nanonext/src/nng/src/core/lmq.c | 1 nanonext-1.10.0/nanonext/src/nng/src/core/message.c | 40 nanonext-1.10.0/nanonext/src/nng/src/core/message.h | 1 nanonext-1.10.0/nanonext/src/nng/src/core/msgqueue.c | 1 nanonext-1.10.0/nanonext/src/nng/src/core/options.h | 2 nanonext-1.10.0/nanonext/src/nng/src/core/pipe.c | 14 nanonext-1.10.0/nanonext/src/nng/src/core/pipe.h | 5 nanonext-1.10.0/nanonext/src/nng/src/core/platform.h | 11 nanonext-1.10.0/nanonext/src/nng/src/core/protocol.h | 3 nanonext-1.10.0/nanonext/src/nng/src/core/sockaddr.c |only nanonext-1.10.0/nanonext/src/nng/src/core/socket.c | 34 nanonext-1.10.0/nanonext/src/nng/src/core/sockfd.c | 4 nanonext-1.10.0/nanonext/src/nng/src/core/stream.c | 14 nanonext-1.10.0/nanonext/src/nng/src/core/url.c | 2 nanonext-1.10.0/nanonext/src/nng/src/nng.c | 358 ++++- nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_clock.c | 31 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_debug.c | 12 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_ipcconn.c | 14 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_pollq_epoll.c | 2 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_pollq_kqueue.c | 2 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_pollq_port.c | 2 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_resolv_gai.c | 49 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_sockaddr.c | 30 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_tcpconn.c | 13 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_tcpdial.c | 12 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_tcplisten.c | 13 nanonext-1.10.0/nanonext/src/nng/src/platform/posix/posix_udp.c | 121 + nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_clock.c | 31 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_debug.c | 17 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_io.c | 6 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_ipcconn.c | 159 +- nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_ipclisten.c | 38 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_resolv.c | 43 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_sockaddr.c | 12 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_tcp.h | 2 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_tcpconn.c | 187 +- nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_tcpdial.c | 16 nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_tcplisten.c | 281 ++-- nanonext-1.10.0/nanonext/src/nng/src/platform/windows/win_udp.c | 88 + nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/bus0/bus.c | 5 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pair0/pair.c | 9 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pair1/pair.c | 15 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pair1/pair1_poly.c | 631 +++++----- nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pipeline0/pull.c | 19 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pipeline0/push.c | 5 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pubsub0/pub.c | 5 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pubsub0/sub.c | 129 +- nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/pubsub0/xsub.c | 13 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/reqrep0/rep.c | 53 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/reqrep0/req.c | 17 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/reqrep0/xrep.c | 19 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/reqrep0/xreq.c | 17 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/survey0/respond.c | 53 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/survey0/survey.c | 45 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/survey0/xrespond.c | 19 nanonext-1.10.0/nanonext/src/nng/src/sp/protocol/survey0/xsurvey.c | 19 nanonext-1.10.0/nanonext/src/nng/src/sp/transport.c | 10 nanonext-1.10.0/nanonext/src/nng/src/sp/transport.h | 4 nanonext-1.10.0/nanonext/src/nng/src/sp/transport/ipc/ipc.c | 71 - nanonext-1.10.0/nanonext/src/nng/src/sp/transport/tcp/tcp.c | 22 nanonext-1.10.0/nanonext/src/nng/src/sp/transport/tls/tls.c | 24 nanonext-1.10.0/nanonext/src/nng/src/sp/transport/ws/websocket.c | 4 nanonext-1.10.0/nanonext/src/nng/src/supplemental/base64/base64.c | 18 nanonext-1.10.0/nanonext/src/nng/src/supplemental/base64/base64.h | 18 nanonext-1.10.0/nanonext/src/nng/src/supplemental/http/http_api.h | 1 nanonext-1.10.0/nanonext/src/nng/src/supplemental/http/http_server.c | 5 nanonext-1.10.0/nanonext/src/nng/src/supplemental/tls/mbedtls/tls.c | 232 ++- nanonext-1.10.0/nanonext/src/nng/src/supplemental/tls/tls_common.c | 93 - nanonext-1.10.0/nanonext/src/nng_structs.h | 2 nanonext-1.10.0/nanonext/src/proto.c | 12 nanonext-1.10.0/nanonext/src/server.c | 6 nanonext-1.10.0/nanonext/src/sync.c | 8 nanonext-1.10.0/nanonext/src/thread.c | 6 nanonext-1.10.0/nanonext/src/tls.c | 4 nanonext-1.10.0/nanonext/tests/tests.R | 41 nanonext-1.10.0/nanonext/tools |only nanonext-1.10.0/nanonext/vignettes/v02-protocols.Rmd | 47 nanonext-1.9.1/nanonext/configure.ucrt |only nanonext-1.9.1/nanonext/configure.win |only nanonext-1.9.1/nanonext/src/mbedtls/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/mbedtls/cmake |only nanonext-1.9.1/nanonext/src/mbedtls/include/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/mbedtls/include/mbedtls/cmac.h |only nanonext-1.9.1/nanonext/src/mbedtls/include/mbedtls/ssl_cache.h |only nanonext-1.9.1/nanonext/src/mbedtls/include/mbedtls/ssl_cookie.h |only nanonext-1.9.1/nanonext/src/mbedtls/include/mbedtls/ssl_ticket.h |only nanonext-1.9.1/nanonext/src/mbedtls/include/mbedtls/timing.h |only nanonext-1.9.1/nanonext/src/mbedtls/library/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/mbedtls/library/block_cipher.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/cmac.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/hkdf.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/net_sockets.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/ssl_cache.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/ssl_cookie.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/ssl_debug_helpers_generated.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/ssl_ticket.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/timing.c |only nanonext-1.9.1/nanonext/src/mbedtls/library/x509write_csr.c |only nanonext-1.9.1/nanonext/src/nng/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/cmake |only nanonext-1.9.1/nanonext/src/nng/include/nng/supplemental/util/options.h |only nanonext-1.9.1/nanonext/src/nng/src/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/core/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/platform/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/platform/posix/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/platform/windows/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/bus0/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/pair0/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/pair1/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/pipeline0/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/pubsub0/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/reqrep0/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/protocol/survey0/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/transport/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/transport/inproc/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/transport/ipc/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/transport/socket/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/transport/tcp/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/transport/tls/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/sp/transport/ws/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/base64/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/http/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/sha1/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/tls/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/tls/mbedtls/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/util |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/websocket/CMakeLists.txt |only nanonext-1.9.1/nanonext/src/nng/src/supplemental/websocket/stub.c |only 193 files changed, 4463 insertions(+), 1788 deletions(-)
Title: Autodiff for Influence Function Based Estimates
Description: Implements an S7 class for estimates based on influence functions,
with forward mode automatic differentiation defined for standard arithmetic
operations.
Author: Nicholas Williams [aut, cre, cph]
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>
Diff between ife versions 0.2.3 dated 2026-02-07 and 0.2.5 dated 2026-07-01
DESCRIPTION | 6 ++-- MD5 | 13 +++++----- NAMESPACE | 2 + NEWS.md | 8 ++++++ R/influence_func_estimand.R | 49 ++++++++++++++++++++++++---------------- R/std_error.R | 24 ++++++++----------- man/ife_constructor.Rd | 21 ++++++++++++----- tests/testthat/test-std_error.R |only 8 files changed, 75 insertions(+), 48 deletions(-)
Title: Analysis of Evolutionary Rates in an OU Framework
Description: Estimates rates for continuous character evolution under Brownian motion and Ornstein-Uhlenbeck based Hansen models that allow both the strength of the pull and stochastic motion to vary across selective regimes. Beaulieu et al. (2012).
Author: Jeremy M. Beaulieu [aut, cre],
Brian O'Meara [aut]
Maintainer: Jeremy M. Beaulieu <jmbeauli@uark.edu>
Diff between OUwie versions 2.10 dated 2022-06-15 and 3.0.2 dated 2026-07-01
OUwie-2.10/OUwie/README.md |only OUwie-3.0.2/OUwie/DESCRIPTION | 29 + OUwie-3.0.2/OUwie/MD5 | 61 +- OUwie-3.0.2/OUwie/NAMESPACE | 12 OUwie-3.0.2/OUwie/R/OUwie.R | 243 ++++++++--- OUwie-3.0.2/OUwie/R/OUwie.anc.R | 87 +++- OUwie-3.0.2/OUwie/R/OUwie.boot.R | 32 - OUwie-3.0.2/OUwie/R/OUwie.contour.r | 4 OUwie-3.0.2/OUwie/R/OUwie.dredge.R | 204 ++++++++- OUwie-3.0.2/OUwie/R/OUwie.fixed.R | 71 ++- OUwie-3.0.2/OUwie/R/OUwie.format.R |only OUwie-3.0.2/OUwie/R/OUwie.sim.R | 104 +++-- OUwie-3.0.2/OUwie/R/adjust_bounds.R | 4 OUwie-3.0.2/OUwie/R/check.identify.R | 11 OUwie-3.0.2/OUwie/R/varcov.ou.R | 434 +++++++++++++-------- OUwie-3.0.2/OUwie/R/vcvbypass.functions.R | 124 ++++-- OUwie-3.0.2/OUwie/R/weight.mat.R | 407 ++++++++++++------- OUwie-3.0.2/OUwie/build/vignette.rds |binary OUwie-3.0.2/OUwie/inst/doc/OUwie_2.1_adds.R | 47 +- OUwie-3.0.2/OUwie/inst/doc/OUwie_2.1_adds.Rmd | 14 OUwie-3.0.2/OUwie/inst/doc/OUwie_2.1_adds.pdf |binary OUwie-3.0.2/OUwie/inst/doc/calculationUpdate.R |only OUwie-3.0.2/OUwie/inst/doc/calculationUpdate.Rmd |only OUwie-3.0.2/OUwie/inst/doc/calculationUpdate.pdf |only OUwie-3.0.2/OUwie/man/OUwie.Rd | 12 OUwie-3.0.2/OUwie/man/OUwie.anc.Rd | 5 OUwie-3.0.2/OUwie/man/OUwie.boot.Rd | 4 OUwie-3.0.2/OUwie/man/OUwie.dredge.Rd | 11 OUwie-3.0.2/OUwie/man/OUwie.fixed.Rd | 7 OUwie-3.0.2/OUwie/man/OUwie.format.Rd |only OUwie-3.0.2/OUwie/man/OUwie.sim.Rd | 6 OUwie-3.0.2/OUwie/tests/testthat/test-likelihood.R | 31 - OUwie-3.0.2/OUwie/tests/testthat/test-restart.R | 4 OUwie-3.0.2/OUwie/vignettes/OUwie_2.1_adds.Rmd | 14 OUwie-3.0.2/OUwie/vignettes/calculationUpdate.Rmd |only 35 files changed, 1384 insertions(+), 598 deletions(-)
Title: Monte Carlo Simulations of Time Changes in Sequences
Description: Generates replicated sets of sequences with Monte Carlo simulated timing changes and computes various indicators for evaluating effects of timing uncertainty on sequence analysis results. See Ritschard, G. and Liao, T.F. (2026): "Assessing the Impact of Timing Errors in Sequence Analysis". International Journal of Social Research Methodology <doi:10.1080/13645579.2026.2666297>.
Author: Gilbert Ritschard [aut, cre, cph] ,
Tim F. Liao [ctb]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between MCseqReplic versions 1.0.0 dated 2026-04-29 and 1.1.0 dated 2026-07-01
MCseqReplic-1.0.0/MCseqReplic/R/seqdistMCSE.R |only MCseqReplic-1.0.0/MCseqReplic/man/seqdistMCSE.Rd |only MCseqReplic-1.1.0/MCseqReplic/DESCRIPTION | 32 ++- MCseqReplic-1.1.0/MCseqReplic/MD5 | 52 +++-- MCseqReplic-1.1.0/MCseqReplic/NAMESPACE | 15 + MCseqReplic-1.1.0/MCseqReplic/R/MCclustcomp.R | 23 +- MCseqReplic-1.1.0/MCseqReplic/R/MCclustqual.R | 179 +++++++++++++++++--- MCseqReplic-1.1.0/MCseqReplic/R/MCcomgrp.R |only MCseqReplic-1.1.0/MCseqReplic/R/MCdisscorr.R | 1 MCseqReplic-1.1.0/MCseqReplic/R/MCmdscorr.R | 18 +- MCseqReplic-1.1.0/MCseqReplic/R/MCmethods.R | 3 MCseqReplic-1.1.0/MCseqReplic/R/MCmisc.R | 15 + MCseqReplic-1.1.0/MCseqReplic/R/MCratios.R | 9 - MCseqReplic-1.1.0/MCseqReplic/R/MCseqReplicate.R | 8 MCseqReplic-1.1.0/MCseqReplic/R/MCseqdistSE.R | 2 MCseqReplic-1.1.0/MCseqReplic/R/seqMCsple.R |only MCseqReplic-1.1.0/MCseqReplic/build |only MCseqReplic-1.1.0/MCseqReplic/inst/CITATION | 8 MCseqReplic-1.1.0/MCseqReplic/inst/NEWS.Rd | 38 ++++ MCseqReplic-1.1.0/MCseqReplic/inst/REFERENCES.bib |only MCseqReplic-1.1.0/MCseqReplic/inst/doc |only MCseqReplic-1.1.0/MCseqReplic/man/MCclustcomp.Rd | 18 +- MCseqReplic-1.1.0/MCseqReplic/man/MCclustqual.Rd | 67 ++++++- MCseqReplic-1.1.0/MCseqReplic/man/MCcompgrp.Rd |only MCseqReplic-1.1.0/MCseqReplic/man/MCmdscorr.Rd | 7 MCseqReplic-1.1.0/MCseqReplic/man/MCratios.Rd | 8 MCseqReplic-1.1.0/MCseqReplic/man/MCseqReplicate.Rd | 3 MCseqReplic-1.1.0/MCseqReplic/man/MCseqdistSE.Rd | 2 MCseqReplic-1.1.0/MCseqReplic/man/print.MCratios.Rd | 2 MCseqReplic-1.1.0/MCseqReplic/vignettes |only 30 files changed, 408 insertions(+), 102 deletions(-)
Title: Help with Preparing a New Version of an R Package
Description: Helps to prepare a release. Before releasing an R package it is important to update the DESCRIPTION file and the changelog. This package prepares these files and also updates the versions according to the branches. It relies heavily on the 'desc' packages.
Author: Tanguy Barthelemy [aut, cre, art]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between releaser versions 1.1.1 dated 2026-06-08 and 1.2.0 dated 2026-07-01
DESCRIPTION | 6 +-- MD5 | 36 ++++++++++---------- NAMESPACE | 1 NEWS.md | 10 +++-- R/cran-check.R | 25 +++++++++++++- R/get_information.R | 14 +++---- R/update_description.R | 64 ++++++++++++++++++++++++++++++++---- README.md | 31 +++++++++-------- inst/WORDLIST | 1 man/change_remotes_field.Rd | 7 ++- man/check.Rd | 13 +++++++ man/check_docs.Rd | 8 ++++ man/get_changes.Rd | 7 ++- man/get_different_future_version.Rd | 4 +- man/get_github_branches.Rd | 4 +- man/get_latest_version.Rd | 4 +- man/print.releaser_doc_check.Rd |only man/set_latest_deps_version.Rd | 10 +++-- man/set_rjdverse_remotes.Rd |only man/update_news_md.Rd | 7 ++- 20 files changed, 180 insertions(+), 72 deletions(-)
Title: Data Sets for Keith McNulty's Handbook of Regression Modeling in
People Analytics
Description: Data sets for statistical inference modeling related to People Analytics.
Contains various data sets from the book 'Handbook of Regression Modeling in People Analytics'
by Keith McNulty (2026).
Author: Keith McNulty [aut, cre]
Maintainer: Keith McNulty <keith.mcnulty@gmail.com>
Diff between peopleanalyticsdata versions 0.2.1 dated 2021-04-13 and 0.2.2 dated 2026-07-01
DESCRIPTION | 17 +++++++++-------- LICENSE | 2 +- MD5 | 21 +++++++++++++++------ NEWS.md | 6 ++++++ R/data-absenteeism.R |only R/data-complaints.R |only R/data-selection.R |only R/data-speed_dating.R | 2 +- README.md | 3 +-- data/absenteeism.rda |only data/complaints.rda |only data/selection.rda |only man/absenteeism.Rd |only man/complaints.Rd |only man/selection.Rd |only man/speed_dating.Rd | 2 +- 16 files changed, 34 insertions(+), 19 deletions(-)
More information about peopleanalyticsdata at CRAN
Permanent link
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>. Shift-scale (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>)
and multivariate (Klein et al, 2022, <DOI:10.1111/sjos.12501>) transformation models
are part of this package. A package vignette is available from <DOI:10.32614/CRAN.package.mlt.docreg> and
more convenient user interfaces to many models from <DOI:10.32614/CRAN.package.tram>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.8-0 dated 2026-04-14 and 1.8-1 dated 2026-07-01
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/mmlt.R | 2 +- build/partial.rdb |binary cleanup | 4 ++++ inst/NEWS.Rd | 8 ++++++++ 6 files changed, 23 insertions(+), 11 deletions(-)
Title: Post-Processing of Markov Chain Monte Carlo Simulations for
Chronological Modelling
Description: Statistical analysis of archaeological dates and groups of
dates. This package allows to post-process Markov Chain Monte Carlo
(MCMC) simulations from 'ChronoModel' <https://chronomodel.com/>,
'Oxcal' <https://c14.arch.ox.ac.uk/oxcal.html> or 'BCal'
<https://bcal.shef.ac.uk/>. It provides functions for the study of
rhythms of the long term from the posterior distribution of a series
of dates (tempo and activity plot). It also allows the estimation and
visualization of time ranges from the posterior distribution of groups
of dates (e.g. duration, transition and hiatus between successive
phases) as described in Philippe and Vibet (2020)
<doi:10.18637/jss.v093.c01>.
Author: Anne Philippe [aut, cre] ,
Marie-Anne Vibet [aut] ,
Nicolas Frerebeau [aut] ,
Thomas S. Dye [ctb] ,
Nantes Universite [fnd] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>
Diff between ArchaeoPhases versions 2.1.0 dated 2025-09-26 and 2.1.1 dated 2026-07-01
DESCRIPTION | 10 +- MD5 | 159 +++++++++++++++++++------------------- NAMESPACE | 13 +-- NEWS.md | 5 + R/AllGenerics.R | 28 +++++- R/ArchaeoPhases-package.R | 5 - R/activity.R | 2 R/coerce.R | 23 +++++ README.md | 63 +++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/ArchaeoPhases.Rmd | 2 inst/doc/ArchaeoPhases.html | 37 ++++---- inst/doc/allen.Rmd | 2 inst/doc/allen.html | 12 +- inst/doc/import.Rmd | 2 inst/doc/import.html | 9 +- man/ActivityEvents-class.Rd | 4 man/AgeDepthModel-class.Rd | 2 man/ArchaeoPhases-package.Rd | 3 man/CumulativeEvents-class.Rd | 4 man/DurationsMCMC-class.Rd | 4 man/EventsMCMC-class.Rd | 4 man/MCMC-class.Rd | 2 man/OccurrenceEvents-class.Rd | 4 man/PhasesMCMC-class.Rd | 2 man/TimeRange-class.Rd | 2 man/activity.Rd | 16 +-- man/allen_analyze.Rd | 30 +++---- man/allen_analyze_relations.Rd | 30 +++---- man/allen_complement.Rd | 30 +++---- man/allen_composition.Rd | 30 +++---- man/allen_converse.Rd | 30 +++---- man/allen_illustrate.Rd | 30 +++---- man/allen_illustrate_relations.Rd | 30 +++---- man/allen_intersect.Rd | 30 +++---- man/allen_joint_concurrency.Rd | 34 ++++---- man/allen_observe.Rd | 32 +++---- man/allen_observe_frequency.Rd | 32 +++---- man/allen_plot.Rd | 30 +++---- man/allen_relate_intervals.Rd | 2 man/allen_relation.Rd | 30 +++---- man/allen_relation_code.Rd | 30 +++---- man/allen_union.Rd | 30 +++---- man/as.array.Rd |only man/as_coda.Rd | 12 +- man/as_events.Rd | 14 +-- man/as_phases.Rd | 14 +-- man/bind.Rd | 14 +-- man/boundaries.Rd | 10 +- man/bury.Rd | 14 +-- man/check.Rd | 14 +-- man/data.frame.Rd | 14 --- man/duration.Rd | 6 - man/elapse.Rd | 10 +- man/hiatus.Rd | 12 +- man/interpolate.Rd | 4 man/interval_credible.Rd | 12 +- man/interval_hdr.Rd | 12 +- man/mcmc_events.Rd | 2 man/mcmc_phases.Rd | 2 man/names.Rd | 9 -- man/occurrence.Rd | 14 +-- man/older.Rd | 2 man/phases.Rd | 8 - man/plot_events.Rd | 6 - man/plot_phases.Rd | 6 - man/read_bcal.Rd | 14 +-- man/read_chronomodel.Rd | 16 +-- man/read_oxcal.Rd | 14 +-- man/sensitivity.Rd | 10 +- man/sort.Rd | 11 -- man/sort.list.Rd | 11 -- man/subset.Rd | 10 -- man/summary.Rd | 12 +- man/tempo.Rd | 16 +-- man/transition.Rd | 10 +- vignettes/ArchaeoPhases.Rmd | 2 vignettes/allen.Rmd | 2 vignettes/import.Rmd | 2 81 files changed, 619 insertions(+), 603 deletions(-)
Title: SDTM Test Data for the 'Pharmaverse' Family of Packages
Description: A set of Study Data Tabulation Model (SDTM) datasets from the
Clinical Data Interchange Standards Consortium (CDISC) pilot project
used for testing and developing Analysis Data Model (ADaM) datasets
inside the pharmaverse family of packages. SDTM dataset specifications
are described in the CDISC SDTM implementation guide, accessible by
creating a free account on <https://www.cdisc.org/>.
Author: Lina Patil [aut, cre],
Stefan Bundfuss [aut] ,
Kristin Dahnert [aut],
Fanny Gautier [aut] ,
Edoardo Mancini [aut] ,
Tomoyuki Namai [aut],
Vinh Nguyen [aut],
Kiran Peddamudium [aut],
Gerardo Jose Rodriguez [aut] ,
Vladyslav Shuliar [aut] ,
Cytel Inc. [...truncated...]
Maintainer: Lina Patil <lina.patil@cytel.com>
Diff between pharmaversesdtm versions 1.4.1 dated 2026-03-30 and 1.5.0 dated 2026-07-01
DESCRIPTION | 13 ++++++++----- MD5 | 27 +++++++++++++++------------ NEWS.md | 15 +++++++++++++++ R/lb_neuro.R | 5 +++-- R/oe_ophtha.R | 4 +++- R/rs_onco_lymphoma.R |only README.md | 2 ++ data/lb_neuro.rda |binary data/oe_ophtha.rda |binary data/rs_onco_lymphoma.rda |only inst/WORDLIST | 7 +++++-- inst/extdata/sdtms-specs.json | 8 ++++++++ man/lb_neuro.Rd | 5 +++-- man/oe_ophtha.Rd | 4 +++- man/pharmaversesdtm-package.Rd | 2 ++ man/rs_onco_lymphoma.Rd |only 16 files changed, 67 insertions(+), 25 deletions(-)
More information about pharmaversesdtm at CRAN
Permanent link
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 0.2.0 dated 2026-03-11 and 0.3.0 dated 2026-07-01
DESCRIPTION | 6 - MD5 | 12 +-- NEWS.md | 14 +++ R/Orthanc.R | 142 +++++++++++++++++++++++++++++++++++++--- R/filtering.R | 2 man/Orthanc.Rd | 33 +++++++++ man/find_and_filter_patients.Rd | 2 7 files changed, 191 insertions(+), 20 deletions(-)
Title: Quantitative Analysis and Visualization of LUCC
Description: Tools for the analysis of land use and cover (LUC) time series. It
includes support for loading spatiotemporal raster data and synthesized
spatial plotting. Several LUC change (LUCC) metrics in regular or irregular
time intervals can be extracted and visualized through one- and multistep
sankey and chord diagrams. A complete intensity analysis according to
Aldwaik and Pontius (2012) <doi:10.1016/j.landurbplan.2012.02.010> is
implemented, including tools for the generation of standardized multilevel
output graphics.
Author: Reginal Exavier [aut, cre] ,
Peter Zeilhofer [aut]
Maintainer: Reginal Exavier <reginalexavier@rocketmail.com>
This is a re-admission after prior archival of version 1.0.3 dated 2024-05-03
Diff between OpenLand versions 1.0.3 dated 2024-05-03 and 1.0.4 dated 2026-07-01
DESCRIPTION | 14 MD5 | 89 +- NEWS.md | 11 R/contingencyTable.R | 380 ++++---- R/data.R | 2 R/demolandscape.R | 173 ++-- R/generalfunctions.R | 472 ++++++----- R/generic_method.R | 86 +- R/intensityAnalysis.R | 1001 ++++++++++++----------- R/intensityClass.R | 525 +++++------- R/otherplots.R | 1115 +++++++++++++------------- R/plotMethods.R | 1042 ++++++++++++------------ R/rasters_input.R | 169 ++- README.md | 69 - build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST |only inst/doc/openland_vignette.R | 235 ++--- inst/doc/openland_vignette.Rmd | 798 +++++++++--------- inst/doc/openland_vignette.html | 735 ++++++----------- man/SL_2002_2014.Rd | 2 man/acc_changes.Rd | 10 man/barplotLand.Rd | 31 man/chordDiagramLand.Rd | 28 man/contingencyTable.Rd | 17 man/dot-demo_landscape.Rd | 8 man/dot-openland_try_download_and_load_rda.Rd |only man/figures/README-cat_level-1.png |binary man/figures/README-chordDiagram-1.png |binary man/figures/README-ng_plot-1.png |binary man/intensityAnalysis.Rd | 25 man/netgrossplot.Rd | 29 man/plot.Rd | 9 man/sankeyLand.Rd | 37 man/summary_dir.Rd | 11 man/summary_map.Rd | 9 tests/spelling.R |only tests/testthat/Rplots.pdf |binary tests/testthat/test_contingencyTable.R | 128 +- tests/testthat/test_demolandscape.R | 27 tests/testthat/test_generalfunctions.R | 292 +++++- tests/testthat/test_inputrasters.R | 72 - tests/testthat/test_intensityAnalysis.R | 208 ++-- tests/testthat/test_intensityClasses.R | 216 ++--- tests/testthat/test_plots.R | 116 +- vignettes/openland_vignette.Rmd | 798 +++++++++--------- vignettes/papers_OpenLand.bib | 2 47 files changed, 4687 insertions(+), 4304 deletions(-)
Title: Machine Learning and Visualization
Description: Machine learning and visualization package with an 'S7' backend
featuring comprehensive type checking and validation, paired with an efficient functional
user-facing API. train(), cluster(), and decomp() provide one-call access to supervised and
unsupervised learning. All configuration steps are performed using setup functions and
validated. A single call to train() handles preprocessing, hyperparameter tuning, and testing
with nested resampling. Supports 'data.frame', 'data.table', and 'tibble' inputs, parallel
execution, and interactive visualizations. The package first appeared in E.D. Gennatas (2017)
<https://repository.upenn.edu/entities/publication/d81892ea-3087-4b71-a6f5-739c58626d64>.
Author: E.D. Gennatas [aut, cre, cph]
Maintainer: E.D. Gennatas <gennatas@gmail.com>
Diff between rtemis versions 1.0.0 dated 2026-03-26 and 1.2.7 dated 2026-07-01
rtemis-1.0.0/rtemis/R/00_S7init.R |only rtemis-1.0.0/rtemis/R/07_Supervised.R |only rtemis-1.0.0/rtemis/R/08_MassUni.R |only rtemis-1.0.0/rtemis/R/09_ClusteringConfig.R |only rtemis-1.0.0/rtemis/R/10_Clustering.R |only rtemis-1.0.0/rtemis/R/11_DecompositionConfig.R |only rtemis-1.0.0/rtemis/R/12_Decomposition.R |only rtemis-1.0.0/rtemis/R/13_Themes.R |only rtemis-1.0.0/rtemis/R/14_SuperConfig.R |only rtemis-1.0.0/rtemis/R/15_CheckData.R |only rtemis-1.0.0/rtemis/R/16_S7utils.R |only rtemis-1.0.0/rtemis/R/ddSci.R |only rtemis-1.0.0/rtemis/R/msg.R |only rtemis-1.0.0/rtemis/R/utils_checks.R |only rtemis-1.0.0/rtemis/man/clean_colnames.Rd |only rtemis-1.0.0/rtemis/man/clean_names.Rd |only rtemis-1.0.0/rtemis/man/ddSci.Rd |only rtemis-1.0.0/rtemis/man/describe.factor.Rd |only rtemis-1.0.0/rtemis/man/labelify.Rd |only rtemis-1.0.0/rtemis/man/present.list.Rd |only rtemis-1.0.0/rtemis/man/rtemis_colors.Rd |only rtemis-1.0.0/rtemis/man/write_toml.Rd |only rtemis-1.2.7/rtemis/DESCRIPTION | 33 rtemis-1.2.7/rtemis/MD5 | 406 ++--- rtemis-1.2.7/rtemis/NAMESPACE | 30 rtemis-1.2.7/rtemis/R/00_init.R |only rtemis-1.2.7/rtemis/R/01_ExecutionConfig.R | 77 rtemis-1.2.7/rtemis/R/02_Hyperparameters.R | 161 +- rtemis-1.2.7/rtemis/R/03_Metrics.R | 140 + rtemis-1.2.7/rtemis/R/04_Preprocessor.R | 16 rtemis-1.2.7/rtemis/R/05_Resampler.R | 55 rtemis-1.2.7/rtemis/R/06_Tuner.R | 55 rtemis-1.2.7/rtemis/R/07_ClusteringConfig.R |only rtemis-1.2.7/rtemis/R/08_Clustering.R |only rtemis-1.2.7/rtemis/R/09_DecompositionConfig.R |only rtemis-1.2.7/rtemis/R/10_Decomposition.R |only rtemis-1.2.7/rtemis/R/11_Session.R |only rtemis-1.2.7/rtemis/R/12_Supervised.R |only rtemis-1.2.7/rtemis/R/13_MassUni.R |only rtemis-1.2.7/rtemis/R/14_Themes.R |only rtemis-1.2.7/rtemis/R/15_SuperConfig.R |only rtemis-1.2.7/rtemis/R/16_DecomposeConfig.R |only rtemis-1.2.7/rtemis/R/17_ClusterConfig.R |only rtemis-1.2.7/rtemis/R/18_CheckData.R |only rtemis-1.2.7/rtemis/R/19_S7utils.R |only rtemis-1.2.7/rtemis/R/algorithmDB.R | 91 - rtemis-1.2.7/rtemis/R/calibrate.R | 7 rtemis-1.2.7/rtemis/R/check_input_data.R | 99 - rtemis-1.2.7/rtemis/R/cluster.R | 59 rtemis-1.2.7/rtemis/R/cluster_CMeans.R | 4 rtemis-1.2.7/rtemis/R/cluster_DBSCAN.R | 6 rtemis-1.2.7/rtemis/R/cluster_flexclust.R | 4 rtemis-1.2.7/rtemis/R/conditions.R |only rtemis-1.2.7/rtemis/R/decomp.R | 62 rtemis-1.2.7/rtemis/R/decomp_ICA.R | 52 rtemis-1.2.7/rtemis/R/decomp_Isomap.R | 8 rtemis-1.2.7/rtemis/R/decomp_NMF.R | 39 rtemis-1.2.7/rtemis/R/decomp_PCA.R | 32 rtemis-1.2.7/rtemis/R/decomp_UMAP.R | 35 rtemis-1.2.7/rtemis/R/decomp_tSNE.R | 8 rtemis-1.2.7/rtemis/R/draw_3Dscatter.R | 26 rtemis-1.2.7/rtemis/R/draw_bar.R | 15 rtemis-1.2.7/rtemis/R/draw_box.R | 38 rtemis-1.2.7/rtemis/R/draw_confusion.R | 25 rtemis-1.2.7/rtemis/R/draw_dist.R | 21 rtemis-1.2.7/rtemis/R/draw_graphjs.R | 13 rtemis-1.2.7/rtemis/R/draw_heatmap.R | 28 rtemis-1.2.7/rtemis/R/draw_leaflet.R | 8 rtemis-1.2.7/rtemis/R/draw_pie.R | 6 rtemis-1.2.7/rtemis/R/draw_protein.R | 8 rtemis-1.2.7/rtemis/R/draw_pvals.R | 2 rtemis-1.2.7/rtemis/R/draw_roc.R | 232 ++ rtemis-1.2.7/rtemis/R/draw_scatter.R | 23 rtemis-1.2.7/rtemis/R/draw_spectrogram.R | 23 rtemis-1.2.7/rtemis/R/draw_survfit.R | 2 rtemis-1.2.7/rtemis/R/draw_ts.R | 7 rtemis-1.2.7/rtemis/R/draw_varimp.R | 10 rtemis-1.2.7/rtemis/R/draw_volcano.R | 39 rtemis-1.2.7/rtemis/R/draw_xt.R | 31 rtemis-1.2.7/rtemis/R/fmt.R | 530 ------ rtemis-1.2.7/rtemis/R/massGLM.R | 59 rtemis-1.2.7/rtemis/R/metrics.R | 226 -- rtemis-1.2.7/rtemis/R/preprocess.R | 156 - rtemis-1.2.7/rtemis/R/present.R | 24 rtemis-1.2.7/rtemis/R/read.R | 40 rtemis-1.2.7/rtemis/R/read_config.R |only rtemis-1.2.7/rtemis/R/reexports.R |only rtemis-1.2.7/rtemis/R/resample.R | 7 rtemis-1.2.7/rtemis/R/rtemis-package.R | 13 rtemis-1.2.7/rtemis/R/rtemis_color_system.R | 109 - rtemis-1.2.7/rtemis/R/train.R | 436 ++++- rtemis-1.2.7/rtemis/R/train_CART.R | 17 rtemis-1.2.7/rtemis/R/train_GAM.R | 50 rtemis-1.2.7/rtemis/R/train_GLM.R | 19 rtemis-1.2.7/rtemis/R/train_GLMNET.R | 57 rtemis-1.2.7/rtemis/R/train_Isotonic.R | 28 rtemis-1.2.7/rtemis/R/train_LightCART.R | 9 rtemis-1.2.7/rtemis/R/train_LightGBM.R | 24 rtemis-1.2.7/rtemis/R/train_LightRF.R | 11 rtemis-1.2.7/rtemis/R/train_LightRuleFit.R | 23 rtemis-1.2.7/rtemis/R/train_Ranger.R | 42 rtemis-1.2.7/rtemis/R/train_SVM.R | 39 rtemis-1.2.7/rtemis/R/train_TabNet.R | 24 rtemis-1.2.7/rtemis/R/tune.R | 18 rtemis-1.2.7/rtemis/R/tune_GridSearch.R | 195 +- rtemis-1.2.7/rtemis/R/utils.R | 23 rtemis-1.2.7/rtemis/R/utils_art.R | 8 rtemis-1.2.7/rtemis/R/utils_async.R | 20 rtemis-1.2.7/rtemis/R/utils_color.R | 63 rtemis-1.2.7/rtemis/R/utils_data.R | 33 rtemis-1.2.7/rtemis/R/utils_data.table.R | 10 rtemis-1.2.7/rtemis/R/utils_date.R | 3 rtemis-1.2.7/rtemis/R/utils_df.R | 30 rtemis-1.2.7/rtemis/R/utils_exec.R | 15 rtemis-1.2.7/rtemis/R/utils_files.R | 2 rtemis-1.2.7/rtemis/R/utils_io.R | 95 - rtemis-1.2.7/rtemis/R/utils_lightgbm.R | 1 rtemis-1.2.7/rtemis/R/utils_palettes.R | 18 rtemis-1.2.7/rtemis/R/utils_plotly.R | 14 rtemis-1.2.7/rtemis/R/utils_print.R | 1028 ------------- rtemis-1.2.7/rtemis/R/utils_rt.R | 1 rtemis-1.2.7/rtemis/R/utils_rules.R | 2 rtemis-1.2.7/rtemis/R/utils_strings.R | 558 ------- rtemis-1.2.7/rtemis/R/utils_supervised.R | 86 - rtemis-1.2.7/rtemis/R/utils_uniprot.R | 1 rtemis-1.2.7/rtemis/R/write_config.R |only rtemis-1.2.7/rtemis/R/zzz.R | 26 rtemis-1.2.7/rtemis/README.md | 49 rtemis-1.2.7/rtemis/inst/WORDLIST |only rtemis-1.2.7/rtemis/man/apply_decomp.Rd |only rtemis-1.2.7/rtemis/man/available_algorithms.Rd | 11 rtemis-1.2.7/rtemis/man/available_draw.Rd | 7 rtemis-1.2.7/rtemis/man/calibrate.Rd | 2 rtemis-1.2.7/rtemis/man/classification_metrics.Rd | 2 rtemis-1.2.7/rtemis/man/cluster.Rd | 10 rtemis-1.2.7/rtemis/man/decomp.Rd | 9 rtemis-1.2.7/rtemis/man/describe.Rd | 40 rtemis-1.2.7/rtemis/man/df_movecolumn.Rd | 3 rtemis-1.2.7/rtemis/man/dot-list_to_DecompositionConfig.Rd |only rtemis-1.2.7/rtemis/man/dot-list_to_Hyperparameters.Rd |only rtemis-1.2.7/rtemis/man/dot-list_to_ResamplerConfig.Rd |only rtemis-1.2.7/rtemis/man/dot-list_to_TunerConfig.Rd |only rtemis-1.2.7/rtemis/man/draw_3Dscatter.Rd | 14 rtemis-1.2.7/rtemis/man/draw_bar.Rd | 15 rtemis-1.2.7/rtemis/man/draw_box.Rd | 23 rtemis-1.2.7/rtemis/man/draw_confusion.Rd | 12 rtemis-1.2.7/rtemis/man/draw_dist.Rd | 14 rtemis-1.2.7/rtemis/man/draw_graphjs.Rd | 10 rtemis-1.2.7/rtemis/man/draw_heatmap.Rd | 28 rtemis-1.2.7/rtemis/man/draw_leaflet.Rd | 8 rtemis-1.2.7/rtemis/man/draw_pie.Rd | 6 rtemis-1.2.7/rtemis/man/draw_protein.Rd | 4 rtemis-1.2.7/rtemis/man/draw_pvals.Rd | 2 rtemis-1.2.7/rtemis/man/draw_roc.Rd | 4 rtemis-1.2.7/rtemis/man/draw_scatter.Rd | 10 rtemis-1.2.7/rtemis/man/draw_spectrogram.Rd | 18 rtemis-1.2.7/rtemis/man/draw_ts.Rd | 4 rtemis-1.2.7/rtemis/man/draw_varimp.Rd | 5 rtemis-1.2.7/rtemis/man/draw_volcano.Rd | 9 rtemis-1.2.7/rtemis/man/draw_xt.Rd | 2 rtemis-1.2.7/rtemis/man/exc.Rd | 2 rtemis-1.2.7/rtemis/man/feature_names.Rd | 2 rtemis-1.2.7/rtemis/man/features.Rd | 2 rtemis-1.2.7/rtemis/man/figures/logo.svg | 35 rtemis-1.2.7/rtemis/man/get_factor_names.Rd | 2 rtemis-1.2.7/rtemis/man/get_palette.Rd | 2 rtemis-1.2.7/rtemis/man/get_varimp.Rd |only rtemis-1.2.7/rtemis/man/inc.Rd | 2 rtemis-1.2.7/rtemis/man/inspect.Rd | 2 rtemis-1.2.7/rtemis/man/massGLM.Rd | 7 rtemis-1.2.7/rtemis/man/matchcases.Rd | 2 rtemis-1.2.7/rtemis/man/numeric_features.Rd |only rtemis-1.2.7/rtemis/man/outcome.Rd | 2 rtemis-1.2.7/rtemis/man/outcome_name.Rd | 2 rtemis-1.2.7/rtemis/man/plot.MassGLM.Rd | 4 rtemis-1.2.7/rtemis/man/plot_manhattan.Rd | 4 rtemis-1.2.7/rtemis/man/plot_roc.Rd | 2 rtemis-1.2.7/rtemis/man/plot_true_pred.Rd | 2 rtemis-1.2.7/rtemis/man/plot_varimp.Rd | 2 rtemis-1.2.7/rtemis/man/preprocess.Rd | 2 rtemis-1.2.7/rtemis/man/preprocessed.Rd | 2 rtemis-1.2.7/rtemis/man/present.Rd | 2 rtemis-1.2.7/rtemis/man/previewcolor.Rd | 14 rtemis-1.2.7/rtemis/man/read.Rd | 8 rtemis-1.2.7/rtemis/man/read_config.Rd | 38 rtemis-1.2.7/rtemis/man/reexports.Rd |only rtemis-1.2.7/rtemis/man/resample.Rd | 2 rtemis-1.2.7/rtemis/man/roc_curve.Rd |only rtemis-1.2.7/rtemis/man/rtemis-package.Rd | 17 rtemis-1.2.7/rtemis/man/rtemis_conditions.Rd |only rtemis-1.2.7/rtemis/man/set_outcome.Rd | 2 rtemis-1.2.7/rtemis/man/set_positive_class.Rd |only rtemis-1.2.7/rtemis/man/setup_CMeans.Rd | 2 rtemis-1.2.7/rtemis/man/setup_ClusterConfig.Rd |only rtemis-1.2.7/rtemis/man/setup_DBSCAN.Rd | 2 rtemis-1.2.7/rtemis/man/setup_DecomposeConfig.Rd |only rtemis-1.2.7/rtemis/man/setup_ExecutionConfig.Rd | 11 rtemis-1.2.7/rtemis/man/setup_HardCL.Rd | 2 rtemis-1.2.7/rtemis/man/setup_ICA.Rd | 8 rtemis-1.2.7/rtemis/man/setup_Isomap.Rd | 2 rtemis-1.2.7/rtemis/man/setup_KMeans.Rd | 2 rtemis-1.2.7/rtemis/man/setup_NMF.Rd | 12 rtemis-1.2.7/rtemis/man/setup_NeuralGas.Rd | 2 rtemis-1.2.7/rtemis/man/setup_PCA.Rd | 7 rtemis-1.2.7/rtemis/man/setup_Preprocessor.Rd | 10 rtemis-1.2.7/rtemis/man/setup_Ranger.Rd | 69 rtemis-1.2.7/rtemis/man/setup_SuperConfig.Rd | 19 rtemis-1.2.7/rtemis/man/setup_SuperConfigLive.Rd |only rtemis-1.2.7/rtemis/man/setup_TabNet.Rd | 2 rtemis-1.2.7/rtemis/man/setup_UMAP.Rd | 8 rtemis-1.2.7/rtemis/man/setup_tSNE.Rd | 2 rtemis-1.2.7/rtemis/man/show_color_key.Rd |only rtemis-1.2.7/rtemis/man/to_json.Rd |only rtemis-1.2.7/rtemis/man/train.Rd | 22 rtemis-1.2.7/rtemis/man/uniprot_get.Rd | 3 rtemis-1.2.7/rtemis/man/write_config.Rd |only rtemis-1.2.7/rtemis/tests/testthat/test_ClusterConfig.R |only rtemis-1.2.7/rtemis/tests/testthat/test_Clustering.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_DecomposeConfig.R |only rtemis-1.2.7/rtemis/tests/testthat/test_Decomposition.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_Hyperparameters.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_Metrics.R | 11 rtemis-1.2.7/rtemis/tests/testthat/test_Preprocessor.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_SuperConfig.R | 106 - rtemis-1.2.7/rtemis/tests/testthat/test_SuperConfigLive.R |only rtemis-1.2.7/rtemis/tests/testthat/test_Supervised.R | 14 rtemis-1.2.7/rtemis/tests/testthat/test_Theme.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_Tuner.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_checks.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_colorsystem.R | 11 rtemis-1.2.7/rtemis/tests/testthat/test_draw.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_idx.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_massGLM.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_strings.R | 2 rtemis-1.2.7/rtemis/tests/testthat/test_to_json.R |only 235 files changed, 3209 insertions(+), 3853 deletions(-)
Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. 'pathfindR' is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
'pathfindR' also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in 'pathfindR' are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. 'pathfindR [...truncated...]
Author: Ege Ulgen [cre, cph] ,
Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 3.0.1 dated 2026-06-29 and 3.0.2 dated 2026-07-01
DESCRIPTION | 13 MD5 | 24 NEWS.md | 9 R/enrichment.R | 2 build/vignette.rds |binary inst/doc/comparing_results.html | 4 inst/doc/intro_vignette.html | 397 +++++----------- inst/doc/non_hs_analysis.html | 489 +++++++++----------- inst/doc/obtain_data.html | 4 inst/doc/visualization_vignette.html | 16 man/enrichment_analyses.Rd | 2 tests/testthat/test-enrichment.R | 9 tests/testthat/test-search-and-enrichment-wrapper.R | 146 +++-- 13 files changed, 497 insertions(+), 618 deletions(-)
Title: Methods for Optimizing Scales of Effect
Description: A tool for optimizing scales of effect when modeling ecological processes in space. Specifically, the scale parameter of a distance-weighted kernel distribution is identified for all environmental layers included in the model. Includes functions to assist in model selection, model evaluation, efficient transformation of raster surfaces using fast Fourier transformation, and projecting models. For more details see Peterman (2026) <doi:10.1007/s10980-025-02267-x>.
Author: Bill Peterman [aut, cre]
Maintainer: Bill Peterman <Peterman.73@osu.edu>
Diff between multiScaleR versions 0.6.13 dated 2026-04-18 and 0.7.0 dated 2026-07-01
DESCRIPTION | 12 MD5 | 151 +- NAMESPACE | 8 NEWS | 371 +++++ R/RcppExports.R | 16 R/aic_tab.R | 330 +++-- R/diagnostics.R | 64 R/estimate_multiscale_ram.R |only R/kernel_bins.R |only R/kernel_dist.R | 134 +- R/kernel_prep.R | 327 ++++- R/kernel_scale.raster.R | 251 +++ R/kernel_scale_fn.R | 721 ++++++++--- R/landscape_metrics.R |only R/marginal_effects.R | 198 ++- R/multiScale_optim.R | 688 +++++++++- R/parallel_helpers.R | 309 ++-- R/plot_kernel.R | 58 R/plot_method.R | 31 R/print_methods.R | 76 + R/profile_sigma.R | 164 ++ R/scale_type.R | 69 - R/scale_vars.R |only R/sim_dat.R | 101 + R/sim_dat_unmarked.R | 179 +- R/sim_rast.R | 76 - R/surface_metrics.R |only R/validation_helpers.R | 87 + README.md | 2 build/partial.rdb |only build/vignette.rds |binary inst/doc/landscape_metric_covariates.R |only inst/doc/landscape_metric_covariates.Rmd |only inst/doc/landscape_metric_covariates.html |only inst/doc/multiScaleR_Guide.R | 474 +++---- inst/doc/multiScaleR_Guide.Rmd | 370 +++-- inst/doc/multiScaleR_Guide.html | 1620 +++++++++++-------------- inst/doc/quickstart.R | 50 inst/doc/quickstart.Rmd | 163 +- inst/doc/quickstart.html | 265 ++-- inst/doc/spatial_projection_clamping.R | 8 inst/doc/spatial_projection_clamping.Rmd | 20 inst/doc/spatial_projection_clamping.html | 162 +- inst/doc/surface_metric_covariates.R |only inst/doc/surface_metric_covariates.Rmd |only inst/doc/surface_metric_covariates.html |only inst/extdata/opt_umf_p.rds |only inst/extdata/vignette_cache.rds |only man/aic_tab.Rd | 215 +-- man/bic_tab.Rd | 36 man/diagnostics.Rd | 65 - man/estimate_multiscale_ram.Rd |only man/kernel_dist.Rd | 55 man/kernel_prep.Rd | 250 ++- man/kernel_scale.raster.Rd | 164 +- man/kernel_scale_fn.Rd | 8 man/msr_vars.Rd |only man/multiScaleR-package.Rd | 5 man/multiScale_optim.Rd | 238 +++ man/plot.multiScaleR.Rd | 33 man/plot_kernel.Rd | 64 man/plot_marginal_effects.Rd | 150 +- man/profile_sigma.Rd | 56 man/sim_dat.Rd | 112 + man/sim_dat_unmarked.Rd | 156 +- man/sim_rast.Rd | 84 - src/RcppExports.cpp | 66 + src/init.c | 8 src/landscape_metrics_cpp.cpp |only src/surface_metrics_cpp.cpp |only tests/testthat/test-coverage-expansion.R | 4 tests/testthat/test-estimate-multiscale-ram.R |only tests/testthat/test-internals-and-helpers.R | 4 tests/testthat/test-kernel-bins.R |only tests/testthat/test-landscape-metrics.R |only tests/testthat/test-optimization-workflow.R | 883 ++++++++++--- tests/testthat/test-raster-and-plotting.R | 391 ++++-- tests/testthat/test-simulation-and-selection.R | 67 + tests/testthat/test-surface-metrics.R |only tools |only vignettes/landscape_metric_covariates.Rmd |only vignettes/multiScaleR_Guide.Rmd | 370 +++-- vignettes/quickstart.Rmd | 163 +- vignettes/spatial_projection_clamping.Rmd | 20 vignettes/surface_metric_covariates.Rmd |only 85 files changed, 7699 insertions(+), 3523 deletions(-)
Title: Base Class and Methods for 'gson' Format
Description: Provides a lightweight container and exchange format for gene set collections. It stores gene set membership, names, gene identifiers, species, versions, and source metadata, with utilities for reading, writing, validating, and converting gene set data for enrichment analysis and related workflows.
Author: Guangchuang Yu [aut, cre, cph]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between gson versions 0.1.0 dated 2023-03-06 and 0.2.0 dated 2026-07-01
DESCRIPTION | 23 MD5 | 46 NAMESPACE | 52 NEWS.md | 13 R/00-AllClasses.R | 101 - R/GMT.R | 139 - R/IO.R | 153 - R/gson-package.R |only R/gson.R | 77 R/gsonList.R | 20 R/methods.R |only R/print.R | 80 R/utilities.r |only R/validate.R |only README.md |only inst/extdata/wikipathways-20220310-gmt-Homo_sapiens.gmt | 1448 ++++++++-------- man/GSON-class.Rd | 80 man/IO.Rd | 58 man/as.data.frame.GSON.Rd |only man/extract.GSON.Rd |only man/gson-package.Rd |only man/gson.Rd | 110 - man/gsonList.Rd | 34 man/read-gmt.Rd | 59 man/show-methods.Rd | 42 man/validate_gson.Rd |only tests |only 27 files changed, 1334 insertions(+), 1201 deletions(-)
Title: A Fast Algorithm for Kernel Quantile Regression
Description: Implements fast algorithms for kernel quantile regression and
related models, including non-crossing kernel quantile regression and
regularized linear quantile regression. The methods are described in
Tang, Gu and Wang (2026) <doi:10.1080/10618600.2025.2541004>.
Author: Qian Tang [aut, cre],
Yuwen Gu [aut],
Boxiang Wang [aut]
Maintainer: Qian Tang <qian-tang@uiowa.edu>
Diff between fastkqr versions 1.0.0 dated 2024-05-13 and 1.0.1 dated 2026-07-01
fastkqr-1.0.0/fastkqr/R/utilities.R |only fastkqr-1.0.1/fastkqr/DESCRIPTION | 27 +-- fastkqr-1.0.1/fastkqr/MD5 | 63 ++++--- fastkqr-1.0.1/fastkqr/NAMESPACE | 11 - fastkqr-1.0.1/fastkqr/NEWS.md |only fastkqr-1.0.1/fastkqr/R/cv.kqr.R | 103 ++++++++++-- fastkqr-1.0.1/fastkqr/R/cv.nckqr.R | 96 ++++++++--- fastkqr-1.0.1/fastkqr/R/cv.qr.R |only fastkqr-1.0.1/fastkqr/R/helpers.R |only fastkqr-1.0.1/fastkqr/R/kqr-methods.R | 79 +++++---- fastkqr-1.0.1/fastkqr/R/kqr.R | 75 ++++++--- fastkqr-1.0.1/fastkqr/R/nckqr-methods.R | 96 ++++++----- fastkqr-1.0.1/fastkqr/R/nckqr.R | 98 ++++++++--- fastkqr-1.0.1/fastkqr/R/qr-methods.R |only fastkqr-1.0.1/fastkqr/R/qr.R |only fastkqr-1.0.1/fastkqr/build/vignette.rds |binary fastkqr-1.0.1/fastkqr/inst/doc/fastkqr.R | 61 +++++-- fastkqr-1.0.1/fastkqr/inst/doc/fastkqr.Rmd | 141 ++++++++--------- fastkqr-1.0.1/fastkqr/inst/doc/fastkqr.html | 193 +++++++++-------------- fastkqr-1.0.1/fastkqr/man/coef.cv.fastlqr.Rd |only fastkqr-1.0.1/fastkqr/man/coef.fastlqr.Rd |only fastkqr-1.0.1/fastkqr/man/coef.kqr.Rd | 31 +-- fastkqr-1.0.1/fastkqr/man/coef.nckqr.Rd | 35 ++-- fastkqr-1.0.1/fastkqr/man/cv.kqr.Rd | 47 ++++- fastkqr-1.0.1/fastkqr/man/cv.nckqr.Rd | 38 +++- fastkqr-1.0.1/fastkqr/man/cv.qr.Rd |only fastkqr-1.0.1/fastkqr/man/kqr.Rd | 22 +- fastkqr-1.0.1/fastkqr/man/nckqr.Rd | 27 +-- fastkqr-1.0.1/fastkqr/man/predict.cv.fastlqr.Rd |only fastkqr-1.0.1/fastkqr/man/predict.fastlqr.Rd |only fastkqr-1.0.1/fastkqr/man/predict.kqr.Rd | 15 - fastkqr-1.0.1/fastkqr/man/predict.nckqr.Rd | 21 +- fastkqr-1.0.1/fastkqr/man/qr.Rd |only fastkqr-1.0.1/fastkqr/src/fast_kqr.f90 | 34 ++-- fastkqr-1.0.1/fastkqr/src/fast_nckqr.f90 | 22 ++ fastkqr-1.0.1/fastkqr/src/fast_qr.f90 |only fastkqr-1.0.1/fastkqr/src/init.c | 40 +++- fastkqr-1.0.1/fastkqr/src/utilities.f90 | 198 +++++++++++++++++++++++- fastkqr-1.0.1/fastkqr/vignettes/fastkqr.Rmd | 141 ++++++++--------- 39 files changed, 1094 insertions(+), 620 deletions(-)
Title: 'C++' Implementations of Functional Enrichment Analysis
Description: Fast implementations of functional enrichment analysis methods using 'C++' via 'Rcpp'.
Currently provides Over-Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA),
Weighted Enrichment Analysis for ORA and GSEA, Network-based Set Enrichment Analysis (NSEA),
multi-layer network-based enrichment, and multi-omics integration workflows. Additional
features include early fusion at the feature level, late fusion at the pathway level,
multi-omics contribution tracing, topology-aware explanation helpers, Bayesian term
selection, and extremely fast Random Walk with Restart (RWR) using 'RcppEigen'. The
enrichment methods build on GSEA by Subramanian et al. (2005)
<doi:10.1073/pnas.0506580102>, the multilevel strategy derived from 'fgsea'
by Korotkevich et al. (2021) <doi:10.1101/060012>, and network-based
enrichment ideas described by Glaab et al. (2012)
<doi:10.1093/bioinformatics/bts389>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between enrichit versions 0.1.5 dated 2026-06-16 and 0.2.0 dated 2026-07-01
enrichit-0.1.5/enrichit/build/vignette.rds |only enrichit-0.1.5/enrichit/inst |only enrichit-0.1.5/enrichit/vignettes |only enrichit-0.2.0/enrichit/DESCRIPTION | 31 ++- enrichit-0.2.0/enrichit/MD5 | 78 +++++--- enrichit-0.2.0/enrichit/NAMESPACE | 27 ++ enrichit-0.2.0/enrichit/NEWS.md | 57 ++++- enrichit-0.2.0/enrichit/R/00-AllClasses.R | 100 +++++++++- enrichit-0.2.0/enrichit/R/AllGenerics.R | 4 enrichit-0.2.0/enrichit/R/RcppExports.R | 13 + enrichit-0.2.0/enrichit/R/gsea.R | 51 +++++ enrichit-0.2.0/enrichit/R/mnsea.R |only enrichit-0.2.0/enrichit/R/mnsea_contribution.R |only enrichit-0.2.0/enrichit/R/mnsea_subnetwork.R |only enrichit-0.2.0/enrichit/R/multi_omics.R |only enrichit-0.2.0/enrichit/R/nsea.R |only enrichit-0.2.0/enrichit/R/omics_contribution.R |only enrichit-0.2.0/enrichit/R/ora.R | 49 ++++- enrichit-0.2.0/enrichit/R/ora_gson.R | 16 + enrichit-0.2.0/enrichit/R/print.R | 86 ++++++++ enrichit-0.2.0/enrichit/README.md | 126 +++++++----- enrichit-0.2.0/enrichit/man/aggregate_enrichment.Rd |only enrichit-0.2.0/enrichit/man/aggregate_omics.Rd |only enrichit-0.2.0/enrichit/man/classify_omics_pattern.Rd |only enrichit-0.2.0/enrichit/man/collapse_multilayer_scores.Rd |only enrichit-0.2.0/enrichit/man/enrichit-package.Rd | 9 enrichit-0.2.0/enrichit/man/extract_mnsea_subnetwork.Rd |only enrichit-0.2.0/enrichit/man/geneID.Rd | 2 enrichit-0.2.0/enrichit/man/geneInCategory.Rd | 2 enrichit-0.2.0/enrichit/man/get_mnsea_contribution.Rd |only enrichit-0.2.0/enrichit/man/get_omics_contribution.Rd |only enrichit-0.2.0/enrichit/man/gsea.Rd | 3 enrichit-0.2.0/enrichit/man/gsea_gson.Rd | 3 enrichit-0.2.0/enrichit/man/harmonize_ids.Rd |only enrichit-0.2.0/enrichit/man/mnsea.Rd |only enrichit-0.2.0/enrichit/man/mnseaResult-class.Rd |only enrichit-0.2.0/enrichit/man/mnsea_gson.Rd |only enrichit-0.2.0/enrichit/man/nsea.Rd |only enrichit-0.2.0/enrichit/man/nseaResult-class.Rd |only enrichit-0.2.0/enrichit/man/nsea_gson.Rd |only enrichit-0.2.0/enrichit/man/ora.Rd | 4 enrichit-0.2.0/enrichit/man/ora_gson.Rd | 3 enrichit-0.2.0/enrichit/man/prepare_multilayer_network.Rd |only enrichit-0.2.0/enrichit/man/prepare_network.Rd |only enrichit-0.2.0/enrichit/man/propagate_multilayer.Rd |only enrichit-0.2.0/enrichit/man/select_features_for_ora.Rd |only enrichit-0.2.0/enrichit/man/show-methods.Rd | 14 + enrichit-0.2.0/enrichit/src/RcppExports.cpp | 17 + enrichit-0.2.0/enrichit/src/nsea.cpp |only enrichit-0.2.0/enrichit/tests/testthat/test-accessors.R |only enrichit-0.2.0/enrichit/tests/testthat/test-gsea.R | 136 ++++++++++++++ enrichit-0.2.0/enrichit/tests/testthat/test-mnsea.R |only enrichit-0.2.0/enrichit/tests/testthat/test-multi-omics.R |only enrichit-0.2.0/enrichit/tests/testthat/test-nsea.R |only enrichit-0.2.0/enrichit/tests/testthat/test-ora.R | 64 ++++++ 55 files changed, 780 insertions(+), 115 deletions(-)
Title: Ensembles of Caret Models
Description: Functions for creating ensembles of caret models: caretList()
and caretStack(). caretList() is a convenience function for fitting multiple
caret::train() models to the same dataset. caretStack() will make linear or
non-linear combinations of these models, using a caret::train() model as a
meta-model.
Author: Zachary A. Deane-Mayer [aut, cre, cph],
Jared E. Knowles [ctb],
Anton Lopez [ctb]
Maintainer: Zachary A. Deane-Mayer <zach.mayer@gmail.com>
Diff between caretEnsemble versions 4.0.1 dated 2024-09-12 and 4.0.2 dated 2026-07-01
DESCRIPTION | 14 - MD5 | 55 ++++--- NAMESPACE | 4 NEWS.md | 99 ++++++++----- R/caretList.R | 58 +++++-- R/caretPredict.R | 37 ++-- R/caretStack.R | 87 ++++++++++- R/plot_variable_importance.R |only build/vignette.rds |binary inst/data-raw/test-all_models.R | 5 inst/doc/Version-4.0-New-Features.html | 97 ++++++------- inst/doc/caretEnsemble-intro.html | 11 - man/add_cross_group_stats.Rd |only man/caretEnsemble.Rd | 7 man/caretList.Rd | 7 man/caretModelSpec.Rd | 2 man/caretPredict.Rd | 10 + man/caretStack.Rd | 8 + man/caretTrain.Rd | 10 + man/check_original_features.Rd |only man/extractBestPreds.Rd | 4 man/figures/README-greedy-stack-6-plot-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/plot_group.Rd |only man/plot_variable_importance.Rd |only man/predict.caretList.Rd | 11 + man/predict.caretStack.Rd | 3 man/prepare_importance.Rd |only man/varImp.caretStack.Rd | 2 tests/testthat/test-caretList.R | 4 tests/testthat/test-caretStack.R | 186 +++++++++++++++++++++++++ tests/testthat/test-plot_variable_importance.R |only 32 files changed, 551 insertions(+), 170 deletions(-)
Title: Time Series Analysis Toolkit Based on Symbolic Aggregate
Discretization, i.e. SAX
Description: Implements time series z-normalization, SAX, HOT-SAX, VSM, SAX-VSM, RePair, and RRA
algorithms facilitating time series motif (i.e., recurrent pattern), discord (i.e., anomaly),
and characteristic pattern discovery along with interpretable time series classification.
Author: Pavel Senin [aut, cre]
Maintainer: Pavel Senin <seninp@gmail.com>
Diff between jmotif versions 1.2.1 dated 2025-12-22 and 1.3.0 dated 2026-07-01
DESCRIPTION | 6 MD5 | 50 +-- R/RcppExports.R | 27 + README.md | 176 ++++++++---- inst/include/jmotif.h | 89 +++++- man/find_discords_brute_force.Rd | 9 man/find_discords_hotsax.Rd | 7 man/find_discords_rra.Rd | 10 src/RcppExports.cpp | 28 + src/discord.cpp | 52 ++- src/distance.cpp | 21 + src/hot-sax.cpp | 60 ++-- src/paa.cpp | 8 src/repair.cpp | 20 - src/repair_priority_queue.cpp | 433 ++++++------------------------ src/rra.cpp | 237 ++++++++++++---- src/sax.cpp | 6 src/visit_registry.cpp | 18 + src/znorm.cpp | 6 tests/testthat/test_SAX_simple.R | 10 tests/testthat/test_SAX_strategies.R | 13 tests/testthat/test_SAX_via_window.R | 5 tests/testthat/test_discord_brute_force.R | 26 - tests/testthat/test_discord_hot_sax.R | 13 tests/testthat/test_discord_rra.R | 9 tests/testthat/test_znorm.R | 18 - 26 files changed, 762 insertions(+), 595 deletions(-)
Title: High-Dimensional Factor-Analytic Representation Modeling and
Metrics
Description: The goal of 'HAMMER' is to provide factor analytic representation
learning and associated determinacy metrics for very-high-dimensional data.
It projects high-dimensional data onto low-dimensional generative latent
sources and assesses the uncertainty in the projection. The projection is
distribution-free, scale-equivariant, and efficient. For details, see
Peeters (2026) <doi:10.48550/arXiv.2606.28854>.
Author: Carel F.W. Peeters [aut, cre, cph]
Maintainer: Carel F.W. Peeters <carel.peeters@wur.nl>
Diff between HAMMER versions 1.0 dated 2026-06-08 and 1.1 dated 2026-07-01
DESCRIPTION | 11 ++++++----- MD5 | 19 ++++++++++--------- NEWS.md | 10 ++++++++++ R/HAMMER-package.R | 8 ++++++++ R/HAMMER.R | 46 ++++++++++++++++++++++++++++++++++++---------- build |only man/HAMMER-package.Rd | 10 ++++++++++ man/HAMMER.determinacy.Rd | 6 ++++-- man/HAMMER.dimension.Rd | 15 ++++++++++++--- man/HAMMER.estimate.Rd | 6 ++++-- man/HAMMER.score.Rd | 6 ++++-- 11 files changed, 104 insertions(+), 33 deletions(-)
Title: Functions for Epidemiological Analysis using Population Data
Description: Enables computation of epidemiological statistics, including
those where counts or mortality rates of the reference population are
used. Currently supported: excess hazard models (Dickman, Sloggett,
Hills, and Hakulinen (2012) <doi:10.1002/sim.1597>), rates, mean
survival times, relative/net survival (in particular the Ederer II
(Ederer and Heise (1959)) and Pohar Perme (Pohar Perme, Stare, and
Esteve (2012) <doi:10.1111/j.1541-0420.2011.01640.x>) estimators), and
standardized incidence and mortality ratios, all of which can be
easily adjusted for by covariates such as age. Fast splitting and
aggregation of 'Lexis' objects (from package 'Epi') and other
computations achieved using 'data.table'.
Author: Joonas Miettinen [cre, aut] ,
Matti Rantanen [aut],
Karri Seppa [ctb]
Maintainer: Joonas Miettinen <joonas.miettinen@cancer.fi>
Diff between popEpi versions 0.4.14 dated 2026-02-12 and 0.5.0 dated 2026-07-01
popEpi-0.4.14/popEpi/man/Lexis_fpa.Rd |only popEpi-0.4.14/popEpi/tests/testthat/test_prevtab.R |only popEpi-0.4.14/popEpi/tests/testthat/test_splitting_randomly_on_fixed_data.R |only popEpi-0.4.14/popEpi/tests/testthat/test_splitting_randomly_on_random_data.R |only popEpi-0.5.0/popEpi/DESCRIPTION | 28 popEpi-0.5.0/popEpi/LICENSE | 2 popEpi-0.5.0/popEpi/MD5 | 261 +- popEpi-0.5.0/popEpi/NAMESPACE | 7 popEpi-0.5.0/popEpi/NEWS.md | 34 popEpi-0.5.0/popEpi/R/Lexis_funs.R |only popEpi-0.5.0/popEpi/R/S3_definitions.R | 815 ++++-- popEpi-0.5.0/popEpi/R/Surv.R | 66 popEpi-0.5.0/popEpi/R/aggregating.R | 321 +- popEpi-0.5.0/popEpi/R/data_document.R | 16 popEpi-0.5.0/popEpi/R/direct_adjusting.R | 12 popEpi-0.5.0/popEpi/R/evaluation.R | 436 ++- popEpi-0.5.0/popEpi/R/flexyargs.R | 17 popEpi-0.5.0/popEpi/R/fractional_years.R | 30 popEpi-0.5.0/popEpi/R/incidence_rates.R | 244 + popEpi-0.5.0/popEpi/R/incidence_rates_utils.R | 86 popEpi-0.5.0/popEpi/R/lexpand.R | 620 +++- popEpi-0.5.0/popEpi/R/long_df_and_array.R | 76 popEpi-0.5.0/popEpi/R/ltable.R | 84 popEpi-0.5.0/popEpi/R/mean_survival.R | 417 ++- popEpi-0.5.0/popEpi/R/popEpi-package.R | 9 popEpi-0.5.0/popEpi/R/pophaz.R | 12 popEpi-0.5.0/popEpi/R/prevalence.R | 142 - popEpi-0.5.0/popEpi/R/relative_poisson.R | 365 +- popEpi-0.5.0/popEpi/R/relative_poisson_net_survival.R | 67 popEpi-0.5.0/popEpi/R/sir.R | 1273 ++++++---- popEpi-0.5.0/popEpi/R/sir_utils.R | 75 popEpi-0.5.0/popEpi/R/splitLexisDT.R | 134 - popEpi-0.5.0/popEpi/R/splitMulti.R | 125 popEpi-0.5.0/popEpi/R/splitting_utility_functions.R | 1019 ++++---- popEpi-0.5.0/popEpi/R/startup_message.R | 49 popEpi-0.5.0/popEpi/R/survival_aggregated.R | 732 +++-- popEpi-0.5.0/popEpi/R/survival_lexis.R | 346 +- popEpi-0.5.0/popEpi/R/survival_utility_functions.R | 606 +++- popEpi-0.5.0/popEpi/R/sysdata.rda |only popEpi-0.5.0/popEpi/R/utility_functions.R | 814 +++--- popEpi-0.5.0/popEpi/R/weighted_table.R | 414 ++- popEpi-0.5.0/popEpi/R/wip_lexis_merge.R |only popEpi-0.5.0/popEpi/R/wip_lexis_split_merge_aggregate.R |only popEpi-0.5.0/popEpi/R/wip_lexis_utils.R |only popEpi-0.5.0/popEpi/R/wip_prev_lexis.R |only popEpi-0.5.0/popEpi/R/wip_surv_args.R |only popEpi-0.5.0/popEpi/R/wip_surv_estimate.R |only popEpi-0.5.0/popEpi/R/wip_surv_individual_weights.R |only popEpi-0.5.0/popEpi/R/wip_surv_lexis.R |only popEpi-0.5.0/popEpi/R/wip_surv_utils.R |only popEpi-0.5.0/popEpi/R/wip_utils.R |only popEpi-0.5.0/popEpi/R/wip_utils_cut.R |only popEpi-0.5.0/popEpi/R/wip_utils_dataset.R |only popEpi-0.5.0/popEpi/R/wip_utils_dt.R |only popEpi-0.5.0/popEpi/R/wip_utils_regex.R |only popEpi-0.5.0/popEpi/R/wip_utils_unit_test.R |only popEpi-0.5.0/popEpi/README.md | 69 popEpi-0.5.0/popEpi/build/partial.rdb |binary popEpi-0.5.0/popEpi/build/vignette.rds |binary popEpi-0.5.0/popEpi/inst/WORDLIST | 6 popEpi-0.5.0/popEpi/inst/doc/sir.R | 7 popEpi-0.5.0/popEpi/inst/doc/sir.Rmd | 8 popEpi-0.5.0/popEpi/inst/doc/sir.html | 6 popEpi-0.5.0/popEpi/inst/doc/survtab_examples.R | 7 popEpi-0.5.0/popEpi/inst/doc/survtab_examples.Rmd | 8 popEpi-0.5.0/popEpi/inst/doc/survtab_examples.html | 6 popEpi-0.5.0/popEpi/man/ICSS.Rd | 9 popEpi-0.5.0/popEpi/man/RPL.Rd | 10 popEpi-0.5.0/popEpi/man/Surv.Rd | 74 popEpi-0.5.0/popEpi/man/adjust.Rd | 5 popEpi-0.5.0/popEpi/man/aggre.Rd | 15 popEpi-0.5.0/popEpi/man/array_df_ratetable_utils.Rd | 5 popEpi-0.5.0/popEpi/man/as.Date.yrs.Rd | 5 popEpi-0.5.0/popEpi/man/as.aggre.Rd | 15 popEpi-0.5.0/popEpi/man/cast_simple.Rd | 5 popEpi-0.5.0/popEpi/man/cut_bound.Rd | 5 popEpi-0.5.0/popEpi/man/direct_standardization.Rd | 4 popEpi-0.5.0/popEpi/man/fac2num.Rd | 5 popEpi-0.5.0/popEpi/man/flexible_argument.Rd | 7 popEpi-0.5.0/popEpi/man/get.yrs.Rd | 5 popEpi-0.5.0/popEpi/man/is_leap_year.Rd | 5 popEpi-0.5.0/popEpi/man/lexis_funs.Rd |only popEpi-0.5.0/popEpi/man/lexpand.Rd | 23 popEpi-0.5.0/popEpi/man/lines.sirspline.Rd | 12 popEpi-0.5.0/popEpi/man/lines.survmean.Rd | 8 popEpi-0.5.0/popEpi/man/lines.survtab.Rd | 19 popEpi-0.5.0/popEpi/man/ltable.Rd | 5 popEpi-0.5.0/popEpi/man/meanpop_fi.Rd | 2 popEpi-0.5.0/popEpi/man/plot.sir.Rd | 5 popEpi-0.5.0/popEpi/man/plot.sirspline.Rd | 12 popEpi-0.5.0/popEpi/man/plot.survmean.Rd | 8 popEpi-0.5.0/popEpi/man/plot.survtab.Rd | 19 popEpi-0.5.0/popEpi/man/poisson.ci.Rd | 5 popEpi-0.5.0/popEpi/man/popEpi-package.Rd | 3 popEpi-0.5.0/popEpi/man/popmort.Rd | 2 popEpi-0.5.0/popEpi/man/print.survtab.Rd | 14 popEpi-0.5.0/popEpi/man/rate.Rd | 27 popEpi-0.5.0/popEpi/man/rate_ratio.Rd | 9 popEpi-0.5.0/popEpi/man/relpois.Rd | 29 popEpi-0.5.0/popEpi/man/relpois_ag.Rd | 29 popEpi-0.5.0/popEpi/man/robust_values.Rd | 5 popEpi-0.5.0/popEpi/man/rpcurve.Rd | 11 popEpi-0.5.0/popEpi/man/setaggre.Rd | 15 popEpi-0.5.0/popEpi/man/sibr.Rd | 4 popEpi-0.5.0/popEpi/man/sir.Rd | 35 popEpi-0.5.0/popEpi/man/sir_exp.Rd | 24 popEpi-0.5.0/popEpi/man/sir_ratio.Rd | 17 popEpi-0.5.0/popEpi/man/sire.Rd | 4 popEpi-0.5.0/popEpi/man/sirspline.Rd | 36 popEpi-0.5.0/popEpi/man/splitLexisDT.Rd | 21 popEpi-0.5.0/popEpi/man/splitMulti.Rd | 28 popEpi-0.5.0/popEpi/man/stdpop101.Rd | 4 popEpi-0.5.0/popEpi/man/stdpop18.Rd | 4 popEpi-0.5.0/popEpi/man/summary.aggre.Rd | 10 popEpi-0.5.0/popEpi/man/summary.survtab.Rd | 19 popEpi-0.5.0/popEpi/man/survmean.Rd | 33 popEpi-0.5.0/popEpi/man/survtab.Rd | 39 popEpi-0.5.0/popEpi/man/survtab_ag.Rd | 39 popEpi-0.5.0/popEpi/tests/testthat.R | 12 popEpi-0.5.0/popEpi/tests/testthat/test_aggre.R | 239 + popEpi-0.5.0/popEpi/tests/testthat/test_call_with_arg_list__.R |only popEpi-0.5.0/popEpi/tests/testthat/test_epi.R | 47 popEpi-0.5.0/popEpi/tests/testthat/test_expo.R | 79 popEpi-0.5.0/popEpi/tests/testthat/test_infer_cut_args.R |only popEpi-0.5.0/popEpi/tests/testthat/test_lexis_crop.R |only popEpi-0.5.0/popEpi/tests/testthat/test_lexpand.R | 648 +++-- popEpi-0.5.0/popEpi/tests/testthat/test_rate.R | 902 +++++-- popEpi-0.5.0/popEpi/tests/testthat/test_relpois_mean_curve.R | 63 popEpi-0.5.0/popEpi/tests/testthat/test_sir.R | 820 ++++-- popEpi-0.5.0/popEpi/tests/testthat/test_splitLexisDT.R | 155 - 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Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate
cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random
effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>.
Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray,
Ghosh-Lin, Binomial regression) with fast computation of influence functions.
Author: Klaus K. Holst [aut, cre],
Thomas Scheike [aut]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.3.10 dated 2026-05-23 and 1.3.11 dated 2026-07-01
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mets-1.3.11/mets/inst/doc/phreg_rct.Rmd | 304 +++ mets-1.3.11/mets/inst/doc/phreg_rct.html | 31 mets-1.3.11/mets/inst/doc/quantitative-twin.Rmd | 151 + mets-1.3.11/mets/inst/doc/quantitative-twin.html | 28 mets-1.3.11/mets/inst/doc/recurrent-events.Rmd | 455 ++++- mets-1.3.11/mets/inst/doc/recurrent-events.html | 55 mets-1.3.11/mets/inst/doc/rmst-ate.Rmd | 213 ++ mets-1.3.11/mets/inst/doc/rmst-ate.html | 31 mets-1.3.11/mets/inst/doc/survival-ate.Rmd | 236 ++ mets-1.3.11/mets/inst/doc/survival-ate.html | 33 mets-1.3.11/mets/inst/doc/time-to-event-family-studies-arev.Rmd | 841 ++++++++-- mets-1.3.11/mets/inst/doc/time-to-event-family-studies-arev.html | 377 ++-- mets-1.3.11/mets/inst/doc/twostage-survival.Rmd | 754 ++++++++ mets-1.3.11/mets/inst/doc/twostage-survival.html | 29 mets-1.3.11/mets/inst/doc/while-alive.Rmd | 189 ++ mets-1.3.11/mets/inst/doc/while-alive.html | 29 mets-1.3.11/mets/man/IC.binreg.Rd |only mets-1.3.11/mets/man/binreg.Rd | 28 mets-1.3.11/mets/man/binregStrata.Rd |only mets-1.3.11/mets/man/binreg_IPTW.Rd |only mets-1.3.11/mets/man/brier_binreg.Rd |only mets-1.3.11/mets/man/estimate.binregCV.Rd |only mets-1.3.11/mets/man/mediatorSurv.Rd | 2 mets-1.3.11/mets/man/print.summary_binregCV_multi.Rd |only mets-1.3.11/mets/man/recregIPCW.Rd | 2 mets-1.3.11/mets/man/resmeanIPCW.Rd | 2 mets-1.3.11/mets/man/summary.binregCV.Rd |only mets-1.3.11/mets/man/summary.binregCV_list.Rd |only mets-1.3.11/mets/man/survivalG.Rd | 2 mets-1.3.11/mets/man/survival_twostage.Rd | 2 mets-1.3.11/mets/man/test_logrankRecurrent.Rd | 5 mets-1.3.11/mets/src/RcppExports.cpp | 4 mets-1.3.11/mets/src/fastcox.cpp | 75 mets-1.3.11/mets/src/sim-tools.cpp | 14 mets-1.3.11/mets/vignettes/basic-dutils.Rmd | 551 +++++- mets-1.3.11/mets/vignettes/binomial-family.Rmd | 436 ++++- mets-1.3.11/mets/vignettes/binomial-twin.Rmd | 405 ++++ mets-1.3.11/mets/vignettes/binreg-TRS.Rmd | 434 ++++- mets-1.3.11/mets/vignettes/binreg-ate.Rmd | 271 +++ mets-1.3.11/mets/vignettes/binreg.Rmd | 134 + mets-1.3.11/mets/vignettes/cifreg.Rmd | 202 ++ mets-1.3.11/mets/vignettes/cooking-survival-data.Rmd | 392 ++++ mets-1.3.11/mets/vignettes/cumulative-cost.Rmd | 245 ++ mets-1.3.11/mets/vignettes/glm-utility.Rmd | 100 + mets-1.3.11/mets/vignettes/haplo-discrete-ttp.Rmd | 171 +- mets-1.3.11/mets/vignettes/interval-discrete-survival.Rmd | 180 +- mets-1.3.11/mets/vignettes/marginal-cox.Rmd | 135 + mets-1.3.11/mets/vignettes/mediation-survival.Rmd | 325 +++ mets-1.3.11/mets/vignettes/phreg_rct.Rmd | 304 +++ mets-1.3.11/mets/vignettes/quantitative-twin.Rmd | 151 + mets-1.3.11/mets/vignettes/recurrent-events.Rmd | 455 ++++- mets-1.3.11/mets/vignettes/rmst-ate.Rmd | 213 ++ mets-1.3.11/mets/vignettes/survival-ate.Rmd | 236 ++ mets-1.3.11/mets/vignettes/time-to-event-family-studies-arev.Rmd | 841 ++++++++-- mets-1.3.11/mets/vignettes/twostage-survival.Rmd | 754 ++++++++ mets-1.3.11/mets/vignettes/while-alive.Rmd | 189 ++ 125 files changed, 14416 insertions(+), 2362 deletions(-)
Title: Columnar Query Engine for Larger-than-RAM Data
Description: A minimal columnar query engine with lazy execution on datasets
larger than RAM. Provides 'dplyr'-like verbs (filter(), select(), mutate(),
group_by(), summarise(), joins, window functions) and common aggregations
(n(), sum(), mean(), min(), max(), sd(), first(), last()) backed by a
pure C11 pull-based execution engine and a custom on-disk format ('.vtr').
Reads and writes 'GeoTIFF' (including tiled and 'BigTIFF' layouts) and a
tiled raster format ('.vec') with overview pyramids and time cubes for
larger-than-RAM raster data. Streams vector operations (spatial transforms,
point-in-polygon and nearest-feature joins including a two-sided
grid-partitioned join, select-by-location, clip, erase, dissolve,
'rasterization', 'polygonization', and contouring) through 'sf', and runs
raster operations (zonal statistics, focal windows, terrain derivatives,
resample or 'reproject' warp, polygon masking, map algebra, and 'mosaicking')
in native C or over the tiled '.vec' format, one batch or tile at [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between vectra versions 0.9.1 dated 2026-06-29 and 0.9.8 dated 2026-07-01
DESCRIPTION | 18 MD5 | 183 +++-- NAMESPACE | 32 + NEWS.md | 246 +++++++ R/embedding.R |only R/expr.R | 115 +++ R/geom_expr.R |only R/joins.R | 85 ++ R/network.R |only R/resample.R |only R/spatial.R | 954 ++++++++++++++++++++++++++++-- R/spatial_topology.R |only R/windows.R | 32 - README.md | 53 + build/vignette.rds |binary inst/doc/coverage-topology.R |only inst/doc/coverage-topology.Rmd |only inst/doc/coverage-topology.html |only inst/doc/engine.html | 4 inst/doc/formats.html | 54 - inst/doc/geometry-expressions.R |only inst/doc/geometry-expressions.Rmd |only inst/doc/geometry-expressions.html |only inst/doc/indexing.Rmd | 13 inst/doc/indexing.html | 30 inst/doc/joins.Rmd | 4 inst/doc/joins.html | 10 inst/doc/large-data.Rmd | 10 inst/doc/large-data.html | 23 inst/doc/networks.R |only inst/doc/networks.Rmd |only inst/doc/networks.html |only inst/doc/offload.Rmd | 12 inst/doc/offload.html | 40 - inst/doc/quickstart.R | 13 inst/doc/quickstart.Rmd | 14 inst/doc/quickstart.html | 33 - inst/doc/schema.Rmd | 8 inst/doc/schema.html | 14 inst/doc/sdm.html | 4 inst/doc/spatial.R | 14 inst/doc/spatial.Rmd | 26 inst/doc/spatial.html | 52 - inst/doc/streaming-spatial.R | 41 + inst/doc/streaming-spatial.Rmd | 90 ++ inst/doc/streaming-spatial.html | 423 ++++++++----- inst/doc/string-ops.Rmd | 2 inst/doc/string-ops.html | 17 man/as_embedding.Rd |only man/embedding_distance.Rd |only man/floor_time.Rd |only man/geom_expressions.Rd |only man/interval_join.Rd |only man/resample.Rd |only man/rolling.Rd |only man/spatial_centerline.Rd |only man/spatial_construct.Rd |only man/spatial_eliminate.Rd |only man/spatial_explode.Rd |only man/spatial_knn.Rd |only man/spatial_line_merge.Rd |only man/spatial_locate.Rd |only man/spatial_network.Rd |only man/spatial_overlay.Rd | 46 + man/spatial_polygonize.Rd |only man/spatial_route.Rd |only man/spatial_service_area.Rd |only man/spatial_simplify.Rd |only man/spatial_smooth.Rd |only man/spatial_snap.Rd |only man/spatial_snap_grid.Rd |only man/spatial_split.Rd |only man/spatial_topology.Rd |only src/edt.c | 4 src/expr.c | 7 src/expr.h | 30 src/expr_datetime.c | 78 ++ src/expr_geom.c |only src/expr_vec.c |only src/focal.c | 4 src/fuzzy_join.c | 274 -------- src/fuzzy_join.h | 14 src/init.c | 11 src/interval_join.c |only src/interval_join.h |only src/join_partition.c |only src/join_partition.h |only src/network.c |only src/r_bridge.h | 6 src/r_bridge_core.c | 61 + src/r_bridge_nodes.c | 84 ++ src/vec_distance.h |only src/vec_omp.h | 28 src/vtr_overlay.c | 4 src/vtr_spatial.c | 4 src/warp.c | 4 src/window.c | 151 ++++ src/window.h | 9 tests/testthat/test-embedding.R |only tests/testthat/test-geom-expr.R |only tests/testthat/test-interval-join.R |only tests/testthat/test-network.R |only tests/testthat/test-resample.R |only tests/testthat/test-rolling.R |only tests/testthat/test-spatial-construct.R |only tests/testthat/test-spatial-explode.R |only tests/testthat/test-spatial-knn.R |only tests/testthat/test-spatial-overlay-two.R |only tests/testthat/test-spatial-smooth.R |only tests/testthat/test-spatial-snap.R |only tests/testthat/test-spatial-split.R |only tests/testthat/test-spatial-topology.R |only vignettes/coverage-topology.Rmd |only vignettes/geometry-expressions.Rmd |only vignettes/indexing.Rmd | 13 vignettes/joins.Rmd | 4 vignettes/large-data.Rmd | 10 vignettes/networks.Rmd |only vignettes/offload.Rmd | 12 vignettes/quickstart.Rmd | 14 vignettes/schema.Rmd | 8 vignettes/spatial.Rmd | 26 vignettes/streaming-spatial.Rmd | 90 ++ vignettes/string-ops.Rmd | 2 124 files changed, 2829 insertions(+), 838 deletions(-)
Title: Struct-Like Data Type Checking and Enforcement
Description: Enforcement of field types in lists. A drop-in tool to allow for
dynamic input data that might be questionably parsed or cast to be coerced
into the specific desired format in a reasonably performant manner.
Author: Samuel Sapire [aut, cre, cph],
Sean Barrett [ctb]
Maintainer: Samuel Sapire <sapires@protonmail.com>
Diff between structenforcement versions 0.3.0 dated 2026-06-30 and 0.3.1 dated 2026-07-01
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ src/functions.c | 19 ++++++++++--------- tests/testthat/test-type_check.R | 1 + tests/testthat/test-type_check_each.R | 24 ++++++++++++++++++++++++ 6 files changed, 47 insertions(+), 17 deletions(-)
More information about structenforcement at CRAN
Permanent link
Title: Groupwise Statistics, LSmeans, Linear Estimates, Utilities
Description: Utility package containing: Main categories: Working with grouped data: 'do' something to data when stratified 'by' some variables. General linear estimates. Data handling utilities. Functional programming, in particular restrict functions to a smaller domain. Miscellaneous functions for data handling. Model stability in connection with model selection. Miscellaneous other tools.
Author: Ulrich Halekoh [aut, cph],
Soeren Hoejsgaard [aut, cre, cph]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between doBy versions 4.7.1 dated 2025-12-02 and 4.7.2 dated 2026-07-01
doBy-4.7.1/doBy/man/beets.Rd |only doBy-4.7.1/doBy/man/carcass.Rd |only doBy-4.7.1/doBy/man/child_growth.Rd |only doBy-4.7.1/doBy/man/codstom.Rd |only doBy-4.7.1/doBy/man/crickets.Rd |only doBy-4.7.1/doBy/man/crimeRate.Rd |only doBy-4.7.1/doBy/man/crime_rate.Rd |only doBy-4.7.1/doBy/man/cropyield.Rd |only doBy-4.7.1/doBy/man/data-wine.Rd |only doBy-4.7.1/doBy/man/dietox.Rd |only doBy-4.7.1/doBy/man/fatacid.Rd |only doBy-4.7.1/doBy/man/fev.Rd |only doBy-4.7.1/doBy/man/haldCement.Rd |only doBy-4.7.1/doBy/man/income.Rd |only doBy-4.7.1/doBy/man/math_teachers.Rd |only doBy-4.7.1/doBy/man/milkman.Rd |only doBy-4.7.1/doBy/man/nir_milk.Rd |only doBy-4.7.1/doBy/man/potatoes.Rd |only doBy-4.7.1/doBy/man/shoes.Rd |only doBy-4.7.2/doBy/DESCRIPTION | 15 doBy-4.7.2/doBy/MD5 | 104 ++-- doBy-4.7.2/doBy/NAMESPACE | 10 doBy-4.7.2/doBy/NEWS.md | 9 doBy-4.7.2/doBy/R/DATA_doby.R | 46 +- doBy-4.7.2/doBy/R/NAMESPACE_doby.R | 14 doBy-4.7.2/doBy/R/by_lmBy.R | 11 doBy-4.7.2/doBy/R/by_scaleBy.R | 2 doBy-4.7.2/doBy/R/compute_on_forecast.R | 582 ++++++++++++++++++++++---- doBy-4.7.2/doBy/R/data_firstobs_lastobs.R | 3 doBy-4.7.2/doBy/R/doby_utilities.R | 3 doBy-4.7.2/doBy/R/lag_data.R |only doBy-4.7.2/doBy/R/linest_LSmeans.R | 3 doBy-4.7.2/doBy/R/linest_compute.R | 3 doBy-4.7.2/doBy/R/linest_utilities.R | 7 doBy-4.7.2/doBy/R/model_stability.r | 322 +++++--------- doBy-4.7.2/doBy/R/modelling.R | 160 +++---- doBy-4.7.2/doBy/build/vignette.rds |binary doBy-4.7.2/doBy/inst/doc/doby.html | 22 doBy-4.7.2/doBy/inst/doc/pipe_arithmetic.html | 6 doBy-4.7.2/doBy/inst/doc/sectioning_fun.html | 59 +- doBy-4.7.2/doBy/inst/doc/vtools.html | 6 doBy-4.7.2/doBy/man/add_pred.Rd | 18 doBy-4.7.2/doBy/man/add_resid.Rd | 10 doBy-4.7.2/doBy/man/align_coefs.Rd | 33 - doBy-4.7.2/doBy/man/by-lmby.Rd | 7 doBy-4.7.2/doBy/man/cv_glm_fitlist.Rd | 6 doBy-4.7.2/doBy/man/data_beets.Rd |only doBy-4.7.2/doBy/man/data_berkeley_growth.Rd |only doBy-4.7.2/doBy/man/data_carcass.Rd |only doBy-4.7.2/doBy/man/data_codstom.Rd |only doBy-4.7.2/doBy/man/data_crickets.Rd |only doBy-4.7.2/doBy/man/data_crimeRate.Rd |only doBy-4.7.2/doBy/man/data_crime_rate.Rd |only doBy-4.7.2/doBy/man/data_cropyield.Rd |only doBy-4.7.2/doBy/man/data_dietox.Rd |only doBy-4.7.2/doBy/man/data_fatacid.Rd |only doBy-4.7.2/doBy/man/data_fev.Rd |only doBy-4.7.2/doBy/man/data_haldCement.Rd |only doBy-4.7.2/doBy/man/data_income.Rd |only doBy-4.7.2/doBy/man/data_math_teachers.Rd |only doBy-4.7.2/doBy/man/data_milkman.Rd |only doBy-4.7.2/doBy/man/data_nir_milk.Rd |only doBy-4.7.2/doBy/man/data_potatoes.Rd |only doBy-4.7.2/doBy/man/data_shoes.Rd |only doBy-4.7.2/doBy/man/data_wine.Rd |only doBy-4.7.2/doBy/man/generate_data_list.Rd | 26 + doBy-4.7.2/doBy/man/get_formulas.Rd | 4 doBy-4.7.2/doBy/man/is_estimable.Rd | 2 doBy-4.7.2/doBy/man/lag_data.Rd |only doBy-4.7.2/doBy/man/model_stability_glm.Rd | 75 +++ doBy-4.7.2/doBy/man/response.Rd | 6 doBy-4.7.2/doBy/man/set_list_set_matrix.Rd | 4 doBy-4.7.2/doBy/man/transform_forecast.Rd | 74 ++- 73 files changed, 1082 insertions(+), 570 deletions(-)
Title: General Modules for 'teal' Applications
Description: Prebuilt 'shiny' modules containing tools for viewing data,
visualizing data, understanding missing and outlier values within your
data and performing simple data analysis. This extends 'teal'
framework that supports reproducible research and analysis.
Author: Dony Unardi [aut, cre],
Dawid Kaledkowski [aut],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Ondrej Slama [ctb],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Nikolas Burkoff [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal.modules.general versions 0.6.0 dated 2025-12-03 and 0.7.0 dated 2026-07-01
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More information about teal.modules.general at CRAN
Permanent link
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of Hoehle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>.
A novel CUSUM approach combining logistic and multinomial logistic
modeling is also included. The package contains several real-world data
sets, the ability to simulate outbreak data, and to visualize the
results of the monitoring in a temporal, spatial or spatio-temporal
fashion. A recent overview of the available mon [...truncated...]
Author: Michael Hoehle [aut, ths] ,
Sebastian Meyer [aut, cre] ,
Michaela Paul [aut],
Leonhard Held [ctb, ths] ,
Howard Burkom [ctb],
Thais Correa [ctb],
Mathias Hofmann [ctb],
Christian Lang [ctb],
Juliane Manitz [ctb],
Sophie Reichert [ctb],
Andrea Riebler [...truncated...]
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between surveillance versions 1.25.0 dated 2025-06-25 and 1.26.0 dated 2026-07-01
DESCRIPTION | 20 +-- MD5 | 188 ++++++++++++++++----------------- NAMESPACE | 13 -- NEWS.md | 20 +++ R/AllClass.R | 2 R/addSeason2formula.R | 8 - R/algo_call.R | 2 R/algo_farrington.R | 32 ++--- R/disProg.R | 2 R/epidataCS_methods.R | 2 R/epidataCS_plot.R | 28 ++-- R/farringtonFlexible.R | 91 ++++----------- R/functionTable.R | 15 +- R/hhh4.R | 10 - R/hhh4_W_powerlaw.R | 53 ++++++++- R/hhh4_amplitudeShift.R | 23 ++-- R/hhh4_methods.R | 4 R/hhh4_simulate.R | 11 + R/knox.R | 10 - R/makeControl.R | 4 R/options.R | 2 R/spatial_tools.R | 4 R/sts.R | 28 ++-- R/sts_toLatex.R | 16 -- R/sysdata.rda |binary R/twinstim.R | 16 +- R/twinstim_intensity.R | 9 + R/twinstim_methods.R | 27 +--- R/twinstim_simulation.R | 6 - R/zzz.R | 12 -- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary data/datalist |only demo/v77i11.R | 1 inst/CITATION | 3 inst/REFERENCES.bib |only inst/doc/glrnb.R | 2 inst/doc/glrnb.Rnw | 6 - inst/doc/glrnb.pdf |binary inst/doc/hhh4.R | 2 inst/doc/hhh4.Rnw | 18 +-- inst/doc/hhh4.pdf |binary inst/doc/hhh4_spacetime.Rnw | 23 ++-- inst/doc/hhh4_spacetime.pdf |binary inst/doc/monitoringCounts.R | 2 inst/doc/monitoringCounts.Rnw | 12 +- inst/doc/monitoringCounts.pdf |binary inst/doc/surveillance.R | 2 inst/doc/surveillance.Rnw | 6 - inst/doc/surveillance.pdf |binary inst/doc/twinSIR.Rnw | 11 + inst/doc/twinSIR.pdf |binary inst/doc/twinstim.R | 1 inst/doc/twinstim.Rnw | 56 +++++---- inst/doc/twinstim.pdf |binary man/LRCUSUM.runlength.Rd | 2 man/addSeason2formula.Rd | 11 + man/algo.quality.Rd | 4 man/epidata.Rd | 2 man/epidataCS.Rd | 4 man/epidataCS_plot.Rd | 1 man/hagelloch.Rd | 4 man/hhh4.Rd | 8 - man/hhh4_formula.Rd | 4 man/hhh4_methods.Rd | 2 man/hhh4_plot.Rd | 2 man/hhh4_validation.Rd | 2 man/knox.Rd | 3 man/macros/linkSPclass.Rd | 2 man/macros/vignette.Rd |only man/measles.weser.Rd | 2 man/stsplot_time.Rd | 11 + man/surveillance-defunct.Rd | 4 man/surveillance-package.Rd | 100 ++++++++++------- man/surveillance.options.Rd | 2 man/toLatex.sts.Rd | 3 man/twinSIR.Rd | 2 man/twinSIR_intensityplot.Rd | 2 man/twinstim.Rd | 4 man/twinstim_iaf.Rd | 2 man/twinstim_iafplot.Rd | 2 man/twinstim_methods.Rd | 8 - man/twinstim_plot.Rd | 2 tests/testthat/test-hhh4+derivatives.R | 14 ++ tests/testthat/test-toLatex.sts.R | 2 tests/testthat/test-twinstim_misc.R | 12 ++ vignettes/fixjss.sty |only vignettes/glrnb.Rnw | 6 - vignettes/hhh4.Rnw | 18 +-- vignettes/hhh4_spacetime.Rnw | 23 ++-- vignettes/monitoringCounts.Rnw | 12 +- vignettes/monitoringCounts.bib | 9 - vignettes/references.bib | 153 +------------------------- vignettes/surveillance.Rnw | 6 - vignettes/twinSIR.Rnw | 11 + vignettes/twinstim.Rnw | 56 +++++---- 97 files changed, 651 insertions(+), 671 deletions(-)
Title: High Throughput Phenotyping (HTP) Data Analysis
Description: Phenotypic analysis of data coming from high throughput
phenotyping (HTP) platforms, including different types of outlier detection,
spatial analysis, and parameter estimation. The package is being developed
within the EPPN2020 project (<https://cordis.europa.eu/project/id/731013>).
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r/>).
Author: Emilie J Millet [aut] ,
Maria Xose Rodriguez Alvarez [aut] ,
Diana Marcela Perez Valencia [aut] ,
Isabelle Sanchez [aut],
Nadine Hilgert [aut],
Bart-Jan van Rossum [aut, cre] ,
Fred van Eeuwijk [aut] ,
Martin Boer [aut]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenHTP versions 1.0.9.2 dated 2026-05-21 and 1.0.9.3 dated 2026-07-01
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview_HTP.html | 4 ++-- inst/tinytest/serieOut |binary inst/tinytest/splineEst |binary inst/tinytest/test_detectSerieOut.R | 9 ++++----- inst/tinytest/test_fitSpline.R | 2 +- tests/tinytest.R | 5 ++--- 11 files changed, 29 insertions(+), 27 deletions(-)
Title: Make Interactive 'PRISMA' Flow Diagrams
Description: Systematic reviews should be described in a high degree of
methodological detail. The 'PRISMA' Statement calls for a high level of
reporting detail in systematic reviews and meta-analyses. An integral part
of the methodological description of a review is a flow diagram.
This package produces an interactive flow diagram that conforms to the
'PRISMA2020' preprint. When made interactive, the reader/user can click
on each box and be directed to another website or file online (e.g. a
detailed description of the screening methods, or a list of excluded full
texts), with a mouse-over tool tip that describes the information linked
to in more detail. Interactive versions can be saved as HTML files,
whilst static versions for inclusion in manuscripts can be saved as
HTML, PDF, PNG, SVG, PS or WEBP files.
Author: Neal Haddaway [aut] ,
Luke McGuinness [aut] ,
Chris Pritchard [aut, cre] ,
Brennan Chapman [ctb],
Hossam Hammady [ctb],
Anders Kolstad [ctb] ,
Shreya Dimri [ctb] ,
Matt Lloyd Jones [ctb] ,
John-o Kulas [ctb]
Maintainer: Chris Pritchard <chris@christopherpritchard.co.uk>
Diff between PRISMA2020 versions 1.1.1 dated 2023-02-09 and 1.1.4 dated 2026-07-01
PRISMA2020-1.1.1/PRISMA2020/R/utils.R |only PRISMA2020-1.1.4/PRISMA2020/DESCRIPTION | 39 PRISMA2020-1.1.4/PRISMA2020/LICENSE | 2 PRISMA2020-1.1.4/PRISMA2020/MD5 | 56 PRISMA2020-1.1.4/PRISMA2020/NAMESPACE | 4 PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_add_hyperlink.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_calc_filetype.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_data.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_default_or_csv.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_flowdiagram.R | 1355 +++----------- PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_format.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_gen_tmp_svg.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_get.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_insert_js.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_interactive.R |only PRISMA2020-1.1.4/PRISMA2020/R/PRISMA_save.R |only PRISMA2020-1.1.4/PRISMA2020/R/defunct.R |only PRISMA2020-1.1.4/PRISMA2020/R/globals.R | 6 PRISMA2020-1.1.4/PRISMA2020/R/imports.R |only PRISMA2020-1.1.4/PRISMA2020/README.md | 1 PRISMA2020-1.1.4/PRISMA2020/inst/extdata/PRISMA.csv | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_add_hyperlink_.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_calc_filetype_.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_data.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_default_or_csv_.Rd |only PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_flowdiagram.Rd | 16 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_format_number_.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_format_reasons_.Rd |only PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_gen_tmp_svg_.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_get_height_.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_get_pos_.Rd | 12 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_insert_js_.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_interactive_.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_parse_reasons_.Rd |only PRISMA2020-1.1.4/PRISMA2020/man/PRISMA_save.Rd | 16 PRISMA2020-1.1.4/PRISMA2020/man/read_PRISMAdata.Rd | 2 PRISMA2020-1.1.4/PRISMA2020/man/sr_flow_interactive.Rd | 2 37 files changed, 482 insertions(+), 1047 deletions(-)
Title: Functions for University of Auckland Course STATS 201/208 Data
Analysis
Description: A set of functions used in teaching STATS 201/208 Data Analysis at
the University of Auckland. The functions are designed to make parts of R more
accessible to a large undergraduate population who are mostly not statistics
majors.
Author: Brant Deppa [aut] ,
James Curran [aut, cre] ,
Hannah Yun [ctb],
Rachel Fewster [ctb],
Russell Millar [ctb],
Ben Stevenson [ctb],
Andrew Balemi [ctb],
Chris Wild [ctb],
Sophie Jones [ctb],
Dineika Chandra [ctb],
Brendan McArdle [ctb]
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between s20x versions 3.2.2 dated 2026-01-14 and 3.3.0 dated 2026-07-01
DESCRIPTION | 25 MD5 | 320 +++++++---- NAMESPACE | 227 +++++--- NEWS.md |only R/autocor.plot.R | 83 +-- R/boxqq.r | 103 --- R/casestudy.R | 137 +++-- R/ciReg.R | 58 +- R/cooks20x.R | 77 +- R/crosstabs.R | 168 +++--- R/displayPairs.R | 280 +++++----- R/eovcheck.R | 465 +++++++++++------ R/estimateContrasts.R | 95 +-- R/estimateContrasts1.R | 101 ++- R/estimateContrasts2.R | 107 ++- R/freq1way.r | 307 ++++++----- R/getVersion.R | 33 - R/graphics-parameter-helpers.R |only R/interactionPlots.R | 11 R/internal-predict-helper.R |only R/layout20x.R | 49 - R/levene.test.R | 140 ++--- R/listCaseStudies.R | 107 ++- R/modcheck.R | 135 ---- R/model-diagnostic-helpers.R |only R/modelcheck.R | 328 ++++++++++-- R/multipleComp.R | 113 ++-- R/normcheck.R | 613 ++++++++++++++++++---- R/openCaseStudy.R | 127 +++- R/pairs20x.R | 232 +++++++- R/plotting-engine-helpers.R |only R/predict20x.R | 199 ++++--- R/predictCount.R | 132 ++-- R/predictGLM.R | 173 +++--- R/propslsd.new.R | 121 ++-- R/residPlot.R | 132 ++-- R/rowdistr.r | 675 +++++++++++++++--------- R/rr.r | 21 R/s20x-data.R | 576 ++++++++++++--------- R/s20x-package.R | 21 R/skewness.r | 49 - R/stripqq.r | 100 --- R/summary1way.R | 238 +++++--- R/summary2way.R | 920 +++++++++++++++++----------------- R/summaryStats.R | 393 +++++++------- R/trendscatter.R | 243 ++++---- R/tslm.R |only README.md | 137 +++-- data/airpass.df.rda |binary data/nzalc.df.rda |only data/nzarrivals.df.rda |only inst/case_studies/CS10_3.Rmd | 4 inst/case_studies/CS11_3.Rmd | 6 inst/case_studies/CS12_4.Rmd | 4 inst/case_studies/CS14_3.Rmd | 2 inst/case_studies/CS14_4.Rmd | 2 inst/case_studies/CS15_3.Rmd | 2 inst/case_studies/CS15_4.Rmd | 4 inst/case_studies/CS5_2.Rmd | 6 inst/case_studies/CS6_3.Rmd | 2 inst/case_studies/CS6_4.Rmd | 2 inst/case_studies/CS8_3.Rmd | 2 inst/case_studies/CS9_6.Rmd | 2 inst/extdata/Galton3.csv | 396 +++++++------- man/anova.tslm.Rd |only man/apples.df.Rd | 26 man/arousal.df.Rd | 6 man/autocor.plot.Rd |only man/autocorPlot.Rd | 4 man/beer.df.Rd | 4 man/body.df.Rd | 37 - man/books.df.Rd | 10 man/boxqq.Rd | 28 - man/bursary.df.Rd | 4 man/butterfat.df.Rd | 6 man/camplake.df.Rd | 6 man/captureOptionalName.Rd |only man/casestudy.Rd | 16 man/chalk.df.Rd | 6 man/ciReg.Rd | 2 man/computer.df.Rd | 4 man/cooks20x.Rd | 4 man/course.df.Rd | 30 - man/course2way.df.Rd | 6 man/crosstabs.Rd | 17 man/diamonds.df.Rd | 4 man/displayPairs.Rd | 20 man/drawPlot.Rd |only man/eovcheck.Rd | 52 + man/estimateContrasts.Rd | 38 - man/estimateContrasts1.Rd |only man/estimateContrasts2.Rd |only man/extractTslmErrorSpec.Rd |only man/extractTslmFit.Rd |only man/fire.df.Rd | 6 man/formatTslmAnovaTable.Rd |only man/formatTslmResidualTypeLabel.Rd |only man/freq1way.Rd | 14 man/fruitfly.df.Rd | 4 man/getModelResidualFittedData.Rd |only man/getTslmArParameters.Rd |only man/getTslmCoefficientTable.Rd |only man/getTslmDiagnosticData.Rd |only man/getTslmErrorTerms.Rd |only man/getTslmResidualDf.Rd |only man/getTslmTimeValues.Rd |only man/getVersion.Rd | 6 man/house.df.Rd | 4 man/incomes.df.Rd | 5 man/interactionPlots.Rd | 11 man/isTslmErrorTerm.Rd |only man/lakemary.df.Rd | 4 man/layout20x.Rd | 19 man/listCaseStudies.Rd | 6 man/makeTslmModelData.Rd |only man/matchPlottingEngine.Rd |only man/matchTslmResidualType.Rd |only man/mazda.df.Rd | 4 man/mening.df.Rd | 7 man/mergers.df.Rd | 5 man/modcheck.Rd | 68 -- man/modelcheck.Rd | 82 ++- man/mozart.df.Rd | 6 man/multipleComp.Rd | 15 man/nail.df.Rd | 4 man/normcheck.Rd | 122 +++- man/nzalc.df.Rd |only man/nzarrivals.df.Rd |only man/openCaseStudy.Rd | 18 man/oysters.df.Rd | 8 man/pairs20x.Rd | 30 - man/parseTslmFormula.Rd |only man/peru.df.Rd | 10 man/plotTslmResiduals.Rd |only man/plotTslmTimeResiduals.Rd |only man/predict20x.Rd | 47 + man/predictCount.Rd | 36 - man/predictGLM.Rd | 35 - man/prepCrosstabList.Rd |only man/print.s20xModelcheck_ggplot2.Rd |only man/print.s20xNormcheck_ggplot2.Rd |only man/printOutput.Rd |only man/propslsd.new.Rd | 3 man/rain.df.Rd | 6 man/removeTslmErrorTerms.Rd |only man/requirePlottingPackage.Rd |only man/requireSuggestedPackage.Rd |only man/residPlot.Rd | 6 man/resolveCaseStudyDestinationDir.Rd |only man/resolveCaseStudyOutputArgs.Rd |only man/rowdistr.Rd | 16 man/rr.Rd | 2 man/s20x-package.Rd | 18 man/s20x_ggplot2_base_theme.Rd |only man/saveGraphicsParameters.Rd |only man/seeds.df.Rd | 6 man/sentenceCase.Rd |only man/sheep.df.Rd | 9 man/skewness.Rd | 4 man/skulls.df.Rd | 4 man/snapper.df.Rd | 9 man/soyabean.df.Rd | 6 man/stripqq.Rd | 35 - man/summary1way.Rd | 31 - man/summary2way.Rd | 41 - man/summaryStats.Rd | 60 +- man/teach.df.Rd | 6 man/technitron.df.Rd | 16 man/thyroid.df.Rd | 8 man/toothpaste.df.Rd | 4 man/trendscatter.Rd | 7 man/tslm.Rd |only man/zoo.df.Rd | 12 tests |only 174 files changed, 6011 insertions(+), 4209 deletions(-)
Title: HTTP Web Server for R
Description: An HTTP web server for R with a documented API to interface between R and the server. The documentation contains the Rook specification and details for building and running Rook applications. To get started, be sure and read the 'Rook' help file first.
Author: Jeffrey Horner [aut],
Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between Rook versions 1.2 dated 2022-11-07 and 1.2.1 dated 2026-06-30
DESCRIPTION | 18 +++++++++++++----- MD5 | 2 +- 2 files changed, 14 insertions(+), 6 deletions(-)
Title: Distributions, Statistics and Tests Derived from Random Matrix
Theory
Description: Functions for working with the Tracy-Widom laws and other distributions
related to the eigenvalues of large Wishart matrices.
The tables for computing the Tracy-Widom densities and distribution
functions were computed by functions were computed by Momar Dieng's MATLAB package "RMLab". This package is part of a collaboration between Iain Johnstone, Zongming Ma, Patrick Perry, and Morteza Shahram.
Author: Iain M. Johnstone [aut],
Zongming Ma [aut],
Patrick O. Perry [aut],
Morteza Shahram [aut],
Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between RMTstat versions 0.3.1 dated 2022-04-12 and 0.3.2 dated 2026-06-30
DESCRIPTION | 32 ++++++++++++++++++++++++++------ MD5 | 4 ++-- inst/CITATION | 31 +++++++++++++++++++++++-------- 3 files changed, 51 insertions(+), 16 deletions(-)
Title: Multivariate Spatio-Temporal Models using Structural Equations
Description: Fits a wide variety of multivariate spatio-temporal models
with simultaneous and lagged interactions among variables (including
vector autoregressive spatio-temporal ('VAST') dynamics)
for areal, continuous, or network spatial domains.
It includes time-variable, space-variable, and space-time-variable
interactions using dynamic structural equation models ('DSEM')
as expressive interface, and the 'mgcv' package to specify splines
via the formula interface. See Thorson et al. (2025)
<doi:10.1111/geb.70035> for more details.
Author: James T. Thorson [aut, cre] ,
Sean C. Anderson [aut]
Maintainer: James T. Thorson <James.Thorson@noaa.gov>
Diff between tinyVAST versions 1.6.0 dated 2026-05-18 and 1.6.1 dated 2026-06-30
DESCRIPTION | 14 ++-- MD5 | 42 ++++++------ NAMESPACE | 3 NEWS.md | 10 +++ R/fit.R | 8 +- R/make_dsem_ram.R | 11 +-- R/make_sem_ram.R | 8 +- R/methods.R | 8 +- R/predict.R | 111 ++++++++++++++++++++++++++++++---- R/sem_imports.R |only R/utility.R | 22 +++--- inst/doc/dsem.html | 58 ++++++++--------- inst/doc/mgcv.html | 4 - inst/doc/multiple_data.html | 2 inst/doc/spatial.html | 4 - inst/doc/spatial_factor_analysis.html | 12 +-- man/integrate_output.Rd | 62 ++++++++++++++++++ man/make_dsem_ram.Rd | 17 +---- man/make_sem_ram.Rd | 17 +---- man/sample_variable.Rd | 22 +++--- src/tinyVAST.cpp | 1 tests/testthat/Rplots.pdf |only tests/testthat/test-dsem.R | 52 ++++++++------- 23 files changed, 320 insertions(+), 168 deletions(-)
Title: Interactive Visualization of MSE Results
Description: A framework for visualizing and exploring results of a Management
Strategy Evaluation (MSE). The publication quality figures and tables
can be developed directly from the R console, or interactively explored
with the 'Slick' App. For more details, see the 'Slick' website
<https://slick.bluematterscience.com>.
Author: Adrian Hordyk [aut, cre],
Tom Carruthers [aut],
Quang Huynh [aut],
Shana Miller [aut]
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>
Diff between Slick versions 1.0.1 dated 2026-02-27 and 1.0.2 dated 2026-06-30
DESCRIPTION | 8 ++++---- MD5 | 38 +++++++++++++++++++------------------- NEWS.md | 7 +++++-- R/class_Check.R | 2 +- R/fct_plotBoxplot.R | 19 +++++++++++-------- R/fct_plotSpider.R | 4 ++++ R/mod_Boxplot.R | 15 --------------- R/mod_Boxplot_overall.R | 4 ++-- R/mod_Metadata.R | 2 +- R/mod_Sidebar.R | 2 +- R/mod_Spider_MP.R | 1 + R/mod_Tradeoff.R | 2 +- R/mod_subtitle.R | 2 +- man/Make_Slick.Rd | 2 +- man/NewSlick.Rd | 2 +- man/PMnorm.Rd | 2 +- man/Quilt-methods.Rd | 3 ++- man/TimeLab.Rd | 2 +- man/plotBoxplot.Rd | 2 +- man/show.Rd | 4 ++-- 20 files changed, 60 insertions(+), 63 deletions(-)
Title: SQLite Interface for R
Description: Embeds the SQLite database engine in R and provides an
interface compliant with the DBI package. The source for the SQLite
engine and for various extensions is included.
System libraries will never be consulted because this package relies
on static linking for the plugins it includes; this also ensures a
consistent experience across all installations. Optionally, when
libcurl is available at build time, an experimental HTTP/HTTPS
virtual file system (VFS) can be enabled to allow read-only access
to remote immutable SQLite database files via URIs.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
D. Richard Hipp [ctb] ,
Dan Kennedy [ctb] ,
Joe Mistachkin [ctb] ,
SQLite Authors [ctb] ,
Liam Healy [ctb] ,
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RSQLite versions 3.53.2 dated 2026-06-17 and 3.53.3 dated 2026-06-30
RSQLite-3.53.2/RSQLite/tests/testthat/helper-aspell.R |only RSQLite-3.53.3/RSQLite/.aspell/DBI.rds |binary RSQLite-3.53.3/RSQLite/.aspell/defaults.R | 2 RSQLite-3.53.3/RSQLite/DESCRIPTION | 8 RSQLite-3.53.3/RSQLite/MD5 | 17 RSQLite-3.53.3/RSQLite/NEWS.md | 11 RSQLite-3.53.3/RSQLite/README.md | 167 --- RSQLite-3.53.3/RSQLite/src/vendor/extensions/csv.c | 9 RSQLite-3.53.3/RSQLite/src/vendor/extensions/http.c | 58 - RSQLite-3.53.3/RSQLite/src/vendor/extensions/series.c | 40 RSQLite-3.53.3/RSQLite/src/vendor/sqlite3/sqlite3.c | 783 +++++++++++------- RSQLite-3.53.3/RSQLite/src/vendor/sqlite3/sqlite3.h | 16 12 files changed, 637 insertions(+), 474 deletions(-)
Title: JSON Graphics Device
Description: A graphics device that translates R plotting operations into JSON
and streams them over a local connection to an external display
application. The device acts as a pure recorder with no rendering
dependencies; all rendering occurs in that application (e.g. a 'VS Code'
extension or a web browser). Official display applications are available
from the project homepage.
Author: Grant McDermott [aut, cre],
Tatsuya Shima [aut],
Dave Gamble [cph] ,
cJSON contributors [cph]
Maintainer: Grant McDermott <contact@grantmcdermott.com>
Diff between jgd versions 0.1.0 dated 2026-04-29 and 0.1.1 dated 2026-06-30
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 15 +++++++++++++++ R/jgd-package.R | 5 +++++ R/jgd.R | 21 +++++++++++++++------ man/jgd-package.Rd | 6 +++++- man/jgd.Rd | 24 +++++++++++++++++++----- man/jgd_ext.Rd | 2 +- src/device.c | 3 +++ src/transport.c | 24 +++++++++++++----------- 10 files changed, 89 insertions(+), 37 deletions(-)
Title: A Universal Approach for Causal Mediation Analysis
Description: This program realizes a universal estimation approach that accommodates
multi-category variables and effect scales, making up for the deficiencies
of the existing approaches when dealing with non-binary exposures and
complex models. The estimation via bootstrapping can simultaneously provide results of
causal mediation on risk difference (RD), odds ratio (OR) and risk ratio (RR) scales with tests of the effects' difference.
The estimation is also applicable to many other settings, e.g., moderated mediation, inconsistent covariates,
panel data, etc. The high flexibility and compatibility
make it possible to apply for any type of model, greatly meeting the needs of
current empirical researches.
Author: Tianbao Zhou [aut, cre],
Xinghao Li [aut],
Lin Liu* [aut]
Maintainer: Tianbao Zhou <michaelzhou@buaa.edu.cn>
Diff between unvs.med versions 1.1.0 dated 2026-01-27 and 1.1.1 dated 2026-06-30
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 3 +++ R/potentialoutcome_facX.R | 6 ++++-- R/potentialoutcome_numX.R | 6 ++++-- 5 files changed, 20 insertions(+), 13 deletions(-)
Title: Group Sequential Design with Non-Constant Effect
Description: The goal of 'gsDesign2' is to enable fixed or group sequential
design under non-proportional hazards. To enable highly flexible enrollment,
time-to-event and time-to-dropout assumptions, 'gsDesign2' offers piecewise
constant enrollment, failure rates, and dropout rates for a stratified
population. This package includes three methods for designs:
average hazard ratio, weighted logrank tests in Yung and Liu (2019)
<doi:10.1111/biom.13196>, and MaxCombo tests.
Substantial flexibility on top of what is in the 'gsDesign' package
is intended for selecting boundaries.
Author: Keaven Anderson [aut],
Yujie Zhao [aut, cre],
Yilong Zhang [aut],
John Blischak [aut],
Yihui Xie [aut],
Nan Xiao [aut],
Jianxiao Yang [aut],
Amin Shirazi [ctb],
Ruixue Wang [ctb],
Yi Cui [ctb],
Ping Yang [ctb],
Xin Tong Li [ctb],
Chenxiang Li [ctb],
[...truncated...]
Maintainer: Yujie Zhao <yujie.zhao@merck.com>
Diff between gsDesign2 versions 1.1.8 dated 2026-02-12 and 1.1.9 dated 2026-06-30
gsDesign2-1.1.8/gsDesign2/R/gs_cp_npe.R |only gsDesign2-1.1.8/gsDesign2/man/gs_cp_npe.Rd |only gsDesign2-1.1.8/gsDesign2/tests/testthat |only gsDesign2-1.1.8/gsDesign2/tests/testthat.R |only gsDesign2-1.1.9/gsDesign2/DESCRIPTION | 8 gsDesign2-1.1.9/gsDesign2/MD5 | 241 +++--- gsDesign2-1.1.9/gsDesign2/NAMESPACE | 4 gsDesign2-1.1.9/gsDesign2/NEWS.md | 30 gsDesign2-1.1.9/gsDesign2/R/expected_time.R | 2 gsDesign2-1.1.9/gsDesign2/R/globals.R | 3 gsDesign2-1.1.9/gsDesign2/R/gs_bound_summary.R | 11 gsDesign2-1.1.9/gsDesign2/R/gs_cp.R |only gsDesign2-1.1.9/gsDesign2/R/gs_cp_npe1.R |only gsDesign2-1.1.9/gsDesign2/R/gs_cp_npe2.R |only gsDesign2-1.1.9/gsDesign2/R/gs_cp_simple.R |only gsDesign2-1.1.9/gsDesign2/R/gs_design_ahr.R | 103 +- gsDesign2-1.1.9/gsDesign2/R/gs_design_npe.R | 22 gsDesign2-1.1.9/gsDesign2/R/gs_design_rd.R | 2 gsDesign2-1.1.9/gsDesign2/R/gs_info_ahr.R | 3 gsDesign2-1.1.9/gsDesign2/R/gs_info_rd.R | 33 gsDesign2-1.1.9/gsDesign2/R/gs_power_npe.R | 14 gsDesign2-1.1.9/gsDesign2/R/gs_power_rd.R | 2 gsDesign2-1.1.9/gsDesign2/R/gs_update_ahr.R | 3 gsDesign2-1.1.9/gsDesign2/R/pw_info.R | 6 gsDesign2-1.1.9/gsDesign2/R/sequential_pval.R |only gsDesign2-1.1.9/gsDesign2/R/summary.R | 2 gsDesign2-1.1.9/gsDesign2/R/text_summary.R | 58 + gsDesign2-1.1.9/gsDesign2/R/utils.R | 26 gsDesign2-1.1.9/gsDesign2/README.md | 64 + gsDesign2-1.1.9/gsDesign2/inst/doc/gsDesign2.html | 770 +++++++++++----------- gsDesign2-1.1.9/gsDesign2/man/gs_cp.Rd |only gsDesign2-1.1.9/gsDesign2/man/gs_cp_simple.Rd |only gsDesign2-1.1.9/gsDesign2/man/gs_design_rd.Rd | 2 gsDesign2-1.1.9/gsDesign2/man/gs_info_rd.Rd | 15 gsDesign2-1.1.9/gsDesign2/man/gs_power_rd.Rd | 2 gsDesign2-1.1.9/gsDesign2/man/sequential_pval.Rd |only gsDesign2-1.1.9/gsDesign2/tests/test-all.R |only gsDesign2-1.1.9/gsDesign2/tests/testit |only 38 files changed, 748 insertions(+), 678 deletions(-)
Title: Interactive Virtualized Data Explorer Grid Widget
Description: Provides an interactive, virtualized data explorer widget for 'R'.
Built on 'React' (via 'reactR') and 'htmlwidgets', it offers column-type
detection, multi-value checkbox filtering, sorting, column visibility
toggling, virtual scrolling for large datasets, and a full-viewport modal.
Includes 'dtsmartr_launch()' with an interactive, zero-code file upload wizard
using 'datamods'. Widgets can be embedded in 'R Markdown' / 'Quarto' documents,
'Shiny' applications, or exported as standalone HTML files via 'save_dtsmartr()'.
Author: Nikhil Wagh [aut, cre]
Maintainer: Nikhil Wagh <nmw1986@gmail.com>
Diff between dtsmartr versions 0.1.0 dated 2026-06-16 and 0.2.0 dated 2026-06-30
DESCRIPTION | 9 +++---- MD5 | 40 ++++++++++++++++++++++++------- NAMESPACE | 2 + R/dtsmartr.R | 49 ++++++++++++++++++++++++++++++++++++--- R/dtsmartr_launch.R | 4 +-- README.md | 23 ++++++++++++++++++ build |only inst/doc |only inst/htmlwidgets/dtsmartr.js | 2 - inst/htmlwidgets/dtsmartr.js.map | 2 - man/dtsmart_lite.Rd |only man/dtsmartr_options.Rd | 6 +++- tests/testthat/test-dtsmartr.R | 18 ++++++++++++-- vignettes |only 14 files changed, 132 insertions(+), 23 deletions(-)
Title: Solvers for Maximum Weight Connected Subgraph Problem and Its
Variants
Description: Algorithms for solving various Maximum
Weight Connected Subgraph Problems, including variants with
budget constraints, cardinality constraints, weighted edges and signals.
The package represents an R interface to high-efficient solvers based on
relax-and-cut approach (Álvarez-Miranda E., Sinnl M. (2017) <doi:10.1016/j.cor.2017.05.015>)
mixed-integer programming (Loboda A., Artyomov M., and Sergushichev A. (2016) <doi:10.1007/978-3-319-43681-4_17>)
and simulated annealing.
Author: Alexander Loboda [aut, cre],
Nikolay Poperechnyi [aut],
Eduardo Alvarez-Miranda [aut],
Markus Sinnl [aut],
Alexey Sergushichev [aut],
Paul Hosler Jr. [cph] ,
www.hamcrest.org [cph] ,
Barak Naveh and Contributors [cph] ,
The Apache Software Foundation [...truncated...]
Maintainer: Alexander Loboda <aleks.loboda@gmail.com>
Diff between mwcsr versions 0.1.11 dated 2026-05-11 and 0.1.12 dated 2026-06-30
DESCRIPTION | 6 MD5 | 12 - R/rnc_sgmwcs.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/tutorial.html | 461 +++++++++++++++++++++++----------------------- tests/testthat/test_rnc.R | 10 7 files changed, 253 insertions(+), 237 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 1.1.5 dated 2026-06-03 and 1.1.6 dated 2026-06-30
DESCRIPTION | 8 +++---- MD5 | 20 ++++++++++-------- NAMESPACE | 4 +++ NEWS.md | 9 ++++++++ R/Compute_Gene_AUC_ROC.R |only README.md | 35 +++++++++++++++++++++++++++++++++ man/Celltype_Compare.Rd | 3 +- man/Celltype_annotation_Cellmarker2.Rd | 3 +- man/Celltype_annotation_Excel.Rd | 3 +- man/Celltype_annotation_PanglaoDB.Rd | 3 +- man/Celltype_annotation_Seurat.Rd | 3 +- man/Compute_Gene_AUC_ROC.Rd |only 12 files changed, 73 insertions(+), 18 deletions(-)
Title: Access EPA 'ATTAINS' Data
Description: An R interface to United States Environmental Protection Agency (EPA)
Assessment, Total Maximum Daily Load (TMDL) Tracking and Implementation System
('ATTAINS') data. 'ATTAINS' is the EPA database used to track information
provided by states about water quality assessments conducted under federal
Clean Water Act requirements. ATTAINS information and API information is available at <https://www.epa.gov/waterdata/attains>.
Author: Michael Schramm [aut, cre, cph]
Maintainer: Michael Schramm <mpschramm@gmail.com>
Diff between rATTAINS versions 1.1.0 dated 2025-12-09 and 1.2.0 dated 2026-06-30
DESCRIPTION | 8 LICENSE | 4 MD5 | 132 +- NAMESPACE | 64 - NEWS.md | 167 +- R/actions.R | 500 ++++---- R/assessment_units.R | 378 +++--- R/assessments.R | 494 ++++---- R/domain_values.R | 191 +-- R/huc12_summary.R | 220 +-- R/internal.R | 203 +-- R/plans.R | 268 ++-- R/rATTAINS-package.R | 50 R/state_summary.R | 265 ++-- R/survey.R | 257 ++-- README.md | 451 +++---- build/vignette.rds |binary inst/CITATION | 36 inst/doc/Introduction.R | 63 - inst/doc/Introduction.Rmd | 228 +-- inst/doc/Introduction.html | 1281 ++++++++++----------- man/actions.Rd | 270 ++-- man/assessment_units.Rd | 202 +-- man/assessments.Rd | 276 ++-- man/domain_values.Rd | 96 - man/huc12_summary.Rd | 90 - man/plans.Rd | 140 +- man/rATTAINS-package.Rd | 53 man/state_summary.Rd | 114 - man/surveys.Rd | 112 - tests/fixtures/actions_chr_works.yml | 101 - tests/fixtures/actions_unnest_works.yml | 101 - tests/fixtures/actions_works.yml | 101 - tests/fixtures/assessment_units_chr_works.yml | 79 - tests/fixtures/assessment_units_unnest_works.yml | 79 - tests/fixtures/assessment_units_works.yml | 79 - tests/fixtures/assessments_chr_works.yml | 69 - tests/fixtures/assessments_unnest_works.yml | 69 - tests/fixtures/assessments_works.yml | 69 - tests/fixtures/domains_works.yml | 1390 ++++++++++++++++++++++- tests/fixtures/huc12_chr_works.yml | 144 +- tests/fixtures/huc12_unnest_works.yml | 131 +- tests/fixtures/huc12_works.yml | 131 +- tests/fixtures/plans_chr_works.yml | 815 ++++++++++--- tests/fixtures/plans_summary_works.yml | 204 +-- tests/fixtures/plans_unnest_works.yml | 1063 ++++++++++------- tests/fixtures/plans_works.yml | 815 ++++++++++--- tests/fixtures/single_domain.yml | 55 tests/fixtures/state_summary_chr_works.yml | 353 ++++- tests/fixtures/state_summary_unnest_works.yml | 353 ++++- tests/fixtures/state_summary_works.yml | 353 ++++- tests/fixtures/survey_chr_works.yml | 471 +++---- tests/fixtures/survey_unnest_works.yml | 471 +++---- tests/fixtures/survey_works.yml | 471 +++---- tests/testthat.R | 8 tests/testthat/setup-rATTAINS.R | 24 tests/testthat/test-actions.R | 63 - tests/testthat/test-assessment_units.R | 60 tests/testthat/test-assessments.R | 66 - tests/testthat/test-domain_values.R | 50 tests/testthat/test-huc12_summary.R | 62 - tests/testthat/test-plans.R | 80 - tests/testthat/test-state_summary.R | 89 - tests/testthat/test-survey.R | 60 vignettes/Introduction.Rmd | 228 +-- vignettes/_vcr |only 66 files changed, 9151 insertions(+), 6219 deletions(-)
Title: Extracting a Data Portion
Description: Provides simple methods to extract data portions from various objects.
The relative portion size and the way the portion is selected can be chosen.
Author: Lennart Oelschlaeger [aut, cre]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between portion versions 0.1.2 dated 2025-06-10 and 0.1.3 dated 2026-06-30
DESCRIPTION | 8 MD5 | 20 - NAMESPACE | 22 - NEWS.md | 38 +- R/portion-package.R | 16 R/portion.R | 770 +++++++++++++++++++++++++++--------------- README.md | 254 +++++++------ man/portion-package.Rd | 53 +- man/portion.Rd | 238 ++++++------ tests/testthat.R | 24 - tests/testthat/test-portion.R | 533 +++++++++++++++++------------ 11 files changed, 1173 insertions(+), 803 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. Designed for real-world data that violates symmetry, linearity, or distributional assumptions, NNS delivers a comprehensive suite of advanced statistical techniques, including: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic superiority / dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995, Second edition: <https://ovvo-financial.github.io/NNS/book/>).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb],
Rasheed Khoshnaw [ctb]
Maintainer: Fred Viole <ovvo.open.source@gmail.com>
Diff between NNS versions 12.1 dated 2026-06-05 and 13.0 dated 2026-06-30
DESCRIPTION | 19 MD5 | 208 ++--- NAMESPACE | 14 R/ARMA.R | 39 R/ARMA_optim.R | 41 - R/Binary_ANOVA.R | 10 R/Boost.R | 55 - R/Causal_matrix.R | 4 R/Copula.R | 1 R/Dependence.R | 26 R/LPM_UPM_VaR.R | 407 +++++++++- R/Multivariate_Regression.R | 440 ++++------- R/NNS_Distance.R | 37 R/NNS_Distance_bulk.R | 96 ++ R/NNS_MC.R | 4 R/NNS_VAR.R | 152 ++- R/NNS_meboot.R | 113 +- R/Normalization.R | 8 R/Partial_Moments.R | 86 +- R/Partition_Map.R | 26 R/RcppExports.R | 28 R/Regression.R | 568 ++++++++------ R/SD_Cluster.R | 6 R/Stack.R | 8 R/dy_d_wrt.R | 50 - R/dy_dx.R | 55 - R/gvload.R | 36 R/print_methods.R |only README.md | 4 inst/NNS_before_after_test.R |only inst/doc/NNSvignette_01_Overview.R | 7 inst/doc/NNSvignette_01_Overview.Rmd | 11 inst/doc/NNSvignette_01_Overview.html | 384 ++++----- inst/doc/NNSvignette_02_Partial_Moments.R | 2 inst/doc/NNSvignette_02_Partial_Moments.Rmd | 6 inst/doc/NNSvignette_03_Correlation_and_Dependence.R | 3 inst/doc/NNSvignette_03_Correlation_and_Dependence.Rmd | 7 inst/doc/NNSvignette_03_Correlation_and_Dependence.html | 5 inst/doc/NNSvignette_04_Normalization_and_Rescaling.R | 2 inst/doc/NNSvignette_04_Normalization_and_Rescaling.Rmd | 6 inst/doc/NNSvignette_04_Normalization_and_Rescaling.html | 5 inst/doc/NNSvignette_05_Sampling.R | 15 inst/doc/NNSvignette_05_Sampling.Rmd | 25 inst/doc/NNSvignette_05_Sampling.html | 51 + inst/doc/NNSvignette_06_Comparing_Distributions.R | 3 inst/doc/NNSvignette_06_Comparing_Distributions.Rmd | 7 inst/doc/NNSvignette_06_Comparing_Distributions.html | 7 inst/doc/NNSvignette_07_Clustering_and_Regression.R | 3 inst/doc/NNSvignette_07_Clustering_and_Regression.Rmd | 9 inst/doc/NNSvignette_07_Clustering_and_Regression.html | 368 +++------ inst/doc/NNSvignette_08_Classification.R | 3 inst/doc/NNSvignette_08_Classification.Rmd | 7 inst/doc/NNSvignette_08_Classification.html | 52 - inst/doc/NNSvignette_09_Forecasting.R | 3 inst/doc/NNSvignette_09_Forecasting.Rmd | 7 inst/doc/NNSvignette_09_Forecasting.html | 5 man/Co.LPM.Rd | 80 +- man/Co.LPM_nD.Rd | 58 - man/Co.LPM_nD.batch.Rd |only man/Co.UPM.Rd | 80 +- man/Co.UPM_nD.Rd | 58 - man/D.LPM.Rd | 78 - man/D.UPM.Rd | 78 - man/DPM_nD.Rd | 58 - man/LPM.VaR.Rd | 2 man/LPM.ratio.Rd | 78 - man/NNS.MC.Rd | 134 +-- man/NNS.Rd | 59 - man/NNS.SD.cluster.Rd | 134 +-- man/NNS.SS.Rd | 252 +++--- man/NNS.boost.Rd | 194 ++-- man/NNS.dep.Rd | 92 +- man/NNS.gravity.Rd | 58 - man/NNS.meboot.Rd | 6 man/NNS.mode.Rd | 62 - man/NNS.moments.Rd | 76 - man/NNS.part.Rd | 10 man/NNS.reg.Rd | 374 ++++----- man/NNS.rescale.Rd | 102 +- man/PM.matrix.Rd | 112 +- man/UPM.VaR.Rd | 4 man/UPM.ratio.Rd | 72 - man/dy.dx.Rd | 88 +- src/NNS_dep.cpp | 591 +++++--------- src/NNS_distance.cpp | 600 +++++++++------ src/NNS_part.cpp | 244 +++--- src/RcppExports.cpp | 100 ++ src/central_tendencies.cpp | 54 - src/central_tendencies.h | 5 src/internal_functions.cpp | 511 +++--------- src/nns_reg_points.cpp |only src/partial_moments.cpp | 483 ++++++++++-- src/partial_moments.h | 368 ++++++++- src/table_ops.cpp |only tests/testthat/Rplots.pdf |binary tests/testthat/test_ANOVA.R | 6 tests/testthat/test_NNS_reg_infinite.R |only tests/testthat/test_Partial_Moments.R | 8 tests/testthat/test_Partition_Map.R | 11 vignettes/NNSvignette_01_Overview.Rmd | 11 vignettes/NNSvignette_02_Partial_Moments.Rmd | 6 vignettes/NNSvignette_03_Correlation_and_Dependence.Rmd | 7 vignettes/NNSvignette_04_Normalization_and_Rescaling.Rmd | 6 vignettes/NNSvignette_05_Sampling.Rmd | 25 vignettes/NNSvignette_06_Comparing_Distributions.Rmd | 7 vignettes/NNSvignette_07_Clustering_and_Regression.Rmd | 9 vignettes/NNSvignette_08_Classification.Rmd | 7 vignettes/NNSvignette_09_Forecasting.Rmd | 7 108 files changed, 5097 insertions(+), 3912 deletions(-)
Title: Linear Mixed Models
Description: Implements Expectation/Conditional Maximization Either (ECME),
rapidly converging algorithms, and Bayesian inference for linear mixed
models following Schafer (1998), "Some Improved Procedures for Linear
Mixed Models", Department of Statistics, The Pennsylvania State
University.
Author: Joseph L. Schafer [aut] ,
Jing hua Zhao [cre]
Maintainer: Jing hua Zhao <jinghuazhao@hotmail.com>
Diff between lmm versions 1.4 dated 2023-08-19 and 1.5 dated 2026-06-30
lmm-1.4/lmm/inst/doc/lmm-tr.Rnw |only lmm-1.4/lmm/inst/doc/lmm-tr.pdf |only lmm-1.4/lmm/vignettes/lmm-tr.Rnw |only lmm-1.5/lmm/ChangeLog | 4 ++++ lmm-1.5/lmm/DESCRIPTION | 35 ++++++++++++++++++++++------------- lmm-1.5/lmm/MD5 | 12 ++++++------ lmm-1.5/lmm/build/vignette.rds |binary lmm-1.5/lmm/inst/doc/lmm.Rnw |only lmm-1.5/lmm/inst/doc/lmm.pdf |only lmm-1.5/lmm/vignettes/lmm.Rnw |only 10 files changed, 32 insertions(+), 19 deletions(-)
Title: A Traceability Focused Grammar of Clinical Data Summary
Description: A traceability focused tool created to simplify the data manipulation necessary to create clinical summaries.
Author: Eli Miller [aut] ,
Mike Stackhouse [aut, cre] ,
Ashley Tarasiewicz [aut],
Nathan Kosiba [ctb] ,
Sadchla Mascary [ctb],
Andrew Bates [ctb],
Shiyu Chen [ctb],
Oleksii Mikryukov [ctb],
Atorus Research LLC [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between Tplyr versions 1.3.2 dated 2026-02-26 and 1.3.3 dated 2026-06-30
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/sort.R | 13 +++++++++---- inst/doc/Tplyr.html | 12 ++++++------ tests/testthat/test-sort.R | 41 +++++++++++++++++++++++++++++++++++++++++ 6 files changed, 69 insertions(+), 18 deletions(-)
Title: Tiny Logging Interface to 'rspdlite' Wrapping 'spdlite' C++20
Logging
Description: Just how 'spdl' provides a nice and consistent interface to 'spdlog' (via
'RcppSpdlog'), this package does so for 'spdlite', the lightweight header-only C++-20
logging library that provides a lighter version of 'spdlog'. This package is essentially
a thin shim around it for a more compact interface from both R and C++.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tl versions 0.0.1 dated 2026-06-22 and 0.0.2 dated 2026-06-30
ChangeLog | 30 ++++++++++++++++++++++++++++++ DESCRIPTION | 14 ++++++++------ MD5 | 17 +++++++++-------- NAMESPACE | 1 + R/tl.R | 26 ++++++++++++++++++++++++-- README.md | 17 ++++++++++++++--- build/partial.rdb |binary inst/NEWS.Rd |only inst/include/tl.h | 23 +++++++++++++++++++++++ man/trace.Rd | 10 ++++++++++ 10 files changed, 119 insertions(+), 19 deletions(-)
Title: Stochastic Tree Ensembles (XBART and BART) for Supervised
Learning and Causal Inference
Description: Flexible stochastic tree ensemble software.
Robust implementations of Bayesian Additive Regression Trees (BART)
(Chipman, George, McCulloch (2010) <doi:10.1214/09-AOAS285>)
for supervised learning and Bayesian Causal Forests (BCF)
(Hahn, Murray, Carvalho (2020) <doi:10.1214/19-BA1195>)
for causal inference. Enables model serialization and parallel sampling
and provides a low-level interface for custom stochastic forest samplers.
Includes the grow-from-root algorithm for accelerated forest sampling
(He and Hahn (2021) <doi:10.1080/01621459.2021.1942012>),
a log-linear leaf model for forest-based heteroskedasticity (Murray (2020) <doi:10.1080/01621459.2020.1813587>),
and the cloglog BART model of Alam and Linero (2025) <doi:10.48550/arXiv.2502.00606> for ordinal outcomes.
Author: Drew Herren [aut, cre] ,
Richard Hahn [aut],
Jared Murray [aut],
Carlos Carvalho [aut],
Jingyu He [aut],
Pedro Lima [ctb],
Entejar Alam [ctb],
stochtree contributors [cph],
Eigen contributors [cph] ,
xgboost contributors [cph] ,
treelite contributors [...truncated...]
Maintainer: Drew Herren <drewherrenopensource@gmail.com>
Diff between stochtree versions 0.4.4 dated 2026-06-08 and 0.4.5 dated 2026-06-30
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ R/bart.R | 2 +- configure | 18 +++++++++--------- configure.ac | 2 +- tests/testthat/test-bart.R | 30 ++++++++++++++++++++++++++++++ 7 files changed, 57 insertions(+), 20 deletions(-)
Title: Dimension Reduction, Regression and Discrimination for
Chemometrics
Description: Data exploration and prediction with focus on high dimensional data and chemometrics.
The package was initially designed about partial least squares regression and discrimination models and variants, in particular locally weighted PLS models (LWPLS). Then, it has been expanded to many other methods for analyzing high dimensional data.
The name 'rchemo' comes from the fact that the package is orientated to chemometrics, but most of the provided methods are fully generic to other domains.
Functions such as transform(), predict(), coef() and summary() are available. Tuning the predictive models is facilitated by generic functions gridscore() (validation dataset) and gridcv() (cross-validation). Faster versions are also available for models based on latent variables (LVs) (gridscorelv() and gridcvlv()) and ridge regularization (gridscorelb() and gridcvlb()).
Author: Marion Brandolini-Bunlon [aut, cre],
Benoit Jaillais [aut],
Jean-Michel Roger [aut],
Matthieu Lesnoff [aut]
Maintainer: Marion Brandolini-Bunlon <marion.brandolini-bunlon@inrae.fr>
Diff between rchemo versions 0.1-3 dated 2024-09-11 and 0.1-4 dated 2026-06-30
DESCRIPTION | 7 +++-- MD5 | 52 ++++++++++++++++++++++++++++------------ NAMESPACE | 9 ++++++ R/consensuspca.R |only R/consensuspcanipals.R |only R/consensuspcanipals2.R |only R/covsel.R | 29 ++++++++++++++-------- R/covsellmr.R |only R/covselprobda.R |only R/covselrda.R |only R/lda.R | 6 ++++ R/mbplsr.R | 39 +++++++++++++++++++++++++----- R/nipals.R |only R/onAttach.r | 2 - R/qda.R | 5 +++ R/scores.r | 3 +- README.md | 4 +-- build |only data/Zhang2023.rda |only inst/NEWS.md | 23 ++++++++++++----- inst/doc |only inst/rchemo_functions_github.md | 6 ++++ man/Zhang2023.Rd |only man/consensuspca.Rd |only man/covsel.Rd | 9 ++++-- man/covselda.Rd |only man/covsellmr.Rd |only man/mbplsr_mbplsda_allsteps.Rd | 8 +++--- man/nipals.Rd |only man/pca.Rd | 27 +++++++++++++------- man/soplsr_soplsda_allsteps.Rd | 8 +++--- vignettes |only 32 files changed, 172 insertions(+), 65 deletions(-)
Title: Latent Space Item Response Model
Description: Analysis of dichotomous, ordinal, and continuous response data using latent space item response model ('LSIRM'). Provides 1PL and 2PL 'LSIRM' for binary response data as described in Jeon et al. (2021) <doi:10.1007/s11336-021-09762-5>, graded response models ('GRM') for ordinal data (De Carolis et al., 2025, <doi:10.1080/00273171.2025.2605678>), and extensions for continuous response data. Supports Bayesian model selection with spike-and-slab priors, adaptive MCMC algorithms, and methods for handling missing data under missing at random ('MAR') and missing completely at random ('MCAR') assumptions. Provides various diagnostic plots to inspect the latent space and summaries of estimated parameters.
Author: Dongyoung Go [aut],
Gwanghee Kim [aut, cre],
Jina Park [aut],
Ickhoon Jin [ctb],
Minjeong Jeon [ctb]
Maintainer: Gwanghee Kim <musagh08@yonsei.ac.kr>
Diff between lsirm12pl versions 2.0.2 dated 2026-05-29 and 2.0.3 dated 2026-06-30
lsirm12pl-2.0.2/lsirm12pl/NEWS.md |only lsirm12pl-2.0.3/lsirm12pl/DESCRIPTION | 8 lsirm12pl-2.0.3/lsirm12pl/MD5 | 95 +++--- lsirm12pl-2.0.3/lsirm12pl/R/diagnostic.lsirm.R | 4 lsirm12pl-2.0.3/lsirm12pl/R/gof.lsirm.R | 22 - lsirm12pl-2.0.3/lsirm12pl/R/lsirm.R | 148 +++++----- lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_fixed_gamma.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_fixed_gamma_mar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_fixed_gamma_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_mar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_mar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_mcar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_fixed_gamma.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_fixed_gamma_mar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_fixed_gamma_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_mar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_mcar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_o.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_o.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_fixed_gamma.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_fixed_gamma_mar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_fixed_gamma_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_mar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_mar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_mcar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_fixed_gamma.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_fixed_gamma_mar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_fixed_gamma_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_mar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_mcar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_o.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_o.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirmgrm.R | 6 lsirm12pl-2.0.3/lsirm12pl/R/lsirmgrm2pl.R | 6 lsirm12pl-2.0.3/lsirm12pl/R/onepl.R | 6 lsirm12pl-2.0.3/lsirm12pl/R/plot.lsirm.R | 25 - lsirm12pl-2.0.3/lsirm12pl/R/twopl.R | 6 lsirm12pl-2.0.3/lsirm12pl/man/onepl.Rd | 2 lsirm12pl-2.0.3/lsirm12pl/man/twopl.Rd | 2 lsirm12pl-2.0.3/lsirm12pl/src/lsm.cpp | 11 lsirm12pl-2.0.3/lsirm12pl/src/utility_cpp.cpp | 7 49 files changed, 218 insertions(+), 198 deletions(-)
Title: Latent Variable Models
Description: A general implementation of Structural Equation Models
with latent variables (MLE, 2SLS, and composite likelihood
estimators) with both continuous, censored, and ordinal
outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>).
Mixture latent variable models and non-linear latent variable models
(Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>).
The package also provides methods for graph exploration (d-separation,
back-door criterion), simulation of general non-linear latent variable
models, and estimation of influence functions for a broad range of
statistical models.
Author: Klaus K. Holst [aut, cre],
Benedikt Sommer [ctb],
Brice Ozenne [ctb],
Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between lava versions 1.9.1 dated 2026-05-14 and 1.9.2 dated 2026-06-30
DESCRIPTION | 6 MD5 | 153 +++++----- NAMESPACE | 7 NEWS.md | 20 + R/IC.R | 6 R/Inverse.R | 3 R/addhook.R | 2 R/assoc.R | 2 R/contr.R | 4 R/correlation.R | 35 +- R/diagtest.R | 45 +-- R/effects.R | 5 R/estimate.array.R | 1 R/estimate.default.R | 433 +++++++++++------------------ R/estimate.formula.R | 12 R/estimate.glm.R | 7 R/estimate.list.R | 6 R/estimate_calculus.R | 108 +++++-- R/eventTime.R | 5 R/fix.R | 3 R/glmest.R | 302 +++++++++++++------- R/gof.R | 5 R/iid.R | 2 R/information.R | 6 R/interactive.R | 2 R/multipletesting.R | 28 - R/procformula.R | 13 R/regression.R | 11 R/score.R | 8 R/sim.default.R | 72 ++++ R/spaghetti.R | 2 R/stack.R |binary R/summary.estimate.R |only R/twostage.R | 13 R/utils.R | 2 R/var_ic.R | 8 R/zib.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/correlation.R | 11 inst/doc/correlation.Rmd | 13 inst/doc/correlation.html | 132 +++++--- inst/doc/influencefunction.R | 24 - inst/doc/influencefunction.Rmd | 26 - inst/doc/influencefunction.html | 384 +++++++++++++------------ inst/doc/nonlinear.R | 2 inst/doc/nonlinear.Rmd | 2 inst/doc/nonlinear.html | 200 +++++-------- man/IC.default.Rd | 9 man/Inverse.Rd | 5 man/c.estimate.Rd |only man/c.summary.estimate.Rd |only man/constrain-set.Rd | 17 - man/covariance.Rd | 2 man/estimate.array.Rd | 3 man/estimate.default.Rd | 186 ++++++------ man/estimate.formula.Rd |only man/estimate.glm.Rd |only man/estimate.list.Rd |only man/gof.Rd | 5 man/iid.Rd | 4 man/information.Rd |only man/merge.estimate.Rd |only man/plotConf.Rd | 2 man/predict_glm.Rd |only man/regression-set.Rd | 14 man/rmvar.Rd | 4 man/score.Rd |only man/sim.default.Rd | 15 + man/stack.estimate.Rd | 4 man/summary.estimate.Rd |only man/var_ic.Rd |only tests/testthat/test-estimate-deprecation.R |only tests/testthat/test-estimate-id.R |only tests/testthat/test-estimate_default.R | 86 ++--- tests/testthat/test-influence.R | 19 - tests/testthat/test-merge-estimate.R | 43 ++ tests/testthat/test-model.R | 59 +++ tests/testthat/test-predict_glm.R |only tests/testthat/test-procformula.R |only tests/testthat/test-score-glm.R |only tests/testthat/test-simdef.R | 105 ++++++- tests/testthat/test-summary-estimate.R |only tests/testthat/test-summary-requires-IC.R |only vignettes/correlation.Rmd | 13 vignettes/influencefunction.Rmd | 26 - vignettes/nonlinear.Rmd | 2 87 files changed, 1611 insertions(+), 1145 deletions(-)
Title: Bayesian Exposure-Response Analysis Tools
Description: Suite of tools that facilitate
exposure-response analysis using Bayesian methods. The package
provides a streamlined workflow for fitting types of models that are
commonly used in exposure-response analysis - linear and Emax for continuous
endpoints, logistic linear and logistic Emax for binary endpoints, as well
as performing simulation and visualization. Learn more about the workflow
at <https://genentech.github.io/BayesERbook/>.
Author: Kenta Yoshida [aut, cre] ,
Francois Mercier [aut] ,
Danielle Navarro [aut] ,
Genentech, Inc. [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between BayesERtools versions 0.2.6 dated 2026-06-13 and 0.2.7 dated 2026-06-30
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 8 ++++++++ R/dev_ermod_lin.R | 18 +++++++++++++----- R/plot_ermod_exp_cov_sel.R | 2 +- README.md | 24 +++++++++++------------- man/figures/README-ermod_bin-1.png |binary man/figures/README-ermod_bin_cov_sel-1.png |binary man/figures/README-plot_coveff-1.png |binary tests/testthat/test-dev_ermod_lin.R | 11 +++++++++-- 10 files changed, 54 insertions(+), 33 deletions(-)
Title: Calculate Confidence Intervals
Description: This calculates a variety of different CIs for proportions
and difference of proportions that are commonly used in the
pharmaceutical industry including Wald, Wilson, Clopper-Pearson,
Agresti-Coull and Jeffreys for proportions. And Miettinen-Nurminen
(1985) <doi:10.1002/sim.4780040211>, Wald, Haldane, and Mee
<https://www.lexjansen.com/wuss/2016/127_Final_Paper_PDF.pdf> for
difference in proportions.
Author: Christina Fillmore [aut, cre] ,
GlaxoSmithKline Research & Development Limited [cph, fnd],
Mike Sprys [aut],
Dan Lythgoe [aut]
Maintainer: Christina Fillmore <christina.e.fillmore@gsk.com>
Diff between cicalc versions 0.2.1 dated 2026-05-08 and 0.2.2 dated 2026-06-30
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/prop_ci.R | 2 +- R/prop_ci_common_risk.R | 10 ++++++---- R/prop_ci_mn.R | 2 +- tests/testthat/_snaps/prop_ci_common_risk.md | 12 ++++++------ 7 files changed, 29 insertions(+), 21 deletions(-)
Title: Compute Soil Carbon Fluxes for the National Ecological
Observatory Network Sites
Description: Acquires and synthesizes soil carbon fluxes at sites located in the National Ecological Observatory Network (NEON). Provides flux estimates and associated uncertainty as well as key environmental measurements (soil water, temperature, CO2 concentration) that are used to compute soil fluxes.
Author: John Zobitz [aut, cre] ,
Edward Ayres [aut] ,
Katie O'Rourke [ctb] ,
Zoey Werbin [ctb],
Lajntxiag Lee [ctb],
Ridwan Abdi [ctb] ,
Dijone Mehmeti [ctb] ,
Ly Xiong [ctb]
Maintainer: John Zobitz <zobitz@augsburg.edu>
Diff between neonSoilFlux versions 3.0.0 dated 2025-11-22 and 4.0.0 dated 2026-06-30
neonSoilFlux-3.0.0/neonSoilFlux/R/NEONSoils-package.R |only neonSoilFlux-4.0.0/neonSoilFlux/DESCRIPTION | 8 neonSoilFlux-4.0.0/neonSoilFlux/MD5 | 61 +- neonSoilFlux-4.0.0/neonSoilFlux/NEWS.md | 5 neonSoilFlux-4.0.0/neonSoilFlux/R/acquire_neon_data.R | 63 ++ neonSoilFlux-4.0.0/neonSoilFlux/R/check_qf_flags.R | 22 neonSoilFlux-4.0.0/neonSoilFlux/R/compute_monthly_mean.R | 19 neonSoilFlux-4.0.0/neonSoilFlux/R/compute_neon_flux.R | 22 neonSoilFlux-4.0.0/neonSoilFlux/R/correct_env_data.R | 10 neonSoilFlux-4.0.0/neonSoilFlux/R/get_neon_api_token.R |only neonSoilFlux-4.0.0/neonSoilFlux/R/neonSoilFlux-package.R |only neonSoilFlux-4.0.0/neonSoilFlux/R/neon_api_token.R |only neonSoilFlux-4.0.0/neonSoilFlux/R/reprocess_vswc.R | 16 neonSoilFlux-4.0.0/neonSoilFlux/R/sjer_flux_2022_06.R | 6 neonSoilFlux-4.0.0/neonSoilFlux/R/swc_correct.R | 11 neonSoilFlux-4.0.0/neonSoilFlux/README.md | 53 +- neonSoilFlux-4.0.0/neonSoilFlux/build/vignette.rds |binary neonSoilFlux-4.0.0/neonSoilFlux/data/sjer_env_data_2022_06.rda |binary neonSoilFlux-4.0.0/neonSoilFlux/data/sjer_flux_2022_06.rda |binary neonSoilFlux-4.0.0/neonSoilFlux/data/sjer_megapit_data_2022_06.rda |binary neonSoilFlux-4.0.0/neonSoilFlux/inst/CITATION |only neonSoilFlux-4.0.0/neonSoilFlux/inst/doc/using-neonSoilFlux.R | 15 neonSoilFlux-4.0.0/neonSoilFlux/inst/doc/using-neonSoilFlux.Rmd | 93 ++- neonSoilFlux-4.0.0/neonSoilFlux/inst/doc/using-neonSoilFlux.html | 238 +++++----- neonSoilFlux-4.0.0/neonSoilFlux/man/acquire_neon_data.Rd | 23 neonSoilFlux-4.0.0/neonSoilFlux/man/compute_monthly_mean.Rd | 11 neonSoilFlux-4.0.0/neonSoilFlux/man/compute_neon_flux.Rd | 22 neonSoilFlux-4.0.0/neonSoilFlux/man/correct_env_data.Rd | 10 neonSoilFlux-4.0.0/neonSoilFlux/man/get_neon_api_token.Rd |only neonSoilFlux-4.0.0/neonSoilFlux/man/neonSoilFlux-package.Rd | 2 neonSoilFlux-4.0.0/neonSoilFlux/man/neon_api_token.Rd |only neonSoilFlux-4.0.0/neonSoilFlux/man/reprocess_vswc.Rd | 12 neonSoilFlux-4.0.0/neonSoilFlux/man/sjer_flux_2022_06.Rd | 6 neonSoilFlux-4.0.0/neonSoilFlux/man/swc_correct.Rd | 11 neonSoilFlux-4.0.0/neonSoilFlux/vignettes/using-neonSoilFlux.Rmd | 93 ++- 35 files changed, 572 insertions(+), 260 deletions(-)
Title: Solving Linear Inverse Models
Description: Functions that (1) find the minimum/maximum of a linear or quadratic function:
min or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(a_i*x_i)
subject to equality constraints Ex=f and/or inequality constraints Gx>=h,
(2) sample an underdetermined- or overdetermined system Ex=f subject to Gx>=h, and if applicable Ax~=b,
(3) solve a linear system Ax=B for the unknown x. It includes banded and tridiagonal linear systems.
Author: Karline Soetaert [aut, cre],
Karel Van den Meersche [aut],
Dick van Oevelen [aut],
Charles L. Lawson [ctb] ,
Richard J. Hanson [ctb] ,
Jack Dongarra [ctb] ,
Cleve Moler [ctb]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between limSolve versions 2.0.2 dated 2026-06-03 and 2.0.3 dated 2026-06-30
DESCRIPTION | 6 MD5 | 28 +-- R/lsei.R | 48 +++-- inst/CITATION | 1 inst/doc/limSolve.R | 2 inst/doc/limSolve.Rmd | 4 inst/doc/limSolve.html | 94 ++++------ man/E_coli.Rd | 3 man/limSolve.rd | 1 man/lsei.Rd | 417 +++++++++++++++++++++++---------------------- man/xsample.Rd | 1 src/colrow.f | 3 src/inverse.f | 406 +++++++++++++++++++++++--------------------- src/solve.f | 446 ++++--------------------------------------------- vignettes/limSolve.Rmd | 4 15 files changed, 564 insertions(+), 900 deletions(-)
Title: Latent Binary Bayesian Neural Networks Using 'torch'
Description: Latent binary Bayesian neural networks (LBBNNs) are implemented using
'torch', an R interface to the LibTorch backend. Supports mean-field variational
inference as well as flexible variational posteriors using normalizing flows.
The standard LBBNN implementation follows Hubin and Storvik (2024) <doi:10.3390/math12060788>,
using the local reparametrization trick as in Skaaret-Lund et al. (2024)
<https://openreview.net/pdf?id=d6kqUKzG3V>. Input-skip connections are also supported,
as described in Høyheim et al. (2025) <doi:10.48550/arXiv.2503.10496>.
Author: Lars Skaaret-Lund [aut, cre],
Aliaksandr Hubin [aut],
Eirik Hoeyheim [aut]
Maintainer: Lars Skaaret-Lund <lars.skaaret-lund@nmbu.no>
Diff between LBBNN versions 0.1.5 dated 2026-04-23 and 0.1.6 dated 2026-06-30
LBBNN-0.1.5/LBBNN/inst/doc/LBBNN_tutorial.R |only LBBNN-0.1.5/LBBNN/inst/doc/LBBNN_tutorial.Rmd |only LBBNN-0.1.5/LBBNN/inst/doc/LBBNN_tutorial.html |only LBBNN-0.1.5/LBBNN/tests/testthat/test_lbbnn_predictions.R |only LBBNN-0.1.5/LBBNN/vignettes/LBBNN_tutorial.Rmd |only LBBNN-0.1.6/LBBNN/DESCRIPTION | 6 LBBNN-0.1.6/LBBNN/MD5 | 86 +++- LBBNN-0.1.6/LBBNN/NAMESPACE | 1 LBBNN-0.1.6/LBBNN/NEWS.md | 12 LBBNN-0.1.6/LBBNN/R/LBBNN_Model.R | 48 +- LBBNN-0.1.6/LBBNN/R/Layers.R | 150 +++++++- LBBNN-0.1.6/LBBNN/R/Train_validate.R | 175 ++++++---- LBBNN-0.1.6/LBBNN/R/local_explanations.R | 25 - LBBNN-0.1.6/LBBNN/R/overwrite_functions.R | 160 +++++---- LBBNN-0.1.6/LBBNN/R/plotting_graphs.R | 37 +- LBBNN-0.1.6/LBBNN/R/utils_torch.R | 52 ++ LBBNN-0.1.6/LBBNN/README.md | 144 ++++---- LBBNN-0.1.6/LBBNN/build/vignette.rds |binary LBBNN-0.1.6/LBBNN/inst/doc/convolutional_architecture.R |only LBBNN-0.1.6/LBBNN/inst/doc/convolutional_architecture.Rmd |only LBBNN-0.1.6/LBBNN/inst/doc/convolutional_architecture.html |only LBBNN-0.1.6/LBBNN/inst/doc/getting_started.R |only LBBNN-0.1.6/LBBNN/inst/doc/getting_started.Rmd |only LBBNN-0.1.6/LBBNN/inst/doc/getting_started.html |only LBBNN-0.1.6/LBBNN/inst/doc/small_dataset_classification.R |only LBBNN-0.1.6/LBBNN/inst/doc/small_dataset_classification.Rmd |only LBBNN-0.1.6/LBBNN/inst/doc/small_dataset_classification.html |only LBBNN-0.1.6/LBBNN/inst/doc/variable_selection_linear_data.R |only LBBNN-0.1.6/LBBNN/inst/doc/variable_selection_linear_data.Rmd |only LBBNN-0.1.6/LBBNN/inst/doc/variable_selection_linear_data.html |only LBBNN-0.1.6/LBBNN/inst/doc/variable_selection_non_linear_data.R |only LBBNN-0.1.6/LBBNN/inst/doc/variable_selection_non_linear_data.Rmd |only LBBNN-0.1.6/LBBNN/inst/doc/variable_selection_non_linear_data.html |only LBBNN-0.1.6/LBBNN/man/density_initialization.Rd | 6 LBBNN-0.1.6/LBBNN/man/figures/README-unnamed-chunk-6-1.png |binary LBBNN-0.1.6/LBBNN/man/figures/README-unnamed-chunk-8-1.png |binary LBBNN-0.1.6/LBBNN/man/get_local_explanations_gradient.Rd | 5 LBBNN-0.1.6/LBBNN/man/init_weight_mean.Rd |only LBBNN-0.1.6/LBBNN/man/lbbnn_conv2d.Rd | 21 - LBBNN-0.1.6/LBBNN/man/lbbnn_linear.Rd | 21 - LBBNN-0.1.6/LBBNN/man/lbbnn_net.Rd | 20 - LBBNN-0.1.6/LBBNN/man/plot_local_explanations_gradient.Rd | 5 LBBNN-0.1.6/LBBNN/man/predict.lbbnn_net.Rd | 4 LBBNN-0.1.6/LBBNN/man/resolve_device.Rd |only LBBNN-0.1.6/LBBNN/man/train_lbbnn.Rd | 15 LBBNN-0.1.6/LBBNN/man/validate_lbbnn.Rd | 5 LBBNN-0.1.6/LBBNN/tests/testthat/test_active_path_computation.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_alpha_validity.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_binary_classification.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_conv_layer.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_forward_pass_MPM.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_multi_output_regression.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_multiclass_classification.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_predict_behavior.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_smoke_training.R | 4 LBBNN-0.1.6/LBBNN/tests/testthat/test_validate_behavior.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_windows_batch_shape.R | 12 LBBNN-0.1.6/LBBNN/vignettes/convolutional_architecture.Rmd |only LBBNN-0.1.6/LBBNN/vignettes/getting_started.Rmd |only LBBNN-0.1.6/LBBNN/vignettes/small_dataset_classification.Rmd |only LBBNN-0.1.6/LBBNN/vignettes/variable_selection_linear_data.Rmd |only LBBNN-0.1.6/LBBNN/vignettes/variable_selection_non_linear_data.Rmd |only 62 files changed, 697 insertions(+), 317 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) (fast) simulation of random fields, b) inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Flexible covariance models for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. Se [...truncated...]
Author: Moreno Bevilacqua [aut, cre, cph],
Victor Morales-Onate [ctb],
Francisco Cuevas-Pacheco [ctb],
Christian Caamano-Carrillo [ctb]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 2.2.4 dated 2026-06-15 and 2.2.5 dated 2026-06-30
GeoModels-2.2.4/GeoModels/man/NuisParam.rd |only GeoModels-2.2.5/GeoModels/DESCRIPTION | 8 GeoModels-2.2.5/GeoModels/MD5 | 164 ++-- GeoModels-2.2.5/GeoModels/NAMESPACE | 3 GeoModels-2.2.5/GeoModels/R/GeoFit.r | 2 GeoModels-2.2.5/GeoModels/R/GeoFit2.R | 2 GeoModels-2.2.5/GeoModels/R/GeoNeighIndex.R | 208 +++++ GeoModels-2.2.5/GeoModels/R/GeoSim.r | 60 + GeoModels-2.2.5/GeoModels/R/GeoSimCopula.R | 79 +- GeoModels-2.2.5/GeoModels/R/GeoSimcond.R | 299 +++++--- GeoModels-2.2.5/GeoModels/R/GeoVarest.R |only GeoModels-2.2.5/GeoModels/R/GeoVarestbootstrap.R | 71 + GeoModels-2.2.5/GeoModels/R/TB.R | 44 - GeoModels-2.2.5/GeoModels/man/Anomalies.Rd | 6 GeoModels-2.2.5/GeoModels/man/CheckBiv.Rd | 2 GeoModels-2.2.5/GeoModels/man/CheckDistance.Rd | 12 GeoModels-2.2.5/GeoModels/man/CheckST.Rd | 8 GeoModels-2.2.5/GeoModels/man/CheckSph.Rd | 8 GeoModels-2.2.5/GeoModels/man/CkCorrModel.Rd | 10 GeoModels-2.2.5/GeoModels/man/CkInput.Rd | 146 +-- GeoModels-2.2.5/GeoModels/man/CkLikelihood.Rd | 16 GeoModels-2.2.5/GeoModels/man/CkModel.Rd | 6 GeoModels-2.2.5/GeoModels/man/CkType.Rd | 6 GeoModels-2.2.5/GeoModels/man/CompIndLik2.Rd | 138 +-- GeoModels-2.2.5/GeoModels/man/CompLik.Rd | 158 ++-- GeoModels-2.2.5/GeoModels/man/CompLik2.Rd | 184 ++-- GeoModels-2.2.5/GeoModels/man/CorrParam.Rd | 24 GeoModels-2.2.5/GeoModels/man/CorrelationPar.Rd | 12 GeoModels-2.2.5/GeoModels/man/Corrsas.Rd | 30 GeoModels-2.2.5/GeoModels/man/GeoAniso.Rd | 16 GeoModels-2.2.5/GeoModels/man/GeoCV.Rd | 102 +- GeoModels-2.2.5/GeoModels/man/GeoCorrFct.Rd | 66 - GeoModels-2.2.5/GeoModels/man/GeoCorrFct_Cop.Rd | 50 - GeoModels-2.2.5/GeoModels/man/GeoCovDisplay.Rd | 24 GeoModels-2.2.5/GeoModels/man/GeoCovariogram.Rd | 158 ++-- GeoModels-2.2.5/GeoModels/man/GeoCovmatrix.Rd | 669 +++++++++--------- GeoModels-2.2.5/GeoModels/man/GeoDistances.Rd | 40 - GeoModels-2.2.5/GeoModels/man/GeoDosocores.Rd | 52 - GeoModels-2.2.5/GeoModels/man/GeoFit.Rd | 486 ++++++------- GeoModels-2.2.5/GeoModels/man/GeoFit2.Rd | 272 +++---- GeoModels-2.2.5/GeoModels/man/GeoKrig.Rd | 327 ++++---- GeoModels-2.2.5/GeoModels/man/GeoKrigWeights.Rd | 158 ++-- GeoModels-2.2.5/GeoModels/man/GeoKrigloc.Rd | 307 ++++---- GeoModels-2.2.5/GeoModels/man/GeoKriglocWeights.Rd | 150 ++-- GeoModels-2.2.5/GeoModels/man/GeoNA.Rd | 68 - GeoModels-2.2.5/GeoModels/man/GeoNeighIndex.Rd | 204 ++--- GeoModels-2.2.5/GeoModels/man/GeoNeighbSelect.Rd | 240 +++--- GeoModels-2.2.5/GeoModels/man/GeoNeighborhood.Rd | 147 +-- GeoModels-2.2.5/GeoModels/man/GeoOutlier.Rd | 117 +-- GeoModels-2.2.5/GeoModels/man/GeoPit.Rd | 22 GeoModels-2.2.5/GeoModels/man/GeoQQ.Rd | 24 GeoModels-2.2.5/GeoModels/man/GeoResiduals.Rd | 34 GeoModels-2.2.5/GeoModels/man/GeoScatterplot.Rd | 87 +- GeoModels-2.2.5/GeoModels/man/GeoScores.Rd | 346 ++++----- GeoModels-2.2.5/GeoModels/man/GeoSim.Rd | 220 +++-- GeoModels-2.2.5/GeoModels/man/GeoSimCopula.Rd | 157 ++-- GeoModels-2.2.5/GeoModels/man/GeoSimapprox.Rd | 197 ++--- GeoModels-2.2.5/GeoModels/man/GeoSimcond.Rd | 142 +-- GeoModels-2.2.5/GeoModels/man/GeoTestIsotropy.Rd | 66 - GeoModels-2.2.5/GeoModels/man/GeoTest_supp.Rd | 60 - GeoModels-2.2.5/GeoModels/man/GeoTests.Rd | 120 +-- GeoModels-2.2.5/GeoModels/man/GeoVarest.Rd |only GeoModels-2.2.5/GeoModels/man/GeoVarestbootstrap.Rd | 75 +- GeoModels-2.2.5/GeoModels/man/GeoVariogram.Rd | 265 +++---- GeoModels-2.2.5/GeoModels/man/GeoWls.Rd | 202 ++--- GeoModels-2.2.5/GeoModels/man/GeovariogramDir.Rd | 116 +-- GeoModels-2.2.5/GeoModels/man/Lik.Rd | 168 ++-- GeoModels-2.2.5/GeoModels/man/MargParam.Rd | 18 GeoModels-2.2.5/GeoModels/man/MatDecomp.Rd | 10 GeoModels-2.2.5/GeoModels/man/Matrixfun.Rd | 16 GeoModels-2.2.5/GeoModels/man/NuisParam.Rd |only GeoModels-2.2.5/GeoModels/man/NuisParam2.Rd | 18 GeoModels-2.2.5/GeoModels/man/SimCE.Rd | 26 GeoModels-2.2.5/GeoModels/man/StartParam.Rd | 96 +- GeoModels-2.2.5/GeoModels/man/WlsStart.Rd | 100 +- GeoModels-2.2.5/GeoModels/man/getInvC.Rd | 60 - GeoModels-2.2.5/GeoModels/man/plot.GeoCorrFct.Rd | 26 GeoModels-2.2.5/GeoModels/man/plot.GeoVariogram.Rd | 20 GeoModels-2.2.5/GeoModels/man/plot.GeoVariogramDir.Rd | 34 GeoModels-2.2.5/GeoModels/man/rainNLD.Rd | 8 GeoModels-2.2.5/GeoModels/man/sp2Geo.Rd | 14 GeoModels-2.2.5/GeoModels/man/spanish_wind.Rd | 6 GeoModels-2.2.5/GeoModels/man/winds.Rd | 12 GeoModels-2.2.5/GeoModels/man/winds.coords.Rd | 16 GeoModels-2.2.5/GeoModels/src/CorrelationFunction.c | 256 ++++-- 85 files changed, 4438 insertions(+), 3958 deletions(-)
Title: Disaster Victim Identification
Description: Joint DNA-based disaster victim identification (DVI), as
described in Vigeland and Egeland (2021)
<doi:10.21203/rs.3.rs-296414/v1>. Identification is performed by
optimising the joint likelihood of all victim samples and reference
individuals. Individual identification probabilities, conditional on
all available information, are derived from the joint solution in the
form of posterior pairing probabilities. 'dvir' is part of the
'pedsuite' collection of packages for pedigree analysis.
Author: Magnus Dehli Vigeland [aut, cre] ,
Thore Egeland [aut]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between dvir versions 3.4.1 dated 2026-05-15 and 3.4.2 dated 2026-06-30
dvir-3.4.1/dvir/man/figures/README-example-plot1-1.png |only dvir-3.4.1/dvir/man/figures/README-example-plot2-1.png |only dvir-3.4.1/dvir/man/figures/README-solution-1.png |only dvir-3.4.2/dvir/DESCRIPTION | 14 dvir-3.4.2/dvir/MD5 | 95 ++--- dvir-3.4.2/dvir/NAMESPACE | 12 dvir-3.4.2/dvir/NEWS.md | 26 + dvir-3.4.2/dvir/R/amDrivenDVI.R | 24 + dvir-3.4.2/dvir/R/dviCompare.R | 200 ++++------- dvir-3.4.2/dvir/R/dviData.R | 22 - dvir-3.4.2/dvir/R/dviGLR.R | 2 dvir-3.4.2/dvir/R/dviGridSize.R |only dvir-3.4.2/dvir/R/dviJoint.R | 156 ++++---- dvir-3.4.2/dvir/R/dviSim.R | 24 - dvir-3.4.2/dvir/R/dviSolve.R | 132 ++++--- dvir-3.4.2/dvir/R/dvir-package.R | 2 dvir-3.4.2/dvir/R/expand.grid.nodup.R | 128 +++---- dvir-3.4.2/dvir/R/findExcluded.R | 4 dvir-3.4.2/dvir/R/findUndisputed.R | 14 dvir-3.4.2/dvir/R/formatSummary.R | 4 dvir-3.4.2/dvir/R/jointDVI.R | 108 ++---- dvir-3.4.2/dvir/R/mergePM.R | 6 dvir-3.4.2/dvir/R/ncomb.R | 18 - dvir-3.4.2/dvir/R/pairwiseGLR.R | 8 dvir-3.4.2/dvir/R/pairwiseLR.R | 54 +-- dvir-3.4.2/dvir/R/plotDVI.R | 71 ++- dvir-3.4.2/dvir/R/relabelDVI.R | 2 dvir-3.4.2/dvir/R/setPairing.R | 18 - dvir-3.4.2/dvir/R/subsetDVI.R | 2 dvir-3.4.2/dvir/R/utils.R | 19 - dvir-3.4.2/dvir/README.md | 306 ++++++++--------- dvir-3.4.2/dvir/build/partial.rdb |binary dvir-3.4.2/dvir/man/dviCompare.Rd | 61 +-- dvir-3.4.2/dvir/man/dviGLR.Rd | 2 dvir-3.4.2/dvir/man/dviGridSize.Rd |only dvir-3.4.2/dvir/man/dviJoint.Rd | 16 dvir-3.4.2/dvir/man/dviSolve.Rd | 17 dvir-3.4.2/dvir/man/expand.grid.nodup.Rd | 55 ++- dvir-3.4.2/dvir/man/figures/README-example2-plot-1.png |only dvir-3.4.2/dvir/man/figures/README-fire-plot-1.png |only dvir-3.4.2/dvir/man/findExcluded.Rd | 2 dvir-3.4.2/dvir/man/findUndisputed.Rd | 3 dvir-3.4.2/dvir/man/jointDVI.Rd | 8 dvir-3.4.2/dvir/man/mergePM.Rd | 4 dvir-3.4.2/dvir/man/ncomb.Rd | 14 dvir-3.4.2/dvir/man/pairwiseLR.Rd | 3 dvir-3.4.2/dvir/man/plotDVI.Rd | 3 dvir-3.4.2/dvir/man/setPairing.Rd | 2 dvir-3.4.2/dvir/man/swapOrientation.Rd | 4 dvir-3.4.2/dvir/tests |only 50 files changed, 842 insertions(+), 823 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 1.0.2 dated 2026-03-11 and 1.0.3 dated 2026-06-30
DESCRIPTION | 8 - MD5 | 89 +++++++-------- NEWS.md | 6 + R/blocking.R | 221 ++++++++++++++++++++------------------- R/controls.R | 46 ++++---- R/data.R | 2 R/est_block_error.R | 8 - R/eval.R | 26 ++-- R/internals.R |only R/method_annoy.R | 2 R/method_hnsw.R | 2 R/method_mlpack.R | 9 - R/method_nnd.R | 2 R/methods.R | 100 ++++++++++++++++- R/reclin2_pair_ann.R | 37 ++---- README.md | 17 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/v1-deduplication.R | 9 - inst/doc/v1-deduplication.Rmd | 14 +- inst/doc/v1-deduplication.html | 16 +- inst/doc/v2-reclin.html | 14 +- inst/doc/v3-integration.Rmd | 2 inst/doc/v3-integration.html | 46 ++------ inst/tinytest/test_annoy.R | 9 + inst/tinytest/test_blocking.R | 169 +++++++++++++++++++++++++++++ inst/tinytest/test_data.R | 1 inst/tinytest/test_hnsw.R | 9 + inst/tinytest/test_mlpack.R | 13 +- inst/tinytest/test_reclin2.R | 65 +++++++++++ inst/tinytest/test_true_blocks.R | 99 ++++++++++++++++- man/RLdata500.Rd | 2 man/blocking.Rd | 28 ++-- man/control_kd.Rd | 6 - man/control_lsh.Rd | 2 man/control_nnd.Rd | 2 man/controls_ann.Rd | 10 - man/controls_txt.Rd | 2 man/est_block_error.Rd | 8 - man/method_hnsw.Rd | 2 man/method_mlpack.Rd | 2 man/method_nnd.Rd | 2 man/pair_ann.Rd | 13 +- tests/tinytest.R | 3 vignettes/v1-deduplication.Rmd | 14 +- vignettes/v3-integration.Rmd | 2 46 files changed, 780 insertions(+), 359 deletions(-)