Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Description: Implements spatial and spatiotemporal GLMMs (Generalized Linear
Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial
Differential Equation) Gaussian Markov random field approximation to
Gaussian random fields. One common application is for spatially explicit
species distribution models (SDMs).
See Anderson et al. (2025) <doi:10.18637/jss.v115.i02>.
Author: Sean C. Anderson [aut, cre] ,
Eric J. Ward [aut] ,
Philina A. English [aut] ,
Lewis A. K. Barnett [aut] ,
James T. Thorson [aut, cph] ,
Joe Watson [ctb] ,
Julia Indivero [ctb] ,
Jillian C. Dunic [ctb] ,
Joseph Barss [ctb],
Cole C. Monnahan [ctb, cph] [...truncated...]
Maintainer: Sean C. Anderson <sean@seananderson.ca>
Diff between sdmTMB versions 1.0.0 dated 2026-01-24 and 1.1.0 dated 2026-07-03
DESCRIPTION | 12 MD5 | 173 +++--- NAMESPACE | 3 NEWS.md | 245 ++++++--- R/areal.R |only R/check.R | 78 +-- R/covariate-diffusion.R |only R/cross-val.R | 34 - R/crs.R | 14 R/data.R | 42 + R/dharma.R | 33 - R/emmeans.R | 3 R/extra-optimization.R | 9 R/families.R | 11 R/fit.R | 487 ++++++++++++++----- R/gather-spread.R | 40 + R/get-index-sims.R | 12 R/get-range-edge.R | 2 R/index.R | 165 +++++- R/mesh.R | 7 R/methods.R | 22 R/parsing.R | 40 + R/predict.R | 324 ++++++++++-- R/print.R | 104 +++- R/priors.R | 16 R/project.R | 18 R/residuals.R | 115 +++- R/tidy.R | 322 ++++++++++-- R/tmb-sim.R | 118 ++++ R/utils.R | 49 + R/visreg.R | 16 build/partial.rdb |binary build/vignette.rds |binary data/ohio_df.rda |only data/ohio_sf.rda |only inst/COPYRIGHTS | 8 inst/doc/model-description.Rmd | 119 +++- inst/doc/model-description.html | 230 ++++++-- man/Effect.sdmTMB.Rd | 2 man/add_utm_columns.Rd | 14 man/dharma_residuals.Rd | 30 - man/emmeans.sdmTMB.Rd | 3 man/families.Rd | 7 man/get_index.Rd | 47 + man/get_index_sims.Rd | 12 man/get_pars.Rd | 4 man/get_range_edge.Rd | 2 man/make_areal_domain.Rd |only man/make_mesh.Rd | 10 man/nonlocal_formula_plots.Rd |only man/ohio_sf.Rd |only man/predict.sdmTMB.Rd | 91 ++- man/priors.Rd | 16 man/project.Rd | 18 man/reexports.Rd | 2 man/residuals.sdmTMB.Rd | 15 man/run_extra_optimization.Rd | 2 man/sdmTMB.Rd | 121 +++- man/sdmTMB_cv.Rd | 20 man/sdmTMBcontrol.Rd | 40 + man/simulate.sdmTMB.Rd | 8 man/simulate_new.Rd | 41 + man/surveydata.Rd | 8 man/tidy.sdmTMB.Rd | 23 man/update.sdmTMB.Rd | 16 man/visreg_delta.Rd | 16 src/covariate-diffusion.h |only src/sdmTMB.cpp | 401 +++++++++++---- src/utils.h | 80 --- tests/testthat/test-1-visreg.R | 1 tests/testthat/test-2-fit-less-basic.R | 4 tests/testthat/test-3-spatial-varying.R | 142 ++++- tests/testthat/test-5-residuals.R | 99 +++ tests/testthat/test-9-mvn-simulation.R | 4 tests/testthat/test-areal-domain.R |only tests/testthat/test-areal-ohio-regression.R |only tests/testthat/test-betabinomial.R | 33 - tests/testthat/test-covariate-diffusion-fit.R |only tests/testthat/test-covariate-diffusion-grid.R |only tests/testthat/test-covariate-diffusion-output.R |only tests/testthat/test-covariate-diffusion-parse.R |only tests/testthat/test-covariate-diffusion-plot.R |only tests/testthat/test-covariate-diffusion-plumbing.R |only tests/testthat/test-covariate-diffusion-predict.R |only tests/testthat/test-covariate-diffusion-projection.R |only tests/testthat/test-covariate-diffusion-regression.R |only tests/testthat/test-covariate-diffusion-simulation.R |only tests/testthat/test-cross-validation.R | 82 +++ tests/testthat/test-deprecated-args.R | 5 tests/testthat/test-factor-levels.R | 74 ++ tests/testthat/test-index.R | 76 ++ tests/testthat/test-parameter-bounds.R | 12 tests/testthat/test-random-effects.R | 207 +++++++- tests/testthat/test-random-intercepts.R | 12 tests/testthat/test-rsr.R |only tests/testthat/test-time-varying.R | 41 - vignettes/model-description.Rmd | 119 +++- vignettes/refs.bib | 32 + 98 files changed, 3692 insertions(+), 1171 deletions(-)
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
plssem-0.1.2/plssem/R/predict.R |only plssem-0.1.2/plssem/R/scale_transform_ordered.R |only plssem-0.1.2/plssem/man/implied_construct_corr.Rd |only plssem-0.1.2/plssem/man/implied_indicator_corr.Rd |only plssem-0.1.3/plssem/DESCRIPTION | 13 plssem-0.1.3/plssem/MD5 | 195 +- plssem-0.1.3/plssem/NAMESPACE | 26 plssem-0.1.3/plssem/R/00model_classes.R | 56 plssem-0.1.3/plssem/R/bootstrap.R | 194 ++ plssem-0.1.3/plssem/R/datasets.R | 10 plssem-0.1.3/plssem/R/fit_measures.R | 212 ++ plssem-0.1.3/plssem/R/formatted_objects.R | 6 plssem-0.1.3/plssem/R/gls.R |only plssem-0.1.3/plssem/R/ho_helpers.R | 47 plssem-0.1.3/plssem/R/mcpls.R | 585 ++++++- plssem-0.1.3/plssem/R/mcpls_robbins_monro.R | 169 +- plssem-0.1.3/plssem/R/model_accessors.R | 15 plssem-0.1.3/plssem/R/model_constructors.R | 4 plssem-0.1.3/plssem/R/model_generics.R | 338 ++++ plssem-0.1.3/plssem/R/model_partable.R | 114 + plssem-0.1.3/plssem/R/model_partable_print.R |only plssem-0.1.3/plssem/R/model_partable_utils.R | 80 - plssem-0.1.3/plssem/R/model_specification.R | 226 ++- plssem-0.1.3/plssem/R/model_state.R | 42 plssem-0.1.3/plssem/R/model_syntax.R | 98 + plssem-0.1.3/plssem/R/modsem_internals.R | 14 plssem-0.1.3/plssem/R/pls.R | 103 - plssem-0.1.3/plssem/R/pls_data.R | 82 - plssem-0.1.3/plssem/R/pls_fit.R | 181 +- plssem-0.1.3/plssem/R/pls_inspect.R |only plssem-0.1.3/plssem/R/pls_msg.R | 2 plssem-0.1.3/plssem/R/pls_predict.R |only plssem-0.1.3/plssem/R/pls_steps.R | 2 plssem-0.1.3/plssem/R/pls_threshold_struct.R |only plssem-0.1.3/plssem/R/pls_unstandardized.R |only plssem-0.1.3/plssem/R/plsc_dijkstra.R | 18 plssem-0.1.3/plssem/R/simulate_data.R | 278 ++- plssem-0.1.3/plssem/R/utils.R | 40 plssem-0.1.3/plssem/R/utils_matrices.R | 9 plssem-0.1.3/plssem/R/utils_tmp.R | 36 plssem-0.1.3/plssem/R/zzz.R | 38 plssem-0.1.3/plssem/build/vignette.rds |binary plssem-0.1.3/plssem/inst/doc/categorical-models.R | 45 plssem-0.1.3/plssem/inst/doc/categorical-models.Rmd | 3 plssem-0.1.3/plssem/inst/doc/categorical-models.html | 453 +----- plssem-0.1.3/plssem/inst/doc/higher-order.R | 45 plssem-0.1.3/plssem/inst/doc/higher-order.Rmd | 3 plssem-0.1.3/plssem/inst/doc/higher-order.html | 472 +----- plssem-0.1.3/plssem/inst/doc/interaction-models.R | 47 plssem-0.1.3/plssem/inst/doc/interaction-models.Rmd | 3 plssem-0.1.3/plssem/inst/doc/interaction-models.html | 503 +----- plssem-0.1.3/plssem/inst/doc/linear-models.R | 41 plssem-0.1.3/plssem/inst/doc/linear-models.Rmd | 3 plssem-0.1.3/plssem/inst/doc/linear-models.html | 448 +---- plssem-0.1.3/plssem/inst/doc/mc-pls.R | 207 +- plssem-0.1.3/plssem/inst/doc/mc-pls.Rmd | 3 plssem-0.1.3/plssem/inst/doc/mc-pls.html | 516 +----- plssem-0.1.3/plssem/inst/doc/missing-imputation.R | 6 plssem-0.1.3/plssem/inst/doc/missing-imputation.Rmd | 6 plssem-0.1.3/plssem/inst/doc/missing-imputation.html | 415 +---- plssem-0.1.3/plssem/inst/doc/multilevel-models.R | 87 - 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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 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| 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
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-05-25 1.0-1
2025-03-08 1.0-0.1
2021-05-27 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-06-17 1.5-3
2026-06-03 1.5-2
2025-05-11 1.5-1
2021-05-12 1.5-0
2020-01-20 1.4-2
2020-01-09 1.4-1
2019-07-10 1.4-0
2018-08-24 1.3-5
2016-02-15 1.3-3
2014-02-04 1.3-2
2013-12-11 1.3-1
2013-09-18 1.3-0
2013-01-29 1.2-2
2012-08-13 1.2-1
2012-06-21 1.2-0
2012-03-16 1.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-06-19 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-05-11 1.0.0
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(-)