Title: Modular Cohort-Building Framework for Analytical Dashboards
Description: You can easily add advanced cohort-building component
to your analytical dashboard or simple 'Shiny' app.
Then you can instantly start building cohorts using multiple
filters of different types, filtering datasets, and filtering steps.
Filters can be complex and data-specific, and together
with multiple filtering steps you can use complex filtering rules.
The cohort-building sidebar panel allows you to easily
work with filters, add and remove filtering steps.
It helps you with handling missing values during filtering,
and provides instant filtering feedback with filter feedback plots.
The GUI panel is not only compatible with native shiny
bookmarking, but also provides reproducible R code.
Author: Krystian Igras [cre, aut],
Kamil Wais [aut],
Adam Forys [ctb]
Maintainer: Krystian Igras <krystian8207@gmail.com>
Diff between shinyCohortBuilder versions 0.4.0 dated 2026-02-25 and 1.0.0 dated 2026-07-05
shinyCohortBuilder-0.4.0/shinyCohortBuilder/man/autofilter.Rd |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/DESCRIPTION | 33 shinyCohortBuilder-1.0.0/shinyCohortBuilder/MD5 | 149 + shinyCohortBuilder-1.0.0/shinyCohortBuilder/NAMESPACE | 14 shinyCohortBuilder-1.0.0/shinyCohortBuilder/NEWS.md | 24 shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/actions.R | 765 ++++++---- shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/app.R | 14 shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/cb_layer.R | 351 ++++ shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/chat.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/control_utils.R | 196 ++ shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/feedback_html.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/filter_date_range.R | 59 shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/filter_datetime_range.R | 83 - shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/filter_discrete.R | 392 +++-- shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/filter_discrete_text.R | 157 -- shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/filter_multi_discrete.R | 210 +- shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/filter_query.R | 114 + shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/filter_range.R | 266 ++- shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/renders.R | 468 ++++-- shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/shinyCohortBuilder-package.R | 18 shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/source.R | 47 shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/source_tblist.R | 248 +-- shinyCohortBuilder-1.0.0/shinyCohortBuilder/R/ui_utils.R | 93 + shinyCohortBuilder-1.0.0/shinyCohortBuilder/README.md | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/build/vignette.rds |binary shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/custom-gui-layer.R | 42 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/custom-gui-layer.Rmd | 46 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/custom-gui-layer.html | 53 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/gui-filter-layer.R | 21 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/gui-filter-layer.Rmd | 25 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/gui-filter-layer.html | 70 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/package-options.Rmd | 30 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/package-options.html | 133 + shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/shinyCohortBuilder.R | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/shinyCohortBuilder.Rmd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/shinyCohortBuilder.html | 118 - shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/doc/updating-source.html | 3 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/www/scb.css | 277 +++ shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/www/scb.js | 10 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/www/scb.min.css | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/inst/www/scb.min.js | 199 ++ shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/available-filters-choices.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/cb_chat.Rd |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/cb_ui.Rd | 67 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/demo_app.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/dot-render_filter.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/gui-filter-layer.Rd | 45 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/gui.Rd | 4 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/keep_na_input.Rd | 3 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/rendering-custom-attrition.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/rendering-filters.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/rendering-step-attrition.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/scb_icons.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/scb_labels.Rd | 2 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/trigger-action.Rd | 23 shinyCohortBuilder-1.0.0/shinyCohortBuilder/man/updating-data-statistics.Rd | 6 shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/apps |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/helper-shinytest2.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/setup.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-cb_input.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-cb_layer.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-cb_server.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-cb_ui.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-defaults.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-domains.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-filter_discrete.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-filter_helpers.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-filter_range.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-pre_post_stats.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-render_filter.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-shinytest2.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-should-run-step-on-render.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-source_tblist.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-trigger_action.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui-basic.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui-configure-step.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui-feedback.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui-matrix-add-step.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui-matrix-update-filter.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui-run-button.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui-stats.R |only shinyCohortBuilder-1.0.0/shinyCohortBuilder/tests/testthat/test-ui_utils.R | 8 shinyCohortBuilder-1.0.0/shinyCohortBuilder/vignettes/custom-gui-layer.Rmd | 46 shinyCohortBuilder-1.0.0/shinyCohortBuilder/vignettes/gui-filter-layer.Rmd | 25 shinyCohortBuilder-1.0.0/shinyCohortBuilder/vignettes/package-options.Rmd | 30 shinyCohortBuilder-1.0.0/shinyCohortBuilder/vignettes/shinyCohortBuilder.Rmd | 2 86 files changed, 3453 insertions(+), 1558 deletions(-)
More information about shinyCohortBuilder at CRAN
Permanent link
Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Statistics to locate and tag peaks and valleys and to label plots
with the equation of a fitted polynomial model by ordinary least squares,
major axis, quantile and robust and resistant regression approaches. Line
and model equation for Normal mixture models. Labels for P-value,
R^2 or adjusted R^2 or information criteria for fitted models; parametric
and non-parametric correlation; ANOVA table or summary table for fitted
models as plot insets; annotations for multiple pairwise
comparisons with adjusted P-values. Model fit classes for which suitable
methods are provided by package 'broom' and 'broom.mixed' are supported as
well as user-defined wrappers on model fit functions, allowing model
selection and conditional labelling. Scales and stats to
build volcano and quadrant plots based on
outcomes, fold changes, p-values and false discovery rates.
Author: Pedro J. Aphalo [aut, cre] ,
Kamil Slowikowski [ctb] ,
Samer Mouksassi [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpmisc versions 0.7.0 dated 2026-03-23 and 1.0.0 dated 2026-07-05
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ggpmisc-1.0.0/ggpmisc/R/utilities-fm.R | 94 ggpmisc-1.0.0/ggpmisc/R/utilities-labels.R | 183 ggpmisc-1.0.0/ggpmisc/README.md | 30 ggpmisc-1.0.0/ggpmisc/build/partial.rdb |binary ggpmisc-1.0.0/ggpmisc/build/vignette.rds |binary ggpmisc-1.0.0/ggpmisc/inst/doc/cheat-sheet.Rmd | 71 ggpmisc-1.0.0/ggpmisc/inst/doc/cheat-sheet.html | 223 ggpmisc-1.0.0/ggpmisc/inst/doc/user-guide.R | 658 +- ggpmisc-1.0.0/ggpmisc/inst/doc/user-guide.Rmd | 1049 ++- ggpmisc-1.0.0/ggpmisc/inst/doc/user-guide.html | 2844 +++++----- ggpmisc-1.0.0/ggpmisc/man/FC_format.Rd | 16 ggpmisc-1.0.0/ggpmisc/man/check_limit_to.Rd |only ggpmisc-1.0.0/ggpmisc/man/check_output_type.Rd | 7 ggpmisc-1.0.0/ggpmisc/man/check_poly_formula.Rd | 94 ggpmisc-1.0.0/ggpmisc/man/decode_label_names.Rd |only ggpmisc-1.0.0/ggpmisc/man/distrmix_helper_fun.Rd | 29 ggpmisc-1.0.0/ggpmisc/man/extract_weights.Rd | 54 ggpmisc-1.0.0/ggpmisc/man/figures/README-readme-03a-1.png |binary ggpmisc-1.0.0/ggpmisc/man/figures/README-unnamed-chunk-1-1.png |binary 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Title: Species Distribution Modeling with H3 Grids
Description: Provides tools for species distribution modeling using H3
hexagonal grids (Uber Technologies Inc., 2022, <https://h3geo.org>).
Facilitates retrieval of species occurrence records, generation of H3 grids,
computation of landscape metrics, and preparation of spatial data for modern
species distribution models workflows. Designed for biodiversity and landscape ecology research.
Author: Manuel Spinola [aut, cre]
Maintainer: Manuel Spinola <mspinola10@gmail.com>
Diff between h3sdm versions 0.1.6 dated 2026-06-15 and 0.1.7 dated 2026-07-05
DESCRIPTION | 9 ++-- MD5 | 21 +++++---- NAMESPACE | 1 NEWS.md | 17 +++++++ R/h3sdm_aoa.R | 101 ++++++++++++++++++++++++++++++++++++++-------- R/h3sdm_workflow.R | 18 +++++++- R/h3sdm_workflow_checks.R |only R/h3sdm_workflows.R | 40 ++++++++++++++---- inst/doc/h3sdm.html | 36 ++++++++-------- man/h3sdm_aoa.Rd | 17 ++++++- man/h3sdm_workflow.Rd | 14 +++++- man/h3sdm_workflows.Rd | 37 +++++++++++++--- 12 files changed, 241 insertions(+), 70 deletions(-)
Title: Complex-Valued Lasso and Complex-Valued Graphical Lasso
Description: Implements 'glmnet'-style complex-valued lasso (CLASSO) and
complex-valued graphical lasso (CGLASSO) via a pathwise coordinate
descent algorithm for complex-valued parameters, using an isomorphism
between complex numbers and 2x2 orthogonal matrices. Also provides a
full inference pipeline for high-dimensional sparse spectral precision
matrices, including data-driven bandwidth selection, one-step
debiasing, asymptotic variance estimation, entry-wise confidence
regions, and FDR-controlled hypothesis testing. Supporting tools for
cross-validation, simulation, coefficient extraction, and plotting are
included. See Deb, Kuceyeski, and Basu (2024)
<doi:10.48550/arXiv.2401.11128> and Deb, Kim, and Basu (2026)
<doi:10.48550/arXiv.2606.07986>.
Author: Younghoon Kim [aut, cre],
Navonil Deb [aut],
Sumanta Basu [aut]
Maintainer: Younghoon Kim <ykim124@ua.edu>
This is a re-admission after prior archival of version 1.0.0 dated 2025-09-17
Diff between cxreg versions 1.0.0 dated 2025-09-17 and 1.1.2 dated 2026-07-05
cxreg-1.0.0/cxreg/man/buildPredmat.default.Rd |only cxreg-1.0.0/cxreg/man/dft.X.Rd |only cxreg-1.0.0/cxreg/man/fixm.Rd |only cxreg-1.1.2/cxreg/DESCRIPTION | 36 ++-- cxreg-1.1.2/cxreg/MD5 | 139 ++++++++++------- cxreg-1.1.2/cxreg/NAMESPACE | 17 +- cxreg-1.1.2/cxreg/NEWS.md |only cxreg-1.1.2/cxreg/R/buildPremat.default.R | 90 +++++------ cxreg-1.1.2/cxreg/R/cglasso.R | 129 ++++++++-------- cxreg-1.1.2/cxreg/R/cglassoFlex.R | 139 ++++------------- cxreg-1.1.2/cxreg/R/classo.R | 103 +++++++----- cxreg-1.1.2/cxreg/R/classo.control.R | 133 +++++++--------- cxreg-1.1.2/cxreg/R/classoFlex.R | 123 +++------------ cxreg-1.1.2/cxreg/R/coef.classo.R | 18 +- cxreg-1.1.2/cxreg/R/coef.cv.classo.R | 47 +++-- cxreg-1.1.2/cxreg/R/cv.classo.R | 53 +++--- cxreg-1.1.2/cxreg/R/cv.classo.raw.R | 206 ++++++++++++------------- cxreg-1.1.2/cxreg/R/cv.classofit.R | 20 +- cxreg-1.1.2/cxreg/R/cvstats.R | 27 ++- cxreg-1.1.2/cxreg/R/cvtype.R | 46 +++-- cxreg-1.1.2/cxreg/R/cxreg-package.R | 133 +++++++++++----- cxreg-1.1.2/cxreg/R/data-documentation.R | 61 ++++++- cxreg-1.1.2/cxreg/R/decglasso.R |only cxreg-1.1.2/cxreg/R/error.bars.R | 32 ++-- cxreg-1.1.2/cxreg/R/family.classo.R | 27 ++- cxreg-1.1.2/cxreg/R/gcvFlex.R |only cxreg-1.1.2/cxreg/R/getOptcv.classo.R | 29 +-- cxreg-1.1.2/cxreg/R/inference.R |only cxreg-1.1.2/cxreg/R/lambda.interp.R | 97 ++++++++---- cxreg-1.1.2/cxreg/R/nonzeroCoef.R | 106 ++++++++----- cxreg-1.1.2/cxreg/R/plot.cglasso.R | 189 +++++++++++------------ cxreg-1.1.2/cxreg/R/plot.classo.R | 12 - cxreg-1.1.2/cxreg/R/plot.cv.classo.R | 71 ++++---- cxreg-1.1.2/cxreg/R/plotCoef.R | 207 +++++++++++--------------- cxreg-1.1.2/cxreg/R/predict.classo.R | 142 ++++++++--------- cxreg-1.1.2/cxreg/R/predict.cv.classo.R | 80 ++++------ cxreg-1.1.2/cxreg/R/print.classo.R | 15 + cxreg-1.1.2/cxreg/R/print.cv.classo.R | 19 +- cxreg-1.1.2/cxreg/R/spectral.functions.R |only cxreg-1.1.2/cxreg/R/var.cov.R |only cxreg-1.1.2/cxreg/README.md |only cxreg-1.1.2/cxreg/build |only cxreg-1.1.2/cxreg/inst |only cxreg-1.1.2/cxreg/man/buildPredmat.Rd | 27 ++- cxreg-1.1.2/cxreg/man/cglasso.Rd | 38 ++-- cxreg-1.1.2/cxreg/man/cglasso.path.Rd | 62 ++----- cxreg-1.1.2/cxreg/man/cglasso_example.Rd | 36 +++- cxreg-1.1.2/cxreg/man/classo-internal.Rd | 7 cxreg-1.1.2/cxreg/man/classo.Rd | 30 +-- cxreg-1.1.2/cxreg/man/classo.control.Rd | 40 ++--- cxreg-1.1.2/cxreg/man/classo.path.Rd | 14 - cxreg-1.1.2/cxreg/man/classo_example.Rd | 35 +++- cxreg-1.1.2/cxreg/man/coef.cv.classo.Rd |only cxreg-1.1.2/cxreg/man/cv.classo.Rd | 32 ++-- cxreg-1.1.2/cxreg/man/cxreg-package.Rd | 108 ++++++++++--- cxreg-1.1.2/cxreg/man/cxreg.Rd | 8 - cxreg-1.1.2/cxreg/man/decglasso.Rd |only cxreg-1.1.2/cxreg/man/dft.all.Rd |only cxreg-1.1.2/cxreg/man/dft.j.Rd |only cxreg-1.1.2/cxreg/man/error.bars.Rd |only cxreg-1.1.2/cxreg/man/family.classo.Rd |only cxreg-1.1.2/cxreg/man/fhat_at.Rd |only cxreg-1.1.2/cxreg/man/lambda.interp.Rd |only cxreg-1.1.2/cxreg/man/nonzeroCoef.Rd |only cxreg-1.1.2/cxreg/man/plot.cglasso.Rd | 31 ++- cxreg-1.1.2/cxreg/man/plot.classo.Rd | 2 cxreg-1.1.2/cxreg/man/plot.cv.classo.Rd | 20 +- cxreg-1.1.2/cxreg/man/plotCoef.Rd |only cxreg-1.1.2/cxreg/man/predict.classo.Rd | 60 +++---- cxreg-1.1.2/cxreg/man/predict.cv.classo.Rd | 33 +--- cxreg-1.1.2/cxreg/man/print.cv.classo.Rd | 9 - cxreg-1.1.2/cxreg/man/select_m.Rd |only cxreg-1.1.2/cxreg/man/spec.fdr.Rd |only cxreg-1.1.2/cxreg/man/spec.test.Rd |only cxreg-1.1.2/cxreg/man/var.cov.Rd |only cxreg-1.1.2/cxreg/src/Makevars.win.txt |only cxreg-1.1.2/cxreg/src/cglassocd_scaled.f | 2 cxreg-1.1.2/cxreg/src/classo_init.cpp | 26 --- cxreg-1.1.2/cxreg/src/classocd_warm.f | 4 cxreg-1.1.2/cxreg/tests |only cxreg-1.1.2/cxreg/vignettes |only 81 files changed, 1632 insertions(+), 1538 deletions(-)
Title: Microstructure Information from Diffusion Imaging
Description: An implementation of a taxonomy of models of restricted diffusion
in biological tissues parametrized by the tissue geometry (axis, diameter,
density, etc.). This is primarily used in the context of diffusion magnetic
resonance (MR) imaging to model the MR signal attenuation in the presence of
diffusion gradients. The goal is to provide tools to simulate the MR signal
attenuation predicted by these models under different experimental
conditions. The package feeds a companion 'shiny' app available at
<https://midi-pastrami.apps.math.cnrs.fr> that serves as a graphical
interface to the models and tools provided by the package. Models currently
available are the ones in Neuman (1974) <doi:10.1063/1.1680931>, Van
Gelderen et al. (1994) <doi:10.1006/jmrb.1994.1038>, Stanisz et al. (1997)
<doi:10.1002/mrm.1910370115>, Soderman & Jonsson (1995)
<doi:10.1006/jmra.1995.0014> and Callaghan (1995)
<doi:10.1006/jmra.1995.1055>.
Author: Aymeric Stamm [aut, cre]
Maintainer: Aymeric Stamm <aymeric.stamm@cnrs.fr>
Diff between midi versions 0.1.0 dated 2024-04-03 and 0.2.0 dated 2026-07-05
midi-0.1.0/midi/R/cylinder-radial-compartment.R |only midi-0.1.0/midi/R/samplers.R |only midi-0.1.0/midi/man/CylinderRadialCompartment.Rd |only midi-0.1.0/midi/tests/testthat/test-samplers.R |only midi-0.2.0/midi/DESCRIPTION | 18 midi-0.2.0/midi/MD5 | 79 +- midi-0.2.0/midi/NAMESPACE | 6 midi-0.2.0/midi/NEWS.md | 41 + midi-0.2.0/midi/R/base-compartment.R |only midi-0.2.0/midi/R/circularly-shaped-compartments.R |only midi-0.2.0/midi/R/constants.R | 23 midi-0.2.0/midi/R/cylinder-bundle-compartment.R | 271 ++++------ midi-0.2.0/midi/R/cylinder-bundle-geometry.R | 37 - midi-0.2.0/midi/R/cylinder-compartment.R | 107 +-- midi-0.2.0/midi/R/distributions.R |only midi-0.2.0/midi/R/free-compartment.R |only midi-0.2.0/midi/R/rcylinders.R |only midi-0.2.0/midi/R/sphere-compartment.R |only midi-0.2.0/midi/R/sysdata.rda |binary midi-0.2.0/midi/R/utils.R | 47 + midi-0.2.0/midi/README.md | 72 +- midi-0.2.0/midi/build/partial.rdb |binary midi-0.2.0/midi/man/BaseCompartment.Rd |only midi-0.2.0/midi/man/BaseDistribution.Rd |only midi-0.2.0/midi/man/CallaghanCompartment.Rd | 50 - midi-0.2.0/midi/man/CircularlyShapedCompartment.Rd |only midi-0.2.0/midi/man/CylinderBundleCompartment.Rd | 237 ++------ midi-0.2.0/midi/man/CylinderCompartment.Rd | 190 ++----- midi-0.2.0/midi/man/FreeCompartment.Rd |only midi-0.2.0/midi/man/GammaDistribution.Rd |only midi-0.2.0/midi/man/NeumanCompartment.Rd | 50 - midi-0.2.0/midi/man/SodermanCompartment.Rd | 50 - midi-0.2.0/midi/man/SphereCompartment.Rd |only midi-0.2.0/midi/man/StaniszCompartment.Rd | 50 - midi-0.2.0/midi/man/VanGelderenCompartment.Rd | 50 - midi-0.2.0/midi/man/WatsonDistribution.Rd |only midi-0.2.0/midi/man/bvalue.Rd |only midi-0.2.0/midi/man/figures/README-unnamed-chunk-4-1.png |binary midi-0.2.0/midi/man/figures/README-unnamed-chunk-5-1.png |only midi-0.2.0/midi/man/midi-package.Rd | 11 midi-0.2.0/midi/man/rcylinders.Rd |only midi-0.2.0/midi/tests/testthat/test-callaghan-compartment.R | 15 midi-0.2.0/midi/tests/testthat/test-cylinder-bundle-compartment.R | 41 + midi-0.2.0/midi/tests/testthat/test-cylinder-bundle-geometry.R |only midi-0.2.0/midi/tests/testthat/test-cylinder-compartment.R | 26 midi-0.2.0/midi/tests/testthat/test-distributions.R |only midi-0.2.0/midi/tests/testthat/test-neuman-compartment.R | 17 midi-0.2.0/midi/tests/testthat/test-rcylinders.R |only midi-0.2.0/midi/tests/testthat/test-soderman-compartment.R | 15 midi-0.2.0/midi/tests/testthat/test-sphere-compartment.R |only midi-0.2.0/midi/tests/testthat/test-stanisz-compartment.R | 15 midi-0.2.0/midi/tests/testthat/test-utils.R |only midi-0.2.0/midi/tests/testthat/test-vangelderen-compartment.R | 15 53 files changed, 787 insertions(+), 746 deletions(-)
Title: Creates Define XML Documents
Description: Creates 'define.xml' documents used for regulatory
submissions based on spreadsheet metadata. Can also help
create metadata and generate HTML data explorer.
Author: David Bosak [aut, cre],
Aheer Alvi [aut],
Jonathan Stallings [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between defineR versions 0.0.5 dated 2025-12-15 and 0.0.6 dated 2026-07-05
defineR-0.0.5/defineR/tests/testthat/output/check.sdtm.pdf |only defineR-0.0.6/defineR/DESCRIPTION | 6 defineR-0.0.6/defineR/MD5 | 28 defineR-0.0.6/defineR/NEWS.md | 4 defineR-0.0.6/defineR/R/create_adam_xml.R | 2 defineR-0.0.6/defineR/R/create_sdtm_xml.R | 2 defineR-0.0.6/defineR/R/write.R | 2 defineR-0.0.6/defineR/inst/extdata/adam/define.xml | 26 defineR-0.0.6/defineR/inst/extdata/sdtm/define.xml | 12 defineR-0.0.6/defineR/tests/testthat/adam/define.xml | 26 defineR-0.0.6/defineR/tests/testthat/metadata/demo/SDTM_METADATA3_CN.xlsx |only defineR-0.0.6/defineR/tests/testthat/output/define.adam.xml | 300 +++++----- defineR-0.0.6/defineR/tests/testthat/output/define.sdtm.html | 20 defineR-0.0.6/defineR/tests/testthat/output/define.sdtm.xml | 38 - defineR-0.0.6/defineR/tests/testthat/test-write.R | 31 + defineR-0.0.6/defineR/tests/testthat/xlsx/SDTM_METADATA.xlsx |binary 16 files changed, 249 insertions(+), 248 deletions(-)
Title: Dynamic Copula VAR Models for Time-Varying Dependence
Description: Fits Bayesian copula vector autoregressive models for bivariate
time series with dynamic, regime-switching, and constant dependence
structures. The package includes simulation, data preparation,
estimation with 'Stan' through 'rstan' or 'cmdstanr', posterior
summaries, diagnostics, trajectory extraction, fitted and predictive
summaries, and approximate leave-one-out cross-validation model
comparison for supported fits. For Bayesian computation and model
comparison, see Carpenter et al. (2017)
<doi:10.18637/jss.v076.i01> and Vehtari, Gelman and Gabry (2017)
<doi:10.1007/s11222-016-9696-4>.
Author: Benedikt Lugauer [aut, cre]
Maintainer: Benedikt Lugauer <benedikt.lugauer@uni-leipzig.de>
Diff between dcvar versions 0.2.0 dated 2026-04-27 and 0.9.3 dated 2026-07-05
DESCRIPTION | 8 MD5 | 287 +++-- NAMESPACE | 46 NEWS.md | 395 +++++++ R/applicability.R |only R/as-data-frame.R | 5 R/backend.R | 74 + R/constant_fit-class.R | 7 R/covariate_fit-class.R | 33 R/data-preparation.R | 559 +++++++++- R/dcvar-package.R | 16 R/dcvar_fit-class.R | 49 R/diagnostics.R | 231 +++- R/extract.R | 1032 +++++++++++++++++-- R/fit-constant.R | 68 - R/fit-covariate.R | 93 + R/fit-dcvar.R | 210 +++ R/fit-hmm.R | 143 ++ R/fit-multilevel.R | 132 +- R/fit-sem.R | 149 ++ R/hmm_fit-class.R | 69 + R/interpret.R | 35 R/loo.R | 71 - R/margins.R | 364 +++++- R/metrics.R | 52 R/multilevel_fit-class.R | 194 +++ R/pit.R | 201 +++ R/plot-trajectories.R | 24 R/plot.R | 286 ++++- R/predict.R | 350 ++++++ R/sem_fit-class.R | 177 +++ R/simulate-breakpoint.R | 23 R/simulate-multilevel.R | 135 ++ R/simulate-sem.R | 156 ++ R/simulate.R | 347 ++++-- R/stan-utils.R | 84 + R/trajectories.R | 44 R/tv_fit-class.R |only R/utils.R | 415 +++++++ README.md | 138 +- inst/CITATION | 2 inst/doc/model-comparison.R | 64 + inst/doc/model-comparison.Rmd | 123 ++ inst/doc/model-comparison.html | 203 ++- inst/doc/simulation-tools.html | 2 inst/stan/constant_EG.stan | 11 inst/stan/constant_GG.stan | 2 inst/stan/constant_NCl.stan | 13 inst/stan/constant_SNG.stan | 2 inst/stan/constant_copula_var.stan | 4 inst/stan/constant_mixed.stan |only inst/stan/constant_mixed_clayton.stan |only inst/stan/dcvar_EG_ncp.stan | 11 inst/stan/dcvar_GG_ncp.stan | 2 inst/stan/dcvar_SNG_ncp.stan | 2 inst/stan/dcvar_covariate_ncp.stan | 2 inst/stan/dcvar_covariate_nodrift.stan | 2 inst/stan/dcvar_dynamic.stan |only inst/stan/dcvar_mixed_ncp.stan |only inst/stan/dcvar_model_ncp.stan | 6 inst/stan/dcvar_tv_mixed.stan |only inst/stan/functions/clayton_copula.stan | 15 inst/stan/functions/ncp_random_walk.stan | 23 inst/stan/functions/softplus.stan |only inst/stan/functions/var_residuals.stan | 18 inst/stan/hmm_EG.stan | 28 inst/stan/hmm_GG.stan | 9 inst/stan/hmm_SNG.stan | 9 inst/stan/hmm_copula_model.stan | 14 inst/stan/hmm_mixed.stan |only inst/stan/hmm_switching.stan |only inst/stan/multilevel_copula_var.stan | 14 inst/stan/multilevel_mixed.stan |only inst/stan/multilevel_tv_mixed.stan |only inst/stan/sem_mixed.stan |only inst/stan/sem_naive_mixed.stan |only inst/stan/sem_tv_mixed.stan |only man/applicability_check.Rd |only man/as.data.frame.dcvar_model_fit.Rd | 5 man/compute_param_metrics.Rd | 4 man/compute_rho_metrics.Rd | 12 man/dcvar-package.Rd | 16 man/dcvar.Rd | 83 + man/dcvar_compare.Rd | 10 man/dcvar_constant.Rd | 24 man/dcvar_constant_fit-methods.Rd | 4 man/dcvar_covariate.Rd | 7 man/dcvar_fit-methods.Rd | 3 man/dcvar_hmm.Rd | 45 man/dcvar_hmm_fit-methods.Rd | 3 man/dcvar_multilevel.Rd | 51 man/dcvar_multilevel_fit-methods.Rd | 23 man/dcvar_sem.Rd | 62 - man/dcvar_sem_fit-methods.Rd | 16 man/dcvar_stan_path.Rd | 10 man/dcvar_tv_fit-methods.Rd |only man/dependence_summary.Rd | 6 man/fitted.dcvar_hmm_fit.Rd |only man/fitted.dcvar_model_fit.Rd | 19 man/hmm_state_params.Rd |only man/hmm_states.Rd | 5 man/interpret_rho_trajectory.Rd | 11 man/loo.dcvar.Rd | 16 man/phi_trajectory.Rd |only man/pit_values.Rd | 6 man/plot_phi_trajectory.Rd |only man/plot_rho.Rd | 3 man/plot_sigma_trajectory.Rd |only man/plot_trajectories.Rd | 4 man/predict.dcvar_hmm_fit.Rd |only man/predict.dcvar_model_fit.Rd | 11 man/prepare_constant_data.Rd | 16 man/prepare_dcvar_covariate_data.Rd | 4 man/prepare_dcvar_data.Rd | 45 man/prepare_hmm_data.Rd | 13 man/prepare_multilevel_data.Rd | 27 man/prepare_sem_data.Rd | 32 man/print.dcvar_applicability.Rd |only man/print.dcvar_multilevel_tv_summary.Rd |only man/print.dcvar_sem_tv_summary.Rd |only man/print.dcvar_tv_summary.Rd |only man/rho_decreasing.Rd | 4 man/rho_increasing.Rd | 4 man/rho_trajectory.Rd | 9 man/sigma_trajectory.Rd |only man/simulate_breakpoint_data.Rd | 8 man/simulate_dcvar.Rd | 56 - man/simulate_dcvar_multilevel.Rd | 42 man/simulate_dcvar_sem.Rd | 45 man/var_params.Rd | 19 tests/testthat/helper-fits.R | 457 ++++++++ tests/testthat/test-applicability.R |only tests/testthat/test-constant-clayton.R | 19 tests/testthat/test-convergence.R | 3 tests/testthat/test-covariate.R | 20 tests/testthat/test-data-preparation-extensions.R | 29 tests/testthat/test-data-preparation.R | 64 + tests/testthat/test-dcvar-dynamic-equivalence.R |only tests/testthat/test-diagnostics.R | 50 tests/testthat/test-extract.R | 34 tests/testthat/test-fit-cmdstanr.R | 44 tests/testthat/test-fit-constant-mixed.R |only tests/testthat/test-fit-mixed-dynamic.R |only tests/testthat/test-fit-mixed-hier.R |only tests/testthat/test-fit-multilevel-tv.R |only tests/testthat/test-fit-multilevel.R | 129 ++ tests/testthat/test-fit-sem-tv.R |only tests/testthat/test-fit-sem.R | 125 ++ tests/testthat/test-fit-tv-sem-multilevel-recovery.R |only tests/testthat/test-fit-tv.R |only tests/testthat/test-hmm-switching.R |only tests/testthat/test-loo-compare.R | 34 tests/testthat/test-margins.R | 139 ++ tests/testthat/test-metrics.R | 27 tests/testthat/test-multilevel-exponential.R | 28 tests/testthat/test-reproducibility.R |only tests/testthat/test-sem-naive.R | 71 + tests/testthat/test-simulate-margins.R | 65 + tests/testthat/test-simulate-multilevel.R | 60 - tests/testthat/test-simulate-orientation.R |only tests/testthat/test-simulate-sem.R | 35 tests/testthat/test-simulate-tv.R |only tests/testthat/test-stan-utils.R | 15 tests/testthat/test-validation-edges.R | 32 vignettes/model-comparison.Rmd | 123 ++ 165 files changed, 8503 insertions(+), 1166 deletions(-)
Title: Statistical Tools for Modelling Climate-Health Impacts
Description: Tools for producing climate-health indicators and supporting
official statistics from health and climate data. Implements analytical
workflows for temperature-related mortality, wildfire smoke exposure,
air pollution, suicides related to extreme heat, malaria, and
diarrhoeal disease outcomes, with utilities for descriptive statistics, model
validation, attributable fraction and attributable number estimation,
relative risk estimation, minimum mortality temperature estimation,
and plotting for reporting. These six indicators are endorsed by
the United Nations Statistical Commission for inclusion in the
Global Set of Environment and Climate Change Statistics.
Implemented methods include distributed lag non-linear models (DLNM),
quasi-Poisson time-series regression, case-crossover analysis,
Bayesian spatio-temporal models using the Integrated Nested Laplace
Approximation ('INLA'), and multivariate meta-analysis for
sub-national estimates. The package is based on methods developed
in the S [...truncated...]
Author: Charlie Browning [aut],
Kenechi Omeke [aut, cre],
Etse Yawo Dzakpa [aut],
Gladin Jose [aut],
Matt Pearce [aut],
Ellie Watkins [aut],
Claire Hunt [aut],
Beatrice Byukusenge [aut],
Cassien Habyarimana [aut],
Venuste Nyagahakwa [aut],
Felix Scarbrough [ [...truncated...]
Maintainer: Kenechi Omeke <climate.health@ons.gov.uk>
Diff between climatehealth versions 1.0.2 dated 2026-06-09 and 1.0.3 dated 2026-07-05
DESCRIPTION | 8 MD5 | 64 ++--- NEWS.md | 17 + R/mental_health.R | 14 + R/temp_mortality.R | 199 ++++++++-------- R/wildfire.R | 15 - README.md | 416 +++++++++++++++++------------------ man/extract_means_for_geography.Rd | 4 man/hc_add_national_data.Rd | 7 man/hc_adf.Rd | 2 man/hc_attr.Rd | 12 - man/hc_attr_tables.Rd | 6 man/hc_create_crossbasis.Rd | 7 man/hc_model_combo_res.Rd | 4 man/hc_model_validation.Rd | 12 - man/hc_plot_af_cold_monthly.Rd | 2 man/hc_plot_af_heat_monthly.Rd | 2 man/hc_plot_ar_cold_monthly.Rd | 2 man/hc_plot_ar_heat_monthly.Rd | 2 man/hc_plot_attr_cold_totals.Rd | 2 man/hc_plot_attr_heat_totals.Rd | 2 man/hc_plot_rr.Rd | 2 man/hc_predict_subnat.Rd | 2 man/hc_quasipoisson_dlnm.Rd | 2 man/hc_read_data.Rd | 12 - man/hc_rr_results.Rd | 4 man/hc_save_results.Rd | 2 man/join_health_and_climate_data.Rd | 3 man/suicides_heat_do_analysis.Rd | 3 man/temp_mortality_do_analysis.Rd | 38 +-- man/wildfire_do_analysis.Rd | 2 tests/testthat/test_temp_mortality.R | 101 ++++++-- tests/testthat/test_wildfire.R | 37 ++- 33 files changed, 565 insertions(+), 442 deletions(-)
Title: Automated Functional Annotation of Genetic Variants and Linked
Proxies
Description: To automated functional annotation of genetic variants and linked proxies. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.
Author: Alireza Ani [aut, cre],
Zoha Kamali [aut],
Ahmad Vaez [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between SNPannotator versions 1.4.7 dated 2026-06-08 and 1.4.8 dated 2026-07-05
DESCRIPTION | 8 - MD5 | 23 ++--- NAMESPACE | 1 R/aaa.R | 2 R/configFile_funcs.R | 24 ++--- R/ensembl_funcs.R | 174 +++++++++++++++++++++++++++++++++++++++++++ R/eqtl_funcs.R | 2 R/eqtl_graph_funcs.R | 3 R/gwascat_graph_funcs.R | 2 R/merge_funcs.R | 35 +++++--- R/misc_files.R | 10 ++ inst/extdata/demo_config.ini | 20 ++-- man/findSynonyms.Rd |only 13 files changed, 251 insertions(+), 53 deletions(-)
Title: Tour Methods for Multivariate Data Visualisation
Description: Implements geodesic interpolation and basis
generation functions that allow you to create new tour
methods from R.
Author: Hadley Wickham [aut, ctb] ,
Dianne Cook [aut, cre] ,
Nick Spyrison [ctb] ,
Ursula Laa [ctb] ,
H. Sherry Zhang [ctb] ,
Stuart Lee [ctb]
Maintainer: Dianne Cook <dicook@monash.edu>
Diff between tourr versions 1.2.7 dated 2026-05-15 and 1.2.8 dated 2026-07-05
DESCRIPTION | 6 +++--- MD5 | 17 ++++++++++------- NAMESPACE | 5 +++++ NEWS.md | 6 ++++++ R/display-dependence.r |only R/history.r | 18 +++++++----------- R/tour-dependence.r | 27 ++++++++++++++++++++++++--- build/vignette.rds |binary man/basis_dep_init.Rd |only man/dependence_tour.Rd | 4 ++-- man/display_dependence.Rd |only 11 files changed, 57 insertions(+), 26 deletions(-)
Title: Extra String Manipulation Functions
Description: There are some things that I wish were easier with the
'stringr' or 'stringi' packages. The foremost of these is the
extraction of numbers from strings. 'stringr' and 'stringi' make you
figure out the regular expression for yourself; 'strex' takes care of
this for you. There are many other handy functionalities in 'strex'.
Contributions to this package are encouraged; it is intended as a
miscellany of string manipulation functions that cannot be found in
'stringi' or 'stringr'.
Author: Rory Nolan [aut, cre]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between strex versions 2.0.1 dated 2024-10-03 and 2.1.0 dated 2026-07-05
DESCRIPTION | 10 ++++---- MD5 | 34 ++++++++++++++--------------- NEWS.md | 6 +++++ R/extract-nums.R | 9 +++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/alphordering-numbers.html | 9 ++++--- inst/doc/argument-matching.R | 14 +++++++++++ inst/doc/argument-matching.html | 9 ++++--- inst/doc/before-and-after.html | 9 ++++--- inst/doc/detection.html | 9 ++++--- inst/doc/important-miscellany.R | 2 + inst/doc/important-miscellany.html | 9 ++++--- inst/doc/numbers-in-strings.html | 9 ++++--- tests/testthat/test-extract-non-numerics.R | 11 +++++++++ tests/testthat/test-extract-nums.R | 15 ++++++++++++ tests/testthat/test-num-before.R | 17 ++++++++++++++ tests/testthat/test-split-by-nums.R | 7 +++++ 18 files changed, 131 insertions(+), 48 deletions(-)
Title: Fast Molecular Clock Dating of Phylogenetic Trees with Rate
Variation
Description: Functions for estimating times of common ancestry and molecular clock rates of evolution using a variety of evolutionary models, parametric and nonparametric bootstrap confidence intervals, methods for detecting outlier lineages, root-to-tip regression, and a statistical test for selecting molecular clock models. For more details see Volz and Frost (2017) <doi:10.1093/ve/vex025>.
Author: Erik Volz [aut, cre]
Maintainer: Erik Volz <erik.volz@gmail.com>
Diff between treedater versions 1.0.2 dated 2025-09-03 and 2.0.0 dated 2026-07-05
DESCRIPTION | 16 ++- MD5 | 17 ++- NAMESPACE | 2 NEWS.md |only R/treedater.R | 2 R/treedater0.R | 228 ++++++++++++++++++++++++++++++++++++++++++++++++----- build/vignette.rds |binary inst/doc/h3n2.html | 150 +++++++++++++++++----------------- man/dater.Rd | 4 tests |only 10 files changed, 307 insertions(+), 112 deletions(-)
Title: Generalized L-Moments Estimation for Extreme Value Distributions
Description: Provides generalized L-moments estimation methods for the
generalized extreme value ('GEV') distribution. Implements both stationary
'GEV' and non-stationary 'GEV11' models where location and scale parameters
vary with time. Includes various penalty functions (Martins-Stedinger,
Park, Cannon, Coles-Dixon) for shape parameter regularization.
Also provides model averaging estimation ('ma.gev') that combines MLE and
L-moment methods with multiple weighting schemes for robust high quantile
estimation. The 'GLME' methodology is described in Shin et al. (2025a)
<doi:10.48550/arXiv.2512.20385>. The non-stationary L-moment method
is based on Shin et al. (2025b) <doi:10.1007/s42952-025-00325-3>.
The model averaging method is described in Shin et al. (2026)
<doi:10.1007/s00477-025-03167-x>.
See also Hosking (1990) <doi:10.1111/j.2517-6161.1990.tb01775.x> for
L-moments theory and Martins and Stedinger (2000)
<doi:10.1029/1999WR900330> for penalized likelihood methods [...truncated...]
Author: Yonggwan Shin [aut, cre] ,
Seokkap Ko [aut, ctb] ,
Jihong Park [ctb] ,
Yire Shin [aut, dtc] ,
Jeong-Soo Park [aut, ths]
Maintainer: Yonggwan Shin <syg.stat@etri.re.kr>
Diff between GLmom versions 1.3.1 dated 2026-02-27 and 2.0.0 dated 2026-07-05
GLmom-1.3.1/GLmom/data/Trehafod.rda |only GLmom-1.3.1/GLmom/data/streamflow.rda |only GLmom-1.3.1/GLmom/man/Trehafod.Rd |only GLmom-1.3.1/GLmom/man/gev11.GLD.Rd |only GLmom-1.3.1/GLmom/man/init.glme.gev11.Rd |only GLmom-1.3.1/GLmom/man/obj.lme.gev11.Rd |only GLmom-1.3.1/GLmom/man/optim.glme.gev11.Rd |only GLmom-1.3.1/GLmom/man/pk.beta.ns.Rd |only GLmom-1.3.1/GLmom/man/pk.beta.stnary.Rd |only GLmom-1.3.1/GLmom/man/streamflow.Rd |only GLmom-1.3.1/GLmom/man/strup.glme.gev11.Rd |only GLmom-2.0.0/GLmom/DESCRIPTION | 14 GLmom-2.0.0/GLmom/MD5 | 106 +- GLmom-2.0.0/GLmom/NAMESPACE | 25 GLmom-2.0.0/GLmom/NEWS.md | 110 ++ GLmom-2.0.0/GLmom/R/GN16.gev11.R |only GLmom-2.0.0/GLmom/R/data.R | 67 - GLmom-2.0.0/GLmom/R/glme.gev.R | 633 ++++-------- GLmom-2.0.0/GLmom/R/glme.gev11.R | 1480 +++++++----------------------- GLmom-2.0.0/GLmom/R/lme.gev11.R |only GLmom-2.0.0/GLmom/R/magev.R | 6 GLmom-2.0.0/GLmom/R/magev_helpers.R | 61 + GLmom-2.0.0/GLmom/R/magev_plots.R | 16 GLmom-2.0.0/GLmom/R/methods.R |only GLmom-2.0.0/GLmom/R/nsgev.R | 70 - GLmom-2.0.0/GLmom/R/penalty.R |only GLmom-2.0.0/GLmom/R/ran.gev.R |only GLmom-2.0.0/GLmom/R/strup.gev11.R |only GLmom-2.0.0/GLmom/build/partial.rdb |binary GLmom-2.0.0/GLmom/man/Befun.Rd | 2 GLmom-2.0.0/GLmom/man/GLmom-methods.Rd |only GLmom-2.0.0/GLmom/man/GN16.gev11.Rd |only GLmom-2.0.0/GLmom/man/MS_pk.Rd | 4 GLmom-2.0.0/GLmom/man/PhliuAgromet.Rd | 14 GLmom-2.0.0/GLmom/man/boot.cov.Rd |only GLmom-2.0.0/GLmom/man/check.penalty.Rd |only GLmom-2.0.0/GLmom/man/find_max_beta.pk.Rd |only GLmom-2.0.0/GLmom/man/fun.lme.gev11.Rd |only GLmom-2.0.0/GLmom/man/gado.prop_11.Rd | 26 GLmom-2.0.0/GLmom/man/glme.gev.Rd | 72 + GLmom-2.0.0/GLmom/man/glme.gev11.Rd | 97 + GLmom-2.0.0/GLmom/man/glme.like.Rd | 16 GLmom-2.0.0/GLmom/man/gof.ene_all.Rd | 16 GLmom-2.0.0/GLmom/man/init.glme.Rd | 41 GLmom-2.0.0/GLmom/man/lme.gev11.Rd |only GLmom-2.0.0/GLmom/man/lmoms.md.park.Rd | 23 GLmom-2.0.0/GLmom/man/ma.gev.Rd | 4 GLmom-2.0.0/GLmom/man/magev.ksensplot.Rd | 4 GLmom-2.0.0/GLmom/man/magev.qqplot.Rd | 6 GLmom-2.0.0/GLmom/man/magev.rlplot.Rd | 6 GLmom-2.0.0/GLmom/man/make.qmax.gev11.Rd | 23 GLmom-2.0.0/GLmom/man/nllh.glme.gev11.Rd | 14 GLmom-2.0.0/GLmom/man/nsgev.Rd | 13 GLmom-2.0.0/GLmom/man/opt.glme.gev11.Rd |only GLmom-2.0.0/GLmom/man/pargev.kfix.Rd | 4 GLmom-2.0.0/GLmom/man/penalty.fun.Rd |only GLmom-2.0.0/GLmom/man/pk.beta.Rd |only GLmom-2.0.0/GLmom/man/pk.norm.stnary.Rd | 6 GLmom-2.0.0/GLmom/man/qns.gev11.Rd | 2 GLmom-2.0.0/GLmom/man/qns.gev_all.Rd | 2 GLmom-2.0.0/GLmom/man/quagev.NS.Rd | 5 GLmom-2.0.0/GLmom/man/ran.gev_all.Rd |only GLmom-2.0.0/GLmom/man/sel.para_all.Rd | 22 GLmom-2.0.0/GLmom/man/set.para.model.Rd | 2 GLmom-2.0.0/GLmom/man/strup.gev11.Rd |only GLmom-2.0.0/GLmom/man/time.m.gev11.Rd | 27 GLmom-2.0.0/GLmom/man/trans.gum01.Rd |only GLmom-2.0.0/GLmom/man/wls.gev11.Rd | 24 GLmom-2.0.0/GLmom/tests/test.R | 126 ++ 69 files changed, 1306 insertions(+), 1883 deletions(-)
Title: Automated Gene Identification for Post-GWAS and QTL Analysis
Description: Facilitates the post-Genome Wide Association Studies (GWAS) and Quantitative Trait Loci (QTL) analysis of identifying candidate genes within user-defined search window, based on the identified Single Nucleotide Polymorphisms (SNPs) as given by Mazumder AK (2024) <doi:10.1038/s41598-024-66903-3>. It supports candidate gene analysis for wheat and rice. Just import your GWAS result as explained in the sample_data file and the function does all the manual search and retrieve candidate genes for you, while exporting the results into ready-to-use output.
Author: Rajamani Nirmalaruban [aut, cre, cph],
R. Suvitha [aut],
Rajbir Yadav [aut],
Meda Alekya [aut],
Amit Kumar Mazumder [aut],
Thirumurugan Sathya [aut],
Subramani Sugumar [aut],
Prashanth babu [aut],
Manjeet Kumar [aut],
Kiran B Gaikwad [aut],
Naresh Ku [...truncated...]
Maintainer: Rajamani Nirmalaruban <nirmalaruban97@gmail.com>
Diff between geneNR versions 2.0.1 dated 2025-03-29 and 3.0.0 dated 2026-07-05
DESCRIPTION | 12 MD5 | 25 + NEWS.md | 9 R/geneQTL.R | 108 ++++++-- R/geneSNP.R | 172 +++++++------ R/geneSNPcustom.R | 174 +++++++------ inst/doc/geneNR_1.R | 122 +++++---- inst/doc/geneNR_1.Rmd | 332 ++++++++++---------------- inst/doc/geneNR_1.html | 531 ++++++++++++++++++++++++------------------ inst/extdata/sample_crop.gff3 |only man/geneQTL.Rd | 17 - man/geneSNP.Rd | 24 + man/geneSNPcustom.Rd | 19 + vignettes/geneNR_1.Rmd | 332 ++++++++++---------------- 14 files changed, 1012 insertions(+), 865 deletions(-)
Title: Psychometric Analysis with Rasch Measurement Theory
Description: Streamlines reproducible Rasch measurement theory analyses
for ordinal item-response data, combining estimation routines from
'eRm', 'psychotools', 'mirt', 'iarm', and 'lavaan' with consistent
diagnostic, plotting, and reporting layers. Covers the four basic
psychometric criteria summarised by Christensen et al. (2021)
<doi:10.1111/sms.13908> -- unidimensionality, local independence,
ordered response category thresholds, and invariance across
subgroups -- together with item fit, targeting, reliability,
category functioning, and descriptive item-response plots. A
distinguishing feature is the use of simulation-based critical
values to replace rule-of-thumb cutoffs for conditional infit mean-square,
Yen's Q3 local-dependence statistic, the largest residual-PCA eigenvalue,
ordinal CFA fit indices, and partial-gamma DIF and local-dependence
coefficients, optionally augmented with multiplicity-corrected bootstrap
p-values. Outputs are knitr::kable() tables and
'ggplot2' figures suitab [...truncated...]
Author: Magnus Johansson [aut, cre] ,
Nicklas Korsell [ctb] ,
Mirka Henninger [ctb] ,
Jan Radek [ctb]
Maintainer: Magnus Johansson <pgmj@pm.me>
Diff between easyRasch2 versions 0.8.0 dated 2026-06-08 and 1.0.0 dated 2026-07-05
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Title: Arbitrary Dimensional Clifford Algebras
Description: A suite of routines for Clifford algebras, using the
'Map' class of the Standard Template Library. Canonical
reference: Hestenes (1987, ISBN 90-277-1673-0, "Clifford algebra
to geometric calculus"). Special cases including Lorentz transforms,
quaternion multiplication, and Grassmann algebra, are discussed.
Vignettes presenting conformal geometric algebra, quaternions and
split quaternions, dual numbers, and Lorentz transforms are
included. The package follows 'disordR' discipline.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between clifford versions 1.2-0 dated 2026-06-30 and 1.2-0-1 dated 2026-07-05
DESCRIPTION | 6 ++-- MD5 | 42 +++++++++++++++---------------- NEWS.md | 3 ++ build/partial.rdb |binary inst/doc/clifford.pdf |binary inst/doc/complex_clifford.html | 3 +- inst/doc/conformal_algebra_clifford.html | 3 +- inst/doc/cramer_clifford.html | 3 +- inst/doc/determinants_clifford.html | 3 +- inst/doc/dual_quaternion_clifford.R | 1 inst/doc/dual_quaternion_clifford.Rmd | 1 inst/doc/dual_quaternion_clifford.html | 5 ++- inst/doc/getcoeffs.html | 3 +- inst/doc/lorentz_clifford.html | 3 +- inst/doc/pauli_clifford.html | 3 +- inst/doc/pseudoscalar.html | 3 +- inst/doc/quaternion_clifford.R | 1 inst/doc/quaternion_clifford.Rmd | 1 inst/doc/quaternion_clifford.html | 5 ++- inst/doc/signature.html | 3 +- vignettes/dual_quaternion_clifford.Rmd | 1 vignettes/quaternion_clifford.Rmd | 1 22 files changed, 51 insertions(+), 43 deletions(-)
Title: Representation for Glycan Compositions and Structures
Description: Computational representations of glycan compositions and structures,
including details such as linkages, anomers, and substituents. Supports varying
levels of monosaccharide specificity (e.g., "Hex" or "Gal") and ambiguous linkages.
Provides robust parsing and generation of IUPAC-condensed structure strings.
Optimized for vectorized operations on glycan structures, with efficient handling
of duplications. As the cornerstone of the glycoverse ecosystem, this package
delivers the foundational data structures that power glycomics and glycoproteomics
analysis workflows.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyrepr versions 0.12.1 dated 2026-06-19 and 0.13.0 dated 2026-07-05
glyrepr-0.12.1/glyrepr/man/get_anomer_pos.Rd |only glyrepr-0.13.0/glyrepr/DESCRIPTION | 17 glyrepr-0.13.0/glyrepr/MD5 | 79 - glyrepr-0.13.0/glyrepr/NAMESPACE | 8 glyrepr-0.13.0/glyrepr/NEWS.md | 22 glyrepr-0.13.0/glyrepr/R/color-utils.R | 6 glyrepr-0.13.0/glyrepr/R/composition.R | 12 glyrepr-0.13.0/glyrepr/R/fill-anomer-pos.R | 2 glyrepr-0.13.0/glyrepr/R/iupac-to-structure.R | 61 - glyrepr-0.13.0/glyrepr/R/linkage.R | 5 glyrepr-0.13.0/glyrepr/R/monosaccharide.R | 31 glyrepr-0.13.0/glyrepr/R/smap.R | 505 ++-------- glyrepr-0.13.0/glyrepr/R/structure-level.R | 4 glyrepr-0.13.0/glyrepr/R/structure-tables.R |only glyrepr-0.13.0/glyrepr/R/structure.R | 189 ++- glyrepr-0.13.0/glyrepr/R/substituent.R | 94 + glyrepr-0.13.0/glyrepr/R/validate-helper.R | 50 glyrepr-0.13.0/glyrepr/inst/doc/glycan-graph.html | 6 glyrepr-0.13.0/glyrepr/inst/doc/glyrepr.html | 8 glyrepr-0.13.0/glyrepr/inst/doc/smap.R | 2 glyrepr-0.13.0/glyrepr/inst/doc/smap.Rmd | 2 glyrepr-0.13.0/glyrepr/inst/doc/smap.html | 18 glyrepr-0.13.0/glyrepr/man/get_structure_level.Rd | 4 glyrepr-0.13.0/glyrepr/man/glycan_structure.Rd | 16 glyrepr-0.13.0/glyrepr/man/glyrepr-package.Rd | 5 glyrepr-0.13.0/glyrepr/man/has_linkages.Rd | 2 glyrepr-0.13.0/glyrepr/man/infer_anomer_pos.Rd |only glyrepr-0.13.0/glyrepr/man/smap.Rd | 17 glyrepr-0.13.0/glyrepr/man/smap2.Rd | 18 glyrepr-0.13.0/glyrepr/man/smap_unique.Rd | 6 glyrepr-0.13.0/glyrepr/man/spmap.Rd | 18 glyrepr-0.13.0/glyrepr/man/structure_tables.Rd |only glyrepr-0.13.0/glyrepr/tests/testthat/test-color-substituents.R | 2 glyrepr-0.13.0/glyrepr/tests/testthat/test-composition.R | 28 glyrepr-0.13.0/glyrepr/tests/testthat/test-iupac-to-structure.R | 57 + glyrepr-0.13.0/glyrepr/tests/testthat/test-monosaccharide.R | 35 glyrepr-0.13.0/glyrepr/tests/testthat/test-smap.R | 119 -- glyrepr-0.13.0/glyrepr/tests/testthat/test-structure-level.R | 5 glyrepr-0.13.0/glyrepr/tests/testthat/test-structure-tables.R |only glyrepr-0.13.0/glyrepr/tests/testthat/test-structure.R | 54 + glyrepr-0.13.0/glyrepr/tests/testthat/test-substituent.R | 11 glyrepr-0.13.0/glyrepr/tests/testthat/test-validate-helper.R | 14 glyrepr-0.13.0/glyrepr/vignettes/smap.Rmd | 2 43 files changed, 811 insertions(+), 723 deletions(-)
Title: Geometric Morphometric Analyses of 2D and 3D Landmark Data
Description: Read and manipulate landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams [aut, cre],
Michael Collyer [aut],
Antigoni Kaliontzopoulou [aut],
Erica Baken [aut]
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 4.1.0 dated 2026-03-14 and 4.1.1 dated 2026-07-05
DESCRIPTION | 6 - MD5 | 35 +++++----- NEWS.md | 11 +++ R/compare.CR.R | 2 R/compare.physign.z.r | 2 R/compare.pls.r | 13 +++ R/geomorph.support.code.r | 2 R/geomorph.utils.r | 2 R/integration.test.r | 34 +++++++-- R/phylo.integration.r | 37 ++++++++-- R/physignal.z.r | 7 +- R/plotAllSpecimens.r | 1 R/plotOutliers.r | 2 R/shared.support.code.R | 160 ++++------------------------------------------ R/two.b.pls.r | 2 README.md | 2 man/integration.test.Rd | 13 +++ man/phylo.integration.Rd | 12 ++- tests/testthat/Rplots.pdf |only 19 files changed, 147 insertions(+), 196 deletions(-)
Title: Convenience Functions for Arrays
Description: Some convenient functions to work with arrays.
Author: Claudia Beleites [aut, cre]
Maintainer: Claudia Beleites <Claudia.Beleites@chemometrix.eu>
Diff between arrayhelpers versions 1.1-0 dated 2020-02-04 and 1.1-1 dated 2026-07-05
arrayhelpers-1.1-0/arrayhelpers/tests/tests.R |only arrayhelpers-1.1-1/arrayhelpers/DESCRIPTION | 29 +++++++----- arrayhelpers-1.1-1/arrayhelpers/MD5 | 16 +++--- arrayhelpers-1.1-1/arrayhelpers/R/apply.R | 2 arrayhelpers-1.1-1/arrayhelpers/R/arrayhelpers-package.R |only arrayhelpers-1.1-1/arrayhelpers/R/arrayhelpers.R | 9 --- arrayhelpers-1.1-1/arrayhelpers/man/arrayhelpers-package.Rd | 24 +++++++-- arrayhelpers-1.1-1/arrayhelpers/man/ensuredim.Rd | 2 arrayhelpers-1.1-1/arrayhelpers/man/makeNd.Rd | 2 arrayhelpers-1.1-1/arrayhelpers/tests/testthat |only arrayhelpers-1.1-1/arrayhelpers/tests/testthat.R |only 11 files changed, 46 insertions(+), 38 deletions(-)
Title: Statistical Tools for Immune Correlates Analysis of Vaccine
Clinical Trial Data
Description: Various semiparametric and nonparametric statistical tools for
immune correlates analysis of vaccine clinical trial data. This includes
calculation of summary statistics and estimation of risk, vaccine efficacy,
controlled effects (controlled risk and controlled vaccine efficacy), and
mediation effects (natural direct effect, natural indirect effect,
proportion mediated). See Gilbert P, Fong Y, Kenny A, and Carone, M (2022)
<doi:10.1093/biostatistics/kxac024> and Fay MP and Follmann DA (2023)
<doi:10.48550/arXiv.2208.06465>.
Author: Avi Kenny [aut, cre]
Maintainer: Avi Kenny <avi.kenny@gmail.com>
Diff between vaccine versions 1.3.1 dated 2025-09-07 and 1.4.0 dated 2026-07-05
DESCRIPTION | 8 +- MD5 | 23 +++-- NAMESPACE | 1 NEWS.md | 13 +++ R/est_cox.R | 153 ++++++++++++++++++++++++++++++++------ R/est_med.R | 198 +++++++++++++++++++++++++++++++++----------------- R/est_np.R | 16 ++-- R/est_overall.R | 40 ++++++++-- R/params.R | 31 +++++++ R/zzz.R | 5 + inst/doc/vaccine.html | 15 ++- man/est_med.Rd | 5 + man/params_med_cox.Rd |only 13 files changed, 384 insertions(+), 124 deletions(-)
Title: Extreme Value Modeling for r-Largest Order Statistics
Description: Tools for extreme value modeling based on the r-largest
order statistics framework. The package provides functions for
parameter estimation via maximum likelihood, return level
estimation with standard errors, profile likelihood-based
confidence intervals, random sample generation, and entropy
difference tests for selecting the number of order statistics r.
Several r-largest order statistics models are implemented,
including the four-parameter kappa (rK4D), generalized logistic
(rGLO), generalized Gumbel (rGGD), logistic (rLD), and Gumbel
(rGD) distributions. The rK4D methodology is described in
Shin et al. (2022) <doi:10.1016/j.wace.2022.100533>, the rGLO
model in Shin and Park (2024) <doi:10.1007/s00477-023-02642-7>,
and the rGGD model in Shin and Park (2025)
<doi:10.1038/s41598-024-83273-y>. The underlying distributions
are related to the kappa distribution of Hosking (1994)
<doi:10.1017/CBO9780511529443>, the generalized logistic
distribution discussed by Ah [...truncated...]
Author: Yire Shin [aut, cre] ,
Jeong-Soo Park [aut, ths]
Maintainer: Yire Shin <shinyire87@gmail.com>
Diff between evmr versions 0.1.0 dated 2026-03-29 and 0.2.0 dated 2026-07-05
evmr-0.1.0/evmr/R/bevern.R |only evmr-0.1.0/evmr/R/oykel.R |only evmr-0.1.0/evmr/data/bevern.rda |only evmr-0.1.0/evmr/data/oykel.rda |only evmr-0.1.0/evmr/man/bevern.Rd |only evmr-0.1.0/evmr/man/oykel.Rd |only evmr-0.2.0/evmr/DESCRIPTION | 8 evmr-0.2.0/evmr/MD5 | 181 ++--- evmr-0.2.0/evmr/NAMESPACE | 84 +- evmr-0.2.0/evmr/NEWS.md |only evmr-0.2.0/evmr/R/bangkok.R | 66 +- evmr-0.2.0/evmr/R/evmr.R | 205 +++--- evmr-0.2.0/evmr/R/qgd.R | 110 +-- evmr-0.2.0/evmr/R/qggd.R | 178 ++--- evmr-0.2.0/evmr/R/qglo.R | 180 ++--- evmr-0.2.0/evmr/R/qk4d.R | 250 +++---- evmr-0.2.0/evmr/R/qld.R | 120 +-- evmr-0.2.0/evmr/R/rgd.fit.R | 470 +++++++------- evmr-0.2.0/evmr/R/rgd.prof.R | 329 +++++----- evmr-0.2.0/evmr/R/rgd.rl.R | 155 ++-- evmr-0.2.0/evmr/R/rgd.summary.R | 224 +++--- evmr-0.2.0/evmr/R/rgdr.R | 144 ++-- evmr-0.2.0/evmr/R/rggd.fit.R | 648 ++++++++++---------- evmr-0.2.0/evmr/R/rggd.prof.R | 483 +++++++-------- evmr-0.2.0/evmr/R/rggd.rl.R | 183 ++--- evmr-0.2.0/evmr/R/rggd.summary.R | 232 +++---- evmr-0.2.0/evmr/R/rggdEd.R | 278 ++++---- evmr-0.2.0/evmr/R/rggdEdtest.R | 204 +++--- evmr-0.2.0/evmr/R/rggdLh.R | 195 ++---- evmr-0.2.0/evmr/R/rggdr.R | 220 +++--- evmr-0.2.0/evmr/R/rglo.fit.R | 757 +++++++++++------------ evmr-0.2.0/evmr/R/rglo.prof.R | 513 +++++++-------- evmr-0.2.0/evmr/R/rglo.rl.R | 200 ++---- evmr-0.2.0/evmr/R/rglo.summary.R | 294 ++++----- evmr-0.2.0/evmr/R/rgloEd.R | 216 +++--- evmr-0.2.0/evmr/R/rgloEdtest.R | 223 +++--- evmr-0.2.0/evmr/R/rgloLh.R | 195 ++---- evmr-0.2.0/evmr/R/rglor.R | 224 +++--- evmr-0.2.0/evmr/R/rk4d.fit.R | 932 ++++++++++++++--------------- evmr-0.2.0/evmr/R/rk4d.prof.R | 517 +++++++--------- evmr-0.2.0/evmr/R/rk4d.rl.R | 222 +++--- evmr-0.2.0/evmr/R/rk4d.summary.R | 327 ++++------ evmr-0.2.0/evmr/R/rk4dEd.R | 260 ++++---- evmr-0.2.0/evmr/R/rk4dEdtest.R | 210 +++--- evmr-0.2.0/evmr/R/rk4dLh.R | 202 ++---- evmr-0.2.0/evmr/R/rk4dr.R | 250 +++---- evmr-0.2.0/evmr/R/rld.fit.R | 653 ++++++++++---------- evmr-0.2.0/evmr/R/rld.prof.R | 460 +++++++------- evmr-0.2.0/evmr/R/rld.rl.R | 185 ++--- evmr-0.2.0/evmr/R/rld.summary.R | 282 ++++---- evmr-0.2.0/evmr/R/rldr.R | 201 ++---- evmr-0.2.0/evmr/build/partial.rdb |binary evmr-0.2.0/evmr/man/bangkok.Rd | 86 +- evmr-0.2.0/evmr/man/evmr.Rd | 63 - evmr-0.2.0/evmr/man/qgd.Rd | 64 - evmr-0.2.0/evmr/man/qggd.Rd | 88 +- evmr-0.2.0/evmr/man/qglo.Rd | 86 +- evmr-0.2.0/evmr/man/qk4d.Rd | 102 +-- evmr-0.2.0/evmr/man/qld.Rd | 64 - evmr-0.2.0/evmr/man/rgd.fit.Rd | 202 +++--- evmr-0.2.0/evmr/man/rgd.prof.Rd | 94 +- evmr-0.2.0/evmr/man/rgd.rl.Rd | 86 +- evmr-0.2.0/evmr/man/rgd.summary.Rd | 150 ++-- evmr-0.2.0/evmr/man/rgdr.Rd | 78 +- evmr-0.2.0/evmr/man/rggd.fit.Rd | 198 +++--- evmr-0.2.0/evmr/man/rggd.prof.Rd | 110 +-- evmr-0.2.0/evmr/man/rggd.rl.Rd | 86 +- evmr-0.2.0/evmr/man/rggd.summary.Rd | 158 ++-- evmr-0.2.0/evmr/man/rggdEd.Rd | 108 +-- evmr-0.2.0/evmr/man/rggdEdtest.Rd | 134 ++-- evmr-0.2.0/evmr/man/rggdLh.Rd | 81 +- evmr-0.2.0/evmr/man/rggdr.Rd | 92 +- evmr-0.2.0/evmr/man/rglo.fit.Rd | 215 +++--- evmr-0.2.0/evmr/man/rglo.prof.Rd | 114 +-- evmr-0.2.0/evmr/man/rglo.rl.Rd | 108 +-- evmr-0.2.0/evmr/man/rglo.summary.Rd | 175 ++--- evmr-0.2.0/evmr/man/rgloEd.Rd | 122 +-- evmr-0.2.0/evmr/man/rgloEdtest.Rd | 142 ++-- evmr-0.2.0/evmr/man/rgloLh.Rd | 83 -- evmr-0.2.0/evmr/man/rglor.Rd | 107 +-- evmr-0.2.0/evmr/man/rk4d.fit.Rd | 258 ++++---- evmr-0.2.0/evmr/man/rk4d.prof.Rd | 113 +-- evmr-0.2.0/evmr/man/rk4d.rl.Rd | 112 +-- evmr-0.2.0/evmr/man/rk4d.summary.Rd | 204 ++---- evmr-0.2.0/evmr/man/rk4dEd.Rd | 116 +-- evmr-0.2.0/evmr/man/rk4dEdtest.Rd | 139 +--- evmr-0.2.0/evmr/man/rk4dLh.Rd | 73 -- evmr-0.2.0/evmr/man/rk4dr.Rd | 122 +-- evmr-0.2.0/evmr/man/rld.fit.Rd | 202 +++--- evmr-0.2.0/evmr/man/rld.prof.Rd | 108 +-- evmr-0.2.0/evmr/man/rld.rl.Rd | 101 +-- evmr-0.2.0/evmr/man/rld.summary.Rd | 163 ++--- evmr-0.2.0/evmr/man/rldr.Rd | 95 +- evmr-0.2.0/evmr/tests/testthat.R | 24 evmr-0.2.0/evmr/tests/testthat/test-evmr.R | 320 ++++----- 95 files changed, 8676 insertions(+), 9140 deletions(-)
Title: Subset and Flag Data Frames with Times by the Use of Periods
Description: Data frames with time information are subset and flagged with period information. Data frames with times are dealt as timeDF objects and periods are represented as periodDF objects.
Author: Toshihiro Umehara [aut, cre]
Maintainer: Toshihiro Umehara <toshi@niceume.com>
Diff between timeDF versions 0.9.1 dated 2024-04-28 and 0.9.2 dated 2026-07-05
DESCRIPTION | 10 ++++----- MD5 | 28 +++++++++++++-------------- R/condense_periodDF.R | 5 ++++ R/examine_with_date_periods.R | 13 ++++++------ R/examine_with_time_periods.R | 13 ++++++------ R/examine_with_time_periods_within_a_day.R | 11 +++++----- R/extract_with_periodDF.R | 28 ++++++++++++++++++--------- R/flag_with_periodDF.R | 16 ++++++++++++--- R/listTimeDF.R | 2 - README.md | 8 +++---- build/partial.rdb |binary inst/unit_tests/test_extract_with_periodDF.R | 6 ++--- inst/unit_tests/test_flag_with_periodDF.R | 4 +-- man/extract_with_periodDF.Rd | 5 ++-- man/flag_with_periodDF.Rd | 5 ++-- 15 files changed, 92 insertions(+), 62 deletions(-)
Title: Minimalist Theme and Vignette Kit for 'pkgdown' and R Markdown
Description: Provides a minimalist 'ggplot2' theme, colour scales, and
'pkgdown' template built around a curated colour palette system
inspired by Josef Albers' colour theory
(Albers (1963, ISBN:978-0-300-17935-4) "Interaction of Color").
Includes helpers to apply consistent theming to 'ggplot2' plots, 'gt'
tables, and 'bslib' Bootstrap 5 sites, along with one-command setup
functions for adopting the style across an R package.
Author: Bradley R. Buchsbaum [aut, cre]
Maintainer: Bradley R. Buchsbaum <brad.buchsbaum@gmail.com>
Diff between albersdown versions 1.0.0 dated 2026-04-01 and 2.0.0 dated 2026-07-05
DESCRIPTION | 8 MD5 | 133 NAMESPACE | 1 R/bs_theme.R | 27 R/gt_albers.R | 4 R/migrate_albersdown.R | 2 R/register_fonts.R |only R/theme_albers.R | 53 R/use_albers.R | 10 R/use_albersdown.R | 470 ++ build/vignette.rds |binary inst/doc/design-notes.R | 32 inst/doc/design-notes.Rmd | 49 inst/doc/design-notes.html | 1755 ++++++++- inst/doc/getting-started.R | 31 inst/doc/getting-started.Rmd | 48 inst/doc/getting-started.html | 1751 ++++++++- inst/doc/interaction.R |only inst/doc/interaction.Rmd |only inst/doc/interaction.html |only inst/doc/proof-ochre-structural.R |only inst/doc/proof-ochre-structural.Rmd |only inst/doc/proof-ochre-structural.html |only inst/doc/proof-teal-study.R |only inst/doc/proof-teal-study.Rmd |only inst/doc/proof-teal-study.html |only inst/doc/theme-lab.R | 42 inst/doc/theme-lab.Rmd | 167 inst/doc/theme-lab.html | 1891 ++++++++- inst/doc/theme-showcase.R | 97 inst/doc/theme-showcase.Rmd | 160 inst/doc/theme-showcase.html | 1934 ++++++++-- inst/fonts |only inst/pkgdown/assets/albers.css | 429 +- inst/pkgdown/assets/albers.js | 2 inst/pkgdown/assets/fonts |only inst/rmarkdown/templates/albers_vignette/skeleton/albers-header.html |only inst/rmarkdown/templates/albers_vignette/skeleton/albers.css | 429 +- inst/rmarkdown/templates/albers_vignette/skeleton/fonts |only inst/rmarkdown/templates/albers_vignette/skeleton/skeleton.Rmd | 33 man/albers_bs_theme.Rd | 2 man/albers_presets.Rd | 12 man/albers_register_fonts.Rd |only man/dot-albers_direction_font.Rd |only man/dot-albers_font_available.Rd |only man/dot-preset_colors.Rd | 6 man/gt_albers.Rd | 2 man/migrate_albersdown.Rd | 2 man/theme_albers.Rd | 15 man/theme_albers_void.Rd | 15 man/use_albers_vignettes.Rd | 8 man/use_albersdown.Rd | 12 tests/testthat/test-migrate-albersdown.R | 408 ++ vignettes/albers-header.html |only vignettes/albers.css | 429 +- vignettes/albers.js | 33 vignettes/design-notes.Rmd | 49 vignettes/fonts |only vignettes/getting-started.Rmd | 48 vignettes/interaction.Rmd |only vignettes/proof-ochre-structural.Rmd |only vignettes/proof-teal-study.Rmd |only vignettes/theme-lab.Rmd | 167 vignettes/theme-showcase.Rmd | 160 64 files changed, 9386 insertions(+), 1540 deletions(-)
Title: Detect Population Structure Within Phylogenetic Trees
Description: Algorithms for detecting population structure from the history of
coalescent events recorded in phylogenetic trees. This method classifies each
tip and internal node of a tree into disjoint sets characterized by similar
coalescent patterns.
Author: Erik Volz [aut, cre] ,
Fabricia F. Nascimento [ctb] ,
Vinicius B. Franceschi [ctb]
Maintainer: Erik Volz <erik.volz@gmail.com>
Diff between treestructure versions 0.7.0 dated 2025-09-27 and 1.0.1 dated 2026-07-05
DESCRIPTION | 15 - MD5 | 56 +++--- NEWS.md |only R/RcppExports.R | 4 R/m13.R | 262 ++++++++++++++++++++++++----- build/vignette.rds |binary inst/doc/false_discovery_rate.R |only inst/doc/false_discovery_rate.Rmd |only inst/doc/false_discovery_rate.html |only inst/doc/supportValues.R | 86 +++++---- inst/doc/supportValues.Rmd | 169 ++++++++++--------- inst/doc/supportValues.html | 302 +++++++++++++++++++--------------- inst/doc/treestructure.R | 24 +- inst/doc/treestructure.Rmd | 129 +++++++++----- inst/doc/treestructure.html | 306 ++++++++++++++++++++++------------- inst/doc/updating_treestructure.Rmd | 5 inst/doc/updating_treestructure.html | 78 +++++--- inst/trestruct_chindex.rds |binary inst/trestruct_res.rds |binary inst/trestruct_res_nobt.rds |binary inst/trestruct_res_nobt_mcs20.rds |only inst/vignette_fwer.rds |only inst/vignette_hetero.rds |only man/treestructure.test.Rd | 10 - man/trestruct.Rd | 75 +++++++- src/RcppExports.cpp | 13 + src/uv_ranksum_moments.cpp |only src/uv_ranksum_nulldist0.cpp | 60 +++--- tests |only vignettes/false_discovery_rate.Rmd |only vignettes/supportValues.Rmd | 169 ++++++++++--------- vignettes/treestructure.Rmd | 129 +++++++++----- vignettes/updating_treestructure.Rmd | 5 33 files changed, 1217 insertions(+), 680 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features like
the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
mikefc [cph] ,
Yann Collet [cph] ,
Posit, PBC [cph, fnd]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between rlang versions 1.2.0 dated 2026-04-06 and 1.3.0 dated 2026-07-05
DESCRIPTION | 43 MD5 | 345 ++-- NEWS.md | 10 R/hash.R | 31 R/nse-inject.R | 3 R/utils.R | 3 man/abort.Rd | 2 man/are_na.Rd | 2 man/as_name.Rd | 4 man/as_string.Rd | 2 man/box.Rd | 2 man/call2.Rd | 2 man/check_data_frame.Rd | 4 man/check_dots_empty.Rd | 6 man/check_dots_unnamed.Rd | 6 man/check_dots_used.Rd | 6 man/check_type_number.Rd | 6 man/check_type_scalar.Rd | 6 man/cnd_muffle.Rd | 8 man/defusing-advanced.Rd | 2 man/dot-data.Rd | 2 man/englue.Rd | 3 man/env_bind.Rd | 2 man/env_get.Rd | 2 man/hash.Rd | 29 man/inherits_any.Rd | 2 man/is_function.Rd | 2 man/is_integerish.Rd | 2 man/missing.Rd | 13 man/names_inform_repair.Rd | 2 man/new_function.Rd | 2 man/new_node.Rd | 2 man/ns_env.Rd | 2 man/return_from.Rd | 2 man/rlang-package.Rd | 1 man/splice-operator.Rd | 4 man/stop_input_type.Rd | 4 man/switch_type.Rd | 2 man/topic-condition-formatting.Rd | 2 man/try_fetch.Rd | 2 man/vector-coercion.Rd | 2 man/with_env.Rd | 2 src/capture.c | 27 src/internal/arg.c | 505 +++--- src/internal/ast-rotate.c | 478 ++--- src/internal/ast-rotate.h | 50 src/internal/attr.c | 404 ++-- src/internal/call.c | 425 ++--- src/internal/call.h | 1 src/internal/cnd-handlers.c | 145 - src/internal/cnd.c | 381 ++-- src/internal/decl/arg-decl.h | 20 src/internal/decl/ast-rotate-decl.h | 26 src/internal/decl/attr-decl.h | 36 src/internal/decl/call-decl.h | 27 src/internal/decl/cnd-decl.h | 22 src/internal/decl/cnd-handlers-decl.h | 3 src/internal/decl/dots-decl.h | 29 src/internal/decl/encoding-decl.h | 18 src/internal/decl/env-binding-decl.h | 13 src/internal/decl/hash-decl.h | 10 src/internal/decl/names-decl.h | 21 src/internal/decl/standalone-types-check-decl.h | 30 src/internal/decl/vec-decl.h | 14 src/internal/dots-ellipsis.c | 60 src/internal/dots.c | 2003 ++++++++++++------------ src/internal/dots.h | 51 src/internal/encoding.c | 219 +- src/internal/env-binding.c | 599 +++---- src/internal/env.c | 89 - src/internal/eval-tidy.c | 906 +++++----- src/internal/eval.c | 35 src/internal/exported.c | 1239 +++++++------- src/internal/file.c | 46 src/internal/fn.c | 40 src/internal/globals.c | 2 src/internal/globals.h | 4 src/internal/hash.c | 584 ++++-- src/internal/internal.c | 769 +++++---- src/internal/internal.h | 45 src/internal/names.c | 320 +-- src/internal/nse-defuse.c | 11 src/internal/nse-inject.c | 630 +++---- src/internal/nse-inject.h | 80 src/internal/parse.c | 969 ++++++----- src/internal/parse.h | 130 - src/internal/quo.c | 109 - src/internal/quo.h | 7 src/internal/replace-na.c | 400 ++-- src/internal/squash.c | 551 +++--- src/internal/squash.h | 9 src/internal/standalone-types-check.c | 327 +-- src/internal/sym-unescape.c | 274 +-- src/internal/tests.c | 151 - src/internal/utils.c | 338 ++-- src/internal/utils.h | 29 src/internal/vec-raw.c | 83 src/internal/vec.c | 343 ++-- src/internal/vec.h | 36 src/internal/weakref.c | 33 src/rlang/arg.c | 14 src/rlang/arg.h | 11 src/rlang/attrib.c | 56 src/rlang/attrib.h | 54 src/rlang/c-utils.c | 42 src/rlang/c-utils.h | 220 +- src/rlang/call.c | 87 - src/rlang/call.h | 2 src/rlang/cnd.c | 225 +- src/rlang/cnd.h | 90 - src/rlang/debug.c | 29 src/rlang/debug.h | 1 src/rlang/decl/df-decl.h | 6 src/rlang/decl/dict-decl.h | 27 src/rlang/decl/dyn-list-of-decl.h | 10 src/rlang/decl/env-decl.h | 27 src/rlang/decl/obj-decl.h | 12 src/rlang/decl/walk-decl.h | 65 src/rlang/df.c | 86 - src/rlang/df.h | 12 src/rlang/dict.c | 462 ++--- src/rlang/dict.h | 37 src/rlang/dots-info.c | 36 src/rlang/dyn-array.c | 193 +- src/rlang/dyn-array.h | 344 ++-- src/rlang/dyn-list-of.c | 398 ++-- src/rlang/dyn-list-of.h | 86 - src/rlang/env-binding.c | 377 ++-- src/rlang/env-binding.h | 29 src/rlang/env.c | 398 ++-- src/rlang/env.h | 98 - src/rlang/eval.c | 265 +-- src/rlang/eval.h | 370 ++-- src/rlang/export.c | 12 src/rlang/export.h | 19 src/rlang/fn.c | 48 src/rlang/fn.h | 75 src/rlang/formula.c | 137 - src/rlang/formula.h | 1 src/rlang/globals.c | 158 - src/rlang/globals.h | 141 - src/rlang/node.c | 104 - src/rlang/node.h | 118 - src/rlang/obj.c | 198 +- src/rlang/obj.h | 138 - src/rlang/parse.c | 39 src/rlang/parse.h | 1 src/rlang/quo.c | 12 src/rlang/quo.h | 1 src/rlang/rlang-types.h | 210 +- src/rlang/rlang.c | 146 - src/rlang/rlang.h | 22 src/rlang/session.c | 84 - src/rlang/session.h | 1 src/rlang/stack.c | 113 - src/rlang/stack.h | 6 src/rlang/state.h | 19 src/rlang/sym.c | 69 src/rlang/sym.h | 16 src/rlang/vec-chr.c | 102 - src/rlang/vec-chr.h | 47 src/rlang/vec-lgl.c | 163 - src/rlang/vec-lgl.h | 2 src/rlang/vec.c | 457 ++--- src/rlang/vec.h | 844 ++++------ src/rlang/vendor.c | 3 src/rlang/vendor.h | 2 src/rlang/walk.c | 835 +++++----- src/rlang/walk.h | 186 +- src/version.c | 4 tests/testthat/_snaps/c-api.md | 4 tests/testthat/_snaps/hash.md |only tests/testthat/test-env-binding.R | 15 tests/testthat/test-hash.R | 314 +++ 174 files changed, 12303 insertions(+), 11517 deletions(-)
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
<doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
JJ Allaire [aut] ,
Kevin Ushey [aut] ,
Qiang Kou [aut] ,
Nathan Russell [aut],
Inaki Ucar [aut] ,
Doug Bates [aut] ,
John Chambers [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 1.1.1-1.1 dated 2026-04-24 and 1.1.2 dated 2026-07-05
ChangeLog | 243 +++++++++- DESCRIPTION | 9 MD5 | 122 ++--- R/Attributes.R | 20 R/RcppLdpath.R | 6 README.md | 8 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 64 ++ inst/bib/Rcpp.bib | 69 +- inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-jss-2011.pdf |binary inst/doc/Rcpp-libraries.pdf |binary inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.pdf |binary inst/include/Rcpp/DataFrame.h | 9 inst/include/Rcpp/Environment.h | 5 inst/include/Rcpp/Function.h | 13 inst/include/Rcpp/Nullable.h | 19 inst/include/Rcpp/Promise.h | 3 inst/include/Rcpp/api/meat/Rcpp_eval.h | 2 inst/include/Rcpp/config.h | 11 inst/include/Rcpp/date_datetime/Datetime.h | 7 inst/include/Rcpp/exceptions.h | 13 inst/include/Rcpp/exceptions_impl.h | 34 + inst/include/Rcpp/internal/r_vector.h | 18 inst/include/Rcpp/proxy/AttributeProxy.h | 18 inst/include/Rcpp/proxy/NamesProxy.h | 23 inst/include/Rcpp/sugar/functions/cumprod.h | 13 inst/include/Rcpp/sugar/functions/cumsum.h | 5 inst/include/Rcpp/sugar/functions/diff.h | 11 inst/include/Rcpp/sugar/functions/max.h | 15 inst/include/Rcpp/sugar/functions/min.h | 15 inst/include/Rcpp/sugar/functions/rowSums.h | 184 ++----- inst/include/Rcpp/sugar/functions/sum.h | 7 inst/include/Rcpp/sugar/operators/Comparator_With_One_Value.h | 5 inst/include/Rcpp/sugar/operators/minus.h | 21 inst/include/Rcpp/sugar/operators/plus.h | 20 inst/include/Rcpp/sugar/operators/times.h | 19 inst/include/Rcpp/sugar/sugar.h | 4 inst/include/Rcpp/sugar/tools/safe_math.h |only inst/include/Rcpp/vector/ListOf.h | 9 inst/include/Rcpp/vector/Vector.h | 15 inst/tinytest/cpp/ListOf.cpp | 10 inst/tinytest/cpp/Vector.cpp | 16 inst/tinytest/cpp/attributes_extended.cpp |only inst/tinytest/cpp/sugar.cpp | 92 +++ inst/tinytest/cpp/sugar_safe_math.cpp |only inst/tinytest/cpp/sugar_safe_math_fallback.cpp |only inst/tinytest/test_attributes_extended.R |only inst/tinytest/test_compile_attributes_errors.R |only inst/tinytest/test_cppfunction_errors.R |only inst/tinytest/test_dataframe.R | 10 inst/tinytest/test_global_rostream.R | 2 inst/tinytest/test_listof.R | 12 inst/tinytest/test_misc.R | 2 inst/tinytest/test_sourcecpp_errors.R |only inst/tinytest/test_sugar.R | 88 +++ inst/tinytest/test_vector.R | 13 src/attributes.cpp | 16 tests/tinytest.R | 3 66 files changed, 899 insertions(+), 424 deletions(-)
Title: Calculates Bond Values and Interest Rate Curves for Finance
Description: Values different types of assets and calibrates discount curves
for quantitative financial analysis. It covers fixed coupon assets,
floating note assets, interest and cross currency swaps with different
payment frequencies. Enables the calibration of spot, instantaneous forward
and basis curves, making it a powerful tool for accurate and flexible bond
valuation and curve generation. The valuation and calibration techniques
presented here are consistent with industry standards and incorporates
author's own calculations. Tuckman, B., Serrat, A. (2022, ISBN: 978-1-119-83555-4).
Author: Camilo Diaz [aut, cre, com],
Andres Galeano [aut],
Julian Rojas [aut],
Quantil S.A.S [aut, cph]
Maintainer: Camilo Diaz <kamodiaz@gmail.com>
This is a re-admission after prior archival of version 0.3.2 dated 2025-07-06
Diff between QuantBondCurves versions 0.3.2 dated 2025-07-06 and 0.3.3 dated 2026-07-05
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/bondValuation.R | 6 +++--- man/valuation.bonds.Rd | 4 ++-- man/valuation.swaps.Rd | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-)
More information about QuantBondCurves at CRAN
Permanent link
Title: Draws Overview of Outliers (O3) Plots
Description: Potential outliers are identified for all combinations of a dataset's variables. O3 plots are described in Unwin(2019) <doi:10.1080/10618600.2019.1575226>. The available methods are FastPCS() from the package 'FastPCS', mvBACON() from 'robustX', adjOutlyingness() from 'robustbase', DectectDeviatingCells() from 'cellWise', covMcd() from 'robustbase'.
Author: Antony Unwin [aut, cre, cph]
Maintainer: Antony Unwin <unwin@math.uni-augsburg.de>
Diff between OutliersO3 versions 0.6.3 dated 2020-04-24 and 0.7 dated 2026-07-05
DESCRIPTION | 19 - MD5 | 67 +++-- NAMESPACE | 2 NEWS | 4 NEWS.md |only R/O3a.R | 23 -- R/O3plotM.R | 9 R/O3plotT.R | 8 R/O3prep.R | 11 README.md | 13 - build/vignette.rds |binary inst/doc/DrawingO3plots.R | 8 inst/doc/DrawingO3plots.Rmd | 34 +-- inst/doc/DrawingO3plots.html | 350 ++++++++++++++++++++----------- inst/doc/MultTolLevels.R | 15 - inst/doc/MultTolLevels.Rmd | 27 -- inst/doc/MultTolLevels.html | 311 ++++++++++++++++----------- inst/doc/PCPsO3.R | 9 inst/doc/PCPsO3.Rmd | 13 - inst/doc/PCPsO3.html | 276 ++++++++++++++---------- inst/doc/xtraO3methods.R | 2 inst/doc/xtraO3methods.Rmd | 6 inst/doc/xtraO3methods.html | 238 +++++++++++++-------- man/Election2005.Rd | 2 man/O3plotColours.Rd | 2 man/O3plotM.Rd | 6 man/O3plotT.Rd | 2 man/O3prep.Rd | 17 - man/OutliersO3.Rd | 6 man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary vignettes/DrawingO3plots.Rmd | 34 +-- vignettes/MultTolLevels.Rmd | 27 -- vignettes/PCPsO3.Rmd | 13 - vignettes/xtraO3methods.Rmd | 6 35 files changed, 905 insertions(+), 655 deletions(-)
Title: Lag Penalized Weighted Correlation for Time Series Clustering
Description: Computes a time series distance measure for clustering based on weighted correlation and introduction of lags. The lags capture delayed responses in a time series dataset. The timepoints must be specified. T. Chandereng, A. Gitter (2020) <doi:10.1186/s12859-019-3324-1>.
Author: Thevaa Chandereng [aut, cre, cph] ,
Anthony Gitter [aut, cph]
Maintainer: Thevaa Chandereng <thevaasiinen@gmail.com>
This is a re-admission after prior archival of version 1.0.0 dated 2020-01-23
Diff between LPWC versions 1.0.0 dated 2020-01-23 and 1.0.1 dated 2026-07-05
DESCRIPTION | 17 +++--- MD5 | 14 ++--- NEWS.md | 8 +++ README.md | 4 - build/vignette.rds |binary inst/CITATION | 2 inst/doc/LPWC.R | 140 ++++++++++++++++++++++++++--------------------------- inst/doc/LPWC.html | 130 +++++++++++++++++++++++++++++-------------------- 8 files changed, 176 insertions(+), 139 deletions(-)
Title: Bridging Log-Odds Ratios and Correspondence Analysis via
Closeness-of-Concordance Measures
Description: Provides a unified analytical workflow that bridges conventional
binary and multinomial logistic regression with singly-ordered (SONSCA)
and doubly-ordered (DONSCA) nonsymmetric correspondence analysis.
Log-odds ratios (LORs) from logistic regression are re-expressed as
cosine theta estimates and closeness-of-concordance measures (CCMs) --
including Yule's Q, Yule's Y, and r_meta -- on the familiar [-1, +1]
scale introduced by Kim and Grochowalski (2019)
<doi:10.1007/s00357-018-9277-7>. Bootstrap confidence intervals for
cosine theta are provided throughout. The package is intended to help
clinical and medical researchers interpret association strength from
logistic regression in an intuitive, correlation-like metric, and to
connect conventional regression results with geometric correspondence
analysis visualisations.
Author: Se-Kang Kim [aut, cre]
Maintainer: Se-Kang Kim <se-kang.kim@bcm.edu>
Diff between lorbridge versions 0.1.0 dated 2026-04-21 and 0.1.1 dated 2026-07-05
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction.html | 4 ++-- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Draw Gene Arrow Maps in 'ggplot2'
Description: A 'ggplot2' extension for drawing gene arrow maps.
Author: David Wilkins [aut, cre],
Zachary Kurtz [ctb]
Maintainer: David Wilkins <david@wilkox.org>
Diff between gggenes versions 0.6.0 dated 2025-12-14 and 0.7.0 dated 2026-07-05
DESCRIPTION | 28 MD5 | 109 +- NAMESPACE | 7 NEWS.md | 52 + R/compose_grob.R |only R/data.R | 2 R/geom_feature.R | 184 ++-- R/geom_feature_label.R | 209 +--- R/geom_gene_arrow.R | 191 ++-- R/geom_gene_label.R | 153 +-- R/geom_subgene_arrow.R | 450 +++------- R/geom_subgene_label.R | 134 +- R/geom_terminator.R | 125 +- R/geom_terminator_label.R | 209 +--- R/gggenes-package.R | 1 R/make_alignment_dummies.R | 81 + R/theme_genes.R | 56 - R/utilities.R | 350 ++----- README.md | 15 build/vignette.rds |binary inst/WORDLIST | 16 inst/doc/introduction-to-gggenes.html | 6 man/figures/README-geom_gene_arrow-1.png |binary man/figures/README-labelled_genes-1.png |binary man/figures/README-make_alignment_dummies-1.png |binary man/figures/README-reversing_direction-1.png |binary man/figures/README-subgene_labels-1.png |binary man/figures/README-subgenes-1.png |binary man/figures/README-theme_genes-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/geom_feature.Rd | 8 man/geom_feature_label.Rd | 16 man/geom_gene_label.Rd | 4 man/geom_subgene_label.Rd | 4 man/geom_terminator.Rd | 6 man/geom_terminator_label.Rd | 12 man/gggenes-package.Rd | 5 tests/testthat/Rplots.pdf |only tests/testthat/_snaps/feature/geom-feature-and-geom-feature-label-in-polar-coordinates.svg | 48 - tests/testthat/_snaps/feature/oriented-feature-labels-in-polar-coordinates.svg |only tests/testthat/_snaps/gene_arrow/gene-arrow-and-label-in-cartesian-coordinates.svg | 168 +-- tests/testthat/_snaps/gene_arrow/gene-arrow-and-label-in-flipped-coordinates.svg | 168 +-- tests/testthat/_snaps/gene_arrow/gene-arrow-and-label-in-polar-coordinates.svg | 60 - tests/testthat/_snaps/subgene_arrow/subgene-arrow-and-label-in-cartesian-coordinates.svg | 310 +++--- tests/testthat/_snaps/subgene_arrow/subgene-arrow-and-label-in-flipped-coordinates.svg | 310 +++--- tests/testthat/_snaps/subgene_arrow/subgene-arrow-in-polar-coordinates.svg |only tests/testthat/_snaps/subgene_arrow/subgene-label-in-polar-coordinates.svg |only tests/testthat/_snaps/terminator/terminator-and-label-in-polar-coordinates.svg | 40 tests/testthat/helpers.R | 106 ++ tests/testthat/test-compose_grob.R |only tests/testthat/test-feature.R | 245 ++++- tests/testthat/test-gene_arrow.R | 126 ++ tests/testthat/test-make_alignment_dummies.R | 115 ++ tests/testthat/test-reverse_strand.R |only tests/testthat/test-subgene_arrow.R | 269 +++++ tests/testthat/test-terminator.R | 144 ++- tests/testthat/test-utilities.R |only vignettes/articles |only 60 files changed, 2536 insertions(+), 2006 deletions(-)
Title: Object-Oriented Implementation of Dose Escalation Designs
Description: Implements a wide range of dose escalation
designs. The focus is on model-based designs, ranging from classical and
modern continual reassessment methods (CRMs) based on dose-limiting toxicity
endpoints to dual-endpoint designs taking into account a biomarker/efficacy
outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy
to setup a new design with custom JAGS code. However, it is also possible to
implement 3+3 designs for comparison or models with non-Bayesian estimation.
The whole package is written in a modular form in the S4 class system, making it
very flexible for adaptation to new models, escalation or stopping rules.
Further details are presented in
Sabanés Bové et al. (2019) <doi:10.18637/jss.v089.i10>.
Author: Daniel Sabanes Bove [aut, cre] ,
Wai Yin Yeung [aut],
Burak Kuersad Guenhan [aut],
Giuseppe Palermo [aut],
Thomas Jaki [aut],
Jiawen Zhu [aut],
Ziwei Liao [aut],
Dimitris Kontos [aut],
Marlene Schulte-Goebel [aut],
Doug Kelkhoff [aut] ,
Oliver Boix [ [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between crmPack versions 2.1.0 dated 2026-01-30 and 2.2.0 dated 2026-07-05
crmPack-2.1.0/crmPack/inst/doc/ordinal-crm.R |only crmPack-2.1.0/crmPack/inst/doc/parallel_computing_with_extensions.R |only crmPack-2.1.0/crmPack/inst/doc/simulations.R |only crmPack-2.1.0/crmPack/inst/doc/tidy_method.R |only crmPack-2.1.0/crmPack/inst/doc/trial_analysis.R |only crmPack-2.1.0/crmPack/inst/doc/trial_backfill.R |only crmPack-2.1.0/crmPack/inst/doc/trial_backfill.pdf |only crmPack-2.1.0/crmPack/inst/doc/trial_definition.R |only crmPack-2.1.0/crmPack/inst/doc/trial_simulation.R |only crmPack-2.1.0/crmPack/inst/doc/upgrading_from_the_old_crmPack.R |only crmPack-2.1.0/crmPack/vignettes/trial_backfill.html |only crmPack-2.2.0/crmPack/DESCRIPTION | 37 crmPack-2.2.0/crmPack/MD5 | 614 +- crmPack-2.2.0/crmPack/NAMESPACE | 134 crmPack-2.2.0/crmPack/NEWS.md | 13 crmPack-2.2.0/crmPack/R/Backfill-class.R | 5 crmPack-2.2.0/crmPack/R/Backfill-methods.R | 24 crmPack-2.2.0/crmPack/R/Backfill-validity.R | 14 crmPack-2.2.0/crmPack/R/Data-class.R | 270 crmPack-2.2.0/crmPack/R/Data-methods.R | 626 ++ crmPack-2.2.0/crmPack/R/Data-validity.R | 165 crmPack-2.2.0/crmPack/R/Design-class.R | 167 crmPack-2.2.0/crmPack/R/Design-methods.R | 541 + crmPack-2.2.0/crmPack/R/Design-validity.R | 43 crmPack-2.2.0/crmPack/R/HierarchicalDesign-class.R |only crmPack-2.2.0/crmPack/R/HierarchicalDesign-methods.R |only crmPack-2.2.0/crmPack/R/HierarchicalDesign-validity.R |only crmPack-2.2.0/crmPack/R/HierarchicalModel-class.R |only crmPack-2.2.0/crmPack/R/Model-class.R | 277 crmPack-2.2.0/crmPack/R/Model-methods.R | 428 + crmPack-2.2.0/crmPack/R/Model-validity.R | 376 + crmPack-2.2.0/crmPack/R/Rules-class.R | 116 crmPack-2.2.0/crmPack/R/Rules-methods.R | 465 + crmPack-2.2.0/crmPack/R/Rules-validity.R | 13 crmPack-2.2.0/crmPack/R/Samples-class.R | 61 crmPack-2.2.0/crmPack/R/Samples-methods.R | 559 + crmPack-2.2.0/crmPack/R/Samples-validity.R | 48 crmPack-2.2.0/crmPack/R/Simulations-class.R | 536 + crmPack-2.2.0/crmPack/R/Simulations-methods.R | 1027 +++ crmPack-2.2.0/crmPack/R/Simulations-validity.R | 98 crmPack-2.2.0/crmPack/R/TwoDrugsCombo-class.R |only crmPack-2.2.0/crmPack/R/crmPack-package.R | 15 crmPack-2.2.0/crmPack/R/fromQuantiles.R | 87 crmPack-2.2.0/crmPack/R/helpers.R | 27 crmPack-2.2.0/crmPack/R/helpers_backfill.R | 26 crmPack-2.2.0/crmPack/R/helpers_jags.R | 11 crmPack-2.2.0/crmPack/R/helpers_knitr_Design.R | 70 crmPack-2.2.0/crmPack/R/helpers_knitr_GeneralData.R | 74 crmPack-2.2.0/crmPack/R/helpers_knitr_GeneralModel.R | 223 crmPack-2.2.0/crmPack/R/helpers_knitr_Increments.R | 56 crmPack-2.2.0/crmPack/R/helpers_rules.R | 37 crmPack-2.2.0/crmPack/R/mcmc.R | 199 crmPack-2.2.0/crmPack/build/partial.rdb |binary crmPack-2.2.0/crmPack/build/vignette.rds |binary crmPack-2.2.0/crmPack/inst/WORDLIST | 28 crmPack-2.2.0/crmPack/inst/doc/combo_designs.Rmd |only crmPack-2.2.0/crmPack/inst/doc/combo_designs.html |only crmPack-2.2.0/crmPack/inst/doc/comparison_decider.Rmd |only crmPack-2.2.0/crmPack/inst/doc/comparison_decider.html 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crmPack-2.2.0/crmPack/vignettes/vignettes.bib | 16 366 files changed, 18365 insertions(+), 4860 deletions(-)
Title: Search Download and Handle Data from Copernicus Marine Service
Information
Description: Subset and download data from EU Copernicus Marine
Service Information: <https://data.marine.copernicus.eu>.
Import data on the oceans physical and biogeochemical state
from Copernicus into R without the need of external software.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between CopernicusMarine versions 0.4.6 dated 2026-04-07 and 0.4.7 dated 2026-07-05
DESCRIPTION | 14 - MD5 | 85 +++--- NAMESPACE | 1 NEWS.md | 9 R/cms_catalogue_entry.R | 41 +-- R/cms_cite_product.r | 47 +-- R/cms_download_native.R | 501 ++++++++++++++++++++++------------------ R/cms_download_subset.r | 6 R/cms_glossary.R | 1 R/cms_login.r | 265 ++++++++++----------- R/cms_product_details.r | 73 ++--- R/cms_product_metadata.r | 65 ++--- R/cms_product_services.r | 79 +++--- R/cms_products_list.r | 204 ++++++++-------- R/cms_wmts.r | 3 R/translate.R | 251 ++++++++++---------- README.md | 2 build/vignette.rds |binary inst/doc/glossary.R | 30 +- inst/doc/glossary.Rmd | 32 +- inst/doc/glossary.html | 6 inst/doc/product-info.html | 2 inst/doc/proxy.html | 2 inst/doc/translate.html | 4 inst/glossary.rdata |binary man/CopernicusMarine-package.Rd | 7 man/account.Rd | 5 man/cms_cite_product.Rd | 12 man/cms_download_native.Rd | 16 + man/cms_download_subset.Rd | 10 man/cms_get_client_info.Rd | 6 man/cms_glossary.Rd | 6 man/cms_login.Rd | 5 man/cms_native_proxy.Rd | 10 man/cms_native_s3.Rd |only man/cms_product_details.Rd | 12 man/cms_product_metadata.Rd | 9 man/cms_product_services.Rd | 12 man/cms_products_list.Rd | 12 man/cms_translate.Rd | 8 man/cms_wmts.Rd | 5 man/cms_zarr_proxy.Rd | 10 tests/testthat/test_native.r | 144 +++++------ vignettes/glossary.Rmd | 32 +- 44 files changed, 1121 insertions(+), 923 deletions(-)
More information about CopernicusMarine at CRAN
Permanent link
Title: Identifying Unique Multilocus Genotypes where Genotyping Error
and Missing Data may be Present
Description: Tools for the identification of unique multilocus genotypes when
both genotyping error and missing data may be present. Includes a data
pre-screening utility to analyze pairwise locus overlap and protect against
underlying mathematical sorting constraints. Targeted for use with large
datasets and databases containing multiple samples of each individual (a common
situation in conservation genetics, particularly in non-invasive wildlife
sampling applications). Functions explicitly incorporate missing data and can
tolerate allele mismatches created by genotyping error. If you use this package,
please cite the original publication in Molecular Ecology Resources (Galpern
et al., 2012), the details for which can be generated using
citation('allelematch'). The complete user manual and analytical tutorials
are included locally as an R vignette and can be accessed within an active R
session using vignette('allelematch').
Author: Paul Galpern [aut],
Micheline Manseau [aut],
Pete Hettinga [aut],
Karen Smith [aut],
Paul Wilson [aut],
Todd Cross [cre]
Maintainer: Todd Cross <todd.cross@gmail.com>
Diff between allelematch versions 2.5.5 dated 2025-07-26 and 2.6.0 dated 2026-07-05
allelematch-2.5.5/allelematch/build/partial.rdb |only allelematch-2.6.0/allelematch/DESCRIPTION | 28 allelematch-2.6.0/allelematch/MD5 | 22 allelematch-2.6.0/allelematch/NAMESPACE | 29 allelematch-2.6.0/allelematch/R/allelematch.r | 4606 +++++---------- allelematch-2.6.0/allelematch/build/vignette.rds |only allelematch-2.6.0/allelematch/data/amExample5.RData |binary allelematch-2.6.0/allelematch/inst/doc |only allelematch-2.6.0/allelematch/man/allelematch-package.Rd | 120 allelematch-2.6.0/allelematch/man/amPreCheck.Rd |only allelematch-2.6.0/allelematch/vignettes |only 11 files changed, 1711 insertions(+), 3094 deletions(-)
Title: Linear Innovations State Space Unobserved Components Model
Description: Unobserved components time series model using the linear innovations state space representation (single source of error) with choice of error distributions and option for dynamic variance. Methods for estimation using automatic differentiation, automatic model selection and ensembling, prediction, filtering, simulation and backtesting. Based on the model described in Hyndman et al (2012) <doi:10.1198/jasa.2011.tm09771>.
Author: Alexios Galanos [aut, cre]
Maintainer: Alexios Galanos <alexios@4dscape.com>
Diff between tsissm versions 1.0.2 dated 2025-07-12 and 1.0.3 dated 2026-07-05
DESCRIPTION | 6 - MD5 | 36 ++++---- NAMESPACE | 1 NEWS.md | 22 +++++ R/capabilities.R |only R/constraint.R | 103 ++++++++++++++++++++++++ R/estimation.R | 9 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/demo_ensembling.R | 2 inst/doc/demo_ensembling.Rmd | 2 inst/doc/demo_ensembling.html | 149 ++++++++++------------------------- inst/doc/demo_filtering.html | 7 - inst/doc/demo_missing_data.html | 13 +-- inst/doc/demo_variance_dynamics.html | 58 ++++++------- inst/doc/issm_introduction.pdf |binary man/estimate.Rd | 9 +- man/tsissm_capabilities.Rd |only tests/longtests/test-backtest.R | 14 --- vignettes/demo_ensembling.Rmd | 2 20 files changed, 252 insertions(+), 181 deletions(-)
Title: Draw Treemaps in 'ggplot2'
Description: Provides 'ggplot2' geoms for drawing treemaps.
Author: David Wilkins [aut, cre] ,
Bob Rudis [ctb]
Maintainer: David Wilkins <david@wilkox.org>
Diff between treemapify versions 2.6.0 dated 2025-12-14 and 2.6.1 dated 2026-07-05
treemapify-2.6.0/treemapify/R/a-rect.R |only treemapify-2.6.1/treemapify/DESCRIPTION | 15 - treemapify-2.6.1/treemapify/MD5 | 47 ++--- treemapify-2.6.1/treemapify/NAMESPACE | 3 treemapify-2.6.1/treemapify/NEWS.md | 26 ++ treemapify-2.6.1/treemapify/R/geom_treemap_subgroup_border.R | 9 treemapify-2.6.1/treemapify/R/geom_treemap_subgroup_text.R | 9 treemapify-2.6.1/treemapify/R/treemap_fixed.R | 4 treemapify-2.6.1/treemapify/R/treemap_squarified.R | 4 treemapify-2.6.1/treemapify/R/treemapify-package.R | 2 treemapify-2.6.1/treemapify/R/treemapify.R | 48 ++++- treemapify-2.6.1/treemapify/README.md | 2 treemapify-2.6.1/treemapify/build/vignette.rds |binary treemapify-2.6.1/treemapify/inst/WORDLIST | 2 treemapify-2.6.1/treemapify/inst/doc/introduction-to-treemapify.html | 4 treemapify-2.6.1/treemapify/man/figures/animated_treemap.gif |binary treemapify-2.6.1/treemapify/man/geom_treemap_subgroup_border.Rd | 2 treemapify-2.6.1/treemapify/man/treemapify-ggproto.Rd | 2 treemapify-2.6.1/treemapify/man/treemapify-package.Rd | 6 treemapify-2.6.1/treemapify/man/treemapify.Rd | 18 + treemapify-2.6.1/treemapify/tests/testthat/test_G20.R | 2 treemapify-2.6.1/treemapify/tests/testthat/test_geoms.R | 71 +++++++ treemapify-2.6.1/treemapify/tests/testthat/test_layout_functions.R | 4 treemapify-2.6.1/treemapify/tests/testthat/test_plots.R | 2 treemapify-2.6.1/treemapify/tests/testthat/test_treemapify.R | 93 +++++++++- 25 files changed, 300 insertions(+), 75 deletions(-)
Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal, and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled. For regression versions of the methods, Monte Carlo and asymptotic methods are used.
Author: Ivair Ramos Silva [aut, cre],
Martin Kulldorff [aut]
Maintainer: Ivair Ramos Silva <ivair@ufop.edu.br>
Diff between Sequential versions 4.6.0 dated 2026-04-21 and 4.6.1 dated 2026-07-05
DESCRIPTION | 10 +- MD5 | 14 +- NAMESPACE | 3 R/Analyze.Multinomial.R | 187 ++++++++++++++++++++++++++-------------- R/AnalyzeSetUp.Multinomial.R | 7 - man/Analyze.Multinomial.Rd | 6 - man/AnalyzeSetUp.Multinomial.Rd | 5 - man/Sequential-package.Rd | 13 +- 8 files changed, 155 insertions(+), 90 deletions(-)
Title: A 'Shiny' Gadget for Interactive 'QRA' Visualizations
Description: Upload raster data and easily create interactive quantitative risk analysis 'QRA' visualizations. Select
from numerous color palettes, base-maps, and different configurations.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
Diff between QRAGadget versions 0.3.0 dated 2023-06-23 and 0.4 dated 2026-07-05
QRAGadget-0.3.0/QRAGadget/R/tableinput.R |only QRAGadget-0.3.0/QRAGadget/inst/images/InputOutput.png |only QRAGadget-0.3.0/QRAGadget/inst/images/map.png |only QRAGadget-0.3.0/QRAGadget/inst/images/map2.png |only QRAGadget-0.3.0/QRAGadget/inst/images/preferences.png |only QRAGadget-0.3.0/QRAGadget/inst/images/raster.png |only QRAGadget-0.3.0/QRAGadget/inst/tableinput |only QRAGadget-0.3.0/QRAGadget/man/matrixInput.Rd |only QRAGadget-0.4/QRAGadget/DESCRIPTION | 30 +- QRAGadget-0.4/QRAGadget/MD5 | 35 +- QRAGadget-0.4/QRAGadget/NAMESPACE | 20 - QRAGadget-0.4/QRAGadget/NEWS.md | 26 + QRAGadget-0.4/QRAGadget/R/QRAGadget.R | 248 ++++++++++-------- QRAGadget-0.4/QRAGadget/README.md | 116 +++----- QRAGadget-0.4/QRAGadget/build |only QRAGadget-0.4/QRAGadget/inst/CITATION |only QRAGadget-0.4/QRAGadget/inst/doc |only QRAGadget-0.4/QRAGadget/inst/images/InputOutput.PNG |only QRAGadget-0.4/QRAGadget/inst/images/Map2.PNG |only QRAGadget-0.4/QRAGadget/inst/images/map.PNG |only QRAGadget-0.4/QRAGadget/inst/images/preferences.PNG |only QRAGadget-0.4/QRAGadget/inst/images/raster.PNG |only QRAGadget-0.4/QRAGadget/man/QRAGadget.Rd | 4 QRAGadget-0.4/QRAGadget/tests |only QRAGadget-0.4/QRAGadget/vignettes |only 25 files changed, 259 insertions(+), 220 deletions(-)
Title: Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Gaussian finite mixture models fitted via EM algorithm for
model-based clustering, classification, and density estimation,
including Bayesian regularization, dimension reduction for
visualisation, and resampling-based inference.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut] ,
Luca Scrucca [aut, cre] ,
Thomas Brendan Murphy [ctb] ,
Michael Fop [ctb]
Maintainer: Luca Scrucca <luca.scrucca@unibo.it>
Diff between mclust versions 6.1.2 dated 2025-10-31 and 6.1.3 dated 2026-07-05
DESCRIPTION | 8 ++-- MD5 | 25 ++++++------- NAMESPACE | 6 +++ NEWS.md | 7 +++ R/bootstrap.R | 2 - R/mclust.R | 20 +++++++--- R/mclustda.R | 2 - R/util.R | 37 +++++++++++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/mclust.html | 96 +++++++++++++++++++++++++-------------------------- man/hypvol.Rd | 2 - man/simulate.Rd |only src/mclust.f | 3 + 14 files changed, 135 insertions(+), 73 deletions(-)
Title: Fit Text Inside a Box in 'ggplot2'
Description: A 'ggplot2' extension to fit text into a box by growing, shrinking or wrapping the text.
Author: David Wilkins [aut, cre],
Brady Johnston [ctb]
Maintainer: David Wilkins <david@wilkox.org>
Diff between ggfittext versions 0.10.3 dated 2025-12-13 and 0.10.4 dated 2026-07-05
DESCRIPTION | 8 - MD5 | 63 ++++---- NEWS.md | 23 +++ R/data.R | 44 +++--- R/geom_bar_text.R | 47 +++--- R/geom_fit_text.R | 212 ++++++++++++++++++------------ README.md | 18 +- build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/introduction-to-ggfittext.R | 5 inst/doc/introduction-to-ggfittext.Rmd | 30 +++- inst/doc/introduction-to-ggfittext.html | 96 +++++++------ man/animals_rich.Rd | 2 man/figures/README-hero-1.png |binary man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-16-1.png |binary man/figures/README-unnamed-chunk-17-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/geom_fit_text.Rd | 39 +++-- man/ggfittext-package.Rd | 5 man/gold.Rd | 2 tests/testthat/Rplots.pdf |only tests/testthat/test-geom_bar_text.R | 103 ++++++++++++++ tests/testthat/test-geom_fit_text.R | 180 +++++++++++++++++++++++++ vignettes/introduction-to-ggfittext.Rmd | 30 +++- 33 files changed, 670 insertions(+), 239 deletions(-)
Title: Fuzzy C-Means for Fuzzy Data
Description: Implements a fuzzy clustering approach for ordinal Likert-type data
using triangular fuzzy numbers (TFNs). The package extends the classical
fuzzy C-means algorithm to better handle uncertainty in ordinal scales and
includes automatic selection of the number of clusters using the Xie-Beni
validity index. References: Coppi, R., D'Urso, P., and Giordani, P. (2012),
"Fuzzy and possibilistic clustering for fuzzy data", <doi:10.1016/j.csda.2010.09.013>. Xie, X. L. and Beni, G.
(1991), "A validity measure for fuzzy clustering", <doi:10.1109/34.85677>.
Author: Jose Ortigas [aut, cre]
Maintainer: Jose Ortigas <jose.ortigas@unmsm.edu.pe>
Diff between fcmfd versions 0.1.1 dated 2026-05-23 and 0.1.2 dated 2026-07-05
fcmfd-0.1.1/fcmfd/R/data_sim_likert_0_10.R |only fcmfd-0.1.1/fcmfd/R/prototype_matrix.R |only fcmfd-0.1.1/fcmfd/data/sim_likert_0_10.rda |only fcmfd-0.1.1/fcmfd/man/prototype_matrix.Rd |only fcmfd-0.1.1/fcmfd/man/sim_likert_0_10.Rd |only fcmfd-0.1.2/fcmfd/DESCRIPTION | 6 fcmfd-0.1.2/fcmfd/MD5 | 48 +- fcmfd-0.1.2/fcmfd/NAMESPACE | 6 fcmfd-0.1.2/fcmfd/NEWS.md | 13 fcmfd-0.1.2/fcmfd/R/cluster_size.R |only fcmfd-0.1.2/fcmfd/R/data_sim_likert7.R | 50 +- fcmfd-0.1.2/fcmfd/R/membership_quality.R |only fcmfd-0.1.2/fcmfd/R/plot_dictionary.R | 206 +++++++++- fcmfd-0.1.2/fcmfd/R/plot_prototypes.R | 388 ++++++++++++++++++-- fcmfd-0.1.2/fcmfd/R/plot_xb.R | 58 ++ fcmfd-0.1.2/fcmfd/R/prototype_results.R |only fcmfd-0.1.2/fcmfd/R/students_wellbeing.R |only fcmfd-0.1.2/fcmfd/README.md | 87 ++-- fcmfd-0.1.2/fcmfd/build/vignette.rds |binary fcmfd-0.1.2/fcmfd/data/students_wellbeing.rda |only fcmfd-0.1.2/fcmfd/inst/doc/fcmTFN-introduction.R | 8 fcmfd-0.1.2/fcmfd/inst/doc/fcmTFN-introduction.Rmd | 24 - fcmfd-0.1.2/fcmfd/inst/doc/fcmTFN-introduction.html | 104 +++-- fcmfd-0.1.2/fcmfd/man/cluster_size.Rd |only fcmfd-0.1.2/fcmfd/man/membership_quality.Rd |only fcmfd-0.1.2/fcmfd/man/plot_dictionary.Rd | 9 fcmfd-0.1.2/fcmfd/man/plot_prototypes.Rd | 13 fcmfd-0.1.2/fcmfd/man/plot_xb.Rd | 8 fcmfd-0.1.2/fcmfd/man/prototype_results.Rd |only fcmfd-0.1.2/fcmfd/man/sim_likert7.Rd | 51 +- fcmfd-0.1.2/fcmfd/man/students_wellbeing.Rd |only fcmfd-0.1.2/fcmfd/vignettes/fcmTFN-introduction.Rmd | 24 - 32 files changed, 841 insertions(+), 262 deletions(-)
Title: Download Spatial Datasets of Peru
Description: Provides access to official spatial datasets of Peru as 'sf'
objects in 'R'. Includes administrative boundaries from the National
Institute of Statistics and Informatics (INEI) <https://ide.inei.gob.pe/>
and protected natural areas from the National Service of Natural Areas
Protected by the State (SERNANP)
<https://www.gob.pe/institucion/sernanp/pages/21261-acceder-a-informacion-espacial-de-las-area-naturales-protegidas-visor-de-informacion-geografica>.
Harmonizes attributes, coordinate reference systems, and topology to
support consistent spatial analysis and visualization.
Author: Paul E. Santos Andrade [aut, cre, cph]
Maintainer: Paul E. Santos Andrade <paulefrens@gmail.com>
Diff between geoperu versions 0.0.0.2 dated 2024-04-01 and 0.0.1 dated 2026-07-05
geoperu-0.0.0.2/geoperu/man/check_connection.Rd |only geoperu-0.0.0.2/geoperu/man/check_connection_anp.Rd |only geoperu-0.0.0.2/geoperu/man/download_gpkg.Rd |only geoperu-0.0.0.2/geoperu/man/download_gpkg_anp.Rd |only geoperu-0.0.0.2/geoperu/man/download_metadata.Rd |only geoperu-0.0.0.2/geoperu/man/download_metadata_anp.Rd |only geoperu-0.0.0.2/geoperu/man/load_gpkg.Rd |only geoperu-0.0.0.2/geoperu/man/select_data_level.Rd |only geoperu-0.0.0.2/geoperu/man/select_data_type.Rd |only geoperu-0.0.0.2/geoperu/man/select_metadata.Rd |only geoperu-0.0.0.2/geoperu/man/select_metadata_anp.Rd |only geoperu-0.0.1/geoperu/DESCRIPTION | 25 geoperu-0.0.1/geoperu/LICENSE | 4 geoperu-0.0.1/geoperu/MD5 | 49 geoperu-0.0.1/geoperu/NAMESPACE | 8 geoperu-0.0.1/geoperu/NEWS.md |only geoperu-0.0.1/geoperu/R/distritos.R | 13 geoperu-0.0.1/geoperu/R/get_anp_peru.R | 150 + geoperu-0.0.1/geoperu/R/get_geo_peru.R | 138 + geoperu-0.0.1/geoperu/R/global.R | 68 geoperu-0.0.1/geoperu/R/utils.R | 780 ++-------- geoperu-0.0.1/geoperu/README.md | 128 + geoperu-0.0.1/geoperu/inst/CITATION | 20 geoperu-0.0.1/geoperu/inst/figures |only geoperu-0.0.1/geoperu/man/figures/README-unnamed-chunk-2-1.png |binary geoperu-0.0.1/geoperu/man/figures/README-unnamed-chunk-3-1.png |binary geoperu-0.0.1/geoperu/man/figures/logo.png |only geoperu-0.0.1/geoperu/man/get_anp_peru.Rd | 61 geoperu-0.0.1/geoperu/man/get_geo_peru.Rd | 90 - geoperu-0.0.1/geoperu/man/peru.Rd | 45 geoperu-0.0.1/geoperu/tests |only 31 files changed, 663 insertions(+), 916 deletions(-)