Title: Simplified Statistical Analysis with Plain-English
Interpretation
Description: A toolkit for common statistical analyses including descriptive statistics, Student's t-tests (one-sample, independent, and paired), one-way and two-way Analysis of Variance (ANOVA), Multivariate Analysis of Variance (MANOVA), chi-square tests, correlation analysis, simple and multiple linear regression, logistic regression, and non-parametric tests (Mann-Whitney U, Wilcoxon Signed Rank, and Kruskal-Wallis). Each function automatically interprets results in plain English, reporting effect sizes, confidence intervals, and p-value interpretations. Post-hoc tests are automatically applied following significant results. A master function automatically detects the appropriate test based on the structure of the input data. Methods are based on Cohen, J. (1988) <doi:10.4324/9780203771587>, Tukey, J. W. (1949) <doi:10.2307/3001913>, and Shapiro and Wilk (1965) <doi:10.2307/2333709>.
Author: Uwakmfon Paul [aut, cre, cph]
Maintainer: Uwakmfon Paul <uwakmfon31@gmail.com>
Diff between statease versions 1.1.0 dated 2026-05-16 and 1.2.0 dated 2026-06-02
DESCRIPTION | 14 +- MD5 | 35 ++++-- NAMESPACE | 23 ++++ NEWS.md | 2 R/analyze.R | 174 ++++++++++++++++++++++++-------- R/anova2_interpret.R | 230 +++++++++++++++++++++++++++---------------- R/logistic_interpret.R |only R/manova_interpret.R |only R/mlr_interpret.R |only R/nonparam_interpret.R |only R/statease-package.R | 3 README.md | 99 +++++++++++++++++- build |only inst |only man/analyze.Rd | 30 +++++ man/anova2_interpret.Rd | 10 + man/kruskal_interpret.Rd |only man/logistic_interpret.Rd |only man/mannwhitney_interpret.Rd |only man/manova_interpret.Rd |only man/mlr_interpret.Rd |only man/statease.Rd | 1 man/wilcoxon_interpret.Rd |only vignettes |only 24 files changed, 469 insertions(+), 152 deletions(-)
Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Tools for fitting self-validated ensemble models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) in small-sample design-of-experiments and related workflows, using elastic net and relaxed elastic net regression via 'glmnet' (Friedman et al. (2010) <doi:10.18637/jss.v033.i01>). Fractional random-weight bootstraps with anti-correlated validation copies are used to tune penalty paths by validation-weighted AIC/BIC. Supports Gaussian and binomial responses, deterministic expansion helpers for shared factor spaces, prediction with bootstrap uncertainty, and a random-search optimizer that respects mixture constraints and combines multiple responses via desirability functions. Also includes a permutation-based whole-model test for Gaussian SVEM fits (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). Package code was drafted with assistance from generative AI tools.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 3.2.0 dated 2026-01-23 and 3.2.1 dated 2026-06-02
DESCRIPTION | 10 ++--- MD5 | 17 +++++----- NEWS | 15 +++++--- R/SVEMnet.R | 28 ++++++++++------ R/glmnet_compat.R |only R/glmnet_with_cv.R | 83 ++++++++++++++++++++++++++++++------------------- build/partial.rdb |binary man/SVEMnet-package.Rd | 5 ++ man/SVEMnet.Rd | 4 +- man/glmnet_with_cv.Rd | 8 +++- 10 files changed, 106 insertions(+), 64 deletions(-)
Title: Likelihood-Based Inference for Joint Modeling of Correlated
Count and Binary Outcomes with Extra Variability and Zeros
Description: Inference approach for jointly modeling correlated count and binary outcomes. This formulation allows simultaneous modeling of zero inflation via the Bernoulli component while providing a more accurate assessment of the Hierarchical Zero-Inflated Poisson's parsimony (Lizandra C. Fabio, Jalmar M. F. Carrasco, Victor H. Lachos and Ming-Hui Chen, Likelihood-based inference for joint modeling of correlated count and binary outcomes with extra variability and zeros, 2026, under submission).
Author: Lizandra C. Fabio [aut],
Jalmar M. F. Carrasco [aut, cre],
Victor H. Lachos [aut],
Ming-Hui Chen [aut]
Maintainer: Jalmar M. F. Carrasco <carrasco.jalmar@ufba.br>
Diff between HZIP versions 0.1.1 dated 2025-12-19 and 0.1.2 dated 2026-06-02
DESCRIPTION | 10 MD5 | 34 +- NAMESPACE | 18 - R/RcppExports.R | 70 ++-- R/envelope.R | 111 +++++- R/generics.R |only R/hzip.R | 825 ++++++++++++++++++++++++++++++------------------- R/residuals.R | 391 +++++++++++++---------- R/simulate.R |only R/testDisp.R |only R/testZI.R |only R/utils.R | 58 +++ man/envelope.HZIP.Rd | 49 ++ man/hzip.Rd | 158 +++++++-- man/print.hzip_test.Rd |only man/residuals.HZIP.Rd | 89 ++++- man/simulate.HZIP.Rd |only man/testDisp.HZIP.Rd |only man/testDisp.Rd |only man/testZI.HZIP.Rd |only man/testZI.Rd |only src/HZIP.cpp | 527 ++++++++++++++++++++----------- src/RcppExports.cpp | 16 23 files changed, 1545 insertions(+), 811 deletions(-)
Title: Taxonomic Distance and Phylogenetic Lineage Computation
Description: Computes phylogenetic distances between any two taxa using
hierarchical lineage data retrieved from The Taxonomicon
<http://taxonomicon.taxonomy.nl>, a comprehensive curated classification
of all life based on Systema Naturae 2000 (Brands, 1989
<http://taxonomicon.taxonomy.nl>). Given any two taxon names, retrieves their
full lineages, identifies the most recent common ancestor (MRCA),
and computes a dissimilarity index based on lineage depth. Outputs
native dist objects, enabling direct integration with the R statistical
ecosystem for hierarchical clustering, principal coordinate analysis (PCoA),
and multivariate ecological analyses. Supports individual distance queries,
pairwise distance matrices, clade filtering, and lineage utilities.
Author: Rodrigo Fonseca Villa [aut, cre]
Maintainer: Rodrigo Fonseca Villa <rodrigo03.villa@gmail.com>
Diff between taxodist versions 0.4.0 dated 2026-05-25 and 0.5.0 dated 2026-06-02
DESCRIPTION | 9 +++--- MD5 | 26 ++++++++++++-------- NAMESPACE | 3 ++ NEWS.md | 18 +++++++++++++ R/data.R |only R/distance.R | 2 - R/fetch.R | 53 +++++++++++++++++++++++++++++------------ data |only inst/WORDLIST | 16 +++++++++++- inst/doc/introduction.Rmd | 4 --- inst/doc/introduction.html | 8 +++--- man/cache_info.Rd |only man/focal_distances.Rd |only man/print.taxodist_focal.Rd |only man/taxobase.Rd |only tests/testthat/test-distance.R | 38 ++++++++++++++++++++++++++++- vignettes/introduction.Rmd | 4 --- 17 files changed, 139 insertions(+), 42 deletions(-)
Title: Datasets and Utilities for Essentials of Statistics for the
Behavioral Sciences
Description: Provides instructional datasets and simple wrapper functions
for selected analyses used in 'Essentials of Statistics for the
Behavioral Sciences' (Gravetter et al., 2026).
The package is intended to support textbook examples by distributing
data in a form that is easy for students and instructors to access
within R. Current functionality includes packaged datasets and
convenience wrappers for functions from 'ez', 'pwr', and 'WebPower'
for analysis of variance and statistical power calculations.
Author: James Witnauer [aut, cre]
Maintainer: James Witnauer <jwitnaue@brockport.edu>
Diff between essentialstools versions 0.1.4 dated 2026-05-18 and 0.1.6 dated 2026-06-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++++--- R/SleepData.R |only build |only data/EVData.rda |binary data/SleepData.rda |only data/music.rda |binary man/SleepData.Rd |only 8 files changed, 10 insertions(+), 6 deletions(-)
More information about essentialstools at CRAN
Permanent link
Title: Client for Delphi's 'Epidata' API
Description: The Delphi 'Epidata' API provides real-time access to
epidemiological surveillance data for influenza, 'COVID-19', and other
diseases for the USA at various geographical resolutions, both from
official government sources such as the Center for Disease Control
(CDC) and Google Trends and private partners such as Facebook and
Change 'Healthcare'. It is built and maintained by the Carnegie Mellon
University Delphi research group. To cite this API: David C. Farrow,
Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni'
'Rosenfeld' (2015). Delphi 'Epidata' API.
<https://github.com/cmu-delphi/delphi-epidata>.
Author: Logan Brooks [aut],
Dmitry Shemetov [aut],
Samuel Gratzl [aut],
David Weber [ctb, cre],
Nat DeFries [ctb],
Alex Reinhart [ctb],
Daniel J. McDonald [ctb],
Kean Ming Tan [ctb],
Will Townes [ctb],
George Haff [ctb],
Kathryn Mazaitis [ctb]
Maintainer: David Weber <davidweb@andrew.cmu.edu>
Diff between epidatr versions 1.2.2 dated 2025-11-17 and 1.2.4 dated 2026-06-02
epidatr-1.2.2/epidatr/R/avail_endpoints.R |only epidatr-1.2.2/epidatr/man/fetch_classic.Rd |only epidatr-1.2.2/epidatr/man/request_impl.Rd |only epidatr-1.2.2/epidatr/tests/testthat/data |only epidatr-1.2.2/epidatr/tests/testthat/generate_test_data.R |only epidatr-1.2.2/epidatr/tests/testthat/test-request.R |only epidatr-1.2.4/epidatr/DESCRIPTION | 24 epidatr-1.2.4/epidatr/MD5 | 180 +- epidatr-1.2.4/epidatr/NAMESPACE | 24 epidatr-1.2.4/epidatr/NEWS.md | 33 epidatr-1.2.4/epidatr/R/auth.R | 15 epidatr-1.2.4/epidatr/R/cache.R | 29 epidatr-1.2.4/epidatr/R/check.R | 163 + epidatr-1.2.4/epidatr/R/constants.R | 4 epidatr-1.2.4/epidatr/R/covidcast.R | 42 epidatr-1.2.4/epidatr/R/endpoints.R | 964 +++++++---- epidatr-1.2.4/epidatr/R/epidatacall.R | 265 +-- epidatr-1.2.4/epidatr/R/model.R | 94 - epidatr-1.2.4/epidatr/R/request.R | 143 - epidatr-1.2.4/epidatr/R/utils.R | 126 - epidatr-1.2.4/epidatr/build/vignette.rds |binary epidatr-1.2.4/epidatr/inst/doc/epidatr.R | 162 + epidatr-1.2.4/epidatr/inst/doc/epidatr.Rmd | 46 epidatr-1.2.4/epidatr/inst/doc/epidatr.html | 452 +---- epidatr-1.2.4/epidatr/inst/doc/signal-discovery.R | 112 - epidatr-1.2.4/epidatr/inst/doc/signal-discovery.Rmd | 55 epidatr-1.2.4/epidatr/inst/doc/signal-discovery.html | 469 ----- epidatr-1.2.4/epidatr/inst/doc/v5-api-demo.R |only epidatr-1.2.4/epidatr/inst/doc/v5-api-demo.Rmd |only epidatr-1.2.4/epidatr/inst/doc/v5-api-demo.html |only epidatr-1.2.4/epidatr/inst/doc/versioned-data.R | 114 - epidatr-1.2.4/epidatr/inst/doc/versioned-data.Rmd | 4 epidatr-1.2.4/epidatr/inst/doc/versioned-data.html | 523 ----- epidatr-1.2.4/epidatr/man/avail_endpoints.Rd | 2 epidatr-1.2.4/epidatr/man/cast_api_queries.Rd |only epidatr-1.2.4/epidatr/man/check_epidata_result.Rd |only epidatr-1.2.4/epidatr/man/check_is_recent.Rd | 2 epidatr-1.2.4/epidatr/man/clear_cache.Rd | 2 epidatr-1.2.4/epidatr/man/covidcast_epidata.Rd | 4 epidatr-1.2.4/epidatr/man/create_epidata_field_info.Rd |only epidatr-1.2.4/epidatr/man/do_request.Rd | 40 epidatr-1.2.4/epidatr/man/dot-epidatr_shared_params.Rd |only epidatr-1.2.4/epidatr/man/epidata_call.Rd | 25 epidatr-1.2.4/epidatr/man/epidata_meta.Rd |only epidatr-1.2.4/epidatr/man/fetch_args_list.Rd | 9 epidatr-1.2.4/epidatr/man/filter_by_timeset.Rd |only epidatr-1.2.4/epidatr/man/format_item.Rd | 2 epidatr-1.2.4/epidatr/man/format_list.Rd | 2 epidatr-1.2.4/epidatr/man/get_api_key.Rd | 15 epidatr-1.2.4/epidatr/man/get_wildcard_equivalent_dates.Rd | 2 epidatr-1.2.4/epidatr/man/parse_signal.Rd | 21 epidatr-1.2.4/epidatr/man/parse_value.Rd |only epidatr-1.2.4/epidatr/man/pub_covid_hosp_facility.Rd | 14 epidatr-1.2.4/epidatr/man/pub_covid_hosp_facility_lookup.Rd | 18 epidatr-1.2.4/epidatr/man/pub_covid_hosp_state_timeseries.Rd | 54 epidatr-1.2.4/epidatr/man/pub_covidcast.Rd | 57 epidatr-1.2.4/epidatr/man/pub_covidcast_meta.Rd | 50 epidatr-1.2.4/epidatr/man/pub_delphi.Rd | 18 epidatr-1.2.4/epidatr/man/pub_dengue_nowcast.Rd | 22 epidatr-1.2.4/epidatr/man/pub_ecdc_ili.Rd | 50 epidatr-1.2.4/epidatr/man/pub_flusurv.Rd | 55 epidatr-1.2.4/epidatr/man/pub_fluview.Rd | 60 epidatr-1.2.4/epidatr/man/pub_fluview_clinical.Rd | 57 epidatr-1.2.4/epidatr/man/pub_fluview_meta.Rd | 15 epidatr-1.2.4/epidatr/man/pub_gft.Rd | 27 epidatr-1.2.4/epidatr/man/pub_kcdc_ili.Rd | 51 epidatr-1.2.4/epidatr/man/pub_meta.Rd | 9 epidatr-1.2.4/epidatr/man/pub_nidss_dengue.Rd | 23 epidatr-1.2.4/epidatr/man/pub_nidss_flu.Rd | 53 epidatr-1.2.4/epidatr/man/pub_nowcast.Rd | 24 epidatr-1.2.4/epidatr/man/pub_paho_dengue.Rd | 51 epidatr-1.2.4/epidatr/man/pub_wiki.Rd | 22 epidatr-1.2.4/epidatr/man/pvt_cdc.Rd | 23 epidatr-1.2.4/epidatr/man/pvt_dengue_sensors.Rd | 25 epidatr-1.2.4/epidatr/man/pvt_ght.Rd | 23 epidatr-1.2.4/epidatr/man/pvt_meta_norostat.Rd | 13 epidatr-1.2.4/epidatr/man/pvt_norostat.Rd | 23 epidatr-1.2.4/epidatr/man/pvt_quidel.Rd | 23 epidatr-1.2.4/epidatr/man/pvt_sensors.Rd | 27 epidatr-1.2.4/epidatr/man/pvt_twitter.Rd | 22 epidatr-1.2.4/epidatr/man/request_epidata.Rd |only epidatr-1.2.4/epidatr/man/validate_date_input.Rd |only epidatr-1.2.4/epidatr/man/validate_timeset_input.Rd |only epidatr-1.2.4/epidatr/man/validate_version_query.Rd |only epidatr-1.2.4/epidatr/tests/testthat/_snaps |only epidatr-1.2.4/epidatr/tests/testthat/helper-live.R |only epidatr-1.2.4/epidatr/tests/testthat/helper-mocks.R |only epidatr-1.2.4/epidatr/tests/testthat/test-cache.R | 91 - epidatr-1.2.4/epidatr/tests/testthat/test-check.R | 25 epidatr-1.2.4/epidatr/tests/testthat/test-covidcast.R | 14 epidatr-1.2.4/epidatr/tests/testthat/test-endpoints.R | 653 +------ epidatr-1.2.4/epidatr/tests/testthat/test-epidatacall.R | 247 +- epidatr-1.2.4/epidatr/tests/testthat/test-live.R |only epidatr-1.2.4/epidatr/tests/testthat/test-model.R | 120 - epidatr-1.2.4/epidatr/tests/testthat/test-utils.R | 60 epidatr-1.2.4/epidatr/vignettes/epidatr.Rmd | 46 epidatr-1.2.4/epidatr/vignettes/signal-discovery.Rmd | 55 epidatr-1.2.4/epidatr/vignettes/v5-api-demo.Rmd |only epidatr-1.2.4/epidatr/vignettes/versioned-data.Rmd | 4 99 files changed, 3127 insertions(+), 3266 deletions(-)
Title: Clinical Table Styling Tools and Utilities
Description: The primary motivation of this package is to take the things that are great about the R packages 'flextable' <https://davidgohel.github.io/flextable/> and 'officer' <https://davidgohel.github.io/officer/>, take the standard and complex pieces of formatting clinical tables for regulatory use, and simplify the tedious pieces.
Author: Mike Stackhouse [aut, cre] ,
Ross Didenko [aut],
Yevhenii Boiko [aut],
Marat Zakirov [ctb],
Roman Rogoza [ctb],
Atorus Research, Inc. [cph],
Incyte Corporation [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between clinify versions 0.3.0 dated 2025-07-07 and 0.3.1 dated 2026-06-02
DESCRIPTION | 8 MD5 | 32 - R/pagination.R | 10 R/slice_clintable.R | 6 R/styles.R | 9 build/vignette.rds |binary inst/doc/clinify.html | 24 inst/doc/defaults.R | 2 inst/doc/defaults.Rmd | 2 inst/doc/defaults.html | 2 inst/doc/end_to_end.html | 2 inst/doc/pagination.html | 26 inst/doc/titles_footnotes.html | 8 tests/testthat/_snaps/pagenums.md | 44 - tests/testthat/_snaps/write.md | 1012 ---------------------------------- tests/testthat/test-slice_clintable.R | 17 vignettes/defaults.Rmd | 2 17 files changed, 111 insertions(+), 1095 deletions(-)
Title: Vis-NIR Spectral Analysis Wrapper
Description: Originally designed application in the context of
resource-limited plant research and breeding programs, 'waves'
provides an open-source solution to spectral data processing and model
development by bringing useful packages together into a streamlined
pipeline. This package is wrapper for functions related to the
analysis of point visible and near-infrared reflectance measurements.
It includes visualization, filtering, aggregation, preprocessing,
cross-validation set formation, model training, and prediction
functions to enable open-source association of spectral and reference
data. This package is documented in a peer-reviewed manuscript in the
Plant Phenome Journal <doi:10.1002/ppj2.20012>. Specialized
cross-validation schemes are described in detail in Jarquín et al.
(2017) <doi:10.3835/plantgenome2016.12.0130>. Example data is from
Ikeogu et al. (2017) <doi:10.1371/journal.pone.0188918>.
Author: Jenna Hershberger [aut, cre] ,
Michael Gore [ths],
NSF BREAD IOS-1543958 [fnd]
Maintainer: Jenna Hershberger <jmh579@cornell.edu>
Diff between waves versions 0.2.6 dated 2025-10-30 and 0.2.7 dated 2026-06-02
DESCRIPTION | 10 +-- MD5 | 46 +++++++++--------- NEWS.md | 16 ++++++ R/aggregate_spectra.R | 2 R/data.R | 3 - R/plot_spectra.R | 10 +-- R/predict_spectra.R | 13 +---- R/pretreat_spectra.R | 4 - R/save_model.R | 8 +-- R/test_spectra.R | 26 ++++------ R/train_spectra.R | 94 ++++++++++++++++++++++-------------- R/utils.R | 44 +++++++++-------- build/vignette.rds |binary inst/doc/waves.R | 4 + inst/doc/waves.Rmd | 4 + inst/doc/waves.html | 122 +++++++++++++++--------------------------------- man/ikeogu.2017.Rd | 3 - man/plot_spectra.Rd | 2 man/predict_spectra.Rd | 2 man/pretreat_spectra.Rd | 4 - man/save_model.Rd | 8 +-- man/test_spectra.Rd | 8 +-- man/train_spectra.Rd | 10 +-- vignettes/waves.Rmd | 4 + 24 files changed, 220 insertions(+), 227 deletions(-)
Title: 'LuaJIT' Scripting
Description: An interface to 'LuaJIT' <https://luajit.org>, a just-in-time
compiler for the 'Lua' scripting language <https://www.lua.org>. Allows
users to run 'Lua' code from 'R'.
Author: Mike Pall [aut, cph] ,
Lua.org, PUC-Rio [cph] ,
Nicholas Davies [cre, ctb, cph] ,
Scott Lembcke, Howling Moon Software [ctb, cph]
Maintainer: Nicholas Davies <nicholas.davies@lshtm.ac.uk>
Diff between luajr versions 0.2.2 dated 2026-02-16 and 0.3.0 dated 2026-06-02
luajr-0.2.2/luajr/R/lua_internal.R |only luajr-0.2.2/luajr/R/lua_parallel.R |only luajr-0.2.2/luajr/inst/doc/objects.R |only luajr-0.2.2/luajr/inst/doc/objects.Rmd |only luajr-0.2.2/luajr/inst/doc/objects.html |only luajr-0.2.2/luajr/man/lua_parallel.Rd |only luajr-0.2.2/luajr/src/lua_api.cpp |only luajr-0.2.2/luajr/src/lua_internal.cpp |only luajr-0.2.2/luajr/tests/testthat/test-basic_v.R |only luajr-0.2.2/luajr/tests/testthat/test-character_v.R |only luajr-0.2.2/luajr/vignettes/objects.Rmd |only luajr-0.3.0/luajr/DESCRIPTION | 10 luajr-0.3.0/luajr/MD5 | 147 - luajr-0.3.0/luajr/NAMESPACE | 1 luajr-0.3.0/luajr/NEWS.md | 28 luajr-0.3.0/luajr/R/lua.R | 4 luajr-0.3.0/luajr/R/lua_func.R | 284 ++- luajr-0.3.0/luajr/R/lua_mode.R | 12 luajr-0.3.0/luajr/R/lua_module.R | 49 luajr-0.3.0/luajr/R/lua_open.R | 3 luajr-0.3.0/luajr/R/luajr-package.R | 24 luajr-0.3.0/luajr/R/zzz.R | 20 luajr-0.3.0/luajr/build/vignette.rds |binary luajr-0.3.0/luajr/configure | 5 luajr-0.3.0/luajr/configure.win | 5 luajr-0.3.0/luajr/inst/Lua/R.lua |only luajr-0.3.0/luajr/inst/Lua/luajr.lua | 1713 ++++++++++---------- luajr-0.3.0/luajr/inst/doc/R-module.R |only luajr-0.3.0/luajr/inst/doc/R-module.Rmd |only luajr-0.3.0/luajr/inst/doc/R-module.html |only luajr-0.3.0/luajr/inst/doc/benchmarks.R |only luajr-0.3.0/luajr/inst/doc/benchmarks.Rmd |only luajr-0.3.0/luajr/inst/doc/benchmarks.html |only luajr-0.3.0/luajr/inst/doc/luajr-module.R |only luajr-0.3.0/luajr/inst/doc/luajr-module.Rmd |only luajr-0.3.0/luajr/inst/doc/luajr-module.html |only luajr-0.3.0/luajr/inst/doc/luajr.R | 131 - luajr-0.3.0/luajr/inst/doc/luajr.Rmd | 426 +--- luajr-0.3.0/luajr/inst/doc/luajr.html | 724 ++------ luajr-0.3.0/luajr/inst/doc/modules.Rmd | 63 luajr-0.3.0/luajr/inst/doc/modules.html | 77 luajr-0.3.0/luajr/inst/include/luajr.h | 33 luajr-0.3.0/luajr/inst/include/luajr_funcs.h | 33 luajr-0.3.0/luajr/inst/include/luajr_luajit.h | 4 luajr-0.3.0/luajr/man/lua_func.Rd | 113 - luajr-0.3.0/luajr/man/lua_module.Rd | 21 luajr-0.3.0/luajr/man/lua_open.Rd | 3 luajr-0.3.0/luajr/man/luajr-package.Rd | 25 luajr-0.3.0/luajr/src/luajit/src/lib_base.c | 4 luajr-0.3.0/luajr/src/luajit/src/lib_debug.c | 2 luajr-0.3.0/luajr/src/luajit/src/lib_ffi.c | 3 luajr-0.3.0/luajr/src/luajit/src/lib_jit.c | 4 luajr-0.3.0/luajr/src/luajit/src/lib_package.c | 2 luajr-0.3.0/luajr/src/luajit/src/lj_carith.c | 2 luajr-0.3.0/luajr/src/luajit/src/lj_cparse.c | 2 luajr-0.3.0/luajr/src/luajit/src/lj_crecord.c | 2 luajr-0.3.0/luajr/src/luajit/src/lj_ffrecord.c | 6 luajr-0.3.0/luajr/src/luajit/src/lj_gc.c | 6 luajr-0.3.0/luajr/src/luajit/src/lj_luajr.c |only luajr-0.3.0/luajr/src/luajit/src/ljamalg.c | 2 luajr-0.3.0/luajr/src/luajrstdr.cpp | 103 - luajr-0.3.0/luajr/src/module.cpp | 64 luajr-0.3.0/luajr/src/parallel.cpp | 330 +-- luajr-0.3.0/luajr/src/push_to.cpp | 914 ++++++---- luajr-0.3.0/luajr/src/run_func.cpp | 146 + luajr-0.3.0/luajr/src/setup.cpp | 83 luajr-0.3.0/luajr/src/shared.h | 124 + luajr-0.3.0/luajr/src/state.cpp | 134 + luajr-0.3.0/luajr/src/tools.cpp | 38 luajr-0.3.0/luajr/tests/testthat/test-attributes.R | 10 luajr-0.3.0/luajr/tests/testthat/test-character.R |only luajr-0.3.0/luajr/tests/testthat/test-environment.R |only luajr-0.3.0/luajr/tests/testthat/test-func.R | 337 +++ luajr-0.3.0/luajr/tests/testthat/test-integer.R |only luajr-0.3.0/luajr/tests/testthat/test-is_na.R |only luajr-0.3.0/luajr/tests/testthat/test-list.R | 179 +- luajr-0.3.0/luajr/tests/testthat/test-logical.R |only luajr-0.3.0/luajr/tests/testthat/test-module.R | 6 luajr-0.3.0/luajr/tests/testthat/test-names.R |only luajr-0.3.0/luajr/tests/testthat/test-numeric.R |only luajr-0.3.0/luajr/tests/testthat/test-parallel.R | 175 +- luajr-0.3.0/luajr/tests/testthat/test-rfunction.R |only luajr-0.3.0/luajr/tests/testthat/test-rmodule.R |only luajr-0.3.0/luajr/tests/testthat/test-sexp.R |only luajr-0.3.0/luajr/tests/testthat/test-subset.R |only luajr-0.3.0/luajr/tests/testthat/test-types.R | 40 luajr-0.3.0/luajr/tools/luajit_relver.txt | 2 luajr-0.3.0/luajr/vignettes/R-module.Rmd |only luajr-0.3.0/luajr/vignettes/benchmarks.Rmd |only luajr-0.3.0/luajr/vignettes/images |only luajr-0.3.0/luajr/vignettes/luajr-module.Rmd |only luajr-0.3.0/luajr/vignettes/luajr.Rmd | 426 +--- luajr-0.3.0/luajr/vignettes/modules.Rmd | 63 93 files changed, 3728 insertions(+), 3439 deletions(-)
Title: Multivariate Joint Modeling for Longitudinal and Time-to-Event
Outcomes with 'INLA'
Description: Estimation of joint models for multivariate longitudinal markers (with various distributions available) and survival outcomes (possibly accounting for competing risks) with Integrated Nested Laplace Approximations (INLA). The flexible and user friendly function joint() facilitates the use of the fast and reliable inference technique implemented in the 'INLA' package for joint modeling. More details are given in the help page of the joint() function (accessible via ?joint in the R console) and the vignette associated to the joint() function (accessible via vignette("INLAjoint") in the R console).
Author: Denis Rustand [cre, aut] ,
Elias Teixeira Krainski [aut] ,
Haavard Rue [aut] ,
Janet van Niekerk [aut]
Maintainer: Denis Rustand <INLAjoint@gmail.com>
Diff between INLAjoint versions 25.11.10 dated 2025-11-10 and 26.6.2 dated 2026-06-02
DESCRIPTION | 14 MD5 | 30 + NAMESPACE | 16 R/joint.R | 85 +++- R/joint.compare.R |only R/joint.run.R | 2 R/plot.INLAjoint.R | 21 - R/predict.INLAjoint.R | 699 +++++++++++++++++++++++++++-------------- R/score_predictions.R |only R/setupFonctions.R | 10 R/summary.INLAjoint.R | 24 + R/zzz.R | 26 - build/vignette.rds |binary man/INLAjoint.object.Rd | 4 man/joint.compare.Rd |only man/plot.score_predictions.Rd |only man/predict.INLAjoint.Rd | 7 man/print.score_predictions.Rd |only man/score_predictions.Rd |only 19 files changed, 620 insertions(+), 318 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor
Analysis-1 (Parafac) model or Parallel Factor Analysis-2 (Parafac2) model fit to
a three-way or four-way data array. See Harshman and Lundy (1994):
<doi:10.1016/0167-9473(94)90132-5>. Classification using principal component
analysis (PCA) fit to a two-way data matrix is also supported. Uses component
weights from one mode of a Parafac, Parafac2, or PCA model as features to tune
parameters for one or more classification methods via a k-fold cross-validation
procedure. Allows for constraints on different tensor modes. Allows for
inclusion of additional features alongside features generated by the component
model. Supports penalized logistic regression, support vector machine, random
forest, feed-forward neural network, regularized discriminant analysis, and
gradient boosting machine. Supports binary and multiclass classification.
Predicts class labels or class probabilities and calculates multiple
classification performanc [...truncated...]
Author: Matthew A. Asisgress [aut, cre]
Maintainer: Matthew A. Asisgress <mattgress@protonmail.ch>
Diff between cpfa versions 1.2-9 dated 2026-05-07 and 1.3.0 dated 2026-06-02
ChangeLog | 24 ++++++++++ DESCRIPTION | 19 ++++---- MD5 | 43 ++++++++++-------- NAMESPACE | 7 +-- R/alignmod.R |only R/cpfa.R | 57 ++++++++++++++++++------ R/cpm.R | 4 - R/cutback.R |only R/imphelper.R |only R/kcv.plr.R | 13 +++-- R/pficpfa.R |only R/plotcpfa.R | 11 +++- R/postalign.R |only R/predict.tunecpfa.R | 17 ------- R/repsums.R |only R/simcpfa.R | 4 - R/tunecpfa.R | 2 inst/doc/cpfa.R | 28 +++++++++++- inst/doc/cpfa.Rmd | 67 +++++++++++++++++++++++++++- inst/doc/cpfa.pdf |binary man/cpfa-internals.Rd | 5 ++ man/cpfa.Rd | 116 ++++++++++++++++++++++++++++++++++++-------------- man/pficpfa.Rd |only man/plotcpfa.Rd | 6 +- man/tunecpfa.Rd | 12 ++--- vignettes/cpfa.Rmd | 67 +++++++++++++++++++++++++++- 26 files changed, 382 insertions(+), 120 deletions(-)
Title: Simulated Point-Pattern via Vectorized Parameterization
Description: An intuitive interface to simulate superimposed (marked) point patterns with vectorized parameterization of random point pattern and distribution of marks.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe.random versions 0.3.0 dated 2026-05-19 and 0.3.1 dated 2026-06-02
DESCRIPTION | 10 +++---- MD5 | 8 ++--- NAMESPACE | 3 -- R/rppp.R | 77 +++++++++++++++++++++++++++++++++----------------------- man/dot-rppp.Rd | 32 ++++++++++++++--------- 5 files changed, 75 insertions(+), 55 deletions(-)
More information about groupedHyperframe.random at CRAN
Permanent link
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph] ,
Emmanuel Paradis [cph] ,
Robert Noble [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 2.3.0 dated 2026-04-23 and 2.4.0 dated 2026-06-02
DESCRIPTION | 10 MD5 | 575 +- NAMESPACE | 1034 +-- NEWS.md | 35 R/AddTip.R | 550 +- R/ArtificialExtinction.R | 242 R/Cherries.R | 68 R/ClusterTable.R | 254 R/Combinatorics.R | 696 +- R/Consensus.R | 320 - R/ConsistentSplits.R | 84 R/Decompose.R | 330 - R/DropTip.R | 710 +- R/EdgeRatio.R | 70 R/ImposeConstraint.R | 278 - R/Information.R | 522 - R/KeptPaths.R | 94 R/KeptVerts.R | 126 R/LongBranchScore.R | 150 R/MatchNodes.R | 216 R/MatchStrings.R | 66 R/PaintTree.R |only R/PathLengths.R | 96 R/PhyToString.R | 284 - R/RUtreebalance.R | 648 +- R/RcppExports-manual.R | 64 R/RcppExports.R | 8 R/ReadMrBayes.R | 190 R/ReadTntTree.R | 580 +- R/Reweight.R | 2 R/RoguePlot.R | 618 +- R/SplitFunctions.R | 912 +-- R/Splits.R | 1336 ++-- R/Stemwardness.R | 218 R/Support.R | 398 - R/TipTimedTree.R | 100 R/TopologyOnly.R | 84 R/TotalCopheneticIndex.R | 316 - R/TreeNumber.R | 1166 ++-- R/TreeTools-package.R | 50 R/Treeness.R | 116 R/as.matrix.R | 30 R/as.multiPhylo.R | 152 R/data.R | 180 R/helper_functions.R | 200 R/match.R | 496 - R/mst.R | 158 R/parse_files.R | 2042 ++++--- R/phylo.R | 642 +- R/sort.R | 156 R/split_analysis.R | 162 R/tree_ancestors.R | 220 R/tree_comparison.R | 86 R/tree_descendants.R | 277 - R/tree_display.R | 292 - R/tree_generation.R | 1002 +-- R/tree_information.R | 206 R/tree_numbering.R | 1468 ++--- R/tree_properties.R | 1028 +-- R/tree_rearrangement.R | 1294 ++-- R/tree_shape.R | 572 +- R/tree_write.R | 262 R/zzz.R | 68 build/partial.rdb |binary data/brewer.R | 40 data/nRootedShapes.R | 114 data/nUnrootedShapes.R | 124 inst/CITATION | 34 inst/REFERENCES.bib | 767 +- inst/WORDLIST | 228 inst/apa-old-doi-prefix.csl | 4546 ++++++++--------- inst/doc/filesystem-navigation.Rmd | 104 inst/doc/filesystem-navigation.html | 4 inst/doc/load-data.Rmd | 428 - inst/doc/load-data.html | 4 inst/doc/load-trees.Rmd | 250 inst/doc/load-trees.html | 4 inst/extdata/input/dataset.nex | 44 inst/extdata/input/notes.nex | 54 inst/extdata/output/named.tre | 6 inst/extdata/output/numbered.tre | 8 inst/extdata/tests/ape-tree.nex | 10 inst/extdata/tests/continuous.nex | 44 inst/extdata/tests/encoding.nex | 48 inst/extdata/tests/parse-nexus.nexus | 510 - inst/extdata/tests/taxon-notes.nex | 48 inst/extdata/tests/tnt-amp-continuation.tnt |only inst/extdata/tests/tnt-bare-tree.tnt | 2 inst/extdata/tests/tnt-cp1252-taxa.tnt |only inst/extdata/tests/tnt-dna.tnt | 42 inst/extdata/tests/tnt-matrix.tnt | 294 - inst/extdata/tests/tnt-midline-xread.tnt |only inst/extdata/tests/tnt-multiline-comment.tnt |only inst/extdata/tests/tnt-multiline-taxa.tnt |only inst/extdata/tests/tnt-multitaxon-line.tnt |only inst/extdata/tests/tnt-namedtree.tre | 8 inst/extdata/tests/tnt-smartquote-taxa.tnt |only inst/extdata/tests/tnt-taxon-taxonomy.tnt |only inst/extdata/tests/tnt-tree.tre | 46 inst/extdata/tests/tnt-trees-and-matrix.tnt | 58 inst/extdata/tests/tnt-xgroup.tnt |only man/AddTip.Rd | 280 - man/AncestorEdge.Rd | 107 man/ApeTime.Rd | 54 man/ArtificialExtinction.Rd | 216 man/CharacterInformation.Rd | 86 man/Cherries.Rd | 108 man/CladeSizes.Rd | 97 man/CladisticInfo.Rd | 144 man/ClusterTable-methods.Rd | 94 man/ClusterTable.Rd | 160 man/CollapseNode.Rd | 162 man/CompatibleSplits.Rd | 108 man/Consensus.Rd | 126 man/ConsensusWithout.Rd | 212 man/ConstrainedNJ.Rd | 108 man/Decompose.Rd | 167 man/DescendantEdges.Rd | 163 man/DoubleFactorial.Rd | 132 man/DropTip.Rd | 280 - man/EdgeAncestry.Rd | 125 man/EdgeDistances.Rd | 105 man/EdgeRatio.Rd | 92 man/EndSentence.Rd | 64 man/ExtractTaxa.Rd | 90 man/GenerateTree.Rd | 195 man/Hamming.Rd | 156 man/ImposeConstraint.Rd | 148 man/J1Index.Rd | 190 man/KeptPaths.Rd | 132 man/KeptVerts.Rd | 138 man/LabelSplits.Rd | 172 man/LeafLabelInterchange.Rd | 118 man/ListAncestors.Rd | 205 man/Lobo.data.Rd | 66 man/LongBranch.Rd | 130 man/MRCA.Rd | 135 man/MSTEdges.Rd | 146 man/MakeTreeBinary.Rd | 108 man/MatchEdges.Rd | 139 man/MatchStrings.Rd | 80 man/MatrixToPhyDat.Rd | 157 man/MorphoBankDecode.Rd | 58 man/N1Spr.Rd | 76 man/NDescendants.Rd | 96 man/NJTree.Rd | 82 man/NPartitionPairs.Rd | 102 man/NRooted.Rd | 268 - man/NSplits.Rd | 172 man/NTip.Rd | 140 man/NewickTree.Rd | 54 man/Neworder.Rd | 128 man/NexusTokensToInteger.Rd |only man/NodeDepth.Rd | 127 man/NodeNumbers.Rd | 115 man/NodeOrder.Rd | 109 man/PaintTree.Rd |only man/PairwiseDistances.Rd | 82 man/PathLengths.Rd | 118 man/PhyToString.Rd | 213 man/PolarizeSplits.Rd | 70 man/ReadCharacters.Rd | 301 - man/ReadMrBayesTrees.Rd | 110 man/ReadTntTree.Rd | 248 man/Renumber.Rd | 118 man/RenumberTips.Rd | 140 man/Reorder.Rd | 553 +- man/Reweight.Rd | 157 man/RightmostCharacter.Rd | 72 man/RoguePlot.Rd | 240 man/RootNode.Rd | 105 man/RootTree.Rd | 190 man/SampleOne.Rd | 84 man/SortTree.Rd | 184 man/SplitConsistent.Rd | 90 man/SplitFrequency.Rd | 173 man/SplitInformation.Rd | 256 man/SplitMatchProbability.Rd | 94 man/Splits.Rd | 216 man/SplitsInBinaryTree.Rd | 162 man/Stemwardness.Rd | 198 man/Subsplit.Rd | 96 man/Subtree.Rd | 122 man/SupportColour.Rd | 142 man/TipLabels.Rd | 252 man/TipTimedTree.Rd | 140 man/TipsInSplits.Rd | 144 man/TopologyOnly.Rd | 46 man/TotalCopheneticIndex.Rd | 188 man/TreeIsRooted.Rd | 86 man/TreeNumber.Rd | 432 - man/TreeShape.Rd | 318 - man/TreeTools-package.Rd | 85 man/Treeness.Rd | 114 man/TreesMatchingSplit.Rd | 92 man/TreesMatchingTree.Rd | 98 man/TrivialSplits.Rd | 96 man/TrivialTree.Rd | 125 man/Unquote.Rd | 64 man/UnrootedTreesMatchingSplit.Rd | 96 man/UnshiftTree.Rd | 116 man/WriteTntCharacters.Rd | 140 man/as.Newick.Rd | 96 man/as.multiPhylo.Rd | 106 man/brewer.Rd | 66 man/dot-RandomParent.Rd | 54 man/doubleFactorials.Rd | 52 man/edge_to_splits.Rd | 98 man/is.TreeNumber.Rd | 64 man/logDoubleFactorials.Rd | 46 man/match.Splits.Rd | 136 man/match.multiPhylo.Rd | 144 man/nRootedShapes.Rd | 56 man/print.TreeNumber.Rd | 44 man/root_on_node.Rd | 58 man/sapply64.Rd | 164 man/sort.multiPhylo.Rd | 114 man/xor.Rd | 62 src/RcppExports.cpp | 18 src/consensus.cpp | 587 +- tests/figs/rogueplot.svg | 68 tests/spelling.R | 8 tests/testthat.R | 8 tests/testthat/_snaps/RoguePlot/rogueplot-poly.svg | 82 tests/testthat/_snaps/RoguePlot/rogueplot-simple.svg | 94 tests/testthat/_snaps/RoguePlot/rogueplot-trees1.svg | 106 tests/testthat/_snaps/RoguePlot/rogueplot-trees2.svg | 82 tests/testthat/_snaps/Support/labelsplits-nameless.svg | 172 tests/testthat/_snaps/Support/labelsplits-names.svg | 148 tests/testthat/_snaps/Support/labelsplits.svg | 148 tests/testthat/_snaps/mst/mst-plotting.svg | 142 tests/testthat/_snaps/tree_display/sorted-tree.svg | 270 - tests/testthat/test-AddTip.R | 356 - tests/testthat/test-ArtificialExtinction.R | 94 tests/testthat/test-Cherries.R | 24 tests/testthat/test-ClusterTable.R | 284 - tests/testthat/test-Decompose.R | 152 tests/testthat/test-DropTip.R | 516 - tests/testthat/test-EdgeRatio.R | 18 tests/testthat/test-FirstMatchingSplit.R | 68 tests/testthat/test-ImposeConstraint.R | 296 - tests/testthat/test-KeptPaths.R | 40 tests/testthat/test-KeptVerts.R | 172 tests/testthat/test-LongBranchScore.R | 36 tests/testthat/test-MatchNodes.R | 148 tests/testthat/test-MatchStrings.R | 26 tests/testthat/test-PaintTree.R |only tests/testthat/test-PathLengths.R | 70 tests/testthat/test-PhyToString.R | 150 tests/testthat/test-RUtreebalance.R | 128 tests/testthat/test-ReadMrBayes.R | 8 tests/testthat/test-ReadTntTree.R | 396 - tests/testthat/test-Reweight.R | 92 tests/testthat/test-RoguePlot.R | 362 - tests/testthat/test-SplitConsistent.R | 72 tests/testthat/test-SplitFunctions.R | 452 - tests/testthat/test-Splits.R | 1184 ++-- tests/testthat/test-Stemwardness.R | 28 tests/testthat/test-Support.R | 222 tests/testthat/test-TipTimedTree.R | 28 tests/testthat/test-TopologyOnly.R | 54 tests/testthat/test-TotalCopheneticIndex.R | 152 tests/testthat/test-TreeNumber.R | 360 - tests/testthat/test-Treeness.R | 38 tests/testthat/test-as.matrix.R | 14 tests/testthat/test-as.multiPhylo.R | 70 tests/testthat/test-combinatorics.R | 178 tests/testthat/test-consensus.R | 22 tests/testthat/test-helper_functions.R | 22 tests/testthat/test-information.R | 84 tests/testthat/test-int_to_tree.cpp.R | 130 tests/testthat/test-match.R | 58 tests/testthat/test-mst.R | 84 tests/testthat/test-parsers.R | 570 +- tests/testthat/test-phylo.R | 112 tests/testthat/test-root_tree.h.R | 226 tests/testthat/test-sort.R | 44 tests/testthat/test-split_analysis.R | 22 tests/testthat/test-splits.cpp.R | 74 tests/testthat/test-tree_ancestors.R | 40 tests/testthat/test-tree_comparison.R | 48 tests/testthat/test-tree_descendants.R | 168 tests/testthat/test-tree_display.R | 128 tests/testthat/test-tree_generation-random.R | 90 tests/testthat/test-tree_generation.R | 449 - tests/testthat/test-tree_information.R | 38 tests/testthat/test-tree_numbering.R | 882 +-- tests/testthat/test-tree_properties.R | 364 - tests/testthat/test-tree_rearrange.R | 830 +-- tests/testthat/test-tree_shape.R | 318 - tests/testthat/test-tree_write.R | 98 tests/testthat/testdata/nonPreCons.nex | 48 vignettes/filesystem-navigation.Rmd | 104 vignettes/load-data.Rmd | 428 - vignettes/load-trees.Rmd | 250 295 files changed, 31432 insertions(+), 30746 deletions(-)
Title: Database Connection Management and Utilities for 'dbverse'
Description: Provides an R6-based project container for managing 'DuckDB'
connections, reconnecting lazy database tables after session restarts, and
storing metadata for database-backed objects used by packages in the
'dbverse'. The package supplies S4 base classes and generics for
database-backed data, helpers for validating 'DuckDB' connections and table
names, utilities for creating persistent database views, and methods for
writing and restoring pinned lazy tables through the 'pins' package. These
tools help package authors and analysts keep database paths, cached
connections, and table references synchronized across interactive sessions
and project directories.
Author: Edward C. Ruiz [aut, cre] ,
Jiaji George Chen [aut],
Ruben Dries [aut]
Maintainer: Edward C. Ruiz <ecr7407@gmail.com>
Diff between dbProject versions 0.1.0 dated 2026-05-07 and 0.1.1 dated 2026-06-02
DESCRIPTION | 8 MD5 | 22 +- NEWS.md | 24 ++ R/connection-methods.R | 17 - R/connection-registry.R | 52 ++-- R/dbMatrix-pin.R | 5 R/dbProject-R6.R | 24 ++ R/dbSpatial-pin.R | 5 inst/doc/connection-management.html | 320 +++++++++++++++-------------- inst/doc/getting_started.html | 355 +++++++++++++++++---------------- inst/doc/troubleshooting.html | 277 ++++++++++++++----------- tests/testthat/test-dbData-reconnect.R | 27 ++ 12 files changed, 648 insertions(+), 488 deletions(-)
Title: Bayesian Power Analysis Using 'brms' and 'INLA'
Description: Provides tools for Bayesian power analysis and assurance calculations using the statistical frameworks of 'brms' and 'INLA'. Includes simulation-based approaches, support for multiple decision rules (direction, threshold, ROPE), sequential designs, and visualisation helpers. Methods are based on Kruschke (2014, ISBN:9780124058880) "Doing Bayesian Data Analysis: A Tutorial with R, JAGS, and Stan", O'Hagan & Stevens (2001) <doi:10.1177/0272989X0102100307> "Bayesian Assessment of Sample Size for Clinical Trials of Cost-Effectiveness", Kruschke (2018) <doi:10.1177/2515245918771304> "Rejecting or Accepting Parameter Values in Bayesian Estimation", Rue et al. (2009) <doi:10.1111/j.1467-9868.2008.00700.x> "Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations", and Bürkner (2017) <doi:10.18637/jss.v080.i01> "brms: An R Package for Bayesian Multilevel Models using Stan".
Author: Tony Myers [aut, cre]
Maintainer: Tony Myers <admyers@aol.com>
Diff between powerbrmsINLA versions 1.1.1 dated 2025-11-16 and 1.2.0 dated 2026-06-02
DESCRIPTION | 11 MD5 | 104 ++-- NAMESPACE | 11 NEWS.md | 57 ++ R/added_plotting_functions.R | 7 R/compute-assurance.R |only R/data-generator.R | 4 R/decision-helpers.R | 611 ++++++++++++++++++------ R/diagnostics.R |only R/engine-main.R | 196 ++++++- R/engine-sequential.R | 39 + R/engine-two-stage.R | 3 R/globals.R | 9 R/imports.R | 2 R/plotting-assurance.R |only R/plotting-bf.R | 20 R/plotting-decision.R | 20 R/plotting-power.R | 39 + R/plotting-precision.R | 31 - R/plotting-robustness.R | 19 R/utils-data-model.R | 234 ++++++++- R/utils-helpers.R | 200 +++++-- build |only inst |only man/add_decision_overlay.Rd | 2 man/assurance_prior_weights.Rd |only man/brms_inla_power.Rd | 78 ++- man/brms_inla_power_sequential.Rd | 4 man/compute_assurance.Rd |only man/decide_sample_size.Rd | 144 ++++- man/dot-brms_to_inla_formula2.Rd | 7 man/dot-compute_weights_from_dist.Rd |only man/dot-eval_prior_density.Rd |only man/dot-map_brms_priors_to_inla.Rd | 23 man/dot-sample_sd_spec.Rd |only man/dot-scale_fill_viridis_discrete.Rd | 6 man/dot-to_inla_family.Rd | 11 man/plot_assurance_curve.Rd |only man/plot_assurance_with_robustness.Rd | 9 man/plot_bf_assurance_curve.Rd | 8 man/plot_bf_assurance_curve_smooth.Rd | 8 man/plot_decision_assurance_curve.Rd | 10 man/plot_decision_threshold_contour.Rd | 2 man/plot_design_prior.Rd |only man/plot_interaction_surface.Rd | 7 man/plot_power_assurance_overlay.Rd |only man/plot_power_contour.Rd | 16 man/plot_power_heatmap.Rd | 14 man/plot_precision_assurance_curve.Rd | 11 man/plot_precision_fan_chart.Rd | 9 man/print.brms_inla_power.Rd |only man/print.powerbrmsINLA_assurance.Rd |only man/print.powerbrmsINLA_sample_size.Rd |only man/validate_inla_vs_brms.Rd |only man/validate_sd_spec.Rd |only tests/testthat/test-assurance-plots.R |only tests/testthat/test-compute_assurance.R |only tests/testthat/test-decide-sample-size.R |only tests/testthat/test-diagnostics.R |only tests/testthat/test-prior-bridge.R |only tests/testthat/test-utils.R | 2 tests/testthat/test-validation-bayesassurance.R |only tests/testthat/test-validation-classical.R |only tests/testthat/test-variance-uncertainty.R |only vignettes |only 65 files changed, 1562 insertions(+), 426 deletions(-)
Title: Download Data from Mexico's Air Quality Information System
Description: Easy-to-use functions for downloading air quality data from
the Mexican National Air Quality Information System (SINAICA). Allows
you to query pollution and meteorological parameters from more than a
hundred monitoring stations located throughout Mexico. See
<https://sinaica.inecc.gob.mx> for more information.
Author: Diego Valle-Jones [aut, cre]
Maintainer: Diego Valle-Jones <diego@diegovalle.net>
Diff between rsinaica versions 1.1.1 dated 2026-02-27 and 1.2.0 dated 2026-06-02
DESCRIPTION | 8 - MD5 | 36 ++++--- NEWS.md | 26 +++++ R/data.R | 6 - R/sinaica_station_data.R | 61 ++++++++----- R/sinaica_station_params_and_dates.R | 39 ++++++-- R/utils.R | 52 ++++++++++- data/stations_sinaica.rda |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/rsinaica-package.Rd | 5 + man/sinaica_station_data.Rd | 38 +++++--- man/sinaica_station_dates.Rd | 16 ++- man/sinaica_station_params.Rd | 16 ++- man/stations_sinaica.Rd | 6 - tests/testthat/test-sinaica_param_data.R |only tests/testthat/test-sinaica_params_and_dates.R | 36 +++++++ tests/testthat/test-sinaica_station_data.R | 23 +++-- tests/testthat/test-stations_sinaica.R |only tests/testthat/test-utils.R | 114 ++++++++++++++++++++++++- 20 files changed, 394 insertions(+), 88 deletions(-)
Title: Visualize the Results of Risk-of-Bias (ROB) Assessments
Description: Helps users in quickly visualizing risk-of-bias
assessments performed as part of a systematic review. It allows users to
create weighted bar-plots of the distribution of risk-of-bias judgments
within each bias domain, in addition to traffic-light plots of the
specific domain-level judgments for each study. The resulting figures are
of publication quality and are formatted according the risk-of-bias
assessment tool use to perform the assessments. Currently, the supported
tools are ROB2.0 (for randomized controlled trials; Sterne et al (2019)
<doi:10.1136/bmj.l4898>), ROBINS-I (for non-randomised studies of
interventions; Sterne et al (2016) <doi:10.1136/bmj.i4919>), and QUADAS-2
(for diagnostic accuracy studies; Whiting et al (2011)
<doi:10.7326/0003-4819-155-8-201110180-00009>).
Author: Luke McGuinness [aut, cre],
Emily Kothe [ctb]
Maintainer: Luke McGuinness <luke@robvis.org>
Diff between robvis versions 0.3.0 dated 2019-11-22 and 0.3.1 dated 2026-06-02
DESCRIPTION | 12 - MD5 | 14 - NEWS.md | 7 README.md | 14 - build/vignette.rds |binary inst/CITATION | 4 inst/doc/Introduction_to_robvis.R | 40 ++-- inst/doc/Introduction_to_robvis.html | 345 +++++++---------------------------- 8 files changed, 125 insertions(+), 311 deletions(-)
Title: Actuarial Tools for Insurance Pricing Models
Description: Provides actuarial tools and building blocks for analysing,
modelling, refining, and validating insurance rating models. Designed to
support common GLM-based pricing tasks and the translation of statistical
model output into practical tariff structures. The package supports the
construction of insurance tariff classes using a data-driven approach, based
on the methodology of Antonio and Valdez
(2012) <doi:10.1007/s10182-011-0152-7>.
Author: Martin Haringa [aut, cre]
Maintainer: Martin Haringa <mtharinga@gmail.com>
Diff between insurancerating versions 0.7.5 dated 2024-10-09 and 0.8.0 dated 2026-06-02
insurancerating-0.7.5/insurancerating/R/deprecated.R |only insurancerating-0.7.5/insurancerating/R/gam_fit.R |only insurancerating-0.7.5/insurancerating/R/histbin.R |only insurancerating-0.7.5/insurancerating/R/model_rating_factors.R |only insurancerating-0.7.5/insurancerating/R/truncated_severity.R |only insurancerating-0.7.5/insurancerating/man/autoplot.bootstrap_rmse.Rd |only insurancerating-0.7.5/insurancerating/man/autoplot.constructtariffclasses.Rd |only insurancerating-0.7.5/insurancerating/man/autoplot.fitgam.Rd |only insurancerating-0.7.5/insurancerating/man/autoplot.restricted.Rd |only insurancerating-0.7.5/insurancerating/man/autoplot.riskfactor.Rd |only insurancerating-0.7.5/insurancerating/man/autoplot.smooth.Rd |only insurancerating-0.7.5/insurancerating/man/autoplot.truncated_dist.Rd |only insurancerating-0.7.5/insurancerating/man/autoplot.univariate.Rd |only insurancerating-0.7.5/insurancerating/man/figures |only insurancerating-0.7.5/insurancerating/man/summary.reduce.Rd |only insurancerating-0.7.5/insurancerating/tests/testthat/test_reduce.R |only insurancerating-0.8.0/insurancerating/DESCRIPTION | 36 insurancerating-0.8.0/insurancerating/MD5 | 250 - insurancerating-0.8.0/insurancerating/NAMESPACE | 114 insurancerating-0.8.0/insurancerating/NEWS.md | 242 + insurancerating-0.8.0/insurancerating/R/data_MTPL.R | 62 insurancerating-0.8.0/insurancerating/R/excess_loss.R |only insurancerating-0.8.0/insurancerating/R/fisher_classify.R |only insurancerating-0.8.0/insurancerating/R/gam_construct_tariff_classes.R | 655 ++ insurancerating-0.8.0/insurancerating/R/gam_riskfactor.R |only insurancerating-0.8.0/insurancerating/R/model_add_prediction.R | 229 insurancerating-0.8.0/insurancerating/R/model_get_data.R | 734 ++- insurancerating-0.8.0/insurancerating/R/model_performance.R | 146 insurancerating-0.8.0/insurancerating/R/model_performance_bootstrap_rmse.R | 480 +- insurancerating-0.8.0/insurancerating/R/model_performance_overdispersion.R | 152 insurancerating-0.8.0/insurancerating/R/model_performance_residuals.R | 272 - insurancerating-0.8.0/insurancerating/R/model_rating_table.R |only insurancerating-0.8.0/insurancerating/R/model_rating_table_deprecated.R |only insurancerating-0.8.0/insurancerating/R/model_rating_table_plot.R |only insurancerating-0.8.0/insurancerating/R/model_refinement.R | 2320 +++++++--- insurancerating-0.8.0/insurancerating/R/model_refinement_plot.R |only insurancerating-0.8.0/insurancerating/R/oud_model_rating_factors.R |only insurancerating-0.8.0/insurancerating/R/oud_model_refinement.R |only insurancerating-0.8.0/insurancerating/R/outlier_histogram.R |only insurancerating-0.8.0/insurancerating/R/severity_distribution.R |only insurancerating-0.8.0/insurancerating/R/time_period_to_months.R | 309 - insurancerating-0.8.0/insurancerating/R/time_reduce.R | 440 + insurancerating-0.8.0/insurancerating/R/time_rows_per_date.R | 207 insurancerating-0.8.0/insurancerating/R/truncated_distributions.R |only insurancerating-0.8.0/insurancerating/R/univariate.R | 1122 +++- insurancerating-0.8.0/insurancerating/R/utils.R | 625 -- insurancerating-0.8.0/insurancerating/R/utils_refinement.R | 568 ++ insurancerating-0.8.0/insurancerating/R/utils_univariate.R |only insurancerating-0.8.0/insurancerating/R/zzz.R | 5 insurancerating-0.8.0/insurancerating/build |only insurancerating-0.8.0/insurancerating/inst |only insurancerating-0.8.0/insurancerating/man/MTPL.Rd | 32 insurancerating-0.8.0/insurancerating/man/MTPL2.Rd | 26 insurancerating-0.8.0/insurancerating/man/active_rows_by_date.Rd |only insurancerating-0.8.0/insurancerating/man/add_observed_experience.Rd |only insurancerating-0.8.0/insurancerating/man/add_prediction.Rd | 66 insurancerating-0.8.0/insurancerating/man/add_relativities.Rd |only insurancerating-0.8.0/insurancerating/man/add_restriction.Rd |only insurancerating-0.8.0/insurancerating/man/add_smoothing.Rd |only insurancerating-0.8.0/insurancerating/man/add_tariff_segments.Rd |only insurancerating-0.8.0/insurancerating/man/allocate_excess_loss.Rd |only insurancerating-0.8.0/insurancerating/man/apply_excess_loading.Rd |only insurancerating-0.8.0/insurancerating/man/assess_excess_threshold.Rd |only insurancerating-0.8.0/insurancerating/man/autoplot.bootstrap_performance.Rd |only insurancerating-0.8.0/insurancerating/man/autoplot.check_residuals.Rd | 23 insurancerating-0.8.0/insurancerating/man/autoplot.excess_loss_allocation.Rd |only insurancerating-0.8.0/insurancerating/man/autoplot.excess_threshold_assessment.Rd |only insurancerating-0.8.0/insurancerating/man/autoplot.factor_analysis.Rd |only insurancerating-0.8.0/insurancerating/man/autoplot.rating_refinement.Rd |only insurancerating-0.8.0/insurancerating/man/autoplot.rating_table.Rd |only insurancerating-0.8.0/insurancerating/man/autoplot.riskfactor_gam.Rd |only insurancerating-0.8.0/insurancerating/man/autoplot.tariff_segments.Rd |only insurancerating-0.8.0/insurancerating/man/autoplot.truncated_severity.Rd |only insurancerating-0.8.0/insurancerating/man/biggest_reference.Rd | 32 insurancerating-0.8.0/insurancerating/man/bootstrap_performance.Rd |only insurancerating-0.8.0/insurancerating/man/bootstrap_rmse.Rd | 70 insurancerating-0.8.0/insurancerating/man/calculate_excess_loss.Rd |only insurancerating-0.8.0/insurancerating/man/check_overdispersion.Rd | 47 insurancerating-0.8.0/insurancerating/man/check_residuals.Rd | 79 insurancerating-0.8.0/insurancerating/man/construct_model_points.Rd | 87 insurancerating-0.8.0/insurancerating/man/construct_tariff_classes.Rd | 95 insurancerating-0.8.0/insurancerating/man/default_extrapolation_break_size.Rd |only insurancerating-0.8.0/insurancerating/man/derive_tariff_segments.Rd |only insurancerating-0.8.0/insurancerating/man/edit_smoothing.Rd |only insurancerating-0.8.0/insurancerating/man/extract_model_data.Rd |only insurancerating-0.8.0/insurancerating/man/factor_analysis.Rd |only insurancerating-0.8.0/insurancerating/man/fisher.Rd | 35 insurancerating-0.8.0/insurancerating/man/fisher_classify.Rd |only insurancerating-0.8.0/insurancerating/man/fit_gam.Rd | 84 insurancerating-0.8.0/insurancerating/man/fit_truncated_dist.Rd | 114 insurancerating-0.8.0/insurancerating/man/fit_truncated_severity.Rd |only insurancerating-0.8.0/insurancerating/man/histbin.Rd | 52 insurancerating-0.8.0/insurancerating/man/make_stars.Rd |only insurancerating-0.8.0/insurancerating/man/merge_date_ranges.Rd |only insurancerating-0.8.0/insurancerating/man/model_data.Rd | 14 insurancerating-0.8.0/insurancerating/man/model_performance.Rd | 24 insurancerating-0.8.0/insurancerating/man/outlier_histogram.Rd |only insurancerating-0.8.0/insurancerating/man/period_to_months.Rd | 43 insurancerating-0.8.0/insurancerating/man/plot_severity_distribution.Rd |only insurancerating-0.8.0/insurancerating/man/prepare_refinement.Rd |only insurancerating-0.8.0/insurancerating/man/print.excess_loss_allocation.Rd |only insurancerating-0.8.0/insurancerating/man/print.excess_threshold_assessment.Rd |only insurancerating-0.8.0/insurancerating/man/rating_factors.Rd | 59 insurancerating-0.8.0/insurancerating/man/rating_factors2.Rd |only insurancerating-0.8.0/insurancerating/man/rating_grid.Rd |only insurancerating-0.8.0/insurancerating/man/rating_table.Rd |only insurancerating-0.8.0/insurancerating/man/reduce.Rd | 68 insurancerating-0.8.0/insurancerating/man/reexports.Rd | 4 insurancerating-0.8.0/insurancerating/man/refit.Rd |only insurancerating-0.8.0/insurancerating/man/refit_glm.Rd | 22 insurancerating-0.8.0/insurancerating/man/relativities.Rd |only insurancerating-0.8.0/insurancerating/man/restrict_coef.Rd | 75 insurancerating-0.8.0/insurancerating/man/rgammat.Rd | 37 insurancerating-0.8.0/insurancerating/man/risk_factor_gam.Rd |only insurancerating-0.8.0/insurancerating/man/riskfactor_gam.Rd |only insurancerating-0.8.0/insurancerating/man/rlnormt.Rd | 36 insurancerating-0.8.0/insurancerating/man/rmse.Rd | 27 insurancerating-0.8.0/insurancerating/man/rows_per_date.Rd | 54 insurancerating-0.8.0/insurancerating/man/scale_second_axis.Rd |only insurancerating-0.8.0/insurancerating/man/set_reference_level.Rd |only insurancerating-0.8.0/insurancerating/man/smooth_coef.Rd | 123 insurancerating-0.8.0/insurancerating/man/split_level.Rd |only insurancerating-0.8.0/insurancerating/man/split_periods_to_months.Rd |only insurancerating-0.8.0/insurancerating/man/split_relativities.Rd |only insurancerating-0.8.0/insurancerating/man/summary.excess_loss_allocation.Rd |only insurancerating-0.8.0/insurancerating/man/summary.excess_threshold_assessment.Rd |only insurancerating-0.8.0/insurancerating/man/univariate.Rd | 55 insurancerating-0.8.0/insurancerating/man/update_glm.Rd | 23 insurancerating-0.8.0/insurancerating/tests/testthat/test_add_prediction.R |only insurancerating-0.8.0/insurancerating/tests/testthat/test_bootstrap_rmse.R | 174 insurancerating-0.8.0/insurancerating/tests/testthat/test_construct_tariff_classes.R | 122 insurancerating-0.8.0/insurancerating/tests/testthat/test_excess_loss.R |only insurancerating-0.8.0/insurancerating/tests/testthat/test_fisher.R |only insurancerating-0.8.0/insurancerating/tests/testthat/test_fitgam.R | 167 insurancerating-0.8.0/insurancerating/tests/testthat/test_model_get_data.R | 258 - insurancerating-0.8.0/insurancerating/tests/testthat/test_model_rating_factors.R | 241 - insurancerating-0.8.0/insurancerating/tests/testthat/test_model_refinement.R | 354 + insurancerating-0.8.0/insurancerating/tests/testthat/test_outlier_histogram.R |only insurancerating-0.8.0/insurancerating/tests/testthat/test_overdispersion.R | 93 insurancerating-0.8.0/insurancerating/tests/testthat/test_residuals.R |only insurancerating-0.8.0/insurancerating/tests/testthat/test_set_reference_level.R |only insurancerating-0.8.0/insurancerating/tests/testthat/test_severity_distribution.R |only insurancerating-0.8.0/insurancerating/tests/testthat/test_smoothing.R | 6 insurancerating-0.8.0/insurancerating/tests/testthat/test_time_utils.R |only insurancerating-0.8.0/insurancerating/tests/testthat/test_truncated_distributions.R |only insurancerating-0.8.0/insurancerating/tests/testthat/test_univariate.R | 240 - insurancerating-0.8.0/insurancerating/vignettes |only 147 files changed, 8497 insertions(+), 3632 deletions(-)
More information about insurancerating at CRAN
Permanent link
Title: Iterative Bias Reduction
Description: Multivariate smoothing using iterative bias reduction with kernel, thin plate splines, Duchon splines or low rank splines.
Author: Pierre-Andre Cornillon [aut, cre],
Nicolas Hengartner [aut],
Eric Matzner-Lober [aut]
Maintainer: Pierre-Andre Cornillon <pierre-andre.cornillon@univ-rennes2.fr>
Diff between ibr versions 2.4-1 dated 2026-05-11 and 2.4-2 dated 2026-06-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/ibr.fit.R | 16 ++++++++++++---- man/forward.Rd | 2 +- man/ibr.Rd | 4 +++- man/ibr.fit.Rd | 6 ++++-- 6 files changed, 29 insertions(+), 17 deletions(-)
Title: Separation of Diffusive and Ebullitive Fluxes
Description: Separates diffusive and ebullitive (bubble) fluxes from
continuous concentration measurements using a running variance approach.
Ebullitive events are identified when the running variance exceeds a
user-set threshold. Diffusive fluxes are calculated via linear regression
on the non-ebullitive portion of the data. See Sø et al. (2024)
<doi:10.1029/2024JG008035> for details.
Author: Jonas Stage Soe [aut, cre] ,
Kaj Sand-Jensen [ctb] ,
Theis Kragh [ctb]
Maintainer: Jonas Stage Soe <Jonassoe@biology.sdu.dk>
Diff between FluxSeparator versions 1.0.1 dated 2026-03-29 and 2.0.0 dated 2026-06-02
DESCRIPTION | 13 +++++++------ MD5 | 13 +++++++++---- NAMESPACE | 36 ++++++++++++++++++++++++++++++++++++ NEWS.md | 6 ++++++ R/FluxSeparatorApp.R |only R/FluxSeparator_PACKAGE.R | 22 +++++++++++++++++++--- R/diff_flux_func.R |only R/ebul_flux_func.R |only inst/shiny |only man/FluxSeparatorApp.Rd |only 10 files changed, 77 insertions(+), 13 deletions(-)
Title: Intraclass Correlation Coefficient (ICC) Design, Calculation and
Interactive 'shiny' Toolkit
Description: A comprehensive toolkit for intraclass correlation coefficient (ICC) analysis,
integrating three core functionalities: (1) Closed-form sample size calculation for ICC
estimation with assurance probability, based on Zou (2012) <doi:10.1002/sim.5466>;
(2) Full implementation of all 10 ICC types (6 common + 4 supplementary) for point
estimation, exact confidence interval calculation, and formal hypothesis testing,
following the methods of McGraw & Wong (1996) <doi:10.1037/1082-989X.1.1.30> and
the standard decision framework; (3) An interactive 'shiny' application that guides users
through ICC type selection, performs calculations, and provides reliability evaluation
based on the Koo & Li (2016) <doi:10.1016/j.jcm.2016.02.012> criteria.
Compared to existing packages, it provides a unified decision workflow and supports
all less common ICC variants.
Author: Ziyu Liu [aut, cre],
Ruilin Ma [aut],
Chenge Gao [aut],
Yundan Zhang [aut]
Maintainer: Ziyu Liu <1755454769@qq.com>
Diff between ICCDesign versions 0.1.0 dated 2026-05-27 and 0.1.1 dated 2026-06-02
DESCRIPTION | 6 ++--- MD5 | 5 ++-- NEWS.md |only R/utils-calc.R | 62 +++++++++++++++++++++++++++++++++++++++++---------------- 4 files changed, 51 insertions(+), 22 deletions(-)
More information about DENSaftertransform at CRAN
Permanent link
Title: High Performance Tables Using 'Cheetah Grid'
Description: An R interface to 'Cheetah Grid', a high-performance JavaScript table widget.
'cheetahR' allows users to render millions of rows in just a few milliseconds,
making it an excellent alternative to other R table widgets. The package wraps
the 'Cheetah Grid' JavaScript functions and makes them readily available for R users.
The underlying grid implementation is based on 'Cheetah Grid'
<https://github.com/future-architect/cheetah-grid>.
Author: Olajoke Oladipo [aut, cre],
David Granjon [aut],
cynkra GmbH [fnd]
Maintainer: Olajoke Oladipo <olajoke@cynkra.com>
Diff between cheetahR versions 0.3.0 dated 2025-07-21 and 0.4.0 dated 2026-06-02
DESCRIPTION | 8 MD5 | 34 +-- NAMESPACE | 1 NEWS.md | 7 R/cheetah_utils.R | 30 ++ R/cheetahr_shiny_utils.R |only R/utils.R | 21 +- README.md | 15 - build/vignette.rds |binary inst/doc/cheetahR.R | 66 ++++++ inst/doc/cheetahR.html | 374 +++++++++++++++++++++++++++++------- inst/doc/cheetahR.qmd | 106 ++++++++++ inst/examples |only inst/htmlwidgets/cheetah.js | 2 inst/htmlwidgets/cheetah.js.map |only man/cheetahr_shiny_utils.Rd |only man/column_def.Rd | 22 ++ man/get_grid_data.Rd |only tests/testthat/test-get_grid_data.R |only tests/testthat/test-utils.R | 47 ++++ vignettes/cheetahR.qmd | 106 ++++++++++ 21 files changed, 742 insertions(+), 97 deletions(-)
More information about actigraph.sleepr at CRAN
Permanent link
Title: Working with United States ZIP Code and ZIP Code Tabulation Area
Data
Description: Provides a set of functions for working with American postal codes,
which are known as ZIP Codes. These include accessing ZIP Code to ZIP Code
Tabulation Area (ZCTA) crosswalks, retrieving demographic data for ZCTAs, and
tabulating demographic data for three-digit ZCTAs.
Author: Christopher Prener [aut, cre] ,
Timothy Wiemken [aut] ,
Angela Cook [aut]
Maintainer: Christopher Prener <Christopher.Prener@pfizer.com>
Diff between zippeR versions 0.1.2 dated 2025-04-25 and 0.2.0 dated 2026-06-02
DESCRIPTION | 26 +- MD5 | 111 ++++----- NEWS.md | 22 + R/zi_aggregate.R | 210 +++++++++++------ R/zi_convert.R | 36 +- R/zi_crosswalk.R | 182 ++++++++++----- R/zi_get_demographics.R | 85 ++++--- R/zi_get_geometry.R | 259 +++++++++++++-------- R/zi_globals.R | 2 R/zi_label.R | 93 ++++--- R/zi_list_zctas.R | 58 +++- R/zi_load_crosswalk.R | 181 ++++++++------- R/zi_load_labels.R | 64 +++-- R/zi_load_labels_list.R | 13 - R/zi_mo_hud.R | 1 R/zi_mo_pop.R | 3 R/zi_mo_usps.R | 1 R/zi_mo_zcta3.R | 1 R/zi_prep_hud.R | 46 ++- R/zi_utils.R | 74 +++--- R/zi_validate.R | 77 +++--- README.md | 30 ++ build/vignette.rds |binary inst/WORDLIST |only inst/doc/converting-zips.Rmd | 21 - inst/doc/converting-zips.html | 91 +++---- inst/doc/three-digit-zips.Rmd | 2 inst/doc/three-digit-zips.html | 6 inst/extdata |only man/zi_aggregate.Rd | 22 + man/zi_convert.Rd | 8 man/zi_crosswalk.Rd | 52 ++-- man/zi_get_demographics.Rd | 19 + man/zi_get_geometry.Rd | 34 +- man/zi_label.Rd | 29 +- man/zi_list_zctas.Rd | 5 man/zi_load_crosswalk.Rd | 29 +- man/zi_load_labels.Rd | 13 - man/zi_load_labels_list.Rd | 5 man/zi_mo_hud.Rd | 2 man/zi_mo_pop.Rd | 4 man/zi_mo_usps.Rd | 2 man/zi_mo_zcta3.Rd | 2 man/zi_repair.Rd | 2 tests/testthat/helper-skip.R |only tests/testthat/test_zi_aggregate.R | 362 +++++++++++++++++++++++++++--- tests/testthat/test_zi_convert.R |only tests/testthat/test_zi_crosswalk.R | 204 ++++++++++++++++ tests/testthat/test_zi_get_demographics.R | 79 +++++- tests/testthat/test_zi_get_geometry.R | 120 +++++++-- tests/testthat/test_zi_label.R |only tests/testthat/test_zi_list_zctas.R | 30 +- tests/testthat/test_zi_load_crosswalk.R | 103 ++++++++ tests/testthat/test_zi_load_hud.R |only tests/testthat/test_zi_load_labels.R |only tests/testthat/test_zi_load_labels_list.R |only tests/testthat/test_zi_prep_hud.R |only tests/testthat/test_zi_repair.R | 14 - tests/testthat/test_zi_validate.R | 12 vignettes/converting-zips.Rmd | 21 - vignettes/three-digit-zips.Rmd | 2 61 files changed, 2025 insertions(+), 845 deletions(-)
Title: Nonlinear Dependence and Lead-Lag Analysis via Chatterjee's Xi
Description: Computes Chatterjee's non-parametric correlation coefficient for time series data. It extends the original metric to time series analysis by providing the univariate Xi-Autocorrelation Function (Xi-ACF), directional Xi-Cross-Correlation Function (Xi-CCF), and multivariate network evaluation matrices. The package allows users to test for non-linear dependence using Iterative Amplitude Adjusted Fourier Transform (IAAFT) and Multivariate IAAFT (MIAAFT) surrogate data with strict Family-Wise Error Rate ('FWER') control via Max-statistic approaches. Methodologies are based on Chatterjee (2021) <doi:10.1080/01621459.2020.1758115>, surrogate data testing methods by Schreiber and Schmitz (1996) <doi:10.1103/PhysRevLett.77.635>, and local structural identification by Watanabe (2026) <doi:10.2139/ssrn.6829431>.
Author: Yasunori Watanabe [aut, cre]
Maintainer: Yasunori Watanabe <watanabe.yasunori@outlook.com>
Diff between xiacf versions 0.6.1 dated 2026-05-31 and 0.6.2 dated 2026-06-02
DESCRIPTION | 11 ++++++----- MD5 | 31 ++++++++++++++++--------------- NAMESPACE | 1 + NEWS.md | 16 ++++++++++++++++ R/extract.R | 4 ++-- R/utils.R | 4 ++-- R/xi_acf.R | 2 +- R/xi_ccf.R | 27 +++++---------------------- R/xi_matrix.R | 4 +--- R/xi_rolling_acf.R | 8 ++++++-- R/xi_rolling_ccf.R | 8 ++++++-- man/extract_xi_acf.Rd | 9 +++++---- man/extract_xi_ccf.Rd | 9 +++++---- man/reexports.Rd | 2 +- man/run_rolling_xi_acf.Rd | 3 +++ man/run_rolling_xi_ccf.Rd | 3 +++ tests/testthat/setup.R |only 17 files changed, 79 insertions(+), 63 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 3.6-0 dated 2026-04-02 and 3.6-1 dated 2026-06-02
DESCRIPTION | 16 +- MD5 | 56 +++++----- NEWS | 8 + build/vignette.rds |binary inst/doc/NAobjects.R | 2 inst/doc/NAobjects.pdf |binary inst/doc/bugfixes.R | 2 inst/doc/bugfixes.Rnw | 9 + inst/doc/bugfixes.pdf |binary inst/doc/datasets.R | 2 inst/doc/datasets.pdf |binary inst/doc/fv.R | 2 inst/doc/fv.pdf |binary inst/doc/getstart.R | 2 inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 2 inst/doc/replicated.R | 2 inst/doc/replicated.pdf |binary inst/doc/shapefiles.R | 2 inst/doc/shapefiles.pdf |binary inst/doc/spatstatKnetsize.txt | 1 inst/doc/updates.R | 25 ++-- inst/doc/updates.Rnw | 235 +++++++++++++++++++++++++++++++++++++++--- inst/doc/updates.pdf |binary inst/info/packagesizes.txt | 2 man/macros/defns.Rd | 1 man/spatstat-package.Rd | 13 +- vignettes/bugfixes.Rnw | 9 + vignettes/updates.Rnw | 235 +++++++++++++++++++++++++++++++++++++++--- 29 files changed, 525 insertions(+), 101 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gabriel Staples [ctb],
Gerhard W [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 5.1.1 dated 2026-05-28 and 5.1.2 dated 2026-06-02
DESCRIPTION | 6 +- MD5 | 25 +++++------ NAMESPACE | 1 NEWS.md | 15 ++++++ R/etNew.R | 5 ++ R/geom-cens.R | 87 +++++++++++++++++++++++++--------------- R/rxode2.R | 29 ++++++++++++- R/rxode2_md5.R | 2 R/utils.R | 3 + inst/doc/rxode2-syntax.html | 26 +++++------ inst/include/rxode2parseVer.h | 4 - man/stat_cens.Rd | 15 +++++- tests/testthat.R | 14 ++++-- tests/testthat/test-geom-cens.R |only 14 files changed, 159 insertions(+), 73 deletions(-)
Title: Read and Write 'las' and 'laz' Binary File Formats Used for
Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://community.asprs.org/leadership-restricted/leadership-content/public-documents/standards>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.4 <https://laszip.org/>.
Author: Jean-Romain Roussel [aut, cre, cph],
Florian De Boissieu [aut, ctb] ,
Martin Isenburg [cph] ,
David Auty [ctb] ,
Pierrick Marie [ctb] ,
Tiago de Conto [ctb]
Maintainer: Jean-Romain Roussel <info@r-lidar.com>
Diff between rlas versions 1.9.2 dated 2026-05-21 and 1.9.3 dated 2026-06-02
rlas-1.9.2/rlas/inst/tinytest/test-remote.R |only rlas-1.9.3/rlas/DESCRIPTION | 6 rlas-1.9.3/rlas/MD5 | 17 - rlas-1.9.3/rlas/NEWS.md | 3 rlas-1.9.3/rlas/src/LASzip/integercompressor.cpp | 24 +- rlas-1.9.3/rlas/src/LASzip/lasreaditemcompressed_v3.cpp | 83 +++----- rlas-1.9.3/rlas/src/LASzip/lasreaditemcompressed_v4.cpp | 148 ++++++-------- rlas-1.9.3/rlas/src/LASzip/lasreaditemraw.hpp | 16 - rlas-1.9.3/rlas/src/LASzip/laswriteitemcompressed_v3.cpp | 152 ++++++--------- rlas-1.9.3/rlas/src/LASzip/laswriteitemcompressed_v4.cpp | 152 ++++++--------- 10 files changed, 273 insertions(+), 328 deletions(-)
Title: NASA POWER API Client
Description: An API client for NASA POWER global meteorology, surface
solar energy and climatology data API. POWER (Prediction Of Worldwide
Energy Resources) data are freely available for download with varying
spatial resolutions dependent on the original data and with several
temporal resolutions depending on the POWER parameter and community.
This work is funded through the NASA Earth Science Directorate Applied
Science Program. For more on the data themselves, the methodologies
used in creating, a web-based data viewer and web access, please see
<https://power.larc.nasa.gov/>.
Author: Adam H. Sparks [aut, cre] ,
Scott Chamberlain [rev] ,
Hazel Kavili [rev] ,
Alison Boyer [rev] ,
Fernando Miguez [ctb] ,
Maelle Salmon [ctb] ,
Phillip D. Alderman [ctb] ` must use `I` for literal data as of vroom 1.5.0.', see
<https://github.com/ropen [...truncated...]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Diff between nasapower versions 4.2.5 dated 2025-05-31 and 4.3.0 dated 2026-06-02
nasapower-4.2.5/nasapower/tests/fixtures |only nasapower-4.3.0/nasapower/.aspell/defaults.R | 9 nasapower-4.3.0/nasapower/DESCRIPTION | 35 - nasapower-4.3.0/nasapower/MD5 | 68 -- nasapower-4.3.0/nasapower/NEWS.md | 29 nasapower-4.3.0/nasapower/R/get_power.R | 113 ++- nasapower-4.3.0/nasapower/R/internal_functions.R | 275 ++++---- nasapower-4.3.0/nasapower/R/nasapower-options.R |only nasapower-4.3.0/nasapower/R/print_POWER_Info.R | 16 nasapower-4.3.0/nasapower/R/query_groupings.R | 43 - nasapower-4.3.0/nasapower/R/query_parameters.R | 152 ++-- nasapower-4.3.0/nasapower/R/query_surfaces.R | 38 - nasapower-4.3.0/nasapower/R/set_request_options.R |only nasapower-4.3.0/nasapower/R/sysdata.rda |binary nasapower-4.3.0/nasapower/README.md | 54 - nasapower-4.3.0/nasapower/build/vignette.rds |binary nasapower-4.3.0/nasapower/inst/WORDLIST | 14 nasapower-4.3.0/nasapower/inst/doc/nasapower.Rmd | 300 ++++----- nasapower-4.3.0/nasapower/inst/doc/nasapower.html | 332 ++++------ nasapower-4.3.0/nasapower/man/get_power.Rd | 43 - nasapower-4.3.0/nasapower/man/nasapower-options.Rd |only nasapower-4.3.0/nasapower/man/nasapower-package.Rd | 16 nasapower-4.3.0/nasapower/man/query_groupings.Rd | 20 nasapower-4.3.0/nasapower/man/query_parameters.Rd | 52 - nasapower-4.3.0/nasapower/man/query_surfaces.Rd | 15 nasapower-4.3.0/nasapower/tests/testthat/helper-vcr.R | 1 nasapower-4.3.0/nasapower/tests/testthat/helper-webmockr.R |only nasapower-4.3.0/nasapower/tests/testthat/test-options.R |only nasapower-4.3.0/nasapower/tests/testthat/test-query_groupings.R | 94 ++ nasapower-4.3.0/nasapower/tests/testthat/test-query_parameters.R | 188 +++-- nasapower-4.3.0/nasapower/tests/testthat/test-query_surfaces.R | 168 +++-- nasapower-4.3.0/nasapower/vignettes/!precompile.R | 5 nasapower-4.3.0/nasapower/vignettes/nasapower.Rmd | 300 ++++----- nasapower-4.3.0/nasapower/vignettes/nasapower.Rmd.orig | 27 34 files changed, 1339 insertions(+), 1068 deletions(-)
Title: Interactive 'shiny' GUI for the 'earth' Package
Description: Provides a 'shiny'-based graphical user interface for the 'earth'
package, enabling interactive building and exploration of Multivariate
Adaptive Regression Splines (MARS) models. Features include data import
from CSV and 'Excel' files, automatic detection of categorical variables,
interactive control of interaction terms via an allowed matrix,
comprehensive model diagnostics with variable importance and partial
dependence plots, and publication-quality report generation via 'Quarto'.
Author: William Craytor [aut, cre]
Maintainer: William Craytor <bcraytor@proton.me>
Diff between earthUI versions 0.1.3 dated 2026-03-18 and 0.8.0 dated 2026-06-02
earthUI-0.1.3/earthUI/inst/app/sales_grid.R |only earthUI-0.8.0/earthUI/DESCRIPTION | 15 earthUI-0.8.0/earthUI/MD5 | 126 earthUI-0.8.0/earthUI/NAMESPACE | 41 earthUI-0.8.0/earthUI/NEWS.md | 265 earthUI-0.8.0/earthUI/R/build_allowed.R | 24 earthUI-0.8.0/earthUI/R/build_sales_grid.R |only earthUI-0.8.0/earthUI/R/compute_intermediate_output.R |only earthUI-0.8.0/earthUI/R/compute_rca_adjustments.R |only earthUI-0.8.0/earthUI/R/compute_sale_age.R |only earthUI-0.8.0/earthUI/R/detect_types.R | 79 earthUI-0.8.0/earthUI/R/export_report.R | 382 + earthUI-0.8.0/earthUI/R/export_results.R |only earthUI-0.8.0/earthUI/R/export_settings.R |only earthUI-0.8.0/earthUI/R/fit_earth.R | 17 earthUI-0.8.0/earthUI/R/launch.R | 79 earthUI-0.8.0/earthUI/R/locale.R | 47 earthUI-0.8.0/earthUI/R/plot_results.R | 15 earthUI-0.8.0/earthUI/R/regproj.R |only earthUI-0.8.0/earthUI/R/regproj_db.R |only earthUI-0.8.0/earthUI/R/select_sales_grid_comps.R |only earthUI-0.8.0/earthUI/R/settings_db.R | 16 earthUI-0.8.0/earthUI/README.md | 95 earthUI-0.8.0/earthUI/build/vignette.rds |binary earthUI-0.8.0/earthUI/inst/app/global.R | 28 earthUI-0.8.0/earthUI/inst/app/server.R | 3028 +++++++--- earthUI-0.8.0/earthUI/inst/app/ui.R | 1009 ++- earthUI-0.8.0/earthUI/inst/batch_run.R |only earthUI-0.8.0/earthUI/inst/doc/g-functions.html | 18 earthUI-0.8.0/earthUI/inst/doc/getting-started.R | 6 earthUI-0.8.0/earthUI/inst/doc/getting-started.Rmd | 50 earthUI-0.8.0/earthUI/inst/doc/getting-started.html | 101 earthUI-0.8.0/earthUI/inst/doc/user-guide.R | 7 earthUI-0.8.0/earthUI/inst/doc/user-guide.Rmd | 175 earthUI-0.8.0/earthUI/inst/doc/user-guide.html | 274 earthUI-0.8.0/earthUI/inst/extdata/regproj_geo.rds |only earthUI-0.8.0/earthUI/inst/extdata/regproj_reference.json |only earthUI-0.8.0/earthUI/inst/quarto/earth_report.qmd | 147 earthUI-0.8.0/earthUI/inst/quarto/reference.docx |binary earthUI-0.8.0/earthUI/man/auto_export_for_mgcv.Rd |only earthUI-0.8.0/earthUI/man/build_allowed_function.Rd | 17 earthUI-0.8.0/earthUI/man/build_sales_grid.Rd |only earthUI-0.8.0/earthUI/man/city_abbreviation.Rd |only earthUI-0.8.0/earthUI/man/compute_intermediate_output.Rd |only earthUI-0.8.0/earthUI/man/compute_rca_adjustments.Rd |only earthUI-0.8.0/earthUI/man/compute_sale_age.Rd |only earthUI-0.8.0/earthUI/man/convert_quarto_file.Rd |only earthUI-0.8.0/earthUI/man/country_choices.Rd |only earthUI-0.8.0/earthUI/man/country_schema.Rd |only earthUI-0.8.0/earthUI/man/default_regproj_root.Rd |only earthUI-0.8.0/earthUI/man/earthui_prefs_path.Rd |only earthUI-0.8.0/earthUI/man/earthui_prefs_read.Rd |only earthUI-0.8.0/earthUI/man/earthui_prefs_write.Rd |only earthUI-0.8.0/earthUI/man/export_settings.Rd |only earthUI-0.8.0/earthUI/man/generate_quarto_report.Rd |only earthUI-0.8.0/earthUI/man/get_project_settings.Rd |only earthUI-0.8.0/earthUI/man/is_project_dir.Rd |only earthUI-0.8.0/earthUI/man/launch.Rd | 5 earthUI-0.8.0/earthUI/man/os_detect.Rd |only earthUI-0.8.0/earthUI/man/prepare_report_assets.Rd |only earthUI-0.8.0/earthUI/man/regproj_flat_segment.Rd |only earthUI-0.8.0/earthUI/man/regproj_geo_db_connect.Rd |only earthUI-0.8.0/earthUI/man/regproj_geo_db_path.Rd |only earthUI-0.8.0/earthUI/man/regproj_in_files.Rd |only earthUI-0.8.0/earthUI/man/regproj_index_get.Rd |only earthUI-0.8.0/earthUI/man/regproj_index_path.Rd |only earthUI-0.8.0/earthUI/man/regproj_index_put.Rd |only earthUI-0.8.0/earthUI/man/regproj_index_read.Rd |only earthUI-0.8.0/earthUI/man/regproj_index_write.Rd |only earthUI-0.8.0/earthUI/man/regproj_last_file.Rd |only earthUI-0.8.0/earthUI/man/regproj_list_projects.Rd |only earthUI-0.8.0/earthUI/man/regproj_parse_flat.Rd |only earthUI-0.8.0/earthUI/man/regproj_path.Rd |only earthUI-0.8.0/earthUI/man/regproj_projects_db_connect.Rd |only earthUI-0.8.0/earthUI/man/regproj_projects_db_path.Rd |only earthUI-0.8.0/earthUI/man/regproj_reference.Rd |only earthUI-0.8.0/earthUI/man/render_report.Rd | 6 earthUI-0.8.0/earthUI/man/select_sales_grid_comps.Rd |only earthUI-0.8.0/earthUI/man/set_project_settings.Rd |only earthUI-0.8.0/earthUI/man/write_earth_output.Rd |only earthUI-0.8.0/earthUI/man/write_fit_log.Rd |only earthUI-0.8.0/earthUI/tests/testthat/test-detect_types.R | 47 earthUI-0.8.0/earthUI/tests/testthat/test-eval_g_function.R |only earthUI-0.8.0/earthUI/tests/testthat/test-export_report.R | 205 earthUI-0.8.0/earthUI/tests/testthat/test-fit_earth.R | 16 earthUI-0.8.0/earthUI/tests/testthat/test-intermediate_output.R | 25 earthUI-0.8.0/earthUI/tests/testthat/test-plot_g_3d_transposition.R |only earthUI-0.8.0/earthUI/tests/testthat/test-quarto_export.R |only earthUI-0.8.0/earthUI/tests/testthat/test-regproj_db.R |only earthUI-0.8.0/earthUI/tests/testthat/test-regproj_helpers.R |only earthUI-0.8.0/earthUI/tests/testthat/test-regproj_path.R |only earthUI-0.8.0/earthUI/vignettes/getting-started.Rmd | 50 earthUI-0.8.0/earthUI/vignettes/user-guide.Rmd | 175 93 files changed, 5355 insertions(+), 1235 deletions(-)
Title: Survey Instrument Workflows
Description: Supports survey research workflows built around a typed
instrument object (the sframe). Features include visual instrument
design via a browser-based builder or 'Shiny' studio, export to a
self-contained static HTML survey, an embeddable 'Shiny' module, SHA-256
integrity-checked serialisation to the '.sframe' format, multi-page survey
rendering, branching logic, response quality checking, scale scoring,
psychometric diagnostics, analysis-plan execution, model syntax planning,
an interactive response dashboard, codebook generation, and reproducible
HTML reporting.
Author: Mohammed Ali Sharafuddin [aut, cre]
Maintainer: Mohammed Ali Sharafuddin <mohammedali.page@gmail.com>
Diff between surveyframe versions 0.3.0 dated 2026-05-27 and 0.3.1 dated 2026-06-02
DESCRIPTION | 6 MD5 | 125 +- NEWS.md | 74 + R/analysis_plan.R | 6 R/conditions.R | 16 R/dashboard.R | 2 R/export_static_survey.R | 8 R/google_sheets.R | 17 R/launch_studio.R | 2 R/model_layer.R | 4 R/psychometrics.R | 49 R/quality_report.R | 2 R/read_responses.R | 2 R/read_write_sframe.R | 19 R/render_survey.R | 12 R/reporting.R | 4 R/score_scales.R | 2 R/sf_instrument.R | 26 R/studio_builder.R | 2 R/surveyframe-package.R | 13 R/validate_sframe.R | 2 README.md | 199 ++- build/vignette.rds |binary inst/builder/survey_builder.html | 6 inst/doc/analysing-survey-responses.R | 115 -- inst/doc/analysing-survey-responses.Rmd | 187 +-- inst/doc/analysing-survey-responses.html | 803 ++++++++++---- inst/doc/building-survey-instrument.R | 188 +-- inst/doc/building-survey-instrument.Rmd | 247 ++-- inst/doc/building-survey-instrument.html | 295 ++--- inst/doc/efa-cfa-sem-pls-syntax.R | 112 +- inst/doc/efa-cfa-sem-pls-syntax.Rmd | 193 +-- inst/doc/efa-cfa-sem-pls-syntax.html | 515 ++++----- inst/doc/scale-reliability-validity.R | 73 - inst/doc/scale-reliability-validity.Rmd | 157 +- inst/doc/scale-reliability-validity.html | 475 ++------ inst/doc/surveybuilder-gui-overview.R | 14 inst/doc/surveybuilder-gui-overview.Rmd | 147 +- inst/doc/surveybuilder-gui-overview.html | 156 +- inst/doc/surveyframe.R | 637 ++++++++--- inst/doc/surveyframe.Rmd | 910 +++++++++++----- inst/doc/surveyframe.html | 1711 +++++++++++++------------------ inst/shiny/app.R | 8 inst/shiny/dashboard/app.R | 4 inst/shiny/dashboard/www |only inst/shiny/www |only inst/static_survey/template.html | 28 man/efa_report.Rd | 4 man/figures |only man/sf_instrument.Rd | 26 man/surveyframe-package.Rd | 13 tests/testthat/test-0.3.1-fixes.R |only vignettes/analysing-survey-responses.Rmd | 187 +-- vignettes/building-survey-instrument.Rmd | 247 ++-- vignettes/efa-cfa-sem-pls-syntax.Rmd | 193 +-- vignettes/scale-reliability-validity.Rmd | 157 +- vignettes/surveybuilder-gui-overview.Rmd | 147 +- vignettes/surveyframe.Rmd | 910 +++++++++++----- 58 files changed, 5522 insertions(+), 3935 deletions(-)
Title: Hierarchical Piecewise Regression with Smoothed Change-Points
Description: Fits Bayesian hierarchical piecewise regression models with
multiple logistic-smoothed change-points. Non-linear parameters (change-point
locations and transition sharpness) and linear parameters can each be
conditioned on covariates and factors via flexible design matrices.
A random-intercept structure is supported for any parameter. Spike-and-slab
regularization is supported for selecting the number of breakpoints.
Posterior inference uses a Metropolis-within-Gibbs sampler implemented
in 'Rust' for speed. Methods are based on the smooth transition
piecewise regression model of Bacon and Watts (1971) <doi:10.2307/2334389>
and variable selection spike-and-slab priors of Kuo and Mallick (1998)
<https://www.jstor.org/stable/25053023>.
Author: Aidan D Bindoff [aut, cre]
Maintainer: Aidan D Bindoff <aidan.bindoff@utas.edu.au>
Diff between smoothbp versions 0.2.1 dated 2026-06-01 and 0.2.2 dated 2026-06-02
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 4 ++++ R/priors.R | 8 ++++---- R/smoothbp.R | 11 +++++++---- R/smoothbp_ss.R | 3 ++- man/smoothbp.Rd | 2 +- man/update.smoothbp_fit.Rd | 3 ++- src/Makevars.in | 6 +++--- src/Makevars.win.in | 6 +++--- src/rust/src/lib.rs | 36 ++++++++++++++++++++---------------- src/rust/src/model.rs | 15 ++++++++++++++- tools/config.R | 8 +++++++- 13 files changed, 82 insertions(+), 50 deletions(-)
Title: Robust Mixture Regression
Description: Finite mixture models are a popular technique for modelling unobserved heterogeneity or to approximate general distribution functions in a semi-parametric way. They are used in a lot of different areas such as astronomy, biology, economics, marketing or medicine.
This package is the implementation of popular robust mixture regression methods based on different algorithms including: fleximix, finite mixture models and latent class regression; CTLERob, component-wise adaptive trimming likelihood estimation; mixbi, bi-square estimation; mixL, Laplacian distribution; mixt, t-distribution; TLE, trimmed likelihood estimation.
The implemented algorithms includes: CTLERob stands for Component-wise adaptive Trimming Likelihood Estimation based mixture regression; mixbi stands for mixture regression based on bi-square estimation; mixLstands for mixture regression based on Laplacian distribution; TLE stands for Trimmed Likelihood Estimation based mixture regression. For more detail of the algori [...truncated...]
Author: Sha Cao [aut, cph, ths],
Wennan Chang [aut, cre],
Chi Zhang [aut, ctb, ths]
Maintainer: Wennan Chang <changwn.nku@gmail.com>
Diff between RobMixReg versions 1.1.0 dated 2020-08-05 and 1.1.3 dated 2026-06-02
RobMixReg-1.1.0/RobMixReg/data/datalist |only RobMixReg-1.1.3/RobMixReg/DESCRIPTION | 18 +- RobMixReg-1.1.3/RobMixReg/MD5 | 56 ++++--- RobMixReg-1.1.3/RobMixReg/NAMESPACE | 1 RobMixReg-1.1.3/RobMixReg/R/CTLE.short.rob.R | 2 RobMixReg-1.1.3/RobMixReg/R/CWM.short.R |only RobMixReg-1.1.3/RobMixReg/R/mixtureReg.R | 2 RobMixReg-1.1.3/RobMixReg/R/outer2.R | 2 RobMixReg-1.1.3/RobMixReg/README.md | 143 +++++++++---------- RobMixReg-1.1.3/RobMixReg/man/CCLE_data.Rd | 6 RobMixReg-1.1.3/RobMixReg/man/CTLERob-methods.Rd | 4 RobMixReg-1.1.3/RobMixReg/man/InitClusters_i.Rd |only RobMixReg-1.1.3/RobMixReg/man/MLM.Rd | 20 +- RobMixReg-1.1.3/RobMixReg/man/TLE-methods.Rd | 4 RobMixReg-1.1.3/RobMixReg/man/TreatSingularity.Rd |only RobMixReg-1.1.3/RobMixReg/man/calcobj_i.Rd |only RobMixReg-1.1.3/RobMixReg/man/colon_data.Rd | 6 RobMixReg-1.1.3/RobMixReg/man/dmnorm.Rd |only RobMixReg-1.1.3/RobMixReg/man/estimClustPar_i.Rd |only RobMixReg-1.1.3/RobMixReg/man/findClustAssig_i.Rd |only RobMixReg-1.1.3/RobMixReg/man/flexmix_2.Rd | 2 RobMixReg-1.1.3/RobMixReg/man/gaussData.Rd | 6 RobMixReg-1.1.3/RobMixReg/man/getini.Rd |only RobMixReg-1.1.3/RobMixReg/man/lars.lsa.Rd | 11 + RobMixReg-1.1.3/RobMixReg/man/mixLp-methods.Rd | 4 RobMixReg-1.1.3/RobMixReg/man/mixlinrb_bi-methods.Rd | 4 RobMixReg-1.1.3/RobMixReg/man/mixtureReg.Rd | 18 +- RobMixReg-1.1.3/RobMixReg/man/plot_CTLE-methods.Rd | 1 RobMixReg-1.1.3/RobMixReg/man/plot_mixtureReg.Rd | 11 + RobMixReg-1.1.3/RobMixReg/man/restr.diffax_i1.Rd |only RobMixReg-1.1.3/RobMixReg/man/restr.diffax_i2.Rd |only RobMixReg-1.1.3/RobMixReg/man/restr2_eigenv.Rd |only RobMixReg-1.1.3/RobMixReg/man/rmr.Rd | 11 + RobMixReg-1.1.3/RobMixReg/man/simuData.Rd | 6 RobMixReg-1.1.3/RobMixReg/man/ssclmat.Rd |only RobMixReg-1.1.3/RobMixReg/man/trim.cwm.Rd |only 36 files changed, 195 insertions(+), 143 deletions(-)
Title: Create and Maintain a Relational Database of Data from
PubMed/MEDLINE
Description: Provides a simple interface for extracting various elements from
the publicly available PubMed XML files, incorporating PubMed's regular
updates, and combining the data with the NIH Open Citation Collection. See
Schoenbachler and Hughey (2021) <doi:10.7717/peerj.11071>.
Author: Jake Hughey [aut, cre],
Josh Schoenbachler [aut],
Elliot Outland [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Diff between pmparser versions 1.0.25 dated 2026-03-02 and 1.0.26 dated 2026-06-02
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 3 +++ R/get_citation.R | 11 ++++++----- 4 files changed, 16 insertions(+), 12 deletions(-)
Title: Multinomial Logit Models
Description: Maximum likelihood estimation of random utility discrete
choice models. The software is described in Croissant (2020)
<doi:10.18637/jss.v095.i11> and the underlying methods in
Train (2009) <doi:10.1017/CBO9780511805271>.
Author: Yves Croissant [aut, cre]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between mlogit versions 1.1-3 dated 2025-07-12 and 2.0-0 dated 2026-06-02
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Title: GWAS-to-CRISPR Data Pipeline for High-Throughput SNP Target
Extraction
Description: Provides a reproducible pipeline to conduct genome-wide association studies
(GWAS) and extract single-nucleotide polymorphisms (SNPs) for a human trait or
disease. Given aggregated GWAS dataset(s) and a user-defined significance threshold,
the package retrieves significant SNPs from the GWAS Catalog using supported trait
identifiers, annotates their gene context, and can write a
harmonised metadata table in comma-separated values (CSV) format, genomic intervals in the Browser Extensible Data
(BED) format, and sequences in the FASTA (text-based sequence) format with user-defined flanking regions for clustered
regularly interspaced short palindromic repeats (CRISPR) guide design. The existing
efo_id argument is retained for backward compatibility. The package prepares
computational artifacts for downstream workflows; it does not perform biological
causality testing, clinical interpretation, therapeutic design, or wet-lab validation.
For details on the resources and methods see:
Buniello [...truncated...]
Author: Othman S. I. Mohammed [aut, cre],
LEOPARD.LY LTD [cph]
Maintainer: Othman S. I. Mohammed <admin@leopard.ly>
Diff between gwas2crispr versions 0.1.4 dated 2026-05-09 and 0.1.5 dated 2026-06-02
DESCRIPTION | 19 MD5 | 37 + NAMESPACE | 14 NEWS.md | 19 R/fetch_gwas.R | 599 ++++++++++++++++++++---------- R/run_gwas2crispr.R | 108 +++-- R/trait_id.R |only R/variant_coordinates.R |only README.md | 468 ++++++++++++++++++++--- inst/WORDLIST | 8 inst/doc/gwas2crispr.R | 4 inst/doc/gwas2crispr.Rmd | 25 - inst/doc/gwas2crispr.html | 129 +++--- inst/scripts/gwas2crispr.R | 34 + man/fetch_gwas.Rd | 93 ++-- man/gwas2crispr-package.Rd | 56 +- man/run_gwas2crispr.Rd | 145 +++---- tests/testthat/test-fetch_gwas.R | 167 +++++++- tests/testthat/test-run_gwas2crispr.R | 6 tests/testthat/test-variant_coordinates.R |only vignettes/gwas2crispr.Rmd | 25 - 21 files changed, 1377 insertions(+), 579 deletions(-)
Title: Functions for Tabular Reporting
Description: Use a grammar for creating and customizing pretty tables.
The following formats are supported: 'HTML', 'PDF', 'RTF', 'Microsoft
Word', 'Microsoft PowerPoint', R 'Grid Graphics' and 'patchwork'.
'R Markdown', 'Quarto' and the package 'officer' can be used to
produce the result files. The syntax is the same for the user
regardless of the type of output to be produced. A set of functions
allows the creation, definition of cell arrangement, addition of
headers or footers, formatting and definition of cell content with
text and or images. The package also offers a set of high-level
functions that allow tabular reporting of statistical models and the
creation of complex cross tabulations.
Author: David Gohel [aut, cre],
ArData [cph],
Clementine Jager [ctb],
Eli Daniels [ctb],
Panagiotis Skintzos [aut],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb],
Titouan Robert [ctb],
Michael Barrowman [ctb],
Atsushi Yasumoto [ctb],
Paul Julian [ctb],
Sean B [...truncated...]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.9.11 dated 2026-02-13 and 0.9.12 dated 2026-06-02
DESCRIPTION | 19 MD5 | 465 +++++------ NAMESPACE | 8 NEWS.md | 48 + R/00-deprecated.R |only R/00_utils.R | 62 + R/01_fpstruct.R | 463 ++++++++--- R/05_content.R | 73 + R/append_chunk.R | 33 R/as_flextable.R | 474 +++++++---- R/as_flextable.tabular.R | 123 ++ R/as_flextable_gam.R | 125 ++ R/as_flextable_rtables.R |only R/as_flextable_tabulator.R | 301 +++++-- R/augment_rows.R | 358 ++++++-- R/body_add_flextable.R | 34 R/border_fix.R | 49 - R/captions.R | 64 + R/chunk_images.R | 190 +++- R/clintables.R | 152 ++- R/compose.R | 46 - R/defaults.R | 223 +++-- R/df_printer.R | 80 + R/doc-selectors.R | 2 R/docx_str.R | 323 ++++--- R/empty.R | 13 R/flextable.R | 143 ++- R/flextable_sizes.R | 682 ++++++++++++++-- R/footnote.R | 60 - R/format_fun.R | 232 +++-- R/formatters.R | 257 ++++-- R/grid_funs.R | 1255 +++++++++++++++++++----------- R/grid_grobs.R | 405 ++++++--- R/html_str.R | 341 +++++--- R/latex-borders.R | 243 +++-- R/latex_chunks.R | 62 + R/latex_str.R | 356 ++++++-- R/merge_flextable.R | 72 + R/nrowcol.R | 10 R/ooxml-utils.R | 40 R/paginate.R | 60 + R/patchwork.R | 2 R/ph_with.R | 8 R/pptx_str.R | 178 +++- R/printers.R | 221 +++-- R/proc_freq.R | 121 +- R/read_structure.R | 154 ++- R/rtf_str.R | 166 ++- R/runs_as_functions.R | 487 ++++++++--- R/splitters.R |only R/styles.R | 136 +-- R/summarizor.R | 121 +- R/table-properties.R | 7 R/tabpart_mains.R | 51 - R/tabpart_tools.R | 28 R/themes.R | 119 ++ R/utils.R | 68 + R/xtable_to_flextable.R | 79 + R/zz-defunct.R | 5 README.md | 2 build/vignette.rds |binary inst/web_1.1.3/tabwid.js | 5 man/add_body.Rd | 31 man/add_body_row.Rd | 31 man/add_footer.Rd | 31 man/add_footer_lines.Rd | 31 man/add_footer_row.Rd | 31 man/add_header.Rd | 31 man/add_header_lines.Rd | 31 man/add_header_row.Rd | 31 man/add_latex_dep.Rd | 8 man/align.Rd | 34 man/append_chunks.Rd | 13 man/as_b.Rd | 38 man/as_bracket.Rd | 38 man/as_chunk.Rd | 38 man/as_equation.Rd | 38 man/as_flextable.Rd | 21 man/as_flextable.TableTree.Rd |only man/as_flextable.compact_summary.Rd | 33 man/as_flextable.data.frame.Rd | 33 man/as_flextable.gam.Rd | 33 man/as_flextable.glm.Rd | 33 man/as_flextable.grouped_data.Rd | 33 man/as_flextable.htest.Rd | 33 man/as_flextable.kmeans.Rd | 33 man/as_flextable.lm.Rd | 33 man/as_flextable.merMod.Rd | 33 man/as_flextable.pam.Rd | 33 man/as_flextable.summarizor.Rd | 33 man/as_flextable.table.Rd | 33 man/as_flextable.tabular.Rd | 33 man/as_flextable.tabulator.Rd | 33 man/as_flextable.xtable.Rd | 33 man/as_highlight.Rd | 38 man/as_i.Rd | 38 man/as_image.Rd | 50 - man/as_paragraph.Rd | 13 man/as_qmd.Rd | 38 man/as_strike.Rd | 38 man/as_sub.Rd | 38 man/as_sup.Rd | 38 man/as_word_field.Rd | 38 man/autofit.Rd | 43 - man/bg.Rd | 34 man/body_add_flextable.Rd | 6 man/body_replace_flextable_at_bkm.Rd | 7 man/bold.Rd | 34 man/border_inner.Rd | 24 man/border_inner_h.Rd | 24 man/border_inner_v.Rd | 24 man/border_outer.Rd | 24 man/border_remove.Rd | 24 man/colformat_char.Rd | 18 man/colformat_date.Rd | 18 man/colformat_datetime.Rd | 18 man/colformat_double.Rd | 18 man/colformat_image.Rd | 23 man/colformat_int.Rd | 18 man/colformat_lgl.Rd | 18 man/colformat_num.Rd | 18 man/color.Rd | 34 man/colorize.Rd | 38 man/compact_summary.Rd | 33 man/compose.Rd | 13 man/delete_columns.Rd | 31 man/delete_part.Rd | 31 man/delete_rows.Rd | 21 man/df_printer.Rd | 30 man/dim.flextable.Rd | 22 man/dim_pretty.Rd | 22 man/empty_blanks.Rd | 34 man/figures/README-diamonds-dataset-1.png |binary man/figures/README-mtcars-dataset-1.png |binary man/figures/README-simple-example-1.png |binary man/figures/logo.png |binary man/fit_columns.Rd |only man/fit_to_width.Rd | 32 man/flextable-package.Rd | 1 man/flextable.Rd | 4 man/flextable_dim.Rd | 22 man/flextable_to_rmd.Rd | 30 man/fmt_2stats.Rd | 18 man/fmt_avg_dev.Rd | 18 man/fmt_dbl.Rd | 18 man/fmt_header_n.Rd | 18 man/fmt_int.Rd | 18 man/fmt_n_percent.Rd | 18 man/fmt_pct.Rd | 18 man/fmt_signif_after_zeros.Rd | 18 man/font.Rd | 34 man/fontsize.Rd | 34 man/footnote.Rd | 10 man/fp_border_default.Rd | 6 man/fp_text_default.Rd | 6 man/gen_grob.Rd | 30 man/get_flextable_defaults.Rd | 26 man/gg_chunk.Rd | 42 - man/grid_chunk.Rd | 42 - man/height.Rd | 22 man/highlight.Rd | 34 man/hline.Rd | 24 man/hline_bottom.Rd | 24 man/hline_top.Rd | 24 man/hrule.Rd | 22 man/htmltools_value.Rd | 32 man/hyperlink_text.Rd | 38 man/information_data_cell.Rd | 8 man/information_data_chunk.Rd | 8 man/information_data_paragraph.Rd | 8 man/italic.Rd | 34 man/keep_with_next.Rd | 34 man/knit_print.flextable.Rd | 49 - man/labelizor.Rd | 9 man/line_spacing.Rd | 34 man/linerange.Rd | 43 - man/merge_at.Rd | 12 man/merge_h.Rd | 31 man/merge_h_range.Rd | 12 man/merge_none.Rd | 12 man/merge_v.Rd | 12 man/minibar.Rd | 43 - man/ncol_keys.Rd | 22 man/nrow_part.Rd | 22 man/padding.Rd | 40 man/paginate.Rd | 31 man/ph_with.flextable.Rd | 7 man/plot.flextable.Rd | 30 man/plot_chunk.Rd | 41 man/prepend_chunks.Rd | 13 man/print.flextable.Rd | 30 man/regulartable.Rd | 2 man/rotate.Rd | 34 man/roxygen |only man/rtf_add.flextable.Rd | 7 man/save_as_docx.Rd | 30 man/save_as_html.Rd | 30 man/save_as_image.Rd | 30 man/save_as_pptx.Rd | 30 man/save_as_rtf.Rd | 30 man/separate_header.Rd | 31 man/set_flextable_defaults.Rd | 26 man/set_formatter.Rd | 18 man/set_header_footer_df.Rd | 33 man/set_header_labels.Rd | 33 man/set_table_properties.Rd | 14 man/split_columns.Rd |only man/split_rows.Rd |only man/split_to_pages.Rd |only man/style.Rd | 38 man/surround.Rd | 24 man/tab_settings.Rd | 34 man/theme_alafoli.Rd | 26 man/theme_apa.Rd | 26 man/theme_booktabs.Rd | 26 man/theme_borderless.Rd | 26 man/theme_box.Rd | 26 man/theme_tron.Rd | 26 man/theme_tron_legacy.Rd | 26 man/theme_vader.Rd | 26 man/theme_vanilla.Rd | 26 man/theme_zebra.Rd | 26 man/to_html.flextable.Rd | 30 man/use_df_printer.Rd | 6 man/use_flextable_qmd.Rd | 6 man/use_model_printer.Rd | 6 man/valign.Rd | 34 man/vline.Rd | 24 man/vline_left.Rd | 24 man/vline_right.Rd | 24 man/void.Rd | 10 man/width.Rd | 22 man/wrap_flextable.Rd | 30 tests/testthat/test-as_flextable.R | 15 tests/testthat/test-fit_columns.R |only tests/testthat/test-images.R | 59 + tests/testthat/test-latex.R | 24 tests/testthat/test-merge.R | 59 + tests/testthat/test-splitters.R |only 239 files changed, 9421 insertions(+), 4830 deletions(-)
Title: Cell Ranger Output Filtering and Metrics Visualization
Description: Sample and cell filtering as well as visualisation of output metrics from 'Cell Ranger' by Grace X.Y. Zheng et al. (2017) <doi:10.1038/ncomms14049>. 'CRMetrics' allows for easy plotting of output metrics across multiple samples as well as comparative plots including statistical assessments of these. 'CRMetrics' allows for easy removal of ambient RNA using 'SoupX' by Matthew D Young and Sam Behjati (2020) <doi:10.1093/gigascience/giaa151> or 'CellBender' by Stephen J Fleming et al. (2022) <doi:10.1101/791699>. Furthermore, it is possible to preprocess data using 'Pagoda2' by Nikolas Barkas et al. (2021) <https://github.com/kharchenkolab/pagoda2> or 'Seurat' by Yuhan Hao et al. (2021) <doi:10.1016/j.cell.2021.04.048> followed by embedding of cells using 'Conos' by Nikolas Barkas et al. (2019) <doi:10.1038/s41592-019-0466-z>. Finally, doublets can be detected using 'scrublet' by Samuel L. Wolock et al. (2019) <doi:10.1016/j.cels.2018.11.005> or 'D [...truncated...]
Author: Rasmus Rydbirk [aut, cre],
Fabienne Kick [aut],
Henrietta Holze [aut],
Xian Xin [ctb],
Laura Wolbeck [aut]
Maintainer: Rasmus Rydbirk <rrydbirk@bmb.sdu.dk>
Diff between CRMetrics versions 0.3.2 dated 2024-11-07 and 0.3.3 dated 2026-06-02
CRMetrics-0.3.2/CRMetrics/inst/docs/walkthrough.Rmd |only CRMetrics-0.3.3/CRMetrics/DESCRIPTION | 21 CRMetrics-0.3.3/CRMetrics/MD5 | 31 CRMetrics-0.3.3/CRMetrics/NAMESPACE | 2 CRMetrics-0.3.3/CRMetrics/NEWS.md | 8 CRMetrics-0.3.3/CRMetrics/R/CRMetrics.R | 1224 +++++-- CRMetrics-0.3.3/CRMetrics/R/inner_functions.R | 308 + CRMetrics-0.3.3/CRMetrics/README.md | 13 CRMetrics-0.3.3/CRMetrics/man/CRMetrics.Rd | 2364 ++++++--------- CRMetrics-0.3.3/CRMetrics/man/addDetailedMetricsInner.Rd | 4 CRMetrics-0.3.3/CRMetrics/man/addPlotStats.Rd | 2 CRMetrics-0.3.3/CRMetrics/man/addPlotStatsSamples.Rd | 6 CRMetrics-0.3.3/CRMetrics/man/addSummaryMetrics.Rd | 4 CRMetrics-0.3.3/CRMetrics/man/checkCompMeta.Rd | 4 CRMetrics-0.3.3/CRMetrics/man/getH5Paths.Rd | 8 CRMetrics-0.3.3/CRMetrics/man/read10xH5.Rd | 7 CRMetrics-0.3.3/CRMetrics/man/readFlex.Rd |only CRMetrics-0.3.3/CRMetrics/man/readParse.Rd |only 18 files changed, 2315 insertions(+), 1691 deletions(-)
Title: Unified Interface for AI Model Providers
Description: A production-grade AI toolkit for R featuring a layered
architecture (Specification, Utilities, Providers, Core), request
interception support, robust error handling with exponential retry
delays, support for multiple AI model providers ('OpenAI',
'Anthropic', etc.), local small language model inference,
distributed 'MCP' ecosystem, multi-agent orchestration, progressive
knowledge loading through skills, and a global skill store for
sharing AI capabilities.
Author: Yonghe Xia [aut, cre]
Maintainer: Yonghe Xia <xiayh17@gmail.com>
Diff between aisdk versions 1.4.11 dated 2026-05-30 and 1.4.12 dated 2026-06-02
DESCRIPTION | 6 - MD5 | 18 +++-- NAMESPACE | 7 ++ NEWS.md | 17 +++++ R/image_model.R | 41 ++++++++++++ R/utils_http.R | 12 +++ R/utils_registry.R | 102 ++++++++++++++++++++++++++++--- man/api_endpoint_urls.Rd |only man/finalize_image_artifacts.Rd |only man/materialize_image_upload.Rd |only man/normalize_image_input_for_json.Rd |only man/normalize_image_input_to_url_like.Rd |only tests/testthat/test-companion-provider.R |only 13 files changed, 185 insertions(+), 18 deletions(-)
Title: Adirondack Long-Term Lake Data
Description: Package for the access and distribution of long-term lake datasets from 28 lakes in the Adirondack Park, northern New York state. Includes a wide variety of physical, chemical, and biological parameters originally described in Farrell et al. 2018 <doi:10.1038/sdata.2018.59>. Water chemistry and nutrient records are extended through 2024 using data from the USGS AQ Samples database, including new columns for surface temperature, UV-254 absorbance, and a program flag distinguishing AEAP integrated samples from ALTM surface grabs. The underlying figshare archive <doi:10.6084/m9.figshare.32305479> additionally contains chemistry records for 25 ALTM-only lakes; the package restricts to the 28 originals for consistency with the published dataset.
Author: Jeremy Farrell [aut, cre],
Luke Winslow [aut],
Taylor Leach [aut],
Tobi Hahn [aut]
Maintainer: Jeremy Farrell <jeremyfarrell@gmail.com>
Diff between adklakedata versions 0.6.4 dated 2025-11-28 and 0.7.1 dated 2026-06-02
DESCRIPTION | 10 - LICENSE | 2 MD5 | 56 +++---- NAMESPACE | 30 +-- NEWS.md |only R/aaa.R | 8 - R/adk_data.R | 126 ++++++++++------ R/adk_metadata.R | 44 ++--- R/check_dl_data.R | 168 +++++++++++----------- R/check_dl_file.R | 144 +++++++++--------- build |only inst/extdata/BlueLine2014Poly.shp.xml | 72 ++++----- inst/extdata/master.csv | 4 inst/extdata/metadata/crustacean.txt | 26 +-- inst/extdata/metadata/lake_characteristics.txt | 28 +-- inst/extdata/metadata/nldas_drivers_1979_2016.txt | 20 +- inst/extdata/metadata/nutrients.txt | 28 +-- inst/extdata/metadata/phyto.txt | 32 ++-- inst/extdata/metadata/rotifer.txt | 26 +-- inst/extdata/metadata/secchi.txt | 12 - inst/extdata/metadata/temp_do_profiles.txt | 10 - inst/extdata/metadata/waterchem.txt | 58 +++---- inst/extdata/metadata/zoop_biomass_conversion.txt | 22 +- man/adk_data.Rd | 8 + man/adk_metadata.Rd | 42 ++--- man/check_dl_data.Rd | 34 ++-- man/local_path.Rd | 48 +++--- man/set_local_path.Rd | 44 ++--- tests/testthat.R | 8 - tests/testthat/test_data_dl_access.R | 62 ++++---- 30 files changed, 607 insertions(+), 565 deletions(-)
Title: Descriptive Statistics, Transition Plots, and More
Description: Utilities for common medical-statistics graphics
and tables, including automatic creation of publication-ready "Table 1"
summaries; transition (Sankey) plots; flow-chart helpers that extend the
grid package; Bézier lines and arrows; and a singular-value-decomposition-
based variable-selection method.
Author: Max Gordon [aut, cre]
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 3.2.0 dated 2026-03-06 and 3.3.0 dated 2026-06-02
Gmisc-3.2.0/Gmisc/tests/testthat/_snaps |only Gmisc-3.3.0/Gmisc/DESCRIPTION | 8 Gmisc-3.3.0/Gmisc/MD5 | 138 Gmisc-3.3.0/Gmisc/NAMESPACE | 6 Gmisc-3.3.0/Gmisc/NEWS.md | 10 Gmisc-3.3.0/Gmisc/R/Gmisc.R | 4 Gmisc-3.3.0/Gmisc/R/assert.R | 2 Gmisc-3.3.0/Gmisc/R/boxGrobs_align.R | 28 Gmisc-3.3.0/Gmisc/R/boxGrobs_boxGrob.R | 59 Gmisc-3.3.0/Gmisc/R/boxGrobs_boxPropGrob.R | 2 Gmisc-3.3.0/Gmisc/R/boxGrobs_connect.R | 31 Gmisc-3.3.0/Gmisc/R/boxGrobs_connect_pr_helpers.R | 111 Gmisc-3.3.0/Gmisc/R/boxGrobs_connect_pr_many_to_one_boxes.R | 20 Gmisc-3.3.0/Gmisc/R/boxGrobs_connect_pr_one_to_many_boxes.R | 20 Gmisc-3.3.0/Gmisc/R/boxGrobs_connect_pr_single_boxes.R | 49 Gmisc-3.3.0/Gmisc/R/boxGrobs_connect_strategies.R | 27 Gmisc-3.3.0/Gmisc/R/boxGrobs_distance.R | 2 Gmisc-3.3.0/Gmisc/R/boxGrobs_equalizeWidths.R |only Gmisc-3.3.0/Gmisc/R/boxGrobs_move.R | 49 Gmisc-3.3.0/Gmisc/R/boxGrobs_s3_connect.R | 24 Gmisc-3.3.0/Gmisc/R/boxGrobs_spread_npc_norm_helpers.R | 1 Gmisc-3.3.0/Gmisc/build/vignette.rds |binary Gmisc-3.3.0/Gmisc/inst/doc/Descriptives.Rmd | 4 Gmisc-3.3.0/Gmisc/inst/doc/Descriptives.html | 28 Gmisc-3.3.0/Gmisc/inst/doc/Grid-based_flowcharts.R | 222 - Gmisc-3.3.0/Gmisc/inst/doc/Grid-based_flowcharts.Rmd | 226 + Gmisc-3.3.0/Gmisc/inst/doc/Grid-based_flowcharts.html | 1710 +++++----- Gmisc-3.3.0/Gmisc/inst/doc/Transition-class.Rmd | 2 Gmisc-3.3.0/Gmisc/inst/doc/Transition-class.html | 6 Gmisc-3.3.0/Gmisc/inst/doc/transitionPlot.R | 2 Gmisc-3.3.0/Gmisc/inst/doc/transitionPlot.Rmd | 3 Gmisc-3.3.0/Gmisc/inst/doc/transitionPlot.html | 8 Gmisc-3.3.0/Gmisc/man/Gmisc-package.Rd | 9 Gmisc-3.3.0/Gmisc/man/align.Rd | 42 Gmisc-3.3.0/Gmisc/man/append.Rd | 27 Gmisc-3.3.0/Gmisc/man/assert.Rd | 2 Gmisc-3.3.0/Gmisc/man/box.Rd | 47 Gmisc-3.3.0/Gmisc/man/boxHeaderGrob.Rd | 27 Gmisc-3.3.0/Gmisc/man/boxPropGrob.Rd | 27 Gmisc-3.3.0/Gmisc/man/boxShapes.Rd | 29 Gmisc-3.3.0/Gmisc/man/connect.Rd | 63 Gmisc-3.3.0/Gmisc/man/coords.Rd | 27 Gmisc-3.3.0/Gmisc/man/describeFactors.Rd | 12 Gmisc-3.3.0/Gmisc/man/describeMean.Rd | 12 Gmisc-3.3.0/Gmisc/man/describeMedian.Rd | 12 Gmisc-3.3.0/Gmisc/man/describeProp.Rd | 12 Gmisc-3.3.0/Gmisc/man/distance.Rd | 27 Gmisc-3.3.0/Gmisc/man/equalizeWidths.Rd |only Gmisc-3.3.0/Gmisc/man/figCapNo.Rd | 6 Gmisc-3.3.0/Gmisc/man/figCapNoLast.Rd | 6 Gmisc-3.3.0/Gmisc/man/figCapNoNext.Rd | 6 Gmisc-3.3.0/Gmisc/man/flowchart.Rd | 27 Gmisc-3.3.0/Gmisc/man/getDescriptionStatsBy.Rd | 12 Gmisc-3.3.0/Gmisc/man/getPval.Rd | 12 Gmisc-3.3.0/Gmisc/man/has.Rd | 4 Gmisc-3.3.0/Gmisc/man/insert.Rd | 27 Gmisc-3.3.0/Gmisc/man/move.Rd | 27 Gmisc-3.3.0/Gmisc/man/moveBox.Rd | 27 Gmisc-3.3.0/Gmisc/man/retrieve.Rd | 4 Gmisc-3.3.0/Gmisc/man/set_column_labels.Rd | 4 Gmisc-3.3.0/Gmisc/man/set_column_units.Rd | 4 Gmisc-3.3.0/Gmisc/man/spread.Rd | 42 Gmisc-3.3.0/Gmisc/tests/testthat/test-align-pipeline.R | 21 Gmisc-3.3.0/Gmisc/tests/testthat/test-boxGrob-padding-option.R |only Gmisc-3.3.0/Gmisc/tests/testthat/test-docx_document.R | 2 Gmisc-3.3.0/Gmisc/tests/testthat/test-equalizeWidths.R |only Gmisc-3.3.0/Gmisc/tests/testthat/test-s3-api-design.R | 90 Gmisc-3.3.0/Gmisc/tests/testthat/test-spread-move-deep-path.R | 24 Gmisc-3.3.0/Gmisc/vignettes/Descriptives.Rmd | 4 Gmisc-3.3.0/Gmisc/vignettes/Grid-based_flowcharts.Rmd | 226 + Gmisc-3.3.0/Gmisc/vignettes/Transition-class.Rmd | 2 Gmisc-3.3.0/Gmisc/vignettes/transitionPlot.Rmd | 3 72 files changed, 2360 insertions(+), 1397 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-05-19 0.1.2