Title: Liquid Glass Design Themes for 'shiny' Applications
Description: Provides drop-in Liquid Glass themes for 'shiny'. Call
glass_theme() and pass the result as theme = to fluidPage(),
navbarPage(), or any 'bslib'-aware page function to get
translucent surfaces, backdrop blur, and system typography on
'Bootstrap' components. Includes light and dark presets with
runtime switching and an OS-following 'auto' mode, an iOS-style
intensity control from Ultra Clear to Tinted, optional
persistence of the look, named wallpaper scenes, helpers to
match 'ggplot2', 'plotly', 'gt', and 'DT' output to the glass pack,
a flatten mode for print and screenshots, and documented CSS tokens.
Author: Eric Anderson [aut, cre, cph]
Maintainer: Eric Anderson <eric.ray.anderson@gmail.com>
Diff between shinyglass versions 0.3.0 dated 2026-09-09 and 0.4.0 dated 2026-09-20
DESCRIPTION | 11 MD5 | 86 ++-- NAMESPACE | 10 NEWS.md | 61 ++ R/glass-flatten.R |only R/glass-intensity.R | 6 R/glass-page.R | 10 R/glass-plots.R | 162 ++++++- R/glass-theme.R | 146 +++++-- R/glass-tokens.R |only R/shinyglass-package.R | 13 README.md | 21 - build/vignette.rds |binary inst/WORDLIST | 94 +++- inst/doc/compatibility.Rmd | 7 inst/doc/compatibility.html | 18 inst/doc/playground.Rmd | 2 inst/doc/playground.html | 7 inst/doc/theming.R | 19 inst/doc/theming.Rmd | 106 ++++- inst/doc/theming.html | 220 ++++++++-- inst/examples/bslib-dashboard.R | 57 +- inst/examples/chrome-kitchen-sink.R | 4 inst/examples/intensity-slider-demo.R | 5 inst/examples/plotly-gt-demo.R | 28 - inst/js/shiny-glass.js | 315 ++++++++++++++- inst/scss/glass.scss | 707 +++++++++++++++++++++++++++++++--- man/dt_options_glass.Rd |only man/glass_add_tokens.Rd |only man/glass_css_tokens.Rd |only man/glass_flatten.Rd |only man/glass_intensity_slider.Rd | 4 man/glass_page.Rd | 6 man/glass_plot_colors.Rd | 9 man/glass_plot_surface_input.Rd |only man/glass_scene_input.Rd |only man/glass_scenes.Rd |only man/glass_theme.Rd | 43 +- man/glass_token_pack.Rd |only man/gt_theme_glass.Rd | 9 man/observe_glass_plot_surface.Rd |only man/observe_glass_scene.Rd |only man/plotly_glass.Rd | 9 man/shinyglass-package.Rd | 12 man/theme_glass.Rd | 13 man/update_glass_theme.Rd | 14 tests/testthat/test-glass-theme.R | 158 +++++++ vignettes/compatibility.Rmd | 7 vignettes/playground.Rmd | 2 vignettes/theming.Rmd | 106 ++++- 50 files changed, 2157 insertions(+), 350 deletions(-)
Title: Simulation and Analysis Tools for Clinical Dose Response
Modeling
Description: Bayesian and ML Emax model fitting, graphics and simulation for clinical dose
response. The summary data from the dose response meta-analyses in
Thomas, Sweeney, and Somayaji (2014) <doi:10.1080/19466315.2014.924876> and
Thomas and Roy (2016) <doi:10.1080/19466315.2016.1256229>
Wu, Banerjee, Jin, Menon, Martin, and Heatherington(2017) <doi:10.1177/0962280216684528>
are included
in the package. The prior distributions for the Bayesian analyses default to
the posterior predictive distributions derived from these references.
Author: Neal Thomas [aut, cre] ,
Jing Wu [aut],
Mike K. Smith [aut],
Budhaditya Goswami [aut],
Satrajit Roychoudhury [aut]
Maintainer: Neal Thomas <snthomas99@gmail.com>
Diff between clinDR versions 2.5.2 dated 2025-10-02 and 2.5.3 dated 2026-09-20
clinDR-2.5.2/clinDR/inst/tests/Rplots.pdf |only clinDR-2.5.3/clinDR/DESCRIPTION | 22 clinDR-2.5.3/clinDR/MD5 | 113 clinDR-2.5.3/clinDR/NAMESPACE | 2 clinDR-2.5.3/clinDR/R/fitEmaxB.R | 42 clinDR-2.5.3/clinDR/R/plot.emaxsimobj.R | 12 clinDR-2.5.3/clinDR/R/plot.fitEmax.R | 24 clinDR-2.5.3/clinDR/R/plot.plotB.R | 24 clinDR-2.5.3/clinDR/R/plotD.R | 6 clinDR-2.5.3/clinDR/R/predict.fitEmaxB.R | 11 clinDR-2.5.3/clinDR/R/print.emaxPrior.R | 1132 ++++++---- clinDR-2.5.3/clinDR/R/randomEmax.R | 2 clinDR-2.5.3/clinDR/build |only clinDR-2.5.3/clinDR/data/metaData.rda |binary clinDR-2.5.3/clinDR/inst/doc |only clinDR-2.5.3/clinDR/inst/models/mrmodel.stan | 19 clinDR-2.5.3/clinDR/inst/shiny/emaxPrior_control.html | 218 + clinDR-2.5.3/clinDR/inst/tests/currentPriors.RData |only clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.densityplot_new.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.densityplot_old.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.emaxsimBobj_new.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.emaxsimBobj_old.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.emaxsimobj_new.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.emaxsimobj_old.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.fitEmaxB_new.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.fitEmaxB_old.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.fitEmax_new.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.fitEmax_old.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.plotB_new.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.plotB_old.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.plotD_new.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.plotD_old.pdf |binary clinDR-2.5.3/clinDR/inst/tests/runIndvidualTests.R | 1 clinDR-2.5.3/clinDR/inst/tests/runIndvidualTests2.R | 46 clinDR-2.5.3/clinDR/inst/tests/test.checkMonoEmaxlocalParm.R | 28 clinDR-2.5.3/clinDR/inst/tests/test.compareTvsMix.R |only clinDR-2.5.3/clinDR/inst/tests/test.compareTvsMix2.R |only clinDR-2.5.3/clinDR/inst/tests/test.emaxsimBlocalParm.R | 62 clinDR-2.5.3/clinDR/inst/tests/test.emaxsimBlocalParmMix.R |only clinDR-2.5.3/clinDR/inst/tests/test.fitEmaxBlocalParm.R | 87 clinDR-2.5.3/clinDR/inst/tests/test.fitEmaxBlocalParmMix.R |only clinDR-2.5.3/clinDR/inst/tests/test.fitEmaxBlocalParmtmp.R |only clinDR-2.5.3/clinDR/inst/tests/test.print.emaxPrior.R | 196 + clinDR-2.5.3/clinDR/man/emaxPrior.control.Rd | 267 +- clinDR-2.5.3/clinDR/man/print.emaxPrior.Rd | 101 clinDR-2.5.3/clinDR/man/randomEmax.Rd | 3 clinDR-2.5.3/clinDR/man/runSimulations.Rd | 3 clinDR-2.5.3/clinDR/vignettes |only 48 files changed, 1631 insertions(+), 790 deletions(-)
Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic
regression, naive Bayes, neural networks, classification and regression trees,
model evaluation, collaborative filtering, decision analysis, and simulation.
The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.model versions 1.6.11 dated 2026-04-15 and 1.6.12 dated 2026-09-20
radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/cf_summary.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/dtree_model.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/dtree_plot_final.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/dtree_plot_initial.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/dtree_sensitivity.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/evalbin_confusion.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/evalbin_lift_gains.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/evalbin_logistic.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/evalreg_nn.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/evalreg_summary_plot.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/logistic_dvd-full.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/logistic_dvd.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/logistic_plot.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/logistic_predict.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/logistic_predict_data.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/logistic_summary.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/mnl_choice_shares.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/mnl_plot.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/mnl_predict.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/mnl_summary.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_catalog_F_critical.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_catalog_F_test.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_catalog_prob_calc.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_catalog_summary.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_diamonds_corr.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_diamonds_dashboard.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_diamonds_hist.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_diamonds_res_vs_pred.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_diamonds_scatter.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_ideal_corr.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_ideal_dashboard.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_ideal_hist.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_ideal_res_vs_pred.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_ideal_scatter.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_ideal_summary.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_corr.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_dashboard.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_hist.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_res_vs_pred.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_scatter.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_summary.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_viz_scatter.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/simulater_repeat.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/simulater_repeat_plot.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/simulater_sim.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/simulater_sim_plot.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/simulater_view.png |only radiant.model-1.6.12/radiant.model/DESCRIPTION | 10 radiant.model-1.6.12/radiant.model/MD5 | 105 --- radiant.model-1.6.12/radiant.model/NAMESPACE | 310 +++++----- radiant.model-1.6.12/radiant.model/NEWS.md | 6 radiant.model-1.6.12/radiant.model/R/crtree.R | 8 radiant.model-1.6.12/radiant.model/R/logistic.R | 17 radiant.model-1.6.12/radiant.model/R/mnl.R | 10 radiant.model-1.6.12/radiant.model/R/nn.R | 31 - radiant.model-1.6.12/radiant.model/R/regress.R | 20 radiant.model-1.6.12/radiant.model/inst/app/tools/analysis/logistic_ui.R | 24 radiant.model-1.6.12/radiant.model/inst/app/tools/analysis/regress_ui.R | 24 radiant.model-1.6.12/radiant.model/inst/app/tools/help/crs.md | 2 radiant.model-1.6.12/radiant.model/inst/app/tools/help/dtree.Rmd | 8 radiant.model-1.6.12/radiant.model/inst/app/tools/help/dtree.md | 8 radiant.model-1.6.12/radiant.model/inst/app/tools/help/evalbin.md | 8 radiant.model-1.6.12/radiant.model/inst/app/tools/help/evalreg.md | 6 radiant.model-1.6.12/radiant.model/inst/app/tools/help/logistic.Rmd | 14 radiant.model-1.6.12/radiant.model/inst/app/tools/help/logistic.md | 14 radiant.model-1.6.12/radiant.model/inst/app/tools/help/mnl.Rmd | 8 radiant.model-1.6.12/radiant.model/inst/app/tools/help/mnl.md | 8 radiant.model-1.6.12/radiant.model/inst/app/tools/help/regress.Rmd | 46 - radiant.model-1.6.12/radiant.model/inst/app/tools/help/regress.md | 46 - radiant.model-1.6.12/radiant.model/inst/app/tools/help/simulater.Rmd | 10 radiant.model-1.6.12/radiant.model/inst/app/tools/help/simulater.md | 10 radiant.model-1.6.12/radiant.model/man/crtree.Rd | 2 radiant.model-1.6.12/radiant.model/man/logistic.Rd | 9 radiant.model-1.6.12/radiant.model/man/mnl.Rd | 2 radiant.model-1.6.12/radiant.model/man/nn.Rd | 2 radiant.model-1.6.12/radiant.model/man/regress.Rd | 6 radiant.model-1.6.12/radiant.model/tests/testthat/test_nn_predict.R |only radiant.model-1.6.12/radiant.model/tests/testthat/test_standardize.R |only 78 files changed, 436 insertions(+), 338 deletions(-)
Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving,
viewing, visualizing, summarizing, transforming, and combining data. It also
contains functionality to generate reproducible reports of the analyses
conducted in the application.
Author: Vincent Nijs [aut, cre],
Niklas von Hertzen [aut]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.data versions 1.6.8 dated 2025-09-16 and 1.6.9 dated 2026-09-20
DESCRIPTION | 15 +- MD5 | 24 ++-- NAMESPACE | 262 +++++++++++++++++++++++++------------------- NEWS.md | 4 R/explore.R | 2 R/pivotr.R | 2 R/view.R | 4 README.md | 4 inst/app/radiant.R | 9 + inst/app/tools/app/about.md | 4 man/dtab.data.frame.Rd | 2 man/reexports.Rd | 18 +-- tests/testthat/test_funs.R | 10 - 13 files changed, 206 insertions(+), 154 deletions(-)
Title: G-Functions
Description: Modified versions of the lag() and summary() functions: glag() and gsummary(). The prefix 'g' is a reminder of who to blame if things do not work as they should.
Author: Genaro Sucarrat [aut, cre]
Maintainer: Genaro Sucarrat <gsucarrat@gmail.com>
Diff between gfunctions versions 1.2 dated 2026-08-21 and 1.3 dated 2026-09-20
DESCRIPTION | 8 +-- MD5 | 9 ++- NEWS | 14 +++++ R/gfunctions-internal.R |only R/gfunctions-source-code.R | 108 +++++++++++++++++++++++++++++++++++++++------ man/gfunctions-package.Rd | 6 +- 6 files changed, 121 insertions(+), 24 deletions(-)
Title: Simulate Experimental and Behavioural Data from a Portable
Design Specification
Description: Generative simulation of experimental and behavioural data sets from a
portable JavaScript Object Notation (JSON) design specification shared with the
'Python' package of the same name.
Supports user-specified fixed effect sizes, crossed by-subject and by-item random
intercepts and slopes, predictors measured with error, realistic response families
(Gaussian, lognormal, shifted lognormal, ex-Gaussian, Bernoulli, Poisson, ordinal and
Beta), and simulation-based power and precision-based design analysis, including the
Type S and Type M errors of Gelman and Carlin (2014)
<doi:10.1177/1745691614551642> and a region of practical equivalence. A shared
cross-language random-number generator means that, given the same specification and
seed, the R and 'Python' implementations produce identical data: exactly for the
Gaussian family and for any family with rounding set, and to within the last unit in
the last place for families applying a transcendental function to the linear
predictor, wh [...truncated...]
Author: Pablo Bernabeu [aut, cre]
Maintainer: Pablo Bernabeu <pcbernabeu@gmail.com>
Diff between pilotr versions 0.3.0 dated 2026-09-12 and 0.3.1 dated 2026-09-20
DESCRIPTION | 6 MD5 | 12 NEWS.md | 835 +++++++++++++++++++++++---------------------- R/spec_builder.R | 117 +++--- man/generate_r_script.Rd | 9 man/spec_json.Rd | 16 tests/testthat/test-core.R | 56 +++ 7 files changed, 587 insertions(+), 464 deletions(-)
Title: Mode Estimation
Description: Provides estimators of the mode of univariate
data or univariate distributions.
Author: Paul Poncet [aut, cre]
Maintainer: Paul Poncet <paulponcet@yahoo.fr>
Diff between modeest versions 2.4.0 dated 2019-11-18 and 2.5.0 dated 2026-09-20
DESCRIPTION | 11 MD5 | 72 ++--- NAMESPACE | 62 ++-- NEWS.md | 71 ++--- R/asselin.R | 169 +++++------- R/deal.ties.R | 33 +- R/distrMode.R | 653 ++++++++++++++++++---------------------------- R/distributionsList.R | 12 R/grenander.R | 170 +++++------- R/hrm.R | 126 ++++---- R/hsm.R | 173 +++++------- R/lientz.R | 235 +++++++--------- R/meanshift.R | 141 ++++------ R/methodsList.R | 12 R/mlv.R | 276 ++++++++----------- R/naive.R | 79 ++--- R/parzen.R | 168 +++++------ R/skewness.R | 113 +++----- R/tsybakov.R | 167 +++++------ R/venter.R | 218 +++++++-------- R/vieu.R | 116 +++----- man/asselin.Rd | 102 +++---- man/distrMode.Rd | 687 ++++++++++++++++++++----------------------------- man/grenander.Rd | 180 ++++++------ man/hrm.Rd | 160 +++++------ man/hsm.Rd | 160 +++++------ man/lientz.Rd | 226 ++++++++-------- man/meanshift.Rd | 134 ++++----- man/mlv.Rd | 256 +++++++++--------- man/modeest-package.Rd | 2 man/naive.Rd | 116 ++++---- man/parzen.Rd | 194 ++++++------- man/reexports.Rd | 32 +- man/skewness.Rd | 138 ++++----- man/tsybakov.Rd | 204 +++++++------- man/venter.Rd | 220 +++++++-------- man/vieu.Rd | 122 ++++---- 37 files changed, 2833 insertions(+), 3177 deletions(-)
Title: Block Designs for Observational Studies
Description: Creates block designs of fixed size J with at least one treated
and control unit per block. Blocks larger than pairs better
distinguish effects caused by a treatment from unmeasured confounding in
assignment of individuals to treatment. Somewhat counterintuitively,
blocks larger than pairs can use more units while attaining better
covariate balance and block homogeneity. A forthcoming manuscript
by Brumberg and Rosenbaum details the design.
Author: Katherine Brumberg [aut, cre] ,
Paul Rosenbaum [aut]
Maintainer: Katherine Brumberg <kbrum@umich.edu>
Diff between observationalBlocks versions 1.0.0 dated 2026-04-10 and 1.1.0 dated 2026-09-20
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 22 +++++++++++++--------- NEWS.md | 5 +++++ R/blockMatch.R | 11 +++++++---- R/seedMatch.R | 9 +++++---- man/blockMatch.Rd | 7 ++++--- tests/testthat/test-blockMatch.R | 23 +++++++++++++++++++++++ 8 files changed, 68 insertions(+), 31 deletions(-)
More information about observationalBlocks at CRAN
Permanent link
Title: Multivariate Spatio-Temporal Models using Structural Equations
Description: Fits a wide variety of multivariate spatio-temporal models
with simultaneous and lagged interactions among variables (including
vector autoregressive spatio-temporal ('VAST') dynamics)
for areal, continuous, or network spatial domains.
It includes time-variable, space-variable, and space-time-variable
interactions using dynamic structural equation models ('DSEM')
as expressive interface, and the 'mgcv' package to specify splines
via the formula interface. See Thorson et al. (2025)
<doi:10.1111/geb.70035> for more details.
Author: James T. Thorson [aut, cre] ,
Sean C. Anderson [aut]
Maintainer: James T. Thorson <James.Thorson@noaa.gov>
This is a re-admission after prior archival of version 1.6.2 dated 2026-07-14
Diff between tinyVAST versions 1.6.2 dated 2026-07-14 and 1.6.3 dated 2026-09-20
tinyVAST-1.6.2/tinyVAST/inst/doc/dsem.R |only tinyVAST-1.6.2/tinyVAST/inst/doc/dsem.Rmd |only tinyVAST-1.6.2/tinyVAST/inst/doc/dsem.html |only tinyVAST-1.6.2/tinyVAST/inst/doc/mgcv.R |only tinyVAST-1.6.2/tinyVAST/inst/doc/mgcv.Rmd |only tinyVAST-1.6.2/tinyVAST/inst/doc/mgcv.html |only tinyVAST-1.6.2/tinyVAST/inst/doc/multiple_data.R |only tinyVAST-1.6.2/tinyVAST/inst/doc/multiple_data.Rmd |only tinyVAST-1.6.2/tinyVAST/inst/doc/multiple_data.html |only tinyVAST-1.6.2/tinyVAST/inst/doc/spatial.R |only tinyVAST-1.6.2/tinyVAST/inst/doc/spatial.Rmd |only tinyVAST-1.6.2/tinyVAST/inst/doc/spatial.html |only tinyVAST-1.6.2/tinyVAST/inst/doc/spatial_factor_analysis.R |only tinyVAST-1.6.2/tinyVAST/inst/doc/spatial_factor_analysis.Rmd |only tinyVAST-1.6.2/tinyVAST/inst/doc/spatial_factor_analysis.html |only tinyVAST-1.6.2/tinyVAST/vignettes/dsem.Rmd |only tinyVAST-1.6.2/tinyVAST/vignettes/mgcv.Rmd |only tinyVAST-1.6.2/tinyVAST/vignettes/multiple_data.Rmd |only tinyVAST-1.6.2/tinyVAST/vignettes/spatial.Rmd |only tinyVAST-1.6.2/tinyVAST/vignettes/spatial_factor_analysis.Rmd |only tinyVAST-1.6.3/tinyVAST/DESCRIPTION | 8 tinyVAST-1.6.3/tinyVAST/MD5 | 36 --- tinyVAST-1.6.3/tinyVAST/NEWS.md | 4 tinyVAST-1.6.3/tinyVAST/R/fit.R | 2 tinyVAST-1.6.3/tinyVAST/R/internal.R | 2 tinyVAST-1.6.3/tinyVAST/build/vignette.rds |binary tinyVAST-1.6.3/tinyVAST/inst/doc/model-description.html | 97 ++++------ tinyVAST-1.6.3/tinyVAST/src/utils.h | 2 tinyVAST-1.6.3/tinyVAST/tests/testthat.R | 4 29 files changed, 66 insertions(+), 89 deletions(-)
Title: Simulate Parametric and Semi-Parametric Survival Times with
Object-Oriented Design
Description: Simulate parametric and semi-parametric survival times through a
consistent, reusable interface for each distribution, using an
object-oriented design. Supported distributions include Exponential,
Weibull, Gompertz, Log-Logistic, Log-Normal, and Piecewise Exponential.
Random variates can be generated under Proportional Hazards, Accelerated
Failure Time, and Extended Hazards models, as well as under renewal and
non-homogeneous Poisson recurrent event processes, following the methods
described by Bender (2003) <doi:10.5282/UBM/EPUB.1716> and Leemis (1987)
in Operations Research, 35(6), 892-894.
Author: Aponte John [aut, cre, cph]
Maintainer: Aponte John <john.j.aponte@gmail.com>
Diff between survobj versions 3.1.1 dated 2024-08-16 and 3.2.0 dated 2026-09-20
DESCRIPTION | 26 +- MD5 | 106 ++++---- NAMESPACE | 56 ++-- NEWS.md | 32 ++ R/exponential_class.R | 12 R/gompertz_class.R | 34 +- R/loglogistic_class.R | 18 - R/lognormal_class.R | 37 +-- R/multiple_events.R | 10 R/piecewise_exponential_class.R | 32 +- R/survival_class.R | 69 +++-- R/utils.R | 12 R/weibull_class.R | 16 - README.md | 167 +++++++++---- build/partial.rdb |only build/vignette.rds |binary inst/WORDLIST | 31 +- inst/doc/example_distributions.Rmd | 82 +++--- inst/doc/example_distributions.html | 398 ++++++++++++++++----------------- inst/doc/simulation_distributions.R | 23 + inst/doc/simulation_distributions.Rmd | 106 ++++++++ inst/doc/simulation_distributions.html | 159 ++++++++++--- inst/doc/simulation_recurent.R | 136 +++++------ inst/doc/simulation_recurent.Rmd | 8 inst/doc/simulation_recurent.html | 81 +++--- inst/doc/simulation_trials.R | 72 ++--- inst/doc/simulation_trials.Rmd | 14 - inst/doc/simulation_trials.html | 47 +-- inst/doc/simulation_trials2.R | 76 +++--- inst/doc/simulation_trials2.Rmd | 28 +- inst/doc/simulation_trials2.html | 70 ++--- man/SURVIVAL.Rd | 27 +- man/censor_event.Rd | 8 man/fx_h_time.Rd | 4 man/is_single_number.Rd | 2 man/nhpp.Rd | 6 man/renewal.Rd | 4 man/s_exponential.Rd | 2 man/s_factory.Rd | 12 man/s_gompertz.Rd | 18 + man/s_loglogistic.Rd | 6 man/s_lognormal.Rd | 8 man/s_piecewise.Rd | 14 - man/s_weibull.Rd | 6 man/survobj-package.Rd | 9 tests/testthat/test_s_gompertz.R | 31 ++ tests/testthat/test_s_lognormal.R | 37 +++ tests/testthat/test_s_piecewise.R | 26 +- tests/testthat/test_survival_class.R |only vignettes/example_distributions.Rmd | 82 +++--- vignettes/references.bib | 25 ++ vignettes/simulation_distributions.Rmd | 106 ++++++++ vignettes/simulation_recurent.Rmd | 8 vignettes/simulation_trials.Rmd | 14 - vignettes/simulation_trials2.Rmd | 28 +- 55 files changed, 1517 insertions(+), 924 deletions(-)
Title: Smoothed Empirical Likelihood
Description: Empirical likelihood methods for asymptotically efficient
estimation of models based on conditional or unconditional moment
restrictions; see Kitamura, Tripathi & Ahn (2004)
<doi:10.1111/j.1468-0262.2004.00550.x> and Owen (2013)
<doi:10.1002/cjs.11183>.
Kernel-based non-parametric methods for density/regression estimation and
numerical routines for empirical likelihood maximisation are implemented in
'Rcpp' for speed.
Author: Andrei Victorovitch Kostyrka [aut, cre]
Maintainer: Andrei Victorovitch Kostyrka <andrei.kostyrka@gmail.com>
Diff between smoothemplik versions 0.0.17 dated 2025-10-29 and 0.0.18 dated 2026-09-20
smoothemplik-0.0.17/smoothemplik/R/catch-routine-registration.R |only smoothemplik-0.0.17/smoothemplik/src/kernelsm.h |only smoothemplik-0.0.17/smoothemplik/src/test-kernelsmoothers.cpp |only smoothemplik-0.0.17/smoothemplik/src/test-runner.cpp |only smoothemplik-0.0.17/smoothemplik/tests/testthat/test-cpp.R |only smoothemplik-0.0.18/smoothemplik/DESCRIPTION | 10 smoothemplik-0.0.18/smoothemplik/MD5 | 29 - smoothemplik-0.0.18/smoothemplik/NEWS.md | 3 smoothemplik-0.0.18/smoothemplik/R/zzz.R | 2 smoothemplik-0.0.18/smoothemplik/build/partial.rdb |binary smoothemplik-0.0.18/smoothemplik/build/vignette.rds |binary smoothemplik-0.0.18/smoothemplik/inst/CITATION | 12 smoothemplik-0.0.18/smoothemplik/inst/doc/choice-of-SEL-weights.html | 65 +-- smoothemplik-0.0.18/smoothemplik/inst/doc/non-parametric-rcpp.html | 87 ++-- smoothemplik-0.0.18/smoothemplik/src/RcppExports.cpp | 25 - smoothemplik-0.0.18/smoothemplik/src/kernelsmoothers.cpp | 177 ++++++---- smoothemplik-0.0.18/smoothemplik/tests/testthat/test-kernelFun.R | 51 ++ smoothemplik-0.0.18/smoothemplik/tests/testthat/test-svdlm.R | 2 18 files changed, 285 insertions(+), 178 deletions(-)
Title: Small Area Estimation Hierarchical Bayes for Spatial Beta Model
Description: Provides several functions and datasets for area-level Small Area Estimation using the Hierarchical Bayesian (HB) method. Model-based estimators are designed for variables of interest that follow a Beta distribution (proportions bounded between 0 and 1). The package supports both non-spatial and spatial models based on Simultaneous Autoregressive (SAR) and Leroux Conditional Autoregressive (CAR) structures for area-level random effects, with optional survey design effect (DEFF) adjustments for sampling variances. In addition, it provides utility functions for constructing spatial weights matrices and performing spatial autocorrelation diagnostics. The 'runjags' package is used to obtain posterior estimates via Markov Chain Monte Carlo (MCMC) with parallel computing capabilities. For references, see Rao and Molina (2015) <doi:10.1002/9781118735855>, Liu et al. (2014) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2014001/article/14030-eng.pdf>, Kubacki and Jedrzejczak (2016) [...truncated...]
Author: Boby Iwan [aut, cre],
Cucu Sumarni [aut]
Maintainer: Boby Iwan <bobyiwanboby2122@gmail.com>
Diff between saeHB.Spatial.Beta versions 0.1.1 dated 2026-08-24 and 0.2.0 dated 2026-09-20
DESCRIPTION | 10 - MD5 | 76 ++++---- NAMESPACE | 3 R/beta_lerouxcar.R | 118 ++++++++---- R/beta_nonspatial.R | 118 ++++++++---- R/beta_sar.R | 131 ++++++++++---- R/betadeff_lerouxcar.R | 107 ++++++++--- R/betadeff_nonspatial.R | 107 ++++++++--- R/betadeff_sar.R | 112 ++++++++---- R/build_w.R | 39 +++- R/databeta.R | 2 R/moran_test.R | 4 R/saeHB.Spatial.Beta_package.R | 15 - README.md | 212 +++++++++++------------ inst/doc/saeHB_Spatial_Beta.R | 19 -- inst/doc/saeHB_Spatial_Beta.Rmd | 46 ++--- inst/doc/saeHB_Spatial_Beta.html | 274 +++++++++++++++--------------- man/beta_lerouxcar.Rd | 7 man/beta_nonspatial.Rd | 7 man/beta_sar.Rd | 7 man/betadeff_lerouxcar.Rd | 7 man/betadeff_nonspatial.Rd | 7 man/betadeff_sar.Rd | 7 man/build_w.Rd | 25 ++ man/databeta.Rd | 2 man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-example-3.png |binary man/moran_test.Rd | 2 man/saeHB.Spatial.Beta-package.Rd | 13 - tests/testthat/test-beta_lerouxcar.R | 20 ++ tests/testthat/test-beta_nonspatial.R | 20 ++ tests/testthat/test-beta_sar.R | 20 ++ tests/testthat/test-betadeff_lerouxcar.R | 20 ++ tests/testthat/test-betadeff_nonspatial.R | 20 ++ tests/testthat/test-betadeff_sar.R | 20 ++ tests/testthat/test-build_w.R | 55 ++++-- tests/testthat/test-moran_test.R | 69 ++----- vignettes/saeHB_Spatial_Beta.Rmd | 46 ++--- 39 files changed, 1124 insertions(+), 643 deletions(-)
More information about saeHB.Spatial.Beta at CRAN
Permanent link
Title: Profile Analysis of Multivariate Data in R
Description: A suite of multivariate methods and data visualization
tools to implement profile analysis and cross-validation techniques described in
Davison & Davenport (2002) <DOI: 10.1037/1082-989X.7.4.468>, Bulut (2013), and other published and unpublished resources.
The package includes routines to perform criterion-related profile analysis, profile analysis
via multidimensional scaling, moderated profile analysis, generalizability theory, profile analysis by group, and a
within-person factor model to derive score profiles.
Author: Okan Bulut [aut],
Christopher David Desjardins [aut, cre]
Maintainer: Christopher David Desjardins <cddesjardins@gmail.com>
Diff between profileR versions 0.3-5 dated 2018-04-19 and 0.3-6 dated 2026-09-20
DESCRIPTION | 25 +++++---- MD5 | 36 +++++++++----- NEWS | 9 +++ R/cpa.R | 11 +--- R/paos.R | 9 +-- R/pr.R | 134 +++++++++++++++++++++++++---------------------------- R/profileplot.R | 8 +-- README.md | 115 ++++++++++++++++++++++++++++++++++++++++----- build |only inst |only man/PS.Rd | 2 man/cpa.Rd | 10 +++ man/figures |only man/interest.Rd | 2 man/paos.Rd | 2 man/pcv.Rd | 10 +++ man/profileplot.Rd | 10 +++ vignettes |only 18 files changed, 252 insertions(+), 131 deletions(-)
Title: Identify Reference Periods in Brazil's PNADC Survey Data
Description: Identifies reference periods (months, fortnights, and weeks) in
Brazil's quarterly PNADC (Pesquisa Nacional por Amostra de Domicilios
Continua) survey data and computes calibrated weights for sub-quarterly
analysis. The core algorithm uses IBGE (Instituto Brasileiro de Geografia
e Estatistica) 'Parada Tecnica' (technical break) rules combined with
respondent birthdates to determine which temporal period each survey
observation refers to. Period identification follows a nested hierarchy
enforced by construction: fortnights require months, weeks require
fortnights. Achieves approximately 97% monthly determination rate with
the full series (2012-2025). Strict fortnight and week rates are
approximately 9% and 3% respectively, as they cannot leverage
cross-quarter panel aggregation. Experimental strategies (probabilistic
assignment and UPA (Primary Sampling Unit) aggregation) further improve
these determination rates. The package provides adaptive hierarchical
weight calibration (4/2/1 cell [...truncated...]
Author: Rogerio Barbosa [aut, cre] ,
Marcos Hecksher [aut]
Maintainer: Rogerio Barbosa <rogerio.barbosa@iesp.uerj.br>
Diff between PNADCperiods versions 0.1.2 dated 2026-04-28 and 0.1.3 dated 2026-09-20
DESCRIPTION | 16 ++--- MD5 | 82 ++++++++++++++------------- NEWS.md | 57 ++++++++++++++++++ R/PNADCperiods-package.R | 6 + R/fetch-sidra-population.R | 16 ----- R/fetch-sidra-series.R | 13 ---- R/mensalize-sidra-series.R | 53 +++++++---------- R/sidra-api-v3.R |only README.md | 10 +-- inst/CITATION | 25 ++++++-- inst/doc/annual-poverty-analysis.Rmd | 13 ++-- inst/doc/annual-poverty-analysis.html | 34 ++++++----- inst/doc/applied-examples.Rmd | 13 ++-- inst/doc/applied-examples.html | 26 +++++--- inst/doc/complex-survey-design.Rmd | 13 ++-- inst/doc/complex-survey-design.html | 18 +++-- inst/doc/download-and-prepare.Rmd | 13 ++-- inst/doc/download-and-prepare.html | 12 ++- inst/doc/getting-started.Rmd | 19 +++--- inst/doc/getting-started.html | 20 ++++-- inst/doc/how-it-works.Rmd | 13 ++-- inst/doc/how-it-works.html | 12 ++- inst/doc/sidra-mensalization.Rmd | 13 ++-- inst/doc/sidra-mensalization.html | 12 ++- man/PNADCperiods-package.Rd | 6 + man/fetch-sidra-population.Rd | 20 +++--- man/fetch_monthly_population.Rd | 6 + man/fetch_sidra_rolling_quarters.Rd | 10 +++ man/mensalize_sidra_series.Rd | 11 ++- man/utils-validation.Rd | 18 ++--- tests/testthat/helper-sidra-v3-fixtures.R |only tests/testthat/test-derived-propagation.R | 11 ++- tests/testthat/test-fetch-sidra-population.R | 42 ++++--------- tests/testthat/test-fetch-sidra-series.R | 12 +-- tests/testthat/test-mensalize-pure-cumsum.R |only tests/testthat/test-pnadc-apply-periods.R | 2 tests/testthat/test-sidra-api-v3.R |only vignettes/annual-poverty-analysis.Rmd | 13 ++-- vignettes/applied-examples.Rmd | 13 ++-- vignettes/complex-survey-design.Rmd | 13 ++-- vignettes/download-and-prepare.Rmd | 13 ++-- vignettes/getting-started.Rmd | 19 +++--- vignettes/how-it-works.Rmd | 13 ++-- vignettes/sidra-mensalization.Rmd | 13 ++-- 44 files changed, 460 insertions(+), 284 deletions(-)
Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Creates styled tables for data presentation. Export to HTML, LaTeX,
RTF, 'Word', 'Excel', 'PowerPoint', 'typst', SVG and PNG. Simple, modern
interface to manipulate borders, size, position, captions, colours,
text styles and number formatting. Table cells can span multiple rows and/or columns.
Includes a 'huxreg' function to create regression tables, and 'quick_*'
one-liners to print tables to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 6.0.1 dated 2026-09-15 and 6.0.2 dated 2026-09-20
DESCRIPTION | 8 +- MD5 | 32 ++++---- NAMESPACE | 23 ++++-- NEWS.md | 9 ++ R/captions.R | 22 ++++- R/markdown.R | 3 R/properties-table.R | 5 - README.md | 154 ++++++++++------------------------------- inst/doc/huxreg.html | 2 inst/doc/huxtable.html | 12 +-- man/caption.Rd | 5 - man/huxtable-FAQ.Rd | 1 man/huxtable-news.Rd | 10 ++ man/huxtable-options.Rd | 1 man/huxtable-package.Rd | 1 tests/testthat/bones.png |binary tests/testthat/test-captions.R | 28 +++++++ 17 files changed, 158 insertions(+), 158 deletions(-)
Title: Access to CAPES Data
Description: Provides simplified access to the data from the Catalog of Theses and Dissertations
of the Brazilian Coordination for the Improvement of Higher Education Personnel (CAPES, <https://catalogodeteses.capes.gov.br>)
for the years 1987 through 2024. The dataset includes variables such as Higher Education
Institution (institution), Area of Concentration (area), Graduate Program Name (program_name),
Type of Work (type), Language of Work (language), Author Identification (author), Abstract
(abstract), Advisor Identification (advisor), Development Region (region), State (state).
Author: Andre Leite [aut, cre],
Hugo Vasconcelos Medeiros [aut],
Dalson Figueiredo Filho [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between capesR versions 0.1.0 dated 2024-12-19 and 0.2.0 dated 2026-09-20
capesR-0.1.0/capesR/data/years_osf.rda |only capesR-0.1.0/capesR/man/years_osf.Rd |only capesR-0.2.0/capesR/DESCRIPTION | 30 ++-- capesR-0.2.0/capesR/MD5 | 23 +-- capesR-0.2.0/capesR/NEWS.md |only capesR-0.2.0/capesR/R/capes.R | 169 +++++++++++++++---------- capesR-0.2.0/capesR/README.md | 20 ++ capesR-0.2.0/capesR/build/vignette.rds |binary capesR-0.2.0/capesR/data/capes_years.rda |only capesR-0.2.0/capesR/inst/doc/capesR.Rmd | 10 - capesR-0.2.0/capesR/inst/doc/capesR.html | 23 ++- capesR-0.2.0/capesR/man/capes_years.Rd |only capesR-0.2.0/capesR/man/download_capes_data.Rd | 26 +++ capesR-0.2.0/capesR/man/read_capes_data.Rd | 4 capesR-0.2.0/capesR/vignettes/capesR.Rmd | 10 - 15 files changed, 200 insertions(+), 115 deletions(-)
Title: Tidy Drift Detection for Monitored Machine Learning Models
Description: Detects concept drift and data drift in streams produced by
deployed machine learning models, using a tidy interface that composes
with the 'tidymodels' ecosystem. Detectors are specified, fitted on a
baseline period, and advanced over new batches of observations,
returning tibbles annotated with warning and drift flags. A catalogue
of 22 sequential drift detectors is provided. Error-based methods
include the Drift Detection Method (DDM) of Gama et al. (2004)
<doi:10.1007/978-3-540-28645-5_29>, the Early Drift Detection Method
(EDDM) of Baena-Garcia et al. (2006), the Hoeffding's inequality
based Drift Detection Methods (HDDM) of Frias-Blanco et al. (2015)
<doi:10.1109/TKDE.2014.2345382>, and the Exponentially Weighted
Moving Average (EWMA) chart of Ross et al. (2012)
<doi:10.1016/j.patrec.2011.08.019>. Distribution-based methods
include Adaptive Windowing (ADWIN) of Bifet and Gavalda (2007)
<doi:10.1137/1.9781611972771.42>, Kolmogorov-Smirnov Windowing
(KSWIN) [...truncated...]
Author: Joao Paulo Assis Bonifacio [aut, cre] ,
Geraldo Magela da Cruz Pereira [aut] ,
Pedro Mambelli Fernandes [aut]
Maintainer: Joao Paulo Assis Bonifacio <jpab.27@hotmail.com>
Diff between deriva versions 0.1.0 dated 2026-08-03 and 0.2.0 dated 2026-09-20
DESCRIPTION | 13 - MD5 | 119 +++++---- NEWS.md | 63 ++++ R/advance.R | 87 +++--- R/augment.R | 61 ++-- R/autoplot.R | 196 ++++++++------- R/data.R |only R/detect_drift.R | 57 ++-- R/drift_detector.R | 159 +++++++++--- R/engine.R | 62 +++- R/fit.R | 160 ++++++++---- R/method-adwin.R | 291 +++++++++++----------- R/method-fhddm.R | 66 ++--- R/method-fhddms.R | 96 +++---- R/method-fisher.R | 209 ++++++++-------- R/method-kswin.R | 62 ++-- R/method-mddm.R | 118 ++++----- R/method-seed.R | 297 +++++++++++----------- R/method-seqdrift2.R | 157 ++++++------ R/method-wstd.R | 129 +++++---- R/param-checks.R |only R/registry.R | 67 ++--- R/tidy-glance.R | 78 +++--- R/validate.R | 111 +++++--- R/zzz.R | 63 ++++ README.md | 232 +++++++++-------- build/partial.rdb |only build/vignette.rds |binary data |only inst/WORDLIST | 56 ++-- inst/doc/deriva.R | 27 -- inst/doc/deriva.Rmd | 351 +++++++++++++-------------- inst/doc/deriva.html | 254 ++++++++++--------- inst/doc/distribution-detectors.R |only inst/doc/distribution-detectors.Rmd |only inst/doc/distribution-detectors.html |only man/advance.Rd | 78 +++--- man/augment.drift_detector_fit.Rd | 59 ++-- man/autoplot.drift_detector_fit.Rd | 46 +-- man/credit_monitoring.Rd |only man/deriva-package.Rd | 11 man/detect_drift.Rd | 68 ++--- man/drift_detector.Rd | 80 ++++-- man/sensor_monitoring.Rd |only man/tidy.drift_detector_fit.Rd | 41 +-- tests/testthat/fixtures/regression-flags.rds |only tests/testthat/helper-bundled.R |only tests/testthat/test-advance.R | 70 ++--- tests/testthat/test-adwin.R | 58 ++-- tests/testthat/test-bridge.R | 63 ++-- tests/testthat/test-column-safety.R |only tests/testthat/test-edge-inputs.R |only tests/testthat/test-fhddm.R | 38 +- tests/testthat/test-fhddms.R | 40 +-- tests/testthat/test-flag-contract.R |only tests/testthat/test-ftdd.R | 78 +++--- tests/testthat/test-keep.R |only tests/testthat/test-kswin.R | 85 +++--- tests/testthat/test-mddm.R | 64 ++-- tests/testthat/test-param-checks.R |only tests/testthat/test-param-validation.R |only tests/testthat/test-registry.R | 65 ++--- tests/testthat/test-regression-flags.R |only tests/testthat/test-rng.R |only tests/testthat/test-seed.R | 139 +++++++--- tests/testthat/test-seqdrift2.R | 78 +++--- tests/testthat/test-spec.R | 45 +-- tests/testthat/test-wstd.R | 129 +++++---- vignettes/deriva.Rmd | 351 +++++++++++++-------------- vignettes/distribution-detectors.Rmd |only 70 files changed, 2920 insertions(+), 2407 deletions(-)
Title: Zero-Modified Complex 'Tri-Parametric' Pearson Distribution for
Overdispersed Count Data
Description: Implements zero-modified versions of the Complex 'Tri-Parametric'
Pearson distribution for overdispersed count data. The package addresses
limitations of existing implementations when the parameter b approaches
zero. It provides distribution functions, maximum likelihood estimation,
and diagnostic tools for modeling count data with excess zeros. The
methodology is based on 'Rodriguez-Avi' and coauthors (2003)
<doi:10.1007/s00362-002-0134-7>.
Author: Rasheedat Oladoja [aut, cre]
Maintainer: Rasheedat Oladoja <roladoja@ttu.edu>
Diff between zmctp versions 0.1.2 dated 2026-07-22 and 0.1.3 dated 2026-09-20
DESCRIPTION | 6 +-- MD5 | 15 ++++---- NEWS.md | 39 ++++++++++++++++++++++ R/ctp_fit.R | 77 ++++++++++++++++++++++++++++++++++++--------- R/dctp.R | 31 ++++++++++++------ R/methods.R | 8 ++++ R/zictp_fit.R | 47 ++++++++++++++++++++++----- inst/doc/introduction.html | 17 ++++----- tests/testthat/test-fit.R |only 9 files changed, 188 insertions(+), 52 deletions(-)
Title: Create Pharmacometric Models
Description: Provides a user interface to create or modify pharmacometric
models for various modeling and simulation software platforms.
Author: Sebastien Bihorel [cre, aut]
Maintainer: Sebastien Bihorel <sb.pmlab@gmail.com>
Diff between pmxcode versions 0.3.1 dated 2025-09-07 and 0.3.2 dated 2026-09-20
DESCRIPTION | 6 LICENSE | 2 MD5 | 16 - NEWS.md | 3 R/new_model_server.R | 8 R/utils_nonmem.R | 52 +++-- build/vignette.rds |binary inst/doc/covariates.html | 472 +++++++++++++++++++++++++++++++++-------------- inst/doc/library.html | 442 +++++++++++++++++++++++++++++--------------- 9 files changed, 688 insertions(+), 313 deletions(-)
Title: Mixture Models for Clustering and Classification
Description: An implementation of 14 parsimonious mixture models for model-based clustering or model-based classification. Gaussian, Student's t, generalized hyperbolic, variance-gamma or skew-t mixtures are available. All approaches work with missing data. Celeux and Govaert (1995) <doi:10.1016/0031-3203(94)00125-6>, Browne and McNicholas (2014) <doi:10.1007/s11634-013-0139-1>, Browne and McNicholas (2015) <doi:10.1002/cjs.11246>.
Author: Nik Pocuca [aut] ,
Ryan P. Browne [aut] ,
Paul D. McNicholas [aut, cre] ,
Alexa A. Sochaniwsky [aut]
Maintainer: Paul D. McNicholas <mcnicholas@math.mcmaster.ca>
Diff between mixture versions 2.2.0 dated 2025-12-18 and 2.2.1 dated 2026-09-20
ChangeLog | 3 + DESCRIPTION | 8 ++-- MD5 | 80 ++++++++++++++++++++-------------------- R/RcppExports.R | 20 +++++----- R/gh_mixture.R | 12 ++++-- R/mixture.R | 12 ++++-- R/pcm.R | 4 +- R/st_mixture.R | 12 ++++-- R/t_mixture.R | 12 ++++-- R/vg_mixture.R | 12 ++++-- man/ARI.Rd | 2 - man/MAP.Rd | 2 - man/e_step.Rd | 2 - man/get_best_model.Rd | 2 - man/ghpcm.Rd | 7 ++- man/gpcm.Rd | 7 ++- man/main_loop.Rd | 7 ++- man/main_loop_gh.Rd | 7 ++- man/main_loop_st.Rd | 7 ++- man/main_loop_t.Rd | 7 ++- man/main_loop_vg.Rd | 7 ++- man/mixture.Rd | 4 +- man/pcm.Rd | 7 ++- man/stpcm.Rd | 7 ++- man/tpcm.Rd | 7 ++- man/vgpcm.Rd | 7 ++- man/z_ig_kmeans.Rd | 2 - man/z_ig_random_hard.Rd | 2 - man/z_ig_random_soft.Rd | 2 - src/Cluster_Error.hpp | 2 - src/GH_Model/GH_Mixture_Model.h | 3 + src/RcppExports.cpp | 45 ++++++++++++---------- src/ST_Model/ST_Mixture_Model.h | 3 + src/T_Model/General_Methods.hpp | 5 ++ src/T_Model/T_Mixture_Model.hpp | 1 src/VG_Model/VG_Mixture_Model.h | 3 + src/ghpcm_arma.hpp | 6 ++- src/gpcm_arma.hpp | 15 ++++++- src/stpcm_arma.hpp | 5 +- src/tpcm_arma.hpp | 5 +- src/vgpcm_arma.hpp | 5 +- 41 files changed, 226 insertions(+), 142 deletions(-)
Title: Soundscape Spectral Metrics
Description: Accessible and flexible implementation of spectral ecoacoustic indices. The functions were design to accommodate a variety of sampling designs. Users can tailor calculations by specifying spectrogram time bin size, amplitude thresholds and normality tests. By simplifying computation and standardizing reproducible methods, the package aims to support ecoacoustics studies.
Author: Arthur Igor da Fonseca-Freire [aut, cre, cph],
Weslley Geremias dos Santos [aut],
Lucas Rodriguez Forti [aut]
Maintainer: Arthur Igor da Fonseca-Freire <arthur.igorr@gmail.com>
Diff between Ruido versions 1.1.0 dated 2026-09-01 and 1.1.1 dated 2026-09-20
DESCRIPTION | 6 +-- MD5 | 18 +++++----- R/activity.R | 82 +++++++++++++++++++++++++------------------------- R/bgNoise.R | 2 - R/internalFunctions.R | 5 +-- R/noise.matrix.R | 5 +-- R/singleSat.R | 61 +++++++++++++++++++++++-------------- man/ENTspec.Rd | 4 +- man/activity.Rd | 14 ++++---- man/singleSat.Rd | 9 ++++- 10 files changed, 115 insertions(+), 91 deletions(-)
Title: Powerful 'SAS' Inspired Concepts for more Efficient Bigger
Outputs
Description: The main goal is to make descriptive evaluations easier to create bigger and more complex outputs in less time with less code. Introducing format containers with multilabels <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p06ciqes4eaqo6n0zyqtz9p21nfb.htm>, a more powerful summarise which is capable to output every possible combination of the provided grouping variables in one go <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p0jvbbqkt0gs2cn1lo4zndbqs1pe.htm>, tabulation functions which can create any table in different styles <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/n1ql5xnu0k3kdtn11gwa5hc7u435.htm> and other more readable functions. The code is optimized to work fast even with datasets of over a million observations.
Author: Tim Siebenmorgen [aut, cre, cph]
Maintainer: Tim Siebenmorgen <qol_package@proton.me>
Diff between qol versions 1.3.4 dated 2026-08-21 and 1.3.5 dated 2026-09-20
DESCRIPTION | 6 MD5 | 116 NEWS.md | 67 R/any_table.R | 7690 ++++++++++++++++++------------------ R/apply_format.R | 387 - R/build_master.R | 91 R/compute.R | 1113 ++--- R/conversion.R | 873 ++-- R/create_format.R | 947 ++-- R/crosstabs.R | 59 R/dummy_data.R | 828 ++- R/excel_helpers.R | 54 R/export_with_style.R | 84 R/frequencies.R | 134 R/globals.R | 192 R/if_else.R | 3716 ++++++++--------- R/import_export.R | 67 R/internal.R | 2 R/loading.R | 2188 +++++----- R/multi_join.R | 950 ++-- R/options.R | 10 R/recode.R | 11 R/renaming.R | 799 +-- R/retain.R | 1 R/small_helpers.R | 30 R/sort_plus.R | 2 R/statistics.R | 9 R/strings.R | 777 +-- R/summarise_plus.R | 3156 +++++++------- R/transpose_plus.R | 1495 ++++-- README.md | 2 inst/tinytest/test-any_table.R | 4 inst/tinytest/test-compute.R | 294 - inst/tinytest/test-create_format.R | 81 inst/tinytest/test-crosstabs.R | 2 inst/tinytest/test-dummy_data.R | 18 inst/tinytest/test-frequencies.R | 16 inst/tinytest/test-if_else.R | 1404 +++--- inst/tinytest/test-loading.R | 902 ++-- inst/tinytest/test-multi_join.R | 461 +- inst/tinytest/test-options.R | 2 inst/tinytest/test-recode.R | 21 inst/tinytest/test-renaming.R | 152 inst/tinytest/test-strings.R | 597 +- inst/tinytest/test-summarise_plus.R | 2180 +++++----- inst/tinytest/test-transpose_plus.R | 686 +-- man/any_table.Rd | 4 man/build_master.Rd | 2 man/combine_into_workbook.Rd | 21 man/crosstabs.Rd | 2 man/dummy_data.Rd | 14 man/export_with_style.Rd | 2 man/frequencies.Rd | 2 man/import_export.Rd | 2 man/qol_options.Rd | 2 man/run_scripts.Rd | 7 man/sort_plus.Rd | 2 man/summarise_plus.Rd | 4 man/transpose_plus.Rd | 43 59 files changed, 17262 insertions(+), 15521 deletions(-)
Title: Summarises Package & Function Usage
Description: Consistent with 'knitr' syntax highlighting, 'usedthese' adds
a summary table of package & function usage to a Quarto document and
enables aggregation of usage across a website.
Author: Carl Goodwin [aut, cre, cph]
Maintainer: Carl Goodwin <carl.goodwin@quantumjitter.com>
Diff between usedthese versions 0.5.0 dated 2024-06-26 and 0.5.1 dated 2026-09-20
DESCRIPTION | 12 ++--- MD5 | 24 +++++------ NAMESPACE | 74 ++++++++++++++++++++---------------- NEWS.md | 4 + R/used_there.R | 7 --- R/usedthese-package.R | 2 README.md | 61 +++++++++-------------------- build/vignette.rds |binary inst/doc/multipage.html | 31 +++++++-------- inst/doc/usedthese.html | 65 ++++++++++++++++--------------- man/usedthese-package.Rd | 5 ++ tests/testthat/_snaps/used_there.md | 13 +++++- tests/testthat/test-used_there.R | 15 +++++++ 13 files changed, 167 insertions(+), 146 deletions(-)
Title: A Comprehensive and Intuitive R Package for Stepwise Regression
Analysis
Description: Stepwise regression is a statistical technique used for model selection. This package streamlines stepwise regression analysis by supporting multiple regression types(linear, Cox, logistic, Poisson, Gamma, and negative binomial), incorporating popular selection strategies(forward, backward, bidirectional, and subset), and offering essential metrics. It enables users to apply multiple selection strategies and metrics in a single function call, visualize variable selection processes, and export results in various formats. StepReg offers a data-splitting option to address potential issues with invalid statistical inference and a randomized forward selection option to avoid overfitting. We validated StepReg's accuracy using public datasets within the SAS software environment. For an interactive web interface, users can install the companion 'StepRegShiny' package. The methodology is described in Li et al. (2026) <doi:10.32614/RJ-2026-005>.
Author: Junhui Li [cre, aut] ,
Kai Hu [aut],
Xiaohuan Lu [aut],
Sushmita N Nayak [ctb, aut],
Cesar Bautista Sotelo [ctb, aut],
Michael A Lodato [ctb, aut],
Wenxin Liu [aut],
Lihua Julie Zhu [aut]
Maintainer: Junhui Li <junhui.li11@umassmed.edu>
Diff between StepReg versions 1.6.7 dated 2026-08-31 and 1.6.8 dated 2026-09-20
DESCRIPTION | 13 +- MD5 | 14 +- NAMESPACE | 22 ++-- NEWS.md | 30 +++++ R/fastUtils.R |only R/report.R | 17 +-- R/stepwise.R | 16 ++ R/stepwiseUtils.R | 219 +++++++++++++++++++++++++++------------- tests/testthat/test_fast_path.R |only 9 files changed, 228 insertions(+), 103 deletions(-)
Title: Statistical Tools for African National Statistics Institutes
Description: A comprehensive statistical toolbox for National Statistics
Institutes (INS) in Africa. Provides functions for survey data import
('KoboToolbox', 'ODK', 'CSPro', 'Excel', 'Stata', 'SPSS'), data
processing and validation, weighted statistical analysis (descriptive
statistics, cross-tabulations, regression, Human Development Index (HDI),
Multidimensional Poverty Index (MPI) following Alkire and Foster (2011)
<doi:10.1093/oep/gpr051>, inequalities), visualization (age pyramids,
thematic maps, official charts) and dissemination ('SDMX' export, 'DDI'
metadata, anonymization, Word/PDF reports). Designed to work in
resource-constrained environments, offline and in French.
Author: Dikers Amoko [aut, cre, ctb],
Josue Honore Dasse [ctb]
Maintainer: Dikers Amoko <diamoko@gmail.com>
Diff between statAfrikR versions 0.1.0 dated 2026-04-03 and 0.2.0 dated 2026-09-20
DESCRIPTION | 48 +- MD5 | 264 +++++++++-- NAMESPACE | 116 +++++ NEWS.md | 189 +++++++- R/analyse.R | 185 -------- R/bien_etre.R |only R/cartographie.R |only R/catalogue_indicateurs.R |only R/collecte.R | 22 R/dashboard.R |only R/data.R |only R/demographie.R |only R/diffusion.R | 41 + R/emploi.R |only R/genre.R |only R/harmonisation_geo.R |only R/inegalites.R |only R/ipm.R |only R/odd.R |only R/pauvrete.R |only R/pib.R |only R/rapports.R |only R/sante.R |only R/sondage.R |only R/statAfrikR-package.R | 37 + R/tableaux.R |only R/traitement.R | 16 R/validation_ins.R |only R/visualisation.R | 4 data |only inst/INS_READINESS.md |only inst/doc/demarrage-rapide.R | 4 inst/doc/demarrage-rapide.Rmd | 4 inst/doc/demarrage-rapide.html | 4 inst/doc/enquete-ponderee.R | 379 +++++++++-------- inst/doc/enquete-ponderee.Rmd | 96 +++- inst/doc/enquete-ponderee.html | 557 ++++++------------------- inst/doc/indicateurs-odd.R | 465 ++++++++++---------- inst/doc/indicateurs-odd.Rmd | 56 +- inst/doc/indicateurs-odd.html | 428 ++++--------------- inst/rmd |only man/accouchements_assistes.Rd |only man/analyse_regression.Rd | 2 man/analyse_spatiale.Rd | 2 man/analyser_non_reponse.Rd |only man/anemie.Rd |only man/anonymiser_donnees.Rd | 7 man/autonomisation_femmes.Rd |only man/bonheur_declare.Rd |only man/calcul_deff.Rd |only man/calcul_fgt.Rd |only man/calcul_gini.Rd |only man/calcul_ipm.Rd | 138 ++++-- man/calcul_ipm_national.Rd |only man/calculer_deflateur.Rd |only man/calibrer_poids.Rd |only man/carte_choroplethe.Rd |only man/carte_exporter.Rd |only man/carte_import.Rd |only man/carte_ipm.Rd |only man/carte_joindre.Rd |only man/carte_pauvrete.Rd |only man/carte_thematique.Rd | 2 man/carte_zones.Rd |only man/catalogue_indicateurs.Rd |only man/check_na.Rd | 2 man/check_types.Rd | 2 man/coherence_demo.Rd |only man/comparer_ipm.Rd |only man/comparer_pib.Rd |only man/compresser_package_diffusion.Rd | 2 man/confiance_institutions.Rd |only man/courbe_lorenz.Rd |only man/creer_design.Rd |only man/decomposer_fgt.Rd |only man/decomposer_inegalite.Rd | 2 man/decomposer_ipm.Rd |only man/decomposer_theil.Rd |only man/detecter_ecarts_geo.Rd |only man/emaciation.Rd |only man/emploi_informel.Rd |only man/emploi_vulnerable.Rd |only man/exporter_code_dashboard.Rd |only man/exporter_excel_ins.Rd |only man/exporter_graphique.Rd | 2 man/exporter_sdmx.Rd | 2 man/fusion_datasets.Rd | 2 man/generer_bulletin.Rd |only man/generer_metadonnees_ddi.Rd | 2 man/generer_rapport.Rd | 2 man/generer_rapport_enquete.Rd |only man/generer_rapport_odd.Rd |only man/graphique_fgt.Rd |only man/graphique_ipm.Rd |only man/handicap_prevalence.Rd |only man/harmoniser_regions.Rd | 2 man/harmoniser_zones.Rd |only man/import_cspro.Rd | 2 man/import_csv.Rd | 2 man/import_excel.Rd | 2 man/import_kobo.Rd | 2 man/import_odk.Rd | 2 man/import_sas.Rd | 2 man/import_spss.Rd | 2 man/import_stata.Rd | 2 man/imputer_valeurs.Rd | 2 man/indice_atkinson.Rd |only man/indice_palma.Rd |only man/insuffisance_ponderale.Rd |only man/lancer_dashboard.Rd |only man/lister_templates.Rd |only man/mariage_precoce.Rd |only man/migrer_nomenclature.Rd |only man/mortalite_5ans.Rd |only man/myers.Rd |only man/nettoyer_libelles.Rd | 2 man/odd_catalogue.Rd |only man/odd_indicateur.Rd |only man/parite_education.Rd |only man/part_quintile.Rd |only man/pauvrete_travail.Rd |only man/perception_economique.Rd |only man/privations_ressenties.Rd |only man/protection_sociale.Rd |only man/pyramide_age.Rd |only man/rapport_harmonisation.Rd |only man/rapport_qualite_demo.Rd |only man/rapport_qualite_sondage.Rd |only man/ratio_masculinite.Rd |only man/recoder_variable.Rd | 2 man/retard_croissance.Rd |only man/saf_cameroun_departements.Rd |only man/saf_cedeao.Rd |only man/saf_cemac.Rd |only man/saf_eau.Rd |only man/saf_pays_afrique.Rd |only man/saf_rca_prefectures.Rd |only man/saf_sadc.Rd |only man/saf_senegal_regions.Rd |only man/saf_subdivisions_afrique.Rd |only man/sante_mentale.Rd |only man/satisfaction_vie.Rd |only man/sentiment_securite.Rd |only man/sous_emploi_temps.Rd |only man/standardiser_ages.Rd | 2 man/statAfrikR-package.Rd | 19 man/stat_descr.Rd | 2 man/suivre_revisions_pib.Rd |only man/supprimer_doublons.Rd | 2 man/tab_croisee.Rd | 2 man/table_concordance.Rd |only man/tableau_bien_etre_subjectif.Rd |only man/tableau_bord_pib.Rd |only man/tableau_croise_ins.Rd |only man/tableau_descriptif.Rd |only man/tableau_fgt.Rd |only man/tableau_genre.Rd |only man/tableau_inegalites.Rd |only man/tableau_ipm.Rd |only man/tableau_marche_travail.Rd |only man/tableau_odd.Rd |only man/tableau_sante.Rd |only man/taux_activite.Rd |only man/taux_croissance.Rd |only man/taux_emploi.Rd |only man/taux_sous_utilisation.Rd |only man/tracer_flux_traitement.Rd | 2 man/travail_enfants.Rd |only man/vaccination.Rd |only man/valider_coherence_geo.Rd |only man/valider_dictionnaire.Rd | 2 man/valider_poids.Rd |only man/valider_qualite_donnees.Rd | 2 man/valider_statistique_ins.Rd |only man/violence_basee_genre.Rd |only man/whipple.Rd |only tests/testthat/test-analyse.R | 83 +-- tests/testthat/test-bien_etre.R |only tests/testthat/test-cartographie.R |only tests/testthat/test-catalogue_indicateurs.R |only tests/testthat/test-dashboard.R |only tests/testthat/test-demographie.R |only tests/testthat/test-emploi.R |only tests/testthat/test-genre.R |only tests/testthat/test-harmonisation_geo.R |only tests/testthat/test-inegalites.R |only tests/testthat/test-ipm.R |only tests/testthat/test-odd.R |only tests/testthat/test-pauvrete.R |only tests/testthat/test-pib.R |only tests/testthat/test-rapports.R |only tests/testthat/test-reference_methodologique.R |only tests/testthat/test-sante.R |only tests/testthat/test-sondage.R |only tests/testthat/test-tableaux.R |only tests/testthat/test-validation_ins.R |only vignettes/demarrage-rapide.Rmd | 4 vignettes/enquete-ponderee.Rmd | 96 +++- vignettes/indicateurs-odd.Rmd | 56 +- 199 files changed, 1700 insertions(+), 1680 deletions(-)
Title: A Modern and Flexible Data Pipeline for 'SurveyCTO'
Description: A modern and flexible R client for the 'SurveyCTO', a mobile and
offline data collection platform, providing a modern and consistent interface for
programmatic access to server resources. Built on top of the 'httr2' package,
it enables secure and efficient data retrieval and returns analysis-ready
data through optional tidying. It includes functions to create, upload, and
download server datasets, in addition to fetching form data, files, and
submission attachments. Robust authentication and request handling make the
package suitable for automated survey monitoring and downstream analysis.
Author: Gutama Girja Urago [aut, cre, cph]
Maintainer: Gutama Girja Urago <girjagutama@gmail.com>
Diff between ctoclient versions 0.1.0 dated 2026-03-28 and 0.2.0 dated 2026-09-20
ctoclient-0.1.0/ctoclient/tests/testthat/_datasets/band_members/records/upload-0002f6-POST.json |only ctoclient-0.2.0/ctoclient/DESCRIPTION | 17 ctoclient-0.2.0/ctoclient/MD5 | 84 - ctoclient-0.2.0/ctoclient/NAMESPACE | 127 - ctoclient-0.2.0/ctoclient/NEWS.md | 39 ctoclient-0.2.0/ctoclient/R/cto_connect.R | 307 ++-- ctoclient-0.2.0/ctoclient/R/cto_dataset_create.R | 313 ++-- ctoclient-0.2.0/ctoclient/R/cto_dataset_delete.R | 128 - ctoclient-0.2.0/ctoclient/R/cto_dataset_download.R | 180 +- ctoclient-0.2.0/ctoclient/R/cto_dataset_info.R | 67 ctoclient-0.2.0/ctoclient/R/cto_form_attachment.R | 286 +-- ctoclient-0.2.0/ctoclient/R/cto_form_data.R | 605 ++++---- ctoclient-0.2.0/ctoclient/R/cto_form_data_attachment.R | 255 +-- ctoclient-0.2.0/ctoclient/R/cto_form_definition.R | 248 +-- ctoclient-0.2.0/ctoclient/R/cto_form_docx.R |only ctoclient-0.2.0/ctoclient/R/cto_form_dofile.R | 126 + ctoclient-0.2.0/ctoclient/R/cto_form_files.R | 465 +++--- ctoclient-0.2.0/ctoclient/R/zzz.R | 729 ++++++++-- ctoclient-0.2.0/ctoclient/README.md | 182 -- ctoclient-0.2.0/ctoclient/build |only ctoclient-0.2.0/ctoclient/inst/doc |only ctoclient-0.2.0/ctoclient/man/cto_connect.Rd | 174 +- ctoclient-0.2.0/ctoclient/man/cto_dataset_create.Rd | 194 +- ctoclient-0.2.0/ctoclient/man/cto_dataset_delete.Rd | 86 - ctoclient-0.2.0/ctoclient/man/cto_dataset_download.Rd | 108 - ctoclient-0.2.0/ctoclient/man/cto_dataset_info.Rd | 62 ctoclient-0.2.0/ctoclient/man/cto_dataset_list.Rd | 96 - ctoclient-0.2.0/ctoclient/man/cto_docx_palette.Rd |only ctoclient-0.2.0/ctoclient/man/cto_form_attachment.Rd | 154 +- ctoclient-0.2.0/ctoclient/man/cto_form_data.Rd | 177 +- ctoclient-0.2.0/ctoclient/man/cto_form_data_attachment.Rd | 148 +- ctoclient-0.2.0/ctoclient/man/cto_form_docx.Rd |only ctoclient-0.2.0/ctoclient/man/cto_form_dofile.Rd | 132 - ctoclient-0.2.0/ctoclient/man/cto_form_languages.Rd | 252 +-- ctoclient-0.2.0/ctoclient/man/cto_form_metadata.Rd | 156 +- ctoclient-0.2.0/ctoclient/man/figures |only ctoclient-0.2.0/ctoclient/tests/testthat/_datasets/band_members/records/upload-f8492c-POST.json |only ctoclient-0.2.0/ctoclient/tests/testthat/_metadata/roles.R | 24 ctoclient-0.2.0/ctoclient/tests/testthat/_metadata/users.R | 24 ctoclient-0.2.0/ctoclient/tests/testthat/fixtures |only ctoclient-0.2.0/ctoclient/tests/testthat/test-ctoclient.R | 59 ctoclient-0.2.0/ctoclient/tests/testthat/test-docx.R |only ctoclient-0.2.0/ctoclient/tests/testthat/test-dofile.R |only ctoclient-0.2.0/ctoclient/tests/testthat/test-form-data.R |only ctoclient-0.2.0/ctoclient/tests/testthat/test-form-id-cache.R |only ctoclient-0.2.0/ctoclient/tests/testthat/test-utils.R |only ctoclient-0.2.0/ctoclient/vignettes |only 47 files changed, 3348 insertions(+), 2656 deletions(-)
Title: Isotopic Tracer Analysis Using MCMC
Description: Implements Bayesian models to analyze data from tracer addition
experiments. The implemented method was originally described in the article
"A New Method to Reconstruct Quantitative Food Webs and Nutrient Flows from
Isotope Tracer Addition Experiments" by López-Sepulcre et al. (2020)
<doi:10.1086/708546>.
Author: Andres Lopez-Sepulcre [aut] ,
Matthieu Bruneaux [aut, cre]
Maintainer: Matthieu Bruneaux <matthieu.bruneaux@gmail.com>
This is a re-admission after prior archival of version 1.1.8 dated 2025-03-07
Diff between isotracer versions 1.1.8 dated 2025-03-07 and 1.1.9 dated 2026-09-20
DESCRIPTION | 14 MD5 | 208 - NAMESPACE | 78 NEWS.md | 6 R/ui_predictions.R | 52 README.md | 22 build/vignette.rds |binary inst/doc/case-study-collins-2016.Rmd | 31 inst/doc/case-study-collins-2016.html | 342 - inst/doc/tutorial-010-quick-start.Rmd | 12 inst/doc/tutorial-010-quick-start.html | 253 - inst/doc/tutorial-020-replication.Rmd | 8 inst/doc/tutorial-020-replication.html | 257 - inst/doc/tutorial-030-steady-state-comps.Rmd | 24 inst/doc/tutorial-030-steady-state-comps.html | 293 - inst/doc/tutorial-040-pulse-drip-events.Rmd | 21 inst/doc/tutorial-040-pulse-drip-events.html | 354 - inst/doc/tutorial-050-fixed-effects.Rmd | 51 inst/doc/tutorial-050-fixed-effects.html | 339 - inst/doc/tutorial-060-units-priors.Rmd | 2 inst/doc/tutorial-060-units-priors.html | 137 inst/doc/tutorial-070-prior-predictive-checks.Rmd | 2 inst/doc/tutorial-070-prior-predictive-checks.html | 18 inst/doc/tutorial-080-mcmc-output-format.Rmd | 10 inst/doc/tutorial-080-mcmc-output-format.html | 181 inst/doc/tutorial-090-post-run-analyses.Rmd | 10 inst/doc/tutorial-090-post-run-analyses.html | 209 - inst/doc/tutorial-100-posterior-predictive-checks.Rmd | 21 inst/doc/tutorial-100-posterior-predictive-checks.html | 251 - inst/doc/tutorial-110-derived-parameters.Rmd | 12 inst/doc/tutorial-110-derived-parameters.html | 229 - inst/doc/tutorial-120-howto-simulations.Rmd | 40 inst/doc/tutorial-120-howto-simulations.html | 309 - inst/doc/tutorial-130-parameter-identifiability.Rmd | 25 inst/doc/tutorial-130-parameter-identifiability.html | 256 - man/filter.Rd | 7 man/isotracer-package.Rd | 1 man/reexports.Rd | 6 src/stanExports_networkModel.cc | 34 src/stanExports_networkModel.h | 1980 ++++++++-- tests/testthat/test-helpers_projection-simulation.R | 2 tests/testthat/test-integration.R | 15 tests/testthat/test-steady-states-flows-pred.R | 17 tests/testthat/test-ui_getters.R | 2 tests/testthat/test-ui_model-building.R | 2 tests/testthat/test-ui_others.R | 2 tests/testthat/test-ui_plotting.R | 5 tests/testthat/test-ui_predictions.R | 5 tests/testthat/test-ui_projection.R | 2 tests/testthat/test-ui_run-mcmc.R | 5 tests/testthat/test-ui_sankey-plotting.R | 5 tests/testthat/test-ui_topology.R | 5 vignettes/case-study-collins-2016.Rmd | 31 vignettes/figures/z-fig-010-unnamed-chunk-8-1.jpeg |binary vignettes/figures/z-fig-030-unnamed-chunk-24-1.jpeg |binary vignettes/figures/z-fig-030-unnamed-chunk-26-1.jpeg |binary vignettes/figures/z-fig-030-unnamed-chunk-27-1.jpeg |binary vignettes/figures/z-fig-040-unnamed-chunk-14-1.jpeg |binary vignettes/figures/z-fig-040-unnamed-chunk-16-1.jpeg |binary vignettes/figures/z-fig-040-unnamed-chunk-29-1.jpeg |binary vignettes/figures/z-fig-040-unnamed-chunk-31-1.jpeg |binary vignettes/figures/z-fig-050-unnamed-chunk-21-1.jpeg |binary vignettes/figures/z-fig-050-unnamed-chunk-23-1.jpeg |binary vignettes/figures/z-fig-050-unnamed-chunk-25-1.jpeg |binary vignettes/figures/z-fig-050-unnamed-chunk-26-1.jpeg |binary vignettes/figures/z-fig-050-unnamed-chunk-28-1.jpeg |binary vignettes/figures/z-fig-080-unnamed-chunk-16-1.jpeg |binary vignettes/figures/z-fig-100-unnamed-chunk-12-1.jpeg |binary vignettes/figures/z-fig-100-unnamed-chunk-12-2.jpeg |binary vignettes/figures/z-fig-100-unnamed-chunk-13-1.jpeg |binary vignettes/figures/z-fig-100-unnamed-chunk-14-1.jpeg |binary vignettes/figures/z-fig-100-unnamed-chunk-8-1.jpeg |binary vignettes/figures/z-fig-120-unnamed-chunk-20-1.jpeg |binary vignettes/figures/z-fig-120-unnamed-chunk-22-1.jpeg |binary vignettes/figures/z-fig-120-unnamed-chunk-28-1.jpeg |binary vignettes/figures/z-fig-120-unnamed-chunk-30-1.jpeg |binary vignettes/figures/z-fig-120-unnamed-chunk-30-2.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-28-1.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-31-1.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-34-1.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-39-1.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-42-1.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-47-1.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-48-1.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-8-1.jpeg |binary vignettes/figures/z-fig-cs-li-2017-unnamed-chunk-26-1.jpeg |binary vignettes/figures/z-fig-cs-li-2017-unnamed-chunk-26-2.jpeg |binary vignettes/figures/z-fig-cs-li-2017-unnamed-chunk-28-1.jpeg |binary vignettes/figures/z-fig-cs-li-2017-unnamed-chunk-8-1.jpeg |binary vignettes/figures/z-fig-cs-mcroy-1970-unnamed-chunk-22-1.jpeg |binary vignettes/figures/z-fig-cs-mcroy-1970-unnamed-chunk-23-1.jpeg |binary vignettes/figures/z-fig-cs-mcroy-1970-unnamed-chunk-9-1.jpeg |binary vignettes/tutorial-010-quick-start.Rmd | 12 vignettes/tutorial-020-replication.Rmd | 8 vignettes/tutorial-030-steady-state-comps.Rmd | 24 vignettes/tutorial-040-pulse-drip-events.Rmd | 21 vignettes/tutorial-050-fixed-effects.Rmd | 51 vignettes/tutorial-060-units-priors.Rmd | 2 vignettes/tutorial-070-prior-predictive-checks.Rmd | 2 vignettes/tutorial-080-mcmc-output-format.Rmd | 10 vignettes/tutorial-090-post-run-analyses.Rmd | 10 vignettes/tutorial-100-posterior-predictive-checks.Rmd | 21 vignettes/tutorial-110-derived-parameters.Rmd | 12 vignettes/tutorial-120-howto-simulations.Rmd | 40 vignettes/tutorial-130-parameter-identifiability.Rmd | 25 105 files changed, 3907 insertions(+), 2534 deletions(-)
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
some of which were ported from S-plus in the 1990s.
For graphics, have pretty (Log-scale) axes eaxis(), an enhanced Tukey-Anscombe
plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()',
pretty arrows, etc.
For robustness, have a robust F test and robust range().
For system support, notably on Linux, provides 'Sys.*()' functions with
more access to system and CPU information.
Finally, miscellaneous utilities such as simple efficient prime numbers,
integer codes, Duplicated(), toLatex.numeric() and is.whole().
Author: Martin Maechler [aut, cre] ,
Werner Stahel [ctb] , f.robftest, last,
p.scales, p.dnorm),
Andreas Ruckstuhl [ctb] , p.profileTraces,
p.res.2x),
Christian Keller [ctb] , p.tachoPlot),
Kjetil Halvorsen [ctb] , ecdf.ksCI),
Alain Hauser [ctb] , is.whole,
[...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.1-25 dated 2026-08-03 and 1.1-26 dated 2026-09-20
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 3 ++- R/misc-goodies.R | 9 +++++++++ inst/NEWS.Rd | 16 +++++++++++----- man/formatN.Rd | 24 +++++++++++++++--------- 6 files changed, 48 insertions(+), 26 deletions(-)
Title: Sound Synthesis and Acoustic Analysis
Description: Parametric source-filter synthesis of harmonic-noise signals, such
as animal vocalizations and human voice, with control over pitch, formants,
noise, amplitude modulation, nonlinear phenomena, and morphing. General signal
processing tools for audio analysis and manipulation: pitch tracking, formant
and vocal tract length estimation, reassigned and auditory spectrograms,
modulation spectra and psychoacoustic roughness, self-similarity and
surprisal, audio segmentation, pitch and formant shifting, etc. Includes four
interactive web apps for audio synthesis, annotation, formant analysis, and
manually correcting pitch contours.
Reference: Anikin (2019) <doi:10.3758/s13428-018-1095-7>.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <andrey.anikin@cogsci.se>
Diff between soundgen versions 2.9.0 dated 2026-02-24 and 3.0.0 dated 2026-09-20
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- soundgen-3.0.0/soundgen/R/windowFunctions.R |only soundgen-3.0.0/soundgen/README.md | 157 soundgen-3.0.0/soundgen/data/IR.rda |only soundgen-3.0.0/soundgen/data/detectNLP_training_nonv.rda |binary soundgen-3.0.0/soundgen/data/detectNLP_training_synth.rda |binary soundgen-3.0.0/soundgen/data/presets.rda |binary soundgen-3.0.0/soundgen/data/speechEx.rda |only soundgen-3.0.0/soundgen/inst/shiny/annotation_app/server.R | 873 +-- soundgen-3.0.0/soundgen/inst/shiny/annotation_app/ui.R | 236 soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/annotation_app.css | 6 soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/annotation_app.js | 81 soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/annotation_app_shinyjs.js | 109 soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/annotate.png |binary soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/backward.png |binary soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/delete.png |binary 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soundgen-3.0.0/soundgen/man/stft_simple.Rd |only soundgen-3.0.0/soundgen/man/timeStretch.Rd | 61 soundgen-3.0.0/soundgen/man/transplantEnv.Rd | 39 soundgen-3.0.0/soundgen/man/transplantFormants.Rd | 184 soundgen-3.0.0/soundgen/man/winFun.Rd |only 427 files changed, 24035 insertions(+), 20894 deletions(-)
Title: Power Under Multiplicity Project
Description: Estimates power, minimum detectable effect size (MDES) and sample size requirements. The context is multilevel randomized experiments with multiple outcomes. The estimation takes into account the use of multiple testing procedures. Development of this package was supported by a grant from the Institute of Education Sciences (R305D170030). For a full package description, including a detailed technical appendix, see <doi:10.18637/jss.v108.i06>.
Author: Luke Miratrix [aut, cre] ,
Kristen Hunter [aut] ,
Zarni Htet [aut],
Kristin Porter [aut],
MDRC [cph],
Institute of Education Sciences [fnd]
Maintainer: Luke Miratrix <luke_miratrix@gse.harvard.edu>
Diff between PUMP versions 1.0.4 dated 2025-03-12 and 1.0.5 dated 2026-09-20
PUMP-1.0.4/PUMP/tests/testthat/test-powerup.R |only PUMP-1.0.4/PUMP/vignettes/pump_demo_cache |only PUMP-1.0.4/PUMP/vignettes/pump_demo_files |only PUMP-1.0.5/PUMP/DESCRIPTION | 15 - PUMP-1.0.5/PUMP/MD5 | 148 +++-------------- PUMP-1.0.5/PUMP/NAMESPACE | 9 - PUMP-1.0.5/PUMP/R/model_fitting.R | 9 - PUMP-1.0.5/PUMP/R/plots.R | 8 PUMP-1.0.5/PUMP/R/pumpresult.R | 11 + PUMP-1.0.5/PUMP/build/partial.rdb |binary PUMP-1.0.5/PUMP/build/vignette.rds |binary PUMP-1.0.5/PUMP/inst/doc/pump_demo.html | 107 ++++++------ PUMP-1.0.5/PUMP/inst/doc/pump_sample_demo.html | 60 ++++-- PUMP-1.0.5/PUMP/inst/doc/pump_simulate.html | 5 PUMP-1.0.5/PUMP/man/PUMP-package.Rd | 1 PUMP-1.0.5/PUMP/man/get_pval_tstat.Rd | 11 - PUMP-1.0.5/PUMP/man/pump_mdes_grid.Rd | 6 PUMP-1.0.5/PUMP/man/pump_power_grid.Rd | 6 PUMP-1.0.5/PUMP/man/pump_sample_grid.Rd | 6 PUMP-1.0.5/PUMP/man/pumpresult.Rd | 2 PUMP-1.0.5/PUMP/tests/testthat/Rplots.pdf |binary PUMP-1.0.5/PUMP/tests/testthat/test-pump_sample.R | 6 PUMP-1.0.5/PUMP/tests/testthat/test-update_functions.R | 76 ++++++++ PUMP-1.0.5/PUMP/vignettes/output/ICCgrid.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/MDEScalc.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/MDEScalcmin1.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/MDESwithNumZero.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/numzerogrid.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/othercorrections.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/powICC.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/powR2.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/powbase.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/rhogrid.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/samplesizecalc.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/samplesizeverify.RDS |binary 35 files changed, 244 insertions(+), 242 deletions(-)
Title: Retrieve, Transform and Analyze the Barcode of Life Data Systems
Data
Description: Facilitates retrieval, transformation and analysis of the data
from the Barcode of Life Data Systems (BOLD) database <https://boldsystems.org/>.
This package allows both public and private user data to be easily downloaded into the R
environment using a variety of inputs such as: IDs (processid, sampleid), BINs, dataset codes,
project codes, taxonomy, geography etc. It provides frictionless data conversion
into formats compatible with other R-packages and third-party tools,
as well as functions for sequence alignment & clustering, biodiversity analysis and spatial mapping.
Author: Sameer Padhye [aut, cre],
Liliana Ballesteros-Mejia [aut],
Timothy Agda [aut],
Jireh Agda [aut],
Sujeevan Ratnasingham [aut]
Maintainer: Sameer Padhye <spadhye@uoguelph.ca>
Diff between BOLDconnectR versions 1.0.2 dated 2026-08-19 and 1.0.3 dated 2026-09-20
DESCRIPTION | 8 - MD5 | 16 +- NAMESPACE | 212 ++++++++++++++++-------------- NEWS.md | 3 R/external.bold.fields.info.R | 71 ++++++---- R/helper.functions.4.bold.public.search.R | 38 +++-- README.md | 4 inst/doc/boldconnectr_workflow.html | 20 +- man/base_url_parse.Rd | 4 9 files changed, 219 insertions(+), 157 deletions(-)
Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine
copula modeling. The 'rvinecopulib' package implements the core features of the
popular 'VineCopula' package, in particular inference algorithms for both vine
copula and bivariate copula models. Advantages over 'VineCopula' are a sleeker
and more modern API, improved performances, especially in high dimensions,
nonparametric and multi-parameter families, and the ability to model discrete
variables. The 'rvinecopulib' package includes 'vinecopulib' as header-only
C++ library (currently version 1.0.0). Thus users do not need to install
'vinecopulib' itself in order to use 'rvinecopulib'. Since their initial
releases, 'vinecopulib' is licensed under the MIT License, and 'rvinecopulib'
is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>
Diff between rvinecopulib versions 0.7.3.1.0 dated 2025-06-13 and 1.0.0.1.0 dated 2026-09-20
rvinecopulib-0.7.3.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_bobyqa.hpp |only rvinecopulib-0.7.3.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_optional.hpp |only rvinecopulib-1.0.0.1.0/rvinecopulib/DESCRIPTION | 22 rvinecopulib-1.0.0.1.0/rvinecopulib/MD5 | 307 rvinecopulib-1.0.0.1.0/rvinecopulib/NAMESPACE | 69 rvinecopulib-1.0.0.1.0/rvinecopulib/NEWS.md | 117 rvinecopulib-1.0.0.1.0/rvinecopulib/R/RcppExports.R | 84 rvinecopulib-1.0.0.1.0/rvinecopulib/R/as_rvine_structure.R | 21 rvinecopulib-1.0.0.1.0/rvinecopulib/R/bicop.R | 24 rvinecopulib-1.0.0.1.0/rvinecopulib/R/bicop_methods.R | 268 rvinecopulib-1.0.0.1.0/rvinecopulib/R/getters.R | 3 rvinecopulib-1.0.0.1.0/rvinecopulib/R/margins.R |only rvinecopulib-1.0.0.1.0/rvinecopulib/R/pairs_copula_data.R | 4 rvinecopulib-1.0.0.1.0/rvinecopulib/R/rosenblatt.R | 136 rvinecopulib-1.0.0.1.0/rvinecopulib/R/rvine_structure.R | 30 rvinecopulib-1.0.0.1.0/rvinecopulib/R/rvinecopulib.R | 104 rvinecopulib-1.0.0.1.0/rvinecopulib/R/tools.R | 260 rvinecopulib-1.0.0.1.0/rvinecopulib/R/truncate_model.R | 9 rvinecopulib-1.0.0.1.0/rvinecopulib/R/vcov.R |only rvinecopulib-1.0.0.1.0/rvinecopulib/R/vine.R | 579 rvinecopulib-1.0.0.1.0/rvinecopulib/R/vine_methods.R | 226 rvinecopulib-1.0.0.1.0/rvinecopulib/R/vinecop.R | 103 rvinecopulib-1.0.0.1.0/rvinecopulib/R/vinecop_methods.R | 316 rvinecopulib-1.0.0.1.0/rvinecopulib/R/vinecop_plot.R | 2 rvinecopulib-1.0.0.1.0/rvinecopulib/README.md | 349 rvinecopulib-1.0.0.1.0/rvinecopulib/build |only rvinecopulib-1.0.0.1.0/rvinecopulib/inst/doc |only rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib-wrappers.hpp | 59 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib.hpp | 11 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/LICENSE |only rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/REVISION |only rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/abstract.hpp | 176 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/archimedean.hpp | 65 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/bb1.hpp | 54 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/bb6.hpp | 54 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/bb7.hpp | 54 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/bb8.hpp | 54 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/class.hpp | 296 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/clayton.hpp | 60 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/elliptical.hpp | 24 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/extreme_value.hpp | 63 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/family.hpp | 96 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/fit_controls.hpp | 33 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/frank.hpp | 58 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/gaussian.hpp | 52 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/gumbel.hpp | 60 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/abstract.ipp | 570 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/archimedean.ipp | 74 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/bb1.ipp | 2514 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/bb6.ipp | 3633 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/bb7.ipp | 2770 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/bb8.ipp | 3581 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/class.ipp | 1648 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/clayton.ipp | 549 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Title: Bayesian Probit Choice Modeling
Description: Fits Bayesian probit models for binary, multinomial, ordered, and ranked
choices in cross-sectional and panel data. Correlated or uncorrelated normal
and log-normal random coefficients, finite mixtures, sparse finite
mixtures, and Dirichlet process mixtures describe preference
heterogeneity. Multiple Gibbs chains produce posterior draws for
diagnostics and choice prediction. Empirical model data can be
supplied as a data frame or simulated from the requested specification.
For an overarching treatment of the methodology, see Oelschlaeger (2026)
<https://pub.uni-bielefeld.de/record/3014719>. The latent-class model is
described in Oelschlaeger and Bauer (2021)
<https://trid.trb.org/view/1759753>.
Author: Lennart Oelschlaeger [aut, cre] ,
Dietmar Bauer [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between RprobitB versions 1.2.0 dated 2025-08-25 and 2.0.0 dated 2026-09-20
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Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Wenping Wang [aut],
Audrey Lavenu [ctb],
Ben Goodrich [ctb],
David Ardia [cph],
Dirk Eddelbuettel [cph],
Elizabeth Eskow [ctb],
Emmanuelle Comets [ctb],
Hadley Wickham [ctb],
Hajar Besbassi [ctb],
Hidde van de Beek [ctb],
[...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 7.0.2 dated 2026-08-04 and 7.1.0 dated 2026-09-20
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nlmixr2est-7.1.0/nlmixr2est/R/preProcessZeroOmega.R | 92 nlmixr2est-7.1.0/nlmixr2est/R/preProcessZeroTheta.R | 37 nlmixr2est-7.1.0/nlmixr2est/R/print.R | 352 nlmixr2est-7.1.0/nlmixr2est/R/priors.R |only nlmixr2est-7.1.0/nlmixr2est/R/qrpem.R | 29 nlmixr2est-7.1.0/nlmixr2est/R/resid.R | 1027 nlmixr2est-7.1.0/nlmixr2est/R/rstudio.R | 6 nlmixr2est-7.1.0/nlmixr2est/R/rxNamedModel.R | 112 nlmixr2est-7.1.0/nlmixr2est/R/rxsolve.R | 278 nlmixr2est-7.1.0/nlmixr2est/R/saem.R | 1500 - nlmixr2est-7.1.0/nlmixr2est/R/saemControl.R | 466 nlmixr2est-7.1.0/nlmixr2est/R/saemIov.R |only nlmixr2est-7.1.0/nlmixr2est/R/saemPhi1Inner.R |only nlmixr2est-7.1.0/nlmixr2est/R/saemPseudoEta.R |only nlmixr2est-7.1.0/nlmixr2est/R/saemPseudoEtaFinalize.R |only nlmixr2est-7.1.0/nlmixr2est/R/saemPseudoEtaSelect.R |only nlmixr2est-7.1.0/nlmixr2est/R/saemRxUiGet.R | 698 nlmixr2est-7.1.0/nlmixr2est/R/saemRxUiGetModel.R | 471 nlmixr2est-7.1.0/nlmixr2est/R/saem_fit.R | 388 nlmixr2est-7.1.0/nlmixr2est/R/saem_fit_aux.R | 786 nlmixr2est-7.1.0/nlmixr2est/R/sessioninfo.R | 103 nlmixr2est-7.1.0/nlmixr2est/R/sharedControl.R | 80 nlmixr2est-7.1.0/nlmixr2est/R/simModelCache.R |only nlmixr2est-7.1.0/nlmixr2est/R/simulate.R | 37 nlmixr2est-7.1.0/nlmixr2est/R/sourceCppFunction.R | 4 nlmixr2est-7.1.0/nlmixr2est/R/splitModelRxUiGet.R | 99 nlmixr2est-7.1.0/nlmixr2est/R/timing.R | 82 nlmixr2est-7.1.0/nlmixr2est/R/trust.R |only nlmixr2est-7.1.0/nlmixr2est/R/uninformativeEtas.R | 193 nlmixr2est-7.1.0/nlmixr2est/R/uobyqa.R | 378 nlmixr2est-7.1.0/nlmixr2est/R/update.R | 6 nlmixr2est-7.1.0/nlmixr2est/R/utils.R | 94 nlmixr2est-7.1.0/nlmixr2est/R/vae.R | 404 nlmixr2est-7.1.0/nlmixr2est/R/vaeCovColinear.R |only nlmixr2est-7.1.0/nlmixr2est/R/vaeCovSelectL0.R | 53 nlmixr2est-7.1.0/nlmixr2est/R/vaeCovShapes.R | 323 nlmixr2est-7.1.0/nlmixr2est/R/vaeData.R | 728 nlmixr2est-7.1.0/nlmixr2est/R/vaeDecoder.R | 17 nlmixr2est-7.1.0/nlmixr2est/R/vaeFit.R | 335 nlmixr2est-7.1.0/nlmixr2est/R/vaeGrad.R | 166 nlmixr2est-7.1.0/nlmixr2est/R/vaeInner.R | 162 nlmixr2est-7.1.0/nlmixr2est/R/vaeOutput.R | 235 nlmixr2est-7.1.0/nlmixr2est/R/validate.R | 21 nlmixr2est-7.1.0/nlmixr2est/R/vi.R | 297 nlmixr2est-7.1.0/nlmixr2est/R/viData.R | 96 nlmixr2est-7.1.0/nlmixr2est/R/vpc.R | 116 nlmixr2est-7.1.0/nlmixr2est/R/zzz.R | 70 nlmixr2est-7.1.0/nlmixr2est/build |only nlmixr2est-7.1.0/nlmixr2est/inst/benchmarks/benchmark-focei-hessian-method.R |only nlmixr2est-7.1.0/nlmixr2est/inst/benchmarks/benchmark-trust-inner.R |only nlmixr2est-7.1.0/nlmixr2est/inst/benchmarks/benchmark-trust-outer.R |only nlmixr2est-7.1.0/nlmixr2est/inst/benchmarks/results |only nlmixr2est-7.1.0/nlmixr2est/inst/benchmarks/runtime-benchmarks.R | 21 nlmixr2est-7.1.0/nlmixr2est/inst/doc |only nlmixr2est-7.1.0/nlmixr2est/inst/include/nlmixr2estFoceiPtr.h |only nlmixr2est-7.1.0/nlmixr2est/inst/include/nlmixr2estLikContrib.h |only nlmixr2est-7.1.0/nlmixr2est/inst/include/nlmixr2estLikContribPtr.h |only nlmixr2est-7.1.0/nlmixr2est/inst/include/nlmixr2estNlmPtr.h |only nlmixr2est-7.1.0/nlmixr2est/inst/reprex_fbio_eta_parallel.R | 17 nlmixr2est-7.1.0/nlmixr2est/inst/tools/genQrpemBaseline.R |only nlmixr2est-7.1.0/nlmixr2est/inst/tools/workaround.R | 47 nlmixr2est-7.1.0/nlmixr2est/man/bobyqaControl.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/dot-augPredIpredModel.Rd | 3 nlmixr2est-7.1.0/nlmixr2est/man/dot-deparseFinal.Rd | 2 nlmixr2est-7.1.0/nlmixr2est/man/dot-nlmixr2estFoceiPtrs.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/dot-nlmixr2estLikContribPtrs.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/dot-nlmixr2estNlmPtrs.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/dot-sensEtaOrTheta.Rd | 23 nlmixr2est-7.1.0/nlmixr2est/man/emviControl.Rd | 17 nlmixr2est-7.1.0/nlmixr2est/man/foceiControl.Rd | 431 nlmixr2est-7.1.0/nlmixr2est/man/foceiLikIterPrintStart.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/foceiLikLoad.Rd | 56 nlmixr2est-7.1.0/nlmixr2est/man/foceiLikRun.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/getBaseSimModelFit.Rd | 6 nlmixr2est-7.1.0/nlmixr2est/man/getValidNlmixrControl.Rd | 31 nlmixr2est-7.1.0/nlmixr2est/man/impCovControl.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/impmapControl.Rd | 240 nlmixr2est-7.1.0/nlmixr2est/man/lbfgsb3cControl.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/n1qn1Control.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/newuoaControl.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/nlmControl.Rd | 44 nlmixr2est-7.1.0/nlmixr2est/man/nlmObjectiveSetup.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/nlmUnscalePar.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/nlminbControl.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/nlmixr2Est.Rd | 64 nlmixr2est-7.1.0/nlmixr2est/man/nlmixr2GradFun.Rd | 2 nlmixr2est-7.1.0/nlmixr2est/man/nlmixr2NlmeControl.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/nlsControl.Rd | 71 nlmixr2est-7.1.0/nlmixr2est/man/nmGetDistributionSaemLines.Rd | 6 nlmixr2est-7.1.0/nlmixr2est/man/nmObjGetControl.Rd | 5 nlmixr2est-7.1.0/nlmixr2est/man/nmObjHandleControlObject.Rd | 5 nlmixr2est-7.1.0/nlmixr2est/man/optimControl.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/postFinalObjectHooks.Rd | 2 nlmixr2est-7.1.0/nlmixr2est/man/preFinalParTableHooks.Rd | 2 nlmixr2est-7.1.0/nlmixr2est/man/preProcessHooks.Rd | 2 nlmixr2est-7.1.0/nlmixr2est/man/predict.nlmixr2FitCore.Rd | 48 nlmixr2est-7.1.0/nlmixr2est/man/registerEstInterceptor.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/rsControl.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/saControl.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/saemControl.Rd | 151 nlmixr2est-7.1.0/nlmixr2est/man/setCov-set.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/setCov.Rd | 100 nlmixr2est-7.1.0/nlmixr2est/man/setCovAllMethods.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/setCovOptions.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/setCovValue.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/setOfv.Rd | 3 nlmixr2est-7.1.0/nlmixr2est/man/tableControl.Rd | 3 nlmixr2est-7.1.0/nlmixr2est/man/trustControl.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/uobyqaControl.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/vaeControl.Rd | 117 nlmixr2est-7.1.0/nlmixr2est/man/vaeCovariates.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/src/Makevars.in | 31 nlmixr2est-7.1.0/nlmixr2est/src/RcppExports.cpp | 353 nlmixr2est-7.1.0/nlmixr2est/src/censEst.h | 130 nlmixr2est-7.1.0/nlmixr2est/src/foceiGrad.cpp | 545 nlmixr2est-7.1.0/nlmixr2est/src/foceiGrad.h | 53 nlmixr2est-7.1.0/nlmixr2est/src/imp.cpp | 1039 nlmixr2est-7.1.0/nlmixr2est/src/imp.h | 53 nlmixr2est-7.1.0/nlmixr2est/src/impQrng.h |only nlmixr2est-7.1.0/nlmixr2est/src/init.c | 90 nlmixr2est-7.1.0/nlmixr2est/src/inner.cpp |11271 ++++++++-- nlmixr2est-7.1.0/nlmixr2est/src/inner.h | 5 nlmixr2est-7.1.0/nlmixr2est/src/likContribUtil.h |only nlmixr2est-7.1.0/nlmixr2est/src/logSumExp.h |only nlmixr2est-7.1.0/nlmixr2est/src/nearPD.cpp | 12 nlmixr2est-7.1.0/nlmixr2est/src/nlm.cpp | 460 nlmixr2est-7.1.0/nlmixr2est/src/nmParallel.h |only nlmixr2est-7.1.0/nlmixr2est/src/nmParallelCore.h |only nlmixr2est-7.1.0/nlmixr2est/src/nmSeqSeed.h |only nlmixr2est-7.1.0/nlmixr2est/src/np.h | 15 nlmixr2est-7.1.0/nlmixr2est/src/npag.cpp | 84 nlmixr2est-7.1.0/nlmixr2est/src/npb.cpp | 79 nlmixr2est-7.1.0/nlmixr2est/src/npde.cpp | 30 nlmixr2est-7.1.0/nlmixr2est/src/odeSwap.cpp | 486 nlmixr2est-7.1.0/nlmixr2est/src/odeSwap.h | 61 nlmixr2est-7.1.0/nlmixr2est/src/rxomp.h | 3 nlmixr2est-7.1.0/nlmixr2est/src/saem.cpp | 2043 + nlmixr2est-7.1.0/nlmixr2est/src/scale.h | 26 nlmixr2est-7.1.0/nlmixr2est/src/slice.cpp | 9 nlmixr2est-7.1.0/nlmixr2est/src/truncNorm.h |only nlmixr2est-7.1.0/nlmixr2est/src/trustHessianUpdate.h |only nlmixr2est-7.1.0/nlmixr2est/src/uninformativeEtas.cpp | 17 nlmixr2est-7.1.0/nlmixr2est/src/vaeEncoder.cpp | 14 nlmixr2est-7.1.0/nlmixr2est/tests/testthat.R | 197 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/baselines/gradref-foce-newton-stall.rds |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/baselines/gradref-ll-multiple-endpoint.rds |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/baselines/gradref-lnorm-domain-clamp-867.rds |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/baselines/qrpem-baseline-ref.rds |binary nlmixr2est-7.1.0/nlmixr2est/tests/testthat/helper-gradref.R | 14 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/helper-lincmt-carry-ll.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/helper-lincmt-carry.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/helper-quiet.R | 35 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/helper-vae-resid.R | 25 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/helper-wang2007.R | 240 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/helper-zzz-fits.R | 74 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-00-reload-ll.R | 10 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-addCwres.R | 100 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-agq-cov.R | 59 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-agq-fast-grad.R | 145 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-ar-est.R | 37 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-augpred.R | 107 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-bad-print.R | 10 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-benchmarking.R | 27 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-bounded-transform.R | 72 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-broom.R | 348 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cens-dist-warn.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cloneEnv-cycle.R | 8 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-control-infer.R | 4 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-control.R | 65 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cor-no-cov-1038.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-analytic-defaults.R | 13 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-analytic.R | 1423 - nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-condition.R | 11 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-decouple-saimp.R | 38 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-decouple.R | 18 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-fdfull-install.R | 77 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-focei.R | 76 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-mu.R | 9 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-robust.R | 14 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-scope-swap.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-setcov-generic.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cwres.R | 35 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-data-assert.R | 38 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-dde-focei.R | 29 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-est-type-list.R | 1 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-etaMat.R | 38 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-fitSim.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-fix-cov.R | 41 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-fix-eta.R | 12 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