Title: Visualization of Regression Models
Description: Provides a convenient interface for constructing plots to
visualize the fit of regression models arising from a wide variety
of models in R ('lm', 'glm', 'coxph', 'rlm', 'gam', 'locfit', 'lmer',
'randomForest', etc.)
Author: Patrick Breheny [aut, cre] ,
Woodrow Burchett [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between visreg versions 2.8.1 dated 2026-07-08 and 3.0.0 dated 2026-07-28
visreg-2.8.1/visreg/R/Response.R |only visreg-2.8.1/visreg/R/Terms.R |only visreg-2.8.1/visreg/R/abbrNum.R |only visreg-2.8.1/visreg/R/collapseVisregList.R |only visreg-2.8.1/visreg/R/factorAxis.R |only visreg-2.8.1/visreg/R/factorPlot.R |only visreg-2.8.1/visreg/R/fillFrame.R |only visreg-2.8.1/visreg/R/getXY.R |only visreg-2.8.1/visreg/R/ggContPlot.R |only visreg-2.8.1/visreg/R/ggFactorPlot.R |only visreg-2.8.1/visreg/R/makeYName.R |only visreg-2.8.1/visreg/R/parseFormula.R |only visreg-2.8.1/visreg/R/plotVisreg2d.R |only visreg-2.8.1/visreg/R/plotVisregList.R |only visreg-2.8.1/visreg/R/printCond.R |only visreg-2.8.1/visreg/R/se.mlm.R |only visreg-2.8.1/visreg/R/setupCond.R |only visreg-2.8.1/visreg/R/setupD.R |only visreg-2.8.1/visreg/R/setupF.R |only visreg-2.8.1/visreg/R/setupV.R |only visreg-2.8.1/visreg/R/setupV2.R |only visreg-2.8.1/visreg/R/setupX.R |only visreg-2.8.1/visreg/R/subsetV.R |only visreg-2.8.1/visreg/R/toplegend.R |only visreg-2.8.1/visreg/R/visregFactorPanel.R |only visreg-2.8.1/visreg/R/visregLatticePlot.R |only visreg-2.8.1/visreg/R/visregList.R |only visreg-2.8.1/visreg/R/visregOverlayPlot.R |only visreg-2.8.1/visreg/R/visregPanel.R |only visreg-2.8.1/visreg/R/visregPlot.R |only visreg-2.8.1/visreg/R/visregPred.R |only visreg-2.8.1/visreg/R/visregResid.R |only visreg-2.8.1/visreg/inst/doc/visreg.rmd |only visreg-2.8.1/visreg/inst/tinytest/_enhances_glmmTMB.R |only visreg-2.8.1/visreg/inst/tinytest/_lme4predict.R |only visreg-2.8.1/visreg/inst/tinytest/_xtrans.r |only visreg-2.8.1/visreg/inst/tinytest/ggplot.R |only visreg-2.8.1/visreg/inst/tinytest/visregList.R |only visreg-2.8.1/visreg/man/visregList.Rd |only visreg-2.8.1/visreg/vignettes/visreg.rmd |only visreg-3.0.0/visreg/DESCRIPTION | 15 visreg-3.0.0/visreg/MD5 | 172 +++--- visreg-3.0.0/visreg/NAMESPACE | 9 visreg-3.0.0/visreg/NEWS.md | 91 ++- visreg-3.0.0/visreg/R/abbr_num.R |only visreg-3.0.0/visreg/R/build_visreg.R |only visreg-3.0.0/visreg/R/build_visreg2d.R |only visreg-3.0.0/visreg/R/collapse.R |only visreg-3.0.0/visreg/R/collapse_visreg_list.R |only visreg-3.0.0/visreg/R/compute_response.R |only visreg-3.0.0/visreg/R/compute_terms.R |only visreg-3.0.0/visreg/R/factor_axis_2d.R |only visreg-3.0.0/visreg/R/fill_frame.R |only visreg-3.0.0/visreg/R/finalize_visreg.R |only visreg-3.0.0/visreg/R/get_xy.R |only visreg-3.0.0/visreg/R/gg_cont_plot.R |only visreg-3.0.0/visreg/R/gg_factor_plot.R |only visreg-3.0.0/visreg/R/interacting_vars.R |only visreg-3.0.0/visreg/R/locate_source_data.R |only visreg-3.0.0/visreg/R/make_y_name.R |only visreg-3.0.0/visreg/R/parse_formula.R |only visreg-3.0.0/visreg/R/persp-visreg2d.R |only visreg-3.0.0/visreg/R/persp3d-visreg2d.R |only visreg-3.0.0/visreg/R/plot-visreg.R | 253 +++------ visreg-3.0.0/visreg/R/plot-visreg2d.R |only visreg-3.0.0/visreg/R/plot-visreg_list.R |only visreg-3.0.0/visreg/R/prep_2d_axes.R |only visreg-3.0.0/visreg/R/print_cond.R |only visreg-3.0.0/visreg/R/refit_if_needed.R |only visreg-3.0.0/visreg/R/resolve_trans.R |only visreg-3.0.0/visreg/R/se_mlm.R |only visreg-3.0.0/visreg/R/setup_cond.R |only visreg-3.0.0/visreg/R/setup_contrast_data.R |only visreg-3.0.0/visreg/R/setup_data.R |only visreg-3.0.0/visreg/R/setup_frame.R |only visreg-3.0.0/visreg/R/subset.R | 16 visreg-3.0.0/visreg/R/subset_xy.R |only visreg-3.0.0/visreg/R/visreg-package.R | 6 visreg-3.0.0/visreg/R/visreg.R | 292 ++++------ visreg-3.0.0/visreg/R/visreg2d.R | 151 ++--- visreg-3.0.0/visreg/R/visreg_coef.R | 4 visreg-3.0.0/visreg/R/visreg_list.R |only visreg-3.0.0/visreg/R/visreg_pred.R |only visreg-3.0.0/visreg/R/visreg_resid.R |only visreg-3.0.0/visreg/R/zzz.R |only visreg-3.0.0/visreg/README.md | 20 visreg-3.0.0/visreg/build/vignette.rds |binary visreg-3.0.0/visreg/inst/doc/visreg.R | 36 - visreg-3.0.0/visreg/inst/doc/visreg.html | 382 +++++++------- visreg-3.0.0/visreg/inst/doc/visreg.qmd |only visreg-3.0.0/visreg/inst/tinytest/_enhances-glmmTMB.R |only visreg-3.0.0/visreg/inst/tinytest/enhances-MASS.R | 30 - visreg-3.0.0/visreg/inst/tinytest/enhances-betareg.R | 12 visreg-3.0.0/visreg/inst/tinytest/enhances-gamlss.R | 14 visreg-3.0.0/visreg/inst/tinytest/enhances-gamm4.R | 16 visreg-3.0.0/visreg/inst/tinytest/enhances-gbm.R | 43 - visreg-3.0.0/visreg/inst/tinytest/enhances-lme4.R | 45 - visreg-3.0.0/visreg/inst/tinytest/enhances-loess.R | 8 visreg-3.0.0/visreg/inst/tinytest/enhances-nlme.R | 32 - visreg-3.0.0/visreg/inst/tinytest/enhances-nnet.R | 22 visreg-3.0.0/visreg/inst/tinytest/enhances-quantreg.R | 36 - visreg-3.0.0/visreg/inst/tinytest/enhances-randomForest.R | 12 visreg-3.0.0/visreg/inst/tinytest/enhances-rms.R |only visreg-3.0.0/visreg/inst/tinytest/enhances-svm.R | 22 visreg-3.0.0/visreg/inst/tinytest/errors.R |only visreg-3.0.0/visreg/inst/tinytest/missing-data.R | 97 +-- visreg-3.0.0/visreg/inst/tinytest/subset.R | 10 visreg-3.0.0/visreg/inst/tinytest/top.R | 45 - visreg-3.0.0/visreg/inst/tinytest/unusual-formulas.R | 61 +- visreg-3.0.0/visreg/inst/tinytest/visreg-contrast.R | 51 + visreg-3.0.0/visreg/inst/tinytest/visreg-coxph.R | 37 - visreg-3.0.0/visreg/inst/tinytest/visreg-glm.R | 59 +- visreg-3.0.0/visreg/inst/tinytest/visreg-interactions.R | 156 ++++- visreg-3.0.0/visreg/inst/tinytest/visreg-lm.R | 159 ++--- visreg-3.0.0/visreg/inst/tinytest/visreg-mlm.R | 67 +- visreg-3.0.0/visreg/inst/tinytest/visreg2d-glm.R | 23 visreg-3.0.0/visreg/inst/tinytest/visreg2d-lm.R | 92 +-- visreg-3.0.0/visreg/inst/tinytest/visreg_list.R |only visreg-3.0.0/visreg/inst/tinytest/weight-char.r | 14 visreg-3.0.0/visreg/man/collapse.Rd |only visreg-3.0.0/visreg/man/persp.visreg2d.Rd |only visreg-3.0.0/visreg/man/plot.visreg.Rd | 164 ++---- visreg-3.0.0/visreg/man/plot.visreg2d.Rd | 95 +-- visreg-3.0.0/visreg/man/subset.visreg.Rd | 16 visreg-3.0.0/visreg/man/visreg-package.Rd | 4 visreg-3.0.0/visreg/man/visreg.Rd | 253 ++++----- visreg-3.0.0/visreg/man/visreg2d.Rd | 123 ++-- visreg-3.0.0/visreg/man/visreg_list.Rd |only visreg-3.0.0/visreg/vignettes/visreg.qmd |only 129 files changed, 1735 insertions(+), 1530 deletions(-)
Title: Revert Spreadsheet Date Auto-Conversion to the Numbers Typed
Description: Spreadsheets silently turn entries such as '30.3' into dates, so
the imported data carry date serials instead of the numbers that were
typed. Reading the workbook directly recovers those numbers without
guesswork: an 'xlsx' file states its own date system, and records which
cells are formatted as dates and in which field order, so the values to
repair are identified from the file rather than inferred from their
magnitude. Functions are also provided for data already imported, where
that evidence is no longer available, using conservative and configurable
detection.
Author: Hercules R. Freitas [aut, cre, cph]
Maintainer: Hercules R. Freitas <hercules.freitas@uerj.br>
Diff between unexcel versions 0.1.0 dated 2025-10-08 and 0.2.0 dated 2026-07-28
unexcel-0.1.0/unexcel/README |only unexcel-0.1.0/unexcel/inst/doc/unexcel.R |only unexcel-0.1.0/unexcel/inst/doc/unexcel.Rmd |only unexcel-0.1.0/unexcel/inst/doc/unexcel.html |only unexcel-0.1.0/unexcel/vignettes/unexcel.Rmd |only unexcel-0.2.0/unexcel/DESCRIPTION | 48 +- unexcel-0.2.0/unexcel/MD5 | 46 +- unexcel-0.2.0/unexcel/NAMESPACE | 11 unexcel-0.2.0/unexcel/NEWS.md |only unexcel-0.2.0/unexcel/R/restore.R | 299 +++++++++++------ unexcel-0.2.0/unexcel/R/serial.R |only unexcel-0.2.0/unexcel/R/unexcel-package.R |only unexcel-0.2.0/unexcel/R/xlsx-api.R |only unexcel-0.2.0/unexcel/R/xlsx-parse.R |only unexcel-0.2.0/unexcel/README.md |only unexcel-0.2.0/unexcel/build/vignette.rds |binary unexcel-0.2.0/unexcel/inst/doc/excel-date-systems.R |only unexcel-0.2.0/unexcel/inst/doc/excel-date-systems.Rmd |only unexcel-0.2.0/unexcel/inst/doc/excel-date-systems.html |only unexcel-0.2.0/unexcel/inst/doc/getting-started.R |only unexcel-0.2.0/unexcel/inst/doc/getting-started.Rmd |only unexcel-0.2.0/unexcel/inst/doc/getting-started.html |only unexcel-0.2.0/unexcel/inst/extdata |only unexcel-0.2.0/unexcel/man/excel_date_cells.Rd |only unexcel-0.2.0/unexcel/man/excel_date_columns.Rd |only unexcel-0.2.0/unexcel/man/excel_date_system.Rd |only unexcel-0.2.0/unexcel/man/excel_origin.Rd |only unexcel-0.2.0/unexcel/man/excel_sheets.Rd |only unexcel-0.2.0/unexcel/man/figures |only unexcel-0.2.0/unexcel/man/fix_serial_columns.Rd | 63 ++- unexcel-0.2.0/unexcel/man/restore_day_month.Rd | 81 +++- unexcel-0.2.0/unexcel/man/serial_to_day_month.Rd |only unexcel-0.2.0/unexcel/man/unexcel-package.Rd |only unexcel-0.2.0/unexcel/man/unexcel_xlsx.Rd |only unexcel-0.2.0/unexcel/tests |only unexcel-0.2.0/unexcel/vignettes/excel-date-systems.Rmd |only unexcel-0.2.0/unexcel/vignettes/getting-started.Rmd |only 37 files changed, 378 insertions(+), 170 deletions(-)
Title: Detect and Remove Chimeras from Amplicon Sequence Analysis Data
Description: Detect and remove chimeras from your amplicon sequence analysis
using reference-based or de novo approaches. The 'rchime' package
implements the 'VSEARCH' algorithms described in Rognes et al. (2016)
<doi:10.7717/peerj.2584>. 'VSEARCH' builds on the work of Edgar,R.C. et al.
(2011) <doi:10.1093/bioinformatics/btr381>.
Author: Sarah Westcott [aut] ,
Pat Schloss [cph, cre] ,
Torbjorn Rognes [cph],
Frederic Mahe [cph],
Tomas Flouri [cph],
Christopher Quince [cph],
Ben Nichols [cph]
Maintainer: Pat Schloss <pschloss@umich.edu>
Diff between rchime versions 0.1.0 dated 2026-07-23 and 0.1.1 dated 2026-07-28
rchime-0.1.0/rchime/man/rchime.data.frame.Rd |only rchime-0.1.0/rchime/man/rchime.strollur.Rd |only rchime-0.1.1/rchime/DESCRIPTION | 6 rchime-0.1.1/rchime/MD5 | 44 rchime-0.1.1/rchime/NEWS.md | 6 rchime-0.1.1/rchime/R/rchime.R | 550 +++--------- rchime-0.1.1/rchime/README.md | 35 rchime-0.1.1/rchime/inst/CITATION | 4 rchime-0.1.1/rchime/inst/doc/chimera_report.R | 13 rchime-0.1.1/rchime/inst/doc/chimera_report.Rmd | 13 rchime-0.1.1/rchime/inst/doc/chimera_report.html | 146 +-- rchime-0.1.1/rchime/inst/doc/denovo_based_detection.R | 42 rchime-0.1.1/rchime/inst/doc/denovo_based_detection.Rmd | 65 - rchime-0.1.1/rchime/inst/doc/denovo_based_detection.html | 203 +--- rchime-0.1.1/rchime/inst/doc/reference_based_detection.R | 13 rchime-0.1.1/rchime/inst/doc/reference_based_detection.Rmd | 25 rchime-0.1.1/rchime/inst/doc/reference_based_detection.html | 145 +-- rchime-0.1.1/rchime/man/rchime.Rd | 60 + rchime-0.1.1/rchime/src/cpu.cc | 153 +-- rchime-0.1.1/rchime/tests/testthat/test-rchime_dataframe.R | 239 ++--- rchime-0.1.1/rchime/tests/testthat/test-rchime_strollur.R | 298 +++--- rchime-0.1.1/rchime/vignettes/chimera_report.Rmd | 13 rchime-0.1.1/rchime/vignettes/denovo_based_detection.Rmd | 65 - rchime-0.1.1/rchime/vignettes/reference_based_detection.Rmd | 25 24 files changed, 845 insertions(+), 1318 deletions(-)
Title: Penalized Estimation for Latent Variable Models with 'lavaan'
Description: Extends the popular 'lavaan' package by adding penalized
estimation capabilities. It supports penalty on individual parameters
as well as the difference between parameters.
Author: Hok Chio Lai [aut, cre]
Maintainer: Hok Chio (Mark) Lai <marklhc@gmail.com>
Diff between plavaan versions 0.0.1 dated 2025-12-30 and 0.0.2 dated 2026-07-28
DESCRIPTION | 10 MD5 | 53 +- NAMESPACE | 4 NEWS.md | 9 R/alf.R | 10 R/multistart.R |only R/penalized.R | 263 ++++++++---- README.md | 4 build/vignette.rds |binary inst/doc/approximate-invariance.Rmd | 3 inst/doc/approximate-invariance.html | 61 +- inst/doc/negative-loading.R |only inst/doc/negative-loading.Rmd |only inst/doc/negative-loading.html |only inst/doc/penalized-cat.R | 2 inst/doc/penalized-cat.Rmd | 4 inst/doc/penalized-cat.html | 732 ++++++++++++++++++----------------- inst/doc/penalized-fa.html | 281 ++++++------- inst/doc/penalized-multistart.R |only inst/doc/penalized-multistart.Rmd |only inst/doc/penalized-multistart.html |only inst/doc/standard-errors.R | 36 - inst/doc/standard-errors.Rmd | 37 - inst/doc/standard-errors.html | 108 ++--- man/penalized_est.Rd | 12 man/penalized_est_multistart.Rd |only tests/testthat/test-alf.R | 1 tests/testthat/test-multistart.R |only vignettes/approximate-invariance.Rmd | 3 vignettes/negative-loading.Rmd |only vignettes/penalized-cat.Rmd | 4 vignettes/penalized-multistart.Rmd |only vignettes/standard-errors.Rmd | 37 - 33 files changed, 871 insertions(+), 803 deletions(-)
Title: Univariate and Bivariate Latent Change Score Modelling
Description: Helper functions to implement univariate and bivariate latent change score models in R using the 'lavaan' package.
For details about Latent Change Score Modeling (LCSM) see McArdle (2009) <doi:10.1146/annurev.psych.60.110707.163612> and Grimm, An, McArdle, Zonderman and Resnick (2012) <doi:10.1080/10705511.2012.659627>.
The package automatically generates 'lavaan' syntax for different model specifications and varying timepoints.
The 'lavaan' syntax generated by this package can be returned and further specifications can be added manually.
Longitudinal plots as well as simplified path diagrams can be created to visualise data and model specifications.
Estimated model parameters and fit statistics can be extracted as data frames.
Data for different univariate and bivariate LCSM can be simulated by specifying estimates for model parameters to explore their effects.
This package combines the strengths of other R packages like 'lavaan', 'broom', and 'semPlot' by generating 'lava [...truncated...]
Author: Milan Wiedemann [aut, cre] ,
Graham M Thew [ctb] ,
Urska Kosir [ctb] ,
Anke Ehlers [ths] ,
Mental Health Research UK [fnd]
Maintainer: Milan Wiedemann <milan.wiedemann@gmail.com>
Diff between lcsm versions 0.3.2 dated 2023-02-25 and 0.3.3 dated 2026-07-28
DESCRIPTION | 21 +-- MD5 | 60 +++++----- NEWS.md | 4 R/data.R | 92 +++++++--------- R/fit_lcsm.R | 61 ++++------ R/sim_lcsm_data.R | 176 +++++++++++++++++++++---------- R/specify_lcsm_lavaan_syntax.R | 52 ++++----- README.md | 95 +++++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/lcsm-parameters.R | 2 inst/doc/lcsm-parameters.html | 3 inst/doc/v0-longitudinal-plots.R | 10 - inst/doc/v0-longitudinal-plots.html | 31 +++-- inst/doc/v1-lavaan-syntax.R | 2 inst/doc/v1-lavaan-syntax.html | 1 inst/doc/v2-path-diagrams.R | 6 - inst/doc/v2-path-diagrams.html | 9 - inst/doc/v3-extract-tutorial.R | 2 inst/doc/v3-extract-tutorial.html | 33 +---- inst/doc/v4-simulate-data.R | 6 - inst/doc/v4-simulate-data.html | 23 ++-- man/data_bi_lcsm.Rd | 42 +++---- man/data_uni_lcsm.Rd | 22 +-- man/figures/README-unnamed-chunk-3-1.png |binary man/fit_bi_lcsm.Rd | 38 +++--- man/fit_uni_lcsm.Rd | 15 +- man/lcsm_data.Rd | 22 +-- man/sim_bi_lcsm.Rd | 2 man/specify_bi_lcsm.Rd | 46 ++++---- tests/testthat/test-sim-data.R | 4 31 files changed, 471 insertions(+), 409 deletions(-)
Title: Download Data from the World Inequality Database
Description: Download data from the online World Inequality Database directly
into R. Data are retrieved from WID.world's online data service. The World
Inequality Database is an extensive source on the historical evolution of
the distribution of income and wealth both within and between countries. It
relies on the combined effort of an international network of over a hundred
researchers covering more than seventy countries from all continents.
Author: Thomas Blanchet [aut],
Ignacio Flores [cre]
Maintainer: Ignacio Flores <stats@wid.world>
Diff between wid versions 0.0.2 dated 2026-07-08 and 0.0.3 dated 2026-07-28
DESCRIPTION | 13 - MD5 | 19 + NEWS.md |only R/check-args.R | 90 ++++----- R/download-wid.R | 87 +++++--- R/get-requests.R | 10 - README.md | 4 man/download_wid.Rd | 32 +-- tests/testthat/test_download.R | 29 +- tests/testthat/test_download_contract.R | 310 ++++++++++++++++++++++++-------- tests/testthat/test_get_requests.R | 4 11 files changed, 399 insertions(+), 199 deletions(-)
Title: Stabilize Function Arguments
Description: A set of consistent, opinionated functions to quickly check
function arguments, coerce them to the desired configuration, or
deliver informative error messages when that is not possible.
Author: Jon Harmon [aut, cre, cph]
Maintainer: Jon Harmon <jonthegeek@gmail.com>
Diff between stbl versions 0.3.0 dated 2026-04-04 and 0.4.0 dated 2026-07-28
stbl-0.3.0/stbl/man/dot-are_not_dbl_ish_chr.Rd |only stbl-0.3.0/stbl/man/dot-are_not_int_ish_chr.Rd |only stbl-0.3.0/stbl/man/dot-to_cls_from_list.Rd |only stbl-0.4.0/stbl/DESCRIPTION | 14 stbl-0.4.0/stbl/MD5 | 368 +++++--- stbl-0.4.0/stbl/NAMESPACE | 49 - stbl-0.4.0/stbl/NEWS.md | 130 +- stbl-0.4.0/stbl/R/aaa-conditions.R | 403 +++++---- stbl-0.4.0/stbl/R/aaa-shared_params.R | 8 stbl-0.4.0/stbl/R/are_dbl_ish.R | 19 stbl-0.4.0/stbl/R/are_fct_ish.R | 15 stbl-0.4.0/stbl/R/are_fn_ish.R |only stbl-0.4.0/stbl/R/are_int_ish.R | 26 stbl-0.4.0/stbl/R/are_lgl_ish.R | 5 stbl-0.4.0/stbl/R/c_api.R |only stbl-0.4.0/stbl/R/check.R | 33 stbl-0.4.0/stbl/R/cls_unexported.R | 37 stbl-0.4.0/stbl/R/pkg_abort.R | 164 ++- stbl-0.4.0/stbl/R/pkg_inform.R |only stbl-0.4.0/stbl/R/pkg_warn.R |only stbl-0.4.0/stbl/R/specify_cls.R | 31 stbl-0.4.0/stbl/R/stabilize_chr.R | 35 stbl-0.4.0/stbl/R/stabilize_dbl.R | 9 stbl-0.4.0/stbl/R/stabilize_df.R | 6 stbl-0.4.0/stbl/R/stabilize_lst.R | 8 stbl-0.4.0/stbl/R/stbl-package.R | 2 stbl-0.4.0/stbl/R/to.R |only stbl-0.4.0/stbl/R/to_chr.R | 164 +++ stbl-0.4.0/stbl/R/to_dbl.R | 67 - stbl-0.4.0/stbl/R/to_df.R | 14 stbl-0.4.0/stbl/R/to_fct.R | 57 - stbl-0.4.0/stbl/R/to_fn.R |only stbl-0.4.0/stbl/R/to_int.R | 129 ++ stbl-0.4.0/stbl/R/to_lgl.R | 49 - stbl-0.4.0/stbl/R/to_lst.R | 15 stbl-0.4.0/stbl/R/to_null.R | 3 stbl-0.4.0/stbl/R/utils-conditions.R |only stbl-0.4.0/stbl/R/utils.R | 17 stbl-0.4.0/stbl/README.md | 2 stbl-0.4.0/stbl/build/vignette.rds |binary stbl-0.4.0/stbl/inst/include |only stbl-0.4.0/stbl/man/are_chr_ish.Rd | 18 stbl-0.4.0/stbl/man/are_dbl_ish.Rd | 18 stbl-0.4.0/stbl/man/are_fct_ish.Rd | 30 stbl-0.4.0/stbl/man/are_fn_ish.Rd |only stbl-0.4.0/stbl/man/are_int_ish.Rd | 18 stbl-0.4.0/stbl/man/are_lgl_ish.Rd | 18 stbl-0.4.0/stbl/man/c_x_to_y.Rd |only stbl-0.4.0/stbl/man/dot-are_not_fct_ish_chr.Rd | 44 stbl-0.4.0/stbl/man/dot-call_specified_fn.Rd | 5 stbl-0.4.0/stbl/man/dot-capture_first_pkg_condition.Rd |only stbl-0.4.0/stbl/man/dot-check_all_named.Rd | 2 stbl-0.4.0/stbl/man/dot-check_cast_failures.Rd | 3 stbl-0.4.0/stbl/man/dot-check_chr_to_int_failures.Rd | 7 stbl-0.4.0/stbl/man/dot-check_cpx_to_int_failures.Rd |only stbl-0.4.0/stbl/man/dot-check_dbl_to_int_failures.Rd |only stbl-0.4.0/stbl/man/dot-check_function_allowed.Rd | 2 stbl-0.4.0/stbl/man/dot-check_is_not_primitive.Rd | 2 stbl-0.4.0/stbl/man/dot-check_lst_failures.Rd |only stbl-0.4.0/stbl/man/dot-check_na.Rd | 5 stbl-0.4.0/stbl/man/dot-check_not_jagged.Rd | 6 stbl-0.4.0/stbl/man/dot-check_scalar.Rd | 5 stbl-0.4.0/stbl/man/dot-check_size.Rd | 5 stbl-0.4.0/stbl/man/dot-check_x_no_more_than_y.Rd | 2 stbl-0.4.0/stbl/man/dot-chr_from_fn_sym.Rd |only stbl-0.4.0/stbl/man/dot-chr_from_op_call.Rd |only stbl-0.4.0/stbl/man/dot-cli_escape.Rd | 38 stbl-0.4.0/stbl/man/dot-cli_mark.Rd | 40 stbl-0.4.0/stbl/man/dot-coerce_fct_levels.Rd | 2 stbl-0.4.0/stbl/man/dot-coerce_fct_levels_impl.Rd | 3 stbl-0.4.0/stbl/man/dot-coerce_fct_to_na.Rd | 46 - stbl-0.4.0/stbl/man/dot-collapse_dash.Rd | 36 stbl-0.4.0/stbl/man/dot-compile_dash.Rd | 36 stbl-0.4.0/stbl/man/dot-compile_pkg_condition_classes.Rd | 44 stbl-0.4.0/stbl/man/dot-compile_pkg_error_classes.Rd | 44 stbl-0.4.0/stbl/man/dot-compile_pkg_message_classes.Rd |only stbl-0.4.0/stbl/man/dot-compile_pkg_warning_classes.Rd |only stbl-0.4.0/stbl/man/dot-construct_specification_fn.Rd | 78 - stbl-0.4.0/stbl/man/dot-construct_stabilizer_symbol.Rd | 44 stbl-0.4.0/stbl/man/dot-describe_failure_chr.Rd | 48 - stbl-0.4.0/stbl/man/dot-elements_are_cls_ish.Rd | 30 stbl-0.4.0/stbl/man/dot-expect_pkg_condition_snapshot.Rd |only stbl-0.4.0/stbl/man/dot-fast_false.Rd | 37 stbl-0.4.0/stbl/man/dot-find_failures.Rd | 48 - stbl-0.4.0/stbl/man/dot-glue2.Rd | 47 - stbl-0.4.0/stbl/man/dot-has_regex_pattern.Rd | 59 - stbl-0.4.0/stbl/man/dot-is_allowed_null.Rd | 48 - stbl-0.4.0/stbl/man/dot-is_covr_count_call.Rd |only stbl-0.4.0/stbl/man/dot-maybe_check_dupes.Rd | 38 stbl-0.4.0/stbl/man/dot-maybe_qualify_fn_name.Rd |only stbl-0.4.0/stbl/man/dot-same_fn.Rd |only stbl-0.4.0/stbl/man/dot-shared-params-check.Rd | 24 stbl-0.4.0/stbl/man/dot-shared-params.Rd | 3 stbl-0.4.0/stbl/man/dot-shared-return-conditions.Rd |only stbl-0.4.0/stbl/man/dot-stabilize_cls.Rd | 3 stbl-0.4.0/stbl/man/dot-stabilize_cls_scalar.Rd | 3 stbl-0.4.0/stbl/man/dot-stbl_abort.Rd | 79 - stbl-0.4.0/stbl/man/dot-stbl_inform.Rd |only stbl-0.4.0/stbl/man/dot-stbl_warn.Rd |only stbl-0.4.0/stbl/man/dot-stop_bad_levels.Rd | 6 stbl-0.4.0/stbl/man/dot-stop_cant_coerce.Rd | 3 stbl-0.4.0/stbl/man/dot-stop_function.Rd | 3 stbl-0.4.0/stbl/man/dot-stop_if_anon_fn.Rd |only stbl-0.4.0/stbl/man/dot-stop_incompatible.Rd | 3 stbl-0.4.0/stbl/man/dot-stop_must.Rd | 3 stbl-0.4.0/stbl/man/dot-stop_null.Rd | 3 stbl-0.4.0/stbl/man/dot-strip_covr_from_expr.Rd |only stbl-0.4.0/stbl/man/dot-to_chr_impl.Rd |only stbl-0.4.0/stbl/man/dot-to_cls_from_fct.Rd | 3 stbl-0.4.0/stbl/man/dot-to_cls_scalar.Rd | 3 stbl-0.4.0/stbl/man/dot-to_df_vector.Rd | 4 stbl-0.4.0/stbl/man/dot-to_null.Rd | 3 stbl-0.4.0/stbl/man/dot-to_num_from_complex.Rd | 3 stbl-0.4.0/stbl/man/dot-validate_named_elements.Rd | 3 stbl-0.4.0/stbl/man/expect_pkg_error_snapshot.Rd | 7 stbl-0.4.0/stbl/man/expect_pkg_message_classes.Rd |only stbl-0.4.0/stbl/man/expect_pkg_message_snapshot.Rd |only stbl-0.4.0/stbl/man/expect_pkg_warning_classes.Rd |only stbl-0.4.0/stbl/man/expect_pkg_warning_snapshot.Rd |only stbl-0.4.0/stbl/man/figures |only stbl-0.4.0/stbl/man/grapes-and-and-grapes.Rd | 46 - stbl-0.4.0/stbl/man/object_type.Rd | 48 - stbl-0.4.0/stbl/man/pkg_abort.Rd | 118 +- stbl-0.4.0/stbl/man/pkg_inform.Rd |only stbl-0.4.0/stbl/man/pkg_warn.Rd |only stbl-0.4.0/stbl/man/reexports.Rd | 34 stbl-0.4.0/stbl/man/specify_chr.Rd | 21 stbl-0.4.0/stbl/man/specify_dbl.Rd | 21 stbl-0.4.0/stbl/man/specify_df.Rd | 21 stbl-0.4.0/stbl/man/specify_fct.Rd | 21 stbl-0.4.0/stbl/man/specify_int.Rd | 21 stbl-0.4.0/stbl/man/specify_lgl.Rd | 21 stbl-0.4.0/stbl/man/specify_lst.Rd | 23 stbl-0.4.0/stbl/man/stabilize_arg.Rd | 18 stbl-0.4.0/stbl/man/stabilize_chr.Rd | 50 - stbl-0.4.0/stbl/man/stabilize_dbl.Rd | 25 stbl-0.4.0/stbl/man/stabilize_df.Rd | 29 stbl-0.4.0/stbl/man/stabilize_fct.Rd | 27 stbl-0.4.0/stbl/man/stabilize_int.Rd | 25 stbl-0.4.0/stbl/man/stabilize_lgl.Rd | 25 stbl-0.4.0/stbl/man/stabilize_lst.Rd | 27 stbl-0.4.0/stbl/man/stabilize_present.Rd | 27 stbl-0.4.0/stbl/man/stbl-package.Rd | 55 - stbl-0.4.0/stbl/man/to.Rd |only stbl-0.4.0/stbl/man/to_df.Rd | 7 stbl-0.4.0/stbl/man/to_fn.Rd |only stbl-0.4.0/stbl/man/to_lst.Rd | 19 stbl-0.4.0/stbl/src |only stbl-0.4.0/stbl/tests/testthat/_problems |only stbl-0.4.0/stbl/tests/testthat/_snaps/aaa-conditions.md | 15 stbl-0.4.0/stbl/tests/testthat/_snaps/check.md | 186 ++-- stbl-0.4.0/stbl/tests/testthat/_snaps/pkg_inform.md |only stbl-0.4.0/stbl/tests/testthat/_snaps/pkg_warn.md |only stbl-0.4.0/stbl/tests/testthat/_snaps/to.md |only stbl-0.4.0/stbl/tests/testthat/_snaps/to_chr.md | 126 +- stbl-0.4.0/stbl/tests/testthat/_snaps/to_df.md | 140 +-- stbl-0.4.0/stbl/tests/testthat/_snaps/to_fct.md | 20 stbl-0.4.0/stbl/tests/testthat/_snaps/to_fn.md |only stbl-0.4.0/stbl/tests/testthat/_snaps/to_int.md | 80 + stbl-0.4.0/stbl/tests/testthat/_snaps/to_lst.md | 20 stbl-0.4.0/stbl/tests/testthat/helper-callable_c_functions.R |only stbl-0.4.0/stbl/tests/testthat/helper-wrap.R | 1 stbl-0.4.0/stbl/tests/testthat/test-aaa-conditions.R | 22 stbl-0.4.0/stbl/tests/testthat/test-are_fct_ish.R | 6 stbl-0.4.0/stbl/tests/testthat/test-are_fn_ish.R |only stbl-0.4.0/stbl/tests/testthat/test-are_int_ish.R | 6 stbl-0.4.0/stbl/tests/testthat/test-c_api.R |only stbl-0.4.0/stbl/tests/testthat/test-callable_c_functions.R |only stbl-0.4.0/stbl/tests/testthat/test-cls_unexported.R | 57 - stbl-0.4.0/stbl/tests/testthat/test-pkg_abort.R | 53 + stbl-0.4.0/stbl/tests/testthat/test-pkg_inform.R |only stbl-0.4.0/stbl/tests/testthat/test-pkg_warn.R |only stbl-0.4.0/stbl/tests/testthat/test-specify_cls.R | 3 stbl-0.4.0/stbl/tests/testthat/test-specify_df.R | 3 stbl-0.4.0/stbl/tests/testthat/test-stabilize_chr.R | 5 stbl-0.4.0/stbl/tests/testthat/test-stabilize_df.R | 10 stbl-0.4.0/stbl/tests/testthat/test-stabilize_lst.R | 488 +++++------ stbl-0.4.0/stbl/tests/testthat/test-to.R |only stbl-0.4.0/stbl/tests/testthat/test-to_chr.R | 259 +++-- stbl-0.4.0/stbl/tests/testthat/test-to_df.R | 19 stbl-0.4.0/stbl/tests/testthat/test-to_fct.R | 37 stbl-0.4.0/stbl/tests/testthat/test-to_fn.R |only stbl-0.4.0/stbl/tests/testthat/test-to_int.R | 55 + stbl-0.4.0/stbl/tests/testthat/test-to_lst.R | 23 stbl-0.4.0/stbl/tests/testthat/test-utils-conditions.R |only 185 files changed, 3131 insertions(+), 2226 deletions(-)
Title: Genotyping Triploids/Tetraploids (or Diploids) from Luminescence
Data
Description: Genotyping of triploid individuals from luminescence data (marker probeset A and B). Works also for diploids and tetraploids.
Three main functions: Create_Dataset_from_file() to build dataset ; Clustering_parallele_from_dir() that regroups individuals with a same genotype based on proximity and
Genotyping_parallele_from_dir() that assigns a genotype to each cluster. For Shiny interface use: launch_GenoShiny().
Author: Julien Roche [aut, cre],
Florence Phocas [aut],
Mathieu Besson [aut],
Pierre Patrice [aut],
Marc Vandeputte [aut],
Francois Allal [aut],
Pierrick Haffray [aut]
Maintainer: Julien Roche <julien.roche@inrae.fr>
Diff between GenoTriplo versions 1.1.3 dated 2025-03-25 and 2.2.1 dated 2026-07-28
GenoTriplo-1.1.3/GenoTriplo/R/GenoTriplo_to_clust.R |only GenoTriplo-1.1.3/GenoTriplo/R/GenoTriplo_to_geno.R |only GenoTriplo-1.1.3/GenoTriplo/data |only GenoTriplo-1.1.3/GenoTriplo/inst/sh |only GenoTriplo-1.1.3/GenoTriplo/man/Create_Dataset.Rd |only GenoTriplo-1.1.3/GenoTriplo/man/GenoTriplo_to_clust.Rd |only GenoTriplo-1.1.3/GenoTriplo/man/GenoTriplo_to_geno.Rd |only GenoTriplo-1.1.3/GenoTriplo/man/Run_Clustering.Rd |only GenoTriplo-1.1.3/GenoTriplo/man/Run_Genotyping.Rd |only GenoTriplo-2.2.1/GenoTriplo/DESCRIPTION | 21 GenoTriplo-2.2.1/GenoTriplo/MD5 | 58 GenoTriplo-2.2.1/GenoTriplo/NAMESPACE | 19 GenoTriplo-2.2.1/GenoTriplo/R/App_GenoTriploShiny.R | 1017 +++------- GenoTriplo-2.2.1/GenoTriplo/R/function_GenoTot_pop_dif.R | 13 GenoTriplo-2.2.1/GenoTriplo/R/function_GenoTot_pop_same.R | 324 +-- GenoTriplo-2.2.1/GenoTriplo/R/function_clustering.R | 186 - GenoTriplo-2.2.1/GenoTriplo/R/function_create_dataset.R | 242 +- GenoTriplo-2.2.1/GenoTriplo/R/function_create_genofiles.R |only GenoTriplo-2.2.1/GenoTriplo/R/function_keepMarkerdiplo.R | 320 +-- GenoTriplo-2.2.1/GenoTriplo/R/function_keepMarkertetra.R |only GenoTriplo-2.2.1/GenoTriplo/R/function_keepMarkertriplo.R | 530 ++--- GenoTriplo-2.2.1/GenoTriplo/R/function_manage_keepMarker.R |only GenoTriplo-2.2.1/GenoTriplo/R/function_run_clustering.R | 156 - GenoTriplo-2.2.1/GenoTriplo/R/function_run_genotyping.R | 322 +-- GenoTriplo-2.2.1/GenoTriplo/inst/extdata |only GenoTriplo-2.2.1/GenoTriplo/man/Clustering.Rd | 21 GenoTriplo-2.2.1/GenoTriplo/man/Clustering_from_dir.Rd |only GenoTriplo-2.2.1/GenoTriplo/man/Clustering_from_file.Rd |only GenoTriplo-2.2.1/GenoTriplo/man/Clustering_parallele_from_dir.Rd |only GenoTriplo-2.2.1/GenoTriplo/man/Create_Dataset_from_file.Rd |only GenoTriplo-2.2.1/GenoTriplo/man/Genotyping_from_file.Rd |only GenoTriplo-2.2.1/GenoTriplo/man/Genotyping_parallele_from_dir.Rd |only GenoTriplo-2.2.1/GenoTriplo/man/create_genofiles.Rd |only GenoTriplo-2.2.1/GenoTriplo/man/launch_GenoShiny.Rd | 6 34 files changed, 1464 insertions(+), 1771 deletions(-)
Title: Dynamic Water Balance a Hydrological Model
Description: A tool for hydrologic modelling using the Budyko
framework and the Dynamic Water Balance model with Dynamical Dimension
Search algorithm to calibrate the model and analyze the outputs from
interactive graphics. It allows to calculate the water availability
in basins and also some water fluxes represented by
the structure of the model.
See Zhang, L., N., Potter, K., Hickel, Y., Zhang, Q., Shao (2008) <DOI:10.1016/j.jhydrol.2008.07.021> "Water balance modeling over variable time scales based on the Budyko framework - Model development and testing", Journal of Hydrology, 360, 117–131.
See Tolson, B., C., Shoemaker (2007) <DOI:10.1029/2005WR004723> "Dynamically dimensioned search algorithm for computationally efficient watershed model calibration", Water Resources Research, 43, 1–16.
Author: Nicolas Duque [aut] ,
Carolina Vega [aut] ,
Jeffer Canon [aut],
Pedro Arboleda [aut] ,
David Zamora [aut, cre] ,
Camila Garcia [cot]
Maintainer: David Zamora <dazamoraa@unal.edu.co>
This is a re-admission after prior archival of version 1.0.0 dated 2020-08-18
Diff between DWBmodelUN versions 1.0.0 dated 2020-08-18 and 2.0.1 dated 2026-07-28
DWBmodelUN-1.0.0/DWBmodelUN/data/datalist |only DWBmodelUN-2.0.1/DWBmodelUN/DESCRIPTION | 30 DWBmodelUN-2.0.1/DWBmodelUN/MD5 | 73 DWBmodelUN-2.0.1/DWBmodelUN/NAMESPACE | 2 DWBmodelUN-2.0.1/DWBmodelUN/NEWS.md |only DWBmodelUN-2.0.1/DWBmodelUN/R/Coord_comparison.R | 194 DWBmodelUN-2.0.1/DWBmodelUN/R/DWBCalculator.R | 208 DWBmodelUN-2.0.1/DWBmodelUN/R/Sogamoso.R | 15 DWBmodelUN-2.0.1/DWBmodelUN/R/buildGRUmaps.R | 95 DWBmodelUN-2.0.1/DWBmodelUN/R/cellBasins.R | 71 DWBmodelUN-2.0.1/DWBmodelUN/R/dds.R | 205 DWBmodelUN-2.0.1/DWBmodelUN/R/funFU.R | 13 DWBmodelUN-2.0.1/DWBmodelUN/R/graphDWB.R | 380 DWBmodelUN-2.0.1/DWBmodelUN/R/init_state.R | 67 DWBmodelUN-2.0.1/DWBmodelUN/R/printVar.R | 97 DWBmodelUN-2.0.1/DWBmodelUN/R/readSetup.R | 46 DWBmodelUN-2.0.1/DWBmodelUN/R/upForcing.R | 166 DWBmodelUN-2.0.1/DWBmodelUN/R/varBasins.R | 17 DWBmodelUN-2.0.1/DWBmodelUN/README.md | 291 DWBmodelUN-2.0.1/DWBmodelUN/build/vignette.rds |binary DWBmodelUN-2.0.1/DWBmodelUN/inst/doc/examples_dwbmodel.R | 28 DWBmodelUN-2.0.1/DWBmodelUN/inst/doc/examples_dwbmodel.Rmd | 43 DWBmodelUN-2.0.1/DWBmodelUN/inst/doc/examples_dwbmodel.html | 6642 +++++++++++- DWBmodelUN-2.0.1/DWBmodelUN/man/Coord_comparison.Rd | 6 DWBmodelUN-2.0.1/DWBmodelUN/man/GRU.Rd | 5 DWBmodelUN-2.0.1/DWBmodelUN/man/basins.Rd | 7 DWBmodelUN-2.0.1/DWBmodelUN/man/buildGRUmaps.Rd | 12 DWBmodelUN-2.0.1/DWBmodelUN/man/cellBasins.Rd | 8 DWBmodelUN-2.0.1/DWBmodelUN/man/dds.Rd | 10 DWBmodelUN-2.0.1/DWBmodelUN/man/figures |only DWBmodelUN-2.0.1/DWBmodelUN/man/funFU.Rd | 5 DWBmodelUN-2.0.1/DWBmodelUN/man/graphDWB.Rd | 20 DWBmodelUN-2.0.1/DWBmodelUN/man/init_state.Rd | 22 DWBmodelUN-2.0.1/DWBmodelUN/man/printVar.Rd | 14 DWBmodelUN-2.0.1/DWBmodelUN/man/readSetup.Rd | 12 DWBmodelUN-2.0.1/DWBmodelUN/man/sogamoso.Rd | 2 DWBmodelUN-2.0.1/DWBmodelUN/man/upForcing.Rd | 43 DWBmodelUN-2.0.1/DWBmodelUN/vignettes/examples_dwbmodel.Rmd | 43 38 files changed, 7856 insertions(+), 1036 deletions(-)
Title: Tests for Variance Homogeneity
Description: Performs 18 omnibus tests yielding a total of 28 distinct methodological variations for testing the composite hypothesis of variance homogeneity.
Author: Gozde Cosar [aut],
Muhammed Ali Yilmaz [aut],
Merve Kasikci [aut],
Osman Dag [aut, cre]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between vartest versions 1.5 dated 2026-04-22 and 1.6 dated 2026-07-28
DESCRIPTION | 10 MD5 | 6 man/select_vartest.Rd | 4 tests/testthat/testthat-vht.R | 614 +++++++++++++++++++++++++++++++++--------- 4 files changed, 493 insertions(+), 141 deletions(-)
Title: A Hypothesis Testing Framework for Validating an Assay for
Precision
Description: A common way of validating a biological assay for is through a
procedure, where m levels of an analyte are measured with n replicates at each
level, and if all m estimates of the coefficient of variation (CV) are less
than some prespecified level, then the assay is declared validated for precision
within the range of the m analyte levels. Two limitations of this procedure are:
there is no clear statistical statement of precision upon passing, and it is
unclear how to modify the procedure for assays with constant standard deviation.
We provide tools to convert such a procedure into a set of m hypothesis tests.
This reframing motivates the m:n:q procedure, which upon completion delivers
a 100q% upper confidence limit on the CV. Additionally, for a post-validation
assay output of y, the method gives an ``effective standard deviation interval''
of log(y) plus or minus r, which is a 68% confidence interval on log(mu), where
mu is the expected value of the assay output for that sample. Furth [...truncated...]
Author: Michael C Sachs [aut, cre],
Michael P Fay [aut]
Maintainer: Michael C Sachs <sachsmc@gmail.com>
Diff between testassay versions 0.1.1 dated 2020-06-03 and 0.1.3 dated 2026-07-28
DESCRIPTION | 20 MD5 | 22 NEWS | 52 - R/testassay.R | 6 README.md | 28 build/vignette.rds |binary inst/CITATION | 32 - inst/doc/GIAValidationExample.R | 164 ++--- inst/doc/GIAValidationExample.html | 1111 ++++++++++++++++++++----------------- man/lognormConstCVCI.Rd | 2 man/normConstCVCI.Rd | 2 man/testassay.Rd | 2 12 files changed, 798 insertions(+), 643 deletions(-)
Title: Stochastic Metafrontier Analysis
Description: Implements stochastic metafrontier analysis for productivity and
performance benchmarking across firms operating under different
technologies. Contains routines for the deterministic metafrontier envelope
of O'Donnell et al. (2008) <doi:10.1007/s00181-007-0119-4> via linear and
quadratic programming, and the stochastic metafrontier of Huang et al.
(2014) <doi:10.1007/s11123-014-0402-2>. Also supports latent class
stochastic metafrontier analysis and sample selection correction stochastic
metafrontier models. Depends on the 'sfaR' package by Dakpo et al. (2023)
<https://CRAN.R-project.org/package=sfaR>.
Author: Sulman Olieko Owili [aut, cre]
Maintainer: Sulman Olieko Owili <oliekosulman@gmail.com>
Diff between smfa versions 1.0.0 dated 2026-04-28 and 1.0.1 dated 2026-07-28
DESCRIPTION | 9 MD5 | 56 NEWS.md | 26 R/smfa.R | 50 R/startup_msg.R | 6 README.md | 2339 ++++++++++++++++++------ inst/CITATION | 2 inst/doc/efficiency-extraction.R | 45 inst/doc/efficiency-extraction.Rmd | 45 inst/doc/efficiency-extraction.html | 730 ++++--- inst/doc/getting-started.R | 29 inst/doc/getting-started.Rmd | 29 inst/doc/getting-started.html | 542 ++--- inst/doc/sfacross-metafrontier.R | 37 inst/doc/sfacross-metafrontier.Rmd | 37 inst/doc/sfacross-metafrontier.html | 2623 +++++++++++++-------------- inst/doc/sfalcmcross-metafrontier.R | 35 inst/doc/sfalcmcross-metafrontier.Rmd | 35 inst/doc/sfalcmcross-metafrontier.html | 1271 ++++++------- inst/doc/sfaselectioncross-metafrontier.R | 35 inst/doc/sfaselectioncross-metafrontier.Rmd | 35 inst/doc/sfaselectioncross-metafrontier.html | 1804 +++++++++--------- man/smfa.Rd | 49 tests |only vignettes/efficiency-extraction.Rmd | 45 vignettes/getting-started.Rmd | 29 vignettes/sfacross-metafrontier.Rmd | 37 vignettes/sfalcmcross-metafrontier.Rmd | 35 vignettes/sfaselectioncross-metafrontier.Rmd | 35 29 files changed, 5978 insertions(+), 4072 deletions(-)
Title: 'Constrained Quantile Regression with B-Splines'
Description: Quantile regression with B-splines under shape constraints.
The initial version with cubic splines is now augmented with splines
of degree 1 to 4. Constraints for degrees 3 (monotone) and 4
(monotone and convex) use the Karlin-Studden SOCP characterization
for the sign of the polynomial, while other constraints applied
at the knots are added as linear problems. The method for cubic
splines is described in Abbes (2026) <doi:10.5281/zenodo.17427913>.
Other formulations are simple consequences of the other given
references. This R implementation is intended for demonstration
and prototyping. All B-spline and polynomial functions have been
rewritten for consistency. An equivalent Python package is available
at <https://pypi.org/project/BsplineQuantRegpy/>.
Author: Alexandre Abbes [aut, cre]
Maintainer: Alexandre Abbes <alexandre.abbes@proton.me>
Diff between BsplineQuantReg versions 0.2.1 dated 2026-07-24 and 0.2.2 dated 2026-07-28
BsplineQuantReg-0.2.1/BsplineQuantReg/demo/monotonicity.R |only BsplineQuantReg-0.2.1/BsplineQuantReg/man/print.quantile_spline.Rd |only BsplineQuantReg-0.2.2/BsplineQuantReg/DESCRIPTION | 11 BsplineQuantReg-0.2.2/BsplineQuantReg/MD5 | 100 +-- BsplineQuantReg-0.2.2/BsplineQuantReg/NAMESPACE | 10 BsplineQuantReg-0.2.2/BsplineQuantReg/NEWS | 27 BsplineQuantReg-0.2.2/BsplineQuantReg/R/bspline-base.R | 318 ++++++++-- BsplineQuantReg-0.2.2/BsplineQuantReg/R/bspline-eval.R | 313 +++++---- BsplineQuantReg-0.2.2/BsplineQuantReg/R/bspline_deriv.R |only BsplineQuantReg-0.2.2/BsplineQuantReg/R/constraints.R | 8 BsplineQuantReg-0.2.2/BsplineQuantReg/R/cubic-regression.R | 14 BsplineQuantReg-0.2.2/BsplineQuantReg/R/imports.R | 2 BsplineQuantReg-0.2.2/BsplineQuantReg/R/linear-regression.R | 6 BsplineQuantReg-0.2.2/BsplineQuantReg/R/polynomial-utils.R | 8 BsplineQuantReg-0.2.2/BsplineQuantReg/R/quadratic-regression.R | 27 BsplineQuantReg-0.2.2/BsplineQuantReg/R/quantile-regression.R | 37 - BsplineQuantReg-0.2.2/BsplineQuantReg/R/quartic-regression.R | 12 BsplineQuantReg-0.2.2/BsplineQuantReg/R/test_bsqr.R |only BsplineQuantReg-0.2.2/BsplineQuantReg/README.md | 17 BsplineQuantReg-0.2.2/BsplineQuantReg/demo/00Index | 17 BsplineQuantReg-0.2.2/BsplineQuantReg/demo/comprehensive.R | 35 - BsplineQuantReg-0.2.2/BsplineQuantReg/demo/convexity.R | 20 BsplineQuantReg-0.2.2/BsplineQuantReg/demo/degrees_comparison.R | 155 ++-- BsplineQuantReg-0.2.2/BsplineQuantReg/demo/demo_der3.R | 61 - BsplineQuantReg-0.2.2/BsplineQuantReg/demo/derivative2.R |only BsplineQuantReg-0.2.2/BsplineQuantReg/demo/logistic.R | 16 BsplineQuantReg-0.2.2/BsplineQuantReg/demo/monotonicity_basic.R |only BsplineQuantReg-0.2.2/BsplineQuantReg/demo/temperature.R | 8 BsplineQuantReg-0.2.2/BsplineQuantReg/demo/temperature2.R | 8 BsplineQuantReg-0.2.2/BsplineQuantReg/inst/References.bib | 4 BsplineQuantReg-0.2.2/BsplineQuantReg/man/Bspline_base.Rd | 16 BsplineQuantReg-0.2.2/BsplineQuantReg/man/Bspline_base_deriv.Rd |only BsplineQuantReg-0.2.2/BsplineQuantReg/man/Bspline_deriv.Rd | 22 BsplineQuantReg-0.2.2/BsplineQuantReg/man/Bsplinetopp.Rd |only BsplineQuantReg-0.2.2/BsplineQuantReg/man/SplineConstQuantRegBs1.Rd | 2 BsplineQuantReg-0.2.2/BsplineQuantReg/man/SplineConstQuantRegBs2.Rd | 10 BsplineQuantReg-0.2.2/BsplineQuantReg/man/SplineConstQuantRegBs3.Rd | 4 BsplineQuantReg-0.2.2/BsplineQuantReg/man/SplineConstQuantRegBs4.Rd | 2 BsplineQuantReg-0.2.2/BsplineQuantReg/man/SplineCubicQuant.Rd | 12 BsplineQuantReg-0.2.2/BsplineQuantReg/man/SplineLinearQuant.Rd | 2 BsplineQuantReg-0.2.2/BsplineQuantReg/man/SplineQuadraticQuant.Rd | 10 BsplineQuantReg-0.2.2/BsplineQuantReg/man/SplineQuarticQuant.Rd | 2 BsplineQuantReg-0.2.2/BsplineQuantReg/man/apply_karlin_cubic.Rd | 4 BsplineQuantReg-0.2.2/BsplineQuantReg/man/apply_karlin_quadratic.Rd | 2 BsplineQuantReg-0.2.2/BsplineQuantReg/man/apply_linear_constraint.Rd | 2 BsplineQuantReg-0.2.2/BsplineQuantReg/man/bs_direct.Rd | 2 BsplineQuantReg-0.2.2/BsplineQuantReg/man/get_parameters.Rd | 8 BsplineQuantReg-0.2.2/BsplineQuantReg/man/make_spline.Rd | 22 BsplineQuantReg-0.2.2/BsplineQuantReg/man/makpp.Rd | 16 BsplineQuantReg-0.2.2/BsplineQuantReg/man/print.callable_pp.Rd |only BsplineQuantReg-0.2.2/BsplineQuantReg/man/print.callable_spline.Rd | 2 BsplineQuantReg-0.2.2/BsplineQuantReg/man/print.non_callable_pp.Rd |only BsplineQuantReg-0.2.2/BsplineQuantReg/man/print.non_callable_spline.Rd |only BsplineQuantReg-0.2.2/BsplineQuantReg/man/quantile_spline.Rd | 8 BsplineQuantReg-0.2.2/BsplineQuantReg/man/reduce_pol.Rd | 4 BsplineQuantReg-0.2.2/BsplineQuantReg/man/spline_eval.Rd | 16 BsplineQuantReg-0.2.2/BsplineQuantReg/man/test_karlin_simple.Rd |only 57 files changed, 873 insertions(+), 529 deletions(-)
More information about BsplineQuantReg at CRAN
Permanent link
Title: Bayesian Reliability Estimation
Description: Functionality for reliability estimates. For 'unidimensional' tests:
Coefficient alpha, 'Guttman's' lambda-2/-4/-6, the Greatest lower
bound and coefficient omega_u ('unidimensional') in a Bayesian and a frequentist version.
For multidimensional tests: omega_t (total) and omega_h (hierarchical).
The results include confidence and credible intervals, the
probability of a coefficient being larger than a cutoff,
and a check for the factor models, necessary for the omega coefficients.
The method for the Bayesian 'unidimensional' estimates, except for omega_u,
is sampling from the posterior inverse 'Wishart' for the
covariance matrix based measures (see 'Murphy', 2007,
<https://groups.seas.harvard.edu/courses/cs281/papers/murphy-2007.pdf>).
The Bayesian omegas (u, t, and h) are obtained by
'Gibbs' sampling from the conditional posterior distributions of
(1) the single factor model, (2) the second-order factor model, (3) the bi-factor model,
(4) the correlated factor model
('Lee', 2007 [...truncated...]
Author: Julius M. Pfadt [aut, cre] ,
Don van den Bergh [aut] ,
Joris Goosen [aut]
Maintainer: Julius M. Pfadt <julius.pfadt@gmail.com>
Diff between Bayesrel versions 0.7.8 dated 2025-03-24 and 0.7.9 dated 2026-07-28
DESCRIPTION | 20 +++++++++++--------- MD5 | 9 +++++---- NEWS.md |only R/bomegasMultiGibbs.R | 9 ++++++++- build/partial.rdb |binary inst/tinytest/test_strel.R | 4 ++-- 6 files changed, 26 insertions(+), 16 deletions(-)
Title: Tree-Spatial Scan Statistic for Cluster Detection
Description: Implements the tree-spatial scan statistic for detecting clusters
that combine both spatial and hierarchical structures, as proposed by
Cancado et al. (2025) <doi:10.1007/s10651-025-00670-w>. The method extends
Kulldorff (1997) <doi:10.1080/03610929708831995> circular spatial scan
statistic and the tree-based scan statistic of Kulldorff et al. (2003)
<doi:10.1111/1541-0420.00039> by searching for anomalies in both
geographic regions and branches of hierarchical trees simultaneously. The
package also provides standalone implementations of Kulldorff's circular
spatial scan statistic and the tree-based scan statistic. Statistical
significance is assessed via Monte Carlo simulation under a Poisson or
binomial model, with optional 'OpenMP' parallelization.
Author: Allan Quadros [aut, cre] ,
Andre L. F. Cancado [aut]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between treeSS versions 0.2.5 dated 2026-07-11 and 0.2.6 dated 2026-07-28
DESCRIPTION | 14 +++++--------- MD5 | 6 +++--- NEWS.md | 6 ++++++ man/treeSS-package.Rd | 2 -- 4 files changed, 14 insertions(+), 14 deletions(-)
Title: GCC Estimation of the Multilevel Factor Model
Description: Provides methods for model selection, estimation, inference, and simulation for the
multilevel factor model, based on the principal component estimation and generalised
canonical correlation approach. Details can be found in "Generalised Canonical Correlation
Estimation of the Multilevel Factor Model." Lin and Shin (2025) <doi:10.2139/ssrn.4295429>.
Author: Rui Lin [aut, cre],
Yongcheol Shin [aut]
Maintainer: Rui Lin <ruilin1081@gmail.com>
Diff between GCCfactor versions 1.2.0 dated 2026-07-27 and 1.2.1 dated 2026-07-28
DESCRIPTION | 6 MD5 | 6 NAMESPACE | 2 R/utility_functions.R | 387 +++++++++++++++++++++++++------------------------- 4 files changed, 201 insertions(+), 200 deletions(-)
Title: Contextualizing Tests
Description: Dissects a package environment or 'covr' coverage object in order to cross
reference tested code with the lines that are evaluated, as well as linking
those evaluated lines to the documentation that they are described within.
Connecting these three pieces of information provides a mechanism of
linking tests to documented behaviors.
Author: Doug Kelkhoff [aut] ,
Szymon Maksymiuk [aut, cre] ,
Andrew McNeil [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Szymon Maksymiuk <sz.maksymiuk@gmail.com>
Diff between covtracer versions 0.0.2 dated 2026-01-30 and 0.0.3 dated 2026-07-28
DESCRIPTION | 8 +- MD5 | 73 +++++++++++++------------ NAMESPACE | 4 + NEWS.md | 5 + R/Rd_df.R | 31 +++++++++- R/getSrcFilepath.R | 5 + R/list_of_srcref.R | 15 ++++- R/obj_namespace_name.R | 2 R/pseudo_srcref.R | 6 +- R/srcref_df.R | 17 +++-- R/srcrefs.R | 29 ++++++++- R/test_description.R | 6 +- R/test_trace_df.R | 10 ++- R/traceability.R |only R/utils.R | 2 build/vignette.rds |binary inst/doc/combining_srcref_data.html | 59 ++++++++++---------- inst/doc/plotting_test_paths.html | 7 +- inst/doc/working_with_srcrefs.html | 21 +++---- man/coverage_check_has_recorded_tests.Rd | 6 +- man/coverage_get_tests.Rd | 6 +- man/coverage_has_recorded_tests.Rd | 6 +- man/pkg_srcrefs.Rd | 6 +- man/pkg_srcrefs_df.Rd | 6 +- man/srcref_namespace.Rd |only man/test_srcrefs.Rd | 6 +- man/test_srcrefs_df.Rd | 6 +- man/trace_srcrefs.Rd | 6 +- man/trace_srcrefs_df.Rd | 6 +- tests/testthat/test_Rd_df.R | 32 ++++++++++ tests/testthat/test_case_list_obj.R | 10 +++ tests/testthat/test_case_no_evaluable_code.R | 2 tests/testthat/test_case_no_exports.R | 2 tests/testthat/test_match_containing_srcrefs.R | 13 ++-- tests/testthat/test_srcrefs.R | 18 ++++-- tests/testthat/test_test_description.R | 58 ++++++++++++++----- tests/testthat/test_test_trace_df.R | 4 + tests/testthat/test_trace_mapping.R | 4 + tests/testthat/test_traceability.R |only 39 files changed, 330 insertions(+), 167 deletions(-)
Title: Camera Trap Data Management and Analysis Framework
Description: Management and analysis of camera trap wildlife data through
an integrated workflow. Provides functions for image/video
organization and metadata extraction, species/individual
identification. Creates detection histories for occupancy and spatial
capture-recapture analyses, with support for multi-season studies.
Includes tools for fitting community occupancy models in JAGS and
NIMBLE, and an interactive dashboard for survey data visualization and
analysis. Features visualization of species distributions and activity
patterns, plus export capabilities for GIS and reports. Emphasizes
automation and reproducibility while maintaining flexibility for
different study designs.
Author: Juergen Niedballa [aut, cre] ,
Alexandre Courtiol [aut] ,
Rahel Sollmann [aut] ,
John Mathai [ctb],
Seth Timothy Wong [ctb] ,
An The Truong Nguyen [ctb] ,
Azlan bin Mohamed [ctb] ,
Andrew Tilker [ctb] ,
Roshan Guharajan [ctb] ,
Ioannis Alexiou [ctb] [...truncated...]
Maintainer: Juergen Niedballa <camtrapr@gmail.com>
Diff between camtrapR versions 3.0.4 dated 2026-04-30 and 3.1.0 dated 2026-07-28
camtrapR-3.0.4/camtrapR/R/readcamtrapDP.R |only camtrapR-3.0.4/camtrapR/inst/pictures/full_size_for_ocr/StationA/mousedeer_detections.jpg |only camtrapR-3.0.4/camtrapR/man/readcamtrapDP.Rd |only camtrapR-3.0.4/camtrapR/tests/testthat/fixtures/sample_camtrap_dp_data/tdwg_camtrap-dp_1.0.2_example.zip |only camtrapR-3.0.4/camtrapR/tests/testthat/test-readcamtrapDP.R |only camtrapR-3.1.0/camtrapR/DESCRIPTION | 32 camtrapR-3.1.0/camtrapR/MD5 | 169 camtrapR-3.1.0/camtrapR/NAMESPACE | 35 camtrapR-3.1.0/camtrapR/NEWS.md | 70 camtrapR-3.1.0/camtrapR/R/aaa_classes.r |only camtrapR-3.1.0/camtrapR/R/aggregateStations.R | 37 camtrapR-3.1.0/camtrapR/R/cameraOperation.R | 44 camtrapR-3.1.0/camtrapR/R/camtrapR-package.R | 294 camtrapR-3.1.0/camtrapR/R/communityModel.R | 254 camtrapR-3.1.0/camtrapR/R/createCovariates.R | 57 camtrapR-3.1.0/camtrapR/R/data.R |only camtrapR-3.1.0/camtrapR/R/detectionHistory.R | 55 camtrapR-3.1.0/camtrapR/R/filterRecordTable.R | 10 camtrapR-3.1.0/camtrapR/R/plot.R | 15 camtrapR-3.1.0/camtrapR/R/predict.R | 1 camtrapR-3.1.0/camtrapR/R/readCamtrapDP.R |only camtrapR-3.1.0/camtrapR/R/readWildlifeInsights.R | 32 camtrapR-3.1.0/camtrapR/R/recordTable.R | 15 camtrapR-3.1.0/camtrapR/R/recordTableIndividual.R | 15 camtrapR-3.1.0/camtrapR/R/simulateCamtrapData.R |only camtrapR-3.1.0/camtrapR/R/surveyDashboard.R | 3226 ++++++---- camtrapR-3.1.0/camtrapR/R/variousOtherHelperFunctions.R | 167 camtrapR-3.1.0/camtrapR/README.md | 126 camtrapR-3.1.0/camtrapR/build/vignette.rds |binary camtrapR-3.1.0/camtrapR/data/camtraps.rda |binary camtrapR-3.1.0/camtrapR/data/camtrapsMultiSeason.rda |binary camtrapR-3.1.0/camtrapR/data/recordTableIndividualSample.rda |binary camtrapR-3.1.0/camtrapR/data/recordTableIndividualSampleMultiSeason.rda |binary camtrapR-3.1.0/camtrapR/data/recordTableSample.rda |binary camtrapR-3.1.0/camtrapR/data/recordTableSampleMultiSeason.rda |binary camtrapR-3.1.0/camtrapR/inst/dashboard_help/communityModels_help.html | 38 camtrapR-3.1.0/camtrapR/inst/dashboard_help/covariateExtraction_help.html | 3 camtrapR-3.1.0/camtrapR/inst/dashboard_help/csv_upload_help.html |only camtrapR-3.1.0/camtrapR/inst/dashboard_help/detectionHistories_help.html | 6 camtrapR-3.1.0/camtrapR/inst/dashboard_help/goodnessOfFit_help.html | 5 camtrapR-3.1.0/camtrapR/inst/dashboard_help/singleSpeciesOccupancy_help.html | 6 camtrapR-3.1.0/camtrapR/inst/dashboard_help/speciesAccum_help.html | 4 camtrapR-3.1.0/camtrapR/inst/doc/camtrapr1.pdf |binary camtrapR-3.1.0/camtrapR/inst/doc/camtrapr2.pdf |binary camtrapR-3.1.0/camtrapR/inst/doc/camtrapr3.pdf |binary camtrapR-3.1.0/camtrapR/inst/doc/camtrapr4.pdf |binary camtrapR-3.1.0/camtrapR/inst/doc/camtrapr5.html | 3220 +++------ camtrapR-3.1.0/camtrapR/inst/doc/camtrapr5.html.asis | 2 camtrapR-3.1.0/camtrapR/inst/doc/camtrapr6.html |only camtrapR-3.1.0/camtrapR/inst/doc/camtrapr6.html.asis |only camtrapR-3.1.0/camtrapR/inst/sample_data |only camtrapR-3.1.0/camtrapR/man/cameraOperation.Rd | 15 camtrapR-3.1.0/camtrapR/man/camtrapR-package.Rd | 198 camtrapR-3.1.0/camtrapR/man/camtraps.Rd | 27 camtrapR-3.1.0/camtrapR/man/camtrapsMultiSeason.Rd | 67 camtrapR-3.1.0/camtrapR/man/communityModel.Rd | 8 camtrapR-3.1.0/camtrapR/man/createCovariates.Rd | 38 camtrapR-3.1.0/camtrapR/man/detectionHistory.Rd | 10 camtrapR-3.1.0/camtrapR/man/dplyr_reconstruct.records.Rd |only camtrapR-3.1.0/camtrapR/man/filterRecordTable.Rd | 5 camtrapR-3.1.0/camtrapR/man/fit-commOccu-method.Rd | 2 camtrapR-3.1.0/camtrapR/man/plot.camOp.Rd |only camtrapR-3.1.0/camtrapR/man/plot_coef-commOccu-method.Rd | 2 camtrapR-3.1.0/camtrapR/man/print.camOp.Rd |only camtrapR-3.1.0/camtrapR/man/print.cams.Rd |only camtrapR-3.1.0/camtrapR/man/print.cams_dp.Rd |only camtrapR-3.1.0/camtrapR/man/print.detHist.Rd |only camtrapR-3.1.0/camtrapR/man/print.records.Rd |only camtrapR-3.1.0/camtrapR/man/readCamtrapDP.Rd |only camtrapR-3.1.0/camtrapR/man/readWildlifeInsights.Rd | 10 camtrapR-3.1.0/camtrapR/man/recordTable.Rd | 8 camtrapR-3.1.0/camtrapR/man/recordTableIndividual.Rd | 6 camtrapR-3.1.0/camtrapR/man/recordTableIndividualSample.Rd | 18 camtrapR-3.1.0/camtrapR/man/recordTableIndividualSampleMultiSeason.Rd | 31 camtrapR-3.1.0/camtrapR/man/recordTableSample.Rd | 15 camtrapR-3.1.0/camtrapR/man/recordTableSampleMultiSeason.Rd | 39 camtrapR-3.1.0/camtrapR/man/simulateCamtrapData.Rd |only camtrapR-3.1.0/camtrapR/man/sub-.camOp.Rd |only camtrapR-3.1.0/camtrapR/man/sub-.detHist.Rd |only camtrapR-3.1.0/camtrapR/man/sub-.records.Rd |only camtrapR-3.1.0/camtrapR/man/summary.camOp.Rd |only camtrapR-3.1.0/camtrapR/man/summary.records.Rd |only camtrapR-3.1.0/camtrapR/man/surveyDashboard.Rd | 17 camtrapR-3.1.0/camtrapR/man/timeShiftTable.Rd | 13 camtrapR-3.1.0/camtrapR/tests/testthat/Rplots.pdf |only camtrapR-3.1.0/camtrapR/tests/testthat/apps |only camtrapR-3.1.0/camtrapR/tests/testthat/fixtures/sample_camtrap_dp_data/datapackage_no_vernacularNames.json |only camtrapR-3.1.0/camtrapR/tests/testthat/test-app-surveyDashboard_builtin.R |only camtrapR-3.1.0/camtrapR/tests/testthat/test-app-surveyDashboard_camtrapdp.R |only camtrapR-3.1.0/camtrapR/tests/testthat/test-communityModels.R | 31 camtrapR-3.1.0/camtrapR/tests/testthat/test-readCamtrapDP.R |only camtrapR-3.1.0/camtrapR/tests/testthat/test-simulateCamtrapData.R |only camtrapR-3.1.0/camtrapR/tests/testthat/test-surveyDashboard.R | 218 camtrapR-3.1.0/camtrapR/tests/testthat/test-surveyReport.R | 30 camtrapR-3.1.0/camtrapR/tests/testthat/test-workflow_simulated_data.R |only camtrapR-3.1.0/camtrapR/tests/testthat/test_createCovariates.R | 7 camtrapR-3.1.0/camtrapR/tests/testthat/test_detectionHistory.R | 3 camtrapR-3.1.0/camtrapR/tests/testthat/test_recordTable.R | 24 camtrapR-3.1.0/camtrapR/vignettes/camtrapr5.html.asis | 2 camtrapR-3.1.0/camtrapR/vignettes/camtrapr6.html.asis |only 100 files changed, 4568 insertions(+), 4214 deletions(-)
Title: Korean National Assembly Data for Political Science Education
Description: Provides ready-to-use datasets from the Korean National Assembly
(assemblies 20 through 22, 2016-2026) for teaching quantitative methods in
political science. Includes legislator metadata, bill proposals, roll call
votes, asset declarations, and policy seminar records. Designed as a Korean
politics counterpart to packages like 'palmerpenguins', enabling students to
practice regression, panel data analysis, text analysis, and network analysis
with real legislative data. Roll call vote data and spatial voting models are
described in Poole and Rosenthal (1985) <doi:10.2307/2111172>. Legislative
data is sourced from the Korean National Assembly Open API.
Author: Kyusik Yang [aut, cre]
Maintainer: Kyusik Yang <kyusik.yang@nyu.edu>
Diff between assemblykor versions 0.1.2 dated 2026-04-15 and 0.1.3 dated 2026-07-28
DESCRIPTION | 6 MD5 | 53 ++-- NAMESPACE | 1 NEWS.md | 34 ++ R/data.R | 21 - R/download.R | 124 +++++++++ R/zzz.R | 14 - README.md | 15 - inst/CITATION | 2 inst/cheatsheet/assemblykor-cheatsheet.Rmd | 6 inst/doc/codebook.Rmd | 4 inst/doc/codebook.html | 4 inst/doc/introduction.html | 16 - inst/doc/quickstart.html | 4 inst/rmd-tutorials/04-panel-data.Rmd | 7 inst/rmd-tutorials/05-text-analysis.Rmd | 128 +++++++++- inst/shinyapps/04-panel-data/04-panel-data.Rmd | 7 inst/shinyapps/05-text-analysis/05-text-analysis.Rmd | 128 +++++++++- inst/shinyapps/assemblykor-tutorials/assemblykor-tutorials.Rmd | 68 ++++- inst/tutorials/04-panel-data/04-panel-data.Rmd | 7 inst/tutorials/05-text-analysis/05-text-analysis.Rmd | 72 +++++ man/assemblykor-package.Rd | 7 man/get_bill_texts.Rd | 3 man/get_proposers.Rd | 3 man/get_speech_tokens.Rd |only man/seminars.Rd | 6 man/wealth.Rd | 8 vignettes/codebook.Rmd | 4 28 files changed, 636 insertions(+), 116 deletions(-)
Title: Word and Document Vector Models
Description: Create dense vector representation of words and documents using 'quanteda'. Implements Word2vec (Mikolov et al., 2013) <doi:10.48550/arXiv.1310.4546>, Doc2vec (Le & Mikolov, 2014) <doi:10.48550/arXiv.1405.4053> and Latent Semantic Analysis (Deerwester et al., 1990) <doi:10.1002/(SICI)1097-4571(199009)41:6%3C391::AID-ASI1%3E3.0.CO;2-9>.
Author: Kohei Watanabe [aut, cre, cph] ,
Jan Wijffels [aut] ,
BNOSAC [cph] ,
Max Fomichev [ctb, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between wordvector versions 0.6.2 dated 2026-04-06 and 0.6.3 dated 2026-07-28
DESCRIPTION | 13 +++-- MD5 | 28 ++++++------ NEWS.md | 5 ++ R/word2vec.R | 13 +++++ man/as.matrix.Rd | 4 + src/word2vec/trainThread.cpp | 90 ++++++++++++++++++++--------------------- src/word2vec/trainThread.hpp | 16 +++---- src/word2vec/word2vec.cpp | 10 ++-- src/word2vec/word2vec.hpp | 14 +++--- src/wordvector.cpp | 2 tests/misc/test_large.R | 13 +---- tests/misc/test_small.R | 19 ++++---- tests/spelling.R | 6 +- tests/testthat/test-utils.R | 7 +++ tests/testthat/test-word2vec.R | 8 ++- 15 files changed, 134 insertions(+), 114 deletions(-)
Title: MCMC Sampling from 'TMB' Model Object using 'Stan'
Description: Enables all 'rstan' functionality for a 'TMB' model object, in particular MCMC sampling and chain visualization. Sampling can be performed with or without Laplace approximation for the random effects. This is demonstrated in Monnahan & Kristensen (2018) <DOI:10.1371/journal.pone.0197954>.
Author: Kasper Kristensen [aut, cre]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between tmbstan versions 1.1.0 dated 2026-03-20 and 1.2.0 dated 2026-07-28
tmbstan-1.1.0/tmbstan/inst/model226.stan |only tmbstan-1.2.0/tmbstan/DESCRIPTION | 11 ++-- tmbstan-1.2.0/tmbstan/MD5 | 16 ++++- tmbstan-1.2.0/tmbstan/NEWS | 7 ++ tmbstan-1.2.0/tmbstan/build |only tmbstan-1.2.0/tmbstan/inst/doc |only tmbstan-1.2.0/tmbstan/inst/model.hpp |only tmbstan-1.2.0/tmbstan/inst/model.stan | 15 ++++- tmbstan-1.2.0/tmbstan/src/include/model.hpp |only tmbstan-1.2.0/tmbstan/tools/autogen.R | 77 +--------------------------- tmbstan-1.2.0/tmbstan/vignettes |only 11 files changed, 42 insertions(+), 84 deletions(-)
Title: Analysis Tools for 'PsyToolkit'
Description: Analyses and reports questionnaire and experiment data exported from 'PsyToolkit'. The package reads downloaded study folders, parses questionnaire structure, optionally merges demographic exports from CloudResearch or Prolific, and produces summary overviews of responses and completion times. It also provides helper functions to extract and aggregate experiment measures and survey variables, and to export results to spreadsheet files for further analysis and archiving. See Stoet (2017) <doi:10.1177/0098628316677643> for the 'PsyToolkit' platform.
Author: Gijsbert Stoet [cre, aut]
Maintainer: Gijsbert Stoet <stoet@gmx.co.uk>
Diff between PsyToolkit versions 1.1.4 dated 2026-03-07 and 1.1.6 dated 2026-07-28
DESCRIPTION | 10 +-- MD5 | 21 +++--- NAMESPACE | 3 R/psytkExport.r | 57 ++++++++++++++---- R/psytkParseSurvey.r | 10 ++- R/psytkReadData.r | 146 ++++++++++++++++++++++++++++++++++++++++-------- R/psytkReport.r | 24 ++++--- R/psytkUtils.r | 100 +++++++++++++++++++++++++++++--- man/lst.Rd |only man/psytkExpDiagnose.Rd |only man/psytkExport.Rd | 9 +- man/psytkExtractCall.Rd |only man/psytkReadData.Rd | 4 - 13 files changed, 308 insertions(+), 76 deletions(-)
Title: Hexagonal Binning Routines
Description: Binning and plotting functions for hexagonal bins.
Author: Dan Carr [aut],
Nicholas Lewin-Koh [aut],
Martin Maechler [aut],
Deepayan Sarkar [aut],
Edzer Pebesma [cre]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between hexbin versions 1.28.5 dated 2024-11-13 and 1.28.6 dated 2026-07-28
DESCRIPTION | 8 - MD5 | 16 +- build/vignette.rds |binary inst/doc/hexagon_binning.R | 2 inst/doc/hexagon_binning.pdf |binary man/plotMAhex.Rd | 2 src/hbin.f | 8 - src/hcell.f | 8 - tests/hdiffplot.Rout.save | 322 +++++++++++++++++++++---------------------- 9 files changed, 182 insertions(+), 184 deletions(-)
Title: Generate Random Tree-Like Images
Description: A generative art system for producing tree-like
images using a stochastic branching process to create the
structures. The package includes tools for generating the data
structures and visualising them in a variety of styles.
Author: Danielle Navarro [aut, cre, cph]
Maintainer: Danielle Navarro <djnavarro@protonmail.com>
Diff between flametree versions 0.1.3 dated 2021-11-29 and 0.2.0 dated 2026-07-28
DESCRIPTION | 30 +++++---- MD5 | 36 +++++------ NEWS.md | 39 +++++++++++- R/checks.R | 46 +++++++++++++- R/grow.R | 124 ++++++++++++++++++++++++++------------- R/plot.R | 77 ++++++++++++++---------- R/save.R | 21 ++---- R/sparks.R | 11 +-- R/zzz.R | 3 README.md | 7 +- inst |only man/figures/README-example-1.png |binary man/flametree_grow.Rd | 47 +++++++++++--- man/flametree_plot.Rd | 17 ++--- man/flametree_save.Rd | 17 +---- man/sparks.Rd | 11 +-- tests/spelling.R |only tests/testthat/test-checks.R | 52 ++++++++++++++++ tests/testthat/test-grow.R | 78 ++++++++++++++++++++++++ tests/testthat/test-save.R | 15 ++++ 20 files changed, 472 insertions(+), 159 deletions(-)
Title: A Wrap Around the 'DistillerSR' APIs
Description: Interface to 'DistillerSR' APIs. See
<https://apidocs.evidencepartners.com/> for more details.
Author: Lorenzo Copelli [aut] ,
Fulvio Barizzone [aut] ,
Dayana Stephanie Buzle [aut] ,
Rafael Vieira [aut] ,
Luca Belmonte [aut, cre]
Maintainer: Luca Belmonte <luca.belmonte@efsa.europa.eu>
Diff between distilleR versions 1.0.0 dated 2026-04-23 and 1.1.0 dated 2026-07-28
DESCRIPTION | 8 +-- MD5 | 51 ++++++++++++++----------- NAMESPACE | 4 + R/buildAuthenticationRequest.R | 4 - R/buildServiceRequest.R | 27 ++++++------- R/getAsyncReportResult.R |only R/getAsyncReportStatus.R |only R/getAuthenticationToken.R | 12 ++--- R/getProjects.R | 13 +++--- R/getReport.R | 18 ++++---- R/getReportAsync.R |only R/getReports.R | 8 ++- R/handleHTTPErrors.R | 19 ++++++--- R/parseCSVResponse.R | 8 +-- R/parseJSONResponse.R | 4 - R/parseXLSXResponse.R | 4 - R/performRequest.R | 4 - inst/doc/distilleR.R | 36 +++++++++++++++++ inst/doc/distilleR.Rmd | 59 +++++++++++++++++++++++++++-- inst/doc/distilleR.html | 57 ++++++++++++++++++++++++++-- man/getAsyncReportResult.Rd |only man/getAsyncReportStatus.Rd |only man/getAuthenticationToken.Rd | 12 ++--- man/getProjects.Rd | 7 +-- man/getReport.Rd | 15 +++---- man/getReportAsync.Rd |only man/getReports.Rd | 7 +-- tests/testthat/test-getAsyncReportResult.R |only tests/testthat/test-getAsyncReportStatus.R |only tests/testthat/test-getReportAsync.R |only vignettes/distilleR.Rmd | 59 +++++++++++++++++++++++++++-- 31 files changed, 329 insertions(+), 107 deletions(-)
Title: Web-Based Interactive Omics Visualization
Description: Tool-set of modules for creating web-based applications that use plot based strategies to visualize and analyze multi-omics data.
This package utilizes the 'shiny' and 'plotly' frameworks to provide a user friendly dashboard for interactive plotting.
Author: Hendrik Schultheis [aut, cre],
Jens Preussner [aut],
Looso Mario [aut]
Maintainer: Hendrik Schultheis <hendrik.schultheis@mpi-bn.mpg.de>
This is a re-admission after prior archival of version 2.4.2 dated 2021-04-19
Diff between wilson versions 2.4.2 dated 2021-04-19 and 2.4.4 dated 2026-07-28
DESCRIPTION | 12 - MD5 | 39 +-- NAMESPACE | 1 NEWS.md | 7 R/clarion.R | 22 + R/function.R | 55 ++-- R/global.R | 52 +++- R/installer.R | 7 R/parser.R | 2 R/zzz.R | 2 README.md | 6 build/vignette.rds |binary inst/doc/intro.html | 261 ++++++++++++++++++++-- man/Clarion.Rd | 475 +++++++++++++++++++++-------------------- man/create_logger.Rd |only man/install_app.Rd | 4 man/log_message.Rd | 4 man/parse_MaxQuant.Rd | 2 man/set_logger.Rd | 42 +-- tests/testthat/test-logging.R | 13 - tests/testthat/test_mqparser.R | 20 + 21 files changed, 679 insertions(+), 347 deletions(-)
Title: Bayesian Vector Autoregressions with Steady-State Priors
Description: Provides estimation of Bayesian vector autoregression
(BVAR) models with steady-state priors via 'Stan', along with
functions for unconditional and conditional forecasting, as well as impulse
response analysis. For details on the steady-state BVAR model
see Villani (2009) <doi:10.1002/jae.1065>.
Author: Mark Becker [aut, cre, cph]
Maintainer: Mark Becker <mark.jw.becker@gmail.com>
Diff between SteadyStateBVAR versions 0.1.0 dated 2026-07-24 and 0.1.1 dated 2026-07-28
DESCRIPTION | 6 MD5 | 96 - NAMESPACE | 1 NEWS.md | 8 R/SteadyStateBVAR-package.R | 2 R/bvar.R | 9 R/forecast.R | 41 R/priors.R | 4 README.md | 22 inst/doc/AR1-stochastic-volatility-steady-state-BVAR.Rmd | 232 ++-- inst/doc/AR1-stochastic-volatility-steady-state-BVAR.html | 244 ++-- inst/doc/Homoscedastic-steady-state-BVAR.Rmd | 240 ++-- inst/doc/Homoscedastic-steady-state-BVAR.html | 255 ++-- inst/doc/RW-stochastic-volatility-steady-state-BVAR.Rmd | 228 ++-- inst/doc/RW-stochastic-volatility-steady-state-BVAR.html | 236 ++-- inst/stan/steady_state_bvar_AR1_stochastic_volatility.stan | 6 inst/stan/steady_state_bvar_RW_stochastic_volatility.stan | 6 inst/stan/steady_state_bvar_homoscedastic_inverse_wishart_prior.stan | 2 inst/stan/steady_state_bvar_homoscedastic_jeffreys_prior.stan | 2 man/IRF.Rd | 180 +-- man/KoopKorobilis2010.Rd | 56 - man/SteadyStateBVAR-package.Rd | 58 - man/Villani2009.Rd | 66 - man/bvar.Rd | 201 +-- man/conditional_forecast.Rd | 198 +-- man/fit.Rd | 458 ++++---- man/forecast.Rd | 162 +-- man/ppi.Rd | 96 - man/priors.Rd | 536 +++++----- man/restrict_beta.Rd | 124 +- man/setup.Rd | 80 - man/stochastic_volatility_plot.Rd | 218 ++-- man/summary.bvar.Rd | 148 +- src/stanExports_steady_state_bvar_AR1_stochastic_volatility.h | 22 src/stanExports_steady_state_bvar_RW_stochastic_volatility.h | 22 src/stanExports_steady_state_bvar_homoscedastic_inverse_wishart_prior.h | 6 src/stanExports_steady_state_bvar_homoscedastic_jeffreys_prior.h | 6 vignettes/AR1-stochastic-volatility-steady-state-BVAR.Rmd | 232 ++-- vignettes/AR1-stochastic-volatility-steady-state-BVAR.Rmd.orig | 6 vignettes/Homoscedastic-steady-state-BVAR.Rmd | 240 ++-- vignettes/Homoscedastic-steady-state-BVAR.Rmd.orig | 2 vignettes/RW-stochastic-volatility-steady-state-BVAR.Rmd | 228 ++-- vignettes/RW-stochastic-volatility-steady-state-BVAR.Rmd.orig | 4 vignettes/precompile.R | 16 vignettes/vignettes |only 45 files changed, 2515 insertions(+), 2490 deletions(-)
More information about SteadyStateBVAR at CRAN
Permanent link
Title: (Standardised) Major Axis Estimation and Testing Routines
Description: Methods for fitting bivariate lines in
allometry using the major axis (MA) or standardised major axis (SMA), and
for making inferences about such lines. The available methods of inference
include confidence intervals and one-sample tests for slope and elevation,
testing for a common slope or elevation amongst several allometric lines,
constructing a confidence interval for a common slope or elevation, and
testing for no shift along a common axis, amongst several samples.
See Warton et al. 2012 <doi:10.1111/j.2041-210X.2011.00153.x> for methods description.
Author: David Warton [aut],
Remko Duursma [aut],
Daniel Falster [aut, cre] ,
Sara Taskinen [aut],
Fonti Kar [aut]
Maintainer: Daniel Falster <daniel.falster@unsw.edu.au>
Diff between smatr versions 3.4-8 dated 2018-03-18 and 3.5-1 dated 2026-07-28
smatr-3.4-8/smatr/R/logLik_sma.R |only smatr-3.4-8/smatr/man/com.ci.Rd |only smatr-3.4-8/smatr/man/nicePlot.Rd |only smatr-3.5-1/smatr/DESCRIPTION | 49 + smatr-3.5-1/smatr/MD5 | 147 ++-- smatr-3.5-1/smatr/NAMESPACE | 93 +- smatr-3.5-1/smatr/NEWS.md |only smatr-3.5-1/smatr/R/alpha.fun.R | 41 - smatr-3.5-1/smatr/R/b.com.est.R | 153 ++-- smatr-3.5-1/smatr/R/coef.sma.R | 43 - smatr-3.5-1/smatr/R/com.ci.R | 107 +-- smatr-3.5-1/smatr/R/confint.sma.R |only smatr-3.5-1/smatr/R/defineAxis.R | 63 + smatr-3.5-1/smatr/R/elev.com.R | 278 +++++-- smatr-3.5-1/smatr/R/elev.test.R | 228 ++++-- smatr-3.5-1/smatr/R/fitted.sma.R | 207 +++-- smatr-3.5-1/smatr/R/ggplot.sma.R |only smatr-3.5-1/smatr/R/huber.M.R | 102 +- smatr-3.5-1/smatr/R/leaflife.R |only smatr-3.5-1/smatr/R/leafmeas.R |only smatr-3.5-1/smatr/R/line.cis.R | 371 ++++++---- smatr-3.5-1/smatr/R/logLik.sma.R |only smatr-3.5-1/smatr/R/lr.b.com.R | 70 + smatr-3.5-1/smatr/R/ma.R | 10 smatr-3.5-1/smatr/R/makeLogMinor.R | 39 - smatr-3.5-1/smatr/R/meas.est.R | 148 ++-- smatr-3.5-1/smatr/R/multcompmatrix.R | 100 +- smatr-3.5-1/smatr/R/nicePlot.R | 116 +-- smatr-3.5-1/smatr/R/plot.sma.R | 562 +++++++++------- smatr-3.5-1/smatr/R/predict.sma.R | 13 smatr-3.5-1/smatr/R/print.sma.R | 329 ++++----- smatr-3.5-1/smatr/R/residuals.sma.R | 20 smatr-3.5-1/smatr/R/robust.factor.R | 108 +-- smatr-3.5-1/smatr/R/seqLog.R | 23 smatr-3.5-1/smatr/R/shift.com.R | 318 +++++---- smatr-3.5-1/smatr/R/slope.com.R | 498 +++++++++----- smatr-3.5-1/smatr/R/slope.test.R | 347 ++++++--- smatr-3.5-1/smatr/R/sma.R | 1121 ++++++++++++++++++-------------- smatr-3.5-1/smatr/R/smatr.R |only smatr-3.5-1/smatr/R/summary.sma.R | 20 smatr-3.5-1/smatr/R/utils.R |only smatr-3.5-1/smatr/README.md | 102 +- smatr-3.5-1/smatr/build |only smatr-3.5-1/smatr/inst/CITATION | 42 - smatr-3.5-1/smatr/inst/doc |only smatr-3.5-1/smatr/man/alpha.fun.Rd | 44 - smatr-3.5-1/smatr/man/b.com.est.Rd | 52 - smatr-3.5-1/smatr/man/coef.sma.Rd | 52 - smatr-3.5-1/smatr/man/confint.sma.Rd |only smatr-3.5-1/smatr/man/defineAxis.Rd |only smatr-3.5-1/smatr/man/elev.com.Rd | 215 +++--- smatr-3.5-1/smatr/man/elev.test.Rd | 203 +++-- smatr-3.5-1/smatr/man/figures |only smatr-3.5-1/smatr/man/fitted.sma.Rd | 77 +- smatr-3.5-1/smatr/man/gamma.fun.Rd |only smatr-3.5-1/smatr/man/get_coef.Rd |only smatr-3.5-1/smatr/man/ggplot.sma.Rd |only smatr-3.5-1/smatr/man/huber.M.Rd |only smatr-3.5-1/smatr/man/leaflife.Rd | 69 + smatr-3.5-1/smatr/man/leafmeas.Rd | 65 - smatr-3.5-1/smatr/man/line.cis.Rd | 216 +++--- smatr-3.5-1/smatr/man/lr.b.com.Rd | 41 - smatr-3.5-1/smatr/man/ma.Rd |only smatr-3.5-1/smatr/man/makeLogMinor.Rd | 61 - smatr-3.5-1/smatr/man/make_plot_data.Rd |only smatr-3.5-1/smatr/man/meas.est.Rd | 116 +-- smatr-3.5-1/smatr/man/multcompmatrix.Rd | 94 +- smatr-3.5-1/smatr/man/plot.sma.Rd | 251 ++++--- smatr-3.5-1/smatr/man/predict.sma.Rd |only smatr-3.5-1/smatr/man/print.sma.Rd | 45 - smatr-3.5-1/smatr/man/residuals.sma.Rd | 51 - smatr-3.5-1/smatr/man/robust.factor.Rd |only smatr-3.5-1/smatr/man/seqLog.Rd | 64 - smatr-3.5-1/smatr/man/shift.com.Rd | 232 +++--- smatr-3.5-1/smatr/man/slope.com.Rd | 299 +++++--- smatr-3.5-1/smatr/man/slope.test.Rd | 220 +++--- smatr-3.5-1/smatr/man/sma.Rd | 425 +++++++----- smatr-3.5-1/smatr/man/smatr-package.Rd | 151 ++-- smatr-3.5-1/smatr/man/summary.sma.Rd | 49 - smatr-3.5-1/smatr/tests |only smatr-3.5-1/smatr/vignettes |only 81 files changed, 5387 insertions(+), 3573 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 vendored 'SUNDIALS'
'CVODE' sources and headers are released under the BSD-3-Clause license.
The information is available in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Aaron Collier [ctb] ,
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Ashley Crawford [ctb] ,
Awad H. Al-Mohy [ctb],
Bill Denney [ctb] ,
Cleve Moler [ctb],
Cody J. Balos [ctb] ,
Dan Shumaker [ctb] ,
Dan [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 5.1.4 dated 2026-07-20 and 5.1.5 dated 2026-07-28
rxode2-5.1.4/rxode2/tests/testthat/433.qs2 |only rxode2-5.1.4/rxode2/tests/testthat/etTrans-drop.qs2 |only rxode2-5.1.4/rxode2/tests/testthat/etTrans1.qs2 |only rxode2-5.1.4/rxode2/tests/testthat/keep-756.qs2 |only rxode2-5.1.4/rxode2/tests/testthat/lincmt-solve-focei-sol.qs2 |only rxode2-5.1.4/rxode2/tests/testthat/test-data-setup.qs2 |only rxode2-5.1.4/rxode2/tests/testthat/test-etTrans-1.qs2 |only rxode2-5.1.4/rxode2/tests/testthat/test-etTrans-780.qs2 |only rxode2-5.1.4/rxode2/tests/testthat/test-example-3-1.qs2 |only rxode2-5.1.4/rxode2/tests/testthat/test-infusion-bolus.qs2 |only rxode2-5.1.4/rxode2/tests/testthat/test-issue-393.qs2 |only rxode2-5.1.4/rxode2/tests/testthat/test-issue-398.qs2 |only rxode2-5.1.4/rxode2/tests/testthat/test-issue-430.qs2 |only rxode2-5.1.4/rxode2/tests/testthat/test-issue-468.qs2 |only rxode2-5.1.5/rxode2/DESCRIPTION | 48 - rxode2-5.1.5/rxode2/MD5 | 355 +++++--- rxode2-5.1.5/rxode2/NAMESPACE | 6 rxode2-5.1.5/rxode2/NEWS.md | 240 +++++ rxode2-5.1.5/rxode2/R/d.R | 61 - rxode2-5.1.5/rxode2/R/dde.R | 88 +- rxode2-5.1.5/rxode2/R/elu.R | 6 rxode2-5.1.5/rxode2/R/et-helpers.R | 4 rxode2-5.1.5/rxode2/R/et-methods.R | 20 rxode2-5.1.5/rxode2/R/et.R | 250 +++++- rxode2-5.1.5/rxode2/R/etNew.R | 54 + rxode2-5.1.5/rxode2/R/etVctrs.R | 21 rxode2-5.1.5/rxode2/R/gelu.R | 4 rxode2-5.1.5/rxode2/R/lrelu.R | 4 rxode2-5.1.5/rxode2/R/piping.R | 24 rxode2-5.1.5/rxode2/R/prelu.R | 4 rxode2-5.1.5/rxode2/R/print.R | 14 rxode2-5.1.5/rxode2/R/relu.R | 4 rxode2-5.1.5/rxode2/R/rxRaw.R | 22 rxode2-5.1.5/rxode2/R/rxode-options.R | 74 - rxode2-5.1.5/rxode2/R/rxode2.R | 29 rxode2-5.1.5/rxode2/R/rxode2_md5.R | 2 rxode2-5.1.5/rxode2/R/rxsolve.R | 77 + rxode2-5.1.5/rxode2/R/selu.R | 4 rxode2-5.1.5/rxode2/R/softplus.R | 4 rxode2-5.1.5/rxode2/R/swish.R | 4 rxode2-5.1.5/rxode2/R/tran.R | 1 rxode2-5.1.5/rxode2/R/ui-assign-parts.R | 13 rxode2-5.1.5/rxode2/R/utils.R | 24 rxode2-5.1.5/rxode2/build/vendor-sundials.R | 106 ++ rxode2-5.1.5/rxode2/cleanup | 1 rxode2-5.1.5/rxode2/cleanup.win | 1 rxode2-5.1.5/rxode2/inst/COPYRIGHTS | 11 rxode2-5.1.5/rxode2/inst/doc/rxode2-syntax.html | 26 rxode2-5.1.5/rxode2/inst/include/rxode2.h | 72 - rxode2-5.1.5/rxode2/inst/include/rxode2parseVer.h | 4 rxode2-5.1.5/rxode2/inst/tools/workaround.R | 54 + rxode2-5.1.5/rxode2/man/ELU.Rd | 4 rxode2-5.1.5/rxode2/man/GELU.Rd | 2 rxode2-5.1.5/rxode2/man/PReLU.Rd | 2 rxode2-5.1.5/rxode2/man/ReLU.Rd | 2 rxode2-5.1.5/rxode2/man/SELU.Rd | 2 rxode2-5.1.5/rxode2/man/Swish.Rd | 2 rxode2-5.1.5/rxode2/man/dELU.Rd | 2 rxode2-5.1.5/rxode2/man/dGELU.Rd | 2 rxode2-5.1.5/rxode2/man/dPReLU.Rd | 2 rxode2-5.1.5/rxode2/man/dReLU.Rd | 2 rxode2-5.1.5/rxode2/man/dSELU.Rd | 2 rxode2-5.1.5/rxode2/man/dSwish.Rd | 2 rxode2-5.1.5/rxode2/man/dlReLU.Rd | 2 rxode2-5.1.5/rxode2/man/dsoftplus.Rd | 2 rxode2-5.1.5/rxode2/man/lReLU.Rd | 2 rxode2-5.1.5/rxode2/man/odeMethodToInt.Rd | 4 rxode2-5.1.5/rxode2/man/rxLastCompile.Rd | 2 rxode2-5.1.5/rxode2/man/rxRawToC.Rd | 4 rxode2-5.1.5/rxode2/man/rxSerialize.Rd | 4 rxode2-5.1.5/rxode2/man/rxSolve.Rd | 50 - rxode2-5.1.5/rxode2/man/rxStateOde.Rd | 3 rxode2-5.1.5/rxode2/man/softplus.Rd | 2 rxode2-5.1.5/rxode2/src/Makevars.in | 9 rxode2-5.1.5/rxode2/src/extraDosing.h | 15 rxode2-5.1.5/rxode2/src/init.c | 3 rxode2-5.1.5/rxode2/src/par_solve.cpp | 6 rxode2-5.1.5/rxode2/src/par_solve.h | 19 rxode2-5.1.5/rxode2/src/qs.cpp | 13 rxode2-5.1.5/rxode2/src/rxData.cpp | 22 rxode2-5.1.5/rxode2/src/sundials_inc |only rxode2-5.1.5/rxode2/src/sundials_sundials_linearsolver.c | 4 rxode2-5.1.5/rxode2/src/sundials_sundials_matrix.c | 4 rxode2-5.1.5/rxode2/src/sundials_sundials_memory.c | 6 rxode2-5.1.5/rxode2/src/sundials_sundials_nonlinearsolver.c | 4 rxode2-5.1.5/rxode2/src/sundials_sundials_nvector.c | 4 rxode2-5.1.5/rxode2/src/sundials_sunlinsol_dense.c | 2 rxode2-5.1.5/rxode2/src/sundials_sunnonlinsol_newton.c | 2 rxode2-5.1.5/rxode2/src/utilc.cpp | 42 + rxode2-5.1.5/rxode2/tests/testthat/433.rds |only rxode2-5.1.5/rxode2/tests/testthat/Rplots.pdf |only rxode2-5.1.5/rxode2/tests/testthat/etTrans-prepfit.rds |only rxode2-5.1.5/rxode2/tests/testthat/etTrans1.rds |only rxode2-5.1.5/rxode2/tests/testthat/keep-756.rds |only rxode2-5.1.5/rxode2/tests/testthat/lincmt-solve-focei-sol.rds |only rxode2-5.1.5/rxode2/tests/testthat/nmtest-evid4.rds |only rxode2-5.1.5/rxode2/tests/testthat/nodup-keep-ev.rds |only rxode2-5.1.5/rxode2/tests/testthat/test-activation.R | 312 +++---- rxode2-5.1.5/rxode2/tests/testthat/test-cbind-study-individual.R | 36 rxode2-5.1.5/rxode2/tests/testthat/test-data-setup.rds |only rxode2-5.1.5/rxode2/tests/testthat/test-data-table.R | 4 rxode2-5.1.5/rxode2/tests/testthat/test-dde.R | 103 ++ rxode2-5.1.5/rxode2/tests/testthat/test-dsl.R | 35 rxode2-5.1.5/rxode2/tests/testthat/test-et.R | 416 +++++++++- rxode2-5.1.5/rxode2/tests/testthat/test-etTrans-780.rds |only rxode2-5.1.5/rxode2/tests/testthat/test-etTrans.R | 164 +-- rxode2-5.1.5/rxode2/tests/testthat/test-example-3-1.R | 4 rxode2-5.1.5/rxode2/tests/testthat/test-example-3-1.rds |only rxode2-5.1.5/rxode2/tests/testthat/test-infusion-bolus.R | 4 rxode2-5.1.5/rxode2/tests/testthat/test-infusion-bolus.rds |only rxode2-5.1.5/rxode2/tests/testthat/test-issue-393.rds |only rxode2-5.1.5/rxode2/tests/testthat/test-issue-398.rds |only rxode2-5.1.5/rxode2/tests/testthat/test-issue-430.rds |only rxode2-5.1.5/rxode2/tests/testthat/test-issue-468.rds |only rxode2-5.1.5/rxode2/tests/testthat/test-keep.R | 4 rxode2-5.1.5/rxode2/tests/testthat/test-lincmt-alag-batch.R |only rxode2-5.1.5/rxode2/tests/testthat/test-lincmt-solve.R | 216 ++--- rxode2-5.1.5/rxode2/tests/testthat/test-modelargs.R | 25 rxode2-5.1.5/rxode2/tests/testthat/test-nmtest.R | 114 +- rxode2-5.1.5/rxode2/tests/testthat/test-nodup-keep.R | 2 rxode2-5.1.5/rxode2/tests/testthat/test-omp-num-threads.R |only rxode2-5.1.5/rxode2/tests/testthat/test-par-solve.R | 4 rxode2-5.1.5/rxode2/tests/testthat/test-raw.R | 36 rxode2-5.1.5/rxode2/tests/testthat/test-rxIs.R | 4 rxode2-5.1.5/rxode2/tests/testthat/test-rxode-issue-393.R | 4 rxode2-5.1.5/rxode2/tests/testthat/test-rxode-issue-398.R | 4 rxode2-5.1.5/rxode2/tests/testthat/test-rxode-issue-430.R | 4 rxode2-5.1.5/rxode2/tests/testthat/test-rxode-issue-433.R | 4 rxode2-5.1.5/rxode2/tests/testthat/test-rxode-issue-468.R | 2 rxode2-5.1.5/rxode2/tests/testthat/test-s3-delayed-register.R |only rxode2-5.1.5/rxode2/tests/testthat/test-sigdig-tol.R |only rxode2-5.1.5/rxode2/tests/testthat/test-sim-err-670.R | 400 ++++----- rxode2-5.1.5/rxode2/tests/testthat/test-udf.R | 414 +++++---- rxode2-5.1.5/rxode2/tests/testthat/test-ui-piping.R | 95 ++ rxode2-5.1.5/rxode2/tests/testthat/test-yeojohnson-derivative.R |only 135 files changed, 3083 insertions(+), 1319 deletions(-)
Title: 'date' C++ Header Library for Date and Time Functionality
Description: A header-only C++ library is provided with support
for dates, time zones, ISO weeks, Julian dates, and Islamic dates.
'date' offers extensive date and time functionality for the C++11,
C++14 and C++17 standards and was written by Howard Hinnant and released
under the MIT license. A slightly modified version has been accepted
(along with 'tz.h') as part of C++20. This package regroups all
header files from the upstream repository by Howard Hinnant so that
other R packages can use them in their C++ code. At present, few of
the types have explicit 'Rcpp' wrappers though these may be added as
needed.
Author: Dirk Eddelbuettel [aut, cre] ,
Howard Hinnant [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppDate versions 0.0.6 dated 2025-05-29 and 0.0.7 dated 2026-07-28
ChangeLog | 20 +++ DESCRIPTION | 8 - MD5 | 16 +-- build/partial.rdb |binary inst/NEWS.Rd | 7 + inst/include/date.h | 33 ++++-- inst/include/iso_week.h | 12 +- inst/include/ptz.h | 241 +++++++++++++++++++++++++++--------------------- inst/include/tz.h | 3 9 files changed, 211 insertions(+), 129 deletions(-)
Title: MAny-Group MAtching
Description: Balancing quasi-experimental field research for effects of covariates is fundamental for drawing causal inference. (Propensity Score) Matching deals with this issue but current
techniques are restricted to binary treatment variables. Moreover, they provide several solutions without providing a comprehensive framework on choosing the best model. The
MAGMA R-package addresses these restrictions by offering nearest neighbor matching based on Propensity Scores or the Mahalanobis Distance for two to four groups. It also includes the option to match data of a 2x2 design. In addition,
MAGMA includes a framework for evaluating the post-matching balance. The package includes functions for the matching process and matching reporting. We provide a General tutorial on
MAGMA and a tutorial for Mahalanobis Distance Matching as vignettes. More information on MAGMA can be found in Feuchter, M. D., Urban, J., Scherrer V., Breit, M. L., and Preckel F. (2022) <https://osf.io/p47nc/>.
Author: Julian Urban [aut, cre],
Markus D. Feuchter [aut],
Vsevolod Scherrer [aut],
Moritz L. Breit [aut],
Franzis Preckel [aut]
Maintainer: Julian Urban <julian.urban@uni-potsdam.de>
Diff between MAGMA.R versions 1.0.4 dated 2025-05-26 and 1.1 dated 2026-07-28
MAGMA.R-1.0.4/MAGMA.R/man/distance_estimator.Rd |only MAGMA.R-1.1/MAGMA.R/DESCRIPTION | 20 MAGMA.R-1.1/MAGMA.R/MD5 | 61 MAGMA.R-1.1/MAGMA.R/NAMESPACE | 95 MAGMA.R-1.1/MAGMA.R/R/Desc_function.R | 1 MAGMA.R-1.1/MAGMA.R/R/Inner_MAGMA_functions.R | 90 MAGMA.R-1.1/MAGMA.R/R/MAGMA_exact_function.R | 298 + MAGMA.R-1.1/MAGMA.R/R/MAGMA_function.R | 480 +- MAGMA.R-1.1/MAGMA.R/R/Non_parametric_descs.R | 4 MAGMA.R-1.1/MAGMA.R/R/Pillai_functions.R | 2 MAGMA.R-1.1/MAGMA.R/R/Visualizing_MAGMA_functions.R | 64 MAGMA.R-1.1/MAGMA.R/R/d_ratio_functions.R | 4 MAGMA.R-1.1/MAGMA.R/R/mean_g_functions.R | 4 MAGMA.R-1.1/MAGMA.R/build/partial.rdb |binary MAGMA.R-1.1/MAGMA.R/build/vignette.rds |binary MAGMA.R-1.1/MAGMA.R/inst/doc/MDM_Vignette.R |only MAGMA.R-1.1/MAGMA.R/inst/doc/MDM_Vignette.Rmd |only MAGMA.R-1.1/MAGMA.R/inst/doc/MDM_Vignette.html |only MAGMA.R-1.1/MAGMA.R/inst/doc/Vignette.R | 90 MAGMA.R-1.1/MAGMA.R/inst/doc/Vignette.Rmd | 56 MAGMA.R-1.1/MAGMA.R/inst/doc/Vignette.html | 1786 +++++----- MAGMA.R-1.1/MAGMA.R/man/MAGMA.Rd | 23 MAGMA.R-1.1/MAGMA.R/man/MAGMA_exact.Rd | 24 MAGMA.R-1.1/MAGMA.R/man/Plot_MAGMA.Rd | 6 MAGMA.R-1.1/MAGMA.R/man/Table_MAGMA.Rd | 8 MAGMA.R-1.1/MAGMA.R/man/initial_unbalance.Rd | 5 MAGMA.R-1.1/MAGMA.R/vignettes/Balance_2x2_MDM.rds |only MAGMA.R-1.1/MAGMA.R/vignettes/Balance_2x2_exact_MDM.rds |only MAGMA.R-1.1/MAGMA.R/vignettes/Balance_gifted_MDM.rds |only MAGMA.R-1.1/MAGMA.R/vignettes/Balance_gifted_exact_MDM.rds |only MAGMA.R-1.1/MAGMA.R/vignettes/Balance_tar_MDM.rds |only MAGMA.R-1.1/MAGMA.R/vignettes/Balance_tar_exact_MDM.rds |only MAGMA.R-1.1/MAGMA.R/vignettes/MDM_Vignette.Rmd |only MAGMA.R-1.1/MAGMA.R/vignettes/Vignette.Rmd | 56 MAGMA.R-1.1/MAGMA.R/vignettes/data_2x2_matched_MDM.rds |only MAGMA.R-1.1/MAGMA.R/vignettes/data_2x2_matched_exact_MDM.rds |only MAGMA.R-1.1/MAGMA.R/vignettes/data_gifted_matched_MDM.rds |only MAGMA.R-1.1/MAGMA.R/vignettes/data_gifted_matched_exact_MDM.rds |only MAGMA.R-1.1/MAGMA.R/vignettes/data_tar_matched_MDM.rds |only MAGMA.R-1.1/MAGMA.R/vignettes/data_tar_matched_exact_MDM.rds |only 40 files changed, 1805 insertions(+), 1372 deletions(-)
Title: Robust Probabilistic Matching of Company Names
Description: A pipeline for matching messy company name strings against a clean dictionary (e.g., 'Orbis').
Implements a cascading strategy: Exact -> Fuzzy ('zoomerjoin') -> 'FTS5' ('SQLite') -> Rarity Weighted.
Name normalization covers German, French, Italian and English legal forms and conventions,
which suits multilingual registers such as the Swiss one.
Normalization discards detail, so several dictionary entries can collapse onto one string;
these groups are matched once and a crosswalk back to every original entry is retained.
References: Beniamino Green (2025) <https://github.com/beniaminogreen/zoomerjoin>; <https://www.sqlite.org/fts5.html>.
Author: Giulian Etingin-Frati [aut, cre]
Maintainer: Giulian Etingin-Frati <etingin-frati@kof.ethz.ch>
Diff between firmmatchr versions 0.1.3 dated 2026-03-06 and 0.2.0 dated 2026-07-28
DESCRIPTION | 25 + MD5 | 35 +- NAMESPACE | 73 ++--- NEWS.md | 147 ++++++++-- R/crosswalk.R |only R/engines.R | 28 + R/globals.R | 20 - R/match_pipeline.R | 570 +++++++++++++++++++++++++++------------- R/normalize.R | 310 +++++++++++++++++---- README.md | 420 +++++++++++++++++++---------- inst/WORDLIST | 13 man/azure_chat_request.Rd | 70 ++-- man/company_name_stopwords.Rd |only man/dict_crosswalk.Rd |only man/expand_matches.Rd |only man/match_companies.Rd | 214 +++++++++------ man/normalize_company_name.Rd | 128 +++++++- man/validate_matches_llm.Rd | 134 ++++----- tests/testthat/helper-quiet.R |only tests/testthat/test-match.R | 278 +++++++++++++++++-- tests/testthat/test-normalize.R | 201 +++++++++++++- 21 files changed, 1924 insertions(+), 742 deletions(-)
Title: EM Algorithm for Model-Based Clustering of Finite Mixture
Gaussian Distribution
Description: EM algorithms and several efficient
initialization methods for model-based clustering of finite
mixture Gaussian distribution with unstructured dispersion
in both of unsupervised and semi-supervised learning.
Author: Wei-Chen Chen [aut, cre],
Ranjan Maitra [aut],
Volodymyr Melnykov [ctb],
Dan Nettleton [ctb],
David Faden [ctb],
Rouben Rostamian [ctb],
R Core team [ctb]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between EMCluster versions 0.2-17 dated 2025-01-08 and 0.2-18 dated 2026-07-28
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/EMCluster-guide.pdf |binary vignettes/EMCluster-include/EMCluster.bib | 12 ++++++++++-- 5 files changed, 21 insertions(+), 10 deletions(-)
Title: Robust Distance-Based Visualization and Analysis of Mixed-Type
Data
Description: Robust distance-based methods applied to matrices and data frames, producing distance matrices that can be used as input for various visualization techniques such as graphs, heatmaps, or multidimensional scaling configurations. See Boj and Grané (2024) <doi:10.1016/j.seps.2024.101992>, Boj et al. (2026) <doi:10.1007/s10260-026-00860-1>, and Grané et al. (2026) <doi:10.1007/s10182-026-00565-6>.
Author: Marcos Alvarez [aut],
Eva Boj [aut, cre],
Aurea Grane [aut]
Maintainer: Eva Boj <evaboj@ub.edu>
Diff between dbrobust versions 1.1.0 dated 2026-07-23 and 1.1.1 dated 2026-07-28
DESCRIPTION | 10 - MD5 | 14 - NEWS.md | 7 R/robust_distances.R | 11 - build/partial.rdb |binary inst/REFERENCES.bib | 127 ++++++++-------- man/calculate_distances.Rd | 356 ++++++++++++++++++++++----------------------- man/robust_distances.Rd | 11 - 8 files changed, 280 insertions(+), 256 deletions(-)
Title: Cosmic Insights: Statistical Frameworks for Astronomers
Description: A comprehensive toolkit for astronomical and cosmological
computations. Provides functions for angular coordinate conversions
(degrees, hours-minutes-seconds, degrees-minutes-seconds, and radians),
access to fundamental physical constants, queries to the Gaia Archive TAP
(Table Access Protocol) service, cosmological distance calculations,
early-universe thermal physics including photon density, 'Saha' equation
solutions, and a full thermal-cosmology module covering the Hubble rate in
the radiation-dominated era, effective relativistic degrees of freedom,
entropy density, equilibrium yields, the Boltzmann relic-abundance
('pebble') equation for WIMP freeze-out, the freeze-out temperature solver,
and the Peebles equation for hydrogen recombination. Also includes the
Drake equation for estimating the number of communicating extraterrestrial
civilisations in the Milky Way.
Author: Samrit Pramanik [aut, cre] ,
Kazi Abu Rousan [aut]
Maintainer: Samrit Pramanik <samrit.2442@gmail.com>
Diff between astronomR versions 0.1.0 dated 2026-05-27 and 0.3.0 dated 2026-07-28
DESCRIPTION | 20 +-- LICENSE | 2 MD5 | 28 +++- NAMESPACE | 10 + NEWS.md | 60 ++++++++- R/00_constants.R | 2 R/07_drake_equation.R |only R/08_thermal_cosmology.R |only README.md | 212 +++++++++++++++++++++++++++----- inst/cran_submission_checklist.md |only man/boltzmann_pebble_rhs.Rd |only man/constants_df.Rd | 10 - man/drake_equation.Rd |only man/entropy_density.Rd |only man/equilibrium_number_density.Rd |only man/equilibrium_yield.Rd |only man/freeze_out_xf.Rd |only man/g_star_eff.Rd |only man/hubble_radiation.Rd |only man/peebles_rhs.Rd |only man/solve_relic_abundance.Rd |only tests/testthat/test-thermal_cosmology.R |only 22 files changed, 293 insertions(+), 51 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-07 1.1.0
2015-11-13 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-18 1.2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-05 0.2.9
2023-03-05 0.2.8
2022-08-22 0.2.5
2022-01-25 0.2.1
2022-01-12 0.2.0
2021-10-13 0.1.9
2021-09-30 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-22 1.0
2021-06-07 0.9
2020-04-29 0.8
Title: 'DuckDB' High Throughput Sequencing File Formats Reader
Extension
Description: Bundles the 'duckhts' 'DuckDB' extension for reading High Throughput
Sequencing file formats with 'DuckDB'. The 'DuckDB' C extension API
<https://duckdb.org/docs/stable/clients/c/api> and its 'htslib' dependency are
compiled from vendored sources during package installation. James K Bonfield and co-authors (2021) <doi:10.1093/gigascience/giab007>. VariantKey / RegionKey support follows Nicola Asuni (2018) <doi:10.1101/473744>.
Author: Sounkou Mahamane Toure [aut, cre],
James K Bonfield, John Marshall,Petr Danecek ,Heng Li , Valeriu Ohan,
Andrew Whitwham,Thomas Keane , Robert M Davies [ctb] ,
Brent Pedersen [cph] ,
Giulio Genovese [cph] ,
Nicola Asuni [cph] ,
Devon Ryan [cph] ,
Duc [...truncated...]
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>
Diff between Rduckhts versions 1.5.0-0.1.0 dated 2026-07-24 and 1.5.1-0.1.3 dated 2026-07-28
DESCRIPTION | 10 MD5 | 150 +++--- NAMESPACE | 1 NEWS.md | 42 + R/bootstrap.R | 34 - R/duckhts.R | 187 ++++++-- configure | 51 +- configure.win | 85 +++ inst/duckhts_extension/bam_bed_coverage.c | 35 - inst/duckhts_extension/bcf_reader.c | 11 inst/duckhts_extension/bcftools_norm_udf.c | 3 inst/duckhts_extension/cgranges.c | 2 inst/duckhts_extension/cgranges_api.c | 224 ---------- inst/duckhts_extension/duckvep/duckvep_annotate.c | 18 inst/duckhts_extension/duckvep/duckvep_model.c | 3 inst/duckhts_extension/duckvep/duckvep_sql.c | 57 +- inst/duckhts_extension/duckvep/duckvep_variant_tile.c | 8 inst/duckhts_extension/duckvep/duckvep_variant_tile.h | 7 inst/duckhts_extension/duckvep/kernel/include/duckvep_kernel.h | 6 inst/duckhts_extension/duckvep/kernel/src/duckvep_delta.c | 18 inst/duckhts_extension/duckvep/kernel/src/duckvep_delta.h | 2 inst/duckhts_extension/duckvep/kernel/src/duckvep_event.h | 59 ++ inst/duckhts_extension/duckvep/kernel/src/duckvep_kernel.c | 96 +++- inst/duckhts_extension/duckvep/kernel/src/duckvep_projection.c | 65 ++ inst/duckhts_extension/duckvep/kernel/src/duckvep_projection.h | 8 inst/duckhts_extension/fastq_qc.c | 8 inst/duckhts_extension/libBigWig/bwRead.c | 2 inst/duckhts_extension/liftover_udf.c | 4 inst/duckhts_extension/mosdepth_table.c | 5 inst/duckhts_extension/samtools_idxstats_table.c | 9 inst/duckhts_extension/vep_parser.c | 4 inst/function_catalog/functions.md | 2 inst/function_catalog/functions.tsv | 2 inst/function_catalog/functions.yaml | 2 inst/htslib_config.R.in | 1 inst/tinytest/test_bam_bed_coverage.R | 5 inst/tinytest/test_bam_file_offset.R | 7 inst/tinytest/test_basic.R | 5 inst/tinytest/test_bcf.R | 15 inst/tinytest/test_bcf_regression.R | 15 inst/tinytest/test_bcftools_norm.R | 5 inst/tinytest/test_bigwig.R | 4 inst/tinytest/test_bin_counts.R | 5 inst/tinytest/test_cgranges_api.R | 5 inst/tinytest/test_cigar_utils.R | 5 inst/tinytest/test_connection.R |only inst/tinytest/test_convert_parquet.R | 14 inst/tinytest/test_duckvep.R | 59 ++ inst/tinytest/test_fastq_qc.R | 4 inst/tinytest/test_htslib_contract.R | 17 inst/tinytest/test_indexes_bgzip.R | 5 inst/tinytest/test_integration.R | 10 inst/tinytest/test_intervals.R | 5 inst/tinytest/test_liftover.R | 5 inst/tinytest/test_liftover_stress.R | 5 inst/tinytest/test_mosdepth.R | 5 inst/tinytest/test_multi.R | 4 inst/tinytest/test_munge.R | 5 inst/tinytest/test_munge_threading.R | 5 inst/tinytest/test_parallel_empty_contigs.R | 5 inst/tinytest/test_pileup.R | 6 inst/tinytest/test_quality_encoding.R | 4 inst/tinytest/test_samtools_idxstats.R | 5 inst/tinytest/test_score.R | 5 inst/tinytest/test_seq_ops.R | 6 inst/tinytest/test_variantkey_regionkey.R | 5 man/detect_complex_types.Rd | 3 man/duckhts_load.Rd | 6 man/extract_array_element.Rd | 3 man/extract_map_data.Rd | 3 man/rduckhts_bam.Rd | 3 man/rduckhts_bcf.Rd | 3 man/rduckhts_connect.Rd |only man/rduckhts_htslib_config.Rd | 3 man/rduckhts_htslib_info.Rd | 5 man/rduckhts_load.Rd | 26 - man/rduckhts_simd_backend.Rd | 3 77 files changed, 840 insertions(+), 689 deletions(-)
Title: Nonparametric Multiple Change Point Detection Using Wild Binary
Segmentation
Description: Implements nonparametric multiple change-point detection for
univariate sequences using Wild Binary Segmentation, as described in
Ross (2026) "Nonparametric Detection of Multiple Location-Scale Change
Points via Wild Binary Segmentation"
<doi:10.48550/arXiv.2107.01742>. The package provides Mann--Whitney,
Mood, Lepage, Cramér--von Mises, and modified Baumgartner rank-based
statistics, together with method-specific thresholds for controlling
the probability of incorrectly detecting a change point in a homogeneous
sequence.
Author: Gordon J. Ross [aut, cre]
Maintainer: Gordon J. Ross <gordon.ross@ed.ac.uk>
Diff between npwbs versions 0.3.0 dated 2026-05-02 and 0.4.0 dated 2026-07-28
DESCRIPTION | 24 +++- MD5 | 24 ++-- NAMESPACE | 4 NEWS.md | 8 + R/RcppExports.R |only R/package-functions.R | 275 ++++++++++++++++++-------------------------------- R/sysdata.rda |binary inst/CITATION | 4 man/detectChanges.Rd | 15 +- src |only tests/test-package.R | 163 ++++++++++++++++------------- 11 files changed, 244 insertions(+), 273 deletions(-)
Title: Liu Regression with Liu Biasing Parameters and Statistics
Description: Linear Liu regression coefficient's estimation and testing with different Liu related measures such as MSE, R-squared etc.
REFERENCES
i. Akdeniz and Kaciranlar (1995) \doi{10.1080/03610929508831585}
ii. Druilhet and Mom (2008) \doi{10.1016/j.jmva.2006.06.011}
iii. Imdadullah, Aslam, and Saima (2017)
iv. Liu (1993) \doi{10.1080/03610929308831027}
v. Liu (2001) \doi{10.1016/j.jspi.2010.05.030}.
Author: Imdad Ullah Muhammad [aut, cre] ,
Aslam Muhammad [aut, ctb]
Maintainer: Imdad Ullah Muhammad <mimdadasad@gmail.com>
Diff between liureg versions 1.1.2 dated 2018-04-08 and 1.1.3 dated 2026-07-28
DESCRIPTION | 36 +++++++++++++++++++++--------------- MD5 | 31 ++++++++++++++++--------------- build |only inst/CITATION | 48 +++++++++++++++++++----------------------------- inst/NEWS.Rd | 13 +++++++++++++ man/dest.Rd | 8 ++++---- man/hatl.Rd | 2 +- man/infoliu.Rd | 6 +++--- man/liu.Rd | 6 +++--- man/lstats.liu.Rd | 10 +++++----- man/plot.biasliu.Rd | 2 +- man/plot.infoliu.Rd | 2 +- man/plot.liu.Rd | 2 +- man/press.liu.Rd | 8 ++++---- man/residuals.liu.Rd | 4 ++-- man/summary.liu.Rd | 4 ++-- man/vcov.liu.Rd | 6 +++--- 17 files changed, 99 insertions(+), 89 deletions(-)
Title: Bayesian Latent Gaussian Modelling using INLA and Extensions
Description: Facilitates spatial and general latent Gaussian modelling using
integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>).
Additionally, extends the GAM-like model class to more general nonlinear predictor
expressions, and implements a log Gaussian Cox process likelihood for
modelling univariate and spatial point processes based on ecological survey data.
Model components are specified with general inputs and mapping methods to the
latent variables, and the predictors are specified via general R expressions,
with separate expressions for each observation likelihood model in
multi-likelihood models. A prediction method based on fast Monte Carlo sampling
allows posterior prediction of general expressions of the latent variables.
Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019)
<doi:10.1111/2041-210X.13168>.
Author: Finn Lindgren [aut, cre, cph] ,
Fabian E. Bachl [aut, cph] ,
David L. Borchers [ctb, dtc, cph] ,
Daniel Simpson [ctb, cph] ,
Lindesay Scott-Howard [ctb, dtc, cph] ,
Andy Seaton [ctb] ,
Man Ho Suen [ctb, cph] ,
Pierre Roudier [ctb, cph] ,
Tim Meehan [ [...truncated...]
Maintainer: Finn Lindgren <finn.lindgren@gmail.com>
Diff between inlabru versions 2.14.1 dated 2026-05-01 and 2.15.0 dated 2026-07-28
inlabru-2.14.1/inlabru/inst/misc/2d_lgcp_residuals_functions_sf.R |only inlabru-2.14.1/inlabru/man/bm_mesh_B.Rd |only inlabru-2.14.1/inlabru/man/bru_log_new.Rd |only inlabru-2.14.1/inlabru/man/ibm_linear.Rd |only inlabru-2.14.1/inlabru/man/predict.bru.Rd |only inlabru-2.14.1/inlabru/tests/testthat/f.txt |only inlabru-2.14.1/inlabru/tests/testthat/test-mapper.R |only inlabru-2.14.1/inlabru/tests/testthat/test-skips.R |only inlabru-2.15.0/inlabru/DESCRIPTION | 74 inlabru-2.15.0/inlabru/MD5 | 370 - inlabru-2.15.0/inlabru/NAMESPACE | 129 inlabru-2.15.0/inlabru/NEWS.md | 41 inlabru-2.15.0/inlabru/R/access_trace.R | 9 inlabru-2.15.0/inlabru/R/bru.gof.R | 26 inlabru-2.15.0/inlabru/R/bru.inference.R | 2083 +++++----- inlabru-2.15.0/inlabru/R/bru_conversion.R | 12 inlabru-2.15.0/inlabru/R/bru_index.R | 53 inlabru-2.15.0/inlabru/R/bru_input.R | 191 inlabru-2.15.0/inlabru/R/bru_is.R | 193 inlabru-2.15.0/inlabru/R/bru_sp.R | 41 inlabru-2.15.0/inlabru/R/data.gorillas.R | 2 inlabru-2.15.0/inlabru/R/data.mexdolphin.R | 4 inlabru-2.15.0/inlabru/R/deltaIC.R | 2 inlabru-2.15.0/inlabru/R/effect.R | 597 +- inlabru-2.15.0/inlabru/R/environment.R | 226 - inlabru-2.15.0/inlabru/R/fmesher.R | 7 inlabru-2.15.0/inlabru/R/gcpo.R |only inlabru-2.15.0/inlabru/R/ggplot.R | 196 inlabru-2.15.0/inlabru/R/hexagon_tiling.R | 29 inlabru-2.15.0/inlabru/R/hierarchical_basis.R | 52 inlabru-2.15.0/inlabru/R/inla.R | 257 - inlabru-2.15.0/inlabru/R/inlabru-package.R | 6 inlabru-2.15.0/inlabru/R/inlabru-reexports.R |only inlabru-2.15.0/inlabru/R/legacy_methods.R |only inlabru-2.15.0/inlabru/R/local_testthat.R | 50 inlabru-2.15.0/inlabru/R/mapper_collect.R | 163 inlabru-2.15.0/inlabru/R/mapper_expr.R |only inlabru-2.15.0/inlabru/R/mapper_repeat.R | 63 inlabru-2.15.0/inlabru/R/mapper_sum.R | 76 inlabru-2.15.0/inlabru/R/mappers.R | 956 ++-- inlabru-2.15.0/inlabru/R/model.R | 1358 +++--- inlabru-2.15.0/inlabru/R/nlinla.R | 162 inlabru-2.15.0/inlabru/R/object_upgrade.R | 164 inlabru-2.15.0/inlabru/R/plotsample.R | 46 inlabru-2.15.0/inlabru/R/pred_expr.R | 200 inlabru-2.15.0/inlabru/R/rgl.R | 78 inlabru-2.15.0/inlabru/R/sampling.R | 90 inlabru-2.15.0/inlabru/R/spatstat.R | 26 inlabru-2.15.0/inlabru/R/spde.R | 78 inlabru-2.15.0/inlabru/R/stack.R | 10 inlabru-2.15.0/inlabru/R/tidiers.R |only inlabru-2.15.0/inlabru/R/track_plotting.R | 164 inlabru-2.15.0/inlabru/R/transformation.R | 8 inlabru-2.15.0/inlabru/R/used.R | 409 + inlabru-2.15.0/inlabru/R/utils.R | 173 inlabru-2.15.0/inlabru/README.md | 145 inlabru-2.15.0/inlabru/build/partial.rdb |binary inlabru-2.15.0/inlabru/build/vignette.rds |binary inlabru-2.15.0/inlabru/inst/doc/articles.html | 6 inlabru-2.15.0/inlabru/inst/doc/classes.html | 358 + inlabru-2.15.0/inlabru/inst/doc/component.html | 2 inlabru-2.15.0/inlabru/inst/doc/linearapprox.html | 8 inlabru-2.15.0/inlabru/inst/doc/prediction_scores.html | 64 inlabru-2.15.0/inlabru/inst/misc/2d_lgcp_residuals_functions.R | 129 inlabru-2.15.0/inlabru/inst/misc/2d_lgcp_residuals_functions_sp.R |only inlabru-2.15.0/inlabru/man/augment.bru.Rd |only inlabru-2.15.0/inlabru/man/bm_aggregate.Rd | 48 inlabru-2.15.0/inlabru/man/bm_collect.Rd | 45 inlabru-2.15.0/inlabru/man/bm_const.Rd | 48 inlabru-2.15.0/inlabru/man/bm_expr.Rd |only inlabru-2.15.0/inlabru/man/bm_factor.Rd | 48 inlabru-2.15.0/inlabru/man/bm_fm_mesh_1d.Rd | 47 inlabru-2.15.0/inlabru/man/bm_fmesher.Rd | 45 inlabru-2.15.0/inlabru/man/bm_harmonics.Rd | 48 inlabru-2.15.0/inlabru/man/bm_index.Rd | 50 inlabru-2.15.0/inlabru/man/bm_linear.Rd | 48 inlabru-2.15.0/inlabru/man/bm_logitaverage.Rd | 48 inlabru-2.15.0/inlabru/man/bm_logsumexp.Rd | 48 inlabru-2.15.0/inlabru/man/bm_marginal.Rd | 54 inlabru-2.15.0/inlabru/man/bm_matrix.Rd | 48 inlabru-2.15.0/inlabru/man/bm_multi.Rd | 47 inlabru-2.15.0/inlabru/man/bm_pipe.Rd | 48 inlabru-2.15.0/inlabru/man/bm_reparam.Rd | 48 inlabru-2.15.0/inlabru/man/bm_repeat.Rd | 45 inlabru-2.15.0/inlabru/man/bm_scale.Rd | 48 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inlabru-2.15.0/inlabru/tests/testthat/test-multi_like.R | 27 inlabru-2.15.0/inlabru/tests/testthat/test-response_size.R | 100 inlabru-2.15.0/inlabru/tests/testthat/test-tidiers.R |only 202 files changed, 8982 insertions(+), 5457 deletions(-)
Title: Gradient Projection Factor Rotation
Description: Gradient projection algorithms for orthogonal and oblique rotation
of factor loadings matrices in factor analysis. Implements a comprehensive
set of rotation criteria including quartimax, quartimin, oblimin, geomin,
simplimax, the Crawford-Ferguson family, and target rotation, among others.
Supports multiple random starts. For details see Bernaards and Jennrich (2005)
<doi:10.1177/0013164404272507>.
Author: Coen Bernaards [aut, cre],
Paul Gilbert [aut],
Robert Jennrich [aut]
Maintainer: Coen Bernaards <cab.gparotation@gmail.com>
Diff between GPArotation versions 2026.6-1 dated 2026-06-18 and 2026.7-1 dated 2026-07-28
DESCRIPTION | 6 MD5 | 46 - NEWS | 7 data/Thurstone.rda |binary inst/doc/GPA1guide.pdf |binary inst/doc/GPA2local.pdf |binary inst/doc/GPA3bifactor.pdf |binary inst/doc/GPA4fitstats.pdf |binary man/00.GPArotation.Rd | 1 man/Thurstone.Rd | 22 tests/Harman.R | 4 tests/Jennrich2002.R | 80 -- tests/KaiserNormalization.R | 6 tests/MASSoblimin.R | 4 tests/Revelle.R | 2 tests/Thurstone.R | 4 tests/WansbeekMeijer.R | 4 tests/diagnosticsTests.R |only tests/errormessages.R | 4 tests/legacyVsBB_extra.R |only tests/lp.R | 132 +-- tests/print-GPArotation.R | 4 tests/rotations.R | 1587 +++++++++++++++++++++----------------------- tests/rotationsRS.R | 968 ++++++++++++-------------- tests/varimaxVarimax.R | 4 25 files changed, 1344 insertions(+), 1541 deletions(-)
Title: Tools for Fast Computing and Visualizing Euclidean Minimum
Spanning Trees
Description: Fast and easy computation of Euclidean Minimum Spanning Trees (EMST) from data,
relying on the R API for 'mlpack' - the C++ Machine Learning Library (Curtin et. al., 2013).
'emstreeR' uses the Dual-Tree Boruvka (March, Ram, Gray, 2010, <doi:10.1145/1835804.1835882>),
which is theoretically and empirically the fastest algorithm for computing an EMST. This package also provides
functions and an S3 method for readily visualizing Minimum Spanning Trees (MST) using either the
style of the 'base', 'scatterplot3d', or 'ggplot2' libraries; and functions to export the MST output to shapefiles.
Author: Allan Quadros [aut, cre],
Duncan Garmonsway [ctb]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between emstreeR versions 3.1.3 dated 2025-12-17 and 3.2.0 dated 2026-07-28
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/ComputeMST.R | 6 +++++- 3 files changed, 12 insertions(+), 8 deletions(-)
Title: Plots the CHOIR Body Map
Description: Collection of utility functions for visualizing
body map data collected with the Collaborative Health Outcomes
Information Registry.
Author: Eric Cramer [aut, cre] ,
Stanford University School of Medicine [cph, fnd]
Maintainer: Eric Cramer <dev.emc503@gmail.com>
Diff between CHOIRBM versions 0.0.2 dated 2021-02-15 and 0.0.3 dated 2026-07-28
DESCRIPTION | 16 MD5 | 84 +++- NAMESPACE | 24 + NEWS.md | 51 +- R/agg_choirbm_list.R |only R/comp_choirbm_chi.R |only R/comp_choirbm_glm.R |only R/comp_choirbm_ztest.R |only R/comp_cooccurrence.R |only R/convert_bodymap.R |only R/convert_bodymaps.R |only R/gen_example_data.R | 66 +-- R/globals.R | 2 R/num_areas.R |only R/plot_cooccurrence.R |only R/plot_female_choirbm.R | 72 +-- R/plot_male_choirbm.R | 70 +-- R/plot_nareas_histogram.R |only R/prep_bodymap.R |only R/string_to_map.R | 72 ++- R/validation.R | 64 +-- README.md | 202 +++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/calc-cooccurrence.R |only inst/doc/calc-cooccurrence.Rmd |only inst/doc/calc-cooccurrence.html |only inst/doc/choir-db-ex.R |only inst/doc/choir-db-ex.Rmd |only inst/doc/choir-db-ex.html |only inst/doc/compare-choirbms.R |only inst/doc/compare-choirbms.Rmd |only inst/doc/compare-choirbms.html |only inst/doc/convert_bodymaps.R |only inst/doc/convert_bodymaps.Rmd |only inst/doc/convert_bodymaps.html |only inst/doc/plot-one-patient.R | 32 - inst/doc/plot-one-patient.Rmd | 74 ++-- inst/doc/plot-one-patient.html | 570 +++++++++++++++++++++---------- inst/img |only man/CHOIRBM-package.Rd | 6 man/agg_choirbm_list.Rd |only man/comp_choirbm_chi.Rd |only man/comp_choirbm_glm.Rd |only man/comp_choirbm_ztest.Rd |only man/comp_cooccurrence.Rd |only man/convert_bodymap.Rd |only man/convert_bodymaps.Rd |only man/num_areas.Rd |only man/plot_cooccurrence.Rd |only man/plot_nareas_histogram.Rd |only man/prep_bodymaps.Rd |only man/string_to_map.Rd | 9 tests/testthat.R | 8 tests/testthat/test-agg-choirbm-list.R |only tests/testthat/test-comp-choirbm-glm.R |only tests/testthat/test-comp-concurrence.R |only tests/testthat/test-comp_choirbm_ztest.R |only tests/testthat/test-num_areas.R |only tests/testthat/test-string-to-map.R | 44 +- vignettes/calc-cooccurrence.Rmd |only vignettes/choir-db-ex.Rmd |only vignettes/compare-choirbms.Rmd |only vignettes/convert_bodymaps.Rmd |only vignettes/plot-one-patient.Rmd | 74 ++-- 65 files changed, 932 insertions(+), 608 deletions(-)
Title: Analyze Multiple Exposure Realizations in Association Studies
Description: Analyze association studies with multiple realizations of a noisy or uncertain exposure. These can be obtained from e.g. a two-dimensional Monte Carlo dosimetry system (Simon et al 2015 <doi:10.1667/RR13729.1>) to characterize exposure uncertainty.
The implemented methods are regression calibration (Carroll et al. 2006 <doi:10.1201/9781420010138>), extended
regression calibration (Little et al. 2023 <doi:10.1038/s41598-023-42283-y>), Monte Carlo maximum
likelihood (Stayner et al. 2007 <doi:10.1667/RR0677.1>), frequentist model averaging (Kwon et al. 2023 <doi:10.1371/journal.pone.0290498>),
and Bayesian model averaging (Kwon et al. 2016 <doi:10.1002/sim.6635>). Supported model families are
Gaussian, binomial, multinomial, Poisson, proportional hazards, and conditional logistic.
Author: Sander Roberti [aut, cre] ,
William Wheeler [aut],
Deukwoo Kwon [aut] ,
Ruth Pfeiffer [ctb] ,
NCI [cph, fnd]
Maintainer: Sander Roberti <statspackages@sanderroberti.nl>
Diff between ameras versions 0.5.1 dated 2026-07-16 and 0.5.2 dated 2026-07-28
DESCRIPTION | 10 MD5 | 56 +-- NEWS.md | 17 + R/ameras.R | 1 R/likelihoods.R | 262 ++++++++++++++++-- R/methods-fma-bma.R | 32 +- R/methods-rc-mcml.R | 19 + R/modifier-design.R | 37 +- R/optimization.R | 3 R/timing.R | 4 R/utils.R | 56 ++- README.md | 24 - inst/doc/confidenceintervals.html | 14 inst/doc/modelfitting.html | 416 ++++++++++++++--------------- inst/doc/parallelfma.Rmd | 13 inst/doc/parallelfma.html | 30 +- inst/doc/relativeriskmodels.html | 12 inst/doc/standardanalysis.html | 4 inst/doc/transformations.html | 10 man/ameras-package.Rd | 2 man/ameras.Rd | 10 man/confint.Rd | 6 man/summary.Rd | 6 tests/testthat/test-fma-assembler.R | 3 tests/testthat/test-fma-edge-cases.R | 34 ++ tests/testthat/test-modifier-formulas.R | 132 ++++++++- tests/testthat/test-optimization-helpers.R | 5 tests/testthat/test-timing.R | 21 - vignettes/parallelfma.Rmd | 13 29 files changed, 861 insertions(+), 391 deletions(-)
Title: Parametric Statistical Modelling and Inference for the
'spatstat' Family
Description: Functionality for parametric statistical modelling and inference for spatial data,
mainly spatial point patterns, in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Supports parametric modelling, formal statistical inference, and model validation.
Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope t [...truncated...]
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb, cph],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Julian Gilbey [ctb],
Yongtao [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.model versions 3.7-1 dated 2026-05-29 and 3.7-2 dated 2026-07-28
DESCRIPTION | 16 MD5 | 103 ++--- NAMESPACE | 11 NEWS | 67 +++ R/addvar.R | 716 +++++++++++++++++++++++------------------ R/aucmodel.R | 3 R/detPPF-class.R | 8 R/detpointprocfamilyfun.R | 4 R/dppm.R | 4 R/dppmclass.R | 7 R/ic.kppm.R | 7 R/kppm.R | 19 - R/kppmMinCon.R | 4 R/mincontrast.R | 27 - R/objsurf.R | 353 ++++++++++++++++---- R/palmdiagnose.R | 46 +- R/parres.R | 45 ++ R/rhohat.R | 6 R/rhohat.slrm.R | 6 R/sysdata.rda |binary R/vcov.kppm.R | 12 build/partial.rdb |binary inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/HierHard.Rd | 18 - man/HierStrauss.Rd | 18 - man/HierStraussHard.Rd | 17 man/LennardJones.Rd | 14 man/Penttinen.Rd | 5 man/addvar.Rd | 66 +++ man/auc.ppm.Rd | 6 man/cdf.test.Rd | 6 man/cdf.test.mppm.Rd | 10 man/dppm.Rd | 22 + man/kppm.Rd | 16 man/macros/defns.Rd | 30 + man/objsurf.Rd | 18 - man/palmdiagnose.Rd | 30 + man/parres.Rd | 9 man/plot.kppm.Rd | 8 man/ppm.Rd | 20 - man/profilepl.Rd | 16 man/rhohat.Rd | 11 man/slrm.Rd | 30 - man/spatstat.model-internal.Rd | 9 man/spatstat.model-package.Rd | 86 +++- man/vcov.dppm.Rd |only man/vcov.kppm.Rd | 4 man/vcov.ppm.Rd | 15 tests/testsD.R | 13 tests/testsL.R | 30 - tests/testsT.R | 57 --- tests/testsUtoZ.R | 11 53 files changed, 1332 insertions(+), 729 deletions(-)
More information about spatstat.model at CRAN
Permanent link
Title: Benchmarking and Visualization Toolkit for Penalized Cox Models
Description: Creates nomogram visualizations for penalized Cox regression
models, with the support of reproducible survival model building,
validation, calibration, and comparison for high-dimensional data.
Author: Nan Xiao [aut, cre] ,
Qing-Song Xu [aut],
Miao-Zhu Li [aut],
Frank Harrell [ctb] ,
Sergej Potapov [ctb] ,
Werner Adler [ctb] ,
Matthias Schmid [ctb]
Maintainer: Nan Xiao <me@nanx.me>
Diff between hdnom versions 6.2.0 dated 2026-05-12 and 6.2.1 dated 2026-07-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 7 +++++++ R/2_2_convert_model.R | 2 +- build/vignette.rds |binary 5 files changed, 15 insertions(+), 8 deletions(-)
Title: Extensible Derivative Pricing and Risk Analytics
Description: Tools for pricing and analysing financial derivatives under
the classical lognormal diffusion model and geometric Brownian motion
assumptions. The package provides analytical European option prices,
Monte Carlo pricing with antithetic and control variates, confidence
intervals, finite-difference Greeks, and path simulation for
path-dependent payoffs. The simulation interfaces accept user-defined
payoff functions, enabling transparent construction of custom contracts
while reporting numerical uncertainty.
Author: Amit Kumar Jha [aut, cre, cph]
Maintainer: Amit Kumar Jha <jha.8@iitj.ac.in>
Diff between CustomDerivative versions 0.1.1 dated 2023-09-30 and 0.2.0 dated 2026-07-28
CustomDerivative-0.1.1/CustomDerivative/R/custom.R |only CustomDerivative-0.1.1/CustomDerivative/tests/testthat/test-custom_derivative.R |only CustomDerivative-0.2.0/CustomDerivative/DESCRIPTION | 31 CustomDerivative-0.2.0/CustomDerivative/MD5 | 27 CustomDerivative-0.2.0/CustomDerivative/NAMESPACE | 19 CustomDerivative-0.2.0/CustomDerivative/NEWS.md |only CustomDerivative-0.2.0/CustomDerivative/R/black-scholes.R |only CustomDerivative-0.2.0/CustomDerivative/R/greeks.R |only CustomDerivative-0.2.0/CustomDerivative/R/legacy-r6.R |only CustomDerivative-0.2.0/CustomDerivative/R/monte-carlo.R |only CustomDerivative-0.2.0/CustomDerivative/R/path-dependent.R |only CustomDerivative-0.2.0/CustomDerivative/R/validation.R |only CustomDerivative-0.2.0/CustomDerivative/README.md |only CustomDerivative-0.2.0/CustomDerivative/man/CustomDerivative.Rd | 313 ++-------- CustomDerivative-0.2.0/CustomDerivative/man/asian_call_payoff.Rd |only CustomDerivative-0.2.0/CustomDerivative/man/black_scholes_price.Rd |only CustomDerivative-0.2.0/CustomDerivative/man/down_and_out_call_payoff.Rd |only CustomDerivative-0.2.0/CustomDerivative/man/finite_difference_greeks.Rd |only CustomDerivative-0.2.0/CustomDerivative/man/payoff_helpers.Rd |only CustomDerivative-0.2.0/CustomDerivative/man/price_european_mc.Rd |only CustomDerivative-0.2.0/CustomDerivative/man/price_path_dependent_mc.Rd |only CustomDerivative-0.2.0/CustomDerivative/man/simulate_gbm_paths.Rd |only CustomDerivative-0.2.0/CustomDerivative/tests/testthat.R |only CustomDerivative-0.2.0/CustomDerivative/tests/testthat/test-legacy-api.R |only CustomDerivative-0.2.0/CustomDerivative/tests/testthat/test-pricing.R |only 25 files changed, 151 insertions(+), 239 deletions(-)
More information about CustomDerivative at CRAN
Permanent link
Title: An IMAP Client for R
Description: A session-based IMAP client that implements the full functionality of
the IMAP4rev1 protocol (RFC 3501), allowing virtually all e-mail operations to be
performed from within R, paving the way for e-mail data analysis.
Author: Allan Quadros [aut, cre] ,
Paul Smith [ctb],
Kurt Hornik [ctb]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between mRpostman versions 1.2.2 dated 2026-07-11 and 1.4.0 dated 2026-07-28
DESCRIPTION | 8 +++--- MD5 | 31 +++++++++++++++++++---- NAMESPACE | 4 +++ R/clean-fetch-results.R | 3 ++ R/clean-msg-text.R | 34 ++++++++++++++++++++++---- R/enron-sandbox.R |only R/ingest-maildir.R |only R/populate-sandbox.R |only R/sandbox-corpus.R |only README.md | 26 +++++++++++++++++++ build/vignette.rds |binary inst/doc/sandbox.R |only inst/doc/sandbox.Rmd |only inst/doc/sandbox.html |only inst/docker |only man/enron_sandbox.Rd |only man/ingest_maildir.Rd |only man/populate_sandbox.Rd |only man/sandbox_corpus.Rd |only tests/testthat/test-clean-msg-text-encoding.R |only tests/testthat/test-enron-header-date.R |only tests/testthat/test-sandbox-corpus.R |only vignettes/sandbox.Rmd |only 23 files changed, 92 insertions(+), 14 deletions(-)
Title: Grouped Hyper Data Frame
Description: To aggregate a hyper data frame, defined in the package 'spatstat.geom', according to a grouping structure. To facilitate downstream analysis based on a "grouped" hyper data frame. The author has retired from academic research. Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications. Backward compatibility with user-code published in <doi:10.1093/bioinformatics/btaf430> is not maintained in versions >= 0.4.0 (June 2026) of this package. The authors of those publications are the appropriate contacts for reproducibility inquiries.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe versions 0.4.3 dated 2026-06-21 and 0.4.4 dated 2026-07-28
groupedHyperframe-0.4.3/groupedHyperframe/R/vectorlist.R |only groupedHyperframe-0.4.3/groupedHyperframe/data/Ki67.rda |only groupedHyperframe-0.4.3/groupedHyperframe/man/Ki67.Rd |only groupedHyperframe-0.4.3/groupedHyperframe/man/as.vectorlist.Rd |only groupedHyperframe-0.4.4/groupedHyperframe/DESCRIPTION | 10 +-- groupedHyperframe-0.4.4/groupedHyperframe/MD5 | 25 +++---- groupedHyperframe-0.4.4/groupedHyperframe/NAMESPACE | 8 -- groupedHyperframe-0.4.4/groupedHyperframe/R/0PACKAGE.R | 19 +---- groupedHyperframe-0.4.4/groupedHyperframe/R/aggregate.hyperframe.R | 2 groupedHyperframe-0.4.4/groupedHyperframe/R/aggregate2.R | 2 groupedHyperframe-0.4.4/groupedHyperframe/R/aug4gam.R | 6 - groupedHyperframe-0.4.4/groupedHyperframe/R/data_doc.R | 33 ---------- groupedHyperframe-0.4.4/groupedHyperframe/R/is_vectorlist.R |only groupedHyperframe-0.4.4/groupedHyperframe/build/partial.rdb |binary groupedHyperframe-0.4.4/groupedHyperframe/man/groupedHyperframe-package.Rd | 2 groupedHyperframe-0.4.4/groupedHyperframe/man/is.vectorlist.Rd | 2 16 files changed, 30 insertions(+), 79 deletions(-)
More information about groupedHyperframe at CRAN
Permanent link
Title: General-to-Specific (GETS) Modelling and Indicator Saturation
Methods
Description: Automated General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting and testing for structural breaks in the mean, see Pretis, Reade and Sucarrat (2018) <doi:10.18637/jss.v086.i03> for an overview of the package. In advanced use, the estimator and diagnostics tests can be fully user-specified, see Sucarrat (2021) <doi:10.32614/RJ-2021-024>.
Author: Genaro Sucarrat [aut, cre] ,
Felix Pretis [aut],
James Reade [aut],
Jonas Kurle [ctb],
Moritz Schwarz [ctb]
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between gets versions 0.38 dated 2024-07-14 and 0.40 dated 2026-07-28
gets-0.38/gets/man/as.arx.lm.Rd |only gets-0.40/gets/DESCRIPTION | 20 gets-0.40/gets/MD5 | 81 gets-0.40/gets/NAMESPACE | 5 gets-0.40/gets/NEWS | 36 gets-0.40/gets/R/gets-base-source.R | 105 gets-0.40/gets/R/gets-internal.R | 2 gets-0.40/gets/R/gets-isat-source.R | 2677 ++++++++++------ gets-0.40/gets/R/gets-larch-source.R | 66 gets-0.40/gets/R/gets-lm-source.R | 25 gets-0.40/gets/R/gets-logitx-source.R | 14 gets-0.40/gets/build/partial.rdb |binary gets-0.40/gets/data/hpdata.rda |binary gets-0.40/gets/data/infldata.rda |binary gets-0.40/gets/data/so2data.rda |binary gets-0.40/gets/data/sp500data.rda |binary gets-0.40/gets/inst/doc/introduction.Rnw | 17 gets-0.40/gets/inst/doc/introduction.pdf |binary gets-0.40/gets/inst/doc/user-defined-gets-and-isat.Rnw | 14 gets-0.40/gets/inst/doc/user-defined-gets-and-isat.pdf |binary gets-0.40/gets/man/ISMatricesLoop.Rd |only gets-0.40/gets/man/ISadditionalblocksearch.Rd |only gets-0.40/gets/man/ISblocksFun.Rd |only gets-0.40/gets/man/arx.Rd | 8 gets-0.40/gets/man/as.arx.Rd |only gets-0.40/gets/man/as.isat.Rd |only gets-0.40/gets/man/as.lm.Rd | 2 gets-0.40/gets/man/blocksFun.Rd | 2 gets-0.40/gets/man/coef.larch.Rd | 2 gets-0.40/gets/man/create.ISmatrices.Rd |only gets-0.40/gets/man/diagnostics.Rd | 2 gets-0.40/gets/man/distorttest.Rd | 4 gets-0.40/gets/man/distorttestboot.Rd | 4 gets-0.40/gets/man/gets-package.Rd | 10 gets-0.40/gets/man/gets.larch.Rd | 10 gets-0.40/gets/man/getsm.Rd | 6 gets-0.40/gets/man/hpdata.Rd | 21 gets-0.40/gets/man/isat.Rd | 44 gets-0.40/gets/man/larch.Rd | 4 gets-0.40/gets/man/regressorsVariance.Rd | 8 gets-0.40/gets/tests |only gets-0.40/gets/vignettes/introduction.Rnw | 17 gets-0.40/gets/vignettes/user-defined-gets-and-isat.Rnw | 14 43 files changed, 2036 insertions(+), 1184 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-18 0.8.1
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and scientific writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Yoel Diaz-Saucedo [aut] ,
Maria Belen Kistner [ctb] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between inti versions 0.7.1 dated 2026-06-22 and 0.7.2 dated 2026-07-28
inti-0.7.1/inti/inst/extdata/_extensions/scihub/ReadMe.qmd |only inti-0.7.1/inti/inst/extdata/_extensions/scihub/design |only inti-0.7.1/inti/inst/extdata/_extensions/scihub/files/images |only inti-0.7.1/inti/inst/extdata/_extensions/scihub/manuscript/Figure_1.jpg |only inti-0.7.2/inti/DESCRIPTION | 8 inti-0.7.2/inti/MD5 | 72 - inti-0.7.2/inti/NEWS.md | 9 inti-0.7.2/inti/R/design_augmented.R | 555 +++++--- inti-0.7.2/inti/R/design_split.R | 36 inti-0.7.2/inti/R/design_split_rcbd.R | 64 inti-0.7.2/inti/R/plot_augmented_design.R | 631 ++++++++- inti-0.7.2/inti/R/plot_split_rcbd_design.R | 658 ++++++++-- inti-0.7.2/inti/R/plot_standard_design.R | 623 ++++++--- inti-0.7.2/inti/R/rticle.R | 197 ++ inti-0.7.2/inti/R/tarpuy_design.R | 19 inti-0.7.2/inti/R/tarpuy_plex.R | 18 inti-0.7.2/inti/R/tarpuy_plotdesign.R | 269 +++- inti-0.7.2/inti/R/utils.R | 46 inti-0.7.2/inti/R/yupana_mvr.R | 14 inti-0.7.2/inti/README.md | 15 inti-0.7.2/inti/build/partial.rdb |binary inti-0.7.2/inti/build/vignette.rds |binary inti-0.7.2/inti/inst/CITATION | 75 - inti-0.7.2/inti/inst/doc/apps.html | 2 inti-0.7.2/inti/inst/extdata/_extensions/scihub/_quarto.yml |only inti-0.7.2/inti/inst/extdata/_extensions/scihub/analysis.qmd | 21 inti-0.7.2/inti/inst/extdata/_extensions/scihub/article.qmd | 23 inti-0.7.2/inti/inst/extdata/_extensions/scihub/files/phenomics.qmd |only inti-0.7.2/inti/inst/extdata/_extensions/scihub/index.qmd |only inti-0.7.2/inti/inst/extdata/_extensions/scihub/labels.qmd |only inti-0.7.2/inti/inst/extdata/_extensions/scihub/library |only inti-0.7.2/inti/inst/extdata/_extensions/scihub/manuscript/Figure-1.jpg |only inti-0.7.2/inti/inst/extdata/_extensions/scihub/scihub.proj | 8 inti-0.7.2/inti/inst/tarpuy/rsconnect/shinyapps.io/inkaverse/tarpuy.dcf | 2 inti-0.7.2/inti/inst/tarpuy/server.R | 297 +++- inti-0.7.2/inti/inst/tarpuy/ui.R | 214 +-- inti-0.7.2/inti/inst/yupana/rsconnect/shinyapps.io/inkaverse/yupana.dcf | 2 inti-0.7.2/inti/man/design_augmented.Rd | 12 inti-0.7.2/inti/man/plot_augmented_design.Rd | 139 +- inti-0.7.2/inti/man/plot_split_rcbd_design.Rd | 126 + inti-0.7.2/inti/man/plot_standard_design.Rd | 249 +-- inti-0.7.2/inti/man/tarpuy_plotdesign.Rd | 124 + 42 files changed, 3348 insertions(+), 1180 deletions(-)
Title: Conduct Simulation Study of Bayesian Optimal Interval Design
with BOIN-ET Family
Description: Bayesian optimal interval based on both efficacy and toxicity outcomes (BOIN-ET) design is a model-assisted oncology phase I/II trial design, aiming to establish an optimal biological dose accounting for efficacy and toxicity in the framework of dose-finding. Some extensions of BOIN-ET design are also available to allow for time-to-event efficacy and toxicity outcomes based on cumulative and pending data (time-to-event BOIN-ET: TITE-BOIN-ET), ordinal graded efficacy and toxicity outcomes (generalized BOIN-ET: gBOIN-ET), and their combination (TITE-gBOIN-ET). 'boinet' is a package to implement the BOIN-ET design family and supports the conduct of simulation studies to assess operating characteristics of BOIN-ET, TITE-BOIN-ET, gBOIN-ET, and TITE-gBOIN-ET, where users can choose design parameters in flexible and straightforward ways depending on their own application.
Author: Yusuke Yamaguchi [aut, cre],
Kentaro Takeda [aut]
Maintainer: Yusuke Yamaguchi <yamagubed@gmail.com>
Diff between boinet versions 1.5.0 dated 2025-10-26 and 1.6.0 dated 2026-07-28
DESCRIPTION | 6 MD5 | 18 NEWS.md | 5 R/boinet.R | 4 R/gboinet.R | 4 R/tite.boinet.R | 4 R/tite.gboinet.R | 4 inst/doc/gt_integration_vignette.html | 799 +++++++++++++++---------------- inst/doc/quarto_workflow_vignette.html | 231 ++++---- inst/doc/result_formatting_vignette.html | 4 10 files changed, 543 insertions(+), 536 deletions(-)
Title: Missing Data Imputation and Model Checking
Description: The mi package provides functions for data manipulation, imputing missing values in an approximate Bayesian framework, diagnostics of the models used to generate the imputations, confidence-building mechanisms to validate some of the assumptions of the imputation algorithm, and functions to analyze multiply imputed data sets with the appropriate degree of sampling uncertainty.
Author: Andrew Gelman [ctb],
Jennifer Hill [ctb],
Yu-Sung Su [aut],
Masanao Yajima [ctb],
Maria Pittau [ctb],
Ben Goodrich [cre, aut],
Yajuan Si [ctb],
Jon Kropko [aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between mi versions 1.2 dated 2025-09-02 and 1.3.1 dated 2026-07-27
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/mi_vignette.Rmd | 2 +- inst/doc/mi_vignette.pdf |binary tests/missing_data.frame.R | 2 +- tests/missing_variable.R | 3 ++- vignettes/mi_vignette.Rmd | 2 +- 9 files changed, 17 insertions(+), 16 deletions(-)
Title: Entity Relationship Diagrams Builder
Description: Build entity relationship diagrams (ERD) to specify the nature of the relationship between tables in a database.
Author: Jonathan Wood [aut] ,
Guillermo Basulto-Elias [aut, cre]
Maintainer: Guillermo Basulto-Elias <basulto@iastate.edu>
Diff between ERDbuilder versions 1.0.0 dated 2024-04-01 and 2.0.0 dated 2026-07-27
DESCRIPTION | 17 MD5 | 42 + NAMESPACE | 5 NEWS.md | 6 R/create_erd.R | 27 - R/dev_examples.R |only R/helper-erd-fixtures.R |only R/perform_join.R | 6 R/render_erd.R | 7 R/suggest_relationships.R |only R/validate_erd.R |only README.md | 615 +++++++++++++++++++++------- build/vignette.rds |binary inst/doc/order_of_entities.R | 284 ++++++------ inst/doc/order_of_entities.Rmd | 10 inst/doc/order_of_entities.html | 119 ++--- inst/doc/step_by_step.html | 604 ++++++++++++++------------- man/create_erd.Rd | 5 man/figures/logo.png |only man/format_relationships.Rd |only man/is_valid_erd.Rd |only man/suggest_relationships.Rd |only man/validate_erd.Rd |only tests/testthat/helper-erd-fixtures.R |only tests/testthat/test-render_erd.R | 28 + tests/testthat/test-suggest_relationships.R |only tests/testthat/test-validate_erd.R |only vignettes/order_of_entities.Rmd | 10 28 files changed, 1124 insertions(+), 661 deletions(-)
Title: Tools to Fit Flexible Parametric Curves
Description: Model selection tools and 'selfStart' functions to fit parametric curves in 'nls', 'nlsList' and 'nlme' frameworks.
Author: Stephen Oswald [aut, cre]
Maintainer: Stephen Oswald <steve.oswald@psu.edu>
Diff between FlexParamCurve versions 1.5-7 dated 2025-08-26 and 1.5-8 dated 2026-07-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/SSposnegRichards.R | 6 +++--- inst/NEWS.Rd | 6 ++++++ 4 files changed, 16 insertions(+), 10 deletions(-)
More information about FlexParamCurve at CRAN
Permanent link
Title: Actuarial Risk Modeling and Life Contingencies
Description: Provides functions for actuarial risk modeling, including survival models,
life annuities, multiple-decrement models, and mortality improvement projections.
The package is designed to align with standard actuarial notation and supports
teaching, exam preparation, and reproducible actuarial analysis. The methods are
based on standard actuarial references including Camilli, Duncan and London (2014,
ISBN:9781625423474) "Models for Quantifying Risk" and Dickson, Hardy and Waters
(2020, ISBN:9781108478083) "Actuarial Mathematics for Life Contingent Risks".
Author: Nii Okine [aut, cre]
Maintainer: Nii Okine <okinean@appstate.edu>
Diff between mqriskR versions 0.1.0 dated 2026-04-27 and 0.1.1 dated 2026-07-27
mqriskR-0.1.0/mqriskR/R/numerical_utils.R |only mqriskR-0.1.0/mqriskR/R/reserve_ch11_ext.R |only mqriskR-0.1.0/mqriskR/man/Abarxy.Rd |only mqriskR-0.1.0/mqriskR/man/Abarxy1.Rd |only mqriskR-0.1.0/mqriskR/man/Abarxy2.Rd |only mqriskR-0.1.0/mqriskR/man/Abarxybar.Rd |only mqriskR-0.1.0/mqriskR/man/Abaryx1.Rd |only mqriskR-0.1.0/mqriskR/man/Abaryx2.Rd |only mqriskR-0.1.0/mqriskR/man/Axy.Rd |only mqriskR-0.1.0/mqriskR/man/Axybar.Rd |only mqriskR-0.1.0/mqriskR/man/Axybarn.Rd |only mqriskR-0.1.0/mqriskR/man/Axybarn1.Rd |only mqriskR-0.1.0/mqriskR/man/Axyn.Rd |only mqriskR-0.1.0/mqriskR/man/Axyn1.Rd |only mqriskR-0.1.0/mqriskR/man/abarx_y.Rd |only mqriskR-0.1.0/mqriskR/man/abarxy_ch12.Rd |only mqriskR-0.1.0/mqriskR/man/abarxybar_ch12.Rd |only mqriskR-0.1.0/mqriskR/man/abary_x.Rd |only mqriskR-0.1.0/mqriskR/man/adotxy.Rd |only mqriskR-0.1.0/mqriskR/man/adotxybar.Rd |only mqriskR-0.1.0/mqriskR/man/adotxybarn.Rd |only mqriskR-0.1.0/mqriskR/man/adotxyn.Rd |only mqriskR-0.1.0/mqriskR/man/alphaF.Rd |only mqriskR-0.1.0/mqriskR/man/annuity_mthly_accum_due.Rd |only mqriskR-0.1.0/mqriskR/man/annuity_mthly_accum_immediate.Rd |only mqriskR-0.1.0/mqriskR/man/annuity_mthly_deferred_due.Rd |only mqriskR-0.1.0/mqriskR/man/annuity_mthly_deferred_immediate.Rd |only mqriskR-0.1.0/mqriskR/man/annuity_mthly_temp_due.Rd |only mqriskR-0.1.0/mqriskR/man/annuity_mthly_temp_immediate.Rd |only mqriskR-0.1.0/mqriskR/man/annuity_mthly_whole_due.Rd |only mqriskR-0.1.0/mqriskR/man/annuity_mthly_whole_immediate.Rd |only mqriskR-0.1.0/mqriskR/man/ax_improved.Rd |only mqriskR-0.1.0/mqriskR/man/ax_y.Rd |only mqriskR-0.1.0/mqriskR/man/axn_improved.Rd |only mqriskR-0.1.0/mqriskR/man/axy_ch12.Rd |only mqriskR-0.1.0/mqriskR/man/axybar_ch12.Rd |only mqriskR-0.1.0/mqriskR/man/axybarn_ch12.Rd |only mqriskR-0.1.0/mqriskR/man/axyn_ch12.Rd |only mqriskR-0.1.0/mqriskR/man/ay_x.Rd |only mqriskR-0.1.0/mqriskR/man/betaF.Rd |only mqriskR-0.1.0/mqriskR/man/ch12_multilife_cont_params.Rd |only mqriskR-0.1.0/mqriskR/man/chapter15_spot_interest_apv.Rd |only mqriskR-0.1.0/mqriskR/man/chapter15_variable_interest_apv.Rd |only mqriskR-0.1.0/mqriskR/man/dot-find_upper_t.Rd |only mqriskR-0.1.0/mqriskR/man/dot-safe_integrate.Rd |only mqriskR-0.1.0/mqriskR/man/meanVx.Rd |only mqriskR-0.1.0/mqriskR/man/mortality_improvement.Rd |only mqriskR-0.1.0/mqriskR/man/multilife_ch12.Rd |only mqriskR-0.1.0/mqriskR/man/multilife_ch12_ext.Rd |only mqriskR-0.1.0/mqriskR/man/nExy.Rd |only mqriskR-0.1.0/mqriskR/man/nExybar.Rd |only mqriskR-0.1.0/mqriskR/man/naxn_improved.Rd |only mqriskR-0.1.0/mqriskR/man/premium_ch9.Rd |only mqriskR-0.1.0/mqriskR/man/px_proj.Rd |only mqriskR-0.1.0/mqriskR/man/pxtau_ul.Rd |only mqriskR-0.1.0/mqriskR/man/qx_proj.Rd |only mqriskR-0.1.0/mqriskR/man/reserve_ch10.Rd |only mqriskR-0.1.0/mqriskR/man/reserve_ch10_ext.Rd |only mqriskR-0.1.0/mqriskR/man/reserve_ch11.Rd |only mqriskR-0.1.0/mqriskR/man/reserve_ch11_ext.Rd |only mqriskR-0.1.0/mqriskR/man/reserve_deferred_insurance_ch10.Rd |only mqriskR-0.1.0/mqriskR/man/tVEx.Rd |only mqriskR-0.1.0/mqriskR/man/tVFx.Rd |only mqriskR-0.1.0/mqriskR/man/tVGx.Rd |only mqriskR-0.1.0/mqriskR/man/tpx_improved.Rd |only mqriskR-0.1.0/mqriskR/man/tpxtau_ul.Rd |only mqriskR-0.1.0/mqriskR/man/tpxy.Rd |only mqriskR-0.1.0/mqriskR/man/tpxybar.Rd |only mqriskR-0.1.0/mqriskR/man/tqxy.Rd |only mqriskR-0.1.0/mqriskR/man/tqxy1.Rd |only mqriskR-0.1.0/mqriskR/man/tqxy2.Rd |only mqriskR-0.1.0/mqriskR/man/tqxybar.Rd |only mqriskR-0.1.0/mqriskR/man/tqyx1.Rd |only mqriskR-0.1.0/mqriskR/man/tqyx2.Rd |only mqriskR-0.1.0/mqriskR/man/tsVx.Rd |only mqriskR-0.1.0/mqriskR/man/tsVxn.Rd |only mqriskR-0.1.0/mqriskR/man/tsVxn1.Rd |only mqriskR-0.1.0/mqriskR/tests/testthat/test-reserve_ch11_ext.R |only mqriskR-0.1.1/mqriskR/DESCRIPTION | 8 mqriskR-0.1.1/mqriskR/MD5 | 570 +-- mqriskR-0.1.1/mqriskR/NEWS.md |only mqriskR-0.1.1/mqriskR/R/annuity_annual.R | 476 +-- mqriskR-0.1.1/mqriskR/R/annuity_approximations.R | 19 mqriskR-0.1.1/mqriskR/R/annuity_mthly.R | 395 +- mqriskR-0.1.1/mqriskR/R/annuity_relationships.R | 286 + mqriskR-0.1.1/mqriskR/R/annuity_varying_payments.R | 426 +- mqriskR-0.1.1/mqriskR/R/chapter14_multiple_decrement.R | 968 ++---- mqriskR-0.1.1/mqriskR/R/chapter15_variable_interest.R | 994 +++--- mqriskR-0.1.1/mqriskR/R/chapter16_universal_life.R | 780 +++-- mqriskR-0.1.1/mqriskR/R/chapter17_profit_analysis.R | 582 ++- mqriskR-0.1.1/mqriskR/R/chapter18_pensions.R | 1057 +++++- mqriskR-0.1.1/mqriskR/R/decrement_ch13_ext.R | 1074 +++++- mqriskR-0.1.1/mqriskR/R/insurance_continuous.R | 182 - mqriskR-0.1.1/mqriskR/R/insurance_discrete.R | 154 mqriskR-0.1.1/mqriskR/R/insurance_mthly.R | 226 - mqriskR-0.1.1/mqriskR/R/insurance_utils.R | 90 mqriskR-0.1.1/mqriskR/R/insurance_varying_benefits.R | 257 + mqriskR-0.1.1/mqriskR/R/interest_theory.R | 259 + mqriskR-0.1.1/mqriskR/R/life_table_conversions.R | 24 mqriskR-0.1.1/mqriskR/R/life_table_core.R | 228 + mqriskR-0.1.1/mqriskR/R/life_table_expectations.R | 236 - mqriskR-0.1.1/mqriskR/R/life_table_fractional.R | 117 mqriskR-0.1.1/mqriskR/R/life_table_select.R | 156 - mqriskR-0.1.1/mqriskR/R/mortality_improvement.R | 291 - mqriskR-0.1.1/mqriskR/R/mqriskR-package.R | 6 mqriskR-0.1.1/mqriskR/R/multilife_ch12.R | 1547 +++++++--- mqriskR-0.1.1/mqriskR/R/multilife_ch12_ext.R | 1287 ++++++-- mqriskR-0.1.1/mqriskR/R/premium_ch9.R | 805 +++-- mqriskR-0.1.1/mqriskR/R/reserve_ch10.R | 200 - mqriskR-0.1.1/mqriskR/R/reserve_ch10_ext.R | 1547 +++++++--- mqriskR-0.1.1/mqriskR/R/reserve_ch11.R | 1478 ++++++--- mqriskR-0.1.1/mqriskR/R/survival_models.R | 402 +- mqriskR-0.1.1/mqriskR/README.md | 84 mqriskR-0.1.1/mqriskR/build/vignette.rds |binary mqriskR-0.1.1/mqriskR/inst/extdata/LifeTable.csv |only mqriskR-0.1.1/mqriskR/inst/extdata/LifeTable.xls |binary mqriskR-0.1.1/mqriskR/inst/scripts/ch02/ch02_listings.R | 2 mqriskR-0.1.1/mqriskR/inst/scripts/ch04/ch04_examples_exercises.R | 28 mqriskR-0.1.1/mqriskR/inst/scripts/ch04/ch04_listings.R | 2 mqriskR-0.1.1/mqriskR/man/AAL_PUC_db.Rd | 33 mqriskR-0.1.1/mqriskR/man/AAL_TUC_db.Rd | 25 mqriskR-0.1.1/mqriskR/man/AB_cae.Rd | 17 mqriskR-0.1.1/mqriskR/man/AB_fas.Rd | 21 mqriskR-0.1.1/mqriskR/man/APV_NR_db.Rd | 25 mqriskR-0.1.1/mqriskR/man/APV_gross_premiums.Rd | 26 mqriskR-0.1.1/mqriskR/man/AS_path.Rd | 48 mqriskR-0.1.1/mqriskR/man/AS_path_md.Rd | 26 mqriskR-0.1.1/mqriskR/man/AV_path_ul_typeA.Rd | 49 mqriskR-0.1.1/mqriskR/man/AV_path_ul_typeB.Rd | 49 mqriskR-0.1.1/mqriskR/man/AVz_dc.Rd | 30 mqriskR-0.1.1/mqriskR/man/Abarx.Rd | 2 mqriskR-0.1.1/mqriskR/man/Abarxj_md.Rd | 30 mqriskR-0.1.1/mqriskR/man/Abarxn.Rd | 3 mqriskR-0.1.1/mqriskR/man/Abarxn1.Rd | 3 mqriskR-0.1.1/mqriskR/man/Ax_m.Rd | 4 mqriskR-0.1.1/mqriskR/man/Axj_md.Rd | 41 mqriskR-0.1.1/mqriskR/man/Axn1_m.Rd | 4 mqriskR-0.1.1/mqriskR/man/Axn_m.Rd | 3 mqriskR-0.1.1/mqriskR/man/DAbarxn1.Rd | 3 mqriskR-0.1.1/mqriskR/man/DAxn1.Rd | 3 mqriskR-0.1.1/mqriskR/man/DbarAbarxn1.Rd | 3 mqriskR-0.1.1/mqriskR/man/ELtx.Rd | 10 mqriskR-0.1.1/mqriskR/man/GI_cont.Rd | 23 mqriskR-0.1.1/mqriskR/man/GI_disc.Rd | 2 mqriskR-0.1.1/mqriskR/man/GMF_rollforward_ul.Rd | 10 mqriskR-0.1.1/mqriskR/man/GM_cont.Rd | 23 mqriskR-0.1.1/mqriskR/man/GM_disc.Rd | 2 mqriskR-0.1.1/mqriskR/man/GT_cont.Rd | 26 mqriskR-0.1.1/mqriskR/man/GT_disc.Rd | 4 mqriskR-0.1.1/mqriskR/man/GTg_disc.Rd | 49 mqriskR-0.1.1/mqriskR/man/IAbarx.Rd | 3 mqriskR-0.1.1/mqriskR/man/IAxn1.Rd | 3 mqriskR-0.1.1/mqriskR/man/IRR_profit.Rd | 15 mqriskR-0.1.1/mqriskR/man/IbarAbarx.Rd | 3 mqriskR-0.1.1/mqriskR/man/IbarAbarxn1.Rd | 3 mqriskR-0.1.1/mqriskR/man/Income_dc.Rd | 10 mqriskR-0.1.1/mqriskR/man/NC_EAN_db.Rd | 12 mqriskR-0.1.1/mqriskR/man/NC_PUC_db.Rd | 19 mqriskR-0.1.1/mqriskR/man/NC_TUC_db.Rd | 25 mqriskR-0.1.1/mqriskR/man/NPV_partial.Rd | 13 mqriskR-0.1.1/mqriskR/man/NPV_profit.Rd | 14 mqriskR-0.1.1/mqriskR/man/PAB_cae.Rd | 29 mqriskR-0.1.1/mqriskR/man/PAB_fas.Rd | 35 mqriskR-0.1.1/mqriskR/man/Pbar_trapz_ms.Rd | 49 mqriskR-0.1.1/mqriskR/man/Pi_signature.Rd | 21 mqriskR-0.1.1/mqriskR/man/PnAdotx.Rd | 33 mqriskR-0.1.1/mqriskR/man/Pnax.Rd | 33 mqriskR-0.1.1/mqriskR/man/Pr_vector_disc.Rd | 59 mqriskR-0.1.1/mqriskR/man/S0.Rd | 25 mqriskR-0.1.1/mqriskR/man/S0_to_lx.Rd | 4 mqriskR-0.1.1/mqriskR/man/V_zeroized.Rd | 38 mqriskR-0.1.1/mqriskR/man/Vprefloor_crvm_ul.Rd | 13 mqriskR-0.1.1/mqriskR/man/ag38_prefunding_ratio.Rd | 10 mqriskR-0.1.1/mqriskR/man/ag38_reserve_ul.Rd | 25 mqriskR-0.1.1/mqriskR/man/annuity_annual.Rd | 82 mqriskR-0.1.1/mqriskR/man/annuity_approximations.Rd | 5 mqriskR-0.1.1/mqriskR/man/annuity_approximations_udd.Rd | 10 mqriskR-0.1.1/mqriskR/man/annuity_approximations_woolhouse2.Rd | 2 mqriskR-0.1.1/mqriskR/man/annuity_approximations_woolhouse3.Rd | 2 mqriskR-0.1.1/mqriskR/man/annuity_certain.Rd | 17 mqriskR-0.1.1/mqriskR/man/annuity_mthly.Rd | 55 mqriskR-0.1.1/mqriskR/man/annuity_relationships.Rd | 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mqriskR-0.1.1/mqriskR/man/ex_temp_complete_tab.Rd | 7 mqriskR-0.1.1/mqriskR/man/ex_temp_curtate_tab.Rd | 4 mqriskR-0.1.1/mqriskR/man/fnk_from_z.Rd | 21 mqriskR-0.1.1/mqriskR/man/forward_matrix_from_z.Rd | 19 mqriskR-0.1.1/mqriskR/man/fractional_duration_reserves.Rd |only mqriskR-0.1.1/mqriskR/man/fractional_duration_term_endowment_reserves.Rd |only mqriskR-0.1.1/mqriskR/man/full_preliminary_term.Rd |only mqriskR-0.1.1/mqriskR/man/fx.Rd | 26 mqriskR-0.1.1/mqriskR/man/fx_tab.Rd | 3 mqriskR-0.1.1/mqriskR/man/gain_loss_md.Rd | 46 mqriskR-0.1.1/mqriskR/man/gross_premium_expense_reserves.Rd |only mqriskR-0.1.1/mqriskR/man/hazard0.Rd | 21 mqriskR-0.1.1/mqriskR/man/htVx.Rd | 10 mqriskR-0.1.1/mqriskR/man/iMA_eiul.Rd | 17 mqriskR-0.1.1/mqriskR/man/iP_eiul.Rd | 7 mqriskR-0.1.1/mqriskR/man/i_credit_eiul.Rd | 22 mqriskR-0.1.1/mqriskR/man/insurance_continuous.Rd | 17 mqriskR-0.1.1/mqriskR/man/insurance_discrete.Rd | 21 mqriskR-0.1.1/mqriskR/man/insurance_mthly.Rd | 18 mqriskR-0.1.1/mqriskR/man/insurance_utils.Rd | 4 mqriskR-0.1.1/mqriskR/man/insurance_varying_benefits.Rd | 17 mqriskR-0.1.1/mqriskR/man/interest_convert.Rd | 22 mqriskR-0.1.1/mqriskR/man/joint_life_annuities.Rd |only mqriskR-0.1.1/mqriskR/man/joint_life_insurance.Rd |only mqriskR-0.1.1/mqriskR/man/last_survivor_annuities.Rd |only mqriskR-0.1.1/mqriskR/man/last_survivor_insurance.Rd |only mqriskR-0.1.1/mqriskR/man/life_table.Rd | 16 mqriskR-0.1.1/mqriskR/man/lx.Rd | 4 mqriskR-0.1.1/mqriskR/man/lx_select.Rd | 2 mqriskR-0.1.1/mqriskR/man/lx_to_S0.Rd | 4 mqriskR-0.1.1/mqriskR/man/markov_nstep_prob.Rd | 23 mqriskR-0.1.1/mqriskR/man/md_table.Rd | 30 mqriskR-0.1.1/mqriskR/man/mortality_improvement_projection.Rd |only mqriskR-0.1.1/mqriskR/man/mqriskR-package.Rd | 11 mqriskR-0.1.1/mqriskR/man/multilife_contingent_probabilities.Rd |only mqriskR-0.1.1/mqriskR/man/multilife_pure_endowments.Rd |only mqriskR-0.1.1/mqriskR/man/multilife_survival_probabilities.Rd |only mqriskR-0.1.1/mqriskR/man/nAbarx.Rd | 2 mqriskR-0.1.1/mqriskR/man/nAx.Rd | 2 mqriskR-0.1.1/mqriskR/man/nAx_m.Rd | 2 mqriskR-0.1.1/mqriskR/man/nEx.Rd | 2 mqriskR-0.1.1/mqriskR/man/ndx.Rd | 4 mqriskR-0.1.1/mqriskR/man/nkqx.Rd | 3 mqriskR-0.1.1/mqriskR/man/nmxq.Rd | 2 mqriskR-0.1.1/mqriskR/man/nmxq_select.Rd | 2 mqriskR-0.1.1/mqriskR/man/npx.Rd | 4 mqriskR-0.1.1/mqriskR/man/npx_select.Rd | 4 mqriskR-0.1.1/mqriskR/man/npxtau_md.Rd | 25 mqriskR-0.1.1/mqriskR/man/nqx.Rd | 4 mqriskR-0.1.1/mqriskR/man/nqx_select.Rd | 2 mqriskR-0.1.1/mqriskR/man/nqxj_md.Rd | 32 mqriskR-0.1.1/mqriskR/man/nqxtau_md.Rd | 24 mqriskR-0.1.1/mqriskR/man/premium_functions.Rd |only mqriskR-0.1.1/mqriskR/man/profit_margin.Rd | 10 mqriskR-0.1.1/mqriskR/man/pv_cashflows.Rd | 4 mqriskR-0.1.1/mqriskR/man/pv_spot_cashflows.Rd | 26 mqriskR-0.1.1/mqriskR/man/px_to_lx.Rd | 2 mqriskR-0.1.1/mqriskR/man/pxtau.Rd | 8 mqriskR-0.1.1/mqriskR/man/qx_dep_cf.Rd | 12 mqriskR-0.1.1/mqriskR/man/qx_dep_sudd.Rd | 17 mqriskR-0.1.1/mqriskR/man/qx_tab.Rd | 4 mqriskR-0.1.1/mqriskR/man/qx_to_lx.Rd | 4 mqriskR-0.1.1/mqriskR/man/qxprime_mudd.Rd | 14 mqriskR-0.1.1/mqriskR/man/qxprime_sudd.Rd | 17 mqriskR-0.1.1/mqriskR/man/qxtau.Rd | 8 mqriskR-0.1.1/mqriskR/man/replacement_ratio_db.Rd | 15 mqriskR-0.1.1/mqriskR/man/replacement_ratio_dc.Rd | 31 mqriskR-0.1.1/mqriskR/man/reversionary_annuities.Rd |only mqriskR-0.1.1/mqriskR/man/rt_ul.Rd | 11 mqriskR-0.1.1/mqriskR/man/salary_scale.Rd | 13 mqriskR-0.1.1/mqriskR/man/select_life_table.Rd | 2 mqriskR-0.1.1/mqriskR/man/solve_yield.Rd | 6 mqriskR-0.1.1/mqriskR/man/spot_interest_apvs.Rd |only mqriskR-0.1.1/mqriskR/man/survival_models.Rd | 30 mqriskR-0.1.1/mqriskR/man/tVbarAbarx.Rd | 10 mqriskR-0.1.1/mqriskR/man/tVbarx.Rd | 10 mqriskR-0.1.1/mqriskR/man/tVnAdotx.Rd | 33 mqriskR-0.1.1/mqriskR/man/tVnEx.Rd | 10 mqriskR-0.1.1/mqriskR/man/tVnax.Rd | 32 mqriskR-0.1.1/mqriskR/man/tVx.Rd | 10 mqriskR-0.1.1/mqriskR/man/tVx_m.Rd | 10 mqriskR-0.1.1/mqriskR/man/tVx_ret.Rd | 37 mqriskR-0.1.1/mqriskR/man/tVxn.Rd | 10 mqriskR-0.1.1/mqriskR/man/tVxn1.Rd | 10 mqriskR-0.1.1/mqriskR/man/tVxn1_ret.Rd | 32 mqriskR-0.1.1/mqriskR/man/tVxn_ret.Rd | 34 mqriskR-0.1.1/mqriskR/man/thiele_backward_path.Rd | 32 mqriskR-0.1.1/mqriskR/man/thiele_backward_step.Rd | 36 mqriskR-0.1.1/mqriskR/man/thiele_dVdt.Rd | 22 mqriskR-0.1.1/mqriskR/man/thiele_dVdt_01.Rd | 53 mqriskR-0.1.1/mqriskR/man/thiele_path_01.Rd | 36 mqriskR-0.1.1/mqriskR/man/tp00_tp01_euler.Rd | 37 mqriskR-0.1.1/mqriskR/man/tpx.Rd | 26 mqriskR-0.1.1/mqriskR/man/tpx_tab.Rd | 3 mqriskR-0.1.1/mqriskR/man/tpx_tau_cf.Rd | 17 mqriskR-0.1.1/mqriskR/man/tpxprimej_cf.Rd | 14 mqriskR-0.1.1/mqriskR/man/tqx.Rd | 21 mqriskR-0.1.1/mqriskR/man/tqxj_cf.Rd | 21 mqriskR-0.1.1/mqriskR/man/tqxprime_mudd.Rd | 15 mqriskR-0.1.1/mqriskR/man/tqxprimej_cf.Rd | 14 mqriskR-0.1.1/mqriskR/man/ul_persistency.Rd |only mqriskR-0.1.1/mqriskR/man/varLtx.Rd | 10 mqriskR-0.1.1/mqriskR/man/var_Abarx.Rd | 3 mqriskR-0.1.1/mqriskR/man/var_Abarxn1.Rd | 4 mqriskR-0.1.1/mqriskR/man/var_Ax_m.Rd | 3 mqriskR-0.1.1/mqriskR/man/var_Axn1.Rd | 3 mqriskR-0.1.1/mqriskR/man/variable_interest_apvs.Rd |only mqriskR-0.1.1/mqriskR/man/vt_var.Rd | 24 mqriskR-0.1.1/mqriskR/man/z_from_coupon_annual.Rd | 16 mqriskR-0.1.1/mqriskR/man/z_from_coupon_semi.Rd | 24 mqriskR-0.1.1/mqriskR/man/z_from_fn1.Rd | 21 mqriskR-0.1.1/mqriskR/tests/testthat/test-annuity_annual.R | 23 mqriskR-0.1.1/mqriskR/tests/testthat/test-annuity_mthly.R | 29 mqriskR-0.1.1/mqriskR/tests/testthat/test-annuity_relationships.R | 30 mqriskR-0.1.1/mqriskR/tests/testthat/test-annuity_varying_payments.R | 39 mqriskR-0.1.1/mqriskR/tests/testthat/test-ch01-interest.R | 40 mqriskR-0.1.1/mqriskR/tests/testthat/test-chapter14_multiple_decrement.R | 358 ++ mqriskR-0.1.1/mqriskR/tests/testthat/test-chapter15_variable_interest.R | 237 + mqriskR-0.1.1/mqriskR/tests/testthat/test-chapter16_universal_life.R | 404 ++ mqriskR-0.1.1/mqriskR/tests/testthat/test-chapter17_profit_analysis.R | 458 ++ mqriskR-0.1.1/mqriskR/tests/testthat/test-chapter18_pensions.R | 536 +++ mqriskR-0.1.1/mqriskR/tests/testthat/test-decrement_ch13_ext.R | 262 + mqriskR-0.1.1/mqriskR/tests/testthat/test-insurance_continuous.R | 22 mqriskR-0.1.1/mqriskR/tests/testthat/test-insurance_discrete.R | 20 mqriskR-0.1.1/mqriskR/tests/testthat/test-insurance_mthly.R | 24 mqriskR-0.1.1/mqriskR/tests/testthat/test-life_table_core.R | 42 mqriskR-0.1.1/mqriskR/tests/testthat/test-mortality_improvement.R | 37 mqriskR-0.1.1/mqriskR/tests/testthat/test-multilife_ch12.R | 354 ++ mqriskR-0.1.1/mqriskR/tests/testthat/test-multilife_ch12_ext.R | 260 + mqriskR-0.1.1/mqriskR/tests/testthat/test-premium_ch9.R | 143 mqriskR-0.1.1/mqriskR/tests/testthat/test-reserve_ch10.R | 188 + mqriskR-0.1.1/mqriskR/tests/testthat/test-reserve_ch10_ext.R | 263 + mqriskR-0.1.1/mqriskR/tests/testthat/test-reserve_ch11.R | 572 +++ mqriskR-0.1.1/mqriskR/tests/testthat/test-survival_models.R | 2 336 files changed, 17137 insertions(+), 7592 deletions(-)
Title: Access the Our World in Data Chart API
Description: Retrieve data from the Our World in Data (OWID) Chart API
<https://docs.owid.io/projects/etl/api/>. OWID provides public access to
more than 4,000 charts focusing on global problems such as poverty,
disease, hunger, climate change, war, existential risks, and inequality.
Author: Christoph Scheuch [aut, cre, cph]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between owidapi versions 0.1.1 dated 2025-06-23 and 0.1.2 dated 2026-07-27
DESCRIPTION | 10 - MD5 | 39 +++-- NEWS.md | 16 ++ R/helpers.R | 28 +++- R/owid_get_catalog.R | 120 +++++++++++++---- R/owid_search.R | 11 + README.md | 223 +++++++++++++++++--------------- man/owid_get.Rd | 2 man/owid_get_catalog.Rd | 6 man/owid_get_metadata.Rd | 2 man/owid_output.Rd | 2 man/owid_search.Rd | 13 + man/owidapi-package.Rd | 2 tests/testthat/fixtures |only tests/testthat/helper-mocks.R |only tests/testthat/test-api-contract.R |only tests/testthat/test-owid_get.R | 127 ++++++++++++------ tests/testthat/test-owid_get_catalog.R | 129 ++++++++++++++++-- tests/testthat/test-owid_get_metadata.R | 40 ++++- 19 files changed, 536 insertions(+), 234 deletions(-)
Title: Continuous Wavelet Transformation for Spectroscopy
Description: Fast application of Continuous Wavelet Transformation ('CWT') on time
series with special attention to spectroscopy. It is written using
data.table and 'C++' language and in some functions it is possible to
use parallel processing to speed-up the computation over samples. Currently,
only the second derivative of a Gaussian wavelet function is implemented.
Author: J. Antonio Guzman Q. [cre, aut, cph]
Maintainer: J. Antonio Guzman Q. <antguz06@gmail.com>
Diff between CWT versions 0.2.1 dated 2024-06-27 and 0.2.3 dated 2026-07-27
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS.md | 15 +++++++++++++++ R/CWT.R | 19 +++++++++++-------- R/resampling_FWHM.R | 3 ++- man/CWT-package.Rd | 5 +++++ man/resampling_FWHM.Rd | 3 ++- src/resampling_FWHM.cpp | 3 ++- 8 files changed, 50 insertions(+), 24 deletions(-)
Title: An API Client for the Environmental Data Initiative Repository
Description: A client for the Environmental Data Initiative repository REST API. The 'EDI' data repository <https://portal.edirepository.org/nis/home.jsp> is for publication and reuse of ecological data with emphasis on metadata accuracy and completeness. It is built upon the 'PASTA+' software stack <https://pastaplus-core.readthedocs.io/en/latest/index.html#> and was developed in collaboration with the US 'LTER' Network <https://lternet.edu/>. 'EDIutils' includes functions to search and access existing data, evaluate and upload new data, and assist other data management tasks common to repository users.
Author: Colin Smith [aut, cre] ,
Corinna Gries [ctb] ,
Jasmine Lai [rev] ,
Rodrigo Pires [rev]
Maintainer: Colin Smith <colin.smith@wisc.edu>
Diff between EDIutils versions 2.1.0 dated 2026-05-05 and 3.0.0 dated 2026-07-27
DESCRIPTION | 6 MD5 | 322 +++++++++++----------- NAMESPACE | 5 NEWS.md | 15 + R/check_status_create.R | 4 R/check_status_evaluate.R | 4 R/check_status_update.R | 4 R/create_data_package.R | 2 R/create_data_package_archive.R | 2 R/create_event_subscription.R | 2 R/create_journal_citation.R | 2 R/create_reservation.R | 2 R/delete_event_subscription.R | 2 R/delete_journal_citation.R | 2 R/delete_reservation.R | 2 R/evaluate_data_package.R | 2 R/execute_event_subscription.R | 2 R/get_audit_count.R | 2 R/get_audit_csv_report.R | 2 R/get_audit_record.R | 2 R/get_audit_report.R | 2 R/get_docid_reads.R | 2 R/get_event_subscription.R | 2 R/get_event_subscription_schema.R | 2 R/get_journal_citation.R | 2 R/get_packageid_reads.R | 2 R/get_provenance_metadata.R | 2 R/get_recent_uploads.R | 2 R/is_authorized.R | 2 R/list_active_reservations.R | 2 R/list_data_descendants.R | 2 R/list_data_entities.R | 2 R/list_data_package_citations.R | 2 R/list_data_package_identifiers.R | 2 R/list_data_package_revisions.R | 2 R/list_data_package_scopes.R | 2 R/list_data_sources.R | 2 R/list_deleted_data_packages.R | 2 R/list_principal_owner_citations.R | 2 R/list_recent_changes.R | 2 R/list_recent_uploads.R | 2 R/list_reservation_identifiers.R | 2 R/list_service_methods.R | 2 R/list_user_data_packages.R | 2 R/list_working_on.R | 2 R/login.R | 109 ++++--- R/logout.R | 1 R/query_event_subscriptions.R | 2 R/read_data_entity.R | 2 R/read_data_entity_checksum.R | 2 R/read_data_entity_name.R | 2 R/read_data_entity_names.R | 2 R/read_data_entity_resource_metadata.R | 2 R/read_data_entity_size.R | 2 R/read_data_entity_sizes.R | 2 R/read_data_package.R | 2 R/read_data_package_archive.R | 2 R/read_data_package_citation.R | 6 R/read_data_package_doi.R | 2 R/read_data_package_error.R | 2 R/read_data_package_from_doi.R | 2 R/read_data_package_report.R | 4 R/read_data_package_report_checksum.R | 2 R/read_data_package_report_resource_metadata.R | 2 R/read_data_package_resource_metadata.R | 2 R/read_evaluate_report.R | 4 R/read_metadata.R | 2 R/read_metadata_checksum.R | 2 R/read_metadata_dublin_core.R | 2 R/read_metadata_format.R | 2 R/read_metadata_resource_metadata.R | 2 R/search_data_packages.R | 4 R/update_data_package.R | 2 R/utilities.R | 94 ++++++ README.md | 14 inst/doc/evaluate_and_upload.R | 16 - inst/doc/evaluate_and_upload.Rmd | 22 - inst/doc/evaluate_and_upload.html | 42 +- inst/doc/retrieve_downloads.R | 6 inst/doc/retrieve_downloads.Rmd | 9 inst/doc/retrieve_downloads.html | 14 inst/doc/tests_requiring_authentication.Rmd | 6 inst/doc/tests_requiring_authentication.html | 13 man/check_status_create.Rd | 12 man/check_status_evaluate.Rd | 12 man/check_status_update.Rd | 12 man/create_data_package.Rd | 12 man/create_data_package_archive.Rd | 6 man/create_dn.Rd | 6 man/create_event_subscription.Rd | 12 man/create_journal_citation.Rd | 10 man/create_reservation.Rd | 8 man/delete_event_subscription.Rd | 12 man/delete_journal_citation.Rd | 10 man/delete_reservation.Rd | 8 man/evaluate_data_package.Rd | 12 man/execute_event_subscription.Rd | 12 man/get_audit_count.Rd | 14 man/get_audit_csv_report.Rd | 14 man/get_audit_record.Rd | 14 man/get_audit_report.Rd | 14 man/get_docid_reads.Rd | 14 man/get_event_subscription.Rd | 12 man/get_event_subscription_schema.Rd | 12 man/get_journal_citation.Rd | 10 man/get_packageid_reads.Rd | 14 man/get_recent_uploads.Rd | 14 man/is_authorized.Rd | 6 man/list_active_reservations.Rd | 8 man/list_data_descendants.Rd | 22 - man/list_data_entities.Rd | 22 - man/list_data_package_citations.Rd | 10 man/list_data_package_identifiers.Rd | 22 - man/list_data_package_revisions.Rd | 22 - man/list_data_package_scopes.Rd | 22 - man/list_data_sources.Rd | 22 - man/list_deleted_data_packages.Rd | 22 - man/list_principal_owner_citations.Rd | 10 man/list_recent_changes.Rd | 22 - man/list_recent_uploads.Rd | 22 - man/list_reservation_identifiers.Rd | 8 man/list_service_methods.Rd | 22 - man/list_user_data_packages.Rd | 22 - man/login.Rd | 37 +- man/logout.Rd | 8 man/query_event_subscriptions.Rd | 12 man/read_data_entity.Rd | 52 +-- man/read_data_entity_checksum.Rd | 52 +-- man/read_data_entity_name.Rd | 52 +-- man/read_data_entity_names.Rd | 52 +-- man/read_data_entity_resource_metadata.Rd | 52 +-- man/read_data_entity_size.Rd | 52 +-- man/read_data_entity_sizes.Rd | 52 +-- man/read_data_package.Rd | 52 +-- man/read_data_package_archive.Rd | 52 +-- man/read_data_package_citation.Rd | 52 +-- man/read_data_package_doi.Rd | 52 +-- man/read_data_package_error.Rd | 52 +-- man/read_data_package_from_doi.Rd | 52 +-- man/read_data_package_report.Rd | 52 +-- man/read_data_package_report_checksum.Rd | 52 +-- man/read_data_package_report_resource_metadata.Rd | 52 +-- man/read_data_package_report_summary.Rd | 52 +-- man/read_data_package_resource_metadata.Rd | 52 +-- man/read_evaluate_report.Rd | 52 +-- man/read_evaluate_report_summary.Rd | 52 +-- man/read_metadata.Rd | 52 +-- man/read_metadata_checksum.Rd | 52 +-- man/read_metadata_dublin_core.Rd | 52 +-- man/read_metadata_entity.Rd | 52 +-- man/read_metadata_format.Rd | 52 +-- man/read_metadata_resource_metadata.Rd | 52 +-- man/update_data_package.Rd | 12 tests/testthat/setup-EDIutils.R | 8 tests/testthat/test_create_data_package_archive.R | 5 tests/testthat/test_get_audit_record.R | 4 tests/testthat/test_list_recent_changes.R | 3 tests/testthat/test_read_data_package_from_doi.R | 26 - tests/testthat/test_utilities.R | 74 +++++ vignettes/evaluate_and_upload.Rmd | 22 - vignettes/retrieve_downloads.Rmd | 9 vignettes/tests_requiring_authentication.Rmd | 6 162 files changed, 1625 insertions(+), 1357 deletions(-)
Title: Automated Selection and Visualisation of Statistical Hypothesis
Tests
Description: Automated test selection, visualised. 'visStatistics'
automatically selects and visualises statistical hypothesis tests
comparing two vectors, based on their class and distribution. Visual
outputs, including box plots, bar charts, regression
lines with confidence bands, mosaic plots, residual plots, and Q-Q
plots, are annotated with relevant test statistics, assumption checks,
and post-hoc analyses where applicable. The algorithmic workflow
shifts attention from ad-hoc test selection to visual diagnostic
assessment and statistical interpretation. It is particularly suited
for server-side R applications, where end users interact solely
through a web interface to select data groups and receive a complete
visual statistical analysis automatically. The same automation makes
it useful in time-constrained contexts such as statistical consulting,
where it reduces effort spent on test selection and leaves more room
for interpretation. The implemented tests cover the most frequently
applied i [...truncated...]
Author: Sabine Schilling [cre, aut, cph] ,
Peter Kauf [ctb]
Maintainer: Sabine Schilling <sabineschilling@gmx.ch>
Diff between visStatistics versions 0.2.0 dated 2026-05-12 and 0.3.0 dated 2026-07-27
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visStatistics-0.3.0/visStatistics/R/get_samples_fact_inputfile.R | 77 visStatistics-0.3.0/visStatistics/R/graphics_args.R |only visStatistics-0.3.0/visStatistics/R/levene.test.R | 87 visStatistics-0.3.0/visStatistics/R/opening_saving_Cairo.R | 86 visStatistics-0.3.0/visStatistics/R/qq_lm_envelope.R |only visStatistics-0.3.0/visStatistics/R/test_and_visuals.R | 761 + visStatistics-0.3.0/visStatistics/R/vis_anova.R | 172 visStatistics-0.3.0/visStatistics/R/vis_lm_assumptions.R | 410 - visStatistics-0.3.0/visStatistics/R/vis_numeric.R | 380 visStatistics-0.3.0/visStatistics/R/visstat.R | 271 visStatistics-0.3.0/visStatistics/R/visstat_core.R | 854 +- visStatistics-0.3.0/visStatistics/R/visstat_methods.R | 84 visStatistics-0.3.0/visStatistics/build/vignette.rds |binary visStatistics-0.3.0/visStatistics/inst/WORDLIST | 108 visStatistics-0.3.0/visStatistics/inst/comparison |only visStatistics-0.3.0/visStatistics/inst/doc/visStatistics.R | 542 - 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Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre] ,
Mike Johnson [aut] ,
Marc Weber [ctb] ,
Josh Erickson [ctb],
Lauren Koenig [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 1.5.0 dated 2026-05-26 and 1.5.1 dated 2026-07-27
DESCRIPTION | 6 MD5 | 221 +-- NEWS.md | 5 R/arcrest_tools.R | 560 ++++---- R/boundary_datasets.R | 60 R/calc_network.R | 128 - R/get_drainage_area_estimates.R | 2 R/get_hydro.R | 714 +++++----- R/get_network.R | 836 ++++++------ R/get_nhdplus.R | 308 ++-- R/get_nhdplushr.R | 698 +++++----- R/get_nldi.R | 554 +++---- R/get_oaproc.R | 970 ++++++------- R/map_nhdplus.R | 408 ++--- R/oafeat_tools.R | 994 +++++++------- R/plot_nhdplus.R | 1532 +++++++++++----------- R/prep_nhdplus.R | 532 +++---- R/rebuild_topology.R | 130 - R/rescale_catchments.R | 490 +++---- R/run_plus_attributes.R | 420 +++--- R/subset_nhdplus.R | 1456 ++++++++++---------- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/get_3dhp_data.R | 132 - inst/doc/get_3dhp_data.Rmd | 266 +-- inst/doc/get_3dhp_data.html | 77 - inst/doc/get_data_overview.R | 422 +++--- inst/doc/get_data_overview.html | 548 ++----- inst/doc/indexing.R | 292 ++-- inst/doc/indexing.Rmd | 532 +++---- inst/doc/indexing.html | 337 +--- inst/doc/nhdplusTools.R | 350 ++--- inst/doc/nhdplusTools.Rmd | 678 ++++----- inst/doc/nhdplusTools.html | 237 --- inst/doc/nhdplushr.R | 190 +- inst/doc/nhdplushr.html | 239 +-- inst/doc/plot_nhdplus.R | 258 +-- inst/doc/plot_nhdplus.html | 113 - inst/extdata/3dhp_yahara_flowlines.R | 46 inst/extdata/get_hr_data.R | 158 +- inst/extdata/sample_data.R | 18 inst/extdata/utils.R | 88 - man/add_plus_network_attributes.Rd | 112 - man/align_nhdplus_names.Rd | 58 man/calculate_arbolate_sum.Rd | 72 - man/calculate_total_drainage_area.Rd | 70 - man/disambiguate_flowline_indexes.Rd | 142 +- man/download_rf1.Rd | 62 man/get_DD.Rd | 84 - man/get_UM.Rd | 88 - man/get_UT.Rd | 76 - man/get_characteristics_metadata.Rd | 68 man/get_drainage_area_estimates.Rd | 2 man/get_elev_along_path.Rd | 110 - man/get_geoconnex_reference.Rd | 110 - man/get_hr_data.Rd | 72 - man/get_nhdplushr.Rd | 166 +- man/get_nldi_basin.Rd | 130 - man/get_nldi_index.Rd | 70 - man/get_raindrop_trace.Rd | 84 - man/get_sorted.Rd | 96 - man/get_split_catchment.Rd | 178 +- man/get_streamlevel.Rd | 96 - man/get_streamorder.Rd | 76 - man/get_terminal.Rd | 62 man/get_vaa_path.Rd | 74 - man/get_waterbody_index.Rd | 88 - man/get_wb_outlet.Rd | 68 man/get_xs_point.Rd | 90 - man/get_xs_points.Rd | 96 - man/map_nhdplus.Rd | 168 +- man/navigate_network.Rd | 142 +- man/navigate_nldi.Rd | 124 - man/nhdplusTools_cache_settings.Rd | 48 man/nhdplusTools_data_dir.Rd | 52 man/nhdplus_path.Rd | 58 man/prepare_nhdplus.Rd | 122 - man/subset_rpu.Rd | 76 - man/subset_vpu.Rd | 76 - tests/testthat.R | 6 tests/testthat/data/prep_test_data.R | 94 - tests/testthat/helper.R | 104 - tests/testthat/test_00_plot_bbox_nhdplus.R | 48 tests/testthat/test_00_plot_integration_nhdplus.R | 198 +- tests/testthat/test_00_plot_local_extra_nhdplus.R | 84 - tests/testthat/test_00_plot_local_nhdplus.R | 122 - tests/testthat/test_00_plot_nhdplus.R | 442 +++--- tests/testthat/test_02_subset.R | 440 +++--- tests/testthat/test_02_subset_extras.R | 374 ++--- tests/testthat/test_03_get_functions.R | 766 +++++------ tests/testthat/test_align_nhdplus_names.R | 18 tests/testthat/test_arcrest.R | 134 - tests/testthat/test_boundary_data.R | 16 tests/testthat/test_calc_network.R | 210 +-- tests/testthat/test_geoconnex.R | 102 - tests/testthat/test_get_3dhp.R | 74 - tests/testthat/test_get_codes.R | 260 +-- tests/testthat/test_get_geometry.R | 140 +- tests/testthat/test_get_nhdphr.R | 46 tests/testthat/test_get_path.R | 314 ++-- tests/testthat/test_get_vaa.R | 322 ++-- tests/testthat/test_map_nhdplus.R | 44 tests/testthat/test_navigate.R | 182 +- tests/testthat/test_nhdplusTools.R | 362 ++--- tests/testthat/test_rescale_catchments.R | 238 +-- tests/testthat/test_run_plus_attributes.R | 170 +- tests/testthat/test_wb_index.R | 86 - vignettes/get_3dhp_data.Rmd | 266 +-- vignettes/hydrogeofetch.html |only vignettes/indexing.Rmd | 532 +++---- vignettes/nhdplusTools.Rmd | 678 ++++----- 112 files changed, 12801 insertions(+), 13444 deletions(-)
Title: Vertical Profiles of Biological Signals in Weather Radar Data
Description: 'R' implementation of the 'vol2bird' software for generating vertical profiles
of birds and other biological signals in weather radar data. See Dokter et al.
(2011) <doi:10.1098/rsif.2010.0116> for a paper describing the methodology.
Author: Anders Henja [aut] ,
Adriaan M. Dokter [aut, cre] ,
Alexander Tedeschi [ctb] ,
Tsung-Yu Lin [ctb] ,
Subranshu Maji [ctb] ,
Daniel Sheldon [ctb] ,
Bart Kranstauber [ctb] ,
Jurriaan H. Spaaks [ctb] ,
Lourens Veen [ctb] ,
Iwan Holleman [ctb] ,
Hidde Lei [...truncated...]
Maintainer: Adriaan M. Dokter <vol2birdr@cornell.edu>
Diff between vol2birdR versions 1.3.0 dated 2026-06-09 and 1.3.1 dated 2026-07-27
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 4 ++++ R/vol2bird.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary man/branch.Rd | 4 ---- man/install_config.Rd | 4 ---- man/rsl2odim.Rd | 2 +- man/vol2bird.Rd | 2 +- man/vol2birdR-package.Rd | 1 + src/includes/libvol2bird/constants.h | 6 +++--- src/librave/composite.c | 8 ++++---- src/librave/odim_io_utilities.c | 4 ++-- src/librave/proj_wkt_helper.c | 6 +++--- src/librave/rave_attribute.c | 3 ++- src/libvol2bird/libvol2bird.c | 2 +- 17 files changed, 44 insertions(+), 46 deletions(-)
Title: Reporting Tools for 'shiny' Modules
Description: Prebuilt 'shiny' modules containing tools for the generation
of 'rmarkdown' reports, supporting reproducible research and analysis.
Author: Dawid Kaledkowski [aut] ,
Kartikeya Kirar [aut] ,
Marcin Kosinski [aut],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Mahmoud Hallal [aut],
Chendi Liao [rev],
Dony Unardi [rev, cre],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal.reporter versions 0.6.2 dated 2026-06-29 and 0.6.3 dated 2026-07-27
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/Reporter.R | 8 ++++---- inst/WORDLIST | 1 - inst/doc/teal-report-class.html | 18 +++++++++--------- 6 files changed, 29 insertions(+), 24 deletions(-)
Title: Access 'Office for Budget Responsibility' Data
Description: Provides clean, tidy access to data published by the 'Office for
Budget Responsibility' ('OBR'), the UK's independent fiscal watchdog. Covers
the Public Finances Databank (outturn for PSNB, PSND, receipts, and
expenditure since 1946), the Historical Official Forecasts Database (every
'OBR' forecast since 2010), the Economic and Fiscal Outlook detailed forecast
tables (five-year projections from the latest Budget), the Welfare Trends
Report (incapacity benefit spending and caseloads), and the Fiscal Risks and
Sustainability Report (50-year state pension projections). All returned
objects carry provenance metadata recording the source URL, publication
vintage, retrieval time, and file fingerprint, so analyses can be audited
and reproduced. Data is downloaded from the 'OBR' on first use and cached
locally for subsequent calls. Data is sourced from the 'OBR' website
<https://obr.uk>.
Author: Charles Coverdale [aut, cre]
Maintainer: Charles Coverdale <charlesfcoverdale@gmail.com>
Diff between obr versions 0.2.5 dated 2026-04-14 and 0.5.1 dated 2026-07-27
DESCRIPTION | 21 + MD5 | 123 +++++++--- NAMESPACE | 22 + NEWS.md | 292 +++++++++++++++++++++++- R/compare.R |only R/efo.R | 262 ++++++++++++++++----- R/efo_catalogue.R |only R/efo_dispatcher.R |only R/fiscal_rules.R |only R/fiscal_sustainability.R | 154 ++++-------- R/forecast_panel.R |only R/forecast_revisions.R |only R/forecasts.R | 117 +++++++-- R/globals.R | 11 R/obr-package.R | 2 R/policy_measures.R |only R/public_finances.R | 185 +++++++++------ R/tbl.R |only R/utils.R | 186 +++++++++++++-- R/vintages.R |only R/welfare.R | 124 ++++++---- README.md | 336 ++++++++++++++++++++-------- build |only inst/CITATION | 9 inst/WORDLIST | 35 ++ inst/doc |only man/as.data.frame.obr_tbl.Rd |only man/get_efo_economy.Rd | 41 ++- man/get_efo_fiscal.Rd | 37 ++- man/get_efo_table.Rd |only man/get_expenditure.Rd | 12 - man/get_forecast_revisions.Rd |only man/get_forecasts.Rd | 33 +- man/get_incapacity_caseloads.Rd | 18 - man/get_incapacity_spending.Rd | 14 - man/get_pension_projections.Rd | 56 +--- man/get_policy_measures.Rd |only man/get_psnb.Rd | 13 - man/get_psnd.Rd | 10 man/get_public_finances.Rd | 14 - man/get_receipts.Rd | 11 man/get_welfare_spending.Rd | 22 - man/list_efo_economy_measures.Rd | 6 man/list_forecast_series.Rd | 8 man/obr-package.Rd | 3 man/obr_actual_vs_forecast.Rd |only man/obr_as_of.Rd |only man/obr_compare_vintages.Rd |only man/obr_efo_catalogue.Rd |only man/obr_efo_vintages.Rd |only man/obr_fiscal_rules.Rd |only man/obr_forecast_panel.Rd |only man/obr_pin.Rd |only man/obr_pinned.Rd |only man/obr_provenance.Rd |only man/obr_unpin.Rd |only man/policy_measures_summary.Rd |only man/print.obr_tbl.Rd |only man/sub-.obr_tbl.Rd |only man/summary.obr_tbl.Rd |only tests/testthat/test-compare.R |only tests/testthat/test-efo-table.R |only tests/testthat/test-efo.R | 92 +++++-- tests/testthat/test-fiscal-rules.R |only tests/testthat/test-fiscal-sustainability.R | 65 +---- tests/testthat/test-forecast-panel.R |only tests/testthat/test-forecast-revisions.R |only tests/testthat/test-forecasts.R | 44 ++- tests/testthat/test-policy-measures.R |only tests/testthat/test-public-finances.R | 74 ++++-- tests/testthat/test-tbl.R |only tests/testthat/test-utils.R | 67 +++++ tests/testthat/test-vintages.R |only tests/testthat/test-welfare.R | 51 +++- vignettes |only 75 files changed, 1825 insertions(+), 745 deletions(-)
Title: Dynamical Systems Approach to Infectious Disease Epidemiology
(Ecology/Evolution)
Description: Exploration of simulation models (apps) of various infectious disease transmission dynamics scenarios.
The purpose of the package is to help individuals learn
about infectious disease epidemiology (ecology/evolution) from a dynamical systems perspective.
All apps include explanations of the underlying models and instructions on what to do with the models.
Author: Andreas Handel [aut, cre] ,
Cody Dailey [ctb],
Isaac Chun-Hai Fung [ctb],
Ronald Galiwango [ctb],
Salil Goyal [ctb],
Spencer Hall [ctb],
Ben Listyg [ctb],
Brian McKay [ctb],
John Rossow [ctb],
Sina Solaimanpour [ctb],
Alexis Vittengl [ctb],
Henok Wol [...truncated...]
Maintainer: Andreas Handel <andreas.handel@gmail.com>
Diff between DSAIDE versions 0.9.6 dated 2023-08-23 and 1.0.0 dated 2026-07-27
DESCRIPTION | 18 - MD5 | 84 ++--- NEWS.md | 5 R/DSAIDE-package.R | 2 build/vignette.rds |binary inst/DSAIDE/app.R | 6 inst/appinformation/basicsir_documentation.Rmd | 2 inst/doc/DSAIDE.R | 40 +- inst/doc/DSAIDE.Rmd | 14 inst/doc/DSAIDE.html | 68 ++-- man/DSAIDE-package.Rd | 8 man/dsaidemenu.Rd | 40 +- man/flu1918data.Rd | 60 +-- man/generate_documentation.Rd | 52 +-- man/generate_fctcall.Rd | 46 +- man/generate_ggplot.Rd | 100 +++--- man/generate_plotly.Rd | 98 +++--- man/generate_shinyinput.Rd | 102 +++--- man/norodata.Rd | 62 ++-- man/run_model.Rd | 72 ++-- man/simulate_Characteristics_of_ID_ode.Rd | 212 ++++++------- man/simulate_Complex_ID_Control_ode.Rd | 294 +++++++++---------- man/simulate_Drug_Resistance_Evolution_stochastic.Rd | 206 ++++++------- man/simulate_Environmental_Transmission_model_ode.Rd | 194 ++++++------ man/simulate_Host_Heterogeneity_Model_ode.Rd | 212 ++++++------- man/simulate_SEIRSd_model_stochastic.Rd | 188 ++++++------ man/simulate_SIRSd_model_ode.Rd | 176 +++++------ man/simulate_SIRSd_model_stochastic.Rd | 170 +++++----- man/simulate_SIR_model_discrete.Rd | 158 +++++----- man/simulate_SIR_model_ode.Rd | 158 +++++----- man/simulate_SIR_modelexploration.Rd | 212 ++++++------- man/simulate_SIR_usanalysis.Rd | 228 +++++++------- man/simulate_Vector_transmission_model_ode.Rd | 194 ++++++------ man/simulate_directtransmission_ode.Rd | 166 +++++----- man/simulate_flu_fit.Rd | 222 +++++++------- man/simulate_idcontrolmultigroup_ode.Rd | 290 +++++++++--------- man/simulate_idcontrolmultioutbreak_ode.Rd | 170 +++++----- man/simulate_idpatterns_ode.Rd | 210 ++++++------- man/simulate_idsurveillance_ode.Rd | 182 +++++------ man/simulate_idvaccine_ode.Rd | 170 +++++----- man/simulate_multipathogen_ode.Rd | 168 +++++----- man/simulate_noro_fit.Rd | 186 ++++++------ vignettes/DSAIDE.Rmd | 14 43 files changed, 2630 insertions(+), 2629 deletions(-)
Title: Tidy Tools for Actuarial Mathematics and Life Contingencies
Description: Provides tidyverse-aligned tools for actuarial mathematics
and life contingencies, including life tables, survival probabilities,
actuarial present values of cash flows, life annuities, life insurance,
premiums, reserves, multiple-life calculations, Monte Carlo simulation,
and deterministic cash-flow diagrams. The package emphasizes clear
actuarial notation, reproducible workflows, and pipe-friendly tools for
actuarial education and applied actuarial analysis.
Author: Julian Fajardo [aut, cre]
Maintainer: Julian Fajardo <julian.fajardo1908@gmail.com>
Diff between tidyactuarial versions 0.1.5 dated 2026-07-27 and 0.1.6 dated 2026-07-27
DESCRIPTION | 6 MD5 | 8 NEWS.md | 13 R/simulate_lifetime.R | 965 +++++++++++++------------- tests/testthat/test-cran-multilife-workflow.R | 82 +- 5 files changed, 562 insertions(+), 512 deletions(-)
Title: NHANES Data Search, Preview, and Download Tools
Description: Search, preview, and download datasets from the National Health and Nutrition Examination Survey (NHANES) across survey cycles. The package provides functions to identify relevant datasets by keyword, inspect available .XPT files before downloading, and organize retrieved data locally. Data are retrieved from the NHANES web services available at <https://wwwn.cdc.gov/nchs/nhanes/> .
Author: Sushma Dahal [aut, cre]
Maintainer: Sushma Dahal <sushdahal@gmail.com>
Diff between nhanesdiva versions 1.0.0 dated 2026-05-19 and 1.0.2 dated 2026-07-27
DESCRIPTION | 6 +++--- MD5 | 10 ++++++---- NEWS.md |only R/get_nhanes_data.R | 6 ++++-- R/nhanes_download_utilities.R | 2 +- README.md |only inst/extdata/nhanes_map.rds |binary 7 files changed, 14 insertions(+), 10 deletions(-)
Title: Miscellaneous Statistical Functions Used in 'guide-R'
Description: Companion package for the manual
'guide-R : Guide pour l’analyse de données d’enquêtes avec R' available at
<https://larmarange.github.io/guide-R/>. 'guideR' implements miscellaneous
functions introduced in 'guide-R' to facilitate statistical analysis and
manipulation of survey data.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between guideR versions 0.9.0 dated 2026-01-08 and 0.10.0 dated 2026-07-27
DESCRIPTION | 17 +++---- MD5 | 68 +++++++++++++++-------------- NAMESPACE | 5 ++ NEWS.md | 11 +++- R/add_interactions_by_step.R | 2 R/combine_answers.R | 2 R/contributions.R |only R/long_to_periods.R | 8 +-- R/long_to_seq.R | 8 +-- R/periods_to_long.R | 4 - R/plot_categorical.R | 2 R/plot_continuous.R | 2 R/plot_means.R | 2 R/plot_multiple_answers.R | 5 -- R/plot_proportions.R | 2 R/plot_trajectories.R | 12 ++--- R/proportion.R | 2 R/titanic.R | 11 ++++ inst/WORDLIST | 10 ++++ man/add_interactions_by_step.Rd | 2 man/contributions.Rd |only man/da.svyglm.fit.Rd |only man/grouped_tbl_pivot_wider.Rd | 2 man/gtsummary_themes.Rd | 6 +- man/gtsummary_utilities.Rd | 4 - man/guideR-package.Rd | 53 ++++++++++++----------- man/install_dependencies.Rd | 2 man/leading_zeros.Rd | 76 ++++++++++++++++----------------- man/long_to_seq.Rd | 4 - man/median_iqr.Rd | 2 man/plot_multiple_answers.Rd | 2 man/plot_proportions.Rd | 2 man/proportion.Rd | 2 man/round_preserve_sum.Rd | 82 ++++++++++++++++++------------------ man/safe_pal.Rd | 6 +- man/titanic.Rd | 36 +++++++-------- tests/testthat/test-contributions.R |only 37 files changed, 244 insertions(+), 210 deletions(-)
Title: Universal Design-Oriented Enhancements for 'ggplot2'
Description: A collection of enhancements to 'ggplot2', with a focus on creating Universally Designed, accessible graphs easily and quickly.
Author: Alex Bajcz [aut, cre]
Maintainer: Alex Bajcz <bajcz003@umn.edu>
Diff between ggplotplus versions 0.5.5 dated 2026-06-17 and 0.5.6 dated 2026-07-27
DESCRIPTION | 9 MD5 | 29 +- NAMESPACE | 3 NEWS.md | 5 R/S7Classes.R | 3 R/UserFacingCoreFunctions.R | 389 ++++++++++++++++++++++++++++++++- R/middleware.R | 110 +++++++++ R/s7methods.R | 59 ++++- README.md | 191 +++++++++++++--- man/dot-get_visible_panel_ranges.Rd |only man/dot-has_any_barCol_geom.Rd |only man/dot-is_between.Rd |only man/dot-is_log10_transformed_scale.Rd |only man/gridlines_plus.Rd | 6 man/scale_focus_plus.Rd |only man/theme_plus.Rd | 7 tests/testthat/Rplots.pdf |only tests/testthat/test-Coaching.R | 130 +++++++++++ tests/testthat/test-scale_focus_plus.R |only 19 files changed, 885 insertions(+), 56 deletions(-)
Title: Bass-Ackwards Hierarchical Structural Analysis
Description: Implements Goldberg's (2006) <doi:10.1016/j.jrp.2006.01.001>
bass-ackwards method and modern descendants for hierarchical structural
analysis. Extracts solutions from 1 to k factors using principal
component analysis (PCA), exploratory factor analysis (EFA), or
exploratory structural equation modeling (ESEM) engines, then
characterizes the hierarchy via between-level factor-score
correlations computed via exact linear algebra (Waller, 2007,
<doi:10.1016/j.jrp.2006.08.005>) or materialized scores. Includes the
Forbes (2023) <doi:10.1037/met0000546> extension for redundancy pruning
and all-levels cross-correlations.
Author: Jeffrey M. Girard [aut, cre] ,
Miriam K. Forbes [cph] , CC-BY 4.0)
Maintainer: Jeffrey M. Girard <me@jmgirard.com>
Diff between ackwards versions 0.1.1 dated 2026-07-24 and 0.2.0 dated 2026-07-27
DESCRIPTION | 6 MD5 | 112 - NEWS.md | 105 + R/ackwards.R | 73 R/autoplot.R | 266 ++- R/engine_esem.R | 2 R/layout.R | 455 ++++- R/prune.R | 174 +- R/suggest_k.R | 111 - R/utils.R | 43 README.md | 24 inst/doc/ackwards-engines.Rmd | 225 +- inst/doc/ackwards-engines.html | 224 +- inst/doc/ackwards-forbes.Rmd | 759 +++++++-- inst/doc/ackwards-forbes.html | 820 ++++++++-- inst/doc/ackwards-forbes2023.Rmd | 5 inst/doc/ackwards-forbes2023.html | 4 inst/doc/ackwards-girard.Rmd | 33 inst/doc/ackwards-girard.html | 60 inst/doc/ackwards-intro.Rmd | 50 inst/doc/ackwards-intro.html | 82 - inst/doc/ackwards-ordinal.Rmd | 5 inst/doc/ackwards-ordinal.html | 4 inst/doc/ackwards-suggest-k.Rmd | 61 inst/doc/ackwards-suggest-k.html | 122 - inst/doc/ackwards-visualization.Rmd | 94 + inst/doc/ackwards-visualization.html | 182 +- man/ackwards.Rd | 33 man/autoplot.ackwards.Rd | 68 man/ba_layout.Rd | 46 man/prune.Rd | 48 man/suggest_k.Rd | 5 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/layout.md |only tests/testthat/_snaps/print-snapshot.md | 75 tests/testthat/test-boot_edges.R | 18 tests/testthat/test-ci-path-filters.R |only tests/testthat/test-compute_edges.R | 109 + tests/testthat/test-esem.R | 8 tests/testthat/test-fork-safety.R |only tests/testthat/test-layout.R | 520 ++++++ tests/testthat/test-ledger-anchors.R |only tests/testthat/test-print-snapshot.R | 89 + tests/testthat/test-prune.R | 290 +++ tests/testthat/test-suggest_k.R | 30 tests/testthat/test-vignette-freshness.R |only vignettes/ackwards-engines.Rmd | 225 +- vignettes/ackwards-forbes.Rmd | 759 +++++++-- vignettes/ackwards-forbes2023.Rmd | 5 vignettes/ackwards-girard.Rmd | 33 vignettes/ackwards-intro.Rmd | 50 vignettes/ackwards-ordinal.Rmd | 5 vignettes/ackwards-suggest-k.Rmd | 61 vignettes/ackwards-visualization.Rmd | 94 + vignettes/assets/ackwards-intro-suggest_k_plot-1.png |binary vignettes/assets/ackwards-suggest-k-autoplot-1.png |binary vignettes/assets/ackwards-visualization-drop-pruned-secondary-1.png |only vignettes/assets/ackwards-visualization-drop-pruned-secondary-2.png |only vignettes/assets/ackwards-visualization-manual-order-1.png |only vignettes/assets/ackwards-visualization-node-size-1.png |only vignettes/assets/ackwards-visualization-show-items-1.png |only vignettes/assets/ackwards-visualization-suggest_k_plot-1.png |binary 62 files changed, 5425 insertions(+), 1247 deletions(-)
Title: R Code for Mark Analysis
Description: An interface to the software package MARK that constructs input
files for MARK and extracts the output. MARK was developed by Gary White
and is freely available at <http://www.phidot.org/software/mark/downloads/>
but is not open source.
Author: Simon Bonner [cre],
Jeff Laake [aut],
Eldar Rakhimberdiev [ctb],
Ben Augustine [ctb],
Daniel Turek [ctb],
Brett McClintock [ctb],
Jim Hines [ctb],
Bret Collier [ctb],
Jay Rotella [ctb],
David Pavlacky [ctb],
Andrew Paul [ctb],
Luke Eberhart- Phillips [...truncated...]
Maintainer: Simon Bonner <simon.bonner@uwo.ca>
Diff between RMark versions 3.0.8 dated 2026-06-14 and 3.1.0 dated 2026-07-27
DESCRIPTION | 33 +++++++++++++++++++-------------- MD5 | 12 ++++++------ NEWS | 13 +++++++++++++ R/mark.R | 3 ++- R/release.gof.R | 2 ++ R/run.mark.model.R | 15 ++++++++++----- R/zzz.R | 3 ++- 7 files changed, 54 insertions(+), 27 deletions(-)
Title: Nonnegative Matrix Factorization
Description: Nonnegative matrix factorization (NMF) is a technique to factorize a matrix with nonnegative values into the product of two matrices. Covariates are also allowed. Parallel computing is an option to enhance the speed and high-dimensional and large scale (and/or sparse) data are allowed. Relevant papers include: Sevinc V., Kontemeniotis N., Perdikis T. and Tsagris M. (2026). Non-negative matrix factorization using the R package nnmf <doi:10.48550/arXiv.2607.20084>, Wang Y. X. and Zhang Y. J. (2012). Nonnegative matrix factorization: A comprehensive review. IEEE Transactions on Knowledge and Data Engineering, 25(6): 1336-1353 <doi:10.1109/TKDE.2012.51> and Kim H. and Park H. (2008). Nonnegative matrix factorization based on alternating nonnegativity constrained least squares and active set method. SIAM Journal on Matrix Analysis and Applications, 30(2): 713-730 <doi:10.1137/07069239X>.
Author: Michail Tsagris [aut, cre],
Nikolaos Kontemeniotis [aut],
Christos Adam [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between nnmf versions 1.4 dated 2026-04-12 and 1.6 dated 2026-07-27
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- man/init.Rd | 4 ++++ man/nmf.manh.Rd | 4 ++++ man/nmf.qp.Rd | 8 ++++++-- man/nmf.sqp.Rd | 4 ++++ man/nmfqp.cv.Rd | 5 ++++- man/nmfqp.pred.Rd | 4 ++++ man/nmfqp.reg.Rd | 4 ++++ man/nnmf-package.Rd | 8 ++++++-- 10 files changed, 50 insertions(+), 19 deletions(-)
Title: Reproducible Language-Model Agents for Research
Description: Large language model agents as governed research instruments,
built on 'LLMR'. The package supports designed conversations and factorial
experiments with declared tools and budgets. Each run produces an
inspectable record that can be archived and checked.
Author: Ali Sanaei [aut, cre]
Maintainer: Ali Sanaei <sanaei@uchicago.edu>
Diff between LLMRagent versions 0.8.0 dated 2026-07-21 and 0.8.1 dated 2026-07-27
LLMRagent-0.8.0/LLMRagent/R/calibrate.R |only LLMRagent-0.8.0/LLMRagent/R/sandbox.R |only LLMRagent-0.8.0/LLMRagent/R/society.R |only LLMRagent-0.8.0/LLMRagent/R/superbrain.R |only LLMRagent-0.8.0/LLMRagent/inst/doc/super-brain.R |only LLMRagent-0.8.0/LLMRagent/inst/doc/super-brain.Rmd |only LLMRagent-0.8.0/LLMRagent/inst/doc/super-brain.html |only LLMRagent-0.8.0/LLMRagent/inst/doc/validity-robustness-and-calibration.R |only LLMRagent-0.8.0/LLMRagent/inst/doc/validity-robustness-and-calibration.Rmd |only LLMRagent-0.8.0/LLMRagent/inst/doc/validity-robustness-and-calibration.html |only LLMRagent-0.8.0/LLMRagent/man/agent_calibrate.Rd |only LLMRagent-0.8.0/LLMRagent/man/agent_population.Rd |only LLMRagent-0.8.0/LLMRagent/man/as_llmrcontent_validation.Rd |only LLMRagent-0.8.0/LLMRagent/man/attach_calibration.Rd |only LLMRagent-0.8.0/LLMRagent/man/collect_measures.Rd |only LLMRagent-0.8.0/LLMRagent/man/contamination_report.Rd |only LLMRagent-0.8.0/LLMRagent/man/diagnostics.agent_calibration.Rd |only LLMRagent-0.8.0/LLMRagent/man/exposure_matrix.Rd |only LLMRagent-0.8.0/LLMRagent/man/hash_workflow.Rd |only LLMRagent-0.8.0/LLMRagent/man/report.society.Rd |only LLMRagent-0.8.0/LLMRagent/man/sandbox_tool.Rd |only LLMRagent-0.8.0/LLMRagent/man/society.Rd |only LLMRagent-0.8.0/LLMRagent/man/step_interaction.Rd |only LLMRagent-0.8.0/LLMRagent/man/think_harder.Rd |only LLMRagent-0.8.0/LLMRagent/tests/testthat/_problems |only LLMRagent-0.8.0/LLMRagent/tests/testthat/test-calibrate.R |only LLMRagent-0.8.0/LLMRagent/tests/testthat/test-sandbox.R |only LLMRagent-0.8.0/LLMRagent/tests/testthat/test-society.R |only LLMRagent-0.8.0/LLMRagent/tests/testthat/test-superbrain.R |only LLMRagent-0.8.0/LLMRagent/tests/testthat/testthat-problems.rds |only LLMRagent-0.8.0/LLMRagent/vignettes/super-brain.Rmd |only LLMRagent-0.8.0/LLMRagent/vignettes/validity-robustness-and-calibration.Rmd |only LLMRagent-0.8.1/LLMRagent/DESCRIPTION | 31 LLMRagent-0.8.1/LLMRagent/MD5 | 204 +--- LLMRagent-0.8.1/LLMRagent/NAMESPACE | 28 LLMRagent-0.8.1/LLMRagent/NEWS.md | 17 LLMRagent-0.8.1/LLMRagent/R/00_package.R | 4 LLMRagent-0.8.1/LLMRagent/R/agent.R | 167 ++- LLMRagent-0.8.1/LLMRagent/R/agent_run.R | 19 LLMRagent-0.8.1/LLMRagent/R/approval.R | 121 +- LLMRagent-0.8.1/LLMRagent/R/archive.R | 72 + LLMRagent-0.8.1/LLMRagent/R/claim_type.R | 65 - LLMRagent-0.8.1/LLMRagent/R/delegation.R | 2 LLMRagent-0.8.1/LLMRagent/R/experiment.R | 13 LLMRagent-0.8.1/LLMRagent/R/fanout_synthesis.R |only LLMRagent-0.8.1/LLMRagent/R/manifest.R | 57 - LLMRagent-0.8.1/LLMRagent/R/memory.R | 24 LLMRagent-0.8.1/LLMRagent/R/methods_llmr.R | 28 LLMRagent-0.8.1/LLMRagent/R/persistence.R | 14 LLMRagent-0.8.1/LLMRagent/R/persona.R | 36 LLMRagent-0.8.1/LLMRagent/R/presets.R | 9 LLMRagent-0.8.1/LLMRagent/R/robustness.R | 18 LLMRagent-0.8.1/LLMRagent/R/tool_governance.R | 58 - LLMRagent-0.8.1/LLMRagent/README.md | 362 +++++-- LLMRagent-0.8.1/LLMRagent/build/vignette.rds |binary LLMRagent-0.8.1/LLMRagent/inst/ai/LLMRagent.md | 457 +++++----- LLMRagent-0.8.1/LLMRagent/inst/doc/designed-conversations.R | 2 LLMRagent-0.8.1/LLMRagent/inst/doc/designed-conversations.Rmd | 13 LLMRagent-0.8.1/LLMRagent/inst/doc/designed-conversations.html | 17 LLMRagent-0.8.1/LLMRagent/inst/doc/fanout-synthesis.R |only LLMRagent-0.8.1/LLMRagent/inst/doc/fanout-synthesis.Rmd |only LLMRagent-0.8.1/LLMRagent/inst/doc/fanout-synthesis.html |only LLMRagent-0.8.1/LLMRagent/inst/doc/getting-started.R | 9 LLMRagent-0.8.1/LLMRagent/inst/doc/getting-started.Rmd | 27 LLMRagent-0.8.1/LLMRagent/inst/doc/getting-started.html | 50 - LLMRagent-0.8.1/LLMRagent/inst/doc/governed-tools-and-human-review.R | 4 LLMRagent-0.8.1/LLMRagent/inst/doc/governed-tools-and-human-review.Rmd | 18 LLMRagent-0.8.1/LLMRagent/inst/doc/governed-tools-and-human-review.html | 23 LLMRagent-0.8.1/LLMRagent/inst/doc/provenance-and-archiving.R | 2 LLMRagent-0.8.1/LLMRagent/inst/doc/provenance-and-archiving.Rmd | 47 - LLMRagent-0.8.1/LLMRagent/inst/doc/provenance-and-archiving.html | 60 - LLMRagent-0.8.1/LLMRagent/inst/doc/validity-robustness-and-claims.R |only LLMRagent-0.8.1/LLMRagent/inst/doc/validity-robustness-and-claims.Rmd |only LLMRagent-0.8.1/LLMRagent/inst/doc/validity-robustness-and-claims.html |only LLMRagent-0.8.1/LLMRagent/inst/doc/workflows.Rmd | 13 LLMRagent-0.8.1/LLMRagent/inst/doc/workflows.html | 16 LLMRagent-0.8.1/LLMRagent/man/Agent-class.Rd | 12 LLMRagent-0.8.1/LLMRagent/man/LLMRagent-package.Rd | 4 LLMRagent-0.8.1/LLMRagent/man/agent.Rd | 5 LLMRagent-0.8.1/LLMRagent/man/agent_as_tool.Rd | 2 LLMRagent-0.8.1/LLMRagent/man/agent_experiment.Rd | 7 LLMRagent-0.8.1/LLMRagent/man/agent_fanout_synthesis.Rd |only LLMRagent-0.8.1/LLMRagent/man/agent_manifest.Rd | 19 LLMRagent-0.8.1/LLMRagent/man/agent_robustness.Rd | 4 LLMRagent-0.8.1/LLMRagent/man/agent_tool.Rd | 9 LLMRagent-0.8.1/LLMRagent/man/archive_agent_study.Rd | 17 LLMRagent-0.8.1/LLMRagent/man/as_agent_run.Rd | 3 LLMRagent-0.8.1/LLMRagent/man/budget.Rd | 17 LLMRagent-0.8.1/LLMRagent/man/figures/logo.png |binary LLMRagent-0.8.1/LLMRagent/man/hash_tool_spec.Rd | 10 LLMRagent-0.8.1/LLMRagent/man/interview.Rd | 9 LLMRagent-0.8.1/LLMRagent/man/llm_claim_lint.Rd | 12 LLMRagent-0.8.1/LLMRagent/man/mark_claim_type.Rd | 23 LLMRagent-0.8.1/LLMRagent/man/memory.Rd | 4 LLMRagent-0.8.1/LLMRagent/man/persona_audit.Rd | 8 LLMRagent-0.8.1/LLMRagent/man/persona_variants.Rd | 10 LLMRagent-0.8.1/LLMRagent/man/report.agent_run.Rd | 9 LLMRagent-0.8.1/LLMRagent/man/resume_run.Rd | 13 LLMRagent-0.8.1/LLMRagent/man/robustness-axes.Rd | 6 LLMRagent-0.8.1/LLMRagent/man/save_agent.Rd | 6 LLMRagent-0.8.1/LLMRagent/tests/testthat/helper-fake.R | 4 LLMRagent-0.8.1/LLMRagent/tests/testthat/test-agent.R | 55 + LLMRagent-0.8.1/LLMRagent/tests/testthat/test-claim-type.R | 39 LLMRagent-0.8.1/LLMRagent/tests/testthat/test-experiment.R | 9 LLMRagent-0.8.1/LLMRagent/tests/testthat/test-fanout-synthesis.R |only LLMRagent-0.8.1/LLMRagent/tests/testthat/test-governance.R | 122 ++ LLMRagent-0.8.1/LLMRagent/tests/testthat/test-inspector.R | 15 LLMRagent-0.8.1/LLMRagent/tests/testthat/test-memory.R | 31 LLMRagent-0.8.1/LLMRagent/tests/testthat/test-persistence.R | 14 LLMRagent-0.8.1/LLMRagent/tests/testthat/test-persona.R | 7 LLMRagent-0.8.1/LLMRagent/tests/testthat/test-provenance.R | 93 +- LLMRagent-0.8.1/LLMRagent/tests/testthat/test-robustness.R | 21 LLMRagent-0.8.1/LLMRagent/tests/testthat/test-workflow.R | 14 LLMRagent-0.8.1/LLMRagent/vignettes/designed-conversations.Rmd | 13 LLMRagent-0.8.1/LLMRagent/vignettes/fanout-synthesis.Rmd |only LLMRagent-0.8.1/LLMRagent/vignettes/getting-started.Rmd | 27 LLMRagent-0.8.1/LLMRagent/vignettes/governed-tools-and-human-review.Rmd | 18 LLMRagent-0.8.1/LLMRagent/vignettes/provenance-and-archiving.Rmd | 47 - LLMRagent-0.8.1/LLMRagent/vignettes/validity-robustness-and-claims.Rmd |only LLMRagent-0.8.1/LLMRagent/vignettes/workflows.Rmd | 13 120 files changed, 1720 insertions(+), 1138 deletions(-)
Title: Classes and Methods for "Class Discovery" with Microarrays or
Proteomics
Description: Defines the classes used for "class discovery" problems
in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class
discovery primarily consists of unsupervised clustering methods with
attempts to assess their statistical significance.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between ClassDiscovery versions 3.4.9 dated 2025-09-03 and 3.4.10 dated 2026-07-27
DESCRIPTION | 10 - MD5 | 26 ++-- NAMESPACE | 1 build/vignette.rds |binary inst/doc/maha-test.R | 2 inst/doc/maha-test.pdf |binary inst/doc/oompa-cd.R | 2 inst/doc/oompa-cd.pdf |binary tests/test02.1-just.R | 2 tests/test02.1-just.Rout.save | 74 ++++++----- tests/test03-boot.R | 2 tests/test03-boot.Rout.save | 254 ++++++++++++++++++++--------------------- tests/test04-perturb.R | 2 tests/test04-perturb.Rout.save | 254 ++++++++++++++++++++--------------------- 14 files changed, 319 insertions(+), 310 deletions(-)
More information about ClassDiscovery at CRAN
Permanent link
Title: Communication-Efficient Varying Coefficient Mixed-Effects Models
Description: Scalable inference for Varying Coefficient Mixed-Effects
Models (VCMMs) with large, correlated random effects. Implements
sufficient-statistics, one-step communication-efficient surrogate
likelihood, and SVD-stabilized (Singular Value Decomposition)
estimators with Kronecker and separable covariance structures.
Implements the methodology of Jalili and Lin (2025)
<doi:10.48550/arXiv.2511.12732>.
Author: Lida Jalili [aut, cre],
Li-Hsiang Lin [aut]
Maintainer: Lida Jalili <lchalangarjalilideh1@gsu.edu>
Diff between cevcmm versions 0.1.3 dated 2026-07-24 and 0.1.4 dated 2026-07-27
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 18 ++++++++++++++++++ inst/doc/od-migration.html | 2 +- src/compute_sufficient_stats_cpp.cpp | 20 +++++++++++++++----- 5 files changed, 41 insertions(+), 13 deletions(-)
Title: Flexible, Interactive 'shiny' Modules for Almost Any Plot
Description: Offers a core selection of interactivity-first 'shiny' modules for many
plot types meant to serve as flexible building blocks for applications and
as the base for more complex modules. These modules
allow for the rapid and convenient construction of 'shiny' apps with very few lines
of code and decouple plotting from the underlying data. These modules allow
for full plot aesthetic customization by the end user through UI inputs. Utility
functions for simple UI organization, automated UI tooltips, and additional
plot enhancements are also provided. Includes a multi-panel figure builder app
for arranging multiple modules together in a free-form layout.
Author: Jared Andrews [aut, cre] ,
Jacob Martin [aut]
Maintainer: Jared Andrews <jared.andrews07@gmail.com>
Diff between VizModules versions 0.2.0 dated 2026-06-16 and 0.3.0 dated 2026-07-27
VizModules-0.2.0/VizModules/R/ternaryPlot.R |only VizModules-0.2.0/VizModules/R/ternaryPlot_module_app.R |only VizModules-0.2.0/VizModules/R/ternaryPlot_module_server.R |only VizModules-0.2.0/VizModules/R/ternaryPlot_module_ui.R |only VizModules-0.2.0/VizModules/data/example_roles.rda |only VizModules-0.2.0/VizModules/inst/apps/test_areaPlot |only VizModules-0.2.0/VizModules/inst/apps/test_barPlot |only VizModules-0.2.0/VizModules/inst/apps/test_boxPlot |only VizModules-0.2.0/VizModules/inst/apps/test_dotPlot |only VizModules-0.2.0/VizModules/inst/apps/test_linePlot |only VizModules-0.2.0/VizModules/inst/apps/test_piePlot |only VizModules-0.2.0/VizModules/inst/apps/test_scatterPlot |only VizModules-0.2.0/VizModules/inst/apps/test_volcanoPlot |only VizModules-0.2.0/VizModules/man/INTERNAL_add_ablines.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_add_hlines.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_add_plot_config.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_add_reference_lines.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_add_vlines.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_adjusted_axis_label.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_apply_axis_title_to_annotations.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_apply_facet_subplot_spacing.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_apply_legend_styling.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_apply_plotly_newshape.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_apply_render_margins.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_apply_subplot_axis_styling.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_apply_title_layout.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_axis_titles_as_annotations.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_build_facet_annotations.Rd |only VizModules-0.2.0/VizModules/man/INTERNAL_build_facet_panel_borders.Rd |only 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VizModules-0.3.0/VizModules/man/plotthis_BarPlotOutputUI.Rd | 2 VizModules-0.3.0/VizModules/man/plotthis_BoxPlotApp.Rd | 15 VizModules-0.3.0/VizModules/man/plotthis_BoxPlotOutputUI.Rd | 2 VizModules-0.3.0/VizModules/man/plotthis_DensityPlotApp.Rd | 15 VizModules-0.3.0/VizModules/man/plotthis_DensityPlotOutputUI.Rd | 2 VizModules-0.3.0/VizModules/man/plotthis_DotPlotApp.Rd | 15 VizModules-0.3.0/VizModules/man/plotthis_DotPlotInputsUI.Rd | 14 VizModules-0.3.0/VizModules/man/plotthis_DotPlotOutputUI.Rd | 2 VizModules-0.3.0/VizModules/man/plotthis_HistogramApp.Rd | 15 VizModules-0.3.0/VizModules/man/plotthis_HistogramOutputUI.Rd | 2 VizModules-0.3.0/VizModules/man/plotthis_SplitBarPlotApp.Rd | 15 VizModules-0.3.0/VizModules/man/plotthis_SplitBarPlotInputsUI.Rd | 8 VizModules-0.3.0/VizModules/man/plotthis_SplitBarPlotOutputUI.Rd | 2 VizModules-0.3.0/VizModules/man/plotthis_ViolinPlotApp.Rd | 15 VizModules-0.3.0/VizModules/man/plotthis_ViolinPlotOutputUI.Rd | 2 VizModules-0.3.0/VizModules/man/radarPlotApp.Rd | 15 VizModules-0.3.0/VizModules/man/radarPlotOutputUI.Rd | 2 VizModules-0.3.0/VizModules/man/recycle_line_style.Rd |only VizModules-0.3.0/VizModules/man/register_model_backend.Rd |only VizModules-0.3.0/VizModules/man/reset_axes_inputs.Rd |only VizModules-0.3.0/VizModules/man/reset_legend_inputs.Rd |only VizModules-0.3.0/VizModules/man/reset_lines_inputs.Rd |only VizModules-0.3.0/VizModules/man/reset_plotly_inputs.Rd |only VizModules-0.3.0/VizModules/man/resolve_facet_layout.Rd |only VizModules-0.3.0/VizModules/man/resolve_facet_sharing.Rd |only VizModules-0.3.0/VizModules/man/setup_auto_update_logic.Rd | 18 VizModules-0.3.0/VizModules/man/setup_manual_edits.Rd |only VizModules-0.3.0/VizModules/man/string_to_linetypes.Rd |only VizModules-0.3.0/VizModules/man/uniform_axes_inputs_ui.Rd |only VizModules-0.3.0/VizModules/man/uniform_legend_inputs_ui.Rd |only VizModules-0.3.0/VizModules/man/uniform_lines_inputs_ui.Rd |only VizModules-0.3.0/VizModules/man/uniform_plotly_inputs_ui.Rd |only VizModules-0.3.0/VizModules/man/updateMultiDynamicInput.Rd |only VizModules-0.3.0/VizModules/tests/testthat/test-figureBuilder.R |only VizModules-0.3.0/VizModules/tests/testthat/test-linePlot.R | 16 VizModules-0.3.0/VizModules/tests/testthat/test-plot_mods.R | 447 ++-- VizModules-0.3.0/VizModules/tests/testthat/test-scatterPlot.R | 45 VizModules-0.3.0/VizModules/tests/testthat/test-ui_utils.R |only VizModules-0.3.0/VizModules/vignettes/adding-a-new-module.Rmd | 70 VizModules-0.3.0/VizModules/vignettes/custom-model-lines.Rmd |only VizModules-0.3.0/VizModules/vignettes/custom-modules.Rmd | 37 VizModules-0.3.0/VizModules/vignettes/custom-shiny-inputs.Rmd |only VizModules-0.3.0/VizModules/vignettes/defaults-and-hiding.Rmd |only VizModules-0.3.0/VizModules/vignettes/quick-start.Rmd | 6 VizModules-0.3.0/VizModules/vignettes/statistical-testing.Rmd |only 289 files changed, 6683 insertions(+), 5254 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, implicitly supports parallel processing with high-quality random number
generation, and provides tools for managing high-performance computing (HPC) array jobs
submitted to schedulers such as SLURM. For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb],
Mikko Roenkkoe [aut],
Moritz Ketzer [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.25 dated 2026-03-31 and 2.26 dated 2026-07-27
SimDesign-2.25/SimDesign/tests/tests/mysim-1 |only SimDesign-2.25/SimDesign/tests/tests/mysim-1rds |only SimDesign-2.26/SimDesign/DESCRIPTION | 14 SimDesign-2.26/SimDesign/MD5 | 88 ++--- SimDesign-2.26/SimDesign/NAMESPACE | 6 SimDesign-2.26/SimDesign/NEWS.md | 27 + SimDesign-2.26/SimDesign/R/Design.R | 8 SimDesign-2.26/SimDesign/R/RobbinsMonro.R | 3 SimDesign-2.26/SimDesign/R/SimCollect.R | 6 SimDesign-2.26/SimDesign/R/SimDesign.R | 1 SimDesign-2.26/SimDesign/R/SimResults.R | 2 SimDesign-2.26/SimDesign/R/SimSolve.R | 2 SimDesign-2.26/SimDesign/R/analysis.R | 26 + SimDesign-2.26/SimDesign/R/descript.R | 89 ++++- SimDesign-2.26/SimDesign/R/reSummarise.R | 86 ++++- SimDesign-2.26/SimDesign/R/runArraySimulation.R | 41 ++ SimDesign-2.26/SimDesign/R/runSimulation.R | 38 +- SimDesign-2.26/SimDesign/R/summary_functions.R | 13 SimDesign-2.26/SimDesign/R/util.R | 93 +++++ SimDesign-2.26/SimDesign/inst/doc/Catch_errors.html | 29 + SimDesign-2.26/SimDesign/inst/doc/Fixed_obj_fun.html | 10 SimDesign-2.26/SimDesign/inst/doc/HPC-computing.R | 2 SimDesign-2.26/SimDesign/inst/doc/HPC-computing.Rmd | 9 SimDesign-2.26/SimDesign/inst/doc/HPC-computing.html | 15 SimDesign-2.26/SimDesign/inst/doc/MultipleAnalyses.R | 10 SimDesign-2.26/SimDesign/inst/doc/MultipleAnalyses.Rmd | 10 SimDesign-2.26/SimDesign/inst/doc/MultipleAnalyses.html | 4 SimDesign-2.26/SimDesign/inst/doc/Parallel-computing.html | 4 SimDesign-2.26/SimDesign/inst/doc/Saving-results.html | 46 ++ SimDesign-2.26/SimDesign/inst/doc/SimDesign-intro.html | 174 +++++------ SimDesign-2.26/SimDesign/man/CheckPackages.Rd |only SimDesign-2.26/SimDesign/man/createDesign.Rd | 3 SimDesign-2.26/SimDesign/man/descript.Rd | 42 +- SimDesign-2.26/SimDesign/man/reSummarise.Rd | 41 ++ SimDesign-2.26/SimDesign/man/reexports.Rd | 3 SimDesign-2.26/SimDesign/man/runArraySimulation.Rd | 13 SimDesign-2.26/SimDesign/man/runSimulation.Rd | 33 +- SimDesign-2.26/SimDesign/man/timeFormater.Rd | 5 SimDesign-2.26/SimDesign/tests/tests/mpi/slurm.slurm | 3 SimDesign-2.26/SimDesign/tests/tests/mpi/slurm_par.slurm | 3 SimDesign-2.26/SimDesign/tests/tests/test-01-core.R | 48 ++- SimDesign-2.26/SimDesign/tests/tests/test-02-aggregate.R | 2 SimDesign-2.26/SimDesign/tests/tests/test-03-array.R | 25 + SimDesign-2.26/SimDesign/tests/tests/test-04-prepare.R | 2 SimDesign-2.26/SimDesign/tests/tests/test-06-robbins-monro.R |only SimDesign-2.26/SimDesign/vignettes/HPC-computing.Rmd | 9 SimDesign-2.26/SimDesign/vignettes/MultipleAnalyses.Rmd | 10 47 files changed, 776 insertions(+), 322 deletions(-)
Title: R6-Based ML Learners for 'mlexperiments'
Description: Enhances 'mlexperiments'
<https://CRAN.R-project.org/package=mlexperiments> with additional
machine learning ('ML') learners. The package provides R6-based
learners for the following algorithms: 'glmnet'
<https://CRAN.R-project.org/package=glmnet>, 'ranger'
<https://CRAN.R-project.org/package=ranger>, 'xgboost'
<https://CRAN.R-project.org/package=xgboost>, and 'lightgbm'
<https://CRAN.R-project.org/package=lightgbm>. These can be used
directly with the 'mlexperiments' R package.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mllrnrs versions 0.0.8 dated 2026-01-17 and 0.0.9 dated 2026-07-27
DESCRIPTION | 8 MD5 | 74 +-- R/learner_glmnet.R | 11 R/learner_lightgbm.R | 15 R/learner_ranger.R | 11 R/learner_xgboost.R | 13 build/vignette.rds |binary inst/doc/mllrnrs_glmnet_binary.R | 300 +++++++++------ inst/doc/mllrnrs_glmnet_binary.html | 328 ++++++++++------ inst/doc/mllrnrs_glmnet_binary.qmd | 302 +++++++++------ inst/doc/mllrnrs_glmnet_multiclass.html | 3 inst/doc/mllrnrs_glmnet_regression.html | 3 inst/doc/mllrnrs_lightgbm_binary.R | 559 ++++++++-------------------- inst/doc/mllrnrs_lightgbm_binary.html | 586 ++++++++---------------------- inst/doc/mllrnrs_lightgbm_binary.qmd | 559 ++++++++-------------------- inst/doc/mllrnrs_lightgbm_multiclass.html | 3 inst/doc/mllrnrs_lightgbm_regression.html | 3 inst/doc/mllrnrs_ranger_binary.R | 469 ++++++++++++++---------- inst/doc/mllrnrs_ranger_binary.html | 496 +++++++++++++++---------- inst/doc/mllrnrs_ranger_binary.qmd | 469 ++++++++++++++---------- inst/doc/mllrnrs_ranger_multiclass.html | 3 inst/doc/mllrnrs_ranger_regression.html | 3 inst/doc/mllrnrs_xgboost_binary.R | 197 +++++----- inst/doc/mllrnrs_xgboost_binary.html | 236 ++++++------ inst/doc/mllrnrs_xgboost_binary.qmd | 197 +++++----- inst/doc/mllrnrs_xgboost_multiclass.html | 3 inst/doc/mllrnrs_xgboost_regression.html | 3 man/LearnerGlmnet.Rd | 108 ++--- man/LearnerLightgbm.Rd | 114 ++--- man/LearnerRanger.Rd | 96 ++-- man/LearnerXgboost.Rd | 112 ++--- tests/testthat/test-binary.R | 15 tests/testthat/test-multiclass.R | 1 tests/testthat/test-regression.R | 1 vignettes/mllrnrs_glmnet_binary.qmd | 302 +++++++++------ vignettes/mllrnrs_lightgbm_binary.qmd | 559 ++++++++-------------------- vignettes/mllrnrs_ranger_binary.qmd | 469 ++++++++++++++---------- vignettes/mllrnrs_xgboost_binary.qmd | 197 +++++----- 38 files changed, 3401 insertions(+), 3427 deletions(-)
Title: Forecasting Models for Intermittent Time Series
Description: Extends the 'fable' framework to support forecasting methods
specifically designed for intermittent time series data, where demand
occurs sporadically with many zero values. All methods produce probabilistic
forecasts returned as 'distributional' objects. The returned forecasts can be
used to evaluate accuracy, plot and print the results seamlessly with 'fable'.
The methods include:
Harvey, Fernandes (1989) <doi:10.1080/07350015.1989.10509750>,
Willemain, Smart, Schwarz (2004) <doi:10.1016/S0169-2070(03)00013-X>,
Zhou, Viswanathan (2011) <doi:10.1016/j.ijpe.2010.09.021>,
Snyder, Ord, Beaumont (2012) <doi:10.1016/j.ijforecast.2011.03.009>,
Kolassa (2016) <doi:10.1016/j.ijforecast.2015.12.004>,
Hasni, Aguir, Babai, Jemai (2019) <doi:10.1080/00207543.2018.1424375>,
Damato, Azzimonti, Corani (2025) <doi:10.1016/j.ijforecast.2025.10.001>,
Sbrana (2025) <doi:10.1080/01605682.2025.2569661>.
Author: Stefano Damato [aut, cre, cph] ,
Lorenzo Zambon [aut] ,
Dario Azzimonti [aut]
Maintainer: Stefano Damato <stefanodamato128@gmail.com>
Diff between fable.intermittent versions 0.1.1 dated 2026-06-24 and 0.2.0 dated 2026-07-27
fable.intermittent-0.1.1/fable.intermittent/R/dist_tweedie.R |only fable.intermittent-0.1.1/fable.intermittent/man/dist_tweedie.Rd |only fable.intermittent-0.1.1/fable.intermittent/man/tweedie.Rd |only fable.intermittent-0.1.1/fable.intermittent/src/tweedie.cpp |only fable.intermittent-0.1.1/fable.intermittent/tests/testthat/test-dist_tweedie.R |only fable.intermittent-0.2.0/fable.intermittent/DESCRIPTION | 11 +- fable.intermittent-0.2.0/fable.intermittent/MD5 | 25 ++--- fable.intermittent-0.2.0/fable.intermittent/NAMESPACE | 19 ---- fable.intermittent-0.2.0/fable.intermittent/NEWS.md | 12 ++ fable.intermittent-0.2.0/fable.intermittent/R/RcppExports.R | 12 -- fable.intermittent-0.2.0/fable.intermittent/R/data.R | 36 +++++++ fable.intermittent-0.2.0/fable.intermittent/R/fable.intermittent-package.R | 1 fable.intermittent-0.2.0/fable.intermittent/R/twees.R | 1 fable.intermittent-0.2.0/fable.intermittent/README.md | 23 +---- fable.intermittent-0.2.0/fable.intermittent/data/pasta.rda |only fable.intermittent-0.2.0/fable.intermittent/man/pasta.Rd |only fable.intermittent-0.2.0/fable.intermittent/src/RcppExports.cpp | 46 ---------- 17 files changed, 77 insertions(+), 109 deletions(-)
More information about fable.intermittent at CRAN
Permanent link
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data
mining tasks such as clustering and classification. The development of
this package was supported in part by NSF IIS-0948893, NSF CMMI
1728612, and NIH R21HG005912. Hahsler et al (2017)
<doi:10.18637/jss.v076.i14>.
Author: Michael Hahsler [aut, cre, cph] ,
Matthew Bolanos [ctb],
John Forrest [ctb],
Matthias Carnein [ctb],
Dennis Assenmacher [ctb],
Dalibor Krleza [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 2.0-3 dated 2025-03-12 and 2.0.6 dated 2026-07-27
DESCRIPTION | 14 +- MD5 | 198 ++++++++++++++--------------- NEWS.md | 16 ++ R/DSC_Reachability.R | 2 R/DSC_Static.R | 4 R/DSD_MG.R | 32 ++-- R/DSD_Memory.R | 4 R/DSD_mlbenchData.R | 41 ++---- R/MGC.R | 67 +++++---- R/ellipse.R | 4 R/evaluate.DSC.R | 4 README.md | 19 ++ build/partial.rdb |binary build/vignette.rds |binary inst/README_files/DSOutlier_DBSTREAM-1.png |binary inst/README_files/Dstream-1.png |binary inst/README_files/stream-1.png |binary inst/doc/extending_stream.R | 2 inst/doc/extending_stream.Rnw | 2 inst/doc/extending_stream.pdf |binary inst/doc/stream.R | 2 inst/doc/stream.Rnw | 12 - inst/doc/stream.pdf |binary man/DSAggregate.Rd | 26 +-- man/DSAggregate_Sample.Rd | 6 man/DSAggregate_Window.Rd | 6 man/DSC.Rd | 46 +++--- man/DSC_BICO.Rd | 16 +- man/DSC_BIRCH.Rd | 16 +- man/DSC_DBSCAN.Rd | 14 +- man/DSC_DBSTREAM.Rd | 30 ++-- man/DSC_DStream.Rd | 30 ++-- man/DSC_EA.Rd | 14 +- man/DSC_Hierarchical.Rd | 14 +- man/DSC_Kmeans.Rd | 14 +- man/DSC_Macro.Rd | 40 ++--- man/DSC_Micro.Rd | 42 +++--- man/DSC_R.Rd | 26 +-- man/DSC_Reachability.Rd | 16 +- man/DSC_Sample.Rd | 16 +- man/DSC_SlidingWindow.Rd | 40 ++--- man/DSC_Static.Rd | 26 +-- man/DSC_TwoStage.Rd | 34 ++-- man/DSC_Window.Rd | 16 +- man/DSC_evoStream.Rd | 24 +-- man/DSClassifier.Rd | 24 +-- man/DSClassifier_SlidingWindow.Rd | 4 man/DSD.Rd | 42 +++--- man/DSD_BarsAndGaussians.Rd | 42 +++--- man/DSD_Benchmark.Rd | 42 +++--- man/DSD_Cubes.Rd | 42 +++--- man/DSD_Gaussians.Rd | 42 +++--- man/DSD_MG.Rd | 74 +++++----- man/DSD_Memory.Rd | 42 +++--- man/DSD_Mixture.Rd | 42 +++--- man/DSD_NULL.Rd | 42 +++--- man/DSD_ReadDB.Rd | 46 +++--- man/DSD_ReadStream.Rd | 42 +++--- man/DSD_Target.Rd | 42 +++--- man/DSD_UniformNoise.Rd | 42 +++--- man/DSD_mlbenchData.Rd | 42 +++--- man/DSD_mlbenchGenerator.Rd | 42 +++--- man/DSF.Rd | 62 ++++----- man/DSF_Convolve.Rd | 16 +- man/DSF_Downsample.Rd | 16 +- man/DSF_ExponentialMA.Rd | 16 +- man/DSF_FeatureSelection.Rd | 16 +- man/DSF_Func.Rd | 16 +- man/DSF_Scale.Rd | 16 +- man/DSF_dplyr.Rd | 20 +- man/DSOutlier.Rd | 26 +-- man/DSRegressor.Rd | 24 +-- man/DSRegressor_SlidingWindow.Rd | 4 man/DST.Rd | 20 +- man/DST_SlidingWindow.Rd | 20 +- man/DST_WriteStream.Rd | 20 +- man/MGC.Rd | 67 +++++---- man/animate_cluster.Rd | 38 ++--- man/animate_data.Rd | 52 +++---- man/close_stream.Rd | 42 +++--- man/evaluate.DSC.Rd | 36 ++--- man/evaluate.Rd | 26 +-- man/get_assignment.Rd | 26 +-- man/get_points.Rd | 42 +++--- man/plot.DSC.Rd | 34 ++-- man/plot.DSD.Rd | 50 +++---- man/predict.Rd | 46 +++--- man/prune_clusters.Rd | 26 +-- man/read_saveDSC.Rd | 28 ++-- man/recluster.Rd | 26 +-- man/reset_stream.Rd | 42 +++--- man/stream-package.Rd | 7 + man/stream_pipeline.Rd | 22 +-- man/update.Rd | 20 +- src/BICO.cpp | 2 src/DBSTREAM.cpp | 2 tests/testthat/test-DSD.R | 2 vignettes/extending_stream.Rnw | 2 vignettes/stream.Rnw | 12 - vignettes/stream.bib | 64 ++++----- 100 files changed, 1347 insertions(+), 1288 deletions(-)
Title: Model Context Protocol Servers and Clients
Description: Implements the Model Context Protocol (MCP). Users can start
'R'-based servers, serving functions as tools for large language
models to call before responding to the user in MCP-compatible apps
like 'Claude Desktop' and 'Claude Code', with options to run those
tools inside of interactive 'R' sessions. On the other end, when 'R'
is the client via the 'ellmer' package, users can register tools from
third-party MCP servers to integrate additional context into chats.
Author: Simon Couch [aut, cre] ,
Winston Chang [aut] ,
Charlie Gao [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between mcptools versions 1.0.0 dated 2026-07-02 and 1.0.1 dated 2026-07-27
DESCRIPTION | 10 - MD5 | 53 ++++---- NEWS.md | 49 ++++++++ R/aaa.R | 1 R/client-auth.R | 92 +++++++++++++-- R/client-http.R | 69 ++++++++++- R/client.R | 230 +++++++++++++++++++++++++++----------- R/mcptools-package.R | 11 - R/server.R | 57 +++++++-- R/session.R | 189 +++++++++++++++++++++++++------ R/socket-auth.R |only R/socket-dir.R |only R/tools.R | 183 ++++++++++++++++++++++++------ R/utils.R | 194 ++++++++++++++++++++++++++++++++ inst/doc/server.Rmd | 2 inst/doc/server.html | 36 +++-- man/client.Rd | 13 +- man/server.Rd | 14 ++ tests/testthat/helper.R | 7 + tests/testthat/setup.R |only tests/testthat/test-client-auth.R | 171 ++++++++++++++++++++++++---- tests/testthat/test-client-http.R | 183 +++++++++++++++++++++++++++++- tests/testthat/test-client.R | 14 ++ tests/testthat/test-server.R | 27 +++- tests/testthat/test-session.R | 119 +++++++++++++++++++ tests/testthat/test-socket-auth.R |only tests/testthat/test-socket-dir.R |only tests/testthat/test-tools.R | 157 +++++++++++++++++++++++++ tests/testthat/test-utils.R | 76 ++++++++++++ vignettes/server.Rmd | 2 30 files changed, 1710 insertions(+), 249 deletions(-)
Title: Likelihood-Based Confidence Interval in Structural Equation
Models
Description: Forms likelihood-based confidence intervals
(LBCIs) for parameters in structural equation modeling,
introduced in Cheung and Pesigan (2023)
<doi:10.1080/10705511.2023.2183860>. Currently
implements the algorithm illustrated by Pek and Wu
(2018) <doi:10.1037/met0000163>, and supports the robust
LBCI proposed by Falk (2018)
<doi:10.1080/10705511.2017.1367254>.
Author: Shu Fai Cheung [aut, cre] ,
Ivan Jacob Agaloos Pesigan [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semlbci versions 0.12.0 dated 2026-07-08 and 0.12.1 dated 2026-07-27
DESCRIPTION | 6 MD5 | 44 NEWS.md | 19 R/check_sem_out.R | 12 R/ci_bound_wn_i.R | 7 R/set_start_wn.R | 13 README.md | 2 inst/doc/loglike.Rmd | 340 +++--- inst/doc/loglike.html | 8 inst/doc/semlbci.Rmd | 35 inst/doc/semlbci.html | 672 ++++++------ inst/doc/technical_searching_one_bound.Rmd | 1049 +++++++++---------- inst/doc/technical_searching_one_bound.html | 235 ++-- tests/testthat/test-lav_mod_to_ram.R | 64 - tests/testthat/test-semlbci_wn_mg_ustd_pa_user_eq.R | 6 tests/testthat/test-semlbci_wn_mg_ustd_sem_user_eq.R | 6 vignettes/loglike.Rmd | 340 +++--- vignettes/loglike.Rmd.original | 4 vignettes/loglike_plot_a-1.png |binary vignettes/loglike_plot_ab-1.png |binary vignettes/semlbci.Rmd | 35 vignettes/semlbci.Rmd.original | 6 vignettes/technical_searching_one_bound.Rmd | 1049 +++++++++---------- 23 files changed, 2028 insertions(+), 1924 deletions(-)
Title: Influential Cases in Structural Equation Modeling
Description: Sensitivity analysis in structural equation modeling using
influence measures and diagnostic plots. Support leave-one-out casewise
sensitivity analysis presented by Pek and MacCallum (2011)
<doi:10.1080/00273171.2011.561068> and approximate casewise influence
using scores and casewise likelihood. An introduction to
the package can be found in Cheung and Lai (2026)
<doi:10.1080/00273171.2026.2634293>.
Author: Shu Fai Cheung [aut, cre] ,
Mark Hok Chio Lai [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semfindr versions 0.2.0 dated 2026-03-06 and 0.2.1 dated 2026-07-27
DESCRIPTION | 8 MD5 | 124 ++-- NEWS.md | 24 R/approx_check.R | 12 R/generic_index_plot.R | 27 R/lavaan_rerun.R | 14 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/casewise_scores.Rmd | 4 inst/doc/casewise_scores.html | 14 inst/doc/selecting_cases.html | 10 inst/doc/semfindr.Rmd | 4 inst/doc/semfindr.html | 42 - inst/doc/user_id.Rmd | 253 +++++++- inst/doc/user_id.html | 283 ++++++++-- man/est_change_plot.Rd | 8 man/est_change_raw.Rd | 4 man/index_plot.Rd | 11 man/influence_plot.Rd | 8 man/lavaan_rerun.Rd | 8 man/pars_id.Rd | 2 man/pars_id_to_lorg.Rd | 6 man/semfindr-package.Rd | 1 tests/testthat/test-est_change_loo_multi_select_by_op.R | 4 tests/testthat/test-est_change_raw_approx_multi.R | 3 tests/testthat/test-est_change_raw_approx_multi_labelled.R | 3 tests/testthat/test-est_change_raw_loo_multi.R | 24 tests/testthat/test-est_change_raw_loo_multi_select_by_op.R | 49 + tests/testthat/test-lavaan_rerun_multi_nonconvergence.R | 15 vignettes/articles/user_fun-1.png |binary vignettes/articles/user_fun2-1.png |binary vignettes/articles/user_function.Rmd | 48 + vignettes/articles/user_function.Rmd.original | 23 vignettes/casewise_scores.Rmd | 4 vignettes/compare-approx-gcd-1.png |binary vignettes/compare-est-change-1.png |binary vignettes/plot-change-chisq-1.png |binary vignettes/plot-change-rmsea-1.png |binary vignettes/semfindr.Rmd | 4 vignettes/semfindr_est_chagne_plot_fig-1.png |binary vignettes/semfindr_est_change_gcd_plot_approx_std_fig-1.png |binary vignettes/semfindr_est_change_gcd_plot_approx_std_fig_2-1.png |binary vignettes/semfindr_est_change_gcd_plot_fig-1.png |binary vignettes/semfindr_est_change_gcd_plot_fig_2-1.png |binary vignettes/semfindr_est_change_plot_approx_fig-1.png |binary vignettes/semfindr_est_change_plot_approx_fig_2-1.png |binary vignettes/semfindr_est_change_plot_approx_fig_3-1.png |binary vignettes/semfindr_est_change_plot_fig_2-1.png |binary vignettes/semfindr_est_change_plot_fig_3-1.png |binary vignettes/semfindr_gcd_gof_md_plot_approx_fig-1.png |binary vignettes/semfindr_gcd_gof_md_plot_fig-1.png |binary vignettes/semfindr_gcd_gof_plot_approx_fig-1.png |binary vignettes/semfindr_gcd_gof_plot_fig-1.png |binary vignettes/semfindr_gcd_plot_approx_fig-1.png |binary vignettes/semfindr_gcd_plot_fig-1.png |binary vignettes/semfindr_md_plot_approx_fig-1.png |binary vignettes/semfindr_md_plot_fig-1.png |binary vignettes/user_id.Rmd | 253 +++++++- vignettes/user_id_gcd_gof_md_plot_fig-1.png |binary vignettes/user_id_gcd_gof_plot_fig-1.png |binary vignettes/user_id_gcd_plot_fig-1.png |binary vignettes/user_id_md_plot_fig-1.png |binary 63 files changed, 1004 insertions(+), 295 deletions(-)
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'.
For example, the 'parallelFor()' function can be used to convert the work of
a standard serial "for" loop into a parallel one and the 'parallelReduce()'
function can be used for accumulating aggregate or other values.
Author: Kevin Ushey [aut, cre] ,
JJ Allaire [aut],
Romain Francois [aut, cph],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] ,
Hamada S. Badr [ctb] ,
Dirk Eddelbuettel [aut] ,
Intel [aut, cph] ,
UXL Foundation [aut, cph] ,
Microsoft [cph],
Posit, PB [...truncated...]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between RcppParallel versions 6.1.0 dated 2026-07-25 and 6.1.1 dated 2026-07-27
DESCRIPTION | 6 +-- MD5 | 6 +-- NEWS.md | 14 ++++++++ tools/config/configure.R | 81 +---------------------------------------------- 4 files changed, 22 insertions(+), 85 deletions(-)
Title: Utilities for Geo-Spatial Cluster Detection and Significance
Classification
Description: Provides utilities for manipulating time series of location-based counts of events to detect geo-spatial clusters. Significance of these clusters is determined using a set of models that classify based on a learned relationship between observed and the log(observed/expected) ratio of counts. The approach implemented here is similar to prospective space-time estimation of clusters using the scan statistic.
Author: Luke C. Mullany [aut, cre],
Howard S. Burkom [aut]
Maintainer: Luke C. Mullany <luke.mullany@jhuapl.edu>
Diff between gsClusterDetect versions 1.0.0 dated 2026-03-23 and 1.0.1 dated 2026-07-27
DESCRIPTION | 26 +++--- MD5 | 61 +++++++++++---- NAMESPACE | 3 NEWS.md | 15 +++ R/cluster_functions.R | 117 +++++++++++++++++++++++------- R/data.R | 15 +++ R/location_functions.R | 56 ++++++++++++-- R/mapping_functions.R |only R/sysdata.rda |binary README.md | 16 +++- build |only data/states.rda |only inst |only man/create_dist_list.Rd | 12 +-- man/dot-clean_up_alert_table.Rd |only man/find_clusters.Rd | 15 +-- man/gen_nearby_case_info.Rd | 6 - man/generate_case_grids.Rd | 7 + man/generate_observed_expected.Rd | 11 +- man/get_point_data.Rd |only man/gsClusterDetect-package.Rd | 6 + man/map_clusters.Rd |only man/map_clusters_ggplot.Rd |only man/map_clusters_plotly.Rd |only man/prepare_map_data.Rd |only man/sf_to_plotly_polygons.Rd |only man/state_distance_matrix.Rd |only man/states.Rd |only man/validate_clusters.Rd |only man/validate_sf_file.Rd |only tests/testthat/test-cluster-compression.R | 12 ++- tests/testthat/test-cluster-find.R | 4 - tests/testthat/test-location-functions.R | 37 +++++++++ tests/testthat/test-mapping_functions.R |only vignettes |only 35 files changed, 320 insertions(+), 99 deletions(-)
More information about gsClusterDetect at CRAN
Permanent link
Title: Set Alpha Based on Sample Size Using Bayes Factors
Description: Sets the alpha level for coefficients in a regression model
as a decreasing function of the sample size through the use of
Jeffreys' Approximate Bayes factor. You tell alphaN() your sample
size, and it tells you to which value you must lower alpha to avoid
Lindley's Paradox. For details, see Wulff and Taylor (2024)
<doi:10.1177/14761270231214429>. Alpha can also be calibrated to the
effect-size and moment Bayes factors of Klauer, Meyer-Grant, and
Kellen (2025) <doi:10.3758/s13423-024-02612-2>, which center the
alternative hypothesis on an effect size of your choosing.
Author: Jesper Wulff [aut, cre] ,
Luke Taylor [aut]
Maintainer: Jesper Wulff <jwulff@econ.au.dk>
Diff between alphaN versions 0.2.0 dated 2026-07-12 and 0.3.0 dated 2026-07-27
DESCRIPTION | 11 - MD5 | 61 +++++--- NAMESPACE | 14 ++ NEWS.md | 85 ++++++++++++ R/JAB.R | 40 ++++- R/JAB_plot.R | 34 +++- R/alphaN.R | 92 +++++++++---- R/alphaN_plot.R | 123 ++++++++++++----- R/alphaN_power.R |only R/alphaN_report.R |only R/klauer.R | 221 +++++++++++++++++++++++++++----- R/klauerBF.R |only R/n_effective.R |only README.md | 132 ++++++++++++++++++- inst/CITATION | 20 ++ inst/WORDLIST | 33 +++- inst/doc/intro-alphaN.R | 12 + inst/doc/intro-alphaN.Rmd | 31 ++++ inst/doc/intro-alphaN.html | 51 ++++++- man/JAB.Rd | 21 ++- man/alphaN.Rd | 99 ++++++++++---- man/alphaN_plot.Rd | 42 +++++- man/alphaN_power.Rd |only man/alphaN_power_plot.Rd |only man/alphaN_report.Rd |only man/figures/README-JAB-plot-1.png |binary man/figures/README-alphaN-plot-1.png |binary man/figures/README-power-plot-1.png |only man/klauerBF.Rd |only man/n_effective.Rd |only tests/testthat/test-JAB.R | 18 ++ tests/testthat/test-alphaN_report.R |only tests/testthat/test-crossval.R |only tests/testthat/test-klauer-regression.R |only tests/testthat/test-klauerBF.R |only tests/testthat/test-n_effective.R |only tests/testthat/test-numerics.R |only tests/testthat/test-plots.R | 16 ++ tests/testthat/test-power.R |only vignettes/intro-alphaN.Rmd | 31 ++++ 40 files changed, 986 insertions(+), 201 deletions(-)
Title: Poisson Lognormal Models
Description: The Poisson-lognormal model and variants (Chiquet,
Mariadassou and Robin, 2021 <doi:10.3389/fevo.2021.588292>) can be
used for a variety of multivariate problems when count data are at
play, including principal component analysis for count data,
discriminant analysis, model-based clustering and network inference.
Implements variational algorithms to fit such models accompanied with
a set of functions for visualization and diagnostic.
Author: Julien Chiquet [aut, cre] ,
Mahendra Mariadassou [aut] ,
Stephane Robin [aut],
Francois Gindraud [aut],
Julie Aubert [ctb],
Bastien Batardiere [ctb],
Giovanni Poggiato [ctb],
Cole Trapnell [ctb],
Maddy Duran [ctb]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between PLNmodels versions 1.2.2 dated 2025-03-21 and 1.3.0 dated 2026-07-27
PLNmodels-1.2.2/PLNmodels/inst/simus_ZIPLN |only PLNmodels-1.2.2/PLNmodels/man/figures/PLN-1.png |only PLNmodels-1.2.2/PLNmodels/man/figures/PLNLDA-1.png |only PLNmodels-1.2.2/PLNmodels/man/figures/PLNPCA-1.png |only PLNmodels-1.2.2/PLNmodels/man/figures/PLNPCA-2.png |only PLNmodels-1.2.2/PLNmodels/man/figures/PLNnetwork-1.png |only PLNmodels-1.2.2/PLNmodels/man/figures/PLNnetwork-2.png |only PLNmodels-1.2.2/PLNmodels/src/lambertW.cpp |only PLNmodels-1.2.2/PLNmodels/src/lambertW.h |only PLNmodels-1.2.2/PLNmodels/src/optim_diag_cov.cpp |only PLNmodels-1.2.2/PLNmodels/src/optim_fixed_cov.cpp |only PLNmodels-1.2.2/PLNmodels/src/optim_full_cov.cpp |only PLNmodels-1.2.2/PLNmodels/src/optim_rank_cov.cpp |only PLNmodels-1.2.2/PLNmodels/src/optim_spherical.cpp |only PLNmodels-1.2.2/PLNmodels/src/optim_zi-pln.cpp |only PLNmodels-1.2.2/PLNmodels/tests/testthat/_snaps |only PLNmodels-1.2.2/PLNmodels/vignettes/article |only PLNmodels-1.3.0/PLNmodels/DESCRIPTION | 30 PLNmodels-1.3.0/PLNmodels/MD5 | 273 ++- PLNmodels-1.3.0/PLNmodels/NAMESPACE | 19 PLNmodels-1.3.0/PLNmodels/NEWS.md | 49 PLNmodels-1.3.0/PLNmodels/R/PLN.R | 71 PLNmodels-1.3.0/PLNmodels/R/PLNLDA.R | 51 PLNmodels-1.3.0/PLNmodels/R/PLNLDAfit-class.R | 55 PLNmodels-1.3.0/PLNmodels/R/PLNPCA.R | 107 - PLNmodels-1.3.0/PLNmodels/R/PLNPCAfamily-class.R | 91 + PLNmodels-1.3.0/PLNmodels/R/PLNPCAfit-class.R | 282 +++ PLNmodels-1.3.0/PLNmodels/R/PLNfit-S3methods.R | 94 + PLNmodels-1.3.0/PLNmodels/R/PLNfit-class.R | 467 +++--- PLNmodels-1.3.0/PLNmodels/R/PLNmixture.R | 48 PLNmodels-1.3.0/PLNmodels/R/PLNmixturefamily-class.R | 18 PLNmodels-1.3.0/PLNmodels/R/PLNmixturefit-class.R | 26 PLNmodels-1.3.0/PLNmodels/R/PLNmodels-package.R | 2 PLNmodels-1.3.0/PLNmodels/R/PLNnetwork.R | 79 - PLNmodels-1.3.0/PLNmodels/R/PLNnetworkfamily-class.R | 76 - PLNmodels-1.3.0/PLNmodels/R/PLNnetworkfit-class.R | 41 PLNmodels-1.3.0/PLNmodels/R/RcppExports.R | 156 +- PLNmodels-1.3.0/PLNmodels/R/ZIPLN.R | 29 PLNmodels-1.3.0/PLNmodels/R/ZIPLNfit-S3methods.R | 85 + PLNmodels-1.3.0/PLNmodels/R/ZIPLNfit-class.R | 237 +-- PLNmodels-1.3.0/PLNmodels/R/ZIPLNnetwork.R | 16 PLNmodels-1.3.0/PLNmodels/R/microcosm.R |only PLNmodels-1.3.0/PLNmodels/R/plot_utils.R | 53 PLNmodels-1.3.0/PLNmodels/R/utils-zipln.R | 19 PLNmodels-1.3.0/PLNmodels/R/utils.R | 201 ++ PLNmodels-1.3.0/PLNmodels/R/zzz.R | 1 PLNmodels-1.3.0/PLNmodels/build/partial.rdb |binary PLNmodels-1.3.0/PLNmodels/build/vignette.rds |binary PLNmodels-1.3.0/PLNmodels/data/microcosm.rda |only PLNmodels-1.3.0/PLNmodels/inst/WORDLIST | 48 PLNmodels-1.3.0/PLNmodels/inst/doc/Import_data.Rmd | 2 PLNmodels-1.3.0/PLNmodels/inst/doc/Import_data.html | 12 PLNmodels-1.3.0/PLNmodels/inst/doc/PLN.Rmd | 4 PLNmodels-1.3.0/PLNmodels/inst/doc/PLN.html | 106 - PLNmodels-1.3.0/PLNmodels/inst/doc/PLNLDA.Rmd | 2 PLNmodels-1.3.0/PLNmodels/inst/doc/PLNLDA.html | 736 +++++----- PLNmodels-1.3.0/PLNmodels/inst/doc/PLNPCA.R | 9 PLNmodels-1.3.0/PLNmodels/inst/doc/PLNPCA.Rmd | 15 PLNmodels-1.3.0/PLNmodels/inst/doc/PLNPCA.html | 251 +-- PLNmodels-1.3.0/PLNmodels/inst/doc/PLNmixture.R | 9 PLNmodels-1.3.0/PLNmodels/inst/doc/PLNmixture.Rmd | 15 PLNmodels-1.3.0/PLNmodels/inst/doc/PLNmixture.html | 123 - PLNmodels-1.3.0/PLNmodels/inst/doc/PLNnetwork.R | 29 PLNmodels-1.3.0/PLNmodels/inst/doc/PLNnetwork.Rmd | 54 PLNmodels-1.3.0/PLNmodels/inst/doc/PLNnetwork.html | 309 ++-- PLNmodels-1.3.0/PLNmodels/inst/doc/Trichoptera.Rmd | 2 PLNmodels-1.3.0/PLNmodels/inst/doc/Trichoptera.html | 18 PLNmodels-1.3.0/PLNmodels/inst/doc/ZIPLN.R |only PLNmodels-1.3.0/PLNmodels/inst/doc/ZIPLN.Rmd |only PLNmodels-1.3.0/PLNmodels/inst/doc/ZIPLN.html |only PLNmodels-1.3.0/PLNmodels/man/AIC.PLNfit.Rd |only PLNmodels-1.3.0/PLNmodels/man/AIC.ZIPLNfit.Rd |only PLNmodels-1.3.0/PLNmodels/man/BIC.PLNfit.Rd |only PLNmodels-1.3.0/PLNmodels/man/BIC.ZIPLNfit.Rd |only PLNmodels-1.3.0/PLNmodels/man/ICL.Rd |only PLNmodels-1.3.0/PLNmodels/man/Networkfamily.Rd | 321 ++-- PLNmodels-1.3.0/PLNmodels/man/PLN.Rd | 2 PLNmodels-1.3.0/PLNmodels/man/PLNLDA.Rd | 21 PLNmodels-1.3.0/PLNmodels/man/PLNLDA_param.Rd | 15 PLNmodels-1.3.0/PLNmodels/man/PLNLDAfit.Rd | 431 ++--- PLNmodels-1.3.0/PLNmodels/man/PLNLDAfit_diagonal.Rd | 130 - PLNmodels-1.3.0/PLNmodels/man/PLNPCA.Rd | 9 PLNmodels-1.3.0/PLNmodels/man/PLNPCA_param.Rd | 74 - PLNmodels-1.3.0/PLNmodels/man/PLNPCAfamily.Rd | 263 +-- PLNmodels-1.3.0/PLNmodels/man/PLNPCAfit.Rd | 594 ++++---- PLNmodels-1.3.0/PLNmodels/man/PLN_param.Rd | 35 PLNmodels-1.3.0/PLNmodels/man/PLNfamily.Rd | 253 +-- PLNmodels-1.3.0/PLNmodels/man/PLNfit.Rd | 497 +++--- PLNmodels-1.3.0/PLNmodels/man/PLNfit_diagonal.Rd | 247 +-- PLNmodels-1.3.0/PLNmodels/man/PLNfit_fixedcov.Rd | 161 +- PLNmodels-1.3.0/PLNmodels/man/PLNfit_genpop.Rd |only PLNmodels-1.3.0/PLNmodels/man/PLNfit_spherical.Rd | 119 - PLNmodels-1.3.0/PLNmodels/man/PLNmixture.Rd | 9 PLNmodels-1.3.0/PLNmodels/man/PLNmixture_param.Rd | 66 PLNmodels-1.3.0/PLNmodels/man/PLNmixturefamily.Rd | 287 ++- PLNmodels-1.3.0/PLNmodels/man/PLNmixturefit.Rd | 379 ++--- PLNmodels-1.3.0/PLNmodels/man/PLNmodels-package.Rd | 1 PLNmodels-1.3.0/PLNmodels/man/PLNnetwork.Rd | 2 PLNmodels-1.3.0/PLNmodels/man/PLNnetwork_param.Rd | 100 + PLNmodels-1.3.0/PLNmodels/man/PLNnetworkfamily.Rd | 137 - PLNmodels-1.3.0/PLNmodels/man/PLNnetworkfit.Rd | 240 +-- PLNmodels-1.3.0/PLNmodels/man/ZIPLN.Rd | 2 PLNmodels-1.3.0/PLNmodels/man/ZIPLN_param.Rd | 13 PLNmodels-1.3.0/PLNmodels/man/ZIPLNfit.Rd | 373 ++--- PLNmodels-1.3.0/PLNmodels/man/ZIPLNfit_diagonal.Rd | 101 - PLNmodels-1.3.0/PLNmodels/man/ZIPLNfit_fixed.Rd | 101 - PLNmodels-1.3.0/PLNmodels/man/ZIPLNfit_sparse.Rd | 199 +- PLNmodels-1.3.0/PLNmodels/man/ZIPLNfit_spherical.Rd | 101 - PLNmodels-1.3.0/PLNmodels/man/ZIPLNnetwork.Rd | 2 PLNmodels-1.3.0/PLNmodels/man/ZIPLNnetwork_param.Rd | 14 PLNmodels-1.3.0/PLNmodels/man/ZIPLNnetworkfamily.Rd | 147 + PLNmodels-1.3.0/PLNmodels/man/compute_PLN_starting_point.Rd | 25 PLNmodels-1.3.0/PLNmodels/man/compute_ZIPLN_starting_point.Rd |only PLNmodels-1.3.0/PLNmodels/man/figures/README-pln-corrplot-1.png |only PLNmodels-1.3.0/PLNmodels/man/figures/README-plnlda-1.png |only PLNmodels-1.3.0/PLNmodels/man/figures/README-plnmixture-1.png |only PLNmodels-1.3.0/PLNmodels/man/figures/README-plnnetwork-1.png |only PLNmodels-1.3.0/PLNmodels/man/figures/README-plnpca-1.png |only PLNmodels-1.3.0/PLNmodels/man/logLik.PLNfit.Rd |only PLNmodels-1.3.0/PLNmodels/man/logLik.ZIPLNfit.Rd |only PLNmodels-1.3.0/PLNmodels/man/microcosm.Rd |only PLNmodels-1.3.0/PLNmodels/man/predict.ZIPLNfit.Rd | 4 PLNmodels-1.3.0/PLNmodels/src/RcppExports.cpp | 570 +++++-- PLNmodels-1.3.0/PLNmodels/src/builtin_optim_pln.h |only PLNmodels-1.3.0/PLNmodels/src/builtin_optim_zipln.h |only PLNmodels-1.3.0/PLNmodels/src/builtin_plnpca.h |only PLNmodels-1.3.0/PLNmodels/src/covariance_pln.h |only PLNmodels-1.3.0/PLNmodels/src/covariance_plnpca.h |only PLNmodels-1.3.0/PLNmodels/src/covariance_zipln.h |only PLNmodels-1.3.0/PLNmodels/src/nlopt_optim_pln.h |only PLNmodels-1.3.0/PLNmodels/src/nlopt_optim_zipln.h |only PLNmodels-1.3.0/PLNmodels/src/nlopt_wrapper.cpp | 36 PLNmodels-1.3.0/PLNmodels/src/nlopt_wrapper.h | 10 PLNmodels-1.3.0/PLNmodels/src/optim_genet_cov.cpp | 13 PLNmodels-1.3.0/PLNmodels/src/optim_zipln_mstep.cpp |only PLNmodels-1.3.0/PLNmodels/src/packing.cpp | 14 PLNmodels-1.3.0/PLNmodels/src/packing.h | 2 PLNmodels-1.3.0/PLNmodels/src/utils.h | 141 + PLNmodels-1.3.0/PLNmodels/src/wrappers_builtin_optim_pln.cpp |only PLNmodels-1.3.0/PLNmodels/src/wrappers_builtin_optim_plnpca.cpp |only PLNmodels-1.3.0/PLNmodels/src/wrappers_builtin_optim_zipln.cpp |only PLNmodels-1.3.0/PLNmodels/src/wrappers_nlopt_optim_pln.cpp |only PLNmodels-1.3.0/PLNmodels/src/wrappers_nlopt_optim_plnpca.cpp |only PLNmodels-1.3.0/PLNmodels/src/wrappers_nlopt_optim_zipln.cpp |only PLNmodels-1.3.0/PLNmodels/tests/testthat/Rplots.pdf |binary PLNmodels-1.3.0/PLNmodels/tests/testthat/test-backends.R |only PLNmodels-1.3.0/PLNmodels/tests/testthat/test-import-utils.R | 44 PLNmodels-1.3.0/PLNmodels/tests/testthat/test-pln-genpop.R |only PLNmodels-1.3.0/PLNmodels/tests/testthat/test-pln.R | 43 PLNmodels-1.3.0/PLNmodels/tests/testthat/test-plnfit.R | 80 + PLNmodels-1.3.0/PLNmodels/tests/testthat/test-plnlda-fit.R | 22 PLNmodels-1.3.0/PLNmodels/tests/testthat/test-plnnetworkfit.R | 40 PLNmodels-1.3.0/PLNmodels/tests/testthat/test-plnpcafit.R | 58 PLNmodels-1.3.0/PLNmodels/tests/testthat/test-standard-error.R | 2 PLNmodels-1.3.0/PLNmodels/tests/testthat/test-zipln.R | 20 PLNmodels-1.3.0/PLNmodels/tests/testthat/test-ziplnfit.R | 39 PLNmodels-1.3.0/PLNmodels/vignettes/Import_data.Rmd | 2 PLNmodels-1.3.0/PLNmodels/vignettes/PLN.Rmd | 4 PLNmodels-1.3.0/PLNmodels/vignettes/PLNLDA.Rmd | 2 PLNmodels-1.3.0/PLNmodels/vignettes/PLNPCA.Rmd | 15 PLNmodels-1.3.0/PLNmodels/vignettes/PLNmixture.Rmd | 15 PLNmodels-1.3.0/PLNmodels/vignettes/PLNnetwork.Rmd | 54 PLNmodels-1.3.0/PLNmodels/vignettes/Trichoptera.Rmd | 2 PLNmodels-1.3.0/PLNmodels/vignettes/ZIPLN.Rmd |only PLNmodels-1.3.0/PLNmodels/vignettes/articles |only PLNmodels-1.3.0/PLNmodels/vignettes/bib |only 166 files changed, 6375 insertions(+), 4748 deletions(-)
Title: Object-Oriented Implementation of Dose Escalation Designs
Description: Implements a wide range of dose escalation
designs. The focus is on model-based designs, ranging from classical and
modern continual reassessment methods (CRMs) based on dose-limiting toxicity
endpoints to dual-endpoint designs taking into account a biomarker/efficacy
outcome. Bayesian inference is performed via MCMC sampling in JAGS, and it is easy
to setup a new design with custom JAGS code. However, it is also possible to
implement 3+3 designs for comparison or models with non-Bayesian estimation.
The whole package is written in a modular form in the S4 class system, making it
very flexible for adaptation to new models, escalation or stopping rules.
Further details are presented in
Sabanés Bové et al. (2019) <doi:10.18637/jss.v089.i10>.
Author: Daniel Sabanes Bove [aut, cre] ,
Wai Yin Yeung [aut],
Burak Kuersad Guenhan [aut],
Giuseppe Palermo [aut],
Thomas Jaki [aut],
Jiawen Zhu [aut],
Ziwei Liao [aut],
Dimitris Kontos [aut],
Marlene Schulte-Goebel [aut],
Doug Kelkhoff [aut] ,
Oliver Boix [ [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between crmPack versions 2.2.0 dated 2026-07-05 and 2.2.1 dated 2026-07-27
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ build/partial.rdb |binary tests/testthat/test-helpers_design.R | 8 ++++---- tests/testthat/test-helpers_knitr.R | 2 +- tests/testthat/test-mcmc.R | 10 ++++++---- 7 files changed, 26 insertions(+), 18 deletions(-)
Title: Posetic Data Analysis
Description: Build and manipulate partially ordered sets (posets), to perform some data analysis
on them and to implement multi-criteria decision making procedures. Several efficient ways for generating linear extensions are implemented, together with functions for building mutual ranking probabilities, incomparability, dominance and separation scores (Fattore, M., De Capitani, L., Avellone, A., Suardi, A. (2024). A fuzzy posetic toolbox for multi-criteria evaluation on ordinal data systems. ANNALS OF OPERATIONS RESEARCH <doi:10.1007/s10479-024-06352-3>).
Author: Alessandro Avellone [aut, cre],
Lucio De Capitani [aut],
Marco Fattore [aut]
Maintainer: Alessandro Avellone <alessandro.avellone@unimib.it>
Diff between poseticDataAnalysis versions 1.1.0 dated 2026-05-18 and 1.1.1 dated 2026-07-27
DESCRIPTION | 6 MD5 | 40 +++--- R/00package-class.R | 13 +- R/00package-exports.R | 24 +++ R/BubleyDyerMRPGenerator.R | 13 -- R/BuildBubleyDyerEvaluationGenerator.R | 13 -- R/BuildBubleyDyerSeparationGenerator.R | 13 -- R/LEBubleyDyer.R | 17 +- build/partial.rdb |binary man/BubleyDyerEvaluationGenerator-class.Rd | 2 man/BubleyDyerGenerator-class.Rd | 2 man/BubleyDyerMRPGenerator-class.Rd | 2 man/BubleyDyerMRPGenerator.Rd | 2 man/BubleyDyerSeparationGenerator-class.Rd | 2 man/BuildBubleyDyerEvaluationGenerator.Rd | 2 man/BuildBubleyDyerSeparationGenerator.Rd | 2 man/LEBubleyDyer.Rd | 2 src/dimensionalityReduction.cpp | 1 src/dimensionalityReduction.h | 1 src/displayMessage.h | 7 - src/rwrapper.cpp | 181 +++++++++++++++++++---------- 21 files changed, 221 insertions(+), 124 deletions(-)
More information about poseticDataAnalysis at CRAN
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Title: Conditional Inference Trees with Stacked Multiple Imputation
Description: Implements the stacked-imputation workflow for conditional
inference trees ('ctree') described in Sherlock et al. (2026)
<doi:10.1080/00273171.2026.2661244>. When data contain missing values,
multiply imputed datasets (e.g., from 'mice') are stacked vertically
and a single 'ctree' is fit on the combined data. To correct for the
artificially inflated sample size introduced by stacking, every
node-level test statistic is divided by the number of imputations M,
the node-level p-values are recomputed from the chi-squared reference
distribution 'ctree' uses (including its multiplicity adjustment across
candidate splitting variables), and the tree is compressed bottom-up
(the Stack/M correction). Degrees of freedom are derived for each node
and each candidate variable, so univariate, bivariate and
higher-dimensional outcomes are all handled, as are unordered factor
predictors, whose degrees of freedom depend on how many levels remain
in a node. The result is a conservative but interpre [...truncated...]
Author: Phillip Sherlock [aut, cre]
Maintainer: Phillip Sherlock <phillip.sherlock@ufl.edu>
Diff between ctreeMI versions 0.3.0 dated 2026-07-25 and 1.0.0 dated 2026-07-27
ctreeMI-0.3.0/ctreeMI/R/zzz.R |only ctreeMI-0.3.0/ctreeMI/man/rescale_alpha.Rd |only ctreeMI-1.0.0/ctreeMI/DESCRIPTION | 28 ctreeMI-1.0.0/ctreeMI/MD5 | 44 ctreeMI-1.0.0/ctreeMI/NAMESPACE | 4 ctreeMI-1.0.0/ctreeMI/NEWS.md | 112 + ctreeMI-1.0.0/ctreeMI/R/ctree_stacked.R | 55 ctreeMI-1.0.0/ctreeMI/R/methods.R | 14 ctreeMI-1.0.0/ctreeMI/R/node_table.R | 76 + ctreeMI-1.0.0/ctreeMI/R/stackM.R | 664 ++++++---- ctreeMI-1.0.0/ctreeMI/R/utils.R | 71 - ctreeMI-1.0.0/ctreeMI/build/partial.rdb |binary ctreeMI-1.0.0/ctreeMI/man/check_stackM_extraction.Rd |only ctreeMI-1.0.0/ctreeMI/man/ctreeMI-package.Rd | 119 + ctreeMI-1.0.0/ctreeMI/man/ctree_stacked.Rd | 295 ++-- ctreeMI-1.0.0/ctreeMI/man/node_table.Rd | 113 - ctreeMI-1.0.0/ctreeMI/man/print.ctreeMI.Rd | 32 ctreeMI-1.0.0/ctreeMI/man/print.ctreeMI_nodes.Rd |only ctreeMI-1.0.0/ctreeMI/man/print.ctreeMI_report.Rd |only ctreeMI-1.0.0/ctreeMI/man/prune_stackM.Rd |only ctreeMI-1.0.0/ctreeMI/man/report_ctreeMI.Rd | 77 - ctreeMI-1.0.0/ctreeMI/man/rescale_statistic.Rd |only ctreeMI-1.0.0/ctreeMI/man/stack_imputations.Rd | 65 ctreeMI-1.0.0/ctreeMI/man/summary.ctreeMI.Rd | 38 ctreeMI-1.0.0/ctreeMI/tests/testthat/test-ctreeMI.R | 111 + ctreeMI-1.0.0/ctreeMI/tests/testthat/test-stackM-correction.R | 9 ctreeMI-1.0.0/ctreeMI/tests/testthat/test-stackM-numerics.R |only 27 files changed, 1205 insertions(+), 722 deletions(-)
Title: Collinearity Detection using Redefined Variance Inflation Factor
and Graphical Methods
Description: The detection of troubling approximate collinearity in a multiple linear regression model is a classical problem in Econometrics. This package is focused on determining whether or not the degree of approximate multicollinearity in a multiple linear regression model is of concern, meaning that it affects the statistical analysis (i.e. individual significance tests) of the model. This objective is achieved by using the variance inflation factor redefined and the scatterplot between the variance inflation factor and the coefficient of variation. For more details see Salmerón R., García C.B. and García J. (2018) <doi:10.1080/00949655.2018.1463376>, Salmerón, R., Rodríguez, A. and García C. (2020) <doi:10.1007/s00180-019-00922-x>, Salmerón, R., García, C.B, Rodríguez, A. and García, C. (2022) <doi:10.32614/RJ-2023-010>, Salmerón, R., García, C.B. and García, J. (2025) <doi:10.1007/s10614-024-10575-8> and Salmerón, R., García, C.B, García J. (2023, working paper) < [...truncated...]
Author: R. Salmeron [aut, cre],
C.B. Garcia [aut]
Maintainer: R. Salmeron <romansg@ugr.es>
Diff between rvif versions 3.2 dated 2025-10-09 and 3.2.1 dated 2026-07-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- tests/testthat/test-cv_vif.R | 2 +- tests/testthat/test-rvifs.R | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Generate SVG Information Cards with Embedded Fonts and Badges
Description: Create self-contained SVG information cards with embedded 'Google
Fonts', shields-style badges, and custom logos. Cards are fully
portable SVG files ideal for dashboards, reports, and web applications.
Includes functions to export cards to PNG and PDF formats and display them in
'R Markdown' and 'Quarto' documents.
Author: Andre Leite [aut, cre],
Marcos Wasiliew [aut],
Hugo Vasconcelos [aut],
Carlos Amorim [aut],
Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between cardargus versions 0.2.3 dated 2026-06-14 and 0.2.5 dated 2026-07-27
cardargus-0.2.3/cardargus/man/start_chrome_session.Rd |only cardargus-0.2.3/cardargus/man/write_svg_html_temp.Rd |only cardargus-0.2.5/cardargus/DESCRIPTION | 20 cardargus-0.2.5/cardargus/MD5 | 66 + cardargus-0.2.5/cardargus/NAMESPACE | 1 cardargus-0.2.5/cardargus/NEWS.md | 71 ++ cardargus-0.2.5/cardargus/R/cards.R | 4 cardargus-0.2.5/cardargus/R/chrome.R | 405 ++++++++---- cardargus-0.2.5/cardargus/R/conversion.R | 97 ++ cardargus-0.2.5/cardargus/R/fonts.R | 28 cardargus-0.2.5/cardargus/R/knitr.R | 28 cardargus-0.2.5/cardargus/R/utils.R | 7 cardargus-0.2.5/cardargus/R/zzz.R | 30 cardargus-0.2.5/cardargus/README.md | 33 cardargus-0.2.5/cardargus/inst/doc/export.R | 19 cardargus-0.2.5/cardargus/inst/doc/export.Rmd | 38 + cardargus-0.2.5/cardargus/inst/doc/export.html | 258 ++++--- cardargus-0.2.5/cardargus/man/batch_svg_to_base64_chrome.Rd | 10 cardargus-0.2.5/cardargus/man/batch_svg_to_png_chrome.Rd | 10 cardargus-0.2.5/cardargus/man/build_svg_html.Rd |only cardargus-0.2.5/cardargus/man/cardargus-package.Rd | 4 cardargus-0.2.5/cardargus/man/chrome_session.Rd |only cardargus-0.2.5/cardargus/man/chrome_session_alive.Rd |only cardargus-0.2.5/cardargus/man/close_chrome_session.Rd |only cardargus-0.2.5/cardargus/man/convert_svg_with_session.Rd | 16 cardargus-0.2.5/cardargus/man/figures/cardargus_card.png |binary cardargus-0.2.5/cardargus/man/font_cache_dir.Rd | 7 cardargus-0.2.5/cardargus/man/load_svg_page.Rd |only cardargus-0.2.5/cardargus/man/running_under_check.Rd |only cardargus-0.2.5/cardargus/man/save_card_for_knitr.Rd | 6 cardargus-0.2.5/cardargus/man/svg_to_pdf.Rd |only cardargus-0.2.5/cardargus/man/svg_to_pdf_chrome.Rd | 14 cardargus-0.2.5/cardargus/man/svg_to_png.Rd | 11 cardargus-0.2.5/cardargus/man/svg_to_png_chrome.Rd | 16 cardargus-0.2.5/cardargus/man/wait_for_page_ready.Rd |only cardargus-0.2.5/cardargus/tests/testthat/test-chrome.R |only cardargus-0.2.5/cardargus/tests/testthat/test-conversion.R | 21 cardargus-0.2.5/cardargus/tests/testthat/test-fonts.R |only cardargus-0.2.5/cardargus/tests/testthat/test-utils.R | 4 cardargus-0.2.5/cardargus/vignettes/export.Rmd | 38 + 40 files changed, 897 insertions(+), 365 deletions(-)
Title: Tools for 'iNZight'
Description: Provides a collection of wrapper functions for common variable and dataset manipulation workflows primarily used by 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions. Additionally, many of the functions return the 'tidyverse' code used to obtain the result in an effort to bridge the gap between GUI and coding.
Author: Tom Elliott [aut, cre] ,
Daniel Barnett [aut],
Yiwen He [aut],
Zhaoming Su [aut],
Lushi Cai [ctb],
Akshay Gupta [ctb],
Owen Jin [ctb],
Christoph Knopf [ctb]
Maintainer: Tom Elliott <tom.elliott@auckland.ac.nz>
This is a re-admission after prior archival of version 2.0.3 dated 2025-07-29
Diff between iNZightTools versions 2.0.3 dated 2025-07-29 and 2.0.4 dated 2026-07-27
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/aggregate.R | 20 ++++++++++---------- R/helpers.R | 11 +++++++---- R/import_data.R | 2 +- R/mutate.R | 18 +++++++++++++----- tests/testthat/casdict.csv | 2 +- tests/testthat/test_helpers.R | 15 +++++++++++++++ tests/testthat/test_missing_to_cat.R | 30 ++++++++++++++++++++++++++++++ 9 files changed, 88 insertions(+), 32 deletions(-)
Title: German Election Database (GERDA)
Description: Provides tools to download datasets of German elections
covering local, state, federal, mayoral, European Parliament, and county
(Kreistag) elections, with federal county-level coverage from 1953 and
other families extending through 2025. The package supplies turnout, vote
shares, and derived indicators at the municipal and county level, including
geographically harmonized datasets that account for changes in municipal
boundaries over time and incorporate mail-in voting districts. Bundled data
includes county-level INKAR covariates (1995-2022) and municipality-level
Zensus 2022 indicators. Data is sourced from
<https://github.com/awiedem/german_election_data>.
Author: Hanno Hilbig [aut, cre]
Maintainer: Hanno Hilbig <hhilbig@ucdavis.edu>
Diff between gerda versions 0.8.0 dated 2026-07-24 and 0.8.1 dated 2026-07-27
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 9 +++++++++ R/gerda_cache.R | 3 ++- R/gerda_covariates.R | 5 +++-- R/load_gerda_web.R | 8 ++++++-- man/clear_gerda_cache.Rd | 3 ++- man/gerda_covariates.Rd | 5 +++-- man/load_gerda_web.Rd | 8 ++++++-- 9 files changed, 42 insertions(+), 21 deletions(-)
Title: Formal Concept Analysis
Description: Provides tools to perform fuzzy formal concept analysis, presented in Wille (1982) <doi:10.1007/978-3-642-01815-2_23> and in Ganter and Obiedkov (2016) <doi:10.1007/978-3-662-49291-8>. It provides functions to load and save a formal context, extract its concept lattice and implications. In addition, one can use the implications to compute semantic closures of fuzzy sets and, thus, build recommendation systems. Boolean Matrix Factorization (BMF) is provided by several algorithms (such as GreConD, ASSO, RSF, RSF-ES, GreEss, PaNDa+, and Hyper+).
Author: Domingo Lopez Rodriguez [aut, cre] ,
Angel Mora [aut]
Maintainer: Domingo Lopez Rodriguez <dominlopez78@gmail.com>
Diff between fcaR versions 1.5.0 dated 2026-02-13 and 2.1.0 dated 2026-07-27
DESCRIPTION | 31 - MD5 | 201 +++++++--- NAMESPACE | 10 NEWS.md | 73 +++ R/RcppExports.R | 145 ++++++- R/add_col.R | 2 R/bond_lattice.R |only R/bonds.R |only R/build_sparse_matrix.R | 17 R/compute_closure_fuzzy.R | 5 R/concept_lattice.R | 203 ++++++++++- R/concept_set.R | 34 + R/datasets.R | 22 + R/experimental_blocks.R |only R/experimental_preconcepts.R |only R/fcaR_helpers.R |only R/fcaRviz.R |only R/formal_context.R | 513 +++++++++++++++++++--------- R/implication_set.R | 197 ++++++++-- R/intersection.R | 6 R/lattice_plot.R | 241 +++++++++---- R/logics.R | 25 - R/options.R | 4 R/rule_set.R | 29 + R/subsets.R | 4 R/to_fraction.R | 21 + build/vignette.rds |binary data/guesswho.rda |only inst/doc/bonds.R |only inst/doc/bonds.Rmd |only inst/doc/bonds.html |only inst/doc/concept_lattice.R | 4 inst/doc/concept_lattice.Rmd | 13 inst/doc/concept_lattice.html | 309 ++++++++-------- inst/doc/creating_contexts.R | 28 - inst/doc/creating_contexts.Rmd | 4 inst/doc/creating_contexts.html | 122 ------ inst/doc/fuzzy_fca.html | 69 +-- inst/doc/implications.R | 7 inst/doc/implications.Rmd | 16 inst/doc/implications.html | 41 +- inst/doc/lattice_properties.R | 8 inst/doc/lattice_properties.Rmd | 20 + inst/doc/lattice_properties.html | 32 + inst/doc/lattice_visualization.html | 10 inst/doc/matrix_factorization.R | 62 +-- inst/doc/matrix_factorization.Rmd | 175 ++++++--- inst/doc/matrix_factorization.html | 345 ++++++++++++------ inst/rstudio/addins.dcf | 5 inst/shiny-examples |only man/BondLattice.Rd |only man/ConceptLattice.Rd | 79 ++++ man/ConceptSet.Rd | 22 - man/FormalContext.Rd | 179 ++++++++- man/ImplicationSet.Rd | 20 + man/RuleSet.Rd | 14 man/attribute_set.Rd |only man/bonds.Rd |only man/bonds_mcis.Rd |only man/bonds_standard.Rd |only man/fcaR-package.Rd | 2 man/guesswho.Rd |only man/is_bond.Rd |only man/iterative_recommender.Rd |only man/lattice_plot.Rd | 6 man/object_set.Rd |only man/recommendation_table.Rd |only man/run_fcaRviz.Rd |only src/Logics.cpp | 43 -- src/Logics.h | 6 src/MatrixFactorization.cpp | 392 --------------------- src/RSF_ES_attr.cpp |only src/RSF_attr.cpp |only src/RcppExports.cpp | 456 ++++++++++++++++++++---- src/algorithm1_opt.cpp |only src/arrow_relations.cpp |only src/asso.cpp |only src/aux_functions.h | 5 src/binary_do_optimized.cpp |only src/closure_cpp.cpp |only src/experimental_blocks_cpp.cpp |only src/fastcbo.cpp | 2 src/fcaR_bitset.h |only src/fcaR_utils.h |only src/fuzzy_do.cpp | 68 +-- src/grecond.cpp |only src/greess.cpp |only src/hyper_inclose.cpp |only src/hyper_plus_optimized.cpp |only src/inclose.cpp | 2 src/lattice_algorithms.cpp | 39 +- src/lincbo.cpp |only src/my_tests.cpp | 46 -- src/nextclosure.cpp | 193 +++++++--- src/panda_versions.cpp |only src/poset_metrics.cpp |only src/protoconcepts.cpp |only src/standard_bonds_opt.cpp |only src/vector_operations.cpp | 68 --- tests/testthat/Rplots.pdf |binary tests/testthat/test-arrow_advanced.R |only tests/testthat/test-arrow_relations.R |only tests/testthat/test-bonds.R |only tests/testthat/test-concept_lattice.R | 2 tests/testthat/test-coverage_sniper.R | 365 +++++++++++++++++++ tests/testthat/test-direct_optimal_binary.R |only tests/testthat/test-factorization.R | 67 ++- tests/testthat/test-formal_context.R | 3 tests/testthat/test-helpers.R |only tests/testthat/test-implication_set.R | 2 tests/testthat/test-lincbo.R |only tests/testthat/test-protoconcepts.R |only tests/testthat/test-standard_context.R |only vignettes/bonds.Rmd |only vignettes/concept_lattice.Rmd | 13 vignettes/creating_contexts.Rmd | 4 vignettes/implications.Rmd | 16 vignettes/lattice_properties.Rmd | 20 + vignettes/matrix_factorization.Rmd | 175 ++++++--- 119 files changed, 3558 insertions(+), 1804 deletions(-)
Title: Fast Survival Analysis and Simulation for Clinical Trials
Description: Provides fast alternatives to standard survival analysis functions
in the 'survival' package, together with tools for time-to-event trial
simulation and sequential analysis. The estimation and testing functions
cover a single-time-point Kaplan-Meier estimator (survfit_fast()), log-rank
tests including weighted and stratified variants (survdiff_fast()), a
closed-form hazard ratio estimator based on the Pike-Halley Estimator method
(coxph_fast()), restricted mean survival time (rmst_fast()), window mean
survival time (wmst_fast()), milestone survival comparison
(milestone_fast()), median survival time (medsurv_fast()), the max-combo
test (maxcombo_fast()), the robust modestly-weighted log-rank test
(rmw_fast()), the weighted Kaplan-Meier (Pepe-Fleming) test (wkm_fast()),
the average hazard with survival weight (ahsw_fast()), and the
Kalbfleisch-Prentice average hazard ratio (ahr_fast()). The simulation
layer generates individual patient data (simdata_fast()), performs interim
or sequenti [...truncated...]
Author: Gosuke Homma [aut, cre]
Maintainer: Gosuke Homma <my.name.is.gosuke@gmail.com>
Diff between FastSurvival versions 0.1.0 dated 2026-05-27 and 0.2.0 dated 2026-07-27
FastSurvival-0.1.0/FastSurvival/src/simdata_core.cpp |only FastSurvival-0.2.0/FastSurvival/DESCRIPTION | 50 FastSurvival-0.2.0/FastSurvival/LICENSE | 2 FastSurvival-0.2.0/FastSurvival/MD5 | 197 + FastSurvival-0.2.0/FastSurvival/NAMESPACE | 35 FastSurvival-0.2.0/FastSurvival/NEWS.md | 143 FastSurvival-0.2.0/FastSurvival/R/FastSurvival-package.R | 159 - FastSurvival-0.2.0/FastSurvival/R/RcppExports.R | 374 ++ FastSurvival-0.2.0/FastSurvival/R/ahr_fast.R |only FastSurvival-0.2.0/FastSurvival/R/ahsw_fast.R |only FastSurvival-0.2.0/FastSurvival/R/analysis_fast.R |only FastSurvival-0.2.0/FastSurvival/R/coxph_fast.R | 415 +- FastSurvival-0.2.0/FastSurvival/R/gen_scenario_fast.R |only FastSurvival-0.2.0/FastSurvival/R/kmcurve_fast.R |only FastSurvival-0.2.0/FastSurvival/R/maxcombo_fast.R |only FastSurvival-0.2.0/FastSurvival/R/medsurv_fast.R |only FastSurvival-0.2.0/FastSurvival/R/milestone_fast.R |only FastSurvival-0.2.0/FastSurvival/R/pairwise_fast.R |only FastSurvival-0.2.0/FastSurvival/R/plot.kmcurve_fast.R |only FastSurvival-0.2.0/FastSurvival/R/plot.scenario_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.ahr_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.ahsw_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.coxph_fast.R | 172 - FastSurvival-0.2.0/FastSurvival/R/print.kmcurve_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.maxcombo_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.medsurv_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.milestone_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.rmst_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.rmw_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.scenario_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.simsummary_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.survdiff_fast.R | 97 FastSurvival-0.2.0/FastSurvival/R/print.survfit_fast.R | 132 FastSurvival-0.2.0/FastSurvival/R/print.wkm_fast.R |only FastSurvival-0.2.0/FastSurvival/R/print.wmst_fast.R |only FastSurvival-0.2.0/FastSurvival/R/rmst_fast.R |only FastSurvival-0.2.0/FastSurvival/R/rmw_fast.R |only FastSurvival-0.2.0/FastSurvival/R/signif_legend.R |only FastSurvival-0.2.0/FastSurvival/R/signif_star.R |only FastSurvival-0.2.0/FastSurvival/R/simdata_fast.R | 1454 +++++++--- FastSurvival-0.2.0/FastSurvival/R/simsummary_fast.R |only FastSurvival-0.2.0/FastSurvival/R/survdiff_fast.R | 574 ++- FastSurvival-0.2.0/FastSurvival/R/survfit_fast.R | 338 +- FastSurvival-0.2.0/FastSurvival/R/wkm_fast.R |only FastSurvival-0.2.0/FastSurvival/R/wmst_fast.R |only FastSurvival-0.2.0/FastSurvival/README.md | 385 ++ FastSurvival-0.2.0/FastSurvival/build/vignette.rds |binary FastSurvival-0.2.0/FastSurvival/inst/WORDLIST |only FastSurvival-0.2.0/FastSurvival/inst/doc/FastSurvival.R | 150 - FastSurvival-0.2.0/FastSurvival/inst/doc/FastSurvival.Rmd | 370 -- FastSurvival-0.2.0/FastSurvival/inst/doc/FastSurvival.html | 393 -- FastSurvival-0.2.0/FastSurvival/inst/doc/compare-logrank-rmst.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/compare-logrank-rmst.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/compare-logrank-rmst.html |only FastSurvival-0.2.0/FastSurvival/inst/doc/correlated-pfs-os-gsd.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/correlated-pfs-os-gsd.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/correlated-pfs-os-gsd.html |only FastSurvival-0.2.0/FastSurvival/inst/doc/group-sequential-design.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/group-sequential-design.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/group-sequential-design.html |only FastSurvival-0.2.0/FastSurvival/inst/doc/investigate-freidlin-and-korn.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/investigate-freidlin-and-korn.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/investigate-freidlin-and-korn.html |only FastSurvival-0.2.0/FastSurvival/inst/doc/mrct-regional-consistency.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/mrct-regional-consistency.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/mrct-regional-consistency.html |only FastSurvival-0.2.0/FastSurvival/inst/doc/multi-arm-pairwise.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/multi-arm-pairwise.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/multi-arm-pairwise.html |only FastSurvival-0.2.0/FastSurvival/inst/doc/speed-comparison.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/speed-comparison.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/speed-comparison.html |only FastSurvival-0.2.0/FastSurvival/inst/doc/validation.R |only FastSurvival-0.2.0/FastSurvival/inst/doc/validation.Rmd |only FastSurvival-0.2.0/FastSurvival/inst/doc/validation.html |only FastSurvival-0.2.0/FastSurvival/man/FastSurvival-package.Rd | 116 FastSurvival-0.2.0/FastSurvival/man/ahr_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/ahr_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/ahsw_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/ahsw_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/analysis_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/combo_logrank_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/coxph_fast.Rd | 47 FastSurvival-0.2.0/FastSurvival/man/figures |only FastSurvival-0.2.0/FastSurvival/man/gen_scenario_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/km_core.Rd | 15 FastSurvival-0.2.0/FastSurvival/man/kmcurve_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/maxcombo_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/medsurv_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/milestone_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/pairwise_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/plot.kmcurve_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/plot.scenario_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.ahr_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.ahsw_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.kmcurve_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.maxcombo_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.medsurv_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.milestone_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.rmst_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.rmw_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.scenario_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.simsummary_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.survdiff_fast.Rd | 5 FastSurvival-0.2.0/FastSurvival/man/print.wkm_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/print.wmst_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/rmst_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/rmst_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/rmw_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/rmw_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/simdata_fast.Rd | 393 +- FastSurvival-0.2.0/FastSurvival/man/simsummary_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/stratified_logrank_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/stratified_weighted_logrank_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/survdiff_fast.Rd | 192 + FastSurvival-0.2.0/FastSurvival/man/survfit_fast.Rd | 14 FastSurvival-0.2.0/FastSurvival/man/weighted_logrank_core.Rd |only FastSurvival-0.2.0/FastSurvival/man/wkm_fast.Rd |only FastSurvival-0.2.0/FastSurvival/man/wmst_fast.Rd |only FastSurvival-0.2.0/FastSurvival/src/RcppExports.cpp | 333 ++ FastSurvival-0.2.0/FastSurvival/src/ahr_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/ahsw_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/analysis_loop_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/combo_logrank_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/km_core.cpp | 70 FastSurvival-0.2.0/FastSurvival/src/logrank_core.cpp | 21 FastSurvival-0.2.0/FastSurvival/src/medsurv_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/milestone_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/pihe_core.cpp | 65 FastSurvival-0.2.0/FastSurvival/src/rmst_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/rmw_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/simdata_core_full.cpp |only FastSurvival-0.2.0/FastSurvival/src/simdata_core_id.cpp |only FastSurvival-0.2.0/FastSurvival/src/stratified_logrank_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/stratified_weighted_logrank_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/weighted_logrank_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/wkm_core.cpp |only FastSurvival-0.2.0/FastSurvival/src/wmst_core.cpp |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-ahr_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-ahsw_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-analysis_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-coxph_fast.R | 4 FastSurvival-0.2.0/FastSurvival/tests/testthat/test-kmcurve_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-maxcombo_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-medsurv_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-milestone_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-pairwise_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-rmst_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-rmw_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-simdata_fast.R | 473 ++- FastSurvival-0.2.0/FastSurvival/tests/testthat/test-simdata_fast_id.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-simdata_fast_karm.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-simsummary_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-survdiff_fast.R | 517 ++- FastSurvival-0.2.0/FastSurvival/tests/testthat/test-wkm_fast.R |only FastSurvival-0.2.0/FastSurvival/tests/testthat/test-wmst_fast.R |only FastSurvival-0.2.0/FastSurvival/vignettes/FastSurvival.Rmd | 370 -- FastSurvival-0.2.0/FastSurvival/vignettes/compare-logrank-rmst.Rmd |only FastSurvival-0.2.0/FastSurvival/vignettes/correlated-pfs-os-gsd.Rmd |only FastSurvival-0.2.0/FastSurvival/vignettes/group-sequential-design.Rmd |only FastSurvival-0.2.0/FastSurvival/vignettes/investigate-freidlin-and-korn.Rmd |only FastSurvival-0.2.0/FastSurvival/vignettes/mrct-regional-consistency.Rmd |only FastSurvival-0.2.0/FastSurvival/vignettes/multi-arm-pairwise.Rmd |only FastSurvival-0.2.0/FastSurvival/vignettes/speed-comparison.Rmd |only FastSurvival-0.2.0/FastSurvival/vignettes/validation.Rmd |only 165 files changed, 5263 insertions(+), 2812 deletions(-)
Title: Density Deconvolution Using Bayesian Semiparametric Methods
Description: Estimates the density of a variable in a measurement error setup, potentially with an excess of zero values. For more details see Sarkar (2021). <doi:10.1080/01621459.2020.1782220>.
Author: Blake Moya [aut],
Mainak Manna [cre, aut],
Abhra Sarkar [aut],
The University of Texas at Austin [cph, fnd]
Maintainer: Mainak Manna <mainakmanna29@utexas.edu>
Diff between BayesDecon versions 0.1.6 dated 2026-03-14 and 0.1.7 dated 2026-07-27
DESCRIPTION | 8 +++---- MD5 | 7 +++--- R/bdeconv.R | 61 ++++++++++++++++++++++++++++++++------------------------- inst |only man/bdeconv.Rd | 26 ++++++++++++++---------- 5 files changed, 58 insertions(+), 44 deletions(-)
Title: Simulation of Simple and Complex Survival Data
Description: Simulation of simple and complex survival data including recurrent and multiple events and competing risks. See Moriña D, Navarro A. (2014) <doi:10.18637/jss.v059.i02> and Moriña D, Navarro A. (2017) <doi:10.1080/03610918.2016.1175621>.
Author: David Morina Soler [aut, cre] ,
Albert Navarro [aut]
Maintainer: David Morina Soler <david.morina@uab.cat>
Diff between survsim versions 1.1.8 dated 2021-12-14 and 1.1.9 dated 2026-07-27
DESCRIPTION | 15 ++++++------ MD5 | 4 +-- inst/CITATION | 71 +++++++++++++++++++++++++++++++--------------------------- 3 files changed, 49 insertions(+), 41 deletions(-)
Title: Propagation of Uncertainty
Description: Propagation of uncertainty using higher-order Taylor expansion and Monte Carlo simulation. Calculations of propagated uncertainties are based on matrix calculus including covariance structure according to Arras 1998 <doi:10.3929/ethz-a-010113668> (first order), Wang & Iyer 2005 <doi:10.1088/0026-1394/42/5/011> (second order) and BIPM Supplement 1 (Monte Carlo) <doi:10.59161/JCGM101-2008>.
Author: Andrej-Nikolai Spiess [aut, cre]
Maintainer: Andrej-Nikolai Spiess <draspiess@gmail.com>
Diff between propagate versions 1.1-0 dated 2026-02-25 and 1.2-0 dated 2026-07-27
DESCRIPTION | 8 - MD5 | 13 +- NEWS | 4 R/distr-densities.R | 298 ++++++++++++++++++++++++++++------------------------ R/fitDistr.R | 11 + R/propagate.R | 31 +++-- build |only man/propagate.Rd | 4 8 files changed, 208 insertions(+), 161 deletions(-)
Title: Regression Models for Ordinal Data
Description: Implementation of cumulative link (mixed) models also known
as ordered regression models, proportional odds models, proportional
hazards models for grouped survival times and ordered logit/probit/...
models. Estimation is via maximum likelihood and mixed models are fitted
with the Laplace approximation and adaptive Gauss-Hermite quadrature.
Multiple random effect terms are allowed and they may be nested, crossed or
partially nested/crossed. Restrictions of symmetry and equidistance can be
imposed on the thresholds (cut-points/intercepts). Standard model
methods are available (summary, anova, drop-methods, step,
confint, predict etc.) in addition to profile methods and slice
methods for visualizing the likelihood function and checking
convergence.
Author: Rune Haubo Bojesen Christensen [aut, cre]
Maintainer: Rune Haubo Bojesen Christensen <rune.haubo@gmail.com>
Diff between ordinal versions 2025.12-29 dated 2026-01-10 and 2026.7-26 dated 2026-07-27
DESCRIPTION | 14 ++++++++------ MD5 | 20 ++++++++++---------- NEWS | 4 ++++ build/vignette.rds |binary inst/doc/clm_article.R | 2 -- inst/doc/clm_article.Rnw | 2 +- inst/doc/clm_article.pdf |binary inst/doc/clmm2_tutorial.R | 2 -- inst/doc/clmm2_tutorial.pdf |binary tests/testCLM.R | 4 ++-- vignettes/clm_article.Rnw | 2 +- 11 files changed, 26 insertions(+), 24 deletions(-)
Title: Linear, Quadratic, and Rational Optimization
Description: Solver for linear, quadratic, and rational programs with linear, quadratic, and rational constraints. A unified interface to different R packages is provided. Optimization problems are transformed into equivalent formulations and solved by the respective package. For example, quadratic programming problems with linear, quadratic and rational constraints can be solved by augmented Lagrangian minimization using package 'alabama', or by sequential quadratic programming using solver 'slsqp'. Alternatively, they can be reformulated as optimization problems with second order cone constraints and solved with package 'cccp'.
Author: Robin Wellmann [aut, cre]
Maintainer: Robin Wellmann <ro.wellmann@gmail.com>
Diff between optiSolve versions 1.0 dated 2021-10-13 and 1.0.1 dated 2026-07-27
DESCRIPTION | 26 +++++++++++++++++--------- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 3 +-- R/adjust.R | 8 ++++---- R/asdefinite.R | 4 ++-- R/call_cccp.R | 16 ++++++++-------- R/call_cccp2.R | 10 +++++----- R/f2fun.R | 6 +++--- R/getSover.R | 8 ++++---- R/getX.R | 2 +- R/reduce.R | 6 +++--- R/simplify.R | 4 ++-- R/validate.R | 6 +++--- build/partial.rdb |binary data/myQ.rda |binary data/myQ1.rda |binary data/myQ2.rda |binary data/phenotype.rda |binary 18 files changed, 70 insertions(+), 63 deletions(-)
Title: A Flexible Class for Messy Dates
Description: Contains a set of tools for constructing and coercing
into and from the "mdate" class.
This date class implements ISO 8601-2:2019(E) and
allows regular dates and times to be annotated
to express unspecified date or time components,
approximate or uncertain components,
ranges, and sets of dates.
The package therefore retains, represents, and reasons about data and time imprecision,
resolving to a single data/time only on demand.
This is useful for describing and analysing temporal information,
whether historical or recent, where date or time precision may vary.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Jael Tan [ctb] ,
Nathan Werth [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between messydates versions 1.0.0 dated 2026-07-16 and 1.1.0 dated 2026-07-27
DESCRIPTION | 7 - MD5 | 68 +++++----- NAMESPACE | 5 NEWS.md | 112 ++++++++++++++++++ R/class_mdate.R | 32 ++--- R/class_methods.R | 50 ++++++-- R/coerce_from_messydate.R | 2 R/coerce_to_messydate.R | 205 ++++++++++++++++++++++++++------- R/convert_contract.R | 25 ++++ R/convert_expand.R | 94 ++++++++++++++- R/convert_sequence.R | 49 +------ R/operate_proportional.R | 7 + R/operate_set.R | 7 + R/operate_statements.R | 6 R/resolve_extrema.R | 4 R/resolve_tendency.R | 10 + R/validate_input.R |only README.md | 18 ++ man/class_methods.Rd | 24 +++ man/coerce_from.Rd | 2 man/coerce_to.Rd | 32 ++++- man/convert_contract.Rd | 10 + man/convert_sequence.Rd | 6 man/md_problems.Rd |only man/operate_proportional.Rd | 8 + man/operate_set.Rd | 8 + man/operate_statements.Rd | 6 man/resolve_tendency.Rd | 10 + tests/testthat/test-class_create.R | 22 +++ tests/testthat/test-coerce_from.R | 12 + tests/testthat/test-coerce_resolve.R | 21 ++- tests/testthat/test-coerce_to.R | 94 ++++++++++++++- tests/testthat/test-convert_contract.R | 16 ++ tests/testthat/test-convert_expand.R | 35 +++++ tests/testthat/test-convert_sequence.R | 17 ++ tests/testthat/test-operate_set.R | 14 ++ 36 files changed, 862 insertions(+), 176 deletions(-)
Title: Get Gene Sets for Gene Enrichment Analysis
Description: Gene sets are fundamental for gene enrichment analysis. The package 'geneset' enables querying
gene sets from public databases including 'GO' (Gene Ontology Consortium. (2004) <doi:10.1093/nar/gkh036>),
'KEGG' (Minoru et al. (2000) <doi:10.1093/nar/28.1.27>),
'WikiPathway' (Marvin et al. (2020) <doi:10.1093/nar/gkaa1024>),
'MsigDb' (Arthur et al. (2015) <doi:10.1016/j.cels.2015.12.004>),
'Reactome' (David et al. (2011) <doi:10.1093/nar/gkq1018>),
'MeSH' (Ish et al. (2014) <doi:10.4103/0019-5413.139827>),
'DisGeNET' (Janet et al. (2017) <doi:10.1093/nar/gkw943>),
'Disease Ontology' (Lynn et al. (2011) <doi:10.1093/nar/gkr972>),
'Network of Cancer Genes' (Dimitra et al. (2019) <doi:10.1186/s13059-018-1612-0>) and
'COVID-19' (Maxim et al. (2020) <doi:10.21203/rs.3.rs-28582/v1>).
Gene sets are stored in the list object which provides data frame of 'geneset' and 'geneset_name'.
The 'geneset' has two columns of term ID and gene ID. [...truncated...]
Author: Yunze Liu [aut, cre]
Maintainer: Yunze Liu <jieandze1314@gmail.com>
Diff between geneset versions 0.2.7 dated 2022-11-20 and 0.2.8 dated 2026-07-27
DESCRIPTION | 12 +- MD5 | 14 +- R/getGO.R | 4 R/getKEGG.R | 2 R/getMsigdb.R | 194 ++++++++++++++++++++++++++++++------- R/utilities.R | 285 ++++++++++++++++++++++++++++++++++++++----------------- README.md | 19 +-- man/getMsigdb.Rd | 32 ++++-- 8 files changed, 406 insertions(+), 156 deletions(-)
Title: Greenhouse Gas Flux Calculation from Chamber Measurements
Description: Functions for greenhouse gas flux calculation from chamber
measurements.
Author: Roland Fuss [aut, cre] ,
Roman Hueppi [ctb]
Maintainer: Roland Fuss <roland.fuss@thuenen.de>
Diff between gasfluxes versions 0.7 dated 2024-08-16 and 0.7-2 dated 2026-07-27
DESCRIPTION | 13 ++++++------- MD5 | 18 +++++++++--------- NEWS.md | 3 +++ build/vignette.rds |binary inst/doc/gasfluxes-howto.Rmd | 2 +- inst/doc/gasfluxes-howto.html | 17 +++++++++-------- man/gasfluxes-package.Rd | 5 +++++ tests/testthat/test_aggfluxes.R | 4 ++-- tests/testthat/test_fitting.R | 14 +++++++------- vignettes/gasfluxes-howto.Rmd | 2 +- 10 files changed, 43 insertions(+), 35 deletions(-)
Title: Exploratory Data Analysis for the 'spatstat' Family
Description: Functionality for exploratory data analysis and nonparametric analysis of
spatial data, mainly spatial point patterns,
in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
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 correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Warick Brown [cph],
Achmad Choiruddin [ctb],
Ya-Mei Chang [ctb],
Jean-Francois Coeurjolly [ctb],
Lucia Cobo Sanchez [ctb, cph],
Ottma [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.explore versions 3.8-1 dated 2026-05-24 and 3.8-2 dated 2026-07-27
DESCRIPTION | 10 ++-- MD5 | 52 +++++++++++++------------ NAMESPACE | 4 + NEWS | 39 ++++++++++++++++++ R/Kinhom.R | 2 R/Kmulti.inhom.R | 81 +++++++++++++++++++++++++-------------- R/densityAdaptiveKernel.ppp.R | 54 ++++---------------------- R/densityVoronoi.R | 3 - R/pcfinhom.R | 38 ++++++++++-------- R/pcfmulti.inhom.R | 60 +++++++++++++++++----------- R/rhohat.R | 31 ++++++++++---- R/smoothAdaptiveKernel.ppp.R |only build/partial.rdb |binary inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/Kcross.inhom.Rd | 2 man/Kdot.inhom.Rd | 2 man/Kmulti.inhom.Rd | 9 +++- man/SmoothAdaptiveKernel.Rd |only man/cdf.test.Rd | 6 +- man/densityVoronoi.Rd | 30 ++++++++++---- man/macros/defns.Rd | 30 +++++++++++--- man/pcfmulti.inhom.Rd | 7 +++ man/plot.cdftest.Rd | 3 - man/rhohat.Rd | 11 ++++- man/spatstat.explore-internal.Rd | 6 -- man/spatstat.explore-package.Rd | 18 ++++++-- tests/testsT.R | 10 +++- 28 files changed, 317 insertions(+), 193 deletions(-)
More information about spatstat.explore at CRAN
Permanent link
Title: Inverse-Regression Estimation of Radioactive Doses
Description: Radioactive doses estimation using individual chromosomal
aberrations information. See Higueras M, Puig P, Ainsbury E,
Rothkamm K. (2015) <doi:10.1088/0952-4746/35/3/557>.
Author: David Morina Soler [aut, cre] ,
Manuel Higueras [aut],
Pedro Puig [aut]
Maintainer: David Morina Soler <david.morina@uab.cat>
Diff between radir versions 1.0.4 dated 2019-07-03 and 1.0.5 dated 2026-07-27
DESCRIPTION | 24 +++++++++++---- MD5 | 18 +++++------ R/ci.dose.radir.R | 2 - R/dose.distr.R | 2 - R/lines.dose.radir.R | 2 - R/plot.dose.radir.R | 2 - R/pr.dose.radir.R | 2 - R/summary.dose.radir.R | 2 - inst/CITATION | 75 ++++++++++++++++++++++++++----------------------- man/radir-package.Rd | 6 +-- 10 files changed, 75 insertions(+), 60 deletions(-)
Title: Optimum Threshold Estimation
Description: Functions that provide point and interval estimations of optimum thresholds for continuous diagnostic tests. The methodology used is based on minimizing an overall cost function in the two- and three-state settings. We also provide functions for sample size determination and estimation of diagnostic accuracy measures. We also include graphical tools. The statistical methodology used here can be found in Perez-Jaume et al (2017) <doi:10.18637/jss.v082.i04> and in Skaltsa et al (2010, 2012) <doi:10.1002/bimj.200900294>, <doi:10.1002/sim.4369>.
Author: Sara Perez-Jaume [aut, cre] ,
Natalia Pallares [aut] ,
Konstantina Skaltsa [aut]
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.9.6 dated 2026-05-14 and 2.10.0 dated 2026-07-27
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/ThresholdROC-2states.R | 14 +++++++------- R/diagnostic.R | 10 +++++----- man/chemo.Rd | 2 +- man/diagnostic.Rd | 14 ++++++++++---- man/lines-thres2.Rd | 20 ++++++++++++++++---- man/lines-thres3.Rd | 20 ++++++++++++++++---- man/plot-thres2.Rd | 28 ++++++++++++++++++++++------ man/plot-thres3.Rd | 22 +++++++++++++++++----- man/plotCostROC.Rd | 6 +++++- man/thres2.Rd | 36 ++++++++++++++++++++++++++++-------- man/thres3.Rd | 40 ++++++++++++++++++++++++++++++++-------- man/thresTH2.Rd | 20 +++++++++++++++----- man/thresTH3.Rd | 26 +++++++++++++++++++++----- 15 files changed, 213 insertions(+), 81 deletions(-)
Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages.
Generates random spatial patterns of points according to many simple rules (complete spatial randomness,
Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns
(thinning, random shift, jittering), simulated realisations of random point processes including
simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes
(using direct, Brix-Kendall, or hybrid algorithms),
log-Gaussian Cox processes, product shot noise cluster processes
and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm,
alternating Gibbs sampler, or coupling-from-the-past perfect simulation).
Also generates random spatial patterns of line segments,
random tessellations, and random images (random noise, random mosaics).
Excludes random generation on a linear network,
which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb, cph],
David Bryant [ctb, cph],
Ya-Mei Chang [ctb, cph],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Dominic Sc [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.random versions 3.5-0 dated 2026-05-24 and 3.5-1 dated 2026-07-27
DESCRIPTION | 12 ++++++------ MD5 | 23 ++++++++++++----------- NAMESPACE | 1 + NEWS | 12 ++++++++++++ R/randompp3.R | 2 +- R/randomtess.R | 38 +++++++++++++++++++++++++++++++++++++- build/partial.rdb |binary inst/doc/packagesizes.txt | 1 + inst/info/packagesizes.txt | 1 + man/macros/defns.Rd | 30 +++++++++++++++++++++++------- man/rpoisDirichletTess.Rd |only man/rpoislinetess.Rd | 6 ++++-- man/spatstat.random-package.Rd | 6 ++++-- 13 files changed, 102 insertions(+), 30 deletions(-)
More information about spatstat.random at CRAN
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Title: Unidimensional Item Response Theory Modeling
Description: Fit unidimensional item response theory (IRT) models to test
data, which includes both dichotomous and polytomous items, calibrate
pretest item parameters, estimate examinees' abilities, and examine
the IRT model-data fit on item-level in different ways as well as provide
useful functions related to IRT analyses such as IRT model-data fit
evaluation and differential item functioning analysis.
The bring.flexmirt() and write.flexmirt() functions were written by modifying
the read.flexmirt() function (Pritikin & Falk (2022) <doi:10.1177/0146621620929431>).
The bring.bilog() and bring.parscale() functions were written by modifying the read.bilog()
and read.parscale() functions, respectively (Weeks (2010) <doi:10.18637/jss.v035.i12>).
The bisection() function was written by modifying the bisection() function
(Howard (2017, ISBN:9780367657918)). The code of the inverse test characteristic curve
scoring in the est_score() function was written by modifying the irt.eq.tse() func [...truncated...]
Author: Hwanggyu Lim [aut, cre],
Craig S. Wells [ctb],
James Howard [ctb],
Joshua Pritikin [ctb],
Jonathan P Weeks [ctb],
Jorge Gonzalez [ctb],
David Magis [ctb]
Maintainer: Hwanggyu Lim <hglim83@gmail.com>
Diff between irtQ versions 1.1.0 dated 2026-06-07 and 1.2.0 dated 2026-07-27
DESCRIPTION | 16 - MD5 | 125 +++++----- NAMESPACE | 8 NEWS.md | 95 +++++++ R/EM.R | 2 R/LSAT6.R | 2 R/SimCAT_DC.R | 4 R/catsib.R | 12 - R/collapse_ftable.R | 2 R/crdif.R | 12 - R/est_irt.R | 27 +- R/est_item.R | 8 R/est_mg.R | 37 +-- R/est_score.R | 10 R/estimation.R | 6 R/find_cut.R |only R/gradient.R | 10 R/grdif.R | 2 R/hessian.R | 10 R/inv_tcc.R | 4 R/irtQ-package.R | 34 +- R/irtfit.R | 8 R/likelihood.R | 4 R/llike_score.R | 2 R/loglike_item.R | 10 R/optim_fns.R | 492 ++++++++++++++++++++--------------------- R/panel_info.R |only R/pcd2.R | 84 ++++++- R/plot_traceline.R | 2 R/print.R | 160 +++++++++++++ R/reval_mst.R | 64 ----- R/ripd.R | 248 +++++++++++++++++++- R/run_mst.R |only R/shape_df.R | 4 R/shape_df_fipc.R | 2 R/simIPD.R |only R/simMST.R | 25 +- R/sx2_fit.R | 2 README.md | 113 +++++---- build/partial.rdb |binary data/simIPD.rda |only data/simMST.rda |binary man/LSAT6.Rd | 2 man/catsib.Rd | 14 - man/crdif.Rd | 12 - man/est_irt.Rd | 24 +- man/est_item.Rd | 8 man/est_mg.Rd | 44 +-- man/est_score.Rd | 6 man/find_cut.Rd |only man/grdif.Rd | 2 man/irtQ-package.Rd | 34 +- man/irtfit.Rd | 8 man/llike_score.Rd | 2 man/panel_info.Rd |only man/pcd2.Rd | 88 ++++++- man/plot.find_cut.Rd |only man/plot.info.Rd | 2 man/plot.traceline.Rd | 4 man/reval_mst.Rd | 8 man/ripd.Rd | 247 +++++++++++++++++++- man/run_mst.Rd |only man/shape_df.Rd | 4 man/shape_df_fipc.Rd | 2 man/simCAT_DC.Rd | 4 man/simIPD.Rd |only man/simMST.Rd | 25 +- man/sx2_fit.Rd | 2 tests/testthat/test-find_cut.R |only 69 files changed, 1525 insertions(+), 663 deletions(-)
Title: Generalized Hermite Distribution
Description: Probability functions and other utilities for the generalized Hermite distribution.
Author: David Morina Soler [aut, cre],
Manuel Higueras [aut],
Pedro Puig [aut],
Maria Oliveira [aut]
Maintainer: David Morina Soler <david.morina@uab.cat>
Diff between hermite versions 1.1.2 dated 2018-05-17 and 1.2.1 dated 2026-07-27
DESCRIPTION | 27 ++++++++++++++++++++++----- MD5 | 10 +++++----- R/glm.hermite.R | 6 +++--- man/glm.hermite.Rd | 18 ++++++++---------- man/hermite-package.Rd | 2 +- man/phermite.Rd | 6 +++--- 6 files changed, 42 insertions(+), 27 deletions(-)
Title: Utilities Powering the Globe and Mail's Data Journalism Template
Description: Core functions necessary for using The Globe and Mail's R data journalism template, 'startr', along with utilities for day-to-day data journalism tasks, such as reading and writing files, producing graphics and cleaning up datasets.
Author: Tom Cardoso [aut, cre] ,
Michael Pereira [ctb],
The Globe and Mail Inc. [cph]
Maintainer: Tom Cardoso <tcardoso@globeandmail.com>
Diff between upstartr versions 0.1.2 dated 2024-01-09 and 0.2.0 dated 2026-07-27
DESCRIPTION | 14 +++++++------- MD5 | 15 +++++++++------ NEWS.md | 23 +++++++++++++++++++++++ R/init.R | 13 ++++++++++++- R/run.R | 19 +++++++++++++++++-- R/write.R | 6 +++++- man/initialize_startr.Rd | 10 +++++++++- tests/testthat/test-init.R |only tests/testthat/test-run.R |only tests/testthat/test-write.R |only 10 files changed, 82 insertions(+), 18 deletions(-)
Title: Helper Functions for Creating Tutorials
Description: Helper functions for creating, editing, and testing tutorials
created with the 'learnr' package. Provides a simple method for allowing
students to download their answers to tutorial questions. For examples
of its use, see the 'r4ds.tutorials' package.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Diff between tutorial.helpers versions 0.6.1 dated 2025-12-23 and 0.7.0 dated 2026-07-27
tutorial.helpers-0.6.1/tutorial.helpers/R/set_positron_settings.R |only tutorial.helpers-0.6.1/tutorial.helpers/R/set_r_profile_settings.R |only tutorial.helpers-0.6.1/tutorial.helpers/inst/doc/books.html |only tutorial.helpers-0.6.1/tutorial.helpers/inst/doc/books.qmd |only tutorial.helpers-0.6.1/tutorial.helpers/inst/doc/instructions.R |only tutorial.helpers-0.6.1/tutorial.helpers/inst/doc/instructions.html |only tutorial.helpers-0.6.1/tutorial.helpers/inst/doc/instructions.qmd |only tutorial.helpers-0.6.1/tutorial.helpers/inst/rmarkdown |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/new-window.png |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/positron-interface.jpeg |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/run-tutorial.png |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/send-tutorial-to-browser.png |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/terminal-1.png |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/terminal-2.png |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/terminal-3.png |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/images/terminal-4.png |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/getting-started/tutorial.html |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/introduction-to-python |only tutorial.helpers-0.6.1/tutorial.helpers/inst/tutorials/introduction-to-r |only tutorial.helpers-0.6.1/tutorial.helpers/inst/www |only tutorial.helpers-0.6.1/tutorial.helpers/man/set_positron_settings.Rd |only tutorial.helpers-0.6.1/tutorial.helpers/man/set_rprofile_settings.Rd |only tutorial.helpers-0.6.1/tutorial.helpers/tests/testthat/test-set_positron_settings.R |only tutorial.helpers-0.6.1/tutorial.helpers/tests/testthat/test-set_rprofile_settings.R |only tutorial.helpers-0.6.1/tutorial.helpers/vignettes/books.qmd |only tutorial.helpers-0.6.1/tutorial.helpers/vignettes/instructions.qmd |only tutorial.helpers-0.7.0/tutorial.helpers/DESCRIPTION | 15 tutorial.helpers-0.7.0/tutorial.helpers/MD5 | 164 - tutorial.helpers-0.7.0/tutorial.helpers/NAMESPACE | 18 tutorial.helpers-0.7.0/tutorial.helpers/NEWS.md | 16 tutorial.helpers-0.7.0/tutorial.helpers/R/check_current_tutorial.R | 3 tutorial.helpers-0.7.0/tutorial.helpers/R/check_key_vars.R | 11 tutorial.helpers-0.7.0/tutorial.helpers/R/check_membership.R | 29 tutorial.helpers-0.7.0/tutorial.helpers/R/check_tutorial_defaults.R | 4 tutorial.helpers-0.7.0/tutorial.helpers/R/determine_code_chunk_name.R | 5 tutorial.helpers-0.7.0/tutorial.helpers/R/determine_exercise_number.R | 28 tutorial.helpers-0.7.0/tutorial.helpers/R/download_google_drive.R | 13 tutorial.helpers-0.7.0/tutorial.helpers/R/format_tutorial.R | 14 tutorial.helpers-0.7.0/tutorial.helpers/R/gather_submissions.R | 28 tutorial.helpers-0.7.0/tutorial.helpers/R/globals.R | 2 tutorial.helpers-0.7.0/tutorial.helpers/R/make_exercise.R | 2 tutorial.helpers-0.7.0/tutorial.helpers/R/match_questions.R | 15 tutorial.helpers-0.7.0/tutorial.helpers/R/open_github_pages.R | 13 tutorial.helpers-0.7.0/tutorial.helpers/R/show_file.R | 120 - tutorial.helpers-0.7.0/tutorial.helpers/R/submission_functions.R | 3 tutorial.helpers-0.7.0/tutorial.helpers/R/submissions_answers.R | 20 tutorial.helpers-0.7.0/tutorial.helpers/R/submissions_summary.R | 179 - tutorial.helpers-0.7.0/tutorial.helpers/R/utils.R | 6 tutorial.helpers-0.7.0/tutorial.helpers/R/write_answers.R | 14 tutorial.helpers-0.7.0/tutorial.helpers/README.md | 42 tutorial.helpers-0.7.0/tutorial.helpers/build/vignette.rds |binary tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/addins.R | 28 tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/addins.html | 229 +- tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/addins.qmd | 72 tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/ai.R | 350 ++- tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/ai.html | 1041 +++++++--- tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/ai.qmd | 629 ++++-- tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/downloads.html | 144 + tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/testing.html | 152 + tutorial.helpers-0.7.0/tutorial.helpers/inst/doc/testing.qmd | 8 tutorial.helpers-0.7.0/tutorial.helpers/inst/extdata |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/cs-copilot-keep-editor.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/cs-copilot-keep-summary.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/cs-open-copilot-chat.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/cs-run-source.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/gs-1.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/gs-2.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/gs-3.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/gs-4.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/gs-5.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/gs-6.png |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/images/neo-cs.gif |only tutorial.helpers-0.7.0/tutorial.helpers/inst/tutorials/getting-started/tutorial.Rmd | 908 +++++--- tutorial.helpers-0.7.0/tutorial.helpers/man/check_current_tutorial.Rd | 4 tutorial.helpers-0.7.0/tutorial.helpers/man/check_key_vars.Rd | 7 tutorial.helpers-0.7.0/tutorial.helpers/man/check_membership.Rd | 11 tutorial.helpers-0.7.0/tutorial.helpers/man/check_tutorial_defaults.Rd | 4 tutorial.helpers-0.7.0/tutorial.helpers/man/dot-check_quarto.Rd | 4 tutorial.helpers-0.7.0/tutorial.helpers/man/gather_submissions.Rd | 5 tutorial.helpers-0.7.0/tutorial.helpers/man/match_questions.Rd | 13 tutorial.helpers-0.7.0/tutorial.helpers/man/open_github_pages.Rd | 2 tutorial.helpers-0.7.0/tutorial.helpers/man/show_file.Rd | 19 tutorial.helpers-0.7.0/tutorial.helpers/man/strip_pagedtable_html.Rd |only tutorial.helpers-0.7.0/tutorial.helpers/man/submissions_answers.Rd | 4 tutorial.helpers-0.7.0/tutorial.helpers/man/submissions_summary.Rd | 4 tutorial.helpers-0.7.0/tutorial.helpers/man/write_answers.Rd | 4 tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/fixtures/show_file_pagedtable_test.qmd |only tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/fixtures/show_file_python_test.qmd |only tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-check_membership.R | 79 tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-determine_code_chunk_name.R | 9 tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-determine_exercise_number.R | 21 tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-format_tutorial.R | 34 tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-match_questions.R | 46 tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-open_github_pages.R |only tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-render.R | 18 tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-show_file.R | 132 + tutorial.helpers-0.7.0/tutorial.helpers/tests/testthat/test-submissions_summary.R | 70 tutorial.helpers-0.7.0/tutorial.helpers/vignettes/addins.qmd | 72 tutorial.helpers-0.7.0/tutorial.helpers/vignettes/ai.qmd | 629 ++++-- tutorial.helpers-0.7.0/tutorial.helpers/vignettes/testing.qmd | 8 100 files changed, 3925 insertions(+), 1599 deletions(-)
More information about tutorial.helpers at CRAN
Permanent link
Title: Tidy Tools for Actuarial Mathematics and Life Contingencies
Description: Provides tidyverse-aligned tools for actuarial mathematics
and life contingencies, including life tables, survival probabilities,
actuarial present values of cash flows, life annuities, life insurance,
premiums, reserves, multiple-life calculations, Monte Carlo simulation,
and deterministic cash-flow diagrams. The package emphasizes clear
actuarial notation, reproducible workflows, and pipe-friendly tools for
actuarial education and applied actuarial analysis.
Author: Julian Fajardo [aut, cre]
Maintainer: Julian Fajardo <julian.fajardo1908@gmail.com>
Diff between tidyactuarial versions 0.1.4 dated 2026-06-01 and 0.1.5 dated 2026-07-27
DESCRIPTION | 8 MD5 | 275 +++-- NAMESPACE | 161 +-- NEWS.md | 2 R/accumulation_factor.R |only R/amort_schedule_general.R |only R/annuity_x.R | 61 - R/annuity_xy.R | 135 ++ R/contract_components.R |only R/contract_components_xy_corrected.R |only R/convexity_cash_flow.R |only R/discount_factor.R |only R/duration_cash_flow.R |only R/globals.R | 200 --- R/imports.R |only R/mc-utils.R | 149 ++ R/mc_annuity.R | 70 + R/mc_insurance.R | 88 + R/mc_loss.R | 620 +++++++---- R/mc_multilife_status.R | 351 +++++- R/mc_premium.R | 705 ++++++++----- R/mc_reserve.R | 1014 ++++++++++++------- R/plot_cash_flow.R | 146 ++ R/premium_gross.R | 577 ++++++++--- R/premium_x.R | 656 +++++++----- R/premium_xy.R | 1193 ++++++++++------------ R/reserve_x.R | 1240 ++++++++++++++--------- R/reserve_xy.R | 1311 +++++++++---------------- R/simulate_life_mc.R | 966 +++++++++++------- R/simulate_lifetime.R | 553 ++++++---- R/simulate_lifetimes.R | 533 +++++++--- R/solve_value_v3.R |only man/a_angle.Rd | 318 +++--- man/accumulation_factor.Rd |only man/add_insurance.Rd |only man/add_premium_schedule.Rd |only man/amort_schedule.Rd | 295 ++--- man/amort_schedule_general.Rd |only man/annuity_arith.Rd | 292 ++--- man/annuity_geom.Rd | 330 +++--- man/annuity_multi.Rd | 298 ++--- man/annuity_x.Rd | 402 +++---- man/annuity_xy.Rd | 385 +++---- man/apv_life_flow.Rd | 248 ++-- man/bond_book_value.Rd | 346 +++--- man/bond_callable_price.Rd | 356 +++--- man/bond_cash_flows.Rd | 102 - man/bond_convexity.Rd | 272 ++--- man/bond_duration.Rd | 298 ++--- man/bond_price.Rd | 274 ++--- man/bond_ytm.Rd | 244 ++-- man/bonds_sample.Rd | 144 +- man/cash_flows_sample.Rd | 140 +- man/commutation_table.Rd | 150 +- man/convexity_cash_flow.Rd |only man/discount_factor.Rd |only man/discount_factor_spot.Rd | 198 +-- man/dot-annuity_factor_count.Rd | 36 man/dot-annuity_payment_count.Rd | 38 man/dot-life_mc_collect_old_args.Rd | 32 man/dot-mc_annuity_payment_times_annual.Rd | 56 - man/dot-mc_annuity_payment_times_fractional.Rd | 76 - man/dot-mc_assert_character_scalar.Rd | 40 man/dot-mc_assert_column.Rd | 44 man/dot-mc_assert_numeric_column.Rd | 44 man/dot-mc_assert_numeric_scalar.Rd | 76 - man/dot-mc_assert_positive_integer.Rd | 40 man/dot-mc_discount_factor.Rd | 72 - man/dot-mc_effective_rate.Rd | 96 - man/dot-mc_normalize_i_type.Rd | 36 man/dot-mc_payment_times.Rd | 46 man/dot-mc_quantile_names.Rd | 36 man/dot-mc_reserve_benefit_info.Rd | 44 man/dot-resolve_life_mc_inputs.Rd | 38 man/dot-simulate_lifetime_inverse_lx.Rd | 55 - man/dot-validate_mc_common.Rd | 40 man/duration_cash_flow.Rd |only man/e_x.Rd | 152 +- man/forward_rate.Rd | 338 +++--- man/future_value.Rd | 215 ++-- man/fv_flow.Rd | 287 ++--- man/immunize_duration.Rd | 274 ++--- man/immunize_duration_convexity.Rd | 274 ++--- man/insurance_variable_k.Rd | 396 +++---- man/insurance_x.Rd | 334 +++--- man/insurance_xj.Rd | 304 ++--- man/insurance_xy.Rd | 350 +++--- man/interest_equivalents.Rd | 174 +-- man/irr_flow.Rd | 241 ++-- man/irr_flow_multi.Rd | 265 ++--- man/life_contract.Rd | 238 ++-- man/lifetable.Rd | 372 +++---- man/loans_sample.Rd | 140 +- man/lt_tau.Rd | 82 - man/mc_annuity.Rd | 550 +++++----- man/mc_insurance.Rd | 535 +++++----- man/mc_loss.Rd | 412 +++---- man/mc_multilife_status.Rd | 164 ++- man/mc_premium.Rd | 441 +++----- man/mc_reserve.Rd | 519 +++------ man/md_table.Rd | 150 +- man/mortality_colombia_tables.Rd | 150 +- man/mortality_law_table.Rd | 404 +++---- man/mortality_world_sample_2015_2023.Rd | 120 +- man/mortality_world_sample_2023.Rd | 116 +- man/multiple_decrement_sample.Rd | 136 +- man/plot_cash_flow.Rd | 321 +++--- man/plot_immunization_gap.Rd | 200 +-- man/plot_km.Rd | 172 +-- man/portfolio_convexity.Rd | 262 ++-- man/portfolio_duration.Rd | 264 ++--- man/premium_gross.Rd | 324 +++--- man/premium_x.Rd | 436 ++++---- man/premium_xy.Rd | 405 ++++--- man/present_value.Rd | 217 ++-- man/pv_flow.Rd | 263 ++--- man/reserve_x.Rd | 361 +++--- man/reserve_xy.Rd | 332 ++---- man/s_angle.Rd | 316 +++--- man/simulate_annuity_x.Rd | 270 ++--- man/simulate_insurance_x.Rd | 236 +--- man/simulate_lifetime.Rd | 297 ++--- man/simulate_lifetimes.Rd | 170 ++- man/sinking_fund_schedule.Rd | 273 ++--- man/soa08lt.Rd | 136 +- man/solve_value.Rd |only man/standardize_interest.Rd | 184 +-- man/summary_mc.Rd | 184 +-- man/t_Ex.Rd | 282 ++--- man/t_px.Rd | 118 +- man/t_pxy.Rd | 218 ++-- man/t_qxj.Rd | 142 +- man/yield_curve.Rd | 282 ++--- tests/testthat.R | 24 tests/testthat/test-accumulation_factor.R |only tests/testthat/test-amort_schedule_general.R |only tests/testthat/test-annuity_x-fractional.R |only tests/testthat/test-annuity_xy-v2.R |only tests/testthat/test-contract_components-xy.R |only tests/testthat/test-convexity_cash_flow.R |only tests/testthat/test-discount_factor.R |only tests/testthat/test-duration_cash_flow.R |only tests/testthat/test-mc-utils-v2.R |only tests/testthat/test-mc_annuity-v2.R |only tests/testthat/test-mc_insurance-v2.R |only tests/testthat/test-mc_loss-v2.R |only tests/testthat/test-mc_multilife_status-v2.R |only tests/testthat/test-mc_premium-v2.R |only tests/testthat/test-mc_reserve_v2.R |only tests/testthat/test-plot_cash_flow.R |only tests/testthat/test-premium_gross-v2.R |only tests/testthat/test-premium_x-v2.R |only tests/testthat/test-premium_xy-v2.R |only tests/testthat/test-reserve_x-v2.R |only tests/testthat/test-reserve_xy-two-tables.R |only tests/testthat/test-reserve_xy-v2.R |only tests/testthat/test-simulate_life_mc-v2.R |only tests/testthat/test-simulate_lifetime-v2.R |only tests/testthat/test-simulate_lifetimes-v2.R |only tests/testthat/test-solve_value_v2.R |only 160 files changed, 16855 insertions(+), 15018 deletions(-)
Title: Personalized Treatment Evaluator
Description: We provide inference for personalized medicine models. Namely, we answer the questions: (1) how much better does a purported personalized recommendation engine for treatments do over a business-as-usual approach and (2) is that difference statistically significant?
Author: Adam Kapelner [aut, cre],
Alina Levine [aut],
Justin Bleich [aut]
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between PTE versions 1.7 dated 2019-01-30 and 2.0 dated 2026-07-27
PTE-1.7/PTE/R/create_PTE_results_object.R |only PTE-1.7/PTE/R/create_cutoffs_for_K_fold_cv.R |only PTE-1.7/PTE/R/create_raw_results_matrix.R |only PTE-1.7/PTE/R/plot.R |only PTE-1.7/PTE/R/print_and_summary.R |only PTE-1.7/PTE/R/run_model_on_left_out_record_results_and_cleanup.R |only PTE-2.0/PTE/CHANGELOG | 14 PTE-2.0/PTE/DESCRIPTION | 31 PTE-2.0/PTE/MD5 | 61 PTE-2.0/PTE/NAMESPACE | 27 PTE-2.0/PTE/R/PTE.R | 80 - PTE-2.0/PTE/R/RcppExports.R |only PTE-2.0/PTE/R/bootstrap_inference.R | 661 ++++++---- PTE-2.0/PTE/R/helpers.R |only PTE-2.0/PTE/R/plot_and_summarize.R |only PTE-2.0/PTE/R/select_optimal_m_prop.R |only PTE-2.0/PTE/R/zzz.R | 6 PTE-2.0/PTE/cleanup |only PTE-2.0/PTE/configure |only PTE-2.0/PTE/configure.win |only PTE-2.0/PTE/man/PTE.Rd | 46 PTE-2.0/PTE/man/PTE_bootstrap_inference.Rd | 395 +++-- PTE-2.0/PTE/man/continuous_example.Rd | 32 PTE-2.0/PTE/man/plot.PTE_bootstrap_results.Rd | 48 PTE-2.0/PTE/man/print.PTE_bootstrap_results.Rd | 48 PTE-2.0/PTE/man/select_optimal_m_prop.Rd |only PTE-2.0/PTE/man/summary.PTE_bootstrap_results.Rd | 48 PTE-2.0/PTE/man/survival_example.Rd | 36 PTE-2.0/PTE/src |only PTE-2.0/PTE/tests |only 30 files changed, 928 insertions(+), 605 deletions(-)
Title: Estimation and Diagnostics for Many-Facet Measurement Models
Description: Native R implementation of many-facet ordered-response
measurement models with arbitrary facet counts, rating-scale and
partial-credit parameterizations, a bounded generalized partial-credit
extension, and both marginal and joint maximum likelihood estimation.
The package provides a fit / diagnose / report pipeline covering
anchoring, linking, bias and differential-functioning screening, and
publication-oriented reporting summaries, with reproducibility manifests
for replay. See 'Andrich'
(1978) <doi:10.1007/BF02293814>, 'Masters' (1982)
<doi:10.1007/BF02296272>, and 'Muraki' (1992)
<doi:10.1177/014662169201600206> for the underlying ordered-response
models.
Author: Ryuya Komuro [aut, cre, cph]
Maintainer: Ryuya Komuro <ryuya.komuro.c4@tohoku.ac.jp>
Diff between mfrmr versions 0.2.1 dated 2026-06-12 and 0.2.2 dated 2026-07-27
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mfrmr-0.2.2/mfrmr/man/plot_rater_severity_profile.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_reliability_snapshot.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_residual_matrix.Rd | 11 mfrmr-0.2.2/mfrmr/man/plot_residual_pca.Rd | 4 mfrmr-0.2.2/mfrmr/man/plot_residual_qq.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_shrinkage_funnel.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_threshold_ladder.Rd | 4 mfrmr-0.2.2/mfrmr/man/plot_unexpected.Rd | 2 mfrmr-0.2.2/mfrmr/man/plot_wright_unified.Rd | 93 mfrmr-0.2.2/mfrmr/man/precision_review_report.Rd | 8 mfrmr-0.2.2/mfrmr/man/predict_mfrm_population.Rd | 14 mfrmr-0.2.2/mfrmr/man/predict_mfrm_units.Rd | 14 mfrmr-0.2.2/mfrmr/man/print.mfrm_apa_text.Rd | 2 mfrmr-0.2.2/mfrmr/man/q3_statistic.Rd | 87 mfrmr-0.2.2/mfrmr/man/rater_halo_network_analysis.Rd | 3 mfrmr-0.2.2/mfrmr/man/rater_network_analysis.Rd | 3 mfrmr-0.2.2/mfrmr/man/rating_scale_table.Rd | 4 mfrmr-0.2.2/mfrmr/man/recode_missing_codes.Rd | 5 mfrmr-0.2.2/mfrmr/man/recommend_mfrm_design.Rd | 2 mfrmr-0.2.2/mfrmr/man/reference_case_benchmark.Rd | 4 mfrmr-0.2.2/mfrmr/man/reporting_checklist.Rd | 16 mfrmr-0.2.2/mfrmr/man/review_conquest_overlap.Rd | 55 mfrmr-0.2.2/mfrmr/man/review_mfrm_anchors.Rd | 5 mfrmr-0.2.2/mfrmr/man/run_mfrm_facets.Rd | 16 mfrmr-0.2.2/mfrmr/man/run_qc_pipeline.Rd | 3 mfrmr-0.2.2/mfrmr/man/sample_mfrm_plausible_values.Rd | 14 mfrmr-0.2.2/mfrmr/man/shrinkage_report.Rd | 2 mfrmr-0.2.2/mfrmr/man/simulate_mfrm_data.Rd | 21 mfrmr-0.2.2/mfrmr/man/specifications_report.Rd | 7 mfrmr-0.2.2/mfrmr/man/subset_connectivity_report.Rd | 2 mfrmr-0.2.2/mfrmr/man/summary.apa_table.Rd | 2 mfrmr-0.2.2/mfrmr/man/summary.mfrm_apa_outputs.Rd | 2 mfrmr-0.2.2/mfrmr/man/summary.mfrm_bias.Rd | 6 mfrmr-0.2.2/mfrmr/man/summary.mfrm_bundle.Rd | 13 mfrmr-0.2.2/mfrmr/man/summary.mfrm_data_description.Rd | 15 mfrmr-0.2.2/mfrmr/man/summary.mfrm_design_evaluation.Rd | 8 mfrmr-0.2.2/mfrmr/man/summary.mfrm_diagnostic_screening.Rd | 4 mfrmr-0.2.2/mfrmr/man/summary.mfrm_diagnostics.Rd | 28 mfrmr-0.2.2/mfrmr/man/summary.mfrm_facet_dashboard.Rd | 2 mfrmr-0.2.2/mfrmr/man/summary.mfrm_facets_run.Rd | 2 mfrmr-0.2.2/mfrmr/man/summary.mfrm_fit.Rd | 125 mfrmr-0.2.2/mfrmr/man/summary.mfrm_person_fit_indices.Rd | 6 mfrmr-0.2.2/mfrmr/man/summary.mfrm_plausible_values.Rd | 14 mfrmr-0.2.2/mfrmr/man/summary.mfrm_population_prediction.Rd | 8 mfrmr-0.2.2/mfrmr/man/summary.mfrm_signal_detection.Rd | 8 mfrmr-0.2.2/mfrmr/man/summary.mfrm_summary_table_bundle.Rd | 3 mfrmr-0.2.2/mfrmr/man/summary.mfrm_unit_prediction.Rd | 14 mfrmr-0.2.2/mfrmr/man/unexpected_after_bias_table.Rd | 11 mfrmr-0.2.2/mfrmr/man/unexpected_response_table.Rd | 2 mfrmr-0.2.2/mfrmr/tests/testthat.R | 17 mfrmr-0.2.2/mfrmr/tests/testthat/helper-fixtures.R | 21 mfrmr-0.2.2/mfrmr/tests/testthat/test-anchor-equating.R | 2 mfrmr-0.2.2/mfrmr/tests/testthat/test-api-error-and-edge-contracts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-api-guard-paths.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-api-public-method-contracts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-as-ggplot.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-as-kable.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-attach-diagnostics.R | 23 mfrmr-0.2.2/mfrmr/tests/testthat/test-bias-collection.R | 24 mfrmr-0.2.2/mfrmr/tests/testthat/test-bubble-chart.R | 27 mfrmr-0.2.2/mfrmr/tests/testthat/test-bundle-dispatch-contracts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-bundle-summary-privacy.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-calc-subsets-parity.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-ci-api-consistency.R | 7 mfrmr-0.2.2/mfrmr/tests/testthat/test-compatibility-aliases.R | 29 mfrmr-0.2.2/mfrmr/tests/testthat/test-console-output-contract.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-core-behavior-contracts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-core-edge-paths.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-core-workflow.R | 64 mfrmr-0.2.2/mfrmr/tests/testthat/test-cran-smoke.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-data-and-citation.R | 6 mfrmr-0.2.2/mfrmr/tests/testthat/test-data-design-audit.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-data-processing.R | 12 mfrmr-0.2.2/mfrmr/tests/testthat/test-diagnostic-screening-validation.R | 2 mfrmr-0.2.2/mfrmr/tests/testthat/test-dif-module.R | 128 mfrmr-0.2.2/mfrmr/tests/testthat/test-documentation-terminology.R | 688 -- mfrmr-0.2.2/mfrmr/tests/testthat/test-draw-and-plot-contracts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-edge-cases.R | 37 mfrmr-0.2.2/mfrmr/tests/testthat/test-estimation-core.R | 167 mfrmr-0.2.2/mfrmr/tests/testthat/test-example-datasets.R | 107 mfrmr-0.2.2/mfrmr/tests/testthat/test-example-policy.R | 156 mfrmr-0.2.2/mfrmr/tests/testthat/test-exception-regression.R | 9 mfrmr-0.2.2/mfrmr/tests/testthat/test-export-bundles.R | 365 + mfrmr-0.2.2/mfrmr/tests/testthat/test-export-mfrm.R | 34 mfrmr-0.2.2/mfrmr/tests/testthat/test-facet-equivalence.R | 34 mfrmr-0.2.2/mfrmr/tests/testthat/test-facet-interactions.R | 2 mfrmr-0.2.2/mfrmr/tests/testthat/test-facets-column-contract.R | 19 mfrmr-0.2.2/mfrmr/tests/testthat/test-facets-metric-contract.R | 38 mfrmr-0.2.2/mfrmr/tests/testthat/test-facets-mode-api.R | 13 mfrmr-0.2.2/mfrmr/tests/testthat/test-facets-summary-profile.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-first-use-readiness-contracts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-fit-pathway.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-gpcm-capability-matrix.R | 279 mfrmr-0.2.2/mfrmr/tests/testthat/test-gpcm-fair-average.R | 21 mfrmr-0.2.2/mfrmr/tests/testthat/test-gpcm-verification.R | 28 mfrmr-0.2.2/mfrmr/tests/testthat/test-import-full.R | 39 mfrmr-0.2.2/mfrmr/tests/testthat/test-information-module.R | 10 mfrmr-0.2.2/mfrmr/tests/testthat/test-marginal-fit-diagnostics.R | 9 mfrmr-0.2.2/mfrmr/tests/testthat/test-mathematical-consistency.R | 18 mfrmr-0.2.2/mfrmr/tests/testthat/test-mfrm-results.R | 150 mfrmr-0.2.2/mfrmr/tests/testthat/test-missing-codes-integration.R | 110 mfrmr-0.2.2/mfrmr/tests/testthat/test-mml-cpp11-backend.R | 4 mfrmr-0.2.2/mfrmr/tests/testthat/test-model-choice-review.R | 60 mfrmr-0.2.2/mfrmr/tests/testthat/test-namespace-contract.R | 35 mfrmr-0.2.2/mfrmr/tests/testthat/test-numerical-validation.R | 10 mfrmr-0.2.2/mfrmr/tests/testthat/test-output-guide.R | 203 mfrmr-0.2.2/mfrmr/tests/testthat/test-output-stability.R | 51 mfrmr-0.2.2/mfrmr/tests/testthat/test-parameter-recovery.R | 18 mfrmr-0.2.2/mfrmr/tests/testthat/test-plot-customization.R | 22 mfrmr-0.2.2/mfrmr/tests/testthat/test-plotting-extras.R | 49 mfrmr-0.2.2/mfrmr/tests/testthat/test-q3-and-person-fit.R | 112 mfrmr-0.2.2/mfrmr/tests/testthat/test-qc-pipeline.R | 53 mfrmr-0.2.2/mfrmr/tests/testthat/test-recovery-simulation.R | 14 mfrmr-0.2.2/mfrmr/tests/testthat/test-reference-benchmark.R | 96 mfrmr-0.2.2/mfrmr/tests/testthat/test-regression-edge-paths.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-replay-roundtrip.R | 5 mfrmr-0.2.2/mfrmr/tests/testthat/test-report-functions.R | 43 mfrmr-0.2.2/mfrmr/tests/testthat/test-reporting-and-facets-edge-paths.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-reporting-checklist.R | 2 mfrmr-0.2.2/mfrmr/tests/testthat/test-reporting-edge-paths.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-reporting-method-contracts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-results-readiness-propagation.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-shrinkage.R | 17 mfrmr-0.2.2/mfrmr/tests/testthat/test-simulation-design.R | 981 +-- mfrmr-0.2.2/mfrmr/tests/testthat/test-summary-reporting-blocks.R | 18 mfrmr-0.2.2/mfrmr/tests/testthat/test-summary-table-bundle.R | 324 - mfrmr-0.2.2/mfrmr/tests/testthat/test-vignette-artifacts.R |only mfrmr-0.2.2/mfrmr/tests/testthat/test-wright-facets-style.R |only mfrmr-0.2.2/mfrmr/vignettes/mfrmr-facets-migration.Rmd | 125 mfrmr-0.2.2/mfrmr/vignettes/mfrmr-gpcm-scope.Rmd | 116 mfrmr-0.2.2/mfrmr/vignettes/mfrmr-linking-and-dff.Rmd | 30 mfrmr-0.2.2/mfrmr/vignettes/mfrmr-mml-and-marginal-fit.Rmd | 90 mfrmr-0.2.2/mfrmr/vignettes/mfrmr-reporting-and-apa.Rmd | 103 mfrmr-0.2.2/mfrmr/vignettes/mfrmr-visual-diagnostics.Rmd | 103 mfrmr-0.2.2/mfrmr/vignettes/mfrmr-workflow.Rmd | 338 - 363 files changed, 21097 insertions(+), 11812 deletions(-)
Title: Modified Generalized Estimating Equations for Small-Sample Data
Description: Analyze small-sample clustered or longitudinal data using modified
generalized estimating equations with bias-adjusted covariance estimator.
The package provides any combination of three modified generalized
estimating equations and 11 bias-adjusted covariance estimators.
Author: Ryota Ishii [aut, cre],
Kazushi Maruo [ctb],
Masahiko Gosho [ctb]
Maintainer: Ryota Ishii <r.ishii0808@gmail.com>
Diff between geess versions 1.0.1 dated 2026-04-27 and 1.0.2 dated 2026-07-27
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/geess.R | 8 ++++---- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: GCC Estimation of the Multilevel Factor Model
Description: Provides methods for model selection, estimation, inference, and simulation for the
multilevel factor model, based on the principal component estimation and generalised
canonical correlation approach. Details can be found in "Generalised Canonical Correlation
Estimation of the Multilevel Factor Model." Lin and Shin (2025) <doi:10.2139/ssrn.4295429>.
Author: Rui Lin [aut, cre],
Yongcheol Shin [aut]
Maintainer: Rui Lin <ruilin1081@gmail.com>
Diff between GCCfactor versions 1.1.6 dated 2026-04-18 and 1.2.0 dated 2026-07-27
DESCRIPTION | 8 MD5 | 15 R/2D_functions.R | 381 ++++++++++++------------ R/internal_functions.R | 184 ++++++----- R/main_functions.R | 57 ++- R/vcov_functions.R | 754 +++++++++++++++++++++++++------------------------ README.md |only man/GCC.Rd | 21 - man/multilevel.Rd | 20 - 9 files changed, 766 insertions(+), 674 deletions(-)
Title: An R Package for Stepwise Cluster Analysis
Description: A statistical tool for multivariate modeling and clustering using stepwise cluster analysis. The modeling output of rSCA is constructed as a cluster tree to represent the complicated relationships between multiple dependent and independent variables. A free tool (named rSCA Tree Generator) for visualizing the cluster tree from rSCA is also released and it can be downloaded at <rscatree.weebly.com>.
Author: Xiuquan Wang [aut] ,
Xiuquan Wang [cre]
Maintainer: Xiuquan (Xander) Wang <xiuquan.wang@gmail.com>
Diff between rSCA versions 3.1 dated 2020-03-10 and 3.2 dated 2026-07-26
DESCRIPTION | 24 +++++++++++++++++------- MD5 | 4 ++-- man/rSCA.modeling.Rd | 2 +- 3 files changed, 20 insertions(+), 10 deletions(-)
Title: Google's Compact Language Detector 3
Description: Google's Compact Language Detector 3 is a neural network model for language
identification and the successor of 'cld2' (available from CRAN). The algorithm is still
experimental and takes a novel approach to language detection with different properties
and outcomes. It can be useful to combine this with the Bayesian classifier results
from 'cld2'. See <https://github.com/google/cld3#readme> for more information.
Author: Jeroen Ooms [aut, cre] ,
Google Inc [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between cld3 versions 1.6.1 dated 2024-10-04 and 1.6.2 dated 2026-07-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 3 +++ src/Makevars.win | 39 ++++++++++++++++++++++++++++----------- 4 files changed, 38 insertions(+), 18 deletions(-)
Title: Binary Image Thinning Algorithms
Description: Thinning (skeletonization) algorithms for binary raster
images. Provides seven algorithms behind a single dispatching
function: Zhang-Suen (Zhang and Suen 1984)
<doi:10.1145/357994.358023>, Guo-Hall (Guo and Hall 1989)
<doi:10.1145/62065.62074>, a 2-D adaptation of Lee
(Lee, Kashyap, and Chu 1994) <doi:10.1006/cgip.1994.1042>, K3M
(Saeed, Tabedzki, Rybnik, and Adamski 2010)
<doi:10.2478/v10006-010-0024-4>, the parallel form commonly
attributed to Hilditch (1969, in 'Machine Intelligence 4'),
OPTA / SPTA (Naccache and Shinghal 1984), and Holt and colleagues
(1987) <doi:10.1145/12527.12531>. Also provides the medial axis
transform (Blum 1967) and a distance transform implementation
following Felzenszwalb and Huttenlocher (2012)
<doi:10.4086/toc.2012.v008a019>. The thin() API selects the
algorithm by name, defaulting to Zhang-Suen. Complements the
morphology in the 'EBImage' package, which does not provide a
thinning operator.
Author: Bill Denney [aut, cre]
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Diff between thinr versions 0.2.0 dated 2026-05-27 and 0.3.0 dated 2026-07-26
thinr-0.2.0/thinr/R/thin_image.R |only thinr-0.2.0/thinr/man/thinImage.Rd |only thinr-0.3.0/thinr/DESCRIPTION | 14 thinr-0.3.0/thinr/MD5 | 59 - thinr-0.3.0/thinr/NAMESPACE | 1 thinr-0.3.0/thinr/NEWS.md | 56 + thinr-0.3.0/thinr/R/distance_transform.R | 10 thinr-0.3.0/thinr/R/medial_axis.R | 2 thinr-0.3.0/thinr/R/thin.R | 77 +- thinr-0.3.0/thinr/R/thinr-package.R | 13 thinr-0.3.0/thinr/README.md | 11 thinr-0.3.0/thinr/build/partial.rdb |binary thinr-0.3.0/thinr/build/vignette.rds |binary thinr-0.3.0/thinr/inst/WORDLIST | 16 thinr-0.3.0/thinr/inst/doc/choosing-a-method.R | 6 thinr-0.3.0/thinr/inst/doc/choosing-a-method.Rmd | 28 thinr-0.3.0/thinr/inst/doc/choosing-a-method.html | 186 ++--- thinr-0.3.0/thinr/inst/doc/correctness-properties.R |only thinr-0.3.0/thinr/inst/doc/correctness-properties.Rmd |only thinr-0.3.0/thinr/inst/doc/correctness-properties.html |only thinr-0.3.0/thinr/man/distance_transform.Rd | 10 thinr-0.3.0/thinr/man/medial_axis.Rd | 2 thinr-0.3.0/thinr/man/thin.Rd | 39 - thinr-0.3.0/thinr/man/thinr-package.Rd | 13 thinr-0.3.0/thinr/src/distance_transform.cpp | 17 thinr-0.3.0/thinr/src/hilditch.cpp | 42 - thinr-0.3.0/thinr/src/lee.cpp | 7 thinr-0.3.0/thinr/src/opta.cpp | 103 +- thinr-0.3.0/thinr/tests/testthat/test-coercion-helpers.R |only thinr-0.3.0/thinr/tests/testthat/test-distance-transform.R | 40 + thinr-0.3.0/thinr/tests/testthat/test-medial-axis.R | 25 thinr-0.3.0/thinr/tests/testthat/test-thin.R | 468 ++++++++++++- thinr-0.3.0/thinr/vignettes/choosing-a-method.Rmd | 28 thinr-0.3.0/thinr/vignettes/correctness-properties.Rmd |only 34 files changed, 1017 insertions(+), 256 deletions(-)
Title: Generates Multivariate Nonnormal Data and Determines How Many
Factors to Retain
Description: The GenDataSample() and GenDataPopulation() functions create,
respectively, a sample or population of multivariate nonnormal data
using methods described in Ruscio and Kaczetow (2008). Both of these
functions call a FactorAnalysis() function to reproduce a correlation
matrix. The EFACompData() function allows users to determine how many
factors to retain in an exploratory factor analysis of an empirical data
set using a method described in Ruscio and Roche (2012). The latter
function uses populations of comparison data created by calling the
GenDataPopulation() function.
<DOI: 10.1080/00273170802285693>.
<DOI: 10.1037/a0025697>.
Author: John Ruscio [aut, cre]
Maintainer: John Ruscio <ruscio@tcnj.edu>
Diff between RGenData versions 1.0 dated 2018-11-14 and 1.0.1 dated 2026-07-26
DESCRIPTION | 15 +++++++++------ MD5 | 6 +++--- man/GenDataPopulation.Rd | 4 ++-- man/GenDataSample.Rd | 2 +- 4 files changed, 15 insertions(+), 12 deletions(-)
Title: Polyspherical Kernel Density Estimation
Description: Kernel density estimation on the polysphere, (hyper)sphere, and
circle. Includes functions for density estimation, regression estimation,
ridge estimation, bandwidth selection, kernels, samplers, and homogeneity
tests. Companion package to García-Portugués and Meilán-Vila (2025)
<doi:10.1080/01621459.2025.2521898> and García-Portugués and Meilán-Vila
(2023) <doi:10.1007/978-3-031-32729-2_4>.
Author: Eduardo Garcia-Portugues [aut, cre] ,
Andrea Meilan-Vila [ctb]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Diff between polykde versions 1.2.0 dated 2026-07-25 and 1.2.1 dated 2026-07-26
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 6 +++++- tests/testthat/Rplots.pdf |binary tests/testthat/tests_bwd.R | 1 + tests/testthat/tests_distr.R | 7 +++++-- tests/testthat/tests_grad_hess.R | 1 + tests/testthat/tests_kde.R | 3 ++- tests/testthat/tests_kre.R | 8 -------- tests/testthat/tests_samplers.R | 10 ++++++++++ tests/testthat/tests_tests.R | 5 ++++- 11 files changed, 42 insertions(+), 27 deletions(-)
Title: Just Analysis Methods Base
Description: Just analysis methods ('jam') base functions
focused on bioinformatics.
Version- and gene-centric alphanumeric sort,
unique name and version assignment, colorized console and 'HTML' output,
color ramp and palette manipulation,
'Rmarkdown' cache import, styled 'Excel' worksheet import and export,
interpolated raster output from smooth scatter and image plots,
list to delimited vector, efficient list tools.
Author: James M. Ward [aut, cre, cph]
Maintainer: James M. Ward <jmw86069@gmail.com>
This is a re-admission after prior archival of version 1.0.4 dated 2025-03-23
Diff between jamba versions 1.0.4 dated 2025-03-23 and 1.0.5 dated 2026-07-26
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Title: 'DataSHIELD' RO-Crate Governance Functions
Description: Tools for wrapping 'DataSHIELD' analyses into RO-Crate
(Research Object Crate) objects. Provides functions to create structured
metadata for federated data analysis projects, enabling governance
tracking of data access, project membership, analysis execution and
output validation across distributed data sources.
Author: Roberto Villegas-Diaz [aut, cre] ,
Becca Wilson [aut] ,
Olly Butters [aut] ,
Stuart Wheater [aut] ,
University of Liverpool [cph]
Maintainer: Roberto Villegas-Diaz <r.villegas-diaz@outlook.com>
Diff between dsROCrate versions 0.1.0 dated 2026-06-01 and 0.2.0 dated 2026-07-26
DESCRIPTION | 10 MD5 | 94 +- NAMESPACE | 34 NEWS.md | 32 R/audit.R | 37 R/audit_engine.R | 68 - R/backend-generic.R |only R/backend-opal.R |only R/check_permissions.R | 25 R/dsROCrate.R | 15 R/print.R | 53 + R/report.R | 23 R/safe-call-utils.R |only R/safe-call.R |only R/safe-reference.R |only R/safe-symbol-utils.R |only R/safe-symbol.R |only R/safe_data.R | 12 R/safe_output.R | 245 ++++- R/safe_people.R | 10 R/safe_project.R | 77 - R/safe_setting.R | 16 R/symbol-registry.R |only R/utils-armadillo.R | 5 R/utils-audit.R | 39 R/utils-connection.R | 118 -- R/utils-cr8tor.R | 74 + R/utils-opal.R | 98 -- R/utils-safe_data.R | 2 R/utils-safe_people.R | 71 + R/utils-safe_project.R | 2 inst/WORDLIST | 23 inst/doc/audit-permissions.R | 4 inst/doc/audit-permissions.Rmd | 7 inst/doc/audit-permissions.html | 5 inst/doc/getting-started.html | 1378 +++++--------------------------- man/armadillo_login.Rd | 5 man/check_permissions.Rd | 9 man/init.Rd | 5 man/report.Rd | 6 man/safe_data.Rd | 5 man/safe_output.Rd | 5 man/safe_people.Rd | 5 man/safe_project.Rd | 37 man/safe_setting.Rd | 5 tests/testthat/helper-mock-opal.R |only tests/testthat/test-audit.R |only tests/testthat/test-audit_engine.R |only tests/testthat/test-check_permissions.R |only tests/testthat/test-dsROCrate-package.R | 4 tests/testthat/test-report.R | 8 tests/testthat/test-utils-opal.R | 4 tests/testthat/test-utils-safe_people.R | 68 + vignettes/audit-permissions.Rmd | 7 54 files changed, 1093 insertions(+), 1657 deletions(-)
Title: R/Weka Interface
Description: An R interface to Weka (Version 3.9.3).
Weka is a collection of machine learning algorithms for data mining
tasks written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Package 'RWeka' contains the interface code, the
Weka jar is in a separate package 'RWekajars'. For more information
on Weka see <https://www.cs.waikato.ac.nz/ml/weka/>.
Author: Kurt Hornik [aut, cre] ,
Christian Buchta [ctb],
Torsten Hothorn [ctb],
Alexandros Karatzoglou [ctb],
David Meyer [ctb],
Achim Zeileis [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between RWeka versions 0.4-49 dated 2026-07-13 and 0.4-50 dated 2026-07-26
RWeka-0.4-49/RWeka/inst/arff/diabetes.arff |only RWeka-0.4-50/RWeka/CHANGELOG | 12 ++++++++++++ RWeka-0.4-50/RWeka/DESCRIPTION | 6 +++--- RWeka-0.4-50/RWeka/MD5 | 11 +++++------ RWeka-0.4-50/RWeka/build/partial.rdb |binary RWeka-0.4-50/RWeka/inst/doc/RWeka.pdf |binary RWeka-0.4-50/RWeka/man/Weka_classifier_trees.Rd | 12 ------------ 7 files changed, 20 insertions(+), 21 deletions(-)
Title: Visualizations of Paired Comparisons
Description: Convert a logical vector or a vector of p-values or a correlation,
difference, or distance matrix into a display identifying the pairs for
which the differences were not significantly different. Designed for use
in conjunction with the output of functions like TukeyHSD, dist (stats),
simint, simtest, csimint, csimtest (multcomp), friedmanmc, kruskalmc (pgirmess).
Author: Spencer Graves [aut],
Hans-Peter Piepho [aut],
Luciano Selzer [aut, cre],
Sundar Dorai-Raj [ctb]
Maintainer: Luciano Selzer <luciano.selzer@gmail.com>
Diff between multcompView versions 0.1-11 dated 2026-02-16 and 0.1-12 dated 2026-07-26
DESCRIPTION | 11 +++++++---- MD5 | 21 ++++++++++++++------- NEWS.md |only R/multcompLetters.R | 16 ++++++++-------- R/multcompTs.R | 6 +----- R/vec2mat.R | 26 -------------------------- man/multcompLetters.Rd | 9 +++------ man/multcompTs.Rd | 6 +----- man/vec2mat.Rd | 26 -------------------------- tests |only 10 files changed, 34 insertions(+), 87 deletions(-)
Title: Extra Functionality for the 'xpose' Package
Description: Adding some at-present missing functionality, or functions
unlikely to be added to the base 'xpose' package. This includes some
diagnostic plots that have been missing in translation from 'xpose4',
but also some useful features that truly extend the capabilities of what
can be done with 'xpose'. These extensions include the concept of a set of
'xpose' objects, and diagnostics for likelihood-based models.
Author: John Prybylski [aut, cre, cph]
Maintainer: John Prybylski <jprybylski@gmail.com>
Diff between xpose.xtras versions 0.1.4 dated 2026-04-21 and 0.2.0 dated 2026-07-26
DESCRIPTION | 22 MD5 | 231 ++++--- NAMESPACE | 40 + NEWS.md | 49 + R/bbr.R |only R/categorical.R | 333 ++++++++++- R/colinearity.R | 244 ++++++++ R/confusion.R | 6 R/covariates.R | 159 +++++ R/fit_stats.R |only R/fixes.R | 206 ++++++ R/modavg_xpdb.R | 18 R/nlmixr_examples.R | 55 + R/process_preset.R |only R/utils.R | 12 R/xp_xtras.R | 90 ++ R/xplot_binned.R |only R/xplot_forest.R |only R/xplot_heatmap.R |only R/xplot_pairs.R | 8 R/xpose.xtras-package.R | 2 R/xpose_set.R | 65 +- R/xset_features.R | 2 R/xset_plots.R | 30 R/xtra_labs.R |only R/xtra_pars.R | 905 +++++++++++++++++++++++++++++- R/xtra_plot_all.R |only R/xtra_plots.R | 186 ++++++ R/xtra_watermark.R |only R/xtras_options.R |only R/zzz.R | 21 README.md | 8 build/partial.rdb |binary build/vignette.rds |binary data/pheno_base.rda |binary data/pheno_final.rda |binary data/pheno_saem.rda |binary data/pheno_set.rda |binary data/pkpd_m3.rda |binary data/pkpd_m3_df.rda |binary data/vismo_dtmm.rda |binary data/vismo_pomod.rda |binary data/vismodegib.rda |binary data/xpdb_set.rda |binary data/xpdb_x.rda |binary inst/WORDLIST | 45 + inst/doc/a01-the-xp_xtra-object.R | 30 inst/doc/a01-the-xp_xtra-object.Rmd | 43 + inst/doc/a01-the-xp_xtra-object.html | 136 +++- inst/doc/a02-xpose-sets.R | 4 inst/doc/a02-xpose-sets.Rmd | 7 inst/doc/a02-xpose-sets.html | 131 ++-- inst/doc/a03-useful_plots.R | 16 inst/doc/a03-useful_plots.Rmd | 29 inst/doc/a03-useful_plots.html | 63 +- inst/doc/a04-plot-output-and-options.R |only inst/doc/a04-plot-output-and-options.Rmd |only inst/doc/a04-plot-output-and-options.html |only man/add_cov_association.Rd |only man/add_process_preset.Rd |only man/add_watermark.Rd |only man/apply_default_labs.Rd |only man/catdv_vs_ipred.Rd |only man/catdv_vs_occ.Rd |only man/check_levels.Rd | 5 man/cormat.Rd |only man/cov_forest.Rd |only man/diagnose_constants.Rd | 2 man/figures/README-cormat-1.png |only man/figures/README-m3-1.png |binary man/figures/README-m3_roc-1.png |binary man/focus_xpdb.Rd | 28 man/get_cov_matrix.Rd |only man/get_xtras_option.Rd |only man/ggsave_xp.Rd |only man/grapes-p-grapes.Rd | 4 man/ind_plots_sample.Rd |only man/is_franken_xpdb.Rd |only man/join_backfill.Rd |only man/left_join_x.Rd |only man/levelers.Rd | 8 man/list_dv_probs.Rd | 4 man/logLik.xpose_data.Rd |only man/modify_xpdb.Rd | 2 man/nlmixr_example.Rd | 7 man/patch_condn.Rd |only man/persist_process_presets.Rd |only man/plot.xpose_data.Rd |only man/prm_cov.Rd |only man/reexports.Rd | 2 man/set_default_labs.Rd |only man/set_default_plots.Rd |only man/set_default_watermark.Rd |only man/set_dv_probs.Rd | 10 man/set_option.Rd | 9 man/set_var_levels.Rd | 9 man/set_var_types.Rd | 6 man/set_var_types.default.Rd | 6 man/set_var_types.xp_xtra.Rd | 6 man/set_var_types_x.Rd | 6 man/set_xtras_options.Rd |only man/summarise_xpdb.Rd | 2 man/val2lvl.Rd | 5 man/xp_from_bbr.Rd |only man/xplot_binned.Rd |only man/xplot_forest.Rd |only man/xplot_heatmap.Rd |only man/xpose.xtras-package.Rd | 5 man/xset_fitstats.Rd |only tests/testthat/helper-bbr.R |only tests/testthat/test-bbr.R |only tests/testthat/test-categorical.R | 309 ++++++++++ tests/testthat/test-colinearity.R |only tests/testthat/test-confusion.R | 77 ++ tests/testthat/test-covariates.R | 204 ++++++ tests/testthat/test-diag_constants.R | 75 ++ tests/testthat/test-fit_stats.R |only tests/testthat/test-fixes.R | 498 ++++++++++++++++ tests/testthat/test-modavg_xpdb.R | 30 tests/testthat/test-nlmixr2.R | 305 +++++++++- tests/testthat/test-process_preset.R |only tests/testthat/test-utils.R | 22 tests/testthat/test-xp_xtras.R | 120 +++ tests/testthat/test-xplot_binned.R |only tests/testthat/test-xplot_boxplot.R | 24 tests/testthat/test-xplot_forest.R |only tests/testthat/test-xplot_heatmap.R |only tests/testthat/test-xplot_pairs.R | 243 ++++++++ tests/testthat/test-xplot_rocplot.R | 83 ++ tests/testthat/test-xpose_set.R | 120 +++ tests/testthat/test-xset_features.R | 22 tests/testthat/test-xset_plots.R | 94 +++ tests/testthat/test-xset_shark.R | 21 tests/testthat/test-xset_waterfall.R | 16 tests/testthat/test-xtra_labs.R |only tests/testthat/test-xtra_pars.R | 559 ++++++++++++++++++ tests/testthat/test-xtra_plot_all.R |only tests/testthat/test-xtra_plots.R | 148 ++++ tests/testthat/test-xtra_watermark.R |only tests/testthat/test-xtras_options.R |only tests/testthat/test-zzz.R |only vignettes/a01-the-xp_xtra-object.Rmd | 43 + vignettes/a02-xpose-sets.Rmd | 7 vignettes/a03-useful_plots.Rmd | 29 vignettes/a04-plot-output-and-options.Rmd |only 145 files changed, 6061 insertions(+), 310 deletions(-)
Title: Publication Toolkit for Water, Sanitation and Hygiene (WASH)
Data
Description: A toolkit to set up an R data package in a consistent structure. Automates tasks like tidy data export, data dictionary documentation, README and website creation, and citation management.
Author: Mian Zhong [aut] ,
Margaux Goetschmann [aut] ,
Colin Walder [aut] ,
Lars Schoebitz [aut, cre] ,
Global Health Engineering, ETH Zurich [cph]
Maintainer: Lars Schoebitz <lschoebitz@ethz.ch>
Diff between washr versions 1.0.1 dated 2024-11-07 and 1.0.2 dated 2026-07-26
DESCRIPTION | 26 +++++----- MD5 | 47 ++++++++++--------- NEWS.md | 23 +++++++++ R/setup_dictionary.R | 16 ------ R/setup_readme.R | 13 ++++- R/setup_roxygen.R | 8 --- R/setup_website.R | 6 -- R/update_citation.R | 59 +++++++++++++++--------- R/update_description.R | 26 ++++++++-- build/vignette.rds |binary inst/doc/washr.R | 6 +- inst/doc/washr.html | 5 +- man/fill_dictionary.Rd | 8 --- man/setup_dictionary.Rd | 8 --- man/setup_readme.Rd | 6 ++ man/setup_roxygen.Rd | 8 --- man/setup_website.Rd | 6 -- man/update_citation.Rd | 20 +++----- man/update_description.Rd | 3 + tests/testthat/_snaps |only tests/testthat/helper.R | 23 ++------- tests/testthat/test_setup_rawdata.R | 1 tests/testthat/test_setup_readme.R | 21 ++++++++ tests/testthat/test_update_citation.R |only tests/testthat/test_update_description.R | 76 +++++++++++++++++++++++++++++-- 25 files changed, 257 insertions(+), 158 deletions(-)
Title: High-Dimensional Undirected Graph Estimation
Description: Provides a general framework for
high-dimensional undirected graph estimation. It integrates
data preprocessing, neighborhood screening, graph estimation,
and model selection techniques into a pipeline. In
preprocessing stage, the nonparanormal(npn) transformation is
applied to help relax the normality assumption. In the graph
estimation stage, the graph structure is estimated by
Meinshausen-Buhlmann graph estimation, the graphical lasso,
or the TIGER (tuning-insensitive graph estimation and
regression) method, and the first two can be further
accelerated by the lossy screening rule preselecting the
neighborhood of each variable by correlation thresholding. We
target on high-dimensional data analysis usually d >> n, and
the computation is memory-optimized using the sparse matrix
output. We also provide a computationally efficient approach,
correlation thresholding graph estimation. Three
regularization/thresholding parameter selection methods are
included in this package: (1)stab [...truncated...]
Author: Haoming Jiang [aut],
Xinyu Fei [aut],
Han Liu [aut],
Kathryn Roeder [aut],
John Lafferty [aut],
Larry Wasserman [aut],
Xingguo Li [aut],
Tuo Zhao [aut, cre]
Maintainer: Tuo Zhao <tourzhao@gatech.edu>
Diff between huge versions 1.6 dated 2026-04-13 and 2.0.0 dated 2026-07-26
huge-1.6/huge/inst/doc/huge-content.pdf |only huge-2.0.0/huge/DESCRIPTION | 15 huge-2.0.0/huge/MD5 | 103 - huge-2.0.0/huge/NAMESPACE | 1 huge-2.0.0/huge/NEWS.md | 272 +++ huge-2.0.0/huge/R/RcppExports.R | 12 huge-2.0.0/huge/R/huge-internal.R | 332 ++++ huge-2.0.0/huge/R/huge-package.R | 1 huge-2.0.0/huge/R/huge.R | 96 - huge-2.0.0/huge/R/huge.ct.R | 98 - huge-2.0.0/huge/R/huge.generator.R | 163 +- huge-2.0.0/huge/R/huge.glasso.R | 46 huge-2.0.0/huge/R/huge.inference.R | 113 + huge-2.0.0/huge/R/huge.mb.R | 97 - huge-2.0.0/huge/R/huge.npn.R | 56 huge-2.0.0/huge/R/huge.plot.R | 21 huge-2.0.0/huge/R/huge.roc.R | 36 huge-2.0.0/huge/R/huge.select.R | 319 +++- huge-2.0.0/huge/R/huge.tiger.R | 113 + huge-2.0.0/huge/build |only huge-2.0.0/huge/configure | 95 + huge-2.0.0/huge/configure.ac | 22 huge-2.0.0/huge/inst/doc/huge.pdf |binary huge-2.0.0/huge/man/huge.Rd | 52 huge-2.0.0/huge/man/huge.ct.Rd | 26 huge-2.0.0/huge/man/huge.generator.Rd | 33 huge-2.0.0/huge/man/huge.glasso.Rd | 21 huge-2.0.0/huge/man/huge.inference.Rd | 12 huge-2.0.0/huge/man/huge.mb.Rd | 19 huge-2.0.0/huge/man/huge.npn.Rd | 6 huge-2.0.0/huge/man/huge.roc.Rd | 4 huge-2.0.0/huge/man/huge.select.Rd | 11 huge-2.0.0/huge/man/huge.tiger.Rd | 26 huge-2.0.0/huge/man/plot.sim.Rd | 2 huge-2.0.0/huge/src/Makevars.in | 1 huge-2.0.0/huge/src/Makevars.win | 1 huge-2.0.0/huge/src/RIC.cpp | 43 huge-2.0.0/huge/src/RcppExports.cpp | 35 huge-2.0.0/huge/src/SPMBgraph.cpp | 56 huge-2.0.0/huge/src/SPMBgraphsqrt.cpp | 83 - huge-2.0.0/huge/src/huge/blas_config.h | 8 huge-2.0.0/huge/src/huge/huge_core.h | 27 huge-2.0.0/huge/src/huge_core.cpp | 1328 ++++++++++++++++--- huge-2.0.0/huge/src/huge_r_threads.h |only huge-2.0.0/huge/src/hugeglasso.cpp | 30 huge-2.0.0/huge/tests/testthat/test-ct.R | 158 ++ huge-2.0.0/huge/tests/testthat/test-generator.R | 277 +++ huge-2.0.0/huge/tests/testthat/test-glasso.R | 236 +++ huge-2.0.0/huge/tests/testthat/test-graphics-state.R |only huge-2.0.0/huge/tests/testthat/test-inference.R | 156 ++ huge-2.0.0/huge/tests/testthat/test-invariants.R |only huge-2.0.0/huge/tests/testthat/test-mb.R | 123 + huge-2.0.0/huge/tests/testthat/test-regressions.R |only huge-2.0.0/huge/tests/testthat/test-select.R | 358 +++++ huge-2.0.0/huge/tests/testthat/test-tiger.R | 546 +++++++ huge-2.0.0/huge/tests/testthat/test-validation.R |only 56 files changed, 4918 insertions(+), 771 deletions(-)
Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] ,
Edward Burn [aut] ,
Theresa Burkard [aut] ,
Yuchen Guo [ctb] ,
Marti Catala [ctb] ,
Mike Du [ctb] ,
Xintong Li [ctb] ,
Ross Williams [ctb] ,
Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between DrugExposureDiagnostics versions 1.1.9 dated 2026-06-30 and 1.1.10 dated 2026-07-26
DESCRIPTION | 6 +++--- MD5 | 12 +++++++----- NEWS.md | 3 +++ R/checkTimeBetween.R | 14 ++++++++++++-- inst/doc/IntroductionToDrugExposureDiagnostics.html | 6 +++--- inst/shiny/ResultsExplorer/dataTest |only inst/testCases |only tests/testthat/test-SyntheaSqlServer.R | 12 ++++++++---- 8 files changed, 36 insertions(+), 17 deletions(-)
More information about DrugExposureDiagnostics at CRAN
Permanent link
Title: Optimal, Fast, and Reproducible Univariate Clustering
Description: Fast, optimal, and reproducible univariate
clustering by dynamic programming. Four problems are solved, including
univariate k-means (Wang & Song 2011) <doi:10.32614/RJ-2011-015>
(Song & Zhong 2020) <doi:10.1093/bioinformatics/btaa613>, k-median,
k-segments, and multi-channel weighted k-means. Dynamic programming
is used to minimize the sum of (weighted) within-cluster distances
using respective metrics. It substantially outperforms heuristic
clustering in both efficiency and accuracy as the number of clusters
increases. Multi-channel weighted k-means groups multiple univariate
signals into k clusters. An auxiliary function generates histograms
adaptive to patterns in data. This package provides a powerful set
of tools for univariate data analysis with guaranteed optimality,
efficiency, and reproducibility, useful for peak calling on temporal,
spatial, and spectral data in addition to univariate clustering.
Author: Joe Song [aut, cre] ,
Hua Zhong [aut] ,
Haizhou Wang [aut]
Maintainer: Joe Song <joemsong@nmsu.edu>
Diff between Ckmeans.1d.dp versions 4.3.5 dated 2023-08-19 and 4.3.6 dated 2026-07-26
DESCRIPTION | 26 ++++++------ MD5 | 26 ++++++------ NEWS.md | 17 +++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/Ckmeans.1d.dp.R | 10 ++-- inst/doc/Ckmeans.1d.dp.html | 92 +++++++++++++++++++++---------------------- inst/doc/Weights.html | 4 - inst/doc/ahist.R | 14 +++--- inst/doc/ahist.html | 15 +++---- man/Ckmeans.1d.dp.Rd | 18 +++++++- man/plot.Cksegs.1d.dp.Rd | 4 - tests/testthat/Rplots.pdf |binary tests/testthat/test_MC_WUC.R | 9 ++++ 14 files changed, 137 insertions(+), 98 deletions(-)
Title: Flexible Bayesian Optimization
Description: A modern and flexible approach to Bayesian Optimization / Model
Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox
providing both ready-to-use optimization algorithms as well as their fundamental
building blocks allowing for straightforward implementation of custom
algorithms. Single- and multi-objective optimization is supported as well as
mixed continuous, categorical and conditional search spaces. Moreover, using
'mlr3mbo' for hyperparameter optimization of machine learning models within the
'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use
optimization algorithms include Efficient Global Optimization by Jones et al.
(1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006)
<doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008)
<doi:10.1007/978-3-540-87700-4_78>.
Author: Marc Becker [cre, aut] ,
Lennart Schneider [aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Florian Pfisterer [aut] ,
Martin Binder [aut],
Sebastian Fischer [aut] ,
Michael H. Buselli [cph],
Wessel Dankers [cph],
Carlos Fonseca [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3mbo versions 1.2.0 dated 2026-07-21 and 1.2.1 dated 2026-07-26
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ README.md | 20 ++++++++++---------- inst/CITATION | 6 +++--- tests/testthat/test_ResultAssignerArchive.R | 2 +- tests/testthat/test_ResultAssignerSurrogate.R | 2 +- tests/testthat/test_TunerADBO.R | 2 +- tests/testthat/test_TunerAsyncMbo.R | 2 +- 9 files changed, 32 insertions(+), 28 deletions(-)
Title: Gaussian Model Invariant by Permutation Symmetry
Description: Find the permutation symmetry group such that the covariance
matrix of the given data is approximately invariant under it.
Discovering such a permutation decreases the number of observations
needed to fit a Gaussian model, which is of great use when it is
smaller than the number of variables. Even if that is not the case,
the covariance matrix found with 'gips' approximates the actual
covariance with less statistical error. The methods implemented in
this package are described in Graczyk et al. (2022)
<doi:10.1214/22-AOS2174>. Documentation about 'gips' is
provided via its website at <https://przechoj.github.io/gips/> and
the paper by Chojecki, Morgen, Kołodziejek
(2025, <doi:10.18637/jss.v112.i07>).
Author: Adam Przemyslaw Chojecki [aut, cre] ,
Pawel Morgen [aut],
Bartosz Kolodziejek [aut]
Maintainer: Adam Przemyslaw Chojecki <adam.prze.choj@gmail.com>
Diff between gips versions 1.2.3 dated 2025-03-18 and 1.3.0 dated 2026-07-26
gips-1.2.3/gips/R/gips_class.R |only gips-1.2.3/gips/man/figures/README-example_mean_known4-1.png |only gips-1.2.3/gips/tests/testthat/Rplots.pdf |only gips-1.3.0/gips/DESCRIPTION | 28 gips-1.3.0/gips/MD5 | 127 + gips-1.3.0/gips/NAMESPACE | 2 gips-1.3.0/gips/NEWS.md | 78 + gips-1.3.0/gips/R/RcppExports.R |only gips-1.3.0/gips/R/calculate_gamma_function.R | 83 - gips-1.3.0/gips/R/find_MAP.R | 365 +++-- gips-1.3.0/gips/R/get_structure_constants.R | 2 gips-1.3.0/gips/R/gips_constructors.R |only gips-1.3.0/gips/R/gips_methods.R |only gips-1.3.0/gips/R/gips_perm_class.R | 36 gips-1.3.0/gips/R/gips_plot.R |only gips-1.3.0/gips/R/log_posteriori_of_gips.R | 253 +++ gips-1.3.0/gips/R/prepare_orthogonal_matrix.R | 65 - gips-1.3.0/gips/R/project_matrix.R | 192 -- gips-1.3.0/gips/R/rcpp.R |only gips-1.3.0/gips/R/sysdata.rda |binary gips-1.3.0/gips/R/utils.R | 29 gips-1.3.0/gips/README.md | 24 gips-1.3.0/gips/inst/WORDLIST | 18 gips-1.3.0/gips/inst/doc/Optimizers.R | 122 + gips-1.3.0/gips/inst/doc/Optimizers.Rmd | 164 ++ gips-1.3.0/gips/inst/doc/Optimizers.html | 524 +++++--- gips-1.3.0/gips/inst/doc/Theory.Rmd | 26 gips-1.3.0/gips/inst/doc/Theory.html | 84 - gips-1.3.0/gips/inst/doc/gips.R | 88 + gips-1.3.0/gips/inst/doc/gips.Rmd | 157 ++ gips-1.3.0/gips/inst/doc/gips.html | 244 ++- gips-1.3.0/gips/man/AIC.gips.Rd | 10 gips-1.3.0/gips/man/as.character.gips.Rd | 4 gips-1.3.0/gips/man/as.character.gips_perm.Rd | 2 gips-1.3.0/gips/man/calculate_gamma_function.Rd | 12 gips-1.3.0/gips/man/compare_posteriories_of_perms.Rd | 11 gips-1.3.0/gips/man/figures/README-example_mean_known1_1-1.png |binary gips-1.3.0/gips/man/figures/README-example_mean_known3_1-1.png |binary gips-1.3.0/gips/man/figures/README-example_mean_known6-1.png |binary gips-1.3.0/gips/man/figures/README-example_mean_unknown2-1.png |binary gips-1.3.0/gips/man/figures/README-example_mean_unknown4-1.png |binary gips-1.3.0/gips/man/find_MAP.Rd | 32 gips-1.3.0/gips/man/forget_perms.Rd | 4 gips-1.3.0/gips/man/get_probabilities_from_gips.Rd | 13 gips-1.3.0/gips/man/get_structure_constants.Rd | 2 gips-1.3.0/gips/man/gips.Rd | 70 - gips-1.3.0/gips/man/gips_perm.Rd | 4 gips-1.3.0/gips/man/logLik.gips.Rd | 13 gips-1.3.0/gips/man/log_posteriori_of_gips.Rd | 19 gips-1.3.0/gips/man/plot.gips.Rd | 75 - gips-1.3.0/gips/man/prepare_orthogonal_matrix.Rd | 9 gips-1.3.0/gips/man/print.gips.Rd | 17 gips-1.3.0/gips/man/print.gips_perm.Rd | 2 gips-1.3.0/gips/man/project_matrix.Rd | 22 gips-1.3.0/gips/man/summary.gips.Rd | 25 gips-1.3.0/gips/src |only gips-1.3.0/gips/tests/testthat/test-calculate_gamma_function.R | 104 + gips-1.3.0/gips/tests/testthat/test-find_MAP.R | 39 gips-1.3.0/gips/tests/testthat/test-gips_class.R | 641 ++-------- gips-1.3.0/gips/tests/testthat/test-gips_mult.R |only gips-1.3.0/gips/tests/testthat/test-gips_perm_class.R | 21 gips-1.3.0/gips/tests/testthat/test-gips_plot.R |only gips-1.3.0/gips/tests/testthat/test-log_posteriori_of_gips.R | 57 gips-1.3.0/gips/tests/testthat/test-plot_multi.R |only gips-1.3.0/gips/tests/testthat/test-prepare_orthogonal_matrix.R | 18 gips-1.3.0/gips/tests/testthat/test-project_matrix.R | 121 - gips-1.3.0/gips/tests/testthat/test-utils.R | 28 gips-1.3.0/gips/vignettes/Optimizers.Rmd | 164 ++ gips-1.3.0/gips/vignettes/Theory.Rmd | 26 gips-1.3.0/gips/vignettes/gips.Rmd | 157 ++ 70 files changed, 2891 insertions(+), 1542 deletions(-)
Title: Diagnostic Test Accuracy Meta-Analysis using Template Model
Builder
Description: Fits the hierarchical summary receiver operating characteristic (HSROC) model of
Rutter and Gatsonis (2001) <doi:10.1002/sim.942>, the bivariate binomial-normal model of
Reitsma et al. (2005) <doi:10.1016/j.jclinepi.2005.02.022>, the threshold-based bivariate
time-to-event model of Hoyer et al. (2018) <doi:10.1002/jrsm.1273>, and the latent class
extensions of Liu et al. (2015) <doi:10.1111/biom.12264> for diagnostic studies without
a perfect reference standard. Provides subgroup analyses, HSROC meta-regression,
likelihood-ratio tests, summary ROC plots, and coupled forest plots.
Author: Claus Nowak [aut, cre]
Maintainer: Claus Nowak <claus.nowak@donau-uni.ac.at>
Diff between dtametaTMB versions 0.1.0 dated 2026-07-16 and 0.1.1 dated 2026-07-26
dtametaTMB-0.1.0/dtametaTMB/R/TMB.R |only dtametaTMB-0.1.0/dtametaTMB/R/getesti_V_g.R |only dtametaTMB-0.1.1/dtametaTMB/DESCRIPTION | 17 dtametaTMB-0.1.1/dtametaTMB/MD5 | 154 +- dtametaTMB-0.1.1/dtametaTMB/NAMESPACE | 33 dtametaTMB-0.1.1/dtametaTMB/R/LogLik.R | 72 dtametaTMB-0.1.1/dtametaTMB/R/as_revman.R | 265 +++ dtametaTMB-0.1.1/dtametaTMB/R/check2_data.R |only dtametaTMB-0.1.1/dtametaTMB/R/dtametaTMB.R | 7 dtametaTMB-0.1.1/dtametaTMB/R/fitReitsma.R | 34 dtametaTMB-0.1.1/dtametaTMB/R/fitReitsmaLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/fitReitsmaSubgroup.R | 52 dtametaTMB-0.1.1/dtametaTMB/R/fitReitsmaSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/fitRutterGatsonis.R | 14 dtametaTMB-0.1.1/dtametaTMB/R/fitRutterGatsonisLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/fitRutterGatsonisReg.R | 4 dtametaTMB-0.1.1/dtametaTMB/R/fitRutterGatsonisSubgroup.R | 2 dtametaTMB-0.1.1/dtametaTMB/R/fitRutterGatsonisSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/forestCochrane.R | 13 dtametaTMB-0.1.1/dtametaTMB/R/forestCochraneLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/forestCochraneSubgroup.R | 46 dtametaTMB-0.1.1/dtametaTMB/R/forestCochraneSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/getWEIGHTSLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/pap.R |only dtametaTMB-0.1.1/dtametaTMB/R/plotHoyerAFT.R | 2 dtametaTMB-0.1.1/dtametaTMB/R/plotReitsma.R | 22 dtametaTMB-0.1.1/dtametaTMB/R/plotReitsmaLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/plotReitsmaSubgroup.R | 4 dtametaTMB-0.1.1/dtametaTMB/R/plotReitsmaSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/plotRutterGatsonis.R | 2 dtametaTMB-0.1.1/dtametaTMB/R/plotRutterGatsonisLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/plotRutterGatsonisSubgroup.R | 4 dtametaTMB-0.1.1/dtametaTMB/R/plotRutterGatsonisSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/plot_SESPGRID.R | 4 dtametaTMB-0.1.1/dtametaTMB/R/printHoyerAFT.R | 11 dtametaTMB-0.1.1/dtametaTMB/R/printReitsma.R | 20 dtametaTMB-0.1.1/dtametaTMB/R/printReitsmaLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/printReitsmaSubgroup.R | 18 dtametaTMB-0.1.1/dtametaTMB/R/printReitsmaSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/printRutterGatsonis.R | 14 dtametaTMB-0.1.1/dtametaTMB/R/printRutterGatsonisLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/printRutterGatsonisReg.R | 9 dtametaTMB-0.1.1/dtametaTMB/R/printRutterGatsonisSubgroup.R | 10 dtametaTMB-0.1.1/dtametaTMB/R/printRutterGatsonisSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/rename_hsrocsubLCA_rows.R |only dtametaTMB-0.1.1/dtametaTMB/R/rename_reitsubLCA_rows.R |only dtametaTMB-0.1.1/dtametaTMB/R/schuetz.R | 4 dtametaTMB-0.1.1/dtametaTMB/R/summaryReitsmaLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/summaryReitsmaSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/summaryRutterGatsonis.R | 2 dtametaTMB-0.1.1/dtametaTMB/R/summaryRutterGatsonisLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/summaryRutterGatsonisSubgroupLCA.R |only dtametaTMB-0.1.1/dtametaTMB/R/tub.R |only dtametaTMB-0.1.1/dtametaTMB/README.md | 37 dtametaTMB-0.1.1/dtametaTMB/build/vignette.rds |binary dtametaTMB-0.1.1/dtametaTMB/data/pap.rda |only dtametaTMB-0.1.1/dtametaTMB/data/tub.rda |only dtametaTMB-0.1.1/dtametaTMB/inst/doc/LCA.R |only dtametaTMB-0.1.1/dtametaTMB/inst/doc/LCA.pdf |only dtametaTMB-0.1.1/dtametaTMB/inst/doc/LCA.qmd |only dtametaTMB-0.1.1/dtametaTMB/inst/doc/Meta-Regression.R | 38 dtametaTMB-0.1.1/dtametaTMB/inst/doc/Meta-Regression.pdf |binary dtametaTMB-0.1.1/dtametaTMB/inst/doc/Meta-Regression.qmd | 49 dtametaTMB-0.1.1/dtametaTMB/inst/doc/dtametaTMB.R | 4 dtametaTMB-0.1.1/dtametaTMB/inst/doc/dtametaTMB.pdf |binary dtametaTMB-0.1.1/dtametaTMB/inst/doc/dtametaTMB.qmd | 121 - dtametaTMB-0.1.1/dtametaTMB/man/anova.dtametaTMB.Rd | 12 dtametaTMB-0.1.1/dtametaTMB/man/as_revman.dtametaTMB.Rd | 19 dtametaTMB-0.1.1/dtametaTMB/man/dtametaTMB.Rd | 15 dtametaTMB-0.1.1/dtametaTMB/man/fitReitsmaLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/fitReitsmaSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/fitRutterGatsonisLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/fitRutterGatsonisSubgroup.Rd | 2 dtametaTMB-0.1.1/dtametaTMB/man/fitRutterGatsonisSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/forest.CochraneLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/forest.CochraneSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/logLik.dtametaTMB.Rd | 12 dtametaTMB-0.1.1/dtametaTMB/man/pap.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/plot.ReitsmaLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/plot.ReitsmaSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/plot.RutterGatsonisLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/plot.RutterGatsonisSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/print.ReitsmaLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/print.ReitsmaSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/print.RutterGatsonisLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/print.RutterGatsonisSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/schuetz.Rd | 4 dtametaTMB-0.1.1/dtametaTMB/man/summary.ReitsmaLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/summary.ReitsmaSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/summary.RutterGatsonis.Rd | 2 dtametaTMB-0.1.1/dtametaTMB/man/summary.RutterGatsonisLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/summary.RutterGatsonisSubgroupLCA.Rd |only dtametaTMB-0.1.1/dtametaTMB/man/tub.Rd |only dtametaTMB-0.1.1/dtametaTMB/src/TMB/ReitsmaLCA.hpp |only dtametaTMB-0.1.1/dtametaTMB/src/TMB/ReitsmaSubgroupLCA.hpp |only dtametaTMB-0.1.1/dtametaTMB/src/TMB/RutterGatsonisLCA.hpp |only dtametaTMB-0.1.1/dtametaTMB/src/TMB/RutterGatsonisSubgroupLCA.hpp |only dtametaTMB-0.1.1/dtametaTMB/src/TMB/dtametaTMB_TMBExports.cpp | 12 dtametaTMB-0.1.1/dtametaTMB/tests/testthat/test-fitLCA.R |only dtametaTMB-0.1.1/dtametaTMB/tests/testthat/test-fitReitsmaSubgroup.R | 2 dtametaTMB-0.1.1/dtametaTMB/tests/testthat/test-plotLCA.R |only dtametaTMB-0.1.1/dtametaTMB/tests/testthat/test-plotReitsmaSubgroup.R |only dtametaTMB-0.1.1/dtametaTMB/vignettes/LCA.html |only dtametaTMB-0.1.1/dtametaTMB/vignettes/LCA.qmd |only dtametaTMB-0.1.1/dtametaTMB/vignettes/Meta-Regression.html | 767 ++++++---- dtametaTMB-0.1.1/dtametaTMB/vignettes/Meta-Regression.qmd | 49 dtametaTMB-0.1.1/dtametaTMB/vignettes/dtametaTMB.html | 439 ++--- dtametaTMB-0.1.1/dtametaTMB/vignettes/dtametaTMB.qmd | 121 - 108 files changed, 1653 insertions(+), 891 deletions(-)
Title: Demographic Analysis
Description: Tool for demographic modeling and analysis, combining stochastic
simulation-based projections with classic demographic methods. Provides
utilities for disaggregating population data using Karup-King interpolation,
fitting Brass relational logit models, calculating fertility and mortality
metrics, building complete and abridged life tables with model-based
separation factors, estimating child mortality indirectly from children
ever born and surviving (Brass-Trussell method), decomposing and
standardizing rates, and performing hierarchical subnational population
projections. Relational life table estimation and interpolation
methods are described in Brass (1975) "Methods for Estimating Fertility and
Mortality from Limited and Defective Data", Preston et al. (2001,
ISBN:978-0631226161) "Demography: Measuring and Modeling Population
Processes", Siegel and Swanson (2004, ISBN:978-0126419559) "The Methods and
Materials of Demography", and Raftery et al. (2012) "Bayesian probabilistic
populat [...truncated...]
Author: Edward Owusu Manu [aut, cre]
Maintainer: Edward Owusu Manu <edward.manu@statsghana.gov.gh>
Diff between DemogAnr versions 0.1.0 dated 2026-07-23 and 0.2.0 dated 2026-07-26
DESCRIPTION | 15 +- MD5 | 55 +++++++--- NAMESPACE | 46 ++++++++ NEWS.md | 78 +++++++++++---- R/CDR_ASDR.R | 16 ++- R/Dem-package.R | 5 R/Fertility.R | 17 +++ R/age_quality.R |only R/child_mortality_indirect.R |only R/data.R | 40 +++++++ R/globals.R | 8 + R/lifetables.R | 176 +++++++++++++++++++++++++--------- R/newPPP.R | 27 +++++ R/plots.R |only R/standardization.R |only data/ghmort2021.rda |only data/ghpop2021.rda |only man/DemogAnr-package.Rd | 2 man/age_ratio.Rd |only man/chm_brass.Rd |only man/decompose_LE.Rd |only man/decompose_rates.Rd |only man/dem.cdr.Rd | 5 man/dem.fert.Rd | 5 man/ghmort2021.Rd |only man/ghpop2021.Rd |only man/lifetable.Rd | 60 +++++++++-- man/myers.Rd |only man/project_population.Rd | 5 man/pyramid.Rd |only man/sex_ratio.Rd |only man/standardize.Rd |only man/un_age_sex_accuracy.Rd |only man/whipple.Rd |only tests/testthat/test-age-quality.R |only tests/testthat/test-chm-brass.R |only tests/testthat/test-lifetable-nax.R |only tests/testthat/test-plots.R |only tests/testthat/test-projections.R | 4 tests/testthat/test-standardization.R |only 40 files changed, 463 insertions(+), 101 deletions(-)
Title: Bayesian Generalized Linear Models (IID Samples)
Description: Provides Bayesian linear and generalized linear model fitting
with independent and identically distributed (iid) posterior samples. The
main functions mirror R's lm() and glm() interfaces while adding prior
family specifications for Gaussian, Poisson, binomial, and Gamma models
with log-concave likelihoods. Sampling for supported non-conjugate models
uses accept-reject methods based on likelihood subgradients as in Nygren
and Nygren (2006) <doi:10.1198/016214506000000357>. The package also
includes tools for prior setup, posterior summaries, prediction,
diagnostics, simulation, vignettes, and optional 'OpenCL' acceleration for
larger models.
Author: Kjell Nygren [aut, cre],
The R Core Team [ctb, cph] ,
The R Foundation [cph] ,
Ross Ihaka [ctb, cph] ,
Robert Gentleman [ctb, cph] ,
Simon Davies [ctb] ,
Morten Welinder [ctb, cph] ,
Martin Maechler [ctb]
Maintainer: Kjell Nygren <kjell.a.nygren@gmail.com>
Diff between glmbayes versions 0.9.7 dated 2026-07-19 and 0.9.72 dated 2026-07-26
DESCRIPTION | 8 - MD5 | 90 ++++++++-------- NEWS.md | 15 ++ build/partial.rdb |binary configure.win | 9 - inst/doc/Chapter-01.html | 12 +- inst/doc/Chapter-02-S01.html | 4 inst/doc/Chapter-02-S02.html | 4 inst/doc/Chapter-02-S03.html | 4 inst/doc/Chapter-02-S04.html | 4 inst/doc/Chapter-02-S05.html | 4 inst/doc/Chapter-03.html | 4 inst/doc/Chapter-04.html | 4 inst/doc/Chapter-05.html | 164 +++++++++++++++--------------- inst/doc/Chapter-06.html | 168 +++++++++++++++---------------- inst/doc/Chapter-07.html | 4 inst/doc/Chapter-08.html | 50 ++++----- inst/doc/Chapter-09.html | 82 +++++++-------- inst/doc/Chapter-10.html | 82 +++++++-------- inst/doc/Chapter-11.html | 50 ++++----- inst/doc/Chapter-13.html | 12 +- inst/doc/Chapter-14.html | 34 +++--- inst/doc/Chapter-17.html | 18 +-- inst/doc/Chapter-18.html | 4 inst/doc/Chapter-A01.html | 22 ++-- inst/doc/Chapter-A02.html | 4 inst/doc/Chapter-A03.html | 120 +++++++++++----------- inst/doc/Chapter-A04.html | 4 inst/doc/Chapter-A05.html | 4 inst/doc/Chapter-A06.html | 4 inst/doc/Chapter-A07.html | 4 inst/doc/Chapter-A08.html | 4 inst/doc/Chapter-A09.html | 4 inst/doc/Chapter-A10.html | 4 inst/doc/Chapter-A11.html | 4 inst/doc/Chapter-A12.html | 4 inst/examples/Ex_Prior_Setup.R | 27 +++- inst/examples/Ex_pfamily.R | 15 ++ inst/examples/Ex_rGamma_reg.R | 6 - inst/examples/Ex_rNormalGamma_reg.R | 5 inst/examples/Ex_rNormal_reg.R | 18 ++- inst/examples/Ex_rindepNormalGamma_reg.R | 6 - man/Prior_Setup.Rd | 27 +++- man/pfamily.Rd | 15 ++ man/simfuncs.Rd | 35 ++++-- src/Makevars.win | 4 46 files changed, 633 insertions(+), 537 deletions(-)
Title: Genetic Tools for Colony Management
Description: Provides genetic tools for colony management and is a derivation
of the work in Amanda Vinson and Michael J Raboin (2015)
<https://pmc.ncbi.nlm.nih.gov/articles/PMC4671785/> "A Practical
Approach for Designing Breeding Groups to Maximize Genetic Diversity in a
Large Colony of Captive Rhesus Macaques ('Macaca' 'mulatta')".
It provides a 'Shiny' application with an exposed API.
The application supports five groups of functions:
(1) Quality control of studbooks contained in text files or 'Excel'
workbooks and of pedigrees within 'LabKey' Electronic Health Records
(EHR);
(2) Creation of pedigrees from a list of animals using the 'LabKey' EHR
integration;
(3) Creation and display of an age by sex pyramid plot of the living
animals within the designated pedigree;
(4) Generation of genetic value analysis reports; and
(5) Creation of potential breeding groups with and without proscribed sex
ratios and defined maximum kinships.
Author: Michael Raboin [aut],
Terry Therneau [aut],
Amanda Vinson [aut, dtc],
R. Mark Sharp [aut, cre, cph, dtc] ,
Matthew Schultz [aut] ,
Southwest National Primate Research Center NIH grant P51 RR13986 [fnd],
Oregon National Primate Research Center grant P [...truncated...]
Maintainer: R. Mark Sharp <rmsharp@me.com>
This is a re-admission after prior archival of version 1.0.8 dated 2025-07-25
Diff between nprcgenekeepr versions 1.0.8 dated 2025-07-25 and 2.0.0 dated 2026-07-26
nprcgenekeepr-1.0.8/nprcgenekeepr/R/agePyramidPlot.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/R/fixGenotypeCols.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/R/getLogo.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/R/getMinParentAge.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/R/getSimSires.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/R/makeGrpNum.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/R/nprcgenekeeper.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/inst/_pkgdown.yml |only nprcgenekeepr-1.0.8/nprcgenekeepr/inst/application |only nprcgenekeepr-1.0.8/nprcgenekeepr/inst/extdata/software_design_doc.qmd |only nprcgenekeepr-1.0.8/nprcgenekeepr/inst/extdata/submission.txt |only nprcgenekeepr-1.0.8/nprcgenekeepr/inst/extdata/trulyUnknownParents.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/man/getLogo.Rd |only nprcgenekeepr-1.0.8/nprcgenekeepr/man/nprcgenekeepr.Rd |only nprcgenekeepr-1.0.8/nprcgenekeepr/tests/testthat/test_fixGenotypeCols.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/tests/testthat/test_getLogo.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/tests/testthat/test_getMinParentAge.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/tests/testthat/test_makeGeneticDiversityDashboard.R |only nprcgenekeepr-1.0.8/nprcgenekeepr/vignettes/manual_components/_bg_algorithm.Rmd |only nprcgenekeepr-1.0.8/nprcgenekeepr/vignettes/manual_components/_bg_formation.Rmd |only nprcgenekeepr-2.0.0/nprcgenekeepr/DESCRIPTION | 31 nprcgenekeepr-2.0.0/nprcgenekeepr/LICENSE | 2 nprcgenekeepr-2.0.0/nprcgenekeepr/MD5 | 1266 + nprcgenekeepr-2.0.0/nprcgenekeepr/NAMESPACE | 170 nprcgenekeepr-2.0.0/nprcgenekeepr/NEWS.md | 269 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addAnimalsWithNoRelative.R | 21 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addBackSecondParents.R | 11 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addErrTxt.R | 9 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addGenotype.R | 27 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addGroupOfUnusedAnimals.R | 14 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addIdRecords.R | 20 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addKinshipValueCount.R | 15 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addParents.R | 10 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addSexAndAgeToGroup.R | 20 nprcgenekeepr-2.0.0/nprcgenekeepr/R/addUIds.R | 23 nprcgenekeepr-2.0.0/nprcgenekeepr/R/allTrueNoNA.R | 9 nprcgenekeepr-2.0.0/nprcgenekeepr/R/alleleFreq.R | 15 nprcgenekeepr-2.0.0/nprcgenekeepr/R/appServer.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/R/appUI.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/R/applyKinshipOverrides.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/R/applyKinshipOverridesToMatrix.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/R/assertRequiredColsPresent.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/R/assignAlleles.R | 13 nprcgenekeepr-2.0.0/nprcgenekeepr/R/autoIdFormat.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/R/calcA.R | 32 nprcgenekeepr-2.0.0/nprcgenekeepr/R/calcAge.R | 13 nprcgenekeepr-2.0.0/nprcgenekeepr/R/calcFE.R | 61 nprcgenekeepr-2.0.0/nprcgenekeepr/R/calcFEFG.R | 90 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nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSiteConfig.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSummaryStats.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSummaryStats_coverage.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSummaryStats_ggplots.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSummaryStats_kinshipOverrides.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSummaryStats_parity.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSummaryStats_popovers.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_modSummaryStats_relationships.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_moduleContract.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_monolith_removed.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_muffleIncompleteFinalLine.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_normalizeGvReport.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_obfuscateDate.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_obfuscateId.R | 19 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_obfuscatePed.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_orderReport.R | 110 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_pkgdown_reference_config.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_prepareKinshipOverrides.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_print.summary.nprcgenekeeprErr.R | 5 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_print.summary.nprcgenekeeprGV.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_qcStudbook.R | 113 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_rankSubjects.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_readKinshipOverrides.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_removeAutoGenIds.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_removeDuplicates.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_removeEarlyDates.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_removeUninformativeFounders.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_removeUnknownAnimals.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_reportGV.R | 712 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_resetGroup.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_resetPopulation.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_resolveBreedingAge.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_rhesusGenotypes.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_rhesusPedigree.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_runModularApp_alias.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_runQcStudbook.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_saveDataframesAsFiles.R | 23 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_setExit.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_setLabKeyDefaults.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_sexCodes.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_shinytest2_workflow_coverage.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_shouldShowChangedColsTab.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_shouldShowOripTab.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_species_first_class.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_summarizeKinshipValues.R | 54 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_summary.nprcgenekeeprErr.R | 11 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_summary.nprcgenekeeprGV.R | 47 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_trimPedigree.R | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_vignettes_no_deprecated_minParentAge.R |only nprcgenekeepr-2.0.0/nprcgenekeepr/tests/testthat/test_withinIntegerRange.R | 5 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/a2interactive.Rmd | 34 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/gvaConvergence.Rmd |only nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_breeding_group_algorithm.Rmd | 9 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_breeding_group_formation.Rmd | 98 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_genetic_value_analysis.Rmd | 105 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_genome_uniqueness_algorithm.Rmd | 7 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_gv_and_bg_desc.Rmd | 49 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_input.Rmd | 84 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_introduction.Rmd | 2 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_pedigree_browser.Rmd | 78 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_running_shiny_application.Rmd | 3 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/manual_components/_summary_statistics.Rmd | 99 nprcgenekeepr-2.0.0/nprcgenekeepr/vignettes/simulatedKValues.Rmd | 83 775 files changed, 15263 insertions(+), 10318 deletions(-)
Title: Minimization Tool for Pharmacokinetic-Pharmacodynamic Data
Analysis
Description: This is a set of minimization tools (maximum likelihood estimation and least square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner's book "Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications" 5th ed. (ISBN:9198299107). Examples include linear and nonlinear compartmental model, turn-over model, single or multiple dosing bolus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling, Emax model, inhibitory model, tolerance model, oscillating response model, enantiomer interaction model, effect compartment model, drug-drug interaction model, receptor occupancy model, and rebound phenomena model.
Author: Kyun-Seop Bae [aut, cre, cph]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between wnl versions 0.8.5 dated 2026-03-07 and 0.8.6 dated 2026-07-26
DESCRIPTION | 10 +++-- MD5 | 30 ++++++++-------- R/ExpandDH.R | 16 +++++--- R/Objs.R | 6 +++ R/SolComp3.R | 20 +++++++---- R/cmpChi.R | 14 ++++--- R/hSkew.R | 16 ++++---- R/nComp.R | 7 ++- R/nlr.R | 32 ++++++++++------- R/pComp.R | 15 ++++---- R/pProf.R | 2 - R/wnl5.R | 6 --- inst/NEWS.Rd | 101 +++++++++++++++++++++++++++++++------------------------- man/SolComp3.Rd | 2 - man/nlr.Rd | 4 +- man/wnl5.Rd | 4 +- 16 files changed, 163 insertions(+), 122 deletions(-)
Title: Power Analysis of Flexible ANOVA Designs and Related Tests
Description: Provides functions for conducting power analysis in ANOVA designs, including between-, within-, and mixed-factor designs, with full support for both main effects and interactions. The package allows calculation of statistical power, required total sample size, significance level, and minimal detectable effect sizes expressed as partial eta squared or Cohen's f for ANOVA terms and planned contrasts. In addition, complementary functions are included for common related tests such as t-tests and correlation tests, making the package a convenient toolkit for power analysis in experimental psychology and related fields.
Author: Hiroyuki Muto [aut, cre]
Maintainer: Hiroyuki Muto <mutopsy@omu.ac.jp>
Diff between pwranova versions 1.0.3 dated 2026-01-19 and 1.1.5 dated 2026-07-26
DESCRIPTION | 6 MD5 | 44 - NEWS.md | 29 R/cohensf_to_peta2.r | 84 +- R/peta2_to_cohensf.r | 84 +- R/pwranova.r | 737 +++++++++++----------- R/pwrcontrast.r | 33 - R/pwrcortest.r | 70 +- R/pwrttest.r | 58 + README.md | 373 +++++++---- inst/CITATION | 27 man/pwranova.Rd | 12 man/pwrcontrast.Rd | 2 man/pwrcortest.Rd | 29 man/pwrttest.Rd | 31 tests/testthat/expected/expected_pwranova.csv | 53 + tests/testthat/expected/expected_pwrcortest.csv | 26 tests/testthat/expected/expected_pwrttest.csv | 24 tests/testthat/test-cohensf_to_peta2.r | 62 + tests/testthat/test-peta2_to_cohensf.r | 72 +- tests/testthat/test-pwranova.r | 511 +++++++-------- tests/testthat/test-pwrcortest.r | 107 +++ tests/testthat/test-pwrttest.r | 777 ++++++++++++------------ 23 files changed, 1863 insertions(+), 1388 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Author: George Moroz [aut, cre] ,
Kirill Koncha [ctb] ,
Mikhail Leonov [ctb],
Anna Smirnova [ctb],
Ekaterina Zalivina [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.1.25 dated 2026-03-02 and 1.1.26 dated 2026-07-26
DESCRIPTION | 8 +-- MD5 | 60 ++++++++++++------------- NEWS | 7 ++ R/autotyp.feature.R | 14 ++++- R/grambank.feature.R | 23 +++++---- R/uralex.feature.R | 13 ++++- R/wals.feature.R | 4 + inst/doc/lingtypology_creating_maps.html | 4 - inst/doc/lingtypology_db_API.html | 4 - inst/doc/lingtypology_dplyr.html | 4 - inst/doc/lingtypology_glottolog_functions.html | 4 - inst/doc/lingtypology_intro.html | 4 - man/abvd.Rd | 2 man/autotyp.Rd | 2 man/autotyp.feature.Rd | 4 + man/bantu.Rd | 2 man/circassian.Rd | 2 man/countries.Rd | 2 man/eurasianphonology.Rd | 2 man/glottolog.Rd | 2 man/grambank.feature.Rd | 6 +- man/iso_639.Rd | 2 man/oto_mangueanIC.Rd | 2 man/phoible.Rd | 2 man/phonological_profiles.Rd | 2 man/providers.Rd | 2 man/soundcomparisons.Rd | 2 man/uralex.Rd | 2 man/uralex.feature.Rd | 4 + man/wals.Rd | 2 man/wals.feature.Rd | 2 31 files changed, 113 insertions(+), 82 deletions(-)
Title: Penalized Likelihood Factor Analysis via Nonconvex Penalty
Description: Computes the penalized maximum likelihood estimates of factor loadings and unique variances for various tuning parameters. The pathwise coordinate descent along with EM algorithm is used. This package also includes a graphical tool which outputs path diagrams, heatmaps, goodness-of-fit indices and model selection criteria for each regularization parameter (Yamamoto, M., Hirose, K. and Nagata, H., 2017 <doi:10.1007/s41237-016-0007-3>). The user can change the regularization parameter interactively with a built-in self-contained HTML viewer (no additional packages required), which is helpful to find a suitable value of regularization parameter. As a penalty, we can choose either the minimax concave penalty (Hirose, K. and Yamamoto, M., 2015 <doi:10.1007/s11222-014-9458-0>; Hirose, K. and Yamamoto, M., 2014 <doi:10.1016/j.csda.2014.05.011>) or the product-based elastic net penalty (Hirose, K. and Terada, Y., 2023 <doi:10.1007/s11336-022-09868-4>).
Author: Kei Hirose [aut, cre] ,
Michio Yamamoto [aut],
Haruhisa Nagata [aut]
Maintainer: Kei Hirose <mail@keihirose.com>
Diff between fanc versions 2.3.13 dated 2026-06-04 and 2.4.0 dated 2026-07-26
DESCRIPTION | 15 MD5 | 23 NAMESPACE | 36 - R/fanc.R | 32 R/out.fanc.R | 7 R/plot.fanc.R | 1818 ++++++++++++++++++++--------------------------------- R/select.fanc.R | 7 man/fanc.Rd | 346 ++++------ man/out.fanc.Rd | 31 man/plot.fanc.Rd | 73 +- man/select.fanc.Rd | 32 src/fanc.c | 6 tests |only 13 files changed, 1041 insertions(+), 1385 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-10 1.3.2
2014-08-21 1.3.1
2014-01-15 1.3.0
2013-10-30 1.2.1
2013-10-14 1.2
2013-09-26 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-23 1.0.4
2025-03-10 1.0.2
Title: Extrema-Weighted Feature Extraction
Description: Extrema-weighted feature extraction for varying length functional data. Functional data analysis method that performs dimensionality reduction based on predefined features and allows for quantile weighting. Method implemented as presented in van den Boom et al. (2018) <doi:10.1093/bioinformatics/bty120>.
Author: Willem van den Boom [aut, cre]
Maintainer: Willem van den Boom <willem@wvdboom.nl>
Diff between xwf versions 0.2-3 dated 2020-02-20 and 0.2-4 dated 2026-07-26
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 12 ++++++------ R/xwfGridsearch.R | 2 +- man/XWFpValues.Rd | 16 +++++++++++++--- man/xwf.Rd | 19 +++++++++++++++---- man/xwfGridsearch.Rd | 20 +++++++++++++++----- 7 files changed, 56 insertions(+), 25 deletions(-)
Title: Interface to the 'MinIO' Client
Description: An R interface to the 'MinIO' Client. The 'MinIO' Client ('mc')
provides a modern alternative to UNIX commands like 'ls', 'cat', 'cp',
'mirror', 'diff', 'find' etc. It supports 'filesystems' and Amazon "S3"
compatible cloud storage service ("AWS" Signature v2 and v4).
This package provides convenience functions for installing the 'MinIO'
client and running any operations, as described in the official
documentation, <https://docs.min.io/aistor/reference/cli/>.
This package provides a flexible and high-performance alternative to 'aws.s3'.
Author: Carl Boettiger [aut, cre] ,
Markus Skyttner [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between minioclient versions 0.0.6 dated 2023-11-07 and 0.0.7 dated 2026-07-26
DESCRIPTION | 11 ++++++----- MD5 | 26 ++++++++++++++------------ NEWS.md | 14 ++++++++++++++ R/install_mc.R | 15 +++++++++++---- R/mc.R | 2 +- R/mc_sql.R | 13 +++++++++++-- README.md | 8 ++++---- man/install_mc.Rd | 2 +- man/mc.Rd | 2 +- man/mc_alias_set.Rd | 2 +- man/mc_sql.Rd | 2 +- tests/testthat/helper-s3-select.R |only tests/testthat/test-mc.R | 5 ++++- tests/testthat/test-mc_bin.R |only tests/testthat/test-s3-select.R | 17 +++++++++++------ 15 files changed, 80 insertions(+), 39 deletions(-)
Title: Measuring Disparity
Description: A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.
Author: Thomas Guillerme [aut, cre, cph] ,
Jack Hatfield [aut, cph],
Mark Puttick [aut, cph],
Caleb Scutt [aut, cph]
Maintainer: Thomas Guillerme <guillert@tcd.ie>
Diff between dispRity versions 1.9 dated 2024-11-13 and 1.9.12 dated 2026-07-25
DESCRIPTION | 20 MD5 | 71 - NEWS.md | 61 + R/MCMCglmm.subsets.R | 3 R/chrono.subsets.R | 13 R/chrono.subsets_fun.R | 2 R/custom.subsets.R | 8 R/custom.subsets_fun.R | 2 R/dispRity.R | 6 R/dispRity.covar.projections.R | 2 R/dispRity.metric.R | 3 R/dispRity.utilities.R | 19 R/dispRity_fun.R | 79 + R/multi.ace.R | 1266 ++++++++++++++++------------ R/multi.ace_fun.R | 174 ++- R/plot.dispRity_fun.R | 6 R/print.dispRity.R | 30 R/reduce.space.R | 1 R/sanitizing.R | 5 R/summary.dispRity.R | 6 build/partial.rdb |binary data/BeckLee_ages.rda |binary data/BeckLee_disparity.rda |binary data/BeckLee_mat50.rda |binary data/BeckLee_mat99.rda |binary data/BeckLee_tree.rda |binary data/charadriiformes.rda |binary data/demo_data.rda |binary data/disparity.rda |binary inst/vignettes/Developer_resources.Rmd | 1 inst/vignettes/select_disparity_metrics.Rmd |only man/chrono.subsets.Rd | 4 man/dispRity-package.Rd | 7 man/dispRity.covar.projections.Rd | 2 man/multi.ace.Rd | 73 + man/reduce.space.Rd | 1 src/char.diff.c | 3 37 files changed, 1161 insertions(+), 707 deletions(-)
Title: Mapping Data for 'usmap' Package
Description: Provides a container for data used by the 'usmap' package.
The data used by 'usmap' has been extracted into this package so that the
file size of the 'usmap' package can be reduced greatly. The data in this
package will be updated roughly once per year as new map data files are
provided by the US Census Bureau.
Author: Paolo Di Lorenzo [aut, cre]
Maintainer: Paolo Di Lorenzo <paolo@dilorenzo.org>
Diff between usmapdata versions 1.0.0 dated 2025-08-22 and 1.1.0 dated 2026-07-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++++-- NEWS.md | 7 ++++++- inst/extdata/2025 |only 4 files changed, 16 insertions(+), 7 deletions(-)
Title: Tests for Rotational Symmetry on the Hypersphere
Description: Implementation of the tests for rotational symmetry on the
hypersphere proposed in García-Portugués, Paindaveine and Verdebout (2020)
<doi:10.1080/01621459.2019.1665527>. The package also implements the
proposed distributions on the hypersphere, based on the tangent-normal
decomposition, and allows for the replication of the data application
considered in the paper.
Author: Eduardo Garcia-Portugues [aut, cre] ,
Davy Paindaveine [aut],
Thomas Verdebout [aut]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Diff between rotasym versions 1.2.0 dated 2025-07-27 and 1.3.1 dated 2026-07-25
DESCRIPTION | 11 -- MD5 | 70 +++++++------ NEWS.md | 17 +++ R/ACG.R | 50 ++++----- R/TE.R | 40 +++---- R/TM.R | 40 +++---- R/auxiliary.R | 5 R/cosines-signs.R | 119 ++++++++++------------ R/data.R | 60 +++++------ R/estimators.R | 55 ++++------ R/rotasym-package.R | 15 +- R/tang-norm.R | 130 +++++++++++-------------- R/tests.R | 176 +++++++++++++++------------------- R/unif.R | 38 +++---- R/vMF.R | 83 ++++++++-------- build/partial.rdb |binary man/ACG.Rd | 53 ++++------ man/check_unit_norm.Rd | 7 - man/cosines-signs.Rd | 114 ++++++++++------------ man/estimators.Rd | 57 +++++------ man/figures |only man/rotasym-package.Rd | 14 +- man/sunspots.Rd | 60 +++++------ man/tang-norm-decomp.Rd | 123 +++++++++++------------ man/tangent-elliptical.Rd | 47 ++++----- man/tangent-vMF.Rd | 47 ++++----- man/test_rotasym.Rd | 170 +++++++++++++++----------------- man/unif.Rd | 36 +++--- man/vMF.Rd | 69 +++++-------- src/vMF.cpp | 7 - tests/testthat/helper-distributions.R |only tests/testthat/test_ACG.R |only tests/testthat/test_TE.R |only tests/testthat/test_TM.R |only tests/testthat/test_auxiliary.R |only tests/testthat/test_cosines_signs.R |only tests/testthat/test_estimators.R |only tests/testthat/test_g_vMF.R |only tests/testthat/test_tang_norm.R |only tests/testthat/test_test_rotasym.R |only tests/testthat/test_unif.R |only tests/testthat/test_vMF.R | 41 +++++++ 42 files changed, 845 insertions(+), 909 deletions(-)
Title: Dynamically Generate 'Quarto' Syntax
Description: Provides helper functions to work programmatically within a 'Quarto' document. It allows
the user to create section headers, tabsets, divs, and spans, and formats these objects
into 'Quarto' syntax when printed into a document.
Author: Danielle Navarro [aut, cre, cph]
Maintainer: Danielle Navarro <djnavarro@protonmail.com>
Diff between quartose versions 0.1.0 dated 2025-07-09 and 0.2.0 dated 2026-07-25
DESCRIPTION | 26 ++--- MD5 | 32 +++--- NAMESPACE | 2 NEWS.md | 69 +++++++++++++ R/class.R | 68 +++++++++---- R/format.R | 126 ++++++++++++++++++++---- R/print.R | 46 ++++++-- R/validate.R | 63 ++++++++++++ README.md | 26 +++++ inst/WORDLIST | 15 ++ man/as_quarto_graphic.Rd |only man/quarto_format.Rd | 23 +++- man/quarto_object.Rd | 22 ++-- man/quarto_print.Rd | 11 ++ tests/testthat/Rplots.pdf |only tests/testthat/helper-graphics.R |only tests/testthat/test-format.R | 196 +++++++++++++++++++++++++++++++++++++- tests/testthat/test-integration.R |only tests/testthat/test-validate.R | 119 ++++++++++++++++++++++- 19 files changed, 753 insertions(+), 91 deletions(-)
Title: Visualizations for 'mlr3'
Description: Visualization package of the 'mlr3' ecosystem. It features
plots for mlr3 objects such as tasks, learners, predictions, benchmark
results, tuning instances and filters via the 'autoplot()' generic of
'ggplot2'. The package draws plots with the 'viridis' color palette
and applies the minimal theme. Visualizations include barplots,
boxplots, histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [aut] ,
Patrick Schratz [aut] ,
Raphael Sonabend [aut] ,
Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Damir Pulatov [ctb],
John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3viz versions 0.11.0 dated 2026-02-22 and 0.11.1 dated 2026-07-25
DESCRIPTION | 8 MD5 | 140 - NEWS.md | 5 R/BenchmarkResult.R | 29 R/EnsembleFSResult.R | 91 R/Filter.R | 19 R/LearnerClassif.R | 37 R/LearnerClassifCVGlmnet.R | 14 R/LearnerClassifGlmnet.R | 17 R/LearnerClassifRpart.R | 35 R/LearnerClustHierarchical.R | 22 R/LearnerRegr.R | 42 R/LearnerRegrCVGlmnet.R | 14 R/LearnerRegrGlmnet.R | 14 R/LearnerRegrRpart.R | 27 R/OptimInstanceBatchSingleCrit.R | 164 + R/Prediction.R | 3 R/PredictionClassif.R | 30 R/PredictionClust.R | 14 R/PredictionRegr.R | 77 R/ResampleResult.R | 158 - R/Task.R | 3 R/TaskClassif.R | 46 R/TaskClust.R | 30 R/TaskRegr.R | 53 R/TuningInstanceBatchSingleCrit.R | 22 R/as_precrec.R | 9 R/helper.R | 7 R/plot_learner_prediction.R | 8 README.md | 2 build/partial.rdb |binary man/autoplot.BenchmarkResult.Rd | 9 man/autoplot.EnsembleFSResult.Rd | 6 man/autoplot.Filter.Rd | 2 man/autoplot.LearnerClassif.Rd | 4 man/autoplot.LearnerClassifGlmnet.Rd | 7 man/autoplot.LearnerClassifRpart.Rd | 6 man/autoplot.LearnerClustHierarchical.Rd | 5 man/autoplot.LearnerRegr.Rd | 2 man/autoplot.OptimInstanceBatchSingleCrit.Rd | 2 man/autoplot.PredictionClassif.Rd | 5 man/autoplot.PredictionClust.Rd | 2 man/autoplot.PredictionRegr.Rd | 11 man/autoplot.ResampleResult.Rd | 8 man/autoplot.TaskClassif.Rd | 2 man/autoplot.TaskClust.Rd | 2 man/autoplot.TaskRegr.Rd | 2 man/autoplot.TuningInstanceBatchSingleCrit.Rd | 2 man/figures/logo.png |binary man/mlr3viz-package.Rd | 1 man/plot_learner_prediction.Rd | 8 man/reexports.Rd | 2 tests/testthat/_snaps/BenchmarkResult/bmr-boxplot.svg | 52 tests/testthat/_snaps/BenchmarkResult/bmr-holdout-ci.svg | 52 tests/testthat/_snaps/BenchmarkResult/bmr-holdout-roc.svg | 4 tests/testthat/_snaps/BenchmarkResult/bmr-prc.svg | 18 tests/testthat/_snaps/BenchmarkResult/bmr-roc.svg | 8 tests/testthat/_snaps/LearnerClassif/learner-classif-prob.svg | 1053 ++-------- tests/testthat/_snaps/LearnerClassif/learner-classif-response.svg | 1035 ++------- tests/testthat/_snaps/plot_learner_prediction/learner-prediction-binary-prob.svg | 36 tests/testthat/_snaps/plot_learner_prediction/learner-prediction-categorical.svg | 18 tests/testthat/setup.R | 1 tests/testthat/test_BenchmarkResult.R | 30 tests/testthat/test_EnsembleFSResult.R | 10 tests/testthat/test_LearnerClassif.R | 4 tests/testthat/test_LearnerClassifCVGlmnet.R | 4 tests/testthat/test_LearnerRegr.R | 1 tests/testthat/test_OptimInstanceSingleCrit.R | 3 tests/testthat/test_PredictionClust.R | 4 tests/testthat/test_ResampleResult.R | 35 tests/testthat/test_TuningInstanceSingleCrit.R | 3 71 files changed, 1464 insertions(+), 2135 deletions(-)
Title: Hyperparameter Optimization for 'mlr3'
Description: Hyperparameter optimization package of the 'mlr3' ecosystem.
It features highly configurable search spaces via the 'paradox'
package and finds optimal hyperparameter configurations for any 'mlr3'
learner. 'mlr3tuning' works with several optimization algorithms e.g.
Random Search, Iterated Racing, Bayesian Optimization (in 'mlr3mbo')
and Hyperband (in 'mlr3hyperband'). Moreover, it can automatically
optimize learners and estimate the performance of optimized models
with nested resampling.
Author: Marc Becker [cre, aut] ,
Michel Lang [aut] ,
Jakob Richter [aut] ,
Bernd Bischl [aut] ,
Daniel Schalk [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 1.6.0 dated 2026-03-16 and 1.6.1 dated 2026-07-25
mlr3tuning-1.6.0/mlr3tuning/tests/testthat/helper_rush.R |only mlr3tuning-1.6.1/mlr3tuning/DESCRIPTION | 10 mlr3tuning-1.6.1/mlr3tuning/MD5 | 292 +++--- mlr3tuning-1.6.1/mlr3tuning/NEWS.md | 34 mlr3tuning-1.6.1/mlr3tuning/R/ArchiveAsyncTuning.R | 121 +- mlr3tuning-1.6.1/mlr3tuning/R/ArchiveAsyncTuningFrozen.R | 98 +- mlr3tuning-1.6.1/mlr3tuning/R/ArchiveBatchTuning.R | 84 + mlr3tuning-1.6.1/mlr3tuning/R/AutoTuner.R | 204 +++- mlr3tuning-1.6.1/mlr3tuning/R/CallbackAsyncTuning.R | 115 +- mlr3tuning-1.6.1/mlr3tuning/R/CallbackBatchTuning.R | 102 +- mlr3tuning-1.6.1/mlr3tuning/R/ContextAsyncTuning.R | 22 mlr3tuning-1.6.1/mlr3tuning/R/ContextBatchTuning.R | 24 mlr3tuning-1.6.1/mlr3tuning/R/ObjectiveTuning.R | 18 mlr3tuning-1.6.1/mlr3tuning/R/ObjectiveTuningAsync.R | 42 mlr3tuning-1.6.1/mlr3tuning/R/ObjectiveTuningBatch.R | 46 - mlr3tuning-1.6.1/mlr3tuning/R/Tuner.R | 46 - mlr3tuning-1.6.1/mlr3tuning/R/TunerAsync.R | 8 mlr3tuning-1.6.1/mlr3tuning/R/TunerAsyncDesignPoints.R | 4 mlr3tuning-1.6.1/mlr3tuning/R/TunerAsyncFromOptimizerAsync.R | 113 +- mlr3tuning-1.6.1/mlr3tuning/R/TunerAsyncGridSearch.R | 22 mlr3tuning-1.6.1/mlr3tuning/R/TunerAsyncRandomSearch.R | 20 mlr3tuning-1.6.1/mlr3tuning/R/TunerBatch.R | 32 mlr3tuning-1.6.1/mlr3tuning/R/TunerBatchCmaes.R | 23 mlr3tuning-1.6.1/mlr3tuning/R/TunerBatchDesignPoints.R | 4 mlr3tuning-1.6.1/mlr3tuning/R/TunerBatchFromBatchOptimizer.R | 124 +- mlr3tuning-1.6.1/mlr3tuning/R/TunerBatchGenSA.R | 5 mlr3tuning-1.6.1/mlr3tuning/R/TunerBatchGridSearch.R | 10 mlr3tuning-1.6.1/mlr3tuning/R/TunerBatchInternal.R | 38 mlr3tuning-1.6.1/mlr3tuning/R/TunerBatchIrace.R | 34 mlr3tuning-1.6.1/mlr3tuning/R/TunerBatchNLoptr.R | 12 mlr3tuning-1.6.1/mlr3tuning/R/TunerBatchRandomSearch.R | 4 mlr3tuning-1.6.1/mlr3tuning/R/TuningInstanceAsyncMulticrit.R | 81 + mlr3tuning-1.6.1/mlr3tuning/R/TuningInstanceAsyncSingleCrit.R | 58 - mlr3tuning-1.6.1/mlr3tuning/R/TuningInstanceBatchMulticrit.R | 61 - mlr3tuning-1.6.1/mlr3tuning/R/TuningInstanceBatchSingleCrit.R | 78 + mlr3tuning-1.6.1/mlr3tuning/R/TuningInstanceMultiCrit.R | 11 mlr3tuning-1.6.1/mlr3tuning/R/TuningInstanceSingleCrit.R | 12 mlr3tuning-1.6.1/mlr3tuning/R/as_search_space.R | 11 mlr3tuning-1.6.1/mlr3tuning/R/as_tuner.R | 18 mlr3tuning-1.6.1/mlr3tuning/R/assertions.R | 38 mlr3tuning-1.6.1/mlr3tuning/R/auto_tuner.R | 7 mlr3tuning-1.6.1/mlr3tuning/R/bibentries.R | 3 mlr3tuning-1.6.1/mlr3tuning/R/extract_inner_tuning_archives.R | 40 mlr3tuning-1.6.1/mlr3tuning/R/extract_inner_tuning_results.R | 43 mlr3tuning-1.6.1/mlr3tuning/R/helper.R | 24 mlr3tuning-1.6.1/mlr3tuning/R/mlr_callbacks.R | 139 ++- mlr3tuning-1.6.1/mlr3tuning/R/mlr_tuners.R | 36 mlr3tuning-1.6.1/mlr3tuning/R/sugar.R | 22 mlr3tuning-1.6.1/mlr3tuning/R/tune.R | 42 mlr3tuning-1.6.1/mlr3tuning/R/tune_nested.R | 5 mlr3tuning-1.6.1/mlr3tuning/R/zzz.R | 24 mlr3tuning-1.6.1/mlr3tuning/README.md | 17 mlr3tuning-1.6.1/mlr3tuning/build/partial.rdb |binary mlr3tuning-1.6.1/mlr3tuning/build/vignette.rds |binary mlr3tuning-1.6.1/mlr3tuning/inst/CITATION | 4 mlr3tuning-1.6.1/mlr3tuning/inst/testthat/helper_expectations.R | 9 mlr3tuning-1.6.1/mlr3tuning/inst/testthat/helper_misc.R | 29 mlr3tuning-1.6.1/mlr3tuning/inst/testthat/helper_tuner.R | 9 mlr3tuning-1.6.1/mlr3tuning/man/ArchiveAsyncTuning.Rd | 331 +++---- mlr3tuning-1.6.1/mlr3tuning/man/ArchiveAsyncTuningFrozen.Rd | 303 +++--- mlr3tuning-1.6.1/mlr3tuning/man/ArchiveBatchTuning.Rd | 319 +++---- mlr3tuning-1.6.1/mlr3tuning/man/AutoTuner.Rd | 447 +++++----- mlr3tuning-1.6.1/mlr3tuning/man/CallbackAsyncTuning.Rd | 75 - mlr3tuning-1.6.1/mlr3tuning/man/CallbackBatchTuning.Rd | 75 - mlr3tuning-1.6.1/mlr3tuning/man/ContextAsyncTuning.Rd | 60 - mlr3tuning-1.6.1/mlr3tuning/man/ContextBatchTuning.Rd | 62 - mlr3tuning-1.6.1/mlr3tuning/man/ObjectiveTuning.Rd | 146 +-- mlr3tuning-1.6.1/mlr3tuning/man/ObjectiveTuningAsync.Rd | 57 - mlr3tuning-1.6.1/mlr3tuning/man/ObjectiveTuningBatch.Rd | 135 +-- mlr3tuning-1.6.1/mlr3tuning/man/Tuner.Rd | 219 ++-- mlr3tuning-1.6.1/mlr3tuning/man/TunerAsync.Rd | 110 +- mlr3tuning-1.6.1/mlr3tuning/man/TunerAsyncFromOptimizerAsync.Rd | 131 +- mlr3tuning-1.6.1/mlr3tuning/man/TunerBatch.Rd | 184 ++-- mlr3tuning-1.6.1/mlr3tuning/man/TunerBatchFromOptimizerBatch.Rd | 130 +- mlr3tuning-1.6.1/mlr3tuning/man/TuningInstanceAsyncMultiCrit.Rd | 223 ++-- mlr3tuning-1.6.1/mlr3tuning/man/TuningInstanceAsyncSingleCrit.Rd | 225 ++--- mlr3tuning-1.6.1/mlr3tuning/man/TuningInstanceBatchMultiCrit.Rd | 227 ++--- mlr3tuning-1.6.1/mlr3tuning/man/TuningInstanceBatchSingleCrit.Rd | 230 ++--- mlr3tuning-1.6.1/mlr3tuning/man/TuningInstanceMultiCrit.Rd | 124 +- mlr3tuning-1.6.1/mlr3tuning/man/TuningInstanceSingleCrit.Rd | 124 +- mlr3tuning-1.6.1/mlr3tuning/man/auto_tuner.Rd | 61 - mlr3tuning-1.6.1/mlr3tuning/man/callback_async_tuning.Rd | 10 mlr3tuning-1.6.1/mlr3tuning/man/callback_batch_tuning.Rd | 11 mlr3tuning-1.6.1/mlr3tuning/man/extract_inner_tuning_archives.Rd | 3 mlr3tuning-1.6.1/mlr3tuning/man/extract_inner_tuning_results.Rd | 3 mlr3tuning-1.6.1/mlr3tuning/man/figures/logo.png |binary mlr3tuning-1.6.1/mlr3tuning/man/mlr3tuning-package.Rd | 1 mlr3tuning-1.6.1/mlr3tuning/man/mlr3tuning.async_freeze_archive.Rd | 3 mlr3tuning-1.6.1/mlr3tuning/man/mlr3tuning.async_mlflow.Rd | 6 mlr3tuning-1.6.1/mlr3tuning/man/mlr3tuning.backup.Rd | 4 mlr3tuning-1.6.1/mlr3tuning/man/mlr3tuning.measures.Rd | 5 mlr3tuning-1.6.1/mlr3tuning/man/mlr3tuning.one_se_rule.Rd | 10 mlr3tuning-1.6.1/mlr3tuning/man/mlr_tuners.Rd | 7 mlr3tuning-1.6.1/mlr3tuning/man/mlr_tuners_async_design_points.Rd | 68 - mlr3tuning-1.6.1/mlr3tuning/man/mlr_tuners_async_grid_search.Rd | 70 - mlr3tuning-1.6.1/mlr3tuning/man/mlr_tuners_async_random_search.Rd | 68 - mlr3tuning-1.6.1/mlr3tuning/man/mlr_tuners_cmaes.Rd | 102 +- mlr3tuning-1.6.1/mlr3tuning/man/mlr_tuners_design_points.Rd | 95 +- mlr3tuning-1.6.1/mlr3tuning/man/mlr_tuners_gensa.Rd | 108 +- mlr3tuning-1.6.1/mlr3tuning/man/mlr_tuners_grid_search.Rd | 101 +- mlr3tuning-1.6.1/mlr3tuning/man/mlr_tuners_internal.Rd | 106 +- mlr3tuning-1.6.1/mlr3tuning/man/mlr_tuners_irace.Rd | 135 +-- mlr3tuning-1.6.1/mlr3tuning/man/mlr_tuners_nloptr.Rd | 106 +- mlr3tuning-1.6.1/mlr3tuning/man/mlr_tuners_random_search.Rd | 95 +- mlr3tuning-1.6.1/mlr3tuning/man/reexports.Rd | 4 mlr3tuning-1.6.1/mlr3tuning/man/ti.Rd | 34 mlr3tuning-1.6.1/mlr3tuning/man/ti_async.Rd | 34 mlr3tuning-1.6.1/mlr3tuning/man/tune.Rd | 59 - mlr3tuning-1.6.1/mlr3tuning/man/tune_nested.Rd | 13 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/_snaps/Tuner.md | 2 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/helper.R | 17 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/setup.R | 3 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_ArchiveAsyncTuning.R | 289 +++++- mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_ArchiveAsyncTuningFrozen.R | 61 + mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_ArchiveBatchTuning.R | 226 ++++- mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_AutoTuner.R | 427 +++++++-- mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_CallbackAsyncTuning.R | 369 +++----- mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_CallbackBatchTuning.R | 312 +++--- mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_ObjectiveTuningAsync.R | 8 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_ObjectiveTuningBatch.R | 26 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_Tuner.R | 217 +++- mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_TunerAsyncDesignPoints.R | 8 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_TunerAsyncGridSearch.R | 8 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_TunerAsyncRandomSearch.R | 8 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_TunerBatchCmaes.R | 5 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_TunerBatchFromOptimizerBatch.R | 2 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_TunerBatchGenSA.R | 20 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_TunerBatchGridSearch.R | 8 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_TunerBatchIrace.R | 60 + mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_TunerBatchRandomSearch.R | 1 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_TunerInternal.R | 6 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_TuningInstanceAsyncMultiCrit.R | 105 +- mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_TuningInstanceAsyncSingleCrit.R | 115 +- mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_TuningInstanceBatchMultiCrit.R | 114 +- mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_TuningInstanceBatchSingleCrit.R | 227 +++-- mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_as_search_space.R | 8 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_as_tuner.R |only mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_auto_tuner.R | 40 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_error_handling.R | 34 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_extract_inner_tuning_archives.R | 216 ++++ mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_extract_inner_tuning_results.R | 179 +++- mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_lgr.R | 25 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_mlr_callbacks.R | 277 ++++-- mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_ti.R | 14 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_ti_async.R | 14 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_trafos.R | 26 mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_tune.R | 55 + mlr3tuning-1.6.1/mlr3tuning/tests/testthat/test_tune_nested.R | 11 148 files changed, 6824 insertions(+), 4510 deletions(-)
Title: Automated Data Quality Checks for Recurring Dataset Deliveries
Description: Automates quality verification of recurring external dataset deliveries.
For each new file arrival, it runs single-snapshot quality checks, compares
the file to the previous delivery, writes a self-contained 'HTML' report, and
records summary statistics in a local 'SQLite' database for long-term trend
tracking. Supports 'CSV' and fixed-width formats. Custom organisation-specific
checks can be supplied as plain R files.
Author: Mick Mioduszewski [aut, cre]
Maintainer: Mick Mioduszewski <mick@mioduszewski.net>
Diff between dqcheckr versions 0.2.5 dated 2026-07-18 and 0.3.0 dated 2026-07-25
DESCRIPTION | 10 - MD5 | 88 ++++++--- NAMESPACE | 6 NEWS.md | 312 +++++++++++++++++++++++++++++++++++ R/checks_custom.R | 21 ++ R/checks_generic.R | 34 +++ R/compare.R | 20 +- R/drift.R | 213 ++++++++++++++++++++--- R/generate.R |only R/ingest.R | 25 ++ R/run_check.R | 49 ++++- R/snapshot.R | 97 ++++++++++ R/sniff.R |only R/utils.R | 204 ++++++++++++++++++++-- R/validate.R |only R/vocabulary.R |only build/vignette.rds |binary inst/doc/dqcheckr.Rmd | 12 + inst/doc/dqcheckr.html | 14 + inst/doc/specification.R | 2 inst/doc/specification.Rmd | 19 ++ inst/doc/specification.html | 103 ++++++++++- inst/doc/workflow.R |only inst/doc/workflow.Rmd |only inst/doc/workflow.html |only inst/templates/drift_report.qmd | 36 ++++ man/check_numeric_stats.Rd | 5 man/dq_result.Rd | 4 man/generate_dataset_config.Rd |only man/generate_global_config.Rd |only man/infer_col_type.Rd | 7 man/list_runs.Rd |only man/print.dqcheckr_validation.Rd |only man/run_dq_check.Rd | 19 +- man/sniff_dataset.Rd |only man/validate_config.Rd |only tests/testthat/test-checks-custom.R | 64 +++++++ tests/testthat/test-checks.R | 65 +++++++ tests/testthat/test-col-threshold.R | 93 ++++++++++ tests/testthat/test-compare.R | 43 ++++ tests/testthat/test-drift.R | 308 ++++++++++++++++++++++++++++++++++ tests/testthat/test-encoding.R | 59 +++--- tests/testthat/test-generate.R |only tests/testthat/test-ingest.R | 40 ++-- tests/testthat/test-integration.R | 14 - tests/testthat/test-list-runs.R |only tests/testthat/test-run-validation.R |only tests/testthat/test-snapshot.R | 46 +++++ tests/testthat/test-sniff.R |only tests/testthat/test-utils.R | 75 +++++++- tests/testthat/test-validate.R |only tests/testthat/test-vocabulary.R |only vignettes/dqcheckr.Rmd | 12 + vignettes/specification.Rmd | 19 ++ vignettes/workflow.Rmd |only 55 files changed, 1915 insertions(+), 223 deletions(-)
Title: Builds the 'TinyCC' Command-Line Interface and Library for 'C'
Scripting in 'R'
Description: Builds the 'TinyCC' (Tiny 'C' Compiler) command-line interface
and library for package use in 'R'. The package compiles 'TinyCC' from source and
provides R functions to interact with the compiler. 'TinyCC' can be
used for header preprocessing, just-in-time compilation of 'C' code in
'R', and lightweight 'C' scripting workflows.
Author: Sounkou Mahamane Toure [aut, cre],
Mike Cheng [cph] ,
Adam Dunkels [ctb] ,
Swedish Institute of Computer Science [cph] ,
Fabrice Bellard and TinyCC authors [cph]
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>
Diff between Rtinycc versions 0.1.12 dated 2026-07-19 and 0.1.15 dated 2026-07-25
Rtinycc-0.1.12/Rtinycc/src/tinycc-e273cf4.tar.gz |only Rtinycc-0.1.15/Rtinycc/DESCRIPTION | 6 Rtinycc-0.1.15/Rtinycc/MD5 | 32 Rtinycc-0.1.15/Rtinycc/NEWS.md | 15 Rtinycc-0.1.15/Rtinycc/R/ffi.R | 3 Rtinycc-0.1.15/Rtinycc/R/knitr_engine.R | 2 Rtinycc-0.1.15/Rtinycc/README.md | 498 +++++++++- Rtinycc-0.1.15/Rtinycc/TODO | 90 + Rtinycc-0.1.15/Rtinycc/configure | 85 + Rtinycc-0.1.15/Rtinycc/inst/LICENSE.note | 6 Rtinycc-0.1.15/Rtinycc/inst/doc/compilation-and-call-overhead.html | 20 Rtinycc-0.1.15/Rtinycc/inst/doc/ffi-helpers.html | 8 Rtinycc-0.1.15/Rtinycc/inst/doc/getting-started.html | 12 Rtinycc-0.1.15/Rtinycc/inst/tinytest/test_libtcc.R | 28 Rtinycc-0.1.15/Rtinycc/man/figures/README-io_uring-demo-1.png |binary Rtinycc-0.1.15/Rtinycc/src/tinycc-199f07b.tar.gz |only Rtinycc-0.1.15/Rtinycc/tools/run_tcc_minimal_test.sh | 9 Rtinycc-0.1.15/Rtinycc/tools/vendortinycc.R | 2 18 files changed, 726 insertions(+), 90 deletions(-)
Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing
with 'Stan' <https://mc-stan.org>, including functions to set up the required
package structure, S3 generics and default methods to unify function naming
across 'Stan'-based R packages, and vignettes with recommendations for
developers.
Author: Jonah Gabry [aut],
Ben Goodrich [aut],
Martin Lysy [aut],
Andrew Johnson [aut, cre],
Hamada S. Badr [ctb],
Marco Colombo [ctb],
Stefan Siegert [ctb],
Visruth Srimath Kandali [ctb],
Trustees of Columbia University [cph]
Maintainer: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Diff between rstantools versions 2.6.0 dated 2026-01-10 and 2.7.0 dated 2026-07-25
DESCRIPTION | 32 ++- MD5 | 24 +- NEWS.md | 7 R/rstan_config.R | 64 +++++++ R/stanc_exceptions.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/developer-guidelines.html | 2 inst/doc/minimal-rstan-package.R | 143 ++++++++-------- inst/doc/minimal-rstan-package.Rmd | 21 +- inst/doc/minimal-rstan-package.html | 303 ++++++------------------------------ inst/stanc.2.32.js |only man/rstantools-package.Rd | 2 vignettes/minimal-rstan-package.Rmd | 21 +- 14 files changed, 242 insertions(+), 377 deletions(-)
Title: Tools for Managing Classes on GitHub
Description: Interface for the GitHub API that enables efficient
management of courses on GitHub. It has a functionality for
managing organizations, teams, repositories, and users on GitHub
and helps automate most of the tedious and repetitive tasks
around creating and distributing assignments.
Author: Colin Rundel [aut, cre],
Mine Cetinkaya-Rundel [aut],
Therese Anders [ctb]
Maintainer: Colin Rundel <rundel@gmail.com>
Diff between ghclass versions 0.4.0 dated 2026-05-07 and 0.4.1 dated 2026-07-25
ghclass-0.4.0/ghclass/R/branch_protect.R |only ghclass-0.4.1/ghclass/DESCRIPTION | 19 - ghclass-0.4.1/ghclass/MD5 | 144 +++++------ ghclass-0.4.1/ghclass/NAMESPACE | 6 ghclass-0.4.1/ghclass/NEWS.md | 28 ++ ghclass-0.4.1/ghclass/R/action_artifacts.R | 4 ghclass-0.4.1/ghclass/R/action_artifacts_download.R | 10 ghclass-0.4.1/ghclass/R/action_badge.R | 11 ghclass-0.4.1/ghclass/R/action_run_logs.R | 1 ghclass-0.4.1/ghclass/R/action_runs.R | 2 ghclass-0.4.1/ghclass/R/action_runtime.R | 3 ghclass-0.4.1/ghclass/R/action_workflows.R | 2 ghclass-0.4.1/ghclass/R/branch.R | 6 ghclass-0.4.1/ghclass/R/github_api_limit.R | 57 ++++ ghclass-0.4.1/ghclass/R/github_token.R | 41 +-- ghclass-0.4.1/ghclass/R/github_whoami.R | 11 ghclass-0.4.1/ghclass/R/issue_close.R | 3 ghclass-0.4.1/ghclass/R/local_repo_anonymize.R |only ghclass-0.4.1/ghclass/R/local_repo_clone.R | 10 ghclass-0.4.1/ghclass/R/local_repo_pull.R | 4 ghclass-0.4.1/ghclass/R/local_repo_push.R | 17 - ghclass-0.4.1/ghclass/R/local_repo_rename.R | 21 - ghclass-0.4.1/ghclass/R/org.R | 5 ghclass-0.4.1/ghclass/R/org_admins.R | 19 - ghclass-0.4.1/ghclass/R/org_create_assignment.R | 12 ghclass-0.4.1/ghclass/R/org_invite.R | 2 ghclass-0.4.1/ghclass/R/org_members.R | 6 ghclass-0.4.1/ghclass/R/org_pending.R | 1 ghclass-0.4.1/ghclass/R/org_repo_forking.R | 4 ghclass-0.4.1/ghclass/R/org_repo_search.R | 4 ghclass-0.4.1/ghclass/R/org_repo_stats.R | 13 ghclass-0.4.1/ghclass/R/org_repos.R | 15 - ghclass-0.4.1/ghclass/R/org_sitrep.R | 5 ghclass-0.4.1/ghclass/R/org_teams_v4.R | 5 ghclass-0.4.1/ghclass/R/org_workflow_permissions.R | 2 ghclass-0.4.1/ghclass/R/repo.R | 5 ghclass-0.4.1/ghclass/R/repo_collaborators.R | 1 ghclass-0.4.1/ghclass/R/repo_issues.R | 13 ghclass-0.4.1/ghclass/R/repo_modify_file.R | 2 ghclass-0.4.1/ghclass/R/repo_n_commits.R | 15 - ghclass-0.4.1/ghclass/R/repo_prs.R | 16 - ghclass-0.4.1/ghclass/R/repo_remove_team.R | 2 ghclass-0.4.1/ghclass/R/repo_style.R | 5 ghclass-0.4.1/ghclass/R/team.R | 4 ghclass-0.4.1/ghclass/R/team_invite.R | 2 ghclass-0.4.1/ghclass/R/team_members.R | 36 +- ghclass-0.4.1/ghclass/R/team_pending.R | 44 +-- ghclass-0.4.1/ghclass/R/team_repos.R | 36 +- ghclass-0.4.1/ghclass/R/team_roster.R |only ghclass-0.4.1/ghclass/R/user_repos.R | 5 ghclass-0.4.1/ghclass/R/util_args.R | 18 - ghclass-0.4.1/ghclass/R/util_general.R | 9 ghclass-0.4.1/ghclass/R/util_github.R | 70 +++-- ghclass-0.4.1/ghclass/R/util_github_v4.R | 84 +++++- ghclass-0.4.1/ghclass/R/util_local_repo.R | 2 ghclass-0.4.1/ghclass/R/util_repo.R | 35 -- ghclass-0.4.1/ghclass/R/util_safely.R | 20 - ghclass-0.4.1/ghclass/R/util_suggests.R | 26 - ghclass-0.4.1/ghclass/R/util_team.R | 9 ghclass-0.4.1/ghclass/README.md | 23 - ghclass-0.4.1/ghclass/man/action_badge.Rd | 12 ghclass-0.4.1/ghclass/man/branch.Rd | 2 ghclass-0.4.1/ghclass/man/figures/lifecycle-experimental.svg |only ghclass-0.4.1/ghclass/man/ghclass-internal.Rd | 4 ghclass-0.4.1/ghclass/man/github_api_limit.Rd | 31 ++ ghclass-0.4.1/ghclass/man/local_repo_anonymize.Rd |only ghclass-0.4.1/ghclass/man/local_repo_rename.Rd | 13 ghclass-0.4.1/ghclass/man/org_details.Rd | 5 ghclass-0.4.1/ghclass/man/repo_details.Rd | 2 ghclass-0.4.1/ghclass/man/repo_file.Rd | 19 - ghclass-0.4.1/ghclass/man/repo_style.Rd | 6 ghclass-0.4.1/ghclass/man/repo_user.Rd | 2 ghclass-0.4.1/ghclass/man/team.Rd | 2 ghclass-0.4.1/ghclass/man/team_members.Rd | 2 ghclass-0.4.1/ghclass/man/team_roster.Rd |only ghclass-0.4.1/ghclass/tests |only 76 files changed, 671 insertions(+), 404 deletions(-)
Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'.
For example, the 'parallelFor()' function can be used to convert the work of
a standard serial "for" loop into a parallel one and the 'parallelReduce()'
function can be used for accumulating aggregate or other values.
Author: Kevin Ushey [aut, cre] ,
JJ Allaire [aut],
Romain Francois [aut, cph],
Gregory Vandenbrouck [aut],
Marcus Geelnard [aut, cph] ,
Hamada S. Badr [ctb] ,
Dirk Eddelbuettel [aut] ,
Intel [aut, cph] ,
UXL Foundation [aut, cph] ,
Microsoft [cph],
Posit, PB [...truncated...]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between RcppParallel versions 6.0.0 dated 2026-07-23 and 6.1.0 dated 2026-07-25
RcppParallel-6.0.0/RcppParallel/inst/tests/runit.distance.R |only RcppParallel-6.0.0/RcppParallel/inst/tests/runit.innerproduct.R |only RcppParallel-6.0.0/RcppParallel/inst/tests/runit.sum.R |only RcppParallel-6.0.0/RcppParallel/inst/tests/runit.transform.R |only RcppParallel-6.0.0/RcppParallel/inst/tests/runit.truefalse_macros.R |only RcppParallel-6.0.0/RcppParallel/tests/doRUnit.R |only RcppParallel-6.1.0/RcppParallel/DESCRIPTION | 10 RcppParallel-6.1.0/RcppParallel/MD5 | 43 - RcppParallel-6.1.0/RcppParallel/NAMESPACE | 1 RcppParallel-6.1.0/RcppParallel/NEWS.md | 127 +++- RcppParallel-6.1.0/RcppParallel/R/fork.R |only RcppParallel-6.1.0/RcppParallel/R/tbb.R | 17 RcppParallel-6.1.0/RcppParallel/R/test.R |only RcppParallel-6.1.0/RcppParallel/R/utils.R | 17 RcppParallel-6.1.0/RcppParallel/R/zzz.R | 34 + RcppParallel-6.1.0/RcppParallel/inst/include/RcppParallel.h | 6 RcppParallel-6.1.0/RcppParallel/inst/include/RcppParallel/Fork.h |only RcppParallel-6.1.0/RcppParallel/man/isProcessForkedChild.Rd |only RcppParallel-6.1.0/RcppParallel/src/init.cpp | 37 + RcppParallel-6.1.0/RcppParallel/src/install.libs.R | 263 +++++++++- RcppParallel-6.1.0/RcppParallel/src/tbb/include/oneapi/tbb/detail/_machine.h | 12 RcppParallel-6.1.0/RcppParallel/tests/test-arch-system-file.R |only RcppParallel-6.1.0/RcppParallel/tests/test-distance.R |only RcppParallel-6.1.0/RcppParallel/tests/test-fork.R |only RcppParallel-6.1.0/RcppParallel/tests/test-innerproduct.R |only RcppParallel-6.1.0/RcppParallel/tests/test-install-libs.R |only RcppParallel-6.1.0/RcppParallel/tests/test-scalable-allocator.R |only RcppParallel-6.1.0/RcppParallel/tests/test-sum.R |only RcppParallel-6.1.0/RcppParallel/tests/test-transform.R |only RcppParallel-6.1.0/RcppParallel/tests/test-truefalse-macros.R |only RcppParallel-6.1.0/RcppParallel/tools/config/cleanup.R | 9 RcppParallel-6.1.0/RcppParallel/tools/config/configure.R | 48 + 32 files changed, 532 insertions(+), 92 deletions(-)
Title: Generalized L-Moments Estimation for Extreme Value Distributions
Description: Provides generalized L-moments estimation methods for the
generalized extreme value ('GEV') distribution. Implements both stationary
'GEV' and non-stationary 'GEV11' models where location and scale parameters
vary with time. Includes various penalty functions (Martins-Stedinger,
Park, Cannon, Coles-Dixon) for shape parameter regularization.
Also provides model averaging estimation ('ma.gev') that combines MLE and
L-moment methods with multiple weighting schemes for robust high quantile
estimation. The 'GLME' methodology is described in Shin et al. (2025a)
<doi:10.48550/arXiv.2512.20385>. The non-stationary L-moment method
is based on Shin et al. (2025b) <doi:10.1007/s42952-025-00325-3>.
The model averaging method is described in Shin et al. (2026)
<doi:10.1007/s00477-025-03167-x>.
See also Hosking (1990) <doi:10.1111/j.2517-6161.1990.tb01775.x> for
L-moments theory and Martins and Stedinger (2000)
<doi:10.1029/1999WR900330> for penalized likelihood methods [...truncated...]
Author: Yonggwan Shin [aut, cre] ,
Seokkap Ko [aut, ctb] ,
Jihong Park [ctb] ,
Yire Shin [aut, dtc] ,
Jeong-Soo Park [aut, ths]
Maintainer: Yonggwan Shin <syg.stat@etri.re.kr>
Diff between GLmom versions 2.0.0 dated 2026-07-05 and 2.0.1 dated 2026-07-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 19 +++++++++++++++++++ R/glme.gev.R | 2 +- R/glme.gev11.R | 2 +- R/penalty.R | 6 +++--- build/partial.rdb |binary 7 files changed, 33 insertions(+), 14 deletions(-)
Title: Certified Partial Eigenvalue and Singular Value Computation
Description: Computes the top-k singular triplets or eigenpairs of large
sparse and structured matrices: the computation behind principal component
analysis on big sparse data, spectral embeddings, and low-rank
approximation. Every result carries a numerical certificate with
residuals, a backward-error bound, orthogonality loss, and a pass/fail
flag, and bounds that can only be estimated are reported as such rather
than passed. Centered, scaled, and composed operators are solved through
native 'C++' kernels without forming dense matrices. Drop-in replacements
for the 'RSpectra' interface are included.
Author: Bradley Buchsbaum [aut, cre, cph]
Maintainer: Bradley Buchsbaum <brad.buchsbaum@gmail.com>
Diff between eigencore versions 1.0.1 dated 2026-07-24 and 1.0.2 dated 2026-07-25
DESCRIPTION | 6 ++-- MD5 | 15 ++++++----- NEWS.md | 11 ++++++++ inst/benchmarks/bench-readme.R | 4 ++- inst/doc/benchmarks.R | 15 +++++++++++ inst/doc/benchmarks.Rmd | 15 +++++++++++ inst/doc/benchmarks.html | 38 +++++++++++++++--------------- tests/testthat/test-profmem-portability.R |only vignettes/benchmarks.Rmd | 15 +++++++++++ 9 files changed, 86 insertions(+), 33 deletions(-)
Title: Conditional Inference Trees with Stacked Multiple Imputation
Description: Implements the stacked-imputation workflow for conditional
inference trees ('ctree') described in Sherlock et al. (2026)
<doi:10.1080/00273171.2026.2661244>. When data contain missing values,
multiply imputed datasets (e.g., from 'mice') are stacked vertically
and a single 'ctree' is fit on the combined data. To correct for the
artificially inflated sample size introduced by stacking, each
node-level test statistic is divided by the number of imputations M
and its p-value recomputed before nodes are pruned (the Stack/M
correction), producing a conservative but interpretable single tree
that incorporates imputation uncertainty without requiring pooling of
structurally different trees. Also exports stack_imputations(),
rescale_statistic() and prune_stackM() as standalone utilities. The
underlying 'ctree' algorithm is provided by 'partykit'
(Hothorn & Zeileis, 2015; Hothorn, Hornik & Zeileis, 2006
<doi:10.1198/106186006X133933>).
Author: Phillip Sherlock [aut, cre]
Maintainer: Phillip Sherlock <phillip.sherlock@ufl.edu>
Diff between ctreeMI versions 0.2.0 dated 2026-07-23 and 0.3.0 dated 2026-07-25
DESCRIPTION | 19 ++-- MD5 | 20 ++--- NEWS.md | 48 ++++++++++++ R/ctree_stacked.R | 125 ++++++++++++++++++++++---------- R/methods.R | 18 +++- R/node_table.R | 20 +++-- R/stackM.R |only R/utils.R | 54 ++++++++++--- build/partial.rdb |binary tests/testthat/test-ctreeMI.R | 15 ++- tests/testthat/test-node-table.R | 3 tests/testthat/test-stackM-correction.R |only 12 files changed, 235 insertions(+), 87 deletions(-)
Title: Sparse Learning with Convex and Concave Penalties
Description: Fast regularization paths for sparse Gaussian, binomial, Poisson,
square-root-lasso, and multinomial models with lasso, smoothly clipped
absolute deviation, or minimax concave penalties. Computation uses
pathwise coordinate optimization, active-set updates, warm starts,
screening rules, Proximal Newton iterations, quadratic majorization, and
adaptive local linear approximation where appropriate. Core solvers are
implemented in C++, and coefficient paths are returned as
Matrix-compatible objects.
Author: Jason Ge [aut],
Xingguo Li [aut],
Haoming Jiang [aut],
Mengdi Wang [aut],
Tong Zhang [aut],
Han Liu [aut],
Tuo Zhao [aut, cre],
Gael Guennebaud [ctb] ,
Benoit Jacob [ctb] ,
Eigen Library Authors [cph]
Maintainer: Tuo Zhao <tourzhao@gatech.edu>
Diff between picasso versions 1.5 dated 2026-03-12 and 2.0.1 dated 2026-07-25
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picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h | 43 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/CwiseNullaryOp.h | 171 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/CwiseUnaryOp.h | 12 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/CwiseUnaryView.h | 24 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/DenseBase.h | 174 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h | 46 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/DenseStorage.h | 230 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/Diagonal.h | 44 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/DiagonalMatrix.h | 52 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/DiagonalProduct.h | 2 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/Dot.h | 20 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/EigenBase.h | 19 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/ForceAlignedAccess.h | 12 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/Fuzzy.h | 6 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/GeneralProduct.h | 30 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/GenericPacketMath.h | 751 + picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/GlobalFunctions.h | 73 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/IO.h | 47 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/IndexedView.h |only picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/Inverse.h | 19 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/Map.h | 14 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/MapBase.h | 13 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/MathFunctions.h | 928 +- picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/MathFunctionsImpl.h | 137 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/Matrix.h | 158 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/MatrixBase.h | 50 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picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/TriangularMatrix.h | 168 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/VectorBlock.h | 10 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/VectorwiseOp.h | 229 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/Visitor.h | 166 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/AVX/Complex.h | 179 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/AVX/MathFunctions.h | 467 - picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/AVX/PacketMath.h | 1260 ++ picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/AVX/TypeCasting.h | 66 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/AVX512/Complex.h |only picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/AVX512/MathFunctions.h | 441 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/AVX512/PacketMath.h | 1983 +++- picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/AVX512/TypeCasting.h |only picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/AltiVec/Complex.h | 317 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/AltiVec/MathFunctions.h | 270 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/AltiVec/MatrixProduct.h |only picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h |only picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h |only picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/AltiVec/PacketMath.h | 2344 ++++- picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/CUDA/Complex.h | 315 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/Default/BFloat16.h |only picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/Default/ConjHelper.h | 116 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/Core/arch/Default/GenericPacketMathFunctions.h |only 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picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseCore/SparseCompressedBase.h | 51 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseCore/SparseCwiseBinaryOp.h | 26 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseCore/SparseCwiseUnaryOp.h | 6 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseCore/SparseDenseProduct.h | 38 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseCore/SparseMatrix.h | 143 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseCore/SparseMatrixBase.h | 17 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseCore/SparseProduct.h | 14 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseCore/SparseRef.h | 14 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseCore/SparseSelfAdjointView.h | 7 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseCore/SparseUtil.h | 8 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseCore/SparseVector.h | 2 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseCore/SparseView.h | 1 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseLU/SparseLU.h | 176 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseLU/SparseLU_Memory.h | 2 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h | 78 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseLU/SparseLU_column_dfs.h | 4 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseLU/SparseLU_gemm_kernel.h | 2 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseLU/SparseLU_panel_bmod.h | 2 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SparseQR/SparseQR.h | 25 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/StlSupport/StdDeque.h | 14 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/StlSupport/StdList.h | 4 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/StlSupport/StdVector.h | 4 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/SuperLUSupport/SuperLUSupport.h | 14 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/UmfPackSupport/UmfPackSupport.h | 214 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/misc/blas.h | 4 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/misc/lapacke.h | 9 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/plugins/ArrayCwiseBinaryOps.h | 30 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/plugins/ArrayCwiseUnaryOps.h | 166 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/plugins/BlockMethods.h | 926 + picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/plugins/CommonCwiseUnaryOps.h | 14 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/plugins/IndexedViewMethods.h |only picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/plugins/MatrixCwiseBinaryOps.h | 8 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/plugins/MatrixCwiseUnaryOps.h | 10 picasso-2.0.1/picasso/src/include/eigen3/Eigen/src/plugins/ReshapedMethods.h |only picasso-2.0.1/picasso/src/include/picasso/actgd.hpp | 28 picasso-2.0.1/picasso/src/include/picasso/actnewton.hpp | 70 picasso-2.0.1/picasso/src/include/picasso/c_api.hpp | 286 picasso-2.0.1/picasso/src/include/picasso/multinomial_actnewton.hpp |only picasso-2.0.1/picasso/src/include/picasso/multinomial_lla.hpp |only picasso-2.0.1/picasso/src/include/picasso/multinomial_objective.hpp |only picasso-2.0.1/picasso/src/include/picasso/objective.hpp | 387 picasso-2.0.1/picasso/src/include/picasso/solver_params.hpp | 10 picasso-2.0.1/picasso/src/internal |only picasso-2.0.1/picasso/src/objective/gaussian_cov_update.cpp | 154 picasso-2.0.1/picasso/src/objective/gaussian_naive_update.cpp | 77 picasso-2.0.1/picasso/src/objective/glm.cpp | 448 picasso-2.0.1/picasso/src/objective/multinomial_objective.cpp |only picasso-2.0.1/picasso/src/objective/sqrtmse.cpp | 161 picasso-2.0.1/picasso/src/picasso-all0.cpp | 4 picasso-2.0.1/picasso/src/picasso_R.cpp | 588 + picasso-2.0.1/picasso/src/solver/actgd.cpp | 322 picasso-2.0.1/picasso/src/solver/actnewton.cpp | 1000 +- picasso-2.0.1/picasso/src/solver/multinomial_actnewton.cpp |only picasso-2.0.1/picasso/src/solver/multinomial_lla.cpp |only picasso-2.0.1/picasso/src/solver/solver_params.cpp | 17 picasso-2.0.1/picasso/tests |only picasso-2.0.1/picasso/vignettes/vignette.Rnw | 174 336 files changed, 30978 insertions(+), 11987 deletions(-)
Title: Optimal Pairing and Matching via Linear Assignment
Description: Solves optimal pairing and matching problems using linear assignment
algorithms. Provides implementations of the Hungarian method (Kuhn 1955)
<doi:10.1002/nav.3800020109>, Jonker-Volgenant shortest path algorithm
(Jonker and Volgenant 1987) <doi:10.1007/BF02278710>, Auction algorithm
(Bertsekas 1988) <doi:10.1007/BF02186476>, cost-scaling
(Goldberg and Kennedy 1995) <doi:10.1007/BF01585996>, scaling algorithms
(Gabow and Tarjan 1989) <doi:10.1137/0218069>, push-relabel (Goldberg and
Tarjan 1988) <doi:10.1145/48014.61051>, and Sinkhorn entropy-regularized
transport (Cuturi 2013) <doi:10.48550/arxiv.1306.0895>. Designed for
matching plots, sites, samples, or any pairwise optimization problem.
Supports rectangular matrices, forbidden assignments, data frame inputs,
batch solving, k-best solutions, and pixel-level image morphing for
visualization. Includes automatic preprocessing with variable health
checks, multiple scaling methods (standardized, [...truncated...]
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between couplr versions 1.5.0 dated 2026-07-19 and 1.5.3 dated 2026-07-25
DESCRIPTION | 20 MD5 | 171 +- NAMESPACE | 3 NEWS.md | 104 + R/RcppExports.R | 8 R/animate.R | 6 R/lap_solve.R | 116 + R/lap_solve_batch.R | 22 R/matching_constraints.R | 36 R/matching_core.R | 117 + R/matching_distance.R | 41 R/matching_distance_cache.R | 95 + R/matching_full.R | 17 R/matching_lazy.R |only R/matching_memory.R |only R/matching_messages.R | 10 R/matching_parallel.R | 5 README.md | 6 inst/doc/algorithms.R | 1103 +++++++++--------- inst/doc/algorithms.Rmd | 17 inst/doc/algorithms.html | 97 + inst/doc/comparison.Rmd | 9 inst/doc/comparison.html | 22 inst/doc/getting-started.html | 4 inst/doc/matching-workflows.Rmd | 13 inst/doc/matching-workflows.html | 26 inst/doc/pixel-morphing.html | 4 inst/doc/troubleshooting.R | 17 inst/doc/troubleshooting.Rmd | 52 inst/doc/troubleshooting.html | 287 ++-- man/assignment.Rd | 23 man/build_cost_matrix.Rd | 20 man/compute_distances.Rd | 18 man/dot-assignment_lazy.Rd |only man/dot-blocks_parallel.Rd | 3 man/dot-couples_blocked.Rd | 3 man/dot-couples_single.Rd | 3 man/estimate_dense_matrix_mb.Rd |only man/full_match.Rd | 10 man/get_free_ram_mb.Rd |only man/lazy_cost_spec_inv_cov.Rd |only man/lazy_pair_distances.Rd |only man/match_couples.Rd | 28 man/match_couples_blocked.Rd | 3 man/match_couples_single.Rd | 3 man/new_lazy_cost_spec.Rd |only man/resolve_memory_mode.Rd |only man/transpose_lazy_cost_spec.Rd |only src/Makevars | 6 src/Makevars.win | 6 src/RcppExports.cpp | 40 src/core/lap_cost_source_traits.h |only src/core/lap_cost_view.h |only src/core/lap_lazy_types.h |only src/core/lap_types.h | 49 src/core/lap_utils.cpp | 60 src/core/lap_utils.h | 64 - src/core/lap_utils_rcpp.cpp | 128 +- src/core/lap_utils_rcpp.h | 32 src/rcpp_interface.cpp | 28 src/solvers/greedy_matching.cpp | 12 src/solvers/jv_core.cpp | 31 src/solvers/jv_core.h | 24 src/solvers/network_simplex/solve_network_simplex.cpp | 19 src/solvers/orlin_ahuja/orlin_solve.cpp | 4 src/solvers/solve_auction.cpp | 234 ++- src/solvers/solve_auction.h | 13 src/solvers/solve_auction_lazy_rcpp.cpp |only src/solvers/solve_bottleneck.cpp | 4 src/solvers/solve_bruteforce.cpp | 4 src/solvers/solve_csa.cpp | 15 src/solvers/solve_csflow.cpp | 4 src/solvers/solve_cycle_cancel.cpp | 11 src/solvers/solve_hk01.cpp | 8 src/solvers/solve_hungarian.cpp | 4 src/solvers/solve_jv.cpp | 43 src/solvers/solve_jv.h | 12 src/solvers/solve_jv_duals.cpp | 4 src/solvers/solve_jv_lazy_rcpp.cpp |only src/solvers/solve_lapmod.cpp | 8 src/solvers/solve_munkres.cpp | 39 src/solvers/solve_push_relabel.cpp | 4 src/solvers/solve_ramshaw_tarjan.cpp | 11 src/solvers/solve_sinkhorn.cpp | 4 src/solvers/solve_ssap_bucket.cpp | 106 + src/solvers/solve_ssp.cpp | 11 tests/testthat/test-animate-widget.R |only tests/testthat/test-assignment-lazy.R |only tests/testthat/test-coverage-90-final.R | 5 tests/testthat/test-distance-cache-coverage.R | 2 tests/testthat/test-match-couples-lazy.R |only tests/testthat/test-memory-mode.R |only vignettes/algorithms.Rmd | 17 vignettes/comparison.Rmd | 9 vignettes/matching-workflows.Rmd | 13 vignettes/troubleshooting.Rmd | 52 96 files changed, 2436 insertions(+), 1246 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, single step (<doi:10.1534/g3.119.400728>),
univariate and multivariate (<doi:10.1186/s12711-022-00730-w>, <doi:10.1093/genetics/iyae179>),
with optional kernel term and sampling techniques (<doi:10.1186/s12859-017-1582-3>).
Author: Alencar Xavier [aut, cre] ,
William Muir [aut],
David Habier [aut],
Kyle Kocak [aut],
Shizhong Xu [aut],
Katy Rainey [aut]
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 2.2.17 dated 2025-12-11 and 2.2.18 dated 2026-07-25
bWGR-2.2.17/bWGR/src/Rcpp20230423.cpp |only bWGR-2.2.18/bWGR/DESCRIPTION | 8 bWGR-2.2.18/bWGR/MD5 | 8 bWGR-2.2.18/bWGR/man/bWGR.Rd | 4 bWGR-2.2.18/bWGR/src/Rcpp20260726ai.cpp |only bWGR-2.2.18/bWGR/src/RcppExports.cpp | 396 ++++++++++++++++---------------- 6 files changed, 208 insertions(+), 208 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library aiming towards
a good balance between speed and ease of use. It provides high-level syntax and
functionality deliberately similar to Matlab. It is useful for algorithm development
directly in C++, or quick conversion of research code into production environments.
It provides efficient classes for vectors, matrices and cubes where dense and sparse
matrices are supported. Integer, floating point and complex numbers are supported.
A sophisticated expression evaluator (based on template meta-programming) automatically
combines several operations to increase speed and efficiency. Dynamic evaluation
automatically chooses optimal code paths based on detected matrix structures.
Matrix decompositions are provided through integration with LAPACK, or one of its
high performance drop-in replacements (such as 'MKL' or 'OpenBLAS'). It can
automatically use 'OpenMP' multi-threading (parallelisation) to speed up
computationally expensive operations [...truncated...]
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Doug Bates [aut] ,
Binxiang Ni [aut],
Conrad Sanderson [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 15.4.0-1 dated 2026-06-19 and 15.4.2-1 dated 2026-07-25
ChangeLog | 34 +++- DESCRIPTION | 8 - MD5 | 78 ++++----- build/partial.rdb |binary build/vignette.rds |binary configure | 18 +- configure.ac | 2 inst/NEWS.Rd | 19 ++ inst/include/armadillo_bits/Mat_bones.hpp | 6 inst/include/armadillo_bits/Mat_meat.hpp | 60 +++++++ inst/include/armadillo_bits/SpBase_bones.hpp | 2 inst/include/armadillo_bits/SpBase_meat.hpp | 10 - inst/include/armadillo_bits/SpGlue_bones.hpp | 3 inst/include/armadillo_bits/SpGlue_meat.hpp | 3 inst/include/armadillo_bits/SpMat_bones.hpp | 3 inst/include/armadillo_bits/SpMat_meat.hpp | 7 inst/include/armadillo_bits/SpOp_bones.hpp | 3 inst/include/armadillo_bits/SpOp_meat.hpp | 3 inst/include/armadillo_bits/SpSubview_bones.hpp | 3 inst/include/armadillo_bits/SpSubview_col_list_bones.hpp | 2 inst/include/armadillo_bits/SpSubview_col_list_meat.hpp | 11 + inst/include/armadillo_bits/SpSubview_meat.hpp | 3 inst/include/armadillo_bits/arma_version.hpp | 2 inst/include/armadillo_bits/diskio_meat.hpp | 2 inst/include/armadillo_bits/memory.hpp | 10 - inst/include/armadillo_bits/mtSpOp_meat.hpp | 2 inst/include/armadillo_bits/mtSpReduceOp_bones.hpp | 3 inst/include/armadillo_bits/mtSpReduceOp_meat.hpp | 11 + inst/include/armadillo_bits/op_diagmat_bones.hpp | 11 + inst/include/armadillo_bits/op_diagmat_meat.hpp | 106 +++++++++---- inst/include/armadillo_bits/op_diagvec_bones.hpp | 18 ++ inst/include/armadillo_bits/op_diagvec_meat.hpp | 101 ++++++++++-- inst/include/armadillo_bits/op_repelem_bones.hpp | 2 inst/include/armadillo_bits/op_repelem_meat.hpp | 17 ++ inst/include/armadillo_bits/op_vectorise_bones.hpp | 2 inst/include/armadillo_bits/op_vectorise_meat.hpp | 118 +-------------- inst/include/armadillo_bits/spdiagview_bones.hpp | 3 inst/include/armadillo_bits/spdiagview_meat.hpp | 11 + inst/include/armadillo_bits/spop_diagmat_bones.hpp | 7 inst/include/armadillo_bits/spop_diagmat_meat.hpp | 29 +++ 40 files changed, 480 insertions(+), 253 deletions(-)
Title: Polyspherical Kernel Density Estimation
Description: Kernel density estimation on the polysphere, (hyper)sphere, and
circle. Includes functions for density estimation, regression estimation,
ridge estimation, bandwidth selection, kernels, samplers, and homogeneity
tests. Companion package to García-Portugués and Meilán-Vila (2025)
<doi:10.1080/01621459.2025.2521898> and García-Portugués and Meilán-Vila
(2023) <doi:10.1007/978-3-031-32729-2_4>.
Author: Eduardo Garcia-Portugues [aut, cre] ,
Andrea Meilan-Vila [ctb]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Diff between polykde versions 1.1.7 dated 2025-07-27 and 1.2.0 dated 2026-07-25
polykde-1.1.7/polykde/tests/testthat/tests_grad-hess.R |only polykde-1.2.0/polykde/DESCRIPTION | 20 - polykde-1.2.0/polykde/MD5 | 141 +++---- polykde-1.2.0/polykde/NEWS.md | 17 polykde-1.2.0/polykde/R/RcppExports.R | 174 +++++---- polykde-1.2.0/polykde/R/angles.R | 28 - polykde-1.2.0/polykde/R/bwd.R | 208 +++++++--- polykde-1.2.0/polykde/R/data.R | 25 - polykde-1.2.0/polykde/R/distr.R | 10 polykde-1.2.0/polykde/R/euler.R | 223 ++++++----- polykde-1.2.0/polykde/R/kernels.R | 31 - polykde-1.2.0/polykde/R/kre.R | 42 +- polykde-1.2.0/polykde/R/mise.R | 99 +++-- polykde-1.2.0/polykde/R/polykde-package.R | 6 polykde-1.2.0/polykde/R/samplers.R | 298 ++++++++------- polykde-1.2.0/polykde/R/sreps.R | 48 +- polykde-1.2.0/polykde/R/sysdata.rda |binary polykde-1.2.0/polykde/R/tests.R | 73 ++- polykde-1.2.0/polykde/R/utils.R | 327 ++++++++++++----- polykde-1.2.0/polykde/R/zzz.R | 22 - polykde-1.2.0/polykde/build/partial.rdb |binary polykde-1.2.0/polykde/inst/CITATION | 20 + polykde-1.2.0/polykde/inst/WORDLIST | 3 polykde-1.2.0/polykde/man/angles_to_polysph.Rd | 4 polykde-1.2.0/polykde/man/angles_to_sph.Rd | 10 polykde-1.2.0/polykde/man/angles_to_torus.Rd | 8 polykde-1.2.0/polykde/man/bw_cv_kre_polysph.Rd | 23 - polykde-1.2.0/polykde/man/bw_cv_polysph.Rd | 60 ++- polykde-1.2.0/polykde/man/bw_lcv_min_epa.Rd | 4 polykde-1.2.0/polykde/man/bw_mrot_polysph.Rd | 24 - polykde-1.2.0/polykde/man/bw_rot_polysph.Rd | 35 + polykde-1.2.0/polykde/man/clean_euler_ridge.Rd | 86 ++-- polykde-1.2.0/polykde/man/comp_ind_dj.Rd | 6 polykde-1.2.0/polykde/man/d_mvmf_polysph.Rd | 12 polykde-1.2.0/polykde/man/dist_polysph.Rd | 18 polykde-1.2.0/polykde/man/eff_kern.Rd | 32 + polykde-1.2.0/polykde/man/euler_ridge.Rd | 178 ++++++--- polykde-1.2.0/polykde/man/fib_latt.Rd | 2 polykde-1.2.0/polykde/man/figures |only polykde-1.2.0/polykde/man/grad_hess_kde_polysph.Rd | 36 + polykde-1.2.0/polykde/man/hammer_to_sph.Rd | 2 polykde-1.2.0/polykde/man/hippocampus.Rd | 25 - polykde-1.2.0/polykde/man/hom_test_polysph.Rd | 38 + polykde-1.2.0/polykde/man/index_ridge.Rd | 135 ++++--- polykde-1.2.0/polykde/man/interp_polysph.Rd | 4 polykde-1.2.0/polykde/man/kde_polysph.Rd | 43 +- polykde-1.2.0/polykde/man/kernel.Rd | 21 - polykde-1.2.0/polykde/man/kre_polysph.Rd | 32 - polykde-1.2.0/polykde/man/log_cv_kde_polysph.Rd | 26 - polykde-1.2.0/polykde/man/polykde-package.Rd | 6 polykde-1.2.0/polykde/man/proj_grad_kde_polysph.Rd | 35 + polykde-1.2.0/polykde/man/proj_polysph.Rd | 11 polykde-1.2.0/polykde/man/r_g_kern.Rd | 2 polykde-1.2.0/polykde/man/r_kde_polysph.Rd | 63 +-- polykde-1.2.0/polykde/man/r_kern_polysph.Rd | 113 +++-- polykde-1.2.0/polykde/man/r_mvmf_polysph.Rd | 14 polykde-1.2.0/polykde/man/r_path_s1r.Rd | 145 ++++--- polykde-1.2.0/polykde/man/r_unif_polysph.Rd | 2 polykde-1.2.0/polykde/man/r_vmf_polysph.Rd | 3 polykde-1.2.0/polykde/man/view_srep.Rd | 86 +++- polykde-1.2.0/polykde/src/euler.cpp | 104 +++-- polykde-1.2.0/polykde/src/grad-hess.cpp | 36 + polykde-1.2.0/polykde/src/kde.cpp | 33 + polykde-1.2.0/polykde/src/utils.cpp | 43 +- polykde-1.2.0/polykde/tests/testthat/Rplots.pdf |binary polykde-1.2.0/polykde/tests/testthat/tests_angles.R | 5 polykde-1.2.0/polykde/tests/testthat/tests_bwd.R | 84 +++- polykde-1.2.0/polykde/tests/testthat/tests_distr.R | 22 + polykde-1.2.0/polykde/tests/testthat/tests_grad_hess.R |only polykde-1.2.0/polykde/tests/testthat/tests_kde.R | 5 polykde-1.2.0/polykde/tests/testthat/tests_mise.R | 41 ++ polykde-1.2.0/polykde/tests/testthat/tests_tests.R | 22 + polykde-1.2.0/polykde/tests/testthat/tests_utils.R | 251 ++++++++++--- 73 files changed, 2482 insertions(+), 1323 deletions(-)
Title: Detect Text Reuse and Document Similarity
Description: Tools for measuring similarity among documents and detecting
passages which have been reused. Implements shingled n-gram, skip n-gram,
and other tokenizers; similarity/dissimilarity functions; pairwise
comparisons; minhash and locality sensitive hashing algorithms; and a
version of the Smith-Waterman local alignment algorithm suitable for
natural language.
Author: Lincoln Mullen [aut] ,
Yaoxiang Li [aut, cre]
Maintainer: Yaoxiang Li <liyaoxiang@outlook.com>
Diff between textreuse versions 1.0.1 dated 2026-05-07 and 1.0.2 dated 2026-07-25
DESCRIPTION | 12 ++++----- MD5 | 42 ++++++++++++++++---------------- NEWS.md | 25 +++++++++++++------ R/align_local.R | 2 - R/lsh.R | 8 +++--- R/lsh_candidates.R | 3 +- R/lsh_probability.R | 3 +- R/minhash.R | 2 - R/textreuse-package.r | 4 +-- README.md | 11 +++----- build/vignette.rds |binary inst/doc/textreuse-alignment.html | 4 +-- inst/doc/textreuse-introduction.html | 10 +++---- inst/doc/textreuse-minhash.html | 45 +++++++++++++++++------------------ inst/doc/textreuse-pairwise.html | 4 +-- man/align_local.Rd | 2 - man/lsh.Rd | 2 - man/lsh_probability.Rd | 3 +- man/minhash_generator.Rd | 2 - man/reexports.Rd | 2 - man/textreuse-package.Rd | 9 +++---- tests/testthat/test-lsh.R | 1 22 files changed, 104 insertions(+), 92 deletions(-)
Title: Cumulative Calibration Assessment for Prediction Models
Description: Tools for visualization of, and inference on, the calibration of prediction models on the cumulative domain. This provides a method for evaluating calibration of risk prediction models without having to group the data or use tuning parameters (e.g., loess bandwidth). This package implements the methodology described in Sadatsafavi and Petkau (2024) <doi:10.1002/sim.10138>. The core of the package is cumulcalib(), which takes in vectors of binary responses and predicted risks. The package also implements non-parametric assessment of the calibration of individualized treatment effect (ITE) models using data from a randomized trial, via cumulcalibITE(), as described in Sadatsafavi et al. (2025) <doi:10.48550/arXiv.2512.08140>. The plot() and summary() methods are implemented for the results returned by cumulcalib() and cumulcalibITE().
Author: Mohsen Sadatsafavi [aut, cre]
Maintainer: Mohsen Sadatsafavi <mohsen.sadatsafavi@ubc.ca>
Diff between cumulcalib versions 0.0.1 dated 2024-06-13 and 0.1.0 dated 2026-07-25
cumulcalib-0.0.1/cumulcalib/tests/testthat/test-test.R |only cumulcalib-0.1.0/cumulcalib/DESCRIPTION | 14 cumulcalib-0.1.0/cumulcalib/LICENSE | 4 cumulcalib-0.1.0/cumulcalib/MD5 | 65 cumulcalib-0.1.0/cumulcalib/NAMESPACE | 3 cumulcalib-0.1.0/cumulcalib/NEWS.md | 38 cumulcalib-0.1.0/cumulcalib/R/core.R | 1273 +++++----- cumulcalib-0.1.0/cumulcalib/R/cumulcalib-package.R | 24 cumulcalib-0.1.0/cumulcalib/R/plot.R |only cumulcalib-0.1.0/cumulcalib/README.md | 47 cumulcalib-0.1.0/cumulcalib/build/partial.rdb |binary cumulcalib-0.1.0/cumulcalib/build/vignette.rds |binary cumulcalib-0.1.0/cumulcalib/inst/WORDLIST | 9 cumulcalib-0.1.0/cumulcalib/inst/doc/tutorial.Rmd | 384 +-- cumulcalib-0.1.0/cumulcalib/inst/doc/tutorial.html | 262 -- cumulcalib-0.1.0/cumulcalib/inst/doc/tutorialITE.R |only cumulcalib-0.1.0/cumulcalib/inst/doc/tutorialITE.Rmd |only cumulcalib-0.1.0/cumulcalib/inst/doc/tutorialITE.html |only cumulcalib-0.1.0/cumulcalib/man/cumulcalib-package.Rd | 42 cumulcalib-0.1.0/cumulcalib/man/cumulcalib.Rd | 64 cumulcalib-0.1.0/cumulcalib/man/cumulcalibITE.Rd |only cumulcalib-0.1.0/cumulcalib/man/figures/README-example-1.png |binary cumulcalib-0.1.0/cumulcalib/man/pKolmogorov.Rd | 38 cumulcalib-0.1.0/cumulcalib/man/pMAD_BM.Rd | 38 cumulcalib-0.1.0/cumulcalib/man/pMAD_BM_c.Rd | 62 cumulcalib-0.1.0/cumulcalib/man/plot.cumulcalib.Rd | 109 cumulcalib-0.1.0/cumulcalib/man/print.cumulcalib.Rd |only cumulcalib-0.1.0/cumulcalib/man/print.summary.cumulcalib.Rd |only cumulcalib-0.1.0/cumulcalib/man/qKolmogorov.Rd | 34 cumulcalib-0.1.0/cumulcalib/man/qMAD_BM.Rd | 34 cumulcalib-0.1.0/cumulcalib/man/qMAD_BM_c.Rd | 38 cumulcalib-0.1.0/cumulcalib/man/summary.cumulcalib.Rd | 64 cumulcalib-0.1.0/cumulcalib/tests/testthat.R | 24 cumulcalib-0.1.0/cumulcalib/tests/testthat/test-cumulcalib.R |only cumulcalib-0.1.0/cumulcalib/tests/testthat/test-cumulcalibITE.R |only cumulcalib-0.1.0/cumulcalib/tests/testthat/test-distributions.R |only cumulcalib-0.1.0/cumulcalib/tests/testthat/test-plot.R |only cumulcalib-0.1.0/cumulcalib/tests/testthat/test-print.R |only cumulcalib-0.1.0/cumulcalib/tests/testthat/test-summary.R |only cumulcalib-0.1.0/cumulcalib/vignettes/tutorial.Rmd | 384 +-- cumulcalib-0.1.0/cumulcalib/vignettes/tutorialITE.Rmd |only 41 files changed, 1657 insertions(+), 1397 deletions(-)
Title: Probabilistic Decomposition of Archaeological Palimpsests
Description: Probabilistic framework for the analysis of archaeological
palimpsests based on the Stratigraphic Entanglement Field (SEF).
Integrates spatial proximity, stratigraphic depth, chronological
overlap, and cultural similarity to estimate latent depositional
phases via diagonal Gaussian mixture Expectation-Maximisation (EM).
Provides the Stratigraphic Entanglement Index (SEI), Excavation
Stratigraphic Energy (ESE), and Palimpsest Dissolution Index (PDI)
for quantifying depositional coherence, detecting intrusive finds,
and measuring palimpsest formation. Includes simulation, diagnostics,
phase-count selection, publication-quality plots, and Geographic
Information System (GIS) export via 'sf'. Methods are described in Cocca (2026)
<https://github.com/enzococca/palimpsestr>.
Author: Enzo Cocca [aut, cre]
Maintainer: Enzo Cocca <enzo.ccc@gmail.com>
Diff between palimpsestr versions 0.10.0 dated 2026-04-09 and 0.24.0 dated 2026-07-25
DESCRIPTION | 13 MD5 | 188 +-- NAMESPACE | 14 NEWS.md | 398 ++++++ R/app.R |only R/bootstrap.R | 16 R/chronology.R |only R/cv.R | 50 R/data.R | 43 R/db_connect.R | 452 +++++++ R/diagnostics.R | 27 R/ese.R | 13 R/export_report.R |only R/fit.R | 344 +++++ R/gg_model_plots.R |only R/gg_plots.R | 42 R/harris.R | 37 R/longevity.R |only R/optimize.R | 58 R/recommend.R |only R/sei.R | 23 R/simulate.R | 8 R/utils.R | 401 ++++++ README.md | 13 build/partial.rdb |only build/vignette.rds |binary data/villa_romana.rda |binary inst/doc/introduction.R | 91 + inst/doc/introduction.Rmd | 221 +++ inst/doc/introduction.html | 1556 +++++++++++++++++--------- inst/rmarkdown |only inst/shiny |only man/adjusted_rand_index.Rd | 10 man/archaeo_sim.Rd | 4 man/as_phase_table.Rd | 15 man/as_plotly.Rd | 38 man/as_sf_links.Rd | 4 man/as_sf_phase.Rd | 4 man/bootstrap_sef.Rd | 10 man/chronology_from_oxcal.Rd |only man/chronology_from_rcarbon.Rd |only man/compare_k.Rd | 36 man/confusion_matrix.Rd | 10 man/cv_sef.Rd | 16 man/detect_intrusions.Rd | 41 man/ese.Rd | 20 man/export_results.Rd | 6 man/export_sef_report.Rd |only man/fit_sef.Rd | 116 + man/gg_bootstrap.Rd | 38 man/gg_compare_k.Rd | 38 man/gg_confusion.Rd | 38 man/gg_convergence.Rd | 38 man/gg_cv.Rd | 38 man/gg_direction.Rd |only man/gg_energy.Rd | 38 man/gg_entropy.Rd | 38 man/gg_intrusions.Rd | 38 man/gg_longevity.Rd |only man/gg_map.Rd | 38 man/gg_outliers.Rd |only man/gg_phase_composition.Rd |only man/gg_phase_profile.Rd | 38 man/gg_phasefield.Rd | 38 man/gg_unit_coherence.Rd |only man/gg_weights.Rd | 38 man/harris_from_contexts.Rd | 35 man/launch_app.Rd |only man/load_geometries.Rd | 5 man/local_sei.Rd | 6 man/optimize_weights.Rd | 29 man/palimpsestr-package.Rd | 5 man/pdi.Rd | 27 man/phase_composition.Rd |only man/phase_diagnostic_table.Rd | 15 man/phase_transition_matrix.Rd | 6 man/plot_energy.Rd | 38 man/plot_entropy.Rd | 38 man/plot_phasefield.Rd | 38 man/plot_sei_profile.Rd | 38 man/predict_phase.Rd | 15 man/read_db.Rd | 5 man/read_harris.Rd | 6 man/read_pyarchinit.Rd |only man/recommend_setup.Rd |only man/reorder_phases.Rd | 8 man/sef_summary.Rd | 8 man/sei_matrix.Rd | 14 man/sei_sparse.Rd | 14 man/type_longevity.Rd |only man/us_summary_table.Rd | 6 man/validate_phases_harris.Rd | 6 man/villa_romana.Rd | 43 tests/testthat/test-basic.R | 7 tests/testthat/test-chrono-uncertainty.R |only tests/testthat/test-chronology-oxcal.R |only tests/testthat/test-chronology-rcarbon.R |only tests/testthat/test-class-multinomial.R |only tests/testthat/test-cv.R | 12 tests/testthat/test-directional-intrusions.R |only tests/testthat/test-export-report.R |only tests/testthat/test-feature-improvements.R |only tests/testthat/test-gg-model-plots.R |only tests/testthat/test-harris.R | 14 tests/testthat/test-intrusion-type.R |only tests/testthat/test-new-features.R | 6 tests/testthat/test-noise-component.R |only tests/testthat/test-noise-scoring.R |only tests/testthat/test-read-pyarchinit.R |only tests/testthat/test-recommend-setup.R |only tests/testthat/test-statistical-correctness.R |only tests/testthat/test-strat-dynamic.R |only tests/testthat/test-type-longevity.R |only vignettes/introduction.Rmd | 221 +++ 114 files changed, 4292 insertions(+), 1167 deletions(-)
Title: Convert Identifiers in Biological Databases
Description: Identifiers in biological databases connect different levels
of metadata, phenotype data or genotype data. This tool is designed to
easily convert identifiers within or between different biological
databases (Wang, Shixiang, et al. (2021) <DOI:10.1371/journal.pgen.1009557>).
Author: Shixiang Wang [aut, cre]
Maintainer: Shixiang Wang <w_shixiang@163.com>
This is a re-admission after prior archival of version 0.3.4 dated 2023-03-14
Diff between IDConverter versions 0.3.4 dated 2023-03-14 and 0.4.0 dated 2026-07-25
IDConverter-0.3.4/IDConverter/R/globalVars.R |only IDConverter-0.4.0/IDConverter/DESCRIPTION | 23 +- IDConverter-0.4.0/IDConverter/MD5 | 65 +++--- IDConverter-0.4.0/IDConverter/NAMESPACE | 5 IDConverter-0.4.0/IDConverter/NEWS.md | 51 ++++ IDConverter-0.4.0/IDConverter/R/IDConverter-package.R | 8 IDConverter-0.4.0/IDConverter/R/annotables-data.R | 28 +- IDConverter-0.4.0/IDConverter/R/build_annotables.R |only IDConverter-0.4.0/IDConverter/R/common_human_and_mouse_ids.R | 44 +++- IDConverter-0.4.0/IDConverter/R/convert_hm_orthologs.R |only IDConverter-0.4.0/IDConverter/R/load_data.R | 61 ++++- IDConverter-0.4.0/IDConverter/R/pair_gdc_samples.R |only IDConverter-0.4.0/IDConverter/R/parse_gdc_uuid.R | 5 IDConverter-0.4.0/IDConverter/README.md | 106 ++++++---- IDConverter-0.4.0/IDConverter/build/partial.rdb |binary IDConverter-0.4.0/IDConverter/build/vignette.rds |only IDConverter-0.4.0/IDConverter/data/icgc.rda |binary IDConverter-0.4.0/IDConverter/data/pcawg_full.rda |binary IDConverter-0.4.0/IDConverter/data/pcawg_simple.rda |binary IDConverter-0.4.0/IDConverter/data/tcga.rda |binary IDConverter-0.4.0/IDConverter/inst/doc |only IDConverter-0.4.0/IDConverter/man/IDConverter-package.Rd | 5 IDConverter-0.4.0/IDConverter/man/build_annotables.Rd |only IDConverter-0.4.0/IDConverter/man/convert_hm_genes.Rd | 16 + IDConverter-0.4.0/IDConverter/man/convert_hm_orthologs.Rd |only IDConverter-0.4.0/IDConverter/man/convert_icgc.Rd | 2 IDConverter-0.4.0/IDConverter/man/convert_pcawg.Rd | 4 IDConverter-0.4.0/IDConverter/man/convert_tcga.Rd | 2 IDConverter-0.4.0/IDConverter/man/load_data.Rd | 11 - IDConverter-0.4.0/IDConverter/man/ls_annotables.Rd | 22 +- IDConverter-0.4.0/IDConverter/man/pair_gdc_samples.Rd |only IDConverter-0.4.0/IDConverter/man/parse_gdc_file_uuid.Rd | 7 IDConverter-0.4.0/IDConverter/man/resolve_gene_aliases.Rd |only IDConverter-0.4.0/IDConverter/tests/testthat/test-roxytest-testexamples-convert_custom.R | 4 IDConverter-0.4.0/IDConverter/tests/testthat/test-roxytest-testexamples-convert_icgc.R | 16 - IDConverter-0.4.0/IDConverter/tests/testthat/test-roxytest-testexamples-convert_pcawg.R | 20 - IDConverter-0.4.0/IDConverter/tests/testthat/test-roxytest-testexamples-convert_tcga.R | 14 - IDConverter-0.4.0/IDConverter/vignettes |only 38 files changed, 360 insertions(+), 159 deletions(-)