Title: Bayesian Estimation of Naloxone Kit Number Under-Reporting
Description: Bayesian model and associated tools for generating estimates of
total naloxone kit numbers distributed and used from naloxone kit orders
data. Provides functions for generating simulated data of naloxone kit use
and functions for generating samples from the posterior.
Author: Mike Irvine [aut, cre, cph] ,
Samantha Bardwell [ctb],
Andrew Johnson [ctb]
Maintainer: Mike Irvine <mike.irvine@bccdc.ca>
Diff between bennu versions 0.3.1 dated 2025-07-25 and 0.3.2 dated 2025-10-09
DESCRIPTION | 10 MD5 | 33 NEWS.md | 5 R/est_naloxone.R | 580 +++--- README.md | 197 +- build/vignette.rds |binary configure | 2 configure.win | 11 inst/doc/Introduction.R | 268 +- inst/doc/Introduction.html | 1397 +++++++-------- inst/doc/simulation_validation_experiments.R | 344 +-- inst/doc/simulation_validation_experiments.html | 1130 ++++++------ man/figures/README-example-1.png |binary src/Makevars |only src/stanExports_distribution_covariate_model.cc | 34 src/stanExports_distribution_covariate_model.h | 2155 +++++++++++------------- tests/testthat/test-kit_summary_table.R | 60 tests/testthat/test-plot_kit_use.R | 72 18 files changed, 3113 insertions(+), 3185 deletions(-)
Title: Bayesian Statistics for 2D/3D Transformations
Description: Fits 2D and 3D geometric transformations via 'Stan' probabilistic programming engine (
Stan Development Team (2021) <https://mc-stan.org>). Returns posterior distribution for individual
parameters of the fitted distribution. Allows for computation of LOO and WAIC information criteria
(Vehtari A, Gelman A, Gabry J (2017) <doi:10.1007/s11222-016-9696-4>) as well as Bayesian R-squared
(Gelman A, Goodrich B, Gabry J, and Vehtari A (2018) <doi:10.1080/00031305.2018.1549100>).
Author: Alexander Pastukhov [aut, cre] ,
Claus-Christian Carbon [aut]
Maintainer: Alexander (Sasha) Pastukhov <pastukhov.alexander@gmail.com>
Diff between TriDimRegression versions 1.0.2 dated 2023-09-13 and 1.0.3 dated 2025-10-09
DESCRIPTION | 15 MD5 | 38 NEWS.md | 11 R/TriDimRegression-package.R | 2 R/coef.R | 4 R/predict.R | 4 R/variable_summary.R | 4 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/calibration.html | 19 inst/doc/comparing_faces.html | 7 inst/doc/transformation_matrices.html | 6 man/TriDimRegression-package.Rd | 3 man/coef.tridim_transformation.Rd | 4 man/predict.tridim_transformation.Rd | 4 man/variable_summary.Rd | 4 man/waic.tridim_transformation.Rd | 2 src/stanExports_tridim_transformation.cc | 34 src/stanExports_tridim_transformation.h | 2393 ++++++++++++++++++------------- 20 files changed, 1549 insertions(+), 1007 deletions(-)
More information about TriDimRegression at CRAN
Permanent link
Title: Geostatistical Modeling of Spatially Referenced Data
Description: Geostatistical analysis of continuous and count data.
Implements stationary Gaussian processes with Matérn correlation for spatial prediction,
as described in Diggle and Giorgi (2019, ISBN: 978-1-138-06102-7).
Author: Emanuele Giorgi [aut, cre] ,
Claudio Fronterre [ctb]
Maintainer: Emanuele Giorgi <e.giorgi@bham.ac.uk>
Diff between RiskMap versions 0.1.0 dated 2024-06-25 and 1.0.0 dated 2025-10-09
DESCRIPTION | 32 MD5 | 61 NAMESPACE | 59 R/abund_sma.R |only R/auxiliary.R | 1077 +++++++++++++-- R/globals.R |only R/infect_sma.R |only R/mda_modelling.R |only R/package-imports.R |only R/parameter_estimation.R | 1814 +++++++++++++++---------- R/spatial_prediction.R | 2264 +++++++++++++++++++++++++++++--- R/tz_covariates.R |only R/tz_malaria.R |only README.md | 96 - build |only data/abund_sma.rdata |only data/infect_sma.rdata |only data/tz_covariates.rdata |only data/tz_malaria.rdata |only man/Laplace_sampling_MCMC.Rd | 101 + man/abund_sma.Rd |only man/assess_pp.Rd |only man/assess_sim.Rd |only man/check_mcmc.Rd |only man/compute_ID_coords.Rd |only man/convex_hull_sf.Rd |only man/dast.Rd |only man/figures |only man/glgpm.Rd | 8 man/glgpm_sim.Rd | 8 man/infect_sma.Rd |only man/maxim.integrand.Rd | 5 man/plot_AnPIT.Rd |only man/plot_mda.Rd |only man/plot_score.Rd |only man/plot_sim_surf.Rd |only man/pred_over_grid.Rd | 2 man/pred_target_grid.Rd | 11 man/pred_target_shp.Rd | 94 - man/print.summary.RiskMap.sim.res.Rd |only man/print.summary.RiskMap.spatial.cv.Rd |only man/summary.RiskMap.sim.res.Rd |only man/summary.RiskMap.spatial.cv.Rd |only man/surf_sim.Rd |only man/to_table.Rd | 29 man/tz_covariates.Rd |only man/tz_malaria.Rd |only man/update_predictors.Rd |only 48 files changed, 4397 insertions(+), 1264 deletions(-)
Title: Transfer 'REDCap' Data to Database
Description: Transfer 'REDCap' (Research Electronic Data Capture) data to a database,
specifically optimized for 'DuckDB'.
Processes data in chunks to handle large datasets without exceeding available memory.
Features include data labeling, coded value conversion, and hearing a "quack" sound on success.
Author: Dylan Pieper [aut, cre]
Maintainer: Dylan Pieper <dylanpieper@gmail.com>
Diff between redquack versions 0.2.0 dated 2025-05-14 and 0.3.0 dated 2025-10-09
redquack-0.2.0/redquack/man/figures/redquack-hex.png |only redquack-0.2.0/redquack/tests/testthat/helper-redcap.R |only redquack-0.2.0/redquack/tests/testthat/test-redcap_to_duckdb.R |only redquack-0.3.0/redquack/DESCRIPTION | 21 redquack-0.3.0/redquack/MD5 | 36 redquack-0.3.0/redquack/NAMESPACE | 41 redquack-0.3.0/redquack/NEWS.md | 30 redquack-0.3.0/redquack/R/collect_labeled.R |only redquack-0.3.0/redquack/R/collect_list.R |only redquack-0.3.0/redquack/R/helpers.R | 462 +++++++ redquack-0.3.0/redquack/R/optimize_data_types.R | 34 redquack-0.3.0/redquack/R/redcap_to_db.R | 653 +++++++--- redquack-0.3.0/redquack/README.md | 243 ++- redquack-0.3.0/redquack/man/close_duckdb.Rd |only redquack-0.3.0/redquack/man/collect_labeled.Rd |only redquack-0.3.0/redquack/man/collect_list.Rd |only redquack-0.3.0/redquack/man/figures/redquack.png |only redquack-0.3.0/redquack/man/inspect.Rd |only redquack-0.3.0/redquack/man/list_to_env.Rd |only redquack-0.3.0/redquack/man/metadata.Rd |only redquack-0.3.0/redquack/man/redcap_log.Rd |only redquack-0.3.0/redquack/man/redcap_to_db.Rd | 93 - redquack-0.3.0/redquack/man/remove_duckdb.Rd |only redquack-0.3.0/redquack/man/save_parquet.Rd |only redquack-0.3.0/redquack/man/tbl_redcap.Rd |only redquack-0.3.0/redquack/man/transfer_log.Rd |only redquack-0.3.0/redquack/man/use_duckdb.Rd |only redquack-0.3.0/redquack/tests/testthat/helpers.R |only redquack-0.3.0/redquack/tests/testthat/test-redcap_to_db.R |only 29 files changed, 1293 insertions(+), 320 deletions(-)
Title: Extreme Risk Measures
Description: A set of procedures for estimating risks related to extreme events via risk measures such as Expectile, Value-at-Risk, etc. is provided. Estimation methods for univariate independent observations and temporal dependent observations are available. The methodology is extended to the case of independent multidimensional observations. The statistical inference is performed through parametric and non-parametric estimators. Inferential procedures such as confidence intervals, confidence regions and hypothesis testing are obtained by exploiting the asymptotic theory. Adapts the methodologies derived in Padoan and Stupfler (2022) <doi:10.3150/21-BEJ1375>, Davison et al. (2023) <doi:10.1080/07350015.2022.2078332>, Daouia et al. (2018) <doi:10.1111/rssb.12254>, Drees (2000) <doi:10.1214/aoap/1019487617>, Drees (2003) <doi:10.3150/bj/1066223272>, de Haan and Ferreira (2006) <doi:10.1007/0-387-34471-3>, de Haan et al. (2016) <doi:10.1007/s00780-015-0287-6> [...truncated...]
Author: Simone Padoan [cre, aut],
Gilles Stupfler [aut],
Carlotta Pacifici [aut]
Maintainer: Simone Padoan <simone.padoan@unibocconi.it>
Diff between ExtremeRisks versions 0.0.4-1 dated 2025-04-26 and 0.0.5 dated 2025-10-09
ExtremeRisks-0.0.4-1/ExtremeRisks/R/Estimation.r |only ExtremeRisks-0.0.4-1/ExtremeRisks/R/Expectiles.r |only ExtremeRisks-0.0.4-1/ExtremeRisks/R/MultiEstimation.r |only ExtremeRisks-0.0.4-1/ExtremeRisks/R/Simulation.r |only ExtremeRisks-0.0.4-1/ExtremeRisks/R/UniEstimation.r |only ExtremeRisks-0.0.5/ExtremeRisks/DESCRIPTION | 23 +++---- ExtremeRisks-0.0.5/ExtremeRisks/MD5 | 41 +++++++++---- ExtremeRisks-0.0.5/ExtremeRisks/NAMESPACE | 16 +++-- ExtremeRisks-0.0.5/ExtremeRisks/R/Estimation.R |only ExtremeRisks-0.0.5/ExtremeRisks/R/Expectiles.R |only ExtremeRisks-0.0.5/ExtremeRisks/R/MultiEstimation.R |only ExtremeRisks-0.0.5/ExtremeRisks/R/Prediction.R |only ExtremeRisks-0.0.5/ExtremeRisks/R/Simulation.R |only ExtremeRisks-0.0.5/ExtremeRisks/R/UniEstimation.R |only ExtremeRisks-0.0.5/ExtremeRisks/inst |only ExtremeRisks-0.0.5/ExtremeRisks/man/Bqgpd_c.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/Bqgpd_d.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/MultiHTailIndex.Rd | 2 ExtremeRisks-0.0.5/ExtremeRisks/man/cpost_stat.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/estMultiExpectiles.Rd | 2 ExtremeRisks-0.0.5/ExtremeRisks/man/estPOT.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/expectiles.Rd | 2 ExtremeRisks-0.0.5/ExtremeRisks/man/extBQuant.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/extBQuantx.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/extMultiQuantile.Rd | 2 ExtremeRisks-0.0.5/ExtremeRisks/man/fitdGPD.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/plotBayes.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/predDens.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/predDensx.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/predMultiExpectiles.Rd | 2 ExtremeRisks-0.0.5/ExtremeRisks/man/predQuant.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/quantF.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/scedastic.test.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/schedastic.test.Rd |only ExtremeRisks-0.0.5/ExtremeRisks/man/testTailHomo.Rd |only 35 files changed, 54 insertions(+), 36 deletions(-)
Title: 'KorAP' Web Service Client Package
Description: A client package that makes the 'KorAP' web service API accessible from R. The corpus analysis platform 'KorAP' has been developed as a scientific tool to make potentially large, stratified and multiply annotated corpora, such as the 'German Reference Corpus DeReKo' or the 'Corpus of the Contemporary Romanian Language CoRoLa', accessible for linguists to let them verify hypotheses and to find interesting patterns in real language use. The 'RKorAPClient' package provides access to 'KorAP' and the corpora behind it for user-created R code, as a programmatic alternative to the 'KorAP' web user-interface. You can learn more about 'KorAP' and use it directly on 'DeReKo' at <https://korap.ids-mannheim.de/>.
Author: Marc Kupietz [aut, cre],
Nils Diewald [ctb],
Leibniz Institute for the German Language [cph, fnd]
Maintainer: Marc Kupietz <kupietz@ids-mannheim.de>
Diff between RKorAPClient versions 1.2.0 dated 2025-09-10 and 1.2.1 dated 2025-10-09
DESCRIPTION | 8 MD5 | 10 NEWS.md | 6 R/KorAPQuery.R | 480 +++++++++++--------------------- tests/testthat/test-fetchAnnotations.R | 28 + tests/testthat/test-parse-annotations.R | 47 ++- 6 files changed, 264 insertions(+), 315 deletions(-)
Title: Query 'R' Versions, Including 'r-release' and 'r-oldrel'
Description: Query the main 'R' 'SVN' repository to find the
versions 'r-release' and 'r-oldrel' refer to, and also all previous
'R' versions and their release dates.
Author: Gabor Csardi [aut, cre],
Jeroen Ooms [ctb],
R Consortium [fnd],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between rversions versions 2.1.2 dated 2022-08-31 and 3.0.0 dated 2025-10-09
rversions-2.1.2/rversions/R/keep-head.R |only rversions-2.1.2/rversions/R/nicks.R |only rversions-2.1.2/rversions/R/urls.R |only rversions-3.0.0/rversions/DESCRIPTION | 20 rversions-3.0.0/rversions/MD5 | 213 ++++++ rversions-3.0.0/rversions/NAMESPACE | 14 rversions-3.0.0/rversions/NEWS.md | 18 rversions-3.0.0/rversions/R/api.R |only rversions-3.0.0/rversions/R/available.R |only rversions-3.0.0/rversions/R/compat-vctrs.R |only rversions-3.0.0/rversions/R/current-os.R |only rversions-3.0.0/rversions/R/iso-date.R |only rversions-3.0.0/rversions/R/json.R |only rversions-3.0.0/rversions/R/linux-distros.R |only rversions-3.0.0/rversions/R/macos.R | 25 rversions-3.0.0/rversions/R/platform.R |only rversions-3.0.0/rversions/R/rematch2.R |only rversions-3.0.0/rversions/R/resolve.R |only rversions-3.0.0/rversions/R/rtools-versions.R |only rversions-3.0.0/rversions/R/rversions.R | 90 -- rversions-3.0.0/rversions/R/tarball.R | 14 rversions-3.0.0/rversions/R/utils.R | 27 rversions-3.0.0/rversions/R/win.R | 14 rversions-3.0.0/rversions/README.md | 319 +++++----- rversions-3.0.0/rversions/man/available.Rd |only rversions-3.0.0/rversions/man/current_r_platform.Rd |only rversions-3.0.0/rversions/man/linux_distros.Rd |only rversions-3.0.0/rversions/man/r_oldrel.Rd | 21 rversions-3.0.0/rversions/man/r_release.Rd | 21 rversions-3.0.0/rversions/man/r_release_macos.Rd | 27 rversions-3.0.0/rversions/man/r_release_tarball.Rd | 21 rversions-3.0.0/rversions/man/r_release_win.Rd | 21 rversions-3.0.0/rversions/man/r_versions.Rd | 2 rversions-3.0.0/rversions/man/resolve.Rd |only rversions-3.0.0/rversions/man/rtools_versions.Rd |only rversions-3.0.0/rversions/man/rversions-package.Rd | 1 rversions-3.0.0/rversions/tests/testthat.R | 4 rversions-3.0.0/rversions/tests/testthat/_snaps |only rversions-3.0.0/rversions/tests/testthat/fixtures |only rversions-3.0.0/rversions/tests/testthat/helper-mock.R |only rversions-3.0.0/rversions/tests/testthat/helper-proxy.R |only rversions-3.0.0/rversions/tests/testthat/helper.R |only rversions-3.0.0/rversions/tests/testthat/test-api.R |only rversions-3.0.0/rversions/tests/testthat/test-available.R |only rversions-3.0.0/rversions/tests/testthat/test-linux-distros.R |only rversions-3.0.0/rversions/tests/testthat/test-macos.R |only rversions-3.0.0/rversions/tests/testthat/test-platform.R |only rversions-3.0.0/rversions/tests/testthat/test-resolve.R |only rversions-3.0.0/rversions/tests/testthat/test-rtools-versions.R |only rversions-3.0.0/rversions/tests/testthat/test-rversions.R | 39 - rversions-3.0.0/rversions/tests/testthat/test-tarball.R |only rversions-3.0.0/rversions/tests/testthat/test-utils.R |only rversions-3.0.0/rversions/tests/testthat/test-win.R |only 53 files changed, 614 insertions(+), 297 deletions(-)
Title: Scans R Projects for Vulnerable Third Party Dependencies
Description: Collects a list of your third party R packages, and scans
them with the 'OSS' Index provided by 'Sonatype', reporting back on
any vulnerabilities that are found in the third party packages you
use.
Author: Jeffry Hesse [aut],
Brittany Belle [aut],
Colin Gillespie [aut, cre] ,
Dan Rollo [aut],
Josiah Parry [aut] ,
Sonatype [cph]
Maintainer: Colin Gillespie <csgillespie@gmail.com>
Diff between oysteR versions 0.1.1 dated 2021-01-10 and 0.1.4 dated 2025-10-09
oysteR-0.1.1/oysteR/R/deprecated.R |only oysteR-0.1.1/oysteR/man/audit_deps.Rd |only oysteR-0.1.1/oysteR/tests/testthat/test-get_vulnerabilities.R |only oysteR-0.1.4/oysteR/DESCRIPTION | 57 +--- oysteR-0.1.4/oysteR/MD5 | 44 ++- oysteR-0.1.4/oysteR/NAMESPACE | 5 oysteR-0.1.4/oysteR/NEWS.md | 20 + oysteR-0.1.4/oysteR/R/audit.R | 33 +- oysteR-0.1.4/oysteR/R/cache.R | 24 + oysteR-0.1.4/oysteR/R/call_os_index.R | 123 ++++------ oysteR-0.1.4/oysteR/R/expect_secure.R | 11 oysteR-0.1.4/oysteR/R/file_audits.R | 72 +++++ oysteR-0.1.4/oysteR/R/get_token.R |only oysteR-0.1.4/oysteR/R/get_vulnerabilities.R | 47 ++- oysteR-0.1.4/oysteR/R/print.R | 10 oysteR-0.1.4/oysteR/R/utils.R | 37 ++- oysteR-0.1.4/oysteR/build |only oysteR-0.1.4/oysteR/inst/doc |only oysteR-0.1.4/oysteR/man/audit.Rd | 5 oysteR-0.1.4/oysteR/man/audit_conda.Rd |only oysteR-0.1.4/oysteR/man/audit_installed_r_pkgs.Rd | 5 oysteR-0.1.4/oysteR/tests/testthat/environment.yml |only oysteR-0.1.4/oysteR/tests/testthat/test-audit.R | 10 oysteR-0.1.4/oysteR/tests/testthat/test-audit_pkg.R | 4 oysteR-0.1.4/oysteR/tests/testthat/test-cache.R | 5 oysteR-0.1.4/oysteR/tests/testthat/test-env-yml.R |only oysteR-0.1.4/oysteR/tests/testthat/test-get_token.R |only oysteR-0.1.4/oysteR/vignettes |only 28 files changed, 313 insertions(+), 199 deletions(-)
Title: Generalized Linear Mixed Models using Template Model Builder
Description: Fit linear and generalized linear mixed models with various
extensions, including zero-inflation. The models are fitted using maximum
likelihood estimation via 'TMB' (Template Model Builder). Random effects are
assumed to be Gaussian on the scale of the linear predictor and are integrated
out using the Laplace approximation. Gradients are calculated using automatic
differentiation.
Author: Mollie Brooks [aut, cre] ,
Ben Bolker [aut] ,
Kasper Kristensen [aut],
Martin Maechler [aut] ,
Arni Magnusson [aut] ,
Maeve McGillycuddy [ctb],
Hans Skaug [aut] ,
Anders Nielsen [aut] ,
Casper Berg [aut] ,
Koen van Bentham [aut],
Nafis Sadat [ctb] ,
[...truncated...]
Maintainer: Mollie Brooks <mollieebrooks@gmail.com>
Diff between glmmTMB versions 1.1.12 dated 2025-08-18 and 1.1.13 dated 2025-10-09
DESCRIPTION | 12 +-- MD5 | 70 ++++++++++---------- NAMESPACE | 3 R/denom_df.R |only R/emmeans.R | 66 +++++++++++++++--- R/enum.R | 3 R/family.R | 16 +++- R/glmmTMB.R | 83 ++++++++++++++++++----- R/methods.R | 112 ++++++++++++++++++-------------- inst/NEWS.Rd | 36 +++++++++- inst/doc/covstruct.R | 1 inst/doc/covstruct.html | 37 ++++++---- inst/doc/covstruct.rmd | 6 - inst/doc/glmmTMB.pdf |binary inst/doc/hacking.html | 4 - inst/doc/mcmc.html | 8 +- inst/doc/miscEx.html | 4 - inst/doc/model_evaluation.pdf |binary inst/doc/parallel.html | 4 - inst/doc/priors.R | 7 +- inst/doc/priors.html | 11 +-- inst/doc/priors.rmd | 7 +- inst/doc/sim.html | 6 - inst/doc/troubleshooting.html | 4 - inst/vignette_data/model_evaluation.rda |binary man/dof_KR.Rd |only man/getME.glmmTMB.Rd | 2 man/glmmTMB.Rd | 4 - man/residuals.glmmTMB.Rd | 1 man/summary.glmmTMB.Rd |only src/glmmTMB.cpp | 35 ++++++---- tests/testthat/test-basics.R | 9 +- tests/testthat/test-ddf.R |only tests/testthat/test-downstream.R | 4 - tests/testthat/test-predict.R | 93 ++++++++++++++++++++++++++ tests/testthat/test-varstruc.R | 32 +++++++++ vignettes/covstruct.rmd | 6 - vignettes/priors.rmd | 7 +- 38 files changed, 495 insertions(+), 198 deletions(-)
Title: The P-Model and BiomeE Modelling Framework
Description: Implements the Simulating Optimal FUNctioning framework for
site-scale simulations of ecosystem processes, including model
calibration. It contains 'Fortran 90' modules for the P-model (Stocker
et al. (2020) <doi:10.5194/gmd-13-1545-2020>), SPLASH
(Davis et al. (2017) <doi:10.5194/gmd-10-689-2017>)
and BiomeE (Weng et al. (2015)
<doi:10.5194/bg-12-2655-2015>).
Author: Benjamin Stocker [aut, cre] ,
Koen Hufkens [aut] ,
Josefa Aran Paredes [aut] ,
Laura Marques [ctb] ,
Mayeul Marcadella [ctb] ,
Ensheng Weng [ctb] ,
Fabian Bernhard [aut] ,
Geocomputation and Earth Observation, University of Bern [cph, fnd]
Maintainer: Benjamin Stocker <benjamin.stocker@gmail.com>
Diff between rsofun versions 5.0.0 dated 2024-11-28 and 5.1.0 dated 2025-10-09
rsofun-5.0.0/rsofun/R/init_dates_dataframe.R |only rsofun-5.0.0/rsofun/R/zzz.R |only rsofun-5.0.0/rsofun/src/classdefs.mod.f90 |only rsofun-5.0.0/rsofun/src/datatypes.mod.f90 |only rsofun-5.0.0/rsofun/src/interface_biosphere_biomee.mod.f90 |only rsofun-5.0.0/rsofun/src/params_siml_biomee.mod.f90 |only rsofun-5.0.0/rsofun/src/sofun_r.f90 |only rsofun-5.0.0/rsofun/src/vegetation_biomee.mod.f90 |only rsofun-5.0.0/rsofun/tests/testthat/test-ancillary-functions.R |only rsofun-5.0.0/rsofun/vignettes/files/biomee_use.Rmd__biomee_gs_leuning_output___out.RDS |only rsofun-5.0.0/rsofun/vignettes/files/biomee_use.Rmd__biomee_p_model_output___calibrated_out.RDS |only rsofun-5.0.0/rsofun/vignettes/files/biomee_use.Rmd__biomee_p_model_output___out.RDS |only rsofun-5.1.0/rsofun/DESCRIPTION | 30 rsofun-5.1.0/rsofun/MD5 | 205 - rsofun-5.1.0/rsofun/NAMESPACE | 4 rsofun-5.1.0/rsofun/R/calib_sofun.R | 64 rsofun-5.1.0/rsofun/R/cost_likelihood_biomee.R | 32 rsofun-5.1.0/rsofun/R/cost_likelihood_pmodel.R | 16 rsofun-5.1.0/rsofun/R/cost_rmse_biomee.R | 4 rsofun-5.1.0/rsofun/R/data.R | 211 + rsofun-5.1.0/rsofun/R/luluc.R |only rsofun-5.1.0/rsofun/R/run_biomee_f_bysite.R | 1233 ++++++---- rsofun-5.1.0/rsofun/R/run_pmodel_f_bysite.R | 493 ++- rsofun-5.1.0/rsofun/R/run_pmodel_onestep_f_bysite.R |only rsofun-5.1.0/rsofun/R/runread_biomee_f.R | 141 - rsofun-5.1.0/rsofun/R/runread_pmodel_f.R | 16 rsofun-5.1.0/rsofun/build/vignette.rds |binary rsofun-5.1.0/rsofun/data/biomee_gs_leuning_drivers.rda |binary rsofun-5.1.0/rsofun/data/biomee_gs_leuning_output.rda |binary rsofun-5.1.0/rsofun/data/biomee_p_model_drivers.rda |binary rsofun-5.1.0/rsofun/data/biomee_p_model_luluc_drivers.rda |only rsofun-5.1.0/rsofun/data/biomee_p_model_luluc_output.rda |only rsofun-5.1.0/rsofun/data/biomee_p_model_output.rda |binary rsofun-5.1.0/rsofun/data/p_model_output.rda |binary rsofun-5.1.0/rsofun/data/p_model_output_vcmax25.rda |binary rsofun-5.1.0/rsofun/inst/CITATION | 16 rsofun-5.1.0/rsofun/inst/doc/biomee_luluc.R |only rsofun-5.1.0/rsofun/inst/doc/biomee_luluc.Rmd |only rsofun-5.1.0/rsofun/inst/doc/biomee_luluc.html |only rsofun-5.1.0/rsofun/inst/doc/biomee_use.R | 267 +- rsofun-5.1.0/rsofun/inst/doc/biomee_use.Rmd | 185 + rsofun-5.1.0/rsofun/inst/doc/biomee_use.html | 331 +- rsofun-5.1.0/rsofun/inst/doc/data_format.html | 26 rsofun-5.1.0/rsofun/inst/doc/new_cost_function.R | 395 +-- rsofun-5.1.0/rsofun/inst/doc/new_cost_function.Rmd | 172 + rsofun-5.1.0/rsofun/inst/doc/new_cost_function.html | 568 ++-- rsofun-5.1.0/rsofun/inst/doc/pmodel_use.R | 234 + rsofun-5.1.0/rsofun/inst/doc/pmodel_use.Rmd | 242 + rsofun-5.1.0/rsofun/inst/doc/pmodel_use.html | 320 +- rsofun-5.1.0/rsofun/inst/doc/sensitivity_analysis.R | 619 ++--- rsofun-5.1.0/rsofun/inst/doc/sensitivity_analysis.Rmd | 412 +-- rsofun-5.1.0/rsofun/inst/doc/sensitivity_analysis.html | 545 ++-- rsofun-5.1.0/rsofun/man/biomee_gs_leuning_drivers.Rd | 170 - rsofun-5.1.0/rsofun/man/biomee_gs_leuning_output.Rd | 3 rsofun-5.1.0/rsofun/man/biomee_p_model_drivers.Rd | 2 rsofun-5.1.0/rsofun/man/biomee_p_model_luluc_drivers.Rd |only rsofun-5.1.0/rsofun/man/biomee_p_model_luluc_output.Rd |only rsofun-5.1.0/rsofun/man/biomee_p_model_output.Rd | 3 rsofun-5.1.0/rsofun/man/build_luc_matrix.Rd |only rsofun-5.1.0/rsofun/man/calib_sofun.Rd | 11 rsofun-5.1.0/rsofun/man/cost_likelihood_biomee.Rd | 13 rsofun-5.1.0/rsofun/man/cost_likelihood_pmodel.Rd | 8 rsofun-5.1.0/rsofun/man/cost_rmse_biomee.Rd | 4 rsofun-5.1.0/rsofun/man/init_dates_dataframe.Rd | 2 rsofun-5.1.0/rsofun/man/p_model_drivers.Rd | 8 rsofun-5.1.0/rsofun/man/p_model_output.Rd | 2 rsofun-5.1.0/rsofun/man/p_model_output_vcmax25.Rd | 2 rsofun-5.1.0/rsofun/man/run_biomee_f_bysite.Rd | 261 -- rsofun-5.1.0/rsofun/man/run_pmodel_f_bysite.Rd | 80 rsofun-5.1.0/rsofun/man/run_pmodel_onestep_f_bysite.Rd |only rsofun-5.1.0/rsofun/man/runread_biomee_f.Rd | 34 rsofun-5.1.0/rsofun/man/runread_pmodel_f.Rd | 16 rsofun-5.1.0/rsofun/src/Makevars | 105 rsofun-5.1.0/rsofun/src/aggregated_tile_biomee.mod.f90 |only rsofun-5.1.0/rsofun/src/biosphere_biomee.mod.f90 | 287 -- rsofun-5.1.0/rsofun/src/biosphere_pmodel.mod.f90 | 28 rsofun-5.1.0/rsofun/src/cohort_biomee.mod.f90 |only rsofun-5.1.0/rsofun/src/cohort_linked_list_biomee.mod.f90 |only rsofun-5.1.0/rsofun/src/common_fluxes.mod.f90 |only rsofun-5.1.0/rsofun/src/forcing_siterun_biomee.mod.f90 | 33 rsofun-5.1.0/rsofun/src/forcing_siterun_pmodel.mod.f90 | 33 rsofun-5.1.0/rsofun/src/gpp_biomee.mod.f90 | 311 +- rsofun-5.1.0/rsofun/src/gpp_pmodel.mod.f90 | 194 - rsofun-5.1.0/rsofun/src/grid_siterun.mod.f90 | 117 rsofun-5.1.0/rsofun/src/interface_biosphere_pmodel.mod.f90 | 8 rsofun-5.1.0/rsofun/src/interface_in_biosphere_biomee.mod.f90 |only rsofun-5.1.0/rsofun/src/interface_out_biosphere_biomee.mod.f90 |only rsofun-5.1.0/rsofun/src/lu_tile_biomee.mod.f90 |only rsofun-5.1.0/rsofun/src/main_biomee.mod.f90 |only rsofun-5.1.0/rsofun/src/main_pmodel.mod.f90 |only rsofun-5.1.0/rsofun/src/orgpool.mod.f90 |only rsofun-5.1.0/rsofun/src/params_core.mod.f90 | 168 - rsofun-5.1.0/rsofun/src/params_siml_pmodel.mod.f90 | 2 rsofun-5.1.0/rsofun/src/photosynth_pmodel.mod.f90 | 399 +-- rsofun-5.1.0/rsofun/src/plant_pmodel.mod.f90 | 88 rsofun-5.1.0/rsofun/src/product_pools_biomee.mod.f90 |only rsofun-5.1.0/rsofun/src/sofunutils.mod.f90 | 34 rsofun-5.1.0/rsofun/src/soil_biomee.mod.f90 | 158 - rsofun-5.1.0/rsofun/src/soiltemp_sitch.mod.f90 | 108 rsofun-5.1.0/rsofun/src/tile_pmodel.mod.f90 | 88 rsofun-5.1.0/rsofun/src/track_vegetation_d13c.mod.f90 |only rsofun-5.1.0/rsofun/src/vegetation_processes_biomee.mod.f90 |only rsofun-5.1.0/rsofun/src/vegetation_tile_biomee.mod.f90 |only rsofun-5.1.0/rsofun/src/waterbal_splash.mod.f90 | 8 rsofun-5.1.0/rsofun/src/wrappersc.c | 434 +-- rsofun-5.1.0/rsofun/tests/testthat.R | 10 rsofun-5.1.0/rsofun/tests/testthat/_snaps |only rsofun-5.1.0/rsofun/tests/testthat/helpers.R |only rsofun-5.1.0/rsofun/tests/testthat/test-calibration-biomee.R | 5 rsofun-5.1.0/rsofun/tests/testthat/test-calibration-pmodel.R | 1 rsofun-5.1.0/rsofun/tests/testthat/test-likelihoods.R |only rsofun-5.1.0/rsofun/tests/testthat/test-model-runs-snapshot-biomee.R |only rsofun-5.1.0/rsofun/tests/testthat/test-model-runs.R | 504 +++- rsofun-5.1.0/rsofun/tests/testthat/test-quantitative-validation.R | 2 rsofun-5.1.0/rsofun/vignettes/biomee_luluc.Rmd |only rsofun-5.1.0/rsofun/vignettes/biomee_use.Rmd | 185 + rsofun-5.1.0/rsofun/vignettes/files/biomee_luluc.Rmd__biomee_p_model_luluc_driver.RDS |only rsofun-5.1.0/rsofun/vignettes/files/biomee_use.Rmd__biomee_p_model_output___pars.RDS |only rsofun-5.1.0/rsofun/vignettes/files/biomee_use.Rmd__out.RDS |only rsofun-5.1.0/rsofun/vignettes/files/biomee_use.Rmd__out2.RDS |only rsofun-5.1.0/rsofun/vignettes/files/new_cost_function.Rmd__par_calib_join.RDS |only rsofun-5.1.0/rsofun/vignettes/files/new_cost_function.Rmd__pars_calib_likelihood.RDS |only rsofun-5.1.0/rsofun/vignettes/files/new_cost_function.Rmd__pars_calib_mae.RDS |only rsofun-5.1.0/rsofun/vignettes/files/pmodel_runs.rds |only rsofun-5.1.0/rsofun/vignettes/files/sensitivity_analysis.Rmd__par_calib.RDS |binary rsofun-5.1.0/rsofun/vignettes/new_cost_function.Rmd | 172 + rsofun-5.1.0/rsofun/vignettes/pmodel_use.Rmd | 242 + rsofun-5.1.0/rsofun/vignettes/sensitivity_analysis.Rmd | 412 +-- 128 files changed, 6461 insertions(+), 5075 deletions(-)
Title: Supporting Functions Maintained by Zhen Lu
Description: Miscellaneous functions commonly used by LuLab. This package aims to help more researchers on epidemiology to perform data management and visualization more efficiently.
Author: Zhen Lu [aut, cre]
Maintainer: Zhen Lu <luzh29@mail2.sysu.edu.cn>
Diff between lulab.utils versions 0.0.4 dated 2024-10-07 and 1.0.0 dated 2025-10-09
lulab.utils-0.0.4/lulab.utils/man/Table1.Rd |only lulab.utils-1.0.0/lulab.utils/DESCRIPTION | 20 lulab.utils-1.0.0/lulab.utils/LICENSE |only lulab.utils-1.0.0/lulab.utils/MD5 | 51 - lulab.utils-1.0.0/lulab.utils/NAMESPACE | 5 lulab.utils-1.0.0/lulab.utils/NEWS.md | 8 lulab.utils-1.0.0/lulab.utils/R/SCI_TFL.R | 411 ++++---- lulab.utils-1.0.0/lulab.utils/R/lulab.utils-package.R | 16 lulab.utils-1.0.0/lulab.utils/R/regression_utilities.R |only lulab.utils-1.0.0/lulab.utils/R/utilities.R | 491 +++++----- lulab.utils-1.0.0/lulab.utils/README.md | 42 lulab.utils-1.0.0/lulab.utils/build/vignette.rds |binary lulab.utils-1.0.0/lulab.utils/inst/WORDLIST |only lulab.utils-1.0.0/lulab.utils/inst/doc/lulab_utils.Rmd | 44 lulab.utils-1.0.0/lulab.utils/inst/doc/lulab_utils.html | 3 lulab.utils-1.0.0/lulab.utils/man/check_cha.Rd | 72 - lulab.utils-1.0.0/lulab.utils/man/check_wget.Rd | 50 - lulab.utils-1.0.0/lulab.utils/man/extract_logistic_model.Rd |only lulab.utils-1.0.0/lulab.utils/man/lulab.utils-package.Rd | 2 lulab.utils-1.0.0/lulab.utils/man/round2.Rd |only lulab.utils-1.0.0/lulab.utils/man/test_mirror.Rd | 60 - lulab.utils-1.0.0/lulab.utils/man/use_wget.Rd | 66 - lulab.utils-1.0.0/lulab.utils/tests/spelling.R |only lulab.utils-1.0.0/lulab.utils/tests/testthat.R | 24 lulab.utils-1.0.0/lulab.utils/tests/testthat/test-Table1.R | 51 - lulab.utils-1.0.0/lulab.utils/tests/testthat/test-check_cha.R | 18 lulab.utils-1.0.0/lulab.utils/tests/testthat/test-check_wget.R | 16 lulab.utils-1.0.0/lulab.utils/tests/testthat/test-test_mirror.R | 22 lulab.utils-1.0.0/lulab.utils/tests/testthat/test-use_wget.R | 50 - lulab.utils-1.0.0/lulab.utils/vignettes/lulab_utils.Rmd | 44 30 files changed, 800 insertions(+), 766 deletions(-)
Title: Graphs and Tables for OMOP Results
Description: Provides methods to transform omop_result objects into
formatted tables and figures, facilitating the visualisation of study
results working with the Observational Medical Outcomes Partnership
(OMOP) Common Data Model.
Author: Marti Catala [aut] ,
Nuria Mercade-Besora [aut, cre] ,
Yuchen Guo [ctb] ,
Elin Rowlands [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Edward Burn [ctb]
Maintainer: Nuria Mercade-Besora <nuria.mercadebesora@ndorms.ox.ac.uk>
Diff between visOmopResults versions 1.3.0 dated 2025-10-05 and 1.3.1 dated 2025-10-09
DESCRIPTION | 6 MD5 | 32 - R/plottingThemes.R | 306 +++++++--------- data/data.rda |binary inst/createMockReportData.R | 6 inst/doc/a01_tables.html | 558 ++++++++++++++--------------- inst/doc/a02_plots.R | 2 inst/doc/a02_plots.Rmd | 594 +++++++++++++++---------------- inst/doc/a02_plots.html | 42 +- inst/doc/a03_quarto_reports.R | 3 inst/doc/a03_quarto_reports.Rmd | 541 ++++++++++++++-------------- inst/doc/a03_quarto_reports.html | 12 inst/doc/a04_shiny_apps.Rmd | 738 +++++++++++++++++++-------------------- inst/doc/a04_shiny_apps.html | 29 - vignettes/a02_plots.Rmd | 594 +++++++++++++++---------------- vignettes/a03_quarto_reports.Rmd | 541 ++++++++++++++-------------- vignettes/a04_shiny_apps.Rmd | 738 +++++++++++++++++++-------------------- 17 files changed, 2359 insertions(+), 2383 deletions(-)
More information about visOmopResults at CRAN
Permanent link
Title: Manipulation of Matched Phylogenies and Data using 'data.table'
Description: An implementation that combines trait data and a phylogenetic tree (or trees) into a
single object of class 'treedata.table'. The resulting object can be easily
manipulated to simultaneously change the trait- and tree-level sampling.
Currently implemented functions allow users to use a 'data.table' syntax when
performing operations on the trait dataset within the 'treedata.table' object.
For more details see Roman-Palacios et al. (2021) <doi:10.7717/peerj.12450>.
Author: Josef Uyeda [aut] ,
Cristian Roman-Palacios [aut, cre] ,
April Wright [aut] ,
Luke Harmon [ctb],
Hugo Gruson [rev],
Kari Norman [rev]
Maintainer: Cristian Roman-Palacios <cromanpa@arizona.edu>
This is a re-admission after prior archival of version 0.1.0 dated 2020-09-30
Diff between treedata.table versions 0.1.0 dated 2020-09-30 and 0.1.1 dated 2025-10-09
treedata.table-0.1.0/treedata.table/inst/doc/E_Preprint.R |only treedata.table-0.1.0/treedata.table/inst/doc/E_Preprint.Rmd |only treedata.table-0.1.0/treedata.table/inst/doc/E_Preprint.html |only treedata.table-0.1.0/treedata.table/vignettes/E_Preprint.Rmd |only treedata.table-0.1.0/treedata.table/vignettes/media |only treedata.table-0.1.1/treedata.table/DESCRIPTION | 37 - treedata.table-0.1.1/treedata.table/MD5 | 66 - treedata.table-0.1.1/treedata.table/R/as.treedata.table.R | 30 treedata.table-0.1.1/treedata.table/R/droptreedata.table.R | 6 treedata.table-0.1.1/treedata.table/R/extractVector.R | 4 treedata.table-0.1.1/treedata.table/R/init.R |only treedata.table-0.1.1/treedata.table/R/pulltreedata.table.R | 2 treedata.table-0.1.1/treedata.table/R/tdt.R | 2 treedata.table-0.1.1/treedata.table/R/tdt_methods.R | 4 treedata.table-0.1.1/treedata.table/R/treedata.table.R | 10 treedata.table-0.1.1/treedata.table/build/vignette.rds |binary treedata.table-0.1.1/treedata.table/inst/doc/AA_treedata.table_intro_english.Rmd | 18 treedata.table-0.1.1/treedata.table/inst/doc/AA_treedata.table_intro_english.html | 338 ++++++--- treedata.table-0.1.1/treedata.table/inst/doc/AB_treedata.table_intro_spanish.Rmd | 14 treedata.table-0.1.1/treedata.table/inst/doc/AB_treedata.table_intro_spanish.html | 340 ++++++---- treedata.table-0.1.1/treedata.table/inst/doc/B_multiphylo_treedata.table.Rmd | 10 treedata.table-0.1.1/treedata.table/inst/doc/B_multiphylo_treedata.table.html | 238 ++++--- treedata.table-0.1.1/treedata.table/inst/doc/C_PartialMatching.Rmd | 2 treedata.table-0.1.1/treedata.table/inst/doc/C_PartialMatching.html | 253 ++++--- treedata.table-0.1.1/treedata.table/inst/doc/D_AdditionalFunctions_treedata.table.Rmd | 2 treedata.table-0.1.1/treedata.table/inst/doc/D_AdditionalFunctions_treedata.table.html | 234 ++++-- treedata.table-0.1.1/treedata.table/man/head.treedata.table.Rd | 3 treedata.table-0.1.1/treedata.table/man/sub-.treedata.table.Rd | 7 treedata.table-0.1.1/treedata.table/man/sub-sub-.treedata.table.Rd | 3 treedata.table-0.1.1/treedata.table/man/tail.treedata.table.Rd | 3 treedata.table-0.1.1/treedata.table/tests/testthat/test.treedata.table.R | 12 treedata.table-0.1.1/treedata.table/vignettes/AA_treedata.table_intro_english.Rmd | 18 treedata.table-0.1.1/treedata.table/vignettes/AB_treedata.table_intro_spanish.Rmd | 14 treedata.table-0.1.1/treedata.table/vignettes/B_multiphylo_treedata.table.Rmd | 10 treedata.table-0.1.1/treedata.table/vignettes/C_PartialMatching.Rmd | 2 treedata.table-0.1.1/treedata.table/vignettes/D_AdditionalFunctions_treedata.table.Rmd | 2 36 files changed, 1014 insertions(+), 670 deletions(-)
More information about treedata.table at CRAN
Permanent link
Title: A Unified Data Layer for Large-Scale Single-Cell, Spatial and
Bulk Immunomics
Description: Provides a unified data layer for single-cell, spatial and bulk
T-cell and B-cell immune receptor repertoire data. Think AnnData or SeuratObject,
but for AIRR data, a.k.a. Adaptive Immune Receptor Repertoire, VDJ-seq, RepSeq, or
VDJ sequencing data.
Author: Vadim I. Nazarov [aut, cre]
Maintainer: Vadim I. Nazarov <support@immunomind.com>
Diff between immundata versions 0.0.3 dated 2025-09-04 and 0.0.5 dated 2025-10-09
DESCRIPTION | 17 - MD5 | 33 +- NAMESPACE | 2 R/core_immundata.R | 14 R/io_immundata_write.R | 9 R/operations_external_annotate_seurat.R |only R/operations_utils.R | 2 R/test_utils.R | 9 README.md | 165 +++------- inst/extdata/single_cell/immundata-lb6.csv/annotations.parquet |binary inst/extdata/single_cell/immundata-lb6.csv/metadata.json | 2 inst/extdata/single_cell/immundata-lt6.csv/annotations.parquet |binary inst/extdata/single_cell/immundata-lt6.csv/metadata.json | 2 man/ImmunData.Rd | 4 man/annotate_seurat.Rd |only man/get_test_idata.Rd | 1 man/get_test_immundata.Rd |only man/immundata-package.Rd | 5 man/write_immundata.Rd | 7 19 files changed, 136 insertions(+), 136 deletions(-)
Title: Goodness-of-Fit Testing for Structural Equation Models
Description: Supports eigenvalue block-averaging p-values (Foldnes, Grønneberg, 2018) <doi:10.1080/10705511.2017.1373021>,
penalized eigenvalue block-averaging p-values (Foldnes, Moss, Grønneberg, 2024) <doi:10.1080/10705511.2024.2372028>, penalized
regression p-values (Foldnes, Moss, Grønneberg, 2024) <doi:10.1080/10705511.2024.2372028>, as well as traditional p-values such as Satorra-Bentler. All p-values can
be calculated using unbiased or biased gamma estimates (Du, Bentler, 2022) <doi:10.1080/10705511.2022.2063870>
and two choices of chi square statistics.
Author: Jonas Moss [aut, cre] ,
Njal Foldnes [ctb] ,
Steffen Groenneberg [ctb]
Maintainer: Jonas Moss <jonas.moss.statistics@gmail.com>
This is a re-admission after prior archival of version 0.5.0 dated 2024-01-18
Diff between semTests versions 0.5.0 dated 2024-01-18 and 0.7.1 dated 2025-10-09
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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 3.1 dated 2025-09-05 and 3.2 dated 2025-10-09
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Title: Knock Errors Off Nice Guesses
Description: Miscellaneous functions and data used in psychological research and teaching. Keng
currently has a built-in dataset depress, and could (1) scale a vector; (2) compute the cut-off
values of Pearson's r with known sample size; (3) test the significance and compute the post-hoc
power for Pearson's r with known sample size; (4) conduct a priori power analysis and plan the
sample size for Pearson's r; (5) compare lm()'s fitted outputs using R-squared, f_squared,
post-hoc power, and PRE (Proportional Reduction in Error, also called partial R-squared or
partial Eta-squared); (6) calculate PRE from partial correlation, Cohen's f, or f_squared;
(7) conduct a priori power analysis and plan the sample size for one or a set of predictors in
regression analysis; (8) conduct post-hoc power analysis for one or a set of predictors in
regression analysis with known sample size; (9) randomly pick numbers for Chinese Super Lotto
and Double Color Balls; (10) assess course objective achievement in Outcome- [...truncated...]
Author: Qingyao Zhang [aut, cre]
Maintainer: Qingyao Zhang <qingyaozhang@outlook.com>
Diff between Keng versions 2025.9.1 dated 2025-08-31 and 2025.10.8 dated 2025-10-09
DESCRIPTION | 8 - MD5 | 56 ++++++----- NAMESPACE | 2 NEWS.md | 5 + R/assess_coa.R | 71 +++++++++++--- R/pick_sl.R | 120 ++++++++++++------------ R/power_lm.R | 125 ++++++++----------------- R/power_r.R | 118 +++++++---------------- R/powered_lm.R |only R/powered_r.R |only R/print.Keng_power.R | 8 - README.md | 195 ++++++++++++++++++++------------------- inst/doc/PRE.html | 5 - inst/doc/assessCOA.R | 12 +- inst/doc/assessCOA.Rmd | 6 - inst/doc/assessCOA.html | 121 ++++++++++++------------ inst/doc/commonSampleSizes.html | 23 ---- inst/doc/partialRegression.html | 5 - inst/doc/planSampleSize.html | 14 +- man/assess_coa.Rd | 21 +++- man/pick_sl.Rd | 2 man/power_lm.Rd | 15 --- man/power_r.Rd | 12 -- man/powered_lm.Rd |only man/powered_r.Rd |only tests/testthat/test-assess_coa.R | 26 +++-- tests/testthat/test-power_lm.R | 4 tests/testthat/test-power_r.R | 7 - tests/testthat/test-powered_lm.R |only tests/testthat/test-powered_r.R |only tests/testthat/test-test_r.R | 8 - vignettes/assessCOA.Rmd | 6 - 32 files changed, 471 insertions(+), 524 deletions(-)
Title: Measurement Units for R Vectors
Description: Support for measurement units in R vectors, matrices
and arrays: automatic propagation, conversion, derivation
and simplification of units; raising errors in case of unit
incompatibility. Compatible with the POSIXct, Date and difftime
classes. Uses the UNIDATA udunits library and unit database for
unit compatibility checking and conversion.
Documentation about 'units' is provided in the paper by Pebesma, Mailund &
Hiebert (2016, <doi:10.32614/RJ-2016-061>), included in this package as a
vignette; see 'citation("units")' for details.
Author: Edzer Pebesma [aut, cre] ,
Thomas Mailund [aut],
Tomasz Kalinowski [aut],
James Hiebert [ctb],
Inaki Ucar [aut] ,
Thomas Lin Pedersen [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between units versions 0.8-7 dated 2025-03-11 and 1.0-0 dated 2025-10-09
DESCRIPTION | 15 - MD5 | 77 ++--- NAMESPACE | 9 NEWS.md | 26 + R/RcppExports.R | 4 R/arith.R | 54 +-- R/conversion.R | 6 R/init.R | 2 R/make_units.R | 250 +++++------------ R/options.R | 12 R/scale_units.R | 120 +++++--- R/symbolic_units.R | 106 +++++-- R/tidyverse.R | 4 R/udunits.R | 19 - build/vignette.rds |binary configure | 18 - inst/doc/measurement_units_in_R.html | 17 - inst/doc/units.R | 1 inst/doc/units.Rmd | 1 inst/doc/units.html | 126 ++++---- man/convert_to_base.Rd |only man/matrixOps.units.Rd |only man/scale_units.Rd | 48 ++- man/udunits2.Rd | 12 man/units.Rd | 64 +--- man/units_options.Rd | 6 src/RcppExports.cpp | 38 -- src/tokenizer.cpp |only src/udunits.cpp | 50 +-- tests/testthat/_snaps/plot/ggplot2-other-alpha.svg |only tests/testthat/_snaps/plot/ggplot2-other-color.svg |only tests/testthat/_snaps/plot/ggplot2-other-fill.svg |only tests/testthat/_snaps/plot/ggplot2-other-linewidth.svg |only tests/testthat/_snaps/plot/ggplot2-other-radius.svg |only tests/testthat/_snaps/plot/ggplot2-other-size-area.svg |only tests/testthat/_snaps/plot/ggplot2-other-size.svg |only tests/testthat/_snaps/plot/ggplot2-range.svg |only tests/testthat/_snaps/tidyverse.md | 11 tests/testthat/test_arith.R | 11 tests/testthat/test_plot.R | 57 +++ tests/testthat/test_symbolic_units.R | 29 + tests/testthat/test_tidyverse.R | 4 tests/testthat/test_udunits.R | 8 tests/testthat/test_unit_creation.R | 87 ++--- vignettes/units.Rmd | 1 45 files changed, 715 insertions(+), 578 deletions(-)
Title: Minimization Methods for Ill-Conditioned Problems
Description: Implementation of methods for minimizing ill-conditioned problems. Currently only includes regularized (quasi-)newton optimization (Kanzow and Steck et al. (2023), <doi:10.1007/s12532-023-00238-4>).
Author: Bert van der Veen [aut, cre]
Maintainer: Bert van der Veen <bert_van_der_veen@hotmail.com>
Diff between minic versions 1.0.2 dated 2025-06-05 and 1.0.3 dated 2025-10-09
DESCRIPTION | 8 +-- MD5 | 8 +-- NEWS.md | 8 +++ README.md | 2 src/minic.cpp | 148 +++++++++++++++++++++++++++++++++++----------------------- 5 files changed, 107 insertions(+), 67 deletions(-)
Title: Tidy and Streamlined Metabolomics Data Workflows
Description: Facilitate tasks typically encountered during metabolomics data analysis including data import, filtering, missing value imputation (Stacklies et al. (2007) <doi:10.1093/bioinformatics/btm069>, Stekhoven et al. (2012) <doi:10.1093/bioinformatics/btr597>, Tibshirani et al. (2017) <doi:10.18129/B9.BIOC.IMPUTE>, Troyanskaya et al. (2001) <doi:10.1093/bioinformatics/17.6.520>), normalization (Bolstad et al. (2003) <doi:10.1093/bioinformatics/19.2.185>, Dieterle et al. (2006) <doi:10.1021/ac051632c>, Zhao et al. (2020) <doi:10.1038/s41598-020-72664-6>) transformation, centering and scaling (Van Den Berg et al. (2006) <doi:10.1186/1471-2164-7-142>) as well as statistical tests and plotting. 'metamorphr' introduces a tidy (Wickham et al. (2019) <doi:10.21105/joss.01686>) format for metabolomics data and is designed to make it easier to build elaborate analysis workflows and to integrate them with 'tidyverse' packages including 'dplyr' and [...truncated...]
Author: Yannik Schermer [aut, cre, cph]
Maintainer: Yannik Schermer <yannik.schermer@chem.rptu.de>
Diff between metamorphr versions 0.1.1 dated 2025-09-01 and 0.2.0 dated 2025-10-09
DESCRIPTION | 8 MD5 | 35 ++-- NAMESPACE | 4 NEWS.md | 10 + R/data.R | 24 ++ R/internal_functions.R | 45 +++++ R/misc.R | 194 ++++++++++++++++++++++++ R/sysdata.rda |binary README.md | 6 data/atoms.rda |only inst/doc/conjugate-screening.html | 4 man/atoms.Rd |only man/calc_km.Rd |only man/calc_kmd.Rd |only man/calc_nominal_km.Rd |only man/figures/functions.svg | 2 man/figures/logo.png |only man/formula_to_mass.Rd |only man/metamorphr-package.Rd | 4 tests/testthat/test-calc_kmd.R |only tests/testthat/test-formula_to_mass.R |only tests/testthat/test-impute_knn.R | 2 tests/testthat/test-normalize_quantile_smooth.R | 4 23 files changed, 319 insertions(+), 23 deletions(-)
Title: Matrix Functions for Teaching and Learning Linear Algebra and
Multivariate Statistics
Description: A collection of matrix functions for teaching and learning matrix
linear algebra as used in multivariate statistical methods. Many of these functions are
designed for tutorial purposes in learning matrix algebra ideas using R. In some
cases, functions are provided for concepts available elsewhere in R, but where
the function call or name is not obvious. In other cases, functions are provided
to show or demonstrate an algorithm. In addition, a collection of functions are
provided for drawing vector diagrams in 2D and 3D and for rendering matrix
expressions and equations in LaTeX.
Author: Michael Friendly [aut, cre] ,
John Fox [aut] ,
Phil Chalmers [aut] ,
Georges Monette [ctb] ,
Gaston Sanchez [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between matlib versions 1.0.0 dated 2024-10-02 and 1.0.1 dated 2025-10-09
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Title: Client for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@lamin.ai>
Diff between laminr versions 1.1.1 dated 2025-05-15 and 1.2.0 dated 2025-10-09
laminr-1.1.1/laminr/man/lamin_connect.Rd |only laminr-1.1.1/laminr/man/lamin_delete.Rd |only laminr-1.1.1/laminr/man/lamin_disconnect.Rd |only laminr-1.1.1/laminr/man/lamin_init.Rd |only laminr-1.1.1/laminr/man/lamin_login.Rd |only laminr-1.1.1/laminr/man/lamin_logout.Rd |only laminr-1.1.1/laminr/man/lamin_save.Rd |only laminr-1.2.0/laminr/DESCRIPTION | 18 laminr-1.2.0/laminr/MD5 | 61 - laminr-1.2.0/laminr/NAMESPACE | 9 laminr-1.2.0/laminr/R/Registry.R | 22 laminr-1.2.0/laminr/R/checks.R | 19 laminr-1.2.0/laminr/R/file_loaders.R | 18 laminr-1.2.0/laminr/R/file_openers.R | 8 laminr-1.2.0/laminr/R/import.R | 27 laminr-1.2.0/laminr/R/lamin_cli.R | 428 +++++++---- laminr-1.2.0/laminr/R/lamindb.R | 108 +- laminr-1.2.0/laminr/R/laminr-package.R | 4 laminr-1.2.0/laminr/R/packages.R | 96 +- laminr-1.2.0/laminr/R/require.R | 115 ++ laminr-1.2.0/laminr/R/reticulate-utils.R | 46 + laminr-1.2.0/laminr/R/status.R |only laminr-1.2.0/laminr/R/temporary-instance.R |only laminr-1.2.0/laminr/R/ui.R | 16 laminr-1.2.0/laminr/R/utils.R | 136 ++- laminr-1.2.0/laminr/R/zzz.R | 2 laminr-1.2.0/laminr/build/vignette.rds |binary laminr-1.2.0/laminr/man/get_current_lamin_instance.Rd | 2 laminr-1.2.0/laminr/man/get_current_lamin_settings.Rd |only laminr-1.2.0/laminr/man/get_current_lamin_user.Rd | 2 laminr-1.2.0/laminr/man/import_module.Rd | 4 laminr-1.2.0/laminr/man/lamin_cli.Rd |only laminr-1.2.0/laminr/man/laminr_status.Rd |only laminr-1.2.0/laminr/man/require_module.Rd | 7 laminr-1.2.0/laminr/man/use_temporary_instance.Rd |only laminr-1.2.0/laminr/tests/testthat/setup.R | 33 laminr-1.2.0/laminr/tests/testthat/test-file_loaders.R | 29 laminr-1.2.0/laminr/tests/testthat/test-status.R |only laminr-1.2.0/laminr/tests/testthat/test-temporary-instance.R |only 39 files changed, 884 insertions(+), 326 deletions(-)
Title: Check Color Palettes for Problems with Color Vision Deficiency
Description: Compare color palettes with simulations of color vision deficiencies - deuteranopia, protanopia, and tritanopia.
It includes calculation of distances between colors, and creating summaries of differences between a color palette and simulations of color vision deficiencies.
This work was inspired by the blog post at <https://www.datawrapper.de/blog/colorblind-check>.
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between colorblindcheck versions 1.0.2 dated 2023-05-13 and 1.0.4 dated 2025-10-09
DESCRIPTION | 13 +++--- MD5 | 32 +++++++++------- NAMESPACE | 1 R/palette_plot.R | 44 ++++++++++++++++++---- README.md | 16 ++------ build/vignette.rds |binary inst/doc/intro-to-colorblindcheck.R | 4 +- inst/doc/intro-to-colorblindcheck.Rmd | 2 - inst/doc/intro-to-colorblindcheck.html | 62 +++++++++++++++---------------- man/colorblindcheck-package.Rd | 4 +- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/logo.png |only man/palette_bivariate_plot.Rd | 8 +++- man/palette_plot.Rd | 5 ++ tests/testthat/_snaps |only tests/testthat/test-plot.R | 7 +++ vignettes/intro-to-colorblindcheck.Rmd | 2 - 17 files changed, 123 insertions(+), 77 deletions(-)
More information about colorblindcheck at CRAN
Permanent link
Title: 'StreamCatTools'
Description: Tools for using the 'StreamCat' and 'LakeCat' API and
interacting with the 'StreamCat' and 'LakeCat' database.
Convenience functions in the package wrap the API for 'StreamCat'
on <https://api.epa.gov/StreamCat/streams/metrics>.
Author: Marc Weber [aut, cre],
Ryan Hill [ctb],
Travis Hudson [ctb],
Allen Brookes [ctb],
David Rebhuhn [ctb],
Michael Dumelle [ctb],
Zachary Smith [ctb]
Maintainer: Marc Weber <weber.marc@epa.gov>
Diff between StreamCatTools versions 0.7.0 dated 2025-09-15 and 0.8.0 dated 2025-10-09
DESCRIPTION | 13 ++- MD5 | 60 +++++++++-------- NAMESPACE | 2 NEWS.md | 9 ++ R/lc_get_comid.R | 2 R/lc_get_data.R | 22 ++++-- R/lc_get_params.R | 117 +++++++++++++++++++++++++++++++-- R/sc_get_comid.R | 9 +- R/sc_get_data.R | 24 +++++- R/sc_get_params.R | 124 +++++++++++++++++++++++++++++++++--- README.md | 3 inst/doc/Applications.html | 4 - inst/doc/Introduction.R | 2 inst/doc/Introduction.Rmd | 2 inst/doc/Introduction.html | 2 inst/doc/LakeCat.R | 2 inst/doc/LakeCat.Rmd | 2 inst/doc/LakeCat.html | 14 ++-- man/lc_get_comid.Rd | 2 man/lc_get_data.Rd | 2 man/lc_get_metric_names.Rd |only man/lc_get_params.Rd | 8 +- man/lc_nlcd.Rd | 2 man/sc_get_comid.Rd | 5 - man/sc_get_data.Rd | 2 man/sc_get_metric_names.Rd |only man/sc_get_params.Rd | 9 +- man/sc_nlcd.Rd | 2 tests/testthat/test-lc_get_params.R | 24 +++--- tests/testthat/test-sc_get_params.R | 33 +++++++++ vignettes/Introduction.Rmd | 2 vignettes/LakeCat.Rmd | 2 32 files changed, 393 insertions(+), 113 deletions(-)
More information about StreamCatTools at CRAN
Permanent link
Title: Work with Open Road Traffic Casualty Data from Great Britain
Description: Work with and download road traffic casualty data from Great
Britain. Enables access to the UK's official road safety statistics,
'STATS19'. Enables users to specify a download directory for the data,
which can be set permanently by adding `STATS19_DOWNLOAD_DIRECTORY=/path/to/a/dir`
to your `.Renviron` file, which can be opened with `usethis::edit_r_environ()`.
The data is provided as a series of `.csv` files.
This package downloads, reads-in and formats the data, making it suitable
for analysis. See the stats19 vignette for details. Data available from
1979 to 2024. See the official data series at
<https://www.data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-accidents-safety-data>.
The package is described in a paper in the Journal of Open Source Software
(Lovelace et al. 2019) <doi:10.21105/joss.01181>.
See
Gilardi et al. (2022) <doi:10.1111/rssa.12823>,
Vidal-Tortosa et al. (2021) <doi:10.1016/j.jth.2021.101291>,
Tait et al. (2023) <doi:10.101 [...truncated...]
Author: Robin Lovelace [aut, cre] ,
Malcolm Morgan [aut] ,
Layik Hama [aut] ,
Mark Padgham [aut] ,
David Ranzolin [rev],
Adam Sparks [rev, ctb] ,
Ivo Wengraf [ctb],
RAC Foundation [fnd],
Blaise Kelly [aut]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stats19 versions 3.3.1 dated 2025-01-15 and 3.4.0 dated 2025-10-09
DESCRIPTION | 61 MD5 | 62 NAMESPACE | 1 NEWS.md | 12 R/adjustments.R | 7 R/dl.R | 35 R/format.R | 2 R/get.R | 24 R/read.R | 12 R/utils.R | 71 build/vignette.rds |binary data/file_names.rda |binary data/stats19_schema.rda |binary data/stats19_variables.rda |binary inst/doc/blog.html | 8 inst/doc/factsheet.R |only inst/doc/factsheet.Rmd |only inst/doc/factsheet.html |only inst/doc/stats19-training-setup.html | 4 inst/doc/stats19-training.html | 23 inst/doc/stats19-vehicles.html | 4 inst/doc/stats19.R | 25 inst/doc/stats19.Rmd | 35 inst/doc/stats19.html |10145 +++++++++++++++++++++++++++++++++-- man/dl_stats19.Rd | 13 man/find_file_name.Rd | 1 man/get_data_directory.Rd | 7 man/get_stats19.Rd | 19 man/get_stats19_adjustments.Rd | 2 man/get_url.Rd | 2 man/read_collisions.Rd | 8 man/read_vehicles.Rd | 4 vignettes/factsheet.Rmd |only vignettes/stats19.Rmd | 35 34 files changed, 9983 insertions(+), 639 deletions(-)
Title: Statistical Modeling
Description: A collection of algorithms and functions to aid statistical modeling. Includes limiting dilution analysis (aka ELDA), growth curve comparisons, mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Also includes advanced generalized linear model functions including Tweedie and Digamma distributional families, secure convergence and exact distributional calculations for unit deviances.
Author: Gordon Smyth [cre, aut],
Lizhong Chen [aut],
Yifang Hu [ctb],
Peter Dunn [ctb],
Belinda Phipson [ctb],
Yunshun Chen [ctb]
Maintainer: Gordon Smyth <smyth@wehi.edu.au>
Diff between statmod versions 1.5.0 dated 2023-01-06 and 1.5.1 dated 2025-10-09
DESCRIPTION | 34 +++++++-- MD5 | 12 +-- build/partial.rdb |binary inst/CITATION | 180 ++++++++++++++++++++++++++---------------------- inst/NEWS | 6 + man/expectedDeviance.Rd | 19 ++++- man/glmscoretest.Rd | 2 7 files changed, 160 insertions(+), 93 deletions(-)
Title: Sparsity by Worst-Case Quadratic Penalties
Description: Fits classical sparse regression models with
efficient active set algorithms by solving quadratic problems as described by
Grandvalet, Chiquet and Ambroise (2017) <doi:10.48550/arXiv.1210.2077>. Also provides a few
methods for model selection purpose (cross-validation, stability selection).
Author: Julien Chiquet [aut, cre]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between quadrupen versions 0.2-12 dated 2024-06-25 and 0.2-13 dated 2025-10-09
DESCRIPTION | 13 +-- MD5 | 34 ++++---- NEWS.md | 6 + R/crossval-class.R | 12 +-- R/crossval.R | 4 - R/init.R | 2 R/quadrupen-class.R | 4 - R/stability-class.R | 8 +- R/stability.R | 4 - build/partial.rdb |binary demo/quad_breg.R | 2 inst/WORDLIST | 8 -- man/crossval.Rd | 4 - man/stability.Rd | 4 - src/Makevars | 4 - src/Makevars.win | 6 - src/elastic_net.cpp | 208 ++++++++++++++++++++++++++-------------------------- src/quadratic.cpp | 6 - 18 files changed, 168 insertions(+), 161 deletions(-)
Title: Lightweight Reproducible Reporting
Description: Distributed reproducible computing framework, adopting
ideas from git, docker and other software. By defining a
lightweight interface around the inputs and outputs of an
analysis, a lot of the repetitive work for reproducible research
can be automated. We define a simple format for organising and
describing work that facilitates collaborative reproducible
research and acknowledges that all analyses are run multiple times
over their lifespans.
Author: Rich FitzJohn [aut, cre],
Robert Ashton [aut],
Martin Eden [aut],
Alex Hill [aut],
Wes Hinsley [aut],
Mantra Kusumgar [aut],
Paul Lietar [aut],
James Thompson [aut],
Katy Gaythorpe [aut],
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between orderly versions 1.4.3 dated 2021-09-22 and 2.0.0 dated 2025-10-09
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Title: Genome Polarization via Diagnostic Index Expectation
Maximization
Description: Implements a likelihood-based method for genome polarization, identifying
which alleles of SNV markers belong to either side of a barrier to gene flow. The
approach co-estimates individual assignment, barrier strength, and divergence between
sides, with direct application to studies of hybridization. Includes VCF-to-diem
conversion and input checks, support for mixed ploidy and parallelization, and tools
for visualization and diagnostic outputs. Based on diagnostic index expectation
maximization as described in Baird et al. (2023) <doi:10.1111/2041-210X.14010>.
Author: Natalia Martinkova [aut, cre] ,
Stuart Baird [aut]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Diff between diemr versions 1.5 dated 2025-09-11 and 1.5.1 dated 2025-10-09
DESCRIPTION | 24 +- MD5 | 50 +++-- NAMESPACE | 1 NEWS.md | 10 + R/ModelOfDiagnostic.r | 3 R/diem.r | 26 +- R/emPolarise.r | 6 R/extdata.r | 29 +-- R/hybridIndex.r |only R/importPolarized.r | 54 +++--- R/pHetErrOnStateCount.r | 7 R/plotDeFinetti.r | 24 +- R/plotMarkerAxis.r | 40 ++-- R/plotPolarized.r | 14 - R/rank2map.r | 6 R/smoothPolarizedGenotypes.r | 5 R/variantSites.r | 20 +- R/vcf2diem.r | 87 ++++++---- README.md |only inst/doc/Importing-data-for-genome-polarisation.html | 4 inst/doc/Understanding-genome-polarisation-output-files.html | 4 inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.html | 4 man/hybridIndex.Rd |only man/rank2map.Rd | 2 man/smoothPolarizedGenotypes.Rd | 7 man/variantSites.Rd | 6 man/vcf2diem.Rd | 29 ++- tests/testthat/test_hybridIndex.r |only 28 files changed, 259 insertions(+), 203 deletions(-)
Title: Bootstrap for State Space Models
Description: Provides a streamlined and user-friendly framework for
bootstrapping in state space models, particularly when the number of
subjects/units (n) exceeds one, a scenario commonly encountered in
social and behavioral sciences. The parametric bootstrap implemented
here was developed and applied in Pesigan, Russell, and Chow (2025)
<doi:10.1037/met0000779>.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph] ,
Michael A. Russell [ctb] ,
Sy-Miin Chow [ctb]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between bootStateSpace versions 1.0.2 dated 2025-02-14 and 1.0.3 dated 2025-10-09
DESCRIPTION | 43 ++++++++++++++++++++++----------- MD5 | 12 ++++----- NEWS.md | 6 ++++ R/bootStateSpace-methods.R | 54 +++++++++++++++++++++++------------------- build/partial.rdb |binary inst/CITATION | 38 ++++++++++++++++++----------- man/bootStateSpace-package.Rd | 8 +++++- 7 files changed, 102 insertions(+), 59 deletions(-)
More information about bootStateSpace at CRAN
Permanent link
More information about CopernicusClimate at CRAN
Permanent link
Title: Weibull Analysis for Reliability Engineering
Description: Life data analysis in the graphical tradition of Waloddi Weibull. Methods derived from Robert B. Abernethy (2008, ISBN 0-965306-3-2), Wayne Nelson (1982, ISBN: 9780471094586), William Q. Meeker and Lois A. Escobar (1998, ISBN: 1-471-14328-6), John I. McCool, (2012, ISBN: 9781118217986).
Author: David Silkworth [aut],
Jurgen Symynck [aut],
Jacob Ormerod [cre],
OpenReliability.org [cph]
Maintainer: Jacob Ormerod <jake@openreliability.org>
Diff between WeibullR versions 1.2.1 dated 2022-06-25 and 1.2.4 dated 2025-10-09
WeibullR-1.2.1/WeibullR/README.md |only WeibullR-1.2.4/WeibullR/DESCRIPTION | 9 ++---- WeibullR-1.2.4/WeibullR/MD5 | 13 ++++----- WeibullR-1.2.4/WeibullR/R/plot.wblr.R | 18 ++++++------ WeibullR-1.2.4/WeibullR/man/options.wblr.Rd | 22 +++++++-------- WeibullR-1.2.4/WeibullR/man/wblr.Rd | 40 ++++++++++++++++------------ WeibullR-1.2.4/WeibullR/man/wblr.conf.Rd | 16 +++++------ WeibullR-1.2.4/WeibullR/src/Makevars | 1 8 files changed, 61 insertions(+), 58 deletions(-)
Title: 'Rcpp' Integration for 'CGAL'
Description: Creates a header only package to link to the 'CGAL'
(Computational Geometry Algorithms Library)
header files in 'Rcpp'. There are a variety of potential uses for
the software such as Hilbert sorting, K-D Tree nearest neighbors,
and convex hull algorithms. For more information about how to use the header files,
see the 'CGAL' documentation at <https://www.cgal.org>. Currently
downloads version 6.1 of the 'CGAL' header files.
Author: Eric Dunipace [aut, cre] ,
Tyler Morgan-Wall [ctb],
The CGAL Project [cph]
Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>
Diff between RcppCGAL versions 6.0.1 dated 2025-01-08 and 6.1 dated 2025-10-09
DESCRIPTION | 19 +-- MD5 | 18 +- NEWS.md | 4 R/zzz.R | 2 build/vignette.rds |binary inst/AUTHORS | 225 ++++++++++++++++++++---------------- inst/doc/Installation.html | 9 - inst/include/CGAL_zip.tar.xz |binary man/RcppCGAL-package.Rd | 2 tools/config/downloader_functions.R | 113 +++++++++++++++++- 10 files changed, 269 insertions(+), 123 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 4.1.0 dated 2025-08-29 and 4.1.1 dated 2025-10-09
DESCRIPTION | 8 MD5 | 72 ++++---- NAMESPACE | 14 + NEWS.md | 30 +++ R/addCwres.R | 2 R/augPred.R | 6 R/broom.R | 18 +- R/cov.R | 2 R/focei.R | 5 R/foceiControl.R | 20 ++ R/iov.R | 329 +++++++++++++++++++++++++++++++++++++-- R/mix.R |only R/nlmixr2Keywords.R | 1 R/nlmixr2_md5.R | 2 R/nmObjGet.R | 37 +++- R/nmObjGetEtaMat.R |only R/ofv.R | 2 R/preProcessZeroOmega.R | 77 +++++++++ R/print.R | 22 ++ R/saem.R | 2 R/saemControl.R | 5 R/simulate.R | 20 +- R/vpc.R | 17 +- R/zzz.R | 14 + data/nlmixr2Keywords.rda |binary man/dot-downgradeEtas.Rd |only man/dot-iniS3.Rd |only man/foceiControl.Rd | 16 + man/nlmixr2.Rd | 87 +++++----- man/nlmixr2Keywords.Rd | 1 man/nlmixr2iovLogvarCv.Rd |only man/rmEta.Rd |only man/rmdhunks/nlmixr2Keywords.Rmd | 3 man/saemControl.Rd | 16 + src/Makevars.in | 2 src/inner.cpp | 10 - src/scale.h | 7 tests/testthat/test-augpred.R | 33 +++ tests/testthat/test-iov.R | 58 ++++++ tests/testthat/test-mix.R |only tests/testthat/test-piping.R |only 41 files changed, 804 insertions(+), 134 deletions(-)
Title: Estimation and Prediction Methods for High-Dimensional Mixed
Frequency Time Series Data
Description: The 'midasml' package implements estimation and prediction methods for high-dimensional mixed-frequency (MIDAS) time-series and panel data regression models. The regularized MIDAS models are estimated using orthogonal (e.g. Legendre) polynomials and sparse-group LASSO (sg-LASSO) estimator. For more information on the 'midasml' approach see Babii, Ghysels, and Striaukas (2021, JBES forthcoming) <doi:10.1080/07350015.2021.1899933>. The package is equipped with the fast implementation of the sg-LASSO estimator by means of proximal block coordinate descent. High-dimensional mixed frequency time-series data can also be easily manipulated with functions provided in the package.
Author: Jonas Striaukas [cre, aut],
Andrii Babii [aut],
Jad Beyhum [aut],
Eric Ghysels [aut],
Alex Kostrov [ctb]
Maintainer: Jonas Striaukas <jonas.striaukas@gmail.com>
Diff between midasml versions 0.1.10 dated 2022-04-29 and 0.1.11 dated 2025-10-09
DESCRIPTION | 11 +++++++---- MD5 | 10 +++++++--- NAMESPACE | 7 ++++--- R/fa.sglfit.R |only R/predict.fa.sglfit.R |only man/fa.sglfit.Rd |only man/midasml-package.Rd | 7 +++++++ man/predict.fa.sglfit.Rd |only 8 files changed, 25 insertions(+), 10 deletions(-)
Title: Generalized Random Forests
Description: Forest-based statistical estimation and inference.
GRF provides non-parametric methods for heterogeneous treatment effects estimation
(optionally using right-censored outcomes, multiple treatment arms or outcomes, or instrumental variables),
as well as least-squares regression, quantile regression, and survival regression,
all with support for missing covariates.
Author: Julie Tibshirani [aut],
Susan Athey [aut],
Rina Friedberg [ctb],
Vitor Hadad [ctb],
David Hirshberg [ctb],
Luke Miner [ctb],
Erik Sverdrup [aut, cre],
Stefan Wager [aut],
Marvin Wright [ctb]
Maintainer: Erik Sverdrup <erik.sverdrup@monash.edu>
Diff between grf versions 2.4.0 dated 2024-11-15 and 2.5.0 dated 2025-10-09
DESCRIPTION | 8 - MD5 | 68 +++++----- R/RcppExports.R | 4 R/causal_survival_forest.R | 4 R/lm_forest.R | 28 +--- R/rank_average_treatment.R | 2 R/survival_forest.R | 10 + man/causal_survival_forest.Rd | 4 man/lm_forest.Rd | 14 -- man/predict.lm_forest.Rd | 14 -- man/rank_average_treatment_effect.Rd | 2 man/survival_forest.Rd | 9 + src/RcppExports.cpp | 9 - src/SurvivalForestBindings.cpp | 3 src/src/forest/ForestTrainers.cpp | 4 src/src/forest/ForestTrainers.h | 2 src/src/splitting/AcceleratedSurvivalSplittingRule.cpp |only src/src/splitting/AcceleratedSurvivalSplittingRule.h |only src/src/splitting/SurvivalSplittingRule.cpp | 10 - src/src/splitting/SurvivalSplittingRule.h | 4 src/src/splitting/factory/CausalSurvivalSplittingRuleFactory.cpp | 3 src/src/splitting/factory/CausalSurvivalSplittingRuleFactory.h | 1 src/src/splitting/factory/InstrumentalSplittingRuleFactory.cpp | 1 src/src/splitting/factory/InstrumentalSplittingRuleFactory.h | 1 src/src/splitting/factory/MultiCausalSplittingRuleFactory.cpp | 1 src/src/splitting/factory/MultiCausalSplittingRuleFactory.h | 1 src/src/splitting/factory/MultiRegressionSplittingRuleFactory.cpp | 1 src/src/splitting/factory/MultiRegressionSplittingRuleFactory.h | 1 src/src/splitting/factory/ProbabilitySplittingRuleFactory.cpp | 1 src/src/splitting/factory/ProbabilitySplittingRuleFactory.h | 1 src/src/splitting/factory/RegressionSplittingRuleFactory.cpp | 1 src/src/splitting/factory/RegressionSplittingRuleFactory.h | 1 src/src/splitting/factory/SplittingRuleFactory.h | 1 src/src/splitting/factory/SurvivalSplittingRuleFactory.cpp | 10 + src/src/splitting/factory/SurvivalSplittingRuleFactory.h | 7 - src/src/tree/TreeTrainer.cpp | 2 36 files changed, 132 insertions(+), 101 deletions(-)
Title: Generate Fully-Sequential Space-Filling Designs Inside a Unit
Hypercube
Description: Provides three methods to generate fully-sequential space-filling designs inside a unit hypercube. A 'fully-sequential space-filling design' means a sequence of nested designs (as the design size varies from one point up to some maximum number of points) with the design points added one at a time and such that the design at each size has good space-filling properties. Two methods target the minimum pairwise distance criterion and generate maximin designs, among which one method is more efficient when design size is large. One method targets the maximum hole size criterion and uses a heuristic to generate what is closer to a minimax design.
Author: Boyang Shang [aut, cre],
Daniel W. Apley [aut]
Maintainer: Boyang Shang <boyangshang2015@u.northwestern.edu>
Diff between FSSF versions 0.1.1 dated 2020-02-05 and 0.1.2 dated 2025-10-09
DESCRIPTION | 21 ++++++++++++++------- MD5 | 12 ++++++------ man/FSSF_b.Rd | 2 +- src/Makevars | 2 -- src/Makevars.win | 2 -- src/RcppExports.cpp | 5 +++++ src/kd_split.cpp | 6 +++--- 7 files changed, 29 insertions(+), 21 deletions(-)
Title: Data Analysis and Graphics Data and Functions
Description: Functions and data sets used in examples and exercises in the
text Maindonald, J.H. and Braun, W.J. (2003, 2007, 2010) "Data
Analysis and Graphics Using R", and in an upcoming Maindonald,
Braun, and Andrews text that builds on this earlier text.
Author: John H Maindonald [aut],
W. John Braun [aut, cre]
Maintainer: W. John Braun <john.braun@ubc.ca>
Diff between DAAG versions 1.25.6 dated 2024-05-26 and 1.25.7 dated 2025-10-09
DESCRIPTION | 19 +++++-- MD5 | 26 +++++----- build/vignette.rds |binary inst/doc/simulate-regdiags.R | 42 ++++++++-------- inst/doc/simulate-regdiags.html | 101 ++++++++++++++++++++++----------------- inst/doc/simulate-varselect.R | 12 ++-- inst/doc/simulate-varselect.html | 65 +++++++++++++++---------- man/DAAGtheme.Rd | 11 ++-- man/greatLakes.Rd | 4 - man/hotspots.Rd | 2 man/hurricNamed.Rd | 4 - man/nassCDS.Rd | 1 man/nasshead.Rd | 1 man/zzDAAGxdb.Rd | 2 14 files changed, 164 insertions(+), 126 deletions(-)
Title: Cluster Analysis via Random Partition Distributions
Description: Cluster analysis is performed using pairwise distance information and a random partition distribution. The method is
implemented for two random partition distributions. It draws samples and then obtains and plots clustering estimates.
An implementation of a selection algorithm is provided for the mass parameter of the partition distribution. Since
pairwise distances are the principal input to this procedure, it is most comparable to the hierarchical and k-medoids
clustering methods. The method is Dahl, Andros, Carter (2022+) <doi:10.1002/sam.11602>.
Author: David B. Dahl [aut, cre] ,
R. Jacob Andros [aut] ,
J. Brandon Carter [aut] ,
Alex Crichton [ctb] ,
Brendan Zabarauskas [ctb] ,
David B. Dahl [ctb] ,
David Tolnay [ctb] ,
Jim Turner [ctb] ,
Jorge Aparicio [ctb] ,
Josh Stone [ctb] ,
Mikhail Vorotilov [ [...truncated...]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between caviarpd versions 0.3.20 dated 2025-06-02 and 0.3.21 dated 2025-10-09
DESCRIPTION | 10 ++--- MD5 | 22 +++++------ NEWS | 4 ++ src/rust/epa/src/clust.rs | 4 +- src/rust/epa/src/epa.rs | 2 - src/rust/rbindings/src/lib.rs | 5 ++ src/rust/roxido/Cargo.lock | 8 ++-- src/rust/roxido/src/lib.rs | 78 ++++++++++++++++++++++++++++++++++++--- src/rust/roxido_macro/Cargo.lock | 8 ++-- src/rust/roxido_macro/src/lib.rs | 4 +- src/rust/vendor.tar.gz |binary tools/build_rust_library.R | 3 + 12 files changed, 112 insertions(+), 36 deletions(-)