Title: Interactive Overlays on 'shiny' Plots
Description: Provides rectangular elements that can be dragged and resized over
plots in 'shiny' apps. This may be useful in applications where users need
to mark regions on the plot for further input or processing.
Author: Nick Davies [aut, cre, cph]
Maintainer: Nick Davies <nicholas.davies@lshtm.ac.uk>
Diff between overshiny versions 0.1.0 dated 2025-07-22 and 0.1.1 dated 2025-08-28
overshiny-0.1.0/overshiny/inst/www/overshiny.css |only overshiny-0.1.1/overshiny/DESCRIPTION | 10 overshiny-0.1.1/overshiny/MD5 | 26 + overshiny-0.1.1/overshiny/NAMESPACE | 1 overshiny-0.1.1/overshiny/NEWS.md | 6 overshiny-0.1.1/overshiny/R/panel.R | 64 ++++ overshiny-0.1.1/overshiny/R/ui.R | 34 +- overshiny-0.1.1/overshiny/README.md | 8 overshiny-0.1.1/overshiny/inst/doc/overshiny.R | 264 +++++++++---------- overshiny-0.1.1/overshiny/inst/doc/overshiny.Rmd | 101 ++++++- overshiny-0.1.1/overshiny/inst/doc/overshiny.html | 304 +++++++++++++--------- overshiny-0.1.1/overshiny/inst/www/overshiny |only overshiny-0.1.1/overshiny/man/remargin.Rd |only overshiny-0.1.1/overshiny/man/useOverlay.Rd | 17 - overshiny-0.1.1/overshiny/vignettes/overshiny.Rmd | 101 ++++++- 15 files changed, 629 insertions(+), 307 deletions(-)
Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Description: A DBI-compatible interface to ODBC databases.
Author: Jim Hester [aut],
Hadley Wickham [aut, cre],
Oliver Gjoneski [aut],
Simon Couch [aut],
lexicalunit [cph] ,
Google Inc. [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between odbc versions 1.6.1 dated 2025-03-27 and 1.6.2 dated 2025-08-28
DESCRIPTION | 8 MD5 | 58 - NEWS.md | 22 R/dbi-driver.R | 5 R/dbi-result.R | 18 R/driver-databricks.R | 5 R/driver-db2.R | 6 R/driver-snowflake.R | 9 R/driver-sql-server.R | 16 R/odbc-connection.R | 24 R/odbc-package.R | 2 R/utils.R | 48 - build/vignette.rds |binary inst/doc/benchmarks.html | 5 inst/doc/develop.html | 5 inst/doc/setup.html | 5 man/SQLServer.Rd | 17 src/cctz/Makefile | 1 src/cctz/include/time_zone.h | 7 src/cctz/src/time_zone_fixed.cc |only src/cctz/src/time_zone_fixed.h |only src/cctz/src/time_zone_lookup.cc | 11 src/nanodbc/nanodbc.cpp | 1192 ++++++++++++++++++++++++++++++-- src/nanodbc/nanodbc.h | 269 +++++++ src/odbc_result.cpp | 418 +++++++---- src/odbc_result.h | 127 ++- src/r_types.h | 1 src/utils.cpp | 39 - tests/testthat/_snaps/utils.md | 8 tests/testthat/test-driver-sql-server.R | 86 ++ tests/testthat/test-utils.R | 29 31 files changed, 2145 insertions(+), 296 deletions(-)
Title: The Tidymodels Extension for Time Series Modeling
Description: The time series forecasting framework for use with the 'tidymodels' ecosystem.
Models include ARIMA, Exponential Smoothing, and additional time series models
from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition"
(<https://otexts.com/fpp2/>).
Refer to "Prophet: forecasting at scale"
(<https://research.facebook.com/blog/2017/02/prophet-forecasting-at-scale/>.).
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime versions 1.3.1 dated 2024-10-22 and 1.3.2 dated 2025-08-28
DESCRIPTION | 8 MD5 | 67 ++++---- NEWS.md | 7 R/parsnip-arima_boost.R | 9 - R/utils-calc-accuracy.R |only R/utils-control-par.R | 181 ++++++++++++++-------- R/yardstick-metric-sets.R | 213 +++++++++++--------------- inst/doc/getting-started-with-modeltime.html | 124 +++++++-------- man/Adam_predict_impl.Rd | 2 man/Arima_predict_impl.Rd | 2 man/Auto_adam_predict_impl.Rd | 2 man/arima_boost.Rd | 9 - man/arima_xgboost_predict_impl.Rd | 2 man/croston_predict_impl.Rd | 2 man/ets_predict_impl.Rd | 2 man/maape.Rd | 21 ++ man/maape_vec.Rd | 17 +- man/metric_sets.Rd | 15 - man/naive_predict_impl.Rd | 2 man/nnetar_predict_impl.Rd | 2 man/parallel_start.Rd | 45 +++-- man/prophet_predict_impl.Rd | 2 man/prophet_xgboost_predict_impl.Rd | 2 man/smooth_predict_impl.Rd | 2 man/snaive_predict_impl.Rd | 2 man/stlm_arima_predict_impl.Rd | 2 man/stlm_ets_predict_impl.Rd | 2 man/summarize_accuracy_metrics.Rd | 33 ++-- man/tbats_predict_impl.Rd | 2 man/temporal_hier_predict_impl.Rd | 2 man/theta_predict_impl.Rd | 2 man/window_function_predict_impl.Rd | 2 tests/testthat/test-algo-adam_reg-Adam.R | 129 +++++++-------- tests/testthat/test-algo-adam_reg-auto_adam.R | 127 ++++++--------- tests/testthat/test-tune_workflows.R | 9 - 35 files changed, 532 insertions(+), 518 deletions(-)
Title: Sensitivity Analyses for Unmeasured Confounding and Other Biases
in Observational Studies and Meta-Analyses
Description: Conducts sensitivity analyses for unmeasured confounding, selection bias, and measurement error (individually or in combination; VanderWeele & Ding (2017) <doi:10.7326/M16-2607>; Smith & VanderWeele (2019) <doi:10.1097/EDE.0000000000001032>; VanderWeele & Li (2019) <doi:10.1093/aje/kwz133>; Smith, Mathur, & VanderWeele (2021) <doi:10.1097/EDE.0000000000001380>). Also conducts sensitivity analyses for unmeasured confounding in meta-analyses (Mathur & VanderWeele (2020a) <doi:10.1080/01621459.2018.1529598>; Mathur & VanderWeele (2020b) <doi:10.1097/EDE.0000000000001180>) and for additive measures of effect modification (Mathur et al., <doi:10.1093/ije/dyac073>).
Author: Maya B. Mathur [cre, aut],
Louisa H. Smith [aut],
Peng Ding [aut],
Tyler J. VanderWeele [aut]
Maintainer: Maya B. Mathur <mmathur@stanford.edu>
Diff between EValue versions 4.1.3 dated 2021-10-28 and 4.1.4 dated 2025-08-28
DESCRIPTION | 16 - MD5 | 34 +-- R/biases.R | 2 R/multi_bound.R | 2 R/multi_evalue.R | 4 build/vignette.rds |binary inst/CITATION | 18 - inst/doc/meta-analysis.R | 2 inst/doc/meta-analysis.html | 228 +++++++++++++-------- inst/doc/multiple-bias-examples.R | 2 inst/doc/multiple-bias-examples.html | 198 +++++++++++-------- inst/doc/multiple-bias.R | 6 inst/doc/multiple-bias.html | 364 ++++++++++++++++++++++++----------- inst/doc/selection-bias.R | 2 inst/doc/selection-bias.html | 135 ++++++------ inst/doc/unmeasured-confounding.R | 2 inst/doc/unmeasured-confounding.html | 217 ++++++++++++-------- man/multi_bias.Rd | 2 18 files changed, 759 insertions(+), 475 deletions(-)
Title: Compute and Plot Zonohedra from Vector Generators
Description: Computes a zonohedron from real vector generators. The package also computes zonogons (2D zonotopes) and zonosegs (1D zonotopes). An elementary S3 class for matroids is included, which supports matroids with rank 3, 2, and 1. Optimization methods are taken from Heckbert (1985) <https://www.cs.cmu.edu/~ph/zono.ps.gz>.
Author: Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between zonohedra versions 0.4-0 dated 2025-01-31 and 0.5-0 dated 2025-08-28
DESCRIPTION | 17 MD5 | 112 ++--- NAMESPACE | 4 NEWS.md | 13 R/matroid.R | 30 - R/trans2.R | 40 +- R/utils.R | 35 + R/zonogon.R | 47 +- R/zonohedron.R | 416 ++++++++++++++++++-- README.md |only build/vignette.rds |binary inst/doc/matroids.html | 20 - inst/doc/raytrace.html | 35 - inst/doc/transitions.html | 34 - inst/doc/zonohedra-guide.R | 37 + inst/doc/zonohedra-guide.Rmd | 100 ++++- inst/doc/zonohedra-guide.html | 837 ++++++++++++++++++++++++++++++++++++++---- inst/doc/zonotopes.html | 28 - man/boundarypgramdata.Rd | 2 man/genlist.Rd | 3 man/inside.Rd | 2 man/inside2trans.Rd | 4 man/invertboundary.Rd | 2 man/lintransform.Rd | 2 man/matroid-getters.Rd | 2 man/matroid-props.Rd | 2 man/matroid.Rd | 2 man/minkowskisum.Rd | 2 man/plot2trans.Rd | 2 man/plothighertrans.Rd | 2 man/plotpolygon.Rd | 2 man/raytrace2trans.Rd | 2 man/section2trans.Rd | 2 man/simplify.Rd | 6 man/transitionsdf.Rd | 4 man/zonogon-getmetrics.Rd | 4 man/zonogon-invert.Rd | 4 man/zonogon-plot.Rd | 6 man/zonogon-raytrace.Rd | 2 man/zonogon-section.Rd | 10 man/zonogon.Rd | 4 man/zonohedron-as.mesh3d.Rd |only man/zonohedron-plot.Rd | 4 man/zonohedron-raytrace.Rd | 1 man/zonohedron-section.Rd | 6 man/zonohedron.Rd | 4 man/zonoseg-invert.Rd | 8 man/zonoseg.Rd | 10 man/zonotope-getters.Rd | 2 man/zonotope-props.Rd | 2 src/dupAtomMatHash.cpp | 292 +++++++------- src/flVecMap.cpp |only src/flVecMap.h |only src/init.c | 14 src/matroid.c | 111 +++-- src/nanotimer_windows.h |only src/rcSetHash.h | 120 +++--- src/rcVec.h | 23 - tests/test-mesh3d.R |only vignettes/zonohedra-guide.Rmd | 100 ++++- 60 files changed, 1897 insertions(+), 678 deletions(-)
Title: Generate Analysis Results Programmes Using ARS Metadata
Description: Analysis Results Standard (ARS), a foundational standard by CDISC
(Clinical Data Interchange Standards Consortium), provides a logical
data model for metadata describing all components to calculate Analysis Results.
<https://www.cdisc.org/standards/foundational/analysis-results-standard>
Using 'siera' package, ARS metadata is ingested (JSON or Excel format),
producing programmes to generate Analysis Results Datasets (ARDs).
Author: Malan Bosman [aut, cre],
Clymb Clinical [cph, fnd]
Maintainer: Malan Bosman <malanbos@gmail.com>
Diff between siera versions 0.5.2 dated 2025-08-25 and 0.5.3 dated 2025-08-28
DESCRIPTION | 6 - MD5 | 12 +- NEWS.md | 46 ++++++----- R/readARS.R | 171 +++++++++++++++++++++++++++++++++--------- README.md | 2 inst/doc/Getting_started.html | 2 man/ARD_script_example.Rd | 44 +++++----- 7 files changed, 196 insertions(+), 87 deletions(-)
Title: Implementation of Several Phenotype-Based Family Genetic Risk
Scores
Description: Implementation of several phenotype-based family genetic risk scores
with unified input data and data preparation functions to help facilitate
the required data preparation and management. The implemented family genetic
risk scores are the extended liability threshold model conditional on family history
from Pedersen (2022) <doi:10.1016/j.ajhg.2022.01.009> and Pedersen (2023) <https://www.nature.com/articles/s41467-023-41210-z>,
Pearson-Aitken Family Genetic Risk Scores from Krebs (2024) <doi:10.1016/j.ajhg.2024.09.009>,
and family genetic risk score from Kendler (2021) <doi:10.1001/jamapsychiatry.2021.0336>.
Author: Emil Michael Pedersen [aut, cre],
Jette Steinbach [aut],
Lucas Rasmussen [ctb],
Morten Dybdahl Krebs [aut]
Maintainer: Emil Michael Pedersen <emp@ph.au.dk>
This is a re-admission after prior archival of version 1.0.0 dated 2025-07-07
Diff between LTFGRS versions 1.0.0 dated 2025-07-07 and 1.0.1 dated 2025-08-28
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- README.md | 4 ++-- inst/doc/LTFGRS_workflow_prediction.html | 12 ++++++------ man/LTFGRS-package.Rd | 2 +- tests/testthat/test-Gibbs-sampler.R | 2 ++ 6 files changed, 22 insertions(+), 20 deletions(-)
Title: Hierarchical Model of Species Communities
Description: Hierarchical Modelling of Species Communities (HMSC) is
a model-based approach for analyzing community ecological data.
This package implements it in the Bayesian framework with Gibbs
Markov chain Monte Carlo (MCMC) sampling (Tikhonov et al. (2020)
<doi:10.1111/2041-210X.13345>).
Author: Gleb Tikhonov [aut],
Otso Ovaskainen [aut, cre] ,
Jari Oksanen [aut],
Melinda de Jonge [aut],
Oystein Opedal [aut],
Tad Dallas [aut]
Maintainer: Otso Ovaskainen <otso.t.ovaskainen@jyu.fi>
Diff between Hmsc versions 3.0-13 dated 2022-08-11 and 3.3-7 dated 2025-08-28
DESCRIPTION | 15 MD5 | 118 ++-- NAMESPACE | 19 R/Hmsc.R | 26 - R/HmscRandomLevel.R | 12 R/biPlot.R | 4 R/c.Hmsc.R | 4 R/computeDataParameters.R | 457 ++++++++++-------- R/computeInitialParameters.R | 17 R/computePredictedValues.R | 10 R/computePredictor.HmscRandomLevel.R |only R/computeSAIR.R |only R/computeVariancePartitioning.R | 16 R/computeWAIC.R | 5 R/coralCombine.R |only R/coralGetRareSpeciesPriors.R |only R/coralGetXDataExt.R |only R/coralPlotBeta.R |only R/coralPredict.R |only R/coralPreprocess.R |only R/coralSplitToBatches.R |only R/coralTrain.R |only R/getPostEstimate.R | 2 R/importPosteriorFromHPC.R |only R/plotBeta.R | 12 R/plotGamma.R | 6 R/plotVariancePartitioning.R | 2 R/predict.R | 94 ++- R/prepareGradient.R | 4 R/print.Hmsc.R | 4 R/sampleMcmc.R | 743 +++++++++++++++++------------- R/updateBetaLambda.R | 6 R/updateBetaSel.R | 20 R/updateEta.R | 25 - R/updateGamma2.R | 8 R/updateGammaEta.R | 47 - R/updateGammaV.R | 2 R/updateInvSigma.R | 8 R/updateZ.R | 8 R/updatewRRR.R | 13 R/utils.R |only README.md | 7 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.md | 24 inst/doc/vignette_1_univariate.pdf |binary inst/doc/vignette_2_multivariate_low.pdf |binary inst/doc/vignette_3_multivariate_high.pdf |binary inst/doc/vignette_4_spatial.pdf |binary inst/doc/vignette_5_performance.pdf |binary man/Hmsc.Rd | 13 man/biPlot.Rd | 2 man/computeDataParameters.Rd | 5 man/computeInitialParameters.Rd | 6 man/computeSAIR.Rd |only man/coralCombine.Rd |only man/coralGetRareSpeciesPriors.Rd |only man/coralGetXDataExt.Rd |only man/coralPlotBeta.Rd |only man/coralPredict.Rd |only man/coralPreprocess.Rd |only man/coralSplitToBatches.Rd |only man/coralTrain.Rd |only man/importPosteriorFromHPC.Rd |only man/plotBeta.Rd | 6 man/plotGamma.Rd | 6 man/predict.Hmsc.Rd | 17 man/sampleMcmc.Rd | 11 tests/Examples/Hmsc-Ex.Rout.save | 81 ++- tests/testthat/test-initialParameters.R | 3 tests/testthat/test-sampling.R | 14 71 files changed, 1127 insertions(+), 775 deletions(-)
Title: Multivariate Analysis with Optimal Scaling
Description: Implements various Gifi methods in a user-friendly way: categorical principal component analysis (princals), multiple correspondence analysis (homals), monotone regression analysis (morals).
Author: Patrick Mair [aut, cre],
Jan De Leeuw [aut],
Patrick J. F. Groenen [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between Gifi versions 0.4-0 dated 2022-10-03 and 1.0-0 dated 2025-08-28
DESCRIPTION | 13 +++++++------ MD5 | 34 ++++++++++++++++++++++++++-------- R/princals.R | 5 +---- build |only inst/NEWS.Rd | 10 ++++++++-- inst/doc |only man/homals.Rd | 2 +- man/morals.Rd | 2 +- man/plot.homals.Rd | 4 +--- man/plot.princals.Rd | 11 +---------- man/princals.Rd | 4 ++-- vignettes |only 12 files changed, 48 insertions(+), 37 deletions(-)
Title: A 'shiny' App for Reproducible QA/QC of Eddy Covariance Data
Description: An interactive 'shiny'-based tool for exploration and quality
assurance and quality control (QA/QC) of eddy covariance flux tower
data processing. It generates data-point removal code via
user-directed selection from a scatterplot, and can export a cleaned
.csv with removed points set to NA plus an R script for
reproducibility. Reference: Key (2025) <DOI:10.5281/zenodo.15597159>.
Author: Kesondra Key [aut, cre]
Maintainer: Kesondra Key <keyke@iu.edu>
Diff between fluxtools versions 0.6.0 dated 2025-08-27 and 0.6.2 dated 2025-08-28
DESCRIPTION | 8 - MD5 | 9 +- R/zzz-deps.R |only README.md | 6 - inst/app/app.R | 183 +++++++++++++++++++++++++-------------------- inst/doc/introduction.html | 6 - 6 files changed, 120 insertions(+), 92 deletions(-)
Title: Confidence and Consistency of Predictive Distribution Models
Description: Calculate confidence and consistency that measure the
goodness-of-fit and transferability of predictive/potential distribution
models (including species distribution models) as described by Somodi &
Bede-Fazekas et al. (2024) <doi:10.1016/j.ecolmodel.2024.110667>.
Author: Akos Bede-Fazekas [aut, cre] ,
Imelda Somodi [aut] ,
Zoltan Botta-Dukat [ctb]
Maintainer: Akos Bede-Fazekas <bfakos@ecolres.hu>
This is a re-admission after prior archival of version 0.3.1 dated 2024-03-17
Diff between confcons versions 0.3.1 dated 2024-03-17 and 0.3.2 dated 2025-08-28
DESCRIPTION | 19 - MD5 | 24 - NEWS.md | 5 README.md | 5 inst/doc/introduction_to_confcons.R | 58 +++- inst/doc/introduction_to_confcons.Rmd | 73 ++++- inst/doc/introduction_to_confcons.html | 462 +++++++++++++++++++-------------- tests/testthat.R | 13 tests/testthat/test_confidence.R | 134 ++++----- tests/testthat/test_consistence.R | 68 ++-- tests/testthat/test_measures.R | 210 +++++++-------- tests/testthat/test_thresholds.R | 102 +++---- vignettes/introduction_to_confcons.Rmd | 73 ++++- 13 files changed, 768 insertions(+), 478 deletions(-)
Title: Simulate, Evaluate, and Analyze Dose Finding Trials with
Bayesian MCPMod
Description: Bayesian MCPMod (Fleischer et al. (2022)
<doi:10.1002/pst.2193>) is an innovative method that improves the
traditional MCPMod by systematically incorporating historical data,
such as previous placebo group data. This R package offers functions
for simulating, analyzing, and evaluating Bayesian MCPMod trials with
normally distributed endpoints. It enables the assessment of trial
designs incorporating historical data across various true
dose-response relationships and sample sizes. Robust mixture prior
distributions, such as those derived with the Meta-Analytic-Predictive
approach (Schmidli et al. (2014) <doi:10.1111/biom.12242>), can be
specified for each dose group. Resulting mixture posterior
distributions are used in the Bayesian Multiple Comparison Procedure
and modeling steps. The modeling step also includes a weighted model
averaging approach (Pinheiro et al. (2014) <doi:10.1002/sim.6052>).
Estimated dose-response relationships can be bootstrapped and
visualize [...truncated...]
Author: Boehringer Ingelheim Pharma GmbH & Co. KG [cph, fnd],
Stephan Wojciekowski [aut, cre],
Lars Andersen [aut],
Jonas Schick [ctb],
Sebastian Bossert [aut]
Maintainer: Stephan Wojciekowski <stephan.wojciekowski@boehringer-ingelheim.com>
Diff between BayesianMCPMod versions 1.1.0 dated 2025-03-07 and 1.2.0 dated 2025-08-28
DESCRIPTION | 18 - MD5 | 70 ++-- NEWS.md | 48 +- R/BMCPMod.R | 623 ++++++++++++++++++++---------------- R/bootstrapping.R | 85 +++- R/modeling.R | 163 ++++++--- R/plot.R | 30 - R/posterior.R | 307 ++++++++--------- R/s3methods.R | 96 +++-- build/vignette.rds |binary inst/WORDLIST | 44 +- inst/doc/Simulation_Comparison.html | 6 inst/doc/Simulation_Example.R | 8 inst/doc/Simulation_Example.Rmd | 10 inst/doc/Simulation_Example.html | 7 inst/doc/analysis_normal.R | 31 - inst/doc/analysis_normal.Rmd | 34 + inst/doc/analysis_normal.html | 131 +++---- man/assessDesign.Rd | 6 man/getBootstrapQuantiles.Rd | 2 man/getBootstrapSamples.Rd | 2 man/getContr.Rd | 18 - man/getCritProb.Rd | 8 man/getMED.Rd | 2 man/getModelFits.Rd | 5 man/getPosterior.Rd | 11 man/performBayesianMCP.Rd | 8 man/performBayesianMCPMod.Rd | 12 tests/testthat/setup.R | 312 ++++++++++++++++-- tests/testthat/test-BMCPMod.R | 177 +++++----- tests/testthat/test-modelling.R | 2 tests/testthat/test-plot.R | 1 tests/testthat/test-posterior.R | 39 +- tests/testthat/test-s3methods.R | 47 +- vignettes/Simulation_Example.Rmd | 10 vignettes/analysis_normal.Rmd | 34 + 36 files changed, 1466 insertions(+), 941 deletions(-)
More information about BayesianMCPMod at CRAN
Permanent link
Title: Choice of Omega in the BAC Algorithm
Description: The Bayesian Adjustment for Confounding (BAC) algorithm (Wang et al., 2012)
can be used to estimate the causal effect of a continuous exposure on a continuous outcome.
This package provides an approximate sensitivity analysis of BAC with regards to the
hyperparameter omega. BACprior also provides functions to guide the user in their choice
of an appropriate omega value. The method is based on Lefebvre, Atherton and Talbot (2014).
Author: Denis Talbot [aut, cre] ,
Genevieve Lefebvre [aut] ,
Juli Atherton [aut]
Maintainer: Denis Talbot <denis.talbot@fmed.ulaval.ca>
Diff between BACprior versions 2.1.1 dated 2023-10-10 and 2.1.2 dated 2025-08-28
ChangeLog | 3 ++ DESCRIPTION | 21 +++++++++++--- MD5 | 8 ++--- man/BACprior-package.Rd | 68 ++++++++++++++++++++++++------------------------ man/BACprior.lm.Rd | 2 - 5 files changed, 58 insertions(+), 44 deletions(-)
Title: Perform Inference on Algorithm-Agnostic Variable Importance
Description: Calculate point estimates of and valid confidence intervals for
nonparametric, algorithm-agnostic variable importance measures in high and low dimensions,
using flexible estimators of the underlying regression functions. For more information
about the methods, please see Williamson et al. (Biometrics, 2020), Williamson et al. (JASA, 2021), and Williamson and Feng (ICML, 2020).
Author: Brian D. Williamson [aut, cre] ,
Jean Feng [ctb],
Charlie Wolock [ctb],
Noah Simon [ths] ,
Marco Carone [ths]
Maintainer: Brian D. Williamson <brian.d.williamson@kp.org>
Diff between vimp versions 2.3.5 dated 2025-07-23 and 2.3.6 dated 2025-08-28
DESCRIPTION | 6 MD5 | 44 +-- NEWS.md | 10 R/est_predictiveness.R | 7 R/est_predictiveness_cv.R | 7 R/estimate_type_predictiveness.R | 12 R/measure_ppv.R | 16 - R/measure_sensitivity.R | 8 inst/doc/introduction-to-vimp.html | 6 inst/doc/ipcw-vim.html | 4 inst/doc/precomputed-regressions.html | 4 inst/doc/types-of-vims.html | 4 tests/testthat/test-average_vim.R | 26 +- tests/testthat/test-avg_value.R | 2 tests/testthat/test-binary_outcomes.R | 19 + tests/testthat/test-bootstrap.R | 152 +++++------ tests/testthat/test-continuous_outcomes.R | 2 tests/testthat/test-cv_vim.R | 8 tests/testthat/test-ipcw.R | 338 +++++++------------------- tests/testthat/test-merge_vim.R | 2 tests/testthat/test-predictiveness_measures.R | 4 tests/testthat/test-sp_vim.R | 12 tests/testthat/test-vim.R | 4 23 files changed, 299 insertions(+), 398 deletions(-)
Title: Test Analysis Modules
Description: Includes marginal maximum likelihood estimation and joint maximum
likelihood estimation for unidimensional and multidimensional
item response models. The package functionality covers the
Rasch model, 2PL model, 3PL model, generalized partial credit model,
multi-faceted Rasch model, nominal item response model,
structured latent class model, mixture distribution IRT models,
and located latent class models. Latent regression models and
plausible value imputation are also supported. For details see
Adams, Wilson and Wang, 1997 <doi:10.1177/0146621697211001>,
Adams, Wilson and Wu, 1997 <doi:10.3102/10769986022001047>,
Formann, 1982 <doi:10.1002/bimj.4710240209>,
Formann, 1992 <doi:10.1080/01621459.1992.10475229>.
Author: Alexander Robitzsch [aut, cre] ,
Thomas Kiefer [aut],
Margaret Wu [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between TAM versions 4.2-21 dated 2024-02-19 and 4.3-25 dated 2025-08-28
DESCRIPTION | 27 +++- MD5 | 104 +++++++++--------- R/DescribeBy.R | 7 - R/IRT.cv.R | 4 R/IRT.informationCurve.R | 8 - R/IRT.linearCFA.R | 23 ++- R/RcppExports.R | 2 R/Scale.R | 10 - R/add.colnames.resp.R | 4 R/anova.tam.R | 21 +-- R/change.grep.lavpartable.R | 12 +- R/extend.label.group.R | 14 +- R/tam.jml.R | 14 +- R/tam.linking.R | 12 +- R/tam.mml.2pl.R | 2 R/tam.mml.wle2.R | 3 R/tam_irf_3pl.R | 2 R/tam_jml_version1.R | 41 +++---- R/tam_jml_wle.R | 22 ++- R/tam_linking_2studies.R | 42 ++++--- R/tam_linking_2studies_create_M_SD.R | 18 +-- R/tam_linking_2studies_create_M_SD_rownames.R | 9 - R/tam_linking_chain.R | 31 ++--- R/tam_linking_extract_list.R | 4 R/tam_linking_extract_parameters.R | 5 R/tam_linking_extract_parameters_trait_distribution.R | 13 +- R/tam_linking_function_haebara_loss.R | 12 +- R/tam_linking_include_list.R | 4 R/tam_linking_irf_discrepancy.R | 10 - R/tam_linking_joint.R | 44 +++---- R/tam_linking_joint_calc_probs.R | 4 R/tam_linking_output_summary.R | 22 +-- R/tam_linking_transform_item_parameters.R | 8 - R/tam_mml_2pl_mstep_slope.R | 16 +- R/tamcat.R | 7 - R/weighted_quantile.R | 8 - R/weighted_quantile_type_selection.R | 5 R/weighted_table.R | 11 + R/weighted_var.R | 4 build/partial.rdb |binary inst/CITATION | 3 inst/NEWS | 14 ++ man/IRT.residuals.Rd | 7 - man/IRT.threshold.Rd | 19 +-- man/tam.jml.Rd | 42 ++++++- man/tam.linking.Rd | 7 - man/tam.wle.Rd | 5 src/RcppExports.cpp | 2 src/init.c | 2 src/tam_rcpp_calc_exp.cpp | 5 src/tam_rcpp_calc_prob.cpp | 7 - src/tam_rcpp_calc_suff_stat.cpp | 11 - src/tam_rcpp_ctt.cpp | 8 - 53 files changed, 422 insertions(+), 319 deletions(-)
Title: Fast and Robust Multi-Scale Graph Clustering
Description: A graph community detection algorithm that aims to be performant
on large graphs and robust, returning consistent results across runs.
SpeakEasy 2 (SE2), the underlying algorithm, is described in Chris Gaiteri,
David R. Connell & Faraz A. Sultan et al. (2023)
<doi:10.1186/s13059-023-03062-0>. The core algorithm is written in 'C',
providing speed and keeping the memory requirements low. This implementation
can take advantage of multiple computing cores without increasing memory
usage. SE2 can detect community structure across scales, making it a good
choice for biological data, which often has hierarchical structure. Graphs
can be passed to the algorithm as adjacency matrices using base 'R'
matrices, the 'Matrix' library, 'igraph' graphs, or any data that can be
coerced into a matrix.
Author: David Connell [aut, cre, cph] ,
Chris Gaiteri [cph] ,
Gabor Csardi [cph, ctb] ,
Tamas Nepusz [cph, ctb] ,
Szabolcs Horvat [cph, ctb] ,
Vincent Traag [cph, ctb] ,
Fabio Zanini [cph, ctb] ,
Daniel Noom [cph, ctb] ,
The igraph development team [cph] ,
F [...truncated...]
Maintainer: David Connell <david32@dcon.addy.io>
Diff between speakeasyR versions 0.1.5 dated 2025-04-03 and 0.1.6 dated 2025-08-28
speakeasyR-0.1.5/speakeasyR/src/se2/vendor/igraph/CODE_OF_CONDUCT.md |only speakeasyR-0.1.6/speakeasyR/DESCRIPTION | 9 speakeasyR-0.1.6/speakeasyR/MD5 | 221 ++++---- speakeasyR-0.1.6/speakeasyR/NEWS.md | 6 speakeasyR-0.1.6/speakeasyR/configure | 18 speakeasyR-0.1.6/speakeasyR/configure.ac | 2 speakeasyR-0.1.6/speakeasyR/inst/doc/speakeasyR.html | 17 speakeasyR-0.1.6/speakeasyR/src/include/igraph_version.h | 4 speakeasyR-0.1.6/speakeasyR/src/se2/CMakeLists.txt | 39 + speakeasyR-0.1.6/speakeasyR/src/se2/benchmarks |only speakeasyR-0.1.6/speakeasyR/src/se2/src/speakeasy2/se2_core.c | 8 speakeasyR-0.1.6/speakeasyR/src/se2/src/speakeasy2/se2_knn_graph.c | 32 - speakeasyR-0.1.6/speakeasyR/src/se2/src/speakeasy2/se2_label.c | 52 +- speakeasyR-0.1.6/speakeasyR/src/se2/src/speakeasy2/se2_order_nodes.c | 4 speakeasyR-0.1.6/speakeasyR/src/se2/src/speakeasy2/se2_partitions.c | 68 +- speakeasyR-0.1.6/speakeasyR/src/se2/src/speakeasy2/se2_partitions.h | 3 speakeasyR-0.1.6/speakeasyR/src/se2/src/speakeasy2/se2_random.c | 6 speakeasyR-0.1.6/speakeasyR/src/se2/src/speakeasy2/se2_random.h | 1 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/CMakeLists.txt | 16 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/CHANGELOG.md | 98 +++ speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/CONTRIBUTING.md | 10 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/CONTRIBUTORS.md | 176 +++---- speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/CONTRIBUTORS.txt | 6 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph.h | 5 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_adjlist.h | 5 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_arpack.h | 3 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_array_pmt.h | 20 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_attributes.h | 1 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_bitset.h | 3 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_bitset_list.h | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_constants.h | 11 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_cycles.h | 59 ++ speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_decls.h | 20 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_error.h | 29 - speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_interface.h | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_microscopic_update.h | 8 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_motifs.h | 8 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_operators.h | 4 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_random.h | 7 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_statusbar.h | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_structural.h | 15 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_strvector.h | 4 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_types.h | 4 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_vector_list.h | 6 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/include/igraph_vector_pmt.h | 41 + speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/community/community_misc.c | 65 +- speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/community/edge_betweenness.c | 18 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/community/leading_eigenvector.c | 21 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/community/leiden.c | 40 + speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/community/louvain.c | 40 + speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/community/modularity.c | 89 +-- speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/community/optimal_modularity.c | 28 - speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/community/spinglass/NetDataTypes.h | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/community/spinglass/clustertool.cpp | 9 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/community/spinglass/pottsmodel_2.cpp | 8 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/community/voronoi.c | 4 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/community/walktrap/walktrap.cpp | 5 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/community/walktrap/walktrap_communities.cpp | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/community/walktrap/walktrap_communities.h | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/config.h.in | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/constructors/adjacency.c | 30 - speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/constructors/atlas.c | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/constructors/basic_constructors.c | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/constructors/circulant.c | 5 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/constructors/famous.c | 5 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/constructors/full.c | 4 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/constructors/lattices.c | 112 ++-- speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/constructors/lcf.c | 5 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/constructors/regular.c | 25 - speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/bitset.c | 68 ++ speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/bitset_list.c | 10 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/error.c | 3 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/interruption.c | 3 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/interruption.h | 3 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/matrix.pmt | 27 - speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/memory.c | 37 - speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/progress.c | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/set.c | 29 - speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/set.h | 29 - speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/sparsemat.c | 22 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/statusbar.c | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/strvector.c | 20 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/typed_list.pmt | 138 ++--- speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/core/vector.pmt | 247 ++++++---- speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/cycles |only speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/graph/adjlist.c | 28 - speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/graph/caching.c | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/graph/cattributes.c | 4 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/graph/type_common.c | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/graph/type_indexededgelist.c | 90 ++- speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/graph/visitors.c | 4 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/internal/glpk_support.h | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/internal/gmp_internal.h | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/linalg/arpack_internal.h | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/linalg/blas.c | 8 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/linalg/blas_internal.h | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/linalg/lapack.c | 18 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/linalg/lapack_internal.h | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/math/safe_intop.c | 8 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/math/safe_intop.h | 2 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/properties/basic_properties.c | 15 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/properties/complete.c | 13 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/properties/degrees.c | 4 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/properties/loops.c | 4 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/properties/multiplicity.c | 21 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/properties/neighborhood.c | 127 ++--- speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/properties/trees.c | 23 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/properties/triangles.c | 245 +++++---- speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/properties/triangles_template.h | 4 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/properties/triangles_template1.h | 4 speakeasyR-0.1.6/speakeasyR/src/se2/vendor/igraph/src/random/random.c | 31 + 111 files changed, 1741 insertions(+), 1146 deletions(-)
Title: Regularized Mediation Analysis
Description: Mediation analysis for multiple mediators by penalized structural equation models with different types of penalties depending on whether there are multiple mediators and only one exposure and one outcome variable (using sparse group lasso) or multiple exposures, multiple mediators, and multiple outcome variables (using lasso, L1, penalties).
Author: Jason Sinnwell [aut, cre] ,
Daniel Schaid [aut]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Diff between regmed versions 2.1.0 dated 2023-01-20 and 2.1.5 dated 2025-08-28
regmed-2.1.0/regmed/inst/doc/GPL.txt |only regmed-2.1.0/regmed/inst/doc/LICENSE |only regmed-2.1.0/regmed/inst/doc/LICENSE.mayo |only regmed-2.1.5/regmed/DESCRIPTION | 15 regmed-2.1.5/regmed/MD5 | 22 regmed-2.1.5/regmed/build/partial.rdb |binary regmed-2.1.5/regmed/build/vignette.rds |binary regmed-2.1.5/regmed/inst/copyrights |only regmed-2.1.5/regmed/inst/doc/regmed.R | 14 regmed-2.1.5/regmed/inst/doc/regmed.html | 549 ++++++++++++------- regmed-2.1.5/regmed/man/mvregmed.graph.attributes.Rd | 2 regmed-2.1.5/regmed/src/Makevars | 2 regmed-2.1.5/regmed/src/Makevars.win | 8 13 files changed, 396 insertions(+), 216 deletions(-)
Title: Interactive Dendrograms for Visualizing Hierarchical Clusters
with Prototypes
Description: Shiny app to interactively visualize hierarchical clustering with prototypes.
For details on hierarchical clustering with prototypes, see
Bien and Tibshirani (2011) <doi:10.1198/jasa.2011.tm10183>. This package currently launches the application.
Author: Andee Kaplan [aut, cre],
Jacob Bien [aut],
Mike Bostock [cph] ,
Brian Reavis [cph]
Maintainer: Andee Kaplan <andee.kaplan@colostate.edu>
Diff between protoshiny versions 0.1.0 dated 2022-05-18 and 0.1.1 dated 2025-08-28
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/as.protoclust.R | 6 +++--- R/extdata.R | 2 +- man/as.protoclust.Rd | 6 +++--- man/words.Rd | 2 +- 7 files changed, 22 insertions(+), 18 deletions(-)
Title: Barycenter Methods for Spatial Point Patterns
Description: Computes a point pattern in R^2 or on a graph that is representative of a collection of many data patterns. The result is an approximate barycenter (also known as Fréchet mean or prototype) based on a transport-transform metric. Possible choices include Optimal SubPattern Assignment (OSPA) and Spike Time metrics. Details can be found in Müller, Schuhmacher and Mateu (2020) <doi:10.1007/s11222-020-09932-y>.
Author: Raoul Mueller [aut],
Dominic Schuhmacher [aut, cre]
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>
Diff between ttbary versions 0.3-1 dated 2022-11-16 and 0.3-2 dated 2025-08-28
DESCRIPTION | 14 +++++++------- MD5 | 18 +++++++++--------- NEWS | 11 ++++++++++- R/data.R | 2 +- R/ppdist.R | 8 ++++---- build/partial.rdb |binary man/kmeansbary.Rd | 1 + man/plotmatch.Rd | 2 +- man/pplist-data.Rd | 2 +- man/sumppdist.Rd | 6 +++--- 10 files changed, 37 insertions(+), 27 deletions(-)
Title: Access the 'Strava' API
Description: Functions to access data from the 'Strava v3 API' <https://developers.strava.com/>.
Author: Marcus W. Beck [cre],
Pedro Villarroel [aut],
Daniel Padfield [aut],
Lorenzo Gaborini [aut],
Niklas von Maltzahn [aut]
Maintainer: Marcus W. Beck <mbafs2012@gmail.com>
Diff between rStrava versions 1.3.2 dated 2024-10-23 and 1.3.3 dated 2025-08-28
rStrava-1.3.2/rStrava/R/achievement_fun.R |only rStrava-1.3.2/rStrava/R/ratelimit.R |only rStrava-1.3.2/rStrava/R/trophy_fun.R |only rStrava-1.3.2/rStrava/man/achievement_fun.Rd |only rStrava-1.3.2/rStrava/man/ratelimit.Rd |only rStrava-1.3.2/rStrava/man/trophy_fun.Rd |only rStrava-1.3.3/rStrava/DESCRIPTION | 10 - rStrava-1.3.3/rStrava/MD5 | 56 ++---- rStrava-1.3.3/rStrava/NAMESPACE | 3 rStrava-1.3.3/rStrava/NEWS.md | 6 rStrava-1.3.3/rStrava/R/athlind_fun.R | 14 - rStrava-1.3.3/rStrava/R/compile_activity_streams.R | 5 rStrava-1.3.3/rStrava/R/follow_fun.R | 11 - rStrava-1.3.3/rStrava/R/get_athlete.R | 4 rStrava-1.3.3/rStrava/R/get_basic.R | 4 rStrava-1.3.3/rStrava/R/get_pages.R | 131 +++++++-------- rStrava-1.3.3/rStrava/R/get_starred.R | 2 rStrava-1.3.3/rStrava/R/get_streams.R | 4 rStrava-1.3.3/rStrava/R/location_fun.R | 5 rStrava-1.3.3/rStrava/R/monthly_fun.R | 6 rStrava-1.3.3/rStrava/R/recent_fun.R | 12 - rStrava-1.3.3/rStrava/R/url_athlete.R | 2 rStrava-1.3.3/rStrava/man/compile_activity_streams.Rd | 3 rStrava-1.3.3/rStrava/man/figures/unnamed-chunk-12-1.png |binary rStrava-1.3.3/rStrava/man/figures/unnamed-chunk-13-1.png |binary rStrava-1.3.3/rStrava/man/figures/unnamed-chunk-13-2.png |binary rStrava-1.3.3/rStrava/man/figures/unnamed-chunk-17-1.png |binary rStrava-1.3.3/rStrava/man/get_athlete.Rd | 2 rStrava-1.3.3/rStrava/man/get_basic.Rd | 2 rStrava-1.3.3/rStrava/man/get_laps.Rd | 66 +++---- rStrava-1.3.3/rStrava/man/get_pages.Rd | 4 rStrava-1.3.3/rStrava/man/seltime_fun.Rd | 52 ++--- 32 files changed, 201 insertions(+), 203 deletions(-)
Title: Resampling Tools for Time Series Forecasting
Description: A 'modeltime' extension that implements forecast resampling tools
that assess time-based model performance and stability for a single time series,
panel data, and cross-sectional time series analysis.
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime.resample versions 0.2.3 dated 2023-04-12 and 0.2.4 dated 2025-08-28
DESCRIPTION | 19 LICENSE | 4 MD5 | 75 NAMESPACE | 90 - NEWS.md | 8 R/00_global_variables.R | 10 R/00_imports.R | 10 R/data.R | 52 R/modeltime_fit_resamples.R | 452 ++--- R/modeltime_resample_accuracy.R | 237 +- R/plot_modeltime_resamples.R | 372 ++-- R/tidyquant-theme-compat.R | 378 ++-- R/utils-pipe.R | 22 R/utils-resamples.R | 180 +- R/utils-tidy-eval.R | 92 - R/utils-timetk.R | 86 README.md | 325 +-- build/vignette.rds |binary inst/doc/getting-started.R | 128 - inst/doc/getting-started.Rmd | 305 +-- inst/doc/getting-started.html | 1915 ++++++++++----------- inst/doc/panel-data.R | 328 +-- inst/doc/panel-data.Rmd | 623 +++---- inst/doc/panel-data.html | 2299 +++++++++++++------------- man/figures/logo.png |only man/get_target_text_from_resamples.Rd | 54 man/m750_training_resamples_fitted.Rd | 74 man/mdl_time_fit_resamples.Rd | 52 man/modeltime_fit_resamples.Rd | 160 - man/modeltime_resample_accuracy.Rd | 180 +- man/pipe.Rd | 24 man/plot_modeltime_resamples.Rd | 236 +- man/tidyeval.Rd | 100 - man/time_series_cv.Rd | 82 man/unnest_modeltime_resamples.Rd | 76 tests/testthat.R | 29 tests/testthat/test-modeltime_fit_resamples.R | 253 +- vignettes/getting-started.Rmd | 305 +-- vignettes/panel-data.Rmd | 623 +++---- 39 files changed, 5195 insertions(+), 5063 deletions(-)
More information about modeltime.resample at CRAN
Permanent link
Title: Ensemble Algorithms for Time Series Forecasting with Modeltime
Description: A 'modeltime' extension that implements time series ensemble forecasting methods including model averaging,
weighted averaging, and stacking. These techniques are popular methods
to improve forecast accuracy and stability.
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime.ensemble versions 1.0.4 dated 2024-07-19 and 1.0.5 dated 2025-08-28
DESCRIPTION | 8 MD5 | 10 R/ensemble_model_spec.R | 9 inst/doc/getting-started-with-modeltime-ensemble.html | 20 inst/doc/nested-ensembles.html | 686 +++++++++--------- inst/doc/recursive-ensembles.html | 170 ++-- 6 files changed, 450 insertions(+), 453 deletions(-)
More information about modeltime.ensemble at CRAN
Permanent link
Title: Outlier Detection Using Invariant Coordinate Selection
Description: Multivariate outlier detection is performed using invariant coordinates where the package offers different methods to choose the appropriate components. ICS is a general multivariate technique with many applications in multivariate analysis. ICSOutlier offers a selection of functions for automated detection of outliers in the data based on a fitted ICS object or by specifying the dataset and the scatters of interest. The current implementation targets data sets with only a small percentage of outliers.
Author: Klaus Nordhausen [aut, cre] ,
Aurore Archimbaud [aut] ,
Anne Ruiz-Gazen [aut]
Maintainer: Klaus Nordhausen <klausnordhausenR@gmail.com>
Diff between ICSOutlier versions 0.4-0 dated 2023-12-13 and 0.4-1 dated 2025-08-28
DESCRIPTION | 16 +++++++++------- MD5 | 10 +++++----- NEWS | 5 +++++ build/partial.rdb |binary man/ics.distances.Rd | 2 +- man/icsOut-class.Rd | 2 +- 6 files changed, 21 insertions(+), 14 deletions(-)
Title: Tidy Tools for Forecasting
Description: Tidies up the forecasting modeling and prediction work flow,
extends the 'broom' package
with 'sw_tidy', 'sw_glance', 'sw_augment', and 'sw_tidy_decomp' functions
for various forecasting models,
and enables converting 'forecast' objects to
"tidy" data frames with 'sw_sweep'.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between sweep versions 0.2.5 dated 2023-07-06 and 0.2.6 dated 2025-08-28
sweep-0.2.5/sweep/man/figures/sweep-logo.png |only sweep-0.2.5/sweep/man/sweep_package.Rd |only sweep-0.2.6/sweep/DESCRIPTION | 25 sweep-0.2.6/sweep/MD5 | 144 sweep-0.2.6/sweep/NAMESPACE | 96 sweep-0.2.6/sweep/NEWS.md | 66 sweep-0.2.6/sweep/R/global_vars.R | 4 sweep-0.2.6/sweep/R/sales_data.R | 68 sweep-0.2.6/sweep/R/sw_augment.R | 80 sweep-0.2.6/sweep/R/sw_glance.R | 82 sweep-0.2.6/sweep/R/sw_sweep.R | 333 - sweep-0.2.6/sweep/R/sw_tidy.R | 99 sweep-0.2.6/sweep/R/sw_tidy_decomp.R | 92 sweep-0.2.6/sweep/R/sweep-package.R | 46 sweep-0.2.6/sweep/R/tidiers_HoltWinters.R | 371 - sweep-0.2.6/sweep/R/tidiers_StructTS.R | 277 - sweep-0.2.6/sweep/R/tidiers_arima.R | 305 - sweep-0.2.6/sweep/R/tidiers_bats.R | 375 - sweep-0.2.6/sweep/R/tidiers_decomposed_ts.R | 141 sweep-0.2.6/sweep/R/tidiers_ets.R | 413 +- sweep-0.2.6/sweep/R/tidiers_nnetar.R | 271 - sweep-0.2.6/sweep/R/tidiers_stl.R | 348 - sweep-0.2.6/sweep/R/utils-broom.R | 264 - sweep-0.2.6/sweep/R/utils-forecast.R | 304 - sweep-0.2.6/sweep/README.md | 255 - sweep-0.2.6/sweep/build/vignette.rds |binary sweep-0.2.6/sweep/inst/doc/SW00_Introduction_to_sweep.R | 312 - sweep-0.2.6/sweep/inst/doc/SW00_Introduction_to_sweep.Rmd | 600 +-- sweep-0.2.6/sweep/inst/doc/SW00_Introduction_to_sweep.html | 1904 ++++------ sweep-0.2.6/sweep/inst/doc/SW01_Forecasting_Time_Series_Groups.R | 266 - sweep-0.2.6/sweep/inst/doc/SW01_Forecasting_Time_Series_Groups.Rmd | 508 +- sweep-0.2.6/sweep/inst/doc/SW01_Forecasting_Time_Series_Groups.html | 1643 ++++---- sweep-0.2.6/sweep/inst/doc/SW02_Forecasting_Multiple_Models.R | 331 - sweep-0.2.6/sweep/inst/doc/SW02_Forecasting_Multiple_Models.Rmd | 605 +-- sweep-0.2.6/sweep/inst/doc/SW02_Forecasting_Multiple_Models.html | 1664 ++++---- sweep-0.2.6/sweep/man/add_index.Rd | 34 sweep-0.2.6/sweep/man/arima_string.Rd | 34 sweep-0.2.6/sweep/man/bats_string.Rd | 30 sweep-0.2.6/sweep/man/bike_sales.Rd | 90 sweep-0.2.6/sweep/man/figures/logo.png |only sweep-0.2.6/sweep/man/reexports.Rd | 32 sweep-0.2.6/sweep/man/sw_augment.Rd | 66 sweep-0.2.6/sweep/man/sw_augment.default.Rd | 38 sweep-0.2.6/sweep/man/sw_augment_columns.Rd | 42 sweep-0.2.6/sweep/man/sw_glance.Rd | 70 sweep-0.2.6/sweep/man/sw_glance.default.Rd | 38 sweep-0.2.6/sweep/man/sw_sweep.Rd | 133 sweep-0.2.6/sweep/man/sw_tidy.Rd | 87 sweep-0.2.6/sweep/man/sw_tidy.default.Rd | 38 sweep-0.2.6/sweep/man/sw_tidy_decomp.Rd | 98 sweep-0.2.6/sweep/man/sweep-package.Rd |only sweep-0.2.6/sweep/man/tbats_string.Rd | 30 sweep-0.2.6/sweep/man/tidiers_HoltWinters.Rd | 195 - sweep-0.2.6/sweep/man/tidiers_StructTS.Rd | 171 sweep-0.2.6/sweep/man/tidiers_arima.Rd | 193 - sweep-0.2.6/sweep/man/tidiers_bats.Rd | 193 - sweep-0.2.6/sweep/man/tidiers_decomposed_ts.Rd | 95 sweep-0.2.6/sweep/man/tidiers_ets.Rd | 201 - sweep-0.2.6/sweep/man/tidiers_nnetar.Rd | 171 sweep-0.2.6/sweep/man/tidiers_stl.Rd | 182 sweep-0.2.6/sweep/man/validate_index.Rd | 34 sweep-0.2.6/sweep/tests/testthat.R | 22 sweep-0.2.6/sweep/tests/testthat/test_sw_sweep.R | 345 - sweep-0.2.6/sweep/tests/testthat/test_tidiers_StructTS.R | 113 sweep-0.2.6/sweep/tests/testthat/test_tidiers_arima.R | 213 - sweep-0.2.6/sweep/tests/testthat/test_tidiers_bats_tbats.R | 243 - sweep-0.2.6/sweep/tests/testthat/test_tidiers_decomposed_ts.R | 63 sweep-0.2.6/sweep/tests/testthat/test_tidiers_ets.R | 137 sweep-0.2.6/sweep/tests/testthat/test_tidiers_hw.R | 160 sweep-0.2.6/sweep/tests/testthat/test_tidiers_lm.R | 65 sweep-0.2.6/sweep/tests/testthat/test_tidiers_nnetar.R | 142 sweep-0.2.6/sweep/tests/testthat/test_tidiers_stl.R | 85 sweep-0.2.6/sweep/vignettes/SW00_Introduction_to_sweep.Rmd | 600 +-- sweep-0.2.6/sweep/vignettes/SW01_Forecasting_Time_Series_Groups.Rmd | 508 +- sweep-0.2.6/sweep/vignettes/SW02_Forecasting_Multiple_Models.Rmd | 605 +-- 75 files changed, 8957 insertions(+), 8931 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb],
Christine Laney [aut, ctb],
Nathan Mietkiewicz [aut, ctb],
Eric Sokol [aut, ctb],
Kaelin Cawley [aut, ctb],
NEON [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 3.0.0 dated 2025-07-22 and 3.0.1 dated 2025-08-28
DESCRIPTION | 13 +++++++------ MD5 | 22 +++++++++++----------- NEWS.md | 12 ++++++++++++ R/byTileAOP.R | 5 +++-- R/datasetQuery.R | 28 ++++++++++++++++++++++------ R/getZipUrls.R | 2 +- R/loadByProduct.R | 2 +- R/schemaFromVar.R | 10 ++++++++-- R/stackDataFilesArrow.R | 4 ++-- R/stackFromStore.R | 8 ++++---- R/tokenCheck.R | 19 ++++++++++++++----- README.md | 21 ++++++++++----------- 12 files changed, 95 insertions(+), 51 deletions(-)
Title: Toolkit for Regression Analysis of Kazakhstan Banking Sector
Data
Description: Tool is created for regression, prediction and forecast analysis of macroeconomic and credit data.
The package includes functions from existing R packages adapted for banking sector of Kazakhstan.
The purpose of the package is to optimize statistical functions for easier interpretation for bank analysts and non-statisticians.
Author: Timur Abilkassymov [aut],
Shyngys Shuneyev [aut],
Alua Makhmetova [aut],
Sultan Zhaparov [aut, cre]
Maintainer: Sultan Zhaparov <saldau.sultan@gmail.com>
Diff between AFR versions 0.3.6 dated 2024-09-06 and 0.3.7 dated 2025-08-28
DESCRIPTION | 6 MD5 | 22 R/macroKZ.R | 2 build/vignette.rds |binary data/macroKZ.rda |binary inst/doc/Data-transformation.R | 54 - inst/doc/Data-transformation.html | 1141 ++++++++++++++++++-------------------- inst/doc/Diagnostic-tests.R | 72 +- inst/doc/Diagnostic-tests.html | 1116 ++++++++++++++++++------------------- inst/doc/Regression-model.R | 48 - inst/doc/Regression-model.html | 819 +++++++++++++-------------- man/macroKZ.Rd | 2 12 files changed, 1632 insertions(+), 1650 deletions(-)
Title: Win Time Methods for Time-to-Event Data in Clinical Trials
Description: Performs an analysis of time-to-event clinical trial data using various "win time" methods,
including 'ewt', 'ewtr', 'rmt', 'ewtp', 'rewtp', 'ewtpr', 'rewtpr', 'max', 'wtr', 'rwtr', 'pwt', and 'rpwt'. These methods are used to calculate and compare
treatment effects on ordered composite endpoints. The package handles event times, event indicators, and treatment
arm indicators and supports calculations on observed and resampled data. Detailed explanations of each method and
usage examples are provided in "Use of win time for ordered composite endpoints in clinical trials," by Troendle et al.
(2024)<https://pubmed.ncbi.nlm.nih.gov/38417455/>. For more information, see the package documentation or the vignette titled "Introduction to wintime."
Author: James Troendle [aut, cre],
Samuel Lawrence [aut]
Maintainer: James Troendle <james.troendle@nih.gov>
Diff between wintime versions 0.4.0 dated 2025-06-30 and 0.4.1 dated 2025-08-28
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/ewtpr.R | 16 ++++++++-------- R/rewtpr.R | 15 ++++++++------- R/wintime.R | 8 ++++---- inst/doc/wintime_vignette.html | 6 +++--- man/wintime.Rd | 2 +- 7 files changed, 33 insertions(+), 32 deletions(-)
Title: Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis
Tests
Description: Compute and plot predictions, slopes, marginal means, and comparisons (contrasts, risk ratios, odds, etc.) for over 100 classes of statistical and machine learning models in R. Conduct linear and non-linear hypothesis tests, or equivalence tests. Calculate uncertainty estimates using the delta method, bootstrapping, or simulation-based inference. Details can be found in Arel-Bundock, Greifer, and Heiss (2024) <doi:10.18637/jss.v111.i09>.
Author: Vincent Arel-Bundock [aut, cre, cph] ,
Noah Greifer [ctb] ,
Etienne Bacher [ctb] ,
Grant McDermott [ctb] ,
Andrew Heiss [ctb]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between marginaleffects versions 0.28.0 dated 2025-06-25 and 0.29.0 dated 2025-08-28
marginaleffects-0.28.0/marginaleffects/R/complete_levels.R |only marginaleffects-0.28.0/marginaleffects/R/config.R |only marginaleffects-0.28.0/marginaleffects/R/get_contrast_data.R |only marginaleffects-0.28.0/marginaleffects/R/get_contrast_data_character.R |only marginaleffects-0.28.0/marginaleffects/R/get_contrast_data_factor.R |only marginaleffects-0.28.0/marginaleffects/R/get_contrast_data_logical.R |only marginaleffects-0.28.0/marginaleffects/R/get_contrast_data_numeric.R |only marginaleffects-0.28.0/marginaleffects/R/get_contrasts.R |only marginaleffects-0.28.0/marginaleffects/R/get_model_matrix_attribute.R |only marginaleffects-0.28.0/marginaleffects/R/recall.R |only marginaleffects-0.28.0/marginaleffects/R/sanitize_hypothesis.R |only marginaleffects-0.28.0/marginaleffects/man/complete_levels.Rd |only marginaleffects-0.29.0/marginaleffects/DESCRIPTION | 113 - marginaleffects-0.29.0/marginaleffects/MD5 | 262 ++-- marginaleffects-0.29.0/marginaleffects/NAMESPACE | 20 marginaleffects-0.29.0/marginaleffects/NEWS.md | 34 marginaleffects-0.29.0/marginaleffects/R/add_hypothesis.R |only marginaleffects-0.29.0/marginaleffects/R/add_rowid.R |only marginaleffects-0.29.0/marginaleffects/R/attributes.R |only marginaleffects-0.29.0/marginaleffects/R/backtransform.R | 5 marginaleffects-0.29.0/marginaleffects/R/broom.R | 13 marginaleffects-0.29.0/marginaleffects/R/by.R | 5 marginaleffects-0.29.0/marginaleffects/R/class.R |only marginaleffects-0.29.0/marginaleffects/R/comparisons.R | 362 ++--- marginaleffects-0.29.0/marginaleffects/R/components.R |only marginaleffects-0.29.0/marginaleffects/R/datagrid.R | 615 +++------- marginaleffects-0.29.0/marginaleffects/R/equivalence.R | 25 marginaleffects-0.29.0/marginaleffects/R/get_ci.R | 58 marginaleffects-0.29.0/marginaleffects/R/get_comparisons.R |only marginaleffects-0.29.0/marginaleffects/R/get_comparisons_data.R |only marginaleffects-0.29.0/marginaleffects/R/get_comparisons_data_character.R |only marginaleffects-0.29.0/marginaleffects/R/get_comparisons_data_factor.R |only marginaleffects-0.29.0/marginaleffects/R/get_comparisons_data_logical.R |only marginaleffects-0.29.0/marginaleffects/R/get_comparisons_data_numeric.R |only marginaleffects-0.29.0/marginaleffects/R/get_dataset.R | 174 +- marginaleffects-0.29.0/marginaleffects/R/get_degrees_of_freedom.R | 71 - marginaleffects-0.29.0/marginaleffects/R/get_draws.R | 20 marginaleffects-0.29.0/marginaleffects/R/get_hypotheses.R |only marginaleffects-0.29.0/marginaleffects/R/get_model_matrix.R | 72 + marginaleffects-0.29.0/marginaleffects/R/get_modeldata.R | 267 ---- marginaleffects-0.29.0/marginaleffects/R/get_predict.R | 98 + marginaleffects-0.29.0/marginaleffects/R/get_predictions.R |only marginaleffects-0.29.0/marginaleffects/R/get_se_delta.R | 70 - marginaleffects-0.29.0/marginaleffects/R/get_vcov.R | 9 marginaleffects-0.29.0/marginaleffects/R/github_issue.R | 1 marginaleffects-0.29.0/marginaleffects/R/hush.R | 2 marginaleffects-0.29.0/marginaleffects/R/hypotheses.R | 315 +---- marginaleffects-0.29.0/marginaleffects/R/hypotheses_joint.R | 67 - marginaleffects-0.29.0/marginaleffects/R/hypothesis.R | 4 marginaleffects-0.29.0/marginaleffects/R/hypothesis_formula.R | 17 marginaleffects-0.29.0/marginaleffects/R/hypothesis_function.R | 17 marginaleffects-0.29.0/marginaleffects/R/hypothesis_string.R | 6 marginaleffects-0.29.0/marginaleffects/R/imputation.R | 114 + marginaleffects-0.29.0/marginaleffects/R/inferences.R | 102 - marginaleffects-0.29.0/marginaleffects/R/inferences_boot.R | 28 marginaleffects-0.29.0/marginaleffects/R/inferences_conformal.R | 54 marginaleffects-0.29.0/marginaleffects/R/inferences_fwb.R | 69 - marginaleffects-0.29.0/marginaleffects/R/inferences_rsample.R | 43 marginaleffects-0.29.0/marginaleffects/R/inferences_simulation.R | 46 marginaleffects-0.29.0/marginaleffects/R/methods.R | 6 marginaleffects-0.29.0/marginaleffects/R/methods_MASS.R | 34 marginaleffects-0.29.0/marginaleffects/R/methods_MCMCglmm.R | 14 marginaleffects-0.29.0/marginaleffects/R/methods_afex.R | 8 marginaleffects-0.29.0/marginaleffects/R/methods_aod.R | 16 marginaleffects-0.29.0/marginaleffects/R/methods_betareg.R | 60 marginaleffects-0.29.0/marginaleffects/R/methods_bife.R | 9 marginaleffects-0.29.0/marginaleffects/R/methods_biglm.R | 20 marginaleffects-0.29.0/marginaleffects/R/methods_brms.R | 25 marginaleffects-0.29.0/marginaleffects/R/methods_crch.R | 6 marginaleffects-0.29.0/marginaleffects/R/methods_dataframe.R | 2 marginaleffects-0.29.0/marginaleffects/R/methods_dbarts.R | 27 marginaleffects-0.29.0/marginaleffects/R/methods_fixest.R | 37 marginaleffects-0.29.0/marginaleffects/R/methods_flexsurv.R | 14 marginaleffects-0.29.0/marginaleffects/R/methods_gamlss.R | 26 marginaleffects-0.29.0/marginaleffects/R/methods_glmmTMB.R | 23 marginaleffects-0.29.0/marginaleffects/R/methods_glmtoolbox.R | 6 marginaleffects-0.29.0/marginaleffects/R/methods_mhurdle.R | 8 marginaleffects-0.29.0/marginaleffects/R/methods_mice.R |only marginaleffects-0.29.0/marginaleffects/R/methods_mlogit.R | 10 marginaleffects-0.29.0/marginaleffects/R/methods_mlr3.R | 17 marginaleffects-0.29.0/marginaleffects/R/methods_nnet.R | 19 marginaleffects-0.29.0/marginaleffects/R/methods_ordinal.R | 17 marginaleffects-0.29.0/marginaleffects/R/methods_quantreg.R | 24 marginaleffects-0.29.0/marginaleffects/R/methods_rms.R | 13 marginaleffects-0.29.0/marginaleffects/R/methods_robustlmm.R | 14 marginaleffects-0.29.0/marginaleffects/R/methods_rstpm2.R | 6 marginaleffects-0.29.0/marginaleffects/R/methods_sampleSelection.R | 19 marginaleffects-0.29.0/marginaleffects/R/methods_stats.R | 6 marginaleffects-0.29.0/marginaleffects/R/methods_survey.R | 49 marginaleffects-0.29.0/marginaleffects/R/methods_survival.R | 13 marginaleffects-0.29.0/marginaleffects/R/methods_systemfit.R | 26 marginaleffects-0.29.0/marginaleffects/R/methods_tidymodels.R | 25 marginaleffects-0.29.0/marginaleffects/R/methods_tobit1.R | 6 marginaleffects-0.29.0/marginaleffects/R/package.R | 4 marginaleffects-0.29.0/marginaleffects/R/pad.R |only marginaleffects-0.29.0/marginaleffects/R/plot.R | 6 marginaleffects-0.29.0/marginaleffects/R/plot_build.R | 26 marginaleffects-0.29.0/marginaleffects/R/plot_comparisons.R | 65 - marginaleffects-0.29.0/marginaleffects/R/plot_predictions.R | 78 - marginaleffects-0.29.0/marginaleffects/R/plot_slopes.R | 33 marginaleffects-0.29.0/marginaleffects/R/predictions.R | 543 ++------ marginaleffects-0.29.0/marginaleffects/R/print.R | 114 - marginaleffects-0.29.0/marginaleffects/R/prune.R |only marginaleffects-0.29.0/marginaleffects/R/sanitize_condition.R | 39 marginaleffects-0.29.0/marginaleffects/R/sanitize_conf_level.R | 3 marginaleffects-0.29.0/marginaleffects/R/sanitize_estimator.R | 2 marginaleffects-0.29.0/marginaleffects/R/sanitize_interaction.R | 2 marginaleffects-0.29.0/marginaleffects/R/sanitize_newdata.R | 248 ++-- marginaleffects-0.29.0/marginaleffects/R/sanitize_numderiv.R | 5 marginaleffects-0.29.0/marginaleffects/R/sanitize_reserved.R | 15 marginaleffects-0.29.0/marginaleffects/R/sanitize_variables.R | 535 ++++++-- marginaleffects-0.29.0/marginaleffects/R/sanity.R | 14 marginaleffects-0.29.0/marginaleffects/R/sanity_by.R | 22 marginaleffects-0.29.0/marginaleffects/R/sanity_dots.R | 2 marginaleffects-0.29.0/marginaleffects/R/sanity_model.R | 35 marginaleffects-0.29.0/marginaleffects/R/sanity_multcomp.R |only marginaleffects-0.29.0/marginaleffects/R/settings.R | 48 marginaleffects-0.29.0/marginaleffects/R/slopes.R | 130 -- marginaleffects-0.29.0/marginaleffects/R/tinytest.R | 141 ++ marginaleffects-0.29.0/marginaleffects/R/type_dictionary.R | 1 marginaleffects-0.29.0/marginaleffects/R/utils.R | 69 - marginaleffects-0.29.0/marginaleffects/R/zzz.R | 4 marginaleffects-0.29.0/marginaleffects/build/partial.rdb |binary marginaleffects-0.29.0/marginaleffects/build/vignette.rds |binary marginaleffects-0.29.0/marginaleffects/inst/WORDLIST | 6 marginaleffects-0.29.0/marginaleffects/man/comparisons.Rd | 18 marginaleffects-0.29.0/marginaleffects/man/components.marginaleffects.Rd |only marginaleffects-0.29.0/marginaleffects/man/datagrid.Rd | 19 marginaleffects-0.29.0/marginaleffects/man/expect_comparisons.Rd |only marginaleffects-0.29.0/marginaleffects/man/expect_hypotheses.Rd |only marginaleffects-0.29.0/marginaleffects/man/expect_predictions.Rd | 2 marginaleffects-0.29.0/marginaleffects/man/extract_calling_function.Rd |only marginaleffects-0.29.0/marginaleffects/man/get_dataset.Rd | 1 marginaleffects-0.29.0/marginaleffects/man/get_draws.Rd | 4 marginaleffects-0.29.0/marginaleffects/man/get_model_matrix.Rd | 4 marginaleffects-0.29.0/marginaleffects/man/get_predict.Rd | 133 +- marginaleffects-0.29.0/marginaleffects/man/get_vcov.Rd | 30 marginaleffects-0.29.0/marginaleffects/man/hypotheses.Rd | 19 marginaleffects-0.29.0/marginaleffects/man/inferences.Rd | 22 marginaleffects-0.29.0/marginaleffects/man/marginaleffects_internal-class.Rd |only marginaleffects-0.29.0/marginaleffects/man/new_marginaleffects_internal.Rd |only marginaleffects-0.29.0/marginaleffects/man/plot_comparisons.Rd | 6 marginaleffects-0.29.0/marginaleffects/man/plot_predictions.Rd | 4 marginaleffects-0.29.0/marginaleffects/man/plot_slopes.Rd | 7 marginaleffects-0.29.0/marginaleffects/man/predictions.Rd | 17 marginaleffects-0.29.0/marginaleffects/man/prune.marginaleffects.Rd |only marginaleffects-0.29.0/marginaleffects/man/reexports.Rd | 6 marginaleffects-0.29.0/marginaleffects/man/sanitize_model_specific.Rd | 20 marginaleffects-0.29.0/marginaleffects/man/set_coef.Rd | 5 marginaleffects-0.29.0/marginaleffects/man/slopes.Rd | 57 150 files changed, 3075 insertions(+), 3272 deletions(-)
More information about marginaleffects at CRAN
Permanent link
Title: Global Triangular and Penta-Hexagonal Grids Based on Tessellated
Icosahedra
Description: Implementation of icosahedral grids in three dimensions. The spherical-triangular tessellation can be set to create grids with custom resolutions. Both the primary triangular and their inverted penta-hexagonal grids can be calculated. Additional functions are provided that allow plotting of the grids and associated data, the interaction of the grids with other raster and vector objects, and treating the grids as a graphs.
Author: Adam T. Kocsis [cre, aut] ,
Deutsche Forschungsgemeinschaft [fnd],
FAU GeoZentrum Nordbayern [fnd]
Maintainer: Adam T. Kocsis <adam.t.kocsis@gmail.com>
Diff between icosa versions 0.11.1 dated 2024-08-16 and 0.12.0 dated 2025-08-28
icosa-0.11.1/icosa/man/figures |only icosa-0.11.1/icosa/man/gridensity.Rd |only icosa-0.12.0/icosa/DESCRIPTION | 19 - icosa-0.12.0/icosa/MD5 | 88 ++++--- icosa-0.12.0/icosa/NAMESPACE | 10 icosa-0.12.0/icosa/NEWS.md | 53 ++++ icosa-0.12.0/icosa/R/data-facelayer-basic.R | 31 ++ icosa-0.12.0/icosa/R/data-facelayer-graphs.R | 54 ++++ icosa-0.12.0/icosa/R/data-facelayer-resample.R | 135 +---------- icosa-0.12.0/icosa/R/data-grapply.R |only icosa-0.12.0/icosa/R/data-gridlayer-attributes.R | 6 icosa-0.12.0/icosa/R/data-gridlayer-basic.R | 5 icosa-0.12.0/icosa/R/data-gridlayer-subset.R | 8 icosa-0.12.0/icosa/R/data.R | 18 + icosa-0.12.0/icosa/R/grid-attributes.R | 171 +++++++++++++- icosa-0.12.0/icosa/R/grid-build.R | 57 +++- icosa-0.12.0/icosa/R/grid-graphs.R | 257 +++++++++++++++++++++ icosa-0.12.0/icosa/R/grid-lookup.R | 42 ++- icosa-0.12.0/icosa/R/grid-move.R | 76 +++--- icosa-0.12.0/icosa/R/grid-obj.R |only icosa-0.12.0/icosa/R/grid-resample.R | 20 + icosa-0.12.0/icosa/R/plot-rgl-grid.R | 2 icosa-0.12.0/icosa/R/utils-conversion.R | 12 - icosa-0.12.0/icosa/R/utils-spherical.R | 273 ++++++++++++++++++++--- icosa-0.12.0/icosa/R/zzz.R | 5 icosa-0.12.0/icosa/build/vignette.rds |binary icosa-0.12.0/icosa/data/hexguide.RData |binary icosa-0.12.0/icosa/data/triguide.RData |binary icosa-0.12.0/icosa/man/arcs.Rd | 3 icosa-0.12.0/icosa/man/face2nb.Rd |only icosa-0.12.0/icosa/man/grapply.Rd |only icosa-0.12.0/icosa/man/hexagrid-class.Rd | 2 icosa-0.12.0/icosa/man/hexguide.Rd | 9 icosa-0.12.0/icosa/man/holes.Rd |only icosa-0.12.0/icosa/man/icosa.Rd | 2 icosa-0.12.0/icosa/man/occupied.Rd | 4 icosa-0.12.0/icosa/man/patches.Rd |only icosa-0.12.0/icosa/man/resample.Rd | 14 - icosa-0.12.0/icosa/man/rotate.Rd | 58 ++++ icosa-0.12.0/icosa/man/rpsphere.Rd | 2 icosa-0.12.0/icosa/man/saveOBJ.Rd |only icosa-0.12.0/icosa/man/spacing.Rd |only icosa-0.12.0/icosa/man/surfacearea.Rd | 10 icosa-0.12.0/icosa/man/surfacecentroid.Rd | 17 + icosa-0.12.0/icosa/man/trigrid-class.Rd | 2 icosa-0.12.0/icosa/man/triguide.Rd | 9 icosa-0.12.0/icosa/man/trishape.Rd | 2 icosa-0.12.0/icosa/man/vertexradius.Rd |only icosa-0.12.0/icosa/src/RcppExports.cpp | 13 + icosa-0.12.0/icosa/src/init.c | 2 icosa-0.12.0/icosa/src/rotation.cpp |only 51 files changed, 1162 insertions(+), 329 deletions(-)
Title: Representation of DET Curve with Confidence Intervals
Description: Builds both ROC (Receiver Operating Characteristic) and DET (Detection Error Tradeoff) curves from a set of predictors, which are the
results of a binary classification system. The curves give a general vision of the performance of the classifier,
and are useful for comparing performance of different systems.
Author: Garcia-Rodenas, Alvaro [aut],
Franco, Manuel [aut],
Vivo, Juana-Maria [aut],
Fernandez-Breis, Jesualdo T. [aut],
Font, Roberto [aut],
Curran, James [cre]
Maintainer: "Curran, James" <j.curran@auckland.ac.nz>
This is a re-admission after prior archival of version 3.0.1 dated 2021-04-02
Diff between DET versions 3.0.1 dated 2021-04-02 and 3.0.2 dated 2025-08-28
DESCRIPTION | 24 +- MD5 | 19 +- NAMESPACE | 1 R/detc.R | 424 ++++++++++++++++++++++++------------------------- R/internalFunctions.R | 295 +++++++++++++++++----------------- R/measures.R | 94 +++++----- R/ovarianCancer-data.R | 82 ++++----- R/show.R | 62 +++---- README.md |only build |only inst |only man/ovarianCancer.Rd | 26 +-- 12 files changed, 523 insertions(+), 504 deletions(-)
Title: Phylogenetics for the Environmental Sciences
Description: Eco-phylogenetic and community phylogenetic analyses.
Keeps community ecological and phylogenetic data matched up and
comparable using 'comparative.comm' objects. Wrappers for common
community phylogenetic indices ('pez.shape', 'pez.evenness',
'pez.dispersion', and 'pez.dissimilarity' metrics). Implementation
of Cavender-Bares (2004) correlation of phylogenetic and
ecological matrices ('fingerprint.regression'). Phylogenetic
Generalised Linear Mixed Models (PGLMMs; 'pglmm') following Ives &
Helmus (2011) and Rafferty & Ives (2013). Simulation of null
assemblages, traits, and phylogenies ('scape', 'sim.meta.comm').
Author: William D. Pearse [aut, cre],
Marc W. Cadotte [aut],
Jeannine Cavender-Bares [aut],
Anthony R. Ives [aut],
Caroline Tucker [aut],
Steve C. Walker [aut],
Matthew R. Helmus [aut]
Maintainer: William D. Pearse <will.pearse@gmail.com>
Diff between pez versions 1.2-4 dated 2022-08-31 and 1.2-5 dated 2025-08-28
DESCRIPTION | 40 ++++++++++++++++++++--- MD5 | 68 ++++++++++++++++++++-------------------- NEWS | 7 ++++ R/comparative.comm.R | 4 +- R/dispersion.R | 2 - R/eco.trait.regression.R | 4 +- R/fingerprint.regression.R | 2 - R/laja.R | 2 - R/metric.null.R | 2 - R/metrics.R | 8 ++-- R/pez-package.R | 3 - R/pglmm.R | 2 + R/phy.signal.R | 2 - R/scape.R | 7 ++-- R/utility.R | 4 +- build/vignette.rds |binary inst/CITATION | 25 +++++++++++++- inst/doc/pez-intro.pdf |binary inst/doc/pez-pglmm-overview.pdf |binary man/cc.manip.Rd | 2 - man/comparative.comm.Rd | 2 - man/drop_tip.Rd | 4 +- man/eco.xxx.regression.Rd | 4 +- man/fingerprint.regression.Rd | 2 - man/generic.metrics.Rd | 10 ++--- man/laja.Rd | 2 - man/pez.Rd | 2 - man/pez.dispersion.Rd | 6 +-- man/pez.metrics.Rd | 8 ++-- man/pglmm.Rd | 3 + man/phy.build.Rd | 2 - man/phy.signal.Rd | 2 - man/scape.Rd | 7 ++-- man/sim.meta.Rd | 2 - man/sim.phy.Rd | 4 -- 35 files changed, 149 insertions(+), 95 deletions(-)
Title: Bootstrap Based Goodness-of-Fit Tests
Description: Bootstrap based goodness-of-fit tests. It allows
to perform rigorous statistical tests to check if a chosen
model family is correct based on the marked empirical
process. The implemented algorithms are described in
(Dikta and Scheer (2021) <doi:10.1007/978-3-030-73480-0>)
and can be applied
to generalized linear models without any further implementation
effort. As far as certain linearity conditions are fulfilled
the resampling scheme are also applicable beyond generalized
linear models. This is reflected in the software architecture
which allows to reuse the resampling scheme by implementing
only certain interfaces for models that are not supported
natively by the package.
Author: Marsel Scheer [aut, cre],
Gerhard Dikta [aut]
Maintainer: Marsel Scheer <scheer@freescience.de>
Diff between bootGOF versions 0.1.0 dated 2021-06-24 and 0.1.1 dated 2025-08-28
bootGOF-0.1.0/bootGOF/tests/testthat |only bootGOF-0.1.0/bootGOF/tests/testthat.R |only bootGOF-0.1.1/bootGOF/DESCRIPTION | 12 bootGOF-0.1.1/bootGOF/MD5 | 81 - bootGOF-0.1.1/bootGOF/NAMESPACE | 1 bootGOF-0.1.1/bootGOF/NEWS.md |only bootGOF-0.1.1/bootGOF/R/GOF_model.R | 15 bootGOF-0.1.1/bootGOF/R/GOF_model_info_extractor.R | 6 bootGOF-0.1.1/bootGOF/R/GOF_model_resample.R | 8 bootGOF-0.1.1/bootGOF/R/GOF_model_simulator.R | 15 bootGOF-0.1.1/bootGOF/R/GOF_model_test.R | 24 bootGOF-0.1.1/bootGOF/R/GOF_model_trainer.R | 10 bootGOF-0.1.1/bootGOF/R/Rn1_statistic.R | 12 bootGOF-0.1.1/bootGOF/README.md | 156 +- bootGOF-0.1.1/bootGOF/build/vignette.rds |binary bootGOF-0.1.1/bootGOF/inst/doc/Architecture.R | 12 bootGOF-0.1.1/bootGOF/inst/doc/Architecture.html | 38 bootGOF-0.1.1/bootGOF/inst/doc/New-Models.R | 2 bootGOF-0.1.1/bootGOF/inst/doc/New-Models.html | 603 +++++----- bootGOF-0.1.1/bootGOF/inst/tinytest/test_GOF_model.R | 87 - bootGOF-0.1.1/bootGOF/inst/tinytest/test_GOF_model_info_extractor.R | 12 bootGOF-0.1.1/bootGOF/inst/tinytest/test_GOF_model_resample.R | 7 bootGOF-0.1.1/bootGOF/inst/tinytest/test_GOF_model_simulator.R | 27 bootGOF-0.1.1/bootGOF/inst/tinytest/test_GOF_model_test.R | 45 bootGOF-0.1.1/bootGOF/inst/tinytest/test_GOF_model_trainer.R | 10 bootGOF-0.1.1/bootGOF/inst/tinytest/test_Rn1_statistic.R | 6 bootGOF-0.1.1/bootGOF/man/GOF_glm_info_extractor.Rd | 30 bootGOF-0.1.1/bootGOF/man/GOF_glm_sim_param.Rd | 12 bootGOF-0.1.1/bootGOF/man/GOF_glm_trainer.Rd | 12 bootGOF-0.1.1/bootGOF/man/GOF_lm_info_extractor.Rd | 30 bootGOF-0.1.1/bootGOF/man/GOF_lm_sim_param.Rd | 12 bootGOF-0.1.1/bootGOF/man/GOF_lm_trainer.Rd | 12 bootGOF-0.1.1/bootGOF/man/GOF_model_info_extractor.Rd | 24 bootGOF-0.1.1/bootGOF/man/GOF_model_resample.Rd | 24 bootGOF-0.1.1/bootGOF/man/GOF_model_simulator.Rd | 12 bootGOF-0.1.1/bootGOF/man/GOF_model_test.Rd | 30 bootGOF-0.1.1/bootGOF/man/GOF_model_trainer.Rd | 15 bootGOF-0.1.1/bootGOF/man/GOF_sim_wild_rademacher.Rd | 18 bootGOF-0.1.1/bootGOF/man/Rn1_CvM.Rd | 18 bootGOF-0.1.1/bootGOF/man/Rn1_KS.Rd | 18 bootGOF-0.1.1/bootGOF/man/Rn1_statistic.Rd | 12 bootGOF-0.1.1/bootGOF/man/rrademacher.Rd | 1 bootGOF-0.1.1/bootGOF/tests/tinytest.R | 4 43 files changed, 807 insertions(+), 666 deletions(-)
Title: Mediterranean Landscape Simulation
Description: Simulate forest hydrology, forest function and dynamics over landscapes [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>]. Parallelization is allowed in several simulation functions and simulations may be conducted including spatial processes such as lateral water transfer and seed dispersal.
Author: Miquel De Caceres [aut, cre],
Aitor Ameztegui [aut] ,
Maria Gonzalez [aut] ,
Nuria Aquilue [aut],
Daniel Caviedes-Voullieme [aut],
Mario Morales-Hernandez [aut],
Mario Beltran [ctb],
Rodrigo Balaguer-Romano [ctb] ,
Roberto Molowny-Horas [ctb]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between medfateland versions 2.6.0 dated 2025-04-23 and 2.7.0 dated 2025-08-28
DESCRIPTION | 18 - MD5 | 48 ++- NAMESPACE | 3 R/RcppExports.R | 24 - R/add_topography.R | 24 + R/check_inputs.R | 87 ++++-- R/default_watershed_control.R | 6 R/impute_forests.R | 44 +++ R/initialize_landscape.R | 42 ++- R/model_land.R | 125 ++-------- R/overland_routing.R | 34 -- R/plot.spwb_land.R |only R/shinyplot_land.R | 157 ++++++++---- man/check_inputs.Rd | 8 man/default_watershed_control.Rd | 2 man/forest_parametrization.Rd | 18 + man/initialize_landscape.Rd | 12 man/overland_routing.Rd | 13 - man/plot.spwb_land.Rd |only man/spwb_land.Rd | 8 man/spwb_land_day.Rd | 2 src/RcppExports.cpp | 84 ++---- src/tetis.cpp | 485 ++++++++++++++++++--------------------- src/tetis_channel.cpp |only src/tetis_channel.h |only tests/testthat/test-checks.R | 7 tests/testthat/test_land.R | 20 + 27 files changed, 652 insertions(+), 619 deletions(-)
Title: Network Reverse Engineering with Approximate Bayesian
Computation
Description: We developed an inference tool based on approximate Bayesian computation to decipher network data and assess the strength of the inferred links between network's actors. It is a new multi-level approximate Bayesian computation (ABC) approach. At the first level, the method captures the global properties of the network, such as a scale-free structure and clustering coefficients, whereas the second level is targeted to capture local properties, including the probability of each couple of genes being linked. Up to now, Approximate Bayesian Computation (ABC) algorithms have been scarcely used in that setting and, due to the computational overhead, their application was limited to a small number of genes. On the contrary, our algorithm was made to cope with that issue and has low computational cost. It can be used, for instance, for elucidating gene regulatory network, which is an important step towards understanding the normal cell physiology and complex pathological phenotype. Reverse-eng [...truncated...]
Author: Frederic Bertrand [cre, aut] ,
Myriam Maumy-Bertrand [aut] ,
Khadija Musayeva [ctb],
Nicolas Jung [ctb],
Universite de Strasbourg [cph],
CNRS [cph]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between networkABC versions 0.8-1 dated 2022-10-18 and 0.9-0 dated 2025-08-28
networkABC-0.8-1/networkABC/man/networkABC.Rd |only networkABC-0.9-0/networkABC/DESCRIPTION | 21 - networkABC-0.9-0/networkABC/MD5 | 47 +- networkABC-0.9-0/networkABC/NEWS.md | 6 networkABC-0.9-0/networkABC/R/abc.R | 30 + networkABC-0.9-0/networkABC/R/randABC-package.R | 11 networkABC-0.9-0/networkABC/R/show.R | 1 networkABC-0.9-0/networkABC/README.md | 29 + networkABC-0.9-0/networkABC/build/vignette.rds |binary networkABC-0.9-0/networkABC/inst/CITATION | 15 networkABC-0.9-0/networkABC/inst/_pkgdown.yml |only networkABC-0.9-0/networkABC/inst/doc/vignette.R | 42 +- networkABC-0.9-0/networkABC/inst/doc/vignette.html | 337 +++++++++--------- networkABC-0.9-0/networkABC/man/abc.Rd | 2 networkABC-0.9-0/networkABC/man/networkABC-package.Rd |only networkABC-0.9-0/networkABC/src/Makevars | 3 networkABC-0.9-0/networkABC/src/abc_R.c | 134 +++---- networkABC-0.9-0/networkABC/src/alloc2d.c |only networkABC-0.9-0/networkABC/src/alloc2d.h |only networkABC-0.9-0/networkABC/src/network_random_R.c | 2 networkABC-0.9-0/networkABC/tests |only 21 files changed, 377 insertions(+), 303 deletions(-)
Title: Detecting Group Disturbances from Longitudinal Observations
Description: Provides an algorithm to detect and characterize disturbances (start, end dates, intensity) that can occur at different hierarchical levels by studying the dynamics of longitudinal observations at the unit level and group level based on Nadaraya-Watson's smoothing curves, but also a shiny app which allows to visualize the observations and the detected disturbances. Finally the package provides a dataframe mimicking a pig farming system subsected to disturbances simulated according to Le et al.(2022) <doi:10.1016/j.animal.2022.100496>.
Author: Tom Rohmer [aut, cre],
Vincent Le [aut],
Ingrid David [aut]
Maintainer: Tom Rohmer <tom.rohmer@inrae.fr>
Diff between UpDown versions 1.2.1 dated 2023-07-20 and 1.2.3 dated 2025-08-28
DESCRIPTION | 9 +++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 2 +- R/Up.R | 43 ++++++++++--------------------------------- R/tools.R | 50 ++------------------------------------------------ R/validation.R | 2 +- README.md | 2 +- man/PigDisturbance.Rd | 5 ++--- man/PigFarming.Rd | 5 ++--- man/UpDown.Rd | 7 ++----- man/UpDownApp.Rd | 9 +++------ 11 files changed, 39 insertions(+), 115 deletions(-)
More information about searchAnalyzeR at CRAN
Permanent link
Title: Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io',
and 'RPubs'
Description: Programmatic deployment interface for 'RPubs',
'shinyapps.io', and 'Posit Connect'. Supported content types include R
Markdown documents, Shiny applications, Plumber APIs, plots, and
static web content.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Hadley Wickham [aut],
Jonathan McPherson [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between rsconnect versions 1.5.0 dated 2025-06-26 and 1.5.1 dated 2025-08-28
rsconnect-1.5.0/rsconnect/tests/testthat/quarto-proj-r-shiny |only rsconnect-1.5.1/rsconnect/DESCRIPTION | 6 rsconnect-1.5.1/rsconnect/MD5 | 26 +- rsconnect-1.5.1/rsconnect/NEWS.md | 11 rsconnect-1.5.1/rsconnect/R/accounts.R | 5 rsconnect-1.5.1/rsconnect/R/client-connect.R | 14 - rsconnect-1.5.1/rsconnect/R/cookies.R | 31 ++ rsconnect-1.5.1/rsconnect/tests/testthat/helper-content.R | 54 ++++ rsconnect-1.5.1/rsconnect/tests/testthat/helper.R | 24 ++ rsconnect-1.5.1/rsconnect/tests/testthat/test-appMetadata-quarto.R | 31 +- rsconnect-1.5.1/rsconnect/tests/testthat/test-bundle.R | 7 rsconnect-1.5.1/rsconnect/tests/testthat/test-client-connect.R | 120 ---------- rsconnect-1.5.1/rsconnect/tests/testthat/test-cookies.R | 19 + rsconnect-1.5.1/rsconnect/tests/testthat/test-writeManifest.R | 18 + 14 files changed, 190 insertions(+), 176 deletions(-)
Title: Inference on the Generalization Error
Description: Confidence interval and resampling methods for inference on
the generalization error.
Author: Sebastian Fischer [cre, aut] ,
Hannah Schulz-Kuempel [aut]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mlr3inferr versions 0.1.0 dated 2025-01-13 and 0.2.0 dated 2025-08-28
mlr3inferr-0.1.0/mlr3inferr/R/MeasureCI.R |only mlr3inferr-0.1.0/mlr3inferr/R/MeasureCIConZ.R |only mlr3inferr-0.1.0/mlr3inferr/R/MeasureCICorT.R |only mlr3inferr-0.1.0/mlr3inferr/R/MeasureCIHoldout.R |only mlr3inferr-0.1.0/mlr3inferr/R/MeasureCIWaldCV.R |only mlr3inferr-0.1.0/mlr3inferr/man/mlr_measures_ci_con_z.Rd |only mlr3inferr-0.1.0/mlr3inferr/man/mlr_measures_ci_cor_t.Rd |only mlr3inferr-0.1.0/mlr3inferr/man/mlr_measures_ci_holdout.Rd |only mlr3inferr-0.1.0/mlr3inferr/man/mlr_measures_ci_ncv.Rd |only mlr3inferr-0.1.0/mlr3inferr/man/mlr_measures_ci_wald_cv.Rd |only mlr3inferr-0.1.0/mlr3inferr/tests/testthat/test_MeasureAbstractCI.R |only mlr3inferr-0.1.0/mlr3inferr/tests/testthat/test_MeasureCI.R |only mlr3inferr-0.1.0/mlr3inferr/tests/testthat/test_MeasureCIConZ.R |only mlr3inferr-0.1.0/mlr3inferr/tests/testthat/test_MeasureCIHoldout.R |only mlr3inferr-0.1.0/mlr3inferr/tests/testthat/test_MeasureCINestedCV.R |only mlr3inferr-0.1.0/mlr3inferr/tests/testthat/test_MeasureCIWaldCV.R |only mlr3inferr-0.2.0/mlr3inferr/DESCRIPTION | 29 ++-- mlr3inferr-0.2.0/mlr3inferr/MD5 | 61 +++++----- mlr3inferr-0.2.0/mlr3inferr/NEWS.md |only mlr3inferr-0.2.0/mlr3inferr/R/MeasureAbstractCi.R | 5 mlr3inferr-0.2.0/mlr3inferr/R/MeasureCi.R |only mlr3inferr-0.2.0/mlr3inferr/R/MeasureCiConZ.R |only mlr3inferr-0.2.0/mlr3inferr/R/MeasureCiCorT.R |only mlr3inferr-0.2.0/mlr3inferr/R/MeasureCiHoldout.R |only mlr3inferr-0.2.0/mlr3inferr/R/MeasureCiNestedCV.R | 17 +- mlr3inferr-0.2.0/mlr3inferr/R/MeasureCiWaldCV.R |only mlr3inferr-0.2.0/mlr3inferr/R/ResamplingNestedCV.R | 18 ++ mlr3inferr-0.2.0/mlr3inferr/R/ResamplingPairedSubsampling.R | 10 - mlr3inferr-0.2.0/mlr3inferr/README.md | 51 ++++++-- mlr3inferr-0.2.0/mlr3inferr/man/figures/README-unnamed-chunk-5-1.png |binary mlr3inferr-0.2.0/mlr3inferr/man/mlr_measures_abstract_ci.Rd | 6 mlr3inferr-0.2.0/mlr3inferr/man/mlr_measures_ci.Rd | 2 mlr3inferr-0.2.0/mlr3inferr/man/mlr_measures_ci.con_z.Rd |only mlr3inferr-0.2.0/mlr3inferr/man/mlr_measures_ci.cor_t.Rd |only mlr3inferr-0.2.0/mlr3inferr/man/mlr_measures_ci.holdout.Rd |only mlr3inferr-0.2.0/mlr3inferr/man/mlr_measures_ci.ncv.Rd |only mlr3inferr-0.2.0/mlr3inferr/man/mlr_measures_ci.wald_cv.Rd |only mlr3inferr-0.2.0/mlr3inferr/man/mlr_resamplings_ncv.Rd | 9 + mlr3inferr-0.2.0/mlr3inferr/man/mlr_resamplings_paired_subsampling.Rd | 8 - mlr3inferr-0.2.0/mlr3inferr/tests/testthat/helpers.R | 8 - mlr3inferr-0.2.0/mlr3inferr/tests/testthat/test_MeasureAbstractCi.R |only mlr3inferr-0.2.0/mlr3inferr/tests/testthat/test_MeasureCi.R |only mlr3inferr-0.2.0/mlr3inferr/tests/testthat/test_MeasureCiConZ.R |only mlr3inferr-0.2.0/mlr3inferr/tests/testthat/test_MeasureCiHoldout.R |only mlr3inferr-0.2.0/mlr3inferr/tests/testthat/test_MeasureCiNestedCV.R |only mlr3inferr-0.2.0/mlr3inferr/tests/testthat/test_MeasureCiWaldCV.R |only mlr3inferr-0.2.0/mlr3inferr/tests/testthat/test_ResamplingNestedCV.R | 6 mlr3inferr-0.2.0/mlr3inferr/tests/testthat/test_ResamplingPairedSubsampling.R | 4 48 files changed, 148 insertions(+), 86 deletions(-)
Title: Display Idiomatic Code to Construct Most R Objects
Description: Prints code that can be used to recreate R objects. In a
sense it is similar to 'base::dput()' or 'base::deparse()' but
'constructive' strives to use idiomatic constructors.
Author: Antoine Fabri [aut, cre],
Kirill Mueller [ctb] ,
Jacob Scott [ctb],
cynkra GmbH [fnd]
Maintainer: Antoine Fabri <antoine.fabri@gmail.com>
Diff between constructive versions 1.1.0 dated 2025-01-10 and 1.2.0 dated 2025-08-28
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Title: ARMA Models to Value Stock Options
Description: Providing ways to estimate the value of European stock options
given historical stock price data. It includes functions for calculating option values
based on autoregressive–moving-average (ARMA) models and generates information about these models.
This package is made to be easy to understand and for financial analysis capabilities.
Author: Brian MacCarvill [aut, cre]
Maintainer: Brian MacCarvill <brianmaccarvills@gmail.com>
Diff between armaOptions versions 1.0.0 dated 2025-07-11 and 1.0.1 dated 2025-08-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 16 +++++++++++----- README.md | 4 ++-- 4 files changed, 20 insertions(+), 14 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution
data. Data are typically regular time series and air quality
measurement, meteorological data and dispersion model output can be
analysed. The package is described in Carslaw and Ropkins (2012,
<doi:10.1016/j.envsoft.2011.09.008>) and subsequent papers.
Author: David Carslaw [aut, cre] ,
Jack Davison [aut] ,
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 2.18-2 dated 2024-03-11 and 2.19.0 dated 2025-08-28
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openair-2.19.0/openair/R/polarFreq.R | 923 +-- openair-2.19.0/openair/R/polarPlot.R | 3648 ++++++------ openair-2.19.0/openair/R/quickText.R | 393 - openair-2.19.0/openair/R/rollingMean.R |only openair-2.19.0/openair/R/runRegression.R | 305 - openair-2.19.0/openair/R/samp.boot.block.R | 5 openair-2.19.0/openair/R/scatterPlot.R | 4062 +++++++------- openair-2.19.0/openair/R/selectByDate.R |only openair-2.19.0/openair/R/selectRunning.R | 235 openair-2.19.0/openair/R/senTheil.R | 48 openair-2.19.0/openair/R/smoothTrend.R | 1212 ++-- openair-2.19.0/openair/R/splitByDate.R |only openair-2.19.0/openair/R/summaryPlot.R | 1241 ++-- openair-2.19.0/openair/R/timeAverage.R | 1323 ++-- openair-2.19.0/openair/R/timePlot.R | 1635 +++-- openair-2.19.0/openair/R/timeProp.R | 755 +- openair-2.19.0/openair/R/timeVariation.R | 2756 +++++---- openair-2.19.0/openair/R/trajCluster.R | 615 +- openair-2.19.0/openair/R/trajLevel.R | 1347 ++-- openair-2.19.0/openair/R/trajPlot.R | 350 - openair-2.19.0/openair/R/trendLevel.R | 1355 ++-- openair-2.19.0/openair/R/utilities.R | 2022 ++---- openair-2.19.0/openair/R/windRose.R | 2078 +++---- openair-2.19.0/openair/R/zzz.R | 94 openair-2.19.0/openair/README.md | 337 - openair-2.19.0/openair/build/partial.rdb |binary openair-2.19.0/openair/inst/CITATION | 42 openair-2.19.0/openair/inst/WORDLIST | 991 +-- openair-2.19.0/openair/man/TaylorDiagram.Rd | 557 - openair-2.19.0/openair/man/TheilSen.Rd | 588 +- openair-2.19.0/openair/man/aqStats.Rd | 228 openair-2.19.0/openair/man/bootMeans.Rd |only openair-2.19.0/openair/man/calcFno2.Rd | 489 - openair-2.19.0/openair/man/calcPercentile.Rd | 189 openair-2.19.0/openair/man/calendarPlot.Rd | 469 - openair-2.19.0/openair/man/conditionalEval.Rd | 378 - openair-2.19.0/openair/man/conditionalQuantile.Rd | 350 - openair-2.19.0/openair/man/corPlot.Rd | 307 - openair-2.19.0/openair/man/cutData.Rd | 296 - openair-2.19.0/openair/man/drawOpenKey.Rd | 355 - openair-2.19.0/openair/man/figures/feature-banner.png |only openair-2.19.0/openair/man/figures/logo.png |binary openair-2.19.0/openair/man/importADMS.Rd | 387 - openair-2.19.0/openair/man/importEurope.Rd | 132 openair-2.19.0/openair/man/importImperial.Rd |only openair-2.19.0/openair/man/importMeta.Rd | 222 openair-2.19.0/openair/man/importTraj.Rd | 309 - openair-2.19.0/openair/man/importUKAQ-wrapper.Rd | 495 - openair-2.19.0/openair/man/importUKAQ.Rd | 464 - openair-2.19.0/openair/man/linearRelation.Rd | 279 openair-2.19.0/openair/man/modStats.Rd | 355 - openair-2.19.0/openair/man/mydata.Rd | 100 openair-2.19.0/openair/man/openColours.Rd | 243 openair-2.19.0/openair/man/openair-package.Rd | 264 openair-2.19.0/openair/man/percentileRose.Rd | 417 - openair-2.19.0/openair/man/polarAnnulus.Rd | 558 - openair-2.19.0/openair/man/polarCluster.Rd | 809 +- openair-2.19.0/openair/man/polarDiff.Rd | 617 +- openair-2.19.0/openair/man/polarFreq.Rd | 487 - openair-2.19.0/openair/man/polarPlot.Rd | 956 +-- openair-2.19.0/openair/man/pollutionRose.Rd | 447 - openair-2.19.0/openair/man/quickText.Rd | 95 openair-2.19.0/openair/man/rollingMean.Rd | 137 openair-2.19.0/openair/man/runRegression.Rd | 155 openair-2.19.0/openair/man/scatterPlot.Rd | 763 +- openair-2.19.0/openair/man/selectByDate.Rd | 159 openair-2.19.0/openair/man/selectRunning.Rd | 152 openair-2.19.0/openair/man/smoothTrend.Rd | 464 - openair-2.19.0/openair/man/splitByDate.Rd | 118 openair-2.19.0/openair/man/summaryPlot.Rd | 376 - openair-2.19.0/openair/man/timeAverage.Rd | 421 - openair-2.19.0/openair/man/timePlot.Rd | 654 +- openair-2.19.0/openair/man/timeProp.Rd | 313 - openair-2.19.0/openair/man/timeVariation.Rd | 664 +- openair-2.19.0/openair/man/trajCluster.Rd | 329 - openair-2.19.0/openair/man/trajLevel.Rd | 582 +- openair-2.19.0/openair/man/trajPlot.Rd | 377 - openair-2.19.0/openair/man/trendLevel.Rd | 419 - openair-2.19.0/openair/man/windRose.Rd | 543 - openair-2.19.0/openair/tests |only 125 files changed, 40712 insertions(+), 36959 deletions(-)
Title: Interactive Viewing of Spatial Data in R
Description: Quickly and conveniently create interactive
visualisations of spatial data with or without background maps.
Attributes of displayed features are fully queryable via pop-up
windows. Additional functionality includes methods to visualise true-
and false-color raster images and bounding boxes.
Author: Tim Appelhans [cre, aut],
Florian Detsch [aut],
Christoph Reudenbach [aut],
Stefan Woellauer [aut],
Spaska Forteva [ctb],
Thomas Nauss [ctb],
Edzer Pebesma [ctb],
Kenton Russell [ctb],
Michael Sumner [ctb],
Jochen Darley [ctb],
Pierre Roudier [ctb],
[...truncated...]
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between mapview versions 2.11.2 dated 2023-10-13 and 2.11.3 dated 2025-08-28
DESCRIPTION | 17 +++--- MD5 | 98 +++++++++++++++++----------------- NAMESPACE | 11 +-- NEWS | 24 ++++++-- NEWS.md | 48 ++++++++++------- R/color.R | 4 - R/cubeView.R | 4 - R/extent.R | 8 +- R/fgb.R | 2 R/files.R | 4 - R/leafletControls.R | 5 + R/legend.R | 121 ++++++++++++++++++++++++++++--------------- R/mapView.R | 81 +++++++++++++++------------- R/mapshot.R | 4 - R/mapview-package.R | 64 ++++++++-------------- R/mapviewControls.R | 2 R/ops.R | 7 ++ R/options.R | 31 +++++------ R/plainView.R | 4 - R/print.R | 8 -- R/projection.R | 3 + R/raster.R | 31 ++++++++--- R/sf.R | 4 - R/shiny-mapview.R | 4 - R/slideView.R | 2 R/stars.R | 2 R/viewRGB.R | 2 R/watch.R | 4 - README.md | 6 -- data/breweries.rda |binary data/franconia.rda |binary data/trails.rda |binary inst/tinytest/test-mapview.R | 46 ---------------- man/breweries.Rd | 6 +- man/franconia.Rd | 9 ++- man/knit_print.mapview.Rd | 2 man/mapView.Rd | 104 ++++++++++++++++++------------------ man/mapshot.Rd | 4 - man/mapview-defunct.Rd | 104 ++++++++++++++++++------------------ man/mapview-package.Rd | 42 ++++++++++++-- man/mapviewColors.Rd | 4 - man/mapviewOptions.Rd | 35 ++++++------ man/mapviewOutput.Rd | 2 man/mapviewWatcher.Rd | 36 ++++++------ man/ops.Rd | 8 +- man/removeMapJunk.Rd | 12 ++-- man/renderMapview.Rd | 2 man/trails.Rd | 12 ++-- man/viewExtent.Rd | 41 +++++++++++++- man/viewRGB.Rd | 2 50 files changed, 591 insertions(+), 485 deletions(-)
Title: 'leaflet' Extensions for 'mapview'
Description: Provides extensions for packages 'leaflet' & 'mapdeck',
many of which are used by package 'mapview'.
Focus is on functionality readily available in
Geographic Information Systems such as 'Quantum GIS'. Includes functions
to display coordinates of mouse pointer position, query image values via
mouse pointer and zoom-to-layer buttons. Additionally, provides a feature
type agnostic function to add points, lines, polygons to a map.
Author: Tim Appelhans [cre, aut],
Christoph Reudenbach [ctb],
Kenton Russell [ctb],
Jochen Darley [ctb],
Daniel Montague [ctb, cph] ,
Lorenzo Busetto [ctb],
Luigi Ranghetti [ctb],
Miles McBain [ctb],
Sebastian Gatscha [ctb],
Bjoern Harrtell [ctb, cph] ,
Danie [...truncated...]
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between leafem versions 0.2.4 dated 2025-05-01 and 0.2.5 dated 2025-08-28
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS | 7 +++++++ NEWS.md | 7 +++++++ R/file.R | 4 ++-- R/homebutton.R | 4 +++- inst/htmlwidgets/lib/FlatGeoBuf/fgb.js | 4 ++-- man/addRasterRGB.Rd | 20 +++++++++++++------- man/addStarsImage.Rd | 20 +++++++++++++------- 9 files changed, 58 insertions(+), 30 deletions(-)
Title: Ecological Trajectory Analysis
Description: Analysis of temporal changes (i.e. dynamics) of ecological entities, defined as trajectories on a chosen multivariate space, by providing a set of
trajectory metrics and visual representations [De Caceres et al. (2019) <doi:10.1002/ecm.1350>;
and Sturbois et al. (2021) <doi:10.1016/j.ecolmodel.2020.109400>]. Includes functions
to estimate metrics for individual trajectories (length, directionality, angles, ...) as well as
metrics to relate pairs of trajectories (dissimilarity and convergence). Functions are also
provided to estimate the ecological quality of ecosystem with respect to reference conditions
[Sturbois et al. (2023) <doi:10.1002/ecs2.4726>].
Author: Miquel De Caceres [aut, cre] ,
Nicolas Djeghri [aut] ,
Anthony Sturbois [aut] ,
Javier De la Casa [ctb]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between ecotraj versions 1.1.0 dated 2025-05-05 and 1.1.1 dated 2025-08-28
DESCRIPTION | 8 +++--- MD5 | 18 +++++++------- NEWS.md | 5 ++++ R/defineTrajectories.R | 36 ++++++++++++++++++++--------- R/subsetTrajectories.R | 18 ++++++++++++-- R/trajectoryComparison.R | 2 - build/partial.rdb |binary man/defineTrajectories.Rd | 8 ++++-- man/subsetTrajectories.Rd | 14 ++++++++--- tests/testthat/test_TrajectoryDefinition.R | 7 +++++ 10 files changed, 84 insertions(+), 32 deletions(-)
Title: Computational Test for Conditional Independence
Description: Tool for performing computational testing for conditional independence between variables in a dataset. 'CCI' implements permutation in combination with Monte Carlo Cross-Validation in generating null distributions and test statistics. For more details see Computational Test for Conditional Independence (2024) <doi:10.3390/a17080323>.
Author: Christian B. H. Thorjussen [aut, cre] ,
Kristian Hovde Liland [aut]
Maintainer: Christian B. H. Thorjussen <christianbern@gmail.com>
Diff between CCI versions 0.2.1 dated 2025-08-19 and 0.3.1 dated 2025-08-28
DESCRIPTION | 12 MD5 | 96 +- NAMESPACE | 1 R/CCI.direction.R | 342 +++---- R/CCI.pretuner.R | 654 ++++++------- R/CCI.test.R | 486 ++++------ R/QQplot.R | 204 ++-- R/data.R | 1398 ++++++++++++++--------------- R/perm.test.R | 284 ++---- R/plot.R | 134 +- R/reports.R | 90 - R/test.gen.R | 400 ++++---- R/utils.R | 537 +++++------ R/wrappers.R | 490 +++++----- README.md | 1058 +++++++++++----------- inst/CITATION | 30 man/BinaryData.Rd | 46 man/BivMultinominal.Rd | 38 man/BivNonLinearCategorization.Rd | 34 man/CCI.test.Rd | 6 man/ComplexCategorization.Rd | 42 man/ExpLogData.Rd | 34 man/ExpLogThreshold.Rd | 40 man/ExponentialNoise.Rd | 46 man/GridPartition.Rd | 42 man/HardCase.Rd | 42 man/InteractiondData.Rd | 34 man/NonLinNormal.Rd | 42 man/NonLinNormalZs.Rd | 50 - man/NonLinearCategorization.Rd | 38 man/NonLinearData.Rd | 34 man/NormalData.Rd | 34 man/PoissonNoise.Rd | 46 man/PolyData.Rd | 34 man/PolyDecision.Rd | 42 man/QuadThresh.Rd | 40 man/SinCosThreshold.Rd | 40 man/SineGaussianBiv.Rd | 42 man/SineGaussianNoise.Rd | 42 man/TrigData.Rd | 34 man/UniformNoise.Rd | 42 man/add_interaction_terms.Rd | 78 - man/add_poly_terms.Rd | 86 - man/build_formula.Rd | 56 - man/check_formula.Rd | 40 man/clean_formula.Rd | 2 man/get_pvalues.Rd | 70 - man/get_tuned_params.Rd | 34 tests/testthat/testCCI.R | 1797 ++++++++++++++++---------------------- 49 files changed, 4580 insertions(+), 4763 deletions(-)
Title: Comparative Analyses of Phylogenetics and Evolution in R
Description: Functions for performing phylogenetic comparative analyses.
Author: David Orme [aut, cre] ,
Rob Freckleton [aut],
Gavin Thomas [aut],
Thomas Petzoldt [aut],
Susanne Fritz [aut],
Nick Isaac [aut],
Will Pearse [aut]
Maintainer: David Orme <d.orme@imperial.ac.uk>
Diff between caper versions 1.0.3 dated 2023-09-26 and 1.0.4 dated 2025-08-28
CHANGES | 4 +++ DESCRIPTION | 11 +++++---- MD5 | 16 +++++++------- build/vignette.rds |binary inst/doc/caper.R | 1 inst/doc/caper.pdf |binary man/comparative.data.Rd | 53 ++++++++++++++++++++++++++++++++++++++---------- man/macrocaic.Rd | 2 - man/pd.calc.Rd | 5 ++-- 9 files changed, 63 insertions(+), 29 deletions(-)
Title: Simulate Disease Outbreak Line List and Contacts Data
Description: Tools to simulate realistic raw case data for an epidemic in
the form of line lists and contacts using a branching process.
Simulated outbreaks are parameterised with epidemiological parameters
and can have age-structured populations, age-stratified
hospitalisation and death risk and time-varying case fatality risk.
Author: Joshua W. Lambert [aut, cre, cph] ,
Carmen Tamayo Cuartero [aut] ,
Hugo Gruson [ctb, rev] ,
Pratik R. Gupte [ctb, rev] ,
Adam Kucharski [rev] ,
Chris Hartgerink [rev] ,
Sebastian Funk [ctb] ,
London School of Hygiene and Tropical Medicine, LSHTM [cph [...truncated...]
Maintainer: Joshua W. Lambert <joshua.lambert@lshtm.ac.uk>
Diff between simulist versions 0.5.0 dated 2025-03-25 and 0.6.0 dated 2025-08-28
DESCRIPTION | 37 MD5 | 110 NAMESPACE | 1 NEWS.md | 40 R/censor_linelist.R |only R/create_config.R | 2 R/messy_linelist.R | 10 R/sim_contacts.R | 21 R/sim_internal.R | 12 R/sim_linelist.R | 24 R/sim_outbreak.R | 6 R/truncate_linelist.R | 7 R/utils.R | 9 README.md | 41 build/partial.rdb |only build/vignette.rds |binary inst/WORDLIST | 11 inst/doc/age-strat-risks.R | 2 inst/doc/age-strat-risks.html | 3 inst/doc/age-struct-pop.Rmd | 10 inst/doc/age-struct-pop.html | 32 inst/doc/design-principles.Rmd | 2 inst/doc/design-principles.html | 4 inst/doc/reporting-delays-truncation.Rmd | 12 inst/doc/reporting-delays-truncation.html | 34 inst/doc/simulist.html | 51 inst/doc/time-varying-cfr.Rmd | 14 inst/doc/time-varying-cfr.html | 62 inst/doc/vis-linelist.R | 23 inst/doc/vis-linelist.Rmd | 18 inst/doc/vis-linelist.html | 527 +- inst/doc/wrangling-linelist.R | 97 inst/doc/wrangling-linelist.Rmd | 164 inst/doc/wrangling-linelist.html | 5894 +++++++++++++++++++++++- man/censor_linelist.Rd |only man/create_config.Rd | 2 man/figures/simulist_archi.svg | 174 man/messy_linelist.Rd | 8 man/sim_contacts.Rd | 21 man/sim_linelist.Rd | 24 man/sim_outbreak.Rd | 6 man/simulist-package.Rd | 2 man/truncate_linelist.Rd | 4 tests/testthat/_snaps/sim_contacts.md | 240 tests/testthat/_snaps/sim_outbreak.md | 820 +-- tests/testthat/test-censor_linelist.R |only tests/testthat/test-messy_linelist.R | 9 tests/testthat/test-truncate_linelist.R | 14 tests/testthat/testdata/pre_ct.rds |binary tests/testthat/testdata/pre_hospitalisation.rds |binary tests/testthat/testdata/pre_names.rds |binary tests/testthat/testdata/pre_outcome.rds |binary vignettes/age-struct-pop.Rmd | 10 vignettes/design-principles.Rmd | 2 vignettes/reporting-delays-truncation.Rmd | 12 vignettes/time-varying-cfr.Rmd | 14 vignettes/vis-linelist.Rmd | 18 vignettes/wrangling-linelist.Rmd | 164 58 files changed, 7594 insertions(+), 1230 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Description: A rich hierarchy of sparse and dense matrix classes,
including general, symmetric, triangular, and diagonal matrices
with numeric, logical, or pattern entries. Efficient methods for
operating on such matrices, often wrapping the 'BLAS', 'LAPACK',
and 'SuiteSparse' libraries.
Author: Douglas Bates [aut] ,
Martin Maechler [aut, cre] ,
Mikael Jagan [aut] ,
Timothy A. Davis [ctb] ,
pattern="License", full.names=TRUE, recursive=TRUE)),
George Karypis [ctb] ,
Jason Riedy [ctb] and onenormest, Copyright: Regents of the
University of C [...truncated...]
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.7-3 dated 2025-03-11 and 1.7-4 dated 2025-08-28
DESCRIPTION | 26 ++++++++++++++------------ MD5 | 30 +++++++++++++++--------------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 20 ++++++++++++++++++++ inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary inst/include/Matrix/version.h | 4 ++-- src/dense.c | 11 ++++++++--- src/matmult.c | 4 ++-- src/sparse.c | 7 ++++--- src/version.h | 4 ++-- tests/Simple.R | 9 +++++++++ 16 files changed, 76 insertions(+), 39 deletions(-)
Title: Translate Words or Sentences via Online Translators
Description: Useful functions to translate text for multiple languages using online translators.
For example, by translating error messages and descriptive analysis results into a language familiar
to the user, it enables a better understanding of the information, thereby reducing the barriers caused by language.
It offers several helper functions to query gene information to help interpretation of interested genes (e.g., marker genes, differential expression genes),
and provides utilities to translate 'ggplot' graphics. This package is not affiliated with any of the online translators.
The developers do not take responsibility for the invoice it incurs when using this package, especially for exceeding the free quota.
Author: Guangchuang Yu [aut, cre, cph] ,
Guannan Chen [ctb],
Difei Wang [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between fanyi versions 0.0.7 dated 2024-04-13 and 0.0.8 dated 2025-08-28
fanyi-0.0.7/fanyi/README.md |only fanyi-0.0.8/fanyi/DESCRIPTION | 14 ++++----- fanyi-0.0.8/fanyi/MD5 | 21 +++++++------- fanyi-0.0.8/fanyi/NAMESPACE | 4 ++ fanyi-0.0.8/fanyi/NEWS.md | 6 ++++ fanyi-0.0.8/fanyi/R/chatglm.r | 53 ++++++++++--------------------------- fanyi-0.0.8/fanyi/R/deepseek.r |only fanyi-0.0.8/fanyi/R/dictionary.r | 15 ++++++---- fanyi-0.0.8/fanyi/R/qwen.r |only fanyi-0.0.8/fanyi/R/translate.r | 36 +++++++++++++++++++------ fanyi-0.0.8/fanyi/R/zzz.r | 9 ------ fanyi-0.0.8/fanyi/inst/CITATION | 32 ++++++++++++++-------- fanyi-0.0.8/fanyi/man/translate.Rd | 11 ++++++- 13 files changed, 111 insertions(+), 90 deletions(-)
Title: User Oriented Plotting Functions
Description: Plots with high flexibility and easy handling, including
informative regression diagnostics for many models.
Author: Werner A. Stahel [aut, cre],
Martin Maechler [ctb]
Maintainer: Werner A. Stahel <stahel@stat.math.ethz.ch>
Diff between plgraphics versions 1.2 dated 2023-09-29 and 1.3 dated 2025-08-28
DESCRIPTION | 12 +++-- MD5 | 30 ++++++++------ R/pl.R | 80 +++++++++++++++++++++------------------ build/vignette.rds |binary inst/doc/logst.R |only inst/doc/logst.Rnw |only inst/doc/logst.pdf |only inst/doc/pl-description.R | 11 ----- inst/doc/pl-description.Rnw | 88 +++++++++++-------------------------------- inst/doc/pl-description.pdf |binary man/Tobit.Rd | 4 - man/logst.Rd | 42 ++++++++++++++++++++ man/plgraphics-internal.Rd | 2 man/ploptions.Rd | 2 man/ploptions.list.Rd | 2 tests/pl-test.R | 6 ++ vignettes/logst.Rnw |only vignettes/pl-description.Rnw | 88 +++++++++++-------------------------------- 18 files changed, 170 insertions(+), 197 deletions(-)
More information about terminalgraphics at CRAN
Permanent link
Title: Colors for all
Description: Color palettes for all people, including those with color vision deficiency. Popular color palette series have been organized by type and have been scored on several properties such as color-blind-friendliness and fairness (i.e. do colors stand out equally?). Own palettes can also be loaded and analysed. Besides the common palette types (categorical, sequential, and diverging) it also includes cyclic and bivariate color palettes. Furthermore, a color for missing values is assigned to each palette.
Author: Martijn Tennekes [aut, cre],
Marco Puts [ctb],
Achim Zeileis [ctb],
Jakub Nowosad [ctb],
Robin Lovelace [ctb],
Helgasoft [ctb],
Matthew Petroff [ctb],
Olivier Roy [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between cols4all versions 0.8 dated 2024-10-16 and 0.9 dated 2025-08-28
DESCRIPTION | 15 +++--- MD5 | 34 +++++++-------- NEWS.md | 5 ++ R/c4a.R | 54 +++++++++++++++++++----- R/c4a_data.R | 1 R/c4a_default_contrast.R | 1 R/c4a_plot.R | 4 + R/check_pals.R | 10 ++-- R/get_pal_n.R | 27 +++++++++++- R/ggplot2.R | 105 ++++++++++++++++++++++++++++++++++------------- R/onLoad.R | 1 R/process_palette.R | 1 R/sysdata.rda |binary inst/cols4all.bib | 8 +++ man/c4a.Rd | 9 ++-- man/c4a_palettes.Rd | 2 man/cols4all-package.Rd | 6 +- man/scales_ggplot2.Rd | 4 - 18 files changed, 206 insertions(+), 81 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-28 0.1.34
Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Small-area estimation.
Author: Thomas Lumley [aut],
Peter Gao [aut],
Ben Schneider [aut],
"Thomas Lumley" [cre]
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>
Diff between survey versions 4.4-2 dated 2024-03-20 and 4.4-8 dated 2025-08-28
DESCRIPTION | 24 ++++++++++++++++++++---- MD5 | 30 +++++++++++++++--------------- R/survey.R | 1 + build/vignette.rds |binary inst/NEWS | 2 ++ inst/doc/domain.pdf |binary inst/doc/epi.pdf |binary inst/doc/pps.pdf |binary inst/doc/precalibrated.pdf |binary inst/doc/qrule.pdf |binary inst/doc/survey.pdf |binary man/hadamard.Rd | 5 ++--- man/svycoplot.Rd | 4 ++-- man/svycoxph.Rd | 4 ++-- man/svylogrank.Rd | 2 +- src/arma_multistage.cpp | 4 ++-- 16 files changed, 47 insertions(+), 29 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data sets,
regression models, and more. The code to create the tables is concise
and highly customizable. Data frames can be summarized with any
function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] ,
Joseph Larmarange [aut] ,
Michael Curry [aut] ,
Emily de la Rua [aut] ,
Jessica Lavery [aut] ,
Karissa Whiting [aut] ,
Emily C. Zabor [aut] ,
Xing Bai [ctb],
Malcolm Barrett [ctb] ,
Esther Drill [ctb] ,
Jessica Flynn [c [...truncated...]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 2.3.0 dated 2025-07-03 and 2.4.0 dated 2025-08-28
DESCRIPTION | 32 LICENSE | 2 MD5 | 368 ++--- NAMESPACE | 3 NEWS.md | 32 R/add_ci.R | 2 R/add_ci.tbl_svysummary.R | 2 R/add_difference.R | 2 R/add_difference.tbl_svysummary.R | 2 R/add_difference_row.R | 2 R/add_glance.R | 2 R/add_global_p.R | 2 R/add_n.R | 2 R/add_n_regression.R | 2 R/add_nevent.R | 2 R/add_overall_ard.R | 8 R/add_p.R | 2 R/add_p.tbl_continuous.R | 2 R/add_p.tbl_cross.R | 2 R/add_p.tbl_survfit.R | 2 R/add_p.tbl_svysummary.R | 2 R/add_q.R | 2 R/add_variable_group_header.R | 2 R/add_vif.R | 4 R/assign_summary_digits.R | 2 R/brdg_continuous.R | 2 R/brdg_hierarchical.R | 16 R/brdg_summary.R | 6 R/brdg_wide_summary.R | 2 R/combine_terms.R | 1 R/deprecated.R | 7 R/dim.R |only R/filter_hierarchical.R | 76 - R/gather_ard.R | 1 R/glance_fun.R | 2 R/global_pvalue_fun.R | 6 R/inline_text.tbl_regression.R | 2 R/inline_text.tbl_uvregression.R | 2 R/modify.R | 6 R/modify_abbreviation.R | 2 R/modify_column_merge.R | 2 R/plot.R | 1 R/sort_hierarchical.R | 94 - R/tbl_ard_continuous.R | 6 R/tbl_ard_hierarchical.R | 4 R/tbl_ard_summary.R | 22 R/tbl_ard_wide_summary.R | 16 R/tbl_continuous.R | 4 R/tbl_custom_summary.R | 2 R/tbl_hierarchical.R | 6 R/tbl_likert.R | 3 R/tbl_regression.R | 2 R/tbl_split.R | 106 + R/tbl_stack.R | 75 - R/tbl_strata.R | 4 R/tbl_strata_nested_stack.R | 2 R/tbl_summary.R | 10 R/tbl_svysummary.R | 23 R/tbl_uvregression.R | 3 R/tbl_wide_summary.R | 7 R/utils-add_p_tests.R | 29 R/utils-tbl_custom_summary.R | 4 build/vignette.rds |binary inst/doc/gtsummary_definition.html | 1100 ++++++++-------- man/add_ci.Rd | 2 man/add_ci.tbl_svysummary.Rd | 2 man/add_difference.tbl_summary.Rd | 2 man/add_difference.tbl_svysummary.Rd | 2 man/add_difference_row.tbl_summary.Rd | 2 man/add_glance.Rd | 2 man/add_global_p.Rd | 2 man/add_n_regression.Rd | 2 man/add_n_summary.Rd | 2 man/add_nevent_regression.Rd | 2 man/add_overall_ard.Rd | 8 man/add_p.tbl_continuous.Rd | 2 man/add_p.tbl_summary.Rd | 2 man/add_p.tbl_survfit.Rd | 2 man/add_p.tbl_svysummary.Rd | 2 man/add_q.Rd | 2 man/add_variable_group_header.Rd | 2 man/add_vif.Rd | 2 man/brdg_continuous.Rd | 2 man/brdg_summary.Rd | 6 man/brdg_wide_summary.Rd | 2 man/dim.gtsummary.Rd |only man/filter_hierarchical.Rd | 87 + man/glance_fun_s3.Rd | 2 man/global_pvalue_fun.Rd | 2 man/gtsummary-package.Rd | 1 man/inline_text.tbl_regression.Rd | 2 man/inline_text.tbl_uvregression.Rd | 2 man/modify.Rd | 4 man/modify_abbreviation.Rd | 2 man/modify_column_merge.Rd | 2 man/plot.Rd | 3 man/proportion_summary.Rd | 3 man/ratio_summary.Rd | 1 man/sort_hierarchical.Rd | 55 man/tbl_ard_continuous.Rd | 6 man/tbl_ard_hierarchical.Rd | 4 man/tbl_ard_summary.Rd | 12 man/tbl_ard_wide_summary.Rd | 6 man/tbl_hierarchical.Rd | 5 man/tbl_likert.Rd | 1 man/tbl_regression.Rd | 2 man/tbl_split_by.Rd | 26 man/tbl_stack.Rd | 13 man/tbl_strata.Rd | 2 man/tbl_summary.Rd | 2 man/tbl_svysummary.Rd | 2 man/tbl_uvregression.Rd | 2 man/tbl_wide_summary.Rd | 1 tests/testthat/_snaps/add_stat_label.tbl_ard_summary.md | 12 tests/testthat/_snaps/filter_hierarchical.md | 12 tests/testthat/_snaps/sort_hierarchical.md | 2 tests/testthat/_snaps/tbl_ard_continuous.md | 24 tests/testthat/_snaps/tbl_ard_summary.md | 29 tests/testthat/_snaps/tbl_ard_wide_summary.md | 17 tests/testthat/_snaps/tbl_split.md | 13 tests/testthat/_snaps/tbl_stack.md | 15 tests/testthat/_snaps/tbl_svysummary.md | 2 tests/testthat/test-add_ci.tbl_summary.R | 2 tests/testthat/test-add_ci.tbl_svysummary.R | 2 tests/testthat/test-add_difference.tbl_svysummary.R | 2 tests/testthat/test-add_glance.R | 2 tests/testthat/test-add_global_p.tbl_regression.R | 2 tests/testthat/test-add_global_p.tbl_uvregression.R | 2 tests/testthat/test-add_n.tbl_regression.R | 2 tests/testthat/test-add_nevent.tbl_regression.R | 2 tests/testthat/test-add_overall.tbl_ard_summary.R | 8 tests/testthat/test-add_overall.tbl_hierarchical.R | 2 tests/testthat/test-add_p.tbl_continuous.R | 1 tests/testthat/test-add_p.tbl_cross.R | 24 tests/testthat/test-add_p.tbl_survfit.R | 2 tests/testthat/test-add_p.tbl_svysummary.R | 2 tests/testthat/test-add_stat.R | 1 tests/testthat/test-add_stat_label.tbl_ard_summary.R | 20 tests/testthat/test-add_variable_group_header.R | 2 tests/testthat/test-add_vif.R | 2 tests/testthat/test-as_flex_table.R | 2 tests/testthat/test-as_gt.R | 2 tests/testthat/test-as_hux_table.R | 3 tests/testthat/test-as_kable.R | 2 tests/testthat/test-as_kable_extra.R | 2 tests/testthat/test-as_tibble.R | 2 tests/testthat/test-bold_p.R | 1 tests/testthat/test-combine_terms.R | 2 tests/testthat/test-custom_tidiers.R | 2 tests/testthat/test-filter_hierarchical.R | 91 + tests/testthat/test-gather_ard.R | 10 tests/testthat/test-inline_text.R | 2 tests/testthat/test-modify_abbreviation.R | 2 tests/testthat/test-modify_bold_italic.R | 2 tests/testthat/test-modify_caption.R | 6 tests/testthat/test-modify_column_alignment.R | 2 tests/testthat/test-modify_column_hide.R | 2 tests/testthat/test-modify_column_merge.R | 2 tests/testthat/test-modify_fmt_fun.R | 2 tests/testthat/test-modify_footnote.R | 4 tests/testthat/test-modify_header.R | 4 tests/testthat/test-modify_missing_symbol.R | 2 tests/testthat/test-modify_spanning_header.R | 6 tests/testthat/test-modify_table_body.R | 2 tests/testthat/test-modify_table_styling.R | 2 tests/testthat/test-remove_row_type.R | 2 tests/testthat/test-select_helpers.R | 2 tests/testthat/test-separate_p_footnotes.R | 2 tests/testthat/test-show_header_names.R | 4 tests/testthat/test-sort_filter_p.R | 2 tests/testthat/test-sort_hierarchical.R | 60 tests/testthat/test-tbl_ard_continuous.R | 26 tests/testthat/test-tbl_ard_hierarchical.R | 40 tests/testthat/test-tbl_ard_summary.R | 72 - tests/testthat/test-tbl_ard_wide_summary.R | 20 tests/testthat/test-tbl_butcher.R | 2 tests/testthat/test-tbl_hierarchical.R | 10 tests/testthat/test-tbl_merge.R | 4 tests/testthat/test-tbl_regression.R | 2 tests/testthat/test-tbl_split.R | 32 tests/testthat/test-tbl_stack.R | 9 tests/testthat/test-tbl_strata.R | 5 tests/testthat/test-tbl_summary.R | 4 tests/testthat/test-tbl_survfit.R | 2 tests/testthat/test-theme_elements_gtsummary.R | 2 tests/testthat/test-theme_gtsummary.R | 2 186 files changed, 1803 insertions(+), 1309 deletions(-)