Title: Create Useful Summaries of the Portal Data
Description: Download and generate summaries for the rodent,
plant, ant, and weather data from the Portal Project. Portal is a
long-term (and ongoing) experimental monitoring site in the Chihuahuan
desert. The raw data files can be found at
<https://github.com/weecology/portaldata>.
Author: Glenda M. Yenni [aut, cre] ,
Hao Ye [aut] ,
Erica M. Christensen [aut] ,
Juniper L. Simonis [aut] ,
Ellen K. Bledsoe [aut] ,
Renata M. Diaz [aut] ,
Shawn D. Taylor [aut] ,
Ethan P, White [aut] ,
S.K. Morgan Ernest [aut] ,
Weecology [cph]
Maintainer: Glenda M. Yenni <glenda@weecology.org>
Diff between portalr versions 0.4.4 dated 2025-06-30 and 0.4.5 dated 2026-01-28
DESCRIPTION | 8 MD5 | 23 +- NEWS.md | 9 + R/NDVI.R | 20 ++ R/download_data.R | 6 README.md | 6 build/vignette.rds |binary inst/doc/portal_researcher_examples.html | 27 +-- inst/doc/rodent-abundance-demo.html | 49 ++--- man/load_datafile.Rd | 2 man/ndvi.Rd | 3 tests/testthat/_snaps/99-regression.md |only tests/testthat/test-99-regression.R | 269 +++++++++++++------------------ 13 files changed, 205 insertions(+), 217 deletions(-)
Title: Scraper for National Hockey League Data
Description: Scrapes and cleans data from the 'NHL' and 'ESPN' APIs into data.frames and lists. Wraps 125+ endpoints documented in <https://github.com/RentoSaijo/nhlscraper/wiki> from high-level multi-season summaries and award winners to low-level decisecond replays and bookmakers' odds, making them more accessible. Features cleaning and visualization tools, primarily for play-by-plays.
Author: Rento Saijo [aut, cre, cph] ,
Lars Skytte [ctb]
Maintainer: Rento Saijo <rentosaijo0527@gmail.com>
Diff between nhlscraper versions 0.4.1 dated 2025-12-17 and 0.4.2 dated 2026-01-28
nhlscraper-0.4.1/nhlscraper/tests/testthat/test-shifts.R |only nhlscraper-0.4.2/nhlscraper/DESCRIPTION | 8 nhlscraper-0.4.2/nhlscraper/MD5 | 55 nhlscraper-0.4.2/nhlscraper/NAMESPACE | 13 nhlscraper-0.4.2/nhlscraper/NEWS.md | 12 nhlscraper-0.4.2/nhlscraper/R/Clean.R | 1308 +++------- nhlscraper-0.4.2/nhlscraper/R/Game.R | 132 - nhlscraper-0.4.2/nhlscraper/R/GameOld.R | 28 nhlscraper-0.4.2/nhlscraper/R/Load.R | 73 nhlscraper-0.4.2/nhlscraper/README.md | 4 nhlscraper-0.4.2/nhlscraper/build/vignette.rds |binary nhlscraper-0.4.2/nhlscraper/inst/doc/example.Rmd | 2 nhlscraper-0.4.2/nhlscraper/inst/doc/example.html | 2 nhlscraper-0.4.2/nhlscraper/man/add_on_ice_players.Rd |only nhlscraper-0.4.2/nhlscraper/man/boxscore.Rd | 3 nhlscraper-0.4.2/nhlscraper/man/calculate_angle.Rd | 21 nhlscraper-0.4.2/nhlscraper/man/calculate_distance.Rd | 21 nhlscraper-0.4.2/nhlscraper/man/count_goals_shots.Rd | 28 nhlscraper-0.4.2/nhlscraper/man/flag_is_home.Rd | 18 nhlscraper-0.4.2/nhlscraper/man/flag_is_rebound.Rd | 24 nhlscraper-0.4.2/nhlscraper/man/flag_is_rush.Rd | 22 nhlscraper-0.4.2/nhlscraper/man/get_shift_charts.Rd | 2 nhlscraper-0.4.2/nhlscraper/man/normalize_coordinates.Rd | 26 nhlscraper-0.4.2/nhlscraper/man/shift_chart.Rd |only nhlscraper-0.4.2/nhlscraper/man/shift_charts.Rd |only nhlscraper-0.4.2/nhlscraper/man/shifts.Rd | 7 nhlscraper-0.4.2/nhlscraper/man/strip_game_id.Rd | 21 nhlscraper-0.4.2/nhlscraper/man/strip_situation_code.Rd | 27 nhlscraper-0.4.2/nhlscraper/man/strip_time_period.Rd | 23 nhlscraper-0.4.2/nhlscraper/tests/testthat/test-shift_chart.R |only nhlscraper-0.4.2/nhlscraper/vignettes/example.Rmd | 2 31 files changed, 785 insertions(+), 1097 deletions(-)
Title: Latent Class Discriminant Analysis
Description: Providing a method for Local Discrimination via Latent Class Models. The approach is described in <https://www.r-project.org/conferences/useR-2009/abstracts/pdf/Bucker.pdf>.
Author: Michael Buecker [aut, cre]
Maintainer: Michael Buecker <michael.buecker@fh-muenster.de>
Diff between lcda versions 0.3.2 dated 2024-02-15 and 0.3.3 dated 2026-01-28
DESCRIPTION | 20 ++++++++++++++------ MD5 | 23 ++++++++++++++++------- R/cclcda.default.R | 3 +++ R/cclcda2.default.R | 9 +++++---- R/lcda.default.R | 4 +++- R/validate_inputs.R |only README.md |only build |only inst |only man/cclcda.Rd | 6 +++--- man/cclcda2.Rd | 6 +++--- man/lcda.Rd | 2 +- tests |only vignettes |only 14 files changed, 48 insertions(+), 25 deletions(-)
Title: Local Large Language Model Inference Engine
Description: Enables R users to run large language models locally using 'GGUF' model files
and the 'llama.cpp' inference engine. Provides a complete R interface for loading models,
generating text completions, and streaming responses in real-time. Supports local
inference without requiring cloud APIs or internet connectivity, ensuring complete
data privacy and control. Based on the 'llama.cpp' project by Georgi Gerganov (2023) <https://github.com/ggml-org/llama.cpp>.
Author: Pawan Rama Mali [aut, cre, cph],
Georgi Gerganov [aut, cph] ,
The ggml authors [cph] ,
Jeffrey Quesnelle [ctb, cph] ,
Bowen Peng [ctb, cph] ,
pi6am [ctb] ,
Ivan Yurchenko [ctb] ,
Dirk Eddelbuettel [ctb, rev]
Maintainer: Pawan Rama Mali <prm@outlook.in>
Diff between edgemodelr versions 0.1.4 dated 2026-01-22 and 0.1.5 dated 2026-01-28
DESCRIPTION | 28 ++++----- MD5 | 26 ++++---- R/api.R | 36 +++++------ R/ollama.R | 6 - inst/CITATION | 2 man/edge_benchmark.Rd | 2 man/edge_clean_cache.Rd | 2 man/edge_find_gguf_models.Rd | 2 man/edge_find_ollama_models.Rd | 2 man/edge_load_ollama_model.Rd | 2 man/edge_small_model_config.Rd | 102 ++++++++++++++++----------------- man/test_ollama_model_compatibility.Rd | 2 src/bindings.cpp | 20 +++--- src/ggml/ggml-backend-reg.cpp | 16 ++--- 14 files changed, 124 insertions(+), 124 deletions(-)
Title: MCMC Estimation of Bayesian Vectorautoregressions
Description: Efficient Markov Chain Monte Carlo (MCMC) algorithms for the
fully Bayesian estimation of vectorautoregressions (VARs) featuring
stochastic volatility (SV). Implements state-of-the-art shrinkage
priors following Gruber & Kastner (2025) <doi:10.1016/j.ijforecast.2025.02.001>.
Efficient equation-per-equation estimation following Kastner & Huber
(2020) <doi:10.1002/for.2680> and Carrerio et al. (2021)
<doi:10.1016/j.jeconom.2021.11.010>.
Author: Luis Gruber [cph, aut, cre] ,
Stefan Haan [aut],
Gregor Kastner [aut, ths]
Maintainer: Luis Gruber <Luis.Gruber@aau.at>
Diff between bayesianVARs versions 0.1.5 dated 2024-11-13 and 0.1.6 dated 2026-01-28
DESCRIPTION | 30 MD5 | 78 NAMESPACE | 7 NEWS.md | 10 R/RcppExports.R | 20 R/bvar_wrapper.R | 1486 ++++----- R/data.R | 8 R/irf.R |only R/plots.R | 1511 +++++----- R/utility_functions.R | 4974 ++++++++++++++++++--------------- README.md | 13 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/bayesianVARs-vignette.R | 7 inst/doc/bayesianVARs-vignette.Rmd | 377 +- inst/doc/bayesianVARs-vignette.pdf |binary inst/doc/irf-vignette.R |only inst/doc/irf-vignette.Rmd |only inst/doc/irf-vignette.html |only inst/doc/scalability-vignette.R |only inst/doc/scalability-vignette.html |only inst/doc/scalability-vignette.qmd |only man/bvar.Rd | 63 man/extractB0.Rd |only man/irf.Rd |only man/plot.bayesianVARs_irf.Rd |only man/plot.bayesianVARs_residuals.Rd |only man/posterior_heatmap.Rd | 61 man/residuals.bayesianVARs_bvar.Rd |only man/specify_prior_phi.Rd | 8 man/specify_prior_sigma.Rd | 2 man/specify_structural_restrictions.Rd |only man/summary.bayesianVARs_bvar.Rd | 5 man/usmacro_growth.Rd | 8 src/RcppExports.cpp | 80 src/bvar_cpp.cpp | 83 src/irf.cpp |only src/sample_coefficients.h | 33 src/utilities_cpp.cpp | 44 src/utilities_cpp.h |only tests/testthat/setup-all.R | 144 tests/testthat/test-bvar.R | 681 +++- tests/testthat/test-irf.R |only vignettes/bayesianVARs-vignette.Rmd | 377 +- vignettes/huge.bib |only vignettes/huge_all_combinations.RData |only vignettes/irf-vignette.Rmd |only vignettes/irfs.bib |only vignettes/ref.bib | 728 ++-- vignettes/scalability-vignette.qmd |only 51 files changed, 6083 insertions(+), 4755 deletions(-)
Title: Excess Hazard Modelling Considering Inappropriate Mortality
Rates
Description: Fits relative survival regression models with or without proportional excess hazards and with the additional possibility to correct for background mortality by one or more parameter(s). These models are relevant when the observed mortality in the studied group is not comparable to that of the general population or in population-based studies where the available life tables used for net survival estimation are insufficiently stratified. In the latter case, the proposed model by Touraine et al. (2020) <doi:10.1177/0962280218823234> can be used. The user can also fit a model that relaxes the proportional expected hazards assumption considered in the Touraine et al. excess hazard model. This extension was proposed by Mba et al. (2020) <doi:10.1186/s12874-020-01139-z> to allow non-proportional effects of the additional variable on the general population mortality. In non-population-based studies, researchers can identify non-comparability source of bias in terms of expected mort [...truncated...]
Author: Juste Goungounga [aut, cre] ,
Hadrien Charvat [aut] ,
Darlin Mba [aut] ,
Nathalie Graffeo [aut] ,
Roch Giorgi [aut]
Maintainer: Juste Goungounga <juste.goungounga@ehesp.fr>
Diff between xhaz versions 2.0.2 dated 2024-06-29 and 2.1.0 dated 2026-01-28
DESCRIPTION | 45 - MD5 | 110 +- NAMESPACE | 13 R/AIC.bsplines.R | 5 R/AIC.constant.R | 5 R/AIC.mexhazLT.R | 4 R/BIC.bsplines.R | 4 R/BIC.constant.R | 6 R/BIC.mexhazLT.R | 4 R/alpha_stripper.R |only R/as.predxhaz_list.R |only R/as_predxhaz.R |only R/ccr.mevents.R | 1 R/coercion_as_xhaz.R |only R/duplicate.R | 7 R/esteve_ph_optim_maxim_function.R | 10 R/exphaz.R | 209 +---- R/exphaz_years.R | 773 +++++++------------- R/formulaLT.R | 3 R/giorgi.tdph.maxim.R | 4 R/imports.R |only R/mexhazLT.R | 6 R/plot.predxhaz.R | 59 - R/pred_list.R |only R/predict.xhaz.bsplines.R | 226 +----- R/predict.xhaz.constant.R | 259 +----- R/predxhaz_list.R |only R/print.xhaz.predxhaz.R | 2 R/utils-predxhaz.R |only R/without_breakpoint_without_cut.R | 1010 +++++++-------------------- R/xhaz.R | 8 build/vignette.rds |binary data/ccr.mevents.rda |binary inst/doc/introduction.R | 4 inst/doc/introduction.Rmd | 8 inst/doc/introduction.html | 851 +++++++++++----------- inst/doc/rescaling_excess_hazard_models.R | 176 +++- inst/doc/rescaling_excess_hazard_models.Rmd | 195 +++-- inst/doc/rescaling_excess_hazard_models.html | 884 +++++++++++++---------- man/AIC.bsplines.Rd | 5 man/AIC.constant.Rd | 5 man/AIC.mexhazLT.Rd | 4 man/BIC.bsplines.Rd | 4 man/BIC.constant.Rd | 6 man/BIC.mexhazLT.Rd | 4 man/as.predxhaz.Rd |only man/as.predxhaz_list.Rd |only man/as.xhaz.Rd |only man/ccr.mevents.Rd | 1 man/duplicate.Rd | 7 man/exphaz.Rd | 6 man/mexhazLT.Rd | 2 man/plot.predxhaz.Rd | 13 man/plot.predxhaz_list.Rd |only man/pred_list.Rd |only man/predict.bsplines.Rd | 2 man/print.predxhaz.Rd | 2 man/xhaz-package.Rd | 12 man/xhaz.Rd | 6 tests/testthat/test-as-xhaz.R |only vignettes/README_files |only vignettes/introduction.Rmd | 8 vignettes/rescaling_excess_hazard_models.Rmd | 195 +++-- 63 files changed, 2296 insertions(+), 2877 deletions(-)
Title: Approximate Bayesian Latent Variable Analysis
Description: Implements approximate Bayesian inference for Structural
Equation Models (SEM) using a custom adaptation of the Integrated
Nested Laplace Approximation as described in Rue et al. (2009)
<doi:10.1111/j.1467-9868.2008.00700.x>. Provides a computationally
efficient alternative to Markov Chain Monte Carlo (MCMC) for Bayesian
estimation, allowing users to fit latent variable models using the
'lavaan' syntax.
Author: Haziq Jamil [aut, cre, cph] ,
Havard Rue [ctb] ,
Alvin Bong [ctb]
Maintainer: Haziq Jamil <haziq.jamil@gmail.com>
Diff between INLAvaan versions 0.2.2 dated 2026-01-27 and 0.2.3 dated 2026-01-28
INLAvaan-0.2.2/INLAvaan/R/qsn.R |only INLAvaan-0.2.2/INLAvaan/tests/testthat/test-qsn.R |only INLAvaan-0.2.3/INLAvaan/DESCRIPTION | 6 INLAvaan-0.2.3/INLAvaan/MD5 | 28 INLAvaan-0.2.3/INLAvaan/NEWS.md | 7 INLAvaan-0.2.3/INLAvaan/R/create_lav_from_inlavaan_internal.R | 2 INLAvaan-0.2.3/INLAvaan/R/inlavaan.R | 5 INLAvaan-0.2.3/INLAvaan/R/qsnorm_fast.R |only INLAvaan-0.2.3/INLAvaan/README.md | 381 ++-------- INLAvaan-0.2.3/INLAvaan/inst/doc/INLAvaan.html | 109 +- INLAvaan-0.2.3/INLAvaan/inst/doc/mediation.html | 38 INLAvaan-0.2.3/INLAvaan/inst/doc/mediation.qmd | 3 INLAvaan-0.2.3/INLAvaan/man/figures/README-fig-compare-poldem-1.png |binary INLAvaan-0.2.3/INLAvaan/tests/testthat/test-mvn_loglik.R | 4 INLAvaan-0.2.3/INLAvaan/tests/testthat/test-qsnorm_fast.R |only INLAvaan-0.2.3/INLAvaan/tests/testthat/test-variance_estimation.R | 2 INLAvaan-0.2.3/INLAvaan/vignettes/mediation.qmd | 3 17 files changed, 188 insertions(+), 400 deletions(-)
Title: Feature-Based Clustering of Longitudinal Trajectories
Description: Identifies clusters of individual longitudinal trajectories. In the spirit of Leffondre et al. (2004), the procedure involves identifying each trajectory to a point in the space of measures. In this context, a measure is a quantity meant to capture a certain characteristic feature of the trajectory. The points in the space of measures are then clustered using a version of spectral clustering.
Author: Marie-Pierre Sylvestre [aut],
Laurence Boulanger [aut, cre],
Gillis Delmas Tchouangue Dinkou [ctb],
Dan Vatnik [ctb]
Maintainer: Laurence Boulanger <laurence.boulanger@umontreal.ca>
Diff between traj versions 2.2.1 dated 2025-02-01 and 3.0.0 dated 2026-01-28
traj-2.2.1/traj/R/CalinskiHarabasz.R |only traj-2.2.1/traj/R/CheckCorrelation.R |only traj-2.2.1/traj/R/Step1Measures.R |only traj-2.2.1/traj/R/Step2Selection.R |only traj-2.2.1/traj/R/Step3Clusters.R |only traj-2.2.1/traj/build |only traj-2.2.1/traj/inst |only traj-2.2.1/traj/man/Step1Measures.Rd |only traj-2.2.1/traj/man/Step2Selection.Rd |only traj-2.2.1/traj/man/Step3Clusters.Rd |only traj-2.2.1/traj/vignettes |only traj-3.0.0/traj/DESCRIPTION | 13 traj-3.0.0/traj/MD5 | 33 -- traj-3.0.0/traj/NAMESPACE | 25 - traj-3.0.0/traj/NEWS.md | 11 traj-3.0.0/traj/R/plot.trajClusters.R | 453 +++++-------------------------- traj-3.0.0/traj/R/quiet.R |only traj-3.0.0/traj/R/spect.R |only traj-3.0.0/traj/R/trajClusters.R |only traj-3.0.0/traj/R/trajMeasures.R |only traj-3.0.0/traj/R/trajReduce.R |only traj-3.0.0/traj/man/plot.trajClusters.Rd | 116 +++---- traj-3.0.0/traj/man/traj-package.Rd | 4 traj-3.0.0/traj/man/trajClusters.Rd |only traj-3.0.0/traj/man/trajMeasures.Rd |only traj-3.0.0/traj/man/trajReduce.Rd |only 26 files changed, 182 insertions(+), 473 deletions(-)
Title: Transcription Elongation Profiling
Description: The general principle relies on calculating the cumulative signal of nascent
RNA sequencing over the gene body of any given gene or transcription unit.
'tepr' can identify transcription attenuation sites by comparing profile to
a null model which assumes uniform read density over the entirety of the
transcription unit. It can also identify increased or diminished
transcription attenuation by comparing two conditions. Besides rigorous
statistical testing and high sensitivity, a major feature of 'tepr' is its
ability to provide the elongation pattern of each individual gene, including
the position of the main attenuation point when such a phenomenon occurs.
Using 'tepr', users can visualize and refine genome-wide aggregated analyses
of elongation patterns to robustly identify effects specific to subsets of
genes. These metrics are suitable for internal comparisons (between genes in
each condition) and for studying elongation of the same gene in different
conditions or comparing it to a p [...truncated...]
Author: Nicolas Descostes [cre],
Victor Billon [aut],
Gael Cristofari [aut]
Maintainer: Nicolas Descostes <nicolas.descostes@gmail.com>
Diff between tepr versions 1.1.13 dated 2025-12-11 and 1.1.14 dated 2026-01-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ R/plotmulti.R | 35 ++++++++++++++++++++--------------- inst/doc/tepr.html | 4 ++-- 5 files changed, 32 insertions(+), 24 deletions(-)
Title: Allocate Samples Among Strata
Description: Functions for the design process of survey sampling, with specific tools for multi-wave and multi-phase designs. Perform optimum allocation using Neyman (1934) <doi:10.2307/2342192> or Wright (2012) <doi:10.1080/00031305.2012.733679> allocation, split strata based on quantiles or values of known variables, randomly select samples from strata, allocate sampling waves iteratively, and organize a complex survey design. Also includes a Shiny application for observing the effects of different strata splits. A paper on this package was published in the Journal of Statistical Software <doi:10.18637/jss.v114.i10>.
Author: Jasper Yang [aut, cre],
Pamela Shaw [aut],
Bryan Shepherd [ctb],
Thomas Lumley [ctb],
Gustavo Amorim [rev]
Maintainer: Jasper Yang <jbyang@uw.edu>
Diff between optimall versions 1.3.0 dated 2025-09-08 and 1.3.1 dated 2026-01-28
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ inst/doc/Multiwave-Estimation.R | 4 ++-- inst/doc/Multiwave-Estimation.Rmd | 4 ++-- inst/doc/Multiwave-Estimation.html | 4 ++-- inst/doc/optimall-vignette.html | 2 +- vignettes/Multiwave-Estimation.Rmd | 4 ++-- 8 files changed, 23 insertions(+), 19 deletions(-)
Title: Multi-Fidelity Computer Experiments Using the Tuo-Wu-Yu Model
Description: This R function implements the nonstationary Kriging model
proposed by Tuo, Wu and Yu (2014) <DOI:10.1080/00401706.2013.842935>
for analyzing multi-fidelity computer outputs. This function computes
the maximum likelihood estimates for the model parameters as well
as the predictive means and variances of the exact solution.
Author: Wenjia Wang [aut, cre],
Rui Tuo [aut],
C. F. Jeff Wu [aut]
Maintainer: Wenjia Wang <1992wangwenjia@gmail.com>
This is a re-admission after prior archival of version 0.1.0 dated 2017-05-12
Diff between diffMeshGP versions 0.1.0 dated 2017-05-12 and 0.1.1 dated 2026-01-28
DESCRIPTION | 27 ++-- MD5 | 7 - NAMESPACE | 2 R/GPdiffMesh.R | 379 +++++++++++++++++++++++++++++++++++---------------------- tests |only 5 files changed, 262 insertions(+), 153 deletions(-)
Title: Robust Linear Mixed Effects Models
Description: Implements the Robust Scoring Equations estimator to fit linear
mixed effects models robustly.
Robustness is achieved by modification of the scoring equations
combined with the Design Adaptive Scale approach.
Author: Manuel Koller [aut, cre]
Maintainer: Manuel Koller <kollerma@proton.me>
Diff between robustlmm versions 3.3-3 dated 2025-05-26 and 3.4-2 dated 2026-01-28
DESCRIPTION | 15 ++++++----- MD5 | 37 ++++++++++++++++------------ NAMESPACE | 2 + R/AllClass.R | 35 ++++++++++++++++++++++++++ R/accessors.R | 28 ++++++++++++++++----- R/asymptoticEfficiency.R | 2 - R/generateLongitudinalDatasets.R |only R/plotLongitudinalBySubject.R |only R/processFile.R | 12 ++++++--- R/rlmer.R | 39 +++++++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/rlmer.Rnw | 8 +++--- inst/doc/rlmer.pdf |binary inst/doc/simulationStudies.pdf |binary man/generateLongitudinalDatasets.Rd |only man/partialMoment_standardNormal.Rd | 2 - man/plotLongitudinalBySubject.Rd |only tests/test_generateLongitudinalDatasets.R |only vignettes/rlmer.Rnw | 8 +++--- vignettes/rlmer.bib | 20 +++++++-------- vignettes/rlmer.sty | 2 - vignettes/simulationStudies.bib | 5 +-- 22 files changed, 157 insertions(+), 58 deletions(-)
Title: Robust Survey Statistics Estimation
Description: Robust (outlier-resistant) estimators of finite population
characteristics like of means, totals, ratios, regression, etc. Available
methods are M- and GM-estimators of regression, weight reduction,
trimming, and winsorization. The package extends the 'survey'
<https://CRAN.R-project.org/package=survey> package.
Author: Beat Hulliger [aut] ,
Tobias Schoch [aut, cre] ,
Martin Sterchi [ctr, com],
R-core [ctb, cph]
Maintainer: Tobias Schoch <tobias.schoch@fhnw.ch>
Diff between robsurvey versions 0.7 dated 2024-08-22 and 0.7-1 dated 2026-01-28
DESCRIPTION | 11 +-- MD5 | 76 ++++++++++++----------- NAMESPACE | 10 ++- NEWS.md | 14 ++++ R/class_svyreg_rob.R | 4 - R/class_svystat_rob.R | 43 +++++++++++-- R/mer.R | 2 R/robsurvey-internal.R | 107 ++++++++++++++++++++------------- R/svymean_dalen.R | 40 ++++-------- R/svymean_huber.R | 39 +++--------- R/svymean_trimmed.R | 33 ++-------- R/svymean_tukey.R | 48 +++++--------- R/svymean_winsorized.R | 68 ++++++-------------- R/within_tolerance.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/Handling_of_NA_and_domains.md |only inst/doc/basic.R | 8 +- inst/doc/basic.html | 8 +- inst/doc/doc_comparison.pdf |binary inst/doc/doc_greg.pdf |binary inst/doc/doc_regression_covariance.pdf |binary inst/doc/greg.R | 10 +-- inst/doc/regression.R | 10 +-- inst/doc/rht.R | 8 +- inst/doc/rht.html | 4 - man/class_svystat_rob.Rd | 13 +++- man/sampling.Rd | 8 +- man/within_tolerance.Rd |only src/huber2.c | 2 src/mallows.c | 2 src/psifunctions.c | 2 src/regression.c | 2 src/regression_cov.c | 4 - src/regression_scale.c | 2 src/robsurvey_error.c | 2 src/sampling.c | 2 src/trimmedwinsorized.c | 2 src/wquantile.c | 2 tests/check_functions.R | 10 ++- tests/domain.R |only 41 files changed, 306 insertions(+), 290 deletions(-)
Title: Build Reproducible Analytical Pipelines with 'Nix'
Description: Streamlines the creation of reproducible analytical pipelines using
'default.nix' expressions generated via the 'rix' package for reproducibility. Define
derivations in 'R', 'Python' or 'Julia', chain them into a composition of pure
functions and build the resulting pipeline using 'Nix' as the underlying
end-to-end build tool. Functions to plot the pipeline as a directed acyclic
graph are included, as well as functions to load and inspect intermediary results
for interactive analysis. User experience heavily inspired by the 'targets' package.
Author: Bruno Rodrigues [aut, cre] ,
William Michael Landau [rev]
for rOpenSci, see
<https://github.com/ropensci/software-review/issues/706>),
Anthony Martinez [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>)
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rixpress versions 0.10.1 dated 2025-10-14 and 0.11.2 dated 2026-01-28
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Title: Reproducible Data Science Environments with 'Nix'
Description: Simplifies the creation of reproducible data science environments
using the 'Nix' package manager, as described in
Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()`
function generates a complete description of the environment as a
`default.nix` file, which can then be built using 'Nix'. This results in
project specific software environments with pinned versions of R, packages,
linked system dependencies, and other tools or programming languages such
as Python or Julia. Additional helpers make it easy to run R code in
'Nix' software environments for testing and production.
Author: Bruno Rodrigues [aut, cre] ,
Philipp Baumann [aut] ,
David Watkins [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>),
Jacob Wujiciak-Jens [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/62 [...truncated...]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rix versions 0.17.4 dated 2026-01-16 and 0.18.1 dated 2026-01-28
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Title: Kernel Functions and Tools for Machine Learning Applications
Description: Kernel functions for diverse types of data (including, but not
restricted to: nonnegative and real vectors, real matrices, categorical
and ordinal variables, sets, strings), plus other utilities like kernel
similarity, kernel Principal Components Analysis (PCA) and features'
importance for Support Vector Machines (SVMs), which expand other 'R'
packages like 'kernlab'.
Author: Elies Ramon [aut, cre, cph]
Maintainer: Elies Ramon <eramon@everlyrusher.com>
Diff between kerntools versions 1.2.0 dated 2025-02-19 and 1.2.1 dated 2026-01-28
DESCRIPTION | 9 +++-- MD5 | 32 ++++++++++---------- NAMESPACE | 1 NEWS.md | 6 +++ R/importancies.R | 2 - R/kernel_functions.R | 4 +- R/kernel_study.R | 2 - README.md | 14 +++++++-- inst/WORDLIST | 4 ++ inst/doc/Kernel-PCA-and-CIA.html | 14 ++++----- inst/doc/Kernel-functions.Rmd | 4 +- inst/doc/Kernel-functions.html | 60 +++++++++++++++++++-------------------- inst/doc/kerntools.Rmd | 2 - inst/doc/kerntools.html | 46 ++++++++++++++--------------- man/vonNeumann.Rd | 2 - vignettes/Kernel-functions.Rmd | 4 +- vignettes/kerntools.Rmd | 2 - 17 files changed, 113 insertions(+), 95 deletions(-)
More information about EQUALPrognosis at CRAN
Permanent link
More information about DataQualityDashboard at CRAN
Permanent link
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 0.4.2 dated 2025-12-17 and 0.4.3 dated 2026-01-28
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/ewt.R | 2 +- R/ewtp.R | 15 +++++++++++++++ R/km.R | 18 ++++++++++++------ R/rmt.R | 18 ++++++++++++++++-- R/wintime.R | 32 +++++++++++++++++++++++++------- inst/doc/wintime_vignette.html | 36 ++++++++++++++++++------------------ 8 files changed, 97 insertions(+), 44 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 1.3.5 dated 2025-12-10 and 1.3.6 dated 2026-01-28
DESCRIPTION | 6 MD5 | 608 - NAMESPACE | 560 - NEWS.md | 4 R/OMOPGenerics-package.R | 24 R/addSettings.R | 156 R/arrange.R | 60 R/assert.R | 1740 ++-- R/casting.R | 184 R/cdmFromTables.R | 208 R/cdmSelect.R | 100 R/classAchillesTable.R | 262 R/classCdmReference.R | 2222 ++--- R/classCdmSource.R | 300 R/classCdmTable.R | 466 - R/classCodelist.R | 530 - R/classCodelistWithDetails.R | 322 R/classCohortTable.R | 1598 ++-- R/classConceptSetExpression.R | 446 - R/classOmopTable.R | 274 R/classSummarisedResult.R | 1958 ++--- R/cohortCodelist.R | 352 R/cohortCount.R | 164 R/columns.R | 506 - R/combineStrata.R | 92 R/compute.R | 216 R/exportCodelist.R | 144 R/exportConceptSetExpression.R | 146 R/exportSummarisedResult.R | 426 - R/filter.R | 468 - R/importCodelist.R | 110 R/importConceptSetExpression.R | 199 R/importSummarisedResult.R | 200 R/indexes.R | 510 - R/logger.R | 816 +- R/methodAttrition.R | 170 R/methodBind.R | 730 - R/methodCdmDisconnect.R | 114 R/methodCdmTableFromSource.R | 76 R/methodDropSourceTable.R | 132 R/methodDropTable.R | 66 R/methodInsertCdmTo.R | 76 R/methodInsertFromSource.R | 88 R/methodInsertTable.R | 170 R/methodListSourceTables.R | 80 R/methodReadSourceTable.R | 124 R/methodSettings.R | 242 R/methodSuppress.R | 474 - R/methodTidy.R | 184 R/omopDataFolder.R | 92 R/overwriteClasses.R | 860 +- R/pivot.R | 216 R/recordCohortAttrition.R | 292 R/split.R | 630 - R/summary.R | 968 +- R/unite.R | 476 - R/utilities.R | 662 - R/validate.R | 2186 ++--- README.md | 628 - build/vignette.rds |binary inst/WORDLIST | 42 inst/cohorts_for_mock/oa_desc.json | 176 inst/cohorts_for_mock/oa_no_desc.json | 174 inst/concepts_for_mock/oa_desc.json | 24 inst/concepts_for_mock/oa_no_desc.json | 24 inst/doc/cdm_reference.R | 54 inst/doc/cdm_reference.Rmd | 200 inst/doc/cdm_reference.html | 1187 +-- inst/doc/codelists.R | 156 inst/doc/codelists.Rmd | 208 inst/doc/codelists.html | 911 +- inst/doc/cohorts.R | 224 inst/doc/cohorts.Rmd | 444 - inst/doc/cohorts.html | 1323 +-- inst/doc/expanding_omopgenerics.R | 284 inst/doc/expanding_omopgenerics.Rmd | 598 - inst/doc/expanding_omopgenerics.html | 1315 +-- inst/doc/logging.R | 190 inst/doc/logging.Rmd | 276 inst/doc/logging.html | 1084 +- inst/doc/reexport.R | 12 inst/doc/reexport.Rmd | 202 inst/doc/reexport.html | 684 - inst/doc/summarised_result.R | 472 - inst/doc/summarised_result.Rmd | 898 +- inst/doc/summarised_result.html | 8687 +++++++++++------------ inst/doc/suppression.R | 94 inst/doc/suppression.Rmd | 190 inst/doc/suppression.html | 1019 +- inst/not_all_concept_sets/acetaminophen.json | 24 inst/not_all_concept_sets/cohort_def.json | 5706 +++++++-------- inst/not_all_concept_sets/influenza.json | 24 man/achillesColumns.Rd | 60 man/achillesTables.Rd | 48 man/addSettings.Rd | 102 man/additionalColumns.Rd | 96 man/assertCharacter.Rd | 82 man/assertChoice.Rd | 80 man/assertClass.Rd | 76 man/assertDate.Rd | 80 man/assertList.Rd | 80 man/assertLogical.Rd | 74 man/assertNumeric.Rd | 92 man/assertTable.Rd | 88 man/assertTrue.Rd | 40 man/attrition.Rd | 34 man/attrition.cohort_table.Rd | 94 man/bind.Rd | 34 man/bind.cohort_table.Rd | 118 man/bind.summarised_result.Rd | 100 man/cash-.cdm_reference.Rd | 86 man/cash-set-.cdm_reference.Rd | 88 man/cdmClasses.Rd | 34 man/cdmDisconnect.Rd | 76 man/cdmFromTables.Rd | 92 man/cdmName.Rd | 86 man/cdmReference.Rd | 82 man/cdmSelect.Rd | 54 man/cdmSource.Rd | 88 man/cdmSourceType.Rd | 84 man/cdmTableFromSource.Rd | 50 man/cdmVersion.Rd | 84 man/checkCohortRequirements.Rd | 86 man/cohortCodelist.Rd | 148 man/cohortColumns.Rd | 54 man/cohortCount.Rd | 102 man/cohortTables.Rd | 50 man/collect.cdm_reference.Rd | 86 man/collect.cohort_table.Rd | 38 man/combineStrata.Rd | 54 man/compute.cdm_table.Rd | 72 man/createIndexes.Rd | 38 man/createLogFile.Rd | 70 man/createTableIndex.Rd | 38 man/dropSourceTable.Rd | 40 man/dropTable.Rd | 44 man/emptyAchillesTable.Rd | 52 man/emptyCdmReference.Rd | 50 man/emptyCodelist.Rd | 36 man/emptyCodelistWithDetails.Rd | 36 man/emptyCohortTable.Rd | 98 man/emptyConceptSetExpression.Rd | 36 man/emptyOmopTable.Rd | 84 man/emptySummarisedResult.Rd | 48 man/estimateTypeChoices.Rd | 42 man/existingIndexes.Rd | 40 man/expectedIndexes.Rd | 40 man/exportCodelist.Rd | 44 man/exportConceptSetExpression.Rd | 44 man/exportSummarisedResult.Rd | 72 man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-stable.svg | 58 man/figures/lifecycle-superseded.svg | 42 man/filterAdditional.Rd | 96 man/filterGroup.Rd | 96 man/filterSettings.Rd | 102 man/filterStrata.Rd | 96 man/getCohortId.Rd | 40 man/getCohortName.Rd | 40 man/getPersonIdentifier.Rd | 46 man/groupColumns.Rd | 94 man/importCodelist.Rd | 40 man/importConceptSetExpression.Rd | 40 man/importSummarisedResult.Rd | 46 man/insertCdmTo.Rd | 38 man/insertFromSource.Rd | 44 man/insertTable.Rd | 100 man/isResultSuppressed.Rd | 80 man/isTableEmpty.Rd | 34 man/listSourceTables.Rd | 34 man/logMessage.Rd | 82 man/newAchillesTable.Rd | 42 man/newCdmReference.Rd | 98 man/newCdmSource.Rd | 38 man/newCdmTable.Rd | 42 man/newCodelist.Rd | 34 man/newCodelistWithDetails.Rd | 36 man/newCohortTable.Rd | 144 man/newConceptSetExpression.Rd | 36 man/newLocalSource.Rd | 42 man/newOmopTable.Rd | 42 man/newSummarisedResult.Rd | 136 man/numberRecords.Rd | 72 man/numberSubjects.Rd | 72 man/omopColumns.Rd | 72 man/omopDataFolder.Rd | 52 man/omopTableFields.Rd | 34 man/omopTables.Rd | 50 man/omopgenerics-package.Rd | 72 man/pivotEstimates.Rd | 102 man/print.cdm_reference.Rd | 84 man/print.codelist.Rd | 50 man/print.codelist_with_details.Rd | 56 man/print.concept_set_expression.Rd | 74 man/readSourceTable.Rd | 38 man/recordCohortAttrition.Rd | 124 man/reexports.Rd | 38 man/resultColumns.Rd | 46 man/resultPackageVersion.Rd | 34 man/settings.Rd | 34 man/settings.cohort_table.Rd | 106 man/settings.summarised_result.Rd | 96 man/settingsColumns.Rd | 98 man/sourceType.Rd | 34 man/splitAdditional.Rd | 106 man/splitAll.Rd | 110 man/splitGroup.Rd | 106 man/splitStrata.Rd | 108 man/statusIndexes.Rd | 42 man/strataColumns.Rd | 94 man/sub-sub-.cdm_reference.Rd | 86 man/sub-subset-.cdm_reference.Rd | 42 man/summariseLogFile.Rd | 84 man/summary.cdm_reference.Rd | 82 man/summary.cdm_source.Rd | 46 man/summary.cohort_table.Rd | 92 man/summary.summarised_result.Rd | 86 man/suppress.Rd | 38 man/suppress.summarised_result.Rd | 120 man/tableName.Rd | 82 man/tableSource.Rd | 82 man/tidy.summarised_result.Rd | 106 man/tidyColumns.Rd | 96 man/tmpPrefix.Rd | 40 man/toSnakeCase.Rd | 46 man/transformToSummarisedResult.Rd | 108 man/uniqueId.Rd | 46 man/uniqueTableName.Rd | 42 man/uniteAdditional.Rd | 80 man/uniteGroup.Rd | 70 man/uniteStrata.Rd | 70 man/validateAchillesTable.Rd | 56 man/validateAgeGroupArgument.Rd | 88 man/validateCdmArgument.Rd | 132 man/validateCdmTable.Rd | 42 man/validateCohortArgument.Rd | 156 man/validateCohortIdArgument.Rd | 130 man/validateColumn.Rd | 82 man/validateConceptSetArgument.Rd | 78 man/validateNameArgument.Rd | 82 man/validateNameLevel.Rd | 58 man/validateNameStyle.Rd | 94 man/validateNewColumn.Rd | 64 man/validateOmopTable.Rd | 56 man/validateResultArgument.Rd | 116 man/validateStrataArgument.Rd | 60 man/validateWindowArgument.Rd | 60 tests/testthat.R | 24 tests/testthat/_snaps/utilities.md | 46 tests/testthat/setup.R | 326 tests/testthat/test-addSettings.R | 104 tests/testthat/test-assert.R | 728 - tests/testthat/test-casting.R | 60 tests/testthat/test-cdmFromTables.R | 346 tests/testthat/test-cdmSelect.R | 20 tests/testthat/test-classCdmReference.R | 186 tests/testthat/test-classCdmSource.R | 120 tests/testthat/test-classCodelist.R | 170 tests/testthat/test-classCodelistWithDetails.R | 194 tests/testthat/test-classCohortTable.R | 1052 +- tests/testthat/test-classConceptSetExpression.R | 368 tests/testthat/test-classLocalSource.R | 14 tests/testthat/test-classSummarisedResult.R | 916 +- tests/testthat/test-cohortCodelist.R | 418 - tests/testthat/test-columns.R | 148 tests/testthat/test-combineStrata.R | 54 tests/testthat/test-emptyObjects.R | 140 tests/testthat/test-exportCodelist.R | 104 tests/testthat/test-exportConceptSetExpression.R | 132 tests/testthat/test-exportSummarisedResult.R | 172 tests/testthat/test-filter.R | 346 tests/testthat/test-importCodelist.R | 90 tests/testthat/test-importConceptSetExpression.R | 252 tests/testthat/test-importSummarisedResult.R | 320 tests/testthat/test-logger.R | 132 tests/testthat/test-methodBind.R | 564 - tests/testthat/test-methodCdmDisconnect.R | 36 tests/testthat/test-methodComputeTable.R | 56 tests/testthat/test-methodDropSourceTable.R | 74 tests/testthat/test-methodGetCdmSource.R | 6 tests/testthat/test-methodInsertFromSource.R | 38 tests/testthat/test-methodInsertTable.R | 26 tests/testthat/test-methodListSourceTables.R | 12 tests/testthat/test-methodReadSourceTable.R | 52 tests/testthat/test-methodSummary.R | 256 tests/testthat/test-methodSuppress.R | 510 - tests/testthat/test-methodTidy.R | 156 tests/testthat/test-omopDataFolder.R | 18 tests/testthat/test-overwriteClasses.R | 162 tests/testthat/test-pivot.R | 52 tests/testthat/test-prefix.R | 60 tests/testthat/test-recordCohortAttrition.R | 384 - tests/testthat/test-split.R | 248 tests/testthat/test-unite.R | 164 tests/testthat/test-utilities.R | 556 - tests/testthat/test-validate.R | 952 +- vignettes/cdm_reference.Rmd | 200 vignettes/codelists.Rmd | 208 vignettes/cohorts.Rmd | 444 - vignettes/expanding_omopgenerics.Rmd | 598 - vignettes/logging.Rmd | 276 vignettes/reexport.Rmd | 202 vignettes/summarised_result.Rmd | 898 +- vignettes/suppression.Rmd | 190 305 files changed, 39159 insertions(+), 39088 deletions(-)
Title: Facilitate Analysis of Proteomic Data from Olink
Description: A collection of functions to facilitate analysis of proteomic
data from Olink, primarily NPX data that has been exported from Olink
Software. The functions also work on QUANT data from
Olink by log- transforming the QUANT data. The functions are focused
on reading data, facilitating data wrangling and quality control
analysis, performing statistical analysis and generating figures to
visualize the results of the statistical analysis. The goal of this
package is to help users extract biological insights from proteomic
data run on the Olink platform.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Klev Diamanti [aut] ,
Amrita Kar [aut] ,
Lei Conze [aut] [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyze versions 4.4.0 dated 2025-12-02 and 4.5.0 dated 2026-01-28
OlinkAnalyze-4.4.0/OlinkAnalyze/man/olink_normalization_product_format.Rd |only OlinkAnalyze-4.5.0/OlinkAnalyze/DESCRIPTION | 6 OlinkAnalyze-4.5.0/OlinkAnalyze/MD5 | 64 OlinkAnalyze-4.5.0/OlinkAnalyze/NEWS.md | 11 OlinkAnalyze-4.5.0/OlinkAnalyze/R/Olink_ordinalRegression.R | 2 OlinkAnalyze-4.5.0/OlinkAnalyze/R/Read_NPX_data.R | 29 OlinkAnalyze-4.5.0/OlinkAnalyze/R/olink_lod.R | 2 OlinkAnalyze-4.5.0/OlinkAnalyze/R/olink_normalization.R | 44 OlinkAnalyze-4.5.0/OlinkAnalyze/R/olink_normalization_format.R |only OlinkAnalyze-4.5.0/OlinkAnalyze/R/olink_normalization_product.R | 204 - OlinkAnalyze-4.5.0/OlinkAnalyze/R/olink_normalization_utils.R | 79 OlinkAnalyze-4.5.0/OlinkAnalyze/R/pca_plot.R | 167 + OlinkAnalyze-4.5.0/OlinkAnalyze/inst/doc/LOD.Rmd | 6 OlinkAnalyze-4.5.0/OlinkAnalyze/inst/doc/LOD.html | 32 OlinkAnalyze-4.5.0/OlinkAnalyze/inst/doc/OutlierExclusion.html | 24 OlinkAnalyze-4.5.0/OlinkAnalyze/inst/doc/Vignett.html | 26 OlinkAnalyze-4.5.0/OlinkAnalyze/inst/doc/bridging_crossproduct.html | 2 OlinkAnalyze-4.5.0/OlinkAnalyze/inst/doc/bridging_introduction.html | 94 OlinkAnalyze-4.5.0/OlinkAnalyze/inst/doc/plate_randomizer.html | 4 OlinkAnalyze-4.5.0/OlinkAnalyze/man/olink_format_oid_no_overlap.Rd |only OlinkAnalyze-4.5.0/OlinkAnalyze/man/olink_format_rm_ext_ctrl.Rd |only OlinkAnalyze-4.5.0/OlinkAnalyze/man/olink_norm_input_assay_overlap.Rd | 2 OlinkAnalyze-4.5.0/OlinkAnalyze/man/olink_normalization.Rd | 3 OlinkAnalyze-4.5.0/OlinkAnalyze/man/olink_normalization_format.Rd |only OlinkAnalyze-4.5.0/OlinkAnalyze/man/olink_normalization_qs.Rd | 2 OlinkAnalyze-4.5.0/OlinkAnalyze/man/olink_pca_plot.Rd | 2 OlinkAnalyze-4.5.0/OlinkAnalyze/tests/testthat/_snaps/Read_NPX_data.md | 24 OlinkAnalyze-4.5.0/OlinkAnalyze/tests/testthat/_snaps/npxProcessing.md | 130 OlinkAnalyze-4.5.0/OlinkAnalyze/tests/testthat/test-Read_NPX_data.R | 17 OlinkAnalyze-4.5.0/OlinkAnalyze/tests/testthat/test-olink_lod.R | 3 OlinkAnalyze-4.5.0/OlinkAnalyze/tests/testthat/test-olink_normalization.R | 1496 +++++++++- OlinkAnalyze-4.5.0/OlinkAnalyze/tests/testthat/test-olink_normalization_format.R |only OlinkAnalyze-4.5.0/OlinkAnalyze/tests/testthat/test-olink_normalization_product.R | 416 -- OlinkAnalyze-4.5.0/OlinkAnalyze/tests/testthat/test-olink_normalization_utils.R | 418 ++ OlinkAnalyze-4.5.0/OlinkAnalyze/tests/testthat/test-pca_plot.R | 181 + OlinkAnalyze-4.5.0/OlinkAnalyze/vignettes/LOD.Rmd | 6 36 files changed, 2386 insertions(+), 1110 deletions(-)
Title: Import, Manipulate and Explore the Results of an 'Antares'
Simulation
Description: Import, manipulate and explore results generated by 'Antares', a
powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems
(more information about 'Antares' here : <https://antares-simulator.org/>).
Author: Tatiana Vargas [aut, cre],
Jalal-Edine ZAWAM [aut],
Frederic Breant [ctb],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
Victor Perrier [ctb],
Etienne Sanchez [ctb],
Assil Mansouri [ctb],
Clement Berthet [ctb],
Kamel Kemiha [c [...truncated...]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>
Diff between antaresRead versions 2.9.3 dated 2025-11-06 and 3.0.0 dated 2026-01-28
DESCRIPTION | 6 MD5 | 18 - NEWS.md | 10 R/importOutput.R | 99 +++++++-- R/setSimulationPath.R | 49 +++- R/setSimulationPathAPI.R | 24 +- R/zzz.R | 2 inst/doc/antaresRead.html | 4 inst/variables_selection/ref_thematic_by_version/ref_930.csv | 1 tests/testthat/test-getStartDate.R | 116 +++++++++++ 10 files changed, 272 insertions(+), 57 deletions(-)
Title: A Finer Way to Render 3D Illustrated Objects in 'grid' Using
Affine Transformations
Description: Dilate, permute, project, reflect, rotate, shear, and translate 2D and 3D points. Supports parallel projections including oblique projections such as the cabinet projection as well as axonometric projections such as the isometric projection. Use 'grid's "affine transformation" feature to render illustrated flat surfaces.
Author: Trevor L. Davis [aut, cre]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between affiner versions 0.1.3 dated 2024-12-02 and 0.2.1 dated 2026-01-28
affiner-0.1.3/affiner/R/hooks.r |only affiner-0.1.3/affiner/R/import-standalone-s3-register.R |only affiner-0.2.1/affiner/DESCRIPTION | 12 affiner-0.2.1/affiner/LICENSE | 4 affiner-0.2.1/affiner/MD5 | 116 - affiner-0.2.1/affiner/NAMESPACE | 61 affiner-0.2.1/affiner/NEWS.md | 16 affiner-0.2.1/affiner/R/R_to_AA.r | 83 affiner-0.2.1/affiner/R/affine-methods.r | 76 affiner-0.2.1/affiner/R/affine.r | 588 +++---- affiner-0.2.1/affiner/R/affineGrob.r | 58 affiner-0.2.1/affiner/R/affiner_options.r | 31 affiner-0.2.1/affiner/R/angle.r | 405 ++-- affiner-0.2.1/affiner/R/as_coord.r | 375 ++-- affiner-0.2.1/affiner/R/autolayer.r | 38 affiner-0.2.1/affiner/R/coord-methods.r | 554 +++--- affiner-0.2.1/affiner/R/coord.r | 697 ++++---- affiner-0.2.1/affiner/R/distance.r | 156 - affiner-0.2.1/affiner/R/has_intersection.r |only affiner-0.2.1/affiner/R/intersection.r |only affiner-0.2.1/affiner/R/is_congruent.r | 38 affiner-0.2.1/affiner/R/is_degenerate.r |only affiner-0.2.1/affiner/R/is_equivalent.r |only affiner-0.2.1/affiner/R/is_methods.r | 6 affiner-0.2.1/affiner/R/is_parallel.r |only affiner-0.2.1/affiner/R/isocubeGrob.r | 214 +- affiner-0.2.1/affiner/R/isotoxal_2ngon_inner_radius.r |only affiner-0.2.1/affiner/R/line_plane-methods.r | 88 - affiner-0.2.1/affiner/R/line_plane.r | 338 ++-- affiner-0.2.1/affiner/R/normal.r | 120 - affiner-0.2.1/affiner/R/plot.r | 43 affiner-0.2.1/affiner/R/roxygen2_inline.r |only affiner-0.2.1/affiner/R/standalone-affine-settings.r | 249 +- affiner-0.2.1/affiner/R/standardize.r |only affiner-0.2.1/affiner/R/trigonometry.r | 102 - affiner-0.2.1/affiner/R/zzz.r | 14 affiner-0.2.1/affiner/build/vignette.rds |binary affiner-0.2.1/affiner/inst/doc/affiner.R | 8 affiner-0.2.1/affiner/inst/doc/affiner.Rmd | 8 affiner-0.2.1/affiner/inst/doc/affiner.html | 4 affiner-0.2.1/affiner/inst/doc/geometry.Rmd | 2 affiner-0.2.1/affiner/inst/doc/geometry.html | 2 affiner-0.2.1/affiner/man/cross_product3d.Rd | 3 affiner-0.2.1/affiner/man/graphics.Rd | 2 affiner-0.2.1/affiner/man/has_intersection.Rd |only affiner-0.2.1/affiner/man/intersection.Rd |only affiner-0.2.1/affiner/man/is_equivalent.Rd |only affiner-0.2.1/affiner/man/is_parallel.Rd |only affiner-0.2.1/affiner/man/isocubeGrob.Rd | 94 - affiner-0.2.1/affiner/man/isotoxal_2ngon_inner_radius.Rd |only affiner-0.2.1/affiner/tests/testthat/test-affine-settings.r | 74 affiner-0.2.1/affiner/tests/testthat/test-affine.r | 836 +++++----- affiner-0.2.1/affiner/tests/testthat/test-affineGrob.r | 16 affiner-0.2.1/affiner/tests/testthat/test-affiner_options.r | 8 affiner-0.2.1/affiner/tests/testthat/test-angle.r | 273 +-- affiner-0.2.1/affiner/tests/testthat/test-coord.r | 758 ++++----- affiner-0.2.1/affiner/tests/testthat/test-distance.r | 83 affiner-0.2.1/affiner/tests/testthat/test-intersection.r |only affiner-0.2.1/affiner/tests/testthat/test-is_parallel.r |only affiner-0.2.1/affiner/tests/testthat/test-isocubeGrob.r | 24 affiner-0.2.1/affiner/tests/testthat/test-isotoxal_2ngon_inner_radius.r |only affiner-0.2.1/affiner/tests/testthat/test-line.r | 139 - affiner-0.2.1/affiner/tests/testthat/test-plane.r | 64 affiner-0.2.1/affiner/tests/testthat/test-plot.r | 114 - affiner-0.2.1/affiner/tests/testthat/test-point.r | 49 affiner-0.2.1/affiner/tests/testthat/test-trigonometry.r | 30 affiner-0.2.1/affiner/vignettes/affiner.Rmd | 8 affiner-0.2.1/affiner/vignettes/geometry.Rmd | 2 68 files changed, 3760 insertions(+), 3323 deletions(-)
Title: Summarise and Visualise Characteristics of Patients in the OMOP
CDM
Description: Summarise and visualise the characteristics of patients in data
mapped to the Observational Medical Outcomes Partnership (OMOP) common data
model (CDM).
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [ctb] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Marta Alcalde [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between CohortCharacteristics versions 1.1.0 dated 2025-11-19 and 1.1.1 dated 2026-01-28
DESCRIPTION | 23 MD5 | 244 NAMESPACE | 108 NEWS.md | 190 R/CohortCharacteristics-package.R | 56 R/benchmarkCohortCharacteristics.R | 528 R/checks.R | 252 R/documentationHelpers.R | 193 R/plot.R | 405 R/plotCharacteristics.R | 326 R/plotCohortAttrition.R | 840 - R/plotCohortCount.R | 158 R/plotCohortOverlap.R | 242 R/plotCohortTiming.R | 366 R/plotComparedLargeScaleCharacteristics.R | 318 R/plotLargeScaleCharacteristics.R | 154 R/reexports.R | 160 R/summariseCharacteristics.R | 1334 - R/summariseCohortAttrition.R | 246 R/summariseCohortCodelist.R | 350 R/summariseCohortCount.R | 112 R/summariseCohortOverlap.R | 476 R/summariseCohortTiming.R | 490 R/summariseLargeScaleCharacteristics.R | 1295 - R/table.R | 254 R/tableCharacteristics.R | 137 R/tableCohortAttrition.R | 120 R/tableCohortCount.R | 120 R/tableCohortOverlap.R | 136 R/tableCohortTiming.R | 180 R/tableLargeScaleCharacteristics.R | 526 R/utilities.R | 135 README.md | 624 build/vignette.rds |binary inst/WORDLIST | 124 inst/doc/summarise_characteristics.R | 322 inst/doc/summarise_characteristics.Rmd | 456 inst/doc/summarise_characteristics.html |12399 +++++++-------- inst/doc/summarise_cohort_overlap.R | 134 inst/doc/summarise_cohort_overlap.Rmd | 198 inst/doc/summarise_cohort_overlap.html | 3150 +-- inst/doc/summarise_cohort_timing.R | 164 inst/doc/summarise_cohort_timing.Rmd | 224 inst/doc/summarise_cohort_timing.html | 3184 +-- inst/doc/summarise_large_scale_characteristics.R | 134 inst/doc/summarise_large_scale_characteristics.Rmd | 224 inst/doc/summarise_large_scale_characteristics.html | 6179 +++---- man/CohortCharacteristics-package.Rd | 78 man/availablePlotColumns.Rd | 54 man/availableTableColumns.Rd | 58 man/benchmarkCohortCharacteristics.Rd | 86 man/cohortDoc.Rd | 24 man/cohortIdDoc.Rd | 26 man/figures/attrition.svg | 40 man/figures/lifecycle-archived.svg | 42 man/figures/lifecycle-defunct.svg | 42 man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-maturing.svg | 42 man/figures/lifecycle-questioning.svg | 42 man/figures/lifecycle-soft-deprecated.svg | 42 man/figures/lifecycle-stable.svg | 58 man/figures/lifecycle-superseded.svg | 42 man/mockCohortCharacteristics.Rd | 90 man/plotCharacteristics.Rd | 175 man/plotCohortAttrition.Rd | 110 man/plotCohortCount.Rd | 125 man/plotCohortOverlap.Rd | 111 man/plotCohortTiming.Rd | 167 man/plotComparedLargeScaleCharacteristics.Rd | 147 man/plotDoc.Rd | 47 man/plotLargeScaleCharacteristics.Rd | 127 man/reexports.Rd | 50 man/resultDoc.Rd | 24 man/strataDoc.Rd | 26 man/summariseCharacteristics.Rd | 268 man/summariseCohortAttrition.Rd | 64 man/summariseCohortCodelist.Rd | 84 man/summariseCohortCount.Rd | 70 man/summariseCohortOverlap.Rd | 84 man/summariseCohortTiming.Rd | 102 man/summariseLargeScaleCharacteristics.Rd | 164 man/tableCharacteristics.Rd | 132 man/tableCohortAttrition.Rd | 132 man/tableCohortCodelist.Rd | 80 man/tableCohortCount.Rd | 132 man/tableCohortOverlap.Rd | 140 man/tableCohortTiming.Rd | 164 man/tableDoc.Rd | 76 man/tableLargeScaleCharacteristics.Rd | 138 man/tableTopLargeScaleCharacteristics.Rd | 135 man/timeScaleDoc.Rd | 24 man/uniqueCombinationsDoc.Rd | 26 tests/manual/test-sqltest.R | 188 tests/spelling.R | 10 tests/testthat.R | 24 tests/testthat/setup.R | 118 tests/testthat/test-benchmarkCohortCharacteristics.R | 44 tests/testthat/test-plotCharacteristics.R | 472 tests/testthat/test-plotCohortAttrition.R | 82 tests/testthat/test-plotCohortCount.R | 50 tests/testthat/test-plotCohortOverlap.R | 214 tests/testthat/test-plotCohortTiming.R | 508 tests/testthat/test-plotLargeScaleCharacteristics.R | 328 tests/testthat/test-summariseCharacteristics.R | 3404 ++-- tests/testthat/test-summariseCohortAttrition.R | 60 tests/testthat/test-summariseCohortCodelist.R | 130 tests/testthat/test-summariseCohortCount.R | 52 tests/testthat/test-summariseCohortOverlap.R | 587 tests/testthat/test-summariseCohortTiming.R | 313 tests/testthat/test-summariseLargeScaleCharacteristics.R | 885 - tests/testthat/test-table.R | 18 tests/testthat/test-tableCharacteristics.R | 258 tests/testthat/test-tableCohortAttrition.R | 24 tests/testthat/test-tableCohortCount.R | 32 tests/testthat/test-tableCohortOverlap.R | 152 tests/testthat/test-tableCohortTiming.R | 226 tests/testthat/test-tableLargeScaleCharacteristics.R | 380 tests/testthat/test-utilities.R | 52 vignettes/summarise_characteristics.Rmd | 456 vignettes/summarise_cohort_overlap.Rmd | 198 vignettes/summarise_cohort_timing.Rmd | 224 vignettes/summarise_large_scale_characteristics.Rmd | 224 123 files changed, 25975 insertions(+), 25702 deletions(-)
More information about CohortCharacteristics at CRAN
Permanent link
Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the
OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped
to the Observational Medical Outcomes Partnership (OMOP) common data model.
New users and prevalent users cohorts can be generated and their
characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] ,
Mike Du [ctb] ,
Yuchen Guo [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Xintong Li [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Nuria Mercade-Besora [aut] ,
Xihang Chen [aut]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between DrugUtilisation versions 1.0.5 dated 2025-11-19 and 1.1.0 dated 2026-01-28
DrugUtilisation-1.0.5/DrugUtilisation/vignettes/daily_dose_calculation.html |only DrugUtilisation-1.0.5/DrugUtilisation/vignettes/drug_restart.html |only DrugUtilisation-1.0.5/DrugUtilisation/vignettes/indication.html |only DrugUtilisation-1.0.5/DrugUtilisation/vignettes/mock_data.html |only DrugUtilisation-1.0.5/DrugUtilisation/vignettes/summarise_treatments.html |only DrugUtilisation-1.0.5/DrugUtilisation/vignettes/treatment_discontinuation.html |only DrugUtilisation-1.1.0/DrugUtilisation/DESCRIPTION | 6 DrugUtilisation-1.1.0/DrugUtilisation/MD5 | 263 DrugUtilisation-1.1.0/DrugUtilisation/NAMESPACE | 152 DrugUtilisation-1.1.0/DrugUtilisation/NEWS.md | 240 DrugUtilisation-1.1.0/DrugUtilisation/R/DrugUtilisation-package.R | 21 DrugUtilisation-1.1.0/DrugUtilisation/R/addDrugUtilisation.R | 2318 - DrugUtilisation-1.1.0/DrugUtilisation/R/addIntersect.R | 836 DrugUtilisation-1.1.0/DrugUtilisation/R/benchmarkDrugUtilisation.R | 502 DrugUtilisation-1.1.0/DrugUtilisation/R/cohortUtilities.R | 476 DrugUtilisation-1.1.0/DrugUtilisation/R/dailyDose.R | 532 DrugUtilisation-1.1.0/DrugUtilisation/R/data.R | 46 DrugUtilisation-1.1.0/DrugUtilisation/R/documentationHelpers.R | 450 DrugUtilisation-1.1.0/DrugUtilisation/R/erafyCohort.R | 210 DrugUtilisation-1.1.0/DrugUtilisation/R/generateAtcCohortSet.R | 158 DrugUtilisation-1.1.0/DrugUtilisation/R/generateDrugUtilisationCohortSet.R | 366 DrugUtilisation-1.1.0/DrugUtilisation/R/generateIngredientCohortSet.R | 344 DrugUtilisation-1.1.0/DrugUtilisation/R/mockDrugUtilisation.R | 1200 DrugUtilisation-1.1.0/DrugUtilisation/R/pattern.R | 348 DrugUtilisation-1.1.0/DrugUtilisation/R/plots.R | 1208 DrugUtilisation-1.1.0/DrugUtilisation/R/reexports.R | 102 DrugUtilisation-1.1.0/DrugUtilisation/R/require.R | 706 DrugUtilisation-1.1.0/DrugUtilisation/R/summariseDrugRestart.R | 914 DrugUtilisation-1.1.0/DrugUtilisation/R/summariseDrugUtilisation.R | 406 DrugUtilisation-1.1.0/DrugUtilisation/R/summariseIntersect.R | 828 DrugUtilisation-1.1.0/DrugUtilisation/R/summariseProportionOfPatientsCovered.R | 648 DrugUtilisation-1.1.0/DrugUtilisation/R/tables.R | 888 DrugUtilisation-1.1.0/DrugUtilisation/R/validate.R | 152 DrugUtilisation-1.1.0/DrugUtilisation/README.md | 408 DrugUtilisation-1.1.0/DrugUtilisation/build/vignette.rds |binary DrugUtilisation-1.1.0/DrugUtilisation/inst/CITATION | 22 DrugUtilisation-1.1.0/DrugUtilisation/inst/Concept/asthma.json | 36 DrugUtilisation-1.1.0/DrugUtilisation/inst/acetaminophen.json | 24 DrugUtilisation-1.1.0/DrugUtilisation/inst/concepts/acetaminophen.json | 24 DrugUtilisation-1.1.0/DrugUtilisation/inst/concepts/influenza.json | 24 DrugUtilisation-1.1.0/DrugUtilisation/inst/doc/create_cohorts.R | 1082 DrugUtilisation-1.1.0/DrugUtilisation/inst/doc/create_cohorts.Rmd | 1690 - DrugUtilisation-1.1.0/DrugUtilisation/inst/doc/create_cohorts.html | 2375 - DrugUtilisation-1.1.0/DrugUtilisation/inst/doc/drug_utilisation.R | 336 DrugUtilisation-1.1.0/DrugUtilisation/inst/doc/drug_utilisation.Rmd | 602 DrugUtilisation-1.1.0/DrugUtilisation/inst/doc/drug_utilisation.html |16185 +++++----- DrugUtilisation-1.1.0/DrugUtilisation/inst/pattern_assessment_for_dose_final.csv | 84 DrugUtilisation-1.1.0/DrugUtilisation/man/DrugUtilisation-package.Rd | 82 DrugUtilisation-1.1.0/DrugUtilisation/man/addCumulativeDose.Rd | 132 DrugUtilisation-1.1.0/DrugUtilisation/man/addCumulativeQuantity.Rd | 124 DrugUtilisation-1.1.0/DrugUtilisation/man/addDailyDose.Rd |only DrugUtilisation-1.1.0/DrugUtilisation/man/addDaysExposed.Rd | 132 DrugUtilisation-1.1.0/DrugUtilisation/man/addDaysPrescribed.Rd | 124 DrugUtilisation-1.1.0/DrugUtilisation/man/addDrugRestart.Rd | 118 DrugUtilisation-1.1.0/DrugUtilisation/man/addDrugUtilisation.Rd | 220 DrugUtilisation-1.1.0/DrugUtilisation/man/addIndication.Rd | 170 DrugUtilisation-1.1.0/DrugUtilisation/man/addInitialDailyDose.Rd | 132 DrugUtilisation-1.1.0/DrugUtilisation/man/addInitialExposureDuration.Rd | 124 DrugUtilisation-1.1.0/DrugUtilisation/man/addInitialQuantity.Rd | 124 DrugUtilisation-1.1.0/DrugUtilisation/man/addNumberEras.Rd | 132 DrugUtilisation-1.1.0/DrugUtilisation/man/addNumberExposures.Rd | 124 DrugUtilisation-1.1.0/DrugUtilisation/man/addTimeToExposure.Rd | 124 DrugUtilisation-1.1.0/DrugUtilisation/man/addTreatment.Rd | 144 DrugUtilisation-1.1.0/DrugUtilisation/man/benchmarkDrugUtilisation.Rd | 86 DrugUtilisation-1.1.0/DrugUtilisation/man/cdmDoc.Rd | 24 DrugUtilisation-1.1.0/DrugUtilisation/man/censorDateDoc.Rd | 26 DrugUtilisation-1.1.0/DrugUtilisation/man/cohortDoc.Rd | 24 DrugUtilisation-1.1.0/DrugUtilisation/man/cohortGapEra.Rd | 78 DrugUtilisation-1.1.0/DrugUtilisation/man/cohortIdDoc.Rd | 26 DrugUtilisation-1.1.0/DrugUtilisation/man/compNameDoc.Rd | 26 DrugUtilisation-1.1.0/DrugUtilisation/man/conceptSetDoc.Rd | 24 DrugUtilisation-1.1.0/DrugUtilisation/man/daysPrescribedDoc.Rd | 26 DrugUtilisation-1.1.0/DrugUtilisation/man/drugUtilisationDoc.Rd | 92 DrugUtilisation-1.1.0/DrugUtilisation/man/erafyCohort.Rd | 102 DrugUtilisation-1.1.0/DrugUtilisation/man/gapEraDoc.Rd | 26 DrugUtilisation-1.1.0/DrugUtilisation/man/generateAtcCohortSet.Rd | 138 DrugUtilisation-1.1.0/DrugUtilisation/man/generateDrugUtilisationCohortSet.Rd | 146 DrugUtilisation-1.1.0/DrugUtilisation/man/generateIngredientCohortSet.Rd | 154 DrugUtilisation-1.1.0/DrugUtilisation/man/indexDateDoc.Rd | 26 DrugUtilisation-1.1.0/DrugUtilisation/man/ingredientConceptIdDoc.Rd | 26 DrugUtilisation-1.1.0/DrugUtilisation/man/mockDrugUtilisation.Rd | 90 DrugUtilisation-1.1.0/DrugUtilisation/man/nameStyleDoc.Rd | 24 DrugUtilisation-1.1.0/DrugUtilisation/man/newNameDoc.Rd | 26 DrugUtilisation-1.1.0/DrugUtilisation/man/numberExposuresDoc.Rd | 26 DrugUtilisation-1.1.0/DrugUtilisation/man/patternTable.Rd | 56 DrugUtilisation-1.1.0/DrugUtilisation/man/patternsWithFormula.Rd | 38 DrugUtilisation-1.1.0/DrugUtilisation/man/plotDoc.Rd | 58 DrugUtilisation-1.1.0/DrugUtilisation/man/plotDrugRestart.Rd | 130 DrugUtilisation-1.1.0/DrugUtilisation/man/plotDrugUtilisation.Rd | 182 DrugUtilisation-1.1.0/DrugUtilisation/man/plotIndication.Rd | 148 DrugUtilisation-1.1.0/DrugUtilisation/man/plotProportionOfPatientsCovered.Rd | 114 DrugUtilisation-1.1.0/DrugUtilisation/man/plotTreatment.Rd | 124 DrugUtilisation-1.1.0/DrugUtilisation/man/reexports.Rd | 56 DrugUtilisation-1.1.0/DrugUtilisation/man/requireDrugInDateRange.Rd | 102 DrugUtilisation-1.1.0/DrugUtilisation/man/requireIsFirstDrugEntry.Rd | 84 DrugUtilisation-1.1.0/DrugUtilisation/man/requireObservationBeforeDrug.Rd | 98 DrugUtilisation-1.1.0/DrugUtilisation/man/requirePriorDrugWashout.Rd | 104 DrugUtilisation-1.1.0/DrugUtilisation/man/restrictIncidentDoc.Rd | 28 DrugUtilisation-1.1.0/DrugUtilisation/man/resultDoc.Rd | 24 DrugUtilisation-1.1.0/DrugUtilisation/man/strataDoc.Rd | 26 DrugUtilisation-1.1.0/DrugUtilisation/man/summariseDoseCoverage.Rd | 90 DrugUtilisation-1.1.0/DrugUtilisation/man/summariseDrugRestart.Rd | 140 DrugUtilisation-1.1.0/DrugUtilisation/man/summariseDrugUtilisation.Rd | 228 DrugUtilisation-1.1.0/DrugUtilisation/man/summariseIndication.Rd | 174 DrugUtilisation-1.1.0/DrugUtilisation/man/summariseProportionOfPatientsCovered.Rd | 96 DrugUtilisation-1.1.0/DrugUtilisation/man/summariseTreatment.Rd | 126 DrugUtilisation-1.1.0/DrugUtilisation/man/tableDoc.Rd | 90 DrugUtilisation-1.1.0/DrugUtilisation/man/tableDoseCoverage.Rd | 144 DrugUtilisation-1.1.0/DrugUtilisation/man/tableDrugRestart.Rd | 158 DrugUtilisation-1.1.0/DrugUtilisation/man/tableDrugUtilisation.Rd | 158 DrugUtilisation-1.1.0/DrugUtilisation/man/tableIndication.Rd | 156 DrugUtilisation-1.1.0/DrugUtilisation/man/tableProportionOfPatientsCovered.Rd | 154 DrugUtilisation-1.1.0/DrugUtilisation/man/tableTreatment.Rd | 154 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat.R | 24 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/_snaps/addDrugUtilisation.md | 144 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/setup.R | 140 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-addDrugUtilisation.R | 942 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-benchmarkDrugUtilisation.R | 56 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-dailyDose.R | 564 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-erafyCohort.R | 152 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-generateDrugUtilisationCohortSet.R | 510 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-generatedAtcCohortSet.R | 66 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-generatedIngredientCohortSet.R | 2 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-indication.R | 1334 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-patterns.R | 130 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-plotProportionOfPatientsCovered.R | 298 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-plotTreatment.R | 178 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-plots.R | 518 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-require.R | 1270 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-summariseDrugRestart.R | 624 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-summariseDrugUtilisation.R | 220 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-summariseProportionOfPatientsCovered.R | 1192 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-summariseTreatment.R | 150 DrugUtilisation-1.1.0/DrugUtilisation/tests/testthat/test-tables.R | 946 DrugUtilisation-1.1.0/DrugUtilisation/vignettes/create_cohorts.Rmd | 1690 - DrugUtilisation-1.1.0/DrugUtilisation/vignettes/drug_utilisation.Rmd | 602 136 files changed, 27733 insertions(+), 27693 deletions(-)
More information about DrugUtilisation at CRAN
Permanent link
Title: Rmetrics - Chronological and Calendar Objects
Description: The 'timeDate' class fulfils the conventions of the ISO 8601
standard as well as of the ANSI C and POSIX standards. Beyond
these standards it provides the "Financial Center" concept
which allows to handle data records collected in different time
zones and mix them up to have always the proper time stamps with
respect to your personal financial center, or alternatively to the GMT
reference time. It can thus also handle time stamps from historical
data records from the same time zone, even if the financial
centers changed day light saving times at different calendar
dates.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Martin Maechler [ctb] ,
Joe W. Byers [ctb],
Georgi N. Boshnakov [cre, aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between timeDate versions 4051.111 dated 2025-10-17 and 4052.112 dated 2026-01-28
DESCRIPTION | 12 +-- MD5 | 108 +++++++++++++++++----------------- NAMESPACE | 7 -- NEWS.md | 39 +++++++++--- R/base-c.R | 9 -- R/base-diff.R | 9 -- R/base-difftimeDate.R | 9 -- R/base-length.R | 8 -- R/base-rep.R | 9 -- R/base-rev.R | 9 -- R/base-sample.R | 9 -- R/base-sort.R | 11 --- R/base-subset.R | 53 +---------------- R/base-summary.R | 18 +---- R/base-unique.R | 9 -- R/calendar-dayOfWeek.R | 17 ----- R/calendar-endpoints.R | 4 - R/calendar-isDaily.R | 88 +++++++++++----------------- R/calendar-isWeekday.R | 33 +--------- R/calendar-periods.R | 25 -------- R/holiday-NERC.R | 5 - R/holiday-NYSE.R | 95 +++++++++++++++--------------- R/holiday-TSX.R | 76 ++++++++++++++++-------- R/holiday-ZURICH.R | 8 -- R/holiday.R | 86 ++++++++++++++++++++++----- R/methods-as.R | 94 +++--------------------------- R/methods-getDataPart.R | 4 - R/methods-mathOps.R | 74 +++++------------------ R/methods-names.R | 4 - R/methods-plot.R | 54 ++++++++--------- R/methods-show.R | 4 - R/options-RmetricsOptions.R | 26 +------- R/stats-blockStart.R | 37 +++-------- R/stats-frequency.R | 47 ++++++++++----- R/stats-kurtosis.R | 111 ++++++++++------------------------- R/stats-na.fail.R | 9 -- R/stats-skewness.R | 104 ++++++++++----------------------- R/stats-start.R | 47 ++------------- R/stats-window.R | 127 +++++++++++++++++++++-------------------- R/timeDate-Calendar.R | 55 ++++++++--------- R/timeDate-Sequence.R | 20 +----- R/timeDate-Sys.timeDate.R | 9 -- R/timeDate-finCenter.R | 33 +++------- R/timeDate-generateDST.R | 18 ++--- R/timeDate-rulesFinCenter.R | 8 -- R/tzone.R | 28 --------- inst/_pkgdown.yml | 1 inst/pkgdown.yml | 16 ++--- inst/unitTests/runit.Subsets.R | 52 ++++++++-------- man/00timeDate-package.Rd | 3 man/calendar-isRegular.Rd | 5 - man/holiday.Rd | 94 +++++++++++++++++++++++++----- man/options-RmetricsOptions.Rd | 25 +++++--- man/stats-window.Rd | 22 ------- tests/doRUnit.R | 2 55 files changed, 754 insertions(+), 1135 deletions(-)
Title: Feel at Home using R, Thanks to Shortcuts Functions Making it
Simple
Description: A collection of personal functions designed to simplify and
streamline common R programming tasks. This package provides reusable
tools and shortcuts for frequently used calculations and workflows.
Author: Raphael Flambard [aut, cre],
Adrien Cocuaud [ctb]
Maintainer: Raphael Flambard <raphael@ralpha.fr>
This is a re-admission after prior archival of version 1.1.0 dated 2025-09-15
Diff between R.AlphA.Home versions 1.1.0 dated 2025-09-15 and 2.0.2 dated 2026-01-28
DESCRIPTION | 34 - MD5 | 112 ++-- NAMESPACE | 129 ++--- NEWS.md | 193 +++++--- R/Rtimer.R | 134 ++--- R/cols_pad.R | 65 +- R/compareVars.R | 100 ++-- R/countSwitches.R | 189 +++----- R/foldAllBr.R | 588 ++++++++++++------------- R/globalVariables.R | 191 ++++---- R/importAll.R | 433 +++++++++--------- R/left_join_checks.R | 331 +++++++------- R/loadCheck.R | 63 +- R/lum_0_100.R | 73 +-- R/printif.R | 102 ++-- R/quickExport.R | 72 +-- R/quickSave.R | 149 +++--- R/ralpha_fold.R | 488 ++++++++++---------- R/ralpha_unfold.R | 460 +++++++++---------- R/rdate.R | 107 ++-- R/ret_lum.R | 70 +- R/root.R | 71 ++- R/sepThsd.R | 64 +- R/setOption.R | 92 +-- R/shiny_lum_0_100.R | 78 +-- R/show_diff.R | 229 +++++++-- R/timer.R | 178 +++---- R/utils-position.R | 266 +++++------ README.md | 186 +++---- inst/rstudio/addins.dcf | 20 man/Rtimer.Rd | 18 man/cols_pad.Rd | 64 +- man/compareVars.Rd | 94 +-- man/countSwitches.Rd | 144 +++--- man/foldAllBr.Rd | 96 ++-- man/importAll.Rd | 174 +++---- man/left_join_checks.Rd | 152 +++--- man/lum_0_100.Rd | 46 - man/printif.Rd | 106 ++-- man/quickExport.Rd | 98 ++-- man/quickSave.Rd | 72 +-- man/ralpha_fold.Rd | 60 +- man/ralpha_unfold.Rd | 110 ++-- man/rdate.Rd | 92 +-- man/ret_lum.Rd | 68 +- man/root.Rd | 77 ++- man/sepThsd.Rd | 70 +- man/setOption.Rd | 82 +-- man/shiny_lum_0_100.Rd | 42 - man/show_diff.Rd | 6 man/timer.Rd | 128 ++--- tests/testthat.R | 24 - tests/testthat/test-Rtimer.R |only tests/testthat/test-cols_pad.r | 108 ++-- tests/testthat/test-compareVars.R |only tests/testthat/test-other_not_tested.R |only tests/testthat/test-printif.R |only tests/testthat/test-rdate.R |only tests/testthat/test-ret_lum.R |only tests/testthat/test-sepThsd.R |only tests/testthat/test_session5_stringi_removal.R |only 61 files changed, 3688 insertions(+), 3510 deletions(-)
Title: Monte Carlo Simulation for Structural Equation Modeling
Description: Provides tools to conduct Monte Carlo simulations under different conditions (e.g., varying sample size, data normality) for structural equation models (SEMs).
Data can be simulated based on user-defined factor loadings and correlations, with optional non-normality added via Fleishman's power method (1978) <doi:10.1007/BF02293811>.
Once generated, models can be estimated using 'lavaan'. This package facilitates testing model performance across multiple simulation scenarios.
When data generation is completed (or when generated data sets are given) model tests can also be run.
Please cite as "Orçan, F. (2021). MonteCarloSEM An R Package to Simulate Data for SEM. International Journal of Assessment Tools in Education, 8 (3), 704-713."
Author: Fatih Orcan [aut, cre]
Maintainer: Fatih Orcan <fatihorcan84@gmail.com>
Diff between MonteCarloSEM versions 0.0.8 dated 2024-04-05 and 2.0.0 dated 2026-01-28
DESCRIPTION | 27 +++++++++++++++------------ MD5 | 46 ++++++++++++++++++++++++---------------------- NAMESPACE | 3 +++ R/Categorize.R | 13 ++++++++----- R/Input_fcors.R | 16 ++++++++-------- R/Input_floads.R | 18 ++++++++++-------- R/MAR.R | 38 +++++++++++++++++++++----------------- R/MCAR.R | 29 ++++++++++++++++------------- R/MNAR.R | 34 +++++++++++++++++++--------------- R/cov.mtx.R |only R/run.sem.sim.R | 43 +++++++++++++++++++++---------------------- R/sim_Categoric.R | 32 +++++++++++++++++--------------- R/sim_Normal.R | 28 ++++++++++++++++------------ R/sim_Skewed.R | 36 +++++++++++++++++++++--------------- man/MAR.data.Rd | 38 +++++++++++++++++++++----------------- man/MCAR.data.Rd | 28 +++++++++++++++------------- man/MNAR.data.Rd | 32 +++++++++++++++++--------------- man/categorize.Rd | 12 +++++++----- man/cov.mtx.Rd |only man/fcors.value.Rd | 15 +++++++-------- man/fit.simulation.Rd | 36 +++++++++++++++++------------------- man/loading.value.Rd | 16 ++++++++-------- man/sim.categoric.Rd | 31 ++++++++++++++++--------------- man/sim.normal.Rd | 27 +++++++++++++++------------ man/sim.skewed.Rd | 35 ++++++++++++++++++++--------------- 25 files changed, 342 insertions(+), 291 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.7.1 dated 2025-12-09 and 1.0.0 dated 2026-01-28
DESCRIPTION | 6 MD5 | 55 ++-- NAMESPACE | 1 NEWS.md | 33 ++ R/MaestroPipeline.R | 281 +++++++++++++++++++----- R/MaestroPipelineList.R | 87 +++---- R/MaestroSchedule.R | 47 +++- R/build_schedule_entry.R | 59 ++--- R/get_run_sequence.R |only R/utils.R | 22 + inst/doc/maestro-1-quick-start.html | 6 inst/doc/maestro-3-advanced-scheduling.html | 14 - inst/doc/maestro-4-directed-acyclic-graphs.html | 28 +- inst/doc/maestro-5-logging.html | 64 ++--- inst/doc/maestro-5-logging.qmd | 2 inst/doc/maestro-8-conditionals.html | 40 +-- man/MaestroPipeline.Rd | 35 ++ man/MaestroPipelineList.Rd | 38 +-- man/MaestroSchedule.Rd | 33 ++ man/figures/README-/unnamed-chunk-3.svg | 2 man/get_run_sequence.Rd |only tests/testthat/_snaps/MaestroPipeline.md | 24 -- tests/testthat/_snaps/conditionals.md | 4 tests/testthat/_snaps/dags.md | 102 ++++++++ tests/testthat/test-MaestroPipeline.R | 3 tests/testthat/test-build_schedule_entry.R | 19 + tests/testthat/test-dags.R | 194 ++++++++++++++++ tests/testthat/test-get_run_sequence.R |only tests/testthat/test-run_schedule.R | 42 +++ vignettes/maestro-5-logging.qmd | 2 30 files changed, 947 insertions(+), 296 deletions(-)
Title: Power Analysis via Data Simulation for (Generalized) Linear
Mixed Effects Models
Description: Conduct a priori power analyses via Monte-Carlo style data simulation for linear and generalized linear mixed-effects models (LMMs/GLMMs). Provides a user-friendly workflow with helper functions to easily define fixed and random effects as well as diagnostic functions to evaluate the adequacy of the results of the power analysis.
Author: Markus Grill [aut, cre]
Maintainer: Markus Grill <markus.grill@uni-wh.de>
Diff between PowRPriori versions 0.1.1 dated 2025-12-14 and 0.1.2 dated 2026-01-28
PowRPriori-0.1.1/PowRPriori/inst/extdata/power_results_vignette.rds |only PowRPriori-0.1.2/PowRPriori/DESCRIPTION | 6 PowRPriori-0.1.2/PowRPriori/MD5 | 29 PowRPriori-0.1.2/PowRPriori/NEWS.md | 23 PowRPriori-0.1.2/PowRPriori/R/power_sim.R | 64 PowRPriori-0.1.2/PowRPriori/R/utils.R | 88 PowRPriori-0.1.2/PowRPriori/R/visualization.R | 47 PowRPriori-0.1.2/PowRPriori/inst/doc/Workflow-Example.R | 153 + PowRPriori-0.1.2/PowRPriori/inst/doc/Workflow-Example.Rmd | 338 ++- PowRPriori-0.1.2/PowRPriori/inst/doc/Workflow-Example.html | 1110 ++++++---- PowRPriori-0.1.2/PowRPriori/inst/extdata/power_results_workflow.rds |only PowRPriori-0.1.2/PowRPriori/man/define_design.Rd | 2 PowRPriori-0.1.2/PowRPriori/man/dot-plot_data.Rd | 2 PowRPriori-0.1.2/PowRPriori/man/plot_sim_model.Rd | 12 PowRPriori-0.1.2/PowRPriori/man/power_sim.Rd | 4 PowRPriori-0.1.2/PowRPriori/vignettes/Workflow-Example.Rmd | 338 ++- PowRPriori-0.1.2/PowRPriori/vignettes/references.bib |only 17 files changed, 1624 insertions(+), 592 deletions(-)
Title: Assess Study Cohorts Using a Common Data Model
Description: Phenotype study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model. Diagnostics
are run at the database, code list, cohort, and population level to assess
whether study cohorts are ready for research.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Xihang Chen [aut] ,
Marta Alcalde-Herraiz [aut] ,
Nuria Mercade-Besora [aut] ,
Albert Prats-Uribe [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between PhenotypeR versions 0.3.0 dated 2026-01-12 and 0.3.1 dated 2026-01-28
DESCRIPTION | 10 MD5 | 41 - R/codelistDiagnostics.R | 11 R/cohortDiagnostics.R | 14 R/documentationHelper.R | 13 R/phenotypeDiagnostics.R | 21 R/shinyDiagnostics.R | 2 inst/doc/CodelistDiagnostics.html | 880 +++++++++++++++--------------- inst/doc/DatabaseDiagnostics.html | 840 ++++++++++++++-------------- inst/doc/PhenotypeExpectations.html | 24 inst/doc/PopulationDiagnostics.html | 220 +++---- inst/doc/ShinyDiagnostics.html | 24 inst/shiny/global.R | 2 inst/shiny/scripts/preprocess.R | 17 inst/shiny/server.R | 19 inst/shiny/ui.R | 17 man/codelistDiagnostics.Rd | 7 man/cohortDiagnostics.Rd | 2 man/cohortSampleDoc.Rd | 2 man/measurementSampleDoc.Rd |only man/phenotypeDiagnostics.Rd | 8 tests/testthat/test-codelistDiagnostics.R | 18 22 files changed, 1139 insertions(+), 1053 deletions(-)
Title: Evolutionary Parameter Estimation for 'Repast Simphony' Models
Description: The EvoPER, Evolutionary Parameter Estimation for Individual-based Models is an extensible
package providing optimization driven parameter estimation methods using metaheuristics and
evolutionary computation techniques (Particle Swarm Optimization, Simulated Annealing, Ant Colony Optimization
for continuous domains, Tabu Search, Evolutionary Strategies, ...) which could be more efficient and require,
in some cases, fewer model evaluations than alternatives relying on experimental design. Currently there
are built in support for models developed with 'Repast Simphony' Agent-Based framework (<https://repast.github.io/>)
and with NetLogo (<https://www.netlogo.org/>) which are the most used frameworks for Agent-based modeling.
Author: Antonio Prestes Garcia [aut, cre],
Alfonso Rodriguez-Paton [aut, ths]
Maintainer: Antonio Prestes Garcia <antonio.pgarcia@alumnos.upm.es>
Diff between evoper versions 0.5.0 dated 2018-08-30 and 0.6.0 dated 2026-01-28
DESCRIPTION | 17 ++---- MD5 | 82 +++++++++++++++-------------- NAMESPACE | 13 +++- NEWS | 8 ++ R/abm-ga.R |only R/abm-tabu.R | 2 R/class-options.R | 27 +++++++++ R/evoper.R | 55 +++++++++++++++---- R/netlogo-helper.R | 14 ++-- R/test-functions.R | 42 +++++++------- inst/examples/netlogo-predator-prey-ees2.R | 14 ++-- man/GetLogLevel.Rd |only man/NLWrapper.GetParameter.Rd | 2 man/NLWrapper.Model.Rd | 4 - man/NLWrapper.Run.Rd | 11 +++ man/NLWrapper.RunExperiment.Rd | 2 man/NLWrapper.SetParameter.Rd | 2 man/OptionsGA-class.Rd |only man/SetLogLevel.Rd |only man/abm.ga.Rd |only man/compare.algorithms1.Rd | 6 +- man/contourplothelper.Rd | 12 +++- man/f0.ackley.Rd | 2 man/f0.ackley4.Rd | 2 man/f0.bohachevsky.Rd | 2 man/f0.bohachevsky4.Rd | 2 man/f0.cigar.Rd | 2 man/f0.cigar4.Rd | 2 man/f0.griewank.Rd | 2 man/f0.griewank4.Rd | 2 man/f0.rosenbrock4.Rd | 2 man/f0.rosenbrockn.Rd | 2 man/f0.schaffer.Rd | 2 man/f0.schaffer4.Rd | 2 man/f0.schwefel.Rd | 2 man/f0.schwefel4.Rd | 2 man/f1.ackley.Rd | 2 man/f1.bohachevsky.Rd | 2 man/f1.cigar.Rd | 2 man/f1.griewank.Rd | 2 man/f1.rosenbrockn.Rd | 2 man/f1.schaffer.Rd | 2 man/f1.schwefel.Rd | 2 tests/testthat/_problems |only tests/testthat/test-metaheuristics.R | 24 ++++++++ 45 files changed, 252 insertions(+), 127 deletions(-)
Title: Extreme Value Analyses with Missing Data
Description: Performs likelihood-based extreme value inferences with
adjustment for the presence of missing values based on Simpson and
Northrop (2026). A Generalised Extreme Value
distribution is fitted to block maxima using maximum likelihood estimation,
with the location and scale parameters reflecting the numbers of
non-missing raw values in each block. A Bayesian version is also provided.
For the purposes of comparison, there are options to make no adjustment for
missing values or to discard any block maximum for which greater than a
percentage of the underlying raw values are missing. Example datasets
containing missing values are provided.
Author: Paul J. Northrop [aut, cre, cph],
Emma S. Simpson [aut, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between evmissing versions 1.0.0 dated 2026-01-08 and 1.0.1 dated 2026-01-28
DESCRIPTION | 10 ++--- MD5 | 29 +++++++------- NEWS.md |only R/evmissing-internal.R | 71 +++++++++++++++++------------------- R/evmissing-package.R | 7 ++- R/methods_confint_gev.R | 6 ++- R/methods_confint_return_level.R | 6 ++- R/methods_evmissing.R | 4 +- R/methods_return_level.R | 4 +- README.md | 14 +++---- man/confint_gev_methods.Rd | 3 + man/confint_return_level_methods.Rd | 3 + man/evmissing-internal.Rd | 3 - man/evmissing-package.Rd | 7 ++- man/evmissing_methods.Rd | 4 +- man/return_level_methods.Rd | 4 +- 16 files changed, 89 insertions(+), 86 deletions(-)
Title: Ensemble Models for Lactation Curves
Description: Lactation curves describe temporal changes in milk yield and are key to breeding and managing dairy animals more efficiently. The use of ensemble modeling, which consists of combining predictions from multiple models, has the potential to yields more accurate and robust estimates of lactation patterns than relying solely on single model estimates. The package EMOTIONS fits 47 models for lactation curves and creates ensemble models using model averaging based on Akaike information criterion (AIC), Bayesian information criterion (BIC), root mean square percentage error (RMSPE) and mean squared error (MAE), variance of the predictions, cosine similarity for each model's predictions, and Bayesian Model Average (BMA). The daily production values predicted through the ensemble models can be used to estimate resilience indicators in the package. The package allows the graphical visualization of the model ranks and the predicted lactation curves. Additionally, the packages allows the user to d [...truncated...]
Author: Pablo Fonseca [aut, cre],
Marcos Prates [aut],
Aroa Suarez-Vega [aut],
Ruth Arribas Gonzalo [aut],
Beatriz Gutierrez-Gil [aut],
Juan Jose Arranz [aut]
Maintainer: Pablo Fonseca <p.fonseca@csic.es>
Diff between EMOTIONS versions 1.0 dated 2025-06-18 and 1.1 dated 2026-01-28
DESCRIPTION | 14 MD5 | 86 NAMESPACE | 114 R/BMAweight_gamma.R | 132 R/CosSquaredWeight.R | 54 R/GetLacModelsMetrics.R | 86 R/LacCurveFit.R | 91 R/LacData.R | 38 R/ModelRankRange.R | 60 R/ModelsLac.R | 712 +-- R/ParDef.R | 118 R/PlotMilkLoss.R |only R/PlotWeightLac.R | 53 R/ResInd.R | 237 - R/RidgeModels.R | 63 R/VarWeight.R | 36 R/global_variables.R | 11 R/imp_my.R |only R/milkloss_detect.R |only R/model_pars.R | 36 R/models_EMOTIONS.R | 42 README.md | 216 - build/vignette.rds |binary data/models_EMOTIONS.rda |binary inst/doc/EMOTIONS.R | 287 - inst/doc/EMOTIONS.Rmd | 765 ++- inst/doc/EMOTIONS.html | 1962 +++++----- man/BMAweight_gamma.Rd | 44 man/CosSquaredWeight.Rd | 40 man/GetLacModelsMetrics.Rd | 44 man/LacCurveFit.Rd | 80 man/LacData.Rd | 8 man/ModelRankRange.Rd | 38 man/ModelsLac.Rd | 87 man/ParDef.Rd | 44 man/PlotMilkLoss.Rd |only man/PlotWeightLac.Rd | 92 man/ResInd.Rd | 74 man/RidgeModels.Rd | 38 man/VarWeight.Rd | 40 man/imp_my.Rd |only man/milkloss_detect.Rd |only man/model_pars.Rd | 4 man/models_EMOTIONS.Rd | 10 vignettes/EMOTIONS.Rmd | 765 ++- vignettes/rsconnect/documents/EMOTIONS.Rmd/rpubs.com/rpubs/Document.dcf | 20 vignettes/rsconnect/documents/EnsembleLacs.Rmd/rpubs.com/rpubs/Document.dcf | 20 47 files changed, 3675 insertions(+), 2986 deletions(-)
Title: Generic PK/PD Simulation Platform Campsis
Description: A generic, easy-to-use and intuitive
pharmacokinetic/pharmacodynamic (PK/PD) simulation platform based on
the R packages 'rxode2' and 'mrgsolve'. Campsis provides an
abstraction layer over the underlying processes of defining a PK/PD
model, assembling a custom dataset and running a simulation. The
package has a strong dependency on the R package 'campsismod', which
allows models to be read from and written to files, including through
a JSON-based interface, and to be adapted further on the fly in the R
environment. In addition, 'campsis' allows users to assemble datasets
in an intuitive manner, including via a JSON-based interface to import
Campsis datasets defined using formal JSON schemas distributed with
the package. Once the dataset is ready, the package prepares the
simulation, calls 'rxode2' or 'mrgsolve' (at the user's choice), and
returns the results for the given model, dataset and desired
simulation settings. The package itself is licensed under the GPL (>=
3); the JSON sc [...truncated...]
Author: Nicolas Luyckx [aut, cre]
Maintainer: Nicolas Luyckx <nicolas.luyckx@calvagone.com>
Diff between campsis versions 1.7.0 dated 2025-04-04 and 1.8.1 dated 2026-01-28
campsis-1.7.0/campsis/man/getFurrrScheduling.Rd |only campsis-1.7.0/campsis/tests/testthat/_snaps/testDefaultPlots/scatterplot-colour-scenario.svg |only campsis-1.7.0/campsis/tests/testthat/_snaps/testDefaultPlots/scatterplot-no-colour.svg |only campsis-1.7.0/campsis/tests/testthat/_snaps/testDefaultPlots/shadedplot-colour-arm-strat-wt.svg |only campsis-1.7.0/campsis/tests/testthat/_snaps/testDefaultPlots/shadedplot-colour-arm-wt-strat-wt.svg |only campsis-1.7.0/campsis/tests/testthat/_snaps/testDefaultPlots/shadedplot-colour-scenario.svg |only campsis-1.7.0/campsis/tests/testthat/_snaps/testDefaultPlots/spaghettiplot-colour-arm-strat-wt.svg |only campsis-1.7.0/campsis/tests/testthat/_snaps/testDefaultPlots/spaghettiplot-colour-scenario.svg |only campsis-1.7.0/campsis/tests/testthat/_snaps/testSimulateReplicates/vpc-specified-outfun.svg |only campsis-1.8.1/campsis/DESCRIPTION | 67 - campsis-1.8.1/campsis/LICENSE.note |only campsis-1.8.1/campsis/MD5 | 207 +++- campsis-1.8.1/campsis/NAMESPACE | 436 +++++----- campsis-1.8.1/campsis/NEWS.md | 11 campsis-1.8.1/campsis/R/arm.R | 2 campsis-1.8.1/campsis/R/bootstrap.R | 18 campsis-1.8.1/campsis/R/check.R | 18 campsis-1.8.1/campsis/R/covariate.R | 11 campsis-1.8.1/campsis/R/dataset.R | 75 + campsis-1.8.1/campsis/R/dataset_config.R | 8 campsis-1.8.1/campsis/R/default_settings.R |only campsis-1.8.1/campsis/R/distribution.R | 117 ++ campsis-1.8.1/campsis/R/dose_adaptation.R | 9 campsis-1.8.1/campsis/R/events.R | 2 campsis-1.8.1/campsis/R/generic.R | 25 campsis-1.8.1/campsis/R/hardware_settings.R | 13 campsis-1.8.1/campsis/R/json_interface.R |only campsis-1.8.1/campsis/R/observations.R | 95 +- campsis-1.8.1/campsis/R/observations_set.R | 10 campsis-1.8.1/campsis/R/plan_setup.R | 8 campsis-1.8.1/campsis/R/protocol.R | 9 campsis-1.8.1/campsis/R/repeated_schedule.R | 31 campsis-1.8.1/campsis/R/scenario.R | 52 - campsis-1.8.1/campsis/R/scenario_action.R |only campsis-1.8.1/campsis/R/scenario_actions.R |only campsis-1.8.1/campsis/R/scenarios.R | 19 campsis-1.8.1/campsis/R/seed.R | 4 campsis-1.8.1/campsis/R/simulate.R | 139 ++- campsis-1.8.1/campsis/R/simulate_preprocess.R | 5 campsis-1.8.1/campsis/R/simulation_settings.R | 40 campsis-1.8.1/campsis/R/time_vector.R |only campsis-1.8.1/campsis/R/treatment.R | 17 campsis-1.8.1/campsis/R/treatment_entry.R | 48 + campsis-1.8.1/campsis/R/utilities.R | 31 campsis-1.8.1/campsis/build/vignette.rds |binary campsis-1.8.1/campsis/inst/doc/campsis.html | 11 campsis-1.8.1/campsis/inst/extdata |only campsis-1.8.1/campsis/man/CyclicSchedule.Rd | 38 campsis-1.8.1/campsis/man/DefaultSettings.Rd |only campsis-1.8.1/campsis/man/DosingSchedule.Rd |only campsis-1.8.1/campsis/man/Observations.Rd | 4 campsis-1.8.1/campsis/man/RepeatAtSchedule.Rd | 38 campsis-1.8.1/campsis/man/ReplaceAction.Rd |only campsis-1.8.1/campsis/man/Scenario.Rd | 4 campsis-1.8.1/campsis/man/TimeSequence.Rd |only campsis-1.8.1/campsis/man/TimeVector.Rd |only campsis-1.8.1/campsis/man/applyAction.Rd |only campsis-1.8.1/campsis/man/as.numeric-time_sequence-method.Rd |only campsis-1.8.1/campsis/man/as.numeric-time_vector-method.Rd |only campsis-1.8.1/campsis/man/binomial_distribution-class.Rd |only campsis-1.8.1/campsis/man/bolus_wrapper-class.Rd | 18 campsis-1.8.1/campsis/man/cyclic_schedule-class.Rd | 34 campsis-1.8.1/campsis/man/default_settings-class.Rd |only campsis-1.8.1/campsis/man/discrete_distribution-class.Rd |only campsis-1.8.1/campsis/man/dosing_schedule-class.Rd |only campsis-1.8.1/campsis/man/getCampsisOption.Rd |only campsis-1.8.1/campsis/man/getCampsisOptions.Rd |only campsis-1.8.1/campsis/man/getCompartmentMapping.Rd | 40 campsis-1.8.1/campsis/man/getSeed.Rd | 2 campsis-1.8.1/campsis/man/getSplittingConfiguration.Rd | 4 campsis-1.8.1/campsis/man/getTimes.Rd | 20 campsis-1.8.1/campsis/man/infusion_wrapper-class.Rd | 18 campsis-1.8.1/campsis/man/jsonToCampsisDataset.Rd |only campsis-1.8.1/campsis/man/jsonToCampsisSettings.Rd |only campsis-1.8.1/campsis/man/length-cyclic_schedule-method.Rd | 34 campsis-1.8.1/campsis/man/length-repeat_at_schedule-method.Rd | 34 campsis-1.8.1/campsis/man/lognormal_distribution-class.Rd |only campsis-1.8.1/campsis/man/normal_distribution-class.Rd |only campsis-1.8.1/campsis/man/observations-class.Rd | 4 campsis-1.8.1/campsis/man/openJSON.Rd |only campsis-1.8.1/campsis/man/repeatSchedule.Rd | 56 - campsis-1.8.1/campsis/man/repeat_at_schedule-class.Rd | 30 campsis-1.8.1/campsis/man/repeated_schedule-class.Rd | 18 campsis-1.8.1/campsis/man/replace_action-class.Rd |only campsis-1.8.1/campsis/man/scenario-class.Rd | 6 campsis-1.8.1/campsis/man/scenario_action-class.Rd |only campsis-1.8.1/campsis/man/scenario_actions-class.Rd |only campsis-1.8.1/campsis/man/setLabel.Rd | 5 campsis-1.8.1/campsis/man/simulation_settings-class.Rd | 2 campsis-1.8.1/campsis/man/time_sequence-class.Rd |only campsis-1.8.1/campsis/man/time_vector-class.Rd |only campsis-1.8.1/campsis/man/undefined_schedule-class.Rd | 18 campsis-1.8.1/campsis/man/uniform_distribution-class.Rd |only campsis-1.8.1/campsis/man/unwrapTreatment.Rd | 84 - campsis-1.8.1/campsis/man/updateADDL.Rd | 92 +- campsis-1.8.1/campsis/man/updateAmount.Rd | 92 +- campsis-1.8.1/campsis/man/updateII.Rd | 92 +- campsis-1.8.1/campsis/man/updateRepeat.Rd | 92 +- campsis-1.8.1/campsis/tests/testthat/_snaps/testDefaultPlots/scatterplot-colour-scenario-mrgsolve.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testDefaultPlots/scatterplot-colour-scenario-rxode2.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testDefaultPlots/scatterplot-no-colour-mrgsolve.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testDefaultPlots/scatterplot-no-colour-rxode2.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testDefaultPlots/shadedplot-colour-arm-strat-wt-mrgsolve.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testDefaultPlots/shadedplot-colour-arm-strat-wt-rxode2.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testDefaultPlots/shadedplot-colour-arm-wt-strat-wt-mrgsolve.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testDefaultPlots/shadedplot-colour-arm-wt-strat-wt-rxode2.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testDefaultPlots/shadedplot-colour-scenario-mrgsolve.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testDefaultPlots/shadedplot-colour-scenario-rxode2.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testDefaultPlots/spaghettiplot-colour-arm-strat-wt-mrgsolve.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testDefaultPlots/spaghettiplot-colour-arm-strat-wt-rxode2.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testDefaultPlots/spaghettiplot-colour-scenario-mrgsolve.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testDefaultPlots/spaghettiplot-colour-scenario-rxode2.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testSimulateReplicates/vpc-specified-outfun-mrgsolve-a.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testSimulateReplicates/vpc-specified-outfun-mrgsolve-b.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testSimulateReplicates/vpc-specified-outfun-mrgsolve-c.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testSimulateReplicates/vpc-specified-outfun-rxode2-a.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testSimulateReplicates/vpc-specified-outfun-rxode2-b.svg |only campsis-1.8.1/campsis/tests/testthat/_snaps/testSimulateReplicates/vpc-specified-outfun-rxode2-c.svg |only campsis-1.8.1/campsis/tests/testthat/json_examples |only campsis-1.8.1/campsis/tests/testthat/testDefaultPlots.R | 44 - campsis-1.8.1/campsis/tests/testthat/testJSONInterface.R |only campsis-1.8.1/campsis/tests/testthat/testObservations.R | 12 campsis-1.8.1/campsis/tests/testthat/testSettings.R | 9 campsis-1.8.1/campsis/tests/testthat/testSimulateBolusInfusionSameCmt.R | 4 campsis-1.8.1/campsis/tests/testthat/testSimulateReplicates.R | 6 campsis-1.8.1/campsis/tests/testthat/testSimulateScenarios.R | 16 campsis-1.8.1/campsis/tests/testthat/testUtils.R | 23 127 files changed, 1631 insertions(+), 900 deletions(-)
Title: Bhavcopy and Live Market Data from National Stock Exchange (NSE)
& Bombay Stock Exchange (BSE) India
Description: Download Current & Historical Bhavcopy. Get Live Market data from NSE India of Equities and Derivatives (F&O) segment. Data source <https://www.nseindia.com/>.
Author: Nandan Patil [cre, aut]
Maintainer: Nandan Patil <tryanother609@gmail.com>
Diff between nser versions 1.5.8 dated 2026-01-10 and 1.6.0 dated 2026-01-28
DESCRIPTION | 8 ++++---- MD5 | 21 ++++++++++++++------- NAMESPACE | 1 + R/nseopen.R | 6 +++--- R/nseopenfo.R |only build/vignette.rds |binary inst/doc/nseopen.Rmd | 3 ++- inst/doc/nseopen.html | 3 +-- inst/doc/nseopenfo.R |only inst/doc/nseopenfo.Rmd |only inst/doc/nseopenfo.html |only inst/npofo.py |only man/nseopenfo.Rd |only vignettes/nseopen.Rmd | 3 ++- vignettes/nseopenfo.Rmd |only 15 files changed, 27 insertions(+), 18 deletions(-)
Title: Connector Between 'mlr3' and 'OpenML'
Description: Provides an interface to 'OpenML.org' to list and download
machine learning data, tasks and experiments. The 'OpenML' objects can
be automatically converted to 'mlr3' objects. For a more
sophisticated interface with more upload options, see
the 'OpenML' package.
Author: Michel Lang [aut] ,
Sebastian Fischer [cre, aut]
Maintainer: Sebastian Fischer <sebf.fischer@gmail.com>
Diff between mlr3oml versions 0.11.0 dated 2025-08-26 and 0.12.0 dated 2026-01-28
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- NEWS.md | 5 +++++ R/cache.R | 32 ++++++++++++++++---------------- R/download_parquet.R | 2 +- R/list_oml_data.R | 3 ++- man/list_oml.Rd | 1 + man/oml_object.Rd | 2 +- src/init.c | 2 +- tests/testthat/test_OMLData.R | 4 ++-- tests/testthat/test_OMLTask.R | 2 ++ tests/testthat/test_cache.R | 16 ++++++++-------- tests/testthat/test_list_oml_data.R | 9 +++++++++ tests/testthat/test_manual.R | 8 ++++---- 14 files changed, 70 insertions(+), 52 deletions(-)
Title: Spatiotemporal Nutrient Balance Analysis Across Agricultural and
Municipal Systems
Description: A comprehensive framework for analyzing agricultural nutrient
balances across multiple spatial scales (county, 'HUC8', 'HUC2') with
integration of wastewater treatment plant ('WWTP') effluent loads for both
nitrogen and phosphorus. Supports classification of spatial units as
nutrient sources, sinks, or balanced areas based on agricultural surplus
and deficit calculations. Includes visualization tools, spatial transition
probability analysis, and nutrient flow network mapping. Built-in datasets
include agricultural nutrient balance data from the Nutrient Use Geographic
Information System ('NuGIS'; The Fertilizer Institute and Plant Nutrition
Canada, 1987-2016) <https://nugis.tfi.org/tabular_data/> and U.S. Environmental
Protection Agency ('EPA') wastewater discharge data from the 'ECHO' Discharge
Monitoring Report ('DMR') Loading Tool (2007-2016)
<https://echo.epa.gov/trends/loading-tool/water-pollution-search>. Data
are downloaded on demand from the Open Science Framework ( [...truncated...]
Author: Olatunde D. Akanbi [aut, cre, cph] ,
Vibha Mandayam [aut] ,
Atharva Gupta [aut] ,
K. Colton Flynn [aut] ,
Jeffrey Yarus [aut] ,
Erika I. Barcelos [aut, cph] ,
Roger H. French [aut, cph]
Maintainer: Olatunde D. Akanbi <olatunde.akanbi@case.edu>
Diff between manureshed versions 0.1.1 dated 2026-01-26 and 0.1.2 dated 2026-01-28
DESCRIPTION | 6 MD5 | 35 ++-- NAMESPACE | 4 NEWS.md | 7 R/regional_comparison_functions.R |only R/utils.R | 38 ++++ inst/cheatsheet |only inst/doc/advanced-features.html | 4 inst/doc/custom-efficiency-analyis.html | 4 inst/doc/data-integration.html | 4 inst/doc/getting-started.R | 4 inst/doc/getting-started.Rmd | 8 inst/doc/getting-started.html | 280 ++++++++++++++++---------------- inst/doc/visualization-guide.html | 4 man/compare_regions.Rd |only man/create_regional_plots.Rd |only man/create_regional_summary.Rd |only man/get_region_definitions.Rd |only man/list_regions.Rd |only man/view_cheatsheet.Rd |only tests/testthat/test-workflows.R | 2 vignettes/getting-started.Rmd | 8 22 files changed, 242 insertions(+), 166 deletions(-)
Title: Extended Joint Models for Longitudinal and Time-to-Event Data
Description: Fit joint models for longitudinal and time-to-event data under the Bayesian approach. Multiple longitudinal outcomes of mixed type (continuous/categorical) and multiple event times (competing risks and multi-state processes) are accommodated. Rizopoulos (2012, ISBN:9781439872864).
Author: Dimitris Rizopoulos [aut, cre] ,
Pedro Miranda-Afonso [aut] ,
Grigorios Papageorgiou [aut]
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes2 versions 0.5-7 dated 2025-06-16 and 0.6-0 dated 2026-01-28
DESCRIPTION | 16 MD5 | 48 - NAMESPACE | 38 - NEWS.md | 13 R/RcppExports.R | 4 R/accuracy_measures.R | 12 R/accuracy_measures_Cox.R | 3 R/basic_methods.R | 1375 ++++++++++++++++++++++++++++++++++++++++--- R/help_functions.R | 805 ++++++++++++++++++++----- R/jm.R | 151 +++- R/optimal_model.R |only R/predict_funs.R | 91 ++ README.md | 11 man/JMbayes2.Rd | 6 man/coda_methods.Rd | 6 man/consensus.Rd |only man/jm.Rd | 49 + man/ppcheck.Rd |only man/rc_setup.Rd | 4 man/sliced_model_generics.Rd |only man/slicer.Rd |only man/variogram.Rd |only src/JMbayes2_Surv.h | 19 src/Makevars | 6 src/Makevars.win | 4 src/RcppExports.cpp | 12 src/init.c | 14 src/mcmc_fit.cpp | 70 +- 28 files changed, 2368 insertions(+), 389 deletions(-)
Title: Modified Poisson Regression for Binary Outcome and Related
Methods
Description: Modified Poisson, logistic and least-squares regression analyses for binary outcomes of Zou (2004) <doi:10.1093/aje/kwh090>, Noma (2025)<Forthcoming>, and Cheung (2007) <doi:10.1093/aje/kwm223> have been standard multivariate analysis methods to estimate risk ratio and risk difference in clinical and epidemiological studies. This R package involves an easy-to-handle function to implement these analyses by simple commands. Missing data analysis tools (multiple imputation) are also involved. In addition, recent studies have shown the ordinary robust variance estimator possibly has serious bias under small or moderate sample size situations for these methods. This package also provides computational tools to calculate alternative accurate confidence intervals.
Author: Hisashi Noma [aut, cre]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between rqlm versions 4.2-2 dated 2025-12-22 and 4.3-1 dated 2026-01-28
DESCRIPTION | 12 ++++++------ MD5 | 10 ++++++---- NAMESPACE | 3 ++- NEWS.md | 4 ++++ R/SumStat.r |only man/SumStat.Rd |only man/ttemsm.Rd | 6 +++--- 7 files changed, 21 insertions(+), 14 deletions(-)
Title: Robust Inference for Covariate Adjustment in Randomized Clinical
Trials
Description: Performs robust estimation and inference when using covariate adjustment and/or covariate-adaptive randomization in randomized clinical trials.
Ting Ye, Jun Shao, Yanyao Yi, Qinyuan Zhao (2023) <doi:10.1080/01621459.2022.2049278>.
Ting Ye, Marlena Bannick, Yanyao Yi, Jun Shao (2023) <doi:10.1080/24754269.2023.2205802>.
Ting Ye, Jun Shao, Yanyao Yi (2023) <doi:10.1093/biomet/asad045>.
Marlena Bannick, Jun Shao, Jingyi Liu, Yu Du, Yanyao Yi, Ting Ye (2024) <doi:10.1093/biomet/asaf029>.
Xiaoyu Qiu, Yuhan Qian, Jaehwan Yi, Jinqiu Wang, Yu Du, Yanyao Yi, Ting Ye (2025) <doi:10.48550/arXiv.2408.12541>.
Author: Marlena Bannick [cre, aut] ,
Yuhan Qian [aut],
Ting Ye [aut],
Yanyao Yi [aut],
Faith Bian [aut]
Maintainer: Marlena Bannick <marlena.bannick@outlook.com>
Diff between RobinCar versions 1.0.0 dated 2025-05-24 and 1.1.0 dated 2026-01-28
DESCRIPTION | 10 ++-- MD5 | 18 ++++---- NAMESPACE | 3 + NEWS.md | 6 ++ R/robincar-contrast.R | 70 +++++++++++++++++++++++++++++++ R/robincar-tte.R | 2 README.md | 13 ++++- build/partial.rdb |binary man/robincar_tte.Rd | 2 tests/testthat/test-contrast.R | 90 +++++++++++++++++++++++++++++++++++++++++ 10 files changed, 194 insertions(+), 20 deletions(-)
Title: Network Meta-Analysis Based on Multivariate Meta-Analysis and
Meta-Regression Models
Description: Network meta-analysis tools based on contrast-based approach using the multivariate meta-analysis and meta-regression models (Noma et al. (2025) <doi:10.1101/2025.09.15.25335823>). Comprehensive analysis tools for network meta-analysis and meta-regression (e.g., synthesis analysis, ranking analysis, and creating league table) are available through simple commands. For inconsistency assessment, the local and global inconsistency tests based on the Higgins' design-by-treatment interaction model are available. In addition, the side-splitting methods and Jackson's random inconsistency model can be applied. Standard graphical tools for network meta-analysis, including network plots, ranked forest plots, and transitivity analyses, are also provided. For the synthesis analyses, the Noma-Hamura's improved REML (restricted maximum likelihood)-based methods (Noma et al. (2023) <doi:10.1002/jrsm.1652> <doi:10.1002/jrsm.1651>) are adopted as the default methods.
Author: Hisashi Noma [aut, cre] ,
Kazushi Maruo [aut],
Shiro Tanaka [aut],
Toshi A. Furukawa [aut]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between NMA versions 2.1-2 dated 2026-01-11 and 3.1-1 dated 2026-01-28
DESCRIPTION | 10 +-- MD5 | 56 +++++++++--------- NAMESPACE | 13 ++++ NEWS.md | 4 + R/SumPMA.r | 105 ++++++++++++++++++++++++++++++++--- R/global.ict.r | 88 ++++++++++++++++++++++++++++- R/local.ict.r | 51 ++++++++++++++++- R/nma.r | 155 ++++++++++++++++++++++++++++++++++++++++++++++++++-- R/nmaQ.r | 62 ++++++++++++++++++++ R/nmafunnel.r | 26 ++++++++ R/nmaleague.r | 29 +++++++++ R/nmarank.r | 62 ++++++++++++++++++-- R/nmareg.r | 63 ++++++++++++++++++++- R/nmaweight.r | 58 ++++++++++++++++--- R/random.icm.r | 70 ++++++++++++++++++++++- R/sidesplit.r | 106 ++++++++++++++++++++++++++++++++--- R/transitivity.r | 36 +++++++++++- man/SumPMA.Rd | 3 - man/global.ict.Rd | 4 + man/local.ict.Rd | 4 + man/nma.Rd | 4 + man/nmaQ.Rd | 4 + man/nmaleague.Rd | 2 man/nmarank.Rd | 4 + man/nmareg.Rd | 4 + man/nmaweight.Rd | 4 + man/random.icm.Rd | 4 + man/sidesplit.Rd | 4 + man/transitivity.Rd | 4 + 29 files changed, 941 insertions(+), 98 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data management
system with support for the Structured Query Language (SQL). This
package includes all of DuckDB and an R Database Interface (DBI)
connector.
Author: Hannes Muehleisen [aut] ,
Mark Raasveldt [aut] ,
Kirill Mueller [cre] ,
Stichting DuckDB Foundation [cph],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrocher [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckdb versions 1.4.3 dated 2025-12-10 and 1.4.4 dated 2026-01-28
DESCRIPTION | 6 +- MD5 | 74 ++++++++++++++++---------------- NEWS.md | 17 +++++++ R/cpp11.R | 4 + R/relational.R | 24 ++++++++++ R/rethrow-gen.R | 10 ++++ R/version.R | 2 README.md | 31 ++++++++++--- inst/include/cpp11.hpp | 4 - inst/include/cpp11/R.hpp | 4 - inst/include/cpp11/altrep.hpp | 4 - inst/include/cpp11/as.hpp | 4 - inst/include/cpp11/attribute_proxy.hpp | 4 - inst/include/cpp11/data_frame.hpp | 62 ++++++++++++-------------- inst/include/cpp11/declarations.hpp | 4 - inst/include/cpp11/doubles.hpp | 4 - inst/include/cpp11/environment.hpp | 4 - inst/include/cpp11/external_pointer.hpp | 8 ++- inst/include/cpp11/function.hpp | 7 +-- inst/include/cpp11/integers.hpp | 4 - inst/include/cpp11/list.hpp | 11 ++-- inst/include/cpp11/list_of.hpp | 4 - inst/include/cpp11/logicals.hpp | 4 - inst/include/cpp11/matrix.hpp | 4 - inst/include/cpp11/named_arg.hpp | 6 +- inst/include/cpp11/protect.hpp | 4 - inst/include/cpp11/r_bool.hpp | 4 - inst/include/cpp11/r_string.hpp | 4 - inst/include/cpp11/r_vector.hpp | 14 +++--- inst/include/cpp11/raws.hpp | 4 - inst/include/cpp11/sexp.hpp | 9 +-- inst/include/cpp11/strings.hpp | 4 - src/cpp11.cpp | 8 +++ src/duckdb.tar.xz |binary src/relational.cpp | 25 ++++++++++ tests/testthat/_snaps/relational.md | 25 ++++++++++ tests/testthat/test-relational.R | 54 +++++++++++++++++++++++ tests/testthat/test-types.R | 1 38 files changed, 325 insertions(+), 141 deletions(-)
Title: Interactive Structural Equation Modeling (SEM) and Multi-Group
Path Diagrams
Description: Provides an interactive workflow for visualizing structural equation modeling (SEM), multi-group path diagrams, and network diagrams in R. Users can directly manipulate nodes and edges to create publication-quality figures while maintaining statistical model integrity. Supports integration with 'lavaan', 'OpenMx', 'tidySEM', and 'blavaan' etc. Features include parameter-based aesthetic mapping, generative AI assistance, and complete reproducibility by exporting metadata for script-based workflows.
Author: Seung Hyun Min [aut, cre]
Maintainer: Seung Hyun Min <seung.min@mail.mcgill.ca>
Diff between ggsem versions 0.9.8 dated 2026-01-17 and 0.9.9 dated 2026-01-28
ggsem-0.9.8/ggsem/man/reproduce_network.Rd |only ggsem-0.9.8/ggsem/man/reproduce_sem.Rd |only ggsem-0.9.9/ggsem/DESCRIPTION | 6 ggsem-0.9.9/ggsem/MD5 | 20 ggsem-0.9.9/ggsem/NAMESPACE | 3 ggsem-0.9.9/ggsem/R/ggsem_app.R | 36 ggsem-0.9.9/ggsem/R/ggsem_silent.R | 23 ggsem-0.9.9/ggsem/R/metadata_to_ggplot.R | 13 ggsem-0.9.9/ggsem/R/reproduce_metadata.R | 6 ggsem-0.9.9/ggsem/R/utils_graph.R | 9 ggsem-0.9.9/ggsem/R/utils_model.R | 182 +- ggsem-0.9.9/ggsem/inst/shiny/app.R | 1960 ++++++++++------------------- 12 files changed, 884 insertions(+), 1374 deletions(-)
Title: Generalized Association Plots
Description: Provides a comprehensive framework for visualizing associations and interaction structures in matrix-formatted data using Generalized Association Plots (GAP). The package implements multiple proximity computation methods (e.g., correlation, distance metrics), ordering techniques including hierarchical clustering (HCT) and Rank-2-Ellipse (R2E) seriation, and optional flipping strategies to enhance visual symmetry. It supports a variety of covariate-based color annotations, allows flexible customization of layout and output, and is suitable for analyzing multivariate data across domains such as social sciences, genomics, and medical research. The method is based on Generalized Association Plots introduced by Chen (2002) <https://www3.stat.sinica.edu.tw/statistica/J12N1/J12N11/J12N11.html> and further extended by Wu, Tien, and Chen (2010) <doi:10.1016/j.csda.2008.09.029>.
Author: Shu-Yu Lin [aut, cre],
Chiun-How Kao [aut, ctb],
Chun-Houh Chen [aut, ctb]
Maintainer: Shu-Yu Lin <shuyuuu89@gmail.com>
Diff between GAPR versions 0.1.4 dated 2025-06-06 and 0.1.5 dated 2026-01-28
DESCRIPTION | 8 LICENSE | 4 MD5 | 8 R/GAP_function.R | 5043 +++++++++++++++++++++++++++---------------------------- man/GAP.Rd | 8 5 files changed, 2555 insertions(+), 2516 deletions(-)
Title: Sorted L1 Penalized Estimation
Description: Efficient implementations for Sorted L-One Penalized Estimation
(SLOPE): generalized linear models regularized with the sorted L1-norm
(Bogdan et al. 2015). Supported models include
ordinary least-squares regression, binomial regression, multinomial
regression, and Poisson regression. Both dense and sparse predictor
matrices are supported. In addition, the package features predictor
screening rules that enable fast and efficient solutions to high-dimensional
problems.
Author: Johan Larsson [aut, cre] ,
Jonas Wallin [aut] ,
Malgorzata Bogdan [aut] ,
Ewout van den Berg [aut],
Chiara Sabatti [aut],
Emmanuel Candes [aut],
Evan Patterson [aut],
Weijie Su [aut],
Jakub Kala [aut],
Krystyna Grzesiak [aut],
Mathurin Massias [aut], [...truncated...]
Maintainer: Johan Larsson <johan@jolars.co>
Diff between SLOPE versions 1.2.0 dated 2025-11-11 and 2.0.0 dated 2026-01-28
DESCRIPTION | 10 +- MD5 | 122 ++++++++++++++++-------------- NAMESPACE | 6 + NEWS.md | 29 +++++++ R/coef.R | 20 ++-- R/cv.R | 45 ++++++++++- R/data.R | 15 +-- R/deviance.R | 2 R/interpolate_coefficients.R | 2 R/interpolate_penalty.R | 2 R/plot.R | 154 ++++++++++++++++++++++++++++++-------- R/plot_diagnostics.R | 2 R/predict.R | 38 +++++++-- R/print.R | 2 R/refit.R |only R/score.R | 2 R/setup_diagnostics.R | 2 R/slope.R | 8 + R/summary.R |only R/train_slope.R | 11 -- README.md | 8 + build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 7 - inst/doc/introduction.R | 2 inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 37 ++++----- inst/doc/models.R |only inst/doc/models.Rmd |only inst/doc/models.html |only inst/doc/solvers.html | 13 +-- inst/include/slope/normalize.h | 21 ++++- inst/include/slope/slope.h | 31 ++++++- inst/include/slope/utils.h | 47 +++++++++++ man/SLOPE-package.Rd | 2 man/SLOPE.Rd | 6 + man/abalone.Rd | 7 - man/coef.SLOPE.Rd | 9 +- man/createFolds.Rd | 2 man/cvSLOPE.Rd | 23 ++++- man/deviance.SLOPE.Rd | 7 - man/glioma.Rd | 2 man/heart.Rd | 2 man/interpolateCoefficients.Rd | 4 man/interpolatePenalty.Rd | 4 man/plot.SLOPE.Rd | 29 +++++-- man/plot.TrainedSLOPE.Rd | 8 - man/plotClusters.Rd | 2 man/plotDiagnostics.Rd | 2 man/predict.SLOPE.Rd | 26 ++++-- man/print.SLOPE.Rd | 7 - man/print.summary_SLOPE.Rd |only man/print.summary_TrainedSLOPE.Rd |only man/refit.Rd |only man/score.Rd | 5 - man/setup_diagnostics.Rd | 4 man/student.Rd | 2 man/summary.SLOPE.Rd |only man/summary.TrainedSLOPE.Rd |only man/trainSLOPE.Rd | 16 --- man/wine.Rd | 2 src/rcpp_slope.cpp | 10 ++ tests/testthat/test-assertions.R | 3 tests/testthat/test-plotting.R | 59 ++++++++++++++ tests/testthat/test-summary.R |only vignettes/SLOPE.bib | 23 +++++ vignettes/introduction.Rmd | 2 vignettes/models.Rmd |only 68 files changed, 670 insertions(+), 238 deletions(-)
Title: Read and Write 'las' and 'laz' Binary File Formats Used for
Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://community.asprs.org/leadership-restricted/leadership-content/public-documents/standards>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.4 <https://laszip.org/>.
Author: Jean-Romain Roussel [aut, cre, cph],
Florian De Boissieu [aut, ctb] ,
Martin Isenburg [cph] ,
David Auty [ctb] ,
Pierrick Marie [ctb] ,
Tiago de Conto [ctb]
Maintainer: Jean-Romain Roussel <info@r-lidar.com>
Diff between rlas versions 1.8.2 dated 2025-05-16 and 1.8.3 dated 2026-01-28
DESCRIPTION | 14 +++++++------- MD5 | 24 ++++++++++++------------ NEWS.md | 5 +++++ R/altrep.R | 8 +++++++- R/header_tools.r | 4 ++-- R/readLAS.r | 4 ++-- R/writeLAS.r | 2 +- man/crs_tools.Rd | 2 +- man/extra_bytes_attribute_tools.Rd | 2 +- man/read.las.Rd | 2 +- man/read.lasheader.Rd | 2 +- man/write.las.Rd | 2 +- src/altrep_compact_replication.cpp | 12 ++++++++++-- 13 files changed, 51 insertions(+), 32 deletions(-)
Title: An API Generator for R
Description: Gives the ability to automatically generate and serve an HTTP
API from R functions using the annotations in the R documentation
around your functions.
Author: Barret Schloerke [cre, aut] ,
Jeff Allen [aut, ccp],
Bruno Tremblay [ctb],
Frans van Dunne [ctb],
Sebastiaan Vandewoude [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between plumber versions 1.3.2 dated 2025-12-23 and 1.3.3 dated 2026-01-28
DESCRIPTION | 6 +- MD5 | 13 ++-- NEWS.md | 8 ++ R/ui.R | 91 +++++++++++++++++++++----------- tests/testthat/files/include/test.html | 2 tests/testthat/test-parser.R | 1 tests/testthat/test-swagger-redirects.R |only tests/testthat/test-ui-apipath.R | 10 ++- 8 files changed, 86 insertions(+), 45 deletions(-)
Title: Non Linear Least Squares with Inequality Constraints
Description: We solve non linear least squares problems with optional
equality and/or inequality constraints. Non linear iterations are
globalized with back-tracking method. Linear problems are solved by
dense QR decomposition from 'LAPACK' which can limit the size of
treated problems. On the other side, we avoid condition number
degradation which happens in classical quadratic programming approach.
Inequality constraints treatment on each non
linear iteration is based on 'NNLS' method (by Lawson and Hanson).
We provide an original function 'lsi_ln' for solving linear least squares
problem with inequality constraints in least norm sens. Thus if Jacobian of
the problem is rank deficient a solution still can be provided.
However, truncation errors are probable in this case.
Equality constraints are treated by using a basis of Null-space.
User defined function calculating residuals must return a list having
residual vector (not their squared sum) and Jacobian. If Jacobian is
not in the returned list, [...truncated...]
Author: Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between nlsic versions 1.1.1 dated 2025-06-27 and 1.2.0 dated 2026-01-28
DESCRIPTION | 8 +- MD5 | 15 ++-- NAMESPACE | 2 NEWS.md | 11 ++- R/nlsic.R | 148 +++++++++++++++++++++++++++---------------- inst/unitTests/runit.nlsic.R | 3 man/g.Rd |only man/ls_ln.Rd | 2 man/nlsic.Rd | 4 - 9 files changed, 125 insertions(+), 68 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis (Balduzzi et al., 2023) <doi:10.18637/jss.v106.i02> and supporting Schwarzer et al. (2015) <doi:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <doi:10.1002/jrsm.1058>;
- additive network meta-analysis for combinations of treatments (Rücker et al., 2020) <doi:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <doi:10.1002/sim.8158>, or penalised logistic regression (Evrenoglou et al., 2022) <doi:10.1002/sim.9562>;
- rankograms and ranking of treatments by the Surface under the cumulative ranking curve (SUCRA) (Salanti et al., 2013) <doi:10.1016/j.jclinepi.2010.03.016>;
- ranking of treatments using P-scores (frequentist analogue of SUCRAs without resampling) according to [...truncated...]
Author: Gerta Ruecker [aut] ,
Ulrike Krahn [aut],
Jochem Koenig [aut] ,
Orestis Efthimiou [aut] ,
Annabel Davies [aut] ,
Theodoros Papakonstantinou [aut] ,
Theodoros Evrenoglou [ctb] ,
Krzysztof Ciomek [ctb] ,
Nana-Adjoa Kwarteng [ctb] ,
Guido Schwarzer [aut, [...truncated...]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between netmeta versions 3.2-0 dated 2025-04-10 and 3.3-1 dated 2026-01-28
DESCRIPTION | 40 ++++---- MD5 | 103 +++++++++++---------- NAMESPACE | 9 + NEWS.md | 78 ++++++++++++++++ R/contribution.matrix.R | 151 ++++++++++++++++++++------------ R/crossnma2netmeta.R | 4 R/decomp.design.R | 3 R/forest.netbind.R | 27 +++-- R/forest.netmeta.R | 2 R/gemtc2netmeta.R |only R/hatmatrix.R | 11 +- R/meta-chk.R | 4 R/netbind.R | 62 +++++++------ R/netcomb.R | 5 - R/netcontrib.R | 68 +++++++++++--- R/netgraph.netconnection.R | 20 +++- R/netgraph.netmeta.R | 15 ++- R/netheat.R | 3 R/netimpact.R | 2 R/netleague.R | 13 ++ R/netmeasures.R | 3 R/netmeta-internal.R | 26 +++-- R/netmeta-package.R | 14 ++ R/netmeta.R | 51 +++++++--- R/netmetareg-internal.R | 5 - R/netmetareg.R | 88 ++++++++++-------- R/netrank.R | 16 +-- R/netsplit.R | 16 ++- R/print.netmeta.R | 42 ++++---- R/print.rankogram.R | 2 R/print.summary.netmeta.R | 133 ++++++++++++++++++++-------- R/rankogram.netmeta.R | 7 - R/studycontribution.R |only R/summary.netconnection.R | 14 ++ R/textmeth.R | 3 R/updateversion.R | 8 + build/vignette.rds |binary data/Linde2016.rda |binary inst/doc/netmeta-workflow.R |only inst/doc/netmeta-workflow.Rmd |only inst/doc/netmeta-workflow.pdf |only inst/doc/netmeta.pdf |binary man/crossnma2netmeta.Rd | 2 man/forest.netmeta.Rd | 2 man/gemtc2netmeta.Rd |only man/netcontrib.Rd | 42 ++++++-- man/netgraph.netconnection.Rd | 9 + man/netimpact.Rd | 2 man/netleague.Rd | 4 man/netmeta-package.Rd | 8 + man/netmeta.Rd | 5 - man/netrank.Rd | 4 man/netsplit.Rd | 7 - man/rankogram.netmeta.Rd | 2 vignettes/netmeta-workflow-diagram.pdf |only vignettes/netmeta-workflow-diagram.pptx |only vignettes/netmeta-workflow.Rmd |only 57 files changed, 754 insertions(+), 381 deletions(-)
Title: Miscellaneous 3D Plots
Description: A collection of miscellaneous 3d plots, including
isosurfaces.
Author: Luke Tierney [aut, cre],
Dai Feng [aut]
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between misc3d versions 0.9-1 dated 2021-10-07 and 0.9-2 dated 2026-01-28
DESCRIPTION | 16 ++++++++++------ MD5 | 4 ++-- inst/CITATION | 5 ++--- 3 files changed, 14 insertions(+), 11 deletions(-)
Title: R Markdown Format for Flexible Dashboards
Description: Format for converting an R Markdown document to a grid
oriented dashboard. The dashboard flexibly adapts the size of it's
components to the containing web page.
Author: Garrick Aden-Buie [aut, cre] ,
Carson Sievert [aut] ,
Richard Iannone [aut] ,
JJ Allaire [aut],
Barbara Borges [aut],
Posit Software, PBC [cph, fnd],
Keen IO [ctb, cph] ,
Abdullah Almsaeed [ctb, cph] ,
Jonas Mosbech [ctb, cph] ,
Noel Bossart [ctb, cp [...truncated...]
Maintainer: Garrick Aden-Buie <garrick@posit.co>
Diff between flexdashboard versions 0.6.2 dated 2023-08-11 and 0.6.3 dated 2026-01-28
DESCRIPTION | 15 ++++++++------- MD5 | 18 +++++++++--------- NEWS.md | 8 ++++++++ R/bslib.R | 8 +++++++- R/flex_dashboard.R | 4 ++-- inst/www/flex_dashboard/flexdashboard.min.css | 2 +- inst/www/flex_dashboard/flexdashboard.scss | 5 +++++ man/flex_dashboard.Rd | 6 +++--- tests/testthat/_snaps/format.md | 4 ++-- tests/testthat/test_built_css.R | 9 ++++++--- 10 files changed, 51 insertions(+), 28 deletions(-)