Title: Lagged and Moving-Average Exposure Features for Aeroallergen
Epidemiology
Description: Deterministic, group-safe utilities that transform daily
environmental exposure series (pollen and spore counts, with support for
other time-varying exposures such as ozone and particulate matter) into
analysis-ready lagged and moving-average exposure features. Functions
validate temporal regularity, assign ISO 8601 weeks and configurable
seasons, impute missing daily values transparently, and construct lagged
and windowed exposures suitable for environmental epidemiology and public
health analyses.
Author: Felix E. Rivera-Mariani [aut, cre]
Maintainer: Felix E. Rivera-Mariani <felixrm@friveram.com>
Diff between SporeLag versions 0.1.1 dated 2026-08-04 and 0.1.2 dated 2026-10-06
DESCRIPTION | 8 - MD5 | 20 +- NEWS.md | 11 + README.md | 23 +-- build/vignette.rds |binary inst/CITATION | 2 inst/WORDLIST | 2 inst/doc/getting-started.R | 107 +++++++++++++++ inst/doc/getting-started.Rmd | 272 ++++++++++++++++++++++++++++++++++++++ inst/doc/getting-started.html | 294 +++++++++++++++++++++++++++++++++++++++++- vignettes/getting-started.Rmd | 272 ++++++++++++++++++++++++++++++++++++++ 11 files changed, 979 insertions(+), 32 deletions(-)
Title: Forecast Verification Routines for Ensemble Forecasts of Weather
and Climate
Description: A collection of forecast verification routines developed for the SPECS
FP7 project. The emphasis is on comparative verification of ensemble forecasts of weather and climate.
Author: Stefan Siegert [aut, cre],
Jonas Bhend [ctb],
Igor Kroener [ctb],
Matteo De Felice [ctb]
Maintainer: Stefan Siegert <s.siegert@exeter.ac.uk>
Diff between SpecsVerification versions 0.5-3 dated 2020-02-26 and 0.5-4 dated 2026-10-06
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/FitAkdParameters.R | 2 +- R/SpecsVerification.R | 3 ++- R/eurotempforecast.R | 2 +- build/partial.rdb |binary man/FitAkdParameters.Rd | 2 +- man/SpecsVerification.Rd | 3 ++- man/eurotempforecast.Rd | 2 +- 9 files changed, 20 insertions(+), 18 deletions(-)
More information about SpecsVerification at CRAN
Permanent link
Title: Data Sonification - Turning Data into Sound
Description: Sonification (or audification) is the process of representing data by sounds in the audible range. This package provides the R function sonify() that transforms univariate data, sampled at regular or irregular intervals, into a continuous sound with time-varying frequency. The ups and downs in frequency represent the ups and downs in the data. Sonify provides a substitute for R's plot function to simplify data analysis for the visually impaired.
Author: Stefan Siegert [aut, cre],
Robin Williams [aut]
Maintainer: Stefan Siegert <s.siegert@exeter.ac.uk>
Diff between sonify versions 0.0-1 dated 2017-02-01 and 0.1-0 dated 2026-10-06
DESCRIPTION | 16 +++++--- MD5 | 10 +++-- NAMESPACE | 1 NEWS.md |only R/sonify.R | 104 ++++++++++++++++++++++++++++++++++++++-------------------- man/sonify.Rd | 50 ++++++++++++++++++--------- tests |only 7 files changed, 118 insertions(+), 63 deletions(-)
Title: Deep Compositional Spatial Models
Description: Deep compositional spatial models are standard spatial covariance
models coupled with an injective warping function of the spatial
domain. The warping function is constructed through a composition
of multiple elemental injective functions in a deep-learning
framework. The package implements two cases for the univariate setting; first,
when these warping functions are known up to some weights that
need to be estimated, and, second, when the weights in each layer are random.
In the multivariate setting only the former case is available.
Estimation and inference is done using `tensorflow`, which makes use of
graphics processing units.
For more details see Zammit-Mangion et al. (2022) <doi:10.1080/01621459.2021.1887741>,
Vu et al. (2022) <doi:10.5705/ss.202020.0156>,
Vu et al. (2023) <doi:10.1016/j.spasta.2023.100742>, and
Shao et al. (2025) <doi:10.48550/arXiv.2505.12548>.
Author: Andrew Zammit-Mangion [aut],
Quan Vu [aut, cre],
Xuanjie Shao [aut]
Maintainer: Quan Vu <quanvustats@gmail.com>
Diff between deepspat versions 0.3.4 dated 2026-09-30 and 0.3.5 dated 2026-10-06
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/predict.deepspat_MSP.R | 18 ++++++++++++++---- 4 files changed, 25 insertions(+), 11 deletions(-)
Title: An R Package to Extend 'ACER ConQuest'
Description: Extends 'ACER ConQuest' through a family of functions
designed to improve graphical outputs and help with advanced analysis
(e.g., differential item functioning). Allows R users to call
'ACER ConQuest' from within R and read 'ACER ConQuest' System Files
(generated by the command `put` <https://conquestmanual.acer.org/s4-00.html#put>).
Requires 'ACER ConQuest' version 5.40 or later.
A demonstration version can be downloaded from <https://shop.acer.org/collections/acer-conquest-5>.
Author: Dan Cloney [aut, cre] ,
Ray Adams [aut]
Maintainer: Dan Cloney <dan.cloney@acer.org>
Diff between conquestr versions 1.5.5 dated 2025-08-23 and 1.8.2 dated 2026-10-06
DESCRIPTION | 12 MD5 | 85 - NAMESPACE | 81 - NEWS.md | 32 R/RcppExports.R | 336 +++++ R/ReadConQuestLibrary.R | 1250 +-------------------- R/ReadConQuestState.R | 63 - R/conquestr.R | 60 - R/conquestrFunc.R | 50 R/generateHelpers.R | 208 +-- R/itanalHelpers.R | 76 - R/plotRout.R | 80 + R/residHelpers.R | 23 R/showHelpers.R | 62 - build/vignette.rds |binary inst/doc/data-cleaning-functions-in-conquestr.html | 4 inst/doc/generateResponses.html | 71 - inst/doc/intro-to-conquestr.Rmd | 2 inst/doc/intro-to-conquestr.html | 8 inst/doc/itanal-in-conquestr.html | 4 inst/doc/plotting.html | 10 inst/doc/responseProbs.html | 10 inst/doc/test_item_review_sheet_markdown.html | 10 inst/extdata/ex1_unident.cqc |only inst/extdata/ex1_unident.dat |only inst/extdata/ex1_unident_xsi.txt |only inst/extdata/mysysfile_unident.cqs |only man/DecompressSys.Rd | 7 man/ReadSys.Rd | 5 man/ReadTermsList.Rd | 6 man/cnvrtItemParam.Rd | 9 man/genResponses.Rd | 2 man/genResponsesCpp.Rd |only man/lcs.Rd |only man/lcs_vec.Rd |only man/plotRout.Rd | 3 man/q3ExpCorrect.Rd | 3 man/replaceInVector.Rd | 4 man/simplepCpp.Rd |only man/steigerStat.Rd | 11 src/RcppExports.cpp | 948 +++++++++++++++ src/generateCq.cpp |only src/readCq.cpp |only src/utilsCq.cpp | 66 + tests/testthat/test-DecompressSys.R |only tests/testthat/test-cqReader.R |only tests/testthat/test-genHelpers.R | 120 ++ tests/testthat/test-getCqItanal.R | 24 tests/testthat/test-getCqRespModel.R |only vignettes/intro-to-conquestr.Rmd | 2 50 files changed, 2140 insertions(+), 1607 deletions(-)
Title: Mining NB-Frequent Itemsets and NB-Precise Rules
Description: NBMiner is an implementation of the model-based mining algorithm for mining NB-frequent itemsets and NB-precise rules. Michael Hahsler (2006) <doi:10.1007/s10618-005-0026-2>.
Author: Michael Hahsler [aut, cre, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesNBMiner versions 0.1.9 dated 2025-12-09 and 0.1.10 dated 2026-10-06
DESCRIPTION | 16 +-- MD5 | 29 +++-- NEWS.md | 12 +- R/Agrawal_data.R | 4 R/NBMiner.R | 132 ++++++++++++++++-------- R/NBMinerParameters.R | 176 ++++++++++++++++++++------------- README.md | 87 +++++++++------- build/partial.rdb |binary build/vignette.rds |only inst/doc |only man/Agrawal.Rd | 5 man/NBMiner.Rd | 121 +++++++++++++++------- man/NBMinerParameters.Rd | 94 ++++++++++++----- man/figures/README-NB_estimation-1.png |only tests |only vignettes |only 16 files changed, 439 insertions(+), 237 deletions(-)
Title: Vehicle Routing Problem Solver Built on 'PyVRP'
Description: A 'tidyverse'-style interface to high-performance vehicle routing
problem (VRP) solving. Vendors the C++ core of the 'PyVRP' solver
(<https://github.com/PyVRP/PyVRP>) and rewires it through 'cpp11', with no
'Python' runtime dependency. Supports the capacitated VRP, time windows,
multiple depots, heterogeneous fleets, prize-collecting and multi-trip
variants, driven by an iterated local search metaheuristic.
Author: Andre Leite [aut, cre] ,
Marcos Wasiliew [aut] ,
Hugo Vasconcelos [aut] ,
Carlos Amorim [aut] ,
Diogo Bezerra [aut] ,
Julia Nascimento Barreto [aut] ,
Niels Wouda [ctb, cph] ,
Thibaut Vidal [cph] ,
ORTEC [cph]
Maintainer: Andre Leite <leite@castlab.org>
Diff between vrpr versions 0.2.1 dated 2026-09-30 and 0.2.2 dated 2026-10-06
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ inst/CITATION | 5 +++-- inst/doc/vrpr.html | 2 +- src/vendor/pyvrp/Client.cpp | 1 + src/vendor/pyvrp/VehicleType.cpp | 1 + 7 files changed, 22 insertions(+), 12 deletions(-)
Title: Data and 'Shiny' Application for the Tv Show 'SouthPark'
Description: Ratings, votes, swear words and sentiments are analysed for the show 'SouthPark' through a 'Shiny' application after web scraping from 'IMDB' and the website <https://southpark.fandom.com/wiki/South_Park_Archives>.
Author: Amalan Mahendran [aut, cre]
Maintainer: Amalan Mahendran <amalan0595@gmail.com>
Diff between SouthParkRshiny versions 1.0.0 dated 2024-03-09 and 1.1.1 dated 2026-10-06
SouthParkRshiny-1.0.0/SouthParkRshiny/R/Basic_plots.R |only SouthParkRshiny-1.0.0/SouthParkRshiny/R/N_Grams_plots.R |only SouthParkRshiny-1.0.0/SouthParkRshiny/R/Ratings_Votes_plots.R |only SouthParkRshiny-1.0.0/SouthParkRshiny/R/Sentiment_Four_plots.R |only SouthParkRshiny-1.0.0/SouthParkRshiny/R/Sentiment_General_plots.R |only SouthParkRshiny-1.0.0/SouthParkRshiny/R/Sentiment_Support_plots.R |only SouthParkRshiny-1.0.0/SouthParkRshiny/R/Swear_Words_plots.R |only SouthParkRshiny-1.0.0/SouthParkRshiny/data/Basic_plots.rda |only SouthParkRshiny-1.0.0/SouthParkRshiny/data/N_Grams_plots.rda |only SouthParkRshiny-1.0.0/SouthParkRshiny/data/Ratings_Votes_plots.rda |only SouthParkRshiny-1.0.0/SouthParkRshiny/data/Sentiment_Four_plots.rda |only SouthParkRshiny-1.0.0/SouthParkRshiny/data/Sentiment_General_plots.rda |only SouthParkRshiny-1.0.0/SouthParkRshiny/data/Sentiment_Support_plots.rda |only SouthParkRshiny-1.0.0/SouthParkRshiny/data/Swear_Words_plots.rda |only SouthParkRshiny-1.0.0/SouthParkRshiny/man/Basic_plots.Rd |only SouthParkRshiny-1.0.0/SouthParkRshiny/man/N_Grams_plots.Rd |only SouthParkRshiny-1.0.0/SouthParkRshiny/man/Ratings_Votes_plots.Rd |only SouthParkRshiny-1.0.0/SouthParkRshiny/man/Sentiment_Four_plots.Rd |only SouthParkRshiny-1.0.0/SouthParkRshiny/man/Sentiment_General_plots.Rd |only SouthParkRshiny-1.0.0/SouthParkRshiny/man/Sentiment_Support_plots.Rd |only SouthParkRshiny-1.0.0/SouthParkRshiny/man/Swear_Words_plots.Rd |only SouthParkRshiny-1.1.1/SouthParkRshiny/DESCRIPTION | 25 SouthParkRshiny-1.1.1/SouthParkRshiny/LICENSE | 2 SouthParkRshiny-1.1.1/SouthParkRshiny/MD5 | 88 ++- SouthParkRshiny-1.1.1/SouthParkRshiny/NAMESPACE | 18 SouthParkRshiny-1.1.1/SouthParkRshiny/R/Basic_Plots.R |only SouthParkRshiny-1.1.1/SouthParkRshiny/R/Cooccurrence_Plots.R |only SouthParkRshiny-1.1.1/SouthParkRshiny/R/Friends_Sentiment_Plots.R |only SouthParkRshiny-1.1.1/SouthParkRshiny/R/N_Grams_Plots.R |only SouthParkRshiny-1.1.1/SouthParkRshiny/R/Ratings_Votes_Plots.R |only SouthParkRshiny-1.1.1/SouthParkRshiny/R/Sentiment_General_Plots.R |only SouthParkRshiny-1.1.1/SouthParkRshiny/R/Support_Sentiment_Plots.R |only SouthParkRshiny-1.1.1/SouthParkRshiny/R/Swear_Words_Plots.R |only SouthParkRshiny-1.1.1/SouthParkRshiny/R/Transition_Plots.R |only SouthParkRshiny-1.1.1/SouthParkRshiny/R/app_server.R | 275 +++++++--- SouthParkRshiny-1.1.1/SouthParkRshiny/R/app_ui.R | 103 ++- SouthParkRshiny-1.1.1/SouthParkRshiny/R/run_app.R | 18 SouthParkRshiny-1.1.1/SouthParkRshiny/data/Basic_Plots.rda |only SouthParkRshiny-1.1.1/SouthParkRshiny/data/Cooccurrence_Plots.rda |only SouthParkRshiny-1.1.1/SouthParkRshiny/data/Friends_Sentiment_Plots.rda |only SouthParkRshiny-1.1.1/SouthParkRshiny/data/N_Grams_Plots.rda |only SouthParkRshiny-1.1.1/SouthParkRshiny/data/Ratings_Votes_Plots.rda |only SouthParkRshiny-1.1.1/SouthParkRshiny/data/Sentiment_General_Plots.rda |only SouthParkRshiny-1.1.1/SouthParkRshiny/data/SouthPark_IMDB_Data.rda |binary SouthParkRshiny-1.1.1/SouthParkRshiny/data/SouthPark_Script_Data.rda |binary SouthParkRshiny-1.1.1/SouthParkRshiny/data/Southpark_Summary.rda |binary SouthParkRshiny-1.1.1/SouthParkRshiny/data/Support_Sentiment_Plots.rda |only SouthParkRshiny-1.1.1/SouthParkRshiny/data/Swear_Words_Plots.rda |only SouthParkRshiny-1.1.1/SouthParkRshiny/data/Transition_Plots.rda |only SouthParkRshiny-1.1.1/SouthParkRshiny/inst/Images |only SouthParkRshiny-1.1.1/SouthParkRshiny/inst/app/www/Images |only SouthParkRshiny-1.1.1/SouthParkRshiny/inst/golem-config.yml | 2 SouthParkRshiny-1.1.1/SouthParkRshiny/man/Basic_Plots.Rd |only SouthParkRshiny-1.1.1/SouthParkRshiny/man/Cooccurrence_Plots.Rd |only SouthParkRshiny-1.1.1/SouthParkRshiny/man/Friends_Sentiment_Plots.Rd |only SouthParkRshiny-1.1.1/SouthParkRshiny/man/N_Grams_Plots.Rd |only SouthParkRshiny-1.1.1/SouthParkRshiny/man/Ratings_Votes_Plots.Rd |only SouthParkRshiny-1.1.1/SouthParkRshiny/man/Sentiment_General_Plots.Rd |only SouthParkRshiny-1.1.1/SouthParkRshiny/man/Support_Sentiment_Plots.Rd |only SouthParkRshiny-1.1.1/SouthParkRshiny/man/Swear_Words_Plots.Rd |only SouthParkRshiny-1.1.1/SouthParkRshiny/man/Transition_Plots.Rd |only 61 files changed, 363 insertions(+), 168 deletions(-)
More information about SouthParkRshiny at CRAN
Permanent link
Title: (Standardised) Major Axis Estimation and Testing Routines
Description: Methods for fitting bivariate lines in
allometry using the major axis (MA) or standardised major axis (SMA), and
for making inferences about such lines. The available methods of inference
include confidence intervals and one-sample tests for slope and elevation,
testing for a common slope or elevation amongst several allometric lines,
constructing a confidence interval for a common slope or elevation, and
testing for no shift along a common axis, amongst several samples.
See Warton et al. 2012 <doi:10.1111/j.2041-210X.2011.00153.x> for methods description.
Author: David Warton [aut],
Remko Duursma [aut],
Daniel Falster [aut, cre] ,
Sara Taskinen [aut],
Fonti Kar [aut]
Maintainer: Daniel Falster <daniel.falster@unsw.edu.au>
Diff between smatr versions 3.5-1 dated 2026-07-28 and 3.5-2 dated 2026-10-06
smatr-3.5-1/smatr/man/defineAxis.Rd |only smatr-3.5-1/smatr/man/huber.M.Rd |only smatr-3.5-2/smatr/DESCRIPTION | 6 +-- smatr-3.5-2/smatr/MD5 | 41 ++++++++++++------------ smatr-3.5-2/smatr/NAMESPACE | 9 +++++ smatr-3.5-2/smatr/NEWS.md | 9 +++++ smatr-3.5-2/smatr/R/alpha.fun.R | 30 ++++++++--------- smatr-3.5-2/smatr/R/b.com.est.R | 1 smatr-3.5-2/smatr/R/com.ci.R | 2 - smatr-3.5-2/smatr/R/defineAxis.R | 11 +----- smatr-3.5-2/smatr/R/huber.M.R | 9 +---- smatr-3.5-2/smatr/R/lr.b.com.R | 1 smatr-3.5-2/smatr/R/makeLogMinor.R | 7 +--- smatr-3.5-2/smatr/R/nicePlot.R | 15 +------- smatr-3.5-2/smatr/R/seqLog.R | 5 +- smatr-3.5-2/smatr/R/utils.R | 9 +---- smatr-3.5-2/smatr/README.md | 12 +++++-- smatr-3.5-2/smatr/build/vignette.rds |binary smatr-3.5-2/smatr/man/alpha.fun.Rd | 10 ++++- smatr-3.5-2/smatr/man/com.ci.Rd |only smatr-3.5-2/smatr/man/makeLogMinor.Rd | 6 +-- smatr-3.5-2/smatr/man/plotutils.Rd |only smatr-3.5-2/smatr/man/seqLog.Rd | 4 +- smatr-3.5-2/smatr/tests/testthat/test-exports.R |only 24 files changed, 96 insertions(+), 91 deletions(-)
Title: Profile Analysis via Multidimensional Scaling
Description: Implements Profile Analysis via Multidimensional Scaling (PAMS)
for the identification of population-level core response profiles from
cross-sectional and longitudinal person-score data. Each person profile
is decomposed into a level component (the person mean) and a pattern
component (ipsatized subscores). PAMS uses nonmetric multidimensional
scaling via the SMACOF algorithm to identify a small number of core
profiles that represent the central response patterns in a sample of any
size. Bootstrap standard errors and bias-corrected and accelerated (BCa)
confidence intervals for individual core profile coordinates are
estimated, enabling significance testing of coordinates that is not
available in other profile analysis methods such as cluster profile
analysis or latent profile analysis. Person-level weights, R-squared
values, and partial correlations with core profiles are also estimated, allowing
individual profiles to be interpreted in terms of the core profile
structure. PAMS can be [...truncated...]
Author: Se-Kang Kim [aut, cre] ,
Donghoh Kim [aut]
Maintainer: Se-Kang Kim <sekangandroid@gmail.com>
Diff between pams versions 0.1.0 dated 2026-03-31 and 0.2.0 dated 2026-10-06
.aspell |only DESCRIPTION | 20 - MD5 | 34 + NAMESPACE | 17 NEWS.md |only R/BootSmacof.R | 822 +++++++++++++++++++++++------------------------- R/internal.R |only R/methods.R |only README.md | 53 +-- build/partial.rdb |binary build/vignette.rds |only demo/00Index | 2 demo/PAMS_analysis.R | 526 +++--------------------------- inst/CITATION |only inst/WORDLIST | 1 inst/doc |only man/BootSmacof.Rd | 95 ++--- man/plot.pams_fit.Rd |only man/summary.pams_fit.Rd |only tests |only vignettes |only 21 files changed, 573 insertions(+), 997 deletions(-)
Title: Clustering of Sites with Species Data
Description: Clustering algorithm developed for use with plot inventories of species. It groups plots by subsets of diagnostic species rather than overall species composition. There is an unsupervised and a supervised mode, the latter accepting suggestions for species with greater weight and cluster medoids.
Author: Sebastian Schmidtlein [aut, cre] ,
Jason Collison [aut],
Robin Pfannendoerfer [aut],
Lubomir Tichy [ctb]
Maintainer: Sebastian Schmidtlein <schmidtlein@kit.edu>
Diff between isopam versions 3.6 dated 2026-03-27 and 3.7 dated 2026-10-06
DESCRIPTION | 11 +++-- MD5 | 6 +-- NAMESPACE | 4 +- R/isopam.R | 111 +++++++++++++++++++++++++++++++++++++++++++----------------- 4 files changed, 92 insertions(+), 40 deletions(-)
Title: Mixture Cure Rate Models with Flexible Link Functions via the EM
Algorithm
Description: Fits mixture cure rate models by the Expectation-Maximization (EM)
algorithm. The incidence component (the probability of being uncured)
accepts the logit, probit, cauchit, power logit and reversed power logit
link functions, and the
latency component accepts the exponential, Rayleigh, Weibull, log-normal,
log-logistic and inverse Gaussian distributions. The package provides
parameter estimates with standard errors, simulation of data from the
model, and diagnostic tools based on residuals and simulated envelopes.
The methods build on Berkson and Gage (1952) <doi:10.2307/2281318>,
Dempster, Laird and Rubin (1977) <doi:10.1111/j.2517-6161.1977.tb01600.x>
and Bazán, Torres-Avilés, Suzuki and Louzada (2017) <doi:10.1002/asmb.2215>.
Author: Chaeyeon Yoo [aut],
Dipak K. Dey [aut],
Victor H. Lachos [aut],
Jalmar M. F. Carrasco [aut, cre]
Maintainer: Jalmar M. F. Carrasco <carrasco.jalmar@ufba.br>
Diff between EMGCR versions 0.2.0 dated 2025-11-18 and 0.3.0 dated 2026-10-06
EMGCR-0.2.0/EMGCR/R/liver2.R |only EMGCR-0.2.0/EMGCR/data/liver2.rda |only EMGCR-0.2.0/EMGCR/man/liver2.Rd |only EMGCR-0.3.0/EMGCR/DESCRIPTION | 42 +++- EMGCR-0.3.0/EMGCR/MD5 | 34 +-- EMGCR-0.3.0/EMGCR/NAMESPACE | 2 EMGCR-0.3.0/EMGCR/NEWS.md |only EMGCR-0.3.0/EMGCR/R/liver.R | 28 +-- EMGCR-0.3.0/EMGCR/R/mleMCR.R | 285 +++++++++++++++++++-------------- EMGCR-0.3.0/EMGCR/R/plotMCR.R | 50 ++--- EMGCR-0.3.0/EMGCR/R/qqMCR.R | 14 + EMGCR-0.3.0/EMGCR/R/rMCM.R | 36 ++-- EMGCR-0.3.0/EMGCR/R/residualsMCR.R | 46 +++-- EMGCR-0.3.0/EMGCR/data/liver.rda |binary EMGCR-0.3.0/EMGCR/man/MCRfit.Rd | 46 +++-- EMGCR-0.3.0/EMGCR/man/liver.Rd | 29 +-- EMGCR-0.3.0/EMGCR/man/plot.MCR.Rd | 18 +- EMGCR-0.3.0/EMGCR/man/qqMCR.Rd | 13 + EMGCR-0.3.0/EMGCR/man/rMCM.Rd | 25 +- EMGCR-0.3.0/EMGCR/man/residuals.MCR.Rd | 16 + 20 files changed, 398 insertions(+), 286 deletions(-)
Title: Modelling Compositional Data with Zero Values
Description: Modelling structural zeros in compositional data using a conditional logistic normal model as described by Aitchison (1986), where MLE (Maximum Likelihood Estimation) is performed via the EM (Expectation-Maximization) algorithm. The relevant paper is Alzeley and Tsagris (2026) <doi:10.48550/arXiv.2608.29954>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositionalcln versions 1.0 dated 2026-09-22 and 1.1 dated 2026-10-06
DESCRIPTION | 12 +-- MD5 | 42 ++++++++--- NAMESPACE | 11 +- R/boot.clnmle.R |only R/boot.clnreg.R | 152 ++++++++++++++++++++++++++++++++++++---- R/cln.bcr.R |only R/cln.biplot.R |only R/cln.condregs.R |only R/cln.cr.R |only R/cln.james.R |only R/cln.mle.R | 32 ++++---- R/cln.pca.R |only R/cln.reg.R | 122 ++++++++++++++++++++++++++++---- R/cln.regs.R |only R/cln.residplot.R |only R/fbed.cln.R |only man/Compositionalcln-package.Rd | 4 - man/boot.clnmle.Rd |only man/boot.clnreg.Rd | 4 - man/cln.bcr.Rd |only man/cln.biplot.Rd |only man/cln.condregs.Rd |only man/cln.contour.Rd | 7 - man/cln.cr.Rd |only man/cln.james.Rd |only man/cln.mle.Rd | 2 man/cln.pca.Rd |only man/cln.reg.Rd | 9 +- man/cln.regs.Rd |only man/cln.residplot.Rd |only man/fbed.cln.Rd |only man/ternary.Rd | 6 - 32 files changed, 325 insertions(+), 78 deletions(-)
More information about Compositionalcln at CRAN
Permanent link
Title: "Risk Model Regression and Analysis with Complex Non-Linear
Models"
Description: Performs risk analysis using general non-linear models. Risk models can be the sum or product of terms. Each term is the product of exponential/linear functions of covariates. Additionally sub-terms can be defined as a sum of exponential, linear threshold, and step functions. Cox Proportional hazards <https://en.wikipedia.org/wiki/Proportional_hazards_model>, Poisson <https://en.wikipedia.org/wiki/Poisson_regression>, and Fine-Gray competing risks <https://www.publichealth.columbia.edu/research/population-health-methods/competing-risk-analysis> regression are supported. This work was sponsored by NASA Grants 80NSSC19M0161 and 80NSSC23M0129 through a subcontract from the National Council on Radiation Protection and Measurements (NCRP). The computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CNS-1006860, EPS-1006860, EPS-0919443, ACI-1440548, CHE-1726332, and NIH P20GM113109.
Author: Eric King-Giunta [aut, cre] ,
Amir Bahadori [ctb] ,
Dan Andresen [ctb] ,
Linda Walsh [ctb] ,
Benjamin French [ctb] ,
Lawrence Dauer [ctb] ,
John Boice Jr [ctb] ,
Kansas State University [cph],
NASA [fnd],
NCRP [fnd],
NRC [fnd]
Maintainer: Eric King-Giunta <egiunta@ksu.edu>
Diff between Colossus versions 1.6.2 dated 2026-09-22 and 1.6.3 dated 2026-10-06
DESCRIPTION | 6 +++--- MD5 | 34 +++++++++++++++++----------------- NEWS.md | 4 ++++ R/plot_types.R | 35 +---------------------------------- inst/WORDLIST | 1 + inst/doc/Alt_Run_Opt.html | 8 ++++---- inst/doc/Logistic.html | 10 +++++----- inst/doc/Matched_Case_Control.html | 6 +++--- inst/doc/Plotting_And_Analysis.html | 2 +- inst/doc/Residual.Rmd | 2 +- inst/doc/Residual.html | 7 ++++--- inst/doc/SMR_Analysis.html | 4 ++-- inst/doc/Starting-Description.html | 4 ++-- inst/doc/Wald_and_Log_Bound.html | 12 ++++++------ src/Grouping.cpp | 9 +++++++++ src/Plot_Extensions.cpp | 9 +++++++++ tests/testthat/test-CoxPlot.R | 7 +++++++ vignettes/Residual.Rmd | 2 +- 18 files changed, 80 insertions(+), 82 deletions(-)
Title: Linear p-Wasserstein Projections
Description: Performs Wasserstein projections from the predictive distributions of any model into the space of predictive distributions of linear models. We utilize L1 penalties to also reduce the complexity of the model space. This package employs the methods as described in Dunipace, Eric and Lorenzo Trippa (2020) <doi:10.48550/arXiv.2012.09999>.
Author: Eric Dunipace [aut, cre] ,
Clemens Schmid [ctb] ,
Espen Bernton [ctb] ,
Mathieu Gerber [ctb] ,
Pierre Jacob [ctb] ,
Bin Dai [ctb] ,
Jared Huling [ctb] ,
Yixuan Qiu [ctb] ,
Dominic Schuhmacher [ctb] ,
Nicolas Bonneel [ctb]
Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>
Diff between WpProj versions 0.2.3 dated 2025-02-05 and 0.3 dated 2026-10-06
DESCRIPTION | 28 - MD5 | 131 ++-- NAMESPACE | 16 NEWS.md | 30 + R/HC.R | 1 R/W1L1.R | 10 R/W2IP.R | 298 ++++++++--- R/W2L1.R | 25 R/WInftyL1.R | 15 R/WPL0.R | 15 R/WPVI.R | 16 R/WP_rsquared.R | 9 R/WPremoveone.R | 2 R/WPsimulatedAnnealing.R | 20 R/WPstepwise.R | 16 R/WpProj-package.R | 3 R/WpProj.R | 39 - R/combine.dist.compare.R | 17 R/distanceCompare.R | 19 R/extractCoefficients.R | 7 R/globals.R |only R/lp_functions.R | 21 R/options.R | 26 R/palette.R |only R/plot_dist.R | 219 +++++--- R/ridgePlot.R | 10 R/utils.R | 81 +++ README.md | 27 - build/partial.rdb |binary inst/WORDLIST | 38 - man/HC.Rd | 1 man/L0_method_options.Rd | 2 man/L1_method_options.Rd | 2 man/W1L1.Rd | 4 man/W2IP.Rd | 13 man/WInfL1.Rd | 4 man/WPL0.Rd | 2 man/WPR2.Rd | 1 man/WPSA.Rd | 2 man/WPSW.Rd | 2 man/WPVI.Rd | 3 man/WpProj-package.Rd | 5 man/WpProj.Rd | 16 man/binary_program_method_options.Rd | 7 man/combine.WPR2.Rd | 1 man/distCompare.Rd | 5 man/figures/README-example_continued_plot_noecho-1.png |binary man/figures/README-r2_plots_noecho-1.png |binary man/figures/README-ridgeplots2_noecho-1.png |binary man/figures/README-ridgeplots_noecho-1.png |binary man/plot-distcompare-method.Rd | 2 man/reexports.Rd | 2 man/ridgePlot.Rd | 5 man/simulated_annealing_method_options.Rd | 2 man/stepwise_method_options.Rd | 2 src/W2penalized.cpp | 2 src/utils.h | 2 tests/testthat/test-W1L1.R | 23 tests/testthat/test-W2IP.R | 143 +++++ tests/testthat/test-W2L1.R | 65 ++ tests/testthat/test-WInftyL1.R | 23 tests/testthat/test-WPL0.R | 58 -- tests/testthat/test-WPL1.R | 26 tests/testthat/test-WPR2.R | 221 +++++--- tests/testthat/test-WpSLIM.R | 447 +++++++++++++---- tests/testthat/test-argument_options.R | 200 +++++-- tests/testthat/test-distanceCompare.R | 193 +++++-- tests/testthat/test-parallel.R |only 68 files changed, 1894 insertions(+), 731 deletions(-)
Title: Infers Novel Immunoglobulin Alleles from Sequencing Data
Description: Infers the V genotype of an individual from immunoglobulin (Ig)
repertoire sequencing data (AIRR-Seq, Rep-Seq). Includes detection of
any novel alleles. This information is then used to correct existing V
allele calls from among the sample sequences.
Citations:
Gadala-Maria, et al (2015) <doi:10.1073/pnas.1417683112>,
Gadala-Maria, et al (2019) <doi:10.3389/fimmu.2019.00129>.
Author: Daniel Gadala-Maria [aut],
Susanna Marquez [aut, cre],
Moriah Cohen [aut],
Ayelet Peres [aut],
Jason Vander Heiden [aut],
Gur Yaari [aut],
Steven Kleinstein [aut, cph]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between tigger versions 1.1.3 dated 2026-04-17 and 1.2.0 dated 2026-10-06
DESCRIPTION | 14 - MD5 | 35 ++-- NAMESPACE | 148 ++++++++++------- NEWS.md | 53 ++++++ R/bayesian.R | 31 +++ R/functions.R | 353 +++++++++++++++++++++++++++++++++++++----- R/tigger.R | 6 README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Tigger-Vignette.Rmd | 10 - inst/doc/Tigger-Vignette.pdf |binary man/genotypeFasta.Rd | 18 ++ man/inferGenotypeBayesian.Rd | 10 + man/plotGenotype.Rd | 8 man/plotGenotypeConfidence.Rd |only man/reassignAlleles.Rd | 53 ++++++ man/tigger-package.Rd | 6 vignettes/Tigger-Vignette.Rmd | 10 - 19 files changed, 611 insertions(+), 148 deletions(-)
Title: Miscellaneous Functions for Working with 'stars' Rasters
Description: Miscellaneous functions for working with 'stars' objects, mainly single-band rasters. Currently includes functions for: (1) focal filtering, (2) detrending of Digital Elevation Models, (3) calculating flow length, (4) calculating the Convergence Index, (5) calculating topographic aspect and topographic slope.
Author: Michael Dorman [aut, cre]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between starsExtra versions 0.2.8 dated 2024-01-13 and 0.2.9 dated 2026-10-06
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 24 ++++++++++++------------ NEWS.md | 7 ++++++- R/layer_to_matrix.R | 3 +++ build/vignette.rds |binary data/carmel.rda |binary inst/doc/intro.R | 18 +++++++++--------- inst/doc/intro.html | 29 +++++++++++++---------------- inst/tinytest/test-focal2.R | 27 ++++++++++++--------------- inst/tinytest/test-focal2r.R | 23 +++++++++-------------- inst/tinytest/test-layer_values_matrix.R | 16 +++++++++++----- man/starsExtra-package.Rd | 5 +++++ 13 files changed, 85 insertions(+), 77 deletions(-)
Title: Persistence Homology Utilities
Description: A low-level package for hosting persistence data. It is part of the
'TDAverse' suite of packages, which is designed to provide a collection of
packages for enabling machine learning and data science tasks using
persistent homology. Implements a class for hosting persistence data, a
number of coercers from and to already existing and used data structures
from other packages and functions to compute distances between persistence
diagrams. A formal definition and study of bottleneck and Wasserstein
distances can be found in Bubenik, Scott and Stanley (2023)
<doi:10.1007/s41468-022-00103-8>. Their implementation in 'phutil' relies on
the 'C++' Hera library developed by Kerber, Morozov and Nigmetov (2017)
<doi:10.1145/3064175>.
Author: Aymeric Stamm [aut, cre] ,
Jason Cory Brunson [aut] ,
Michael Kerber [ctb] ,
Dmitriy Morozov [ctb] ,
Arnur Nigmetov [ctb]
Maintainer: Aymeric Stamm <aymeric.stamm@cnrs.fr>
Diff between phutil versions 0.0.2 dated 2026-04-17 and 0.0.3 dated 2026-10-06
phutil-0.0.2/phutil/src/Makevars |only phutil-0.0.3/phutil/DESCRIPTION | 8 - phutil-0.0.3/phutil/MD5 | 63 +++++----- phutil-0.0.3/phutil/NEWS.md | 10 + phutil-0.0.3/phutil/R/distances.R | 13 +- phutil-0.0.3/phutil/R/persistence-class.R | 2 phutil-0.0.3/phutil/build/partial.rdb |binary phutil-0.0.3/phutil/build/vignette.rds |binary phutil-0.0.3/phutil/cleanup |only phutil-0.0.3/phutil/cleanup.win |only phutil-0.0.3/phutil/configure |only phutil-0.0.3/phutil/configure.win |only phutil-0.0.3/phutil/inst/doc/persistence-class.html | 11 + phutil-0.0.3/phutil/inst/doc/validation-benchmark.html | 13 +- phutil-0.0.3/phutil/inst/tinytest/test-persistence-class.R | 4 phutil-0.0.3/phutil/man/arch_spirals.Rd | 2 phutil-0.0.3/phutil/man/distances.Rd | 13 +- phutil-0.0.3/phutil/man/pairwise-distances.Rd | 2 phutil-0.0.3/phutil/man/persistence_sample.Rd | 2 phutil-0.0.3/phutil/man/phutil-package.Rd | 1 phutil-0.0.3/phutil/man/trefoils.Rd | 2 phutil-0.0.3/phutil/src/Makevars.in |only phutil-0.0.3/phutil/src/README.md |only phutil-0.0.3/phutil/src/hera/bottleneck.h | 2 phutil-0.0.3/phutil/src/hera/bottleneck/basic_defs_bt.h | 2 phutil-0.0.3/phutil/src/hera/bottleneck/bottleneck_detail.h | 2 phutil-0.0.3/phutil/src/hera/bottleneck/def_debug_bt.h | 2 phutil-0.0.3/phutil/src/hera/bottleneck/neighb_oracle.h | 4 phutil-0.0.3/phutil/src/hera/common.h | 12 - phutil-0.0.3/phutil/src/hera/common/diagram_point.h | 7 - phutil-0.0.3/phutil/src/hera/dnn/geometry/euclidean-dynamic.h | 2 phutil-0.0.3/phutil/src/hera/wasserstein/auction_oracle_kdtree_restricted.h | 4 phutil-0.0.3/phutil/src/hera/wasserstein/auction_params.h | 2 phutil-0.0.3/phutil/src/hera/wasserstein/auction_result.h | 2 phutil-0.0.3/phutil/src/hera/wasserstein/basic_defs_ws.h | 4 phutil-0.0.3/phutil/src/hera/wasserstein/def_debug_ws.h | 2 36 files changed, 113 insertions(+), 80 deletions(-)
Title: Limited Memory BFGS Minimizer with Bounds on Parameters with
optim() 'C' Interface
Description: Interfacing to Nocedal et al. L-BFGS-B.3.0
(See <http://users.iems.northwestern.edu/~nocedal/lbfgsb.html>)
limited memory BFGS minimizer with bounds on parameters.
This is a fork of 'lbfgsb3'.
This registers a 'R' compatible 'C' interface to L-BFGS-B.3.0 that uses the same
function types and optimization as the optim() function (see writing 'R' extensions
and source for details). This package also adds more stopping criteria as well
as allowing the adjustment of more tolerances.
Author: Matthew L Fidler [aut, cre] ,
John C Nash [aut],
Ciyou Zhu [aut],
Richard Byrd [aut],
Jorge Nocedal [aut],
Jose Luis Morales [aut]
Maintainer: Matthew L Fidler <matthew.fidler@gmail.com>
Diff between lbfgsb3c versions 2024-3.5 dated 2024-09-17 and 2026-3.5 dated 2026-10-06
lbfgsb3c-2024-3.5/lbfgsb3c/src/timer.f |only lbfgsb3c-2026-3.5/lbfgsb3c/DESCRIPTION | 15 lbfgsb3c-2026-3.5/lbfgsb3c/MD5 | 35 lbfgsb3c-2026-3.5/lbfgsb3c/NEWS.md | 40 lbfgsb3c-2026-3.5/lbfgsb3c/R/RcppExports.R | 8 lbfgsb3c-2026-3.5/lbfgsb3c/R/lbfgsb3.R | 12 lbfgsb3c-2026-3.5/lbfgsb3c/build/vignette.rds |binary lbfgsb3c-2026-3.5/lbfgsb3c/inst/doc/lbfgsb3c.R | 106 - lbfgsb3c-2026-3.5/lbfgsb3c/inst/doc/lbfgsb3c.Rmd | 2 lbfgsb3c-2026-3.5/lbfgsb3c/inst/doc/lbfgsb3c.html | 704 +++++++----- lbfgsb3c-2026-3.5/lbfgsb3c/inst/include/lbfgsb3ptr.h | 18 lbfgsb3c-2026-3.5/lbfgsb3c/man/lbfgsb3c.Rd | 1 lbfgsb3c-2026-3.5/lbfgsb3c/src/Makevars |only lbfgsb3c-2026-3.5/lbfgsb3c/src/Makevars.win |only lbfgsb3c-2026-3.5/lbfgsb3c/src/RcppExports.cpp | 22 lbfgsb3c-2026-3.5/lbfgsb3c/src/init.c | 19 lbfgsb3c-2026-3.5/lbfgsb3c/src/lbfgsb3x.cpp | 309 +---- lbfgsb3c-2026-3.5/lbfgsb3c/src/lbfgsb_cpp.cpp |only lbfgsb3c-2026-3.5/lbfgsb3c/src/lbfgsb_cpp.h |only lbfgsb3c-2026-3.5/lbfgsb3c/src/threadtest.cpp |only lbfgsb3c-2026-3.5/lbfgsb3c/tests/testthat/test-cpp-engine.R |only lbfgsb3c-2026-3.5/lbfgsb3c/vignettes/lbfgsb3c.Rmd | 2 22 files changed, 693 insertions(+), 600 deletions(-)
Title: Generalized Additive Models for Location Scale and Shape
Description: Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.
Author: Mikis Stasinopoulos [aut, cre, cph] ,
Robert Rigby [aut] ,
Vlasios Voudouris [ctb],
Calliope Akantziliotou [ctb],
Marco Enea [ctb],
Daniil Kiose [ctb] ,
Achim Zeileis [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@gre.ac.uk>
Diff between gamlss versions 5.5-0 dated 2025-08-19 and 5.5-5 dated 2026-10-06
gamlss-5.5-0/gamlss/R/FitTail.R |only gamlss-5.5-0/gamlss/R/gamlss_test.R |only gamlss-5.5-5/gamlss/DESCRIPTION | 8 - gamlss-5.5-5/gamlss/MD5 | 41 ++--- gamlss-5.5-5/gamlss/NAMESPACE | 10 + gamlss-5.5-5/gamlss/NEWS.md | 107 +++++++++----- gamlss-5.5-5/gamlss/R/DropAddStepGAIC-Parallel.R | 12 - gamlss-5.5-5/gamlss/R/LR-test-12-06-2013.R | 14 + gamlss-5.5-5/gamlss/R/centilesPLOT.R | 169 +++++++++++------------ gamlss-5.5-5/gamlss/R/chooseDistParallel.R | 2 gamlss-5.5-5/gamlss/R/extra.R | 42 ++++- gamlss-5.5-5/gamlss/R/gamlssML.R | 6 gamlss-5.5-5/gamlss/R/gamlssVGD_23_12_21.R | 2 gamlss-5.5-5/gamlss/R/lms.R | 14 - gamlss-5.5-5/gamlss/R/loglogSurv.R |only gamlss-5.5-5/gamlss/R/pb.R | 114 +++++++++------ gamlss-5.5-5/gamlss/R/pb_goingtozero.R | 39 +++-- gamlss-5.5-5/gamlss/README.md | 6 gamlss-5.5-5/gamlss/build/partial.rdb |binary gamlss-5.5-5/gamlss/man/IC.Rd | 37 ++--- gamlss-5.5-5/gamlss/man/Rsq.Rd | 3 gamlss-5.5-5/gamlss/man/centiles.split.Rd | 4 gamlss-5.5-5/gamlss/man/gamlssVGD.Rd | 4 23 files changed, 374 insertions(+), 260 deletions(-)
Title: An Interface to Brazilian Public Health Data
Description: Retrieves public health data from the Department of Informatics
('DATASUS') of the Brazilian Unified Health System ('Sistema Unico de
Saude', 'SUS') through its online tabulation service and open-data catalog.
It covers the Mortality Information System ('SIM'), Live Birth Information
System ('SINASC'), Hospital Information System of the Unified Health System
('SIH/SUS'), Outpatient Information System of the Unified Health System
('SIA/SUS'), National Register of Health Establishments ('CNES'),
Notifiable Diseases Information System ('SINAN'), National Immunization
Program ('PNI'), Cancer Information System ('SISCAN'), and Food and
Nutrition Surveillance System ('SISVAN'). Contemporary sources from the
'OpenDataSUS' portal include Events Supposedly Attributable to Vaccination
or Immunization ('ESAVI'), influenza-like illness notifications from
'e-SUS Notifica', individual vaccination doses, coronavirus disease 2019
(COVID-19) hospital occupancy, and record-level mortality, live-birth an [...truncated...]
Author: Renato Prado Siqueira [aut, cre]
Maintainer: Renato Prado Siqueira <rpradosiqueira@gmail.com>
Diff between datasus versions 0.16.1 dated 2026-09-05 and 0.16.2 dated 2026-10-06
DESCRIPTION | 6 +- MD5 | 19 ++++--- NEWS.md | 7 ++ R/tabnet-client.R | 25 +++++++++- README.md | 21 +++++++- inst/doc/Introduction_to_datasus.html | 4 - inst/doc/accessing-datasus.html | 4 - inst/doc/geography-and-analysis.html | 73 +++++++++++++----------------- inst/doc/large-files-and-microdata.html | 24 ++++----- inst/doc/modern-surveillance.html | 4 - tests/testthat/test-tabnet-filter-codes.R |only 11 files changed, 112 insertions(+), 75 deletions(-)
Title: Field Planning and Biostatistics Utilities
Description: A toolkit for agricultural trial planning, experimental design,
and applied biostatistics. Supports generating field designs such as Latin
Square, Alpha-Lattice (Patterson and Williams, 1976
<doi:10.2307/2335087>), and Factorial layouts, with automatic fieldbook
creation and layout sketching. Includes a built-in QR Code engine (powered
by the 'Nayuki' C library <https://github.com/nayuki/QR-Code-generator>)
for generating printable plot labels in PDF. Also provides descriptive
statistics utilities for quantitative variables following Field, Miles,
and Field (2012, ISBN:978-1-4462-0045-2).
Author: Tiago Olivoto [aut, cre]
Maintainer: Tiago Olivoto <tiagoolivoto@gmail.com>
Diff between beautils versions 0.2.0 dated 2026-06-24 and 0.3.0 dated 2026-10-06
DESCRIPTION | 31 +++--- MD5 | 78 +++++++++++------ NAMESPACE | 99 ++++++++++++++-------- NEWS.md | 23 +++++ R/beautils-package.R |only R/conf_int.R |only R/design_alpha_lattice.R | 63 ++++++-------- R/design_augmented.R | 20 ++-- R/design_full_factorial.R | 29 +++--- R/design_latin_square.R | 133 +++++++++++++++++++++++------ R/design_prep.R |only R/design_rectangular_lattice.R |only R/design_split_plot.R | 130 ++++++++++++++++++++++------ R/design_square_lattice.R |only R/design_strip_plot.R | 153 ++++++++++++++++++++++++---------- R/design_unifatorial.R | 37 ++++---- R/stats_core.R | 4 R/utils-internal.R | 9 ++ R/utils_etiquetas.R | 29 +++++- R/utils_ttest.R |only R/utils_uuid.R |only build |only inst/COPYRIGHTS |only man/alpha_lattice.Rd | 7 - man/augmented.Rd | 5 - man/beautils-package.Rd |only man/conf_int.Rd |only man/create_label.Rd | 4 man/full_factorial.Rd | 15 +-- man/latin_square.Rd | 19 ++-- man/make_qrcode.Rd | 12 ++ man/prep_design.Rd |only man/rectangular_lattice.Rd |only man/reexports.Rd | 4 man/split_plot.Rd | 22 +++- man/square_lattice.Rd |only man/strip_plot.Rd | 23 +++-- man/t_test.Rd |only man/t_test_paired.Rd |only man/unifatorial.Rd | 13 +- man/utils_sets.Rd | 4 man/uuid_generator.Rd |only src |only tests/testthat/test-conf_int.R |only tests/testthat/test-utils_etiquetas.R | 28 ++++++ tests/testthat/test-utils_planning.R | 2 tests/testthat/test-uuid.R |only 47 files changed, 693 insertions(+), 303 deletions(-)
Title: Mixed Models for Repeated Measures
Description: Mixed models for repeated measures (MMRM) are a popular
choice for analyzing longitudinal continuous outcomes in randomized
clinical trials and beyond; see Cnaan, Laird and Slasor (1997)
<doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E>
for a tutorial and Mallinckrodt, Lane, Schnell, Peng and Mancuso
(2008) <doi:10.1177/009286150804200402> for a review. This package
implements MMRM based on the marginal linear model without random
effects using Template Model Builder ('TMB') which enables fast and
robust model fitting. Users can specify a variety of covariance
matrices, weight observations, fit models with restricted or standard
maximum likelihood inference, perform hypothesis testing with
Satterthwaite or Kenward-Roger adjustment, and extract least square
means estimates by using 'emmeans'.
Author: Daniel Sabanes Bove [aut, cre] ,
Liming Li [aut] ,
Julia Dedic [aut],
Doug Kelkhoff [aut],
Kevin Kunzmann [aut],
Brian Matthew Lang [aut],
Christian Stock [aut],
Ya Wang [aut],
Craig Gower-Page [ctb],
Dan James [aut],
Jonathan Sidi [aut],
Daniel Leib [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@rconis.com>
Diff between mmrm versions 0.3.18 dated 2026-06-19 and 0.3.19 dated 2026-10-06
DESCRIPTION | 8 MD5 | 89 ++-- NAMESPACE | 38 +- NEWS.md | 13 R/fit.R | 22 - R/interop-emmeans.R | 7 R/kenwardroger.R | 181 ++++++--- R/utils.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 32 + inst/doc/algorithm.Rmd | 137 ++++--- inst/doc/algorithm.html | 191 +++++----- inst/doc/introduction.html | 29 + inst/doc/kenward.Rmd | 335 ++++++++++++++---- inst/doc/kenward.html | 446 +++++++++++++++++------- inst/doc/mmrm_review_methods.html | 93 ++--- inst/doc/satterthwaite.Rmd | 197 +++++++--- inst/doc/satterthwaite.html | 286 ++++++++++----- man/h_check_columns_nested.Rd | 2 man/h_check_fits_all_data_same.Rd | 2 man/h_df_1d_kr.Rd | 4 man/h_df_md_kr.Rd | 3 man/h_get_kr_comp.Rd | 17 man/h_kr_df.Rd | 2 man/h_var_adj.Rd | 12 man/h_var_adj_contracted.Rd |only man/mmrm.Rd | 4 src/derivatives.h | 42 +- src/empirical.cpp | 2 src/exports.cpp | 9 src/jacobian.cpp | 2 src/kr_comp.cpp | 145 +++++-- src/kr_comp.h |only src/test-derivatives.cpp | 31 + src/test-kr_comp.cpp |only src/utils.h | 4 tests/testthat/_snaps/kenwardroger.md | 8 tests/testthat/helper-kenwardroger.R |only tests/testthat/test-emmeans.R | 33 + tests/testthat/test-fit.R | 12 tests/testthat/test-kenwardroger.R | 310 ++++++++++++++++ tests/testthat/test-kr-integrated.R |only tests/testthat/test-satterthwaite.R | 20 + vignettes/algorithm.Rmd | 137 ++++--- vignettes/kenward.Rmd | 335 ++++++++++++++---- vignettes/satterthwaite.Rmd | 197 +++++++--- vignettes/subsections/_intro-customizations.Rmd | 16 48 files changed, 2514 insertions(+), 943 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020)
<DOI:10.18637/jss.v092.i01>. Shift-scale (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>)
and multivariate (Klein et al, 2022, <DOI:10.1111/sjos.12501>) transformation models
are part of this package. A package vignette is available from <DOI:10.32614/CRAN.package.mlt.docreg> and
more convenient user interfaces to many models from <DOI:10.32614/CRAN.package.tram>.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.8-2 dated 2026-08-21 and 1.8-3 dated 2026-10-06
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/R.R | 2 ++ build/partial.rdb |binary inst/NEWS.Rd | 9 +++++++++ 5 files changed, 18 insertions(+), 7 deletions(-)
Title: Make 'PICRUSt2' Output Analysis and Visualization Easier
Description: Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) <doi:10.1093/bioinformatics/btad470>.
Author: Chen Yang [aut, cre],
Liangliang Zhang [aut]
Maintainer: Chen Yang <cafferychen7850@gmail.com>
Diff between ggpicrust2 versions 2.5.17 dated 2026-06-05 and 2.5.19 dated 2026-10-06
DESCRIPTION | 8 MD5 | 187 +- NAMESPACE | 1 NEWS.md | 539 +++++++- R/color_themes.R | 123 + R/compare_daa_results.R | 221 ++- R/compare_gsea_daa.R | 383 ++++- R/compare_metagenome_results.R | 667 ++++++++- R/data_utils.R | 1080 +++++++++++++++- R/ggpicrust2.R | 194 +- R/gsea_pathway_annotation.R | 149 -- R/import_MicrobiomeAnalyst_daa_results.R | 215 ++- R/ko2kegg_abundance.R | 95 + R/legend_annotation_utils.R | 130 + R/pathway_annotation.R | 135 +- R/pathway_daa.R | 1470 +++++++++++++++++----- R/pathway_errorbar.R | 412 +++--- R/pathway_errorbar_table.R | 125 + R/pathway_gsea.R | 1175 +++++++++++++---- R/pathway_heatmap.R | 461 ++++-- R/pathway_pca.R | 294 ++-- R/pathway_ridgeplot.R | 472 ++++--- R/pathway_volcano.R | 64 R/taxa_contribution.R | 452 +++++- R/taxa_contribution_viz.R | 378 ++++- R/visualize_gsea.R | 666 +++++++-- R/zzz.R | 3 README.md | 1389 +++----------------- build/vignette.rds |binary inst/doc/gsea_analysis.R | 103 - inst/doc/gsea_analysis.Rmd | 240 ++- inst/doc/gsea_analysis.html | 612 ++++----- inst/doc/using_ggpicrust2.R | 135 +- inst/doc/using_ggpicrust2.Rmd | 239 ++- inst/doc/using_ggpicrust2.html | 390 +++-- man/aggregate_taxa_contributions.Rd | 36 man/calculate_rank_metric.Rd | 20 man/compare_daa_results.Rd | 24 man/compare_gsea_daa.Rd | 46 man/compare_metagenome_results.Rd | 83 + man/compute_correlation_distance.Rd |only man/create_gradient_colors.Rd | 4 man/create_heatmap_plot.Rd | 7 man/create_network_plot.Rd | 3 man/dot-as_color_vector.Rd | 6 man/filter_gene_sets_to_ranked_universe.Rd |only man/get_color_theme.Rd | 7 man/ggpicrust2.Rd | 113 - man/gsea_pathway_annotation.Rd | 5 man/import_MicrobiomeAnalyst_daa_results.Rd | 27 man/ko2kegg_abundance.Rd | 39 man/ko_to_go_reference.Rd | 6 man/pathway_annotation.Rd | 45 man/pathway_daa.Rd | 78 + man/pathway_errorbar.Rd | 186 +- man/pathway_errorbar_table.Rd | 38 man/pathway_gsea.Rd | 122 + man/pathway_heatmap.Rd | 58 man/pathway_pca.Rd | 27 man/pathway_ridgeplot.Rd | 25 man/pathway_volcano.Rd | 10 man/prepare_gene_sets.Rd | 5 man/read_contrib_file.Rd | 10 man/read_strat_file.Rd | 2 man/resolve_limma_contrast.Rd |only man/run_fgsea.Rd | 14 man/run_limma_gsea.Rd | 9 man/safe_extract.Rd | 4 man/smart_color_selection.Rd | 3 man/taxa_contribution_bar.Rd | 26 man/taxa_contribution_heatmap.Rd | 21 man/visualize_gsea.Rd | 60 tests/testthat/test-color-themes.R |only tests/testthat/test-compare_gsea_daa.R |only tests/testthat/test-compare_metagenome_results.R | 365 +++++ tests/testthat/test-core-audit-followup.R | 199 ++ tests/testthat/test-data_utils.R | 134 ++ tests/testthat/test-find_sample_column.R | 30 tests/testthat/test-first-principles-fixes.R | 347 +++++ tests/testthat/test-ggpicrust2-return-structure.R | 257 +++ tests/testthat/test-go_pathway_support.R | 1 tests/testthat/test-gsea-transformation.R |only tests/testthat/test-gsea_pathway_annotation.R | 52 tests/testthat/test-ko2kegg_abundance.R | 97 + tests/testthat/test-legend_annotation_utils.R |only tests/testthat/test-pathway_annotation.R | 164 ++ tests/testthat/test-pathway_daa.R | 1291 ++++++++++++++++++- tests/testthat/test-pathway_errorbar.R | 284 ++++ tests/testthat/test-pathway_errorbar_table.R | 221 +++ tests/testthat/test-pathway_gsea.R | 945 ++++++++++++++ tests/testthat/test-pathway_heatmap.R | 352 +++++ tests/testthat/test-pathway_pca.R | 219 +++ tests/testthat/test-pathway_ridgeplot.R | 395 +++++ tests/testthat/test-pathway_volcano.R | 110 + tests/testthat/test-taxa_contribution.R | 692 ++++++++++ tests/testthat/test-visualize_gsea.R | 525 +++++++ vignettes/gsea_analysis.Rmd | 240 ++- vignettes/using_ggpicrust2.Rmd | 239 ++- 98 files changed, 16920 insertions(+), 4615 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-27 0.1.0
More information about datazoom.saude at CRAN
Permanent link
Title: ICESat-2 Data Analysis for Land and Vegetation
Description: Provides tools for downloading, reading, processing, visualizing,
and exporting NASA's ICESat-2 ATL03 (Global Geolocated Photon
Data) and ATL08 (Land and Vegetation Height) products. Supports
photon- and segment-level analysis, spatial sampling, gridding,
statistical and machine-learning modeling, and integration with
'Google Earth Engine' (<https://earthengine.google.com/>) for
wall-to-wall mapping of vegetation structure and other land
attributes.
Author: Carlos Alberto Silva [aut, cph, cre],
Caio Hamamura [aut, cph],
Cesar Alvites [aut, ctb],
Alexander J. Gaskins [aut, ctb],
Sunil Arya [ctb, cph] ),
David Mount [ctb, cph] ),
University of Maryland [cph] ),
Chuck Gantz [ctb] ,
Cole Krehbiel [ctb]
Maintainer: Carlos Alberto Silva <c.silva@ufl.edu>
Diff between ICESat2VegR versions 0.0.3 dated 2026-09-28 and 0.0.4 dated 2026-10-06
DESCRIPTION | 6 +-- MD5 | 22 +++++++------- R/earthaccess.R | 53 +++++++++++++++++++---------------- R/extract.R | 8 ++++- R/model_tools.R | 2 - configure | 6 +-- configure.ac | 4 +- src/ANNIndex.cpp | 9 +++-- src/Makevars.ucrt | 6 +-- tests/testthat/test-ann-index.R |only tests/testthat/test-configure.R | 31 +++++++++++++++++++- tests/testthat/test-extract-errors.R |only tests/testthat/test-spatial.R | 40 ++++++++++++++++++++++++-- 13 files changed, 131 insertions(+), 56 deletions(-)
Title: Forensic Pedigree Analysis and Relatedness Inference
Description: Forensic applications of pedigree analysis, including
likelihood ratios for relationship testing, general relatedness
inference, marker simulation, and power analysis. 'forrel' is part of
the 'pedsuite', a collection of packages for pedigree analysis,
further described in the book 'Pedigree Analysis in R' (Vigeland,
2021, ISBN:9780128244302). Several functions deal specifically with
power analysis in missing person cases, implementing methods described
in Vigeland et al. (2020) <doi:10.1016/j.fsigen.2020.102376>. Methods
for checking pairwise relationships are described in Egeland and
Vigeland (2025) <doi:10.1016/j.fsigen.2025.103270>. Data exchange with
the 'Familias' software (Egeland et al. (2000)
<doi:10.1016/S0379-0738(00)00147-X>) is supported through the
'pedFamilias' package.
Author: Magnus Dehli Vigeland [aut, cre] ,
Thore Egeland [ctb]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between forrel versions 1.9.0 dated 2026-06-28 and 1.10.0 dated 2026-10-06
forrel-1.10.0/forrel/DESCRIPTION | 16 +- forrel-1.10.0/forrel/MD5 | 68 ++++---- forrel-1.10.0/forrel/NAMESPACE | 48 +++--- forrel-1.10.0/forrel/NEWS.md | 19 ++ forrel-1.10.0/forrel/R/LRpower.R | 86 ++++++---- forrel-1.10.0/forrel/R/LRpowerPlot.R |only forrel-1.10.0/forrel/R/MPPsims.R | 42 ++--- forrel-1.10.0/forrel/R/checkPairwise.R | 2 forrel-1.10.0/forrel/R/exclusionPower.R | 28 ++- forrel-1.10.0/forrel/R/expectedLR.R | 76 +++++---- forrel-1.10.0/forrel/R/ibdBootstrap.R | 4 forrel-1.10.0/forrel/R/ibdEstimate.R | 100 ++++++------ forrel-1.10.0/forrel/R/kinshipLR.R | 114 +++++++------- forrel-1.10.0/forrel/R/missingPersonIP.R | 134 ++++++++++------- forrel-1.10.0/forrel/R/powerPlot.R | 30 ++- forrel-1.10.0/forrel/R/profileSim.R | 21 -- forrel-1.10.0/forrel/R/quickLR.R | 2 forrel-1.10.0/forrel/R/randomPersonEP.R | 4 forrel-1.10.0/forrel/R/utils.R | 26 ++- forrel-1.10.0/forrel/README.md | 17 -- forrel-1.10.0/forrel/build/partial.rdb |binary forrel-1.10.0/forrel/man/LRpower.Rd | 53 +++--- forrel-1.10.0/forrel/man/LRpowerPlot.Rd |only forrel-1.10.0/forrel/man/MPPsims.Rd | 42 ++--- forrel-1.10.0/forrel/man/MPpowerPlot.Rd |only forrel-1.10.0/forrel/man/exclusionPower.Rd | 12 + forrel-1.10.0/forrel/man/expectedLR.Rd | 48 ++---- forrel-1.10.0/forrel/man/figures/README-triangle-1.png |binary forrel-1.10.0/forrel/man/forrel-package.Rd | 2 forrel-1.10.0/forrel/man/ibdEstimate.Rd | 97 +++++------- forrel-1.10.0/forrel/man/kinshipLR.Rd | 112 ++++++-------- forrel-1.10.0/forrel/man/missingPersonEP.Rd | 5 forrel-1.10.0/forrel/man/missingPersonIP.Rd | 84 ++++++---- forrel-1.10.0/forrel/man/randomPersonEP.Rd | 5 forrel-1.10.0/forrel/tests/testthat/test-expectedLR.R |only forrel-1.10.0/forrel/tests/testthat/test-kinshipLR.R | 3 forrel-1.9.0/forrel/man/powerPlot.Rd |only forrel-1.9.0/forrel/man/showInTriangle.Rd |only 38 files changed, 706 insertions(+), 594 deletions(-)
Title: Package Checks for 'rOpenSci'
Description: Check whether a package is ready for submission to the 'rOpenSci'
peer review system ('rOpenSci' authors (2026) <doi:10.5281/zenodo.2553043>
"'rOpenSci' Packages: Development, Maintenance, and Peer Review").
Incorporates the 'goodpractice' package and many additional checks,
including aspects related to maintenance of online public code
repositories.
Author: Mark Padgham [aut, cre] ,
Maelle Salmon [aut],
Jacob Wujciak-Jens [aut] ,
Kelli F. Johnson [ctb] ,
Eunseop Kim [aut] ,
Katrina Brock [ctb] ,
Andy Teucher [aut] ,
Eric R. Scott [aut]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between pkgcheck versions 0.3.2 dated 2026-10-02 and 0.3.3 dated 2026-10-06
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NEWS.md | 6 ++++++ R/check-orcid-ror.R | 5 +++++ inst/doc/autotest-pkgcheck-gp.html | 4 ++-- inst/doc/environment.html | 4 ++-- inst/doc/extending-checks.html | 4 ++-- inst/doc/list-checks.html | 4 ++-- tests/testthat/_snaps/pkgcheck/checks0.html | 3 ++- tests/testthat/_snaps/pkgcheck/checks0.md | 5 ++++- tests/testthat/_snaps/pkgcheck/checks1.html | 3 ++- tests/testthat/_snaps/pkgcheck/checks1.md | 5 ++++- tests/testthat/test-check-ci.R | 2 ++ tests/testthat/test-check-orcid-ror.R | 2 +- 14 files changed, 50 insertions(+), 29 deletions(-)
Title: São Paulo Metro Passenger Demand Data
Description: Provides passenger demand data for the São Paulo metro system,
covering 2012 to 2026. Datasets include monthly passenger entries and
transported counts by line, average weekday passengers transported
by station, daily station entries, and spatial geometries for metro and
commuter train lines and stations. The bundled datasets are a fixed snapshot, so
analyses stay reproducible and examples run offline. More recent data
is published to 'GitHub' releases as the upstream sources are updated,
and read_metro_demand() downloads, caches, and reads it, optionally
pinned to a dated monthly batch.
Author: Vinicius Oike [aut, cre, cph]
Maintainer: Vinicius Oike <viniciusoike@gmail.com>
Diff between metrosp versions 1.2.1 dated 2026-09-03 and 2.0.0 dated 2026-10-06
metrosp-1.2.1/metrosp/data/lines.rda |only metrosp-1.2.1/metrosp/data/passengers_entrance.rda |only metrosp-1.2.1/metrosp/data/passengers_transported.rda |only metrosp-1.2.1/metrosp/data/station_averages.rda |only metrosp-1.2.1/metrosp/data/station_daily.rda |only metrosp-1.2.1/metrosp/data/station_inauguration.rda |only metrosp-1.2.1/metrosp/data/stations.rda |only metrosp-1.2.1/metrosp/inst/doc/data-dictionary.R |only metrosp-1.2.1/metrosp/man/lines.Rd |only metrosp-1.2.1/metrosp/man/passengers_entrance.Rd |only metrosp-1.2.1/metrosp/man/passengers_transported.Rd |only metrosp-1.2.1/metrosp/man/station_averages.Rd |only metrosp-1.2.1/metrosp/man/station_daily.Rd |only metrosp-1.2.1/metrosp/man/station_inauguration.Rd |only metrosp-1.2.1/metrosp/man/stations.Rd |only metrosp-1.2.1/metrosp/tests/testthat/test-dashboard-helpers.R |only metrosp-2.0.0/metrosp/DESCRIPTION | 24 metrosp-2.0.0/metrosp/LICENSE | 2 metrosp-2.0.0/metrosp/MD5 | 86 - metrosp-2.0.0/metrosp/NAMESPACE | 4 metrosp-2.0.0/metrosp/NEWS.md | 93 + metrosp-2.0.0/metrosp/R/cache.R | 243 +- metrosp-2.0.0/metrosp/R/data.R | 291 +-- metrosp-2.0.0/metrosp/R/read_metro_demand.R | 298 ++- metrosp-2.0.0/metrosp/README.md | 80 metrosp-2.0.0/metrosp/build/vignette.rds |binary metrosp-2.0.0/metrosp/data/calendar_spo.rda |binary metrosp-2.0.0/metrosp/data/line_entries_monthly.rda |only metrosp-2.0.0/metrosp/data/line_transported_monthly.rda |only metrosp-2.0.0/metrosp/data/rail_lines.rda |only metrosp-2.0.0/metrosp/data/rail_stations.rda |only metrosp-2.0.0/metrosp/data/station_entries_daily.rda |only metrosp-2.0.0/metrosp/data/station_transported_monthly.rda |only metrosp-2.0.0/metrosp/inst/WORDLIST | 18 metrosp-2.0.0/metrosp/inst/doc/data-dictionary.html | 831 +++------- metrosp-2.0.0/metrosp/inst/doc/data-dictionary.qmd | 430 +---- metrosp-2.0.0/metrosp/inst/doc/getting_started.R | 39 metrosp-2.0.0/metrosp/inst/doc/getting_started.html | 342 ++-- metrosp-2.0.0/metrosp/inst/doc/getting_started.qmd | 86 - metrosp-2.0.0/metrosp/man/calendar_spo.Rd | 12 metrosp-2.0.0/metrosp/man/figures/timespan_line_entries_monthly.png |only metrosp-2.0.0/metrosp/man/figures/timespan_line_transported_monthly.png |only metrosp-2.0.0/metrosp/man/figures/timespan_station_entries_daily.png |only metrosp-2.0.0/metrosp/man/figures/timespan_station_transported_monthly.png |only metrosp-2.0.0/metrosp/man/line_entries_monthly.Rd |only metrosp-2.0.0/metrosp/man/line_transported_monthly.Rd |only metrosp-2.0.0/metrosp/man/metro_colors.Rd | 2 metrosp-2.0.0/metrosp/man/metrosp_cache.Rd |only metrosp-2.0.0/metrosp/man/metrosp_cache_clear.Rd |only metrosp-2.0.0/metrosp/man/rail_lines.Rd |only metrosp-2.0.0/metrosp/man/rail_stations.Rd |only metrosp-2.0.0/metrosp/man/read_metro_demand.Rd |only metrosp-2.0.0/metrosp/man/station_entries_daily.Rd |only metrosp-2.0.0/metrosp/man/station_transported_monthly.Rd |only metrosp-2.0.0/metrosp/tests/testthat/helper-checks.R | 514 +++++- metrosp-2.0.0/metrosp/tests/testthat/test-cache.R | 216 +- metrosp-2.0.0/metrosp/tests/testthat/test-datasets.R | 235 ++ metrosp-2.0.0/metrosp/tests/testthat/test-geo-datasets.R | 100 - metrosp-2.0.0/metrosp/tests/testthat/test-pipeline-readers.R |only metrosp-2.0.0/metrosp/tests/testthat/test-read-metro-demand.R | 468 +++++ metrosp-2.0.0/metrosp/vignettes/data-dictionary.qmd | 430 +---- metrosp-2.0.0/metrosp/vignettes/getting_started.qmd | 86 - 62 files changed, 2867 insertions(+), 2063 deletions(-)
Title: Scalable Bayesian Disease Mapping Models for High-Dimensional
Data
Description: Implements several spatial and spatio-temporal scalable disease mapping models for high-dimensional count data using the INLA technique for approximate Bayesian inference in latent Gaussian models (Orozco-Acosta et al., 2021 <doi:10.1016/j.spasta.2021.100496>; Orozco-Acosta et al., 2023 <doi:10.1016/j.cmpb.2023.107403> and Vicente et al., 2023 <doi:10.1007/s11222-023-10263-x>). The creation and develpment of this package has been supported by Project MTM2017-82553-R (AEI/FEDER, UE) and Project PID2020-113125RB-I00/MCIN/AEI/10.13039/501100011033. It has also been partially funded by the Public University of Navarra (project PJUPNA2001).
Author: Aritz Adin [aut, cre] ,
Erick Orozco-Acosta [aut] ,
Maria Dolores Ugarte [aut]
Maintainer: Aritz Adin <aritz.adin@unavarra.es>
Diff between bigDM versions 0.5.8 dated 2026-08-19 and 0.5.9 dated 2026-10-06
bigDM-0.5.8/bigDM/R/random_partition.R |only bigDM-0.5.9/bigDM/DESCRIPTION | 10 - bigDM-0.5.9/bigDM/MD5 | 53 +++++----- bigDM-0.5.9/bigDM/NAMESPACE | 6 + bigDM-0.5.9/bigDM/NEWS | 5 bigDM-0.5.9/bigDM/R/MCAR_INLA.R | 75 ++++++++++++-- bigDM-0.5.9/bigDM/R/Mmodel_bym2.R |only bigDM-0.5.9/bigDM/R/Mmodel_icar.R | 5 bigDM-0.5.9/bigDM/R/Mmodel_lcar.R | 6 - bigDM-0.5.9/bigDM/R/Mmodel_pcar.R | 4 bigDM-0.5.9/bigDM/R/bigDM-package.R | 6 - bigDM-0.5.9/bigDM/R/clustering_partition.R | 20 --- bigDM-0.5.9/bigDM/R/divide_carto.R | 16 --- bigDM-0.5.9/bigDM/R/grid_partition.R |only bigDM-0.5.9/bigDM/R/kmeans_partition.R |only bigDM-0.5.9/bigDM/R/mergeINLA.R | 24 ++-- bigDM-0.5.9/bigDM/README.md | 9 + bigDM-0.5.9/bigDM/build/partial.rdb |binary bigDM-0.5.9/bigDM/inst/CITATION | 4 bigDM-0.5.9/bigDM/man/MCAR_INLA.Rd | 4 bigDM-0.5.9/bigDM/man/Mmodel_bym2.Rd |only bigDM-0.5.9/bigDM/man/Mmodel_compute_cor.Rd | 4 bigDM-0.5.9/bigDM/man/Mmodel_icar.Rd | 6 - bigDM-0.5.9/bigDM/man/Mmodel_lcar.Rd | 7 + bigDM-0.5.9/bigDM/man/Mmodel_pcar.Rd | 5 bigDM-0.5.9/bigDM/man/bigDM-package.Rd | 6 - bigDM-0.5.9/bigDM/man/clustering_partition.Rd | 20 --- bigDM-0.5.9/bigDM/man/divide_carto.Rd | 16 --- bigDM-0.5.9/bigDM/man/grid_partition.Rd |only bigDM-0.5.9/bigDM/man/kmeans_partition.Rd |only bigDM-0.5.9/bigDM/man/random_partition.Rd | 137 ++------------------------ 31 files changed, 208 insertions(+), 240 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] ,
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 1.3.0 dated 2026-09-29 and 1.3.1 dated 2026-10-06
renv-1.3.0/renv/inst/repos/src/contrib/renv_1.3.0.tar.gz |only renv-1.3.1/renv/DESCRIPTION | 6 renv-1.3.1/renv/MD5 | 112 ++-- renv-1.3.1/renv/NEWS.md | 123 ++++ renv-1.3.1/renv/R/available-packages.R | 8 renv-1.3.1/renv/R/cache.R | 37 + renv-1.3.1/renv/R/dependencies.R | 2 renv-1.3.1/renv/R/description.R | 10 renv-1.3.1/renv/R/embed.R | 6 renv-1.3.1/renv/R/ext.R | 11 renv-1.3.1/renv/R/files.R | 7 renv-1.3.1/renv/R/graph.R | 263 ++++++++-- renv-1.3.1/renv/R/hydrate.R | 21 renv-1.3.1/renv/R/install.R | 39 - renv-1.3.1/renv/R/lockfile-validate.R | 5 renv-1.3.1/renv/R/mask.R | 34 + renv-1.3.1/renv/R/package.R | 3 renv-1.3.1/renv/R/pak.R | 120 ++++ renv-1.3.1/renv/R/progress.R | 5 renv-1.3.1/renv/R/project.R | 44 + renv-1.3.1/renv/R/restore.R | 17 renv-1.3.1/renv/R/retrieve.R | 32 + renv-1.3.1/renv/R/scope.R | 8 renv-1.3.1/renv/R/sysreqs.R | 304 ++++++++++- renv-1.3.1/renv/R/update.R | 2 renv-1.3.1/renv/R/vendor.R | 71 ++ renv-1.3.1/renv/R/zzz.R | 5 renv-1.3.1/renv/inst/config.yml | 2 renv-1.3.1/renv/inst/doc/ci.html | 28 - renv-1.3.1/renv/inst/doc/docker.Rmd | 4 renv-1.3.1/renv/inst/doc/docker.html | 14 renv-1.3.1/renv/inst/doc/rsconnect.html | 2 renv-1.3.1/renv/inst/repos/src/contrib/PACKAGES | 4 renv-1.3.1/renv/inst/repos/src/contrib/PACKAGES.gz |binary renv-1.3.1/renv/inst/repos/src/contrib/PACKAGES.rds |binary renv-1.3.1/renv/inst/repos/src/contrib/renv_1.3.1.tar.gz |only renv-1.3.1/renv/man/config.Rd | 2 renv-1.3.1/renv/man/embed.Rd | 6 renv-1.3.1/renv/man/sysreqs.Rd | 83 ++- renv-1.3.1/renv/man/vendor.Rd | 1 renv-1.3.1/renv/tests/testthat/_snaps/sysreqs.md | 2 renv-1.3.1/renv/tests/testthat/helper-git.R | 79 ++- renv-1.3.1/renv/tests/testthat/helper-vendor.R |only renv-1.3.1/renv/tests/testthat/test-available-packages.R | 19 renv-1.3.1/renv/tests/testthat/test-cache.R | 181 +++++++ renv-1.3.1/renv/tests/testthat/test-description.R | 21 renv-1.3.1/renv/tests/testthat/test-ffi.R | 27 + renv-1.3.1/renv/tests/testthat/test-graph.R | 149 +++++ renv-1.3.1/renv/tests/testthat/test-hydrate.R | 14 renv-1.3.1/renv/tests/testthat/test-install.R | 370 ++++++++++++++ renv-1.3.1/renv/tests/testthat/test-lockfile-validate.R | 19 renv-1.3.1/renv/tests/testthat/test-pak.R | 218 ++++++++ renv-1.3.1/renv/tests/testthat/test-progress.R |only renv-1.3.1/renv/tests/testthat/test-restore.R | 158 ++++++ renv-1.3.1/renv/tests/testthat/test-retrieve.R | 35 + renv-1.3.1/renv/tests/testthat/test-scope.R | 28 + renv-1.3.1/renv/tests/testthat/test-sysreqs.R | 382 ++++++++++++++- renv-1.3.1/renv/tests/testthat/test-vendor.R | 183 +++++++ renv-1.3.1/renv/vignettes/docker.Rmd | 4 59 files changed, 3068 insertions(+), 262 deletions(-)
Title: Psychometric Analysis with Rasch Measurement Theory
Description: Streamlines reproducible Rasch measurement theory analyses
for ordinal item-response data, combining estimation routines from
'eRm', 'psychotools', 'mirt', 'iarm', and 'lavaan' with consistent
diagnostic, plotting, and reporting layers. Covers the four basic
psychometric criteria summarised by Christensen et al. (2021)
<doi:10.1111/sms.13908> -- unidimensionality, local independence,
ordered response category thresholds, and invariance across
subgroups -- together with item fit, targeting, reliability,
category functioning, and descriptive item-response plots. A
distinguishing feature is the use of simulation-based critical
values to replace rule-of-thumb cutoffs for conditional infit mean-square,
item-rest-score gamma, Yen's Q3 local-dependence statistic, the largest residual-PCA eigenvalue,
ordinal CFA fit indices, and partial-gamma DIF and local-dependence
coefficients, optionally augmented with multiplicity-corrected bootstrap
p-values. Outputs are knitr::kable() tables and
' [...truncated...]
Author: Magnus Johansson [aut, cre] ,
Nicklas Korsell [ctb] ,
Mirka Henninger [ctb] ,
Jan Radek [ctb]
Maintainer: Magnus Johansson <pgmj@pm.me>
Diff between easyRasch2 versions 1.3.1 dated 2026-09-13 and 1.4.0 dated 2026-10-06
easyRasch2-1.3.1/easyRasch2/vignettes/easyRasch2.Rmd.orig |only easyRasch2-1.4.0/easyRasch2/DESCRIPTION | 8 easyRasch2-1.4.0/easyRasch2/MD5 | 104 - easyRasch2-1.4.0/easyRasch2/NAMESPACE | 2 easyRasch2-1.4.0/easyRasch2/NEWS.md | 64 + easyRasch2-1.4.0/easyRasch2/R/bootstrap_restscore.R | 17 easyRasch2-1.4.0/easyRasch2/R/cfa_cutoff.R | 30 easyRasch2-1.4.0/easyRasch2/R/conditional_infit.R | 35 easyRasch2-1.4.0/easyRasch2/R/conditional_infit_mi.R | 12 easyRasch2-1.4.0/easyRasch2/R/dif_partgam.R | 614 ++++++---- easyRasch2-1.4.0/easyRasch2/R/infit_cutoff.R | 2 easyRasch2-1.4.0/easyRasch2/R/infitcutoff_plot.R | 5 easyRasch2-1.4.0/easyRasch2/R/item_parameters.R | 7 easyRasch2-1.4.0/easyRasch2/R/item_restscore.R | 411 ++++++ easyRasch2-1.4.0/easyRasch2/R/item_restscore_cutoff.R |only easyRasch2-1.4.0/easyRasch2/R/item_restscore_plot.R |only easyRasch2-1.4.0/easyRasch2/R/ld_partgam.R | 36 easyRasch2-1.4.0/easyRasch2/R/local_dependence.R | 71 - easyRasch2-1.4.0/easyRasch2/R/locdep_q3_plot.R | 6 easyRasch2-1.4.0/easyRasch2/R/person_change.R | 84 + easyRasch2-1.4.0/easyRasch2/R/reliability.R | 4 easyRasch2-1.4.0/easyRasch2/R/residual_pca.R | 11 easyRasch2-1.4.0/easyRasch2/R/utils-multiplicity.R | 19 easyRasch2-1.4.0/easyRasch2/R/utils-theta.R | 47 easyRasch2-1.4.0/easyRasch2/R/utils-validation.R | 165 ++ easyRasch2-1.4.0/easyRasch2/R/zzz_reproducibility.R | 1 easyRasch2-1.4.0/easyRasch2/README.md | 9 easyRasch2-1.4.0/easyRasch2/inst/doc/easyRasch2.Rmd | 79 - easyRasch2-1.4.0/easyRasch2/inst/doc/easyRasch2.html | 222 ++- easyRasch2-1.4.0/easyRasch2/man/RMUreliability.Rd | 4 easyRasch2-1.4.0/easyRasch2/man/RMdifGamma.Rd | 58 easyRasch2-1.4.0/easyRasch2/man/RMdifGammaCutoff.Rd | 115 + easyRasch2-1.4.0/easyRasch2/man/RMdifGammaPlot.Rd | 14 easyRasch2-1.4.0/easyRasch2/man/RMitemInfit.Rd | 34 easyRasch2-1.4.0/easyRasch2/man/RMitemRestscore.Rd | 156 ++ easyRasch2-1.4.0/easyRasch2/man/RMitemRestscoreBoot.Rd | 17 easyRasch2-1.4.0/easyRasch2/man/RMitemRestscoreCutoff.Rd |only easyRasch2-1.4.0/easyRasch2/man/RMitemRestscorePlot.Rd |only easyRasch2-1.4.0/easyRasch2/man/RMlocdepGamma.Rd | 9 easyRasch2-1.4.0/easyRasch2/man/RMlocdepQ3Cutoff.Rd | 5 easyRasch2-1.4.0/easyRasch2/man/RMpersonChange.Rd | 84 + easyRasch2-1.4.0/easyRasch2/man/easyRasch2-package.Rd | 2 easyRasch2-1.4.0/easyRasch2/man/easyRasch2-reproducibility.Rd | 1 easyRasch2-1.4.0/easyRasch2/man/run_restscore_sim_parallel.Rd |only easyRasch2-1.4.0/easyRasch2/man/run_restscore_sim_sequential.Rd |only easyRasch2-1.4.0/easyRasch2/man/run_single_restscore_sim.Rd |only easyRasch2-1.4.0/easyRasch2/tests/testthat/test-cfa_cutoff.R | 36 easyRasch2-1.4.0/easyRasch2/tests/testthat/test-cutoff_sample_check.R |only easyRasch2-1.4.0/easyRasch2/tests/testthat/test-dif-flagging-defaults.R |only easyRasch2-1.4.0/easyRasch2/tests/testthat/test-extreme_only_categories.R |only easyRasch2-1.4.0/easyRasch2/tests/testthat/test-infit_cutoff_plot.R | 4 easyRasch2-1.4.0/easyRasch2/tests/testthat/test-item_restscore_cutoff.R |only easyRasch2-1.4.0/easyRasch2/tests/testthat/test-local_dependence.R | 45 easyRasch2-1.4.0/easyRasch2/tests/testthat/test-parallel-reproducibility.R | 28 easyRasch2-1.4.0/easyRasch2/tests/testthat/test-partgam_dif.R | 20 easyRasch2-1.4.0/easyRasch2/tests/testthat/test-reliability_curve.R | 34 easyRasch2-1.4.0/easyRasch2/vignettes/easyRasch2.Rmd | 79 - easyRasch2-1.4.0/easyRasch2/vignettes/figures/rasch-dif-cicc-1.png |binary easyRasch2-1.4.0/easyRasch2/vignettes/figures/rasch-targeting-1.png |binary 59 files changed, 2177 insertions(+), 633 deletions(-)
Title: Simplification of scRNA-Seq Data by Merging Together Similar
Cells
Description: Aggregates large single-cell data into metacell dataset by merging together gene expression of very similar cells. 'SuperCell' uses 'velocyto.R' <doi:10.1038/s41586-018-0414-6> <https://github.com/velocyto-team/velocyto.R> for RNA velocity and 'WeightedCluster' <doi:10.12682/lives.2296-1658.2013.24> <https://mephisto.unige.ch/weightedcluster/> for weighted clustering on metacells. We also recommend installing 'scater' Bioconductor package <doi:10.18129/B9.bioc.scater> <https://bioconductor.org/packages/release/bioc/html/scater.html>.
Author: Mariia Bilous [aut],
Matei Teleman [cre]
Maintainer: Matei Teleman <matei.teleman@unil.ch>
Diff between SuperCell versions 1.1 dated 2025-12-16 and 1.2 dated 2026-10-06
DESCRIPTION | 8 +-- MD5 | 6 +- inst/doc/a_SuperCell.html | 57 ++++++++++------------ tests/testthat/test_data_load_and_manipulations.R | 4 - 4 files changed, 36 insertions(+), 39 deletions(-)
Title: Spatial MIDAS Models Using INLA
Description: Provides tools for fitting spatial Mixed-Data Sampling (MIDAS) regression models using Integrated Nested Laplace Approximation (INLA) (Rue et al., 2009) <doi:10.1111/j.1467-9868.2008.00700.x>. The package is designed for settings where responses and explanatory variables are observed at different temporal frequencies and supports both constant and spatially varying regression coefficients.
Author: Stephen Jun Villejo [aut, cre],
Havard Rue [aut],
Marta Blangiardo [aut]
Maintainer: Stephen Jun Villejo <s.villejo@imperial.ac.uk>
Diff between midasINLA versions 0.1.1 dated 2026-10-01 and 0.1.2 dated 2026-10-06
DESCRIPTION | 29 +++++++-- MD5 | 20 ++++-- R/estimation_functions.R | 21 +++++++ README.md | 137 +++++++++++++++++++++++------------------------ build/vignette.rds |binary inst/doc/midasINLA.R | 45 +++++++++++++-- inst/doc/midasINLA.Rmd | 132 +++++++++++++++++++++++++++++---------------- inst/doc/midasINLA.html | 100 +++++++++++++++++++--------------- man/figures |only vignettes/figures |only vignettes/midasINLA.Rmd | 132 +++++++++++++++++++++++++++++---------------- 11 files changed, 388 insertions(+), 228 deletions(-)
Title: Composite Indicators Functions
Description: A collection of functions to calculate Composite Indicators methods, focusing, in particular, on the normalisation and weighting-aggregation steps, as described in OECD Handbook on constructing composite indicators: methodology and user guide, 2008, 'Vidoli' and 'Fusco' and 'Mazziotta' <doi:10.1007/s11205-014-0710-y>, 'Mazziotta' and 'Pareto' (2016) <doi:10.1007/s11205-015-0998-2>, 'Van Puyenbroeck and 'Rogge' <doi:10.1016/j.ejor.2016.07.038> and other authors.
Author: Francesco Vidoli [aut, cre],
Elisa Fusco [aut]
Maintainer: Francesco Vidoli <fvidoli@gmail.com>
Diff between Compind versions 3.6 dated 2026-07-10 and 3.7 dated 2026-10-06
DESCRIPTION | 8 +- MD5 | 24 +++--- NEWS | 10 ++ R/ci_bod_var_w.R | 2 R/ci_generalized_mean.R | 18 ++-- R/ci_rbod_dir.R | 5 - R/ci_rbod_mdir.R | 162 ++++++++++++++++++++++++------------------ R/plot_M_robust_ci.R | 17 +++- inst/doc/Compind_vignette.pdf |binary man/ci_generalized_mean.Rd | 4 - man/ci_ogwa.Rd | 2 man/ci_rbod_mdir.Rd | 27 ++++--- man/plot_M_robust_ci.Rd | 14 ++- 13 files changed, 182 insertions(+), 111 deletions(-)
Title: Headless Venn Diagram Analysis and Rendering
Description: Headless companion to the 'Venn Diagram Lab' web tool
(<https://www.venndiagramlab.org/>). Build, render, and statistically
analyze Venn / 'UpSet' diagrams from 'CSV' / 'TSV' / 'GMT' / 'GMX'
inputs. Provides the same 44 SVG models, intersection / 'Jaccard' /
hypergeometric statistics, and PDF report layout as the web tool,
with byte-equivalent 'TSV' exports (parity-tested against the
published Python package). Integrates with 'ggplot2', 'tidygraph',
and 'broom'.
Author: Zoltan Dul [aut, cre] ,
Marton Oelbei [aut] ,
N. Shaun B. Thomas [aut],
Azeddine Si Ammour [aut] ,
Attila Csikasz-Nagy [aut]
Maintainer: Zoltan Dul <zoltan.dul@gmail.com>
Diff between vennDiagramLab versions 2.4.2 dated 2026-06-10 and 2.9.0 dated 2026-10-06
DESCRIPTION | 18 MD5 | 69 NAMESPACE | 8 NEWS.md | 49 R/classes.R | 5 R/data-quality.R |only R/json-export.R |only R/network-export.R |only R/render-pdf.R | 4 R/statistics.R | 265 ++ R/tsv-export.R | 145 + README.md | 64 inst/extdata/samples/dataset_mock_gene_sets.csv | 196 - inst/extdata/samples/dataset_mock_streaming_platforms.csv | 1602 +++++++------- man/StatisticsResult-class.Rd | 5 man/analyze_data_quality.Rd |only man/fold_enrichment_ci.Rd |only man/one_vs_rest_enrichment.Rd |only man/to_network_graphml.Rd |only man/to_network_sif.Rd |only man/to_one_vs_rest_tsv.Rd |only man/to_result_json.Rd |only man/to_statistics_tsv.Rd | 8 man/validate_dataset.Rd |only tests/testthat/fixtures |only tests/testthat/test-data-quality.R |only tests/testthat/test-json-export.R |only tests/testthat/test-network-export.R |only tests/testthat/test-parity-json.R |only tests/testthat/test-parity-network-export.R |only tests/testthat/test-parity-one-vs-rest.R |only tests/testthat/test-parity-with-webapp.R | 54 tests/testthat/test-render-pdf.R | 11 tests/testthat/test-statistics.R | 118 + tests/testthat/test-tsv-export.R | 28 35 files changed, 1651 insertions(+), 998 deletions(-)
More information about vennDiagramLab at CRAN
Permanent link
Title: R Interface to Proximal Interior Point Quadratic Programming
Solver
Description: An embedded proximal interior point quadratic programming solver, which can solve dense and sparse quadratic programs, described in Schwan, Jiang, Kuhn, and Jones (2023) <doi:10.48550/arXiv.2304.00290>. Combining an infeasible interior point method with the proximal method of multipliers, the algorithm can handle ill-conditioned convex quadratic programming problems without the need for linear independence of the constraints. The solver is written in header only 'C++ 14' leveraging the 'Eigen' library for vectorized linear algebra. For small dense problems, vectorized instructions and cache locality can be exploited more efficiently. Allocation free problem updates and re-solves are also provided.
Author: Balasubramanian Narasimhan [aut, cre],
Roland Schwan [aut, cph],
Yuning Jiang [aut],
Daniel Kuhn [aut],
Colin N. Jones [aut]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between piqp versions 0.6.4 dated 2026-10-02 and 0.6.4.1 dated 2026-10-06
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 14 ++++++++++++++ inst/doc/piqp.html | 2 +- src/Makevars | 6 ++++++ src/r_patches/piqp.patch | 18 ++++++++++++++++++ 6 files changed, 47 insertions(+), 9 deletions(-)
Title: 'C++' Implementations of Functional Enrichment Analysis
Description: Fast implementations of functional enrichment analysis methods using 'C++' via 'Rcpp'.
Currently provides Over-Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA),
Weighted Enrichment Analysis for ORA and GSEA, Network-based Set Enrichment Analysis (NSEA),
multi-layer network-based enrichment, and multi-omics integration workflows. Additional
features include early fusion at the feature level, late fusion at the pathway level,
multi-omics contribution tracing, topology-aware explanation helpers, Bayesian term
selection, and extremely fast Random Walk with Restart (RWR) using 'RcppEigen'. The
enrichment methods build on GSEA by Subramanian et al. (2005)
<doi:10.1073/pnas.0506580102>, the multilevel strategy derived from 'fgsea'
by Korotkevich et al. (2021) <doi:10.1101/060012>, and network-based
enrichment ideas described by Glaab et al. (2012)
<doi:10.1093/bioinformatics/bts389>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between enrichit versions 0.2.5 dated 2026-09-24 and 0.2.6 dated 2026-10-06
DESCRIPTION | 6 - MD5 | 49 ++++---- NEWS.md | 34 +++++- R/converters.R | 178 ++++++++++++++++++++------------ R/gsea.R | 50 +++++++-- R/mnsea.R | 16 ++ R/nsea.R | 30 +++-- R/ora_gson.R | 10 + R/print.R | 8 - R/utilities.R | 73 ++++++++++++- README.md | 30 ++--- man/as_enrichResult.Rd | 25 ++++ man/as_gseaResult.Rd | 22 +++- man/gsea.Rd | 13 ++ man/gsea_gson.Rd | 15 ++ man/gsea_leading_edge_details.Rd |only man/mnsea.Rd | 8 + man/mnsea_gson.Rd | 8 + man/nsea.Rd | 14 +- man/nsea_gson.Rd | 14 +- man/ora_gson.Rd | 8 + src/RcppExports.cpp | 4 src/gsea.cpp | 47 ++++---- src/nsea.cpp | 2 tests/testthat/test-converters.R | 19 +++ tests/testthat/test-gsea.R | 214 +++++++++++++++++++++++++++++++++++++++ 26 files changed, 709 insertions(+), 188 deletions(-)
Title: Query and Standardize Biodiversity Occurrences in Peru
Description: Facilitates the retrieval, spatial validation, and integration
of flora and fauna occurrence records across administrative units (districts
and provinces) in Peru. Retrieves official boundary geometries via
'geoperu', queries and consolidates observations from the Global Biodiversity
Information Facility (GBIF, <https://www.gbif.org/>) and 'iNaturalist'
(<https://www.inaturalist.org/>), and standardizes attributes into a unified
Darwin Core aligned structure. Designed for biodiversity assessments and
spatial workflows within user-defined areas of interest.
Author: Paul E. Santos Andrade [aut, cre, cph]
Maintainer: Paul E. Santos Andrade <paulefrens@gmail.com>
Diff between peruocc versions 0.1.0 dated 2026-09-21 and 0.1.1 dated 2026-10-06
DESCRIPTION | 6 +- MD5 | 20 +++---- NEWS.md | 6 ++ R/config.R | 7 ++ README.md | 84 +++++++++++++----------------- inst/doc/busqueda_poligono_usuario.html | 14 ++--- inst/doc/getting_started.html | 44 +++++++-------- inst/doc/visualizacion_y_exportacion.html | 16 ++--- man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-7-2.png |binary tests/testthat/test-project-utils.R | 2 11 files changed, 102 insertions(+), 97 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of discrete response data using
unidimensional and multidimensional item analysis models under the Item
Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>).
Exploratory and confirmatory item factor analysis models
are estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier models are available for modeling item testlets using
dimension reduction EM algorithms, while multiple group analyses and
mixed effects designs are included for detecting differential item, bundle,
and test functioning, and for modeling item and person covariates.
Finally, latent class models such as the DINA, DINO, multidimensional latent class,
mixture IRT models, and zero-inflated response models are supported, as well
as a wide family of probabilistic unfolding models.
Author: Phil Chalmers [aut, cre] ,
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb],
Lennart Schneider [ctb],
David King [ctb],
Chen-Wei Liu [ctb],
Ogreden Oguzhan [ctb],
Samuel [...truncated...]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.47 dated 2026-08-20 and 1.48 dated 2026-10-06
DESCRIPTION | 6 MD5 | 48 ++--- NEWS.md | 19 ++ R/03-estimation.R | 2 R/05-model.elements.R | 8 R/DIF.R | 46 +++++ R/EMstep.group.R | 12 + R/empirical_plot.R | 269 +++++++++++++++++++++++++++++---- R/itemstats.R | 57 ++++-- R/pirt.R | 6 R/utils.R | 13 + README.md | 3 man/DIF.Rd | 44 +++++ man/empirical_plot.Rd | 103 +++++++++++- man/itemstats.Rd | 21 ++ man/pirt.Rd | 6 tests/testthat/test-01-mirtOne.R | 5 tests/testthat/test-02-mirtTwo.R | 4 tests/testthat/test-03-bfactor.R | 7 tests/testthat/test-04-multipleGroup.R | 4 tests/testthat/test-07-mixedmirt.R | 7 tests/testthat/test-10-extras.R | 7 tests/testthat/test-11-discrete.R | 2 tests/testthat/test-14-unfolding.R | 2 tests/testthat/test-16-DCIRT.R | 7 25 files changed, 586 insertions(+), 122 deletions(-)
Title: Information Matrices for 'lmeStruct' and 'glsStruct' Objects
Description: Provides analytic derivatives and information matrices for
fitted linear mixed effects (lme) models and generalized least squares (gls) models
estimated using lme() (from package 'nlme') and gls() (from package 'nlme'), respectively.
The package includes functions for estimating the sampling variance-covariance of variance
component parameters using the inverse Fisher information. The variance components include
the parameters of the random effects structure (for lme models), the variance structure,
and the correlation structure. The expected and average forms of the Fisher information matrix
are used in the calculations, and models estimated by full maximum likelihood or
restricted maximum likelihood are supported. The package also includes a function for estimating
standardized mean difference effect sizes (Pustejovsky, Hedges, and Shadish (2014) <DOI:10.3102/1076998614547577>)
based on fitted lme or gls models.
Author: James Pustejovsky [aut] ,
Man Chen [aut, cre]
Maintainer: Man Chen <manchen9005@gmail.com>
Diff between lmeInfo versions 0.3.2 dated 2023-04-17 and 0.3.3 dated 2026-10-06
DESCRIPTION | 11 - MD5 | 24 +-- NAMESPACE | 38 ++++-- NEWS.md | 5 R/build-variance-matrices.R | 6 R/derivatives.R | 94 +++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/Information-matrices-for-fitted-LME-models.R | 2 inst/doc/Information-matrices-for-fitted-LME-models.html | 10 - tests/testthat/test-equivalent-pdClasses.R | 6 tests/testthat/test-multi-model-g_mlm.R | 15 +- tests/testthat/test-variance-structures.R | 6 13 files changed, 138 insertions(+), 79 deletions(-)
Title: Manifest-Based Dependency Conflict Detection for Sandboxed and
Desktop R Sessions
Description: Lightweight, offline-first checking of R package dependencies
against the currently installed environment, without requiring a full
project lockfile. Verifies a declared manifest of package versions,
including version constraints declared by transitive dependencies,
reports session-level snapshot differences (including stale versions
still loaded in a running session), detects packages shadowed by another
library, and offers single-package version rollback. Designed for hosted
notebooks (e.g. Kaggle, Colab, Binder) where 'renv'-style lockfile
ownership is impractical, and equally usable on a normal desktop.
Author: Samruddhi Amol Shah [aut, cre],
Kartik Patel [aut],
Amrit Pal [ctb]
Maintainer: Samruddhi Amol Shah <samruddhi.bitnbyte@gmail.com>
Diff between depguard versions 0.1.0 dated 2026-09-24 and 0.2.0 dated 2026-10-06
depguard-0.1.0/depguard/man/print.depguard_snapshot.Rd |only depguard-0.2.0/depguard/DESCRIPTION | 33 depguard-0.2.0/depguard/MD5 | 67 +- depguard-0.2.0/depguard/NAMESPACE | 26 depguard-0.2.0/depguard/NEWS.md |only depguard-0.2.0/depguard/R/check.R | 400 +++++++----- depguard-0.2.0/depguard/R/depguard-package.R | 63 - depguard-0.2.0/depguard/R/env.R |only depguard-0.2.0/depguard/R/fix.R | 237 +++++-- depguard-0.2.0/depguard/R/healthcheck.R | 75 +- depguard-0.2.0/depguard/R/libs.R |only depguard-0.2.0/depguard/R/manifest.R | 238 +++++-- depguard-0.2.0/depguard/R/snapshot.R | 315 ++++++--- depguard-0.2.0/depguard/R/utils.R |only depguard-0.2.0/depguard/R/versions.R |only depguard-0.2.0/depguard/README.md | 196 +++-- depguard-0.2.0/depguard/build/vignette.rds |binary depguard-0.2.0/depguard/inst/WORDLIST | 38 - depguard-0.2.0/depguard/inst/doc/kaggle-colab-workflow.R | 27 depguard-0.2.0/depguard/inst/doc/kaggle-colab-workflow.Rmd | 261 ++++--- depguard-0.2.0/depguard/inst/doc/kaggle-colab-workflow.html | 115 ++- depguard-0.2.0/depguard/man/dep_check.Rd | 114 ++- depguard-0.2.0/depguard/man/dep_diff.Rd | 56 + depguard-0.2.0/depguard/man/dep_env.Rd |only depguard-0.2.0/depguard/man/dep_fix.Rd | 100 +-- depguard-0.2.0/depguard/man/dep_healthcheck.Rd | 68 +- depguard-0.2.0/depguard/man/dep_libraries.Rd |only depguard-0.2.0/depguard/man/dep_manifest.Rd | 85 +- depguard-0.2.0/depguard/man/dep_manifest_freeze.Rd |only depguard-0.2.0/depguard/man/dep_manifest_read.Rd | 39 - depguard-0.2.0/depguard/man/dep_snapshot.Rd | 65 + depguard-0.2.0/depguard/man/depguard-package.Rd | 106 +-- depguard-0.2.0/depguard/tests/testthat/helper-depguard.R |only depguard-0.2.0/depguard/tests/testthat/test-check.R | 243 ++++++- depguard-0.2.0/depguard/tests/testthat/test-env.R |only depguard-0.2.0/depguard/tests/testthat/test-fix.R |only depguard-0.2.0/depguard/tests/testthat/test-healthcheck.R |only depguard-0.2.0/depguard/tests/testthat/test-libs.R |only depguard-0.2.0/depguard/tests/testthat/test-manifest.R | 123 +++ depguard-0.2.0/depguard/tests/testthat/test-snapshot.R | 158 ++++ depguard-0.2.0/depguard/tests/testthat/test-versions.R |only depguard-0.2.0/depguard/vignettes/kaggle-colab-workflow.Rmd | 261 ++++--- 42 files changed, 2403 insertions(+), 1106 deletions(-)
More information about causaljudgment at CRAN
Permanent link
Title: Build 'Tidyverse'-Style Meta-Packages from Local Package Files
Description: Turns a curated set of package archives (.tar.gz, .zip) into one
meta-package in the style of the 'tidyverse', so that a group of
interdependent packages can be distributed and installed as a single
unit. The generated meta-package records the exact archive versions it
was built from and installs its components in dependency order, so that
whoever receives it does not have to work out which package to install
first.
The component archives are copied into the generated meta-package, so it
is the only artifact that has to be distributed and no directory has to be
agreed on between machines. Resolves dependencies by building a graph with
topological ordering and cycle detection, classifies them as local or
external, and detects implicit dependencies by scanning source code.
Installation needs no repository access unless a component depends on a
package that only exists in one, which suits teams working behind
institutional firewalls. Generates the complete meta-package scaffold,
including [...truncated...]
Author: Sebastian Lucas [aut, cre] ,
Richard Detomasi [ctb]
Maintainer: Sebastian Lucas <sebalucas@gmail.com>
Diff between bigbang versions 0.5.0 dated 2026-10-02 and 0.5.1 dated 2026-10-06
DESCRIPTION | 6 MD5 | 20 NEWS.md | 22 R/create_metapackage.R | 8 R/dependencies.R | 423 ++++++++++------ R/install_local_pkg.R | 10 R/scaffold.R | 2 R/templates-engine.R | 243 +++++++-- inst/doc/getting-started.html | 4 man/install_local_pkg.Rd | 11 tests/testthat/fixtures/round068-qualified-runtime.txt |only tests/testthat/test-round068-speed-and-lazy-reexports.R |only 12 files changed, 554 insertions(+), 195 deletions(-)
Title: Designing Stated Preference Experiments
Description: Contemporary software commonly used to design stated preference experiments are expensive and the code is closed source. This is a free software package with an easy to use interface to make flexible stated preference experimental designs using state-of-the-art methods. For an overview of stated choice experimental design theory, see e.g., Rose, J. M. & Bliemer, M. C. J. (2014) in Hess S. & Daly. A. <doi:10.4337/9781781003152>. The package website can be accessed at <https://spdesign.edsandorf.me>. We acknowledge funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant INSPiRE (Grant agreement ID: 793163). The package features in Mariel et al. (2025) Environmental Valuation with Discrete Choice Experiments in R. (<doi:10.1007/978-3-031-89338-4>).
Author: Erlend Dancke Sandorf [aut, cre],
Danny Campbell [aut]
Maintainer: Erlend Dancke Sandorf <erlend.dancke.sandorf@nmbu.no>
Diff between spdesign versions 0.0.6 dated 2026-07-02 and 0.0.7 dated 2026-10-06
spdesign-0.0.6/spdesign/man/define_base_x_j.Rd |only spdesign-0.0.6/spdesign/man/fits_lvl_occurrences.Rd |only spdesign-0.0.6/spdesign/man/remove_prior.Rd |only spdesign-0.0.7/spdesign/DESCRIPTION | 10 spdesign-0.0.7/spdesign/MD5 | 113 +- spdesign-0.0.7/spdesign/NAMESPACE | 2 spdesign-0.0.7/spdesign/NEWS.md | 30 spdesign-0.0.7/spdesign/R/assertions.R | 120 ++ spdesign-0.0.7/spdesign/R/block.R | 74 - spdesign-0.0.7/spdesign/R/candidate-set.R |only spdesign-0.0.7/spdesign/R/design.R | 116 +- spdesign-0.0.7/spdesign/R/efficiency-criteria.R | 3 spdesign-0.0.7/spdesign/R/evaluate.R | 24 spdesign-0.0.7/spdesign/R/exclusions-and-conditions.R | 32 spdesign-0.0.7/spdesign/R/extract.R | 10 spdesign-0.0.7/spdesign/R/federov.R | 426 ++++------ spdesign-0.0.7/spdesign/R/full-factorial.R | 46 - spdesign-0.0.7/spdesign/R/parsing.R | 79 + spdesign-0.0.7/spdesign/R/random.R | 255 +++-- spdesign-0.0.7/spdesign/R/remove.R | 8 spdesign-0.0.7/spdesign/R/rsc.R | 260 +++--- spdesign-0.0.7/spdesign/R/spdesign-package.R | 1 spdesign-0.0.7/spdesign/R/utils.R | 13 spdesign-0.0.7/spdesign/R/xj.R | 149 +-- spdesign-0.0.7/spdesign/inst/WORDLIST |only spdesign-0.0.7/spdesign/inst/doc/examples.R | 5 spdesign-0.0.7/spdesign/inst/doc/examples.html | 69 - spdesign-0.0.7/spdesign/inst/doc/syntax.Rmd | 33 spdesign-0.0.7/spdesign/inst/doc/syntax.html | 78 + spdesign-0.0.7/spdesign/man/align_x_j.Rd |only spdesign-0.0.7/spdesign/man/as_whole_word.Rd |only spdesign-0.0.7/spdesign/man/build_candidate_set.Rd |only spdesign-0.0.7/spdesign/man/combine_profiles.Rd |only spdesign-0.0.7/spdesign/man/define_profiles.Rd |only spdesign-0.0.7/spdesign/man/define_x_j.Rd | 34 spdesign-0.0.7/spdesign/man/exclude.Rd | 10 spdesign-0.0.7/spdesign/man/extract_all_names.Rd | 5 spdesign-0.0.7/spdesign/man/federov.Rd | 53 - spdesign-0.0.7/spdesign/man/full_factorial.Rd | 35 spdesign-0.0.7/spdesign/man/generate_design.Rd | 17 spdesign-0.0.7/spdesign/man/invalid_dummy_coding.Rd |only spdesign-0.0.7/spdesign/man/lvl_violation.Rd |only spdesign-0.0.7/spdesign/man/pair_param_terms.Rd |only spdesign-0.0.7/spdesign/man/random.Rd | 9 spdesign-0.0.7/spdesign/man/random_design_candidate.Rd | 27 spdesign-0.0.7/spdesign/man/rsc.Rd | 9 spdesign-0.0.7/spdesign/man/spdesign-package.Rd | 2 spdesign-0.0.7/spdesign/man/unlisted_levels.Rd |only spdesign-0.0.7/spdesign/man/utility_formula.Rd | 7 spdesign-0.0.7/spdesign/tests/testthat/test-apply-restrictions.R | 38 spdesign-0.0.7/spdesign/tests/testthat/test-assertions.R | 107 ++ spdesign-0.0.7/spdesign/tests/testthat/test-block.R |only spdesign-0.0.7/spdesign/tests/testthat/test-candidate-set.R |only spdesign-0.0.7/spdesign/tests/testthat/test-design.R |only spdesign-0.0.7/spdesign/tests/testthat/test-distributions.R | 8 spdesign-0.0.7/spdesign/tests/testthat/test-efficiency-criteria.R | 18 spdesign-0.0.7/spdesign/tests/testthat/test-extract.R | 19 spdesign-0.0.7/spdesign/tests/testthat/test-full-factorial.R | 48 - spdesign-0.0.7/spdesign/tests/testthat/test-level-occurrence.R | 33 spdesign-0.0.7/spdesign/tests/testthat/test-priors.R | 10 spdesign-0.0.7/spdesign/tests/testthat/test-random.R |only spdesign-0.0.7/spdesign/tests/testthat/test-utility.R | 62 + spdesign-0.0.7/spdesign/tests/testthat/test-utils.R | 13 spdesign-0.0.7/spdesign/tests/testthat/test-xj.R |only spdesign-0.0.7/spdesign/vignettes/examples/mnl-design-with-sq-and-names.R | 6 spdesign-0.0.7/spdesign/vignettes/examples/mnl-design-with-supplied-candidate-set.R | 5 spdesign-0.0.7/spdesign/vignettes/syntax.Rmd | 33 67 files changed, 1521 insertions(+), 1043 deletions(-)
Title: R Interface to the 'SparseDiffEngine' Sparse Differentiation
Backend
Description: Bindings for the 'SparseDiffEngine' C library, the sparse
Jacobian and Hessian differentiation backend used by 'CVXPY' for its
Disciplined Nonlinear Programming (DNLP) extension. Provides low-level
routines for building nonlinear expression graphs and evaluating sparse
derivatives, intended as a backend for higher-level modeling layers such
as 'CVXR'. This is the R analog of the 'sparsediffpy' Python
package and wraps the same C library.
Author: Balasubramanian Narasimhan [aut, cre],
Daniel Cederberg [aut, cph] ,
William Zijie Zhang [aut, cph]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between sparsediff versions 0.4.0 dated 2026-06-08 and 0.6.1 dated 2026-10-06
sparsediff-0.4.0/sparsediff/src/sparsediffengine/include/utils/matrix_BTA.h |only sparsediff-0.4.0/sparsediff/src/sparsediffengine/src/utils/matrix_BTA.c |only sparsediff-0.6.1/sparsediff/DESCRIPTION | 11 sparsediff-0.6.1/sparsediff/MD5 | 199 + sparsediff-0.6.1/sparsediff/NAMESPACE | 14 sparsediff-0.6.1/sparsediff/NEWS.md |only sparsediff-0.6.1/sparsediff/R/cpp11.R | 40 sparsediff-0.6.1/sparsediff/R/sparsediff-atoms.R | 137 + sparsediff-0.6.1/sparsediff/R/sparsediff-package.R | 42 sparsediff-0.6.1/sparsediff/R/sparsediff-problem.R | 49 sparsediff-0.6.1/sparsediff/R/version.R | 2 sparsediff-0.6.1/sparsediff/build/vignette.rds |binary sparsediff-0.6.1/sparsediff/cleanup | 10 sparsediff-0.6.1/sparsediff/inst/doc/sparsediff.html | 2 sparsediff-0.6.1/sparsediff/man/engine_version.Rd | 2 sparsediff-0.6.1/sparsediff/man/sparsediff-affine.Rd | 15 sparsediff-0.6.1/sparsediff/man/sparsediff-bivariate.Rd | 14 sparsediff-0.6.1/sparsediff/man/sparsediff-elementwise.Rd | 17 sparsediff-0.6.1/sparsediff/man/sparsediff-getters.Rd |only sparsediff-0.6.1/sparsediff/man/sparsediff-leaves.Rd | 4 sparsediff-0.6.1/sparsediff/man/sparsediff-matrix.Rd | 66 sparsediff-0.6.1/sparsediff/man/sparsediff-oracle.Rd | 47 sparsediff-0.6.1/sparsediff/man/sparsediff-package.Rd | 45 sparsediff-0.6.1/sparsediff/man/sparsediff-problem.Rd | 5 sparsediff-0.6.1/sparsediff/man/sparsediff-reduction.Rd | 5 sparsediff-0.6.1/sparsediff/src/Makevars.in | 9 sparsediff-0.6.1/sparsediff/src/cblas_compat/sparsediff_cblas.h | 5 sparsediff-0.6.1/sparsediff/src/cblas_shim.c | 11 sparsediff-0.6.1/sparsediff/src/cpp11.cpp | 81 sparsediff-0.6.1/sparsediff/src/sparsediff.cpp | 205 ++ sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/atoms/affine.h | 12 sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/atoms/non_elementwise_full_dom.h | 10 sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/subexpr.h | 29 sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/utils/Vec_macros.h | 19 sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/utils/cblas_wrapper.h | 8 sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/utils/matmul_dispatchers.h |only sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/utils/matrix.h | 15 sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/utils/mini_numpy.h | 3 sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/utils/permuted_dense.h | 183 - sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/utils/permuted_dense_linalg.h |only sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/utils/r_io.h | 12 sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/utils/stacked_pd.h |only sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/utils/stacked_pd_kron_linalg.h |only sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/utils/stacked_pd_linalg.h |only sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/utils/tracked_alloc.h | 72 sparsediff-0.6.1/sparsediff/src/sparsediffengine/include/utils/utils.h | 30 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/add.c | 2 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/broadcast.c | 4 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/convolve.c | 16 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/diag_mat.c | 5 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/diag_vec.c | 4 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/hstack.c | 23 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/index.c | 12 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/kron.c |only sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/left_matmul.c | 141 - sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/neg.c | 2 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/parameter.c | 2 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/promote.c | 2 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/reshape.c | 2 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/right_matmul.c | 8 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/scalar_mult.c | 5 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/sum.c | 42 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/trace.c | 12 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/transpose.c | 6 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/upper_tri.c | 5 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/variable.c | 2 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/vector_mult.c | 7 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/affine/vstack.c | 4 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/bivariate_full_dom/matmul.c | 49 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/bivariate_full_dom/multiply.c | 45 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/bivariate_restricted_dom/quad_over_lin.c | 10 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/bivariate_restricted_dom/rel_entr.c | 2 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/bivariate_restricted_dom/rel_entr_scalar_vector.c | 5 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/bivariate_restricted_dom/rel_entr_vector_scalar.c | 5 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/elementwise_full_dom/common.c | 13 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/elementwise_full_dom/power.c | 2 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/elementwise_restricted_dom/common.c | 2 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/other/prod.c | 2 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/other/prod_axis_one.c | 14 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/other/prod_axis_zero.c | 14 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/atoms/other/quad_form.c | 262 ++ sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/expr.c | 24 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/old-code/linear_op.c | 6 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/old-code/old_permuted_dense.c | 44 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/problem.c | 80 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/COO_matrix.c | 28 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/CSC_matrix.c | 40 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/CSR_matrix.c | 20 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/CSR_sum.c | 4 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/int_double_pair.c | 4 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/linalg_dense_sparse_matmuls.c | 21 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/linalg_sparse_matmuls.c | 111 - sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/matmul_dispatchers.c |only sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/matrix_sum.c | 4 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/mini_numpy.c | 15 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/permuted_dense.c | 999 +++------- sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/permuted_dense_linalg.c |only sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/sparse_matrix.c | 78 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/stacked_pd.c |only sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/stacked_pd_coalesce.c |only sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/stacked_pd_kron_linalg.c |only sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/stacked_pd_linalg.c |only sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/tracked_alloc.c | 1 sparsediff-0.6.1/sparsediff/src/sparsediffengine/src/utils/utils.c | 75 sparsediff-0.6.1/sparsediff/tests |only 105 files changed, 2305 insertions(+), 1410 deletions(-)
Title: Nonparametric Multiple Change Point Detection Using Wild Binary
Segmentation
Description: Implements nonparametric multiple change-point detection for
univariate sequences using Wild Binary Segmentation, as described in
Ross (2026) "Nonparametric Detection of Multiple Location-Scale Change
Points via Wild Binary Segmentation"
<doi:10.48550/arXiv.2107.01742>. The package provides Mann--Whitney,
Mood, Lepage, Cramér--von Mises, modified Baumgartner, standardised
Zhang Z_C, and standardised Anderson--Darling rank-based statistics,
together with method-specific thresholds for controlling
the probability of incorrectly detecting a change point in a homogeneous
sequence.
Author: Gordon J. Ross [aut, cre]
Maintainer: Gordon J. Ross <gordon.ross@ed.ac.uk>
Diff between npwbs versions 0.5.0 dated 2026-08-04 and 1.0 dated 2026-10-06
npwbs-0.5.0/npwbs/NEWS.md |only npwbs-1.0/npwbs/DESCRIPTION | 12 - npwbs-1.0/npwbs/MD5 | 23 +- npwbs-1.0/npwbs/R/RcppExports.R | 8 npwbs-1.0/npwbs/R/package-functions.R | 205 +++++++++++++++++------ npwbs-1.0/npwbs/R/sysdata.rda |binary npwbs-1.0/npwbs/R/zhang.R | 2 npwbs-1.0/npwbs/inst/DEVELOPMENT_STATUS |only npwbs-1.0/npwbs/man/detectChanges.Rd | 22 +- npwbs-1.0/npwbs/src/RcppExports.cpp | 24 ++ npwbs-1.0/npwbs/src/anderson_darling.cpp |only npwbs-1.0/npwbs/src/lepage.cpp | 8 npwbs-1.0/npwbs/tests/test-next-merge-contract.R |only npwbs-1.0/npwbs/tests/test-package.R | 17 + npwbs-1.0/npwbs/tests/test-sampler-regression.R |only 15 files changed, 233 insertions(+), 88 deletions(-)