Title: Watch the File System for Changes
Description: R binding for 'libfswatch', a file system monitoring library.
Watch files, or directories recursively, for changes in the
background. Log activity, or call an R function, upon every change
event.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd] ,
Enrico M. Crisostomo [cph] ,
Alan Dipert [cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between watcher versions 0.1.5 dated 2025-12-01 and 0.1.6 dated 2026-05-08
watcher-0.1.5/watcher/src/fswatch-5c443d2p.tar.gz |only watcher-0.1.6/watcher/DESCRIPTION | 19 +- watcher-0.1.6/watcher/MD5 | 86 ++++++++++-- watcher-0.1.6/watcher/NEWS.md | 4 watcher-0.1.6/watcher/README.md | 15 +- watcher-0.1.6/watcher/cleanup | 2 watcher-0.1.6/watcher/cleanup.win | 2 watcher-0.1.6/watcher/configure | 149 ++++++++++++---------- watcher-0.1.6/watcher/configure.ucrt | 25 +-- watcher-0.1.6/watcher/configure.win | 28 +--- watcher-0.1.6/watcher/man/watcher-package.Rd | 7 + watcher-0.1.6/watcher/src/Makevars.in | 19 ++ watcher-0.1.6/watcher/src/Makevars.ucrt | 19 ++ watcher-0.1.6/watcher/src/Makevars.win | 19 ++ watcher-0.1.6/watcher/src/fswatch |only watcher-0.1.6/watcher/tools |only 16 files changed, 264 insertions(+), 130 deletions(-)
Title: Shared Memory for R Objects
Description: Share R objects across processes on the same machine via a
single copy in 'POSIX' shared memory (Linux, macOS) or a 'Win32' file
mapping (Windows). Every process reads from the same physical pages
through the R Alternative Representation ('ALTREP') framework, giving
lazy, zero-copy access. Shared objects serialize compactly as their
shared memory name rather than their full contents.
Author: Charlie Gao [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between mori versions 0.1.0 dated 2026-04-21 and 0.2.0 dated 2026-05-08
DESCRIPTION | 10 MD5 | 32 - NEWS.md | 8 R/share.R | 89 ++-- README.md | 208 ++++------ man/figures/mori-diagram.svg | 100 +++-- man/map_shared.Rd | 20 - man/mori-package.Rd | 5 man/share.Rd | 57 +- man/shared_name.Rd | 11 src/altrep.c | 708 +++++++++++++++++++++--------------- src/mori.h | 18 src/shm.c | 99 +++-- tests/testthat/test-api.R | 188 ++++++++- tests/testthat/test-cow.R | 62 +++ tests/testthat/test-nested.R | 5 tests/testthat/test-serialization.R | 15 17 files changed, 1068 insertions(+), 567 deletions(-)
Title: Dyad Ratios Algorithm for Latent Variable Estimation
Description: Implements the Dyad Ratios algorithm for estimating latent
variables from time-series survey data. The algorithm estimates a
latent mood dimension (or two dimensions) from a set of issue opinion
series. Supports annual, quarterly, monthly, and daily aggregation
intervals, optional exponential smoothing, and up to two latent
dimensions. Input data can be provided as a data frame or read from
delimited text files. Based on Stimson's 'MCalc' C++ program.
See Stimson (2018) <doi:10.1177/0759106318761614> for more details.
Author: James Stimson [aut] ,
Dave Armstrong [cre, aut]
Maintainer: Dave Armstrong <davearmstrong.ps@gmail.com>
Diff between DyadRatios versions 1.4 dated 2026-04-08 and 2.0 dated 2026-05-08
DyadRatios-1.4/DyadRatios/R/aggregate.R |only DyadRatios-1.4/DyadRatios/R/boot_dr.R |only DyadRatios-1.4/DyadRatios/R/document_data.R |only DyadRatios-1.4/DyadRatios/R/dominate.R |only DyadRatios-1.4/DyadRatios/R/esmooth.R |only DyadRatios-1.4/DyadRatios/R/extract.R |only DyadRatios-1.4/DyadRatios/R/findper.R |only DyadRatios-1.4/DyadRatios/R/iscorr.R |only DyadRatios-1.4/DyadRatios/R/plot.extract.R |only DyadRatios-1.4/DyadRatios/R/print.extract.R |only DyadRatios-1.4/DyadRatios/R/residmi.R |only DyadRatios-1.4/DyadRatios/R/summary.extract.R |only DyadRatios-2.0/DyadRatios/DESCRIPTION | 41 + DyadRatios-2.0/DyadRatios/MD5 | 55 +- DyadRatios-2.0/DyadRatios/NAMESPACE | 25 - DyadRatios-2.0/DyadRatios/R/RcppExports.R |only DyadRatios-2.0/DyadRatios/R/data_document.R |only DyadRatios-2.0/DyadRatios/R/dyad_ratios.R |only DyadRatios-2.0/DyadRatios/R/dyadratios-package.R |only DyadRatios-2.0/DyadRatios/R/get_mood.R | 51 +- DyadRatios-2.0/DyadRatios/R/globals.R |only DyadRatios-2.0/DyadRatios/R/methods.R |only DyadRatios-2.0/DyadRatios/inst/doc/extract-vignette.R | 41 - DyadRatios-2.0/DyadRatios/inst/doc/extract-vignette.Rmd | 41 - DyadRatios-2.0/DyadRatios/inst/doc/extract-vignette.html | 346 ++++++++------- DyadRatios-2.0/DyadRatios/inst/examples |only DyadRatios-2.0/DyadRatios/man/boot_dr.Rd | 177 ++++--- DyadRatios-2.0/DyadRatios/man/dyadratios-package.Rd |only DyadRatios-2.0/DyadRatios/man/extract.Rd | 217 +++++---- DyadRatios-2.0/DyadRatios/man/get_mood.Rd | 34 + DyadRatios-2.0/DyadRatios/man/jennings.Rd | 2 DyadRatios-2.0/DyadRatios/man/plot.boot_dr.Rd |only DyadRatios-2.0/DyadRatios/man/plot.extract.Rd | 34 - DyadRatios-2.0/DyadRatios/man/print.extract.Rd | 27 - DyadRatios-2.0/DyadRatios/man/summary.extract.Rd | 28 - DyadRatios-2.0/DyadRatios/src |only DyadRatios-2.0/DyadRatios/tests |only DyadRatios-2.0/DyadRatios/vignettes/extract-vignette.Rmd | 41 - 38 files changed, 640 insertions(+), 520 deletions(-)
Title: Access to Global Sub-National Income Data
Description: Provides access to granular sub-national income data from the
MCC-PIK Database Of Sub-national Economic Output (DOSE). The package
downloads and processes the data from its open repository on 'Zenodo'
(<https://zenodo.org/records/20035157>). Functions are provided to
fetch data at multiple geographic levels, match coordinates to
administrative regions, and access associated geometries.
Author: Pablo Garcia Guzman [aut, cre, cph]
Maintainer: Pablo Garcia Guzman <garciagp@ebrd.com>
Diff between subincomeR versions 0.4.0 dated 2025-09-11 and 0.5.0 dated 2026-05-08
DESCRIPTION | 11 LICENSE | 4 MD5 | 34 - NAMESPACE | 38 - NEWS.md | 8 R/getDOSE.R | 270 ++++---- R/getDOSE_geom.r | 346 +++++----- R/matchDOSE.R | 332 +++++----- README.md | 134 ++-- build/vignette.rds |binary inst/WORDLIST | 65 +- inst/doc/regional-convergence.R | 316 +++++----- inst/doc/regional-convergence.html | 1169 ++++++++++++++++++------------------- man/figures/map.png |binary man/getDOSE.Rd | 106 +-- man/matchDOSE.Rd | 174 ++--- man/subincomeR-package.Rd | 2 tests/spelling.R | 6 18 files changed, 1513 insertions(+), 1502 deletions(-)
Title: Optimized Data Analysis System for AI-Based Text Processing
Description: Extracts machine-readable variables from natural language text using
AI APIs. Optimized for speed and cost efficiency through parallel processing
and direct CSV-formatted responses from language models. Supports multiple AI
providers with robust error handling and automatic retry mechanisms for
failed extractions.
Author: Gabriel Loenn [aut, cre],
Sebastian Schutte [ctb]
Maintainer: Gabriel Loenn <g.e.lonn@stv.uio.no>
Diff between rapidcodeR versions 0.1.0 dated 2026-03-10 and 0.1.1 dated 2026-05-08
DESCRIPTION | 12 +- MD5 | 12 +- NAMESPACE | 1 R/calculate_overlap.R | 186 +++++++++++++++++++++++++--------------------- R/track_progress.R | 3 man/calculate_overlap.Rd | 32 ++++--- man/rapidcodeR-package.Rd | 7 + 7 files changed, 141 insertions(+), 112 deletions(-)
Title: Scalable and Flexible Derivation of Custom-Time Bioclimatic and
Environmental Summary Variables
Description: Provides an efficient tool for creating custom-time bioclimatic and derived environmental
summary variables from user-supplied raster data for user-defined timeframes. The package overcomes
computational bottlenecks by automatically switching between an in-memory framework using the 'terra'
package to maximize speed for smaller datasets, and an on-disk tiling framework for rasters that exceed
available RAM, leveraging 'exactextractr' and 'Rfast' to process data in chunks. The core functions,
derive_bioclim() and derive_statistics(), offer a unified interface with flexibility for custom time
periods beyond standard quarters and the use of fixed temporal indices, facilitating the creation of
temporally-matched environmental variables for ecological and biogeographical modeling. Visit
the package website <https://gepinillab.github.io/fastbioclim/> to find tutorials in English and Spanish.
Author: Gonzalo E. Pinilla-Buitrago [aut, cre] ,
Luis Osorio-Olvera [aut]
Maintainer: Gonzalo E. Pinilla-Buitrago <gepinillab@gmail.com>
Diff between fastbioclim versions 0.4.1 dated 2026-03-10 and 0.4.2 dated 2026-05-08
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS.md | 4 ++++ README.md | 11 +++++++++++ inst/CITATION |only 5 files changed, 22 insertions(+), 6 deletions(-)
Title: Result Stability Checks for Empirical R Projects
Description: Lightweight helpers for checking whether empirical results remain
substantively unchanged across code revisions, platform differences,
and package updates. The package supports regression-style testing of
derived datasets, statistical model outputs, tables, and plots, helping
researchers detect unintended result drift early and distinguish material
from non-material changes in empirical workflows.
Author: Dianyi Yang [aut, cre, ctb]
Maintainer: Dianyi Yang <dianyi.yang@politics.ox.ac.uk>
Diff between resultcheck versions 0.2.0 dated 2026-05-03 and 0.2.1 dated 2026-05-08
DESCRIPTION | 8 MD5 | 18 NEWS.md | 4 R/sandbox.R | 313 ++++++++----- R/snapshot.R | 731 ++++++++++++++++++++++---------- inst/extdata/snapshot-method-defaults.R | 196 ++++---- tests/testthat/test-example-project.R | 33 + tests/testthat/test-integration.R | 27 - tests/testthat/test-sandbox.R | 31 - tests/testthat/test-snapshot.R | 263 ++++++++--- 10 files changed, 1079 insertions(+), 545 deletions(-)
Title: J&J Innovative Medicine ADaM Test Data
Description: A set of Analysis Data Model (ADaM) datasets constructed by
modifying the ADaM datasets in the 'pharmaverseadam' package to meet J&J Innovative Medicine's
standard data structure for Clinical and Statistical Programming.
Author: David Munoz Tord [aut, cre],
Nicholas Masel [aut],
Joe Kovach [aut],
Mahesh Divakaran [ctb],
J&J Innovative Medicine [cph, fnd]
Maintainer: David Munoz Tord <david.munoztord@mailbox.org>
Diff between pharmaverseadamjnj versions 0.0.4 dated 2026-05-07 and 0.0.5 dated 2026-05-08
DESCRIPTION | 9 +-- MD5 | 64 +++++++++++------------ NEWS.md | 26 --------- R/adae.R | 16 ++--- R/adaeocmq.R | 16 ++--- R/adeg.R | 3 - R/adex.R | 10 +-- R/adlb.R | 5 + R/adpc.R | 4 - R/adsl.R | 16 +---- R/advs.R | 16 ----- data/adae.rda |binary data/adaeocmq.rda |binary data/adagocmq.rda |binary data/adcm.rda |binary data/addili.rda |binary data/adeg.rda |binary data/adex.rda |binary data/adexsum.rda |binary data/adlb.rda |binary data/adpc.rda |binary data/adsl.rda |binary data/adttesaf.rda |binary data/advs.rda |binary inst/WORDLIST | 147 +++++++++++++++++++++++++----------------------------- man/adae.Rd | 16 ++--- man/adaeocmq.Rd | 16 ++--- man/adeg.Rd | 3 - man/adex.Rd | 10 +-- man/adlb.Rd | 5 + man/adpc.Rd | 4 - man/adsl.Rd | 16 +---- man/advs.Rd | 16 ----- 33 files changed, 173 insertions(+), 245 deletions(-)
More information about pharmaverseadamjnj at CRAN
Permanent link
Title: A Unified Time Series Event Detection Framework
Description: By analyzing time series, it is possible to observe significant changes in the behavior of observations that frequently characterize events. Events present themselves as anomalies, change points, or motifs. In the literature, there are several methods for detecting events. However, searching for a suitable time series method is a complex task, especially considering that the nature of events is often unknown. This work presents Harbinger, a framework for integrating and analyzing event detection methods. Harbinger contains several state-of-the-art methods described in Salles et al. (2020) <doi:10.5753/sbbd.2020.13626>.
Author: Eduardo Ogasawara [aut, ths, cre] ,
Antonio Castro [aut],
Antonio Mello [aut],
Diego Carvalho [ctb],
Eduardo Bezerra [ctb],
Ellen Paixao [aut],
Fernando Fraga [aut],
Heraldo Borges [aut],
Igor Andrade [aut],
Isabele Rocha [aut],
Janio Lima [aut],
Jan [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between harbinger versions 1.2.767 dated 2026-02-10 and 2.0.707 dated 2026-05-08
DESCRIPTION | 53 +++++++------ MD5 | 128 ++++++++++++++++++--------------- NAMESPACE | 21 +++++ R/data.R | 8 +- R/hanc_ml.R | 20 ++--- R/hanct_dtw.R | 11 +- R/hanct_kmeans.R | 13 +-- R/hanr_fbiad.R | 11 +- R/hanr_fft.R | 4 - R/hanr_fft_amoc.R | 14 +-- R/hanr_fft_amoc_cusum.R | 19 ---- R/hanr_fft_binseg.R | 15 +-- R/hanr_fft_binseg_cusum.R | 20 +---- R/hanr_fft_sma.R | 13 --- R/hanr_remd.R | 11 +- R/hanr_rtad.R | 42 ++++++---- R/har_ensemble.R | 61 ++++++--------- R/har_ensemble_fuzzy.R |only R/har_eval.R | 9 +- R/har_eval_soft.R | 10 +- R/har_plot.R | 2 R/har_plot_ensemble.R |only R/harbinger.R | 22 ++--- R/harbinger_utils.R | 151 ++++++++++++++++++++------------------- R/hcp_bocpd.R |only R/hcp_chow.R | 7 - R/hcp_garch.R | 6 + R/hcp_gft.R | 2 R/hcp_kswin.R |only R/hcp_page_hinkley.R |only R/hcp_scp.R | 29 +++++-- R/hcp_waypoint.R |only R/hdis_mp.R | 2 R/hmo_mp.R | 2 README.md | 143 ++++++++++++++++++++---------------- build/partial.rdb |binary man/detect.Rd | 4 - man/detect.har_ensemble_fuzzy.Rd |only man/examples_anomalies.Rd | 1 man/examples_changepoints.Rd | 1 man/examples_harbinger.Rd | 1 man/examples_motifs.Rd | 1 man/hanct_dtw.Rd | 11 +- man/hanct_kmeans.Rd | 13 +-- man/hanr_fbiad.Rd | 9 +- man/hanr_fft.Rd | 4 - man/hanr_fft_amoc.Rd | 14 +-- man/hanr_fft_amoc_cusum.Rd | 19 ---- man/hanr_fft_binseg.Rd | 15 +-- man/hanr_fft_binseg_cusum.Rd | 20 +---- man/hanr_fft_sma.Rd | 13 --- man/hanr_remd.Rd | 11 +- man/hanr_rtad.Rd | 20 +++-- man/har_ensemble.Rd | 3 man/har_ensemble_fuzzy.Rd |only man/har_ensemble_plot.Rd |only man/har_ensemble_plot_models.Rd |only man/har_eval.Rd | 7 - man/har_eval_soft.Rd | 4 - man/har_plot.Rd | 2 man/harbinger.Rd | 4 - man/hcp_binseg.Rd | 2 man/hcp_bocpd.Rd |only man/hcp_chow.Rd | 5 - man/hcp_garch.Rd | 6 + man/hcp_kswin.Rd |only man/hcp_page_hinkley.Rd |only man/hcp_scp.Rd | 16 +++- man/hcp_waypoint.Rd |only man/hdis_mp.Rd | 2 man/hmo_mp.Rd | 2 tests |only 72 files changed, 533 insertions(+), 526 deletions(-)
Title: Univariate and Multivariate Model-Based Clustering in
Group-Specific Functional Subspaces
Description: The funHDDC algorithm allows to cluster functional univariate (Bouveyron and Jacques, 2011, <doi:10.1007/s11634-011-0095-6>) or multivariate data (Schmutz et al., 2018) by modeling each group within a specific functional subspace.
Author: A Schmutz [aut],
J. Jacques & C. Bouveyron [aut],
Julien Jacques [cre]
Maintainer: Julien Jacques <julien.jacques@univ-lyon2.fr>
This is a re-admission after prior archival of version 2.3.1 dated 2021-03-17
Diff between funHDDC versions 2.3.1 dated 2021-03-17 and 2.3.1.1 dated 2026-05-08
DESCRIPTION | 24 MD5 | 22 R/funHDDC.R | 20 R/mfpca.R | 12 R/predict.funHDDC.R | 2 build/vignette.rds |binary inst/doc/funHDDC.R | 110 ++-- inst/doc/funHDDC.html | 1230 ++++++++++++++++++++++++++++++++----------------- man/funHDDC.Rd | 121 ++-- man/plot.fd.Rd | 8 man/predict.funHDDC.Rd | 99 +-- man/slopeHeuristic.Rd | 78 +-- 12 files changed, 1066 insertions(+), 660 deletions(-)
Title: Methods for ''A Fast Alternative for the R x C Ecological
Inference Case''
Description: Estimates the probability matrix for the R×C Ecological Inference problem using the Expectation-Maximization Algorithm with four approximation methods for the E-Step, and an exact method as well. It also provides a bootstrap function to estimate the standard deviation of the estimated probabilities. In addition, it has functions that aggregate rows optimally to have more reliable estimates in cases of having few data points. For comparing the probability estimates of two groups, a Wald test routine is implemented. The library has data from the first round of the Chilean Presidential Election 2021 and can also generate synthetic election data. Methods described in Thraves, Charles; Ubilla, Pablo; Hermosilla, Daniel (2024) ''A Fast Ecological Inference Algorithm for the R×C case'' <doi:10.2139/ssrn.4832834>.
Author: Charles Thraves [aut] ,
Pablo Ubilla [aut] ,
Daniel Hermosilla [aut, cre]
Maintainer: Daniel Hermosilla <daniel.hermosilla.r@ug.uchile.cl>
Diff between fastei versions 0.0.0.12 dated 2026-01-09 and 0.0.16 dated 2026-05-08
DESCRIPTION | 12 MD5 | 98 ++++--- NAMESPACE | 4 R/RcppExports.R | 8 R/data-utils.R | 5 R/eim-S3.R |only R/eim-class.R | 415 +++++--------------------------- R/fastei-package.R | 6 R/instancer.R | 2 R/internal.R | 555 +++++++++++++++++++++++++++++++++++++++++++- README.md | 11 inst/doc/demonstration.Rmd | 2 inst/doc/demonstration.html | 127 ++++------ man/eim.Rd | 3 man/fastei-package.Rd | 9 man/get_agg_opt.Rd | 6 man/get_agg_proxy.Rd | 2 man/get_eim_chile.Rd | 4 man/plot.eim.Rd |only man/run_em.Rd | 27 +- man/simulate_election.Rd | 3 src/LP.c | 296 +++++++++++++++++++++-- src/LP.h | 7 src/MCMC.c | 8 src/MCMC.h | 3 src/RcppExports.cpp | 33 ++ src/bootstrap.c | 1 src/exact.c | 8 src/exact.h | 1 src/globals.h | 7 src/main.c | 47 +++ src/main.h | 13 + src/main_symmetric.c |only src/main_symmetric.h |only src/multinomial.c | 8 src/multinomial.h | 3 src/multivariate-cdf.c | 8 src/multivariate-cdf.h | 1 src/multivariate-pdf.c | 66 +++-- src/multivariate-pdf.h | 1 src/utils_matrix.c | 38 +-- src/utils_matrix.h | 16 + src/wrapper.cpp | 171 ++++++++++--- src/wrapper.h | 13 - tests |only vignettes/demonstration.Rmd | 2 46 files changed, 1442 insertions(+), 608 deletions(-)
More information about contagionchannels at CRAN
Permanent link
Title: Bayesian "Now-Cast" Estimation of Event Probabilities in
Multi-Party Democracies
Description: An implementation of a Bayesian framework for the opinion poll
based estimation of event probabilities in multi-party electoral systems
(Bender and Bauer (2018) <doi:10.21105/joss.00606>).
Author: Andreas Bender [aut, cre] ,
Alexander Bauer [aut] ,
Rebekka Schade [ctb]
Maintainer: Andreas Bender <bender.at.R@gmail.com>
This is a re-admission after prior archival of version 0.6.24 dated 2022-08-17
Diff between coalitions versions 0.6.24 dated 2022-08-17 and 0.6.27 dated 2026-05-08
coalitions-0.6.24/coalitions/man/pool_austria.Rd |only coalitions-0.6.24/coalitions/man/scrape_austria.Rd |only coalitions-0.6.27/coalitions/DESCRIPTION | 21 - coalitions-0.6.27/coalitions/MD5 | 116 +++--- coalitions-0.6.27/coalitions/NAMESPACE | 12 coalitions-0.6.27/coalitions/NEWS.md | 26 + coalitions-0.6.27/coalitions/R/DHondt.R | 28 + coalitions-0.6.27/coalitions/R/coalition-probability.R | 36 +- coalitions-0.6.27/coalitions/R/entry-probabilities.R | 2 coalitions-0.6.27/coalitions/R/hare_niemeyer.R | 2 coalitions-0.6.27/coalitions/R/plot_survey.R | 1 coalitions-0.6.27/coalitions/R/pooling.R | 34 - coalitions-0.6.27/coalitions/R/prettify.R | 2 coalitions-0.6.27/coalitions/R/saint-lague-scheppers.R | 25 + coalitions-0.6.27/coalitions/R/scrapers.R | 175 +++------- coalitions-0.6.27/coalitions/R/seat-distribution.R | 10 coalitions-0.6.27/coalitions/R/survey-helpers.R | 19 - coalitions-0.6.27/coalitions/R/sysdata.rda |binary coalitions-0.6.27/coalitions/R/utils-pipe.R | 1 coalitions-0.6.27/coalitions/README.md | 22 - coalitions-0.6.27/coalitions/data/party_colors_de.rda |binary coalitions-0.6.27/coalitions/data/party_labels_de.rda |binary coalitions-0.6.27/coalitions/data/surveys_sample.rda |binary coalitions-0.6.27/coalitions/inst/CITATION | 51 +- coalitions-0.6.27/coalitions/man/as_survey.Rd | 3 coalitions-0.6.27/coalitions/man/calculate_prob.Rd | 5 coalitions-0.6.27/coalitions/man/calculate_probs.Rd | 4 coalitions-0.6.27/coalitions/man/collapse_parties.Rd | 5 coalitions-0.6.27/coalitions/man/dHondt.Rd | 10 coalitions-0.6.27/coalitions/man/effective_samplesize.Rd | 4 coalitions-0.6.27/coalitions/man/extract_num.Rd | 3 coalitions-0.6.27/coalitions/man/filter_superior.Rd | 4 coalitions-0.6.27/coalitions/man/get_eligible.Rd | 4 coalitions-0.6.27/coalitions/man/get_entryprobability.Rd | 2 coalitions-0.6.27/coalitions/man/get_meta.Rd | 4 coalitions-0.6.27/coalitions/man/get_n.Rd | 4 coalitions-0.6.27/coalitions/man/get_pooled.Rd | 5 coalitions-0.6.27/coalitions/man/get_probabilities.Rd | 7 coalitions-0.6.27/coalitions/man/get_seats.Rd | 2 coalitions-0.6.27/coalitions/man/get_superior.Rd | 8 coalitions-0.6.27/coalitions/man/get_surveys.Rd | 9 coalitions-0.6.27/coalitions/man/gg_survey.Rd | 3 coalitions-0.6.27/coalitions/man/hare_niemeyer.Rd | 2 coalitions-0.6.27/coalitions/man/has_majority.Rd | 4 coalitions-0.6.27/coalitions/man/have_majority.Rd | 6 coalitions-0.6.27/coalitions/man/paste_coalitions.Rd | 4 coalitions-0.6.27/coalitions/man/pipe.Rd | 3 coalitions-0.6.27/coalitions/man/pool_surveys.Rd | 6 coalitions-0.6.27/coalitions/man/prettify.Rd | 4 coalitions-0.6.27/coalitions/man/redistribute.Rd | 6 coalitions-0.6.27/coalitions/man/sanitize_colnames.Rd | 4 coalitions-0.6.27/coalitions/man/sanitize_strings.Rd | 4 coalitions-0.6.27/coalitions/man/scrape.Rd | 21 - coalitions-0.6.27/coalitions/man/sls.Rd | 9 coalitions-0.6.27/coalitions/man/try_readHTML.Rd | 3 coalitions-0.6.27/coalitions/tests/testthat/test-basic-functions.R | 19 - coalitions-0.6.27/coalitions/tests/testthat/test-pooling.R | 16 coalitions-0.6.27/coalitions/tests/testthat/test-scrapers.R | 69 +-- coalitions-0.6.27/coalitions/tests/testthat/test-survey-helpers.R | 8 coalitions-0.6.27/coalitions/tests/testthat/test-workflow.R | 4 60 files changed, 478 insertions(+), 383 deletions(-)
Title: Logistic Biplot Estimation Using Machine Learning Algorithms
Description: Implements methods for fitting logistic biplot models to
multivariate binary data. The logistic biplot represents individuals
as points and binary variables as directed vectors in a low-dimensional
subspace; the orthogonal projection of each individual onto a variable
vector approximates the expected probability that the corresponding
characteristic is present. Available fitting methods include conjugate
gradient algorithms, a coordinate descent Majorization-Minimization
(MM) algorithm, and a block coordinate descent algorithm based on data
projection that supports matrices with missing values and allows new
individuals to be projected as supplementary rows without refitting
the model. A cross-validation procedure is provided to select the
number of latent dimensions k.
References: Babativa-Marquez and Vicente-Villardon (2021)
<doi:10.3390/math9162015>;
Vicente-Villardon and Galindo (2006, ISBN:9780470973196).
Author: Jose Giovany Babativa-Marquez [cre, aut]
Maintainer: Jose Giovany Babativa-Marquez <jgbabativam@unal.edu.co>
This is a re-admission after prior archival of version 1.1.0 dated 2022-04-22
Diff between BiplotML versions 1.1.0 dated 2022-04-22 and 1.1.1 dated 2026-05-08
BiplotML-1.1.0/BiplotML/R/bootBLB.R |only BiplotML-1.1.0/BiplotML/README.md |only BiplotML-1.1.0/BiplotML/man/bootBLB.Rd |only BiplotML-1.1.1/BiplotML/DESCRIPTION | 43 + BiplotML-1.1.1/BiplotML/MD5 | 58 +- BiplotML-1.1.1/BiplotML/NAMESPACE | 45 - BiplotML-1.1.1/BiplotML/NEWS.md |only BiplotML-1.1.1/BiplotML/R/BinaryFunctions.R | 480 ++++++++++--------- BiplotML-1.1.1/BiplotML/R/LogBip.R | 300 +++++++----- BiplotML-1.1.1/BiplotML/R/Methylation.R | 35 - BiplotML-1.1.1/BiplotML/R/SVD_MM.R | 159 +++--- BiplotML-1.1.1/BiplotML/R/cv_LogBip.R | 259 ++++++---- BiplotML-1.1.1/BiplotML/R/fitted_LB.R | 43 - BiplotML-1.1.1/BiplotML/R/gradientDesc.R | 220 ++++---- BiplotML-1.1.1/BiplotML/R/performanceBLB.R | 219 ++++---- BiplotML-1.1.1/BiplotML/R/plotBLB.R | 637 +++++++++++++++++--------- BiplotML-1.1.1/BiplotML/R/predict_LB.R | 188 ++++--- BiplotML-1.1.1/BiplotML/R/proj_LogBip.R | 171 ++++-- BiplotML-1.1.1/BiplotML/R/simBin.R | 125 ++--- BiplotML-1.1.1/BiplotML/R/zzz.R |only BiplotML-1.1.1/BiplotML/build |only BiplotML-1.1.1/BiplotML/inst/CITATION | 30 - BiplotML-1.1.1/BiplotML/man/LogBip.Rd | 142 +++-- BiplotML-1.1.1/BiplotML/man/Methylation.Rd | 28 - BiplotML-1.1.1/BiplotML/man/cv_LogBip.Rd | 51 +- BiplotML-1.1.1/BiplotML/man/fitted_LB.Rd | 24 BiplotML-1.1.1/BiplotML/man/gradientDesc.Rd | 59 +- BiplotML-1.1.1/BiplotML/man/performanceBLB.Rd | 64 +- BiplotML-1.1.1/BiplotML/man/plotBLB.Rd | 130 +++-- BiplotML-1.1.1/BiplotML/man/pred_LB.Rd | 38 + BiplotML-1.1.1/BiplotML/man/proj_LogBip.Rd | 63 +- BiplotML-1.1.1/BiplotML/man/sdv_MM.Rd | 48 + BiplotML-1.1.1/BiplotML/man/simBin.Rd | 39 - 33 files changed, 2214 insertions(+), 1484 deletions(-)
Title: Landscape Meteorology Tools
Description: Functions to estimate weather variables at any position of a landscape [De Caceres et al. (2018) <doi:10.1016/j.envsoft.2018.08.003>].
Author: Miquel De Caceres [aut, cre] ,
Victor Granda [aut] ,
Nicolas Martin [aut] ,
Antoine Cabon [aut]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between meteoland versions 2.2.6 dated 2026-02-18 and 2.2.7 dated 2026-05-08
DESCRIPTION | 10 - MD5 | 30 ++-- NEWS.md | 3 R/RcppExports.R | 15 -- R/tidy_interpolation_cross_validation.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/reshaping-meteo.html | 206 ++++++++++++++++---------------- inst/doc/tidy-meteoland.html | 204 ++++++++++++++++--------------- inst/include/meteoland/pet_c.hpp | 1 inst/include/meteoland/radiation_c.hpp | 1 inst/include/meteoland/utils_c.hpp | 2 man/interpolator_calibration.Rd | 5 src/radiation.cpp | 7 - src/temperature.cpp | 3 src/utils.cpp | 5 16 files changed, 244 insertions(+), 250 deletions(-)
Title: A Basic Set of Functions for Compositional Data Analysis
Description: A minimum set of functions to perform compositional data analysis
using the log-ratio approach introduced by John Aitchison (1982). Main functions
have been implemented in c++ for better performance.
Author: Marc Comas-Cufi [aut, cre]
Maintainer: Marc Comas-Cufi <mcomas@imae.udg.edu>
Diff between coda.base versions 1.0.5 dated 2026-03-04 and 1.0.6 dated 2026-05-08
coda.base-1.0.5/coda.base/data/statistitian_time.RData |only coda.base-1.0.5/coda.base/man/statistitian_time.Rd |only coda.base-1.0.5/coda.base/man/zero_na_conditional_obasis.Rd |only coda.base-1.0.6/coda.base/DESCRIPTION | 7 coda.base-1.0.6/coda.base/MD5 | 61 + coda.base-1.0.6/coda.base/NAMESPACE | 10 coda.base-1.0.6/coda.base/R/RcppExports.R | 12 coda.base-1.0.6/coda.base/R/basis.R | 8 coda.base-1.0.6/coda.base/R/compositional_ops.R |only coda.base-1.0.6/coda.base/R/data.R | 6 coda.base-1.0.6/coda.base/R/tabu_search.R |only coda.base-1.0.6/coda.base/R/utils.R | 385 +++++++-- coda.base-1.0.6/coda.base/R/zero_replacement_imputation.R | 395 ++-------- coda.base-1.0.6/coda.base/build/partial.rdb |only coda.base-1.0.6/coda.base/data/statistician_time.RData |only coda.base-1.0.6/coda.base/inst/doc/coordinates.html | 6 coda.base-1.0.6/coda.base/inst/doc/features.html | 22 coda.base-1.0.6/coda.base/inst/doc/principal_balances.html | 25 coda.base-1.0.6/coda.base/man/closure.Rd |only coda.base-1.0.6/coda.base/man/coda_replacement.Rd | 27 coda.base-1.0.6/coda.base/man/conditional_obasis.Rd | 68 + coda.base-1.0.6/coda.base/man/dist.Rd | 6 coda.base-1.0.6/coda.base/man/dist_coda.Rd |only coda.base-1.0.6/coda.base/man/partial_pb_constrained.Rd |only coda.base-1.0.6/coda.base/man/partial_pb_exact.Rd |only coda.base-1.0.6/coda.base/man/partial_pb_tabu_search.Rd |only coda.base-1.0.6/coda.base/man/pb_basis.Rd | 3 coda.base-1.0.6/coda.base/man/pb_tabu_search.Rd |only coda.base-1.0.6/coda.base/man/perturbation.Rd |only coda.base-1.0.6/coda.base/man/powering.Rd |only coda.base-1.0.6/coda.base/man/random_composition_with_fixed_pb.Rd |only coda.base-1.0.6/coda.base/man/statistician_time.Rd |only coda.base-1.0.6/coda.base/src/RcppExports.cpp | 52 + coda.base-1.0.6/coda.base/src/balance_incremental.h |only coda.base-1.0.6/coda.base/src/coda_replacement.cpp | 2 coda.base-1.0.6/coda.base/src/partial_pb_exact.cpp |only coda.base-1.0.6/coda.base/src/principal_balances_incremental.cpp |only coda.base-1.0.6/coda.base/src/tabu_search.cpp |only coda.base-1.0.6/coda.base/src/tabu_search_neighbouhood.cpp |only coda.base-1.0.6/coda.base/tests |only 40 files changed, 648 insertions(+), 447 deletions(-)
Title: Calculate Confidence Intervals
Description: This calculates a variety of different CIs for proportions
and difference of proportions that are commonly used in the
pharmaceutical industry including Wald, Wilson, Clopper-Pearson,
Agresti-Coull and Jeffreys for proportions. And Miettinen-Nurminen
(1985) <doi:10.1002/sim.4780040211>, Wald, Haldane, and Mee
<https://www.lexjansen.com/wuss/2016/127_Final_Paper_PDF.pdf> for
difference in proportions.
Author: Christina Fillmore [aut, cre] ,
GlaxoSmithKline Research & Development Limited [cph, fnd],
Mike Sprys [aut],
Dan Lythgoe [aut]
Maintainer: Christina Fillmore <christina.e.fillmore@gsk.com>
Diff between cicalc versions 0.2.0 dated 2026-01-07 and 0.2.1 dated 2026-05-08
DESCRIPTION | 9 ++- MD5 | 12 ++--- NEWS.md | 3 + R/prop_ci.R | 4 - R/prop_ci_mn.R | 61 ++++++++++++++++---------- man/ci_prop_clopper_pearson.Rd | 4 - tests/testthat/test-prop_ci_mn.R | 89 ++++++++++++++++++++++++++++++++++++++- 7 files changed, 142 insertions(+), 40 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb],
Zoe Clarke [ctb]
Maintainer: Samuel Marsh <sccustomize@gmail.com>
Diff between scCustomize versions 3.2.4 dated 2025-12-11 and 3.3.0 dated 2026-05-08
scCustomize-3.2.4/scCustomize/R/QC_Utilities_Seurat.R |only scCustomize-3.3.0/scCustomize/DESCRIPTION | 14 scCustomize-3.3.0/scCustomize/MD5 | 101 - scCustomize-3.3.0/scCustomize/NAMESPACE | 2 scCustomize-3.3.0/scCustomize/NEWS.md | 28 scCustomize-3.3.0/scCustomize/R/Internal_Utilities.R | 4 scCustomize-3.3.0/scCustomize/R/LIGER_Utilities.R | 3 scCustomize-3.3.0/scCustomize/R/Plotting_QC_Seq_10X.R | 671 ++++++---- scCustomize-3.3.0/scCustomize/R/Plotting_QC_Seurat.R | 357 ++++- scCustomize-3.3.0/scCustomize/R/Plotting_Seurat.R | 458 ++++++ scCustomize-3.3.0/scCustomize/R/Plotting_Statistics.R | 92 + scCustomize-3.3.0/scCustomize/R/Plotting_Utilities_Internal.R | 60 scCustomize-3.3.0/scCustomize/R/Read_Write_Data.R | 424 ++++++ scCustomize-3.3.0/scCustomize/R/Utilities.R | 2 scCustomize-3.3.0/scCustomize/R/Utilities_Objects.R | 19 scCustomize-3.3.0/scCustomize/R/Utilities_QC_Seurat.R |only scCustomize-3.3.0/scCustomize/man/Add_CellBender_Diff.Rd | 2 scCustomize-3.3.0/scCustomize/man/Add_Cell_Complexity.Rd | 2 scCustomize-3.3.0/scCustomize/man/Add_Cell_QC_Metrics.Rd | 13 scCustomize-3.3.0/scCustomize/man/Add_Hemo.Rd | 2 scCustomize-3.3.0/scCustomize/man/Add_MALAT1_Threshold.Rd | 6 scCustomize-3.3.0/scCustomize/man/Add_Mito_Ribo.Rd | 2 scCustomize-3.3.0/scCustomize/man/Add_Top_Gene_Pct.Rd | 2 scCustomize-3.3.0/scCustomize/man/ElbowPlot_scCustom.Rd | 14 scCustomize-3.3.0/scCustomize/man/Extract_Sample_Meta.Rd | 8 scCustomize-3.3.0/scCustomize/man/Plot_Cells_per_Sample.Rd | 22 scCustomize-3.3.0/scCustomize/man/QC_Histogram.Rd | 8 scCustomize-3.3.0/scCustomize/man/QC_Plot_GenevsFeature.Rd | 8 scCustomize-3.3.0/scCustomize/man/QC_Plot_UMIvsFeature.Rd | 8 scCustomize-3.3.0/scCustomize/man/QC_Plot_UMIvsGene.Rd | 8 scCustomize-3.3.0/scCustomize/man/QC_Plots_Combined_Vln.Rd | 8 scCustomize-3.3.0/scCustomize/man/QC_Plots_Complexity.Rd | 8 scCustomize-3.3.0/scCustomize/man/QC_Plots_Feature.Rd | 8 scCustomize-3.3.0/scCustomize/man/QC_Plots_Genes.Rd | 8 scCustomize-3.3.0/scCustomize/man/QC_Plots_Mito.Rd | 8 scCustomize-3.3.0/scCustomize/man/QC_Plots_UMIs.Rd | 8 scCustomize-3.3.0/scCustomize/man/Read_Velocity.Rd |only scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_Alignment_Combined.Rd | 9 scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_Antisense.Rd | 9 scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_Basic_Combined.Rd | 9 scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_Exonic.Rd | 9 scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_Genes.Rd | 9 scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_Genome.Rd | 9 scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_Intergenic.Rd | 9 scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_Intronic.Rd | 9 scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_Number_Cells.Rd | 9 scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_Reads_in_Cells.Rd | 9 scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_Reads_per_Cell.Rd | 9 scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_Saturation.Rd | 9 scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_Total_Genes.Rd | 9 scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_Transcriptome.Rd | 9 scCustomize-3.3.0/scCustomize/man/Seq_QC_Plot_UMIs.Rd | 9 scCustomize-3.3.0/scCustomize/man/exAM_Scoring.Rd | 6 53 files changed, 1987 insertions(+), 542 deletions(-)
Title: Lagrangian Multiplier Smoothing Splines for Smooth Function
Estimation
Description: Implements Lagrangian multiplier smoothing splines for flexible
nonparametric regression and function estimation. Provides tools for fitting,
prediction, and inference using a constrained optimization approach to
enforce smoothness. Supports generalized linear models, Weibull accelerated
failure time (AFT) models, Cox proportional hazards models,
quadratic programming constraints, and customizable working-correlation
structures, with options for parallel fitting. The core spline construction
builds on Ezhov et al. (2018) <doi:10.1515/jag-2017-0029>.
Quadratic-programming and SQP details follow Goldfarb & Idnani (1983)
<doi:10.1007/BF02591962> and Nocedal & Wright (2006)
<doi:10.1007/978-0-387-40065-5>. For smoothing spline and penalized spline
background, see Wahba (1990) <doi:10.1137/1.9781611970128> and Wood (2017)
<doi:10.1201/9781315370279>. For variance-component and correlation-parameter
estimation, see Searle et al. (2006) <ISBN:978-04700 [...truncated...]
Author: Matthew Davis [aut, cre]
Maintainer: Matthew Davis <matthewlouisdavis@gmail.com>
Diff between lgspline versions 1.0.2 dated 2026-04-13 and 1.1.0 dated 2026-05-08
DESCRIPTION | 22 MD5 | 172 NEWS.md | 13 R/HelperFunctions.R | 1142 +- R/RcppExports.R | 6 R/blockfit_solve.R | 4782 ++++---- R/get_B.R | 7965 +++++++------- R/globals.R |only R/lgspline-details.R | 3802 +++--- R/lgspline.R | 853 - R/methods.R | 7726 ++++++------- R/prior_loglik.R | 103 R/process_qp.R | 711 + R/solver_utils.R | 647 + R/tune_Lambda.R | 1305 +- R/weibull_helpers.R | 2138 +-- inst/WORDLIST | 8 man/Details.Rd | 562 man/armaInv.Rd | 2 man/blockfit_solve.Rd | 37 man/compute_Lambda.Rd | 32 man/compute_dG_u_dlambda_xy.Rd | 3 man/compute_trace_H.Rd | 9 man/dot-active_set_refine.Rd | 7 man/dot-active_set_refine_full.Rd |only man/dot-active_set_refine_woodbury.Rd |only man/dot-bf_case_gauss_gee.Rd | 42 man/dot-bf_case_gauss_no_corr.Rd | 2 man/dot-bf_case_glm_gee.Rd | 7 man/dot-bf_case_glm_no_corr.Rd | 1 man/dot-bf_inner_weighted.Rd | 1 man/dot-bf_lagrangian_project.Rd | 4 man/dot-bf_split_components.Rd | 3 man/dot-build_deriv_qp.Rd | 15 man/dot-build_tuning_env.Rd | 2 man/dot-check_kkt_full.Rd |only man/dot-check_kkt_partitionwise.Rd | 3 man/dot-check_kkt_partitionwise_woodbury.Rd |only man/dot-compute_gcvu_gradient.Rd | 13 man/dot-constraint_col_scales.Rd |only man/dot-damped_bfgs.Rd | 9 man/dot-detect_qp_global.Rd | 7 man/dot-fit_coefficients.Rd | 4 man/dot-get_B_gaussian_nocorr.Rd | 2 man/dot-get_B_gee_gaussian.Rd | 8 man/dot-get_B_gee_glm.Rd | 2 man/dot-get_B_gee_glm_woodbury.Rd | 23 man/dot-get_B_gee_woodbury.Rd | 13 man/dot-get_B_glm_nocorr.Rd | 4 man/dot-lagrangian_project.Rd | 7 man/dot-lagrangian_project_full.Rd |only man/dot-lagrangian_project_woodbury.Rd | 18 man/dot-solver_active_set.Rd |only man/dot-solver_build_active_qp_info.Rd |only man/dot-solver_build_augmented_constraints.Rd |only man/dot-solver_build_constraint_rhs.Rd |only man/dot-solver_check_primal_feasibility.Rd |only man/dot-solver_detect_qp_global.Rd | 9 man/dot-solver_recover_active_multipliers.Rd |only man/dot-solver_resolve_active_set.Rd |only man/dot-solver_stabilize_working_weights.Rd |only man/dot-try_woodbury_active_set.Rd |only man/dot-tune_grid_search.Rd | 2 man/dot-woodbury_decompose_V.Rd | 9 man/dot-woodbury_halfsqrt_components.Rd | 25 man/dot-woodbury_redecompose_weighted.Rd | 8 man/dot-woodbury_transform_constraint_matrix.Rd |only man/dot-woodbury_transform_constraint_matrix_transpose.Rd |only man/generate_posterior.Rd | 4 man/get_B.Rd | 14 man/get_B_verification_examples.Rd | 6 man/gramMatrix.Rd | 4 man/lgspline-package.Rd | 2 man/lgspline.Rd | 438 man/lgspline.fit.Rd | 337 man/logLik.lgspline.Rd | 24 man/make_constraint_matrix.Rd | 10 man/prior_loglik.Rd | 20 man/process_qp.Rd | 88 man/softplus.Rd | 4 man/std.Rd | 8 man/tune_Lambda.Rd | 137 src/cpp_functions.cpp | 27 tests/testthat/test-advanced.R | 120 tests/testthat/test-cox.R | 304 tests/testthat/test-fitting.R | 60 tests/testthat/test-glm-sqp.R | 247 tests/testthat/test-methods.R | 84 tests/testthat/test-negbin.R | 512 tests/testthat/test-parallel-qr.R |only tests/testthat/test-parallel.R | 41 tests/testthat/test-plotting.R | 12 tests/testthat/test-predictions.R | 17 tests/testthat/test-tuning-criterion.R | 1199 +- tests/testthat/test-utilities.R | 20 tests/testthat/test_correlation_structure.R | 396 tests/testthat/test_qp_observations_list.R |only 97 files changed, 20316 insertions(+), 16109 deletions(-)
Title: Event Classification, Visualization and Analysis of Eye Tracking
Data
Description: Functions for analysing eye tracking data, including event detection, visualizations and area of interest (AOI) based analyses.
The package includes implementations of the IV-T, I-DT, adaptive velocity threshold, and Identification by two means clustering (I2MC) algorithms.
See separate documentation for each function. The principles underlying I-VT and I-DT algorithms are described in Salvucci & Goldberg (2000) <doi:10.1145/355017.355028>.
Two-means clustering is described in Hessels et al. (2017), <doi: 10.3758/s13428-016-0822-1>.
The adaptive velocity threshold algorithm is described in Nyström & Holmqvist (2010),<doi:10.3758/BRM.42.1.188>.
A documentation of the 'kollaR' can be found in Kleberg et al (2026) <doi:10.3758/s13428-025-02903-z>. Cite this paper when using 'kollaR'
See a demonstration in the URL.
Author: Johan Lundin Kleberg [aut, cre]
Maintainer: Johan Lundin Kleberg <johan.lundin.kleberg@su.se>
Diff between kollaR versions 1.1.3 dated 2026-02-25 and 1.1.4 dated 2026-05-08
DESCRIPTION | 10 - MD5 | 20 +- NAMESPACE | 2 R/AnalysisFunctions.R | 386 +++++++++++++++++++++++++----------------- R/PreprocessingFunctions.R | 14 + R/VisualizationFunctions.R | 11 - man/aoi_test.Rd | 18 + man/calculate_rms.Rd | 10 - man/draw_aois.Rd | 19 -- man/plot_algorithm_results.Rd | 6 man/plot_filter_results.Rd | 5 11 files changed, 301 insertions(+), 200 deletions(-)
Title: ICA-Based Matrix/Tensor Decomposition
Description: Some functions for performing ICA, MICA, Group ICA, and Multilinear ICA are implemented.
ICA, MICA/Group ICA, and Multilinear ICA extract statistically independent components from single matrix, multiple matrices, and single tensor, respectively.
For the details of these methods, see the reference section of GitHub README.md <https://github.com/rikenbit/iTensor>.
Author: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between iTensor versions 1.0.2 dated 2023-04-28 and 1.0.4 dated 2026-05-08
DESCRIPTION | 10 - MD5 | 37 ++-- NAMESPACE | 2 R/MultilinearICA.R | 10 - R/groupICA_internal.R |only R/toyModel.R | 1 build/vignette.rds |binary inst/NEWS | 13 + inst/doc/iTensor-1.html | 268 ++++++++++++++++------------------- inst/doc/iTensor-2.html | 220 +++++++++++++--------------- inst/doc/iTensor-3.html | 227 +++++++++++++---------------- man/ICA2.Rd | 4 man/MultilinearICA.Rd | 3 tests/testthat.R | 7 tests/testthat/test-CorrIndex.R |only tests/testthat/test-GroupICA.R | 140 +++++++++++++----- tests/testthat/test-ICA.R | 6 tests/testthat/test-ICA2.R | 44 +++-- tests/testthat/test-MICA.R | 4 tests/testthat/test-MultilinearICA.R | 10 + tests/testthat/test-toyModel.R |only 21 files changed, 522 insertions(+), 484 deletions(-)
Title: Pipeline Audit Trails and Data Diagnostics for 'tidyverse'
Workflows
Description: Provides pipeline audit trails and data diagnostics for
'tidyverse' workflows. The audit trail system captures lightweight
metadata snapshots at each step of a pipeline, building a structured
record without storing the data itself. Operation-aware taps enrich
snapshots with join match rates and filter drop statistics.
Trails can be serialized to 'JSON' or 'RDS' and exported as
self-contained 'HTML' visualizations. Also includes diagnostic
functions for interactive data analysis including frequency tables,
string quality auditing, and data comparison.
Author: Fernando Cordeiro [aut, cre, cph]
Maintainer: Fernando Cordeiro <fernandolpcordeiro@gmail.com>
Diff between tidyaudit versions 0.2.0 dated 2026-03-24 and 0.2.1 dated 2026-05-08
DESCRIPTION | 8 ++-- MD5 | 62 +++++++++++++++++----------------- NEWS.md | 11 ++++++ R/audit-transform.R | 16 ++++++-- build/vignette.rds |binary inst/doc/tidyaudit.html | 28 +++++++-------- man/audit_diff.Rd | 10 ++--- man/audit_export.Rd | 10 ++--- man/audit_report.Rd | 10 ++--- man/audit_tap.Rd | 10 ++--- man/audit_trail.Rd | 10 ++--- man/audit_transform.Rd | 12 +++--- man/compare_tables.Rd | 8 ++-- man/diagnose_nas.Rd | 12 +++--- man/diagnose_strings.Rd | 12 +++--- man/filter_drop.Rd | 4 +- man/filter_keep.Rd | 4 +- man/filter_tap.Rd | 2 - man/get_summary_table.Rd | 12 +++--- man/join_tap.Rd | 4 +- man/read_trail.Rd | 10 ++--- man/summarize_column.Rd | 12 +++--- man/tab.Rd | 12 +++--- man/tab_tap.Rd | 10 ++--- man/tidyaudit-package.Rd | 5 ++ man/trail_to_df.Rd | 10 ++--- man/trail_to_list.Rd | 12 +++--- man/validate_join.Rd | 8 ++-- man/validate_primary_keys.Rd | 8 ++-- man/validate_var_relationship.Rd | 8 ++-- man/write_trail.Rd | 10 ++--- tests/testthat/test-audit-transform.R | 18 +++++++++ 32 files changed, 205 insertions(+), 163 deletions(-)
Title: Non-Negative Tensor Decomposition
Description: Some functions for performing non-negative matrix factorization, non-negative CANDECOMP/PARAFAC (CP) decomposition, non-negative Tucker decomposition, and generating toy model data. See Andrzej Cichock et al (2009) and the reference section of GitHub README.md <https://github.com/rikenbit/nnTensor>, for details of the methods.
Author: Koki Tsuyuzaki [aut, cre],
Itoshi Nikaido [aut]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between nnTensor versions 1.3.0 dated 2024-05-13 and 1.4.0 dated 2026-05-08
DESCRIPTION | 11 - MD5 | 37 ++- NAMESPACE | 7 R/NMF.R | 132 ++++++++++++- R/PSDTF.R |only R/ZITNMF.R |only R/nnTensor-internal.R | 216 ++++++++++++++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/bibliography.bib |only inst/doc/nnTensor-1.html | 130 ++++++------- inst/doc/nnTensor-2.html | 197 +++++++++----------- inst/doc/nnTensor-3.html | 243 ++++++++++++------------- inst/doc/nnTensor-4.R | 20 +- inst/doc/nnTensor-4.Rmd | 20 +- inst/doc/nnTensor-4.html | 406 +++++++++++++++++++++---------------------- man/NMF.Rd | 84 ++++++++ man/PSDTF.Rd |only man/ZITNMF.Rd |only tests/testthat/test_NMF.R | 11 + tests/testthat/test_PSDTF.R |only tests/testthat/test_ZITNMF.R |only vignettes/nnTensor-4.Rmd | 20 +- 23 files changed, 958 insertions(+), 576 deletions(-)
Title: Fast and Flexible Implementations of Exploratory Factor Analysis
Tools
Description: Provides functions to perform exploratory factor analysis (EFA) procedures and compare their solutions. The goal is to provide state-of-the-art factor retention methods and a high degree of flexibility in the EFA procedures. This way, for example, implementations from R 'psych' and 'SPSS' can be compared. Moreover, functions for Schmid-Leiman transformation and the computation of omegas are provided. To speed up the analyses, some of the iterative procedures, like principal axis factoring (PAF), are implemented in C++.
Author: Markus Steiner [aut, cre],
Silvia Grieder [aut],
William Revelle [ctb],
Max Auerswald [ctb],
Morten Moshagen [ctb],
John Ruscio [ctb],
Brendan Roche [ctb],
Urbano Lorenzo-Seva [ctb],
David Navarro-Gonzalez [ctb],
Johan Braeken [ctb],
Andreas Soteriad [...truncated...]
Maintainer: Markus Steiner <markus.d.steiner@gmail.com>
Diff between EFAtools versions 0.7.0 dated 2026-04-30 and 0.7.1 dated 2026-05-08
DESCRIPTION | 6 MD5 | 30 +- NEWS.md | 10 R/EFA.R | 11 - R/EFA_POOLED.R | 8 R/FACTOR_SCORES.R | 25 ++ R/ROTATE_OBLQ.R | 22 +- R/ROTATE_ORTH.R | 18 + inst/doc/EFAtools.html | 270 +++++++++++++------------- inst/doc/Replicate_SPSS_psych.html | 376 ++++++++++++++++++------------------- man/EFA.Rd | 6 man/FACTOR_SCORES.Rd | 23 ++ tests/testthat/test-EFA.R | 4 tests/testthat/test-ROTATE_OBLQ.R | 28 +- tests/testthat/test-ROTATE_ORTH.R | 12 - tests/testthat/test-SL.R | 4 16 files changed, 464 insertions(+), 389 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385>, Wilson (2025) <DOI:10.1002/mrm.30462> and
spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] ,
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin.wilson111@gmail.com>
Diff between spant versions 3.9.0 dated 2026-02-23 and 4.0.0 dated 2026-05-08
DESCRIPTION | 12 +- MD5 | 60 +++++++------ NAMESPACE | 9 + NEWS.md | 11 ++ R/ants_utils.R |only R/dicom_reader.R | 3 R/fit_svs.R | 61 +++++++++---- R/fit_svs_edited.R | 59 +++++++++--- R/fmrs.R | 28 +++++- R/mrs_read_dicom.R | 17 ++- R/qm_simulation.R | 6 - R/rats.R | 27 ++++- R/utils.R | 5 - build/vignette.rds |binary inst/cli_scripts/spant_fit_svs | 4 inst/doc/abfit-baseline-opts.html | 18 +-- inst/doc/spant-basis-simulation.html | 8 - inst/doc/spant-intro.html | 138 +++++++++++++++--------------- inst/doc/spant-metabolite-simulation.html | 10 +- inst/doc/spant-preprocessing.html | 14 +-- man/faceoff.Rd |only man/fit_svs.Rd | 21 ++-- man/fit_svs_edited.Rd | 21 ++-- man/get_ants_dir.Rd |only man/get_spant_resources_dir.Rd |only man/install_ants.Rd |only man/install_faceoff.Rd |only man/install_oasis_template.Rd |only man/mr_data2bids.Rd | 2 man/reexports.Rd | 2 man/segment_t1_ants.Rd |only man/segment_t1_fsl.Rd | 4 man/segment_t1_rpyants.Rd |only man/set_ants_dir.Rd |only man/sim_basis.Rd | 2 man/spant-package.Rd | 5 + 36 files changed, 345 insertions(+), 202 deletions(-)
Title: Self-Controlled Case Series
Description: Execute the self-controlled case series (SCCS) design using observational
data in the OMOP Common Data Model. Extracts all necessary data from the database and
transforms it to the format required for SCCS. Age and season can be modeled
using splines assuming constant hazard within calendar months. Event-dependent
censoring of the observation period can be corrected for. Many exposures can be
included at once (MSCCS), with regularization on all coefficients except for the
exposure of interest. Includes diagnostics for all major assumptions of the SCCS.
Author: Martijn Schuemie [aut, cre],
Patrick Ryan [aut],
Trevor Shaddox [aut],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SelfControlledCaseSeries versions 6.1.4 dated 2026-03-26 and 6.1.5 dated 2026-05-08
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 10 ++++++++++ R/RunAnalyses.R | 2 +- R/SccsDataConversion.R | 18 ++++-------------- R/ScriDataConversion.R | 7 ++----- inst/doc/MultipleAnalyses.pdf |binary inst/doc/ResultsSchema.pdf |binary inst/doc/SingleStudies.pdf |binary tests/testthat/test-eraConstruction.R | 1 + tests/testthat/test-eunomia.R | 10 +++++++++- 11 files changed, 41 insertions(+), 35 deletions(-)
More information about SelfControlledCaseSeries at CRAN
Permanent link
Title: R Interface to the 'OKX' REST API
Description: Provides lightweight R wrappers for the 'OKX' REST API, covering
endpoints for market data, trading, account management, asset balances,
and copy trading. The upstream API reference is available at
<https://www.okx.com/docs-v5/en/>.
Author: Oliver Zhou [aut, cre],
Lily Li [aut]
Maintainer: Oliver Zhou <oliver.yxzhou@gmail.com>
Diff between okxr versions 0.2.4 dated 2026-04-28 and 0.4.5 dated 2026-05-08
DESCRIPTION | 17 MD5 | 214 +- NAMESPACE | 115 + NEWS.md | 206 ++ R/def_constants.R | 1511 +++++++++++++++- R/utils_auth.R | 7 R/utils_parser.R | 38 R/utils_request_helpers.R | 62 R/wrappers_get_account.R | 582 ++++++ R/wrappers_get_asset.R | 264 ++ R/wrappers_get_copy_trade.R | 321 +++ R/wrappers_get_market.R | 702 +++++++ R/wrappers_get_trade.R | 303 +++ R/wrappers_post_asset.R |only R/wrappers_post_configure.R | 302 +++ R/wrappers_post_trade.R | 497 +++++ README.md | 141 + man/dot-execute_get_action.Rd | 7 man/dot-gets.Rd | 2 man/dot-make_parser.Rd | 29 man/dot-posts.Rd | 2 man/get_account_adjust_leverage_info.Rd |only man/get_account_balance.Rd | 9 man/get_account_bills_history_archive.Rd |only man/get_account_collateral_assets.Rd |only man/get_account_config.Rd | 7 man/get_account_greeks.Rd |only man/get_account_instruments.Rd |only man/get_account_interest_accrued.Rd |only man/get_account_interest_limits.Rd |only man/get_account_interest_rate.Rd |only man/get_account_leverage_info.Rd | 14 man/get_account_max_avail_size.Rd |only man/get_account_max_loan.Rd |only man/get_account_max_size.Rd |only man/get_account_max_withdrawal.Rd |only man/get_account_mmp_config.Rd |only man/get_account_move_positions_history.Rd |only man/get_account_position_risk.Rd |only man/get_account_position_tiers.Rd |only man/get_account_positions.Rd | 7 man/get_account_positions_history.Rd | 7 man/get_account_precheck_set_delta_neutral.Rd |only man/get_account_risk_state.Rd |only man/get_account_set_account_switch_precheck.Rd |only man/get_account_spot_borrow_repay_history.Rd |only man/get_account_subaccount_balances.Rd |only man/get_account_subaccount_max_withdrawal.Rd |only man/get_account_subtypes.Rd |only man/get_account_trade_fee.Rd |only man/get_asset_asset_valuation.Rd |only man/get_asset_bills.Rd |only man/get_asset_bills_history.Rd |only man/get_asset_convert_currencies.Rd |only man/get_asset_convert_currency_pair.Rd |only man/get_asset_convert_history.Rd |only man/get_asset_deposit_history.Rd | 34 man/get_asset_deposit_withdraw_status.Rd |only man/get_asset_exchange_list.Rd |only man/get_asset_non_tradable_assets.Rd |only man/get_asset_transfer_state.Rd |only man/get_asset_withdrawal_history.Rd | 34 man/get_copy_trade_config.Rd |only man/get_copy_trade_current_subpos.Rd | 26 man/get_copy_trade_historical_subpos.Rd | 26 man/get_copy_trade_instruments.Rd |only man/get_copy_trade_my_leaders.Rd | 6 man/get_copy_trade_profit_sharing_details.Rd |only man/get_copy_trade_public_config.Rd |only man/get_copy_trade_public_copy_traders.Rd |only man/get_copy_trade_public_current_subpositions.Rd |only man/get_copy_trade_public_lead_traders.Rd |only man/get_copy_trade_public_pnl.Rd |only man/get_copy_trade_public_preference_currency.Rd |only man/get_copy_trade_public_stats.Rd |only man/get_copy_trade_public_subpositions_history.Rd |only man/get_copy_trade_public_weekly_pnl.Rd |only man/get_copy_trade_settings.Rd | 14 man/get_copy_trade_total_profit_sharing.Rd |only man/get_copy_trade_total_unrealized_profit_sharing.Rd |only man/get_copy_trade_unrealized_profit_sharing_details.Rd |only man/get_market_block_ticker.Rd |only man/get_market_block_tickers.Rd |only man/get_market_books.Rd | 7 man/get_market_candles.Rd | 6 man/get_market_exchange_rate.Rd |only man/get_market_history_candles.Rd | 16 man/get_market_history_index_candles.Rd |only man/get_market_history_mark_price_candles.Rd |only man/get_market_index_candles.Rd |only man/get_market_index_components.Rd |only man/get_market_index_tickers.Rd |only man/get_market_mark_price_candles.Rd |only man/get_market_option_instrument_family_trades.Rd |only man/get_market_platform_24_volume.Rd |only man/get_market_trades.Rd | 7 man/get_public_block_trades.Rd |only man/get_public_convert_contract_coin.Rd |only man/get_public_delivery_exercise_history.Rd |only man/get_public_discount_rate_interest_free_quota.Rd |only man/get_public_economic_calendar.Rd |only man/get_public_estimated_price.Rd |only man/get_public_estimated_settlement_info.Rd |only man/get_public_funding_rate.Rd | 6 man/get_public_instrument_tick_bands.Rd |only man/get_public_instruments.Rd | 8 man/get_public_insurance_fund.Rd |only man/get_public_interest_rate_loan_quota.Rd |only man/get_public_mark_price.Rd | 6 man/get_public_opt_summary.Rd |only man/get_public_option_trades.Rd |only man/get_public_position_tiers.Rd |only man/get_public_premium_history.Rd |only man/get_public_price_limit.Rd | 6 man/get_public_settlement_history.Rd |only man/get_public_underlying.Rd |only man/get_trade_account_rate_limit.Rd |only man/get_trade_easy_convert_currency_list.Rd |only man/get_trade_easy_convert_history.Rd |only man/get_trade_fills.Rd | 6 man/get_trade_fills_history.Rd | 6 man/get_trade_one_click_repay_currency_list.Rd |only man/get_trade_one_click_repay_currency_list_v2.Rd |only man/get_trade_one_click_repay_history.Rd |only man/get_trade_one_click_repay_history_v2.Rd |only man/get_trade_order.Rd | 5 man/get_trade_order_algo.Rd |only man/get_trade_orders_algo_history.Rd |only man/get_trade_orders_algo_pending.Rd |only man/get_trade_orders_history.Rd |only man/get_trade_orders_history_7d.Rd | 29 man/get_trade_orders_history_archive.Rd |only man/get_trade_orders_pending.Rd | 7 man/okxr-package.Rd | 5 man/post_account_account_level_switch_preset.Rd |only man/post_account_mmp_config.Rd |only man/post_account_mmp_reset.Rd |only man/post_account_move_positions.Rd |only man/post_account_position_margin_balance.Rd |only man/post_account_set_account_level.Rd |only man/post_account_set_auto_loan.Rd |only man/post_account_set_auto_repay.Rd |only man/post_account_set_collateral_assets.Rd |only man/post_account_set_fee_type.Rd |only man/post_account_set_greeks.Rd |only man/post_account_set_leverage.Rd | 3 man/post_account_set_position_mode.Rd |only man/post_account_spot_manual_borrow_repay.Rd |only man/post_asset_cancel_withdrawal.Rd |only man/post_asset_convert_estimate_quote.Rd |only man/post_asset_convert_trade.Rd |only man/post_asset_transfer.Rd |only man/post_asset_withdrawal.Rd |only man/post_trade_amend_algos.Rd |only man/post_trade_amend_batch_orders.Rd |only man/post_trade_amend_order.Rd |only man/post_trade_batch_orders.Rd |only man/post_trade_cancel_algos.Rd |only man/post_trade_cancel_all_after.Rd |only man/post_trade_cancel_batch_orders.Rd |only man/post_trade_cancel_order.Rd | 13 man/post_trade_mass_cancel.Rd |only man/post_trade_order_precheck.Rd |only man/set_okxr_options.Rd | 6 tests/testthat/test-request-helpers.R | 24 tests/testthat/test-wrapper-queries.R | 944 +++++++++ 166 files changed, 6286 insertions(+), 330 deletions(-)
Title: Minimalist Async Evaluation Framework for R
Description: Evaluates R expressions asynchronously and in parallel,
locally or distributed across networks. An official parallel cluster
type for R. Built on 'nanonext' and 'NNG', its non-polling,
event-driven architecture scales from a laptop to thousands of
processes across high-performance computing clusters and cloud
platforms. Features FIFO scheduling with task cancellation and bounded
queues, promises for reactive programming, 'OpenTelemetry' distributed
tracing, and custom serialization for cross-language data types.
Author: Charlie Gao [aut, cre] ,
Joe Cheng [ctb],
Posit Software, PBC [cph, fnd] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@posit.co>
Diff between mirai versions 2.6.1 dated 2026-03-02 and 2.7.0 dated 2026-05-08
mirai-2.6.1/mirai/R/dispatcher.R |only mirai-2.6.1/mirai/man/dispatcher.Rd |only mirai-2.7.0/mirai/DESCRIPTION | 19 + mirai-2.7.0/mirai/MD5 | 78 +++---- mirai-2.7.0/mirai/NAMESPACE | 10 - mirai-2.7.0/mirai/NEWS.md | 22 ++ mirai-2.7.0/mirai/R/daemons.R | 132 +++++++------ mirai-2.7.0/mirai/R/launchers.R | 190 ++++++++++++++----- mirai-2.7.0/mirai/R/map.R | 11 - mirai-2.7.0/mirai/R/mirai-package.R | 14 - mirai-2.7.0/mirai/R/mirai.R | 181 ++++++++++++------ mirai-2.7.0/mirai/R/next.R | 5 mirai-2.7.0/mirai/README.md | 204 +++++++++----------- mirai-2.7.0/mirai/build/vignette.rds |binary mirai-2.7.0/mirai/inst/doc/mirai.Rmd | 9 mirai-2.7.0/mirai/inst/doc/mirai.html | 9 mirai-2.7.0/mirai/inst/doc/v01-reference.Rmd | 245 +++++++++++++++++++------ mirai-2.7.0/mirai/inst/doc/v01-reference.html | 205 +++++++++++++++----- mirai-2.7.0/mirai/inst/doc/v06-packages.Rmd | 4 mirai-2.7.0/mirai/inst/doc/v06-packages.html | 2 mirai-2.7.0/mirai/inst/doc/v07-questions.Rmd | 2 mirai-2.7.0/mirai/inst/doc/v07-questions.html | 2 mirai-2.7.0/mirai/man/call_mirai.Rd | 3 mirai-2.7.0/mirai/man/cluster_config.Rd | 5 mirai-2.7.0/mirai/man/collect_mirai.Rd | 4 mirai-2.7.0/mirai/man/daemons.Rd | 30 ++- mirai-2.7.0/mirai/man/dot-flat.Rd | 9 mirai-2.7.0/mirai/man/everywhere.Rd | 3 mirai-2.7.0/mirai/man/figures/architecture.svg | 120 +++++------- mirai-2.7.0/mirai/man/http_config.Rd | 41 ++++ mirai-2.7.0/mirai/man/make_cluster.Rd | 2 mirai-2.7.0/mirai/man/mirai-package.Rd | 11 - mirai-2.7.0/mirai/man/mirai.Rd | 37 +++ mirai-2.7.0/mirai/man/nextstream.Rd | 5 mirai-2.7.0/mirai/man/ssh_config.Rd | 8 mirai-2.7.0/mirai/man/status.Rd | 16 + mirai-2.7.0/mirai/tests/tests.R | 177 ++++++++++++++++-- mirai-2.7.0/mirai/vignettes/mirai.Rmd | 9 mirai-2.7.0/mirai/vignettes/v01-reference.Rmd | 245 +++++++++++++++++++------ mirai-2.7.0/mirai/vignettes/v06-packages.Rmd | 4 mirai-2.7.0/mirai/vignettes/v07-questions.Rmd | 2 41 files changed, 1433 insertions(+), 642 deletions(-)
Title: Create Layout Plots of Biological Culture Plates and Microplates
Description: Enables users to create simple plots of biological culture plates as well as microplates. Both continuous and discrete values can be plotted onto the plate layout.
Author: Jan-Philipp Quast [aut, cre]
Maintainer: Jan-Philipp Quast <jpquast.software@gmail.com>
Diff between ggplate versions 0.2.0 dated 2026-01-09 and 0.3.0 dated 2026-05-08
DESCRIPTION | 6 +++--- MD5 | 16 +++++++++------- NEWS.md | 4 ++++ R/data.R | 13 +++++++++++-- R/plate_plot.R | 27 ++++++++++++++++++++++++--- README.md | 4 ++-- data/data_continuous_1536_Aa.rda |only man/data_continuous_1536.Rd | 4 ++-- man/data_continuous_1536_Aa.Rd |only man/plate_plot.Rd | 9 +++++++++ 10 files changed, 64 insertions(+), 19 deletions(-)
Title: Comparative Cohort Method with Large Scale Propensity and
Outcome Models
Description: Functions for performing comparative cohort studies
in an observational database in the Observational Medical Outcomes Partnership (OMOP) Common
Data Model. Can extract all necessary data from a database. This implements large-scale
propensity scores (LSPS) as described in Tian et al. (2018) <doi:10.1093/ije/dyy120>,
using a large set of covariates, including for example all drugs, diagnoses, procedures,
as well as age, comorbidity indexes, etc. Large scale regularized regression is used to
fit the propensity and outcome models as described in Suchard et al. (2013) <doi:10.1145/2414416.2414791>.
Functions are included for trimming, stratifying, (variable and fixed ratio) matching and
weighting by propensity scores, as well as diagnostic functions, such as propensity score distribution
plots and plots showing covariate balance before and after matching and/or trimming. Supported
outcome models are (conditional) logistic regression, (conditional) Poisson regression, and
(stra [...truncated...]
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Patrick Ryan [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between CohortMethod versions 6.0.1 dated 2026-03-21 and 6.0.2 dated 2026-05-08
DESCRIPTION | 8 +++---- MD5 | 20 +++++++++---------- NEWS.md | 10 +++++++++ R/DataLoadingSaving.R | 17 +++++++++++++++- R/PsFunctions.R | 2 - R/RunAnalyses.R | 9 +++++++- README.md | 44 +++++++++++++++++++++--------------------- inst/doc/MultipleAnalyses.pdf |binary inst/doc/ResultsSchema.html | 4 +-- inst/doc/SingleStudies.pdf |binary man/createPs.Rd | 2 - 11 files changed, 75 insertions(+), 41 deletions(-)
Title: Early Detection of Public Health Threats from Social Media Data
Description: It allows you to automatically monitor trends of social media messages by time, place and topic aiming at detecting public health threats early through the detection of signals (i.e., an unusual increase in the number of messages per time, topic and location). It was designed to focus on infectious diseases, and it can be extended to all hazards or other fields of study by modifying the topics and keywords. More information on the original package 'epitweetr' is available in the peer-review publication Espinosa et al. (2022) <doi:10.2807/1560-7917.ES.2022.27.39.2200177>.
Author: Laura Espinosa [aut, fnd, cre] ,
Francisco Orchard [aut, ctr] ,
Gianfranco Spiteri [ctb, fnd],
Ariana Wijermans [ctb] ,
Thomas Mollet [ctb] ,
Adrian Prodan [ctb],
Martin Norling [ctb],
Enrique Delgado [ctb],
Thomas Czernichow [ctb],
Maria Prieto Gonz [...truncated...]
Maintainer: Laura Espinosa <laura.espinosa@ecdc.europa.eu>
Diff between episomer versions 3.0.34 dated 2026-04-20 and 3.0.35 dated 2026-05-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/plans.R | 4 ++-- java/ecdc-episomer-bundle_2.13-1.0-source.zip |binary 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Integrated Analysis and Visualization of Microbiome Data
Description: A toolkit for working with Biological Observation Matrix ('BIOM') files.
Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and
beta diversity (including 'UniFrac'). Summarize counts by taxonomic level.
Subset based on metadata. Generate visualizations and statistical analyses.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between rbiom versions 2.2.1 dated 2025-06-27 and 3.1.0 dated 2026-05-08
rbiom-2.2.1/rbiom/R/rbiom-deprecated.r |only rbiom-2.2.1/rbiom/data |only rbiom-2.2.1/rbiom/man/adiv_matrix.Rd |only rbiom-2.2.1/rbiom/man/rarefy_cols.Rd |only rbiom-2.2.1/rbiom/man/rbiom-deprecated.Rd |only rbiom-2.2.1/rbiom/src |only rbiom-2.2.1/rbiom/tests/testthat/test-rbiom-deprecated.r |only rbiom-3.1.0/rbiom/DESCRIPTION | 33 rbiom-3.1.0/rbiom/MD5 | 215 +--- rbiom-3.1.0/rbiom/NAMESPACE | 105 - rbiom-3.1.0/rbiom/R/adiv_table.r | 222 ++-- rbiom-3.1.0/rbiom/R/apcoa.r | 2 rbiom-3.1.0/rbiom/R/as_rbiom.r | 81 + rbiom-3.1.0/rbiom/R/bdiv_heatmap.r | 71 - rbiom-3.1.0/rbiom/R/bdiv_ord_plot.r | 35 rbiom-3.1.0/rbiom/R/bdiv_ord_table.r | 33 rbiom-3.1.0/rbiom/R/bdiv_table.r | 330 ++---- rbiom-3.1.0/rbiom/R/biom_merge.r | 89 + rbiom-3.1.0/rbiom/R/biom_ply.r | 8 rbiom-3.1.0/rbiom/R/boxplot.r | 36 rbiom-3.1.0/rbiom/R/cache.r | 2 rbiom-3.1.0/rbiom/R/clustering.r | 15 rbiom-3.1.0/rbiom/R/convert.r | 160 ++- rbiom-3.1.0/rbiom/R/corrplot.r | 32 rbiom-3.1.0/rbiom/R/data.r | 47 rbiom-3.1.0/rbiom/R/distmat_stats.r | 2 rbiom-3.1.0/rbiom/R/documentation.r | 79 + rbiom-3.1.0/rbiom/R/import_table.r | 4 rbiom-3.1.0/rbiom/R/rarefy.r | 789 +++++++++++---- rbiom-3.1.0/rbiom/R/rbiom_objects.r | 52 rbiom-3.1.0/rbiom/R/read_biom.r | 156 +- rbiom-3.1.0/rbiom/R/read_tree.r | 65 - rbiom-3.1.0/rbiom/R/reexport.r | 13 rbiom-3.1.0/rbiom/R/s3_methods.r | 16 rbiom-3.1.0/rbiom/R/speed_ups.r | 2 rbiom-3.1.0/rbiom/R/stats_table.r | 15 rbiom-3.1.0/rbiom/R/taxa_heatmap.r | 4 rbiom-3.1.0/rbiom/R/taxa_stacked.r | 3 rbiom-3.1.0/rbiom/R/taxa_table.r | 29 rbiom-3.1.0/rbiom/R/utils.r | 25 rbiom-3.1.0/rbiom/R/validate.r | 129 ++ rbiom-3.1.0/rbiom/R/write_biom.r | 180 +-- rbiom-3.1.0/rbiom/R/write_xlsx.r | 10 rbiom-3.1.0/rbiom/R/zzz.r | 7 rbiom-3.1.0/rbiom/README.md | 90 + rbiom-3.1.0/rbiom/build/partial.rdb |binary rbiom-3.1.0/rbiom/exec/rbiom_subtree.r | 2 rbiom-3.1.0/rbiom/man/adiv_boxplot.Rd | 17 rbiom-3.1.0/rbiom/man/adiv_corrplot.Rd | 15 rbiom-3.1.0/rbiom/man/adiv_stats.Rd | 15 rbiom-3.1.0/rbiom/man/adiv_table.Rd | 80 + rbiom-3.1.0/rbiom/man/babies.Rd | 10 rbiom-3.1.0/rbiom/man/bdiv_boxplot.Rd | 36 rbiom-3.1.0/rbiom/man/bdiv_clusters.Rd | 43 rbiom-3.1.0/rbiom/man/bdiv_corrplot.Rd | 34 rbiom-3.1.0/rbiom/man/bdiv_heatmap.Rd | 38 rbiom-3.1.0/rbiom/man/bdiv_ord_plot.Rd | 32 rbiom-3.1.0/rbiom/man/bdiv_ord_table.Rd | 37 rbiom-3.1.0/rbiom/man/bdiv_stats.Rd | 40 rbiom-3.1.0/rbiom/man/bdiv_table.Rd | 108 +- rbiom-3.1.0/rbiom/man/bdply.Rd | 11 rbiom-3.1.0/rbiom/man/biom_inflate.Rd |only rbiom-3.1.0/rbiom/man/biom_relativize.Rd |only rbiom-3.1.0/rbiom/man/biom_rescale.Rd |only rbiom-3.1.0/rbiom/man/convert_to.Rd | 67 - rbiom-3.1.0/rbiom/man/distmat_stats.Rd | 2 rbiom-3.1.0/rbiom/man/documentation_default.Rd | 67 - rbiom-3.1.0/rbiom/man/export.Rd | 3 rbiom-3.1.0/rbiom/man/figures/README-bdiv-1.png |binary rbiom-3.1.0/rbiom/man/figures/README-bdiv-2.png |binary rbiom-3.1.0/rbiom/man/figures/README-bdiv-3.png |binary rbiom-3.1.0/rbiom/man/figures/README-taxa-1.png |binary rbiom-3.1.0/rbiom/man/figures/README-taxa-2.png |binary rbiom-3.1.0/rbiom/man/gems.Rd | 10 rbiom-3.1.0/rbiom/man/hmp50.Rd | 10 rbiom-3.1.0/rbiom/man/matrix_ops.Rd |only rbiom-3.1.0/rbiom/man/modify_metadata.Rd | 4 rbiom-3.1.0/rbiom/man/rare_corrplot.Rd | 21 rbiom-3.1.0/rbiom/man/rare_multiplot.Rd | 17 rbiom-3.1.0/rbiom/man/rare_stacked.Rd | 5 rbiom-3.1.0/rbiom/man/rarefy.Rd | 90 + rbiom-3.1.0/rbiom/man/reexports.Rd | 11 rbiom-3.1.0/rbiom/man/sample_sums.Rd | 7 rbiom-3.1.0/rbiom/man/slice_metadata.Rd | 17 rbiom-3.1.0/rbiom/man/speed.Rd | 2 rbiom-3.1.0/rbiom/man/subset.Rd | 4 rbiom-3.1.0/rbiom/man/suggest_inflate_depths.Rd |only rbiom-3.1.0/rbiom/man/suggest_rarefy_depth.Rd |only rbiom-3.1.0/rbiom/man/taxa_boxplot.Rd | 5 rbiom-3.1.0/rbiom/man/taxa_clusters.Rd | 3 rbiom-3.1.0/rbiom/man/taxa_corrplot.Rd | 5 rbiom-3.1.0/rbiom/man/taxa_heatmap.Rd | 7 rbiom-3.1.0/rbiom/man/taxa_map.Rd | 3 rbiom-3.1.0/rbiom/man/taxa_matrix.Rd | 7 rbiom-3.1.0/rbiom/man/taxa_stacked.Rd | 7 rbiom-3.1.0/rbiom/man/taxa_stats.Rd | 5 rbiom-3.1.0/rbiom/man/taxa_sums.Rd | 5 rbiom-3.1.0/rbiom/man/with.Rd | 4 rbiom-3.1.0/rbiom/man/write_biom.Rd | 18 rbiom-3.1.0/rbiom/tests/testthat/_test_distance.r | 2 rbiom-3.1.0/rbiom/tests/testthat/inputs/biom.hdf5 |only rbiom-3.1.0/rbiom/tests/testthat/test-adiv_table.r | 18 rbiom-3.1.0/rbiom/tests/testthat/test-bdiv_heatmap.r | 4 rbiom-3.1.0/rbiom/tests/testthat/test-bdiv_ord_plot.r | 4 rbiom-3.1.0/rbiom/tests/testthat/test-bdiv_table.r | 50 rbiom-3.1.0/rbiom/tests/testthat/test-biom_ply.r | 50 rbiom-3.1.0/rbiom/tests/testthat/test-convert.r | 35 rbiom-3.1.0/rbiom/tests/testthat/test-rarefy.r | 22 rbiom-3.1.0/rbiom/tests/testthat/test-read_biom.r | 13 rbiom-3.1.0/rbiom/tests/testthat/test-write_biom.r | 2 110 files changed, 2563 insertions(+), 1747 deletions(-)
Title: Analysis of Experimental Data using ANOVA and Mean Comparison
Description: Provides tools for designing and analyzing agricultural
experiments. It includes functions for generating randomized
treatment layouts for standard experimental designs such as
Completely Randomized Design (CRD), Randomized Block Design (RBD),
Latin Square Design (LSD), Factorial Randomized Block Design
(FRBD), split-plot design, and strip-plot design. The package
implements one-factor and two-factor analysis of variance (ANOVA)
and offers multiple comparison procedures, including Least
Significant Difference (lsd), Tukey, and Duncan tests, to compare
treatment means in single-factor and factorial experiments. The
methods follow classical experimental design principles described
in Gomez and Gomez (1984, Statistical Procedures for Agricultural Research, John Wiley & Sons, New York).
Author: Santosh Patil [aut, cre] ,
Yogesh Garde [aut]
Maintainer: Santosh Patil <patil.sgstat@gmail.com>
Diff between PGaovR versions 0.1.0 dated 2026-04-28 and 0.1.1 dated 2026-05-08
DESCRIPTION | 8 MD5 | 9 NEWS.md |only R/FDlay.R | 655 +++++++++++++++++++++++++++++------------------------------ R/SFaov.R | 255 +++++++++++----------- R/data-doc.R | 12 - 6 files changed, 473 insertions(+), 466 deletions(-)
Title: Argentina's Spatial Data Toolbox
Description: Collection of tools that facilitates data access and workflow for spatial analysis of Argentina. Includes historical information from censuses, administrative limits at different levels of aggregation, location of human settlements, among others. Since it is expected that the majority of users will be Spanish-speaking, the documentation of the package prioritizes this language, although an effort is made to also offer annotations in English.
Author: Juan Pablo Ruiz Nicolini [aut, cre, cph] ,
Patricio Del Boca [aut],
Juan Gabriel Juara [aut]
Maintainer: Juan Pablo Ruiz Nicolini <juanpabloruiznicolini@gmail.com>
Diff between geoAr versions 1.0.0 dated 2024-03-03 and 1.2.2 dated 2026-05-08
DESCRIPTION | 23 MD5 | 55 NAMESPACE | 27 NEWS.md | 39 R/georefar.R | 1897 +++++++++++++++++++++++++++------- README.md | 13 build/vignette.rds |binary inst/doc/geoAr_geofacet.Rmd | 356 +++--- inst/doc/geoAr_leaflet.Rmd | 118 +- man/geoAr.Rd | 3 man/get_asentamientos.Rd | 10 man/get_calles.Rd | 32 man/get_departamentos.Rd | 10 man/get_geodata_dump.Rd |only man/get_localidades.Rd | 10 man/get_localidades_censales.Rd | 10 man/get_municipios.Rd | 10 man/get_provincias.Rd | 8 man/normalizar_direccion.Rd | 20 man/post_asentamientos_bulk.Rd |only man/post_calles_bulk.Rd |only man/post_departamentos_bulk.Rd |only man/post_direcciones_bulk.Rd |only man/post_localidades_bulk.Rd |only man/post_localidades_censales_bulk.Rd |only man/post_municipios_bulk.Rd |only man/post_provincias_bulk.Rd |only man/post_ubicacion_bulk.Rd |only man/replace_null_with_na.Rd |only vignettes/geoAr_geofacet.Rmd | 356 +++--- vignettes/geoAr_geofacet.Rmd.orig | 200 +-- vignettes/geoAr_leaflet.Rmd | 118 +- vignettes/geoAr_leaflet.Rmd.orig | 116 +- vignettes/georefar.Rmd.orig | 276 ++-- 34 files changed, 2515 insertions(+), 1192 deletions(-)
Title: Distribution-Free Goodness-of-Fit Testing for Regression
Description: Implements the distribution-free goodness-of-fit regression testing
procedure, introduced by Estate Khmaladze (2021, <doi:10.1007/s10463-021-00786-3>)
to test whether or not the mean structure of a parametric model belongs to a
specified model family. The test is implemented for general mean functions
with minimal distributional assumptions as well as common models (e.g., lm,
glm) with the usual model assumptions.
Author: Jesse Miller [aut, cre]
Maintainer: Jesse Miller <smallepsilon@proton.me>
Diff between distfreereg versions 1.1 dated 2025-07-02 and 1.2 dated 2026-05-08
distfreereg-1.1/distfreereg/R/combine_dfr_arg_lists.R |only distfreereg-1.1/distfreereg/R/distfreereg.default.R |only distfreereg-1.1/distfreereg/R/distfreereg.formula.R |only distfreereg-1.1/distfreereg/R/distfreereg.function.R |only distfreereg-1.1/distfreereg/R/distfreereg.glm.R |only distfreereg-1.1/distfreereg/R/distfreereg.lm.R |only distfreereg-1.1/distfreereg/R/distfreereg.lmerMod.R |only distfreereg-1.1/distfreereg/R/distfreereg.nls.R |only distfreereg-1.1/distfreereg/R/validate_args_distfreereg_default.R |only distfreereg-1.1/distfreereg/R/validate_args_distfreereg_formula.R |only distfreereg-1.1/distfreereg/R/validate_args_distfreereg_function.R |only distfreereg-1.1/distfreereg/R/validate_args_distfreereg_glm.R |only distfreereg-1.1/distfreereg/R/validate_args_distfreereg_lm.R |only distfreereg-1.1/distfreereg/R/validate_args_distfreereg_lmerMod.R |only distfreereg-1.1/distfreereg/R/validate_args_distfreereg_nls.R |only distfreereg-1.1/distfreereg/R/validate_extra_arg_list.R |only distfreereg-1.2/distfreereg/DESCRIPTION | 23 distfreereg-1.2/distfreereg/MD5 | 221 distfreereg-1.2/distfreereg/NAMESPACE | 24 distfreereg-1.2/distfreereg/NEWS.md | 193 distfreereg-1.2/distfreereg/R/all.equal.compare.R | 25 distfreereg-1.2/distfreereg/R/calc_epsp.R | 17 distfreereg-1.2/distfreereg/R/calc_p.R | 12 distfreereg-1.2/distfreereg/R/compare.R | 70 distfreereg-1.2/distfreereg/R/confband.R | 40 distfreereg-1.2/distfreereg/R/confband_Sigma_hat.R | 13 distfreereg-1.2/distfreereg/R/confband_radii.R | 23 distfreereg-1.2/distfreereg/R/confint.distfreereg.R | 2 distfreereg-1.2/distfreereg/R/create_confband.R | 54 distfreereg-1.2/distfreereg/R/define_data_for_res_order.R | 17 distfreereg-1.2/distfreereg/R/define_r.R | 1 distfreereg-1.2/distfreereg/R/distfreereg.R | 305 + distfreereg-1.2/distfreereg/R/fill_covariance_list.R | 139 distfreereg-1.2/distfreereg/R/fit_model.R |only distfreereg-1.2/distfreereg/R/get_X.R |only distfreereg-1.2/distfreereg/R/get_X.default.R |only distfreereg-1.2/distfreereg/R/get_X.lmerMod.R |only distfreereg-1.2/distfreereg/R/get_X.nls.R |only distfreereg-1.2/distfreereg/R/get_Y.R |only distfreereg-1.2/distfreereg/R/get_Y.default.R |only distfreereg-1.2/distfreereg/R/get_Y.lmerMod.R |only distfreereg-1.2/distfreereg/R/get_Y.nls.R |only distfreereg-1.2/distfreereg/R/get_cov.R | 4 distfreereg-1.2/distfreereg/R/get_cov.default.R |only distfreereg-1.2/distfreereg/R/get_cov.glm.R | 2 distfreereg-1.2/distfreereg/R/get_cov.lm.R | 2 distfreereg-1.2/distfreereg/R/get_cov.lmerMod.R | 2 distfreereg-1.2/distfreereg/R/get_cov.nls.R | 2 distfreereg-1.2/distfreereg/R/get_data.default.R | 4 distfreereg-1.2/distfreereg/R/get_fitted_values.R |only distfreereg-1.2/distfreereg/R/get_fitted_values.default.R |only distfreereg-1.2/distfreereg/R/get_fitted_values.function.R |only distfreereg-1.2/distfreereg/R/get_fitted_values.lmerMod.R |only distfreereg-1.2/distfreereg/R/get_fitted_values.nls.R |only distfreereg-1.2/distfreereg/R/get_jacobian.R | 2 distfreereg-1.2/distfreereg/R/get_jacobian.function.R |only distfreereg-1.2/distfreereg/R/get_jacobian.glm.R | 9 distfreereg-1.2/distfreereg/R/get_jacobian.lm.R | 7 distfreereg-1.2/distfreereg/R/get_jacobian.lmerMod.R | 7 distfreereg-1.2/distfreereg/R/get_jacobian.nls.R | 7 distfreereg-1.2/distfreereg/R/get_theta_hat.R |only distfreereg-1.2/distfreereg/R/get_theta_hat.default.R |only distfreereg-1.2/distfreereg/R/get_theta_hat.function.R |only distfreereg-1.2/distfreereg/R/get_theta_hat.lmerMod.R |only distfreereg-1.2/distfreereg/R/ks.test.compare.R | 21 distfreereg-1.2/distfreereg/R/plot.compare.R | 500 - distfreereg-1.2/distfreereg/R/plot.distfreereg.R | 198 distfreereg-1.2/distfreereg/R/print.distfreereg.R | 11 distfreereg-1.2/distfreereg/R/refit_model.R |only distfreereg-1.2/distfreereg/R/rejection.R | 8 distfreereg-1.2/distfreereg/R/simulate_response.default.R | 2 distfreereg-1.2/distfreereg/R/simulate_response.function.R | 4 distfreereg-1.2/distfreereg/R/simulate_response.nls.R | 4 distfreereg-1.2/distfreereg/R/strict_match.R | 6 distfreereg-1.2/distfreereg/R/update.distfreereg.R | 270 distfreereg-1.2/distfreereg/R/validate_args_compare.R | 4 distfreereg-1.2/distfreereg/R/validate_args_distfreereg.R |only distfreereg-1.2/distfreereg/R/validate_args_plot.compare.R | 2 distfreereg-1.2/distfreereg/R/validate_args_plot.distfreereg.R | 10 distfreereg-1.2/distfreereg/R/validate_args_rejection.R | 4 distfreereg-1.2/distfreereg/R/validate_weights.R |only distfreereg-1.2/distfreereg/R/validate_weights.default.R |only distfreereg-1.2/distfreereg/R/validate_weights.glm.R |only distfreereg-1.2/distfreereg/build/partial.rdb |binary distfreereg-1.2/distfreereg/build/vignette.rds |binary distfreereg-1.2/distfreereg/inst/doc/v1_introduction.html | 1762 +++--- distfreereg-1.2/distfreereg/inst/doc/v1_introduction.rmd | 939 +-- distfreereg-1.2/distfreereg/inst/doc/v2_compare.html | 1058 +-- distfreereg-1.2/distfreereg/inst/doc/v2_compare.rmd | 77 distfreereg-1.2/distfreereg/inst/doc/v3_plotting.html | 1380 ++-- distfreereg-1.2/distfreereg/inst/doc/v3_plotting.rmd | 40 distfreereg-1.2/distfreereg/inst/doc/v4_parameter-estimation.html | 1330 ++-- distfreereg-1.2/distfreereg/inst/doc/v4_parameter-estimation.rmd | 116 distfreereg-1.2/distfreereg/inst/doc/v5_advanced-options.html | 1526 ++--- distfreereg-1.2/distfreereg/inst/doc/v5_advanced-options.rmd | 152 distfreereg-1.2/distfreereg/man/asymptotics.Rd | 2 distfreereg-1.2/distfreereg/man/coef.distfreereg.Rd | 2 distfreereg-1.2/distfreereg/man/compare.Rd | 308 - distfreereg-1.2/distfreereg/man/confint.distfreereg.Rd | 18 distfreereg-1.2/distfreereg/man/distfreereg.Rd | 751 +- distfreereg-1.2/distfreereg/man/fitted.distfreereg.Rd | 2 distfreereg-1.2/distfreereg/man/formula.distfreereg.Rd | 2 distfreereg-1.2/distfreereg/man/ks.test.compare.Rd | 9 distfreereg-1.2/distfreereg/man/plot.compare.Rd | 129 distfreereg-1.2/distfreereg/man/plot.distfreereg.Rd | 290 - distfreereg-1.2/distfreereg/man/predict.distfreereg.Rd | 2 distfreereg-1.2/distfreereg/man/print.compare.Rd | 2 distfreereg-1.2/distfreereg/man/print.distfreereg.Rd | 2 distfreereg-1.2/distfreereg/man/rejection.Rd | 40 distfreereg-1.2/distfreereg/man/residuals.distfreereg.Rd | 8 distfreereg-1.2/distfreereg/man/update.distfreereg.Rd | 52 distfreereg-1.2/distfreereg/man/vcov.distfreereg.Rd | 36 distfreereg-1.2/distfreereg/tests/0-01_preliminaries.R | 3 distfreereg-1.2/distfreereg/tests/0-01_preliminaries.Rout.save | 169 distfreereg-1.2/distfreereg/tests/1-01_distfreereg_function.R | 195 distfreereg-1.2/distfreereg/tests/1-01_distfreereg_function.Rout.save | 2773 +++++----- distfreereg-1.2/distfreereg/tests/1-02_distfreereg_lm.R | 34 distfreereg-1.2/distfreereg/tests/1-02_distfreereg_lm.Rout.save | 872 +-- distfreereg-1.2/distfreereg/tests/1-03_distfreereg_nls.R | 69 distfreereg-1.2/distfreereg/tests/1-03_distfreereg_nls.Rout.save | 123 distfreereg-1.2/distfreereg/tests/1-04_distfreereg_glm.Rout.save | 38 distfreereg-1.2/distfreereg/tests/1-05_distfreereg_lmerMod.Rout.save | 26 distfreereg-1.2/distfreereg/tests/1-06_other.R | 8 distfreereg-1.2/distfreereg/tests/1-06_other.Rout.save | 31 distfreereg-1.2/distfreereg/tests/2-01_compare.R | 112 distfreereg-1.2/distfreereg/tests/2-01_compare.Rout.save | 2447 ++++---- distfreereg-1.2/distfreereg/vignettes/bibliography.bib | 17 distfreereg-1.2/distfreereg/vignettes/v1_introduction.rmd | 939 +-- distfreereg-1.2/distfreereg/vignettes/v2_compare.rmd | 77 distfreereg-1.2/distfreereg/vignettes/v3_plotting.rmd | 40 distfreereg-1.2/distfreereg/vignettes/v4_parameter-estimation.rmd | 116 distfreereg-1.2/distfreereg/vignettes/v5_advanced-options.rmd | 152 132 files changed, 11041 insertions(+), 9506 deletions(-)
Title: Columnar Query Engine for Larger-than-RAM Data
Description: A minimal columnar query engine with lazy execution on datasets
larger than RAM. Provides 'dplyr'-like verbs (filter(), select(), mutate(),
group_by(), summarise(), joins, window functions) and common aggregations
(n(), sum(), mean(), min(), max(), sd(), first(), last()) backed by a
pure C11 pull-based execution engine and a custom on-disk format ('.vtr').
Reads and writes 'GeoTIFF' (including tiled and 'BigTIFF' layouts) and a
tiled raster format ('.vec') with overview pyramids and time cubes for
larger-than-RAM raster data.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
This is a re-admission after prior archival of version 0.5.1 dated 2026-04-21
Diff between vectra versions 0.5.1 dated 2026-04-21 and 0.6.2 dated 2026-05-08
DESCRIPTION | 12 LICENSE | 4 MD5 | 328 ++--- NAMESPACE | 15 NEWS.md | 601 +++++---- R/across.R | 296 ++-- R/bind.R | 176 +- R/block.R | 218 +-- R/collect.R | 62 R/delete.R | 78 - R/diff.R | 164 +- R/explain.R | 76 - R/index.R | 118 - R/print.R | 154 +- R/raster.R |only R/reframe.R | 134 +- R/schema.R | 580 ++++----- R/tbl.R | 639 ++++++---- R/verbs_basic.R | 486 +++---- R/verbs_grouping.R | 706 +++++------ R/verbs_utility.R | 900 +++++++------- R/windows.R | 242 +-- R/write.R | 136 ++ R/zzz.R | 96 - README.md | 36 build/vignette.rds |binary configure | 16 configure.win | 7 inst/benchmarks/bench_core.R | 690 +++++----- inst/doc/engine.html | 4 inst/doc/formats.Rmd | 920 +++++++------- inst/doc/formats.html | 8 inst/doc/indexing.html | 8 inst/doc/joins.html | 4 inst/doc/large-data.Rmd | 1852 ++++++++++++++--------------- inst/doc/large-data.html | 4 inst/doc/quickstart.html | 4 inst/doc/schema.Rmd | 796 ++++++------ inst/doc/schema.html | 4 inst/doc/string-ops.Rmd | 2024 ++++++++++++++++---------------- inst/doc/string-ops.html | 4 man/across.Rd | 66 - man/append_vtr.Rd | 78 - man/arrange.Rd | 66 - man/bind_rows.Rd | 86 - man/block_fuzzy_lookup.Rd | 94 - man/block_lookup.Rd | 78 - man/collect.Rd | 56 man/count.Rd | 80 - man/create_index.Rd | 78 - man/cross_join.Rd | 66 - man/delete_vtr.Rd | 84 - man/desc.Rd | 48 man/diff_vtr.Rd | 116 - man/distinct.Rd | 68 - man/explain.Rd | 52 man/filter.Rd | 76 - man/fuzzy_join.Rd | 100 - man/glimpse.Rd | 58 man/group_by.Rd | 52 man/has_index.Rd | 56 man/head.vectra_node.Rd | 42 man/left_join.Rd | 120 - man/link.Rd | 66 - man/lookup.Rd | 130 +- man/materialize.Rd | 66 - man/mutate.Rd | 76 - man/print.vectra_node.Rd | 38 man/pull.Rd | 52 man/reframe.Rd | 54 man/relocate.Rd | 60 man/rename.Rd | 52 man/select.Rd | 52 man/slice.Rd | 52 man/slice_head.Rd | 88 - man/summarise.Rd | 94 - man/tbl.Rd | 52 man/tbl_csv.Rd | 58 man/tbl_sqlite.Rd | 68 - man/tbl_tiff.Rd | 78 - man/tbl_xlsx.Rd | 74 - man/tiff_band_names.Rd |only man/tiff_crs.Rd |only man/tiff_extract_points.Rd | 96 - man/tiff_metadata.Rd | 56 man/transmute.Rd | 52 man/ungroup.Rd | 52 man/vec_build_overviews.Rd |only man/vec_close_raster.Rd |only man/vec_extract_points.Rd |only man/vec_open_raster.Rd |only man/vec_raster_layout.Rd |only man/vec_raster_times.Rd |only man/vec_read_pixel_series.Rd |only man/vec_read_time_slice.Rd |only man/vec_read_window.Rd |only man/vec_to_tiff.Rd |only man/vec_write_raster.Rd |only man/vec_write_time_cube.Rd |only man/vtr_schema.Rd | 90 - man/write_csv.Rd | 62 man/write_sqlite.Rd | 66 - man/write_tiff.Rd | 129 +- src/block.c | 15 src/collect.c | 40 src/csv_scan.c | 22 src/expr_string.c | 4 src/fuzzy_join.c | 13 src/grow.h |only src/init.c | 50 src/miniz/UPSTREAM | 90 - src/r_bridge.c | 16 src/r_bridge.h | 7 src/r_bridge_io.c | 131 +- src/r_bridge_raster.c |only src/tdc/VENDORED_FROM | 2 src/tdc/src/entropy/lz.c | 8 src/tdc/src/entropy/lz_streams.c | 11 src/tdc/src/model/float_pred_helpers.h | 26 src/tdc/src/model/pred2d.c | 547 ++++++++ src/tdc/src/model/pred2d_internal.h | 25 src/tdc/src/model/pred3d.c | 86 - src/tdc/src/model/pred3d_float.c | 29 src/tiff_format.c | 1633 ++++++++++++++++++++----- src/tiff_format.h | 72 + src/tiff_write.c | 49 src/tiff_write.h | 20 src/vec_omp.h | 19 src/vec_raster.c |only src/vec_raster.h |only src/vtr1_tdc.c | 10 src/vtr_diff.c | 10 tests/testthat.R | 8 tests/testthat/test-agg.R | 278 ++-- tests/testthat/test-append-delete.R | 496 +++---- tests/testthat/test-binary-search.R | 192 +-- tests/testthat/test-codec-tdc.R | 226 +-- tests/testthat/test-compression.R | 1020 ++++++++-------- tests/testthat/test-count-tally.R | 122 - tests/testthat/test-csv.R | 258 ++-- tests/testthat/test-datetime.R | 246 +-- tests/testthat/test-edge-cases.R | 288 ++-- tests/testthat/test-expressions.R | 512 ++++---- tests/testthat/test-filter.R | 644 +++++----- tests/testthat/test-full-join.R | 352 ++--- tests/testthat/test-groupby.R | 298 ++-- tests/testthat/test-index.R | 250 +-- tests/testthat/test-joins.R | 846 ++++++------- tests/testthat/test-levenshtein.R | 490 +++---- tests/testthat/test-mutate.R | 122 - tests/testthat/test-new-aggs.R | 440 +++--- tests/testthat/test-new-aggs2.R | 260 ++-- tests/testthat/test-optimize.R | 340 ++--- tests/testthat/test-project.R | 38 tests/testthat/test-raster.R |only tests/testthat/test-resolve-propagate.R | 410 +++--- tests/testthat/test-schema.R | 494 +++---- tests/testthat/test-sql-scan.R | 294 ++-- tests/testthat/test-tidyselect.R | 194 +-- tests/testthat/test-tiff-bigtiff.R |only tests/testthat/test-tiff-extract.R | 198 +-- tests/testthat/test-tiff-geotiff.R |only tests/testthat/test-tiff-scan.R | 310 ++-- tests/testthat/test-tiff-typed.R | 306 ++-- tests/testthat/test-topn.R | 362 ++--- tests/testthat/test-types.R | 210 +-- tests/testthat/test-verbs.R | 732 +++++------ tests/testthat/test-vtr1-tdc.R | 800 ++++++------ tests/testthat/test-vtr1.R | 192 +-- tests/testthat/test-windows.R | 436 +++--- tests/testthat/test-write-vtr-node.R | 148 +- tests/testthat/test-xlsx-scan.R | 216 +-- vignettes/formats.Rmd | 920 +++++++------- vignettes/large-data.Rmd | 1852 ++++++++++++++--------------- vignettes/schema.Rmd | 796 ++++++------ vignettes/string-ops.Rmd | 2024 ++++++++++++++++---------------- 176 files changed, 19984 insertions(+), 17606 deletions(-)
Title: Generalized Linear Models with Slab and Shrinkage Estimators
Description: Provides a flexible framework for fitting generalized linear models (GLMs)
with slab and shrinkage estimators. Methods include the Stein estimator (St),
Diagonal Shrinkage (DSh), Simple Slab Regression (SR), Generalized Slab Regression (GSR),
Ledoit-Wolf Linear Shrinkage (LW), Quadratic-Inverse Shrinkage (QIS),
and Shrinkage (Sh), all integrated into the iteratively reweighted least squares (IRLS)
algorithm. This approach enhances estimation accuracy, convergence, and robustness
in the presence of multicollinearity. The best-fitting model is selected based on
the Akaike Information Criterion (AIC). Methods are related to methods described in
Marschner (2011) <doi:10.32614/RJ-2011-012>,
Asimit et al. (2025) <https://openaccess.city.ac.uk/id/eprint/35005/>,
Ledoit and Wolf (2004) <doi:10.1016/S0047-259X(03)00096-4>, and
Ledoit and Wolf (2022) <doi:10.3150/20-BEJ1315>.
Author: Ziwei Chen [aut, cre] ,
Vali Asimit [aut] ,
Claudio Senatore [aut]
Maintainer: Ziwei Chen <Ziwei.Chen.3@citystgeorges.ac.uk>
Diff between savvyGLM versions 0.1.2 dated 2026-05-03 and 0.1.4 dated 2026-05-08
DESCRIPTION | 9 MD5 | 18 R/savvy_glm.fit2.R | 3 R/savvy_glm2.R | 3 inst/doc/savvyGLM.R | 38 -- inst/doc/savvyGLM.Rmd | 48 -- inst/doc/savvyGLM.html | 912 ++++++++++++++++++++++++------------------------- man/savvy_glm.fit2.Rd | 3 man/savvy_glm2.Rd | 3 vignettes/savvyGLM.Rmd | 48 -- 10 files changed, 507 insertions(+), 578 deletions(-)
Title: Merging of Satellite Datasets with Ground Observations using
Random Forests
Description: S3 implementation of the Random Forest MErging Procedure (RF-MEP), which combines two or more satellite-based datasets (e.g., precipitation products, topography) with ground observations to produce a new dataset with improved spatio-temporal distribution of the target field. In particular, this package was developed to merge different Satellite-based Rainfall Estimates (SREs) with measurements from rain gauges, in order to obtain a new precipitation dataset where the time series in the rain gauges are used to correct different types of errors present in the SREs. However, this package might be used to merge other hydrological/environmental gridded datasets with point observations. For details, see Baez-Villanueva et al. (2020) <doi:10.1016/j.rse.2019.111606>. Bugs / comments / questions / collaboration of any kind are very welcomed.
Author: Mauricio Zambrano-Bigiarini [aut, cre, cph] ,
Oscar M. Baez-Villanueva [aut, cph] ,
Juan Giraldo-Osorio [ctb]
Maintainer: Mauricio Zambrano-Bigiarini <mzb.devel@gmail.com>
This is a re-admission after prior archival of version 0.1-10 dated 2020-05-22
Diff between RFmerge versions 0.1-10 dated 2020-05-22 and 0.3-3 dated 2026-05-08
RFmerge-0.1-10/RFmerge/NEWS |only RFmerge-0.1-10/RFmerge/R/buffer_dist.R |only RFmerge-0.1-10/RFmerge/data/ValparaisoSHP.RData |only RFmerge-0.1-10/RFmerge/inst/doc/RFmerge-RainfallExample-minimal.R |only RFmerge-0.1-10/RFmerge/inst/doc/RFmerge-RainfallExample-minimal.Rmd |only RFmerge-0.1-10/RFmerge/inst/doc/RFmerge-RainfallExample-minimal.pdf |only RFmerge-0.1-10/RFmerge/man/ValparaisoSHP.Rd |only RFmerge-0.1-10/RFmerge/vignettes/RFmerge-RainfallExample-minimal.Rmd |only RFmerge-0.3-3/RFmerge/DESCRIPTION | 29 RFmerge-0.3-3/RFmerge/MD5 | 38 RFmerge-0.3-3/RFmerge/NAMESPACE | 5 RFmerge-0.3-3/RFmerge/NEWS.md |only RFmerge-0.3-3/RFmerge/R/RFmerge.R | 891 +++++----- RFmerge-0.3-3/RFmerge/R/zl.R | 4 RFmerge-0.3-3/RFmerge/build/partial.rdb |binary RFmerge-0.3-3/RFmerge/build/vignette.rds |binary RFmerge-0.3-3/RFmerge/inst/CITATION | 35 RFmerge-0.3-3/RFmerge/inst/doc/RFmerge-RainfallExample-link.Rmd |only RFmerge-0.3-3/RFmerge/inst/doc/RFmerge-RainfallExample-link.html |only RFmerge-0.3-3/RFmerge/inst/extdata/ValparaisoSHP.cpg |only RFmerge-0.3-3/RFmerge/inst/extdata/ValparaisoSHP.dbf |only RFmerge-0.3-3/RFmerge/inst/extdata/ValparaisoSHP.prj |only RFmerge-0.3-3/RFmerge/inst/extdata/ValparaisoSHP.shp |only RFmerge-0.3-3/RFmerge/inst/extdata/ValparaisoSHP.shx |only RFmerge-0.3-3/RFmerge/man/RFmerge-package.Rd | 31 RFmerge-0.3-3/RFmerge/man/RFmerge.Rd | 70 RFmerge-0.3-3/RFmerge/man/ValparaisoPPts.Rd | 12 RFmerge-0.3-3/RFmerge/man/figures |only RFmerge-0.3-3/RFmerge/vignettes/RFmerge-RainfallExample-link.Rmd |only 29 files changed, 631 insertions(+), 484 deletions(-)
Title: For Writing Geneva Graduate Institute Documents
Description: A set of tools for writing documents
according to Geneva Graduate Institute conventions and regulations.
The most common use is for writing and compiling theses or thesis
chapters, as drafts or for examination with correct preamble formatting.
However, the package also offers users to create HTML presentation
slides with 'xaringan', complete problem sets, format posters, and,
for course instructors, prepare a syllabus.
The package includes additional functions for institutional color palettes,
an institutional 'ggplot' theme, a function for counting manuscript words,
and a bibliographical analysis toolkit.
Author: James Hollway [aut, cre, cph] ,
Bernhard Bieri [ctb] ,
Henrique Sposito [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between iheiddown versions 0.9.7 dated 2022-11-09 and 0.9.9 dated 2026-05-08
DESCRIPTION | 21 MD5 | 76 +-- NEWS.md | 16 R/bibfix.R | 8 R/count_words.R | 38 - R/zzz.R | 2 README.md | 12 build/vignette.rds |binary inst/_bookdown.yml | 2 inst/doc/poster.R | 4 inst/doc/poster.Rmd | 2 inst/doc/poster.html | 24 - inst/doc/presentations.R | 78 +-- inst/doc/presentations.Rmd | 10 inst/doc/presentations.html | 223 +++++----- inst/doc/problemset.R | 4 inst/doc/problemset.html | 135 +++--- inst/doc/syllabus.R | 4 inst/doc/syllabus.html | 22 inst/doc/thesis.R | 4 inst/doc/thesis.Rmd | 6 inst/doc/thesis.html | 29 - inst/rmarkdown/lua/color-text.lua | 2 inst/rmarkdown/templates/iheiddown_poster/skeleton/packages.bib | 2 inst/rmarkdown/templates/presentation/skeleton/assets/myBib.bib | 2 inst/rmarkdown/templates/presentation/skeleton/skeleton.Rmd | 4 inst/rmarkdown/templates/problemset/skeleton/references.bib | 2 inst/rmarkdown/templates/syllabus/skeleton/references.bib | 4 inst/rmarkdown/templates/thesis/skeleton/01-introduction.Rmd | 2 inst/rmarkdown/templates/thesis/skeleton/05-conclusion.Rmd | 4 inst/rmarkdown/templates/thesis/skeleton/98-appendices.Rmd | 2 inst/rmarkdown/templates/thesis/skeleton/_bookdown.yml | 2 inst/rmarkdown/templates/thesis/skeleton/bib/references.bib | 2 inst/rmarkdown/templates/thesis/skeleton/front-matter/abbreviations.aux |only inst/rmarkdown/templates/thesis/skeleton/skeleton.Rmd | 2 tests/testthat/test-countwords.R | 7 tests/testthat/test.Rmd |only vignettes/poster.Rmd | 2 vignettes/presentations.Rmd | 10 vignettes/thesis.Rmd | 6 40 files changed, 403 insertions(+), 372 deletions(-)
Title: Easy Study of Patient DICOM Data in Oncology
Description: Read, process, and export DICOM and DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, with patient-oriented 2D-3D visualization.
Author: Cathy Fontbonne [aut, cre] ,
Jean-Marc Fontbonne [aut] ,
Nathan Azemar [ctb]
Maintainer: Cathy Fontbonne <contact.espadon@lpccaen.in2p3.fr>
Diff between espadon versions 1.11.3 dated 2025-11-17 and 1.11.5 dated 2026-05-08
espadon-1.11.3/espadon/build/stage23.rdb |only espadon-1.11.5/espadon/DESCRIPTION | 22 espadon-1.11.5/espadon/MD5 | 479 +- espadon-1.11.5/espadon/NAMESPACE | 1 espadon-1.11.5/espadon/NEWS.md | 18 espadon-1.11.5/espadon/R/Rdcm_inventory.R | 120 espadon-1.11.5/espadon/R/Rdcm_upgrade.R | 46 espadon-1.11.5/espadon/R/add_margin.R | 56 espadon-1.11.5/espadon/R/add_shape.R | 86 espadon-1.11.5/espadon/R/bin_closing.R | 52 espadon-1.11.5/espadon/R/bin_clustering.R | 37 espadon-1.11.5/espadon/R/bin_dilation.R | 52 espadon-1.11.5/espadon/R/bin_erosion.R | 48 espadon-1.11.5/espadon/R/bin_from_roi.R | 321 - espadon-1.11.5/espadon/R/bin_from_vol.R | 28 espadon-1.11.5/espadon/R/bin_intersection.R | 35 espadon-1.11.5/espadon/R/bin_inversion.R | 20 espadon-1.11.5/espadon/R/bin_opening.R | 49 espadon-1.11.5/espadon/R/bin_shape.R | 559 +- espadon-1.11.5/espadon/R/bin_subtraction.R | 34 espadon-1.11.5/espadon/R/bin_sum.R | 35 espadon-1.11.5/espadon/R/castlow_str.R | 7 espadon-1.11.5/espadon/R/castup_str.R | 7 espadon-1.11.5/espadon/R/contour.R | 16 espadon-1.11.5/espadon/R/dicom_browser.R | 18 espadon-1.11.5/espadon/R/dicom_get_UID.R | 84 espadon-1.11.5/espadon/R/dicom_parser.R | 135 espadon-1.11.5/espadon/R/dicom_patient_anonymiser.R | 52 espadon-1.11.5/espadon/R/dicom_raw_data_anonymizer.R | 326 - espadon-1.11.5/espadon/R/dicom_raw_data_loader.R | 4 espadon-1.11.5/espadon/R/dicom_set_tag_value.R | 254 - espadon-1.11.5/espadon/R/dicom_tag_dictionary.R | 2 espadon-1.11.5/espadon/R/dicom_tag_parser.R | 61 espadon-1.11.5/espadon/R/dicom_to_Rdcm_converter.R | 68 espadon-1.11.5/espadon/R/dicom_viewer.R | 156 espadon-1.11.5/espadon/R/display_2D_histo.R | 127 espadon-1.11.5/espadon/R/display_3D_contour.R | 88 espadon-1.11.5/espadon/R/display_3D_mesh.R | 16 espadon-1.11.5/espadon/R/display_3D_sections.R | 68 espadon-1.11.5/espadon/R/display_3D_stack.R | 95 espadon-1.11.5/espadon/R/display_DVH.R | 23 espadon-1.11.5/espadon/R/display_DVH_pc.R | 22 espadon-1.11.5/espadon/R/display_dV_dx.R | 19 espadon-1.11.5/espadon/R/display_histo.R | 24 espadon-1.11.5/espadon/R/display_kplane.R | 62 espadon-1.11.5/espadon/R/display_legend.R | 43 espadon-1.11.5/espadon/R/display_obj_links.R | 398 -- espadon-1.11.5/espadon/R/display_palette.R | 91 espadon-1.11.5/espadon/R/display_plane.R | 400 -- espadon-1.11.5/espadon/R/dist_mesh.R | 191 - espadon-1.11.5/espadon/R/dist_to_conformity.R | 9 espadon-1.11.5/espadon/R/err_metrics_from_roi.R | 80 espadon-1.11.5/espadon/R/espadon-package.R | 90 espadon-1.11.5/espadon/R/espadon_class.R | 6 espadon-1.11.5/espadon/R/espadon_hidden.R | 3430 ++++++++---------- espadon-1.11.5/espadon/R/export.R | 1326 +++--- espadon-1.11.5/espadon/R/fan_beam.R | 13 espadon-1.11.5/espadon/R/fan_planar.R | 40 espadon-1.11.5/espadon/R/fan_sphere.R | 39 espadon-1.11.5/espadon/R/fan_to_voxel.R | 119 espadon-1.11.5/espadon/R/get_extreme_pt.R | 55 espadon-1.11.5/espadon/R/get_ijk_from_index.R | 7 espadon-1.11.5/espadon/R/get_ijk_from_xyz.R | 23 espadon-1.11.5/espadon/R/get_line.R | 24 espadon-1.11.5/espadon/R/get_obj_connection.R | 80 espadon-1.11.5/espadon/R/get_plane.R | 166 espadon-1.11.5/espadon/R/get_rigid_M.R | 29 espadon-1.11.5/espadon/R/get_roi_connection.R | 38 espadon-1.11.5/espadon/R/get_value_from_ijk.R | 47 espadon-1.11.5/espadon/R/get_value_from_mesh.R | 143 espadon-1.11.5/espadon/R/get_value_from_xyz.R | 50 espadon-1.11.5/espadon/R/get_volume_from_bin.R | 35 espadon-1.11.5/espadon/R/get_volume_from_roi.R | 39 espadon-1.11.5/espadon/R/get_xyz_from_index.R | 22 espadon-1.11.5/espadon/R/grid_equal.R | 22 espadon-1.11.5/espadon/R/histo_2D.R | 139 espadon-1.11.5/espadon/R/histo_DVH.R | 46 espadon-1.11.5/espadon/R/histo_from_bin.R | 55 espadon-1.11.5/espadon/R/histo_from_roi.R | 102 espadon-1.11.5/espadon/R/histo_vol.R | 57 espadon-1.11.5/espadon/R/load_Rdcm_raw_data.R | 165 espadon-1.11.5/espadon/R/load_T_MAT.R | 52 espadon-1.11.5/espadon/R/load_obj_data.R | 28 espadon-1.11.5/espadon/R/load_obj_from_Rdcm.R | 52 espadon-1.11.5/espadon/R/load_obj_from_dicom.R | 48 espadon-1.11.5/espadon/R/load_patient_from_Rdcm.R | 153 espadon-1.11.5/espadon/R/load_patient_from_dicom.R | 167 espadon-1.11.5/espadon/R/mesh_from_bin.R | 72 espadon-1.11.5/espadon/R/mesh_in_new_ref.R | 32 espadon-1.11.5/espadon/R/mesh_repair.R | 130 espadon-1.11.5/espadon/R/mesh_spheric_proj.R | 201 - espadon-1.11.5/espadon/R/nesting_bin.R | 111 espadon-1.11.5/espadon/R/nesting_cube.R | 128 espadon-1.11.5/espadon/R/nesting_roi.R | 144 espadon-1.11.5/espadon/R/obj_create.R | 31 espadon-1.11.5/espadon/R/orientation_create.R | 44 espadon-1.11.5/espadon/R/pal_RVV.R | 64 espadon-1.11.5/espadon/R/pal_rainbow.R | 29 espadon-1.11.5/espadon/R/plot.R | 415 +- espadon-1.11.5/espadon/R/polyg.R | 14 espadon-1.11.5/espadon/R/ref_add.R | 141 espadon-1.11.5/espadon/R/ref_cutplane_add.R | 43 espadon-1.11.5/espadon/R/ref_remove.R | 47 espadon-1.11.5/espadon/R/ref_srctodest_add.R | 117 espadon-1.11.5/espadon/R/rt_chi_index.R | 120 espadon-1.11.5/espadon/R/rt_gamma_index.R | 158 espadon-1.11.5/espadon/R/rt_indices_from_bin.R | 124 espadon-1.11.5/espadon/R/rt_indices_from_roi.R | 1471 ++----- espadon-1.11.5/espadon/R/save_T_MAT.R | 71 espadon-1.11.5/espadon/R/save_to_Rdcm.R | 77 espadon-1.11.5/espadon/R/select_names.R | 46 espadon-1.11.5/espadon/R/set_ref_obj.R | 42 espadon-1.11.5/espadon/R/sp_similarity_from_bin.R | 75 espadon-1.11.5/espadon/R/sp_similarity_from_mesh.R | 74 espadon-1.11.5/espadon/R/struct_clustering.R | 107 espadon-1.11.5/espadon/R/struct_create.R | 106 espadon-1.11.5/espadon/R/struct_from_bin.R | 122 espadon-1.11.5/espadon/R/struct_from_mesh.R | 299 - espadon-1.11.5/espadon/R/struct_in_new_ref.R | 39 espadon-1.11.5/espadon/R/struct_merge.R | 100 espadon-1.11.5/espadon/R/struct_update_roiinfo.R | 11 espadon-1.11.5/espadon/R/study_deployment.R | 161 espadon-1.11.5/espadon/R/toy_dicom_raw.R | 8 espadon-1.11.5/espadon/R/toy_load_patient.R | 481 +- espadon-1.11.5/espadon/R/toy_rtdose.R | 240 - espadon-1.11.5/espadon/R/vector_product.R | 15 espadon-1.11.5/espadon/R/vol_abserror.R | 24 espadon-1.11.5/espadon/R/vol_border_tuning.R | 43 espadon-1.11.5/espadon/R/vol_copy.R | 25 espadon-1.11.5/espadon/R/vol_create.R | 76 espadon-1.11.5/espadon/R/vol_error.R | 24 espadon-1.11.5/espadon/R/vol_from_bin.R | 49 espadon-1.11.5/espadon/R/vol_gradient.R | 35 espadon-1.11.5/espadon/R/vol_in_new_ref.R | 44 espadon-1.11.5/espadon/R/vol_median.R | 29 espadon-1.11.5/espadon/R/vol_oversampling.R | 64 espadon-1.11.5/espadon/R/vol_regrid.R | 147 espadon-1.11.5/espadon/R/vol_repair.R | 85 espadon-1.11.5/espadon/R/vol_subsampling.R | 58 espadon-1.11.5/espadon/R/vol_sum.R | 44 espadon-1.11.5/espadon/R/xlsx_from_Rdcm.R | 92 espadon-1.11.5/espadon/R/xlsx_from_dcm.R | 61 espadon-1.11.5/espadon/build/partial.rdb |binary espadon-1.11.5/espadon/build/vignette.rds |binary espadon-1.11.5/espadon/inst/doc/espadon_overview.html | 32 espadon-1.11.5/espadon/man/Rdcm.inventory.Rd | 19 espadon-1.11.5/espadon/man/Rdcm.upgrade.Rd | 20 espadon-1.11.5/espadon/man/add.margin.Rd | 100 espadon-1.11.5/espadon/man/add.shape.Rd | 18 espadon-1.11.5/espadon/man/bin.clustering.Rd | 5 espadon-1.11.5/espadon/man/dicom.set.tag.value.Rd | 6 espadon-1.11.5/espadon/man/display.DVH.Rd | 2 espadon-1.11.5/espadon/man/display.dV_dx.Rd | 2 espadon-1.11.5/espadon/man/display.kplane.Rd | 2 espadon-1.11.5/espadon/man/espadon-package.Rd | 73 espadon-1.11.5/espadon/man/espadon.class.Rd | 2 espadon-1.11.5/espadon/man/export.Rd | 2 espadon-1.11.5/espadon/man/get.obj.connection.Rd | 6 espadon-1.11.5/espadon/man/get.plane.Rd | 36 espadon-1.11.5/espadon/man/get.rigid.M.Rd | 6 espadon-1.11.5/espadon/man/get.roi.connection.Rd | 8 espadon-1.11.5/espadon/man/get.value.from.ijk.Rd | 12 espadon-1.11.5/espadon/man/get.value.from.mesh.Rd | 22 espadon-1.11.5/espadon/man/get.value.from.xyz.Rd | 8 espadon-1.11.5/espadon/man/get.volume.from.bin.Rd | 22 espadon-1.11.5/espadon/man/get.volume.from.roi.Rd | 12 espadon-1.11.5/espadon/man/get.xyz.from.index.Rd | 8 espadon-1.11.5/espadon/man/grid.equal.Rd | 8 espadon-1.11.5/espadon/man/histo.2D.Rd | 24 espadon-1.11.5/espadon/man/histo.DVH.Rd | 16 espadon-1.11.5/espadon/man/histo.from.bin.Rd | 34 espadon-1.11.5/espadon/man/histo.from.roi.Rd | 14 espadon-1.11.5/espadon/man/histo.vol.Rd | 8 espadon-1.11.5/espadon/man/load.Rdcm.raw.data.Rd | 22 espadon-1.11.5/espadon/man/load.T.MAT.Rd | 18 espadon-1.11.5/espadon/man/load.obj.data.Rd | 16 espadon-1.11.5/espadon/man/load.obj.from.Rdcm.Rd | 22 espadon-1.11.5/espadon/man/load.obj.from.dicom.Rd | 18 espadon-1.11.5/espadon/man/load.patient.from.Rdcm.Rd | 20 espadon-1.11.5/espadon/man/load.patient.from.dicom.Rd | 24 espadon-1.11.5/espadon/man/mesh.from.bin.Rd | 10 espadon-1.11.5/espadon/man/mesh.in.new.ref.Rd | 12 espadon-1.11.5/espadon/man/mesh.repair.Rd | 14 espadon-1.11.5/espadon/man/mesh.spheric.proj.Rd | 26 espadon-1.11.5/espadon/man/nesting.bin.Rd | 16 espadon-1.11.5/espadon/man/nesting.cube.Rd | 14 espadon-1.11.5/espadon/man/nesting.roi.Rd | 30 espadon-1.11.5/espadon/man/obj.create.Rd | 8 espadon-1.11.5/espadon/man/orientation.create.Rd | 8 espadon-1.11.5/espadon/man/pal.RVV.Rd | 12 espadon-1.11.5/espadon/man/pal.rainbow.Rd | 12 espadon-1.11.5/espadon/man/plot.Rd | 48 espadon-1.11.5/espadon/man/ref.add.Rd | 8 espadon-1.11.5/espadon/man/ref.cutplane.add.Rd | 6 espadon-1.11.5/espadon/man/ref.remove.Rd | 10 espadon-1.11.5/espadon/man/ref.srctodest.add.Rd | 10 espadon-1.11.5/espadon/man/rt.chi.index.Rd | 36 espadon-1.11.5/espadon/man/rt.gamma.index.Rd | 28 espadon-1.11.5/espadon/man/rt.indices.from.bin.Rd | 26 espadon-1.11.5/espadon/man/rt.indices.from.roi.Rd | 249 - espadon-1.11.5/espadon/man/save.T.MAT.Rd | 12 espadon-1.11.5/espadon/man/save.to.Rdcm.Rd | 14 espadon-1.11.5/espadon/man/select.names.Rd | 8 espadon-1.11.5/espadon/man/set.reference.obj.Rd | 6 espadon-1.11.5/espadon/man/sp.similarity.from.bin.Rd | 16 espadon-1.11.5/espadon/man/sp.similarity.from.mesh.Rd | 16 espadon-1.11.5/espadon/man/struct.clustering.Rd | 26 espadon-1.11.5/espadon/man/struct.create.Rd | 14 espadon-1.11.5/espadon/man/struct.from.bin.Rd | 14 espadon-1.11.5/espadon/man/struct.from.mesh.Rd | 6 espadon-1.11.5/espadon/man/struct.in.new.ref.Rd | 6 espadon-1.11.5/espadon/man/struct.merge.Rd | 20 espadon-1.11.5/espadon/man/study.deployment.Rd | 28 espadon-1.11.5/espadon/man/toy.dicom.raw.Rd | 2 espadon-1.11.5/espadon/man/toy.load.patient.Rd | 4 espadon-1.11.5/espadon/man/vector.product.Rd | 2 espadon-1.11.5/espadon/man/vol.abserror.Rd | 16 espadon-1.11.5/espadon/man/vol.copy.Rd | 6 espadon-1.11.5/espadon/man/vol.create.Rd | 14 espadon-1.11.5/espadon/man/vol.error.Rd | 16 espadon-1.11.5/espadon/man/vol.from.bin.Rd | 16 espadon-1.11.5/espadon/man/vol.gradient.Rd | 8 espadon-1.11.5/espadon/man/vol.in.new.ref.Rd | 6 espadon-1.11.5/espadon/man/vol.median.Rd | 8 espadon-1.11.5/espadon/man/vol.oversampling.Rd | 18 espadon-1.11.5/espadon/man/vol.regrid.Rd | 20 espadon-1.11.5/espadon/man/vol.repair.Rd | 22 espadon-1.11.5/espadon/man/vol.subsampling.Rd | 18 espadon-1.11.5/espadon/man/vol.sum.Rd | 6 espadon-1.11.5/espadon/man/xlsx.from.Rdcm.Rd | 24 espadon-1.11.5/espadon/man/xlsx.from.dcm.Rd | 10 espadon-1.11.5/espadon/src/dicombrowser.cpp | 11 espadon-1.11.5/espadon/src/fansphereC.cpp | 14 espadon-1.11.5/espadon/src/gammaindex.cpp | 2 espadon-1.11.5/espadon/src/getvaluefromijkC.cpp | 2 espadon-1.11.5/espadon/src/labelbrowser.cpp | 2 espadon-1.11.5/espadon/src/meshinfront.cpp | 1 espadon-1.11.5/espadon/src/ouline2voxC.cpp | 61 espadon-1.11.5/espadon/src/polygtoolsC.cpp | 8 espadon-1.11.5/espadon/src/ptinpolygonC.cpp | 3 espadon-1.11.5/espadon/src/ptnearestC.cpp | 7 241 files changed, 9242 insertions(+), 11082 deletions(-)
Title: Optimal Categorisation of Continuous Variables in Prediction
Models
Description: Allows the user to categorise a continuous predictor variable in a logistic or a Cox proportional hazards regression setting, by maximising the discriminative ability of the model. I Barrio, I Arostegui, MX Rodriguez-Alvarez, JM Quintana (2015) <doi:10.1177/0962280215601873>. I Barrio, MX Rodriguez-Alvarez, L Meira-Machado, C Esteban, I Arostegui (2017) <https://www.idescat.cat/sort/sort411/41.1.3.barrio-etal.pdf>.
Author: Irantzu Barrio [aut, cre],
Maria Xose Rodriguez-Alvarez [aut],
Inmaculada Arostegui [ctb],
Diana Marcela Perez [ctb]
Maintainer: Irantzu Barrio <irantzu.barrio@ehu.eus>
This is a re-admission after prior archival of version 1.4 dated 2025-10-30
Diff between CatPredi versions 1.4 dated 2025-10-30 and 2.0 dated 2026-05-08
CatPredi-1.4/CatPredi/man/CatPredi-package.Rd |only CatPredi-2.0/CatPredi/DESCRIPTION | 17 CatPredi-2.0/CatPredi/MD5 | 90 ++-- CatPredi-2.0/CatPredi/NAMESPACE | 42 +- CatPredi-2.0/CatPredi/R/auc.opt.corrected.R | 84 ++-- CatPredi-2.0/CatPredi/R/backaddfor.R | 20 - CatPredi-2.0/CatPredi/R/backaddfor.cind.R | 158 ++++---- CatPredi-2.0/CatPredi/R/calculate.AUC.R | 6 CatPredi-2.0/CatPredi/R/calculate.CPE.R | 52 +- CatPredi-2.0/CatPredi/R/calculate.cind.R | 6 CatPredi-2.0/CatPredi/R/catpredi.R | 164 +++++++- CatPredi-2.0/CatPredi/R/catpredi.survival.R | 153 ++++++-- CatPredi-2.0/CatPredi/R/cindex.categorization.R | 28 - CatPredi-2.0/CatPredi/R/cindex.opt.corrected.R | 16 CatPredi-2.0/CatPredi/R/comp.cutpoints.R | 90 ++++ CatPredi-2.0/CatPredi/R/comp.cutpoints.survival.R | 240 ++++++++---- CatPredi-2.0/CatPredi/R/compare.AUC.ht.R | 259 ++++++++------ CatPredi-2.0/CatPredi/R/controlcatpredi.R | 47 ++ CatPredi-2.0/CatPredi/R/controlcatpredi.survival.R | 46 ++ CatPredi-2.0/CatPredi/R/coxcpe.R | 4 CatPredi-2.0/CatPredi/R/cpe.opt.corrected.R | 78 ++-- CatPredi-2.0/CatPredi/R/globalVariables.R |only CatPredi-2.0/CatPredi/R/plot.catpredi.R | 92 +++- CatPredi-2.0/CatPredi/R/plot.catpredi.survival.R | 65 ++- CatPredi-2.0/CatPredi/R/print.catpredi.R | 109 ++--- CatPredi-2.0/CatPredi/R/print.catpredi.survival.R | 181 ++++----- CatPredi-2.0/CatPredi/R/print.comp.cutpoints.R | 3 CatPredi-2.0/CatPredi/R/print.comp.cutpoints.binary.R | 3 CatPredi-2.0/CatPredi/R/print.comp.cutpoints.survival.R | 5 CatPredi-2.0/CatPredi/R/print.summary.catpredi.R | 7 CatPredi-2.0/CatPredi/R/print.summary.catpredi.survival.R | 1 CatPredi-2.0/CatPredi/R/select.cutpoint.auc.R | 8 CatPredi-2.0/CatPredi/R/select.cutpoint.cind.R | 10 CatPredi-2.0/CatPredi/R/select.cutpoint.cpe.R | 58 +-- CatPredi-2.0/CatPredi/R/summary.catpredi.R | 61 +++ CatPredi-2.0/CatPredi/R/summary.catpredi.survival.R | 49 ++ CatPredi-2.0/CatPredi/man/catpredi.Rd | 257 +++++++------ CatPredi-2.0/CatPredi/man/catpredi.survival.Rd | 212 ++++++----- CatPredi-2.0/CatPredi/man/comp.cutpoints.Rd | 106 ++--- CatPredi-2.0/CatPredi/man/comp.cutpoints.survival.Rd | 153 ++++---- CatPredi-2.0/CatPredi/man/compare.AUC.ht.Rd | 161 ++++---- CatPredi-2.0/CatPredi/man/controlcatpredi.Rd | 65 ++- CatPredi-2.0/CatPredi/man/controlcatpredi.survival.Rd | 84 ++-- CatPredi-2.0/CatPredi/man/plot.catpredi.Rd | 120 +++--- CatPredi-2.0/CatPredi/man/plot.catpredi.survival.Rd | 78 ++-- CatPredi-2.0/CatPredi/man/summary.catpredi.Rd | 108 ++--- CatPredi-2.0/CatPredi/man/summary.catpredi.survival.Rd | 124 +++--- 47 files changed, 2267 insertions(+), 1453 deletions(-)
Title: Bayesian Prevalence-Incidence Mixture Model
Description: Models time-to-event data from interval-censored
screening studies. It accounts for latent prevalence at baseline and
incorporates misclassification due to imperfect test sensitivity. For usage
details, see the package vignette "BayesPIM_intro". Further details can be
found in Klausch, Lissenberg-Witte and Coupé (2026)
<doi:10.1002/sim.70433>.
Author: Thomas Klausch [aut, cre]
Maintainer: Thomas Klausch <t.klausch@amsterdamumc.nl>
This is a re-admission after prior archival of version 1.0.0 dated 2025-03-22
Diff between BayesPIM versions 1.0.0 dated 2025-03-22 and 1.0.1 dated 2026-05-08
DESCRIPTION | 19 MD5 | 43 - NAMESPACE | 1 R/BayesPIM_package.r | 25 R/RcppExports.R | 70 - R/bayes2S_v6.r | 1496 +++++++++++++++++++++------------------- R/bayes2S_v6_seq.r | 1355 +++++++++++++++++++----------------- R/datgen.r | 400 +++++----- R/search.prop.sd.r | 226 +++--- R/search.prop.sd_seq.r | 226 +++--- R/validate_bayes_2S_inputs.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/BayesPIM_intro.R | 422 +++++------ inst/doc/BayesPIM_intro.Rmd | 629 ++++++++--------- inst/doc/BayesPIM_intro.html | 1590 +++++++++++++++++++++---------------------- man/BayesPIM-package.Rd | 7 man/bayes.2S.Rd | 10 man/bayes.2S_seq.Rd | 15 man/gen.dat.Rd | 4 man/search.prop.sd.Rd | 2 man/search.prop.sd_seq.Rd | 6 vignettes/BayesPIM_intro.Rmd | 629 ++++++++--------- 23 files changed, 3705 insertions(+), 3470 deletions(-)
Title: Record Linkage Based on an Entropy-Maximizing Classifier
Description: The goal of 'automatedRecLin' is to perform record linkage (also known as entity resolution) in unsupervised or supervised settings. It compares pairs of records from two datasets using selected comparison functions to estimate the probability or density ratio between matched and non-matched records. Based on these estimates, it predicts a set of matches that maximizes entropy. For details see: Lee et al. (2022) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2022001/article/00007-eng.htm>, Vo et al. (2023) <https://ideas.repec.org/a/eee/csdana/v179y2023ics0167947322002365.html>, Sugiyama et al. (2008) <doi:10.1007/s10463-008-0197-x>.
Author: Adam Struzik [aut, cre] ,
Maciej Beresewicz [aut, ctb]
Maintainer: Adam Struzik <adastr5@st.amu.edu.pl>
Diff between automatedRecLin versions 1.0.1 dated 2025-12-13 and 1.1.0 dated 2026-05-08
DESCRIPTION | 21 MD5 | 61 - NAMESPACE | 4 NEWS.md | 24 R/bootstrap.R |only R/comparators.R | 10 R/comparison_vectors.R | 128 ++ R/controls.R | 8 R/data.R | 78 + R/internals.R | 1092 ++++++++++++++++++++++ R/methods.R | 69 + R/predict.R | 319 +----- R/supervised_learning.R | 261 ++--- R/unsupervised_learning.R | 1486 ++++++++++++++++++++++++------- README.md | 64 - build/partial.rdb |binary build/vignette.rds |only data/census.rda |only data/cis.rda |only inst/doc |only inst/tinytest/test_mec.R | 43 inst/tinytest/test_mec_blocking.R |only inst/tinytest/test_supervised_learning.R | 63 + man/census.Rd |only man/cis.Rd |only man/comparison_vectors.Rd | 14 man/control_kliep.Rd | 8 man/custom_rec_lin_model.Rd | 12 man/est_se_bootstrap.Rd |only man/jarowinkler_complement.Rd | 10 man/mec.Rd | 23 man/mec_blocking.Rd |only man/predict.rec_lin_model.Rd | 21 man/train_rec_lin.Rd | 23 tests/tinytest.R | 2 vignettes |only 36 files changed, 2950 insertions(+), 894 deletions(-)
More information about automatedRecLin at CRAN
Permanent link
Title: Stepwise Clustered Ensemble
Description: Implementation of Stepwise Clustered Ensemble (SCE) and Stepwise Cluster Analysis (SCA) for multivariate data analysis. The package provides comprehensive tools for feature selection, model training, prediction, and evaluation in hydrological and environmental modeling applications. Key functionalities include recursive feature elimination (RFE), Wilks feature importance analysis, model validation through out-of-bag (OOB) validation, and ensemble prediction capabilities. The package supports both single and multivariate response variables, making it suitable for complex environmental modeling scenarios. For more details see Li et al. (2021) <doi:10.5194/hess-25-4947-2021>.
Author: Kailong Li [aut, cre]
Maintainer: Kailong Li <lkl98509509@gmail.com>
Diff between SCE versions 1.1.2 dated 2025-10-04 and 1.1.3 dated 2026-05-08
SCE-1.1.2/SCE/data/Air_quality_testing.rda |only SCE-1.1.2/SCE/data/Air_quality_training.rda |only SCE-1.1.2/SCE/data/Streamflow_testing_10var.rda |only SCE-1.1.2/SCE/data/Streamflow_testing_22var.rda |only SCE-1.1.2/SCE/data/Streamflow_training_10var.rda |only SCE-1.1.2/SCE/data/Streamflow_training_22var.rda |only SCE-1.1.2/SCE/man/Air_quality.Rd |only SCE-1.1.2/SCE/man/Plot_RFE.Rd |only SCE-1.1.2/SCE/man/RFE_SCE.Rd |only SCE-1.1.2/SCE/man/SCA.Rd |only SCE-1.1.2/SCE/man/SCE.Rd |only SCE-1.1.2/SCE/man/Streamflow.Rd |only SCE-1.1.3/SCE/DESCRIPTION | 6 SCE-1.1.3/SCE/MD5 | 56 ++-- SCE-1.1.3/SCE/NAMESPACE | 28 +- SCE-1.1.3/SCE/NEWS.md | 14 + SCE-1.1.3/SCE/R/Model_evaluation.R | 34 +- SCE-1.1.3/SCE/R/Model_simulation.R | 24 - SCE-1.1.3/SCE/R/Prediction.R | 2 SCE-1.1.3/SCE/R/RFE_SCE.R | 14 - SCE-1.1.3/SCE/R/SCA.R | 42 +-- SCE-1.1.3/SCE/R/SCE.R | 321 +++++++++-------------- SCE-1.1.3/SCE/R/Wilks_importance.R | 8 SCE-1.1.3/SCE/README.md | 118 +++----- SCE-1.1.3/SCE/data/air_quality_testing.rda |only SCE-1.1.3/SCE/data/air_quality_training.rda |only SCE-1.1.3/SCE/data/streamflow_testing_10var.rda |only SCE-1.1.3/SCE/data/streamflow_testing_22var.rda |only SCE-1.1.3/SCE/data/streamflow_training_10var.rda |only SCE-1.1.3/SCE/data/streamflow_training_22var.rda |only SCE-1.1.3/SCE/man/air_quality.Rd |only SCE-1.1.3/SCE/man/evaluate.Rd | 10 SCE-1.1.3/SCE/man/importance.Rd | 10 SCE-1.1.3/SCE/man/plot_rfe.Rd |only SCE-1.1.3/SCE/man/predict.Rd | 10 SCE-1.1.3/SCE/man/print.Rd | 10 SCE-1.1.3/SCE/man/rfe_sce.Rd |only SCE-1.1.3/SCE/man/sca.Rd |only SCE-1.1.3/SCE/man/sce.Rd |only SCE-1.1.3/SCE/man/streamflow.Rd |only SCE-1.1.3/SCE/man/summary.Rd | 14 - 41 files changed, 335 insertions(+), 386 deletions(-)
Title: Modified Generalized Estimating Equations for Binary Outcome
Description: Analyze small-sample clustered or longitudinal data with binary
outcome using modified generalized estimating equations (GEE) with
bias-adjusted covariance estimator. The package provides any combination of
three GEE methods and 12 covariance estimators.
Author: Ryota Ishii [aut, cre],
Tomohiro Ohigashi [ctb],
Kazushi Maruo [ctb],
Masahiko Gosho [ctb]
Maintainer: Ryota Ishii <r.ishii0808@gmail.com>
Diff between geessbin versions 1.0.1 dated 2025-12-02 and 1.0.2 dated 2026-05-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 3 +++ R/sqrtmat.R | 3 ++- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Fitting Linear Models with Endogenous Regressors using Latent
Instrumental Variables
Description: Fits linear models with endogenous regressor using latent instrumental variable approaches.
The methods included in the package are Lewbel's (1997) <doi:10.2307/2171884> higher moments approach as well as
Lewbel's (2012) <doi:10.1080/07350015.2012.643126> heteroscedasticity approach, Park and Gupta's (2012) <doi:10.1287/mksc.1120.0718> joint estimation method
that uses Gaussian copula and Kim and Frees's (2007) <doi:10.1007/s11336-007-9008-1> multilevel generalized
method of moment approach that deals with endogeneity in a multilevel setting.
These are statistical techniques to address the endogeneity problem where no external instrumental variables are needed.
See the publication related to this package in the Journal of Statistical Software for more details: <doi:10.18637/jss.v107.i03>.
Note that with version 2.0.0 sweeping changes were introduced which greatly improve functionality and usability but break backwards compatibility.
Author: Raluca Gui [cre, aut],
Markus Meierer [aut],
Rene Algesheimer [aut],
Patrik Schilter [aut],
Kimberly-Anne Lew Chuk Wai [aut]
Maintainer: Raluca Gui <raluca.gui@gmail.com>
Diff between REndo versions 2.4.11 dated 2026-03-23 and 2.5.0 dated 2026-05-08
DESCRIPTION | 22 ++++--- MD5 | 42 ++++++++++---- NAMESPACE | 8 ++ NEWS.md | 12 +++- R/data.R | 79 ++++++++++++++++++++++++++++ R/f_checkinput_copulaIMA.R |only R/f_checkinput_copulacorrection.R | 10 --- R/f_checkinput_helperfunctions.R | 21 +++++++ R/f_checkinput_multilevel.R | 25 +++++--- R/f_copulaIMA_fit.R |only R/f_copulaIMA_helpers.R |only R/f_copulaIMA_interface.R |only R/f_copulacorrection_interface.R | 11 ++- R/f_new_rendobase.R | 15 +++++ R/f_new_rendoboots.R | 8 ++ R/f_new_rendobootsdegeneratesremoved.R |only R/f_new_rendocopulaima.R |only R/f_s3_rendobootsdegeneratesremoved.R |only R/f_s3_rendocopulaIMA.R |only data/dataCopIMABinExo.rda |only data/dataCopIMAContExo.rda |only data/dataCopIMAMultiEndo.rda |only man/REndo.Rd | 1 man/copulaCorrection.Rd | 15 +++-- man/copulaIMA.Rd |only man/dataCopIMABinExo.Rd |only man/dataCopIMAContExo.Rd |only man/dataCopIMAMultiEndo.Rd |only tests/testthat/test-correctness_copulaIMA.R |only tests/testthat/test-inputchecks_copulaIMA.R |only tests/testthat/test-runability_copulaIMA.R |only 31 files changed, 218 insertions(+), 51 deletions(-)
Title: Bayesian Regression with Functional Data
Description: Bayesian regression with functional data, including regression with scalar, survival, or functional outcomes. The package allows regression with scalar and functional predictors. Methods are described in Jiang et al. (2025)
"Tutorial on Bayesian Functional Regression Using Stan"
<doi:10.1002/sim.70265>.
Author: Ziren Jiang [aut, cre],
Erjia Cui [aut],
Ciprian Crainiceanu [ctb]
Maintainer: Ziren Jiang <jian0746@umn.edu>
Diff between refundBayes versions 0.5.1 dated 2026-04-07 and 0.6.0 dated 2026-05-08
DESCRIPTION | 10 MD5 | 73 ++- NAMESPACE | 5 NEWS.md |only R/fcox_bayes.R | 9 R/fofr_bayes.R |only R/fosr_bayes.R | 3 R/fpca_bayes.R |only R/refundBayes_plot.R | 257 ++++++++++++ R/refundBayesbasis.R | 69 +++ R/refundBayesdata.R | 235 ++++++++++- R/refundBayesformula.R | 14 R/refundBayesmodel.R | 45 +- R/refundBayesreconfuncoef.R | 8 R/sofr_bayes.R | 5 README.md | 278 ++++--------- build/vignette.rds |binary inst/CITATION |only inst/doc/fcox_bayes_vignette.Rmd | 26 - inst/doc/fcox_bayes_vignette.html | 176 ++++---- inst/doc/fofr_bayes_vignette.R |only inst/doc/fofr_bayes_vignette.Rmd |only inst/doc/fofr_bayes_vignette.html |only inst/doc/fosr_bayes_vignette.Rmd | 13 inst/doc/fosr_bayes_vignette.html | 126 +++--- inst/doc/fpca_bayes_vignette.R |only inst/doc/fpca_bayes_vignette.Rmd |only inst/doc/fpca_bayes_vignette.html |only inst/doc/joint_FPCA_vignette.R |only inst/doc/joint_FPCA_vignette.Rmd |only inst/doc/joint_FPCA_vignette.html |only inst/doc/sofr_bayes_vignette.Rmd | 23 - inst/doc/sofr_bayes_vignette.html | 780 ++++++++++++++++++++------------------ man/fcox_bayes.Rd | 8 man/fofr_bayes.Rd |only man/fosr_bayes.Rd | 2 man/fpca_bayes.Rd |only man/plot.refundBayes.Rd | 30 + man/sofr_bayes.Rd | 4 vignettes/fcox_bayes_vignette.Rmd | 26 - vignettes/figures |only vignettes/fofr_bayes_vignette.Rmd |only vignettes/fosr_bayes_vignette.Rmd | 13 vignettes/fpca_bayes_vignette.Rmd |only vignettes/joint_FPCA_vignette.Rmd |only vignettes/sofr_bayes_vignette.Rmd | 23 - 46 files changed, 1449 insertions(+), 812 deletions(-)
Title: Multiple Comparisons Using Normal Approximation
Description: Multiple contrast tests and simultaneous confidence
intervals based on normal approximation. With implementations for
binomial proportions in a 2xk setting (risk difference and odds ratio),
poly-3-adjusted tumour rates, biodiversity indices (multinomial data)
and expected values under lognormal assumption. Approximative power
calculation for multiple contrast tests of binomial and Gaussian data.
Author: Frank Schaarschmidt [aut, cre],
Daniel Gerhard [aut],
Martin Sill [aut]
Maintainer: Frank Schaarschmidt <schaarschmidt@biostat.uni-hannover.de>
Diff between MCPAN versions 1.1-21 dated 2018-03-22 and 1.1-22 dated 2026-05-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/PQln.Rd | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Download Sea Ice Concentration Data from the NSIDC Climate Data
Record
Description: Programmatic access to NSIDC's sea ice concentration CDR <https://nsidc.org/data/g02202> via ERDAPP server and Sea Ice index <https://nsidc.org/data/g02135>. Supports caching results and optional fixes for some inconsistencies of the raw files.
Author: Elio Campitelli [cre, aut, cph]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between icecdr versions 1.1.0 dated 2026-03-24 and 1.2.0 dated 2026-05-08
icecdr-1.1.0/icecdr/tests/testthat/_vcr/sea_ice_index.yml |only icecdr-1.2.0/icecdr/DESCRIPTION | 12 icecdr-1.2.0/icecdr/MD5 | 27 icecdr-1.2.0/icecdr/NEWS.md | 10 icecdr-1.2.0/icecdr/R/cdr-fix.R | 17 icecdr-1.2.0/icecdr/R/cdr.R | 33 icecdr-1.2.0/icecdr/R/sea_ice_index.R | 4 icecdr-1.2.0/icecdr/README.md | 9 icecdr-1.2.0/icecdr/man/cdr.Rd | 2 icecdr-1.2.0/icecdr/man/convenience.Rd | 8 icecdr-1.2.0/icecdr/man/figures/README-unnamed-chunk-3-1.png |binary icecdr-1.2.0/icecdr/man/icecdr-package.Rd | 7 icecdr-1.2.0/icecdr/tests/testthat/_vcr/bad-range.yml | 24 icecdr-1.2.0/icecdr/tests/testthat/_vcr/sea_index_daily.yml |14792 ---------- icecdr-1.2.0/icecdr/tests/testthat/_vcr/sea_index_monthly.yml | 165 15 files changed, 215 insertions(+), 14895 deletions(-)
Title: Nested Sequential Monte Carlo for the Bayesian Mallows Model
Description: Provides nested sequential Monte Carlo algorithms for performing
sequential inference in the Bayesian Mallows model, which is a widely used
probability model for rank and preference data. The package implements the
SMC2 (Sequential Monte Carlo Squared) algorithm for handling sequentially
arriving rankings and pairwise preferences, including support for complete
rankings, partial rankings, and pairwise comparisons. The methods are based
on Sorensen (2025) <doi:10.1214/25-BA1564>.
Author: Oystein Sorensen [aut, cre]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallowsSMC2 versions 0.2.1 dated 2026-02-04 and 0.3.0 dated 2026-05-08
DESCRIPTION | 8 ++++---- MD5 | 27 ++++++++++++++------------- NEWS.md | 6 ++++++ R/set_smc_options.R | 5 ++++- README.md | 11 ++++++++++- build/partial.rdb |binary inst/CITATION |only inst/REFERENCES.bib | 2 ++ man/set_smc_options.Rd | 7 ++++++- src/options.cpp | 3 ++- src/options.h | 1 + src/particle.cpp | 23 +++++++++++++++++------ src/particle.h | 4 +++- src/rejuvenate.cpp | 37 +++++++++++++++++++++++++++++++++---- src/run_smc.cpp | 3 +-- 15 files changed, 103 insertions(+), 34 deletions(-)
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Title: Comprehensive Geospatiotemporal Analysis and Multimodal
Integration Toolkit
Description: A comprehensive toolkit for geospatiotemporal analysis
featuring 60+ vegetation indices, advanced raster visualization,
universal spatial mapping, water quality analysis, CDL crop analysis,
spatial interpolation, temporal analysis, and terrain analysis.
Designed for agricultural research, environmental monitoring, remote
sensing applications, and publication-quality mapping with support for
any geographic region and robust error handling. Methods include
vegetation indices calculations (Rouse et al. 1974), NDVI and enhanced
vegetation indices (Huete et al. 1997)
<doi:10.1016/S0034-4257(97)00104-1>, (Akanbi et al. 2024)
<doi:10.1007/s41651-023-00164-y>, spatial interpolation techniques
(Cressie 1993, ISBN:9780471002556), water quality indices (McFeeters
1996) <doi:10.1080/01431169608948714>, and crop data layer analysis
(USDA NASS 2024)
<https://www.nass.usda.gov/Research_and_Science/Cropland/>. Funding:
This material is based upon financial support by the Natio [...truncated...]
Author: Olatunde D. Akanbi [aut, cre, cph] ,
Vibha Mandayam [aut] ,
Yinghui Wu [aut] ,
Jeffrey Yarus [aut] ,
Erika I. Barcelos [aut, cph] ,
Roger H. French [aut, cph]
Maintainer: Olatunde D. Akanbi <olatunde.akanbi@case.edu>
Diff between geospatialsuite versions 0.1.1 dated 2025-11-05 and 0.2.0 dated 2026-05-08
DESCRIPTION | 11 MD5 | 140 - NAMESPACE | 4 NEWS.md | 131 + R/00-package-info.R | 7 R/02-vegetation-indices.R | 637 ++++-- R/04-crop-analysis.R | 2 R/05-mosaicing.R | 86 R/06-spatial-join.R | 18 R/12-workflows.R | 11 R/13-water-quality.R | 2 R/15-helpers.R | 191 + R/16-data-download.R |only R/16-geocoding-examples.R | 4 R/99-testing.R | 8 README.md |only build/vignette.rds |binary inst/CITATION | 23 inst/doc/agricultural-analysis.R | 13 inst/doc/agricultural-analysis.Rmd | 36 inst/doc/agricultural-analysis.html | 29 inst/doc/analyze-crop-vegetation.R | 17 inst/doc/analyze-crop-vegetation.Rmd | 154 + inst/doc/analyze-crop-vegetation.html | 418 +++ inst/doc/getting-started.R | 581 ++--- inst/doc/getting-started.Rmd | 686 ++---- inst/doc/getting-started.html | 1038 +++++---- inst/doc/performance_benchmark.R |only inst/doc/performance_benchmark.Rmd |only inst/doc/performance_benchmark.html |only inst/doc/spatial-analysis.R | 5 inst/doc/spatial-analysis.Rmd | 23 inst/doc/spatial-analysis.html | 21 inst/doc/spatial-integration.R | 19 inst/doc/spatial-integration.Rmd | 23 inst/doc/spatial-integration.html | 62 inst/doc/vegetation-indices.R | 1131 ++-------- inst/doc/vegetation-indices.Rmd | 1542 ++------------ inst/doc/vegetation-indices.html | 3052 ++++------------------------- inst/doc/water-quality.R | 177 - inst/doc/water-quality.Rmd | 21 inst/doc/water-quality.html | 125 + inst/doc/workflows-case-studies.R | 20 inst/doc/workflows-case-studies.Rmd | 22 inst/doc/workflows-case-studies.html | 1264 ++++++------ inst/extdata |only man/auto_geocode_data.Rd | 2 man/calculate_index_by_type.Rd | 1 man/calculate_vegetation_index.Rd | 22 man/detect_geographic_entities.Rd | 4 man/download_sample_data.Rd |only man/extract_aster_coordinates.Rd | 10 man/geocoding_examples.Rd | 4 man/geospatialsuite-package.Rd | 18 man/get_index_required_bands.Rd |only man/get_sample_data.Rd |only man/list_sample_datasets.Rd |only man/load_sample_data.Rd |only man/select_rasters_for_region.Rd | 19 man/test_geospatialsuite_package_simple.Rd | 2 man/universal_spatial_join.Rd | 18 man/validate_required_bands.Rd | 1 tests/testthat/test-integration.R | 5 tests/testthat/test-workflows.R | 5 vignettes/agricultural-analysis.Rmd | 36 vignettes/analyze-crop-vegetation.Rmd | 154 + vignettes/getting-started.Rmd | 686 ++---- vignettes/performance_benchmark.Rmd |only vignettes/spatial-analysis.Rmd | 23 vignettes/spatial-integration.Rmd | 23 vignettes/vegetation-indices.Rmd | 1542 ++------------ vignettes/water-quality.Rmd | 21 vignettes/workflows-case-studies.Rmd | 22 73 files changed, 5703 insertions(+), 8669 deletions(-)
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