Title: Community Dynamics Metrics
Description: Univariate and multivariate temporal and spatial diversity indices,
rank abundance curves, and community stability measures. The functions
implement measures that are either explicitly temporal and include the
option to calculate them over multiple replicates, or spatial and include
the option to calculate them over multiple time points. Functions fall into
five categories: static diversity indices, temporal diversity indices,
spatial diversity indices, rank abundance curves, and community stability
measures. The diversity indices are temporal and spatial analogs to
traditional diversity indices. Specifically, the package includes functions
to calculate community richness, evenness and diversity at a given point in
space and time. In addition, it contains functions to calculate species
turnover, mean rank shifts, and lags in community similarity between two
time points. Details of the methods are available in
Hallett et al. (2016) <doi:10.1111/2041-210X.12569> and Avolio
et al. ( [...truncated...]
Author: Lauren Hallett [aut] ,
Meghan L. Avolio [aut] ,
Ian T. Carroll [aut] ,
Sydney K. Jones [aut],
A. Andrew M. MacDonald [aut] ,
Dan F. B. Flynn [aut] ,
Peter Slaughter [aut] ,
Julie Ripplinger [aut] ,
Scott L. Collins [aut] ,
Corinna Gries [aut] ,
Matth [...truncated...]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between codyn versions 2.0.5 dated 2020-12-01 and 2.0.6 dated 2026-09-17
codyn-2.0.5/codyn/NEWS |only codyn-2.0.6/codyn/DESCRIPTION | 34 codyn-2.0.6/codyn/MD5 | 106 +- codyn-2.0.6/codyn/NAMESPACE | 22 codyn-2.0.6/codyn/NEWS.md |only codyn-2.0.6/codyn/R/RAC_change.R | 57 - codyn-2.0.6/codyn/R/RAC_difference.R | 82 - codyn-2.0.6/codyn/R/abundance_change.R | 21 codyn-2.0.6/codyn/R/abundance_difference.R | 58 - codyn-2.0.6/codyn/R/codyn-package.R | 137 -- codyn-2.0.6/codyn/R/community_diversity.R | 26 codyn-2.0.6/codyn/R/community_stability.R | 12 codyn-2.0.6/codyn/R/community_structure.R | 31 codyn-2.0.6/codyn/R/curve_change.R | 14 codyn-2.0.6/codyn/R/curve_difference.R | 16 codyn-2.0.6/codyn/R/data.R |only codyn-2.0.6/codyn/R/multivariate_change_and_difference.R | 41 codyn-2.0.6/codyn/R/rank_shift.R | 16 codyn-2.0.6/codyn/R/rate_change.R | 16 codyn-2.0.6/codyn/R/synchrony.R | 12 codyn-2.0.6/codyn/R/temporal_torus_translation.R | 8 codyn-2.0.6/codyn/R/turnover.R | 29 codyn-2.0.6/codyn/R/variance_ratio.R | 12 codyn-2.0.6/codyn/README.md | 8 codyn-2.0.6/codyn/build/vignette.rds |binary codyn-2.0.6/codyn/inst/WORDLIST |only codyn-2.0.6/codyn/inst/doc/Community_Stability_Metrics.R | 46 codyn-2.0.6/codyn/inst/doc/Community_Stability_Metrics.Rmd | 2 codyn-2.0.6/codyn/inst/doc/Community_Stability_Metrics.html | 614 +++++++----- codyn-2.0.6/codyn/inst/doc/Temporal_Diversity_Indices.R | 18 codyn-2.0.6/codyn/inst/doc/Temporal_Diversity_Indices.html | 560 ++++++---- codyn-2.0.6/codyn/inst/doc/codyn_overview.html | 198 ++- codyn-2.0.6/codyn/man/RAC_change.Rd | 59 - codyn-2.0.6/codyn/man/RAC_difference.Rd | 84 - codyn-2.0.6/codyn/man/abundance_change.Rd | 23 codyn-2.0.6/codyn/man/abundance_difference.Rd | 57 - codyn-2.0.6/codyn/man/codyn-package.Rd | 68 - codyn-2.0.6/codyn/man/collins08.Rd | 12 codyn-2.0.6/codyn/man/community_diversity.Rd | 30 codyn-2.0.6/codyn/man/community_stability.Rd | 12 codyn-2.0.6/codyn/man/community_structure.Rd | 31 codyn-2.0.6/codyn/man/confint.cyclic_shift.Rd | 8 codyn-2.0.6/codyn/man/curve_change.Rd | 14 codyn-2.0.6/codyn/man/curve_difference.Rd | 16 codyn-2.0.6/codyn/man/knz_001d.Rd | 12 codyn-2.0.6/codyn/man/mean_rank_shift.Rd | 8 codyn-2.0.6/codyn/man/multivariate_change.Rd | 20 codyn-2.0.6/codyn/man/multivariate_difference.Rd | 21 codyn-2.0.6/codyn/man/pplots.Rd | 16 codyn-2.0.6/codyn/man/rank_shift.Rd | 8 codyn-2.0.6/codyn/man/rate_change.Rd | 6 codyn-2.0.6/codyn/man/rate_change_interval.Rd | 10 codyn-2.0.6/codyn/man/synchrony.Rd | 12 codyn-2.0.6/codyn/man/turnover.Rd | 16 codyn-2.0.6/codyn/man/variance_ratio.Rd | 12 codyn-2.0.6/codyn/vignettes/Community_Stability_Metrics.Rmd | 2 56 files changed, 1417 insertions(+), 1336 deletions(-)
Title: Missing Data for Marked Hawkes Process
Description: Estimation of model parameters for marked Hawkes process.
Accounts for missing data in the estimation of the parameters.
Technical details found in (Tucker et al., 2019 <DOI:10.1016/j.spasta.2018.12.004>).
Author: J. Derek Tucker [aut, cre],
Lyndsay Shand [aut],
Stephen Rowe [aut],
John Lewis [aut]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between stpphawkes versions 0.2.2 dated 2025-03-10 and 0.2.4 dated 2026-09-17
DESCRIPTION | 10 ++-- MD5 | 57 ++++++++++++------------- NAMESPACE | 24 ++++++---- NEWS.md | 3 - R/homog_ppp.R | 5 +- R/inhomo_ppp.R | 19 ++++++-- R/mcmc.R | 18 +++++-- R/simulate_stpp_hawkes.R | 10 ++-- man/stpphawkes.Rd | 1 src/Makevars | 2 src/condInt_mcmc_stpp.cpp | 3 + src/condInt_mcmc_stpp_branching.cpp | 2 src/condInt_mcmc_stpp_branching_md.cpp | 6 ++ src/condInt_mcmc_stpp_branching_nonunif.cpp | 2 src/condInt_mcmc_stpp_branching_nonunif_md.cpp | 6 ++ src/condInt_mcmc_temporal.cpp | 4 + src/condInt_mcmc_temporal_branching.cpp | 2 src/condInt_mcmc_temporal_branching_md.cpp | 4 + src/condInt_mcmc_temporal_md.cpp | 7 ++- src/helper_functions.h | 21 ++++----- src/rng_seed.h |only src/simulate_stpp_hawkes.cpp | 16 ++++--- src/simulate_stpp_hawkes_nonunif.cpp | 16 ++++--- src/spatio_temporal_common.cpp | 11 +++- src/spatio_temporal_common_nonunif.cpp | 12 +++-- src/temporal_catmark.cpp | 2 src/temporal_catmark_common.cpp | 5 ++ src/temporal_catmark_md.cpp | 2 src/temporal_common.cpp | 16 ++++++- src/temporal_contmark.cpp | 2 30 files changed, 193 insertions(+), 95 deletions(-)
Title: Density and Abundance from Distance-Sampling Surveys
Description: Distance-sampling (<doi:10.1007/978-3-319-19219-2>)
is a field survey and analytical method that estimates density and
abundance of survey targets (e.g., animals) when
detection probability declines with observation distance.
Distance-sampling is popular in ecology,
especially when survey targets are observed from aerial platforms (e.g.,
airplane or drone), surface vessels (e.g., boat or truck), or along
walking transects. Analysis involves fitting smooth (parametric) curves to
histograms of observation distances and using those functions to
adjust density estimates for missed targets. Routines included here
fit curves to observation distance histograms, estimate effective
sampling area, density of targets in surveyed areas, and the abundance
of targets in a surrounding study area. Confidence interval estimation
uses built-in bootstrap resampling. Help files are extensive and have been
vetted by multiple authors. Many tutorials are available on the package's
website (URL below).
Author: Trent McDonald [cre, aut],
Jason Carlisle [aut],
Aidan McDonald [aut] ,
Ryan Nielson [ctb] ,
Ben Augustine [ctb] ,
James Griswald [ctb] ,
Patrick McKann [ctb] ,
Lacey Jeroue [ctb] ,
Hoffman Abigail [ctb] ,
Kleinsausser Michael [ctb] ,
Joel Reynolds [ [...truncated...]
Maintainer: Trent McDonald <trent@mcdonalddatasciences.com>
Diff between Rdistance versions 4.4.3 dated 2026-05-14 and 4.5.0 dated 2026-09-17
DESCRIPTION | 13 +-- MD5 | 73 +++++++++++++------- NAMESPACE | 5 + NEWS.md | 79 ++++++++++++++++++++++ R/Oscars.R |only R/abundEstim.R | 151 ++++++++++++++++++++++++------------------- R/bootstrap.R | 39 +++++++---- R/calcLineLength.R |only R/convexPartition.R |only R/dE.single.R | 37 ++++++++-- R/drawTransects.R |only R/exampleSurveyPoly.R |only R/findSpacing.R |only R/huber.start.limits.R | 8 +- R/integrateOneStepLines.R | 7 + R/makeLines.R |only R/makeLinesUtils.R |only R/mlEstimates.R | 4 - R/oneStep.like.R | 5 + R/oneStep.start.limits.R | 12 ++- R/oscarsLimits.R |only R/parseModel.R | 4 - R/pronghornAreas.R |only R/pronghornDfDocumentation.R |only R/setOptimizer.R | 12 ++- R/triangle.start.limits.R | 27 ++++--- R/zzz.R | 4 + data/exampleSurveyPoly.rda |only data/pronghornAreas.rda |only data/pronghornDf.rda |only inst/WORDLIST | 50 +++++++++++++- man/Oscars.Rd |only man/abundEstim.Rd | 46 ++++++------- man/autoDistSamp.Rd | 10 +- man/bootstrap.Rd | 11 ++- man/calcLineLength.Rd |only man/convexPartition.Rd |only man/dE.multi.Rd | 1 man/dE.single.Rd | 1 man/dfuncEstim.Rd | 1 man/drawTransects.Rd |only man/exampleSurveyPoly.Rd |only man/findSpacing.Rd |only man/integrateOneStepLines.Rd | 7 + man/makeLines.Rd |only man/oneBsIter.Rd | 7 + man/oneStep.like.Rd | 5 + man/oscarsLimits.Rd |only man/pronghornDf.Rd |only 49 files changed, 445 insertions(+), 174 deletions(-)
Title: Multivariate Bayesian Regression
Description: Fit, plot, and predict a multivariate response, using an arbitrary
univariate Bayesian regression model to independently fit basis components
(e.g., principal components) of the response (Francom et al., 2025 <DOI:10.1137/24M1644092>).
Author: Gavin Collins [aut, ctb],
J. Derek Tucker [ctb, cre] ,
Sandia National Laboratories [cph, fnd]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between mvBayes versions 1.2.2 dated 2026-07-30 and 1.2.3 dated 2026-09-17
DESCRIPTION | 11 + MD5 | 33 +++-- NAMESPACE | 2 NEWS.md | 3 R/basisSetup.R | 53 +++++++-- R/basisSetupElastic.R | 57 +++++----- R/cv.R | 140 +++++++++++++----------- R/generics.R | 13 +- R/mvBayes.R | 91 +++++++++------- R/mvBayesElastic.R | 41 ++++--- R/rsobol.R | 15 +- R/sobol.R | 248 ++++++++++++++++++++++++++------------------ R/splinet.R | 4 README.md | 2 inst/doc/friedman_demo.html | 86 +++++++-------- man/mvCV.Rd | 3 man/traceplot.Rd | 30 +---- man/traceplot.mvBayes.Rd |only 18 files changed, 480 insertions(+), 352 deletions(-)
Title: Bayesian Projection Pursuit Regression
Description: Bayesian fitting of projection pursuit regression model.
Built to handle continuous and categorical inputs and
scalar output (Collins et al., 2023 <DOI:10.1007/s11222-023-10334-z>).
Author: Gavin Collins [aut, ctb],
J. Derek Tucker [ctb, cre]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between BayesPPR versions 0.1.0 dated 2026-05-18 and 0.2.0 dated 2026-09-17
DESCRIPTION | 10 +++++----- MD5 | 21 +++++++++++---------- NEWS.md | 19 +++++++++++++++++++ R/bppr.R | 37 ++++++++++++++++++++++++++++++------- R/bppr_pca.R | 6 +++++- R/matrix_computation.R | 14 ++++++++++++++ R/pca.R | 21 +++++++++++++++++++-- R/predict.R | 34 ++++++++++++++++++++++------------ R/predict_pca.R | 15 +++++++++++---- R/resume.R | 6 ++++-- README.md | 2 ++ man/figures |only 12 files changed, 142 insertions(+), 43 deletions(-)
Title: 'R' Bindings for 'TMB'
Description: Native 'R' interface to 'TMB' (Template Model Builder) so models can be written entirely in 'R' rather than 'C++'. Automatic differentiation, to any order, is available for a rich subset of 'R' features, including linear algebra for dense and sparse matrices, complex arithmetic, Fast Fourier Transform, probability distributions and special functions. 'RTMB' provides easy access to model fitting and validation following the principles of Kristensen, K., Nielsen, A., Berg, C. W., Skaug, H., & Bell, B. M. (2016) <DOI:10.18637/jss.v070.i05> and Thygesen, U.H., Albertsen, C.M., Berg, C.W. et al. (2017) <DOI:10.1007/s10651-017-0372-4>.
Author: Kasper Kristensen [aut, cre]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between RTMB versions 1.9 dated 2026-03-20 and 2.0 dated 2026-09-17
DESCRIPTION | 8 +- MD5 | 66 +++++++++-------- NAMESPACE | 4 - NEWS | 24 ++++++ R/00roxygen.R | 8 +- R/RcppExports.R | 36 +++++++++ R/advector.R | 65 +++++++++++++++-- R/experimental.R | 49 +++++++++++-- R/integrate.R | 2 R/methods.R | 27 +++++++ R/mvgauss.R | 37 ++++------ R/sdreport.R |only R/sim.R | 9 ++ R/zzz.R | 2 build/vignette.rds |binary inst/doc/RTMB-advanced.html | 4 - inst/doc/RTMB-introduction.html | 6 - inst/doc/RTMB-tips.html | 6 - inst/include/CallRTMB.hpp | 2 inst/include/config.h | 2 inst/tinytest/test-integration_methods.R |only inst/tinytest/test-model-spde.R | 2 inst/tinytest/test-sequential_reduction.R |only man/ADintegrate.Rd | 2 man/Distributions.Rd | 28 ++++++- man/MVgauss.Rd | 2 src/Makevars | 5 + src/Makevars.win | 5 + src/RTMB_tape.cpp | 24 ++++++ src/RcppExports.cpp | 111 ++++++++++++++++++++++++++++++ src/branching.cpp | 2 src/config.h | 2 src/integrate.cpp | 4 - src/lse_sparse.cpp |only src/math.cpp | 34 +++++++++ src/misc.cpp | 2 36 files changed, 482 insertions(+), 98 deletions(-)
Title: Switzerland's Data Series in One Place
Description: Download and import open Swiss economic time series from
'dataseries.org' <https://dataseries.org>, a comprehensive and
up-to-date collection of public data from Switzerland. Series are
retrieved through the public 'dataseries.org' API and imported as a
'data.frame' or 'ts' object.
Author: Christoph Sax [aut, cre, cph],
Jannes Muenchow [ctb]
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between dataseries versions 1.0.0 dated 2026-06-13 and 1.1.0 dated 2026-09-17
DESCRIPTION | 15 ++++++++------- LICENSE |only MD5 | 22 ++++++++++++++-------- NEWS.md | 33 +++++++++++++++++++++++++++++++++ R/catalog.R | 34 +++++++++++++++++++++++++--------- R/utils.R | 34 ++++++++++++++++++++++++++++------ README.md | 26 ++++++++++++++++++++++++-- build |only inst |only man/ds_catalog.Rd | 10 +++++++++- man/ds_search.Rd | 10 +++++++++- tests/testthat/test-helpers.R | 37 +++++++++++++++++++++++++++++++++++++ vignettes |only 13 files changed, 187 insertions(+), 34 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
Posit Software, PBC [cph, fnd],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.60 dated 2026-06-16 and 0.61 dated 2026-09-17
tinytex-0.60/tinytex/tests/test-ci.R |only tinytex-0.60/tinytex/tests/test-cran.R |only tinytex-0.61/tinytex/DESCRIPTION | 6 +++--- tinytex-0.61/tinytex/MD5 | 17 +++++++++-------- tinytex-0.61/tinytex/R/install.R | 2 +- tinytex-0.61/tinytex/R/latex.R | 18 ++++++++++++------ tinytex-0.61/tinytex/man/latexmk.Rd | 9 ++++++--- tinytex-0.61/tinytex/tests/test-all.R |only tinytex-0.61/tinytex/tests/test-ci/bib |only tinytex-0.61/tinytex/tests/test-ci/test-install.R | 5 +++-- tinytex-0.61/tinytex/tests/test-ci/test-latex.R | 11 +++++++++++ 11 files changed, 45 insertions(+), 23 deletions(-)
Title: Manipulate and Analyze Round Robin Dyadic Data
Description: Provides utilities for processing and analyzing dyadic data
collected using a round-robin design, in which each person in a group
rates or interacts with every other person on at least one variable.
Data manipulation functions prepare datasets for dyadic data analysis by
creating the actor and partner dummy variables required by the social
relations model (SRM). Analysis functions implement the SRM using
multilevel modeling via a custom 'nlme' covariance class ('pdSRM'),
following the approach of Snijders and Kenny (1999)
<doi:10.1111/j.1475-6811.1999.tb00204.x> and Knight and Humphrey (2019)
<doi:10.1037/0000115-019>. The package estimates group, actor, partner,
and relationship variance components along with generalized and dyadic
reciprocity correlations, and supports both null and fixed-effects models.
Author: Andrew Knight [aut, cre, cph]
Maintainer: Andrew Knight <knightap@wustl.edu>
Diff between roundRobinR versions 1.0.1 dated 2026-04-21 and 2.0.0 dated 2026-09-17
roundRobinR-1.0.1/roundRobinR/R/createDummies.R |only roundRobinR-1.0.1/roundRobinR/R/srmPseudoRSq.R |only roundRobinR-1.0.1/roundRobinR/R/srmRun.R |only roundRobinR-1.0.1/roundRobinR/R/srmVarPct.R |only roundRobinR-2.0.0/roundRobinR/DESCRIPTION | 12 +- roundRobinR-2.0.0/roundRobinR/MD5 | 42 +++++--- roundRobinR-2.0.0/roundRobinR/NAMESPACE | 10 + roundRobinR-2.0.0/roundRobinR/NEWS.md | 42 ++++++++ roundRobinR-2.0.0/roundRobinR/R/cpsrm.R |only roundRobinR-2.0.0/roundRobinR/R/cpsrm_run.R |only roundRobinR-2.0.0/roundRobinR/R/create_cp_dummies.R |only roundRobinR-2.0.0/roundRobinR/R/create_dummies.R |only roundRobinR-2.0.0/roundRobinR/R/deprecated.R |only roundRobinR-2.0.0/roundRobinR/R/srm_pseudo_rsq.R |only roundRobinR-2.0.0/roundRobinR/R/srm_run.R |only roundRobinR-2.0.0/roundRobinR/R/srm_var_pct.R |only roundRobinR-2.0.0/roundRobinR/build/partial.rdb |binary roundRobinR-2.0.0/roundRobinR/build/vignette.rds |binary roundRobinR-2.0.0/roundRobinR/inst/doc/introduction.html | 77 +++++++++------ roundRobinR-2.0.0/roundRobinR/man/cpsrm.Rd |only roundRobinR-2.0.0/roundRobinR/man/cpsrmRun.Rd |only roundRobinR-2.0.0/roundRobinR/man/cpsrm_run.Rd |only roundRobinR-2.0.0/roundRobinR/man/createDummies.Rd | 51 ++------- roundRobinR-2.0.0/roundRobinR/man/create_cp_dummies.Rd |only roundRobinR-2.0.0/roundRobinR/man/create_dummies.Rd |only roundRobinR-2.0.0/roundRobinR/man/print.cpsrm.Rd |only roundRobinR-2.0.0/roundRobinR/man/srmPseudoRSq.Rd | 58 +---------- roundRobinR-2.0.0/roundRobinR/man/srmRun.Rd | 49 +-------- roundRobinR-2.0.0/roundRobinR/man/srmVarPct.Rd | 43 -------- roundRobinR-2.0.0/roundRobinR/man/srm_pseudo_rsq.Rd |only roundRobinR-2.0.0/roundRobinR/man/srm_run.Rd |only roundRobinR-2.0.0/roundRobinR/man/srm_var_pct.Rd |only roundRobinR-2.0.0/roundRobinR/man/summary.cpsrm.Rd |only 33 files changed, 168 insertions(+), 216 deletions(-)
Title: Neural Networks Made Algebraic
Description: Build, compose, stack, sum, and realize feed-forward neural
networks as algebraic objects. Implements the calculus and constructive
approximations described by Rafi, Padgett, and Nakarmi (2024)
<doi:10.48550/arXiv.2402.01058>, Grohs, Hornung, Jentzen, et al. (2023)
<doi:10.1007/s10444-022-09970-2>, and Jentzen, Kuckuck, and von
Wurstemberger (2023) <doi:10.48550/arXiv.2310.20360>. Includes neural
network polynomials, transcendental-function approximations,
multidimensional maximum convolution, and vectorized batch realization.
Author: Shakil Rafi [aut, cre] ,
Joshua Lee Padgett [aut] ,
Ukash Nakarmi [ctb]
Maintainer: Shakil Rafi <sarafi@uark.edu>
Diff between nnR versions 0.1.0 dated 2024-02-14 and 0.2.0 dated 2026-09-17
nnR-0.1.0/nnR/man/A.Rd |only nnR-0.1.0/nnR/man/A_k.Rd |only nnR-0.1.0/nnR/man/B.Rd |only nnR-0.1.0/nnR/man/C_k.Rd |only nnR-0.1.0/nnR/man/ck.Rd |only nnR-0.2.0/nnR/DESCRIPTION | 33 nnR-0.2.0/nnR/MD5 | 130 +-- nnR-0.2.0/nnR/NAMESPACE | 55 + nnR-0.2.0/nnR/NEWS.md |only nnR-0.2.0/nnR/R/Aff.R | 63 - nnR-0.2.0/nnR/R/Csn.R | 32 nnR-0.2.0/nnR/R/Etr.R | 36 nnR-0.2.0/nnR/R/Id.R | 37 - nnR-0.2.0/nnR/R/MC.R | 78 -- nnR-0.2.0/nnR/R/Mxm.R | 69 - nnR-0.2.0/nnR/R/Nrm.R | 46 - nnR-0.2.0/nnR/R/Phi.R | 18 nnR-0.2.0/nnR/R/Phi_k.R | 24 nnR-0.2.0/nnR/R/Pnm.R |only nnR-0.2.0/nnR/R/Prd.R | 50 - nnR-0.2.0/nnR/R/Pwr.R | 86 +- nnR-0.2.0/nnR/R/Sne.R | 35 nnR-0.2.0/nnR/R/Sqr.R | 59 - nnR-0.2.0/nnR/R/Tay.R | 83 -- nnR-0.2.0/nnR/R/Tun.R | 60 - nnR-0.2.0/nnR/R/Xpn.R | 36 nnR-0.2.0/nnR/R/activations.R | 36 nnR-0.2.0/nnR/R/aux_fun.R | 57 - nnR-0.2.0/nnR/R/comp.R | 142 --- nnR-0.2.0/nnR/R/i.R | 14 nnR-0.2.0/nnR/R/instantiation.R | 126 ++- nnR-0.2.0/nnR/R/is_nn.R | 82 +- nnR-0.2.0/nnR/R/nn_creator.R | 53 - nnR-0.2.0/nnR/R/nn_sum.R | 88 +- nnR-0.2.0/nnR/R/nn_viewer.R | 93 ++ nnR-0.2.0/nnR/R/scalar_mult.R | 76 -- nnR-0.2.0/nnR/R/stacking.R | 156 ++-- nnR-0.2.0/nnR/R/validation.R |only nnR-0.2.0/nnR/README.md |only nnR-0.2.0/nnR/build/vignette.rds |binary nnR-0.2.0/nnR/inst/doc/nnR.R | 36 nnR-0.2.0/nnR/inst/doc/nnR.Rmd | 95 +- nnR-0.2.0/nnR/inst/doc/nnR.html | 692 +++++++++---------- nnR-0.2.0/nnR/man/Aff.Rd | 2 nnR-0.2.0/nnR/man/Csn.Rd | 19 nnR-0.2.0/nnR/man/Etr.Rd | 5 nnR-0.2.0/nnR/man/MC.Rd | 15 nnR-0.2.0/nnR/man/Mxm.Rd | 7 nnR-0.2.0/nnR/man/Pnm.Rd |only nnR-0.2.0/nnR/man/Prd.Rd | 12 nnR-0.2.0/nnR/man/Pwr.Rd | 12 nnR-0.2.0/nnR/man/Sne.Rd | 20 nnR-0.2.0/nnR/man/Sqr.Rd | 14 nnR-0.2.0/nnR/man/Tay.Rd | 19 nnR-0.2.0/nnR/man/Tun.Rd | 2 nnR-0.2.0/nnR/man/Xpn.Rd | 23 nnR-0.2.0/nnR/man/comp.Rd | 1 nnR-0.2.0/nnR/man/create_nn.Rd | 3 nnR-0.2.0/nnR/man/dep.Rd | 2 nnR-0.2.0/nnR/man/draw_nn.Rd |only nnR-0.2.0/nnR/man/figures |only nnR-0.2.0/nnR/man/inst.Rd | 9 nnR-0.2.0/nnR/man/is_nn.Rd | 17 nnR-0.2.0/nnR/man/nn_sum.Rd | 3 nnR-0.2.0/nnR/man/nn_sum_many.Rd |only nnR-0.2.0/nnR/man/param.Rd | 2 nnR-0.2.0/nnR/man/realize_nn.Rd |only nnR-0.2.0/nnR/man/stk.Rd | 7 nnR-0.2.0/nnR/man/stk_many.Rd |only nnR-0.2.0/nnR/man/view_nn.Rd | 3 nnR-0.2.0/nnR/tests/testthat/test-core-correctness.R |only nnR-0.2.0/nnR/tests/testthat/test-nn_viewer.R | 8 nnR-0.2.0/nnR/vignettes/nnR.Rmd | 95 +- nnR-0.2.0/nnR/vignettes/references.bib | 13 74 files changed, 1548 insertions(+), 1541 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis (Balduzzi et al., 2023) <doi:10.18637/jss.v106.i02> and supporting Schwarzer et al. (2015) <doi:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <doi:10.1002/jrsm.1058>;
- additive network meta-analysis for combinations of treatments (Rücker et al., 2020) <doi:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <doi:10.1002/sim.8158>, or penalised logistic regression (Evrenoglou et al., 2022) <doi:10.1002/sim.9562>;
- rankograms and ranking of treatments by the Surface under the cumulative ranking curve (SUCRA) (Salanti et al., 2013) <doi:10.1016/j.jclinepi.2010.03.016>;
- ranking of treatments using P-scores (frequentist analogue of SUCRAs without resampling) according to [...truncated...]
Author: Gerta Ruecker [aut] ,
Ulrike Krahn [aut],
Jochem Koenig [aut] ,
Orestis Efthimiou [aut] ,
Annabel Davies [aut] ,
Theodoros Papakonstantinou [aut] ,
Theodoros Evrenoglou [ctb] ,
Krzysztof Ciomek [ctb] ,
Nana-adjoa Kwarteng [ctb] ,
Noosheen R. Tahmasebi [...truncated...]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between netmeta versions 3.6-1 dated 2026-06-20 and 3.7-0 dated 2026-09-17
DESCRIPTION | 18 +- MD5 | 68 ++++--- NAMESPACE | 365 +++++++++++++++++++++++------------------- NEWS.md | 46 +++++ R/heatplot.netpath.R |only R/netgraph.netmeta.R | 6 R/netleague.R | 22 +- R/netmeta-package.R | 30 ++- R/netpath.R |only R/netpath_internal.R |only R/netposet.R | 143 ++++++++++------ R/netrank.R | 136 ++++++++++----- R/netsplit.R | 58 +++--- R/nettable.R | 5 R/plot.netposet.R | 46 ++++- R/plot.netrank.R | 121 ++++++++++--- R/rankogram.default.R | 41 +++- R/rankogram.netmeta.R | 35 ++-- R/updateversion.R | 6 R/vikor-internal.R |only R/vikor.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/netmeta-workflow.pdf |binary inst/doc/netmeta.pdf |binary man/heatplot.netpath.Rd |only man/netgraph.netmeta.Rd | 6 man/netleague.Rd | 10 - man/netmeta-package.Rd | 16 + man/netpath.Rd |only man/netposet.Rd | 34 ++- man/netrank.Rd | 58 ++++-- man/netsplit.Rd | 5 man/nettable.Rd | 5 man/plot.netposet.Rd | 12 - man/plot.netrank.Rd | 41 +++- man/rankogram.default.Rd | 39 +++- man/rankogram.netmeta.Rd | 35 ++-- man/vikor.Rd |only 39 files changed, 925 insertions(+), 482 deletions(-)
Title: Asymptotic Timing
Description: Computing and visualizing comparative
asymptotic timings of different algorithms and code versions.
Also includes functionality for comparing empirical timings with
expected references such as linear or quadratic,
<https://en.wikipedia.org/wiki/Asymptotic_computational_complexity>
Also includes functionality for measuring asymptotic memory and other
quantities.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between atime versions 2026.4.2 dated 2026-04-04 and 2026.9.17 dated 2026-09-17
DESCRIPTION | 24 +++--- MD5 | 72 ++++++++++---------- NAMESPACE | 1 NEWS | 29 ++++++++ R/atime.R | 62 +++++++++-------- R/references.R | 10 +- R/test.R | 95 ++++++++++++++++---------- R/versions.R | 132 ++++++++++++++++++++++++------------- build/vignette.rds |binary inst/CITATION |only inst/doc/Custom_Plots.R | 2 inst/doc/Custom_Plots.Rmd | 2 inst/doc/Custom_Plots.html | 27 +++---- inst/doc/Custom_References.R | 46 ++++++------- inst/doc/Custom_References.Rmd | 50 +++++++------- inst/doc/Custom_References.html | 141 +++++++++++++++++++--------------------- inst/doc/Custom_Units.R | 6 - inst/doc/Custom_Units.Rmd | 10 +- inst/doc/Custom_Units.html | 38 +++++----- inst/doc/cum_median.html | 24 +++--- inst/doc/regex.html | 34 +++++---- inst/doc/sparse.R | 6 - inst/doc/sparse.Rmd | 6 - inst/doc/sparse.html | 56 ++++++++------- inst/example_tests.R | 7 + man/R_CMD_INSTALL.Rd |only man/atime.Rd | 20 ++++- man/atime_pkg.Rd | 10 +- man/atime_test.Rd | 9 +- man/atime_test_list.Rd | 51 +++++--------- man/atime_versions.Rd | 26 +++++-- man/atime_versions_exprs.Rd | 20 ++++- man/glob_find_replace.Rd | 3 tests/testthat/test-CRAN.R | 76 +++++++++++---------- vignettes/Custom_Plots.Rmd | 2 vignettes/Custom_References.Rmd | 50 +++++++------- vignettes/Custom_Units.Rmd | 10 +- vignettes/sparse.Rmd | 6 - 38 files changed, 646 insertions(+), 517 deletions(-)
Title: Reproducible Code for 'Shiny' Objects
Description: Provides functionality to extract reactive expressions from a 'shiny' application and
convert them into stand-alone R scripts. This enables users to reproduce tables and visualisations
outside the interactive UI, facilitating integration into static reports or automated workflows
without requiring access to the original application source code.
Author: Ashley Baldry [aut, cre]
Maintainer: Ashley Baldry <ashley.baldry@acuityanalytics.com>
Diff between shinyreprex versions 0.2.0 dated 2026-06-29 and 0.3.0 dated 2026-09-17
DESCRIPTION | 15 - LICENSE | 4 MD5 | 53 +++-- NAMESPACE | 3 NEWS.md | 32 +++ R/S7_utils.R | 4 R/call_chunk_if.R | 17 + R/call_chunk_utils.R | 15 + R/chunk_reactive.R | 32 --- R/reactive_expression.R |only R/register_reactives.R |only R/reprex_lockfile.R |only R/reprex_reactive.R | 170 ++++++++--------- R/walk_packages.R |only README.md | 47 ++++ build/vignette.rds |binary inst/WORDLIST | 7 inst/doc/shinyreprex.Rmd | 152 ++++++++++++++- inst/doc/shinyreprex.html | 267 +++++++++++++++++++++------ inst/examples-shiny |only man/assert_reactives.Rd |only man/call_reactive_env.Rd |only man/reactive_expression.Rd |only man/register_reactives.Rd |only man/registered_reactives.Rd |only man/reprex_lockfile.Rd |only man/reprex_packages.Rd |only man/reprex_store.Rd |only man/walk_packages.Rd |only tests/testthat/test-call_chunk_if.R | 184 ++++++++++++++++++ tests/testthat/test-call_chunk_utils.R | 32 +++ tests/testthat/test-canary-shiny-internals.R |only tests/testthat/test-examples-shiny.R |only tests/testthat/test-register_reactives.R |only tests/testthat/test-reprex_lockfile.R |only tests/testthat/test-walk_packages.R |only vignettes/shinyreprex.Rmd | 152 ++++++++++++++- 37 files changed, 975 insertions(+), 211 deletions(-)
Title: Sample Size Calculation Tools
Description: Functions for sample size estimation and simulation in clinical
trials. Includes methods for selecting the best group using the
Indifference-zone approach, as well as designs for non-inferiority,
equivalence, and negative binomial models. For the sample size calculation
for non-inferiority of vaccines, the approach is based on Fleming, Powers,
and Huang (2021) <doi:10.1177/1740774520988244>. The Indifference-zone
approach is based on Sobel and Huyett (1957) <doi:10.1002/j.1538-7305.1957.tb02411.x> and
Bechhofer, Santner, and Goldsman (1995, ISBN:978-0-471-57427-9).
Author: John J. Aponte [aut, cre] ,
Chris Gast [ctb]
Maintainer: John J. Aponte <john.j.aponte@gmail.com>
Diff between ssutil versions 1.1.0 dated 2026-09-06 and 1.2.0 dated 2026-09-17
DESCRIPTION | 8 +- MD5 | 68 +++++++++++------------ NAMESPACE | 2 NEWS.md | 32 ++++++++++ R/multz.R | 50 ++++++++++------- R/prophr.R | 8 +- R/sim_power_best_bin_rank.R | 21 ++++--- R/sim_power_best_binomial.R | 61 ++++++++++++++------ R/sim_power_equivalence_normal.R | 7 ++ R/sim_power_nbinom.R | 33 ++++++++--- R/sim_power_non_inferiority.R | 15 ++++- R/ss_best_binomial.R | 62 +++++++++++++++++++-- R/ss_best_normal.R | 9 +-- R/ss_ni_ve.R | 70 ++++++++++++++++++------ inst/doc/iz_binomial.html | 16 ++--- inst/doc/iz_normal.html | 2 inst/doc/non_inferiority.R | 4 - inst/doc/non_inferiority.Rmd | 12 ++-- inst/doc/non_inferiority.html | 10 +-- man/multp.Rd | 15 +++-- man/multz.Rd | 21 +++---- man/power_best_normal.Rd | 4 - man/prophr.Rd | 4 - man/sim_power_best_bin_rank.Rd | 21 ++++--- man/sim_power_equivalence_normal.Rd | 7 ++ man/sim_power_nbinom.Rd | 10 +++ man/sim_power_ni_normal.Rd | 9 ++- man/ss_ni_ve.Rd | 45 ++++++++++++++- tests/testthat/test-multz.R | 5 + tests/testthat/test-sim_power_nbinom.R | 3 + tests/testthat/test-sim_power_non_inferiority.R | 58 +++++++++++++++++++ tests/testthat/test-ss_best_binomial.R | 51 ++++++++++++----- tests/testthat/test-ss_best_normal.R | 41 +++++++++----- tests/testthat/test-ss_ni_ve.R | 67 +++++++++++++++++++++- vignettes/non_inferiority.Rmd | 12 ++-- 35 files changed, 645 insertions(+), 218 deletions(-)
Title: Sparse and Group Sparse Linear Models
Description: Fits the solution paths of classical sparse regression models with efficient active set algorithms by solving small sub-problems. Include LASSO, SCAD, MCP, (Sparse) Group-LASSO, Cooperative-LASSO, (Group) LAVA, (Generalized) Fused-Lasso and (Generalized) Elastic-Net. Also provides methods for model selection purpose (information criteria, cross-validation, stability selection).
Author: Julien Chiquet [aut, cre]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between quadrupen versions 1.0-0 dated 2026-06-05 and 1.1-0 dated 2026-09-17
DESCRIPTION | 8 MD5 | 134 ++++++------ NEWS.md | 22 ++ R/DataModel-R6Class.R | 20 + R/QuadrupenFit-R6Class.R | 27 +- R/group-lava.R | 2 R/group_sparse_lm.R | 2 R/init.R | 2 R/ridge.R | 3 R/sparse_lm.R | 3 R/utils.R | 2 build/vignette.rds |binary inst/doc/group-sparse-regression.html | 26 +- inst/doc/lava.R | 20 - inst/doc/lava.Rmd | 20 - inst/doc/lava.html | 26 +- inst/doc/structured-signal-recovery.R | 2 inst/doc/structured-signal-recovery.Rmd | 2 inst/doc/structured-signal-recovery.html | 4 man/DataModel.Rd | 23 ++ man/bounded_reg.Rd | 3 man/figures/breg-nostruct-1.png |binary man/figures/bregridge-nostruct-1.png |binary man/figures/bregridge_struct-1.png |binary man/figures/enet-nostruct-1.png |binary man/figures/enet_struct-1.png |binary man/figures/fused-lasso-1.png |binary man/figures/grplasso-l1l2-1.png |binary man/figures/grplasso-l1linf-1.png |binary man/figures/img-cor-struct-1.png |binary man/figures/lasso-nostruct-1.png |binary man/figures/lava-nostruct-1.png |binary man/figures/lava-nostruct-2.png |binary man/figures/lava_struct-1.png |binary man/figures/lava_struct-2.png |binary man/figures/mcp-nostruct-1.png |binary man/figures/ridge-nostruct-1.png |binary man/figures/ridge_struct-1.png |binary man/figures/scad-nostruct-1.png |binary man/figures/sparse-cooplasso-1.png |binary man/figures/sparse-grpenet-l1l2-1.png |binary man/figures/sparse-grplasso-coop-1.png |binary man/figures/sparse-grplasso-l1l2-1.png |binary man/figures/sparse-grplasso-l1linf-1.png |binary man/group_lava.Rd | 3 man/group_sparse_lm.Rd | 3 man/lava.Rd | 3 man/ridge.Rd | 3 man/sparse_lm.Rd | 3 src/Makevars | 3 src/Makevars.win | 5 src/Quadrupen/ActiveSet.h | 330 +++++++++++++++++++++---------- src/Quadrupen/BaseLava.h | 17 + src/Quadrupen/BoundedRegression.cpp | 52 +++- src/Quadrupen/BoundedRegression.h | 3 src/Quadrupen/Optimizer.cpp | 139 ++++++++----- src/Quadrupen/Optimizer.h | 14 + src/Quadrupen/OptimizerGroup.h | 275 +++++++++++++++++-------- src/Quadrupen/OptimizerSparse.h | 49 ++-- src/Quadrupen/PenaltyGroup.cpp | 3 src/Quadrupen/RegressionData.h | 15 + src/Quadrupen/RidgeRegression.cpp | 21 + src/Quadrupen/SparseRegularizer.h | 2 src/wrapper_FusedLasso.cpp | 4 src/wrapper_RidgeRegression.cpp | 5 tests/testthat/dataTest-boundedReg.rds |binary vignettes/lava.Rmd | 20 - vignettes/structured-signal-recovery.Rmd | 2 68 files changed, 876 insertions(+), 449 deletions(-)
Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Author: Myles Lewis [aut, cre] ,
Tom Willis [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between locuszoomr versions 1.0.0 dated 2026-09-03 and 1.1.0 dated 2026-09-17
DESCRIPTION | 8 MD5 | 49 +-- NAMESPACE | 311 +++++++++++-------- NEWS.md | 7 R/genetrack_ly.R | 3 R/genetracks.R | 2 R/locus.R | 60 ++- R/locus_plot.R | 1 R/locus_plotly.R | 53 +++ R/sanity_check.R |only R/scatter_plot.R | 28 + R/scatter_plotly.R | 88 ++++- R/zoom.R | 701 +++++++++++++++++++++++++++----------------- R/zoom_funcs.R |only README.md | 2 inst/doc/locuszoomr.Rmd | 2 inst/doc/locuszoomr.html | 4 inst/doc/zoom_browser.R | 19 + inst/doc/zoom_browser.Rmd | 61 +++ inst/doc/zoom_browser.html | 61 +++ man/locus.Rd | 5 man/locus_plotly.Rd | 15 man/sanity_check.Rd |only man/zoom.Rd | 51 ++- vignettes/dbl_gwas_manh.png |only vignettes/dbl_loc_eqtl.png |only vignettes/locuszoomr.Rmd | 2 vignettes/zoom_browser.Rmd | 61 +++ 28 files changed, 1076 insertions(+), 518 deletions(-)
Title: High Dimensional Geometry, Set Operations, Projection, and
Inference Using Kernel Density Estimation, Support Vector
Machines, and Convex Hulls
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation, support vector machine delineation, and convex hull generation. Applications include modeling trait and niche hypervolumes and species distribution modeling.
Author: Benjamin Blonder [aut, cre],
Cecina Babich Morrow [aut],
Stuart Brown [aut],
Gregoire Butruille [aut],
Daniel Chen [aut],
Alex Laini [aut],
David J. Harris [aut],
Clement Violet [aut]
Maintainer: Benjamin Blonder <benjamin.blonder@berkeley.edu>
Diff between hypervolume versions 3.1.6 dated 2025-06-15 and 3.1.7 dated 2026-09-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/partial.rdb |binary inst/doc/Hypervolume-Resampling.html | 7 ++++--- inst/doc/occupancy.html | 5 +++-- man/hypervolume_distance_point.Rd | 9 ++++----- 6 files changed, 20 insertions(+), 19 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 1.13.0 dated 2026-09-02 and 1.13.1 dated 2026-09-17
DESCRIPTION | 22 ++-- MD5 | 101 ++++++++++----------- NEWS.md | 29 ++++++ R/ArchiveAsync.R | 2 R/ArchiveBatch.R | 2 R/ContextBatch.R | 2 R/Objective.R | 3 R/OptimInstance.R | 4 R/OptimInstanceAsyncMultiCrit.R | 4 R/OptimInstanceAsyncSingleCrit.R | 2 R/OptimInstanceBatch.R | 11 +- R/OptimInstanceBatchMultiCrit.R | 4 R/Optimizer.R | 10 ++ R/OptimizerAsync.R | 9 + R/OptimizerBatchChain.R | 97 ++++++++++++++++---- R/OptimizerBatchFocusSearch.R | 29 ------ R/OptimizerBatchIrace.R | 7 - R/OptimizerBatchNLoptr.R | 13 -- R/OptimizerBatchRandomSearch.R | 2 R/TerminatorRunTime.R | 2 R/assertions.R | 2 R/bb_optimize.R | 2 R/helper.R | 6 - R/mlr_optimizers.R | 2 R/nds_selection.R | 14 +- man/branin.Rd | 4 man/mlr_optimizers_chain.Rd | 13 +- man/mlr_optimizers_nloptr.Rd | 2 man/nds_selection.Rd | 2 man/shrink_ps.Rd | 7 - src/local_search.c | 35 ++++--- src/rc_helpers.c | 4 tests/testthat/test_ArchiveAsync.R | 28 +++++ tests/testthat/test_ArchiveBatch.R | 33 ++++-- tests/testthat/test_CallbackBatch.R | 19 +++ tests/testthat/test_Objective.R | 19 +++ tests/testthat/test_OptimInstanceAsyncMultiCrit.R |only tests/testthat/test_OptimInstanceBatchMultiCrit.R | 15 +++ tests/testthat/test_OptimInstanceBatchSingleCrit.R | 21 ++++ tests/testthat/test_Optimizer.R | 10 ++ tests/testthat/test_OptimizerAsync.R | 76 +++++++++++++++ tests/testthat/test_OptimizerBatchChain.R | 69 ++++++++++++++ tests/testthat/test_OptimizerBatchFocusSearch.R | 50 +++++----- tests/testthat/test_OptimizerBatchIrace.R | 57 +++++++++++ tests/testthat/test_OptimizerBatchLocalSearch.R | 84 +++++++++++++++++ tests/testthat/test_OptimizerBatchNLoptr.R | 16 +++ tests/testthat/test_OptimizerBatchRandomSearch.R | 4 tests/testthat/test_TerminatorRunTime.R | 18 +++ tests/testthat/test_bb_optimize.R | 15 +++ tests/testthat/test_mlr_optimizers.R | 2 tests/testthat/test_mlr_test_functions.R | 8 + tests/testthat/test_nds_selection.R | 17 +++ 52 files changed, 797 insertions(+), 212 deletions(-)
Title: Characteristic-Function De-Heaping Density Estimation
Description: Tuning-free kernel density estimation for heaped and rounded data
using a characteristic-function theory of heaping. Rounding to a grid is
convolution with a box followed by lattice sampling, so the density is
recovered by deconvolving the known box and tapering against a data-driven
noise floor. Provides a box-deconvolution de-heaping estimator, a
superposition variant, and a single combined estimator selected by a
band-capacity gate; grid, heaped-fraction, and mixed-grain readers;
and a spectral higher-order comb detector. Base-R replicas of the
Heitjan-Rubin multiple-imputation and measurement-error deconvolution
methods are included for comparison, and the 'Kernelheaping' stochastic
expectation-maximization estimator is used when installed.
Author: Mitchell A. Thornton [aut, cre]
Maintainer: Mitchell A. Thornton <mitchat@sbcglobal.net>
Diff between adheaping versions 1.0.0 dated 2026-07-24 and 1.1.0 dated 2026-09-17
DESCRIPTION | 10 ++-- MD5 | 22 +++++----- NEWS.md | 31 ++++++++++++++ R/detector.R | 91 +++++++++++++++++++++++++++++++++++--------- build/vignette.rds |binary inst/doc/adheaping.R | 2 inst/doc/adheaping.Rmd | 5 +- inst/doc/adheaping.html | 13 +++--- man/heap_grid.Rd | 5 +- man/heap_lattice.Rd | 46 +++++++++++++++++----- tests/testthat/test-basic.R | 51 ++++++++++++++++++++++++ vignettes/adheaping.Rmd | 5 +- 12 files changed, 227 insertions(+), 54 deletions(-)
Title: Spatial Analysis in Archaeology from Refitting Fragments
Description: Methods to analyse spatial units in archaeology from the refitting relationships between fragments of objects scattered in these units (e.g. stratigraphic layers). Graphs are used to model archaeological observations. The package is mainly based on the 'igraph' package for graph analysis. Functions can: 1) create, manipulate, visualise, and simulate fragmentation graphs, 2) measure the cohesion and admixture of archaeological spatial units, and 3) characterise the topology of a specific set of refitting relationships. A series of published empirical datasets is included. Documentation about 'archeofrag' is provided by a vignette and by the accompanying scientific papers: Plutniak (2021, Journal of Archaeological Science, <doi:10.1016/j.jas.2021.105501>) and Plutniak (2022, Journal of Open Source Software, <doi:10.21105/joss.04335>). This package is complemented by the 'archeofrag.gui' R package, a companion GUI application available at <https://analytics.huma-num.fr/arch [...truncated...]
Author: Sebastien Plutniak [aut, cre]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between archeofrag versions 1.2.4 dated 2026-04-22 and 1.3.0 dated 2026-09-17
archeofrag-1.2.4/archeofrag/data/CuzoulCave.RData |only archeofrag-1.2.4/archeofrag/data/CuzoulSouth.RData |only archeofrag-1.3.0/archeofrag/DESCRIPTION | 10 archeofrag-1.3.0/archeofrag/MD5 | 107 +++++----- archeofrag-1.3.0/archeofrag/NAMESPACE | 3 archeofrag-1.3.0/archeofrag/NEWS.md | 11 - archeofrag-1.3.0/archeofrag/R/frag.edges.weighting.R | 35 +-- archeofrag-1.3.0/archeofrag/R/frag.graph.mirror.R |only archeofrag-1.3.0/archeofrag/R/frag.graph.plot.R | 29 ++ archeofrag-1.3.0/archeofrag/R/frag.layers.admixture.R | 5 archeofrag-1.3.0/archeofrag/R/frag.layers.cohesion.R | 34 ++- archeofrag-1.3.0/archeofrag/R/make_frag_object.R | 3 archeofrag-1.3.0/archeofrag/R/utils.R | 6 archeofrag-1.3.0/archeofrag/TODO | 11 - archeofrag-1.3.0/archeofrag/data/BargerGulch.RData |only archeofrag-1.3.0/archeofrag/data/Bessinaudes.RData |only archeofrag-1.3.0/archeofrag/data/BoutDesVergnes.RData |binary archeofrag-1.3.0/archeofrag/data/ChampParel3.RData |only archeofrag-1.3.0/archeofrag/data/Chauzeys.RData |binary archeofrag-1.3.0/archeofrag/data/CuzoulDeGramatCave.RData |only archeofrag-1.3.0/archeofrag/data/CuzoulDeGramatSouth.RData |only archeofrag-1.3.0/archeofrag/data/Eaton.RData |binary archeofrag-1.3.0/archeofrag/data/EtiollesD71.RData |only archeofrag-1.3.0/archeofrag/data/FontJuvenal.RData |binary archeofrag-1.3.0/archeofrag/data/Fumane.RData |binary archeofrag-1.3.0/archeofrag/data/Geelbek.RData |binary archeofrag-1.3.0/archeofrag/data/GrandeRivoire1stMeso.RData |binary archeofrag-1.3.0/archeofrag/data/GrandeRivoire2ndMeso.RData |binary archeofrag-1.3.0/archeofrag/data/Grotte16.RData |binary archeofrag-1.3.0/archeofrag/data/LiangAbu.RData |binary archeofrag-1.3.0/archeofrag/data/Peyrazet.RData |only archeofrag-1.3.0/archeofrag/data/RueAugusteIsaac35.RData |only archeofrag-1.3.0/archeofrag/data/StCesaire1987.RData |binary archeofrag-1.3.0/archeofrag/data/StCesaire2024.RData |binary archeofrag-1.3.0/archeofrag/data/TaiCave.RData |binary archeofrag-1.3.0/archeofrag/data/TaiSouth.RData |binary archeofrag-1.3.0/archeofrag/data/Villetoureix.RData |only archeofrag-1.3.0/archeofrag/inst/doc/archeofrag-vignette.html | 74 +++--- archeofrag-1.3.0/archeofrag/man/BargerGulch.Rd |only archeofrag-1.3.0/archeofrag/man/Bessinaudes.Rd |only archeofrag-1.3.0/archeofrag/man/BoutDesVergnes.Rd | 8 archeofrag-1.3.0/archeofrag/man/ChampParel3.Rd |only archeofrag-1.3.0/archeofrag/man/Chauzeys.Rd | 19 + archeofrag-1.3.0/archeofrag/man/CuzoulCave.Rd | 24 +- archeofrag-1.3.0/archeofrag/man/CuzoulSouth.Rd | 24 +- archeofrag-1.3.0/archeofrag/man/Eaton.Rd | 2 archeofrag-1.3.0/archeofrag/man/EtiollesD71.Rd |only archeofrag-1.3.0/archeofrag/man/FontJuvenal.Rd | 2 archeofrag-1.3.0/archeofrag/man/Fumane.Rd | 2 archeofrag-1.3.0/archeofrag/man/Geelbek.Rd | 2 archeofrag-1.3.0/archeofrag/man/GrandeRivoire1stMeso.Rd | 2 archeofrag-1.3.0/archeofrag/man/GrandeRivoire2ndMeso.Rd | 2 archeofrag-1.3.0/archeofrag/man/Grotte16.Rd | 2 archeofrag-1.3.0/archeofrag/man/LiangAbu.Rd | 2 archeofrag-1.3.0/archeofrag/man/Peyrazet.Rd |only archeofrag-1.3.0/archeofrag/man/RueAugusteIsaac35.Rd |only archeofrag-1.3.0/archeofrag/man/StCesaire1987.Rd | 2 archeofrag-1.3.0/archeofrag/man/StCesaire2024.Rd | 2 archeofrag-1.3.0/archeofrag/man/TaiCave.Rd | 4 archeofrag-1.3.0/archeofrag/man/Villetoureix.Rd |only archeofrag-1.3.0/archeofrag/man/frag.edges.weighting.Rd | 16 - archeofrag-1.3.0/archeofrag/man/frag.graph.plot.Rd | 3 archeofrag-1.3.0/archeofrag/man/frag.layers.cohesion.Rd | 30 ++ archeofrag-1.3.0/archeofrag/tests/testthat/test-frag.layers.cohesion.R | 90 +++++++- 64 files changed, 377 insertions(+), 189 deletions(-)
Title: Plot FTIR Spectra
Description: The goal of 'PlotFTIR' is to easily and quickly kick-start the production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using 'ggplot2'. The produced plots can be published directly or further modified by 'ggplot2' functions.
L'objectif de 'PlotFTIR' est de démarrer facilement et rapidement la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de 'ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions 'ggplot2'.
Author: Philip Bulsink [aut, cre] ,
Ulrich Makanda [trl] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources [cph]
Maintainer: Philip Bulsink <philip.bulsink@nrcan-rncan.gc.ca>
Diff between PlotFTIR versions 1.3.0 dated 2026-07-21 and 1.3.1 dated 2026-09-17
DESCRIPTION | 11 MD5 | 137 NAMESPACE | 60 NEWS.md | 6 R/PlotFTIR-package.R | 14 R/aaa-shared_params.R | 86 R/data.R | 194 R/error_handling.R |only R/io.R | 2328 ++-- R/manipulations.R | 2033 ++- R/maths.R | 2118 ++- R/plot_ftir.R | 691 - R/utils.R | 553 R/zzz.R | 128 README.md |20581 ------------------------------------ build/vignette.rds |binary data/biodiesel.rda |binary data/sample_spectra.rda |binary inst/doc/plotting_ftir_spectra.R | 448 inst/doc/plotting_ftir_spectra.Rmd | 950 - inst/doc/plotting_ftir_spectra.html | 1896 +-- man/PlotFTIR-package.Rd | 69 man/add_band.Rd | 138 man/add_subtract_scalar.Rd | 104 man/add_wavenumber_marker.Rd | 204 man/average_spectra.Rd | 90 man/biodiesel.Rd | 128 man/check_ftir_data.Rd | 76 man/chemospec_to_plotftir.Rd | 68 man/compress_low_energy.Rd | 104 man/compress_trans.Rd | 46 man/conversion.Rd | 136 man/dot-ggplot.Rd | 70 man/dot-shared-params.Rd | 92 man/get_plot_sample_ids.Rd | 76 man/highlight_sample.Rd | 84 man/intensity_type.Rd | 44 man/ir_to_plotftir.Rd | 74 man/move_plot_legend.Rd | 156 man/normalize_spectra.Rd | 122 man/plot_ftir.Rd | 132 man/plot_ftir_core.Rd | 152 man/plot_ftir_stacked.Rd | 186 man/plotftir_to_chemospec.Rd | 104 man/plotftir_to_ir.Rd | 82 man/print.PlotFTIR_data.Rd | 60 man/read_ftir.Rd | 96 man/read_ftir_directory.Rd | 104 man/recalculate_baseline.Rd | 238 man/rename_plot_sample_ids.Rd | 102 man/sample_spectra.Rd | 100 man/save_plot.Rd | 72 man/zoom_in_on_range.Rd | 86 tests/testthat.R | 24 tests/testthat/_problems |only tests/testthat/helper-bilingual.R |only tests/testthat/test-io.R | 1467 +- tests/testthat/test-manipulations.R | 1129 - tests/testthat/test-maths.R | 3244 ++--- tests/testthat/test-plot_ftir.R | 408 tests/testthat/test-utils.R | 143 tests/testthat/test-zzz.R |only vignettes/peak_fitting.R |only vignettes/peak_fitting.html |only vignettes/plotting_ftir_spectra.Rmd | 950 - 65 files changed, 12502 insertions(+), 30492 deletions(-)
Title: Handling Missing Values with Multivariate Data Analysis
Description: Imputation of incomplete continuous or categorical datasets; Missing values are imputed with a principal component analysis (PCA), a multiple correspondence analysis (MCA) model or a multiple factor analysis (MFA) model; Perform multiple imputation with and in PCA or MCA.
Author: Francois Husson [aut, cre] ,
Julie Josse [aut]
Maintainer: Francois Husson <francois.husson@institut-agro.fr>
Diff between missMDA versions 1.22 dated 2026-07-07 and 1.23 dated 2026-09-17
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 1 + R/MIFAMD.R | 5 +++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/MultipleImputation.html | 18 +++++++++++------- inst/doc/missMDA.html | 18 +++++++++++------- 8 files changed, 39 insertions(+), 25 deletions(-)
Title: Hierarchically Regularized Entropy Balancing
Description: Implements hierarchically regularized entropy balancing proposed by Xu and Yang (2022) <doi:10.1017/pan.2022.12>. The method adjusts the covariate distributions of the control group to match those of the treatment group. 'hbal' automatically expands the covariate space to include higher order terms and uses cross-validation to select variable penalties for the balancing conditions.
Author: Yiqing Xu [aut, cre] ,
Eddie Yang [aut]
Maintainer: Yiqing Xu <yiqingxu@stanford.edu>
Diff between hbal versions 1.2.15 dated 2025-09-10 and 1.3.0 dated 2026-09-17
DESCRIPTION | 13 +- MD5 | 50 ++++++--- NAMESPACE | 2 R/att.R | 240 +++++++++++++++++++++++++++++++++++++++++++---- R/att_abw.R |only R/balanceData.R |only R/classFunctions.R | 19 ++- R/contenderJudges-data.R | 11 +- R/covarExpand.R | 5 R/crossValidate.R | 4 R/hbal.R | 108 ++++++++++++++------- R/lalonde-data.R | 10 + R/onAttach.R | 1 build |only man/att.Rd | 154 ++++++++++++++++++++++++++++-- man/balanceData.Rd |only man/contenderJudges.Rd | 10 + man/covarExpand.Rd | 5 man/crossValidate.Rd | 4 man/dot-onAttach.Rd | 3 man/hbal.Rd | 83 ++++++++++------ man/lalonde.Rd | 9 + man/plot.hbal.Rd | 6 - man/summary.hbal.Rd | 5 tests |only 25 files changed, 612 insertions(+), 130 deletions(-)
Title: Automatic Processing of Terrestrial-Based Technologies Point
Cloud Data for Forestry Purposes
Description: Process automation of point cloud data derived from terrestrial-based technologies such as Terrestrial Laser Scanner (TLS) or Mobile Laser Scanner. 'FORTLS' enables (i) detection of trees and estimation of tree-level attributes (e.g. diameters and heights), (ii) estimation of stand-level variables (e.g. density, basal area, mean and dominant height), (iii) computation of metrics related to important forest attributes estimated in Forest Inventories at stand-level, and (iv) optimization of plot design for combining TLS data and field measured data. Documentation about 'FORTLS' is described in Molina-Valero et al. (2022, <doi:10.1016/j.envsoft.2022.105337>).
Author: Juan Alberto Molina-Valero [aut, cph, cre],
Adela Martinez-Calvo [aut, com],
Juan Gabriel Alvarez-Gonzalez [aut, ths],
Fernando Montes [aut],
Cesar Perez-Cruzado [aut, ths]
Maintainer: Juan Alberto Molina-Valero <jamolinavalero@gmail.com>
This is a re-admission after prior archival of version 2.0.1 dated 2026-04-20
Diff between FORTLS versions 2.0.1 dated 2026-04-20 and 2.0.2 dated 2026-09-17
DESCRIPTION | 8 ++++---- MD5 | 22 ++++++++++++---------- R/install_fortls_python_deps.R | 3 ++- R/normalize.R | 7 ++++--- R/python.functions.R | 13 +++++++++++++ R/tree.detection.multi.scan.R | 2 +- R/tree.detection.single.scan.R | 15 +++++++++++++-- build/partial.rdb |binary inst/doc/plot_design_optimization.html | 6 +++--- inst/doc/tree_level.html | 2 +- inst/python/fit_circles_macif.py |only man/fit_circles_macif.Rd |only man/normalize.Rd | 4 +++- 13 files changed, 56 insertions(+), 26 deletions(-)
Title: Spatial Analysis in Archaeology from Refitting Fragments (GUI)
Description: A 'Shiny' application to access the functionalities and datasets of the 'archeofrag' package for spatial analysis in archaeology from refitting data. Quick and seamless exploration of archaeological refitting datasets, focusing on physical refits only. Features include: built-in documentation and convenient workflow, plot generation and export, anomaly detection in the spatial distribution of refitting connection, exploration of spatial units merging solutions, data export to the 'fabryka' application for spatial orientation analysis, simulation of archaeological site formation processes, support for parallel computing, R code generation to re-execute simulations and ensure reproducibility, code generation for the 'openMOLE' model exploration software. A demonstration of the app is available at <https://analytics.huma-num.fr/archeofrag/>.
Author: Sebastien Plutniak [aut, cre]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between archeofrag.gui versions 1.1.4 dated 2026-01-11 and 1.2.0 dated 2026-09-17
DESCRIPTION | 10 MD5 | 12 NAMESPACE | 8 NEWS.md | 12 R/app_server.R | 1306 ++++++++++++++++++++++++------------------- R/app_ui.R | 114 ++- R/check_weighting_variable.R |only R/make_rubish_data.R |only 8 files changed, 857 insertions(+), 605 deletions(-)
More information about archeofrag.gui at CRAN
Permanent link
Title: Baseline Functions for Actigraphy and Activity Processing and
Analysis
Description: Provides baseline functions for actigraphy and activity data.
This package is intended to be extended by downstream overlays such as
'actiread', 'actimetrics', and 'stepcount'.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between actibase versions 0.5.0 dated 2026-08-21 and 0.6.0 dated 2026-09-17
DESCRIPTION | 6 +++--- MD5 | 16 +++++++++++++--- NAMESPACE | 8 ++++++++ NEWS.md | 3 +++ R/time_to_minute.R |only man/acti_day_index.Rd |only man/acti_day_start.Rd |only man/acti_hms_to_minute.Rd |only man/acti_minute_to_hms.Rd |only man/acti_repeat_time_of_day.Rd |only man/acti_split_intervals_at_midnight.Rd |only man/acti_time_of_day.Rd |only man/acti_time_to_minute.Rd |only tests/testthat/test-time-to-minute.R |only 14 files changed, 27 insertions(+), 6 deletions(-)
Title: Discover, Count, Categorise, Score, Translate and Relate Emoji
in Text
Description: A tidy toolkit for working with the emoji in any text column, such
as social-media posts, product reviews, chat logs or survey responses.
Unicode is awkward to handle and not every code point is an emoji, which
makes emoji statistics fiddly to obtain. 'tidyEmoji' extracts, counts,
categorises, sentiment-scores and emotion-scores emoji, converts them to and
from text (for accessibility and NLP preprocessing), searches the emoji
catalogue, maps emoji co-occurrence and sequences (graph-ready edge lists
and n-grams), measures where and how densely emoji are used, and builds
document-by-emoji feature tables for machine learning, with grapheme-aware
detection (so skin-tone and multi-person sequences stay intact), returning
tidy data frames that slot straight into a 'tidyverse' workflow. It also
quantifies how much annotators disagreed about an emoji (interpretation
risk), extracts the words around each emoji, tracks emoji use over time,
measures text-emoji sentiment mismatch, and applies exp [...truncated...]
Author: Youzhi Yu [aut, cre]
Maintainer: Youzhi Yu <yuyouzhi666@icloud.com>
Diff between tidyEmoji versions 0.3.0 dated 2026-08-04 and 0.4.0 dated 2026-09-17
tidyEmoji-0.3.0/tidyEmoji/vignettes/ata_tweets.csv |only tidyEmoji-0.4.0/tidyEmoji/DESCRIPTION | 26 tidyEmoji-0.4.0/tidyEmoji/MD5 | 164 tidyEmoji-0.4.0/tidyEmoji/NAMESPACE | 21 tidyEmoji-0.4.0/tidyEmoji/NEWS.md | 2568 +++++++++- tidyEmoji-0.4.0/tidyEmoji/R/data.R | 38 tidyEmoji-0.4.0/tidyEmoji/R/emoji-ambiguity.R |only tidyEmoji-0.4.0/tidyEmoji/R/emoji-categorize.R | 60 tidyEmoji-0.4.0/tidyEmoji/R/emoji-context.R |only tidyEmoji-0.4.0/tidyEmoji/R/emoji-dfm.R | 56 tidyEmoji-0.4.0/tidyEmoji/R/emoji-emotion.R | 141 tidyEmoji-0.4.0/tidyEmoji/R/emoji-engine.R | 984 +++ tidyEmoji-0.4.0/tidyEmoji/R/emoji-extraction.R | 48 tidyEmoji-0.4.0/tidyEmoji/R/emoji-incongruity.R |only tidyEmoji-0.4.0/tidyEmoji/R/emoji-lexicon-api.R | 170 tidyEmoji-0.4.0/tidyEmoji/R/emoji-metrics.R | 134 tidyEmoji-0.4.0/tidyEmoji/R/emoji-provenance.R |only tidyEmoji-0.4.0/tidyEmoji/R/emoji-relate.R | 74 tidyEmoji-0.4.0/tidyEmoji/R/emoji-sanitize.R |only tidyEmoji-0.4.0/tidyEmoji/R/emoji-search.R | 58 tidyEmoji-0.4.0/tidyEmoji/R/emoji-sentiment.R | 105 tidyEmoji-0.4.0/tidyEmoji/R/emoji-summary.R | 42 tidyEmoji-0.4.0/tidyEmoji/R/emoji-time.R |only tidyEmoji-0.4.0/tidyEmoji/R/emoji-translate.R | 133 tidyEmoji-0.4.0/tidyEmoji/R/emoji-type.R |only tidyEmoji-0.4.0/tidyEmoji/R/tidyEmoji.R | 169 tidyEmoji-0.4.0/tidyEmoji/R/top-n-emojis.R | 60 tidyEmoji-0.4.0/tidyEmoji/README.md | 95 tidyEmoji-0.4.0/tidyEmoji/inst/CITATION |only tidyEmoji-0.4.0/tidyEmoji/inst/LICENSE.note |only tidyEmoji-0.4.0/tidyEmoji/inst/WORDLIST |only tidyEmoji-0.4.0/tidyEmoji/inst/doc/introduction.R | 152 tidyEmoji-0.4.0/tidyEmoji/inst/doc/introduction.Rmd | 353 + tidyEmoji-0.4.0/tidyEmoji/inst/doc/introduction.html | 1030 ++-- tidyEmoji-0.4.0/tidyEmoji/inst/extdata |only tidyEmoji-0.4.0/tidyEmoji/man/as_emoji_name.Rd | 42 tidyEmoji-0.4.0/tidyEmoji/man/as_emoji_type.Rd |only tidyEmoji-0.4.0/tidyEmoji/man/emoji_adoption_lag.Rd |only tidyEmoji-0.4.0/tidyEmoji/man/emoji_ambiguity.Rd |only 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|only tidyEmoji-0.4.0/tidyEmoji/man/emoji_lexicons.Rd | 8 tidyEmoji-0.4.0/tidyEmoji/man/emoji_ngrams.Rd | 26 tidyEmoji-0.4.0/tidyEmoji/man/emoji_pairs.Rd | 27 tidyEmoji-0.4.0/tidyEmoji/man/emoji_position.Rd | 51 tidyEmoji-0.4.0/tidyEmoji/man/emoji_provenance.Rd |only tidyEmoji-0.4.0/tidyEmoji/man/emoji_ratio.Rd | 28 tidyEmoji-0.4.0/tidyEmoji/man/emoji_risk.Rd |only tidyEmoji-0.4.0/tidyEmoji/man/emoji_sanitize.Rd |only tidyEmoji-0.4.0/tidyEmoji/man/emoji_score.Rd | 77 tidyEmoji-0.4.0/tidyEmoji/man/emoji_search.Rd | 28 tidyEmoji-0.4.0/tidyEmoji/man/emoji_seasonality.Rd |only tidyEmoji-0.4.0/tidyEmoji/man/emoji_sentiment.Rd | 46 tidyEmoji-0.4.0/tidyEmoji/man/emoji_sentiment_lexicon.Rd | 12 tidyEmoji-0.4.0/tidyEmoji/man/emoji_summary.Rd | 16 tidyEmoji-0.4.0/tidyEmoji/man/emoji_to_text.Rd | 24 tidyEmoji-0.4.0/tidyEmoji/man/emoji_token_cost.Rd |only tidyEmoji-0.4.0/tidyEmoji/man/emoji_tokens.Rd | 18 tidyEmoji-0.4.0/tidyEmoji/man/emoji_trend.Rd |only 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More information about spatstat.convert at CRAN
Permanent link
Title: Sparse Marginal Epistasis Test
Description: The Sparse Marginal Epistasis Test is a computationally efficient
genetics method which detects statistical epistasis in complex traits;
see Stamp et al. (2025, <doi:10.1101/2025.01.11.632557>) for details.
Author: Julian Stamp [cre, aut] ,
Lorin Crawford [aut] ,
sriramlab [cph]
Maintainer: Julian Stamp <julian.d.stamp@gmail.com>
This is a re-admission after prior archival of version 0.0.2 dated 2025-08-22
Diff between smer versions 0.0.2 dated 2025-08-22 and 0.0.3 dated 2026-09-17
DESCRIPTION | 8 - MD5 | 23 ++--- NEWS.md | 5 + build/vignette.rds |binary inst/WORDLIST |only inst/doc/smer.html | 86 ++++++++++--------- inst/doc/study-erythroid-differentiation-data.html | 88 ++++++++++---------- inst/doc/tutorial-create-mask-file.html | 88 ++++++++++---------- inst/doc/tutorial-memory-optimization.html | 91 ++++++++++----------- inst/doc/tutorial-simulate-traits.html | 86 ++++++++++--------- src/count_data.cpp | 2 src/hdf5_api.cpp | 1 src/read_genotype_mask.h | 1 13 files changed, 248 insertions(+), 231 deletions(-)
Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
This is a re-admission after prior archival of version 10.1.9 dated 2026-06-16
Diff between rswipl versions 10.1.9 dated 2026-06-16 and 10.1.15 dated 2026-09-17
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rswipl-10.1.15/rswipl/src/swipl-devel/src/pl-umap.c | 6323 +++++++ rswipl-10.1.15/rswipl/src/swipl-devel/src/pl-undo.c | 6 rswipl-10.1.15/rswipl/src/swipl-devel/src/pl-undo.h | 1 rswipl-10.1.15/rswipl/src/swipl-devel/src/pl-util.c | 10 rswipl-10.1.15/rswipl/src/swipl-devel/src/pl-util.h | 1 rswipl-10.1.15/rswipl/src/swipl-devel/src/pl-variant.c | 45 rswipl-10.1.15/rswipl/src/swipl-devel/src/pl-vmi.c | 75 rswipl-10.1.15/rswipl/src/swipl-devel/src/pl-wrap.c | 62 rswipl-10.1.15/rswipl/src/swipl-devel/src/pl-wrap.h | 5 rswipl-10.1.15/rswipl/src/swipl-devel/src/pl-write.c | 1006 - rswipl-10.1.15/rswipl/src/swipl-devel/src/pl-write.h | 2 rswipl-10.1.15/rswipl/src/swipl-devel/src/pl-zip.c | 6 rswipl-10.1.15/rswipl/src/swipl-devel/src/pl-zip.h | 1 rswipl-10.1.15/rswipl/src/swipl-devel/src/swipl.1.in | 21 rswipl-10.1.15/rswipl/src/swipl-devel/src/wasm/pl-wasm.c | 29 rswipl-10.1.15/rswipl/src/swipl-devel/tests/attvar/test_dif.pl | 8 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rswipl-10.1.9/rswipl/src/swipl-devel/tests/core |only 609 files changed, 50007 insertions(+), 12176 deletions(-)
Title: Bindings to 'OpenCV' Computer Vision Library
Description: Exposes some of the available 'OpenCV' <https://opencv.org/> algorithms,
such as a QR code scanner, and edge, body or face detection. These can either be
applied to analyze static images, or to filter live video footage from a camera device.
Author: Jeroen Ooms [aut, cre] ,
Jan Wijffels [aut]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between opencv versions 0.6.0 dated 2026-09-14 and 0.6.1 dated 2026-09-17
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NEWS | 3 +++ 3 files changed, 8 insertions(+), 5 deletions(-)
Title: Migration and Range Change Estimation in R
Description: A set of tools for likelihood-based estimation, model selection and testing of two- and three-range shift and migration models for animal movement data as described in Gurarie et al. (2017) <doi:10.1111/1365-2656.12674>. Provided movement data (X, Y and Time), including irregularly sampled data, functions estimate the time, duration and location of one or two range shifts, as well as the ranging area and auto-correlation structure of the movement. Tests assess, for example, whether the shift was "significant", and whether a two-shift migration was a true return migration.
Author: Eliezer Gurarie [aut, cre],
Faridedin Cheraghi [ctb]
Maintainer: Eliezer Gurarie <egurarie@esf.edu>
Diff between marcher versions 0.0-2 dated 2017-04-12 and 0.0.3 dated 2026-09-17
marcher-0.0-2/marcher/R/estimate_shift.r |only marcher-0.0-2/marcher/R/getArea.r |only marcher-0.0-2/marcher/R/getRSI.r |only marcher-0.0-2/marcher/R/getTau.r |only marcher-0.0-2/marcher/R/locate_shift.r |only marcher-0.0-2/marcher/R/plot.shiftfit.r |only marcher-0.0-2/marcher/R/quickfit.r |only marcher-0.0-2/marcher/R/selectModel.r |only marcher-0.0-2/marcher/R/tests.r |only marcher-0.0.3/marcher/DESCRIPTION | 25 marcher-0.0.3/marcher/MD5 | 90 - marcher-0.0.3/marcher/NAMESPACE | 2 marcher-0.0.3/marcher/NEWS.md | 11 marcher-0.0.3/marcher/R/datasets.R | 2 marcher-0.0.3/marcher/R/estimate_shift.R |only marcher-0.0.3/marcher/R/fitNSD.R | 14 marcher-0.0.3/marcher/R/getArea.R |only marcher-0.0.3/marcher/R/getLikelihood.R | 4 marcher-0.0.3/marcher/R/getMu.R | 11 marcher-0.0.3/marcher/R/getRSI.R |only marcher-0.0.3/marcher/R/getTau.R |only marcher-0.0.3/marcher/R/init.R | 1 marcher-0.0.3/marcher/R/locate_shift.R |only marcher-0.0.3/marcher/R/marcher.R | 30 marcher-0.0.3/marcher/R/plot.shiftfit.R |only marcher-0.0.3/marcher/R/quickfit.R |only marcher-0.0.3/marcher/R/scan_track.R | 4 marcher-0.0.3/marcher/R/selectModel.R |only marcher-0.0.3/marcher/R/simulate_shift.R | 9 marcher-0.0.3/marcher/R/tests.R |only marcher-0.0.3/marcher/README.md | 22 marcher-0.0.3/marcher/build/vignette.rds |binary marcher-0.0.3/marcher/demo/estimate_shift_example.r | 2 marcher-0.0.3/marcher/inst/doc/marcher.R | 110 - marcher-0.0.3/marcher/inst/doc/marcher.Rmd | 30 marcher-0.0.3/marcher/inst/doc/marcher.html | 1130 ++++++++++++++------ marcher-0.0.3/marcher/man/Michela.Rd | 68 - marcher-0.0.3/marcher/man/SimulatedTracks.Rd | 86 - marcher-0.0.3/marcher/man/estimate_shift.Rd | 188 +-- marcher-0.0.3/marcher/man/fitNSD.Rd | 113 +- marcher-0.0.3/marcher/man/getArea.Rd | 67 - marcher-0.0.3/marcher/man/getCov.Rd | 48 marcher-0.0.3/marcher/man/getLikelihood.Rd | 47 marcher-0.0.3/marcher/man/getMu.Rd | 52 marcher-0.0.3/marcher/man/getRSI.Rd | 46 marcher-0.0.3/marcher/man/getTau.Rd | 56 marcher-0.0.3/marcher/man/locate_shift.Rd | 63 - marcher-0.0.3/marcher/man/marcher-package.Rd | 92 - marcher-0.0.3/marcher/man/plot.shiftfit.Rd | 148 +- marcher-0.0.3/marcher/man/quickfit.Rd | 133 +- marcher-0.0.3/marcher/man/scan_track.Rd | 112 + marcher-0.0.3/marcher/man/selectModel.Rd | 181 +-- marcher-0.0.3/marcher/man/simulate_shift.Rd | 114 +- marcher-0.0.3/marcher/man/test_rangeshift.Rd | 82 - marcher-0.0.3/marcher/vignettes/marcher.Rmd | 30 55 files changed, 1942 insertions(+), 1281 deletions(-)
Title: Fast Robust Moments
Description: Fast, numerically robust computation of weighted moments via 'Rcpp'.
Supports computation on vectors and matrices, and Monoidal append of moments.
Moments and cumulants over running fixed length windows can be computed,
as well as over time-based windows.
Moment computations are via a generalization of Welford's method, as described
by Bennett et. (2009) <doi:10.1109/CLUSTR.2009.5289161>.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between fromo versions 0.2.4 dated 2024-11-29 and 0.2.5 dated 2026-09-17
ChangeLog | 16 +++++ DESCRIPTION | 13 ++-- MD5 | 97 +++++++++++++++++------------------ R/RcppExports.R | 88 ++++++++++++++++++++++---------- R/fromo.r | 19 ++++++ R/zzz_centsums.R | 87 ++++++++++++++++++------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/fromo.pdf |binary man/NEWS.Rd | 19 ++++++ man/as.centsums.Rd | 9 ++- man/centcosum-accessor-methods.Rd | 7 +- man/centcosums-class.Rd | 15 ++++- man/centcosums.Rd | 9 ++- man/centsums-accessor-methods.Rd | 10 +++ man/centsums-class.Rd | 7 +- man/centsums.Rd | 29 +--------- man/centsums_join.Rd |only man/firstmoments.Rd | 5 + man/runningadjustments.Rd | 5 + man/runningmean.Rd | 5 + man/runningmoments.Rd | 5 + man/runningquantiles.Rd | 5 + man/t_runningadjustments.Rd | 8 +- man/t_runningmean.Rd | 5 + man/t_runningmoments.Rd | 5 + man/t_runningquantiles.Rd | 5 + man/two_runningmoments.Rd | 5 + man/two_t_runningmoments.Rd | 19 +++--- src/RcppExports.cpp | 9 +-- src/common.h | 4 - src/fromo.cpp | 73 ++++++++++++++++++++------ src/running.cpp | 3 - src/running.h | 30 +++++----- src/runningmean.cpp | 3 - src/runningmean.h | 54 ++++++++++--------- src/t_running.cpp | 4 - src/t_running.h | 30 +++++----- src/t_runningmean.cpp | 3 - src/t_runningmean.h | 1 src/two_running.cpp | 3 - src/two_running.h | 38 +++++++------ src/two_t_running.cpp | 14 ++--- src/two_t_running.h | 39 ++++++++------ src/welford.h | 2 tests/testthat/test-correctness.r | 61 ++++++++++++++++++++++ tests/testthat/test-obj.r | 103 +++++++++++++++++++++++++++++++++++-- tests/testthat/test-running.r | 104 +++++++++++++++++++++++++++++++++++--- tests/testthat/test-trunning.r | 63 +++++++++++++++++++++++ vignettes/fromo.bib | 4 - 50 files changed, 813 insertions(+), 329 deletions(-)
Title: Integration of One-Dimensional Functions with Double Exponential
Formulas
Description: Numerical quadrature of functions of one variable over a finite
or infinite interval with double exponential formulas.
Author: Hiroyuki Okamura [aut, cre]
Maintainer: Hiroyuki Okamura <okamu@hiroshima-u.ac.jp>
This is a re-admission after prior archival of version 0.1.2 dated 2022-05-30
Diff between deformula versions 0.1.2 dated 2022-05-30 and 0.1.3 dated 2026-09-17
deformula-0.1.2/deformula/man/deformula.Rd |only deformula-0.1.3/deformula/DESCRIPTION | 16 ++--- deformula-0.1.3/deformula/MD5 | 22 +++---- deformula-0.1.3/deformula/NEWS.md | 19 +++++- deformula-0.1.3/deformula/R/deformula.R | 28 ++++----- deformula-0.1.3/deformula/R/package.R | 2 deformula-0.1.3/deformula/README.md | 9 +++ deformula-0.1.3/deformula/man/deformula-package.Rd |only deformula-0.1.3/deformula/man/deformula.moneone.Rd | 2 deformula-0.1.3/deformula/man/deformula.zeroinf.Rd | 2 deformula-0.1.3/deformula/src/deformula.h | 45 ++++++++++------ deformula-0.1.3/deformula/tests/testthat/test-moneone.R | 22 +++++++ deformula-0.1.3/deformula/tests/testthat/test-zeroinf.R | 30 ++++++++++ 13 files changed, 141 insertions(+), 56 deletions(-)
Title: Estimate Crown Scorch from Terrestrial LiDAR Scans
Description: Estimates tree crown scorch from terrestrial lidar scans collected with a RIEGL vz400i. The methods follow those described in Cannon et al. (2025, Fire Ecology 21:71, <doi:10.1186/s42408-025-00420-0>).
Author: Jeffery Cannon [aut, cre],
Andrew Whelan [ctb]
Maintainer: Jeffery Cannon <Jeffery.Cannon@jonesctr.org>
This is a re-admission after prior archival of version 0.1.1 dated 2026-01-18
Diff between CrownScorchTLS versions 0.1.1 dated 2026-01-18 and 0.1.2 dated 2026-09-17
DESCRIPTION | 6 - MD5 | 20 ++-- NEWS.md | 10 ++ R/TreeLS_stemPoints_methods.R | 2 R/functions.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/CrownScorchTLS-workflow.html | 9 + man/remove_stem.Rd | 2 man/stemPoints.Rd | 103 ++++++++++----------- man/stm.hough.Rd | 166 +++++++++++++++++----------------- 11 files changed, 167 insertions(+), 155 deletions(-)
More information about CrownScorchTLS at CRAN
Permanent link
Title: Identification and Estimation using Group Testing
Description: Methods for the group testing identification problem: 1) Operating
characteristics (e.g., expected number of tests) for commonly used
hierarchical and array-based algorithms, and 2) Optimal testing
configurations for these same algorithms. Methods for the group testing
estimation problem: 1) Estimation and inference procedures for an overall
prevalence, and 2) Regression modeling for commonly used hierarchical and
array-based algorithms.
Author: Brianna Hitt [aut, cre] ,
Christopher Bilder [aut] ,
Frank Schaarschmidt [aut] ,
Brad Biggerstaff [aut] ,
Christopher McMahan [aut] ,
Joshua Tebbs [aut] ,
Boan Zhang [ctb],
Michael Black [ctb],
Peijie Hou [ctb],
Peng Chen [ctb],
Minh Nguyen [ctb]
Maintainer: Brianna Hitt <brianna.hitt@afacademy.af.edu>
This is a re-admission after prior archival of version 1.3.3 dated 2025-09-13
Diff between binGroup2 versions 1.3.3 dated 2025-09-13 and 1.3.4 dated 2026-09-17
DESCRIPTION | 12 MD5 | 85 - NAMESPACE | 1 NEWS.md | 10 R/RcppExports.R | 86 - R/hivsurv.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/Identification-through-group-testing.R | 396 +++--- inst/doc/Identification-through-group-testing.html | 1263 ++++++++++----------- man/ExpTests.Rd | 2 man/GroupMembershipMatrix.Rd | 12 man/OTC1.Rd | 712 +++++------ man/OTC2.Rd | 674 +++++------ man/Sterrett.Rd | 314 ++--- man/TOD.Rd | 12 man/binGroup2.Rd | 646 +++++----- man/designEst.Rd | 162 +- man/designPower.Rd | 408 +++--- man/expectOrderBeta.Rd | 164 +- man/gtPower.Rd | 254 ++-- man/gtReg.Rd | 674 +++++------ man/gtRegControl.Rd | 100 - man/gtSim.Rd | 324 ++--- man/gtTest.Rd | 198 +-- man/gtWidth.Rd | 160 +- man/halving.Rd | 172 +- man/hivsurv.Rd | 73 - man/informativeArrayProb.Rd | 120 - man/operatingCharacteristics1.Rd | 708 +++++------ man/operatingCharacteristics2.Rd | 832 ++++++------- man/pmf.Rd | 2 man/predict.gtReg.Rd | 168 +- man/print.designPower.Rd | 62 - man/print.gtTest.Rd | 58 man/print.propCI.Rd | 54 man/print.propDiffCI.Rd | 54 man/print.summary.gtReg.Rd | 86 - man/propCI.Rd | 468 +++---- man/propDiffCI.Rd | 310 ++--- man/summary.OTC.Rd | 232 +-- man/summary.gtReg.Rd | 174 +- man/summary.opChar.Rd | 246 ++-- src/Hierarchical.cpp | 68 - 44 files changed, 5288 insertions(+), 5268 deletions(-)
Title: Dataset Dependency Graphs for Leakage-Aware Evaluation
Description: Represent biomedical dataset structure as typed dependency
graphs so that sample provenance, repeated-measure structure, study
design, batch effects, and temporal relationships are explicit and
inspectable. Validates dataset structure, detects sample-level overlap,
derives deterministic split constraints, and produces a tool-agnostic
split specification for leakage-aware evaluation workflows.
Author: Selcuk Korkmaz [aut, cre]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between splitGraph versions 0.3.0 dated 2026-07-03 and 0.4.0 dated 2026-09-17
splitGraph-0.3.0/splitGraph/inst/schema/dependency_graph.schema.json |only splitGraph-0.3.0/splitGraph/inst/schema/split_spec.schema.json |only splitGraph-0.4.0/splitGraph/DESCRIPTION | 11 splitGraph-0.4.0/splitGraph/MD5 | 151 splitGraph-0.4.0/splitGraph/NAMESPACE | 16 splitGraph-0.4.0/splitGraph/NEWS.md | 272 splitGraph-0.4.0/splitGraph/R/constraints.R | 409 splitGraph-0.4.0/splitGraph/R/constructors.R | 82 splitGraph-0.4.0/splitGraph/R/export.R |only splitGraph-0.4.0/splitGraph/R/graph-build-auto.R | 103 splitGraph-0.4.0/splitGraph/R/graph-build.R | 89 splitGraph-0.4.0/splitGraph/R/graph-edit.R |only splitGraph-0.4.0/splitGraph/R/ingest.R | 44 splitGraph-0.4.0/splitGraph/R/methods.R | 128 splitGraph-0.4.0/splitGraph/R/pairwise.R | 225 splitGraph-0.4.0/splitGraph/R/query.R | 248 splitGraph-0.4.0/splitGraph/R/schema-validate.R | 93 splitGraph-0.4.0/splitGraph/R/serialization.R | 338 splitGraph-0.4.0/splitGraph/R/split-spec.R | 274 splitGraph-0.4.0/splitGraph/R/splitGraph-package.R | 170 splitGraph-0.4.0/splitGraph/R/validate.R | 350 splitGraph-0.4.0/splitGraph/README.md | 60 splitGraph-0.4.0/splitGraph/build/vignette.rds |binary splitGraph-0.4.0/splitGraph/inst/bench |only splitGraph-0.4.0/splitGraph/inst/doc/adapter-cookbook.R | 437 - splitGraph-0.4.0/splitGraph/inst/doc/adapter-cookbook.Rmd | 203 splitGraph-0.4.0/splitGraph/inst/doc/adapter-cookbook.html | 1648 ++- splitGraph-0.4.0/splitGraph/inst/doc/case-study-gse60424.R |only splitGraph-0.4.0/splitGraph/inst/doc/case-study-gse60424.Rmd |only splitGraph-0.4.0/splitGraph/inst/doc/case-study-gse60424.html |only splitGraph-0.4.0/splitGraph/inst/doc/cross-language-handoff.R | 174 splitGraph-0.4.0/splitGraph/inst/doc/cross-language-handoff.Rmd | 213 splitGraph-0.4.0/splitGraph/inst/doc/cross-language-handoff.html | 1285 +-- splitGraph-0.4.0/splitGraph/inst/doc/faq-design-notes.R |only splitGraph-0.4.0/splitGraph/inst/doc/faq-design-notes.Rmd |only splitGraph-0.4.0/splitGraph/inst/doc/faq-design-notes.html |only splitGraph-0.4.0/splitGraph/inst/doc/leakage-aware-workflow.R | 1385 +-- splitGraph-0.4.0/splitGraph/inst/doc/leakage-aware-workflow.Rmd | 311 splitGraph-0.4.0/splitGraph/inst/doc/leakage-aware-workflow.html | 4219 +++++----- splitGraph-0.4.0/splitGraph/inst/doc/modeling-structure.R | 387 splitGraph-0.4.0/splitGraph/inst/doc/modeling-structure.Rmd | 259 splitGraph-0.4.0/splitGraph/inst/doc/modeling-structure.html | 1492 ++- splitGraph-0.4.0/splitGraph/inst/doc/quick-start.R |only splitGraph-0.4.0/splitGraph/inst/doc/quick-start.Rmd |only splitGraph-0.4.0/splitGraph/inst/doc/quick-start.html |only splitGraph-0.4.0/splitGraph/inst/extdata |only splitGraph-0.4.0/splitGraph/inst/python/README.md | 18 splitGraph-0.4.0/splitGraph/inst/python/conformance.py | 2 splitGraph-0.4.0/splitGraph/inst/python/pyproject.toml |only splitGraph-0.4.0/splitGraph/inst/python/splitspec/__init__.py | 2 splitGraph-0.4.0/splitGraph/inst/python/splitspec/reader.py | 36 splitGraph-0.4.0/splitGraph/inst/schema/0.3.0 |only splitGraph-0.4.0/splitGraph/man/as_split_spec.Rd | 61 splitGraph-0.4.0/splitGraph/man/build_dependency_graph.Rd | 35 splitGraph-0.4.0/splitGraph/man/depgraph_validation_report.Rd | 5 splitGraph-0.4.0/splitGraph/man/derive_split_constraints.Rd | 10 splitGraph-0.4.0/splitGraph/man/export_graph.Rd |only splitGraph-0.4.0/splitGraph/man/graph_edit.Rd |only splitGraph-0.4.0/splitGraph/man/graph_from_metadata.Rd | 38 splitGraph-0.4.0/splitGraph/man/graph_node_set.Rd | 31 splitGraph-0.4.0/splitGraph/man/pairwise_edges.Rd | 7 splitGraph-0.4.0/splitGraph/man/plot.dependency_graph.Rd |only splitGraph-0.4.0/splitGraph/man/splitgraph_conditions.Rd |only splitGraph-0.4.0/splitGraph/man/validate_json.Rd | 3 splitGraph-0.4.0/splitGraph/man/write_dependency_graph.Rd | 35 splitGraph-0.4.0/splitGraph/man/write_split_spec.Rd | 21 splitGraph-0.4.0/splitGraph/tests/testthat/test-bioleak-contract.R | 97 splitGraph-0.4.0/splitGraph/tests/testthat/test-conditions.R |only splitGraph-0.4.0/splitGraph/tests/testthat/test-constructors.R | 20 splitGraph-0.4.0/splitGraph/tests/testthat/test-contract-0-4-0.R |only splitGraph-0.4.0/splitGraph/tests/testthat/test-deprecations.R | 96 splitGraph-0.4.0/splitGraph/tests/testthat/test-export.R |only splitGraph-0.4.0/splitGraph/tests/testthat/test-graph-edit.R |only splitGraph-0.4.0/splitGraph/tests/testthat/test-graph-from-metadata.R | 65 splitGraph-0.4.0/splitGraph/tests/testthat/test-json-schema.R | 111 splitGraph-0.4.0/splitGraph/tests/testthat/test-methods-coverage.R |only splitGraph-0.4.0/splitGraph/tests/testthat/test-methods.R | 12 splitGraph-0.4.0/splitGraph/tests/testthat/test-performance.R |only splitGraph-0.4.0/splitGraph/tests/testthat/test-python-conformance.R | 30 splitGraph-0.4.0/splitGraph/tests/testthat/test-schema-version.R | 2 splitGraph-0.4.0/splitGraph/tests/testthat/test-serialization.R | 35 splitGraph-0.4.0/splitGraph/tests/testthat/test-split-spec.R | 65 splitGraph-0.4.0/splitGraph/tests/testthat/test-summarized-experiment.R |only splitGraph-0.4.0/splitGraph/tests/testthat/test-validate.R | 12 splitGraph-0.4.0/splitGraph/vignettes/adapter-cookbook.Rmd | 203 splitGraph-0.4.0/splitGraph/vignettes/case-study-gse60424.Rmd |only splitGraph-0.4.0/splitGraph/vignettes/cross-language-handoff.Rmd | 213 splitGraph-0.4.0/splitGraph/vignettes/faq-design-notes.Rmd |only splitGraph-0.4.0/splitGraph/vignettes/leakage-aware-workflow.Rmd | 311 splitGraph-0.4.0/splitGraph/vignettes/modeling-structure.Rmd | 259 splitGraph-0.4.0/splitGraph/vignettes/quick-start.Rmd |only 91 files changed, 10745 insertions(+), 6166 deletions(-)
Title: Calculate Pairwise Distances
Description: A common framework for calculating distance matrices.
Author: Nello Blaser [aut, cre]
Maintainer: Nello Blaser <nello.blaser@uib.no>
Diff between rdist versions 0.0.5 dated 2020-05-04 and 0.0.6 dated 2026-09-17
DESCRIPTION | 9 ++++----- MD5 | 18 +++++++++--------- NEWS.md | 5 ++++- R/RcppExports.R | 6 +++--- R/farthest_point_sampling.R | 4 ++-- R/rdist-package.r | 1 + README.md | 2 -- man/farthest_point_sampling.Rd | 4 ++-- man/rdist.Rd | 1 + src/RcppExports.cpp | 5 +++++ 10 files changed, 31 insertions(+), 24 deletions(-)
Title: Random Hazard Forests
Description: Random Hazard Forests (RHF) extend Random Survival
Forests (RSF) by directly estimating the hazard function and by
accommodating time-dependent covariates through counting-process
style inputs. The package fits tree ensembles for dynamic survival
prediction, returning hazard, cumulative hazard, integrated hazard,
and related performance summaries for training and test data. The
methods build on Random Survival Forests described by Ishwaran et
al. (2008) <doi:10.1214/08-AOAS169> and on nonparametric hazard
modeling with time-dependent covariates described by Lee et
al. (2021) <doi:10.1214/20-AOS2028>.
Author: Hemant Ishwaran [aut],
Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestRHF versions 2.0.3 dated 2026-09-01 and 2.1.0 dated 2026-09-17
DESCRIPTION | 8 - MD5 | 28 +++--- NEWS.md | 9 +- R/auct.rhf.R | 29 ++++++ R/predict.rhf.workhorse.R | 2 R/rhf.workhorse.R | 2 R/utilities_additional.R | 29 ++++-- src/entry.c | 2 src/global.h | 2 src/processEnsemble.c | 10 -- src/processEnsembleCOE.c | 188 ++++++++++++++++++++++++++++++--------------- src/rhfMain.c | 31 +++---- src/shared/stackIncoming.c | 30 +++---- src/stackOutput.c | 10 +- src/survivalTDC.c | 4 15 files changed, 245 insertions(+), 139 deletions(-)
More information about randomForestRHF at CRAN
Permanent link
Title: Causal Analysis for Macroeconomic Time Series (ECM-MARS, BSTS,
Bayesian GLM-AR(1))
Description: Implements three complementary pipelines for causal analysis on macroeconomic time series:
(1) Error-Correction Models with Multivariate Adaptive Regression Splines (ECM-MARS),
(2) Bayesian Structural Time Series (BSTS), and
(3) Bayesian GLM with AR(1) errors validated with Leave-Future-Out (LFO).
Heavy backends (Stan) are optional and never used in examples or tests.
Author: Jose Mauricio Gomez Julian [aut, cre]
Maintainer: Jose Mauricio Gomez Julian <isadore.nabi@pm.me>
Diff between EconCausal versions 1.0.2 dated 2025-10-08 and 1.0.4 dated 2026-09-17
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Title: Generic PK/PD Simulation Platform Campsis
Description: A generic, easy-to-use and intuitive
pharmacokinetic/pharmacodynamic (PK/PD) simulation platform based on
the R packages 'rxode2' and 'mrgsolve'. Campsis provides an
abstraction layer over the underlying processes of defining a PK/PD
model, assembling a custom dataset and running a simulation. The
package has a strong dependency on the R package 'campsismod', which
allows models to be read from and written to files, including through
a JSON-based interface, and to be adapted further on the fly in the R
environment. In addition, 'campsis' allows users to assemble datasets
in an intuitive manner, including via a JSON-based interface to import
Campsis datasets defined using formal JSON schemas distributed with
the package. Once the dataset is ready, the package prepares the
simulation, calls 'rxode2' or 'mrgsolve' (at the user's choice), and
returns the results for the given model, dataset and desired
simulation settings. The package itself is licensed under the GPL (>=
3); the JSON sc [...truncated...]
Author: Nicolas Luyckx [aut, cre]
Maintainer: Nicolas Luyckx <nicolas.luyckx@calvagone.com>
Diff between campsis versions 1.9.0 dated 2026-08-05 and 1.9.1 dated 2026-09-17
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campsis-1.9.1/campsis/man/dosing_only.Rd | 34 campsis-1.9.1/campsis/man/drop_others.Rd | 34 campsis-1.9.1/campsis/man/export_delegate.Rd | 58 - campsis-1.9.1/campsis/man/export_table_delegate.Rd | 60 - campsis-1.9.1/campsis/man/generate_iiv.Rd | 42 campsis-1.9.1/campsis/man/generate_iiv_.Rd | 38 campsis-1.9.1/campsis/man/get_available_time_units.Rd | 28 campsis-1.9.1/campsis/man/get_campsis_option.Rd | 38 campsis-1.9.1/campsis/man/get_campsis_options.Rd | 30 campsis-1.9.1/campsis/man/get_column.Rd | 40 campsis-1.9.1/campsis/man/get_compartment_mapping.Rd | 40 campsis-1.9.1/campsis/man/get_covariates.Rd | 60 - campsis-1.9.1/campsis/man/get_event_covariates.Rd | 60 - campsis-1.9.1/campsis/man/get_fixed_covariates.Rd | 60 - campsis-1.9.1/campsis/man/get_initial_conditions.Rd | 44 campsis-1.9.1/campsis/man/get_iovs.Rd | 52 campsis-1.9.1/campsis/man/get_occasions.Rd | 52 campsis-1.9.1/campsis/man/get_random_seed_value.Rd | 30 campsis-1.9.1/campsis/man/get_seed.Rd | 36 campsis-1.9.1/campsis/man/get_seed_for_dataset_export.Rd | 40 campsis-1.9.1/campsis/man/get_seed_for_iteration.Rd | 40 campsis-1.9.1/campsis/man/get_seed_for_parameters_sampling.Rd | 36 campsis-1.9.1/campsis/man/get_simulation_engine_type.Rd | 36 campsis-1.9.1/campsis/man/get_splitting_configuration.Rd | 40 campsis-1.9.1/campsis/man/get_time_varying_covariates.Rd | 60 - campsis-1.9.1/campsis/man/get_times.Rd | 90 - campsis-1.9.1/campsis/man/import_campsismod_to_namespace.Rd | 30 campsis-1.9.1/campsis/man/iov-class.Rd |only campsis-1.9.1/campsis/man/is_empty_bootstrap.Rd | 36 campsis-1.9.1/campsis/man/json_to_campsis_dataset.Rd | 40 campsis-1.9.1/campsis/man/json_to_campsis_settings.Rd | 40 campsis-1.9.1/campsis/man/left_join_iiv.Rd | 40 campsis-1.9.1/campsis/man/make_vpc_summary.Rd | 68 - campsis-1.9.1/campsis/man/obs_only.Rd | 34 campsis-1.9.1/campsis/man/on_ci.Rd | 30 campsis-1.9.1/campsis/man/on_cran.Rd | 34 campsis-1.9.1/campsis/man/open_json.Rd | 40 campsis-1.9.1/campsis/man/preprocess_arm_column.Rd | 40 campsis-1.9.1/campsis/man/preprocess_dest.Rd | 40 campsis-1.9.1/campsis/man/preprocess_dosing.Rd | 36 campsis-1.9.1/campsis/man/preprocess_events.Rd | 30 campsis-1.9.1/campsis/man/preprocess_ids.Rd | 36 campsis-1.9.1/campsis/man/preprocess_outfun.Rd | 36 campsis-1.9.1/campsis/man/preprocess_outvars.Rd | 40 campsis-1.9.1/campsis/man/preprocess_replicates.Rd | 40 campsis-1.9.1/campsis/man/preprocess_scenarios.Rd | 32 campsis-1.9.1/campsis/man/preprocess_settings.Rd | 40 campsis-1.9.1/campsis/man/preprocess_slices.Rd | 36 campsis-1.9.1/campsis/man/preprocess_tablefun.Rd | 36 campsis-1.9.1/campsis/man/preserve_column_levels.Rd |only campsis-1.9.1/campsis/man/process_arm_labels.Rd | 44 campsis-1.9.1/campsis/man/process_drop_others.Rd | 44 campsis-1.9.1/campsis/man/process_simulate_arguments.Rd | 56 campsis-1.9.1/campsis/man/remove_column_levels.Rd |only campsis-1.9.1/campsis/man/remove_initial_conditions.Rd | 36 campsis-1.9.1/campsis/man/reorder_columns.Rd | 40 campsis-1.9.1/campsis/man/repeat_schedule.Rd | 56 campsis-1.9.1/campsis/man/retrieve_parameter_value.Rd | 46 campsis-1.9.1/campsis/man/rxode_engine-class.Rd | 18 campsis-1.9.1/campsis/man/sample_covariates_list.Rd | 44 campsis-1.9.1/campsis/man/sample_distribution_as_tibble.Rd | 44 campsis-1.9.1/campsis/man/scatterPlot.Rd | 48 campsis-1.9.1/campsis/man/scatter_plot.Rd | 38 campsis-1.9.1/campsis/man/scatter_plot.std_campsis_tbl.Rd | 102 - campsis-1.9.1/campsis/man/scenario-class.Rd | 2 campsis-1.9.1/campsis/man/setLabel.Rd | 46 campsis-1.9.1/campsis/man/setSubjects.Rd | 46 campsis-1.9.1/campsis/man/set_label.Rd | 50 campsis-1.9.1/campsis/man/set_seed.Rd | 34 campsis-1.9.1/campsis/man/set_subjects.Rd | 50 campsis-1.9.1/campsis/man/setupPlanDefault.Rd | 50 campsis-1.9.1/campsis/man/setupPlanSequential.Rd | 36 campsis-1.9.1/campsis/man/setup_plan_default.Rd | 50 campsis-1.9.1/campsis/man/setup_plan_sequential.Rd | 28 campsis-1.9.1/campsis/man/shadedPlot.Rd | 70 - campsis-1.9.1/campsis/man/shaded_plot.Rd | 38 campsis-1.9.1/campsis/man/shaded_plot.std_campsis_tbl.Rd | 118 +- campsis-1.9.1/campsis/man/simulate.Rd | 296 ++--- campsis-1.9.1/campsis/man/simulate_delegate.Rd | 106 - campsis-1.9.1/campsis/man/simulate_delegate_core.Rd | 100 - campsis-1.9.1/campsis/man/simulate_scenarios.Rd | 106 - campsis-1.9.1/campsis/man/simulation_progress-class.Rd | 66 - campsis-1.9.1/campsis/man/solver_settings-class.Rd | 54 campsis-1.9.1/campsis/man/spaghettiPlot.Rd | 44 campsis-1.9.1/campsis/man/spaghetti_plot.Rd | 38 campsis-1.9.1/campsis/man/spaghetti_plot.std_campsis_tbl.Rd | 80 - campsis-1.9.1/campsis/man/standardise_time.Rd | 38 campsis-1.9.1/campsis/man/to_explicit_distribution.Rd | 56 campsis-1.9.1/campsis/man/undefined_distribution-class.Rd | 26 campsis-1.9.1/campsis/man/unite_columns.Rd | 48 campsis-1.9.1/campsis/man/unwrap_treatment.Rd | 84 - campsis-1.9.1/campsis/man/update_addl.Rd | 92 - campsis-1.9.1/campsis/man/update_amount.Rd | 92 - campsis-1.9.1/campsis/man/update_ii.Rd | 92 - campsis-1.9.1/campsis/man/update_repeat.Rd | 92 - campsis-1.9.1/campsis/man/vec_restore.campsis_tbl.Rd | 46 campsis-1.9.1/campsis/man/vpcPlot.Rd | 64 - campsis-1.9.1/campsis/man/vpc_plot.Rd | 38 campsis-1.9.1/campsis/man/vpc_plot.pi_campsis_tbl.Rd | 110 - campsis-1.9.1/campsis/man/vpc_plot.std_campsis_tbl.Rd | 142 +- campsis-1.9.1/campsis/tests/testthat/json_examples/scenarios_example1b.json |only campsis-1.9.1/campsis/tests/testthat/test-dataset.R | 24 campsis-1.9.1/campsis/tests/testthat/test-json_interface.R | 81 + campsis-1.9.1/campsis/tests/testthat/test-occasion.R | 6 campsis-1.9.1/campsis/tests/testthat/test-occasions.R | 4 campsis-1.9.1/campsis/tests/testthat/test-scenario.R | 7 campsis-1.9.1/campsis/tests/testthat/test-scenarios.R | 16 campsis-1.9.1/campsis/tests/testthat/test-show_method.R | 2 campsis-1.9.1/campsis/tests/testthat/test-simulate_iov.R | 31 campsis-1.9.1/campsis/tests/testthat/test-simulate_nocb_locf.R | 2 campsis-1.9.1/campsis/tests/testthat/test-simulate_scenarios.R | 26 campsis-1.9.1/campsis/tests/testthat/test-utils.R | 2 162 files changed, 4240 insertions(+), 3790 deletions(-)
Title: Unsupervised Clustering of Individualized Survival Curves
Description: Tools for clustering individualized survival curves using the
Partitioning Around Medoids (PAM) algorithm, with monotonic enforcement,
optional smoothing, weighted distances (L1/L2), automatic K selection via
silhouette width, prediction for new curves, basic stability checks, and
plotting helpers. The method is described in El Badisy (2026)
<doi:10.1093/bioadv/vbag218>.
Author: Imad El Badisy [aut, cre]
Maintainer: Imad El Badisy <elbadisyimad@gmail.com>
Diff between unsurv versions 0.7.0 dated 2026-08-31 and 0.7.2 dated 2026-09-17
DESCRIPTION | 9 ++++----- MD5 | 8 ++++---- NEWS.md | 14 ++++++++++++++ R/internals.R | 43 ++++++++++++++++++++++++++----------------- inst/doc/unsurv-intro.html | 4 ++-- 5 files changed, 50 insertions(+), 28 deletions(-)
Title: Plant Photobiology Related Functions and Data
Description: Provides functions for quantifying visible (VIS) and ultraviolet
(UV) radiation in relation to the photoreceptors Phytochromes,
Cryptochromes, and UVR8 which are present in plants. It also includes data
sets on the optical properties of plants. Part of the 'r4photobiology'
suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyPlants versions 0.6.1-1 dated 2025-10-04 and 0.6.2 dated 2026-09-17
DESCRIPTION | 20 MD5 | 95 ++- NAMESPACE | 16 NEWS.md | 21 R/D-water-CO2.R |only R/McCree-photosynthesis-mspct.R | 16 R/PQ_redox_state.R |only R/Pfr-Ptot.R | 150 ++++- R/photobiologyPlants.r | 2 R/plant-q-irrads.r | 105 ++-- R/rs-anatomy.R |only README.md | 4 build/partial.rdb |binary build/vignette.rds |binary data/Mattila.rda |only data/McCree.rda |binary inst/doc/r4p-introduction.html | 2 inst/doc/user-guide.R | 97 ++- inst/doc/user-guide.Rmd | 262 +++++++--- inst/doc/user-guide.html | 689 +++++++++++++++++--------- man/Betula_ermanii.mspct.Rd | 100 +-- man/CRYs.mspct.Rd | 94 +-- man/D_water.Rd |only man/ET_ref.Rd | 290 +++++------ man/McCree_photosynthesis.mspct.Rd | 89 +-- man/PHOTs.mspct.Rd | 80 +-- man/PHYs.mspct.Rd | 94 +-- man/PQ_redox_state.Rd |only man/PS1_PS2_k.spct.Rd |only man/Pfr_P_ratio.Rd | 86 +-- man/Pfr_P_ratio_mono.Rd | 64 +- man/Pfr_Ptot.Rd | 205 ++++--- man/Pfr_Ptot_R_FR.Rd | 90 +-- man/Phy_Sigma.Rd | 78 +-- man/Phy_Sigma_FR.Rd | 84 +-- man/Phy_Sigma_R.Rd | 84 +-- man/Phy_reaction_rates.Rd | 136 ++--- man/Solidago_altissima.mspct.Rd | 100 +-- man/UVR8s.mspct.Rd | 88 +-- man/ZTLs.mspct.Rd | 60 +- man/carotenoids.mspct.Rd | 84 +-- man/chlorophylls.mspct.Rd | 156 +++--- man/chlorophylls_fluorescence.mspct.Rd | 132 ++--- man/figures/README-unnamed-chunk-4-1.png |binary man/gs_c_from_gs_w.Rd |only man/molar_vol.Rd |only man/net_irradiance.Rd | 102 +-- man/photobiologyPlants-package.Rd | 117 ++-- man/photon-irradiances.Rd | 365 +++++++------- man/photon-ratios.Rd | 796 +++++++++++++++---------------- man/rs_from_size.Rd |only man/water_vp_sat.Rd | 454 ++++++++--------- tests/testthat/test_gs.R |only vignettes/user-guide.Rmd | 262 +++++++--- 54 files changed, 3224 insertions(+), 2545 deletions(-)
More information about photobiologyPlants at CRAN
Permanent link
Title: Cluster Extension for 'mlr3'
Description: Extends the 'mlr3' package with cluster analysis.
Author: Maximilian Muecke [aut, cre] ,
Damir Pulatov [aut],
Michel Lang [aut] ,
Marc Becker [ctb]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between mlr3cluster versions 0.5.0 dated 2026-08-21 and 0.6.0 dated 2026-09-17
DESCRIPTION | 24 +- MD5 | 214 +++++++++--------- NAMESPACE | 10 NEWS.md | 35 ++ R/LearnerClust.R | 2 R/LearnerClustAffinityPropagation.R | 29 +- R/LearnerClustAgnes.R | 13 - R/LearnerClustBICO.R | 1 R/LearnerClustBIRCH.R | 1 R/LearnerClustCLARA.R | 1 R/LearnerClustCMeans.R | 1 R/LearnerClustCobweb.R | 5 R/LearnerClustDBSCAN.R | 20 + R/LearnerClustDBSCANfpc.R | 10 R/LearnerClustDiana.R | 11 R/LearnerClustEM.R | 7 R/LearnerClustFanny.R | 1 R/LearnerClustFarthestFirst.R | 4 R/LearnerClustFeatureless.R | 5 R/LearnerClustFlexmix.R | 13 - R/LearnerClustGMeans.R | 5 R/LearnerClustGenie.R | 8 R/LearnerClustHDBSCAN.R | 9 R/LearnerClustHclust.R | 17 + R/LearnerClustKCCA.R | 23 - R/LearnerClustKKMeans.R | 10 R/LearnerClustKMeans.R | 1 R/LearnerClustKMeansRcpp.R | 3 R/LearnerClustKModes.R | 6 R/LearnerClustKProto.R | 3 R/LearnerClustMclust.R | 30 ++ R/LearnerClustMeanShift.R | 3 R/LearnerClustMiniBatchKMeans.R | 19 + R/LearnerClustMovMF.R | 1 R/LearnerClustOPTICS.R | 5 R/LearnerClustPAM.R | 3 R/LearnerClustProtoclust.R | 12 - R/LearnerClustSKMeans.R | 1 R/LearnerClustSOM.R | 31 ++ R/LearnerClustSTDBSCAN.R | 11 R/LearnerClustSimpleKMeans.R | 6 R/LearnerClustSpectral.R | 10 R/LearnerClustTclust.R | 16 + R/LearnerClustXMeans.R | 16 + R/MeasureClust.R | 10 R/MeasureClustSimple.R | 110 +++++---- R/PredictionClust.R | 28 +- R/PredictionDataClust.R | 67 +++-- R/TaskClust.R | 5 R/TaskGeneratorBlobs.R |only R/TaskGeneratorMoons.R |only R/as_prediction_clust.R | 22 - R/as_task_clust.R | 50 +++- R/cluster_stats.R | 4 R/default_fallback.R |only R/helper.R | 21 + R/measures.R | 2 R/zzz.R | 61 ++--- README.md | 12 - man/LearnerClust.Rd | 2 man/MeasureClust.Rd | 45 +++ man/PredictionClust.Rd | 10 man/TaskClust.Rd | 5 man/as_prediction_clust.Rd | 3 man/as_task_clust.Rd | 34 ++ man/figures/logo.png |only man/figures/logo.svg |only man/mlr3cluster-package.Rd | 2 man/mlr_learners_clust.MBatchKMeans.Rd | 5 man/mlr_learners_clust.SimpleKMeans.Rd | 1 man/mlr_learners_clust.agnes.Rd | 13 + man/mlr_learners_clust.ap.Rd | 3 man/mlr_learners_clust.cobweb.Rd | 2 man/mlr_learners_clust.dbscan.Rd | 2 man/mlr_learners_clust.diana.Rd | 13 + man/mlr_learners_clust.em.Rd | 2 man/mlr_learners_clust.featureless.Rd | 2 man/mlr_learners_clust.ff.Rd | 1 man/mlr_learners_clust.flexmix.Rd | 6 man/mlr_learners_clust.genie.Rd | 11 man/mlr_learners_clust.hclust.Rd | 20 + man/mlr_learners_clust.kcca.Rd | 8 man/mlr_learners_clust.kkmeans.Rd | 13 + man/mlr_learners_clust.kmodes.Rd | 11 man/mlr_learners_clust.mclust.Rd | 8 man/mlr_learners_clust.protoclust.Rd | 11 man/mlr_learners_clust.som.Rd | 25 +- man/mlr_learners_clust.specc.Rd | 13 + man/mlr_learners_clust.stdbscan.Rd | 2 man/mlr_learners_clust.tclust.Rd | 10 man/mlr_learners_clust.xmeans.Rd | 10 man/mlr_measures_clust.silhouette.Rd | 4 man/mlr_task_generators_blobs.Rd |only man/mlr_task_generators_moons.Rd |only tests/testthat/_snaps/PredictionClust.md | 8 tests/testthat/helper.R | 6 tests/testthat/setup.R | 19 + tests/testthat/teardown.R | 8 tests/testthat/test_LearnerClust.R | 20 + tests/testthat/test_MeasureClust.R | 2 tests/testthat/test_PredictionClust.R | 89 +++++++ tests/testthat/test_as_task_clust.R |only tests/testthat/test_default_fallback.R |only tests/testthat/test_mlr_learners_clust_ap.R | 21 + tests/testthat/test_mlr_learners_clust_cobweb.R | 4 tests/testthat/test_mlr_learners_clust_em.R | 4 tests/testthat/test_mlr_learners_clust_featureless.R | 20 + tests/testthat/test_mlr_learners_clust_ff.R | 3 tests/testthat/test_mlr_learners_clust_flexmix.R | 1 tests/testthat/test_mlr_learners_clust_simplekmeans.R | 3 tests/testthat/test_mlr_learners_clust_stdbscan.R | 5 tests/testthat/test_mlr_learners_clust_xmeans.R | 3 tests/testthat/test_mlr_task_generators.R |only 113 files changed, 1151 insertions(+), 410 deletions(-)
Title: Processing Time Series Data Using the Matching Pursuit Algorithm
Description: Provides tools for analysing and decomposing time series data using the Matching Pursuit (MP) algorithm, a greedy signal decomposition technique that represents complex signals as a linear combination of simpler functions (called atoms) selected from a redundant dictionary. Support for the Orthogonal Matching Pursuit (OMP) variant of the classical MP algorithm is also provided. For more details see Mallat and Zhang (1993) <doi:10.1109/78.258082>, Pati et al. (1993) <doi:10.1109/ACSSC.1993.342465>, Elad (2010) <doi:10.1007/978-1-4419-7011-4> and Różański (2024) <doi:10.1145/3674832>.
Author: Artur Gramacki [aut, cre] ,
Jaroslaw Gramacki [ctb] ,
Piotr T. Rożanski [ctb]
Maintainer: Artur Gramacki <a.gramacki@gmail.com>
Diff between MatchingPursuit versions 1.2.0 dated 2026-08-19 and 1.3.0 dated 2026-09-17
MatchingPursuit-1.2.0/MatchingPursuit/R/mp_omp_pipeline.R |only MatchingPursuit-1.2.0/MatchingPursuit/R/plot.edf.R |only MatchingPursuit-1.2.0/MatchingPursuit/R/plot.mp.R |only MatchingPursuit-1.2.0/MatchingPursuit/R/plot.wfdb.R |only MatchingPursuit-1.2.0/MatchingPursuit/R/topk_atoms.R |only MatchingPursuit-1.2.0/MatchingPursuit/inst/examples |only MatchingPursuit-1.2.0/MatchingPursuit/inst/extdata/00001_lr.db |only MatchingPursuit-1.2.0/MatchingPursuit/inst/extdata/00001_lr.xml |only MatchingPursuit-1.2.0/MatchingPursuit/inst/extdata/EEG_filter_resample_montage.bin |only MatchingPursuit-1.2.0/MatchingPursuit/inst/extdata/EEG_filter_resample_montage.csv |only MatchingPursuit-1.2.0/MatchingPursuit/inst/extdata/EEG_filter_resample_montage.xml |only MatchingPursuit-1.2.0/MatchingPursuit/inst/extdata/sample1.db |only MatchingPursuit-1.2.0/MatchingPursuit/inst/extdata/sample2.db |only MatchingPursuit-1.2.0/MatchingPursuit/inst/extdata/sample2.xml |only MatchingPursuit-1.2.0/MatchingPursuit/inst/extdata/sample3.db |only MatchingPursuit-1.2.0/MatchingPursuit/inst/extdata/sample3_EMPI.xml |only MatchingPursuit-1.2.0/MatchingPursuit/man/mp_omp_pipeline.Rd |only MatchingPursuit-1.2.0/MatchingPursuit/man/plot.edf.Rd |only MatchingPursuit-1.2.0/MatchingPursuit/man/plot.mp.Rd |only MatchingPursuit-1.2.0/MatchingPursuit/man/plot.wfdb.Rd |only MatchingPursuit-1.2.0/MatchingPursuit/man/topk_atoms.Rd |only MatchingPursuit-1.3.0/MatchingPursuit/DESCRIPTION | 31 MatchingPursuit-1.3.0/MatchingPursuit/MD5 | 122 MatchingPursuit-1.3.0/MatchingPursuit/NAMESPACE | 22 MatchingPursuit-1.3.0/MatchingPursuit/NEWS.md | 45 MatchingPursuit-1.3.0/MatchingPursuit/R/as_sig.R | 2 MatchingPursuit-1.3.0/MatchingPursuit/R/clear_cache.R | 2 MatchingPursuit-1.3.0/MatchingPursuit/R/edf-methods.R |only MatchingPursuit-1.3.0/MatchingPursuit/R/empi_execute.R | 33 MatchingPursuit-1.3.0/MatchingPursuit/R/empi_locate.R | 8 MatchingPursuit-1.3.0/MatchingPursuit/R/gabor_projection_fft.R | 132 MatchingPursuit-1.3.0/MatchingPursuit/R/generate_xml_dict.R | 62 MatchingPursuit-1.3.0/MatchingPursuit/R/mp-methods.R |only MatchingPursuit-1.3.0/MatchingPursuit/R/mp_core.R | 296 - MatchingPursuit-1.3.0/MatchingPursuit/R/mp_omp_execute.R | 359 - MatchingPursuit-1.3.0/MatchingPursuit/R/omp_core.R | 457 +- MatchingPursuit-1.3.0/MatchingPursuit/R/omp_reference.R |only MatchingPursuit-1.3.0/MatchingPursuit/R/package.R | 110 MatchingPursuit-1.3.0/MatchingPursuit/R/read_atom_params.R | 5 MatchingPursuit-1.3.0/MatchingPursuit/R/read_gabor_dict.R | 221 - MatchingPursuit-1.3.0/MatchingPursuit/R/sig-methods.R |only MatchingPursuit-1.3.0/MatchingPursuit/R/tf_map.R | 128 MatchingPursuit-1.3.0/MatchingPursuit/R/topk-methods.R |only MatchingPursuit-1.3.0/MatchingPursuit/R/topk_gabor_atoms.R |only MatchingPursuit-1.3.0/MatchingPursuit/R/wfdb-methods.R |only MatchingPursuit-1.3.0/MatchingPursuit/README.md | 322 + MatchingPursuit-1.3.0/MatchingPursuit/inst/doc/MatchingPursuit.R | 358 + MatchingPursuit-1.3.0/MatchingPursuit/inst/doc/MatchingPursuit.Rmd | 1001 +++-- MatchingPursuit-1.3.0/MatchingPursuit/inst/doc/MatchingPursuit.html | 1844 +++++----- MatchingPursuit-1.3.0/MatchingPursuit/inst/extdata/00001_lr.rds |only MatchingPursuit-1.3.0/MatchingPursuit/inst/extdata/EEG_filter_resample_montage.db |binary MatchingPursuit-1.3.0/MatchingPursuit/inst/extdata/eeg_empi_out.rds |only MatchingPursuit-1.3.0/MatchingPursuit/inst/extdata/empi.db |only MatchingPursuit-1.3.0/MatchingPursuit/inst/extdata/one_block.xml | 4 MatchingPursuit-1.3.0/MatchingPursuit/inst/extdata/sample1.rds |only MatchingPursuit-1.3.0/MatchingPursuit/inst/extdata/sample1.xml | 84 MatchingPursuit-1.3.0/MatchingPursuit/inst/extdata/sample1_empi_class.rds |only MatchingPursuit-1.3.0/MatchingPursuit/inst/extdata/sample2.rds |only MatchingPursuit-1.3.0/MatchingPursuit/inst/extdata/sample3.csv | 2 MatchingPursuit-1.3.0/MatchingPursuit/inst/extdata/sample3.xml | 43 MatchingPursuit-1.3.0/MatchingPursuit/man/MatchingPursuit.Rd | 114 MatchingPursuit-1.3.0/MatchingPursuit/man/as_sig.Rd | 2 MatchingPursuit-1.3.0/MatchingPursuit/man/clear_cache.Rd | 2 MatchingPursuit-1.3.0/MatchingPursuit/man/edf-methods.Rd |only MatchingPursuit-1.3.0/MatchingPursuit/man/empi_execute.Rd | 33 MatchingPursuit-1.3.0/MatchingPursuit/man/empi_locate.Rd | 8 MatchingPursuit-1.3.0/MatchingPursuit/man/figures |only MatchingPursuit-1.3.0/MatchingPursuit/man/gabor_projection_fft.Rd | 85 MatchingPursuit-1.3.0/MatchingPursuit/man/generate_xml_dict.Rd | 51 MatchingPursuit-1.3.0/MatchingPursuit/man/mp-methods.Rd |only MatchingPursuit-1.3.0/MatchingPursuit/man/mp_core.Rd | 87 MatchingPursuit-1.3.0/MatchingPursuit/man/mp_omp_execute.Rd | 221 - MatchingPursuit-1.3.0/MatchingPursuit/man/omp_core.Rd | 176 MatchingPursuit-1.3.0/MatchingPursuit/man/omp_reference.Rd |only MatchingPursuit-1.3.0/MatchingPursuit/man/read_atom_params.Rd | 5 MatchingPursuit-1.3.0/MatchingPursuit/man/read_gabor_dict.Rd | 189 - MatchingPursuit-1.3.0/MatchingPursuit/man/sig-methods.Rd |only MatchingPursuit-1.3.0/MatchingPursuit/man/tf_map.Rd | 44 MatchingPursuit-1.3.0/MatchingPursuit/man/topk-methods.Rd |only MatchingPursuit-1.3.0/MatchingPursuit/man/topk_gabor_atoms.Rd |only MatchingPursuit-1.3.0/MatchingPursuit/man/wfdb-methods.Rd |only MatchingPursuit-1.3.0/MatchingPursuit/vignettes/MatchingPursuit.Rmd | 1001 +++-- 82 files changed, 4383 insertions(+), 3328 deletions(-)
More information about MatchingPursuit at CRAN
Permanent link
Title: ISO 3166-1 Country Codes
Description: ISO 3166-1 country codes and ISO 4217 currency codes provided
by the International Organization for Standardization.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between isocountry versions 0.7.0 dated 2026-08-21 and 0.8.0 dated 2026-09-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 14 +++++++++----- data/isocountry.rda |binary 4 files changed, 15 insertions(+), 11 deletions(-)
Title: Connect to an OMOP Common Data Model
Description: Provides tools for working with observational health data in the
Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax.
Common data model database table references are stored in a single compound object along with metadata.
Author: Ger Inberg [aut, cre] ,
Adam Black [aut] ,
Artem Gorbachev [aut],
Edward Burn [aut],
Marti Catala Sabate [aut],
Ioanna Nika [aut]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between CDMConnector versions 2.7.0 dated 2026-08-27 and 2.8.0 dated 2026-09-17
DESCRIPTION | 8 +- MD5 | 44 ++++++----- NEWS.md | 5 + R/cdm.R | 37 ++++------ R/cdmSubset.R | 5 - R/copyCdmTo.R | 1 R/dbSource.R | 12 ++- R/generateCohortSet.R | 4 - R/sysdata.rda |binary R/utils.R | 28 +++++-- inst/csv/OMOP_CDMv5.5_Field_Level.csv |only inst/csv/OMOP_CDMv5.5_Table_Level.csv |only inst/doc/a01_getting-started.html | 70 +++++++++---------- inst/doc/a06_using_cdm_attributes.html | 4 - man/cdmFromCon.Rd | 10 +- man/version.Rd | 2 tests/testthat/test-01-db-DBI.R | 34 ++++++++- tests/testthat/test-02-db-cdm.R | 2 tests/testthat/test-04-db-generateConceptCohortSet.R | 4 - tests/testthat/test-06-db-compute.R | 30 ++++---- tests/testthat/test-14-db-cohortTransformations.R | 3 tests/testthat/test-cdm-extra.R | 33 +------- tests/testthat/test-db-utils.R | 3 tests/testthat/test-utils-extra.R | 34 +++++++++ 24 files changed, 222 insertions(+), 151 deletions(-)
Title: (Bayesian) Additive Voronoi Tessellations
Description: Implements the Bayesian Additive Voronoi Tessellation
model for non-parametric regression, classification and machine learning as
introduced in Stone and Gosling (2025) <doi:10.1080/10618600.2024.2414104>.
This package provides a flexible alternative to BART (Bayesian Additive
Regression Trees) using Voronoi tessellations instead of trees. Users can
fit Bayesian regression and probit classification models, estimate the
associated posterior distributions and make predictions. It is particularly
useful for spatial data analysis, machine learning, complex function
approximation and Bayesian modelling where the underlying structure is
unknown.
Author: Adam Stone [aut] ,
John Paul Gosling [aut, cre] ,
Andrew Iskauskas [aut] ,
Leo Thomson [aut]
Maintainer: John Paul Gosling <john-paul.gosling@durham.ac.uk>
Diff between AddiVortes versions 0.6.9 dated 2026-08-03 and 1.0.1 dated 2026-09-17
AddiVortes-0.6.9/AddiVortes/man/cellIndices.Rd |only AddiVortes-1.0.1/AddiVortes/DESCRIPTION | 31 AddiVortes-1.0.1/AddiVortes/MD5 | 80 AddiVortes-1.0.1/AddiVortes/NAMESPACE | 61 AddiVortes-1.0.1/AddiVortes/NEWS.md | 79 AddiVortes-1.0.1/AddiVortes/R/0_CellIndices.R | 3 AddiVortes-1.0.1/AddiVortes/R/0_CovariateStructure.R | 101 AddiVortes-1.0.1/AddiVortes/R/0_ResponseType.R |only AddiVortes-1.0.1/AddiVortes/R/AddiVortes-package.R | 29 AddiVortes-1.0.1/AddiVortes/R/AddiVortes.R | 318 + AddiVortes-1.0.1/AddiVortes/R/AddiVortesFit.R | 530 +- AddiVortes-1.0.1/AddiVortes/README.md | 28 AddiVortes-1.0.1/AddiVortes/build/vignette.rds |binary AddiVortes-1.0.1/AddiVortes/inst/doc/categorical.R | 56 AddiVortes-1.0.1/AddiVortes/inst/doc/categorical.Rmd | 152 AddiVortes-1.0.1/AddiVortes/inst/doc/categorical.html | 532 +- AddiVortes-1.0.1/AddiVortes/inst/doc/classification.R |only AddiVortes-1.0.1/AddiVortes/inst/doc/classification.Rmd |only AddiVortes-1.0.1/AddiVortes/inst/doc/classification.html |only AddiVortes-1.0.1/AddiVortes/inst/doc/introduction.R | 2 AddiVortes-1.0.1/AddiVortes/inst/doc/introduction.Rmd | 2 AddiVortes-1.0.1/AddiVortes/inst/doc/introduction.html | 12 AddiVortes-1.0.1/AddiVortes/inst/doc/prediction.R | 6 AddiVortes-1.0.1/AddiVortes/inst/doc/prediction.Rmd | 8 AddiVortes-1.0.1/AddiVortes/inst/doc/prediction.html | 56 AddiVortes-1.0.1/AddiVortes/inst/doc/spherical.html | 12 AddiVortes-1.0.1/AddiVortes/man/AddiVortes-package.Rd | 30 AddiVortes-1.0.1/AddiVortes/man/AddiVortes.Rd | 121 AddiVortes-1.0.1/AddiVortes/man/new_AddiVortes.Rd | 25 AddiVortes-1.0.1/AddiVortes/man/plot.AddiVortes.Rd | 5 AddiVortes-1.0.1/AddiVortes/man/predict.AddiVortes.Rd | 50 AddiVortes-1.0.1/AddiVortes/man/traceplots.AddiVortes.Rd | 2 AddiVortes-1.0.1/AddiVortes/man/traceplots.Rd | 18 AddiVortes-1.0.1/AddiVortes/src/addi_vortes_code.cpp | 2106 ++++++---- AddiVortes-1.0.1/AddiVortes/src/init.c | 7 AddiVortes-1.0.1/AddiVortes/tests/testthat/test-AddiVortes-methods.R | 89 AddiVortes-1.0.1/AddiVortes/tests/testthat/test-CRAN-smoke.R | 24 AddiVortes-1.0.1/AddiVortes/tests/testthat/test-CategoricalCovariates.R | 64 AddiVortes-1.0.1/AddiVortes/tests/testthat/test-Friedman.R |only AddiVortes-1.0.1/AddiVortes/tests/testthat/test-classification.R |only AddiVortes-1.0.1/AddiVortes/tests/testthat/test-spherical.R | 4 AddiVortes-1.0.1/AddiVortes/vignettes/categorical.Rmd | 152 AddiVortes-1.0.1/AddiVortes/vignettes/classification.Rmd |only AddiVortes-1.0.1/AddiVortes/vignettes/introduction.Rmd | 2 AddiVortes-1.0.1/AddiVortes/vignettes/prediction.Rmd | 8 45 files changed, 3326 insertions(+), 1479 deletions(-)
Title: Inferential Methods for Multimodal and Other Networks
Description: A set of tools for testing networks.
It includes functions for univariate and multivariate conditional uniform graph
and quadratic assignment procedure testing, and network regression.
The package is a complement to
'Multimodal Political Networks' (2021, ISBN:9781108985000),
and includes various datasets used in the book.
Built on the 'manynet' package, all functions operate with matrices,
edge lists, and 'igraph', 'network', and 'tidygraph' objects,
and on one-mode and two-mode (bipartite) networks.
Author: James Hollway [cre, aut, ctb] ,
Henrique Sposito [ctb] ,
Jael Tan [ctb] ,
Bernhard Bieri [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between migraph versions 1.7.0 dated 2026-08-30 and 1.7.2 dated 2026-09-17
DESCRIPTION | 10 MD5 | 28 NEWS.md | 31 R/model_diffusion.R | 16 R/zzz.R | 25 inst/tutorials/tutorial0/tutorial0.Rmd | 858 +++++++++-- inst/tutorials/tutorial0/tutorial0.html | 2383 +++++++++++++++++++++++++------- man/mpn_bristol.Rd | 4 man/mpn_cow_combined.Rd | 2 man/mpn_elite_usa.Rd | 4 man/mpn_senate.Rd | 4 man/mpn_senate112.Rd | 12 tests/testthat/Rplots.pdf |binary tests/testthat/test-model_distrib.R | 1 tests/testthat/test-zzz.R | 26 15 files changed, 2652 insertions(+), 752 deletions(-)
Title: 'C++' Implementations of Functional Enrichment Analysis
Description: Fast implementations of functional enrichment analysis methods using 'C++' via 'Rcpp'.
Currently provides Over-Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA),
Weighted Enrichment Analysis for ORA and GSEA, Network-based Set Enrichment Analysis (NSEA),
multi-layer network-based enrichment, and multi-omics integration workflows. Additional
features include early fusion at the feature level, late fusion at the pathway level,
multi-omics contribution tracing, topology-aware explanation helpers, Bayesian term
selection, and extremely fast Random Walk with Restart (RWR) using 'RcppEigen'. The
enrichment methods build on GSEA by Subramanian et al. (2005)
<doi:10.1073/pnas.0506580102>, the multilevel strategy derived from 'fgsea'
by Korotkevich et al. (2021) <doi:10.1101/060012>, and network-based
enrichment ideas described by Glaab et al. (2012)
<doi:10.1093/bioinformatics/bts389>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between enrichit versions 0.2.1 dated 2026-08-04 and 0.2.4 dated 2026-09-17
DESCRIPTION | 8 MD5 | 52 +- NAMESPACE | 43 +- NEWS.md | 304 ++++++++------- R/00-AllClasses.R | 336 ++++++++--------- R/AllGenerics.R | 60 +-- R/RcppExports.R | 76 ++- R/accessor.R | 408 ++++++++++----------- R/gsea.R | 872 +++++++++++++++++++++++---------------------- R/gsfilter.R | 92 ++-- R/nsea.R | 793 +++++++++++++++++++++++++++++++--------- R/ora.R | 248 ++++++------ R/ora_gson.R | 468 ++++++++++++------------ R/print.R | 364 +++++++++--------- R/setReadable.R | 306 +++++++-------- R/utilities.R | 13 build/partial.rdb |binary man/gsea.Rd | 7 man/gsea_gson.Rd | 8 man/nsea.Rd | 24 + man/nsea_gson.Rd | 30 + man/prepare_network.Rd | 5 src/RcppExports.cpp | 15 src/gsea_scores.cpp | 94 ++++ tests/testthat/test-gsea.R | 89 ++++ tests/testthat/test-nsea.R | 67 +++ tests/testthat/test-ora.R | 80 ++-- 27 files changed, 2846 insertions(+), 2016 deletions(-)
Title: Survival Regression with Smoothed Error Distribution
Description: Contains, as a main contribution, a function to fit a regression model with possibly right, left or interval
censored observations and with the error distribution expressed as a mixture of G-splines. Core part
of the computation is done in compiled 'C++' written using the 'Scythe' Statistical Library Version 0.3.
The methods implemented in the package have been published in Komárek, Lesaffe and Hilton (2005, J. of Comp. and Graph. Stat.) <doi:10.1198/106186005X63734> and Lesaffre, Komárek and Declerck (2005, Stat. Methods in Med. Res.) <doi:10.1191/0962280205sm417oa>.
Author: Arnost Komarek [aut, cre] ,
Kevin M. Quinn [ctb, cph] ,
Andrew D. Martin [ctb, cph] ,
Daniel B. Pemstein [ctb, cph] ,
Berwin A. Turlach [ctb]
Maintainer: Arnost Komarek <arnost.komarek@matfyz.cuni.cz>
Diff between smoothSurv versions 2.6 dated 2023-12-13 and 2.7 dated 2026-09-17
DESCRIPTION | 25 ++++++++--------- MD5 | 58 ++++++++++++++++++++--------------------- NEWS | 4 ++ man/MP.pseudoinv.Rd | 2 - man/a2c.Rd | 2 - man/c2a.Rd | 2 - man/confint.smoothSurvReg.Rd | 2 - man/derivative.cc3.Rd | 2 - man/derivative.expAD.Rd | 2 - man/dextreme.Rd | 2 - man/dstlogis.Rd | 2 - man/estimTdiff.Rd | 2 - man/eval.Gspline.Rd | 2 - man/fdensity.smoothSurvReg.Rd | 4 ++ man/find.c.Rd | 2 - man/give.c.Rd | 2 - man/hazard.smoothSurvReg.Rd | 4 ++ man/minPenalty.Rd | 2 - man/piece.Rd | 2 - man/plot.smoothSurvReg.Rd | 2 - man/print.estimTdiff.Rd | 2 - man/print.smoothSurvReg.Rd | 2 - man/residuals.smoothSurvReg.Rd | 2 - man/smoothSurvReg.Rd | 2 - man/smoothSurvReg.control.Rd | 2 - man/smoothSurvReg.fit.Rd | 2 - man/smoothSurvReg.object.Rd | 2 - man/std.data.Rd | 2 - man/survfit.smoothSurvReg.Rd | 2 - src/Scythe_Matrix.h | 1 30 files changed, 76 insertions(+), 68 deletions(-)
Title: OIDC Authentication and OAuth Authorization for 'shiny'
Applications
Description: Provides a simple, configurable framework for 'OpenID Connect'
(OIDC) authentication and 'OAuth 2.0' authorization in 'shiny' applications
using 'S7' classes. Defines providers, clients, and tokens, as well
as various supporting functions and a 'shiny' module. Features include
cross-site request forgery (CSRF) protection, state encryption,
'Proof Key for Code Exchange' (PKCE) handling, validation of OIDC identity
tokens (nonces, signatures, claims), automatic user info retrieval for OIDC
and supported 'OAuth' providers, asynchronous flows,
and hooks for audit logging.
Author: Luka Koning [aut, cre, cph]
Maintainer: Luka Koning <koningluka@gmail.com>
Diff between shinyOAuth versions 0.5.0 dated 2026-05-23 and 0.6.0 dated 2026-09-17
shinyOAuth-0.5.0/shinyOAuth/man/state_payload_decrypt_validate.Rd |only shinyOAuth-0.5.0/shinyOAuth/man/state_store_get_remove.Rd |only shinyOAuth-0.6.0/shinyOAuth/DESCRIPTION | 27 shinyOAuth-0.6.0/shinyOAuth/MD5 | 810 shinyOAuth-0.6.0/shinyOAuth/NAMESPACE | 24 shinyOAuth-0.6.0/shinyOAuth/NEWS.md | 240 shinyOAuth-0.6.0/shinyOAuth/R/aaa-api-compatibility.R |only shinyOAuth-0.6.0/shinyOAuth/R/check_oauth21.R |only shinyOAuth-0.6.0/shinyOAuth/R/classes__OAuthClient.R | 5660 +++--- shinyOAuth-0.6.0/shinyOAuth/R/classes__OAuthConnection.R |only shinyOAuth-0.6.0/shinyOAuth/R/classes__OAuthProvider.R | 1433 + shinyOAuth-0.6.0/shinyOAuth/R/classes__OAuthToken.R | 559 shinyOAuth-0.6.0/shinyOAuth/R/connection_credential_lifecycle.R |only shinyOAuth-0.6.0/shinyOAuth/R/connection_owner.R |only shinyOAuth-0.6.0/shinyOAuth/R/connection_store.R |only shinyOAuth-0.6.0/shinyOAuth/R/custom_cache.R | 418 shinyOAuth-0.6.0/shinyOAuth/R/errors__constructors.R | 1702 + shinyOAuth-0.6.0/shinyOAuth/R/errors__events.R | 621 shinyOAuth-0.6.0/shinyOAuth/R/errors__trace.R | 236 shinyOAuth-0.6.0/shinyOAuth/R/methods__client_bearer_req.R | 1871 +- shinyOAuth-0.6.0/shinyOAuth/R/methods__connection.R |only shinyOAuth-0.6.0/shinyOAuth/R/methods__login.R | 6526 +++---- shinyOAuth-0.6.0/shinyOAuth/R/methods__print.R | 836 shinyOAuth-0.6.0/shinyOAuth/R/methods__token.R | 3432 ++- shinyOAuth-0.6.0/shinyOAuth/R/methods__userinfo.R | 2526 +- shinyOAuth-0.6.0/shinyOAuth/R/mtls_registration.R | 1734 + shinyOAuth-0.6.0/shinyOAuth/R/oauth_connections.R |only shinyOAuth-0.6.0/shinyOAuth/R/oauth_connections_server.R |only shinyOAuth-0.6.0/shinyOAuth/R/oauth_connections_ui.R |only shinyOAuth-0.6.0/shinyOAuth/R/oauth_form_post_ui.R | 2299 +- shinyOAuth-0.6.0/shinyOAuth/R/oauth_module_server.R | 9020 ++++++---- shinyOAuth-0.6.0/shinyOAuth/R/oauth_ui.R |only shinyOAuth-0.6.0/shinyOAuth/R/prepare_authorization_request.R |only shinyOAuth-0.6.0/shinyOAuth/R/providers.R | 1360 - shinyOAuth-0.6.0/shinyOAuth/R/providers__apple.R |only shinyOAuth-0.6.0/shinyOAuth/R/providers__oidc_discovery.R | 3033 +-- shinyOAuth-0.6.0/shinyOAuth/R/shinyOAuth-package.R | 48 shinyOAuth-0.6.0/shinyOAuth/R/smart_client.R |only shinyOAuth-0.6.0/shinyOAuth/R/smart_context.R |only shinyOAuth-0.6.0/shinyOAuth/R/smart_discovery.R |only shinyOAuth-0.6.0/shinyOAuth/R/smart_launch.R |only shinyOAuth-0.6.0/shinyOAuth/R/smart_scopes.R |only shinyOAuth-0.6.0/shinyOAuth/R/softeners__options.R | 543 shinyOAuth-0.6.0/shinyOAuth/R/telemetry.R | 3764 ++-- shinyOAuth-0.6.0/shinyOAuth/R/use_shinyOAuth.R | 398 shinyOAuth-0.6.0/shinyOAuth/R/utils__access_token.R |only shinyOAuth-0.6.0/shinyOAuth/R/utils__audit_digest.R | 229 shinyOAuth-0.6.0/shinyOAuth/R/utils__authorization_context.R |only shinyOAuth-0.6.0/shinyOAuth/R/utils__base64url.R | 142 shinyOAuth-0.6.0/shinyOAuth/R/utils__callback_registry.R |only shinyOAuth-0.6.0/shinyOAuth/R/utils__client_resources.R |only shinyOAuth-0.6.0/shinyOAuth/R/utils__connection_credentials.R |only shinyOAuth-0.6.0/shinyOAuth/R/utils__connection_router.R |only shinyOAuth-0.6.0/shinyOAuth/R/utils__crypt_primitives.R | 170 shinyOAuth-0.6.0/shinyOAuth/R/utils__crypt_state.R | 1270 - 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shinyOAuth-0.6.0/shinyOAuth/R/utils__shiny_request_uri.R | 772 shinyOAuth-0.6.0/shinyOAuth/R/utils__shiny_timers.R |only shinyOAuth-0.6.0/shinyOAuth/R/utils__state.R | 2537 +- shinyOAuth-0.6.0/shinyOAuth/R/utils__tls.R |only shinyOAuth-0.6.0/shinyOAuth/R/utils__url_helpers.R | 2022 +- shinyOAuth-0.6.0/shinyOAuth/R/utils__validators.R | 635 shinyOAuth-0.6.0/shinyOAuth/R/zzz.R | 52 shinyOAuth-0.6.0/shinyOAuth/README.md | 331 shinyOAuth-0.6.0/shinyOAuth/build/vignette.rds |binary shinyOAuth-0.6.0/shinyOAuth/inst/doc/advanced-security.R |only shinyOAuth-0.6.0/shinyOAuth/inst/doc/advanced-security.Rmd |only shinyOAuth-0.6.0/shinyOAuth/inst/doc/advanced-security.html |only shinyOAuth-0.6.0/shinyOAuth/inst/doc/audit-logging.R |only shinyOAuth-0.6.0/shinyOAuth/inst/doc/audit-logging.Rmd | 992 - shinyOAuth-0.6.0/shinyOAuth/inst/doc/audit-logging.html | 2344 +- shinyOAuth-0.6.0/shinyOAuth/inst/doc/authentication-flow.R |only shinyOAuth-0.6.0/shinyOAuth/inst/doc/authentication-flow.Rmd | 1129 - shinyOAuth-0.6.0/shinyOAuth/inst/doc/authentication-flow.html | 2032 +- shinyOAuth-0.6.0/shinyOAuth/inst/doc/example-spotify.R | 1138 - 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shinyOAuth-0.6.0/shinyOAuth/tests/testthat/test_state_key.R | 56 shinyOAuth-0.6.0/shinyOAuth/tests/testthat/test_state_store_single_use.R | 146 shinyOAuth-0.6.0/shinyOAuth/vignettes/advanced-security.Rmd |only shinyOAuth-0.6.0/shinyOAuth/vignettes/audit-logging.Rmd | 992 - shinyOAuth-0.6.0/shinyOAuth/vignettes/authentication-flow.Rmd | 1129 - shinyOAuth-0.6.0/shinyOAuth/vignettes/example-spotify.Rmd | 1228 - shinyOAuth-0.6.0/shinyOAuth/vignettes/multiple-authorizations.Rmd |only shinyOAuth-0.6.0/shinyOAuth/vignettes/opentelemetry.Rmd | 960 - shinyOAuth-0.6.0/shinyOAuth/vignettes/package-options.Rmd |only shinyOAuth-0.6.0/shinyOAuth/vignettes/smart-on-fhir.Rmd |only shinyOAuth-0.6.0/shinyOAuth/vignettes/usage.Rmd | 1241 - 532 files changed, 119714 insertions(+), 102254 deletions(-)
Title: Non-Ordered Vectors
Description: Functionality for manipulating values of associative
maps. The package is a dependency for mvp-type
packages that use the STL map class: it traps
plausible idiom that is ill-defined (implementation-specific) and
returns an informative error, rather than returning a possibly
incorrect result. To cite the package in publications please use
Hankin (2022) <doi:10.48550/ARXIV.2210.03856>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between disordR versions 0.9-8-6 dated 2026-03-12 and 0.9-8-7 dated 2026-09-17
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 1 + R/disordR.R | 2 ++ build/vignette.rds |binary inst/doc/disindex.html | 12 ++++++------ inst/doc/disordR.html | 34 +++++++++++++++++----------------- man/misc.Rd | 41 ++++++++++++++++++++++++++++++++++------- man/show.Rd | 4 ++++ 9 files changed, 76 insertions(+), 42 deletions(-)
Title: Tiny 'shiny' Server - Lightweight Multi-App 'shiny' Proxy
Description: A lightweight, 'WebSocket'-enabled proxy server for hosting multiple
'shiny' applications with automatic health monitoring, session management,
and resource cleanup. Provides a simple entry point to run the server using
a JSON configuration file.
Author: Lars Bernhardsson [aut, cre]
Maintainer: Lars Bernhardsson <cran.sherry228@passinbox.com>
Diff between tinyshinyserver versions 0.1.0 dated 2026-01-06 and 0.2.0 dated 2026-09-17
DESCRIPTION | 13 MD5 | 68 +-- NAMESPACE | 22 - NEWS.md | 48 ++ R/config-format.R | 70 ++- R/config.R | 65 ++- R/connection_manager.R | 96 ++++- R/example-config.R | 28 - R/handlers.R | 392 ++++++++++---------- R/management_api.R | 6 R/process_manager.R | 201 ++++++---- R/start_tss.R | 44 -- R/tinyshinyserver-package.R | 8 R/tss_main.R | 15 R/utils.R | 23 - R/validation.R | 12 README.md | 593 +++++++------------------------ inst/examples/config.json | 5 inst/examples/inventory/server.R | 12 inst/examples/inventory/ui.R | 2 inst/templates/management_page.html | 52 +- man/config-format.Rd | 70 ++- man/example-config.Rd | 28 - man/start_tss.Rd | 45 -- man/tinyshinyserver-package.Rd | 13 tests/browser |only tests/testthat/helper-async.R |only tests/testthat/test-async-proxy.R |only tests/testthat/test-config.R | 70 +++ tests/testthat/test-management-api.R | 15 tests/testthat/test-management-csrf.R |only tests/testthat/test-p2-regressions.R |only tests/testthat/test-process-manager.R | 37 + tests/testthat/test-review-regressions.R |only tests/testthat/test-routing.R | 89 ++-- tests/testthat/test-utils.R | 9 tests/testthat/test-validation.R | 8 37 files changed, 1148 insertions(+), 1011 deletions(-)
More information about tinyshinyserver at CRAN
Permanent link
Title: Translate CSS Selectors to XPath Expressions
Description: Translates a CSS selector into an equivalent XPath
expression. This allows us to use CSS selectors when working with
the 'XML' and 'xml2' packages, which can only evaluate XPath
expressions. Also provided are convenience functions for querying
XML and HTML documents with CSS selectors. This package was
originally a port of the Python package 'cssselect'
(<https://cssselect.readthedocs.io/>).
Author: Simon Potter [aut, trl, cre],
Simon Sapin [aut],
Ian Bicking [aut]
Maintainer: Simon Potter <simon@sjp.co.nz>
Diff between selectr versions 0.6-0 dated 2026-06-23 and 0.7-0 dated 2026-09-17
selectr-0.6-0/selectr/.Rinstignore |only selectr-0.6-0/selectr/tests/test-all.R |only selectr-0.7-0/selectr/DESCRIPTION | 19 selectr-0.7-0/selectr/LICENCE | 2 selectr-0.7-0/selectr/MD5 | 85 selectr-0.7-0/selectr/NAMESPACE | 24 selectr-0.7-0/selectr/R/errors.R |only selectr-0.7-0/selectr/R/main.R | 439 +- selectr-0.7-0/selectr/R/ncname.R |only selectr-0.7-0/selectr/R/parser.R | 1365 +++++-- selectr-0.7-0/selectr/R/xpath.R | 1800 +++++++--- selectr-0.7-0/selectr/README.md | 96 selectr-0.7-0/selectr/inst/NEWS.Rd | 361 ++ selectr-0.7-0/selectr/man/css_to_xpath.Rd | 187 - selectr-0.7-0/selectr/man/querySelectorAll.Rd | 253 - selectr-0.7-0/selectr/man/selectors.Rd |only selectr-0.7-0/selectr/tests/testthat.R |only selectr-0.7-0/selectr/tests/testthat/helper-fixtures.R |only selectr-0.7-0/selectr/tests/testthat/test-adjacent-sibling.R | 100 selectr-0.7-0/selectr/tests/testthat/test-error-hierarchy.R |only selectr-0.7-0/selectr/tests/testthat/test-has.R | 266 - selectr-0.7-0/selectr/tests/testthat/test-html-translator.R |only selectr-0.7-0/selectr/tests/testthat/test-main.R | 180 - selectr-0.7-0/selectr/tests/testthat/test-method-registration.R | 14 selectr-0.7-0/selectr/tests/testthat/test-namespaces.R | 412 +- selectr-0.7-0/selectr/tests/testthat/test-nth-child-of.R | 12 selectr-0.7-0/selectr/tests/testthat/test-nth-child.R | 460 +- selectr-0.7-0/selectr/tests/testthat/test-parse-errors.R | 492 ++ selectr-0.7-0/selectr/tests/testthat/test-parser.R | 332 - selectr-0.7-0/selectr/tests/testthat/test-pseudo.R | 655 ++- selectr-0.7-0/selectr/tests/testthat/test-querySelector-XML.R | 213 - selectr-0.7-0/selectr/tests/testthat/test-querySelector-chaining.R |only selectr-0.7-0/selectr/tests/testthat/test-querySelector-default.R | 37 selectr-0.7-0/selectr/tests/testthat/test-querySelector-xml2.R | 188 - selectr-0.7-0/selectr/tests/testthat/test-quoting.R | 90 selectr-0.7-0/selectr/tests/testthat/test-scope.R | 145 selectr-0.7-0/selectr/tests/testthat/test-select-XML.R | 227 - selectr-0.7-0/selectr/tests/testthat/test-select-xml2.R | 528 +- selectr-0.7-0/selectr/tests/testthat/test-selectors-reference.R |only selectr-0.7-0/selectr/tests/testthat/test-series.R | 295 + selectr-0.7-0/selectr/tests/testthat/test-shakespeare-XML.R | 301 - selectr-0.7-0/selectr/tests/testthat/test-shakespeare-xml2.R | 303 - selectr-0.7-0/selectr/tests/testthat/test-specificity.R | 169 selectr-0.7-0/selectr/tests/testthat/test-test-hygiene.R |only selectr-0.7-0/selectr/tests/testthat/test-tokenizer.R | 323 + selectr-0.7-0/selectr/tests/testthat/test-translation.R | 687 ++- selectr-0.7-0/selectr/tests/testthat/test-where.R | 158 selectr-0.7-0/selectr/tests/testthat/test-xmllang-XML.R | 44 selectr-0.7-0/selectr/tests/testthat/test-xmllang-xml2.R | 44 selectr-0.7-0/selectr/tests/testthat/test-xpath.R | 484 ++ 50 files changed, 8183 insertions(+), 3607 deletions(-)
Title: Time Series Regression
Description: Time series regression. The dyn class interfaces ts,
irts(), zoo() and zooreg() time series classes to lm(), glm(),
loess(), quantreg::rq(), MASS::rlm(), MCMCpack::MCMCregress(),
quantreg::rq(), randomForest::randomForest() and other regression
functions allowing those functions to be used with time series
including specifications that may contain lags, diffs and
missing values.
Author: G. Grothendieck [aut],
M. Leeds [cre]
Maintainer: M. Leeds <markleeds2@gmail.com>
Diff between dyn versions 0.2-9.6 dated 2018-03-19 and 0.2-11.0 dated 2026-09-17
DESCRIPTION | 21 +++++++++++++++------ MD5 | 14 +++++++------- NEWS | 20 ++++++++++++++++++++ R/anova.dyn.R | 51 ++++++++++++++++++++++++++++----------------------- R/model.frame.dyn.R | 3 ++- R/update.dyn.R | 17 ++++++++++++++--- demo/dyn-na.R | 2 +- tests/vcovHAC.R | 4 ++-- 8 files changed, 89 insertions(+), 43 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-07-02 1.9
2026-05-22 1.8
2026-01-17 1.7
2025-08-19 1.6
2025-06-13 1.5
2025-05-18 1.4
2025-02-02 1.3
2023-07-15 1.2
2023-07-11 1.1
2023-06-29 1.0
2023-04-24 0.8
2023-04-21 0.7
2023-04-19 0.6
2023-01-17 0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-06-16 10.1.9
2026-05-29 10.1.8
2026-05-12 10.1.7
2026-04-26 10.1.6
2026-03-12 10.1.5
2026-02-23 10.1.4
2026-01-21 10.1.1.1
2026-01-08 10.1.1
2025-12-06 10.0.0
2025-03-21 9.3.21
2025-03-09 9.3.20
2025-01-07 9.3.18
2024-12-04 9.3.16
2024-09-29 9.3.12
2024-09-17 9.3.11
2024-07-09 9.3.7.2
2024-05-13 9.3.5.1
2024-05-01 9.3.5
2024-03-26 9.3.3.1
2024-03-16 9.3.3
2024-01-25 9.1.22
2023-10-31 9.1.17.1
2023-10-16 9.1.17
2023-09-27 9.1.16
2023-09-06 9.1.15
2023-08-07 9.1.12
2023-07-05 9.1.11
2023-05-04 9.1.9
2023-03-24 9.1.8
2023-03-19 9.1.7
2023-02-20 9.1.6
2023-01-27 9.1.4
2023-01-15 9.1.3
2022-12-20 9.1.2
2022-11-09 8.5.20
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-08-26 0.7.4
2022-08-25 0.7.1
2021-05-21 0.7.0
2020-06-30 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-02-19 2.1.0
2024-07-08 2.0.9
2024-06-12 2.0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-06-25 0.9.28
2026-06-18 0.9.27
2026-04-21 0.9.26
2026-02-24 0.9.25
2026-01-14 0.9.24
2025-05-19 0.9.23
2025-03-11 0.9.21
2025-02-15 0.9.20
2024-07-09 0.9.18
2024-05-01 0.9.17
2024-03-28 0.9.16
2024-03-18 0.9.15
2023-06-29 0.9.14
2023-05-08 0.9.13
2023-04-20 0.9.12
2023-01-27 0.9.11
2023-01-12 0.9.10
2023-01-06 0.9.9
2022-12-23 0.9.8
2022-11-12 0.9.6
2022-05-14 0.9.4
2022-05-04 0.9.3
2022-04-29 0.9.2
2022-04-28 0.9.1
2022-04-25 0.9