Title: A Traceability Focused Grammar of Clinical Data Summary
Description: A traceability focused tool created to simplify the data manipulation necessary to create clinical summaries.
Author: Eli Miller [aut] ,
Mike Stackhouse [aut, cre] ,
Ashley Tarasiewicz [aut],
Nathan Kosiba [ctb] ,
Sadchla Mascary [ctb],
Andrew Bates [ctb],
Shiyu Chen [ctb],
Oleksii Mikryukov [ctb],
Atorus Research LLC [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between Tplyr versions 1.3.2 dated 2026-02-26 and 1.3.3 dated 2026-06-30
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/sort.R | 13 +++++++++---- inst/doc/Tplyr.html | 12 ++++++------ tests/testthat/test-sort.R | 41 +++++++++++++++++++++++++++++++++++++++++ 6 files changed, 69 insertions(+), 18 deletions(-)
Title: Tiny Logging Interface to 'rspdlite' Wrapping 'spdlite' C++20
Logging
Description: Just how 'spdl' provides a nice and consistent interface to 'spdlog' (via
'RcppSpdlog'), this package does so for 'spdlite', the lightweight header-only C++-20
logging library that provides a lighter version of 'spdlog'. This package is essentially
a thin shim around it for a more compact interface from both R and C++.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tl versions 0.0.1 dated 2026-06-22 and 0.0.2 dated 2026-06-30
ChangeLog | 30 ++++++++++++++++++++++++++++++ DESCRIPTION | 14 ++++++++------ MD5 | 17 +++++++++-------- NAMESPACE | 1 + R/tl.R | 26 ++++++++++++++++++++++++-- README.md | 17 ++++++++++++++--- build/partial.rdb |binary inst/NEWS.Rd |only inst/include/tl.h | 23 +++++++++++++++++++++++ man/trace.Rd | 10 ++++++++++ 10 files changed, 119 insertions(+), 19 deletions(-)
Title: Stochastic Tree Ensembles (XBART and BART) for Supervised
Learning and Causal Inference
Description: Flexible stochastic tree ensemble software.
Robust implementations of Bayesian Additive Regression Trees (BART)
(Chipman, George, McCulloch (2010) <doi:10.1214/09-AOAS285>)
for supervised learning and Bayesian Causal Forests (BCF)
(Hahn, Murray, Carvalho (2020) <doi:10.1214/19-BA1195>)
for causal inference. Enables model serialization and parallel sampling
and provides a low-level interface for custom stochastic forest samplers.
Includes the grow-from-root algorithm for accelerated forest sampling
(He and Hahn (2021) <doi:10.1080/01621459.2021.1942012>),
a log-linear leaf model for forest-based heteroskedasticity (Murray (2020) <doi:10.1080/01621459.2020.1813587>),
and the cloglog BART model of Alam and Linero (2025) <doi:10.48550/arXiv.2502.00606> for ordinal outcomes.
Author: Drew Herren [aut, cre] ,
Richard Hahn [aut],
Jared Murray [aut],
Carlos Carvalho [aut],
Jingyu He [aut],
Pedro Lima [ctb],
Entejar Alam [ctb],
stochtree contributors [cph],
Eigen contributors [cph] ,
xgboost contributors [cph] ,
treelite contributors [...truncated...]
Maintainer: Drew Herren <drewherrenopensource@gmail.com>
Diff between stochtree versions 0.4.4 dated 2026-06-08 and 0.4.5 dated 2026-06-30
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ R/bart.R | 2 +- configure | 18 +++++++++--------- configure.ac | 2 +- tests/testthat/test-bart.R | 30 ++++++++++++++++++++++++++++++ 7 files changed, 57 insertions(+), 20 deletions(-)
Title: Dimension Reduction, Regression and Discrimination for
Chemometrics
Description: Data exploration and prediction with focus on high dimensional data and chemometrics.
The package was initially designed about partial least squares regression and discrimination models and variants, in particular locally weighted PLS models (LWPLS). Then, it has been expanded to many other methods for analyzing high dimensional data.
The name 'rchemo' comes from the fact that the package is orientated to chemometrics, but most of the provided methods are fully generic to other domains.
Functions such as transform(), predict(), coef() and summary() are available. Tuning the predictive models is facilitated by generic functions gridscore() (validation dataset) and gridcv() (cross-validation). Faster versions are also available for models based on latent variables (LVs) (gridscorelv() and gridcvlv()) and ridge regularization (gridscorelb() and gridcvlb()).
Author: Marion Brandolini-Bunlon [aut, cre],
Benoit Jaillais [aut],
Jean-Michel Roger [aut],
Matthieu Lesnoff [aut]
Maintainer: Marion Brandolini-Bunlon <marion.brandolini-bunlon@inrae.fr>
Diff between rchemo versions 0.1-3 dated 2024-09-11 and 0.1-4 dated 2026-06-30
DESCRIPTION | 7 +++-- MD5 | 52 ++++++++++++++++++++++++++++------------ NAMESPACE | 9 ++++++ R/consensuspca.R |only R/consensuspcanipals.R |only R/consensuspcanipals2.R |only R/covsel.R | 29 ++++++++++++++-------- R/covsellmr.R |only R/covselprobda.R |only R/covselrda.R |only R/lda.R | 6 ++++ R/mbplsr.R | 39 +++++++++++++++++++++++++----- R/nipals.R |only R/onAttach.r | 2 - R/qda.R | 5 +++ R/scores.r | 3 +- README.md | 4 +-- build |only data/Zhang2023.rda |only inst/NEWS.md | 23 ++++++++++++----- inst/doc |only inst/rchemo_functions_github.md | 6 ++++ man/Zhang2023.Rd |only man/consensuspca.Rd |only man/covsel.Rd | 9 ++++-- man/covselda.Rd |only man/covsellmr.Rd |only man/mbplsr_mbplsda_allsteps.Rd | 8 +++--- man/nipals.Rd |only man/pca.Rd | 27 +++++++++++++------- man/soplsr_soplsda_allsteps.Rd | 8 +++--- vignettes |only 32 files changed, 172 insertions(+), 65 deletions(-)
Title: Latent Space Item Response Model
Description: Analysis of dichotomous, ordinal, and continuous response data using latent space item response model ('LSIRM'). Provides 1PL and 2PL 'LSIRM' for binary response data as described in Jeon et al. (2021) <doi:10.1007/s11336-021-09762-5>, graded response models ('GRM') for ordinal data (De Carolis et al., 2025, <doi:10.1080/00273171.2025.2605678>), and extensions for continuous response data. Supports Bayesian model selection with spike-and-slab priors, adaptive MCMC algorithms, and methods for handling missing data under missing at random ('MAR') and missing completely at random ('MCAR') assumptions. Provides various diagnostic plots to inspect the latent space and summaries of estimated parameters.
Author: Dongyoung Go [aut],
Gwanghee Kim [aut, cre],
Jina Park [aut],
Ickhoon Jin [ctb],
Minjeong Jeon [ctb]
Maintainer: Gwanghee Kim <musagh08@yonsei.ac.kr>
Diff between lsirm12pl versions 2.0.2 dated 2026-05-29 and 2.0.3 dated 2026-06-30
lsirm12pl-2.0.2/lsirm12pl/NEWS.md |only lsirm12pl-2.0.3/lsirm12pl/DESCRIPTION | 8 lsirm12pl-2.0.3/lsirm12pl/MD5 | 95 +++--- lsirm12pl-2.0.3/lsirm12pl/R/diagnostic.lsirm.R | 4 lsirm12pl-2.0.3/lsirm12pl/R/gof.lsirm.R | 22 - lsirm12pl-2.0.3/lsirm12pl/R/lsirm.R | 148 +++++----- lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_fixed_gamma.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_fixed_gamma_mar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_fixed_gamma_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_mar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_mar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_mcar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_fixed_gamma.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_fixed_gamma_mar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_fixed_gamma_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_mar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_mcar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_o.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_normal_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_o.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm1pl_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_fixed_gamma.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_fixed_gamma_mar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_fixed_gamma_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_mar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_mar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_mcar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_fixed_gamma.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_fixed_gamma_mar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_fixed_gamma_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_mar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_mcar.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_mcar_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_o.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_normal_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_o.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirm2pl_ss.R | 2 lsirm12pl-2.0.3/lsirm12pl/R/lsirmgrm.R | 6 lsirm12pl-2.0.3/lsirm12pl/R/lsirmgrm2pl.R | 6 lsirm12pl-2.0.3/lsirm12pl/R/onepl.R | 6 lsirm12pl-2.0.3/lsirm12pl/R/plot.lsirm.R | 25 - lsirm12pl-2.0.3/lsirm12pl/R/twopl.R | 6 lsirm12pl-2.0.3/lsirm12pl/man/onepl.Rd | 2 lsirm12pl-2.0.3/lsirm12pl/man/twopl.Rd | 2 lsirm12pl-2.0.3/lsirm12pl/src/lsm.cpp | 11 lsirm12pl-2.0.3/lsirm12pl/src/utility_cpp.cpp | 7 49 files changed, 218 insertions(+), 198 deletions(-)
Title: Latent Variable Models
Description: A general implementation of Structural Equation Models
with latent variables (MLE, 2SLS, and composite likelihood
estimators) with both continuous, censored, and ordinal
outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>).
Mixture latent variable models and non-linear latent variable models
(Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>).
The package also provides methods for graph exploration (d-separation,
back-door criterion), simulation of general non-linear latent variable
models, and estimation of influence functions for a broad range of
statistical models.
Author: Klaus K. Holst [aut, cre],
Benedikt Sommer [ctb],
Brice Ozenne [ctb],
Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between lava versions 1.9.1 dated 2026-05-14 and 1.9.2 dated 2026-06-30
DESCRIPTION | 6 MD5 | 153 +++++----- NAMESPACE | 7 NEWS.md | 20 + R/IC.R | 6 R/Inverse.R | 3 R/addhook.R | 2 R/assoc.R | 2 R/contr.R | 4 R/correlation.R | 35 +- R/diagtest.R | 45 +-- R/effects.R | 5 R/estimate.array.R | 1 R/estimate.default.R | 433 +++++++++++------------------ R/estimate.formula.R | 12 R/estimate.glm.R | 7 R/estimate.list.R | 6 R/estimate_calculus.R | 108 +++++-- R/eventTime.R | 5 R/fix.R | 3 R/glmest.R | 302 +++++++++++++------- R/gof.R | 5 R/iid.R | 2 R/information.R | 6 R/interactive.R | 2 R/multipletesting.R | 28 - R/procformula.R | 13 R/regression.R | 11 R/score.R | 8 R/sim.default.R | 72 ++++ R/spaghetti.R | 2 R/stack.R |binary R/summary.estimate.R |only R/twostage.R | 13 R/utils.R | 2 R/var_ic.R | 8 R/zib.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/correlation.R | 11 inst/doc/correlation.Rmd | 13 inst/doc/correlation.html | 132 +++++--- inst/doc/influencefunction.R | 24 - inst/doc/influencefunction.Rmd | 26 - inst/doc/influencefunction.html | 384 +++++++++++++------------ inst/doc/nonlinear.R | 2 inst/doc/nonlinear.Rmd | 2 inst/doc/nonlinear.html | 200 +++++-------- man/IC.default.Rd | 9 man/Inverse.Rd | 5 man/c.estimate.Rd |only man/c.summary.estimate.Rd |only man/constrain-set.Rd | 17 - man/covariance.Rd | 2 man/estimate.array.Rd | 3 man/estimate.default.Rd | 186 ++++++------ man/estimate.formula.Rd |only man/estimate.glm.Rd |only man/estimate.list.Rd |only man/gof.Rd | 5 man/iid.Rd | 4 man/information.Rd |only man/merge.estimate.Rd |only man/plotConf.Rd | 2 man/predict_glm.Rd |only man/regression-set.Rd | 14 man/rmvar.Rd | 4 man/score.Rd |only man/sim.default.Rd | 15 + man/stack.estimate.Rd | 4 man/summary.estimate.Rd |only man/var_ic.Rd |only tests/testthat/test-estimate-deprecation.R |only tests/testthat/test-estimate-id.R |only tests/testthat/test-estimate_default.R | 86 ++--- tests/testthat/test-influence.R | 19 - tests/testthat/test-merge-estimate.R | 43 ++ tests/testthat/test-model.R | 59 +++ tests/testthat/test-predict_glm.R |only tests/testthat/test-procformula.R |only tests/testthat/test-score-glm.R |only tests/testthat/test-simdef.R | 105 ++++++- tests/testthat/test-summary-estimate.R |only tests/testthat/test-summary-requires-IC.R |only vignettes/correlation.Rmd | 13 vignettes/influencefunction.Rmd | 26 - vignettes/nonlinear.Rmd | 2 87 files changed, 1611 insertions(+), 1145 deletions(-)
Title: Bayesian Exposure-Response Analysis Tools
Description: Suite of tools that facilitate
exposure-response analysis using Bayesian methods. The package
provides a streamlined workflow for fitting types of models that are
commonly used in exposure-response analysis - linear and Emax for continuous
endpoints, logistic linear and logistic Emax for binary endpoints, as well
as performing simulation and visualization. Learn more about the workflow
at <https://genentech.github.io/BayesERbook/>.
Author: Kenta Yoshida [aut, cre] ,
Francois Mercier [aut] ,
Danielle Navarro [aut] ,
Genentech, Inc. [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between BayesERtools versions 0.2.6 dated 2026-06-13 and 0.2.7 dated 2026-06-30
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 8 ++++++++ R/dev_ermod_lin.R | 18 +++++++++++++----- R/plot_ermod_exp_cov_sel.R | 2 +- README.md | 24 +++++++++++------------- man/figures/README-ermod_bin-1.png |binary man/figures/README-ermod_bin_cov_sel-1.png |binary man/figures/README-plot_coveff-1.png |binary tests/testthat/test-dev_ermod_lin.R | 11 +++++++++-- 10 files changed, 54 insertions(+), 33 deletions(-)
Title: Calculate Confidence Intervals
Description: This calculates a variety of different CIs for proportions
and difference of proportions that are commonly used in the
pharmaceutical industry including Wald, Wilson, Clopper-Pearson,
Agresti-Coull and Jeffreys for proportions. And Miettinen-Nurminen
(1985) <doi:10.1002/sim.4780040211>, Wald, Haldane, and Mee
<https://www.lexjansen.com/wuss/2016/127_Final_Paper_PDF.pdf> for
difference in proportions.
Author: Christina Fillmore [aut, cre] ,
GlaxoSmithKline Research & Development Limited [cph, fnd],
Mike Sprys [aut],
Dan Lythgoe [aut]
Maintainer: Christina Fillmore <christina.e.fillmore@gsk.com>
Diff between cicalc versions 0.2.1 dated 2026-05-08 and 0.2.2 dated 2026-06-30
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/prop_ci.R | 2 +- R/prop_ci_common_risk.R | 10 ++++++---- R/prop_ci_mn.R | 2 +- tests/testthat/_snaps/prop_ci_common_risk.md | 12 ++++++------ 7 files changed, 29 insertions(+), 21 deletions(-)
Title: Compute Soil Carbon Fluxes for the National Ecological
Observatory Network Sites
Description: Acquires and synthesizes soil carbon fluxes at sites located in the National Ecological Observatory Network (NEON). Provides flux estimates and associated uncertainty as well as key environmental measurements (soil water, temperature, CO2 concentration) that are used to compute soil fluxes.
Author: John Zobitz [aut, cre] ,
Edward Ayres [aut] ,
Katie O'Rourke [ctb] ,
Zoey Werbin [ctb],
Lajntxiag Lee [ctb],
Ridwan Abdi [ctb] ,
Dijone Mehmeti [ctb] ,
Ly Xiong [ctb]
Maintainer: John Zobitz <zobitz@augsburg.edu>
Diff between neonSoilFlux versions 3.0.0 dated 2025-11-22 and 4.0.0 dated 2026-06-30
neonSoilFlux-3.0.0/neonSoilFlux/R/NEONSoils-package.R |only neonSoilFlux-4.0.0/neonSoilFlux/DESCRIPTION | 8 neonSoilFlux-4.0.0/neonSoilFlux/MD5 | 61 +- neonSoilFlux-4.0.0/neonSoilFlux/NEWS.md | 5 neonSoilFlux-4.0.0/neonSoilFlux/R/acquire_neon_data.R | 63 ++ neonSoilFlux-4.0.0/neonSoilFlux/R/check_qf_flags.R | 22 neonSoilFlux-4.0.0/neonSoilFlux/R/compute_monthly_mean.R | 19 neonSoilFlux-4.0.0/neonSoilFlux/R/compute_neon_flux.R | 22 neonSoilFlux-4.0.0/neonSoilFlux/R/correct_env_data.R | 10 neonSoilFlux-4.0.0/neonSoilFlux/R/get_neon_api_token.R |only neonSoilFlux-4.0.0/neonSoilFlux/R/neonSoilFlux-package.R |only neonSoilFlux-4.0.0/neonSoilFlux/R/neon_api_token.R |only neonSoilFlux-4.0.0/neonSoilFlux/R/reprocess_vswc.R | 16 neonSoilFlux-4.0.0/neonSoilFlux/R/sjer_flux_2022_06.R | 6 neonSoilFlux-4.0.0/neonSoilFlux/R/swc_correct.R | 11 neonSoilFlux-4.0.0/neonSoilFlux/README.md | 53 +- neonSoilFlux-4.0.0/neonSoilFlux/build/vignette.rds |binary neonSoilFlux-4.0.0/neonSoilFlux/data/sjer_env_data_2022_06.rda |binary neonSoilFlux-4.0.0/neonSoilFlux/data/sjer_flux_2022_06.rda |binary neonSoilFlux-4.0.0/neonSoilFlux/data/sjer_megapit_data_2022_06.rda |binary neonSoilFlux-4.0.0/neonSoilFlux/inst/CITATION |only neonSoilFlux-4.0.0/neonSoilFlux/inst/doc/using-neonSoilFlux.R | 15 neonSoilFlux-4.0.0/neonSoilFlux/inst/doc/using-neonSoilFlux.Rmd | 93 ++- neonSoilFlux-4.0.0/neonSoilFlux/inst/doc/using-neonSoilFlux.html | 238 +++++----- neonSoilFlux-4.0.0/neonSoilFlux/man/acquire_neon_data.Rd | 23 neonSoilFlux-4.0.0/neonSoilFlux/man/compute_monthly_mean.Rd | 11 neonSoilFlux-4.0.0/neonSoilFlux/man/compute_neon_flux.Rd | 22 neonSoilFlux-4.0.0/neonSoilFlux/man/correct_env_data.Rd | 10 neonSoilFlux-4.0.0/neonSoilFlux/man/get_neon_api_token.Rd |only neonSoilFlux-4.0.0/neonSoilFlux/man/neonSoilFlux-package.Rd | 2 neonSoilFlux-4.0.0/neonSoilFlux/man/neon_api_token.Rd |only neonSoilFlux-4.0.0/neonSoilFlux/man/reprocess_vswc.Rd | 12 neonSoilFlux-4.0.0/neonSoilFlux/man/sjer_flux_2022_06.Rd | 6 neonSoilFlux-4.0.0/neonSoilFlux/man/swc_correct.Rd | 11 neonSoilFlux-4.0.0/neonSoilFlux/vignettes/using-neonSoilFlux.Rmd | 93 ++- 35 files changed, 572 insertions(+), 260 deletions(-)
Title: Solving Linear Inverse Models
Description: Functions that (1) find the minimum/maximum of a linear or quadratic function:
min or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(a_i*x_i)
subject to equality constraints Ex=f and/or inequality constraints Gx>=h,
(2) sample an underdetermined- or overdetermined system Ex=f subject to Gx>=h, and if applicable Ax~=b,
(3) solve a linear system Ax=B for the unknown x. It includes banded and tridiagonal linear systems.
Author: Karline Soetaert [aut, cre],
Karel Van den Meersche [aut],
Dick van Oevelen [aut],
Charles L. Lawson [ctb] ,
Richard J. Hanson [ctb] ,
Jack Dongarra [ctb] ,
Cleve Moler [ctb]
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between limSolve versions 2.0.2 dated 2026-06-03 and 2.0.3 dated 2026-06-30
DESCRIPTION | 6 MD5 | 28 +-- R/lsei.R | 48 +++-- inst/CITATION | 1 inst/doc/limSolve.R | 2 inst/doc/limSolve.Rmd | 4 inst/doc/limSolve.html | 94 ++++------ man/E_coli.Rd | 3 man/limSolve.rd | 1 man/lsei.Rd | 417 +++++++++++++++++++++++---------------------- man/xsample.Rd | 1 src/colrow.f | 3 src/inverse.f | 406 +++++++++++++++++++++++--------------------- src/solve.f | 446 ++++--------------------------------------------- vignettes/limSolve.Rmd | 4 15 files changed, 564 insertions(+), 900 deletions(-)
Title: Latent Binary Bayesian Neural Networks Using 'torch'
Description: Latent binary Bayesian neural networks (LBBNNs) are implemented using
'torch', an R interface to the LibTorch backend. Supports mean-field variational
inference as well as flexible variational posteriors using normalizing flows.
The standard LBBNN implementation follows Hubin and Storvik (2024) <doi:10.3390/math12060788>,
using the local reparametrization trick as in Skaaret-Lund et al. (2024)
<https://openreview.net/pdf?id=d6kqUKzG3V>. Input-skip connections are also supported,
as described in Høyheim et al. (2025) <doi:10.48550/arXiv.2503.10496>.
Author: Lars Skaaret-Lund [aut, cre],
Aliaksandr Hubin [aut],
Eirik Hoeyheim [aut]
Maintainer: Lars Skaaret-Lund <lars.skaaret-lund@nmbu.no>
Diff between LBBNN versions 0.1.5 dated 2026-04-23 and 0.1.6 dated 2026-06-30
LBBNN-0.1.5/LBBNN/inst/doc/LBBNN_tutorial.R |only LBBNN-0.1.5/LBBNN/inst/doc/LBBNN_tutorial.Rmd |only LBBNN-0.1.5/LBBNN/inst/doc/LBBNN_tutorial.html |only LBBNN-0.1.5/LBBNN/tests/testthat/test_lbbnn_predictions.R |only LBBNN-0.1.5/LBBNN/vignettes/LBBNN_tutorial.Rmd |only LBBNN-0.1.6/LBBNN/DESCRIPTION | 6 LBBNN-0.1.6/LBBNN/MD5 | 86 +++- LBBNN-0.1.6/LBBNN/NAMESPACE | 1 LBBNN-0.1.6/LBBNN/NEWS.md | 12 LBBNN-0.1.6/LBBNN/R/LBBNN_Model.R | 48 +- LBBNN-0.1.6/LBBNN/R/Layers.R | 150 +++++++- LBBNN-0.1.6/LBBNN/R/Train_validate.R | 175 ++++++---- LBBNN-0.1.6/LBBNN/R/local_explanations.R | 25 - LBBNN-0.1.6/LBBNN/R/overwrite_functions.R | 160 +++++---- LBBNN-0.1.6/LBBNN/R/plotting_graphs.R | 37 +- LBBNN-0.1.6/LBBNN/R/utils_torch.R | 52 ++ LBBNN-0.1.6/LBBNN/README.md | 144 ++++---- LBBNN-0.1.6/LBBNN/build/vignette.rds |binary LBBNN-0.1.6/LBBNN/inst/doc/convolutional_architecture.R |only LBBNN-0.1.6/LBBNN/inst/doc/convolutional_architecture.Rmd |only LBBNN-0.1.6/LBBNN/inst/doc/convolutional_architecture.html |only LBBNN-0.1.6/LBBNN/inst/doc/getting_started.R |only LBBNN-0.1.6/LBBNN/inst/doc/getting_started.Rmd |only LBBNN-0.1.6/LBBNN/inst/doc/getting_started.html |only LBBNN-0.1.6/LBBNN/inst/doc/small_dataset_classification.R |only LBBNN-0.1.6/LBBNN/inst/doc/small_dataset_classification.Rmd |only LBBNN-0.1.6/LBBNN/inst/doc/small_dataset_classification.html |only LBBNN-0.1.6/LBBNN/inst/doc/variable_selection_linear_data.R |only LBBNN-0.1.6/LBBNN/inst/doc/variable_selection_linear_data.Rmd |only LBBNN-0.1.6/LBBNN/inst/doc/variable_selection_linear_data.html |only LBBNN-0.1.6/LBBNN/inst/doc/variable_selection_non_linear_data.R |only LBBNN-0.1.6/LBBNN/inst/doc/variable_selection_non_linear_data.Rmd |only LBBNN-0.1.6/LBBNN/inst/doc/variable_selection_non_linear_data.html |only LBBNN-0.1.6/LBBNN/man/density_initialization.Rd | 6 LBBNN-0.1.6/LBBNN/man/figures/README-unnamed-chunk-6-1.png |binary LBBNN-0.1.6/LBBNN/man/figures/README-unnamed-chunk-8-1.png |binary LBBNN-0.1.6/LBBNN/man/get_local_explanations_gradient.Rd | 5 LBBNN-0.1.6/LBBNN/man/init_weight_mean.Rd |only LBBNN-0.1.6/LBBNN/man/lbbnn_conv2d.Rd | 21 - LBBNN-0.1.6/LBBNN/man/lbbnn_linear.Rd | 21 - LBBNN-0.1.6/LBBNN/man/lbbnn_net.Rd | 20 - LBBNN-0.1.6/LBBNN/man/plot_local_explanations_gradient.Rd | 5 LBBNN-0.1.6/LBBNN/man/predict.lbbnn_net.Rd | 4 LBBNN-0.1.6/LBBNN/man/resolve_device.Rd |only LBBNN-0.1.6/LBBNN/man/train_lbbnn.Rd | 15 LBBNN-0.1.6/LBBNN/man/validate_lbbnn.Rd | 5 LBBNN-0.1.6/LBBNN/tests/testthat/test_active_path_computation.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_alpha_validity.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_binary_classification.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_conv_layer.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_forward_pass_MPM.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_multi_output_regression.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_multiclass_classification.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_predict_behavior.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_smoke_training.R | 4 LBBNN-0.1.6/LBBNN/tests/testthat/test_validate_behavior.R |only LBBNN-0.1.6/LBBNN/tests/testthat/test_windows_batch_shape.R | 12 LBBNN-0.1.6/LBBNN/vignettes/convolutional_architecture.Rmd |only LBBNN-0.1.6/LBBNN/vignettes/getting_started.Rmd |only LBBNN-0.1.6/LBBNN/vignettes/small_dataset_classification.Rmd |only LBBNN-0.1.6/LBBNN/vignettes/variable_selection_linear_data.Rmd |only LBBNN-0.1.6/LBBNN/vignettes/variable_selection_non_linear_data.Rmd |only 62 files changed, 697 insertions(+), 317 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) (fast) simulation of random fields, b) inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Flexible covariance models for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. Se [...truncated...]
Author: Moreno Bevilacqua [aut, cre, cph],
Victor Morales-Onate [ctb],
Francisco Cuevas-Pacheco [ctb],
Christian Caamano-Carrillo [ctb]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 2.2.4 dated 2026-06-15 and 2.2.5 dated 2026-06-30
GeoModels-2.2.4/GeoModels/man/NuisParam.rd |only GeoModels-2.2.5/GeoModels/DESCRIPTION | 8 GeoModels-2.2.5/GeoModels/MD5 | 164 ++-- GeoModels-2.2.5/GeoModels/NAMESPACE | 3 GeoModels-2.2.5/GeoModels/R/GeoFit.r | 2 GeoModels-2.2.5/GeoModels/R/GeoFit2.R | 2 GeoModels-2.2.5/GeoModels/R/GeoNeighIndex.R | 208 +++++ GeoModels-2.2.5/GeoModels/R/GeoSim.r | 60 + GeoModels-2.2.5/GeoModels/R/GeoSimCopula.R | 79 +- GeoModels-2.2.5/GeoModels/R/GeoSimcond.R | 299 +++++--- GeoModels-2.2.5/GeoModels/R/GeoVarest.R |only GeoModels-2.2.5/GeoModels/R/GeoVarestbootstrap.R | 71 + GeoModels-2.2.5/GeoModels/R/TB.R | 44 - GeoModels-2.2.5/GeoModels/man/Anomalies.Rd | 6 GeoModels-2.2.5/GeoModels/man/CheckBiv.Rd | 2 GeoModels-2.2.5/GeoModels/man/CheckDistance.Rd | 12 GeoModels-2.2.5/GeoModels/man/CheckST.Rd | 8 GeoModels-2.2.5/GeoModels/man/CheckSph.Rd | 8 GeoModels-2.2.5/GeoModels/man/CkCorrModel.Rd | 10 GeoModels-2.2.5/GeoModels/man/CkInput.Rd | 146 +-- GeoModels-2.2.5/GeoModels/man/CkLikelihood.Rd | 16 GeoModels-2.2.5/GeoModels/man/CkModel.Rd | 6 GeoModels-2.2.5/GeoModels/man/CkType.Rd | 6 GeoModels-2.2.5/GeoModels/man/CompIndLik2.Rd | 138 +-- GeoModels-2.2.5/GeoModels/man/CompLik.Rd | 158 ++-- GeoModels-2.2.5/GeoModels/man/CompLik2.Rd | 184 ++-- GeoModels-2.2.5/GeoModels/man/CorrParam.Rd | 24 GeoModels-2.2.5/GeoModels/man/CorrelationPar.Rd | 12 GeoModels-2.2.5/GeoModels/man/Corrsas.Rd | 30 GeoModels-2.2.5/GeoModels/man/GeoAniso.Rd | 16 GeoModels-2.2.5/GeoModels/man/GeoCV.Rd | 102 +- GeoModels-2.2.5/GeoModels/man/GeoCorrFct.Rd | 66 - GeoModels-2.2.5/GeoModels/man/GeoCorrFct_Cop.Rd | 50 - GeoModels-2.2.5/GeoModels/man/GeoCovDisplay.Rd | 24 GeoModels-2.2.5/GeoModels/man/GeoCovariogram.Rd | 158 ++-- GeoModels-2.2.5/GeoModels/man/GeoCovmatrix.Rd | 669 +++++++++--------- GeoModels-2.2.5/GeoModels/man/GeoDistances.Rd | 40 - GeoModels-2.2.5/GeoModels/man/GeoDosocores.Rd | 52 - GeoModels-2.2.5/GeoModels/man/GeoFit.Rd | 486 ++++++------- GeoModels-2.2.5/GeoModels/man/GeoFit2.Rd | 272 +++---- GeoModels-2.2.5/GeoModels/man/GeoKrig.Rd | 327 ++++---- GeoModels-2.2.5/GeoModels/man/GeoKrigWeights.Rd | 158 ++-- GeoModels-2.2.5/GeoModels/man/GeoKrigloc.Rd | 307 ++++---- GeoModels-2.2.5/GeoModels/man/GeoKriglocWeights.Rd | 150 ++-- GeoModels-2.2.5/GeoModels/man/GeoNA.Rd | 68 - GeoModels-2.2.5/GeoModels/man/GeoNeighIndex.Rd | 204 ++--- GeoModels-2.2.5/GeoModels/man/GeoNeighbSelect.Rd | 240 +++--- GeoModels-2.2.5/GeoModels/man/GeoNeighborhood.Rd | 147 +-- GeoModels-2.2.5/GeoModels/man/GeoOutlier.Rd | 117 +-- GeoModels-2.2.5/GeoModels/man/GeoPit.Rd | 22 GeoModels-2.2.5/GeoModels/man/GeoQQ.Rd | 24 GeoModels-2.2.5/GeoModels/man/GeoResiduals.Rd | 34 GeoModels-2.2.5/GeoModels/man/GeoScatterplot.Rd | 87 +- GeoModels-2.2.5/GeoModels/man/GeoScores.Rd | 346 ++++----- GeoModels-2.2.5/GeoModels/man/GeoSim.Rd | 220 +++-- GeoModels-2.2.5/GeoModels/man/GeoSimCopula.Rd | 157 ++-- GeoModels-2.2.5/GeoModels/man/GeoSimapprox.Rd | 197 ++--- GeoModels-2.2.5/GeoModels/man/GeoSimcond.Rd | 142 +-- GeoModels-2.2.5/GeoModels/man/GeoTestIsotropy.Rd | 66 - GeoModels-2.2.5/GeoModels/man/GeoTest_supp.Rd | 60 - GeoModels-2.2.5/GeoModels/man/GeoTests.Rd | 120 +-- GeoModels-2.2.5/GeoModels/man/GeoVarest.Rd |only GeoModels-2.2.5/GeoModels/man/GeoVarestbootstrap.Rd | 75 +- GeoModels-2.2.5/GeoModels/man/GeoVariogram.Rd | 265 +++---- GeoModels-2.2.5/GeoModels/man/GeoWls.Rd | 202 ++--- GeoModels-2.2.5/GeoModels/man/GeovariogramDir.Rd | 116 +-- GeoModels-2.2.5/GeoModels/man/Lik.Rd | 168 ++-- GeoModels-2.2.5/GeoModels/man/MargParam.Rd | 18 GeoModels-2.2.5/GeoModels/man/MatDecomp.Rd | 10 GeoModels-2.2.5/GeoModels/man/Matrixfun.Rd | 16 GeoModels-2.2.5/GeoModels/man/NuisParam.Rd |only GeoModels-2.2.5/GeoModels/man/NuisParam2.Rd | 18 GeoModels-2.2.5/GeoModels/man/SimCE.Rd | 26 GeoModels-2.2.5/GeoModels/man/StartParam.Rd | 96 +- GeoModels-2.2.5/GeoModels/man/WlsStart.Rd | 100 +- GeoModels-2.2.5/GeoModels/man/getInvC.Rd | 60 - GeoModels-2.2.5/GeoModels/man/plot.GeoCorrFct.Rd | 26 GeoModels-2.2.5/GeoModels/man/plot.GeoVariogram.Rd | 20 GeoModels-2.2.5/GeoModels/man/plot.GeoVariogramDir.Rd | 34 GeoModels-2.2.5/GeoModels/man/rainNLD.Rd | 8 GeoModels-2.2.5/GeoModels/man/sp2Geo.Rd | 14 GeoModels-2.2.5/GeoModels/man/spanish_wind.Rd | 6 GeoModels-2.2.5/GeoModels/man/winds.Rd | 12 GeoModels-2.2.5/GeoModels/man/winds.coords.Rd | 16 GeoModels-2.2.5/GeoModels/src/CorrelationFunction.c | 256 ++++-- 85 files changed, 4438 insertions(+), 3958 deletions(-)
Title: Disaster Victim Identification
Description: Joint DNA-based disaster victim identification (DVI), as
described in Vigeland and Egeland (2021)
<doi:10.21203/rs.3.rs-296414/v1>. Identification is performed by
optimising the joint likelihood of all victim samples and reference
individuals. Individual identification probabilities, conditional on
all available information, are derived from the joint solution in the
form of posterior pairing probabilities. 'dvir' is part of the
'pedsuite' collection of packages for pedigree analysis.
Author: Magnus Dehli Vigeland [aut, cre] ,
Thore Egeland [aut]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between dvir versions 3.4.1 dated 2026-05-15 and 3.4.2 dated 2026-06-30
dvir-3.4.1/dvir/man/figures/README-example-plot1-1.png |only dvir-3.4.1/dvir/man/figures/README-example-plot2-1.png |only dvir-3.4.1/dvir/man/figures/README-solution-1.png |only dvir-3.4.2/dvir/DESCRIPTION | 14 dvir-3.4.2/dvir/MD5 | 95 ++--- dvir-3.4.2/dvir/NAMESPACE | 12 dvir-3.4.2/dvir/NEWS.md | 26 + dvir-3.4.2/dvir/R/amDrivenDVI.R | 24 + dvir-3.4.2/dvir/R/dviCompare.R | 200 ++++------- dvir-3.4.2/dvir/R/dviData.R | 22 - dvir-3.4.2/dvir/R/dviGLR.R | 2 dvir-3.4.2/dvir/R/dviGridSize.R |only dvir-3.4.2/dvir/R/dviJoint.R | 156 ++++---- dvir-3.4.2/dvir/R/dviSim.R | 24 - dvir-3.4.2/dvir/R/dviSolve.R | 132 ++++--- dvir-3.4.2/dvir/R/dvir-package.R | 2 dvir-3.4.2/dvir/R/expand.grid.nodup.R | 128 +++---- dvir-3.4.2/dvir/R/findExcluded.R | 4 dvir-3.4.2/dvir/R/findUndisputed.R | 14 dvir-3.4.2/dvir/R/formatSummary.R | 4 dvir-3.4.2/dvir/R/jointDVI.R | 108 ++---- dvir-3.4.2/dvir/R/mergePM.R | 6 dvir-3.4.2/dvir/R/ncomb.R | 18 - dvir-3.4.2/dvir/R/pairwiseGLR.R | 8 dvir-3.4.2/dvir/R/pairwiseLR.R | 54 +-- dvir-3.4.2/dvir/R/plotDVI.R | 71 ++- dvir-3.4.2/dvir/R/relabelDVI.R | 2 dvir-3.4.2/dvir/R/setPairing.R | 18 - dvir-3.4.2/dvir/R/subsetDVI.R | 2 dvir-3.4.2/dvir/R/utils.R | 19 - dvir-3.4.2/dvir/README.md | 306 ++++++++--------- dvir-3.4.2/dvir/build/partial.rdb |binary dvir-3.4.2/dvir/man/dviCompare.Rd | 61 +-- dvir-3.4.2/dvir/man/dviGLR.Rd | 2 dvir-3.4.2/dvir/man/dviGridSize.Rd |only dvir-3.4.2/dvir/man/dviJoint.Rd | 16 dvir-3.4.2/dvir/man/dviSolve.Rd | 17 dvir-3.4.2/dvir/man/expand.grid.nodup.Rd | 55 ++- dvir-3.4.2/dvir/man/figures/README-example2-plot-1.png |only dvir-3.4.2/dvir/man/figures/README-fire-plot-1.png |only dvir-3.4.2/dvir/man/findExcluded.Rd | 2 dvir-3.4.2/dvir/man/findUndisputed.Rd | 3 dvir-3.4.2/dvir/man/jointDVI.Rd | 8 dvir-3.4.2/dvir/man/mergePM.Rd | 4 dvir-3.4.2/dvir/man/ncomb.Rd | 14 dvir-3.4.2/dvir/man/pairwiseLR.Rd | 3 dvir-3.4.2/dvir/man/plotDVI.Rd | 3 dvir-3.4.2/dvir/man/setPairing.Rd | 2 dvir-3.4.2/dvir/man/swapOrientation.Rd | 4 dvir-3.4.2/dvir/tests |only 50 files changed, 842 insertions(+), 823 deletions(-)
Title: Various Blocking Methods for Entity Resolution
Description: The goal of 'blocking' is to provide blocking methods for record linkage and deduplication using approximate nearest neighbour (ANN) algorithms and graph techniques. It supports multiple ANN implementations via 'rnndescent', 'RcppHNSW', 'RcppAnnoy', and 'mlpack' packages, and provides integration with the 'reclin2' package. The package generates shingles from character strings and similarity vectors for record comparison, and includes evaluation metrics for assessing blocking performance including false positive rate (FPR) and false negative rate (FNR) estimates. For details see: Papadakis et al. (2020) <doi:10.1145/3377455>, Steorts et al. (2014) <doi:10.1007/978-3-319-11257-2_20>, Dasylva and Goussanou (2021) <https://www150.statcan.gc.ca/n1/en/catalogue/12-001-X202100200002>, Dasylva and Goussanou (2022) <doi:10.1007/s42081-022-00153-3>.
Author: Maciej Beresewicz [aut, cre] ,
Adam Struzik [aut, ctr]
Maintainer: Maciej Beresewicz <maciej.beresewicz@ue.poznan.pl>
Diff between blocking versions 1.0.2 dated 2026-03-11 and 1.0.3 dated 2026-06-30
DESCRIPTION | 8 - MD5 | 89 +++++++-------- NEWS.md | 6 + R/blocking.R | 221 ++++++++++++++++++++------------------- R/controls.R | 46 ++++---- R/data.R | 2 R/est_block_error.R | 8 - R/eval.R | 26 ++-- R/internals.R |only R/method_annoy.R | 2 R/method_hnsw.R | 2 R/method_mlpack.R | 9 - R/method_nnd.R | 2 R/methods.R | 100 ++++++++++++++++- R/reclin2_pair_ann.R | 37 ++---- README.md | 17 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/v1-deduplication.R | 9 - inst/doc/v1-deduplication.Rmd | 14 +- inst/doc/v1-deduplication.html | 16 +- inst/doc/v2-reclin.html | 14 +- inst/doc/v3-integration.Rmd | 2 inst/doc/v3-integration.html | 46 ++------ inst/tinytest/test_annoy.R | 9 + inst/tinytest/test_blocking.R | 169 +++++++++++++++++++++++++++++ inst/tinytest/test_data.R | 1 inst/tinytest/test_hnsw.R | 9 + inst/tinytest/test_mlpack.R | 13 +- inst/tinytest/test_reclin2.R | 65 +++++++++++ inst/tinytest/test_true_blocks.R | 99 ++++++++++++++++- man/RLdata500.Rd | 2 man/blocking.Rd | 28 ++-- man/control_kd.Rd | 6 - man/control_lsh.Rd | 2 man/control_nnd.Rd | 2 man/controls_ann.Rd | 10 - man/controls_txt.Rd | 2 man/est_block_error.Rd | 8 - man/method_hnsw.Rd | 2 man/method_mlpack.Rd | 2 man/method_nnd.Rd | 2 man/pair_ann.Rd | 13 +- tests/tinytest.R | 3 vignettes/v1-deduplication.Rmd | 14 +- vignettes/v3-integration.Rmd | 2 46 files changed, 780 insertions(+), 359 deletions(-)
Title: 'shiny' Widgets for 'teal' Applications
Description: Collection of 'shiny' widgets to support 'teal' applications.
Enables the manipulation of application layout and plot or table
settings.
Author: Dawid Kaledkowski [aut],
Pawel Rucki [aut],
Mahmoud Hallal [aut],
Nikolas Burkoff [aut],
Maciej Nasinski [aut],
Konrad Pagacz [aut],
Junlue Zhao [aut],
Dony Unardi [aut, cre],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal.widgets versions 0.6.0 dated 2026-02-24 and 0.6.1 dated 2026-06-30
teal.widgets-0.6.0/teal.widgets/tests/testthat/_snaps/verbatim_popup_ui.md |only teal.widgets-0.6.1/teal.widgets/DESCRIPTION | 18 +-- teal.widgets-0.6.1/teal.widgets/MD5 | 25 ++-- teal.widgets-0.6.1/teal.widgets/NAMESPACE | 10 + teal.widgets-0.6.1/teal.widgets/NEWS.md | 9 + teal.widgets-0.6.1/teal.widgets/R/plot_with_settings.R | 2 teal.widgets-0.6.1/teal.widgets/R/table_with_settings.R | 20 +-- teal.widgets-0.6.1/teal.widgets/R/verbatim_popup.R | 7 - teal.widgets-0.6.1/teal.widgets/inst/WORDLIST | 2 teal.widgets-0.6.1/teal.widgets/man/teal.widgets-package.Rd | 4 teal.widgets-0.6.1/teal.widgets/man/white_small_well.Rd | 2 teal.widgets-0.6.1/teal.widgets/tests/testthat/Rplots.pdf |binary teal.widgets-0.6.1/teal.widgets/tests/testthat/test-plot_with_settings_ui.R | 54 ++++++++-- teal.widgets-0.6.1/teal.widgets/tests/testthat/test-verbatim_popup_ui.R | 6 - 14 files changed, 110 insertions(+), 49 deletions(-)
Title: Exploratory Web Apps for Analyzing Clinical Trials Data
Description: A 'shiny' based interactive exploration framework for
analyzing clinical trials data. 'teal' currently provides a dynamic
filtering facility and different data viewers. 'teal' 'shiny'
applications are built using standard 'shiny' modules.
Author: Dony Unardi [aut, cre],
Dawid Kaledkowski [aut] ,
Pawel Rucki [aut],
Aleksander Chlebowski [aut] ,
Andre Verissimo [aut] ,
Kartikeya Kirar [aut],
Vedha Viyash [aut],
Marcin Kosinski [aut],
Adrian Waddell [aut],
Nina Qi [rev],
Nikolas Burkoff [aut],
M [...truncated...]
Maintainer: Dony Unardi <unardid@gene.com>
Diff between teal versions 1.1.0 dated 2025-11-17 and 1.2.0 dated 2026-06-30
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199 files changed, 37112 insertions(+), 34997 deletions(-)
Title: Automated Soil Profile Classification per WRB 2022, 'SiBCS' 5
and USDA Soil Taxonomy 13
Description: Implements deterministic classification keys for the World
Reference Base for Soil Resources 2022 (4th edition) and the Brazilian
System of Soil Classification ('SiBCS', 5th edition). Provides a unified
profile representation with explicit per-attribute provenance, multimodal
extraction from field reports and photos via vision-language models,
spatial priors from 'SoilGrids' and national soil maps, and gap-filling of
soil attributes from Vis-NIR or MIR spectra via the Open Soil Spectral
Library ('OSSL'). The taxonomic key itself is never delegated to a language
model; LLMs are restricted to schema-validated extraction. Each
classification result reports a key trace, a provenance-aware evidence
grade, and ambiguities that further measurement would resolve.
Author: Hugo Rodrigues [aut, cre]
Maintainer: Hugo Rodrigues <rodrigues.machado.hugo@gmail.com>
Diff between soilKey versions 0.9.155 dated 2026-06-22 and 0.9.157 dated 2026-06-30
DESCRIPTION | 8 - MD5 | 17 +-- NEWS.md | 54 +++++++++ R/spectra-munsell.R | 131 ++++++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/v09_perfil_embrapa_pt.html | 2 inst/rules/usda/subgroups/inceptisols.yaml | 6 - man/predict_munsell_from_spectra.Rd | 12 +- tests/testthat/test-v09156-munsell-illuminant.R |only 10 files changed, 161 insertions(+), 69 deletions(-)
Title: Conduct Additional Modeling and Analysis for 'seminr'
Description: Supplementary tools for evaluating and validating partial least
squares structural equation models estimated with 'seminr'. Provides methods
for predictive model assessment, importance-performance analysis with
necessary condition testing, overfitting diagnostics, measurement model
verification, mediator contribution analysis, unobserved heterogeneity
detection via latent class and prediction-oriented segmentation, and
congruence coefficient testing. All functions accept estimated 'seminr'
model objects and return results with print, summary, and plot methods.
Author: Soumya Ray [aut, ths],
Nicholas Patrick Danks [aut, cre]
Maintainer: Nicholas Patrick Danks <nicholasdanks@hotmail.com>
Diff between seminrExtras versions 1.0.1 dated 2026-05-21 and 1.0.2 dated 2026-06-30
DESCRIPTION | 8 ++--- MD5 | 20 ++++++------- NEWS.md | 23 +++++++++++++++ R/feature_congruence.R | 26 +++++++++++------ build/vignette.rds |binary inst/doc/SEMinRExtras.html | 17 +++++------ tests/fixtures/cvpat1.csv | 6 ++-- tests/testthat/test-congruence.R | 44 ++++++++++++++++++++++++++++++ tests/testthat/test-cvpat-comprehensive.R | 26 ++++++++--------- tests/testthat/test-cvpat.R | 7 ++-- tests/testthat/test-pos.R | 40 ++++++++++----------------- 11 files changed, 142 insertions(+), 75 deletions(-)
Title: Density, Distribution, and Sampling Functions for Evidence
Accumulation Models
Description: Calculate the probability density functions (PDFs) for two threshold evidence
accumulation models (EAMs). These are defined using the following Stochastic
Differential Equation (SDE), dx(t) = v(x(t),t)*dt+D(x(t),t)*dW, where x(t) is
the accumulated evidence at time t, v(x(t),t) is the drift rate, D(x(t),t) is
the noise scale, and W is the standard Wiener process. The boundary conditions
of this process are the upper and lower decision thresholds, represented by b_u(t)
and b_l(t), respectively. Upper threshold b_u(t) > 0, while lower threshold b_l(t) < 0.
The initial condition of this process x(0) = z where b_l(t) < z < b_u(t). We
represent this as the relative start point w = z/(b_u(0)-b_l(0)), defined as
a ratio of the initial threshold location. This package generates the PDF using
the same approach as the 'python' package it is based upon, 'PyBEAM' by Murrow and Holmes
(2023) <doi:10.3758/s13428-023-02162-w>. First, it converts the SDE model into the
forwards Fokke [...truncated...]
Author: Raphael Hartmann [aut, cre] ,
Matthew Murrow [aut]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between ream versions 1.0-10 dated 2025-12-19 and 1.0-12 dated 2026-06-30
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/tools.R | 2 +- build/vignette.rds |binary inst/doc/guideline.html | 4 ++-- src/Model_7P.cpp | 4 ++-- src/R_wrapper.cpp | 8 ++++---- 7 files changed, 18 insertions(+), 18 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models, used in the computation of
marginal means, contrast analysis and predictions. For a list of supported models,
see 'insight::supported_models()'.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Remi Theriault [aut]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between modelbased versions 0.15.0 dated 2026-05-10 and 0.16.0 dated 2026-06-30
modelbased-0.15.0/modelbased/tests/testthat/test-estimate_contrasts_bookexamples.R |only modelbased-0.16.0/modelbased/DESCRIPTION | 12 modelbased-0.16.0/modelbased/MD5 | 92 +- modelbased-0.16.0/modelbased/NEWS.md | 31 modelbased-0.16.0/modelbased/R/estimate_contrasts.R | 122 ++- modelbased-0.16.0/modelbased/R/estimate_grouplevel.R | 153 +++- modelbased-0.16.0/modelbased/R/estimate_means.R | 33 modelbased-0.16.0/modelbased/R/estimate_slopes.R | 21 modelbased-0.16.0/modelbased/R/format.R | 18 modelbased-0.16.0/modelbased/R/get_contexteffects.R | 22 modelbased-0.16.0/modelbased/R/get_emcontrasts.R | 15 modelbased-0.16.0/modelbased/R/get_emmeans.R | 29 modelbased-0.16.0/modelbased/R/get_emtrends.R | 66 + modelbased-0.16.0/modelbased/R/get_inequalitycontrasts.R | 5 modelbased-0.16.0/modelbased/R/get_jointtest.R | 153 ++-- modelbased-0.16.0/modelbased/R/get_marginalcontrasts.R | 79 +- modelbased-0.16.0/modelbased/R/get_marginaleffects_type.R | 117 +-- modelbased-0.16.0/modelbased/R/get_marginalmeans.R | 190 ++++- modelbased-0.16.0/modelbased/R/get_marginaltrends.R | 72 +- modelbased-0.16.0/modelbased/R/p_adjust.R | 3 modelbased-0.16.0/modelbased/R/table_footer.R | 15 modelbased-0.16.0/modelbased/R/utils.R | 4 modelbased-0.16.0/modelbased/build/partial.rdb |binary modelbased-0.16.0/modelbased/build/vignette.rds |binary modelbased-0.16.0/modelbased/inst/WORDLIST | 1 modelbased-0.16.0/modelbased/man/estimate_contrasts.Rd | 151 +++- modelbased-0.16.0/modelbased/man/estimate_grouplevel.Rd | 108 ++- modelbased-0.16.0/modelbased/man/estimate_means.Rd | 33 modelbased-0.16.0/modelbased/man/estimate_slopes.Rd | 54 - modelbased-0.16.0/modelbased/man/get_emmeans.Rd | 70 + modelbased-0.16.0/modelbased/man/modelbased-package.Rd | 1 modelbased-0.16.0/modelbased/man/puppy_love.Rd | 64 - modelbased-0.16.0/modelbased/man/reexports.Rd | 4 modelbased-0.16.0/modelbased/tests/testthat/test-attributes_estimatefun.R | 16 modelbased-0.16.0/modelbased/tests/testthat/test-brms-dpar.R |only modelbased-0.16.0/modelbased/tests/testthat/test-discovr_bookexamples.R |only modelbased-0.16.0/modelbased/tests/testthat/test-estimate_contrasts.R | 8 modelbased-0.16.0/modelbased/tests/testthat/test-estimate_contrasts_context.R | 18 modelbased-0.16.0/modelbased/tests/testthat/test-estimate_contrasts_inequality.R | 20 modelbased-0.16.0/modelbased/tests/testthat/test-estimate_contrasts_post_process.R |only modelbased-0.16.0/modelbased/tests/testthat/test-estimate_expectation.R | 44 - modelbased-0.16.0/modelbased/tests/testthat/test-estimate_grouplevel.R | 92 ++ modelbased-0.16.0/modelbased/tests/testthat/test-estimate_means.R | 354 +++++++--- modelbased-0.16.0/modelbased/tests/testthat/test-estimate_predicted.R | 2 modelbased-0.16.0/modelbased/tests/testthat/test-estimate_slopes.R | 41 + modelbased-0.16.0/modelbased/tests/testthat/test-g_computation.R | 54 + modelbased-0.16.0/modelbased/tests/testthat/test-joint_test.R | 89 +- modelbased-0.16.0/modelbased/tests/testthat/test-keep_iterations.R | 11 modelbased-0.16.0/modelbased/tests/testthat/test-offset.R | 40 - 49 files changed, 1858 insertions(+), 669 deletions(-)
Title: Additional Documentation and Regression Tests for
'stats::free1way()'
Description: Function 'stats::free1way()' implements semiparametrically
efficient population- and permutation-based inference in
distribution-free stratified K-sample oneway layouts. This package
provides additional documentation, including a detailed description
of the implementation, and serves as a home for extensive regression tests.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Frank E Harrell Jr [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between free1way.docreg versions 1.0-1 dated 2026-06-16 and 1.0-2 dated 2026-06-30
DESCRIPTION | 8 MD5 | 14 build/vignette.rds |binary inst/NEWS.Rd | 8 inst/doc/free1way.Rnw | 696 ++++++++++++++++++++++++------------------------- inst/doc/free1way.pdf |binary inst/nuweb/free1way.w | 8 vignettes/free1way.Rnw | 696 ++++++++++++++++++++++++------------------------- 8 files changed, 719 insertions(+), 711 deletions(-)
More information about free1way.docreg at CRAN
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Title: Area-Proportional Euler and Venn Diagrams
Description: Generate area-proportional Euler diagrams
using numerical optimization. A Euler diagram is a generalization of a Venn
diagram, relaxing the criterion that all interactions need to be
represented. Diagrams may be fit with circles, ellipses, squares, and
rectangles via a wide range of inputs and can be visualized in numerous ways.
Author: Johan Larsson [aut, cre, cph] ,
A. Jonathan R. Godfrey [ctb],
Peter Gustafsson [ctb],
David H. Eberly [ctb] ,
Emanuel Huber [ctb] ,
Florian Prive [ctb]
Maintainer: Johan Larsson <johan@jolars.co>
Diff between eulerr versions 8.0.0 dated 2026-05-29 and 8.1.0 dated 2026-06-30
DESCRIPTION | 33 +- LICENSE |only MD5 | 124 +++++---- NEWS.md | 99 ++++++- R/euler-methods.R | 6 R/euler.R | 113 ++++++--- R/eulerr.R | 2 R/eulerr_options.R | 9 R/extendr-wrappers.R | 14 + R/fit_diagram.R | 197 +++++++++++++++ R/geometry.R | 15 + R/label_placement.R | 4 R/parse_input.R | 2 R/plot.euler.R | 41 +-- R/setup_grobs.R | 47 +-- R/tag-grobs.R | 186 ++++++-------- R/utils.R | 74 +++++ R/venn.R | 19 + R/zzz.R | 8 README.md | 40 ++- build/vignette.rds |binary inst/WORDLIST | 44 ++- inst/doc/comparison.R |only inst/doc/comparison.Rmd |only inst/doc/comparison.html |only inst/doc/gallery.html | 22 - inst/doc/introduction.html | 6 inst/doc/loss-functions.Rmd | 6 inst/doc/loss-functions.html | 11 inst/doc/under-the-hood.html | 4 inst/doc/venn-diagrams.html | 10 inst/doc/visualization.html | 14 - man/EULER_PANEL_PAD_PT.Rd | 4 man/build_leader_grob.Rd | 2 man/coef.euler.Rd | 2 man/default_n_threads.Rd |only man/detect_available_cores.Rd |only man/euler.Rd | 85 +++++- man/eulerr-package.Rd | 14 - man/eulerr_options.Rd | 8 man/figures/README-plot_method-1.png |binary man/fit_euler_diagram.Rd | 6 man/fitted.euler.Rd | 4 man/get_bounding_box.Rd | 2 man/is_real.Rd | 2 man/open_measurement_viewport.Rd | 4 man/plot.euler.Rd | 10 man/print.euler.Rd | 4 man/print.eulerr_venn.Rd | 4 man/setup_grobs.Rd | 2 man/venn.Rd | 15 - man/venn_layout.Rd |only src/rust/Cargo.lock | 423 +++++++--------------------------- src/rust/Cargo.toml | 6 src/rust/rust-toolchain.toml | 2 src/rust/src/lib.rs | 329 +++++++++++++++++++------- src/rust/vendor.tar.xz |binary tests/testthat/test-assertions.R | 19 + tests/testthat/test-control.R |only tests/testthat/test-inputs.R | 46 +++ tests/testthat/test-plotting.R | 31 ++ tests/testthat/test-reproducibility.R | 22 + tests/testthat/test-shapes.R | 46 +++ tests/testthat/test-utils.R | 74 +++++ vignettes/benchmark_results.rds |only vignettes/comparison.Rmd |only vignettes/eulerr.bib | 61 ++++ vignettes/loss-functions.Rmd | 6 68 files changed, 1541 insertions(+), 842 deletions(-)
More information about SimplexRegression at CRAN
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Title: Create Upset Plots
Description: Create Upset plots using a combination of 'ggplot2' and 'patchwork'.
Author: Stevie Pederson [aut, cre] ,
Lachlan Baer [ctb]
Maintainer: Stevie Pederson <stephen.pederson.au@gmail.com>
Diff between SimpleUpset versions 0.1.4 dated 2025-11-29 and 0.1.5 dated 2026-06-30
DESCRIPTION | 16 ++++-- MD5 | 22 ++++---- NEWS.md | 6 ++ R/defaults.R | 18 ++++--- R/simpleUpSet.R | 60 ++++++++++++++++------- build/vignette.rds |binary inst/doc/introduction.html | 82 ++++++++++++++++---------------- man/default-layers.Rd | 15 ++++- man/simpleUpSet.Rd | 10 +++ tests/testthat/test-default_layers.R | 12 +++- tests/testthat/test-private_functions.R | 35 +++++++++---- tests/testthat/test-simpleUpSet.R | 18 +++++++ 12 files changed, 196 insertions(+), 98 deletions(-)
Title: Sum of Ranking Differences Statistical Test
Description: We provide an implementation for Sum of Ranking Differences (SRD),
a novel statistical test introduced by Héberger (2010)
<doi:10.1016/j.trac.2009.09.009>. The test allows the comparison of
different solutions through a reference by first performing a rank
transformation on the input, then calculating and comparing the distances
between the solutions and the reference - the latter is measured in the
L1 norm. The reference can be an external benchmark (e.g. an established
gold standard) or can be aggregated from the data. The calculated distances,
called SRD scores, are validated in two ways, see Héberger and Kollár-Hunek
(2011) <doi:10.1002/cem.1320>. A randomization test (also called permutation
test) compares the SRD scores of the solutions to the SRD scores of randomly
generated rankings. The second validation option is cross-validation that
checks whether the rankings generated from the solutions come from the same
distribution or not. For a detailed analysis about the [...truncated...]
Author: Jochen Staudacher [aut, cph, cre] ,
Balazs R. Sziklai [aut, cph] ,
Linus Olsson [aut, cph],
Dennis Horn [ctb],
Alexander Pothmann [ctb],
Ali Tugay Sen [ctb],
Attila Gere [ctb] ,
Karoly Hebeger [ctb]
Maintainer: Jochen Staudacher <jochen.staudacher@hs-kempten.de>
Diff between rSRD versions 0.1.8 dated 2024-11-01 and 0.2.0 dated 2026-06-30
DESCRIPTION | 27 +- MD5 | 75 +++++--- NAMESPACE | 72 +++---- NEWS.md |only R/RcppExports.R | 104 ++--------- R/SRD_utility.R | 326 ++++++----------------------------- R/boxplots.R | 102 +++++++--- R/data_fusion.R | 246 +++++++++++++------------- R/input_validation.R |only R/rSRD-package.R |only R/validation.R | 224 ++++++++++++------------ R/wrappers.R |only build |only inst |only man/calculateCrossValidation.Rd | 12 + man/calculateSRDDistribution.Rd | 59 ++++-- man/calculateSRDDistribution_impl.Rd |only man/calculateSRDValues.Rd | 26 +- man/calculateSRDValues_impl.Rd |only man/plotCrossValidation.Rd | 22 +- man/plotPermTest.Rd | 7 man/rSRD-package.Rd |only man/utilsColorPalette.Rd | 6 man/utilsPreprocessDF.Rd | 2 man/utilsRankingMatrix.Rd | 11 - man/utilsRankingMatrix_impl.Rd |only man/validateSRDInput.Rd |only src/CrossValidationInterface.cpp | 8 src/Cross_Validation.cpp | 36 ++- src/Cross_Validation.h | 6 src/RankingMatrixInterface.cpp | 25 -- src/Ranking_generator.cpp | 83 +++++++- src/Ranking_generator.h | 26 +- src/RcppExports.cpp | 40 ++-- src/SRDDistributionInterface.cpp | 162 ++++++----------- src/SRDValuesInterface.cpp | 45 +--- tests |only vignettes |only 38 files changed, 819 insertions(+), 933 deletions(-)
More information about NeighborFinder at CRAN
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Title: Monthly Climate Data for Germany, Usable for Heating and Cooling
Calculations
Description: This data package contains monthly climate data in Germany, it can be used for heating and
cooling calculations (external temperature, heating / cooling days, solar radiation).
Author: Tobias Loga [aut] ,
Guillaume Behem [aut],
Jens Calisti [cre]
Maintainer: Jens Calisti <jens@tangled.de>
Diff between clidamonger versions 1.5.0 dated 2026-01-30 and 1.6.0 dated 2026-06-30
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 9 ++++++++- README.md | 4 ++-- data/data.sol.rda |binary data/data.ta.hd.rda |binary data/list.station.ta.rda |binary man/data.sol.Rd | 2 +- man/data.ta.hd.Rd | 2 +- man/list.station.ta.Rd | 2 +- 10 files changed, 25 insertions(+), 18 deletions(-)
Title: Simple Functions to Save Time and Memory
Description: Fast and memory-efficient (or 'cheap') tools to facilitate
efficient programming, saving time and memory. It aims to provide
'cheaper' alternatives to common base R functions, as well as some
additional functions.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cheapr versions 1.5.1 dated 2026-04-04 and 1.5.2 dated 2026-06-30
DESCRIPTION | 8 ++-- MD5 | 20 +++++----- NEWS.md | 4 ++ inst/include/cheapr/internal/c_core.h | 6 +++ man/cheapr-package.Rd | 5 ++ src/attrs.cpp | 2 - src/combine.cpp | 68 ++++++++++++++++++---------------- src/lag.cpp | 14 ++++--- src/math.cpp | 2 - src/nas.cpp | 5 +- src/sset.cpp | 26 ++++++------- 11 files changed, 93 insertions(+), 67 deletions(-)
More information about caretMultimodal at CRAN
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Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Martin J [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between performance versions 0.17.0 dated 2026-05-21 and 0.17.1 dated 2026-06-30
DESCRIPTION | 10 MD5 | 38 +-- NAMESPACE | 5 NEWS.md | 30 ++ R/check_dag.R | 3 R/check_group_variation.R | 4 R/check_model.R | 52 +++- R/check_model_diagnostics.R | 321 +++++++++++++++++------------ R/check_overdispersion.R | 54 ++-- R/check_predictions.R | 69 ++---- R/check_priors.R |only R/check_zeroinflation.R | 1 build/partial.rdb |binary man/check_dag.Rd | 4 man/check_group_variation.Rd | 4 man/check_model.Rd | 29 +- man/check_overdispersion.Rd | 12 + man/check_predictions.Rd | 5 man/check_priors.Rd |only tests/testthat/test-check_overdispersion.R | 159 +++++++++++++- tests/testthat/test-check_predictions.R | 311 +++++----------------------- 21 files changed, 616 insertions(+), 495 deletions(-)
Title: Helper Functions for Linear Model Analysis
Description: A collection of helper functions for multiple
regression models fitted by lm(). Most of them are simple
functions for simple tasks which can be done with coding,
but may not be easy for occasional users of R. Most of
the tasks addressed are those sometimes needed when
using the 'manymome' package (Cheung and Cheung, 2023,
<doi:10.3758/s13428-023-02224-z>) and 'stdmod' package
(Cheung, Cheung, Lau, Hui, and Vong, 2022,
<doi:10.1037/hea0001188>). However, they can also be used
in other scenarios.
Author: Shu Fai Cheung [aut, cre]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between lmhelprs versions 0.4.4 dated 2026-03-10 and 0.4.5 dated 2026-06-30
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 10 ++++++++++ R/many_lm_to_partable.R | 2 +- README.md | 6 +++--- build/vignette.rds |binary inst/tinytest/test_semPlotModel.R | 31 +++++++++++++++++++++++++++++++ man/lm_list_to_partable.Rd | 4 ++-- 8 files changed, 58 insertions(+), 17 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: Hierarchical continuous (and discrete) time state space modelling, for linear
and nonlinear systems measured by continuous variables, with limited support for
binary data. The subject specific dynamic system is modelled as a stochastic
differential equation (SDE) or difference equation, measurement models are typically multivariate normal factor models.
Linear mixed effects SDE's estimated via maximum likelihood and optimization are the default.
Nonlinearities, (state dependent parameters) and random effects on all parameters
are possible, using either max likelihood / max a posteriori optimization
(with optional importance sampling) or Stan's Hamiltonian Monte Carlo sampling.
See <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf>
for details. See <https://osf.io/preprints/psyarxiv/4q9ex_v2> for a detailed tutorial.
Priors may be used. For the conceptual overview of the hierarchical Bayesian
linear SDE approach,
see <https://www.research [...truncated...]
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph],
Trustees of Columbia University [cph]
Maintainer: Charles Driver <charles.driver2@uzh.ch>
Diff between ctsem versions 3.10.6 dated 2026-01-27 and 3.11.0 dated 2026-06-30
ctsem-3.10.6/ctsem/R/JKalman.R |only ctsem-3.10.6/ctsem/R/ctFitAuto.R |only ctsem-3.10.6/ctsem/R/ctFitMultiModel.R |only ctsem-3.10.6/ctsem/R/ctStanProfileCI.R |only ctsem-3.10.6/ctsem/R/importanceSamplingBackup.R |only ctsem-3.10.6/ctsem/R/modelchecking.R |only ctsem-3.10.6/ctsem/R/stan_checkdivergences.R |only ctsem-3.10.6/ctsem/R/stan_confidenceRegion.R |only ctsem-3.10.6/ctsem/R/stan_postcalc.R |only ctsem-3.10.6/ctsem/man/ctDensity.Rd |only ctsem-3.10.6/ctsem/man/ctFitAuto.Rd |only ctsem-3.10.6/ctsem/man/ctFitAutoGroupModel.Rd |only ctsem-3.10.6/ctsem/man/ctFitMultiModel.Rd |only ctsem-3.10.6/ctsem/man/ctStanContinuousPars.Rd |only ctsem-3.10.6/ctsem/man/ctStanDiscretePars.Rd |only ctsem-3.10.6/ctsem/man/ctStanDiscreteParsPlot.Rd |only ctsem-3.10.6/ctsem/man/ctStanFit.Rd |only ctsem-3.10.6/ctsem/man/ctStanFitUpdate.Rd |only ctsem-3.10.6/ctsem/man/ctStanGenerate.Rd |only ctsem-3.10.6/ctsem/man/ctStanGenerateFromFit.Rd |only ctsem-3.10.6/ctsem/man/ctStanKalman.Rd |only ctsem-3.10.6/ctsem/man/ctStanModel.Rd |only ctsem-3.10.6/ctsem/man/ctStanParnames.Rd |only ctsem-3.10.6/ctsem/man/ctStanPlotPost.Rd |only ctsem-3.10.6/ctsem/man/ctStanPostPredict.Rd |only ctsem-3.10.6/ctsem/man/ctStanSubjectPars.Rd |only ctsem-3.10.6/ctsem/man/ctStanTIpredeffects.Rd |only ctsem-3.10.6/ctsem/man/stan_checkdivergences.Rd |only ctsem-3.11.0/ctsem/DESCRIPTION | 14 ctsem-3.11.0/ctsem/MD5 | 221 +- ctsem-3.11.0/ctsem/NAMESPACE | 27 ctsem-3.11.0/ctsem/NEWS.md | 12 ctsem-3.11.0/ctsem/R/ctACF.R | 14 ctsem-3.11.0/ctsem/R/ctCheckFit.R | 761 ++++---- ctsem-3.11.0/ctsem/R/ctCompare.R | 4 ctsem-3.11.0/ctsem/R/ctCoverageCheck.R | 82 ctsem-3.11.0/ctsem/R/ctDataHelp.R | 2 ctsem-3.11.0/ctsem/R/ctDiscretePars.R | 250 +- ctsem-3.11.0/ctsem/R/ctEmpiricalBayesFit.R |only ctsem-3.11.0/ctsem/R/ctGenerate.R | 40 ctsem-3.11.0/ctsem/R/ctKalman.R | 34 ctsem-3.11.0/ctsem/R/ctModel.R | 386 ---- ctsem-3.11.0/ctsem/R/ctModelHigherOrder.R | 5 ctsem-3.11.0/ctsem/R/ctModelLatex.R | 31 ctsem-3.11.0/ctsem/R/ctPlotArray.R | 2 ctsem-3.11.0/ctsem/R/ctStanContinuousPars.R | 35 ctsem-3.11.0/ctsem/R/ctStanData.R | 4 ctsem-3.11.0/ctsem/R/ctStanFit.R | 471 ++--- ctsem-3.11.0/ctsem/R/ctStanGenerate.R | 19 ctsem-3.11.0/ctsem/R/ctStanGenerateFromFit.R | 9 ctsem-3.11.0/ctsem/R/ctStanKalman.R | 11 ctsem-3.11.0/ctsem/R/ctStanModel.R | 222 ++ ctsem-3.11.0/ctsem/R/ctStanModelWriter.R | 199 +- ctsem-3.11.0/ctsem/R/ctStanPlotPost.R | 19 ctsem-3.11.0/ctsem/R/ctStanPostPredict.R | 29 ctsem-3.11.0/ctsem/R/ctStanTIpredeffects.R | 15 ctsem-3.11.0/ctsem/R/ctSummarise.R | 28 ctsem-3.11.0/ctsem/R/ctTIpredAuto.R | 71 ctsem-3.11.0/ctsem/R/ctdataupdate.R | 22 ctsem-3.11.0/ctsem/R/ctsem-package.R | 44 ctsem-3.11.0/ctsem/R/ctsemUtils.R | 72 ctsem-3.11.0/ctsem/R/ctsmupdate.R | 4 ctsem-3.11.0/ctsem/R/plot.ctStanFit.R | 34 ctsem-3.11.0/ctsem/R/stan_unconstrainsamples.R | 2 ctsem-3.11.0/ctsem/R/stanoptimis.R | 853 +++++++++- ctsem-3.11.0/ctsem/R/summary.ctStanFit.R | 23 ctsem-3.11.0/ctsem/README.md | 63 ctsem-3.11.0/ctsem/build/partial.rdb |binary ctsem-3.11.0/ctsem/build/vignette.rds |binary ctsem-3.11.0/ctsem/inst/doc/empirical-bayes-fitting.R |only ctsem-3.11.0/ctsem/inst/doc/empirical-bayes-fitting.html |only ctsem-3.11.0/ctsem/inst/doc/empirical-bayes-fitting.qmd |only ctsem-3.11.0/ctsem/inst/doc/hierarchicalmanual.pdf |binary ctsem-3.11.0/ctsem/inst/doc/hierarchicalmanual.rnw | 36 ctsem-3.11.0/ctsem/inst/stan/ctsm.stan | 107 - ctsem-3.11.0/ctsem/inst/stan/ctsmgen.stan | 107 - ctsem-3.11.0/ctsem/man/ctACFresiduals.Rd | 68 ctsem-3.11.0/ctsem/man/ctChisqTest.Rd | 64 ctsem-3.11.0/ctsem/man/ctDiscretePars.Rd |only ctsem-3.11.0/ctsem/man/ctDiscreteParsPlot.Rd |only ctsem-3.11.0/ctsem/man/ctEmpiricalBayesFit.Rd |only ctsem-3.11.0/ctsem/man/ctFit.Rd | 449 ++++- ctsem-3.11.0/ctsem/man/ctFitCovCheck.Rd | 139 + ctsem-3.11.0/ctsem/man/ctFitCovCheckPlot.Rd | 65 ctsem-3.11.0/ctsem/man/ctFitUpdate.Rd |only ctsem-3.11.0/ctsem/man/ctGenerate.Rd | 131 - ctsem-3.11.0/ctsem/man/ctGenerateFromFit.Rd |only ctsem-3.11.0/ctsem/man/ctGenerateFromPriors.Rd |only ctsem-3.11.0/ctsem/man/ctKalman.Rd | 174 +- ctsem-3.11.0/ctsem/man/ctKalmanArray.Rd |only ctsem-3.11.0/ctsem/man/ctModel.Rd | 388 +--- ctsem-3.11.0/ctsem/man/ctModelConvertOMX.Rd |only ctsem-3.11.0/ctsem/man/ctModelCoverage_check.Rd | 86 - ctsem-3.11.0/ctsem/man/ctModelHigherOrder.Rd | 87 - ctsem-3.11.0/ctsem/man/ctModelMatrices.Rd |only ctsem-3.11.0/ctsem/man/ctOptimUncertainty.Rd |only ctsem-3.11.0/ctsem/man/ctPlotArray.Rd | 130 - ctsem-3.11.0/ctsem/man/ctPlotPosterior.Rd |only ctsem-3.11.0/ctsem/man/ctPostPredict.Rd |only ctsem-3.11.0/ctsem/man/ctPredictTIP.Rd | 127 - ctsem-3.11.0/ctsem/man/ctRawParnames.Rd |only ctsem-3.11.0/ctsem/man/ctResiduals.Rd | 62 ctsem-3.11.0/ctsem/man/ctStanUpdModel.Rd | 40 ctsem-3.11.0/ctsem/man/ctSubjectPars.Rd |only ctsem-3.11.0/ctsem/man/ctSummaryMatrices.Rd |only ctsem-3.11.0/ctsem/man/ctTIpredEffects.Rd |only ctsem-3.11.0/ctsem/man/ctsem-package.Rd | 106 - ctsem-3.11.0/ctsem/man/ctstantestdat.Rd | 22 ctsem-3.11.0/ctsem/man/plot.ctStanFit.Rd | 90 - ctsem-3.11.0/ctsem/man/stan_unconstrainsamples.Rd | 92 - ctsem-3.11.0/ctsem/man/stanoptimis.Rd | 219 +- ctsem-3.11.0/ctsem/man/summary.ctEmpiricalBayesFit.Rd |only ctsem-3.11.0/ctsem/man/summary.ctStanFit.Rd | 84 ctsem-3.11.0/ctsem/tests/testthat/ctBinaryBinaryMix.R | 6 ctsem-3.11.0/ctsem/tests/testthat/ctBinaryGaussianMix.R | 6 ctsem-3.11.0/ctsem/tests/testthat/test-bivariatetrait_hmc.R | 25 ctsem-3.11.0/ctsem/tests/testthat/test-bootHessian.R | 4 ctsem-3.11.0/ctsem/tests/testthat/test-bootstrapScoreHessian.R | 14 ctsem-3.11.0/ctsem/tests/testthat/test-corrcheck.R | 38 ctsem-3.11.0/ctsem/tests/testthat/test-ctCoverageCheck.R |only ctsem-3.11.0/ctsem/tests/testthat/test-ctEmpiricalBayesFit.R |only ctsem-3.11.0/ctsem/tests/testthat/test-ctFit-alias.R |only ctsem-3.11.0/ctsem/tests/testthat/test-ctLOO.R | 13 ctsem-3.11.0/ctsem/tests/testthat/test-ctOptimUncertainty.R |only ctsem-3.11.0/ctsem/tests/testthat/test-ctRaschExampleTest.R | 25 ctsem-3.11.0/ctsem/tests/testthat/test-ctStanModel-matrices.R |only ctsem-3.11.0/ctsem/tests/testthat/test-dtVct.R | 10 ctsem-3.11.0/ctsem/tests/testthat/test-fixedvalsunspot.R | 6 ctsem-3.11.0/ctsem/tests/testthat/test-knownFits.R | 17 ctsem-3.11.0/ctsem/tests/testthat/test-nonlinearVlinear.R | 6 ctsem-3.11.0/ctsem/tests/testthat/test-reshaping.R | 3 ctsem-3.11.0/ctsem/tests/testthat/test-stantipred.R | 6 ctsem-3.11.0/ctsem/tests/testthat/test-sunspots.R | 14 ctsem-3.11.0/ctsem/tests/testthat/test-tdeffectvariation_covtest.R | 81 ctsem-3.11.0/ctsem/tests/testthat/test-timevarying.R | 26 ctsem-3.11.0/ctsem/tests/testthat/test-ukfpoptest.R | 34 ctsem-3.11.0/ctsem/tests/testthat/test_behavGenNLcor.R | 2 ctsem-3.11.0/ctsem/vignettes/empirical-bayes-fitting.qmd |only ctsem-3.11.0/ctsem/vignettes/hierarchicalmanual.rnw | 36 139 files changed, 4276 insertions(+), 3103 deletions(-)
Title: Analysis of Interval DAta
Description: Tools for the analysis of interval-valued data, including construction,
visualization, and statistical modeling. The package provides the 'intData' class for
representing interval-valued data, along with functions to aggregate microdata and
to estimate parameters of latent distributions.
Barycenter and covariance matrix estimation is implemented based on the Mallows
distance (Oliveira et al. (2025) <doi:10.48550/arXiv.2407.05105>).
Robust estimation of the symbolic covariance matrix is implemented via the Interval
Minimum Covariance Determinant (IMCD) estimator, enabling outlier detection
based on the robust squared Interval-Mahalanobis distance, as proposed by
Loureiro et al. (2026b) <doi:10.48550/arXiv.2604.26769>.
Explainable outlier detection is supported through Shapley value based decomposition
of the squared robust Interval-Mahalanobis distance, allowing assessment of variable
contributions to outlyingness (Loureiro et al. (2026a) <doi:10.48550/arXiv.2606.26307> [...truncated...]
Author: Catarina P. Loureiro [aut, cre]
Maintainer: Catarina P. Loureiro <catarinapadrela@tecnico.ulisboa.pt>
Diff between AIDA versions 0.1.5 dated 2026-05-12 and 0.2.0 dated 2026-06-30
AIDA-0.1.5/AIDA/R/evaluation_metrics.r |only AIDA-0.1.5/AIDA/man/KL_divergence.Rd |only AIDA-0.1.5/AIDA/man/SYMB.biplot.Rd |only AIDA-0.1.5/AIDA/man/SYMB.pairs.panels.Rd |only AIDA-0.1.5/AIDA/man/angle_error.Rd |only AIDA-0.1.5/AIDA/man/figures/unnamed-chunk-2-1.png |only AIDA-0.1.5/AIDA/man/frobenius_error.Rd |only AIDA-0.2.0/AIDA/DESCRIPTION | 36 + AIDA-0.2.0/AIDA/MD5 | 196 ++++++---- AIDA-0.2.0/AIDA/NAMESPACE | 65 ++- AIDA-0.2.0/AIDA/NEWS.md | 17 AIDA-0.2.0/AIDA/R/IMCD.r | 63 ++- AIDA-0.2.0/AIDA/R/Shapley.r |only AIDA-0.2.0/AIDA/R/data.r | 18 AIDA-0.2.0/AIDA/R/farness.r | 21 - AIDA-0.2.0/AIDA/R/intData_class.r | 329 +++++++++--------- AIDA-0.2.0/AIDA/R/intData_utils.r | 200 ++++++---- AIDA-0.2.0/AIDA/R/int_cov.r | 149 ++++++-- AIDA-0.2.0/AIDA/R/int_distances.r | 149 ++++---- AIDA-0.2.0/AIDA/R/int_outliers.r | 20 - AIDA-0.2.0/AIDA/R/micro2intData.r | 96 ++--- AIDA-0.2.0/AIDA/R/plots.r | 211 +++++++---- AIDA-0.2.0/AIDA/R/plots_Shapley.r |only AIDA-0.2.0/AIDA/README.md |only AIDA-0.2.0/AIDA/build/vignette.rds |binary AIDA-0.2.0/AIDA/inst/CITATION | 6 AIDA-0.2.0/AIDA/inst/WORDLIST | 24 - AIDA-0.2.0/AIDA/inst/doc/IMCD_examples.R | 8 AIDA-0.2.0/AIDA/inst/doc/IMCD_examples.Rmd | 8 AIDA-0.2.0/AIDA/inst/doc/IMCD_examples.html | 4 AIDA-0.2.0/AIDA/inst/doc/Shapley_examples.R |only AIDA-0.2.0/AIDA/inst/doc/Shapley_examples.Rmd |only AIDA-0.2.0/AIDA/inst/doc/Shapley_examples.html |only AIDA-0.2.0/AIDA/inst/doc/intData_examples.R | 2 AIDA-0.2.0/AIDA/inst/doc/intData_examples.Rmd | 6 AIDA-0.2.0/AIDA/inst/doc/intData_examples.html | 17 AIDA-0.2.0/AIDA/man/Centers.Rd | 6 AIDA-0.2.0/AIDA/man/IMCD.Rd | 8 AIDA-0.2.0/AIDA/man/IMah_dist.Rd | 40 +- AIDA-0.2.0/AIDA/man/IMah_dist_pairs.Rd | 29 - AIDA-0.2.0/AIDA/man/LatentCase.Rd | 6 AIDA-0.2.0/AIDA/man/LatentDist.Rd | 6 AIDA-0.2.0/AIDA/man/LatentParam.Rd | 6 AIDA-0.2.0/AIDA/man/LogRanges.Rd | 6 AIDA-0.2.0/AIDA/man/LowerBounds.Rd | 6 AIDA-0.2.0/AIDA/man/Mallows_dist.Rd | 16 AIDA-0.2.0/AIDA/man/NbMicroUnits.Rd | 6 AIDA-0.2.0/AIDA/man/Ranges.Rd | 6 AIDA-0.2.0/AIDA/man/S4-Extract-methods.Rd | 9 AIDA-0.2.0/AIDA/man/UpperBounds.Rd | 6 AIDA-0.2.0/AIDA/man/bigIMCD.Rd | 2 AIDA-0.2.0/AIDA/man/c_step.Rd | 2 AIDA-0.2.0/AIDA/man/cal.E.UU.Rd | 6 AIDA-0.2.0/AIDA/man/colnames.Rd | 6 AIDA-0.2.0/AIDA/man/comparison-methods.Rd | 18 AIDA-0.2.0/AIDA/man/creditcard.Rd | 4 AIDA-0.2.0/AIDA/man/dim.Rd | 6 AIDA-0.2.0/AIDA/man/draw_z.Rd | 2 AIDA-0.2.0/AIDA/man/entrecampos_air_quality.Rd | 2 AIDA-0.2.0/AIDA/man/farness.Rd | 5 AIDA-0.2.0/AIDA/man/figures/README-iris_example-1.png |only AIDA-0.2.0/AIDA/man/get_latent_param.Rd | 31 + AIDA-0.2.0/AIDA/man/get_latent_var.Rd | 21 - AIDA-0.2.0/AIDA/man/head.Rd | 8 AIDA-0.2.0/AIDA/man/intCars.Rd | 6 AIDA-0.2.0/AIDA/man/intData-class.Rd | 8 AIDA-0.2.0/AIDA/man/intData.Rd | 37 +- AIDA-0.2.0/AIDA/man/int_Shapley.Rd |only AIDA-0.2.0/AIDA/man/int_Shapley_decomp.Rd |only AIDA-0.2.0/AIDA/man/int_Shapley_interaction.Rd |only AIDA-0.2.0/AIDA/man/int_cov.Rd | 19 - AIDA-0.2.0/AIDA/man/int_cov_z.Rd | 24 - AIDA-0.2.0/AIDA/man/int_mean_z.Rd | 3 AIDA-0.2.0/AIDA/man/int_outliers.Rd | 11 AIDA-0.2.0/AIDA/man/meanU.Rd | 2 AIDA-0.2.0/AIDA/man/meanU2.Rd | 2 AIDA-0.2.0/AIDA/man/micro2intData.Rd | 28 - AIDA-0.2.0/AIDA/man/names.Rd | 6 AIDA-0.2.0/AIDA/man/ncol.Rd | 6 AIDA-0.2.0/AIDA/man/nrow.Rd | 6 AIDA-0.2.0/AIDA/man/pick10.Rd | 2 AIDA-0.2.0/AIDA/man/plot.Rd | 14 AIDA-0.2.0/AIDA/man/plot_bar_int_Shapley.Rd |only AIDA-0.2.0/AIDA/man/plot_bar_int_Shapley_decomp.Rd |only AIDA-0.2.0/AIDA/man/plot_beeswarm_int_Shapley.Rd |only AIDA-0.2.0/AIDA/man/plot_dist_dist.Rd | 45 +- AIDA-0.2.0/AIDA/man/plot_int_Shapley_inter.Rd |only AIDA-0.2.0/AIDA/man/plot_interval_dist.Rd | 22 - AIDA-0.2.0/AIDA/man/plot_pairs_int.Rd |only AIDA-0.2.0/AIDA/man/plot_radar_int_Shapley.Rd |only AIDA-0.2.0/AIDA/man/plot_scatter_int.Rd |only AIDA-0.2.0/AIDA/man/plot_tile_int_Shapley.Rd |only AIDA-0.2.0/AIDA/man/print.Rd | 4 AIDA-0.2.0/AIDA/man/rbind.Rd |only AIDA-0.2.0/AIDA/man/row.names.Rd | 6 AIDA-0.2.0/AIDA/man/rownames.Rd | 6 AIDA-0.2.0/AIDA/man/safe_solve_cov.Rd |only AIDA-0.2.0/AIDA/man/show.Rd | 6 AIDA-0.2.0/AIDA/man/smallIMCD.Rd | 2 AIDA-0.2.0/AIDA/man/spotify_tracks.Rd | 6 AIDA-0.2.0/AIDA/man/step_it.Rd | 4 AIDA-0.2.0/AIDA/man/summary.Rd | 6 AIDA-0.2.0/AIDA/man/tail.Rd | 8 AIDA-0.2.0/AIDA/tests |only AIDA-0.2.0/AIDA/vignettes/IMCD_examples.Rmd | 8 AIDA-0.2.0/AIDA/vignettes/Shapley_examples.Rmd |only AIDA-0.2.0/AIDA/vignettes/intData_examples.Rmd | 6 AIDA-0.2.0/AIDA/vignettes/references.bib | 9 108 files changed, 1323 insertions(+), 903 deletions(-)
Title: Taxa Waterbeheer Nederland voor R
Description: The TWN-list (Taxa Waterbeheer Nederland) is the Dutch standard for naming
taxons in Dutch Watermanagement. This package makes it easier to use the
TWN-list for ecological analyses. It consists of two parts. First it makes the
TWN-list itself available in R. Second, it has a few functions that make it
easy to perform some basic and often recurring tasks for checking and consulting
taxonomic data from the TWN-list.
Author: Johan van Tent [aut, cre]
Maintainer: Johan van Tent <tentvanjohan@hotmail.com>
Diff between twn versions 0.2.6 dated 2025-09-26 and 0.2.7 dated 2026-06-30
DESCRIPTION | 10 - MD5 | 22 +- NEWS.md | 2 R/sysdata.rda |binary README.md | 8 build/vignette.rds |binary data/twn_lijst.rda |binary data/twn_literatuur.rda |binary data/twn_statuscodes.rda |binary data/twn_taxonlevels.rda |binary inst/doc/krw_beoordeling.html | 385 +++++++++++++++++++++--------------------- man/twn.Rd | 5 12 files changed, 220 insertions(+), 212 deletions(-)
More information about TemporalModelR at CRAN
Permanent link
Title: Data Package for 'pathfindR'
Description: This is a data-only package, containing data needed to run the CRAN
package 'pathfindR', a package for enrichment analysis utilizing active
subnetworks. This package contains protein-protein interaction network data,
data related to gene sets and example input/output data.
Author: Ege Ulgen [cre, cph] ,
Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR.data versions 2.1.0 dated 2024-04-27 and 2.2.0 dated 2026-06-30
DESCRIPTION | 12 ++-- MD5 | 80 ++++++++++++++-------------- NEWS.md | 14 ++++ R/data.R | 70 ++++++++++++------------ R/sysdata.rda |binary data/biocarta_descriptions.rda |binary data/biocarta_genes.rda |binary data/cell_markers_descriptions.rda |binary data/cell_markers_gsets.rda |binary data/example_active_snws.rda |binary data/example_comparison_output.rda |binary data/example_custom_genesets_result.rda |binary data/example_mmu_output.rda |binary data/example_pathfindR_output.rda |binary data/example_pathfindR_output_clustered.rda |binary data/go_all_genes.rda |binary data/kegg_descriptions.rda |binary data/kegg_genes.rda |binary data/mmu_kegg_descriptions.rda |binary data/mmu_kegg_genes.rda |binary data/pathfindR.data_updates.rda |binary data/reactome_descriptions.rda |binary data/reactome_genes.rda |binary man/biocarta_descriptions.Rd | 2 man/biocarta_genes.Rd | 2 man/cell_markers_descriptions.Rd | 4 - man/cell_markers_gsets.Rd | 4 - man/example_active_snws.Rd | 10 +-- man/example_comparison_output.Rd | 4 - man/example_custom_genesets_result.Rd | 2 man/example_mmu_output.Rd | 4 - man/example_pathfindR_output.Rd | 4 - man/example_pathfindR_output_clustered.Rd | 4 - man/go_all_genes.Rd | 4 - man/kegg_descriptions.Rd | 4 - man/kegg_genes.Rd | 4 - man/mmu_kegg_descriptions.Rd | 4 - man/mmu_kegg_genes.Rd | 4 - man/pathfindR.data_updates.Rd | 2 man/reactome_descriptions.Rd | 4 - man/reactome_genes.Rd | 4 - 41 files changed, 130 insertions(+), 116 deletions(-)
More information about pathfindR.data at CRAN
Permanent link
Title: Multiple Imputation for Multivariate Panel or Clustered Data
Description: It provides functions and examples for maximum likelihood estimation for
generalized linear mixed models and Gibbs sampler for multivariate linear
mixed models with incomplete data, as described in Schafer JL (1997)
"Imputation of missing covariates under a multivariate linear mixed model".
Technical report 97-04, Dept. of Statistics, The Pennsylvania State University.
Author: Original by Joseph L. Schafer [aut],
Jing hua Zhao [cre]
Maintainer: Jing hua Zhao <jinghuazhao@hotmail.com>
Diff between pan versions 1.9 dated 2023-08-21 and 2.0 dated 2026-06-30
pan-1.9/pan/inst/doc/pan-tr.Rnw |only pan-1.9/pan/inst/doc/pan-tr.pdf |only pan-1.9/pan/vignettes/pan-tr.Rnw |only pan-2.0/pan/ChangeLog | 9 ++++++++- pan-2.0/pan/DESCRIPTION | 18 +++++++++++++----- pan-2.0/pan/MD5 | 12 ++++++------ pan-2.0/pan/build/vignette.rds |binary pan-2.0/pan/inst/doc/pan.Rnw |only pan-2.0/pan/inst/doc/pan.pdf |only pan-2.0/pan/vignettes/pan.Rnw |only 10 files changed, 27 insertions(+), 12 deletions(-)
Title: 'shiny' Applications for the 'tesselle' Packages
Description: A collection of 'shiny' applications for the 'tesselle'
packages <https://www.tesselle.org/>. This package provides
applications for archaeological data analysis and visualization. These
mainly, but not exclusively, include applications for chronological
modelling (e.g. matrix seriation, aoristic analysis) and count data
analysis (e.g. diversity measures, compositional data analysis).
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between kinesis versions 0.4.0 dated 2026-06-18 and 0.5.0 dated 2026-06-30
DESCRIPTION | 14 +- MD5 | 69 +++++----- NAMESPACE | 3 NEWS.md | 9 + R/calibrate.R | 57 +++++---- R/coda.R | 46 +++++++ R/kinesis-internal.R | 34 +++-- R/kinesis-package.R | 2 R/lm.R | 135 +++++++++++++++++---- R/multivariate.R | 10 - R/plot.R | 35 +++-- R/scatter.R | 31 +++- R/variables.R | 6 README.md | 2 build/partial.rdb |binary inst/app/source/ui.R | 22 --- inst/po/fr/LC_MESSAGES/R-kinesis.mo |binary man/coda_barplot_server.Rd | 1 man/coda_barplot_ui.Rd | 1 man/coda_hclust_server.Rd | 1 man/coda_hclust_ui.Rd | 1 man/coda_hist_server.Rd | 1 man/coda_hist_ui.Rd | 1 man/coda_nav.Rd |only man/coda_outliers_server.Rd | 1 man/coda_outliers_ui.Rd | 1 man/coda_server.Rd | 1 man/coda_summary_server.Rd | 1 man/coda_summary_ui.Rd | 1 man/coda_ui.Rd | 1 man/kinesis-package.Rd | 2 man/logratio_server.Rd | 1 man/logratio_ui.Rd | 1 man/update_input.Rd | 6 po/R-fr.po | 226 ++++++++++++++++++------------------ po/R-kinesis.pot | 210 +++++++++++++++++---------------- 36 files changed, 571 insertions(+), 362 deletions(-)
Title: Estimation in Staggered First Switch Designs, where Groups
Experience their First Treatment Change at Different Points in
Time
Description: Estimation of heterogeneity-robust difference-in-differences estimators, with a binary, discrete, or continuous treatment, in designs where past treatments may affect the current outcome.
Author: Anzony Quispe [aut, cre],
Diego Ciccia [aut],
Felix Knau [aut],
Melitine Malezieux [aut],
Doulo Sow [aut],
Clement de Chaisemartin [aut]
Maintainer: Anzony Quispe <anzony.quispe@gmail.com>
Diff between DIDmultiplegtDYN versions 2.3.4 dated 2026-05-26 and 2.4.0 dated 2026-06-30
DESCRIPTION | 35 ++-- MD5 | 22 +- NAMESPACE | 3 R/RcppExports.R | 8 R/did_multiplegt_avg_cumul.R |only R/did_multiplegt_bootstrap.R | 1 R/did_multiplegt_dyn.R | 354 ++++++++++++++++++++++++++----------------- R/did_multiplegt_main.R | 1 R/did_multiplegt_reset.R |only R/globals.R | 5 man/did_multiplegt_dyn.Rd | 128 ++++++++------- src/RcppExports.cpp | 46 +++++ src/did_loops.cpp | 253 ++++++++++++++++++++++++++++++ 13 files changed, 633 insertions(+), 223 deletions(-)
More information about DIDmultiplegtDYN at CRAN
Permanent link
Title: Arbitrary Dimensional Clifford Algebras
Description: A suite of routines for Clifford algebras, using the
'Map' class of the Standard Template Library. Canonical
reference: Hestenes (1987, ISBN 90-277-1673-0, "Clifford algebra
to geometric calculus"). Special cases including Lorentz transforms,
quaternion multiplication, and Grassmann algebra, are discussed.
Vignettes presenting conformal geometric algebra, quaternions and
split quaternions, dual numbers, and Lorentz transforms are
included. The package follows 'disordR' discipline.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between clifford versions 1.1-3 dated 2025-11-10 and 1.2-0 dated 2026-06-30
DESCRIPTION | 6 - MD5 | 76 +++++++++++++++++------- NEWS.md | 8 ++ R/clifford.R | 48 ++++++++++----- build/partial.rdb |binary build/vignette.rds |binary data/dot.rda |binary inst/doc/clifford.R | 2 inst/doc/clifford.pdf |binary inst/doc/complex_clifford.html | 5 - inst/doc/conformal_algebra_clifford.html | 5 - inst/doc/cramer_clifford.R |only inst/doc/cramer_clifford.Rmd |only inst/doc/cramer_clifford.html |only inst/doc/determinants_clifford.R |only inst/doc/determinants_clifford.Rmd |only inst/doc/determinants_clifford.html |only inst/doc/dual_quaternion_clifford.R |only inst/doc/dual_quaternion_clifford.Rmd |only inst/doc/dual_quaternion_clifford.html |only inst/doc/getcoeffs.R |only inst/doc/getcoeffs.Rmd |only inst/doc/getcoeffs.html |only inst/doc/lorentz_clifford.R |only inst/doc/lorentz_clifford.Rmd |only inst/doc/lorentz_clifford.html |only inst/doc/pauli_clifford.R |only inst/doc/pauli_clifford.Rmd |only inst/doc/pauli_clifford.html |only inst/doc/pseudoscalar.R |only inst/doc/pseudoscalar.Rmd |only inst/doc/pseudoscalar.html |only inst/doc/quaternion_clifford.R |only inst/doc/quaternion_clifford.Rmd |only inst/doc/quaternion_clifford.html |only inst/doc/signature.R | 22 +++---- inst/doc/signature.html | 8 +- man/homog.Rd | 13 ++-- man/involution.Rd | 32 +++++----- man/magnitude.Rd | 25 +++++--- man/minus.Rd | 24 ++++--- man/rcliff.Rd | 5 + man/signature.Rd | 5 - man/term.Rd | 51 +++++++++------- src/clifford.h | 96 +++++++++++++++++-------------- tests/testthat/test_aal.R |only tests/testthat/test_aam.R |only vignettes/clifford.bib | 12 +-- vignettes/cramer_clifford.Rmd |only vignettes/determinants_clifford.Rmd |only vignettes/dual_quaternion_clifford.Rmd |only vignettes/getcoeffs.Rmd |only vignettes/lorentz_clifford.Rmd |only vignettes/pauli_clifford.Rmd |only vignettes/pseudoscalar.Rmd |only vignettes/quaternion_clifford.Rmd |only 56 files changed, 267 insertions(+), 176 deletions(-)
Title: Stochastic Data Envelopment Analysis
Description: Set of functions for Stochastic Data Envelopment Analysis. Chance constrained versions of radial, directional and additive DEA models are implemented, as long as super-efficiency models. See: Cooper, W.W.; Deng, H.; Huang, Z.; Li, S.X. (2002). <doi:10.1057/palgrave.jors.2601433>, Bolós, V.J.; Benítez, R.; Coll-Serrano, V. (2024) <doi:10.1016/j.orp.2024.100307>.
Author: Vicente Bolos [aut, cre],
Vicente Coll-Serrano [aut],
Rafael Benitez Suarez [aut]
Maintainer: Vicente Bolos <vicente.bolos@uv.es>
Diff between SdeaR versions 1.1.0 dated 2026-06-11 and 1.1.1 dated 2026-06-30
DESCRIPTION | 8 ++-- MD5 | 36 +++++++++--------- R/make_deadata_stoch.R | 76 ++++++++++++++++++++++++-------------- R/modelstoch_additive.R | 75 ++++++++++++++++++++++++++----------- R/modelstoch_additive_p.R | 73 ++++++++++++++++++++++++++---------- R/modelstoch_addsupereff.R | 49 +++++++++++++++++++++--- R/modelstoch_dir.R | 73 ++++++++++++++++++++++++++---------- R/modelstoch_dir_dd.R | 73 ++++++++++++++++++++++++++---------- R/modelstoch_radial.R | 73 ++++++++++++++++++++++++++---------- R/modelstoch_radial_supereff.R | 4 +- build/partial.rdb |binary man/make_deadata_stoch.Rd | 76 ++++++++++++++++++++++++-------------- man/modelstoch_additive.Rd | 25 ++++++++---- man/modelstoch_additive_p.Rd | 23 ++++++++--- man/modelstoch_addsupereff.Rd | 15 +++++-- man/modelstoch_dir.Rd | 23 ++++++++--- man/modelstoch_dir_dd.Rd | 23 ++++++++--- man/modelstoch_radial.Rd | 23 ++++++++--- man/modelstoch_radial_supereff.Rd | 4 +- 19 files changed, 517 insertions(+), 235 deletions(-)
Title: Import, Inspect, Analyse, and Report Gazepoint GP3 Exports
Description: Imports, inspects, cleans, summarises, models, and reports
Gazepoint GP3 and Gazepoint Analysis CSV exports. Supports offline
workflows for all-gaze, fixation, pupil, area-of-interest, transition,
time-course, quality-audit, and manuscript-reporting analyses.
Author: Stefanos Balaskas [aut, cre]
Maintainer: Stefanos Balaskas <s.balaskas@ac.upatras.gr>
Diff between gp3tools versions 1.0.1 dated 2026-06-29 and 1.0.2 dated 2026-06-30
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test-fit_gazepoint_gca.R | 7 ++++++- 4 files changed, 16 insertions(+), 7 deletions(-)
Title: Core Utilities for the 'rtemis' Ecosystem
Description: Utilities used across packages of the 'rtemis' ecosystem. Includes the msg()
messaging system and the fmt() formatting system. Provides a library of 'S7' properties,
test_* functions that return logical values, check_* functions that throw informative errors,
and clean_* functions that return validated and coerced values. This code began as part of the
'rtemis' package (<doi:10.32614/CRAN.package.rtemis>).
Author: E.D. Gennatas [aut, cre, cph]
Maintainer: E.D. Gennatas <gennatas@gmail.com>
Diff between rtemis.core versions 0.1.0 dated 2026-05-09 and 0.3.1 dated 2026-06-30
DESCRIPTION | 10 MD5 | 70 +++- NAMESPACE | 30 +- NEWS.md | 68 ++++ R/00_S7_properties.R | 5 R/check.R | 604 +++++++++++++++++++++++++++++++++++------ R/clean.R | 28 + R/core-package.R | 1 R/fmt.R | 61 +++- R/log.R |only R/msg.R | 283 +++++++++++++++++-- R/rtemis_color_system.R | 21 + R/test.R | 2 R/utils_print.R | 156 +++++++--- R/utils_strings.R | 95 +++++- man/abort.Rd |only man/bold.Rd | 8 man/catsize.Rd |only man/check_file_exists.Rd |only man/check_numeric.Rd |only man/collapse_head.Rd |only man/datetime.Rd |only man/dbg.Rd |only man/fmt.Rd | 3 man/fn2label.Rd |only man/format_trace.Rd |only man/get_msg_sink.Rd |only man/get_verbosity.Rd |only man/gray.Rd |only man/highlightbig.Rd |only man/info.Rd |only man/italic.Rd |only man/nay.Rd |only man/objcat.Rd |only man/oxfordcomma.Rd |only man/pad_string.Rd |only man/printls.Rd | 2 man/red.Rd |only man/repr_ls.Rd | 2 man/set_msg_sink.Rd |only man/show_df.Rd |only man/show_table.Rd |only man/strip_ansi.Rd |only man/success.Rd |only man/thin.Rd |only man/warn.Rd |only man/with_msg_sink.Rd |only man/yay.Rd |only tests/testthat/test-check.R | 30 ++ tests/testthat/test-log.R |only tests/testthat/test-msg_sink.R |only tests/testthat/test-utils.R | 11 52 files changed, 1272 insertions(+), 218 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. (2014) "Node-based analysis of species distributions." Methods in Ecology and Evolution 5(11): 1225-1235. <doi:10.1111/2041-210X.12283>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped.
Author: Michael Krabbe Borregaard [aut, cre]
Maintainer: Michael Krabbe Borregaard <mkborregaard@sund.ku.dk>
This is a re-admission after prior archival of version 1.4.3 dated 2025-09-12
Diff between nodiv versions 1.4.3 dated 2025-09-12 and 1.4.4 dated 2026-06-30
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/Nodesig_function.R | 2 +- R/two_color_map.R | 2 +- man/Nodesig.Rd | 2 +- man/plot_nodes_phylo.Rd | 4 ++++ man/plot_points.Rd | 6 +++++- man/two_color_map.Rd | 2 +- tests/testthat/test_adding.R | 4 ++-- 9 files changed, 28 insertions(+), 20 deletions(-)
Title: Conditional Inference Procedures in a Permutation Test Framework
Description: Conditional inference procedures for the general independence
problem including two-sample, K-sample (non-parametric ANOVA),
correlation, censored, ordered and multivariate problems described
in <doi:10.18637/jss.v028.i08>.
Author: Torsten Hothorn [aut, cre] ,
Henric Winell [aut] ,
Kurt Hornik [aut] ,
Mark A. van de Wiel [aut] ,
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between coin versions 1.4-3 dated 2023-09-27 and 1.4-4 dated 2026-06-30
coin-1.4-3/coin/vignettes/LegoCondInf.bib |only coin-1.4-3/coin/vignettes/coin.bib |only coin-1.4-3/coin/vignettes/references.bib |only coin-1.4-4/coin/DESCRIPTION | 24 coin-1.4-4/coin/MD5 | 190 coin-1.4-4/coin/R/Classes.R | 17 coin-1.4-4/coin/R/CorrelationTests.R | 6 coin-1.4-4/coin/R/ExactDistributions.R | 4 coin-1.4-4/coin/R/InitMethods.R | 6 coin-1.4-4/coin/R/LocationTests.R | 8 coin-1.4-4/coin/R/MarginalHomogeneityTests.R | 5 coin-1.4-4/coin/R/Methods.R | 12 coin-1.4-4/coin/R/Print.R | 13 coin-1.4-4/coin/R/ScaleTests.R | 12 coin-1.4-4/coin/R/SurvivalTests.R | 6 coin-1.4-4/coin/R/SymmetryTests.R | 58 coin-1.4-4/coin/R/Transformations.R | 2 coin-1.4-4/coin/R/helpers.R | 26 coin-1.4-4/coin/R/zAccess.R | 25 coin-1.4-4/coin/build/partial.rdb |binary coin-1.4-4/coin/build/vignette.rds |binary coin-1.4-4/coin/inst/NEWS.Rd | 35 coin-1.4-4/coin/inst/REFERENCES.bib |only coin-1.4-4/coin/inst/doc/Implementation.R | 18 coin-1.4-4/coin/inst/doc/Implementation.Rnw | 14 coin-1.4-4/coin/inst/doc/Implementation.pdf |binary coin-1.4-4/coin/inst/doc/LegoCondInf.R | 12 coin-1.4-4/coin/inst/doc/LegoCondInf.Rnw | 21 coin-1.4-4/coin/inst/doc/LegoCondInf.pdf |binary coin-1.4-4/coin/inst/doc/MAXtest.R | 34 coin-1.4-4/coin/inst/doc/MAXtest.Rnw | 17 coin-1.4-4/coin/inst/doc/MAXtest.pdf |binary coin-1.4-4/coin/inst/doc/coin.R | 12 coin-1.4-4/coin/inst/doc/coin.Rnw | 17 coin-1.4-4/coin/inst/doc/coin.pdf |binary coin-1.4-4/coin/man/CWD.Rd | 35 coin-1.4-4/coin/man/ContingencyTests.Rd | 44 coin-1.4-4/coin/man/CorrelationTests.Rd | 16 coin-1.4-4/coin/man/GTSG.Rd | 24 coin-1.4-4/coin/man/IndependenceTest.Rd | 40 coin-1.4-4/coin/man/LocationTests.Rd | 31 coin-1.4-4/coin/man/MarginalHomogeneityTests.Rd | 69 coin-1.4-4/coin/man/MaximallySelectedStatisticsTests.Rd | 59 coin-1.4-4/coin/man/NullDistribution-methods.Rd | 8 coin-1.4-4/coin/man/NullDistribution.Rd | 45 coin-1.4-4/coin/man/PValue-class.Rd | 6 coin-1.4-4/coin/man/PermutationDistribution-methods.Rd | 6 coin-1.4-4/coin/man/ScaleTests.Rd | 38 coin-1.4-4/coin/man/SurvivalTests.Rd | 145 coin-1.4-4/coin/man/SymmetryTest.Rd | 41 coin-1.4-4/coin/man/SymmetryTests.Rd | 51 coin-1.4-4/coin/man/Transformations.Rd | 6 coin-1.4-4/coin/man/VarCovar-class.Rd | 4 coin-1.4-4/coin/man/alpha.Rd | 19 coin-1.4-4/coin/man/alzheimer.Rd | 16 coin-1.4-4/coin/man/asat.Rd | 21 coin-1.4-4/coin/man/coin-package.Rd | 30 coin-1.4-4/coin/man/glioma.Rd | 10 coin-1.4-4/coin/man/hohnloser.Rd | 14 coin-1.4-4/coin/man/jobsatisfaction.Rd | 14 coin-1.4-4/coin/man/malformations.Rd | 32 coin-1.4-4/coin/man/mercuryfish.Rd | 21 coin-1.4-4/coin/man/neuropathy.Rd | 9 coin-1.4-4/coin/man/ocarcinoma.Rd | 21 coin-1.4-4/coin/man/photocar.Rd | 19 coin-1.4-4/coin/man/pvalue-methods.Rd | 59 coin-1.4-4/coin/man/rotarod.Rd | 11 coin-1.4-4/coin/man/treepipit.Rd | 10 coin-1.4-4/coin/man/vision.Rd | 21 coin-1.4-4/coin/src/Helpers.c | 36 coin-1.4-4/coin/src/StreitbergRoehmel.c | 74 coin-1.4-4/coin/src/coin-init.c | 4 coin-1.4-4/coin/src/coin.h | 12 coin-1.4-4/coin/src/vandeWiel.c | 9 coin-1.4-4/coin/tests/Examples/coin-Ex.Rout.save | 6468 +++++++--------- coin-1.4-4/coin/tests/bugfixes.R | 24 coin-1.4-4/coin/tests/bugfixes.Rout.save | 63 coin-1.4-4/coin/tests/comparisons.Rout.save | 8 coin-1.4-4/coin/tests/regtest_2sample.Rout.save | 8 coin-1.4-4/coin/tests/regtest_Ksample.Rout.save | 8 coin-1.4-4/coin/tests/regtest_MTP.Rout.save | 8 coin-1.4-4/coin/tests/regtest_contingency.Rout.save | 8 coin-1.4-4/coin/tests/regtest_correlation.Rout.save | 8 coin-1.4-4/coin/tests/regtest_distribution.Rout.save | 5608 ++++++------- coin-1.4-4/coin/tests/regtest_helpers.R | 36 coin-1.4-4/coin/tests/regtest_helpers.Rout.save | 1790 ++-- coin-1.4-4/coin/tests/regtest_midpvalue.Rout.save | 1602 +-- coin-1.4-4/coin/tests/regtest_names.Rout.save | 848 +- coin-1.4-4/coin/tests/regtest_size.Rout.save | 476 - coin-1.4-4/coin/tests/regtest_trafo.Rout.save | 2454 +++--- coin-1.4-4/coin/vignettes/Implementation.Rnw | 14 coin-1.4-4/coin/vignettes/Implementation.Rout.save | 737 - coin-1.4-4/coin/vignettes/LegoCondInf.Rnw | 21 coin-1.4-4/coin/vignettes/LegoCondInf.Rout.save | 635 - coin-1.4-4/coin/vignettes/MAXtest.Rnw | 17 coin-1.4-4/coin/vignettes/MAXtest.Rout.save | 521 - coin-1.4-4/coin/vignettes/coin.Rnw | 17 coin-1.4-4/coin/vignettes/coin.Rout.save | 412 - 98 files changed, 11696 insertions(+), 11819 deletions(-)
Title: Visualization and Polytomous Modeling of Survival and Competing
Risks
Description: A publication-ready toolkit for modern survival and competing risks
analysis with a minimal, formula-based interface. Both nonparametric
estimation and direct polytomous regression of cumulative incidence
functions (CIFs) are supported. The main functions 'cifcurve()', 'cifplot()',
and 'cifpanel()' estimate survival and CIF curves and produce high-quality
graphics with risk tables, censoring and competing-risk marks, and
multi-panel or inset layouts built on 'ggplot2' and 'ggsurvfit'. The modeling
function 'polyreg()' performs direct polytomous regression for coherent joint
modeling of all cause-specific CIFs to estimate risk ratios, odds ratios, or
subdistribution hazard ratios at user-specified time points. All core
functions adopt a formula-and-data syntax and return tidy and extensible
outputs that integrate smoothly with 'modelsummary', 'broom', and the broader
'tidyverse' ecosystem. Key numerical routines are implemented in C++ via
'Rcpp'.
Author: Shiro Tanaka [aut, cre, cph] ,
Shigetaka Kobari [ctb],
Chisato Honda [ctb]
Maintainer: Shiro Tanaka <gestimation@gmail.com>
Diff between cifmodeling versions 0.9.8 dated 2026-01-10 and 1.0.0 dated 2026-06-30
DESCRIPTION | 10 MD5 | 63 NAMESPACE | 3 NEWS.md | 232 +- R/binregRatioLOP.R |only R/cif-stat-arguments.R | 61 R/cif-visual-arguments.R | 174 - R/cifcurve.R | 1298 ++++++++---- R/cifflowchart.R |only R/cifpanel.R | 2408 +++++++++++----------- R/cifplot.R | 3606 +++++++++++++++++----------------- R/ciftest.R |only R/polyreg.R | 18 build/stage23.rdb |binary inst/doc/v1_overview.R | 8 inst/doc/v1_overview.Rmd | 35 inst/doc/v1_overview.html | 1317 ++++++++++++ inst/doc/v4_examples.html | 2 inst/doc/v5_gallery.Rmd | 2 inst/doc/v5_gallery.html | 6 inst/doc/v7_arguments.Rmd | 12 inst/doc/v7_arguments.html | 35 man/calculate_A12_logrank_weightit.Rd |only man/cif-stat-arguments.Rd | 3 man/cifcurve.Rd | 50 man/cifflowchart.Rd |only man/cifpanel.Rd | 3 man/cifplot.Rd | 3 man/fd_step_safe.Rd |only man/get_weightit_mparts.Rd |only man/polyreg.Rd | 18 tests/testthat/test-calculateCI.R | 1585 ++++++++++---- tests/testthat/test-cifflowchart.R |only tests/testthat/test-ciftest.R |only vignettes/v1_overview.Rmd | 35 vignettes/v5_gallery.Rmd | 2 vignettes/v7_arguments.Rmd | 12 37 files changed, 6719 insertions(+), 4282 deletions(-)
Title: Maki Cointegration Test with Multiple Structural Breaks
Description: Implements the Maki (2012) <doi:10.1016/j.econmod.2012.04.022>
residual-based test for cointegration allowing for an unknown number of
structural breaks. Breaks are located by a sequential procedure and the
cointegrating residual is tested for a unit root with an augmented
Dickey-Fuller (ADF) regression; the test statistic is the minimum ADF
t-statistic over all candidate breaks. Four model specifications are
supported (level shift, level shift with trend, regime shift, and regime
shift with trend) and one to four regressors. The default engine reproduces
the original 'GAUSS' / 'tspdlib' implementation, with an optional break rule
following Maki (2012, Steps 2 and 4). The test runs for any feasible number
of breaks; beyond the five tabulated by Maki, critical values can be
simulated by his Monte-Carlo design. A two-panel diagnostic plot is provided
via 'ggplot2'.
Author: Merwan Roudane [aut, cre, cph]
Maintainer: Merwan Roudane <merwanroudane920@gmail.com>
Diff between makicoint versions 1.0.0 dated 2025-11-04 and 2.0.0 dated 2026-06-30
makicoint-1.0.0/makicoint/R/breaks_1_2.R |only makicoint-1.0.0/makicoint/R/breaks_3_4_5.R |only makicoint-1.0.0/makicoint/R/helper_functions.R |only makicoint-1.0.0/makicoint/R/main_functions.R |only makicoint-1.0.0/makicoint/man/dftau.Rd |only makicoint-1.0.0/makicoint/man/mbreak1.Rd |only makicoint-1.0.0/makicoint/man/mbreak2.Rd |only makicoint-1.0.0/makicoint/man/mbreak21.Rd |only makicoint-1.0.0/makicoint/man/mbreak22.Rd |only makicoint-1.0.0/makicoint/man/opttlag.Rd |only makicoint-1.0.0/makicoint/man/pf.Rd |only makicoint-1.0.0/makicoint/man/print.maki_test.Rd |only makicoint-2.0.0/makicoint/DESCRIPTION | 41 + makicoint-2.0.0/makicoint/MD5 | 42 - makicoint-2.0.0/makicoint/NAMESPACE | 2 makicoint-2.0.0/makicoint/NEWS.md | 56 +- makicoint-2.0.0/makicoint/R/coint_maki.R |only makicoint-2.0.0/makicoint/R/engine.R |only makicoint-2.0.0/makicoint/R/zzz.R |only makicoint-2.0.0/makicoint/README.md | 148 +----- makicoint-2.0.0/makicoint/build/partial.rdb |only makicoint-2.0.0/makicoint/build/vignette.rds |binary makicoint-2.0.0/makicoint/inst/CITATION |only makicoint-2.0.0/makicoint/inst/doc/introduction.R | 123 +---- makicoint-2.0.0/makicoint/inst/doc/introduction.Rmd | 224 ++------- makicoint-2.0.0/makicoint/inst/doc/introduction.html | 433 +++++-------------- makicoint-2.0.0/makicoint/man/coint_maki.Rd | 133 +++-- makicoint-2.0.0/makicoint/man/cv_coint_maki.Rd | 37 - makicoint-2.0.0/makicoint/man/plot.maki_test.Rd |only makicoint-2.0.0/makicoint/tests/testthat/test-maki.R | 181 ++----- makicoint-2.0.0/makicoint/vignettes/introduction.Rmd | 224 ++------- 31 files changed, 580 insertions(+), 1064 deletions(-)
Title: Flexible and Robust GARCH-X Modelling
Description: Flexible and robust estimation and inference of Generalised Autoregressive Conditional Heteroscedasticity (GARCH) models with covariates ('X') based on the results by Francq and Thieu (2019) <doi:10.1017/S0266466617000512>. Coefficients can straightforwardly be set to zero by omission, and quasi maximum likelihood methods ensure estimates are generally consistent and inference valid, even when the standardised innovations are non-normal and/or dependent over time. See Sucarrat (2021) <doi:10.32614/RJ-2021-057> for an overview of the package.
Author: Genaro Sucarrat [aut, cre]
Maintainer: Genaro Sucarrat <gsucarrat@gmail.com>
Diff between garchx versions 1.6 dated 2025-07-09 and 1.7 dated 2026-06-30
DESCRIPTION | 10 +- MD5 | 18 +-- NEWS | 16 +++ R/garchx-internal.R | 4 R/garchx-source-code.R | 237 ++++++++++++++++++++++++++++++++----------------- build/partial.rdb |binary man/coef.garchx.Rd | 5 - man/garchx-package.Rd | 4 man/garchx.Rd | 8 + man/ttest0.Rd | 4 10 files changed, 199 insertions(+), 107 deletions(-)
Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] ,
Edward Burn [aut] ,
Theresa Burkard [aut] ,
Yuchen Guo [ctb] ,
Marti Catala [ctb] ,
Mike Du [ctb] ,
Xintong Li [ctb] ,
Ross Williams [ctb] ,
Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between DrugExposureDiagnostics versions 1.1.8 dated 2026-06-19 and 1.1.9 dated 2026-06-30
DESCRIPTION | 6 ++--- MD5 | 22 ++++++++++---------- NEWS.md | 4 +++ R/executeChecks.R | 13 ++++++++++- R/obscureCounts.R | 10 ++++++++- inst/doc/DrugSig.html | 2 - inst/doc/IntroductionToDrugExposureDiagnostics.html | 6 ++--- inst/doc/VerbatimEndDate.html | 2 - man/executeChecks.Rd | 10 ++++++++- tests/testthat/test-ObscureCounts.R | 21 +++++++++++++++++++ tests/testthat/test-SyntheaSqlServer.R | 5 ++-- tests/testthat/test-executeChecks.R | 16 ++++++++++++++ 12 files changed, 92 insertions(+), 25 deletions(-)
More information about DrugExposureDiagnostics at CRAN
Permanent link
Title: CRAN Task Views
Description: Infrastructure for task views to CRAN-style repositories: Querying task views and installing the associated
packages (client-side tools), generating HTML pages and storing task view information in the repository
(server-side tools).
Author: Achim Zeileis [aut, cre] ,
Kurt Hornik [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between ctv versions 0.9-8 dated 2026-04-15 and 1.0-0 dated 2026-06-30
ctv-0.9-8/ctv/tests |only ctv-1.0-0/ctv/DESCRIPTION | 11 +-- ctv-1.0-0/ctv/MD5 | 17 ++--- ctv-1.0-0/ctv/NEWS.md | 18 +++++ ctv-1.0-0/ctv/R/ctv-client.R | 2 ctv-1.0-0/ctv/README.md | 34 ++++++++-- ctv-1.0-0/ctv/build/vignette.rds |binary ctv-1.0-0/ctv/inst/doc/ctv-howto.Rmd | 15 ++-- ctv-1.0-0/ctv/inst/doc/ctv-howto.html | 115 +++++++++++++++++++++++++++++----- ctv-1.0-0/ctv/vignettes/ctv-howto.Rmd | 15 ++-- 10 files changed, 180 insertions(+), 47 deletions(-)
Title: Struct-Like Data Type Checking and Enforcement
Description: Enforcement of field types in lists. A drop-in tool to allow for
dynamic input data that might be questionably parsed or cast to be coerced
into the specific desired format in a reasonably performant manner.
Author: Samuel Sapire [aut, cre, cph],
Sean Barrett [ctb]
Maintainer: Samuel Sapire <sapires@protonmail.com>
Diff between structenforcement versions 0.2.0 dated 2026-04-07 and 0.3.0 dated 2026-06-30
structenforcement-0.2.0/structenforcement/R/utils.R |only structenforcement-0.3.0/structenforcement/DESCRIPTION | 10 structenforcement-0.3.0/structenforcement/MD5 | 24 structenforcement-0.3.0/structenforcement/NAMESPACE | 1 structenforcement-0.3.0/structenforcement/NEWS.md | 6 structenforcement-0.3.0/structenforcement/R/type_check.R | 129 +- structenforcement-0.3.0/structenforcement/man/bind_as_struct.Rd | 7 structenforcement-0.3.0/structenforcement/man/type_check_each.Rd |only structenforcement-0.3.0/structenforcement/src/functions.c | 605 ++++++++-- structenforcement-0.3.0/structenforcement/src/functions.h | 11 structenforcement-0.3.0/structenforcement/src/registration.c | 2 structenforcement-0.3.0/structenforcement/tests/testthat/helper-fixtures.R |only structenforcement-0.3.0/structenforcement/tests/testthat/test-joining.R | 292 +++- structenforcement-0.3.0/structenforcement/tests/testthat/test-type_check.R | 386 +++--- structenforcement-0.3.0/structenforcement/tests/testthat/test-type_check_each.R |only 15 files changed, 1072 insertions(+), 401 deletions(-)
More information about structenforcement at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-06-18 0.1.2
2025-01-22 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-24 0.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-06-15 0.6.0
2025-10-17 0.5.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-29 0.2.0
2025-02-27 0.1.0