Title: Visualise OMOP Results using 'shiny' Applications
Description: Visualise results obtained from analysing data mapped to the
Observational Medical Outcomes Partnership (OMOP) common data model using
'shiny' applications.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Edward Burn [ctb] ,
Nuria Mercade-Besora [ctb] ,
Elin Rowlands [ctb] ,
Cecilia Campanile [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between OmopViewer versions 0.3.0 dated 2025-04-15 and 0.4.0 dated 2025-07-08
OmopViewer-0.3.0/OmopViewer/inst/doc/configured_panels.R |only OmopViewer-0.3.0/OmopViewer/inst/doc/configured_panels.Rmd |only OmopViewer-0.3.0/OmopViewer/inst/doc/configured_panels.html |only OmopViewer-0.3.0/OmopViewer/vignettes/configured_panels.Rmd |only OmopViewer-0.4.0/OmopViewer/DESCRIPTION | 36 OmopViewer-0.4.0/OmopViewer/MD5 | 84 - OmopViewer-0.4.0/OmopViewer/NAMESPACE | 1 OmopViewer-0.4.0/OmopViewer/R/appDynamic.R | 37 OmopViewer-0.4.0/OmopViewer/R/appStatic.R | 36 OmopViewer-0.4.0/OmopViewer/R/background.R | 2 OmopViewer-0.4.0/OmopViewer/R/buttons.R | 68 + OmopViewer-0.4.0/OmopViewer/R/classes.R | 23 OmopViewer-0.4.0/OmopViewer/R/createServer.R | 74 + OmopViewer-0.4.0/OmopViewer/R/createUi.R | 25 OmopViewer-0.4.0/OmopViewer/R/defaultPanels.R | 30 OmopViewer-0.4.0/OmopViewer/R/functions.R | 267 +---- OmopViewer-0.4.0/OmopViewer/R/omopViewer-package.R | 1 OmopViewer-0.4.0/OmopViewer/R/populatePanelDetailsOptions.R | 34 OmopViewer-0.4.0/OmopViewer/R/sysdata.rda |binary OmopViewer-0.4.0/OmopViewer/R/utilities.R | 3 OmopViewer-0.4.0/OmopViewer/build/vignette.rds |binary OmopViewer-0.4.0/OmopViewer/data/omopViewerPanels.rda |binary OmopViewer-0.4.0/OmopViewer/data/omopViewerResults.rda |binary OmopViewer-0.4.0/OmopViewer/inst/doc/dynamic_app.R |only OmopViewer-0.4.0/OmopViewer/inst/doc/dynamic_app.Rmd |only OmopViewer-0.4.0/OmopViewer/inst/doc/dynamic_app.html |only OmopViewer-0.4.0/OmopViewer/inst/doc/edit_static_content.R | 51 + OmopViewer-0.4.0/OmopViewer/inst/doc/edit_static_content.Rmd | 95 + OmopViewer-0.4.0/OmopViewer/inst/doc/edit_static_content.html | 97 +- OmopViewer-0.4.0/OmopViewer/inst/doc/export_static_app.R | 38 OmopViewer-0.4.0/OmopViewer/inst/doc/export_static_app.Rmd | 106 ++ OmopViewer-0.4.0/OmopViewer/inst/doc/export_static_app.html | 477 ++++++++-- OmopViewer-0.4.0/OmopViewer/inst/functions.R | 262 ----- OmopViewer-0.4.0/OmopViewer/man/exportStaticApp.Rd | 17 OmopViewer-0.4.0/OmopViewer/man/figures |only OmopViewer-0.4.0/OmopViewer/man/getPanel.Rd | 2 OmopViewer-0.4.0/OmopViewer/man/launchDynamicApp.Rd | 2 OmopViewer-0.4.0/OmopViewer/man/omopViewerPanels.Rd | 8 OmopViewer-0.4.0/OmopViewer/man/omopViewerResults.Rd | 10 OmopViewer-0.4.0/OmopViewer/man/panelDetailsFromResult.Rd | 8 OmopViewer-0.4.0/OmopViewer/tests/testthat/test-appStatic.R | 4 OmopViewer-0.4.0/OmopViewer/tests/testthat/test-background.R | 2 OmopViewer-0.4.0/OmopViewer/tests/testthat/test-choices.R | 79 + OmopViewer-0.4.0/OmopViewer/vignettes/dynamic_app.Rmd |only OmopViewer-0.4.0/OmopViewer/vignettes/edit_static_content.Rmd | 95 + OmopViewer-0.4.0/OmopViewer/vignettes/export_static_app.Rmd | 106 ++ 46 files changed, 1466 insertions(+), 714 deletions(-)
Title: Bayesian Longitudinal Regularized Quantile Mixed Model
Description: With high-dimensional omics features, repeated measure ANOVA leads to longitudinal gene-environment interaction studies that have intra-cluster correlations, outlying observations and structured sparsity arising from the ANOVA design. In this package, we have developed robust sparse Bayesian mixed effect models tailored for the above studies (Fan et al. (2025) <doi:10.1093/jrsssc/qlaf027>). An efficient Gibbs sampler has been developed to facilitate fast computation. The Markov chain Monte Carlo algorithms of the proposed and alternative methods are efficiently implemented in 'C++'. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Kun Fan [aut, cre],
Cen Wu [aut]
Maintainer: Kun Fan <kfan@ksu.edu>
Diff between mixedBayes versions 0.1.9 dated 2025-06-27 and 0.1.10 dated 2025-07-08
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 4 ++++ R/LONBGLSS.R | 8 ++++---- R/LONRBGLSS.R | 4 ++-- R/mixedBayes.R | 11 ++++++----- R/selection.R | 8 ++++---- R/selection_nonsparse.R | 8 ++++---- R/selection_sparse.R | 8 ++++---- README.md | 4 ++-- man/selection.Rd | 2 +- src/BGL.cpp | 2 +- src/BLSS.cpp | 6 +++--- 13 files changed, 51 insertions(+), 46 deletions(-)
Title: Spatio-Temporal Point Pattern Methods, Model Fitting,
Diagnostics, Simulation, Local Tests
Description: Toolbox for different kinds of spatio-temporal analyses to be performed on observed point patterns, following the growing stream of literature on point process theory. This R package implements functions to perform different kinds of analyses on point processes, proposed in the papers (Siino, Adelfio, and Mateu 2018<doi:10.1007/s00477-018-1579-0>; Siino et al. 2018<doi:10.1002/env.2463>; Adelfio et al. 2020<doi:10.1007/s00477-019-01748-1>; D’Angelo, Adelfio, and Mateu 2021<doi:10.1016/j.spasta.2021.100534>; D’Angelo, Adelfio, and Mateu 2022<doi:10.1007/s00362-022-01338-4>; D’Angelo, Adelfio, and Mateu 2023<doi:10.1016/j.csda.2022.107679>). The main topics include modeling, statistical inference, and simulation issues on spatio-temporal point processes on Euclidean space and linear networks. Version 1.0.0 has been updated for accompanying the journal publication D Angelo and Adelfio 2025 <doi:10.18637/jss.v113.i10>.
Author: Nicoletta D'Angelo [aut, cre] ,
Giada Adelfio [aut]
Maintainer: Nicoletta D'Angelo <nicoletta.dangelo@unipa.it>
Diff between stopp versions 0.2.4 dated 2024-06-04 and 1.0.0 dated 2025-07-08
DESCRIPTION | 19 +++++++++-------- MD5 | 53 ++++++++++++++++++++++++------------------------- R/globaldiag.R | 4 +-- R/internals.R | 5 ++++ R/localSTLKinhom.R | 2 - R/localdiag.R | 2 - R/localtest.R | 2 - R/plot.globaldiag.R | 2 - R/plot.locstppm.R | 4 +-- R/plot.sepstppm.R | 4 +-- R/plot.stlgcppm.R | 4 +-- R/plot.stlp.R | 2 - R/plot.stppm.R | 4 +-- R/sepstlppm.R | 2 - R/sepstppm.R | 2 - inst |only man/globaldiag.Rd | 4 +-- man/localSTLKinhom.Rd | 2 - man/localdiag.Rd | 2 - man/localtest.Rd | 2 - man/plot.globaldiag.Rd | 2 - man/plot.locstppm.Rd | 4 +-- man/plot.sepstppm.Rd | 4 +-- man/plot.stlgcppm.Rd | 4 +-- man/plot.stlp.Rd | 2 - man/plot.stppm.Rd | 4 +-- man/sepstlppm.Rd | 2 - man/sepstppm.Rd | 2 - 28 files changed, 76 insertions(+), 69 deletions(-)
Title: Real-Time Disease Surveillance
Description: Supports modelling real-time case data to facilitate the real-time
surveillance of infectious diseases and other point phenomena. The package provides automated computational grid generation over
an area of interest with methods to map covariates between geographies, model fitting including spatially aggregated case counts,
and predictions and visualisation. Both Bayesian and maximum likelihood methods are provided. Log-Gaussian Cox Processes are described by
Diggle et al. (2013) <doi:10.1214/13-STS441> and we provide both the low-rank approximation for Gaussian processes
described by Solin and Särkkä (2020) <doi:10.1007/s11222-019-09886-w> and Riutort-Mayol et al (2023) <doi:10.1007/s11222-022-10167-2> and the
nearest neighbour Gaussian process described by Datta et al (2016) <doi:10.1080/01621459.2015.1044091>. 'cmdstanr' can be downloaded at <https://mc-stan.org/cmdstanr/>.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <s.i.watson@bham.ac.uk>
Diff between rts2 versions 0.8.0 dated 2025-06-10 and 0.8.3 dated 2025-07-08
DESCRIPTION | 8 +- MD5 | 24 +++--- R/RcppExports.R | 20 +++++ R/data_functions.R | 13 ++- R/griddata_class.R | 117 +++++++++++++++++++++---------- build/partial.rdb |binary inst/include/rts/regionlinearpredictor.h | 33 +++++++- inst/include/rts/rtsmodelbits.h | 6 - inst/include/rts/rtsregionmodel.h | 11 +- man/create_points.Rd | 2 man/grid.Rd | 4 + src/RcppExports.cpp | 78 ++++++++++++++++++++ src/model_module.cpp | 88 ++++++++++++++++++++++- 13 files changed, 330 insertions(+), 74 deletions(-)
Title: Projection Predictive Feature Selection
Description: Performs projection predictive feature selection for generalized linear
models (Piironen, Paasiniemi, and Vehtari, 2020, <doi:10.1214/20-EJS1711>)
with or without multilevel or additive terms (Catalina, Bürkner, and
Vehtari, 2022, <https://proceedings.mlr.press/v151/catalina22a.html>), for
some ordinal and nominal regression models (Weber, Glass, and Vehtari, 2025,
<doi:10.1007/s00180-024-01506-0>), and for many other regression models
(using the latent projection by Catalina, Bürkner, and Vehtari, 2021,
<doi:10.48550/arXiv.2109.04702>, which can also be applied to most of the
former models). The package is compatible with the 'rstanarm' and 'brms'
packages, but other reference models can also be used. See the vignettes and
the documentation for more information and examples.
Author: Juho Piironen [aut],
Markus Paasiniemi [aut],
Alejandro Catalina [aut],
Frank Weber [aut],
Osvaldo Martin [cre, aut],
Aki Vehtari [aut],
Jonah Gabry [ctb],
Marco Colombo [ctb],
Paul-Christian Buerkner [ctb],
Hamada S. Badr [ctb],
Brian Sullivan [ctb], [...truncated...]
Maintainer: Osvaldo Martin <aloctavodia@gmail.com>
Diff between projpred versions 2.8.0 dated 2023-12-14 and 2.9.0 dated 2025-07-08
DESCRIPTION | 39 - MD5 | 110 +-- NAMESPACE | 3 NEWS.md | 46 + R/cv_varsel.R | 769 +++++++++++++++----------- R/data.R | 16 R/divergence_minimizers.R | 114 +++ R/extend_family.R | 11 R/formula.R | 2 R/glmfun.R | 2 R/latent.R | 45 + R/methods.R | 303 +++++++--- R/misc.R | 178 +++++- R/project.R | 45 + R/projfun.R | 47 + R/projpred-package.R | 126 +++- R/refmodel.R | 21 R/search.R | 6 R/summary_funs.R | 653 ++++++++++++++-------- R/varsel.R | 97 ++- README.md | 23 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 55 + inst/doc/latent.R | 56 - inst/doc/latent.Rmd | 193 +++--- inst/doc/latent.html | 810 +++++++++++----------------- inst/doc/projpred.R | 81 +- inst/doc/projpred.Rmd | 165 +++-- inst/doc/projpred.html | 1028 ++++++++++++++++++------------------ man/cv_varsel.Rd | 129 +++- man/extend_family.Rd | 11 man/internal-global-options.Rd |only man/mesquite.Rd | 10 man/plot.cv_proportions.Rd | 6 man/plot.vsel.Rd | 129 ++-- man/project.Rd | 15 man/projpred-package.Rd | 84 +- man/suggest_size.Rd | 38 - man/summary.vsel.Rd | 89 +-- man/varsel.Rd | 26 man/y_wobs_offs.Rd | 4 tests/testthat/helpers/creators.R |only tests/testthat/helpers/testers.R | 432 +++++++++------ tests/testthat/setup.R | 173 ++++-- tests/testthat/test_as_matrix.R | 6 tests/testthat/test_augdat.R | 14 tests/testthat/test_datafit.R | 15 tests/testthat/test_div_minimizer.R | 34 - tests/testthat/test_methods_vsel.R | 176 +++--- tests/testthat/test_misc.R | 283 +++++++++ tests/testthat/test_parallel.R | 2 tests/testthat/test_proj_predfun.R | 7 tests/testthat/test_varsel.R | 338 ++--------- vignettes/latent.Rmd | 193 +++--- vignettes/projpred.Rmd | 165 +++-- vignettes/references.bib | 36 + 57 files changed, 4389 insertions(+), 3070 deletions(-)
Title: Kernel SHAP
Description: Efficient implementation of Kernel SHAP (Lundberg and Lee,
2017, <doi:10.48550/arXiv.1705.07874>) permutation SHAP, and additive
SHAP for model interpretability. For Kernel SHAP and permutation
SHAP, if the number of features is too large for exact calculations,
the algorithms iterate until the SHAP values are sufficiently precise
in terms of their standard errors. The package integrates smoothly
with meta-learning packages such as 'tidymodels', 'caret' or 'mlr3'.
It supports multi-output models, case weights, and parallel
computations. Visualizations can be done using the R package
'shapviz'.
Author: Michael Mayer [aut, cre] ,
David Watson [aut] ,
Przemyslaw Biecek [ctb]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between kernelshap versions 0.7.0 dated 2024-08-17 and 0.8.0 dated 2025-07-08
kernelshap-0.7.0/kernelshap/man/figures/README-gam-dep.svg |only kernelshap-0.7.0/kernelshap/man/figures/README-gam-imp.svg |only kernelshap-0.7.0/kernelshap/man/figures/README-nn-dep.svg |only kernelshap-0.7.0/kernelshap/man/figures/README-prob-dep.svg |only kernelshap-0.7.0/kernelshap/man/figures/README-rf-dep.svg |only kernelshap-0.8.0/kernelshap/DESCRIPTION | 31 - kernelshap-0.8.0/kernelshap/MD5 | 46 - kernelshap-0.8.0/kernelshap/NEWS.md | 63 ++ kernelshap-0.8.0/kernelshap/R/additive_shap.R | 27 kernelshap-0.8.0/kernelshap/R/kernelshap.R | 275 ++++------ kernelshap-0.8.0/kernelshap/R/permshap.R | 167 ++++-- kernelshap-0.8.0/kernelshap/R/utils.R | 134 +++- kernelshap-0.8.0/kernelshap/R/utils_kernelshap.R | 156 ++--- kernelshap-0.8.0/kernelshap/R/utils_permshap.R | 230 +++++++- kernelshap-0.8.0/kernelshap/README.md | 99 +-- kernelshap-0.8.0/kernelshap/man/additive_shap.Rd | 8 kernelshap-0.8.0/kernelshap/man/figures/README-gam-dep.png |only kernelshap-0.8.0/kernelshap/man/figures/README-gam-imp.png |only kernelshap-0.8.0/kernelshap/man/figures/README-nn-dep.png |only kernelshap-0.8.0/kernelshap/man/figures/README-prob-dep.png |only kernelshap-0.8.0/kernelshap/man/figures/README-rf-dep.png |only kernelshap-0.8.0/kernelshap/man/kernelshap.Rd | 54 - kernelshap-0.8.0/kernelshap/man/permshap.Rd | 71 ++ kernelshap-0.8.0/kernelshap/tests/testthat.R | 24 kernelshap-0.8.0/kernelshap/tests/testthat/test-basic.R | 123 ++-- kernelshap-0.8.0/kernelshap/tests/testthat/test-kernelshap-utils.R | 43 - kernelshap-0.8.0/kernelshap/tests/testthat/test-multioutput.R | 64 +- kernelshap-0.8.0/kernelshap/tests/testthat/test-permshap-utils.R | 59 ++ kernelshap-0.8.0/kernelshap/tests/testthat/test-utils.R | 41 + 29 files changed, 1122 insertions(+), 593 deletions(-)
Title: Authenticated HTTP Request Client for the 'Hakai' API
Description: Initializes a class that obtains API credentials and provides
a method to use those credentials to make GET requests to the 'Hakai'
API server. Usage instructions are documented at
<https://hakaiinstitute.github.io/hakai-api/>.
Author: Sam Albers [aut, cre],
Taylor Denouden [aut],
Brett Johnson [aut],
Nate Rosenstock [ctb],
Chris Davis [ctb],
Hakai Institute [cph]
Maintainer: Sam Albers <sam.albers@hakai.org>
Diff between hakaiApi versions 1.0.3 dated 2025-05-27 and 1.0.4 dated 2025-07-08
DESCRIPTION | 6 - MD5 | 15 +-- NEWS.md | 10 ++ R/client.R | 199 +++++++++++++++++++++++++++++-------------- R/utils.R | 27 ++++- README.md | 4 man/Client.Rd | 59 ++++++++++-- tests/testthat/test-client.R |only tests/testthat/test-utils.R | 46 ++++++--- 9 files changed, 260 insertions(+), 106 deletions(-)
Title: Routines for L1 Estimation
Description: L1 estimation for linear regression using Barrodale and Roberts' method
<doi:10.1145/355616.361024> and the EM algorithm <doi:10.1023/A:1020759012226>.
Estimation of mean and covariance matrix using the multivariate Laplace distribution,
density, distribution function, quantile function and random number generation
for univariate and multivariate Laplace distribution <doi:10.1080/03610929808832115>.
Implementation of Naik and Plungpongpun <doi:10.1007/0-8176-4487-3_7> for the
Generalized spatial median estimator is included.
Author: Felipe Osorio [aut, cre] ,
Tymoteusz Wolodzko [aut]
Maintainer: Felipe Osorio <faosorios.stat@gmail.com>
Diff between L1pack versions 0.52 dated 2025-03-18 and 0.60 dated 2025-07-08
ChangeLog | 4 ++++ DESCRIPTION | 11 ++++++----- MD5 | 24 ++++++++++++++---------- NAMESPACE | 9 +++++---- R/ccc.R |only inst/CITATION | 8 ++++---- man/envelope.Rd | 4 ++++ man/l1ccc.Rd |only src/R_init_L1pack.c | 8 +++++++- src/ccc.f |only src/fitter_equal.c |only src/lad.h | 7 ++++++- src/lad_EM.c | 8 ++++---- src/laplace_fitter.c | 17 +++++++---------- src/spatial_median.c | 14 ++++++++------ 15 files changed, 69 insertions(+), 45 deletions(-)
Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Statistics: locate and tag peaks and valleys; label plot with the
equation of a fitted polynomial or other types of models including major
axis, quantile and robust and resistant regression. Labels for P-value,
R^2 or adjusted R^2 or information criteria for fitted models; parametric
and non-parametric correlation; label with ANOVA table for fitted models;
label with summary table for fitted models; annotations for multiple
comparisons with adjusted P-values. Model fit classes for which suitable
methods are provided by package 'broom' and 'broom.mixed' are supported as
well as user-defined wrappers on model fit functions. Scales and stats to build volcano and quadrant plots based on
outcomes, fold changes, p-values and false discovery rates.
Author: Pedro J. Aphalo [aut, cre] ,
Kamil Slowikowski [ctb] ,
Samer Mouksassi [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpmisc versions 0.6.1 dated 2024-11-14 and 0.6.2 dated 2025-07-08
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Title: Fractional Weighted Bootstrap
Description: An implementation of the fractional weighted bootstrap to be used as a drop-in for functions in
the 'boot' package. The fractional weighted bootstrap (also known as the Bayesian bootstrap) involves drawing
weights randomly that are applied to the data rather than resampling units from the data. See Xu et al. (2020)
<doi:10.1080/00031305.2020.1731599> for details.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between fwb versions 0.4.0 dated 2025-06-11 and 0.5.0 dated 2025-07-08
DESCRIPTION | 18 +- MD5 | 46 +++--- NAMESPACE | 3 NEWS.md | 20 ++ R/bearingcage.R | 8 - R/compute.ci.R |only R/fwb.R | 27 +-- R/fwb.array.R |only R/fwb.ci.R | 278 +++++++++-------------------------------- R/plot.fwb.R | 10 - R/simultaneous.R |only R/summary.fwb.R | 211 ++++++++++++++++++++++++------- R/utils.R | 25 ++- R/vcovFWB.R | 23 ++- R/weighted-statistics.R | 18 +- build/stage23.rdb |binary man/bearingcage.Rd | 8 - man/fwb-package.Rd | 2 man/fwb.Rd | 7 - man/fwb.array.Rd |only man/fwb.ci.Rd | 35 +++-- man/summary.fwb.Rd | 42 ++++-- tests/testthat/helpers.R | 74 ++++++++++ tests/testthat/test-boot.R |only tests/testthat/test-fwb.R | 4 tests/testthat/test-p-values.R |only tests/testthat/test-w_mean.R | 2 27 files changed, 496 insertions(+), 365 deletions(-)
Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models.
Includes Markov Chain Monte Carlo Maximum likelihood and Laplace approximation model fitting for a range of models,
non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily,
robust and bias-corrected standard error estimation, power calculation, data simulation, and more.
See <https://samuel-watson.github.io/glmmr-web/> for a detailed manual.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 1.0.0 dated 2025-04-01 and 1.0.1 dated 2025-07-08
DESCRIPTION | 8 MD5 | 12 R/R6Model.R | 2 build/partial.rdb |binary inst/include/glmmr/modeloptim.hpp | 2 inst/stan/mcml.stan | 70 ++-- src/stanExports_mcml.h | 533 ++++++++++++++------------------------ 7 files changed, 248 insertions(+), 379 deletions(-)
Title: Logging Setup for the 'teal' Family of Packages
Description: Utilizing the 'logger' framework to record events within a
package, specific to 'teal' family of packages. Supports logging
namespaces, hierarchical logging, various log destinations,
vectorization, and more.
Author: Dawid Kaledkowski [aut, cre],
Konrad Pagacz [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.logger versions 0.3.2 dated 2025-02-14 and 0.4.0 dated 2025-07-08
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NEWS.md | 4 ++++ R/register_logger.R | 4 ++-- build/vignette.rds |binary inst/WORDLIST | 1 - 6 files changed, 17 insertions(+), 14 deletions(-)
Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function
(Corless et al, 1996) <doi:10.1007/BF02124750> without the need for
installing the entire GSL.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between lamW versions 2.2.4 dated 2024-06-17 and 2.2.5 dated 2025-07-08
DESCRIPTION | 11 ++++++----- MD5 | 16 ++++++++-------- README.md | 3 +-- build/partial.rdb |binary inst/CITATION | 2 +- inst/NEWS.Rd | 15 +++++++++++++++ inst/tinytest/test_lamW.R | 14 +++++++------- inst/tinytest/test_package_metadata.R | 33 +++++++++++++++++++++++---------- src/lambertW.cpp | 4 +--- 9 files changed, 62 insertions(+), 36 deletions(-)
Title: Actuarial Functions and Heavy Tailed Distributions
Description: Functions and data sets for actuarial science:
modeling of loss distributions; risk theory and ruin theory;
simulation of compound models, discrete mixtures and compound
hierarchical models; credibility theory. Support for many additional
probability distributions to model insurance loss size and
frequency: 23 continuous heavy tailed distributions; the
Poisson-inverse Gaussian discrete distribution; zero-truncated and
zero-modified extensions of the standard discrete distributions.
Support for phase-type distributions commonly used to compute ruin
probabilities. Main reference: <doi:10.18637/jss.v025.i07>.
Implementation of the Feller-Pareto family of distributions:
<doi:10.18637/jss.v103.i06>.
Author: Vincent Goulet [cre, aut] ,
Sebastien Auclair [ctb],
Christophe Dutang [aut] ,
Walter Garcia-Fontes [ctb],
Nicholas Langevin [ctb],
Xavier Milhaud [ctb],
Tommy Ouellet [ctb],
Alexandre Parent [ctb],
Mathieu Pigeon [aut],
Louis-Philippe Pouliot [ctb], [...truncated...]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between actuar versions 3.3-5 dated 2025-01-09 and 3.3-6 dated 2025-07-08
DESCRIPTION | 24 +-- MD5 | 43 +++-- R/coverage.R | 16 ++ R/ruin.R | 34 ++-- R/var-methods.R | 15 +- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 36 ++++ inst/doc/actuar.pdf |binary inst/doc/coverage.pdf |binary inst/doc/credibility.pdf |binary inst/doc/distributions.pdf |binary inst/doc/modeling.pdf |binary inst/doc/risk.pdf |binary inst/doc/simulation.pdf |binary man/ruin.Rd | 24 ++- src/betaint.c | 23 --- src/dpq.c | 315 +++++++++++++++---------------------------- src/dpqphtype.c | 22 +-- src/invgauss.c | 51 +++++- tests/dpqr-tests.R | 101 +++++++++++-- tests/var-methods-tests.R |only vignettes/share/preamble.tex | 2 23 files changed, 390 insertions(+), 316 deletions(-)
Title: Tools to Analyze Repertory Grid Data
Description: Analyze repertory grids, a qualitative-quantitative
data collection technique devised by George A. Kelly in the 1950s. Today, grids are used across
various domains ranging from clinical psychology to marketing. The package contains functions
to quantitatively analyze and visualize repertory grid data (e.g. 'Fransella', 'Bell', & 'Bannister',
2004, ISBN: 978-0-470-09080-0). The package is part of the The package is part of the
<https://openrepgrid.org/> project.
Author: Mark Heckmann [aut, cre, cph] ,
Alejandro Garcia Gutierrez [ctb],
Diego Vitali [ctb]
Maintainer: Mark Heckmann <heckmann.mark@gmail.com>
Diff between OpenRepGrid versions 0.1.17 dated 2025-03-02 and 0.1.18 dated 2025-07-08
OpenRepGrid-0.1.17/OpenRepGrid/man/colorize_matrix_rows.Rd |only OpenRepGrid-0.1.17/OpenRepGrid/man/importExcelInternal.Rd |only OpenRepGrid-0.1.17/OpenRepGrid/man/importTxtInternal.Rd |only OpenRepGrid-0.1.17/OpenRepGrid/man/showMeta.Rd |only OpenRepGrid-0.1.18/OpenRepGrid/DESCRIPTION | 21 OpenRepGrid-0.1.18/OpenRepGrid/MD5 | 126 +- OpenRepGrid-0.1.18/OpenRepGrid/NAMESPACE | 14 OpenRepGrid-0.1.18/OpenRepGrid/NEWS.md | 51 - OpenRepGrid-0.1.18/OpenRepGrid/R/bertin.r | 30 OpenRepGrid-0.1.18/OpenRepGrid/R/calc.r | 17 OpenRepGrid-0.1.18/OpenRepGrid/R/data-openrepgrid.r | 137 ++ OpenRepGrid-0.1.18/OpenRepGrid/R/dev-functions.r | 22 OpenRepGrid-0.1.18/OpenRepGrid/R/distance.R | 9 OpenRepGrid-0.1.18/OpenRepGrid/R/export.r | 264 ++++- OpenRepGrid-0.1.18/OpenRepGrid/R/gridlist.R | 5 OpenRepGrid-0.1.18/OpenRepGrid/R/import.r | 479 ++++++---- OpenRepGrid-0.1.18/OpenRepGrid/R/measures.r | 1 OpenRepGrid-0.1.18/OpenRepGrid/R/openrepgrid.r | 7 OpenRepGrid-0.1.18/OpenRepGrid/R/preferred_poles.R |only OpenRepGrid-0.1.18/OpenRepGrid/R/repgrid-basicops.r | 88 + OpenRepGrid-0.1.18/OpenRepGrid/R/repgrid-output.r | 133 +- OpenRepGrid-0.1.18/OpenRepGrid/R/repgrid-plots.r | 34 OpenRepGrid-0.1.18/OpenRepGrid/R/rgl-3d.r | 79 - OpenRepGrid-0.1.18/OpenRepGrid/R/settings.r | 14 OpenRepGrid-0.1.18/OpenRepGrid/R/utils.r | 72 + OpenRepGrid-0.1.18/OpenRepGrid/build/partial.rdb |binary OpenRepGrid-0.1.18/OpenRepGrid/data/df_construct_columns.RData |only OpenRepGrid-0.1.18/OpenRepGrid/data/df_element_columns.RData |only OpenRepGrid-0.1.18/OpenRepGrid/data/df_long.RData |only OpenRepGrid-0.1.18/OpenRepGrid/inst/examples/example-biplot3d.R |only OpenRepGrid-0.1.18/OpenRepGrid/inst/examples/example-importExcel.R |only OpenRepGrid-0.1.18/OpenRepGrid/inst/examples/example-preferredPoles.R |only OpenRepGrid-0.1.18/OpenRepGrid/inst/examples/example-save-as-excel.R |only OpenRepGrid-0.1.18/OpenRepGrid/inst/examples/example-save-as-worksheet.R |only OpenRepGrid-0.1.18/OpenRepGrid/inst/extdata/grid_01.txt | 9 OpenRepGrid-0.1.18/OpenRepGrid/inst/extdata/grid_01.xlsx |binary OpenRepGrid-0.1.18/OpenRepGrid/inst/extdata/grid_02.xlsx |binary OpenRepGrid-0.1.18/OpenRepGrid/inst/extdata/grid_03.xlsx |only OpenRepGrid-0.1.18/OpenRepGrid/man/OpenRepGrid-overview.Rd | 6 OpenRepGrid-0.1.18/OpenRepGrid/man/alignByIdeal.Rd | 5 OpenRepGrid-0.1.18/OpenRepGrid/man/alignByLoadings.Rd | 5 OpenRepGrid-0.1.18/OpenRepGrid/man/alignByPreferredPole.Rd |only OpenRepGrid-0.1.18/OpenRepGrid/man/biplot2d.Rd | 3 OpenRepGrid-0.1.18/OpenRepGrid/man/biplot3d.Rd | 38 OpenRepGrid-0.1.18/OpenRepGrid/man/biplotDraw.Rd | 4 OpenRepGrid-0.1.18/OpenRepGrid/man/df_construct_columns.Rd |only OpenRepGrid-0.1.18/OpenRepGrid/man/df_element_columns.Rd |only OpenRepGrid-0.1.18/OpenRepGrid/man/df_long.Rd |only OpenRepGrid-0.1.18/OpenRepGrid/man/distanceHartmann.Rd | 4 OpenRepGrid-0.1.18/OpenRepGrid/man/grid_to_df_long.Rd |only OpenRepGrid-0.1.18/OpenRepGrid/man/grid_to_df_wide.Rd |only OpenRepGrid-0.1.18/OpenRepGrid/man/importDataframe.Rd |only OpenRepGrid-0.1.18/OpenRepGrid/man/importExcel.Rd | 117 +- OpenRepGrid-0.1.18/OpenRepGrid/man/importGridcor.Rd | 14 OpenRepGrid-0.1.18/OpenRepGrid/man/importGridstat.Rd | 10 OpenRepGrid-0.1.18/OpenRepGrid/man/importGridsuite.Rd | 10 OpenRepGrid-0.1.18/OpenRepGrid/man/importScivesco.Rd | 10 OpenRepGrid-0.1.18/OpenRepGrid/man/importTxt.Rd | 40 OpenRepGrid-0.1.18/OpenRepGrid/man/preferred-pole.Rd |only OpenRepGrid-0.1.18/OpenRepGrid/man/preferredPolesByIdeal.Rd |only OpenRepGrid-0.1.18/OpenRepGrid/man/print.distance.Rd | 5 OpenRepGrid-0.1.18/OpenRepGrid/man/print.hdistance.Rd | 5 OpenRepGrid-0.1.18/OpenRepGrid/man/randomGrid.Rd | 8 OpenRepGrid-0.1.18/OpenRepGrid/man/roxygen |only OpenRepGrid-0.1.18/OpenRepGrid/man/saveAsExcel.Rd | 53 - OpenRepGrid-0.1.18/OpenRepGrid/man/saveAsWorksheet.Rd |only OpenRepGrid-0.1.18/OpenRepGrid/man/settings.Rd | 3 OpenRepGrid-0.1.18/OpenRepGrid/man/stop_if_not_in_element_range.Rd |only OpenRepGrid-0.1.18/OpenRepGrid/tests/testthat/test-calc.R |only OpenRepGrid-0.1.18/OpenRepGrid/tests/testthat/test-gridlist.R | 6 OpenRepGrid-0.1.18/OpenRepGrid/tests/testthat/test-import-export.R |only OpenRepGrid-0.1.18/OpenRepGrid/tests/testthat/test-preferred-pole.R |only OpenRepGrid-0.1.18/OpenRepGrid/tests/testthat/test-save.R |only OpenRepGrid-0.1.18/OpenRepGrid/tests/testthat/test-utils.R |only OpenRepGrid-0.1.18/OpenRepGrid/tests/testthat/test_bertin.R | 6 OpenRepGrid-0.1.18/OpenRepGrid/tests/testthat/test_biplot.R | 1 OpenRepGrid-0.1.18/OpenRepGrid/tests/testthat/testdata |only 77 files changed, 1374 insertions(+), 591 deletions(-)
Title: Enhance 'Quarto' Project Workflows and Standards
Description: Streamlines 'Quarto' workflows by providing tools for consistent project setup and documentation. Enables portability through reusable metadata, automated project structure creation, and standardized templates. Features include enhanced project initialization, pre-formatted 'Quarto' documents, inclusion of 'Quarto' brand functionality, comprehensive data protection settings, custom styling, and structured documentation generation. Designed to improve efficiency and collaboration in R data science projects by reducing repetitive setup tasks while maintaining consistent formatting across multiple documents.
Author: Kyle Grealis [aut, cre]
Maintainer: Kyle Grealis <kyleGrealis@icloud.com>
Diff between froggeR versions 0.4.0 dated 2025-03-16 and 0.5.0 dated 2025-07-08
DESCRIPTION | 15 + MD5 | 70 +++++---- NAMESPACE | 3 NEWS.md | 23 ++ R/froggeR-package.R | 1 R/quarto_project.R | 75 +++++---- R/save_brand.R |only R/save_variables.R | 22 +- R/utils.R | 1 R/write_brand.R |only R/write_quarto.R | 55 +++---- R/write_variables.R | 13 - README.md | 17 +- build/vignette.rds |binary inst/doc/customizing-quarto.Rmd | 8 - inst/doc/customizing-quarto.html | 18 +- inst/doc/hopping-into-quarto.R | 18 -- inst/doc/hopping-into-quarto.Rmd | 153 ++++++++++--------- inst/doc/hopping-into-quarto.html | 263 ++++++++++++++++------------------ inst/doc/quarto-workflow.R | 26 --- inst/doc/quarto-workflow.Rmd | 131 ++++++---------- inst/doc/quarto-workflow.html | 226 +++++++++++++---------------- inst/gists/basic_quarto.qmd | 41 ----- inst/gists/brand.yml |only inst/gists/config.yml | 1 inst/gists/custom.scss | 29 +++ inst/gists/custom_quarto.qmd | 59 ++----- inst/gists/quarto.yml |only inst/gists/references.bib |only man/figures/write-quarto-example.png |only man/quarto_project.Rd | 33 +--- man/save_brand.Rd |only man/save_variables.Rd | 2 man/write_brand.Rd |only man/write_quarto.Rd | 48 ++---- tests/testthat/test-write_scss.R | 2 tests/testthat/test-write_variables.R | 1 vignettes/customizing-quarto.Rmd | 8 - vignettes/hopping-into-quarto.Rmd | 153 ++++++++++--------- vignettes/quarto-workflow.Rmd | 131 ++++++---------- 40 files changed, 767 insertions(+), 879 deletions(-)
Title: Methods for Correlation Analysis
Description: Lightweight package for computing different kinds
of correlations, such as partial correlations, Bayesian correlations,
multilevel correlations, polychoric correlations, biweight
correlations, distance correlations and more. Part of the 'easystats'
ecosystem. References: Makowski et al. (2020) <doi:10.21105/joss.02306>.
Author: Dominique Makowski [aut, inv] ,
Brenton M. Wiernik [aut, cre] ,
Indrajeet Patil [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Remi Theriault [aut] ,
Mark White [rev],
Maximilian M. Rabe [rev]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>
Diff between correlation versions 0.8.7 dated 2025-03-03 and 0.8.8 dated 2025-07-08
DESCRIPTION | 28 ++-- MD5 | 54 ++++----- NEWS.md | 6 + R/cor_test.R | 11 + R/cor_test_biserial.R | 2 R/cor_test_distance.R | 10 - R/cor_test_freq.R | 1 R/cor_test_percentage.R | 2 R/cor_to_ci.R | 3 R/cor_to_pcor.R | 7 - R/correlation.R | 40 +++++- R/matrix_inverse.R | 1 R/methods_print.R | 1 R/utils_find_correlationtype.R | 1 R/utils_get_combinations.R | 1 R/utils_remove_redundant.R | 2 R/visualisation_recipe.cor_test.R | 2 R/visualisation_recipe.easycormatrix.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/multilevel.R | 42 +++---- inst/doc/multilevel.html | 62 ++-------- inst/doc/types.R | 154 +++++++++++++------------- inst/doc/types.html | 173 +++++++++++++----------------- man/correlation.Rd | 8 + tests/testthat/test-cor_test.R | 19 ++- tests/testthat/test-cor_test_na_present.R | 1 tests/testthat/test-correlation.R | 28 ++++ 28 files changed, 328 insertions(+), 334 deletions(-)
Title: Unbiased Distances for Mixed-Type Data
Description: A comprehensive framework for calculating unbiased distances in datasets
containing mixed-type variables (numerical and categorical). The package implements
a general formulation that ensures multivariate additivity and commensurability,
meaning that variables contribute equally to the overall distance regardless of
their type, scale, or distribution. Supports multiple distance measures including
Gower's distance, Euclidean distance, Manhattan distance, and various categorical
variable distances such as simple matching, Eskin, occurrence frequency, and
association-based distances. Provides tools for variable scaling (standard
deviation, range, robust range, and principal component scaling), and handles
both independent and association-based category dissimilarities. Implements
methods to correct for biases that typically arise from different variable types,
distributions, and number of categories. Particularly useful for cluster analysis,
data visualization, and other distance-based me [...truncated...]
Author: Alfonso Iodice D'Enza [aut],
Angelos Markos [aut, cre],
Michel van de Velden [aut],
Carlo Cavicchia [aut]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between manydist versions 0.4.5 dated 2025-07-02 and 0.4.7 dated 2025-07-08
DESCRIPTION | 6 +-- MD5 | 12 +++---- R/cat_custom_delta.R | 6 +++ R/cat_delta.R | 18 ++++++++++- R/mdist.R | 79 +++++++++++++++++++++++++++++++-------------------- R/ndist.R | 2 - man/mdist.Rd | 14 ++++----- 7 files changed, 87 insertions(+), 50 deletions(-)
Title: Multi-Cohort Selection Bias Correction using IPW and AIPW
Methods
Description: Comprehensive toolkit for addressing selection
bias in binary disease models across diverse non-probability samples, each
with unique selection mechanisms. It utilizes Inverse Probability Weighting
(IPW) and Augmented Inverse Probability Weighting (AIPW) methods to reduce
selection bias effectively in multiple non-probability cohorts by integrating
data from either individual-level or summary-level external sources. The
package also provides a variety of variance estimation techniques. Please
refer to Kundu et al. <doi:10.48550/arXiv.2412.00228>.
Author: Ritoban Kundu [aut],
Michael Kleinsasser [cre]
Maintainer: Michael Kleinsasser <biostat-cran-manager@umich.edu>
Diff between EHRmuse versions 0.0.2.1 dated 2025-01-28 and 0.0.2.2 dated 2025-07-08
DESCRIPTION | 15 ++++++++------- MD5 | 42 +++++++++++++++++++++++++++++++++++++++--- NAMESPACE | 23 +++++++++++++++++++++-- R/AIPW_var_approx.R | 2 +- R/INV.R |only R/Vfun.R |only R/dd.R |only R/dsim.R |only R/gf1.R |only R/gf2.R |only R/gf3.R |only R/gf4.R |only R/gfd1.R |only R/gfd2.R |only R/gfd3.R |only R/gfd4.R |only R/hf1.R |only R/hf2.R |only R/hf3.R |only R/hf4.R |only R/pp.R |only R/psim.R |only R/psim.norm.R |only R/qsim.R |only R/qsim.norm.R |only R/rIG.R |only R/rMIG.R |only R/rsim.R |only R/simglm1.R |only R/simglm2.R |only R/simplexgee.R |only R/simplexreg.R |only R/simplexreg.fit.R |only R/uu.R |only R/var.sim.R |only R/vf.R |only inst |only src |only 38 files changed, 69 insertions(+), 13 deletions(-)
Title: Density, Probability, Quantile ('DPQ') Computations
Description: Computations for approximations and alternatives for the 'DPQ'
(Density (pdf), Probability (cdf) and Quantile) functions for probability
distributions in R.
Primary focus is on (central and non-central) beta, gamma and related
distributions such as the chi-squared, F, and t.
--
For several distribution functions, provide functions implementing formulas from
Johnson, Kotz, and Kemp (1992) <doi:10.1002/bimj.4710360207> and
Johnson, Kotz, and Balakrishnan (1995) for discrete or continuous
distributions respectively.
This is for the use of researchers in these numerical approximation
implementations, notably for my own use in order to improve standard
R pbeta(), qgamma(), ..., etc: {'"dpq"'-functions}.
Author: Martin Maechler [aut, cre] ,
Morten Welinder [ctb] ),
Wolfgang Viechtbauer [ctb] , 2002),
Ross Ihaka [ctb] ,
Marius Hofert [ctb] , lssum),
R-core [ctb] ,
R Foundation [cph]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between DPQ versions 0.5-9 dated 2024-08-23 and 0.6-0 dated 2025-07-08
DESCRIPTION | 20 + LICENSE |only MD5 | 75 +++---- NAMESPACE | 4 R/beta-fns.R | 115 ++++++----- R/dgamma.R | 201 +++++++++++-------- R/utils.R | 6 TODO | 20 + build/partial.rdb |binary build/vignette.rds |binary inst/COPYRIGHTS |only inst/NEWS.Rd | 67 ++++++ inst/doc/Noncentral-Chisq.pdf |binary inst/doc/comp-beta.pdf |binary inst/doc/log1pmx-etc.R | 11 - inst/doc/log1pmx-etc.Rnw | 202 ++++++++++--------- inst/doc/log1pmx-etc.pdf |binary inst/doc/qnorm-asymp.pdf |binary inst/extraR/relErr-plots.R | 8 man/dgamma-utils.Rd | 107 ++++------ man/dltgammaInc.Rd |only man/lgammaP11.Rd |only man/log1pmx.Rd | 28 +- man/logcf.Rd | 43 ++-- man/p1l1.Rd | 51 ++-- man/stirlerr.Rd | 32 ++- src/DPQ-misc.c | 2 src/DPQpkg.h | 10 src/bd0.c | 91 +++++++- src/gamma_inc_T1006.c |only src/init.c | 5 src/logcf.c | 75 +++---- src/pnchisq-it.c | 6 tests/bd0-tst.R | 438 +++++++++++++++++++++++++++++------------- tests/chisq-nonc-ex.R | 16 - tests/dnbinom-tst.R | 239 ++++++++++++++-------- tests/pow-tst.R | 10 tests/ppois-ex.R | 18 - tests/stirlerr-tst.R | 53 ++--- vignettes/R-numerics.bib | 12 + vignettes/log1pmx-etc.Rnw | 202 ++++++++++--------- 41 files changed, 1346 insertions(+), 821 deletions(-)
Title: Indexed Data Frames
Description: Provides extended data frames, with a special data frame column which contains two indexes, with potentially a nesting structure.
Author: Yves Croissant [aut, cre]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between dfidx versions 0.1-2 dated 2025-06-08 and 0.2-0 dated 2025-07-08
DESCRIPTION | 10 +- MD5 | 52 ++++++------ NAMESPACE | 3 NEWS.md | 26 +++++- R/datasets.R | 7 + R/dfidx-package.R | 3 R/dfidx.R | 65 +++++++++------ R/methods.R | 197 ++++++++++++++++++++++++++++++++++++++--------- R/miscellaneous.R | 51 ++++++------ R/model.R | 23 +++-- README.md | 6 - build/partial.rdb |binary build/vignette.rds |binary data/munnell_wide.rda |binary inst/REFERENCES.bib | 10 ++ inst/doc/dfidx.R | 81 +++++++++++++------ inst/doc/dfidx.pdf |binary inst/doc/dfidx.qmd | 181 +++++++++++++++++++++++++++++-------------- inst/tinytest |only man/dfidx.Rd | 24 +++-- man/idx.Rd | 10 +- man/idx_name.Rd | 12 +- man/methods.dfidx.Rd | 50 +++++++++-- man/model.frame.dfidx.Rd | 19 ++-- man/munnell.Rd | 9 +- man/unfold_idx.Rd | 15 ++- tests |only vignettes/dfidx.qmd | 181 +++++++++++++++++++++++++++++-------------- 28 files changed, 712 insertions(+), 323 deletions(-)
Title: Reinforcement Learning Tools for Two-Alternative Forced Choice
Tasks
Description: Tools for building reinforcement learning (RL) models
specifically tailored for Two-Alternative Forced Choice (TAFC) tasks,
commonly employed in psychological research. These models build upon
the foundational principles of model-free reinforcement learning detailed in
Sutton and Barto (2018) <ISBN:9780262039246>. The package allows
for the intuitive definition of RL models using simple if-else
statements. Our approach to constructing and evaluating these
computational models is informed by the guidelines proposed in
Wilson & Collins (2019) <doi:10.7554/eLife.49547>. Example
datasets included with the package are sourced from the work of
Mason et al. (2024) <doi:10.3758/s13423-023-02415-x>.
Author: YuKi [aut, cre]
Maintainer: YuKi <hmz1969a@gmail.com>
Diff between binaryRL versions 0.8.9 dated 2025-06-15 and 0.9.0 dated 2025-07-08
DESCRIPTION | 10 MD5 | 91 +++---- NAMESPACE | 2 R/1_unique_choice.R | 28 +- R/2_arrange_data.R | 19 - R/3_add_NA.R | 44 ++- R/4_set_initial_value.R | 38 +-- R/5_decision_making.R | 412 ++++++++++++++++++++++----------- R/7_digits.R | 3 R/8_output.R | 55 +++- R/binaryRL-package.R |only R/func_epsilon.R | 240 +++++++++++++++---- R/func_eta.R | 218 +++++++++++++---- R/func_gamma.R | 214 +++++++++++++---- R/func_pi.R |only R/func_tau.R | 191 +++++++++++---- R/model_RSTD.R | 26 +- R/model_TD.R | 25 +- R/model_Utility.R | 29 ++ R/process_optimize_para.R | 158 ++++++++---- R/process_recovery_data.R | 144 +++++++++-- R/process_simulate_list.R | 118 +++++++-- R/step1_run_m.R | 564 ++++++++++++++++++++++++++++++---------------- R/step2_rcv_d.R | 282 ++++++++++++++++++----- R/step3_fit_p.R | 248 +++++++++++++++----- R/step4_rpl_e.R | 125 +++++++--- R/summary.binaryRL.R | 51 +++- R/zzz.R | 20 - build |only data/Mason_2024_Exp1.rda |binary data/Mason_2024_Exp2.rda |binary man/Mason_2024_Exp1.Rd | 51 ++-- man/Mason_2024_Exp2.Rd | 51 ++-- man/RSTD.Rd | 25 +- man/TD.Rd | 24 + man/Utility.Rd | 27 ++ man/binaryRL-package.Rd |only man/fit_p.Rd | 342 +++++++++++++++++++-------- man/func_epsilon.Rd | 219 ++++++++++++++--- man/func_eta.Rd | 177 +++++++++++--- man/func_gamma.Rd | 168 ++++++++++--- man/func_pi.Rd |only man/func_tau.Rd | 159 ++++++++++-- man/optimize_para.Rd | 157 ++++++++---- man/rcv_d.Rd | 381 ++++++++++++++++++++++--------- man/recovery_data.Rd | 175 ++++++++++---- man/rpl_e.Rd | 88 ++++++- man/run_m.Rd | 465 ++++++++++++++++++++++++++----------- man/simulate_list.Rd | 127 +++++++--- 49 files changed, 4386 insertions(+), 1605 deletions(-)
Title: Log Execution of Scripts
Description: Logging of scripts suitable for clinical trials using
'Quarto' to create nice human readable logs. 'whirl' enables
execution of scripts in batch, while simultaneously creating logs for
the execution of each script, and providing an overview summary log of
the entire batch execution.
Author: Aksel Thomsen [aut, cre],
Lovemore Gakava [aut],
Cervan Girard [aut],
Kristian Troejelsgaard [aut],
Steffen Falgreen Larsen [aut],
Vladimir Obucina [aut],
Michael Svingel [aut],
Skander Mulder [aut],
Novo Nordisk A/S [cph]
Maintainer: Aksel Thomsen <oath@novonordisk.com>
Diff between whirl versions 0.2.0 dated 2025-04-15 and 0.3.0 dated 2025-07-08
whirl-0.2.0/whirl/R/import-standalone-s3-register.R |only whirl-0.2.0/whirl/R/session.R |only whirl-0.2.0/whirl/R/zzz.R |only whirl-0.2.0/whirl/inst/examples/success_log.html |only whirl-0.2.0/whirl/inst/use_whirl/_whirl.yaml |only whirl-0.2.0/whirl/tests/testthat/scripts/error_log.html |only whirl-0.2.0/whirl/tests/testthat/scripts/py_error_log.html |only whirl-0.2.0/whirl/tests/testthat/scripts/py_success_log.html |only whirl-0.2.0/whirl/tests/testthat/scripts/py_warning_log.html |only whirl-0.2.0/whirl/tests/testthat/scripts/success_log.html |only whirl-0.2.0/whirl/tests/testthat/scripts/warning_log.html |only whirl-0.3.0/whirl/DESCRIPTION | 18 whirl-0.3.0/whirl/MD5 | 101 ++-- whirl-0.3.0/whirl/NAMESPACE | 3 whirl-0.3.0/whirl/NEWS.md | 8 whirl-0.3.0/whirl/R/approvedpkgs.R | 243 ---------- whirl-0.3.0/whirl/R/biocompute.R |only whirl-0.3.0/whirl/R/custom_logging.R | 33 - whirl-0.3.0/whirl/R/internal_run.R | 2 whirl-0.3.0/whirl/R/log.R |only whirl-0.3.0/whirl/R/mdformats.R | 2 whirl-0.3.0/whirl/R/renv.R | 2 whirl-0.3.0/whirl/R/run.R | 16 whirl-0.3.0/whirl/R/status.R | 10 whirl-0.3.0/whirl/R/strace.R | 89 ++- whirl-0.3.0/whirl/R/use_whirl.R | 55 +- whirl-0.3.0/whirl/R/util_queue_summary.R | 54 -- whirl-0.3.0/whirl/R/whirl-options.R | 10 whirl-0.3.0/whirl/R/whirl-package.R | 1 whirl-0.3.0/whirl/R/whirl_queue.R | 48 - whirl-0.3.0/whirl/R/whirl_r_session.R | 155 +++--- whirl-0.3.0/whirl/README.md | 28 - whirl-0.3.0/whirl/build/vignette.rds |binary whirl-0.3.0/whirl/inst/WORDLIST | 25 - whirl-0.3.0/whirl/inst/documents/dummy.qmd | 72 +- whirl-0.3.0/whirl/inst/documents/files.qmd |only whirl-0.3.0/whirl/inst/documents/log.qmd | 185 +++---- whirl-0.3.0/whirl/inst/documents/python.qmd |only whirl-0.3.0/whirl/inst/documents/summary.qmd | 12 whirl-0.3.0/whirl/inst/use_whirl/_biocompute.yml |only whirl-0.3.0/whirl/inst/use_whirl/_parametrics.yml |only whirl-0.3.0/whirl/inst/use_whirl/_whirl.yml |only whirl-0.3.0/whirl/man/run.Rd | 4 whirl-0.3.0/whirl/man/use_biocompute.Rd |only whirl-0.3.0/whirl/man/use_whirl.Rd | 4 whirl-0.3.0/whirl/man/whirl-options-params.Rd | 4 whirl-0.3.0/whirl/man/whirl-options.Rd | 18 whirl-0.3.0/whirl/man/whirl-package.Rd | 2 whirl-0.3.0/whirl/man/write_biocompute.Rd |only whirl-0.3.0/whirl/tests/testthat/_snaps/biocompute.md |only whirl-0.3.0/whirl/tests/testthat/_snaps/custom_logging.md | 11 whirl-0.3.0/whirl/tests/testthat/_snaps/examples.md | 55 -- whirl-0.3.0/whirl/tests/testthat/scripts/_biocompute_parametrics.yml |only whirl-0.3.0/whirl/tests/testthat/scripts/_whirl_biocompute.yaml |only whirl-0.3.0/whirl/tests/testthat/scripts/biocompute.R |only whirl-0.3.0/whirl/tests/testthat/test-approvedpkgs.R | 26 - whirl-0.3.0/whirl/tests/testthat/test-biocompute.R |only whirl-0.3.0/whirl/tests/testthat/test-custom_logging.R | 8 whirl-0.3.0/whirl/tests/testthat/test-examples.R | 46 - whirl-0.3.0/whirl/tests/testthat/test-renv.R | 6 whirl-0.3.0/whirl/tests/testthat/test-run.R | 32 - whirl-0.3.0/whirl/tests/testthat/test-strace.R | 133 +++++ whirl-0.3.0/whirl/tests/testthat/test-use_whirl.R | 6 whirl-0.3.0/whirl/tests/testthat/test-util_queue_summary.R | 26 - 64 files changed, 741 insertions(+), 812 deletions(-)
Title: Generalized Propensity Score Estimation and Matching for
Multiple Groups
Description: Implements the Vector Matching algorithm to match multiple
treatment groups based on previously estimated generalized propensity
scores. The package includes tools for visualizing initial confounder
imbalances, estimating treatment assignment probabilities using various
methods, defining the common support region, performing matching across
multiple groups, and evaluating matching quality. For more details, see
Lopez and Gutman (2017) <doi:10.1214/17-STS612>.
Author: Mateusz Kolek [aut, cre, cph]
Maintainer: Mateusz Kolek <mati.kolek13@gmail.com>
Diff between vecmatch versions 1.1.0 dated 2025-04-24 and 1.2.0 dated 2025-07-08
DESCRIPTION | 18 ++++--- MD5 | 45 +++++++++++-------- NAMESPACE | 8 +++ NEWS.md | 20 ++++++++ R/balqual.R | 40 ++++++++++++++--- R/chk-utils.R | 31 +++++++++++++ R/csregion.R | 46 ++++++++++++++++++-- R/estimate_gps.R | 29 +++++++----- R/mosaic.R | 5 ++ R/optimize_gps.R |only R/raincloud.R | 85 ++++++++++++++++++++++++++++++++----- R/utils.R | 6 ++ build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 3 + inst/doc/optimizing-matching.R |only inst/doc/optimizing-matching.Rmd |only inst/doc/optimizing-matching.html |only inst/doc/vecmatch.html | 30 ++++++------- man/balqual.Rd | 6 ++ man/csregion.Rd | 9 +++ man/estimate_gps.Rd | 3 - man/make_opt_args.Rd |only man/optimize_gps.Rd |only man/raincloud.Rd | 9 +++ man/select_opt.Rd |only tests/testthat/test-optimize_gps.R |only vignettes/optimizing-matching.Rmd |only 28 files changed, 317 insertions(+), 76 deletions(-)
Title: Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data. In
particular representation, manipulation, rate estimation and
simulation for multistate data - the Lexis suite of functions, which
includes interfaces to 'mstate', 'etm' and 'cmprsk' packages.
Contains functions for Age-Period-Cohort and Lee-Carter modeling and
a function for interval censored data and some useful functions for
tabulation and plotting, as well as a number of epidemiological data
sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.59 dated 2025-01-13 and 2.60 dated 2025-07-08
Epi-2.59/Epi/build |only Epi-2.59/Epi/inst/doc/aaflup.R |only Epi-2.59/Epi/inst/doc/aaflup.pdf |only Epi-2.59/Epi/inst/doc/aaflup.rnw |only Epi-2.59/Epi/inst/doc/addLexis.R |only Epi-2.59/Epi/inst/doc/addLexis.pdf |only Epi-2.59/Epi/inst/doc/addLexis.rnw |only Epi-2.59/Epi/inst/doc/crisk.R |only Epi-2.59/Epi/inst/doc/crisk.pdf |only Epi-2.59/Epi/inst/doc/crisk.rnw |only Epi-2.59/Epi/inst/doc/simLexis.R |only Epi-2.59/Epi/inst/doc/simLexis.pdf |only Epi-2.59/Epi/inst/doc/simLexis.rnw |only Epi-2.59/Epi/inst/doc/yll.R |only Epi-2.59/Epi/inst/doc/yll.pdf |only Epi-2.59/Epi/inst/doc/yll.rnw |only Epi-2.59/Epi/vignettes/aaflup.rnw |only Epi-2.59/Epi/vignettes/addLexis.rnw |only Epi-2.59/Epi/vignettes/crisk.rnw |only Epi-2.59/Epi/vignettes/mvall.bat |only Epi-2.59/Epi/vignettes/simLexis.rnw |only Epi-2.59/Epi/vignettes/yll.rnw |only Epi-2.60/Epi/CHANGES | 4 Epi-2.60/Epi/DESCRIPTION | 8 - Epi-2.60/Epi/MD5 | 108 ++++++++++++++++--------- Epi-2.60/Epi/NAMESPACE | 6 + Epi-2.60/Epi/R/AaJ.Lexis.R | 6 - Epi-2.60/Epi/R/ci.lin.R | 36 ++++---- Epi-2.60/Epi/R/float.R | 54 ++++++------ Epi-2.60/Epi/inst/doc/01flup.R |only Epi-2.60/Epi/inst/doc/01flup.pdf |only Epi-2.60/Epi/inst/doc/02addLexis.R |only Epi-2.60/Epi/inst/doc/02addLexis.pdf |only Epi-2.60/Epi/inst/doc/03crisk.R |only Epi-2.60/Epi/inst/doc/03crisk.pdf |only Epi-2.60/Epi/inst/doc/04simLexis.R |only Epi-2.60/Epi/inst/doc/04simLexis.pdf |only Epi-2.60/Epi/inst/doc/05yll.R |only Epi-2.60/Epi/inst/doc/05yll.pdf |only Epi-2.60/Epi/inst/doc/index.html | 25 +++-- Epi-2.60/Epi/man/AaJ.Lexis.Rd | 7 - Epi-2.60/Epi/man/addCov.Lexis.Rd | 7 - Epi-2.60/Epi/man/addDrug.Lexis.Rd | 3 Epi-2.60/Epi/man/float.Rd | 8 + Epi-2.60/Epi/vignettes/01flup-Ieff.pdf |only Epi-2.60/Epi/vignettes/01flup-IeffR.pdf |only Epi-2.60/Epi/vignettes/01flup-box1.pdf |only Epi-2.60/Epi/vignettes/01flup-box4.pdf |only Epi-2.60/Epi/vignettes/01flup-dmL1.pdf |only Epi-2.60/Epi/vignettes/01flup-dmL2.pdf |only Epi-2.60/Epi/vignettes/01flup-dur-int-RR.pdf |only Epi-2.60/Epi/vignettes/01flup-dur-int.pdf |only Epi-2.60/Epi/vignettes/01flup-ins-time.pdf |only Epi-2.60/Epi/vignettes/01flup-mbox.pdf |only Epi-2.60/Epi/vignettes/01flup-mboxr.pdf |only Epi-2.60/Epi/vignettes/01flup-pr-a.pdf |only Epi-2.60/Epi/vignettes/01flup-sep-HR.pdf |only Epi-2.60/Epi/vignettes/01flup-sep-mort.pdf |only Epi-2.60/Epi/vignettes/01flup.rnw |only Epi-2.60/Epi/vignettes/01flup.tex |only Epi-2.60/Epi/vignettes/02addLexis.rnw |only Epi-2.60/Epi/vignettes/02addLexis.tex |only Epi-2.60/Epi/vignettes/03crisk-Sr1.pdf |only Epi-2.60/Epi/vignettes/03crisk-Sr2.pdf |only Epi-2.60/Epi/vignettes/03crisk-boxes.pdf |only Epi-2.60/Epi/vignettes/03crisk-boxes4.pdf |only Epi-2.60/Epi/vignettes/03crisk-boxes5.pdf |only Epi-2.60/Epi/vignettes/03crisk-cR.pdf |only Epi-2.60/Epi/vignettes/03crisk-crates.pdf |only Epi-2.60/Epi/vignettes/03crisk-difrat.pdf |only Epi-2.60/Epi/vignettes/03crisk-difratx.pdf |only Epi-2.60/Epi/vignettes/03crisk-rates-ci.pdf |only Epi-2.60/Epi/vignettes/03crisk-rates-l.pdf |only Epi-2.60/Epi/vignettes/03crisk-rates.pdf |only Epi-2.60/Epi/vignettes/03crisk-stack-ci.pdf |only Epi-2.60/Epi/vignettes/03crisk-stack.pdf |only Epi-2.60/Epi/vignettes/03crisk.rnw |only Epi-2.60/Epi/vignettes/03crisk.tex |only Epi-2.60/Epi/vignettes/04simLexis-boxes.pdf |only Epi-2.60/Epi/vignettes/04simLexis-comp-0.pdf |only Epi-2.60/Epi/vignettes/04simLexis-mort-int.pdf |only Epi-2.60/Epi/vignettes/04simLexis-pstate0.pdf |only Epi-2.60/Epi/vignettes/04simLexis-pstatex.pdf |only Epi-2.60/Epi/vignettes/04simLexis-pstatey.pdf |only Epi-2.60/Epi/vignettes/04simLexis.rnw |only Epi-2.60/Epi/vignettes/04simLexis.tex |only Epi-2.60/Epi/vignettes/05yll-imm.pdf |only Epi-2.60/Epi/vignettes/05yll-states.pdf |only Epi-2.60/Epi/vignettes/05yll-sus.pdf |only Epi-2.60/Epi/vignettes/05yll-tot.pdf |only Epi-2.60/Epi/vignettes/05yll.rnw |only Epi-2.60/Epi/vignettes/05yll.tex |only Epi-2.60/Epi/vignettes/fixall.bat | 58 ++++++------- Epi-2.60/Epi/vignettes/rtall.bat | 10 +- Epi-2.60/Epi/vignettes/rwall.bat | 10 +- 95 files changed, 202 insertions(+), 148 deletions(-)
Title: Tidy and Geospatial Kernel Smoothing
Description: Extensions of the kernel smoothing functions from the 'ks' package for compatibility with the tidyverse and geospatial ecosystems <doi:10.1007/s00180-024-01543-9>.
Author: Tarn Duong [aut, cre]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between eks versions 1.1.0 dated 2025-05-18 and 1.1.1 dated 2025-07-08
CHANGELOG | 10 + DESCRIPTION | 8 - MD5 | 22 ++-- R/prelim.R | 27 ++++- R/sf-ks-prelim.R | 21 +++- R/sf-ks.R | 241 +++++++++++++++++++++++++++++++++++++++-------- R/tidy-ks-prelim.R | 7 - R/tidy-ks.R | 9 - build/vignette.rds |binary inst/doc/tidysf_kde.html | 4 man/tidyst_as_kde.Rd | 3 man/tidyst_kdde.Rd | 15 +- 12 files changed, 291 insertions(+), 76 deletions(-)
Title: Collection of Functions for Working with Age Intervals
Description: Provides a collection of efficient functions for working with
individual ages and corresponding intervals. These include functions for
conversion from an age to an interval, aggregation of ages with associated
counts in to intervals and the splitting of interval counts based on
specified age distributions.
Author: Tim Taylor [aut, cre, cph] ,
Edwin van Leeuwen [aut]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ageutils versions 0.0.9 dated 2025-07-01 and 0.1.0 dated 2025-07-08
DESCRIPTION | 8 MD5 | 36 +-- NAMESPACE | 6 NEWS.md | 24 ++ R/ageutils-package.R | 1 R/breaks_to_interval.R | 8 R/cut_ages.R | 10 R/reaggregate_counts.R | 138 ++++++----- R/reaggregate_rates.R | 97 +++----- R/utils.R | 24 ++ man/breaks_to_interval.Rd | 4 man/cut_ages.Rd | 6 man/reaggregate_counts.Rd | 11 man/reaggregate_rates.Rd | 11 tests/testthat/helpers.R | 372 +++++++++++++++++++++++++++++-- tests/testthat/test-breaks_to_interval.R | 6 tests/testthat/test-cut_ages.R | 16 - tests/testthat/test-reaggregate_counts.R | 54 +++- tests/testthat/test-reaggregate_rates.R | 150 ++++++++++++ 19 files changed, 777 insertions(+), 205 deletions(-)
Title: Simulation Methods for Legislative Redistricting
Description: Enables researchers to sample redistricting plans from a pre-specified
target distribution using Sequential Monte Carlo and Markov Chain Monte Carlo
algorithms. The package allows for the implementation of various constraints in
the redistricting process such as geographic compactness and population parity
requirements. Tools for analysis such as computation of various summary statistics
and plotting functionality are also included. The package implements the SMC
algorithm of McCartan and Imai (2023) <doi:10.1214/23-AOAS1763>, the enumeration
algorithm of Fifield, Imai, Kawahara, and Kenny (2020) <doi:10.1080/2330443X.2020.1791773>,
the Flip MCMC algorithm of Fifield, Higgins, Imai and Tarr (2020) <doi:10.1080/10618600.2020.1739532>,
the Merge-split/Recombination algorithms of Carter et al. (2019) <doi:10.48550/arXiv.1911.01503>
and DeFord et al. (2021) <doi:10.1162/99608f92.eb30390f>, and the Short-burst
optimization algorithm of Cannon et al. (2020) < [...truncated...]
Author: Christopher T. Kenny [aut, cre] ,
Cory McCartan [aut] ,
Ben Fifield [aut] ,
Kosuke Imai [aut] ,
Jun Kawahara [ctb],
Alexander Tarr [ctb],
Michael Higgins [ctb]
Maintainer: Christopher T. Kenny <christopherkenny@fas.harvard.edu>
Diff between redist versions 4.2.0 dated 2024-01-13 and 4.3.0 dated 2025-07-08
redist-4.2.0/redist/src/labeling.cpp |only redist-4.2.0/redist/src/labeling.h |only redist-4.3.0/redist/DESCRIPTION | 44 ++-- redist-4.3.0/redist/MD5 | 118 ++++++------- redist-4.3.0/redist/NAMESPACE | 5 redist-4.3.0/redist/NEWS.md | 9 + redist-4.3.0/redist/R/RcppExports.R | 4 redist-4.3.0/redist/R/adjacency.R | 6 redist-4.3.0/redist/R/cores.R | 3 redist-4.3.0/redist/R/deprecations.R | 4 redist-4.3.0/redist/R/diagnostics.R | 24 +- redist-4.3.0/redist/R/plans_helpers.R | 43 ---- redist-4.3.0/redist/R/proj.R |only redist-4.3.0/redist/R/redist-package.R | 2 redist-4.3.0/redist/R/redist_constr.R | 5 redist-4.3.0/redist/R/redist_map.R | 16 + redist-4.3.0/redist/R/redist_ms.R | 33 ++- redist-4.3.0/redist/R/redist_ms_parallel.R | 99 ++++++----- redist-4.3.0/redist/R/redist_plans.R | 16 + redist-4.3.0/redist/R/redist_shortburst.R | 41 ++-- redist-4.3.0/redist/R/redist_smc.R | 13 - redist-4.3.0/redist/R/utils.R |only redist-4.3.0/redist/build/partial.rdb |binary redist-4.3.0/redist/build/vignette.rds |binary redist-4.3.0/redist/inst/doc/common_args.html | 10 - redist-4.3.0/redist/inst/doc/flip.R | 8 redist-4.3.0/redist/inst/doc/flip.html | 75 ++------ redist-4.3.0/redist/inst/doc/map-preproc.R | 140 ++++++++------- redist-4.3.0/redist/inst/doc/map-preproc.Rmd | 159 +++++++++--------- redist-4.3.0/redist/inst/doc/map-preproc.html | 127 +++++++------- redist-4.3.0/redist/inst/doc/redist.R | 2 redist-4.3.0/redist/inst/doc/redist.Rmd | 8 redist-4.3.0/redist/inst/doc/redist.html | 109 ++++++------ redist-4.3.0/redist/man/avg_by_prec.Rd | 4 redist-4.3.0/redist/man/proj.Rd |only redist-4.3.0/redist/man/pullback.Rd | 2 redist-4.3.0/redist/man/redist-package.Rd | 11 - redist-4.3.0/redist/man/redist.compactness.Rd | 4 redist-4.3.0/redist/man/redist.identify.cores.Rd | 3 redist-4.3.0/redist/man/redist.plot.contr_pfdr.Rd |only redist-4.3.0/redist/man/redist_map.Rd | 4 redist-4.3.0/redist/man/redist_mergesplit.Rd | 3 redist-4.3.0/redist/man/redist_mergesplit_parallel.Rd | 3 redist-4.3.0/redist/man/redist_plans.Rd | 2 redist-4.3.0/redist/man/redist_smc.Rd | 6 redist-4.3.0/redist/man/scorers.Rd | 2 redist-4.3.0/redist/src/RcppExports.cpp | 15 + redist-4.3.0/redist/src/map_calc.cpp | 22 ++ redist-4.3.0/redist/src/map_calc.h | 2 redist-4.3.0/redist/src/merge_split.cpp | 74 ++++---- redist-4.3.0/redist/src/merge_split.h | 3 redist-4.3.0/redist/src/smc.cpp | 111 ++++-------- redist-4.3.0/redist/src/smc.h | 10 - redist-4.3.0/redist/src/tree_op.cpp | 66 +------ redist-4.3.0/redist/src/tree_op.h | 11 - redist-4.3.0/redist/src/wilson.cpp | 47 ++--- redist-4.3.0/redist/src/wilson.h | 9 - redist-4.3.0/redist/tests/testthat/test_burst.R | 6 redist-4.3.0/redist/tests/testthat/test_enumpart.R | 6 redist-4.3.0/redist/tests/testthat/test_ms.R | 4 redist-4.3.0/redist/tests/testthat/test_smc.R | 28 ++- redist-4.3.0/redist/vignettes/map-preproc.Rmd | 159 +++++++++--------- redist-4.3.0/redist/vignettes/redist.Rmd | 8 63 files changed, 884 insertions(+), 864 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 11.3 dated 2025-04-28 and 11.4 dated 2025-07-08
DESCRIPTION | 8 - MD5 | 38 ++++---- R/Partial_Moments.R | 46 ++++++++++ R/RcppExports.R | 37 -------- R/dy_dx.R | 14 +-- README.md | 4 man/Co.LPM.Rd | 74 ++++++++-------- man/Co.UPM.Rd | 74 ++++++++-------- man/D.LPM.Rd | 78 ++++++++--------- man/D.UPM.Rd | 78 ++++++++--------- man/LPM.Rd | 10 +- man/LPM.ratio.Rd | 98 +++++++++++----------- man/PM.matrix.Rd | 106 ++++++++++++------------ man/UPM.Rd | 8 + man/UPM.ratio.Rd | 78 ++++++++--------- src/RcppExports.cpp | 18 ++-- src/partial_moments_rcpp.cpp | 149 ++++++++++++++++++++-------------- src/partial_moments_rcpp.h | 12 ++ tests/testthat/Rplots.pdf |binary tests/testthat/test_Partial_Moments.R | 16 +-- 20 files changed, 503 insertions(+), 443 deletions(-)
Title: Network Meta-Analysis Using Bayesian Methods
Description: Network meta-analyses (mixed treatment comparisons) in the Bayesian
framework using JAGS. Includes methods to assess heterogeneity and
inconsistency, and a number of standard visualizations.
van Valkenhoef et al. (2012) <doi:10.1002/jrsm.1054>;
van Valkenhoef et al. (2015) <doi:10.1002/jrsm.1167>.
Author: Gert van Valkenhoef [aut, cre],
Joel Kuiper [aut]
Maintainer: Gert van Valkenhoef <gert@gertvv.nl>
Diff between gemtc versions 1.0-2 dated 2023-06-21 and 1.1-0 dated 2025-07-08
DESCRIPTION | 22 +++++++++++++++------- MD5 | 17 ++++++++++------- NEWS.md | 7 +++++++ R/likelihoods.R | 5 ++++- R/ll.normal.identity.R | 2 +- R/ll.normal.smd.R |only build/partial.rdb |binary inst/gemtc.likelihood.normal.smd.power.txt |only inst/gemtc.likelihood.normal.smd.txt |only man/mtc.model.Rd | 5 +++++ man/parkinson.Rd | 2 +- 11 files changed, 43 insertions(+), 17 deletions(-)
Title: Dyadic Mixed Model for Pedigree Data
Description: Mixed model analysis for quantitative genetics
with multi-trait responses and pedigree-based partitioning
of individual variation into a range of environmental and
genetic variance components for individual and
maternal effects. Method documented in dmmOverview.pdf; dmm is an
implementation of dispersion mean model described by
Searle et al. (1992) "Variance Components", Wiley, NY.
'DMM' can do 'MINQUE', 'bias-corrected-ML', and 'REML' variance and
covariance component estimates.
Author: Neville Jackson [aut, cre]
Maintainer: Neville Jackson <nanddjackson@bigpond.com>
Diff between dmm versions 3.1-1 dated 2025-02-25 and 3.2-1 dated 2025-07-08
DESCRIPTION | 14 MD5 | 15 R/dmesolve.R | 942 +++++++++++++++++------------------------------ R/fgls.iter.siga.R | 126 ++---- R/fgls.update.R | 88 ---- inst/doc/bugs.txt | 4 inst/doc/dmmOverview.pdf |binary inst/doc/mods.txt | 3 inst/doc/remlmultiv.pdf |only 9 files changed, 435 insertions(+), 757 deletions(-)
Title: Univariate Time Series Forecasting
Description: An engine for univariate time series forecasting using
different regression models in an autoregressive way. The engine
provides an uniform interface for applying the different models.
Furthermore, it is extensible so that users can easily apply their
own regression models to univariate time series forecasting and
benefit from all the features of the engine, such as preprocessings
or estimation of forecast accuracy.
Author: Maria Pilar Frias-Bustamante [aut] ,
Francisco Martinez [aut, cre, cph]
Maintainer: Francisco Martinez <fmartin@ujaen.es>
Diff between utsf versions 1.2.0 dated 2025-05-19 and 1.3.0 dated 2025-07-08
utsf-1.2.0/utsf/R/forecast.R |only utsf-1.2.0/utsf/man/autoplot.utsf.Rd |only utsf-1.2.0/utsf/man/evaluation.Rd |only utsf-1.2.0/utsf/man/forecast.Rd |only utsf-1.2.0/utsf/tests/testthat/test-forecast.R |only utsf-1.3.0/utsf/DESCRIPTION | 10 utsf-1.3.0/utsf/MD5 | 50 + utsf-1.3.0/utsf/NAMESPACE | 12 utsf-1.3.0/utsf/NEWS.md | 22 utsf-1.3.0/utsf/R/do_tuneGrid.R | 80 ++- utsf-1.3.0/utsf/R/estimate_accuracy.R | 165 +++--- utsf-1.3.0/utsf/R/first_differences.R | 8 utsf-1.3.0/utsf/R/main.R |only utsf-1.3.0/utsf/R/plot.R | 22 utsf-1.3.0/utsf/R/print_utsf.R | 40 + utsf-1.3.0/utsf/R/simulations.R |only utsf-1.3.0/utsf/R/utsf-package.R | 18 utsf-1.3.0/utsf/README.md | 10 utsf-1.3.0/utsf/build/vignette.rds |binary utsf-1.3.0/utsf/inst/doc/utsf.R | 130 +++- utsf-1.3.0/utsf/inst/doc/utsf.Rmd | 202 ++++--- utsf-1.3.0/utsf/inst/doc/utsf.html | 612 ++++++++++++----------- utsf-1.3.0/utsf/man/autoplot.utsf_forecast.Rd |only utsf-1.3.0/utsf/man/create_model.Rd |only utsf-1.3.0/utsf/man/efa.Rd |only utsf-1.3.0/utsf/man/figures/README-example-1.png |binary utsf-1.3.0/utsf/man/forecast.utsf.Rd |only utsf-1.3.0/utsf/man/reexports.Rd |only utsf-1.3.0/utsf/man/trend.Rd | 6 utsf-1.3.0/utsf/man/tune_grid.Rd |only utsf-1.3.0/utsf/tests/testthat/test-main.R |only utsf-1.3.0/utsf/vignettes/ro_minimum.png |only utsf-1.3.0/utsf/vignettes/ro_normal.png |only utsf-1.3.0/utsf/vignettes/utsf.Rmd | 202 ++++--- 34 files changed, 970 insertions(+), 619 deletions(-)
Title: Modify and Share Images
Description: Tools for manipulating, visualizing, and exporting raster images in R.
Designed as an educational resource for students learning the basics of remote sensing,
the package provides user-friendly functions to apply color ramps, export RGB composites,
and create multi-frame visualizations. Built on top of the 'terra' and 'ggplot2' packages.
See <https://github.com/ducciorocchini/imageRy> for more details and examples.
Author: Duccio Rocchini [aut],
Ludovico Chieffallo [aut, cre],
Giovanni Andrea Nocera [ctb],
Giacomo Panza [ctb],
Michele Torresani [aut],
Elisa Thouverai [aut]
Maintainer: Ludovico Chieffallo <ludovico.chieffallo2@unibo.it>
Diff between imageRy versions 0.1.1 dated 2025-06-25 and 0.2.0 dated 2025-07-08
DESCRIPTION | 6 ++-- MD5 | 14 ++++----- R/im.classify.R | 77 +++++++++++++++++++++-------------------------------- R/im.import.R | 73 +++++++++++++++++++++++++++----------------------- R/im.list.R | 72 ++++++++++++++++++++++++++++++++++++++----------- man/im.classify.Rd | 32 +--------------------- man/im.import.Rd | 13 ++++---- man/im.list.Rd | 26 ++++++----------- 8 files changed, 154 insertions(+), 159 deletions(-)
Title: Estimation and Simulation of Drifting Semi-Markov Models
Description: Performs parametric and non-parametric estimation and simulation of
drifting semi-Markov processes. The definition of parametric and non-parametric
model specifications is also possible. Furthermore, three different types of
drifting semi-Markov models are considered. These models differ in the number
of transition matrices and sojourn time distributions used for the computation
of a number of semi-Markov kernels, which in turn characterize the drifting
semi-Markov kernel. For the parametric model estimation and specification,
several discrete distributions are considered for the sojourn times: Uniform,
Poisson, Geometric, Discrete Weibull and Negative Binomial. The non-parametric
model specification makes no assumptions about the shape of the sojourn time
distributions. Semi-Markov models are described in:
Barbu, V.S., Limnios, N. (2008) <doi:10.1007/978-0-387-73173-5>.
Drifting Markov models are described in:
Vergne, N. (2008) <doi:10.2202/1544-6115.1326>.
Reliability ind [...truncated...]
Author: Vlad Stefan Barbu [aut] ,
Ioannis Mavrogiannis [aut, cre] ,
Nicolas Vergne [aut]
Maintainer: Ioannis Mavrogiannis <mavrogiannis.ioa@gmail.com>
Diff between dsmmR versions 1.0.5 dated 2024-07-27 and 1.0.7 dated 2025-07-08
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Title: Analysis of Clinical Trials with the Desirability of Outcome
Ranking Methodology
Description: Statistical methods and related graphical representations for the Desirability of Outcome Ranking (DOOR) methodology. The DOOR is a paradigm for the design, analysis, interpretation of clinical trials and other research studies based on the patient centric benefit risk evaluation. The package provides functions for generating summary statistics from individual level/summary level datasets, conduct DOOR probability-based inference, and visualization of the results. For more details of DOOR methodology, see Hamasaki and Evans (2025) <doi:10.1201/9781003390855>. For more explanation of the statistical methods and the graphics, see the technical document and user manual of the DOOR 'Shiny' apps at <https://methods.bsc.gwu.edu>.
Author: Yijie He [aut, cre],
Qihang Wu [ctb],
Toshimitsu Hamasaki [ctb]
Maintainer: Yijie He <yih148@gwu.edu>
Diff between door versions 0.0.1 dated 2025-06-28 and 0.0.2 dated 2025-07-08
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-23 6.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-27 0.1.2
2025-02-27 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-17 0.1.1