Title: Visual Diagnostic Checks for Vector Autoregressive Models
Description: Provides model-agnostic visual diagnostics for vector
autoregressive (VAR) models. Given empirical data, model predictions,
residuals, and optionally simulated data, the package assembles a
multi-panel diagnostic grid: empirical vs. predicted time series, residual
inspection, residuals vs. predictions scatter, and posterior predictive style
checks via simulated trajectories. Output is a 'patchwork' object composed
of 'ggplot2' plots, allowing further customisation via standard
'ggplot2' theme calls. Follows the approach described in
Haslbeck et al. (2026) <doi:10.31234/osf.io/k6uz4_v3>.
Author: Bjoern S. Siepe [aut, cre, cph] ,
Jonas M. B. Haslbeck [aut]
Maintainer: Bjoern S. Siepe <bjoernsiepe+software@gmail.com>
Diff between VARcheck versions 0.1.0 dated 2026-05-19 and 0.1.1 dated 2026-07-13
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 9 +++++++++ R/panels.R | 4 ++-- R/plot_var_check.R | 16 ++++++++++++---- R/plot_var_row.R | 2 +- inst/doc/example-analyses.R | 1 + inst/doc/example-analyses.Rmd | 1 + inst/doc/example-analyses.html | 12 ++++++------ inst/doc/getting-started.html | 17 ++++++++--------- man/plot_var_check.Rd | 7 ++++++- tests/testthat/test-plot_var_check.R | 5 +++++ vignettes/example-analyses.Rmd | 1 + 13 files changed, 67 insertions(+), 38 deletions(-)
Title: Heteroskedasticity-Consistent Inference for Linear Models
Description: Computes heteroskedasticity-consistent covariance matrix
estimators for ordinary least squares regression models. The published HC0
through HC5m estimators implemented in the package follow White (1980)
<doi:10.2307/1912934>, Hinkley (1977)
<doi:10.1080/00401706.1977.10489550>, Horn et al. (1975)
<doi:10.1080/01621459.1975.10479877>, MacKinnon and White (1985)
<doi:10.1016/0304-4076(85)90158-7>, Cribari-Neto (2004)
<doi:10.1016/S0167-9473(02)00366-3>, Cribari-Neto and da Silva
(2011) <doi:10.1007/s10182-010-0141-2>, Cribari-Neto et al. (2007)
<doi:10.1080/03610920601126589>, and Li et al. (2016)
<doi:10.1080/00949655.2016.1198906>. The package also includes HCbeta, a
new estimator proposed by the package authors. It provides normal Wald tests,
confidence intervals, diagnostics, and S3 output for applied inference.
Author: Pedro Rafael D. Marinho [aut, cre] ,
Francisco Cribari-Neto [aut] ,
Marina Oliveira Cunha [aut]
Maintainer: Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>
Diff between hcinfer versions 0.1.0 dated 2026-06-10 and 0.1.1 dated 2026-07-13
DESCRIPTION | 6 +- MD5 | 26 ++++++------ NEWS.md | 5 +- R/data.R | 67 +++++++++++++++++++++++++++---- README.md | 25 +++++++---- data/PublicSchools.rda |binary data/PublicSchools2.rda |only inst/doc/hcinfer-hcbeta.html | 28 ++++++------ man/PublicSchools.Rd | 18 ++++---- man/PublicSchools2.Rd |only man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/hcinfer-package.Rd | 1 tests/testthat/helper-data.R | 1 tests/testthat/test-data.R | 53 ++++++++++++++++++++++++ 15 files changed, 176 insertions(+), 54 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.7.0 dated 2026-07-10 and 1.7.0.1 dated 2026-07-13
DESCRIPTION | 8 +-- MD5 | 24 +++++------ R/GPModel.R | 66 ++++++++++++++++++++++++++++++-- configure | 10 ++-- configure.ac | 10 ++-- man/GPModel.Rd | 5 +- man/GPModel_shared_params.Rd | 29 +++++++++++++- man/fitGPModel.Rd | 5 +- src/include/GPBoost/likelihoods.h | 6 +- src/include/GPBoost/re_model.h | 3 - src/include/GPBoost/re_model_template.h | 17 ++++---- src/include/LightGBM/c_api.h | 3 - src/re_model.cpp | 7 ++- 13 files changed, 148 insertions(+), 45 deletions(-)
Title: Securely Wrangle Dataset According to Data Usage Agreement
Description: Create shareable data sets from raw data files that
contain protected elements. Relying on master crosswalk
files that list restricted variables, package functions
warn users about possible violations of data usage
agreement and prevent writing protected elements.
Author: Benjamin Skinner [aut, cre]
Maintainer: Benjamin Skinner <ben@btskinner.io>
Diff between duawranglr versions 0.6.7 dated 2021-04-15 and 0.6.8 dated 2026-07-13
DESCRIPTION | 31 - MD5 | 22 - NAMESPACE | 1 NEWS.md | 4 R/duawrangler.R | 6 build/vignette.rds |binary inst/doc/duawranglr.Rmd | 2 inst/doc/duawranglr.html | 292 +++++++++++++- inst/doc/securing_data.R | 74 +-- inst/doc/securing_data.html | 865 +++++++++++++++++++++++++++++--------------- man/duawranglr.Rd | 19 vignettes/duawranglr.Rmd | 2 12 files changed, 940 insertions(+), 378 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 3.11.0 dated 2026-06-30 and 3.11.1 dated 2026-07-13
ctsem-3.11.0/ctsem/R/ctCheckFit.R |only ctsem-3.11.0/ctsem/R/ctStanContinuousPars.R |only ctsem-3.11.0/ctsem/R/ctStanData.R |only ctsem-3.11.0/ctsem/R/ctStanFit.R |only ctsem-3.11.0/ctsem/R/ctStanGenerate.R |only ctsem-3.11.0/ctsem/R/ctStanGenerateFromFit.R |only ctsem-3.11.0/ctsem/R/ctStanKalman.R |only ctsem-3.11.0/ctsem/R/ctStanModelWriter.R |only ctsem-3.11.0/ctsem/R/priorcheck.R |only ctsem-3.11.0/ctsem/man/ctAddSamples.Rd |only ctsem-3.11.0/ctsem/man/ctKalman.Rd |only ctsem-3.11.0/ctsem/man/ctStanUpdModel.Rd |only ctsem-3.11.1/ctsem/DESCRIPTION | 8 ctsem-3.11.1/ctsem/MD5 | 119 - ctsem-3.11.1/ctsem/NAMESPACE | 5 ctsem-3.11.1/ctsem/R/ctCoverageCheck.R | 2 ctsem-3.11.1/ctsem/R/ctData.R |only ctsem-3.11.1/ctsem/R/ctDiscretePars.R | 33 ctsem-3.11.1/ctsem/R/ctFit.R |only ctsem-3.11.1/ctsem/R/ctFitCovCheck.R |only ctsem-3.11.1/ctsem/R/ctGenerate.R | 107 + ctsem-3.11.1/ctsem/R/ctGenerateFromFit.R |only ctsem-3.11.1/ctsem/R/ctKalman.R | 261 ++ ctsem-3.11.1/ctsem/R/ctModelLatex.R | 524 ++++- ctsem-3.11.1/ctsem/R/ctModelWriter.R |only ctsem-3.11.1/ctsem/R/ctOptimUncertainty.R |only ctsem-3.11.1/ctsem/R/ctStanModel.R | 16 ctsem-3.11.1/ctsem/R/ctStanPlotPost.R | 19 ctsem-3.11.1/ctsem/R/ctStanPostPredict.R | 11 ctsem-3.11.1/ctsem/R/ctStanTIpredeffects.R | 13 ctsem-3.11.1/ctsem/R/ctSummarise.R | 4 ctsem-3.11.1/ctsem/R/ctsem-package.R | 2 ctsem-3.11.1/ctsem/R/ctsemUtils.R | 56 ctsem-3.11.1/ctsem/R/plot.ctStanFit.R | 8 ctsem-3.11.1/ctsem/R/sdpcor2cov.R | 2 ctsem-3.11.1/ctsem/R/stanoptimis.R | 1078 +----------- ctsem-3.11.1/ctsem/R/summary.ctStanFit.R | 300 +++ ctsem-3.11.1/ctsem/README.md | 4 ctsem-3.11.1/ctsem/inst/doc/empirical-bayes-fitting.html | 90 - ctsem-3.11.1/ctsem/inst/doc/hierarchicalmanual.pdf |binary ctsem-3.11.1/ctsem/inst/doc/hierarchicalmanual.rnw | 6 ctsem-3.11.1/ctsem/man/ctCheckFit.Rd | 2 ctsem-3.11.1/ctsem/man/ctDiscretePars.Rd | 14 ctsem-3.11.1/ctsem/man/ctDiscreteParsPlot.Rd | 16 ctsem-3.11.1/ctsem/man/ctFit.Rd | 41 ctsem-3.11.1/ctsem/man/ctFitAddSamples.Rd |only ctsem-3.11.1/ctsem/man/ctFitCovCheck.Rd | 12 ctsem-3.11.1/ctsem/man/ctFitCovCheckPlot.Rd | 2 ctsem-3.11.1/ctsem/man/ctFitUpdate.Rd | 4 ctsem-3.11.1/ctsem/man/ctFitUpdateModel.Rd |only ctsem-3.11.1/ctsem/man/ctGenerateFromFit.Rd | 12 ctsem-3.11.1/ctsem/man/ctGenerateFromPriors.Rd | 14 ctsem-3.11.1/ctsem/man/ctKalmanArray.Rd | 21 ctsem-3.11.1/ctsem/man/ctModelConvertOMX.Rd | 2 ctsem-3.11.1/ctsem/man/ctModelLatex.Rd | 8 ctsem-3.11.1/ctsem/man/ctOptimUncertainty.Rd | 77 ctsem-3.11.1/ctsem/man/ctPlotPosterior.Rd | 12 ctsem-3.11.1/ctsem/man/ctPostPredict.Rd | 14 ctsem-3.11.1/ctsem/man/ctPredict.Rd |only ctsem-3.11.1/ctsem/man/ctRawParnames.Rd | 2 ctsem-3.11.1/ctsem/man/ctSubjectPars.Rd | 4 ctsem-3.11.1/ctsem/man/ctSummaryMatrices.Rd | 9 ctsem-3.11.1/ctsem/man/ctTIpredEffects.Rd | 15 ctsem-3.11.1/ctsem/man/plot.ctKalmanDF.Rd | 16 ctsem-3.11.1/ctsem/man/plot.ctStanFit.Rd | 2 ctsem-3.11.1/ctsem/man/print.summary.ctStanFit.Rd |only ctsem-3.11.1/ctsem/man/stanoptimis.Rd | 18 ctsem-3.11.1/ctsem/man/summary.ctStanFit.Rd | 4 ctsem-3.11.1/ctsem/tests/testthat/test-ctModelLatex.R |only ctsem-3.11.1/ctsem/tests/testthat/test-ctOptimUncertainty.R | 182 +- ctsem-3.11.1/ctsem/tests/testthat/test-stantipred.R | 5 ctsem-3.11.1/ctsem/vignettes/hierarchicalmanual.rnw | 6 72 files changed, 1610 insertions(+), 1572 deletions(-)
Title: Core Functions to Read and Fit 13c Time Series from Breath Tests
Description: Reads several formats of 13C data (IRIS/Wagner,
BreathID) and CSV. Creates artificial sample data for testing. Fits
Maes/Ghoos, Bluck-Coward self-correcting formula using 'nls', 'nlme'.
Methods to fit breath test curves with Bayesian Stan methods are
refactored to package 'breathteststan'. For a Shiny GUI, see package
'dmenne/breathtestshiny' on github.
Author: Dieter Menne [aut, cre],
Menne Biomed Consulting Tuebingen [cph],
Benjamin Misselwitz [fnd],
Mark Fox [fnd],
Andreas Steingoetter [dtc],
University Hospital of Zurich, Dep. Gastroenterology [fnd, dtc]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between breathtestcore versions 0.8.10 dated 2025-10-28 and 0.8.11 dated 2026-07-13
DESCRIPTION | 8 MD5 | 164 ++++++++++---------- R/breathtest_data.R | 100 ++++++------ R/breathtest_parameters.R | 77 ++++----- R/breathtest_read_function.R | 33 ++-- R/breathtestcore-package.R | 8 R/breathtestcore.R | 59 +++---- R/breathtestfit_broom.R | 103 +++++++----- R/btcore_file.R | 11 - R/cleanup_data.R | 203 ++++++++++++++---------- R/coef_breathtestfit.R | 34 ++-- R/coef_by_group.R | 108 +++++++------ R/coef_diff_by_group.R | 125 ++++++++------- R/dob_to_pdr.R | 48 +++-- R/exp_beta.R | 47 +++-- R/nlme_fit.R | 89 ++++++---- R/nls_fit.R | 127 +++++++++------ R/null_fit.R | 13 - R/plot_breathtestfit.R | 205 +++++++++++++++---------- R/read_any_breathtest.R | 29 +-- R/read_breathid.R | 56 ++++-- R/read_breathid_xml.R | 103 ++++++------ R/read_breathtest_excel.R | 58 ++++--- R/read_iris.R | 62 ++++--- R/read_iris_csv.R | 94 +++++++---- R/sigma.R | 17 -- R/simulate_breathtest_data.R | 165 +++++++++++++------- R/subsample_data.R | 45 +++-- build/vignette.rds |binary inst/doc/data_formats.html | 10 - inst/doc/methods_and_concepts.R | 4 inst/doc/methods_and_concepts.Rmd | 4 inst/doc/methods_and_concepts.html | 12 - man/augment.breathtestfit.Rd | 12 - man/breathtest_data.Rd | 26 +-- man/breathtest_read_function.Rd | 6 man/btcore_file.Rd | 4 man/cleanup_data.Rd | 34 ++-- man/coef.breathtestfit.Rd | 8 man/coef_by_group.Rd | 14 - man/dob_to_pdr.Rd | 6 man/exp_beta.Rd | 10 - man/extract_id.Rd | 4 man/nlme_fit.Rd | 14 - man/nls_fit.Rd | 24 +- man/null_fit.Rd | 6 man/plot.breathtestfit.Rd | 6 man/read_any_breathtest.Rd | 4 man/read_breathid.Rd | 2 man/read_breathtest_excel.Rd | 14 - man/read_iris.Rd | 2 man/read_iris_csv.Rd | 6 man/sigma.breathtestnlmefit.Rd | 2 man/simulate_breathtest_data.Rd | 8 man/subsample_data.Rd | 8 man/t50_bluck_coward.Rd | 22 +- man/t50_maes_ghoos.Rd | 6 man/t50_maes_ghoos_scintigraphy.Rd | 6 man/tidy.breathtestfit.Rd | 6 man/tlag_maes_ghoos.Rd | 6 man/usz_13c.Rd | 4 man/usz_13c_a.Rd | 4 man/usz_13c_d.Rd | 22 +- tests/testthat/test_breathtest_parameters.R | 31 +-- tests/testthat/test_breathtest_read_function.R | 34 ++-- tests/testthat/test_broom.R | 6 tests/testthat/test_cleanup_data.R | 147 +++++++++++------ tests/testthat/test_coef_by_group.R | 85 +++++++--- tests/testthat/test_coef_diff_by_group.R | 81 ++++++--- tests/testthat/test_exp_beta.R | 9 - tests/testthat/test_nlme_fit.R | 74 ++++++--- tests/testthat/test_nls_fit.R | 24 +- tests/testthat/test_plot_breathtestfit.R | 42 ++--- tests/testthat/test_read_any_breathtest.R | 22 +- tests/testthat/test_read_breathid.R | 16 + tests/testthat/test_read_breathid_xml.R | 8 tests/testthat/test_read_excel.R | 61 ++++--- tests/testthat/test_read_iris.R | 53 +++--- tests/testthat/test_read_iris_csv.R | 14 - tests/testthat/test_simulate_breathtest_data.R | 29 ++- tests/testthat/test_subsample_data.R | 10 - tests/testthat/test_usz_13c.R | 32 +-- vignettes/methods_and_concepts.Rmd | 4 83 files changed, 1904 insertions(+), 1395 deletions(-)
More information about breathtestcore at CRAN
Permanent link
Title: Rapid Asynchronous and Distributed Computing
Description: Package to tackle large-scale problems asynchronously across
a distributed network. Employing a database centric model, rush
enables workers to communicate tasks and their results over a shared
'Redis' database. Key features include low task overhead, efficient
caching, and robust error handling. The package powers the
asynchronous optimization algorithms in the 'bbotk' and 'mlr3tuning'
packages.
Author: Marc Becker [cre, aut, cph]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between rush versions 1.1.0 dated 2026-04-24 and 1.2.0 dated 2026-07-13
rush-1.1.0/rush/man/filter_custom_fields.Rd |only rush-1.2.0/rush/DESCRIPTION | 13 rush-1.2.0/rush/MD5 | 59 rush-1.2.0/rush/NAMESPACE | 2 rush-1.2.0/rush/NEWS.md | 75 rush-1.2.0/rush/R/AppenderRedis.R | 49 rush-1.2.0/rush/R/Rush.R | 804 +++++----- rush-1.2.0/rush/R/RushWorker.R | 235 ++ rush-1.2.0/rush/R/assertions.R | 24 rush-1.2.0/rush/R/heartbeat_loops.R | 2 rush-1.2.0/rush/R/helper.R | 16 rush-1.2.0/rush/R/lua_scripts.R |only rush-1.2.0/rush/R/rush_plan.R | 19 rush-1.2.0/rush/R/start_worker.R | 46 rush-1.2.0/rush/R/store_large_object.R | 15 rush-1.2.0/rush/R/zzz.R | 15 rush-1.2.0/rush/README.md | 22 rush-1.2.0/rush/inst/testthat/helper.R | 11 rush-1.2.0/rush/man/AppenderRedis.Rd | 133 - rush-1.2.0/rush/man/Rush.Rd | 1568 +++++++++----------- rush-1.2.0/rush/man/RushWorker.Rd | 331 ++-- rush-1.2.0/rush/man/heartbeat.Rd | 8 rush-1.2.0/rush/man/rush-package.Rd | 26 rush-1.2.0/rush/man/rush_plan.Rd | 13 rush-1.2.0/rush/man/start_worker.Rd | 22 rush-1.2.0/rush/man/store_large_object.Rd | 7 rush-1.2.0/rush/tests/testthat/helper.R | 35 rush-1.2.0/rush/tests/testthat/test-AppenderRedis.R | 9 rush-1.2.0/rush/tests/testthat/test-Rush.R | 445 +++++ rush-1.2.0/rush/tests/testthat/test-RushWorker.R | 193 +- rush-1.2.0/rush/tests/testthat/test-rush_plan.R | 17 rush-1.2.0/rush/tests/testthat/test-start_worker.R |only 32 files changed, 2596 insertions(+), 1618 deletions(-)
Title: Processing and Transforming Relational Event History Data
Description: Efficiently processes relational event history data and transforms them into formats suitable for other packages. The primary objective of this package is to convert event history data into a format that integrates with the packages in 'remverse' and is compatible with various analytical tools (e.g., computing network statistics, estimating tie-oriented or actor-oriented social network models). Second, it can also transform the data into formats compatible with other packages out of 'remverse'. The package processes the data for two types of temporal social network models: tie-oriented modeling framework (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>) and actor-oriented modeling framework (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>).
Author: Giuseppe Arena [aut, cre] ,
Joris Mulder [aut],
Rumana Lakdawala [ctb],
Marlyne Meijerink-Bosman [ctb],
Diana Karimova [ctb],
Fabio Generoso Vieira [ctb],
Mahdi Shafiee Kamalabad [ctb],
Roger Leenders [ctb]
Maintainer: Giuseppe Arena <g.arena@uva.nl>
Diff between remify versions 4.0.0 dated 2026-05-04 and 4.1.0 dated 2026-07-13
remify-4.0.0/remify/inst/tinytest/test-remify2-thin.R |only remify-4.1.0/remify/DESCRIPTION | 8 remify-4.1.0/remify/MD5 | 59 - remify-4.1.0/remify/NAMESPACE | 3 remify-4.1.0/remify/NEWS.md | 5 remify-4.1.0/remify/R/data.R | 5 remify-4.1.0/remify/R/plot.remify.R |only remify-4.1.0/remify/R/remify2.R | 398 ++++--- remify-4.1.0/remify/R/remify_durem.R |only remify-4.1.0/remify/R/remify_util.R | 562 ---------- remify-4.1.0/remify/R/summary_remify.R | 12 remify-4.1.0/remify/inst/datasets |only remify-4.1.0/remify/inst/doc/remify.R | 2 remify-4.1.0/remify/inst/doc/remify.Rmd | 10 remify-4.1.0/remify/inst/doc/remify.html | 32 remify-4.1.0/remify/inst/doc/riskset.R | 2 remify-4.1.0/remify/inst/doc/riskset.Rmd | 10 remify-4.1.0/remify/inst/doc/riskset.html | 26 remify-4.1.0/remify/inst/tinytest/simple-tests.R | 4 remify-4.1.0/remify/inst/tinytest/test-remify-durem.R |only remify-4.1.0/remify/inst/tinytest/test-remify-methods2.R | 25 remify-4.1.0/remify/inst/tinytest/test-remify2-actor.R | 12 remify-4.1.0/remify/inst/tinytest/test-remify2-aggregate_time.R |only remify-4.1.0/remify/inst/tinytest/test-remify2-typed-events.R | 4 remify-4.1.0/remify/inst/tinytest/test-summary-remify.R | 18 remify-4.1.0/remify/inst/tinytest/tests_remify2.R | 7 remify-4.1.0/remify/man/dot-durem_normalize_edgelist.Rd |only remify-4.1.0/remify/man/dot-remify_durem_init.Rd |only remify-4.1.0/remify/man/history.Rd | 7 remify-4.1.0/remify/man/is.remify_durem.Rd |only remify-4.1.0/remify/man/plot.remify.Rd | 56 remify-4.1.0/remify/man/print.remify_durem.Rd |only remify-4.1.0/remify/man/remify.Rd | 93 + remify-4.1.0/remify/man/summary.remify_durem.Rd |only remify-4.1.0/remify/vignettes/remify.Rmd | 10 remify-4.1.0/remify/vignettes/riskset.Rmd | 10 36 files changed, 487 insertions(+), 893 deletions(-)
Title: Correction of Heaping on Individual Level
Description: Provides methods for correcting heaping (digit preference) in
survey data at the individual record level. Age heaping, where respondents
disproportionately report ages ending in 0 or 5, is a common phenomenon that
can distort demographic analyses. Unlike traditional smoothing methods that
only correct aggregated statistics, this package corrects individual values
by replacing a calculated proportion of heaped observations with draws from
fitted truncated distributions (log-normal, normal, or uniform). Supports
5-year and 10-year heaping patterns, single heap correction, survey
weights, and optional covariate-conditional (model-based) correction via
quantile regression forests or linear models to preserve relationships. A
multiple-imputation wrapper repeats the correction to propagate the added
uncertainty into downstream inference.
Author: Matthias Templ [aut, cre] ,
Bernhard Meindl [ctb]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between heaping versions 0.1.0 dated 2026-02-09 and 0.2.0 dated 2026-07-13
DESCRIPTION | 13 MD5 | 27 - NAMESPACE | 2 NEWS.md |only R/correctHeap.R | 582 +++++++++----------------- R/correctHeapsMI.R |only R/heaping-package.R | 30 - R/impute-model.R |only inst/doc/heaping-intro.html | 755 +++++++++++++++++------------------ man/correctHeaps.Rd | 73 ++- man/correctHeapsMI.Rd |only man/correctSingleHeap.Rd | 16 man/heaping-package.Rd | 30 - tests/testthat/test-conditional.R |only tests/testthat/test-correctHeaps.R | 56 ++ tests/testthat/test-correctHeapsMI.R |only tests/testthat/test-heap-ratios.R |only tests/testthat/test-marginal.R |only tests/testthat/test-select.R |only 19 files changed, 771 insertions(+), 813 deletions(-)
Title: Fuzzy Statistical Tools
Description: The main goal of this package is to present various fuzzy statistical tools. It intends to provide an implementation of the theoretical and empirical approaches presented in the book entitled "The signed distance measure in fuzzy statistical analysis. Some theoretical, empirical and programming advances" <doi: 10.1007/978-3-030-76916-1>. For the theoretical approaches, see Berkachy R. and Donze L. (2019) <doi:10.1007/978-3-030-03368-2_1>. For the empirical approaches, see Berkachy R. and Donze L. (2016) <ISBN: 978-989-758-201-1>). Important (non-exhaustive) implementation highlights of this package are as follows: (1) a numerical procedure to estimate the fuzzy difference and the fuzzy square. (2) two numerical methods of fuzzification. (3) a function performing different possibilities of distances, including the signed distance and the generalized signed distance for instance with all its properties. (4) numerical estimations of fuzzy statistical measures such as the [...truncated...]
Author: Redina Berkachy [aut, cre] ,
Laurent Donze [aut]
Maintainer: Redina Berkachy <redina.berkachy@hefr.ch>
Diff between FuzzySTs versions 0.4 dated 2025-07-31 and 0.5 dated 2026-07-13
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++++++---------- NAMESPACE | 5 +++++ NEWS.md | 9 +++++++-- R/PRM_13072026.R |only README.md | 2 +- build/partial.rdb |only build/vignette.rds |binary inst/doc/Vignette_A.html | 7 ++++--- inst/doc/Vignette_B.html | 7 ++++--- inst/doc/Vignette_C.html | 35 ++++++++++++++++++----------------- inst/doc/Vignette_D.html | 1 + inst/doc/Vignette_E.html | 1 + man/FuzzySTs-package.Rd |only man/prm_polygon.Rd |only man/prm_trapezoid.Rd |only man/prm_triangle.Rd |only man/summary_prm.Rd |only man/summary_prm_scores.Rd |only 19 files changed, 63 insertions(+), 40 deletions(-)
Title: Access the 'CDC PLACES' API
Description: Allows users to seamlessly query several 'CDC PLACES' APIs (<https://data.cdc.gov/browse?q=PLACES%20&sortBy=relevance>)
by geography, state, measure, and release year. This package also contains a
function to explore the available measures for each release year.
Author: Brenden Smith [aut, cre]
Maintainer: Brenden Smith <smit2535@msu.edu>
Diff between CDCPLACES versions 1.2.1 dated 2026-05-22 and 1.2.2 dated 2026-07-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 7 +++++++ R/get_places.R | 10 +++++----- R/sysdata.rda |binary 5 files changed, 20 insertions(+), 13 deletions(-)
Title: Nonparametric Bounds for the Average Causal Effect Due to Balke
and Pearl and Extensions
Description: Implementation of the nonparametric bounds for the average
causal effect under an instrumental variable model by Balke and Pearl
(Bounds on Treatment Effects from Studies with Imperfect Compliance,
JASA, 1997, 92, 439, 1171-1176, <doi:10.1080/01621459.1997.10474074>). The package
can calculate bounds for a binary outcome, a binary
treatment/phenotype, and an instrument with either 2 or 3 categories.
The package implements bounds for situations where these 3 variables
are measured in the same dataset (trivariate data) or where the
outcome and instrument are measured in one study and the
treatment/phenotype and instrument are measured in another study
(bivariate data).
Author: Tom Palmer [aut, cre] ,
Roland Ramsahai [aut] ,
Vanessa Didelez [aut] ,
Nuala Sheehan [aut]
Maintainer: Tom Palmer <remlapmot@hotmail.com>
Diff between bpbounds versions 0.1.7 dated 2026-05-24 and 0.1.8 dated 2026-07-13
DESCRIPTION | 6 +- MD5 | 30 ++++++------ NEWS.md | 16 ++++++ R/bpbounds.R | 13 +++++ R/bpbounds_calc_biv_z2.R | 26 ++++++---- R/bpbounds_calc_biv_z3.R | 22 +++++--- R/bpbounds_calc_tri_z2.R | 6 ++ R/bpbounds_calc_tri_z3.R | 8 ++- R/bpbounds_tri_x2y2z3.R | 4 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/bpbounds.Rmd | 5 -- inst/doc/bpbounds.html | 25 ++++------ inst/shiny-examples/myapp/app.R | 65 ++++++++++---------------- tests/testthat/test-bpbounds.R | 100 +++++++++++++++++++++++++++++++--------- vignettes/bpbounds.Rmd | 5 -- 16 files changed, 216 insertions(+), 115 deletions(-)
Title: A Docking Layout Manager for 'blockr'
Description: Building on the docking layout manager provided by 'dockViewR',
this provides a flexible front-end to 'blockr.core'. It provides an extension mechanism which allows for providing means to manipulate a board
object via panel-based user interface components.
Author: Nicolas Bennett [aut, cre],
David Granjon [aut]
Maintainer: Nicolas Bennett <nicolas@cynkra.com>
Diff between blockr.dock versions 0.1.1 dated 2026-04-29 and 0.1.2 dated 2026-07-13
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blockr.dock-0.1.2/blockr.dock/R/utils-serve.R | 51 blockr.dock-0.1.2/blockr.dock/R/utils-ui.R | 110 - blockr.dock-0.1.2/blockr.dock/README.md | 27 blockr.dock-0.1.2/blockr.dock/build/vignette.rds |binary blockr.dock-0.1.2/blockr.dock/inst/assets/css/blockr-dock.css | 229 ++ blockr.dock-0.1.2/blockr.dock/inst/assets/css/sidebar-block.css |only blockr.dock-0.1.2/blockr.dock/inst/assets/css/sidebar-link.css |only blockr.dock-0.1.2/blockr.dock/inst/assets/css/sidebar-server.css |only blockr.dock-0.1.2/blockr.dock/inst/assets/css/sidebar-stack.css |only blockr.dock-0.1.2/blockr.dock/inst/assets/js/sidebar-block.js |only blockr.dock-0.1.2/blockr.dock/inst/assets/js/sidebar-link.js |only blockr.dock-0.1.2/blockr.dock/inst/assets/js/sidebar-server.js |only blockr.dock-0.1.2/blockr.dock/inst/assets/js/sidebar-stack.js |only blockr.dock-0.1.2/blockr.dock/inst/assets/js/view-binding.js | 87 blockr.dock-0.1.2/blockr.dock/inst/doc/layouts.R | 125 - blockr.dock-0.1.2/blockr.dock/inst/doc/layouts.Rmd | 522 +++- blockr.dock-0.1.2/blockr.dock/inst/doc/layouts.html | 692 ++++-- blockr.dock-0.1.2/blockr.dock/inst/examples/edit-add |only blockr.dock-0.1.2/blockr.dock/inst/examples/edit-board |only blockr.dock-0.1.2/blockr.dock/inst/examples/locked-dock/app.R | 5 blockr.dock-0.1.2/blockr.dock/inst/examples/multi-view |only blockr.dock-0.1.2/blockr.dock/inst/examples/serdes |only blockr.dock-0.1.2/blockr.dock/inst/examples/single-page/app.R | 5 blockr.dock-0.1.2/blockr.dock/inst/examples/sized-grid |only blockr.dock-0.1.2/blockr.dock/inst/examples/views/app.R | 23 blockr.dock-0.1.2/blockr.dock/man/action.Rd | 8 blockr.dock-0.1.2/blockr.dock/man/dock-grid.Rd |only blockr.dock-0.1.2/blockr.dock/man/dock-layout.Rd |only blockr.dock-0.1.2/blockr.dock/man/dock.Rd | 64 blockr.dock-0.1.2/blockr.dock/man/extension.Rd | 31 blockr.dock-0.1.2/blockr.dock/man/figures/views.png |binary blockr.dock-0.1.2/blockr.dock/man/ids.Rd | 16 blockr.dock-0.1.2/blockr.dock/man/layout.Rd | 118 - 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Title: Optimize PTSD Diagnostic Criteria
Description: Provides tools for analyzing and optimizing PTSD (Post-Traumatic
Stress Disorder) diagnostic criteria using PCL-5 (PTSD Checklist for DSM-5)
and CAPS-5 (Clinician-Administered PTSD Scale for DSM-5) data. Functions identify optimal subsets of PCL-5 items that maintain
diagnostic accuracy while reducing assessment burden. Includes tools for
both hierarchical (cluster-based) and non-hierarchical symptom combinations,
calculation of diagnostic metrics, and comparison with standard DSM-5
criteria. Model validation is conducted using holdout and cross-validation
methods to assess robustness and generalizability of the results. For more
details see Weidmann et al. (2025) <doi:10.31219/osf.io/6rk72_v1>.
Author: Laura Weidmann [aut] ,
Tobias R. Spiller [aut, cre] ,
Flavio A. Schueepp [aut]
Maintainer: Tobias R. Spiller <tobias.spiller@access.uzh.ch>
Diff between PTSDdiag versions 0.1.0 dated 2026-02-13 and 0.4.1 dated 2026-07-13
PTSDdiag-0.1.0/PTSDdiag/inst/doc/introduction.R |only PTSDdiag-0.1.0/PTSDdiag/inst/doc/introduction.Rmd |only PTSDdiag-0.1.0/PTSDdiag/inst/doc/introduction.html |only PTSDdiag-0.1.0/PTSDdiag/vignettes/introduction.Rmd |only PTSDdiag-0.4.1/PTSDdiag/DESCRIPTION | 21 PTSDdiag-0.4.1/PTSDdiag/MD5 | 119 + PTSDdiag-0.4.1/PTSDdiag/NAMESPACE | 22 PTSDdiag-0.4.1/PTSDdiag/NEWS.md | 455 +++++ PTSDdiag-0.4.1/PTSDdiag/R/alternative_criteria.R |only PTSDdiag-0.4.1/PTSDdiag/R/analysis.R | 793 +++++----- PTSDdiag-0.4.1/PTSDdiag/R/apply_combinations.R |only PTSDdiag-0.4.1/PTSDdiag/R/compare_optimizations.R |only PTSDdiag-0.4.1/PTSDdiag/R/data_preparation.R | 312 +++ PTSDdiag-0.4.1/PTSDdiag/R/definitions.R |only PTSDdiag-0.4.1/PTSDdiag/R/helping_functions.R | 162 -- PTSDdiag-0.4.1/PTSDdiag/R/internals.R |only PTSDdiag-0.4.1/PTSDdiag/R/io_combinations.R |only PTSDdiag-0.4.1/PTSDdiag/R/scenario_plots.R |only PTSDdiag-0.4.1/PTSDdiag/R/scenario_tables.R |only PTSDdiag-0.4.1/PTSDdiag/R/score_all_combinations.R |only PTSDdiag-0.4.1/PTSDdiag/R/scoring_and_diagnosis.R | 85 - PTSDdiag-0.4.1/PTSDdiag/R/simulated_ptsd.R | 16 PTSDdiag-0.4.1/PTSDdiag/R/simulated_ptsd_genpop.R |only PTSDdiag-0.4.1/PTSDdiag/R/validation.R | 557 +++---- PTSDdiag-0.4.1/PTSDdiag/README.md | 55 PTSDdiag-0.4.1/PTSDdiag/build/vignette.rds |binary PTSDdiag-0.4.1/PTSDdiag/data/simulated_ptsd.rda |binary PTSDdiag-0.4.1/PTSDdiag/data/simulated_ptsd_genpop.rda |only PTSDdiag-0.4.1/PTSDdiag/inst/CITATION |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/caps5-workflow.R |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/caps5-workflow.Rmd |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/caps5-workflow.html |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/comparing-criteria.R |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/comparing-criteria.Rmd |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/comparing-criteria.html |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/getting-started.R |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/getting-started.Rmd |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/getting-started.html |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/multi-site-validation.R |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/multi-site-validation.Rmd |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/multi-site-validation.html |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/validation.R |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/validation.Rmd |only PTSDdiag-0.4.1/PTSDdiag/inst/doc/validation.html |only PTSDdiag-0.4.1/PTSDdiag/man/analyze_best_six_symptoms_four_required.Rd | 49 PTSDdiag-0.4.1/PTSDdiag/man/analyze_best_six_symptoms_four_required_clusters.Rd | 50 PTSDdiag-0.4.1/PTSDdiag/man/apply_symptom_combinations.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/as_definitions.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/check_pcl5_data.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/compare_diagnostic_systems.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/compare_optimizations.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/create_caps5_diagnosis.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/create_icd11_diagnosis.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/create_ptsd_diagnosis_nonbinarized.Rd | 6 PTSDdiag-0.4.1/PTSDdiag/man/create_readable_summary.Rd | 13 PTSDdiag-0.4.1/PTSDdiag/man/cross_validation.Rd | 89 - PTSDdiag-0.4.1/PTSDdiag/man/evaluate_definitions.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/extract_definitions.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/holdout_validation.Rd | 75 PTSDdiag-0.4.1/PTSDdiag/man/optimize_combinations.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/optimize_combinations_clusters.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/plot_symptom_frequency.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/print.ptsdiag_comparison.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/read_combinations.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/rename_caps5_columns.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/rename_ptsd_columns.Rd | 30 PTSDdiag-0.4.1/PTSDdiag/man/score_all_combinations.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/simulated_ptsd.Rd | 17 PTSDdiag-0.4.1/PTSDdiag/man/simulated_ptsd_genpop.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/summarize_ptsd.Rd | 4 PTSDdiag-0.4.1/PTSDdiag/man/summarize_ptsd_changes.Rd | 5 PTSDdiag-0.4.1/PTSDdiag/man/summarize_top_combinations.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/symptom_frequency.Rd |only PTSDdiag-0.4.1/PTSDdiag/man/write_combinations.Rd |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-alternative_criteria.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-analysis.R | 293 +++ PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-balanced_accuracy.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-compare_optimizations.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-data.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-data_preparation.R | 194 ++ PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-definitions.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-helping_functions.R | 147 + PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-io_combinations.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-scenario_plots.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-scenario_tables.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-score_all_combinations.R |only PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-scoring_and_diagnosis.R | 26 PTSDdiag-0.4.1/PTSDdiag/tests/testthat/test-validation.R | 328 +++- PTSDdiag-0.4.1/PTSDdiag/vignettes/caps5-workflow.Rmd |only PTSDdiag-0.4.1/PTSDdiag/vignettes/comparing-criteria.Rmd |only PTSDdiag-0.4.1/PTSDdiag/vignettes/getting-started.Rmd |only PTSDdiag-0.4.1/PTSDdiag/vignettes/multi-site-validation.Rmd |only PTSDdiag-0.4.1/PTSDdiag/vignettes/validation.Rmd |only 93 files changed, 2878 insertions(+), 1045 deletions(-)
Title: Fitting the Multinomial Probit Model
Description: Fits the Bayesian multinomial probit model via Markov chain
Monte Carlo. The multinomial probit model is often used to analyze
the discrete choices made by individuals recorded in survey data.
Examples where the multinomial probit model may be useful include the
analysis of product choice by consumers in market research and the
analysis of candidate or party choice by voters in electoral studies.
The MNP package can also fit the model with different choice sets for
each individual, and complete or partial individual choice orderings
of the available alternatives from the choice set. The estimation is
based on the efficient marginal data augmentation algorithm that is
developed by Imai and van Dyk (2005). "A Bayesian Analysis of the
Multinomial Probit Model Using the Data Augmentation." Journal of
Econometrics, Vol. 124, No. 2 (February), pp. 311-334.
<doi:10.1016/j.jeconom.2004.02.002> Detailed examples are given in
Imai and van Dyk (2005). "MNP: R Package for Fitting the Multi [...truncated...]
Author: Kosuke Imai [aut, cre],
David van Dyk [aut],
Hubert Jin [ctb]
Maintainer: Kosuke Imai <imai@harvard.edu>
Diff between MNP versions 3.1-5 dated 2024-06-20 and 3.1-6 dated 2026-07-13
ChangeLog | 3 ++- DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ build/vignette.rds |binary inst/doc/MNP.Rnw | 4 ++-- inst/doc/MNP.pdf |binary vignettes/MNP.Rnw | 4 ++-- 7 files changed, 15 insertions(+), 14 deletions(-)
Title: Continuous Norming
Description: Generates continuous test norms in
psychometrics and biometrics, and analyzing model fit. The package offers
both distribution-free modeling using Taylor polynomials and parametric
modeling using the beta-binomial and the 'Sinh-Arcsinh' distribution.
Originally developed for achievement tests, it is applicable to a wide
range of mental, physical, or other test scores dependent on continuous or
discrete explanatory variables. The package provides several advantages:
It minimizes deviations from representativeness in subsamples, interpolates
between discrete levels of explanatory variables, and significantly reduces
the required sample size compared to conventional norming per age group.
cNORM enables graphical and analytical evaluation of model fit,
accommodates a wide range of scales including those with negative and
descending values, and as well supports conventional norming. It generates
norm tables including confidence intervals. Methods for addressing
representativeness issues are [...truncated...]
Author: Alexandra Lenhard [aut] ,
Wolfgang Lenhard [cre, aut] ,
Sebastian Gary [aut],
WPS Publisher [fnd]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Diff between cNORM versions 3.6.0 dated 2026-06-17 and 3.6.1 dated 2026-07-13
DESCRIPTION | 6 MD5 | 107 - NAMESPACE | 4 NEWS.md | 99 + R/betaBinomial.R | 2347 ++++++++++++++++++-------------------- R/cNORM.R | 11 R/modelling.R | 1633 +++++++++++++------------- R/plot.R | 711 +++++------ inst/doc/BetaBinomial.html | 48 inst/doc/WeightedRegression.html | 41 inst/doc/cNORM-Demo.html | 236 +-- inst/doc/sinh.html | 56 man/autoselect.betabinomial.Rd | 17 man/bb_design_matrix.Rd |only man/bb_distribution.Rd |only man/bb_prepare_data.Rd |only man/bb_resolve_scale.Rd |only man/bestModel.Rd | 70 - man/betaCoefficients.Rd | 33 man/buildFunction.Rd | 1 man/cNORM.Rd | 5 man/checkConsistency.Rd | 38 man/checkWeights.Rd | 29 man/cnorm.betabinomial.Rd | 64 - man/cnorm.betabinomial1.Rd | 44 man/cnorm.betabinomial2.Rd | 42 man/cnorm.cv.Rd | 78 - man/compare.Rd | 17 man/computeWeights.Rd | 170 +- man/derive.Rd | 16 man/diagnostics.betabinomial.Rd | 47 man/getNormScoreSE.Rd | 21 man/log_likelihood.Rd | 20 man/log_likelihood2.Rd | 30 man/modelSummary.Rd | 3 man/normTable.betabinomial.Rd | 30 man/plot.cnormBetaBinomial.Rd | 32 man/plot.cnormBetaBinomial2.Rd | 19 man/plotPercentileSeries.Rd | 46 man/plotSubset.Rd | 49 man/predict.cnormBetaBinomial.Rd | 25 man/predict.cnormBetaBinomial2.Rd | 28 man/predictCoefficients.Rd | 18 man/predictCoefficients2.Rd | 14 man/print.cnorm.Rd | 3 man/printSubset.Rd | 10 man/rangeCheck.Rd | 10 man/regressionFunction.Rd | 3 man/standardizeRakingWeights.Rd | 43 man/subsample_lm.Rd | 26 man/summary.cnorm.Rd | 3 man/summary.cnormBetaBinomial.Rd | 25 man/summary.cnormBetaBinomial2.Rd | 39 man/taylorSwift.Rd | 7 man/weighted.rank.Rd | 46 man/weightedAverageModel.Rd |only tests/testthat/test.modelling.R | 145 ++ 57 files changed, 3553 insertions(+), 3112 deletions(-)
Title: Clinical Publication
Description: Accelerate the process from clinical data to medical publication,
including clinical data cleaning, significant result screening, and the
generation of publish-ready tables and figures.
Author: Yue Niu [aut, cre, cph] ,
Keyun Wang [aut]
Maintainer: Yue Niu <niuyuesam@163.com>
Diff between clinpubr versions 1.4.0 dated 2026-05-24 and 1.4.1 dated 2026-07-13
DESCRIPTION | 32 +- MD5 | 44 +-- NAMESPACE | 6 NEWS.md | 10 R/RcppExports.R |only R/extract_history.R |only R/group_by_range.R |only R/interactions.R | 11 R/misc.R | 8 R/regressions.R | 4 R/to_date.R | 2 R/unit_standardize.R | 16 - R/utils.R | 2 inst/doc/baseline-table.html | 4 inst/doc/data-cleaning.html | 476 ++++++++++++++++----------------- inst/doc/model-evaluation.html | 14 inst/doc/regression-analysis.html | 16 - man/emp_colors.Rd | 5 man/extract_history.Rd |only man/extract_history_single.Rd |only man/group_by_range.Rd |only man/group_by_range_cpp.Rd |only man/regression_basic_results.Rd | 4 src |only tests/testthat/test-extract_history.R |only tests/testthat/test-group_by_range.R |only tests/testthat/test-unit_standardize.R | 92 ++++++ tools |only 28 files changed, 445 insertions(+), 301 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Description: Bayesian network structure learning, parameter learning and inference.
This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, MMPC,
Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing,
Tabu Search, DirectLiNGAM) and hybrid (MMHC, RSMAX2, H2PC) structure learning
algorithms for discrete, Gaussian, conditional Gaussian and zero-inflated
networks, along with many score functions and conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also
implemented. Some utility functions (model comparison and manipulation,
random data generation, arc orientation testing, simple and advanced plots)
are included, as well as support for parameter estimation (maximum likelihood
and Bayesian) and inference, conditional probability queries, interventions,
counterfactuals, cross-validation, bootstrap and model averaging. Development
snapshots with the latest bugfixes are available from
<https://www.bnlearn.com/>.
Author: Marco Scutari [aut, cre],
Tomi Silander [ctb]
Maintainer: Marco Scutari <scutari@bnlearn.com>
Diff between bnlearn versions 5.1 dated 2025-08-20 and 5.2 dated 2026-07-13
bnlearn-5.1/bnlearn/R/utils-elist.R |only bnlearn-5.1/bnlearn/man/bn.class.Rd |only bnlearn-5.1/bnlearn/man/bn.fit.class.Rd |only bnlearn-5.1/bnlearn/man/bn.kcv.class.Rd |only bnlearn-5.1/bnlearn/src/arcs/arcs2elist.c |only bnlearn-5.1/bnlearn/src/bnlearn |only bnlearn-5.1/bnlearn/src/graphs/path.matrix.c |only bnlearn-5.1/bnlearn/src/graphs/rinterface/path.matrix.c |only bnlearn-5.1/bnlearn/src/graphs/sid.c |only bnlearn-5.1/bnlearn/src/predict/predict.c |only bnlearn-5.1/bnlearn/src/scores/dirichlet.averaged.posterior.c |only bnlearn-5.2/bnlearn/Changelog | 66 - bnlearn-5.2/bnlearn/DESCRIPTION | 34 bnlearn-5.2/bnlearn/MD5 | 569 +++++----- bnlearn-5.2/bnlearn/NAMESPACE | 33 bnlearn-5.2/bnlearn/R/all.equal.R |only bnlearn-5.2/bnlearn/R/aracne.R | 8 bnlearn-5.2/bnlearn/R/averaged.fitted.R | 73 + bnlearn-5.2/bnlearn/R/backend-indep.R | 38 bnlearn-5.2/bnlearn/R/backend-s4.R | 5 bnlearn-5.2/bnlearn/R/bootstrap.R | 30 bnlearn-5.2/bnlearn/R/causal.R | 375 +++++- bnlearn-5.2/bnlearn/R/chow.liu.R | 6 bnlearn-5.2/bnlearn/R/ci.test.R | 4 bnlearn-5.2/bnlearn/R/classifiers.R | 7 bnlearn-5.2/bnlearn/R/cpdag.R | 448 +++++++ bnlearn-5.2/bnlearn/R/cpq.R | 2 bnlearn-5.2/bnlearn/R/custom.fit.R | 168 +- bnlearn-5.2/bnlearn/R/cv.R | 2 bnlearn-5.2/bnlearn/R/enumeration.R | 6 bnlearn-5.2/bnlearn/R/fast-iamb.R | 33 bnlearn-5.2/bnlearn/R/fit.R | 87 + bnlearn-5.2/bnlearn/R/fitted.assignment.R | 71 + bnlearn-5.2/bnlearn/R/foreign-read.R | 12 bnlearn-5.2/bnlearn/R/foreign-write.R | 8 bnlearn-5.2/bnlearn/R/frontend-amat.R | 64 + bnlearn-5.2/bnlearn/R/frontend-arcs.R | 7 bnlearn-5.2/bnlearn/R/frontend-averaging.R | 19 bnlearn-5.2/bnlearn/R/frontend-bn.R | 33 bnlearn-5.2/bnlearn/R/frontend-bootstrap.R | 17 bnlearn-5.2/bnlearn/R/frontend-causal.R | 173 ++- bnlearn-5.2/bnlearn/R/frontend-fit.R | 89 + bnlearn-5.2/bnlearn/R/frontend-graph.R | 29 bnlearn-5.2/bnlearn/R/frontend-learning.R | 165 +- bnlearn-5.2/bnlearn/R/frontend-missingdata.R | 8 bnlearn-5.2/bnlearn/R/frontend-packages.R | 10 bnlearn-5.2/bnlearn/R/frontend-plot.R | 30 bnlearn-5.2/bnlearn/R/frontend-predict.R | 24 bnlearn-5.2/bnlearn/R/frontend-print.R | 97 + bnlearn-5.2/bnlearn/R/frontend-queries.R | 2 bnlearn-5.2/bnlearn/R/gRain.R | 4 bnlearn-5.2/bnlearn/R/globals.R | 67 - 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bnlearn-5.2/bnlearn/src/core/sets.h | 1 bnlearn-5.2/bnlearn/src/core/uppertriangular.c | 2 bnlearn-5.2/bnlearn/src/fitted/enums.c | 6 bnlearn-5.2/bnlearn/src/fitted/fitted.c | 38 bnlearn-5.2/bnlearn/src/fitted/fitted.h | 31 bnlearn-5.2/bnlearn/src/fitted/nparams.c | 12 bnlearn-5.2/bnlearn/src/fitted/rinterface/nodes.and.arcs.c |only bnlearn-5.2/bnlearn/src/fitted/topological.sort.c |only bnlearn-5.2/bnlearn/src/globals.c | 23 bnlearn-5.2/bnlearn/src/graphs/graphs.h | 14 bnlearn-5.2/bnlearn/src/graphs/nparams.c |only bnlearn-5.2/bnlearn/src/graphs/path.c | 2 bnlearn-5.2/bnlearn/src/graphs/pdag2dag.c | 5 bnlearn-5.2/bnlearn/src/graphs/random/graph.generation.c | 15 bnlearn-5.2/bnlearn/src/graphs/rinterface/all.equal.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/cache.structure.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/cextend.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/colliders.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/connected.components.c | 4 bnlearn-5.2/bnlearn/src/graphs/rinterface/cpdag.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/nodes.and.arcs.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/nparams.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/shd.c |only bnlearn-5.2/bnlearn/src/graphs/rinterface/sid.c | 425 ++++++- bnlearn-5.2/bnlearn/src/graphs/topological.ordering.c | 18 bnlearn-5.2/bnlearn/src/include/globals.h | 4 bnlearn-5.2/bnlearn/src/include/graph.h | 1 bnlearn-5.2/bnlearn/src/include/register.h | 23 bnlearn-5.2/bnlearn/src/include/sampling.h | 30 bnlearn-5.2/bnlearn/src/inference/likelihood.weighting.c | 61 - bnlearn-5.2/bnlearn/src/inference/loglikelihood/common.c | 2 bnlearn-5.2/bnlearn/src/inference/loglikelihood/conditional.gaussian.c | 50 bnlearn-5.2/bnlearn/src/inference/loglikelihood/discrete.c | 34 bnlearn-5.2/bnlearn/src/inference/loglikelihood/gaussian.c | 18 bnlearn-5.2/bnlearn/src/inference/loglikelihood/loglikelihood.h | 16 bnlearn-5.2/bnlearn/src/inference/loglikelihood/zero.inflated.c |only bnlearn-5.2/bnlearn/src/inference/rbn.c | 503 ++++---- bnlearn-5.2/bnlearn/src/inference/rinterface/cpdist.c | 24 bnlearn-5.2/bnlearn/src/inference/rinterface/likelihood.weighting.c | 28 bnlearn-5.2/bnlearn/src/inference/rinterface/loglikelihood.c | 44 bnlearn-5.2/bnlearn/src/inference/rinterface/rbn.c | 120 ++ bnlearn-5.2/bnlearn/src/learning/averaging/averaging.c | 6 bnlearn-5.2/bnlearn/src/learning/averaging/bootstrap.c | 8 bnlearn-5.2/bnlearn/src/learning/local/mi.matrix.c | 58 - bnlearn-5.2/bnlearn/src/learning/rinterface |only bnlearn-5.2/bnlearn/src/learning/score/hc.cache.lookup.c | 12 bnlearn-5.2/bnlearn/src/learning/score/score.delta.c | 7 bnlearn-5.2/bnlearn/src/learning/score/tabu.c | 2 bnlearn-5.2/bnlearn/src/math/conditional.least.squares.c | 2 bnlearn-5.2/bnlearn/src/math/hypergeometric.c |only bnlearn-5.2/bnlearn/src/math/hypergeometric.h |only bnlearn-5.2/bnlearn/src/math/hyperpoisson.c |only bnlearn-5.2/bnlearn/src/math/hyperpoisson.h |only bnlearn-5.2/bnlearn/src/math/linear.algebra.c | 29 bnlearn-5.2/bnlearn/src/math/reweighted.least.squares.c |only bnlearn-5.2/bnlearn/src/math/reweighted.least.squares.h |only bnlearn-5.2/bnlearn/src/math/sparse.amat.c |only bnlearn-5.2/bnlearn/src/math/sparse.amat.h |only bnlearn-5.2/bnlearn/src/math/xnegbin.c |only bnlearn-5.2/bnlearn/src/math/xnegbin.h |only bnlearn-5.2/bnlearn/src/minimal/common.c | 2 bnlearn-5.2/bnlearn/src/minimal/data.frame.c | 34 bnlearn-5.2/bnlearn/src/minimal/data.frame.h | 2 bnlearn-5.2/bnlearn/src/minimal/tiers.c | 3 bnlearn-5.2/bnlearn/src/parameters/discrete/classic.discrete.c | 1 bnlearn-5.2/bnlearn/src/parameters/discrete/hierarchical.dirichlet.c | 2 bnlearn-5.2/bnlearn/src/parameters/enums.c |only bnlearn-5.2/bnlearn/src/parameters/parameters.h | 26 bnlearn-5.2/bnlearn/src/parameters/rinterface/classic.discrete.c | 1 bnlearn-5.2/bnlearn/src/parameters/rinterface/hierarchical.dirichlet.c | 5 bnlearn-5.2/bnlearn/src/parameters/rinterface/mixture.ordinary.least.squares.c | 6 bnlearn-5.2/bnlearn/src/parameters/rinterface/ordinary.least.squares.c | 2 bnlearn-5.2/bnlearn/src/parameters/rinterface/zero.inflated.c |only bnlearn-5.2/bnlearn/src/predict/map.lw.c | 229 +--- bnlearn-5.2/bnlearn/src/predict/naivebayes.c |only bnlearn-5.2/bnlearn/src/predict/parents.c |only bnlearn-5.2/bnlearn/src/predict/predict.h |only bnlearn-5.2/bnlearn/src/predict/rinterface |only bnlearn-5.2/bnlearn/src/preprocessing/dedup.c | 26 bnlearn-5.2/bnlearn/src/preprocessing/discretize.c | 12 bnlearn-5.2/bnlearn/src/preprocessing/enums.c | 5 bnlearn-5.2/bnlearn/src/preprocessing/preprocessing.h | 2 bnlearn-5.2/bnlearn/src/preprocessing/rinterface/discretize.c | 65 - bnlearn-5.2/bnlearn/src/sanitization/cg.assumptions.c | 4 bnlearn-5.2/bnlearn/src/sanitization/covariance.c | 2 bnlearn-5.2/bnlearn/src/sanitization/data.c | 43 bnlearn-5.2/bnlearn/src/sanitization/data.h | 1 bnlearn-5.2/bnlearn/src/scores/alpha.star.c | 8 bnlearn-5.2/bnlearn/src/scores/cg.loglikelihood.c | 8 bnlearn-5.2/bnlearn/src/scores/cg.nal.c | 6 bnlearn-5.2/bnlearn/src/scores/cg.predictive.loglikelihood.c | 6 bnlearn-5.2/bnlearn/src/scores/custom.score.c | 1 bnlearn-5.2/bnlearn/src/scores/dirichlet.posterior.c | 2 bnlearn-5.2/bnlearn/src/scores/discrete.loglikelihood.c | 4 bnlearn-5.2/bnlearn/src/scores/discrete.nal.c | 4 bnlearn-5.2/bnlearn/src/scores/discrete.predictive.loglikelihood.c | 5 bnlearn-5.2/bnlearn/src/scores/enum.c | 16 bnlearn-5.2/bnlearn/src/scores/gaussian.loglikelihood.c | 5 bnlearn-5.2/bnlearn/src/scores/gaussian.nal.c | 5 bnlearn-5.2/bnlearn/src/scores/gaussian.predictive.loglikelihood.c | 5 bnlearn-5.2/bnlearn/src/scores/graph.priors.c | 14 bnlearn-5.2/bnlearn/src/scores/nml.regret.c | 1 bnlearn-5.2/bnlearn/src/scores/normalized.maximum.likelihood.c | 4 bnlearn-5.2/bnlearn/src/scores/per.node.score.c | 128 +- bnlearn-5.2/bnlearn/src/scores/scores.h | 34 bnlearn-5.2/bnlearn/src/scores/wishart.posterior.c | 22 bnlearn-5.2/bnlearn/src/scores/zero.inflated.coefs.c |only bnlearn-5.2/bnlearn/src/scores/zero.inflated.em.c |only bnlearn-5.2/bnlearn/src/tests/conditional.gaussian/cg.mutual.information.c | 3 bnlearn-5.2/bnlearn/src/tests/discrete/jonckheere.c | 2 bnlearn-5.2/bnlearn/src/tests/discrete/shrinkage.c | 8 bnlearn-5.2/bnlearn/src/tests/enums.c | 5 bnlearn-5.2/bnlearn/src/tests/gaussian/shrinkage.c | 9 bnlearn-5.2/bnlearn/src/tests/patterns.h | 47 bnlearn-5.2/bnlearn/src/tests/patterns/allsubs.test.c | 252 ++-- bnlearn-5.2/bnlearn/src/tests/patterns/ctest.c | 141 +- bnlearn-5.2/bnlearn/src/tests/patterns/roundrobin.test.c | 178 +-- bnlearn-5.2/bnlearn/src/tests/patterns/utest.c | 10 bnlearn-5.2/bnlearn/src/tests/permutation/discrete.monte.carlo.c | 5 bnlearn-5.2/bnlearn/src/tests/permutation/gaussian.monte.carlo.c | 7 bnlearn-5.2/bnlearn/src/tests/rinterface/allsubs.test.c | 62 - bnlearn-5.2/bnlearn/src/tests/rinterface/ctest.c | 56 bnlearn-5.2/bnlearn/src/tests/rinterface/htest.c | 2 bnlearn-5.2/bnlearn/src/tests/rinterface/roundrobin.test.c | 40 bnlearn-5.2/bnlearn/src/tests/rinterface/utest.c | 4 307 files changed, 6569 insertions(+), 4215 deletions(-)
Title: Beta Kernel Process Modeling
Description: Implements the Beta Kernel Process (BKP) for nonparametric modeling of
covariate-dependent binomial probabilities, and the Dirichlet Kernel Process (DKP) for
categorical or multinomial response data. Scalable global-local approximations
are provided through TwinBKP and TwinDKP, using twinning-selected global subsets
and local nearest-neighbour updates.
Functions are included for model fitting, predictive inference with
uncertainty quantification, posterior simulation,
and visualization in one- and two-dimensional input spaces.
Gaussian, Matern 5/2, Matern 3/2, and Wendland kernels are supported,
with hyperparameters selected by multi-start derivative-free optimization.
For more details, see Zhao, Qing, and Xu (2025) <doi:10.48550/arXiv.2508.10447>.
Author: Jiangyan Zhao [cre, aut],
Kunhai Qing [aut],
Jin Xu [aut]
Maintainer: Jiangyan Zhao <zhaojy2017@126.com>
Diff between BKP versions 0.3.0 dated 2026-07-02 and 0.3.1 dated 2026-07-13
DESCRIPTION | 9 MD5 | 27 NEWS.md | 6 R/fit_BKP.R | 849 ++++++++++------------ R/fit_DKP.R | 859 +++++++++++----------- R/plot_BKP.R | 860 +++++++++++----------- R/plot_DKP.R | 820 ++++++++++----------- R/plot_TwinBKP.R | 748 +++++++++---------- R/plot_TwinDKP.R | 1118 ++++++++++++++--------------- README.md | 278 +++++-- inst/CITATION | 2 man/figures/README-bkp-demonstration-1.png |only man/fit_BKP.Rd | 36 man/fit_DKP.Rd | 36 man/plot.Rd | 6 15 files changed, 2909 insertions(+), 2745 deletions(-)
Title: Tools for Choice Model Estimation and Application
Description: Choice models are a widely used technique across numerous scientific disciplines. The Apollo package is a very flexible tool for the estimation and application
of choice models in R. Users are able to write their own
model functions or use a mix of already available ones. Random heterogeneity,
both continuous and discrete and at the level of individuals and
choices, can be incorporated for all models. There is support for both standalone
models and hybrid model structures. Both classical
and Bayesian estimation is available, and multiple discrete
continuous models are covered in addition to discrete choice.
Multi-threading processing is supported for estimation and a large
number of pre and post-estimation routines, including for computing posterior
(individual-level) distributions are available.
For examples, a manual, and a support forum, visit
<https://www.ApolloChoiceModelling.com>. For more information on choice
models see Train, K. (2009) <isbn:978-0-521-74738-7> and [...truncated...]
Author: Stephane Hess [aut, cre],
David Palma [aut],
Thomas Hancock [ctb]
Maintainer: Stephane Hess <S.Hess@leeds.ac.uk>
Diff between apollo versions 0.3.8 dated 2026-05-17 and 0.3.9 dated 2026-07-13
apollo-0.3.8/apollo/R/apollo_cnl2.R |only apollo-0.3.8/apollo/man/apollo_cnl2.Rd |only apollo-0.3.9/apollo/DESCRIPTION | 6 apollo-0.3.9/apollo/MD5 | 309 ++++---- apollo-0.3.9/apollo/NAMESPACE | 1 apollo-0.3.9/apollo/R/apollo_avgInterDraws.R | 9 apollo-0.3.9/apollo/R/apollo_avgIntraDraws.R | 3 apollo-0.3.9/apollo/R/apollo_basTest.R | 3 apollo-0.3.9/apollo/R/apollo_bootstrap.R | 53 + apollo-0.3.9/apollo/R/apollo_checkArguments.R | 26 apollo-0.3.9/apollo/R/apollo_choiceAnalysis.R | 32 apollo-0.3.9/apollo/R/apollo_classAlloc.R | 41 + apollo-0.3.9/apollo/R/apollo_cnl.R | 49 + apollo-0.3.9/apollo/R/apollo_combineModels.R | 7 apollo-0.3.9/apollo/R/apollo_combineResults.R | 57 + apollo-0.3.9/apollo/R/apollo_compareInputs.R | 6 apollo-0.3.9/apollo/R/apollo_conditionals.R | 4 apollo-0.3.9/apollo/R/apollo_dVdB.R | 8 apollo-0.3.9/apollo/R/apollo_deltaMethod.R | 40 - apollo-0.3.9/apollo/R/apollo_detach.R | 4 apollo-0.3.9/apollo/R/apollo_dft.R | 52 + apollo-0.3.9/apollo/R/apollo_diagnostics.R | 13 apollo-0.3.9/apollo/R/apollo_drugChoiceData.R | 2 apollo-0.3.9/apollo/R/apollo_el.R | 74 +- apollo-0.3.9/apollo/R/apollo_emdc.R | 40 - apollo-0.3.9/apollo/R/apollo_estimate.R | 79 +- apollo-0.3.9/apollo/R/apollo_expandLoop.R | 145 +--- apollo-0.3.9/apollo/R/apollo_firstRow.R | 7 apollo-0.3.9/apollo/R/apollo_fitsTest.R | 15 apollo-0.3.9/apollo/R/apollo_fmnl.R | 34 apollo-0.3.9/apollo/R/apollo_fnl.R | 87 ++ apollo-0.3.9/apollo/R/apollo_initialise.R | 2 apollo-0.3.9/apollo/R/apollo_insertComponentName.R | 18 apollo-0.3.9/apollo/R/apollo_insertFunc.R | 20 apollo-0.3.9/apollo/R/apollo_insertOLList.R | 262 +++---- apollo-0.3.9/apollo/R/apollo_insertQuotes.R | 184 ++--- apollo-0.3.9/apollo/R/apollo_lc.R | 40 - apollo-0.3.9/apollo/R/apollo_lcConditionals.R | 16 apollo-0.3.9/apollo/R/apollo_lcEM.R | 133 +++ apollo-0.3.9/apollo/R/apollo_lcUnconditionals.R | 18 apollo-0.3.9/apollo/R/apollo_llCalc.R | 13 apollo-0.3.9/apollo/R/apollo_loadModel.R | 20 apollo-0.3.9/apollo/R/apollo_longToWide.R | 58 + apollo-0.3.9/apollo/R/apollo_lrTest.R | 25 apollo-0.3.9/apollo/R/apollo_makeDraws.R | 20 apollo-0.3.9/apollo/R/apollo_mdcev.R | 37 - apollo-0.3.9/apollo/R/apollo_mdcnev.R | 100 ++ apollo-0.3.9/apollo/R/apollo_mixConditionals.R | 19 apollo-0.3.9/apollo/R/apollo_mixEM.R | 125 ++- apollo-0.3.9/apollo/R/apollo_mixUnconditionals.R | 28 apollo-0.3.9/apollo/R/apollo_mnl.R | 57 + apollo-0.3.9/apollo/R/apollo_mnl_hessian_fix.R |only apollo-0.3.9/apollo/R/apollo_modeChoiceData.R | 6 apollo-0.3.9/apollo/R/apollo_modelOutput.R | 46 + apollo-0.3.9/apollo/R/apollo_modifyUserDefFunc.R | 5 apollo-0.3.9/apollo/R/apollo_nl.R | 93 ++ apollo-0.3.9/apollo/R/apollo_normalDensity.R | 99 ++ apollo-0.3.9/apollo/R/apollo_ol.R | 93 ++ apollo-0.3.9/apollo/R/apollo_op.R | 100 ++ apollo-0.3.9/apollo/R/apollo_outOfSample.R | 101 ++ apollo-0.3.9/apollo/R/apollo_ownModel.R | 45 + apollo-0.3.9/apollo/R/apollo_panelProd.R | 15 apollo-0.3.9/apollo/R/apollo_prediction.R | 153 +++- apollo-0.3.9/apollo/R/apollo_prepareProb.R | 19 apollo-0.3.9/apollo/R/apollo_print.R | 34 apollo-0.3.9/apollo/R/apollo_readBeta.R | 12 apollo-0.3.9/apollo/R/apollo_rrm.R | 81 +- apollo-0.3.9/apollo/R/apollo_saveOutput.R | 114 ++- apollo-0.3.9/apollo/R/apollo_searchStart.R | 590 +++++++++-------- apollo-0.3.9/apollo/R/apollo_setRows.R | 9 apollo-0.3.9/apollo/R/apollo_setWorkDir.R | 43 - apollo-0.3.9/apollo/R/apollo_sharesTest.R | 57 + apollo-0.3.9/apollo/R/apollo_sink.R | 68 + apollo-0.3.9/apollo/R/apollo_speedTest.R | 95 ++ apollo-0.3.9/apollo/R/apollo_swissRouteChoiceData.R | 16 apollo-0.3.9/apollo/R/apollo_timeUseData.R | 21 apollo-0.3.9/apollo/R/apollo_tobit.R | 97 ++ apollo-0.3.9/apollo/R/apollo_unconditionals.R | 38 - apollo-0.3.9/apollo/R/apollo_validate.R | 12 apollo-0.3.9/apollo/R/apollo_validateControl.R | 73 +- apollo-0.3.9/apollo/R/apollo_validateData.R | 23 apollo-0.3.9/apollo/R/apollo_validateInputs.R | 9 apollo-0.3.9/apollo/R/apollo_varList.R | 7 apollo-0.3.9/apollo/R/apollo_varcov.R | 49 + apollo-0.3.9/apollo/R/apollo_weighting.R | 28 apollo-0.3.9/apollo/R/apollo_writeF12.R | 202 ++--- apollo-0.3.9/apollo/R/summary.apollo.R | 2 apollo-0.3.9/apollo/inst/doc/apollofirstexample.html | 28 apollo-0.3.9/apollo/man/apollo_avgInterDraws.Rd | 7 apollo-0.3.9/apollo/man/apollo_avgIntraDraws.Rd | 3 apollo-0.3.9/apollo/man/apollo_bootstrap.Rd | 11 apollo-0.3.9/apollo/man/apollo_choiceAnalysis.Rd | 19 apollo-0.3.9/apollo/man/apollo_classAlloc.Rd | 4 apollo-0.3.9/apollo/man/apollo_cnl.Rd | 6 apollo-0.3.9/apollo/man/apollo_combineModels.Rd | 7 apollo-0.3.9/apollo/man/apollo_combineResults.Rd | 2 apollo-0.3.9/apollo/man/apollo_compareInputs.Rd | 6 apollo-0.3.9/apollo/man/apollo_conditionals.Rd | 4 apollo-0.3.9/apollo/man/apollo_dVdB.Rd | 2 apollo-0.3.9/apollo/man/apollo_deltaMethod.Rd | 8 apollo-0.3.9/apollo/man/apollo_detach.Rd | 4 apollo-0.3.9/apollo/man/apollo_dft.Rd | 10 apollo-0.3.9/apollo/man/apollo_diagnostics.Rd | 12 apollo-0.3.9/apollo/man/apollo_drugChoiceData.Rd | 2 apollo-0.3.9/apollo/man/apollo_el.Rd | 12 apollo-0.3.9/apollo/man/apollo_estimate.Rd | 24 apollo-0.3.9/apollo/man/apollo_expandLoop.Rd | 10 apollo-0.3.9/apollo/man/apollo_firstRow.Rd | 3 apollo-0.3.9/apollo/man/apollo_fitsTest.Rd | 6 apollo-0.3.9/apollo/man/apollo_fmnl.Rd | 10 apollo-0.3.9/apollo/man/apollo_fnl.Rd | 21 apollo-0.3.9/apollo/man/apollo_insertComponentName.Rd | 6 apollo-0.3.9/apollo/man/apollo_insertFunc.Rd | 14 apollo-0.3.9/apollo/man/apollo_insertOLList.Rd | 2 apollo-0.3.9/apollo/man/apollo_insertRRMQuotes.Rd | 2 apollo-0.3.9/apollo/man/apollo_lc.Rd | 10 apollo-0.3.9/apollo/man/apollo_lcConditionals.Rd | 4 apollo-0.3.9/apollo/man/apollo_lcEM.Rd | 10 apollo-0.3.9/apollo/man/apollo_lcUnconditionals.Rd | 6 apollo-0.3.9/apollo/man/apollo_loadModel.Rd | 2 apollo-0.3.9/apollo/man/apollo_longToWide.Rd | 7 apollo-0.3.9/apollo/man/apollo_mdcev.Rd | 12 apollo-0.3.9/apollo/man/apollo_mdcnev.Rd | 10 apollo-0.3.9/apollo/man/apollo_mixConditionals.Rd | 11 apollo-0.3.9/apollo/man/apollo_mixEM.Rd | 12 apollo-0.3.9/apollo/man/apollo_mixUnconditionals.Rd | 2 apollo-0.3.9/apollo/man/apollo_mnl.Rd | 33 apollo-0.3.9/apollo/man/apollo_modeChoiceData.Rd | 6 apollo-0.3.9/apollo/man/apollo_modelOutput.Rd | 9 apollo-0.3.9/apollo/man/apollo_nl.Rd | 8 apollo-0.3.9/apollo/man/apollo_normalDensity.Rd | 10 apollo-0.3.9/apollo/man/apollo_ol.Rd | 11 apollo-0.3.9/apollo/man/apollo_op.Rd | 8 apollo-0.3.9/apollo/man/apollo_outOfSample.Rd | 18 apollo-0.3.9/apollo/man/apollo_ownModel.Rd | 11 apollo-0.3.9/apollo/man/apollo_panelProd.Rd | 8 apollo-0.3.9/apollo/man/apollo_prediction.Rd | 8 apollo-0.3.9/apollo/man/apollo_prepareProb.Rd | 8 apollo-0.3.9/apollo/man/apollo_readBeta.Rd | 4 apollo-0.3.9/apollo/man/apollo_rrm.Rd | 16 apollo-0.3.9/apollo/man/apollo_saveOutput.Rd | 21 apollo-0.3.9/apollo/man/apollo_searchStart.Rd | 10 apollo-0.3.9/apollo/man/apollo_setWorkDir.Rd | 7 apollo-0.3.9/apollo/man/apollo_sharesTest.Rd | 4 apollo-0.3.9/apollo/man/apollo_sink.Rd | 5 apollo-0.3.9/apollo/man/apollo_speedTest.Rd | 8 apollo-0.3.9/apollo/man/apollo_swissRouteChoiceData.Rd | 16 apollo-0.3.9/apollo/man/apollo_timeUseData.Rd | 54 - apollo-0.3.9/apollo/man/apollo_tobit.Rd | 13 apollo-0.3.9/apollo/man/apollo_unconditionals.Rd | 18 apollo-0.3.9/apollo/man/apollo_validateControl.Rd | 24 apollo-0.3.9/apollo/man/apollo_validateData.Rd | 6 apollo-0.3.9/apollo/man/apollo_validateInputs.Rd | 5 apollo-0.3.9/apollo/man/apollo_varList.Rd | 9 apollo-0.3.9/apollo/man/apollo_varcov.Rd | 18 apollo-0.3.9/apollo/man/apollo_weighting.Rd | 4 apollo-0.3.9/apollo/man/apollo_writeF12.Rd | 2 157 files changed, 3679 insertions(+), 1890 deletions(-)
Title: Cross-Platform 'zip' Compression
Description: Cross-Platform 'zip' Compression Library. A replacement for
the 'zip' function, that does not require any additional external
tools on any platform.
Author: Gabor Csardi [aut, cre],
Kuba Podgorski [ctb],
Rich Geldreich [ctb],
Arm Limited [ctb, cph] ),
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between zip versions 3.0.0 dated 2026-06-10 and 3.0.1 dated 2026-07-13
DESCRIPTION | 6 +++--- MD5 | 27 ++++++++++++++------------- NEWS.md | 17 +++++++++++++++++ R/threaded.R | 10 ++++++++++ R/utils.R | 5 +++-- R/zip.R | 3 ++- man/unzip.Rd | 3 ++- src/miniz.c | 21 +++++++++++++++++++++ src/zip.c | 7 +++++-- tests/testthat/_snaps/threaded-unzip.md | 8 ++++++++ tests/testthat/test-threaded-unzip.R | 26 +++++++++++++++++++++++++- tests/testthat/test-unzip.R | 6 +++--- tests/testthat/test-utils.R |only tests/testthat/test-zip.R | 19 +++++++++++++++++-- tools/extra/miniz.patch | 27 +++++++++++++++++++++++++++ 15 files changed, 157 insertions(+), 28 deletions(-)
Title: Time Series Analysis and Computational Finance
Description: Time series analysis and computational finance.
Author: Adrian Trapletti [aut],
Kurt Hornik [aut, cre] ,
Blake LeBaron [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tseries versions 0.10-61 dated 2026-03-26 and 0.10-62 dated 2026-07-13
ChangeLog | 4 ++++ DESCRIPTION | 9 ++++----- MD5 | 24 ++++++++++++------------ build/partial.rdb |binary data/NelPlo.rda |binary data/USeconomic.rda |binary data/bev.rda |binary data/camp.rda |binary data/ice.river.rda |binary data/nino.rda |binary data/tcm.rda |binary data/tcmd.rda |binary man/white.test.Rd | 3 +++ 13 files changed, 23 insertions(+), 17 deletions(-)
Title: Text Analysis Utilities
Description: Utilities for text analysis.
Author: Christian Buchta [aut],
Kurt Hornik [aut, cre] ,
Ingo Feinerer [aut] ,
David Meyer [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tau versions 0.0-28 dated 2026-03-26 and 0.0-29 dated 2026-07-13
DESCRIPTION | 6 ++-- MD5 | 16 ++++++------ R/sysdata.rda |binary build/partial.rdb |binary src/textcnt.c | 6 +++- tests/counting.R | 20 ++++++++-------- tests/counting.Rout.save | 47 ++++++++++++++------------------------ tests/counting_useBytes.R | 20 ++++++++-------- tests/counting_useBytes.Rout.save | 45 +++++++++++++----------------------- 9 files changed, 72 insertions(+), 88 deletions(-)
Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices,
based on index arrays and simple triplet representations, respectively.
Author: Kurt Hornik [aut, cre] ,
David Meyer [aut] ,
Christian Buchta [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between slam versions 0.1-55 dated 2024-11-13 and 0.1-56 dated 2026-07-13
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- man/array.Rd | 5 +++++ tests/stm_rollup.R | 2 +- tests/stm_rollup.Rout.save | 12 +++++------- 5 files changed, 20 insertions(+), 17 deletions(-)
Title: R/Weka Interface
Description: An R interface to Weka (Version 3.9.3).
Weka is a collection of machine learning algorithms for data mining
tasks written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Package 'RWeka' contains the interface code, the
Weka jar is in a separate package 'RWekajars'. For more information
on Weka see <https://www.cs.waikato.ac.nz/ml/weka/>.
Author: Kurt Hornik [aut, cre] ,
Christian Buchta [ctb],
Torsten Hothorn [ctb],
Alexandros Karatzoglou [ctb],
David Meyer [ctb],
Achim Zeileis [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between RWeka versions 0.4-48 dated 2026-03-26 and 0.4-49 dated 2026-07-13
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/RWeka.R | 2 -- inst/doc/RWeka.pdf |binary man/Weka_classifier_trees.Rd | 11 +++++++++++ tests/data_exchange.R | 14 ++++++++++++-- tests/data_exchange.Rout.save | 22 ++++++++++++++++------ 9 files changed, 50 insertions(+), 21 deletions(-)
Title: Apache OpenNLP Tools Interface
Description: An interface to the Apache OpenNLP tools (version 1.5.3).
The Apache OpenNLP library is a machine learning based toolkit for the
processing of natural language text written in Java.
It supports the most common NLP tasks, such as tokenization, sentence
segmentation, part-of-speech tagging, named entity extraction, chunking,
parsing, and coreference resolution.
See <https://opennlp.apache.org/> for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between openNLP versions 0.2-7 dated 2019-10-26 and 0.2-8 dated 2026-07-13
DESCRIPTION | 8 +++--- MD5 | 14 +++++----- man/Maxent_Chunk_Annotator.Rd | 41 +++++++++++++++--------------- man/Maxent_Entity_Annotator.Rd | 49 ++++++++++++++++++------------------- man/Maxent_POS_Tag_Annotator.Rd | 4 +-- man/Maxent_Sent_Token_Annotator.Rd | 4 +-- man/Maxent_Word_Token_Annotator.Rd | 4 +-- man/Parse_Annotator.Rd | 45 ++++++++++++++++----------------- 8 files changed, 83 insertions(+), 86 deletions(-)
Title: Natural Language Processing Infrastructure
Description: Basic classes and methods for Natural Language Processing.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between NLP versions 0.3-2 dated 2024-11-20 and 0.3-3 dated 2026-07-13
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/sysdata.rda |binary build/partial.rdb |binary man/CoNLLTextDocument.Rd | 9 ++++++--- man/Tokenizer.Rd | 2 ++ man/datetime.Rd | 3 +++ man/ngrams.Rd | 3 +++ man/viewers.Rd | 1 + 9 files changed, 27 insertions(+), 15 deletions(-)
Title: Machine Learning Benchmark Problems
Description: A collection of artificial and real-world machine learning
benchmark problems, including, e.g., several
data sets from the UCI repository.
Author: Friedrich Leisch [aut] ,
Evgenia Dimitriadou [aut],
Kurt Hornik [cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between mlbench versions 2.1-8 dated 2026-03-26 and 2.1-9 dated 2026-07-13
DESCRIPTION | 7 ++---- MD5 | 48 +++++++++++++++++++++--------------------- NAMESPACE | 22 +++++++++++++++++-- NEWS | 5 ++++ build/partial.rdb |binary data/BostonHousing.rda |binary data/BostonHousing2.rda |binary data/BreastCancer.rda |binary data/DNA.rda |binary data/Glass.rda |binary data/HouseVotes84.rda |binary data/Ionosphere.rda |binary data/LetterRecognition.rda |binary data/Ozone.rda |binary data/PimaIndiansDiabetes.rda |binary data/PimaIndiansDiabetes2.rda |binary data/Satellite.rda |binary data/Servo.rda |binary data/Shuttle.rda |binary data/Sonar.rda |binary data/Soybean.rda |binary data/Vehicle.rda |binary data/Vowel.rda |binary data/Zoo.rda |binary man/mlbench.hypercube.Rd | 1 25 files changed, 52 insertions(+), 31 deletions(-)
Title: Continuous Time Structural Equation Modelling - Old
'OpenMx'-Based Version
Description: Original 'ctsem' (continuous time structural equation modelling)
functionality, based on the 'OpenMx' software, as described in
Driver, Oud, Voelkle (2017) <doi:10.18637/jss.v077.i05>, with updated details in vignette.
Combines stochastic differential equations representing latent processes with
structural equation measurement models. This package is maintained for consistency with the
original 'ctsem' paper, but for the much newer and more capable 'ctsem' package, see
<https://cran.r-project.org/package=ctsem>.
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph]
Maintainer: Charles Driver <charles.driver2@uzh.ch>
Diff between ctsemOMX versions 2.0.0 dated 2026-03-19 and 2.0.1 dated 2026-07-13
DESCRIPTION | 10 MD5 | 22 R/ctDataHelp.R | 214 ++++---- R/ctDiscretiseData.R | 114 ++-- R/ctLongtowide.r | 308 ++++++------ R/ctModel.R | 1212 ++++++++++++++++++++++++------------------------- R/ctsemOMX-package.R | 140 ++--- build/vignette.rds |binary inst/doc/ctsemOMX.pdf |binary inst/doc/ctsemOMX.rnw | 2 man/ctsemOMX.Rd | 1 vignettes/ctsemOMX.rnw | 2 12 files changed, 1013 insertions(+), 1012 deletions(-)
Title: Creating Composite Plots using 'aplot'
Description: Many complex plots are actually composite plots, such as 'oncoplot', 'funkyheatmap', 'upsetplot', etc. We can produce subplots using 'ggplot2' and combine them to create composite plots using 'aplot'. In this way, it is easy to customize these complex plots, by adding, deleting or modifying subplots in the final plot. This package provides a set of utilities to help users to create subplots and complex plots.
Author: Guangchuang Yu [aut, cre] ,
Shuangbin Xu [ctb] ,
Chun-Hui Gao [ctb] ,
Shensuo Li [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between aplotExtra versions 0.0.4 dated 2025-06-12 and 0.0.5 dated 2026-07-13
DESCRIPTION | 12 +++++++----- MD5 | 17 ++++++++++------- NEWS.md | 9 +++++++++ R/funkyheatmap.R | 6 ++---- R/oncoplot.r | 2 +- R/upset.R | 4 ++-- man/aplotExtra-package.Rd | 5 +++++ man/upset_plot.Rd | 2 +- tests |only 9 files changed, 37 insertions(+), 20 deletions(-)
Title: 'rcpp' Wrapper for 'mecab' Library
Description: R package based on 'Rcpp' for 'MeCab': Yet Another Part-of-Speech and Morphological Analyzer.
It provides install-time engine profiles and dictionaries for Japanese,
Korean, and Mandarin Chinese text. Runtime dictionary selection does not
change the installed engine.
This package utilizes parallel programming for providing highly efficient text preprocessing 'posParallel()' function.
For installation, please refer to README.md file.
Author: Junhewk Kim [aut, cre],
Taku Kudo [aut],
Akiru Kato [ctb],
Patrick Schratz [ctb]
Maintainer: Junhewk Kim <junhewk.kim@gmail.com>
Diff between RcppMeCab versions 0.0.1.6 dated 2026-07-12 and 0.0.1.7 dated 2026-07-13
DESCRIPTION | 20 ++++--- MD5 | 37 +++++++------ NEWS.md | 6 +- R/RcppMeCab-package.r | 7 +- R/dic.R | 21 +++++-- R/pos.r | 16 ++++- R/posParallel.R | 16 ++++- README.md | 108 ++++++++++++++++++++++++++++------------ cleanup | 1 configure | 103 ++++++++++++++++++++++++++++++++------ inst/COPYRIGHTS |only man/RcppMeCab.Rd | 7 +- man/download_dic.Rd | 6 +- man/pos.Rd | 16 ++++- man/posParallel.Rd | 16 ++++- man/set_dic.Rd | 13 ++-- src/Makevars.win | 22 ++++++++ tests/testthat/test_pos_ko.R | 2 tests/testthat/test_pos_zh.R |only tools/mecab-dict-index-main.cpp |only tools/winlibs.R | 26 ++++++++- 21 files changed, 331 insertions(+), 112 deletions(-)
Title: Bayesian Inference Using 'RTMB'
Description: Provides tools for Markov chain Monte Carlo (MCMC) and Maximum A Posteriori (MAP) estimation utilizing the 'RTMB' package. It supports various statistical models including generalized linear mixed models, factor analysis, item response theory, and multidimensional unfolding. The package allows users to easily transition between frequentist and Bayesian paradigms using a unified interface. Automatic differentiation and Laplace approximation follow Kristensen et al. (2016) <doi:10.18637/jss.v070.i05>, and MCMC sampling uses the No-U-Turn Sampler described by Hoffman and Gelman (2014) <https://jmlr.org/papers/v15/hoffman14a.html>.
Author: Hiroshi Shimizu [aut, cre]
Maintainer: Hiroshi Shimizu <simizu706@gmail.com>
Diff between BayesRTMB versions 0.2.1 dated 2026-06-23 and 0.2.3 dated 2026-07-13
DESCRIPTION | 6 MD5 | 74 NAMESPACE | 2 NEWS.md | 22 R/Base_Fit.R | 114 R/RTMB_Model_impl_ast.R | 16 R/distributions.R | 152 R/model.R | 200 + R/parameters.R | 29 R/wrapper_corr.R | 2 R/wrapper_fa.R | 62 R/wrapper_lrt.R | 38 R/wrapper_mixture.R | 33 inst/doc/analysis_reference.R | 3 inst/doc/analysis_reference.Rmd | 8 inst/doc/analysis_reference.html | 135 inst/doc/ja-analysis_reference.Rmd | 3396 +++++++++++----------- inst/doc/ja-wrapper_functions.R | 4 inst/doc/ja-wrapper_functions.Rmd | 4 inst/doc/ja-writing_models.R | 89 inst/doc/ja-writing_models.Rmd | 122 inst/doc/ja-writing_models.html | 546 ++- inst/doc/writing_models.R | 88 inst/doc/writing_models.Rmd | 117 inst/doc/writing_models.html | 163 - inst/examples/ex_fa.R | 30 man/RTMB_Fit_Base.Rd | 20 man/diffusion_lpdf.Rd |only man/distributions.Rd | 6 man/exp_mod_normal_lpdf.Rd |only man/rtmb_fa.Rd | 30 tests/testthat/test-obs-syntax.R |only tests/testthat/test-response-time-distributions.R |only tests/testthat/test-rtmb-containers.R | 13 tests/testthat/test-wrappers.R | 119 vignettes/analysis_reference.Rmd | 8 vignettes/ja-analysis_reference.Rmd | 3396 +++++++++++----------- vignettes/ja-wrapper_functions.Rmd | 4 vignettes/ja-writing_models.Rmd | 122 vignettes/writing_models.Rmd | 117 40 files changed, 5427 insertions(+), 3863 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-05-23 3.1.2
2026-05-19 3.1.0
2026-01-11 3.0.4
2025-09-18 2.1.8
2025-09-02 2.1.6
2024-06-02 2.1.0
2024-04-25 2.0.5
2024-04-16 2.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-17 2.0.11
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-05-18 3.1.1
2026-05-16 3.1.0
2026-01-08 3.0.0
2024-12-12 2.1.2
2024-05-29 2.1.0
2024-04-15 2.0.12
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-01-11 2.1.1
2025-10-14 2.0.9
2025-10-11 2.0.8
2024-05-15 2.0.7
2024-04-15 2.0.6
Title: Bayesian Network Meta-Analysis with Missing Participants
Description: A comprehensive suite of functions to perform and visualise
pairwise and network meta-analysis with aggregate binary or continuous
missing participant outcome data. The package covers core Bayesian one-stage
models implemented in a systematic review with multiple interventions,
including fixed-effect and random-effects network meta-analysis,
meta-regression, and evaluation of the consistency assumption via the
node-splitting approach and the unrelated mean effects model (original and
revised model proposed by Spineli, (2021) <doi:10.1177/0272989X211068005>).
Missing participant outcome data are addressed in all models of the package
(see Spineli, (2019) <doi:10.1186/s12874-019-0731-y>, Spineli et al., (2019)
<doi:10.1002/sim.8207>, Spineli, (2019) <doi:10.1016/j.jclinepi.2018.09.002>,
and Spineli et al., (2021) <doi:10.1177/0962280220983544>).
The robustness to primary analysis results can also be investigated using a
novel intuitive index (see Spineli et [...truncated...]
Author: Loukia Spineli [aut, cre],
Chrysostomos Kalyvas [ctb],
Katerina Papadimitropoulou [ctb]
Maintainer: Loukia Spineli <Spineli.Loukia@mh-hannover.de>
Diff between rnmamod versions 0.5.0 dated 2025-06-13 and 0.5.1 dated 2026-07-13
DESCRIPTION | 25 ++++++------ MD5 | 44 ++++++++++----------- NEWS.md | 4 + R/comp.clustering_function.R | 27 +++++++------ R/dendro.heatmap_function.R | 10 +++- R/distr.characteristics_function.R | 8 +++ R/gower.distance_function.R | 26 +++++++++++- R/kld.inconsistency.user_function.R | 6 ++ R/kld.inconsistency_function.R | 6 ++ R/miss.characteristics_function.R | 9 +++- R/plot.study.dissimilarities_function.R | 2 R/rnmamod.R.R | 59 ++++++++++++++++++++++++----- inst/doc/network_description.html | 13 +++--- inst/doc/perform_network_metaanalysis.html | 9 ++-- man/comp_clustering.Rd | 22 ++++++---- man/dendro_heatmap.Rd | 10 +++- man/distr_characteristics.Rd | 8 +++ man/gower_distance.Rd | 20 +++++++++ man/kld_inconsistency.Rd | 6 ++ man/kld_inconsistency_user.Rd | 6 ++ man/miss_characteristics.Rd | 9 +++- man/plot_study_dissimilarities.Rd | 2 man/rnmamod-package.Rd | 59 ++++++++++++++++++++++++----- 23 files changed, 290 insertions(+), 100 deletions(-)
Title: Interface to 'JDemetra+' 3.x Time Series Analysis Software
Description: Interface to 'JDemetra+' 3.x (<https://github.com/jdemetra>)
time series analysis software. It offers full access to txt, csv, xml
and spreadsheets files which are meant to be read by 'JDemetra+'
Graphical User Interface.
Author: Jean Palate [aut],
Alessandro Piovani [aut, cre],
Tanguy Barthelemy [ctb, art]
Maintainer: Alessandro Piovani <alessandro.piovani@istat.it>
Diff between rjd3providers versions 3.7.1 dated 2026-03-11 and 3.8.0 dated 2026-07-13
rjd3providers-3.7.1/rjd3providers/R/deprecated.R |only rjd3providers-3.7.1/rjd3providers/inst/java/caffeine-3.2.3.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/java-io-base-0.0.35.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/java-io-picocsv-0.0.35.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/java-io-xml-0.0.35.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/java-io-xml-bind-0.0.35.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-spreadsheet-base-api-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-spreadsheet-base-r-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-text-base-api-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-text-base-r-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-toolkit-base-tsp-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-toolkit-base-xml-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/spreadsheet-api-2.5.10.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/spreadsheet-standalone-2.5.10.jar |only rjd3providers-3.7.1/rjd3providers/man/deprecated-rjd3providers.Rd |only rjd3providers-3.8.0/rjd3providers/DESCRIPTION | 14 rjd3providers-3.8.0/rjd3providers/MD5 | 116 rjd3providers-3.8.0/rjd3providers/NAMESPACE | 84 rjd3providers-3.8.0/rjd3providers/NEWS.md | 224 - rjd3providers-3.8.0/rjd3providers/R/jd3spreadsheet.R | 768 +++-- rjd3providers-3.8.0/rjd3providers/R/jd3txt.R | 927 ++++--- rjd3providers-3.8.0/rjd3providers/R/jd3xml.R | 576 ++-- rjd3providers-3.8.0/rjd3providers/R/providers.R | 143 - rjd3providers-3.8.0/rjd3providers/R/rjd3providers-package.R |only rjd3providers-3.8.0/rjd3providers/R/zzz.R | 106 rjd3providers-3.8.0/rjd3providers/README.md | 481 +-- rjd3providers-3.8.0/rjd3providers/inst/extdata/ABS.csv | 852 +++--- rjd3providers-3.8.0/rjd3providers/inst/extdata/Prod.xml | 1286 +++++----- rjd3providers-3.8.0/rjd3providers/inst/java/caffeine-3.2.4.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/java-io-base-0.0.38.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/java-io-picocsv-0.0.38.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/java-io-xml-0.0.38.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/java-io-xml-bind-0.0.38.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/jdplus-spreadsheet-base-api-3.8.0.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/jdplus-spreadsheet-base-r-3.8.0.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/jdplus-text-base-api-3.8.0.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/jdplus-text-base-r-3.8.0.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/jdplus-toolkit-base-tsp-3.8.0.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/jdplus-toolkit-base-xml-3.8.0.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/spreadsheet-api-2.6.0.jar |only rjd3providers-3.8.0/rjd3providers/inst/java/spreadsheet-standalone-2.6.0.jar |only rjd3providers-3.8.0/rjd3providers/java/README | 12 rjd3providers-3.8.0/rjd3providers/man/dot-obs_format.Rd | 68 rjd3providers-3.8.0/rjd3providers/man/dot-obs_gathering.Rd | 68 rjd3providers-3.8.0/rjd3providers/man/dot-spreadsheet_moniker.Rd | 46 rjd3providers-3.8.0/rjd3providers/man/dot-txt_moniker.Rd | 46 rjd3providers-3.8.0/rjd3providers/man/dot-xml_moniker.Rd | 46 rjd3providers-3.8.0/rjd3providers/man/figures/logo.svg | 188 - rjd3providers-3.8.0/rjd3providers/man/get_providers_option.Rd |only rjd3providers-3.8.0/rjd3providers/man/providers_option.Rd |only rjd3providers-3.8.0/rjd3providers/man/rjd3providers-package.Rd |only rjd3providers-3.8.0/rjd3providers/man/set_spreadsheet_paths.Rd | 46 rjd3providers-3.8.0/rjd3providers/man/set_txt_paths.Rd | 46 rjd3providers-3.8.0/rjd3providers/man/set_xml_paths.Rd | 46 rjd3providers-3.8.0/rjd3providers/man/spreadsheet_change_file.Rd | 62 rjd3providers-3.8.0/rjd3providers/man/spreadsheet_content.Rd | 50 rjd3providers-3.8.0/rjd3providers/man/spreadsheet_data.Rd | 92 rjd3providers-3.8.0/rjd3providers/man/spreadsheet_id_to_properties.Rd | 66 rjd3providers-3.8.0/rjd3providers/man/spreadsheet_name.Rd | 40 rjd3providers-3.8.0/rjd3providers/man/spreadsheet_properties_to_id.Rd | 68 rjd3providers-3.8.0/rjd3providers/man/spreadsheet_series.Rd | 98 rjd3providers-3.8.0/rjd3providers/man/txt_change_file.Rd | 62 rjd3providers-3.8.0/rjd3providers/man/txt_content.Rd | 132 - rjd3providers-3.8.0/rjd3providers/man/txt_data.Rd | 132 - rjd3providers-3.8.0/rjd3providers/man/txt_id_to_properties.Rd | 54 rjd3providers-3.8.0/rjd3providers/man/txt_name.Rd | 40 rjd3providers-3.8.0/rjd3providers/man/txt_properties_to_id.Rd | 68 rjd3providers-3.8.0/rjd3providers/man/txt_series.Rd | 140 - rjd3providers-3.8.0/rjd3providers/man/xml_change_file.Rd | 62 rjd3providers-3.8.0/rjd3providers/man/xml_content.Rd | 56 rjd3providers-3.8.0/rjd3providers/man/xml_data.Rd | 64 rjd3providers-3.8.0/rjd3providers/man/xml_id_to_properties.Rd | 56 rjd3providers-3.8.0/rjd3providers/man/xml_name.Rd | 40 rjd3providers-3.8.0/rjd3providers/man/xml_properties_to_id.Rd | 56 rjd3providers-3.8.0/rjd3providers/man/xml_series.Rd | 70 75 files changed, 4048 insertions(+), 3649 deletions(-)
Title: A Comprehensive Toolkit for Environmental Mixtures Analysis
Description: Quantitative characterization of the health impacts associated with exposure to chemical mixtures has received considerable attention in current environmental and epidemiological studies. 'CompMix' package allows practitioners to estimate the health impacts from exposure to chemical mixtures data through various statistical approaches, including Lasso, Elastic net, Bayesian kernel machine regression (BKMR), hierNet, Quantile g-computation, Weighted quantile sum (WQS) and Random forest. Methods and recommendations are described in Hao et al. (2025) <doi:10.1289/EHP15305>.
Author: Wei Hao [aut, cre]
Maintainer: Wei Hao <weihao@umich.edu>
This is a re-admission after prior archival of version 0.1.0 dated 2024-05-22
Diff between CompMix versions 0.1.0 dated 2024-05-22 and 1.1.0 dated 2026-07-13
DESCRIPTION | 15 - MD5 | 9 - NAMESPACE | 2 R/environment_mix_lib_package.R | 324 +++++++++++++--------------------------- inst |only man/Comp.Mix.Rd | 30 ++- 6 files changed, 139 insertions(+), 241 deletions(-)
Title: Clustering-Based K-Nearest Neighbor Regression for Longitudinal
Data
Description: Implements the 'CKNNRLD' algorithm (Clustering-Based K-Nearest
Neighbor Regression for Longitudinal Data) for improving K-Nearest
Neighbor ('KNN') regression on longitudinal data through cluster-based
partitioning and localized prediction. Offers enhanced computational
efficiency and accuracy for high-volume longitudinal datasets. The
acronym 'KNN' stands for K-Nearest Neighbor. References: Loeloe MS,
Tabatabaei SM, Sefidkar R, Mehrparvar AH, Jambarsang S (2025).
"Boosting K-nearest neighbor regression performance for longitudinal
data through a novel learning approach." BMC Bioinformatics, 26, 232.
<doi:10.1186/s12859-025-06205-1>.
Author: Mohammad Sadegh Loeloe [aut, cre],
Seyyed Mohammad Tabatabaei [aut],
Reyhane Sefidkar [aut],
Amir Houshang Mehrparvar [aut],
Sara Jambarsang [aut, ths]
Maintainer: Mohammad Sadegh Loeloe <mslbiostat@gmail.com>
Diff between CKNNRLD versions 0.2.0 dated 2026-07-10 and 0.2.2 dated 2026-07-13
CKNNRLD-0.2.0/CKNNRLD/R/return_model.R |only CKNNRLD-0.2.2/CKNNRLD/DESCRIPTION | 6 +++--- CKNNRLD-0.2.2/CKNNRLD/MD5 | 6 +++--- CKNNRLD-0.2.2/CKNNRLD/R/CKNNRLD.R |only CKNNRLD-0.2.2/CKNNRLD/man/CKNNRLD.Rd | 20 ++++++++++---------- 5 files changed, 16 insertions(+), 16 deletions(-)
Title: Bayesian Simultaneous Credible Bands for Polynomial Regression
Description: Provides functions to construct two-sided Bayesian simultaneous
credible bands (BSCBs) for the regression curve in univariate polynomial
regression over a finite covariate interval. Six methods are implemented,
including Normal-Gamma conjugate priors (with empirical Bayes,
unit-information, and g-prior hyperparameter specifications),
non-conjugate priors fitted via Hamiltonian Monte Carlo (HMC) using
'cmdstanr', and a non-informative independent Jeffreys prior approach.
Also includes functions for computing the empirical simultaneous coverage
rate (ESCR) and posterior simultaneous coverage probability (PSCP),
enabling performance comparison across methods. The methodology is
described in:
Yang, F., Han, Y., Liu, W., & Hall, I. (2026). "Bayesian simultaneous
credible bands for polynomial regression" <doi:10.48550/arXiv.2606.28015>.
Author: Fei Yang [aut, cre]
Maintainer: Fei Yang <fei.yang@manchester.ac.uk>
Diff between BSCB versions 1.0.0 dated 2026-07-10 and 1.0.1 dated 2026-07-13
BSCB-1.0.0/BSCB/inst/BSCB_1.0.0.pdf |only BSCB-1.0.1/BSCB/DESCRIPTION | 8 ++++---- BSCB-1.0.1/BSCB/MD5 | 14 +++++++------- BSCB-1.0.1/BSCB/NEWS.md | 13 +++++++++++-- BSCB-1.0.1/BSCB/R/generate_data.R | 12 ++++++++---- BSCB-1.0.1/BSCB/README.md | 15 +++++++++++++++ BSCB-1.0.1/BSCB/inst/BSCB_1.0.1.pdf |only BSCB-1.0.1/BSCB/inst/doc/BSCB-vignette.html | 19 +++++++++---------- BSCB-1.0.1/BSCB/man/generate_simulation_data.Rd | 9 ++++++--- 9 files changed, 60 insertions(+), 30 deletions(-)
Title: Branding, Theme Application and Navigation Utilities for
'bs4Dash' Dashboards
Description: Provides branding, theme application, and navigation utilities for
applications built with 'bs4Dash' and 'shiny'. Supports configurable
sidebar brand display modes, hover-expand behavior, and theme
customization using CSS variables. Includes complete navbar item helpers,
navbar structure validation, reusable brand configuration, prototype
top-navigation support, and helpers for common navigation bar and footer
layouts.
Author: George Arthur [aut, cre]
Maintainer: George Arthur <prigasgenthian48@gmail.com>
Diff between bs4Dashkit versions 0.2.0 dated 2026-04-21 and 0.3.0 dated 2026-07-13
DESCRIPTION | 18 MD5 | 108 ++- NAMESPACE | 49 - NEWS.md | 303 ++++++--- R/assets.R | 62 + R/nav_buttons.R | 207 ++++++ R/navbar_title.R | 4 R/sidebar.R | 22 R/sidebar_mode.R | 995 +++++++++++++++---------------- R/theme.R | 154 ++-- R/titles.R | 391 +++++++----- R/topnav.R |only R/use_core.R | 216 ++++-- R/utils.R | 242 +++++-- README.md | 224 ++++-- build/vignette.rds |binary inst/app-assets/dash-demo-brand.js |only inst/app-assets/dash-topnav.css |only inst/app-assets/dash-topnav.js |only inst/doc/branding-and-sidebar-modes.R | 26 inst/doc/branding-and-sidebar-modes.Rmd | 132 ++-- inst/doc/branding-and-sidebar-modes.html | 259 ++++---- inst/doc/complete-example-app.R | 23 inst/doc/complete-example-app.Rmd | 57 - inst/doc/complete-example-app.html | 203 +++--- inst/doc/getting-started.R | 25 inst/doc/getting-started.Rmd | 195 +++--- inst/doc/getting-started.html | 132 ++-- inst/doc/global-options.Rmd | 26 inst/doc/global-options.html | 6 inst/doc/navigation-utilities.R | 123 ++- inst/doc/navigation-utilities.Rmd | 250 ++++--- inst/doc/navigation-utilities.html | 382 ++++++----- inst/doc/packaged-examples.R |only inst/doc/packaged-examples.Rmd |only inst/doc/packaged-examples.html |only inst/doc/top-navigation.R |only inst/doc/top-navigation.Rmd |only inst/doc/top-navigation.html |only inst/examples/hardening-regression |only inst/examples/real-shiny-app/app.R | 834 ++++++++++++------------- inst/examples/test-all/app.R | 461 +++++++------- inst/examples/topnav-prototype |only man/dash_brand_options.Rd |only man/dash_nav_help_item.Rd |only man/dash_nav_refresh_item.Rd |only man/dash_nav_status_badge.Rd |only man/dash_nav_status_item.Rd |only man/dash_titles_from.Rd |only man/dash_topnav_options.Rd |only man/use_bs4Dashkit.Rd | 41 - man/use_bs4Dashkit_core.Rd | 135 ++-- man/use_dash_sidebar_behavior.Rd | 46 - man/use_dash_topnav.Rd |only man/validate_bs4dash_navbar.Rd |only tests/testthat/test-dash-titles.R | 477 ++++++++------ tests/testthat/test-nav-buttons.R | 65 +- tests/testthat/test-packaged-examples.R |only tests/testthat/test-theme-presets.R | 110 ++- tests/testthat/test-topnav.R |only tests/testthat/test-use-core.R |only vignettes/branding-and-sidebar-modes.Rmd | 132 ++-- vignettes/complete-example-app.Rmd | 57 - vignettes/getting-started.Rmd | 195 +++--- vignettes/global-options.Rmd | 26 vignettes/navigation-utilities.Rmd | 250 ++++--- vignettes/packaged-examples.Rmd |only vignettes/top-navigation.Rmd |only 68 files changed, 4403 insertions(+), 3260 deletions(-)
Title: Spatial Interpolation using Bayesian Maximum Entropy (BME)
Description: Provides an accessible and robust implementation of core BME
methodologies for spatial prediction. It enables the systematic integration
of heterogeneous data sources including both hard data (precise
measurements) and soft interval data (bounded or uncertain observations)
while incorporating prior knowledge and supporting variogram-based spatial
modeling. The BME methodology is described in Christakos (1990)
<doi:10.1007/BF00890661>, Serre and Christakos (1999)
<doi:10.1007/s004770050029> and Duah (2025, 2026)
<doi:10.1016/j.spasta.2026.100974>.
Author: Kinspride Duah [aut, cre, cph] ,
Yan Sun [aut]
Maintainer: Kinspride Duah <kinspride2020@gmail.com>
Diff between BMEmapping versions 1.2.2 dated 2025-08-19 and 2.0.0 dated 2026-07-13
DESCRIPTION | 18 MD5 | 92 +- NAMESPACE | 15 NEWS.md | 65 - R/bme_cv.R | 138 ++- R/bme_estimate.R | 55 + R/bme_kfcv.R |only R/bme_loocv.R |only R/bme_map.R | 9 R/bme_predict.R | 93 +- R/bme_predict_ci.R |only R/ch_nhmax.R | 3 R/check_x.R | 4 R/combine_data.R |only R/covmat.R | 10 R/covmat_avg.R |only R/cs_nsmax.R | 4 R/data.R | 3 R/exponential.R | 2 R/extended_range.R | 4 R/gaussian.R | 2 R/plot.BMEmapping.R | 452 +++++++++---- R/prob_zk.R | 38 - R/q_bme_cv.R |only R/q_bme_estimate.R |only R/q_bme_kfcv.R |only R/q_bme_loocv.R |only R/q_bme_predict.R |only R/q_bme_predict_ci.R |only R/q_prob_zk.R |only R/spherical.R | 4 R/summary.BMEmapping.R | 15 R/vg_results.R |only R/zzz.R | 3 README.md | 86 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction_to_BMEmapping.R | 294 +++++--- inst/doc/Introduction_to_BMEmapping.Rmd | 578 +++++++++++----- inst/doc/Introduction_to_BMEmapping.html | 1072 ++++++++++++++++++++++--------- man/bme_cv.Rd | 59 + man/bme_map.Rd | 4 man/bme_predict.Rd | 39 - man/bme_predict_ci.Rd |only man/casnowload.Rd | 2 man/plot.BMEmapping.Rd | 19 man/prob_zk.Rd | 22 man/q_bme_cv.Rd |only man/q_bme_predict.Rd |only man/q_bme_predict_ci.Rd |only man/q_prob_zk.Rd |only tests/testthat/test-bme_cv.R | 24 tests/testthat/test-bme_predict.R | 57 + tests/testthat/test-covmat.R | 3 tests/testthat/test-prob_zk.R | 13 vignettes/Introduction_to_BMEmapping.Rmd | 578 +++++++++++----- 56 files changed, 2630 insertions(+), 1249 deletions(-)
Title: Modified Poisson Regression for Binary Outcome and Related
Methods
Description: Modified Poisson, logistic and least-squares regression analyses for binary outcomes of Zou (2004) <doi:10.1093/aje/kwh090>, Noma (2026)<doi:10.1016/j.spl.2026.110698>, and Cheung (2007) <doi:10.1093/aje/kwm223> have been standard multivariate analysis methods to estimate risk ratio and risk difference in clinical and epidemiological studies. This R package involves an easy-to-handle function to implement these analyses by simple commands. Missing data analysis tools (multiple imputation) are also involved. In addition, recent studies have shown the ordinary robust variance estimator possibly has serious bias under small or moderate sample size situations for these methods. This package also provides computational tools to calculate alternative accurate confidence intervals.
Author: Hisashi Noma [aut, cre]
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Diff between rqlm versions 4.3-2 dated 2026-02-28 and 4.4-1 dated 2026-07-13
DESCRIPTION | 8 MD5 | 12 - NAMESPACE | 1 NEWS.md | 4 R/rqlm.r | 622 +++++++++++++++++++++++++++++++++++----------------- man/rqlm-package.Rd | 2 man/rqlm.Rd | 297 ++++++++++++++++++++---- 7 files changed, 680 insertions(+), 266 deletions(-)
Title: A Fast and Flexible Pipeline for Text Classification
Description: A high-level pipeline that simplifies text classification into three streamlined steps:
preprocessing, model training, and standardized prediction.
It unifies the interface for multiple algorithms (including 'glmnet', 'ranger',
'xgboost', and 'naivebayes') and memory-efficient sparse matrix vectorization
methods (Bag-of-Words, Term Frequency, TF-IDF, and Binary). Users can go from
raw text to a fully evaluated sentiment model, complete with ROC-optimized
thresholds, in just a few function calls. The resulting model artifact
automatically aligns the vocabulary of new datasets during the prediction phase,
safely appending predicted classes and probability matrices directly to the
user's original dataframe to preserve metadata.
Author: Alabhya Dahal [aut, cre]
Maintainer: Alabhya Dahal <alabhya.dahal@gmail.com>
Diff between quickSentiment versions 0.3.4 dated 2026-04-16 and 0.3.5 dated 2026-07-13
DESCRIPTION | 6 +-- MD5 | 36 +++++++++--------- NEWS.md | 5 +- R/logit.R | 15 ++++++- R/nb.R | 3 + R/pipeline.R | 25 +++++++++++- R/rf.R | 14 +++++-- R/xgb.R | 13 ++++-- README.md | 2 + inst/WORDLIST | 15 ++++--- inst/doc/introduction-to-quickSentiment.R | 2 + inst/doc/introduction-to-quickSentiment.Rmd | 2 + inst/doc/introduction-to-quickSentiment.html | 52 ++++++++++++++------------- man/logit_model.Rd | 5 ++ man/nb_model.Rd | 11 +++++ man/pipeline.Rd | 3 + man/rf_model.Rd | 11 +++++ man/xgb_model.Rd | 11 +++++ vignettes/introduction-to-quickSentiment.Rmd | 2 + 19 files changed, 162 insertions(+), 71 deletions(-)
More information about quickSentiment at CRAN
Permanent link
Title: Build 'pkgdown' Websites Offline
Description: Provides support for building 'pkgdown' websites without an
internet connection. Works by bundling cached dependencies and
implementing drop-in replacements for key 'pkgdown' functions.
Enables package documentation websites to be built in environments
where internet access is unavailable or restricted.
For more details on generating 'pkgdown' websites, see
Wickham et al. (2025) <doi:10.32614/CRAN.package.pkgdown>.
Author: Nan Xiao [aut, cre, cph] ,
John Blischak [aut] ,
Algolia, Inc. and other contributors [ctb, cph] ,
Aidan Feldman [ctb, cph] ,
Zeno Rocha [ctb, cph] ,
Nick Williams [ctb, cph] ,
Julian Kuehnel [ctb, cph] ,
Kiro Risk [ctb, cph] ,
Khan Academy and other [...truncated...]
Maintainer: Nan Xiao <me@nanx.me>
Diff between pkgdown.offline versions 0.1.2 dated 2025-11-08 and 0.1.3 dated 2026-07-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 11 +++++++++++ R/build.R | 5 +++++ build/partial.rdb |binary build/vignette.rds |binary inst/cache/MD5 | 7 +++++++ man/pkgdown.offline-package.Rd | 1 + 8 files changed, 35 insertions(+), 11 deletions(-)
More information about pkgdown.offline at CRAN
Permanent link
Title: Performing Comprehensive Overlap Assessments
Description: The implementation of a statistical framework for performing overlap assessments on
lists comprising sets of strings (such as lists of gene sets) described in Stoica (2023)
<https://ora.ox.ac.uk/objects/uuid:b0847284-a02f-47ee-88e3-a3c4e0cdb8b1>.
It can assess overlaps of pairs of sets of strings selected either from the same universe or
from different universes, and overlaps of triplets of sets of strings selected from the same
universe. Designed for single-cell RNA-sequencing data analysis applications, but suitable
for other purposes as well.
Author: Andrei-Florian Stoica [aut, cre]
Maintainer: Andrei-Florian Stoica <andreistoica@foxmail.com>
Diff between LISTO versions 0.7.3 dated 2026-04-25 and 0.8.1 dated 2026-07-13
DESCRIPTION | 6 ++-- MD5 | 42 ++++++++++++++++---------------- R/checks.R | 5 +-- R/cutoffs.R | 52 ++++++++++++++++------------------------ R/multiple_testing.R | 5 --- R/prob_counts.R | 1 R/pval_objects.R | 12 +++------ R/run_listo.R | 21 +++++++--------- R/seurat_demo.R | 2 - R/vectors.R | 4 +++ README.md | 10 +++---- man/filterItems.Rd | 2 - man/generateCutoffs.Rd | 16 +++++++----- man/getObjectValues.Rd | 10 +++---- man/mtCorrectDF.Rd | 2 - man/mtCorrectHelper.Rd | 2 - man/mtCorrectV.Rd | 2 - man/pvalObjects.Rd | 20 +++++++++------ man/pvalObjectsCore.Rd | 9 ++++-- man/runLISTO.Rd | 22 +++++++++------- tests/testthat/helper-globals.R | 1 tests/testthat/test-LISTO.R | 30 ++++++++++++----------- 22 files changed, 140 insertions(+), 136 deletions(-)
Title: Delayed Read for 'GDAL' Vector Data Sources
Description: Lazy read for drawings. A 'dplyr' back end for data sources supported by
'GDAL' vector drivers, that allows working with local or remote sources as if they
are in-memory data frames. Basic features work with any drawing format ('GDAL vector
data source') supported by the 'gdalraster' package.
Author: Michael Sumner [aut, cre]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between lazysf versions 0.3.0 dated 2026-02-17 and 0.4.0 dated 2026-07-13
lazysf-0.3.0/lazysf/R/SFSQLConnection.R |only lazysf-0.3.0/lazysf/R/SFSQLDriver.R |only lazysf-0.3.0/lazysf/R/SFSQLResult.R |only lazysf-0.3.0/lazysf/R/utils-pipe.R |only lazysf-0.3.0/lazysf/man/SFSQL.Rd |only lazysf-0.3.0/lazysf/man/SFSQLConnection-class.Rd |only lazysf-0.3.0/lazysf/man/SFSQLDriver-class.Rd |only lazysf-0.3.0/lazysf/man/SFSQLResult-class.Rd |only lazysf-0.3.0/lazysf/man/dbConnect-SFSQLDriver-method.Rd |only lazysf-0.3.0/lazysf/man/pipe.Rd |only lazysf-0.3.0/lazysf/man/st_as_sf.Rd |only lazysf-0.4.0/lazysf/DESCRIPTION | 27 lazysf-0.4.0/lazysf/MD5 | 71 + lazysf-0.4.0/lazysf/NAMESPACE | 61 - lazysf-0.4.0/lazysf/NEWS.md | 150 +++ lazysf-0.4.0/lazysf/R/GDALVectorConnection.R |only lazysf-0.4.0/lazysf/R/GDALVectorDriver.R |only lazysf-0.4.0/lazysf/R/GDALVectorResult.R |only lazysf-0.4.0/lazysf/R/connect.R | 73 + lazysf-0.4.0/lazysf/R/dbplyr.R | 38 lazysf-0.4.0/lazysf/R/helper.R |only lazysf-0.4.0/lazysf/R/lazysf-package.R | 33 lazysf-0.4.0/lazysf/R/lazysf.R | 125 +- lazysf-0.4.0/lazysf/R/sql-query-fields.R |only lazysf-0.4.0/lazysf/R/sql-translation.R |only lazysf-0.4.0/lazysf/R/zzz.R | 41 lazysf-0.4.0/lazysf/README.md | 484 +++++------ lazysf-0.4.0/lazysf/build/vignette.rds |binary lazysf-0.4.0/lazysf/inst/doc/GDALSQL.R | 102 ++ lazysf-0.4.0/lazysf/inst/doc/GDALSQL.Rmd | 247 ++++- lazysf-0.4.0/lazysf/inst/doc/GDALSQL.html | 337 +++++-- lazysf-0.4.0/lazysf/inst/extdata/nc.dbf |only lazysf-0.4.0/lazysf/inst/extdata/nc.gpkg |only lazysf-0.4.0/lazysf/inst/extdata/nc.prj |only lazysf-0.4.0/lazysf/inst/extdata/nc.shp |only lazysf-0.4.0/lazysf/inst/extdata/nc.shx |only lazysf-0.4.0/lazysf/man/GDALSQL.Rd |only lazysf-0.4.0/lazysf/man/GDALVectorConnection-class.Rd |only lazysf-0.4.0/lazysf/man/GDALVectorDriver-class.Rd |only lazysf-0.4.0/lazysf/man/GDALVectorResult-class.Rd |only lazysf-0.4.0/lazysf/man/collect.tbl_GDALVectorConnection.Rd |only lazysf-0.4.0/lazysf/man/dbConnect-GDALVectorDriver-method.Rd |only lazysf-0.4.0/lazysf/man/lazysf-package.Rd | 15 lazysf-0.4.0/lazysf/man/lazysf.Rd | 91 +- lazysf-0.4.0/lazysf/man/reexports.Rd |only lazysf-0.4.0/lazysf/tests |only lazysf-0.4.0/lazysf/vignettes/GDALSQL.Rmd | 247 ++++- 47 files changed, 1396 insertions(+), 746 deletions(-)
Title: A Versatile Visualization Suite
Description: A visualization suite primarily designed for single-cell
RNA-sequencing data analysis applications but well-suited for
other purposes as well. It introduces novel plots to represent two-variable
and frequency data and optimizes some commonly used plotting options
(e.g., correlation, network, density, alluvial and volcano plots)
for ease of usage and flexibility.
Author: Andrei-Florian Stoica [aut, cre]
Maintainer: Andrei-Florian Stoica <andreistoica@foxmail.com>
Diff between henna versions 0.7.5 dated 2026-02-17 and 0.8.5 dated 2026-07-13
DESCRIPTION | 6 ++--- MD5 | 36 +++++++++++++++---------------- R/documentation.R | 4 ++- R/label_points.R | 5 +--- R/rank_plot.R | 5 ++-- R/tile_plot.R | 43 ++++++++++++++++++++++---------------- README.md | 32 +++++++++++++--------------- inst/figures/correlation_plot.png |binary inst/figures/density_plot.png |binary inst/figures/hull_plot.png |binary inst/figures/network_plot.png |binary inst/figures/radial_plot.png |binary inst/figures/rank_plot.png |binary inst/figures/tile_plot.png |binary inst/figures/volcano_plot.png |binary man/documentFun.Rd | 5 +++- man/rankPlot.Rd | 5 +++- man/tilePlot.Rd | 18 ++++++++++++--- tests/testthat/test-henna.R | 12 ++++------ 19 files changed, 97 insertions(+), 74 deletions(-)
Title: Access and Work with HCUP Resources and Datasets
Description: A comprehensive R package for accessing and working with publicly
available and free resources from the Agency for Healthcare Research and Quality
(AHRQ) Healthcare Cost and Utilization Project (HCUP). The package provides
streamlined access to HCUP's Clinical Classifications Software Refined (CCSR)
mapping files and Summary Trend Tables, enabling researchers and analysts to
efficiently map ICD-10-CM diagnosis codes and ICD-10-PCS procedure codes to
CCSR categories and access HCUP statistical reports. Key features include:
direct download from HCUP website, multiple output formats (long/wide/default),
cross-classification support, version management, citation generation, and
intelligent caching. The package does not redistribute HCUP data files but
facilitates direct download from the official HCUP website, ensuring users
always have access to the latest versions and maintain compliance with HCUP
data use policies. This package only accesses free public tools and reports;
it does NOT a [...truncated...]
Author: Vikrant Dev Rathore [aut, cre]
Maintainer: Vikrant Dev Rathore <rathore.vikrant@gmail.com>
Diff between HCUPtools versions 1.0.1 dated 2026-05-11 and 1.0.2 dated 2026-07-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 10 ++++++++++ inst/CITATION | 30 +++++++++++++++++++++++------- inst/doc/HCUPtools.html | 4 ++-- 5 files changed, 42 insertions(+), 16 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor
Analysis-1 (Parafac) model or Parallel Factor Analysis-2 (Parafac2) model fit to
a three-way or four-way data array. See Harshman and Lundy (1994):
<doi:10.1016/0167-9473(94)90132-5>. Classification using principal component
analysis (PCA) fit to a two-way data matrix is also supported. Uses component
weights from one mode of a Parafac, Parafac2, or PCA model as features to tune
parameters for one or more classification methods via a k-fold cross-validation
procedure. Allows for constraints on different tensor modes. Allows for
inclusion of additional features alongside features generated by the component
model. Supports penalized logistic regression, support vector machine, random
forest, feed-forward neural network, regularized discriminant analysis, and
gradient boosting machine. Supports binary and multiclass classification.
Predicts class labels or class probabilities and calculates multiple
classification performanc [...truncated...]
Author: Matthew A. Asisgress [aut, cre]
Maintainer: Matthew A. Asisgress <mattgress@protonmail.ch>
Diff between cpfa versions 1.3.0 dated 2026-06-02 and 1.3.1 dated 2026-07-13
ChangeLog | 14 +++++++++++++- DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/pficpfa.R | 40 ++++++++++++++++++++++++++++++++-------- inst/doc/cpfa.pdf |binary man/cpfa.Rd | 3 ++- 6 files changed, 56 insertions(+), 19 deletions(-)
Title: High-Level Modeling Functions with 'torch'
Description: Provides high-level modeling functions to define and train
models using the 'torch' R package. Models include linear, logistic,
and multinomial regression as well as multilayer perceptrons.
Author: Max Kuhn [aut, cre] ,
Daniel Falbel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between brulee versions 1.1.0 dated 2026-07-02 and 1.1.1 dated 2026-07-13
DESCRIPTION | 6 +- MD5 | 41 +++++++++--------- NEWS.md | 8 +++ R/0_utils.R | 46 +++++++++++++++++++++ R/aaa.R | 46 --------------------- R/chronos2-fit.R | 20 +++++---- R/chronos2-misc.R | 25 ++++++++++- R/tabicl-download.R | 46 +++++++++++---------- R/tabicl-fit.R | 12 +++-- R/training_loop.R | 9 +++- README.md | 70 ++++++++++++++++++-------------- man/brulee_chronos.Rd | 17 ++++--- man/brulee_tab_icl.Rd | 12 +++-- man/tab_icl_download_weights.Rd | 9 ++-- tests/testthat/helper-chronos2.R | 7 ++- tests/testthat/setup.R | 5 -- tests/testthat/test-0_utils.R |only tests/testthat/test-autoint.R | 2 tests/testthat/test-chronos2-misc.R | 65 +++++++++++++++++++++++++++++ tests/testthat/test-resnet-regression.R | 35 ++++++++++++++++ tests/testthat/test-tabicl-download.R | 68 ++++++++++++++++++++++++++++--- tests/testthat/test-tabicl-fit.R | 4 - 22 files changed, 388 insertions(+), 165 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-11 1.1.0
2018-06-15 1.0.0