Title: Fast, Robust Clustering Algorithms for Gene Enrichment Data
Description: Clusters functionally related biological terms from gene set
enrichment results. Terms are compared by the overlap of their gene
sets using Cohen's kappa, the Jaccard index, or the Dice coefficient,
and the resulting similarity matrix is grouped either by agglomerative
hierarchical clustering with single, complete, average, or Ward
linkage, or by the seed-and-merge procedure of the 'DAVID' functional
classification tool. The distance and clustering routines are written
in 'C++' for speed. The methods are described in Huang et al. (2007)
<doi:10.1186/gb-2007-8-9-r183>, Ward (1963)
<doi:10.1080/01621459.1963.10500845>, Cohen (1960)
<doi:10.1177/001316446002000104>, and Jaccard (1912)
<doi:10.1111/j.1469-8137.1912.tb05611.x>.
Author: Junguk Hur [aut, cre] ,
Sarah Hong [aut],
Jane Kim [aut]
Maintainer: Junguk Hur <hurlabshared@gmail.com>
Diff between richCluster versions 2.0.0 dated 2026-09-16 and 2.0.1 dated 2026-09-22
richCluster-2.0.0/richCluster/tests/testthat/test-cpp-units.R |only richCluster-2.0.1/richCluster/DESCRIPTION | 8 +- richCluster-2.0.1/richCluster/MD5 | 11 +-- richCluster-2.0.1/richCluster/NEWS.md | 4 + richCluster-2.0.1/richCluster/inst/doc/workflow.html | 28 +++++----- richCluster-2.0.1/richCluster/tests/testthat/test-instrument-contracts.R | 4 - richCluster-2.0.1/richCluster/tests/testthat/test-t107-diagonal.R | 2 7 files changed, 30 insertions(+), 27 deletions(-)
Title: Simulate Discrete Character Data along Phylogenetic Trees
Description: Tools to simulate morphological traits along phylogenetic trees
with branch lengths representing evolutionary distance or time.
Includes functions for visualizing evolutionary processes along trees
and within morphological character matrices. Methods are described in
Mulvey et al. (2026) <doi:10.1111/2041-210X.70326>.
Author: Laura Mulvey [aut, cre, cph],
Tim Brandler [aut, cph],
Alessio Capobianco [aut, cph],
Rachel Warnock [aut, cph],
Joelle Barido-Sottani [aut, cph]
Maintainer: Laura Mulvey <lauramulvey479@gmail.com>
This is a re-admission after prior archival of version 1.2.0 dated 2026-05-06
Diff between MorphSim versions 1.2.0 dated 2026-05-06 and 1.2.1 dated 2026-09-22
DESCRIPTION | 9 ++++--- MD5 | 16 ++++++------- R/plot.morpho.R | 54 ++++++++++++++++++++++++---------------------- R/reconstruct.tree.R | 21 +++++++++-------- R/sim.morpho.R | 28 +++++++++++++++++++++-- R/write.r | 16 +++++++------ inst/CITATION | 36 +++++++++++++++++------------- man/morphsim_fossilsim.Rd | 5 ---- man/reconstruct.matrix.Rd | 2 - 9 files changed, 108 insertions(+), 79 deletions(-)
Title: Gaussian Mixture Topic Models
Description: Gaussian mixture models (GMM) and k-means for topic analysis of dense document vectors. The underlying clustering functions rely on the Armadillo library (Sanderson & Curtin, 2017) <doi:10.1109/ICSPCS.2017.8270510>.
Author: Kohei Watanabe [aut, cre, cph] ,
Sanderson Conrad [ctb, cph] ,
Curtin Ryan [ctb, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between GMTM versions 0.1.0 dated 2026-09-15 and 0.2.0 dated 2026-09-22
DESCRIPTION | 27 +- MD5 | 49 ++-- NAMESPACE | 56 +++-- NEWS.md | 14 - R/RcppExports.R | 12 - R/gmm.R | 162 ++++++++++----- R/kmeans.R | 229 ++++++++++----------- R/utils.R | 182 ++++++++++++++--- inst/WORDLIST | 19 + man/as.seedwords.Rd |only man/group_matrix.Rd |only man/probability.textmodel_gmm.Rd |only man/reexports.Rd |only man/terms.Rd | 66 +++--- man/textmodel_gmm.Rd | 111 ++++++---- man/textmodel_kmeans.Rd | 87 ++++---- man/topics.Rd | 45 ++-- src/Makevars |only src/Makevars.win |only src/RcppExports.cpp | 31 ++ src/gmm.cpp | 49 +++- src/kmeans.cpp | 12 - tests/data |only tests/misc/benchmark.R | 52 ++-- tests/misc/comparison.R | 174 ++++++++-------- tests/testthat.R | 11 - tests/testthat/test-gmm.R | 414 ++++++++++++++++++++++++++++++++------- tests/testthat/test-kmeans.R | 217 +++++++++++++------- tests/testthat/test-utils.R | 57 +++++ 29 files changed, 1396 insertions(+), 680 deletions(-)
Title: Set Axis Break for 'ggplot2'
Description: An implementation of scale functions for setting axis breaks of a 'gg' plot (S Xu (2021) <doi:10.3389/fgene.2021.774846>).
Author: Guangchuang Yu [aut, cre, cph] ,
Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggbreak versions 0.1.7 dated 2026-03-18 and 0.2.2 dated 2026-09-22
DESCRIPTION | 15 MD5 | 69 - NAMESPACE | 101 - NEWS.md | 198 +-- R/ggbreak-package.R | 6 R/grid-draw-utilities.R | 2159 ++++++++++++++++++++++------------ R/method-ggplot-add.R | 195 +-- R/method-ggplot-grob.R |only R/method-grid-draw.R | 1207 +++++++++++-------- R/method-plot.R | 30 R/method-print.R | 34 R/scales.R | 271 ++-- R/utilities.R | 806 +++++++----- R/zzz.R | 58 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 60 inst/doc/ggbreak.R | 533 ++++---- inst/doc/ggbreak.Rmd | 186 ++ inst/doc/ggbreak.html | 1492 ++++++++++++++--------- man/ggbreak-package.Rd | 1 man/scale-wrap.Rd | 3 man/scale_break.Rd | 155 +- man/scale_cut.Rd | 97 - tests/testthat.R |only tests/testthat/test-api-attributes.R | 22 tests/testthat/test-issue-16.R |only tests/testthat/test-issue-31.R |only tests/testthat/test-issue-33.R |only tests/testthat/test-issue-35.R |only tests/testthat/test-issue-43.R |only tests/testthat/test-issue-46.R |only tests/testthat/test-issue-52.R |only tests/testthat/test-issue-53.R |only tests/testthat/test-issue-55.R |only tests/testthat/test-issue-57.R |only tests/testthat/test-issue-59.R |only tests/testthat/test-issue-64.R |only tests/testthat/test-issue-68.R |only tests/testthat/test-issue-71.R |only tests/testthat/test-issue-73.R |only tests/testthat/test-issue-83.R |only tests/testthat/test-issue-84.R |only tests/testthat/test-issue-85.R |only tests/testthat/test-scale-transform.R |only vignettes/ggbreak.Rmd | 186 ++ 46 files changed, 4957 insertions(+), 2927 deletions(-)
Title: Doubly Regularized Matrix-Variate Regression
Description: The doubly regularized matrix-variate regression solves a low-rank-plus-sparse
structure for matrix-variate generalized linear models through a weighted
combination of nuclear-norm and L1-norm. The methodology implemented by this
package is described in the paper "Doubly Regularized Matrix-Variate Regression".
See Xu, Luo and Jiang <doi:10.1080/10618600.2026.2702534>.
Author: Zengchao Xu [aut, cre, cph],
Shan Luo [aut],
Binyan Jiang [aut]
Maintainer: Zengchao Xu <zengc.xu@aliyun.com>
Diff between drrglm versions 0.3.2 dated 2026-04-20 and 0.4.0 dated 2026-09-22
DESCRIPTION | 16 +++++++--------- MD5 | 25 +++++++++++++------------ NEWS.md | 7 +++++++ R/drr-factor-model.R | 2 +- R/simu-reg-model.R | 2 +- R/simu-zhouandli2014.R | 2 +- R/tune-drrglm.R | 2 +- README.md | 32 ++++++++++++-------------------- build |only man/drrglm-package.Rd | 3 ++- man/simu-reg-model.Rd | 2 +- man/simu_zhouandli2014.Rd | 2 +- man/tune.drrglm.Rd | 2 +- man/tune_drr_factor_model.Rd | 2 +- 14 files changed, 49 insertions(+), 50 deletions(-)
Title: Decorate a 'ggplot' with Associated Information
Description: Supports data-driven composition of a main plot with associated subplots that need precise axis alignment. Unlike general layout-focused tools such as 'cowplot' and 'patchwork', it enables related subplots to be integrated on the top, bottom, left, or right sides of a main plot with matched axes, so that the combined panels can be interpreted as a coherent whole. This design was inspired by the 'Method 2' described in 'ggtree' (G Yu (2018) <doi:10.1093/molbev/msy194>).
Author: Guangchuang Yu [aut, cre] ,
Shuangbin Xu [ctb] ,
Thomas Hackl [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between aplot versions 0.3.1 dated 2026-07-07 and 0.3.2 dated 2026-09-22
aplot-0.3.1/aplot/tests/testthat/Rplots.pdf |only aplot-0.3.2/aplot/DESCRIPTION | 10 aplot-0.3.2/aplot/MD5 | 48 +- aplot-0.3.2/aplot/NAMESPACE | 161 ++++----- aplot-0.3.2/aplot/NEWS.md | 316 ++++++++--------- aplot-0.3.2/aplot/R/aplot-package.R | 6 aplot-0.3.2/aplot/R/axis.R | 392 ++++++++++----------- aplot-0.3.2/aplot/R/cowplot-compat.R |only aplot-0.3.2/aplot/R/insertion.R | 354 +++++++++---------- aplot-0.3.2/aplot/R/method-accessor.R | 108 +++--- aplot-0.3.2/aplot/R/plot-list.R | 446 ++++++++++++------------- aplot-0.3.2/aplot/R/re-export.R | 42 +- aplot-0.3.2/aplot/R/utilities.R | 118 +++--- aplot-0.3.2/aplot/R/zzz.R | 60 +-- aplot-0.3.2/aplot/build/partial.rdb |binary aplot-0.3.2/aplot/inst/CITATION | 86 ++-- aplot-0.3.2/aplot/man/align_axis.Rd | 68 +-- aplot-0.3.2/aplot/man/aplot-package.Rd | 68 +-- aplot-0.3.2/aplot/man/aplot_label.Rd | 54 +-- aplot-0.3.2/aplot/man/as.patchwork.Rd | 32 - aplot-0.3.2/aplot/man/as_grob.gglist.Rd |only aplot-0.3.2/aplot/man/gglist.Rd | 46 +- aplot-0.3.2/aplot/man/gglistGrob.Rd | 34 - aplot-0.3.2/aplot/man/plot-insertion.Rd | 124 +++--- aplot-0.3.2/aplot/man/plot_list.Rd | 116 +++--- aplot-0.3.2/aplot/man/reexports.Rd | 48 +- aplot-0.3.2/aplot/tests/testthat/test-gglist.R |only 27 files changed, 1375 insertions(+), 1362 deletions(-)
Title: Survival Analysis for Recurrent Event Data
Description: Estimation of the survival function of inter-occurrence times
for recurrent event data, using the estimators of Peña, Strawderman and
Hollander (2001) <doi:10.1198/016214501753381922> and Wang and Chang
(1999) <doi:10.1080/01621459.1999.10473831>, and maximum likelihood
estimation under a gamma frailty model. Includes bootstrap comparison
of survival quantiles between groups.
Author: Dolors Pelegri-Siso [aut, cre] ,
Juan R. Gonzalez [aut],
Edsel A. Pena [aut],
Robert L. Strawderman [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>
This is a re-admission after prior archival of version 1.2-2 dated 2012-03-26
Diff between survrec versions 1.2-2 dated 2012-03-26 and 2.0.0 dated 2026-09-22
survrec-1.2-2/survrec/R/survrec.R |only survrec-1.2-2/survrec/man/Survsearch.Rd |only survrec-1.2-2/survrec/man/mlefrailtyfit.Rd |only survrec-1.2-2/survrec/man/plotsurvfitr.Rd |only survrec-1.2-2/survrec/man/printsurvfitr.Rd |only survrec-1.2-2/survrec/man/pshfit.Rd |only survrec-1.2-2/survrec/man/qsearch.Rd |only survrec-1.2-2/survrec/man/summarysurvfitr.Rd |only survrec-1.2-2/survrec/man/wcfit.Rd |only survrec-1.2-2/survrec/src/bootstrap.f |only survrec-1.2-2/survrec/src/survrec.f |only survrec-2.0.0/survrec/DESCRIPTION | 53 ++++- survrec-2.0.0/survrec/INDEX | 42 ++-- survrec-2.0.0/survrec/MD5 | 98 ++++++++-- survrec-2.0.0/survrec/NAMESPACE | 61 ++++-- survrec-2.0.0/survrec/NEWS.md |only survrec-2.0.0/survrec/R/RcppExports.R |only survrec-2.0.0/survrec/R/Survr.R |only survrec-2.0.0/survrec/R/autoplot.survfitr.R |only survrec-2.0.0/survrec/R/data.R |only survrec-2.0.0/survrec/R/deprecated.R |only survrec-2.0.0/survrec/R/mcf.R |only survrec-2.0.0/survrec/R/methods.survfitr.R |only survrec-2.0.0/survrec/R/misc-methods.R |only survrec-2.0.0/survrec/R/mlefrailty_fit.R |only survrec-2.0.0/survrec/R/psh_fit.R |only survrec-2.0.0/survrec/R/search.R |only survrec-2.0.0/survrec/R/survdiffr-methods.R |only survrec-2.0.0/survrec/R/survdiffr.R |only survrec-2.0.0/survrec/R/survfitr.R |only survrec-2.0.0/survrec/R/survrec-package.R |only survrec-2.0.0/survrec/R/theme-survrec.R |only survrec-2.0.0/survrec/R/threads.R |only survrec-2.0.0/survrec/R/utils-internal.R |only survrec-2.0.0/survrec/R/wc_fit.R |only survrec-2.0.0/survrec/README.md |only survrec-2.0.0/survrec/build |only survrec-2.0.0/survrec/data/MMC.rda |binary survrec-2.0.0/survrec/data/colon.rda |binary survrec-2.0.0/survrec/inst |only survrec-2.0.0/survrec/man/MMC.Rd | 55 +++--- survrec-2.0.0/survrec/man/Survr.Rd | 81 +++++--- survrec-2.0.0/survrec/man/as.data.frame.survfitr.Rd |only survrec-2.0.0/survrec/man/autoplot.mcf.Rd |only survrec-2.0.0/survrec/man/autoplot.survdiffr.Rd |only survrec-2.0.0/survrec/man/autoplot.survfitr.Rd |only survrec-2.0.0/survrec/man/colon.Rd | 59 +++--- survrec-2.0.0/survrec/man/mcf.Rd |only survrec-2.0.0/survrec/man/mlefrailty_fit.Rd |only survrec-2.0.0/survrec/man/plot.survfitr.Rd |only survrec-2.0.0/survrec/man/plotEstimators.Rd |only survrec-2.0.0/survrec/man/print.survfitr.Rd |only survrec-2.0.0/survrec/man/psh_fit.Rd |only survrec-2.0.0/survrec/man/q_search.Rd |only survrec-2.0.0/survrec/man/quantile.survfitr.Rd |only survrec-2.0.0/survrec/man/reexports.Rd |only survrec-2.0.0/survrec/man/summary.survdiffr.Rd |only survrec-2.0.0/survrec/man/summary.survfitr.Rd |only survrec-2.0.0/survrec/man/surv_search.Rd |only survrec-2.0.0/survrec/man/survdiffr.Rd | 183 +++++++++++--------- survrec-2.0.0/survrec/man/survfitr.Rd | 135 ++++++-------- survrec-2.0.0/survrec/man/survrec-deprecated.Rd |only survrec-2.0.0/survrec/man/survrec-package.Rd |only survrec-2.0.0/survrec/man/survrecThreads.Rd |only survrec-2.0.0/survrec/man/theme_survrec.Rd |only survrec-2.0.0/survrec/man/wc_fit.Rd |only survrec-2.0.0/survrec/src/Makevars |only survrec-2.0.0/survrec/src/RcppExports.cpp |only survrec-2.0.0/survrec/src/at_risk.cpp |only survrec-2.0.0/survrec/src/at_risk.h |only survrec-2.0.0/survrec/src/bootstrap.cpp |only survrec-2.0.0/survrec/src/bootstrap.h |only survrec-2.0.0/survrec/src/exports.cpp |only survrec-2.0.0/survrec/src/frailty_em.cpp |only survrec-2.0.0/survrec/src/frailty_em.h |only survrec-2.0.0/survrec/src/survrec_data.h |only survrec-2.0.0/survrec/src/wang_chang.cpp |only survrec-2.0.0/survrec/src/wang_chang.h |only survrec-2.0.0/survrec/tests |only survrec-2.0.0/survrec/vignettes |only 80 files changed, 460 insertions(+), 307 deletions(-)
Title: Actuarial Functions for Non-Life Insurance Modelling
Description: Assists actuaries and other insurance modellers in pricing,
reserving and capital modelling for non-life insurance and
reinsurance modelling. Provides functions that help model
excess levels, capping and pure Incurred but not reported
claims (pure IBNR).
Includes capped mean, exposure curves and increased limit
factor curves (ILFs) for LogNormal, Gamma, Pareto, Sliced
LogNormal-Pareto and Sliced Gamma-Pareto distributions.
Includes mean, probability density function (pdf), cumulative
probability function (cdf) and inverse cumulative probability
function for Sliced LogNormal-Pareto and Sliced Gamma-Pareto
distributions.
Includes calculating pure IBNR exposure with LogNormal and
Gamma distribution for reporting delay.
Includes three 'shiny' tools: a claims simulator with reinsurance
structures, a generalised linear model fitting tool, and a claims
frequency and severity distribution fitting tool.
Methods used in the package refer to
Free for All by Yiannis Parizas (2023) <https://www. [...truncated...]
Author: Yiannis Parizas [aut, cre]
Maintainer: Yiannis Parizas <yiannis.parizas@gmail.com>
Diff between NetSimR versions 0.3.0 dated 2026-09-15 and 0.3.1 dated 2026-09-22
NetSimR-0.3.0/NetSimR/tests/CappedMean |only NetSimR-0.3.0/NetSimR/tests/PureIBNR |only NetSimR-0.3.0/NetSimR/tests/SlicedDistributions |only NetSimR-0.3.1/NetSimR/DESCRIPTION | 24 NetSimR-0.3.1/NetSimR/MD5 | 233 NetSimR-0.3.1/NetSimR/NEWS | 511 + NetSimR-0.3.1/NetSimR/R/GLMFittingToolGlobal.R | 196 NetSimR-0.3.1/NetSimR/R/GLMFittingToolServer.R | 335 - NetSimR-0.3.1/NetSimR/R/GLMFittingToolUI.R | 31 NetSimR-0.3.1/NetSimR/R/Gamma.R | 495 - NetSimR-0.3.1/NetSimR/R/LogNormal.R | 281 NetSimR-0.3.1/NetSimR/R/NetSimR.R | 16 NetSimR-0.3.1/NetSimR/R/Pareto.R | 238 NetSimR-0.3.1/NetSimR/R/ShinySimulatorGlobal.R | 71 NetSimR-0.3.1/NetSimR/R/ShinySimulatorReport.R | 2829 +++++----- NetSimR-0.3.1/NetSimR/R/ShinySimulatorServer.R | 140 NetSimR-0.3.1/NetSimR/R/ShinySimulatorSettingsIO.R | 251 NetSimR-0.3.1/NetSimR/R/ShinySimulatorSummary.R | 681 +- NetSimR-0.3.1/NetSimR/R/ShinySimulatorTabs.R | 2523 ++++---- NetSimR-0.3.1/NetSimR/R/ShinySimulatorUI.R | 120 NetSimR-0.3.1/NetSimR/R/SlicecdGammaPareto.R | 453 - NetSimR-0.3.1/NetSimR/R/SlicecdLogNormalPareto.R | 449 - NetSimR-0.3.1/NetSimR/R/csv_safe.R |only NetSimR-0.3.1/NetSimR/R/distribution_fitting_tool_Server.R | 121 NetSimR-0.3.1/NetSimR/R/distribution_fitting_tool_UI.R | 48 NetSimR-0.3.1/NetSimR/R/distribution_fitting_tool_global.R | 187 NetSimR-0.3.1/NetSimR/R/plot_device.R |only NetSimR-0.3.1/NetSimR/R/settings_file.R |only NetSimR-0.3.1/NetSimR/R/simulate_claims.R | 5 NetSimR-0.3.1/NetSimR/README.md | 182 NetSimR-0.3.1/NetSimR/inst/WORDLIST | 77 NetSimR-0.3.1/NetSimR/inst/doc/CappedMean.Rmd | 8 NetSimR-0.3.1/NetSimR/inst/doc/CappedMean.html | 6 NetSimR-0.3.1/NetSimR/inst/doc/PureIBNR.Rmd | 6 NetSimR-0.3.1/NetSimR/inst/doc/PureIBNR.html | 4 NetSimR-0.3.1/NetSimR/inst/doc/SimulateClaims.Rmd | 431 - NetSimR-0.3.1/NetSimR/inst/doc/SimulateClaims.html | 1 NetSimR-0.3.1/NetSimR/inst/doc/SlicedDistributions.Rmd | 8 NetSimR-0.3.1/NetSimR/inst/doc/SlicedDistributions.html | 6 NetSimR-0.3.1/NetSimR/man/ExposureCurveGamma.Rd | 4 NetSimR-0.3.1/NetSimR/man/ExposureCurveLNorm.Rd | 6 NetSimR-0.3.1/NetSimR/man/ExposureCurvePareto.Rd | 2 NetSimR-0.3.1/NetSimR/man/ExposureCurveSlicedGammaPareto.Rd | 5 NetSimR-0.3.1/NetSimR/man/ExposureCurveSlicedLNormPareto.Rd | 5 NetSimR-0.3.1/NetSimR/man/GLMFittingToolServer.Rd | 4 NetSimR-0.3.1/NetSimR/man/GLMFittingToolUI.Rd | 8 NetSimR-0.3.1/NetSimR/man/GammaCappedMean.Rd | 2 NetSimR-0.3.1/NetSimR/man/IGamma.Rd | 52 NetSimR-0.3.1/NetSimR/man/ILFGamma.Rd | 2 NetSimR-0.3.1/NetSimR/man/ILFLNorm.Rd | 2 NetSimR-0.3.1/NetSimR/man/ILFPareto.Rd | 2 NetSimR-0.3.1/NetSimR/man/ILFSlicedGammaPareto.Rd | 5 NetSimR-0.3.1/NetSimR/man/ILFSlicedLNormPareto.Rd | 5 NetSimR-0.3.1/NetSimR/man/LNormCappedMean.Rd | 2 NetSimR-0.3.1/NetSimR/man/NetSimR-package.Rd | 20 NetSimR-0.3.1/NetSimR/man/ParetoCappedMean.Rd | 2 NetSimR-0.3.1/NetSimR/man/ParetoCappedMeanCalc.Rd | 2 NetSimR-0.3.1/NetSimR/man/PureIBNRGamma.Rd | 5 NetSimR-0.3.1/NetSimR/man/PureIBNRLNorm.Rd | 5 NetSimR-0.3.1/NetSimR/man/SlicedGammaParetoCappedMean.Rd | 5 NetSimR-0.3.1/NetSimR/man/SlicedGammaParetoMean.Rd | 9 NetSimR-0.3.1/NetSimR/man/SlicedLNormParetoCappedMean.Rd | 5 NetSimR-0.3.1/NetSimR/man/SlicedLNormParetoMean.Rd | 7 NetSimR-0.3.1/NetSimR/man/apply_deductible_limit.Rd | 3 NetSimR-0.3.1/NetSimR/man/dSlicedGammaPareto.Rd | 5 NetSimR-0.3.1/NetSimR/man/dSlicedLNormPareto.Rd | 5 NetSimR-0.3.1/NetSimR/man/distributionClass-class.Rd | 44 NetSimR-0.3.1/NetSimR/man/distribution_fitting_tool_Server.Rd | 5 NetSimR-0.3.1/NetSimR/man/distribution_fitting_tool_UI.Rd | 8 NetSimR-0.3.1/NetSimR/man/erf.Rd | 2 NetSimR-0.3.1/NetSimR/man/freq_dist_options.Rd | 6 NetSimR-0.3.1/NetSimR/man/freq_dist_parameter_placeholders.Rd | 4 NetSimR-0.3.1/NetSimR/man/max_number_of_pareto_slices.Rd | 4 NetSimR-0.3.1/NetSimR/man/pSlicedGammaPareto.Rd | 11 NetSimR-0.3.1/NetSimR/man/pSlicedLNormPareto.Rd | 11 NetSimR-0.3.1/NetSimR/man/qSlicedGammaPareto.Rd | 11 NetSimR-0.3.1/NetSimR/man/qSlicedLNormPareto.Rd | 11 NetSimR-0.3.1/NetSimR/man/reinsurance_structures_options.Rd | 4 NetSimR-0.3.1/NetSimR/man/run_shiny_distribution_fitting_tool.Rd | 16 NetSimR-0.3.1/NetSimR/man/run_shiny_glm_fitting_tool.Rd | 22 NetSimR-0.3.1/NetSimR/man/run_shiny_simulator.Rd | 4 NetSimR-0.3.1/NetSimR/man/sev_dist_parameter_placeholders.Rd | 4 NetSimR-0.3.1/NetSimR/man/shiny_simulator_server.Rd | 7 NetSimR-0.3.1/NetSimR/man/shiny_simulator_ui.Rd | 9 NetSimR-0.3.1/NetSimR/man/simulate_claims.Rd | 2 NetSimR-0.3.1/NetSimR/man/simulate_function.Rd | 16 NetSimR-0.3.1/NetSimR/tests/testthat.R | 8 NetSimR-0.3.1/NetSimR/tests/testthat/helper-app.R |only NetSimR-0.3.1/NetSimR/tests/testthat/helper-settings.R | 80 NetSimR-0.3.1/NetSimR/tests/testthat/test-app-distribution.R |only NetSimR-0.3.1/NetSimR/tests/testthat/test-app-glm.R |only NetSimR-0.3.1/NetSimR/tests/testthat/test-app-narrow.R |only NetSimR-0.3.1/NetSimR/tests/testthat/test-app-simulator.R |only NetSimR-0.3.1/NetSimR/tests/testthat/test-apply-deductible-limit.R | 116 NetSimR-0.3.1/NetSimR/tests/testthat/test-capped-mean.R | 94 NetSimR-0.3.1/NetSimR/tests/testthat/test-core-review-fixes.R |only NetSimR-0.3.1/NetSimR/tests/testthat/test-core-validation.R | 348 - NetSimR-0.3.1/NetSimR/tests/testthat/test-csv-safe.R |only NetSimR-0.3.1/NetSimR/tests/testthat/test-distribution-moments.R | 154 NetSimR-0.3.1/NetSimR/tests/testthat/test-fit-charts.R | 454 - NetSimR-0.3.1/NetSimR/tests/testthat/test-fit-count-mle.R | 220 NetSimR-0.3.1/NetSimR/tests/testthat/test-fit-nbinom-overdispersed.R |only NetSimR-0.3.1/NetSimR/tests/testthat/test-fit-reading-fixes.R |only NetSimR-0.3.1/NetSimR/tests/testthat/test-fit-unusual-data.R | 713 +- NetSimR-0.3.1/NetSimR/tests/testthat/test-glm-formula-safety.R |only NetSimR-0.3.1/NetSimR/tests/testthat/test-glm-tool-fixes.R |only NetSimR-0.3.1/NetSimR/tests/testthat/test-pkg-fitting-helpers.R | 389 - NetSimR-0.3.1/NetSimR/tests/testthat/test-pkg-fitting-tools.R | 162 NetSimR-0.3.1/NetSimR/tests/testthat/test-pkg-pure-ibnr.R | 268 NetSimR-0.3.1/NetSimR/tests/testthat/test-plot-device.R |only NetSimR-0.3.1/NetSimR/tests/testthat/test-report-review-fixes.R |only NetSimR-0.3.1/NetSimR/tests/testthat/test-report.R | 206 NetSimR-0.3.1/NetSimR/tests/testthat/test-settings-file.R |only NetSimR-0.3.1/NetSimR/tests/testthat/test-settings-io.R | 263 NetSimR-0.3.1/NetSimR/tests/testthat/test-sim-aggregate-order.R | 358 - NetSimR-0.3.1/NetSimR/tests/testthat/test-sim-app-fixes.R |only NetSimR-0.3.1/NetSimR/tests/testthat/test-sim-precision.R | 164 NetSimR-0.3.1/NetSimR/tests/testthat/test-simulate-engine.R | 708 +- NetSimR-0.3.1/NetSimR/tests/testthat/test-simulate-function.R | 373 - NetSimR-0.3.1/NetSimR/tests/testthat/test-simulator-server.R | 73 NetSimR-0.3.1/NetSimR/tests/testthat/test-summarise-simulation.R | 603 +- NetSimR-0.3.1/NetSimR/vignettes/CappedMean.Rmd | 8 NetSimR-0.3.1/NetSimR/vignettes/PureIBNR.Rmd | 6 NetSimR-0.3.1/NetSimR/vignettes/SimulateClaims.Rmd | 431 - NetSimR-0.3.1/NetSimR/vignettes/SlicedDistributions.Rmd | 8 125 files changed, 9893 insertions(+), 7661 deletions(-)
Title: Global Bounded Optimization by the OSCARS-II Algorithm
Description: A collection of general optimization routines based on variants of
the One Side Cut Accelerated Random Search (OSCARS-II) algorithm
(Price et al., 2020, <doi:10.1007/s10898-020-00928-6>). The main function
, 'oscars()', performs black-box optimization of a general (including nonsmooth or
discontinuous) function subject to simple bounds on the unknowns. If all bounds are
finite, oscars searches globally. The main method implements a stochastic direct
search method and is derivative free. Testing shows the OSCARS-II algorithm
usually finds extrema with fewer function evaluations than similar global
derivative-free methods.
Author: Chris Price [aut, cre],
Trent McDonald [aut, ctb]
Maintainer: Chris Price <chrisj.price@canterbury.ac.nz>
Diff between OSCARS versions 0.1.2 dated 2026-05-06 and 0.2.1 dated 2026-09-22
DESCRIPTION | 8 +++--- MD5 | 26 +++++++++++++++------- NAMESPACE | 5 ++++ R/oscars.R | 55 +++++++++++++++++++++++++++++++++++++++++++----- R/oscars.control.R | 6 ++--- R/oscarsQN.R |only R/oscarsQN.control.R |only R/poscars.R |only R/print.oscars.R | 2 - R/print.oscarsQN.R |only R/summary.oscars.R | 4 +-- R/summary.oscarsQN.R |only man/oscars.Rd | 32 ++++++++++++++++++++++++--- man/oscars.control.Rd | 6 ++--- man/oscarsQN.Rd |only man/oscarsQN.control.Rd |only man/poscars.Rd |only man/print.oscarsQN.Rd |only man/summary.oscarsQN.Rd |only 19 files changed, 114 insertions(+), 30 deletions(-)
Title: Assessing and Visualizing Fragility of Clinical Results
Description: A collection of user-friendly functions for assessing fragility of clinical results with binary and survival outcomes. For binary outcomes, the package assesses and visualizes fragility of individual studies (Walsh et al., 2014 <doi:10.1016/j.jclinepi.2013.10.019>; Lin, 2021 <doi:10.1111/jep.13428>), conventional pairwise meta-analyses (Atal et al., 2019 <doi:10.1016/j.jclinepi.2019.03.012>), and network meta-analyses of multiple treatments with binary outcomes (Xing et al., 2020 <doi:10.1016/j.jclinepi.2020.07.003>). The functions for binary outcomes are designed to: 1) calculate the fragility index (i.e., the minimal event status modifications that can alter the significance or non-significance of the original result) and fragility quotient (i.e., fragility index divided by sample size) at a specific significance level; 2) give the cases of event status modifications for altering the result's significance or non-significance and visualize these cases; 3) visua [...truncated...]
Author: Lifeng Lin [aut, cre] ,
Xing Xing [aut] ,
Jiayi Tong [aut] ,
Haitao Chu [aut]
Maintainer: Lifeng Lin <lifenglin@arizona.edu>
Diff between fragility versions 1.6.1 dated 2025-01-23 and 2.0 dated 2026-09-22
DESCRIPTION | 27 ++++++++++++++++----------- MD5 | 12 +++++++++--- NAMESPACE | 45 +++++++++++++++++++++++---------------------- R/frag.surv.R |only R/print.frag.surv.R |only build/partial.rdb |binary data/dat.fis.rda |only man/dat.fis.Rd |only man/frag.surv.Rd |only man/print.frag.surv.Rd |only 10 files changed, 48 insertions(+), 36 deletions(-)
Title: Estimation of Group Means and SDs from Binned Count Data
Description: Estimates group-level means and standard deviations from
binned (coarsened) data, where only the number of cases in each of
several ordered bins is observed and the underlying values are not.
The main function, fast_hetop(), fits the heteroskedastic ordered
probit model of Reardon, Shear, Castellano and Ho (2017)
<doi:10.3102/1076998616666279> one group at a time, solving
closed-form truncated-normal score equations instead of optimizing
jointly over all groups. Runtime is therefore linear in the number
of groups, so thousands of schools, districts or subgroups can be
fitted in under a second. Cut scores may be supplied when an
agency publishes them, or estimated from the data when it does not.
Output includes standard errors and confidence intervals, an
optional empirical Bayes shrinkage estimator, and a per-group
goodness-of-fit test of the within-group normality assumption.
Also included, and deprecated, are mle_hetop() and fh_hetop(),
which fit the same model by joint maxim [...truncated...]
Author: Paul T. von Hippel [aut, cre],
David J. Hunter [aut],
J.R. Lockwood [aut]
Maintainer: Paul T. von Hippel <ph3828@eid.utexas.edu>
Diff between binest versions 0.2-1 dated 2026-06-08 and 0.3-0 dated 2026-09-22
binest-0.2-1/binest/R/bin_means.R |only binest-0.2-1/binest/README |only binest-0.2-1/binest/man/bin_means.Rd |only binest-0.3-0/binest/DESCRIPTION | 45 +- binest-0.3-0/binest/MD5 | 37 +- binest-0.3-0/binest/NAMESPACE | 9 binest-0.3-0/binest/NEWS.md | 423 +++++++++++++++++++++++++++ binest-0.3-0/binest/R/fast_hetop.R |only binest-0.3-0/binest/R/fh_hetop.R | 44 +- binest-0.3-0/binest/README.md | 44 +- binest-0.3-0/binest/build/vignette.rds |binary binest-0.3-0/binest/inst/doc/binest.R | 36 +- binest-0.3-0/binest/inst/doc/binest.Rmd | 439 +++++++++++++++-------------- binest-0.3-0/binest/inst/doc/binest.html | 357 +++++++++++++---------- binest-0.3-0/binest/man/binest-package.Rd | 50 ++- binest-0.3-0/binest/man/fast_hetop.Rd |only binest-0.3-0/binest/man/fh_hetop.Rd | 65 ++-- binest-0.3-0/binest/man/mle_hetop.Rd | 19 - binest-0.3-0/binest/man/triple_goal.Rd | 2 binest-0.3-0/binest/man/tx_g6_math_2018.Rd | 34 +- binest-0.3-0/binest/man/waic_hetop.Rd | 14 binest-0.3-0/binest/vignettes/binest.Rmd | 439 +++++++++++++++-------------- 22 files changed, 1340 insertions(+), 717 deletions(-)
Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages.
Generates random spatial patterns of points according to many simple rules (complete spatial randomness,
Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns
(thinning, random shift, jittering), simulated realisations of random point processes including
simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes
(using direct, Brix-Kendall, or hybrid algorithms),
log-Gaussian Cox processes, product shot noise cluster processes
and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm,
alternating Gibbs sampler, or coupling-from-the-past perfect simulation).
Also generates random spatial patterns of line segments,
random tessellations, and random images (random noise, random mosaics).
Excludes random generation on a linear network,
which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb, cph],
David Bryant [ctb, cph],
Ya-Mei Chang [ctb, cph],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Dominic Sc [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.random versions 3.5-1 dated 2026-07-27 and 3.5-2 dated 2026-09-21
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS | 6 ++++++ R/random.R | 16 +++++++++------- inst/doc/packagesizes.txt | 2 +- inst/info/packagesizes.txt | 2 +- man/spatstat.random-internal.Rd | 2 +- 7 files changed, 29 insertions(+), 21 deletions(-)
More information about spatstat.random at CRAN
Permanent link
Title: Generative UI for 'shiny'
Description: Build interactive user interfaces for 'shiny' applications
through a conversation with a large language model (LLM).
Developers choose a set of reusable components, and the model arranges
and updates those components as the user describes what they need.
Each component's inputs are checked before it is shown, and the model
supplies data rather than executable code. Applications can also save and
replay the sequence of interface changes without contacting a model.
For background on generative user interfaces, see
Leviathan et al. (2026) <doi:10.48550/arXiv.2604.09577>.
Author: Nan Xiao [aut, cre, cph]
Maintainer: Nan Xiao <me@nanx.me>
Diff between shinygenui versions 0.1.0 dated 2026-09-09 and 0.2.0 dated 2026-09-21
DESCRIPTION | 10 +- MD5 | 30 ++++---- NEWS.md | 33 +++++++++ R/engine.R | 4 - R/server.R | 85 ++++++----------------- R/tools.R | 10 +- README.md | 47 ++++++++++++- inst/doc/shinygenui.R | 16 +++- inst/doc/shinygenui.Rmd | 28 +++++-- inst/doc/shinygenui.html | 82 +++++++++++++---------- inst/examples/01-mtcars-explorer/app.R | 117 +++++++++++++++++++++++++++++++-- inst/examples/02-layout/app.R | 38 +++++++++- man/figures |only man/genui_server.Rd | 18 ++--- man/shinygenui-package.Rd | 2 tests/testthat/test-chat.R |only vignettes/shinygenui.Rmd | 28 +++++-- 17 files changed, 390 insertions(+), 158 deletions(-)
Title: Publication-Quality Forest and Funnel Plots with 'ggplot2'
Description: A 'ggplot2' extension that creates publication-quality forest
and funnel plots from 'meta' package objects or tidy data frames. Provides
custom 'ggproto' geometries for study-level confidence intervals with
weight-proportional squares, summary effect diamonds, prediction
intervals, null-effect reference lines, and funnel-plot contours. Supports
subgroup analysis, back-transformation of summary measures, on-the-fly
effect pooling, effect and weight table columns, and journal-specific
layout presets (JAMA, BMJ, RevMan5).
Author: Hercules R. Freitas [aut, cre, cph]
Maintainer: Hercules R. Freitas <hercules.freitas@uerj.br>
Diff between ggmeta versions 0.1.0 dated 2026-07-22 and 0.1.1 dated 2026-09-21
DESCRIPTION | 8 +-- MD5 | 53 +++++++++++--------- NAMESPACE | 84 +++++++++++++++++---------------- NEWS.md | 69 +++++++++++++++++++++++++++ R/fortify.R | 2 R/geom-forest-ci.R | 23 +++++++-- R/ggforest.R | 75 +++++++++++++++++++++++++---- R/ggfunnel.R | 18 ++++++- R/imports.R | 2 R/tidy-meta.R | 69 ++++++++++++++++++++++++--- R/utils.R | 54 +++++++++++++++++++-- README.md | 14 ++++- build/vignette.rds |binary inst/WORDLIST | 4 + inst/doc/customising.html | 8 +-- inst/doc/from-meta-forest.html | 8 +-- inst/doc/getting-started.html | 14 ++--- man/figures/logo.png |only man/fortify.meta.Rd | 2 man/geom_forest_ci.Rd | 9 +++ man/ggforest.Rd | 11 +++- man/ggfunnel.Rd | 2 man/tidy_meta.Rd | 18 ++++++- tests/testthat/test-columns.R | 45 +++++++++++++++++ tests/testthat/test-edge-cases.R |only tests/testthat/test-geoms.R | 50 +++++++++++++++++++ tests/testthat/test-hetstats-caption.R |only tests/testthat/test-meta-types.R | 76 ++++++++++++++++++++++++++++- tests/testthat/test-pooling.R | 79 +++++++++++++++++++++++++++++++ 29 files changed, 677 insertions(+), 120 deletions(-)
Title: Visualise Function Dependencies
Description: Easily create graphs of the inter-relationships between
functions in an environment.
Author: Lewin Appleton-Fox [aut, cre]
Maintainer: Lewin Appleton-Fox <lewin.a.f@gmail.com>
Diff between foodwebr versions 1.0.0 dated 2025-09-30 and 1.1.0 dated 2026-09-21
DESCRIPTION | 9 - MD5 | 16 +- NEWS.md | 8 + R/function-matrix.R | 243 ++++++++++++++++++++++++++--------- README.md | 63 ++++++++- man/function_arg.Rd |only man/functions_called_by.Rd | 19 +- man/functions_passed_by.Rd |only tests/testthat/test-foodweb-matrix.R | 209 +++++++++++++++++++++++++++++- tests/testthat/test-foodweb.R | 15 ++ 10 files changed, 504 insertions(+), 78 deletions(-)
Title: Days Alive and Out of Hospital (DAOH) Calculation
Description: Calculates Days Alive and Out of Hospital (DAOH) from administrative
admission/discharge/mortality data using three algorithms (nights, days, exact)
and three death-handling approaches (midday, midnight, zero).
Includes tools for comparing methods (Bland-Altman, ICC, reclassification), and plotting.
Author: David Cumin [aut, cre]
Maintainer: David Cumin <d.cumin@auckland.ac.nz>
Diff between daoh versions 0.1.0 dated 2026-06-19 and 0.2.6 dated 2026-09-21
DESCRIPTION | 8 - MD5 | 43 +++---- NAMESPACE | 7 - NEWS.md |only R/algorithms.R | 25 +++- R/calc_daoh.R | 239 +++++++++++++++++++++++++++++---------- R/compare.R | 72 +++++++---- R/daoh-package.R | 18 ++ R/plots.R | 67 ++++++++-- inst/doc/getting_started.R | 3 inst/doc/getting_started.Rmd | 3 inst/doc/getting_started.html | 23 +-- man/bland_altman_daoh.Rd | 9 - man/calc_daoh.Rd | 18 ++ man/daoh-package.Rd |only man/daoh_icc.Rd | 7 - man/daoh_reclassify.Rd | 6 man/daoh_reclassify_centile.Rd | 6 man/daoh_summary.Rd | 8 - man/plot_daoh_ba.Rd | 7 - man/plot_daoh_dist.Rd | 22 ++- tests/testthat.R |only tests/testthat/test_algorithms.R | 31 ++++- vignettes/getting_started.Rmd | 3 24 files changed, 457 insertions(+), 168 deletions(-)
Title: Load and Process Passive Acoustic Data
Description: Tools for loading and processing passive acoustic data. Read in data
that has been processed in 'Pamguard' (<https://www.pamguard.org/>), apply a suite
processing functions, and export data for reports or external modeling tools. Parameter
calculations implement methods by Oswald et al (2007) <doi:10.1121/1.2743157>,
Griffiths et al (2020) <doi:10.1121/10.0001229> and Baumann-Pickering et al (2010)
<doi:10.1121/1.3479549>.
Author: Taiki Sakai [aut, cre],
Jay Barlow [ctb],
Emily Griffiths [ctb],
Michael Oswald [ctb],
Simone Baumann-Pickering [ctb],
Julie Oswald [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PAMpal versions 1.5.2 dated 2026-02-26 and 1.6.1 dated 2026-09-21
DESCRIPTION | 10 - MD5 | 28 +- NAMESPACE | 381 ++++++++++++++++++++++------------------ NEWS.md | 14 + R/addRecordings.R | 18 + R/calculateAverageSpectra.R | 33 ++- R/calculateEchoDepth.R | 14 + R/getClipData.R | 175 +++++++++++++++--- R/plotGram.R | 10 - R/wavUtils.R | 41 ++++ R/writeEventClips.R | 59 +++++- man/calculateAverageSpectra.Rd | 2 man/getClipData.Rd | 154 ++++++++-------- man/writeEventClips.Rd | 3 tests/testthat/test-workStudy.R | 10 - 15 files changed, 633 insertions(+), 319 deletions(-)
Title: Packages and Functions for 'CourseKata' Courses
Description: Easily install and load all packages and functions used in
'CourseKata' courses. Aid teaching with helper functions and augment
generic functions to provide cohesion between the network of packages.
Learn more about 'CourseKata' at <https://www.coursekata.org>.
Author: Adam Blake [cre, aut] ,
Ji Son [aut] ,
Jim Stigler [aut] ,
CourseKata [cph]
Maintainer: Adam Blake <adam@coursekata.org>
Diff between coursekata versions 0.20.1 dated 2026-08-22 and 0.21.0 dated 2026-09-21
coursekata-0.20.1/coursekata/R/compat-ggplot2.R |only coursekata-0.20.1/coursekata/tests/testthat/test-compat-ggplot2.R |only coursekata-0.21.0/coursekata/DESCRIPTION | 16 coursekata-0.21.0/coursekata/MD5 | 210 + coursekata-0.21.0/coursekata/NAMESPACE | 32 coursekata-0.21.0/coursekata/NEWS.md | 90 coursekata-0.21.0/coursekata/R/aaa-named-layer-factory.R |only coursekata-0.21.0/coursekata/R/b-arguments.R |only coursekata-0.21.0/coursekata/R/b-model.R |only coursekata-0.21.0/coursekata/R/b-plan.R |only coursekata-0.21.0/coursekata/R/b-source.R |only coursekata-0.21.0/coursekata/R/cutoff-callout.R |only coursekata-0.21.0/coursekata/R/cutoff-layout.R |only coursekata-0.21.0/coursekata/R/cutoff-plan.R | 7 coursekata-0.21.0/coursekata/R/geom-b-text.R |only coursekata-0.21.0/coursekata/R/geom-cutoff.R |only coursekata-0.21.0/coursekata/R/geom-model.R |only coursekata-0.21.0/coursekata/R/geom-resid.R | 686 ----- coursekata-0.21.0/coursekata/R/geom-squareplot.R | 160 + coursekata-0.21.0/coursekata/R/gf_b.R | 892 ------- coursekata-0.21.0/coursekata/R/gf_model.R | 165 - coursekata-0.21.0/coursekata/R/gf_reduce.R | 313 -- coursekata-0.21.0/coursekata/R/gf_resid_fun.R | 23 coursekata-0.21.0/coursekata/R/gf_resid_gf_squaresid.R | 223 - coursekata-0.21.0/coursekata/R/gf_sd_ruler.R | 192 - coursekata-0.21.0/coursekata/R/gf_square_resid_fun.R | 16 coursekata-0.21.0/coursekata/R/gf_squareplot.R | 338 +- coursekata-0.21.0/coursekata/R/guide-cutoff.R |only coursekata-0.21.0/coursekata/R/guide-dgp.R |only coursekata-0.21.0/coursekata/R/layer-b.R |only coursekata-0.21.0/coursekata/R/layer-diagnostics.R |only coursekata-0.21.0/coursekata/R/layer-model.R |only coursekata-0.21.0/coursekata/R/layer-resid.R |only coursekata-0.21.0/coursekata/R/layer-tag.R | 32 coursekata-0.21.0/coursekata/R/model-implied.R | 8 coursekata-0.21.0/coursekata/R/model-infer.R | 118 coursekata-0.21.0/coursekata/R/model-metadata.R |only coursekata-0.21.0/coursekata/R/model-plan.R | 453 ++- coursekata-0.21.0/coursekata/R/plot-pin.R | 200 + coursekata-0.21.0/coursekata/R/plot-spec.R | 246 + coursekata-0.21.0/coursekata/R/position-anchor.R |only coursekata-0.21.0/coursekata/R/position-guide.R |only coursekata-0.21.0/coursekata/R/resid-plan.R |only coursekata-0.21.0/coursekata/R/resid-source.R |only coursekata-0.21.0/coursekata/R/show_cutoffs.R | 376 +- coursekata-0.21.0/coursekata/R/show_overlays.R | 391 +-- coursekata-0.21.0/coursekata/R/stat-b-mark.R |only coursekata-0.21.0/coursekata/R/stat-cutoff.R | 128 - coursekata-0.21.0/coursekata/R/stat-dist-mean.R |only coursekata-0.21.0/coursekata/R/stat-model.R |only coursekata-0.21.0/coursekata/R/stat-panel.R |only coursekata-0.21.0/coursekata/R/theme.R | 246 - coursekata-0.21.0/coursekata/R/utils.R | 19 coursekata-0.21.0/coursekata/README.md | 17 coursekata-0.21.0/coursekata/man/GeomCutoff.Rd |only coursekata-0.21.0/coursekata/man/GeomModel.Rd |only coursekata-0.21.0/coursekata/man/GeomResid.Rd | 6 coursekata-0.21.0/coursekata/man/GeomSquareResid.Rd | 2 coursekata-0.21.0/coursekata/man/StatCutoff.Rd | 95 coursekata-0.21.0/coursekata/man/StatDistMean.Rd |only coursekata-0.21.0/coursekata/man/StatModel.Rd |only coursekata-0.21.0/coursekata/man/StatReduce.Rd |only coursekata-0.21.0/coursekata/man/StatResid.Rd | 9 coursekata-0.21.0/coursekata/man/StatSdRuler.Rd | 71 coursekata-0.21.0/coursekata/man/coursekata_load_theme.Rd | 4 coursekata-0.21.0/coursekata/man/coursekata_unload_theme.Rd | 7 coursekata-0.21.0/coursekata/man/geom_b.Rd |only coursekata-0.21.0/coursekata/man/geom_model.Rd |only coursekata-0.21.0/coursekata/man/geom_resid.Rd |only coursekata-0.21.0/coursekata/man/geom_squareplot.Rd |only coursekata-0.21.0/coursekata/man/gf_b.Rd | 38 coursekata-0.21.0/coursekata/man/gf_model.Rd | 29 coursekata-0.21.0/coursekata/man/gf_reduce.Rd | 24 coursekata-0.21.0/coursekata/man/gf_resid.Rd | 4 coursekata-0.21.0/coursekata/man/gf_resid_fun.Rd | 4 coursekata-0.21.0/coursekata/man/gf_sd_ruler.Rd | 13 coursekata-0.21.0/coursekata/man/gf_square_reduce.Rd | 42 coursekata-0.21.0/coursekata/man/gf_squareplot.Rd | 13 coursekata-0.21.0/coursekata/man/guide_cutoff.Rd |only coursekata-0.21.0/coursekata/man/guide_dgp.Rd |only coursekata-0.21.0/coursekata/man/show_cutoffs.Rd | 40 coursekata-0.21.0/coursekata/man/show_dgp.Rd | 36 coursekata-0.21.0/coursekata/man/show_mean.Rd | 13 coursekata-0.21.0/coursekata/tests/testthat/_snaps/gf_b-visual/gf-b-categorical-arrows.svg | 4 coursekata-0.21.0/coursekata/tests/testthat/_snaps/gf_b-visual/gf-b-continuous-triangle.svg | 350 +- coursekata-0.21.0/coursekata/tests/testthat/_snaps/gf_sd_ruler/gf-sd-ruler-basic.svg | 2 coursekata-0.21.0/coursekata/tests/testthat/_snaps/guide-cutoff |only coursekata-0.21.0/coursekata/tests/testthat/_snaps/show_cutoffs/show-cutoffs-middle-95.svg | 25 coursekata-0.21.0/coursekata/tests/testthat/_snaps/show_cutoffs/show-cutoffs-stacked-three-levels-flipped.svg |only coursekata-0.21.0/coursekata/tests/testthat/_snaps/show_cutoffs/show-cutoffs-stacked-three-levels.svg | 63 coursekata-0.21.0/coursekata/tests/testthat/_snaps/show_overlays/show-dgp-shuffled-b1.svg | 151 - coursekata-0.21.0/coursekata/tests/testthat/helper-coefficient-marks.R |only coursekata-0.21.0/coursekata/tests/testthat/helper-ggplot.R |only coursekata-0.21.0/coursekata/tests/testthat/helper-vdiffr.R | 11 coursekata-0.21.0/coursekata/tests/testthat/test-annotation-composition.R |only coursekata-0.21.0/coursekata/tests/testthat/test-b-layers.R |only coursekata-0.21.0/coursekata/tests/testthat/test-b-source.R |only coursekata-0.21.0/coursekata/tests/testthat/test-docs.R | 12 coursekata-0.21.0/coursekata/tests/testthat/test-geom-b-text.R |only coursekata-0.21.0/coursekata/tests/testthat/test-geom-cutoff.R |only coursekata-0.21.0/coursekata/tests/testthat/test-geom-resid.R | 24 coursekata-0.21.0/coursekata/tests/testthat/test-geom-squareplot.R | 5 coursekata-0.21.0/coursekata/tests/testthat/test-gf_b-visual.R | 352 ++ coursekata-0.21.0/coursekata/tests/testthat/test-gf_b.R | 151 - coursekata-0.21.0/coursekata/tests/testthat/test-gf_model-formula.R | 4 coursekata-0.21.0/coursekata/tests/testthat/test-gf_model-infer.R | 33 coursekata-0.21.0/coursekata/tests/testthat/test-gf_model-visual.R | 14 coursekata-0.21.0/coursekata/tests/testthat/test-gf_model.R | 56 coursekata-0.21.0/coursekata/tests/testthat/test-gf_reduce.R | 53 coursekata-0.21.0/coursekata/tests/testthat/test-gf_resid_fun.R | 16 coursekata-0.21.0/coursekata/tests/testthat/test-gf_resid_gf_squaresid.R | 30 coursekata-0.21.0/coursekata/tests/testthat/test-gf_sd_ruler.R | 19 coursekata-0.21.0/coursekata/tests/testthat/test-gf_square_resid_fun.R | 6 coursekata-0.21.0/coursekata/tests/testthat/test-gf_squareplot.R | 32 coursekata-0.21.0/coursekata/tests/testthat/test-guide-cutoff.R |only coursekata-0.21.0/coursekata/tests/testthat/test-guide-dgp.R |only coursekata-0.21.0/coursekata/tests/testthat/test-layer-factory.R |only coursekata-0.21.0/coursekata/tests/testthat/test-layer-tag.R | 20 coursekata-0.21.0/coursekata/tests/testthat/test-model-layers.R |only coursekata-0.21.0/coursekata/tests/testthat/test-model-plan.R | 63 coursekata-0.21.0/coursekata/tests/testthat/test-model-shared-plan.R |only coursekata-0.21.0/coursekata/tests/testthat/test-plot-modernization.R |only coursekata-0.21.0/coursekata/tests/testthat/test-plot-pin.R | 30 coursekata-0.21.0/coursekata/tests/testthat/test-plot-spec.R | 45 coursekata-0.21.0/coursekata/tests/testthat/test-plotting-integration.R |only coursekata-0.21.0/coursekata/tests/testthat/test-position-guide.R |only coursekata-0.21.0/coursekata/tests/testthat/test-resid-contracts.R |only coursekata-0.21.0/coursekata/tests/testthat/test-resid-layers.R |only coursekata-0.21.0/coursekata/tests/testthat/test-show_cutoffs.R | 1268 ++++++---- coursekata-0.21.0/coursekata/tests/testthat/test-show_overlays.R | 149 - coursekata-0.21.0/coursekata/tests/testthat/test-source-resolution.R |only coursekata-0.21.0/coursekata/tests/testthat/test-squareplot-constructors.R |only coursekata-0.21.0/coursekata/tests/testthat/test-squareplot-lifecycle.R |only coursekata-0.21.0/coursekata/tests/testthat/test-stat-cutoff.R |only coursekata-0.21.0/coursekata/tests/testthat/test-stat-dist-mean.R |only coursekata-0.21.0/coursekata/tests/testthat/test-stat-sd-ruler.R |only coursekata-0.21.0/coursekata/tests/testthat/test-theme.R |only coursekata-0.21.0/coursekata/tools |only 138 files changed, 4714 insertions(+), 4321 deletions(-)
Title: Genome-Wide Nucleic Acid Melting Temperature Profiling and
Multi-Omics Integration
Description: Accurate calculation of nucleic acid melting temperature (Tm) is fundamental to many molecular biology applications, and this software scales Tm analysis from individual sequences to genome‑wide thermodynamic profiling. This package extends Tm analysis from simple sequence level computation to comprehensive genome-wide thermodynamic profiling. It takes four input sources: sequence strings, a FASTA file, an installed 'BSgenome' package named by string, or a 'GRanges' carrying sequences. A 'regions' argument selects what to cover and 'window' and 'slide' set the resolution at which it is tiled. The implementation provides three Tm calculation methods: the Wallace rule (Thein & Wallace, 1986), empirical GC‑content formulas (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991; Untergasser, 2012; von Ahsen, 2001), and nearest‑neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010; Sugimoto, 1 [...truncated...]
Author: Junhui Li [cre, aut] ,
Lihua Julie Zhu [aut]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between TmCalculator versions 1.1.0 dated 2026-09-14 and 1.1.1 dated 2026-09-21
TmCalculator-1.1.0/TmCalculator/inst/doc/tool_comparison.R |only TmCalculator-1.1.0/TmCalculator/inst/doc/tool_comparison.Rmd |only TmCalculator-1.1.0/TmCalculator/inst/doc/tool_comparison.html |only TmCalculator-1.1.0/TmCalculator/inst/extdata/bench_parallel_cluster.csv |only TmCalculator-1.1.0/TmCalculator/inst/extdata/bench_parallel_strategy.csv |only TmCalculator-1.1.0/TmCalculator/inst/extdata/bench_parallel_strategy_tasks.csv.gz |only TmCalculator-1.1.0/TmCalculator/inst/extdata/nn_params_provenance_v1.1.0.md |only TmCalculator-1.1.0/TmCalculator/inst/scripts/app.R |only TmCalculator-1.1.0/TmCalculator/inst/scripts/bench_methods.R |only TmCalculator-1.1.0/TmCalculator/inst/scripts/bench_parallel_cluster.R |only TmCalculator-1.1.0/TmCalculator/inst/scripts/bench_parallel_cluster.lsf |only TmCalculator-1.1.0/TmCalculator/inst/scripts/bench_parallel_strategy.R |only TmCalculator-1.1.0/TmCalculator/inst/scripts/bench_worker.R |only TmCalculator-1.1.0/TmCalculator/inst/scripts/bench_worker.py |only TmCalculator-1.1.0/TmCalculator/inst/scripts/benchmark_hg38.R |only TmCalculator-1.1.0/TmCalculator/inst/scripts/benchmark_tools.R |only TmCalculator-1.1.0/TmCalculator/inst/scripts/make_figure5_two_env.R |only TmCalculator-1.1.0/TmCalculator/inst/scripts/make_table6.R |only TmCalculator-1.1.0/TmCalculator/inst/vignette-source/tool_comparison.Rmd |only TmCalculator-1.1.0/TmCalculator/vignettes/tool_comparison.Rmd |only TmCalculator-1.1.1/TmCalculator/DESCRIPTION | 19 TmCalculator-1.1.1/TmCalculator/MD5 | 107 TmCalculator-1.1.1/TmCalculator/NAMESPACE | 2 TmCalculator-1.1.1/TmCalculator/NEWS.md | 82 TmCalculator-1.1.1/TmCalculator/R/coor_to_genomic_ranges.R | 12 TmCalculator-1.1.1/TmCalculator/R/tm_calculate.R | 360 + TmCalculator-1.1.1/TmCalculator/R/tm_source.R |only TmCalculator-1.1.1/TmCalculator/R/to_genomic_ranges.R | 9 TmCalculator-1.1.1/TmCalculator/README.md | 2 TmCalculator-1.1.1/TmCalculator/build/vignette.rds |binary TmCalculator-1.1.1/TmCalculator/inst/doc/genome_wide_tm_ecoli.R | 188 TmCalculator-1.1.1/TmCalculator/inst/doc/genome_wide_tm_ecoli.Rmd | 417 -- TmCalculator-1.1.1/TmCalculator/inst/doc/genome_wide_tm_ecoli.html | 1080 ++--- TmCalculator-1.1.1/TmCalculator/inst/doc/hg38_performance_parallel.R | 439 -- TmCalculator-1.1.1/TmCalculator/inst/doc/hg38_performance_parallel.Rmd | 1158 +---- TmCalculator-1.1.1/TmCalculator/inst/doc/hg38_performance_parallel.html | 2060 +--------- TmCalculator-1.1.1/TmCalculator/inst/doc/window_size_sensitivity.Rmd | 16 TmCalculator-1.1.1/TmCalculator/inst/doc/window_size_sensitivity.html | 67 TmCalculator-1.1.1/TmCalculator/inst/extdata/bench_hg38_cluster.csv |only TmCalculator-1.1.1/TmCalculator/inst/extdata/bench_hg38_laptop.csv |only TmCalculator-1.1.1/TmCalculator/inst/extdata/nn_params_provenance_v1.1.1.md |only TmCalculator-1.1.1/TmCalculator/inst/scripts/bench_crosstool.R | 6 TmCalculator-1.1.1/TmCalculator/inst/scripts/bench_tm_calculate.R |only TmCalculator-1.1.1/TmCalculator/inst/scripts/bench_tm_calculate.lsf |only TmCalculator-1.1.1/TmCalculator/inst/scripts/bench_tm_calculate_local.sh |only TmCalculator-1.1.1/TmCalculator/inst/scripts/make_figure2.R | 604 -- TmCalculator-1.1.1/TmCalculator/inst/scripts/make_figure3.R | 531 ++ TmCalculator-1.1.1/TmCalculator/inst/scripts/make_figure4.R | 285 - TmCalculator-1.1.1/TmCalculator/inst/scripts/make_figure5.R | 344 - TmCalculator-1.1.1/TmCalculator/inst/scripts/plot_crosstool.R | 6 TmCalculator-1.1.1/TmCalculator/inst/scripts/quick_parallel_mac.R |only TmCalculator-1.1.1/TmCalculator/inst/scripts/setup_cluster_env.sh | 10 TmCalculator-1.1.1/TmCalculator/inst/scripts/test_tm_calculate_merged.R |only TmCalculator-1.1.1/TmCalculator/inst/vignette-source/genome_wide_tm_ecoli.Rmd | 417 -- TmCalculator-1.1.1/TmCalculator/inst/vignette-source/hg38_performance_parallel.Rmd | 1158 +---- TmCalculator-1.1.1/TmCalculator/inst/vignette-source/window_size_sensitivity.Rmd | 16 TmCalculator-1.1.1/TmCalculator/man/TmCalculator-package.Rd | 2 TmCalculator-1.1.1/TmCalculator/man/coor_to_genomic_ranges.Rd | 4 TmCalculator-1.1.1/TmCalculator/man/dot-fasta_lengths.Rd |only TmCalculator-1.1.1/TmCalculator/man/dot-spill_fasta.Rd |only TmCalculator-1.1.1/TmCalculator/man/dot-tm_as_granges.Rd |only TmCalculator-1.1.1/TmCalculator/man/dot-tm_complete_gr.Rd |only TmCalculator-1.1.1/TmCalculator/man/dot-tm_finish.Rd |only TmCalculator-1.1.1/TmCalculator/man/dot-tm_match.Rd |only TmCalculator-1.1.1/TmCalculator/man/dot-tm_model.Rd |only TmCalculator-1.1.1/TmCalculator/man/dot-tm_offsets.Rd |only TmCalculator-1.1.1/TmCalculator/man/dot-tm_regions.Rd |only TmCalculator-1.1.1/TmCalculator/man/dot-tm_run.Rd |only TmCalculator-1.1.1/TmCalculator/man/dot-tm_source.Rd |only TmCalculator-1.1.1/TmCalculator/man/dot-tm_task_bsgenome.Rd |only TmCalculator-1.1.1/TmCalculator/man/dot-tm_task_fasta.Rd |only TmCalculator-1.1.1/TmCalculator/man/dot-tm_tasks.Rd |only TmCalculator-1.1.1/TmCalculator/man/tm_calculate.Rd | 124 TmCalculator-1.1.1/TmCalculator/vignettes/genome_wide_tm_ecoli.Rmd | 417 -- TmCalculator-1.1.1/TmCalculator/vignettes/hg38_performance_parallel.Rmd | 1158 +---- TmCalculator-1.1.1/TmCalculator/vignettes/window_size_sensitivity.Rmd | 16 76 files changed, 4103 insertions(+), 7013 deletions(-)
Title: Miscellaneous Functions for Passive Acoustic Analysis
Description: A collection of miscellaneous functions for passive acoustics.
Much of the content here is adapted to R from code written by other people.
If you have any ideas of functions to add, please contact Taiki Sakai.
Author: Taiki Sakai [aut, cre],
Jay Barlow [ctb],
Julie Oswald [ctb],
Val Schmidt [ctb]
Maintainer: Taiki Sakai <taiki.sakai@noaa.gov>
Diff between PAMmisc versions 1.13.0 dated 2026-04-04 and 1.14.2 dated 2026-09-21
DESCRIPTION | 10 - MD5 | 32 +++--- NAMESPACE | 214 ++++++++++++++++++++++++------------------ NEWS.md | 15 ++ R/createSSP.R | 2 R/erddapToEdinfo.R | 66 ++++++++++++ R/getEdinfo.R | 3 R/matchEnvData.R | 91 +++++++++++++++++ R/ncToData.R | 127 +++++++++++++++++++----- R/ncUtils.R | 32 +++--- R/peakTrough.R | 8 - R/straightPath.R | 10 - data/hycomList.rda |binary man/erddapToEdinfo.Rd | 7 + man/matchEnvData.Rd | 3 man/ncToData.Rd | 6 - tests/testthat/test-envdata.R | 2 17 files changed, 464 insertions(+), 164 deletions(-)
Title: Reading Bibliometric Data from Lattes Platform
Description: A simple API for downloading and reading xml data directly from Lattes <http://lattes.cnpq.br/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetLattesData versions 1.5 dated 2024-05-04 and 1.5.2 dated 2026-09-21
DESCRIPTION | 16 +- MD5 | 34 ++++- NAMESPACE | 1 NEWS.md | 20 +++ R/get_acad_back.R |only R/get_accepted_papers.R |only R/get_awards.R |only R/get_books.R |only R/get_coauthors.R |only R/get_conferences.R |only R/get_cvitae.R |only R/get_employment.R |only R/get_projs.R |only R/get_published_papers.R |only R/get_superv.R |only R/gld_get_lattes_data.R | 201 ++-------------------------------- R/gld_get_lattes_data_from_zip.R | 99 +++++++--------- R/gld_read_lattes_zip.R | 59 +++++++++ R/gld_read_lattes_zip2.R |only R/gld_utils.R | 86 ++++++++++++++ R/globals.R |only build/vignette.rds |binary inst/doc/gld_vignette-ReadLattes.html | 17 +- man/gld_read_zip2.Rd |only tests/testthat/test_gld2.R |only tests/testthat/test_parsing_bugs.R |only 26 files changed, 267 insertions(+), 266 deletions(-)
Title: Tools for Designing, Simulating, and Analyzing Implementation
Rollout Trials
Description: Provides a unified framework for designing, simulating, and analyzing implementation rollout trials, including stepped wedge, sequential rollout, head-to-head, multi-condition, and rollout implementation optimization designs. The package enables users to flexibly specify rollout schedules, incorporate site-level and nested data structures, generate outcomes under rich hierarchical models, and evaluate analytic strategies through simulation-based power analysis. By separating data generation from model fitting, the tools support assessment of bias, Type I error, and robustness to model misspecification. The workflow integrates with standard mixed-effects modeling approaches and the tidyverse ecosystem, offering transparent and reproducible tools for implementation scientists and applied statisticians.
Author: Ian Cero [aut, cre] ,
C. Hendricks Brown [aut]
Maintainer: Ian Cero <ian_cero@urmc.rochester.edu>
Diff between rollout versions 0.1.0 dated 2026-01-13 and 0.2.0 dated 2026-09-21
DESCRIPTION | 12 LICENSE | 4 MD5 | 69 ++--- NAMESPACE | 3 NEWS.md | 9 R/data_generation.R | 322 ++++++++++++------------- R/effect_simulation.R | 94 ++++++- R/model_evaluation.R | 412 ++++++++++++++++++++++++++++++--- R/model_fitting.R | 195 +++++++-------- R/rollout-package.R | 6 man/add_binary_outcome.Rd | 78 +++--- man/add_binomial_outcome.Rd |only man/add_error.Rd | 46 +-- man/add_fixed_effect.Rd | 46 +-- man/add_linear_outcome.Rd | 46 +-- man/add_parameter.Rd | 46 +-- man/add_poisson_outcome.Rd | 64 ++--- man/add_random_effect.Rd | 50 ++-- man/eval_between.Rd | 113 ++++----- man/eval_bias.Rd | 155 +++++++----- man/eval_coverage.Rd |only man/eval_greater_than.Rd | 111 ++++---- man/eval_less_than.Rd | 111 ++++---- man/eval_quantile.Rd | 119 ++++----- man/evaluate_model_results.Rd | 181 +++++++------- man/extract_model_results.Rd | 104 ++++---- man/figures/lifecycle-deprecated.svg | 42 +-- man/figures/lifecycle-experimental.svg | 42 +-- man/figures/lifecycle-stable.svg | 58 ++-- man/figures/lifecycle-superseded.svg | 42 +-- man/fit_models.Rd | 179 +++++++------- man/initialize_replicates.Rd | 46 +-- man/join_info.Rd | 74 ++--- man/pivot_schedule_longer.Rd | 113 ++++----- man/rollout-package.Rd | 59 ++-- tests/testthat/test-data_generation.R | 271 +++++++++++++++++++++ tests/testthat/test-model_evaluation.R |only 37 files changed, 2031 insertions(+), 1291 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Extra
Support Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
support functions like preconditioned fits
<doi:10.1208/s12248-016-9866-5>, boostrap and stepwise covariate
selection.
Author: Matthew Fidler [aut, cre] ,
Vipul Mann [aut],
Vishal Sarsani [aut] ,
Christian Bartels [ctb],
Bill Denney [aut] ,
Omar Elashkar [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2extra versions 5.2.0 dated 2026-08-04 and 5.2.1 dated 2026-09-21
DESCRIPTION | 17 MD5 | 94 - NAMESPACE | 65 - NEWS.md | 101 + R/AICHelpers.R | 5 R/SCM.R | 393 +++++-- R/bayesiancovsel.R | 157 +- R/computingutil.R | 504 ++++----- R/iivSearch.R | 351 +++--- R/knit_printEquation.R | 91 + R/lassocov.R | 388 ++++--- R/linearizefocei.R | 1588 ++++++++++++++++-------------- R/multistart.R |only R/nlmixr2extra-package.R | 1 R/nlmixrFormula.R | 251 +++- R/parsingutil.R | 359 +++--- R/precondition.R | 268 +++-- R/profile.R | 124 +- R/resSearch.R | 58 - R/rxUiLinearize.R | 280 +++-- R/setCov.R | 209 ++- R/theoFitOde.R | 14 R/zzz.R | 1 README.md | 48 data/theoFitOde.rda |binary inst/iivSearch.R | 212 ++-- inst/tools/build.R | 5 man/horseshoeSummardf.Rd | 2 man/lassoSummardf.Rd | 2 man/linearize.Rd | 21 man/linearizePlot.Rd | 3 man/multistart.Rd |only man/multistartControl.Rd |only man/plot.nlmixr2Multistart.Rd |only tests/testthat/test-AICHelpers.R | 5 tests/testthat/test-SCM-backwardSearch.R | 4 tests/testthat/test-SCM-covarSearchAuto.R | 128 ++ tests/testthat/test-bootstrap.R | 56 - tests/testthat/test-computing.R | 34 tests/testthat/test-iivSearch.R | 45 tests/testthat/test-ini-prior-column.R |only tests/testthat/test-knit_printEquation.R | 64 - tests/testthat/test-lasso.R | 22 tests/testthat/test-linearizefocei.R | 858 ++++++++-------- tests/testthat/test-multistart.R |only tests/testthat/test-nlmixrFormula.R | 281 +++-- tests/testthat/test-parsing.R | 160 +-- tests/testthat/test-precondition.R | 101 + tests/testthat/test-profile.R | 66 - tests/testthat/test-resSearch.R | 37 tests/testthat/test-safety.R | 1 51 files changed, 4434 insertions(+), 3040 deletions(-)
Title: Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io',
and 'RPubs'
Description: Programmatic deployment interface for 'RPubs',
'shinyapps.io', and 'Posit Connect'. Supported content types include R
Markdown documents, Shiny applications, Plumber APIs, plots, and
static web content.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Hadley Wickham [aut],
Jonathan McPherson [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between rsconnect versions 1.11.0 dated 2026-08-25 and 1.11.1 dated 2026-09-21
DESCRIPTION | 6 MD5 | 60 NEWS.md | 56 R/appMetadata.R | 12 R/applications.R | 79 R/auth.R | 461 ++++- R/client-connect.R | 17 R/client-connectCloud.R | 198 +- R/deployApp.R | 23 R/deploymentTarget.R | 54 R/options.R |only R/rpubs.R | 2 README.md | 2 man/addAuthorizedUser.Rd | 21 man/options.Rd | 101 - man/removeAuthorizedUser.Rd | 18 man/resendInvitation.Rd | 20 man/showInvited.Rd | 28 man/showUsers.Rd | 33 tests/manual/publishing-dialog.Rmd | 8 tests/testthat/helper.R | 42 tests/testthat/shinyapp-with-absolute-paths/ShinyDocument.Rmd | 7 tests/testthat/shinyapp-with-absolute-paths/ShinyPresentation.Rmd | 6 tests/testthat/shinyapp-with-absolute-paths/server.R | 2 tests/testthat/test-appMetadata.R | 32 tests/testthat/test-applications.R | 143 + tests/testthat/test-auth.R |only tests/testthat/test-bundle.R | 2 tests/testthat/test-client-connect.R | 58 tests/testthat/test-client-connectCloud.R | 832 +++++++++- tests/testthat/test-deployApp.R | 183 ++ tests/testthat/test-deploymentTarget.R | 73 32 files changed, 2272 insertions(+), 307 deletions(-)
Title: Robust Trimmed Clustering
Description: Provides functions for robust trimmed clustering. The methods are
described in Garcia-Escudero (2008) <doi:10.1214/07-AOS515>,
Fritz et al. (2012) <doi:10.18637/jss.v047.i12>,
Garcia-Escudero et al. (2011) <doi:10.1007/s11222-010-9194-z> and others.
Author: Valentin Todorov [aut, cre] ,
Luis Angel Garcia Escudero [aut],
Agustin Mayo Iscar [aut],
Javier Crespo Guerrero [aut],
Heinrich Fritz [aut]
Maintainer: Valentin Todorov <valentin@todorov.at>
Diff between tclust versions 2.2-0 dated 2026-04-26 and 2.2-3 dated 2026-09-21
tclust-2.2-0/tclust/R/myscale.r |only tclust-2.2-0/tclust/inst/tests |only tclust-2.2-3/tclust/ChangeLog | 10 + tclust-2.2-3/tclust/DESCRIPTION | 6 tclust-2.2-3/tclust/MD5 | 31 +--- tclust-2.2-3/tclust/R/DiscrFact.R | 4 tclust-2.2-3/tclust/R/RcppExports.R | 65 ++++---- tclust-2.2-3/tclust/R/ctlcurves.R | 4 tclust-2.2-3/tclust/R/myscale.R |only tclust-2.2-3/tclust/R/print.tclust.R | 13 - tclust-2.2-3/tclust/R/tclust-internal.R | 11 + tclust-2.2-3/tclust/R/tclust.R | 186 ++++++++++++++++++++++-- tclust-2.2-3/tclust/man/estepRR.Rd | 3 tclust-2.2-3/tclust/man/tclust.Rd | 55 ++++++- tclust-2.2-3/tclust/src/GPCM.cpp |only tclust-2.2-3/tclust/src/RcppExports.cpp | 33 +++- tclust-2.2-3/tclust/src/tclust.cpp | 244 ++++++++++++++++++++++++++------ tclust-2.2-3/tclust/src/tclust_types.h | 69 ++++++++- 18 files changed, 596 insertions(+), 138 deletions(-)
Title: Single Cell Oriented Reconstruction of PANDA Individually
Optimized Networks
Description: Constructs cell-type-specific gene regulatory networks from single-cell RNA-sequencing data. The method implements the SCORPION algorithm, which first aggregates individual cells into super-cells and then applies PANDA (Passing Attributes between Networks for Data Assimilation) to infer transcription factor-target regulatory relationships. It also provides statistical methods for differential edge analysis.
Author: Daniel Osorio [aut, cre] ,
Marieke L. Kuijjer [aut]
Maintainer: Daniel Osorio <daniecos@uio.no>
Diff between SCORPION versions 1.3.3 dated 2026-09-02 and 1.3.4 dated 2026-09-21
DESCRIPTION | 6 ++--- MD5 | 6 ++--- R/runSCORPION.R | 54 ++++++++++++++++++++++++++++++------------------ data/scorpionTest.RData |binary 4 files changed, 40 insertions(+), 26 deletions(-)
Title: Adversarial Random Forests
Description: Adversarial random forests (ARFs) recursively partition data
into fully factorized leaves, where features are jointly independent.
The procedure is iterative, with alternating rounds of generation and
discrimination. Data becomes increasingly realistic at each round,
until original and synthetic samples can no longer be reliably
distinguished. This is useful for several unsupervised learning
tasks, such as density estimation and data synthesis. Methods for both
are implemented in this package. ARFs naturally handle unstructured
data with mixed continuous and categorical covariates. They inherit
many of the benefits of random forests, including speed, flexibility,
and solid performance with default parameters. For details, see
Watson et al. (2023)
<https://proceedings.mlr.press/v206/watson23a.html>.
Author: Marvin N. Wright [aut, cre] ,
David S. Watson [aut] ,
Kristin Blesch [aut] ,
Jan Kapar [aut] ,
Lukas Burk [ctb] ,
Martin Jullum [ctb]
Maintainer: Marvin N. Wright <cran@wrig.de>
Diff between arf versions 0.2.4 dated 2025-02-24 and 0.2.5 dated 2026-09-21
arf-0.2.4/arf/tests/testthat/test_expct.R |only arf-0.2.4/arf/vignettes/vignette.R |only arf-0.2.4/arf/vignettes/vignette.html |only arf-0.2.5/arf/DESCRIPTION | 89 +++---- arf-0.2.5/arf/MD5 | 46 ++- arf-0.2.5/arf/NAMESPACE | 33 +- arf-0.2.5/arf/NEWS.md | 9 arf-0.2.5/arf/R/adversarial_rf.R | 45 +-- arf-0.2.5/arf/R/expct.R | 22 + arf-0.2.5/arf/R/forde.R | 14 - arf-0.2.5/arf/R/forge.R | 25 +- arf-0.2.5/arf/R/sample_from_leaves.R |only arf-0.2.5/arf/R/shortcut_functions.R | 10 arf-0.2.5/arf/R/utils.R | 54 +++- arf-0.2.5/arf/README.md | 5 arf-0.2.5/arf/build/vignette.rds |binary arf-0.2.5/arf/inst/doc/arf.R | 14 - arf-0.2.5/arf/inst/doc/arf.html | 197 ++++++++--------- arf-0.2.5/arf/man/adversarial_rf.Rd | 6 arf-0.2.5/arf/man/arf-package.Rd | 7 arf-0.2.5/arf/man/prep_cond.Rd | 2 arf-0.2.5/arf/man/sample_from_leaves.Rd |only arf-0.2.5/arf/tests/testthat/test-arguments.R | 12 - arf-0.2.5/arf/tests/testthat/test-conditions.R | 16 - arf-0.2.5/arf/tests/testthat/test-expct.R |only arf-0.2.5/arf/tests/testthat/test-nomatch.R |only arf-0.2.5/arf/tests/testthat/test-return_types.R | 10 arf-0.2.5/arf/tests/testthat/test-sample_from_leaves.R |only 28 files changed, 349 insertions(+), 267 deletions(-)
Title: Create Tests According to QTI 2.1 Standard
Description: Create tests and tasks compliant with the Question & Test Interoperability (QTI) information model version 2.1. Input sources are Rmd/md description files or S4-class objects. Output formats include standalone zip or xml files. Supports the generation of basic task types (single and multiple choice, order, pair association, matching tables, filling gaps and essay) and provides a comprehensive set of attributes for customizing tests.
Author: Andrey Shevandrin [aut, cre, cph] ,
Petr Bondarenko [ctb] ,
Ivonne Ojeda [ctb],
Johannes Titz [aut, cph] ,
Brian Mottershead [cph] ,
Stiftung fuer Innovation in der Hochschullehre [fnd]
Maintainer: Andrey Shevandrin <shevandrin@gmail.com>
Diff between rqti versions 1.2.1 dated 2026-05-14 and 1.3.0 dated 2026-09-21
rqti-1.2.1/rqti/inst/exercises |only rqti-1.3.0/rqti/DESCRIPTION | 12 rqti-1.3.0/rqti/MD5 | 228 +-- rqti-1.3.0/rqti/NAMESPACE | 11 rqti-1.3.0/rqti/NEWS.md | 42 rqti-1.3.0/rqti/R/AssessmentItem.R | 26 rqti-1.3.0/rqti/R/AssessmentSection.R | 3 rqti-1.3.0/rqti/R/AssessmentTest.R | 11 rqti-1.3.0/rqti/R/AssessmentTestOpal.R | 37 rqti-1.3.0/rqti/R/AssessmentTestOpenOlat.R | 4 rqti-1.3.0/rqti/R/CorrectFeedback.R | 4 rqti-1.3.0/rqti/R/DirectedPair.R | 4 rqti-1.3.0/rqti/R/Entry.R | 3 rqti-1.3.0/rqti/R/Essay.R | 4 rqti-1.3.0/rqti/R/InlineChoice.R | 4 rqti-1.3.0/rqti/R/LMS.R | 176 ++ rqti-1.3.0/rqti/R/ModalFeedback.R | 4 rqti-1.3.0/rqti/R/MultipleChoice.R | 4 rqti-1.3.0/rqti/R/MultipleChoiceTable.R | 4 rqti-1.3.0/rqti/R/NumericGap.R | 4 rqti-1.3.0/rqti/R/OneInColTable.R | 4 rqti-1.3.0/rqti/R/OneInRowTable.R | 4 rqti-1.3.0/rqti/R/Opal.R | 561 ++++++- rqti-1.3.0/rqti/R/Ordering.R | 4 rqti-1.3.0/rqti/R/SingleChoice.R | 4 rqti-1.3.0/rqti/R/TextGap.R | 5 rqti-1.3.0/rqti/R/TextGapOpal.R | 4 rqti-1.3.0/rqti/R/WrongFeedback.R | 4 rqti-1.3.0/rqti/R/character.R | 13 rqti-1.3.0/rqti/R/extract_results.R | 194 +- rqti-1.3.0/rqti/R/helpers.R | 204 ++ rqti-1.3.0/rqti/R/knit_functions.R | 16 rqti-1.3.0/rqti/R/object_builder.R | 14 rqti-1.3.0/rqti/R/qti_test.R | 26 rqti-1.3.0/rqti/R/response_processing.R | 2 rqti-1.3.0/rqti/R/rqti.R | 105 + rqti-1.3.0/rqti/R/section_builder.R | 26 rqti-1.3.0/rqti/R/verify_qti.R | 181 ++ rqti-1.3.0/rqti/README.md | 2 rqti-1.3.0/rqti/inst/QTIJS/index.xml |only rqti-1.3.0/rqti/inst/QTIJS/theme/core.css | 52 rqti-1.3.0/rqti/inst/QTIJS/themecc/style.css | 59 rqti-1.3.0/rqti/inst/extdata |only rqti-1.3.0/rqti/inst/qti_v2p1p2_extension.xsd | 59 rqti-1.3.0/rqti/inst/xsd/imsqti_v2p2.xsd |only rqti-1.3.0/rqti/man/AssessmentSection-class.Rd | 10 rqti-1.3.0/rqti/man/AssessmentTest-class.Rd | 14 rqti-1.3.0/rqti/man/AssessmentTestOpal-class.Rd | 20 rqti-1.3.0/rqti/man/AssessmentTestOpenOlat-class.Rd | 14 rqti-1.3.0/rqti/man/Gap-class.Rd | 4 rqti-1.3.0/rqti/man/InlineChoice-class.Rd | 4 rqti-1.3.0/rqti/man/NumericGap-class.Rd | 4 rqti-1.3.0/rqti/man/TextGap-class.Rd | 4 rqti-1.3.0/rqti/man/TextGapOpal-class.Rd | 4 rqti-1.3.0/rqti/man/addGroupUser-methods.Rd |only rqti-1.3.0/rqti/man/assessmentSection.Rd | 2 rqti-1.3.0/rqti/man/assessmentTest.Rd | 6 rqti-1.3.0/rqti/man/assessmentTestOpal.Rd | 24 rqti-1.3.0/rqti/man/assessmentTestOpenOlat.Rd | 4 rqti-1.3.0/rqti/man/buildAssessmentSection-methods.Rd | 2 rqti-1.3.0/rqti/man/createCourseGroup-methods.Rd |only rqti-1.3.0/rqti/man/createQtiTask-methods.Rd | 4 rqti-1.3.0/rqti/man/createQtiTest-methods.Rd | 6 rqti-1.3.0/rqti/man/createZip-methods.Rd | 4 rqti-1.3.0/rqti/man/create_qti_test.Rd | 8 rqti-1.3.0/rqti/man/dropdown.Rd | 6 rqti-1.3.0/rqti/man/extract_results.Rd | 8 rqti-1.3.0/rqti/man/gap_numeric.Rd | 24 rqti-1.3.0/rqti/man/gap_text.Rd | 2 rqti-1.3.0/rqti/man/getCourseAssessment-methods.Rd |only rqti-1.3.0/rqti/man/getCourseElements-methods.Rd | 4 rqti-1.3.0/rqti/man/getLMSResourceURL-methods.Rd | 2 rqti-1.3.0/rqti/man/getLMSResources-methods.Rd | 2 rqti-1.3.0/rqti/man/getLMSResourcesByName-methods.Rd | 4 rqti-1.3.0/rqti/man/inlineChoice.Rd | 4 rqti-1.3.0/rqti/man/numericGap_doc.Rd | 4 rqti-1.3.0/rqti/man/provide_audio.Rd |only rqti-1.3.0/rqti/man/removeGroupUser-methods.Rd |only rqti-1.3.0/rqti/man/render_opal.Rd | 7 rqti-1.3.0/rqti/man/render_qtijs.Rd | 7 rqti-1.3.0/rqti/man/render_xml.Rd | 2 rqti-1.3.0/rqti/man/section.Rd | 8 rqti-1.3.0/rqti/man/test.Rd | 6 rqti-1.3.0/rqti/man/test4opal.Rd | 12 rqti-1.3.0/rqti/man/textGapOpal_doc.Rd | 4 rqti-1.3.0/rqti/man/textGap_doc.Rd | 4 rqti-1.3.0/rqti/man/upload2LMS-methods.Rd | 10 rqti-1.3.0/rqti/man/upload2opal.Rd | 28 rqti-1.3.0/rqti/man/verify_qti.Rd | 19 rqti-1.3.0/rqti/man/verify_qti_impl.Rd | 12 rqti-1.3.0/rqti/tests/qtijs |only rqti-1.3.0/rqti/tests/testthat/file/rmd/resolution_image.Rmd | 23 rqti-1.3.0/rqti/tests/testthat/file/xml/assessmentResult_candidate_comment.xml |only rqti-1.3.0/rqti/tests/testthat/test-api_lms.R | 740 +++++++++- rqti-1.3.0/rqti/tests/testthat/test-assessment_test.R | 93 + rqti-1.3.0/rqti/tests/testthat/test-character.R | 155 ++ rqti-1.3.0/rqti/tests/testthat/test-correct_feedback.R | 7 rqti-1.3.0/rqti/tests/testthat/test-essay.R | 11 rqti-1.3.0/rqti/tests/testthat/test-extract_results.R | 107 + rqti-1.3.0/rqti/tests/testthat/test-helpers.R | 41 rqti-1.3.0/rqti/tests/testthat/test-helpers_provide_audio.R |only rqti-1.3.0/rqti/tests/testthat/test-helpers_provide_file.R | 26 rqti-1.3.0/rqti/tests/testthat/test-images.R |only rqti-1.3.0/rqti/tests/testthat/test-knit_functions.R | 182 -- rqti-1.3.0/rqti/tests/testthat/test-multiple_choice_table.R | 47 rqti-1.3.0/rqti/tests/testthat/test-object_builder.R | 2 rqti-1.3.0/rqti/tests/testthat/test-qti_exam.R | 13 rqti-1.3.0/rqti/tests/testthat/test-response_processing.R |only rqti-1.3.0/rqti/tests/testthat/test-rmd2qti.R | 20 rqti-1.3.0/rqti/tests/testthat/test-section.R | 11 rqti-1.3.0/rqti/tests/testthat/test-verify_qti.R | 196 ++ rqti-1.3.0/rqti/tests/testthat/test-wrong_feedback.R | 9 112 files changed, 3286 insertions(+), 842 deletions(-)
Title: Track Energy Consumption and Carbon Emissions of R Code
Description: Wraps the Python 'codecarbon' package via 'reticulate' to
measure the energy consumption and estimated carbon emissions of R
code. Provides a self-contained setup routine that installs
'codecarbon' into a dedicated conda environment, and an R-facing
tracker API for measuring a block of code or a longer-running
session.
Author: Beatrice Bock [aut, cre, cph] ,
Rachel Peterson [aut] ,
Dylan Van Bramer [aut]
Maintainer: Beatrice Bock <beabockm@gmail.com>
Diff between CodeCarbonR versions 0.1.0 dated 2026-09-05 and 0.1.1 dated 2026-09-21
DESCRIPTION | 15 ++++++++------- MD5 | 8 ++++---- NEWS.md | 9 +++++++++ README.md | 11 +++++++++++ inst/CITATION | 39 ++++++++++++++++++++++++++++----------- 5 files changed, 60 insertions(+), 22 deletions(-)
Title: Templated Unified Library for Posterior Approximation in
Bayesian Hierarchical Models
Description: A general-purpose engine for fitting Bayesian hierarchical models
with spatial fields, temporal effects, spatially varying coefficients, and
multiple inference backends. Scalable spatial structure includes Hilbert
space approximate Gaussian processes (HSGP; Riutort-Mayol et al. 2023
<doi:10.1007/s11222-022-10167-2>), nearest-neighbor Gaussian processes
(NNGP; Datta et al. 2016 <doi:10.1080/01621459.2015.1044091>), intrinsic
conditional autoregressive models (ICAR; Besag, York, and Mollie 1991
<doi:10.1007/BF00116466>), the reparameterized Besag-York-Mollie model
(BYM2; Riebler et al. 2016 <doi:10.1177/0962280216660421>), and stochastic
partial differential equation fields (SPDE; Lindgren, Rue, and Lindstrom
2011 <doi:10.1111/j.1467-9868.2011.00777.x>). Temporal structure covers
random walks, autoregressive processes, and Gaussian processes. Inference
is tiered by correctness guarantee: exact Hamiltonian Monte Carlo with the
No-U-Turn sampler, Laplace and n [...truncated...]
Author: Gilles Colling [aut, cre, cph] ,
Frances Y. Kuo [ctb, cph] ,
Stephen Joe [ctb, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between tulpa versions 0.2.0 dated 2026-09-09 and 0.5.0 dated 2026-09-21
tulpa-0.2.0/tulpa/inst/include/tulpa/joint_nested_laplace_api.h |only tulpa-0.2.0/tulpa/man/gp_cov_type_for_laplace.Rd |only tulpa-0.2.0/tulpa/man/laplace_diagnostics.Rd |only tulpa-0.2.0/tulpa/man/mcmc_diagnostics.Rd |only tulpa-0.2.0/tulpa/tests/testthat/Rplots.pdf |only tulpa-0.5.0/tulpa/DESCRIPTION | 14 tulpa-0.5.0/tulpa/MD5 | 1076 +-- tulpa-0.5.0/tulpa/NAMESPACE | 175 tulpa-0.5.0/tulpa/NEWS.md | 3391 +++++++++- tulpa-0.5.0/tulpa/R/RcppExports.R | 168 tulpa-0.5.0/tulpa/R/agq.R | 30 tulpa-0.5.0/tulpa/R/bayes_r2.R | 22 tulpa-0.5.0/tulpa/R/brasil.R | 12 tulpa-0.5.0/tulpa/R/categorical_accessors.R |only tulpa-0.5.0/tulpa/R/cila.R | 27 tulpa-0.5.0/tulpa/R/control_check.R | 112 tulpa-0.5.0/tulpa/R/convergence.R | 86 tulpa-0.5.0/tulpa/R/criteria.R | 284 tulpa-0.5.0/tulpa/R/diagnostics.R | 253 tulpa-0.5.0/tulpa/R/diagnostics_generic.R | 229 tulpa-0.5.0/tulpa/R/diagnostics_sim.R | 33 tulpa-0.5.0/tulpa/R/eb.R | 30 tulpa-0.5.0/tulpa/R/em_laplace.R | 2 tulpa-0.5.0/tulpa/R/ep.R | 141 tulpa-0.5.0/tulpa/R/family_loglik.R | 143 tulpa-0.5.0/tulpa/R/family_zi.R | 47 tulpa-0.5.0/tulpa/R/fit_beta_nuts.R | 14 tulpa-0.5.0/tulpa/R/fit_gibbs.R | 341 - tulpa-0.5.0/tulpa/R/fit_laplace.R | 100 tulpa-0.5.0/tulpa/R/fit_spde.R | 110 tulpa-0.5.0/tulpa/R/fit_spde_nested.R | 165 tulpa-0.5.0/tulpa/R/fit_spde_nuts.R | 15 tulpa-0.5.0/tulpa/R/fit_st_nested.R | 399 + tulpa-0.5.0/tulpa/R/fit_st_nested_auto_grid.R | 33 tulpa-0.5.0/tulpa/R/formula.R | 147 tulpa-0.5.0/tulpa/R/glmm_logpost.R | 2 tulpa-0.5.0/tulpa/R/hyper_axis_spec.R | 104 tulpa-0.5.0/tulpa/R/hyper_grid.R | 108 tulpa-0.5.0/tulpa/R/hyper_grid_refine.R | 205 tulpa-0.5.0/tulpa/R/hyper_quadrature.R |only tulpa-0.5.0/tulpa/R/hyperprior_default.R |only tulpa-0.5.0/tulpa/R/imh_laplace.R | 8 tulpa-0.5.0/tulpa/R/inference_modes.R | 485 + tulpa-0.5.0/tulpa/R/kfold.R | 53 tulpa-0.5.0/tulpa/R/laplace_diagnostics.R | 594 - tulpa-0.5.0/tulpa/R/mala.R | 8 tulpa-0.5.0/tulpa/R/marginal_se_spatial.R | 73 tulpa-0.5.0/tulpa/R/methods_generic.R | 625 + tulpa-0.5.0/tulpa/R/methods_interop.R | 3 tulpa-0.5.0/tulpa/R/mode_find.R | 13 tulpa-0.5.0/tulpa/R/multinomial.R | 36 tulpa-0.5.0/tulpa/R/nested_laplace.R | 672 + tulpa-0.5.0/tulpa/R/nested_laplace_auto_grid.R | 814 ++ tulpa-0.5.0/tulpa/R/nested_laplace_joint.R | 1005 ++ tulpa-0.5.0/tulpa/R/nested_laplace_joint_adaptive.R | 7 tulpa-0.5.0/tulpa/R/nested_laplace_joint_backends.R | 58 tulpa-0.5.0/tulpa/R/nested_laplace_joint_batch.R | 451 + tulpa-0.5.0/tulpa/R/nested_laplace_joint_ccd.R | 640 + tulpa-0.5.0/tulpa/R/nested_laplace_joint_ccd_local.R | 47 tulpa-0.5.0/tulpa/R/nested_laplace_joint_helpers.R | 714 +- tulpa-0.5.0/tulpa/R/nested_laplace_joint_hyperpriors.R | 36 tulpa-0.5.0/tulpa/R/nested_laplace_joint_multi.R | 655 + tulpa-0.5.0/tulpa/R/nested_laplace_joint_pareto_k.R | 600 - tulpa-0.5.0/tulpa/R/nested_laplace_moments.R | 596 + tulpa-0.5.0/tulpa/R/nested_laplace_pilot.R |only tulpa-0.5.0/tulpa/R/nested_laplace_re_cov.R | 164 tulpa-0.5.0/tulpa/R/ordinal.R | 64 tulpa-0.5.0/tulpa/R/outer_pareto_candidates.R |only tulpa-0.5.0/tulpa/R/outer_threads.R |only tulpa-0.5.0/tulpa/R/pathfinder.R | 9 tulpa-0.5.0/tulpa/R/plot_diagnostics.R | 162 tulpa-0.5.0/tulpa/R/plot_map.R | 17 tulpa-0.5.0/tulpa/R/posterior_draws.R | 32 tulpa-0.5.0/tulpa/R/posterior_draws_hyper.R |only tulpa-0.5.0/tulpa/R/posterior_draws_joint.R | 20 tulpa-0.5.0/tulpa/R/posterior_predict.R | 483 + tulpa-0.5.0/tulpa/R/priorsense.R | 86 tulpa-0.5.0/tulpa/R/progress_iter.R | 50 tulpa-0.5.0/tulpa/R/prune_screen.R |only tulpa-0.5.0/tulpa/R/psis.R | 182 tulpa-0.5.0/tulpa/R/rational_spde.R | 71 tulpa-0.5.0/tulpa/R/re_cov_gibbs.R | 12 tulpa-0.5.0/tulpa/R/sample_glmm.R | 106 tulpa-0.5.0/tulpa/R/sbc.R | 44 tulpa-0.5.0/tulpa/R/settings.R | 556 + tulpa-0.5.0/tulpa/R/simulate.R | 2 tulpa-0.5.0/tulpa/R/spatial_car.R | 14 tulpa-0.5.0/tulpa/R/spatial_field.R | 100 tulpa-0.5.0/tulpa/R/spatial_gp.R | 63 tulpa-0.5.0/tulpa/R/spatial_rsr_spde.R | 144 tulpa-0.5.0/tulpa/R/spatiotemporal.R | 38 tulpa-0.5.0/tulpa/R/temporal_ar2.R | 12 tulpa-0.5.0/tulpa/R/temporal_field.R | 32 tulpa-0.5.0/tulpa/R/temporal_gp.R | 97 tulpa-0.5.0/tulpa/R/temporal_rtr_posteriors.R | 85 tulpa-0.5.0/tulpa/R/temporal_tvc.R | 105 tulpa-0.5.0/tulpa/R/tgmrf_imh.R | 4 tulpa-0.5.0/tulpa/R/tgmrf_nuts.R | 7 tulpa-0.5.0/tulpa/R/tgmrf_nuts_joint.R | 35 tulpa-0.5.0/tulpa/R/tgmrf_vi.R | 4 tulpa-0.5.0/tulpa/R/tulpa-package.R | 1 tulpa-0.5.0/tulpa/R/tulpa.R | 822 +- tulpa-0.5.0/tulpa/R/validate.R | 35 tulpa-0.5.0/tulpa/R/validate_helpers.R | 7 tulpa-0.5.0/tulpa/R/varcorr.R | 24 tulpa-0.5.0/tulpa/R/warm_start.R | 1 tulpa-0.5.0/tulpa/build/partial.rdb |binary tulpa-0.5.0/tulpa/build/vignette.rds |binary tulpa-0.5.0/tulpa/inst/CITATION | 4 tulpa-0.5.0/tulpa/inst/doc/inference-modes.R | 9 tulpa-0.5.0/tulpa/inst/doc/inference-modes.Rmd | 1115 +-- tulpa-0.5.0/tulpa/inst/doc/inference-modes.html | 38 tulpa-0.5.0/tulpa/inst/doc/model-comparison.R | 16 tulpa-0.5.0/tulpa/inst/doc/model-comparison.Rmd | 18 tulpa-0.5.0/tulpa/inst/doc/model-comparison.html | 20 tulpa-0.5.0/tulpa/inst/doc/priors.Rmd | 1318 +-- tulpa-0.5.0/tulpa/inst/doc/priors.html | 61 tulpa-0.5.0/tulpa/inst/doc/quickstart.R | 10 tulpa-0.5.0/tulpa/inst/doc/quickstart.Rmd | 1607 ++-- tulpa-0.5.0/tulpa/inst/doc/quickstart.html | 46 tulpa-0.5.0/tulpa/inst/doc/reliability-pareto-k.R | 4 tulpa-0.5.0/tulpa/inst/doc/reliability-pareto-k.Rmd | 17 tulpa-0.5.0/tulpa/inst/doc/reliability-pareto-k.html | 30 tulpa-0.5.0/tulpa/inst/doc/sbc.R | 7 tulpa-0.5.0/tulpa/inst/doc/sbc.Rmd | 11 tulpa-0.5.0/tulpa/inst/doc/sbc.html | 12 tulpa-0.5.0/tulpa/inst/doc/spatial-models.R | 9 tulpa-0.5.0/tulpa/inst/doc/spatial-models.Rmd | 32 tulpa-0.5.0/tulpa/inst/doc/spatial-models.html | 37 tulpa-0.5.0/tulpa/inst/doc/temporal-models.R | 11 tulpa-0.5.0/tulpa/inst/doc/temporal-models.Rmd | 43 tulpa-0.5.0/tulpa/inst/doc/temporal-models.html | 50 tulpa-0.5.0/tulpa/inst/doc/tgmrf.Rmd | 15 tulpa-0.5.0/tulpa/inst/doc/tgmrf.html | 40 tulpa-0.5.0/tulpa/inst/include/tulpa/aghq_oracle.h | 14 tulpa-0.5.0/tulpa/inst/include/tulpa/cov_kernel.h |only tulpa-0.5.0/tulpa/inst/include/tulpa/model_data.h | 28 tulpa-0.5.0/tulpa/inst/include/tulpa/param_layout.h | 8 tulpa-0.5.0/tulpa/inst/include/tulpa/tvc_data.h | 12 tulpa-0.5.0/tulpa/inst/include/tulpa/types.h | 10 tulpa-0.5.0/tulpa/man/AIC.tulpa_fit.Rd |only tulpa-0.5.0/tulpa/man/BACKEND_REGISTRY.Rd | 3 tulpa-0.5.0/tulpa/man/agq_fit.Rd | 4 tulpa-0.5.0/tulpa/man/auto_grid.Rd | 37 tulpa-0.5.0/tulpa/man/auto_grid_place.Rd |only tulpa-0.5.0/tulpa/man/auto_select_mode.Rd | 3 tulpa-0.5.0/tulpa/man/build_glmm_logpost.Rd | 12 tulpa-0.5.0/tulpa/man/categorical_accessors.Rd |only tulpa-0.5.0/tulpa/man/compare_models.Rd | 5 tulpa-0.5.0/tulpa/man/confint.tulpa_fit.Rd | 4 tulpa-0.5.0/tulpa/man/criteria_doors.Rd | 79 tulpa-0.5.0/tulpa/man/diagnostics.Rd | 244 tulpa-0.5.0/tulpa/man/dispatch_gibbs_spatial.Rd | 3 tulpa-0.5.0/tulpa/man/dispatch_gibbs_temporal.Rd | 3 tulpa-0.5.0/tulpa/man/dot-assert_finite_model_inputs.Rd | 24 tulpa-0.5.0/tulpa/man/dot-canonical_family.Rd | 11 tulpa-0.5.0/tulpa/man/dot-family_obs_weight.Rd | 19 tulpa-0.5.0/tulpa/man/dot-finalize_fit.Rd | 17 tulpa-0.5.0/tulpa/man/dot-marginal_H_beta_bym2.Rd | 3 tulpa-0.5.0/tulpa/man/dot-spde_mean_marginal_var.Rd | 16 tulpa-0.5.0/tulpa/man/dot-spde_nested_logmarginal_at.Rd | 4 tulpa-0.5.0/tulpa/man/dot-validate_glm_design.Rd | 10 tulpa-0.5.0/tulpa/man/family_names.Rd | 8 tulpa-0.5.0/tulpa/man/fit_spde.Rd | 36 tulpa-0.5.0/tulpa/man/fit_st_nested.Rd | 121 tulpa-0.5.0/tulpa/man/fitted.tulpa_fit.Rd | 5 tulpa-0.5.0/tulpa/man/glmm_weights.Rd | 20 tulpa-0.5.0/tulpa/man/gp_cov_type.Rd |only tulpa-0.5.0/tulpa/man/hyper_axis_spec.Rd | 56 tulpa-0.5.0/tulpa/man/imh_laplace.Rd | 5 tulpa-0.5.0/tulpa/man/is_auto_grid.Rd | 7 tulpa-0.5.0/tulpa/man/laplace_gp_at.Rd | 12 tulpa-0.5.0/tulpa/man/laplace_spde_at.Rd | 12 tulpa-0.5.0/tulpa/man/logLik.tulpa_fit.Rd | 64 tulpa-0.5.0/tulpa/man/mala.Rd | 5 tulpa-0.5.0/tulpa/man/n_divergent.Rd | 8 tulpa-0.5.0/tulpa/man/pathfinder.Rd | 5 tulpa-0.5.0/tulpa/man/posterior_predict.Rd | 44 tulpa-0.5.0/tulpa/man/predict.tulpa_fit.Rd | 23 tulpa-0.5.0/tulpa/man/re_cov_pc_lkj_prior.Rd | 28 tulpa-0.5.0/tulpa/man/residuals.tulpa_fit.Rd | 3 tulpa-0.5.0/tulpa/man/select_backend_for_mode.Rd | 4 tulpa-0.5.0/tulpa/man/select_inference_mode.Rd | 5 tulpa-0.5.0/tulpa/man/simulate.tulpa_fit.Rd | 8 tulpa-0.5.0/tulpa/man/spatial_rsr.Rd | 77 tulpa-0.5.0/tulpa/man/spatial_spde.Rd | 17 tulpa-0.5.0/tulpa/man/spatial_spde_custom.Rd | 15 tulpa-0.5.0/tulpa/man/spatiotemporal_effects.Rd | 5 tulpa-0.5.0/tulpa/man/spatiotemporal_gp.Rd | 7 tulpa-0.5.0/tulpa/man/summary.tulpa_fit.Rd | 8 tulpa-0.5.0/tulpa/man/temporal_ar2.Rd | 4 tulpa-0.5.0/tulpa/man/temporal_tvc.Rd | 44 tulpa-0.5.0/tulpa/man/tulpa-package.Rd | 2 tulpa-0.5.0/tulpa/man/tulpa.Rd | 96 tulpa-0.5.0/tulpa/man/tulpa_batched_pareto_k.Rd |only tulpa-0.5.0/tulpa/man/tulpa_eb.Rd | 25 tulpa-0.5.0/tulpa/man/tulpa_ep.Rd | 29 tulpa-0.5.0/tulpa/man/tulpa_gibbs.Rd | 36 tulpa-0.5.0/tulpa/man/tulpa_grid_axis.Rd |only tulpa-0.5.0/tulpa/man/tulpa_grid_log_quad.Rd |only tulpa-0.5.0/tulpa/man/tulpa_hyper_check_copy_slab.Rd |only tulpa-0.5.0/tulpa/man/tulpa_hyper_copy_slab_density.Rd |only tulpa-0.5.0/tulpa/man/tulpa_hyper_draws.Rd |only tulpa-0.5.0/tulpa/man/tulpa_hyper_grid.Rd | 28 tulpa-0.5.0/tulpa/man/tulpa_hyper_grid_supports.Rd |only tulpa-0.5.0/tulpa/man/tulpa_hyper_slice_home.Rd |only tulpa-0.5.0/tulpa/man/tulpa_iter_progress.Rd |only tulpa-0.5.0/tulpa/man/tulpa_joint_axis_specs_from_grid.Rd |only tulpa-0.5.0/tulpa/man/tulpa_joint_grid_batch.Rd |only tulpa-0.5.0/tulpa/man/tulpa_joint_inner_vcov_blocks.Rd |only tulpa-0.5.0/tulpa/man/tulpa_laplace.Rd | 15 tulpa-0.5.0/tulpa/man/tulpa_multinomial.Rd | 8 tulpa-0.5.0/tulpa/man/tulpa_nested_laplace.Rd | 126 tulpa-0.5.0/tulpa/man/tulpa_nested_laplace_joint.Rd | 404 + tulpa-0.5.0/tulpa/man/tulpa_normalise_weights_safe.Rd |only tulpa-0.5.0/tulpa/man/tulpa_nuts_beta.Rd | 4 tulpa-0.5.0/tulpa/man/tulpa_ordinal.Rd | 7 tulpa-0.5.0/tulpa/man/tulpa_pit.Rd | 32 tulpa-0.5.0/tulpa/man/tulpa_posterior_draws.Rd | 10 tulpa-0.5.0/tulpa/man/tulpa_posterior_draws.tulpa_nested_laplace_joint.Rd | 5 tulpa-0.5.0/tulpa/man/tulpa_powerscale_sensitivity.Rd | 8 tulpa-0.5.0/tulpa/man/tulpa_re_cov_nested.Rd | 56 tulpa-0.5.0/tulpa/man/tulpa_rpg.Rd |only tulpa-0.5.0/tulpa/man/tulpa_sample_glmm.Rd | 40 tulpa-0.5.0/tulpa/man/tulpa_spde_log_hyperprior.Rd |only tulpa-0.5.0/tulpa/man/tulpa_spde_precision_Q.Rd |only tulpa-0.5.0/tulpa/man/tulpa_theta_matrix.Rd |only tulpa-0.5.0/tulpa/man/validate_gp.Rd | 19 tulpa-0.5.0/tulpa/man/validate_temporal_multiscale.Rd | 19 tulpa-0.5.0/tulpa/man/vcov.tulpa_fit.Rd | 3 tulpa-0.5.0/tulpa/src/Makevars.win | 20 tulpa-0.5.0/tulpa/src/RcppExports.cpp | 617 + tulpa-0.5.0/tulpa/src/areal_input_check.h | 63 tulpa-0.5.0/tulpa/src/brasil.h |only tulpa-0.5.0/tulpa/src/brasil_export.cpp |only tulpa-0.5.0/tulpa/src/checkpoint_io.h | 2 tulpa-0.5.0/tulpa/src/cov_kernel_export.cpp |only tulpa-0.5.0/tulpa/src/family_terms_export.cpp | 28 tulpa-0.5.0/tulpa/src/glmm_family_elt.h |only tulpa-0.5.0/tulpa/src/glmm_oracle.h | 60 tulpa-0.5.0/tulpa/src/gpu_nngp_laplace.h | 9 tulpa-0.5.0/tulpa/src/hmc_chain_checkpoint.h | 4 tulpa-0.5.0/tulpa/src/hmc_chain_stack.h | 11 tulpa-0.5.0/tulpa/src/hmc_gp_gradients.h | 2 tulpa-0.5.0/tulpa/src/hmc_gp_nc.h | 2 tulpa-0.5.0/tulpa/src/hmc_gradient_fallback.cpp | 38 tulpa-0.5.0/tulpa/src/hmc_mass_lowrank.h | 5 tulpa-0.5.0/tulpa/src/hmc_mass_st_gmrf.cpp | 26 tulpa-0.5.0/tulpa/src/hmc_nuts_chain.cpp | 33 tulpa-0.5.0/tulpa/src/hmc_nuts_chain_iter_hmc.h | 1 tulpa-0.5.0/tulpa/src/hmc_nuts_chain_iter_nuts.h | 34 tulpa-0.5.0/tulpa/src/hmc_nuts_chain_iter_store.h | 11 tulpa-0.5.0/tulpa/src/hmc_nuts_chain_setup.h | 30 tulpa-0.5.0/tulpa/src/hmc_nuts_mass_init.cpp | 4 tulpa-0.5.0/tulpa/src/hmc_nuts_parallel.cpp | 113 tulpa-0.5.0/tulpa/src/hmc_param_layout.cpp | 111 tulpa-0.5.0/tulpa/src/hmc_sampler_chain_state.h | 12 tulpa-0.5.0/tulpa/src/hmc_sampler_decls.h | 50 tulpa-0.5.0/tulpa/src/hmc_svc.h | 81 tulpa-0.5.0/tulpa/src/hmc_svc_autodiff.h | 11 tulpa-0.5.0/tulpa/src/hmc_temporal.h | 33 tulpa-0.5.0/tulpa/src/hmc_tvc.h | 157 tulpa-0.5.0/tulpa/src/hyperprior_density_export.cpp |only tulpa-0.5.0/tulpa/src/inv_block_extract.h | 41 tulpa-0.5.0/tulpa/src/joint_inner_vcov.cpp | 54 tulpa-0.5.0/tulpa/src/joint_inner_vcov.h | 30 tulpa-0.5.0/tulpa/src/laplace_core.cpp | 76 tulpa-0.5.0/tulpa/src/laplace_core.h | 23 tulpa-0.5.0/tulpa/src/laplace_family_link.h | 22 tulpa-0.5.0/tulpa/src/laplace_family_zi_phi.h | 2 tulpa-0.5.0/tulpa/src/laplace_newton_joint.h | 329 tulpa-0.5.0/tulpa/src/laplace_newton_joint_sparse.h | 400 - tulpa-0.5.0/tulpa/src/laplace_newton_loop.h | 40 tulpa-0.5.0/tulpa/src/laplace_re_priors.h | 64 tulpa-0.5.0/tulpa/src/laplace_spec.cpp | 4 tulpa-0.5.0/tulpa/src/laplace_spec_fit.h | 2 tulpa-0.5.0/tulpa/src/laplace_spec_solve.h | 2 tulpa-0.5.0/tulpa/src/linalg_fast.h | 26 tulpa-0.5.0/tulpa/src/log_post_generic_impl.h | 18 tulpa-0.5.0/tulpa/src/nested_laplace.cpp | 130 tulpa-0.5.0/tulpa/src/nested_laplace_checkpoint.h | 2 tulpa-0.5.0/tulpa/src/nested_laplace_entries.h |only tulpa-0.5.0/tulpa/src/nested_laplace_grid.h | 733 +- tulpa-0.5.0/tulpa/src/nested_laplace_joint_batch.cpp | 600 - tulpa-0.5.0/tulpa/src/nested_laplace_joint_batch.h | 36 tulpa-0.5.0/tulpa/src/nested_laplace_joint_core.h | 123 tulpa-0.5.0/tulpa/src/nested_laplace_joint_multi.cpp | 264 tulpa-0.5.0/tulpa/src/nested_laplace_joint_multi.h | 276 tulpa-0.5.0/tulpa/src/nested_laplace_multi.cpp | 30 tulpa-0.5.0/tulpa/src/nested_laplace_multi.h | 177 tulpa-0.5.0/tulpa/src/nl_entry_inputs.h | 100 tulpa-0.5.0/tulpa/src/nngp_twin_export.cpp | 3 tulpa-0.5.0/tulpa/src/omp_threads.h | 14 tulpa-0.5.0/tulpa/src/pc_prior.h | 48 tulpa-0.5.0/tulpa/src/pg_binomial.cpp | 20 tulpa-0.5.0/tulpa/src/pg_binomial_bym2.cpp | 16 tulpa-0.5.0/tulpa/src/pg_binomial_gp.cpp | 25 tulpa-0.5.0/tulpa/src/pg_binomial_gp_rsr.cpp |only tulpa-0.5.0/tulpa/src/pg_binomial_multiscale_gp.cpp | 41 tulpa-0.5.0/tulpa/src/pg_binomial_rsr.cpp | 52 tulpa-0.5.0/tulpa/src/pg_binomial_temporal.cpp | 75 tulpa-0.5.0/tulpa/src/pg_negbin.cpp | 113 tulpa-0.5.0/tulpa/src/pg_shared.h | 395 + tulpa-0.5.0/tulpa/src/pg_spatial.cpp | 54 tulpa-0.5.0/tulpa/src/pg_spatial.h | 25 tulpa-0.5.0/tulpa/src/re_cov_gibbs.cpp | 23 tulpa-0.5.0/tulpa/src/re_cov_gibbs_sweep.h | 76 tulpa-0.5.0/tulpa/src/row_classes.h |only tulpa-0.5.0/tulpa/src/sampler_log_prob.h |only tulpa-0.5.0/tulpa/src/sampler_model_data.h | 310 tulpa-0.5.0/tulpa/src/sparse_cholesky.cpp | 59 tulpa-0.5.0/tulpa/src/sparse_cholesky.h | 43 tulpa-0.5.0/tulpa/src/spde_laplace.cpp | 61 tulpa-0.5.0/tulpa/src/spde_qbuilder.h | 24 tulpa-0.5.0/tulpa/src/st_null_space.h | 44 tulpa-0.5.0/tulpa/src/st_type_iv_precision.h | 40 tulpa-0.5.0/tulpa/src/temporal_gp_kernel.h | 69 tulpa-0.5.0/tulpa/src/test_ccallable_registry.cpp |only tulpa-0.5.0/tulpa/src/test_helpers.cpp | 118 tulpa-0.5.0/tulpa/src/test_laplace_sample_fixture.cpp |only tulpa-0.5.0/tulpa/src/test_nan_gradient_nuts.cpp | 76 tulpa-0.5.0/tulpa/src/test_pg_nngp_conditional.cpp | 16 tulpa-0.5.0/tulpa/src/test_st_fixture_parse.h |only tulpa-0.5.0/tulpa/src/test_st_hsgp_prior.cpp |only tulpa-0.5.0/tulpa/src/test_st_iv_fixture.cpp | 72 tulpa-0.5.0/tulpa/src/tgmrf_nuts.cpp | 3 tulpa-0.5.0/tulpa/src/tulpa_beta_sampler.cpp | 1 tulpa-0.5.0/tulpa/src/tulpa_generic_sampler.cpp | 6 tulpa-0.5.0/tulpa/src/tulpa_glmm_eta_draws.cpp |only tulpa-0.5.0/tulpa/src/tulpa_glmm_layout_probe.cpp | 4 tulpa-0.5.0/tulpa/src/tulpa_priors_st.h | 227 tulpa-0.5.0/tulpa/src/tulpa_priors_temporal.h | 65 tulpa-0.5.0/tulpa/src/tulpa_priors_tvc.h | 105 tulpa-0.5.0/tulpa/src/tulpa_sample_glmm.cpp | 64 tulpa-0.5.0/tulpa/src/tulpa_shims.cpp | 276 tulpa-0.5.0/tulpa/src/tulpa_shims_nested_laplace.h | 147 tulpa-0.5.0/tulpa/src/tulpa_spde_sampler.cpp | 1 tulpa-0.5.0/tulpa/src/vi_convergence_probe.cpp |only tulpa-0.5.0/tulpa/src/vi_optimizer.h | 79 tulpa-0.5.0/tulpa/src/vi_types.h | 5 tulpa-0.5.0/tulpa/tests/testthat/helper-count-support.R |only tulpa-0.5.0/tulpa/tests/testthat/helper-draws-block.R |only tulpa-0.5.0/tulpa/tests/testthat/helper-joint-icar-fixture.R |only tulpa-0.5.0/tulpa/tests/testthat/helper-laplace-fit-single.R |only tulpa-0.5.0/tulpa/tests/testthat/helper-outer-grid-dump.R | 102 tulpa-0.5.0/tulpa/tests/testthat/helper-phi-placement.R |only tulpa-0.5.0/tulpa/tests/testthat/helper-sbc.R | 81 tulpa-0.5.0/tulpa/tests/testthat/helper-spatial-grid.R |only tulpa-0.5.0/tulpa/tests/testthat/helper-tiers.R | 25 tulpa-0.5.0/tulpa/tests/testthat/test-adjacency.R | 3 tulpa-0.5.0/tulpa/tests/testthat/test-areal-input-check.R | 53 tulpa-0.5.0/tulpa/tests/testthat/test-auto-grid-provenance.R | 100 tulpa-0.5.0/tulpa/tests/testthat/test-auto-picks-a-backend-that-fits.R |only tulpa-0.5.0/tulpa/tests/testthat/test-axis-sd-estimator.R |only tulpa-0.5.0/tulpa/tests/testthat/test-beta-nuts.R | 6 tulpa-0.5.0/tulpa/tests/testthat/test-bound-family-joint-arm.R | 3 tulpa-0.5.0/tulpa/tests/testthat/test-brasil-cpp-oracle.R |only tulpa-0.5.0/tulpa/tests/testthat/test-car-icar-gibbs-alias.R |only tulpa-0.5.0/tulpa/tests/testthat/test-categorical-accessors.R |only tulpa-0.5.0/tulpa/tests/testthat/test-ccallable-registry.R |only tulpa-0.5.0/tulpa/tests/testthat/test-ccd-modefind-budget.R |only tulpa-0.5.0/tulpa/tests/testthat/test-checkpoint-universal.R | 156 tulpa-0.5.0/tulpa/tests/testthat/test-cila.R | 17 tulpa-0.5.0/tulpa/tests/testthat/test-control-check.R | 1 tulpa-0.5.0/tulpa/tests/testthat/test-control-surface-contracts.R |only tulpa-0.5.0/tulpa/tests/testthat/test-convergence.R | 17 tulpa-0.5.0/tulpa/tests/testthat/test-copy-alpha-resolution.R |only tulpa-0.5.0/tulpa/tests/testthat/test-cov-kernel.R | 20 tulpa-0.5.0/tulpa/tests/testthat/test-cpp-kernels.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-criteria-tulpa-fit.R |only tulpa-0.5.0/tulpa/tests/testthat/test-criteria.R | 28 tulpa-0.5.0/tulpa/tests/testthat/test-declared-surface-refusals.R |only tulpa-0.5.0/tulpa/tests/testthat/test-diagnostics-cross-tier.R | 64 tulpa-0.5.0/tulpa/tests/testthat/test-diagnostics-known-answer.R | 1 tulpa-0.5.0/tulpa/tests/testthat/test-diagnostics-report-honesty.R |only tulpa-0.5.0/tulpa/tests/testthat/test-diagnostics-sim.R | 20 tulpa-0.5.0/tulpa/tests/testthat/test-diagnostics.R | 95 tulpa-0.5.0/tulpa/tests/testthat/test-eb-dispersion.R | 1 tulpa-0.5.0/tulpa/tests/testthat/test-eb-marginal.R | 25 tulpa-0.5.0/tulpa/tests/testthat/test-eb.R | 28 tulpa-0.5.0/tulpa/tests/testthat/test-em-laplace-mstep-extra.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-entry-conventions.R |only tulpa-0.5.0/tulpa/tests/testthat/test-ep.R | 21 tulpa-0.5.0/tulpa/tests/testthat/test-export-doors-tulpaobs.R |only tulpa-0.5.0/tulpa/tests/testthat/test-family-count-compiled.R | 3 tulpa-0.5.0/tulpa/tests/testthat/test-family-count-extensions.R | 6 tulpa-0.5.0/tulpa/tests/testthat/test-family-cross-path.R | 10 tulpa-0.5.0/tulpa/tests/testthat/test-family-gate-nan.R | 4 tulpa-0.5.0/tulpa/tests/testthat/test-family-loglik.R | 10 tulpa-0.5.0/tulpa/tests/testthat/test-family-registry-compiled.R |only tulpa-0.5.0/tulpa/tests/testthat/test-family-validation.R | 41 tulpa-0.5.0/tulpa/tests/testthat/test-family-zi.R | 18 tulpa-0.5.0/tulpa/tests/testthat/test-finalize-fit.R | 6 tulpa-0.5.0/tulpa/tests/testthat/test-finite-input-guard-arms.R |only tulpa-0.5.0/tulpa/tests/testthat/test-fit-methods.R | 27 tulpa-0.5.0/tulpa/tests/testthat/test-fit-reads-contract.R |only tulpa-0.5.0/tulpa/tests/testthat/test-fit-st-nested-auto-grid.R | 75 tulpa-0.5.0/tulpa/tests/testthat/test-formula.R | 63 tulpa-0.5.0/tulpa/tests/testthat/test-front-door-argument-contracts.R |only tulpa-0.5.0/tulpa/tests/testthat/test-frontdoor-validation.R | 123 tulpa-0.5.0/tulpa/tests/testthat/test-generic-sampler.R | 10 tulpa-0.5.0/tulpa/tests/testthat/test-gibbs-chain.R |only tulpa-0.5.0/tulpa/tests/testthat/test-gibbs-spatial.R | 66 tulpa-0.5.0/tulpa/tests/testthat/test-gibbs-temporal.R | 14 tulpa-0.5.0/tulpa/tests/testthat/test-gpu-nngp.R | 1 tulpa-0.5.0/tulpa/tests/testthat/test-hyper-axis-domain.R |only tulpa-0.5.0/tulpa/tests/testthat/test-hyper-copy-slab.R |only tulpa-0.5.0/tulpa/tests/testthat/test-hyper-draws.R |only tulpa-0.5.0/tulpa/tests/testthat/test-hyper-prior-coordinate.R |only tulpa-0.5.0/tulpa/tests/testthat/test-hyper-quadrature-refinement.R |only tulpa-0.5.0/tulpa/tests/testthat/test-hyperparameter-coverage.R | 8 tulpa-0.5.0/tulpa/tests/testthat/test-hyperprior-default.R |only tulpa-0.5.0/tulpa/tests/testthat/test-hyperprior-frontdoor.R |only tulpa-0.5.0/tulpa/tests/testthat/test-implicit-diff.R | 1 tulpa-0.5.0/tulpa/tests/testthat/test-inference-dispatch.R | 29 tulpa-0.5.0/tulpa/tests/testthat/test-inference-modes.R | 49 tulpa-0.5.0/tulpa/tests/testthat/test-inner-pareto-k.R | 4 tulpa-0.5.0/tulpa/tests/testthat/test-inner-skew-correction.R | 4 tulpa-0.5.0/tulpa/tests/testthat/test-inner-skew.R | 14 tulpa-0.5.0/tulpa/tests/testthat/test-interval-gaussian.R | 11 tulpa-0.5.0/tulpa/tests/testthat/test-joint-axis-refinable.R |only tulpa-0.5.0/tulpa/tests/testthat/test-joint-fitted-eta-var.R |only tulpa-0.5.0/tulpa/tests/testthat/test-joint-logpost-grad-kinds.R | 18 tulpa-0.5.0/tulpa/tests/testthat/test-joint-multi-hyperprior-blocks.R |only tulpa-0.5.0/tulpa/tests/testthat/test-joint-pareto-k-proposal.R | 18 tulpa-0.5.0/tulpa/tests/testthat/test-kdiag-capture.R | 65 tulpa-0.5.0/tulpa/tests/testthat/test-kfold.R | 31 tulpa-0.5.0/tulpa/tests/testthat/test-laplace-arg-lengths.R | 37 tulpa-0.5.0/tulpa/tests/testthat/test-laplace-exact-gradient.R | 5 tulpa-0.5.0/tulpa/tests/testthat/test-laplace-gp-dispatch.R | 22 tulpa-0.5.0/tulpa/tests/testthat/test-laplace-link-domain.R | 1 tulpa-0.5.0/tulpa/tests/testthat/test-laplace-mode-stationarity.R | 1 tulpa-0.5.0/tulpa/tests/testthat/test-laplace-sample-clone.R | 8 tulpa-0.5.0/tulpa/tests/testthat/test-laplace-spatial-gp-spde-equiv.R | 18 tulpa-0.5.0/tulpa/tests/testthat/test-laplace-spec-builtin-family.R | 45 tulpa-0.5.0/tulpa/tests/testthat/test-laplace-spec.R | 8 tulpa-0.5.0/tulpa/tests/testthat/test-laplace_diagnostics.R | 20 tulpa-0.5.0/tulpa/tests/testthat/test-linpred-evidence.R |only tulpa-0.5.0/tulpa/tests/testthat/test-loglik-quantity-offset.R |only tulpa-0.5.0/tulpa/tests/testthat/test-loglik-sampler-logprob.R |only tulpa-0.5.0/tulpa/tests/testthat/test-marginal-se-gp.R | 29 tulpa-0.5.0/tulpa/tests/testthat/test-methods-interop.R | 43 tulpa-0.5.0/tulpa/tests/testthat/test-miid-recovery.R | 11 tulpa-0.5.0/tulpa/tests/testthat/test-mode-override.R | 9 tulpa-0.5.0/tulpa/tests/testthat/test-nc-field-eta-draws.R |only tulpa-0.5.0/tulpa/tests/testthat/test-nested-fixed-mixture-interval.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-nested-grid-pareto-k-jacobian.R | 10 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-axis-rail.R | 16 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-bym2.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-car-proper.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-cpp.R | 3 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-grid-hessians.R | 29 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-adaptive-grid.R | 11 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-barycentre.R | 173 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-batch-equivalence.R | 341 - tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-batch-response.R | 28 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-box-mass.R | 60 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-bym2.R | 4 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-car-proper.R | 31 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-ccd-local.R | 74 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-ccd.R | 141 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-checkpoint.R | 43 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-descriptor-plane.R | 312 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-fixed-moments.R | 17 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-grid-adaptive.R | 5 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-grid-fixed-parallel.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-hsgp-mo.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-hsgp-svc.R | 9 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-icar.R | 4 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-inner-refresh.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-multi-copy.R | 9 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-multi.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-parallel.R | 6 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-pareto-k.R | 113 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-phi-grid.R | 69 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-phi-prior.R | 42 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-prune-misrank.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-prune.R | 42 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-sigma-pos-prior.R | 85 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-sparse-equivalence.R | 4 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-joint-sparse-parallel.R | 7 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-multi-block.R | 3 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-recovery.R | 125 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace-spatial-recovery.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-nested-laplace.R | 3 tulpa-0.5.0/tulpa/tests/testthat/test-nested-posterior-draws.R | 7 tulpa-0.5.0/tulpa/tests/testthat/test-nl-axis-consumption.R | 84 tulpa-0.5.0/tulpa/tests/testthat/test-nl-entry-forwarding.R | 77 tulpa-0.5.0/tulpa/tests/testthat/test-nl-fitted-var-dedup.R |only tulpa-0.5.0/tulpa/tests/testthat/test-nl-grid-axis-contract.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-nl-grid-cap.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-nl-internal-batch-warning.R |only tulpa-0.5.0/tulpa/tests/testthat/test-nl-interval-support.R | 4 tulpa-0.5.0/tulpa/tests/testthat/test-nl-registry-axis-scope.R | 6 tulpa-0.5.0/tulpa/tests/testthat/test-nl-required-fields.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-nl-single-block-prune.R |only tulpa-0.5.0/tulpa/tests/testthat/test-nl-weight-guard.R | 17 tulpa-0.5.0/tulpa/tests/testthat/test-nngp-coords-arity.R | 4 tulpa-0.5.0/tulpa/tests/testthat/test-nuts-nan-gradient.R | 30 tulpa-0.5.0/tulpa/tests/testthat/test-nuts-progress-scope.R |only tulpa-0.5.0/tulpa/tests/testthat/test-ordinal-fit.R | 4 tulpa-0.5.0/tulpa/tests/testthat/test-outer-grid-dump.R | 70 tulpa-0.5.0/tulpa/tests/testthat/test-outer-grid-edge-mass.R |only tulpa-0.5.0/tulpa/tests/testthat/test-outer-k-budget.R |only tulpa-0.5.0/tulpa/tests/testthat/test-outer-k-tail-one-resolution.R |only tulpa-0.5.0/tulpa/tests/testthat/test-outer-proposal-lever.R |only tulpa-0.5.0/tulpa/tests/testthat/test-outer-skew-rescue.R | 53 tulpa-0.5.0/tulpa/tests/testthat/test-outer-thread-clamp-report.R |only tulpa-0.5.0/tulpa/tests/testthat/test-parallel-equivalence.R | 119 tulpa-0.5.0/tulpa/tests/testthat/test-pc-prior.R | 24 tulpa-0.5.0/tulpa/tests/testthat/test-pg-beta-draw-cov.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-pg-gibbs-thin.R | 15 tulpa-0.5.0/tulpa/tests/testthat/test-pg-icar-conditional.R | 25 tulpa-0.5.0/tulpa/tests/testthat/test-pg-nngp-conditional.R | 24 tulpa-0.5.0/tulpa/tests/testthat/test-pg-spatial-recovery.R | 6 tulpa-0.5.0/tulpa/tests/testthat/test-phi-conditioned-announced.R |only tulpa-0.5.0/tulpa/tests/testthat/test-phi-grid-placement.R |only tulpa-0.5.0/tulpa/tests/testthat/test-phi2-dispersion.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-plot-diagnostics.R |only tulpa-0.5.0/tulpa/tests/testthat/test-plot-map.R | 1 tulpa-0.5.0/tulpa/tests/testthat/test-posterior-draws-joint.R | 67 tulpa-0.5.0/tulpa/tests/testthat/test-posterior-predict-phi-axis.R |only tulpa-0.5.0/tulpa/tests/testthat/test-posterior-predict.R | 39 tulpa-0.5.0/tulpa/tests/testthat/test-predict-zi.R |only tulpa-0.5.0/tulpa/tests/testthat/test-priorsense.R | 85 tulpa-0.5.0/tulpa/tests/testthat/test-progress-control-keys.R |only tulpa-0.5.0/tulpa/tests/testthat/test-progress-eta.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-progress-threads.R | 55 tulpa-0.5.0/tulpa/tests/testthat/test-prune-steep-grid.R |only tulpa-0.5.0/tulpa/tests/testthat/test-psis-cpp.R | 1 tulpa-0.5.0/tulpa/tests/testthat/test-psis.R | 74 tulpa-0.5.0/tulpa/tests/testthat/test-ranef-subspace-debias.R | 63 tulpa-0.5.0/tulpa/tests/testthat/test-rational-spde.R | 6 tulpa-0.5.0/tulpa/tests/testthat/test-re-aghq-multiarm.R | 1 tulpa-0.5.0/tulpa/tests/testthat/test-re-cov-gibbs.R | 17 tulpa-0.5.0/tulpa/tests/testthat/test-re-cov-nested.R | 17 tulpa-0.5.0/tulpa/tests/testthat/test-re-cov-prior.R | 34 tulpa-0.5.0/tulpa/tests/testthat/test-recenter-pilot.R |only tulpa-0.5.0/tulpa/tests/testthat/test-recenter-sd-clamp.R | 4 tulpa-0.5.0/tulpa/tests/testthat/test-rsr-continuous.R |only tulpa-0.5.0/tulpa/tests/testthat/test-sample-glmm-structure.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-sample-glmm.R | 8 tulpa-0.5.0/tulpa/tests/testthat/test-sampler-mass-matrix.R | 3 tulpa-0.5.0/tulpa/tests/testthat/test-sbc-crps.R | 7 tulpa-0.5.0/tulpa/tests/testthat/test-sbc-frontdoor.R | 30 tulpa-0.5.0/tulpa/tests/testthat/test-screen-depth.R |only tulpa-0.5.0/tulpa/tests/testthat/test-selected-inversion.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-settings.R | 161 tulpa-0.5.0/tulpa/tests/testthat/test-sobol.R | 9 tulpa-0.5.0/tulpa/tests/testthat/test-sparse-cholesky.R | 78 tulpa-0.5.0/tulpa/tests/testthat/test-spatial-field.R | 24 tulpa-0.5.0/tulpa/tests/testthat/test-spatial-mcar.R | 22 tulpa-0.5.0/tulpa/tests/testthat/test-spatial-spde-api.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-spde-ccd.R | 64 tulpa-0.5.0/tulpa/tests/testthat/test-spde-fractional-var-norm.R |only tulpa-0.5.0/tulpa/tests/testthat/test-spde-kriging.R | 6 tulpa-0.5.0/tulpa/tests/testthat/test-spde-nu-general.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-spde-re-integrated.R |only tulpa-0.5.0/tulpa/tests/testthat/test-spde-re.R | 22 tulpa-0.5.0/tulpa/tests/testthat/test-st-ar1-gp-density.R |only tulpa-0.5.0/tulpa/tests/testthat/test-st-hsgp-prior.R |only tulpa-0.5.0/tulpa/tests/testthat/test-st-nested.R | 72 tulpa-0.5.0/tulpa/tests/testthat/test-subspace-debias.R | 3 tulpa-0.5.0/tulpa/tests/testthat/test-svc-noncentered-amplitude.R | 124 tulpa-0.5.0/tulpa/tests/testthat/test-svc-nuts-frontdoor.R | 72 tulpa-0.5.0/tulpa/tests/testthat/test-svc-parameterization-equivalence.R |only tulpa-0.5.0/tulpa/tests/testthat/test-temporal-ar1-rho-prior.R | 52 tulpa-0.5.0/tulpa/tests/testthat/test-temporal-ar2.R | 28 tulpa-0.5.0/tulpa/tests/testthat/test-temporal-field.R | 18 tulpa-0.5.0/tulpa/tests/testthat/test-temporal-frontdoor.R | 6 tulpa-0.5.0/tulpa/tests/testthat/test-temporal-gp-parameterization.R | 43 tulpa-0.5.0/tulpa/tests/testthat/test-temporal-gp-period-units.R |only tulpa-0.5.0/tulpa/tests/testthat/test-temporal-grad-equiv.R | 1 tulpa-0.5.0/tulpa/tests/testthat/test-truncated-gaussian.R | 5 tulpa-0.5.0/tulpa/tests/testthat/test-tulpa-entry-nested.R | 15 tulpa-0.5.0/tulpa/tests/testthat/test-tulpa-entry.R | 12 tulpa-0.5.0/tulpa/tests/testthat/test-tulpa-re-cov-frontdoor.R | 2 tulpa-0.5.0/tulpa/tests/testthat/test-tulpa-rpg.R |only tulpa-0.5.0/tulpa/tests/testthat/test-tulpa-spatial-frontdoor.R | 22 tulpa-0.5.0/tulpa/tests/testthat/test-tulpa-spatial-gp-frontdoor.R | 3 tulpa-0.5.0/tulpa/tests/testthat/test-tvc-gp.R |only tulpa-0.5.0/tulpa/tests/testthat/test-tvc-level-identification.R |only tulpa-0.5.0/tulpa/tests/testthat/test-tweedie.R | 53 tulpa-0.5.0/tulpa/tests/testthat/test-varying-coef-accessors.R | 65 tulpa-0.5.0/tulpa/tests/testthat/test-vi-stopping-rule.R |only tulpa-0.5.0/tulpa/tests/testthat/test-warm-start.R | 4 tulpa-0.5.0/tulpa/tests/testthat/test-within-cell-box-uniform.R | 3 tulpa-0.5.0/tulpa/tests/testthat/test-zi-fit.R | 3 tulpa-0.5.0/tulpa/tests/testthat/test-zi-random-effects.R | 5 tulpa-0.5.0/tulpa/vignettes/inference-modes.Rmd | 1115 +-- tulpa-0.5.0/tulpa/vignettes/model-comparison.Rmd | 18 tulpa-0.5.0/tulpa/vignettes/priors.Rmd | 1318 +-- tulpa-0.5.0/tulpa/vignettes/quickstart.Rmd | 1607 ++-- tulpa-0.5.0/tulpa/vignettes/reliability-pareto-k.Rmd | 17 tulpa-0.5.0/tulpa/vignettes/sbc.Rmd | 11 tulpa-0.5.0/tulpa/vignettes/spatial-models.Rmd | 32 tulpa-0.5.0/tulpa/vignettes/temporal-models.Rmd | 43 tulpa-0.5.0/tulpa/vignettes/tgmrf.Rmd | 15 598 files changed, 32227 insertions(+), 12490 deletions(-)
Title: Develop Clinical Prediction Models Using the Common Data Model
Description: A user friendly way to create patient level prediction models using
the Observational Medical Outcomes Partnership Common Data Model. Given a cohort
of interest and an outcome of interest, the package can use data in the Common
Data Model to build a large set of features. These features can then be used to
fit a predictive model with a number of machine learning algorithms. This is
further described in Reps (2017) <doi:10.1093/jamia/ocy032>.
Author: Egill Fridgeirsson [aut, cre],
Jenna Reps [aut],
Martijn Schuemie [aut],
Marc Suchard [aut],
Patrick Ryan [aut],
Peter Rijnbeek [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Egill Fridgeirsson <e.fridgeirsson@erasmusmc.nl>
Diff between PatientLevelPrediction versions 6.6.0 dated 2026-03-09 and 6.7.0 dated 2026-09-21
PatientLevelPrediction-6.6.0/PatientLevelPrediction/vignettes/maintainers |only PatientLevelPrediction-6.7.0/PatientLevelPrediction/DESCRIPTION | 31 PatientLevelPrediction-6.7.0/PatientLevelPrediction/MD5 | 170 + PatientLevelPrediction-6.7.0/PatientLevelPrediction/NAMESPACE | 3 PatientLevelPrediction-6.7.0/PatientLevelPrediction/NEWS.md | 34 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/AndromedaHelperFunctions.R | 72 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/CovariateSummary.R | 19 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/CyclopsModels.R | 390 ++++ PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/CyclopsSettings.R | 178 +- PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/DataSplitting.R | 332 +++ PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/DiagnosePlp.R | 6 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/EvaluatePlp.R | 3 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/ExtractData.R | 13 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/FeatureEngineering.R | 54 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/HelperFunctions.R | 43 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/HyperparameterSettings.R | 33 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/Imputation.R | 35 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/LearningCurve.R | 7 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/ParamChecks.R | 21 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/Predict.R | 21 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/RunPlp.R | 7 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/SaveLoadPlp.R | 15 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/Simulation.R | 839 +++++++++ PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/SklearnToJson.R | 56 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/uploadToDatabase.R | 65 PatientLevelPrediction-6.7.0/PatientLevelPrediction/R/uploadToDatabaseModelDesign.R | 86 PatientLevelPrediction-6.7.0/PatientLevelPrediction/README.md | 11 PatientLevelPrediction-6.7.0/PatientLevelPrediction/build/partial.rdb |only PatientLevelPrediction-6.7.0/PatientLevelPrediction/build/vignette.rds |binary PatientLevelPrediction-6.7.0/PatientLevelPrediction/data/simulationProfile.rda |binary PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/AddingCustomFeatureEngineering.html | 7 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/AddingCustomModels.Rmd | 4 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/AddingCustomModels.html | 13 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/AddingCustomSamples.Rmd | 2 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/AddingCustomSamples.html | 9 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/AddingCustomSplitting.Rmd | 6 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/AddingCustomSplitting.html | 20 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/BenchmarkTasks.html | 4 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/BestPractices.html | 4 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/BuildingMultiplePredictiveModels.Rmd | 2 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/BuildingMultiplePredictiveModels.html | 22 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/BuildingPredictiveModels.R | 10 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/BuildingPredictiveModels.Rmd | 22 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/BuildingPredictiveModels.html | 123 - PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/ClinicalModels.html | 4 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/ConstrainedPredictors.html | 7 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/CreatingLearningCurves.html | 15 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/CreatingNetworkStudies.Rmd | 2 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/CreatingNetworkStudies.html | 6 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/GISExample.html | 11 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/InstallationGuide.R | 12 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/InstallationGuide.Rmd | 40 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/doc/InstallationGuide.html | 55 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/settings/resultsDataModelSpecification.csv | 1 PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/sql/postgresql/migrations/Migration_3-add_model_name.sql |only PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/sql/sql_server/migrations/Migration_3-add_model_name.sql |only PatientLevelPrediction-6.7.0/PatientLevelPrediction/inst/sql/sqlite/migrations/Migration_3-add_model_name.sql |only PatientLevelPrediction-6.7.0/PatientLevelPrediction/man/configurePython.Rd | 14 PatientLevelPrediction-6.7.0/PatientLevelPrediction/man/createHyperparameterSettings.Rd | 8 PatientLevelPrediction-6.7.0/PatientLevelPrediction/man/createLearningCurve.Rd | 7 PatientLevelPrediction-6.7.0/PatientLevelPrediction/man/createNormalizer.Rd | 6 PatientLevelPrediction-6.7.0/PatientLevelPrediction/man/createOutcomeLimitedSplitSettings.Rd |only PatientLevelPrediction-6.7.0/PatientLevelPrediction/man/diagnosePlp.Rd | 6 PatientLevelPrediction-6.7.0/PatientLevelPrediction/man/iterativeImpute.Rd | 2 PatientLevelPrediction-6.7.0/PatientLevelPrediction/man/runPlp.Rd | 7 PatientLevelPrediction-6.7.0/PatientLevelPrediction/man/setBrokenAdaptiveRidge.Rd |only PatientLevelPrediction-6.7.0/PatientLevelPrediction/man/setPythonEnvironment.Rd | 14 PatientLevelPrediction-6.7.0/PatientLevelPrediction/man/simulatePlpBenchmarkData.Rd |only PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/setup.R | 4 PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-LightGBM.R | 4 PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-UploadToDatabase.R | 170 + PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-UploadToDatabaseModelDesign.R | 125 + PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-andromedahelperfunctions.R | 7 PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-barFitState.R |only PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-cyclopsModels.R | 437 ++++ PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-dataSplitting.R | 169 + PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-evaluation.R | 19 PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-helperfunctions.R | 6 PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-hyperparameterSettings.R | 47 PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-normalizers.R | 13 PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-paramchecks.R | 23 PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-resultsDataModelSpecification.R |only PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-simulation.R | 888 +++++++++- PatientLevelPrediction-6.7.0/PatientLevelPrediction/tests/testthat/test-sklearnJson.R | 87 PatientLevelPrediction-6.7.0/PatientLevelPrediction/vignettes/AddingCustomModels.Rmd | 4 PatientLevelPrediction-6.7.0/PatientLevelPrediction/vignettes/AddingCustomSamples.Rmd | 2 PatientLevelPrediction-6.7.0/PatientLevelPrediction/vignettes/AddingCustomSplitting.Rmd | 6 PatientLevelPrediction-6.7.0/PatientLevelPrediction/vignettes/BuildingMultiplePredictiveModels.Rmd | 2 PatientLevelPrediction-6.7.0/PatientLevelPrediction/vignettes/BuildingPredictiveModels.Rmd | 22 PatientLevelPrediction-6.7.0/PatientLevelPrediction/vignettes/CreatingNetworkStudies.Rmd | 2 PatientLevelPrediction-6.7.0/PatientLevelPrediction/vignettes/InstallationGuide.Rmd | 40 91 files changed, 4291 insertions(+), 795 deletions(-)
More information about PatientLevelPrediction at CRAN
Permanent link
Title: Multilevel Descriptive Statistics and Data Preparation
Description: Provides tools for multilevel descriptive statistics and data preparation.
Computes within-group and between-group correlations (via variance decomposition or
two-level structural equation modeling), intraclass correlation coefficients (ICCs),
and descriptive statistics for nested data (e.g., repeated measurements per person),
supporting both frequentist (via 'lme4' or 'lavaan') and Bayesian (via 'brms')
estimation. Results are formatted according to APA standards and can be exported as
tables using 'gt' or 'tinytable'. Also includes functions for decomposing variables
into within-group and between-group components for use in Random Effects
Within-Between (REWB) models.
Author: Felix Dietrich [aut, cre, cph]
Maintainer: Felix Dietrich <mail@felix-dietrich.de>
Diff between mlstats versions 0.1.1 dated 2026-07-15 and 0.1.2 dated 2026-09-21
DESCRIPTION | 6 MD5 | 59 - NEWS.md | 13 R/media_diary.R | 19 R/mldesc.R | 3 R/mlstats_desc_tibble.R | 13 R/mlstats_wb_tibble.R | 9 R/utils.R | 44 R/within_between_correlations.R | 1 README.md | 16 data/media_diary.rda |binary inst/doc/correlation-methods.Rmd | 9 inst/doc/correlation-methods.html | 20 inst/doc/mlstats.Rmd | 9 inst/doc/mlstats.html | 329 +++--- inst/doc/multilevel-descriptives.Rmd | 5 inst/doc/multilevel-descriptives.html | 60 - inst/doc/rewb-models.Rmd | 24 inst/doc/rewb-models.html | 164 +-- inst/doc/tables.R | 7 inst/doc/tables.Rmd | 14 inst/doc/tables.html | 1079 +++++++++++----------- man/media_diary.Rd | 19 tests/testthat/test-media_diary.R |only tests/testthat/test-mldesc.R | 67 + tests/testthat/test-within_between_correlations.R | 61 + vignettes/correlation-methods.Rmd | 9 vignettes/mlstats.Rmd | 9 vignettes/multilevel-descriptives.Rmd | 5 vignettes/rewb-models.Rmd | 24 vignettes/tables.Rmd | 14 31 files changed, 1216 insertions(+), 895 deletions(-)
Title: Tidy Pipelines for the 'Sensor Tower' API
Description: Retrieves mobile app intelligence from the 'Sensor Tower' API
<https://app.sensortower.com/api/docs/app_analysis>. Composes discovery,
metadata, rankings, sales, audience and specialist estimates through
ordinary data frames with explicit identifiers, units and error handling.
Author: Phillip Black [aut, cre]
Maintainer: Phillip Black <pblack@gameeconomistconsulting.com>
Diff between sensortowerR versions 1.0.1 dated 2026-05-14 and 2.0.0 dated 2026-09-21
sensortowerR-1.0.1/sensortowerR/R/app_id_validation.R |only sensortowerR-1.0.1/sensortowerR/R/column_helpers.R |only sensortowerR-1.0.1/sensortowerR/R/constants.R |only sensortowerR-1.0.1/sensortowerR/R/custom_filter_utils.R |only sensortowerR-1.0.1/sensortowerR/R/data_validation.R |only sensortowerR-1.0.1/sensortowerR/R/defunct.R |only sensortowerR-1.0.1/sensortowerR/R/example_data.R |only sensortowerR-1.0.1/sensortowerR/R/formatting_helpers.R |only sensortowerR-1.0.1/sensortowerR/R/globals.R |only sensortowerR-1.0.1/sensortowerR/R/revenue_standardization.R |only sensortowerR-1.0.1/sensortowerR/R/st_active_users.R |only sensortowerR-1.0.1/sensortowerR/R/st_api_diagnostics.R |only sensortowerR-1.0.1/sensortowerR/R/st_app.R |only sensortowerR-1.0.1/sensortowerR/R/st_app_details.R |only sensortowerR-1.0.1/sensortowerR/R/st_app_enriched.R |only sensortowerR-1.0.1/sensortowerR/R/st_app_info.R |only sensortowerR-1.0.1/sensortowerR/R/st_app_lookup.R |only sensortowerR-1.0.1/sensortowerR/R/st_app_tag.R |only sensortowerR-1.0.1/sensortowerR/R/st_batch_app_lookup.R |only sensortowerR-1.0.1/sensortowerR/R/st_batch_metrics.R |only sensortowerR-1.0.1/sensortowerR/R/st_categories.R |only sensortowerR-1.0.1/sensortowerR/R/st_category_rankings.R |only sensortowerR-1.0.1/sensortowerR/R/st_custom_fields.R |only sensortowerR-1.0.1/sensortowerR/R/st_custom_fields_utils.R |only sensortowerR-1.0.1/sensortowerR/R/st_custom_fields_workflow.R |only sensortowerR-1.0.1/sensortowerR/R/st_demographics.R |only sensortowerR-1.0.1/sensortowerR/R/st_facets_metrics.R |only sensortowerR-1.0.1/sensortowerR/R/st_filter.R |only sensortowerR-1.0.1/sensortowerR/R/st_filter_helpers.R |only sensortowerR-1.0.1/sensortowerR/R/st_game_summary.R |only sensortowerR-1.0.1/sensortowerR/R/st_get_unified_mapping.R |only sensortowerR-1.0.1/sensortowerR/R/st_gt_dashboard.R |only sensortowerR-1.0.1/sensortowerR/R/st_id_cache.R |only sensortowerR-1.0.1/sensortowerR/R/st_market_metrics.R |only sensortowerR-1.0.1/sensortowerR/R/st_metrics.R |only sensortowerR-1.0.1/sensortowerR/R/st_publisher_apps.R |only sensortowerR-1.0.1/sensortowerR/R/st_publisher_portfolio.R |only sensortowerR-1.0.1/sensortowerR/R/st_rankings.R |only sensortowerR-1.0.1/sensortowerR/R/st_ratings_review_facets.R |only sensortowerR-1.0.1/sensortowerR/R/st_resolve_ids.R |only sensortowerR-1.0.1/sensortowerR/R/st_retention.R |only sensortowerR-1.0.1/sensortowerR/R/st_retention_facets.R |only sensortowerR-1.0.1/sensortowerR/R/st_sales_report.R |only sensortowerR-1.0.1/sensortowerR/R/st_session_metrics.R |only sensortowerR-1.0.1/sensortowerR/R/st_smart_metrics.R |only sensortowerR-1.0.1/sensortowerR/R/st_top_charts.R |only sensortowerR-1.0.1/sensortowerR/R/st_top_publishers.R |only sensortowerR-1.0.1/sensortowerR/R/st_unified_sales_report.R |only sensortowerR-1.0.1/sensortowerR/R/st_url_parser.R |only sensortowerR-1.0.1/sensortowerR/R/st_yoy_metrics.R |only sensortowerR-1.0.1/sensortowerR/R/utils.R |only sensortowerR-1.0.1/sensortowerR/R/zzz.R |only sensortowerR-1.0.1/sensortowerR/inst/cache |only sensortowerR-1.0.1/sensortowerR/inst/doc/custom-fields.Rmd |only sensortowerR-1.0.1/sensortowerR/inst/doc/custom-fields.html |only sensortowerR-1.0.1/sensortowerR/inst/doc/migrating-to-1.0.Rmd |only sensortowerR-1.0.1/sensortowerR/inst/doc/migrating-to-1.0.html |only sensortowerR-1.0.1/sensortowerR/inst/doc/tidy-active-users.Rmd |only sensortowerR-1.0.1/sensortowerR/inst/doc/tidy-active-users.html |only sensortowerR-1.0.1/sensortowerR/inst/docs |only sensortowerR-1.0.1/sensortowerR/inst/examples |only sensortowerR-1.0.1/sensortowerR/inst/scripts |only sensortowerR-1.0.1/sensortowerR/man/METRIC_MAPPING.Rd |only sensortowerR-1.0.1/sensortowerR/man/NUMERIC_METRIC_PATTERNS.Rd |only sensortowerR-1.0.1/sensortowerR/man/add_custom_filter_params.Rd |only sensortowerR-1.0.1/sensortowerR/man/calculate_yoy_growth.Rd |only sensortowerR-1.0.1/sensortowerR/man/create_custom_filter_example.Rd |only sensortowerR-1.0.1/sensortowerR/man/custom_filter_utils.Rd |only sensortowerR-1.0.1/sensortowerR/man/example_sensortower_data.Rd |only sensortowerR-1.0.1/sensortowerR/man/extract_custom_filter_params.Rd |only sensortowerR-1.0.1/sensortowerR/man/fetch_data_core.Rd |only sensortowerR-1.0.1/sensortowerR/man/fetch_unified_data.Rd |only sensortowerR-1.0.1/sensortowerR/man/filter_helpers.Rd |only sensortowerR-1.0.1/sensortowerR/man/format_arpu.Rd |only sensortowerR-1.0.1/sensortowerR/man/format_currency.Rd |only sensortowerR-1.0.1/sensortowerR/man/format_downloads.Rd |only sensortowerR-1.0.1/sensortowerR/man/format_large_number.Rd |only sensortowerR-1.0.1/sensortowerR/man/format_market_share.Rd |only sensortowerR-1.0.1/sensortowerR/man/format_percent.Rd |only sensortowerR-1.0.1/sensortowerR/man/format_retention.Rd |only sensortowerR-1.0.1/sensortowerR/man/format_users.Rd |only sensortowerR-1.0.1/sensortowerR/man/formatting_helpers.Rd |only sensortowerR-1.0.1/sensortowerR/man/get_custom_filter_docs.Rd |only sensortowerR-1.0.1/sensortowerR/man/id_cache.Rd |only sensortowerR-1.0.1/sensortowerR/man/lookup_category_names.Rd |only sensortowerR-1.0.1/sensortowerR/man/map_game_summary_fields.Rd |only sensortowerR-1.0.1/sensortowerR/man/process_app_details_response.Rd |only sensortowerR-1.0.1/sensortowerR/man/process_game_summary_response.Rd |only sensortowerR-1.0.1/sensortowerR/man/process_ranking_response.Rd |only sensortowerR-1.0.1/sensortowerR/man/sensortowerR-defunct.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_active_users.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_analyze_filter.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_api_diagnostics.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_app_enriched.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_app_tag.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_batch_app_lookup.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_build_filter_url.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_build_web_url.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_clear_app_cache.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_clear_id_cache.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_custom_fields.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_custom_fields_utils.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_custom_fields_values.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_custom_fields_workflow.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_discover_fields.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_extract_filter_id.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_extract_url_params.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_facets_metrics.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_game_summary.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_get_app_names.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_get_filter_collection.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_get_filtered_apps.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_get_unified_mapping.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_gt_dashboard.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_is_valid_filter_id.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_parse_web_url.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_publisher_portfolio.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_ratings_facets.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_retention_facets.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_reviews_by_rating_facets.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_session_metrics.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_test_filter.Rd |only sensortowerR-1.0.1/sensortowerR/man/st_yoy_metrics.Rd |only sensortowerR-1.0.1/sensortowerR/man/standardize_revenue_units.Rd |only sensortowerR-1.0.1/sensortowerR/man/validate_custom_filter_params.Rd |only sensortowerR-1.0.1/sensortowerR/tests/testthat/helper-api-mocks.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/helper-auth.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-active-users-wrapper.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-api-helpers.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-cross-platform.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-custom-tags-processing.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-defunct.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-enrichment.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-id-cache.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-live-smoke.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-os-parameter.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-rhub-cran-checks.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-sensortowerR.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-st_batch_metrics_ids.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-st_filter.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-st_game_summary.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-st_market_metrics.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-st_metrics.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-st_rankings.R |only sensortowerR-1.0.1/sensortowerR/tests/testthat/test-st_yoy_metrics.R |only sensortowerR-1.0.1/sensortowerR/vignettes/custom-fields.Rmd |only sensortowerR-1.0.1/sensortowerR/vignettes/migrating-to-1.0.Rmd |only sensortowerR-1.0.1/sensortowerR/vignettes/tidy-active-users.Rmd |only sensortowerR-2.0.0/sensortowerR/DESCRIPTION | 42 - sensortowerR-2.0.0/sensortowerR/MD5 | 226 +------- sensortowerR-2.0.0/sensortowerR/NAMESPACE | 154 ----- sensortowerR-2.0.0/sensortowerR/NEWS.md |only sensortowerR-2.0.0/sensortowerR/R/core.R |only sensortowerR-2.0.0/sensortowerR/R/discovery.R |only sensortowerR-2.0.0/sensortowerR/R/filters.R |only sensortowerR-2.0.0/sensortowerR/R/metrics.R |only sensortowerR-2.0.0/sensortowerR/R/rankings.R |only sensortowerR-2.0.0/sensortowerR/R/request.R |only sensortowerR-2.0.0/sensortowerR/R/specialists.R |only sensortowerR-2.0.0/sensortowerR/R/utilities.R |only sensortowerR-2.0.0/sensortowerR/README.md | 281 ++-------- sensortowerR-2.0.0/sensortowerR/build/vignette.rds |binary sensortowerR-2.0.0/sensortowerR/inst/doc/pipelines.R |only sensortowerR-2.0.0/sensortowerR/inst/doc/pipelines.Rmd |only sensortowerR-2.0.0/sensortowerR/inst/doc/pipelines.html |only sensortowerR-2.0.0/sensortowerR/inst/doc/recipes.R |only sensortowerR-2.0.0/sensortowerR/inst/doc/recipes.Rmd |only sensortowerR-2.0.0/sensortowerR/inst/doc/recipes.html |only sensortowerR-2.0.0/sensortowerR/inst/recipes |only sensortowerR-2.0.0/sensortowerR/man/st_app.Rd | 48 - sensortowerR-2.0.0/sensortowerR/man/st_app_tags.Rd |only sensortowerR-2.0.0/sensortowerR/man/st_apps.Rd | 37 - sensortowerR-2.0.0/sensortowerR/man/st_cache_info.Rd | 12 sensortowerR-2.0.0/sensortowerR/man/st_categories.Rd | 33 - sensortowerR-2.0.0/sensortowerR/man/st_charts.Rd |only sensortowerR-2.0.0/sensortowerR/man/st_demographics.Rd | 103 --- sensortowerR-2.0.0/sensortowerR/man/st_diagnostics.Rd |only sensortowerR-2.0.0/sensortowerR/man/st_facets.Rd |only sensortowerR-2.0.0/sensortowerR/man/st_fields.Rd |only sensortowerR-2.0.0/sensortowerR/man/st_filter.Rd | 86 --- sensortowerR-2.0.0/sensortowerR/man/st_filter_read.Rd |only sensortowerR-2.0.0/sensortowerR/man/st_market_metrics.Rd | 66 -- sensortowerR-2.0.0/sensortowerR/man/st_metrics.Rd | 106 +-- sensortowerR-2.0.0/sensortowerR/man/st_parse_url.Rd |only sensortowerR-2.0.0/sensortowerR/man/st_publisher_apps.Rd | 88 --- sensortowerR-2.0.0/sensortowerR/man/st_rankings.Rd | 70 +- sensortowerR-2.0.0/sensortowerR/man/st_ratings.Rd |only sensortowerR-2.0.0/sensortowerR/man/st_retention.Rd | 111 --- sensortowerR-2.0.0/sensortowerR/man/st_sessions.Rd |only sensortowerR-2.0.0/sensortowerR/tests/testthat.R | 7 sensortowerR-2.0.0/sensortowerR/tests/testthat/helper-fixtures.R |only sensortowerR-2.0.0/sensortowerR/tests/testthat/test-metrics.R |only sensortowerR-2.0.0/sensortowerR/tests/testthat/test-pipelines.R |only sensortowerR-2.0.0/sensortowerR/tests/testthat/test-recipes.R |only sensortowerR-2.0.0/sensortowerR/tests/testthat/test-requests-filters.R |only sensortowerR-2.0.0/sensortowerR/tests/testthat/test-specialists.R |only sensortowerR-2.0.0/sensortowerR/vignettes/pipelines.Rmd |only sensortowerR-2.0.0/sensortowerR/vignettes/recipes.Rmd |only 198 files changed, 390 insertions(+), 1080 deletions(-)
Title: Reproducible Data Capsules with Provenance and Fallback
Description: Tools for building brick-proof, reproducible, self-contained data
capsules. Resolves open-data sources through the Comprehensive Knowledge
Archive Network ('CKAN', <https://ckan.org/>) package_show and
package_search endpoints, records and verifies provenance with Secure
Hash Algorithm 256 ('SHA-256') digests and Internet Archive 'Wayback
Machine' (<https://web.archive.org/>) snapshots, validates downloaded
data against a pinned schema, and falls back to schema-driven synthetic
data when the real source is unreachable. Run records are captured in a
manifest plus a plain-language summary so any result can be traced back
to its inputs. Distributional drift between a pinned capsule and a fresh
fetch is tested with Kolmogorov-Smirnov, chi-square, population
stability index, Jensen-Shannon divergence and 'Benford' first-digit
screens, because a re-released extract can be statistically identical
yet differ byte-for-byte, and a column can keep its name and type while
having been s [...truncated...]
Author: Vansh Singh Ruhela [aut, cre]
Maintainer: Vansh Singh Ruhela <vsruhela@proton.me>
Diff between rmoriebricklayer versions 0.5.0 dated 2026-09-16 and 0.5.1 dated 2026-09-21
DESCRIPTION | 83 ++++++------- MD5 | 156 ++++++++++++++++-------- NAMESPACE | 28 ++++ NEWS.md | 204 ++++++++++++++++++++++++++++++++ R/aaa_input_guards.R |only R/aaa_local_seed.R |only R/analyse_table.R |only R/areal.R | 21 ++- R/bands.R | 3 R/capsule_template.R |only R/categorical_guard.R |only R/concentration.R | 9 + R/core.R | 16 +- R/core_stats.R | 70 +++++++--- R/crypto_extra.R | 9 + R/custody.R | 8 + R/digest_extra.R | 14 +- R/drift.R | 10 - R/eda.R | 1 R/falsify.R | 2 R/json_gzip.R | 8 + R/json_native.R | 38 +++++ R/lib_capsule.R | 5 R/lib_data_loader.R | 19 ++ R/lib_helpers.R | 24 +++ R/lib_manifest.R | 15 ++ R/lib_synthetic.R | 29 +++- R/power.R | 2 R/print_methods.R | 46 ++++++- R/published_bounds.R |only R/rate.R | 2 R/repro.R | 4 R/revocation.R | 1 R/rule_lib.R | 7 + R/scan_adjust.R |only R/sign.R | 1 R/sketch.R | 19 ++ R/trend.R | 18 +- R/yoy_labels.R | 6 README.md | 31 ++++ build/vignette.rds |binary inst/doc/capsules.html | 2 inst/doc/categorical-integrity.R |only inst/doc/categorical-integrity.Rmd |only inst/doc/categorical-integrity.html |only inst/doc/getting-started.R |only inst/doc/getting-started.Rmd |only inst/doc/getting-started.html |only inst/doc/provenance.html | 10 - inst/doc/tables.html | 18 +- inst/doc/yoy.html | 37 +++-- inst/extdata/otis_a01_individuals.csv |only inst/include/rmoriebricklayer.h | 8 + inst/scripts/setup_and_run.R | 58 ++++++++- man/analyse_table.Rd |only man/audit_categories.Rd |only man/bricklayer_json_to_json.Rd | 4 man/change_envelope.Rd |only man/core_bootstrap_mean.Rd | 3 man/decode_codes.Rd |only man/decode_labelled.Rd |only man/drift_calibrate.Rd |only man/guard_binary.Rd |only man/guard_levels.Rd |only man/guard_recode.Rd |only man/odds_ratio_check.Rd |only man/published_bounds.Rd |only man/recode_manifest.Rd |only man/relabel.Rd |only man/relabel_forensics.Rd |only man/report_analysis.Rd |only man/scan_adjust.Rd |only man/sir.Rd | 3 man/transfer_verify.Rd |only man/use_capsule_template.Rd |only man/verify_marginals.Rd |only man/verify_recode.Rd |only man/write_recode_manifest.Rd |only man/yoy_bounds.Rd |only man/yoy_pvalues.Rd |only src/Makevars | 18 ++ src/Makevars.win | 18 ++ src/init.c | 6 src/morie_core.h | 65 ++++++++-- src/rmbl_core.cpp | 11 + src/rmbl_digest.cpp | 4 src/rmbl_mlkem_core.h | 7 - src/rmbl_series.cpp | 24 +++ src/rmbl_sketch.cpp | 5 src/rmbl_stats.cpp | 51 ++++---- tests/testthat/test-analyse-table.R |only tests/testthat/test-areal.R | 4 tests/testthat/test-bundle-fallbacks.R |only tests/testthat/test-capsule-template.R |only tests/testthat/test-categorical-guard.R |only tests/testthat/test-core-overflow.R |only tests/testthat/test-helper-paths.R | 2 tests/testthat/test-input-contracts.R |only tests/testthat/test-local-seed.R |only tests/testthat/test-trend-scale.R |only tests/testthat/test-ubsan-paths.R |only vignettes/categorical-integrity.Rmd |only vignettes/getting-started.Rmd |only 103 files changed, 1014 insertions(+), 253 deletions(-)
More information about rmoriebricklayer at CRAN
Permanent link
Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
Author: Julian Taylor [aut, cre],
David Butler. [aut]
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
This is a re-admission after prior archival of version 1.0-8 dated 2024-11-01
Diff between ASMap versions 1.0-8 dated 2024-11-01 and 1.1-0 dated 2026-09-21
ASMap-1.0-8/ASMap/vignettes/asmapvignette-concordance.tex |only ASMap-1.1-0/ASMap/DESCRIPTION | 6 - ASMap-1.1-0/ASMap/MD5 | 15 +- ASMap-1.1-0/ASMap/build/vignette.rds |binary ASMap-1.1-0/ASMap/inst/NEWS.Rd | 20 +++ ASMap-1.1-0/ASMap/inst/doc/asmapvignette.R | 78 +++++++------- ASMap-1.1-0/ASMap/inst/doc/asmapvignette.Rnw | 6 - ASMap-1.1-0/ASMap/inst/doc/asmapvignette.pdf |binary ASMap-1.1-0/ASMap/vignettes/asmapvignette.Rnw | 6 - 9 files changed, 75 insertions(+), 56 deletions(-)
Title: Power Calculation for Stepped Wedge Designs
Description: Tools for power and sample size
calculation as well as design diagnostics for
longitudinal mixed model settings, with a focus on stepped wedge designs.
All calculations are oracle estimates i.e. assume random effect variances
to be known (or guessed) in advance.
The method is introduced in Hussey and Hughes (2007) <doi:10.1016/j.cct.2006.05.007>,
extensions are discussed in Li et al. (2020) <doi:10.1177/0962280220932962>.
Author: Philipp Mildenberger [aut, cre] ,
Federico Marini [ctb]
Maintainer: Philipp Mildenberger <pmildenb@uni-mainz.de>
Diff between SteppedPower versions 0.3.5 dated 2024-04-29 and 0.4.0 dated 2026-09-21
SteppedPower-0.3.5/SteppedPower/tests/testthat/test_CovMat.R |only SteppedPower-0.3.5/SteppedPower/tests/testthat/test_DesMat.R |only SteppedPower-0.4.0/SteppedPower/DESCRIPTION | 17 SteppedPower-0.4.0/SteppedPower/LICENSE | 4 SteppedPower-0.4.0/SteppedPower/MD5 | 104 SteppedPower-0.4.0/SteppedPower/NAMESPACE | 100 SteppedPower-0.4.0/SteppedPower/NEWS.md | 137 SteppedPower-0.4.0/SteppedPower/R/InformationContent.R | 66 SteppedPower-0.4.0/SteppedPower/R/SteppedPower_PACKAGE.R | 40 SteppedPower-0.4.0/SteppedPower/R/closed_formulae.R | 250 SteppedPower-0.4.0/SteppedPower/R/construct_CovMat.R | 588 SteppedPower-0.4.0/SteppedPower/R/construct_DesMat.R | 804 - SteppedPower-0.4.0/SteppedPower/R/helper_functions.R | 643 - SteppedPower-0.4.0/SteppedPower/R/wlsPower.R | 1989 +-- SteppedPower-0.4.0/SteppedPower/README.md | 105 SteppedPower-0.4.0/SteppedPower/build/vignette.rds |binary SteppedPower-0.4.0/SteppedPower/inst/doc/Binomial_and_Count_Outcomes.R |only SteppedPower-0.4.0/SteppedPower/inst/doc/Binomial_and_Count_Outcomes.Rmd |only SteppedPower-0.4.0/SteppedPower/inst/doc/Binomial_and_Count_Outcomes.html |only SteppedPower-0.4.0/SteppedPower/inst/doc/Getting_Started.R | 359 SteppedPower-0.4.0/SteppedPower/inst/doc/Getting_Started.Rmd | 1200 - SteppedPower-0.4.0/SteppedPower/inst/doc/Getting_Started.html | 6375 ++++------ SteppedPower-0.4.0/SteppedPower/inst/doc/Incomplete_Designs.R | 95 SteppedPower-0.4.0/SteppedPower/inst/doc/Incomplete_Designs.Rmd | 100 SteppedPower-0.4.0/SteppedPower/inst/doc/Incomplete_Designs.html | 3177 +++- SteppedPower-0.4.0/SteppedPower/inst/vignettes |only SteppedPower-0.4.0/SteppedPower/man/RandEff_to_alpha012.Rd | 78 SteppedPower-0.4.0/SteppedPower/man/RandEff_to_icc.Rd |only SteppedPower-0.4.0/SteppedPower/man/SteppedPower-pkg.Rd | 32 SteppedPower-0.4.0/SteppedPower/man/VarClosed_Kasza.Rd | 114 SteppedPower-0.4.0/SteppedPower/man/VarClosed_Li.Rd | 72 SteppedPower-0.4.0/SteppedPower/man/alpha012_to_RandEff.Rd | 87 SteppedPower-0.4.0/SteppedPower/man/compute_InfoContent.Rd | 60 SteppedPower-0.4.0/SteppedPower/man/compute_glsPower.Rd | 176 SteppedPower-0.4.0/SteppedPower/man/construct_CovBlk.Rd | 90 SteppedPower-0.4.0/SteppedPower/man/construct_CovMat.Rd | 18 SteppedPower-0.4.0/SteppedPower/man/construct_CovSubMat.Rd | 130 SteppedPower-0.4.0/SteppedPower/man/construct_DesMat.Rd | 178 SteppedPower-0.4.0/SteppedPower/man/construct_incompMat.Rd | 66 SteppedPower-0.4.0/SteppedPower/man/construct_timeAdjust.Rd | 78 SteppedPower-0.4.0/SteppedPower/man/construct_trtMat.Rd | 74 SteppedPower-0.4.0/SteppedPower/man/glsPower.Rd | 549 SteppedPower-0.4.0/SteppedPower/man/icc_to_RandEff.Rd |only SteppedPower-0.4.0/SteppedPower/man/plot.DesMat.Rd | 56 SteppedPower-0.4.0/SteppedPower/man/plot.glsPower.Rd | 84 SteppedPower-0.4.0/SteppedPower/man/plot_CellWeights.Rd | 62 SteppedPower-0.4.0/SteppedPower/man/plot_CovMat.Rd | 38 SteppedPower-0.4.0/SteppedPower/man/plot_InfoContent.Rd | 62 SteppedPower-0.4.0/SteppedPower/man/print.DesMat.Rd | 38 SteppedPower-0.4.0/SteppedPower/man/print.glsPower.Rd | 40 SteppedPower-0.4.0/SteppedPower/man/tTestPwr.Rd | 58 SteppedPower-0.4.0/SteppedPower/tests/testthat.R | 8 SteppedPower-0.4.0/SteppedPower/tests/testthat/test_compute_glsPower.R |only SteppedPower-0.4.0/SteppedPower/tests/testthat/test_construct_CovMat.R |only SteppedPower-0.4.0/SteppedPower/tests/testthat/test_construct_DesMat.R |only SteppedPower-0.4.0/SteppedPower/vignettes/Binomial_and_Count_Outcomes.Rmd |only SteppedPower-0.4.0/SteppedPower/vignettes/Getting_Started.Rmd | 1200 - SteppedPower-0.4.0/SteppedPower/vignettes/Incomplete_Designs.Rmd | 100 SteppedPower-0.4.0/SteppedPower/vignettes/references.bib | 590 59 files changed, 11199 insertions(+), 9092 deletions(-)
Title: Simulation and Data Analysis for Plant Breeders
Description: Provides tools for simulation of plant breeding programs
as described, for example, by Melchinger and Frisch
(2023) <doi:10.1007/s00122-023-04446-3>, prediction of
segregation variance (Osthushenrich, Frisch and Herzog
(2017) <doi:10.1371/journal.pone.0188839>), genomic
prediction (Hofheinz and Frisch (2014)
<doi:10.1534/g3.113.010025>), linkage disequilibrium
based haplotype construction, and planning of marker
assisted back crossing programs. It provides an integrated
framework for simulation and analysis of plant breeding
programs.
Author: Matthias Frisch [aut, cre],
Hans Peter Maurer [ctb],
Philipp Heilmann [ctb]
Maintainer: Matthias Frisch <matthias.frisch@uni-giessen.de>
Diff between SelectionTools versions 26.3 dated 2026-09-15 and 26.4 dated 2026-09-21
SelectionTools-26.3/SelectionTools/man/st.simple.ggt.plot.Rd |only SelectionTools-26.4/SelectionTools/DESCRIPTION | 12 SelectionTools-26.4/SelectionTools/MD5 | 150 SelectionTools-26.4/SelectionTools/NAMESPACE | 3 SelectionTools-26.4/SelectionTools/R/SelectionTools01.R | 415 +- SelectionTools-26.4/SelectionTools/R/SelectionTools02.R | 17 SelectionTools-26.4/SelectionTools/R/SelectionTools03.R | 499 --- SelectionTools-26.4/SelectionTools/R/SelectionTools04.R | 1603 ++------- SelectionTools-26.4/SelectionTools/R/SelectionTools05.R |only SelectionTools-26.4/SelectionTools/build/partial.rdb |only SelectionTools-26.4/SelectionTools/build/vignette.rds |binary SelectionTools-26.4/SelectionTools/inst/doc/v-cross.R |only SelectionTools-26.4/SelectionTools/inst/doc/v-cross.Rnw |only SelectionTools-26.4/SelectionTools/inst/doc/v-cross.pdf |only SelectionTools-26.4/SelectionTools/inst/doc/v-hapld.R |only SelectionTools-26.4/SelectionTools/inst/doc/v-hapld.Rnw |only SelectionTools-26.4/SelectionTools/inst/doc/v-hapld.pdf |only SelectionTools-26.4/SelectionTools/inst/doc/v-phase.R |only SelectionTools-26.4/SelectionTools/inst/doc/v-phase.Rnw |only SelectionTools-26.4/SelectionTools/inst/doc/v-phase.pdf |only SelectionTools-26.4/SelectionTools/inst/doc/v-simbp.R | 8 SelectionTools-26.4/SelectionTools/inst/doc/v-simbp.Rnw | 512 --- SelectionTools-26.4/SelectionTools/inst/doc/v-simbp.pdf |binary SelectionTools-26.4/SelectionTools/inst/doc/v-simmd.Rmd | 2 SelectionTools-26.4/SelectionTools/inst/doc/v-simmd.pdf |binary SelectionTools-26.4/SelectionTools/man/cross.Rd | 12 SelectionTools-26.4/SelectionTools/man/define.effects.Rd | 16 SelectionTools-26.4/SelectionTools/man/define.map.Rd | 38 SelectionTools-26.4/SelectionTools/man/dh.Rd | 2 SelectionTools-26.4/SelectionTools/man/get.population.size.Rd | 17 SelectionTools-26.4/SelectionTools/man/gs.cross.eval.es.Rd | 87 SelectionTools-26.4/SelectionTools/man/gs.cross.eval.gd.Rd | 38 SelectionTools-26.4/SelectionTools/man/gs.cross.eval.ma.Rd | 39 SelectionTools-26.4/SelectionTools/man/gs.cross.eval.mi.Rd | 39 SelectionTools-26.4/SelectionTools/man/gs.cross.eval.mu.Rd | 39 SelectionTools-26.4/SelectionTools/man/gs.cross.eval.va.Rd | 54 SelectionTools-26.4/SelectionTools/man/gs.cross.info.Rd | 11 SelectionTools-26.4/SelectionTools/man/gs.esteff.rr.Rd | 65 SelectionTools-26.4/SelectionTools/man/gs.plot.model.fit.Rd | 35 SelectionTools-26.4/SelectionTools/man/load.linkage.map.Rd | 16 SelectionTools-26.4/SelectionTools/man/mab.load.data.Rd | 25 SelectionTools-26.4/SelectionTools/man/mab.simulate.Rd | 41 SelectionTools-26.4/SelectionTools/man/population.concat.Rd | 16 SelectionTools-26.4/SelectionTools/man/read.vcf.Rd |only SelectionTools-26.4/SelectionTools/man/show.phase.Rd |only SelectionTools-26.4/SelectionTools/man/st.calc.ld.Rd | 108 SelectionTools-26.4/SelectionTools/man/st.dataframe.to.STvcf.Rd | 27 SelectionTools-26.4/SelectionTools/man/st.def.hblocks.Rd | 88 SelectionTools-26.4/SelectionTools/man/st.destroy.phase.Rd |only SelectionTools-26.4/SelectionTools/man/st.marker.data.statistics.Rd | 28 SelectionTools-26.4/SelectionTools/man/st.phase.Rd |only SelectionTools-26.4/SelectionTools/man/st.plot.gene.diversity.Rd | 10 SelectionTools-26.4/SelectionTools/man/st.plot.ggt.Rd | 148 SelectionTools-26.4/SelectionTools/man/st.plot.ggt.src.Rd | 66 SelectionTools-26.4/SelectionTools/man/st.recode.hil.Rd | 53 SelectionTools-26.4/SelectionTools/man/st.recode.ref.Rd | 55 SelectionTools-26.4/SelectionTools/man/st.return.performance.data.Rd | 7 SelectionTools-26.4/SelectionTools/man/st.select.phen.Rd | 33 SelectionTools-26.4/SelectionTools/man/st.set.simpop.Rd | 46 SelectionTools-26.4/SelectionTools/man/st.switch.error.Rd |only SelectionTools-26.4/SelectionTools/man/st.write.marker.data.Rd | 21 SelectionTools-26.4/SelectionTools/man/st_mixed.Rd | 22 SelectionTools-26.4/SelectionTools/man/write.vcf.Rd |only SelectionTools-26.4/SelectionTools/src/SelectionTools01.c | 1627 +++++++++- SelectionTools-26.4/SelectionTools/src/SelectionTools02.c | 19 SelectionTools-26.4/SelectionTools/src/SelectionTools03.c |only SelectionTools-26.4/SelectionTools/src/init.c |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-01.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-02.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-03.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-04a.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-04b.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-05a.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-05b.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-06.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-07-101.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-07-102.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-07-103.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-07-104.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-07-105.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-07-106.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-07-107.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-07-108.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-07-109.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-crs-07-110.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-hapLD-fig01.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-hapLD-fig03.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-hapLD-fig05.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-hapLD-fig06.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-hapLD-fig07.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-hapLD-fig08.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-hapLD-fig09.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-hapLD-fig10.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/ex-vis1a-01.pdf |only SelectionTools-26.4/SelectionTools/vignettes/figures/f2-after-phasing.png |only SelectionTools-26.4/SelectionTools/vignettes/figures/f2-before-phasing.png |only SelectionTools-26.4/SelectionTools/vignettes/figures/f2-phased-haplotype-blocks.png |only SelectionTools-26.4/SelectionTools/vignettes/figures/f2-true-phase.png |only SelectionTools-26.4/SelectionTools/vignettes/v-cross.Rnw |only SelectionTools-26.4/SelectionTools/vignettes/v-hapld.Rnw |only SelectionTools-26.4/SelectionTools/vignettes/v-phase.Rnw |only SelectionTools-26.4/SelectionTools/vignettes/v-simbp.Rnw | 512 --- SelectionTools-26.4/SelectionTools/vignettes/v-simmd.Rmd | 2 103 files changed, 3751 insertions(+), 2932 deletions(-)
More information about SelectionTools at CRAN
Permanent link
Title: Construction of Screening Designs for Mixed Level Continuous and
Categorical Factors
Description: Constructs screening designs for experiments involving
continuous and categorical factors with multiple levels. The package
implements methods for constructing mixed-level screening designs,
involving factors with more than two levels. It also evaluates the
statistical performance of screening designs throughdev power to identify
active effects and Type I error rates.
The package implements three methods proposed by Jones, B.,
Lekivetz, R., Majumdar, D. and Nachtsheim, C. (2025)
<doi:10.1080/00401706.2024.2362149> for generating efficient
screening designs involving three-level continuous and two-level
categorical factors for even run sizes.
It also includes Paley Type I and Type II constructions for conference matrices
and pseudo conference matrices obtained using the coordinate exchange algorithm by Jones, B. and Nachtsheim, C. J. (2011)
<doi:10.1080/00224065.2011.11917841> which are used
in the development of these screening designs.
Author: Vyshna I C [aut, cre],
Cini Varghese [aut, ctb],
Safeela Nasrin [aut],
Boyina Devi Priyanka [aut, ctb],
Mohd Harun [aut, ctb],
Anindita Datta [aut, ctb]
Maintainer: Vyshna I C <vyshnaic@gmail.com>
Diff between SCCDdesign versions 0.1.0 dated 2026-09-03 and 0.2.0 dated 2026-09-21
DESCRIPTION | 26 +++++++++++++++----------- MD5 | 14 ++++++++++++-- NAMESPACE | 6 ++++++ R/even_even_design.R |only R/even_odd_design.R |only R/mixed_level_design.R |only R/odd_odd_design.R |only R/simulation.R |only man/even_even_design.Rd |only man/mixed_level_design.Rd |only man/odd_even_design.Rd |only man/odd_odd_design.Rd |only man/simulation.Rd |only 13 files changed, 33 insertions(+), 13 deletions(-)
Title: Download and Read Brazilian Meteorological Data from INMET
Description: Automates the download and processing of historical weather
data from the Brazilian National Institute of Meteorology (INMET).
It provides a cached catalogue of automatic stations, resumable and
validated downloads, and parsers for formatting inconsistencies in raw
CSV files across different years. It removes structural artifacts,
standardizes column names, parses timestamps, and returns data frames ready
for analysis. Data are retrieved from
<https://portal.inmet.gov.br/dadoshistoricos> and
<https://apitempo.inmet.gov.br/estacoes/T>.
Author: Rodrigo Fonseca Villa [aut, cre]
Maintainer: Rodrigo Fonseca Villa <rodrigo03.villa@gmail.com>
Diff between rmet versions 0.1.0 dated 2026-04-21 and 0.2.0 dated 2026-09-21
DESCRIPTION | 22 - MD5 | 51 +-- NAMESPACE | 17 - NEWS.md | 45 ++ R/download.R | 216 +++++++------ R/get.R |only R/read.R | 634 ++++++++++++++++++++++------------------- R/stations.R | 291 +++++++++++++++--- R/utils.R | 191 ++++++++---- README.md | 121 +++++-- inst/CITATION |only inst/WORDLIST | 4 inst/doc/rmet-intro.R | 12 inst/doc/rmet-intro.Rmd | 42 +- inst/doc/rmet-intro.html | 75 +++- man/inmet_cache_clear.Rd | 16 - man/inmet_cache_status.Rd | 17 - man/inmet_download.Rd | 44 -- man/inmet_extract.Rd | 18 - man/inmet_get.Rd |only man/inmet_read.Rd | 55 +-- man/inmet_stations.Rd | 82 ++--- man/rmet-package.Rd | 24 - tests/testthat/test-download.R | 184 +++++++++++ tests/testthat/test-read.R | 209 ++++++++++++- tests/testthat/test-stations.R | 218 +++++++++++++- tests/testthat/test-utils.R | 106 ++++++ vignettes/rmet-intro.Rmd | 42 +- 28 files changed, 1922 insertions(+), 814 deletions(-)
Title: Utility Functions Around 'JDemetra+ 3.0'
Description: R Interface to 'JDemetra+ 3.x'
(<https://github.com/jdemetra>) time series analysis software. It
provides functions allowing to model time series (create outlier
regressors, user-defined calendar regressors, Unobserved Components
AutoRegressive Integrated Moving Average (UCARIMA) models...), to test
the presence of trading days or seasonal effects and also to set
specifications in pre-adjustment and benchmarking when using 'rjd3x13'
or 'rjd3tramoseats'.
Author: Jean Palate [aut],
Alain Quartier-la-Tente [aut] ,
Tanguy Barthelemy [aut, cre, art, cph],
Anna Smyk [aut]
Maintainer: Tanguy Barthelemy <timeserieswithjdemetraandr@gmail.com>
Diff between rjd3toolkit versions 3.8.0 dated 2026-07-08 and 3.9.0 dated 2026-09-21
rjd3toolkit-3.8.0/rjd3toolkit/R/modellingcontext.R |only rjd3toolkit-3.8.0/rjd3toolkit/R/protos.R |only rjd3toolkit-3.8.0/rjd3toolkit/inst/java/jdplus-sa-base-protobuf-3.8.0.jar |only rjd3toolkit-3.8.0/rjd3toolkit/inst/java/jdplus-sa-base-r-3.8.0.jar |only rjd3toolkit-3.8.0/rjd3toolkit/inst/java/jdplus-toolkit-base-protobuf-3.8.0.jar |only rjd3toolkit-3.8.0/rjd3toolkit/inst/java/jdplus-toolkit-base-r-3.8.0.jar |only rjd3toolkit-3.8.0/rjd3toolkit/man/sa_preprocessing.Rd |only rjd3toolkit-3.9.0/rjd3toolkit/DESCRIPTION | 22 rjd3toolkit-3.9.0/rjd3toolkit/MD5 | 323 rjd3toolkit-3.9.0/rjd3toolkit/NAMESPACE | 736 - rjd3toolkit-3.9.0/rjd3toolkit/NEWS.md | 295 rjd3toolkit-3.9.0/rjd3toolkit/R/arima.R | 1380 +-- rjd3toolkit-3.9.0/rjd3toolkit/R/calendars.R | 2271 +++-- rjd3toolkit-3.9.0/rjd3toolkit/R/calendarts.R | 76 rjd3toolkit-3.9.0/rjd3toolkit/R/data.R | 195 rjd3toolkit-3.9.0/rjd3toolkit/R/decomposition.R | 316 rjd3toolkit-3.9.0/rjd3toolkit/R/deprecated.R | 37 rjd3toolkit-3.9.0/rjd3toolkit/R/dictionary.R | 156 rjd3toolkit-3.9.0/rjd3toolkit/R/differencing.R | 481 - rjd3toolkit-3.9.0/rjd3toolkit/R/display.R | 1146 +- rjd3toolkit-3.9.0/rjd3toolkit/R/distributions.R | 574 - rjd3toolkit-3.9.0/rjd3toolkit/R/generics.R | 154 rjd3toolkit-3.9.0/rjd3toolkit/R/jd2r.R | 492 - rjd3toolkit-3.9.0/rjd3toolkit/R/jd3rslts.R | 506 - rjd3toolkit-3.9.0/rjd3toolkit/R/modelling_context.R |only rjd3toolkit-3.9.0/rjd3toolkit/R/options.R |only rjd3toolkit-3.9.0/rjd3toolkit/R/procresults.R | 233 rjd3toolkit-3.9.0/rjd3toolkit/R/protobuf.R | 1423 +-- rjd3toolkit-3.9.0/rjd3toolkit/R/regarima_generic.R | 207 rjd3toolkit-3.9.0/rjd3toolkit/R/regarima_rslts.R | 95 rjd3toolkit-3.9.0/rjd3toolkit/R/rjd3toolkit-package.R | 12 rjd3toolkit-3.9.0/rjd3toolkit/R/spec_benchmarking.R | 202 rjd3toolkit-3.9.0/rjd3toolkit/R/spec_regarima.R | 4082 +++++----- rjd3toolkit-3.9.0/rjd3toolkit/R/splines.R | 295 rjd3toolkit-3.9.0/rjd3toolkit/R/tests_regular.R | 614 - rjd3toolkit-3.9.0/rjd3toolkit/R/tests_seasonality.R | 658 - rjd3toolkit-3.9.0/rjd3toolkit/R/tests_td.R | 267 rjd3toolkit-3.9.0/rjd3toolkit/R/timeseries.R | 1038 +- rjd3toolkit-3.9.0/rjd3toolkit/R/utils.R | 201 rjd3toolkit-3.9.0/rjd3toolkit/R/variables.R | 1215 +- rjd3toolkit-3.9.0/rjd3toolkit/R/zzz.R | 158 rjd3toolkit-3.9.0/rjd3toolkit/README.md | 142 rjd3toolkit-3.9.0/rjd3toolkit/inst/WORDLIST | 200 rjd3toolkit-3.9.0/rjd3toolkit/inst/java/jdplus-sa-base-protobuf-3.9.0.jar |only rjd3toolkit-3.9.0/rjd3toolkit/inst/java/jdplus-sa-base-r-3.9.0.jar |only rjd3toolkit-3.9.0/rjd3toolkit/inst/java/jdplus-toolkit-base-protobuf-3.9.0.jar |only rjd3toolkit-3.9.0/rjd3toolkit/inst/java/jdplus-toolkit-base-r-3.9.0.jar |only rjd3toolkit-3.9.0/rjd3toolkit/inst/proto/modelling.proto | 370 rjd3toolkit-3.9.0/rjd3toolkit/inst/proto/outliers.proto | 62 rjd3toolkit-3.9.0/rjd3toolkit/inst/proto/regarima.proto | 92 rjd3toolkit-3.9.0/rjd3toolkit/inst/proto/sa.proto | 216 rjd3toolkit-3.9.0/rjd3toolkit/inst/proto/toolkit.proto | 846 +- rjd3toolkit-3.9.0/rjd3toolkit/java/README | 12 rjd3toolkit-3.9.0/rjd3toolkit/man/ABS.Rd | 44 rjd3toolkit-3.9.0/rjd3toolkit/man/Births.Rd | 78 rjd3toolkit-3.9.0/rjd3toolkit/man/Electricity.Rd | 54 rjd3toolkit-3.9.0/rjd3toolkit/man/Exports.Rd | 44 rjd3toolkit-3.9.0/rjd3toolkit/man/Imports.Rd | 44 rjd3toolkit-3.9.0/rjd3toolkit/man/Retail.Rd | 44 rjd3toolkit-3.9.0/rjd3toolkit/man/add_outlier.Rd | 146 rjd3toolkit-3.9.0/rjd3toolkit/man/add_usrdefvar.Rd | 233 rjd3toolkit-3.9.0/rjd3toolkit/man/aggregate.Rd | 82 rjd3toolkit-3.9.0/rjd3toolkit/man/arima_difference.Rd | 62 rjd3toolkit-3.9.0/rjd3toolkit/man/arima_model.Rd | 60 rjd3toolkit-3.9.0/rjd3toolkit/man/arima_properties.Rd | 60 rjd3toolkit-3.9.0/rjd3toolkit/man/arima_sum.Rd | 66 rjd3toolkit-3.9.0/rjd3toolkit/man/autocorrelations.Rd | 86 rjd3toolkit-3.9.0/rjd3toolkit/man/bsplines.Rd | 56 rjd3toolkit-3.9.0/rjd3toolkit/man/calendar_td.Rd | 181 rjd3toolkit-3.9.0/rjd3toolkit/man/chained_calendar.Rd | 76 rjd3toolkit-3.9.0/rjd3toolkit/man/chi2distribution.Rd | 90 rjd3toolkit-3.9.0/rjd3toolkit/man/clean_extremities.Rd | 48 rjd3toolkit-3.9.0/rjd3toolkit/man/compare_annual_totals.Rd | 54 rjd3toolkit-3.9.0/rjd3toolkit/man/complete_modelling_context.Rd |only rjd3toolkit-3.9.0/rjd3toolkit/man/data_to_ts.Rd | 50 rjd3toolkit-3.9.0/rjd3toolkit/man/daysOf.Rd | 49 rjd3toolkit-3.9.0/rjd3toolkit/man/deprecated-rjd3toolkit.Rd | 43 rjd3toolkit-3.9.0/rjd3toolkit/man/diagnostics.Rd | 46 rjd3toolkit-3.9.0/rjd3toolkit/man/dictionary.Rd | 62 rjd3toolkit-3.9.0/rjd3toolkit/man/differences.Rd | 52 rjd3toolkit-3.9.0/rjd3toolkit/man/differencing_fast.Rd | 82 rjd3toolkit-3.9.0/rjd3toolkit/man/do_stationary.Rd | 71 rjd3toolkit-3.9.0/rjd3toolkit/man/dot-add_ud_var.Rd | 50 rjd3toolkit-3.9.0/rjd3toolkit/man/dot-likelihood.Rd | 112 rjd3toolkit-3.9.0/rjd3toolkit/man/dot-tsmoniker.Rd | 58 rjd3toolkit-3.9.0/rjd3toolkit/man/easter_dates.Rd | 68 rjd3toolkit-3.9.0/rjd3toolkit/man/easter_day.Rd | 86 rjd3toolkit-3.9.0/rjd3toolkit/man/easter_variable.Rd | 114 rjd3toolkit-3.9.0/rjd3toolkit/man/figures/logo.svg | 1448 +-- rjd3toolkit-3.9.0/rjd3toolkit/man/fixed_day.Rd | 82 rjd3toolkit-3.9.0/rjd3toolkit/man/fixed_week_day.Rd | 82 rjd3toolkit-3.9.0/rjd3toolkit/man/gammadistribution.Rd | 90 rjd3toolkit-3.9.0/rjd3toolkit/man/get_toolkit_option.Rd | 42 rjd3toolkit-3.9.0/rjd3toolkit/man/holidays.Rd | 158 rjd3toolkit-3.9.0/rjd3toolkit/man/intervention_variable.Rd | 192 rjd3toolkit-3.9.0/rjd3toolkit/man/invgammadistribution.Rd | 90 rjd3toolkit-3.9.0/rjd3toolkit/man/invgaussiandistribution.Rd | 76 rjd3toolkit-3.9.0/rjd3toolkit/man/jd3_print.Rd | 100 rjd3toolkit-3.9.0/rjd3toolkit/man/jd3_utilities.Rd | 725 - rjd3toolkit-3.9.0/rjd3toolkit/man/ljungbox.Rd | 72 rjd3toolkit-3.9.0/rjd3toolkit/man/long_term_mean.Rd | 128 rjd3toolkit-3.9.0/rjd3toolkit/man/lp_variable.Rd | 96 rjd3toolkit-3.9.0/rjd3toolkit/man/mad.Rd | 54 rjd3toolkit-3.9.0/rjd3toolkit/man/modelling_context.Rd | 100 rjd3toolkit-3.9.0/rjd3toolkit/man/monotonic_cspline.Rd | 54 rjd3toolkit-3.9.0/rjd3toolkit/man/national_calendar.Rd | 106 rjd3toolkit-3.9.0/rjd3toolkit/man/natural_cspline.Rd | 54 rjd3toolkit-3.9.0/rjd3toolkit/man/normality_tests.Rd | 128 rjd3toolkit-3.9.0/rjd3toolkit/man/outliers_variables.Rd | 148 rjd3toolkit-3.9.0/rjd3toolkit/man/periodic_bsplines.Rd | 60 rjd3toolkit-3.9.0/rjd3toolkit/man/periodic_cspline.Rd | 54 rjd3toolkit-3.9.0/rjd3toolkit/man/periodic_csplines.Rd | 50 rjd3toolkit-3.9.0/rjd3toolkit/man/periodic_dummies.Rd | 84 rjd3toolkit-3.9.0/rjd3toolkit/man/print_calendars.Rd | 82 rjd3toolkit-3.9.0/rjd3toolkit/man/r2jd_calendarts.Rd | 54 rjd3toolkit-3.9.0/rjd3toolkit/man/ramp_variable.Rd | 94 rjd3toolkit-3.9.0/rjd3toolkit/man/rangemean_tstat.Rd | 138 rjd3toolkit-3.9.0/rjd3toolkit/man/rjd3toolkit-package.Rd | 68 rjd3toolkit-3.9.0/rjd3toolkit/man/runstests.Rd | 96 rjd3toolkit-3.9.0/rjd3toolkit/man/sa_decomposition.Rd | 128 rjd3toolkit-3.9.0/rjd3toolkit/man/sarima_decompose.Rd | 54 rjd3toolkit-3.9.0/rjd3toolkit/man/sarima_estimate.Rd | 112 rjd3toolkit-3.9.0/rjd3toolkit/man/sarima_hannan_rissanen.Rd | 90 rjd3toolkit-3.9.0/rjd3toolkit/man/sarima_model.Rd | 98 rjd3toolkit-3.9.0/rjd3toolkit/man/sarima_properties.Rd | 54 rjd3toolkit-3.9.0/rjd3toolkit/man/sarima_random.Rd | 72 rjd3toolkit-3.9.0/rjd3toolkit/man/seasonality_canovahansen.Rd | 88 rjd3toolkit-3.9.0/rjd3toolkit/man/seasonality_canovahansen_trigs.Rd | 84 rjd3toolkit-3.9.0/rjd3toolkit/man/seasonality_combined.Rd | 80 rjd3toolkit-3.9.0/rjd3toolkit/man/seasonality_f.Rd | 68 rjd3toolkit-3.9.0/rjd3toolkit/man/seasonality_friedman.Rd | 66 rjd3toolkit-3.9.0/rjd3toolkit/man/seasonality_kruskalwallis.Rd | 66 rjd3toolkit-3.9.0/rjd3toolkit/man/seasonality_modified_qs.Rd | 70 rjd3toolkit-3.9.0/rjd3toolkit/man/seasonality_periodogram.Rd | 66 rjd3toolkit-3.9.0/rjd3toolkit/man/seasonality_qs.Rd | 66 rjd3toolkit-3.9.0/rjd3toolkit/man/set_arima.Rd | 178 rjd3toolkit-3.9.0/rjd3toolkit/man/set_automodel.Rd | 290 rjd3toolkit-3.9.0/rjd3toolkit/man/set_basic.Rd | 216 rjd3toolkit-3.9.0/rjd3toolkit/man/set_benchmarking.Rd | 156 rjd3toolkit-3.9.0/rjd3toolkit/man/set_easter.Rd | 188 rjd3toolkit-3.9.0/rjd3toolkit/man/set_estimate.Rd | 174 rjd3toolkit-3.9.0/rjd3toolkit/man/set_outlier.Rd | 234 rjd3toolkit-3.9.0/rjd3toolkit/man/set_tradingdays.Rd | 436 - rjd3toolkit-3.9.0/rjd3toolkit/man/set_transform.Rd | 124 rjd3toolkit-3.9.0/rjd3toolkit/man/single_day.Rd | 62 rjd3toolkit-3.9.0/rjd3toolkit/man/special_day.Rd | 140 rjd3toolkit-3.9.0/rjd3toolkit/man/statisticaltest.Rd | 82 rjd3toolkit-3.9.0/rjd3toolkit/man/stock_td.Rd | 86 rjd3toolkit-3.9.0/rjd3toolkit/man/studentdistribution.Rd | 86 rjd3toolkit-3.9.0/rjd3toolkit/man/td.Rd | 140 rjd3toolkit-3.9.0/rjd3toolkit/man/td_canovahansen.Rd | 70 rjd3toolkit-3.9.0/rjd3toolkit/man/td_f.Rd | 138 rjd3toolkit-3.9.0/rjd3toolkit/man/td_timevarying.Rd | 58 rjd3toolkit-3.9.0/rjd3toolkit/man/to_ts.Rd | 70 rjd3toolkit-3.9.0/rjd3toolkit/man/to_tscollection.Rd | 77 rjd3toolkit-3.9.0/rjd3toolkit/man/toolkit_option.Rd | 41 rjd3toolkit-3.9.0/rjd3toolkit/man/tramoseats_spec_default.Rd | 51 rjd3toolkit-3.9.0/rjd3toolkit/man/trigonometric_variables.Rd | 146 rjd3toolkit-3.9.0/rjd3toolkit/man/ts_adjust.Rd | 60 rjd3toolkit-3.9.0/rjd3toolkit/man/ts_interpolate.Rd | 56 rjd3toolkit-3.9.0/rjd3toolkit/man/tsdata_of.Rd | 62 rjd3toolkit-3.9.0/rjd3toolkit/man/ucarima_canonical.Rd | 62 rjd3toolkit-3.9.0/rjd3toolkit/man/ucarima_estimate.Rd | 68 rjd3toolkit-3.9.0/rjd3toolkit/man/ucarima_model.Rd | 70 rjd3toolkit-3.9.0/rjd3toolkit/man/ucarima_wk.Rd | 72 rjd3toolkit-3.9.0/rjd3toolkit/man/weighted_calendar.Rd | 90 rjd3toolkit-3.9.0/rjd3toolkit/man/x13_spec_default.Rd | 50 rjd3toolkit-3.9.0/rjd3toolkit/tests |only 168 files changed, 18126 insertions(+), 16125 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Data
Description: Conduct a noncompartmental analysis with industrial strength.
Some features are
1) Use of CDISC SDTM terms
2) Automatic or manual slope selection
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
5) Steady-state analysis over the dosing interval (AUCTAU, CAVG, CL and Vz from AUCTAU)
6) Installation/Operational Qualification (IQ/OQ) reports in pdf.
After installation, qualify the package in your own environment:
run IQNCA() for Installation Qualification and OQNCA() for Operational
Qualification. Run writeMD5NCA() once after installation so the IQ
file-integrity check passes. To approve a report, sign it digitally in
Adobe Acrobat Reader (generate with sigField=TRUE, or run
addSigFieldNCA(), to add click-to-sign fields), instead of printing and
scanning; or use signPDFNCA()/verifyPDFNCA() for a scriptable signature.
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data [...truncated...]
Author: Kyun-Seop Bae [aut, cre]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between NonCompart versions 0.8.3 dated 2026-08-21 and 0.8.4 dated 2026-09-21
DESCRIPTION | 11 MD5 | 26 R/OQNCA.R | 37 + R/Unit.R | 269 ++++---- R/sNCA.R | 551 +++++++++-------- R/tblNCA.R | 162 ++-- inst/NEWS.Rd | 12 inst/OQ/Reference_Analytic_SS_Extravascular_Linear.csv |only inst/OQ/RptCfg.csv | 2 inst/extdoc/NCA-Formula.pdf |binary man/OQNCA.Rd | 13 man/sNCA.Rd | 35 - man/tblNCA.Rd | 40 - tests/RptCfg.csv | 100 +-- tests/Test-SS.R |only 15 files changed, 715 insertions(+), 543 deletions(-)
Title: Tool for Statistical and Environmental Analysis
Description: Provides a set of accessible and automated functions to apply
statistical models such as Simple Linear Regression (RLS, from the Spanish
'Regresión Lineal Simple'), Multiple Linear Regression (RLM, from the Spanish
'Regresión Lineal Múltiple'), Generalized Linear Models (GLM), and time
series analysis through Autoregressive Integrated Moving Average (ARIMA)
models. Designed to support teaching at the Universidad Autónoma Chapingo,
it facilitates results interpretation and assumption validation through
automatic graphical diagnostics. Developed as part of an undergraduate
thesis at the Universidad Autónoma Chapingo, under the supervision of
Dr. Julio César Buendía Espinoza (thesis advisor), with the participation
of the thesis committee: Diego Ernesto Lira González (secretary), Israel
Lerma Serna (member), Juan Uriel Avelar Roblero (alternate), and Elisa del
Carmen Martínez Ochoa (alternate). Methods for regression and time series
are based on Montgomery et al. (2021, ISBN:978-111957014 [...truncated...]
Author: Dayron Jared Bazan Guzman [aut, cre],
Julio Cesar Buendia Espinoza [aut, ths] ,
Diego Ernesto Lira Gonzalez [ctb] ,
Israel Lerma Serna [ctb] ,
Juan Uriel Avelar Roblero [ctb] ,
Elisa del Carmen Martinez Ochoa [ctb]
Maintainer: Dayron Jared Bazan Guzman <dbazanguzman@gmail.com>
Diff between GREENREG versions 0.1.0 dated 2026-05-29 and 0.1.1 dated 2026-09-21
GREENREG-0.1.0/GREENREG/R/Analisis_datos.R |only GREENREG-0.1.0/GREENREG/R/Regresion_lineal_multiple.R |only GREENREG-0.1.0/GREENREG/R/Regresion_lineal_simple.R |only GREENREG-0.1.0/GREENREG/R/Regresion_logistica.R |only GREENREG-0.1.0/GREENREG/R/Regresion_poisson.R |only GREENREG-0.1.1/GREENREG/DESCRIPTION | 52 +++++++++++-- GREENREG-0.1.1/GREENREG/MD5 | 38 +++++----- GREENREG-0.1.1/GREENREG/NAMESPACE | 1 GREENREG-0.1.1/GREENREG/R/analisis_datos.R |only GREENREG-0.1.1/GREENREG/R/globals.R | 2 GREENREG-0.1.1/GREENREG/R/modelo_ar.R |only GREENREG-0.1.1/GREENREG/R/modelo_arima.R |only GREENREG-0.1.1/GREENREG/R/modelo_arma.R |only GREENREG-0.1.1/GREENREG/R/modelo_ma.R |only GREENREG-0.1.1/GREENREG/R/regresion_lineal_multiple.R |only GREENREG-0.1.1/GREENREG/R/regresion_lineal_simple.R |only GREENREG-0.1.1/GREENREG/R/regresion_logistica.R |only GREENREG-0.1.1/GREENREG/R/regresion_poisson.R |only GREENREG-0.1.1/GREENREG/man/analisis_datos.Rd | 2 GREENREG-0.1.1/GREENREG/man/logistico.Rd | 2 GREENREG-0.1.1/GREENREG/man/modelo_ar.Rd | 63 ++++++++++++++++ GREENREG-0.1.1/GREENREG/man/modelo_arima.Rd | 68 +++++++++++++++++- GREENREG-0.1.1/GREENREG/man/modelo_arma.Rd | 63 ++++++++++++++++ GREENREG-0.1.1/GREENREG/man/modelo_ma.Rd | 62 +++++++++++++++- GREENREG-0.1.1/GREENREG/man/reg_poisson.Rd | 2 GREENREG-0.1.1/GREENREG/man/rlm.Rd | 2 GREENREG-0.1.1/GREENREG/man/rls.Rd | 2 27 files changed, 318 insertions(+), 41 deletions(-)
Title: Objective Bayesian Distribution Fitting
Description: Fits common univariate distributions using registered objective
Bayesian priors, including Jeffreys, reference, and maximal data information
priors, and supports user-defined distributions and priors through an
extensible model specification. Model-specific posterior propriety and
moment conditions are checked before computation when registered or supplied.
Exact simulation, marginalization, slice sampling, adaptive Metropolis, and
user-supplied posterior samplers share a common interface for summaries,
diagnostics, prediction, and pointwise log-likelihood evaluation.
A separate interface fits independently right-censored observations using
the registered complete-data priors, observed-data likelihood sampling or
data augmentation, with sufficient posterior-propriety checks. Optional
post-processing provides WAIC, PSIS-LOO, and DIC for observed-data likelihoods.
The reference-prior framework follows Bernardo (1979)
<doi:10.1111/j.2517-6161.1979.tb01066.x>.
Author: Pedro Luiz Ramos [aut, cre, cph]
Maintainer: Pedro Luiz Ramos <pedro.ramos@uc.cl>
Diff between fitdistrBayes versions 0.2.3 dated 2026-09-09 and 0.5.0 dated 2026-09-21
DESCRIPTION | 16 ++++--- MD5 | 30 ++++++++++--- NAMESPACE | 20 +++++++++ NEWS.md | 42 +++++++++++++++++++ R/criteria.R |only R/fitcensBayes-methods.R |only R/fitcensBayes.R |only R/fitdistrBayes.R | 71 +++++++++++++++++++++++++++++---- README.md | 73 +++++++++++++++++++++++++++++++++- inst/examples/tutorial_criteria.R |only inst/examples/tutorial_fitcensBayes.R |only man/criteria.Rd |only man/fitcensBayes-methods.Rd |only man/fitcensBayes.Rd |only man/fitcensBayes_models.Rd |only man/fitdistrBayes-methods.Rd | 4 + man/fitdistrBayes.Rd | 26 +++++++++--- man/fitdistrBayes_model.Rd | 17 +++++-- tests/censored-helpers.R |only tests/tests_audit_regressions.R |only tests/tests_censored_contracts.R |only tests/tests_censored_sampling.R |only tests/tests_criteria.R |only 23 files changed, 264 insertions(+), 35 deletions(-)
Title: Fast Functional Generalized Estimating Equations via a One-Step
Estimator
Description: Fits functional generalized estimating equations for longitudinal
functional outcomes and covariates using a one-step estimator that is fast
even for large cluster sizes or large numbers of clusters. The package
supports quasi-likelihoods derived from a range of distributions, with
substantial simulations run for quasi-likelihoods derived from Gaussian,
binomial, Poisson, negative binomial, Gamma and beta families. It supports
common link functions and several working correlation structures. An optimized engine
constructs cluster score and sensitivity statistics in one pass, provides
coefficient-space Gaussian cross-validation, analytic-gradient fast cluster
cross-validation, and an experimental sandwich-scaled working restricted
quasi-likelihood selector. Internal compiled routines provide symmetric
positive-definite Cholesky solves and exact tridiagonal precision operations
for irregularly sampled continuous-time AR(1) working correlations.
Uncertainty quantification is based on sand [...truncated...]
Author: Gabriel Loewinger [aut, cre]
Maintainer: Gabriel Loewinger <gloewinger@gmail.com>
Diff between fastFGEE versions 0.2.0 dated 2026-09-15 and 0.2.2 dated 2026-09-21
DESCRIPTION | 6 MD5 | 21 R/RcppExports.R | 4 R/corr_gram.R |only R/working_stats.R | 43 inst/doc/fastFGEE.R | 342 ++--- inst/doc/fastFGEE.Rmd | 923 +++++++-------- inst/doc/fastFGEE.html | 1291 ++++++++++------------ src/RcppExports.cpp | 15 src/corr_gram.cpp |only tests/testthat/test-corr-gram.R |only tests/testthat/test-dependency-and-registration.R | 12 vignettes/fastFGEE.Rmd | 923 +++++++-------- 13 files changed, 1702 insertions(+), 1878 deletions(-)
Title: Client for Delphi's 'Epidata' API
Description: The Delphi 'Epidata' API provides real-time access to
epidemiological surveillance data for influenza, 'COVID-19', and other
diseases for the USA at various geographical resolutions, both from
official government sources such as the Center for Disease Control
(CDC) and Google Trends and private partners such as Facebook and
Change 'Healthcare'. It is built and maintained by the Carnegie Mellon
University Delphi research group. To cite this API: David C. Farrow,
Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni'
'Rosenfeld' (2015). Delphi 'Epidata' API.
<https://github.com/cmu-delphi/delphi-epidata>.
Author: Logan Brooks [aut],
Dmitry Shemetov [aut],
Samuel Gratzl [aut],
David Weber [ctb, cre],
Nat DeFries [ctb],
Alex Reinhart [ctb],
Daniel J. McDonald [ctb],
Kean Ming Tan [ctb],
Will Townes [ctb],
George Haff [ctb],
Kathryn Mazaitis [ctb]
Maintainer: David Weber <davidweb@andrew.cmu.edu>
Diff between epidatr versions 1.3.0 dated 2026-08-28 and 1.4.0 dated 2026-09-21
epidatr-1.3.0/epidatr/inst/doc/v5-api-demo.Rmd |only epidatr-1.3.0/epidatr/inst/doc/v5-api-demo.html |only epidatr-1.3.0/epidatr/vignettes/img/epidatr-unnamed-chunk-9-1.png |only epidatr-1.3.0/epidatr/vignettes/v5-api-demo.Rmd |only epidatr-1.4.0/epidatr/DESCRIPTION | 8 epidatr-1.4.0/epidatr/MD5 | 107 epidatr-1.4.0/epidatr/NAMESPACE | 104 epidatr-1.4.0/epidatr/NEWS.md | 46 epidatr-1.4.0/epidatr/R/check.R | 127 epidatr-1.4.0/epidatr/R/endpoints.R | 146 - epidatr-1.4.0/epidatr/R/epidatacall.R | 30 epidatr-1.4.0/epidatr/R/model.R | 14 epidatr-1.4.0/epidatr/R/request.R | 69 epidatr-1.4.0/epidatr/R/utils.R | 9 epidatr-1.4.0/epidatr/README.md | 144 - epidatr-1.4.0/epidatr/build/vignette.rds |binary epidatr-1.4.0/epidatr/inst/doc/epidatr.Rmd | 579 ++-- epidatr-1.4.0/epidatr/inst/doc/epidatr.html | 1294 +++++----- epidatr-1.4.0/epidatr/inst/doc/migration-guide.Rmd | 306 +- epidatr-1.4.0/epidatr/inst/doc/migration-guide.html | 531 ++-- epidatr-1.4.0/epidatr/inst/doc/signal-discovery.Rmd | 912 +++---- epidatr-1.4.0/epidatr/inst/doc/signal-discovery.html | 1151 ++++---- epidatr-1.4.0/epidatr/inst/doc/versioned-data.Rmd | 269 +- epidatr-1.4.0/epidatr/inst/doc/versioned-data.html | 783 +----- epidatr-1.4.0/epidatr/man/assert_limit_param.Rd |only epidatr-1.4.0/epidatr/man/assert_report_time_param.Rd |only epidatr-1.4.0/epidatr/man/cast_api_queries.Rd | 23 epidatr-1.4.0/epidatr/man/covidcast_epidata.Rd | 6 epidatr-1.4.0/epidatr/man/epidata_aux.Rd | 25 epidatr-1.4.0/epidatr/man/epidata_meta.Rd | 6 epidatr-1.4.0/epidatr/man/fetch_args_list.Rd | 10 epidatr-1.4.0/epidatr/man/format_report_time_bound.Rd |only epidatr-1.4.0/epidatr/man/parse_api_datetimetz.Rd |only epidatr-1.4.0/epidatr/man/validate_version_query.Rd | 13 epidatr-1.4.0/epidatr/man/warn_limit_unsupported.Rd |only epidatr-1.4.0/epidatr/tests/testthat/_snaps/epidatacall.md | 10 epidatr-1.4.0/epidatr/tests/testthat/_snaps/fixtures.md | 59 epidatr-1.4.0/epidatr/tests/testthat/fixtures/aux-data.csv | 72 epidatr-1.4.0/epidatr/tests/testthat/fixtures/cast-archive.csv | 234 - epidatr-1.4.0/epidatr/tests/testthat/fixtures/cast-meta.json | 2 epidatr-1.4.0/epidatr/tests/testthat/fixtures/cast-snapshot.csv | 234 - epidatr-1.4.0/epidatr/tests/testthat/helper-endpoints.R | 1 epidatr-1.4.0/epidatr/tests/testthat/helper-fixtures.R | 4 epidatr-1.4.0/epidatr/tests/testthat/helper-live.R | 18 epidatr-1.4.0/epidatr/tests/testthat/helper-mocks.R | 12 epidatr-1.4.0/epidatr/tests/testthat/setup.R | 11 epidatr-1.4.0/epidatr/tests/testthat/test-check.R | 88 epidatr-1.4.0/epidatr/tests/testthat/test-endpoints.R | 194 - epidatr-1.4.0/epidatr/tests/testthat/test-epidatacall.R | 31 epidatr-1.4.0/epidatr/tests/testthat/test-live-cast.R |only epidatr-1.4.0/epidatr/tests/testthat/test-live.R | 125 epidatr-1.4.0/epidatr/tests/testthat/test-model.R | 21 epidatr-1.4.0/epidatr/vignettes/epidatr.Rmd | 579 ++-- epidatr-1.4.0/epidatr/vignettes/img/epidatr-archive-plot-1.png |only epidatr-1.4.0/epidatr/vignettes/img/epidatr-unnamed-chunk-11-1.png |only epidatr-1.4.0/epidatr/vignettes/img/epidatr-unnamed-chunk-12-1.png |only epidatr-1.4.0/epidatr/vignettes/img/epidatr-unnamed-chunk-13-1.png |only epidatr-1.4.0/epidatr/vignettes/img/epidatr-unnamed-chunk-7-1.png |only epidatr-1.4.0/epidatr/vignettes/img/epidatr-unnamed-chunk-8-1.png |binary epidatr-1.4.0/epidatr/vignettes/migration-guide.Rmd | 306 +- epidatr-1.4.0/epidatr/vignettes/signal-discovery.Rmd | 912 +++---- epidatr-1.4.0/epidatr/vignettes/versioned-data.Rmd | 269 +- 62 files changed, 5337 insertions(+), 4557 deletions(-)
Title: Extinction Date Estimation from Sighting Records
Description: Estimates the historic date of extinction of a species from a
time-ordered record of sighting events. Given a table of sighting counts
per year, computes extinction date estimators from the sighting-record
literature: optimal linear estimation and its Weibull extreme-value
persistence test (Roberts & Solow, 2003; Solow, 2005), constant-rate and
declining-rate persistence tests (Solow, 1993), a sighting-rate persistence
test comparable across records with different observation periods
(McInerny, Roberts, Davy & Cribb, 2006), a classical confidence interval
on the end of a temporal range (Strauss & Sadler, 1989), a
truncation-point extrapolation (Robson & Whitlock, 1964), and a
combinatorial persistence test based on inclusion-exclusion over
sighting-gap occupancy (Burgman, Grimson & Ferson, 1995). Also implements
a nonparametric endpoint test (Solow & Roberts, 2003), a sighting-interval
trend index (Jarić & Ebenhard, 2010), and reliability-adjusted inference
[...truncated...]
Author: Rodrigo Fonseca Villa [aut, cre]
Maintainer: Rodrigo Fonseca Villa <rodrigo03.villa@gmail.com>
Diff between EDE versions 0.1.0 dated 2026-08-07 and 0.2.0 dated 2026-09-21
DESCRIPTION | 22 - MD5 | 80 +++--- NAMESPACE | 29 +- NEWS.md |only R/burgman1995.R | 16 - R/ede-estimate.R | 23 + R/jaric-roberts2014.R |only R/jaric2010.R |only R/mcinerny2006.R | 168 ++++++------ R/ole.R | 39 ++ R/robson1964.R | 18 - R/sighting-data.R | 34 +- R/solow-roberts2003.R |only R/solow1993.R | 41 +-- R/solow1993b.R | 41 +-- R/solow2005.R | 82 ++---- R/strauss1989.R | 20 - README.md | 97 ++++--- inst/doc/EDE.R | 40 +-- inst/doc/EDE.Rmd | 283 ++++++++------------- inst/doc/EDE.html | 418 +++++++++++--------------------- man/burgman1995.Rd | 12 man/ede_estimate.Rd | 1 man/jaric2010.Rd |only man/jaric_roberts2014.Rd |only man/mcinerny2006.Rd | 4 man/ole.Rd | 8 man/robson1964.Rd | 11 man/sighting_data.Rd | 4 man/solow1993.Rd | 12 man/solow1993b.Rd | 9 man/solow2005.Rd | 21 - man/solow_roberts2003.Rd |only man/strauss1989.Rd | 13 tests/testthat/test-burgman1995.R | 27 +- tests/testthat/test-jaric-roberts2014.R |only tests/testthat/test-jaric2010.R |only tests/testthat/test-ole.R | 28 +- tests/testthat/test-print.R | 64 ++-- tests/testthat/test-robson1964.R | 63 ++-- tests/testthat/test-sighting-data.R | 17 - tests/testthat/test-solow-roberts2003.R |only tests/testthat/test-solow.R | 68 +++-- tests/testthat/test-solow1993b.R | 18 + tests/testthat/test-strauss1989.R | 80 +++--- vignettes/EDE.Rmd | 283 ++++++++------------- 46 files changed, 1061 insertions(+), 1133 deletions(-)
Title: ALTREP String Interoperability
Description: Provides infrastructure for interoperable ALTREP character vectors.
Producers of ALTREP string classes can register access methods,
allowing consumers to read supported character vectors through
a common interface without materializing them as ordinary R strings.
Also provides 'charvec', a reference ALTREP string implementation backed
by stable memory slices, with support for efficient and multithreaded
construction.
Author: Travers Ching [aut, cre, cph],
R Consortium [fnd]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between charport versions 0.1.0 dated 2026-09-17 and 0.1.1 dated 2026-09-21
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NEWS.md |only inst/include/charport/charvec/builder.h | 3 ++- inst/include/charport/charvec/store.h | 3 ++- inst/include/charport/interop/reader.h | 11 ++++++----- tests/test_charvec_semantics.R | 12 ------------ 7 files changed, 20 insertions(+), 28 deletions(-)
Title: Download Data from Brazil's Population Census
Description: Easy access to data from Brazil's population censuses. The package
provides a simple and efficient way to download and read the data
sets and the documentation of all the population censuses taken in
and after 1960 in the country. The package is built on top of the
'Arrow' platform <https://arrow.apache.org/docs/r/>, which allows
users to work with larger-than-memory census data using 'dplyr'
familiar functions. <https://arrow.apache.org/docs/r/articles/arrow.html#analyzing-arrow-data-with-dplyr>.
Author: Rafael H. M. Pereira [aut, cre] ,
Rogerio J. Barbosa [aut] ,
Pedro Herculano Souza [ctb],
Diego Rabatone Oliveira [ctb],
Neal Richardson [ctb],
Haydee Svab [ctb],
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between censobr versions 0.6.0 dated 2026-07-29 and 1.0.0 dated 2026-09-21
censobr-0.6.0/censobr/tests/tests_rafa/aaaaaa.R |only censobr-1.0.0/censobr/DESCRIPTION | 25 censobr-1.0.0/censobr/MD5 | 172 censobr-1.0.0/censobr/NAMESPACE | 13 censobr-1.0.0/censobr/NEWS.md | 110 censobr-1.0.0/censobr/R/add_labels_emigration.R | 423 censobr-1.0.0/censobr/R/add_labels_families.R | 430 censobr-1.0.0/censobr/R/add_labels_households.R | 2183 +++ censobr-1.0.0/censobr/R/add_labels_mortality.R | 214 censobr-1.0.0/censobr/R/add_labels_population.R | 6077 +++++++++- censobr-1.0.0/censobr/R/availability.R |only censobr-1.0.0/censobr/R/cache.R | 203 censobr-1.0.0/censobr/R/censobr.R | 24 censobr-1.0.0/censobr/R/data_dictionary.R | 139 censobr-1.0.0/censobr/R/docs_interview_manual.R | 21 censobr-1.0.0/censobr/R/docs_questionnaire.R | 26 censobr-1.0.0/censobr/R/import_microdata22_controlado.R |only censobr-1.0.0/censobr/R/merge_household.R | 333 censobr-1.0.0/censobr/R/onLoad.R | 9 censobr-1.0.0/censobr/R/read_emigration.R | 42 censobr-1.0.0/censobr/R/read_families.R | 35 censobr-1.0.0/censobr/R/read_households.R | 35 censobr-1.0.0/censobr/R/read_mortality.R | 43 censobr-1.0.0/censobr/R/read_population.R | 153 censobr-1.0.0/censobr/R/read_tracts.R | 20 censobr-1.0.0/censobr/R/utils.R | 357 censobr-1.0.0/censobr/README.md | 21 censobr-1.0.0/censobr/build/vignette.rds |binary censobr-1.0.0/censobr/inst/doc/censobr.R | 221 censobr-1.0.0/censobr/inst/doc/censobr.Rmd | 79 censobr-1.0.0/censobr/inst/doc/censobr.html | 165 censobr-1.0.0/censobr/inst/doc/census_tracts_data.R | 296 censobr-1.0.0/censobr/inst/doc/census_tracts_data.Rmd | 9 censobr-1.0.0/censobr/inst/doc/census_tracts_data.html | 588 censobr-1.0.0/censobr/inst/doc/documentation.R | 2 censobr-1.0.0/censobr/inst/doc/documentation.Rmd | 16 censobr-1.0.0/censobr/inst/doc/documentation.html | 29 censobr-1.0.0/censobr/inst/doc/larger_than_memory.R | 92 censobr-1.0.0/censobr/inst/doc/larger_than_memory.html | 105 censobr-1.0.0/censobr/inst/doc/microdata_2022.R |only censobr-1.0.0/censobr/inst/doc/microdata_2022.Rmd |only censobr-1.0.0/censobr/inst/doc/microdata_2022.html |only censobr-1.0.0/censobr/inst/extdata |only censobr-1.0.0/censobr/man/censobr.Rd | 2 censobr-1.0.0/censobr/man/censobr_cache.Rd | 16 censobr-1.0.0/censobr/man/data_dictionary.Rd | 21 censobr-1.0.0/censobr/man/delete_old_cache_dirs.Rd |only censobr-1.0.0/censobr/man/download_is_incomplete.Rd |only censobr-1.0.0/censobr/man/error_arg_not_declared.Rd |only censobr-1.0.0/censobr/man/error_columns_absent.Rd |only censobr-1.0.0/censobr/man/error_merge_households_needs_columns.Rd |only censobr-1.0.0/censobr/man/error_merge_households_years.Rd |only censobr-1.0.0/censobr/man/error_missing_datasets.Rd | 36 censobr-1.0.0/censobr/man/error_missing_years.Rd | 36 censobr-1.0.0/censobr/man/error_year_not_declared.Rd |only censobr-1.0.0/censobr/man/figures/censobr_hexsticker.R | 2 censobr-1.0.0/censobr/man/get_censobr_cache_dir.Rd | 54 censobr-1.0.0/censobr/man/import_microdata22.Rd |only censobr-1.0.0/censobr/man/interview_manual.Rd | 11 censobr-1.0.0/censobr/man/merge_household_var.Rd | 83 censobr-1.0.0/censobr/man/open_censobr_data.Rd |only censobr-1.0.0/censobr/man/prune_old_cache_once.Rd |only censobr-1.0.0/censobr/man/questionnaire.Rd | 12 censobr-1.0.0/censobr/man/read_emigration.Rd | 4 censobr-1.0.0/censobr/man/read_families.Rd | 4 censobr-1.0.0/censobr/man/read_households.Rd | 4 censobr-1.0.0/censobr/man/read_mortality.Rd | 4 censobr-1.0.0/censobr/man/read_population.Rd | 23 censobr-1.0.0/censobr/man/roxygen/templates/columns.R | 4 censobr-1.0.0/censobr/man/schemas_microdata22.Rd |only censobr-1.0.0/censobr/man/warning_microdata22_not_imported.Rd |only censobr-1.0.0/censobr/tests/tests_rafa/make_fixture_microdata22.R |only censobr-1.0.0/censobr/tests/tests_rafa/s3_test.R | 4 censobr-1.0.0/censobr/tests/tests_rafa/test_merge.R | 2 censobr-1.0.0/censobr/tests/tests_rafa/test_rafa.R | 334 censobr-1.0.0/censobr/tests/testthat/test_availability.R |only censobr-1.0.0/censobr/tests/testthat/test_cache_prune.R |only censobr-1.0.0/censobr/tests/testthat/test_data_dictionary.R | 113 censobr-1.0.0/censobr/tests/testthat/test_docs_interview_manual.R | 8 censobr-1.0.0/censobr/tests/testthat/test_docs_questionnaire.R | 13 censobr-1.0.0/censobr/tests/testthat/test_import_microdata22_controlado.R |only censobr-1.0.0/censobr/tests/testthat/test_labels_emigration.R | 19 censobr-1.0.0/censobr/tests/testthat/test_labels_families.R | 47 censobr-1.0.0/censobr/tests/testthat/test_labels_households.R | 71 censobr-1.0.0/censobr/tests/testthat/test_labels_mortality.R | 36 censobr-1.0.0/censobr/tests/testthat/test_labels_population.R | 207 censobr-1.0.0/censobr/tests/testthat/test_labels_types.R |only censobr-1.0.0/censobr/tests/testthat/test_read_emigration.R | 20 censobr-1.0.0/censobr/tests/testthat/test_read_families.R | 15 censobr-1.0.0/censobr/tests/testthat/test_read_households.R | 55 censobr-1.0.0/censobr/tests/testthat/test_read_mortality.R | 46 censobr-1.0.0/censobr/tests/testthat/test_read_population.R | 191 censobr-1.0.0/censobr/tests/testthat/test_read_tracts.R | 14 censobr-1.0.0/censobr/tests/testthat/test_set_censobr_cache_dir.R | 2 censobr-1.0.0/censobr/tests/testthat/test_z_censobr_cache.R | 24 censobr-1.0.0/censobr/tests/testthat/test_zz_graceful_failure.R |only censobr-1.0.0/censobr/vignettes/censobr.Rmd | 79 censobr-1.0.0/censobr/vignettes/census_tracts_data.Rmd | 9 censobr-1.0.0/censobr/vignettes/documentation.Rmd | 16 censobr-1.0.0/censobr/vignettes/microdata_2022.Rmd |only 100 files changed, 11651 insertions(+), 2700 deletions(-)
Title: Genomic Prediction of Hybrid Performance
Description: Performs genomic prediction of hybrid performance using eight statistical methods including GBLUP, BayesB, RKHS, PLS, LASSO, EN, LightGBM and XGBoost along with additive and additive-dominance models. Users are able to incorporate parental phenotypic information in all methods based on their specific needs. (Xu S et al(2017) <doi:10.1534/g3.116.038059>; Xu Y et al (2021) <doi: 10.1111/pbi.13458>).
Author: Yang Xu [aut, cre],
Guangning Yu [aut],
Yanru Cui [aut],
Shizhong Xu [aut],
Chenwu Xu [aut]
Maintainer: Yang Xu <xuyang_89@126.com>
Diff between predhy versions 2.1.2 dated 2025-04-05 and 2.1.3 dated 2026-09-21
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NAMESPACE | 1 + R/convertgen.R | 2 ++ R/cv.R | 4 +++- R/import_packages.R | 2 +- R/predhy.predict.R | 18 +++++++++++++----- R/predhy.predict_NCII.R | 28 +++++++++++++++++++++------- 8 files changed, 51 insertions(+), 24 deletions(-)
Title: A Suite of Routines for Working with Jordan Algebras
Description: A Jordan algebra is an algebraic object originally
designed to study observables in quantum mechanics. Jordan
algebras are commutative but non-associative; they satisfy the
Jordan identity. The package follows the ideas and notation of
K. McCrimmon (2004, ISBN:0-387-95447-3) "A Taste of Jordan
Algebras". To cite the package in publications, please use
Hankin (2023) <doi:10.48550/arXiv.2303.06062>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between jordan versions 1.0-6 dated 2024-07-04 and 1.0-6-1 dated 2026-09-21
DESCRIPTION | 9 +-- MD5 | 20 +++---- R/type_1.R | 129 ++++++++++++++++++++++++++------------------------- R/type_2.R | 91 ++++++++++++++++++++--------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/jordan.Rmd | 1 inst/doc/jordan.html | 62 ++++++++++++------------ man/coerce.Rd | 2 man/jordan.Rd | 18 ++++++- vignettes/jordan.Rmd | 1 11 files changed, 187 insertions(+), 146 deletions(-)
Title: Pretest Probability for Coronary Artery Disease
Description: An application to calculate a patient's pretest probability
(PTP) for obstructive Coronary Artery Disease (CAD) from a collection
of guidelines or studies. Guidelines usually comes from the American
Heart Association (AHA), American College of Cardiology (ACC) or
European Society of Cardiology (ESC). Examples of PTP scores that
comes from studies are the 2020 Winther et al. basic, Risk
Factor-weighted Clinical Likelihood (RF-CL) and Coronary Artery
Calcium Score-weighted Clinical Likelihood (CACS-CL) models
<doi:10.1016/j.jacc.2020.09.585>, 2019 Reeh et al. basic and clinical
models <doi:10.1093/eurheartj/ehy806> and 2017 Fordyce et al. PROMISE
Minimal-Risk Tool <doi:10.1001/jamacardio.2016.5501>. As diagnosis of
CAD involves a costly and invasive coronary angiography procedure for
patients, having a reliable PTP for CAD helps doctors to make better
decisions during patient management. This ensures high risk patients
can be diagnosed and treated early for CAD while [...truncated...]
Author: Jeremy Selva [aut, cre]
Maintainer: Jeremy Selva <jeremy1189.jjs@gmail.com>
Diff between pretestcad versions 1.1.0 dated 2025-09-03 and 1.2.0 dated 2026-09-21
DESCRIPTION | 9 LICENSE | 2 MD5 | 152 ++- NAMESPACE | 10 NEWS.md | 15 R/aha_2012_conference_ptp.R | 13 R/aha_2021_conference_ptp.R | 19 R/cad_consortium_ptp.R | 111 ++ R/chen_2018_ptp.R |only R/come_cct_2025_ptp.R |only R/confirm_ptp.R | 20 R/dcs_ptp.R | 183 +++- R/diamond_forrester_ptp.R | 4 R/esc_2013_conference_ptp.R | 4 R/esc_2019_conference_ptp.R | 34 R/esc_2024_conference_ptp.R | 251 +++--- R/harmonise.R | 25 R/lah_ptp.R | 71 + R/miller_ptp.R |only R/pmrs_ptp.R | 34 R/precise_ptp.R | 78 + R/rasmussen_ptp.R |only R/reeh_ptp.R | 53 + R/utilities.R | 16 R/winther_ptp.R | 114 ++ R/zuo_2025_ptp.R |only README.md | 16 inst/WORDLIST | 18 man/arg_match0_no_na_error_message.Rd | 102 +- man/calculate_aha_2012_tbl_9_ptp.Rd | 198 ++--- man/calculate_aha_2021_ptp.Rd | 237 +++--- man/calculate_cad1_2011_ptp.Rd | 167 ++-- man/calculate_cad2_2012_basic_ptp.Rd | 167 ++-- man/calculate_cad2_2012_clinical_ccs_ptp.Rd | 349 ++++---- man/calculate_cad2_2012_clinical_ptp.Rd | 338 ++++---- man/calculate_chen_2018_mfs_fig_3_ptp.Rd |only man/calculate_chen_2018_mfs_formula_ptp.Rd |only man/calculate_come_cct_2025_ptp.Rd |only man/calculate_come_cct_with_cta_2025_ptp.Rd |only man/calculate_come_cta_alone_2025_ptp.Rd |only man/calculate_confirm_2015_num_of_rf.Rd | 301 +++---- man/calculate_confirm_2015_ptp.Rd | 331 ++++---- man/calculate_dcs_1993_lm_cad_ptp.Rd | 318 ++++---- man/calculate_dcs_1993_pain_index.Rd | 381 ++++----- man/calculate_dcs_1993_risk_factor_index.Rd | 217 ++--- man/calculate_dcs_1993_severe_cad_ptp.Rd | 631 ++++++++-------- man/calculate_dcs_1993_sig_cad_ptp.Rd | 413 +++++----- man/calculate_dcs_1993_vascular_disease_index.Rd | 217 ++--- man/calculate_diamond_forrester_1979_ptp.Rd | 175 ++-- man/calculate_esc_2013_ptp.Rd | 142 +-- man/calculate_esc_2019_ptp.Rd | 256 +++--- man/calculate_esc_2024_fig_4_ptp.Rd | 446 +++++------ man/calculate_esc_2024_fig_4_ptp_simplfied.Rd | 178 ++-- man/calculate_esc_2024_num_of_rf.Rd | 307 +++---- man/calculate_esc_2024_symptom_score.Rd | 193 ++-- man/calculate_lah_2022_clinical_ptp.Rd | 334 ++++---- man/calculate_lah_2022_extended_ptp.Rd | 345 ++++---- man/calculate_miller_2023_lm_50_non_lm_70_cad_ptp.Rd |only man/calculate_miller_2023_vessel_50_cad_ptp.Rd |only man/calculate_precise_2021_clinical_ptp.Rd | 422 +++++----- man/calculate_precise_2021_simple_ptp.Rd | 348 ++++---- man/calculate_prms_2017_ptp.Rd | 461 ++++++----- man/calculate_rasmussen_2025_cacs_cl_ccta_ptp.Rd |only man/calculate_rasmussen_2025_rf_cl_ccta_ptp.Rd |only man/calculate_reeh_2019_basic_ptp.Rd | 185 ++-- man/calculate_reeh_2019_clinical_ptp.Rd | 305 ++++--- man/calculate_winther_2020_basic_ptp.Rd | 192 ++-- man/calculate_winther_2020_cacs_cl_ptp.Rd | 456 ++++++----- man/calculate_winther_2020_rf_cl_ptp.Rd | 440 ++++++----- man/calculate_zuo_2025_predict_ocad_ptp.Rd |only man/check_if_four_categories_are_mutually_exclusive.Rd | 176 ++-- man/check_if_integer.Rd | 94 +- man/check_if_non_negative.Rd | 94 +- man/check_if_numeric.Rd | 112 +- man/check_if_positive.Rd | 102 +- man/check_if_three_categories_are_mutually_exclusive.Rd | 150 +-- man/check_if_two_categories_are_mutually_exclusive.Rd | 132 +-- man/chr_quoted.Rd | 56 - man/harmonise_four_labels.Rd | 459 +++++------ man/harmonise_three_labels.Rd | 376 ++++----- man/harmonise_two_labels.Rd | 301 +++---- tests/testthat/test-chen_2018_ptp.R |only tests/testthat/test-come_cct_2025_ptp.R |only tests/testthat/test-rasmussen_ptp.R |only tests/testthat/test-winther_ptp.R | 1 tests/testthat/test-zuo_2025_ptp.R |only tests/testthat/test_miller_ptp.R |only 87 files changed, 6964 insertions(+), 5893 deletions(-)
Title: Estimation, Diagnostics and Visualization of Conditional
Marginal Effects
Description: Performs estimation, diagnostics, and visualization of conditional marginal effects and group average treatment effects of a treatment on an outcome across different values of a moderator. Optionally integrates with the 'mlr3extralearners' package for additional machine learning backends compatible with the double machine learning estimators. 'mlr3extralearners' is not on CRAN but can be obtained from <https://github.com/mlr-org/mlr3extralearners>.
Author: Yiqing Xu [aut, cre],
Jens Hainmueller [aut],
Jonathan Mummolo [aut],
Tianzhu Qin [aut],
Jiehan Liu [aut],
Ziyi Liu [aut]
Maintainer: Yiqing Xu <yiqingxu@stanford.edu>
Diff between interflex versions 1.4.0 dated 2026-04-10 and 1.4.1 dated 2026-09-21
interflex-1.4.0/interflex/tests/testthat/Rplots.pdf |only interflex-1.4.1/interflex/DESCRIPTION | 8 interflex-1.4.1/interflex/MD5 | 32 interflex-1.4.1/interflex/NAMESPACE | 2 interflex-1.4.1/interflex/NEWS.md | 16 interflex-1.4.1/interflex/R/estimate_cme_plr.R | 15 interflex-1.4.1/interflex/R/interflex.R | 27 interflex-1.4.1/interflex/R/kernel.R | 6319 +++++----- interflex-1.4.1/interflex/R/lasso.R | 8 interflex-1.4.1/interflex/R/plot_pool.R | 12 interflex-1.4.1/interflex/R/predict.R | 2 interflex-1.4.1/interflex/R/raw.R | 12 interflex-1.4.1/interflex/R/uniform.R | 11 interflex-1.4.1/interflex/inst |only interflex-1.4.1/interflex/man/inter_test.Rd | 8 interflex-1.4.1/interflex/man/interflex.Rd | 9 interflex-1.4.1/interflex/tests/testthat/test-bw-select.R |only interflex-1.4.1/interflex/tests/testthat/test-dml.R | 1 interflex-1.4.1/interflex/tests/testthat/test-kernel-adaptive-bw.R |only 19 files changed, 3569 insertions(+), 2913 deletions(-)
Title: Orthogonal Nonlinear Least-Squares Regression
Description: Fits n-dimensional data by means of orthogonal nonlinear least-squares using Levenberg-Marquardt minimization and provides functionality for fit diagnostics and plotting. Delivers the same results as the 'ODRPACK' Fortran implementation described in Boggs et al. (1989) <doi:10.1145/76909.76913>, but is implemented in pure R.
Author: Andrej-Nikolai Spiess [aut, cre]
Maintainer: Andrej-Nikolai Spiess <draspiess@gmail.com>
Diff between onls versions 0.1-4 dated 2025-09-01 and 0.2 dated 2026-09-21
onls-0.1-4/onls/inst/doc/onls.R |only onls-0.1-4/onls/inst/doc/onls.Rnw |only onls-0.1-4/onls/inst/doc/onls.pdf |only onls-0.1-4/onls/vignettes/onls.Rnw |only onls-0.2/onls/DESCRIPTION | 12 onls-0.2/onls/MD5 | 48 - onls-0.2/onls/NAMESPACE | 10 onls-0.2/onls/NEWS | 40 + onls-0.2/onls/R/NIST.R | 28 - onls-0.2/onls/R/S3_functions.R | 559 +++++++++++++++------- onls-0.2/onls/R/fit_functions.R | 188 +++++-- onls-0.2/onls/R/onls.R | 744 ++++++++++++++++++------------ onls-0.2/onls/build/partial.rdb |binary onls-0.2/onls/build/vignette.rds |binary onls-0.2/onls/inst/doc/onls-vignette.R |only onls-0.2/onls/inst/doc/onls-vignette.Rmd |only onls-0.2/onls/inst/doc/onls-vignette.html |only onls-0.2/onls/man/NIST.Rd | 2 onls-0.2/onls/man/check_o.Rd | 84 ++- onls-0.2/onls/man/confint.onls.Rd | 39 - onls-0.2/onls/man/deviance_o.Rd | 9 onls-0.2/onls/man/logLik_o.Rd | 36 + onls-0.2/onls/man/onls.Rd | 418 ++++++++++++---- onls-0.2/onls/man/plot.onls.Rd | 112 +++- onls-0.2/onls/man/print.onls.Rd | 2 onls-0.2/onls/man/residuals_o.Rd | 9 onls-0.2/onls/man/summary.onls.Rd | 27 - onls-0.2/onls/man/x0.Rd | 18 onls-0.2/onls/vignettes/onls-vignette.Rmd |only 29 files changed, 1635 insertions(+), 750 deletions(-)
Title: Goodness-of-Fit Test for Weibull Distribution (Weibullness)
Description: Conducts a goodness-of-fit test for the Weibull distribution (referred to as the weibullness test) and furnishes parameter estimations for both the two-parameter and three-parameter Weibull distributions.
Notably, the threshold parameter is derived through correlation from the Weibull plot. Additionally, this package conducts goodness-of-fit assessments for the exponential, Gumbel, and inverse Weibull distributions, accompanied by parameter estimations.
For more details, see Park (2017) <doi:10.23055/ijietap.2017.24.4.2848>,
Park (2018) <doi:10.1155/2018/6056975>, and Park (2023) <doi:10.3390/math11143156>.
This work was supported by the National Research Foundation of Korea (NRF) grants funded by the Korea government (No. 2022R1A2C1091319).
Author: Chanseok Park [aut, cre]
Maintainer: Chanseok Park <statpnu@gmail.com>
Diff between weibullness versions 1.24.1 dated 2024-01-09 and 2.26.9 dated 2026-09-21
weibullness-1.24.1/weibullness/man/Wdata.Rd |only weibullness-2.26.9/weibullness/DESCRIPTION | 26 +-- weibullness-2.26.9/weibullness/MD5 | 84 +++++----- weibullness-2.26.9/weibullness/NAMESPACE | 10 - weibullness-2.26.9/weibullness/R/Estimate.Gumbel.R | 28 +++ weibullness-2.26.9/weibullness/R/Estimate.RM.R |only weibullness-2.26.9/weibullness/R/Estimate.Weibull.R | 74 +++++++- weibullness-2.26.9/weibullness/R/Estimate.inverse.Weibull.R | 4 weibullness-2.26.9/weibullness/build/partial.rdb |binary weibullness-2.26.9/weibullness/data/Wdata-bunzip2.rda |binary weibullness-2.26.9/weibullness/inst/CITATION | 20 +- weibullness-2.26.9/weibullness/inst/NEWS.Rd | 29 ++- weibullness-2.26.9/weibullness/man/Exponential.ANOVA.Quantiles.Rd | 4 weibullness-2.26.9/weibullness/man/Gumbel.Plot.Quantiles.Rd | 4 weibullness-2.26.9/weibullness/man/IW.Plot.Quantiles.Rd | 10 - weibullness-2.26.9/weibullness/man/Weibull.Plot.Quantiles.Rd | 8 weibullness-2.26.9/weibullness/man/Weibulldata.Rd |only weibullness-2.26.9/weibullness/man/breakdown.pwrm.Rd |only weibullness-2.26.9/weibullness/man/ep.plot.Rd | 3 weibullness-2.26.9/weibullness/man/ep.test.Rd | 6 weibullness-2.26.9/weibullness/man/ep.test.critical.Rd | 7 weibullness-2.26.9/weibullness/man/ep.test.pvalue.Rd | 7 weibullness-2.26.9/weibullness/man/gp.plot.Rd | 3 weibullness-2.26.9/weibullness/man/gp.test.Rd | 7 weibullness-2.26.9/weibullness/man/gp.test.critical.Rd | 7 weibullness-2.26.9/weibullness/man/gp.test.pvalue.Rd | 7 weibullness-2.26.9/weibullness/man/gumbel.gp.Rd | 15 + weibullness-2.26.9/weibullness/man/gumbel.mle.Rd |only weibullness-2.26.9/weibullness/man/inverseWeibull.Rd | 1 weibullness-2.26.9/weibullness/man/invweibull.mle.Rd | 9 - weibullness-2.26.9/weibullness/man/iwp.plot.Rd | 1 weibullness-2.26.9/weibullness/man/iwp.test.Rd | 22 -- weibullness-2.26.9/weibullness/man/iwp.test.critical.Rd | 5 weibullness-2.26.9/weibullness/man/iwp.test.pvalue.Rd | 6 weibullness-2.26.9/weibullness/man/regr.pwrm.Rd |only weibullness-2.26.9/weibullness/man/regr.rm.Rd |only weibullness-2.26.9/weibullness/man/weibull.ic.Rd | 7 weibullness-2.26.9/weibullness/man/weibull.mle.Rd | 6 weibullness-2.26.9/weibullness/man/weibull.pwrm.Rd |only weibullness-2.26.9/weibullness/man/weibull.rm.Rd | 8 weibullness-2.26.9/weibullness/man/weibull.seki.Rd |only weibullness-2.26.9/weibullness/man/weibull.threshold.Rd | 12 - weibullness-2.26.9/weibullness/man/weibull.wp.Rd | 23 -- weibullness-2.26.9/weibullness/man/wmedian.Rd |only weibullness-2.26.9/weibullness/man/wp.plot.Rd | 8 weibullness-2.26.9/weibullness/man/wp.test.Rd | 15 - weibullness-2.26.9/weibullness/man/wp.test.critical.Rd | 5 weibullness-2.26.9/weibullness/man/wp.test.pvalue.Rd | 6 48 files changed, 289 insertions(+), 208 deletions(-)
Title: Liquid Glass Design Themes for 'shiny' Applications
Description: Provides drop-in Liquid Glass themes for 'shiny'. Call
glass_theme() and pass the result as theme = to fluidPage(),
navbarPage(), or any 'bslib'-aware page function to get
translucent surfaces, backdrop blur, and system typography on
'Bootstrap' components. Includes light and dark presets with
runtime switching and an OS-following 'auto' mode, an iOS-style
intensity control from Ultra Clear to Tinted, optional
persistence of the look, named wallpaper scenes, helpers to
match 'ggplot2', 'plotly', 'gt', and 'DT' output to the glass pack,
a flatten mode for print and screenshots, and documented CSS tokens.
Author: Eric Anderson [aut, cre, cph]
Maintainer: Eric Anderson <eric.ray.anderson@gmail.com>
Diff between shinyglass versions 0.3.0 dated 2026-09-09 and 0.4.0 dated 2026-09-20
DESCRIPTION | 11 MD5 | 86 ++-- NAMESPACE | 10 NEWS.md | 61 ++ R/glass-flatten.R |only R/glass-intensity.R | 6 R/glass-page.R | 10 R/glass-plots.R | 162 ++++++- R/glass-theme.R | 146 +++++-- R/glass-tokens.R |only R/shinyglass-package.R | 13 README.md | 21 - build/vignette.rds |binary inst/WORDLIST | 94 +++- inst/doc/compatibility.Rmd | 7 inst/doc/compatibility.html | 18 inst/doc/playground.Rmd | 2 inst/doc/playground.html | 7 inst/doc/theming.R | 19 inst/doc/theming.Rmd | 106 ++++- inst/doc/theming.html | 220 ++++++++-- inst/examples/bslib-dashboard.R | 57 +- inst/examples/chrome-kitchen-sink.R | 4 inst/examples/intensity-slider-demo.R | 5 inst/examples/plotly-gt-demo.R | 28 - inst/js/shiny-glass.js | 315 ++++++++++++++- inst/scss/glass.scss | 707 +++++++++++++++++++++++++++++++--- man/dt_options_glass.Rd |only man/glass_add_tokens.Rd |only man/glass_css_tokens.Rd |only man/glass_flatten.Rd |only man/glass_intensity_slider.Rd | 4 man/glass_page.Rd | 6 man/glass_plot_colors.Rd | 9 man/glass_plot_surface_input.Rd |only man/glass_scene_input.Rd |only man/glass_scenes.Rd |only man/glass_theme.Rd | 43 +- man/glass_token_pack.Rd |only man/gt_theme_glass.Rd | 9 man/observe_glass_plot_surface.Rd |only man/observe_glass_scene.Rd |only man/plotly_glass.Rd | 9 man/shinyglass-package.Rd | 12 man/theme_glass.Rd | 13 man/update_glass_theme.Rd | 14 tests/testthat/test-glass-theme.R | 158 +++++++ vignettes/compatibility.Rmd | 7 vignettes/playground.Rmd | 2 vignettes/theming.Rmd | 106 ++++- 50 files changed, 2157 insertions(+), 350 deletions(-)
Title: Simulation and Analysis Tools for Clinical Dose Response
Modeling
Description: Bayesian and ML Emax model fitting, graphics and simulation for clinical dose
response. The summary data from the dose response meta-analyses in
Thomas, Sweeney, and Somayaji (2014) <doi:10.1080/19466315.2014.924876> and
Thomas and Roy (2016) <doi:10.1080/19466315.2016.1256229>
Wu, Banerjee, Jin, Menon, Martin, and Heatherington(2017) <doi:10.1177/0962280216684528>
are included
in the package. The prior distributions for the Bayesian analyses default to
the posterior predictive distributions derived from these references.
Author: Neal Thomas [aut, cre] ,
Jing Wu [aut],
Mike K. Smith [aut],
Budhaditya Goswami [aut],
Satrajit Roychoudhury [aut]
Maintainer: Neal Thomas <snthomas99@gmail.com>
Diff between clinDR versions 2.5.2 dated 2025-10-02 and 2.5.3 dated 2026-09-20
clinDR-2.5.2/clinDR/inst/tests/Rplots.pdf |only clinDR-2.5.3/clinDR/DESCRIPTION | 22 clinDR-2.5.3/clinDR/MD5 | 113 clinDR-2.5.3/clinDR/NAMESPACE | 2 clinDR-2.5.3/clinDR/R/fitEmaxB.R | 42 clinDR-2.5.3/clinDR/R/plot.emaxsimobj.R | 12 clinDR-2.5.3/clinDR/R/plot.fitEmax.R | 24 clinDR-2.5.3/clinDR/R/plot.plotB.R | 24 clinDR-2.5.3/clinDR/R/plotD.R | 6 clinDR-2.5.3/clinDR/R/predict.fitEmaxB.R | 11 clinDR-2.5.3/clinDR/R/print.emaxPrior.R | 1132 ++++++---- clinDR-2.5.3/clinDR/R/randomEmax.R | 2 clinDR-2.5.3/clinDR/build |only clinDR-2.5.3/clinDR/data/metaData.rda |binary clinDR-2.5.3/clinDR/inst/doc |only clinDR-2.5.3/clinDR/inst/models/mrmodel.stan | 19 clinDR-2.5.3/clinDR/inst/shiny/emaxPrior_control.html | 218 + clinDR-2.5.3/clinDR/inst/tests/currentPriors.RData |only clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.densityplot_new.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.densityplot_old.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.emaxsimBobj_new.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.emaxsimBobj_old.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.emaxsimobj_new.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.emaxsimobj_old.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.fitEmaxB_new.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.fitEmaxB_old.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.fitEmax_new.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.fitEmax_old.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.plotB_new.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.plotB_old.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.plotD_new.pdf |binary clinDR-2.5.3/clinDR/inst/tests/extraGraphics/pdfoutput/output.plotD_old.pdf |binary clinDR-2.5.3/clinDR/inst/tests/runIndvidualTests.R | 1 clinDR-2.5.3/clinDR/inst/tests/runIndvidualTests2.R | 46 clinDR-2.5.3/clinDR/inst/tests/test.checkMonoEmaxlocalParm.R | 28 clinDR-2.5.3/clinDR/inst/tests/test.compareTvsMix.R |only clinDR-2.5.3/clinDR/inst/tests/test.compareTvsMix2.R |only clinDR-2.5.3/clinDR/inst/tests/test.emaxsimBlocalParm.R | 62 clinDR-2.5.3/clinDR/inst/tests/test.emaxsimBlocalParmMix.R |only clinDR-2.5.3/clinDR/inst/tests/test.fitEmaxBlocalParm.R | 87 clinDR-2.5.3/clinDR/inst/tests/test.fitEmaxBlocalParmMix.R |only clinDR-2.5.3/clinDR/inst/tests/test.fitEmaxBlocalParmtmp.R |only clinDR-2.5.3/clinDR/inst/tests/test.print.emaxPrior.R | 196 + clinDR-2.5.3/clinDR/man/emaxPrior.control.Rd | 267 +- clinDR-2.5.3/clinDR/man/print.emaxPrior.Rd | 101 clinDR-2.5.3/clinDR/man/randomEmax.Rd | 3 clinDR-2.5.3/clinDR/man/runSimulations.Rd | 3 clinDR-2.5.3/clinDR/vignettes |only 48 files changed, 1631 insertions(+), 790 deletions(-)
Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic
regression, naive Bayes, neural networks, classification and regression trees,
model evaluation, collaborative filtering, decision analysis, and simulation.
The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.model versions 1.6.11 dated 2026-04-15 and 1.6.12 dated 2026-09-20
radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/cf_summary.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/dtree_model.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/dtree_plot_final.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/dtree_plot_initial.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/dtree_sensitivity.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/evalbin_confusion.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/evalbin_lift_gains.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/evalbin_logistic.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/evalreg_nn.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/evalreg_summary_plot.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/logistic_dvd-full.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/logistic_dvd.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/logistic_plot.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/logistic_predict.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/logistic_predict_data.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/logistic_summary.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/mnl_choice_shares.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/mnl_plot.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/mnl_predict.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/mnl_summary.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_catalog_F_critical.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_catalog_F_test.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_catalog_prob_calc.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_catalog_summary.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_diamonds_corr.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_diamonds_dashboard.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_diamonds_hist.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_diamonds_res_vs_pred.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_diamonds_scatter.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_ideal_corr.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_ideal_dashboard.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_ideal_hist.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_ideal_res_vs_pred.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_ideal_scatter.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_ideal_summary.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_corr.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_dashboard.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_hist.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_res_vs_pred.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_scatter.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_summary.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/regress_log_diamonds_viz_scatter.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/simulater_repeat.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/simulater_repeat_plot.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/simulater_sim.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/simulater_sim_plot.png |only radiant.model-1.6.11/radiant.model/inst/app/tools/help/figures/simulater_view.png |only radiant.model-1.6.12/radiant.model/DESCRIPTION | 10 radiant.model-1.6.12/radiant.model/MD5 | 105 --- radiant.model-1.6.12/radiant.model/NAMESPACE | 310 +++++----- radiant.model-1.6.12/radiant.model/NEWS.md | 6 radiant.model-1.6.12/radiant.model/R/crtree.R | 8 radiant.model-1.6.12/radiant.model/R/logistic.R | 17 radiant.model-1.6.12/radiant.model/R/mnl.R | 10 radiant.model-1.6.12/radiant.model/R/nn.R | 31 - radiant.model-1.6.12/radiant.model/R/regress.R | 20 radiant.model-1.6.12/radiant.model/inst/app/tools/analysis/logistic_ui.R | 24 radiant.model-1.6.12/radiant.model/inst/app/tools/analysis/regress_ui.R | 24 radiant.model-1.6.12/radiant.model/inst/app/tools/help/crs.md | 2 radiant.model-1.6.12/radiant.model/inst/app/tools/help/dtree.Rmd | 8 radiant.model-1.6.12/radiant.model/inst/app/tools/help/dtree.md | 8 radiant.model-1.6.12/radiant.model/inst/app/tools/help/evalbin.md | 8 radiant.model-1.6.12/radiant.model/inst/app/tools/help/evalreg.md | 6 radiant.model-1.6.12/radiant.model/inst/app/tools/help/logistic.Rmd | 14 radiant.model-1.6.12/radiant.model/inst/app/tools/help/logistic.md | 14 radiant.model-1.6.12/radiant.model/inst/app/tools/help/mnl.Rmd | 8 radiant.model-1.6.12/radiant.model/inst/app/tools/help/mnl.md | 8 radiant.model-1.6.12/radiant.model/inst/app/tools/help/regress.Rmd | 46 - radiant.model-1.6.12/radiant.model/inst/app/tools/help/regress.md | 46 - radiant.model-1.6.12/radiant.model/inst/app/tools/help/simulater.Rmd | 10 radiant.model-1.6.12/radiant.model/inst/app/tools/help/simulater.md | 10 radiant.model-1.6.12/radiant.model/man/crtree.Rd | 2 radiant.model-1.6.12/radiant.model/man/logistic.Rd | 9 radiant.model-1.6.12/radiant.model/man/mnl.Rd | 2 radiant.model-1.6.12/radiant.model/man/nn.Rd | 2 radiant.model-1.6.12/radiant.model/man/regress.Rd | 6 radiant.model-1.6.12/radiant.model/tests/testthat/test_nn_predict.R |only radiant.model-1.6.12/radiant.model/tests/testthat/test_standardize.R |only 78 files changed, 436 insertions(+), 338 deletions(-)
Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving,
viewing, visualizing, summarizing, transforming, and combining data. It also
contains functionality to generate reproducible reports of the analyses
conducted in the application.
Author: Vincent Nijs [aut, cre],
Niklas von Hertzen [aut]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.data versions 1.6.8 dated 2025-09-16 and 1.6.9 dated 2026-09-20
DESCRIPTION | 15 +- MD5 | 24 ++-- NAMESPACE | 262 +++++++++++++++++++++++++------------------- NEWS.md | 4 R/explore.R | 2 R/pivotr.R | 2 R/view.R | 4 README.md | 4 inst/app/radiant.R | 9 + inst/app/tools/app/about.md | 4 man/dtab.data.frame.Rd | 2 man/reexports.Rd | 18 +-- tests/testthat/test_funs.R | 10 - 13 files changed, 206 insertions(+), 154 deletions(-)
Title: G-Functions
Description: Modified versions of the lag() and summary() functions: glag() and gsummary(). The prefix 'g' is a reminder of who to blame if things do not work as they should.
Author: Genaro Sucarrat [aut, cre]
Maintainer: Genaro Sucarrat <gsucarrat@gmail.com>
Diff between gfunctions versions 1.2 dated 2026-08-21 and 1.3 dated 2026-09-20
DESCRIPTION | 8 +-- MD5 | 9 ++- NEWS | 14 +++++ R/gfunctions-internal.R |only R/gfunctions-source-code.R | 108 +++++++++++++++++++++++++++++++++++++++------ man/gfunctions-package.Rd | 6 +- 6 files changed, 121 insertions(+), 24 deletions(-)
Title: Simulate Experimental and Behavioural Data from a Portable
Design Specification
Description: Generative simulation of experimental and behavioural data sets from a
portable JavaScript Object Notation (JSON) design specification shared with the
'Python' package of the same name.
Supports user-specified fixed effect sizes, crossed by-subject and by-item random
intercepts and slopes, predictors measured with error, realistic response families
(Gaussian, lognormal, shifted lognormal, ex-Gaussian, Bernoulli, Poisson, ordinal and
Beta), and simulation-based power and precision-based design analysis, including the
Type S and Type M errors of Gelman and Carlin (2014)
<doi:10.1177/1745691614551642> and a region of practical equivalence. A shared
cross-language random-number generator means that, given the same specification and
seed, the R and 'Python' implementations produce identical data: exactly for the
Gaussian family and for any family with rounding set, and to within the last unit in
the last place for families applying a transcendental function to the linear
predictor, wh [...truncated...]
Author: Pablo Bernabeu [aut, cre]
Maintainer: Pablo Bernabeu <pcbernabeu@gmail.com>
Diff between pilotr versions 0.3.0 dated 2026-09-12 and 0.3.1 dated 2026-09-20
DESCRIPTION | 6 MD5 | 12 NEWS.md | 835 +++++++++++++++++++++++---------------------- R/spec_builder.R | 117 +++--- man/generate_r_script.Rd | 9 man/spec_json.Rd | 16 tests/testthat/test-core.R | 56 +++ 7 files changed, 587 insertions(+), 464 deletions(-)
Title: Mode Estimation
Description: Provides estimators of the mode of univariate
data or univariate distributions.
Author: Paul Poncet [aut, cre]
Maintainer: Paul Poncet <paulponcet@yahoo.fr>
Diff between modeest versions 2.4.0 dated 2019-11-18 and 2.5.0 dated 2026-09-20
DESCRIPTION | 11 MD5 | 72 ++--- NAMESPACE | 62 ++-- NEWS.md | 71 ++--- R/asselin.R | 169 +++++------- R/deal.ties.R | 33 +- R/distrMode.R | 653 ++++++++++++++++++---------------------------- R/distributionsList.R | 12 R/grenander.R | 170 +++++------- R/hrm.R | 126 ++++---- R/hsm.R | 173 +++++------- R/lientz.R | 235 +++++++--------- R/meanshift.R | 141 ++++------ R/methodsList.R | 12 R/mlv.R | 276 ++++++++----------- R/naive.R | 79 ++--- R/parzen.R | 168 +++++------ R/skewness.R | 113 +++----- R/tsybakov.R | 167 +++++------ R/venter.R | 218 +++++++-------- R/vieu.R | 116 +++----- man/asselin.Rd | 102 +++---- man/distrMode.Rd | 687 ++++++++++++++++++++----------------------------- man/grenander.Rd | 180 ++++++------ man/hrm.Rd | 160 +++++------ man/hsm.Rd | 160 +++++------ man/lientz.Rd | 226 ++++++++-------- man/meanshift.Rd | 134 ++++----- man/mlv.Rd | 256 +++++++++--------- man/modeest-package.Rd | 2 man/naive.Rd | 116 ++++---- man/parzen.Rd | 194 ++++++------- man/reexports.Rd | 32 +- man/skewness.Rd | 138 ++++----- man/tsybakov.Rd | 204 +++++++------- man/venter.Rd | 220 +++++++-------- man/vieu.Rd | 122 ++++---- 37 files changed, 2833 insertions(+), 3177 deletions(-)
Title: Block Designs for Observational Studies
Description: Creates block designs of fixed size J with at least one treated
and control unit per block. Blocks larger than pairs better
distinguish effects caused by a treatment from unmeasured confounding in
assignment of individuals to treatment. Somewhat counterintuitively,
blocks larger than pairs can use more units while attaining better
covariate balance and block homogeneity. A forthcoming manuscript
by Brumberg and Rosenbaum details the design.
Author: Katherine Brumberg [aut, cre] ,
Paul Rosenbaum [aut]
Maintainer: Katherine Brumberg <kbrum@umich.edu>
Diff between observationalBlocks versions 1.0.0 dated 2026-04-10 and 1.1.0 dated 2026-09-20
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 22 +++++++++++++--------- NEWS.md | 5 +++++ R/blockMatch.R | 11 +++++++---- R/seedMatch.R | 9 +++++---- man/blockMatch.Rd | 7 ++++--- tests/testthat/test-blockMatch.R | 23 +++++++++++++++++++++++ 8 files changed, 68 insertions(+), 31 deletions(-)
More information about observationalBlocks at CRAN
Permanent link
Title: Multivariate Spatio-Temporal Models using Structural Equations
Description: Fits a wide variety of multivariate spatio-temporal models
with simultaneous and lagged interactions among variables (including
vector autoregressive spatio-temporal ('VAST') dynamics)
for areal, continuous, or network spatial domains.
It includes time-variable, space-variable, and space-time-variable
interactions using dynamic structural equation models ('DSEM')
as expressive interface, and the 'mgcv' package to specify splines
via the formula interface. See Thorson et al. (2025)
<doi:10.1111/geb.70035> for more details.
Author: James T. Thorson [aut, cre] ,
Sean C. Anderson [aut]
Maintainer: James T. Thorson <James.Thorson@noaa.gov>
This is a re-admission after prior archival of version 1.6.2 dated 2026-07-14
Diff between tinyVAST versions 1.6.2 dated 2026-07-14 and 1.6.3 dated 2026-09-20
tinyVAST-1.6.2/tinyVAST/inst/doc/dsem.R |only tinyVAST-1.6.2/tinyVAST/inst/doc/dsem.Rmd |only tinyVAST-1.6.2/tinyVAST/inst/doc/dsem.html |only tinyVAST-1.6.2/tinyVAST/inst/doc/mgcv.R |only tinyVAST-1.6.2/tinyVAST/inst/doc/mgcv.Rmd |only tinyVAST-1.6.2/tinyVAST/inst/doc/mgcv.html |only tinyVAST-1.6.2/tinyVAST/inst/doc/multiple_data.R |only tinyVAST-1.6.2/tinyVAST/inst/doc/multiple_data.Rmd |only tinyVAST-1.6.2/tinyVAST/inst/doc/multiple_data.html |only tinyVAST-1.6.2/tinyVAST/inst/doc/spatial.R |only tinyVAST-1.6.2/tinyVAST/inst/doc/spatial.Rmd |only tinyVAST-1.6.2/tinyVAST/inst/doc/spatial.html |only tinyVAST-1.6.2/tinyVAST/inst/doc/spatial_factor_analysis.R |only tinyVAST-1.6.2/tinyVAST/inst/doc/spatial_factor_analysis.Rmd |only tinyVAST-1.6.2/tinyVAST/inst/doc/spatial_factor_analysis.html |only tinyVAST-1.6.2/tinyVAST/vignettes/dsem.Rmd |only tinyVAST-1.6.2/tinyVAST/vignettes/mgcv.Rmd |only tinyVAST-1.6.2/tinyVAST/vignettes/multiple_data.Rmd |only tinyVAST-1.6.2/tinyVAST/vignettes/spatial.Rmd |only tinyVAST-1.6.2/tinyVAST/vignettes/spatial_factor_analysis.Rmd |only tinyVAST-1.6.3/tinyVAST/DESCRIPTION | 8 tinyVAST-1.6.3/tinyVAST/MD5 | 36 --- tinyVAST-1.6.3/tinyVAST/NEWS.md | 4 tinyVAST-1.6.3/tinyVAST/R/fit.R | 2 tinyVAST-1.6.3/tinyVAST/R/internal.R | 2 tinyVAST-1.6.3/tinyVAST/build/vignette.rds |binary tinyVAST-1.6.3/tinyVAST/inst/doc/model-description.html | 97 ++++------ tinyVAST-1.6.3/tinyVAST/src/utils.h | 2 tinyVAST-1.6.3/tinyVAST/tests/testthat.R | 4 29 files changed, 66 insertions(+), 89 deletions(-)
Title: Simulate Parametric and Semi-Parametric Survival Times with
Object-Oriented Design
Description: Simulate parametric and semi-parametric survival times through a
consistent, reusable interface for each distribution, using an
object-oriented design. Supported distributions include Exponential,
Weibull, Gompertz, Log-Logistic, Log-Normal, and Piecewise Exponential.
Random variates can be generated under Proportional Hazards, Accelerated
Failure Time, and Extended Hazards models, as well as under renewal and
non-homogeneous Poisson recurrent event processes, following the methods
described by Bender (2003) <doi:10.5282/UBM/EPUB.1716> and Leemis (1987)
in Operations Research, 35(6), 892-894.
Author: Aponte John [aut, cre, cph]
Maintainer: Aponte John <john.j.aponte@gmail.com>
Diff between survobj versions 3.1.1 dated 2024-08-16 and 3.2.0 dated 2026-09-20
DESCRIPTION | 26 +- MD5 | 106 ++++---- NAMESPACE | 56 ++-- NEWS.md | 32 ++ R/exponential_class.R | 12 R/gompertz_class.R | 34 +- R/loglogistic_class.R | 18 - R/lognormal_class.R | 37 +-- R/multiple_events.R | 10 R/piecewise_exponential_class.R | 32 +- R/survival_class.R | 69 +++-- R/utils.R | 12 R/weibull_class.R | 16 - README.md | 167 +++++++++---- build/partial.rdb |only build/vignette.rds |binary inst/WORDLIST | 31 +- inst/doc/example_distributions.Rmd | 82 +++--- inst/doc/example_distributions.html | 398 ++++++++++++++++----------------- inst/doc/simulation_distributions.R | 23 + inst/doc/simulation_distributions.Rmd | 106 ++++++++ inst/doc/simulation_distributions.html | 159 ++++++++++--- inst/doc/simulation_recurent.R | 136 +++++------ inst/doc/simulation_recurent.Rmd | 8 inst/doc/simulation_recurent.html | 81 +++--- inst/doc/simulation_trials.R | 72 ++--- inst/doc/simulation_trials.Rmd | 14 - inst/doc/simulation_trials.html | 47 +-- inst/doc/simulation_trials2.R | 76 +++--- inst/doc/simulation_trials2.Rmd | 28 +- inst/doc/simulation_trials2.html | 70 ++--- man/SURVIVAL.Rd | 27 +- man/censor_event.Rd | 8 man/fx_h_time.Rd | 4 man/is_single_number.Rd | 2 man/nhpp.Rd | 6 man/renewal.Rd | 4 man/s_exponential.Rd | 2 man/s_factory.Rd | 12 man/s_gompertz.Rd | 18 + man/s_loglogistic.Rd | 6 man/s_lognormal.Rd | 8 man/s_piecewise.Rd | 14 - man/s_weibull.Rd | 6 man/survobj-package.Rd | 9 tests/testthat/test_s_gompertz.R | 31 ++ tests/testthat/test_s_lognormal.R | 37 +++ tests/testthat/test_s_piecewise.R | 26 +- tests/testthat/test_survival_class.R |only vignettes/example_distributions.Rmd | 82 +++--- vignettes/references.bib | 25 ++ vignettes/simulation_distributions.Rmd | 106 ++++++++ vignettes/simulation_recurent.Rmd | 8 vignettes/simulation_trials.Rmd | 14 - vignettes/simulation_trials2.Rmd | 28 +- 55 files changed, 1517 insertions(+), 924 deletions(-)
Title: Smoothed Empirical Likelihood
Description: Empirical likelihood methods for asymptotically efficient
estimation of models based on conditional or unconditional moment
restrictions; see Kitamura, Tripathi & Ahn (2004)
<doi:10.1111/j.1468-0262.2004.00550.x> and Owen (2013)
<doi:10.1002/cjs.11183>.
Kernel-based non-parametric methods for density/regression estimation and
numerical routines for empirical likelihood maximisation are implemented in
'Rcpp' for speed.
Author: Andrei Victorovitch Kostyrka [aut, cre]
Maintainer: Andrei Victorovitch Kostyrka <andrei.kostyrka@gmail.com>
Diff between smoothemplik versions 0.0.17 dated 2025-10-29 and 0.0.18 dated 2026-09-20
smoothemplik-0.0.17/smoothemplik/R/catch-routine-registration.R |only smoothemplik-0.0.17/smoothemplik/src/kernelsm.h |only smoothemplik-0.0.17/smoothemplik/src/test-kernelsmoothers.cpp |only smoothemplik-0.0.17/smoothemplik/src/test-runner.cpp |only smoothemplik-0.0.17/smoothemplik/tests/testthat/test-cpp.R |only smoothemplik-0.0.18/smoothemplik/DESCRIPTION | 10 smoothemplik-0.0.18/smoothemplik/MD5 | 29 - smoothemplik-0.0.18/smoothemplik/NEWS.md | 3 smoothemplik-0.0.18/smoothemplik/R/zzz.R | 2 smoothemplik-0.0.18/smoothemplik/build/partial.rdb |binary smoothemplik-0.0.18/smoothemplik/build/vignette.rds |binary smoothemplik-0.0.18/smoothemplik/inst/CITATION | 12 smoothemplik-0.0.18/smoothemplik/inst/doc/choice-of-SEL-weights.html | 65 +-- smoothemplik-0.0.18/smoothemplik/inst/doc/non-parametric-rcpp.html | 87 ++-- smoothemplik-0.0.18/smoothemplik/src/RcppExports.cpp | 25 - smoothemplik-0.0.18/smoothemplik/src/kernelsmoothers.cpp | 177 ++++++---- smoothemplik-0.0.18/smoothemplik/tests/testthat/test-kernelFun.R | 51 ++ smoothemplik-0.0.18/smoothemplik/tests/testthat/test-svdlm.R | 2 18 files changed, 285 insertions(+), 178 deletions(-)
Title: Small Area Estimation Hierarchical Bayes for Spatial Beta Model
Description: Provides several functions and datasets for area-level Small Area Estimation using the Hierarchical Bayesian (HB) method. Model-based estimators are designed for variables of interest that follow a Beta distribution (proportions bounded between 0 and 1). The package supports both non-spatial and spatial models based on Simultaneous Autoregressive (SAR) and Leroux Conditional Autoregressive (CAR) structures for area-level random effects, with optional survey design effect (DEFF) adjustments for sampling variances. In addition, it provides utility functions for constructing spatial weights matrices and performing spatial autocorrelation diagnostics. The 'runjags' package is used to obtain posterior estimates via Markov Chain Monte Carlo (MCMC) with parallel computing capabilities. For references, see Rao and Molina (2015) <doi:10.1002/9781118735855>, Liu et al. (2014) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2014001/article/14030-eng.pdf>, Kubacki and Jedrzejczak (2016) [...truncated...]
Author: Boby Iwan [aut, cre],
Cucu Sumarni [aut]
Maintainer: Boby Iwan <bobyiwanboby2122@gmail.com>
Diff between saeHB.Spatial.Beta versions 0.1.1 dated 2026-08-24 and 0.2.0 dated 2026-09-20
DESCRIPTION | 10 - MD5 | 76 ++++---- NAMESPACE | 3 R/beta_lerouxcar.R | 118 ++++++++---- R/beta_nonspatial.R | 118 ++++++++---- R/beta_sar.R | 131 ++++++++++---- R/betadeff_lerouxcar.R | 107 ++++++++--- R/betadeff_nonspatial.R | 107 ++++++++--- R/betadeff_sar.R | 112 ++++++++---- R/build_w.R | 39 +++- R/databeta.R | 2 R/moran_test.R | 4 R/saeHB.Spatial.Beta_package.R | 15 - README.md | 212 +++++++++++------------ inst/doc/saeHB_Spatial_Beta.R | 19 -- inst/doc/saeHB_Spatial_Beta.Rmd | 46 ++--- inst/doc/saeHB_Spatial_Beta.html | 274 +++++++++++++++--------------- man/beta_lerouxcar.Rd | 7 man/beta_nonspatial.Rd | 7 man/beta_sar.Rd | 7 man/betadeff_lerouxcar.Rd | 7 man/betadeff_nonspatial.Rd | 7 man/betadeff_sar.Rd | 7 man/build_w.Rd | 25 ++ man/databeta.Rd | 2 man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-example-3.png |binary man/moran_test.Rd | 2 man/saeHB.Spatial.Beta-package.Rd | 13 - tests/testthat/test-beta_lerouxcar.R | 20 ++ tests/testthat/test-beta_nonspatial.R | 20 ++ tests/testthat/test-beta_sar.R | 20 ++ tests/testthat/test-betadeff_lerouxcar.R | 20 ++ tests/testthat/test-betadeff_nonspatial.R | 20 ++ tests/testthat/test-betadeff_sar.R | 20 ++ tests/testthat/test-build_w.R | 55 ++++-- tests/testthat/test-moran_test.R | 69 ++----- vignettes/saeHB_Spatial_Beta.Rmd | 46 ++--- 39 files changed, 1124 insertions(+), 643 deletions(-)
More information about saeHB.Spatial.Beta at CRAN
Permanent link
Title: Profile Analysis of Multivariate Data in R
Description: A suite of multivariate methods and data visualization
tools to implement profile analysis and cross-validation techniques described in
Davison & Davenport (2002) <DOI: 10.1037/1082-989X.7.4.468>, Bulut (2013), and other published and unpublished resources.
The package includes routines to perform criterion-related profile analysis, profile analysis
via multidimensional scaling, moderated profile analysis, generalizability theory, profile analysis by group, and a
within-person factor model to derive score profiles.
Author: Okan Bulut [aut],
Christopher David Desjardins [aut, cre]
Maintainer: Christopher David Desjardins <cddesjardins@gmail.com>
Diff between profileR versions 0.3-5 dated 2018-04-19 and 0.3-6 dated 2026-09-20
DESCRIPTION | 25 +++++---- MD5 | 36 +++++++++----- NEWS | 9 +++ R/cpa.R | 11 +--- R/paos.R | 9 +-- R/pr.R | 134 +++++++++++++++++++++++++---------------------------- R/profileplot.R | 8 +-- README.md | 115 ++++++++++++++++++++++++++++++++++++++++----- build |only inst |only man/PS.Rd | 2 man/cpa.Rd | 10 +++ man/figures |only man/interest.Rd | 2 man/paos.Rd | 2 man/pcv.Rd | 10 +++ man/profileplot.Rd | 10 +++ vignettes |only 18 files changed, 252 insertions(+), 131 deletions(-)
Title: Identify Reference Periods in Brazil's PNADC Survey Data
Description: Identifies reference periods (months, fortnights, and weeks) in
Brazil's quarterly PNADC (Pesquisa Nacional por Amostra de Domicilios
Continua) survey data and computes calibrated weights for sub-quarterly
analysis. The core algorithm uses IBGE (Instituto Brasileiro de Geografia
e Estatistica) 'Parada Tecnica' (technical break) rules combined with
respondent birthdates to determine which temporal period each survey
observation refers to. Period identification follows a nested hierarchy
enforced by construction: fortnights require months, weeks require
fortnights. Achieves approximately 97% monthly determination rate with
the full series (2012-2025). Strict fortnight and week rates are
approximately 9% and 3% respectively, as they cannot leverage
cross-quarter panel aggregation. Experimental strategies (probabilistic
assignment and UPA (Primary Sampling Unit) aggregation) further improve
these determination rates. The package provides adaptive hierarchical
weight calibration (4/2/1 cell [...truncated...]
Author: Rogerio Barbosa [aut, cre] ,
Marcos Hecksher [aut]
Maintainer: Rogerio Barbosa <rogerio.barbosa@iesp.uerj.br>
Diff between PNADCperiods versions 0.1.2 dated 2026-04-28 and 0.1.3 dated 2026-09-20
DESCRIPTION | 16 ++--- MD5 | 82 ++++++++++++++------------- NEWS.md | 57 ++++++++++++++++++ R/PNADCperiods-package.R | 6 + R/fetch-sidra-population.R | 16 ----- R/fetch-sidra-series.R | 13 ---- R/mensalize-sidra-series.R | 53 +++++++---------- R/sidra-api-v3.R |only README.md | 10 +-- inst/CITATION | 25 ++++++-- inst/doc/annual-poverty-analysis.Rmd | 13 ++-- inst/doc/annual-poverty-analysis.html | 34 ++++++----- inst/doc/applied-examples.Rmd | 13 ++-- inst/doc/applied-examples.html | 26 +++++--- inst/doc/complex-survey-design.Rmd | 13 ++-- inst/doc/complex-survey-design.html | 18 +++-- inst/doc/download-and-prepare.Rmd | 13 ++-- inst/doc/download-and-prepare.html | 12 ++- inst/doc/getting-started.Rmd | 19 +++--- inst/doc/getting-started.html | 20 ++++-- inst/doc/how-it-works.Rmd | 13 ++-- inst/doc/how-it-works.html | 12 ++- inst/doc/sidra-mensalization.Rmd | 13 ++-- inst/doc/sidra-mensalization.html | 12 ++- man/PNADCperiods-package.Rd | 6 + man/fetch-sidra-population.Rd | 20 +++--- man/fetch_monthly_population.Rd | 6 + man/fetch_sidra_rolling_quarters.Rd | 10 +++ man/mensalize_sidra_series.Rd | 11 ++- man/utils-validation.Rd | 18 ++--- tests/testthat/helper-sidra-v3-fixtures.R |only tests/testthat/test-derived-propagation.R | 11 ++- tests/testthat/test-fetch-sidra-population.R | 42 ++++--------- tests/testthat/test-fetch-sidra-series.R | 12 +-- tests/testthat/test-mensalize-pure-cumsum.R |only tests/testthat/test-pnadc-apply-periods.R | 2 tests/testthat/test-sidra-api-v3.R |only vignettes/annual-poverty-analysis.Rmd | 13 ++-- vignettes/applied-examples.Rmd | 13 ++-- vignettes/complex-survey-design.Rmd | 13 ++-- vignettes/download-and-prepare.Rmd | 13 ++-- vignettes/getting-started.Rmd | 19 +++--- vignettes/how-it-works.Rmd | 13 ++-- vignettes/sidra-mensalization.Rmd | 13 ++-- 44 files changed, 460 insertions(+), 284 deletions(-)
Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Creates styled tables for data presentation. Export to HTML, LaTeX,
RTF, 'Word', 'Excel', 'PowerPoint', 'typst', SVG and PNG. Simple, modern
interface to manipulate borders, size, position, captions, colours,
text styles and number formatting. Table cells can span multiple rows and/or columns.
Includes a 'huxreg' function to create regression tables, and 'quick_*'
one-liners to print tables to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 6.0.1 dated 2026-09-15 and 6.0.2 dated 2026-09-20
DESCRIPTION | 8 +- MD5 | 32 ++++---- NAMESPACE | 23 ++++-- NEWS.md | 9 ++ R/captions.R | 22 ++++- R/markdown.R | 3 R/properties-table.R | 5 - README.md | 154 ++++++++++------------------------------- inst/doc/huxreg.html | 2 inst/doc/huxtable.html | 12 +-- man/caption.Rd | 5 - man/huxtable-FAQ.Rd | 1 man/huxtable-news.Rd | 10 ++ man/huxtable-options.Rd | 1 man/huxtable-package.Rd | 1 tests/testthat/bones.png |binary tests/testthat/test-captions.R | 28 +++++++ 17 files changed, 158 insertions(+), 158 deletions(-)
Title: Access to CAPES Data
Description: Provides simplified access to the data from the Catalog of Theses and Dissertations
of the Brazilian Coordination for the Improvement of Higher Education Personnel (CAPES, <https://catalogodeteses.capes.gov.br>)
for the years 1987 through 2024. The dataset includes variables such as Higher Education
Institution (institution), Area of Concentration (area), Graduate Program Name (program_name),
Type of Work (type), Language of Work (language), Author Identification (author), Abstract
(abstract), Advisor Identification (advisor), Development Region (region), State (state).
Author: Andre Leite [aut, cre],
Hugo Vasconcelos Medeiros [aut],
Dalson Figueiredo Filho [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between capesR versions 0.1.0 dated 2024-12-19 and 0.2.0 dated 2026-09-20
capesR-0.1.0/capesR/data/years_osf.rda |only capesR-0.1.0/capesR/man/years_osf.Rd |only capesR-0.2.0/capesR/DESCRIPTION | 30 ++-- capesR-0.2.0/capesR/MD5 | 23 +-- capesR-0.2.0/capesR/NEWS.md |only capesR-0.2.0/capesR/R/capes.R | 169 +++++++++++++++---------- capesR-0.2.0/capesR/README.md | 20 ++ capesR-0.2.0/capesR/build/vignette.rds |binary capesR-0.2.0/capesR/data/capes_years.rda |only capesR-0.2.0/capesR/inst/doc/capesR.Rmd | 10 - capesR-0.2.0/capesR/inst/doc/capesR.html | 23 ++- capesR-0.2.0/capesR/man/capes_years.Rd |only capesR-0.2.0/capesR/man/download_capes_data.Rd | 26 +++ capesR-0.2.0/capesR/man/read_capes_data.Rd | 4 capesR-0.2.0/capesR/vignettes/capesR.Rmd | 10 - 15 files changed, 200 insertions(+), 115 deletions(-)
Title: Tidy Drift Detection for Monitored Machine Learning Models
Description: Detects concept drift and data drift in streams produced by
deployed machine learning models, using a tidy interface that composes
with the 'tidymodels' ecosystem. Detectors are specified, fitted on a
baseline period, and advanced over new batches of observations,
returning tibbles annotated with warning and drift flags. A catalogue
of 22 sequential drift detectors is provided. Error-based methods
include the Drift Detection Method (DDM) of Gama et al. (2004)
<doi:10.1007/978-3-540-28645-5_29>, the Early Drift Detection Method
(EDDM) of Baena-Garcia et al. (2006), the Hoeffding's inequality
based Drift Detection Methods (HDDM) of Frias-Blanco et al. (2015)
<doi:10.1109/TKDE.2014.2345382>, and the Exponentially Weighted
Moving Average (EWMA) chart of Ross et al. (2012)
<doi:10.1016/j.patrec.2011.08.019>. Distribution-based methods
include Adaptive Windowing (ADWIN) of Bifet and Gavalda (2007)
<doi:10.1137/1.9781611972771.42>, Kolmogorov-Smirnov Windowing
(KSWIN) [...truncated...]
Author: Joao Paulo Assis Bonifacio [aut, cre] ,
Geraldo Magela da Cruz Pereira [aut] ,
Pedro Mambelli Fernandes [aut]
Maintainer: Joao Paulo Assis Bonifacio <jpab.27@hotmail.com>
Diff between deriva versions 0.1.0 dated 2026-08-03 and 0.2.0 dated 2026-09-20
DESCRIPTION | 13 - MD5 | 119 +++++---- NEWS.md | 63 ++++ R/advance.R | 87 +++--- R/augment.R | 61 ++-- R/autoplot.R | 196 ++++++++------- R/data.R |only R/detect_drift.R | 57 ++-- R/drift_detector.R | 159 +++++++++--- R/engine.R | 62 +++- R/fit.R | 160 ++++++++---- R/method-adwin.R | 291 +++++++++++----------- R/method-fhddm.R | 66 ++--- R/method-fhddms.R | 96 +++---- R/method-fisher.R | 209 ++++++++-------- R/method-kswin.R | 62 ++-- R/method-mddm.R | 118 ++++----- R/method-seed.R | 297 +++++++++++----------- R/method-seqdrift2.R | 157 ++++++------ R/method-wstd.R | 129 +++++---- R/param-checks.R |only R/registry.R | 67 ++--- R/tidy-glance.R | 78 +++--- R/validate.R | 111 +++++--- R/zzz.R | 63 ++++ README.md | 232 +++++++++-------- build/partial.rdb |only build/vignette.rds |binary data |only inst/WORDLIST | 56 ++-- inst/doc/deriva.R | 27 -- inst/doc/deriva.Rmd | 351 +++++++++++++-------------- inst/doc/deriva.html | 254 ++++++++++--------- inst/doc/distribution-detectors.R |only inst/doc/distribution-detectors.Rmd |only inst/doc/distribution-detectors.html |only man/advance.Rd | 78 +++--- man/augment.drift_detector_fit.Rd | 59 ++-- man/autoplot.drift_detector_fit.Rd | 46 +-- man/credit_monitoring.Rd |only man/deriva-package.Rd | 11 man/detect_drift.Rd | 68 ++--- man/drift_detector.Rd | 80 ++++-- man/sensor_monitoring.Rd |only man/tidy.drift_detector_fit.Rd | 41 +-- tests/testthat/fixtures/regression-flags.rds |only tests/testthat/helper-bundled.R |only tests/testthat/test-advance.R | 70 ++--- tests/testthat/test-adwin.R | 58 ++-- tests/testthat/test-bridge.R | 63 ++-- tests/testthat/test-column-safety.R |only tests/testthat/test-edge-inputs.R |only tests/testthat/test-fhddm.R | 38 +- tests/testthat/test-fhddms.R | 40 +-- tests/testthat/test-flag-contract.R |only tests/testthat/test-ftdd.R | 78 +++--- tests/testthat/test-keep.R |only tests/testthat/test-kswin.R | 85 +++--- tests/testthat/test-mddm.R | 64 ++-- tests/testthat/test-param-checks.R |only tests/testthat/test-param-validation.R |only tests/testthat/test-registry.R | 65 ++--- tests/testthat/test-regression-flags.R |only tests/testthat/test-rng.R |only tests/testthat/test-seed.R | 139 +++++++--- tests/testthat/test-seqdrift2.R | 78 +++--- tests/testthat/test-spec.R | 45 +-- tests/testthat/test-wstd.R | 129 +++++---- vignettes/deriva.Rmd | 351 +++++++++++++-------------- vignettes/distribution-detectors.Rmd |only 70 files changed, 2920 insertions(+), 2407 deletions(-)
Title: Zero-Modified Complex 'Tri-Parametric' Pearson Distribution for
Overdispersed Count Data
Description: Implements zero-modified versions of the Complex 'Tri-Parametric'
Pearson distribution for overdispersed count data. The package addresses
limitations of existing implementations when the parameter b approaches
zero. It provides distribution functions, maximum likelihood estimation,
and diagnostic tools for modeling count data with excess zeros. The
methodology is based on 'Rodriguez-Avi' and coauthors (2003)
<doi:10.1007/s00362-002-0134-7>.
Author: Rasheedat Oladoja [aut, cre]
Maintainer: Rasheedat Oladoja <roladoja@ttu.edu>
Diff between zmctp versions 0.1.2 dated 2026-07-22 and 0.1.3 dated 2026-09-20
DESCRIPTION | 6 +-- MD5 | 15 ++++---- NEWS.md | 39 ++++++++++++++++++++++ R/ctp_fit.R | 77 ++++++++++++++++++++++++++++++++++++--------- R/dctp.R | 31 ++++++++++++------ R/methods.R | 8 ++++ R/zictp_fit.R | 47 ++++++++++++++++++++++----- inst/doc/introduction.html | 17 ++++----- tests/testthat/test-fit.R |only 9 files changed, 188 insertions(+), 52 deletions(-)
Title: Create Pharmacometric Models
Description: Provides a user interface to create or modify pharmacometric
models for various modeling and simulation software platforms.
Author: Sebastien Bihorel [cre, aut]
Maintainer: Sebastien Bihorel <sb.pmlab@gmail.com>
Diff between pmxcode versions 0.3.1 dated 2025-09-07 and 0.3.2 dated 2026-09-20
DESCRIPTION | 6 LICENSE | 2 MD5 | 16 - NEWS.md | 3 R/new_model_server.R | 8 R/utils_nonmem.R | 52 +++-- build/vignette.rds |binary inst/doc/covariates.html | 472 +++++++++++++++++++++++++++++++++-------------- inst/doc/library.html | 442 +++++++++++++++++++++++++++++--------------- 9 files changed, 688 insertions(+), 313 deletions(-)
Title: Mixture Models for Clustering and Classification
Description: An implementation of 14 parsimonious mixture models for model-based clustering or model-based classification. Gaussian, Student's t, generalized hyperbolic, variance-gamma or skew-t mixtures are available. All approaches work with missing data. Celeux and Govaert (1995) <doi:10.1016/0031-3203(94)00125-6>, Browne and McNicholas (2014) <doi:10.1007/s11634-013-0139-1>, Browne and McNicholas (2015) <doi:10.1002/cjs.11246>.
Author: Nik Pocuca [aut] ,
Ryan P. Browne [aut] ,
Paul D. McNicholas [aut, cre] ,
Alexa A. Sochaniwsky [aut]
Maintainer: Paul D. McNicholas <mcnicholas@math.mcmaster.ca>
Diff between mixture versions 2.2.0 dated 2025-12-18 and 2.2.1 dated 2026-09-20
ChangeLog | 3 + DESCRIPTION | 8 ++-- MD5 | 80 ++++++++++++++++++++-------------------- R/RcppExports.R | 20 +++++----- R/gh_mixture.R | 12 ++++-- R/mixture.R | 12 ++++-- R/pcm.R | 4 +- R/st_mixture.R | 12 ++++-- R/t_mixture.R | 12 ++++-- R/vg_mixture.R | 12 ++++-- man/ARI.Rd | 2 - man/MAP.Rd | 2 - man/e_step.Rd | 2 - man/get_best_model.Rd | 2 - man/ghpcm.Rd | 7 ++- man/gpcm.Rd | 7 ++- man/main_loop.Rd | 7 ++- man/main_loop_gh.Rd | 7 ++- man/main_loop_st.Rd | 7 ++- man/main_loop_t.Rd | 7 ++- man/main_loop_vg.Rd | 7 ++- man/mixture.Rd | 4 +- man/pcm.Rd | 7 ++- man/stpcm.Rd | 7 ++- man/tpcm.Rd | 7 ++- man/vgpcm.Rd | 7 ++- man/z_ig_kmeans.Rd | 2 - man/z_ig_random_hard.Rd | 2 - man/z_ig_random_soft.Rd | 2 - src/Cluster_Error.hpp | 2 - src/GH_Model/GH_Mixture_Model.h | 3 + src/RcppExports.cpp | 45 ++++++++++++---------- src/ST_Model/ST_Mixture_Model.h | 3 + src/T_Model/General_Methods.hpp | 5 ++ src/T_Model/T_Mixture_Model.hpp | 1 src/VG_Model/VG_Mixture_Model.h | 3 + src/ghpcm_arma.hpp | 6 ++- src/gpcm_arma.hpp | 15 ++++++- src/stpcm_arma.hpp | 5 +- src/tpcm_arma.hpp | 5 +- src/vgpcm_arma.hpp | 5 +- 41 files changed, 226 insertions(+), 142 deletions(-)
Title: Soundscape Spectral Metrics
Description: Accessible and flexible implementation of spectral ecoacoustic indices. The functions were design to accommodate a variety of sampling designs. Users can tailor calculations by specifying spectrogram time bin size, amplitude thresholds and normality tests. By simplifying computation and standardizing reproducible methods, the package aims to support ecoacoustics studies.
Author: Arthur Igor da Fonseca-Freire [aut, cre, cph],
Weslley Geremias dos Santos [aut],
Lucas Rodriguez Forti [aut]
Maintainer: Arthur Igor da Fonseca-Freire <arthur.igorr@gmail.com>
Diff between Ruido versions 1.1.0 dated 2026-09-01 and 1.1.1 dated 2026-09-20
DESCRIPTION | 6 +-- MD5 | 18 +++++----- R/activity.R | 82 +++++++++++++++++++++++++------------------------- R/bgNoise.R | 2 - R/internalFunctions.R | 5 +-- R/noise.matrix.R | 5 +-- R/singleSat.R | 61 +++++++++++++++++++++++-------------- man/ENTspec.Rd | 4 +- man/activity.Rd | 14 ++++---- man/singleSat.Rd | 9 ++++- 10 files changed, 115 insertions(+), 91 deletions(-)
Title: Powerful 'SAS' Inspired Concepts for more Efficient Bigger
Outputs
Description: The main goal is to make descriptive evaluations easier to create bigger and more complex outputs in less time with less code. Introducing format containers with multilabels <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p06ciqes4eaqo6n0zyqtz9p21nfb.htm>, a more powerful summarise which is capable to output every possible combination of the provided grouping variables in one go <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/p0jvbbqkt0gs2cn1lo4zndbqs1pe.htm>, tabulation functions which can create any table in different styles <https://documentation.sas.com/doc/en/pgmsascdc/v_067/proc/n1ql5xnu0k3kdtn11gwa5hc7u435.htm> and other more readable functions. The code is optimized to work fast even with datasets of over a million observations.
Author: Tim Siebenmorgen [aut, cre, cph]
Maintainer: Tim Siebenmorgen <qol_package@proton.me>
Diff between qol versions 1.3.4 dated 2026-08-21 and 1.3.5 dated 2026-09-20
DESCRIPTION | 6 MD5 | 116 NEWS.md | 67 R/any_table.R | 7690 ++++++++++++++++++------------------ R/apply_format.R | 387 - R/build_master.R | 91 R/compute.R | 1113 ++--- R/conversion.R | 873 ++-- R/create_format.R | 947 ++-- R/crosstabs.R | 59 R/dummy_data.R | 828 ++- R/excel_helpers.R | 54 R/export_with_style.R | 84 R/frequencies.R | 134 R/globals.R | 192 R/if_else.R | 3716 ++++++++--------- R/import_export.R | 67 R/internal.R | 2 R/loading.R | 2188 +++++----- R/multi_join.R | 950 ++-- R/options.R | 10 R/recode.R | 11 R/renaming.R | 799 +-- R/retain.R | 1 R/small_helpers.R | 30 R/sort_plus.R | 2 R/statistics.R | 9 R/strings.R | 777 +-- R/summarise_plus.R | 3156 +++++++------- R/transpose_plus.R | 1495 ++++-- README.md | 2 inst/tinytest/test-any_table.R | 4 inst/tinytest/test-compute.R | 294 - inst/tinytest/test-create_format.R | 81 inst/tinytest/test-crosstabs.R | 2 inst/tinytest/test-dummy_data.R | 18 inst/tinytest/test-frequencies.R | 16 inst/tinytest/test-if_else.R | 1404 +++--- inst/tinytest/test-loading.R | 902 ++-- inst/tinytest/test-multi_join.R | 461 +- inst/tinytest/test-options.R | 2 inst/tinytest/test-recode.R | 21 inst/tinytest/test-renaming.R | 152 inst/tinytest/test-strings.R | 597 +- inst/tinytest/test-summarise_plus.R | 2180 +++++----- inst/tinytest/test-transpose_plus.R | 686 +-- man/any_table.Rd | 4 man/build_master.Rd | 2 man/combine_into_workbook.Rd | 21 man/crosstabs.Rd | 2 man/dummy_data.Rd | 14 man/export_with_style.Rd | 2 man/frequencies.Rd | 2 man/import_export.Rd | 2 man/qol_options.Rd | 2 man/run_scripts.Rd | 7 man/sort_plus.Rd | 2 man/summarise_plus.Rd | 4 man/transpose_plus.Rd | 43 59 files changed, 17262 insertions(+), 15521 deletions(-)
Title: Summarises Package & Function Usage
Description: Consistent with 'knitr' syntax highlighting, 'usedthese' adds
a summary table of package & function usage to a Quarto document and
enables aggregation of usage across a website.
Author: Carl Goodwin [aut, cre, cph]
Maintainer: Carl Goodwin <carl.goodwin@quantumjitter.com>
Diff between usedthese versions 0.5.0 dated 2024-06-26 and 0.5.1 dated 2026-09-20
DESCRIPTION | 12 ++--- MD5 | 24 +++++------ NAMESPACE | 74 ++++++++++++++++++++---------------- NEWS.md | 4 + R/used_there.R | 7 --- R/usedthese-package.R | 2 README.md | 61 +++++++++-------------------- build/vignette.rds |binary inst/doc/multipage.html | 31 +++++++-------- inst/doc/usedthese.html | 65 ++++++++++++++++--------------- man/usedthese-package.Rd | 5 ++ tests/testthat/_snaps/used_there.md | 13 +++++- tests/testthat/test-used_there.R | 15 +++++++ 13 files changed, 167 insertions(+), 146 deletions(-)
Title: A Comprehensive and Intuitive R Package for Stepwise Regression
Analysis
Description: Stepwise regression is a statistical technique used for model selection. This package streamlines stepwise regression analysis by supporting multiple regression types(linear, Cox, logistic, Poisson, Gamma, and negative binomial), incorporating popular selection strategies(forward, backward, bidirectional, and subset), and offering essential metrics. It enables users to apply multiple selection strategies and metrics in a single function call, visualize variable selection processes, and export results in various formats. StepReg offers a data-splitting option to address potential issues with invalid statistical inference and a randomized forward selection option to avoid overfitting. We validated StepReg's accuracy using public datasets within the SAS software environment. For an interactive web interface, users can install the companion 'StepRegShiny' package. The methodology is described in Li et al. (2026) <doi:10.32614/RJ-2026-005>.
Author: Junhui Li [cre, aut] ,
Kai Hu [aut],
Xiaohuan Lu [aut],
Sushmita N Nayak [ctb, aut],
Cesar Bautista Sotelo [ctb, aut],
Michael A Lodato [ctb, aut],
Wenxin Liu [aut],
Lihua Julie Zhu [aut]
Maintainer: Junhui Li <junhui.li11@umassmed.edu>
Diff between StepReg versions 1.6.7 dated 2026-08-31 and 1.6.8 dated 2026-09-20
DESCRIPTION | 13 +- MD5 | 14 +- NAMESPACE | 22 ++-- NEWS.md | 30 +++++ R/fastUtils.R |only R/report.R | 17 +-- R/stepwise.R | 16 ++ R/stepwiseUtils.R | 219 +++++++++++++++++++++++++++------------- tests/testthat/test_fast_path.R |only 9 files changed, 228 insertions(+), 103 deletions(-)
Title: Statistical Tools for African National Statistics Institutes
Description: A comprehensive statistical toolbox for National Statistics
Institutes (INS) in Africa. Provides functions for survey data import
('KoboToolbox', 'ODK', 'CSPro', 'Excel', 'Stata', 'SPSS'), data
processing and validation, weighted statistical analysis (descriptive
statistics, cross-tabulations, regression, Human Development Index (HDI),
Multidimensional Poverty Index (MPI) following Alkire and Foster (2011)
<doi:10.1093/oep/gpr051>, inequalities), visualization (age pyramids,
thematic maps, official charts) and dissemination ('SDMX' export, 'DDI'
metadata, anonymization, Word/PDF reports). Designed to work in
resource-constrained environments, offline and in French.
Author: Dikers Amoko [aut, cre, ctb],
Josue Honore Dasse [ctb]
Maintainer: Dikers Amoko <diamoko@gmail.com>
Diff between statAfrikR versions 0.1.0 dated 2026-04-03 and 0.2.0 dated 2026-09-20
DESCRIPTION | 48 +- MD5 | 264 +++++++++-- NAMESPACE | 116 +++++ NEWS.md | 189 +++++++- R/analyse.R | 185 -------- R/bien_etre.R |only R/cartographie.R |only R/catalogue_indicateurs.R |only R/collecte.R | 22 R/dashboard.R |only R/data.R |only R/demographie.R |only R/diffusion.R | 41 + R/emploi.R |only R/genre.R |only R/harmonisation_geo.R |only R/inegalites.R |only R/ipm.R |only R/odd.R |only R/pauvrete.R |only R/pib.R |only R/rapports.R |only R/sante.R |only R/sondage.R |only R/statAfrikR-package.R | 37 + R/tableaux.R |only R/traitement.R | 16 R/validation_ins.R |only R/visualisation.R | 4 data |only inst/INS_READINESS.md |only inst/doc/demarrage-rapide.R | 4 inst/doc/demarrage-rapide.Rmd | 4 inst/doc/demarrage-rapide.html | 4 inst/doc/enquete-ponderee.R | 379 +++++++++-------- inst/doc/enquete-ponderee.Rmd | 96 +++- inst/doc/enquete-ponderee.html | 557 ++++++------------------- inst/doc/indicateurs-odd.R | 465 ++++++++++---------- inst/doc/indicateurs-odd.Rmd | 56 +- inst/doc/indicateurs-odd.html | 428 ++++--------------- inst/rmd |only man/accouchements_assistes.Rd |only man/analyse_regression.Rd | 2 man/analyse_spatiale.Rd | 2 man/analyser_non_reponse.Rd |only man/anemie.Rd |only man/anonymiser_donnees.Rd | 7 man/autonomisation_femmes.Rd |only man/bonheur_declare.Rd |only man/calcul_deff.Rd |only man/calcul_fgt.Rd |only man/calcul_gini.Rd |only man/calcul_ipm.Rd | 138 ++++-- man/calcul_ipm_national.Rd |only man/calculer_deflateur.Rd |only man/calibrer_poids.Rd |only man/carte_choroplethe.Rd |only man/carte_exporter.Rd |only man/carte_import.Rd |only man/carte_ipm.Rd |only man/carte_joindre.Rd |only man/carte_pauvrete.Rd |only man/carte_thematique.Rd | 2 man/carte_zones.Rd |only man/catalogue_indicateurs.Rd |only man/check_na.Rd | 2 man/check_types.Rd | 2 man/coherence_demo.Rd |only man/comparer_ipm.Rd |only man/comparer_pib.Rd |only man/compresser_package_diffusion.Rd | 2 man/confiance_institutions.Rd |only man/courbe_lorenz.Rd |only man/creer_design.Rd |only man/decomposer_fgt.Rd |only man/decomposer_inegalite.Rd | 2 man/decomposer_ipm.Rd |only man/decomposer_theil.Rd |only man/detecter_ecarts_geo.Rd |only man/emaciation.Rd |only man/emploi_informel.Rd |only man/emploi_vulnerable.Rd |only man/exporter_code_dashboard.Rd |only man/exporter_excel_ins.Rd |only man/exporter_graphique.Rd | 2 man/exporter_sdmx.Rd | 2 man/fusion_datasets.Rd | 2 man/generer_bulletin.Rd |only man/generer_metadonnees_ddi.Rd | 2 man/generer_rapport.Rd | 2 man/generer_rapport_enquete.Rd |only man/generer_rapport_odd.Rd |only man/graphique_fgt.Rd |only man/graphique_ipm.Rd |only man/handicap_prevalence.Rd |only man/harmoniser_regions.Rd | 2 man/harmoniser_zones.Rd |only man/import_cspro.Rd | 2 man/import_csv.Rd | 2 man/import_excel.Rd | 2 man/import_kobo.Rd | 2 man/import_odk.Rd | 2 man/import_sas.Rd | 2 man/import_spss.Rd | 2 man/import_stata.Rd | 2 man/imputer_valeurs.Rd | 2 man/indice_atkinson.Rd |only man/indice_palma.Rd |only man/insuffisance_ponderale.Rd |only man/lancer_dashboard.Rd |only man/lister_templates.Rd |only man/mariage_precoce.Rd |only man/migrer_nomenclature.Rd |only man/mortalite_5ans.Rd |only man/myers.Rd |only man/nettoyer_libelles.Rd | 2 man/odd_catalogue.Rd |only man/odd_indicateur.Rd |only man/parite_education.Rd |only man/part_quintile.Rd |only man/pauvrete_travail.Rd |only man/perception_economique.Rd |only man/privations_ressenties.Rd |only man/protection_sociale.Rd |only man/pyramide_age.Rd |only man/rapport_harmonisation.Rd |only man/rapport_qualite_demo.Rd |only man/rapport_qualite_sondage.Rd |only man/ratio_masculinite.Rd |only man/recoder_variable.Rd | 2 man/retard_croissance.Rd |only man/saf_cameroun_departements.Rd |only man/saf_cedeao.Rd |only man/saf_cemac.Rd |only man/saf_eau.Rd |only man/saf_pays_afrique.Rd |only man/saf_rca_prefectures.Rd |only man/saf_sadc.Rd |only man/saf_senegal_regions.Rd |only man/saf_subdivisions_afrique.Rd |only man/sante_mentale.Rd |only man/satisfaction_vie.Rd |only man/sentiment_securite.Rd |only man/sous_emploi_temps.Rd |only man/standardiser_ages.Rd | 2 man/statAfrikR-package.Rd | 19 man/stat_descr.Rd | 2 man/suivre_revisions_pib.Rd |only man/supprimer_doublons.Rd | 2 man/tab_croisee.Rd | 2 man/table_concordance.Rd |only man/tableau_bien_etre_subjectif.Rd |only man/tableau_bord_pib.Rd |only man/tableau_croise_ins.Rd |only man/tableau_descriptif.Rd |only man/tableau_fgt.Rd |only man/tableau_genre.Rd |only man/tableau_inegalites.Rd |only man/tableau_ipm.Rd |only man/tableau_marche_travail.Rd |only man/tableau_odd.Rd |only man/tableau_sante.Rd |only man/taux_activite.Rd |only man/taux_croissance.Rd |only man/taux_emploi.Rd |only man/taux_sous_utilisation.Rd |only man/tracer_flux_traitement.Rd | 2 man/travail_enfants.Rd |only man/vaccination.Rd |only man/valider_coherence_geo.Rd |only man/valider_dictionnaire.Rd | 2 man/valider_poids.Rd |only man/valider_qualite_donnees.Rd | 2 man/valider_statistique_ins.Rd |only man/violence_basee_genre.Rd |only man/whipple.Rd |only tests/testthat/test-analyse.R | 83 +-- tests/testthat/test-bien_etre.R |only tests/testthat/test-cartographie.R |only tests/testthat/test-catalogue_indicateurs.R |only tests/testthat/test-dashboard.R |only tests/testthat/test-demographie.R |only tests/testthat/test-emploi.R |only tests/testthat/test-genre.R |only tests/testthat/test-harmonisation_geo.R |only tests/testthat/test-inegalites.R |only tests/testthat/test-ipm.R |only tests/testthat/test-odd.R |only tests/testthat/test-pauvrete.R |only tests/testthat/test-pib.R |only tests/testthat/test-rapports.R |only tests/testthat/test-reference_methodologique.R |only tests/testthat/test-sante.R |only tests/testthat/test-sondage.R |only tests/testthat/test-tableaux.R |only tests/testthat/test-validation_ins.R |only vignettes/demarrage-rapide.Rmd | 4 vignettes/enquete-ponderee.Rmd | 96 +++- vignettes/indicateurs-odd.Rmd | 56 +- 199 files changed, 1700 insertions(+), 1680 deletions(-)
Title: A Modern and Flexible Data Pipeline for 'SurveyCTO'
Description: A modern and flexible R client for the 'SurveyCTO', a mobile and
offline data collection platform, providing a modern and consistent interface for
programmatic access to server resources. Built on top of the 'httr2' package,
it enables secure and efficient data retrieval and returns analysis-ready
data through optional tidying. It includes functions to create, upload, and
download server datasets, in addition to fetching form data, files, and
submission attachments. Robust authentication and request handling make the
package suitable for automated survey monitoring and downstream analysis.
Author: Gutama Girja Urago [aut, cre, cph]
Maintainer: Gutama Girja Urago <girjagutama@gmail.com>
Diff between ctoclient versions 0.1.0 dated 2026-03-28 and 0.2.0 dated 2026-09-20
ctoclient-0.1.0/ctoclient/tests/testthat/_datasets/band_members/records/upload-0002f6-POST.json |only ctoclient-0.2.0/ctoclient/DESCRIPTION | 17 ctoclient-0.2.0/ctoclient/MD5 | 84 - ctoclient-0.2.0/ctoclient/NAMESPACE | 127 - ctoclient-0.2.0/ctoclient/NEWS.md | 39 ctoclient-0.2.0/ctoclient/R/cto_connect.R | 307 ++-- ctoclient-0.2.0/ctoclient/R/cto_dataset_create.R | 313 ++-- ctoclient-0.2.0/ctoclient/R/cto_dataset_delete.R | 128 - ctoclient-0.2.0/ctoclient/R/cto_dataset_download.R | 180 +- ctoclient-0.2.0/ctoclient/R/cto_dataset_info.R | 67 ctoclient-0.2.0/ctoclient/R/cto_form_attachment.R | 286 +-- ctoclient-0.2.0/ctoclient/R/cto_form_data.R | 605 ++++---- ctoclient-0.2.0/ctoclient/R/cto_form_data_attachment.R | 255 +-- ctoclient-0.2.0/ctoclient/R/cto_form_definition.R | 248 +-- ctoclient-0.2.0/ctoclient/R/cto_form_docx.R |only ctoclient-0.2.0/ctoclient/R/cto_form_dofile.R | 126 + ctoclient-0.2.0/ctoclient/R/cto_form_files.R | 465 +++--- ctoclient-0.2.0/ctoclient/R/zzz.R | 729 ++++++++-- ctoclient-0.2.0/ctoclient/README.md | 182 -- ctoclient-0.2.0/ctoclient/build |only ctoclient-0.2.0/ctoclient/inst/doc |only ctoclient-0.2.0/ctoclient/man/cto_connect.Rd | 174 +- ctoclient-0.2.0/ctoclient/man/cto_dataset_create.Rd | 194 +- ctoclient-0.2.0/ctoclient/man/cto_dataset_delete.Rd | 86 - ctoclient-0.2.0/ctoclient/man/cto_dataset_download.Rd | 108 - ctoclient-0.2.0/ctoclient/man/cto_dataset_info.Rd | 62 ctoclient-0.2.0/ctoclient/man/cto_dataset_list.Rd | 96 - ctoclient-0.2.0/ctoclient/man/cto_docx_palette.Rd |only ctoclient-0.2.0/ctoclient/man/cto_form_attachment.Rd | 154 +- ctoclient-0.2.0/ctoclient/man/cto_form_data.Rd | 177 +- ctoclient-0.2.0/ctoclient/man/cto_form_data_attachment.Rd | 148 +- ctoclient-0.2.0/ctoclient/man/cto_form_docx.Rd |only ctoclient-0.2.0/ctoclient/man/cto_form_dofile.Rd | 132 - ctoclient-0.2.0/ctoclient/man/cto_form_languages.Rd | 252 +-- ctoclient-0.2.0/ctoclient/man/cto_form_metadata.Rd | 156 +- ctoclient-0.2.0/ctoclient/man/figures |only ctoclient-0.2.0/ctoclient/tests/testthat/_datasets/band_members/records/upload-f8492c-POST.json |only ctoclient-0.2.0/ctoclient/tests/testthat/_metadata/roles.R | 24 ctoclient-0.2.0/ctoclient/tests/testthat/_metadata/users.R | 24 ctoclient-0.2.0/ctoclient/tests/testthat/fixtures |only ctoclient-0.2.0/ctoclient/tests/testthat/test-ctoclient.R | 59 ctoclient-0.2.0/ctoclient/tests/testthat/test-docx.R |only ctoclient-0.2.0/ctoclient/tests/testthat/test-dofile.R |only ctoclient-0.2.0/ctoclient/tests/testthat/test-form-data.R |only ctoclient-0.2.0/ctoclient/tests/testthat/test-form-id-cache.R |only ctoclient-0.2.0/ctoclient/tests/testthat/test-utils.R |only ctoclient-0.2.0/ctoclient/vignettes |only 47 files changed, 3348 insertions(+), 2656 deletions(-)
Title: Isotopic Tracer Analysis Using MCMC
Description: Implements Bayesian models to analyze data from tracer addition
experiments. The implemented method was originally described in the article
"A New Method to Reconstruct Quantitative Food Webs and Nutrient Flows from
Isotope Tracer Addition Experiments" by López-Sepulcre et al. (2020)
<doi:10.1086/708546>.
Author: Andres Lopez-Sepulcre [aut] ,
Matthieu Bruneaux [aut, cre]
Maintainer: Matthieu Bruneaux <matthieu.bruneaux@gmail.com>
This is a re-admission after prior archival of version 1.1.8 dated 2025-03-07
Diff between isotracer versions 1.1.8 dated 2025-03-07 and 1.1.9 dated 2026-09-20
DESCRIPTION | 14 MD5 | 208 - NAMESPACE | 78 NEWS.md | 6 R/ui_predictions.R | 52 README.md | 22 build/vignette.rds |binary inst/doc/case-study-collins-2016.Rmd | 31 inst/doc/case-study-collins-2016.html | 342 - inst/doc/tutorial-010-quick-start.Rmd | 12 inst/doc/tutorial-010-quick-start.html | 253 - inst/doc/tutorial-020-replication.Rmd | 8 inst/doc/tutorial-020-replication.html | 257 - inst/doc/tutorial-030-steady-state-comps.Rmd | 24 inst/doc/tutorial-030-steady-state-comps.html | 293 - inst/doc/tutorial-040-pulse-drip-events.Rmd | 21 inst/doc/tutorial-040-pulse-drip-events.html | 354 - inst/doc/tutorial-050-fixed-effects.Rmd | 51 inst/doc/tutorial-050-fixed-effects.html | 339 - inst/doc/tutorial-060-units-priors.Rmd | 2 inst/doc/tutorial-060-units-priors.html | 137 inst/doc/tutorial-070-prior-predictive-checks.Rmd | 2 inst/doc/tutorial-070-prior-predictive-checks.html | 18 inst/doc/tutorial-080-mcmc-output-format.Rmd | 10 inst/doc/tutorial-080-mcmc-output-format.html | 181 inst/doc/tutorial-090-post-run-analyses.Rmd | 10 inst/doc/tutorial-090-post-run-analyses.html | 209 - inst/doc/tutorial-100-posterior-predictive-checks.Rmd | 21 inst/doc/tutorial-100-posterior-predictive-checks.html | 251 - inst/doc/tutorial-110-derived-parameters.Rmd | 12 inst/doc/tutorial-110-derived-parameters.html | 229 - inst/doc/tutorial-120-howto-simulations.Rmd | 40 inst/doc/tutorial-120-howto-simulations.html | 309 - inst/doc/tutorial-130-parameter-identifiability.Rmd | 25 inst/doc/tutorial-130-parameter-identifiability.html | 256 - man/filter.Rd | 7 man/isotracer-package.Rd | 1 man/reexports.Rd | 6 src/stanExports_networkModel.cc | 34 src/stanExports_networkModel.h | 1980 ++++++++-- tests/testthat/test-helpers_projection-simulation.R | 2 tests/testthat/test-integration.R | 15 tests/testthat/test-steady-states-flows-pred.R | 17 tests/testthat/test-ui_getters.R | 2 tests/testthat/test-ui_model-building.R | 2 tests/testthat/test-ui_others.R | 2 tests/testthat/test-ui_plotting.R | 5 tests/testthat/test-ui_predictions.R | 5 tests/testthat/test-ui_projection.R | 2 tests/testthat/test-ui_run-mcmc.R | 5 tests/testthat/test-ui_sankey-plotting.R | 5 tests/testthat/test-ui_topology.R | 5 vignettes/case-study-collins-2016.Rmd | 31 vignettes/figures/z-fig-010-unnamed-chunk-8-1.jpeg |binary vignettes/figures/z-fig-030-unnamed-chunk-24-1.jpeg |binary vignettes/figures/z-fig-030-unnamed-chunk-26-1.jpeg |binary vignettes/figures/z-fig-030-unnamed-chunk-27-1.jpeg |binary vignettes/figures/z-fig-040-unnamed-chunk-14-1.jpeg |binary vignettes/figures/z-fig-040-unnamed-chunk-16-1.jpeg |binary vignettes/figures/z-fig-040-unnamed-chunk-29-1.jpeg |binary vignettes/figures/z-fig-040-unnamed-chunk-31-1.jpeg |binary vignettes/figures/z-fig-050-unnamed-chunk-21-1.jpeg |binary vignettes/figures/z-fig-050-unnamed-chunk-23-1.jpeg |binary vignettes/figures/z-fig-050-unnamed-chunk-25-1.jpeg |binary vignettes/figures/z-fig-050-unnamed-chunk-26-1.jpeg |binary vignettes/figures/z-fig-050-unnamed-chunk-28-1.jpeg |binary vignettes/figures/z-fig-080-unnamed-chunk-16-1.jpeg |binary vignettes/figures/z-fig-100-unnamed-chunk-12-1.jpeg |binary vignettes/figures/z-fig-100-unnamed-chunk-12-2.jpeg |binary vignettes/figures/z-fig-100-unnamed-chunk-13-1.jpeg |binary vignettes/figures/z-fig-100-unnamed-chunk-14-1.jpeg |binary vignettes/figures/z-fig-100-unnamed-chunk-8-1.jpeg |binary vignettes/figures/z-fig-120-unnamed-chunk-20-1.jpeg |binary vignettes/figures/z-fig-120-unnamed-chunk-22-1.jpeg |binary vignettes/figures/z-fig-120-unnamed-chunk-28-1.jpeg |binary vignettes/figures/z-fig-120-unnamed-chunk-30-1.jpeg |binary vignettes/figures/z-fig-120-unnamed-chunk-30-2.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-28-1.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-31-1.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-34-1.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-39-1.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-42-1.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-47-1.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-48-1.jpeg |binary vignettes/figures/z-fig-cs-collins-2016-unnamed-chunk-8-1.jpeg |binary vignettes/figures/z-fig-cs-li-2017-unnamed-chunk-26-1.jpeg |binary vignettes/figures/z-fig-cs-li-2017-unnamed-chunk-26-2.jpeg |binary vignettes/figures/z-fig-cs-li-2017-unnamed-chunk-28-1.jpeg |binary vignettes/figures/z-fig-cs-li-2017-unnamed-chunk-8-1.jpeg |binary vignettes/figures/z-fig-cs-mcroy-1970-unnamed-chunk-22-1.jpeg |binary vignettes/figures/z-fig-cs-mcroy-1970-unnamed-chunk-23-1.jpeg |binary vignettes/figures/z-fig-cs-mcroy-1970-unnamed-chunk-9-1.jpeg |binary vignettes/tutorial-010-quick-start.Rmd | 12 vignettes/tutorial-020-replication.Rmd | 8 vignettes/tutorial-030-steady-state-comps.Rmd | 24 vignettes/tutorial-040-pulse-drip-events.Rmd | 21 vignettes/tutorial-050-fixed-effects.Rmd | 51 vignettes/tutorial-060-units-priors.Rmd | 2 vignettes/tutorial-070-prior-predictive-checks.Rmd | 2 vignettes/tutorial-080-mcmc-output-format.Rmd | 10 vignettes/tutorial-090-post-run-analyses.Rmd | 10 vignettes/tutorial-100-posterior-predictive-checks.Rmd | 21 vignettes/tutorial-110-derived-parameters.Rmd | 12 vignettes/tutorial-120-howto-simulations.Rmd | 40 vignettes/tutorial-130-parameter-identifiability.Rmd | 25 105 files changed, 3907 insertions(+), 2534 deletions(-)
Title: Utilities from 'Seminar fuer Statistik' ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH Zurich,
some of which were ported from S-plus in the 1990s.
For graphics, have pretty (Log-scale) axes eaxis(), an enhanced Tukey-Anscombe
plot, combining histogram and boxplot, 2d-residual plots, a 'tachoPlot()',
pretty arrows, etc.
For robustness, have a robust F test and robust range().
For system support, notably on Linux, provides 'Sys.*()' functions with
more access to system and CPU information.
Finally, miscellaneous utilities such as simple efficient prime numbers,
integer codes, Duplicated(), toLatex.numeric() and is.whole().
Author: Martin Maechler [aut, cre] ,
Werner Stahel [ctb] , f.robftest, last,
p.scales, p.dnorm),
Andreas Ruckstuhl [ctb] , p.profileTraces,
p.res.2x),
Christian Keller [ctb] , p.tachoPlot),
Kjetil Halvorsen [ctb] , ecdf.ksCI),
Alain Hauser [ctb] , is.whole,
[...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.1-25 dated 2026-08-03 and 1.1-26 dated 2026-09-20
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 3 ++- R/misc-goodies.R | 9 +++++++++ inst/NEWS.Rd | 16 +++++++++++----- man/formatN.Rd | 24 +++++++++++++++--------- 6 files changed, 48 insertions(+), 26 deletions(-)
Title: Sound Synthesis and Acoustic Analysis
Description: Parametric source-filter synthesis of harmonic-noise signals, such
as animal vocalizations and human voice, with control over pitch, formants,
noise, amplitude modulation, nonlinear phenomena, and morphing. General signal
processing tools for audio analysis and manipulation: pitch tracking, formant
and vocal tract length estimation, reassigned and auditory spectrograms,
modulation spectra and psychoacoustic roughness, self-similarity and
surprisal, audio segmentation, pitch and formant shifting, etc. Includes four
interactive web apps for audio synthesis, annotation, formant analysis, and
manually correcting pitch contours.
Reference: Anikin (2019) <doi:10.3758/s13428-018-1095-7>.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <andrey.anikin@cogsci.se>
Diff between soundgen versions 2.9.0 dated 2026-02-24 and 3.0.0 dated 2026-09-20
soundgen-2.9.0/soundgen/R/audSpec.R |only soundgen-2.9.0/soundgen/R/defaults.R |only soundgen-2.9.0/soundgen/R/matchPars.R |only soundgen-2.9.0/soundgen/R/nonlinPred.R |only soundgen-2.9.0/soundgen/R/optimize.R |only soundgen-2.9.0/soundgen/R/subharmonics.R |only soundgen-2.9.0/soundgen/data/def_form.rda |only soundgen-2.9.0/soundgen/data/defaults.rda |only soundgen-2.9.0/soundgen/data/defaults_analyze.rda |only soundgen-2.9.0/soundgen/data/defaults_analyze_pitchCand.rda |only soundgen-2.9.0/soundgen/data/notesDict.rda |only soundgen-2.9.0/soundgen/data/permittedValues.rda |only soundgen-2.9.0/soundgen/data/pitchContour.rda |only soundgen-2.9.0/soundgen/data/pitchManual.rda |only soundgen-2.9.0/soundgen/data/segmentManual.rda |only soundgen-2.9.0/soundgen/inst/shiny/annotation_app/www/icons/octaveDown.png |only soundgen-2.9.0/soundgen/inst/shiny/annotation_app/www/icons/octaveUp.png |only soundgen-2.9.0/soundgen/inst/shiny/annotation_app/www/icons/prior.png |only soundgen-2.9.0/soundgen/inst/shiny/annotation_app/www/icons/synth.png |only soundgen-2.9.0/soundgen/inst/shiny/annotation_app/www/icons/unvoice.png |only soundgen-2.9.0/soundgen/inst/shiny/annotation_app/www/icons/update.png |only soundgen-2.9.0/soundgen/inst/shiny/annotation_app/www/icons/voice.png |only soundgen-2.9.0/soundgen/inst/shiny/formant_app/www/icons/octaveDown.png |only soundgen-2.9.0/soundgen/inst/shiny/formant_app/www/icons/octaveUp.png |only soundgen-2.9.0/soundgen/inst/shiny/formant_app/www/icons/prior.png |only soundgen-2.9.0/soundgen/inst/shiny/formant_app/www/icons/unvoice.png |only soundgen-2.9.0/soundgen/inst/shiny/formant_app/www/icons/voice.png |only soundgen-2.9.0/soundgen/inst/shiny/soundgen_main/www |only soundgen-2.9.0/soundgen/man/HzToERB.Rd |only soundgen-2.9.0/soundgen/man/HzToNotes.Rd |only soundgen-2.9.0/soundgen/man/HzToSemitones.Rd |only soundgen-2.9.0/soundgen/man/Mode.Rd |only soundgen-2.9.0/soundgen/man/addPitchCands.Rd |only soundgen-2.9.0/soundgen/man/addPitchJumps.Rd |only soundgen-2.9.0/soundgen/man/addSubh.Rd |only soundgen-2.9.0/soundgen/man/addSubh_per_epoch.Rd |only soundgen-2.9.0/soundgen/man/addVectors.Rd |only soundgen-2.9.0/soundgen/man/analyzeFrame.Rd |only soundgen-2.9.0/soundgen/man/averageMatrices.Rd |only soundgen-2.9.0/soundgen/man/checkInputType.Rd |only soundgen-2.9.0/soundgen/man/convertStringToFormants.Rd |only soundgen-2.9.0/soundgen/man/convert_sec_to_hms.Rd |only soundgen-2.9.0/soundgen/man/costJumps.Rd |only soundgen-2.9.0/soundgen/man/costPerPath.Rd |only soundgen-2.9.0/soundgen/man/dPhase.Rd |only soundgen-2.9.0/soundgen/man/def_form.Rd |only soundgen-2.9.0/soundgen/man/defaults.Rd |only soundgen-2.9.0/soundgen/man/defaults_analyze.Rd |only soundgen-2.9.0/soundgen/man/defaults_analyze_pitchCand.Rd |only soundgen-2.9.0/soundgen/man/detectNLP_training_synth.Rd |only soundgen-2.9.0/soundgen/man/divideIntoSyllables.Rd |only soundgen-2.9.0/soundgen/man/dot-addAM.Rd |only soundgen-2.9.0/soundgen/man/dot-addFormants.Rd |only soundgen-2.9.0/soundgen/man/dot-analyze.Rd |only soundgen-2.9.0/soundgen/man/dot-audSpectrogram.Rd |only soundgen-2.9.0/soundgen/man/dot-bandpass.Rd |only soundgen-2.9.0/soundgen/man/dot-detectNLP.Rd |only soundgen-2.9.0/soundgen/man/dot-fade.Rd |only soundgen-2.9.0/soundgen/man/dot-filterSoundByMS.Rd |only soundgen-2.9.0/soundgen/man/dot-flatEnv.Rd |only soundgen-2.9.0/soundgen/man/dot-flatSpectrum.Rd |only soundgen-2.9.0/soundgen/man/dot-getDuration.Rd |only soundgen-2.9.0/soundgen/man/dot-getLoudness.Rd |only soundgen-2.9.0/soundgen/man/dot-getPitchZc.Rd |only soundgen-2.9.0/soundgen/man/dot-getRMS.Rd |only soundgen-2.9.0/soundgen/man/dot-getSurprisal.Rd |only soundgen-2.9.0/soundgen/man/dot-modulationSpectrum.Rd |only soundgen-2.9.0/soundgen/man/dot-osc.Rd |only soundgen-2.9.0/soundgen/man/dot-phasegram.Rd |only soundgen-2.9.0/soundgen/man/dot-pitchDescriptives.Rd |only soundgen-2.9.0/soundgen/man/dot-prosody.Rd |only soundgen-2.9.0/soundgen/man/dot-resample.Rd |only soundgen-2.9.0/soundgen/man/dot-reverb.Rd |only soundgen-2.9.0/soundgen/man/dot-segment.Rd |only soundgen-2.9.0/soundgen/man/dot-shiftFormants.Rd |only soundgen-2.9.0/soundgen/man/dot-shiftPitch.Rd |only soundgen-2.9.0/soundgen/man/dot-spectrogram.Rd |only soundgen-2.9.0/soundgen/man/dot-ssm.Rd |only soundgen-2.9.0/soundgen/man/dot-timeStretch.Rd |only soundgen-2.9.0/soundgen/man/drawContour.Rd |only soundgen-2.9.0/soundgen/man/drawFreqAxis.Rd |only soundgen-2.9.0/soundgen/man/evaluatePars.Rd |only soundgen-2.9.0/soundgen/man/fart.Rd |only soundgen-2.9.0/soundgen/man/filled.contour.mod.Rd |only soundgen-2.9.0/soundgen/man/filterMS.Rd |only soundgen-2.9.0/soundgen/man/findBursts.Rd |only soundgen-2.9.0/soundgen/man/findElbow.Rd |only soundgen-2.9.0/soundgen/man/findGrad.Rd |only soundgen-2.9.0/soundgen/man/findInflections.Rd |only soundgen-2.9.0/soundgen/man/findJumps.Rd |only soundgen-2.9.0/soundgen/man/findSyllables.Rd |only soundgen-2.9.0/soundgen/man/findVoicedSegments.Rd |only soundgen-2.9.0/soundgen/man/findZeroCrossing.Rd |only soundgen-2.9.0/soundgen/man/flatSpectrum.Rd |only soundgen-2.9.0/soundgen/man/forcePerPath.Rd |only soundgen-2.9.0/soundgen/man/formatPitchManual.Rd |only soundgen-2.9.0/soundgen/man/generateEpoch.Rd |only soundgen-2.9.0/soundgen/man/generateGC.Rd |only soundgen-2.9.0/soundgen/man/generateHarmonics.Rd |only soundgen-2.9.0/soundgen/man/generatePath.Rd |only soundgen-2.9.0/soundgen/man/getAM.Rd |only soundgen-2.9.0/soundgen/man/getAM_env.Rd |only soundgen-2.9.0/soundgen/man/getCPP.Rd |only soundgen-2.9.0/soundgen/man/getCheckerboardKernel.Rd |only soundgen-2.9.0/soundgen/man/getDiscreteContour.Rd |only soundgen-2.9.0/soundgen/man/getDom.Rd |only soundgen-2.9.0/soundgen/man/getFeatureFlux.Rd |only soundgen-2.9.0/soundgen/man/getFormantDispersion.Rd |only soundgen-2.9.0/soundgen/man/getFormants.Rd |only soundgen-2.9.0/soundgen/man/getFrameBank.Rd |only soundgen-2.9.0/soundgen/man/getGlottalCycles.Rd |only soundgen-2.9.0/soundgen/man/getMelSpec.Rd |only soundgen-2.9.0/soundgen/man/getNovelty.Rd |only soundgen-2.9.0/soundgen/man/getPitchAutocor.Rd |only soundgen-2.9.0/soundgen/man/getPitchCep.Rd |only soundgen-2.9.0/soundgen/man/getPitchHps.Rd |only soundgen-2.9.0/soundgen/man/getPitchSpec.Rd |only soundgen-2.9.0/soundgen/man/getPrior.Rd |only soundgen-2.9.0/soundgen/man/getRough.Rd |only soundgen-2.9.0/soundgen/man/getSHR.Rd |only soundgen-2.9.0/soundgen/man/getSigmoid.Rd |only soundgen-2.9.0/soundgen/man/getSmoothSpectrum.Rd |only soundgen-2.9.0/soundgen/man/getSpectralEnvelope.Rd |only soundgen-2.9.0/soundgen/man/getSpectralFlux.Rd |only soundgen-2.9.0/soundgen/man/getSurprisal_matrix.Rd |only soundgen-2.9.0/soundgen/man/getSurprisal_vector.Rd |only soundgen-2.9.0/soundgen/man/guessPhase_GL.Rd |only soundgen-2.9.0/soundgen/man/guessPhase_spsi.Rd |only soundgen-2.9.0/soundgen/man/harmEnergy.Rd |only soundgen-2.9.0/soundgen/man/harmHeight.Rd |only soundgen-2.9.0/soundgen/man/harmHeight_dif.Rd |only soundgen-2.9.0/soundgen/man/harmHeight_peaks.Rd |only soundgen-2.9.0/soundgen/man/htmlPlots.Rd |only soundgen-2.9.0/soundgen/man/hz2mel.Rd |only soundgen-2.9.0/soundgen/man/identifyAndPlay.Rd |only soundgen-2.9.0/soundgen/man/intplNA.Rd |only soundgen-2.9.0/soundgen/man/isNeighbour_mod.Rd |only soundgen-2.9.0/soundgen/man/iso226.Rd |only soundgen-2.9.0/soundgen/man/istft_mod.Rd |only soundgen-2.9.0/soundgen/man/jet.col.Rd |only soundgen-2.9.0/soundgen/man/killDC.Rd |only soundgen-2.9.0/soundgen/man/lockToFormants.Rd |only soundgen-2.9.0/soundgen/man/log01.Rd |only soundgen-2.9.0/soundgen/man/logMatrix.Rd |only soundgen-2.9.0/soundgen/man/logWarpMS.Rd |only soundgen-2.9.0/soundgen/man/logistic.Rd |only soundgen-2.9.0/soundgen/man/logit.Rd |only soundgen-2.9.0/soundgen/man/matchColumns.Rd |only soundgen-2.9.0/soundgen/man/matchLengths.Rd |only soundgen-2.9.0/soundgen/man/medianSmoother.Rd |only soundgen-2.9.0/soundgen/man/modulationSpectrumFragment.Rd |only soundgen-2.9.0/soundgen/man/morphDF.Rd |only soundgen-2.9.0/soundgen/man/morphFormants.Rd |only soundgen-2.9.0/soundgen/man/morphList.Rd |only soundgen-2.9.0/soundgen/man/msToSpec.Rd |only soundgen-2.9.0/soundgen/man/na.trim.Rd |only soundgen-2.9.0/soundgen/man/naiveBayes_dynamicPrior.Rd |only soundgen-2.9.0/soundgen/man/naiveBayes_likelihood.Rd |only soundgen-2.9.0/soundgen/man/naiveBayes_train.Rd |only soundgen-2.9.0/soundgen/man/nonLinearPrediction_mod.Rd |only soundgen-2.9.0/soundgen/man/nonlinPred.Rd |only soundgen-2.9.0/soundgen/man/nonlinStats.Rd |only soundgen-2.9.0/soundgen/man/notesDict.Rd |only soundgen-2.9.0/soundgen/man/objectToString.Rd |only soundgen-2.9.0/soundgen/man/optimizePars.Rd |only soundgen-2.9.0/soundgen/man/pDistr.Rd |only soundgen-2.9.0/soundgen/man/parabPeakInterpol.Rd |only soundgen-2.9.0/soundgen/man/pathfinder.Rd |only soundgen-2.9.0/soundgen/man/pathfinding_fast.Rd |only soundgen-2.9.0/soundgen/man/pathfinding_slow.Rd |only soundgen-2.9.0/soundgen/man/permittedValues.Rd |only soundgen-2.9.0/soundgen/man/phasePropagate.Rd |only soundgen-2.9.0/soundgen/man/phon2sone.Rd |only soundgen-2.9.0/soundgen/man/pitchContour.Rd |only soundgen-2.9.0/soundgen/man/pitchManual.Rd |only soundgen-2.9.0/soundgen/man/plotSpec.Rd |only soundgen-2.9.0/soundgen/man/plotUnrasterized.Rd |only soundgen-2.9.0/soundgen/man/princarg.Rd |only soundgen-2.9.0/soundgen/man/processAudio.Rd |only soundgen-2.9.0/soundgen/man/pseudoLog.Rd |only soundgen-2.9.0/soundgen/man/pseudoLog_undo.Rd |only soundgen-2.9.0/soundgen/man/rbind_fill.Rd |only soundgen-2.9.0/soundgen/man/readAudio.Rd |only soundgen-2.9.0/soundgen/man/reformatAnchors.Rd |only soundgen-2.9.0/soundgen/man/reformatFormants.Rd |only soundgen-2.9.0/soundgen/man/rnorm_truncated2.Rd |only soundgen-2.9.0/soundgen/man/sampleModif.Rd |only soundgen-2.9.0/soundgen/man/scaleNoiseAnchors.Rd |only soundgen-2.9.0/soundgen/man/scaleSPL.Rd |only soundgen-2.9.0/soundgen/man/segmentManual.Rd |only soundgen-2.9.0/soundgen/man/selfsim.Rd |only soundgen-2.9.0/soundgen/man/silenceSegments.Rd |only soundgen-2.9.0/soundgen/man/sinc.Rd |only soundgen-2.9.0/soundgen/man/snake.Rd |only soundgen-2.9.0/soundgen/man/splitContour.Rd |only soundgen-2.9.0/soundgen/man/splitIntoChunks.Rd |only soundgen-2.9.0/soundgen/man/spreadSpec.Rd |only soundgen-2.9.0/soundgen/man/summarizeAnalyze.Rd |only soundgen-2.9.0/soundgen/man/switchColorTheme.Rd |only soundgen-2.9.0/soundgen/man/timeSeriesSummary.Rd |only soundgen-2.9.0/soundgen/man/to_dB.Rd |only soundgen-2.9.0/soundgen/man/updateAnalyze.Rd |only soundgen-2.9.0/soundgen/man/upsampleGC.Rd |only soundgen-2.9.0/soundgen/man/validatePars.Rd |only soundgen-2.9.0/soundgen/man/warpMatrix.Rd |only soundgen-2.9.0/soundgen/man/wiggleAnchors.Rd |only soundgen-2.9.0/soundgen/man/wiggleGC.Rd |only soundgen-2.9.0/soundgen/man/wigglePars.Rd |only soundgen-2.9.0/soundgen/man/writeAudio.Rd |only soundgen-2.9.0/soundgen/man/zeroOne.Rd |only soundgen-3.0.0/soundgen/DESCRIPTION | 30 soundgen-3.0.0/soundgen/MD5 | 613 -- soundgen-3.0.0/soundgen/NAMESPACE | 51 soundgen-3.0.0/soundgen/NEWS | 100 soundgen-3.0.0/soundgen/R/SSM.R | 737 +- soundgen-3.0.0/soundgen/R/am.R | 599 +- soundgen-3.0.0/soundgen/R/amplitude.R | 684 +- soundgen-3.0.0/soundgen/R/analyze.R | 1137 ++-- soundgen-3.0.0/soundgen/R/analyze_utilities.R | 258 - soundgen-3.0.0/soundgen/R/apps.R | 234 soundgen-3.0.0/soundgen/R/audSpectrogram.R |only soundgen-3.0.0/soundgen/R/compareSounds.R | 689 +- soundgen-3.0.0/soundgen/R/data.R | 67 soundgen-3.0.0/soundgen/R/detectNLP.R | 514 +- soundgen-3.0.0/soundgen/R/duration.R | 32 soundgen-3.0.0/soundgen/R/fft.R |only soundgen-3.0.0/soundgen/R/filters.R | 281 - soundgen-3.0.0/soundgen/R/formants.R | 1208 ++-- soundgen-3.0.0/soundgen/R/formants_utilities.R | 169 soundgen-3.0.0/soundgen/R/frequency_scales.R | 335 - soundgen-3.0.0/soundgen/R/getSpec.R |only soundgen-3.0.0/soundgen/R/helpers.R |only soundgen-3.0.0/soundgen/R/interpolate.R |only soundgen-3.0.0/soundgen/R/invertModulSpec.R | 968 ++- soundgen-3.0.0/soundgen/R/invertSpectrogram.R | 259 - soundgen-3.0.0/soundgen/R/io.R | 850 ++- soundgen-3.0.0/soundgen/R/loudness.R | 647 +- soundgen-3.0.0/soundgen/R/loudness_utilities.R | 212 soundgen-3.0.0/soundgen/R/math.R | 1712 ++---- soundgen-3.0.0/soundgen/R/matrix.R |only soundgen-3.0.0/soundgen/R/modulationSpectrum.R | 1120 ++-- soundgen-3.0.0/soundgen/R/modulationSpectrum_utilities.R | 793 +-- soundgen-3.0.0/soundgen/R/morph.R | 236 soundgen-3.0.0/soundgen/R/morph_utilities.R | 74 soundgen-3.0.0/soundgen/R/naiveBayes.R | 629 +- soundgen-3.0.0/soundgen/R/noiseRemoval.R | 207 soundgen-3.0.0/soundgen/R/osc.R | 198 soundgen-3.0.0/soundgen/R/phasegram.R | 883 ++- soundgen-3.0.0/soundgen/R/pitchDescriptives.R | 335 - soundgen-3.0.0/soundgen/R/pitchTrackers.R | 810 +-- soundgen-3.0.0/soundgen/R/pitch_postprocessing.R | 1403 ++--- soundgen-3.0.0/soundgen/R/postprocessing.R | 755 +- soundgen-3.0.0/soundgen/R/presets.R | 68 soundgen-3.0.0/soundgen/R/prosody.R | 181 soundgen-3.0.0/soundgen/R/resample.R | 294 - soundgen-3.0.0/soundgen/R/rolloff.R | 322 - soundgen-3.0.0/soundgen/R/segment.R | 1015 +-- soundgen-3.0.0/soundgen/R/segment_utilities.R | 600 +- soundgen-3.0.0/soundgen/R/shiftFormants.R | 368 - soundgen-3.0.0/soundgen/R/shiftPitch.R | 735 +- soundgen-3.0.0/soundgen/R/smoothContours.R | 535 -- soundgen-3.0.0/soundgen/R/soundgen-package.R | 94 soundgen-3.0.0/soundgen/R/soundgen.R | 1285 ++--- soundgen-3.0.0/soundgen/R/soundgen_utilities.R | 794 ++- soundgen-3.0.0/soundgen/R/source.R | 1099 +--- soundgen-3.0.0/soundgen/R/spectralDescr.R | 522 -- soundgen-3.0.0/soundgen/R/spectrogram.R | 972 +-- soundgen-3.0.0/soundgen/R/stft.R |only soundgen-3.0.0/soundgen/R/surprisal.R | 1143 ++-- soundgen-3.0.0/soundgen/R/sysdata.rda |binary soundgen-3.0.0/soundgen/R/timeStretch.R | 116 soundgen-3.0.0/soundgen/R/vtl.R | 367 - soundgen-3.0.0/soundgen/R/windowFunctions.R |only soundgen-3.0.0/soundgen/README.md | 157 soundgen-3.0.0/soundgen/data/IR.rda |only soundgen-3.0.0/soundgen/data/detectNLP_training_nonv.rda |binary soundgen-3.0.0/soundgen/data/detectNLP_training_synth.rda |binary soundgen-3.0.0/soundgen/data/presets.rda |binary soundgen-3.0.0/soundgen/data/speechEx.rda |only soundgen-3.0.0/soundgen/inst/shiny/annotation_app/server.R | 873 +-- soundgen-3.0.0/soundgen/inst/shiny/annotation_app/ui.R | 236 soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/annotation_app.css | 6 soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/annotation_app.js | 81 soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/annotation_app_shinyjs.js | 109 soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/annotate.png |binary soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/backward.png |binary soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/delete.png |binary soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/forward.png |binary soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/minus.png |binary soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/play.png |binary soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/plus.png |binary soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/snap.png |only soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/stop.png |binary soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/zoomIn.png |binary soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/zoomOut.png |binary soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/icons/zoomSel.png |binary soundgen-3.0.0/soundgen/inst/shiny/annotation_app/www/temp.csv |only soundgen-3.0.0/soundgen/inst/shiny/formant_app/server.R | 2560 ++++------ soundgen-3.0.0/soundgen/inst/shiny/formant_app/ui.R | 438 - soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/formant_app.css | 41 soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/formant_app.js | 86 soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/formant_app_shinyjs.js | 127 soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/icons/annotate.png |binary soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/icons/backward.png |binary soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/icons/delete.png |binary soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/icons/forward.png |binary soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/icons/minus.png |binary soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/icons/play.png |binary soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/icons/plus.png |binary soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/icons/snap.png |only soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/icons/stop.png |binary soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/icons/synth.png |binary soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/icons/update.png |binary soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/icons/zoomIn.png |binary soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/icons/zoomOut.png |binary soundgen-3.0.0/soundgen/inst/shiny/formant_app/www/icons/zoomSel.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/server.R | 320 - soundgen-3.0.0/soundgen/inst/shiny/pitch_app/ui.R | 476 - soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/icons/backward.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/icons/forward.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/icons/octaveDown.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/icons/octaveUp.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/icons/play.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/icons/prior.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/icons/stop.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/icons/synth.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/icons/unvoice.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/icons/update.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/icons/voice.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/icons/zoomIn.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/icons/zoomOut.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/icons/zoomSel.png |binary soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/pitch_app.js | 7 soundgen-3.0.0/soundgen/inst/shiny/pitch_app/www/pitch_app_shinyjs.js | 129 soundgen-3.0.0/soundgen/inst/shiny/soundgen_main/server.R | 502 + soundgen-3.0.0/soundgen/inst/shiny/soundgen_main/ui.R | 409 - soundgen-3.0.0/soundgen/man/HzToOther.Rd | 59 soundgen-3.0.0/soundgen/man/IR.Rd |only soundgen-3.0.0/soundgen/man/acf_fft.Rd |only soundgen-3.0.0/soundgen/man/addAM.Rd | 86 soundgen-3.0.0/soundgen/man/addFormants.Rd | 163 soundgen-3.0.0/soundgen/man/analyze.Rd | 535 -- soundgen-3.0.0/soundgen/man/annotation_app.Rd | 37 soundgen-3.0.0/soundgen/man/audSpectrogram.Rd | 209 soundgen-3.0.0/soundgen/man/bandpass.Rd | 122 soundgen-3.0.0/soundgen/man/beat.Rd | 11 soundgen-3.0.0/soundgen/man/clumper.Rd | 23 soundgen-3.0.0/soundgen/man/compareSounds.Rd | 318 - soundgen-3.0.0/soundgen/man/crossFade.Rd | 100 soundgen-3.0.0/soundgen/man/detectNLP.Rd | 104 soundgen-3.0.0/soundgen/man/detectNLP_training_nonv.Rd | 15 soundgen-3.0.0/soundgen/man/dot-roxygen_defaults.Rd |only soundgen-3.0.0/soundgen/man/estimateVTL.Rd | 47 soundgen-3.0.0/soundgen/man/fade.Rd | 72 soundgen-3.0.0/soundgen/man/figures/README-analysis-1.png |binary soundgen-3.0.0/soundgen/man/figures/README-synthsesis-1.png |binary soundgen-3.0.0/soundgen/man/figures/s.mp3 |binary soundgen-3.0.0/soundgen/man/filterSoundByMS.Rd | 347 - soundgen-3.0.0/soundgen/man/findPeaks.Rd | 45 soundgen-3.0.0/soundgen/man/flatEnv.Rd | 63 soundgen-3.0.0/soundgen/man/formant_app.Rd | 43 soundgen-3.0.0/soundgen/man/gaussianSmooth2D.Rd | 67 soundgen-3.0.0/soundgen/man/generateNoise.Rd | 174 soundgen-3.0.0/soundgen/man/getBandwidth.Rd | 5 soundgen-3.0.0/soundgen/man/getDuration.Rd | 20 soundgen-3.0.0/soundgen/man/getEntropy.Rd | 25 soundgen-3.0.0/soundgen/man/getEnv.Rd | 59 soundgen-3.0.0/soundgen/man/getFormantFilter.Rd |only soundgen-3.0.0/soundgen/man/getHNR.Rd | 102 soundgen-3.0.0/soundgen/man/getIntegerRandomWalk.Rd | 9 soundgen-3.0.0/soundgen/man/getLoudness.Rd | 196 soundgen-3.0.0/soundgen/man/getPeakFreq.Rd | 72 soundgen-3.0.0/soundgen/man/getPitchZc.Rd | 42 soundgen-3.0.0/soundgen/man/getRMS.Rd | 70 soundgen-3.0.0/soundgen/man/getRandomWalk.Rd | 17 soundgen-3.0.0/soundgen/man/getRolloff.Rd | 123 soundgen-3.0.0/soundgen/man/getRoughness.Rd |only soundgen-3.0.0/soundgen/man/getSharpness.Rd |only soundgen-3.0.0/soundgen/man/getSmoothContour.Rd | 98 soundgen-3.0.0/soundgen/man/getSpec.Rd |only soundgen-3.0.0/soundgen/man/getSpecEnv.Rd |only soundgen-3.0.0/soundgen/man/getSurprisal.Rd | 436 + soundgen-3.0.0/soundgen/man/hilbert_exact.Rd |only soundgen-3.0.0/soundgen/man/interpolMatrix.Rd | 34 soundgen-3.0.0/soundgen/man/interpolate.Rd | 170 soundgen-3.0.0/soundgen/man/interpolateNA.Rd |only soundgen-3.0.0/soundgen/man/invertSpectrogram.Rd | 93 soundgen-3.0.0/soundgen/man/matchPars.Rd | 98 soundgen-3.0.0/soundgen/man/mixAtSNR.Rd |only soundgen-3.0.0/soundgen/man/modulationSpectrum.Rd | 486 + soundgen-3.0.0/soundgen/man/morph.Rd | 30 soundgen-3.0.0/soundgen/man/naiveBayes.Rd | 69 soundgen-3.0.0/soundgen/man/noiseRemoval.Rd | 111 soundgen-3.0.0/soundgen/man/normalizeFolder.Rd | 67 soundgen-3.0.0/soundgen/man/osc.Rd | 63 soundgen-3.0.0/soundgen/man/phasegram.Rd | 147 soundgen-3.0.0/soundgen/man/pitchDescriptives.Rd | 64 soundgen-3.0.0/soundgen/man/pitchSmoothPraat.Rd | 21 soundgen-3.0.0/soundgen/man/pitch_app.Rd | 58 soundgen-3.0.0/soundgen/man/playme.Rd | 38 soundgen-3.0.0/soundgen/man/plotMS.Rd | 47 soundgen-3.0.0/soundgen/man/presets.Rd | 3 soundgen-3.0.0/soundgen/man/prosody.Rd | 96 soundgen-3.0.0/soundgen/man/reportCI.Rd | 29 soundgen-3.0.0/soundgen/man/reportTime.Rd | 8 soundgen-3.0.0/soundgen/man/resample.Rd | 109 soundgen-3.0.0/soundgen/man/reverb.Rd | 94 soundgen-3.0.0/soundgen/man/rnorm_truncated.Rd | 34 soundgen-3.0.0/soundgen/man/schwa.Rd | 46 soundgen-3.0.0/soundgen/man/segment.Rd | 328 - soundgen-3.0.0/soundgen/man/segment_ann.Rd |only soundgen-3.0.0/soundgen/man/shiftFormants.Rd | 124 soundgen-3.0.0/soundgen/man/shiftPitch.Rd | 221 soundgen-3.0.0/soundgen/man/soundgen-package.Rd | 28 soundgen-3.0.0/soundgen/man/soundgen.Rd | 559 +- soundgen-3.0.0/soundgen/man/soundgen_app.Rd | 16 soundgen-3.0.0/soundgen/man/specToMS.Rd | 65 soundgen-3.0.0/soundgen/man/specToMS_1D.Rd | 41 soundgen-3.0.0/soundgen/man/spectrogram.Rd | 257 - soundgen-3.0.0/soundgen/man/spectrum.Rd |only soundgen-3.0.0/soundgen/man/speechEx.Rd |only soundgen-3.0.0/soundgen/man/ssm.Rd | 181 soundgen-3.0.0/soundgen/man/stft_simple.Rd |only soundgen-3.0.0/soundgen/man/timeStretch.Rd | 61 soundgen-3.0.0/soundgen/man/transplantEnv.Rd | 39 soundgen-3.0.0/soundgen/man/transplantFormants.Rd | 184 soundgen-3.0.0/soundgen/man/winFun.Rd |only 427 files changed, 24035 insertions(+), 20894 deletions(-)
Title: Power Under Multiplicity Project
Description: Estimates power, minimum detectable effect size (MDES) and sample size requirements. The context is multilevel randomized experiments with multiple outcomes. The estimation takes into account the use of multiple testing procedures. Development of this package was supported by a grant from the Institute of Education Sciences (R305D170030). For a full package description, including a detailed technical appendix, see <doi:10.18637/jss.v108.i06>.
Author: Luke Miratrix [aut, cre] ,
Kristen Hunter [aut] ,
Zarni Htet [aut],
Kristin Porter [aut],
MDRC [cph],
Institute of Education Sciences [fnd]
Maintainer: Luke Miratrix <luke_miratrix@gse.harvard.edu>
Diff between PUMP versions 1.0.4 dated 2025-03-12 and 1.0.5 dated 2026-09-20
PUMP-1.0.4/PUMP/tests/testthat/test-powerup.R |only PUMP-1.0.4/PUMP/vignettes/pump_demo_cache |only PUMP-1.0.4/PUMP/vignettes/pump_demo_files |only PUMP-1.0.5/PUMP/DESCRIPTION | 15 - PUMP-1.0.5/PUMP/MD5 | 148 +++-------------- PUMP-1.0.5/PUMP/NAMESPACE | 9 - PUMP-1.0.5/PUMP/R/model_fitting.R | 9 - PUMP-1.0.5/PUMP/R/plots.R | 8 PUMP-1.0.5/PUMP/R/pumpresult.R | 11 + PUMP-1.0.5/PUMP/build/partial.rdb |binary PUMP-1.0.5/PUMP/build/vignette.rds |binary PUMP-1.0.5/PUMP/inst/doc/pump_demo.html | 107 ++++++------ PUMP-1.0.5/PUMP/inst/doc/pump_sample_demo.html | 60 ++++-- PUMP-1.0.5/PUMP/inst/doc/pump_simulate.html | 5 PUMP-1.0.5/PUMP/man/PUMP-package.Rd | 1 PUMP-1.0.5/PUMP/man/get_pval_tstat.Rd | 11 - PUMP-1.0.5/PUMP/man/pump_mdes_grid.Rd | 6 PUMP-1.0.5/PUMP/man/pump_power_grid.Rd | 6 PUMP-1.0.5/PUMP/man/pump_sample_grid.Rd | 6 PUMP-1.0.5/PUMP/man/pumpresult.Rd | 2 PUMP-1.0.5/PUMP/tests/testthat/Rplots.pdf |binary PUMP-1.0.5/PUMP/tests/testthat/test-pump_sample.R | 6 PUMP-1.0.5/PUMP/tests/testthat/test-update_functions.R | 76 ++++++++ PUMP-1.0.5/PUMP/vignettes/output/ICCgrid.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/MDEScalc.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/MDEScalcmin1.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/MDESwithNumZero.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/numzerogrid.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/othercorrections.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/powICC.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/powR2.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/powbase.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/rhogrid.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/samplesizecalc.RDS |binary PUMP-1.0.5/PUMP/vignettes/output/samplesizeverify.RDS |binary 35 files changed, 244 insertions(+), 242 deletions(-)
Title: Retrieve, Transform and Analyze the Barcode of Life Data Systems
Data
Description: Facilitates retrieval, transformation and analysis of the data
from the Barcode of Life Data Systems (BOLD) database <https://boldsystems.org/>.
This package allows both public and private user data to be easily downloaded into the R
environment using a variety of inputs such as: IDs (processid, sampleid), BINs, dataset codes,
project codes, taxonomy, geography etc. It provides frictionless data conversion
into formats compatible with other R-packages and third-party tools,
as well as functions for sequence alignment & clustering, biodiversity analysis and spatial mapping.
Author: Sameer Padhye [aut, cre],
Liliana Ballesteros-Mejia [aut],
Timothy Agda [aut],
Jireh Agda [aut],
Sujeevan Ratnasingham [aut]
Maintainer: Sameer Padhye <spadhye@uoguelph.ca>
Diff between BOLDconnectR versions 1.0.2 dated 2026-08-19 and 1.0.3 dated 2026-09-20
DESCRIPTION | 8 - MD5 | 16 +- NAMESPACE | 212 ++++++++++++++++-------------- NEWS.md | 3 R/external.bold.fields.info.R | 71 ++++++---- R/helper.functions.4.bold.public.search.R | 38 +++-- README.md | 4 inst/doc/boldconnectr_workflow.html | 20 +- man/base_url_parse.Rd | 4 9 files changed, 219 insertions(+), 157 deletions(-)
Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine
copula modeling. The 'rvinecopulib' package implements the core features of the
popular 'VineCopula' package, in particular inference algorithms for both vine
copula and bivariate copula models. Advantages over 'VineCopula' are a sleeker
and more modern API, improved performances, especially in high dimensions,
nonparametric and multi-parameter families, and the ability to model discrete
variables. The 'rvinecopulib' package includes 'vinecopulib' as header-only
C++ library (currently version 1.0.0). Thus users do not need to install
'vinecopulib' itself in order to use 'rvinecopulib'. Since their initial
releases, 'vinecopulib' is licensed under the MIT License, and 'rvinecopulib'
is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>
Diff between rvinecopulib versions 0.7.3.1.0 dated 2025-06-13 and 1.0.0.1.0 dated 2026-09-20
rvinecopulib-0.7.3.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_bobyqa.hpp |only rvinecopulib-0.7.3.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_optional.hpp |only rvinecopulib-1.0.0.1.0/rvinecopulib/DESCRIPTION | 22 rvinecopulib-1.0.0.1.0/rvinecopulib/MD5 | 307 rvinecopulib-1.0.0.1.0/rvinecopulib/NAMESPACE | 69 rvinecopulib-1.0.0.1.0/rvinecopulib/NEWS.md | 117 rvinecopulib-1.0.0.1.0/rvinecopulib/R/RcppExports.R | 84 rvinecopulib-1.0.0.1.0/rvinecopulib/R/as_rvine_structure.R | 21 rvinecopulib-1.0.0.1.0/rvinecopulib/R/bicop.R | 24 rvinecopulib-1.0.0.1.0/rvinecopulib/R/bicop_methods.R | 268 rvinecopulib-1.0.0.1.0/rvinecopulib/R/getters.R | 3 rvinecopulib-1.0.0.1.0/rvinecopulib/R/margins.R |only rvinecopulib-1.0.0.1.0/rvinecopulib/R/pairs_copula_data.R | 4 rvinecopulib-1.0.0.1.0/rvinecopulib/R/rosenblatt.R | 136 rvinecopulib-1.0.0.1.0/rvinecopulib/R/rvine_structure.R | 30 rvinecopulib-1.0.0.1.0/rvinecopulib/R/rvinecopulib.R | 104 rvinecopulib-1.0.0.1.0/rvinecopulib/R/tools.R | 260 rvinecopulib-1.0.0.1.0/rvinecopulib/R/truncate_model.R | 9 rvinecopulib-1.0.0.1.0/rvinecopulib/R/vcov.R |only rvinecopulib-1.0.0.1.0/rvinecopulib/R/vine.R | 579 rvinecopulib-1.0.0.1.0/rvinecopulib/R/vine_methods.R | 226 rvinecopulib-1.0.0.1.0/rvinecopulib/R/vinecop.R | 103 rvinecopulib-1.0.0.1.0/rvinecopulib/R/vinecop_methods.R | 316 rvinecopulib-1.0.0.1.0/rvinecopulib/R/vinecop_plot.R | 2 rvinecopulib-1.0.0.1.0/rvinecopulib/README.md | 349 rvinecopulib-1.0.0.1.0/rvinecopulib/build |only rvinecopulib-1.0.0.1.0/rvinecopulib/inst/doc |only rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib-wrappers.hpp | 59 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib.hpp | 11 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/LICENSE |only rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/REVISION |only rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/abstract.hpp | 176 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/archimedean.hpp | 65 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/bb1.hpp | 54 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/bb6.hpp | 54 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/bb7.hpp | 54 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/bb8.hpp | 54 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/class.hpp | 296 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/clayton.hpp | 60 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/elliptical.hpp | 24 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/extreme_value.hpp | 63 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/family.hpp | 96 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/fit_controls.hpp | 33 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/frank.hpp | 58 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/gaussian.hpp | 52 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/gumbel.hpp | 60 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/abstract.ipp | 570 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/archimedean.ipp | 74 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/bb1.ipp | 2514 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/bb6.ipp | 3633 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/bb7.ipp | 2770 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/bb8.ipp | 3581 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/class.ipp | 1648 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/clayton.ipp | 549 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/elliptical.ipp | 30 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/extreme_value.ipp | 154 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/family.ipp | 83 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/fit_controls.ipp | 147 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/frank.ipp | 539 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/gaussian.ipp | 475 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/gumbel.ipp | 915 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/indep.ipp | 20 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/joe.ipp | 702 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/kernel.ipp | 102 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/parametric.ipp | 272 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/student.ipp | 1395 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/tawn.ipp | 5082 + rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/tll.ipp | 58 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/implementation/tools_select.ipp | 12 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/indep.hpp | 37 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/joe.hpp | 59 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/kernel.hpp | 46 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/parametric.hpp | 63 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/student.hpp | 114 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/tawn.hpp | 51 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/tll.hpp | 11 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/bicop/tools_select.hpp | 2 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/mainpage.h |only rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/fit_controls.hpp | 118 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/implementation/tools_eigen.ipp | 146 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/implementation/tools_interpolation.ipp | 571 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/implementation/tools_optimization.ipp | 341 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/implementation/tools_stats.ipp | 394 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/implementation/tools_transforms.ipp |only rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/nlohmann_json.hpp |43008 +++++----- rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_batch.hpp | 3 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_constants.hpp | 2 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_eigen.hpp | 123 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_integration.hpp | 70 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_interface.hpp | 3 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_interpolation.hpp | 101 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_optimization.hpp | 91 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_serialization.hpp | 110 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_stats.hpp | 54 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_stats_ghalton.hpp | 2 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_stats_sobol.hpp | 2 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_stl.hpp | 63 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_thread.hpp | 157 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/tools_transforms.hpp |only rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/misc/triangular_array.hpp | 66 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/version.hpp | 9 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/vinecop/class.hpp | 368 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/vinecop/fit_controls.hpp | 89 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/vinecop/implementation/class.ipp | 2640 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/vinecop/implementation/fit_controls.ipp | 177 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/vinecop/implementation/rvine_structure.ipp | 130 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/vinecop/implementation/rvine_trees.ipp |only rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/vinecop/implementation/tools_select.ipp | 1040 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/vinecop/rvine_structure.hpp | 34 rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/vinecop/rvine_trees.hpp |only rvinecopulib-1.0.0.1.0/rvinecopulib/inst/include/vinecopulib/vinecop/tools_select.hpp | 121 rvinecopulib-1.0.0.1.0/rvinecopulib/man/as_margin.Rd |only rvinecopulib-1.0.0.1.0/rvinecopulib/man/bicop.Rd | 4 rvinecopulib-1.0.0.1.0/rvinecopulib/man/bicop_dependence.Rd |only rvinecopulib-1.0.0.1.0/rvinecopulib/man/bicop_methods.Rd | 72 rvinecopulib-1.0.0.1.0/rvinecopulib/man/kde1d_family.Rd |only rvinecopulib-1.0.0.1.0/rvinecopulib/man/mBICV.Rd | 6 rvinecopulib-1.0.0.1.0/rvinecopulib/man/margin_dist.Rd |only rvinecopulib-1.0.0.1.0/rvinecopulib/man/margin_family.Rd |only rvinecopulib-1.0.0.1.0/rvinecopulib/man/margin_family_protocol.Rd |only rvinecopulib-1.0.0.1.0/rvinecopulib/man/margin_protocol.Rd |only rvinecopulib-1.0.0.1.0/rvinecopulib/man/parameter_uncertainty.Rd |only rvinecopulib-1.0.0.1.0/rvinecopulib/man/plot.bicop_dist.Rd | 6 rvinecopulib-1.0.0.1.0/rvinecopulib/man/plot.vinecop_dist.Rd | 2 rvinecopulib-1.0.0.1.0/rvinecopulib/man/predict_bicop.Rd | 2 rvinecopulib-1.0.0.1.0/rvinecopulib/man/predict_vinecop.Rd | 2 rvinecopulib-1.0.0.1.0/rvinecopulib/man/rosenblatt.Rd | 95 rvinecopulib-1.0.0.1.0/rvinecopulib/man/rvinecopulib.Rd | 111 rvinecopulib-1.0.0.1.0/rvinecopulib/man/stats_margin.Rd |only rvinecopulib-1.0.0.1.0/rvinecopulib/man/univariateML_family.Rd |only rvinecopulib-1.0.0.1.0/rvinecopulib/man/vine.Rd | 111 rvinecopulib-1.0.0.1.0/rvinecopulib/man/vine_methods.Rd | 33 rvinecopulib-1.0.0.1.0/rvinecopulib/man/vinecop.Rd | 49 rvinecopulib-1.0.0.1.0/rvinecopulib/man/vinecop_methods.Rd | 106 rvinecopulib-1.0.0.1.0/rvinecopulib/man/zero_inflated.Rd |only rvinecopulib-1.0.0.1.0/rvinecopulib/src/Makevars | 3 rvinecopulib-1.0.0.1.0/rvinecopulib/src/Makevars.win | 2 rvinecopulib-1.0.0.1.0/rvinecopulib/src/RcppExports.cpp | 267 rvinecopulib-1.0.0.1.0/rvinecopulib/src/vinecopulib-interface.cpp | 394 rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/Rplots.pdf | 1518 rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/test_bicop.R | 47 rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/test_bicop_dist.R | 645 rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/test_count_validation.R |only rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/test_discrete.R | 131 rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/test_margins.R |only rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/test_rosenblatt.R | 160 rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/test_rvine_structure.R | 6 rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/test_tools.R | 4 rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/test_truncate_model.R | 27 rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/test_vcov.R |only rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/test_vine.R | 551 rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/test_vine_dist.R | 143 rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/test_vinecop.R | 364 rvinecopulib-1.0.0.1.0/rvinecopulib/tests/testthat/test_vinecop_dist.R | 446 rvinecopulib-1.0.0.1.0/rvinecopulib/vignettes |only 155 files changed, 59320 insertions(+), 26030 deletions(-)
Title: Bayesian Probit Choice Modeling
Description: Fits Bayesian probit models for binary, multinomial, ordered, and ranked
choices in cross-sectional and panel data. Correlated or uncorrelated normal
and log-normal random coefficients, finite mixtures, sparse finite
mixtures, and Dirichlet process mixtures describe preference
heterogeneity. Multiple Gibbs chains produce posterior draws for
diagnostics and choice prediction. Empirical model data can be
supplied as a data frame or simulated from the requested specification.
For an overarching treatment of the methodology, see Oelschlaeger (2026)
<https://pub.uni-bielefeld.de/record/3014719>. The latent-class model is
described in Oelschlaeger and Bauer (2021)
<https://trid.trb.org/view/1759753>.
Author: Lennart Oelschlaeger [aut, cre] ,
Dietmar Bauer [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between RprobitB versions 1.2.0 dated 2025-08-25 and 2.0.0 dated 2026-09-20
RprobitB-1.2.0/RprobitB/R/R_hat.R |only RprobitB-1.2.0/RprobitB/R/RprobitB_data.R |only RprobitB-1.2.0/RprobitB/R/RprobitB_fit.R |only RprobitB-1.2.0/RprobitB/R/RprobitB_gibbs_samples_statistics.R |only RprobitB-1.2.0/RprobitB/R/RprobitB_latent_classes.R |only RprobitB-1.2.0/RprobitB/R/RprobitB_normalization.R |only RprobitB-1.2.0/RprobitB/R/RprobitB_parameter.R |only RprobitB-1.2.0/RprobitB/R/WAIC.R |only RprobitB-1.2.0/RprobitB/R/as_cov_names.R |only RprobitB-1.2.0/RprobitB/R/check_form.R |only RprobitB-1.2.0/RprobitB/R/check_prior.R |only RprobitB-1.2.0/RprobitB/R/choice_probabilities.R |only RprobitB-1.2.0/RprobitB/R/classification.R |only RprobitB-1.2.0/RprobitB/R/coef.RprobitB_fit.R |only RprobitB-1.2.0/RprobitB/R/compute_p_si.R |only RprobitB-1.2.0/RprobitB/R/cov_mix.R |only RprobitB-1.2.0/RprobitB/R/create_lagged_cov.R |only RprobitB-1.2.0/RprobitB/R/data.R |only RprobitB-1.2.0/RprobitB/R/draw_from_prior.R |only RprobitB-1.2.0/RprobitB/R/filter_gibbs_samples.R |only RprobitB-1.2.0/RprobitB/R/fit_model.R |only RprobitB-1.2.0/RprobitB/R/get_cov.R |only RprobitB-1.2.0/RprobitB/R/logLik.RprobitB_fit.R |only RprobitB-1.2.0/RprobitB/R/missing_covariates.R |only RprobitB-1.2.0/RprobitB/R/mml.R |only RprobitB-1.2.0/RprobitB/R/mode_approx.R |only RprobitB-1.2.0/RprobitB/R/model_selection.R |only RprobitB-1.2.0/RprobitB/R/nobs.RprobitB_fit.R |only RprobitB-1.2.0/RprobitB/R/npar.RprobitB_fit.R |only RprobitB-1.2.0/RprobitB/R/overview_effects.R |only RprobitB-1.2.0/RprobitB/R/parameter_labels.R |only RprobitB-1.2.0/RprobitB/R/plotting.R |only RprobitB-1.2.0/RprobitB/R/point_estimates.R |only RprobitB-1.2.0/RprobitB/R/posterior_pars.R |only RprobitB-1.2.0/RprobitB/R/pred_acc.R |only RprobitB-1.2.0/RprobitB/R/predict.RprobitB_fit.R |only RprobitB-1.2.0/RprobitB/R/preference_flip.R |only RprobitB-1.2.0/RprobitB/R/prepare_data.R |only RprobitB-1.2.0/RprobitB/R/simulate_choices.R |only RprobitB-1.2.0/RprobitB/R/sufficient_statistics.R |only RprobitB-1.2.0/RprobitB/R/train_test.R |only RprobitB-1.2.0/RprobitB/R/transform.RprobitB_fit.R |only RprobitB-1.2.0/RprobitB/R/transform_gibbs_samples.R |only RprobitB-1.2.0/RprobitB/R/transform_parameter.R |only RprobitB-1.2.0/RprobitB/R/update.RprobitB_fit.R |only RprobitB-1.2.0/RprobitB/data |only RprobitB-1.2.0/RprobitB/inst/doc/RprobitB.Rmd |only RprobitB-1.2.0/RprobitB/inst/doc/RprobitB.html |only RprobitB-1.2.0/RprobitB/inst/doc/v01_model_definition.R |only RprobitB-1.2.0/RprobitB/inst/doc/v01_model_definition.Rmd |only RprobitB-1.2.0/RprobitB/inst/doc/v01_model_definition.html |only RprobitB-1.2.0/RprobitB/inst/doc/v02_choice_data.R |only RprobitB-1.2.0/RprobitB/inst/doc/v02_choice_data.Rmd |only RprobitB-1.2.0/RprobitB/inst/doc/v02_choice_data.html |only RprobitB-1.2.0/RprobitB/inst/doc/v03_model_fitting.R |only RprobitB-1.2.0/RprobitB/inst/doc/v03_model_fitting.Rmd |only RprobitB-1.2.0/RprobitB/inst/doc/v03_model_fitting.html |only RprobitB-1.2.0/RprobitB/inst/doc/v04_modeling_heterogeneity.R |only RprobitB-1.2.0/RprobitB/inst/doc/v04_modeling_heterogeneity.Rmd |only RprobitB-1.2.0/RprobitB/inst/doc/v04_modeling_heterogeneity.html |only RprobitB-1.2.0/RprobitB/inst/doc/v05_choice_prediction.R |only RprobitB-1.2.0/RprobitB/inst/doc/v05_choice_prediction.Rmd |only RprobitB-1.2.0/RprobitB/inst/doc/v05_choice_prediction.html |only RprobitB-1.2.0/RprobitB/inst/doc/v06_model_selection.R |only RprobitB-1.2.0/RprobitB/inst/doc/v06_model_selection.Rmd |only RprobitB-1.2.0/RprobitB/inst/doc/v06_model_selection.html |only RprobitB-1.2.0/RprobitB/man/R_hat.Rd |only RprobitB-1.2.0/RprobitB/man/RprobitB_data.Rd |only RprobitB-1.2.0/RprobitB/man/RprobitB_fit.Rd |only RprobitB-1.2.0/RprobitB/man/RprobitB_gibbs_samples_statistics.Rd |only RprobitB-1.2.0/RprobitB/man/RprobitB_latent_classes.Rd |only RprobitB-1.2.0/RprobitB/man/RprobitB_normalization.Rd |only RprobitB-1.2.0/RprobitB/man/RprobitB_parameter.Rd |only RprobitB-1.2.0/RprobitB/man/as_cov_names.Rd |only RprobitB-1.2.0/RprobitB/man/check_form.Rd |only RprobitB-1.2.0/RprobitB/man/check_prior.Rd |only RprobitB-1.2.0/RprobitB/man/choice_probabilities.Rd |only RprobitB-1.2.0/RprobitB/man/classification.Rd |only RprobitB-1.2.0/RprobitB/man/compute_choice_probabilities.Rd |only RprobitB-1.2.0/RprobitB/man/compute_p_si.Rd |only RprobitB-1.2.0/RprobitB/man/cov_mix.Rd |only RprobitB-1.2.0/RprobitB/man/create_lagged_cov.Rd |only RprobitB-1.2.0/RprobitB/man/d_to_gamma.Rd |only RprobitB-1.2.0/RprobitB/man/draw_from_prior.Rd |only RprobitB-1.2.0/RprobitB/man/figures/README-coef-1.png |only RprobitB-1.2.0/RprobitB/man/figures/README-fit-1.png |only RprobitB-1.2.0/RprobitB/man/filter_gibbs_samples.Rd |only RprobitB-1.2.0/RprobitB/man/fit_model.Rd |only RprobitB-1.2.0/RprobitB/man/get_cov.Rd |only RprobitB-1.2.0/RprobitB/man/gibbs_sampler.Rd |only RprobitB-1.2.0/RprobitB/man/ll_ordered.Rd |only RprobitB-1.2.0/RprobitB/man/missing_covariates.Rd |only RprobitB-1.2.0/RprobitB/man/mml.Rd |only RprobitB-1.2.0/RprobitB/man/mode_approx.Rd |only RprobitB-1.2.0/RprobitB/man/model_selection.Rd |only RprobitB-1.2.0/RprobitB/man/npar.Rd |only RprobitB-1.2.0/RprobitB/man/overview_effects.Rd |only RprobitB-1.2.0/RprobitB/man/parameter_labels.Rd |only RprobitB-1.2.0/RprobitB/man/plot_acf.Rd |only RprobitB-1.2.0/RprobitB/man/plot_class_allocation.Rd |only RprobitB-1.2.0/RprobitB/man/plot_class_seq.Rd |only RprobitB-1.2.0/RprobitB/man/plot_mixture_contour.Rd |only RprobitB-1.2.0/RprobitB/man/plot_mixture_marginal.Rd |only RprobitB-1.2.0/RprobitB/man/plot_roc.Rd |only RprobitB-1.2.0/RprobitB/man/plot_trace.Rd |only RprobitB-1.2.0/RprobitB/man/point_estimates.Rd |only RprobitB-1.2.0/RprobitB/man/posterior_pars.Rd |only RprobitB-1.2.0/RprobitB/man/pred_acc.Rd |only RprobitB-1.2.0/RprobitB/man/preference_flip.Rd |only RprobitB-1.2.0/RprobitB/man/prepare_data.Rd |only RprobitB-1.2.0/RprobitB/man/sample_allocation.Rd |only RprobitB-1.2.0/RprobitB/man/simulate_choices.Rd |only RprobitB-1.2.0/RprobitB/man/sufficient_statistics.Rd |only RprobitB-1.2.0/RprobitB/man/train_choice.Rd |only RprobitB-1.2.0/RprobitB/man/train_test.Rd |only RprobitB-1.2.0/RprobitB/man/transform.Rd |only RprobitB-1.2.0/RprobitB/man/transform_gibbs_samples.Rd |only RprobitB-1.2.0/RprobitB/man/transform_parameter.Rd |only RprobitB-1.2.0/RprobitB/man/update_Omega.Rd |only RprobitB-1.2.0/RprobitB/man/update_Omega_c.Rd |only RprobitB-1.2.0/RprobitB/man/update_Sigma.Rd |only RprobitB-1.2.0/RprobitB/man/update_U.Rd |only RprobitB-1.2.0/RprobitB/man/update_U_ranked.Rd |only RprobitB-1.2.0/RprobitB/man/update_b.Rd |only RprobitB-1.2.0/RprobitB/man/update_b_c.Rd |only RprobitB-1.2.0/RprobitB/man/update_classes_dp.Rd |only RprobitB-1.2.0/RprobitB/man/update_classes_wb.Rd |only RprobitB-1.2.0/RprobitB/man/update_coefficient.Rd |only RprobitB-1.2.0/RprobitB/man/update_d.Rd |only RprobitB-1.2.0/RprobitB/man/update_m.Rd |only RprobitB-1.2.0/RprobitB/man/update_s.Rd |only RprobitB-1.2.0/RprobitB/man/update_z.Rd |only RprobitB-1.2.0/RprobitB/tests/testthat/_snaps |only RprobitB-1.2.0/RprobitB/tests/testthat/test-RprobitB_parameter.R |only RprobitB-1.2.0/RprobitB/tests/testthat/test-data_management.R |only RprobitB-1.2.0/RprobitB/tests/testthat/test-draw_from_prior.R |only RprobitB-1.2.0/RprobitB/tests/testthat/test-mode_approx.R |only RprobitB-1.2.0/RprobitB/tests/testthat/test-model_evaluation.R |only RprobitB-1.2.0/RprobitB/tests/testthat/test-model_fitting.R |only RprobitB-1.2.0/RprobitB/tests/testthat/test-model_selection.R |only RprobitB-1.2.0/RprobitB/tests/testthat/test-plotting.R |only RprobitB-1.2.0/RprobitB/vignettes/RprobitB.Rmd |only RprobitB-1.2.0/RprobitB/vignettes/img |only RprobitB-1.2.0/RprobitB/vignettes/v01_model_definition.Rmd |only RprobitB-1.2.0/RprobitB/vignettes/v02_choice_data.Rmd |only RprobitB-1.2.0/RprobitB/vignettes/v03_model_fitting.Rmd |only RprobitB-1.2.0/RprobitB/vignettes/v04_modeling_heterogeneity.Rmd |only RprobitB-1.2.0/RprobitB/vignettes/v05_choice_prediction.Rmd |only RprobitB-1.2.0/RprobitB/vignettes/v06_model_selection.Rmd |only RprobitB-2.0.0/RprobitB/DESCRIPTION | 47 RprobitB-2.0.0/RprobitB/MD5 | 263 RprobitB-2.0.0/RprobitB/NAMESPACE | 199 RprobitB-2.0.0/RprobitB/NEWS.md | 170 RprobitB-2.0.0/RprobitB/R/RcppExports.R | 987 +- RprobitB-2.0.0/RprobitB/R/RprobitB-package.R | 216 RprobitB-2.0.0/RprobitB/R/evaluation.R |only RprobitB-2.0.0/RprobitB/R/fit.R |only RprobitB-2.0.0/RprobitB/R/helpers.R |only RprobitB-2.0.0/RprobitB/R/interpret.R |only RprobitB-2.0.0/RprobitB/R/model.R |only RprobitB-2.0.0/RprobitB/R/posterior.R |only RprobitB-2.0.0/RprobitB/R/prediction.R |only RprobitB-2.0.0/RprobitB/README.md | 369 - RprobitB-2.0.0/RprobitB/build/partial.rdb |binary RprobitB-2.0.0/RprobitB/build/vignette.rds |binary RprobitB-2.0.0/RprobitB/inst/REFERENCES.bib | 723 +- RprobitB-2.0.0/RprobitB/inst/doc/v01_get_started.R |only RprobitB-2.0.0/RprobitB/inst/doc/v01_get_started.Rmd |only RprobitB-2.0.0/RprobitB/inst/doc/v01_get_started.html |only RprobitB-2.0.0/RprobitB/inst/doc/v02_model_variants.R |only RprobitB-2.0.0/RprobitB/inst/doc/v02_model_variants.Rmd |only RprobitB-2.0.0/RprobitB/inst/doc/v02_model_variants.html |only RprobitB-2.0.0/RprobitB/inst/doc/v03_heterogeneity.R |only RprobitB-2.0.0/RprobitB/inst/doc/v03_heterogeneity.Rmd |only RprobitB-2.0.0/RprobitB/inst/doc/v03_heterogeneity.html |only RprobitB-2.0.0/RprobitB/inst/doc/v04_prediction.R |only RprobitB-2.0.0/RprobitB/inst/doc/v04_prediction.Rmd |only RprobitB-2.0.0/RprobitB/inst/doc/v04_prediction.html |only RprobitB-2.0.0/RprobitB/inst/doc/v05_model_evaluation.R |only RprobitB-2.0.0/RprobitB/inst/doc/v05_model_evaluation.Rmd |only RprobitB-2.0.0/RprobitB/inst/doc/v05_model_evaluation.html |only RprobitB-2.0.0/RprobitB/man/RprobitB-package.Rd | 135 RprobitB-2.0.0/RprobitB/man/WAIC.Rd | 92 RprobitB-2.0.0/RprobitB/man/as_draws.RprobitB_fit.Rd |only RprobitB-2.0.0/RprobitB/man/bayes_factor.Rd |only RprobitB-2.0.0/RprobitB/man/class_updates.Rd |only RprobitB-2.0.0/RprobitB/man/coef.RprobitB_fit.Rd | 90 RprobitB-2.0.0/RprobitB/man/coefficient_updates.Rd |only RprobitB-2.0.0/RprobitB/man/confint.RprobitB_fit.Rd |only RprobitB-2.0.0/RprobitB/man/figures/README-plot-1.png |only RprobitB-2.0.0/RprobitB/man/figures/logo.png |binary RprobitB-2.0.0/RprobitB/man/fit.Rd |only RprobitB-2.0.0/RprobitB/man/formula.RprobitB_fit.Rd |only RprobitB-2.0.0/RprobitB/man/interpret.Rd |only RprobitB-2.0.0/RprobitB/man/latent_class_diagnostics.Rd |only RprobitB-2.0.0/RprobitB/man/logLik.RprobitB_fit.Rd |only RprobitB-2.0.0/RprobitB/man/loo.RprobitB_fit.Rd |only RprobitB-2.0.0/RprobitB/man/model.frame.RprobitB_fit.Rd |only RprobitB-2.0.0/RprobitB/man/nobs.RprobitB_fit.Rd |only RprobitB-2.0.0/RprobitB/man/plot.RprobitB_fit.Rd | 95 RprobitB-2.0.0/RprobitB/man/predict.RprobitB_fit.Rd | 150 RprobitB-2.0.0/RprobitB/man/print.RprobitB_fit.Rd |only RprobitB-2.0.0/RprobitB/man/print.summary.RprobitB_fit.Rd |only RprobitB-2.0.0/RprobitB/man/reexports.Rd |only RprobitB-2.0.0/RprobitB/man/residuals.RprobitB_fit.Rd |only RprobitB-2.0.0/RprobitB/man/summary.RprobitB_fit.Rd |only RprobitB-2.0.0/RprobitB/man/update.RprobitB_fit.Rd | 199 RprobitB-2.0.0/RprobitB/man/utility_updates.Rd |only RprobitB-2.0.0/RprobitB/man/vcov.RprobitB_fit.Rd |only RprobitB-2.0.0/RprobitB/src/RcppExports.cpp | 249 RprobitB-2.0.0/RprobitB/src/gibbs_sampler.cpp | 3308 +++++----- RprobitB-2.0.0/RprobitB/src/gibbs_sampler.h | 93 RprobitB-2.0.0/RprobitB/src/test-gibbs_sampler.cpp | 502 - RprobitB-2.0.0/RprobitB/tests/testthat.R | 8 RprobitB-2.0.0/RprobitB/tests/testthat/helper.R |only RprobitB-2.0.0/RprobitB/tests/testthat/test-cpp.R | 6 RprobitB-2.0.0/RprobitB/tests/testthat/test-evaluation.R |only RprobitB-2.0.0/RprobitB/tests/testthat/test-fit.R |only RprobitB-2.0.0/RprobitB/tests/testthat/test-helpers.R |only RprobitB-2.0.0/RprobitB/tests/testthat/test-interpret.R |only RprobitB-2.0.0/RprobitB/tests/testthat/test-model.R |only RprobitB-2.0.0/RprobitB/tests/testthat/test-posterior.R |only RprobitB-2.0.0/RprobitB/tests/testthat/test-prediction.R |only RprobitB-2.0.0/RprobitB/tests/testthat/test-sampler.R |only RprobitB-2.0.0/RprobitB/vignettes/v01_get_started.Rmd |only RprobitB-2.0.0/RprobitB/vignettes/v02_model_variants.Rmd |only RprobitB-2.0.0/RprobitB/vignettes/v03_heterogeneity.Rmd |only RprobitB-2.0.0/RprobitB/vignettes/v04_prediction.Rmd |only RprobitB-2.0.0/RprobitB/vignettes/v05_model_evaluation.Rmd |only 229 files changed, 4129 insertions(+), 3772 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Wenping Wang [aut],
Audrey Lavenu [ctb],
Ben Goodrich [ctb],
David Ardia [cph],
Dirk Eddelbuettel [cph],
Elizabeth Eskow [ctb],
Emmanuelle Comets [ctb],
Hadley Wickham [ctb],
Hajar Besbassi [ctb],
Hidde van de Beek [ctb],
[...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 7.0.2 dated 2026-08-04 and 7.1.0 dated 2026-09-20
nlmixr2est-7.0.2/nlmixr2est/man/dot-nlmixr2objectNameAssign.Rd |only nlmixr2est-7.0.2/nlmixr2est/tests/testthat/baselines/gradref-fit-focep-ref-focepluss.rds |only nlmixr2est-7.1.0/nlmixr2est/DESCRIPTION | 16 nlmixr2est-7.1.0/nlmixr2est/MD5 | 1064 nlmixr2est-7.1.0/nlmixr2est/NAMESPACE | 292 nlmixr2est-7.1.0/nlmixr2est/NEWS.md | 2272 ++ nlmixr2est-7.1.0/nlmixr2est/R/RcppExports.R | 181 nlmixr2est-7.1.0/nlmixr2est/R/aaaCranNlmixrThreads.R | 2 nlmixr2est-7.1.0/nlmixr2est/R/addCwres.R | 83 nlmixr2est-7.1.0/nlmixr2est/R/agq.R | 90 nlmixr2est-7.1.0/nlmixr2est/R/assert.R | 29 nlmixr2est-7.1.0/nlmixr2est/R/augPred.R | 172 nlmixr2est-7.1.0/nlmixr2est/R/benchmarking.R | 121 nlmixr2est-7.1.0/nlmixr2est/R/bobyqa.R | 372 nlmixr2est-7.1.0/nlmixr2est/R/broom.R | 75 nlmixr2est-7.1.0/nlmixr2est/R/build.R | 27 nlmixr2est-7.1.0/nlmixr2est/R/cloneNlmixr.R | 4 nlmixr2est-7.1.0/nlmixr2est/R/compat.R | 33 nlmixr2est-7.1.0/nlmixr2est/R/complete.R | 105 nlmixr2est-7.1.0/nlmixr2est/R/cov.R | 814 nlmixr2est-7.1.0/nlmixr2est/R/covControl.R |only nlmixr2est-7.1.0/nlmixr2est/R/covRecompute.R | 158 nlmixr2est-7.1.0/nlmixr2est/R/deparse.R | 80 nlmixr2est-7.1.0/nlmixr2est/R/emviControl.R | 210 nlmixr2est-7.1.0/nlmixr2est/R/estInterceptor.R |only nlmixr2est-7.1.0/nlmixr2est/R/fbvi.R | 4 nlmixr2est-7.1.0/nlmixr2est/R/fitSim.R | 91 nlmixr2est-7.1.0/nlmixr2est/R/fo.R | 94 nlmixr2est-7.1.0/nlmixr2est/R/foce.R | 70 nlmixr2est-7.1.0/nlmixr2est/R/focei.R | 3973 ++- nlmixr2est-7.1.0/nlmixr2est/R/foceiControl.R | 1553 - nlmixr2est-7.1.0/nlmixr2est/R/foceiCov.R | 87 nlmixr2est-7.1.0/nlmixr2est/R/foceiCovAnalytic.R | 5010 +++- nlmixr2est-7.1.0/nlmixr2est/R/foceiCovFdFull.R | 95 nlmixr2est-7.1.0/nlmixr2est/R/foceiFast.R | 12 nlmixr2est-7.1.0/nlmixr2est/R/foceiFull.R |only nlmixr2est-7.1.0/nlmixr2est/R/foceiGradAnalytic.R | 2104 + nlmixr2est-7.1.0/nlmixr2est/R/foceiLik.R | 292 nlmixr2est-7.1.0/nlmixr2est/R/foceiLinCmtAlagSens.R |only nlmixr2est-7.1.0/nlmixr2est/R/foceiLinCmtCarry.R |only nlmixr2est-7.1.0/nlmixr2est/R/foceiLinCmtCarryCompose.R |only nlmixr2est-7.1.0/nlmixr2est/R/foceiLinCmtCarryData.R |only nlmixr2est-7.1.0/nlmixr2est/R/foceiLinCmtCarryEligible.R |only nlmixr2est-7.1.0/nlmixr2est/R/foceiLinCmtCarryEmitJump.R |only nlmixr2est-7.1.0/nlmixr2est/R/foceiLinCmtCarryEvent.R |only nlmixr2est-7.1.0/nlmixr2est/R/foceiLinCmtCarryGates.R |only nlmixr2est-7.1.0/nlmixr2est/R/foceiLinCmtCarryMemo.R |only nlmixr2est-7.1.0/nlmixr2est/R/foceiLinCmtCarryPredCall.R |only nlmixr2est-7.1.0/nlmixr2est/R/foceiLinCmtCarryTheta.R |only nlmixr2est-7.1.0/nlmixr2est/R/focep.R | 71 nlmixr2est-7.1.0/nlmixr2est/R/foi.R | 98 nlmixr2est-7.1.0/nlmixr2est/R/hook.R | 236 nlmixr2est-7.1.0/nlmixr2est/R/iagq.R | 14 nlmixr2est-7.1.0/nlmixr2est/R/ifoce.R | 12 nlmixr2est-7.1.0/nlmixr2est/R/ifocei.R | 10 nlmixr2est-7.1.0/nlmixr2est/R/ifocep.R | 64 nlmixr2est-7.1.0/nlmixr2est/R/ilaplace.R | 14 nlmixr2est-7.1.0/nlmixr2est/R/imp.R | 21 nlmixr2est-7.1.0/nlmixr2est/R/impPsis.R | 43 nlmixr2est-7.1.0/nlmixr2est/R/impmap.R | 900 nlmixr2est-7.1.0/nlmixr2est/R/impmapThetaSens.R | 146 nlmixr2est-7.1.0/nlmixr2est/R/ini.R | 5 nlmixr2est-7.1.0/nlmixr2est/R/iov.R | 1157 - nlmixr2est-7.1.0/nlmixr2est/R/iterPrintControl.R | 133 nlmixr2est-7.1.0/nlmixr2est/R/laplace.R | 75 nlmixr2est-7.1.0/nlmixr2est/R/lbfgsb3c.R | 391 nlmixr2est-7.1.0/nlmixr2est/R/magq.R | 14 nlmixr2est-7.1.0/nlmixr2est/R/md5.R | 4 nlmixr2est-7.1.0/nlmixr2est/R/mfoce.R | 12 nlmixr2est-7.1.0/nlmixr2est/R/mfocei.R | 10 nlmixr2est-7.1.0/nlmixr2est/R/mfocep.R | 64 nlmixr2est-7.1.0/nlmixr2est/R/mix.R | 767 nlmixr2est-7.1.0/nlmixr2est/R/mlaplace.R | 14 nlmixr2est-7.1.0/nlmixr2est/R/model.R | 15 nlmixr2est-7.1.0/nlmixr2est/R/mu2.R | 182 nlmixr2est-7.1.0/nlmixr2est/R/muRefClassify.R | 161 nlmixr2est-7.1.0/nlmixr2est/R/muRefControl.R | 411 nlmixr2est-7.1.0/nlmixr2est/R/muRefLinear.R | 4 nlmixr2est-7.1.0/nlmixr2est/R/n1qn1.R | 356 nlmixr2est-7.1.0/nlmixr2est/R/newuoa.R | 374 nlmixr2est-7.1.0/nlmixr2est/R/nlm.R | 938 nlmixr2est-7.1.0/nlmixr2est/R/nlmShared.R | 181 nlmixr2est-7.1.0/nlmixr2est/R/nlme.R | 423 nlmixr2est-7.1.0/nlmixr2est/R/nlmeRxUiGet.R | 119 nlmixr2est-7.1.0/nlmixr2est/R/nlminb.R | 510 nlmixr2est-7.1.0/nlmixr2est/R/nlmixr2.R | 132 nlmixr2est-7.1.0/nlmixr2est/R/nlmixr2Est.R | 295 nlmixr2est-7.1.0/nlmixr2est/R/nlmixr2EstType.R | 131 nlmixr2est-7.1.0/nlmixr2est/R/nlmixr2_md5.R | 2 nlmixr2est-7.1.0/nlmixr2est/R/nlmixr2global.R | 16 nlmixr2est-7.1.0/nlmixr2est/R/nlmixr2output.R | 342 nlmixr2est-7.1.0/nlmixr2est/R/nlmixrAddObjectiveFunction.R | 28 nlmixr2est-7.1.0/nlmixr2est/R/nlmixrCbind.R | 4 nlmixr2est-7.1.0/nlmixr2est/R/nlmixrGrad.R | 93 nlmixr2est-7.1.0/nlmixr2est/R/nlmixrUpdateObject.R | 17 nlmixr2est-7.1.0/nlmixr2est/R/nls.R | 1032 nlmixr2est-7.1.0/nlmixr2est/R/nmObjGet.R | 574 nlmixr2est-7.1.0/nlmixr2est/R/nmObjGetEtaMat.R | 64 nlmixr2est-7.1.0/nlmixr2est/R/nmObjHandle.R | 75 nlmixr2est-7.1.0/nlmixr2est/R/npBox.R | 21 nlmixr2est-7.1.0/nlmixr2est/R/npCommon.R | 347 nlmixr2est-7.1.0/nlmixr2est/R/npInner.R | 51 nlmixr2est-7.1.0/nlmixr2est/R/npMuExpand.R | 33 nlmixr2est-7.1.0/nlmixr2est/R/npag.R | 35 nlmixr2est-7.1.0/nlmixr2est/R/npb.R | 41 nlmixr2est-7.1.0/nlmixr2est/R/npde.R | 50 nlmixr2est-7.1.0/nlmixr2est/R/odeSwapVerify.R | 58 nlmixr2est-7.1.0/nlmixr2est/R/ofv.R | 269 nlmixr2est-7.1.0/nlmixr2est/R/omegaBlock.R | 148 nlmixr2est-7.1.0/nlmixr2est/R/optim.R | 565 nlmixr2est-7.1.0/nlmixr2est/R/pkpars.R | 3 nlmixr2est-7.1.0/nlmixr2est/R/posthoc.R | 74 nlmixr2est-7.1.0/nlmixr2est/R/preProcessBoundedTransform.R | 304 nlmixr2est-7.1.0/nlmixr2est/R/preProcessCensDistWarn.R |only nlmixr2est-7.1.0/nlmixr2est/R/preProcessCovariatesPresent.R | 21 nlmixr2est-7.1.0/nlmixr2est/R/preProcessDataUi.R | 2 nlmixr2est-7.1.0/nlmixr2est/R/preProcessLinCmtOde.R | 138 nlmixr2est-7.1.0/nlmixr2est/R/preProcessLiteralFix.R | 23 nlmixr2est-7.1.0/nlmixr2est/R/preProcessSaemModeledResid.R |only nlmixr2est-7.1.0/nlmixr2est/R/preProcessVaeNonMuTheta.R | 73 nlmixr2est-7.1.0/nlmixr2est/R/preProcessZeroOmega.R | 92 nlmixr2est-7.1.0/nlmixr2est/R/preProcessZeroTheta.R | 37 nlmixr2est-7.1.0/nlmixr2est/R/print.R | 352 nlmixr2est-7.1.0/nlmixr2est/R/priors.R |only nlmixr2est-7.1.0/nlmixr2est/R/qrpem.R | 29 nlmixr2est-7.1.0/nlmixr2est/R/resid.R | 1027 nlmixr2est-7.1.0/nlmixr2est/R/rstudio.R | 6 nlmixr2est-7.1.0/nlmixr2est/R/rxNamedModel.R | 112 nlmixr2est-7.1.0/nlmixr2est/R/rxsolve.R | 278 nlmixr2est-7.1.0/nlmixr2est/R/saem.R | 1500 - nlmixr2est-7.1.0/nlmixr2est/R/saemControl.R | 466 nlmixr2est-7.1.0/nlmixr2est/R/saemIov.R |only nlmixr2est-7.1.0/nlmixr2est/R/saemPhi1Inner.R |only nlmixr2est-7.1.0/nlmixr2est/R/saemPseudoEta.R |only nlmixr2est-7.1.0/nlmixr2est/R/saemPseudoEtaFinalize.R |only nlmixr2est-7.1.0/nlmixr2est/R/saemPseudoEtaSelect.R |only nlmixr2est-7.1.0/nlmixr2est/R/saemRxUiGet.R | 698 nlmixr2est-7.1.0/nlmixr2est/R/saemRxUiGetModel.R | 471 nlmixr2est-7.1.0/nlmixr2est/R/saem_fit.R | 388 nlmixr2est-7.1.0/nlmixr2est/R/saem_fit_aux.R | 786 nlmixr2est-7.1.0/nlmixr2est/R/sessioninfo.R | 103 nlmixr2est-7.1.0/nlmixr2est/R/sharedControl.R | 80 nlmixr2est-7.1.0/nlmixr2est/R/simModelCache.R |only nlmixr2est-7.1.0/nlmixr2est/R/simulate.R | 37 nlmixr2est-7.1.0/nlmixr2est/R/sourceCppFunction.R | 4 nlmixr2est-7.1.0/nlmixr2est/R/splitModelRxUiGet.R | 99 nlmixr2est-7.1.0/nlmixr2est/R/timing.R | 82 nlmixr2est-7.1.0/nlmixr2est/R/trust.R |only nlmixr2est-7.1.0/nlmixr2est/R/uninformativeEtas.R | 193 nlmixr2est-7.1.0/nlmixr2est/R/uobyqa.R | 378 nlmixr2est-7.1.0/nlmixr2est/R/update.R | 6 nlmixr2est-7.1.0/nlmixr2est/R/utils.R | 94 nlmixr2est-7.1.0/nlmixr2est/R/vae.R | 404 nlmixr2est-7.1.0/nlmixr2est/R/vaeCovColinear.R |only nlmixr2est-7.1.0/nlmixr2est/R/vaeCovSelectL0.R | 53 nlmixr2est-7.1.0/nlmixr2est/R/vaeCovShapes.R | 323 nlmixr2est-7.1.0/nlmixr2est/R/vaeData.R | 728 nlmixr2est-7.1.0/nlmixr2est/R/vaeDecoder.R | 17 nlmixr2est-7.1.0/nlmixr2est/R/vaeFit.R | 335 nlmixr2est-7.1.0/nlmixr2est/R/vaeGrad.R | 166 nlmixr2est-7.1.0/nlmixr2est/R/vaeInner.R | 162 nlmixr2est-7.1.0/nlmixr2est/R/vaeOutput.R | 235 nlmixr2est-7.1.0/nlmixr2est/R/validate.R | 21 nlmixr2est-7.1.0/nlmixr2est/R/vi.R | 297 nlmixr2est-7.1.0/nlmixr2est/R/viData.R | 96 nlmixr2est-7.1.0/nlmixr2est/R/vpc.R | 116 nlmixr2est-7.1.0/nlmixr2est/R/zzz.R | 70 nlmixr2est-7.1.0/nlmixr2est/build |only nlmixr2est-7.1.0/nlmixr2est/inst/benchmarks/benchmark-focei-hessian-method.R |only nlmixr2est-7.1.0/nlmixr2est/inst/benchmarks/benchmark-trust-inner.R |only nlmixr2est-7.1.0/nlmixr2est/inst/benchmarks/benchmark-trust-outer.R |only nlmixr2est-7.1.0/nlmixr2est/inst/benchmarks/results |only nlmixr2est-7.1.0/nlmixr2est/inst/benchmarks/runtime-benchmarks.R | 21 nlmixr2est-7.1.0/nlmixr2est/inst/doc |only nlmixr2est-7.1.0/nlmixr2est/inst/include/nlmixr2estFoceiPtr.h |only nlmixr2est-7.1.0/nlmixr2est/inst/include/nlmixr2estLikContrib.h |only nlmixr2est-7.1.0/nlmixr2est/inst/include/nlmixr2estLikContribPtr.h |only nlmixr2est-7.1.0/nlmixr2est/inst/include/nlmixr2estNlmPtr.h |only nlmixr2est-7.1.0/nlmixr2est/inst/reprex_fbio_eta_parallel.R | 17 nlmixr2est-7.1.0/nlmixr2est/inst/tools/genQrpemBaseline.R |only nlmixr2est-7.1.0/nlmixr2est/inst/tools/workaround.R | 47 nlmixr2est-7.1.0/nlmixr2est/man/bobyqaControl.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/dot-augPredIpredModel.Rd | 3 nlmixr2est-7.1.0/nlmixr2est/man/dot-deparseFinal.Rd | 2 nlmixr2est-7.1.0/nlmixr2est/man/dot-nlmixr2estFoceiPtrs.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/dot-nlmixr2estLikContribPtrs.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/dot-nlmixr2estNlmPtrs.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/dot-sensEtaOrTheta.Rd | 23 nlmixr2est-7.1.0/nlmixr2est/man/emviControl.Rd | 17 nlmixr2est-7.1.0/nlmixr2est/man/foceiControl.Rd | 431 nlmixr2est-7.1.0/nlmixr2est/man/foceiLikIterPrintStart.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/foceiLikLoad.Rd | 56 nlmixr2est-7.1.0/nlmixr2est/man/foceiLikRun.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/getBaseSimModelFit.Rd | 6 nlmixr2est-7.1.0/nlmixr2est/man/getValidNlmixrControl.Rd | 31 nlmixr2est-7.1.0/nlmixr2est/man/impCovControl.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/impmapControl.Rd | 240 nlmixr2est-7.1.0/nlmixr2est/man/lbfgsb3cControl.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/n1qn1Control.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/newuoaControl.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/nlmControl.Rd | 44 nlmixr2est-7.1.0/nlmixr2est/man/nlmObjectiveSetup.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/nlmUnscalePar.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/nlminbControl.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/nlmixr2Est.Rd | 64 nlmixr2est-7.1.0/nlmixr2est/man/nlmixr2GradFun.Rd | 2 nlmixr2est-7.1.0/nlmixr2est/man/nlmixr2NlmeControl.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/nlsControl.Rd | 71 nlmixr2est-7.1.0/nlmixr2est/man/nmGetDistributionSaemLines.Rd | 6 nlmixr2est-7.1.0/nlmixr2est/man/nmObjGetControl.Rd | 5 nlmixr2est-7.1.0/nlmixr2est/man/nmObjHandleControlObject.Rd | 5 nlmixr2est-7.1.0/nlmixr2est/man/optimControl.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/postFinalObjectHooks.Rd | 2 nlmixr2est-7.1.0/nlmixr2est/man/preFinalParTableHooks.Rd | 2 nlmixr2est-7.1.0/nlmixr2est/man/preProcessHooks.Rd | 2 nlmixr2est-7.1.0/nlmixr2est/man/predict.nlmixr2FitCore.Rd | 48 nlmixr2est-7.1.0/nlmixr2est/man/registerEstInterceptor.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/rsControl.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/saControl.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/saemControl.Rd | 151 nlmixr2est-7.1.0/nlmixr2est/man/setCov-set.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/setCov.Rd | 100 nlmixr2est-7.1.0/nlmixr2est/man/setCovAllMethods.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/setCovOptions.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/setCovValue.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/setOfv.Rd | 3 nlmixr2est-7.1.0/nlmixr2est/man/tableControl.Rd | 3 nlmixr2est-7.1.0/nlmixr2est/man/trustControl.Rd |only nlmixr2est-7.1.0/nlmixr2est/man/uobyqaControl.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/man/vaeControl.Rd | 117 nlmixr2est-7.1.0/nlmixr2est/man/vaeCovariates.Rd | 11 nlmixr2est-7.1.0/nlmixr2est/src/Makevars.in | 31 nlmixr2est-7.1.0/nlmixr2est/src/RcppExports.cpp | 353 nlmixr2est-7.1.0/nlmixr2est/src/censEst.h | 130 nlmixr2est-7.1.0/nlmixr2est/src/foceiGrad.cpp | 545 nlmixr2est-7.1.0/nlmixr2est/src/foceiGrad.h | 53 nlmixr2est-7.1.0/nlmixr2est/src/imp.cpp | 1039 nlmixr2est-7.1.0/nlmixr2est/src/imp.h | 53 nlmixr2est-7.1.0/nlmixr2est/src/impQrng.h |only nlmixr2est-7.1.0/nlmixr2est/src/init.c | 90 nlmixr2est-7.1.0/nlmixr2est/src/inner.cpp |11271 ++++++++-- nlmixr2est-7.1.0/nlmixr2est/src/inner.h | 5 nlmixr2est-7.1.0/nlmixr2est/src/likContribUtil.h |only nlmixr2est-7.1.0/nlmixr2est/src/logSumExp.h |only nlmixr2est-7.1.0/nlmixr2est/src/nearPD.cpp | 12 nlmixr2est-7.1.0/nlmixr2est/src/nlm.cpp | 460 nlmixr2est-7.1.0/nlmixr2est/src/nmParallel.h |only nlmixr2est-7.1.0/nlmixr2est/src/nmParallelCore.h |only nlmixr2est-7.1.0/nlmixr2est/src/nmSeqSeed.h |only nlmixr2est-7.1.0/nlmixr2est/src/np.h | 15 nlmixr2est-7.1.0/nlmixr2est/src/npag.cpp | 84 nlmixr2est-7.1.0/nlmixr2est/src/npb.cpp | 79 nlmixr2est-7.1.0/nlmixr2est/src/npde.cpp | 30 nlmixr2est-7.1.0/nlmixr2est/src/odeSwap.cpp | 486 nlmixr2est-7.1.0/nlmixr2est/src/odeSwap.h | 61 nlmixr2est-7.1.0/nlmixr2est/src/rxomp.h | 3 nlmixr2est-7.1.0/nlmixr2est/src/saem.cpp | 2043 + nlmixr2est-7.1.0/nlmixr2est/src/scale.h | 26 nlmixr2est-7.1.0/nlmixr2est/src/slice.cpp | 9 nlmixr2est-7.1.0/nlmixr2est/src/truncNorm.h |only nlmixr2est-7.1.0/nlmixr2est/src/trustHessianUpdate.h |only nlmixr2est-7.1.0/nlmixr2est/src/uninformativeEtas.cpp | 17 nlmixr2est-7.1.0/nlmixr2est/src/vaeEncoder.cpp | 14 nlmixr2est-7.1.0/nlmixr2est/tests/testthat.R | 197 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/baselines/gradref-foce-newton-stall.rds |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/baselines/gradref-ll-multiple-endpoint.rds |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/baselines/gradref-lnorm-domain-clamp-867.rds |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/baselines/qrpem-baseline-ref.rds |binary nlmixr2est-7.1.0/nlmixr2est/tests/testthat/helper-gradref.R | 14 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/helper-lincmt-carry-ll.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/helper-lincmt-carry.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/helper-quiet.R | 35 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/helper-vae-resid.R | 25 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/helper-wang2007.R | 240 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/helper-zzz-fits.R | 74 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-00-reload-ll.R | 10 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-addCwres.R | 100 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-agq-cov.R | 59 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-agq-fast-grad.R | 145 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-ar-est.R | 37 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-augpred.R | 107 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-bad-print.R | 10 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-benchmarking.R | 27 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-bounded-transform.R | 72 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-broom.R | 348 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cens-dist-warn.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cloneEnv-cycle.R | 8 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-control-infer.R | 4 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-control.R | 65 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cor-no-cov-1038.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-analytic-defaults.R | 13 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-analytic.R | 1423 - nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-condition.R | 11 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-decouple-saimp.R | 38 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-decouple.R | 18 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-fdfull-install.R | 77 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-focei.R | 76 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-mu.R | 9 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-robust.R | 14 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-scope-swap.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cov-setcov-generic.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-cwres.R | 35 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-data-assert.R | 38 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-dde-focei.R | 29 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-est-type-list.R | 1 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-etaMat.R | 38 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-fitSim.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-fix-cov.R | 41 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-fix-eta.R | 12 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-fo-control.R | 17 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-1.R | 25 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-bobyqa-retry.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-cens-t-fit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-cens-t.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-cens.R | 183 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-char.R | 22 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-cores-fresh-rx.R | 8 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-det-conditional.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-eta-only.R | 1 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-eta-reset-path-dependence.R | 53 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-event-eta-1016.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-factr-control.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-factr-fit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-family-control.R | 39 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-fast-grad.R | 431 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-fast-methods-fit.R | 64 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-fast-methods.R | 12 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-fast-objective-scale.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-fd-fallbacks.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-foce-plus.R | 151 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-foce-stride.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-full-inner.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-hessian-etastep.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-hessian-method.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-ind-counts-1039.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-inner-conditional.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-inner.R | 106 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-adr-default.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-alag-sens.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-carry-eligible-gates.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-carry-eligible.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-carry-emit-fd.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-carry-emit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-carry-fit-fallback.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-carry-fit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-carry-jump-fit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-carry-jump.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-carry-ll-fit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-carry-ll.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-carry-theta-fit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-carry-theta.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-carry-trans.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-lincmt-phi-engage.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-ll-fast-grad-fit.R | 124 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-ll-fast-grad.R | 49 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-llik.R | 149 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-mceta-1040.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-mceta-empty-cube.R | 4 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-mix-cov.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-mix-grad.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-outer-fd-fallback.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-outer-hessian-api.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-outer-hessian-censor.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-outer-hessian-family.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-outer-hessian-fit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-outer-hessian-nlminb-fit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-outer-hessian-nlminb.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-outer-hessian-tol.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-outer-hessian.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-outer-trust.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-parallel.R | 126 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-pooled-solve-args.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-preprocess.R | 20 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-prior.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-ptrs.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-reproducible.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-shi21-bounds.R | 10 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-syminvchol.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-theta-reset-bounds.R | 15 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-theta-reset.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-trust-inner.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-vid-alloc-1010.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-wang2007-basic.R | 190 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-wang2007-bounded.R | 564 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-wang2007-boxcox-half.R | 679 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-wang2007-boxcox-lnorm.R | 648 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-wang2007-boxcox.R | 1111 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-wang2007-combined.R | 702 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-wang2007-lognormal.R | 604 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-wang2007-power.R | 224 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-wang2007-yeojohnson.R | 125 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-warm.R | 219 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-zero-init-scale.R | 59 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-focei-zero-theta.R | 48 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-foceiLik.R | 116 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-imp-auto.R | 155 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-imp-burnin.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-imp-combsens.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-imp-mapiter.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-imp-mceta.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-imp-mstep-damping.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-imp-parallel.R | 3 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-imp-prior.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-imp-proposal-slow.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-imp-proposal.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-imp-psis.R | 73 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-imp-refit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-imp-tprop.R | 126 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-imp-xi-gamma.R | 179 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-impmap.R | 357 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-ini-ui.R | 2 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-inpar-saem.R | 25 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-integerish-focei-print.R | 30 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-iov-loglik-1000.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-iov-method-gate.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-iov-mifocei-1083.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-iov-same.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-iov-template-copy.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-iov-zero-eta.R | 15 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-iov.R | 60 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-issue-281.R | 15 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-issue-429.R | 5 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-issue-455.R | 35 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-issue-470.R | 6 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-issue-502.R | 162 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-issue-503.R | 21 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-issue-515.R | 3 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-issue-641.R | 9 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-iter-print-ofv-header.R | 68 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-keep.R | 15 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-lik-contrib-fast-grad.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-lik-contrib-methods.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-lik-contrib.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-lincmt-ode-fit.R | 76 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-lincmt-ode.R | 46 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-manual-back-transform.R | 166 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-matexp.R | 302 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-mem-npde-empty.R | 14 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-mfocei.R | 79 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-mix.R | 310 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-model.R | 1 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-mtime-fit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-mtime.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-mu-family.R | 34 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-mu-parhist.R | 52 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-mu-plain-fit.R | 74 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-mu-plain.R | 40 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-mu-timevarying.R | 81 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-muRefClassify.R | 3 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-muRefLinear.R | 14 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-muRefResetOptOut.R | 27 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nearPd.R | 59 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nlm-cens-t.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nlm-cens.R | 102 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nlm-lik-contrib.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nlm-ptrs.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nlm.R | 94 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nlmUnscalePar.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nlme-control.R | 14 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nlme-cov.R | 8 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nlme.R | 64 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nlmixr2output.R | 262 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nlmixr3-load.R | 5 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nlmsetup-fresh-rx.R | 4 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nls.R | 17 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nmobj.R | 67 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nn-outer.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-nonmu.R | 39 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-np-control-surface.R | 15 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-np-endpoint-map.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-np.R | 22 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npag-bimodal.R | 21 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npag-cycle.R | 25 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npag-dispatch.R | 26 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npag-error-models.R | 126 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npag-fit.R | 41 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npag-fixed.R | 11 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npag-general-lik.R | 162 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npag-golden.R | 67 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npag-grid.R | 21 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npag-ipm.R | 15 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npag-mixture.R | 53 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npag-muexpand.R | 48 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npag-npb-cens-978.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npag-psi.R | 18 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npb-fit.R | 43 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-npde.R | 31 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-odeswap-fit.R | 91 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-odeswap.R | 152 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-omega-block.R | 151 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-omega-boundary.R | 18 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-omega-offdiag.R | 66 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-optexpression-ebe.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-optexpression-saem-nlme.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-optim.R | 17 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-ordid-subject-mapping.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-parFixedDf.R | 49 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-piping.R | 18 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-posthoc.R | 11 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-predict.R | 42 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-print.R | 2 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-priors-assert.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-priors-output.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-qrpem-scramble.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-qrpem-slow.R | 186 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-qrpem.R | 70 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-resid-ode-fallback.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-restart.R | 6 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-review-batch2.R | 17 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-rx-model-props.R | 3 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-rxsolve.R | 55 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-rxuideparse.R | 163 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-addprop-estep.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-aic.R | 2 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-auto-nu.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-cov-analytic.R | 20 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-cov-multi-endpoint-904.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-cov-sa.R | 625 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-cov-transpose.R | 17 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-degraded-fit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-drop.R | 131 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-eta-no-phi-1047.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-fixed-omega-report-1073.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-funny-mu.R | 1 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-iov-twolevel-fit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-iov-twolevel.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-logitnorm-probitnorm-resid.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-loglik-focei.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-loglik.R | 385 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-mcmc-diagnostics.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-mcmc-seed-order.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-mix-regress.R | 138 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-mix.R | 473 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-model-pred-dedup.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-modeled-resid-fit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-modeled-resid.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-mu.R | 46 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-nearpd.R | 21 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-no-obs-subject.R | 62 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-no-pop.R | 16 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-nonmutheta.R | 112 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-odeswap-regression.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-phi1-inner.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-phi1-objective.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-resid-cache.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-resid-lambda.R | 146 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-tbs-loglik.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-theo_sd.R | 68 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-saem-translate.R | 290 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-scale-normtype.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-sens-fd.R | 22 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-shi21-hbound.R | 13 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-simModelCache.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-simulation.R | 14 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-single-subject.R | 10 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-split.R | 203 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-splitbolus-interp.R | 79 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-str-est.R | 53 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-subFinal.R | 160 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-table-cmt.R | 93 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-tad-in-models.R | 6 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-timing.R | 35 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-tolFactor.R | 27 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-trust.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-udf.R | 4 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-ui-est-change.R | 3 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-unary-mu.R | 1 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-uninformative-etas-revisit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-uninformative-etas.R | 465 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-update-estimates.R | 8 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-utils.R | 24 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-colinear-fit.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-colinear.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-cov-control.R | 12 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-cov-groups.R | 157 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-cov-shapes.R | 322 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-covariate-accessor.R | 150 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-covariate-estimate.R | 131 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-covariate-selection.R | 168 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-covariate-table.R | 42 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-dataprep.R | 69 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-decoder.R | 19 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-elbo.R | 31 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-encoder.R | 49 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-errmodel.R | 69 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-fit.R | 19 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-fixbounds.R | 51 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-grad-fit.R | 46 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-hockey-fit.R | 39 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-inner.R | 443 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-iov.R | 52 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-l0learn-fit.R | 96 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-l0learn.R | 105 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-ll-grad-fit.R | 76 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-miqp.R | 53 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-mix.R |only nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-neonatal.R | 40 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-nonmutheta-grad.R | 220 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-nonmutheta.R | 115 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-parhist.R | 36 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-residopt.R | 67 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-rvar.R | 29 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vae-train.R | 7 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vi-control.R | 20 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vi-cores.R | 14 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vi-dataprep.R | 6 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vi-fit.R | 186 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vi-focei-agreement.R | 16 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vi-fullbayes.R | 35 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vi-fullrank.R | 32 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vi-grad.R | 168 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vi-inner.R | 3 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vi-neonatal.R | 16 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vi-repro.R | 19 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vi-stan.R | 33 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vpcSim.R | 22 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-vpcSimExpand.R | 6 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-warfarin.R | 13 nlmixr2est-7.1.0/nlmixr2est/tests/testthat/test-zero-omega-restore.R | 15 nlmixr2est-7.1.0/nlmixr2est/vignettes |only 620 files changed, 62262 insertions(+), 21930 deletions(-)
Title: Download Official Spatial Data Sets of Brazil
Description: Easy access to official spatial data sets of Brazil. The package
offers a wide range of spatial data sets available at various
geographic scales and for various years with harmonized attributes,
projection and fixed topology. All functions allow for seamless
integration sf, DuckDB and Arrow.
Author: Rafael H. M. Pereira [aut, cre] ,
Rogerio Jeronimo Barbosa [aut],
Caio Nogueira Goncalves [ctb],
Cecilia do Lago [ctb],
Filipe Cavalcanti [ctb],
Arthur Bazolli [ctb],
Lucas Gelape [ctb],
Rafael Lopes [ctb],
Vinicius Oike [ctb],
Paulo Henrique Fernand [...truncated...]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between geobr versions 2.0.1 dated 2026-06-23 and 2.1.0 dated 2026-09-19
geobr-2.0.1/geobr/man/check_connection.Rd |only geobr-2.0.1/geobr/tests/testthat/test-check_connection.R |only geobr-2.1.0/geobr/DESCRIPTION | 22 geobr-2.1.0/geobr/MD5 | 74 - geobr-2.1.0/geobr/NAMESPACE | 2 geobr-2.1.0/geobr/R/cep_to_state.R | 152 +- geobr-2.1.0/geobr/R/geobr.R | 3 geobr-2.1.0/geobr/R/list_geobr.R | 38 geobr-2.1.0/geobr/R/lookup_muni.R | 337 +++--- geobr-2.1.0/geobr/R/read_addresses.R |only geobr-2.1.0/geobr/R/read_capitals.R | 229 ++-- geobr-2.1.0/geobr/R/read_census_tract.R | 14 geobr-2.1.0/geobr/R/read_country.R | 109 +- geobr-2.1.0/geobr/R/read_health_region.R | 10 geobr-2.1.0/geobr/R/read_pop_arrangements.R | 125 +- geobr-2.1.0/geobr/R/read_region.R | 103 - geobr-2.1.0/geobr/R/read_state.R | 2 geobr-2.1.0/geobr/R/read_statistical_grid.R | 10 geobr-2.1.0/geobr/R/read_urban_concentrations.R | 127 +- geobr-2.1.0/geobr/R/utils.R | 360 ++---- geobr-2.1.0/geobr/build/partial.rdb |binary geobr-2.1.0/geobr/build/vignette.rds |binary geobr-2.1.0/geobr/inst/doc/intro_to_geobr.R | 282 ++--- geobr-2.1.0/geobr/inst/doc/intro_to_geobr.Rmd | 624 +++++------ geobr-2.1.0/geobr/inst/doc/intro_to_geobr.html | 106 - geobr-2.1.0/geobr/man/geobr.Rd | 8 geobr-2.1.0/geobr/man/read_addresses.Rd |only geobr-2.1.0/geobr/man/read_capitals.Rd | 3 geobr-2.1.0/geobr/man/read_census_tract.Rd | 14 geobr-2.1.0/geobr/man/read_state.Rd | 2 geobr-2.1.0/geobr/man/read_statistical_grid.Rd | 15 geobr-2.1.0/geobr/tests/tests_rafa/long_term_cache.R | 704 ++++++------- geobr-2.1.0/geobr/tests/tests_rafa/test_rafa.R | 7 geobr-2.1.0/geobr/tests/testthat/test-cep_to_state.R | 70 - geobr-2.1.0/geobr/tests/testthat/test-download_fallback.R |only geobr-2.1.0/geobr/tests/testthat/test-list_geobr.R | 87 - geobr-2.1.0/geobr/tests/testthat/test-lookup_muni.R | 109 +- geobr-2.1.0/geobr/tests/testthat/test-read_addresses.R |only geobr-2.1.0/geobr/tests/testthat/test-read_capitals.R | 70 - geobr-2.1.0/geobr/tests/testthat/test-read_health_region.R | 101 + geobr-2.1.0/geobr/vignettes/intro_to_geobr.Rmd | 624 +++++------ 41 files changed, 2320 insertions(+), 2223 deletions(-)
Title: Efficiently Using Gaussian Processes with Rcpp and RcppEigen
Description: Contains Rcpp and RcppEigen implementations of matrix operations useful for Gaussian process models, such as the inverse and determinant of a symmetric and positive-definite Toeplitz matrix, sampling from multivariate normal distributions, evaluation of the log-density of a multivariate normal vector, and Bayesian inference for latent variable Gaussian process models with elliptical slice sampling (Murray, Adams, and MacKay 2010).
Author: Giri Gopalan [aut, cre],
Luke Bornn [aut]
Maintainer: Giri Gopalan <gopalan88@gmail.com>
Diff between FastGP versions 1.3 dated 2026-04-29 and 1.4 dated 2026-09-19
DESCRIPTION | 10 +++++----- MD5 | 20 +++++++++++--------- R/RcppExports.R | 8 ++++++++ R/gpfuncs.R | 30 ++++++++++++++++++++++++++++++ R/rcpp_mvn.R | 42 +++++++++++++++++++++++++++++++++++------- demo/FastGPdemo.R | 33 ++++++++++++--------------------- man/ess.Rd | 19 ++++++++++++++----- man/rcpp_matrix_ops.Rd | 11 ++++++++--- man/rcpp_rmvnorm.Rd | 2 ++ src/RcppExports.cpp | 24 ++++++++++++++++++++++++ src/tchol.cpp |only src/toep_det.cpp |only 12 files changed, 149 insertions(+), 50 deletions(-)
Title: Weighted Double Score Matching for Survey-Weighted Causal
Inference
Description: Implements weighted double score matching (WDSM) for estimating
population-level causal effects from complex survey data. Combines
propensity scores and prognostic scores with survey design weights for
matching, survey-weighted imputation within match sets, and Hajek
normalization to target the population average treatment effect (PATE) and
the population average treatment effect on the treated (PATT). Supports
both retrospective (treatment-dependent) and prospective
(treatment-independent) sampling designs. Uses propensity probabilities
and arm-specific prognostic scores for matching, with a complete quadratic
bias correction in each arm's double score. Provides linearization-based
multinomial replication variance estimates and centered normal Wald
confidence intervals, retaining the original matching reuse coefficients
without re-matching. Supplied scores can be held fixed for inference
conditional on those scores. This weight-only interface does not encode
survey strata, clusters, o [...truncated...]
Author: Yukang Zeng [aut, cre],
Guangyu Tong [aut],
Jiaqi Tong [aut],
Haidong Lu [aut],
Bhramar Mukherjee [aut],
Fan Li [aut]
Maintainer: Yukang Zeng <ykzeng2019@gmail.com>
Diff between wdsmatch versions 0.2.0 dated 2026-09-11 and 0.2.1 dated 2026-09-19
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- NEWS.md | 12 ++++++++++++ R/matching.R | 21 ++++++++------------- R/wdsm.R | 7 ++++--- R/wdsm_ties.R |only R/wdsmatchATE.R | 29 ++++++++++++++++++++++++----- R/wdsmatchATT.R | 6 ++++-- man/wdsmatchATE.Rd | 28 ++++++++++++++++++++++++---- man/wdsmatchATT.Rd | 12 +++++++++++- tests/testthat/test-internals.R | 29 ++++++++++++++++++----------- tests/testthat/test-ties.R |only 12 files changed, 120 insertions(+), 52 deletions(-)
Title: Three-Step Estimation for Latent Class Analysis
Description: Implements BCH (Bolck-Croon-Hagenaars) <doi:10.1093/pan/mph001> and ML (Vermunt's maximum likelihood) <doi:10.1093/pan/mpq025> approaches for three-step estimation of latent class models with covariates and distal outcomes, following Bakk, Tekle & Vermunt (2013) <doi:10.1177/0081175012470644>, Bakk, Oberski & Vermunt (2014) <https://www.jstor.org/stable/24573086>, and Bakk & Kuha (2018) <doi:10.1007/s11336-017-9592-7>. Built on 'multilevLCA' (Lyrvall et al., 2025) <doi:10.1080/00273171.2025.2473935> for Step-1 measurement model estimation, this package extends it with support for Gaussian, Poisson, and binomial distal outcome families. Unlike 'poLCA', which relies on one-step estimation and cannot accommodate a measurement model from a different sample, this package uses a stepwise approach to prevent the structural model from influencing latent class formation. Implements correct sandwich variance estimation that propagates measurement u [...truncated...]
Author: Sam Lee [aut, cre, cph] ,
Jay Goodliffe [ctb]
Maintainer: Sam Lee <samlee@arizona.edu>
Diff between tseLCA versions 1.0.2 dated 2026-07-11 and 1.1.0 dated 2026-09-19
DESCRIPTION | 8 MD5 | 66 +- NAMESPACE | 6 NEWS.md | 130 ++++ R/clean.R | 6 R/dgp.R | 6 R/imports.R | 2 R/lca_measurement.R | 664 ++++++++++++++++++++- R/three_step.R | 1139 +++++++++++++++++++++++++++++++------ R/tseLCA-package.R | 12 README.md | 188 +++--- inst/CITATION | 4 inst/WORDLIST | 8 inst/doc/tseLCA-workflow.R | 52 + inst/doc/tseLCA-workflow.Rmd | 126 +++- inst/doc/tseLCA-workflow.html | 1010 +++++++++++++++++++------------- inst/examples/tseLCA_replication.R | 144 ++++ inst/examples/tseLCA_sim.R | 552 +++++++++++------ man/coef.tseLCA_measurement.Rd | 6 man/extract_Y_from_mU.Rd | 2 man/fitZ_from_fit0.Rd | 2 man/fitZ_from_multiLCA.Rd | 22 man/generate_data.Rd | 4 man/lca_indiv_varmat.Rd | 2 man/lca_step1.Rd | 31 + man/lca_step1_startval.Rd |only man/omnibus_test.Rd |only man/permute_fitZ_classes.Rd | 2 man/three_step.Rd | 103 +++ man/tseLCA-package.Rd | 12 man/vcov.tseLCA_measurement.Rd | 5 tests/testthat/test-dgp.R | 2 tests/testthat/test-helpers.R | 2 tests/testthat/test-integration.R | 852 +++++++++++++++++++++++++++ vignettes/tseLCA-workflow.Rmd | 126 +++- 35 files changed, 4262 insertions(+), 1034 deletions(-)
Title: Fast and Scalable Cellwise-Robust Ensemble
Description: Functions to perform robust variable selection and regression using the Fast and Scalable
Cellwise-Robust Ensemble (FSCRE) algorithm. The approach establishes a robust foundation
using the Detect Deviating Cells (DDC) algorithm and robust correlation estimates. It then
employs a competitive ensemble architecture where a robust Least Angle Regression (LARS)
engine proposes candidate variables and cross-validation arbitrates their assignment. A final
robust MM-estimator is applied to the selected predictors.
Author: Anthony Christidis [aut, cre],
Gabriela Cohen-Freue [aut]
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between srlars versions 3.0.1 dated 2026-07-01 and 3.1.0 dated 2026-09-19
DESCRIPTION | 11 - MD5 | 41 +++-- NAMESPACE | 1 NEWS.md | 66 +++++--- R/checkInputData.R | 30 +++ R/checkInputDataCV.R |only R/computeCVError.R | 20 -- R/computeRobustFoundation.R | 6 R/computeRobustLoss.R |only R/cv.srlars.R |only R/performSelectionLoop.R | 90 ++++++++++- R/predict.srlars.R | 323 +++++++++++++++++++--------------------- R/srlars.R | 26 ++- README.md | 217 +++++++++++--------------- build |only inst |only man/checkInputData.Rd | 120 +++++++------- man/checkInputDataCV.Rd |only man/computeRobustLoss.Rd |only man/cv.srlars.Rd |only man/performSelectionLoop.Rd | 191 ++++++++++++----------- man/srlars.Rd | 259 +++++++++++++++++--------------- man/srlars_ensemble_predict.Rd |only tests/testthat/test-cv-srlars.R |only tests/testthat/test-srlars.R | 195 ++++++++++++++++++++++++ vignettes |only 26 files changed, 961 insertions(+), 635 deletions(-)
Title: Stream Network Movement Analyses
Description: Calculating home ranges and movements of animals in complex stream environments
is often challenging, and standard home range estimators do not apply. This
package provides a series of tools for assessing movements in a stream
network, such as calculating the total length of stream used, distances
between points, and movement patterns over time. See Vignette for additional
details. This package was originally released on 'GitHub' under the name 'SNM'.
SNMA was developed for analyses in McKnight et al. (2025) <doi:10.3354/esr01442>
which contains additional examples and information.
Author: Donald T. McKnight [aut, cre]
Maintainer: Donald T. McKnight <donald.mcknight@my.jcu.edu.au>
Diff between SNMA versions 0.1.7 dated 2026-08-26 and 0.1.8 dated 2026-09-19
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/increase.stream.points.R | 9 +++++++-- R/prep.data.R | 4 ++++ inst/doc/SNMA_vignette.R | 20 +++++++++++++++++++- inst/doc/SNMA_vignette.Rmd | 32 +++++++++++++++++++++++++++++++- inst/doc/SNMA_vignette.pdf |binary man/prep.data.Rd | 4 ++++ vignettes/SNMA_vignette.Rmd | 32 +++++++++++++++++++++++++++++++- 9 files changed, 109 insertions(+), 18 deletions(-)
Title: Wasserstein Index Generation (WIG) Model
Description: Efficient implementation of several Optimal Transport algorithms in Fangzhou Xie (2025) <doi:10.48550/arXiv.2504.08722> and the Wasserstein Index Generation (WIG) model in Fangzhou Xie (2020) <doi:10.1016/j.econlet.2019.108874>.
Author: Fangzhou Xie [aut, cre, cph]
Maintainer: Fangzhou Xie <fangzhou.xie@rutgers.edu>
Diff between rwig versions 0.1.0 dated 2026-04-21 and 0.2.0 dated 2026-09-19
rwig-0.1.0/rwig/R/RcppExports.R |only rwig-0.1.0/rwig/src/RcppExports.cpp |only rwig-0.2.0/rwig/DESCRIPTION | 16 rwig-0.2.0/rwig/MD5 | 120 ++- rwig-0.2.0/rwig/NAMESPACE | 3 rwig-0.2.0/rwig/NEWS.md | 44 + rwig-0.2.0/rwig/R/barycenter.R | 142 ---- rwig-0.2.0/rwig/R/check_args.R | 316 ++-------- rwig-0.2.0/rwig/R/cpp.R |only rwig-0.2.0/rwig/R/rwig-package.R | 3 rwig-0.2.0/rwig/R/sinkhorn.R | 100 --- rwig-0.2.0/rwig/R/specs.R | 50 - rwig-0.2.0/rwig/R/utils.R | 15 rwig-0.2.0/rwig/R/wdl.R | 52 - rwig-0.2.0/rwig/R/wig.R | 95 +-- rwig-0.2.0/rwig/R/zzz.R | 72 +- rwig-0.2.0/rwig/README.md | 41 - rwig-0.2.0/rwig/build/partial.rdb |binary rwig-0.2.0/rwig/build/vignette.rds |binary rwig-0.2.0/rwig/configure | 43 - rwig-0.2.0/rwig/configure.ac | 26 rwig-0.2.0/rwig/inst/doc/barycenter.html | 7 rwig-0.2.0/rwig/inst/doc/specs.Rmd | 8 rwig-0.2.0/rwig/inst/doc/specs.html | 10 rwig-0.2.0/rwig/inst/doc/threading.R | 3 rwig-0.2.0/rwig/inst/doc/threading.Rmd | 22 rwig-0.2.0/rwig/inst/doc/threading.html | 21 rwig-0.2.0/rwig/inst/doc/wdl-model.html | 22 rwig-0.2.0/rwig/inst/doc/wig-model.html | 4 rwig-0.2.0/rwig/inst/include/barycenter_impl.hpp | 129 +--- rwig-0.2.0/rwig/inst/include/common.hpp | 19 rwig-0.2.0/rwig/inst/include/cuda_interface.cuh | 11 rwig-0.2.0/rwig/inst/include/cuda_kernels.cuh | 101 +-- rwig-0.2.0/rwig/inst/include/iter_solver.hpp |only rwig-0.2.0/rwig/inst/include/linalg.hpp |only rwig-0.2.0/rwig/inst/include/logdomain.hpp |only rwig-0.2.0/rwig/inst/include/optimizer.hpp | 108 +-- rwig-0.2.0/rwig/inst/include/r_glue.hpp |only rwig-0.2.0/rwig/inst/include/sinkhorn_impl.hpp | 121 +-- rwig-0.2.0/rwig/inst/include/thread_pool.hpp |only rwig-0.2.0/rwig/inst/include/vformat.hpp | 58 - rwig-0.2.0/rwig/inst/include/wdl_impl.hpp | 228 ++----- rwig-0.2.0/rwig/inst/tinytest/test_cuda.R |only rwig-0.2.0/rwig/inst/tinytest/test_utils.R |only rwig-0.2.0/rwig/inst/tinytest/test_wdl_wig.R |only rwig-0.2.0/rwig/man/rwig-package.Rd | 5 rwig-0.2.0/rwig/man/wdl_specs.Rd | 22 rwig-0.2.0/rwig/man/wig.Rd | 5 rwig-0.2.0/rwig/src/barycenter.cpp | 249 +++----- rwig-0.2.0/rwig/src/barycenter_impl_log.cpp | 508 ++++------------ rwig-0.2.0/rwig/src/barycenter_impl_parallel.cpp | 293 ++++----- rwig-0.2.0/rwig/src/check_cuda.cpp | 338 ----------- rwig-0.2.0/rwig/src/cuda_barycenter.cu | 176 ++--- rwig-0.2.0/rwig/src/cuda_kernels.cu | 334 +--------- rwig-0.2.0/rwig/src/cuda_optimizer.cu | 39 - rwig-0.2.0/rwig/src/cuda_sinkhorn.cu | 89 -- rwig-0.2.0/rwig/src/cuda_wdl.cu | 467 ++++++++------- rwig-0.2.0/rwig/src/init.cpp |only rwig-0.2.0/rwig/src/sinkhorn.cpp | 204 ++---- rwig-0.2.0/rwig/src/sinkhorn_impl_log.cpp | 705 +++-------------------- rwig-0.2.0/rwig/src/sinkhorn_impl_vanilla.cpp | 322 ++++------ rwig-0.2.0/rwig/src/tsvd.cpp | 123 ++-- rwig-0.2.0/rwig/src/utils.cpp | 152 ++-- rwig-0.2.0/rwig/src/wdl.cpp | 221 +++---- rwig-0.2.0/rwig/src/wdl_impl.cpp | 397 +++++------- rwig-0.2.0/rwig/vignettes/specs.Rmd | 8 rwig-0.2.0/rwig/vignettes/threading.Rmd | 22 67 files changed, 2309 insertions(+), 4380 deletions(-)
Title: Core Utilities for the 'rtemis' Ecosystem
Description: Utilities used across packages of the 'rtemis' ecosystem. Includes the msg()
messaging system and the fmt() formatting system. Provides a library of 'S7' properties,
test_* functions that return logical values, check_* functions that throw informative errors,
and clean_* functions that return validated and coerced values. This code began as part of the
'rtemis' package (<doi:10.32614/CRAN.package.rtemis>).
Author: E.D. Gennatas [aut, cre, cph]
Maintainer: E.D. Gennatas <gennatas@gmail.com>
Diff between rtemis.core versions 0.3.1 dated 2026-06-30 and 0.4.6 dated 2026-09-19
rtemis.core-0.3.1/rtemis.core/R/00_S7_properties.R |only rtemis.core-0.3.1/rtemis.core/R/01_S7_generics.R |only rtemis.core-0.3.1/rtemis.core/R/rtemis_color_system.R |only rtemis.core-0.3.1/rtemis.core/man/bounded_double_property.Rd |only rtemis.core-0.4.6/rtemis.core/DESCRIPTION | 14 rtemis.core-0.4.6/rtemis.core/LICENSE |only rtemis.core-0.4.6/rtemis.core/MD5 | 181 +++--- rtemis.core-0.4.6/rtemis.core/NAMESPACE | 32 + rtemis.core-0.4.6/rtemis.core/NEWS.md | 167 +++++ rtemis.core-0.4.6/rtemis.core/R/01_rtemis_color_system.R |only rtemis.core-0.4.6/rtemis.core/R/02_S7_prop_factories.R |only rtemis.core-0.4.6/rtemis.core/R/03_S7_properties.R |only rtemis.core-0.4.6/rtemis.core/R/04_S7_generics.R |only rtemis.core-0.4.6/rtemis.core/R/check.R | 282 ++++++++++ rtemis.core-0.4.6/rtemis.core/R/fmt.R | 135 +++- rtemis.core-0.4.6/rtemis.core/R/html.R |only rtemis.core-0.4.6/rtemis.core/R/log.R | 117 +++- rtemis.core-0.4.6/rtemis.core/R/msg.R | 113 +++- rtemis.core-0.4.6/rtemis.core/R/progress.R |only rtemis.core-0.4.6/rtemis.core/R/schema.R |only rtemis.core-0.4.6/rtemis.core/R/schema_contract.R |only rtemis.core-0.4.6/rtemis.core/R/utils_print.R | 76 +- rtemis.core-0.4.6/rtemis.core/R/utils_strings.R | 68 ++ rtemis.core-0.4.6/rtemis.core/README.md | 7 rtemis.core-0.4.6/rtemis.core/man/abort.Rd | 31 - rtemis.core-0.4.6/rtemis.core/man/assert_config_contract.Rd |only rtemis.core-0.4.6/rtemis.core/man/assert_description_language.Rd |only rtemis.core-0.4.6/rtemis.core/man/bold.Rd | 5 rtemis.core-0.4.6/rtemis.core/man/character_scalar.Rd | 7 rtemis.core-0.4.6/rtemis.core/man/check_bounded_double_scalar.Rd |only rtemis.core-0.4.6/rtemis.core/man/check_bounded_integer_scalar.Rd |only rtemis.core-0.4.6/rtemis.core/man/check_optional_bounded_double_scalar.Rd |only rtemis.core-0.4.6/rtemis.core/man/check_optional_bounded_integer_scalar.Rd |only rtemis.core-0.4.6/rtemis.core/man/checkmark.Rd |only rtemis.core-0.4.6/rtemis.core/man/col256.Rd | 5 rtemis.core-0.4.6/rtemis.core/man/crossmark.Rd |only rtemis.core-0.4.6/rtemis.core/man/double_scalar.Rd | 7 rtemis.core-0.4.6/rtemis.core/man/enum.Rd | 2 rtemis.core-0.4.6/rtemis.core/man/fmt.Rd | 5 rtemis.core-0.4.6/rtemis.core/man/fmt_gradient.Rd | 5 rtemis.core-0.4.6/rtemis.core/man/format_trace.Rd | 16 rtemis.core-0.4.6/rtemis.core/man/get_msg_sink.Rd | 6 rtemis.core-0.4.6/rtemis.core/man/get_output_type.Rd | 34 + rtemis.core-0.4.6/rtemis.core/man/gray.Rd | 5 rtemis.core-0.4.6/rtemis.core/man/highlight.Rd | 5 rtemis.core-0.4.6/rtemis.core/man/highlightbig.Rd | 5 rtemis.core-0.4.6/rtemis.core/man/html_div.Rd |only rtemis.core-0.4.6/rtemis.core/man/html_escape.Rd |only rtemis.core-0.4.6/rtemis.core/man/html_li.Rd |only rtemis.core-0.4.6/rtemis.core/man/html_p.Rd |only rtemis.core-0.4.6/rtemis.core/man/html_raw.Rd |only rtemis.core-0.4.6/rtemis.core/man/html_span.Rd |only rtemis.core-0.4.6/rtemis.core/man/html_strong.Rd |only rtemis.core-0.4.6/rtemis.core/man/html_tag.Rd |only rtemis.core-0.4.6/rtemis.core/man/html_ul.Rd |only rtemis.core-0.4.6/rtemis.core/man/integer_scalar.Rd | 8 rtemis.core-0.4.6/rtemis.core/man/italic.Rd | 9 rtemis.core-0.4.6/rtemis.core/man/logical_scalar.Rd | 7 rtemis.core-0.4.6/rtemis.core/man/msgstart.Rd | 6 rtemis.core-0.4.6/rtemis.core/man/nonneg_double_scalar.Rd | 7 rtemis.core-0.4.6/rtemis.core/man/nonneg_double_vector.Rd | 10 rtemis.core-0.4.6/rtemis.core/man/nonneg_integer_scalar.Rd | 10 rtemis.core-0.4.6/rtemis.core/man/objcat.Rd | 11 rtemis.core-0.4.6/rtemis.core/man/optional.Rd | 2 rtemis.core-0.4.6/rtemis.core/man/optional_character_scalar.Rd | 8 rtemis.core-0.4.6/rtemis.core/man/optional_double_scalar.Rd | 8 rtemis.core-0.4.6/rtemis.core/man/optional_integer_scalar.Rd | 8 rtemis.core-0.4.6/rtemis.core/man/optional_logical_scalar.Rd | 8 rtemis.core-0.4.6/rtemis.core/man/optional_nonneg_double_scalar.Rd | 11 rtemis.core-0.4.6/rtemis.core/man/optional_nonneg_double_vector.Rd | 11 rtemis.core-0.4.6/rtemis.core/man/optional_nonneg_integer_scalar.Rd | 11 rtemis.core-0.4.6/rtemis.core/man/optional_pos_double_scalar.Rd | 11 rtemis.core-0.4.6/rtemis.core/man/optional_pos_double_vector.Rd | 8 rtemis.core-0.4.6/rtemis.core/man/optional_pos_integer_scalar.Rd | 11 rtemis.core-0.4.6/rtemis.core/man/optional_prob_scalar.Rd | 8 rtemis.core-0.4.6/rtemis.core/man/optional_prob_vector.Rd | 11 rtemis.core-0.4.6/rtemis.core/man/optional_unit_open_scalar.Rd | 11 rtemis.core-0.4.6/rtemis.core/man/optional_unit_open_vector.Rd | 11 rtemis.core-0.4.6/rtemis.core/man/pos_double_scalar.Rd | 7 rtemis.core-0.4.6/rtemis.core/man/pos_double_vector.Rd | 10 rtemis.core-0.4.6/rtemis.core/man/pos_integer_scalar.Rd | 10 rtemis.core-0.4.6/rtemis.core/man/prob_scalar.Rd | 7 rtemis.core-0.4.6/rtemis.core/man/prob_vector.Rd | 7 rtemis.core-0.4.6/rtemis.core/man/progress_begin.Rd |only rtemis.core-0.4.6/rtemis.core/man/progress_clear.Rd |only rtemis.core-0.4.6/rtemis.core/man/progress_end.Rd |only rtemis.core-0.4.6/rtemis.core/man/progress_lapply.Rd |only rtemis.core-0.4.6/rtemis.core/man/progress_update.Rd |only rtemis.core-0.4.6/rtemis.core/man/prop_bag.Rd |only rtemis.core-0.4.6/rtemis.core/man/prop_boolean.Rd |only rtemis.core-0.4.6/rtemis.core/man/prop_const.Rd |only rtemis.core-0.4.6/rtemis.core/man/prop_float.Rd |only rtemis.core-0.4.6/rtemis.core/man/prop_integer.Rd |only rtemis.core-0.4.6/rtemis.core/man/prop_spec.Rd |only rtemis.core-0.4.6/rtemis.core/man/prop_string.Rd |only rtemis.core-0.4.6/rtemis.core/man/repr.Rd | 2 rtemis.core-0.4.6/rtemis.core/man/repr_S7name.Rd | 3 rtemis.core-0.4.6/rtemis.core/man/repr_ls.Rd | 5 rtemis.core-0.4.6/rtemis.core/man/rtemis_colors.Rd | 2 rtemis.core-0.4.6/rtemis.core/man/set_msg_sink.Rd | 20 rtemis.core-0.4.6/rtemis.core/man/show_df.Rd | 5 rtemis.core-0.4.6/rtemis.core/man/show_table.Rd | 5 rtemis.core-0.4.6/rtemis.core/man/thin.Rd | 5 rtemis.core-0.4.6/rtemis.core/man/unit_open_scalar.Rd | 8 rtemis.core-0.4.6/rtemis.core/man/unit_open_vector.Rd | 7 rtemis.core-0.4.6/rtemis.core/man/warn.Rd | 4 rtemis.core-0.4.6/rtemis.core/man/write_JSONSchema.Rd |only rtemis.core-0.4.6/rtemis.core/man/write_lines.Rd |only rtemis.core-0.4.6/rtemis.core/tests/testthat/test-00_S7_prop_factories.R |only rtemis.core-0.4.6/rtemis.core/tests/testthat/test-00_S7_properties.R | 57 -- rtemis.core-0.4.6/rtemis.core/tests/testthat/test-check.R | 187 ++++++ rtemis.core-0.4.6/rtemis.core/tests/testthat/test-fmt.R |only rtemis.core-0.4.6/rtemis.core/tests/testthat/test-html.R |only rtemis.core-0.4.6/rtemis.core/tests/testthat/test-log.R | 133 ++++ rtemis.core-0.4.6/rtemis.core/tests/testthat/test-progress.R |only rtemis.core-0.4.6/rtemis.core/tests/testthat/test-schema_contract.R |only 116 files changed, 1688 insertions(+), 332 deletions(-)
Title: R Bindings to the 'Mosaic' Visualization Framework
Description: Provides R bindings for 'Mosaic', a declarative grammar for
linked, data-driven visualizations backed by 'DuckDB'. The package supplies
'htmlwidgets' and 'shiny' helpers for rendering 'Mosaic' specifications
from R, including optional browser-side 'DuckDB-WASM' execution and
selection export helpers for exploratory workflows.
Author: Timur Rizvanov [aut, cre],
Edward C. Ruiz [aut],
Ruben Dries [aut, rev],
Dries Lab [fnd] ,
Boston University [fnd] )
Maintainer: Timur Rizvanov <timurr@bu.edu>
Diff between rMosaic versions 0.1.3 dated 2026-06-25 and 0.2.0 dated 2026-09-19
DESCRIPTION | 15 + MD5 | 27 ++- NEWS.md | 43 +++++ R/exportSelection.R | 6 R/mosaic.R | 338 +++++++++++++++++++++++++++++++++++++++++---- R/runMosaicApp.R | 6 R/runMosaicWithExport.R | 6 inst/htmlwidgets/mosaic.js | 102 ++++++++++++- man/mosaic.Rd | 43 ++++- man/runMosaicApp.Rd | 24 ++- man/runMosaicExport.Rd | 24 ++- man/runMosaicWithExport.Rd | 24 ++- tests |only 13 files changed, 593 insertions(+), 65 deletions(-)
Title: R Bindings to 'Deck.gl'
Description: Provides R bindings for 'deck.gl', a 'WebGL' framework for
rendering large interactive spatial and tabular visualizations. The package
supplies 'htmlwidgets' and 'shiny' bindings, supports 'DuckDB'-backed data
hydration, and bundles the JavaScript assets needed to render 'deck.gl'
specifications from R.
Author: Timur Rizvanov [aut, cre],
Edward C. Ruiz [aut],
Ruben Dries [aut, rev],
Dries Lab [fnd] ,
Boston University [fnd] )
Maintainer: Timur Rizvanov <timurr@bu.edu>
Diff between rDeckgl versions 0.1.0 dated 2026-06-01 and 0.2.0 dated 2026-09-19
DESCRIPTION | 13 - MD5 | 20 +- NEWS.md | 69 ++++++++ R/deckgl.R | 292 ++++++++++++++++++++++++++++------ R/json-export.R |only inst/htmlwidgets/deckgl.js | 291 +++++++++++++++++++++++++++++++++ man/deckgl.Rd | 43 ++++- tests/js |only tests/testthat/test-compact-columns.R |only tests/testthat/test-file-transport.R |only tests/testthat/test-hydration-rows.R |only tests/testthat/test-json-export.R |only tests/testthat/test-live-json-rows.R |only 13 files changed, 659 insertions(+), 69 deletions(-)
Title: Understanding Nonlinear Mixed Effects Modeling for Population
Pharmacokinetics
Description: This shows how 'NONMEM' (Beal SL, Sheiner LB, Boeckmann AJ,
Bauer RJ. NONMEM 7.5 Users Guides. Icon plc, 2020) software works.
'NONMEM' classical estimation methods such as 'First Order (FO)
approximation', 'First Order Conditional Estimation (FOCE)', and
'Laplacian approximation' are explained. Functions are also provided
for post-run processing of NONMEM output files, generating PDF or Markdown
diagnostic reports including objective function value analysis,
parameter estimates, prediction and residual diagnostics, empirical
Bayes estimate (EBE) analysis, input data summary, and individual
pharmacokinetic parameter distributions. Helper utilities for
building NONMEM-ready datasets from SDTM-style source tables are
also included.
Author: Kyun-Seop Bae [aut, cre]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between nmw versions 0.5.1 dated 2026-08-21 and 0.6.0 dated 2026-09-19
DESCRIPTION | 12 MD5 | 68 +++-- R/nm_read.R | 1 R/nm_summary.R | 119 ++++++++- R/nmw_run.R | 137 +++++------ R/plot_pairs.R | 174 +++++++------- R/report_ebe.R | 203 +++++++++------- R/report_indipk.R | 77 ++++-- R/report_input.R | 106 ++++---- R/report_ofv.R | 93 ++++--- R/report_output.R | 34 +- R/report_param.R | 126 ++++++---- R/report_pred.R | 115 +++++---- R/report_resid.R | 179 +++++++------- R/report_writer.R |only R/utils_data.R | 444 ++++++++++++++++++------------------ R/utils_report.R | 198 +++++++++++++++- inst/NEWS.Rd | 183 ++++++++++++-- man/AddDefaultNMCols.Rd |only man/AddDefaultTabCols.Rd |only man/InfluencePanel.Rd |only man/NormalizeTabCols.Rd |only man/Outline.Rd | 31 ++ man/PlotUnavailable.Rd |only man/ReadTabFile.Rd |only man/RequireRunFile.Rd |only man/RownamesToColumn.Rd |only man/SumOutEmpty.Rd |only man/nmw_report_ebe.Rd | 22 + man/nmw_report_indipk.Rd | 22 + man/nmw_report_input.Rd | 23 + man/nmw_report_ofv.Rd | 23 + man/nmw_report_output.Rd | 22 + man/nmw_report_param.Rd | 23 + man/nmw_report_pred.Rd | 22 + man/nmw_report_resid.Rd | 23 + man/nmw_run.Rd | 21 + tests/testthat/test-nm_summary.R |only tests/testthat/test-report_writer.R |only tests/testthat/test-reports.R | 215 +++++++++++++++++ tests/testthat/test-utils_report.R | 75 ++++++ 41 files changed, 1934 insertions(+), 857 deletions(-)
Title: Polynomial Maximization Method for Non-Gaussian Regression
Description: Implements the Polynomial Maximization Method ('PMM') for parameter estimation
in linear and time series models when error distributions deviate from normality.
The 'PMM2' variant achieves lower variance parameter estimates compared to ordinary
least squares ('OLS') when errors exhibit significant skewness. The 'PMM3' variant
(S=3) targets symmetric platykurtic error distributions, reducing variance when
excess kurtosis is negative. Includes automatic method selection ('pmm_dispatch'),
linear regression, 'AR'/'MA'/'ARMA'/'ARIMA' models, and bootstrap inference.
Methodology described in Zabolotnii, Warsza, and Tkachenko (2018) <doi:10.1007/978-3-319-77179-3_75>,
Zabolotnii, Tkachenko, and Warsza (2022) <doi:10.1007/978-3-031-03502-9_37>, and
Zabolotnii, Tkachenko, and Warsza (2023) <doi:10.1007/978-3-031-25844-2_21>, and
Zabolotnii (2025) <doi:10.48550/arXiv.2511.07059>.
Author: Serhii Zabolotnii [aut, cre]
Maintainer: Serhii Zabolotnii <zabolotniua@gmail.com>
Diff between EstemPMM versions 0.4.0 dated 2026-05-29 and 0.5.0 dated 2026-09-19
DESCRIPTION | 12 +- MD5 | 52 +++++---- NEWS.md | 139 +++++++++++++++++++++++++ R/pmm2_classes.R | 10 + R/pmm2_ts_main.R | 173 ++++++++++++++++++++++++-------- R/pmm2_ts_methods.R | 93 +++++++++++++---- R/pmm2_ts_recursive.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/bootstrap_inference.html | 8 - inst/doc/pmm2_introduction.html | 8 - inst/doc/pmm2_time_series.html | 28 ++--- inst/doc/pmm3_symmetric_errors.html | 12 +- inst/doc/pmm3_time_series.html | 16 +- inst/doc/seasonal_models.html | 32 ++--- man/EstemPMM-package.Rd | 5 man/TS2fit-class.Rd | 10 + man/ar_pmm2.Rd | 10 + man/arima_pmm2.Rd | 15 ++ man/arma_admissible.Rd |only man/arma_pmm2.Rd | 15 ++ man/arma_recursion.Rd |only man/ma_pmm2.Rd | 15 ++ man/ma_pmm2_fit_recursive.Rd |only man/pmm2_recursive_design.Rd |only man/pmm2_recursive_score.Rd |only man/pmm2_recursive_solve.Rd |only man/ts_pmm2.Rd | 45 +++++++- man/vcov-TS2fit-method.Rd | 39 ++++++- tests/testthat/Rplots.pdf |binary tests/testthat/test-pmm2-recursive-ma.R |only 31 files changed, 568 insertions(+), 169 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson [aut, cre] ,
Evan Sergeant [aut],
Cord Heuer [ctb],
Ian Kopacka [ctb],
Klemens Fuchs [ctb],
Telmo Nunes [ctb],
Cord Heuer [ctb],
Jonathon Marshall [ctb],
Javier Sanchez [ctb],
Ron Thornton [ctb],
Jeno Reiczigel [ctb],
Jim Robison-Cox [ [...truncated...]
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.96 dated 2026-08-03 and 2.0.98 dated 2026-09-19
DESCRIPTION | 8 +- MD5 | 28 +++---- NEWS | 16 +++- R/epi.2by2.R | 139 ++++++++++++++++++++++++++--------- R/epi.evalue.R | 87 +++++++++++---------- R/epi.kappa.R | 49 +++++++++--- build/vignette.rds |binary inst/doc/epiR_descriptive_epi.html | 18 ++-- inst/doc/epiR_diagnostic_tests.html | 28 +++---- inst/doc/epiR_measures_of_assoc.html | 17 ++-- inst/doc/epiR_sample_size.html | 4 - inst/doc/epiR_surveillance.html | 19 ++-- man/epi.2by2.Rd | 4 - man/epi.kappa.Rd | 39 +++++++++ man/epi.mbf.Rd | 4 - 15 files changed, 308 insertions(+), 152 deletions(-)
Title: More Statistical Methods for Composite Material Data
Description: A companion package to
'cmstatr' <https://cran.r-project.org/package=cmstatr>. 'cmstatr' contains
statistical methods that are published in the Composite Materials Handbook,
Volume 1 (2012, ISBN: 978-0-7680-7811-4), while 'cmstatrExt' contains
statistical methods that are not included in that handbook.
Author: Stefan Kloppenborg [aut, cre]
Maintainer: Stefan Kloppenborg <stefan@kloppenborg.ca>
Diff between cmstatrExt versions 0.4.1 dated 2026-03-17 and 0.5.0 dated 2026-09-19
cmstatrExt-0.4.1/cmstatrExt/src/p_equiv.cpp |only cmstatrExt-0.5.0/cmstatrExt/DESCRIPTION | 14 +- cmstatrExt-0.5.0/cmstatrExt/MD5 | 42 ++++--- cmstatrExt-0.5.0/cmstatrExt/NAMESPACE | 3 cmstatrExt-0.5.0/cmstatrExt/NEWS.md |only cmstatrExt-0.5.0/cmstatrExt/R/RcppExports.R | 34 +++++- cmstatrExt-0.5.0/cmstatrExt/R/conflicts.R |only cmstatrExt-0.5.0/cmstatrExt/R/deprecated.R |only cmstatrExt-0.5.0/cmstatrExt/R/zzz.R |only cmstatrExt-0.5.0/cmstatrExt/README.md | 2 cmstatrExt-0.5.0/cmstatrExt/build/vignette.rds |binary cmstatrExt-0.5.0/cmstatrExt/inst/doc/equivalency-p-values.html | 56 +++++----- cmstatrExt-0.5.0/cmstatrExt/inst/extdata |only cmstatrExt-0.5.0/cmstatrExt/man/average_curve_lm.Rd | 2 cmstatrExt-0.5.0/cmstatrExt/man/cmstatrExt-package.Rd | 5 cmstatrExt-0.5.0/cmstatrExt/man/figures/power_sim_dual_example-1.png |binary cmstatrExt-0.5.0/cmstatrExt/man/k_equiv_one_sample.Rd |only cmstatrExt-0.5.0/cmstatrExt/man/p_equiv.Rd | 23 ---- cmstatrExt-0.5.0/cmstatrExt/man/p_equiv_one_sample.Rd |only cmstatrExt-0.5.0/cmstatrExt/man/reexports.Rd | 2 cmstatrExt-0.5.0/cmstatrExt/src/RcppExports.cpp | 22 +++ cmstatrExt-0.5.0/cmstatrExt/src/acceptance.cpp | 6 - cmstatrExt-0.5.0/cmstatrExt/src/k_equiv_one_sample.cpp |only cmstatrExt-0.5.0/cmstatrExt/src/p_equiv_one_sample.cpp |only cmstatrExt-0.5.0/cmstatrExt/src/power_sim.cpp | 21 +-- cmstatrExt-0.5.0/cmstatrExt/src/root.cpp | 4 cmstatrExt-0.5.0/cmstatrExt/tests/testthat/test-equiv-one-sample.R |only 27 files changed, 142 insertions(+), 94 deletions(-)
Title: Fast Strength-t Coverage Verification for Covering Arrays
Description: Verifies that an array covers every t-way interaction, the
certificate check for covering arrays, using compiled C code with
optional 'OpenMP' threading. Supports uniform and mixed-level
(per-column symbol counts) arrays. Missing values mark flexible
("don't care") entries, which contribute nothing to coverage, so a
verified array remains covering however they are filled. Designed
to be easy to embed in other packages: a single C file with a
registered .Call entry point and one R wrapper.
Author: Christopher Smolen [aut, cre]
Maintainer: Christopher Smolen <chrispbsmolen@gmail.com>
Diff between caverify versions 0.1.3 dated 2026-08-23 and 0.2.0 dated 2026-09-19
DESCRIPTION | 16 +++--- MD5 | 12 ++-- NEWS.md | 35 +++++++++++++ R/ca_verify.R | 129 +++++++++++++++++++++++++++++++++++++++---------- man/ca_verify.Rd | 47 +++++++++++++---- src/ca_verify.c | 98 ++++++++++++++++++++++--------------- tests/test-ca_verify.R | 124 +++++++++++++++++++++++++++++++++++++++++++++-- 7 files changed, 367 insertions(+), 94 deletions(-)
Title: Retrieve 'AirNow' Air Quality Observations and Forecasts
Description: Retrieve air quality data via the 'AirNow'
<https://www.airnow.gov/> API.
Author: Brian Connelly [aut, cre, cph]
Maintainer: Brian Connelly <bdc@bconnelly.net>
Diff between airnow versions 0.1.1 dated 2026-03-01 and 0.2.0 dated 2026-09-19
airnow-0.1.1/airnow/R/get_airnow_area.R |only airnow-0.1.1/airnow/R/get_airnow_conditions.R |only airnow-0.1.1/airnow/R/get_airnow_forecast.R |only airnow-0.1.1/airnow/man/get_airnow_area.Rd |only airnow-0.1.1/airnow/man/get_airnow_conditions.Rd |only airnow-0.1.1/airnow/man/get_airnow_forecast.Rd |only airnow-0.1.1/airnow/man/get_airnow_token.Rd |only airnow-0.1.1/airnow/tests/testthat/test-get_airnow_area.R |only airnow-0.2.0/airnow/DESCRIPTION | 11 airnow-0.2.0/airnow/MD5 | 101 ++++- airnow-0.2.0/airnow/NAMESPACE | 7 airnow-0.2.0/airnow/NEWS.md | 56 +++ airnow-0.2.0/airnow/R/api.R | 75 ++++ airnow-0.2.0/airnow/R/aqi.R | 17 airnow-0.2.0/airnow/R/areas.R |only airnow-0.2.0/airnow/R/argument_checks.R | 76 ++++ airnow-0.2.0/airnow/R/credentials.R | 74 ++-- airnow-0.2.0/airnow/R/data.R |only airnow-0.2.0/airnow/R/deprecated.R |only airnow-0.2.0/airnow/R/get_airnow_forecast_history.R |only airnow-0.2.0/airnow/R/get_airnow_forecasts.R |only airnow-0.2.0/airnow/R/get_airnow_monitors.R |only airnow-0.2.0/airnow/R/get_airnow_observations.R |only airnow-0.2.0/airnow/R/get_airnow_reporting_area.R |only airnow-0.2.0/airnow/R/legacy.R |only airnow-0.2.0/airnow/R/normalize.R |only airnow-0.2.0/airnow/R/sysdata.rda |only airnow-0.2.0/airnow/R/utils.R | 51 ++ airnow-0.2.0/airnow/README.md | 66 ++- airnow-0.2.0/airnow/data |only airnow-0.2.0/airnow/inst |only airnow-0.2.0/airnow/man/airnow-deprecated.Rd |only airnow-0.2.0/airnow/man/airnow-package.Rd | 5 airnow-0.2.0/airnow/man/airnow_areas.Rd |only airnow-0.2.0/airnow/man/aqi.Rd | 14 airnow-0.2.0/airnow/man/get_airnow_forecast_history.Rd |only airnow-0.2.0/airnow/man/get_airnow_forecasts.Rd |only airnow-0.2.0/airnow/man/get_airnow_key.Rd |only airnow-0.2.0/airnow/man/get_airnow_monitors.Rd |only airnow-0.2.0/airnow/man/get_airnow_observations.Rd |only airnow-0.2.0/airnow/man/get_airnow_reporting_area.Rd |only airnow-0.2.0/airnow/tests/testthat/forecast_history |only airnow-0.2.0/airnow/tests/testthat/forecasts |only airnow-0.2.0/airnow/tests/testthat/forecasts_nodata |only airnow-0.2.0/airnow/tests/testthat/harness |only airnow-0.2.0/airnow/tests/testthat/helper-cache.R |only airnow-0.2.0/airnow/tests/testthat/helper-live-results.R |only airnow-0.2.0/airnow/tests/testthat/legacy_conditions |only airnow-0.2.0/airnow/tests/testthat/legacy_forecast |only airnow-0.2.0/airnow/tests/testthat/legacy_forecast_date |only airnow-0.2.0/airnow/tests/testthat/monitors |only airnow-0.2.0/airnow/tests/testthat/observations |only airnow-0.2.0/airnow/tests/testthat/observations_nodata |only airnow-0.2.0/airnow/tests/testthat/reporting_area |only airnow-0.2.0/airnow/tests/testthat/resolve_zip |only airnow-0.2.0/airnow/tests/testthat/setup.R |only airnow-0.2.0/airnow/tests/testthat/test-api.R | 81 ++++ airnow-0.2.0/airnow/tests/testthat/test-aqi.R | 41 +- airnow-0.2.0/airnow/tests/testthat/test-areas.R |only airnow-0.2.0/airnow/tests/testthat/test-argument_checks.R | 76 +++- airnow-0.2.0/airnow/tests/testthat/test-ci-runner.R |only airnow-0.2.0/airnow/tests/testthat/test-credentials.R | 62 ++- airnow-0.2.0/airnow/tests/testthat/test-data.R |only airnow-0.2.0/airnow/tests/testthat/test-deprecated.R |only airnow-0.2.0/airnow/tests/testthat/test-get_airnow_conditions.R | 90 +++-- airnow-0.2.0/airnow/tests/testthat/test-get_airnow_forecast.R | 174 +++++++--- airnow-0.2.0/airnow/tests/testthat/test-get_airnow_forecast_history.R |only airnow-0.2.0/airnow/tests/testthat/test-get_airnow_forecasts.R |only airnow-0.2.0/airnow/tests/testthat/test-get_airnow_monitors.R |only airnow-0.2.0/airnow/tests/testthat/test-get_airnow_observations.R |only airnow-0.2.0/airnow/tests/testthat/test-get_airnow_reporting_area.R |only airnow-0.2.0/airnow/tests/testthat/test-harness.R |only airnow-0.2.0/airnow/tests/testthat/test-legacy.R |only airnow-0.2.0/airnow/tests/testthat/test-live.R |only airnow-0.2.0/airnow/tests/testthat/test-normalize.R |only airnow-0.2.0/airnow/tests/testthat/test-utils.R | 55 +++ 76 files changed, 921 insertions(+), 211 deletions(-)
Title: 'DataTables' 2.x for R
Description: A modern R binding for 'DataTables' V2 with modular
extension loading, 'Bootstrap 5' styling, 'Shiny' integration (proxy, events,
inline inputs), server-side processing helpers, and standalone (non-Shiny)
support. Configure 'DataTables' options directly via R lists, a 1:1 mapping
to the 'JavaScript' API.
Author: Andre Leite [aut, cre],
Marcos Wasilew [aut],
Hugo Vasconcelos [aut],
Carlos Amorim [aut],
Diogo Bezerra [aut]
Maintainer: Andre Leite <leite@castlab.org>
Diff between DT2 versions 0.1.2 dated 2026-06-14 and 0.1.3 dated 2026-09-19
DESCRIPTION | 13 MD5 | 54 - NEWS.md | 31 R/dt2.R | 13 R/dt2_formats.R | 2 R/dt2_server_processing.R | 64 + R/dt2_shiny.R | 33 README.md | 13 inst/doc/extensions-guide.Rmd | 3 inst/doc/extensions-guide.html | 123 ++- inst/doc/formatting.html | 124 ++- inst/doc/getting-started.Rmd | 2 inst/doc/getting-started.html | 230 ++++-- inst/doc/js-config.html | 144 +++- inst/doc/shiny-integration.R | 23 inst/doc/shiny-integration.Rmd | 46 + inst/doc/shiny-integration.html | 1065 ++++++++++++++++---------------- inst/htmlwidgets/dt2.js | 92 ++ man/dot-dt2_payload.Rd | 14 man/dt2.Rd | 2 man/dt2_bind_server.Rd | 11 man/dt2_cols_render_js.Rd | 2 man/dt2_ssp_handler.Rd | 13 man/dt2_state.Rd | 34 - tests/testthat/test-server-processing.R | 89 ++ vignettes/extensions-guide.Rmd | 3 vignettes/getting-started.Rmd | 2 vignettes/shiny-integration.Rmd | 46 + 28 files changed, 1522 insertions(+), 769 deletions(-)
Title: Reverse-Correlation Image-Classification Toolbox
Description: Generate stimuli and analyze data of reverse correlation image
classification experiments (psychophysical tasks aimed at visualizing
cognitive mental representations of faces). For the method see Dotsch and
Todorov (2012) <doi:10.1177/1948550611430272>; for a practical primer see
Brinkman, Todorov and Dotsch (2017) <doi:10.1080/10463283.2017.1381469>.
Author: Ron Dotsch [aut, cre]
Maintainer: Ron Dotsch <rdotsch@gmail.com>
Diff between rcicr versions 1.3.0 dated 2026-09-02 and 1.4.1 dated 2026-09-19
rcicr-1.3.0/rcicr/tests/testthat/fixtures/released-formals-1.3.0.rds |only rcicr-1.4.1/rcicr/ChangeLog | 65 -- rcicr-1.4.1/rcicr/DESCRIPTION | 6 rcicr-1.4.1/rcicr/MD5 | 72 +- rcicr-1.4.1/rcicr/NEWS.md | 131 ++++ rcicr-1.4.1/rcicr/R/autoscale.R | 19 rcicr-1.4.1/rcicr/R/ci-inputs.R | 40 + rcicr-1.4.1/rcicr/R/computeCumulativeCICorrelation.R | 8 rcicr-1.4.1/rcicr/R/computeInfoVal2IFC.R | 103 +-- rcicr-1.4.1/rcicr/R/generateCI.R | 54 + rcicr-1.4.1/rcicr/R/generateCI2IFC.R | 2 rcicr-1.4.1/rcicr/R/generateCINoise.R | 8 rcicr-1.4.1/rcicr/R/generateReferenceDistribution.R | 148 +---- rcicr-1.4.1/rcicr/R/generateStimuli2IFC.R | 59 + rcicr-1.4.1/rcicr/R/parallel.R | 10 rcicr-1.4.1/rcicr/R/reference-base.R |only rcicr-1.4.1/rcicr/R/zzz.R | 2 rcicr-1.4.1/rcicr/README.md | 72 +- rcicr-1.4.1/rcicr/inst/doc/reverse-correlation-walkthrough.R | 13 rcicr-1.4.1/rcicr/inst/doc/reverse-correlation-walkthrough.Rmd | 23 rcicr-1.4.1/rcicr/inst/doc/reverse-correlation-walkthrough.html | 296 +++++----- rcicr-1.4.1/rcicr/man/computeCumulativeCICorrelation.Rd | 2 rcicr-1.4.1/rcicr/man/computeInfoVal2IFC.Rd | 15 rcicr-1.4.1/rcicr/man/generateCI.Rd | 4 rcicr-1.4.1/rcicr/man/generateCI2IFC.Rd | 2 rcicr-1.4.1/rcicr/man/generateCINoise.Rd | 2 rcicr-1.4.1/rcicr/man/generateReferenceDistribution2IFC.Rd | 46 + rcicr-1.4.1/rcicr/tests/testthat/fixtures/released-formals-1.4.0.rds |only rcicr-1.4.1/rcicr/tests/testthat/helper-fixtures.R | 18 rcicr-1.4.1/rcicr/tests/testthat/test-base-image-alpha.R |only rcicr-1.4.1/rcicr/tests/testthat/test-fixed-bugs.R | 7 rcicr-1.4.1/rcicr/tests/testthat/test-generateCINoise.R | 25 rcicr-1.4.1/rcicr/tests/testthat/test-generateReferenceDistribution2IFC.R | 132 +++- rcicr-1.4.1/rcicr/tests/testthat/test-independent-reference.R |only rcicr-1.4.1/rcicr/tests/testthat/test-legacy-rdata.R | 70 +- rcicr-1.4.1/rcicr/tests/testthat/test-multi-base-stimuli.R |only rcicr-1.4.1/rcicr/tests/testthat/test-parallel-backend.R |only rcicr-1.4.1/rcicr/tests/testthat/test-reference-from-saved-noise.R |only rcicr-1.4.1/rcicr/tests/testthat/test-released-signatures.R | 6 rcicr-1.4.1/rcicr/tests/testthat/test-trial-validation.R |only rcicr-1.4.1/rcicr/tests/testthat/test-zero-range-scaling.R |only rcicr-1.4.1/rcicr/vignettes/reverse-correlation-walkthrough.Rmd | 23 42 files changed, 865 insertions(+), 618 deletions(-)
Title: Interpolate Munsell Renotation Data from Hue Value/Chroma to
CIE/RGB
Description: Methods for interpolating data in the Munsell color system following the ASTM D-1535 standard. Hues and chromas with decimal values can be interpolated and converted to/from the Munsell color system and CIE xyY, CIE XYZ, CIE Lab, CIE Luv, or RGB. Includes ISCC-NBS color block lookup. Based on the work by Paul Centore, "The Munsell and Kubelka-Munk Toolbox".
Author: Jose Gama [aut, trl],
Paul Centore [aut, cph],
Glenn Davis [aut, cre],
Hugo Rodrigues [ctb]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between munsellinterpol versions 3.5-1 dated 2026-07-30 and 3.6-0 dated 2026-09-19
DESCRIPTION | 8 +-- MD5 | 56 +++++++++++++------------- NEWS.md | 10 ++++ R/ColorDifference.R | 9 ++++ R/Colorlab.R | 48 +++++++++++----------- R/ISCC-NBS.R | 5 +- R/MunsellName.R | 5 +- R/MunsellToxyY.R | 24 +++++++++-- R/conversions.R | 6 ++ R/round.R | 3 + R/utils.R | 77 ++++++++++++++++++++++++++++++++++-- inst/doc/dental.html | 6 +- inst/doc/lightness.pdf |binary inst/doc/lociHC.pdf |binary inst/doc/munsellinterpol-guide.Rmd | 2 inst/doc/munsellinterpol-guide.html | 29 +++++++------ inst/doc/soil.html | 29 +++++++------ man/ColorBlockFromMunsell.Rd | 2 man/MunsellNameFromHVC.Rd | 2 man/MunsellSpecToColorlabFormat.Rd | 5 ++ man/MunsellToLab.Rd | 6 ++ man/MunsellToLuv.Rd | 6 ++ man/MunsellToRGB.Rd | 6 ++ man/MunsellToXYZ.Rd | 6 ++ man/MunsellTosRGB.Rd | 6 ++ man/MunsellToxyY.Rd | 3 - man/NickersonColorDifference.Rd | 6 ++ man/round.Rd | 6 ++ vignettes/munsellinterpol-guide.Rmd | 2 29 files changed, 272 insertions(+), 101 deletions(-)
More information about munsellinterpol at CRAN
Permanent link
Title: Faithful and Scalable MARCXML Parsing
Description: Parses Machine-Readable Cataloging ('MARC 21') XML
<https://www.loc.gov/standards/marcxml/> into a canonical tidy long
representation while preserving leaders, control fields, data fields,
indicators, repeated fields, repeated subfields, and source order.
Provides an in-memory reader for manageable catalogues and a
bounded-memory converter that writes larger collections as 'Parquet'
datasets, with optional local parallel processing.
Author: Lorenzo Isella [aut, cre]
Maintainer: Lorenzo Isella <lorenzo.isella@gmail.com>
Diff between marcxmlr versions 0.1.0 dated 2026-09-12 and 0.2.1 dated 2026-09-19
DESCRIPTION | 12 MD5 | 38 NAMESPACE | 1 NEWS.md | 60 R/marcxml-to-parquet.R | 383 +++++- R/marcxmlr-package.R | 1 R/multi-file-parquet.R |only R/native-parser.R |only R/read-marcxml.R | 70 - R/record-parser.R | 47 README.md | 1477 ++++++++++++++++++------ configure |only inst/NOTICE |only inst/benchmarks/benchmark-native.R |only man/marcxml_to_parquet.Rd | 68 - man/read_marcxml.Rd | 19 src |only tests/testthat/helper-fixtures.R | 25 tests/testthat/test-error-context.R |only tests/testthat/test-native-direct.R |only tests/testthat/test-native-parallel.R |only tests/testthat/test-native-parser.R |only tests/testthat/test-native-stream-reader.R |only tests/testthat/test-parquet-multifile.R |only tests/testthat/test-stream-namespace-fastpath.R |only tools |only 26 files changed, 1758 insertions(+), 443 deletions(-)
Title: Methods for Clustering Mixed-Type Data
Description: Implements methods for clustering mixed-type data,
specifically combinations of continuous and nominal data. Special attention
is paid to the often-overlooked problem of equitably balancing the
contribution of the continuous and categorical variables. This package
implements KAMILA clustering, a novel method for clustering
mixed-type data in the spirit of k-means clustering. It does not require
dummy coding of variables, and is efficient enough to scale to rather large
data sets. Also implemented is Modha-Spangler clustering, which uses a
brute-force strategy to maximize the cluster separation simultaneously in the
continuous and categorical variables. For more information, see Foss, Markatou,
Ray, & Heching (2016) <doi:10.1007/s10994-016-5575-7> and Foss & Markatou
(2018) <doi:10.18637/jss.v083.i13>.
Author: Alexander Foss [aut, cre],
Marianthi Markatou [aut]
Maintainer: Alexander Foss <alexanderhfoss@gmail.com>
Diff between kamila versions 0.1.2 dated 2020-03-13 and 0.2.0 dated 2026-09-19
DESCRIPTION | 18 MD5 | 53 - NAMESPACE | 34 NEWS.md |only R/RcppExports.R | 20 R/calc_approx_bic_deprec.R | 25 R/gen_mixed_data.R | 385 ++++---- R/kamila.R | 1437 +++++++++++++++++------------- R/misc_functions.R | 182 ++- R/modha_spangler.R | 112 +- R/prediction_strength_deprec.R | 197 +--- README.md | 82 + inst/shiny |only man/classifyKamila.Rd | 34 man/dummyCodeFactorDf.Rd | 2 man/genMixedData.Rd | 21 man/gmsClust.Rd | 32 man/kamila-package.Rd | 79 - man/kamila.Rd | 88 + man/wkmeans.Rd | 21 src/RcppExports.cpp | 84 + src/cppfunctions.cpp | 1050 +++++++++++++++++++++ tests/testthat/_snaps |only tests/testthat/test_calc_approx_bic.R |only tests/testthat/test_calc_ps_rcpp.R |only tests/testthat/test_gen_mixed_data.R |only tests/testthat/test_gmsClust.R | 58 + tests/testthat/test_kamila.R | 163 ++- tests/testthat/test_kamila_advanced.R |only tests/testthat/test_kamila_parallel.R |only tests/testthat/test_kamila_regression.R |only tests/testthat/test_misc_functions.R |only tests/testthat/test_prediction_strength.R |only 33 files changed, 2879 insertions(+), 1298 deletions(-)
Title: Client for the Ifo Institute Time Series
Description: Download ifo business survey data and more time series from
ifo institute <https://www.ifo.de/en/ifo-time-series>.
Author: Maximilian Muecke [aut, cre]
Maintainer: Maximilian Muecke <muecke.maximilian@gmail.com>
Diff between ifo versions 0.2.5 dated 2026-08-21 and 0.3.0 dated 2026-09-19
DESCRIPTION | 12 MD5 | 21 NAMESPACE | 1 NEWS.md | 13 R/ifo.R | 112 + README.md | 14 man/figures/README-plotting-1.png |binary man/ifo_business.Rd | 2 man/ifo_climate.Rd | 3 man/ifo_vintage.Rd |only tests/testthat/fixtures/ifo-time-series.html | 1568 +++++++++++++++++++-------- tests/testthat/test-ifo.R | 119 ++ 12 files changed, 1418 insertions(+), 447 deletions(-)
Title: Client for the 'Google Data Commons API V2'
Description: Access the 'Google Data Commons API V2' <https://docs.datacommons.org/api/rest/v2/>.
Data Commons provides programmatic access to statistical and demographic data from
dozens of sources organized in a knowledge graph.
Author: Christoph Scheuch [aut, cre, cph] ,
Teal Emery [aut]
Maintainer: Christoph Scheuch <christoph@tidy-intelligence.com>
Diff between datacommons versions 0.1.0 dated 2025-08-28 and 0.1.1 dated 2026-09-19
DESCRIPTION | 10 +- MD5 | 50 +++++++------ NEWS.md | 12 +++ R/sparql.R | 21 +++++ R/utils.R | 42 +++++++++-- README.md | 53 ++++++++------ build/vignette.rds |binary inst/doc/analyzing-census-data.html | 121 ++++++++++++++++---------------- inst/doc/using-un-data-commons.R |only inst/doc/using-un-data-commons.Rmd |only inst/doc/using-un-data-commons.html |only man/dc_get_classes.Rd | 2 man/dc_get_dcid_by_coordinates.Rd | 2 man/dc_get_dcids_by_name.Rd | 2 man/dc_get_dcids_by_wikidata_id.Rd | 2 man/dc_get_node.Rd | 2 man/dc_get_observations.Rd | 2 man/dc_get_property_values.Rd | 2 man/dc_get_resolve.Rd | 2 man/dc_get_statistical_variables.Rd | 2 man/dc_post_sparql.Rd | 14 +++ man/dc_set_api_key.Rd | 3 man/dc_set_base_url.Rd | 3 man/figures |only tests/testthat/test-sparql.R | 17 ++++ tests/testthat/test-utils.R | 136 ++++++++++++++++++++++++++++++++++++ vignettes/using-un-data-commons.Rmd |only 27 files changed, 371 insertions(+), 129 deletions(-)
Title: Pipeline for Explainable Machine Learning with Functional Data
Description: Implements the Variable importance Explainable Elastic Shape Analysis pipeline for explainable machine learning with functional data inputs. Converts training and testing data functional inputs to elastic shape analysis principal components that account for vertical and/or horizontal variability. Computes feature importance to identify important principal components and visualizes variability captured by functional principal components. See Goode et al. (2025) <doi:10.48550/arXiv.2501.07602> for technical details about the methodology.
Author: Katherine Goode [cre, aut],
J. Derek Tucker [aut],
Sandia National Laboratories [cph, fnd]
Maintainer: Katherine Goode <kjgoode@sandia.gov>
Diff between veesa versions 0.1.7 dated 2025-12-04 and 0.1.8 dated 2026-09-18
veesa-0.1.7/veesa/R/center_pcdirs.R |only veesa-0.1.8/veesa/DESCRIPTION | 13 veesa-0.1.8/veesa/MD5 | 59 +-- veesa-0.1.8/veesa/NAMESPACE | 86 ++-- veesa-0.1.8/veesa/NEWS.md | 29 + veesa-0.1.8/veesa/R/align_pcdirs.R | 5 veesa-0.1.8/veesa/R/center_warping_funs.R | 8 veesa-0.1.8/veesa/R/compute_logloss.R | 12 veesa-0.1.8/veesa/R/compute_nmse.R | 3 veesa-0.1.8/veesa/R/compute_pfi.R | 2 veesa-0.1.8/veesa/R/data_shifted_peaks.R | 2 veesa-0.1.8/veesa/R/plot_pc_diffs.R | 113 ++++-- veesa-0.1.8/veesa/R/plot_pc_directions.R | 60 ++- veesa-0.1.8/veesa/R/prep_testing_data.R | 108 +++++- veesa-0.1.8/veesa/R/prep_training_data.R | 42 +- veesa-0.1.8/veesa/R/simulate_functions.R | 16 veesa-0.1.8/veesa/README.md | 48 ++ veesa-0.1.8/veesa/man/align_pcdirs.Rd | 14 veesa-0.1.8/veesa/man/center_warping_funs.Rd | 4 veesa-0.1.8/veesa/man/compute_pfi.Rd | 3 veesa-0.1.8/veesa/man/plot_pc_diffs.Rd | 6 veesa-0.1.8/veesa/man/plot_pc_directions.Rd | 4 veesa-0.1.8/veesa/man/prep_testing_data.Rd | 48 ++ veesa-0.1.8/veesa/man/prep_training_data.Rd | 34 + veesa-0.1.8/veesa/man/shifted_peaks.Rd | 2 veesa-0.1.8/veesa/man/simulate_functions.Rd | 1 veesa-0.1.8/veesa/tests/testthat/test-align_pcdirs.R |only veesa-0.1.8/veesa/tests/testthat/test-center_warping_funs.R |only veesa-0.1.8/veesa/tests/testthat/test-compute_metrics.R |only veesa-0.1.8/veesa/tests/testthat/test-plot_pc_diffs.R |only veesa-0.1.8/veesa/tests/testthat/test-plot_pc_directions.R | 207 ++++++++---- veesa-0.1.8/veesa/tests/testthat/test-prep_testing_data.R | 104 +++++- veesa-0.1.8/veesa/tests/testthat/test-prep_training_data.R | 35 ++ 33 files changed, 789 insertions(+), 279 deletions(-)
Title: Support Functions for Wrangling and Visualization
Description: Suite of helper functions for data wrangling and visualization.
The only theme for these functions is that they tend towards simple, short, and narrowly-scoped.
These functions are built for tasks that often recur but are not large enough in scope to warrant an ecosystem of interdependent functions.
Author: Nicholas J Lyon [aut, cre, cph]
Maintainer: Nicholas J Lyon <nickjlyon@gmail.com>
Diff between supportR versions 1.6.0 dated 2025-12-21 and 1.6.1 dated 2026-09-18
DESCRIPTION | 16 ++--- MD5 | 17 +++-- NAMESPACE | 7 +- NEWS.md | 94 ++++++++++++++++++------------- R/spellcheck_quarto.r |only README.md | 31 ++-------- build/vignette.rds |binary inst/doc/supportr_03_visualizations.html | 6 - man/spellcheck_quarto.Rd |only man/supportR-package.Rd | 7 +- tests/testthat/test-spellcheck_quarto.r |only 11 files changed, 96 insertions(+), 82 deletions(-)
Title: Analyze Outbreak Models of Multi-Group Populations with
Vaccination
Description: Model infectious disease dynamics in populations
with multiple subgroups having different vaccination rates, transmission
characteristics, and contact patterns. Calculate final and intermediate
outbreak sizes, form age-structured contact models with automatic fetching
of U.S. census data, and explore vaccination scenarios with an interactive
'shiny' dashboard for a model with two subgroups, as described in Nguyen et
al. (2024) <doi:10.1016/j.jval.2024.03.039> and Duong et al. (2026)
<doi:10.1093/ofid/ofaf695.217>.
Author: Damon Toth [aut, cre, cph] ,
Jake Wagoner [aut] ,
Willy Ray [aut],
George Vega Yon [ctb] ,
Centers for Disease Control and Prevention's Center for Forecasting and
Outbreak Analytics [fnd]
Maintainer: Damon Toth <damon.toth@hsc.utah.edu>
Diff between multigroup.vaccine versions 0.1.1 dated 2026-02-09 and 0.1.2 dated 2026-09-18
DESCRIPTION | 8 MD5 | 19 +- NEWS.md | 6 R/contactMatrixPolymod.R | 20 +- build/vignette.rds |binary inst/doc/census_functions_demo.html | 7 inst/doc/contact_matrix_examples.html | 282 ++++++++++++++++---------------- inst/doc/measles_agemodel.html | 48 ++--- inst/doc/run_model_on_command_line.html | 32 +-- inst/extdata/polymod_countries_2005.csv |only man/run_my_app.Rd | 2 11 files changed, 217 insertions(+), 207 deletions(-)
More information about multigroup.vaccine at CRAN
Permanent link
Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov
chains more easily. In addition functions to perform statistical (fitting
and drawing random variates) and probabilistic (analysis of their structural
proprieties) analysis are provided. See Spedicato (2017) <doi:10.32614/RJ-2017-036>.
Some functions for continuous times Markov chains depend on the suggested ctmcd package.
Author: Giorgio Alfredo Spedicato [aut, cre] ,
Tae Seung Kang [aut],
Sai Bhargav Yalamanchi [aut],
Mildenberger Thoralf [ctb] ,
Deepak Yadav [aut],
Ignacio Cordon [aut] ,
Vandit Jain [ctb],
Toni Giorgino [ctb] ,
Richel J.C. Bilderbeek [ctb] ,
Daniel Ebbert [ [...truncated...]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between markovchain versions 1.0.0 dated 2026-08-25 and 1.1.1 dated 2026-09-18
DESCRIPTION | 10 MD5 | 60 +- NAMESPACE | 6 NEWS.md | 14 R/RcppExports.R | 10 R/ctmcProbabilistic.R | 32 + R/entropyRate.R |only R/fitHigherOrder.R | 8 R/fittingFunctions.R | 55 +- R/fundamentalMatrix.R |only R/kemeny.R |only R/probabilistic.R | 472 ++++++++++++------- inst/doc/an_introduction_to_markovchain_package.R | 103 ++++ inst/doc/an_introduction_to_markovchain_package.Rmd | 328 +++++++++---- inst/doc/an_introduction_to_markovchain_package.pdf |binary inst/doc/gsoc_2017_additions.html | 13 inst/doc/higher_order_markov_chains.html | 11 man/autoLump.Rd |only man/entropyRate.Rd |only man/fundamentalMatrix.Rd |only man/is.lumpable.Rd |only man/kemenyConstant.Rd |only man/lump.Rd |only src/RcppExports.cpp | 28 + src/ctmcFittingFunctions.cpp | 41 + src/ctmcProbabilistic.cpp | 23 src/fitHigherOrder.cpp | 52 +- src/fittingFunctions.cpp | 19 src/probabilistic.cpp | 364 +++++++++++--- tests/testthat/test-ctmcFittingFunctions.R |only tests/testthat/test-entropyRate.R |only tests/testthat/test-fitHigherOrder.R |only tests/testthat/test-fundamentalMatrix.R |only tests/testthat/test-input-hardening.R |only tests/testthat/test-kemeny.R |only tests/testthat/test-lumpability.R |only tests/testthat/testHittingProbabilities.R | 45 + vignettes/an_introduction_to_markovchain_package.Rmd | 328 +++++++++---- vignettes/markovchainBiblio.bib | 37 + 39 files changed, 1533 insertions(+), 526 deletions(-)
Title: Tools Developed by the Long Term Ecological Research Community
Description: Set of the data science tools created by various members of the Long Term
Ecological Research (LTER) community. These functions were initially written largely
as standalone operations and have later been aggregated into this package.
Author: Nicholas Lyon [aut, cre] ,
Angel Chen [aut] ,
Miguel C. Leon [ctb] ,
National Science Foundation [fnd] ,
University of California, Santa Barbara [cph]
Maintainer: Nicholas Lyon <nickjlyon@gmail.com>
Diff between ltertools versions 2.1.0 dated 2025-09-02 and 2.1.1 dated 2026-09-18
DESCRIPTION | 14 ++--- MD5 | 19 +++--- NEWS.md | 72 ++++++++++++++++--------- R/check_key.R | 8 ++ R/standardize.R | 11 ++- README.md | 111 ++++++++++------------------------------ build/vignette.rds |binary inst/doc/ltertools.html | 9 +-- man/check_key.Rd | 4 - man/ltertools-package.Rd | 3 - tests/testthat/test-check_key.R |only 11 files changed, 113 insertions(+), 138 deletions(-)
Title: Access the 'Finto' API
Description: Access and retrieve vocabulary data 'Finto' API <https://api.finto.fi/>, which is a centralized service for interoperable thesauri, ontology and classification schemes for different subject areas.
Author: Akewak Jeba [aut, cre] ,
Leo Lahti [aut]
Maintainer: Akewak Jeba <akewak84@gmail.com>
Diff between finto versions 0.1.1 dated 2025-11-24 and 0.1.2 dated 2026-09-18
DESCRIPTION | 17 +- MD5 | 138 ++++++++-------- NAMESPACE | 5 R/data.R |only R/fetch_kanto_info.R | 2 R/fetch_profession_hierarchy.R | 2 R/fetch_profession_info.R | 2 R/get_alphabetical_index_letters.R | 2 R/get_broader_concepts.R | 2 R/get_broader_transitive_concepts.R | 2 R/get_children_concepts.R | 2 R/get_concept_data.R | 2 R/get_concept_groups.R | 2 R/get_concept_labels.R | 2 R/get_concept_labels_vocid.R | 2 R/get_concepts_by_letter.R | 2 R/get_group_members.R | 2 R/get_hierarchy.R | 2 R/get_kanto.R | 273 ++++++++++++++++++++++++++++----- R/get_label_statistics.R | 2 R/get_mappings.R | 2 R/get_modified_concepts.R | 2 R/get_narrower_concepts.R | 2 R/get_narrower_transitive.R | 2 R/get_new_concepts.R | 2 R/get_related_concepts.R | 2 R/get_top_concepts.R | 2 R/get_types.R | 2 R/get_vocabularies.R | 2 R/get_vocabulary_info.R | 2 R/get_vocabulary_statistics.R | 2 R/get_vocabulary_types.R | 2 R/lookup_concept_by_label.R | 2 R/search_concepts.R | 2 R/search_vocabulary_concepts.R | 2 R/utils.R | 15 + R/yso_places.R |only build/vignette.rds |binary man/fennica_subset.Rd |only man/fetch_kanto_info.Rd | 2 man/fetch_profession_hierarchy.Rd | 2 man/fetch_profession_info.Rd | 2 man/get_alphabetical_index_letters.Rd | 2 man/get_broader_concepts.Rd | 2 man/get_broader_transitive_concepts.Rd | 2 man/get_children_concepts.Rd | 2 man/get_concept_data.Rd | 2 man/get_concept_groups.Rd | 2 man/get_concept_labels.Rd | 2 man/get_concept_labels_vocid.Rd | 2 man/get_concepts_by_letter.Rd | 2 man/get_group_members.Rd | 2 man/get_hierarchy.Rd | 2 man/get_kanto.Rd | 11 + man/get_label_statistics.Rd | 2 man/get_mappings.Rd | 2 man/get_modified_concepts.Rd | 2 man/get_narrower_concepts.Rd | 2 man/get_narrower_transitive.Rd | 2 man/get_new_concepts.Rd | 2 man/get_related_concepts.Rd | 2 man/get_top_concepts.Rd | 2 man/get_types.Rd | 2 man/get_vocabularies.Rd | 2 man/get_vocabulary_info.Rd | 2 man/get_vocabulary_statistics.Rd | 2 man/get_vocabulary_types.Rd | 2 man/lookup_concept_by_label.Rd | 2 man/search_concepts.Rd | 2 man/search_vocabulary_concepts.Rd | 2 man/yso_place.Rd |only tests/testthat/test_search_concepts.R | 3 72 files changed, 463 insertions(+), 119 deletions(-)
Title: Dungeons & Dragons Functions for Players and Dungeon Masters
Description: The goal of 'dndR' is to provide a suite of Dungeons & Dragons related functions.
This package is meant to be useful both to players and Dungeon Masters (DMs).
Some functions apply to many tabletop role-playing games (e.g., dice rolling), but others are focused on Fifth Edition (a.k.a. "5e") and where possible both the 2014 and 2024 versions are supported.
Author: Nicholas Lyon [aut, cre, cph] ,
Tim Schatto-Eckrodt [aut] ,
Humberto Nappo [aut] ,
Billy Mitchell [aut]
Maintainer: Nicholas Lyon <nickjlyon@gmail.com>
Diff between dndR versions 3.1.0 dated 2025-06-11 and 3.1.1 dated 2026-09-18
DESCRIPTION | 16 ++--- MD5 | 26 ++++---- NAMESPACE | 6 +- NEWS.md | 112 ++++++++++++++++---------------------- README.md | 37 +++--------- build/vignette.rds |binary inst/doc/dndr_00_dice.html | 16 +++-- inst/doc/dndr_01_characters.html | 40 +++++++------ inst/doc/dndr_02_creatures.html | 37 ++++++------ inst/doc/dndr_03_spells.html | 5 + inst/doc/dndr_04_encounters.html | 5 + inst/doc/dndr_05_visuals.html | 11 ++- inst/doc/dndr_99_dmg-vs-dndr.html | 4 - man/dndR-package.Rd | 4 + 14 files changed, 150 insertions(+), 169 deletions(-)
Title: Prais-Winsten Estimator for AR(1) Serial Correlation
Description: The Prais-Winsten estimator (Prais & Winsten, 1954) takes into account AR(1) serial correlation of the errors in a linear regression model. The procedure recursively estimates the coefficients and the error autocorrelation of the specified model until sufficient convergence of the AR(1) coefficient is attained.
Author: Franz X. Mohr [aut, cre] ,
Michael Skvrňak [ctb]
Maintainer: Franz X. Mohr <franz.x.mohr@outlook.com>
Diff between prais versions 1.1.4 dated 2025-06-25 and 1.2.0 dated 2026-09-18
DESCRIPTION | 18 +-- MD5 | 43 ++++--- NEWS.md | 76 +++++++++++++ R/data.R | 42 +++---- R/prais_winsten.R | 210 +++++++++++++++++++++++++++++------- R/predict.prais.R | 67 +++++++---- R/print.summary.prais.R | 9 + R/pw_transform.R | 93 ++++++++++++++++ R/summary.prais.R | 46 ++------ R/vcovHC.R | 39 +----- R/vcovPC.R | 54 +++++---- build/partial.rdb |binary inst |only man/barium.Rd | 42 +++---- man/prais-package.Rd | 10 + man/prais_winsten.Rd | 274 ++++++++++++++++++++++-------------------------- man/predict.prais.Rd |only man/summary.prais.Rd | 6 - tests |only 19 files changed, 668 insertions(+), 361 deletions(-)
Title: Optimal Survival Cut-Point Discovery for Time-to-Event Analysis
with 'OptSurvCutR'
Description: Provides a robust workflow for optimal cut-point analysis in
time-to-event ('survival') data. Functions determine the optimal number
of cut-points via find_cutpoint_number(), find their precise locations
via find_cutpoint() using systematic or genetic algorithms (via the
'rgenoud' package), and validate stability via bootstrapping using
validate_cutpoint(). Features include covariate adjustment, parallel
processing, and an extensible S3 plotting engine for clinical
dashboards and diagnostics.
Author: Payton Yau [aut, cre, cph] ,
Suhirthakumar Puvanendran [aut]
Maintainer: Payton Yau <tungon@gmail.com>
Diff between OptSurvCutR versions 0.10.0 dated 2026-06-30 and 0.11.1 dated 2026-09-18
DESCRIPTION | 27 MD5 | 66 - NAMESPACE | 176 ++-- NEWS.md | 90 ++ R/engine-genetic.R | 651 +++++++-------- R/engine-systematic.R | 22 R/find_cutpoint.R | 112 ++ R/find_cutpoint_number.R | 1220 +++++++++++------------------ R/plotting_functions.R | 216 +++-- R/utils-permutations.R | 14 R/validate_cutpoint.R | 747 +++++++++-------- R/validate_cutpoint_methods.R | 569 +++++++------ README.md | 291 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/bilirubin.R | 188 +--- inst/doc/bilirubin.Rmd | 769 +++++++++--------- inst/doc/bilirubin.html | 1197 +++++++++++++--------------- inst/doc/crc.R |only inst/doc/crc.Rmd |only inst/doc/crc.html |only man/OptSurvCutR-package.Rd | 1 man/find_cutpoint.Rd | 65 - man/find_cutpoint_number.Rd | 41 man/plot.find_cutpoint.Rd | 5 man/plot_optimisation_curve.Rd | 36 man/validate_cutpoint.Rd | 9 tests/testthat/helper-data.R | 198 ++-- tests/testthat/test-find_cutpoint.R | 6 tests/testthat/test-find_cutpoint_number.R | 8 tests/testthat/test-plotting.R | 18 tests/testthat/test-stability-metric.R |only tests/testthat/test-utils.R | 56 - tests/testthat/test-validate_cutpoint.R | 4 tests/testthat/test-workflow-integration.R |only vignettes/bilirubin.Rmd | 769 +++++++++--------- vignettes/crc.Rmd |only 37 files changed, 3764 insertions(+), 3807 deletions(-)
Title: Download Radar Data for Biological Research
Description: Load polar volume and vertical profile data for
aeroecological research directly into R. With 'getRad' you can access
data from several sources in Europe and the US and standardize it to
facilitate further exploration in tools such as 'bioRad'.
Author: Bart Kranstauber [aut, cre] ,
Pieter Huybrechts [aut] ),
Peter Desmet [aut] ),
Cecilia Nilsson [ctb] ,
Alexander Tedeschi [ctb] ,
Hidde Leijnse [ctb] ,
Bart Hoekstra [ctb] ,
University of Amsterdam [cph] ,
Biodiversa+ [fnd]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between getRad versions 0.3.0 dated 2026-06-11 and 0.4.0 dated 2026-09-18
DESCRIPTION | 14 +++--- MD5 | 84 +++++++++++++++++++------------------ NAMESPACE | 1 NEWS.md | 6 ++ R/get_pvol.R | 63 +++++++++++++++++++++++++-- R/get_pvol_cz.R | 5 +- R/get_pvol_de.R | 36 +++++++++++---- R/get_pvol_ee.R | 12 +++-- R/get_pvol_nl.R | 9 ++- R/get_pvol_ord.R |only R/get_pvol_ro.R | 10 +++- R/get_pvol_sk.R | 5 +- R/get_pvol_uk.R |only R/get_pvol_us.R | 7 ++- R/get_vpts.R | 16 +++---- R/get_vpts_aloft.R | 2 R/get_vpts_birdcast.R | 2 R/get_vpts_coverage_aloft.R | 4 - R/get_vpts_coverage_birdcast.R | 4 - R/get_vpts_coverage_rmi.R | 9 ++- R/get_vpts_local_dark_ecology.R | 3 - R/get_vpts_rmi.R | 8 ++- R/get_weather_radars.R | 12 +++-- R/secrets.R | 4 - R/utils.R | 37 ++++++++-------- R/utils_pvol.R | 7 +-- R/utils_vpts_aloft.R | 4 - R/utils_vpts_rmi.R | 8 +-- R/zzz.R | 1 build/vignette.rds |binary inst/doc/supported_sources.R | 30 ++++++++----- inst/doc/supported_sources.Rmd | 43 ++++++++++++------ inst/doc/supported_sources.html | 42 +++++++++++------- man/get_pvol.Rd | 24 +++++++++- man/get_vpts.Rd | 14 +++--- man/get_weather_radars.Rd | 7 +-- tests/testthat/setup.R |only tests/testthat/test-get_pvol.R | 3 + tests/testthat/test-get_pvol_at.R | 8 ++- tests/testthat/test-get_pvol_fi.R | 8 +++ tests/testthat/test-get_pvol_nl.R | 38 +++++++++++++--- tests/testthat/test-get_pvol_ord.R |only tests/testthat/test-get_pvol_ro.R | 39 +++++++++++++++++ tests/testthat/test-get_pvol_us.R | 17 +++++++ vignettes/supported_sources.Rmd | 43 ++++++++++++------ 45 files changed, 478 insertions(+), 211 deletions(-)
Title: A Collection of Tools for Building Cropping System Models
Description: A collection of tools for designing, implementing,
testing, documenting and visualizing dynamic simulation
cropping system models. Models are specified as a combination of
state variables, parameters, intermediate factors and input data that
define a system of ordinary differential equations. Specified models
can be used to simulate dynamic processes using numerical
integration algorithms.
Author: Phillip D Alderman [aut, cre],
Pratishtha Poudel [aut]
Maintainer: Phillip D Alderman <phillip.alderman@okstate.edu>
Diff between csmbuilder versions 0.1.0 dated 2026-04-03 and 0.1.1 dated 2026-09-18
DESCRIPTION | 10 +- MD5 | 33 ++++---- NAMESPACE | 4 NEWS.md | 14 +++ R/csm_create_data_structure.R | 13 ++- R/csm_render_model.R | 12 +- R/csm_run_sim_group.R |only R/helper_functions.R |only R/utilities.R | 132 -------------------------------- inst/tinytest/test_csm_run_sim_group.R |only inst/tinytest/test_pheno_tt.R | 22 +++-- inst/tinytest/test_pheno_vrn.R | 21 +++-- inst/tinytest/test_simple_wheat.R | 38 ++++++--- inst/tinytest/test_soil_water_balance.R | 66 +++++++++------- man/csm_arr_fr_active.Rd |only man/csm_create_data_structure.Rd | 11 ++ man/csm_get_at_t.Rd | 2 man/csm_hill_down_reg.Rd |only man/csm_hill_up_reg.Rd |only man/csm_mod_arr.Rd | 2 man/csm_run_sim_group.Rd |only 21 files changed, 163 insertions(+), 217 deletions(-)
Title: Tools for the OeNB Data Web Service
Description: Tools to access data from the data web service of the Oesterreichische Nationalbank (OeNB), <https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html>.
Author: Franz X. Mohr [aut, cre]
Maintainer: Franz X. Mohr <franz.x.mohr@outlook.com>
Diff between oenb versions 0.0.2 dated 2021-03-22 and 0.1.0 dated 2026-09-18
DESCRIPTION | 22 +-- MD5 | 62 +++++++-- NEWS.md | 51 ++++++++ R/oenb_attributes.R | 116 ++++++++++-------- R/oenb_data.R | 75 +++++++---- R/oenb_dataset.R | 92 ++++++++------ R/oenb_frequency.R | 88 ++++++++------ R/oenb_metadata.R | 95 +++++++++------ R/oenb_toc.R | 63 +++++----- R/utils.R |only README.md | 308 +++++++++++++++++++++++++------------------------ build/vignette.rds |binary inst/CITATION |only inst/doc/oenb.R | 56 ++++---- inst/doc/oenb.html | 216 ++++++++++++++++++++-------------- man/oenb_attributes.Rd | 63 +++++----- man/oenb_data.Rd | 121 +++++++++---------- man/oenb_dataset.Rd | 57 ++++----- man/oenb_frequency.Rd | 63 +++++----- man/oenb_metadata.Rd | 63 +++++----- man/oenb_toc.Rd | 51 ++++---- tests |only 22 files changed, 947 insertions(+), 715 deletions(-)
Title: Download Weather Data from Japan Meteorological Agency Website
Description: Provides features that allow users to download
weather data published by the Japan Meteorological Agency (JMA) website
(<https://www.jma.go.jp/jma/index.html>). The data includes information
dating back to 1976 and aligns with the categories available on the website.
Additionally, users can process the best track data of typhoons and easily
handle earthquake record files.
Author: Shinya Uryu [aut, cph, cre]
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between jmastats versions 0.3.0 dated 2025-01-27 and 0.3.1 dated 2026-09-18
DESCRIPTION | 11 MD5 | 63 - NEWS.md | 12 R/appdir.R | 32 R/data.R | 12 R/ggplot2_scales.R | 98 +- R/jma_collect.R | 1241 ++++++++++++++++++---------------- R/kishou_feed.R | 47 - R/nearest_station.R | 164 ++-- R/parse_unit.R | 22 R/pivot_tide_level.R | 44 - R/read_eqdb.R | 127 ++- R/read_jma_weather.R | 56 - R/read_tide_level.R | 268 +++---- R/track.R | 143 ++- R/utils.R | 138 ++- README.md | 8 data/earthquake_station.rda |binary data/stations.rda |binary data/tide_station.rda |binary inst/CITATION |only man/earthquake_station.Rd | 4 man/ggplot2-scales.Rd | 4 man/jmastats-package.Rd | 5 man/nearest_station.Rd | 2 man/stations.Rd | 2 man/tide_station.Rd | 6 man/track.Rd | 2 tests/testthat/test-data.R | 10 tests/testthat/test-internals.R | 48 - tests/testthat/test-nearest_station.R | 51 - tests/testthat/test-palette.R | 4 tests/testthat/test-station.R | 18 33 files changed, 1527 insertions(+), 1115 deletions(-)
Title: Faster K-Medoids Clustering Algorithms: FastPAM, FastCLARA,
FastCLARANS
Description: R wrappers of C++ implementation of Faster K-Medoids clustering algorithms (FastPAM, FastCLARA and FastCLARANS) proposed in Erich Schubert, Peter J. Rousseeuw 2019 <doi:10.1007/978-3-030-32047-8_16>.
Author: Xun Li [aut, cre]
Maintainer: Xun Li <lixun910@gmail.com>
Diff between fastkmedoids versions 1.6 dated 2026-03-26 and 1.7 dated 2026-09-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/pam.cpp | 1 + src/pam.h | 1 + 4 files changed, 9 insertions(+), 7 deletions(-)
Title: Conditional Inference Trees with Stacked Multiple Imputation
Description: Implements the stacked-imputation workflow for conditional
inference trees ('ctree') described in Sherlock et al. (2026)
<doi:10.1080/00273171.2026.2661244>. When data contain missing values,
multiply imputed datasets (e.g., from 'mice') are stacked vertically
and a single 'ctree' is fit on the combined data. To correct for the
artificially inflated sample size introduced by stacking, every
node-level test statistic is divided by the number of imputations M,
the node-level p-values are recomputed from the chi-squared reference
distribution 'ctree' uses (including its multiplicity adjustment across
candidate splitting variables), and the tree is compressed bottom-up
(the Stack/M correction). Degrees of freedom are derived for each node
and each candidate variable, so univariate, bivariate and
higher-dimensional outcomes are all handled, as are unordered factor
predictors, whose degrees of freedom depend on how many levels remain
in a node. The result is a single interpretable tree [...truncated...]
Author: Phillip Sherlock [aut, cre]
Maintainer: Phillip Sherlock <phillip.sherlock@ufl.edu>
Diff between ctreeMI versions 1.0.1 dated 2026-08-26 and 1.1.0 dated 2026-09-18
DESCRIPTION | 6 - MD5 | 43 +++++---- NAMESPACE | 7 + NEWS.md | 91 ++++++++++++++++++++ R/confirm.R |only R/ctreeMI-package.R | 49 +++++++--- R/ctree_stacked.R | 29 +++--- R/node_table.R | 2 man/check_stackM_extraction.Rd | 4 man/confirm_ctreeMI.Rd |only man/ctreeMI-package.Rd | 78 +++++++++++------ man/ctree_stacked.Rd | 184 +++++++++++++++++++++-------------------- man/discover_confirm.Rd |only man/node_table.Rd | 24 ++--- man/print.ctreeMI.Rd | 8 - man/print.ctreeMI_nodes.Rd | 6 - man/print.ctreeMI_report.Rd | 4 man/prune_stackM.Rd | 57 ++++++------ man/prune_unconfirmed.Rd |only man/report_confirm.Rd |only man/report_ctreeMI.Rd | 8 - man/rescale_statistic.Rd | 34 +++---- man/split_holdout.Rd |only man/stack_imputations.Rd | 20 ++-- man/summary.ctreeMI.Rd | 14 +-- tests/testthat/test-confirm.R |only 26 files changed, 416 insertions(+), 252 deletions(-)
Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is
the core database application for biobanks. Participant data, once
collected from any data source, must be integrated and stored in a central
data repository under a uniform model. 'Opal' is such a central repository.
It can import, process, validate, query, analyze, report, and export data.
'Opal' is typically used in a research center to analyze the data acquired at
assessment centres. Its ultimate purpose is to achieve seamless
data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal'
web services and to perform operations on the R server side. 'DataSHIELD'
administration tools are also provided.
Author: Yannick Marcon [aut, cre] ,
Amadou Gaye [ctb] ,
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between opalr versions 3.6.1 dated 2026-05-27 and 3.7.0 dated 2026-09-18
DESCRIPTION | 8 ++++---- MD5 | 32 +++++++++++++++++++++----------- NAMESPACE | 8 ++++++++ R/datashield.admin.R | 8 +++++++- R/datashield.quota.R |only R/opal.project.R | 38 ++++++++++++++++++++++++++++---------- R/opal.quota.R |only build/vignette.rds |binary inst/doc/datashield-admin.html | 4 ++-- inst/doc/opal-files.html | 4 ++-- inst/doc/opal-projects.html | 4 ++-- inst/doc/opal-rsession.html | 4 ++-- man/dsadmin.log.Rd | 8 +++++++- man/dsadmin.quota.Rd |only man/dsadmin.quota_delete.Rd |only man/dsadmin.quota_enable.Rd |only man/dsadmin.quota_exists.Rd |only man/dsadmin.quota_save.Rd |only man/dsadmin.quota_usage.Rd |only man/dsadmin.quotas.Rd |only man/opal.project_create.Rd | 11 ++++++++--- man/opal.quotas.Rd |only 22 files changed, 91 insertions(+), 38 deletions(-)
Title: NFL Logo Plots in 'ggplot2' and 'gt'
Description: A set of functions to visualize National Football League
analysis in 'ggplot2' plots and 'gt' tables.
Author: Sebastian Carl [aut, cre]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Diff between nflplotR versions 1.6.0 dated 2025-11-14 and 1.7.0 dated 2026-09-18
DESCRIPTION | 8 ++--- MD5 | 34 ++++++++++++------------ NAMESPACE | 12 +++++--- NEWS.md | 5 +++ R/nfl_team_factors.R | 4 ++ R/sysdata.rda |binary man/geom_lines.Rd | 6 ++-- man/nflplotR-package.Rd | 16 ++++------- man/nflverse_sitrep.Rd | 2 - man/reexports.Rd | 2 - tests/testthat/_snaps/geom_nfl_logos/p1.svg | 20 +++++++------- tests/testthat/_snaps/geom_nfl_logos/p2.svg | 22 +++++++-------- tests/testthat/_snaps/geom_nfl_logos/p3.svg | 20 +++++++------- tests/testthat/_snaps/geom_nfl_wordmarks/p1.svg | 2 - tests/testthat/_snaps/geom_nfl_wordmarks/p2.svg | 2 - tests/testthat/_snaps/scale_nfl/p1.svg | 2 - tests/testthat/_snaps/theme-elements/p1.svg | 4 +- tests/testthat/_snaps/theme-elements/p2.svg | 4 +- 18 files changed, 87 insertions(+), 78 deletions(-)
Title: Access 'Hugging Face' Models and Datasets
Description: Access models and datasets hosted on the 'Hugging Face' Hub
through its Inference Application Programming Interface (API). Run text
classification, embeddings, chat, translation, image, audio, and other
tasks from tidy 'R' workflows without installing 'Python' by default.
Results are returned as data frames or simple 'R' objects so they can be
composed with 'dplyr', 'tidyr', and related tooling. Helpers also support
Hub search, file download, provider discovery, and guarded uploads for
authenticated workflows. Optional local embeddings and text classification
use 'Python' through 'reticulate'.
Author: Alex Farach [aut, cre, cph],
Sam Terfa [aut, cph],
Jack Penzer [aut, cph]
Maintainer: Alex Farach <alexfarach@gmail.com>
Diff between huggingfaceR versions 2.2.0 dated 2026-08-29 and 2.3.0 dated 2026-09-18
DESCRIPTION | 16 LICENSE | 4 MD5 | 384 - NAMESPACE | 220 NEWS.md | 460 + R/auth.R | 374 - R/batch.R | 450 - R/chat.R | 1146 ++-- R/classify-batch.R | 812 +-- R/classify.R | 348 - R/datasets_api.R | 882 ++- R/defaults.R | 140 R/embeddings-batch.R | 524 +- R/embeddings.R | 438 - R/extract.R | 572 +- R/ez.R | 4308 +++++++++--------- R/generate.R | 354 - R/globals.R | 8 R/hub.R | 2220 ++++----- R/huggingface_hub.R | 202 R/inference.R | 776 +-- R/local-python.R |only R/local-validation.R |only R/local.R |only R/models_with_downloads.R | 20 R/multimodal.R | 1086 ++-- R/providers.R | 439 + R/request.R | 677 +- R/sentence-transformers.R | 138 R/text-tasks.R | 886 +-- R/tidymodels.R | 400 - R/tidytext.R | 448 - R/transformers.R | 340 - R/utils-pipe.R | 32 R/utils.R | 276 - R/zzz.R | 602 +- README.md | 887 +-- man/batch_vector.Rd | 44 man/chat.Rd | 54 man/figures/logo.svg | 78 man/hf_api_request.Rd | 80 man/hf_build_request.Rd | 76 man/hf_caption_image.Rd | 98 man/hf_chat.Rd | 174 man/hf_check_inference.Rd | 82 man/hf_classify.Rd | 104 man/hf_classify_batch.Rd | 110 man/hf_classify_chunks.Rd | 118 man/hf_classify_image.Rd | 98 man/hf_classify_local.Rd |only man/hf_classify_zero_shot.Rd | 112 man/hf_classify_zero_shot_batch.Rd | 116 man/hf_cluster_texts.Rd | 80 man/hf_conversation.Rd | 78 man/hf_create_repo.Rd | 80 man/hf_dataset_info.Rd | 48 man/hf_default_model.Rd | 80 man/hf_delete_repo.Rd | 58 man/hf_describe_image.Rd | 94 man/hf_detect_config.Rd | 44 man/hf_detect_objects.Rd | 100 man/hf_download_model.Rd |only man/hf_embed.Rd | 92 man/hf_embed_batch.Rd | 110 man/hf_embed_chunks.Rd | 124 man/hf_embed_local.Rd |only man/hf_embed_text.Rd | 104 man/hf_embed_umap.Rd | 102 man/hf_extract.Rd | 126 man/hf_extract_topics.Rd | 66 man/hf_ez_conversational.Rd | 74 man/hf_ez_conversational_api_inference.Rd | 134 man/hf_ez_conversational_local_inference.Rd | 104 man/hf_ez_fill_mask.Rd | 68 man/hf_ez_fill_mask_api_inference.Rd | 86 man/hf_ez_fill_mask_local_inference.Rd | 48 man/hf_ez_question_answering.Rd | 72 man/hf_ez_question_answering_api_inference.Rd | 92 man/hf_ez_question_answering_local_inference.Rd | 52 man/hf_ez_sentence_similarity.Rd | 100 man/hf_ez_sentence_similarity_api_inference.Rd | 92 man/hf_ez_sentence_similarity_local_inference.Rd | 62 man/hf_ez_summarization.Rd | 74 man/hf_ez_summarization_api_inference.Rd | 128 man/hf_ez_summarization_local_inference.Rd | 98 man/hf_ez_table_question_answering.Rd | 86 man/hf_ez_table_question_answering_api_inference.Rd | 92 man/hf_ez_table_question_answering_local_inference.Rd | 52 man/hf_ez_text2text_generation.Rd | 66 man/hf_ez_text2text_generation_api_inference.Rd | 86 man/hf_ez_text2text_generation_local_inference.Rd | 48 man/hf_ez_text_classification.Rd | 72 man/hf_ez_text_classification_api_inference.Rd | 86 man/hf_ez_text_classification_local_inference.Rd | 48 man/hf_ez_text_generation.Rd | 66 man/hf_ez_text_generation_api_inference.Rd | 140 man/hf_ez_text_generation_local_inference.Rd | 110 man/hf_ez_token_classification.Rd | 88 man/hf_ez_token_classification_api_inference.Rd | 102 man/hf_ez_token_classification_local_inference.Rd | 72 man/hf_ez_translation.Rd | 62 man/hf_ez_translation_api_inference.Rd | 86 man/hf_ez_translation_local_inference.Rd | 48 man/hf_ez_zero_shot_classification.Rd | 80 man/hf_ez_zero_shot_classification_api_inference.Rd | 98 man/hf_ez_zero_shot_classification_local_inference.Rd | 68 man/hf_fill_mask.Rd | 104 man/hf_fill_mask_payload.Rd | 46 man/hf_generate.Rd | 102 man/hf_get_existing_chunks.Rd | 40 man/hf_get_token.Rd | 40 man/hf_hub_download.Rd | 86 man/hf_inference.Rd | 100 man/hf_list_authors.Rd | 50 man/hf_list_datasets.Rd | 50 man/hf_list_languages.Rd | 50 man/hf_list_libraries.Rd | 50 man/hf_list_licenses.Rd | 50 man/hf_list_models.Rd | 50 man/hf_list_providers.Rd | 71 man/hf_list_repo_files.Rd | 74 man/hf_list_tasks.Rd | 52 man/hf_load_AutoModel_for_task.Rd | 74 man/hf_load_dataset.Rd | 106 man/hf_load_local_model.Rd |only man/hf_load_model.Rd | 48 man/hf_load_pipeline.Rd | 66 man/hf_load_sentence_model.Rd | 90 man/hf_load_tokenizer.Rd | 56 man/hf_local_setup.Rd |only man/hf_model_info.Rd | 50 man/hf_nearest_neighbors.Rd | 82 man/hf_ner.Rd | 112 man/hf_parse_response.Rd | 40 man/hf_perform_batch.Rd | 56 man/hf_push_dataset.Rd | 108 man/hf_python_depends.Rd | 52 man/hf_question_answer.Rd | 112 man/hf_question_answering_payload.Rd | 56 man/hf_read_chunks.Rd | 50 man/hf_resolve_dataset.Rd | 40 man/hf_rows_to_tibble.Rd |only man/hf_run_tools.Rd | 72 man/hf_search_datasets.Rd | 88 man/hf_search_models.Rd | 118 man/hf_search_papers.Rd | 52 man/hf_search_spaces.Rd | 78 man/hf_sentence_encode.Rd | 82 man/hf_sentence_similarity_payload.Rd | 56 man/hf_set_device.Rd | 44 man/hf_set_token.Rd | 74 man/hf_similarity.Rd | 58 man/hf_summarization_payload.Rd | 94 man/hf_summarize.Rd | 114 man/hf_table_question_answer.Rd | 106 man/hf_table_question_answering_payload.Rd | 56 man/hf_text2text_generation_payload.Rd | 46 man/hf_text_classification_payload.Rd | 46 man/hf_text_generation_payload.Rd | 104 man/hf_text_to_image.Rd | 119 man/hf_text_to_speech.Rd | 109 man/hf_token_classification_payload.Rd | 60 man/hf_tool.Rd | 72 man/hf_transcribe.Rd | 102 man/hf_translate.Rd | 152 man/hf_translation_payload.Rd | 46 man/hf_upload_file.Rd | 100 man/hf_vectorize.Rd | 48 man/hf_whoami.Rd | 52 man/hf_write_chunk.Rd | 48 man/hf_zero_shot_classification_payload.Rd | 68 man/models_with_downloads.Rd | 44 man/null_coalesce.Rd | 36 man/pipe.Rd | 46 man/step_hf_embed.Rd | 138 tests/testthat.R | 24 tests/testthat/_snaps |only tests/testthat/helper-local.R |only tests/testthat/helper.R | 36 tests/testthat/test-auth.R | 244 - tests/testthat/test-batch.R | 282 - tests/testthat/test-chat.R | 310 - tests/testthat/test-classify-batch.R | 178 tests/testthat/test-classify.R | 138 tests/testthat/test-dataset-rows.R |only tests/testthat/test-datasets.R | 127 tests/testthat/test-defaults.R | 94 tests/testthat/test-embeddings-batch.R | 150 tests/testthat/test-embeddings.R | 206 tests/testthat/test-extract.R | 226 tests/testthat/test-hub.R | 324 - tests/testthat/test-huggingface_hub.R | 56 tests/testthat/test-local-compatibility.R |only tests/testthat/test-local-loading.R |only tests/testthat/test-local-snapshot.R |only tests/testthat/test-local.R |only tests/testthat/test-multimodal.R | 242 - tests/testthat/test-providers.R | 356 - tests/testthat/test-request.R | 276 - tests/testthat/test-text-tasks.R | 392 - tests/testthat/test-transformers.R | 204 201 files changed, 17779 insertions(+), 17366 deletions(-)
Title: Multivariate VAM Fitting
Description: Fits a multivariate value-added model (VAM), see Broatch, Green, and Karl (2018) <doi:10.32614/RJ-2018-033> and Broatch and Lohr (2012) <doi:10.3102/1076998610396900>, with normally distributed test scores and a binary outcome indicator. A pseudo-likelihood approach, Wolfinger (1993) <doi:10.1080/00949659308811554>, is used for the estimation of this joint generalized linear mixed model. The inner loop of the pseudo-likelihood routine (estimation of a linear mixed model) occurs in the framework of the EM algorithm presented by Karl, Yang, and Lohr (2013) <DOI:10.1016/j.csda.2012.10.004>. This material is based upon work supported by the National Science Foundation under grants DRL-1336027 and DRL-1336265.
Author: Andrew Karl [cre, aut] ,
Jennifer Broatch [aut],
Jennifer Green [aut]
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between RealVAMS versions 0.4-6 dated 2024-04-05 and 0.5.0 dated 2026-09-18
DESCRIPTION | 14 - MD5 | 58 ++-- NAMESPACE | 55 ++-- R/REML_Rm.R | 63 ++++ R/R_mstep2.R | 59 ++++ R/RealVAMS-package.R |only R/RealVAMS.R | 343 +++++++++++++++++++++----- R/example.outcome.data.R |only R/example.score.data.R |only R/plot.RealVAMS.R | 255 ++++++++----------- R/print.RealVAMS.R | 43 +-- R/print.summary.RealVAMS.R | 133 +++++----- R/summary.RealVAMS.R | 42 ++- R/validate-inputs.R |only R/vp_cp.R | 572 ++++++++++++++++++++++---------------------- inst/NEWS | 34 ++ man/REML_Rm.Rd | 150 ++++++----- man/R_mstep2.Rd | 136 +++++----- man/RealVAMS-package.Rd | 92 +++---- man/RealVAMS.Rd | 461 ++++++++++++++++++++--------------- man/example.outcome.data.Rd | 146 +++++------ man/example.score.data.Rd | 152 ++++++----- man/plot.Rd | 103 ++++--- man/print.Rd | 49 ++- man/summary.Rd | 77 +++-- man/vp_cp.Rd | 48 +-- src/REML_Rm.cpp | 10 src/R_mstep.cpp | 10 src/init.c | 4 tests |only 30 files changed, 1808 insertions(+), 1301 deletions(-)
Title: Multivariate Generalized Linear Mixed Models for Ranking Sports
Teams
Description: Maximum likelihood estimates are obtained via an EM algorithm with either a first-order or a fully exponential Laplace approximation as documented by Broatch and Karl (2018) <doi:10.48550/arXiv.1710.05284>,
Karl, Yang, and Lohr (2014) <doi:10.1016/j.csda.2013.11.019>, and by
Karl (2012) <doi:10.1515/1559-0410.1471>. Karl and Zimmerman <doi:10.1016/j.jspi.2020.06.004> use this package to illustrate how the home field effect estimator from a mixed model can be biased under nonrandom scheduling.
Author: Andrew T. Karl [cre, aut] ,
Jennifer Broatch [aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between mvglmmRank versions 1.2-5 dated 2026-06-09 and 1.2-6 dated 2026-09-18
DESCRIPTION | 12 MD5 | 82 +++--- NAMESPACE | 11 NEWS | 72 +++-- NEWS.md | 136 ++++++---- R/NB_cre.R | 249 +++++++------------ R/NB_mov.r | 276 ++++++++------------- R/N_mov.r | 483 -------------------------------------- R/PB_cre.R | 379 ++++++++++-------------------- R/binary_cre.R | 239 +++++++----------- R/f2008-data.R |only R/f2009-data.R |only R/f2010-data.R |only R/f2011-data.R |only R/f2012-data.R |only R/game.pred.R | 236 +++++++----------- R/gaussian-helpers.R |only R/mvglmmRank-package.R | 86 +++--- R/mvglmmRank.R | 423 +++++++++++++++++++-------------- R/nba2013-data.R |only R/ncaab2012-data.R |only R/nfl2012-data.R |only R/normal_cre.R | 592 ----------------------------------------------- R/numerical-helpers.R |only R/poisson_cre.R | 268 +++++++-------------- inst/CITATION | 54 ++-- man/NB_cre.Rd | 57 ++-- man/NB_mov.Rd | 57 ++-- man/N_mov.Rd | 52 +--- man/PB_cre.Rd | 64 ++--- man/binary_cre.Rd | 57 ++-- man/f2008.Rd | 66 ++--- man/f2009.Rd | 66 ++--- man/f2010.Rd | 66 ++--- man/f2011.Rd | 66 ++--- man/f2012.Rd | 66 ++--- man/game.pred.Rd | 3 man/gaussian-helpers.Rd |only man/mvglmmRank.Rd | 48 +++ man/nba2013.Rd | 70 ++--- man/ncaab2012.Rd | 68 ++--- man/nfl2012.Rd | 66 ++--- man/normal_cre.Rd | 52 +--- man/numerical-helpers.Rd |only man/poisson_cre.Rd | 64 ++--- tests/testthat |only tests/testthat.R |only 47 files changed, 1661 insertions(+), 2925 deletions(-)
Title: Maximum Likelihood Estimation of Multiple Membership Mixed
Models Used in Value-Added Modeling
Description: An EM algorithm, Karl et al. (2013) <doi:10.1016/j.csda.2012.10.004>,
estimates generalized, reduced generalized, variable, complete, and zero
persistence models by maximum likelihood or restricted maximum likelihood
(the default). These are multiple-membership linear mixed models with
teachers modeled as "G-side" effects and students modeled with either
"G-side" or "R-side" effects; see Mariano et al. (2010)
<doi:10.3102/1076998609346967>.
Author: Andrew Karl [cre, aut] ,
Yan Yang [aut],
Sharon Lohr [aut]
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between GPvam versions 3.2-0 dated 2024-12-12 and 3.3-0 dated 2026-09-18
GPvam-3.2-0/GPvam/man/plot.Rd |only GPvam-3.2-0/GPvam/man/print.Rd |only GPvam-3.2-0/GPvam/man/summary.Rd |only GPvam-3.3-0/GPvam/DESCRIPTION | 22 GPvam-3.3-0/GPvam/MD5 | 79 ++- GPvam-3.3-0/GPvam/NAMESPACE | 100 ++-- GPvam-3.3-0/GPvam/NEWS | 54 ++ GPvam-3.3-0/GPvam/R/GP.csh.R | 176 +++---- GPvam-3.3-0/GPvam/R/GP.un.R | 175 +++---- GPvam-3.3-0/GPvam/R/GPvam-package.R |only GPvam-3.3-0/GPvam/R/GPvam.R | 328 +++++++++++--- GPvam-3.3-0/GPvam/R/REML_Rm.R | 16 GPvam-3.3-0/GPvam/R/R_mstep2.R | 38 + GPvam-3.3-0/GPvam/R/VP.CP.ZP.un.r | 260 +++-------- GPvam-3.3-0/GPvam/R/bias.test.custom.R | 441 ++++++++++--------- GPvam-3.3-0/GPvam/R/data.R |only GPvam-3.3-0/GPvam/R/estimation-helpers.R |only GPvam-3.3-0/GPvam/R/methods.R |only GPvam-3.3-0/GPvam/R/plot.GPvam.R | 240 ++++------ GPvam-3.3-0/GPvam/R/print.GPvam.R | 27 - GPvam-3.3-0/GPvam/R/print.summary.GPvam.R | 35 - GPvam-3.3-0/GPvam/R/rGP.un.R | 175 +++---- GPvam-3.3-0/GPvam/R/summary.GPvam.R | 47 +- GPvam-3.3-0/GPvam/build |only GPvam-3.3-0/GPvam/man/GP.csh.Rd | 51 +- GPvam-3.3-0/GPvam/man/GP.un.Rd | 50 +- GPvam-3.3-0/GPvam/man/GPvam-methods.Rd |only GPvam-3.3-0/GPvam/man/GPvam-package.Rd | 105 ++-- GPvam-3.3-0/GPvam/man/GPvam.Rd | 382 +++++++++------- GPvam-3.3-0/GPvam/man/GPvam.benchmark.Rd | 63 +- GPvam-3.3-0/GPvam/man/REML_Rm.Rd |only GPvam-3.3-0/GPvam/man/R_mstep2.Rd |only GPvam-3.3-0/GPvam/man/VP.CP.ZP.un.Rd | 52 +- GPvam-3.3-0/GPvam/man/bias.test.custom.Rd | 160 ++++-- GPvam-3.3-0/GPvam/man/dot-gpvam_estep.Rd |only GPvam-3.3-0/GPvam/man/dot-gpvam_information.Rd |only GPvam-3.3-0/GPvam/man/dot-gpvam_residual_diagonal.Rd |only GPvam-3.3-0/GPvam/man/dot-gpvam_update_residual.Rd |only GPvam-3.3-0/GPvam/man/plot.GPvam.Rd |only GPvam-3.3-0/GPvam/man/print.GPvam.Rd |only GPvam-3.3-0/GPvam/man/rGP.un.Rd | 51 +- GPvam-3.3-0/GPvam/man/summary.GPvam.Rd |only GPvam-3.3-0/GPvam/man/vam_data.Rd | 131 +++-- GPvam-3.3-0/GPvam/src/REML_Rm.cpp | 8 GPvam-3.3-0/GPvam/src/R_mstep.cpp | 8 GPvam-3.3-0/GPvam/tests |only 46 files changed, 1873 insertions(+), 1401 deletions(-)
Title: Generalized Linear Mixed Models via Fully Exponential Laplace in
EM
Description: Fit generalized linear mixed models (GLMMs) with normal random
effects using first-order Laplace, fully exponential Laplace (FEL) with
mean-only corrections, and FEL with mean and variance-diagonal corrections in
the E-step of an expectation-maximization (EM) algorithm. The current
development version provides a matrix-based interface (y, X, Z) and
supports binary logit and probit, and Poisson log-link models. An EM
framework is used to update fixed effects, random effects, and a single
variance component tau^2 for G = tau^2 I, with staged approximations
(Laplace -> FEL mean-only -> FEL full) for efficiency and stability. A
pseudo-likelihood engine glmmFEL_pl() implements the working-response /
working-weights linearization approach of Wolfinger and O'Connell (1993)
<doi:10.1080/00949659308811554>, and is adapted from the implementation
used in the 'RealVAMS' package (Broatch, Green, and Karl (2018))
<doi:10.32614/RJ-2018-033>. The FEL implementation follows Karl, Yan [...truncated...]
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between glmmFEL versions 1.0.5 dated 2026-01-09 and 1.0.6 dated 2026-09-18
DESCRIPTION | 17 MD5 | 46 - NEWS.md |only R/fe_derivatives.R | 475 +++++------ R/fe_trace.R | 14 R/glmmFEL-benchmarks.R |only R/glmmFEL-helpers.R | 585 +++++++------- R/glmmFEL-methods.R | 431 +++++----- R/glmmFEL-package.R | 107 +- R/glmmFEL.R | 1193 ++++++++++++------------------ R/glmmFEL_PL.R | 517 ++++++------- R/numerical_helpers.R |only build/partial.rdb |binary inst/benchmarks |only man/glmmFEL-benchmarks.Rd |only man/glmmFEL-package.Rd | 63 - man/glmmFEL.Rd | 88 +- man/glmmFEL_pl.Rd | 2 man/logLik.glmmFELMod.Rd | 2 tests/testthat/fixtures |only tests/testthat/test-glmmFEL-matrix-only.R | 974 ++++++++++++------------ tests/testthat/test-numerical-audit.R |only 22 files changed, 2125 insertions(+), 2389 deletions(-)
Title: Bayesian Inference of Binary, Count and Continuous Data in
Toxicology
Description: Advanced methods for a valuable quantitative environmental
risk assessment using Bayesian inference of several type of
toxicological data. 'binary' (e.g., survival, mobility), 'count'
(e.g., reproduction) and 'continuous' (e.g., growth as length,
weight). Estimation procedures can be used without a deep knowledge
of their underlying probabilistic model or inference methods. Rather,
they were designed to behave as well as possible without requiring a
user to provide values for some obscure parameters. That said, models
can also be used as a first step to tailor new models for more
specific situations.
Author: Virgile Baudrot [aut, cre],
Sandrine Charles [aut],
Marie Laure Delignette-Muller [aut],
Nils Kehrein [ctb],
Guillaume Kon-Kam-King [ctb],
Christelle Lopes [ctb],
Philippe Veber [aut]
Maintainer: Virgile Baudrot <virgile.baudrot@qonfluens.com>
Diff between morseDR versions 0.1.2 dated 2025-05-29 and 0.1.3 dated 2026-09-18
DESCRIPTION | 10 ++-- MD5 | 13 +++-- NEWS | 8 +++ R/priorPosterior.R | 1 README.md | 49 ++++++++++++++++++++- inst/doc/models.html | 35 +++++++-------- inst/doc/tutorial.html | 104 ++++++++++++++++++++++------------------------ tests/testthat/Rplots.pdf |only 8 files changed, 137 insertions(+), 83 deletions(-)
Title: Bias Diagnostic for Linear Mixed Models
Description: Provides a function to perform bias diagnostics on linear mixed models fitted with lmer() from the 'lme4' package. Implements permutation tests for assessing the bias of fixed effects, as described in Karl and Zimmerman (2021) <doi:10.1016/j.jspi.2020.06.004>. Karl and Zimmerman (2020) <doi:10.17632/tmynggddfm.1> provide R code for implementing the test using 'mvglmmRank' output. Development of this package was assisted by 'GPT o1-preview' for code structure and documentation.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between mixedbiastest versions 1.0.2 dated 2025-11-30 and 1.0.3 dated 2026-09-18
mixedbiastest-1.0.2/mixedbiastest/tests/testthat/Rplots.pdf |only mixedbiastest-1.0.3/mixedbiastest/DESCRIPTION | 12 mixedbiastest-1.0.3/mixedbiastest/MD5 | 23 mixedbiastest-1.0.3/mixedbiastest/NEWS.md |only mixedbiastest-1.0.3/mixedbiastest/R/list_fixed.R | 5 mixedbiastest-1.0.3/mixedbiastest/R/mixedbiastest.R | 690 ++++------ mixedbiastest-1.0.3/mixedbiastest/build/partial.rdb |binary mixedbiastest-1.0.3/mixedbiastest/man/list_fixed_effects.Rd | 1 mixedbiastest-1.0.3/mixedbiastest/man/mixedbiastest-package.Rd | 5 mixedbiastest-1.0.3/mixedbiastest/man/mixedbiastest.Rd | 20 mixedbiastest-1.0.3/mixedbiastest/tests/testthat.R | 10 mixedbiastest-1.0.3/mixedbiastest/tests/testthat/helper-reference.R |only mixedbiastest-1.0.3/mixedbiastest/tests/testthat/test-lme4-updates.R |only mixedbiastest-1.0.3/mixedbiastest/tests/testthat/test-mixedbiastest.R | 12 mixedbiastest-1.0.3/mixedbiastest/tests/testthat/test-supported-inputs.R |only 15 files changed, 356 insertions(+), 422 deletions(-)
Title: Data & Functions for Working with US ZIP Codes
Description: Make working with ZIP codes in R painless with an integrated dataset of U.S. ZIP codes and functions for working with them.
Search ZIP codes by multiple geographies, including state, county, city & across time zones. Also included are functions for relating
ZIP codes to Census data, geocoding & distance calculations. New
analyses can select an immutable modern data bundle through the
next-generation API, while the historical interface remains
compatible with version 0.3.5 for reproducible research.
Author: Gavin Rozzi [aut, cre]
Maintainer: Gavin Rozzi <gr@gavinrozzi.com>
Diff between zipcodeR versions 0.4.0 dated 2026-09-07 and 0.4.1 dated 2026-09-18
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 14 ++++++++++++++ inst/doc/geographic.html | 2 +- inst/doc/zipcodeR.html | 2 +- tests/testthat/test-04-data-bundles.R | 8 +++++++- 6 files changed, 31 insertions(+), 11 deletions(-)
Title: Solar Potential Calculation for Point Clouds using 'VOSTOK'
Description: Calculate solar potential for LiDAR point clouds using the 'VOSTOK'
(Voxel Octree Solar Toolkit) algorithm. This R program provides an interface to
the original 'VOSTOK' C++ implementation by Bechtold and Hofle (2020), enabling
efficient ray casting and solar position algorithms to compute solar irradiance
for each point while accounting for shadowing effects. Integrates seamlessly with
the 'lidR' package for LiDAR data processing workflows. The original 'VOSTOK'
toolkit is available at <doi:10.11588/data/QNA02B>.
Author: Andrew J. Sanchez Meador [aut, cre],
Sebastian Bechtold [aut] ,
Bernhard Hofle [aut]
Maintainer: Andrew J. Sanchez Meador <andrew.sanchezmeador@nau.edu>
This is a re-admission after prior archival of version 0.2.1 dated 2026-03-25
Diff between vostokR versions 0.2.1 dated 2026-03-25 and 0.2.2 dated 2026-09-18
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 14 +++++++++----- man/vostokR-package.Rd | 1 + 4 files changed, 19 insertions(+), 14 deletions(-)
Title: Utilities to Support Lidar Applications at the Landscape,
Forest, and Tree Scale
Description: Implements algorithms for terrestrial, mobile, and airborne lidar processing, tree detection,
segmentation, and attribute estimation (Donager et al., 2021)
<doi:10.3390/rs13122297>, and a hierarchical patch delineation algorithm
'PatchMorph' (Girvetz & Greco, 2007) <doi:10.1007/s10980-007-9104-8>. Tree
detection uses rasterized point cloud metrics (relative neighborhood density and
verticality) combined with RANSAC cylinder fitting to locate tree boles and estimate
diameter at breast height. Tree segmentation applies graph-theory approaches inspired
by Tao et al. (2015) <doi:10.1016/j.isprsjprs.2015.08.007> with cylinder fitting
methods from de Conto et al. (2017) <doi:10.1016/j.compag.2017.07.019>. PatchMorph
delineates habitat patches across spatial scales using organism-specific thresholds.
Built on 'lidR' (Roussel et al., 2020) <doi:10.1016/j.rse.2020.112061>.
Author: Andrew Sanchez Meador [aut, cre, ctb] ,
Jonathon Donager [aut, ctb] ,
Blackburn Ryan [aut, ctb] ,
Cannon Jeffery [ctb] ,
Tiago de Conto [ctb, cph] ,
Keith O'Hara [ctb, cph]
Maintainer: Andrew Sanchez Meador <Andrew.SanchezMeador@nau.edu>
This is a re-admission after prior archival of version 1.0.4 dated 2026-04-01
Diff between spanner versions 1.0.4 dated 2026-04-01 and 1.0.5 dated 2026-09-18
DESCRIPTION | 15 MD5 | 34 - NAMESPACE | 44 +- NEWS.md | 6 R/Patch_Morph.R | 404 +++++++++++------------ R/PostProcess_TreeLocations.R | 492 ++++++++++++++-------------- R/Segment_Graph.R | 630 ++++++++++++++++++------------------ R/spanner-package.R | 38 +- build/stage23.rdb |binary man/colorize_las.Rd | 180 +++++----- man/compute_pcv.Rd | 72 ++-- man/compute_ssao.Rd | 90 ++--- man/download_naip_for_las.Rd | 126 +++---- man/eigen_metrics.Rd | 126 +++---- man/merge_las_colors.Rd | 124 +++---- man/segment_graph.Rd | 304 ++++++++--------- tests/testthat/test-eigen-metrics.R | 120 +++--- tests/testthat/test-segmentation.R | 224 ++++++------ 18 files changed, 1522 insertions(+), 1507 deletions(-)
Title: Fast Simulation of Bayesian Optimal Interval Designs for Phase I
Trials
Description: Design and evaluate phase I dose-finding trials that use the
Bayesian optimal interval (BOIN) design of Liu and Yuan (2015)
<doi:10.1111/rssc.12089>. Functions are provided to tabulate the decision
boundaries, to simulate trials, to estimate the dose-toxicity curve under a
monotonicity constraint and to select the maximum tolerated dose. The
simulation engine is written in C++ and draws one random variate per
patient in enrollment order, which reproduces the reference implementation
in the 'BOIN' package trial by trial for a given seed. The traditional 3+3
design is provided as a comparator, with operating characteristics obtained
in closed form rather than by simulation.
Author: Gosuke Homma [aut, cre]
Maintainer: Gosuke Homma <my.name.is.gosuke@gmail.com>
Diff between simFastBOIN versions 1.3.2 dated 2025-12-17 and 2.0.0 dated 2026-09-18
simFastBOIN-1.3.2/simFastBOIN/R/get_boin_boundary.R |only simFastBOIN-1.3.2/simFastBOIN/R/get_boin_decision.R |only simFastBOIN-1.3.2/simFastBOIN/R/get_boin_stopping_boundaries.R |only simFastBOIN-1.3.2/simFastBOIN/R/get_pts_and_tox.R |only simFastBOIN-1.3.2/simFastBOIN/R/isotonic_regression.R |only simFastBOIN-1.3.2/simFastBOIN/R/print.boin_multi_summary.R |only simFastBOIN-1.3.2/simFastBOIN/R/print.boin_summary.R |only simFastBOIN-1.3.2/simFastBOIN/R/select_mtd.R |only simFastBOIN-1.3.2/simFastBOIN/man/get_boin_boundary.Rd |only simFastBOIN-1.3.2/simFastBOIN/man/get_boin_decision.Rd |only simFastBOIN-1.3.2/simFastBOIN/man/get_boin_stopping_boundaries.Rd |only simFastBOIN-1.3.2/simFastBOIN/man/get_pts_and_tox.Rd |only simFastBOIN-1.3.2/simFastBOIN/man/isotonic_regression.Rd |only simFastBOIN-1.3.2/simFastBOIN/man/print.boin_multi_summary.Rd |only simFastBOIN-1.3.2/simFastBOIN/man/print.boin_summary.Rd |only simFastBOIN-1.3.2/simFastBOIN/man/select_mtd.Rd |only simFastBOIN-1.3.2/simFastBOIN/tests/testthat/test-get_boin_boundary.R |only simFastBOIN-1.3.2/simFastBOIN/tests/testthat/test-get_boin_decision.R |only simFastBOIN-1.3.2/simFastBOIN/tests/testthat/test-get_boin_stopping_boundaries.R |only simFastBOIN-1.3.2/simFastBOIN/tests/testthat/test-get_pts_and_tox.R |only simFastBOIN-1.3.2/simFastBOIN/tests/testthat/test-isotonic_regression.R |only simFastBOIN-1.3.2/simFastBOIN/tests/testthat/test-select_mtd.R |only simFastBOIN-2.0.0/simFastBOIN/DESCRIPTION | 45 simFastBOIN-2.0.0/simFastBOIN/LICENSE | 2 simFastBOIN-2.0.0/simFastBOIN/MD5 | 124 + simFastBOIN-2.0.0/simFastBOIN/NAMESPACE | 32 simFastBOIN-2.0.0/simFastBOIN/NEWS.md | 298 ++++ simFastBOIN-2.0.0/simFastBOIN/R/RcppExports.R |only simFastBOIN-2.0.0/simFastBOIN/R/as.data.frame.boin_boundary.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_boundary.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_decision_table.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_isotonic.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_lambda.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_p_tox.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_select_mtd.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_simulate.R |only simFastBOIN-2.0.0/simFastBOIN/R/boin_stopping_table.R |only simFastBOIN-2.0.0/simFastBOIN/R/deprecated.R |only simFastBOIN-2.0.0/simFastBOIN/R/oc_3p3.R |only simFastBOIN-2.0.0/simFastBOIN/R/oc_multi_table.R |only simFastBOIN-2.0.0/simFastBOIN/R/plot.boin_decision_table.R |only simFastBOIN-2.0.0/simFastBOIN/R/print.boin_boundary.R |only simFastBOIN-2.0.0/simFastBOIN/R/print.boin_decision_table.R |only simFastBOIN-2.0.0/simFastBOIN/R/print.boin_oc.R |only simFastBOIN-2.0.0/simFastBOIN/R/print.boin_oc_multi.R |only simFastBOIN-2.0.0/simFastBOIN/R/print.boin_trials.R |only simFastBOIN-2.0.0/simFastBOIN/R/print.oc_3p3.R |only simFastBOIN-2.0.0/simFastBOIN/R/simFastBOIN-package.R |only simFastBOIN-2.0.0/simFastBOIN/R/sim_3p3.R |only simFastBOIN-2.0.0/simFastBOIN/R/sim_boin.R | 448 +++--- simFastBOIN-2.0.0/simFastBOIN/R/sim_boin_multi.R | 326 +--- simFastBOIN-2.0.0/simFastBOIN/R/validate.R |only simFastBOIN-2.0.0/simFastBOIN/README.md | 450 +----- simFastBOIN-2.0.0/simFastBOIN/build/vignette.rds |binary simFastBOIN-2.0.0/simFastBOIN/inst/WORDLIST |only simFastBOIN-2.0.0/simFastBOIN/inst/doc/simFastBOIN-introduction.R | 256 +-- simFastBOIN-2.0.0/simFastBOIN/inst/doc/simFastBOIN-introduction.Rmd | 420 ++--- simFastBOIN-2.0.0/simFastBOIN/inst/doc/simFastBOIN-introduction.html | 732 ++++------ simFastBOIN-2.0.0/simFastBOIN/inst/validation |only simFastBOIN-2.0.0/simFastBOIN/man/as.data.frame.boin_boundary.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_boundary.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_decision_table.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_isotonic.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_lambda.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_p_tox.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_select_mtd.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_simulate.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/boin_stopping_table.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/oc_3p3.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/plot.boin_decision_table.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/print.boin_boundary.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/print.boin_decision_table.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/print.boin_oc.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/print.boin_oc_multi.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/print.boin_trials.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/print.oc_3p3.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/simFastBOIN-deprecated.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/simFastBOIN-package.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/sim_3p3.Rd |only simFastBOIN-2.0.0/simFastBOIN/man/sim_boin.Rd | 305 ++-- simFastBOIN-2.0.0/simFastBOIN/man/sim_boin_multi.Rd | 243 +-- simFastBOIN-2.0.0/simFastBOIN/src |only simFastBOIN-2.0.0/simFastBOIN/tests/spelling.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat.R | 8 simFastBOIN-2.0.0/simFastBOIN/tests/testthat/helper-reference.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-3p3.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_boundary.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_decision_table.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_isotonic.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_lambda.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_p_tox.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_reference.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_reference_oc.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_select_mtd.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_simulate.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-boin_stopping_table.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-deprecated.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-mtd_max_estimate.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-overdose.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-plot_methods.R |only simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-print_methods.R | 216 +- simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-sim_boin.R | 340 +--- simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-sim_boin_multi.R | 367 +---- simFastBOIN-2.0.0/simFastBOIN/tests/testthat/test-stay_on_1_of_3.R |only simFastBOIN-2.0.0/simFastBOIN/vignettes/simFastBOIN-introduction.Rmd | 420 ++--- 105 files changed, 2295 insertions(+), 2737 deletions(-)
Title: Acesso aos Dados do 'SIDRA' do IBGE
Description: Functions for accessing and manipulating data from Brazilian
Institute of Geography and Statistics (IBGE)'s API 'SIDRA' (acronym for IBGE
System of Automatic Retrieval) from the new endpoints
at <https://servicodados.ibge.gov.br/api/docs/agregados?versao=3>. Ferramentas para acessar
e manipular dados via API do Sistema IBGE De Recuperação Automática 'SIDRA'
do Instituto Brasileiro de Geografia e Estatística (IBGE).
Author: Rodrigo Emmanuel Santana Borges [cre, aut, cph]
Maintainer: Rodrigo Emmanuel Santana Borges <rodrigo@borges.net.br>
This is a re-admission after prior archival of version 0.1.9 dated 2025-09-06
Diff between sidra versions 0.1.9 dated 2025-09-06 and 0.2.0 dated 2026-09-18
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 8 ++++++++ R/sidra.R | 2 +- R/tab_agr.R | 2 +- R/tab_meta.R | 2 +- R/tab_niveis.R | 2 +- build/vignette.rds |binary inst/doc/sidra.html | 4 ++-- tests/testthat/test-sidra.R | 22 +++++++--------------- tests/testthat/test-tab_agr.R | 15 +++++---------- 11 files changed, 39 insertions(+), 44 deletions(-)
Title: Prepare Data and Trees for Phylogenetic Comparative Methods
Description: Reconcile species names across datasets and phylogenetic trees
for comparative biology workflows. Identifies mismatches due to formatting
differences, taxonomic synonymy, and spelling errors. Produces detailed
reports documenting how each name was resolved, which taxonomic authority
was used, and what remains unresolved. Supports exact matching, name
normalisation, synonym resolution via local taxonomic databases, and
fuzzy matching for likely typos. Detects taxonomic splits and lumps. For
methodological context, see Nakagawa et al. (2026)
<doi:10.32942/X2468Z>.
Author: Shinichi Nakagawa [aut, cre, cph] ,
Santiago Ortega [aut],
Ayumi Mizuno [aut],
Eduardo S.A. Santos [aut],
Malgorzata Lagisz [aut] ,
Bhavya Jain [aut],
Jimuel Jr Celeste [aut],
Sergio Poo Hernandez [aut]
Maintainer: Shinichi Nakagawa <itchyshin@gmail.com>
Diff between prepR4pcm versions 1.0.2 dated 2026-08-25 and 1.0.3 dated 2026-09-18
DESCRIPTION | 8 ++--- MD5 | 26 ++++++++--------- NEWS.md | 4 ++ R/reconcile_accessors.R | 8 ++--- README.md | 2 + inst/doc/bird-workflow.R | 18 +++++------ inst/doc/bird-workflow.html | 44 ++++++----------------------- inst/doc/comparing-tree-backends.html | 6 +-- inst/doc/db-assembly-workflow_mammals.html | 4 +- inst/doc/getting-started.Rmd | 5 +-- inst/doc/getting-started.html | 9 +++-- man/reconcile_mapping.Rd | 8 ++--- tests/testthat/test-authority-mocked.R | 1 vignettes/getting-started.Rmd | 5 +-- 14 files changed, 67 insertions(+), 81 deletions(-)
Title: Transparent and Assisted Linear Modeling Engine
Description: Unified estimation, diagnostics, and reporting for ordinary least
squares (OLS) regression, ANOVA/t-tests, logistic regression, panel data
(fixed/random effects with Hausman test), instrumental variables (2SLS with
weak instrument diagnostics), and difference-in-differences. Designed for
applied researchers in social sciences with integrated "Methodological Customs"
that audit assumptions and provide literature references. All methods
implemented in pure base R without external dependencies beyond stats and
graphics packages.
Author: Manuel Soto-Perez [aut, cre]
Maintainer: Manuel Soto-Perez <msoto@up.edu.mx>
Diff between OLSengine versions 1.1.1 dated 2026-07-31 and 1.2.0 dated 2026-09-18
DESCRIPTION | 6 ++--- MD5 | 18 ++++++++-------- NAMESPACE | 1 NEWS.md | 18 ++++++++++++++++ R/OLS_engine.R | 44 +++++++++++++++++++++++++++++++--------- README.md | 8 +++---- inst/doc/vignette_tutorial.R | 2 - inst/doc/vignette_tutorial.Rmd | 2 - inst/doc/vignette_tutorial.html | 16 +++++++------- vignettes/vignette_tutorial.Rmd | 2 - 10 files changed, 81 insertions(+), 36 deletions(-)
Title: Multivariate Network Meta-Analysis using Bayesian Methods
Description: Tools to conduct Bayesian multivariate network meta-analysis providing
- the single correlation coefficient model by Efthimiou et al. (2015) <doi:10.1093/biostatistics/kxu030>;
- per-outcome consistency checks using the node-splitting method (Dias et al., 2010) <doi:10.1002/sim.3767>;
- per-outcome treatment hierarchies using the surface under the cumulative ranking curve (SUCRA), the probability of best value, or median (or mean) ranks (Salanti et al., 2011) <doi:10.1016/j.jclinepi.2010.03.016>;
- across-outcomes benefit-risk assessment using the VišeKriterijumska Optimizacija I Kompromisno Rešenje (VIKOR) method (Opricovic & Tzeng, 2004) <doi:10.1016/S0377-2217(03)00020-1>;
- convergence checks using trace plots, density plots, or the R-hat statistic;
- forest plots of treatment estimates and consistency checks, scatter plots of per-outcome rankings, Hasse diagrams (Carlsen & Bruggemann, 2014) <doi:10.1002/cem.2569> to visualize the partial order [...truncated...]
Author: Theodoros Evrenoglou [aut, cre] ,
Guido Schwarzer [aut]
Maintainer: Theodoros Evrenoglou <theodoros.evrenoglou@uniklinik-freiburg.de>
Diff between mvnma versions 0.2-0 dated 2026-07-09 and 0.3-0 dated 2026-09-18
mvnma-0.2-0/mvnma/R/mvdata.R |only mvnma-0.2-0/mvnma/man/vikor.Rd |only mvnma-0.3-0/mvnma/DESCRIPTION | 15 mvnma-0.3-0/mvnma/MD5 | 67 mvnma-0.3-0/mvnma/NAMESPACE | 180 +- mvnma-0.3-0/mvnma/NEWS.md | 70 mvnma-0.3-0/mvnma/R/VIKOR.R | 387 +--- mvnma-0.3-0/mvnma/R/as.mcmc.mvnma.R | 180 +- mvnma-0.3-0/mvnma/R/forest.mvnma.R | 420 ++--- mvnma-0.3-0/mvnma/R/forest.netsplit.R |only mvnma-0.3-0/mvnma/R/hasse.R | 201 +- mvnma-0.3-0/mvnma/R/heatplot.mvrank.R | 393 ++-- mvnma-0.3-0/mvnma/R/linechart.R | 255 +-- mvnma-0.3-0/mvnma/R/mvnma-internal.R | 1780 ++++++++++------------ mvnma-0.3-0/mvnma/R/mvnma-package.R | 321 +-- mvnma-0.3-0/mvnma/R/mvnma.R | 1397 +++++++---------- mvnma-0.3-0/mvnma/R/mvnma_code.R | 1137 +++++++------- mvnma-0.3-0/mvnma/R/mvrank.R | 533 +++--- mvnma-0.3-0/mvnma/R/netsplit-internal.R |only mvnma-0.3-0/mvnma/R/netsplit.mvnma.R |only mvnma-0.3-0/mvnma/R/plot.mvrank.R | 189 +- mvnma-0.3-0/mvnma/R/spiechart-internal.R | 72 mvnma-0.3-0/mvnma/R/spiechart.R | 248 +-- mvnma-0.3-0/mvnma/R/updateversion.R |only mvnma-0.3-0/mvnma/R/vikor-internal.R | 354 ++-- mvnma-0.3-0/mvnma/inst/extdata/mvnma_examples.rda |binary mvnma-0.3-0/mvnma/man/as.mcmc.mvnma.Rd | 122 - mvnma-0.3-0/mvnma/man/forest.mvnma.Rd | 184 +- mvnma-0.3-0/mvnma/man/forest.netsplit.mvnma.Rd |only mvnma-0.3-0/mvnma/man/hasse.mvrank.Rd | 124 - mvnma-0.3-0/mvnma/man/heatplot.mvrank.Rd | 218 +- mvnma-0.3-0/mvnma/man/linechart.Rd | 156 - mvnma-0.3-0/mvnma/man/mvnma-package.Rd | 303 +-- mvnma-0.3-0/mvnma/man/mvnma.Rd | 584 +++---- mvnma-0.3-0/mvnma/man/mvrank.Rd | 166 +- mvnma-0.3-0/mvnma/man/netsplit.mvnma.Rd |only mvnma-0.3-0/mvnma/man/plot.mvrank.Rd | 134 - mvnma-0.3-0/mvnma/man/spiechart.Rd | 132 - mvnma-0.3-0/mvnma/man/vikor.mvrank.Rd |only 39 files changed, 5079 insertions(+), 5243 deletions(-)
Title: Dyadic Network Analysis
Description: Contains functions for the MCMC simulation of (multilevel) dyadic network models j2 (Zijlstra, 2017, <doi:10.1080/0022250X.2017.1387858>) and p2 (Van Duijn, Snijders & Zijlstra, 2004, <doi: 10.1046/j.0039-0402.2003.00258.x>), the multilevel p2 model (Zijlstra, Van Duijn & Snijders (2009) <doi: 10.1348/000711007X255336>), and the bidirectional (multilevel) counterpart of the the multilevel p2 model as described in Zijlstra, Van Duijn & Snijders (2009) <doi: 10.1348/000711007X255336>, the (multilevel) b2 model.
Author: Bonne J.H. Zijlstra [aut, cre]
Maintainer: Bonne J.H. Zijlstra <B.J.H.Zijlstra@uva.nl>
Diff between dyads versions 1.2.1 dated 2022-08-17 and 1.2.22.3 dated 2026-09-18
DESCRIPTION | 18 MD5 | 26 - NAMESPACE | 17 R/b2ML.R | 993 +++++++++++++++++++++------------------------ R/internalFunctionsDyads.R | 389 +++++++++++++++++ R/j2.R | 29 - R/j2ML.R |only R/p2.R | 31 - R/p2ML.R | 333 +++++++-------- build/partial.rdb |binary man/b2ML.Rd | 200 ++++----- man/j2.Rd | 156 +++---- man/j2ML.Rd |only man/p2.Rd | 154 +++--- man/p2ML.Rd | 209 ++++----- 15 files changed, 1468 insertions(+), 1087 deletions(-)
Title: Visualisation, Exploration, and Web Communication of
Archaeological Spatial Data
Description: An R 'Shiny' application for visual and statistical exploration and web communication of archaeological spatial data, either remains or sites. It offers interactive 3D and 2D visualisations (cross sections and maps of remains, timeline of the work made in a site) which can be exported in SVG and HTML formats. It performs simple spatial statistics (convex hull, regression surfaces, 2D kernel density estimation) and allows exporting data to other online applications for more complex methods. 'archeoViz' can be used offline locally or deployed on a server, either with interactive input of data or with a static data set. Example is provided at <https://analytics.huma-num.fr/archeoviz/en>.
Author: Sebastien Plutniak [aut, cre] ,
Renata Araujo [ctb] ,
Laura Coltofean [ctb] ,
Nicolas Delsol [ctb] ,
Sara Giardino [ctb] ,
Julian Laabs [ctb]
Maintainer: Sebastien Plutniak <sebastien.plutniak@posteo.net>
Diff between archeoViz versions 1.4.2 dated 2026-07-30 and 1.4.3 dated 2026-09-18
DESCRIPTION | 8 MD5 | 12 NAMESPACE | 2 NEWS.md | 4 R/app_server.R | 302 ++++++++++++++++-------- R/app_ui.R | 1 R/load_interface_terms.R | 576 ++++++++++++++++++++++++++--------------------- 7 files changed, 538 insertions(+), 367 deletions(-)
Title: Functions to Efficiently Access NFL Play by Play Data
Description: A set of functions to access National Football League
play-by-play data from <https://www.nfl.com/>.
Author: Sebastian Carl [aut],
Ben Baldwin [cre, aut],
Lee Sharpe [ctb],
Maksim Horowitz [ctb],
Ron Yurko [ctb],
Samuel Ventura [ctb],
Tan Ho [ctb],
John Edwards [ctb]
Maintainer: Ben Baldwin <bbaldwin206@gmail.com>
Diff between nflfastR versions 5.2.0 dated 2026-02-07 and 6.0.0 dated 2026-09-18
nflfastR-5.2.0/nflfastR/tests/testthat/1999 |only nflfastR-6.0.0/nflfastR/DESCRIPTION | 12 nflfastR-6.0.0/nflfastR/MD5 | 111 nflfastR-6.0.0/nflfastR/NAMESPACE | 33 nflfastR-6.0.0/nflfastR/NEWS.md | 31 nflfastR-6.0.0/nflfastR/R/aggregate_game_stats.R | 750 ---- nflfastR-6.0.0/nflfastR/R/aggregate_game_stats_def.R | 629 --- nflfastR-6.0.0/nflfastR/R/aggregate_game_stats_kicking.R | 193 - nflfastR-6.0.0/nflfastR/R/build_nflfastR_pbp.R | 47 nflfastR-6.0.0/nflfastR/R/build_playstats.R | 31 nflfastR-6.0.0/nflfastR/R/calculate_series_conversion_rates.R | 47 nflfastR-6.0.0/nflfastR/R/calculate_standings.R | 129 nflfastR-6.0.0/nflfastR/R/calculate_stats.R | 417 +- nflfastR-6.0.0/nflfastR/R/data_documentation.R | 5 nflfastR-6.0.0/nflfastR/R/database.R |only nflfastR-6.0.0/nflfastR/R/ep_wp_calculators.R | 38 nflfastR-6.0.0/nflfastR/R/helper_add_cp_cpoe.R | 67 nflfastR-6.0.0/nflfastR/R/helper_add_ep_wp.R | 1789 ++++++---- nflfastR-6.0.0/nflfastR/R/helper_add_fixed_drives.R | 115 nflfastR-6.0.0/nflfastR/R/helper_add_game_data.R | 38 nflfastR-6.0.0/nflfastR/R/helper_add_nflscrapr_mutations.R | 625 ++- nflfastR-6.0.0/nflfastR/R/helper_add_series_data.R | 49 nflfastR-6.0.0/nflfastR/R/helper_add_xpass.R | 35 nflfastR-6.0.0/nflfastR/R/helper_add_xyac.R | 152 nflfastR-6.0.0/nflfastR/R/helper_additional_functions.R | 404 +- nflfastR-6.0.0/nflfastR/R/helper_database_functions.R | 145 nflfastR-6.0.0/nflfastR/R/helper_decode_player_ids.R | 27 nflfastR-6.0.0/nflfastR/R/helper_get_scheds_and_rosters.R | 11 nflfastR-6.0.0/nflfastR/R/helper_scrape_gc.R | 152 nflfastR-6.0.0/nflfastR/R/helper_scrape_nfl.R | 241 + nflfastR-6.0.0/nflfastR/R/helper_tidy_play_stats.R | 200 - nflfastR-6.0.0/nflfastR/R/helper_variable_selector.R | 477 ++ nflfastR-6.0.0/nflfastR/R/nflfastR-package.R | 4 nflfastR-6.0.0/nflfastR/R/report.R | 2 nflfastR-6.0.0/nflfastR/R/save_raw_pbp.R | 92 nflfastR-6.0.0/nflfastR/R/top-level_scraper.R | 48 nflfastR-6.0.0/nflfastR/R/utils.R | 142 nflfastR-6.0.0/nflfastR/data/nfl_stats_variables.rda |binary nflfastR-6.0.0/nflfastR/data/teams_colors_logos.rda |binary nflfastR-6.0.0/nflfastR/man/calculate_player_stats.Rd | 96 nflfastR-6.0.0/nflfastR/man/calculate_player_stats_def.Rd | 27 nflfastR-6.0.0/nflfastR/man/calculate_player_stats_kicking.Rd | 23 nflfastR-6.0.0/nflfastR/man/fast_scraper_roster.Rd | 2 nflfastR-6.0.0/nflfastR/man/nflfastR-package.Rd | 1 nflfastR-6.0.0/nflfastR/man/reexports.Rd | 3 nflfastR-6.0.0/nflfastR/man/report.Rd | 7 nflfastR-6.0.0/nflfastR/man/stat_ids.Rd | 2 nflfastR-6.0.0/nflfastR/man/teams_colors_logos.Rd | 3 nflfastR-6.0.0/nflfastR/man/update_pbp_db.Rd |only nflfastR-6.0.0/nflfastR/tests/testthat/2025 |only nflfastR-6.0.0/nflfastR/tests/testthat/_snaps/build_nflfastR_pbp.md |only nflfastR-6.0.0/nflfastR/tests/testthat/_snaps/stats/calculate_stats.md | 20 nflfastR-6.0.0/nflfastR/tests/testthat/expected_pbp.rds |binary nflfastR-6.0.0/nflfastR/tests/testthat/expected_sc.rds |binary nflfastR-6.0.0/nflfastR/tests/testthat/expected_sc_weekly.rds |binary nflfastR-6.0.0/nflfastR/tests/testthat/games.rds |binary nflfastR-6.0.0/nflfastR/tests/testthat/helpers.R | 68 nflfastR-6.0.0/nflfastR/tests/testthat/test-build_nflfastR_pbp.R | 15 nflfastR-6.0.0/nflfastR/tests/testthat/test-calculate_stats.R | 31 59 files changed, 4103 insertions(+), 3483 deletions(-)
Title: Estimates and Plots Single-Level and Multilevel Latent Class
Models
Description: Efficiently estimates single- and multilevel latent class models with covariates, allowing for output visualization in all specifications. For more technical details, see Lyrvall et al. (2025) <doi:10.1080/00273171.2025.2473935>.
Author: Roberto Di Mari [aut, cre],
Johan Lyrvall [aut],
Zsuzsa Bakk [ctb],
Jennifer Oser [ctb],
Jouni Kuha [ctb]
Maintainer: Roberto Di Mari <roberto.dimari@unict.it>
Diff between multilevLCA versions 2.1.5 dated 2026-08-26 and 2.1.6 dated 2026-09-18
DESCRIPTION | 8 MD5 | 18 - R/RcppExports.R | 8 build/partial.rdb |binary data/dataIEA.rda |binary data/dataTOY.rda |binary src/RcppExports.cpp | 35 --- src/Utils.cpp | 511 ++++++++++++++------------------------------------ src/Utils.h | 2 src/multilevLC_EM.cpp | 274 ++++++++++++++++---------- 10 files changed, 333 insertions(+), 523 deletions(-)
Title: Simultaneous Prediction and Confidence Bands for Functional Data
Description: Computes simultaneous prediction and confidence bands for densely
sampled functional data on a common grid. The calibration builds on the
functional bootstrap approach of Lenhoff et al. (1999)
<doi:10.1016/S0966-6362(98)00043-5>; hierarchical measurement designs are
motivated by Koska et al. (2023)
<doi:10.1016/j.jbiomech.2023.111506>. Independent curves are resampled
individually. Clustered data use an intact-subject bootstrap with equal
subject weighting, and the clustered prediction target is one future
curve from a new subject. Curves are represented by finite Fourier series,
and an 'Rcpp' backend performs the bootstrap calibration.
Author: Daniel Koska [aut, cre, cph]
Maintainer: Daniel Koska <dkoska@proton.me>
Diff between funbootband versions 0.2.0 dated 2025-10-20 and 0.3.0 dated 2026-09-18
DESCRIPTION | 28 +- MD5 | 33 +- NEWS.md | 22 + R/RcppExports.R | 8 R/band.R | 228 ++++++++++++++++--- README.md | 122 +++++----- build/vignette.rds |binary inst/doc/funbootband-intro.R | 136 +++++++---- inst/doc/funbootband-intro.Rmd | 234 ++++++++++++++------ inst/doc/funbootband-intro.html | 434 ++++++++++++++++++++++---------------- inst/examples/clustered_example.R | 85 ++++--- inst/examples/iid_example.R | 59 ++--- inst/validation |only man/band.Rd | 177 +++++++++------ src/RcppExports.cpp | 35 +-- src/band_kernels.cpp | 181 ++++++++++----- tests/testthat/test-band.R | 178 +++++++++++++++ vignettes/funbootband-intro.Rmd | 234 ++++++++++++++------ 18 files changed, 1452 insertions(+), 742 deletions(-)
Title: Text Analysis for All
Description: An R 'shiny' app designed for diverse text analysis tasks, offering a wide range of methodologies tailored to Natural Language Processing (NLP) needs.
It is a versatile, general-purpose tool for analyzing textual data.
'tall' features a comprehensive workflow, including data cleaning, preprocessing, statistical analysis, and visualization, all integrated for effective text analysis.
Author: Massimo Aria [aut, cre, cph] ,
Maria Spano [aut] ,
Luca D'Aniello [aut] ,
Corrado Cuccurullo [ctb] ,
Michelangelo Misuraca [ctb]
Maintainer: Massimo Aria <aria@unina.it>
Diff between tall versions 1.0.0 dated 2026-04-15 and 1.0.1 dated 2026-09-18
DESCRIPTION | 8 MD5 | 50 - NAMESPACE | 80 +- NEWS.md | 350 +++++++++++ R/reinert.R | 8 R/txt_recode_fast.R | 31 - build/partial.rdb |binary inst/tall/collocation.R | 32 - inst/tall/doc_classification.R | 77 +- inst/tall/documents.R | 15 inst/tall/featureroles.R | 121 ++- inst/tall/helpContent.R | 951 +++++++++++++++---------------- inst/tall/import.R | 16 inst/tall/overview.R | 12 inst/tall/preprocessing.R | 42 + inst/tall/settings.R | 94 ++- inst/tall/tallAI.R | 255 +++++--- inst/tall/tallEmbeddings.R | 69 +- inst/tall/tallNLP.R | 63 +- inst/tall/tallSentiment.R | 21 inst/tall/tallTextIO.R | 28 inst/tall/tallTopicModel.R | 218 +++++-- inst/tall/tallUtils.R | 49 + inst/tall/words.R | 15 man/process_multiwords_fast.Rd | 5 tests/testthat/test-process_multiwords.R | 51 + 26 files changed, 1820 insertions(+), 841 deletions(-)
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include 'Microsoft SQL Server', 'Oracle',
'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', 'Snowflake',
'Azure Synapse Analytics Dedicated', 'Apache Spark', 'SQLite', and 'InterSystems IRIS'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.19.6 dated 2026-07-31 and 1.19.7 dated 2026-09-18
DESCRIPTION | 10 +++--- MD5 | 24 +++++++-------- NAMESPACE | 16 ++++++---- NEWS.md | 14 +++++++++ inst/csv/replacementPatterns.csv | 32 +++++++++++--------- inst/doc/UsingSqlRender.pdf |binary tests/testthat/test-translate-duckdb.R | 4 +- tests/testthat/test-translate-impala.R | 6 +-- tests/testthat/test-translate-iris.R | 37 ++++++++++++++++++++++-- tests/testthat/test-translate-oracle.R | 24 +++++++++++++++ tests/testthat/test-translate-postgresql.R | 6 +-- tests/testthat/test-translate-sqlite-extended.R | 8 ++--- tests/testthat/test-translate-sqlite.R | 24 ++++++++++++++- 13 files changed, 151 insertions(+), 54 deletions(-)
Title: Analyse Political Texts
Description: Wrangle and annotate different types of political texts.
It also introduces Urgency Analysis,
a new method for the analysis of urgency in political texts.
Author: Henrique Sposito [cre, aut, ctb],
James Hollway [ctb],
Jael Tan [ctb]
Maintainer: Henrique Sposito <henrique.sposito@graduateinstitute.ch>
Diff between poldis versions 0.1.2 dated 2024-09-04 and 0.2.0 dated 2026-09-18
poldis-0.1.2/poldis/R/US_News_Conferences_1960_1980.R |only poldis-0.1.2/poldis/data/US_News_Conferences_1960_1980.rda |only poldis-0.1.2/poldis/man/US_News_Conferences_1960_1980.Rd |only poldis-0.1.2/poldis/man/extract_date.Rd |only poldis-0.1.2/poldis/man/extract_title.Rd |only poldis-0.1.2/poldis/man/sim_urgency.Rd |only poldis-0.2.0/poldis/DESCRIPTION | 30 poldis-0.2.0/poldis/LICENSE | 4 poldis-0.2.0/poldis/MD5 | 78 - poldis-0.2.0/poldis/NAMESPACE | 85 - poldis-0.2.0/poldis/NEWS.md | 271 ++- poldis-0.2.0/poldis/R/US_inaugural_addresses_1993_2025.R |only poldis-0.2.0/poldis/R/class.R | 60 poldis-0.2.0/poldis/R/priorities.R | 80 - poldis-0.2.0/poldis/R/sysdata.rda |binary poldis-0.2.0/poldis/R/text_tools.R | 708 ++++------ poldis-0.2.0/poldis/R/topic.R | 297 +--- poldis-0.2.0/poldis/R/urgency.R | 425 ++---- poldis-0.2.0/poldis/R/utils.R | 77 - poldis-0.2.0/poldis/README.md | 449 +++--- poldis-0.2.0/poldis/build/partial.rdb |binary poldis-0.2.0/poldis/build/vignette.rds |only poldis-0.2.0/poldis/data/US_inaugural_addresses_1993_2025.rda |only poldis-0.2.0/poldis/inst |only poldis-0.2.0/poldis/man/US_inaugural_addresses_1993_2025.Rd |only poldis-0.2.0/poldis/man/annotate_text.Rd | 49 poldis-0.2.0/poldis/man/extract_context.Rd | 72 - poldis-0.2.0/poldis/man/extract_first_sentence.Rd |only poldis-0.2.0/poldis/man/extract_locations.Rd | 48 poldis-0.2.0/poldis/man/extract_match.Rd | 64 poldis-0.2.0/poldis/man/extract_names.Rd | 46 poldis-0.2.0/poldis/man/extract_text_similarities.Rd | 70 poldis-0.2.0/poldis/man/gather_related_terms.Rd | 87 - poldis-0.2.0/poldis/man/gather_topics.Rd | 75 - poldis-0.2.0/poldis/man/get_urgency.Rd | 124 - poldis-0.2.0/poldis/man/read_pdf.Rd | 34 poldis-0.2.0/poldis/man/select_priorities.Rd | 55 poldis-0.2.0/poldis/man/split_text.Rd | 54 poldis-0.2.0/poldis/tests/testthat.R | 8 poldis-0.2.0/poldis/tests/testthat/helper-spacy.R |only poldis-0.2.0/poldis/tests/testthat/test_priorities.R | 39 poldis-0.2.0/poldis/tests/testthat/test_text_tools.R | 104 - poldis-0.2.0/poldis/tests/testthat/test_topic.R | 26 poldis-0.2.0/poldis/tests/testthat/test_urgency.R | 120 - poldis-0.2.0/poldis/vignettes |only 45 files changed, 1823 insertions(+), 1816 deletions(-)
Title: Time Series Analysis Tool using Linear Layered SDEs
Description: Time series analysis tool using linear layered stochastic
differential equations. The package allows for multiple time
series with correlative and/or causal links between them. Unmeasured causal
processes are allowed to affect the measured processes in a layered structure,
hence the name of the package. In case of causal feedback loops,
the matrix operations (including eigenvalue decompositions) allows for
complex numbers. In this case, cyclic behavior can be expected.
Details can be found in Reitan and Liow (2019)<doi:10.1111/2041-210X.13299>.
Author: Trond Reitan [aut, cre] ,
Lee Hsiang Liow [ctb] ,
Adam T. Kocsis [ctb]
Maintainer: Trond Reitan <trond.reitan@geo.uio.no>
Diff between layeranalyzer versions 0.4.1 dated 2026-08-28 and 0.4.2 dated 2026-09-18
DESCRIPTION | 8 - MD5 | 8 - NEWS.md | 5 build/partial.rdb |binary src/layeranalyzer.cpp | 298 +++++++++++++++++++++++++------------------------- 5 files changed, 166 insertions(+), 153 deletions(-)
Title: Baseline Correction of Spectra
Description: Collection of baseline correction algorithms, along with a framework and a Tcl/Tk enabled GUI for optimising baseline algorithm parameters. Typical use of the package is for removing background effects from spectra originating from various types of spectroscopy and spectrometry, possibly optimizing this with regard to regression or classification results. Correction methods include polynomial fitting, weighted local smoothers and many more.
Author: Kristian Hovde Liland [aut, cre] ,
Bjoern-Helge Mevik [aut],
Roberto Canteri [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between baseline versions 1.3-7 dated 2025-06-18 and 1.3-8 dated 2026-09-18
baseline-1.3-7/baseline/man/PLSRTest-class.Rd |only baseline-1.3-7/baseline/man/baseline-class.Rd |only baseline-1.3-7/baseline/man/baselineAlg-class.Rd |only baseline-1.3-7/baseline/man/baselineAlgResult-class.Rd |only baseline-1.3-7/baseline/man/baselineAlgTest-class.Rd |only baseline-1.3-7/baseline/man/getBaseline.Rd |only baseline-1.3-7/baseline/man/ind.min.Rd |only baseline-1.3-7/baseline/man/name.Rd |only baseline-1.3-7/baseline/man/param.ind.min.Rd |only baseline-1.3-7/baseline/man/predictionResult-class.Rd |only baseline-1.3-7/baseline/man/predictionTest-class.Rd |only baseline-1.3-7/baseline/man/ridgeRegressionTest-class.Rd |only baseline-1.3-8/baseline/DESCRIPTION | 12 baseline-1.3-8/baseline/MD5 | 107 ++++---- baseline-1.3-8/baseline/NAMESPACE | 125 +++++++-- baseline-1.3-8/baseline/NEWS | 12 baseline-1.3-8/baseline/R/baseline.R | 24 + baseline-1.3-8/baseline/R/baseline.package.R | 4 baseline-1.3-8/baseline/R/custom.baseline.R | 8 baseline-1.3-8/baseline/R/datasets.R | 11 baseline-1.3-8/baseline/R/optimWizard.R | 4 baseline-1.3-8/baseline/R/optimisation.R | 189 ++++++++++----- baseline-1.3-8/baseline/R/plotBaseline.R | 2 baseline-1.3-8/baseline/man/PLSRTestClass.Rd |only baseline-1.3-8/baseline/man/XPSdata.Rd | 39 +-- baseline-1.3-8/baseline/man/algorithm.Rd | 25 + baseline-1.3-8/baseline/man/baseline-package.Rd | 78 +++--- baseline-1.3-8/baseline/man/baseline.Rd | 65 ++--- baseline-1.3-8/baseline/man/baseline.TAP.Rd | 68 +++-- baseline-1.3-8/baseline/man/baseline.als.Rd | 57 ++-- baseline-1.3-8/baseline/man/baseline.fillPeaks.Rd | 54 ++-- baseline-1.3-8/baseline/man/baseline.irls.Rd | 43 +-- baseline-1.3-8/baseline/man/baseline.lowpass.Rd | 51 ++-- baseline-1.3-8/baseline/man/baseline.medianWindow.Rd | 53 ++-- baseline-1.3-8/baseline/man/baseline.modpolyfit.Rd | 55 ++-- baseline-1.3-8/baseline/man/baseline.peakDetection.Rd | 110 +++++--- baseline-1.3-8/baseline/man/baseline.rfbaseline.Rd | 95 ++++--- baseline-1.3-8/baseline/man/baseline.rollingBall.Rd | 42 +-- baseline-1.3-8/baseline/man/baseline.shirley.Rd | 106 +++++--- baseline-1.3-8/baseline/man/baselineAlg.Rd |only baseline-1.3-8/baseline/man/baselineAlgClass.Rd |only baseline-1.3-8/baseline/man/baselineAlgResult.Rd |only baseline-1.3-8/baseline/man/baselineAlgResultMethods.Rd |only baseline-1.3-8/baseline/man/baselineAlgTest.Rd |only baseline-1.3-8/baseline/man/baselineAlgorithms.Rd | 26 +- baseline-1.3-8/baseline/man/baselineAlgorithmsGUI.Rd | 24 + baseline-1.3-8/baseline/man/baselineClass.Rd |only baseline-1.3-8/baseline/man/baselineEnv.Rd | 50 ++- baseline-1.3-8/baseline/man/baselineGUI.Rd | 45 ++- baseline-1.3-8/baseline/man/custom.baseline.Rd | 99 ++++--- baseline-1.3-8/baseline/man/doOptim.Rd | 152 ++++++++---- baseline-1.3-8/baseline/man/funcName.Rd | 29 +- baseline-1.3-8/baseline/man/getSpectra.Rd |only baseline-1.3-8/baseline/man/milk.Rd | 46 +-- baseline-1.3-8/baseline/man/optimWizard.Rd | 41 ++- baseline-1.3-8/baseline/man/overall.min.Rd | 35 +- baseline-1.3-8/baseline/man/param.Rd | 38 +-- baseline-1.3-8/baseline/man/plotBaseline.Rd | 106 +++++--- baseline-1.3-8/baseline/man/plotOptim.Rd | 42 +-- baseline-1.3-8/baseline/man/predictionResult.Rd |only baseline-1.3-8/baseline/man/predictionResultMethods.Rd |only baseline-1.3-8/baseline/man/predictionTest.Rd |only baseline-1.3-8/baseline/man/qualMeas.Rd | 111 +++++--- baseline-1.3-8/baseline/man/ridgeRegressionTestClass.Rd |only baseline-1.3-8/baseline/man/runTest.Rd | 82 +++--- baseline-1.3-8/baseline/src/Makevars | 2 baseline-1.3-8/baseline/tools |only 67 files changed, 1438 insertions(+), 929 deletions(-)
Title: Self-Validated Ensemble Models with Lasso and Relaxed Elastic
Net Regression
Description: Implements the self-validated elastic-net and relaxed elastic-net ensemble modeling and multi-response optimization workflow described in Karl (2026) <doi:10.1016/j.chemolab.2026.105660>. Self-validated ensemble models (SVEM; Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) are fitted for small-sample design-of-experiments and related workflows using 'glmnet' (Friedman et al. (2010) <doi:10.18637/jss.v033.i01>). Fractional random-weight bootstraps with anti-correlated validation copies are used to tune penalty paths by validation-weighted AIC/BIC. Supports Gaussian and binomial responses, deterministic expansion helpers for shared factor spaces, prediction with bootstrap uncertainty, and a random-search optimizer that respects mixture constraints and combines multiple responses via desirability functions. Also includes a permutation-based whole-model test for Gaussian SVEM fits (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). Package code was drafte [...truncated...]
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 3.6.0 dated 2026-09-06 and 3.6.2 dated 2026-09-18
SVEMnet-3.6.0/SVEMnet/inst/COPYRIGHTS |only SVEMnet-3.6.0/SVEMnet/tests/testthat/fixtures |only SVEMnet-3.6.2/SVEMnet/DESCRIPTION | 25 SVEMnet-3.6.2/SVEMnet/MD5 | 25 SVEMnet-3.6.2/SVEMnet/NEWS | 10 SVEMnet-3.6.2/SVEMnet/R/SVEMnet.R | 816 +++---- SVEMnet-3.6.2/SVEMnet/R/edf.R |only SVEMnet-3.6.2/SVEMnet/R/fitting_paths.R |only SVEMnet-3.6.2/SVEMnet/R/shasho_fit.R | 255 +- SVEMnet-3.6.2/SVEMnet/R/svem_significance_test_parallel.R | 28 SVEMnet-3.6.2/SVEMnet/man/SVEMnet-package.Rd | 7 SVEMnet-3.6.2/SVEMnet/man/SVEMnet.Rd | 1164 +++++----- SVEMnet-3.6.2/SVEMnet/man/svem_significance_test_parallel.Rd | 16 SVEMnet-3.6.2/SVEMnet/tests/testthat/test-edf-correction.R |only SVEMnet-3.6.2/SVEMnet/tests/testthat/test-shasho-fit.R | 73 SVEMnet-3.6.2/SVEMnet/tests/testthat/test-wmt-hardening-3.4.0.R | 55 16 files changed, 1236 insertions(+), 1238 deletions(-)
Title: Facilitate Analysis of Proteomic Data from Olink
Description: A collection of functions to facilitate analysis of proteomic
data from Olink, primarily NPX data that has been exported from Olink
Software. The functions also work on QUANT data from
Olink by log- transforming the QUANT data. The functions are focused
on reading data, facilitating data wrangling and quality control
analysis, performing statistical analysis and generating figures to
visualize the results of the statistical analysis. The goal of this
package is to help users extract biological insights from proteomic
data run on the Olink platform.
Author: Kathleen Nevola [aut, cre] ,
Marianne Sandin [aut] ,
Jamey Guess [aut] ,
Simon Forsberg [aut] ,
Christoffer Cambronero [aut] ,
Pascal Pucholt [aut] ,
Boxi Zhang [aut] ,
Masoumeh Sheikhi [aut] ,
Klev Diamanti [aut] ,
Amrita Kar [aut] ,
Lei Conze [aut] [...truncated...]
Maintainer: Kathleen Nevola <biostattools@olink.com>
Diff between OlinkAnalyze versions 5.0.2 dated 2026-06-23 and 5.1.0 dated 2026-09-18
OlinkAnalyze-5.0.2/OlinkAnalyze/man/ansi_collapse_quot.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_columns.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_file_exists.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_file_extension.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_is_arrow_object.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_is_boolean.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_is_character.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_is_dataset.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_is_integer.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_is_list.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_is_numeric.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_is_scalar_boolean.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_is_scalar_character.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_is_scalar_integer.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_is_scalar_numeric.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_is_tibble.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_library_installed.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_log_colname.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_npx_update_col_names.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/check_out_df_arg.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/figures/OA_v5.0_flowchart.png |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/norm_internal_rename_cols.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/olink_iqr.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/olink_median.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/olink_median_iqr_outlier.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/olink_normalization_bridgeable.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/olink_normalization_qs.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/remove_all_na_cols.Rd |only OlinkAnalyze-5.0.2/OlinkAnalyze/man/run_check_npx.Rd |only OlinkAnalyze-5.1.0/OlinkAnalyze/DESCRIPTION | 19 OlinkAnalyze-5.1.0/OlinkAnalyze/MD5 | 336 OlinkAnalyze-5.1.0/OlinkAnalyze/NAMESPACE | 8 OlinkAnalyze-5.1.0/OlinkAnalyze/NEWS.md | 16 OlinkAnalyze-5.1.0/OlinkAnalyze/R/Olink_one_non_parametric.R | 99 OlinkAnalyze-5.1.0/OlinkAnalyze/R/check_boolean.R | 6 OlinkAnalyze-5.1.0/OlinkAnalyze/R/check_character.R | 6 OlinkAnalyze-5.1.0/OlinkAnalyze/R/check_columns.R | 4 OlinkAnalyze-5.1.0/OlinkAnalyze/R/check_df.R | 59 OlinkAnalyze-5.1.0/OlinkAnalyze/R/check_file.R | 4 OlinkAnalyze-5.1.0/OlinkAnalyze/R/check_integer.R | 6 OlinkAnalyze-5.1.0/OlinkAnalyze/R/check_library_installed.R | 3 OlinkAnalyze-5.1.0/OlinkAnalyze/R/check_list.R | 3 OlinkAnalyze-5.1.0/OlinkAnalyze/R/check_npx.R | 539 - OlinkAnalyze-5.1.0/OlinkAnalyze/R/check_numeric.R | 6 OlinkAnalyze-5.1.0/OlinkAnalyze/R/clean_npx.R | 99 OlinkAnalyze-5.1.0/OlinkAnalyze/R/dist_plot.R | 56 OlinkAnalyze-5.1.0/OlinkAnalyze/R/get_others.R | 1 OlinkAnalyze-5.1.0/OlinkAnalyze/R/npxProcessing.R | 21 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_anova.R | 40 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_boxplot.R | 23 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_bridge_selector.R | 38 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_class.R |only OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_lmer.R | 34 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_lod.R | 47 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_normalization.R | 342 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_normalization_format.R | 15 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_normalization_n.R | 62 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_normalization_product.R | 10 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_normalization_utils.R | 296 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_ordinal_regression.R | 21 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_outlier_detection_utils.R | 101 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_pathway_enrichment.R | 72 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_pathway_heatmap.R | 9 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_pathway_visualization.R | 9 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_plate_randomizer.R | 152 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_qc_plot.R | 188 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_ttest.R | 14 OlinkAnalyze-5.1.0/OlinkAnalyze/R/olink_wilcox.R | 14 OlinkAnalyze-5.1.0/OlinkAnalyze/R/osi_dist_plot.R | 8 OlinkAnalyze-5.1.0/OlinkAnalyze/R/pca_plot.R | 50 OlinkAnalyze-5.1.0/OlinkAnalyze/R/plot_heatmap.R | 12 OlinkAnalyze-5.1.0/OlinkAnalyze/R/plot_heatmap_helper.R | 13 OlinkAnalyze-5.1.0/OlinkAnalyze/R/plot_is_bridgeable.R | 18 OlinkAnalyze-5.1.0/OlinkAnalyze/R/plot_point_range.R | 18 OlinkAnalyze-5.1.0/OlinkAnalyze/R/plot_umap.R | 31 OlinkAnalyze-5.1.0/OlinkAnalyze/R/plot_volcano.R | 3 OlinkAnalyze-5.1.0/OlinkAnalyze/R/read_npx.R | 43 OlinkAnalyze-5.1.0/OlinkAnalyze/R/read_npx_format.R | 55 OlinkAnalyze-5.1.0/OlinkAnalyze/R/read_npx_utils.R | 87 OlinkAnalyze-5.1.0/OlinkAnalyze/R/read_npx_wide.R | 4 OlinkAnalyze-5.1.0/OlinkAnalyze/R/sysdata.rda |binary OlinkAnalyze-5.1.0/OlinkAnalyze/R/utils.R | 164 OlinkAnalyze-5.1.0/OlinkAnalyze/inst/doc/OlinkAnalyze-Vignette.R | 125 OlinkAnalyze-5.1.0/OlinkAnalyze/inst/doc/OlinkAnalyze-Vignette.Rmd | 294 OlinkAnalyze-5.1.0/OlinkAnalyze/inst/doc/OlinkAnalyze-Vignette.html | 614 - OlinkAnalyze-5.1.0/OlinkAnalyze/man/attach_check_log.Rd |only OlinkAnalyze-5.1.0/OlinkAnalyze/man/attach_check_log_arrow.Rd |only OlinkAnalyze-5.1.0/OlinkAnalyze/man/check_osi.Rd | 4 OlinkAnalyze-5.1.0/OlinkAnalyze/man/clean_npx.Rd | 26 OlinkAnalyze-5.1.0/OlinkAnalyze/man/convert_read_npx_output.Rd | 2 OlinkAnalyze-5.1.0/OlinkAnalyze/man/dot-check_params.Rd | 14 OlinkAnalyze-5.1.0/OlinkAnalyze/man/dot-downstream_fun_args.Rd | 5 OlinkAnalyze-5.1.0/OlinkAnalyze/man/dot-read_npx_args.Rd | 5 OlinkAnalyze-5.1.0/OlinkAnalyze/man/extract_check_log.Rd |only OlinkAnalyze-5.1.0/OlinkAnalyze/man/figures/OA_v5.1_flowchart.png |only OlinkAnalyze-5.1.0/OlinkAnalyze/man/figures/logo.html | 2 OlinkAnalyze-5.1.0/OlinkAnalyze/man/mapping_file_id.Rd | 38 OlinkAnalyze-5.1.0/OlinkAnalyze/man/new_olink_class.Rd |only OlinkAnalyze-5.1.0/OlinkAnalyze/man/norm_internal_adjust.Rd | 102 OlinkAnalyze-5.1.0/OlinkAnalyze/man/norm_internal_adjust_not_ref.Rd | 62 OlinkAnalyze-5.1.0/OlinkAnalyze/man/norm_internal_adjust_ref.Rd | 50 OlinkAnalyze-5.1.0/OlinkAnalyze/man/norm_internal_assay_median.Rd | 78 OlinkAnalyze-5.1.0/OlinkAnalyze/man/norm_internal_bridge.Rd | 88 OlinkAnalyze-5.1.0/OlinkAnalyze/man/norm_internal_cross_product.Rd | 120 OlinkAnalyze-5.1.0/OlinkAnalyze/man/norm_internal_reference_median.Rd | 74 OlinkAnalyze-5.1.0/OlinkAnalyze/man/norm_internal_subset.Rd | 100 OlinkAnalyze-5.1.0/OlinkAnalyze/man/norm_internal_update_maxlod.Rd | 40 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_anova.Rd | 13 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_anova_posthoc.Rd | 13 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_boxplot.Rd | 11 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_bridge_selector.Rd | 12 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_bridgeability_plot.Rd | 16 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_class.Rd |only OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_display_plate_dist.Rd | 1 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_display_plate_layout.Rd | 1 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_dist_plot.Rd | 19 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_format_oid_no_overlap.Rd | 52 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_format_rm_ext_ctrl.Rd | 58 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_heatmap_plot.Rd | 8 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_lmer.Rd | 11 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_lmer_plot.Rd | 16 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_lmer_posthoc.Rd | 13 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_lod.Rd | 29 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_norm_input_check.Rd | 6 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_norm_input_ref_medians.Rd | 42 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_norm_input_validate.Rd | 108 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_norm_product_id.Rd | 50 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_norm_reference_id.Rd | 54 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_normalization.Rd | 35 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_normalization_bridge.Rd | 24 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_normalization_format.Rd | 15 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_normalization_subset.Rd | 32 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_one_non_parametric.Rd | 13 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_one_non_parametric_posthoc.Rd | 16 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_ordinal_regression.Rd | 6 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_ordinal_regression_posthoc.Rd | 9 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_osi_dist_plot.Rd | 5 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_pathway_enrichment.Rd | 14 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_pathway_heatmap.Rd | 9 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_pathway_visualization.Rd | 9 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_pca_plot.Rd | 16 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_plate_randomizer.Rd | 1 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_qc_plot.Rd | 11 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_ttest.Rd | 12 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_umap_plot.Rd | 22 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_volcano_plot.Rd | 3 OlinkAnalyze-5.1.0/OlinkAnalyze/man/olink_wilcox.Rd | 12 OlinkAnalyze-5.1.0/OlinkAnalyze/man/read_npx.Rd | 39 OlinkAnalyze-5.1.0/OlinkAnalyze/man/rm_check_log.Rd |only OlinkAnalyze-5.1.0/OlinkAnalyze/man/serialize_check_log.Rd |only OlinkAnalyze-5.1.0/OlinkAnalyze/man/update_check_log.Rd |only OlinkAnalyze-5.1.0/OlinkAnalyze/man/validate_check_log.Rd |only OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/helper-check.R | 56 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-Olink_one_non_parametric.R | 211 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-check_columns.R | 78 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-check_df.R | 355 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-check_npx.R | 460 - OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-clean_npx.R | 860 + OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-dist_plot.R | 137 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-npxProcessing.R | 94 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_anova.R | 201 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_boxplot.R | 266 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_bridge_selector.R | 98 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_class.R |only OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_color.R | 2 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_lmer.R | 140 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_lod.R | 469 + OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_normalization.R | 4595 +++++++--- OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_normalization_n.R | 1100 +- OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_normalization_utils.R | 2182 ++++ OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_ordinal_regression.R | 442 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_outlier_detection_utils.R |only OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_pathway_enrichment.R | 83 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_plate_randomizer.R | 19 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_qc_plot.R | 140 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_ttest.R | 71 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-olink_wilcox.R | 91 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-osi_dist_plot.R | 44 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-pca_plot.R | 386 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-plot_heatmap.R | 143 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-plot_is_bridgeable.R | 800 + OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-plot_point_range.R | 95 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-plot_umap.R | 129 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-read_npx.R | 368 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-read_npx_format.R | 240 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-read_npx_utils.R | 179 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-read_npx_wide.R | 144 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-read_npx_zip.R | 376 OlinkAnalyze-5.1.0/OlinkAnalyze/tests/testthat/test-utils.R | 813 + OlinkAnalyze-5.1.0/OlinkAnalyze/vignettes/OlinkAnalyze-Vignette.Rmd | 294 190 files changed, 16680 insertions(+), 5444 deletions(-)
Title: Various Methods for the Goodness-of-Fit Problem in D>1
Dimensions
Description: Provides multivariate goodness-of-fit testing with a common
interface for several test statistics. Null models may be simple or include
parameter estimation, with p-values obtained by parametric bootstrap
simulation. The function gof_test_adjusted_pvalue() combines several tests
and computes a p-value adjusted for simultaneous inference. The function
gof_power() estimates test power. The functions hybrid_test() and
hybrid_power() use Monte Carlo samples under the null together with
two-sample procedures. The function run.studies() supports systematic power
comparisons of user-supplied and included methods across case studies. See
the included vignettes for method details and references.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between MDgof versions 1.1.0 dated 2026-08-03 and 1.2.0 dated 2026-09-18
MDgof-1.1.0/MDgof/R/makeTSextra.R |only MDgof-1.2.0/MDgof/DESCRIPTION | 36 MDgof-1.2.0/MDgof/MD5 | 65 MDgof-1.2.0/MDgof/NAMESPACE | 12 MDgof-1.2.0/MDgof/NEWS.md | 7 MDgof-1.2.0/MDgof/R/check.functions.R | 108 - MDgof-1.2.0/MDgof/R/chi_power.R | 138 +- MDgof-1.2.0/MDgof/R/draw_case.R | 79 - MDgof-1.2.0/MDgof/R/gof_power.R | 651 +++++----- MDgof-1.2.0/MDgof/R/gof_test.R | 640 ++++++--- MDgof-1.2.0/MDgof/R/gof_test_adjusted_pvalue.R | 630 ++++----- MDgof-1.2.0/MDgof/R/helper_functions.R |only MDgof-1.2.0/MDgof/R/hybrid_power.R | 20 MDgof-1.2.0/MDgof/R/hybrid_test.R | 25 MDgof-1.2.0/MDgof/R/power_pvals.R | 92 - MDgof-1.2.0/MDgof/R/run.studies.R | 7 MDgof-1.2.0/MDgof/R/signif_digits.R | 62 MDgof-1.2.0/MDgof/R/timecheck.R | 26 MDgof-1.2.0/MDgof/inst/doc/MDgof-Case-Studies.html | 56 MDgof-1.2.0/MDgof/man/MDgof_test-methods.Rd |only MDgof-1.2.0/MDgof/man/as.data.frame.MDgof_power.Rd |only MDgof-1.2.0/MDgof/man/check.functions.Rd | 17 MDgof-1.2.0/MDgof/man/draw_case.Rd | 4 MDgof-1.2.0/MDgof/man/gof_power.Rd | 15 MDgof-1.2.0/MDgof/man/gof_test.Rd | 20 MDgof-1.2.0/MDgof/man/gof_test_adjusted_pvalue.Rd | 7 MDgof-1.2.0/MDgof/man/hybrid_power.Rd | 3 MDgof-1.2.0/MDgof/man/hybrid_test.Rd | 3 MDgof-1.2.0/MDgof/man/makeTSextra.Rd | 5 MDgof-1.2.0/MDgof/man/makemaxProcessor.Rd |only MDgof-1.2.0/MDgof/man/maketypeTS.Rd |only MDgof-1.2.0/MDgof/man/print.MDgof_power.Rd |only MDgof-1.2.0/MDgof/man/run.studies.Rd | 5 MDgof-1.2.0/MDgof/man/signif_digits.Rd | 1 MDgof-1.2.0/MDgof/man/timecheck.Rd | 1 MDgof-1.2.0/MDgof/tests/testthat/test-discrete-custom-TS-signatures.R |only MDgof-1.2.0/MDgof/tests/testthat/test-discrete-matrix-detection.R |only MDgof-1.2.0/MDgof/tests/testthat/test-gof-power-ci.R |only MDgof-1.2.0/MDgof/tests/testthat/test-input-validation.R |only 39 files changed, 1510 insertions(+), 1225 deletions(-)
Title: Interface to Download Meteorological (and Hydrological) Datasets
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories:
OGIMET (<http://ogimet.com/index.phtml.en>),
University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair/>),
Polish Institute of Meteorology and Water Management - National Research Institute (<https://danepubliczne.imgw.pl>),
and National Oceanic & Atmospheric Administration (NOAA).
This package also allows for searching geographical coordinates for each observation and calculate distances to the nearest stations.
Author: Bartosz Czernecki [aut, cre] ,
Arkadiusz Glogowski [aut] ,
Jakub Nowosad [aut] ,
IMGW-PIB [ctb]
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Diff between climate versions 1.4.0 dated 2026-07-10 and 1.4.1 dated 2026-09-18
DESCRIPTION | 6 MD5 | 50 +- NEWS.md | 8 R/hydro_imgw.R | 15 R/hydro_imgw_daily.R | 2 R/hydro_imgw_monthly.R | 2 R/hydro_shortening_imgw.R | 62 +-- R/meteo_imgw.R | 13 R/meteo_imgw_daily.R | 12 R/meteo_imgw_hourly.R | 15 R/meteo_imgw_monthly.R | 15 R/meteo_shortening_imgw.R | 52 +- R/utils.R | 7 README.md | 17 data/imgw_hydro_abbrev.rda |binary data/imgw_meteo_abbrev.rda |binary inst/doc/getstarted.Rmd | 6 inst/doc/getstarted.html | 756 ++++++++++++------------------------------- man/hydro_imgw.Rd | 1 man/hydro_shortening_imgw.Rd | 17 man/meteo_imgw.Rd | 5 man/meteo_imgw_daily.Rd | 6 man/meteo_imgw_hourly.Rd | 5 man/meteo_imgw_monthly.Rd | 11 man/meteo_shortening_imgw.Rd | 12 vignettes/getstarted.Rmd | 6 26 files changed, 378 insertions(+), 723 deletions(-)
Title: Holistic Multimodel Domain Analysis for Exploratory Machine
Learning
Description: Holistic Multimodel Domain Analysis (HMDA) is a robust and transparent framework designed for exploratory machine learning research, aiming to enhance the process of feature assessment and selection. HMDA addresses key limitations of traditional machine learning methods by evaluating the consistency across multiple high-performing models within a fine-tuned modeling grid, thereby improving the interpretability and reliability of feature importance assessments. Specifically, it computes Weighted Mean SHapley Additive exPlanations (WMSHAP), which aggregate feature contributions from multiple models based on weighted performance metrics. HMDA also provides confidence intervals to demonstrate the stability of these feature importance estimates. This framework is particularly beneficial for analyzing complex, multidimensional datasets common in health research, supporting reliable exploration of mental health outcomes such as suicidal ideation, suicide attempts, and other psychological cond [...truncated...]
Author: E. F. Haghish [aut, cre, cph]
Maintainer: E. F. Haghish <haghish@hotmail.com>
Diff between HMDA versions 0.3.0 dated 2026-03-04 and 0.4.1 dated 2026-09-18
DESCRIPTION | 8 ++++---- MD5 | 13 ++++++++++--- NAMESPACE | 5 +++++ R/helpers.R |only R/hmda.fastcompute.globalshap.R |only R/hmda.fastcompute.globalwmshap.R |only R/hmda.init.R | 2 +- R/hmda.rashamon.set.R |only man/hmda.fastcompute.globalshap.Rd |only man/hmda.fastcompute.globalwmshap.Rd |only man/hmda.rashomon.set.Rd |only 11 files changed, 20 insertions(+), 8 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Warick Brown [ctb],
Tilman Davies [ctb],
Ute Hahn [ctb],
Martin Hazelton [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oeh [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.8-2 dated 2026-07-24 and 3.8-3 dated 2026-09-18
DESCRIPTION | 10 ++++----- MD5 | 20 +++++++++--------- NAMESPACE | 1 NEWS | 24 ++++++++++++++++++++-- R/marks.R | 24 +++++++++++++++++++++- R/plot.im.R | 45 +++++++++++++++++++++++++++++------------- R/ripras.R | 5 ++-- inst/doc/packagesizes.txt | 2 - inst/info/packagesizes.txt | 2 - man/ripras.Rd | 5 ++-- man/spatstat.geom-internal.Rd | 2 + 11 files changed, 103 insertions(+), 37 deletions(-)
Title: External jars for 'rjdverse' R Packages
Description: It provides external jars required for the 'rjdverse' (as 'rjd3toolkit', 'rjd3x13' and 'rjd3tramoseats').
Author: Tanguy Barthelemy [aut, cre, cph]
Maintainer: Tanguy Barthelemy <timeserieswithjdemetraandr@gmail.com>
Diff between rjd3jars versions 0.0.5 dated 2026-07-07 and 0.0.6 dated 2026-09-18
rjd3jars-0.0.5/rjd3jars/inst/java/jdplus-sa-base-api-3.8.0.jar |only rjd3jars-0.0.5/rjd3jars/inst/java/jdplus-sa-base-core-3.8.0.jar |only rjd3jars-0.0.5/rjd3jars/inst/java/jdplus-toolkit-base-api-3.8.0.jar |only rjd3jars-0.0.5/rjd3jars/inst/java/jdplus-toolkit-base-core-3.8.0.jar |only rjd3jars-0.0.5/rjd3jars/inst/java/protobuf-java-4.35.1.jar |only rjd3jars-0.0.6/rjd3jars/DESCRIPTION | 21 + rjd3jars-0.0.6/rjd3jars/MD5 | 40 +-- rjd3jars-0.0.6/rjd3jars/NAMESPACE | 22 - rjd3jars-0.0.6/rjd3jars/NEWS.md | 130 +++++----- rjd3jars-0.0.6/rjd3jars/R/java.R |only rjd3jars-0.0.6/rjd3jars/R/rjd3jars-package.R | 12 rjd3jars-0.0.6/rjd3jars/R/utils.R | 116 ++++---- rjd3jars-0.0.6/rjd3jars/R/zzz.R | 110 ++------ rjd3jars-0.0.6/rjd3jars/README.md | 82 +++--- rjd3jars-0.0.6/rjd3jars/inst/WORDLIST | 106 -------- rjd3jars-0.0.6/rjd3jars/inst/java/jdplus-sa-base-api-3.9.0.jar |only rjd3jars-0.0.6/rjd3jars/inst/java/jdplus-sa-base-core-3.9.0.jar |only rjd3jars-0.0.6/rjd3jars/inst/java/jdplus-toolkit-base-api-3.9.0.jar |only rjd3jars-0.0.6/rjd3jars/inst/java/jdplus-toolkit-base-core-3.9.0.jar |only rjd3jars-0.0.6/rjd3jars/inst/java/protobuf-java-4.36.1.jar |only rjd3jars-0.0.6/rjd3jars/java/README | 12 rjd3jars-0.0.6/rjd3jars/man/java-version.Rd | 76 ++--- rjd3jars-0.0.6/rjd3jars/man/reload_dictionaries.Rd | 38 +- rjd3jars-0.0.6/rjd3jars/man/reload_safactories.Rd | 35 +- rjd3jars-0.0.6/rjd3jars/man/reload_tsproviders.Rd | 38 +- rjd3jars-0.0.6/rjd3jars/man/rjd3jars-package.Rd | 49 ++- rjd3jars-0.0.6/rjd3jars/tests |only 27 files changed, 384 insertions(+), 503 deletions(-)
Title: 'Rcpp' Meets 'C++' Arrays
Description: Interoperability between 'Rcpp' and the 'C++11' array and tuple
types. Linking to this package allows fixed-length 'std::array' objects to
be converted to and from equivalent R vectors, and 'std::tuple' objects
converted to lists, via the as() and wrap() functions. There is also
experimental support for 'std::span' from 'C++20'.
Author: Jon Clayden [cre, aut] ,
Dirk Eddelbuettel [aut],
Andrew Johnson [ctb]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RcppArray versions 0.3.0 dated 2023-11-08 and 0.3.1 dated 2026-09-18
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NEWS.md | 5 +++++ README.md | 8 ++++---- inst/include/RcppArray.h | 13 +++++++++++-- src/main.cpp | 2 -- 6 files changed, 31 insertions(+), 19 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Weber et al. (2021) <doi:10.18637/jss.v100.i19>
for details on applying this package while Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> explain details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Lukas A. Widmer [ctb] ,
Daniel Sabanes Bove [ctb] ,
Trustees of Columbia Univers [...truncated...]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.11-0 dated 2026-08-04 and 1.12-0 dated 2026-09-18
DESCRIPTION | 8 MD5 | 126 NAMESPACE | 58 NEWS.md | 66 R/RBesT-package.R | 15 R/asthma.R | 2 R/gMAP-center.R |only R/gMAP.R | 248 R/gMAP_draws.R | 4 R/integrate_gauss_quadrature.R | 16 R/mixjson.R | 68 R/sysdata.rda |binary build/partial.rdb |binary inst/REFERENCES.bib | 77 inst/doc/RBesT.pdf |binary inst/doc/introduction.html | 90 inst/sbc/calibration.md5 | 6 inst/sbc/sbc_report.html | 589 - inst/stan/gMAP.stan | 479 + man/RBesT-package.Rd | 15 man/asthma.Rd | 2 man/mixjson.Rd | 9 src/stanExports_gMAP.cc | 34 src/stanExports_gMAP.h | 3112 +++++++--- tests/testthat/fixtures-compact/gmap_binomial_covariate_mvn_model.json | 40 tests/testthat/fixtures-compact/gmap_binomial_covariate_mvn_theta.json | 176 tests/testthat/fixtures-compact/gmap_binomial_covariate_rows_mvn_model.json | 18 tests/testthat/fixtures-compact/gmap_binomial_covariate_rows_mvn_theta.json | 28 tests/testthat/fixtures-compact/gmap_binomial_covariate_rows_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_covariate_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_extreme_all_response_mvn_model.json | 18 tests/testthat/fixtures-compact/gmap_binomial_extreme_all_response_mvn_theta.json | 28 tests/testthat/fixtures-compact/gmap_binomial_extreme_all_response_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_extreme_no_response_mvn_model.json | 18 tests/testthat/fixtures-compact/gmap_binomial_extreme_no_response_mvn_theta.json | 28 tests/testthat/fixtures-compact/gmap_binomial_extreme_no_response_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_extreme_two_studies_mvn_model.json | 18 tests/testthat/fixtures-compact/gmap_binomial_extreme_two_studies_mvn_theta.json | 36 tests/testthat/fixtures-compact/gmap_binomial_extreme_two_studies_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_fixed_tau_generated_mvn_model.json | 10 tests/testthat/fixtures-compact/gmap_binomial_fixed_tau_generated_mvn_theta.json | 108 tests/testthat/fixtures-compact/gmap_binomial_fixed_tau_generated_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_fixed_tau_mvn_model.json | 10 tests/testthat/fixtures-compact/gmap_binomial_fixed_tau_mvn_theta.json | 108 tests/testthat/fixtures-compact/gmap_binomial_fixed_tau_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_noncontinuous_studies_mvn_model.json | 18 tests/testthat/fixtures-compact/gmap_binomial_noncontinuous_studies_mvn_theta.json | 88 tests/testthat/fixtures-compact/gmap_binomial_noncontinuous_studies_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_single_trial_mvn_model.json | 20 tests/testthat/fixtures-compact/gmap_binomial_single_trial_mvn_theta.json | 12 tests/testthat/fixtures-compact/gmap_binomial_single_trial_spec.R | 2 tests/testthat/fixtures-compact/gmap_binomial_tau_strata_rows_mvn_model.json | 10 tests/testthat/fixtures-compact/gmap_binomial_tau_strata_rows_mvn_theta.json | 26 tests/testthat/fixtures-compact/gmap_binomial_tau_strata_rows_spec.R | 4 tests/testthat/fixtures-mcmc-src/gmap_s2z_prior_pd_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_stepsize_ad95_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_stepsize_ad99_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_switch_off_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_switch_on_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_verbose_binomial_ncp_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_zeta_binomial_cp_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_zeta_binomial_ncp_fixture.R |only tests/testthat/fixtures-mcmc-src/gmap_s2z_zeta_normal_ncp_fixture.R |only tests/testthat/helper-compressed-fixtures.R | 6 tests/testthat/helper-s2z.R |only tests/testthat/test-gMAP-compact-fixtures.R | 4 tests/testthat/test-gMAP-quadrature-approximation.R |only tests/testthat/test-gMAP-s2z-center.R |only tests/testthat/test-gMAP-s2z.R |only tests/testthat/test-mixjson.R | 109 vignettes/REFERENCES.bib | 77 71 files changed, 4350 insertions(+), 1710 deletions(-)
Title: Selecting Variable Subsets
Description: A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria. Theoretical support for the heuristic search methods and exploratory data analysis criteria is in Cadima, Cerdeira, Minhoto (2003, <doi:10.1016/j.csda.2003.11.001>). Theoretical support for the leap and bounds algorithm and the criteria for the general multivariate linear model is in Duarte Silva (2001, <doi:10.1006/jmva.2000.1920>). There is a package vignette "subselect", which includes additional references.
Author: Jorge Orestes Cerdeira [aut],
Pedro Duarte Silva [aut, cre],
Jorge Cadima [aut],
Manuel Minhoto [aut]
Maintainer: Pedro Duarte Silva <psilva@ucp.pt>
Diff between subselect versions 0.16.1 dated 2026-05-04 and 0.16.2 dated 2026-09-18
DESCRIPTION | 8 ++++---- MD5 | 44 ++++++++++++++++++++++---------------------- R/anneal.R | 2 +- R/ccr12.R | 2 +- R/eleaps.R | 2 +- R/genetic.R | 2 +- R/improve.R | 2 +- R/tau2.R | 2 +- R/wald.R | 2 +- R/xi2.R | 2 +- R/zeta2.R | 2 +- build/vignette.rds |binary inst/doc/subselect.R | 2 -- inst/doc/subselect.pdf |binary man/anneal.Rd | 2 +- man/ccr12.Rd | 2 +- man/eleaps.Rd | 2 +- man/genetic.Rd | 2 +- man/improve.Rd | 2 +- man/tau2.Rd | 2 +- man/wald.Rd | 2 +- man/xi2.Rd | 2 +- man/zeta2.Rd | 2 +- 23 files changed, 44 insertions(+), 46 deletions(-)
Title: An Interface to IBGE's SIDRA API
Description: Provides a flexible interface to discover, inspect, plan, and
retrieve aggregate data from the Brazilian Institute of Geography and
Statistics (IBGE) through its SIDRA application programming interfaces.
SIDRA is IBGE's system for retrieving aggregate statistical data.
Author: Renato Prado Siqueira [aut, cre]
Maintainer: Renato Prado Siqueira <rpradosiqueira@gmail.com>
Diff between sidrar versions 0.5.0 dated 2026-08-25 and 0.5.1 dated 2026-09-18
DESCRIPTION | 6 - MD5 | 35 +++--- NEWS.md | 14 ++ R/collect.R | 21 ++- R/fallback.R |only R/get_sidra.R | 30 ++++- R/utils.R | 51 ++++++++ README.md | 36 ++++++ inst/doc/Introduction_to_sidrar.Rmd | 15 ++ inst/doc/Introduction_to_sidrar.html | 17 ++ man/get_sidra.Rd | 14 ++ man/sidra_collect.Rd | 4 man/sidra_provenance.Rd | 2 tests/testthat/helper-fixtures.R | 8 + tests/testthat/test-collect.R | 47 ++++++++ tests/testthat/test-fallback-integration.R |only tests/testthat/test-fallback.R |only tests/testthat/test-live-api.R | 15 ++ tests/testthat/test-utils.R | 168 +++++++++++++++++++++++++++++ vignettes/Introduction_to_sidrar.Rmd | 15 ++ 20 files changed, 467 insertions(+), 31 deletions(-)
Title: Processing and Analyzing Amplicon Sequence Data
Description: Processing and analysis of targeted sequencing data. The package provides a user-friendly interface for core 'VSEARCH' (Rognes et al. (2016), <doi:10.7717/peerj.2584>) functions, in addition to tools for visualization and parameter tuning.
Author: Cassandra Stamsaas [cre, aut],
Lars Snipen [aut],
Torbjoern Rognes [aut],
Hilde Vinje [aut]
Maintainer: Cassandra Stamsaas <cassandra.stamsaas@nmbu.no>
Diff between Rsearch versions 1.1.0 dated 2026-07-20 and 1.2.0 dated 2026-09-18
DESCRIPTION | 8 ++++---- MD5 | 33 +++++++++++++++++---------------- NAMESPACE | 6 ++++-- NEWS.md | 12 ++++++++++++ R/vs_fastq_join.R | 5 ----- R/vs_fastq_mergepairs.R | 9 ++------- R/vs_fastx_trim_filt.R | 11 +++-------- R/vs_merging_lengths.R | 4 ++-- R/vs_optimize_truncee_rate.R | 2 +- R/vs_optimize_truncqual.R | 2 +- README.md | 4 +++- inst/CITATION |only man/vs_fastq_join.Rd | 5 ----- man/vs_fastq_mergepairs.Rd | 9 ++------- man/vs_fastx_trim_filt.Rd | 11 +++-------- man/vs_merging_lengths.Rd | 4 ++-- man/vs_optimize_truncee_rate.Rd | 2 +- man/vs_optimize_truncqual.Rd | 2 +- 18 files changed, 58 insertions(+), 71 deletions(-)
Title: Model Context Protocol Servers and Clients
Description: Implements the Model Context Protocol (MCP). Users can start
'R'-based servers, serving functions as tools for large language
models to call before responding to the user in MCP-compatible apps
like 'Claude Desktop' and 'Claude Code', with options to run those
tools inside of interactive 'R' sessions. On the other end, when 'R'
is the client via the 'ellmer' package, users can register tools from
third-party MCP servers to integrate additional context into chats.
Author: Simon Couch [aut, cre] ,
Winston Chang [aut] ,
Charlie Gao [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Simon Couch <simon.couch@posit.co>
Diff between mcptools versions 1.0.2 dated 2026-08-22 and 1.0.3 dated 2026-09-18
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test-socket-dir.R | 5 ++++- 4 files changed, 14 insertions(+), 7 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 1.4.1 dated 2026-07-13 and 1.4.2 dated 2026-09-18
DESCRIPTION | 12 MD5 | 122 ++++++-- NAMESPACE | 1 NEWS.md | 12 R/RcppExports.R | 18 + R/baseline_table.R | 38 +- R/classif_model_compare.R | 124 +++----- R/extract_history.R | 49 +-- R/interactions.R | 24 - R/misc.R | 21 - R/time_roc.R | 13 R/utils.R | 27 + inst/doc/baseline-table.html | 8 inst/doc/data-cleaning.html | 180 ++++++------ inst/doc/model-evaluation.html | 20 + man/extract_history.Rd | 3 man/extract_history_single.Rd | 45 +-- man/get_var_types.Rd | 5 man/mov_sort_cpp.Rd |only man/test_normality.Rd | 10 man/theme_pub.Rd |only src/RcppExports.cpp | 13 src/merge_ordered_vectors.cpp |only tests/testthat/_snaps/baseline_table.md | 372 ++++++++++++------------- tests/testthat/_snaps/classif_model_compare.md | 20 - tests/testthat/test-baseline_table.R | 26 + tests/testthat/test-extract_history.R | 12 tools/build_skill_docs.R |only tools/skill_docs |only 29 files changed, 684 insertions(+), 491 deletions(-)
Title: Spatial Network Analysis
Description: Interface package for 'sala', the spatial network analysis library
from the 'depthmapX' software application. The R parts of the code are based
on the 'rdepthmap' package. Allows for the analysis of urban and
building-scale networks and provides metrics and methods usually found
within the Space Syntax domain. Methods in this package are described by K.
Al-Sayed, A. Turner, B. Hillier, S. Iida and A. Penn (2014) "Space Syntax
methodology", and also by A. Turner (2004)
<https://discovery.ucl.ac.uk/id/eprint/2651> "Depthmap 4: a researcher's
handbook".
Author: Petros Koutsolampros [cre, aut] ,
Fani Kostourou [ctb] ,
Kimon Krenz [ctb] ,
Alasdair Turner [ctb] ,
Tasos Varoudis [ctb] ,
Christian Sailer [ctb] ,
Eva Friedrich [ctb] ,
University College London [fnd, cph] ,
Spacelab UK [fnd]
Maintainer: Petros Koutsolampros <r-devel@pklampros.net>
Diff between alcyon versions 0.9.0 dated 2026-08-29 and 0.10.0 dated 2026-09-18
DESCRIPTION | 6 MD5 | 440 +++++------ NEWS.md | 13 R/agentAnalysis.R | 6 configure | 5 configure.ac | 5 configure.win | 22 inst/WORDLIST | 2 man/agentAnalysis.Rd | 2 src/Makevars.in | 9 src/Makevars.win | 10 src/analysis_agent.cpp | 6 src/analysis_axial.cpp | 16 src/analysis_vgaShortestPath.cpp | 6 src/communicator.hpp | 14 src/helper_attr.hpp | 3 src/libs/CMakeLists.txt | 31 src/libs/salalib/CMakeLists.txt | 37 src/libs/salalib/REUSE.toml | 3 src/libs/salalib/agents/CMakeLists.txt | 4 src/libs/salalib/agents/agent.cpp | 127 +-- src/libs/salalib/agents/agent.hpp | 37 src/libs/salalib/agents/agentanalysis.cpp | 14 src/libs/salalib/agents/agentanalysis.hpp | 12 src/libs/salalib/agents/agentprogram.cpp | 41 - src/libs/salalib/agents/agentprogram.hpp | 5 src/libs/salalib/alllinemap.cpp | 11 src/libs/salalib/alllinemap.hpp | 9 src/libs/salalib/analysisresult.hpp | 29 src/libs/salalib/attributemap.hpp | 6 src/libs/salalib/attributetable.cpp | 53 - src/libs/salalib/attributetable.hpp | 42 - src/libs/salalib/attributetablehelpers.hpp | 5 src/libs/salalib/attributetableindex.cpp | 15 src/libs/salalib/attributetableindex.hpp | 3 src/libs/salalib/attributetableview.cpp | 3 src/libs/salalib/attributetableview.hpp | 1 src/libs/salalib/axialminimiser.cpp | 6 src/libs/salalib/axialminimiser.hpp | 6 src/libs/salalib/axialmodules/CMakeLists.txt | 10 src/libs/salalib/axialmodules/axialintegration.cpp | 24 src/libs/salalib/axialmodules/axialintegration.hpp | 44 - src/libs/salalib/axialmodules/axiallocal.cpp | 3 src/libs/salalib/axialmodules/axiallocal.hpp | 6 src/libs/salalib/axialmodules/axialstepdepth.cpp | 1 src/libs/salalib/axialmodules/axialstepdepth.hpp | 10 src/libs/salalib/axialpolygons.cpp | 15 src/libs/salalib/axialpolygons.hpp | 6 src/libs/salalib/connector.cpp | 1 src/libs/salalib/connector.hpp | 2 src/libs/salalib/displayparams.hpp | 1 src/libs/salalib/entityparsing.cpp | 3 src/libs/salalib/entityparsing.hpp | 2 src/libs/salalib/exportutils.cpp | 1 src/libs/salalib/fileproperties.hpp | 5 src/libs/salalib/genlib/CMakeLists.txt | 2 src/libs/salalib/genlib/bsptree.cpp | 5 src/libs/salalib/genlib/bsptree.hpp | 3 src/libs/salalib/genlib/comm.hpp | 11 src/libs/salalib/genlib/containerutils.hpp | 1 src/libs/salalib/genlib/edgeu.cpp | 1 src/libs/salalib/genlib/edgeu.hpp | 1 src/libs/salalib/genlib/event2f.hpp | 1 src/libs/salalib/genlib/exceptions.hpp | 1 src/libs/salalib/genlib/line4f.cpp | 136 +-- src/libs/salalib/genlib/line4f.hpp | 20 src/libs/salalib/genlib/pafmath.cpp | 3 src/libs/salalib/genlib/pafmath.hpp | 11 src/libs/salalib/genlib/point2f.cpp | 3 src/libs/salalib/genlib/point2f.hpp | 2 src/libs/salalib/genlib/point3f.hpp | 3 src/libs/salalib/genlib/poly.cpp | 2 src/libs/salalib/genlib/poly.hpp | 2 src/libs/salalib/genlib/readwritehelpers.hpp | 1 src/libs/salalib/genlib/region4f.cpp | 1 src/libs/salalib/genlib/region4f.hpp | 3 src/libs/salalib/genlib/regiontree.cpp | 2 src/libs/salalib/genlib/regiontree.hpp | 1 src/libs/salalib/genlib/simplematrix.hpp | 1 src/libs/salalib/genlib/stringutils.cpp | 6 src/libs/salalib/genlib/xmlparse.cpp | 12 src/libs/salalib/genlib/xmlparse.hpp | 4 src/libs/salalib/geometrygenerators.cpp | 43 - src/libs/salalib/geometrygenerators.hpp | 1 src/libs/salalib/ianalysis.hpp | 17 src/libs/salalib/importtypedefs.hpp | 1 src/libs/salalib/importutils.cpp | 4 src/libs/salalib/importutils.hpp | 5 src/libs/salalib/isovist.cpp | 43 - src/libs/salalib/isovist.hpp | 4 src/libs/salalib/isovistdef.hpp | 1 src/libs/salalib/isovistutils.hpp | 6 src/libs/salalib/latticemap.cpp | 24 src/libs/salalib/latticemap.hpp | 14 src/libs/salalib/layermanager.hpp | 3 src/libs/salalib/layermanagerimpl.cpp | 7 src/libs/salalib/layermanagerimpl.hpp | 5 src/libs/salalib/linkutils.cpp | 5 src/libs/salalib/linkutils.hpp | 2 src/libs/salalib/mapconverter.cpp | 10 src/libs/salalib/mapconverter.hpp | 6 src/libs/salalib/metagraph.hpp | 6 src/libs/salalib/metagraphreadwrite.cpp | 12 src/libs/salalib/metagraphreadwrite.hpp | 9 src/libs/salalib/mgraph_consts.hpp | 1 src/libs/salalib/ngraph.cpp | 8 src/libs/salalib/ngraph.hpp | 3 src/libs/salalib/pafcolor.cpp | 38 src/libs/salalib/pafcolor.hpp | 2 src/libs/salalib/parsers/CMakeLists.txt | 12 src/libs/salalib/parsers/dxfp.cpp | 5 src/libs/salalib/parsers/dxfp.hpp | 6 src/libs/salalib/parsers/mapinfodata.cpp | 16 src/libs/salalib/parsers/mapinfodata.hpp | 5 src/libs/salalib/parsers/ntfp.cpp | 3 src/libs/salalib/parsers/ntfp.hpp | 2 src/libs/salalib/parsers/tigerp.cpp | 5 src/libs/salalib/parsers/tigerp.hpp | 1 src/libs/salalib/pixelbase.cpp | 32 src/libs/salalib/pixelbase.hpp | 2 src/libs/salalib/pixelref.hpp | 4 src/libs/salalib/point.cpp | 2 src/libs/salalib/point.hpp | 5 src/libs/salalib/pushvalues.cpp | 102 +- src/libs/salalib/pushvalues.hpp | 66 - src/libs/salalib/salaprogram.cpp | 13 src/libs/salalib/salaprogram.hpp | 5 src/libs/salalib/salashape.cpp | 16 src/libs/salalib/salashape.hpp | 2 src/libs/salalib/segmmodules/CMakeLists.txt | 26 src/libs/salalib/segmmodules/segmangular.cpp | 11 src/libs/salalib/segmmodules/segmangular.hpp | 13 src/libs/salalib/segmmodules/segmhelpers.hpp | 4 src/libs/salalib/segmmodules/segmmetric.cpp | 21 src/libs/salalib/segmmodules/segmmetric.hpp | 14 src/libs/salalib/segmmodules/segmmetricpd.cpp | 24 src/libs/salalib/segmmodules/segmmetricpd.hpp | 9 src/libs/salalib/segmmodules/segmmetricshortestpath.cpp | 22 src/libs/salalib/segmmodules/segmmetricshortestpath.hpp | 7 src/libs/salalib/segmmodules/segmtopological.cpp | 16 src/libs/salalib/segmmodules/segmtopological.hpp | 14 src/libs/salalib/segmmodules/segmtopologicalpd.cpp | 10 src/libs/salalib/segmmodules/segmtopologicalpd.hpp | 9 src/libs/salalib/segmmodules/segmtopologicalshortestpath.cpp | 9 src/libs/salalib/segmmodules/segmtopologicalshortestpath.hpp | 7 src/libs/salalib/segmmodules/segmtulip.cpp | 81 +- src/libs/salalib/segmmodules/segmtulip.hpp | 29 src/libs/salalib/segmmodules/segmtulipdepth.cpp | 15 src/libs/salalib/segmmodules/segmtulipdepth.hpp | 9 src/libs/salalib/segmmodules/segmtulipleafchoice.cpp | 72 + src/libs/salalib/segmmodules/segmtulipleafchoice.hpp | 23 src/libs/salalib/segmmodules/segmtulipshortestpath.cpp | 15 src/libs/salalib/segmmodules/segmtulipshortestpath.hpp | 8 src/libs/salalib/shapegraph.cpp | 14 src/libs/salalib/shapegraph.hpp | 11 src/libs/salalib/shapemap.cpp | 39 src/libs/salalib/shapemap.hpp | 14 src/libs/salalib/shapemapgroupdata.cpp | 5 src/libs/salalib/shapemapgroupdata.hpp | 6 src/libs/salalib/shaperef.hpp | 1 src/libs/salalib/spacepixel.cpp | 13 src/libs/salalib/spacepixel.hpp | 4 src/libs/salalib/sparksieve2.cpp | 1 src/libs/salalib/sparksieve2.hpp | 4 src/libs/salalib/tidylines.cpp | 5 src/libs/salalib/tidylines.hpp | 4 src/libs/salalib/tolerances.hpp | 1 src/libs/salalib/vgamodules/CMakeLists.txt | 44 - src/libs/salalib/vgamodules/extractlinkdata.hpp | 7 src/libs/salalib/vgamodules/ivga.hpp | 9 src/libs/salalib/vgamodules/ivgaangular.hpp | 16 src/libs/salalib/vgamodules/ivgametric.hpp | 39 src/libs/salalib/vgamodules/ivgatraversing.hpp | 4 src/libs/salalib/vgamodules/ivgavisual.hpp | 7 src/libs/salalib/vgamodules/vgaangular.cpp | 12 src/libs/salalib/vgamodules/vgaangular.hpp | 18 src/libs/salalib/vgamodules/vgaangulardepth.cpp | 5 src/libs/salalib/vgamodules/vgaangulardepth.hpp | 9 src/libs/salalib/vgamodules/vgaangularopenmp.cpp | 11 src/libs/salalib/vgamodules/vgaangularopenmp.hpp | 19 src/libs/salalib/vgamodules/vgaangularshortestpath.cpp | 9 src/libs/salalib/vgamodules/vgaangularshortestpath.hpp | 7 src/libs/salalib/vgamodules/vgaisovist.cpp | 26 src/libs/salalib/vgamodules/vgaisovist.hpp | 11 src/libs/salalib/vgamodules/vgaisovistzone.cpp | 9 src/libs/salalib/vgamodules/vgaisovistzone.hpp | 17 src/libs/salalib/vgamodules/vgametric.cpp | 31 src/libs/salalib/vgamodules/vgametric.hpp | 19 src/libs/salalib/vgamodules/vgametricdepth.cpp | 30 src/libs/salalib/vgamodules/vgametricdepth.hpp | 9 src/libs/salalib/vgamodules/vgametricdepthlinkcost.cpp | 7 src/libs/salalib/vgamodules/vgametricdepthlinkcost.hpp | 8 src/libs/salalib/vgamodules/vgametricopenmp.cpp | 11 src/libs/salalib/vgamodules/vgametricopenmp.hpp | 22 src/libs/salalib/vgamodules/vgametricshortestpath.cpp | 34 src/libs/salalib/vgamodules/vgametricshortestpath.hpp | 10 src/libs/salalib/vgamodules/vgametricshortestpathtomany.cpp | 16 src/libs/salalib/vgamodules/vgametricshortestpathtomany.hpp | 14 src/libs/salalib/vgamodules/vgathroughvision.cpp | 13 src/libs/salalib/vgamodules/vgathroughvision.hpp | 8 src/libs/salalib/vgamodules/vgavisualglobal.cpp | 48 - src/libs/salalib/vgamodules/vgavisualglobal.hpp | 16 src/libs/salalib/vgamodules/vgavisualglobaldepth.cpp | 7 src/libs/salalib/vgamodules/vgavisualglobaldepth.hpp | 9 src/libs/salalib/vgamodules/vgavisualglobalopenmp.cpp | 23 src/libs/salalib/vgamodules/vgavisualglobalopenmp.hpp | 15 src/libs/salalib/vgamodules/vgavisuallocal.cpp | 23 src/libs/salalib/vgamodules/vgavisuallocal.hpp | 7 src/libs/salalib/vgamodules/vgavisuallocaladjmatrix.cpp | 7 src/libs/salalib/vgamodules/vgavisuallocaladjmatrix.hpp | 9 src/libs/salalib/vgamodules/vgavisuallocalopenmp.cpp | 11 src/libs/salalib/vgamodules/vgavisuallocalopenmp.hpp | 9 src/libs/salalib/vgamodules/vgavisualshortestpath.cpp | 6 src/libs/salalib/vgamodules/vgavisualshortestpath.hpp | 8 src/process_convertExternal.cpp | 8 src/process_convertInternal.cpp | 8 src/process_isovist.cpp | 2 src/rcpp_AllLineMap.cpp | 2 src/rcpp_LatticeMap.cpp | 34 src/rcpp_ShapeGraph.cpp | 26 src/rcpp_ShapeMap.cpp | 21 221 files changed, 2036 insertions(+), 1386 deletions(-)
Title: User-Friendly Tables with Color Helpers for Data Exploration
Description: Make it easy to deal with multiple cross-tables in data exploration, by
creating them, manipulating them, and adding color helpers to highlight deviations
(differences from totals, comparisons between lines or columns, contributions to
variance, odds ratios, etc.) and significance (confidence intervals, stars, etc.).
Create the same kind of tables for regression models, with a framework to compare
model effects with their crude/observed counterpart systematically.
All functions render data frames which can be easily manipulated.
All tables can be exported with formats and colors to 'Excel', html and markdown.
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@protonmail.com>
Diff between tabxplor versions 2.0.0 dated 2026-08-29 and 2.0.1 dated 2026-09-18
DESCRIPTION | 8 MD5 | 285 ++-- NAMESPACE | 13 NEWS.md | 75 + R/fmt_class.R | 1613 ++-------------------- R/jmvtab-cache.R | 8 R/jmvtab-export.R | 91 + R/jmvtab.b.R | 7 R/jmvtab.h.R | 64 R/jmvtabreg-cache.R | 4 R/jmvtabreg.b.R | 7 R/jmvtabreg.h.R | 67 R/plots.R | 13 R/reg-assumptions.R | 51 R/reg-cross.R | 2 R/reg-empirical.R | 12 R/reg-estimand.R | 12 R/row-model.R | 77 - R/survey-design.R | 8 R/tab-args.R | 14 R/tab-css.R | 169 ++ R/tab-display.R | 197 ++ R/tab-export-prep.R | 466 ++++-- R/tab-export.R | 5 R/tab-footer.R |only R/tab-leaf.R | 19 R/tab-legend.R |only R/tab-options.R | 57 R/tab-palettes.R | 27 R/tab-render-html.R | 202 +- R/tab-resolve.R | 47 R/tab-steps-legacy.R | 11 R/tab-test-display.R | 10 R/tab-tooltip.R | 2 R/tab-transpose-render.R | 16 R/tab-xl-backend.R | 14 R/tab.R | 39 R/tab_classes.R | 702 ++++++++-- R/tab_md.R | 172 +- R/tab_reg.R | 64 R/tab_xl.R | 189 +- R/utils.R | 144 +- R/zzz-fact-keys.R | 25 README.md | 50 inst/doc/tabxplor-programming.Rmd | 4 inst/doc/tabxplor-programming.html | 147 ++ inst/doc/tabxplor-reading-a-regression.Rmd | 6 inst/doc/tabxplor-reading-a-regression.html | 537 +++++-- inst/doc/tabxplor-reg.R | 2 inst/doc/tabxplor-reg.Rmd | 27 inst/doc/tabxplor-reg.html | 1185 +++++++++------- inst/doc/tabxplor-weights.html | 132 + inst/doc/tabxplor.Rmd | 6 inst/doc/tabxplor.html | 473 ++++-- inst/i18n/fr.json | 267 +-- inst/po/en@quot/LC_MESSAGES/R-tabxplor.mo |binary inst/po/fr/LC_MESSAGES/R-tabxplor.mo |binary inst/tabxplor-1.0/tabxplor.js | 10 man/fct_recode_helper.Rd | 27 man/fmt.Rd | 5 man/fmt_attributes.Rd | 4 man/fmt_fields.Rd | 17 man/new_tab.Rd | 38 man/print.tabxplor_md.Rd |only man/print.tabxplor_tab.Rd | 3 man/set_bars.Rd |only man/set_color_palette.Rd | 4 man/set_footer_tabs.Rd |only man/set_legend_words.Rd |only man/set_subtext.Rd |only man/tab.Rd | 7 man/tab_color_legend.Rd | 2 man/tab_css.Rd | 15 man/tab_footer_text.Rd |only man/tab_html.Rd | 20 man/tab_md.Rd | 22 man/tab_note.Rd |only man/tab_pipe.Rd |only man/tab_reg.Rd | 13 man/tab_xl.Rd | 9 man/tabxplor-display.Rd | 31 man/tabxplor-footer.Rd |only man/tabxplor-options.Rd | 7 po/R-fr.po | 1164 ++++++++-------- po/R-tabxplor.pot | 975 +++++++------ tests/testthat/_golden/f_all_pct.rds |binary tests/testthat/_golden/f_chi2.rds |binary tests/testthat/_golden/f_ci_cell.rds |binary tests/testthat/_golden/f_ci_diff.rds |binary tests/testthat/_golden/f_col_pct.rds |binary tests/testthat/_golden/f_col_ref_ci.rds |binary tests/testthat/_golden/f_col_ref_lvl.rds |binary tests/testthat/_golden/f_col_ref_multi.rds |binary tests/testthat/_golden/f_col_ref_or.rds |binary tests/testthat/_golden/f_col_ref_partial.rds |binary tests/testthat/_golden/f_color_afterci.rds |binary tests/testthat/_golden/f_color_contrib.rds |binary tests/testthat/_golden/f_color_diff.rds |binary tests/testthat/_golden/f_common_base.rds |binary tests/testthat/_golden/f_counts.rds |binary tests/testthat/_golden/f_merge2.rds |binary tests/testthat/_golden/f_or.rds |binary tests/testthat/_golden/f_ref_first.rds |binary tests/testthat/_golden/f_ref_named.rds |binary tests/testthat/_golden/f_row_pct.rds |binary tests/testthat/_golden/f_selfcross.rds |binary tests/testthat/_golden/f_subtab.rds |binary tests/testthat/_golden/f_totcol_each.rds |binary tests/testthat/_golden/m_multi.rds |binary tests/testthat/_golden/n_ci_tabvars.rds |binary tests/testthat/_golden/n_ci_tabvars_all.rds |binary tests/testthat/_golden/n_mean.rds |binary tests/testthat/_golden/n_mean_ci.rds |binary tests/testthat/_golden/n_mean_color.rds |binary tests/testthat/_golden/n_mean_sparse.rds |binary tests/testthat/_golden/n_mean_tottab.rds |binary tests/testthat/_golden/n_mean_w.rds |binary tests/testthat/_golden/totn_drop.rds |binary tests/testthat/_golden/totn_keep.rds |binary tests/testthat/_golden/totn_row_drop.rds |binary tests/testthat/_golden/w_weighted.rds |binary tests/testthat/_snaps/golden.md | 1894 ++++++++++++++++++++++++++- tests/testthat/_snaps/tab-render-html.md | 18 tests/testthat/test-edge-cases.R | 22 tests/testthat/test-fmt.R | 24 tests/testthat/test-i18n.R | 32 tests/testthat/test-jmvtab.R | 26 tests/testthat/test-reg-estimand.R | 10 tests/testthat/test-reg-influence.R | 2 tests/testthat/test-row-model.R | 35 tests/testthat/test-survey-design.R | 30 tests/testthat/test-tab-agg.R | 3 tests/testthat/test-tab-classes.R | 298 ++++ tests/testthat/test-tab-color.R | 80 - tests/testthat/test-tab-display.R | 115 + tests/testthat/test-tab-export-prep.R | 185 ++ tests/testthat/test-tab-footer.R |only tests/testthat/test-tab-legend.R |only tests/testthat/test-tab-md.R | 62 tests/testthat/test-tab-options.R | 28 tests/testthat/test-tab-palettes.R | 34 tests/testthat/test-tab-reg.R | 22 tests/testthat/test-tab-render-html.R | 98 + tests/testthat/test-tab-steps-legacy.R | 19 tests/testthat/test-tab-xl.R | 31 tests/testthat/test-utils.R | 6 vignettes/tabxplor-programming.Rmd | 4 vignettes/tabxplor-reading-a-regression.Rmd | 6 vignettes/tabxplor-reg.Rmd | 27 vignettes/tabxplor.Rmd | 6 150 files changed, 8767 insertions(+), 4567 deletions(-)
Title: Object-Oriented Interface for Offline Change-Point Detection
Description: A collection of efficient implementations of popular offline change-point detection algorithms, featuring a consistent, object-oriented interface for practical use.
Author: Minh Long Nguyen [aut, cre],
Toby Hocking [aut],
Charles Truong [aut]
Maintainer: Minh Long Nguyen <edelweiss611428@gmail.com>
Diff between rupturesRcpp versions 1.0.2 dated 2025-11-23 and 1.0.3 dated 2026-09-18
DESCRIPTION | 7 MD5 | 14 - R/zzz.R | 2 README.md | 11 - src/tmplBinSeg.cpp | 24 --- src/tmplPelt.cpp | 113 +++++--------- src/tmplWindow.cpp | 18 -- tests/testthat/test-segModule_PELT.R | 276 +++-------------------------------- 8 files changed, 91 insertions(+), 374 deletions(-)
Title: Generalized Pareto Distribution and Peaks Over Threshold
Description: Some functions useful to perform a Peak Over Threshold
analysis in univariate and bivariate cases, see Beirlant et al. (2004)
<doi:10.1002/0470012382>. A user guide is available in the vignette.
Author: Christophe Dutang [aut, cre] ,
Mathieu Ribatet [aut]
Maintainer: Christophe Dutang <dutangc@gmail.com>
Diff between POT versions 1.1-11 dated 2024-10-17 and 1.1-12 dated 2026-09-18
POT-1.1-11/POT/inst/ChangeLog |only POT-1.1-12/POT/DESCRIPTION | 15 ++++++--- POT-1.1-12/POT/MD5 | 38 +++++++++++++---------- POT-1.1-12/POT/NAMESPACE | 7 +++- POT-1.1-12/POT/R/graph-qqpareto.R |only POT-1.1-12/POT/R/uvgev-gen-retlev.R |only POT-1.1-12/POT/build/vignette.rds |binary POT-1.1-12/POT/inst/ChangeLog.md |only POT-1.1-12/POT/inst/doc/POT.R | 2 - POT-1.1-12/POT/inst/doc/POT.Rnw | 14 ++++---- POT-1.1-12/POT/inst/doc/POT.pdf |binary POT-1.1-12/POT/man/POT-pkg.Rd | 53 ++++++++++++++++++++++++++++++++- POT-1.1-12/POT/man/fitBvGPD.Rd | 22 +++++++++---- POT-1.1-12/POT/man/fitGPD.Rd | 28 +++++++++++------ POT-1.1-12/POT/man/fitMcGPD.Rd | 23 +++++++++++--- POT-1.1-12/POT/man/fitPP.Rd | 26 ++++++++++++++++ POT-1.1-12/POT/man/qqpareto.Rd |only POT-1.1-12/POT/man/retlev.Rd | 21 +++++++++++-- POT-1.1-12/POT/tests/t-fitbvgpd.R | 4 +- POT-1.1-12/POT/tests/t-fitmcgpd.R | 4 +- POT-1.1-12/POT/tests/t-fituvgpd.R | 16 ++++++++- POT-1.1-12/POT/tests/t-retlev-evdpkg.R |only POT-1.1-12/POT/vignettes/POT.Rnw | 14 ++++---- 23 files changed, 218 insertions(+), 69 deletions(-)
Title: K-Sample Tests for Truncated and/or Censored Data
Description: Nonparametric analysis and comparison of distributions
under left truncation and right censoring. The package includes simulation
routines for truncated and/or censored survival data, nonparametric
distribution comparison methods based on Kolmogorov-Smirnov-type and
Cramér-von Mises-type statistics, and bootstrap routines for p-value
approximation. For methodological details, see Lago, de Uña-Álvarez and
Pardo-Fernández (2025) <doi:10.1007/s11749-024-00948-4>
and Lago, Pardo-Fernández and de Uña-Álvarez (2026)
<doi:10.1007/s10985-026-09713-1>.
Author: Adrian Lago [aut, cre],
Jacobo de Una-Alvarez [aut],
Juan Carlos Pardo-Fernandez [aut]
Maintainer: Adrian Lago <adrian.lago@uvigo.gal>
Diff between ksamplesLTRC versions 0.1.0 dated 2026-07-30 and 0.1.1 dated 2026-09-18
DESCRIPTION | 15 +++++++++------ MD5 | 20 ++++++++++++-------- NAMESPACE | 14 +++++++++----- NEWS.md | 19 +++++++++++++++++++ R/auto_test.R | 9 --------- R/lt_cvm.R | 2 +- R/lt_truncation_estimator.R | 4 ++-- R/ltrc_cvm.R | 2 +- inst/doc/ksamplesLTRC.html | 4 ++-- tests/testthat/test-estimators.R |only tests/testthat/test-simulation.R |only tests/testthat/test-summary-plot.R |only tests/testthat/test-tests.R |only 13 files changed, 55 insertions(+), 34 deletions(-)
Title: Calculate Heat Stress Indices
Description: Calculates heat-stress indices from meteorological observations,
including the physically based wet-bulb globe temperature model described
by Liljegren et al. (2008) <doi:10.1080/15459620802310770>. The package
provides an independently maintained R implementation with row-level
diagnostics, configurable physical controls, and batch processing for the
Liljegren method; it is not a bitwise-compatible port of the original
program, and cross-implementation differences are expected.
Author: Yifei Zheng [aut, cre] ,
Ana Casanueva [aut]
Maintainer: Yifei Zheng <zyf0717@gmail.com>
Diff between HeatStressR versions 2.2.1 dated 2026-08-07 and 2.4.0 dated 2026-09-18
DESCRIPTION | 10 - MD5 | 42 +++--- NEWS | 23 +++ R/HeatStressR.R | 2 R/heat_indices.R | 17 +- R/wbgt-parallel.R | 151 ++++++++++++++----------- R/wbgt.Liljegren.R | 104 +++++++---------- README.md | 22 ++- inst/CITATION | 5 inst/doc/README.md | 4 inst/doc/benchmarking.md | 5 inst/doc/liljegren-inputs.md | 10 + inst/doc/non-liljegren-indices.md | 7 - inst/doc/parallelism.md | 22 +-- man/HeatStressR.Rd | 2 man/heat_indices.Rd | 18 +- man/wbgt.Liljegren.Rd | 19 +-- tests/testthat/test.liljegren-solar-geometry.R |only tests/testthat/test.non-liljegren-kernels.R | 6 tests/testthat/test.wbgt-batch-solvers.R | 4 tests/testthat/test.wbgt-diagnostics.R | 26 ++++ tests/testthat/test.wbgt-parallel.R | 73 +++++++----- tests/testthat/test.wbgt-preprocessing.R |only 23 files changed, 343 insertions(+), 229 deletions(-)
Title: Wearable Accelerometer Data File Readers
Description: Reads data collected from wearable acceleratometers as used in sleep and physical activity research. Currently supports file formats: binary data from 'GENEActiv' <https://activinsights.com/>, .bin-format from GENEA devices (not for sale), and .cwa-format from 'Axivity' <https://axivity.com>. Further, it has functions for reading text files with epoch level aggregates from 'Actical', 'Fitbit', 'Actiwatch', 'ActiGraph', and 'PhilipsHealthBand'. Primarily designed to complement R package GGIR <https://CRAN.R-project.org/package=GGIR>.
Author: Vincent T van Hees [aut, cre],
Patrick Bos [aut] ,
Lena Kushleyeva [ctb],
Jing Hua Zhao [ctb],
Evgeny Mirkes [ctb],
Dan Jackson [ctb],
Jairo H Migueles [ctb],
John Muschelli [ctb],
Jia Ying Chua [ctb],
Medical Research Council UK [cph, fnd],
Acceltin [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIRread versions 1.0.10 dated 2026-08-26 and 1.0.11 dated 2026-09-18
DESCRIPTION | 10 ++++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/readGENEActiv.R | 31 ++++++++++++++++++++++++++----- man/GGIRread-package.Rd | 4 ++-- man/readGENEActiv.Rd | 20 ++++++++++++++------ 6 files changed, 57 insertions(+), 22 deletions(-)
Title: Offline Taxonomic Name Matching Against Darwin Core Backbones
Description: Match taxonomic names against locally stored Darwin Core backbone
databases ('WFO', 'COL', 'GBIF', 'ITIS', 'NCBI Taxonomy', 'Open Tree of Life',
'WoRMS', 'Euro+Med', 'Species Fungorum', 'AlgaeBase', 'FishBase',
'SeaLifeBase', 'Reptile Database', 'LCVP', 'WCVP',
'Mammal Diversity Database', 'AviList', 'LPSN'). Provides offline fuzzy and
exact matching with synonym resolution, hybrid name detection, and a unified
output schema across all sources. All heavy computation runs in the 'vectra'
C11 columnar engine.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between taxify versions 0.5.0 dated 2026-09-02 and 0.5.5 dated 2026-09-18
DESCRIPTION | 12 MD5 | 281 NAMESPACE | 6 NEWS.md | 349 R/add-alien-first-records.R | 157 R/add-bet.R | 158 R/add-bien.R | 152 R/add-data.R | 1302 +- R/add-ecoflora.R | 5 R/add-kew-sid.R | 122 R/add-leda.R | 157 R/add-trait.R | 737 - R/backbones.R | 44 R/backend.R | 364 R/backends-registry.R | 3 R/basionym.R |only R/browse.R | 1059 - R/cache.R | 601 - R/cite.R | 71 R/classification-tree.R | 520 R/clean.R | 1365 +- R/comm2sci.R | 593 - R/content-store.R | 104 R/disambiguate-authorship.R | 20 R/download.R | 252 R/downstream.R | 439 R/enrichment-meta.R | 37 R/enrichment-tr8.R | 360 R/enrichment.R | 415 R/id2name.R | 264 R/inspect.R | 1187 +- R/lock.R | 223 R/manifest.R | 127 R/parse-name.R | 35 R/pick.R | 212 R/reconcile.R | 262 R/region.R | 2212 ++-- R/register.R | 462 R/taxify-long.R | 431 R/taxify-package.R | 171 R/taxify-result.R | 104 R/taxify.R | 305 R/trait-provenance.R |only R/trait-registry.R | 196 R/upstream.R | 261 README.md | 12 inst/doc/enrichments.R | 16 inst/doc/enrichments.Rmd | 77 inst/doc/enrichments.html | 533 inst/doc/large-scale.Rmd | 18 inst/doc/large-scale.html | 40 inst/doc/regions.Rmd | 532 inst/doc/regions.html | 13 inst/exampledb/enrichment/alien_first_records/latest/alien_first_records.vtr |binary inst/exampledb/enrichment/alien_first_records/latest/meta.json | 40 inst/exampledb/enrichment/amphibio/latest/amphibio.vtr |binary inst/exampledb/enrichment/austraits/latest/austraits.vtr |binary inst/exampledb/enrichment/austraits/latest/austraits_references.vtr |only inst/exampledb/enrichment/austraits/latest/meta.json | 17 inst/exampledb/enrichment/bien/latest/bien.vtr |binary inst/exampledb/enrichment/brot/latest/brot.vtr |binary inst/exampledb/enrichment/brot/latest/brot_references.vtr |only inst/exampledb/enrichment/brot/latest/meta.json | 17 inst/exampledb/enrichment/elton_traits/latest/elton_traits.vtr |binary inst/exampledb/enrichment/fishbase/latest/fishbase.vtr |binary inst/exampledb/enrichment/gift/latest/gift.vtr |binary inst/exampledb/enrichment/gift/latest/gift_references.vtr |only inst/exampledb/enrichment/gift/latest/meta.json | 37 inst/exampledb/enrichment/leda/latest/leda.vtr |binary inst/exampledb/enrichment/leda/latest/leda_references.vtr |only inst/exampledb/enrichment/leda/latest/meta.json | 41 inst/exampledb/enrichment/sealifebase/latest/sealifebase.vtr |binary inst/manifest.json | 5392 +++++++++- man/add_alien_first_records.Rd | 51 man/add_bet.Rd | 5 man/add_bien.Rd | 16 man/add_data.Rd | 14 man/add_ecoflora.Rd | 5 man/add_leda.Rd | 31 man/add_trait.Rd | 30 man/backbone_fixed_kingdom.Rd |only man/basionym_placement.Rd |only man/children.Rd | 27 man/cite.Rd | 29 man/class2tree.Rd | 14 man/comm2sci.Rd | 37 man/downstream.Rd | 32 man/enrichment_groups.Rd | 2 man/id2name.Rd | 6 man/inspect.Rd | 24 man/install_backbones.Rd | 18 man/lookup_genus.Rd | 3 man/lowest_common.Rd | 5 man/normalize_kingdom_group.Rd |only man/parse_name.Rd | 7 man/reconcile.Rd | 9 man/sci2comm.Rd | 5 man/score_candidates.Rd | 21 man/synonyms.Rd | 8 man/taxify.Rd | 25 man/taxify_long.Rd | 5 man/taxify_pin.Rd |only man/taxify_regions.Rd | 2 man/taxify_restore.Rd | 17 man/upstream.Rd | 5 tests/testthat/test-abbrev.R | 462 tests/testthat/test-add-data.R | 911 - tests/testthat/test-add-trait.R | 1678 +-- tests/testthat/test-algaebase.R | 312 tests/testthat/test-backbone-content-id.R | 29 tests/testthat/test-backbone-refresh.R |only tests/testthat/test-backbones.R | 17 tests/testthat/test-basionym.R |only tests/testthat/test-clean.R | 677 - tests/testthat/test-col.R | 284 tests/testthat/test-cross-backbone-recovery.R | 47 tests/testthat/test-descendants.R |only tests/testthat/test-doors-all.R |only tests/testthat/test-download.R |only tests/testthat/test-empty-input.R |only tests/testthat/test-enrich-by-group-authorship.R | 45 tests/testthat/test-enrichment-content-id.R | 40 tests/testthat/test-enrichment-grain.R | 2 tests/testthat/test-enrichment-side-paths.R |only tests/testthat/test-euromed.R | 308 tests/testthat/test-exports-direct.R |only tests/testthat/test-fungorum.R | 312 tests/testthat/test-fuzzy-boundary.R | 57 tests/testthat/test-gap-verbs.R | 3 tests/testthat/test-gbif.R | 12 tests/testthat/test-infraspecific-match.R |only tests/testthat/test-inspect.R | 1018 + tests/testthat/test-itis.R | 558 - tests/testthat/test-lock-identity.R |only tests/testthat/test-match.R | 45 tests/testthat/test-meta.R | 281 tests/testthat/test-multi-backend.R | 859 - tests/testthat/test-ncbi.R | 310 tests/testthat/test-new-verbs.R | 4 tests/testthat/test-ott.R | 310 tests/testthat/test-pin.R |only tests/testthat/test-pinned-version.R |only tests/testthat/test-region-marine.R | 5 tests/testthat/test-region.R | 498 tests/testthat/test-session-memo.R |only tests/testthat/test-taxify-forwarding.R |only tests/testthat/test-taxify.R | 700 - tests/testthat/test-trait-provenance.R |only tests/testthat/test-untested-verbs.R | 621 - tests/testthat/test-verb-inputs.R |only tests/testthat/test-vtr-indexes.R |only tests/testthat/test-worms.R | 310 vignettes/enrichments.Rmd | 77 vignettes/large-scale.Rmd | 18 vignettes/regions.Rmd | 532 155 files changed, 20995 insertions(+), 13722 deletions(-)
Title: OIDC Authentication and OAuth Authorization for 'shiny'
Applications
Description: Provides a simple, configurable framework for 'OpenID Connect'
(OIDC) authentication and 'OAuth 2.0' authorization in 'shiny' applications
using 'S7' classes. Defines providers, clients, and tokens, as well
as various supporting functions and a 'shiny' module. Features include
cross-site request forgery (CSRF) protection, state encryption,
'Proof Key for Code Exchange' (PKCE) handling, validation of OIDC identity
tokens (nonces, signatures, claims), automatic user info retrieval for OIDC
and supported 'OAuth' providers, asynchronous flows,
and hooks for audit logging.
Author: Luka Koning [aut, cre, cph]
Maintainer: Luka Koning <koningluka@gmail.com>
Diff between shinyOAuth versions 0.6.0 dated 2026-09-17 and 0.6.1 dated 2026-09-18
DESCRIPTION | 6 MD5 | 738 - NEWS.md | 6 R/connection_credential_lifecycle.R | 438 R/connection_owner.R | 1524 +- R/connection_store.R | 680 R/custom_cache.R | 498 R/errors__constructors.R | 1940 +- R/errors__events.R | 840 - R/errors__trace.R | 236 R/methods__login.R | 7004 +++++----- R/methods__print.R | 894 - R/methods__token.R | 3912 ++--- R/oauth_connections_ui.R | 838 - R/oauth_form_post_ui.R | 3120 ++-- R/oauth_ui.R | 590 R/providers__apple.R | 344 R/shinyOAuth-package.R | 48 R/telemetry.R | 4034 ++--- R/use_shinyOAuth.R | 518 R/utils__audit_digest.R | 250 R/utils__base64url.R | 142 R/utils__callback_registry.R | 518 R/utils__client_resources.R | 102 R/utils__connection_credentials.R | 706 - R/utils__connection_router.R | 334 R/utils__crypt_primitives.R | 170 R/utils__crypt_state.R | 1332 - R/utils__diagnostic_text.R | 410 R/utils__dpop.R | 2230 +-- R/utils__endpoint_auth.R | 650 R/utils__expires.R | 708 - R/utils__http_audit.R | 790 - R/utils__http_media_type.R | 26 R/utils__http_requests.R | 1600 +- R/utils__jwks_fetch.R | 1984 +- R/utils__jwks_keys.R | 1554 +- R/utils__jwt_id_token.R | 1514 +- R/utils__jwt_jarm.R | 2176 +-- R/utils__jwt_jwe.R | 2032 +- R/utils__jwt_parse.R | 2016 +- R/utils__jwt_signing.R | 1720 +- R/utils__key_dependencies.R | 110 R/utils__managed_module.R | 132 R/utils__mtls.R | 1982 +- R/utils__oauth21.R | 664 R/utils__oauth_params.R | 1866 +- R/utils__random.R | 530 R/utils__refresh_scopes.R | 280 R/utils__resource_binding.R | 400 R/utils__scopes.R | 646 R/utils__shiny_context.R | 680 R/utils__shiny_dispatch.R | 774 - R/utils__shiny_otel.R | 1026 - R/utils__shiny_request_uri.R | 874 - R/utils__shiny_timers.R | 192 R/utils__tls.R | 282 R/utils__url_helpers.R | 2256 +-- R/utils__validators.R | 702 - R/zzz.R | 54 README.md | 328 build/vignette.rds |binary inst/doc/advanced-security.R | 544 inst/doc/advanced-security.html | 2117 +-- inst/doc/audit-logging.R | 32 inst/doc/audit-logging.Rmd | 978 - inst/doc/audit-logging.html | 2305 +-- inst/doc/authentication-flow.R | 18 inst/doc/authentication-flow.html | 1959 +- inst/doc/example-spotify.R | 108 inst/doc/example-spotify.Rmd | 242 inst/doc/example-spotify.html | 957 - inst/doc/multiple-authorizations.R | 394 inst/doc/multiple-authorizations.html | 1583 +- inst/doc/opentelemetry.R | 36 inst/doc/opentelemetry.Rmd | 1086 - inst/doc/opentelemetry.html | 2275 +-- inst/doc/package-options.R | 6 inst/doc/package-options.Rmd | 468 inst/doc/package-options.html | 1473 +- inst/doc/smart-on-fhir.R | 332 inst/doc/smart-on-fhir.html | 1675 +- inst/doc/usage.R | 396 inst/doc/usage.Rmd | 1270 - inst/doc/usage.html | 2085 +- inst/examples/client_bearer_req.R | 80 inst/examples/error_on_softened.R | 24 inst/examples/is_ok_host.R | 24 inst/examples/oauth_client_jarm.R | 76 inst/examples/oauth_form_post_ui.R | 110 inst/examples/oauth_module_server.R | 458 inst/examples/oauth_provider_microsoft.R | 244 inst/examples/spotify-dashboard.R | 2350 +-- inst/www/shinyOAuth.js | 480 man/OAuthClient.Rd | 1342 - man/OAuthProvider.Rd | 1082 - man/OAuthToken.Rd | 268 man/check_oauth21.Rd | 174 man/client_bearer_req.Rd | 180 man/custom_cache.Rd | 348 man/error_on_softened.Rd | 90 man/get_userinfo.Rd | 174 man/handle_callback.Rd | 202 man/introspect_token.Rd | 198 man/is_ok_host.Rd | 126 man/oauth_browser_owner.Rd | 256 man/oauth_client.Rd | 1218 - man/oauth_client_mtls_registration.Rd | 160 man/oauth_connection.Rd | 140 man/oauth_connection_store_memory.Rd | 158 man/oauth_connections.Rd | 302 man/oauth_connections_server.Rd | 280 man/oauth_connections_ui.Rd | 234 man/oauth_form_post_ui.Rd | 300 man/oauth_module_server.Rd | 938 - man/oauth_provider.Rd | 1066 - man/oauth_provider_apple.Rd | 122 man/oauth_provider_auth0.Rd | 58 man/oauth_provider_github.Rd | 54 man/oauth_provider_google.Rd | 66 man/oauth_provider_keycloak.Rd | 104 man/oauth_provider_microsoft.Rd | 348 man/oauth_provider_oidc.Rd | 258 man/oauth_provider_oidc_discover.Rd | 428 man/oauth_provider_okta.Rd | 62 man/oauth_provider_slack.Rd | 70 man/oauth_provider_spotify.Rd | 80 man/oauth_ui.Rd | 194 man/perform_client_bearer_req.Rd | 218 man/perform_resource_req.Rd | 314 man/prepare_call.Rd | 168 man/refresh_token.Rd | 292 man/resource_req.Rd | 314 man/revoke_token.Rd | 176 man/shinyOAuth-package.Rd | 58 man/smart_client.Rd | 326 man/smart_context.Rd | 152 man/smart_discover.Rd | 214 man/smart_launch_route.Rd | 158 man/use_shinyOAuth.Rd | 96 tests/browser-authorization-post.cjs | 84 tests/browser-cookie-ack.cjs | 84 tests/browser-cookie-tossing.cjs | 76 tests/browser-malformed-cookie.cjs | 126 tests/browser-origin-binding.cjs | 222 tests/testthat.R | 194 tests/testthat/fixtures/cran-0.5.0-arguments.json | 788 - tests/testthat/fixtures/mtls/ca-cert.pem | 44 tests/testthat/fixtures/mtls/client-cert.pem | 46 tests/testthat/fixtures/mtls/client-key.pem | 56 tests/testthat/fixtures/mtls/generate-san-fixtures.py | 50 tests/testthat/fixtures/mtls/numeric-dns-cert.pem | 36 tests/testthat/fixtures/mtls/typed-san-cert.pem | 38 tests/testthat/helper-async-daemon.R | 276 tests/testthat/helper-form-post-candidates.R | 240 tests/testthat/helper-jwk.R | 30 tests/testthat/helper-mtls.R | 168 tests/testthat/helper-otel.R | 388 tests/testthat/helper-shinytest2.R | 288 tests/testthat/helper-smart-client.R | 198 tests/testthat/teardown-chromote.R | 44 tests/testthat/teardown-otel.R | 2 tests/testthat/test-absolute-uri-syntax.R | 68 tests/testthat/test-absolute-url-validation.R | 620 tests/testthat/test-access-token-characters.R | 188 tests/testthat/test-access-token-duplicate-json.R | 56 tests/testthat/test-acr-enforcement.R | 1208 - tests/testthat/test-async-authorization.R | 618 tests/testthat/test-async-serialization.R | 466 tests/testthat/test-audit-async-options.R | 2804 ++-- tests/testthat/test-audit-async-session-context.R | 228 tests/testthat/test-audit-shiny-context.R | 724 - tests/testthat/test-audit-state-failures.R | 132 tests/testthat/test-auth-query-policy.R | 352 tests/testthat/test-auth-url-scope-reserved.R | 64 tests/testthat/test-authorization-context.R | 502 tests/testthat/test-base64url-helpers.R | 172 tests/testthat/test-basic.R | 48 tests/testthat/test-browser-authorization-post.R | 226 tests/testthat/test-browser-binding-reset.R | 134 tests/testthat/test-browser-bookmarks.R | 434 tests/testthat/test-browser-concurrent-bindings.R | 210 tests/testthat/test-browser-error.R | 70 tests/testthat/test-browser-malformed-cookie.R | 32 tests/testthat/test-browser-navigation.R | 298 tests/testthat/test-browser-origin-binding.R | 120 tests/testthat/test-browser-owner-admission.R | 98 tests/testthat/test-browser-owner-pending.R | 146 tests/testthat/test-browser-token-dos.R | 192 tests/testthat/test-browser-two-port.R | 174 tests/testthat/test-build-hygiene.R | 280 tests/testthat/test-cache-ttl-diagnostics.R | 82 tests/testthat/test-callback-fixed-query.R | 328 tests/testthat/test-claims-parameter.R | 912 - tests/testthat/test-client-assertion-alg-eddsa.R | 232 tests/testthat/test-client-bearer-req-headers.R | 84 tests/testthat/test-client-bearer-req-url-validation.R | 426 tests/testthat/test-client-jwt-defaults.R | 286 tests/testthat/test-client-resources.R | 382 tests/testthat/test-client-secret-basic-encoding.R | 122 tests/testthat/test-coerce-expires-in.R | 10 tests/testthat/test-connection-audit.R | 372 tests/testthat/test-connection-credentials.R | 382 tests/testthat/test-connection-identity.R | 328 tests/testthat/test-connection-request-object.R | 182 tests/testthat/test-connection-store.R | 516 tests/testthat/test-constant-time-compare.R | 162 tests/testthat/test-cookie-path.R | 178 tests/testthat/test-cookie-tossing.R | 32 tests/testthat/test-custom-cache.R | 174 tests/testthat/test-defaults-and-validation.R | 834 - tests/testthat/test-diagnostic-exposure.R | 724 - tests/testthat/test-discovery-auth-methods.R | 1804 +- tests/testthat/test-discovery-hardened.R | 1626 +- tests/testthat/test-discovery-issuer-mismatch.R | 464 tests/testthat/test-discovery-jarm-aliases.R | 126 tests/testthat/test-discovery-jose-case.R | 120 tests/testthat/test-endpoint-auth.R | 748 - tests/testthat/test-endpoint-condition-privacy.R | 284 tests/testthat/test-endpoint-event-redaction.R | 62 tests/testthat/test-error-response-state.R | 1022 - tests/testthat/test-errors-and-audit.R | 1948 +- tests/testthat/test-exact-list-access.R | 426 tests/testthat/test-example-callback-handlers.R | 252 tests/testthat/test-extra-headers.R | 58 tests/testthat/test-form-post-candidate-store.R | 510 tests/testthat/test-form-post-identical-candidates.R | 62 tests/testthat/test-form-post-module-transport.R | 366 tests/testthat/test-form-post-namespaces.R | 242 tests/testthat/test-form-post-response-mode.R | 4162 ++--- tests/testthat/test-get-callback-bridge.R | 626 tests/testthat/test-helper-otel.R | 98 tests/testthat/test-host-config-reminder.R | 40 tests/testthat/test-http-metadata-privacy.R | 186 tests/testthat/test-id-token-audience.R | 266 tests/testthat/test-id-token-claims.R | 592 tests/testthat/test-inbound-ed25519.R | 130 tests/testthat/test-input-validation-guards.R | 718 - tests/testthat/test-integration-authorization-assertions.R | 122 tests/testthat/test-integration-browser-startup.R | 144 tests/testthat/test-integration-error-policy.R | 176 tests/testthat/test-integration-runner.R | 322 tests/testthat/test-introspect-fallback.R | 12 tests/testthat/test-introspect-token.R | 56 tests/testthat/test-introspection-expiry.R | 50 tests/testthat/test-is_ok_host-review.R | 216 tests/testthat/test-issued-at-boundary.R | 148 tests/testthat/test-issued-at-independent-of-store-ttl.R | 48 tests/testthat/test-jar-jarm-live.R | 548 tests/testthat/test-jarm-compression.R | 38 tests/testthat/test-jose-header-fields.R | 754 - tests/testthat/test-jwe-cbc-hmac-vectors.R | 292 tests/testthat/test-jwks-cache-host-policy.R | 1168 - tests/testthat/test-jwks-cache-invalidation.R | 116 tests/testthat/test-jwks-cache-signature.R | 194 tests/testthat/test-jwks-duck-cache.R | 76 tests/testthat/test-jwks-host-allow-only.R | 108 tests/testthat/test-jwks-http-cache.R | 258 tests/testthat/test-jwks-malformed-and-pinning.R | 744 - tests/testthat/test-jwks-operation-metadata.R | 142 tests/testthat/test-jwks-public-extensions.R | 64 tests/testthat/test-jwks-rsa-validation.R | 414 tests/testthat/test-jwks-runtime-discovery.R | 308 tests/testthat/test-jwks-secret-material.R | 36 tests/testthat/test-jwks.R | 752 - tests/testthat/test-jwt-duplicate-members.R | 462 tests/testthat/test-jwt-jwe-roundtrip.R | 198 tests/testthat/test-jwt-temporal-order.R | 108 tests/testthat/test-jwt-uri-identifiers.R | 92 tests/testthat/test-key-normalization.R | 78 tests/testthat/test-leeway-validation.R | 102 tests/testthat/test-literal-protocol-diagnostics.R | 302 tests/testthat/test-managed-module.R | 732 - tests/testthat/test-microsoft-tenant-independent-validation.R | 400 tests/testthat/test-mirai-utils.R | 722 - tests/testthat/test-module-acceptance-deadline.R | 318 tests/testthat/test-module-test-exports.R | 94 tests/testthat/test-mtls-backend.R | 48 tests/testthat/test-mtls-fixture-readiness.R | 184 tests/testthat/test-mtls-model.R | 920 - tests/testthat/test-mtls-registration.R | 722 - tests/testthat/test-mtls-roundtrip.R | 106 tests/testthat/test-mtls-thumbprint-cache.R | 54 tests/testthat/test-multiple-vignette.R | 76 tests/testthat/test-numeric-option-shapes.R | 130 tests/testthat/test-oauth-client-shiny-warning.R | 102 tests/testthat/test-oauth-error-body.R | 664 tests/testthat/test-oauth-error-privacy.R | 218 tests/testthat/test-oauth-ui.R | 146 tests/testthat/test-oidc-standard-claim-types.R | 224 tests/testthat/test-optional-jwt-claims.R | 160 tests/testthat/test-otel-authorization-privacy.R | 140 tests/testthat/test-otel-disable.R | 500 tests/testthat/test-otel-fallback-warning.R | 58 tests/testthat/test-otel-token-outcomes.R | 296 tests/testthat/test-otel-token-type-privacy.R | 180 tests/testthat/test-otel-userinfo-alg.R | 134 tests/testthat/test-outbound-eddsa.R | 320 tests/testthat/test-par.R | 2146 +-- tests/testthat/test-parameter-overrides.R | 160 tests/testthat/test-pkce-s256-encoding.R | 20 tests/testthat/test-print-claims-privacy.R | 44 tests/testthat/test-print-redaction.R | 490 tests/testthat/test-proactive-refresh-credentials.R | 80 tests/testthat/test-provider-fingerprint.R | 640 tests/testthat/test-provider-helpers.R | 1430 +- tests/testthat/test-random-and-validators.R | 238 tests/testthat/test-reauth-lifetime.R | 432 tests/testthat/test-refresh-credential-outcome.R | 346 tests/testthat/test-refresh-iss-aud.R | 1974 +- tests/testthat/test-refresh-races.R | 644 tests/testthat/test-refresh-single-flight.R | 170 tests/testthat/test-refresh-token.R | 4322 +++--- tests/testthat/test-resource-binding.R | 336 tests/testthat/test-resource-indicators.R | 362 tests/testthat/test-resource-redirect-policy.R | 72 tests/testthat/test-response-compression-limit.R | 116 tests/testthat/test-response-json-types.R | 228 tests/testthat/test-response-mode-validation.R | 908 - tests/testthat/test-rs384.R | 144 tests/testthat/test-scope-validation.R | 1795 +- tests/testthat/test-security-vignette.R | 42 tests/testthat/test-security.R | 168 tests/testthat/test-shiny-request-uri.R | 636 tests/testthat/test-shiny-timers.R | 254 tests/testthat/test-shinytest2-helper.R | 40 tests/testthat/test-slack-profiles.R | 108 tests/testthat/test-smart-authorization-details.R | 544 tests/testthat/test-smart-context.R | 914 - tests/testthat/test-smart-contracts.R | 304 tests/testthat/test-smart-discovery.R | 1292 - tests/testthat/test-smart-identity-versions.R | 156 tests/testthat/test-smart-online-negotiation.R | 478 tests/testthat/test-smart-tls-assessment.R | 106 tests/testthat/test-softeners.R | 380 tests/testthat/test-state-envelope-roundtrip.R | 100 tests/testthat/test-state-fuzz-wrapper.R | 242 tests/testthat/test-state-json-structure.R | 54 tests/testthat/test-state-race.R | 178 tests/testthat/test-state-record-consistency.R | 94 tests/testthat/test-state-size-caps.R | 140 tests/testthat/test-state-store-atomic-take.R | 774 - tests/testthat/test-state-store-duck.R | 144 tests/testthat/test-state-store-sealing.R | 106 tests/testthat/test-state-store-signature.R | 132 tests/testthat/test-state-store-strict.R | 816 - tests/testthat/test-tls-policy.R | 372 tests/testthat/test-token-media-type.R | 82 tests/testthat/test-token-stale.R | 84 tests/testthat/test-transport-error-context.R | 52 tests/testthat/test-use-shinyOAuth-referrer-meta.R | 70 tests/testthat/test-userinfo-jwt-crit-and-jwks-refresh.R | 594 tests/testthat/test-userinfo-jwt-fallback.R | 598 tests/testthat/test-userinfo-parse-privacy.R | 280 tests/testthat/test-userinfo-parsing.R | 358 tests/testthat/test-userinfo-selector-validation.R | 310 tests/testthat/test-userinfo-transport.R | 68 tests/testthat/test-utils-crypt-decrypt-rejects.R | 610 tests/testthat/test-utils-http-helpers.R | 1604 +- tests/testthat/test-utils-url-and-scopes.R | 526 tests/testthat/test-validator-na-safe.R | 76 tests/testthat/test-vignette-spotify.R | 340 tests/testthat/test_chromote_cookie.R | 1404 +- tests/testthat/test_state_key.R | 56 tests/testthat/test_state_store_single_use.R | 148 vignettes/audit-logging.Rmd | 978 - vignettes/example-spotify.Rmd | 242 vignettes/opentelemetry.Rmd | 1086 - vignettes/package-options.Rmd | 468 vignettes/usage.Rmd | 1270 - 370 files changed, 97974 insertions(+), 97826 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc] ,
Christoph Burow [aut, trl, dtc] ,
Michael Dietze [aut] ,
Margret C. Fuchs [aut] ,
Christoph Schmidt [aut] ,
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] ,
Norbert Mercier [aut] ,
Rachel K. Smedley [ct [...truncated...]
Maintainer: Sebastian Kreutzer <maintainer_luminescence@r-luminescence.org>
Diff between Luminescence versions 1.3.0 dated 2026-07-22 and 1.3.1 dated 2026-09-18
Luminescence-1.3.0/Luminescence/man/calc_MaxDose.Rd |only Luminescence-1.3.0/Luminescence/man/merge_RLum.Data.Spectrum.Rd |only Luminescence-1.3.1/Luminescence/DESCRIPTION | 26 Luminescence-1.3.1/Luminescence/MD5 | 563 +-- Luminescence-1.3.1/Luminescence/NAMESPACE | 60 Luminescence-1.3.1/Luminescence/NEWS.md | 1656 ++-------- Luminescence-1.3.1/Luminescence/R/Luminescence-generics.R | 60 Luminescence-1.3.1/Luminescence/R/Luminescence-package.R | 4 Luminescence-1.3.1/Luminescence/R/RLum.Analysis-class.R | 31 Luminescence-1.3.1/Luminescence/R/RLum.Data.Curve-class.R | 27 Luminescence-1.3.1/Luminescence/R/RLum.Data.Image-class.R | 14 Luminescence-1.3.1/Luminescence/R/RLum.Data.Spectrum-class.R | 15 Luminescence-1.3.1/Luminescence/R/RLum.Results-class.R | 15 Luminescence-1.3.1/Luminescence/R/Risoe.BINfileData-class.R | 5 Luminescence-1.3.1/Luminescence/R/Risoe.BINfileData2RLum.Analysis.R | 52 Luminescence-1.3.1/Luminescence/R/analyse_Al2O3C_CrossTalk.R | 19 Luminescence-1.3.1/Luminescence/R/analyse_Al2O3C_ITC.R | 10 Luminescence-1.3.1/Luminescence/R/analyse_Al2O3C_Measurement.R | 6 Luminescence-1.3.1/Luminescence/R/analyse_FadingMeasurement.R | 15 Luminescence-1.3.1/Luminescence/R/analyse_IRSAR.RF.R | 168 - Luminescence-1.3.1/Luminescence/R/analyse_SAR.CWOSL.R | 54 Luminescence-1.3.1/Luminescence/R/analyse_SAR.NCF.R | 4 Luminescence-1.3.1/Luminescence/R/analyse_SAR.TL.R | 11 Luminescence-1.3.1/Luminescence/R/analyse_baSAR.R | 2 Luminescence-1.3.1/Luminescence/R/analyse_pIRIRSequence.R | 14 Luminescence-1.3.1/Luminescence/R/calc_AverageDose.R | 2 Luminescence-1.3.1/Luminescence/R/calc_CentralDose.R | 60 Luminescence-1.3.1/Luminescence/R/calc_FadingCorr.R | 4 Luminescence-1.3.1/Luminescence/R/calc_FastRatio.R | 57 Luminescence-1.3.1/Luminescence/R/calc_FiniteMixture.R | 2 Luminescence-1.3.1/Luminescence/R/calc_FuchsLang2001.R | 87 Luminescence-1.3.1/Luminescence/R/calc_Huntley2006.R | 103 Luminescence-1.3.1/Luminescence/R/calc_IEU.R | 4 Luminescence-1.3.1/Luminescence/R/calc_MaxDose.R | 103 Luminescence-1.3.1/Luminescence/R/calc_MinDose.R | 177 - Luminescence-1.3.1/Luminescence/R/calc_MoransI.R | 2 Luminescence-1.3.1/Luminescence/R/calc_OSLLxTxRatio.R | 20 Luminescence-1.3.1/Luminescence/R/calc_SourceDoseRate.R | 48 Luminescence-1.3.1/Luminescence/R/calc_Statistics.R | 45 Luminescence-1.3.1/Luminescence/R/calc_WodaFuchs2008.R | 2 Luminescence-1.3.1/Luminescence/R/calc_gSGC.R | 7 Luminescence-1.3.1/Luminescence/R/calc_gSGC_feldspar.R | 4 Luminescence-1.3.1/Luminescence/R/convert_CW2pLMi.R | 2 Luminescence-1.3.1/Luminescence/R/fit_CWCurve.R | 8 Luminescence-1.3.1/Luminescence/R/fit_DoseResponseCurve.R | 134 Luminescence-1.3.1/Luminescence/R/fit_EmissionSpectra.R | 9 Luminescence-1.3.1/Luminescence/R/fit_IsothermalHolding.R | 5 Luminescence-1.3.1/Luminescence/R/fit_LMCurve.R | 5 Luminescence-1.3.1/Luminescence/R/fit_OSLLifeTimes.R | 10 Luminescence-1.3.1/Luminescence/R/fit_SurfaceExposure.R | 20 Luminescence-1.3.1/Luminescence/R/get_Layout.R | 8 Luminescence-1.3.1/Luminescence/R/internals_RLum.R | 98 Luminescence-1.3.1/Luminescence/R/merge_RLum.Analysis.R | 23 Luminescence-1.3.1/Luminescence/R/merge_RLum.Data.Curve.R | 83 Luminescence-1.3.1/Luminescence/R/merge_RLum.Data.Spectrum.R | 124 Luminescence-1.3.1/Luminescence/R/merge_RLum.R | 36 Luminescence-1.3.1/Luminescence/R/merge_RLum.Results.R | 145 Luminescence-1.3.1/Luminescence/R/merge_Risoe.BINfileData.R | 40 Luminescence-1.3.1/Luminescence/R/plot_AbanicoPlot.R | 703 ++-- Luminescence-1.3.1/Luminescence/R/plot_DRCSummary.R | 11 Luminescence-1.3.1/Luminescence/R/plot_DRTResults.R | 55 Luminescence-1.3.1/Luminescence/R/plot_DetPlot.R | 28 Luminescence-1.3.1/Luminescence/R/plot_DoseResponseCurve.R | 28 Luminescence-1.3.1/Luminescence/R/plot_Histogram.R | 53 Luminescence-1.3.1/Luminescence/R/plot_KDE.R | 81 Luminescence-1.3.1/Luminescence/R/plot_NRt.R | 2 Luminescence-1.3.1/Luminescence/R/plot_RLum.Data.Curve.R | 15 Luminescence-1.3.1/Luminescence/R/plot_RLum.Data.Spectrum.R | 21 Luminescence-1.3.1/Luminescence/R/plot_RLum.R | 13 Luminescence-1.3.1/Luminescence/R/plot_RLum.Results.R | 43 Luminescence-1.3.1/Luminescence/R/plot_RadialPlot.R | 67 Luminescence-1.3.1/Luminescence/R/plot_ViolinPlot.R | 32 Luminescence-1.3.1/Luminescence/R/read_RF2R.R | 75 Luminescence-1.3.1/Luminescence/R/read_XSYG2R.R | 11 Luminescence-1.3.1/Luminescence/R/scale_GammaDose.R | 77 Luminescence-1.3.1/Luminescence/R/verify_SingleGrainData.R | 12 Luminescence-1.3.1/Luminescence/R/write_R2BIN.R | 12 Luminescence-1.3.1/Luminescence/README.md | 11 Luminescence-1.3.1/Luminescence/inst/doc/crosstalk.html | 62 Luminescence-1.3.1/Luminescence/man/Risoe.BINfileData-class.Rd | 2 Luminescence-1.3.1/Luminescence/man/Risoe.BINfileData2RLum.Analysis.Rd | 32 Luminescence-1.3.1/Luminescence/man/analyse_Al2O3C_CrossTalk.Rd | 7 Luminescence-1.3.1/Luminescence/man/analyse_Al2O3C_ITC.Rd | 8 Luminescence-1.3.1/Luminescence/man/analyse_Al2O3C_Measurement.Rd | 2 Luminescence-1.3.1/Luminescence/man/analyse_FadingMeasurement.Rd | 15 Luminescence-1.3.1/Luminescence/man/analyse_IRSAR.RF.Rd | 29 Luminescence-1.3.1/Luminescence/man/analyse_SAR.CWOSL.Rd | 10 Luminescence-1.3.1/Luminescence/man/analyse_SAR.NCF.Rd | 4 Luminescence-1.3.1/Luminescence/man/analyse_SAR.TL.Rd | 4 Luminescence-1.3.1/Luminescence/man/analyse_baSAR.Rd | 2 Luminescence-1.3.1/Luminescence/man/analyse_pIRIRSequence.Rd | 2 Luminescence-1.3.1/Luminescence/man/analyse_portableOSL.Rd | 2 Luminescence-1.3.1/Luminescence/man/apply_CosmicRayRemoval.Rd | 2 Luminescence-1.3.1/Luminescence/man/apply_Crosstalk.Rd | 2 Luminescence-1.3.1/Luminescence/man/apply_EfficiencyCorrection.Rd | 2 Luminescence-1.3.1/Luminescence/man/as.Rd |only Luminescence-1.3.1/Luminescence/man/bin_RLum.Data.Rd | 4 Luminescence-1.3.1/Luminescence/man/calc_AliquotSize.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_AverageDose.Rd | 4 Luminescence-1.3.1/Luminescence/man/calc_CentralDose.Rd | 4 Luminescence-1.3.1/Luminescence/man/calc_CobbleDoseRate.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_CommonDose.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_CosmicDoseRate.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_EED_Model.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_FadingCorr.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_FastRatio.Rd | 7 Luminescence-1.3.1/Luminescence/man/calc_FiniteMixture.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_FuchsLang2001.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_HomogeneityTest.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_Huntley2006.Rd | 12 Luminescence-1.3.1/Luminescence/man/calc_IEU.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_Lamothe2003.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_MinDose.Rd | 106 Luminescence-1.3.1/Luminescence/man/calc_MoransI.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_OSLLxTxDecomposed.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_OSLLxTxRatio.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_SourceDoseRate.Rd | 8 Luminescence-1.3.1/Luminescence/man/calc_Statistics.Rd | 25 Luminescence-1.3.1/Luminescence/man/calc_TLLxTxRatio.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_ThermalLifetime.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_WodaFuchs2008.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_gSGC.Rd | 2 Luminescence-1.3.1/Luminescence/man/calc_gSGC_feldspar.Rd | 2 Luminescence-1.3.1/Luminescence/man/combine_De_Dr.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_Activity2Concentration.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_BIN2CSV.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_CW2pHMi.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_CW2pLM.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_CW2pLMi.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_CW2pPMi.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_Concentration2DoseRate.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_Daybreak2CSV.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_PSL2CSV.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_PSL2Risoe.BINfileData.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_RLum2Risoe.BINfileData.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_SG2MG.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_Second2Gray.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_Wavelength2Energy.Rd | 2 Luminescence-1.3.1/Luminescence/man/convert_XSYG2CSV.Rd | 2 Luminescence-1.3.1/Luminescence/man/correct_PMTLinearity.Rd | 2 Luminescence-1.3.1/Luminescence/man/dot-as.latex.table.Rd | 2 Luminescence-1.3.1/Luminescence/man/extract_IrradiationTimes.Rd | 2 Luminescence-1.3.1/Luminescence/man/extract_ROI.Rd | 2 Luminescence-1.3.1/Luminescence/man/fit_CWCurve.Rd | 2 Luminescence-1.3.1/Luminescence/man/fit_DoseResponseCurve.Rd | 11 Luminescence-1.3.1/Luminescence/man/fit_EmissionSpectra.Rd | 2 Luminescence-1.3.1/Luminescence/man/fit_LMCurve.Rd | 2 Luminescence-1.3.1/Luminescence/man/fit_OSLLifeTimes.Rd | 4 Luminescence-1.3.1/Luminescence/man/fit_SurfaceExposure.Rd | 2 Luminescence-1.3.1/Luminescence/man/fit_ThermalQuenching.Rd | 2 Luminescence-1.3.1/Luminescence/man/get_Layout.Rd | 2 Luminescence-1.3.1/Luminescence/man/get_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/get_rightAnswer.Rd | 2 Luminescence-1.3.1/Luminescence/man/import_Data.Rd | 2 Luminescence-1.3.1/Luminescence/man/length_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/melt_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/merge_RLum.Analysis.Rd | 10 Luminescence-1.3.1/Luminescence/man/merge_RLum.Data.Curve.Rd | 94 Luminescence-1.3.1/Luminescence/man/merge_RLum.Rd | 10 Luminescence-1.3.1/Luminescence/man/merge_RLum.Results.Rd | 11 Luminescence-1.3.1/Luminescence/man/merge_Risoe.BINfileData.Rd | 10 Luminescence-1.3.1/Luminescence/man/metadata.Rd | 2 Luminescence-1.3.1/Luminescence/man/names_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/normalise_RLum.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_AbanicoPlot.Rd | 122 Luminescence-1.3.1/Luminescence/man/plot_DRCSummary.Rd | 10 Luminescence-1.3.1/Luminescence/man/plot_DRTResults.Rd | 10 Luminescence-1.3.1/Luminescence/man/plot_DetPlot.Rd | 14 Luminescence-1.3.1/Luminescence/man/plot_DoseResponseCurve.Rd | 17 Luminescence-1.3.1/Luminescence/man/plot_FilterCombinations.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_GrowthCurve.Rd | 11 Luminescence-1.3.1/Luminescence/man/plot_Histogram.Rd | 31 Luminescence-1.3.1/Luminescence/man/plot_KDE.Rd | 16 Luminescence-1.3.1/Luminescence/man/plot_MoranScatterplot.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_NRt.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_OSLAgeSummary.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_RLum.Analysis.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_RLum.Data.Curve.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_RLum.Data.Image.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 11 Luminescence-1.3.1/Luminescence/man/plot_RLum.Rd | 10 Luminescence-1.3.1/Luminescence/man/plot_RLum.Results.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_ROI.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_RadialPlot.Rd | 19 Luminescence-1.3.1/Luminescence/man/plot_Risoe.BINfileData.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_SingleGrainDisc.Rd | 2 Luminescence-1.3.1/Luminescence/man/plot_ViolinPlot.Rd | 8 Luminescence-1.3.1/Luminescence/man/read_BIN2R.Rd | 2 Luminescence-1.3.1/Luminescence/man/read_BINXLOG2R.Rd | 2 Luminescence-1.3.1/Luminescence/man/read_Daybreak2R.Rd | 2 Luminescence-1.3.1/Luminescence/man/read_HeliosOSL2R.Rd | 2 Luminescence-1.3.1/Luminescence/man/read_PSL2R.Rd | 2 Luminescence-1.3.1/Luminescence/man/read_RF2R.Rd | 16 Luminescence-1.3.1/Luminescence/man/read_SPE2R.Rd | 2 Luminescence-1.3.1/Luminescence/man/read_TIFF2R.Rd | 2 Luminescence-1.3.1/Luminescence/man/read_XSYG2R.Rd | 4 Luminescence-1.3.1/Luminescence/man/remove_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/remove_SignalBackground.Rd | 2 Luminescence-1.3.1/Luminescence/man/replicate_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/report_RLum.Rd | 2 Luminescence-1.3.1/Luminescence/man/sTeve.Rd | 2 Luminescence-1.3.1/Luminescence/man/scale_GammaDose.Rd | 71 Luminescence-1.3.1/Luminescence/man/set_RLum.Rd | 2 Luminescence-1.3.1/Luminescence/man/set_Risoe.BINfileData.Rd | 2 Luminescence-1.3.1/Luminescence/man/smooth_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/sort_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/structure_RLum.Rd | 4 Luminescence-1.3.1/Luminescence/man/subset_SingleGrainData.Rd | 2 Luminescence-1.3.1/Luminescence/man/template_DRAC.Rd | 2 Luminescence-1.3.1/Luminescence/man/trim_RLum.Data.Rd | 2 Luminescence-1.3.1/Luminescence/man/tune_Data.Rd | 2 Luminescence-1.3.1/Luminescence/man/use_DRAC.Rd | 2 Luminescence-1.3.1/Luminescence/man/verify_SingleGrainData.Rd | 2 Luminescence-1.3.1/Luminescence/man/view.Rd | 4 Luminescence-1.3.1/Luminescence/man/write_R2BIN.Rd | 4 Luminescence-1.3.1/Luminescence/man/write_R2TIFF.Rd | 2 Luminescence-1.3.1/Luminescence/man/write_RLum2CSV.Rd | 2 Luminescence-1.3.1/Luminescence/tests/testthat/_data/RF_new_header.rf |only Luminescence-1.3.1/Luminescence/tests/testthat/_data/xsyg-tests/XSYG_broken_2.xsyg |only Luminescence-1.3.1/Luminescence/tests/testthat/setup.R | 16 Luminescence-1.3.1/Luminescence/tests/testthat/test_RLum.Analysis-class.R | 4 Luminescence-1.3.1/Luminescence/tests/testthat/test_RLum.Data.Image.R | 8 Luminescence-1.3.1/Luminescence/tests/testthat/test_Risoe.BINfileData-class.R | 2 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_Al2O3C_CrossTalk.R | 17 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_Al2O3C_ITC.R | 7 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_Al2O3C_Measurement.R | 42 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_FadingMeasurement.R | 37 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_IRSAR.RF.R | 46 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_SAR.CWOSL.R | 43 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_SAR.NCF.R | 7 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_SAR.TL.R | 14 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_baSAR.R | 1 Luminescence-1.3.1/Luminescence/tests/testthat/test_analyse_pIRIRSequence.R | 16 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_AliquotSize.R | 8 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_AverageDose.R | 13 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_CentralDose.R | 16 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_CommonDose.R | 9 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_CosmicDoseRate.R | 4 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_EED_Model.R | 2 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_FadingCorr.R | 10 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_FastRatio.R | 67 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_FiniteMixture.R | 1 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_FuchsLang2001.R | 12 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_HomogeneityTest.R | 4 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_Huntley2006.R | 74 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_IEU.R | 13 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_Lamothe2003.R | 3 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_MinDose.R | 56 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_MoransI.R | 2 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_SourceDoseRate.R | 5 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_Statistics.R | 18 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_ThermalLifetime.R | 9 Luminescence-1.3.1/Luminescence/tests/testthat/test_calc_gSGC.R | 11 Luminescence-1.3.1/Luminescence/tests/testthat/test_convert_Activity2Concentration.R | 2 Luminescence-1.3.1/Luminescence/tests/testthat/test_fit_CWCurve.R | 3 Luminescence-1.3.1/Luminescence/tests/testthat/test_fit_DoseResponseCurve.R | 36 Luminescence-1.3.1/Luminescence/tests/testthat/test_fit_EmissionSpectra.R | 11 Luminescence-1.3.1/Luminescence/tests/testthat/test_fit_LMCurve.R | 5 Luminescence-1.3.1/Luminescence/tests/testthat/test_fit_OSLLifeTimes.R | 9 Luminescence-1.3.1/Luminescence/tests/testthat/test_fit_SurfaceExposure.R | 57 Luminescence-1.3.1/Luminescence/tests/testthat/test_fit_ThermalQuenching.R | 6 Luminescence-1.3.1/Luminescence/tests/testthat/test_internals.R | 64 Luminescence-1.3.1/Luminescence/tests/testthat/test_merge_RLum.Analysis.R | 17 Luminescence-1.3.1/Luminescence/tests/testthat/test_merge_RLum.Data.Curve.R | 6 Luminescence-1.3.1/Luminescence/tests/testthat/test_merge_RLum.Data.Spectrum.R | 3 Luminescence-1.3.1/Luminescence/tests/testthat/test_merge_RLum.R | 8 Luminescence-1.3.1/Luminescence/tests/testthat/test_merge_RLum.Results.R | 30 Luminescence-1.3.1/Luminescence/tests/testthat/test_merge_Risoe.BINfileData.R | 10 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_AbanicoPlot.R | 62 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_DRCSummary.R | 1 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_DRTResults.R | 8 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_DetPlot.R | 20 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_DoseResponseCurve.R | 3 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_Histogram.R | 5 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_KDE.R | 16 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_RLum.Data.Curve.R | 8 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_RLum.Data.Spectrum.R | 22 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_RLum.R | 6 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_RLum.Results.R | 7 Luminescence-1.3.1/Luminescence/tests/testthat/test_plot_RadialPlot.R | 16 Luminescence-1.3.1/Luminescence/tests/testthat/test_read_RF2R.R | 43 Luminescence-1.3.1/Luminescence/tests/testthat/test_read_XSYG2R.R | 9 Luminescence-1.3.1/Luminescence/tests/testthat/test_scale_GammaDose.R | 10 Luminescence-1.3.1/Luminescence/tests/testthat/test_verify_SingleGrainData.R | 25 Luminescence-1.3.1/Luminescence/tests/testthat/test_write_R2BIN.R | 20 285 files changed, 3874 insertions(+), 4010 deletions(-)
Title: ICESat-2 Data Analysis for Land and Vegetation
Description: Provides tools for downloading, reading, processing, visualizing,
and exporting NASA's ICESat-2 ATL03 (Global Geolocated Photon
Data) and ATL08 (Land and Vegetation Height) products. Supports
photon- and segment-level analysis, spatial sampling, gridding,
statistical and machine-learning modeling, and integration with
'Google Earth Engine' (<https://earthengine.google.com/>) for
wall-to-wall mapping of vegetation structure and other land
attributes.
Author: Carlos Alberto Silva [aut, cph, cre],
Caio Hamamura [aut, cph],
Cesar Alvites [aut, ctb],
Alexander J. Gaskins [aut, ctb],
Sunil Arya [ctb, cph] ),
David Mount [ctb, cph] ),
University of Maryland [cph] ),
Chuck Gantz [ctb] ,
Cole Krehbiel [ctb]
Maintainer: Carlos Alberto Silva <c.silva@ufl.edu>
Diff between ICESat2VegR versions 0.0.1 dated 2026-09-11 and 0.0.2 dated 2026-09-18
DESCRIPTION | 6 ++--- MD5 | 32 ++++++++++++++++++++++++------- R/ATLAS_dataDownload.R | 13 +++++------- R/class.icesat2.h5_local.R | 31 ++++++++++-------------------- R/class.icesat2.h5ds_local.R | 14 +++---------- R/zzz.R | 33 ++++++++------------------------ inst/proj |only man/earthdata_login.Rd | 8 +++---- src/Makevars.ucrt |only src/Makevars.ucrt.in |only tests/testthat/test-integration-local.R | 26 +++++++++++++++++++++++-- 11 files changed, 86 insertions(+), 77 deletions(-)
Title: Biodiversity Data from the GBIF Node Network
Description: The Global Biodiversity Information Facility
('GBIF', <https://www.gbif.org>) sources data from an international network
of data providers, known as 'nodes'. Several of these nodes - the "living
atlases" (<https://living-atlases.gbif.org>) - maintain their own web
services using software originally developed by the Atlas of Living
Australia ('ALA', <https://www.ala.org.au>). 'galah' enables the R community
to directly access data and resources hosted by 'GBIF' and its partner nodes.
Author: Martin Westgate [aut, cre],
Dax Kellie [aut],
Shandiya Balasubramaniam [ctb],
Matilda Stevenson [ctb]
Maintainer: Martin Westgate <martin.westgate@csiro.au>
Diff between galah versions 2.2.0 dated 2026-02-11 and 2.3.0 dated 2026-09-18
galah-2.2.0/galah/R/galah_apply_profile.R |only galah-2.2.0/galah/R/galah_bbox.R |only galah-2.2.0/galah/R/galah_filter.R |only galah-2.2.0/galah/R/galah_geolocate.R |only galah-2.2.0/galah/R/galah_group_by.R |only galah-2.2.0/galah/R/galah_identify.R |only galah-2.2.0/galah/R/galah_polygon.R |only galah-2.2.0/galah/R/galah_radius.R |only galah-2.2.0/galah/R/galah_select.R |only galah-2.2.0/galah/tests/testthat/test-galah_apply_profile.R |only galah-2.2.0/galah/tests/testthat/test-galah_bbox.R |only galah-2.2.0/galah/tests/testthat/test-galah_geolocate.R |only galah-2.2.0/galah/tests/testthat/test-galah_group_by.R |only galah-2.2.0/galah/tests/testthat/test-galah_identify.R |only galah-2.2.0/galah/tests/testthat/test-galah_polygon.R |only galah-2.2.0/galah/tests/testthat/test-galah_radius.R |only galah-2.3.0/galah/DESCRIPTION | 6 galah-2.3.0/galah/MD5 | 245 +++--- galah-2.3.0/galah/NAMESPACE | 5 galah-2.3.0/galah/NEWS.md | 28 galah-2.3.0/galah/R/apply_profile.R |only galah-2.3.0/galah/R/atlas_counts.R | 2 galah-2.3.0/galah/R/atlas_distributions.R | 4 galah-2.3.0/galah/R/atlas_media.R | 39 - galah-2.3.0/galah/R/atlas_occurrences.R | 12 galah-2.3.0/galah/R/atlas_species.R | 2 galah-2.3.0/galah/R/atlas_taxonomy.R | 6 galah-2.3.0/galah/R/authenticate.R | 143 +++ galah-2.3.0/galah/R/build_query.R | 69 + galah-2.3.0/galah/R/capture.R | 86 +- galah-2.3.0/galah/R/capture_events.R |only galah-2.3.0/galah/R/capture_files.R | 13 galah-2.3.0/galah/R/capture_metadata.R | 184 ++-- galah-2.3.0/galah/R/capture_metadata_unnest.R | 39 - galah-2.3.0/galah/R/capture_occurrences.R | 86 +- galah-2.3.0/galah/R/capture_occurrences_count.R | 88 -- galah-2.3.0/galah/R/capture_species.R | 22 galah-2.3.0/galah/R/capture_species_count.R | 47 - galah-2.3.0/galah/R/capture_taxa.R | 50 - galah-2.3.0/galah/R/check.R | 389 ++++------ galah-2.3.0/galah/R/check_queue.R | 4 galah-2.3.0/galah/R/collapse_checks.R | 47 - galah-2.3.0/galah/R/collapse_events.R |only galah-2.3.0/galah/R/collapse_metadata.R | 75 + galah-2.3.0/galah/R/collapse_occurrences.R | 6 galah-2.3.0/galah/R/collapse_occurrences_count_atlas.R | 23 galah-2.3.0/galah/R/collapse_query_set.R | 10 galah-2.3.0/galah/R/collect_events.R |only galah-2.3.0/galah/R/collect_metadata.R | 99 +- galah-2.3.0/galah/R/collect_metadata_unnest.R | 198 ++++- galah-2.3.0/galah/R/collect_occurrences.R | 115 +- galah-2.3.0/galah/R/collect_occurrences_count.R | 55 - galah-2.3.0/galah/R/collect_species.R | 2 galah-2.3.0/galah/R/collect_taxa.R | 18 galah-2.3.0/galah/R/compound.R | 66 + galah-2.3.0/galah/R/compute_occurrences.R | 16 galah-2.3.0/galah/R/describe.R |only galah-2.3.0/galah/R/dplyr-collect.R | 4 galah-2.3.0/galah/R/dplyr-compute.R | 2 galah-2.3.0/galah/R/dplyr-filter.R | 21 galah-2.3.0/galah/R/dplyr-glimpse.R | 2 galah-2.3.0/galah/R/dplyr-select.R | 24 galah-2.3.0/galah/R/filter_object_classes.R | 9 galah-2.3.0/galah/R/galah_call.R | 77 + galah-2.3.0/galah/R/galah_config.R | 64 - galah-2.3.0/galah/R/geolocate.R |only galah-2.3.0/galah/R/geolocate_bbox.R |only galah-2.3.0/galah/R/geolocate_polygon.R |only galah-2.3.0/galah/R/geolocate_radius.R |only galah-2.3.0/galah/R/graphics-identify.R |only galah-2.3.0/galah/R/messages.R | 21 galah-2.3.0/galah/R/onload.R | 113 +- galah-2.3.0/galah/R/print.R | 92 +- galah-2.3.0/galah/R/query_API.R | 275 ++++--- galah-2.3.0/galah/R/read_zip.R | 209 +++-- galah-2.3.0/galah/R/search_all.R | 10 galah-2.3.0/galah/R/show_values.R | 40 - galah-2.3.0/galah/R/superseded-functions.R |only galah-2.3.0/galah/R/sysdata.rda |binary galah-2.3.0/galah/R/taxonomic-searches.R | 4 galah-2.3.0/galah/R/tidyr-unnest.R | 15 galah-2.3.0/galah/R/url_lookup.R | 19 galah-2.3.0/galah/R/utilities_caching.R | 12 galah-2.3.0/galah/R/utilities_internal.R | 253 ++++-- galah-2.3.0/galah/inst/doc/quick_start_guide.Rmd | 374 +++++---- galah-2.3.0/galah/inst/doc/quick_start_guide.html | 377 +++++---- galah-2.3.0/galah/man/apply_profile.Rd | 5 galah-2.3.0/galah/man/atlas_.Rd | 14 galah-2.3.0/galah/man/authenticate.Rd | 47 - galah-2.3.0/galah/man/capture.data_request.Rd | 2 galah-2.3.0/galah/man/compound.Rd | 14 galah-2.3.0/galah/man/describe.Rd |only galah-2.3.0/galah/man/figures/atlases_plot.png |binary galah-2.3.0/galah/man/filter.data_request.Rd | 24 galah-2.3.0/galah/man/galah_call.Rd | 24 galah-2.3.0/galah/man/geolocate.Rd | 53 - galah-2.3.0/galah/man/glimpse.data_request.Rd | 4 galah-2.3.0/galah/man/group_by.data_request.Rd | 5 galah-2.3.0/galah/man/identify.data_request.Rd | 5 galah-2.3.0/galah/man/print_galah_objects.Rd | 6 galah-2.3.0/galah/man/read_zip.Rd | 5 galah-2.3.0/galah/man/select.data_request.Rd | 14 galah-2.3.0/galah/man/show_values.Rd | 24 galah-2.3.0/galah/man/superseded_functions.Rd |only galah-2.3.0/galah/man/taxonomic_searches.Rd | 4 galah-2.3.0/galah/man/unnest.Rd | 15 galah-2.3.0/galah/tests/testthat/_snaps/print.md | 35 galah-2.3.0/galah/tests/testthat/test-apply_profile.R |only galah-2.3.0/galah/tests/testthat/test-atlas_events.R |only galah-2.3.0/galah/tests/testthat/test-atlas_media.R | 73 + galah-2.3.0/galah/tests/testthat/test-atlas_occurrences.R | 14 galah-2.3.0/galah/tests/testthat/test-atlas_species.R | 7 galah-2.3.0/galah/tests/testthat/test-authentication.R | 24 galah-2.3.0/galah/tests/testthat/test-describe.R |only galah-2.3.0/galah/tests/testthat/test-dplyr-distinct.R | 3 galah-2.3.0/galah/tests/testthat/test-dplyr-filter.R | 241 +++--- galah-2.3.0/galah/tests/testthat/test-dplyr-group_by.R |only galah-2.3.0/galah/tests/testthat/test-galah_call.R | 42 - galah-2.3.0/galah/tests/testthat/test-galah_filter.R |only galah-2.3.0/galah/tests/testthat/test-geolocate.R |only galah-2.3.0/galah/tests/testthat/test-geolocate_bbox.R |only galah-2.3.0/galah/tests/testthat/test-geolocate_polygon.R |only galah-2.3.0/galah/tests/testthat/test-geolocate_radius.R |only galah-2.3.0/galah/tests/testthat/test-identify.R |only galah-2.3.0/galah/tests/testthat/test-international-Austria.R | 63 - galah-2.3.0/galah/tests/testthat/test-international-Brazil.R | 7 galah-2.3.0/galah/tests/testthat/test-international-Flanders.R | 24 galah-2.3.0/galah/tests/testthat/test-international-GBIF-predicates.R | 49 - galah-2.3.0/galah/tests/testthat/test-international-GBIF.R | 263 ++++-- galah-2.3.0/galah/tests/testthat/test-international-Kew.R | 9 galah-2.3.0/galah/tests/testthat/test-international-Portugal.R | 19 galah-2.3.0/galah/tests/testthat/test-international-Spain.R | 31 galah-2.3.0/galah/tests/testthat/test-international-Sweden.R | 57 - galah-2.3.0/galah/tests/testthat/test-international-UK.R | 24 galah-2.3.0/galah/tests/testthat/test-print.R | 4 galah-2.3.0/galah/tests/testthat/test-request_metadata_select.R | 23 galah-2.3.0/galah/tests/testthat/test-request_metadata_unnest.R | 17 galah-2.3.0/galah/tests/testthat/test-search_all.R | 16 galah-2.3.0/galah/tests/testthat/test-search_taxa.R | 12 galah-2.3.0/galah/tests/testthat/test-show_all.R | 13 galah-2.3.0/galah/tests/testthat/test-show_values.R | 66 + galah-2.3.0/galah/tests/testthat/test-url_lookup.R | 23 galah-2.3.0/galah/vignettes/quick_start_guide.Rmd | 374 +++++---- 143 files changed, 3756 insertions(+), 2358 deletions(-)
Title: Local Influence Diagnostics for the Extreme-Value
Birnbaum-Saunders Regression Model
Description: Implements local influence diagnostics for the Extreme-Value
Birnbaum-Saunders (EVBS) regression model: joint maximum likelihood
estimation, conformal normal curvature diagnostics under three
perturbation schemes (case-weight, response variable, and explanatory
variable), randomized quantile residuals with simulation envelope,
Monte Carlo simulation utilities, and publication-quality density and
diagnostic plots. Version 1.1.0 adds the density, distribution and
quantile functions, the finite upper endpoint, return levels and
expected shortfall, block bootstrap standard errors for serially
dependent series, local influence diagnostics for the generalized
extreme-value regression model, and a GAMLSS family allowing the
tail-shape parameter to depend on covariates. Version 1.2.0 adds a
prospective control chart for endpoint identifiability. The methods
are described in Ospina, Lima, Barros, and Macedo (2026, submitted)
and are applied to monthly maximum wind gust data from Itajai, Brazil.
Author: Raydonal Ospina [aut, cre]
Maintainer: Raydonal Ospina <raydonal@de.ufpe.br>
Diff between evbsreg versions 1.0.0 dated 2026-06-30 and 1.2.0 dated 2026-09-18
DESCRIPTION | 22 ++++++++----- MD5 | 38 ++++++++++++++++++----- NAMESPACE | 15 +++++++++ NEWS.md | 61 +++++++++++++++++++++++++++++++++++-- R/blockboot.R |only R/distribution.R |only R/evbsreg_diagnostics.R | 37 +++++++++++++++++++++- R/evbsreg_residuals.R | 2 - R/gamlss_family.R |only R/gev.R |only R/monitor.R |only README.md | 23 +++++++++++-- build/vignette.rds |binary inst/doc/evbsreg.html | 32 +++++++++---------- man/cnc_diagnostics_gev.Rd |only man/devbs.Rd |only man/evbs_block_boot.Rd |only man/evbs_endpoint.Rd |only man/evbs_monitor.Rd |only man/evbs_return_level.Rd |only man/gev_scores.Rd |only man/gevreg.fit.Rd |only man/logEVBS-dist.Rd |only man/logEVBS.Rd |only man/pevbs.Rd |only man/plot.evbs_monitor.Rd |only man/qevbs.Rd |only tests/testthat/test-distribution.R |only tests/testthat/test-gamlss.R |only tests/testthat/test-gev.R |only tests/testthat/test-monitor.R |only 31 files changed, 190 insertions(+), 40 deletions(-)
Title: Fitting Exact Conditional Logistic Regression with Lasso and
Elastic Net Penalties
Description: Tools for the fitting and cross validation of exact conditional logistic regression models with lasso and elastic net penalties. Uses cyclic coordinate descent and warm starts to compute the entire path efficiently.
Author: Stephen Reid [aut, cre],
Robert Tibshirani [aut]
Maintainer: Stephen Reid <sreid1652@gmail.com>
Diff between clogitL1 versions 1.5 dated 2019-02-02 and 1.6 dated 2026-09-18
DESCRIPTION | 18 ++++++++---- MD5 | 30 ++++++++++---------- R/RcppExports.R | 22 +++++++-------- R/cv.clogitL1.R | 3 -- inst/CITATION | 33 +++++++++------------- man/clogitL1-package.Rd | 2 - man/clogitL1.Rd | 2 - man/cv.clogitL1.Rd | 2 - man/plot.clogitL1.Rd | 2 - man/plot.cv.clogitL1.Rd | 2 - man/print.clogitL1.Rd | 10 +++--- man/summary.clogitL1.Rd | 2 - man/summary.cv.clogitL1.Rd | 2 - src/Makevars | 2 - src/Makevars.win | 1 src/RcppExports.cpp | 66 ++++++++++++++++++++++++++++----------------- 16 files changed, 107 insertions(+), 92 deletions(-)
Title: Fast and Memory-Efficient Base R Table Manipulation
Description: A tabular data manipulation, exploration and validation toolkit
with a base R-style interface (subset, transform, aggregate, merge, split)
and no external computation dependency. Grouping, joins, ordering,
filtering, reshaping and delimited-file reading run in a bundled 'C++'
engine that uses multiple threads for the heavier operations. Grouped
reducers accumulate in compiled code without materialising intermediate
columns, so grouped aggregation and counting allocate close to nothing.
Results are returned as an ordinary data frame with a light 'basetable'
class.
Author: Imad El Badisy [aut, cre]
Maintainer: Imad El Badisy <elbadisyimad@gmail.com>
Diff between basetable versions 1.4.1 dated 2026-09-13 and 1.4.2 dated 2026-09-18
DESCRIPTION | 6 +- MD5 | 25 +++++----- NEWS.md | 12 +++++ R/split.R | 3 + README.md | 8 +++ inst/benchmarks/benchmark-results.md | 28 ++++++------ inst/benchmarks/make-readme-figures.R | 15 +++--- inst/doc/benchmarking.html | 78 +++++++++++++++++----------------- inst/doc/functions-reference.pdf |binary man/figures/benchmark-combined.png |only man/figures/benchmark-memory.png |binary man/figures/benchmark-time.png |binary man/split.Rd | 16 ++++-- tests/testthat/test-split.R | 9 +++ 14 files changed, 120 insertions(+), 80 deletions(-)
Title: Inference on Prototypes from Clusters of Features
Description: Procedures for testing for group-wide signal in clusters of variables. Tests can be performed for single groups in isolation (univariate) or multiple groups together (multivariate). Specific tests include the exact and approximate (un)selective likelihood ratio tests described in Reid et al (2015), the selective F test and marginal screening prototype test of Reid and Tibshirani (2015). User may pre-specify columns to be included in prototype formation, or allow the function to select them itself. A mixture of these two is also possible. Any variable selection is accounted for using the selective inference framework. Options for non-sampling and hit-and-run null reference distributions.
Author: Stephen Reid [aut, cre]
Maintainer: Stephen Reid <sreid1652@gmail.com>
Diff between prototest versions 1.2 dated 2019-02-03 and 1.3 dated 2026-09-18
DESCRIPTION | 19 ++++++++----- MD5 | 14 ++++----- R/RcppExports.R | 10 +++--- build/partial.rdb |binary man/prototest-package.Rd | 10 +++--- man/prototest.multivariate.Rd | 6 ++-- man/prototest.univariate.Rd | 8 ++--- src/RcppExports.cpp | 61 +++++++++++++++++++++++++++--------------- 8 files changed, 76 insertions(+), 52 deletions(-)
Title: Within-Subject Mediation Analysis Using Structural Equation
Modeling
Description: Within-subject mediation analysis using structural equation modeling.
Examine how changes in an outcome variable between two conditions are mediated
through one or more variables. Supports within-subject mediation analysis using
the 'lavaan' package by Rosseel (2012) <doi:10.18637/jss.v048.i02>,
and extends Monte Carlo confidence interval estimation to missing data scenarios
using the 'semmcci' package by Pesigan and Cheung (2023) <doi:10.3758/s13428-023-02114-4>.
Author: Wendie Yang [aut, cre] ,
Shu Fai Cheung [aut]
Maintainer: Wendie Yang <1581075494q@gmail.com>
Diff between wsMed versions 1.0.2 dated 2025-12-11 and 1.1.0 dated 2026-09-18
DESCRIPTION | 6 MD5 | 164 - NAMESPACE | 5 NEWS.md | 34 R/GenerateModelCN.R | 4 R/GenerateModelCP.R | 113 R/GenerateModelCustom.R |only R/GenerateModelP.R | 4 R/GenerateModelPC.R | 102 R/MCMI2.R | 18 R/MClav_MCStd2.R | 81 R/MClav_RAM2Lav2.R | 16 R/MClav_StdLav2.R | 8 R/MClav_StdRAM2.R | 27 R/RunMCMIAnalysis.R | 69 R/WSMed.R | 128 R/analyze_mm_categorical.R | 19 R/analyze_mm_continuous.R | 230 - R/calc_basic_contrasts.R | 13 R/plot-effects.R |only R/plot_moderation_curve.R | 259 - R/print-wsMed.R | 43 R/standardization-internal.R |only R/standardize_moderation.R |only R/wsMed-helper.R | 100 build/vignette.rds |binary inst/doc/GenerateModelCN.Rmd | 55 inst/doc/GenerateModelCN.html | 56 inst/doc/GenerateModelCP.Rmd | 53 inst/doc/GenerateModelCP.html | 54 inst/doc/GenerateModelCustom.Rmd |only inst/doc/GenerateModelCustom.html |only inst/doc/GenerateModelP.Rmd | 45 inst/doc/GenerateModelP.html | 47 inst/doc/GenerateModelPC.Rmd | 53 inst/doc/GenerateModelPC.html | 54 inst/doc/MEMORE_vs_wsMed.Rmd | 264 - inst/doc/MEMORE_vs_wsMed.html | 267 - inst/doc/PlottingEffects.Rmd |only inst/doc/PlottingEffects.html |only inst/doc/StandardizedModeratedMediation.Rmd |only inst/doc/StandardizedModeratedMediation.html |only inst/doc/WsMed.Rmd | 2558 +++++++++------ inst/doc/WsMed.html | 2902 ++++++++++-------- inst/doc/printGM.Rmd | 45 inst/doc/printGM.html | 38 man/GenerateModelCustom.Rd |only man/MCMI2.Rd | 51 man/MCStd2.Rd | 20 man/RAM2Lav2.Rd | 8 man/RunMCMIAnalysis.Rd | 33 man/StdLav2.Rd | 6 man/StdRAM2.Rd | 14 man/analyze_mm_continuous.Rd | 106 man/calc_basic_contrasts.Rd | 57 man/dot-fit_and_mc.Rd | 3 man/dot-make_moderation.Rd | 3 man/plot_conditional_effects.Rd |only man/plot_contrasts.Rd |only man/plot_effects.Rd |only man/plot_moderation_curve.Rd | 75 man/standardize_moderation.Rd |only man/validate_wsMed_inputs.Rd | 3 man/wsMed.Rd | 98 tests/testthat/test-GenerateModelCustom.R |only tests/testthat/test-GenerateModelP.R | 6 tests/testthat/test-ImputeData.R | 2 tests/testthat/test-WsMed.R | 579 +++ tests/testthat/test-analyze-mm-continuous.R | 2 tests/testthat/test-choice-case.R |only tests/testthat/test-effect-plots.R |only tests/testthat/test-print.WsMed.R | 244 + tests/testthat/test-standardization-phase1.R |only tests/testthat/test-standardization-phase2.R |only vignettes/GenerateModelCN.Rmd | 55 vignettes/GenerateModelCN.Rmd.original | 55 vignettes/GenerateModelCP.Rmd | 53 vignettes/GenerateModelCP.Rmd.original | 53 vignettes/GenerateModelCustom.Rmd |only vignettes/GenerateModelCustom.Rmd.original |only vignettes/GenerateModelP.Rmd | 45 vignettes/GenerateModelP.Rmd.original | 45 vignettes/GenerateModelPC.Rmd | 53 vignettes/GenerateModelPC.Rmd.original | 53 vignettes/MEMORE_vs_wsMed.Rmd | 264 - vignettes/MEMORE_vs_wsMed.Rmd.original | 15 vignettes/PlottingEffects.Rmd |only vignettes/PlottingEffects.Rmd.original |only vignettes/StandardizedModeratedMediation.Rmd |only vignettes/StandardizedModeratedMediation.Rmd.original |only vignettes/Wa.png |only vignettes/Wb.png |only vignettes/Wc.png |only vignettes/Wd.png |only vignettes/WsMed.Rmd | 2558 +++++++++------ vignettes/WsMed.Rmd.original | 1411 +++++--- vignettes/printGM.Rmd | 45 vignettes/printGM.Rmd.original | 24 98 files changed, 8526 insertions(+), 5447 deletions(-)
Title: Community Dynamics Metrics
Description: Univariate and multivariate temporal and spatial diversity indices,
rank abundance curves, and community stability measures. The functions
implement measures that are either explicitly temporal and include the
option to calculate them over multiple replicates, or spatial and include
the option to calculate them over multiple time points. Functions fall into
five categories: static diversity indices, temporal diversity indices,
spatial diversity indices, rank abundance curves, and community stability
measures. The diversity indices are temporal and spatial analogs to
traditional diversity indices. Specifically, the package includes functions
to calculate community richness, evenness and diversity at a given point in
space and time. In addition, it contains functions to calculate species
turnover, mean rank shifts, and lags in community similarity between two
time points. Details of the methods are available in
Hallett et al. (2016) <doi:10.1111/2041-210X.12569> and Avolio
et al. ( [...truncated...]
Author: Lauren Hallett [aut] ,
Meghan L. Avolio [aut] ,
Ian T. Carroll [aut] ,
Sydney K. Jones [aut],
A. Andrew M. MacDonald [aut] ,
Dan F. B. Flynn [aut] ,
Peter Slaughter [aut] ,
Julie Ripplinger [aut] ,
Scott L. Collins [aut] ,
Corinna Gries [aut] ,
Matth [...truncated...]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between codyn versions 2.0.5 dated 2020-12-01 and 2.0.6 dated 2026-09-17
codyn-2.0.5/codyn/NEWS |only codyn-2.0.6/codyn/DESCRIPTION | 34 codyn-2.0.6/codyn/MD5 | 106 +- codyn-2.0.6/codyn/NAMESPACE | 22 codyn-2.0.6/codyn/NEWS.md |only codyn-2.0.6/codyn/R/RAC_change.R | 57 - codyn-2.0.6/codyn/R/RAC_difference.R | 82 - codyn-2.0.6/codyn/R/abundance_change.R | 21 codyn-2.0.6/codyn/R/abundance_difference.R | 58 - codyn-2.0.6/codyn/R/codyn-package.R | 137 -- codyn-2.0.6/codyn/R/community_diversity.R | 26 codyn-2.0.6/codyn/R/community_stability.R | 12 codyn-2.0.6/codyn/R/community_structure.R | 31 codyn-2.0.6/codyn/R/curve_change.R | 14 codyn-2.0.6/codyn/R/curve_difference.R | 16 codyn-2.0.6/codyn/R/data.R |only codyn-2.0.6/codyn/R/multivariate_change_and_difference.R | 41 codyn-2.0.6/codyn/R/rank_shift.R | 16 codyn-2.0.6/codyn/R/rate_change.R | 16 codyn-2.0.6/codyn/R/synchrony.R | 12 codyn-2.0.6/codyn/R/temporal_torus_translation.R | 8 codyn-2.0.6/codyn/R/turnover.R | 29 codyn-2.0.6/codyn/R/variance_ratio.R | 12 codyn-2.0.6/codyn/README.md | 8 codyn-2.0.6/codyn/build/vignette.rds |binary codyn-2.0.6/codyn/inst/WORDLIST |only codyn-2.0.6/codyn/inst/doc/Community_Stability_Metrics.R | 46 codyn-2.0.6/codyn/inst/doc/Community_Stability_Metrics.Rmd | 2 codyn-2.0.6/codyn/inst/doc/Community_Stability_Metrics.html | 614 +++++++----- codyn-2.0.6/codyn/inst/doc/Temporal_Diversity_Indices.R | 18 codyn-2.0.6/codyn/inst/doc/Temporal_Diversity_Indices.html | 560 ++++++---- codyn-2.0.6/codyn/inst/doc/codyn_overview.html | 198 ++- codyn-2.0.6/codyn/man/RAC_change.Rd | 59 - codyn-2.0.6/codyn/man/RAC_difference.Rd | 84 - codyn-2.0.6/codyn/man/abundance_change.Rd | 23 codyn-2.0.6/codyn/man/abundance_difference.Rd | 57 - codyn-2.0.6/codyn/man/codyn-package.Rd | 68 - codyn-2.0.6/codyn/man/collins08.Rd | 12 codyn-2.0.6/codyn/man/community_diversity.Rd | 30 codyn-2.0.6/codyn/man/community_stability.Rd | 12 codyn-2.0.6/codyn/man/community_structure.Rd | 31 codyn-2.0.6/codyn/man/confint.cyclic_shift.Rd | 8 codyn-2.0.6/codyn/man/curve_change.Rd | 14 codyn-2.0.6/codyn/man/curve_difference.Rd | 16 codyn-2.0.6/codyn/man/knz_001d.Rd | 12 codyn-2.0.6/codyn/man/mean_rank_shift.Rd | 8 codyn-2.0.6/codyn/man/multivariate_change.Rd | 20 codyn-2.0.6/codyn/man/multivariate_difference.Rd | 21 codyn-2.0.6/codyn/man/pplots.Rd | 16 codyn-2.0.6/codyn/man/rank_shift.Rd | 8 codyn-2.0.6/codyn/man/rate_change.Rd | 6 codyn-2.0.6/codyn/man/rate_change_interval.Rd | 10 codyn-2.0.6/codyn/man/synchrony.Rd | 12 codyn-2.0.6/codyn/man/turnover.Rd | 16 codyn-2.0.6/codyn/man/variance_ratio.Rd | 12 codyn-2.0.6/codyn/vignettes/Community_Stability_Metrics.Rmd | 2 56 files changed, 1417 insertions(+), 1336 deletions(-)
Title: Missing Data for Marked Hawkes Process
Description: Estimation of model parameters for marked Hawkes process.
Accounts for missing data in the estimation of the parameters.
Technical details found in (Tucker et al., 2019 <DOI:10.1016/j.spasta.2018.12.004>).
Author: J. Derek Tucker [aut, cre],
Lyndsay Shand [aut],
Stephen Rowe [aut],
John Lewis [aut]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between stpphawkes versions 0.2.2 dated 2025-03-10 and 0.2.4 dated 2026-09-17
DESCRIPTION | 10 ++-- MD5 | 57 ++++++++++++------------- NAMESPACE | 24 ++++++---- NEWS.md | 3 - R/homog_ppp.R | 5 +- R/inhomo_ppp.R | 19 ++++++-- R/mcmc.R | 18 +++++-- R/simulate_stpp_hawkes.R | 10 ++-- man/stpphawkes.Rd | 1 src/Makevars | 2 src/condInt_mcmc_stpp.cpp | 3 + src/condInt_mcmc_stpp_branching.cpp | 2 src/condInt_mcmc_stpp_branching_md.cpp | 6 ++ src/condInt_mcmc_stpp_branching_nonunif.cpp | 2 src/condInt_mcmc_stpp_branching_nonunif_md.cpp | 6 ++ src/condInt_mcmc_temporal.cpp | 4 + src/condInt_mcmc_temporal_branching.cpp | 2 src/condInt_mcmc_temporal_branching_md.cpp | 4 + src/condInt_mcmc_temporal_md.cpp | 7 ++- src/helper_functions.h | 21 ++++----- src/rng_seed.h |only src/simulate_stpp_hawkes.cpp | 16 ++++--- src/simulate_stpp_hawkes_nonunif.cpp | 16 ++++--- src/spatio_temporal_common.cpp | 11 +++- src/spatio_temporal_common_nonunif.cpp | 12 +++-- src/temporal_catmark.cpp | 2 src/temporal_catmark_common.cpp | 5 ++ src/temporal_catmark_md.cpp | 2 src/temporal_common.cpp | 16 ++++++- src/temporal_contmark.cpp | 2 30 files changed, 193 insertions(+), 95 deletions(-)
Title: Density and Abundance from Distance-Sampling Surveys
Description: Distance-sampling (<doi:10.1007/978-3-319-19219-2>)
is a field survey and analytical method that estimates density and
abundance of survey targets (e.g., animals) when
detection probability declines with observation distance.
Distance-sampling is popular in ecology,
especially when survey targets are observed from aerial platforms (e.g.,
airplane or drone), surface vessels (e.g., boat or truck), or along
walking transects. Analysis involves fitting smooth (parametric) curves to
histograms of observation distances and using those functions to
adjust density estimates for missed targets. Routines included here
fit curves to observation distance histograms, estimate effective
sampling area, density of targets in surveyed areas, and the abundance
of targets in a surrounding study area. Confidence interval estimation
uses built-in bootstrap resampling. Help files are extensive and have been
vetted by multiple authors. Many tutorials are available on the package's
website (URL below).
Author: Trent McDonald [cre, aut],
Jason Carlisle [aut],
Aidan McDonald [aut] ,
Ryan Nielson [ctb] ,
Ben Augustine [ctb] ,
James Griswald [ctb] ,
Patrick McKann [ctb] ,
Lacey Jeroue [ctb] ,
Hoffman Abigail [ctb] ,
Kleinsausser Michael [ctb] ,
Joel Reynolds [ [...truncated...]
Maintainer: Trent McDonald <trent@mcdonalddatasciences.com>
Diff between Rdistance versions 4.4.3 dated 2026-05-14 and 4.5.0 dated 2026-09-17
DESCRIPTION | 13 +-- MD5 | 73 +++++++++++++------- NAMESPACE | 5 + NEWS.md | 79 ++++++++++++++++++++++ R/Oscars.R |only R/abundEstim.R | 151 ++++++++++++++++++++++++------------------- R/bootstrap.R | 39 +++++++---- R/calcLineLength.R |only R/convexPartition.R |only R/dE.single.R | 37 ++++++++-- R/drawTransects.R |only R/exampleSurveyPoly.R |only R/findSpacing.R |only R/huber.start.limits.R | 8 +- R/integrateOneStepLines.R | 7 + R/makeLines.R |only R/makeLinesUtils.R |only R/mlEstimates.R | 4 - R/oneStep.like.R | 5 + R/oneStep.start.limits.R | 12 ++- R/oscarsLimits.R |only R/parseModel.R | 4 - R/pronghornAreas.R |only R/pronghornDfDocumentation.R |only R/setOptimizer.R | 12 ++- R/triangle.start.limits.R | 27 ++++--- R/zzz.R | 4 + data/exampleSurveyPoly.rda |only data/pronghornAreas.rda |only data/pronghornDf.rda |only inst/WORDLIST | 50 +++++++++++++- man/Oscars.Rd |only man/abundEstim.Rd | 46 ++++++------- man/autoDistSamp.Rd | 10 +- man/bootstrap.Rd | 11 ++- man/calcLineLength.Rd |only man/convexPartition.Rd |only man/dE.multi.Rd | 1 man/dE.single.Rd | 1 man/dfuncEstim.Rd | 1 man/drawTransects.Rd |only man/exampleSurveyPoly.Rd |only man/findSpacing.Rd |only man/integrateOneStepLines.Rd | 7 + man/makeLines.Rd |only man/oneBsIter.Rd | 7 + man/oneStep.like.Rd | 5 + man/oscarsLimits.Rd |only man/pronghornDf.Rd |only 49 files changed, 445 insertions(+), 174 deletions(-)
Title: Multivariate Bayesian Regression
Description: Fit, plot, and predict a multivariate response, using an arbitrary
univariate Bayesian regression model to independently fit basis components
(e.g., principal components) of the response (Francom et al., 2025 <DOI:10.1137/24M1644092>).
Author: Gavin Collins [aut, ctb],
J. Derek Tucker [ctb, cre] ,
Sandia National Laboratories [cph, fnd]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between mvBayes versions 1.2.2 dated 2026-07-30 and 1.2.3 dated 2026-09-17
DESCRIPTION | 11 + MD5 | 33 +++-- NAMESPACE | 2 NEWS.md | 3 R/basisSetup.R | 53 +++++++-- R/basisSetupElastic.R | 57 +++++----- R/cv.R | 140 +++++++++++++----------- R/generics.R | 13 +- R/mvBayes.R | 91 +++++++++------- R/mvBayesElastic.R | 41 ++++--- R/rsobol.R | 15 +- R/sobol.R | 248 ++++++++++++++++++++++++++------------------ R/splinet.R | 4 README.md | 2 inst/doc/friedman_demo.html | 86 +++++++-------- man/mvCV.Rd | 3 man/traceplot.Rd | 30 +---- man/traceplot.mvBayes.Rd |only 18 files changed, 480 insertions(+), 352 deletions(-)
Title: Bayesian Projection Pursuit Regression
Description: Bayesian fitting of projection pursuit regression model.
Built to handle continuous and categorical inputs and
scalar output (Collins et al., 2023 <DOI:10.1007/s11222-023-10334-z>).
Author: Gavin Collins [aut, ctb],
J. Derek Tucker [ctb, cre]
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between BayesPPR versions 0.1.0 dated 2026-05-18 and 0.2.0 dated 2026-09-17
DESCRIPTION | 10 +++++----- MD5 | 21 +++++++++++---------- NEWS.md | 19 +++++++++++++++++++ R/bppr.R | 37 ++++++++++++++++++++++++++++++------- R/bppr_pca.R | 6 +++++- R/matrix_computation.R | 14 ++++++++++++++ R/pca.R | 21 +++++++++++++++++++-- R/predict.R | 34 ++++++++++++++++++++++------------ R/predict_pca.R | 15 +++++++++++---- R/resume.R | 6 ++++-- README.md | 2 ++ man/figures |only 12 files changed, 142 insertions(+), 43 deletions(-)
Title: 'R' Bindings for 'TMB'
Description: Native 'R' interface to 'TMB' (Template Model Builder) so models can be written entirely in 'R' rather than 'C++'. Automatic differentiation, to any order, is available for a rich subset of 'R' features, including linear algebra for dense and sparse matrices, complex arithmetic, Fast Fourier Transform, probability distributions and special functions. 'RTMB' provides easy access to model fitting and validation following the principles of Kristensen, K., Nielsen, A., Berg, C. W., Skaug, H., & Bell, B. M. (2016) <DOI:10.18637/jss.v070.i05> and Thygesen, U.H., Albertsen, C.M., Berg, C.W. et al. (2017) <DOI:10.1007/s10651-017-0372-4>.
Author: Kasper Kristensen [aut, cre]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between RTMB versions 1.9 dated 2026-03-20 and 2.0 dated 2026-09-17
DESCRIPTION | 8 +- MD5 | 66 +++++++++-------- NAMESPACE | 4 - NEWS | 24 ++++++ R/00roxygen.R | 8 +- R/RcppExports.R | 36 +++++++++ R/advector.R | 65 +++++++++++++++-- R/experimental.R | 49 +++++++++++-- R/integrate.R | 2 R/methods.R | 27 +++++++ R/mvgauss.R | 37 ++++------ R/sdreport.R |only R/sim.R | 9 ++ R/zzz.R | 2 build/vignette.rds |binary inst/doc/RTMB-advanced.html | 4 - inst/doc/RTMB-introduction.html | 6 - inst/doc/RTMB-tips.html | 6 - inst/include/CallRTMB.hpp | 2 inst/include/config.h | 2 inst/tinytest/test-integration_methods.R |only inst/tinytest/test-model-spde.R | 2 inst/tinytest/test-sequential_reduction.R |only man/ADintegrate.Rd | 2 man/Distributions.Rd | 28 ++++++- man/MVgauss.Rd | 2 src/Makevars | 5 + src/Makevars.win | 5 + src/RTMB_tape.cpp | 24 ++++++ src/RcppExports.cpp | 111 ++++++++++++++++++++++++++++++ src/branching.cpp | 2 src/config.h | 2 src/integrate.cpp | 4 - src/lse_sparse.cpp |only src/math.cpp | 34 +++++++++ src/misc.cpp | 2 36 files changed, 482 insertions(+), 98 deletions(-)
Title: Switzerland's Data Series in One Place
Description: Download and import open Swiss economic time series from
'dataseries.org' <https://dataseries.org>, a comprehensive and
up-to-date collection of public data from Switzerland. Series are
retrieved through the public 'dataseries.org' API and imported as a
'data.frame' or 'ts' object.
Author: Christoph Sax [aut, cre, cph],
Jannes Muenchow [ctb]
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between dataseries versions 1.0.0 dated 2026-06-13 and 1.1.0 dated 2026-09-17
DESCRIPTION | 15 ++++++++------- LICENSE |only MD5 | 22 ++++++++++++++-------- NEWS.md | 33 +++++++++++++++++++++++++++++++++ R/catalog.R | 34 +++++++++++++++++++++++++--------- R/utils.R | 34 ++++++++++++++++++++++++++++------ README.md | 26 ++++++++++++++++++++++++-- build |only inst |only man/ds_catalog.Rd | 10 +++++++++- man/ds_search.Rd | 10 +++++++++- tests/testthat/test-helpers.R | 37 +++++++++++++++++++++++++++++++++++++ vignettes |only 13 files changed, 187 insertions(+), 34 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
Posit Software, PBC [cph, fnd],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.60 dated 2026-06-16 and 0.61 dated 2026-09-17
tinytex-0.60/tinytex/tests/test-ci.R |only tinytex-0.60/tinytex/tests/test-cran.R |only tinytex-0.61/tinytex/DESCRIPTION | 6 +++--- tinytex-0.61/tinytex/MD5 | 17 +++++++++-------- tinytex-0.61/tinytex/R/install.R | 2 +- tinytex-0.61/tinytex/R/latex.R | 18 ++++++++++++------ tinytex-0.61/tinytex/man/latexmk.Rd | 9 ++++++--- tinytex-0.61/tinytex/tests/test-all.R |only tinytex-0.61/tinytex/tests/test-ci/bib |only tinytex-0.61/tinytex/tests/test-ci/test-install.R | 5 +++-- tinytex-0.61/tinytex/tests/test-ci/test-latex.R | 11 +++++++++++ 11 files changed, 45 insertions(+), 23 deletions(-)
Title: Manipulate and Analyze Round Robin Dyadic Data
Description: Provides utilities for processing and analyzing dyadic data
collected using a round-robin design, in which each person in a group
rates or interacts with every other person on at least one variable.
Data manipulation functions prepare datasets for dyadic data analysis by
creating the actor and partner dummy variables required by the social
relations model (SRM). Analysis functions implement the SRM using
multilevel modeling via a custom 'nlme' covariance class ('pdSRM'),
following the approach of Snijders and Kenny (1999)
<doi:10.1111/j.1475-6811.1999.tb00204.x> and Knight and Humphrey (2019)
<doi:10.1037/0000115-019>. The package estimates group, actor, partner,
and relationship variance components along with generalized and dyadic
reciprocity correlations, and supports both null and fixed-effects models.
Author: Andrew Knight [aut, cre, cph]
Maintainer: Andrew Knight <knightap@wustl.edu>
Diff between roundRobinR versions 1.0.1 dated 2026-04-21 and 2.0.0 dated 2026-09-17
roundRobinR-1.0.1/roundRobinR/R/createDummies.R |only roundRobinR-1.0.1/roundRobinR/R/srmPseudoRSq.R |only roundRobinR-1.0.1/roundRobinR/R/srmRun.R |only roundRobinR-1.0.1/roundRobinR/R/srmVarPct.R |only roundRobinR-2.0.0/roundRobinR/DESCRIPTION | 12 +- roundRobinR-2.0.0/roundRobinR/MD5 | 42 +++++--- roundRobinR-2.0.0/roundRobinR/NAMESPACE | 10 + roundRobinR-2.0.0/roundRobinR/NEWS.md | 42 ++++++++ roundRobinR-2.0.0/roundRobinR/R/cpsrm.R |only roundRobinR-2.0.0/roundRobinR/R/cpsrm_run.R |only roundRobinR-2.0.0/roundRobinR/R/create_cp_dummies.R |only roundRobinR-2.0.0/roundRobinR/R/create_dummies.R |only roundRobinR-2.0.0/roundRobinR/R/deprecated.R |only roundRobinR-2.0.0/roundRobinR/R/srm_pseudo_rsq.R |only roundRobinR-2.0.0/roundRobinR/R/srm_run.R |only roundRobinR-2.0.0/roundRobinR/R/srm_var_pct.R |only roundRobinR-2.0.0/roundRobinR/build/partial.rdb |binary roundRobinR-2.0.0/roundRobinR/build/vignette.rds |binary roundRobinR-2.0.0/roundRobinR/inst/doc/introduction.html | 77 +++++++++------ roundRobinR-2.0.0/roundRobinR/man/cpsrm.Rd |only roundRobinR-2.0.0/roundRobinR/man/cpsrmRun.Rd |only roundRobinR-2.0.0/roundRobinR/man/cpsrm_run.Rd |only roundRobinR-2.0.0/roundRobinR/man/createDummies.Rd | 51 ++------- roundRobinR-2.0.0/roundRobinR/man/create_cp_dummies.Rd |only roundRobinR-2.0.0/roundRobinR/man/create_dummies.Rd |only roundRobinR-2.0.0/roundRobinR/man/print.cpsrm.Rd |only roundRobinR-2.0.0/roundRobinR/man/srmPseudoRSq.Rd | 58 +---------- roundRobinR-2.0.0/roundRobinR/man/srmRun.Rd | 49 +-------- roundRobinR-2.0.0/roundRobinR/man/srmVarPct.Rd | 43 -------- roundRobinR-2.0.0/roundRobinR/man/srm_pseudo_rsq.Rd |only roundRobinR-2.0.0/roundRobinR/man/srm_run.Rd |only roundRobinR-2.0.0/roundRobinR/man/srm_var_pct.Rd |only roundRobinR-2.0.0/roundRobinR/man/summary.cpsrm.Rd |only 33 files changed, 168 insertions(+), 216 deletions(-)
Title: Neural Networks Made Algebraic
Description: Build, compose, stack, sum, and realize feed-forward neural
networks as algebraic objects. Implements the calculus and constructive
approximations described by Rafi, Padgett, and Nakarmi (2024)
<doi:10.48550/arXiv.2402.01058>, Grohs, Hornung, Jentzen, et al. (2023)
<doi:10.1007/s10444-022-09970-2>, and Jentzen, Kuckuck, and von
Wurstemberger (2023) <doi:10.48550/arXiv.2310.20360>. Includes neural
network polynomials, transcendental-function approximations,
multidimensional maximum convolution, and vectorized batch realization.
Author: Shakil Rafi [aut, cre] ,
Joshua Lee Padgett [aut] ,
Ukash Nakarmi [ctb]
Maintainer: Shakil Rafi <sarafi@uark.edu>
Diff between nnR versions 0.1.0 dated 2024-02-14 and 0.2.0 dated 2026-09-17
nnR-0.1.0/nnR/man/A.Rd |only nnR-0.1.0/nnR/man/A_k.Rd |only nnR-0.1.0/nnR/man/B.Rd |only nnR-0.1.0/nnR/man/C_k.Rd |only nnR-0.1.0/nnR/man/ck.Rd |only nnR-0.2.0/nnR/DESCRIPTION | 33 nnR-0.2.0/nnR/MD5 | 130 +-- nnR-0.2.0/nnR/NAMESPACE | 55 + nnR-0.2.0/nnR/NEWS.md |only nnR-0.2.0/nnR/R/Aff.R | 63 - nnR-0.2.0/nnR/R/Csn.R | 32 nnR-0.2.0/nnR/R/Etr.R | 36 nnR-0.2.0/nnR/R/Id.R | 37 - nnR-0.2.0/nnR/R/MC.R | 78 -- nnR-0.2.0/nnR/R/Mxm.R | 69 - nnR-0.2.0/nnR/R/Nrm.R | 46 - nnR-0.2.0/nnR/R/Phi.R | 18 nnR-0.2.0/nnR/R/Phi_k.R | 24 nnR-0.2.0/nnR/R/Pnm.R |only nnR-0.2.0/nnR/R/Prd.R | 50 - nnR-0.2.0/nnR/R/Pwr.R | 86 +- nnR-0.2.0/nnR/R/Sne.R | 35 nnR-0.2.0/nnR/R/Sqr.R | 59 - nnR-0.2.0/nnR/R/Tay.R | 83 -- nnR-0.2.0/nnR/R/Tun.R | 60 - nnR-0.2.0/nnR/R/Xpn.R | 36 nnR-0.2.0/nnR/R/activations.R | 36 nnR-0.2.0/nnR/R/aux_fun.R | 57 - nnR-0.2.0/nnR/R/comp.R | 142 --- nnR-0.2.0/nnR/R/i.R | 14 nnR-0.2.0/nnR/R/instantiation.R | 126 ++- nnR-0.2.0/nnR/R/is_nn.R | 82 +- nnR-0.2.0/nnR/R/nn_creator.R | 53 - nnR-0.2.0/nnR/R/nn_sum.R | 88 +- nnR-0.2.0/nnR/R/nn_viewer.R | 93 ++ nnR-0.2.0/nnR/R/scalar_mult.R | 76 -- nnR-0.2.0/nnR/R/stacking.R | 156 ++-- nnR-0.2.0/nnR/R/validation.R |only nnR-0.2.0/nnR/README.md |only nnR-0.2.0/nnR/build/vignette.rds |binary nnR-0.2.0/nnR/inst/doc/nnR.R | 36 nnR-0.2.0/nnR/inst/doc/nnR.Rmd | 95 +- nnR-0.2.0/nnR/inst/doc/nnR.html | 692 +++++++++---------- nnR-0.2.0/nnR/man/Aff.Rd | 2 nnR-0.2.0/nnR/man/Csn.Rd | 19 nnR-0.2.0/nnR/man/Etr.Rd | 5 nnR-0.2.0/nnR/man/MC.Rd | 15 nnR-0.2.0/nnR/man/Mxm.Rd | 7 nnR-0.2.0/nnR/man/Pnm.Rd |only nnR-0.2.0/nnR/man/Prd.Rd | 12 nnR-0.2.0/nnR/man/Pwr.Rd | 12 nnR-0.2.0/nnR/man/Sne.Rd | 20 nnR-0.2.0/nnR/man/Sqr.Rd | 14 nnR-0.2.0/nnR/man/Tay.Rd | 19 nnR-0.2.0/nnR/man/Tun.Rd | 2 nnR-0.2.0/nnR/man/Xpn.Rd | 23 nnR-0.2.0/nnR/man/comp.Rd | 1 nnR-0.2.0/nnR/man/create_nn.Rd | 3 nnR-0.2.0/nnR/man/dep.Rd | 2 nnR-0.2.0/nnR/man/draw_nn.Rd |only nnR-0.2.0/nnR/man/figures |only nnR-0.2.0/nnR/man/inst.Rd | 9 nnR-0.2.0/nnR/man/is_nn.Rd | 17 nnR-0.2.0/nnR/man/nn_sum.Rd | 3 nnR-0.2.0/nnR/man/nn_sum_many.Rd |only nnR-0.2.0/nnR/man/param.Rd | 2 nnR-0.2.0/nnR/man/realize_nn.Rd |only nnR-0.2.0/nnR/man/stk.Rd | 7 nnR-0.2.0/nnR/man/stk_many.Rd |only nnR-0.2.0/nnR/man/view_nn.Rd | 3 nnR-0.2.0/nnR/tests/testthat/test-core-correctness.R |only nnR-0.2.0/nnR/tests/testthat/test-nn_viewer.R | 8 nnR-0.2.0/nnR/vignettes/nnR.Rmd | 95 +- nnR-0.2.0/nnR/vignettes/references.bib | 13 74 files changed, 1548 insertions(+), 1541 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis (Balduzzi et al., 2023) <doi:10.18637/jss.v106.i02> and supporting Schwarzer et al. (2015) <doi:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <doi:10.1002/jrsm.1058>;
- additive network meta-analysis for combinations of treatments (Rücker et al., 2020) <doi:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <doi:10.1002/sim.8158>, or penalised logistic regression (Evrenoglou et al., 2022) <doi:10.1002/sim.9562>;
- rankograms and ranking of treatments by the Surface under the cumulative ranking curve (SUCRA) (Salanti et al., 2013) <doi:10.1016/j.jclinepi.2010.03.016>;
- ranking of treatments using P-scores (frequentist analogue of SUCRAs without resampling) according to [...truncated...]
Author: Gerta Ruecker [aut] ,
Ulrike Krahn [aut],
Jochem Koenig [aut] ,
Orestis Efthimiou [aut] ,
Annabel Davies [aut] ,
Theodoros Papakonstantinou [aut] ,
Theodoros Evrenoglou [ctb] ,
Krzysztof Ciomek [ctb] ,
Nana-adjoa Kwarteng [ctb] ,
Noosheen R. Tahmasebi [...truncated...]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between netmeta versions 3.6-1 dated 2026-06-20 and 3.7-0 dated 2026-09-17
DESCRIPTION | 18 +- MD5 | 68 ++++--- NAMESPACE | 365 +++++++++++++++++++++++------------------- NEWS.md | 46 +++++ R/heatplot.netpath.R |only R/netgraph.netmeta.R | 6 R/netleague.R | 22 +- R/netmeta-package.R | 30 ++- R/netpath.R |only R/netpath_internal.R |only R/netposet.R | 143 ++++++++++------ R/netrank.R | 136 ++++++++++----- R/netsplit.R | 58 +++--- R/nettable.R | 5 R/plot.netposet.R | 46 ++++- R/plot.netrank.R | 121 ++++++++++--- R/rankogram.default.R | 41 +++- R/rankogram.netmeta.R | 35 ++-- R/updateversion.R | 6 R/vikor-internal.R |only R/vikor.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/netmeta-workflow.pdf |binary inst/doc/netmeta.pdf |binary man/heatplot.netpath.Rd |only man/netgraph.netmeta.Rd | 6 man/netleague.Rd | 10 - man/netmeta-package.Rd | 16 + man/netpath.Rd |only man/netposet.Rd | 34 ++- man/netrank.Rd | 58 ++++-- man/netsplit.Rd | 5 man/nettable.Rd | 5 man/plot.netposet.Rd | 12 - man/plot.netrank.Rd | 41 +++- man/rankogram.default.Rd | 39 +++- man/rankogram.netmeta.Rd | 35 ++-- man/vikor.Rd |only 39 files changed, 925 insertions(+), 482 deletions(-)
Title: Asymptotic Timing
Description: Computing and visualizing comparative
asymptotic timings of different algorithms and code versions.
Also includes functionality for comparing empirical timings with
expected references such as linear or quadratic,
<https://en.wikipedia.org/wiki/Asymptotic_computational_complexity>
Also includes functionality for measuring asymptotic memory and other
quantities.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between atime versions 2026.4.2 dated 2026-04-04 and 2026.9.17 dated 2026-09-17
DESCRIPTION | 24 +++--- MD5 | 72 ++++++++++---------- NAMESPACE | 1 NEWS | 29 ++++++++ R/atime.R | 62 +++++++++-------- R/references.R | 10 +- R/test.R | 95 ++++++++++++++++---------- R/versions.R | 132 ++++++++++++++++++++++++------------- build/vignette.rds |binary inst/CITATION |only inst/doc/Custom_Plots.R | 2 inst/doc/Custom_Plots.Rmd | 2 inst/doc/Custom_Plots.html | 27 +++---- inst/doc/Custom_References.R | 46 ++++++------- inst/doc/Custom_References.Rmd | 50 +++++++------- inst/doc/Custom_References.html | 141 +++++++++++++++++++--------------------- inst/doc/Custom_Units.R | 6 - inst/doc/Custom_Units.Rmd | 10 +- inst/doc/Custom_Units.html | 38 +++++----- inst/doc/cum_median.html | 24 +++--- inst/doc/regex.html | 34 +++++---- inst/doc/sparse.R | 6 - inst/doc/sparse.Rmd | 6 - inst/doc/sparse.html | 56 ++++++++------- inst/example_tests.R | 7 + man/R_CMD_INSTALL.Rd |only man/atime.Rd | 20 ++++- man/atime_pkg.Rd | 10 +- man/atime_test.Rd | 9 +- man/atime_test_list.Rd | 51 +++++--------- man/atime_versions.Rd | 26 +++++-- man/atime_versions_exprs.Rd | 20 ++++- man/glob_find_replace.Rd | 3 tests/testthat/test-CRAN.R | 76 +++++++++++---------- vignettes/Custom_Plots.Rmd | 2 vignettes/Custom_References.Rmd | 50 +++++++------- vignettes/Custom_Units.Rmd | 10 +- vignettes/sparse.Rmd | 6 - 38 files changed, 646 insertions(+), 517 deletions(-)
Title: Reproducible Code for 'Shiny' Objects
Description: Provides functionality to extract reactive expressions from a 'shiny' application and
convert them into stand-alone R scripts. This enables users to reproduce tables and visualisations
outside the interactive UI, facilitating integration into static reports or automated workflows
without requiring access to the original application source code.
Author: Ashley Baldry [aut, cre]
Maintainer: Ashley Baldry <ashley.baldry@acuityanalytics.com>
Diff between shinyreprex versions 0.2.0 dated 2026-06-29 and 0.3.0 dated 2026-09-17
DESCRIPTION | 15 - LICENSE | 4 MD5 | 53 +++-- NAMESPACE | 3 NEWS.md | 32 +++ R/S7_utils.R | 4 R/call_chunk_if.R | 17 + R/call_chunk_utils.R | 15 + R/chunk_reactive.R | 32 --- R/reactive_expression.R |only R/register_reactives.R |only R/reprex_lockfile.R |only R/reprex_reactive.R | 170 ++++++++--------- R/walk_packages.R |only README.md | 47 ++++ build/vignette.rds |binary inst/WORDLIST | 7 inst/doc/shinyreprex.Rmd | 152 ++++++++++++++- inst/doc/shinyreprex.html | 267 +++++++++++++++++++++------ inst/examples-shiny |only man/assert_reactives.Rd |only man/call_reactive_env.Rd |only man/reactive_expression.Rd |only man/register_reactives.Rd |only man/registered_reactives.Rd |only man/reprex_lockfile.Rd |only man/reprex_packages.Rd |only man/reprex_store.Rd |only man/walk_packages.Rd |only tests/testthat/test-call_chunk_if.R | 184 ++++++++++++++++++ tests/testthat/test-call_chunk_utils.R | 32 +++ tests/testthat/test-canary-shiny-internals.R |only tests/testthat/test-examples-shiny.R |only tests/testthat/test-register_reactives.R |only tests/testthat/test-reprex_lockfile.R |only tests/testthat/test-walk_packages.R |only vignettes/shinyreprex.Rmd | 152 ++++++++++++++- 37 files changed, 975 insertions(+), 211 deletions(-)
Title: Sample Size Calculation Tools
Description: Functions for sample size estimation and simulation in clinical
trials. Includes methods for selecting the best group using the
Indifference-zone approach, as well as designs for non-inferiority,
equivalence, and negative binomial models. For the sample size calculation
for non-inferiority of vaccines, the approach is based on Fleming, Powers,
and Huang (2021) <doi:10.1177/1740774520988244>. The Indifference-zone
approach is based on Sobel and Huyett (1957) <doi:10.1002/j.1538-7305.1957.tb02411.x> and
Bechhofer, Santner, and Goldsman (1995, ISBN:978-0-471-57427-9).
Author: John J. Aponte [aut, cre] ,
Chris Gast [ctb]
Maintainer: John J. Aponte <john.j.aponte@gmail.com>
Diff between ssutil versions 1.1.0 dated 2026-09-06 and 1.2.0 dated 2026-09-17
DESCRIPTION | 8 +- MD5 | 68 +++++++++++------------ NAMESPACE | 2 NEWS.md | 32 ++++++++++ R/multz.R | 50 ++++++++++------- R/prophr.R | 8 +- R/sim_power_best_bin_rank.R | 21 ++++--- R/sim_power_best_binomial.R | 61 ++++++++++++++------ R/sim_power_equivalence_normal.R | 7 ++ R/sim_power_nbinom.R | 33 ++++++++--- R/sim_power_non_inferiority.R | 15 ++++- R/ss_best_binomial.R | 62 +++++++++++++++++++-- R/ss_best_normal.R | 9 +-- R/ss_ni_ve.R | 70 ++++++++++++++++++------ inst/doc/iz_binomial.html | 16 ++--- inst/doc/iz_normal.html | 2 inst/doc/non_inferiority.R | 4 - inst/doc/non_inferiority.Rmd | 12 ++-- inst/doc/non_inferiority.html | 10 +-- man/multp.Rd | 15 +++-- man/multz.Rd | 21 +++---- man/power_best_normal.Rd | 4 - man/prophr.Rd | 4 - man/sim_power_best_bin_rank.Rd | 21 ++++--- man/sim_power_equivalence_normal.Rd | 7 ++ man/sim_power_nbinom.Rd | 10 +++ man/sim_power_ni_normal.Rd | 9 ++- man/ss_ni_ve.Rd | 45 ++++++++++++++- tests/testthat/test-multz.R | 5 + tests/testthat/test-sim_power_nbinom.R | 3 + tests/testthat/test-sim_power_non_inferiority.R | 58 +++++++++++++++++++ tests/testthat/test-ss_best_binomial.R | 51 ++++++++++++----- tests/testthat/test-ss_best_normal.R | 41 +++++++++----- tests/testthat/test-ss_ni_ve.R | 67 +++++++++++++++++++++- vignettes/non_inferiority.Rmd | 12 ++-- 35 files changed, 645 insertions(+), 218 deletions(-)
Title: Sparse and Group Sparse Linear Models
Description: Fits the solution paths of classical sparse regression models with efficient active set algorithms by solving small sub-problems. Include LASSO, SCAD, MCP, (Sparse) Group-LASSO, Cooperative-LASSO, (Group) LAVA, (Generalized) Fused-Lasso and (Generalized) Elastic-Net. Also provides methods for model selection purpose (information criteria, cross-validation, stability selection).
Author: Julien Chiquet [aut, cre]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between quadrupen versions 1.0-0 dated 2026-06-05 and 1.1-0 dated 2026-09-17
DESCRIPTION | 8 MD5 | 134 ++++++------ NEWS.md | 22 ++ R/DataModel-R6Class.R | 20 + R/QuadrupenFit-R6Class.R | 27 +- R/group-lava.R | 2 R/group_sparse_lm.R | 2 R/init.R | 2 R/ridge.R | 3 R/sparse_lm.R | 3 R/utils.R | 2 build/vignette.rds |binary inst/doc/group-sparse-regression.html | 26 +- inst/doc/lava.R | 20 - inst/doc/lava.Rmd | 20 - inst/doc/lava.html | 26 +- inst/doc/structured-signal-recovery.R | 2 inst/doc/structured-signal-recovery.Rmd | 2 inst/doc/structured-signal-recovery.html | 4 man/DataModel.Rd | 23 ++ man/bounded_reg.Rd | 3 man/figures/breg-nostruct-1.png |binary man/figures/bregridge-nostruct-1.png |binary man/figures/bregridge_struct-1.png |binary man/figures/enet-nostruct-1.png |binary man/figures/enet_struct-1.png |binary man/figures/fused-lasso-1.png |binary man/figures/grplasso-l1l2-1.png |binary man/figures/grplasso-l1linf-1.png |binary man/figures/img-cor-struct-1.png |binary man/figures/lasso-nostruct-1.png |binary man/figures/lava-nostruct-1.png |binary man/figures/lava-nostruct-2.png |binary man/figures/lava_struct-1.png |binary man/figures/lava_struct-2.png |binary man/figures/mcp-nostruct-1.png |binary man/figures/ridge-nostruct-1.png |binary man/figures/ridge_struct-1.png |binary man/figures/scad-nostruct-1.png |binary man/figures/sparse-cooplasso-1.png |binary man/figures/sparse-grpenet-l1l2-1.png |binary man/figures/sparse-grplasso-coop-1.png |binary man/figures/sparse-grplasso-l1l2-1.png |binary man/figures/sparse-grplasso-l1linf-1.png |binary man/group_lava.Rd | 3 man/group_sparse_lm.Rd | 3 man/lava.Rd | 3 man/ridge.Rd | 3 man/sparse_lm.Rd | 3 src/Makevars | 3 src/Makevars.win | 5 src/Quadrupen/ActiveSet.h | 330 +++++++++++++++++++++---------- src/Quadrupen/BaseLava.h | 17 + src/Quadrupen/BoundedRegression.cpp | 52 +++- src/Quadrupen/BoundedRegression.h | 3 src/Quadrupen/Optimizer.cpp | 139 ++++++++----- src/Quadrupen/Optimizer.h | 14 + src/Quadrupen/OptimizerGroup.h | 275 +++++++++++++++++-------- src/Quadrupen/OptimizerSparse.h | 49 ++-- src/Quadrupen/PenaltyGroup.cpp | 3 src/Quadrupen/RegressionData.h | 15 + src/Quadrupen/RidgeRegression.cpp | 21 + src/Quadrupen/SparseRegularizer.h | 2 src/wrapper_FusedLasso.cpp | 4 src/wrapper_RidgeRegression.cpp | 5 tests/testthat/dataTest-boundedReg.rds |binary vignettes/lava.Rmd | 20 - vignettes/structured-signal-recovery.Rmd | 2 68 files changed, 876 insertions(+), 449 deletions(-)
Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Author: Myles Lewis [aut, cre] ,
Tom Willis [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between locuszoomr versions 1.0.0 dated 2026-09-03 and 1.1.0 dated 2026-09-17
DESCRIPTION | 8 MD5 | 49 +-- NAMESPACE | 311 +++++++++++-------- NEWS.md | 7 R/genetrack_ly.R | 3 R/genetracks.R | 2 R/locus.R | 60 ++- R/locus_plot.R | 1 R/locus_plotly.R | 53 +++ R/sanity_check.R |only R/scatter_plot.R | 28 + R/scatter_plotly.R | 88 ++++- R/zoom.R | 701 +++++++++++++++++++++++++++----------------- R/zoom_funcs.R |only README.md | 2 inst/doc/locuszoomr.Rmd | 2 inst/doc/locuszoomr.html | 4 inst/doc/zoom_browser.R | 19 + inst/doc/zoom_browser.Rmd | 61 +++ inst/doc/zoom_browser.html | 61 +++ man/locus.Rd | 5 man/locus_plotly.Rd | 15 man/sanity_check.Rd |only man/zoom.Rd | 51 ++- vignettes/dbl_gwas_manh.png |only vignettes/dbl_loc_eqtl.png |only vignettes/locuszoomr.Rmd | 2 vignettes/zoom_browser.Rmd | 61 +++ 28 files changed, 1076 insertions(+), 518 deletions(-)