Title: Genome Wide Association Studies
Description: Fast single trait Genome Wide Association Studies (GWAS) following
the method described in Kang et al. (2010), <doi:10.1038/ng.548>.
One of a series of statistical genetic packages for streamlining the
analysis of typical plant breeding experiments developed by Biometris.
Author: Bart-Jan van Rossum [aut, cre] ,
Willem Kruijer [aut] ,
Fred van Eeuwijk [ctb] ,
Martin Boer [ctb] ,
Marcos Malosetti [ctb] ,
Daniela Bustos-Korts [ctb] ,
Emilie Millet [ctb] ,
Joao Paulo [ctb] ,
Maikel Verouden [ctb] ,
Ron Wehrens [ctb] ,
Choazhi Zh [...truncated...]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenGWAS versions 1.0.13 dated 2026-02-19 and 1.0.14 dated 2026-09-22
DESCRIPTION | 10 +-- MD5 | 24 ++++---- NAMESPACE | 10 ++- NEWS.md | 4 + R/GWASHelp.R | 67 ++++++++++++++----------- README.md | 8 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/GWAS.html | 91 +++++++++++++++------------------- man/figures/README-manhattanStg-1.png |binary man/figures/README-qtlStgNorm-1.png |binary man/readVcf.Rd | 4 - man/statgenGWAS-package.Rd | 1 13 files changed, 116 insertions(+), 103 deletions(-)
Title: Seasonal Adjustment with TRAMO-SEATS in 'JDemetra+' 3.x
Description: Interface to 'JDemetra+' 3.x (<https://github.com/jdemetra>)
time series analysis software. It offers full access to options and
outputs of 'TRAMO-SEATS' (Time series Regression with ARIMA noise,
Missing values and Outliers - Signal Extraction in ARIMA Time Series),
including 'TRAMO' modelling (ARIMA model with outlier detection and
trading days adjustment). ARIMA = AutoRegressive Integrated Moving
Average.
Author: Jean Palate [aut],
Alain Quartier-la-Tente [aut] ,
Tanguy Barthelemy [aut, cre, art],
Anna Smyk [aut],
Eulalie Delaune [aut]
Maintainer: Tanguy Barthelemy <timeserieswithjdemetraandr@gmail.com>
Diff between rjd3tramoseats versions 3.8.0 dated 2026-07-10 and 3.9.0 dated 2026-09-22
rjd3tramoseats-3.8.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-api-3.8.0.jar |only rjd3tramoseats-3.8.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-core-3.8.0.jar |only rjd3tramoseats-3.8.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-protobuf-3.8.0.jar |only rjd3tramoseats-3.8.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-r-3.8.0.jar |only rjd3tramoseats-3.9.0/rjd3tramoseats/DESCRIPTION | 25 rjd3tramoseats-3.9.0/rjd3tramoseats/MD5 | 86 rjd3tramoseats-3.9.0/rjd3tramoseats/NAMESPACE | 258 - rjd3tramoseats-3.9.0/rjd3tramoseats/NEWS.md | 217 - rjd3tramoseats-3.9.0/rjd3tramoseats/R/deprecated.R | 130 rjd3tramoseats-3.9.0/rjd3tramoseats/R/print.R | 840 ++-- rjd3tramoseats-3.9.0/rjd3tramoseats/R/revisions.R | 269 - rjd3tramoseats-3.9.0/rjd3tramoseats/R/rjd3tramoseats-package.R | 12 rjd3tramoseats-3.9.0/rjd3tramoseats/R/seats.R | 88 rjd3tramoseats-3.9.0/rjd3tramoseats/R/seats_spec.R | 326 - rjd3tramoseats-3.9.0/rjd3tramoseats/R/tramo_generic.R | 162 rjd3tramoseats-3.9.0/rjd3tramoseats/R/tramo_outliers.R | 172 rjd3tramoseats-3.9.0/rjd3tramoseats/R/tramo_spec.R | 248 - rjd3tramoseats-3.9.0/rjd3tramoseats/R/tramoseats.R | 1930 +++++----- rjd3tramoseats-3.9.0/rjd3tramoseats/R/tramoseats_rslts.R | 162 rjd3tramoseats-3.9.0/rjd3tramoseats/R/tramoseats_spec.R | 868 ++-- rjd3tramoseats-3.9.0/rjd3tramoseats/R/utils.R | 52 rjd3tramoseats-3.9.0/rjd3tramoseats/R/zzz.R | 178 rjd3tramoseats-3.9.0/rjd3tramoseats/README.md | 252 - rjd3tramoseats-3.9.0/rjd3tramoseats/inst/WORDLIST | 102 rjd3tramoseats-3.9.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-api-3.9.0.jar |only rjd3tramoseats-3.9.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-core-3.9.0.jar |only rjd3tramoseats-3.9.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-protobuf-3.9.0.jar |only rjd3tramoseats-3.9.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-r-3.9.0.jar |only rjd3tramoseats-3.9.0/rjd3tramoseats/inst/proto/tramoseats.proto | 372 - rjd3tramoseats-3.9.0/rjd3tramoseats/java/README | 12 rjd3tramoseats-3.9.0/rjd3tramoseats/man/deprecated-rjd3tramoseats.Rd | 126 rjd3tramoseats-3.9.0/rjd3tramoseats/man/figures/logo.svg | 1326 +++--- rjd3tramoseats-3.9.0/rjd3tramoseats/man/get_tramoseats_option.Rd | 42 rjd3tramoseats-3.9.0/rjd3tramoseats/man/jd3_utilities.Rd | 64 rjd3tramoseats-3.9.0/rjd3tramoseats/man/refresh.Rd | 426 +- rjd3tramoseats-3.9.0/rjd3tramoseats/man/rjd3tramoseats-package.Rd | 69 rjd3tramoseats-3.9.0/rjd3tramoseats/man/seats_decompose.Rd | 134 rjd3tramoseats-3.9.0/rjd3tramoseats/man/set_seats.Rd | 230 - rjd3tramoseats-3.9.0/rjd3tramoseats/man/terror.Rd | 105 rjd3tramoseats-3.9.0/rjd3tramoseats/man/tramo.Rd | 141 rjd3tramoseats-3.9.0/rjd3tramoseats/man/tramo_forecast.Rd | 89 rjd3tramoseats-3.9.0/rjd3tramoseats/man/tramo_outliers.Rd | 108 rjd3tramoseats-3.9.0/rjd3tramoseats/man/tramoseats.Rd | 154 rjd3tramoseats-3.9.0/rjd3tramoseats/man/tramoseats_dictionary.Rd | 110 rjd3tramoseats-3.9.0/rjd3tramoseats/man/tramoseats_option.Rd | 41 rjd3tramoseats-3.9.0/rjd3tramoseats/man/tramoseats_revisions.Rd | 153 rjd3tramoseats-3.9.0/rjd3tramoseats/man/tramoseats_spec.Rd | 128 rjd3tramoseats-3.9.0/rjd3tramoseats/tests/spelling.R | 14 48 files changed, 5129 insertions(+), 5092 deletions(-)
More information about rjd3tramoseats at CRAN
Permanent link
Title: Credential Chain for Seamless 'OAuth 2.0' Authentication to
'Azure Services'
Description: Implements a credential chain for 'Azure OAuth 2.0' authentication
based on the package 'httr2''s 'OAuth' framework. Sequentially attempts authentication
methods until one succeeds. During development allows interactive
browser-based flows ('Device Code' and 'Auth Code' flows) and non-interactive
flow ('Client Secret') in batch mode.
Author: Pedro Baltazar [aut, cre]
Maintainer: Pedro Baltazar <pedrobtz@gmail.com>
Diff between azr versions 0.3.5 dated 2026-06-26 and 0.3.6 dated 2026-09-22
DESCRIPTION | 8 MD5 | 78 ++++--- NAMESPACE | 2 NEWS.md | 9 R/api-client.R | 24 ++ R/credential-azure-cli.R | 66 +++++- R/default-credential.R | 85 ++++++++ R/utils.R | 169 ++++++++++------- R/zzz.R | 2 man/AuthCodeCredential.Rd | 126 ++++++------ man/AzureCLICredential.Rd | 286 ++++++++++++++--------------- man/CachedTokenCredential.Rd | 163 ++++++++-------- man/ClientSecretCredential.Rd | 121 ++++++------ man/DefaultCredential.Rd | 183 +++++++++--------- man/DeviceCodeCredential.Rd | 113 +++++------ man/InteractiveCredential.Rd | 221 ++++++++++------------ man/ManagedIdentityCredential.Rd | 160 ++++++++-------- man/RefreshTokenCredential.Rd | 180 +++++++++--------- man/WorkloadIdentityCredential.Rd | 187 +++++++++---------- man/api_client.Rd | 374 ++++++++++++++++++-------------------- man/api_graph_resource.Rd | 78 ++++--- man/api_log_analytics_client.Rd | 201 +++++++++----------- man/api_resource.Rd | 85 ++++---- man/api_service.Rd | 65 +++--- man/api_storage_client.Rd | 248 ++++++++++++------------- man/az_config.Rd |only man/azr-package.Rd | 5 man/azr_catalog.Rd | 2 man/azr_catalog_read.Rd | 2 man/azr_catalog_write.Rd | 2 man/azr_dataset.Rd | 2 man/azr_dataset_from_uri.Rd | 2 man/azr_dataset_manifest.Rd | 4 man/azr_dataset_uri.Rd | 2 man/azr_resolve_dataset.Rd | 2 man/azure_authority_hosts.Rd | 4 man/azure_client.Rd | 4 man/azure_services.Rd | 4 man/environment_variables.Rd | 4 man/get_token.Rd | 3 man/get_user_token.Rd |only 41 files changed, 1720 insertions(+), 1556 deletions(-)
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(-)
More information about Compositionalcln at CRAN
Permanent link
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
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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
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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 - 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More information about AI4OfficialStats at CRAN
Permanent link
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(-)