Title: Utilities to Output CDISC SDTM/ADaM XPT Files
Description: Tools to build CDISC compliant data sets and check for CDISC
compliance.
Author: Eli Miller [aut, cre] ,
Ben Straub [aut],
Zelos Zhu [aut],
Ethan Brockmann [aut],
Vedha Viyash [aut],
Andre Verissimo [aut],
Sophie Shapcott [aut],
Celine Piraux [aut],
Kangjie Zhang [aut],
Adrian Chan [aut],
Sadchla Mascary [aut],
Seunghyun Kim [aut [...truncated...]
Maintainer: Eli Miller <Eli.Miller@AtorusResearch.com>
Diff between xportr versions 0.5.0 dated 2026-01-13 and 0.6.0 dated 2026-08-31
DESCRIPTION | 11 MD5 | 86 ++-- NAMESPACE | 14 NEWS.md | 18 R/df_label.R | 8 R/format.R | 12 R/label.R | 13 R/length.R | 8 R/messages.R | 29 + R/metadata.R | 8 R/order.R | 16 R/support-test.R | 38 - R/type.R | 6 R/utils-xportr.R | 35 - R/write.R | 2 R/xportr-package.R | 6 R/xportr.R | 35 - README.md | 42 - build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/agency_standards.html | 88 ++-- inst/doc/deepdive.R | 161 +++---- inst/doc/deepdive.Rmd | 166 ++----- inst/doc/deepdive.html | 687 +++++++++++++------------------- inst/doc/options.R |only inst/doc/options.Rmd |only inst/doc/options.html |only inst/doc/xportr.R | 30 - inst/doc/xportr.Rmd | 32 - inst/doc/xportr.html | 40 - man/metadata.Rd | 8 man/xportr.Rd | 19 tests/testthat/_snaps/label.md | 36 + tests/testthat/test-label.R | 29 + tests/testthat/test-length.R | 220 ++++++++-- tests/testthat/test-messages.R | 52 +- tests/testthat/test-metadata.R | 148 +++--- tests/testthat/test-order.R | 26 - tests/testthat/test-support-for-tests.R | 16 tests/testthat/test-type.R | 42 - tests/testthat/test-utils-xportr.R | 26 - tests/testthat/test-write.R | 26 - tests/testthat/test-xportr.R | 16 vignettes/deepdive.Rmd | 166 ++----- vignettes/options.Rmd |only vignettes/xportr.Rmd | 32 - 46 files changed, 1202 insertions(+), 1252 deletions(-)
Title: Visualize R Data Structures with Trees
Description: A set of tools for inspecting and understanding R data
structures inspired by str(). Includes ast() for visualizing abstract
syntax trees, ref() for showing shared references, cst() for showing
call stack trees, and obj_size() for computing object sizes.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between lobstr versions 1.2.1 dated 2026-04-04 and 1.2.2 dated 2026-08-31
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/size.R | 3 --- man/ast.Rd | 8 ++++---- man/lobstr-package.Rd | 5 +++++ man/ref.Rd | 8 ++++---- man/src.Rd | 8 ++++---- man/sxp.Rd | 8 ++++---- 9 files changed, 38 insertions(+), 32 deletions(-)
Title: Water Quality Assessment and Environmental Compliance in Brazil
Description: Tools to import, clean, validate, and analyze freshwater quality data
in Brazil. Implements water quality indices including the Water Quality Index
('WQI'/'IQA') using the weighted geometric mean following 'CETESB' methodology,
the Trophic State Index ('TSI'/'IET') after Carlson (1977)
<doi:10.4319/lo.1977.22.2.0361> and Lamparelli (2004)
<https://teses.usp.br/teses/disponiveis/41/41134/tde-20032006-075813/publico/TeseLamparelli2004.pdf>,
and the National Sanitation Foundation Water Quality Index ('NSF WQI', Brown
(1970)). The package also checks compliance with Brazilian standard 'CONAMA'
Resolution 357/2005
<https://conama.mma.gov.br/?id=450&option=com_sisconama&task=arquivo.download>
including the legal frequency rule (Art. 15, 80% conformity over six or more
samples per year), and provides seasonal analysis with regional flow-season
calendars, pollutant load computation, exceedance probability estimation, 'IET'
visualization, and multivariate 'PCA' tools f [...truncated...]
Author: Vinicius Saraiva Santos [aut, cre] ,
Fabricio Berton Zanchi [ctb]
Maintainer: Vinicius Saraiva Santos <vinisaraiva@gmail.com>
Diff between tikatuwq versions 0.9.0 dated 2026-06-09 and 0.10.0 dated 2026-08-31
DESCRIPTION | 32 - MD5 | 63 +- NAMESPACE | 2 NEWS.md | 18 R/analysis_text.R | 3 R/conama.R | 38 - R/io_clean.R | 19 R/iqa.R | 368 ++++++++++------ R/iqa_equations.R | 662 +++++++++++++++++++++--------- R/nsfwqi.R | 183 +++----- R/report.R | 3 R/seasonal.R | 54 +- R/utils_sanitize.R | 220 ++++++++- README.md | 200 +++------ inst/CITATION | 5 inst/doc/tikatuwq-methods.html | 46 +- inst/doc/tikatuwq-workflow.html | 30 - inst/doc/tikatuwq.html | 2 man/assign_season.Rd | 27 - man/classify_iqa.Rd | 11 man/conama_check.Rd | 14 man/iqa.Rd | 129 ++--- man/iqa_components.Rd |only man/normalize_param_names.Rd |only man/nsfwqi.Rd | 101 +--- man/render_report.Rd | 2 man/tikatuwq-package.Rd | 5 tests/testthat/test-iqa-cetesb-formulas.R |only tests/testthat/test-iqa-components.R |only tests/testthat/test-iqa-curves.R | 5 tests/testthat/test-iqa-geometric.R | 44 + tests/testthat/test-iqa-inema-benchmark.R |only tests/testthat/test-iqa-solids-tds.R |only tests/testthat/test-iqa-temperature.R |only tests/testthat/test-iqa.R | 16 tests/testthat/test-render_report.R | 21 36 files changed, 1419 insertions(+), 904 deletions(-)
Title: Assessing Risk Predictions for Clustered Data
Description: Assessing and comparing risk prediction rules for clustered data. The method is based on the paper: Rosner B, Qiu W, and Lee MLT.(2013) <doi: 10.1007/s10985-012-9240-6>.
Author: Bernard Rosner [aut, ctb],
Weiliang Qiu [aut, cre],
Meiling T. Lee [aut, ctb]
Maintainer: Weiliang Qiu <Weiliang.Qiu@gmail.com>
Diff between riskPredictClustData versions 0.2.6 dated 2018-11-28 and 0.2.7 dated 2026-08-31
DESCRIPTION | 9 MD5 | 14 NEWS | 215 +- R/functions.R | 2548 +++++++++++++++++------------------ man/print.class.riskPredict.Rd |only man/print.class.riskPredictDiff.Rd |only man/riskPredict.Rd | 264 +-- man/riskPredictDiff.Rd | 286 +-- man/summary.class.riskPredict.Rd |only man/summary.class.riskPredictDiff.Rd |only 10 files changed, 1702 insertions(+), 1634 deletions(-)
More information about riskPredictClustData at CRAN
Permanent link
Title: Data-Derived Graph Construction Utilities
Description: Constructs data-derived graphs from numerical observations using
mutual, shared-neighbor, intersection, geodesic, radius, adaptive-radius,
and minimum-spanning-tree completion methods. Provides graph conversion,
pruning, diagnostics, spectral embedding, endpoint detection, and path
utilities. The implemented graph constructions include methods described by
Jarvis and Patrick (1973) <doi:10.1109/T-C.1973.223640>, Brito et al. (1997)
<doi:10.1016/S0167-7152(96)00213-1>, Berry and Sauer (2019)
<doi:10.3934/fods.2019001>, and Gower and Ross (1969)
<doi:10.2307/2346439>.
Author: Pawel Gajer [aut, cre],
Sunil Arya [ctb] ,
David M. Mount [ctb] ,
University of Maryland [cph] ,
Yixuan Qiu [ctb, cph] ,
Anna Araslanova [ctb, cph] ,
Gael Guennebaud [ctb, cph] ,
Jitse Niesen [ctb, cph] ,
Netherlands eScience Center [ctb, cph]
Maintainer: Pawel Gajer <pgajer@gmail.com>
Diff between dgraphs versions 0.1.0 dated 2026-08-20 and 0.2.0 dated 2026-08-31
dgraphs-0.1.0/dgraphs/R/graph_edit_distance.R |only dgraphs-0.1.0/dgraphs/man/adjlist.to.igraph.Rd |only dgraphs-0.1.0/dgraphs/man/calculate.edit.distances.Rd |only dgraphs-0.1.0/dgraphs/man/cpp.create.rknn.graphs.Rd |only dgraphs-0.1.0/dgraphs/man/create.distance.plot.Rd |only dgraphs-0.1.0/dgraphs/man/deprecated-radius-graph-constructors.Rd |only dgraphs-0.1.0/dgraphs/man/dist.to.knn.Rd |only dgraphs-0.1.0/dgraphs/man/euclidean.distance.Rd |only dgraphs-0.1.0/dgraphs/man/graph.adj.mat.Rd |only dgraphs-0.1.0/dgraphs/man/graph.edit.distance.Rd |only dgraphs-0.1.0/dgraphs/man/load.graph.data.Rd |only dgraphs-0.2.0/dgraphs/DESCRIPTION | 17 dgraphs-0.2.0/dgraphs/MD5 | 220 ++++------ dgraphs-0.2.0/dgraphs/NAMESPACE | 21 dgraphs-0.2.0/dgraphs/NEWS.md | 40 + dgraphs-0.2.0/dgraphs/R/as_igraph.R | 190 ++++++-- dgraphs-0.2.0/dgraphs/R/basic_graphs.R | 119 +++-- dgraphs-0.2.0/dgraphs/R/component_mst_connectivity.R | 37 - dgraphs-0.2.0/dgraphs/R/dgraphs-package.R | 1 dgraphs-0.2.0/dgraphs/R/divergences.R | 3 dgraphs-0.2.0/dgraphs/R/geodesic_distances.R | 5 dgraphs-0.2.0/dgraphs/R/geodesic_stats.R | 28 + dgraphs-0.2.0/dgraphs/R/graph_embedding_spectrum.R | 25 + dgraphs-0.2.0/dgraphs/R/graph_endpoint_geometry.R | 27 + dgraphs-0.2.0/dgraphs/R/graph_fixtures.R | 3 dgraphs-0.2.0/dgraphs/R/graph_pruning.R | 9 dgraphs-0.2.0/dgraphs/R/graph_summary_divergence.R | 24 + dgraphs-0.2.0/dgraphs/R/graph_utils.R | 60 ++ dgraphs-0.2.0/dgraphs/R/grid_graphs.R | 9 dgraphs-0.2.0/dgraphs/R/iknn_selection.R | 17 dgraphs-0.2.0/dgraphs/R/isometry_deviation.R | 9 dgraphs-0.2.0/dgraphs/R/local_extrema.R | 22 + dgraphs-0.2.0/dgraphs/R/path_geodesic_utils.R | 76 ++- dgraphs-0.2.0/dgraphs/R/path_graphs.R | 21 dgraphs-0.2.0/dgraphs/R/radius_graphs.R | 167 ------- dgraphs-0.2.0/dgraphs/R/threshold_distance_graph.R | 5 dgraphs-0.2.0/dgraphs/README.md | 11 dgraphs-0.2.0/dgraphs/build |only dgraphs-0.2.0/dgraphs/inst/doc |only dgraphs-0.2.0/dgraphs/man/as_igraph.Rd | 42 + dgraphs-0.2.0/dgraphs/man/build.iknn.graphs.and.selectk.Rd | 9 dgraphs-0.2.0/dgraphs/man/compare.adj.lists.Rd | 5 dgraphs-0.2.0/dgraphs/man/compare.paths.Rd | 7 dgraphs-0.2.0/dgraphs/man/compute.geodesic.stats.Rd | 13 dgraphs-0.2.0/dgraphs/man/compute.graph.diameter.Rd | 6 dgraphs-0.2.0/dgraphs/man/compute.graph.distance.Rd | 11 dgraphs-0.2.0/dgraphs/man/compute.graph.endpoint.scores.Rd | 13 dgraphs-0.2.0/dgraphs/man/compute.graph.summary.pmf.Rd | 5 dgraphs-0.2.0/dgraphs/man/compute.graph.summary.stability.Rd | 12 dgraphs-0.2.0/dgraphs/man/compute.stability.metrics.Rd | 10 dgraphs-0.2.0/dgraphs/man/compute.vertex.geodesic.stats.Rd | 12 dgraphs-0.2.0/dgraphs/man/convert.adjacency.list.to.adjacency.matrix.Rd | 6 dgraphs-0.2.0/dgraphs/man/convert.adjacency.to.edge.matrix.Rd | 5 dgraphs-0.2.0/dgraphs/man/convert.to.undirected.Rd | 5 dgraphs-0.2.0/dgraphs/man/convert.weighted.adjacency.matrix.to.adjacency.list.Rd | 5 dgraphs-0.2.0/dgraphs/man/count.edges.Rd | 4 dgraphs-0.2.0/dgraphs/man/create.bi.kNN.chain.graph.Rd | 6 dgraphs-0.2.0/dgraphs/man/create.bipartite.graph.Rd | 5 dgraphs-0.2.0/dgraphs/man/create.chain.graph.Rd | 6 dgraphs-0.2.0/dgraphs/man/create.chain.graph.with.offset.Rd | 4 dgraphs-0.2.0/dgraphs/man/create.circular.graph.Rd | 4 dgraphs-0.2.0/dgraphs/man/create.complete.graph.Rd | 5 dgraphs-0.2.0/dgraphs/man/create.empty.graph.Rd | 4 dgraphs-0.2.0/dgraphs/man/create.grid.graph.Rd | 10 dgraphs-0.2.0/dgraphs/man/create.path.graph.Rd | 6 dgraphs-0.2.0/dgraphs/man/create.path.graph.series.Rd | 6 dgraphs-0.2.0/dgraphs/man/create.plm.graph.Rd | 6 dgraphs-0.2.0/dgraphs/man/create.random.graph.Rd | 6 dgraphs-0.2.0/dgraphs/man/create.star.graph.Rd | 5 dgraphs-0.2.0/dgraphs/man/create.subgraph.Rd | 9 dgraphs-0.2.0/dgraphs/man/create.threshold.distance.graph.Rd | 5 dgraphs-0.2.0/dgraphs/man/detect.graph.endpoints.Rd | 16 dgraphs-0.2.0/dgraphs/man/detect.local.extrema.Rd | 12 dgraphs-0.2.0/dgraphs/man/dgraphs-package.Rd | 4 dgraphs-0.2.0/dgraphs/man/edge.diff.Rd | 6 dgraphs-0.2.0/dgraphs/man/estimate.geodesic.distances.Rd | 5 dgraphs-0.2.0/dgraphs/man/extract.edge.lengths.Rd | 6 dgraphs-0.2.0/dgraphs/man/extract.trajectory.edge.lengths.Rd | 6 dgraphs-0.2.0/dgraphs/man/generate.circle.graph.Rd | 6 dgraphs-0.2.0/dgraphs/man/geodesic.core.endpoints.Rd | 10 dgraphs-0.2.0/dgraphs/man/geodesic.disk.Rd | 6 dgraphs-0.2.0/dgraphs/man/geodesic.knn.Rd | 5 dgraphs-0.2.0/dgraphs/man/geodesic.knnx.Rd | 6 dgraphs-0.2.0/dgraphs/man/get.edge.weights.Rd | 6 dgraphs-0.2.0/dgraphs/man/get.shortest.path.Rd | 7 dgraphs-0.2.0/dgraphs/man/graph.connected.components.Rd | 5 dgraphs-0.2.0/dgraphs/man/graph.embedding.Rd | 6 dgraphs-0.2.0/dgraphs/man/graph.geodesic.distances.Rd | 6 dgraphs-0.2.0/dgraphs/man/graph.spectral.embedding.Rd | 6 dgraphs-0.2.0/dgraphs/man/graph.spectrum.Rd | 6 dgraphs-0.2.0/dgraphs/man/graph.summary.divergence.Rd | 10 dgraphs-0.2.0/dgraphs/man/identical.vertex.set.weighted.graph.similarity.Rd | 9 dgraphs-0.2.0/dgraphs/man/isometry.geodesic.diagnostics.Rd | 9 dgraphs-0.2.0/dgraphs/man/jensen.shannon.divergence.Rd | 4 dgraphs-0.2.0/dgraphs/man/join.graphs.Rd | 6 dgraphs-0.2.0/dgraphs/man/minh.limit.Rd | 7 dgraphs-0.2.0/dgraphs/man/nerve.graph.Rd | 5 dgraphs-0.2.0/dgraphs/man/path.dist.Rd | 5 dgraphs-0.2.0/dgraphs/man/path.length.Rd | 4 dgraphs-0.2.0/dgraphs/man/plot2D.colored.graph.Rd | 11 dgraphs-0.2.0/dgraphs/man/rm.self.loops.Rd | 4 dgraphs-0.2.0/dgraphs/man/shortest.path.Rd | 6 dgraphs-0.2.0/dgraphs/man/subdivide.path.Rd | 5 dgraphs-0.2.0/dgraphs/man/summary.rknn_graphs.Rd | 6 dgraphs-0.2.0/dgraphs/man/vertices.Rd | 12 dgraphs-0.2.0/dgraphs/man/wgraph.prune.long.edges.Rd | 10 dgraphs-0.2.0/dgraphs/src/Makevars | 4 dgraphs-0.2.0/dgraphs/src/Makevars.win | 4 dgraphs-0.2.0/dgraphs/src/adaptive_radius_graph_ann.cpp | 12 dgraphs-0.2.0/dgraphs/src/cpp_mstrees.cpp | 30 - dgraphs-0.2.0/dgraphs/src/iknn_graphs.cpp | 59 -- dgraphs-0.2.0/dgraphs/tests/dg7d-installed-self-containment.R | 9 dgraphs-0.2.0/dgraphs/tests/testthat/test-api-0.2.R |only dgraphs-0.2.0/dgraphs/tests/testthat/test-dg6c-path-geodesic-self-hosted.R | 20 dgraphs-0.2.0/dgraphs/tests/testthat/test-exported-examples.R |only dgraphs-0.2.0/dgraphs/tests/testthat/test-rknn-graphs.R | 90 +++- dgraphs-0.2.0/dgraphs/tests/testthat/test-self-hosted-graph-constructors.R | 42 + dgraphs-0.2.0/dgraphs/vignettes |only 118 files changed, 1390 insertions(+), 546 deletions(-)
Title: Model Diagnostics for Accelerated Failure Time Models
Description: A collection of model checking methods for semiparametric
accelerated failure time (AFT) models under the rank-based approach. For the
(computational) efficiency, Gehan's weight is used. It provides functions to
verify whether the observed data fit the specific model assumptions such as
a functional form of each covariate, a link function, and an omnibus test.
The p-value offered in this package is based on the Kolmogorov-type supremum
test and the variance of the proposed test statistics is estimated through
the re-sampling method. Furthermore, a graphical technique to compare the
shape of the observed residual to a number of the approximated realizations
is provided. See the following references; A general model-checking
procedure for semiparametric accelerated failure time models, Statistics and
Computing, 34 (3), 117 <doi:10.1007/s11222-024-10431-7>; Diagnostics for
semiparametric accelerated failure time models with R package 'afttest',
Journal of Statistical Software, to ap [...truncated...]
Author: Woojung Bae [aut, cre] ,
Dongrak Choi [aut] ,
Jun Yan [aut] ,
Sangwook Kang [aut]
Maintainer: Woojung Bae <matt.woojung@gmail.com>
Diff between afttest versions 4.5.3 dated 2026-03-22 and 4.6.1 dated 2026-08-31
DESCRIPTION | 12 +-- MD5 | 20 +++--- NAMESPACE | 54 +++++++++------- R/afttest.R | 156 ++++++++++++++++++++++++++++--------------------- README.md | 114 ++++++++++++++++++++++++++++++++--- inst/CITATION | 6 - inst/bib/afttest.bib | 6 - man/afttest-package.Rd | 1 man/afttest.Rd | 6 + man/afttest.aftgee.Rd | 13 ---- man/afttest.aftsrr.Rd | 18 ++--- 11 files changed, 261 insertions(+), 145 deletions(-)
Title: Weighted Dependence Measures
Description: Provides efficient implementations of weighted dependence measures
and related asymptotic tests for independence. Implemented measures are
the Pearson correlation, Spearman's rho, Kendall's tau, Blomqvist's beta,
Hoeffding's D, and Chatterjee's xi; see, e.g., Nelsen (2006)
<doi:10.1007/0-387-28678-0>, Hollander et al. (2015,
ISBN:9780470387375), and Chatterjee (2021)
<doi:10.1080/01621459.2020.1758115>.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between wdm versions 0.2.6 dated 2025-01-07 and 0.3.0 dated 2026-08-31
wdm-0.2.6/wdm/inst/test/test.cpp |only wdm-0.3.0/wdm/DESCRIPTION | 21 wdm-0.3.0/wdm/MD5 | 94 - wdm-0.3.0/wdm/NEWS.md | 8 wdm-0.3.0/wdm/R/RcppExports.R | 12 wdm-0.3.0/wdm/R/indep_test.R | 55 wdm-0.3.0/wdm/R/methods.R |only wdm-0.3.0/wdm/R/rank_wtd.R | 30 wdm-0.3.0/wdm/R/wdm-package.R | 5 wdm-0.3.0/wdm/R/wdm.R | 79 - wdm-0.3.0/wdm/README.md | 98 - wdm-0.3.0/wdm/build/partial.rdb |binary wdm-0.3.0/wdm/inst/CMakeLists.txt | 2 wdm-0.3.0/wdm/inst/cmake/buildTargets.cmake | 4 wdm-0.3.0/wdm/inst/cmake/compilerDefOpt.cmake | 4 wdm-0.3.0/wdm/inst/cmake/options.cmake | 4 wdm-0.3.0/wdm/inst/cmake/printInfo.cmake | 3 wdm-0.3.0/wdm/inst/include/mainpage.h | 67 - wdm-0.3.0/wdm/inst/include/wdm.hpp | 333 +++-- wdm-0.3.0/wdm/inst/include/wdm/bbeta.hpp | 46 wdm-0.3.0/wdm/inst/include/wdm/cxi.hpp |only wdm-0.3.0/wdm/inst/include/wdm/eigen.hpp | 146 +- wdm-0.3.0/wdm/inst/include/wdm/hoeffd.hpp | 175 +- wdm-0.3.0/wdm/inst/include/wdm/ktau.hpp | 136 +- wdm-0.3.0/wdm/inst/include/wdm/methods.hpp | 53 wdm-0.3.0/wdm/inst/include/wdm/nan_handling.hpp | 119 + wdm-0.3.0/wdm/inst/include/wdm/prho.hpp | 70 - wdm-0.3.0/wdm/inst/include/wdm/random.hpp | 145 +- wdm-0.3.0/wdm/inst/include/wdm/ranks.hpp | 369 ++--- wdm-0.3.0/wdm/inst/include/wdm/srho.hpp | 21 wdm-0.3.0/wdm/inst/include/wdm/utils.hpp | 769 ++++++------ wdm-0.3.0/wdm/inst/test/CMakeLists.txt | 73 + wdm-0.3.0/wdm/inst/test/install |only wdm-0.3.0/wdm/inst/test/test_cxi.cpp |only wdm-0.3.0/wdm/inst/test/test_eigen.cpp |only wdm-0.3.0/wdm/inst/test/test_estimators.cpp |only wdm-0.3.0/wdm/inst/test/test_headers.cpp |only wdm-0.3.0/wdm/inst/test/test_helpers.hpp |only wdm-0.3.0/wdm/inst/test/test_inference.cpp |only wdm-0.3.0/wdm/inst/test/test_input.cpp |only wdm-0.3.0/wdm/inst/test/test_ranks.cpp |only wdm-0.3.0/wdm/man/indep_test.Rd | 35 wdm-0.3.0/wdm/man/rank_wtd.Rd | 17 wdm-0.3.0/wdm/man/wdm-package.Rd | 10 wdm-0.3.0/wdm/man/wdm.Rd | 33 wdm-0.3.0/wdm/src/RcppExports.cpp | 28 wdm-0.3.0/wdm/src/wrappers.cpp | 50 wdm-0.3.0/wdm/tests/testthat/test_chatterjee.R |only wdm-0.3.0/wdm/tests/testthat/test_computations_unweighted.R | 37 wdm-0.3.0/wdm/tests/testthat/test_computations_weighted.R | 4 wdm-0.3.0/wdm/tests/testthat/test_indep_test.R | 2 wdm-0.3.0/wdm/tests/testthat/test_input_validation.R |only wdm-0.3.0/wdm/tests/testthat/test_matrix_interface.R |only wdm-0.3.0/wdm/tests/testthat/test_rank_wtd.R | 6 wdm-0.3.0/wdm/tests/testthat/test_wdm_interface.R | 2 55 files changed, 1776 insertions(+), 1389 deletions(-)
Title: Unsupervised Clustering of Individualized Survival Curves
Description: Tools for clustering individualized survival curves using the
Partitioning Around Medoids (PAM) algorithm, with monotonic enforcement,
optional smoothing, weighted distances (L1/L2), automatic K selection via
silhouette width, prediction for new curves, basic stability checks, and
plotting helpers. The method is described in El Badisy (2026)
<doi:10.1093/bioadv/vbag218>.
Author: Imad El Badisy [aut, cre]
Maintainer: Imad El Badisy <elbadisyimad@gmail.com>
Diff between unsurv versions 0.5.0 dated 2026-03-17 and 0.7.0 dated 2026-08-31
DESCRIPTION | 23 +-- MD5 | 29 ++-- NAMESPACE | 4 NEWS.md | 23 +++ R/compare.R |only R/zzz.R | 5 README.md | 57 +++---- inst/CITATION | 16 +- inst/doc/unsurv-intro.R | 109 ++++++++++++--- inst/doc/unsurv-intro.Rmd | 225 ++++++++++++++++++++++++------- inst/doc/unsurv-intro.html | 293 ++++++++++++++++++++++++++++++----------- inst/extdata |only man/autoplot.unsurv_compare.Rd |only man/dot-km_cluster_medians.Rd |only man/print.unsurv_compare.Rd |only man/unsurv-package.Rd | 2 man/unsurv_compare.Rd |only tests/testthat/test-compare.R |only vignettes/unsurv-intro.Rmd | 225 ++++++++++++++++++++++++------- 19 files changed, 760 insertions(+), 251 deletions(-)
Title: Authentication Helpers for 'Snowflake'
Description: Authentication helpers for 'Snowflake'.
It provides compatibility with authentication approaches supported
by the 'Snowflake Connector for Python' <https://pypi.org/project/snowflake-connector-python>
and the 'Snowflake CLI' <https://pypi.org/project/snowflake-cli>.
Author: Aaron Jacobs [aut],
E. David Aja [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: E. David Aja <david@posit.co>
Diff between snowflakeauth versions 0.2.2 dated 2026-02-25 and 0.3.0 dated 2026-08-31
DESCRIPTION | 6 +-- MD5 | 33 +++++++++++--------- NEWS.md | 13 ++++++++ R/config.R | 7 ++++ R/credentials.R | 40 ++++++++++++++++--------- R/externalbrowser.R | 20 +++++++----- R/keypair.R | 18 +++++++++-- R/oauth.R | 5 +-- R/oauth_authorization_code.R |only R/workload_identity.R | 5 +-- README.md | 3 + man/snowflake_connection.Rd | 3 + tests/testthat/connections.toml | 20 ++++++++++++ tests/testthat/test-config.R | 36 ++++++++++++++++++++++ tests/testthat/test-credentials.R |only tests/testthat/test-keypair.R | 39 ++++++++++++++++++++++++ tests/testthat/test-oauth-authorization-code.R |only tests/testthat/test-oauth.R | 35 +++++++++++++++++++++ tests/testthat/test-workload-identity.R | 18 ++++++----- 19 files changed, 246 insertions(+), 55 deletions(-)
Title: Detect and Remove Unwanted Variation using Negative Controls
Description: Implements the 'RUV' (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. These algorithms were proposed in Gagnon-Bartsch and Speed (2012) <doi:10.1093/nar/gkz433>, Gagnon-Bartsch, Jacob and Speed (2013), and Molania, et. al. (2019) <doi:10.1093/nar/gkz433>. The algorithms require the user to specify a set of negative control variables, as described in the references. The algorithms included in this package are 'RUV-2', 'RUV-4', 'RUV-inv', 'RUV-rinv', 'RUV-I', and RUV-III', along with various supporting algorithms.
Author: Johann Gagnon-Bartsch [aut, cre]
Maintainer: Johann Gagnon-Bartsch <johanngb@umich.edu>
Diff between ruv versions 0.9.7.1 dated 2019-08-30 and 0.9.7.2 dated 2026-08-31
DESCRIPTION | 16 ++++++++++------ MD5 | 30 +++++++++++++++--------------- R/ruv_shiny.R | 6 +++--- man/RUV2.Rd | 6 +++--- man/RUV4.Rd | 6 +++--- man/RUVI.Rd | 4 ++-- man/RUVIII.Rd | 4 ++-- man/RUVinv.Rd | 6 +++--- man/RUVrinv.Rd | 6 +++--- man/getK.Rd | 4 ++-- man/get_empirical_variances.Rd | 2 +- man/invvar.Rd | 2 +- man/randinvvar.Rd | 2 +- man/ruv-package.Rd | 6 +++--- man/sigmashrink.Rd | 4 ++-- man/variance_adjust.Rd | 4 ++-- 16 files changed, 56 insertions(+), 52 deletions(-)
Title: Road Network Projection
Description: Iterative least cost path and minimum spanning tree methods for projecting
forest road networks. The methods connect a set of target points to an existing
road network using 'igraph' <https://igraph.org> to identify least cost routes.
The cost of constructing a road segment between adjacent pixels is determined
by a user supplied weight raster and a weight function; options include the
average of adjacent weight raster values, and a function of the elevation
differences between adjacent cells that penalizes steep grades. These road
network projection methods are intended for integration into R workflows and
modelling frameworks used for forecasting forest change, and can be applied
over multiple time-steps without rebuilding a graph at each time-step.
Author: Sarah Endicott [aut, cre] ,
Kyle Lochhead [aut],
Josie Hughes [aut],
Patrick Kirby [aut],
Her Majesty the Queen in Right of Canada as represented by the Minister
of the Environment [cph] ,
Province of British Columbia [cph]
Maintainer: Sarah Endicott <sarah.endicott@ec.gc.ca>
This is a re-admission after prior archival of version 1.2.1 dated 2026-01-16
Diff between roads versions 1.2.1 dated 2026-01-16 and 1.2.2 dated 2026-08-31
DESCRIPTION | 22 + MD5 | 27 +- NEWS.md | 2 R/getDistFromSource.R | 403 +++++++++++++++++------------------ R/projectRoads.R | 7 README.md | 190 ++++++++-------- inst/WORDLIST |only inst/doc/ReconstructRoadHistory.html | 49 ++-- inst/doc/grade-penalty.html | 28 +- inst/doc/roads-vignette.html | 4 man/getDistFromSource.Rd | 17 - man/getLandingsFromTarget.Rd | 2 man/prepExData.Rd | 2 man/projectRoads.Rd | 7 man/roads-package.Rd | 3 15 files changed, 396 insertions(+), 367 deletions(-)
Title: 'KorAP' Web Service Client Package
Description: A client package that makes the 'KorAP' web service API accessible from R. The corpus analysis platform 'KorAP' has been developed as a scientific tool to make potentially large, stratified and multiply annotated corpora, such as the 'German Reference Corpus DeReKo' or the 'Corpus of the Contemporary Romanian Language CoRoLa', accessible for linguists to let them verify hypotheses and to find interesting patterns in real language use. The 'RKorAPClient' package provides access to 'KorAP' and the corpora behind it for user-created R code, as a programmatic alternative to the 'KorAP' web user-interface. You can learn more about 'KorAP' and use it directly on 'DeReKo' at <https://korap.ids-mannheim.de/>.
Author: Marc Kupietz [aut, cre],
Nils Diewald [ctb],
Leibniz Institute for the German Language [cph, fnd]
Maintainer: Marc Kupietz <kupietz@ids-mannheim.de>
Diff between RKorAPClient versions 1.2.1 dated 2025-10-09 and 1.3.0 dated 2026-08-31
RKorAPClient-1.2.1/RKorAPClient/man/KorAPConnection-class.Rd |only RKorAPClient-1.3.0/RKorAPClient/DESCRIPTION | 10 RKorAPClient-1.3.0/RKorAPClient/MD5 | 52 RKorAPClient-1.3.0/RKorAPClient/NAMESPACE | 167 - RKorAPClient-1.3.0/RKorAPClient/NEWS.md | 12 RKorAPClient-1.3.0/RKorAPClient/R/KorAPConnection.R | 55 RKorAPClient-1.3.0/RKorAPClient/R/collocationAnalysis.R | 1228 +++++++++- RKorAPClient-1.3.0/RKorAPClient/R/collocationScoreQuery.R | 66 RKorAPClient-1.3.0/RKorAPClient/man/KorAPConnection.Rd |only RKorAPClient-1.3.0/RKorAPClient/man/RKorAPClient-package.Rd | 5 RKorAPClient-1.3.0/RKorAPClient/man/association-score-functions.Rd | 4 RKorAPClient-1.3.0/RKorAPClient/man/auth-KorAPConnection-method.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/man/clearAccessToken-KorAPConnection-method.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/man/collocationAnalysis-KorAPConnection-method.Rd | 84 RKorAPClient-1.3.0/RKorAPClient/man/collocationScoreQuery-KorAPConnection-method.Rd | 10 RKorAPClient-1.3.0/RKorAPClient/man/corpusQuery-KorAPConnection-method.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/man/defaultKorAPUrl.Rd |only RKorAPClient-1.3.0/RKorAPClient/man/fetchAll-KorAPQuery-method.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/man/fetchAnnotations-KorAPQuery-method.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/man/fetchNext-KorAPQuery-method.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/man/hc_add_onclick_korap_search.Rd | 4 RKorAPClient-1.3.0/RKorAPClient/man/hc_freq_by_year_ci.Rd | 4 RKorAPClient-1.3.0/RKorAPClient/man/initialize-KorAPConnection-method.Rd | 7 RKorAPClient-1.3.0/RKorAPClient/man/persistAccessToken-KorAPConnection-method.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/man/reexports.Rd | 12 RKorAPClient-1.3.0/RKorAPClient/man/synsemanticStopwords.Rd | 2 RKorAPClient-1.3.0/RKorAPClient/tests/testthat/test-collocations.R | 680 +++++ RKorAPClient-1.3.0/RKorAPClient/tests/testthat/test-fetchAnnotations.R | 9 RKorAPClient-1.3.0/RKorAPClient/tests/testthat/test-korapconnection-signature.R |only 29 files changed, 2208 insertions(+), 217 deletions(-)
Title: Density-Free RIF Decompositions for Unconditional Expectiles
Description: Implements a density-free recentered influence function (RIF)
regression framework for unconditional expectiles, and embeds it in a
two-sample Oaxaca-Blinder decomposition indexed continuously by the
expectile level. Unlike quantile-based RIF decompositions, which require
estimating an inverse density term at each quantile, the expectile RIF
depends only on primitive moments of the outcome distribution and
requires no density estimation, no bandwidth selection, and no kernel
smoothing. The package provides expectile estimation by iteratively
reweighted least squares, closed-form RIF construction, two-sample
composition/structure decomposition across a grid of expectile levels,
bootstrap-based inference, and plotting methods. The underlying
methodology is described in Ndoye (2025), "Semi-Nonparametric
Expectile RIF Regression for Distributional Decomposition," presented at
the 2025 World Congress of the Econometric Society, Seoul, Korea,
<https://www.econometricsociety.org/regional-a [...truncated...]
Author: Abdoul Aziz Ndoye [aut, cre]
Maintainer: Abdoul Aziz Ndoye <abdoulaziz1.ndoye@gmail.com>
Diff between rifexpectile versions 0.1.0 dated 2026-08-30 and 0.1.1 dated 2026-08-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/decompose.R | 2 ++ README.md | 7 ++++++- inst/doc/rifexpectile-intro.html | 6 +++--- 5 files changed, 18 insertions(+), 11 deletions(-)
Title: String Similarity Computation Using 'RapidFuzz'
Description: Provides a high-performance interface for calculating string similarities and distances, leveraging the efficient library 'RapidFuzz' <https://github.com/rapidfuzz/rapidfuzz-cpp>. This package integrates the 'C++' implementation, allowing 'R' users to access cutting-edge algorithms for fuzzy matching and text analysis. Supported metrics include Levenshtein, Damerau-Levenshtein, Hamming, Jaro, Jaro-Winkler, Longest Common Subsequence (LCS), Optimal String Alignment (OSA), Indel, Prefix, and Postfix distances and similarities, as well as multiple fuzzy matching ratios.
Author: Andre Leite [aut, cre],
Hugo Vaconcelos [aut],
Marcos Wasilew [aut],
Carlos Amorim [aut],
Diogo Bezerra [aut],
Max Bachmann [ctb],
Adam Cohen [ctb]
Maintainer: Andre Leite <leite@castlab.org>
Diff between RapidFuzz versions 1.1.0 dated 2026-04-07 and 1.1.1 dated 2026-08-31
DESCRIPTION | 14 +++++++------- MD5 | 20 +++++++++++--------- NEWS.md | 10 +++++++++- R/zzz.R | 2 +- README.md | 7 ++++--- build/vignette.rds |binary inst/doc/introduction.html | 6 +++--- man/figures |only src/rapidfuzz/details/GrowingHashmap.hpp | 2 ++ src/rapidfuzz/details/Range.hpp | 2 ++ src/rapidfuzz/details/types.hpp | 2 ++ 11 files changed, 41 insertions(+), 24 deletions(-)
Title: Prediction Rule Ensembles
Description: Fits prediction rule ensembles (PREs). Largely follows the
procedure for deriving PREs as described in Friedman & Popescu (2008;
<DOI:10.1214/07-AOAS148>), with adjustments and improvements described in
Fokkema (2020; <DOI:10.18637/jss.v092.i12>) and Fokkema & Strobl
(2020; <DOI:10.1037/met0000256>). The main function pre() derives
prediction rule ensembles consisting of rules and/or linear terms for
continuous, binary, count, multinomial, survival and multivariate
continuous responses. Function gpe() derives generalized prediction
ensembles, consisting of rules, hinge and linear functions of the
predictor variables.
Author: Marjolein Fokkema [aut, cre],
Benjamin Christoffersen [aut],
Giorgio Spadaccini [ctb]
Maintainer: Marjolein Fokkema <m.fokkema@fsw.leidenuniv.nl>
Diff between pre versions 1.0.9 dated 2026-06-09 and 1.1.0 dated 2026-08-31
DESCRIPTION | 22 MD5 | 128 NAMESPACE | 1 NEWS.md | 17 R/corplot.R |only R/cvpre.R |only R/explain.R |only R/get_modmat.R |only R/gpe.R | 3 R/interaction_H_statistics.R |only R/partial_dependence_plots.R |only R/pre.R | 4009 ---------- R/pre_S3_methods.R |only R/prune_pre.R |only R/rule_learners.R |only R/shap.R |only R/utils.R | 221 README.md | 188 build/vignette.rds |binary inst/README-figures/README-pairplot-1.png |binary inst/README-figures/README-singleplot-1.png |binary inst/README-figures/README-unnamed-chunk-9-1.png |only inst/doc/Missingness.Rmd | 9 inst/doc/Missingness.html | 42 inst/doc/Tuning.html | 12 inst/doc/relaxed.Rmd | 4 inst/doc/relaxed.html | 26 inst/doc/shap.R |only inst/doc/shap.Rmd |only inst/doc/shap.html |only inst/doc/speed.html | 22 man/RuleMats.Rd |only man/ShapleyMats.Rd |only man/bsnullinteract.Rd | 4 man/coef.gpe.Rd | 2 man/coef.pre.Rd | 4 man/corplot.Rd | 4 man/cvpre.Rd | 4 man/explain.Rd | 9 man/gpe_rules_pre.Rd | 2 man/importance.pre.Rd | 4 man/interact.Rd | 4 man/maxdepth_sampler.Rd | 2 man/pairplot.Rd | 4 man/plot.pre.Rd | 4 man/pre.Rd | 4 man/predict.pre.Rd | 4 man/print.gpe.Rd | 2 man/print.pre.Rd | 4 man/prune_pre.Rd | 2 man/rare_level_sampler.Rd | 2 man/shap.Rd |only man/singleplot.Rd | 4 man/summary.gpe.Rd | 2 man/summary.pre.Rd | 4 tests/testthat.R | 2 tests/testthat/helper.R | 13 tests/testthat/previous_results/PimaIndiansDiabetes_w_pre_LR.RDS |binary tests/testthat/previous_results/PimaIndiansDiabetes_w_pre_no_LR.RDS |binary tests/testthat/previous_results/SHAP.RDS |only tests/testthat/previous_results/SHAP_interact.RDS |only tests/testthat/previous_results/SHAP_marginal.RDS |only tests/testthat/previous_results/gpe_earth_binary.RDS |binary tests/testthat/previous_results/gpe_earth_binary_no_learn.RDS |binary tests/testthat/previous_results/gpe_fit1_binary.RDS |binary tests/testthat/previous_results/gpe_predict_binary_response.RDS |binary tests/testthat/previous_results/gpe_tree_binary_1.RDS |binary tests/testthat/previous_results/gpe_tree_binary_1_w_glm.RDS |binary tests/testthat/previous_results/gpe_tree_binary_2.RDS |binary tests/testthat/test_explain_and_shap.R |only tests/testthat/test_gpe.R | 18 tests/testthat/test_pre_misc.R | 9 vignettes/Missingness.Rmd | 9 vignettes/bib.bib | 63 vignettes/relaxed.Rmd | 4 vignettes/shap.Rmd |only 76 files changed, 616 insertions(+), 4281 deletions(-)
Title: Download and Manage Optional Package Data
Description: Manage optional data for your package. The data can be hosted anywhere, and you have to give a Uniform Resource Locator (URL) for each file. File integrity checks are supported. This is useful for package authors who need to ship more than the 5 Megabyte of data currently allowed by the the Comprehensive R Archive Network (CRAN). Download functions are supposed to be called by users in interactive sessions only.
Author: Tim Schaefer [aut, cre]
Maintainer: Tim Schaefer <ts+code@rcmd.org>
Diff between pkgfilecache versions 0.2.0 dated 2026-08-21 and 0.4.1 dated 2026-08-31
DESCRIPTION | 6 MD5 | 34 +++- NAMESPACE | 5 R/cli.R |only R/filecache.R | 216 ++++++++++++++++++++++++--- R/manifest.R |only exec |only inst/doc/pkgfilecache.R | 44 +++++ inst/doc/pkgfilecache.Rmd | 72 +++++++++ inst/doc/pkgfilecache.html | 220 +++++++++++++++++++--------- man/add_file_download_to_curl_pool.Rd |only man/derive_manifest_urls.Rd |only man/download_files_with_md5_mismatch.Rd | 8 - man/ensure_files_available.Rd | 14 + man/ensure_files_available_from_manifest.Rd |only man/manifest_cli.Rd |only man/manifest_cli_usage.Rd |only man/manifest_script.Rd |only man/read_manifest.Rd |only man/validate_manifest.Rd |only man/write_manifest_from_dir.Rd |only tests/testthat/test-filecache.R | 131 ++++++++++++++++ tests/testthat/test-manifest-cli.R |only tests/testthat/test-manifest.R |only vignettes/pkgfilecache.Rmd | 72 +++++++++ 25 files changed, 712 insertions(+), 110 deletions(-)
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available. The methods are described in
Hothorn et al. (2006) <doi:10.1198/106186006X133933>,
Zeileis et al. (2008) <d [...truncated...]
Author: Torsten Hothorn [aut, cre] ,
Kurt Hornik [aut] ,
Carolin Strobl [aut] ,
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between party versions 1.3-22 dated 2026-08-21 and 1.3-23 dated 2026-08-31
DESCRIPTION | 6 ++--- MD5 | 34 ++++++++++++++++---------------- build/partial.rdb |binary cleanup | 8 +++++++ inst/NEWS.Rd | 13 ++++++++++-- inst/doc/MOB.pdf |binary inst/doc/party.pdf |binary tests/Distributions.Rout.save | 4 +-- tests/LinearStatistic-regtest.Rout.save | 4 +-- tests/Predict-regtest.Rout.save | 4 +-- tests/RandomForest-regtest.R | 2 + tests/RandomForest-regtest.Rout.save | 11 +++------- tests/TestStatistic-regtest.Rout.save | 4 +-- tests/TreeGrow-regtest.Rout.save | 4 +-- tests/Utils-regtest.Rout.save | 4 +-- tests/bugfixes.R | 2 + tests/bugfixes.Rout.save | 11 +++------- tests/mob.Rout.save | 4 +-- 18 files changed, 65 insertions(+), 50 deletions(-)
Title: Optimal Binning and Weight of Evidence Framework for Modeling
Description: High-performance implementation of 37 optimal binning algorithms
(16 categorical, 21 numerical) for Weight of Evidence ('WoE') transformation,
credit scoring, and risk modeling. Includes advanced methods such as Mixed
Integer Linear Programming ('MILP'), Genetic Algorithms, Simulated Annealing,
and Monotonic Regression. Features automatic method selection based on
Information Value ('IV') maximization, strict monotonicity enforcement, and
efficient handling of large datasets via 'Rcpp'. Provides automated variable
screening by Information Value strength and bin ordering, and generation of
the equivalent 'SQL' 'CASE' expressions for in-database scoring. Fully
integrated with the 'tidymodels' ecosystem for building robust machine
learning pipelines.
Based on methods described in Siddiqi (2006) <doi:10.1002/9781119201731>
and Navas-Palencia (2020) <doi:10.48550/arXiv.2001.08025>.
Author: Jose Evandeilton Lopes [aut, cre, cph]
Maintainer: Jose Evandeilton Lopes <evandeilton@gmail.com>
Diff between OptimalBinningWoE versions 1.13.4 dated 2026-08-26 and 1.13.5 dated 2026-08-31
DESCRIPTION | 8 - MD5 | 14 +-- NEWS.md | 53 ++++++++++++ inst/doc/algorithms.html | 30 +++---- inst/doc/industrial-pipeline.html | 8 - inst/doc/introduction.html | 8 - tests/testthat/helper-germancredit.R | 149 ++++++++++++++++++++++++++++++++++- tests/testthat/test-obwoe-sql.R | 28 ++++++ 8 files changed, 262 insertions(+), 36 deletions(-)
More information about OptimalBinningWoE at CRAN
Permanent link
Title: The Nonparametric Classification Methods for Cognitive Diagnosis
Description: Statistical tools for analyzing cognitive diagnosis (CD) data collected from small settings using the nonparametric classification (NPCD) framework. The core methods of the NPCD framework includes the nonparametric classification (NPC) method developed by Chiu and Douglas (2013) <DOI:10.1007/s00357-013-9132-9> and the general NPC (GNPC) method developed by Chiu, Sun, and Bian (2018) <DOI:10.1007/s11336-017-9595-4> and Chiu and Köhn (2019) <DOI:10.1007/s11336-019-09660-x>. An extension of the NPCD framework included in the package is the nonparametric method for multiple-choice items (MC-NPC) developed by Wang, Chiu, and Koehn (2023) <DOI:10.3102/10769986221133088>. Functions associated with various extensions concerning the evaluation, validation, and feasibility of the CD analysis are also provided. These topics include the completeness of Q-matrix, Q-matrix refinement method, as well as Q-matrix estimation.
Author: Chia-Yi Chiu [aut, cph],
Weixuan Xiao [aut, cre],
Hans Friedrich Koehn [aut],
Yu Wang [aut],
Xiran Wen [aut]
Maintainer: Weixuan Xiao <wx2299@tc.columbia.edu>
Diff between NPCDTools versions 1.1.0 dated 2026-03-03 and 1.2.0 dated 2026-08-31
NPCDTools-1.1.0/NPCDTools/R/internal_functions.R |only NPCDTools-1.2.0/NPCDTools/DESCRIPTION | 12 NPCDTools-1.2.0/NPCDTools/MD5 | 30 NPCDTools-1.2.0/NPCDTools/NAMESPACE | 5 NPCDTools-1.2.0/NPCDTools/NEWS.md | 7 NPCDTools-1.2.0/NPCDTools/R/MCNPC.R |only NPCDTools-1.2.0/NPCDTools/R/NPC.R | 16 NPCDTools-1.2.0/NPCDTools/R/TSQE.R | 2 NPCDTools-1.2.0/NPCDTools/R/distractor.check.R | 34 NPCDTools-1.2.0/NPCDTools/R/internal.functions.R |only NPCDTools-1.2.0/NPCDTools/R/mcQ.generate.R |only NPCDTools-1.2.0/NPCDTools/R/mcdat.generate.R |only NPCDTools-1.2.0/NPCDTools/build/partial.rdb |binary NPCDTools-1.2.0/NPCDTools/inst/shiny/GNPC_app/app.R | 1973 +++++++++++--------- NPCDTools-1.2.0/NPCDTools/man/MCNPC.Rd |only NPCDTools-1.2.0/NPCDTools/man/NPC.Rd | 8 NPCDTools-1.2.0/NPCDTools/man/TSQE.Rd | 2 NPCDTools-1.2.0/NPCDTools/man/distractor.check.Rd | 6 NPCDTools-1.2.0/NPCDTools/man/mcQ.generate.Rd |only NPCDTools-1.2.0/NPCDTools/man/mcdat.generate.Rd |only 20 files changed, 1180 insertions(+), 915 deletions(-)
Title: Compute the Coefficient of Determination for Vector or Matrix
Outcomes
Description: Compute the coefficient of determination for outcomes in n-dimensions.
May be useful for multidimensional predictions (such as a multinomial model) or
calculating goodness of fit from latent variable models such as probabilistic
topic models like latent Dirichlet allocation or deterministic topic models
like latent semantic analysis. Based on Jones (2019)
<doi:10.48550/arXiv.1911.11061>.
Author: Tommy Jones [aut, cre] ,
Thomas Nagler [ctb]
Maintainer: Tommy Jones <jones.thos.w@gmail.com>
Diff between mvrsquared versions 0.1.5 dated 2023-07-14 and 0.1.6 dated 2026-08-31
mvrsquared-0.1.5/mvrsquared/man/mvrsquared.Rd |only mvrsquared-0.1.6/mvrsquared/DESCRIPTION | 15 mvrsquared-0.1.6/mvrsquared/MD5 | 28 - mvrsquared-0.1.6/mvrsquared/NEWS.md | 38 ++ mvrsquared-0.1.6/mvrsquared/R/RcppExports.R | 4 mvrsquared-0.1.6/mvrsquared/R/calc_rsquared.R | 59 ++- mvrsquared-0.1.6/mvrsquared/R/mvrsquared.R | 5 mvrsquared-0.1.6/mvrsquared/README.md | 1 mvrsquared-0.1.6/mvrsquared/build/vignette.rds |binary mvrsquared-0.1.6/mvrsquared/inst/WORDLIST | 1 mvrsquared-0.1.6/mvrsquared/inst/doc/getting_started_with_mvrsquared.R | 86 ++--- mvrsquared-0.1.6/mvrsquared/inst/doc/getting_started_with_mvrsquared.html | 31 - mvrsquared-0.1.6/mvrsquared/man/calc_rsquared.Rd | 11 mvrsquared-0.1.6/mvrsquared/man/mvrsquared-package.Rd |only mvrsquared-0.1.6/mvrsquared/src/RcppExports.cpp | 25 + mvrsquared-0.1.6/mvrsquared/src/calc_sum_squares_latent.cpp | 163 ++++++++-- 16 files changed, 324 insertions(+), 143 deletions(-)
Title: Monte Carlo Hypothesis Tests with Sequential Stopping
Description: Performs Monte Carlo hypothesis tests, allowing a couple of different sequential stopping boundaries. For example, a truncated sequential probability ratio test boundary (Fay, Kim and Hachey, 2007 <DOI:10.1198/106186007X257025>) and a boundary proposed by Besag and Clifford, 1991 <DOI:10.1093/biomet/78.2.301>. Gives valid p-values and confidence intervals on p-values.
Author: Michael P. Fay [aut, cre]
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between MChtest versions 1.0-3 dated 2019-05-16 and 1.0-4 dated 2026-08-31
ChangeLog | 8 ++++++++ DESCRIPTION | 14 +++++++++----- MD5 | 10 +++++----- inst/CITATION | 10 ++++------ man/MCbound.precalc1.Rd | 2 +- man/MCtest.Rd | 4 ++-- 6 files changed, 29 insertions(+), 19 deletions(-)
Title: L-Infinity Normalization and Dominant Community State Types
Description: Implements L-infinity normalization for compositional matrices,
assigns samples to dominant features, constructs truncated and
hierarchically refined dominant community state types, and computes
representative landmark profiles. The methods are described in the
accompanying publication <doi:10.48550/arXiv.2503.21543>. Bundled vaginal
and gut microbiome data support reproducible demonstrations of the package
interface; phenotype fields in the stratified gut subset are illustrative
and are not suitable for population-level inference.
Author: Pawel Gajer [aut, cre]
Maintainer: Pawel Gajer <pgajer@gmail.com>
Diff between linf versions 0.2.0 dated 2026-08-21 and 0.3.0 dated 2026-08-31
linf-0.2.0/linf/man/asv.to.linf.csts.Rd |only linf-0.2.0/linf/man/latex.linf.csts.Rd |only linf-0.2.0/linf/man/refine.linf.csts.iter.Rd |only linf-0.3.0/linf/DESCRIPTION | 9 linf-0.3.0/linf/MD5 | 42 linf-0.3.0/linf/NAMESPACE | 3 linf-0.3.0/linf/NEWS.md | 19 linf-0.3.0/linf/R/landmarks.R | 36 linf-0.3.0/linf/R/linf.R | 634 ++++----------- linf-0.3.0/linf/R/transfer_dcsts.R | 12 linf-0.3.0/linf/README.md | 5 linf-0.3.0/linf/data/valencia13k_dcst_depth2_merged.rda |binary linf-0.3.0/linf/data/valencia13k_dcst_depth3_merged.rda |binary linf-0.3.0/linf/inst/doc/linf-intro.html | 6 linf-0.3.0/linf/man/dcst.view.Rd | 16 linf-0.3.0/linf/man/linf.csts.Rd | 13 linf-0.3.0/linf/man/linf.landmarks.Rd | 16 linf-0.3.0/linf/man/normalize.linf.Rd | 10 linf-0.3.0/linf/man/print.linf.csts.Rd | 8 linf-0.3.0/linf/man/refine.linf.csts.Rd | 36 linf-0.3.0/linf/man/summary.linf.csts.Rd | 9 linf-0.3.0/linf/man/transfer.dcsts.Rd | 2 linf-0.3.0/linf/tests/testthat/test-api-cleanup.R |only linf-0.3.0/linf/tests/testthat/test-public-terminology.R | 3 24 files changed, 360 insertions(+), 519 deletions(-)
Title: HMM Toolkit for Inferring IBD Segments from SNP Genotypes
Description: Implements continuous-time hidden Markov models (HMMs) to
infer identity-by-descent (IBD) segments shared by two individuals
from their single-nucleotide polymorphism (SNP) genotypes. Provides
posterior probabilities at each marker (forward-backward algorithm),
prediction of IBD segments (Viterbi algorithm), and functions for
visualising results. Supports both autosomal data and X-chromosomal
data. The current model has two states, non-IBD and IBD1, and is
intended for unilineal relationships. The methodology and package are
described in Vigeland et al. (2026)
<doi:10.1016/j.fsigen.2025.103409>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ibdfindr versions 0.3.1 dated 2025-08-18 and 0.4.0 dated 2026-08-31
ibdfindr-0.3.1/ibdfindr/tests/testthat/_snaps |only ibdfindr-0.4.0/ibdfindr/DESCRIPTION | 15 ibdfindr-0.4.0/ibdfindr/MD5 | 60 +- ibdfindr-0.4.0/ibdfindr/NAMESPACE | 17 ibdfindr-0.4.0/ibdfindr/NEWS.md | 13 ibdfindr-0.4.0/ibdfindr/R/computePR.R | 156 +++--- ibdfindr-0.4.0/ibdfindr/R/data.R | 4 ibdfindr-0.4.0/ibdfindr/R/findIBD.R | 21 ibdfindr-0.4.0/ibdfindr/R/findSegments.R | 29 - ibdfindr-0.4.0/ibdfindr/R/fitHMM.R | 127 +++-- ibdfindr-0.4.0/ibdfindr/R/ibdPosteriors.R | 15 ibdfindr-0.4.0/ibdfindr/R/plotIBD.R | 232 +++++----- ibdfindr-0.4.0/ibdfindr/R/prepForHMM.R | 71 ++- ibdfindr-0.4.0/ibdfindr/R/problemMarkers.R |only ibdfindr-0.4.0/ibdfindr/R/totalLoglik.R | 15 ibdfindr-0.4.0/ibdfindr/R/utils.R | 20 ibdfindr-0.4.0/ibdfindr/README.md | 41 + ibdfindr-0.4.0/ibdfindr/inst |only ibdfindr-0.4.0/ibdfindr/man/brothersX.Rd | 2 ibdfindr-0.4.0/ibdfindr/man/computePR.Rd | 74 +-- ibdfindr-0.4.0/ibdfindr/man/cousinsDemo.Rd | 2 ibdfindr-0.4.0/ibdfindr/man/figures/README-brothersX-plot-1.png |binary ibdfindr-0.4.0/ibdfindr/man/figures/README-cousinsDemo-plot-1.png |binary ibdfindr-0.4.0/ibdfindr/man/findIBD.Rd | 124 ++--- ibdfindr-0.4.0/ibdfindr/man/findSegments.Rd | 96 ++-- ibdfindr-0.4.0/ibdfindr/man/fitHMM.Rd | 161 +++--- ibdfindr-0.4.0/ibdfindr/man/ibdPosteriors.Rd | 90 +-- ibdfindr-0.4.0/ibdfindr/man/ibdfindr-package.Rd | 7 ibdfindr-0.4.0/ibdfindr/man/plotIBD.Rd | 3 ibdfindr-0.4.0/ibdfindr/man/problemMarkers.Rd |only ibdfindr-0.4.0/ibdfindr/man/totalLoglik.Rd | 64 +- ibdfindr-0.4.0/ibdfindr/tests/testthat/test-computePR.R |only ibdfindr-0.4.0/ibdfindr/tests/testthat/test-findIBD.R | 2 ibdfindr-0.4.0/ibdfindr/tests/testthat/test-hmm.R |only 34 files changed, 821 insertions(+), 640 deletions(-)
Title: Analysis of Evolutionary Diversification
Description: Methods for fitting macroevolutionary models to phylogenetic trees
Pennell (2014) <doi:10.1093/bioinformatics/btu181>.
Author: Luke Harmon [aut, cre],
Matthew Pennell [aut],
Chad Brock [aut],
Joseph Brown [aut],
Wendell Challenger [aut],
Jon Eastman [aut],
Rich FitzJohn [aut],
Rich Glor [aut],
Gene Hunt [aut],
Liam Revell [aut],
Graham Slater [aut],
Josef Uyeda [aut],
Jason [...truncated...]
Maintainer: Luke Harmon <lukeh@uidaho.edu>
Diff between geiger versions 2.0.11 dated 2023-04-03 and 2.0.12 dated 2026-08-31
ChangeLog | 68 DESCRIPTION | 45 MD5 | 136 - NAMESPACE | 343 ++-- R/TESTING.R | 1202 +++++++------- R/congruify.R | 910 +++++------ R/deprecated.R | 318 +-- R/disparity.R | 580 +++---- R/diversification.R | 496 +++--- R/edges.R | 452 ++--- R/examples.R | 222 +- R/glomogram.R | 312 +-- R/internal.R | 254 +-- R/likelihood.R | 862 +++++----- R/mecca.R | 3028 ++++++++++++++++++------------------- R/medusa.R | 2650 ++++++++++++++++---------------- R/plotting.R | 1446 ++++++++--------- R/postpred.R | 560 +++--- R/proposals.R | 1738 ++++++++++----------- R/rjmcmc.R | 552 +++--- R/simulation.R | 562 +++--- R/traits-fossil.R | 1538 +++++++++---------- R/traits.R | 2138 +++++++++++++------------- R/utilities-phylo.R | 3790 +++++++++++++++++++++++------------------------ R/utilities-print.R | 680 ++++---- R/utilities-stat.R | 316 +-- README.md | 62 inst/CITATION | 170 +- man/aicm.Rd | 86 - man/aicw.Rd | 66 man/aov.phylo.Rd | 116 - man/bd.ms.Rd | 152 - man/calibrate.mecca.Rd | 178 +- man/calibrate.rjmcmc.Rd | 88 - man/congruify.phylo.Rd | 110 - man/dcount.Rd | 86 - man/drop.extinct.Rd | 96 - man/dtt.Rd | 154 - man/fitContinuous.Rd | 394 ++-- man/fitContinuousMCMC.Rd | 212 +- man/fitDiscrete.Rd | 268 +-- man/gbresolve.Rd | 124 - man/geiger-data.Rd | 234 +- man/geiger-defunct.Rd | 157 - man/geiger-examples.Rd | 22 man/geiger-internal.Rd | 184 +- man/geiger-package.Rd | 48 man/load.rjmcmc.Rd | 116 - man/make.gbm.Rd | 148 - man/mecca.Rd | 296 +-- man/medusa.Rd | 172 +- man/name.check.Rd | 94 - man/nh.test.Rd | 152 - man/nodelabel.phylo.Rd | 254 +-- man/plot.medusa.Rd | 106 - man/pp.mcmc.Rd | 282 +-- man/r8s.phylo.Rd | 150 - man/ratematrix.Rd | 82 - man/rc.Rd | 116 - man/rescale.phylo.Rd | 178 +- man/rjmcmc.bm.Rd | 232 +- man/sim.bd.Rd | 90 - man/sim.bdtree.Rd | 116 - man/sim.char.Rd | 128 - man/startingpt.mecca.Rd | 132 - man/subset.phylo.Rd | 68 man/tips.Rd | 64 man/to.auteur.Rd | 70 man/treedata.Rd | 76 69 files changed, 15680 insertions(+), 15647 deletions(-)
Title: Fast Interpretable Greedy-Tree Sums for Tree Ensembles
Description: Flexible, interpretable machine learning algorithm for additive
tree sums (FIGS). Fits a sum of shallow classification and regression
trees (CART) by greedily minimizing residual impurity, growing a new
tree or deepening an existing one at each step, whichever reduces the
residuals most. Supports regression and two-class classification, variable
importance, bootstrap ensembling and seamless integration with 'parsnip'
and 'tidymodels' workflows. The method is described in Tan et al. (2023)
<doi:10.1073/pnas.2310151122>.
Author: Joao Paulo Assis Bonifacio [aut, cre, cph] ,
Geraldo Magela da Cruz Pereira [aut, cph] ,
Pedro Mambelli Fernandes [aut, cph] ,
Joao Vitor Andrade Alves de Souza [aut, cph]
Maintainer: Joao Paulo Assis Bonifacio <jpab.27@hotmail.com>
Diff between figsr versions 0.1.0 dated 2026-08-31 and 0.1.1 dated 2026-08-31
DESCRIPTION | 10 MD5 | 64 - NAMESPACE | 31 NEWS.md | 121 ++- R/bagging.R | 213 +++-- R/dials.R | 78 +- R/figs_tree.R | 525 +++++++------ R/fit_engine.R | 793 +++++++++++---------- R/plot.R | 400 +++++----- R/predict.R | 203 +++-- R/summary.R | 197 ++--- README.md | 147 ++- inst/WORDLIST | 3 inst/doc/figsr-intro.R | 55 + inst/doc/figsr-intro.Rmd | 175 +++- inst/doc/figsr-intro.html | 234 ++++-- man/bagging_figs.Rd | 88 +- man/figs.Rd | 143 ++- man/figs_tree.Rd | 85 +- man/figsr_importance.Rd | 72 - man/fit_figs.Rd | 106 +- man/max_splits.Rd | 42 - man/max_trees.Rd | 42 - man/plot.figsr_fit.Rd | 68 - man/predict.bagging_figs_fit.Rd | 52 - man/predict.figsr_fit.Rd | 58 - man/predict_figs.Rd | 53 - man/print.figsr_fit.Rd | 52 - man/summary.figsr_fit.Rd | 52 - man/update.figs_tree.Rd |only tests/testthat/test-classification-probabilities.R |only tests/testthat/test-deep-node-values.R |only tests/testthat/test-edge-cases.R |only tests/testthat/test-formula-interface.R |only tests/testthat/test-print-plot.R |only vignettes/figsr-intro.Rmd | 175 +++- 36 files changed, 2564 insertions(+), 1773 deletions(-)
Title: Escalation with Overdose Control
Description: An implementation of a variety of escalation with overdose control designs introduced by Babb, Rogatko and Zacks (1998) <doi:10.1002/(SICI)1097-0258(19980530)17:10%3C1103::AID-SIM793%3E3.0.CO;2-9>. It calculates the next dose as a clinical trial proceeds and performs simulations to obtain operating characteristics.
Author: Marcio A. Diniz [aut, cre, cph]
Maintainer: Marcio A. Diniz <marcio.diniz@mountsinai.org>
This is a re-admission after prior archival of version 0.3.0 dated 2020-06-07
Diff between ewoc versions 0.3.0 dated 2020-06-07 and 0.3.1 dated 2026-08-31
DESCRIPTION | 22 +++++++----- MD5 | 36 ++++++++++----------- NAMESPACE | 8 ++++ NEWS.md | 3 + R/classical_EWOC.R | 1 R/extended_EWOC.R | 3 + R/next_dose.R | 4 +- R/operating_characteristics.R | 39 ++++++++++++---------- R/pdlt.R | 3 + R/ph_EWOC.R | 1 R/plot.R | 15 +++++--- R/response.R | 5 ++ R/stop_rule.R | 28 ++++++++-------- README.md | 72 ++++++++++++++++++++++-------------------- man/opc.Rd | 6 +-- man/stop_rule.Rd | 2 - man/stop_rule_d1classical.Rd | 10 ++--- man/stop_rule_d1extended.Rd | 12 +++---- man/stop_rule_d1ph.Rd | 12 +++---- 19 files changed, 161 insertions(+), 121 deletions(-)
Title: Tools for General Maximum Likelihood Estimation
Description: Methods and functions for fitting maximum likelihood models in R. This package modifies and extends the 'mle' classes in the 'stats4' package.
Author: Ben Bolker [aut, cre] ,
R Development Core Team [aut],
Iago Gine-Vazquez [ctb]
Maintainer: Ben Bolker <bolker@mcmaster.ca>
Diff between bbmle versions 1.0.25.1 dated 2023-12-08 and 1.0.26 dated 2026-08-31
DESCRIPTION | 12 ++-- MD5 | 70 ++++++++++++++-------------- NAMESPACE | 4 - R/IC.R | 7 ++ R/confint.R | 14 +++-- R/mle.R | 110 ++++++++++++++++++++++++++++++-------------- R/mle2-methods.R | 2 R/predict.R | 2 R/profile.R | 8 ++- build/vignette.rds |binary inst/NEWS.Rd | 38 ++++++++++++++- inst/doc/mle2.R | 45 ++++++++++++------ inst/doc/mle2.Rnw | 15 ++---- inst/doc/mle2.pdf |binary inst/doc/quasi.pdf |binary inst/tinytest |only man/BIC-methods.Rd | 7 ++ man/ICtab.Rd | 42 ++++++++++------ man/mle2.Rd | 3 + man/pop_pred_samp.Rd | 3 - man/profile.mle-class.Rd | 9 ++- tests/BIC.R | 16 ++++++ tests/BIC.Rout.save | 25 ++++++++-- tests/ICtab.R | 10 +++- tests/ICtab.Rout.save | 21 +++++--- tests/binomtest1.R | 2 tests/binomtest1.Rout.save | 2 tests/formulatest.R | 8 +-- tests/formulatest.Rout.save | 8 +-- tests/mortanal.R | 6 +- tests/mortanal.Rout.save | 6 +- tests/optimx.R | 57 ++++++++++++++++++++++ tests/optimx.Rout.save | 65 ++++++++++++++++++++++++-- tests/startvals2.R | 6 +- tests/startvals2.Rout.save | 6 +- tests/tinytest.R |only vignettes/mle2.Rnw | 15 ++---- 37 files changed, 465 insertions(+), 179 deletions(-)
Title: Bayesian Averaging for Dynamic Panels
Description: Implements Bayesian model averaging for dynamic panels with weakly
exogenous regressors as described in the paper by
Moral-Benito (2013, <doi:10.1080/07350015.2013.818003>).
The package provides functions to estimate dynamic panel data models
and analyze the results of the estimation.
Author: Krzysztof Beck [aut],
Piotr Cukier [aut],
Marcin Dubel [aut, cre],
Mariusz Szczepanczyk [aut],
Mateusz Wyszynski [aut],
badp authors [cph]
Maintainer: Marcin Dubel <marcindubel@gmail.com>
Diff between badp versions 0.6.0 dated 2026-08-19 and 0.6.1 dated 2026-08-31
DESCRIPTION | 15 ++++++++++----- LICENSE | 4 ++-- MD5 | 6 +++--- NEWS.md | 5 +++++ 4 files changed, 20 insertions(+), 10 deletions(-)
Title: D-Vine Quantile Regression
Description: Implements D-vine quantile regression models with
parametric or nonparametric pair-copulas. See
Kraus and Czado (2017) <doi:10.1016/j.csda.2016.12.009> and
Schallhorn et al. (2017) <doi:10.48550/arXiv.1705.08310>.
Author: Thomas Nagler [aut, cre],
Dani Kraus [ctb]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between vinereg versions 0.12.1 dated 2025-12-10 and 0.13.0 dated 2026-08-31
DESCRIPTION | 7 MD5 | 68 ++--- NAMESPACE | 7 NEWS.md | 47 +++ R/cpit.R | 29 +- R/generics.R | 67 ++++- R/predict.vinereg.R | 19 - R/tools.R | 17 - R/vinereg-package.R |only R/vinereg.R | 105 +++++++- README.md | 116 +++++---- build/partial.rdb |only build/vignette.rds |binary inst/doc/abalone-example.R | 10 inst/doc/abalone-example.Rmd | 29 +- inst/doc/abalone-example.html | 389 ++++++++++++++----------------- inst/doc/bike-rental.R | 12 inst/doc/bike-rental.Rmd | 16 - inst/doc/bike-rental.html | 370 +++++++++++++++-------------- man/cll.Rd | 7 man/cpdf.Rd | 13 - man/cpit.Rd | 12 man/figures/README-unnamed-chunk-1-1.png |binary man/plot_effects.Rd | 14 - man/predict.vinereg.Rd | 11 man/vinereg-methods.Rd |only man/vinereg-package.Rd |only man/vinereg.Rd | 26 +- src/Makevars | 1 src/Makevars.win | 2 src/vinereg.cpp | 22 - tests/testthat/test-generics.R | 13 + tests/testthat/test-predict.R | 12 tests/testthat/test-test-cpit.R | 22 + tests/testthat/test-vinereg.R | 102 ++++++++ vignettes/abalone-example.Rmd | 29 +- vignettes/bike-rental.Rmd | 16 - 37 files changed, 986 insertions(+), 624 deletions(-)
Title: Stationary Vine Copula Models
Description: Provides functionality to fit and simulate from stationary vine
copula models for time series, see Nagler et al. (2022)
<doi:10.1016/j.jeconom.2021.11.015>.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between svines versions 0.2.7 dated 2025-06-12 and 0.3.0 dated 2026-08-31
svines-0.2.7/svines/src/Makevars |only svines-0.2.7/svines/src/Makevars.win |only svines-0.3.0/svines/DESCRIPTION | 18 - svines-0.3.0/svines/MD5 | 87 +++---- svines-0.3.0/svines/NEWS.md | 9 svines-0.3.0/svines/R/returns.R | 15 - svines-0.3.0/svines/R/standard_errors.R | 68 ++++- svines-0.3.0/svines/R/svine.R | 81 +++++- svines-0.3.0/svines/R/svine_methods.R | 22 - svines-0.3.0/svines/R/svinecop.R | 68 ++--- svines-0.3.0/svines/R/svinecop_methods.R | 39 +-- svines-0.3.0/svines/R/tools_select.R | 108 +++++++- svines-0.3.0/svines/README.md | 124 +++++----- svines-0.3.0/svines/build/partial.rdb |binary svines-0.3.0/svines/build/vignette.rds |only svines-0.3.0/svines/cleanup |only svines-0.3.0/svines/cleanup.win |only svines-0.3.0/svines/configure |only svines-0.3.0/svines/configure.win |only svines-0.3.0/svines/inst/CITATION |only svines-0.3.0/svines/inst/doc |only svines-0.3.0/svines/inst/include/svines/implementation/svine_selector.ipp | 54 +++- svines-0.3.0/svines/inst/include/svines/implementation/svinecop.ipp | 57 +++- svines-0.3.0/svines/inst/include/svines/svine_selector.hpp | 4 svines-0.3.0/svines/inst/include/svines/svinecop.hpp | 8 svines-0.3.0/svines/man/figures/README-unnamed-chunk-4-1.png |binary svines-0.3.0/svines/man/figures/README-unnamed-chunk-5-1.png |binary svines-0.3.0/svines/man/figures/README-unnamed-chunk-6-1.png |binary svines-0.3.0/svines/man/returns.Rd | 13 - svines-0.3.0/svines/man/svine.Rd | 18 + svines-0.3.0/svines/man/svine_bootstrap_models.Rd | 7 svines-0.3.0/svines/man/svine_dist.Rd | 10 svines-0.3.0/svines/man/svine_hessian.Rd | 13 - svines-0.3.0/svines/man/svine_loglik.Rd | 4 svines-0.3.0/svines/man/svine_pseudo_residuals.Rd | 14 - svines-0.3.0/svines/man/svine_scores.Rd | 10 svines-0.3.0/svines/man/svine_sim.Rd | 2 svines-0.3.0/svines/man/svinecop.Rd | 36 +- svines-0.3.0/svines/man/svinecop_dist.Rd | 14 - svines-0.3.0/svines/man/svinecop_hessian.Rd | 17 - svines-0.3.0/svines/man/svinecop_loglik.Rd | 4 svines-0.3.0/svines/man/svinecop_pseudo_residuals.Rd | 5 svines-0.3.0/svines/man/svinecop_scores.Rd | 11 svines-0.3.0/svines/man/svinecop_sim.Rd | 2 svines-0.3.0/svines/man/svines-package.Rd | 6 svines-0.3.0/svines/src/Makevars.in |only svines-0.3.0/svines/src/Makevars.win.in |only svines-0.3.0/svines/tests/testthat/test-discrete.R |only svines-0.3.0/svines/tests/testthat/test-svinecop.R | 5 svines-0.3.0/svines/vignettes |only 50 files changed, 658 insertions(+), 295 deletions(-)
Title: Minorization-Maximization via Assembly-Decomposition Technology
Description: A formula-driven framework for maximizing target functions
via the minorization-maximization (MM) algorithm. The package
represents the target as a symbolic expression tree, infers its
curvature via disciplined-convex-programming rules, and constructs
a separable surrogate at each iterate using only Jensen's
inequality and the supporting hyperplane. The driver maximizes the
surrogate via block-coordinate Newton with line search, falling
back to a multivariate step on any non-separable residue. A
formula interface accepts standard R expressions (including
`sum()` reductions and `X %*% theta` design-matrix products) so
statistical models such as Poisson regression can be written in
one line.
Author: Xifen Huang [aut],
Jinfeng Xu [aut],
Jiaqi Gu [aut, cre]
Maintainer: Jiaqi Gu <jiaqigu@usf.edu>
Diff between MMAD versions 3.0.0 dated 2026-07-07 and 3.0.1 dated 2026-08-31
DESCRIPTION | 9 - MD5 | 14 +- NAMESPACE | 10 + R/MMAD-package.R | 1 R/mmad_driver.R | 193 ++++++++++++++++++++++++++++++++++++-- man/mmad.Rd | 21 +++- man/mmad_fit-methods.Rd |only man/mmad_test.Rd |only tests/testthat/test-mmad_driver.R | 115 ++++++++++++++++++++++ 9 files changed, 338 insertions(+), 25 deletions(-)
Title: Mediation Analysis with Missing Data Using Bootstrap
Description: Four methods for mediation analysis with missing data: Listwise deletion, Pairwise deletion, Multiple imputation, and Two Stage Maximum Likelihood algorithm. For MI and TS-ML, auxiliary variables can be included. Bootstrap confidence intervals for mediation effects are obtained. The robust method is also implemented for TS-ML. Since version 1.4, bmem adds the capability to conduct power analysis for mediation models. Details about the methods used can be found in these articles. Zhang and Wang (2003) <doi:10.1007/s11336-012-9301-5>. Zhang (2014) <doi:10.3758/s13428-013-0424-0>.
Author: Zhiyong Zhang [aut, cre],
Lijuan Wang [aut]
Maintainer: Zhiyong Zhang <zhiyongzhang@nd.edu>
Diff between bmem versions 2.2 dated 2025-09-03 and 2.3 dated 2026-08-31
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/power.R | 12 ++++++------ inst/doc/MediationAnalysis.pdf |binary 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 1.2.0 dated 2026-07-02 and 1.3.0 dated 2026-08-31
DESCRIPTION | 6 - MD5 | 49 +++++----- NAMESPACE | 2 NEWS.md | 6 + R/MaestroPipeline.R | 62 +++++++++++++ R/MaestroPipelineList.R | 104 +++++++++++++++++++++++ R/build_schedule.R | 1 R/build_schedule_entry.R | 24 ++++- R/maestro_tags.R | 35 +++++++ R/roxy_maestro.R | 37 ++++++++ inst/doc/maestro-1-quick-start.html | 2 inst/doc/maestro-3-advanced-scheduling.html | 4 inst/doc/maestro-4-directed-acyclic-graphs.html | 18 +-- inst/doc/maestro-4b-directed-acyclic-graphs.html | 38 ++++---- inst/doc/maestro-5-logging.html | 64 +++++++------- inst/doc/maestro-7-tag-reference.html | 24 +++++ inst/doc/maestro-7-tag-reference.qmd | 30 ++++++ inst/doc/maestro-8-conditionals.html | 38 ++++---- man/MaestroPipeline.Rd | 93 ++++++++++++++++++++ man/MaestroPipelineList.Rd | 20 ++++ man/maestro_tags.Rd | 37 ++++++++ tests/testthat/_snaps/fanout.md | 11 ++ tests/testthat/_snaps/get_slot_usage.md | 8 - tests/testthat/test-cascade.R |only tests/testthat/test-fanout.R | 33 +++++++ vignettes/maestro-7-tag-reference.qmd | 30 ++++++ 26 files changed, 658 insertions(+), 118 deletions(-)
Title: Curve Linear Regression via Dimension Reduction
Description: A new methodology for linear regression with both curve response
and curve regressors, which is described in Cho, Goude, Brossat and Yao
(2013) <doi:10.1080/01621459.2012.722900> and (2015)
<doi:10.1007/978-3-319-18732-7_3>. The key idea behind this methodology is
dimension reduction based on a singular value decomposition in a Hilbert
space, which reduces the curve regression problem to several scalar linear
regression problems.
Author: Amandine Pierrot [cre, aut],
Qiwei Yao [ctb],
Haeran Cho [ctb],
Yannig Goude [ctb],
Tony Aldon [ctb],
EDF [cph, fnd]
Maintainer: Amandine Pierrot <amandine.m.pierrot@gmail.com>
Diff between clr versions 0.1.2 dated 2019-07-29 and 0.1.3 dated 2026-08-31
clr-0.1.2/clr/data/datalist |only clr-0.1.3/clr/DESCRIPTION | 25 ++++++++++++++++++------- clr-0.1.3/clr/MD5 | 21 ++++++++++----------- clr-0.1.3/clr/NAMESPACE | 16 ++++++++++------ clr-0.1.3/clr/NEWS.md | 13 +++++++++++++ clr-0.1.3/clr/R/clr.R | 4 ++-- clr-0.1.3/clr/R/gb_load-data.R | 4 ++-- clr-0.1.3/clr/man/clr.Rd | 14 ++++++++++---- clr-0.1.3/clr/man/clust_test.Rd | 6 ++++-- clr-0.1.3/clr/man/clust_train.Rd | 6 ++++-- clr-0.1.3/clr/man/gb_load.Rd | 10 ++++++---- clr-0.1.3/clr/man/predict.clr.Rd | 10 ++++++++-- 12 files changed, 87 insertions(+), 42 deletions(-)
Title: Bayesian Estimation of Dynamic VAR Models using Stan
Description: Bayesian estimation of multilevel Vector Autoregression (VAR) models
using Stan. Supports Gaussian, Binary, and Ordinal (adjacent category) outcome
variables with random effects and customizable priors.
Author: Florian Metwaly [aut, cre, cph]
Maintainer: Florian Metwaly <f.j.metwaly@uva.nl>
Diff between bvarnet versions 1.0.1 dated 2026-06-13 and 1.0.2 dated 2026-08-31
DESCRIPTION | 19 + MD5 | 81 ++++---- NAMESPACE | 3 NEWS.md | 29 ++- R/bayes_factor.R | 129 +++++++++++-- R/bvar.R | 189 +++++++++++++------ R/download_models.R |only R/extract_param.R | 60 ++---- R/extractors.R | 77 +++++--- R/helpers.R | 298 +++++++++++++++++++++++++++---- R/set_priors.R | 13 + R/sim_bvarnet.R | 79 +++----- R/summary.R | 19 + R/to_stan_data.R | 131 +++++++++++-- R/utils.R |only R/zzz.R | 90 ++++++--- README.md | 45 +++- inst/COPYRIGHTS |only inst/doc/Missing-Data.Rmd | 160 +++------------- inst/doc/Missing-Data.html | 244 ++++++++----------------- man/bf_table.Rd | 12 + man/bvar.Rd | 48 ++++ man/bvarnet-package.Rd | 2 man/bvarnet_clear_model_cache.Rd |only man/bvarnet_model_cache_dir.Rd |only man/bvarnet_setup_models.Rd |only man/compare_to_truth.Rd | 6 man/extract_network_matrix.Rd | 10 - man/extract_param.Rd | 22 +- man/extract_random_effects.Rd | 22 ++ man/extract_temporal.Rd | 13 - man/figures |only man/set_priors.Rd | 15 + man/summary.bvarnet.Rd | 7 tests/testthat/helper-fixtures.R | 47 +++- tests/testthat/test-bayes_factor.R | 64 +++--- tests/testthat/test-download-models.R |only tests/testthat/test-draw-ordering.R |only tests/testthat/test-extract_param.R | 23 ++ tests/testthat/test-helpers.R | 192 +++++++++++++++++++ tests/testthat/test-input-validation.R | 29 +++ tests/testthat/test-prior-scaling.R |only tests/testthat/test-summary-extractors.R | 59 ++++++ tests/testthat/test-to_stan_data.R | 111 +++++++++++ tests/testthat/test-utils.R |only vignettes/Missing-Data.Rmd | 160 +++------------- vignettes/Missing-Data.Rmd.orig | 28 +- 47 files changed, 1728 insertions(+), 808 deletions(-)
Title: Bayesian Latent Space Model
Description: Provides a Bayesian latent space
model for complex networks, either weighted or unweighted.
Given an observed input graph, the estimates for the latent coordinates
of the nodes are obtained through a Bayesian MCMC algorithm.
The overall likelihood of the graph depends on a fundamental probability
equation, which is defined so that ties are more likely to exist
between nodes whose latent space coordinates are close.
The package is mainly based on the model by Hoff, Raftery and Handcock (2002)
<doi:10.1198/016214502388618906> and contains some extra features
(e.g., removal of the Procrustean step, weights implemented as
coefficients of the latent distances, 3D plots).
The original code related to the above model was retrieved from
<https://www2.stat.duke.edu/~pdh10/Code/hoff_raftery_handcock_2002_jasa/>.
Users can inspect the MCMC simulation, create and customize insightful
graphical representations or apply clustering techniques.
Author: Alberto Donizetti [aut, cre],
Francesca Ieva [ctb]
Maintainer: Alberto Donizetti <albe.donizetti@gmail.com>
Diff between BLSM versions 0.1.0 dated 2018-04-26 and 0.1.1 dated 2026-08-31
DESCRIPTION | 12 MD5 | 48 +- NAMESPACE | 50 +- NEWS.md | 10 R/RcppExports.R | 238 +++++------ R/blsm.R | 820 +++++++++++++++++++-------------------- R/data.R | 112 ++--- R/package.R | 102 ++-- README.md | 68 +-- man/BLSM.Rd | 92 ++-- man/Z_up.Rd | 58 +- man/alpha_up.Rd | 58 +- man/dst.Rd | 40 - man/estimate_latent_positions.Rd | 216 +++++----- man/example_adjacency_matrix.Rd | 28 - man/example_blsm_obj.Rd | 58 +- man/example_weights_matrix.Rd | 58 +- man/lpY.Rd | 50 +- man/lpYNODE.Rd | 58 +- man/lpz_dist.Rd | 46 +- man/lpz_distNODE.Rd | 46 +- man/mlpY.Rd | 46 +- man/plot_latent_positions.Rd | 70 +-- man/plot_traceplots_acf.Rd | 66 +-- man/proc_crr.Rd | 74 +-- 25 files changed, 1272 insertions(+), 1252 deletions(-)
Title: Interact with Peak Flow Data in the United Kingdom
Description: Obtain information on peak flow data from the National River Flow Archive (NRFA) in the United Kingdom, either from the Peak Flow Dataset files <https://nrfa.ceh.ac.uk/data/peak-flow-dataset> once these have been downloaded to the user's computer or using the NRFA's API. These files are in a format suitable for direct use in the 'WINFAP' software, hence the name of the package.
Author: Ilaria Prosdocimi [aut, cre] ,
Luke Shaw [aut]
Maintainer: Ilaria Prosdocimi <prosdocimi.ilaria@gmail.com>
Diff between winfapReader versions 0.1-7 dated 2026-02-20 and 0.1-7.1 dated 2026-08-31
DESCRIPTION | 8 ++++---- MD5 | 25 +++++++++++++------------ NAMESPACE | 26 ++++++++++++++------------ NEWS.md | 5 ++++- R/known_Oct1.R | 4 +++- R/readerFuncs.R | 27 ++++++++++++++------------- build/vignette.rds |binary data/known_Oct1.rda |binary inst/doc/winfapReader.R | 4 ---- inst/doc/winfapReader.Rmd | 4 ---- inst/doc/winfapReader.html | 12 ++++-------- man/known_Oct1.Rd | 2 +- vignettes/--find-assets.html |only vignettes/winfapReader.Rmd | 4 ---- 14 files changed, 57 insertions(+), 64 deletions(-)
Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen [aut, cre] ,
Gavin L. Simpson [aut] ,
F. Guillaume Blanchet [aut],
Roeland Kindt [aut],
Pierre Legendre [aut],
Peter R. Minchin [aut],
R.B. O'Hara [aut],
Peter Solymos [aut],
M. Henry H. Stevens [aut],
Eduard Szoecs [aut],
Helene Wagner [...truncated...]
Maintainer: Jari Oksanen <jhoksane@gmail.com>
Diff between vegan versions 2.7-5 dated 2026-05-25 and 2.7-6 dated 2026-08-31
DESCRIPTION | 6 +-- MD5 | 58 ++++++++++++++--------------- NEWS.md | 41 ++++++++++++++++++++ R/clamtest.R | 8 ++-- R/decorana.R | 4 +- R/make.cepnames.R | 17 +++++++- R/metaMDS.R | 11 ++--- R/ordimedian.R | 30 +++++++++------ R/ordispider.R | 4 -- R/ordisurf.R | 21 +++++++--- R/plot.decorana.R | 11 ++++- R/print.summary.clamtest.R | 6 ++- R/showvarparts.R | 2 - R/summary.clamtest.R | 8 ++-- R/summary.isomap.R | 1 R/tabasco.R | 13 ++++-- R/text.decorana.R | 8 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/FAQ-vegan.html | 18 +++++---- inst/doc/decision-vegan.pdf |binary inst/doc/diversity-vegan.pdf |binary inst/doc/intro-vegan.pdf |binary inst/doc/partitioning.pdf |binary man/make.cepnames.Rd | 38 ++++++++++++------- man/ordiArrowTextXY.Rd | 2 - man/tolerance.Rd | 34 ++++++++++++----- man/vegemite.Rd | 84 +++++++++++++++++++++---------------------- tests/vegan-tests.R | 26 +++++++++++-- tests/vegan-tests.Rout.save | 51 ++++++++++++++++++++++---- 30 files changed, 334 insertions(+), 168 deletions(-)
Title: Language Support for 'sylly' Package: English
Description: Adds support for the English language to the 'sylly' package. To ask for help, report bugs, suggest feature improvements, or discuss the global development of the package, please consider subscribing to the koRpus-dev mailing list (<https://korpusml.reaktanz.de>).
Author: Meik Michalke [aut, cre]
Maintainer: Meik Michalke <meik.michalke@hhu.de>
Diff between sylly.en versions 0.1-3 dated 2018-03-19 and 0.1-4 dated 2026-08-31
ChangeLog | 4 ++++ DESCRIPTION | 23 ++++++++--------------- MD5 | 23 ++++++++++++----------- R/hyph.en-data.R | 7 +++---- R/hyph.support-en.R | 10 +++++----- R/sylly.en-package.R | 35 +++++++++++++++++++---------------- README.md | 6 +++--- build |only inst/CITATION | 12 ++++++------ inst/NEWS.Rd | 7 +++++++ man/hyph.en.Rd | 13 ++++++------- man/hyph.support.en.Rd | 6 +++--- man/sylly.en-package.Rd | 29 +++++++++++++++++------------ 13 files changed, 93 insertions(+), 82 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 1.6.6 dated 2026-06-04 and 1.6.7 dated 2026-08-31
DESCRIPTION | 33 MD5 | 16 build/partial.rdb |only build/vignette.rds |binary inst/CITATION |only inst/doc/StepReg.R | 393 ---- inst/doc/StepReg.Rmd | 748 --------- inst/doc/StepReg.html | 3942 +++---------------------------------------------- man/StepReg-package.Rd | 15 vignettes/StepReg.Rmd | 748 --------- 10 files changed, 312 insertions(+), 5583 deletions(-)
Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are cumulative probability
distributions which are fitted to toxicity concentrations for
different species as described by Posthuma et al. (2001)
<isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to
fit distributions such as the gamma, log-logistic, log-normal and
log-normal log-normal mixture. Multiple distributions can be averaged
using Akaike Information Criteria. Confidence intervals on hazard
concentrations and proportions are produced by bootstrapping.
Author: Joe Thorley [aut, cre] ,
Rebecca Fisher [aut],
David Fox [aut],
Carl Schwarz [aut],
Angeline Tillmanns [ctb],
Seb Dalgarno [ctb] ,
Kathleen McTavish [ctb],
Heather Thompson [ctb],
Doug Spry [ctb],
Rick van Dam [ctb],
Graham Batley [ctb],
Ali Azizishi [...truncated...]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between ssdtools versions 2.6.0 dated 2026-03-05 and 2.7.0 dated 2026-08-31
ssdtools-2.6.0/ssdtools/tests/testthat/_snaps/hp/hc_fix.csv |only ssdtools-2.6.0/ssdtools/tests/testthat/_snaps/hp/hc_unfix.csv |only ssdtools-2.6.0/ssdtools/tests/testthat/_snaps/hp/hp_30.csv |only ssdtools-2.6.0/ssdtools/tests/testthat/_snaps/weibull/hc_anona.csv |only ssdtools-2.7.0/ssdtools/DESCRIPTION | 24 ssdtools-2.7.0/ssdtools/MD5 | 389 +++--- ssdtools-2.7.0/ssdtools/NAMESPACE | 142 +- ssdtools-2.7.0/ssdtools/NEWS.md | 47 ssdtools-2.7.0/ssdtools/R/bcanz.R | 43 ssdtools-2.7.0/ssdtools/R/boot.R | 116 + ssdtools-2.7.0/ssdtools/R/burrlioz.R | 65 - ssdtools-2.7.0/ssdtools/R/burrrIII3.R | 51 ssdtools-2.7.0/ssdtools/R/censor.R | 14 ssdtools-2.7.0/ssdtools/R/chk.R | 45 ssdtools-2.7.0/ssdtools/R/ci-methods.R | 9 ssdtools-2.7.0/ssdtools/R/cis.R | 5 ssdtools-2.7.0/ssdtools/R/convergence.R | 3 ssdtools-2.7.0/ssdtools/R/devtools-helpers.R | 1 ssdtools-2.7.0/ssdtools/R/dists.R | 8 ssdtools-2.7.0/ssdtools/R/element.R |only ssdtools-2.7.0/ssdtools/R/estimates.R | 4 ssdtools-2.7.0/ssdtools/R/fit-burrlioz.R | 86 - ssdtools-2.7.0/ssdtools/R/fit-dists.R | 212 ++- ssdtools-2.7.0/ssdtools/R/gamma.R | 36 ssdtools-2.7.0/ssdtools/R/getters.R | 13 ssdtools-2.7.0/ssdtools/R/ggplot.R | 168 +- ssdtools-2.7.0/ssdtools/R/ggproto.R | 71 - ssdtools-2.7.0/ssdtools/R/glance.R | 14 ssdtools-2.7.0/ssdtools/R/gof.R | 4 ssdtools-2.7.0/ssdtools/R/gompertz.R | 60 ssdtools-2.7.0/ssdtools/R/hc-burrlioz.R | 12 ssdtools-2.7.0/ssdtools/R/hc.R | 151 +- ssdtools-2.7.0/ssdtools/R/hcp-average.R | 91 + ssdtools-2.7.0/ssdtools/R/hcp-ind.R | 62 - ssdtools-2.7.0/ssdtools/R/hcp-ma.R | 144 +- ssdtools-2.7.0/ssdtools/R/hcp-multi.R | 56 ssdtools-2.7.0/ssdtools/R/hcp-samples.R | 85 + ssdtools-2.7.0/ssdtools/R/hcp-tmbfit.R | 120 + ssdtools-2.7.0/ssdtools/R/hcp-weighted.R | 55 ssdtools-2.7.0/ssdtools/R/hcp.R | 158 ++ ssdtools-2.7.0/ssdtools/R/helpers.R | 31 ssdtools-2.7.0/ssdtools/R/hp.R | 82 - ssdtools-2.7.0/ssdtools/R/internal.R | 9 ssdtools-2.7.0/ssdtools/R/invpareto.R | 39 ssdtools-2.7.0/ssdtools/R/lgumbel.R | 81 - ssdtools-2.7.0/ssdtools/R/llogis-llogis.R | 149 +- ssdtools-2.7.0/ssdtools/R/llogis.R | 47 ssdtools-2.7.0/ssdtools/R/lnorm-lnorm.R | 106 + ssdtools-2.7.0/ssdtools/R/lnorm.R | 36 ssdtools-2.7.0/ssdtools/R/match-moments.R | 28 ssdtools-2.7.0/ssdtools/R/multi.R | 615 ++-------- ssdtools-2.7.0/ssdtools/R/params.R | 9 ssdtools-2.7.0/ssdtools/R/plot-cdf.R | 56 ssdtools-2.7.0/ssdtools/R/plot-cf.R | 5 ssdtools-2.7.0/ssdtools/R/plot-data.R | 126 +- ssdtools-2.7.0/ssdtools/R/pqr.R | 85 + ssdtools-2.7.0/ssdtools/R/predict.R | 75 - ssdtools-2.7.0/ssdtools/R/print.R | 12 ssdtools-2.7.0/ssdtools/R/scales.R | 46 ssdtools-2.7.0/ssdtools/R/seeds.R | 4 ssdtools-2.7.0/ssdtools/R/ssd-plot.R | 266 +++- ssdtools-2.7.0/ssdtools/R/ssdtools-package.R | 2 ssdtools-2.7.0/ssdtools/R/subset.R | 8 ssdtools-2.7.0/ssdtools/R/tidy.R | 5 ssdtools-2.7.0/ssdtools/R/tmb.R | 49 ssdtools-2.7.0/ssdtools/R/utils.R | 29 ssdtools-2.7.0/ssdtools/R/weibull.R | 36 ssdtools-2.7.0/ssdtools/R/wqg.R | 6 ssdtools-2.7.0/ssdtools/README.md | 43 ssdtools-2.7.0/ssdtools/build/vignette.rds |binary ssdtools-2.7.0/ssdtools/inst/doc/faqs.R | 2 ssdtools-2.7.0/ssdtools/inst/doc/faqs.Rmd | 2 ssdtools-2.7.0/ssdtools/inst/doc/faqs.html | 8 ssdtools-2.7.0/ssdtools/inst/doc/ssdtools.html | 36 ssdtools-2.7.0/ssdtools/man/augment.fitdists.Rd | 6 ssdtools-2.7.0/ssdtools/man/dist_data.Rd | 8 ssdtools-2.7.0/ssdtools/man/geom_hcintersect.Rd | 12 ssdtools-2.7.0/ssdtools/man/geom_ssdpoint.Rd | 12 ssdtools-2.7.0/ssdtools/man/geom_ssdsegment.Rd | 12 ssdtools-2.7.0/ssdtools/man/geom_xribbon.Rd | 12 ssdtools-2.7.0/ssdtools/man/glance.fitdists.Rd | 11 ssdtools-2.7.0/ssdtools/man/params.Rd | 4 ssdtools-2.7.0/ssdtools/man/reexports.Rd | 10 ssdtools-2.7.0/ssdtools/man/scale_colour_ssd.Rd | 12 ssdtools-2.7.0/ssdtools/man/ssd_dists.Rd | 6 ssdtools-2.7.0/ssdtools/man/ssd_dists_all.Rd | 6 ssdtools-2.7.0/ssdtools/man/ssd_dists_shiny.Rd | 6 ssdtools-2.7.0/ssdtools/man/ssd_e.Rd | 6 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Title: Stagewise Generalized Estimating Equations
Description: Stagewise techniques implemented with Generalized Estimating Equations to handle individual, group, bi-level, and interaction selection. Stagewise approaches start with an empty model and slowly build the model over several iterations, which yields a 'path' of candidate models from which model selection can be performed. This 'slow brewing' approach gives stagewise techniques a unique flexibility that allows simple incorporation of Generalized Estimating Equations; see Vaughan, G., Aseltine, R., Chen, K., Yan, J., (2017) <doi:10.1111/biom.12669> for details.
Author: Gregory Vaughan [aut, cre],
Kun Chen [ctb],
Jun Yan [ctb]
Maintainer: Gregory Vaughan <gvaughan@bentley.edu>
Diff between sgee versions 0.6-0 dated 2018-01-08 and 0.6-2 dated 2026-08-31
ChangeLog | 460 +++++---- DESCRIPTION | 28 MD5 | 66 - R/bisee.R | 1212 ++++++++++++------------- R/deltaFinder.R | 84 - R/deltaValue.R | 86 - R/evaluateGEE.R | 506 +++++----- R/genCorMat.R | 250 ++--- R/genData.R | 581 +++++++----- R/gsee.R | 588 ++++++------ R/hisee.R | 1075 +++++++++++----------- R/isee.R | 1954 ++++++++++++++++++++--------------------- R/miniSim.R | 396 ++++---- R/plot.sgee.R | 644 ++++++------- R/print.sgee.R | 202 ++-- R/print.sgeeSummary.R | 186 +-- R/samplingDistCalculation.R | 262 ++--- R/see.R | 1279 +++++++++++++------------- R/sgee-package.R | 278 ++--- R/sgee.control.R | 268 ++--- R/subsample.R | 166 +-- R/summary.sgee.R | 670 +++++++------- inst/COPYRIGHT | 36 man/bisee.Rd | 71 + man/genData.Rd | 34 man/hisee.Rd | 36 man/isee.Rd | 69 + man/miniSim.Rd | 18 man/plot.sgee.Rd | 19 man/samplingDistCalculation.Rd | 18 man/see.Rd | 39 man/sgee-package.Rd | 16 man/sgee.control.Rd | 14 man/summary.sgee.Rd | 15 34 files changed, 5980 insertions(+), 5646 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran [aut],
Udaya B. Kogalur [aut, cre]
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 3.6.2 dated 2026-04-19 and 3.7.0 dated 2026-08-31
DESCRIPTION | 8 MD5 | 74 +-- NAMESPACE | 2 NEWS.md | 44 + R/generic.predict.rfsrc.R | 66 +- R/impute.learn.rfsrc.R | 346 ++++++++++++++- R/impute.rfsrc.R | 20 R/plot.survival.rfsrc.R | 450 ++++++++++++++----- R/rfsrc.R | 6 R/rfsrc.news.R | 2 R/utilities.R | 20 R/utilities_impute.R | 74 +++ R/utilities_impute_learn.R | 719 ++++++++++++++++++++++++++++++- R/utilities_survival.R | 1031 ++++++++++++++++++++++++++++++++++++++------- data/breast.rda |binary data/follic.rda |binary data/hd.rda |binary data/housing.rda |binary data/nutrigenomic.rda |binary data/pbc.rda |binary data/peakVO2.rda |binary data/vdv.rda |binary data/veteran.rda |binary data/wihs.rda |binary data/wine.rda |binary man/impute.learn.rfsrc.Rd | 383 +++++++++++----- man/impute.rfsrc.Rd | 26 - man/plot.survival.rfsrc.Rd | 299 +++++++++---- man/predict.rfsrc.Rd | 45 + man/rfsrc.Rd | 30 - src/entry.c | 7 src/entryGeneric.c | 6 src/processEnsemble.c | 56 +- src/rfsrc.c | 17 src/stack.c | 14 src/stackOutput.c | 128 +++-- src/tree.c | 270 ++++++++--- src/tree.h | 4 38 files changed, 3436 insertions(+), 711 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Many Marks, Measures, Memberships, and Motifs for Networks
Description: Many tools for calculating network, node, or tie
marks, measures, motifs and memberships of many different types of networks.
Marks identify structural positions, measures quantify network properties,
memberships classify nodes into groups, and motifs tabulate substructure participation.
All functions operate with all classes of network data covered in 'manynet',
and on directed, undirected, multiplex, multimodal, signed, and other networks.
Author: James Hollway [cre, aut, ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Diff between netrics versions 0.4.0 dated 2026-07-24 and 1.0.1 dated 2026-08-31
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Title: Tools for Multiple Imputation of Missing Data
Description: Tools to perform analyses and combine results from multiple-imputation datasets.
Author: Thomas Lumley [aut, cre]
Maintainer: Thomas Lumley <t.lumley@auckland.ac.nz>
Diff between mitools versions 2.4 dated 2019-04-26 and 2.7 dated 2026-08-31
mitools-2.4/mitools/NEWS |only mitools-2.7/mitools/DESCRIPTION | 15 +++++++++------ mitools-2.7/mitools/MD5 | 16 ++++++++-------- mitools-2.7/mitools/NAMESPACE | 1 + mitools-2.7/mitools/R/PV.R | 2 +- mitools-2.7/mitools/build/vignette.rds |binary mitools-2.7/mitools/data/smi.rda |binary mitools-2.7/mitools/inst/NEWZ |only mitools-2.7/mitools/inst/doc/smi.pdf |binary mitools-2.7/mitools/man/PV.Rd | 2 +- 10 files changed, 20 insertions(+), 16 deletions(-)
Title: Generate Optimal Designs of Accelerated Life Test using
PSO-Based Algorithm
Description: A computationally efficient solution for generating optimal experimental designs in Accelerated Life Testing (ALT). Leveraging a Particle Swarm Optimization (PSO)-based hybrid algorithm, the package identifies optimal test plans that minimize estimation variance under specified failure models and stress profiles. For more detailed, see Lee et al. (2025), Optimal Robust Strategies for Accelerated Life Tests and Fatigue Testing of Polymer Composite Materials <doi:10.1214/25-AOAS2075>.
Author: Hoai-Linh Hoang [aut, cre],
I-Chen Lee [aut],
Ping-Yang Chen [aut],
Ray-Bing Chen [aut],
Weng Kee Wong [aut]
Maintainer: Hoai-Linh Hoang <hoailinh.hoang17@gmail.com>
Diff between minimaxALT versions 1.0.3 dated 2025-12-23 and 1.0.4 dated 2026-08-31
minimaxALT-1.0.3/minimaxALT/R/common.R |only minimaxALT-1.0.3/minimaxALT/R/equivalence_theorem.R |only minimaxALT-1.0.3/minimaxALT/R/summary_methods.R |only minimaxALT-1.0.3/minimaxALT/inst/designs |only minimaxALT-1.0.3/minimaxALT/inst/figures |only minimaxALT-1.0.3/minimaxALT/man/check_equivalence_theorem.Rd |only minimaxALT-1.0.3/minimaxALT/tests/testthat/test-check-equivalence-theorem.R |only minimaxALT-1.0.3/minimaxALT/tests/testthat/test-locally-optimal-design-1factor.R |only minimaxALT-1.0.3/minimaxALT/tests/testthat/test-locally-optimal-design-2factor.R |only minimaxALT-1.0.4/minimaxALT/DESCRIPTION | 14 minimaxALT-1.0.4/minimaxALT/MD5 | 68 + minimaxALT-1.0.4/minimaxALT/NAMESPACE | 15 minimaxALT-1.0.4/minimaxALT/NEWS.md | 4 minimaxALT-1.0.4/minimaxALT/R/check_optimality.R |only minimaxALT-1.0.4/minimaxALT/R/extract_design.R |only minimaxALT-1.0.4/minimaxALT/R/helpers.R |only minimaxALT-1.0.4/minimaxALT/R/minimaxALT-package.R | 6 minimaxALT-1.0.4/minimaxALT/R/minimaxALT.R | 381 ++++------ minimaxALT-1.0.4/minimaxALT/R/plot.R |only minimaxALT-1.0.4/minimaxALT/R/print.R |only minimaxALT-1.0.4/minimaxALT/R/setup.R | 132 ++- minimaxALT-1.0.4/minimaxALT/R/summary.R |only minimaxALT-1.0.4/minimaxALT/build |only minimaxALT-1.0.4/minimaxALT/inst/doc |only minimaxALT-1.0.4/minimaxALT/man/check_optimality.Rd |only minimaxALT-1.0.4/minimaxALT/man/extract_design.Rd |only minimaxALT-1.0.4/minimaxALT/man/find_optimal_alt.Rd | 79 +- minimaxALT-1.0.4/minimaxALT/man/initialize_values.Rd | 30 minimaxALT-1.0.4/minimaxALT/man/minimaxALT-package.Rd | 2 minimaxALT-1.0.4/minimaxALT/man/plot.OptimalALT.Rd |only minimaxALT-1.0.4/minimaxALT/man/print.DesignInfo.Rd |only minimaxALT-1.0.4/minimaxALT/man/print.InitialValue.Rd |only minimaxALT-1.0.4/minimaxALT/man/print.OptimalALT.Rd |only minimaxALT-1.0.4/minimaxALT/man/print.OptimalityCheck.Rd |only minimaxALT-1.0.4/minimaxALT/man/print.PSOInfo.Rd |only minimaxALT-1.0.4/minimaxALT/man/pso_setting.Rd | 15 minimaxALT-1.0.4/minimaxALT/man/set_design_info.Rd | 10 minimaxALT-1.0.4/minimaxALT/man/summary.OptimalALT.Rd |only minimaxALT-1.0.4/minimaxALT/man/update_optimality_check.Rd |only minimaxALT-1.0.4/minimaxALT/src/psoMain.cpp | 144 ++- minimaxALT-1.0.4/minimaxALT/tests/testthat.R | 1 minimaxALT-1.0.4/minimaxALT/tests/testthat/helper-data.R |only minimaxALT-1.0.4/minimaxALT/tests/testthat/test-class.R |only minimaxALT-1.0.4/minimaxALT/tests/testthat/test-extract.R |only minimaxALT-1.0.4/minimaxALT/tests/testthat/test-models.R |only minimaxALT-1.0.4/minimaxALT/tests/testthat/test-multiple-factors.R |only minimaxALT-1.0.4/minimaxALT/tests/testthat/test-reproducibility.R |only minimaxALT-1.0.4/minimaxALT/vignettes |only 48 files changed, 487 insertions(+), 414 deletions(-)
Title: Lexicons for Text Analysis
Description: A collection of lexical hash tables, dictionaries, and word lists.
Author: Tyler Rinker [aut, cre, cph],
University of Notre Dame [dtc, cph],
Department of Knowledge Technologies [dtc, cph],
Unicode, Inc. [dtc, cph],
John Higgins [dtc, cph],
Grady Ward [dtc],
Heiko Possel [dtc],
Michal Boleslav Mechura [dtc, cph],
Bing Liu [...truncated...]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between lexicon versions 1.2.1 dated 2019-03-21 and 1.3.2 dated 2026-08-31
lexicon-1.2.1/lexicon/NEWS |only lexicon-1.2.1/lexicon/data/datalist |only lexicon-1.3.2/lexicon/DESCRIPTION | 10 lexicon-1.3.2/lexicon/MD5 | 338 +- lexicon-1.3.2/lexicon/NAMESPACE | 20 lexicon-1.3.2/lexicon/R/available_data.R | 100 lexicon-1.3.2/lexicon/R/cliches.R | 64 lexicon-1.3.2/lexicon/R/common_names.R | 24 lexicon-1.3.2/lexicon/R/constraining_loughran_mcdonald.R | 46 lexicon-1.3.2/lexicon/R/freq_first_names.R | 38 lexicon-1.3.2/lexicon/R/freq_last_names.R | 36 lexicon-1.3.2/lexicon/R/function_words.R | 29 lexicon-1.3.2/lexicon/R/grady_augmented.R | 32 lexicon-1.3.2/lexicon/R/hash_emoticons.R | 50 lexicon-1.3.2/lexicon/R/hash_grady_pos.R | 118 - lexicon-1.3.2/lexicon/R/hash_internet_slang.R | 40 lexicon-1.3.2/lexicon/R/hash_lemmas.R | 1120 ++++----- lexicon-1.3.2/lexicon/R/hash_nrc_emotion.R | 44 lexicon-1.3.2/lexicon/R/hash_sentiment_emojis.R | 362 +-- lexicon-1.3.2/lexicon/R/hash_sentiment_huliu.R | 62 lexicon-1.3.2/lexicon/R/hash_sentiment_jockers.R | 90 lexicon-1.3.2/lexicon/R/hash_sentiment_jockers_rinker.R | 52 lexicon-1.3.2/lexicon/R/hash_sentiment_loughran_mcdonald.R | 58 lexicon-1.3.2/lexicon/R/hash_sentiment_nrc.R | 70 lexicon-1.3.2/lexicon/R/hash_sentiment_senticnet.R | 66 lexicon-1.3.2/lexicon/R/hash_sentiment_sentiword.R | 58 lexicon-1.3.2/lexicon/R/hash_sentiment_slangsd.R | 78 lexicon-1.3.2/lexicon/R/hash_sentiment_socal_google.R | 54 lexicon-1.3.2/lexicon/R/hash_valence_shifters.R | 106 lexicon-1.3.2/lexicon/R/key_contractions.R | 32 lexicon-1.3.2/lexicon/R/key_corporate_social_responsibility.R | 54 lexicon-1.3.2/lexicon/R/key_grade.R | 32 lexicon-1.3.2/lexicon/R/key_ratings.R | 36 lexicon-1.3.2/lexicon/R/key_regressive_imagery.R | 126 - lexicon-1.3.2/lexicon/R/lexicon-package.R | 20 lexicon-1.3.2/lexicon/R/modal_loughran_mcdonald.R | 54 lexicon-1.3.2/lexicon/R/nrc_emotions.R | 70 lexicon-1.3.2/lexicon/R/pos_action_verb.R | 42 lexicon-1.3.2/lexicon/R/pos_df_irregular_nouns.R | 50 lexicon-1.3.2/lexicon/R/pos_df_pronouns.R | 44 lexicon-1.3.2/lexicon/R/pos_interjections.R | 24 lexicon-1.3.2/lexicon/R/pos_preposition.R | 20 lexicon-1.3.2/lexicon/R/profanity_alvarez.R | 26 lexicon-1.3.2/lexicon/R/profanity_arr_bad.R | 28 lexicon-1.3.2/lexicon/R/profanity_banned.R | 32 lexicon-1.3.2/lexicon/R/profanity_racist.R | 72 lexicon-1.3.2/lexicon/R/profanity_zac_anger.R | 34 lexicon-1.3.2/lexicon/R/sw_dolch.R | 36 lexicon-1.3.2/lexicon/R/sw_fry_100.R | 34 lexicon-1.3.2/lexicon/R/sw_fry_1000.R | 28 lexicon-1.3.2/lexicon/R/sw_fry_200.R | 34 lexicon-1.3.2/lexicon/R/sw_fry_25.R | 34 lexicon-1.3.2/lexicon/R/sw_jockers.R | 26 lexicon-1.3.2/lexicon/R/sw_loughran_mcdonald.R | 80 lexicon-1.3.2/lexicon/R/sw_lucene.R | 60 lexicon-1.3.2/lexicon/R/sw_mallet.R | 206 - lexicon-1.3.2/lexicon/R/sw_python.R | 86 lexicon-1.3.2/lexicon/R/utils.R | 152 - lexicon-1.3.2/lexicon/README.md | 652 ++--- lexicon-1.3.2/lexicon/data/cliches.rda |binary lexicon-1.3.2/lexicon/data/common_names.rda |binary lexicon-1.3.2/lexicon/data/constraining_loughran_mcdonald.rda |binary lexicon-1.3.2/lexicon/data/emojis_sentiment.rda |binary lexicon-1.3.2/lexicon/data/freq_first_names.rda |binary lexicon-1.3.2/lexicon/data/freq_last_names.rda |binary lexicon-1.3.2/lexicon/data/function_words.rda |binary lexicon-1.3.2/lexicon/data/grady_augmented.rda |binary lexicon-1.3.2/lexicon/data/hash_emojis.rda |binary lexicon-1.3.2/lexicon/data/hash_emojis_identifier.rda |binary lexicon-1.3.2/lexicon/data/hash_emoticons.rda |binary lexicon-1.3.2/lexicon/data/hash_grady_pos.rda |binary lexicon-1.3.2/lexicon/data/hash_internet_slang.rda |binary lexicon-1.3.2/lexicon/data/hash_lemmas.rda |binary lexicon-1.3.2/lexicon/data/hash_nrc_emotions.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_emojis.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_huliu.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_jockers_rinker.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_loughran_mcdonald.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_nrc.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_senticnet.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_sentiword.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_slangsd.rda |binary lexicon-1.3.2/lexicon/data/hash_sentiment_socal_google.rda |binary lexicon-1.3.2/lexicon/data/hash_valence_shifters.rda |binary lexicon-1.3.2/lexicon/data/key_contractions.rda |binary lexicon-1.3.2/lexicon/data/key_corporate_social_responsibility.rda |binary lexicon-1.3.2/lexicon/data/key_grade.rda |binary lexicon-1.3.2/lexicon/data/key_rating.rda |binary lexicon-1.3.2/lexicon/data/key_regressive_imagery.rda |binary lexicon-1.3.2/lexicon/data/modal_loughran_mcdonald.rda |binary lexicon-1.3.2/lexicon/data/nrc_emotions.rda |binary lexicon-1.3.2/lexicon/data/pos_action_verb.rda |binary lexicon-1.3.2/lexicon/data/pos_df_irregular_nouns.rda |binary lexicon-1.3.2/lexicon/data/pos_df_pronouns.rda |binary lexicon-1.3.2/lexicon/data/pos_interjections.rda |binary lexicon-1.3.2/lexicon/data/pos_preposition.rda |binary lexicon-1.3.2/lexicon/data/profanity_alvarez.rda |binary lexicon-1.3.2/lexicon/data/profanity_arr_bad.rda |binary lexicon-1.3.2/lexicon/data/profanity_banned.rda |binary lexicon-1.3.2/lexicon/data/profanity_racist.rda |binary lexicon-1.3.2/lexicon/data/profanity_zac_anger.rda |binary lexicon-1.3.2/lexicon/data/sw_dolch.rda |binary lexicon-1.3.2/lexicon/data/sw_fry_100.rda |binary lexicon-1.3.2/lexicon/data/sw_fry_1000.rda |binary lexicon-1.3.2/lexicon/data/sw_fry_200.rda |binary lexicon-1.3.2/lexicon/data/sw_fry_25.rda |binary lexicon-1.3.2/lexicon/data/sw_jockers.rda |binary lexicon-1.3.2/lexicon/data/sw_loughran_mcdonald_long.rda |binary lexicon-1.3.2/lexicon/data/sw_loughran_mcdonald_short.rda |binary lexicon-1.3.2/lexicon/data/sw_lucene.rda |binary lexicon-1.3.2/lexicon/data/sw_mallet.rda |binary lexicon-1.3.2/lexicon/data/sw_python.rda |binary lexicon-1.3.2/lexicon/inst/CITATION | 40 lexicon-1.3.2/lexicon/inst/dev_kit/test_valence_shifter.R | 100 lexicon-1.3.2/lexicon/man/available_data.Rd | 56 lexicon-1.3.2/lexicon/man/cliches.Rd | 84 lexicon-1.3.2/lexicon/man/common_names.Rd | 36 lexicon-1.3.2/lexicon/man/constraining_loughran_mcdonald.Rd | 66 lexicon-1.3.2/lexicon/man/emojis_sentiment.Rd | 90 lexicon-1.3.2/lexicon/man/freq_first_names.Rd | 50 lexicon-1.3.2/lexicon/man/freq_last_names.Rd | 48 lexicon-1.3.2/lexicon/man/function_words.Rd | 49 lexicon-1.3.2/lexicon/man/grady_augmented.Rd | 48 lexicon-1.3.2/lexicon/man/hash_emojis.Rd | 118 - lexicon-1.3.2/lexicon/man/hash_emojis_identifier.Rd | 120 - lexicon-1.3.2/lexicon/man/hash_emoticons.Rd | 70 lexicon-1.3.2/lexicon/man/hash_grady_pos.Rd | 94 lexicon-1.3.2/lexicon/man/hash_internet_slang.Rd | 54 lexicon-1.3.2/lexicon/man/hash_lemmas.Rd | 1136 +++++----- lexicon-1.3.2/lexicon/man/hash_nrc_emotions.Rd | 58 lexicon-1.3.2/lexicon/man/hash_sentiment_emojis.Rd | 88 lexicon-1.3.2/lexicon/man/hash_sentiment_huliu.Rd | 70 lexicon-1.3.2/lexicon/man/hash_sentiment_jockers.Rd | 48 lexicon-1.3.2/lexicon/man/hash_sentiment_jockers_rinker.Rd | 62 lexicon-1.3.2/lexicon/man/hash_sentiment_loughran_mcdonald.Rd | 80 lexicon-1.3.2/lexicon/man/hash_sentiment_nrc.Rd | 88 lexicon-1.3.2/lexicon/man/hash_sentiment_senticnet.Rd | 80 lexicon-1.3.2/lexicon/man/hash_sentiment_sentiword.Rd | 76 lexicon-1.3.2/lexicon/man/hash_sentiment_slangsd.Rd | 92 lexicon-1.3.2/lexicon/man/hash_sentiment_socal_google.Rd | 72 lexicon-1.3.2/lexicon/man/hash_valence_shifters.Rd | 88 lexicon-1.3.2/lexicon/man/key_contractions.Rd | 42 lexicon-1.3.2/lexicon/man/key_corporate_social_responsibility.Rd | 66 lexicon-1.3.2/lexicon/man/key_grade.Rd | 42 lexicon-1.3.2/lexicon/man/key_rating.Rd | 42 lexicon-1.3.2/lexicon/man/key_regressive_imagery.Rd | 142 - lexicon-1.3.2/lexicon/man/key_sentiment_jockers.Rd | 48 lexicon-1.3.2/lexicon/man/lexicon.Rd | 76 lexicon-1.3.2/lexicon/man/modal_loughran_mcdonald.Rd | 80 lexicon-1.3.2/lexicon/man/nrc_emotions.Rd | 90 lexicon-1.3.2/lexicon/man/pos_action_verb.Rd | 52 lexicon-1.3.2/lexicon/man/pos_df_irregular_nouns.Rd | 62 lexicon-1.3.2/lexicon/man/pos_df_pronouns.Rd | 56 lexicon-1.3.2/lexicon/man/pos_interjections.Rd | 38 lexicon-1.3.2/lexicon/man/pos_preposition.Rd | 30 lexicon-1.3.2/lexicon/man/profanity_alvarez.Rd | 46 lexicon-1.3.2/lexicon/man/profanity_arr_bad.Rd | 48 lexicon-1.3.2/lexicon/man/profanity_banned.Rd | 52 lexicon-1.3.2/lexicon/man/profanity_racist.Rd | 88 lexicon-1.3.2/lexicon/man/profanity_zac_anger.Rd | 50 lexicon-1.3.2/lexicon/man/sw_dolch.Rd | 52 lexicon-1.3.2/lexicon/man/sw_fry_100.Rd | 50 lexicon-1.3.2/lexicon/man/sw_fry_1000.Rd | 44 lexicon-1.3.2/lexicon/man/sw_fry_200.Rd | 50 lexicon-1.3.2/lexicon/man/sw_fry_25.Rd | 50 lexicon-1.3.2/lexicon/man/sw_jockers.Rd | 40 lexicon-1.3.2/lexicon/man/sw_loughran_mcdonald_long.Rd | 66 lexicon-1.3.2/lexicon/man/sw_loughran_mcdonald_short.Rd | 58 lexicon-1.3.2/lexicon/man/sw_lucene.Rd | 74 lexicon-1.3.2/lexicon/man/sw_mallet.Rd | 224 - lexicon-1.3.2/lexicon/man/sw_python.Rd | 102 171 files changed, 5336 insertions(+), 5174 deletions(-)
Title: A Functionally Oriented Interface for Integrating 'Julia' with R
Description: Allows to import functions and whole packages from 'Julia' in R.
Imported 'Julia' functions can directly be called as R functions.
Data structures can be translated between 'Julia' and R.
More details can also be found in the corresponding article
<doi:10.18637/jss.v101.i06>.
Author: Stefan Lenz [aut, cre] ,
Harald Binder [aut, ths] ,
Angelo D'Ambrosio [ctb] ,
June Choe [ctb] ,
Bjarke Hautop Kristensen [ctb]
Maintainer: Stefan Lenz <stefan-m-lenz@web.de>
Diff between JuliaConnectoR versions 1.1.5 dated 2026-01-08 and 1.1.6 dated 2026-08-31
DESCRIPTION | 16 ++++--- MD5 | 26 +++++------ R/connecting.R | 32 +++++++++----- R/main.R | 5 ++ R/writing.R | 32 ++++++++++---- inst/Julia/communicating.jl | 32 +++++++++++--- inst/Julia/evaluating.jl | 4 - inst/Julia/handling_dataframes.jl | 3 - inst/Julia/writing.jl | 32 +++++++------- inst/examples/iris-example/iris-example.R | 2 inst/examples/iris-example/iris-example.jl | 4 - man/JuliaConnectoR-package.Rd | 9 ++++ tests/testthat/helper.R | 9 ++++ tests/testthat/test.R | 64 +++++++++++++++++++++++++++-- 14 files changed, 202 insertions(+), 68 deletions(-)
More information about JuliaConnectoR at CRAN
Permanent link
Title: Functionalities for the 'INLA' Package
Description: Contain code to work with a C struct, in short cgeneric, to
define a Gaussian Markov random (GMRF) model. The cgeneric contain
code to specify GMRF elements such as the graph and the precision
matrix, and also the initial and prior for its parameters, useful for
model inference. It can be accessed from a C program and is the
recommended way to implement new GMRF models in the 'INLA' package
(<https://www.r-inla.org>). The 'INLAtools' implement functions to
evaluate each one of the model specifications from R. The implemented
functionalities leverage the use of 'cgeneric' models and provide a
way to debug the code as well to work with the prior for the model
parameters and to sample from it. The `generic0` can be used to
implement intrinsic models with the scaling as proposed in Sørbye &
Rue (2014) <doi:10.1016/j.spasta.2013.06.004>, and the required
constraints. A very useful functionality is the Kronecker product
method that creates a new model from multiple cgen [...truncated...]
Author: Elias Teixeira Krainski [cre, aut, cph] ,
Finn Lindgren [aut] ,
Haavard Rue’ [aut]
Maintainer: Elias Teixeira Krainski <elias.krainski@kaust.edu.sa>
Diff between INLAtools versions 0.1.4 dated 2026-05-04 and 0.1.5 dated 2026-08-31
DESCRIPTION | 10 - MD5 | 22 +- NAMESPACE | 18 + R/aaaaa.R | 2 R/cgeneric.R | 4 R/cgeneric_generic0.R | 2 R/cgeneric_get.R | 11 + R/kronecker.R | 39 +++- demo/kronecker.R | 4 man/cgeneric-class.Rd | 4 src/INLAtools.h | 56 +++-- src/cgeneric_kronecker.c | 444 +++++++++++++++++++++++------------------------ 12 files changed, 333 insertions(+), 283 deletions(-)
Title: Make 'ggplot2' Fully Accessible by Generating Alternative Text
Description: Generates concise alternative text for data visualizations created
with 'ggplot2'. Descriptions are produced by inspecting plot layers, labels,
scales, and facets, with support for multiple languages and alternative text
stored in plot metadata.
Author: Joseph Barbier [aut, cre, cph]
Maintainer: Joseph Barbier <joseph@ysunflower.com>
Diff between ggalttext versions 0.3.0 dated 2026-06-25 and 0.4.0 dated 2026-08-31
DESCRIPTION | 6 +- MD5 | 12 ++-- R/describe_helpers.R | 24 +++++++++ R/language.R | 3 + R/parse.R | 34 ++++++++++--- README.md | 26 ++++------ tests/testthat/test-generate-alt-text.R | 83 ++++++++++++++++++++++++++++++++ 7 files changed, 158 insertions(+), 30 deletions(-)
Title: Identifies Parameters in a Tree-Shaped SCM
Description: Implements the algorithm by Briefs and Bläser (2025) <https://openreview.net/forum?id=8PHOPPH35D>, based on the approach of Gupta and Bläser (2024) <doi:10.1609/aaai.v38i18.30023>. It determines, for a structural causal model (SCM) whose directed edges form a tree, whether each parameter is unidentifiable, 1-identifiable or 2-identifiable (other cases cannot occur), using a randomized algorithm with provable running time O(n^3 log^2 n).
Author: Yasmine Briefs [aut, cre],
Markus Blaeser [aut]
Maintainer: Yasmine Briefs <ybriefs@mpi-inf.mpg.de>
Diff between fasttreeid versions 1.0.1 dated 2025-11-18 and 1.0.2 dated 2026-08-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/algebra.h | 1 + src/random.cpp | 2 +- src/random.h | 1 + 5 files changed, 10 insertions(+), 8 deletions(-)
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Description: An integrated set of tools for thermodynamic calculations in
aqueous geochemistry and geobiochemistry. Functions are provided for writing
balanced reactions to form species from user-selected basis species and for
calculating the standard molal properties of species and reactions, including
the standard Gibbs energy and equilibrium constant. Calculations of the
non-equilibrium chemical affinity and equilibrium chemical activity of species
can be portrayed on diagrams as a function of temperature, pressure, or
activity of basis species; in two dimensions, this gives a maximum affinity or
predominance diagram. The diagrams have formatted chemical formulas and axis
labels, and water stability limits can be added to Eh-pH, oxygen fugacity-
temperature, and other diagrams with a redox variable. The package has been
developed to handle common calculations in aqueous geochemistry, such as
solubility due to complexation of metal ions, mineral buffers of redox or pH,
and changing the basis spec [...truncated...]
Author: Jeffrey Dick [aut, cre]
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between CHNOSZ versions 2.2.0 dated 2025-06-20 and 2.3.0 dated 2026-08-31
CHNOSZ-2.2.0/CHNOSZ/R/examples.R |only CHNOSZ-2.2.0/CHNOSZ/demo/gold.R |only CHNOSZ-2.2.0/CHNOSZ/demo/sum_S.R |only CHNOSZ-2.2.0/CHNOSZ/inst/TODO |only CHNOSZ-2.2.0/CHNOSZ/inst/extdata/OBIGT/SLOP98.csv |only CHNOSZ-2.2.0/CHNOSZ/inst/extdata/OBIGT/testing/IGEM.csv |only CHNOSZ-2.2.0/CHNOSZ/inst/tinytest/test-util.R |only CHNOSZ-2.2.0/CHNOSZ/src/count_letters.c |only CHNOSZ-2.3.0/CHNOSZ/DESCRIPTION | 8 CHNOSZ-2.3.0/CHNOSZ/MD5 | 284 - CHNOSZ-2.3.0/CHNOSZ/NAMESPACE | 12 CHNOSZ-2.3.0/CHNOSZ/R/AD.R | 4 CHNOSZ-2.3.0/CHNOSZ/R/JANAF.to.OBIGT.R |only CHNOSZ-2.3.0/CHNOSZ/R/add.OBIGT.R | 61 CHNOSZ-2.3.0/CHNOSZ/R/affinity.R | 42 CHNOSZ-2.3.0/CHNOSZ/R/basis.R | 5 CHNOSZ-2.3.0/CHNOSZ/R/diagram.R | 8 CHNOSZ-2.3.0/CHNOSZ/R/equilibrate.R | 4 CHNOSZ-2.3.0/CHNOSZ/R/info.R | 8 CHNOSZ-2.3.0/CHNOSZ/R/mosaic.R | 65 CHNOSZ-2.3.0/CHNOSZ/R/phosphorylate.R |only CHNOSZ-2.3.0/CHNOSZ/R/protein.info.R | 20 CHNOSZ-2.3.0/CHNOSZ/R/solubility.R | 78 CHNOSZ-2.3.0/CHNOSZ/R/subcrt.R | 67 CHNOSZ-2.3.0/CHNOSZ/R/thermo.R | 2 CHNOSZ-2.3.0/CHNOSZ/R/thermo.plot.R |only CHNOSZ-2.3.0/CHNOSZ/R/util.affinity.R | 106 CHNOSZ-2.3.0/CHNOSZ/R/util.data.R | 19 CHNOSZ-2.3.0/CHNOSZ/R/util.formula.R | 34 CHNOSZ-2.3.0/CHNOSZ/R/util.legend.R | 6 CHNOSZ-2.3.0/CHNOSZ/R/util.misc.R | 28 CHNOSZ-2.3.0/CHNOSZ/R/util.plot.R | 156 CHNOSZ-2.3.0/CHNOSZ/R/util.protein.R | 2 CHNOSZ-2.3.0/CHNOSZ/R/water.R | 2 CHNOSZ-2.3.0/CHNOSZ/README.md | 10 CHNOSZ-2.3.0/CHNOSZ/build/partial.rdb |binary CHNOSZ-2.3.0/CHNOSZ/build/vignette.rds |binary CHNOSZ-2.3.0/CHNOSZ/demo/00Index | 13 CHNOSZ-2.3.0/CHNOSZ/demo/ATP_hydrolysis.R |only CHNOSZ-2.3.0/CHNOSZ/demo/NaCl.R | 58 CHNOSZ-2.3.0/CHNOSZ/demo/Pourbaix.R | 2 CHNOSZ-2.3.0/CHNOSZ/demo/aluminum.R | 12 CHNOSZ-2.3.0/CHNOSZ/demo/arsenic.R | 81 CHNOSZ-2.3.0/CHNOSZ/demo/buffer.R | 2 CHNOSZ-2.3.0/CHNOSZ/demo/chalcocite.R |only CHNOSZ-2.3.0/CHNOSZ/demo/comproportionation.R | 9 CHNOSZ-2.3.0/CHNOSZ/demo/contour.R | 124 CHNOSZ-2.3.0/CHNOSZ/demo/demos.R |only CHNOSZ-2.3.0/CHNOSZ/demo/demos_png.R |only CHNOSZ-2.3.0/CHNOSZ/demo/examples.R |only CHNOSZ-2.3.0/CHNOSZ/demo/examples_png.R |only CHNOSZ-2.3.0/CHNOSZ/demo/glycinate.R | 1 CHNOSZ-2.3.0/CHNOSZ/demo/gold1.R |only CHNOSZ-2.3.0/CHNOSZ/demo/gold2.R |only CHNOSZ-2.3.0/CHNOSZ/demo/minsol.R | 38 CHNOSZ-2.3.0/CHNOSZ/demo/mosaic.R | 6 CHNOSZ-2.3.0/CHNOSZ/demo/neodymium.R |only CHNOSZ-2.3.0/CHNOSZ/demo/phosphorylate.R |only CHNOSZ-2.3.0/CHNOSZ/demo/potassium.R | 9 CHNOSZ-2.3.0/CHNOSZ/demo/references.R | 2 CHNOSZ-2.3.0/CHNOSZ/demo/saturation.R | 4 CHNOSZ-2.3.0/CHNOSZ/demo/sphalerite.R | 2 CHNOSZ-2.3.0/CHNOSZ/demo/sulfur.R |only CHNOSZ-2.3.0/CHNOSZ/demo/uranyl.R | 12 CHNOSZ-2.3.0/CHNOSZ/inst/CHECKLIST | 11 CHNOSZ-2.3.0/CHNOSZ/inst/NEWS.Rd | 457 + CHNOSZ-2.3.0/CHNOSZ/inst/doc/FAQ.R | 167 CHNOSZ-2.3.0/CHNOSZ/inst/doc/FAQ.Rmd | 196 CHNOSZ-2.3.0/CHNOSZ/inst/doc/FAQ.html | 2109 +++++-- CHNOSZ-2.3.0/CHNOSZ/inst/doc/OBIGT.R | 30 CHNOSZ-2.3.0/CHNOSZ/inst/doc/OBIGT.Rmd | 66 CHNOSZ-2.3.0/CHNOSZ/inst/doc/OBIGT.bib | 196 CHNOSZ-2.3.0/CHNOSZ/inst/doc/OBIGT.html | 4040 ++++++++++----- CHNOSZ-2.3.0/CHNOSZ/inst/doc/anintro.R | 108 CHNOSZ-2.3.0/CHNOSZ/inst/doc/anintro.Rmd | 63 CHNOSZ-2.3.0/CHNOSZ/inst/doc/anintro.html | 645 +- CHNOSZ-2.3.0/CHNOSZ/inst/doc/custom_data.html | 1207 +++- CHNOSZ-2.3.0/CHNOSZ/inst/doc/eos-regress.html | 209 CHNOSZ-2.3.0/CHNOSZ/inst/doc/multi-metal.R | 40 CHNOSZ-2.3.0/CHNOSZ/inst/doc/multi-metal.Rmd | 28 CHNOSZ-2.3.0/CHNOSZ/inst/doc/multi-metal.html | 2441 +++++---- CHNOSZ-2.3.0/CHNOSZ/inst/extdata/Berman/sympy.R | 4 CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/SLOP98-a.csv |only CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/SLOP98-b.csv |only CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv | 107 CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv | 213 CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/inorganic_liq.csv |only CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv | 567 -- CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/organic_cr.csv | 7 CHNOSZ-2.3.0/CHNOSZ/inst/extdata/OBIGT/organic_gas.csv | 1 CHNOSZ-2.3.0/CHNOSZ/inst/extdata/misc/C-127.txt |only CHNOSZ-2.3.0/CHNOSZ/inst/extdata/misc/Fe-001.txt |only CHNOSZ-2.3.0/CHNOSZ/inst/extdata/misc/OBIGT_check.csv | 338 - CHNOSZ-2.3.0/CHNOSZ/inst/extdata/misc/S-004.txt |only CHNOSZ-2.3.0/CHNOSZ/inst/extdata/thermo/refs.csv | 114 CHNOSZ-2.3.0/CHNOSZ/inst/extdata/thermo/stoich.csv.xz |binary CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-AD.R | 39 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-EOSregress.R | 43 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-JANAF.to.OBIGT.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-S_liq.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-affinity.R | 31 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-diagram.R | 63 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-equilibrate.R | 6 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-logK.to.OBIGT.R | 49 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-makeup.R | 22 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-mix.R | 33 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-mod.buffer.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-mosaic.R | 22 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-nonideal.R | 13 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-phosphorylate.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-protein.info.R | 19 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-rank.affinity.R | 2 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-subcrt.R | 36 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-taxonomy.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.data.R | 26 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.expression.R | 30 CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.formula.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.legend.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.misc.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.protein.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.units.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-util.water.R |only CHNOSZ-2.3.0/CHNOSZ/inst/tinytest/test-water.R | 11 CHNOSZ-2.3.0/CHNOSZ/man/Berman.Rd | 10 CHNOSZ-2.3.0/CHNOSZ/man/CHNOSZ-package.Rd | 6 CHNOSZ-2.3.0/CHNOSZ/man/DEW.Rd | 4 CHNOSZ-2.3.0/CHNOSZ/man/EOSregress.Rd | 6 CHNOSZ-2.3.0/CHNOSZ/man/IAPWS95.Rd | 2 CHNOSZ-2.3.0/CHNOSZ/man/JANAF.to.OBIGT.Rd |only CHNOSZ-2.3.0/CHNOSZ/man/NaCl.Rd | 2 CHNOSZ-2.3.0/CHNOSZ/man/add.OBIGT.Rd | 12 CHNOSZ-2.3.0/CHNOSZ/man/affinity.Rd | 24 CHNOSZ-2.3.0/CHNOSZ/man/basis.Rd | 4 CHNOSZ-2.3.0/CHNOSZ/man/diagram.Rd | 22 CHNOSZ-2.3.0/CHNOSZ/man/equilibrate.Rd | 2 CHNOSZ-2.3.0/CHNOSZ/man/examples.Rd | 137 CHNOSZ-2.3.0/CHNOSZ/man/extdata.Rd | 48 CHNOSZ-2.3.0/CHNOSZ/man/ionize.aa.Rd | 6 CHNOSZ-2.3.0/CHNOSZ/man/logK.to.OBIGT.Rd | 9 CHNOSZ-2.3.0/CHNOSZ/man/mix.Rd | 4 CHNOSZ-2.3.0/CHNOSZ/man/mod.buffer.Rd | 6 CHNOSZ-2.3.0/CHNOSZ/man/mosaic.Rd | 26 CHNOSZ-2.3.0/CHNOSZ/man/nonideal.Rd | 18 CHNOSZ-2.3.0/CHNOSZ/man/phosphorylate.Rd |only CHNOSZ-2.3.0/CHNOSZ/man/protein.info.Rd | 10 CHNOSZ-2.3.0/CHNOSZ/man/solubility.Rd | 71 CHNOSZ-2.3.0/CHNOSZ/man/stack_mosaic.Rd | 8 CHNOSZ-2.3.0/CHNOSZ/man/subcrt.Rd | 30 CHNOSZ-2.3.0/CHNOSZ/man/thermo.Rd | 10 CHNOSZ-2.3.0/CHNOSZ/man/thermo.plot.Rd |only CHNOSZ-2.3.0/CHNOSZ/man/util.data.Rd | 6 CHNOSZ-2.3.0/CHNOSZ/man/util.formula.Rd | 2 CHNOSZ-2.3.0/CHNOSZ/man/util.legend.Rd | 10 CHNOSZ-2.3.0/CHNOSZ/man/util.plot.Rd | 71 CHNOSZ-2.3.0/CHNOSZ/man/util.protein.Rd | 2 CHNOSZ-2.3.0/CHNOSZ/man/util.water.Rd | 4 CHNOSZ-2.3.0/CHNOSZ/man/water.Rd | 22 CHNOSZ-2.3.0/CHNOSZ/src/H2O92D.f | 300 - CHNOSZ-2.3.0/CHNOSZ/vignettes/FAQ.Rmd | 196 CHNOSZ-2.3.0/CHNOSZ/vignettes/OBIGT.Rmd | 66 CHNOSZ-2.3.0/CHNOSZ/vignettes/OBIGT.bib | 196 CHNOSZ-2.3.0/CHNOSZ/vignettes/anintro.Rmd | 63 CHNOSZ-2.3.0/CHNOSZ/vignettes/multi-metal.Rmd | 28 CHNOSZ-2.3.0/CHNOSZ/vignettes/vig.bib | 8 164 files changed, 10330 insertions(+), 6336 deletions(-)
Title: A Byte-Pair-Encoding (BPE) Tokenizer for OpenAI's Large Language
Models
Description: A thin wrapper around the tiktoken-rs crate, allowing to encode text into Byte-Pair-Encoding (BPE) tokens and decode tokens back to text. This is useful to understand how Large Language Models (LLMs) perceive text.
Author: David Zimmermann-Kollenda [aut, cre],
Roger Zurawicki [aut] ,
Authors of the dependent Rust crates [aut]
Maintainer: David Zimmermann-Kollenda <david_j_zimmermann@hotmail.com>
Diff between rtiktoken versions 0.11.0.2 dated 2026-08-21 and 0.11.0.3 dated 2026-08-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ src/Makevars.in | 12 +++++++++--- src/Makevars.win.in | 13 +++++++++---- 5 files changed, 33 insertions(+), 14 deletions(-)
Title: Interface to the 'Pharmpy' 'Pharmacometrics' Library
Description: Interface to the 'Pharmpy' 'pharmacometrics' library. The 'Reticulate' package is used to interface Python from R.
Author: Rikard Nordgren [aut, cre, cph],
Stella Belin [aut, cph],
Mats O. Karlsson [sad],
Andrew C. Hooker [sad],
Xiaomei Chen [sad],
Sebastian Ueckert [sad] ,
Simon Buatois [rev],
Joao A. Abrantes [rev],
Emilie Schindler [rev],
F. Hoffmann-La Roche Ltd. [fn [...truncated...]
Maintainer: Rikard Nordgren <rikard.nordgren@uu.se>
Diff between pharmr versions 2.1.1 dated 2026-05-28 and 2.2.0 dated 2026-08-31
pharmr-2.1.1/pharmr/man/reset_indices_results.Rd |only pharmr-2.1.1/pharmr/man/set_unit.Rd |only pharmr-2.2.0/pharmr/DESCRIPTION | 16 pharmr-2.2.0/pharmr/MD5 | 77 pharmr-2.2.0/pharmr/NAMESPACE | 13 pharmr-2.2.0/pharmr/R/check_setup.R | 2 pharmr-2.2.0/pharmr/R/functions_wrapper.R | 2104 ++++------ pharmr-2.2.0/pharmr/R/install.R | 2 pharmr-2.2.0/pharmr/R/internals.R | 170 pharmr-2.2.0/pharmr/R/overloads.R | 7 pharmr-2.2.0/pharmr/R/utils.R | 28 pharmr-2.2.0/pharmr/R/zzz.R | 10 pharmr-2.2.0/pharmr/README.md | 2 pharmr-2.2.0/pharmr/man/add_administration.Rd |only pharmr-2.2.0/pharmr/man/add_arm.Rd |only pharmr-2.2.0/pharmr/man/add_observations.Rd |only pharmr-2.2.0/pharmr/man/annotate_unit.Rd |only pharmr-2.2.0/pharmr/man/calculate_bic.Rd | 12 pharmr-2.2.0/pharmr/man/calculate_epsilon_gradient_expression.Rd | 2 pharmr-2.2.0/pharmr/man/calculate_eta_gradient_expression.Rd | 2 pharmr-2.2.0/pharmr/man/convert_unit.Rd | 4 pharmr-2.2.0/pharmr/man/create_datainfo.Rd |only pharmr-2.2.0/pharmr/man/create_dataset_from_design.Rd |only pharmr-2.2.0/pharmr/man/create_symbol.Rd | 2 pharmr-2.2.0/pharmr/man/create_trial_design.Rd |only pharmr-2.2.0/pharmr/man/fit.Rd | 11 pharmr-2.2.0/pharmr/man/get_central_volume_and_clearance.Rd | 2 pharmr-2.2.0/pharmr/man/get_individual_prediction_expression.Rd | 2 pharmr-2.2.0/pharmr/man/get_observation_expression.Rd | 2 pharmr-2.2.0/pharmr/man/get_omegas.Rd | 2 pharmr-2.2.0/pharmr/man/get_population_prediction_expression.Rd | 2 pharmr-2.2.0/pharmr/man/get_sigmas.Rd | 2 pharmr-2.2.0/pharmr/man/get_thetas.Rd | 2 pharmr-2.2.0/pharmr/man/read_datainfo.Rd |only pharmr-2.2.0/pharmr/man/reset_dataset.Rd |only pharmr-2.2.0/pharmr/man/reset_index.Rd | 4 pharmr-2.2.0/pharmr/man/run_amd.Rd | 8 pharmr-2.2.0/pharmr/man/run_linearize.Rd | 12 pharmr-2.2.0/pharmr/man/run_qa.Rd | 6 pharmr-2.2.0/pharmr/man/run_retries.Rd | 8 pharmr-2.2.0/pharmr/man/set_covariates.Rd | 4 pharmr-2.2.0/pharmr/man/set_dataset.Rd | 8 pharmr-2.2.0/pharmr/man/set_index.Rd |only pharmr-2.2.0/pharmr/man/set_property.Rd | 2 pharmr-2.2.0/pharmr/man/write_datainfo.Rd |only pharmr-2.2.0/pharmr/tests/testthat/test-reset_index.R | 8 46 files changed, 1186 insertions(+), 1352 deletions(-)
Title: Predict and Map Oyster Growth Suitability from Environmental
Data
Description: Predicts spatial suitability for oyster growth from environmental
survey data using Analytic Hierarchy Process (AHP) weighted scoring.
Users supply sensor data from Acoustic Doppler Current Profilers (ADCP),
Conductivity-Temperature-Depth (CTD) sensors, bathymetric sonar, and
sidescan sonar, specify a target species, and receive per-location
suitability scores, a five-band 'GeoTIFF' heatmap for 'QGIS', contour
lines, and a formatted PDF or HTML report. Supports seventeen species across
global aquaculture regions, including Ostrea edulis, Magallana gigas,
Crassostrea virginica, Crassostrea hongkongensis, and thirteen further
species; see list_species(). Includes ocean acidification scoring via
in-house aragonite saturation state (Omega_arag) calculation using
Lueker et al. (2000) <doi:10.1016/S0304-4203(00)00022-0> and Mucci (1983)
<doi:10.1357/002224083788520153> equilibrium constants (no external
dependencies), variable impact diagnostics (variable_impact()), fine-scale
ha [...truncated...]
Author: T Tucker [aut, cre]
Maintainer: T Tucker <tristantucker48@gmail.com>
Diff between oystermapR versions 1.4.0 dated 2026-05-15 and 1.5.0 dated 2026-08-31
DESCRIPTION | 25 - MD5 | 192 +++++---- NAMESPACE | 6 NEWS.md | 88 ++++ R/anthropogenic.R | 16 R/aragonite.R |only R/area_summary.R |only R/backscatter.R | 38 - R/batch_compare.R | 20 - R/bayesian_update.R | 102 +++-- R/climate_projection.R | 31 - R/connectivity.R | 18 R/disease_risk.R | 20 - R/export_geotiff.R | 51 +- R/hab_risk.R | 22 - R/habitat_utils.R | 17 R/ingest_rasters.R | 9 R/ingest_sensors.R | 59 +- R/interpolation.R | 21 - R/larval_dispersal.R | 37 - R/planning.R | 32 - R/plot_tolerance.R |only R/predation_risk.R | 17 R/predict_oyster.R | 38 + R/report.R | 2 R/score_variables.R | 169 +++++++- R/seasonal_composite.R | 18 R/sediment_stability.R | 17 R/settlement.R | 18 R/spatial_smooth.R | 12 R/species_tolerances.R | 534 ++++++++++++++++++++++++++- R/summary_pdf.R | 11 R/survey_compare.R | 18 R/survey_qc.R | 30 - R/tidal_correction.R | 42 +- R/validate.R | 62 +-- R/variable_importance.R | 44 -- R/water_quality.R | 17 R/wave_exposure.R | 15 README.md | 183 ++++++++- inst/doc/example-bay-survey.R | 88 ++++ inst/doc/example-bay-survey.Rmd | 233 ++++++++++- inst/doc/example-bay-survey.html | 269 +++++++++++-- inst/extdata/example_bay_ctd.csv | 162 ++++---- inst/extdata/sample_survey.csv | 402 ++++++++++---------- man/add_intertidal_flag.Rd | 17 man/add_shellfish_classification.Rd | 17 man/add_suitability_ci.Rd | 10 man/analyse_connectivity.Rd | 14 man/area_summary.Rd |only man/assess_gear_feasibility.Rd | 11 man/auto_tidal_correct.Rd | 20 - man/calculate_aragonite.Rd |only man/classify_substrate_from_backscatter.Rd | 20 - man/compare_species.Rd | 20 - man/compare_surveys.Rd | 18 man/composite_seasonal.Rd | 14 man/correct_to_chart_datum.Rd | 22 - man/dot-auto_calculate_aragonite.Rd |only man/dot-estimate_cell_size_m.Rd |only man/dot-run_patch_analysis.Rd |only man/estimate_chlorophyll_from_backscatter.Rd | 18 man/export_contours.Rd | 9 man/export_geotiff.Rd | 23 - man/generate_report.Rd | 2 man/generate_summary_pdf.Rd | 11 man/get_tolerance_posteriors.Rd | 4 man/identify_resilient_sites.Rd | 9 man/interpolate_survey.Rd | 16 man/load_tolerance_update.Rd | 35 + man/merge_sensor_data.Rd | 19 man/permutation_importance.Rd | 20 - man/plot_tolerance.Rd |only man/predict_oyster.Rd | 31 - man/project_suitability.Rd | 20 - man/qc_survey_data.Rd | 25 - man/read_aanderaa_csv.Rd | 2 man/read_generic_csv.Rd | 14 man/read_nortek_adcp.Rd | 7 man/read_nortek_aquadopp.Rd | 2 man/read_rdi_adcp.Rd | 2 man/read_sonar_tif.Rd | 2 man/read_soundings_xyz.Rd | 7 man/reset_tolerance_update.Rd | 2 man/save_tolerance_update.Rd | 32 + man/score_anthropogenic_disturbance.Rd | 16 man/score_disease_risk.Rd | 15 man/score_economic_viability.Rd | 19 man/score_hab_risk.Rd | 22 - man/score_larval_connectivity.Rd | 30 - man/score_predation_risk.Rd | 17 man/score_sediment_stability.Rd | 17 man/score_settlement.Rd | 18 man/score_wave_exposure.Rd | 15 man/sensitivity_analysis.Rd | 24 - man/smooth_suitability.Rd | 12 man/spatial_block_cv.Rd | 27 - man/stack_surveys.Rd | 13 man/update_species_tolerances.Rd | 37 - man/validate_against_records.Rd | 25 - man/variable_impact.Rd |only vignettes/example-bay-survey.Rmd | 233 ++++++++++- 102 files changed, 2832 insertions(+), 1408 deletions(-)
Title: Optimal Two-Stage Designs for Ordered Categorical Outcomes
Description: Functions to design and simulate optimal two-stage randomized
controlled trials (RCTs) with ordered categorical outcomes, supporting
rank-based tests and group-sequential decision rules. Methods build on
classical and modern rank tests and two-stage/Group-Sequential designs,
e.g., Park (2025) <doi: 10.1371/journal.pone.0318211>. The functions
'rule()', 'op()' and 'design_table()' provide a single entry point for
constructing designs, evaluating their operating characteristics, and
tabulating several designs at once. The earlier functions, one for each
combination of test statistic and stopping rule, are retained and still
return the same values, but they are deprecated: each warns and names its
replacement, and they will be removed in the next version. Please see the
package reference manual and the vignette for details.
Author: Yeonhee Park [aut, cre],
Yudi Wang [aut],
Zhanpeng Xu [aut]
Maintainer: Yeonhee Park <yeonheepark@skku.edu>
Diff between OptOTrials versions 1.0.2 dated 2025-09-05 and 1.0.3 dated 2026-08-31
DESCRIPTION | 20 ++++-- MD5 | 116 ++++++++++++++++++++---------------- NAMESPACE | 30 +++++---- NEWS.md |only R/Decision_rule_M.F.R | 6 + R/Decision_rule_M.FS.R | 28 ++++++-- R/Decision_rule_M_1stage.R | 6 + R/Decision_rule_S.F.R | 10 ++- R/Decision_rule_S.FS.R | 35 ++++++++-- R/Decision_rule_S_1stage.R | 10 ++- R/Decision_rule_W.F.R | 6 + R/Decision_rule_W.FS.R | 26 ++++++-- R/Decision_rule_W_1stage.R | 6 + R/Proportional_odds_assumption.R | 43 ++++++++----- R/QR_fun.R | 4 + R/V_S.over.nk.R | 4 + R/W_W.R | 4 + R/deprecated.R |only R/effect-size.R |only R/op.1stage.R | 6 + R/op.F.R | 6 + R/op.FS.R | 15 +++- R/op.R |only R/p2_fun.R | 5 + R/p_minus.R | 4 + R/p_plus.R | 4 + R/pq_fun.R | 4 + R/print-methods.R |only R/rule.R |only R/ruleF.R | 24 ++++--- R/ruleFS.R | 90 ++++++++++++++------------- R/theta.R | 4 + R/utils-validate.R |only build/partial.rdb |binary build/vignette.rds |only inst |only man/Decision_rule_M.F.Rd | 38 ++++++++--- man/Decision_rule_M.FS.Rd | 44 +++++++++---- man/Decision_rule_M_1stage.Rd | 26 ++++++-- man/Decision_rule_S.F.Rd | 35 ++++++++-- man/Decision_rule_S.FS.Rd | 41 +++++++++--- man/Decision_rule_S_1stage.Rd | 26 ++++++-- man/Decision_rule_W.F.Rd | 35 ++++++++-- man/Decision_rule_W.FS.Rd | 41 +++++++++--- man/Decision_rule_W_1stage.Rd | 23 +++++-- man/OptOTrials-deprecated.Rd |only man/OptOTrials-package.Rd | 10 ++- man/Proportional_odds_assumption.Rd | 19 ++++- man/QR_fun.Rd | 12 ++- man/V_S.over.nk.Rd | 15 +++- man/W_W.Rd | 10 ++- man/design_table.Rd |only man/op.1stage.Rd | 34 ++++++++-- man/op.F.Rd | 39 +++++++++--- man/op.FS.Rd | 42 ++++++++++--- man/op.Rd |only man/p2_fun.Rd | 6 + man/p_minus.Rd | 10 ++- man/p_plus.Rd | 10 ++- man/pq_fun.Rd | 10 ++- man/rule.Rd |only man/ruleF.Rd | 34 ++++++++-- man/ruleFS.Rd | 34 ++++++++-- man/theta.Rd | 9 +- vignettes |only 65 files changed, 794 insertions(+), 325 deletions(-)
Title: Markov Decision Processes Toolbox
Description: The Markov Decision Processes (MDP) toolbox proposes functions related to the resolution of discrete-time Markov Decision Processes: finite horizon, value iteration, policy iteration, linear programming algorithms with some variants and also proposes some functions related to Reinforcement Learning.
Author: Iadine Chades [aut],
Guillaume Chapron [aut, cre],
Marie-Josee Cros [aut],
Frederick Garcia [aut],
Regis Sabbadin [aut]
Maintainer: Guillaume Chapron <gchapron@carnivoreconservation.org>
Diff between MDPtoolbox versions 4.0.3 dated 2017-03-03 and 4.0.4 dated 2026-08-31
DESCRIPTION | 32 ++++++++++++++++++++++++++------ MD5 | 4 ++-- man/mdp_example_forest.Rd | 2 +- 3 files changed, 29 insertions(+), 9 deletions(-)
Title: Advice on R Package Building
Description: Give advice about good practices when building R packages.
Advice includes functions and syntax to avoid, package structure, code
complexity, code formatting, etc.
Author: Mark Padgham [aut, cre] ,
Ascent Digital Services UK Limited [cph] ,
Karina Marks [aut] ,
Daniel de Bortoli [aut] ,
Gabor Csardi [aut],
Hannah Frick [aut],
Owen Jones [aut] ,
Hannah Alexander [aut],
Ana Simmons [ctb] ,
Fabian Scheipl [ctb] ,
Athanasi [...truncated...]
Maintainer: Mark Padgham <mark@ropensci.org>
Diff between goodpractice versions 1.1.0 dated 2026-06-05 and 1.2.0 dated 2026-08-31
goodpractice-1.1.0/goodpractice/tests/testthat/good_tidyverse/R/good_style.R |only goodpractice-1.1.0/goodpractice/tests/testthat/good_tidyverse/tests/testthat/test-good_style.R |only goodpractice-1.2.0/goodpractice/DESCRIPTION | 10 goodpractice-1.2.0/goodpractice/MD5 | 109 +++--- goodpractice-1.2.0/goodpractice/NAMESPACE | 36 +- goodpractice-1.2.0/goodpractice/NEWS.md | 179 +++++----- goodpractice-1.2.0/goodpractice/R/api.R | 92 +++++ goodpractice-1.2.0/goodpractice/R/chk_code_structure.R | 6 goodpractice-1.2.0/goodpractice/R/chk_description.R | 38 +- goodpractice-1.2.0/goodpractice/R/chk_lintr.R | 7 goodpractice-1.2.0/goodpractice/R/chk_rd.R | 2 goodpractice-1.2.0/goodpractice/R/chk_roxygen2.R | 8 goodpractice-1.2.0/goodpractice/R/chk_tidyverse.R | 22 - goodpractice-1.2.0/goodpractice/R/chk_urlchecker.R | 2 goodpractice-1.2.0/goodpractice/R/customization.R | 1 goodpractice-1.2.0/goodpractice/R/gp.R | 11 goodpractice-1.2.0/goodpractice/R/lists.R | 7 goodpractice-1.2.0/goodpractice/R/package.R | 1 goodpractice-1.2.0/goodpractice/R/prep_lintr.R | 1 goodpractice-1.2.0/goodpractice/R/prep_roxygen2.R | 3 goodpractice-1.2.0/goodpractice/R/prep_urlchecker.R | 2 goodpractice-1.2.0/goodpractice/R/print.R | 1 goodpractice-1.2.0/goodpractice/R/treesitter.R | 2 goodpractice-1.2.0/goodpractice/README.md | 99 +++-- goodpractice-1.2.0/goodpractice/build/vignette.rds |binary goodpractice-1.2.0/goodpractice/inst/doc/custom_checks.html | 6 goodpractice-1.2.0/goodpractice/inst/doc/goodpractice.Rmd | 4 goodpractice-1.2.0/goodpractice/inst/doc/goodpractice.html | 48 +- goodpractice-1.2.0/goodpractice/inst/doc/gp4developers.R |only goodpractice-1.2.0/goodpractice/inst/doc/gp4developers.Rmd |only goodpractice-1.2.0/goodpractice/inst/doc/gp4developers.html |only goodpractice-1.2.0/goodpractice/inst/skills |only goodpractice-1.2.0/goodpractice/man/all_check_groups.Rd | 10 goodpractice-1.2.0/goodpractice/man/all_checks.Rd | 10 goodpractice-1.2.0/goodpractice/man/checks.Rd | 3 goodpractice-1.2.0/goodpractice/man/checks_by_group.Rd | 10 goodpractice-1.2.0/goodpractice/man/customization.Rd | 7 goodpractice-1.2.0/goodpractice/man/default_checks.Rd | 10 goodpractice-1.2.0/goodpractice/man/describe_check.Rd | 10 goodpractice-1.2.0/goodpractice/man/describe_check_groups.Rd | 10 goodpractice-1.2.0/goodpractice/man/export_json.Rd | 6 goodpractice-1.2.0/goodpractice/man/failed_checks.Rd | 3 goodpractice-1.2.0/goodpractice/man/failed_positions.Rd | 7 goodpractice-1.2.0/goodpractice/man/goodpractice-package.Rd | 4 goodpractice-1.2.0/goodpractice/man/gp.Rd | 5 goodpractice-1.2.0/goodpractice/man/learn_skill_gp.Rd |only goodpractice-1.2.0/goodpractice/man/print.goodPractice.Rd | 6 goodpractice-1.2.0/goodpractice/man/results.Rd | 8 goodpractice-1.2.0/goodpractice/man/tidyverse_checks.Rd | 10 goodpractice-1.2.0/goodpractice/man/use_skill_gp.Rd |only goodpractice-1.2.0/goodpractice/tests/testthat/_snaps/describe-check.md | 3 goodpractice-1.2.0/goodpractice/tests/testthat/good_tidyverse/R/good-style_name.R |only goodpractice-1.2.0/goodpractice/tests/testthat/good_tidyverse/tests/testthat/test-good-style_name.R |only goodpractice-1.2.0/goodpractice/tests/testthat/helper-dotfiles.R |only goodpractice-1.2.0/goodpractice/tests/testthat/test-api.R | 8 goodpractice-1.2.0/goodpractice/tests/testthat/test-check-selection.R | 4 goodpractice-1.2.0/goodpractice/tests/testthat/test-gp.R | 45 -- goodpractice-1.2.0/goodpractice/tests/testthat/test-integrity.R | 3 goodpractice-1.2.0/goodpractice/tests/testthat/test-skill-gp.R |only goodpractice-1.2.0/goodpractice/tests/testthat/test-tidyverse.R | 17 goodpractice-1.2.0/goodpractice/vignettes/goodpractice.Rmd | 4 goodpractice-1.2.0/goodpractice/vignettes/gp4developers.Rmd |only 62 files changed, 597 insertions(+), 303 deletions(-)
Title: Generalized Additive Latent and Mixed Models
Description: Estimates generalized additive latent and
mixed models using maximum marginal likelihood,
as defined in Sorensen et al. (2023)
<doi:10.1007/s11336-023-09910-z>, which is an extension of Rabe-Hesketh and
Skrondal (2004)'s unifying framework for multilevel latent variable
modeling <doi:10.1007/BF02295939>. Efficient computation is done using sparse
matrix methods, Laplace approximation, and automatic differentiation. The
framework includes generalized multilevel models with heteroscedastic
residuals, mixed response types, factor loadings, smoothing splines,
crossed random effects, and combinations thereof. Syntax for model
formulation is close to 'lme4' (Bates et al. (2015)
<doi:10.18637/jss.v067.i01>) and 'PLmixed' (Rockwood and Jeon (2019)
<doi:10.1080/00273171.2018.1516541>).
Author: Oeystein Soerensen [aut, cre] ,
Douglas Bates [ctb],
Ben Bolker [ctb],
Martin Maechler [ctb],
Allan Leal [ctb],
Fabian Scheipl [ctb],
Steven Walker [ctb],
Simon Wood [ctb]
Maintainer: Oeystein Soerensen <oystein.sorensen@psykologi.uio.no>
Diff between galamm versions 0.4.0 dated 2025-12-21 and 0.4.1 dated 2026-08-31
DESCRIPTION | 14 MD5 | 231 +++++++-------- NAMESPACE | 50 +-- NEWS.md |only R/galamm-package.R | 2 README.md | 75 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/galamm.Rmd | 38 +- inst/doc/galamm.html | 113 +++---- inst/doc/glmm_factor.Rmd | 18 - inst/doc/glmm_factor.html | 68 ++-- inst/doc/latent_observed_interaction.Rmd | 12 inst/doc/latent_observed_interaction.html | 29 - inst/doc/lmm_factor.Rmd | 77 ++--- inst/doc/lmm_factor.html | 152 ++++----- inst/doc/lmm_heteroscedastic.Rmd | 6 inst/doc/lmm_heteroscedastic.html | 11 inst/doc/mixed_response.Rmd | 26 - inst/doc/mixed_response.html | 62 +--- inst/doc/optimization.Rmd | 12 inst/doc/optimization.html | 23 - inst/doc/posterior_sampling.Rmd | 2 inst/doc/posterior_sampling.html | 11 inst/doc/scaling.Rmd | 8 inst/doc/scaling.html | 23 - inst/doc/semiparametric.Rmd | 88 ++--- inst/doc/semiparametric.html | 188 ++++++------ man/VarCorr.Rd | 44 +- man/anova.galamm.Rd | 12 man/appraise.galamm.Rd | 44 +- man/coef.galamm.Rd | 44 +- man/cognition.Rd | 2 man/confint.galamm.Rd | 44 +- man/derivatives.galamm.Rd | 44 +- man/deviance.galamm.Rd | 44 +- man/diet.Rd | 2 man/draw.galamm.Rd | 12 man/epilep.Rd | 2 man/extract_optim_parameters.galamm.Rd | 4 man/factor_loadings.galamm.Rd | 44 +- man/family.galamm.Rd | 44 +- man/figures/README-unnamed-chunk-9-1.png |binary man/fitted.galamm.Rd | 44 +- man/fixef.Rd | 44 +- man/formula.galamm.Rd | 44 +- man/galamm-package.Rd | 11 man/galamm.Rd | 8 man/galammObject.Rd | 12 man/galamm_control.Rd | 8 man/gfam.Rd | 8 man/hsced.Rd | 2 man/latent_covariates.Rd | 2 man/latent_covariates_long.Rd | 2 man/lifespan.Rd | 2 man/llikAIC.Rd | 44 +- man/logLik.galamm.Rd | 44 +- man/model.frame.galamm.Rd | 44 +- man/mresp.Rd | 2 man/mresp_hsced.Rd | 2 man/nobs.galamm.Rd | 44 +- man/plot.galamm.Rd | 4 man/plot_smooth.galamm.Rd | 12 man/predict.galamm.Rd | 44 +- man/print.VarCorr.galamm.Rd | 44 +- man/print.galamm.Rd | 12 man/print.summary.galamm.Rd | 12 man/qqmath.galamm.Rd | 4 man/ranef.galamm.Rd | 44 +- man/residuals.galamm.Rd | 44 +- man/response.Rd | 44 +- man/sigma.galamm.Rd | 44 +- man/sl.Rd | 8 man/summary.galamm.Rd | 12 man/t2l.Rd | 8 man/vcov.galamm.Rd | 44 +- tests/testthat/_snaps/galamm-lmm.md | 16 - vignettes/galamm.Rmd | 38 +- vignettes/glmm_factor.Rmd | 18 - vignettes/glmm_factor_binomial_diagnostic-1.png |binary vignettes/glmm_factor_poisson_diagnostic-1.png |binary vignettes/latent-observed-smooth-1.png |binary vignettes/latent_observed_interaction.Rmd | 12 vignettes/lmm_factor.Rmd | 77 ++--- vignettes/lmm_factor_diagnostic_plot-1.png |binary vignettes/lmm_heteroscedastic.Rmd | 6 vignettes/mixed_response.Rmd | 26 - vignettes/optimization.Rmd | 12 vignettes/posterior_sampling.Rmd | 2 vignettes/scaling-glmm-plot-1.png |binary vignettes/scaling-hsced-plot-1.png |binary vignettes/scaling-lmm-plot-1.png |binary vignettes/scaling-semiparametric-binomial-plot-1.png |binary vignettes/scaling-semiparametric-gaussian-plot-1.png |binary vignettes/scaling.Rmd | 8 vignettes/semiparametric-gamm-binomial-1.png |binary vignettes/semiparametric-gamm4-binomial-1.png |binary vignettes/semiparametric-gaussian-by-factor1-1.png |binary vignettes/semiparametric-gaussian-by-factor2-1.png |binary vignettes/semiparametric-gaussian-factor-1.png |binary vignettes/semiparametric-gaussian-gamm-smooth1-1.png |binary vignettes/semiparametric-gaussian-gamm-smooth2-1.png |binary vignettes/semiparametric-gaussian-gamm-smooth2-2.png |binary vignettes/semiparametric-gaussian-gamm4-diagnostic-1.png |binary vignettes/semiparametric-gaussian-gamm4-smooth-1.png |binary vignettes/semiparametric-mixed-by-factor1-1.png |binary vignettes/semiparametric-mixed-by-factor2-1.png |binary vignettes/semiparametric-spaghetti-plot-1.png |binary vignettes/semiparametric.Rmd | 88 ++--- vignettes/unnamed-chunk-10-1.png |binary vignettes/unnamed-chunk-12-1.png |binary vignettes/unnamed-chunk-15-1.png |binary vignettes/unnamed-chunk-20-1.png |binary vignettes/unnamed-chunk-28-1.png |binary vignettes/unnamed-chunk-29-1.png |binary vignettes/unnamed-chunk-3-1.png |binary vignettes/unnamed-chunk-6-1.png |binary 117 files changed, 1365 insertions(+), 1410 deletions(-)
Title: String Interpolation for Documents, Reports and Apps
Description: Extra strength 'glue' for data-driven templates. String
interpolation for 'Shiny' apps or 'R Markdown' and 'knitr'-powered
'Quarto' documents, built on the 'glue' and 'whisker' packages.
Author: Garrick Aden-Buie [aut, cre] ,
Kushagra Gour [ctb] ,
The mustache.js community [ctb]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
This is a re-admission after prior archival of version 1.0.0 dated 2023-09-19
Diff between epoxy versions 1.0.0 dated 2023-09-19 and 1.0.1 dated 2026-08-31
DESCRIPTION | 11 +- MD5 | 108 ++++++++++++------------ NAMESPACE | 8 + NEWS.md | 5 + R/engines.R | 26 +++-- R/epoxy.R | 29 ++++-- R/epoxy_transform_html.R | 17 ++- R/epoxy_transform_inline.R | 64 +++++++------- R/epoxy_use.R | 8 + R/shiny.R | 40 ++++++-- R/transformers.R | 52 ++++++++--- R/utils-knitr.R | 4 R/utils.R | 19 +++- R/zzz.R | 5 - README.md | 2 build/vignette.rds |binary inst/doc/epoxy-report.Rmd | 4 inst/doc/epoxy-report.html | 17 ++- inst/doc/epoxy-script.html | 1 inst/doc/epoxy-shiny.html | 25 ++--- inst/doc/inline-reporting.Rmd | 4 inst/doc/inline-reporting.html | 13 +- inst/examples/word-list/server.R | 40 +++++--- inst/examples/word-list/ui.R | 46 +++++----- man/epoxy-package.Rd | 5 + man/epoxy.Rd | 4 man/epoxy_mustache.Rd | 4 man/epoxy_transform.Rd | 6 - man/epoxy_transform_html.Rd | 8 - man/epoxy_transform_inline.Rd | 10 +- man/epoxy_transform_one_shot.Rd | 2 man/epoxy_use.Rd | 2 man/fragments/setup.Rmd | 2 man/render_epoxy.Rd | 4 man/ui_epoxy_html.Rd | 6 - man/ui_epoxy_markdown.Rd | 10 +- man/ui_epoxy_mustache.Rd | 12 +- man/use_epoxy_knitr_engines.Rd | 2 tests/testthat/_snaps/epoxy_transform_inline.md | 6 - tests/testthat/_snaps/transformers.md | 2 tests/testthat/apps/no-shiny/app.R | 4 tests/testthat/helpers.R | 29 ++++-- tests/testthat/test-engines.R | 17 ++- tests/testthat/test-epoxy.R | 13 ++ tests/testthat/test-epoxy_transform_html.R | 16 ++- tests/testthat/test-epoxy_transform_inline.R | 4 tests/testthat/test-epoxy_use.R | 11 +- tests/testthat/test-shiny.R | 44 +++++++-- tests/testthat/test-shiny_ui_epoxy_html-list.R | 6 - tests/testthat/test-shiny_ui_epoxy_markdown.R | 1 tests/testthat/test-shiny_ui_epoxy_mustache.R | 1 tests/testthat/test-shiny_word-list.R | 1 tests/testthat/test-transformers.R | 33 ++++++- vignettes/epoxy-report.Rmd | 4 vignettes/inline-reporting.Rmd | 4 55 files changed, 501 insertions(+), 320 deletions(-)
Title: Extract Subsequences from GenBank Annotations
Description: Extraction of subsequences into FASTA files from GenBank annotations where gene names may vary among accessions. Borstein & O'Meara (2018) <doi:10.7717/peerj.5179>.
Author: Samuel R. Borstein [aut, cre] ,
Brian O'Meara [aut]
Maintainer: Samuel R. Borstein <sam@borstein.com>
Diff between AnnotationBustR versions 1.3.0 dated 2020-09-24 and 2.0 dated 2026-08-31
DESCRIPTION | 40 +- MD5 | 58 +-- NAMESPACE | 2 R/AnnotationBust.R | 609 ++++++++++----------------------- R/DataDoc.R | 30 - R/FindLongestSeq.R | 67 ++- R/HelperFunctions.R |only R/MergeSearchTerms.R | 55 +- R/globals.R |only R/pkgname.R | 7 build/vignette.rds |binary data/cpDNAterms.RData |binary data/mtDNAterms.RData |binary data/mtDNAtermsPlants.RData |binary data/rDNAterms.RData |binary inst/CITATION | 39 -- inst/doc/AnnotationBustR-vignette.R | 12 inst/doc/AnnotationBustR-vignette.Rmd | 179 ++++----- inst/doc/AnnotationBustR-vignette.html | 604 ++++++++++++++++++++++---------- man/AnnotationBust.Rd | 90 ++-- man/AnnotationBustR.Rd | 7 man/FindLongestSeq.Rd | 12 man/MergeSearchTerms.Rd | 47 +- man/cpDNAterms.Rd | 8 man/mtDNAterms.Rd | 8 man/mtDNAtermsPlants.Rd | 6 man/rDNAterms.Rd | 8 tests/testthat/test_AnnotationBust.R | 34 - tests/testthat/test_FindLongestSeq.R | 14 tests/testthat/test_MergeSearchTerms.R | 33 - vignettes/AnnotationBustR-vignette.Rmd | 179 ++++----- 31 files changed, 1091 insertions(+), 1057 deletions(-)
More information about AnnotationBustR at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-25 0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-08-21 0.0.6
2025-07-12 0.0.5
2025-07-06 0.0.4
2025-05-16 0.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-16 0.2-1
2009-02-20 0.2
2008-08-01 0.1
Title: A Compendium of Bayesian Statistical Routines Written in 'C++'
Description: This is a compendium of 'C++' routines useful for Bayesian statistics. We steal
other people's 'C++' code, repurpose it, and export it so developers of 'R'
packages can use it in their 'C++' code. We actually don't steal anything, or
claim that Thomas Bayes did, but copy code that is compatible with our GPL 3
licence, fully acknowledging the authorship of the original code.
Author: Tomasz Wozniak [aut, cre] ,
Xiaolei Wang [aut] ,
Longcan Li [aut] ,
Jianying Shelly Xie [aut] ,
Filip Reierson [aut] ,
Kenyon Ng [aut]
Maintainer: Tomasz Wozniak <wozniak.tom@pm.me>
Diff between StealLikeBayes versions 1.0 dated 2025-12-02 and 2.0 dated 2026-08-31
StealLikeBayes-1.0/StealLikeBayes/R/rnorm1_precision_sampler.R |only StealLikeBayes-1.0/StealLikeBayes/inst/tinytest/test_rnorm1_precision_sampler.R |only StealLikeBayes-1.0/StealLikeBayes/man/rnorm1_precision_sampler.Rd |only StealLikeBayes-1.0/StealLikeBayes/src/rnorm1_precision_sampler.cpp |only StealLikeBayes-1.0/StealLikeBayes/src/rnorm1_precision_sampler.h |only StealLikeBayes-2.0/StealLikeBayes/DESCRIPTION | 14 StealLikeBayes-2.0/StealLikeBayes/MD5 | 55 +- StealLikeBayes-2.0/StealLikeBayes/NAMESPACE | 4 StealLikeBayes-2.0/StealLikeBayes/NEWS.md | 11 StealLikeBayes-2.0/StealLikeBayes/R/rgennorm.R | 2 StealLikeBayes-2.0/StealLikeBayes/R/rgig1.R |only StealLikeBayes-2.0/StealLikeBayes/R/rig2.R |only StealLikeBayes-2.0/StealLikeBayes/R/rmvnorm1_precision_sampler.R |only StealLikeBayes-2.0/StealLikeBayes/R/sample_variances_horseshoe.R | 25 + StealLikeBayes-2.0/StealLikeBayes/R/sample_variances_normal_gamma.R | 19 StealLikeBayes-2.0/StealLikeBayes/README.md | 10 StealLikeBayes-2.0/StealLikeBayes/build |only StealLikeBayes-2.0/StealLikeBayes/inst/include/StealLikeBayes_RcppExports.h | 89 +++- StealLikeBayes-2.0/StealLikeBayes/inst/tinytest/test_rgig1.R |only StealLikeBayes-2.0/StealLikeBayes/inst/tinytest/test_rig2.R |only StealLikeBayes-2.0/StealLikeBayes/inst/tinytest/test_rmvnorm1_precision_sampler.R |only StealLikeBayes-2.0/StealLikeBayes/man/StealLikeBayes-package.Rd | 13 StealLikeBayes-2.0/StealLikeBayes/man/rgennorm.Rd | 2 StealLikeBayes-2.0/StealLikeBayes/man/rgig1.Rd |only StealLikeBayes-2.0/StealLikeBayes/man/rig2.Rd |only StealLikeBayes-2.0/StealLikeBayes/man/rmvnorm1_precision_sampler.Rd |only StealLikeBayes-2.0/StealLikeBayes/man/sample_variances_horseshoe.Rd | 24 - StealLikeBayes-2.0/StealLikeBayes/man/sample_variances_normal_gamma.Rd | 17 StealLikeBayes-2.0/StealLikeBayes/src/RcppExports.cpp | 200 +++++++--- StealLikeBayes-2.0/StealLikeBayes/src/rgig1.cpp |only StealLikeBayes-2.0/StealLikeBayes/src/rgig1.h |only StealLikeBayes-2.0/StealLikeBayes/src/rig2.cpp |only StealLikeBayes-2.0/StealLikeBayes/src/rig2.h |only StealLikeBayes-2.0/StealLikeBayes/src/rmvnorm1_precision_sampler.cpp |only StealLikeBayes-2.0/StealLikeBayes/src/rmvnorm1_precision_sampler.h |only StealLikeBayes-2.0/StealLikeBayes/src/sample_variances_horseshoe.cpp | 18 StealLikeBayes-2.0/StealLikeBayes/src/sample_variances_horseshoe.h | 4 StealLikeBayes-2.0/StealLikeBayes/src/sample_variances_normal_gamma.cpp | 25 - StealLikeBayes-2.0/StealLikeBayes/src/sample_variances_normal_gamma.h | 4 39 files changed, 396 insertions(+), 140 deletions(-)
More information about StealLikeBayes at CRAN
Permanent link
Title: Rational Approximations of Fractional Stochastic Partial
Differential Equations
Description: Functions that compute rational approximations of fractional elliptic stochastic partial differential equations. The package also contains functions for common statistical usage of these approximations. The main references for rSPDE are Bolin, Simas and Xiong (2023) <doi:10.1080/10618600.2023.2231051> for the covariance-based method and Bolin and Kirchner (2020) <doi:10.1080/10618600.2019.1665537> for the operator-based rational approximation. These can be generated by the citation function in R.
Author: David Bolin [cre, aut],
Alexandre Simas [aut],
Finn Lindgren [ctb]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between rSPDE versions 2.5.2 dated 2026-01-26 and 2.6.0 dated 2026-08-31
DESCRIPTION | 19 MD5 | 99 +-- NAMESPACE | 85 +- NEWS.md | 16 R/fractional.computations.R | 86 ++ R/fractional.operators.R | 14 R/hybrid.spde.R |only R/inla_rspde.R | 98 +-- R/inla_rspde_1d.R | 53 - R/inla_rspde_anisotropic.R | 24 R/inla_rspde_hybrid.R |only R/inla_rspde_intrinsic.R | 46 - R/inla_rspde_spacetime.R | 27 R/inla_safe.R |only R/inlabru_rspde.R | 108 +-- R/posterior_crossvalidation.R |only R/rSPDE-package.R | 13 R/rspde_lme.R | 419 ++++++++++-- R/util.R | 683 ++++++++++++++++++--- build/vignette.rds |binary demo |only inst/doc/rSPDE_package.html | 4 man/augment.rspde_lme.Rd | 2 man/bru_get_mapper.inla_rspde.Rd | 17 man/glance.rspde_lme.Rd | 4 man/hybrid.spde.Rd |only man/posterior_crossvalidation.Rd |only man/predict.hybrid_spde.Rd |only man/predict.inla_rspde_matern1d.Rd | 21 man/rSPDE-package.Rd | 3 man/rspde.anistropic2d.Rd | 9 man/rspde.hybrid.matern.Rd |only man/rspde.intrinsic.Rd | 11 man/rspde.make.A.Rd | 7 man/rspde.make.index.Rd | 20 man/rspde.matern.Rd | 9 man/rspde.matern.intrinsic.Rd | 9 man/rspde.matern1d.Rd | 9 man/rspde.metric_graph.Rd | 2 man/rspde.result.Rd | 17 man/rspde.spacetime.Rd | 18 man/rspde_lme.Rd | 7 man/rspde_safe_inla.Rd |only man/simulate.hybrid_spde.Rd |only man/spde.make.A.Rd | 5 man/spde.matern.operators.Rd | 7 man/summary.rspde_result.Rd | 17 man/update.CBrSPDEobj.Rd | 5 man/update.hybrid_spde.Rd |only man/update.rSPDEobj.Rd | 5 tests/testthat/setup.R |only tests/testthat/test.cgeneric_builtin.R |only tests/testthat/test.fem.R |only tests/testthat/test.inla_rspde.R |only tests/testthat/test.inlabru_rspde.R | 4 tests/testthat/test.posterior_crossvalidation.R |only tests/testthat/test.rspde_lme_optim_errors.R | 27 tests/testthat/test.rspde_lme_predict_precompute.R |only tests/testthat/test_hybrid_spde.R |only tests/testthat/test_inla_rspde_hybrid.R |only 60 files changed, 1476 insertions(+), 553 deletions(-)
Title: Bayesian Age-Period-Cohort Modeling and Prediction
Description: Bayesian Age-Period-Cohort Modeling and Prediction using efficient Markov Chain Monte Carlo Methods. This is the R version of the previous BAMP software as described in Volker Schmid and Leonhard Held (2007) <DOI:10.18637/jss.v021.i08> Bayesian Age-Period-Cohort Modeling and Prediction - BAMP, Journal of Statistical Software 21:8. This package includes checks of convergence using Gelman's R.
Author: Volker Schmid [aut, cre] ,
Florian Geressen [ctb],
Leonhard Held [ctb],
Evi Rainer [ctb],
Chris Kypridemos [aut]
Maintainer: Volker Schmid <volker.schmid@lmu.de>
Diff between bamp versions 2.2.0 dated 2026-06-21 and 3.0.0 dated 2026-08-31
DESCRIPTION | 16 - MD5 | 47 ++-- NAMESPACE | 3 NEWS.md | 42 ++++ R/bamp.R | 302 ++++++++++++++++++++++++++------ R/check_apc.R | 192 +++++++++++++++----- R/effects_apc.R | 187 +++++++++++++++---- R/pg_engine.R |only R/plot_apc.R | 65 ++++-- R/predict_apc.R | 80 ++++++-- R/print_apc.R | 15 + R/select_model.R |only README.md | 40 ++-- inst/CITATION | 2 inst/tinytest |only man/bamp.Rd | 133 +++++++++++++- man/checkConvergence.Rd | 30 ++- man/effects.apc.Rd | 51 +++++ man/plot.apc.Rd | 24 ++ man/selectModel.Rd |only src/bamp.cc | 5 src/block.cc | 2 src/init.c | 13 + src/pg_engine.c |only tests |only vignettes/publications/publications.Rmd | 8 26 files changed, 1010 insertions(+), 247 deletions(-)
Title: A High-Performance Taxonomic Database Interface
Description: Provides fast access to many commonly used taxonomic authorities
in a uniform Darwin Core format. Tables are read directly from
versioned Parquet snapshots, streamed from cloud storage or from a
local copy, and queried with familiar 'dplyr' verbs.
Author: Carl Boettiger [aut, cre] ,
Kari Norman [aut] ,
Jorrit Poelen [aut] ,
Scott Chamberlain [aut] ,
Noam Ross [ctb] ,
Mattia Ghilardi [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between taxadb versions 0.2.1 dated 2023-03-08 and 0.3.0 dated 2026-08-31
taxadb-0.2.1/taxadb/R/parse_schema.R |only taxadb-0.2.1/taxadb/R/taxadb_dir.R |only taxadb-0.2.1/taxadb/R/td_create.R |only taxadb-0.2.1/taxadb/R/tl_import.R |only taxadb-0.2.1/taxadb/inst/doc/backends.R |only taxadb-0.2.1/taxadb/inst/doc/backends.Rmd |only taxadb-0.2.1/taxadb/inst/doc/backends.html |only taxadb-0.2.1/taxadb/inst/extdata/common_itis_test.tsv.bz2 |only taxadb-0.2.1/taxadb/inst/extdata/dwc_itis_test.tsv.bz2 |only taxadb-0.2.1/taxadb/inst/extdata/prov.json |only taxadb-0.2.1/taxadb/inst/extdata/schema.json |only taxadb-0.2.1/taxadb/man/tl_import.Rd |only taxadb-0.2.1/taxadb/tests/testthat/test-tl_import.R |only taxadb-0.2.1/taxadb/vignettes/backends.Rmd |only taxadb-0.3.0/taxadb/DESCRIPTION | 39 - taxadb-0.3.0/taxadb/MD5 | 126 ++-- taxadb-0.3.0/taxadb/NAMESPACE | 26 taxadb-0.3.0/taxadb/NEWS.md | 152 +++++ taxadb-0.3.0/taxadb/R/build_col.R |only taxadb-0.3.0/taxadb/R/build_fishbase.R |only taxadb-0.3.0/taxadb/R/build_gbif.R |only taxadb-0.3.0/taxadb/R/build_itis.R |only taxadb-0.3.0/taxadb/R/build_ncbi.R |only taxadb-0.3.0/taxadb/R/build_ott.R |only taxadb-0.3.0/taxadb/R/build_utils.R |only taxadb-0.3.0/taxadb/R/clean_names.R | 7 taxadb-0.3.0/taxadb/R/filter_by.R | 25 taxadb-0.3.0/taxadb/R/filter_id.R | 4 taxadb-0.3.0/taxadb/R/fuzzy_filter.R | 6 taxadb-0.3.0/taxadb/R/get_ids.R | 5 taxadb-0.3.0/taxadb/R/get_names.R | 22 taxadb-0.3.0/taxadb/R/manifest.R |only taxadb-0.3.0/taxadb/R/providers.R |only taxadb-0.3.0/taxadb/R/taxa_tbl.R | 65 +- taxadb-0.3.0/taxadb/R/taxadb_source.R |only taxadb-0.3.0/taxadb/R/td_build.R |only taxadb-0.3.0/taxadb/R/td_connect.R | 137 +++-- taxadb-0.3.0/taxadb/R/td_download.R |only taxadb-0.3.0/taxadb/R/td_validate.R |only taxadb-0.3.0/taxadb/README.md | 366 ++++++++++---- taxadb-0.3.0/taxadb/build/vignette.rds |binary taxadb-0.3.0/taxadb/inst/WORDLIST | 54 +- taxadb-0.3.0/taxadb/inst/doc/data-sources.Rmd | 155 ++++- taxadb-0.3.0/taxadb/inst/doc/data-sources.html | 279 ++++++---- taxadb-0.3.0/taxadb/inst/extdata/common_itis_test.parquet |binary taxadb-0.3.0/taxadb/inst/extdata/dwc_itis_test.parquet |binary taxadb-0.3.0/taxadb/inst/scripts |only taxadb-0.3.0/taxadb/man/available_providers.Rd |only taxadb-0.3.0/taxadb/man/available_versions.Rd |only taxadb-0.3.0/taxadb/man/build_col.Rd |only taxadb-0.3.0/taxadb/man/build_dir.Rd |only taxadb-0.3.0/taxadb/man/build_fishbase.Rd |only taxadb-0.3.0/taxadb/man/build_gbif.Rd |only taxadb-0.3.0/taxadb/man/build_itis.Rd |only taxadb-0.3.0/taxadb/man/build_ncbi.Rd |only taxadb-0.3.0/taxadb/man/build_ott.Rd |only taxadb-0.3.0/taxadb/man/common_contains.Rd | 2 taxadb-0.3.0/taxadb/man/common_starts_with.Rd | 2 taxadb-0.3.0/taxadb/man/filter_by.Rd | 14 taxadb-0.3.0/taxadb/man/filter_common.Rd | 12 taxadb-0.3.0/taxadb/man/filter_id.Rd | 16 taxadb-0.3.0/taxadb/man/filter_name.Rd | 12 taxadb-0.3.0/taxadb/man/filter_rank.Rd | 12 taxadb-0.3.0/taxadb/man/fuzzy_filter.Rd | 4 taxadb-0.3.0/taxadb/man/get_ids.Rd | 4 taxadb-0.3.0/taxadb/man/get_names.Rd | 4 taxadb-0.3.0/taxadb/man/latest_version.Rd |only taxadb-0.3.0/taxadb/man/list_snapshots.Rd |only taxadb-0.3.0/taxadb/man/name_contains.Rd | 4 taxadb-0.3.0/taxadb/man/name_starts_with.Rd | 4 taxadb-0.3.0/taxadb/man/taxa_tbl.Rd | 22 taxadb-0.3.0/taxadb/man/taxadb_dir.Rd | 18 taxadb-0.3.0/taxadb/man/taxadb_provider_info.Rd |only taxadb-0.3.0/taxadb/man/taxadb_providers.Rd |only taxadb-0.3.0/taxadb/man/taxadb_repo.Rd |only taxadb-0.3.0/taxadb/man/taxadb_uri.Rd |only taxadb-0.3.0/taxadb/man/td_build.Rd |only taxadb-0.3.0/taxadb/man/td_connect.Rd | 49 + taxadb-0.3.0/taxadb/man/td_create.Rd | 68 -- taxadb-0.3.0/taxadb/man/td_disconnect.Rd | 6 taxadb-0.3.0/taxadb/man/td_download.Rd |only taxadb-0.3.0/taxadb/man/td_manifest.Rd |only taxadb-0.3.0/taxadb/man/td_validate.Rd |only taxadb-0.3.0/taxadb/man/td_write_metadata.Rd |only taxadb-0.3.0/taxadb/tests/testthat/test-clean_names.R | 3 taxadb-0.3.0/taxadb/tests/testthat/test-id-formats.R |only taxadb-0.3.0/taxadb/tests/testthat/test-taxadb_source.R |only taxadb-0.3.0/taxadb/tests/testthat/test-td_validate.R |only taxadb-0.3.0/taxadb/vignettes/data-sources.Rmd | 155 ++++- 89 files changed, 1307 insertions(+), 572 deletions(-)
Title: Sequential Poisson Sampling
Description: Sequential Poisson sampling is a variation of Poisson sampling for
drawing probability-proportional-to-size samples with a given number of
units, and is commonly used for price-index surveys. This package gives
functions to draw stratified sequential Poisson samples according to the
method by Ohlsson (1998, ISSN:0282-423X), as well as other order sample
designs by Rosén (1997, <doi:10.1016/S0378-3758(96)00186-3>), and generate
approximate bootstrap replicate weights according to the generalized
bootstrap method by Beaumont and Patak
(2012, <doi:10.1111/j.1751-5823.2011.00166.x>).
Author: Steve Martin [aut, cre, cph] ,
Justin Francis [ctb]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between sps versions 0.6.4 dated 2026-07-19 and 0.7.0 dated 2026-08-31
sps-0.6.4/sps/LICENSE |only sps-0.7.0/sps/DESCRIPTION | 14 - sps-0.7.0/sps/MD5 | 66 +++--- sps-0.7.0/sps/NEWS.md | 15 + sps-0.7.0/sps/R/expected_coverage.R | 6 sps-0.7.0/sps/R/inclusion_prob.R | 62 ++---- sps-0.7.0/sps/R/prop_allocation.R | 16 - sps-0.7.0/sps/R/sps.R | 74 ++----- sps-0.7.0/sps/R/sps_iterator.R | 9 sps-0.7.0/sps/R/sps_repweights.R | 37 +-- sps-0.7.0/sps/R/utils.R |only sps-0.7.0/sps/R/zzz.R | 7 sps-0.7.0/sps/README.md | 153 +++++++--------- sps-0.7.0/sps/build/partial.rdb |binary sps-0.7.0/sps/build/vignette.rds |binary sps-0.7.0/sps/inst/CITATION | 2 sps-0.7.0/sps/inst/REFERENCES.R |only sps-0.7.0/sps/inst/WORDLIST |only sps-0.7.0/sps/inst/doc/performance.Rmd |only sps-0.7.0/sps/inst/doc/performance.html |only sps-0.7.0/sps/inst/doc/sps.R | 8 sps-0.7.0/sps/inst/doc/sps.Rmd | 16 + sps-0.7.0/sps/inst/doc/sps.html | 208 ++++------------------ sps-0.7.0/sps/inst/doc/take-all.R | 2 sps-0.7.0/sps/inst/doc/take-all.Rmd | 18 + sps-0.7.0/sps/inst/doc/take-all.html | 13 - sps-0.7.0/sps/inst/tinytest/test-inclusion_prob.R | 1 sps-0.7.0/sps/inst/tinytest/test-sps.R | 19 +- sps-0.7.0/sps/inst/tinytest/test-zzz.R |only sps-0.7.0/sps/man/inclusion_prob.Rd | 13 - sps-0.7.0/sps/man/prop_allocation.Rd | 8 sps-0.7.0/sps/man/sps-package.Rd | 4 sps-0.7.0/sps/man/sps.Rd | 36 +-- sps-0.7.0/sps/man/sps_repweights.Rd | 33 +-- sps-0.7.0/sps/tests/spelling.R |only sps-0.7.0/sps/vignettes/performance.Rmd |only sps-0.7.0/sps/vignettes/performance.Rmd.orig |only sps-0.7.0/sps/vignettes/sps.Rmd | 16 + sps-0.7.0/sps/vignettes/take-all.Rmd | 18 + 39 files changed, 351 insertions(+), 523 deletions(-)
Title: Similarity Retrieval and Local Learning for Spectral
Chemometrics
Description: Functions for dissimilarity analysis and machine learning in complex
spectral data sets, including memory-based learning (MBL), optimal subset
search and selection, and retrieval-based modelling with model libraries.
Supports local learning, optimisation of spectral libraries, and
ensemble prediction from precomputed models. Most of these functions are
based on the methods presented in Ramirez-Lopez et al. (2013)
<doi:10.1016/j.geoderma.2012.12.014>, Ramirez-Lopez et al. (2026a)
<doi:10.1016/j.aca.2026.345682>, and Ramirez-Lopez et al. (2026b)
<doi:10.1016/j.aca.2026.345651>.
Author: Leonardo Ramirez-Lopez [aut, cre] ,
Antoine Stevens [aut, ctb] ,
Claudio Orellano [ctb]
Maintainer: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Diff between resemble versions 3.0.0 dated 2026-04-20 and 3.0.1 dated 2026-08-31
resemble-3.0.0/resemble/inst/doc/building-a-library-of-models-with-liblex.R |only resemble-3.0.0/resemble/inst/doc/building-a-library-of-models-with-liblex.html |only resemble-3.0.0/resemble/inst/doc/building-a-library-of-models-with-liblex.qmd |only resemble-3.0.0/resemble/inst/doc/classical-mbl.R |only resemble-3.0.0/resemble/inst/doc/classical-mbl.html |only resemble-3.0.0/resemble/inst/doc/classical-mbl.qmd |only resemble-3.0.0/resemble/inst/doc/dimensionality-reduction.R |only resemble-3.0.0/resemble/inst/doc/dimensionality-reduction.html |only resemble-3.0.0/resemble/inst/doc/dimensionality-reduction.qmd |only resemble-3.0.0/resemble/inst/doc/estimating-dissimilarity-between-spectra.R |only resemble-3.0.0/resemble/inst/doc/estimating-dissimilarity-between-spectra.html |only resemble-3.0.0/resemble/inst/doc/estimating-dissimilarity-between-spectra.qmd |only resemble-3.0.0/resemble/inst/doc/evolutionary-subset-search.R |only resemble-3.0.0/resemble/inst/doc/evolutionary-subset-search.html |only resemble-3.0.0/resemble/inst/doc/evolutionary-subset-search.qmd |only resemble-3.0.0/resemble/inst/doc/intro.R |only resemble-3.0.0/resemble/inst/doc/intro.html |only resemble-3.0.0/resemble/inst/doc/intro.qmd |only resemble-3.0.0/resemble/inst/doc/nearest-neighbor-search.R |only resemble-3.0.0/resemble/inst/doc/nearest-neighbor-search.html |only resemble-3.0.0/resemble/inst/doc/nearest-neighbor-search.qmd |only resemble-3.0.0/resemble/inst/doc/simple-global-models.R |only resemble-3.0.0/resemble/inst/doc/simple-global-models.html |only resemble-3.0.0/resemble/inst/doc/simple-global-models.qmd |only resemble-3.0.0/resemble/man/figures/mbl.png |only resemble-3.0.0/resemble/vignettes/building-a-library-of-models-with-liblex.qmd |only resemble-3.0.0/resemble/vignettes/classical-mbl.qmd |only resemble-3.0.0/resemble/vignettes/dimensionality-reduction.qmd |only resemble-3.0.0/resemble/vignettes/estimating-dissimilarity-between-spectra.qmd |only resemble-3.0.0/resemble/vignettes/evolutionary-subset-search.qmd |only resemble-3.0.0/resemble/vignettes/intro.qmd |only resemble-3.0.0/resemble/vignettes/nearest-neighbor-search.qmd |only resemble-3.0.0/resemble/vignettes/simple-global-models.qmd |only resemble-3.0.1/resemble/DESCRIPTION | 20 - resemble-3.0.1/resemble/MD5 | 123 +++++----- resemble-3.0.1/resemble/NAMESPACE | 2 resemble-3.0.1/resemble/NEWS.md | 9 resemble-3.0.1/resemble/R/AAA.R | 7 resemble-3.0.1/resemble/R/RcppExports.R | 12 resemble-3.0.1/resemble/R/diss_correlation.R | 16 - resemble-3.0.1/resemble/R/diss_evaluate.R | 10 resemble-3.0.1/resemble/R/diss_methods.R | 49 ++- resemble-3.0.1/resemble/R/gesearch.R | 15 - resemble-3.0.1/resemble/R/liblex.R | 29 +- resemble-3.0.1/resemble/R/local_helpers.R | 1 resemble-3.0.1/resemble/R/resemble.R | 17 - resemble-3.0.1/resemble/R/sid.R | 2 resemble-3.0.1/resemble/README.md | 58 +++- resemble-3.0.1/resemble/build/stage23.rdb |binary resemble-3.0.1/resemble/build/vignette.rds |binary resemble-3.0.1/resemble/inst/doc/aa-intro.R |only resemble-3.0.1/resemble/inst/doc/aa-intro.html |only resemble-3.0.1/resemble/inst/doc/aa-intro.qmd |only resemble-3.0.1/resemble/inst/doc/ab-dimensionality-reduction.R |only resemble-3.0.1/resemble/inst/doc/ab-dimensionality-reduction.html |only resemble-3.0.1/resemble/inst/doc/ab-dimensionality-reduction.qmd |only resemble-3.0.1/resemble/inst/doc/ac-estimating-dissimilarity-between-spectra.R |only resemble-3.0.1/resemble/inst/doc/ac-estimating-dissimilarity-between-spectra.html |only resemble-3.0.1/resemble/inst/doc/ac-estimating-dissimilarity-between-spectra.qmd |only resemble-3.0.1/resemble/inst/doc/ad-nearest-neighbor-search.R |only resemble-3.0.1/resemble/inst/doc/ad-nearest-neighbor-search.html |only resemble-3.0.1/resemble/inst/doc/ad-nearest-neighbor-search.qmd |only resemble-3.0.1/resemble/inst/doc/ae-simple-global-models.R |only resemble-3.0.1/resemble/inst/doc/ae-simple-global-models.html |only resemble-3.0.1/resemble/inst/doc/ae-simple-global-models.qmd |only resemble-3.0.1/resemble/inst/doc/af-classical-mbl.R |only resemble-3.0.1/resemble/inst/doc/af-classical-mbl.html |only resemble-3.0.1/resemble/inst/doc/af-classical-mbl.qmd |only resemble-3.0.1/resemble/inst/doc/ag-evolutionary-subset-search.R |only resemble-3.0.1/resemble/inst/doc/ag-evolutionary-subset-search.html |only resemble-3.0.1/resemble/inst/doc/ag-evolutionary-subset-search.qmd |only resemble-3.0.1/resemble/inst/doc/ah-building-a-library-of-models-with-liblex.R |only resemble-3.0.1/resemble/inst/doc/ah-building-a-library-of-models-with-liblex.html |only resemble-3.0.1/resemble/inst/doc/ah-building-a-library-of-models-with-liblex.qmd |only resemble-3.0.1/resemble/inst/logo.R | 2 resemble-3.0.1/resemble/man/diss_correlation.Rd | 15 - resemble-3.0.1/resemble/man/diss_cosine.Rd | 11 resemble-3.0.1/resemble/man/diss_euclidean.Rd | 11 resemble-3.0.1/resemble/man/diss_mahalanobis.Rd | 5 resemble-3.0.1/resemble/man/figures/mbl_example.png |only resemble-3.0.1/resemble/man/gesearch.Rd | 12 resemble-3.0.1/resemble/man/liblex.Rd | 27 +- resemble-3.0.1/resemble/man/mbl.Rd | 2 resemble-3.0.1/resemble/man/resemble-package.Rd | 16 - resemble-3.0.1/resemble/man/sid.Rd | 2 resemble-3.0.1/resemble/src/RcppExports.cpp | 11 resemble-3.0.1/resemble/src/diss_helpers.cpp | 17 + resemble-3.0.1/resemble/tests/setup.R |only resemble-3.0.1/resemble/vignettes/aa-intro.qmd |only resemble-3.0.1/resemble/vignettes/ab-dimensionality-reduction.qmd |only resemble-3.0.1/resemble/vignettes/ac-estimating-dissimilarity-between-spectra.qmd |only resemble-3.0.1/resemble/vignettes/ad-nearest-neighbor-search.qmd |only resemble-3.0.1/resemble/vignettes/ae-simple-global-models.qmd |only resemble-3.0.1/resemble/vignettes/af-classical-mbl.qmd |only resemble-3.0.1/resemble/vignettes/ag-evolutionary-subset-search.qmd |only resemble-3.0.1/resemble/vignettes/ah-building-a-library-of-models-with-liblex.qmd |only 96 files changed, 302 insertions(+), 199 deletions(-)
Title: Signal and Image Processing Toolbox for Analyzing Intracranial
Electroencephalography Data
Description: Implemented fast and memory-efficient Notch-filter,
Welch-periodogram, discrete wavelet spectrogram for minutes of
high-resolution signals, fast 3D convolution, image registration,
3D mesh manipulation; providing fundamental toolbox for intracranial
Electroencephalography (iEEG) pipelines.
Documentation and examples about 'RAVE' project are provided at
<https://rave.wiki>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for
details.
Author: Zhengjia Wang [aut, cre] ,
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph] ,
Karim Rahim [cph, ctb] ,
Thomas Possidente [cph, ctb] ,
Michael Prerau [cph, ctb] ,
Marcus Geelnard [ctb, cph] ,
Stefan Schlag [...truncated...]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravetools versions 0.3.0 dated 2026-08-21 and 0.3.1 dated 2026-08-31
DESCRIPTION | 9 MD5 | 38 +- NEWS.md | 6 R/RcppExports.R | 4 R/aaa.R | 16 + R/vcg-collision.R | 249 ++++++++++++++++--- R/vcg.R | 51 +++ README.md | 62 ++++ build/vignette.rds |only inst/doc |only man/vcg_detect_collision.Rd | 196 ++++++++++++--- man/vcg_smooth.Rd | 5 src/RcppExports.cpp | 8 src/reg_linear.cpp | 6 src/reg_syn.cpp | 4 src/vcgCollision.cpp | 364 ++++++++++++++++++++++------ src/vcgCommon.cpp | 11 src/vcgCommon.h | 9 tests/testthat/test-vcg-collision.R | 460 +++++++++++++++++++++++++++--------- tests/testthat/test-vcg-mesh-io.R |only vignettes |only 21 files changed, 1203 insertions(+), 295 deletions(-)
Title: Administrative Boundaries and Static Map Tiles for Spain
Description: Administrative boundaries of Spain at several levels
(Autonomous Communities and Cities, provinces, municipalities and
'NUTS'), based on 'GISCO' from 'Eurostat'
<https://ec.europa.eu/eurostat/web/gisco> and 'CartoBase ANE' from
'Instituto Geográfico Nacional' <https://www.ign.es/>. Includes tools
to download and process static map tiles and a 'leaflet' plugin for
Spanish public administration tile providers.
Author: Diego Hernangomez [aut, cre, cph] ,
Eurostat [cph] ,
Instituto Geografico Nacional [cph] ,
Francisco J. Goerlich [ctb]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between mapSpain versions 1.2.0 dated 2026-06-17 and 1.2.1 dated 2026-08-31
mapSpain-1.2.0/mapSpain/tests/testthat/_snaps/esp-get-ccaa-siane.md |only mapSpain-1.2.0/mapSpain/tests/testthat/_snaps/esp-get-prov-siane.md |only mapSpain-1.2.0/mapSpain/tests/testthat/helpers.R |only mapSpain-1.2.1/mapSpain/DESCRIPTION | 10 mapSpain-1.2.1/mapSpain/MD5 | 341 +++++----- mapSpain-1.2.1/mapSpain/NAMESPACE | 8 mapSpain-1.2.1/mapSpain/NEWS.md | 63 - mapSpain-1.2.1/mapSpain/R/addProviderEspTiles.R | 9 mapSpain-1.2.1/mapSpain/R/data.R | 32 mapSpain-1.2.1/mapSpain/R/esp-cache.R | 52 - mapSpain-1.2.1/mapSpain/R/esp-check-access.R | 25 mapSpain-1.2.1/mapSpain/R/esp-dict.R | 41 - mapSpain-1.2.1/mapSpain/R/esp-get-attributions.R | 24 mapSpain-1.2.1/mapSpain/R/esp-get-can-box.R | 10 mapSpain-1.2.1/mapSpain/R/esp-get-capimun.R | 19 mapSpain-1.2.1/mapSpain/R/esp-get-ccaa-siane.R | 15 mapSpain-1.2.1/mapSpain/R/esp-get-ccaa.R | 13 mapSpain-1.2.1/mapSpain/R/esp-get-comarca.R | 21 mapSpain-1.2.1/mapSpain/R/esp-get-countries-siane.R | 27 mapSpain-1.2.1/mapSpain/R/esp-get-grid-BDN.R | 13 mapSpain-1.2.1/mapSpain/R/esp-get-grid-EEA.R | 8 mapSpain-1.2.1/mapSpain/R/esp-get-grid-ESDAC.R | 13 mapSpain-1.2.1/mapSpain/R/esp-get-grid-MTN.R | 14 mapSpain-1.2.1/mapSpain/R/esp-get-gridmap.R | 16 mapSpain-1.2.1/mapSpain/R/esp-get-hydrobasin.R | 7 mapSpain-1.2.1/mapSpain/R/esp-get-hypsobath.R | 10 mapSpain-1.2.1/mapSpain/R/esp-get-landwater.R | 35 - mapSpain-1.2.1/mapSpain/R/esp-get-munic-siane.R | 5 mapSpain-1.2.1/mapSpain/R/esp-get-munic.R | 11 mapSpain-1.2.1/mapSpain/R/esp-get-nuts.R | 19 mapSpain-1.2.1/mapSpain/R/esp-get-prov-siane.R | 7 mapSpain-1.2.1/mapSpain/R/esp-get-prov.R | 15 mapSpain-1.2.1/mapSpain/R/esp-get-railway.R | 31 mapSpain-1.2.1/mapSpain/R/esp-get-roads.R | 24 mapSpain-1.2.1/mapSpain/R/esp-get-simpl.R | 10 mapSpain-1.2.1/mapSpain/R/esp-get-spain-siane.R | 6 mapSpain-1.2.1/mapSpain/R/esp-get-spain.R | 11 mapSpain-1.2.1/mapSpain/R/esp-get-tiles.R | 56 - mapSpain-1.2.1/mapSpain/R/esp-make-provider.R | 2 mapSpain-1.2.1/mapSpain/R/esp-move-can.R | 16 mapSpain-1.2.1/mapSpain/R/esp-siane-bulk-download.R | 17 mapSpain-1.2.1/mapSpain/R/sysdata.rda |binary mapSpain-1.2.1/mapSpain/R/utils-convert-names.R | 20 mapSpain-1.2.1/mapSpain/R/utils-country.R | 18 mapSpain-1.2.1/mapSpain/R/utils-dict.R | 10 mapSpain-1.2.1/mapSpain/R/utils-get-tiles.R | 33 mapSpain-1.2.1/mapSpain/R/utils-sf.R | 24 mapSpain-1.2.1/mapSpain/R/utils-url.R | 83 +- mapSpain-1.2.1/mapSpain/R/utils.R | 75 +- mapSpain-1.2.1/mapSpain/README.md | 31 mapSpain-1.2.1/mapSpain/build/partial.rdb |binary mapSpain-1.2.1/mapSpain/build/vignette.rds |binary mapSpain-1.2.1/mapSpain/data/esp_codelist.rda |binary mapSpain-1.2.1/mapSpain/data/esp_nuts_2024.rda |binary mapSpain-1.2.1/mapSpain/data/esp_tiles_providers.rda |binary mapSpain-1.2.1/mapSpain/data/pobmun25.rda |binary mapSpain-1.2.1/mapSpain/inst/doc/imagery.html | 11 mapSpain-1.2.1/mapSpain/inst/doc/mapSpain.html | 35 - mapSpain-1.2.1/mapSpain/inst/doc/mapSpain.qmd | 34 mapSpain-1.2.1/mapSpain/inst/schemaorg.json | 4 mapSpain-1.2.1/mapSpain/man/addProviderEspTiles.Rd | 3 mapSpain-1.2.1/mapSpain/man/esp_clear_cache.Rd | 5 mapSpain-1.2.1/mapSpain/man/esp_codelist.Rd | 3 mapSpain-1.2.1/mapSpain/man/esp_dict.Rd | 16 mapSpain-1.2.1/mapSpain/man/esp_get_attributions.Rd |only mapSpain-1.2.1/mapSpain/man/esp_get_can_box.Rd | 8 mapSpain-1.2.1/mapSpain/man/esp_get_capimun.Rd | 68 - mapSpain-1.2.1/mapSpain/man/esp_get_ccaa.Rd | 49 - mapSpain-1.2.1/mapSpain/man/esp_get_ccaa_siane.Rd | 47 - mapSpain-1.2.1/mapSpain/man/esp_get_comarca.Rd | 47 - mapSpain-1.2.1/mapSpain/man/esp_get_countries_siane.Rd | 48 - mapSpain-1.2.1/mapSpain/man/esp_get_grid_BDN.Rd | 29 mapSpain-1.2.1/mapSpain/man/esp_get_grid_EEA.Rd | 9 mapSpain-1.2.1/mapSpain/man/esp_get_grid_ESDAC.Rd | 25 mapSpain-1.2.1/mapSpain/man/esp_get_grid_MTN.Rd | 26 mapSpain-1.2.1/mapSpain/man/esp_get_gridmap.Rd | 26 mapSpain-1.2.1/mapSpain/man/esp_get_hydrobasin.Rd | 29 mapSpain-1.2.1/mapSpain/man/esp_get_hypsobath.Rd | 29 mapSpain-1.2.1/mapSpain/man/esp_get_landwater.Rd | 27 mapSpain-1.2.1/mapSpain/man/esp_get_munic.Rd | 47 - mapSpain-1.2.1/mapSpain/man/esp_get_munic_siane.Rd | 46 - mapSpain-1.2.1/mapSpain/man/esp_get_nuts.Rd | 50 - mapSpain-1.2.1/mapSpain/man/esp_get_prov.Rd | 53 - mapSpain-1.2.1/mapSpain/man/esp_get_prov_siane.Rd | 50 - mapSpain-1.2.1/mapSpain/man/esp_get_railway.Rd | 25 mapSpain-1.2.1/mapSpain/man/esp_get_roads.Rd | 23 mapSpain-1.2.1/mapSpain/man/esp_get_simpl.Rd | 34 mapSpain-1.2.1/mapSpain/man/esp_get_spain.Rd | 45 - mapSpain-1.2.1/mapSpain/man/esp_get_spain_siane.Rd | 39 - mapSpain-1.2.1/mapSpain/man/esp_get_tiles.Rd | 26 mapSpain-1.2.1/mapSpain/man/esp_make_provider.Rd | 9 mapSpain-1.2.1/mapSpain/man/esp_move_can.Rd | 16 mapSpain-1.2.1/mapSpain/man/esp_nuts_2024.Rd | 7 mapSpain-1.2.1/mapSpain/man/esp_set_cache_dir.Rd | 17 mapSpain-1.2.1/mapSpain/man/esp_siane_bulk_download.Rd | 41 - mapSpain-1.2.1/mapSpain/man/esp_tiles_providers.Rd | 12 mapSpain-1.2.1/mapSpain/man/figures/README-tile-1.png |binary mapSpain-1.2.1/mapSpain/man/pobmun25.Rd | 3 mapSpain-1.2.1/mapSpain/man/roxygen/meta.R | 8 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/addProviderEspTiles.md | 6 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-cache.md | 20 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-dict.md | 31 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-attributions.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-can-box.md | 14 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-capimun.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-ccaa.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-comarca.md | 23 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-countries-siane.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-grid-BDN.md | 6 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-grid-EEA.md | 2 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-grid-ESDAC.md |only mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-grid-MTN.md |only mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-gridmap.md | 2 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-hydrobasin.md | 8 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-hypsobath.md |only mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-landwater.md | 16 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-munic-siane.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-munic.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-nuts.md | 28 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-prov.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-railway.md | 4 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-roads.md |only mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-simpl.md | 2 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-get-tiles.md | 17 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/esp-move-can.md | 6 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/utils-convert-names.md | 59 - mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/utils-country.md | 22 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/utils-dict.md | 2 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/utils-get-tiles.md | 28 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/utils-sf.md | 7 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/utils-url.md | 4 mapSpain-1.2.1/mapSpain/tests/testthat/_snaps/utils.md | 34 mapSpain-1.2.1/mapSpain/tests/testthat/helper.R |only mapSpain-1.2.1/mapSpain/tests/testthat/test-addProviderEspTiles.R | 7 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-cache.R | 216 ++++-- mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-check-access.R | 38 - mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-dict.R | 4 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-attributions.R | 2 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-can-box.R | 2 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-capimun.R | 26 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-ccaa-siane.R | 48 - mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-ccaa.R | 4 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-comarca.R | 21 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-countries-siane.R | 32 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-grid-BDN.R | 18 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-grid-EEA.R | 2 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-grid-ESDAC.R | 33 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-grid-MTN.R | 14 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-gridmap.R | 2 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-hydrobasin.R | 23 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-hypsobath.R | 31 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-landwater.R | 42 - mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-munic-siane.R | 24 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-munic.R | 9 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-nuts.R | 77 -- mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-prov-siane.R | 54 - mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-prov.R | 4 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-railway.R | 23 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-roads.R | 28 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-simpl.R | 16 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-spain-siane.R | 13 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-spain.R | 13 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-stations.R | 14 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-get-tiles.R | 155 ++-- mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-make-provider.R | 4 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-move-can.R | 16 mapSpain-1.2.1/mapSpain/tests/testthat/test-esp-siane-bulk-download.R | 24 mapSpain-1.2.1/mapSpain/tests/testthat/test-utils-convert-names.R | 6 mapSpain-1.2.1/mapSpain/tests/testthat/test-utils-country.R | 6 mapSpain-1.2.1/mapSpain/tests/testthat/test-utils-dict.R | 4 mapSpain-1.2.1/mapSpain/tests/testthat/test-utils-get-tiles.R | 92 +- mapSpain-1.2.1/mapSpain/tests/testthat/test-utils-sf.R | 21 mapSpain-1.2.1/mapSpain/tests/testthat/test-utils-url.R | 106 ++- mapSpain-1.2.1/mapSpain/tests/testthat/test-utils.R | 36 - mapSpain-1.2.1/mapSpain/vignettes/mapSpain.qmd | 34 mapSpain-1.2.1/mapSpain/vignettes/thematic-1.png |binary 176 files changed, 2282 insertions(+), 1931 deletions(-)
Title: Add Ipea Editorial Standards to 'ggplot2' Graphics
Description: Convenient functions to create 'ggplot2' graphics following the
editorial guidelines of the Institute for Applied Economic
Research (Ipea).
Author: Pedro Ferreira [aut, cre],
Pedro Jorge [aut],
Daniel Lima [aut],
Gustavo Coelho [aut],
Rafael H. M. Pereira [aut],
Lucas Mation [aut],
Fabio Vaz [ctb],
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Pedro Ferreira <pedro.ferreira2@ipea.gov.br>
Diff between ipeaplot versions 0.5.4 dated 2026-07-09 and 1.0.0 dated 2026-08-31
ipeaplot |only 1 file changed
Title: Graph Drawing with Intelligent Placement (GRIP)
Description: Implements GRIP multiscale graph layout with a unified choice
between hop-count and geometry-aware edge-length graph metrics in 2D and
3D. Provides layout scoring, candidate
comparison, multiscale trace diagnostics, synthetic graph families,
and advanced experimental geodesic-KK utilities for weighted-layout
evaluation and polish. Based on Gajer and Kobourov (2002)
<doi:10.7155/jgaa.00052> and Gajer, Goodrich and Kobourov (2004)
<doi:10.1016/j.comgeo.2004.03.014>.
Author: Pawel Gajer [aut, cre]
Maintainer: Pawel Gajer <pgajer@gmail.com>
Diff between grip versions 0.1.3 dated 2026-08-21 and 0.2.0 dated 2026-08-31
grip-0.1.3/grip/R/deprecated_api.R |only grip-0.1.3/grip/man/deprecated-grip-api.Rd |only grip-0.1.3/grip/man/gmds.result.Rd |only grip-0.1.3/grip/man/grip.compare.layouts.Rd |only grip-0.1.3/grip/man/grip.optimize.edge.kk.layout.Rd |only grip-0.1.3/grip/man/grip.prepare.edge.kk.Rd |only grip-0.1.3/grip/man/grip.score.layout.Rd |only grip-0.2.0/grip/DESCRIPTION | 6 grip-0.2.0/grip/MD5 | 177 +- grip-0.2.0/grip/NAMESPACE | 93 - grip-0.2.0/grip/NEWS.md | 13 grip-0.2.0/grip/R/data-hmp_gc.R |only grip-0.2.0/grip/R/export_examples.R |only grip-0.2.0/grip/R/gmds_layout_interface.R | 61 grip-0.2.0/grip/R/graph_helpers.R | 640 ++++------ grip-0.2.0/grip/R/grip-0.2-migration.R |only grip-0.2.0/grip/R/grip_quality.R | 60 grip-0.2.0/grip/README.md | 15 grip-0.2.0/grip/data/hmp.gc.rda |only grip-0.2.0/grip/inst/doc/grip-examples.html | 12 grip-0.2.0/grip/inst/doc/grip-real-data.html | 188 +- grip-0.2.0/grip/inst/extdata/hmp_gc |only grip-0.2.0/grip/inst/extdata/hmp_u01_gc_coarse/PROVENANCE.md | 29 grip-0.2.0/grip/inst/extdata/hmp_u01_gc_coarse/vignette_results.rds |binary grip-0.2.0/grip/inst/extdata/vs_alternatives/BENCHMARK_PROVENANCE.md |only grip-0.2.0/grip/inst/extdata/vs_alternatives/benchmark_results.rds |binary grip-0.2.0/grip/inst/scripts |only grip-0.2.0/grip/man/build.weighted.misf.Rd | 10 grip-0.2.0/grip/man/compare.layouts.Rd | 9 grip-0.2.0/grip/man/cube_mask_pattern_helpers.Rd | 14 grip-0.2.0/grip/man/cylinder_surface_helpers.Rd | 22 grip-0.2.0/grip/man/edge.kk.Rd | 12 grip-0.2.0/grip/man/edge.length.density.stiffness.Rd | 7 grip-0.2.0/grip/man/edge.repulsive.stage.Rd | 12 grip-0.2.0/grip/man/edge.repulsive.state.Rd | 12 grip-0.2.0/grip/man/geodesic.kk.Rd | 9 grip-0.2.0/grip/man/geometry.diagnostics.Rd | 11 grip-0.2.0/grip/man/globalrep.weighted.grip.Rd | 11 grip-0.2.0/grip/man/graph.riemannian.star.structure.Rd | 9 grip-0.2.0/grip/man/graph_generators.Rd | 386 ------ grip-0.2.0/grip/man/grip-0.2-migration.Rd |only grip-0.2.0/grip/man/hmp.gc.Rd |only grip-0.2.0/grip/man/irregular_annulus_surface_helpers.Rd | 22 grip-0.2.0/grip/man/irregular_ball_solid_helpers.Rd | 24 grip-0.2.0/grip/man/irregular_double_torus_surface_helpers.Rd | 27 grip-0.2.0/grip/man/irregular_pair_of_pants_surface_helpers.Rd | 26 grip-0.2.0/grip/man/irregular_rectangle_surface_helpers.Rd | 71 - grip-0.2.0/grip/man/irregular_shell_solid_helpers.Rd | 25 grip-0.2.0/grip/man/irregular_sphere_surface_helpers.Rd | 22 grip-0.2.0/grip/man/irregular_torus_surface_helpers.Rd | 23 grip-0.2.0/grip/man/kary_tree_weighted_graph_helpers.Rd | 5 grip-0.2.0/grip/man/kernel.gram.gkk.Rd | 12 grip-0.2.0/grip/man/landmark.geodesic.kk.Rd | 11 grip-0.2.0/grip/man/mask_pattern_helpers.Rd | 11 grip-0.2.0/grip/man/menger_sponge_surface_helpers.Rd | 19 grip-0.2.0/grip/man/mesh_surface_helpers.Rd | 26 grip-0.2.0/grip/man/metric.mds.Rd | 7 grip-0.2.0/grip/man/misf.geodesic.kk.Rd | 14 grip-0.2.0/grip/man/occupied_mesh_surface_helpers.Rd | 26 grip-0.2.0/grip/man/perforated_grid_helpers.Rd | 12 grip-0.2.0/grip/man/porous_cube_surface_helpers.Rd | 62 grip-0.2.0/grip/man/prepare.edge.kk.Rd | 6 grip-0.2.0/grip/man/prepare.geodesic.kk.Rd | 6 grip-0.2.0/grip/man/prepare.graph.geodesic.mds.Rd | 6 grip-0.2.0/grip/man/prepare.landmark.geodesic.kk.Rd | 8 grip-0.2.0/grip/man/recursive_cube_mask_surface_helpers.Rd | 23 grip-0.2.0/grip/man/recursive_mask_grid_surface_helpers.Rd | 23 grip-0.2.0/grip/man/recursive_tetrahedron_mask_surface_helpers.Rd | 17 grip-0.2.0/grip/man/recursive_triangle_mask_surface_helpers.Rd | 19 grip-0.2.0/grip/man/repulsive.stage.Rd | 10 grip-0.2.0/grip/man/repulsive.state.Rd | 8 grip-0.2.0/grip/man/sampled_rectangle_surface_helpers.Rd | 46 grip-0.2.0/grip/man/score.geodesic.kk.Rd | 9 grip-0.2.0/grip/man/score.gmds.Rd | 9 grip-0.2.0/grip/man/score.landmark.geodesic.kk.Rd | 11 grip-0.2.0/grip/man/score.layout.Rd | 11 grip-0.2.0/grip/man/score.misf.geodesic.kk.Rd | 11 grip-0.2.0/grip/man/sierpinski_carpet_surface_helpers.Rd | 20 grip-0.2.0/grip/man/sierpinski_tetrahedron_surface_helpers.Rd | 16 grip-0.2.0/grip/man/sierpinski_triangle_surface_helpers.Rd | 18 grip-0.2.0/grip/man/sphere_surface_helpers.Rd | 23 grip-0.2.0/grip/man/tetrahedron_mask_helpers.Rd | 7 grip-0.2.0/grip/man/torus_surface_helpers.Rd | 22 grip-0.2.0/grip/man/triangle_mask_helpers.Rd | 7 grip-0.2.0/grip/man/triangulated_annulus_surface_helpers.Rd | 22 grip-0.2.0/grip/man/triangulated_pair_of_pants_surface_helpers.Rd | 24 grip-0.2.0/grip/man/triangulated_polyhedron_surface_helpers.Rd | 19 grip-0.2.0/grip/man/vicsek_surface_helpers.Rd | 22 grip-0.2.0/grip/man/weighted.grip.nd.Rd | 11 grip-0.2.0/grip/tests/testthat/test-edge-isometric-gkk.R | 52 grip-0.2.0/grip/tests/testthat/test-gmds-layout-interface.R | 2 grip-0.2.0/grip/tests/testthat/test-graph-helpers.R | 186 +- grip-0.2.0/grip/tests/testthat/test-hmp-gc.R |only grip-0.2.0/grip/tests/testthat/test-layout-metric-dispatch.R | 28 grip-0.2.0/grip/tests/testthat/test-layout-quality.R | 20 grip-0.2.0/grip/tests/testthat/test-public-api.R |only 96 files changed, 1190 insertions(+), 1795 deletions(-)
Title: Tools for Managing Classes on GitHub
Description: Interface for the GitHub API that enables efficient
management of courses on GitHub. It has a functionality for
managing organizations, teams, repositories, and users on GitHub
and helps automate most of the tedious and repetitive tasks
around creating and distributing assignments.
Author: Colin Rundel [aut, cre],
Mine Cetinkaya-Rundel [aut],
Therese Anders [ctb]
Maintainer: Colin Rundel <rundel@gmail.com>
Diff between ghclass versions 0.4.1 dated 2026-07-25 and 0.4.2 dated 2026-08-31
DESCRIPTION | 8 +- MD5 | 31 +++++---- NAMESPACE | 2 NEWS.md | 12 +++ R/github_token.R | 119 +++++++++++++++++++++++++++++++++++--- R/org_allows_forking.R | 5 + R/org_sitrep.R | 110 ++++++++++++++++++----------------- R/org_workflow_permissions.R | 5 + R/repo.R | 6 + R/repo_tree.R |only R/team_roster.R | 3 R/util_github.R | 8 ++ R/util_safely.R | 113 +++++++++++++++++++++++++----------- R/util_scopes.R |only man/github_token.Rd | 24 +++++++ man/repo_file.Rd | 12 +++ man/team_roster.Rd | 3 tests/testthat/test-util_scopes.R |only 18 files changed, 344 insertions(+), 117 deletions(-)
Title: An R Tool for Streamlining Database Joins
Description: Simplifies and automates the process of exploring and merging
data from relational databases. This package allows users to discover
table relationships, create a map of all possible joins, and generate
executable plans to merge data based on a structured metadata framework.
Author: Akshat Maurya [aut, cre],
David Shilane [aut]
Maintainer: Akshat Maurya <codingmaster902@gmail.com>
Diff between DBmaps versions 0.1.0 dated 2025-09-08 and 0.1.1 dated 2026-08-31
DESCRIPTION | 12 MD5 | 26 - NEWS.md | 13 R/generate_code.R | 14 R/join_plan.R | 158 +++---- R/map_joins.R | 48 +- build/vignette.rds |binary inst/doc/DBmaps-introduction.html | 633 ++++++++++++++---------------- inst/doc/defining-table-metadata.html | 417 +++++++++---------- inst/doc/discovering-join-paths.html | 229 +++++----- inst/doc/generating-aggregation-code.html | 231 +++++----- inst/doc/join-plan.html | 293 ++++++------- man/create_join_plan.Rd | 48 -- man/generate_aggregation_code.Rd | 9 14 files changed, 1033 insertions(+), 1098 deletions(-)
Title: Interactive Command-Line Menus
Description: Provides interactive command-line menu functionality with
single and multiple selection menus, keyboard navigation (arrow keys or
vi-style j/k), preselection, and graceful fallback for non-interactive
environments. Inspired by tools such as 'inquirer.js'
<https://github.com/SBoudrias/Inquirer.js>, 'pick'
<https://github.com/aisk/pick>, and 'survey'
<https://github.com/AlecAivazis/survey>. Designed to be lightweight and
easy to integrate into 'R' packages and scripts.
Author: Petr Čala [aut, cre]
Maintainer: Petr Čala <61505008@fsv.cuni.cz>
Diff between climenu versions 0.1.8 dated 2026-07-08 and 0.2.0 dated 2026-08-31
DESCRIPTION | 8 MD5 | 32 +-- NAMESPACE | 1 NEWS.md | 10 + R/checkbox.R | 113 ++++++++--- R/menu.R | 30 ++- R/select.R | 96 +++++++-- R/utils.R | 178 +++++++++++++++--- inst/doc/climenu.R | 29 ++- inst/doc/climenu.Rmd | 41 +++- inst/doc/climenu.html | 290 ++++++++++++++++-------------- man/checkbox.Rd | 29 ++- man/menu.Rd | 24 ++ man/select.Rd | 34 +++ tests/testthat/test-fallback.R | 30 +-- tests/testthat/test-labels-descriptions.R |only tests/testthat/test-render-frame.R |only vignettes/climenu.Rmd | 41 +++- 18 files changed, 704 insertions(+), 282 deletions(-)
Title: An Efficient and Deterministic Method for Identifying
Topological Domains in Genomes
Description: The 'TopDom' method identifies topological domains in genomes from Hi-C sequence data (Shin et al., 2016 <doi:10.1093/nar/gkv1505>). The authors published an implementation of their method as an R script (two different versions; also available in this package). This package originates from those original 'TopDom' R scripts and provides help pages adopted from the original 'TopDom' PDF documentation. It also provides a small number of bug fixes to the original code.
Author: Henrik Bengtsson [aut, cre, cph] ,
Hanjun Shin [aut, ctr, cph],
Harris Lazaris [ctr, cph] ,
Gangqing Hu [ctr, cph] ,
Xianghong Zhou [ctr]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between TopDom versions 0.10.1 dated 2021-05-06 and 0.10.2 dated 2026-08-31
TopDom-0.10.1/TopDom/NEWS |only TopDom-0.10.2/TopDom/.Rinstignore |only TopDom-0.10.2/TopDom/DESCRIPTION | 39 ++++++---- TopDom-0.10.2/TopDom/MD5 | 33 +++++--- TopDom-0.10.2/TopDom/NAMESPACE | 42 ++++++----- TopDom-0.10.2/TopDom/NEWS.md |only TopDom-0.10.2/TopDom/R/TopDom.R | 57 ++++++++++---- TopDom-0.10.2/TopDom/R/exdata.R | 15 ++- TopDom-0.10.2/TopDom/R/overlapScores.R | 8 +- TopDom-0.10.2/TopDom/README.md | 15 +-- TopDom-0.10.2/TopDom/build |only TopDom-0.10.2/TopDom/inst/CITATION | 80 +++++++++------------ TopDom-0.10.2/TopDom/inst/WORDLIST | 24 ++++++ TopDom-0.10.2/TopDom/man/TopDom-data.Rd | 15 ++- TopDom-0.10.2/TopDom/man/TopDom.Rd | 21 ++--- TopDom-0.10.2/TopDom/man/overlapScores.Rd | 8 +- TopDom-0.10.2/TopDom/tests/TopDom-options.R |only TopDom-0.10.2/TopDom/tests/countsPerRegion.R |only TopDom-0.10.2/TopDom/tests/ggplot.R |only TopDom-0.10.2/TopDom/tests/legacy-api.R |only TopDom-0.10.2/TopDom/tests/overlapScores-methods.R |only TopDom-0.10.2/TopDom/tests/readHiC.R |only TopDom-0.10.2/TopDom/tests/subsetByRegion.R |only TopDom-0.10.2/TopDom/tests/utils.R |only 24 files changed, 211 insertions(+), 146 deletions(-)
Title: Least Squares Sparse Principal Components Analysis
Description: Implements least-squares sparse principal component analysis with cardinality constraints. The package has an efficient C++ backend and provides functions for fitting, summarizing, comparing, and visualizing sparse principal component models. The approach follows Merola (2015) <doi:10.1111/anzs.12128> and Merola and Chen (2019) <doi:10.1016/j.jmva.2019.04.001>.
Author: Giovanni Maria Merola [aut, cre]
Maintainer: Giovanni Maria Merola <merolagio@gmail.com>
Diff between spca versions 1.1.1 dated 2026-07-10 and 1.1.3 dated 2026-08-31
spca-1.1.1/spca/R/helpers_and_validation.R |only spca-1.1.1/spca/R/utilities_and_cpp_wrappers.R |only spca-1.1.1/spca/inst/doc/spca_extended_vignette.R |only spca-1.1.1/spca/inst/doc/spca_extended_vignette.Rmd |only spca-1.1.1/spca/inst/doc/spca_extended_vignette.html |only spca-1.1.1/spca/man/figures/spca_Logo.png |only spca-1.1.1/spca/man/figures/spca_Logo_bordered.png |only spca-1.1.1/spca/man/show_contributions_spca.Rd |only spca-1.1.1/spca/vignettes/figures/spca_Logo.png |only spca-1.1.1/spca/vignettes/figures/spca_Logo_bordered.png |only spca-1.1.1/spca/vignettes/spca_extended_vignette.Rmd |only spca-1.1.3/spca/DESCRIPTION | 12 spca-1.1.3/spca/MD5 | 163 ++++--- spca-1.1.3/spca/NAMESPACE | 15 spca-1.1.3/spca/NEWS.md | 31 + spca-1.1.3/spca/R/Internal_utilities_and_cpp_wrappers.R |only spca-1.1.3/spca/R/accessors_for_obsolete.R |only spca-1.1.3/spca/R/compare_spca.R | 143 +++--- spca-1.1.3/spca/R/datasets.R | 4 spca-1.1.3/spca/R/imports.R | 2 spca-1.1.3/spca/R/methods_and_functions.R |only spca-1.1.3/spca/R/pca.R | 190 +-------- spca-1.1.3/spca/R/pca_methods.R |only spca-1.1.3/spca/R/plot.spca.R | 209 ++++------ spca-1.1.3/spca/R/print.spca.R | 35 - spca-1.1.3/spca/R/spca-package.R | 85 ++-- spca-1.1.3/spca/R/spca.R | 142 +++--- spca-1.1.3/spca/R/summary.spca.R | 40 - spca-1.1.3/spca/R/validation.R |only spca-1.1.3/spca/README.md | 52 +- spca-1.1.3/spca/build/vignette.rds |binary spca-1.1.3/spca/inst/doc/spca_extended.R |only spca-1.1.3/spca/inst/doc/spca_extended.Rmd |only spca-1.1.3/spca/inst/doc/spca_extended.html |only spca-1.1.3/spca/inst/doc/spca_intro.R | 3 spca-1.1.3/spca/inst/doc/spca_intro.Rmd | 22 - spca-1.1.3/spca/inst/doc/spca_intro.html | 104 ++-- spca-1.1.3/spca/man/aggregate_by_group.Rd | 90 ++-- spca-1.1.3/spca/man/change_loadings_sign_spca.Rd | 27 - spca-1.1.3/spca/man/change_sign.Rd |only spca-1.1.3/spca/man/change_weights_sign_spca.Rd |only spca-1.1.3/spca/man/compare_spca.Rd | 44 +- spca-1.1.3/spca/man/figures/README-pca_checks-1.png |binary spca-1.1.3/spca/man/figures/README-pca_checks-2.png |binary spca-1.1.3/spca/man/figures/README-pca_checks-3.png |only spca-1.1.3/spca/man/figures/spca_logo_octagon.png |only spca-1.1.3/spca/man/holzinger.Rd | 2 spca-1.1.3/spca/man/holzinger_scales.Rd | 4 spca-1.1.3/spca/man/is.spca.Rd | 14 spca-1.1.3/spca/man/new_spca.Rd | 16 spca-1.1.3/spca/man/pca.Rd | 11 spca-1.1.3/spca/man/plot.spca.Rd | 26 - spca-1.1.3/spca/man/print.spca.Rd | 18 spca-1.1.3/spca/man/qqplot_spca.Rd |only spca-1.1.3/spca/man/screeplot_spca.Rd |only spca-1.1.3/spca/man/show_correlations.Rd |only spca-1.1.3/spca/man/show_weights.Rd |only spca-1.1.3/spca/man/spca-package.Rd | 57 +- spca-1.1.3/spca/man/spca.Rd | 26 - spca-1.1.3/spca/man/spca_object.Rd | 32 + spca-1.1.3/spca/man/spca_screeplot.Rd | 40 - spca-1.1.3/spca/man/summary.spca.Rd | 22 - spca-1.1.3/spca/man/wachter_qqplot.Rd | 71 +-- spca-1.1.3/spca/src/pca.cpp | 34 - spca-1.1.3/spca/src/spca_fat.cpp | 46 +- spca-1.1.3/spca/src/spca_tall.cpp | 52 +- spca-1.1.3/spca/src/support_fat.cpp | 18 spca-1.1.3/spca/src/support_tall.cpp | 72 +-- spca-1.1.3/spca/src/utility_wrappers.cpp | 6 spca-1.1.3/spca/tests/testthat/helper-data.R | 12 spca-1.1.3/spca/tests/testthat/test-compare-plot.R | 84 ++-- spca-1.1.3/spca/tests/testthat/test-methods.R | 202 +++++++-- spca-1.1.3/spca/tests/testthat/test-new-spca.R | 4 spca-1.1.3/spca/tests/testthat/test-pca-plots.R | 140 ++++++ spca-1.1.3/spca/tests/testthat/test-pca.R | 6 spca-1.1.3/spca/tests/testthat/test-spca-power-methods.R | 2 spca-1.1.3/spca/tests/testthat/test-spca-selection.R | 2 spca-1.1.3/spca/tests/testthat/test-spca-structure.R | 10 spca-1.1.3/spca/tests/testthat/test-spca-validation.R | 4 spca-1.1.3/spca/vignettes/Extended_vignette_material/spca_JSS_article_results.rda |binary spca-1.1.3/spca/vignettes/figures/barplot-1.png |binary spca-1.1.3/spca/vignettes/figures/circplot-1.png |binary spca-1.1.3/spca/vignettes/figures/compare-1.png |binary spca-1.1.3/spca/vignettes/figures/groupplot-1.png |binary spca-1.1.3/spca/vignettes/figures/heatmap-1.png |binary spca-1.1.3/spca/vignettes/figures/intro-circular-1.png |binary spca-1.1.3/spca/vignettes/figures/intro-groups-1.png |binary spca-1.1.3/spca/vignettes/figures/intro-heatmap-1.png |binary spca-1.1.3/spca/vignettes/figures/intro-methods-1.png |binary spca-1.1.3/spca/vignettes/figures/intro-pca_checks-1.png |binary spca-1.1.3/spca/vignettes/figures/intro-pca_checks-2.png |binary spca-1.1.3/spca/vignettes/figures/intro-spca90-1.png |binary spca-1.1.3/spca/vignettes/figures/pca-1.png |binary spca-1.1.3/spca/vignettes/figures/qqplot-1.png |binary spca-1.1.3/spca/vignettes/figures/spca_logo_octagon.png |only spca-1.1.3/spca/vignettes/spca_extended.Rmd |only spca-1.1.3/spca/vignettes/spca_intro.Rmd | 22 - 97 files changed, 1320 insertions(+), 1148 deletions(-)
Title: SHAP Visualizations
Description: Visualizations for SHAP (SHapley Additive exPlanations), such
as waterfall plots, force plots, various types of importance plots,
dependence plots, and interaction plots. These plots act on a
'shapviz' object created from a matrix of SHAP values and a
corresponding feature dataset. Wrappers for the R packages 'xgboost',
'lightgbm', 'fastshap', 'shapr', 'h2o', 'treeshap', 'DALEX', and
'kernelshap' are added for convenience. By separating visualization
and computation, it is possible to display factor variables in graphs,
even if the SHAP values are calculated by a model that requires
numerical features. The plots are inspired by those provided by the
'shap' package in Python, but there is no dependency on it.
Author: Michael Mayer [aut, cre],
Adrian Stando [ctb]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between shapviz versions 0.10.3 dated 2025-10-13 and 0.10.4 dated 2026-08-31
shapviz-0.10.3/shapviz/man/figures/README-bee.svg |only shapviz-0.10.4/shapviz/DESCRIPTION | 10 shapviz-0.10.4/shapviz/MD5 | 72 - shapviz-0.10.4/shapviz/NEWS.md | 10 shapviz-0.10.4/shapviz/R/collapse_shap.R | 6 shapviz-0.10.4/shapviz/R/shapviz.R | 4 shapviz-0.10.4/shapviz/R/sv_dependence.R | 21 shapviz-0.10.4/shapviz/R/sv_dependence2D.R | 9 shapviz-0.10.4/shapviz/R/sv_force.R | 5 shapviz-0.10.4/shapviz/R/sv_importance.R | 2 shapviz-0.10.4/shapviz/R/sv_interaction.R | 5 shapviz-0.10.4/shapviz/R/sv_waterfall.R | 8 shapviz-0.10.4/shapviz/build/vignette.rds |binary shapviz-0.10.4/shapviz/data/miami.rda |binary shapviz-0.10.4/shapviz/inst/doc/basic_use.Rmd | 10 shapviz-0.10.4/shapviz/inst/doc/basic_use.html | 49 shapviz-0.10.4/shapviz/inst/doc/geographic.html | 15 shapviz-0.10.4/shapviz/inst/doc/multiple_output.html | 10 shapviz-0.10.4/shapviz/inst/doc/tidymodels.Rmd | 9 shapviz-0.10.4/shapviz/inst/doc/tidymodels.html | 37 shapviz-0.10.4/shapviz/man/collapse_shap.Rd | 6 shapviz-0.10.4/shapviz/man/figures/README-bee.png |only shapviz-0.10.4/shapviz/man/figures/README-dep.png |binary shapviz-0.10.4/shapviz/man/figures/README-force.svg | 507 ++++++++-- shapviz-0.10.4/shapviz/man/figures/README-imp.svg | 402 ++++++- shapviz-0.10.4/shapviz/man/figures/README-waterfall.svg | 495 ++++++++- shapviz-0.10.4/shapviz/man/figures/VIGNETTE-tidy-class-normal-dep1.png |binary shapviz-0.10.4/shapviz/man/figures/VIGNETTE-tidy-class-normal-imp.png |binary shapviz-0.10.4/shapviz/man/shapviz-package.Rd | 5 shapviz-0.10.4/shapviz/man/shapviz.Rd | 4 shapviz-0.10.4/shapviz/man/sv_dependence.Rd | 21 shapviz-0.10.4/shapviz/man/sv_dependence2D.Rd | 9 shapviz-0.10.4/shapviz/man/sv_force.Rd | 5 shapviz-0.10.4/shapviz/man/sv_importance.Rd | 4 shapviz-0.10.4/shapviz/man/sv_interaction.Rd | 7 shapviz-0.10.4/shapviz/man/sv_waterfall.Rd | 8 shapviz-0.10.4/shapviz/vignettes/basic_use.Rmd | 10 shapviz-0.10.4/shapviz/vignettes/tidymodels.Rmd | 9 38 files changed, 1431 insertions(+), 343 deletions(-)
Title: Functions for Pre-Processing Data for Multivariate Data
Visualisation using Tours
Description: This is a companion to the book Cook, D. and Laa, U. (2023) <https://dicook.github.io/mulgar_book/>
"Interactively exploring high-dimensional data and models in R".
by Cook and Laa. It contains useful functions for processing data in preparation for
visualising with a tour. There are also several sample data sets.
Author: Dianne Cook [aut, cre] ,
Ursula Laa [aut]
Maintainer: Dianne Cook <dicook@monash.edu>
Diff between mulgar versions 1.0.5 dated 2025-04-06 and 1.0.8 dated 2026-08-31
DESCRIPTION | 12 ++++++------ MD5 | 12 +++++++----- NEWS.md | 12 ++++++++++++ R/data.R | 13 +++++++++++++ R/pca.R | 4 +--- data/fake_trees.rda |only man/fake_trees.Rd |only man/mulgar-package.Rd | 1 + 8 files changed, 40 insertions(+), 14 deletions(-)
Title: Dynamic Multi-Species Size Spectrum Modelling
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Gustav Delius [cre, aut, cph] ,
Finlay Scott [aut, cph],
Julia Blanchard [aut, cph] ,
Ken Andersen [aut, cph] ,
Richard Southwell [ctb, cph]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 3.3.0 dated 2026-08-24 and 3.4.0 dated 2026-08-31
mizer-3.3.0/mizer/inst/limit_cycle.R |only mizer-3.3.0/mizer/man/assertExtensionChain.Rd |only mizer-3.3.0/mizer/man/baseMizerClass.Rd |only mizer-3.3.0/mizer/man/clearExtensionChain.Rd |only mizer-3.3.0/mizer/man/compareExtensionChains.Rd |only mizer-3.3.0/mizer/man/defineExtensionClasses.Rd |only mizer-3.3.0/mizer/man/defineOrCheckClass.Rd |only mizer-3.3.0/mizer/man/dispatchExtensions.Rd |only mizer-3.3.0/mizer/man/formatExtensionChain.Rd |only mizer-3.3.0/mizer/man/getRegisteredExtensions.Rd |only mizer-3.3.0/mizer/man/isSuffixChain.Rd |only mizer-3.3.0/mizer/man/providesDispatchMethods.Rd |only mizer-3.3.0/mizer/man/registerExtension.Rd |only mizer-3.3.0/mizer/man/registerExtensions.Rd |only mizer-3.3.0/mizer/man/usesExtensionDispatch.Rd |only mizer-3.4.0/mizer/DESCRIPTION | 8 mizer-3.4.0/mizer/MD5 | 259 +-- mizer-3.4.0/mizer/NAMESPACE | 18 mizer-3.4.0/mizer/NEWS.md | 268 +++ mizer-3.4.0/mizer/R/ArraySpeciesBySize-class.R | 81 mizer-3.4.0/mizer/R/ArrayTimeBySpeciesBySize-class.R | 18 mizer-3.4.0/mizer/R/MizerParams-class.R | 230 +- mizer-3.4.0/mizer/R/MizerScan-class.R | 8 mizer-3.4.0/mizer/R/MizerSim-class.R | 84 - mizer-3.4.0/mizer/R/calibrate.R | 25 mizer-3.4.0/mizer/R/diffusion.R | 2 mizer-3.4.0/mizer/R/extension.R | 180 ++ mizer-3.4.0/mizer/R/generic_methods.R | 15 mizer-3.4.0/mizer/R/getSteadyResidual.R | 636 ++++++- mizer-3.4.0/mizer/R/helpers.R | 163 + mizer-3.4.0/mizer/R/indicator_functions.R | 100 + mizer-3.4.0/mizer/R/info_signals.R | 32 mizer-3.4.0/mizer/R/manipulate_species.R | 27 mizer-3.4.0/mizer/R/plots.R | 14 mizer-3.4.0/mizer/R/project.R | 45 mizer-3.4.0/mizer/R/project_methods.R | 48 mizer-3.4.0/mizer/R/rate_functions.R | 35 mizer-3.4.0/mizer/R/registerExtensions.R | 563 ------ mizer-3.4.0/mizer/R/saveParams.R | 95 - mizer-3.4.0/mizer/R/scanModel.R | 2 mizer-3.4.0/mizer/R/setFishing.R | 54 mizer-3.4.0/mizer/R/setMetadata.R | 9 mizer-3.4.0/mizer/R/species_params.R | 611 ++++++- mizer-3.4.0/mizer/R/steady.R | 145 + mizer-3.4.0/mizer/R/steadyNewton.R | 21 mizer-3.4.0/mizer/R/steadyState.R | 32 mizer-3.4.0/mizer/R/summary_methods.R | 26 mizer-3.4.0/mizer/R/upgrade.R | 20 mizer-3.4.0/mizer/R/validSpeciesParams.R | 21 mizer-3.4.0/mizer/R/zzz.R | 2 mizer-3.4.0/mizer/data/NS_params.rda |binary mizer-3.4.0/mizer/data/NS_sim.rda |binary mizer-3.4.0/mizer/inst/WORDLIST | 60 mizer-3.4.0/mizer/inst/doc/mizer_vignette.html | 4 mizer-3.4.0/mizer/inst/llms.txt | 24 mizer-3.4.0/mizer/inst/skills/analyse-and-plot/SKILL.md | 9 mizer-3.4.0/mizer/inst/skills/analyse-and-plot/quick-reference.md | 5 mizer-3.4.0/mizer/inst/skills/analyse-stability/SKILL.md | 12 mizer-3.4.0/mizer/inst/skills/build-model/SKILL.md | 7 mizer-3.4.0/mizer/inst/skills/calibrate-model/SKILL.md | 13 mizer-3.4.0/mizer/inst/skills/change-parameters/SKILL.md | 64 mizer-3.4.0/mizer/inst/skills/change-parameters/quick-reference.md | 2 mizer-3.4.0/mizer/inst/skills/create-extension-package/SKILL.md | 438 ++--- mizer-3.4.0/mizer/inst/skills/extend-mizer/SKILL.md | 157 + mizer-3.4.0/mizer/inst/skills/run-simulation/SKILL.md | 9 mizer-3.4.0/mizer/inst/skills/upgrade-extension-package |only mizer-3.4.0/mizer/inst/skills/upgrade-mizer-code/SKILL.md | 350 +++- mizer-3.4.0/mizer/inst/skills/upgrade-mizer-code/references/mizer-3.2.md | 11 mizer-3.4.0/mizer/inst/skills/upgrade-mizer-code/references/mizer-3.3.md | 840 ++++------ mizer-3.4.0/mizer/inst/skills/upgrade-mizer-code/references/mizer-3.4.md |only mizer-3.4.0/mizer/inst/skills/use-extension-packages/SKILL.md | 166 - mizer-3.4.0/mizer/man/MizerParams-class.Rd | 6 mizer-3.4.0/mizer/man/MizerScan.Rd | 8 mizer-3.4.0/mizer/man/MizerSim-class.Rd | 6 mizer-3.4.0/mizer/man/NOther.Rd | 5 mizer-3.4.0/mizer/man/addSpecies.Rd | 2 mizer-3.4.0/mizer/man/coerceToExtensionClass.Rd | 26 mizer-3.4.0/mizer/man/completeSpeciesParams.Rd | 88 - mizer-3.4.0/mizer/man/distanceSSLogN.Rd | 34 mizer-3.4.0/mizer/man/dot-hasSlot.Rd |only mizer-3.4.0/mizer/man/ensureExtensionNamespaces.Rd | 4 mizer-3.4.0/mizer/man/extensionRequirements.Rd | 6 mizer-3.4.0/mizer/man/extensionVersions.Rd | 2 mizer-3.4.0/mizer/man/extension_needs_upgrading.Rd | 4 mizer-3.4.0/mizer/man/getEncounter.Rd | 2 mizer-3.4.0/mizer/man/getMeanWeight.Rd | 52 mizer-3.4.0/mizer/man/getSteadyResidual.Rd | 137 + mizer-3.4.0/mizer/man/get_f0_default.Rd | 8 mizer-3.4.0/mizer/man/get_gamma_default.Rd | 8 mizer-3.4.0/mizer/man/indicator_functions.Rd | 1 mizer-3.4.0/mizer/man/initialNOther-set.Rd | 5 mizer-3.4.0/mizer/man/isSteady.Rd | 23 mizer-3.4.0/mizer/man/length_at_size.Rd |only mizer-3.4.0/mizer/man/mizerEncounter.Rd | 2 mizer-3.4.0/mizer/man/objectExtensions.Rd | 4 mizer-3.4.0/mizer/man/other_mort.Rd |only mizer-3.4.0/mizer/man/plotYield.Rd | 3 mizer-3.4.0/mizer/man/project.Rd | 30 mizer-3.4.0/mizer/man/projectUntilSettled.Rd | 7 mizer-3.4.0/mizer/man/reconcileSpeciesParams.Rd |only mizer-3.4.0/mizer/man/recordExtension.Rd | 32 mizer-3.4.0/mizer/man/runExtensionUpgrades.Rd | 2 mizer-3.4.0/mizer/man/saveParams.Rd | 23 mizer-3.4.0/mizer/man/setComponent.Rd | 5 mizer-3.4.0/mizer/man/setMetadata.Rd | 9 mizer-3.4.0/mizer/man/setRateFunction.Rd | 5 mizer-3.4.0/mizer/man/signal_defaulted_length_weight.Rd |only mizer-3.4.0/mizer/man/signal_removed_species_params.Rd |only mizer-3.4.0/mizer/man/simExtensionClass.Rd | 4 mizer-3.4.0/mizer/man/slot-set.Rd |only mizer-3.4.0/mizer/man/slot.Rd |only mizer-3.4.0/mizer/man/slotNames.Rd |only mizer-3.4.0/mizer/man/species_params.Rd | 64 mizer-3.4.0/mizer/man/species_size_range_mask.Rd |only mizer-3.4.0/mizer/man/summary.Rd | 16 mizer-3.4.0/mizer/man/upgrade_s4_to_s3.Rd |only mizer-3.4.0/mizer/man/validObject.Rd |only mizer-3.4.0/mizer/man/validSpeciesParams.Rd | 90 - mizer-3.4.0/mizer/tests/testthat/_snaps/indicator_functions.md | 8 mizer-3.4.0/mizer/tests/testthat/helper.R | 28 mizer-3.4.0/mizer/tests/testthat/test-ArraySpeciesBySize-class.R | 41 mizer-3.4.0/mizer/tests/testthat/test-ArrayTimeBySpeciesBySize-class.R | 14 mizer-3.4.0/mizer/tests/testthat/test-MizerParams-class.R | 10 mizer-3.4.0/mizer/tests/testthat/test-MizerSim-class.R | 25 mizer-3.4.0/mizer/tests/testthat/test-backwards_compatibility.R | 8 mizer-3.4.0/mizer/tests/testthat/test-calibrate.R | 22 mizer-3.4.0/mizer/tests/testthat/test-extension.R | 122 + mizer-3.4.0/mizer/tests/testthat/test-getOscillationModeSim.R | 2 mizer-3.4.0/mizer/tests/testthat/test-getSteadyResidual.R | 347 ++++ mizer-3.4.0/mizer/tests/testthat/test-indicator_functions.R | 68 mizer-3.4.0/mizer/tests/testthat/test-manipulate_species.R | 27 mizer-3.4.0/mizer/tests/testthat/test-plots.R | 11 mizer-3.4.0/mizer/tests/testthat/test-project.R | 37 mizer-3.4.0/mizer/tests/testthat/test-project_methods.R | 14 mizer-3.4.0/mizer/tests/testthat/test-project_n.R | 2 mizer-3.4.0/mizer/tests/testthat/test-registerExtensions.R | 293 --- mizer-3.4.0/mizer/tests/testthat/test-saveParams.R | 109 + mizer-3.4.0/mizer/tests/testthat/test-scanModel.R | 12 mizer-3.4.0/mizer/tests/testthat/test-second_order_summary.R | 12 mizer-3.4.0/mizer/tests/testthat/test-second_order_w.R | 2 mizer-3.4.0/mizer/tests/testthat/test-setFishing.R | 53 mizer-3.4.0/mizer/tests/testthat/test-species_params.R | 558 ++++++ mizer-3.4.0/mizer/tests/testthat/test-steady.R | 171 ++ mizer-3.4.0/mizer/tests/testthat/test-steadyState.R | 31 mizer-3.4.0/mizer/tests/testthat/test-upgrade.R | 20 145 files changed, 6072 insertions(+), 2766 deletions(-)
Title: Data Analysis for IP Addresses and Networks
Description: Classes and functions for working with IP (Internet Protocol)
addresses and networks, inspired by the Python 'ipaddress' module.
Offers full support for both IPv4 and IPv6 (Internet Protocol versions
4 and 6) address spaces. It is specifically designed to work well with
the 'tidyverse'.
Author: David Hall [aut, cre]
Maintainer: David Hall <david.hall.physics@gmail.com>
Diff between ipaddress versions 1.0.3 dated 2025-08-22 and 1.0.4 dated 2026-08-31
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 4 ++++ R/address_ranges.R | 4 ++-- build/vignette.rds |binary inst/doc/ip-data.html | 5 +++-- inst/doc/recipes.R | 4 ++-- inst/doc/recipes.html | 34 ++++++++++++++-------------------- inst/include/ipaddress/IpAddress.h | 1 + man/exclude_networks.Rd | 4 ++-- man/ip_to_binary.Rd | 8 ++++---- man/ip_to_bytes.Rd | 10 +++++----- man/ip_to_hex.Rd | 8 ++++---- man/ip_to_integer.Rd | 8 ++++---- man/ipaddress-package.Rd | 7 ++++++- 15 files changed, 69 insertions(+), 64 deletions(-)
Title: General Bivariate Copula Theory and Many Utility Functions
Description: Extensive functions for bivariate copula (bicopula) computations and related operations
for bicopula theory. The lower, upper, product, and select other bicopula are implemented along
with operations including the diagonal, survival copula, dual of a copula, co-copula, and
numerical bicopula density. Level sets, horizontal and vertical sections are supported. Numerical
derivatives and inverses of a bicopula are provided through which simulation is implemented.
Bicopula composition, convex combination, asymmetry extension, and products also are provided.
Support extends to the Kendall Function as well as the Lmoments thereof. Kendall Tau,
Spearman Rho and Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer-
Wolff Sigma, tail dependency, tail order, skewness, and bivariate Lmoments are implemented, and
positive/negative quadrant dependency, left (right) increasing (decreasing) are available.
Other features include Kullback-Leibler Divergence, Vuong Procedure, spectral measure, [...truncated...]
Author: William Asquith [aut, cre]
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between copBasic versions 2.2.15 dated 2026-07-22 and 2.2.16 dated 2026-08-31
DESCRIPTION | 8 - MD5 | 41 +++++--- NEWS | 18 +++ R/CIRCcop.R | 9 + man/EuvCOP.Rd | 4 man/EvuCOP.Rd | 4 man/FGMcop.Rd | 6 - man/GLcop.Rd | 4 man/LzCOPpermsym.Rd | 4 man/MOcop.Rd | 2 man/derCOPinv.Rd | 60 ++++++------- man/figures/chck_wolfCOPtestCIRC_plot.jpg |only man/figures/chck_wolfCOPtestCIRC_plot.pdf |only man/figures/chck_wolfCOPtestCL_plotA.jpg |only man/figures/chck_wolfCOPtestCL_plotA.pdf |only man/figures/chck_wolfCOPtestCL_plotB.jpg |only man/figures/chck_wolfCOPtestCL_plotB.pdf |only man/footCOP.Rd | 6 - man/giniCOP.Rd | 138 +++++++++++++++--------------- man/hoefCOP.Rd | 24 +++-- man/joint.curvesCOP.Rd | 47 +++++----- man/joint.curvesCOP2.Rd | 23 ++--- man/wolfCOP.Rd | 2 man/wolfCOPtest.Rd | 42 ++++++--- man/wolfCOPtest_check.Rd |only 25 files changed, 249 insertions(+), 193 deletions(-)
Title: Cross-Entropy Clustering
Description: Splits data into Gaussian type clusters using the Cross-Entropy
Clustering ('CEC') method. This method allows for the simultaneous use of
various types of Gaussian mixture models, for performing the reduction of
unnecessary clusters, and for discovering new clusters by splitting them.
'CEC' is based on the work of Spurek, P. and Tabor, J. (2014)
<doi:10.1016/j.patcog.2014.03.006>.
Author: Kamieniecki Konrad [aut, cph],
Spurek Przemyslaw [ctb],
Simon Garnier [cre, ctb, cph]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between CEC versions 0.11.3 dated 2026-02-04 and 0.12.0 dated 2026-08-31
CEC-0.11.3/CEC/R/tests.R |only CEC-0.11.3/CEC/inst |only CEC-0.11.3/CEC/tests/run.cec.tests.R |only CEC-0.12.0/CEC/DESCRIPTION | 27 +++--- CEC-0.12.0/CEC/MD5 | 110 ++++++++++++++------------ CEC-0.12.0/CEC/NEWS.md | 37 ++++++++ CEC-0.12.0/CEC/R/cec.R | 112 +++++++++++++++++++-------- CEC-0.12.0/CEC/R/cec.params.R | 9 -- CEC-0.12.0/CEC/R/init.centers.R | 12 ++ CEC-0.12.0/CEC/R/model.covariance.R | 2 CEC-0.12.0/CEC/R/plot.cec.R | 8 + CEC-0.12.0/CEC/R/utils.R | 23 ----- CEC-0.12.0/CEC/README.md | 4 CEC-0.12.0/CEC/man/cec.Rd | 27 +++++- CEC-0.12.0/CEC/src/cec_r.cpp | 104 ++++++++++++++----------- CEC-0.12.0/CEC/src/cec_r.h | 5 - CEC-0.12.0/CEC/src/cec_starter.cpp | 12 ++ CEC-0.12.0/CEC/src/cec_starter.h | 7 + CEC-0.12.0/CEC/src/cluster.h | 36 ++++---- CEC-0.12.0/CEC/src/cov.h | 81 ++++++++++++++----- CEC-0.12.0/CEC/src/exceptions.h | 12 -- CEC-0.12.0/CEC/src/models/cov_utils.cpp | 21 +++-- CEC-0.12.0/CEC/src/models/fixed_covariance.h | 4 CEC-0.12.0/CEC/src/models/model.h | 6 - CEC-0.12.0/CEC/src/parallel_starter.h | 56 ++++++++----- CEC-0.12.0/CEC/src/params.h | 10 +- CEC-0.12.0/CEC/src/r_ext_ptr.h | 4 CEC-0.12.0/CEC/src/r_params.cpp | 5 - CEC-0.12.0/CEC/src/r_utils.h | 6 - CEC-0.12.0/CEC/src/split_starter.cpp | 19 +++- CEC-0.12.0/CEC/src/split_starter.h | 2 CEC-0.12.0/CEC/src/starter.cpp | 29 +++++- CEC-0.12.0/CEC/src/starter.h | 7 - CEC-0.12.0/CEC/src/vec.h | 4 CEC-0.12.0/CEC/tests/testthat |only CEC-0.12.0/CEC/tests/testthat.R |only 36 files changed, 514 insertions(+), 287 deletions(-)
Title: Standardized Metrics Based on the CDC and WHO Growth Charts
Description: Calculation of sex- and age-standardized growth metrics using
the LMS method (lambda-mu-sigma). The package includes functions for the CDC
Growth Charts (cdc_z) and the WHO Charts (who_z). Because CDC recommends
using the WHO Charts for children under 24 months and the CDC Charts among
older children, there can be large differences at age 2.0 years. For example,
a girl weighing 9.9 kg would be at the WHO 10th percentile on the day before
her second birthday, but at the CDC 2nd percentile the following day.
The 'gradual_z' function reduces the differences among 2- to 5-year-olds
by taking a weighted average of the CDC and WHO z-scores.
Author: David Freedman [aut, cre] ,
Carrie Daymont [ctb]
Maintainer: David Freedman <DavidSFreedman@gmail.com>
Diff between cdcanthro versions 0.3.0 dated 2026-07-28 and 0.4.0 dated 2026-08-31
cdcanthro-0.3.0/cdcanthro/R/cdcanthro.R |only cdcanthro-0.3.0/cdcanthro/R/sysdata.rda |only cdcanthro-0.3.0/cdcanthro/man/cdcanthro.Rd |only cdcanthro-0.4.0/cdcanthro/DESCRIPTION | 49 ++++++++++++--------- cdcanthro-0.4.0/cdcanthro/MD5 | 28 +++++++----- cdcanthro-0.4.0/cdcanthro/NAMESPACE | 7 ++- cdcanthro-0.4.0/cdcanthro/NEWS.md | 22 ++++++++- cdcanthro-0.4.0/cdcanthro/R/cdc_z.R |only cdcanthro-0.4.0/cdcanthro/R/grad_Z.R |only cdcanthro-0.4.0/cdcanthro/R/utils-anthro.R |only cdcanthro-0.4.0/cdcanthro/R/who_z.R |only cdcanthro-0.4.0/cdcanthro/R/zzz.R |only cdcanthro-0.4.0/cdcanthro/data/NHanes.rda |binary cdcanthro-0.4.0/cdcanthro/data/cdc_ref_data.rda |binary cdcanthro-0.4.0/cdcanthro/data/who_ref_data.rda |only cdcanthro-0.4.0/cdcanthro/man/NHanes.Rd | 3 - cdcanthro-0.4.0/cdcanthro/man/cdc_ref_data.Rd | 2 cdcanthro-0.4.0/cdcanthro/man/cdc_z.Rd |only cdcanthro-0.4.0/cdcanthro/man/cdcanthro-package.Rd |only cdcanthro-0.4.0/cdcanthro/man/gradual_z.Rd |only cdcanthro-0.4.0/cdcanthro/man/who_ref_data.Rd |only cdcanthro-0.4.0/cdcanthro/man/who_z.Rd |only 22 files changed, 74 insertions(+), 37 deletions(-)
Title: Get Network Representation of an R Package
Description: Tools from the domain of graph theory can be used to quantify the complexity
and vulnerability to failure of a software package. That is the guiding philosophy
of this package. 'pkgnet' provides tools to analyze the dependencies between functions
in an R package and between its imported packages. See the pkgnet website for vignettes
and other supplementary information.
Author: Brian Burns [aut, cre],
James Lamb [aut],
Jay Qi [aut]
Maintainer: Brian Burns <brian.burns.opensource@gmail.com>
Diff between pkgnet versions 0.6.0 dated 2026-01-27 and 0.6.1 dated 2026-08-31
DESCRIPTION | 6 - MD5 | 16 ++-- NEWS.md | 11 +++ R/FunctionReporter.R | 79 +++++++++++++++++++----- README.md | 1 tests/testthat/test-DependencyReporter-class.R | 5 - tests/testthat/test-FunctionReporter-class.R | 49 +++++++++++--- tests/testthat/test-InheritanceReporter-class.R | 7 -- tests/testthat/test-plotting.R | 18 ----- 9 files changed, 124 insertions(+), 68 deletions(-)
Title: Topological Data Analysis: Mapper Algorithm
Description: The Mapper algorithm from Topological Data Analysis, the steps are as follows 1. Define a filter (lens) function on the data. 2. Perform clustering within each level set. 3. Generate a complex from the clustering results.
Author: ChiChien Wang [aut, cre, trl],
Paul Pearson [ctb],
Daniel Muellner [ctb],
Gurjeet Singh [ctb]
Maintainer: ChiChien Wang <kennywang2003@gmail.com>
Diff between MapperAlgo versions 1.1.0 dated 2026-04-13 and 1.2.0 dated 2026-08-31
DESCRIPTION | 15 +- MD5 | 33 ++--- NAMESPACE | 12 + R/Cluster.R | 17 -- R/ClusterMlr3.R |only R/GMapper.R | 2 R/GridSearch.R | 1 R/MapperAlgo.R | 52 ++++++-- R/MapperCorrelation.R | 3 R/Plotter.R | 264 ++++++++++++++++++++++++++++++++++++++++- README.md | 26 +--- inst/example/TestingFMapper.R | 9 - inst/example/TestingGMapper.R | 15 +- inst/example/TestingMapper.R | 40 ++++-- man/MapperAlgo.Rd | 7 - man/MapperCorrelation.Rd | 9 - man/MapperPlotter.Rd | 17 ++ man/MapperPlotter3D.Rd |only man/perform_clustering_mlr3.Rd |only 19 files changed, 412 insertions(+), 110 deletions(-)
Title: Progress Bar with Remaining Time Forecast Method
Description: A simple progress bar showing estimated remaining time.
Multiple forecast methods and user defined forecast method for
the remaining time are supported.
Author: Yangzhuoran Yang [aut, cre]
Maintainer: Yangzhuoran Yang <yangyangzhuoran@gmail.com>
This is a re-admission after prior archival of version 0.1.0 dated 2020-04-28
Diff between lazybar versions 0.1.0 dated 2020-04-28 and 0.1.1 dated 2026-08-31
lazybar-0.1.0/lazybar/R/lpblapply.R |only lazybar-0.1.1/lazybar/DESCRIPTION | 16 lazybar-0.1.1/lazybar/MD5 | 13 lazybar-0.1.1/lazybar/NAMESPACE | 1 lazybar-0.1.1/lazybar/NEWS.md | 11 lazybar-0.1.1/lazybar/R/LazyBar.R | 527 ++++++++++++++------------- lazybar-0.1.1/lazybar/README.md | 168 ++++---- lazybar-0.1.1/lazybar/man/lazyProgressBar.Rd | 2 8 files changed, 386 insertions(+), 352 deletions(-)
Title: Read Data from European Data Format (EDF and EDF+) Files
Description: Import physiologic data stored in
the European Data Format (EDF and EDF+) into R.
Both EDF and EDF+ files are supported. Discontinuous
EDF+ files are not yet supported.
Author: Andreas Henelius [aut, cre],
Finnish Institute of Occupational Health [cph]
Maintainer: Andreas Henelius <andreas.henelius@iki.fi>
Diff between edf versions 1.0.0 dated 2016-04-22 and 1.0.1 dated 2026-08-31
DESCRIPTION | 15 +++++++++------ LICENSE | 2 +- MD5 | 27 ++++++++++++++------------- R/edf.R | 7 +++---- R/read_edf.R | 6 +++--- build |only man/create.variable.name.Rd | 1 - man/edf.Rd | 26 +++++++++++++++++++++++--- man/edf.char.to.num.Rd | 1 - man/parse.edf.annotations.Rd | 1 - man/parse.edf.global.header.Rd | 1 - man/parse.edf.signal.header.Rd | 1 - man/parse.event.Rd | 1 - man/read.edf.Rd | 7 +++---- man/trim.end.Rd | 1 - 15 files changed, 56 insertions(+), 41 deletions(-)
Title: Calculate Distance Measures for DataFrames
Description: It provides functions that calculate Mahalanobis distance, Euclidean distance, Manhattan distance, Chebyshev distance, Hamming distance, Canberra distance, Minkowski dissimilarity (distance defined for p >= 1), Cosine dissimilarity, Bhattacharyya dissimilarity, Jaccard distance, Hellinger distance, Bray-Curtis dissimilarity, Sorensen-Dice dissimilarity between each pair of species in a list of data frames. These statistics are fundamental in various fields, such as cluster analysis, classification, and other applications of machine learning and data mining, where assessing similarity or dissimilarity between data is crucial. The package is designed to be flexible and easily integrated into data analysis workflows, providing reliable tools for evaluating distances in multidimensional contexts.
Author: Flavio Gioia [aut, cre]
Maintainer: Flavio Gioia <flaviogioia.fg@gmail.com>
Diff between cmahalanobis versions 1.0.0 dated 2025-09-14 and 1.1.0 dated 2026-08-31
DESCRIPTION | 13 MD5 | 117 NAMESPACE | 17 R/cmahalanobis.R | 8009 ++++++++++++---------- README.md |only inst/CITATION |only inst/rmarkdown/template_report_cbhattacharyya.Rmd | 577 + inst/rmarkdown/template_report_cbraycurtis.Rmd | 528 - inst/rmarkdown/template_report_ccanberra.Rmd | 523 - inst/rmarkdown/template_report_cchebyshev.Rmd | 508 - inst/rmarkdown/template_report_ccosine.Rmd | 514 - inst/rmarkdown/template_report_ceuclide.Rmd | 499 - inst/rmarkdown/template_report_chamming.Rmd | 509 - inst/rmarkdown/template_report_chellinger.Rmd | 566 + inst/rmarkdown/template_report_cjaccard.Rmd | 539 - inst/rmarkdown/template_report_cmahalanobis.Rmd | 560 + inst/rmarkdown/template_report_cmanhattan.Rmd | 516 - inst/rmarkdown/template_report_cminkowski.Rmd | 521 - inst/rmarkdown/template_report_csorensendice.Rmd | 506 - man/cbhattacharyya.Rd | 119 man/cbraycurtis.Rd | 120 man/ccanberra.Rd | 119 man/cchebyshev.Rd | 47 man/ccosine.Rd | 119 man/ceuclide.Rd | 49 man/chamming.Rd | 119 man/chellinger.Rd | 120 man/cjaccard.Rd | 121 man/cmahalanobis.Rd | 51 man/cmanhattan.Rd | 47 man/cminkowski.Rd | 49 man/csorensendice.Rd | 118 man/figures |only man/generate_report_cbhattacharyya.Rd | 39 man/generate_report_cbraycurtis.Rd | 39 man/generate_report_ccanberra.Rd | 43 man/generate_report_cchebyshev.Rd | 39 man/generate_report_ccosine.Rd | 105 man/generate_report_ceuclide.Rd | 39 man/generate_report_chamming.Rd | 106 man/generate_report_chellinger.Rd | 107 man/generate_report_cjaccard.Rd | 107 man/generate_report_cmahalanobis.Rd | 42 man/generate_report_cmanhattan.Rd | 38 man/generate_report_cminkowski.Rd | 45 man/generate_report_csorensendice.Rd | 39 man/pvaluescbatt.Rd | 110 man/pvaluescbrcu.Rd | 41 man/pvaluesccanb.Rd | 109 man/pvaluesccheb.Rd | 47 man/pvaluesccosi.Rd | 109 man/pvaluesceucl.Rd | 45 man/pvalueschamm.Rd | 111 man/pvalueschell.Rd | 109 man/pvaluescjacc.Rd | 110 man/pvaluescmaha.Rd | 48 man/pvaluescmanh.Rd | 45 man/pvaluescmink.Rd | 53 man/pvaluescsore.Rd | 109 tests/testthat.R | 24 tests/testthat/cmahalanobis.R | 7879 ++++++++++++--------- 61 files changed, 15704 insertions(+), 10253 deletions(-)
Title: Meta Fuzzy Functions
Description: Implements Meta Fuzzy Functions (MFFs) for regression Tak and Ucan (2026) <doi:10.1016/j.asoc.2026.114592> by aggregating predictions from multiple base learners using membership weights learned in the prediction space of validation set. The package supports fuzzy and crisp meta-ensemble structures via Fuzzy C-Means (FCM) Tak (2018) <doi:10.1016/j.asoc.2018.08.009>, Possibilistic FCM (PFCM) Tak (2021) <doi:10.1016/j.ins.2021.01.024>, Gustafson–Kessel (GK) clustering, and k-means, and provides a workflow to (i) generate validation/test prediction matrices from common regression learners (linear and penalized regression via 'glmnet', random forests, gradient boosting with 'xgboost' and 'lightgbm'), (ii) fit cluster-wise meta fuzzy functions and compute membership-based weights, (iii) tune clustering-related hyperparameters (number of clusters/functions, fuzziness exponent, possibilistic regularization) via grid search on validation loss, and (iv) predict on new/test pre [...truncated...]
Author: Nihat Tak [aut, cre],
Sadik Coban [ctb]
Maintainer: Nihat Tak <nihattak@gmail.com>
Diff between MFF versions 0.2.3 dated 2026-08-24 and 0.2.4 dated 2026-08-31
DESCRIPTION | 10 +- MD5 | 43 +++++----- NEWS.md | 17 ++++ R/MFF-package.R | 2 R/evaluate.R | 19 ++++ R/methods-mff.R | 92 ++++++++++++++++++++-- R/mff.R | 67 +++++++++++----- R/predict.mff.R | 29 ++++-- R/tune.mff.R | 158 ++++++++++++++++++++++++++++++-------- R/utils-clustering.R | 53 ++++++++++++ R/utils-validation.R |only inst/doc/mff-workflow.R | 4 inst/doc/mff-workflow.Rmd | 13 +++ inst/doc/mff-workflow.html | 88 ++++++++++++--------- man/MFF-package.Rd | 2 man/mff.Rd | 9 +- man/plot.mff.Rd | 26 ++++-- man/tune.mff.Rd | 12 ++ tests/testthat/test-evaluate.R | 7 + tests/testthat/test-methods-mff.R | 13 +++ tests/testthat/test-mff-predict.R | 47 +++++++++++ tests/testthat/test-tune-mff.R | 72 +++++++++++++++++ vignettes/mff-workflow.Rmd | 13 +++ 23 files changed, 649 insertions(+), 147 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-15 2.6.3
2023-08-08 2.6.2
2022-12-20 2.6.1
2022-05-20 2.6.0
2022-01-26 2.5.1
2022-01-17 2.5.0
2021-11-26 2.4.0
2021-10-26 2.3.0
2021-09-23 2.2.0
2021-07-27 2.1.0
2021-02-24 2.0.1
2021-02-22 2.0.0
2021-01-20 1.10.0
2020-11-17 1.9.1
2020-11-11 1.9.0
2020-09-25 1.8.1
2020-08-10 1.8.0
2020-07-02 1.7.1
2020-05-14 1.7.0
2020-03-17 1.6.0
2020-02-16 1.5.1
2020-01-08 1.5.0
2019-12-19 1.4.0
2019-12-06 1.3.0
2019-11-28 1.2.1
2019-11-14 1.2.0
2019-10-23 1.1.0
2019-10-20 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-13 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-30 1.0.5
2023-09-13 1.0.4
2023-08-30 1.0.3
2020-10-06 1.0.2
2020-04-15 1.0.1
2020-04-01 1.0.0
2020-03-31 0.1.0