Title: Lightweight Tables via JSON Specs and JavaScript
Description: A lightweight grammar of tables. Build a table by declaring a JSON
spec (titles, spanners, row groups, footnotes, formatting functions, etc.); a tiny
vanilla JavaScript runtime builds the HTML table from the spec on page
load. Cells can hold inline plots (error bars, dot plots, mini line and bar charts) drawn
as SVG in the browser from the numbers alone. Tables can optionally be made
interactive (sorting, searching, filtering, pagination, column hiding,
expandable row detail, and CSV download) via a separate extension loaded
only when requested. No 'sass', no 'V8', no 'htmlwidgets' — just base
R and 'xfun' ('htmltools' is used only for the optional Shiny binding and
for embedding tables in other HTML output).
Author: Yihui Xie [aut, cre, cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between lt versions 0.4 dated 2026-09-01 and 0.5 dated 2026-10-16
lt-0.4/lt/tests/helper.R |only lt-0.4/lt/tests/test-ci/test-js.R |only lt-0.5/lt/DESCRIPTION | 24 lt-0.5/lt/MD5 | 118 +++- lt-0.5/lt/NAMESPACE | 14 lt-0.5/lt/NEWS.md | 22 lt-0.5/lt/R/interactive.R |only lt-0.5/lt/R/lt.R | 52 +- lt-0.5/lt/R/reexports.R |only lt-0.5/lt/R/render.R | 336 ++++++++----- lt-0.5/lt/R/shiny.R | 59 +- lt-0.5/lt/R/tab.R | 442 ++++++++++++++++-- lt-0.5/lt/README.md | 57 ++ lt-0.5/lt/inst/js/run-lt.js | 13 lt-0.5/lt/inst/www/lt-binding.js | 2 lt-0.5/lt/inst/www/lt-interactive.css |only lt-0.5/lt/inst/www/lt-interactive.js |only lt-0.5/lt/inst/www/lt-plot.css |only lt-0.5/lt/inst/www/lt-plot.js |only lt-0.5/lt/inst/www/lt.css | 61 -- lt-0.5/lt/inst/www/lt.js | 613 ------------------------- lt-0.5/lt/man/format.lt_tbl.Rd | 4 lt-0.5/lt/man/lt-package.Rd | 2 lt-0.5/lt/man/lt.Rd | 2 lt-0.5/lt/man/lt_align.Rd | 8 lt-0.5/lt/man/lt_css.Rd | 6 lt-0.5/lt/man/lt_date.Rd | 8 lt-0.5/lt/man/lt_dependency.Rd |only lt-0.5/lt/man/lt_dotplot.Rd |only lt-0.5/lt/man/lt_errorbar.Rd |only lt-0.5/lt/man/lt_export.Rd | 6 lt-0.5/lt/man/lt_footnote.Rd | 7 lt-0.5/lt/man/lt_format.Rd | 8 lt-0.5/lt/man/lt_group.Rd | 2 lt-0.5/lt/man/lt_header.Rd | 4 lt-0.5/lt/man/lt_hide.Rd |only lt-0.5/lt/man/lt_html.Rd | 7 lt-0.5/lt/man/lt_indent.Rd | 2 lt-0.5/lt/man/lt_interactive.Rd |only lt-0.5/lt/man/lt_label.Rd | 12 lt-0.5/lt/man/lt_merge.Rd | 6 lt-0.5/lt/man/lt_move.Rd | 8 lt-0.5/lt/man/lt_note.Rd | 2 lt-0.5/lt/man/lt_output.Rd | 2 lt-0.5/lt/man/lt_spanner.Rd | 5 lt-0.5/lt/man/lt_sparkline.Rd |only lt-0.5/lt/man/lt_spec.Rd |only lt-0.5/lt/man/lt_style.Rd | 7 lt-0.5/lt/man/lt_sub.Rd | 7 lt-0.5/lt/man/lt_width.Rd | 11 lt-0.5/lt/man/lt_wrap.Rd |only lt-0.5/lt/man/print.lt_tbl.Rd | 4 lt-0.5/lt/man/reexports.Rd |only lt-0.5/lt/tests/test-ci/helper.R |only lt-0.5/lt/tests/test-ci/test-controls-js.R |only lt-0.5/lt/tests/test-ci/test-detail-js.R |only lt-0.5/lt/tests/test-ci/test-export-js.R |only lt-0.5/lt/tests/test-ci/test-filter-api-js.R |only lt-0.5/lt/tests/test-ci/test-filter-js.R |only lt-0.5/lt/tests/test-ci/test-filter-typed-js.R |only lt-0.5/lt/tests/test-ci/test-fmt-js.R |only lt-0.5/lt/tests/test-ci/test-footnote-js.R |only lt-0.5/lt/tests/test-ci/test-group-js.R |only lt-0.5/lt/tests/test-ci/test-hide-js.R |only lt-0.5/lt/tests/test-ci/test-merge-js.R |only lt-0.5/lt/tests/test-ci/test-missing-js.R |only lt-0.5/lt/tests/test-ci/test-pager-js.R |only lt-0.5/lt/tests/test-ci/test-plot-js.R |only lt-0.5/lt/tests/test-ci/test-render-js.R |only lt-0.5/lt/tests/test-ci/test-resize-js.R |only lt-0.5/lt/tests/test-ci/test-search-js.R |only lt-0.5/lt/tests/test-ci/test-sort-js.R |only lt-0.5/lt/tests/test-ci/test-spanner-js.R |only lt-0.5/lt/tests/test-ci/test-style-js.R |only lt-0.5/lt/tests/test-ci/test-view-js.R |only lt-0.5/lt/tests/testit/test-interactive.R |only lt-0.5/lt/tests/testit/test-lt.R | 53 +- lt-0.5/lt/tests/testit/test-render.R | 144 ++++- lt-0.5/lt/tests/testit/test-snap.md | 35 + lt-0.5/lt/tests/testit/test-tab.R | 359 +++++++------- 80 files changed, 1339 insertions(+), 1195 deletions(-)
Title: Track 'ggplot2' Calls
Description: Provides a way to log 'ggplot' component calls, which can be
useful for debugging and understanding how 'ggplot' objects are created.
The logged calls can be printed, saved, and re-executed to reproduce the
original 'ggplot' object.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between gglogger versions 0.1.8 dated 2026-04-14 and 0.1.9 dated 2026-10-16
DESCRIPTION | 6 +-- MD5 | 5 +- NEWS.md |only R/zzz.R | 101 ++++++++++++++++++++++++++++++++++++++++++------------------ 4 files changed, 77 insertions(+), 35 deletions(-)
Title: Sampling Design for Spatially Explicit Capture-Recapture
Description: Tools for designing spatially explicit capture-recapture studies of animal populations. This is primarily a simulation manager for package 'secr'. Extensions in version 2.5.0 include costing and evaluation of detector spacing.
Author: Murray Efford [aut, cre] ,
Ian Durbach [ctb]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secrdesign versions 2.10.1 dated 2026-01-08 and 2.10.3 dated 2026-10-16
DESCRIPTION | 10 MD5 | 26 NEWS | 790 ++++++------- R/estimateSummary.R | 392 +++--- R/methods.R | 1170 +++++++++---------- R/run.scenarios.R | 2242 +++++++++++++++++++------------------ R/scenarioSummary.R | 577 ++++----- R/select.stats.R | 348 ++--- R/utility.R | 281 ++-- R/validate.R | 58 man/estimateSummary.Rd | 488 ++++---- man/run.scenarios.Rd | 788 ++++++------- man/secrdesign-package.Rd | 204 +-- tests/testthat/test-dynamictraps.R | 42 14 files changed, 3792 insertions(+), 3624 deletions(-)
Title: Parametric Modal Regression with Right Censoring
Description: Implements parametric modal regression for continuous positive
distributions of the exponential family and beyond (e.g., Log-Logistic,
Birnbaum-Saunders, Log-t) under right censoring. Provides functions to link the
conditional mode to a linear predictor using alternative parameterizations. Includes maximum
likelihood estimation via numerical optimization, asymptotic inference based on
the observed Fisher information matrix, and model diagnostics using randomized
quantile residuals. See Galarza and Lachos (2026) <doi:10.48550/arXiv.2603.07099>.
Author: Christian Galarza [aut, cre],
Victor Lachos [aut]
Maintainer: Christian Galarza <chedgala@espol.edu.ec>
Diff between ModalCens versions 0.2.0 dated 2026-08-21 and 0.3.0 dated 2026-10-16
DESCRIPTION | 14 +++++----- MD5 | 14 +++++----- NAMESPACE | 2 + NEWS.md | 14 ++++++++++ R/methods.R | 3 ++ R/modal_reg.R | 73 ++++++++++++++++++++++++++++++++++++++++++++++++++---- README.md | 35 ++++++++++++++++++++++--- man/modal_cens.Rd | 25 ++++++++++++++++-- 8 files changed, 153 insertions(+), 27 deletions(-)
Title: Detecting, Decomposing, and Stress-Testing Temporal Change in
Repeated Decision Systems
Description: Tools for detecting, decomposing, and testing temporal change in
repeated binary decision systems. Decomposes each change in the decision
rate into inflow (uptake) and outflow (reversal) through the
marginal-transition identity, separates net change from gross turnover,
and splits aggregate change into within-group and composition components
with a symmetric midpoint decomposition. A unit-level cluster bootstrap
gives intervals for every component and a global test of process
stability with family-wise-adjusted contrasts and simultaneous confidence
bands. Also provides prevalence and transition drift summaries, entropy
trends, group-differential drift, change-point diagnostics, robustness and
sensitivity analyses, an integrated audit, and a simulator for stable,
marginal, masked, abrupt, group-masked, and composition-change scenarios.
Complements the 'decisionpaths' package. Applications include algorithmic
audit, AI governance, education, health, and organisational research.
Author: Subir Hait [aut, cre]
Maintainer: Subir Hait <haitsubi@msu.edu>
Diff between DecisionDrift versions 0.1.0 dated 2026-04-16 and 0.2.0 dated 2026-10-16
DESCRIPTION | 44 - MD5 | 54 +- NAMESPACE | 12 NEWS.md | 56 ++ R/dd_audit.R | 664 +++++++++++++++++----------- R/dd_changepoint.R | 433 +++++++++--------- R/dd_cluster_bootstrap.R |only R/dd_decompose.R |only R/dd_engine.R |only R/dd_global_test.R |only R/dd_group_decompose.R |only R/dd_indices.R | 225 +++++---- R/dd_simulate.R |only R/dd_transition.R | 315 +++++++------ README.md | 65 ++ build/vignette.rds |binary inst/WORDLIST | 54 +- inst/doc/DecisionDrift.R | 39 + inst/doc/DecisionDrift.Rmd | 832 ++++++++++++++++++++---------------- inst/doc/DecisionDrift.html | 419 ++++++++++++++---- inst/simulation |only man/dd_audit.Rd | 80 ++- man/dd_changepoint.Rd | 16 man/dd_cluster_bootstrap.Rd |only man/dd_decompose.Rd |only man/dd_global_test.Rd |only man/dd_group_decompose.Rd |only man/dd_indices.Rd | 13 man/dd_simulate.Rd |only man/dd_transition.Rd | 26 - man/plot.dd_decompose.Rd |only man/plot.dd_global_test.Rd |only man/plot.dd_group_decompose.Rd |only tests/testthat/test-DecisionDrift.R | 735 +++++++++++++++---------------- tests/testthat/test-v020.R |only vignettes/DecisionDrift.Rmd | 832 ++++++++++++++++++++---------------- 36 files changed, 2903 insertions(+), 2011 deletions(-)
Title: Lightweight 'CUDA' Numerical Computing
Description: Provides a lightweight interface to graphics processing unit
(GPU)-accelerated numerical computing using 'CUDA'. Dense tensors, sparse
matrices, decompositions, distances, exact nearest neighbours, clustering,
graph workflows, and embeddings share one consistent interface. The native
backend discovers the 'NVIDIA CUDA Driver API', 'cuBLAS', and 'cuSOLVER'
libraries at runtime without bundling 'LibTorch' or the 'CUDA Runtime'.
Stage-level provenance records the backend, device, and data transfers used
by each result. A portable implementation supports package validation on
systems without 'CUDA'. Background for the included Leiden community
detection and uniform manifold approximation and projection methods is given
by Traag, Waltman and van Eck (2019)
<doi:10.1038/s41598-019-41695-z> and McInnes et al. (2018)
<doi:10.21105/joss.00861>, respectively.
Author: Yaoxiang Li [aut, cre]
Maintainer: Yaoxiang Li <liyaoxiang@outlook.com>
Diff between cudaverse versions 0.4.1 dated 2026-09-10 and 0.4.2 dated 2026-10-16
DESCRIPTION | 6 MD5 | 242 NAMESPACE | 142 NEWS.md | 309 R/algorithms.R | 3788 +++---- R/backend-native.R | 1839 +-- R/backend.R | 1684 +-- R/cudaverse-package.R | 10 R/embeddings.R | 1564 +-- R/graph.R | 858 - R/memory.R | 308 R/provenance.R | 1440 +- R/sparse.R | 1632 +-- R/tensor.R | 2479 ++-- README.md | 353 build/partial.rdb |only build/vignette.rds |binary inst/WORDLIST | 85 inst/benchmarks/README.md | 294 inst/benchmarks/contract.csv | 34 inst/benchmarks/dense.R | 34 inst/benchmarks/pca-knn.R | 28 inst/benchmarks/sparse.R | 30 inst/doc/backend-provenance.R | 148 inst/doc/backend-provenance.Rmd | 344 inst/doc/backend-provenance.html | 1028 +- inst/doc/backend-support.R | 114 inst/doc/backend-support.Rmd | 246 inst/doc/backend-support.html | 1053 +- inst/doc/getting-started.R | 197 inst/doc/getting-started.Rmd | 351 inst/doc/getting-started.html | 1021 +- inst/doc/gpu-setup.R | 83 inst/doc/gpu-setup.Rmd | 389 inst/doc/gpu-setup.html | 1100 +- inst/doc/performance.R | 13 inst/doc/performance.Rmd | 272 inst/doc/performance.html | 1052 +- inst/kernels/SHA256SUMS | 2 inst/kernels/cudaverse_dense_kernels.ptx | 164 inst/reports/THIRD_PARTY_LICENSES.md | 42 inst/reports/backend-capability-matrix.csv | 80 inst/reports/benchmarks/CP05-SMOKE.md | 80 inst/reports/benchmarks/CP07-FULL-CHECK.log | 2 inst/reports/benchmarks/CP07-FULL-RUN.log | 68 inst/reports/benchmarks/CP07-FULL-SUMMARY-CHECK.log | 2 inst/reports/benchmarks/CP07-FULL.json |10102 ++++++++++---------- inst/reports/benchmarks/CP07-FULL.md | 196 inst/reports/benchmarks/CP07-SMOKE.json | 2922 ++--- inst/reports/benchmarks/CP07-SMOKE.md | 124 inst/reports/native/STAGE1.md | 124 inst/reports/native/STAGE2.md | 124 inst/reports/native/STAGE3.md | 136 inst/reports/native/STAGE4.md | 170 inst/reports/native/STAGE5-CONSOLIDATION.md | 168 inst/reports/native/consolidation-rtx2000.json | 2590 ++--- inst/reports/native/phase2-rtx2000.json | 3320 +++--- inst/reports/native/phase3-rtx2000.json | 2310 ++-- inst/reports/native/phase4-rtx2000.json | 2612 ++--- inst/reports/native/session-contract-rtx2000.json | 88 inst/reports/native/stage1-rtx2000.json | 840 - inst/reports/sbom.cdx.json | 126 man/as_adjacency_matrix.Rd | 46 man/cuda_available.Rd | 38 man/cuda_diagnostics.Rd | 58 man/cuda_diffusion_map.Rd | 102 man/cuda_distance.Rd | 92 man/cuda_kmeans.Rd | 116 man/cuda_knn.Rd | 120 man/cuda_knn_graph.Rd | 80 man/cuda_leiden.Rd | 60 man/cuda_louvain.Rd | 60 man/cuda_memory_info.Rd | 74 man/cuda_pca.Rd | 98 man/cuda_sparse.Rd | 86 man/cuda_svd.Rd | 72 man/cuda_tensor.Rd | 72 man/cuda_tsne.Rd | 92 man/cuda_umap.Rd | 110 man/cudatensor-subset.Rd | 84 man/cudaverse-package.Rd | 62 man/dimnames.cudasparse.Rd | 36 man/embedding_coordinates.Rd | 50 man/figures/cudaverse-logo.svg | 240 man/figures/logo.svg | 204 man/predict.cuda_kmeans.Rd | 100 man/predict.cuda_pca.Rd | 90 man/sparse_info.Rd | 42 man/sparse_matmul_dense.Rd | 48 man/sparse_matvec.Rd | 44 man/sparse_normalize.Rd | 80 man/sparse_row_sums.Rd | 50 man/t.cudasparse.Rd | 48 man/tensor_matmul.Rd | 22 man/tensor_reshape.Rd | 62 man/to_dgCMatrix.Rd | 40 src/native_backend.cpp | 104 tests/testthat.R | 8 tests/testthat/helper-torch.R | 20 tests/testthat/setup-backends.R | 6 tests/testthat/test-algorithms.R | 1740 +-- tests/testthat/test-backend-contract.R | 2198 ++-- tests/testthat/test-base-topk.R | 384 tests/testthat/test-benchmark-contract.R | 68 tests/testthat/test-capability-matrix.R | 42 tests/testthat/test-embeddings.R | 194 tests/testthat/test-graph.R | 350 tests/testthat/test-memory.R | 306 tests/testthat/test-native-backend.R | 3929 +++---- tests/testthat/test-provenance-algorithms.R | 514 - tests/testthat/test-provenance-embeddings.R | 392 tests/testthat/test-provenance-graph.R | 250 tests/testthat/test-provenance-sparse.R | 258 tests/testthat/test-public-backend-conformance.R | 906 - tests/testthat/test-sce-input.R | 580 - tests/testthat/test-sparse.R | 558 - tests/testthat/test-tensor.R | 886 - tests/testthat/test-tf32.R |only vignettes/backend-provenance.Rmd | 344 vignettes/backend-support.Rmd | 246 vignettes/getting-started.Rmd | 351 vignettes/gpu-setup.Rmd | 389 vignettes/performance.Rmd | 272 123 files changed, 34782 insertions(+), 34153 deletions(-)
Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Description: Implements spatial and spatiotemporal GLMMs (Generalized Linear
Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial
Differential Equation) Gaussian Markov random field approximation to
Gaussian random fields. One common application is for spatially explicit
species distribution models (SDMs).
See Anderson et al. (2025) <doi:10.18637/jss.v115.i02>.
Author: Sean C. Anderson [aut, cre] ,
Eric J. Ward [aut] ,
Philina A. English [aut] ,
Lewis A. K. Barnett [aut] ,
James T. Thorson [aut, cph] ,
Joe Watson [ctb] ,
Julia Indivero [ctb] ,
Jillian C. Dunic [ctb] ,
Joseph Barss [ctb],
Cole C. Monnahan [ctb, cph] [...truncated...]
Maintainer: Sean C. Anderson <sean@seananderson.ca>
Diff between sdmTMB versions 1.1.0 dated 2026-07-03 and 1.2.0 dated 2026-10-16
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Title: Shape Constrained Additive Models
Description: Generalized additive models under shape
constraints on the component functions of the linear predictor.
Models can include multiple shape-constrained (univariate
and bivariate) and unconstrained terms. Routines of the
package 'mgcv' are used to set up the model matrix, print,
and plot the results. Multiple smoothing parameter
estimation by the Generalized Cross Validation or similar.
See Pya and Wood (2015) <doi:10.1007/s11222-013-9448-7>
for an overview. A broad selection of shape-constrained
smoothers, linear functionals of smooths with shape constraints,
and Gaussian models with AR1 residuals.
Author: Natalya Pya [aut, cre]
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-22 dated 2026-03-12 and 1.2-23 dated 2026-10-16
ChangeLog | 10 DESCRIPTION | 8 MD5 | 29 +- NAMESPACE | 11 - R/bivar.smooth.const.R | 303 ++++++++++++++++++++++++++++-- R/check.analytical.R | 6 R/plot.r | 9 R/predict.scam.R | 18 + R/scam.r | 11 - build/partial.rdb |binary man/Predict.matrix.mpi.smooth.Rd | 4 man/model.matrix.scam.Rd |only man/scam.Rd | 2 man/smooth.construct.tedi.smooth.spec.Rd |only man/smooth.construct.tedmd.smooth.spec.Rd | 28 +- man/smooth.construct.tedmi.smooth.spec.Rd | 29 +- man/smooth.construct.teid.smooth.spec.Rd |only 17 files changed, 399 insertions(+), 69 deletions(-)
Title: Programmatically Collect Normalized News from (Almost) Any
Website
Description: Programmatically collect normalized news from
(almost) any website. An 'R' clone of the
<https://github.com/kotartemiy/newscatcher> 'Python' module.
Author: Novica Nakov [aut, cre],
Teofil Nakov [ctb],
Artem Bugara [ctb],
Discindo [cph]
Maintainer: Novica Nakov <nnovica@gmail.com>
Diff between newscatcheR versions 0.1.2 dated 2023-09-20 and 0.1.3 dated 2026-10-16
newscatcheR-0.1.2/newscatcheR/inst/doc/newscatcheR.Rmd |only newscatcheR-0.1.2/newscatcheR/vignettes/newscatcheR.Rmd |only newscatcheR-0.1.3/newscatcheR/DESCRIPTION | 16 newscatcheR-0.1.3/newscatcheR/LICENSE | 4 newscatcheR-0.1.3/newscatcheR/MD5 | 68 newscatcheR-0.1.3/newscatcheR/NAMESPACE | 16 newscatcheR-0.1.3/newscatcheR/NEWS.md | 16 newscatcheR-0.1.3/newscatcheR/R/check_url.R | 61 newscatcheR-0.1.3/newscatcheR/R/describe_url.R | 60 newscatcheR-0.1.3/newscatcheR/R/filter_helpers.R | 90 - newscatcheR-0.1.3/newscatcheR/R/filter_urls.R | 170 +- newscatcheR-0.1.3/newscatcheR/R/get_headlines.R | 66 newscatcheR-0.1.3/newscatcheR/R/get_news.R | 108 - newscatcheR-0.1.3/newscatcheR/R/package_rss.R | 34 newscatcheR-0.1.3/newscatcheR/README.md | 332 ++-- newscatcheR-0.1.3/newscatcheR/build/vignette.rds |binary newscatcheR-0.1.3/newscatcheR/inst/CITATION |only newscatcheR-0.1.3/newscatcheR/inst/doc/newscatcheR.R | 73 - newscatcheR-0.1.3/newscatcheR/inst/doc/newscatcheR.html | 692 +++------- newscatcheR-0.1.3/newscatcheR/inst/doc/newscatcheR.qmd |only newscatcheR-0.1.3/newscatcheR/man/check_url.Rd | 42 newscatcheR-0.1.3/newscatcheR/man/describe_url.Rd | 50 newscatcheR-0.1.3/newscatcheR/man/figures |only newscatcheR-0.1.3/newscatcheR/man/filter_urls.Rd | 72 - newscatcheR-0.1.3/newscatcheR/man/get_headlines.Rd | 82 - newscatcheR-0.1.3/newscatcheR/man/get_news.Rd | 74 - newscatcheR-0.1.3/newscatcheR/man/newscatcheR-package.Rd | 8 newscatcheR-0.1.3/newscatcheR/man/package_rss.Rd | 56 newscatcheR-0.1.3/newscatcheR/man/show_countries.Rd | 44 newscatcheR-0.1.3/newscatcheR/man/show_languages.Rd | 42 newscatcheR-0.1.3/newscatcheR/man/show_topics.Rd | 44 newscatcheR-0.1.3/newscatcheR/tests/testthat.R | 8 newscatcheR-0.1.3/newscatcheR/tests/testthat/test-check_url.R | 17 newscatcheR-0.1.3/newscatcheR/tests/testthat/test-decribe_url.R | 16 newscatcheR-0.1.3/newscatcheR/tests/testthat/test-filter_urls.R | 111 - newscatcheR-0.1.3/newscatcheR/tests/testthat/test-get_headlines.R | 29 newscatcheR-0.1.3/newscatcheR/tests/testthat/test-get_news.R | 58 newscatcheR-0.1.3/newscatcheR/vignettes/newscatcheR.qmd |only 38 files changed, 1213 insertions(+), 1346 deletions(-)
Title: Markov Random Field Models for Image Analysis
Description: Model fitting, sampling and visualization
for the (Hidden) Markov Random Field model with pairwise interactions and
general interaction structure from
Freguglia, Garcia & Bicas (2020) <doi:10.1002/env.2613>,
which has many popular models used in 2-dimensional lattices
as particular cases, like the Ising Model and Potts Model.
A complete manuscript describing the package is available in
Freguglia & Garcia (2022) <doi:10.18637/jss.v101.i08>.
Author: Victor Freguglia [aut, cre]
Maintainer: Victor Freguglia <victorfreguglia@gmail.com>
Diff between mrf2d versions 1.0 dated 2022-01-25 and 1.0.3 dated 2026-10-16
DESCRIPTION | 17 MD5 | 152 +-- NAMESPACE | 92 +- NEWS.md | 64 - R/RcppExports.R | 142 +-- R/array_vector_conversions.R | 356 +++---- R/basis_functions.R | 216 ++-- R/cpmrf2d.R | 76 - R/example_data.R | 124 +- R/family.R | 112 +- R/fit_ghm.R | 456 +++++----- R/fit_icm.R | 36 R/fit_sa.R | 330 +++---- R/hmrfout.R | 116 +- R/mrf2d.R | 16 R/mrfi_class.R | 368 ++++---- R/mrfi_methods.R | 374 ++++---- R/mrfout.R | 293 +++--- R/plot.R | 156 +-- R/pseudo_likelihood.R | 328 +++---- R/rmrf.R | 438 ++++----- R/suf_stat.R | 402 ++++---- R/zzz.R | 12 README.md | 277 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 32 inst/REFERENCES.bib | 158 +-- inst/doc/mrf2d-family.R | 48 - inst/doc/mrf2d-family.Rmd | 168 +-- inst/doc/mrf2d-family.html | 872 +++++++++---------- inst/doc/three-dimensions-on-mrf2d.R | 150 +-- inst/doc/three-dimensions-on-mrf2d.Rmd | 348 +++---- inst/doc/three-dimensions-on-mrf2d.html | 1118 +++++++++++++------------ man/Z_potts.Rd | 50 - man/basis_functions.Rd | 90 +- man/bold5000.Rd | 60 - man/cpmrf2d.Rd | 86 - man/data_examples.Rd | 64 - man/dplot.Rd | 108 +- man/fit_ghm.Rd | 236 ++--- man/fit_pl.Rd | 138 +-- man/fit_sa.Rd | 252 ++--- man/hmrfout.Rd | 50 - man/mrf2d-family.Rd | 138 +-- man/mrf2d-package.Rd | 59 - man/mrfi-class.Rd | 336 +++---- man/mrfout.Rd | 50 - man/pl_mrf2d.Rd | 92 +- man/plot.mrfi.Rd | 98 +- man/rmrf2d.Rd | 250 ++--- man/rmrf2d_mc.Rd | 140 +-- man/smr_array.Rd | 128 +- man/smr_stat.Rd | 132 +- src/Makevars |only src/Makevars.win |only src/conditional_probability.cpp | 64 - src/gibbs_sampler_mrf.cpp | 4 src/pseudo_likelihood.cpp | 127 ++ tests/testthat.R | 8 tests/testthat/test-array_vector_conversions.R | 50 - tests/testthat/test-basis_functions.R | 44 tests/testthat/test-cohist.R | 6 tests/testthat/test-cp_mrf2d.R | 38 tests/testthat/test-fit_ghm.R | 92 +- tests/testthat/test-fit_icm.R | 8 tests/testthat/test-fit_sa.R | 30 tests/testthat/test-hmrfout.R | 52 - tests/testthat/test-mrfi_class.R | 116 +- tests/testthat/test-mrfout.R | 74 - tests/testthat/test-plot.R | 8 tests/testthat/test-pseudo_likelihood.R | 88 - tests/testthat/test-rmrf2d.R | 106 +- tests/testthat/test-rmrf2d_mc.R | 14 tests/testthat/test-smr_functions.R | 58 - tests/testthat/test-suf_stat.R | 70 - vignettes/mrf2d-family.Rmd | 168 +-- vignettes/three-dimensions-on-mrf2d.Rmd | 348 +++---- 78 files changed, 6112 insertions(+), 5865 deletions(-)
Title: Dirichlet Regression
Description: Implements Dirichlet regression models.
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier <marco_maier@posteo.de>
Diff between DirichletReg versions 0.7-2 dated 2025-05-30 and 0.7-3 dated 2026-10-16
.Rinstignore | 2 DESCRIPTION | 20 MD5 | 68 - NAMESPACE | 88 - NEWS | 137 +- R/DR_LL_alt.R | 2 R/DR_LL_common.R | 2 R/DR_data.R | 224 +-- R/DirichReg.R | 6 R/Dirichlet.R | 8 R/plot_DRdata_4d.R | 2 R/print.DirichletRegModel.R | 5 R/summary.DirichletRegModel.R | 6 R/sysdata.rda |binary R/zzz.R | 10 build/partial.rdb |binary build/vignette.rds |binary data/ArcticLake.RData |binary data/BloodSamples.RData |binary data/GlacialTills.RData |binary data/ReadingSkills.RData |binary data/Rocks.RData |binary inst/CITATION | 10 inst/NEWS.Rd | 59 - inst/NEWS.pdf |binary inst/doc/DirichletReg-vig.R | 397 +++--- inst/doc/DirichletReg-vig.Rmd | 19 inst/doc/DirichletReg-vig.html | 1770 +++++++++++++++--------------- src/c_msg_translation.h |only src/ddirichlet.c | 17 src/init.c | 5 src/rdirichlet.c | 7 tests/testthat.R | 7 tests/testthat/test-ArcticTests_AltPar.R | 383 +++--- tests/testthat/test-ArcticTests_CommPar.R | 446 +++---- tests/testthat/test-DR_data.R |only vignettes/DirichletReg-vig.Rmd | 19 37 files changed, 1875 insertions(+), 1844 deletions(-)
Title: Tidy Data and Workflow Layer for Epidemic Nowcasting
Description: Defines tidy data structures and package-agnostic workflows for
epidemiological nowcasting. The 'tbl_now' class records event, report, and
revision dates alongside strata, covariates tagged by model component,
censoring, and reporting-delay metadata while remaining compatible with 'dplyr'. Tools
support validation, manipulation, diagnostics, visualization, format
conversion, retrospective evaluation, and multiple modelling engines. The
'tbl_nowcast' class standardizes probabilistic predictions for plotting,
scoring, comparison, and ensembling.
Author: Rodrigo Zepeda-Tello [aut, cre] ,
Rami Yaari [aut] ,
Matteo Perini [aut] ,
Teresa Yamana [ctb] ,
Jeffrey Shaman [ctb] ,
Columbia University in the City of New York [cph, fnd]
Maintainer: Rodrigo Zepeda-Tello <rzepeda17@gmail.com>
Diff between tbl.now versions 1.0.0 dated 2026-09-21 and 1.2.0 dated 2026-10-16
DESCRIPTION | 27 - MD5 | 104 +++-- NAMESPACE | 16 NEWS.md | 151 ++++++++ R/add_temporal_effects.R | 108 ++++- R/adders_changers_and_removers.R | 192 ++++++++++ R/align_weeks.R | 3 R/backtest_checkpoint.R |only R/backtest_combine.R |only R/compute_temporal_effects.R | 22 - R/converters.R | 108 ++++- R/diagnose.R | 27 + R/dplyr_generics.R | 19 + R/getters.R | 23 + R/nowcast_ensemble.R | 94 ++++- R/nowcast_methods.R | 79 ++++ R/nowcast_score.R | 445 ++++++++++++++++++++---- R/pillar_exts.R | 18 R/revision.R | 6 R/simulate_batch.R | 7 R/tbl_now.R | 43 ++ R/temporal_effects.R | 18 R/tidy.R | 46 +- R/to_count.R | 10 R/update.R | 3 R/utils.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/tbl.now.html | 6 man/add.Rd | 43 ++ man/add_temporal_effects.Rd | 21 - man/backtest_combine.Rd |only man/nowcast_backtest.Rd | 95 +++++ man/nowcast_data_getters.Rd | 14 man/nowcast_ensemble.Rd | 22 + man/nowcast_weights.Rd | 22 + man/tbl.now-package.Rd | 2 man/tbl_now.Rd | 13 man/temporal_effects.Rd | 20 - man/tidy.delay_distribution.Rd | 4 tests/testthat/test-backtest-checkpoint.R |only tests/testthat/test-backtest-combine.R |only tests/testthat/test-backtest-common-targets.R |only tests/testthat/test-backtest-parallel.R |only tests/testthat/test-batch_screen.R | 13 tests/testthat/test-changers.R | 63 +++ tests/testthat/test-complete_zeroes.R | 6 tests/testthat/test-converter-epidist.R | 43 +- tests/testthat/test-converter-epinow2.R | 6 tests/testthat/test-converters.R | 4 tests/testthat/test-engines-covariates.R | 2 tests/testthat/test-nowcast_backends.R | 54 ++ tests/testthat/test-nowcast_ensemble.R | 118 ++++++ tests/testthat/test-nowcast_score.R | 30 + tests/testthat/test-temporal_effects.R | 30 - tests/testthat/test-temporal_effects_calendar.R |only tests/testthat/test-tidy.R | 46 +- 57 files changed, 1963 insertions(+), 286 deletions(-)
Title: Design and Analysis of Intertidal Chamber Experiments
Description: Facilitates the design and analysis of intertidal chamber
experiments as described in Pham & Sokolova (2026)
<doi:10.64898/2026.09.28.754745>. It supports generating experimental
profiles for 'ElectricBlue' intertidal chambers, reading log files,
and checking actual chamber conditions against designed profiles. It
also helps read log files from 'EnvLogger' robomussels (or temperature
loggers) and 'Pulse V2' heart rate loggers, and provides an algorithm
to extract heart rates from 'Pulse V2' records. The acronym stands for
Research Assistant in Marine Biology at the University of Rostock.
Author: Duy Nghia Pham [aut, cre] ,
Inna M. Sokolova [ctb]
Maintainer: Duy Nghia Pham <nghiapham@yandex.com>
Diff between rambur versions 0.5.5 dated 2026-10-16 and 0.5.6 dated 2026-10-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/pulse.hr.R | 8 +++++--- man/pulse.hr.Rd | 8 +++++--- 4 files changed, 17 insertions(+), 13 deletions(-)
Title: Extract from the Scottish Health and Social Care Open Data
Platform
Description: Extract and interact with data from the Scottish Health and
Social Care Open Data platform <https://www.opendata.nhs.scot>.
Author: Public Health Scotland [cph],
Csilla Scharle [cre, aut],
James Hayes [aut] ,
David Aikman [aut],
Ross Hull [aut],
Haritha Jagadeesh [aut],
Simon Barnes [ctb]
Maintainer: Csilla Scharle <csilla.scharle2@phs.scot>
Diff between phsopendata versions 1.1.0 dated 2026-05-06 and 1.1.1 dated 2026-10-16
phsopendata-1.1.0/phsopendata/R/utils-pipe.R |only phsopendata-1.1.0/phsopendata/man/pipe.Rd |only phsopendata-1.1.1/phsopendata/DESCRIPTION | 15 - phsopendata-1.1.1/phsopendata/MD5 | 40 +- phsopendata-1.1.1/phsopendata/NAMESPACE | 2 phsopendata-1.1.1/phsopendata/NEWS.md | 23 - phsopendata-1.1.1/phsopendata/R/get_dataset_additional_info.R | 6 phsopendata-1.1.1/phsopendata/R/get_latest_resource_id.R | 2 phsopendata-1.1.1/phsopendata/R/get_resource.R | 8 phsopendata-1.1.1/phsopendata/R/get_resource_sql.R | 6 phsopendata-1.1.1/phsopendata/R/list_datasets.R | 4 phsopendata-1.1.1/phsopendata/R/list_resources.R | 4 phsopendata-1.1.1/phsopendata/README.md | 150 ++++++---- phsopendata-1.1.1/phsopendata/inst/WORDLIST | 5 phsopendata-1.1.1/phsopendata/man/get_dataset_additional_info.Rd | 4 phsopendata-1.1.1/phsopendata/man/get_resource.Rd | 4 phsopendata-1.1.1/phsopendata/man/get_resource_sql.Rd | 4 phsopendata-1.1.1/phsopendata/man/list_datasets.Rd | 4 phsopendata-1.1.1/phsopendata/man/list_resources.Rd | 4 phsopendata-1.1.1/phsopendata/tests/testthat/test-add_context.R | 8 phsopendata-1.1.1/phsopendata/tests/testthat/test-get_resource.R | 2 phsopendata-1.1.1/phsopendata/tests/testthat/test-use_dump_check.R | 6 22 files changed, 183 insertions(+), 118 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Plot
Functions
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for
'ggplot2' plotting methods for 'nlmixr2' objects.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [ctb] ,
Wenping Wang [aut],
Vipul Mann [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2plot versions 5.2.0 dated 2026-09-22 and 5.2.1 dated 2026-10-16
DESCRIPTION | 6 MD5 | 41 ++- NEWS.md | 60 +++++ R/modelDiagram.R | 160 ++++++++++++--- R/plot.bsv.R | 162 +++++++++++---- R/plot.nlmixr2.R | 325 ++++++++++++++++++++----------- R/plot.nlmixr2AugPred.R | 129 ++++++++---- R/rxEvents.R |only R/vpcPlot.R | 145 +++++++++++-- build/vignette.rds |binary inst/doc/events.R |only inst/doc/events.Rmd |only inst/doc/events.html |only inst/doc/model-diagrams.html | 10 tests/testthat/Rplots.pdf |only tests/testthat/helper-figure-envs.R |only tests/testthat/test-augpred-log.R | 22 ++ tests/testthat/test-bsv-etas.R |only tests/testthat/test-event-hooks.R |only tests/testthat/test-gglist-integration.R | 2 tests/testthat/test-model-diagram.R | 201 ++++++++++++------- tests/testthat/test-plots-bootstrap.R |only tests/testthat/test-plots-bsv.R | 78 +++++++ tests/testthat/test-plots.R | 43 ++++ tests/testthat/test-vpc-data.R | 1 tests/testthat/test-vpcPlot.R |only vignettes/events.Rmd |only 27 files changed, 1048 insertions(+), 337 deletions(-)
Title: Use 'nlmixr2' to Interact with Open Source and Commercial
Software
Description: Run other estimation and simulation software via the 'nlmixr2' (Fidler et al (2019)
<doi:10.1002/psp4.12445>) interface including 'PKNCA', 'NONMEM' and 'Monolix'. It also converts
'nlmixr2'/'rxode2' models to 'PopED' optimal design databases (Fidler et al (2024)
<doi:10.70534/XUMG6226>). While not required, you can
get/install the 'lixoftConnectors' package in the 'Monolix' installation, as
described at the following url
<https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When
'lixoftConnectors' is available, 'Monolix' can be run directly instead of setting up
command line usage.
Author: Matthew Fidler [aut, cre] ,
Bill Denney [aut] ,
Theodoros Papathanasiou [ctb],
Nook Fulloption [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between babelmixr2 versions 0.1.11 dated 2025-11-28 and 0.1.12 dated 2026-10-16
babelmixr2-0.1.11/babelmixr2/tests/testthat/bad-nonmem-data-convert.qs2 |only babelmixr2-0.1.12/babelmixr2/DESCRIPTION | 21 babelmixr2-0.1.12/babelmixr2/MD5 | 211 - babelmixr2-0.1.12/babelmixr2/NAMESPACE | 312 +- babelmixr2-0.1.12/babelmixr2/NEWS.md | 555 +++ babelmixr2-0.1.12/babelmixr2/R/as.nlmixr2monolixr2rx.R | 27 babelmixr2-0.1.12/babelmixr2/R/as.nlmixr2nonmem2rx.R | 377 +- babelmixr2-0.1.12/babelmixr2/R/convert.R | 508 ++- babelmixr2-0.1.12/babelmixr2/R/fitCache.R |only babelmixr2-0.1.12/babelmixr2/R/fmeMcmc.R | 224 + babelmixr2-0.1.12/babelmixr2/R/linCmt.R |only babelmixr2-0.1.12/babelmixr2/R/monolix.R | 530 +++ babelmixr2-0.1.12/babelmixr2/R/monolixControl.R | 24 babelmixr2-0.1.12/babelmixr2/R/monolixNlmixr2est.R | 201 + babelmixr2-0.1.12/babelmixr2/R/monolixPriors.R |only babelmixr2-0.1.12/babelmixr2/R/monolixReadData.R | 76 babelmixr2-0.1.12/babelmixr2/R/monolixRxUiGet.R | 3 babelmixr2-0.1.12/babelmixr2/R/monolixRxUiGetJacobian.R | 2 babelmixr2-0.1.12/babelmixr2/R/monolixRxUiGetMlxtranDatafile.R | 5 babelmixr2-0.1.12/babelmixr2/R/monolixRxUiGetMlxtranFit.R | 5 babelmixr2-0.1.12/babelmixr2/R/monolixRxUiGetMlxtranIndividual.R | 14 babelmixr2-0.1.12/babelmixr2/R/monolixRxUiGetMlxtranLongitudinal.R | 13 babelmixr2-0.1.12/babelmixr2/R/monolixRxUiGetMlxtranParameters.R | 68 babelmixr2-0.1.12/babelmixr2/R/monolixRxUiGetMonolixModel.R | 374 ++ babelmixr2-0.1.12/babelmixr2/R/nlmer.R |only babelmixr2-0.1.12/babelmixr2/R/nlmerControl.R |only babelmixr2-0.1.12/babelmixr2/R/nlmerRxUiGet.R |only babelmixr2-0.1.12/babelmixr2/R/nmGetDistributionMonolixLines.R | 17 babelmixr2-0.1.12/babelmixr2/R/nmGetDistributionNonmemLines.R | 2 babelmixr2-0.1.12/babelmixr2/R/nonmem.R | 1469 +++++++-- babelmixr2-0.1.12/babelmixr2/R/nonmemControl.R | 77 babelmixr2-0.1.12/babelmixr2/R/nonmemFailure.R |only babelmixr2-0.1.12/babelmixr2/R/nonmemNlmixr2est.R | 153 babelmixr2-0.1.12/babelmixr2/R/nonmemReadData.R | 144 babelmixr2-0.1.12/babelmixr2/R/nonmemRxUiGet.R | 4 babelmixr2-0.1.12/babelmixr2/R/nonmemRxUiGetErr.R | 24 babelmixr2-0.1.12/babelmixr2/R/nonmemRxUiGetEst.R | 23 babelmixr2-0.1.12/babelmixr2/R/nonmemRxUiGetInput.R | 26 babelmixr2-0.1.12/babelmixr2/R/nonmemRxUiGetModel.R | 138 babelmixr2-0.1.12/babelmixr2/R/nonmemRxUiGetOmega.R | 33 babelmixr2-0.1.12/babelmixr2/R/nonmemRxUiGetPk.R | 529 ++- babelmixr2-0.1.12/babelmixr2/R/nonmemRxUiGetPrior.R |only babelmixr2-0.1.12/babelmixr2/R/nonmemRxUiGetSub.R | 15 babelmixr2-0.1.12/babelmixr2/R/nonmemRxUiGetTable.R | 10 babelmixr2-0.1.12/babelmixr2/R/pknca.R | 1283 +++++++- babelmixr2-0.1.12/babelmixr2/R/poped.R | 248 + babelmixr2-0.1.12/babelmixr2/R/pruneIf.R |only babelmixr2-0.1.12/babelmixr2/R/pseudoOptim.R | 95 babelmixr2-0.1.12/babelmixr2/R/reexport.R | 4 babelmixr2-0.1.12/babelmixr2/R/reexports.R | 6 babelmixr2-0.1.12/babelmixr2/R/saemix.R |only babelmixr2-0.1.12/babelmixr2/R/saemixControl.R |only babelmixr2-0.1.12/babelmixr2/R/sigdigControl.R |only babelmixr2-0.1.12/babelmixr2/R/units.R | 11 babelmixr2-0.1.12/babelmixr2/R/utils.R | 37 babelmixr2-0.1.12/babelmixr2/R/zzz.R | 16 babelmixr2-0.1.12/babelmixr2/build |only babelmixr2-0.1.12/babelmixr2/inst/CITATION | 22 babelmixr2-0.1.12/babelmixr2/inst/WORDLIST | 67 babelmixr2-0.1.12/babelmixr2/inst/err-boxCox.txt | 22 babelmixr2-0.1.12/babelmixr2/inst/err-cens-limit.txt | 28 babelmixr2-0.1.12/babelmixr2/inst/err-cens.txt | 7 babelmixr2-0.1.12/babelmixr2/inst/err-lnorm.txt | 8 babelmixr2-0.1.12/babelmixr2/inst/err-logit.txt | 3 babelmixr2-0.1.12/babelmixr2/inst/err-logitYeoJohnson.txt | 34 babelmixr2-0.1.12/babelmixr2/inst/err-yeoJohnson.txt | 32 babelmixr2-0.1.12/babelmixr2/inst/poped/ex.10.PKPD.HCV.adaptive-dosing.babelmixr2.R |only babelmixr2-0.1.12/babelmixr2/inst/poped/ex.10.PKPD.HCV.dose-and-tinf.babelmixr2.R |only babelmixr2-0.1.12/babelmixr2/inst/stress |only babelmixr2-0.1.12/babelmixr2/man/babel.poped.database.Rd | 8 babelmixr2-0.1.12/babelmixr2/man/dot-nlmerCurrentFormula.Rd |only babelmixr2-0.1.12/babelmixr2/man/dot-nlmerNlmerFun.Rd |only babelmixr2-0.1.12/babelmixr2/man/fmeMcmcControl.Rd | 325 -- babelmixr2-0.1.12/babelmixr2/man/modelUnitConversion.Rd | 6 babelmixr2-0.1.12/babelmixr2/man/monolixControl.Rd | 73 babelmixr2-0.1.12/babelmixr2/man/nlmixr2Est.nlmer.Rd |only babelmixr2-0.1.12/babelmixr2/man/nlmixr2Est.pknca.Rd | 9 babelmixr2-0.1.12/babelmixr2/man/nlmixr2NlmerControl.Rd |only babelmixr2-0.1.12/babelmixr2/man/nonmemControl.Rd | 47 babelmixr2-0.1.12/babelmixr2/man/pkncaControl.Rd | 3 babelmixr2-0.1.12/babelmixr2/man/popedControl.Rd | 32 babelmixr2-0.1.12/babelmixr2/man/pseudoOptimControl.Rd | 313 -- babelmixr2-0.1.12/babelmixr2/man/reexports.Rd | 17 babelmixr2-0.1.12/babelmixr2/man/rxUiGet.loadPruneNlmer.Rd |only babelmixr2-0.1.12/babelmixr2/man/rxUiGet.loadPruneNlmerSens.Rd |only babelmixr2-0.1.12/babelmixr2/man/rxUiGet.nlmerEnv.Rd |only babelmixr2-0.1.12/babelmixr2/man/rxUiGet.nlmerFormula.Rd |only babelmixr2-0.1.12/babelmixr2/man/rxUiGet.nlmerHdTheta.Rd |only babelmixr2-0.1.12/babelmixr2/man/rxUiGet.nlmerModel0.Rd |only babelmixr2-0.1.12/babelmixr2/man/rxUiGet.nlmerParams.Rd |only babelmixr2-0.1.12/babelmixr2/man/rxUiGet.nlmerRandomFormula.Rd |only babelmixr2-0.1.12/babelmixr2/man/rxUiGet.nlmerSensModel.Rd |only babelmixr2-0.1.12/babelmixr2/man/rxUiGet.nlmerStart.Rd |only babelmixr2-0.1.12/babelmixr2/man/rxUiGet.nlmerThetaSens.Rd |only babelmixr2-0.1.12/babelmixr2/man/rxUiGet.nlmerThetas.Rd |only babelmixr2-0.1.12/babelmixr2/man/saemixControl.Rd |only babelmixr2-0.1.12/babelmixr2/man/simplifyUnit.Rd | 6 babelmixr2-0.1.12/babelmixr2/src/classicReverse.cpp | 41 babelmixr2-0.1.12/babelmixr2/src/poped.cpp | 28 babelmixr2-0.1.12/babelmixr2/src/transform.cpp | 4 babelmixr2-0.1.12/babelmixr2/tests/testthat.R | 68 babelmixr2-0.1.12/babelmixr2/tests/testthat/bad-nonmem-data-convert.rds |only babelmixr2-0.1.12/babelmixr2/tests/testthat/monolix2024-priors.zip |only babelmixr2-0.1.12/babelmixr2/tests/testthat/nonmem-pktime.zip |only babelmixr2-0.1.12/babelmixr2/tests/testthat/one.cmt-nonmem |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-as-nlmixr2-pktime.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-as-nlmixr2.R | 149 babelmixr2-0.1.12/babelmixr2/tests/testthat/test-c-integer-safety.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-convert.R | 4 babelmixr2-0.1.12/babelmixr2/tests/testthat/test-fmeMcmc.R | 157 + babelmixr2-0.1.12/babelmixr2/tests/testthat/test-iterPrintControl.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-linCmt.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-monolix-2024-priors.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-monolix-priors.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-monolix-prune.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-monolix.R | 988 +++++- babelmixr2-0.1.12/babelmixr2/tests/testthat/test-monolix2rx-ss.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-nlmer.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-nonmem-cens.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-nonmem-est.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-nonmem-failure.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-nonmem-monolix-nlmixr2lib.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-nonmem-monolix-stress.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-nonmem-prior.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-nonmem-prune.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-nonmem-read.R | 100 babelmixr2-0.1.12/babelmixr2/tests/testthat/test-nonmem.R | 1478 ++++++++- babelmixr2-0.1.12/babelmixr2/tests/testthat/test-pknca.R | 1533 +++++++++- babelmixr2-0.1.12/babelmixr2/tests/testthat/test-poped.R | 328 ++ babelmixr2-0.1.12/babelmixr2/tests/testthat/test-psuedoOptim.R | 22 babelmixr2-0.1.12/babelmixr2/tests/testthat/test-saemix.R |only babelmixr2-0.1.12/babelmixr2/tests/testthat/test-sigdig.R |only 132 files changed, 11414 insertions(+), 2462 deletions(-)
Title: Scale Mixture of Skew-Normal Linear Mixed Models
Description: It fits scale mixture of skew-normal linear mixed models using either an expectation–maximization (EM) type algorithm or its accelerated version (Damped Anderson Acceleration with Epsilon Monotonicity, DAAREM), including some possibilities for modeling the within-subject dependence <doi:10.18637/jss.v115.i07>.
Author: Fernanda L. Schumacher [aut, cre] ,
Larissa A. Matos [aut] ,
Victor H. Lachos [aut] ,
Katherine A. L. Valeriano [aut] ,
Nicholas Henderson [ctb],
Ravi Varadhan [ctb]
Maintainer: Fernanda L. Schumacher <fernandalschumacher@gmail.com>
Diff between skewlmm versions 1.1.3 dated 2026-01-18 and 1.1.5 dated 2026-10-16
skewlmm-1.1.3/skewlmm/R/smnCens_allfunctions.R |only skewlmm-1.1.3/skewlmm/R/smnCens_prin.R |only skewlmm-1.1.3/skewlmm/man/fitted.SMNCens.Rd |only skewlmm-1.1.3/skewlmm/man/mahalDist.SMNCens.Rd |only skewlmm-1.1.3/skewlmm/man/plot.SMNCens.Rd |only skewlmm-1.1.3/skewlmm/man/plot.mahalDist.SMNCens.Rd |only skewlmm-1.1.3/skewlmm/man/predict.SMNCens.Rd |only skewlmm-1.1.3/skewlmm/man/print.SMNCens.Rd |only skewlmm-1.1.3/skewlmm/man/residuals.SMNCens.Rd |only skewlmm-1.1.3/skewlmm/man/rsmsn.clmm.Rd |only skewlmm-1.1.3/skewlmm/man/smn.clmm.Rd |only skewlmm-1.1.3/skewlmm/man/summary.SMNCens.Rd |only skewlmm-1.1.5/skewlmm/DESCRIPTION | 16 ++- skewlmm-1.1.5/skewlmm/MD5 | 63 ++++++-------- skewlmm-1.1.5/skewlmm/NAMESPACE | 28 ------ skewlmm-1.1.5/skewlmm/NEWS.md | 13 ++- skewlmm-1.1.5/skewlmm/R/mainfunctions.R | 68 ++++++++++++---- skewlmm-1.1.5/skewlmm/R/residuals.R | 39 +++++---- skewlmm-1.1.5/skewlmm/R/sve_derivates.R |only skewlmm-1.1.5/skewlmm/R/sve_mainfunctions.R |only skewlmm-1.1.5/skewlmm/README.md | 54 +++++++++--- skewlmm-1.1.5/skewlmm/inst/CITATION | 39 ++++----- skewlmm-1.1.5/skewlmm/man/UTIdata.Rd | 3 skewlmm-1.1.5/skewlmm/man/acfresid.Rd | 2 skewlmm-1.1.5/skewlmm/man/boot_par.Rd | 3 skewlmm-1.1.5/skewlmm/man/coef.Rd | 10 -- skewlmm-1.1.5/skewlmm/man/confint.Rd | 24 ++++- skewlmm-1.1.5/skewlmm/man/criteria.Rd | 8 - skewlmm-1.1.5/skewlmm/man/figures/README-example1-1.png |binary skewlmm-1.1.5/skewlmm/man/figures/README-example2-1.png |binary skewlmm-1.1.5/skewlmm/man/figures/README-example2-2.png |binary skewlmm-1.1.5/skewlmm/man/figures/README-example2-3.png |binary skewlmm-1.1.5/skewlmm/man/fixef.Rd | 6 - skewlmm-1.1.5/skewlmm/man/lmmControl.Rd | 6 - skewlmm-1.1.5/skewlmm/man/ranef.Rd | 10 -- skewlmm-1.1.5/skewlmm/man/smn.lmm.Rd | 4 skewlmm-1.1.5/skewlmm/man/smsn.lmm.Rd | 4 skewlmm-1.1.5/skewlmm/man/update.Rd | 14 +-- skewlmm-1.1.5/skewlmm/tests |only 39 files changed, 236 insertions(+), 178 deletions(-)
Title: Model Visualisation Toolbox for 'easystats' and 'ggplot2'
Description: Provides plotting utilities supporting packages in the 'easystats'
ecosystem (<https://github.com/easystats/easystats>) and some extra themes,
geoms, and scales for 'ggplot2'. Color scales are based on
<https://materialui.co/>.
References: Lüdecke et al. (2021) <doi:10.21105/joss.03393>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, inv] ,
Indrajeet Patil [aut] ,
Mattan S. Ben-Shachar [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Remi Theriault [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Jeffrey R. Stevens [ctb] ,
Julius Bogomolo [...truncated...]
Maintainer: Daniel Luedecke <officialeasystats@gmail.com>
Diff between see versions 0.14.2 dated 2026-09-01 and 0.15.0 dated 2026-10-16
see-0.14.2/see/man/ggplot2-ggproto.Rd |only see-0.15.0/see/DESCRIPTION | 18 see-0.15.0/see/MD5 | 77 see-0.15.0/see/NEWS.md | 129 see-0.15.0/see/R/geom_binomdensity.R | 6 see-0.15.0/see/R/geom_violindot.R | 374 + see-0.15.0/see/R/geom_violinhalf.R | 481 +- see-0.15.0/see/R/plot.check_collinearity.R | 32 see-0.15.0/see/R/plot.check_heteroscedasticity.R | 8 see-0.15.0/see/R/plot.check_homogeneity.R | 24 see-0.15.0/see/R/plot.check_model.R | 171 see-0.15.0/see/R/plot.check_outliers.dots.R | 9 see-0.15.0/see/R/plot.check_outliers.scree.R | 17 see-0.15.0/see/R/plot.equivalence_test.R | 8 see-0.15.0/see/R/plot.estimate_contrasts.R | 1170 +++++ see-0.15.0/see/R/plot.means_by_group.R | 33 see-0.15.0/see/R/plot.parameters_sem.R | 19 see-0.15.0/see/R/plot.rope.R | 2 see-0.15.0/see/R/plots.R | 13 see-0.15.0/see/inst/WORDLIST | 2 see-0.15.0/see/man/geom_violindot.Rd | 100 see-0.15.0/see/man/geom_violinhalf.Rd | 98 see-0.15.0/see/man/plot.see_check_collinearity.Rd | 6 see-0.15.0/see/man/plot.see_check_heteroscedasticity.Rd | 6 see-0.15.0/see/man/plot.see_check_model.Rd | 9 see-0.15.0/see/man/plot.see_dw_groupmeans.Rd | 9 see-0.15.0/see/man/plot.see_estimate_contrasts.Rd | 181 see-0.15.0/see/tests/testthat/helper-violinhalf.R |only see-0.15.0/see/tests/testthat/test-check_model_few_values.R |only see-0.15.0/see/tests/testthat/test-check_model_show_smooth.R |only see-0.15.0/see/tests/testthat/test-check_model_theme.R | 2 see-0.15.0/see/tests/testthat/test-geom_binomdensity.R | 29 see-0.15.0/see/tests/testthat/test-geom_violindot.R |only see-0.15.0/see/tests/testthat/test-geom_violinhalf.R |only see-0.15.0/see/tests/testthat/test-plot.check_collinearity.R | 149 see-0.15.0/see/tests/testthat/test-plot.check_outliers.R | 39 see-0.15.0/see/tests/testthat/test-plot.estimate_contrasts.R | 2187 ++++++++++ see-0.15.0/see/tests/testthat/test-plot.means_by_group.R |only see-0.15.0/see/tests/testthat/test-plot.parameters_sem.R |only see-0.15.0/see/tests/testthat/test-plot.rope.R | 2 see-0.15.0/see/tests/testthat/test-vdiffr_check_model.R | 55 see-0.15.0/see/tests/testthat/test-vdiffr_check_predictions.R | 24 see-0.15.0/see/tests/testthat/test-vdiffr_geoms_coords.R | 61 see-0.15.0/see/tests/testthat/test-vdiffr_lighthouse.R |only 44 files changed, 5185 insertions(+), 365 deletions(-)
Title: 'Rcpp' Bindings for the 'simdjson' Header-Only Library for
'JSON' Parsing
Description: The 'JSON' format is ubiquitous for data interchange, and the
'simdjson' library written by Daniel Lemire (and many contributors) provides a
high-performance parser for these files which by relying on parallel 'SIMD'
instruction manages to parse these files as faster than disk speed. See the
<doi:10.48550/arXiv.1902.08318> paper for more details about 'simdjson'. This
package parses 'JSON' from string, file, or remote URLs under a variety of
settings.
Author: Dirk Eddelbuettel [aut, cre] ,
Brendan Knapp [aut] ,
Daniel Lemire [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSimdJson versions 0.1.16 dated 2026-10-09 and 0.1.17 dated 2026-10-16
RcppSimdJson-0.1.16/RcppSimdJson/src/Makevars |only RcppSimdJson-0.1.17/RcppSimdJson/ChangeLog | 28 RcppSimdJson-0.1.17/RcppSimdJson/DESCRIPTION | 8 RcppSimdJson-0.1.17/RcppSimdJson/MD5 | 23 RcppSimdJson-0.1.17/RcppSimdJson/README.md | 35 RcppSimdJson-0.1.17/RcppSimdJson/build/partial.rdb |binary RcppSimdJson-0.1.17/RcppSimdJson/cleanup | 2 RcppSimdJson-0.1.17/RcppSimdJson/configure |only RcppSimdJson-0.1.17/RcppSimdJson/inst/NEWS.Rd | 12 RcppSimdJson-0.1.17/RcppSimdJson/inst/examples/simpleBenchmark.R | 2 RcppSimdJson-0.1.17/RcppSimdJson/inst/examples/simpleParseBenchmark.R | 2 RcppSimdJson-0.1.17/RcppSimdJson/inst/include/simdjson.cpp | 83 RcppSimdJson-0.1.17/RcppSimdJson/inst/include/simdjson.h | 2653 +++++++--- RcppSimdJson-0.1.17/RcppSimdJson/src/Makevars.in |only 14 files changed, 2225 insertions(+), 623 deletions(-)
Title: Statistical Analysis of Count Data and Quantal Data
Description: Methods for statistical analysis of count data and quantal data.
For the analysis of count data an implementation of the Closure Principle Computational Approach Test ("CPCAT") is provided (Lehmann, R et al. (2016) <doi:10.1007/s00477-015-1079-4>), as well as an implementation of a "Dunnett GLM" approach using either a Quasi-Poisson, a negative binomial or a Poisson regression (Hothorn, L, Kluxen, F (2020) <doi:10.1101/2020.01.15.907881>).
For the analysis of quantal data an implementation of the Closure Principle Fisher–Freeman–Halton test ("CPFISH") is provided (Lehmann, R et al. (2018) <doi:10.1007/s00477-017-1392-1>). P-values and no/lowest observed (adverse) effect concentration values are calculated.
All implemented methods include further functions to evaluate the power and the minimum detectable difference using a bootstrapping approach.
A model-agnostic, simulation-calibrated diagnostic for overdispersion in grouped count data is provided to support the choic [...truncated...]
Author: Benjamin Daniels [cre, aut] ,
Christian Dietrich [aut],
Thomas Graeff [aut],
Magnus Wang [aut]
Maintainer: Benjamin Daniels <benjamin.daniels@rwth-aachen.de>
Diff between qountstat versions 0.1.1 dated 2025-02-21 and 0.2.0 dated 2026-10-16
DESCRIPTION | 26 - MD5 | 45 +- NAMESPACE | 1 NEWS |only R/CPCAT.R | 76 +++- R/CPCATbMDD.R | 3 R/CPFISHPower.R | 2 R/CPFISHbMDD.R | 2 R/DunnettGLM.R | 177 ++++++++++ R/DunnettGLMPower.R | 34 ++ R/DunnettGLMbMDD.R | 40 ++ R/MultiGroupTestBMDD.R | 34 +- R/MultiGroupTestPower.R | 19 - R/OverdispersionTest.R |only inst |only man/CPCAT.Rd | 35 +- man/CPCAT.bMDD.Rd | 3 man/Dunnett.GLM.Rd | 93 +++++ man/Dunnett.GLM.bMDD.Rd | 40 ++ man/Dunnett.GLM.power.Rd | 34 ++ man/MSSR.statistic.Rd |only man/Multi.group.test.bMDD.Rd | 8 man/Multi.group.test.power.Rd | 4 man/Overdispersion.test.Rd |only man/calibrate.c.alpha.Rd |only man/run.overdispersion.diagnostic.Rd |only tests/testthat/tests.R | 568 +++++++++++++++++++++++++++++++++++ 27 files changed, 1149 insertions(+), 95 deletions(-)
Title: Euclidean Climatch Algorithm
Description: An interface for performing climate matching using the Euclidean "Climatch" algorithm. Functions provide a vector of climatch scores (0-10) for each location (i.e., grid cell) within the recipient region, the percent of climatch scores >= a threshold value, and mean climatch score. Tools for parallelization and visualizations are also provided. Note that the floor function that rounds the climatch score down to the nearest integer has been removed in this implementation and the “Climatch” algorithm, also referred to as the “Climate” algorithm, is described in: Crombie, J., Brown, L., Lizzio, J., & Hood, G. (2008). “Climatch user manual”. The method for the percent score is described in: Howeth, J.G., Gantz, C.A., Angermeier, P.L., Frimpong, E.A., Hoff, M.H., Keller, R.P., Mandrak, N.E., Marchetti, M.P., Olden, J.D., Romagosa, C.M., and Lodge, D.M. (2016). <doi:10.1111/ddi.12391>.
Author: Justin A. G. Hubbard [aut, cre] ,
D. Andrew R. Drake [aut],
Nicholas E. Mandrak [aut]
Maintainer: Justin A. G. Hubbard <justin.hubbard@alumni.utoronto.ca>
Diff between Euclimatch versions 1.0.2 dated 2024-10-03 and 1.0.3 dated 2026-10-16
DESCRIPTION | 19 +++++++++++-------- MD5 | 4 +++- tests |only 3 files changed, 14 insertions(+), 9 deletions(-)
Title: Mathematical Modeling of Infectious Disease Dynamics
Description: Tools for simulating mathematical models of infectious disease dynamics.
Epidemic model classes include deterministic compartmental models, stochastic
individual-contact models, and stochastic network models. Network models use the
robust statistical methods of exponential-family random graph models (ERGMs)
from the Statnet suite of software packages in R. Standard templates for epidemic
modeling include SI, SIR, and SIS disease types. EpiModel features an API for
extending these templates to address novel scientific research aims. Full
methods for EpiModel are detailed in Jenness et al. (2018, <doi:10.18637/jss.v084.i08>).
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Adrien Le Guillou [aut],
Chad Klumb [aut],
Skye Bender-deMoll [ctb]
Maintainer: Samuel Jenness <samuel.m.jenness@emory.edu>
Diff between EpiModel versions 2.6.2 dated 2026-09-16 and 2.7.0 dated 2026-10-16
EpiModel-2.6.2/EpiModel/man/generate_random_params.Rd |only EpiModel-2.6.2/EpiModel/man/get_param_set.Rd |only EpiModel-2.6.2/EpiModel/man/param_random.Rd |only EpiModel-2.7.0/EpiModel/DESCRIPTION | 18 EpiModel-2.7.0/EpiModel/MD5 | 265 +-- EpiModel-2.7.0/EpiModel/NAMESPACE | 17 EpiModel-2.7.0/EpiModel/NEWS.md | 92 + EpiModel-2.7.0/EpiModel/R/EpiModel-package.R | 7 EpiModel-2.7.0/EpiModel/R/as.data.frame.R | 2 EpiModel-2.7.0/EpiModel/R/by_infection_duration.R |only EpiModel-2.7.0/EpiModel/R/dcm.R | 33 EpiModel-2.7.0/EpiModel/R/dcm.inputs.R | 41 EpiModel-2.7.0/EpiModel/R/dendo.R | 3 EpiModel-2.7.0/EpiModel/R/edgelists.R | 4 EpiModel-2.7.0/EpiModel/R/get.R | 342 +--- EpiModel-2.7.0/EpiModel/R/icm.inputs.R | 1 EpiModel-2.7.0/EpiModel/R/merge.R | 430 ++++- EpiModel-2.7.0/EpiModel/R/net.controls.R |only EpiModel-2.7.0/EpiModel/R/net.fn.accessor.R | 431 ++++- EpiModel-2.7.0/EpiModel/R/net.fn.logs.R | 4 EpiModel-2.7.0/EpiModel/R/net.fn.modules.R | 2 EpiModel-2.7.0/EpiModel/R/net.fn.param_df.R | 21 EpiModel-2.7.0/EpiModel/R/net.fn.record.R | 137 + EpiModel-2.7.0/EpiModel/R/net.fn.restart_point.R |only EpiModel-2.7.0/EpiModel/R/net.fn.scenarios.R | 146 + EpiModel-2.7.0/EpiModel/R/net.fn.track.attrs.R |only EpiModel-2.7.0/EpiModel/R/net.fn.utils.R | 343 ++-- EpiModel-2.7.0/EpiModel/R/net.helpers.R | 72 EpiModel-2.7.0/EpiModel/R/net.inputs.R | 596 +++---- EpiModel-2.7.0/EpiModel/R/net.mod.infection.R | 66 EpiModel-2.7.0/EpiModel/R/net.mod.init.R | 195 ++ EpiModel-2.7.0/EpiModel/R/net.mod.nwupdate.R | 11 EpiModel-2.7.0/EpiModel/R/net.mod.prevalence.R | 110 - EpiModel-2.7.0/EpiModel/R/net.mod.recovery.R | 48 EpiModel-2.7.0/EpiModel/R/net.mod.simnet.R | 87 + EpiModel-2.7.0/EpiModel/R/net.mod.summary.R | 40 EpiModel-2.7.0/EpiModel/R/net.mod.trackers.R | 4 EpiModel-2.7.0/EpiModel/R/net.mod.updater.R | 40 EpiModel-2.7.0/EpiModel/R/net.mod.vital.R | 24 EpiModel-2.7.0/EpiModel/R/netcensus.R |only EpiModel-2.7.0/EpiModel/R/netclique.R |only EpiModel-2.7.0/EpiModel/R/netdx.R | 48 EpiModel-2.7.0/EpiModel/R/netest.R | 32 EpiModel-2.7.0/EpiModel/R/netsim.R | 85 - EpiModel-2.7.0/EpiModel/R/network.R | 211 ++ EpiModel-2.7.0/EpiModel/R/plot.comp_plot.R | 6 EpiModel-2.7.0/EpiModel/R/plot.dcm.R | 20 EpiModel-2.7.0/EpiModel/R/plot.epi.data.frame.R | 2 EpiModel-2.7.0/EpiModel/R/plot.icm.R | 6 EpiModel-2.7.0/EpiModel/R/plot.netdx.R | 4 EpiModel-2.7.0/EpiModel/R/plot.netsim.R | 17 EpiModel-2.7.0/EpiModel/R/plot.stat_table.R | 12 EpiModel-2.7.0/EpiModel/R/print.R | 76 - EpiModel-2.7.0/EpiModel/R/reachable.R | 17 EpiModel-2.7.0/EpiModel/R/saveout.R | 47 EpiModel-2.7.0/EpiModel/R/summary.R | 12 EpiModel-2.7.0/EpiModel/R/update.R | 60 EpiModel-2.7.0/EpiModel/R/utils.R | 3 EpiModel-2.7.0/EpiModel/inst/doc/Intro.R | 6 EpiModel-2.7.0/EpiModel/inst/doc/Intro.Rmd | 16 EpiModel-2.7.0/EpiModel/inst/doc/Intro.html | 74 EpiModel-2.7.0/EpiModel/inst/doc/attributes-and-summary-statistics.R | 97 - EpiModel-2.7.0/EpiModel/inst/doc/attributes-and-summary-statistics.Rmd | 190 +- EpiModel-2.7.0/EpiModel/inst/doc/attributes-and-summary-statistics.html | 210 +- EpiModel-2.7.0/EpiModel/inst/doc/model-parameters.R | 154 -- EpiModel-2.7.0/EpiModel/inst/doc/model-parameters.Rmd | 196 +- EpiModel-2.7.0/EpiModel/inst/doc/model-parameters.html | 749 +++++----- EpiModel-2.7.0/EpiModel/inst/doc/network-objects.R | 115 + EpiModel-2.7.0/EpiModel/inst/doc/network-objects.Rmd | 247 +++ EpiModel-2.7.0/EpiModel/inst/doc/network-objects.html | 504 ++++++ EpiModel-2.7.0/EpiModel/man/EpiModel-package.Rd | 4 EpiModel-2.7.0/EpiModel/man/add_vertices.Rd | 17 EpiModel-2.7.0/EpiModel/man/arrive_nodes.Rd | 6 EpiModel-2.7.0/EpiModel/man/as.phylo.transmat.Rd | 3 EpiModel-2.7.0/EpiModel/man/assign_groups.Rd |only EpiModel-2.7.0/EpiModel/man/auto_update_attr.Rd | 4 EpiModel-2.7.0/EpiModel/man/brewer_ramp.Rd | 3 EpiModel-2.7.0/EpiModel/man/by_infection_duration.Rd |only EpiModel-2.7.0/EpiModel/man/control.dcm.Rd | 27 EpiModel-2.7.0/EpiModel/man/control.net.Rd | 51 EpiModel-2.7.0/EpiModel/man/create_scenario_list.Rd | 22 EpiModel-2.7.0/EpiModel/man/dcm.Rd | 5 EpiModel-2.7.0/EpiModel/man/delete_vertices.Rd | 17 EpiModel-2.7.0/EpiModel/man/depart_nodes.Rd | 6 EpiModel-2.7.0/EpiModel/man/get_attr.Rd |only EpiModel-2.7.0/EpiModel/man/get_attr_at.Rd |only EpiModel-2.7.0/EpiModel/man/get_attr_history.Rd | 17 EpiModel-2.7.0/EpiModel/man/get_attr_prop.Rd | 13 EpiModel-2.7.0/EpiModel/man/get_epi.Rd |only EpiModel-2.7.0/EpiModel/man/get_nwparam.Rd | 6 EpiModel-2.7.0/EpiModel/man/get_param.Rd |only EpiModel-2.7.0/EpiModel/man/get_sims.Rd | 5 EpiModel-2.7.0/EpiModel/man/get_transmat.Rd | 4 EpiModel-2.7.0/EpiModel/man/init_nets.Rd | 5 EpiModel-2.7.0/EpiModel/man/initialize.net.Rd | 21 EpiModel-2.7.0/EpiModel/man/make_networkDynamic.Rd |only EpiModel-2.7.0/EpiModel/man/make_restart_point.Rd | 88 - EpiModel-2.7.0/EpiModel/man/merge.icm.Rd | 12 EpiModel-2.7.0/EpiModel/man/merge.netsim.Rd | 51 EpiModel-2.7.0/EpiModel/man/move_to_group.Rd |only EpiModel-2.7.0/EpiModel/man/multilayer.Rd | 27 EpiModel-2.7.0/EpiModel/man/net-accessor.Rd | 201 -- EpiModel-2.7.0/EpiModel/man/net-controls.Rd |only EpiModel-2.7.0/EpiModel/man/netcensus.Rd |only EpiModel-2.7.0/EpiModel/man/netclique.Rd |only EpiModel-2.7.0/EpiModel/man/netdx.Rd | 33 EpiModel-2.7.0/EpiModel/man/netest.Rd | 32 EpiModel-2.7.0/EpiModel/man/netsim.Rd | 52 EpiModel-2.7.0/EpiModel/man/param.net.Rd | 121 - EpiModel-2.7.0/EpiModel/man/param.net_to_table.Rd | 8 EpiModel-2.7.0/EpiModel/man/plot.dcm.Rd | 3 EpiModel-2.7.0/EpiModel/man/plot.epi.data.frame.Rd | 3 EpiModel-2.7.0/EpiModel/man/plot.icm.Rd | 6 EpiModel-2.7.0/EpiModel/man/plot.netdx.Rd | 7 EpiModel-2.7.0/EpiModel/man/plot.netsim.Rd | 9 EpiModel-2.7.0/EpiModel/man/print.netsim.Rd | 3 EpiModel-2.7.0/EpiModel/man/reachable-nodes.Rd | 15 EpiModel-2.7.0/EpiModel/man/record_attr_history.Rd | 74 EpiModel-2.7.0/EpiModel/man/record_raw_object.Rd | 21 EpiModel-2.7.0/EpiModel/man/sample_groups.Rd |only EpiModel-2.7.0/EpiModel/man/tracked_attrs_record.Rd |only EpiModel-2.7.0/EpiModel/man/tracked_attrs_set_ref.Rd |only EpiModel-2.7.0/EpiModel/man/trim_netest.Rd | 12 EpiModel-2.7.0/EpiModel/man/truncate_sim.Rd | 20 EpiModel-2.7.0/EpiModel/man/update_list.Rd | 11 EpiModel-2.7.0/EpiModel/man/use_scenario.Rd | 3 EpiModel-2.7.0/EpiModel/tests/testthat/Rplots.pdf |binary EpiModel-2.7.0/EpiModel/tests/testthat/test-accessors.R | 79 + EpiModel-2.7.0/EpiModel/tests/testthat/test-by-infection-duration.R |only EpiModel-2.7.0/EpiModel/tests/testthat/test-cumulative_edgelist.R | 41 EpiModel-2.7.0/EpiModel/tests/testthat/test-dcm.R | 82 + EpiModel-2.7.0/EpiModel/tests/testthat/test-get.R | 252 +-- EpiModel-2.7.0/EpiModel/tests/testthat/test-merge.R | 453 +++++- EpiModel-2.7.0/EpiModel/tests/testthat/test-multinets.R | 2 EpiModel-2.7.0/EpiModel/tests/testthat/test-net-inputs-validation.R | 51 EpiModel-2.7.0/EpiModel/tests/testthat/test-netattr.R | 95 + EpiModel-2.7.0/EpiModel/tests/testthat/test-netcensus.R |only EpiModel-2.7.0/EpiModel/tests/testthat/test-netclique.R |only EpiModel-2.7.0/EpiModel/tests/testthat/test-netsim.R | 52 EpiModel-2.7.0/EpiModel/tests/testthat/test-newmodules.R | 406 +++-- EpiModel-2.7.0/EpiModel/tests/testthat/test-print.R | 2 EpiModel-2.7.0/EpiModel/tests/testthat/test-tracked-attrs.R |only EpiModel-2.7.0/EpiModel/tests/testthat/test-truncate-restart.R | 538 +++++++ EpiModel-2.7.0/EpiModel/vignettes/Intro.Rmd | 16 EpiModel-2.7.0/EpiModel/vignettes/attributes-and-summary-statistics.Rmd | 190 +- EpiModel-2.7.0/EpiModel/vignettes/model-parameters.Rmd | 196 +- EpiModel-2.7.0/EpiModel/vignettes/network-objects.Rmd | 247 +++ 147 files changed, 7152 insertions(+), 3446 deletions(-)
Title: Time Series with Matrix Profile
Description: A toolkit implementing the Matrix Profile concept
that was created by CS-UCR
<http://www.cs.ucr.edu/~eamonn/MatrixProfile.html>.
Author: Francisco Bischoff [aut, cre] ,
Michael Yeh [res, ccp, ctb] ,
Diego Silva [res, ccp, ctb] ,
Yan Zhu [res, ccp, ctb] ,
Hoang Dau [res, ccp, ctb] ,
Michele Linardi [res, ccp, ctb]
Maintainer: Francisco Bischoff <fbischoff@med.up.pt>
Diff between tsmp versions 0.4.16 dated 2025-12-04 and 0.5.1 dated 2026-10-16
tsmp-0.4.16/tsmp/R/RcppExports.R |only tsmp-0.4.16/tsmp/R/annotations.R |only tsmp-0.4.16/tsmp/R/mass-pre-w.R |only tsmp-0.4.16/tsmp/R/mass-pre.R |only tsmp-0.4.16/tsmp/R/mass.R |only tsmp-0.4.16/tsmp/R/mass_v2.R |only tsmp-0.4.16/tsmp/R/mass_v3.R |only tsmp-0.4.16/tsmp/R/mass_weighted.R |only tsmp-0.4.16/tsmp/R/mpx.R |only tsmp-0.4.16/tsmp/R/scrimp.R |only tsmp-0.4.16/tsmp/R/stamp-par.R |only tsmp-0.4.16/tsmp/R/stamp.R |only tsmp-0.4.16/tsmp/R/stomp-par.R |only tsmp-0.4.16/tsmp/R/stomp.R |only tsmp-0.4.16/tsmp/R/sysdata.rda |only tsmp-0.4.16/tsmp/man/fast_avg_sd.Rd |only tsmp-0.4.16/tsmp/man/fast_movavg.Rd |only tsmp-0.4.16/tsmp/man/fast_movsd.Rd |only tsmp-0.4.16/tsmp/man/mass-deprecated.Rd |only tsmp-0.4.16/tsmp/man/mass_pre.Rd |only tsmp-0.4.16/tsmp/man/mass_pre_w.Rd |only tsmp-0.4.16/tsmp/man/mass_v2.Rd |only tsmp-0.4.16/tsmp/man/mass_v3.Rd |only tsmp-0.4.16/tsmp/man/mass_weighted.Rd |only tsmp-0.4.16/tsmp/man/mpx.Rd |only tsmp-0.4.16/tsmp/man/read.Rd |only tsmp-0.4.16/tsmp/man/scrimp.Rd |only tsmp-0.4.16/tsmp/man/stamp.Rd |only tsmp-0.4.16/tsmp/man/stomp.Rd |only tsmp-0.4.16/tsmp/man/write.Rd |only tsmp-0.4.16/tsmp/src |only tsmp-0.4.16/tsmp/tests/fontconfig-helper.R |only tsmp-0.5.1/tsmp/DESCRIPTION | 23 tsmp-0.5.1/tsmp/MD5 | 268 +-- tsmp-0.5.1/tsmp/NAMESPACE | 44 tsmp-0.5.1/tsmp/NEWS | 196 +- tsmp-0.5.1/tsmp/NEWS.md | 50 tsmp-0.5.1/tsmp/R/analyze.R | 3 tsmp-0.5.1/tsmp/R/annotation_vectors.R |only tsmp-0.5.1/tsmp/R/compute.R | 118 - tsmp-0.5.1/tsmp/R/dist_profile.R | 270 ++- tsmp-0.5.1/tsmp/R/find-chains.R | 7 tsmp-0.5.1/tsmp/R/find-discord.R | 21 tsmp-0.5.1/tsmp/R/find-motifs.R | 12 tsmp-0.5.1/tsmp/R/find-snippet.R | 19 tsmp-0.5.1/tsmp/R/fluss.R | 54 tsmp-0.5.1/tsmp/R/misc.R | 758 ++-------- tsmp-0.5.1/tsmp/R/mpdist.R | 79 - tsmp-0.5.1/tsmp/R/mstomp-par.R | 343 ---- tsmp-0.5.1/tsmp/R/mstomp.R | 275 --- tsmp-0.5.1/tsmp/R/plot.R | 186 +- tsmp-0.5.1/tsmp/R/pmp.R | 50 tsmp-0.5.1/tsmp/R/print.R | 24 tsmp-0.5.1/tsmp/R/salient.R | 61 tsmp-0.5.1/tsmp/R/sdts-train.R | 28 tsmp-0.5.1/tsmp/R/serialize.R | 79 - tsmp-0.5.1/tsmp/R/simple.R | 18 tsmp-0.5.1/tsmp/R/stompi.R | 24 tsmp-0.5.1/tsmp/R/subset.R | 95 - tsmp-0.5.1/tsmp/R/tsmp-package.R | 33 tsmp-0.5.1/tsmp/R/tsmp.R | 143 + tsmp-0.5.1/tsmp/R/valmod.R | 61 tsmp-0.5.1/tsmp/R/zzz.R | 58 tsmp-0.5.1/tsmp/README.md | 124 + tsmp-0.5.1/tsmp/build/vignette.rds |binary tsmp-0.5.1/tsmp/data/datalist | 5 tsmp-0.5.1/tsmp/inst/API-v0.5.1 |only tsmp-0.5.1/tsmp/inst/WORDLIST | 46 tsmp-0.5.1/tsmp/inst/benchmarks |only tsmp-0.5.1/tsmp/inst/doc/press.R | 14 tsmp-0.5.1/tsmp/inst/doc/press.Rmd | 16 tsmp-0.5.1/tsmp/inst/doc/press.html | 53 tsmp-0.5.1/tsmp/inst/schemaorg.json | 6 tsmp-0.5.1/tsmp/man/analyze.Rd | 10 tsmp-0.5.1/tsmp/man/as.matrixprofile.Rd | 3 tsmp-0.5.1/tsmp/man/as_ts_data.Rd |only tsmp-0.5.1/tsmp/man/av_apply.Rd | 14 tsmp-0.5.1/tsmp/man/av_complexity.Rd | 14 tsmp-0.5.1/tsmp/man/av_hardlimit_artifact.Rd | 14 tsmp-0.5.1/tsmp/man/av_motion_artifact.Rd | 14 tsmp-0.5.1/tsmp/man/av_stop_word.Rd | 14 tsmp-0.5.1/tsmp/man/av_zerocrossing.Rd | 14 tsmp-0.5.1/tsmp/man/compute.Rd | 10 tsmp-0.5.1/tsmp/man/discords.Rd | 10 tsmp-0.5.1/tsmp/man/dist_profile.Rd | 30 tsmp-0.5.1/tsmp/man/figures/dependency_plot-1.png |binary tsmp-0.5.1/tsmp/man/find_discord.Rd | 8 tsmp-0.5.1/tsmp/man/find_motif.Rd | 9 tsmp-0.5.1/tsmp/man/find_snippet.Rd | 10 tsmp-0.5.1/tsmp/man/floss.Rd | 14 tsmp-0.5.1/tsmp/man/floss_cac.Rd | 18 tsmp-0.5.1/tsmp/man/floss_extract.Rd | 14 tsmp-0.5.1/tsmp/man/fluss.Rd | 14 tsmp-0.5.1/tsmp/man/fluss_cac.Rd | 18 tsmp-0.5.1/tsmp/man/fluss_extract.Rd | 14 tsmp-0.5.1/tsmp/man/fluss_score.Rd | 18 tsmp-0.5.1/tsmp/man/get_data.Rd | 3 tsmp-0.5.1/tsmp/man/ipaa.Rd |only tsmp-0.5.1/tsmp/man/min_mp_idx.Rd | 3 tsmp-0.5.1/tsmp/man/motifs.Rd | 10 tsmp-0.5.1/tsmp/man/mpdist.Rd | 5 tsmp-0.5.1/tsmp/man/mstomp.Rd | 22 tsmp-0.5.1/tsmp/man/paa.Rd |only tsmp-0.5.1/tsmp/man/pmp.Rd | 9 tsmp-0.5.1/tsmp/man/pmp_upper_bound.Rd | 2 tsmp-0.5.1/tsmp/man/read_json.Rd |only tsmp-0.5.1/tsmp/man/remove_class.Rd | 3 tsmp-0.5.1/tsmp/man/salient_subsequences.Rd | 2 tsmp-0.5.1/tsmp/man/sdts_predict.Rd | 6 tsmp-0.5.1/tsmp/man/sdts_score.Rd | 6 tsmp-0.5.1/tsmp/man/sdts_train.Rd | 12 tsmp-0.5.1/tsmp/man/set_data.Rd | 3 tsmp-0.5.1/tsmp/man/simple_fast.Rd | 2 tsmp-0.5.1/tsmp/man/tsmp-deprecated.Rd | 22 tsmp-0.5.1/tsmp/man/tsmp-package.Rd |only tsmp-0.5.1/tsmp/man/tsmp.Rd | 38 tsmp-0.5.1/tsmp/man/valmod.Rd | 13 tsmp-0.5.1/tsmp/man/visualize.Rd | 10 tsmp-0.5.1/tsmp/man/write_json.Rd |only tsmp-0.5.1/tsmp/tests/spelling.R | 10 tsmp-0.5.1/tsmp/tests/testthat.R | 8 tsmp-0.5.1/tsmp/tests/testthat/Rplots.pdf |only tsmp-0.5.1/tsmp/tests/testthat/_snaps/plot-print.md |only tsmp-0.5.1/tsmp/tests/testthat/_snaps/plot-print/plot-salient.svg | 230 +-- tsmp-0.5.1/tsmp/tests/testthat/_snaps/visualize/visualize.svg | 2 tsmp-0.5.1/tsmp/tests/testthat/_snaps/visualize/visualize2.svg | 2 tsmp-0.5.1/tsmp/tests/testthat/helper.R |only tsmp-0.5.1/tsmp/tests/testthat/test-analyze.R | 17 tsmp-0.5.1/tsmp/tests/testthat/test-annotation.R | 18 tsmp-0.5.1/tsmp/tests/testthat/test-as-ts-data.R |only tsmp-0.5.1/tsmp/tests/testthat/test-basics.R | 17 tsmp-0.5.1/tsmp/tests/testthat/test-compute.R | 23 tsmp-0.5.1/tsmp/tests/testthat/test-discords.R | 1 tsmp-0.5.1/tsmp/tests/testthat/test-find-chains.R | 3 tsmp-0.5.1/tsmp/tests/testthat/test-find-discord.R | 2 tsmp-0.5.1/tsmp/tests/testthat/test-fluss.R | 1 tsmp-0.5.1/tsmp/tests/testthat/test-mass-agressive.R | 3 tsmp-0.5.1/tsmp/tests/testthat/test-misc.R | 1 tsmp-0.5.1/tsmp/tests/testthat/test-motifs.R | 1 tsmp-0.5.1/tsmp/tests/testthat/test-mpdist.R | 1 tsmp-0.5.1/tsmp/tests/testthat/test-mstomp-search.R | 1 tsmp-0.5.1/tsmp/tests/testthat/test-na-handling.R |only tsmp-0.5.1/tsmp/tests/testthat/test-plot-print.R | 182 +- tsmp-0.5.1/tsmp/tests/testthat/test-salient.R | 1 tsmp-0.5.1/tsmp/tests/testthat/test-sdts.R | 3 tsmp-0.5.1/tsmp/tests/testthat/test-serialize.R | 51 tsmp-0.5.1/tsmp/tests/testthat/test-simple.R | 1 tsmp-0.5.1/tsmp/tests/testthat/test-stamps.R | 127 - tsmp-0.5.1/tsmp/tests/testthat/test-stomp-search.R | 3 tsmp-0.5.1/tsmp/tests/testthat/test-stress-stamps.R | 33 tsmp-0.5.1/tsmp/tests/testthat/test-subset.R | 1 tsmp-0.5.1/tsmp/tests/testthat/test-valmod.R | 2 tsmp-0.5.1/tsmp/tests/testthat/test-visualize.R | 24 tsmp-0.5.1/tsmp/vignettes/press.Rmd | 16 154 files changed, 2177 insertions(+), 2727 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph] ,
Emmanuel Paradis [cph] ,
Robert Noble [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 2.4.1 dated 2026-09-10 and 2.5.0 dated 2026-10-16
DESCRIPTION | 8 MD5 | 531 - NAMESPACE | 1048 +-- NEWS.md | 21 R/AddTip.R | 550 +- R/Cherries.R | 68 R/ClusterTable.R | 254 R/Combinatorics.R | 696 +- R/ConsistentSplits.R | 84 R/Decompose.R | 330 - R/EdgeRatio.R | 70 R/ImposeConstraint.R | 278 - R/KeptPaths.R | 94 R/LongBranchScore.R | 150 R/MatchNodes.R | 253 R/MatchStrings.R | 66 R/PathLengths.R | 96 R/PhyToString.R | 284 - R/RUtreebalance.R | 648 +- R/RcppExports-manual.R | 70 R/RcppExports.R | 12 R/ReadMrBayes.R | 190 R/ReadTntTree.R | 580 +- R/Reweight.R | 220 R/SplitFunctions.R | 912 +-- R/Splits.R | 1336 ++-- R/Stemwardness.R | 218 R/TipTimedTree.R | 100 R/TopologyOnly.R | 84 R/TreeNumber.R | 1166 ++-- R/Treeness.R | 116 R/as.matrix.R | 30 R/as.multiPhylo.R | 152 R/data.R | 180 R/helper_functions.R | 200 R/match.R | 496 - R/mst.R | 158 R/sort.R | 156 R/split_analysis.R | 162 R/tree_ancestors.R | 220 R/tree_comparison.R | 86 R/tree_display.R | 292 - R/tree_generation.R | 1006 +-- R/tree_information.R | 206 R/tree_numbering.R | 22 R/tree_shape.R | 572 +- R/tree_write.R | 262 build/partial.rdb |binary data/brewer.R | 40 data/nRootedShapes.R | 114 data/nUnrootedShapes.R | 124 inst/CITATION | 36 inst/REFERENCES.bib | 778 +- inst/WORDLIST | 206 inst/apa-old-doi-prefix.csl | 4551 ++++++++--------- inst/doc/filesystem-navigation.Rmd | 104 inst/doc/filesystem-navigation.html | 4 inst/doc/load-data.Rmd | 428 - inst/doc/load-data.html | 4 inst/doc/load-trees.Rmd | 250 inst/doc/load-trees.html | 4 inst/extdata/input/dataset.nex | 44 inst/extdata/input/notes.nex | 54 inst/extdata/output/named.tre | 6 inst/extdata/output/numbered.tre | 8 inst/extdata/tests/ape-tree.nex | 10 inst/extdata/tests/continuous.nex | 44 inst/extdata/tests/encoding.nex | 48 inst/extdata/tests/parse-nexus.nexus | 510 - inst/extdata/tests/statelabels-semicolon.nex | 58 inst/extdata/tests/taxon-notes.nex | 48 inst/extdata/tests/tnt-amp-continuation.tnt | 20 inst/extdata/tests/tnt-bare-tree.tnt | 2 inst/extdata/tests/tnt-cp1252-taxa.tnt | 12 inst/extdata/tests/tnt-dna.tnt | 42 inst/extdata/tests/tnt-matrix.tnt | 294 - inst/extdata/tests/tnt-midline-xread.tnt | 12 inst/extdata/tests/tnt-multiline-comment.tnt | 26 inst/extdata/tests/tnt-multiline-taxa.tnt | 26 inst/extdata/tests/tnt-multitaxon-line.tnt | 10 inst/extdata/tests/tnt-namedtree.tre | 8 inst/extdata/tests/tnt-smartquote-taxa.tnt | 24 inst/extdata/tests/tnt-taxon-taxonomy.tnt | 14 inst/extdata/tests/tnt-tree.tre | 46 inst/extdata/tests/tnt-trees-and-matrix.tnt | 58 inst/extdata/tests/tnt-xgroup.tnt | 32 inst/include/TreeTools/SplitList.h | 120 inst/include/TreeTools/edge_to_splits.h |only man/AddTip.Rd | 280 - man/AncestorEdge.Rd | 108 man/ApeTime.Rd | 54 man/ArtificialExtinction.Rd | 216 man/CharacterInformation.Rd | 86 man/Cherries.Rd | 108 man/CladeSizes.Rd | 98 man/CladisticInfo.Rd | 144 man/ClusterTable-methods.Rd | 94 man/ClusterTable.Rd | 160 man/CollapseNode.Rd | 162 man/CompatibleSplits.Rd | 108 man/Consensus.Rd | 156 man/ConsensusWithout.Rd | 212 man/ConstrainedNJ.Rd | 108 man/Decompose.Rd | 168 man/DescendantEdges.Rd | 164 man/DoubleFactorial.Rd | 132 man/DropTip.Rd | 280 - man/EdgeAncestry.Rd | 126 man/EdgeDistances.Rd | 106 man/EdgeRatio.Rd | 92 man/EndSentence.Rd | 64 man/ExtractTaxa.Rd | 90 man/GenerateTree.Rd | 202 man/Hamming.Rd | 156 man/ImposeConstraint.Rd | 148 man/J1Index.Rd | 190 man/KeptPaths.Rd | 132 man/KeptVerts.Rd | 138 man/LabelSplits.Rd | 172 man/LeafLabelInterchange.Rd | 118 man/ListAncestors.Rd | 192 man/Lobo.data.Rd | 66 man/LongBranch.Rd | 130 man/MRCA.Rd | 136 man/MSTEdges.Rd | 146 man/MakeTreeBinary.Rd | 108 man/MatchEdges.Rd | 155 man/MatchStrings.Rd | 80 man/MatrixToPhyDat.Rd | 158 man/MorphoBankDecode.Rd | 58 man/N1Spr.Rd | 76 man/NDescendants.Rd | 100 man/NJTree.Rd | 82 man/NPartitionPairs.Rd | 102 man/NRooted.Rd | 268 - man/NSplits.Rd | 172 man/NTip.Rd | 140 man/NewickTree.Rd | 54 man/Neworder.Rd | 128 man/NexusTokensToInteger.Rd | 128 man/NodeDepth.Rd | 128 man/NodeNumbers.Rd | 116 man/NodeOrder.Rd | 110 man/PaintTree.Rd | 196 man/PairwiseDistances.Rd | 82 man/PathLengths.Rd | 118 man/PhyToString.Rd | 214 man/PolarizeSplits.Rd | 70 man/ReadCharacters.Rd | 314 - man/ReadMrBayesTrees.Rd | 110 man/ReadTntTree.Rd | 248 man/Renumber.Rd | 118 man/RenumberTips.Rd | 140 man/Reorder.Rd | 550 +- man/Reweight.Rd | 158 man/RightmostCharacter.Rd | 72 man/RoguePlot.Rd | 240 man/RootNode.Rd | 106 man/RootTree.Rd | 190 man/SampleOne.Rd | 84 man/SortTree.Rd | 184 man/SplitConsistent.Rd | 90 man/SplitFrequency.Rd | 180 man/SplitInformation.Rd | 256 man/SplitMatchProbability.Rd | 94 man/Splits.Rd | 216 man/SplitsInBinaryTree.Rd | 162 man/Stemwardness.Rd | 198 man/Subsplit.Rd | 96 man/Subtree.Rd | 122 man/SupportColour.Rd | 142 man/TipLabels.Rd | 252 man/TipTimedTree.Rd | 140 man/TipsInSplits.Rd | 144 man/TopologyOnly.Rd | 46 man/TotalCopheneticIndex.Rd | 188 man/TreeIsRooted.Rd | 86 man/TreeNumber.Rd | 432 - man/TreeShape.Rd | 318 - man/TreeTools-package.Rd | 96 man/Treeness.Rd | 114 man/TreesMatchingSplit.Rd | 92 man/TreesMatchingTree.Rd | 98 man/TrivialSplits.Rd | 96 man/TrivialTree.Rd | 126 man/Unquote.Rd | 64 man/UnrootedTreesMatchingSplit.Rd | 96 man/UnshiftTree.Rd | 116 man/WriteTntCharacters.Rd | 140 man/as.Newick.Rd | 96 man/as.multiPhylo.Rd | 106 man/brewer.Rd | 66 man/dot-RandomParent.Rd | 54 man/doubleFactorials.Rd | 52 man/edge_to_splits.Rd | 98 man/is.TreeNumber.Rd | 64 man/logDoubleFactorials.Rd | 46 man/match.Splits.Rd | 136 man/match.multiPhylo.Rd | 144 man/nRootedShapes.Rd | 56 man/print.TreeNumber.Rd | 44 man/root_on_node.Rd | 66 man/sapply64.Rd | 164 man/sort.multiPhylo.Rd | 114 man/xor.Rd | 62 src/RcppExports.cpp | 42 src/match_nodes.cpp |only src/splits.cpp | 51 src/tips_in_splits.cpp | 6 tests/figs/rogueplot.svg | 68 tests/spelling.R | 37 tests/testthat.R | 8 tests/testthat/_snaps/RoguePlot/rogueplot-poly.svg | 82 tests/testthat/_snaps/RoguePlot/rogueplot-simple.svg | 94 tests/testthat/_snaps/RoguePlot/rogueplot-trees1.svg | 106 tests/testthat/_snaps/RoguePlot/rogueplot-trees2.svg | 82 tests/testthat/_snaps/Support/labelsplits-nameless.svg | 172 tests/testthat/_snaps/Support/labelsplits-names.svg | 148 tests/testthat/_snaps/Support/labelsplits.svg | 148 tests/testthat/_snaps/mst/mst-plotting.svg | 142 tests/testthat/_snaps/tree_display/sorted-tree.svg | 270 - tests/testthat/test-ArtificialExtinction.R | 94 tests/testthat/test-Cherries.R | 24 tests/testthat/test-ClusterTable.R | 284 - tests/testthat/test-Decompose.R | 152 tests/testthat/test-EdgeRatio.R | 18 tests/testthat/test-FirstMatchingSplit.R | 68 tests/testthat/test-KeptPaths.R | 40 tests/testthat/test-KeptVerts.R | 172 tests/testthat/test-LongBranchScore.R | 36 tests/testthat/test-MatchNodes.R | 251 tests/testthat/test-MatchStrings.R | 26 tests/testthat/test-PathLengths.R | 70 tests/testthat/test-PhyToString.R | 150 tests/testthat/test-RUtreebalance.R | 128 tests/testthat/test-ReadMrBayes.R | 8 tests/testthat/test-Reweight.R | 92 tests/testthat/test-SplitConsistent.R | 72 tests/testthat/test-SplitFunctions.R | 452 - tests/testthat/test-Stemwardness.R | 28 tests/testthat/test-TipTimedTree.R | 28 tests/testthat/test-TopologyOnly.R | 54 tests/testthat/test-TreeNumber.R | 360 - tests/testthat/test-Treeness.R | 38 tests/testthat/test-as.matrix.R | 14 tests/testthat/test-as.multiPhylo.R | 70 tests/testthat/test-combinatorics.R | 178 tests/testthat/test-edge_to_splits.h.R |only tests/testthat/test-helper_functions.R | 22 tests/testthat/test-information.R | 84 tests/testthat/test-int_to_tree.cpp.R | 130 tests/testthat/test-match.R | 58 tests/testthat/test-mst.R | 84 tests/testthat/test-root_tree.h.R | 278 - tests/testthat/test-sort.R | 44 tests/testthat/test-split_analysis.R | 22 tests/testthat/test-splits.cpp.R | 74 tests/testthat/test-tree_ancestors.R | 40 tests/testthat/test-tree_comparison.R | 48 tests/testthat/test-tree_descendants.R | 168 tests/testthat/test-tree_display.R | 128 tests/testthat/test-tree_generation-random.R | 90 tests/testthat/test-tree_information.R | 38 tests/testthat/test-tree_numbering.R | 27 tests/testthat/testdata/nonPreCons.nex | 48 vignettes/filesystem-navigation.Rmd | 104 vignettes/load-data.Rmd | 428 - vignettes/load-trees.Rmd | 250 268 files changed, 23019 insertions(+), 22628 deletions(-)
Title: Load Census TIGER/Line Shapefiles
Description: Download TIGER/Line shapefiles from the United States Census
Bureau
(<https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html>)
and load into R as 'sf' objects.
Author: Kyle Walker [aut, cre],
Bob Rudis [ctb],
Eli Pousson [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between tigris versions 2.2.1 dated 2025-04-16 and 2.3.0 dated 2026-10-16
tigris-2.2.1/tigris/man/tigris.Rd |only tigris-2.3.0/tigris/DESCRIPTION | 41 tigris-2.3.0/tigris/MD5 | 159 + tigris-2.3.0/tigris/NAMESPACE | 19 tigris-2.3.0/tigris/NEWS | 16 tigris-2.3.0/tigris/R/center_of_pop.R |only tigris-2.3.0/tigris/R/enumeration_units.R | 670 +++----- tigris-2.3.0/tigris/R/geocode.R | 93 - tigris-2.3.0/tigris/R/helpers.R | 635 +++---- tigris-2.3.0/tigris/R/landmarks.R | 73 tigris-2.3.0/tigris/R/legislative.R | 218 +- tigris-2.3.0/tigris/R/metro_areas.R | 274 +-- tigris-2.3.0/tigris/R/national.R | 108 - tigris-2.3.0/tigris/R/native.R | 136 - tigris-2.3.0/tigris/R/places.R | 107 - tigris-2.3.0/tigris/R/pumas.R | 58 tigris-2.3.0/tigris/R/request.R |only tigris-2.3.0/tigris/R/shift_geometry.R | 291 ++- tigris-2.3.0/tigris/R/states.R | 55 tigris-2.3.0/tigris/R/tigris-package.R | 21 tigris-2.3.0/tigris/R/transportation.R | 173 -- tigris-2.3.0/tigris/R/utils.R | 833 ++++++++-- tigris-2.3.0/tigris/R/water.R | 129 - tigris-2.3.0/tigris/R/zzz.R | 47 tigris-2.3.0/tigris/README.md | 69 tigris-2.3.0/tigris/data/fips_codes.rda |binary tigris-2.3.0/tigris/man/address_ranges.Rd | 14 tigris-2.3.0/tigris/man/alaska_native_regional_corporations.Rd | 14 tigris-2.3.0/tigris/man/area_water.Rd | 10 tigris-2.3.0/tigris/man/block_groups.Rd | 24 tigris-2.3.0/tigris/man/blocks.Rd | 24 tigris-2.3.0/tigris/man/call_geolocator.Rd | 3 tigris-2.3.0/tigris/man/call_geolocator_latlon.Rd | 10 tigris-2.3.0/tigris/man/coastline.Rd | 10 tigris-2.3.0/tigris/man/combined_statistical_areas.Rd | 14 tigris-2.3.0/tigris/man/congressional_districts.Rd | 12 tigris-2.3.0/tigris/man/core_based_statistical_areas.Rd | 14 tigris-2.3.0/tigris/man/counties.Rd | 24 tigris-2.3.0/tigris/man/county_subdivisions.Rd | 32 tigris-2.3.0/tigris/man/divisions.Rd | 10 tigris-2.3.0/tigris/man/erase_water.Rd | 2 tigris-2.3.0/tigris/man/landmarks.Rd | 4 tigris-2.3.0/tigris/man/linear_water.Rd | 10 tigris-2.3.0/tigris/man/load_tiger.Rd | 4 tigris-2.3.0/tigris/man/load_tiger_doc_template.Rd | 8 tigris-2.3.0/tigris/man/metro_divisions.Rd | 14 tigris-2.3.0/tigris/man/military.Rd | 4 tigris-2.3.0/tigris/man/nation.Rd | 10 tigris-2.3.0/tigris/man/native_areas.Rd | 17 tigris-2.3.0/tigris/man/new_england.Rd | 14 tigris-2.3.0/tigris/man/places.Rd | 28 tigris-2.3.0/tigris/man/population_centers.Rd |only tigris-2.3.0/tigris/man/primary_roads.Rd | 14 tigris-2.3.0/tigris/man/primary_secondary_roads.Rd | 14 tigris-2.3.0/tigris/man/pumas.Rd | 24 tigris-2.3.0/tigris/man/rails.Rd | 14 tigris-2.3.0/tigris/man/regions.Rd | 10 tigris-2.3.0/tigris/man/roads.Rd | 26 tigris-2.3.0/tigris/man/school_districts.Rd | 24 tigris-2.3.0/tigris/man/shift_geometry.Rd | 28 tigris-2.3.0/tigris/man/state_legislative_districts.Rd | 10 tigris-2.3.0/tigris/man/states.Rd | 24 tigris-2.3.0/tigris/man/tigris-package.Rd |only tigris-2.3.0/tigris/man/tracts.Rd | 24 tigris-2.3.0/tigris/man/tribal_block_groups.Rd | 14 tigris-2.3.0/tigris/man/tribal_census_tracts.Rd | 14 tigris-2.3.0/tigris/man/tribal_subdivisions_national.Rd | 14 tigris-2.3.0/tigris/man/urban_areas.Rd | 17 tigris-2.3.0/tigris/man/validate_county.Rd |only tigris-2.3.0/tigris/man/validate_state.Rd |only tigris-2.3.0/tigris/man/voting_districts.Rd | 10 tigris-2.3.0/tigris/man/zctas.Rd | 24 tigris-2.3.0/tigris/tests/testthat/_snaps |only tigris-2.3.0/tigris/tests/testthat/setup.R |only tigris-2.3.0/tigris/tests/testthat/test-enumeration_units.R |only tigris-2.3.0/tigris/tests/testthat/test-geocode.R |only tigris-2.3.0/tigris/tests/testthat/test-landmarks.R |only tigris-2.3.0/tigris/tests/testthat/test-legislative.R |only tigris-2.3.0/tigris/tests/testthat/test-lookup_helper.R |only tigris-2.3.0/tigris/tests/testthat/test-metro_areas.R |only tigris-2.3.0/tigris/tests/testthat/test-national.R |only tigris-2.3.0/tigris/tests/testthat/test-native.R |only tigris-2.3.0/tigris/tests/testthat/test-places.R |only tigris-2.3.0/tigris/tests/testthat/test-population_centers.R |only tigris-2.3.0/tigris/tests/testthat/test-pumas.R |only tigris-2.3.0/tigris/tests/testthat/test-rbind_tigris.R |only tigris-2.3.0/tigris/tests/testthat/test-request.R |only tigris-2.3.0/tigris/tests/testthat/test-shift_geometry.R |only tigris-2.3.0/tigris/tests/testthat/test-states.R |only tigris-2.3.0/tigris/tests/testthat/test-transportation.R |only tigris-2.3.0/tigris/tests/testthat/test-utils.R |only tigris-2.3.0/tigris/tests/testthat/test-water.R |only tigris-2.3.0/tigris/tests/testthat/test_lookup_helper.R | 24 93 files changed, 2578 insertions(+), 2306 deletions(-)
Title: Tools for Simulation of Evapotranspiration of Field Crops and
Soil Water Balance
Description: Supports the calculation of meteorological characteristics in
evapotranspiration research and reference crop evapotranspiration, and offers
three models to simulate crop evapotranspiration and soil water balance in
the field, including single crop coefficient and dual crop coefficient,
as well as the Shuttleworth-Wallace model. These calculations mainly refer to
Allen et al. (1998, ISBN:92-5-104219-5), Teh (2006, ISBN:1-58-112-998-X), and
Liu et al. (2006) <doi:10.1016/j.agwat.2006.01.018>.
Author: Minguo Liu [aut, cre],
Huimin Yang [dtc, fnd]
Maintainer: Minguo Liu <liumg@nwafu.edu.cn>
Diff between simET versions 1.0.3 dated 2023-08-19 and 1.0.5 dated 2026-10-16
DESCRIPTION | 22 MD5 | 61 - NAMESPACE | 9 R/Estimate.R | 7 R/calculate_ReferenceEvapotranspiration.R | 4 R/calculate_meteorlogy.R | 4 R/calculate_soil.R | 222 ++-- R/convert.R | 381 +++---- R/data.R | 28 R/model_DualKc.R | 1079 ++++++++++--------- R/model_Shuttleworth_Wallace.R | 1511 ++++++++++++++-------------- R/model_Single_Kc.R | 817 +++++++-------- build |only data/FIalfalfa.rda |binary data/SDIalfalfa.rda |binary man/FIalfalfa.Rd | 8 man/Kcb_adj_for_DualKc.Rd | 2 man/Model_DualKc.Rd | 11 man/Model_SW.Rd | 19 man/Model_single_Kc.Rd | 11 man/SDIalfalfa.Rd | 8 man/cal_DeepPercolation.Rd | 35 man/cal_Dei_for_DualKc.Rd | 3 man/cal_Kc_max_for_DualKc.Rd | 2 man/cal_capillaryRise.Rd | 16 man/cal_reductionFactorForT.Rd | 2 man/convert_Fahrenheit_to_degreesCelsius.Rd | 9 man/convert_Kelvin_to_degreesCelsius.Rd |only man/convert_degreesCelsius_to_Fahrenheit.Rd | 7 man/convert_degreesCelsius_to_Kelvin.Rd |only man/create_modelDF.Rd | 30 man/estimate_goodnessOfFit.Rd | 3 man/simET-package.Rd | 45 33 files changed, 2267 insertions(+), 2089 deletions(-)
Title: Semiparametric Least Squares Inference for Causal Effects
Description: Several causal effects are measured using least squares regressions and basis function approximations. Backward and forward selection methods based on different criteria are used to select the basis functions.
Author: Pierre Chausse Developer [aut, cre],
Mihai Giurcanu Developer [aut]
Maintainer: Pierre Chausse Developer <pchausse@uwaterloo.ca>
Diff between causalSLSE versions 0.4-1 dated 2025-08-29 and 0.4-2 dated 2026-10-16
causalSLSE-0.4-1/causalSLSE/inst/CITATION |only causalSLSE-0.4-1/causalSLSE/src/rsum.f90 |only causalSLSE-0.4-2/causalSLSE/DESCRIPTION | 11 +++++++---- causalSLSE-0.4-2/causalSLSE/MD5 | 14 +++++++------- causalSLSE-0.4-2/causalSLSE/NEWS |only causalSLSE-0.4-2/causalSLSE/build/partial.rdb |only causalSLSE-0.4-2/causalSLSE/build/vignette.rds |binary causalSLSE-0.4-2/causalSLSE/inst/doc/causalSLSE.pdf |binary causalSLSE-0.4-2/causalSLSE/man/nsw.Rd | 2 +- causalSLSE-0.4-2/causalSLSE/src/causal.f | 14 +++++++------- 10 files changed, 22 insertions(+), 19 deletions(-)
Title: Penalized Transformation Models
Description: Partially penalized versions of specific transformation models
implemented in package 'mlt'. Available models include a fully parametric version
of the Cox model, other parametric survival models (Weibull, etc.), normal and
transformed-normal (Box-Cox type) linear models, and continuous outcome logistic
regression. Models can be specified via a formula interface. Hyperparameter tuning
is facilitated through model-based optimization functionalities from package 'mlr3mbo'.
The accompanying vignette describes the methodology used in 'tramnet' in detail.
Transformation models and model-based optimization are described in
Hothorn et al. (2019) <doi:10.1111/sjos.12291> and
Bischl et al. (2017) <doi:10.48550/arXiv.1703.03373>, respectively.
Author: Lucas Kook [cre, aut],
Balint Tamasi [ctb],
Sandra Siegfried [ctb],
Samuel Pawel [ctb],
Torsten Hothorn [ctb]
Maintainer: Lucas Kook <lucasheinrich.kook@gmail.com>
Diff between tramnet versions 0.0-991 dated 2026-03-10 and 0.1-0 dated 2026-10-16
tramnet-0.0-991/tramnet/tests/Colr-pen.R |only tramnet-0.0-991/tramnet/vignettes/RJournal.sty |only tramnet-0.1-0/tramnet/DESCRIPTION | 34 - tramnet-0.1-0/tramnet/MD5 | 82 +- tramnet-0.1-0/tramnet/NAMESPACE | 95 ++- tramnet-0.1-0/tramnet/NEWS.md |only tramnet-0.1-0/tramnet/R/cvl_tramnet.R | 118 +++- tramnet-0.1-0/tramnet/R/methods.R | 579 +++++++++++++++++---- tramnet-0.1-0/tramnet/R/package.R |only tramnet-0.1-0/tramnet/R/prof_lambda.R | 203 +++++-- tramnet-0.1-0/tramnet/R/tramnet.R | 346 ++++++++---- tramnet-0.1-0/tramnet/R/tramnet_formula.R |only tramnet-0.1-0/tramnet/R/tramnet_mbo.R | 330 +++++++++-- tramnet-0.1-0/tramnet/build/vignette.rds |binary tramnet-0.1-0/tramnet/inst/doc/tramnet.R | 58 +- tramnet-0.1-0/tramnet/inst/doc/tramnet.Rnw | 145 +++-- tramnet-0.1-0/tramnet/inst/doc/tramnet.pdf |binary tramnet-0.1-0/tramnet/man/Coxphnet.Rd |only tramnet-0.1-0/tramnet/man/coef.tramnet.Rd | 19 tramnet-0.1-0/tramnet/man/coef.tramnet_Lm.Rd | 28 - tramnet-0.1-0/tramnet/man/cvl_tramnet.Rd | 20 tramnet-0.1-0/tramnet/man/elnet_obj.Rd | 20 tramnet-0.1-0/tramnet/man/estfun.tramnet.Rd | 21 tramnet-0.1-0/tramnet/man/lasso_obj.Rd | 11 tramnet-0.1-0/tramnet/man/logLik.tramnet.Rd | 32 - tramnet-0.1-0/tramnet/man/mbo_recommended.Rd | 17 tramnet-0.1-0/tramnet/man/mbo_tramnet.Rd | 74 ++ tramnet-0.1-0/tramnet/man/model.matrix.tramnet.Rd |only tramnet-0.1-0/tramnet/man/plot.tramnet.Rd | 26 tramnet-0.1-0/tramnet/man/plot_path.Rd | 9 tramnet-0.1-0/tramnet/man/predict.tramnet.Rd | 20 tramnet-0.1-0/tramnet/man/print.summary.tramnet.Rd | 16 tramnet-0.1-0/tramnet/man/print.tramnet.Rd | 13 tramnet-0.1-0/tramnet/man/prof_alpha.Rd | 20 tramnet-0.1-0/tramnet/man/prof_lambda.Rd | 20 tramnet-0.1-0/tramnet/man/residuals.tramnet.Rd | 20 tramnet-0.1-0/tramnet/man/ridge_obj.Rd | 11 tramnet-0.1-0/tramnet/man/simulate.tramnet.Rd | 19 tramnet-0.1-0/tramnet/man/summary.tramnet.Rd | 15 tramnet-0.1-0/tramnet/man/tramnet.Rd | 80 ++ tramnet-0.1-0/tramnet/tests/testthat |only tramnet-0.1-0/tramnet/tests/testthat.R |only tramnet-0.1-0/tramnet/vignettes/cache.rda |binary tramnet-0.1-0/tramnet/vignettes/kook-hothorn.bib | 11 tramnet-0.1-0/tramnet/vignettes/tramnet.Rnw | 145 +++-- 45 files changed, 1975 insertions(+), 682 deletions(-)
Title: Geometric Features and Footprint Comparison for 'sf' Objects
Description: Extracts reproducible geometric and urban-morphology descriptors from
polygon and multipart polygon building footprints stored as 'sf' objects,
including area, perimeter, compactness, shape, topology, convexity, orientation,
and optional building-height and floor-area metrics. Compares polygon footprints
across periods using the intersection-over-union (Jaccard) index (Jaccard,
1912) <doi:10.1111/j.1469-8137.1912.tb05611.x> to identify new constructions,
potential demolitions, and footprint changes. Supports vector file formats
readable by 'sf', including Shapefiles and GeoPackage (GPKG) vector files with
named layers, optional boundary clipping, and reprojection to a common coordinate
reference system. Returned 'sf' objects preserve source attributes and geometry
for spatial analysis and downstream workflows, with optional parallel processing
using 'future' for larger feature-extraction jobs.
Author: Jonathan Cohen [aut, cre]
Maintainer: Jonathan Cohen <cohen.jota@gmail.com>
Diff between geomorphR versions 0.2.0 dated 2026-10-13 and 0.2.1 dated 2026-10-16
DESCRIPTION | 6 MD5 | 12 - NEWS.md | 12 + R/extract_geometric_features.R | 149 +++++++++++------------ README.md | 85 ++++++++++--- inst/examples/compare_footprints.R | 34 ++++- tests/testthat/test_extract_geometric_features.R | 55 ++++++++ 7 files changed, 248 insertions(+), 105 deletions(-)
Title: Apply Function to Elements in Parallel using Futures
Description: Implementations of apply(), by(), eapply(), lapply(), Map(), .mapply(), mapply(), replicate(), sapply(), tapply(), and vapply() that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster. These future_*apply() functions come with the same pros and cons as the corresponding base-R *apply() functions but with the additional feature of being able to be processed via the future framework <doi:10.32614/RJ-2021-048>.
Author: Henrik Bengtsson [aut, cre, cph] ,
R Core Team [cph, ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.apply versions 1.20.2 dated 2026-02-20 and 1.21.0 dated 2026-10-16
future.apply-1.20.2/future.apply/inst/testme/_prologue/995.detrius-connections.R |only future.apply-1.20.2/future.apply/inst/testme/test-rng.R |only future.apply-1.20.2/future.apply/tests/test-rng.R |only future.apply-1.21.0/future.apply/.Rinstignore |only future.apply-1.21.0/future.apply/DESCRIPTION | 14 future.apply-1.21.0/future.apply/MD5 | 91 +++--- future.apply-1.21.0/future.apply/NAMESPACE | 50 ++- future.apply-1.21.0/future.apply/NEWS.md | 71 ++++ future.apply-1.21.0/future.apply/R/001.import_future_functions.R | 6 future.apply-1.21.0/future.apply/R/condition-handlers.R | 7 future.apply-1.21.0/future.apply/R/future_apply.R | 34 +- future.apply-1.21.0/future.apply/R/future_by.R | 6 future.apply-1.21.0/future.apply/R/future_kernapply.R | 32 +- future.apply-1.21.0/future.apply/R/future_lapply.R | 24 + future.apply-1.21.0/future.apply/R/future_mapply.R | 118 +++++--- future.apply-1.21.0/future.apply/R/future_tapply.R | 2 future.apply-1.21.0/future.apply/R/future_vapply.R | 78 ++++- future.apply-1.21.0/future.apply/R/future_xapply.R | 30 +- future.apply-1.21.0/future.apply/R/globals.R | 4 future.apply-1.21.0/future.apply/R/makeChunks.R | 11 future.apply-1.21.0/future.apply/R/options.R | 5 future.apply-1.21.0/future.apply/R/utils,conditions.R | 22 - future.apply-1.21.0/future.apply/R/utils,future.R |only future.apply-1.21.0/future.apply/R/utils-debug.R | 10 future.apply-1.21.0/future.apply/R/utils.R | 12 future.apply-1.21.0/future.apply/R/zzz.R | 3 future.apply-1.21.0/future.apply/build/vignette.rds |binary future.apply-1.21.0/future.apply/inst/doc/future.apply-1-overview.html | 18 - future.apply-1.21.0/future.apply/inst/testme/_prologue/030.imports.R | 3 future.apply-1.21.0/future.apply/inst/testme/_prologue/995.detritus-connections.R |only future.apply-1.21.0/future.apply/inst/testme/run.R | 8 future.apply-1.21.0/future.apply/inst/testme/test-future_Filter.R | 12 future.apply-1.21.0/future.apply/inst/testme/test-future_apply.R | 17 + future.apply-1.21.0/future.apply/inst/testme/test-future_by.R | 56 +++ future.apply-1.21.0/future.apply/inst/testme/test-future_kernapply.R | 51 +++ future.apply-1.21.0/future.apply/inst/testme/test-future_lapply,RNG.R | 6 future.apply-1.21.0/future.apply/inst/testme/test-future_lapply.R | 68 ++++ future.apply-1.21.0/future.apply/inst/testme/test-future_mapply.R | 5 future.apply-1.21.0/future.apply/inst/testme/test-future_tapply.R | 6 future.apply-1.21.0/future.apply/inst/testme/test-future_vapply.R | 144 +++++++++- future.apply-1.21.0/future.apply/inst/testme/test-makeChunks.R |only future.apply-1.21.0/future.apply/inst/testme/test-rng,disposable.R |only future.apply-1.21.0/future.apply/man/future.apply.Rd | 8 future.apply-1.21.0/future.apply/man/future.apply.options.Rd | 2 future.apply-1.21.0/future.apply/man/future_apply.Rd | 7 future.apply-1.21.0/future.apply/man/future_by.Rd | 2 future.apply-1.21.0/future.apply/man/future_lapply.Rd | 19 - future.apply-1.21.0/future.apply/man/future_mapply.Rd | 28 + future.apply-1.21.0/future.apply/man/makeChunks.Rd | 5 future.apply-1.21.0/future.apply/tests/incl/start,load-only.R | 3 future.apply-1.21.0/future.apply/tests/test-makeChunks.R |only future.apply-1.21.0/future.apply/tests/test-rng,disposable.R |only 52 files changed, 819 insertions(+), 279 deletions(-)
Title: R Interface to the 'COIN-OR' 'Clp' Linear Programming Solver
Description: Solves linear programs with 'Clp', the simplex and interior
point code of the 'COIN-OR' project <https://github.com/coin-or/Clp>.
Provides a one-call solver interface for dense and sparse constraint
matrices, and complete low level bindings to the 'Clp' callable library
covering problem construction, warm starts, presolve options, basis
access and 'MPS' files. A compatibility layer reproduces the interface
of the archived 'clpAPI' package so that existing code keeps working.
'Clp' itself is not bundled and must be installed on the system; the
'Rtools' toolchain supplies it on 'Windows', from 'Rtools' 4.3 on.
Author: Sam Lovick [aut, cre]
Maintainer: Sam Lovick <sam@lovickconsulting.com>
Diff between coinclp versions 0.1.1 dated 2026-09-16 and 0.1.2 dated 2026-10-16
DESCRIPTION | 8 ++++---- LICENSE |only MD5 | 9 +++++---- NEWS.md | 13 +++++++++++++ README.md | 10 ++++++++-- inst/COPYRIGHTS | 23 +++++++++++++++++------ 6 files changed, 47 insertions(+), 16 deletions(-)
More information about SynthesizerPlus at CRAN
Permanent link
Title: Spatial Concentration and Radius-Based Risk Calculations
Description: Provides computational building blocks for fixed-radius spatial
aggregation, weighted circle-placement problems, hotspot detection, and
polygon-based spatial summaries. The package focuses on efficient
determination of the sum of observations within a given radius, identifying
areas of high local concentration, and aggregating point data to polygon
geometries. These methods are useful for applications such as insurance,
urban analytics, environmental exposure analysis, and other spatial point
pattern workflows. The fixed-radius circle placement problem is discussed
by Chazelle and Lee (1986) <doi:10.1007/BF02238188>, and
related maximum covering problems are described by Church (1974)
<doi:10.1007/BF01942293>.
Author: Martin Haringa [aut, cre]
Maintainer: Martin Haringa <mtharinga@gmail.com>
Diff between spatialrisk versions 0.8.3 dated 2026-09-30 and 0.8.4 dated 2026-10-16
spatialrisk-0.8.3/spatialrisk/man/figures |only spatialrisk-0.8.4/spatialrisk/DESCRIPTION | 6 - spatialrisk-0.8.4/spatialrisk/MD5 | 45 ++++------ spatialrisk-0.8.4/spatialrisk/NEWS.md | 11 ++ spatialrisk-0.8.4/spatialrisk/R/choropleth.R | 17 +++ spatialrisk-0.8.4/spatialrisk/R/deprecated.R | 9 +- spatialrisk-0.8.4/spatialrisk/R/deprecated_highest_concentration.R | 34 +++---- spatialrisk-0.8.4/spatialrisk/R/highest_concentration_terra.R | 16 ++- spatialrisk-0.8.4/spatialrisk/R/hotspot-workflow.R | 13 ++ spatialrisk-0.8.4/spatialrisk/R/map_points.R | 12 ++ spatialrisk-0.8.4/spatialrisk/inst/doc/fixed-radius-concentration.html | 24 ++--- spatialrisk-0.8.4/spatialrisk/inst/doc/visualisation.R | 4 spatialrisk-0.8.4/spatialrisk/inst/doc/visualisation.Rmd | 13 ++ spatialrisk-0.8.4/spatialrisk/inst/doc/visualisation.html | 10 ++ spatialrisk-0.8.4/spatialrisk/man/choropleth.Rd | 14 ++- spatialrisk-0.8.4/spatialrisk/man/map_points.Rd | 9 +- spatialrisk-0.8.4/spatialrisk/man/plot.conc.Rd | 7 + spatialrisk-0.8.4/spatialrisk/man/plot.hotspot.Rd | 8 + spatialrisk-0.8.4/spatialrisk/man/plot.neighborhood.Rd | 7 + spatialrisk-0.8.4/spatialrisk/man/prepare_spatialrisk.Rd | 12 ++ spatialrisk-0.8.4/spatialrisk/tests/testthat/test-map-basemaps.R |only spatialrisk-0.8.4/spatialrisk/vignettes/visualisation.Rmd | 13 ++ 22 files changed, 207 insertions(+), 77 deletions(-)
Title: Stratigraphic Plug Alignment for Integrating Plug-Based and XRF
Data
Description: Implements the Stratigraphic Plug Alignment (SPA) procedure for
integrating sparsely sampled plug-based measurements (e.g., total organic
carbon, porosity, mineralogy) with high-resolution X-ray fluorescence
(XRF) geochemical data. SPA uses linear interpolation via the base
approx() function with constrained extrapolation (rule = 1) to preserve
stratigraphic order and avoid estimation beyond observed depths. The
method aligns all datasets to a common depth grid, enabling high-resolution
multivariate analysis and stratigraphic interpretation of core-based
datasets such as those from the Utica and Point Pleasant formations.
See R Core Team (2025)
<https://stat.ethz.ch/R-manual/R-devel/library/stats/html/stats-package.html>
and Omodolor (2025)
<http://rave.ohiolink.edu/etdc/view?acc_num=case175262671767524>
for methodological background and geological context.
Author: Hope E. Omodolor [aut] ,
Jeffrey M. Yarus [aut],
Roger H. French [cre]
Maintainer: Roger H. French <rxf131@case.edu>
Diff between spaAlign versions 0.0.7 dated 2026-10-09 and 0.0.8 dated 2026-10-16
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- NEWS.md | 6 ++++-- man/figures/logo.png |only 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Runtime Type Checking
Description: Provides a lightweight runtime type system for 'R' that enables
developers to declare and enforce variable types during execution.
Inspired by 'TypeScript', the package introduces intuitive syntax for
annotating variables and validating data structures, helping catch
type-related errors early and making 'R' code more robust and easier
to maintain.
Author: Mohamed El Fodil Ihaddaden [aut, cre]
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between sicher versions 0.1.1 dated 2026-06-04 and 0.2.0 dated 2026-10-16
DESCRIPTION | 11 MD5 | 62 ++- NAMESPACE | 39 + NEWS.md | 72 +++ R/engine.R |only R/infer_type.R | 14 R/main.R | 716 +++++++++++++++++++---------------- R/object_helpers.R |only R/parse.R |only R/schema.R |only R/typed_vars.R |only R/types_extra.R |only README.md | 462 ++++++++++++++++++++-- man/Coerce.Rd |only man/Date.Rd |only man/DateTime.Rd |only man/Default.Rd |only man/DiscriminatedUnion.Rd |only man/Environment.Rd |only man/Factor.Rd |only man/FunctionOf.Rd |only man/InstanceOf.Rd |only man/Lazy.Rd |only man/MatrixOf.Rd |only man/NonNegative.Rd |only man/Nullable.Rd |only man/Positive.Rd |only man/Record.Rd |only man/Refine.Rd |only man/Tuple.Rd |only man/Unique.Rd |only man/Whole.Rd |only man/branded-types.Rd |only man/check_type.Rd | 17 man/create_dataframe_type.Rd | 6 man/create_list_type.Rd | 9 man/infer_type.Rd | 2 man/intersection-operator.Rd |only man/is_type.Rd |only man/length-modifiers.Rd |only man/object-helpers.Rd |only man/parse_as.Rd |only man/print.sicher_parse_result.Rd |only man/print.sicher_readonly.Rd |only man/to_json_schema.Rd |only man/type_of.Rd |only man/untype.Rd |only man/validate_json.Rd |only tests/testthat/test-new-types.R |only tests/testthat/test-objects-schema.R |only tests/testthat/test-parse.R |only tests/testthat/test-sicher.R | 78 +-- 52 files changed, 1040 insertions(+), 448 deletions(-)
Title: An Automated Cleaning Tool for Semantic and Linguistic Data
Description: Implements several functions that automates the cleaning and spell-checking of text data. Also converges, finalizes, removes plurals and continuous strings, and puts text data in binary format for semantic network analysis. Uses the 'SemNetDictionaries' package to make the cleaning process more accurate, efficient, and reproducible.
Author: Alexander P. Christensen [aut, cre]
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNetCleaner versions 1.3.7 dated 2025-05-08 and 2.0.0 dated 2026-10-16
SemNetCleaner-1.3.7/SemNetCleaner/R/bad.response.R |only SemNetCleaner-1.3.7/SemNetCleaner/R/best.guess.R |only SemNetCleaner-1.3.7/SemNetCleaner/R/bin2resp.R |only SemNetCleaner-1.3.7/SemNetCleaner/R/qwerty.dist.R |only SemNetCleaner-1.3.7/SemNetCleaner/R/read.data.R |only SemNetCleaner-1.3.7/SemNetCleaner/R/resp2bin.R |only SemNetCleaner-1.3.7/SemNetCleaner/R/utils-SemNetCleaner.R |only SemNetCleaner-1.3.7/SemNetCleaner/build/vignette.rds |only SemNetCleaner-1.3.7/SemNetCleaner/inst/Automated |only SemNetCleaner-1.3.7/SemNetCleaner/inst/doc |only SemNetCleaner-1.3.7/SemNetCleaner/man/bad.response.Rd |only SemNetCleaner-1.3.7/SemNetCleaner/man/best.guess.Rd |only SemNetCleaner-1.3.7/SemNetCleaner/man/bin2resp.Rd |only SemNetCleaner-1.3.7/SemNetCleaner/man/qwerty.dist.Rd |only SemNetCleaner-1.3.7/SemNetCleaner/man/read.data.Rd |only SemNetCleaner-1.3.7/SemNetCleaner/man/resp2bin.Rd |only SemNetCleaner-1.3.7/SemNetCleaner/vignettes |only SemNetCleaner-2.0.0/SemNetCleaner/DESCRIPTION | 22 SemNetCleaner-2.0.0/SemNetCleaner/MD5 | 110 - SemNetCleaner-2.0.0/SemNetCleaner/NAMESPACE | 41 SemNetCleaner-2.0.0/SemNetCleaner/NEWS | 602 +++-- SemNetCleaner-2.0.0/SemNetCleaner/R/advance_wizard.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/auto_spellcheck.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/automated_edit.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/bad_response.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/best_guess.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/binary_to_responses.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/brit_us_conversion.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/build_answer_burst.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/change_format.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/convert2snafu.R | 156 - SemNetCleaner-2.0.0/SemNetCleaner/R/convert_miss.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/correct_changes.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/correct_data.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/correct_data_free.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/correspondence_matrix.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/finalize_textcleaner.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/help_window.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/helpers.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/ind_word_check.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/legacy.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/multiple_words.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/obtain_id.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/pluralize.R | 330 +-- SemNetCleaner-2.0.0/SemNetCleaner/R/prep_spellcheck_dictionary.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/qwerty_distance.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/read_data.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/read_uploaded_file.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/response_splitter.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/responses_to_binary.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/search_shiny.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/singularize.R | 582 +++-- SemNetCleaner-2.0.0/SemNetCleaner/R/spellcheck_dictionary.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/spellcheck_menu.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/textcleaner.R | 1045 ++++++++-- SemNetCleaner-2.0.0/SemNetCleaner/R/textcleaner_help.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/textcleaner_shiny.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/walk_through.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/wizard_menu_labels.R |only SemNetCleaner-2.0.0/SemNetCleaner/R/zzz.R | 30 SemNetCleaner-2.0.0/SemNetCleaner/build/partial.rdb |only SemNetCleaner-2.0.0/SemNetCleaner/inst/Shiny |only SemNetCleaner-2.0.0/SemNetCleaner/inst/WORDLIST |only SemNetCleaner-2.0.0/SemNetCleaner/man/advance_wizard.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/automated_edit_server.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/automated_edit_ui.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/bad_response.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/best_guess.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/binary_to_responses.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/build_answer_burst.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/convert2snafu.Rd | 22 SemNetCleaner-2.0.0/SemNetCleaner/man/finalize_textcleaner.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/make_shiny_search_fn.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/pluralize.Rd | 2 SemNetCleaner-2.0.0/SemNetCleaner/man/prepare_automated_for_review.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/qwerty_distance.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/read_data.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/read_uploaded_file.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/responses_to_binary.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/textcleaner.Rd | 202 + SemNetCleaner-2.0.0/SemNetCleaner/man/textcleaner_shiny.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/wizard_menu_labels.Rd |only SemNetCleaner-2.0.0/SemNetCleaner/man/wizard_response_letters.Rd |only 83 files changed, 2240 insertions(+), 904 deletions(-)
Title: Integral Analysis of Diversity Based on Hill Numbers
Description: Measures and compares the diversity of biological communities
(e.g. tables of operational taxonomic units (OTUs), amplicon sequence
variants (ASVs) or metagenome-assembled genomes (MAGs)) based on Hill
numbers, in a unified framework for neutral, phylogenetic and functional
diversity measurement, diversity partitioning, (dis)similarity
measurement, diversity profiles, evenness, redundancy and attribution of
Hill power-sum weight to taxa and sets. The
statistical framework encompasses richness, Shannon and Simpson
diversity, Faith's phylogenetic diversity (PD), Rao's quadratic entropy
and Sorensen- and UniFrac-type dissimilarities, all grounded in a single
Hill-number framework. Methods are described in Jost (2007)
<doi:10.1890/06-1736.1>, Chao et al. (2010)
<doi:10.1098/rstb.2010.0272>, Chiu et al. (2014) <doi:10.1890/12-0960.1>
and reviewed in Alberdi & Gilbert (2019) <doi:10.1111/1755-0998.13014>.
Optional import adapters interoperate with the Bioconductor [...truncated...]
Author: Antton Alberdi [aut, cre]
Maintainer: Antton Alberdi <antton.alberdi@sund.ku.dk>
Diff between hilldiv3 versions 3.0.0 dated 2026-10-06 and 3.1.1 dated 2026-10-16
DESCRIPTION | 9 - MD5 | 21 +-- NAMESPACE | 1 NEWS.md | 24 +++ R/engine-alpha.R | 26 +++ R/hillshare.R |only README.md | 81 ++++++++++-- inst/doc/hilldiv3.R | 6 inst/doc/hilldiv3.Rmd | 34 +++++ inst/doc/hilldiv3.html | 268 +++++++++++++++++++++++----------------- man/hillshare.Rd |only tests/testthat/test-hillshare.R |only vignettes/hilldiv3.Rmd | 34 +++++ 13 files changed, 366 insertions(+), 138 deletions(-)
Title: Cumulative Standardized Binomial EWMA for Multiple Stream
Processes
Description: Implements the Cumulative Standardized Binomial Exponentially Weighted Moving Average (CSB-EWMA) control chart for monitoring multiple independent streams with binomial outcomes. Provides exact variance calculations, adaptive control limits, post-hoc identification with multiple testing corrections (Bonferroni, Holm, Benjamini-Hochberg), and visualization tools. The method is described in Muritala et al. (2026) <doi:10.48550/arXiv.2601.09968>.
Author: Faruk Muritala [aut, cre],
Austin Brown [aut],
Dhrubajyoti Ghosh [aut],
Sherry Ni [aut]
Maintainer: Faruk Muritala <fmurital@students.kennesaw.edu>
Diff between csbewma versions 1.1.0 dated 2026-09-09 and 1.2.0 dated 2026-10-16
DESCRIPTION | 6 ++--- MD5 | 21 ++++++++++--------- NEWS.md | 34 ++++++++++++++++++++++++++++++ R/chart.R | 44 +++++++++++++++++++++++++++++++++------- R/posthoc.R | 18 +++++++++++++--- R/utils.R | 30 ++++++++++++++++++++------- man/calculate_pvalues.Rd | 8 ++++++- man/csb_ewma.Rd | 5 +++- man/dichotomize_data.Rd | 11 +++++++++- man/identify_ooc.Rd | 4 ++- man/run_csb_ewma.Rd | 12 ++++++++++ tests/testthat/test-vector-p0.R |only 12 files changed, 158 insertions(+), 35 deletions(-)
More information about ClimateAnomaly at CRAN
Permanent link
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by
using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.
Author: Matthijs S. Berends [aut, cre] ,
Dennis Souverein [aut, ctb] ,
Erwin E. A. Hassing [aut, ctb],
Aislinn Cook [ctb] ,
Andrew P. Norgan [ctb] ,
Anita Williams [ctb] ,
Annick Lenglet [ctb] ,
Anthony Underwood [ctb] ,
Anton Mymrikov [ctb],
Bart C. Meijer [...truncated...]
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>
Diff between AMR versions 3.0.1 dated 2025-09-20 and 3.1.0 dated 2026-10-16
AMR-3.0.1/AMR/R/custom_eucast_rules.R |only AMR-3.0.1/AMR/R/eucast_rules.R |only AMR-3.0.1/AMR/man/custom_eucast_rules.Rd |only AMR-3.0.1/AMR/man/eucast_rules.Rd |only AMR-3.0.1/AMR/tests/testthat/test-eucast_rules.R |only AMR-3.1.0/AMR/DESCRIPTION | 27 AMR-3.1.0/AMR/MD5 | 371 ++-- AMR-3.1.0/AMR/NAMESPACE | 79 AMR-3.1.0/AMR/NEWS.md | 193 ++ AMR-3.1.0/AMR/R/aa_amr-package.R | 6 AMR-3.1.0/AMR/R/aa_globals.R | 61 AMR-3.1.0/AMR/R/aa_helper_functions.R | 705 ++++--- AMR-3.1.0/AMR/R/aa_helper_pm_functions.R | 7 AMR-3.1.0/AMR/R/aa_options.R | 31 AMR-3.1.0/AMR/R/aa_session_cache.R |only AMR-3.1.0/AMR/R/ab.R | 259 +- AMR-3.1.0/AMR/R/ab_from_text.R | 4 AMR-3.1.0/AMR/R/ab_property.R | 48 AMR-3.1.0/AMR/R/age.R | 14 AMR-3.1.0/AMR/R/amr_course.R |only AMR-3.1.0/AMR/R/amr_selectors.R | 102 - AMR-3.1.0/AMR/R/antibiogram.R | 1259 +++++++++----- AMR-3.1.0/AMR/R/atc_online.R | 8 AMR-3.1.0/AMR/R/av.R | 12 AMR-3.1.0/AMR/R/av_from_text.R | 4 AMR-3.1.0/AMR/R/av_property.R | 12 AMR-3.1.0/AMR/R/availability.R | 2 AMR-3.1.0/AMR/R/bug_drug_combinations.R | 89 AMR-3.1.0/AMR/R/count.R | 54 AMR-3.1.0/AMR/R/custom_antimicrobials.R | 383 ++++ AMR-3.1.0/AMR/R/custom_interpretive_rules.R |only AMR-3.1.0/AMR/R/custom_mdro_guideline.R | 25 AMR-3.1.0/AMR/R/custom_microorganisms.R | 31 AMR-3.1.0/AMR/R/data.R | 104 - AMR-3.1.0/AMR/R/disk.R | 57 AMR-3.1.0/AMR/R/export_biosample.R | 2 AMR-3.1.0/AMR/R/first_isolate.R | 63 AMR-3.1.0/AMR/R/g.test.R | 18 AMR-3.1.0/AMR/R/get_episode.R | 4 AMR-3.1.0/AMR/R/ggplot_pca.R | 4 AMR-3.1.0/AMR/R/ggplot_sir.R | 24 AMR-3.1.0/AMR/R/guess_ab_col.R | 35 AMR-3.1.0/AMR/R/interpretive_rules.R |only AMR-3.1.0/AMR/R/italicise_taxonomy.R | 2 AMR-3.1.0/AMR/R/join_microorganisms.R | 8 AMR-3.1.0/AMR/R/key_antimicrobials.R | 27 AMR-3.1.0/AMR/R/kurtosis.R | 2 AMR-3.1.0/AMR/R/like.R | 7 AMR-3.1.0/AMR/R/mdro.R | 226 +- AMR-3.1.0/AMR/R/mean_amr_distance.R | 4 AMR-3.1.0/AMR/R/mic.R | 80 AMR-3.1.0/AMR/R/mo.R | 557 +++--- AMR-3.1.0/AMR/R/mo_matching_score.R | 8 AMR-3.1.0/AMR/R/mo_property.R | 197 +- AMR-3.1.0/AMR/R/mo_source.R | 52 AMR-3.1.0/AMR/R/pca.R | 14 AMR-3.1.0/AMR/R/plotting.R | 602 +++--- AMR-3.1.0/AMR/R/proportion.R | 100 - AMR-3.1.0/AMR/R/random.R | 31 AMR-3.1.0/AMR/R/resistance_predict.R | 12 AMR-3.1.0/AMR/R/sir.R | 987 +++++++--- AMR-3.1.0/AMR/R/sir_calc.R | 150 + AMR-3.1.0/AMR/R/sir_combine.R |only AMR-3.1.0/AMR/R/sir_df.R | 12 AMR-3.1.0/AMR/R/skewness.R | 2 AMR-3.1.0/AMR/R/sysdata.rda |binary AMR-3.1.0/AMR/R/tidymodels.R |only AMR-3.1.0/AMR/R/top_n_microorganisms.R | 83 AMR-3.1.0/AMR/R/translate.R | 179 + AMR-3.1.0/AMR/R/vctrs.R | 12 AMR-3.1.0/AMR/R/whocc.R | 4 AMR-3.1.0/AMR/R/zz_deprecated.R | 12 AMR-3.1.0/AMR/R/zzz.R | 55 AMR-3.1.0/AMR/README.md | 22 AMR-3.1.0/AMR/data/antibiotics.rda |binary AMR-3.1.0/AMR/data/antimicrobials.rda |binary AMR-3.1.0/AMR/data/clinical_breakpoints.rda |binary AMR-3.1.0/AMR/data/esbl_isolates.rda |only AMR-3.1.0/AMR/data/example_isolates.rda |binary AMR-3.1.0/AMR/data/intrinsic_resistant.rda |binary AMR-3.1.0/AMR/data/microorganisms.codes.rda |binary AMR-3.1.0/AMR/data/microorganisms.groups.rda |binary AMR-3.1.0/AMR/data/microorganisms.rda |binary AMR-3.1.0/AMR/inst/CITATION | 2 AMR-3.1.0/AMR/inst/doc/AMR_for_Python.Rmd | 42 AMR-3.1.0/AMR/inst/doc/AMR_for_Python.html | 66 AMR-3.1.0/AMR/inst/doc/welcome_to_AMR.Rmd | 12 AMR-3.1.0/AMR/inst/doc/welcome_to_AMR.html | 32 AMR-3.1.0/AMR/man/AMR-deprecated.Rd | 3 AMR-3.1.0/AMR/man/AMR-options.Rd | 24 AMR-3.1.0/AMR/man/AMR.Rd | 47 AMR-3.1.0/AMR/man/WHOCC.Rd | 2 AMR-3.1.0/AMR/man/ab_from_text.Rd | 12 AMR-3.1.0/AMR/man/ab_property.Rd | 18 AMR-3.1.0/AMR/man/add_custom_antimicrobials.Rd | 24 AMR-3.1.0/AMR/man/age_groups.Rd | 3 AMR-3.1.0/AMR/man/amr-tidymodels.Rd |only AMR-3.1.0/AMR/man/amr_course.Rd |only AMR-3.1.0/AMR/man/antibiogram.Rd | 411 ++-- AMR-3.1.0/AMR/man/antimicrobial_selectors.Rd | 197 +- AMR-3.1.0/AMR/man/antimicrobials.Rd | 28 AMR-3.1.0/AMR/man/as.ab.Rd | 20 AMR-3.1.0/AMR/man/as.av.Rd | 2 AMR-3.1.0/AMR/man/as.disk.Rd | 7 AMR-3.1.0/AMR/man/as.mic.Rd | 26 AMR-3.1.0/AMR/man/as.mo.Rd | 53 AMR-3.1.0/AMR/man/as.sir.Rd | 199 +- AMR-3.1.0/AMR/man/atc_online.Rd | 8 AMR-3.1.0/AMR/man/av_from_text.Rd | 12 AMR-3.1.0/AMR/man/av_property.Rd | 2 AMR-3.1.0/AMR/man/bug_drug_combinations.Rd | 64 AMR-3.1.0/AMR/man/clinical_breakpoints.Rd | 44 AMR-3.1.0/AMR/man/count.Rd | 109 - AMR-3.1.0/AMR/man/custom_interpretive_rules.Rd |only AMR-3.1.0/AMR/man/custom_mdro_guideline.Rd | 38 AMR-3.1.0/AMR/man/dosage.Rd | 4 AMR-3.1.0/AMR/man/esbl_isolates.Rd |only AMR-3.1.0/AMR/man/example_isolates.Rd | 4 AMR-3.1.0/AMR/man/export_ncbi_biosample.Rd | 10 AMR-3.1.0/AMR/man/first_isolate.Rd | 58 AMR-3.1.0/AMR/man/g.test.Rd | 32 AMR-3.1.0/AMR/man/ggplot_pca.Rd | 42 AMR-3.1.0/AMR/man/ggplot_sir.Rd | 97 - AMR-3.1.0/AMR/man/guess_ab_col.Rd | 8 AMR-3.1.0/AMR/man/interpretive_rules.Rd |only AMR-3.1.0/AMR/man/intrinsic_resistant.Rd | 6 AMR-3.1.0/AMR/man/key_antimicrobials.Rd | 32 AMR-3.1.0/AMR/man/like.Rd | 5 AMR-3.1.0/AMR/man/mdro.Rd | 64 AMR-3.1.0/AMR/man/microorganisms.Rd | 86 AMR-3.1.0/AMR/man/microorganisms.codes.Rd | 7 AMR-3.1.0/AMR/man/microorganisms.groups.Rd | 4 AMR-3.1.0/AMR/man/mo_matching_score.Rd | 4 AMR-3.1.0/AMR/man/mo_property.Rd | 418 +++- AMR-3.1.0/AMR/man/mo_source.Rd | 12 AMR-3.1.0/AMR/man/pca.Rd | 19 AMR-3.1.0/AMR/man/plot.Rd | 207 +- AMR-3.1.0/AMR/man/proportion.Rd | 166 + AMR-3.1.0/AMR/man/random.Rd | 30 AMR-3.1.0/AMR/man/resistance_predict.Rd | 84 AMR-3.1.0/AMR/man/sir_combine.Rd |only AMR-3.1.0/AMR/man/top_n_microorganisms.Rd | 36 AMR-3.1.0/AMR/man/translate.Rd | 10 AMR-3.1.0/AMR/tests/testthat.R | 2 AMR-3.1.0/AMR/tests/testthat/helper-functions.R | 2 AMR-3.1.0/AMR/tests/testthat/helper-microorganisms.R |only AMR-3.1.0/AMR/tests/testthat/test-_deprecated.R | 15 AMR-3.1.0/AMR/tests/testthat/test-_misc.R | 33 AMR-3.1.0/AMR/tests/testthat/test-ab.R | 2 AMR-3.1.0/AMR/tests/testthat/test-ab_from_text.R | 5 AMR-3.1.0/AMR/tests/testthat/test-ab_property.R | 9 AMR-3.1.0/AMR/tests/testthat/test-age.R | 2 AMR-3.1.0/AMR/tests/testthat/test-amr_selectors.R | 6 AMR-3.1.0/AMR/tests/testthat/test-antibiogram.R | 130 + AMR-3.1.0/AMR/tests/testthat/test-atc_online.R | 2 AMR-3.1.0/AMR/tests/testthat/test-av.R | 2 AMR-3.1.0/AMR/tests/testthat/test-av_from_text.R | 2 AMR-3.1.0/AMR/tests/testthat/test-av_property.R | 2 AMR-3.1.0/AMR/tests/testthat/test-availability.R | 2 AMR-3.1.0/AMR/tests/testthat/test-bug_drug_combinations.R | 20 AMR-3.1.0/AMR/tests/testthat/test-count.R | 58 AMR-3.1.0/AMR/tests/testthat/test-custom_antimicrobials.R | 188 ++ AMR-3.1.0/AMR/tests/testthat/test-custom_microorganisms.R | 2 AMR-3.1.0/AMR/tests/testthat/test-data-microorganisms.R |only AMR-3.1.0/AMR/tests/testthat/test-data.R | 542 +++++- AMR-3.1.0/AMR/tests/testthat/test-disk.R | 2 AMR-3.1.0/AMR/tests/testthat/test-first_isolate.R | 2 AMR-3.1.0/AMR/tests/testthat/test-g.test.R | 6 AMR-3.1.0/AMR/tests/testthat/test-get_episode.R | 2 AMR-3.1.0/AMR/tests/testthat/test-ggplot_sir.R | 25 AMR-3.1.0/AMR/tests/testthat/test-guess_ab_col.R | 2 AMR-3.1.0/AMR/tests/testthat/test-interpretive_rules.R |only AMR-3.1.0/AMR/tests/testthat/test-italicise_taxonomy.R | 2 AMR-3.1.0/AMR/tests/testthat/test-join_microorganisms.R | 2 AMR-3.1.0/AMR/tests/testthat/test-key_antimicrobials.R | 2 AMR-3.1.0/AMR/tests/testthat/test-kurtosis.R | 2 AMR-3.1.0/AMR/tests/testthat/test-like.R | 2 AMR-3.1.0/AMR/tests/testthat/test-mdro.R | 69 AMR-3.1.0/AMR/tests/testthat/test-mean_amr_distance.R | 2 AMR-3.1.0/AMR/tests/testthat/test-mic.R | 2 AMR-3.1.0/AMR/tests/testthat/test-mo.R | 61 AMR-3.1.0/AMR/tests/testthat/test-mo_property.R | 23 AMR-3.1.0/AMR/tests/testthat/test-mo_source.R |only AMR-3.1.0/AMR/tests/testthat/test-pca.R | 2 AMR-3.1.0/AMR/tests/testthat/test-plotting.R | 92 + AMR-3.1.0/AMR/tests/testthat/test-proportion.R | 36 AMR-3.1.0/AMR/tests/testthat/test-random.R | 19 AMR-3.1.0/AMR/tests/testthat/test-session_cache.R |only AMR-3.1.0/AMR/tests/testthat/test-sir.R | 344 +++ AMR-3.1.0/AMR/tests/testthat/test-sir_combine.R |only AMR-3.1.0/AMR/tests/testthat/test-skewness.R | 2 AMR-3.1.0/AMR/tests/testthat/test-tidymodels.R |only AMR-3.1.0/AMR/tests/testthat/test-top_n_microorganisms.R | 2 AMR-3.1.0/AMR/tests/testthat/test-translate.R | 18 AMR-3.1.0/AMR/tests/testthat/test-vctrs.R | 2 AMR-3.1.0/AMR/tests/testthat/test-zzz.R | 74 AMR-3.1.0/AMR/tests/tinytest.R.old | 44 AMR-3.1.0/AMR/vignettes/AMR_for_Python.Rmd | 42 AMR-3.1.0/AMR/vignettes/welcome_to_AMR.Rmd | 12 199 files changed, 8543 insertions(+), 3874 deletions(-)
Title: Estimate a Sparse Mixed Frequency Gaussian Factor Model Using a
Two-Step Procedure
Description: Estimate a sparse Gaussian state-space model with mixed frequency
data via sparse principal components analysis and the Kalman filter
and smoother. For more details see Franjic and Schweikert (2024) <doi:10.2139/ssrn.4733872>.
Author: Domenic Franjic [aut, cre]
Maintainer: Domenic Franjic <franjic@uni-hohenheim.de>
Diff between TwoStepSDFM versions 0.2.2 dated 2026-05-19 and 0.3.0 dated 2026-10-16
DESCRIPTION | 9 MD5 | 60 - NAMESPACE | 1 NEWS.md | 2 R/ImputeData.R |only R/KalmanFilterSmoother.R | 896 ++++++++-------- R/Nowcast.R | 8 R/PlotterHelper.R | 320 ++--- R/SparcePCA.R | 974 +++++++++--------- R/TwoStepDenseDFM.R | 10 R/TwoStepSDFM.R | 16 R/data.R | 122 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/IntroTwoStepSDFM.html | 76 - inst/include/Internals/ElNetSolve.h | 8 inst/include/Internals/Orders.h | 6 inst/include/Internals/SparseDFM.h | 87 - man/crossVal.Rd | 420 +++---- man/factor_model.Rd | 82 - man/imputeMonthlyData.Rd |only man/kalmanFilterSmoother.Rd | 286 ++--- man/mixed_freq_factor_model.Rd | 84 - man/noOfFactors.Rd | 188 +-- man/nowcast.Rd | 396 +++---- man/predict.SDFMFit.Rd | 2 man/simFM.Rd | 448 ++++---- man/sparsePCA.Rd | 322 ++--- man/twoStepDenseDFM.Rd | 268 ++-- src/DataGen.cpp | 6 src/Orders.cpp | 4 src/RWrapperSparseUnivariateKalmanFilterSnmoother.cpp | 6 32 files changed, 2567 insertions(+), 2540 deletions(-)
Title: Base Functions for the 'DescToolsX' Ecosystem
Description: Provides the low level utilities on which the 'DescToolsX'
ecosystem is built. Covered are data manipulation and reshaping,
predicates for data inspection and validation, vector and string
operations, handling of labels and metadata, and routines from
number theory and combinatorics. All functions share a common
naming and argument scheme and are implemented as S3 generics
wherever several input types are meaningful, with performance
critical parts written in C++. The package is self contained and
can be used on its own, independently of the higher level packages
of the suite.
Author: Andri Signorell [aut, cre] ,
R Core Team [ctb],
Hans W. Borchers [ctb],
Daniel Chessel [ctb],
Nicholas Cooper [ctb],
Stephane Dray [ctb],
Martin Elff [ctb],
Michael Friendly [ctb],
Friedrich Leisch [ctb],
Thomas Lumley [ctb],
Martin Maechler [ctb],
N [...truncated...]
Maintainer: Andri Signorell <andri@signorell.net>
Diff between bedrock versions 0.1.16 dated 2026-10-01 and 0.1.20 dated 2026-10-16
bedrock-0.1.16/bedrock/R/fileExistURL.R |only bedrock-0.1.16/bedrock/R/isURL.R |only bedrock-0.1.16/bedrock/R/parseSASDatalines.R |only bedrock-0.1.16/bedrock/man/courseData.Rd |only bedrock-0.1.16/bedrock/man/fileExistURL.Rd |only bedrock-0.1.16/bedrock/man/isURL.Rd |only bedrock-0.1.16/bedrock/man/parseSASDatalines.Rd |only bedrock-0.1.16/bedrock/tests/testthat/test-fileExistURL.R |only bedrock-0.1.16/bedrock/tests/testthat/test-isURL.R |only bedrock-0.1.16/bedrock/tests/testthat/test-parseSASDatalines.R |only bedrock-0.1.20/bedrock/DESCRIPTION | 6 bedrock-0.1.20/bedrock/MD5 | 172 ++-- bedrock-0.1.20/bedrock/NAMESPACE | 12 bedrock-0.1.20/bedrock/NEWS.md | 69 + bedrock-0.1.20/bedrock/R/asCDateFmt.R | 18 bedrock-0.1.20/bedrock/R/auditNames.R |only bedrock-0.1.20/bedrock/R/between-operators.R | 10 bedrock-0.1.20/bedrock/R/callIf.R | 24 bedrock-0.1.20/bedrock/R/char-ascii-conversion.R | 8 bedrock-0.1.20/bedrock/R/checks.R | 12 bedrock-0.1.20/bedrock/R/closest.R | 36 - bedrock-0.1.20/bedrock/R/concepts.R | 14 bedrock-0.1.20/bedrock/R/courseData.R | 10 bedrock-0.1.20/bedrock/R/crossProdN.R | 26 bedrock-0.1.20/bedrock/R/dataDescription.R | 8 bedrock-0.1.20/bedrock/R/factorize.R | 36 - bedrock-0.1.20/bedrock/R/funCalls.R | 6 bedrock-0.1.20/bedrock/R/intervals.R | 8 bedrock-0.1.20/bedrock/R/isEuclid.R | 12 bedrock-0.1.20/bedrock/R/isPrime.R | 20 bedrock-0.1.20/bedrock/R/isUrl.R |only bedrock-0.1.20/bedrock/R/parseSasDatalines.R |only bedrock-0.1.20/bedrock/R/permn.R | 8 bedrock-0.1.20/bedrock/R/printCharMatrix.R | 28 bedrock-0.1.20/bedrock/R/rankX.R | 219 ++---- bedrock-0.1.20/bedrock/R/recycle.R | 28 bedrock-0.1.20/bedrock/R/renameX.R | 356 +++++----- bedrock-0.1.20/bedrock/R/sortX.R | 84 +- bedrock-0.1.20/bedrock/R/toBaseR.R | 217 +++--- bedrock-0.1.20/bedrock/R/untable.R | 14 bedrock-0.1.20/bedrock/R/urlExists.R |only bedrock-0.1.20/bedrock/R/winsorize.R | 26 bedrock-0.1.20/bedrock/README.md | 10 bedrock-0.1.20/bedrock/man/Cards.Rd | 2 bedrock-0.1.20/bedrock/man/Pizza.Rd | 2 bedrock-0.1.20/bedrock/man/Roulette.Rd | 2 bedrock-0.1.20/bedrock/man/Tarot.Rd | 2 bedrock-0.1.20/bedrock/man/asCDateFmt.Rd | 18 bedrock-0.1.20/bedrock/man/auditNames.Rd |only bedrock-0.1.20/bedrock/man/between-operators.Rd | 10 bedrock-0.1.20/bedrock/man/buildPath.Rd | 6 bedrock-0.1.20/bedrock/man/callIf.Rd | 20 bedrock-0.1.20/bedrock/man/char-ascii-conversion.Rd | 7 bedrock-0.1.20/bedrock/man/checkConfLevel.Rd | 9 bedrock-0.1.20/bedrock/man/closest.Rd | 28 bedrock-0.1.20/bedrock/man/concepts.Rd | 8 bedrock-0.1.20/bedrock/man/crossProdN.Rd | 4 bedrock-0.1.20/bedrock/man/dataDescription.Rd | 4 bedrock-0.1.20/bedrock/man/factorize.Rd | 18 bedrock-0.1.20/bedrock/man/findDownload.Rd | 6 bedrock-0.1.20/bedrock/man/funArgs.Rd | 1 bedrock-0.1.20/bedrock/man/funCalls.Rd | 5 bedrock-0.1.20/bedrock/man/funKeywords.Rd | 1 bedrock-0.1.20/bedrock/man/funList.Rd | 1 bedrock-0.1.20/bedrock/man/intervals.Rd | 10 bedrock-0.1.20/bedrock/man/isEuclid.Rd | 4 bedrock-0.1.20/bedrock/man/isFilePath.Rd | 82 +- bedrock-0.1.20/bedrock/man/isPrime.Rd | 8 bedrock-0.1.20/bedrock/man/isUrl.Rd |only bedrock-0.1.20/bedrock/man/parseSasDatalines.Rd |only bedrock-0.1.20/bedrock/man/pdfManual.Rd | 2 bedrock-0.1.20/bedrock/man/peekFile.Rd | 2 bedrock-0.1.20/bedrock/man/permn.Rd | 4 bedrock-0.1.20/bedrock/man/printCharMatrix.Rd | 8 bedrock-0.1.20/bedrock/man/rdLabels.Rd | 1 bedrock-0.1.20/bedrock/man/rdTitle.Rd | 1 bedrock-0.1.20/bedrock/man/readCourseData.Rd |only bedrock-0.1.20/bedrock/man/readDownload.Rd | 2 bedrock-0.1.20/bedrock/man/recycle.Rd | 12 bedrock-0.1.20/bedrock/man/renameX.Rd | 9 bedrock-0.1.20/bedrock/man/sortX.Rd | 28 bedrock-0.1.20/bedrock/man/splitPath.Rd | 4 bedrock-0.1.20/bedrock/man/toBaseR.Rd | 23 bedrock-0.1.20/bedrock/man/untable.Rd | 8 bedrock-0.1.20/bedrock/man/urlExists.Rd |only bedrock-0.1.20/bedrock/man/winsorize.Rd | 14 bedrock-0.1.20/bedrock/tests/testthat/test-auditNames.R |only bedrock-0.1.20/bedrock/tests/testthat/test-checks.R | 9 bedrock-0.1.20/bedrock/tests/testthat/test-closest.R | 6 bedrock-0.1.20/bedrock/tests/testthat/test-course.R | 32 bedrock-0.1.20/bedrock/tests/testthat/test-intervals.R | 48 - bedrock-0.1.20/bedrock/tests/testthat/test-permn.R | 10 bedrock-0.1.20/bedrock/tests/testthat/test-printCharMatrix.R | 12 bedrock-0.1.20/bedrock/tests/testthat/test-recycle.R | 10 bedrock-0.1.20/bedrock/tests/testthat/test-sortX.R | 14 bedrock-0.1.20/bedrock/tests/testthat/test-urlExists.R |only bedrock-0.1.20/bedrock/tests/testthat/test-winsorize.R | 16 bedrock-0.1.20/bedrock/vignettes/Combinatorics.docx |only 98 files changed, 1062 insertions(+), 968 deletions(-)
Title: Simple and Fast Date Manipulation on Character Strings
Description: Provides simple and fast date manipulation functions operating on
character strings in one of three formats: 'DD.MM.YYYY' (default),
'YYYY-MM-DD' or 'YYYYMMDD'. The format is chosen once per R session.
Functions include extraction of day, month, and year components,
computation of differences between two dates, and addition or subtraction
of months.
"DD" is ignored in the calculations, therefore a date like 31.02.2026 is a valid
in- or output. That's why it is so fast.
Author: Prem Lueers [aut, cre]
Maintainer: Prem Lueers <prem@lueers.net>
Diff between theRefdate versions 1.0.0 dated 2026-03-23 and 1.1.0 dated 2026-10-16
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Title: Fast Simulation of Bayesian Optimal Interval Designs for Phase I
Trials
Description: Design and evaluate phase I dose-finding trials that use the
Bayesian optimal interval (BOIN) design of Liu and Yuan (2015)
<doi:10.1111/rssc.12089>. Functions are provided to tabulate the decision
boundaries, to simulate trials, to estimate the dose-toxicity curve under a
monotonicity constraint and to select the maximum tolerated dose. The
simulation engine is written in C++ and draws one random variate per
patient in enrollment order, which reproduces the reference implementation
in the 'BOIN' package trial by trial for a given seed. The traditional 3+3
design is provided as a comparator, with operating characteristics obtained
in closed form rather than by simulation. For toxicity that is observed
late, the time-to-event BOIN design is provided with the two estimators of
Yuan and colleagues (2018) <doi:10.1158/1078-0432.CCR-18-0246> and Lin and
Yuan (2020) <doi:10.1093/biostatistics/kxz007>. Patients who arrive while
the dose escalation waits can be backfilled to [...truncated...]
Author: Gosuke Homma [aut, cre]
Maintainer: Gosuke Homma <my.name.is.gosuke@gmail.com>
Diff between simFastBOIN versions 2.0.0 dated 2026-09-18 and 2.1.0 dated 2026-10-16
DESCRIPTION | 27 + MD5 | 171 +++++++++-- NAMESPACE | 31 ++ NEWS.md | 272 +++++++++++++++++ R/RcppExports.R | 32 ++ R/as_comb_count_array.R |only R/backfill_oc.R |only R/backfill_oc_multi_table.R |only R/backfill_simulate.R |only R/be_boin_simulate.R |only R/bf_boin_simulate.R |only R/check_p_true_matrix.R |only R/check_start_combination.R |only R/comb_boin_next.R |only R/comb_boin_select_mtd.R |only R/comb_boin_simulate.R |only R/comb_oc_multi_table.R |only R/comb_oc_table.R |only R/decision_table_3p3.R |only R/decision_table_3p3_notes.R |only R/decision_table_3p3_rows.R |only R/normalize_backfill_scenarios.R |only R/normalize_comb_scenarios.R |only R/plot.boin_decision_table.R | 4 R/plot.comb_boin_next.R |only R/plot.decision_table_3p3.R |only R/plot.tite_boin_decision_table.R |only R/print.backfill_oc.R |only R/print.backfill_oc_multi.R |only R/print.backfill_trials.R |only R/print.comb_boin_next.R |only R/print.comb_boin_oc.R |only R/print.comb_boin_oc_multi.R |only R/print.comb_boin_trials.R |only R/print.decision_table_3p3.R |only R/print.tite_boin_decision_table.R |only R/print.tite_boin_oc.R |only R/print.tite_boin_oc_multi.R |only R/print.tite_boin_trials.R |only R/simFastBOIN-package.R | 52 +++ R/sim_be_boin.R |only R/sim_be_boin_multi.R |only R/sim_bf_boin.R |only R/sim_bf_boin_multi.R |only R/sim_comb_boin.R |only R/sim_comb_boin_multi.R |only R/sim_tite_boin.R |only R/sim_tite_boin_multi.R |only R/tite_boin_bounds.R |only R/tite_boin_decision_table.R |only R/tite_boin_display_rows.R |only R/tite_boin_simulate.R |only R/tite_oc_multi_table.R |only R/tite_rules.R |only README.md | 294 ++++++++++++++++++- build/partial.rdb |only build/vignette.rds |binary inst/WORDLIST | 33 ++ inst/doc/simFastBOIN-backfill.R |only inst/doc/simFastBOIN-backfill.Rmd |only inst/doc/simFastBOIN-backfill.html |only inst/doc/simFastBOIN-combination.R |only inst/doc/simFastBOIN-combination.Rmd |only inst/doc/simFastBOIN-combination.html |only inst/doc/simFastBOIN-introduction.R | 3 inst/doc/simFastBOIN-introduction.Rmd | 14 inst/doc/simFastBOIN-introduction.html | 60 ++- inst/doc/simFastBOIN-tite.R |only inst/doc/simFastBOIN-tite.Rmd |only inst/doc/simFastBOIN-tite.html |only inst/validation/compare-comb-with-BOIN.R |only inst/validation/compare-with-LinYin2017.R |only inst/validation/compare-with-Zhao2024.R |only man/be_boin_simulate.Rd |only man/bf_boin_simulate.Rd |only man/comb_boin_next.Rd |only man/comb_boin_select_mtd.Rd |only man/comb_boin_simulate.Rd |only man/decision_table_3p3.Rd |only man/plot.comb_boin_next.Rd |only man/plot.decision_table_3p3.Rd |only man/plot.tite_boin_decision_table.Rd |only man/print.backfill_oc.Rd |only man/print.backfill_oc_multi.Rd |only man/print.backfill_trials.Rd |only man/print.comb_boin_next.Rd |only man/print.comb_boin_oc.Rd |only man/print.comb_boin_oc_multi.Rd |only man/print.comb_boin_trials.Rd |only man/print.decision_table_3p3.Rd |only man/print.tite_boin_decision_table.Rd |only man/print.tite_boin_oc.Rd |only man/print.tite_boin_oc_multi.Rd |only man/print.tite_boin_trials.Rd |only man/simFastBOIN-package.Rd | 49 +++ man/sim_be_boin.Rd |only man/sim_be_boin_multi.Rd |only man/sim_bf_boin.Rd |only man/sim_bf_boin_multi.Rd |only man/sim_comb_boin.Rd |only man/sim_comb_boin_multi.Rd |only man/sim_tite_boin.Rd |only man/sim_tite_boin_multi.Rd |only man/tite_boin_decision_table.Rd |only man/tite_boin_simulate.Rd |only src/RcppExports.cpp | 244 +++++++++++++++ src/backfill.cpp |only src/backfill_core.h |only src/comb.cpp |only src/comb_core.h |only src/tite.cpp |only src/tite_core.h |only tests/testthat/fixtures |only tests/testthat/helper-reference.R | 16 - tests/testthat/test-backfill_replay_cpp.R |only tests/testthat/test-be_boin_simulate.R |only tests/testthat/test-bf_boin_simulate.R |only tests/testthat/test-comb_boin_next.R |only tests/testthat/test-comb_boin_reference_oc.R |only tests/testthat/test-comb_boin_select_mtd.R |only tests/testthat/test-comb_boin_simulate.R |only tests/testthat/test-decision_table_3p3.R |only tests/testthat/test-plot.comb_boin_next.R |only tests/testthat/test-plot.decision_table_3p3.R |only tests/testthat/test-plot.tite_boin_decision_table.R |only tests/testthat/test-plot_methods.R | 11 tests/testthat/test-print.backfill_oc.R |only tests/testthat/test-print.backfill_oc_multi.R |only tests/testthat/test-print.backfill_trials.R |only tests/testthat/test-print.comb_boin_next.R |only tests/testthat/test-print.comb_boin_oc.R |only tests/testthat/test-print.comb_boin_oc_multi.R |only tests/testthat/test-print.comb_boin_trials.R |only tests/testthat/test-print.decision_table_3p3.R |only tests/testthat/test-print.tite_boin_decision_table.R |only tests/testthat/test-print.tite_boin_oc.R |only tests/testthat/test-print.tite_boin_oc_multi.R |only tests/testthat/test-print.tite_boin_trials.R |only tests/testthat/test-sim_be_boin.R |only tests/testthat/test-sim_be_boin_multi.R |only tests/testthat/test-sim_bf_boin.R |only tests/testthat/test-sim_bf_boin_multi.R |only tests/testthat/test-sim_comb_boin.R |only tests/testthat/test-sim_comb_boin_multi.R |only tests/testthat/test-sim_tite_boin.R |only tests/testthat/test-sim_tite_boin_multi.R |only tests/testthat/test-tite_boin_decision_table.R |only tests/testthat/test-tite_boin_simulate.R |only tests/testthat/test-tite_decision_cpp.R |only vignettes/simFastBOIN-backfill.Rmd |only vignettes/simFastBOIN-combination.Rmd |only vignettes/simFastBOIN-introduction.Rmd | 14 vignettes/simFastBOIN-tite.Rmd |only 153 files changed, 1266 insertions(+), 61 deletions(-)
Title: 'S7' Framework for Schema-Validated YAML Configuration
Description: Provides a generic framework for working with YAML (YAML
Ain't Markup Language) configuration files. Uses 'ajv' (Another JSON
Schema Validator) via 'QuickJSR' to validate configurations against
JSON Schema definitions. Configuration objects inherit from 'S7'
classes and base lists, supporting downstream extension through custom
classes and methods.
Author: Aksel Thomsen [aut, cre],
Matthew Phelps [aut],
Novo Nordisk A/S [cph],
Evgeny Poberezkin [cph] ,
Vincent Le Goff [cph]
Maintainer: Aksel Thomsen <oath@novonordisk.com>
Diff between S7schema versions 0.1.2 dated 2026-08-21 and 0.2.0 dated 2026-10-16
S7schema-0.1.2/S7schema/inst/licenses/argparse-LICENSE |only S7schema-0.1.2/S7schema/inst/licenses/js-yaml-LICENSE |only S7schema-0.1.2/S7schema/inst/licenses/require-from-string-LICENSE |only S7schema-0.2.0/S7schema/DESCRIPTION | 38 S7schema-0.2.0/S7schema/LICENSE.note | 3 S7schema-0.2.0/S7schema/MD5 | 61 S7schema-0.2.0/S7schema/NEWS.md | 20 S7schema-0.2.0/S7schema/R/validate-config.R | 22 S7schema-0.2.0/S7schema/R/validator.R | 86 S7schema-0.2.0/S7schema/R/y_S7schema.R | 39 S7schema-0.2.0/S7schema/R/yaml.R | 39 S7schema-0.2.0/S7schema/R/z_document.R | 4 S7schema-0.2.0/S7schema/inst/WORDLIST | 15 S7schema-0.2.0/S7schema/inst/bundle.js | 4709 +--------- S7schema-0.2.0/S7schema/inst/doc/S7schema.html | 26 S7schema-0.2.0/S7schema/inst/doc/use-in-package.html | 13 S7schema-0.2.0/S7schema/inst/licenses/fast-uri-LICENSE | 4 S7schema-0.2.0/S7schema/man/S7schema.Rd | 26 S7schema-0.2.0/S7schema/man/document_schema.Rd | 2 S7schema-0.2.0/S7schema/man/to_yaml.Rd | 35 S7schema-0.2.0/S7schema/man/validate_config.Rd | 26 S7schema-0.2.0/S7schema/man/validator.Rd | 29 S7schema-0.2.0/S7schema/tests/testthat/_snaps/validate-config.md |only S7schema-0.2.0/S7schema/tests/testthat/input/date_string.yml |only S7schema-0.2.0/S7schema/tests/testthat/input/empty.yml |only S7schema-0.2.0/S7schema/tests/testthat/input/merge_key.yml |only S7schema-0.2.0/S7schema/tests/testthat/input/no_string.yml |only S7schema-0.2.0/S7schema/tests/testthat/input/precision.yml |only S7schema-0.2.0/S7schema/tests/testthat/input/r_types.yml |only S7schema-0.2.0/S7schema/tests/testthat/schemas/invalid_type.json |only S7schema-0.2.0/S7schema/tests/testthat/schemas/maximum.json |only S7schema-0.2.0/S7schema/tests/testthat/schemas/merge.json |only S7schema-0.2.0/S7schema/tests/testthat/schemas/nullable.json |only S7schema-0.2.0/S7schema/tests/testthat/schemas/precision.json |only S7schema-0.2.0/S7schema/tests/testthat/schemas/r_types.json |only S7schema-0.2.0/S7schema/tests/testthat/schemas/strings.json |only S7schema-0.2.0/S7schema/tests/testthat/test-validate-config.R | 235 S7schema-0.2.0/S7schema/tests/testthat/test-validator.R | 20 S7schema-0.2.0/S7schema/tests/testthat/test-y_schema.R | 26 S7schema-0.2.0/S7schema/tests/testthat/test-yaml.R | 48 40 files changed, 1324 insertions(+), 4202 deletions(-)
Title: Crop-Specific Functions and Parameters for APSIM Next Generation
Lentil Model
Description: Provides lentil-specific functions, processes and parameter sets used by
lentil model in the Agricultural Production Systems sIMulator ('APSIM') Next Generation.
Includes tools for crop process calculations, parameter management and customisation,
enabling users to explore, modify and apply lentil model components.
Author: Bangyou Zheng [aut, cre]
Maintainer: Bangyou Zheng <zheng.bangyou@gmail.com>
Diff between rapsimng.lentil versions 0.1.0 dated 2026-09-24 and 0.1.1 dated 2026-10-16
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/options.R | 10 ++++++---- README.md | 6 ++++++ man/lentil.Rd | 3 +-- tests/testthat/test-options.R | 12 +++++++++--- tests/testthat/test-thermal_time.R | 4 ++-- 7 files changed, 35 insertions(+), 22 deletions(-)
More information about rapsimng.lentil at CRAN
Permanent link
Title: Compatibility Notice for Stock Synthesis Tools
Description: Provides a compatibility notice for users of the 'r4ss' Stock
Synthesis tools. Active development and current releases are available
from GitHub <https://github.com/r4ss/r4ss>. This package supplies the
canonical repository location and migration guidance.
Author: Ian G. Taylor [aut, cre],
Ian J. Stewart [aut],
Allan C. Hicks [aut],
Tommy M. Garrison [aut],
Andre E. Punt [aut],
R.I.C. Chris Francis [aut],
John R. Wallace [aut],
Chantel R. Wetzel [aut],
James T. Thorson [aut],
Yukio Takeuchi [aut],
Kotaro Ono [ [...truncated...]
Maintainer: Ian G. Taylor <Ian.Taylor@noaa.gov>
Diff between r4ss versions 1.44.0 dated 2022-05-26 and 1.44.1 dated 2026-10-16
r4ss-1.44.0/r4ss/R/NegLogInt_Fn.R |only r4ss-1.44.0/r4ss/R/PinerPlot.R |only r4ss-1.44.0/r4ss/R/RebuildPlot.R |only r4ss-1.44.0/r4ss/R/SSMethod.Cond.TA1.8.R |only r4ss-1.44.0/r4ss/R/SSMethod.TA1.8.R |only r4ss-1.44.0/r4ss/R/SS_ForeCatch.R |only r4ss-1.44.0/r4ss/R/SS_RunJitter.R |only r4ss-1.44.0/r4ss/R/SS_Sensi_plot.R |only r4ss-1.44.0/r4ss/R/SS_changepars.R |only r4ss-1.44.0/r4ss/R/SS_decision_table_stuff.R |only r4ss-1.44.0/r4ss/R/SS_doRetro.R |only r4ss-1.44.0/r4ss/R/SS_fitbiasramp.R |only r4ss-1.44.0/r4ss/R/SS_html.R |only r4ss-1.44.0/r4ss/R/SS_makeHTMLdiagnostictable.R |only r4ss-1.44.0/r4ss/R/SS_output.R |only r4ss-1.44.0/r4ss/R/SS_parlines.R |only r4ss-1.44.0/r4ss/R/SS_plots.R |only r4ss-1.44.0/r4ss/R/SS_profile.R |only r4ss-1.44.0/r4ss/R/SS_read.R |only r4ss-1.44.0/r4ss/R/SS_read_summary.R |only r4ss-1.44.0/r4ss/R/SS_readctl.R |only r4ss-1.44.0/r4ss/R/SS_readctl_3.24.R |only r4ss-1.44.0/r4ss/R/SS_readctl_3.30.R |only r4ss-1.44.0/r4ss/R/SS_readdat.R |only 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r4ss-1.44.0/r4ss/R/SS_writestarter.R |only r4ss-1.44.0/r4ss/R/SS_writewtatage.R |only r4ss-1.44.0/r4ss/R/SSbiologytables.R |only r4ss-1.44.0/r4ss/R/SSbootstrap.R |only r4ss-1.44.0/r4ss/R/SSexecutivesummary.r |only r4ss-1.44.0/r4ss/R/SSgetMCMC.R |only r4ss-1.44.0/r4ss/R/SSgetoutput.R |only r4ss-1.44.0/r4ss/R/SSmakeMmatrix.R |only r4ss-1.44.0/r4ss/R/SSmohnsrho.R |only r4ss-1.44.0/r4ss/R/SSplotAgeMatrix.R |only r4ss-1.44.0/r4ss/R/SSplotBiology.R |only r4ss-1.44.0/r4ss/R/SSplotCatch.R |only r4ss-1.44.0/r4ss/R/SSplotCohortCatch.R |only r4ss-1.44.0/r4ss/R/SSplotComparisons.R |only r4ss-1.44.0/r4ss/R/SSplotComps.R |only r4ss-1.44.0/r4ss/R/SSplotData.R |only r4ss-1.44.0/r4ss/R/SSplotDiscard.R |only r4ss-1.44.0/r4ss/R/SSplotDynamicB0.R |only r4ss-1.44.0/r4ss/R/SSplotIndices.R |only r4ss-1.44.0/r4ss/R/SSplotMCMC_ExtraSelex.R |only r4ss-1.44.0/r4ss/R/SSplotMnwt.R |only r4ss-1.44.0/r4ss/R/SSplotMovementMap.R |only r4ss-1.44.0/r4ss/R/SSplotMovementRates.R |only r4ss-1.44.0/r4ss/R/SSplotNumbers.R |only r4ss-1.44.0/r4ss/R/SSplotPars.R |only r4ss-1.44.0/r4ss/R/SSplotProfile.R |only r4ss-1.44.0/r4ss/R/SSplotRecdevs.R |only r4ss-1.44.0/r4ss/R/SSplotRecdist.R |only r4ss-1.44.0/r4ss/R/SSplotRetroDevs.R |only r4ss-1.44.0/r4ss/R/SSplotRetroRecruits.R |only r4ss-1.44.0/r4ss/R/SSplotSPR.R |only r4ss-1.44.0/r4ss/R/SSplotSelex.R |only r4ss-1.44.0/r4ss/R/SSplotSexRatio.R |only r4ss-1.44.0/r4ss/R/SSplotSpawnrecruit.R |only r4ss-1.44.0/r4ss/R/SSplotSummaryF.R |only r4ss-1.44.0/r4ss/R/SSplotTags.R |only r4ss-1.44.0/r4ss/R/SSplotTimeseries.R |only r4ss-1.44.0/r4ss/R/SSplotYield.R |only r4ss-1.44.0/r4ss/R/SSsummarize.R |only r4ss-1.44.0/r4ss/R/SStableComparisons.R |only r4ss-1.44.0/r4ss/R/SSunavailableSpawningOutput.R |only r4ss-1.44.0/r4ss/R/TSCplot.R |only r4ss-1.44.0/r4ss/R/bubble3.R |only r4ss-1.44.0/r4ss/R/check_inputlist.R |only r4ss-1.44.0/r4ss/R/check_model.R |only r4ss-1.44.0/r4ss/R/copy_SS_inputs.R |only r4ss-1.44.0/r4ss/R/file_increment.R |only r4ss-1.44.0/r4ss/R/getADMBHessian.R |only r4ss-1.44.0/r4ss/R/get_SIS_info.R |only r4ss-1.44.0/r4ss/R/get_comments.r |only r4ss-1.44.0/r4ss/R/get_ncol.R |only r4ss-1.44.0/r4ss/R/helper_fxns.R |only r4ss-1.44.0/r4ss/R/make_multifig.R |only r4ss-1.44.0/r4ss/R/make_multifig_sexratio.R |only r4ss-1.44.0/r4ss/R/mcmc.nuisance.R |only r4ss-1.44.0/r4ss/R/mcmc.out.R |only r4ss-1.44.0/r4ss/R/mountains.R |only r4ss-1.44.0/r4ss/R/plotCI.R |only r4ss-1.44.0/r4ss/R/populate_multiple_folders.R |only r4ss-1.44.0/r4ss/R/r4ss_logo.R |only r4ss-1.44.0/r4ss/R/read.admbFit.R |only r4ss-1.44.0/r4ss/R/run_SS_models.R |only r4ss-1.44.0/r4ss/R/selShapes.R |only r4ss-1.44.0/r4ss/R/stackpoly.R |only r4ss-1.44.0/r4ss/R/write_fwf4.r |only r4ss-1.44.0/r4ss/inst |only r4ss-1.44.0/r4ss/man/DoProjectPlots.Rd |only r4ss-1.44.0/r4ss/man/NegLogInt_Fn.Rd |only r4ss-1.44.0/r4ss/man/PinerPlot.Rd |only r4ss-1.44.0/r4ss/man/SSMethod.Cond.TA1.8.Rd |only r4ss-1.44.0/r4ss/man/SSMethod.TA1.8.Rd |only r4ss-1.44.0/r4ss/man/SS_ForeCatch.Rd |only r4ss-1.44.0/r4ss/man/SS_RunJitter.Rd |only r4ss-1.44.0/r4ss/man/SS_Sensi_plot.Rd |only r4ss-1.44.0/r4ss/man/SS_changepars.Rd |only r4ss-1.44.0/r4ss/man/SS_decision_table_stuff.Rd |only r4ss-1.44.0/r4ss/man/SS_doRetro.Rd |only r4ss-1.44.0/r4ss/man/SS_fitbiasramp.Rd |only r4ss-1.44.0/r4ss/man/SS_html.Rd |only r4ss-1.44.0/r4ss/man/SS_makeHTMLdiagnostictable.Rd |only r4ss-1.44.0/r4ss/man/SS_output.Rd |only r4ss-1.44.0/r4ss/man/SS_parlines.Rd |only r4ss-1.44.0/r4ss/man/SS_plots.Rd |only r4ss-1.44.0/r4ss/man/SS_profile.Rd |only r4ss-1.44.0/r4ss/man/SS_read.Rd |only r4ss-1.44.0/r4ss/man/SS_read_summary.Rd |only r4ss-1.44.0/r4ss/man/SS_readctl.Rd |only r4ss-1.44.0/r4ss/man/SS_readctl_3.24.Rd |only r4ss-1.44.0/r4ss/man/SS_readctl_3.30.Rd |only r4ss-1.44.0/r4ss/man/SS_readdat.Rd |only r4ss-1.44.0/r4ss/man/SS_readdat_2.00.Rd |only r4ss-1.44.0/r4ss/man/SS_readdat_3.00.Rd |only r4ss-1.44.0/r4ss/man/SS_readdat_3.24.Rd |only r4ss-1.44.0/r4ss/man/SS_readdat_3.30.Rd |only r4ss-1.44.0/r4ss/man/SS_readforecast.Rd |only r4ss-1.44.0/r4ss/man/SS_readpar_3.24.Rd |only r4ss-1.44.0/r4ss/man/SS_readpar_3.30.Rd |only r4ss-1.44.0/r4ss/man/SS_readstarter.Rd |only r4ss-1.44.0/r4ss/man/SS_readwtatage.Rd |only r4ss-1.44.0/r4ss/man/SS_recdevs.Rd |only r4ss-1.44.0/r4ss/man/SS_splitdat.Rd |only r4ss-1.44.0/r4ss/man/SS_tune_comps.Rd |only r4ss-1.44.0/r4ss/man/SS_varadjust.Rd |only r4ss-1.44.0/r4ss/man/SS_write.Rd |only r4ss-1.44.0/r4ss/man/SS_writectl.Rd |only r4ss-1.44.0/r4ss/man/SS_writectl_3.24.Rd |only r4ss-1.44.0/r4ss/man/SS_writectl_3.30.Rd |only r4ss-1.44.0/r4ss/man/SS_writedat.Rd |only r4ss-1.44.0/r4ss/man/SS_writedat_3.24.Rd |only r4ss-1.44.0/r4ss/man/SS_writedat_3.30.Rd |only r4ss-1.44.0/r4ss/man/SS_writeforecast.Rd |only r4ss-1.44.0/r4ss/man/SS_writepar_3.24.Rd |only r4ss-1.44.0/r4ss/man/SS_writepar_3.30.Rd |only r4ss-1.44.0/r4ss/man/SS_writestarter.Rd |only r4ss-1.44.0/r4ss/man/SS_writewtatage.Rd |only r4ss-1.44.0/r4ss/man/SSbiologytables.Rd |only r4ss-1.44.0/r4ss/man/SSbootstrap.Rd |only r4ss-1.44.0/r4ss/man/SSdiagsTime2Year.Rd |only r4ss-1.44.0/r4ss/man/SSexecutivesummary.Rd |only r4ss-1.44.0/r4ss/man/SSgetMCMC.Rd |only r4ss-1.44.0/r4ss/man/SSgetoutput.Rd |only r4ss-1.44.0/r4ss/man/SSmakeMmatrix.Rd |only r4ss-1.44.0/r4ss/man/SSmohnsrho.Rd |only r4ss-1.44.0/r4ss/man/SSplotAgeMatrix.Rd |only r4ss-1.44.0/r4ss/man/SSplotBiology.Rd |only r4ss-1.44.0/r4ss/man/SSplotCatch.Rd |only r4ss-1.44.0/r4ss/man/SSplotCohortCatch.Rd |only r4ss-1.44.0/r4ss/man/SSplotComparisons.Rd |only r4ss-1.44.0/r4ss/man/SSplotComps.Rd |only r4ss-1.44.0/r4ss/man/SSplotData.Rd |only r4ss-1.44.0/r4ss/man/SSplotDiscard.Rd |only r4ss-1.44.0/r4ss/man/SSplotDynamicB0.Rd |only r4ss-1.44.0/r4ss/man/SSplotIndices.Rd |only r4ss-1.44.0/r4ss/man/SSplotMCMC_ExtraSelex.Rd |only r4ss-1.44.0/r4ss/man/SSplotMnwt.Rd |only r4ss-1.44.0/r4ss/man/SSplotMovementMap.Rd |only r4ss-1.44.0/r4ss/man/SSplotMovementRates.Rd |only r4ss-1.44.0/r4ss/man/SSplotNumbers.Rd |only r4ss-1.44.0/r4ss/man/SSplotPars.Rd |only r4ss-1.44.0/r4ss/man/SSplotProfile.Rd |only r4ss-1.44.0/r4ss/man/SSplotRecdevs.Rd |only r4ss-1.44.0/r4ss/man/SSplotRecdist.Rd |only r4ss-1.44.0/r4ss/man/SSplotRetroRecruits.Rd |only r4ss-1.44.0/r4ss/man/SSplotSPR.Rd |only r4ss-1.44.0/r4ss/man/SSplotSelex.Rd |only r4ss-1.44.0/r4ss/man/SSplotSexRatio.Rd |only r4ss-1.44.0/r4ss/man/SSplotSpawnrecruit.Rd |only r4ss-1.44.0/r4ss/man/SSplotSummaryF.Rd |only r4ss-1.44.0/r4ss/man/SSplotTags.Rd |only r4ss-1.44.0/r4ss/man/SSplotTimeseries.Rd |only r4ss-1.44.0/r4ss/man/SSplotYield.Rd |only r4ss-1.44.0/r4ss/man/SSsummarize.Rd |only r4ss-1.44.0/r4ss/man/SStableComparisons.Rd |only r4ss-1.44.0/r4ss/man/SSunavailableSpawningOutput.Rd |only r4ss-1.44.0/r4ss/man/TSCplot.Rd |only r4ss-1.44.0/r4ss/man/add_legend.Rd |only r4ss-1.44.0/r4ss/man/bubble3.Rd |only r4ss-1.44.0/r4ss/man/check_inputlist.Rd |only r4ss-1.44.0/r4ss/man/check_model.Rd |only r4ss-1.44.0/r4ss/man/copy_SS_inputs.Rd |only r4ss-1.44.0/r4ss/man/file_increment.Rd |only r4ss-1.44.0/r4ss/man/getADMBHessian.Rd |only r4ss-1.44.0/r4ss/man/get_SIS_info.Rd |only r4ss-1.44.0/r4ss/man/get_comments.Rd |only r4ss-1.44.0/r4ss/man/get_dat_new_name.Rd |only r4ss-1.44.0/r4ss/man/get_last_phase.Rd |only r4ss-1.44.0/r4ss/man/get_tuning_table.Rd |only r4ss-1.44.0/r4ss/man/get_tv_parlabs.Rd |only r4ss-1.44.0/r4ss/man/is.wholenumber.Rd |only r4ss-1.44.0/r4ss/man/make_multifig.Rd |only r4ss-1.44.0/r4ss/man/make_multifig_sexratio.Rd |only r4ss-1.44.0/r4ss/man/mcmc.nuisance.Rd |only r4ss-1.44.0/r4ss/man/mcmc.out.Rd |only r4ss-1.44.0/r4ss/man/mountains.Rd |only r4ss-1.44.0/r4ss/man/plotCI.Rd |only r4ss-1.44.0/r4ss/man/populate_multiple_folders.Rd |only r4ss-1.44.0/r4ss/man/r4ss_logo.Rd |only r4ss-1.44.0/r4ss/man/read.admbFit.Rd |only r4ss-1.44.0/r4ss/man/rich.colors.short.Rd |only r4ss-1.44.0/r4ss/man/run_SS_models.Rd |only r4ss-1.44.0/r4ss/man/save_png.Rd |only r4ss-1.44.0/r4ss/man/selShapes.Rd |only r4ss-1.44.0/r4ss/man/sspar.Rd |only r4ss-1.44.0/r4ss/man/stackpoly.Rd |only r4ss-1.44.0/r4ss/man/translate_3.30_to_3.24_Q_setup.Rd |only r4ss-1.44.0/r4ss/man/translate_3.30_to_3.24_var_adjust.Rd |only r4ss-1.44.0/r4ss/man/write_fwf4.Rd |only r4ss-1.44.1/r4ss/DESCRIPTION | 124 +++--- r4ss-1.44.1/r4ss/MD5 | 253 -------------- r4ss-1.44.1/r4ss/NAMESPACE | 183 ---------- r4ss-1.44.1/r4ss/NEWS.md | 71 --- r4ss-1.44.1/r4ss/R/r4ss-package.R | 50 +- r4ss-1.44.1/r4ss/README.md | 70 --- r4ss-1.44.1/r4ss/man/r4ss-package.Rd | 69 --- r4ss-1.44.1/r4ss/man/r4ss_repository.Rd |only r4ss-1.44.1/r4ss/tests |only 243 files changed, 122 insertions(+), 698 deletions(-)
Title: Tool for Statistical and Environmental Analysis
Description: Provides a set of accessible and automated functions to apply
statistical models such as Simple Linear Regression (RLS, from the Spanish
'Regresión Lineal Simple'), Multiple Linear Regression (RLM, from the Spanish
'Regresión Lineal Múltiple'), Generalized Linear Models (GLM), and time
series analysis through Autoregressive Integrated Moving Average (ARIMA)
models. Designed to support teaching at the Universidad Autónoma Chapingo,
it facilitates results interpretation and assumption validation through
automatic graphical diagnostics. Developed as part of an undergraduate
thesis at the Universidad Autónoma Chapingo, under the supervision of
Dr. Julio César Buendía Espinoza (thesis advisor), with the participation
of the thesis committee: Diego Ernesto Lira González (secretary), Israel
Lerma Serna (member), Juan Uriel Avelar Roblero (alternate), and Elisa del
Carmen Martínez Ochoa (alternate). Methods for regression and time series
are based on Montgomery, Peck & Vining (2021, Introd [...truncated...]
Author: Dayron Jared Bazan Guzman [aut, cre],
Julio Cesar Buendia Espinoza [aut, ths] ,
Diego Ernesto Lira Gonzalez [rev] ,
Israel Lerma Serna [rev] ,
Juan Uriel Avelar Roblero [rev] ,
Elisa del Carmen Martinez Ochoa [rev]
Maintainer: Dayron Jared Bazan Guzman <dbazanguzman@gmail.com>
Diff between GREENREG versions 0.1.1 dated 2026-09-21 and 0.1.2 dated 2026-10-16
GREENREG-0.1.1/GREENREG/R/'Modelo_Autoregresivo_Integrado_de_Media_Movil_(ARIMA).R' |only GREENREG-0.1.1/GREENREG/R/'Modelo_Autoregresivo_de_media_movil_(ARMA).R' |only GREENREG-0.1.1/GREENREG/R/'Modelo_Autorregresivo_(AR).R' |only GREENREG-0.1.1/GREENREG/R/'Modelo_media_movil_(MA).R' |only GREENREG-0.1.1/GREENREG/man/analisis_datos.Rd |only GREENREG-0.1.1/GREENREG/man/logistico.Rd |only GREENREG-0.1.1/GREENREG/man/modelo_ar.Rd |only GREENREG-0.1.1/GREENREG/man/modelo_arima.Rd |only GREENREG-0.1.1/GREENREG/man/modelo_arma.Rd |only GREENREG-0.1.1/GREENREG/man/modelo_ma.Rd |only GREENREG-0.1.1/GREENREG/man/reg_poisson.Rd |only GREENREG-0.1.1/GREENREG/man/rlm.Rd |only GREENREG-0.1.1/GREENREG/man/rls.Rd |only GREENREG-0.1.2/GREENREG/DESCRIPTION | 33 GREENREG-0.1.2/GREENREG/MD5 | 83 GREENREG-0.1.2/GREENREG/NAMESPACE | 9 GREENREG-0.1.2/GREENREG/NEWS.md |only GREENREG-0.1.2/GREENREG/R/analisis_datos.R | 976 +++--- GREENREG-0.1.2/GREENREG/R/datos_anomalia_temperatura.R | 52 GREENREG-0.1.2/GREENREG/R/datos_nivel_presa.R | 52 GREENREG-0.1.2/GREENREG/R/datos_rendimiento_maiz.R | 52 GREENREG-0.1.2/GREENREG/R/datos_roya_cafe.R | 54 GREENREG-0.1.2/GREENREG/R/datos_tala_ilegal_poisson.R | 58 GREENREG-0.1.2/GREENREG/R/deprecated.R |only GREENREG-0.1.2/GREENREG/R/globals.R | 38 GREENREG-0.1.2/GREENREG/R/modelo_ar.R | 1226 ++++---- GREENREG-0.1.2/GREENREG/R/modelo_arima.R | 1455 +++++----- GREENREG-0.1.2/GREENREG/R/modelo_arma.R | 1114 +++---- GREENREG-0.1.2/GREENREG/R/modelo_ma.R | 1278 ++++---- GREENREG-0.1.2/GREENREG/R/regresion_lineal_multiple.R | 1275 ++++---- GREENREG-0.1.2/GREENREG/R/regresion_lineal_simple.R | 920 +++--- GREENREG-0.1.2/GREENREG/R/regresion_logistica.R | 1166 ++++---- GREENREG-0.1.2/GREENREG/R/regresion_poisson.R | 1176 ++++---- GREENREG-0.1.2/GREENREG/README.md |only GREENREG-0.1.2/GREENREG/build |only GREENREG-0.1.2/GREENREG/inst |only GREENREG-0.1.2/GREENREG/man/datos_anomalia_temperatura.Rd | 14 GREENREG-0.1.2/GREENREG/man/datos_nivel_presa.Rd | 10 GREENREG-0.1.2/GREENREG/man/datos_rendimiento_maiz.Rd | 22 GREENREG-0.1.2/GREENREG/man/datos_roya_cafe.Rd | 26 GREENREG-0.1.2/GREENREG/man/datos_tala_ilegal_poisson.Rd | 18 GREENREG-0.1.2/GREENREG/man/greenreg_analisis_datos.Rd |only GREENREG-0.1.2/GREENREG/man/greenreg_logistico.Rd |only GREENREG-0.1.2/GREENREG/man/greenreg_modelo_ar.Rd |only GREENREG-0.1.2/GREENREG/man/greenreg_modelo_arima.Rd |only GREENREG-0.1.2/GREENREG/man/greenreg_modelo_arma.Rd |only GREENREG-0.1.2/GREENREG/man/greenreg_modelo_ma.Rd |only GREENREG-0.1.2/GREENREG/man/greenreg_reg_poisson.Rd |only GREENREG-0.1.2/GREENREG/man/greenreg_rlm.Rd |only GREENREG-0.1.2/GREENREG/man/greenreg_rls.Rd |only GREENREG-0.1.2/GREENREG/tests |only GREENREG-0.1.2/GREENREG/vignettes |only 52 files changed, 5759 insertions(+), 5348 deletions(-)
Title: 'DataSHIELD' RO-Crate Governance Functions
Description: Tools for wrapping 'DataSHIELD' analyses into RO-Crate
(Research Object Crate) objects. Provides functions to create structured
metadata for federated data analysis projects, enabling governance
tracking of data access, project membership, analysis execution and
output validation across distributed data sources.
Author: Roberto Villegas-Diaz [aut, cre] ,
Becca Wilson [aut] ,
Olly Butters [aut] ,
Stuart Wheater [aut] ,
University of Liverpool [cph]
Maintainer: Roberto Villegas-Diaz <r.villegas-diaz@outlook.com>
Diff between dsROCrate versions 0.2.3 dated 2026-09-24 and 0.2.4 dated 2026-10-16
DESCRIPTION | 6 MD5 | 107 NEWS.md | 78 R/audit.R | 11 R/audit_engine.R | 4 R/backend-opal.R | 4 R/dsROCrate.R | 8 R/params.R |only R/report.R | 12 R/safe-call.R | 2 R/safe_data.R | 2 R/safe_output.R | 54 R/safe_people.R | 6 R/safe_project.R | 8 R/safe_setting.R | 2 R/symbol-registry.R | 2 R/utils-date.R | 61 R/utils-opal.R | 6 R/utils-safe_data.R | 1 R/utils-safe_output.R | 3 R/utils-safe_people.R | 1 R/utils-safe_project.R | 3 R/utils-safe_setting.R | 1 README.md | 131 build/vignette.rds |binary inst/WORDLIST | 14 inst/doc/audit-permissions.R | 9 inst/doc/audit-permissions.Rmd | 149 inst/doc/audit-permissions.html | 244 inst/doc/auditing-studies.R |only inst/doc/auditing-studies.Rmd |only inst/doc/auditing-studies.html |only inst/doc/building-crates.R |only inst/doc/building-crates.Rmd |only inst/doc/building-crates.html |only inst/doc/deploy-local-datashield-server-with-opal.R | 16 inst/doc/deploy-local-datashield-server-with-opal.Rmd | 223 inst/doc/deploy-local-datashield-server-with-opal.html | 224 inst/doc/getting-started.R | 396 - inst/doc/getting-started.Rmd | 596 - inst/doc/getting-started.html | 5983 ----------------- man/audit.Rd | 11 man/init.Rd | 6 man/report.Rd | 7 man/safe_data.Rd | 6 man/safe_output.Rd | 6 man/safe_people.Rd | 10 man/safe_project.Rd | 6 man/safe_setting.Rd | 6 man/shared_params.Rd |only tests/testthat/test-audit_engine.R | 6 tests/testthat/test-report.R | 3 tests/testthat/test-safe-call.R | 2 tests/testthat/test-safe_output.R | 8 tests/testthat/test-utils-date.R |only vignettes/audit-permissions.Rmd | 149 vignettes/auditing-studies.Rmd |only vignettes/building-crates.Rmd |only vignettes/deploy-local-datashield-server-with-opal.Rmd | 223 vignettes/getting-started.Rmd | 596 - 60 files changed, 1601 insertions(+), 7811 deletions(-)
Title: Planning and Analyzing Dose Finding Experiments
Description: The DoseFinding package provides functions for the design and analysis
of dose-finding experiments (with focus on pharmaceutical Phase
II clinical trials). It provides functions for: multiple contrast
tests, fitting non-linear dose-response models (using Bayesian and
non-Bayesian estimation), calculating optimal designs and an
implementation of the MCPMod methodology (Pinheiro et al. (2014)
<doi:10.1002/sim.6052>).
Author: Bjoern Bornkamp [aut] ,
Jose Pinheiro [aut],
Frank Bretz [aut],
Ludger Sandig [aut],
Marius Thomas [aut, cre],
Daniel Sabanes Bove [aut] ,
Carina Miller [ctb],
Novartis Pharma AG [cph, fnd]
Maintainer: Marius Thomas <marius.thomas@novartis.com>
Diff between DoseFinding versions 1.4-1 dated 2025-07-09 and 1.4-2 dated 2026-10-16
DoseFinding-1.4-1/DoseFinding/vignettes/american-statistical-association.csl |only DoseFinding-1.4-1/DoseFinding/vignettes/refs.bib |only DoseFinding-1.4-2/DoseFinding/DESCRIPTION | 15 DoseFinding-1.4-2/DoseFinding/MD5 | 243 - DoseFinding-1.4-2/DoseFinding/NAMESPACE | 131 DoseFinding-1.4-2/DoseFinding/NEWS.md | 805 +-- DoseFinding-1.4-2/DoseFinding/R/DesignMCPModApp.R | 30 DoseFinding-1.4-2/DoseFinding/R/DoseFinding-package.R | 911 +-- DoseFinding-1.4-2/DoseFinding/R/MCPMod.R | 793 +-- DoseFinding-1.4-2/DoseFinding/R/MCTtest.R | 686 +- DoseFinding-1.4-2/DoseFinding/R/MCTtest_helpers.R | 132 DoseFinding-1.4-2/DoseFinding/R/Mods.R | 1190 ++--- DoseFinding-1.4-2/DoseFinding/R/Mods_helpers.R | 1556 +++--- DoseFinding-1.4-2/DoseFinding/R/bFitMod.R | 799 +-- DoseFinding-1.4-2/DoseFinding/R/bFitMod_helpers.R | 528 +- DoseFinding-1.4-2/DoseFinding/R/bMCTtest.R | 637 +- DoseFinding-1.4-2/DoseFinding/R/bMCTtest_helpers.R | 122 DoseFinding-1.4-2/DoseFinding/R/drmodels.R | 381 - DoseFinding-1.4-2/DoseFinding/R/fitMod.R | 1691 +++---- DoseFinding-1.4-2/DoseFinding/R/fitMod_helpers.R | 1165 ++--- DoseFinding-1.4-2/DoseFinding/R/guesst.R | 420 - DoseFinding-1.4-2/DoseFinding/R/maFitMod.R | 459 - DoseFinding-1.4-2/DoseFinding/R/optContr.R | 497 +- DoseFinding-1.4-2/DoseFinding/R/optContr_helpers.R | 190 DoseFinding-1.4-2/DoseFinding/R/optDesign.R | 1142 ++-- DoseFinding-1.4-2/DoseFinding/R/optDesign_helpers.R | 338 - DoseFinding-1.4-2/DoseFinding/R/planMod.R | 885 +-- DoseFinding-1.4-2/DoseFinding/R/planMod_helpers.R | 464 +- DoseFinding-1.4-2/DoseFinding/R/powMCT.R | 379 - DoseFinding-1.4-2/DoseFinding/R/powMCTInterim.R | 329 - DoseFinding-1.4-2/DoseFinding/R/powMCT_helpers.R | 376 - DoseFinding-1.4-2/DoseFinding/R/sampSize.R | 854 +-- DoseFinding-1.4-2/DoseFinding/README.md | 274 - DoseFinding-1.4-2/DoseFinding/build/partial.rdb |only DoseFinding-1.4-2/DoseFinding/build/vignette.rds |binary DoseFinding-1.4-2/DoseFinding/inst/REFERENCES.bib |only DoseFinding-1.4-2/DoseFinding/inst/american-statistical-association.csl |only DoseFinding-1.4-2/DoseFinding/inst/doc/analysis_normal.R | 156 DoseFinding-1.4-2/DoseFinding/inst/doc/analysis_normal.Rmd | 564 +- DoseFinding-1.4-2/DoseFinding/inst/doc/analysis_normal.html | 1420 +++--- DoseFinding-1.4-2/DoseFinding/inst/doc/binary_data.R | 260 - 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DoseFinding-1.4-2/DoseFinding/inst/doc/sample_size.html | 1207 ++--- DoseFinding-1.4-2/DoseFinding/inst/doc/time_to_event_data.R |only DoseFinding-1.4-2/DoseFinding/inst/doc/time_to_event_data.Rmd |only DoseFinding-1.4-2/DoseFinding/inst/doc/time_to_event_data.html |only DoseFinding-1.4-2/DoseFinding/man/DesignMCPModApp.Rd | 35 DoseFinding-1.4-2/DoseFinding/man/DoseFinding-package.Rd | 205 DoseFinding-1.4-2/DoseFinding/man/IBScovars.Rd | 63 DoseFinding-1.4-2/DoseFinding/man/MCPMod.Rd | 490 -- DoseFinding-1.4-2/DoseFinding/man/MCTpval.Rd | 136 DoseFinding-1.4-2/DoseFinding/man/MCTtest.Rd | 333 - DoseFinding-1.4-2/DoseFinding/man/Mods.Rd | 440 - DoseFinding-1.4-2/DoseFinding/man/bFitMod.Rd | 445 - DoseFinding-1.4-2/DoseFinding/man/bMCTtest.Rd | 405 - DoseFinding-1.4-2/DoseFinding/man/biom.Rd | 50 DoseFinding-1.4-2/DoseFinding/man/critVal.Rd | 90 DoseFinding-1.4-2/DoseFinding/man/defBnds.Rd | 92 DoseFinding-1.4-2/DoseFinding/man/drmodels.Rd | 500 +- DoseFinding-1.4-2/DoseFinding/man/figures/README-example1-1.png |binary DoseFinding-1.4-2/DoseFinding/man/figures/README-example3-1.png |binary DoseFinding-1.4-2/DoseFinding/man/fitMod.Rd | 524 +- DoseFinding-1.4-2/DoseFinding/man/glycobrom.Rd | 124 DoseFinding-1.4-2/DoseFinding/man/guesst.Rd | 270 - 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DoseFinding-1.4-2/DoseFinding/tests/testthat.R | 22 DoseFinding-1.4-2/DoseFinding/tests/testthat/generate_test_datasets.R | 206 DoseFinding-1.4-2/DoseFinding/tests/testthat/test-DesignMCPModApp.R | 12 DoseFinding-1.4-2/DoseFinding/tests/testthat/test-MCPMod.R | 74 DoseFinding-1.4-2/DoseFinding/tests/testthat/test-MCTtest.R | 486 +- DoseFinding-1.4-2/DoseFinding/tests/testthat/test-Mods.R | 392 - DoseFinding-1.4-2/DoseFinding/tests/testthat/test-bFitMod.R | 218 DoseFinding-1.4-2/DoseFinding/tests/testthat/test-bMCTtest.R | 562 +- DoseFinding-1.4-2/DoseFinding/tests/testthat/test-drmodels.R | 64 DoseFinding-1.4-2/DoseFinding/tests/testthat/test-fitMod.R | 589 +- DoseFinding-1.4-2/DoseFinding/tests/testthat/test-guesst.R | 198 DoseFinding-1.4-2/DoseFinding/tests/testthat/test-maFitMod.R | 406 - DoseFinding-1.4-2/DoseFinding/tests/testthat/test-optContr.R | 444 - DoseFinding-1.4-2/DoseFinding/tests/testthat/test-optDesign.R | 626 +- DoseFinding-1.4-2/DoseFinding/tests/testthat/test-planMod.R | 282 - DoseFinding-1.4-2/DoseFinding/tests/testthat/test-powMCT.R | 200 DoseFinding-1.4-2/DoseFinding/tests/testthat/test-powMCTBinCount.R | 228 DoseFinding-1.4-2/DoseFinding/tests/testthat/test-powMCTInterim.R | 376 - DoseFinding-1.4-2/DoseFinding/tests/testthat/test-sampSize.R | 426 - DoseFinding-1.4-2/DoseFinding/vignettes/analysis_normal.Rmd | 564 +- DoseFinding-1.4-2/DoseFinding/vignettes/binary_data.Rmd | 604 +- DoseFinding-1.4-2/DoseFinding/vignettes/children/settings.txt | 16 DoseFinding-1.4-2/DoseFinding/vignettes/faq.Rmd | 788 +-- DoseFinding-1.4-2/DoseFinding/vignettes/longitudinal_data.Rmd | 1132 ++-- DoseFinding-1.4-2/DoseFinding/vignettes/mult_regimen.Rmd | 609 +- DoseFinding-1.4-2/DoseFinding/vignettes/overview.Rmd | 162 DoseFinding-1.4-2/DoseFinding/vignettes/sample_size.Rmd | 452 - DoseFinding-1.4-2/DoseFinding/vignettes/time_to_event_data.Rmd |only 127 files changed, 27519 insertions(+), 27613 deletions(-)
Title: Structured Messages and Options
Description: Provides a structured framework for consistent user
communication and configuration management for package developers.
Author: Aksel Thomsen [aut, cre] ,
Mathias Lerbech Jeppesen [aut],
Cervan Girard [aut],
Kristian Troejelsgaard [aut],
Lovemore Gakava [aut],
Steffen Falgreen Larsen [aut],
Vladimir Obucina [aut],
Novo Nordisk A/S [cph]
Maintainer: Aksel Thomsen <oath@novonordisk.com>
Diff between zephyr versions 0.1.3 dated 2025-08-22 and 0.1.4 dated 2026-10-16
DESCRIPTION | 14 ++--- MD5 | 41 ++++++++------ NAMESPACE | 2 NEWS.md | 7 ++ R/options.R | 58 ++++++++++++++++++-- R/use_zephyr.R | 2 R/utils.R | 23 ++++++-- R/verbosity_level.R | 27 +++++++++ inst/WORDLIST | 2 man/create_option.Rd | 2 man/set_option.Rd |only man/set_verbosity_level.Rd |only man/use_zephyr.Rd | 2 man/verbosity_level.Rd | 4 - man/zephyr-package.Rd | 2 tests/testthat/_snaps/integration.md | 13 +--- tests/testthat/_snaps/use_zephyr.md | 2 tests/testthat/test-integration.R | 94 ++++++++++++++++++++++------------ tests/testthat/test-options.R | 38 +++++++++++++ tests/testthat/test-utils.R | 22 +++++++ tests/testthat/test-verbosity_level.R | 10 +++ tests/testthat/test.pkg.nested.envs |only 22 files changed, 280 insertions(+), 85 deletions(-)
Title: Fetch Data from Yahoo Finance API
Description: Obtain historical and near real time data related to stocks, index
and currencies from the Yahoo Finance API. This package is community maintained
and is not officially supported by 'Yahoo'. The accuracy of data is only as
correct as provided on <https://finance.yahoo.com/>.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between yahoofinancer versions 0.5.0 dated 2026-05-21 and 0.6.1 dated 2026-10-16
yahoofinancer-0.5.0/yahoofinancer/tests/testthat/query1.finance.yahoo.com |only yahoofinancer-0.5.0/yahoofinancer/tests/testthat/query2.finance.yahoo.com |only yahoofinancer-0.5.0/yahoofinancer/tests/testthat/test-market-summary.R |only yahoofinancer-0.6.1/yahoofinancer/DESCRIPTION | 15 yahoofinancer-0.6.1/yahoofinancer/LICENSE | 2 yahoofinancer-0.6.1/yahoofinancer/MD5 | 243 yahoofinancer-0.6.1/yahoofinancer/NAMESPACE | 6 yahoofinancer-0.6.1/yahoofinancer/NEWS.md | 106 yahoofinancer-0.6.1/yahoofinancer/R/api_request.R |only yahoofinancer-0.6.1/yahoofinancer/R/base.R | 328 yahoofinancer-0.6.1/yahoofinancer/R/functional_api.R |only yahoofinancer-0.6.1/yahoofinancer/R/indice.R | 134 yahoofinancer-0.6.1/yahoofinancer/R/others.R | 629 - yahoofinancer-0.6.1/yahoofinancer/R/ticker.R | 479 yahoofinancer-0.6.1/yahoofinancer/R/tickers.R | 370 yahoofinancer-0.6.1/yahoofinancer/R/utils.R | 145 yahoofinancer-0.6.1/yahoofinancer/R/validate.R |only yahoofinancer-0.6.1/yahoofinancer/R/yahoofinancer.R | 36 yahoofinancer-0.6.1/yahoofinancer/README.md | 299 yahoofinancer-0.6.1/yahoofinancer/build |only yahoofinancer-0.6.1/yahoofinancer/inst |only yahoofinancer-0.6.1/yahoofinancer/man/Indice-class.Rd | 282 yahoofinancer-0.6.1/yahoofinancer/man/Ticker-class.Rd | 258 yahoofinancer-0.6.1/yahoofinancer/man/Tickers.Rd | 44 yahoofinancer-0.6.1/yahoofinancer/man/YahooFinanceBase-class.Rd | 258 yahoofinancer-0.6.1/yahoofinancer/man/currency_converter.Rd | 38 yahoofinancer-0.6.1/yahoofinancer/man/get_currencies.Rd | 16 yahoofinancer-0.6.1/yahoofinancer/man/get_market_summary.Rd | 32 yahoofinancer-0.6.1/yahoofinancer/man/get_trending.Rd | 24 yahoofinancer-0.6.1/yahoofinancer/man/validate.Rd | 59 yahoofinancer-0.6.1/yahoofinancer/man/yf_download_prices.Rd |only yahoofinancer-0.6.1/yahoofinancer/man/yf_get_financials.Rd |only yahoofinancer-0.6.1/yahoofinancer/man/yf_get_index_quotes.Rd |only yahoofinancer-0.6.1/yahoofinancer/man/yf_get_market_stats.Rd |only yahoofinancer-0.6.1/yahoofinancer/tests/testthat/api |only yahoofinancer-0.6.1/yahoofinancer/tests/testthat/helper-mocks.R | 190 yahoofinancer-0.6.1/yahoofinancer/tests/testthat/samples/insights_1.json | 5182 +++++----- yahoofinancer-0.6.1/yahoofinancer/tests/testthat/samples/insights_2.json | 4890 ++++----- yahoofinancer-0.6.1/yahoofinancer/tests/testthat/samples/insights_3.json | 22 yahoofinancer-0.6.1/yahoofinancer/tests/testthat/samples/rec_aapl.json | 64 yahoofinancer-0.6.1/yahoofinancer/tests/testthat/samples/rec_btc_usd.json | 64 yahoofinancer-0.6.1/yahoofinancer/tests/testthat/samples/rec_msft.json | 64 yahoofinancer-0.6.1/yahoofinancer/tests/testthat/samples/ts_redacted.json | 10 yahoofinancer-0.6.1/yahoofinancer/tests/testthat/setup-httptest2.R |only yahoofinancer-0.6.1/yahoofinancer/tests/testthat/test-currency.R | 250 yahoofinancer-0.6.1/yahoofinancer/tests/testthat/test-functional_api.R |only yahoofinancer-0.6.1/yahoofinancer/tests/testthat/test-index-success.R | 80 yahoofinancer-0.6.1/yahoofinancer/tests/testthat/test-index.R | 152 yahoofinancer-0.6.1/yahoofinancer/tests/testthat/test-market_summary.R |only yahoofinancer-0.6.1/yahoofinancer/tests/testthat/test-parse_chart_data.R |only yahoofinancer-0.6.1/yahoofinancer/tests/testthat/test-smoke-live.R |only yahoofinancer-0.6.1/yahoofinancer/tests/testthat/test-ticker-success.R | 597 - yahoofinancer-0.6.1/yahoofinancer/tests/testthat/test-ticker.R | 502 yahoofinancer-0.6.1/yahoofinancer/tests/testthat/test-tickers.R | 358 yahoofinancer-0.6.1/yahoofinancer/tests/testthat/test-trending.R | 54 yahoofinancer-0.6.1/yahoofinancer/tests/testthat/test-utils.R | 94 yahoofinancer-0.6.1/yahoofinancer/tests/testthat/test-validate.R |only yahoofinancer-0.6.1/yahoofinancer/tests/testthat/test-vignettes.R |only yahoofinancer-0.6.1/yahoofinancer/tools |only yahoofinancer-0.6.1/yahoofinancer/vignettes |only 60 files changed, 8876 insertions(+), 7500 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible
outcome to evaluate the effectiveness of a new therapy (the true endpoint) is
difficult to measure. In such a situation, it can be an effective strategy to
replace the true endpoint by a (bio)marker that is easier to measure and that
allows for a prediction of the treatment effect on the true endpoint (a
surrogate endpoint). The package 'Surrogate' allows for an evaluation of the
appropriateness of a candidate surrogate endpoint based on the meta-analytic,
information-theoretic, and causal-inference frameworks. Part of this software
has been developed using funding provided from the European Union's Seventh
Framework Programme for research, technological development and demonstration
(Grant Agreement no 602552), the Special Research Fund (BOF) of Hasselt
University (BOF-number: BOF2OCPO3), GlaxoSmithKline Biologicals, Baekeland
Mandaat (HBC.2022.0145), and Johnson & Johnson Innovative Medicine.
Author: Wim Van Der Elst [cre, aut],
Florian Stijven [aut],
Fenny Ong [aut],
Dries De Witte [aut],
Gokce Deliorman [aut],
Paul Meyvisch [aut],
Alvaro Poveda [aut],
Ariel Alonso [aut],
Hannah Ensor [aut],
Christoper Weir [aut],
Geert Molenberghs [aut]
Maintainer: Wim Van Der Elst <wim.vanderelst@gmail.com>
Diff between Surrogate versions 3.4.2 dated 2026-06-03 and 3.4.3 dated 2026-10-16
Surrogate-3.4.2/Surrogate/data/ARMD_S.rda |only Surrogate-3.4.2/Surrogate/man/ARMD_S.Rd |only Surrogate-3.4.3/Surrogate/DESCRIPTION | 7 Surrogate-3.4.3/Surrogate/MD5 | 519 +- Surrogate-3.4.3/Surrogate/NAMESPACE | 18 Surrogate-3.4.3/Surrogate/NEWS.md | 2 Surrogate-3.4.3/Surrogate/R/AA.MultS.R | 114 Surrogate-3.4.3/Surrogate/R/Bootstrap.MEP.BinBin.R | 340 - Surrogate-3.4.3/Surrogate/R/CausalDiagramBinBin.R | 750 +-- Surrogate-3.4.3/Surrogate/R/CausalDiagramContCont.R | 196 Surrogate-3.4.3/Surrogate/R/CbC.R | 350 - Surrogate-3.4.3/Surrogate/R/Data.Processing.R | 100 Surrogate-3.4.3/Surrogate/R/ECT.R | 52 Surrogate-3.4.3/Surrogate/R/FederatedApproachStage1.R | 324 - Surrogate-3.4.3/Surrogate/R/FederatedApproachStage2.R | 626 +- Surrogate-3.4.3/Surrogate/R/FixedBinBinIT.r | 606 +- Surrogate-3.4.3/Surrogate/R/FixedBinContIT.r | 756 +-- Surrogate-3.4.3/Surrogate/R/FixedContBinIT.r | 546 +- Surrogate-3.4.3/Surrogate/R/FixedContContIT.r | 482 - Surrogate-3.4.3/Surrogate/R/FixedDiscrDiscrIT.R | 1188 ++-- Surrogate-3.4.3/Surrogate/R/ICA.BinBin.Grid.Full.R | 1372 ++--- Surrogate-3.4.3/Surrogate/R/ICA.BinBin.Grid.Sample.Uncert.R | 1524 +++--- Surrogate-3.4.3/Surrogate/R/ICA.BinCont.BS.R | 250 - Surrogate-3.4.3/Surrogate/R/ICA.Cont.Cont.MultS.R | 550 +- Surrogate-3.4.3/Surrogate/R/ICA.Cont.Cont.MultS_alt.R | 220 Surrogate-3.4.3/Surrogate/R/ICA.ContCont.MultS.MPC.R | 380 - Surrogate-3.4.3/Surrogate/R/ICA.ContCont.MultS.PC.R | 258 - Surrogate-3.4.3/Surrogate/R/ICA.Sample.ControlTreat.R | 286 - Surrogate-3.4.3/Surrogate/R/ICABinBin.R | 1446 ++--- Surrogate-3.4.3/Surrogate/R/ICABinBinCounterAssum.R | 406 - Surrogate-3.4.3/Surrogate/R/ICA_ContCont_copula.R | 176 Surrogate-3.4.3/Surrogate/R/ICA_OrdCont_copula.R | 378 - Surrogate-3.4.3/Surrogate/R/ICA_OrdOrd_copula.R | 324 - Surrogate-3.4.3/Surrogate/R/ICA_SurvSurv_copula.R | 298 - Surrogate-3.4.3/Surrogate/R/ICA_alpha_ContCont.R | 332 - Surrogate-3.4.3/Surrogate/R/ICA_contcont_long_galecki.R | 197 Surrogate-3.4.3/Surrogate/R/ICA_contcont_long_ri.R | 564 -- Surrogate-3.4.3/Surrogate/R/ICA_contcont_long_ri_nested.R |only Surrogate-3.4.3/Surrogate/R/ICA_contcont_long_shared_ri.R |only Surrogate-3.4.3/Surrogate/R/ICA_t.R | 86 Surrogate-3.4.3/Surrogate/R/ISTE.ContCont.R | 758 +-- Surrogate-3.4.3/Surrogate/R/ITCI-Dvine-inference-utils.R | 1112 ++-- Surrogate-3.4.3/Surrogate/R/LongToWide.R | 20 Surrogate-3.4.3/Surrogate/R/MICA.Sample.ContCont.R | 372 - Surrogate-3.4.3/Surrogate/R/MICAContCont.R | 390 - Surrogate-3.4.3/Surrogate/R/MarginalProbs.R | 92 Surrogate-3.4.3/Surrogate/R/MaxEntICABinBin.R | 690 +- Surrogate-3.4.3/Surrogate/R/MaxEntSPFBinBin.R | 682 +- Surrogate-3.4.3/Surrogate/R/MetaAnalyticSurvBin.R | 1752 +++---- Surrogate-3.4.3/Surrogate/R/MetaAnalyticSurvCat.R | 1760 +++---- Surrogate-3.4.3/Surrogate/R/MetaAnalyticSurvCont.R | 1922 +++---- Surrogate-3.4.3/Surrogate/R/MetaAnalyticSurvSurv.R | 2344 ++++----- Surrogate-3.4.3/Surrogate/R/MinSurrContCont.R | 158 Surrogate-3.4.3/Surrogate/R/MixedContContIT.R | 330 - Surrogate-3.4.3/Surrogate/R/MufixedContCont.MultS.R | 550 +- Surrogate-3.4.3/Surrogate/R/MumixedContCont.MultS.R | 306 - Surrogate-3.4.3/Surrogate/R/PPE.BinBin.R | 454 - Surrogate-3.4.3/Surrogate/R/PROC.BinBin.R | 158 Surrogate-3.4.3/Surrogate/R/Plot.FixedDiscrDiscrIT.R | 32 Surrogate-3.4.3/Surrogate/R/Pos.Def.Matrices.R | 76 Surrogate-3.4.3/Surrogate/R/Pred.TrialT.ContCont.R | 250 - Surrogate-3.4.3/Surrogate/R/Prentice.R | 134 Surrogate-3.4.3/Surrogate/R/SPF.BinCont.R | 356 - Surrogate-3.4.3/Surrogate/R/Schizo_PANSS_BPRS.R |only Surrogate-3.4.3/Surrogate/R/Sim.Data.Counterfactuals.R | 66 Surrogate-3.4.3/Surrogate/R/Sim.Data.MTS.R | 168 Surrogate-3.4.3/Surrogate/R/Sim.Data.STS.R | 46 Surrogate-3.4.3/Surrogate/R/SimDataCounterfactualsBinBin.R | 428 - Surrogate-3.4.3/Surrogate/R/SimDataSTSBinBin.R | 562 +- Surrogate-3.4.3/Surrogate/R/SummaryITContCont.R | 160 Surrogate-3.4.3/Surrogate/R/SummaryMaxEntSPFBinBin.R | 58 Surrogate-3.4.3/Surrogate/R/SummaryMetaAnalyticSTSContCont.R | 102 Surrogate-3.4.3/Surrogate/R/SummaryTrialLevelMA.R | 36 Surrogate-3.4.3/Surrogate/R/Surrogate-package.R | 14 Surrogate-3.4.3/Surrogate/R/TrialLevelIT.R | 74 Surrogate-3.4.3/Surrogate/R/TrialLevelMA.R | 82 Surrogate-3.4.3/Surrogate/R/TwoStageSurvSurv.R | 150 Surrogate-3.4.3/Surrogate/R/comb27.BinBin.R | 550 +- Surrogate-3.4.3/Surrogate/R/copula_utils.R | 1310 ++--- Surrogate-3.4.3/Surrogate/R/fit_model_BinCont_copula.R | 1006 ++-- Surrogate-3.4.3/Surrogate/R/fit_model_ContCont_copula.R | 660 +- Surrogate-3.4.3/Surrogate/R/fit_model_OrdCont_copula.R | 792 +-- Surrogate-3.4.3/Surrogate/R/fit_model_OrdOrd_copula.R | 612 +- Surrogate-3.4.3/Surrogate/R/fit_model_SurvSurv.R | 1094 ++-- Surrogate-3.4.3/Surrogate/R/goodness_of_fit_copula_models.R | 732 +- Surrogate-3.4.3/Surrogate/R/likelihood_copula_models.R | 260 - Surrogate-3.4.3/Surrogate/R/longitudinal_ica_utils.R |only Surrogate-3.4.3/Surrogate/R/longitudinal_model_fit.R |only Surrogate-3.4.3/Surrogate/R/longitudinal_model_summary.R |only Surrogate-3.4.3/Surrogate/R/plot.BinContCombnIT.R | 76 Surrogate-3.4.3/Surrogate/R/plot.Fano.BinBin.R | 272 - Surrogate-3.4.3/Surrogate/R/plot.InfoTheoretic.R | 58 Surrogate-3.4.3/Surrogate/R/plot.MaxEntContCont.R | 54 Surrogate-3.4.3/Surrogate/R/plot.MaxEntSPF.BinBin.R | 380 - Surrogate-3.4.3/Surrogate/R/plot.MetaAnalyticSTS.R | 48 Surrogate-3.4.3/Surrogate/R/plot.PPE.BinBin.R | 104 Surrogate-3.4.3/Surrogate/R/plot.SurvSurv.R | 80 Surrogate-3.4.3/Surrogate/R/plot.TrialLevelIT.R | 26 Surrogate-3.4.3/Surrogate/R/plot.TrialLevelMA.R | 38 Surrogate-3.4.3/Surrogate/R/plot.TwoStageSurvSurv.R | 42 Surrogate-3.4.3/Surrogate/R/plot.comb27.BinBin.R | 50 Surrogate-3.4.3/Surrogate/R/plot_ICABinCont.R | 216 Surrogate-3.4.3/Surrogate/R/plot_MaxEntICABinBin.R | 46 Surrogate-3.4.3/Surrogate/R/plot_SPF.BinCont.R | 208 Surrogate-3.4.3/Surrogate/R/plot_SPPBinBin.R | 2492 +++++----- Surrogate-3.4.3/Surrogate/R/prepare_longitudinal_data.R |only Surrogate-3.4.3/Surrogate/R/sensitivity_analysis_SurvSurv.R | 876 +-- Surrogate-3.4.3/Surrogate/R/sensitivity_analysis_copula.R | 516 +- Surrogate-3.4.3/Surrogate/R/sensitivity_intervals.R | 442 - Surrogate-3.4.3/Surrogate/R/summary.Fano.BinBin.R | 284 - Surrogate-3.4.3/Surrogate/R/summary.FixedDIscrDiscrIT.R | 78 Surrogate-3.4.3/Surrogate/R/summary.MuContCont.MultS.R | 114 Surrogate-3.4.3/Surrogate/R/summary.PPE.BinBin.R | 132 Surrogate-3.4.3/Surrogate/R/summary.SurvSurv.R | 66 Surrogate-3.4.3/Surrogate/R/summary.TrialLevelIT.R | 30 Surrogate-3.4.3/Surrogate/R/summary.TwoStageSurvSurv.R | 42 Surrogate-3.4.3/Surrogate/R/summaryBinContCombnIT.R | 104 Surrogate-3.4.3/Surrogate/R/summary_ICABinCont.R | 72 Surrogate-3.4.3/Surrogate/R/summary_MaxEntContCont.R | 36 Surrogate-3.4.3/Surrogate/R/summary_MaxEntICABinBin.R | 42 Surrogate-3.4.3/Surrogate/R/summary_SPFBinCont.R | 216 Surrogate-3.4.3/Surrogate/R/utils.R | 50 Surrogate-3.4.3/Surrogate/data/Schizo_PANSS_BPRS.rda |only Surrogate-3.4.3/Surrogate/man/AA.MultS.Rd | 148 Surrogate-3.4.3/Surrogate/man/ARMD.MultS.Rd | 42 Surrogate-3.4.3/Surrogate/man/ARMD.Rd | 40 Surrogate-3.4.3/Surrogate/man/BimixedCbCContCont.Rd | 224 Surrogate-3.4.3/Surrogate/man/Bootstrap.MEP.BinBin.Rd | 100 Surrogate-3.4.3/Surrogate/man/CausalDiagramBinBin.Rd | 138 Surrogate-3.4.3/Surrogate/man/CausalDiagramContCont.Rd | 112 Surrogate-3.4.3/Surrogate/man/Dvine_ICA_confint.Rd | 130 Surrogate-3.4.3/Surrogate/man/ECT.Rd | 70 Surrogate-3.4.3/Surrogate/man/Fano.BinBin.Rd | 136 Surrogate-3.4.3/Surrogate/man/FederatedApproachStage1.Rd | 274 - Surrogate-3.4.3/Surrogate/man/FederatedApproachStage2.Rd | 318 - Surrogate-3.4.3/Surrogate/man/FixedBinBinIT.Rd | 286 - Surrogate-3.4.3/Surrogate/man/ICA.BinCont.BS.Rd | 190 Surrogate-3.4.3/Surrogate/man/ICA.ContCont.MultS.MPC.Rd | 226 Surrogate-3.4.3/Surrogate/man/ICA.ContCont.MultS.PC.Rd | 190 Surrogate-3.4.3/Surrogate/man/ICA.ContCont.MultS.Rd | 186 Surrogate-3.4.3/Surrogate/man/ICA.ContCont.Mult_alt.Rd | 196 Surrogate-3.4.3/Surrogate/man/ICA.Sample.ControlTreat.Rd | 120 Surrogate-3.4.3/Surrogate/man/ICAContCont.Rd | 1 Surrogate-3.4.3/Surrogate/man/ICA_alpha_ContCont.Rd | 48 Surrogate-3.4.3/Surrogate/man/ICA_contcont_long_galecki.Rd | 87 Surrogate-3.4.3/Surrogate/man/ICA_contcont_long_ri.Rd | 252 - Surrogate-3.4.3/Surrogate/man/ICA_contcont_long_ri_nested.Rd |only Surrogate-3.4.3/Surrogate/man/ICA_contcont_long_shared_ri.Rd |only Surrogate-3.4.3/Surrogate/man/ICA_given_model_constructor.Rd | 162 Surrogate-3.4.3/Surrogate/man/ICA_given_model_constructor_SurvSurv.Rd | 144 Surrogate-3.4.3/Surrogate/man/ICA_t.Rd | 44 Surrogate-3.4.3/Surrogate/man/ISTE.ContCont.Rd | 246 Surrogate-3.4.3/Surrogate/man/MaxEntICAContCont.Rd | 116 Surrogate-3.4.3/Surrogate/man/MetaAnalyticSurvBin.Rd | 176 Surrogate-3.4.3/Surrogate/man/MetaAnalyticSurvCat.Rd | 172 Surrogate-3.4.3/Surrogate/man/MetaAnalyticSurvCont.Rd | 180 Surrogate-3.4.3/Surrogate/man/MetaAnalyticSurvSurv.Rd | 186 Surrogate-3.4.3/Surrogate/man/MixedContContIT.Rd | 256 - Surrogate-3.4.3/Surrogate/man/MufixedContCont.MultS.Rd | 230 Surrogate-3.4.3/Surrogate/man/MumixedContCont.MultS.Rd | 198 Surrogate-3.4.3/Surrogate/man/PANSS.Rd | 54 Surrogate-3.4.3/Surrogate/man/PROC.BinBin.Rd | 134 Surrogate-3.4.3/Surrogate/man/Plot.PredTrialTContCont.Rd | 98 Surrogate-3.4.3/Surrogate/man/Pred.TrialT.ContCont.Rd | 202 Surrogate-3.4.3/Surrogate/man/R2Lambda_from_covariance.Rd |only Surrogate-3.4.3/Surrogate/man/Schizo.Rd | 50 Surrogate-3.4.3/Surrogate/man/Schizo_BinCont.Rd | 50 Surrogate-3.4.3/Surrogate/man/Schizo_PANSS.Rd | 62 Surrogate-3.4.3/Surrogate/man/Schizo_PANSS_BPRS.Rd |only Surrogate-3.4.3/Surrogate/man/Single.Trial.RE.AA.Rd | 28 Surrogate-3.4.3/Surrogate/man/SurvSurv.Rd | 202 Surrogate-3.4.3/Surrogate/man/association_gof_copula.Rd | 120 Surrogate-3.4.3/Surrogate/man/binary_continuous_loglik.Rd | 76 Surrogate-3.4.3/Surrogate/man/cdf_fun.Rd | 56 Surrogate-3.4.3/Surrogate/man/clayton_loglik_copula_scale.Rd | 86 Surrogate-3.4.3/Surrogate/man/colorectal.rd | 58 Surrogate-3.4.3/Surrogate/man/colorectal4.rd | 58 Surrogate-3.4.3/Surrogate/man/comb27.BinBin.Rd | 136 Surrogate-3.4.3/Surrogate/man/compute_ICA.Rd | 64 Surrogate-3.4.3/Surrogate/man/compute_ICA_BinCont.Rd | 134 Surrogate-3.4.3/Surrogate/man/compute_ICA_ContCont.Rd | 162 Surrogate-3.4.3/Surrogate/man/compute_ICA_OrdCont.Rd | 154 Surrogate-3.4.3/Surrogate/man/compute_ICA_OrdOrd.Rd | 154 Surrogate-3.4.3/Surrogate/man/compute_ICA_SurvSurv.Rd | 188 Surrogate-3.4.3/Surrogate/man/constructor_ICA_estimator.Rd | 54 Surrogate-3.4.3/Surrogate/man/continuous_continuous_loglik.Rd | 120 Surrogate-3.4.3/Surrogate/man/delta_method_log_mutinfo.Rd | 136 Surrogate-3.4.3/Surrogate/man/estimate_ICA_BinCont.Rd | 52 Surrogate-3.4.3/Surrogate/man/estimate_ICA_ContCont.Rd | 50 Surrogate-3.4.3/Surrogate/man/estimate_ICA_OrdCont.Rd | 118 Surrogate-3.4.3/Surrogate/man/estimate_ICA_OrdOrd.Rd | 54 Surrogate-3.4.3/Surrogate/man/estimate_marginal.Rd | 60 Surrogate-3.4.3/Surrogate/man/estimate_mutual_information_SurvSurv.Rd | 60 Surrogate-3.4.3/Surrogate/man/extract_longitudinal_parameters.Rd |only Surrogate-3.4.3/Surrogate/man/figures/lifecycle-archived.svg | 42 Surrogate-3.4.3/Surrogate/man/figures/lifecycle-defunct.svg | 42 Surrogate-3.4.3/Surrogate/man/figures/lifecycle-deprecated.svg | 42 Surrogate-3.4.3/Surrogate/man/figures/lifecycle-experimental.svg | 42 Surrogate-3.4.3/Surrogate/man/figures/lifecycle-maturing.svg | 42 Surrogate-3.4.3/Surrogate/man/figures/lifecycle-questioning.svg | 42 Surrogate-3.4.3/Surrogate/man/figures/lifecycle-soft-deprecated.svg | 42 Surrogate-3.4.3/Surrogate/man/figures/lifecycle-stable.svg | 58 Surrogate-3.4.3/Surrogate/man/figures/lifecycle-superseded.svg | 42 Surrogate-3.4.3/Surrogate/man/fit_copula_ContCont.Rd | 126 Surrogate-3.4.3/Surrogate/man/fit_copula_OrdCont.Rd | 294 - Surrogate-3.4.3/Surrogate/man/fit_copula_OrdOrd.Rd | 158 Surrogate-3.4.3/Surrogate/man/fit_copula_model_BinCont.Rd | 168 Surrogate-3.4.3/Surrogate/man/fit_copula_submodel_BinCont.Rd | 94 Surrogate-3.4.3/Surrogate/man/fit_copula_submodel_ContCont.Rd | 172 Surrogate-3.4.3/Surrogate/man/fit_copula_submodel_OrdCont.Rd | 156 Surrogate-3.4.3/Surrogate/man/fit_copula_submodel_OrdOrd.Rd | 128 Surrogate-3.4.3/Surrogate/man/fit_longitudinal_surrogate_model.Rd |only Surrogate-3.4.3/Surrogate/man/fit_model_SurvSurv.Rd | 272 - Surrogate-3.4.3/Surrogate/man/frank_loglik_copula_scale.Rd | 86 Surrogate-3.4.3/Surrogate/man/gaussian_loglik_copula_scale.Rd | 86 Surrogate-3.4.3/Surrogate/man/gumbel_loglik_copula_scale.Rd | 86 Surrogate-3.4.3/Surrogate/man/log_likelihood_copula_model.Rd | 142 Surrogate-3.4.3/Surrogate/man/loglik_copula_scale.Rd | 128 Surrogate-3.4.3/Surrogate/man/longitudinal_fit_stats.Rd |only Surrogate-3.4.3/Surrogate/man/longitudinal_matrix_diagnostics.Rd |only Surrogate-3.4.3/Surrogate/man/make_longitudinal_re_endpoint_specific.Rd |only Surrogate-3.4.3/Surrogate/man/make_longitudinal_re_none.Rd |only Surrogate-3.4.3/Surrogate/man/make_longitudinal_re_shared_by_arm.Rd |only Surrogate-3.4.3/Surrogate/man/marginal_distribution.Rd | 70 Surrogate-3.4.3/Surrogate/man/marginal_gof_copula.Rd | 122 Surrogate-3.4.3/Surrogate/man/marginal_gof_plots_scr.Rd | 80 Surrogate-3.4.3/Surrogate/man/model_fit_measures.Rd | 90 Surrogate-3.4.3/Surrogate/man/new_vine_copula_fit.Rd | 56 Surrogate-3.4.3/Surrogate/man/new_vine_copula_ss_fit.Rd | 92 Surrogate-3.4.3/Surrogate/man/ordinal_continuous_loglik.Rd | 250 - Surrogate-3.4.3/Surrogate/man/ordinal_ordinal_loglik.Rd | 148 Surrogate-3.4.3/Surrogate/man/ordinal_to_cutpoints.Rd | 52 Surrogate-3.4.3/Surrogate/man/pdf_fun.Rd | 56 Surrogate-3.4.3/Surrogate/man/plot.Fano.BinBin.Rd | 134 Surrogate-3.4.3/Surrogate/man/plot.ICA.ContCont.Mult.Rd | 150 Surrogate-3.4.3/Surrogate/man/plot.ISTE.ContCont.Rd | 146 Surrogate-3.4.3/Surrogate/man/plot.MaxEntContCont.Rd | 104 Surrogate-3.4.3/Surrogate/man/plot.MetaAnalyticSurvBin.Rd | 60 Surrogate-3.4.3/Surrogate/man/plot.MetaAnalyticSurvCat.Rd | 58 Surrogate-3.4.3/Surrogate/man/plot.MetaAnalyticSurvCont.Rd | 60 Surrogate-3.4.3/Surrogate/man/plot.MetaAnalyticSurvSurv.Rd | 58 Surrogate-3.4.3/Surrogate/man/plot.PPE.BinBin.Rd | 142 Surrogate-3.4.3/Surrogate/man/plot.SPPBinBin.Rd | 116 Surrogate-3.4.3/Surrogate/man/plot.comb27.BinBin.Rd | 108 Surrogate-3.4.3/Surrogate/man/plot.vine_copula_fit.Rd | 124 Surrogate-3.4.3/Surrogate/man/prepare_longitudinal_surrogate_data.Rd |only Surrogate-3.4.3/Surrogate/man/print.MetaAnalyticSurvBin.Rd | 58 Surrogate-3.4.3/Surrogate/man/print.MetaAnalyticSurvCat.Rd | 56 Surrogate-3.4.3/Surrogate/man/print.MetaAnalyticSurvCont.Rd | 58 Surrogate-3.4.3/Surrogate/man/print.MetaAnalyticSurvSurv.Rd | 56 Surrogate-3.4.3/Surrogate/man/print.vine_copula_fit.Rd | 34 Surrogate-3.4.3/Surrogate/man/prostate.Rd | 60 Surrogate-3.4.3/Surrogate/man/sample_copula_parameters.Rd | 150 Surrogate-3.4.3/Surrogate/man/sample_deltas_BinCont.Rd | 180 Surrogate-3.4.3/Surrogate/man/sample_dvine.Rd | 120 Surrogate-3.4.3/Surrogate/man/sensitivity_analysis_BinCont_copula.Rd | 454 - Surrogate-3.4.3/Surrogate/man/sensitivity_analysis_SurvSurv_copula.Rd | 622 +- Surrogate-3.4.3/Surrogate/man/sensitivity_analysis_copula.Rd | 486 - Surrogate-3.4.3/Surrogate/man/sensitivity_intervals_Dvine.Rd | 286 - Surrogate-3.4.3/Surrogate/man/summary.FederatedApproachStage2.Rd | 172 Surrogate-3.4.3/Surrogate/man/summary.MetaAnalyticSurvBin.Rd | 58 Surrogate-3.4.3/Surrogate/man/summary.MetaAnalyticSurvCat.Rd | 56 Surrogate-3.4.3/Surrogate/man/summary.MetaAnalyticSurvCont.Rd | 58 Surrogate-3.4.3/Surrogate/man/summary.MetaAnalyticSurvSurv.Rd | 56 Surrogate-3.4.3/Surrogate/man/summary_level_bootstrap_ICA.Rd | 196 Surrogate-3.4.3/Surrogate/man/summary_longitudinal_ica.Rd |only Surrogate-3.4.3/Surrogate/man/twostep_BinCont.Rd | 106 Surrogate-3.4.3/Surrogate/man/twostep_SurvSurv.Rd | 132 Surrogate-3.4.3/Surrogate/tests/testthat/test-ICA_contcont_long_galecki.R | 179 Surrogate-3.4.3/Surrogate/tests/testthat/test-ICA_contcont_long_ri.R | 479 - Surrogate-3.4.3/Surrogate/tests/testthat/test-ICA_contcont_long_ri_nested.R |only Surrogate-3.4.3/Surrogate/tests/testthat/test-ICA_contcont_long_shared_ri.R |only Surrogate-3.4.3/Surrogate/tests/testthat/test-fit_longitudinal_surrogate_model.R |only Surrogate-3.4.3/Surrogate/tests/testthat/test-longitudinal_utils_data.R |only 274 files changed, 32010 insertions(+), 32495 deletions(-)
Title: Conducting and Visualizing Specification Curve Analyses
Description: Provides utilities for conducting specification curve analyses (Simonsohn, Simmons & Nelson, 2020, <doi:10.1038/s41562-020-0912-z>) or multiverse analyses (Steegen, Tuerlinckx, Gelman & Vanpaemel, 2016, <doi:10.1177/1745691616658637>) including functions to setup, run, evaluate, and plot all specifications, as well as to conduct inference on the specification curve based on resampling under the null.
Author: Philipp K. Masur [aut, cre] ,
Michael Scharkow [aut]
Maintainer: Philipp K. Masur <phil.masur@gmail.com>
Diff between specr versions 1.0.0 dated 2023-01-20 and 1.1.0 dated 2026-10-16
specr-1.0.0/specr/R/example_data.4.R |only specr-1.0.0/specr/vignettes/man |only specr-1.0.0/specr/vignettes/parallel-bayesian-models.Rmd.orig |only specr-1.0.0/specr/vignettes/parallelization.Rmd.orig |only specr-1.1.0/specr/DESCRIPTION | 26 specr-1.1.0/specr/MD5 | 178 +- specr-1.1.0/specr/NAMESPACE | 17 specr-1.1.0/specr/NEWS.md | 89 + specr-1.1.0/specr/R/data.R |only specr-1.1.0/specr/R/generics.r | 522 +++++- specr-1.1.0/specr/R/helpers.R | 72 specr-1.1.0/specr/R/helpers_old.R | 14 specr-1.1.0/specr/R/icc_specs.r | 25 specr-1.1.0/specr/R/infer_curve.R |only specr-1.1.0/specr/R/plot_choices.r | 20 specr-1.1.0/specr/R/plot_curve.r | 23 specr-1.1.0/specr/R/plot_decisiontree.r | 27 specr-1.1.0/specr/R/plot_samplesizes.r | 7 specr-1.1.0/specr/R/plot_specs.r | 12 specr-1.1.0/specr/R/plot_summary.r | 16 specr-1.1.0/specr/R/plot_variance.r | 6 specr-1.1.0/specr/R/reexports.R | 2 specr-1.1.0/specr/R/run_specs.r | 34 specr-1.1.0/specr/R/setup.R | 137 + specr-1.1.0/specr/R/setup_specs.r | 15 specr-1.1.0/specr/R/specr-package.r | 12 specr-1.1.0/specr/R/specr.R | 131 - 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Title: The Self-Controlled Case Series Method
Description: Various self-controlled case series models used to investigate
associations between time-varying exposures such as vaccines or
other drugs or non drug exposures and an adverse event can be
fitted. Detailed information on the self-controlled case series
method and its extensions with more examples can be found in
Farrington, P., Whitaker, H., and Ghebremichael-Weldeselassie, Y.
(2018, ISBN: 978-1-4987-8159-6. Self-controlled Case Series studies: A modelling Guide with R. Boca Raton: Chapman & Hall/CRC Press) and
<https://sccs-studies.info>.
Author: Yonas Ghebremichael Weldeselassie [aut, cre],
Heather Whitaker [aut],
Paddy Farrington [aut]
Maintainer: Yonas Ghebremichael Weldeselassie <yonas.weldeselassie@open.ac.uk>
Diff between SCCS versions 1.7 dated 2024-04-01 and 1.8 dated 2026-10-16
DESCRIPTION | 31 + MD5 | 6 R/semisccs.R | 877 +++++++++++++++++++++++++++---------------------------- R/standardsccs.R | 1 4 files changed, 464 insertions(+), 451 deletions(-)
Title: Lagged Weighted Quantile Sum Regression
Description: Wrapper functions for the implementation of lagged weighted
quantile sum regression, as per 'Gennings et al' (2020)
<doi:10.1016/j.envres.2020.109529>.
Author: Paul Curtin [aut, cre],
Stefano Renzetti [aut],
Chris Gennings [aut]
Maintainer: Paul Curtin <paul.c.p.curtin@gmail.com>
This is a re-admission after prior archival of version 0.5.0 dated 2021-03-04
Diff between lwqs versions 0.5.0 dated 2021-03-04 and 0.5.1 dated 2026-10-16
lwqs-0.5.0/lwqs/inst/doc/lwqs-vignette.R |only lwqs-0.5.0/lwqs/inst/doc/lwqs-vignette.Rmd |only lwqs-0.5.0/lwqs/inst/doc/lwqs-vignette.html |only lwqs-0.5.0/lwqs/vignettes/lwqs-vignette.Rmd |only lwqs-0.5.1/lwqs/DESCRIPTION | 26 - lwqs-0.5.1/lwqs/MD5 | 26 - lwqs-0.5.1/lwqs/NAMESPACE | 4 lwqs-0.5.1/lwqs/NEWS.md |only lwqs-0.5.1/lwqs/R/lwqs.R | 262 ++++++++------ lwqs-0.5.1/lwqs/build/vignette.rds |binary lwqs-0.5.1/lwqs/inst/doc/lwqs_vignette.Rmd |only lwqs-0.5.1/lwqs/inst/doc/lwqs_vignette.html |only lwqs-0.5.1/lwqs/man/extract_mixture.Rd | 14 lwqs-0.5.1/lwqs/man/extract_weights.Rd | 13 lwqs-0.5.1/lwqs/man/lwqs.Rd | 26 - lwqs-0.5.1/lwqs/man/lwqs_data.Rd | 8 lwqs-0.5.1/lwqs/vignettes/lwqs-fig-unnamed-chunk-13-1.png |only lwqs-0.5.1/lwqs/vignettes/lwqs-fig-unnamed-chunk-4-1.png |only lwqs-0.5.1/lwqs/vignettes/lwqs_vignette.Rmd |only 19 files changed, 226 insertions(+), 153 deletions(-)
Title: Content Analysis in R: Integrated Qualitative (LLMs) and
Quantitative Pipeline
Description: Provides an integrated pipeline for content analysis
combining qualitative coding assisted by large language models (LLMs)
with classical quantitative text analysis. Includes modules for
pre-processing (tokenization, stopwords for Brazilian Portuguese),
descriptive statistics, keyness, co-occurrence networks, word clouds
(including comparative and X-ray variants), sentiment analysis via
OpLexicon, Latent Dirichlet Allocation (LDA), inter-coder
reliability metrics (Krippendorff, Gwet), and modern visualizations
based on ggplot2. Special focus on Brazilian corpora and
political-institutional codebooks. Inspired by Maerz and Benoit (2025)
<https://quallmer.github.io/quallmer/>.
Author: Anderson Henrique [aut, cre]
Maintainer: Anderson Henrique <anderson.henrique@usp.br>
Diff between acR versions 0.4.0 dated 2026-10-14 and 0.6.0 dated 2026-10-16
DESCRIPTION | 8 MD5 | 333 ++-- NAMESPACE | 26 NEWS.md | 1197 +++++++++------- R/ac_ca.R |only R/ac_chat_local.R | 4 R/ac_clean.R | 4 R/ac_cluster.R | 519 +++---- R/ac_collocations.R |only R/ac_cooccurrence.R | 466 +++--- R/ac_corpus.R | 4 R/ac_count.R | 335 ++-- R/ac_dictionary.R |only R/ac_dictionary_validate.R |only R/ac_emotion.R |only R/ac_estimate_tokens.R | 30 R/ac_export.R | 22 R/ac_fetch_camara.R | 24 R/ac_fetch_senado.R | 18 R/ac_import.R | 16 R/ac_keyness.R | 52 R/ac_kwic.R |only R/ac_lda.R | 939 +++++++------ R/ac_lexical_diversity.R |only R/ac_plot_cluster.R | 6 R/ac_plot_cooccurrence.R | 4 R/ac_plot_keyness.R | 315 ++-- R/ac_plot_tf_idf.R | 357 ++-- R/ac_plot_top_terms.R | 332 ++-- R/ac_plot_wordcloud_comparative.R | 750 +++++----- R/ac_plot_zipf.R |only R/ac_qual_code.R | 1723 ++++++++++++------------ R/ac_qual_codebook.R | 44 R/ac_qual_irr.R | 734 +++++----- R/ac_qual_models.R | 4 R/ac_qual_reliability.R | 1717 ++++++++++++----------- R/ac_qual_report.R | 1560 ++++++++++----------- R/ac_qual_search_literature.R | 20 R/ac_readability.R |only R/ac_sentiment.R | 677 +++++---- R/ac_temporal.R |only R/ac_tf_idf.R | 30 R/ac_theme.R | 2 R/ac_tokenize.R | 433 +++--- R/ac_top_terms.R | 243 +-- R/ac_wordcloud.R | 8 R/ac_wordscores.R |only R/globals.R | 79 - R/is_ac_corpus.R | 2 R/stopwords_pt_br.R | 4 README.md | 1062 +++++++------- build/vignette.rds |binary inst/doc/analise-proposicoes.R | 4 inst/doc/analise-proposicoes.Rmd | 952 +++++++------ inst/doc/analise-proposicoes.html | 111 + inst/doc/cluster.R | 35 inst/doc/cluster.Rmd | 949 ++++++++----- inst/doc/cluster.html | 329 +++- inst/doc/introducao-acR.R | 38 inst/doc/introducao-acR.Rmd | 525 ++++--- inst/doc/introducao-acR.html | 304 +--- inst/doc/lda.R | 142 + inst/doc/lda.Rmd | 891 +++++++----- inst/doc/lda.html | 653 +++++---- inst/doc/llm-local-em-escala.R | 6 inst/doc/llm-local-em-escala.Rmd | 428 ++--- inst/doc/llm-local-em-escala.html | 43 inst/doc/qualitativo-llm.R | 8 inst/doc/qualitativo-llm.Rmd | 1331 +++++++++--------- inst/doc/qualitativo-llm.html | 323 +++- inst/doc/quantitativo.R | 302 +++- inst/doc/quantitativo.Rmd | 1672 ++++++++++++++++++----- inst/doc/quantitativo.html | 1338 +++++++++++++++++- inst/doc/quickstart.R | 27 inst/doc/quickstart.Rmd | 193 +- inst/doc/quickstart.html | 41 inst/doc/replicabilidade.R | 34 inst/doc/replicabilidade.Rmd | 666 ++++----- inst/doc/replicabilidade.html | 391 +---- inst/doc/sentimento.R | 53 inst/doc/sentimento.Rmd | 774 ++++++---- inst/doc/sentimento.html | 398 ++++- man/acR-package.Rd | 115 - 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man/ac_qual_codebook.Rd | 6 man/ac_qual_codebook_add.Rd | 4 man/ac_qual_codebook_history.Rd | 4 man/ac_qual_codebook_hybrid.Rd | 4 man/ac_qual_codebook_merge.Rd | 2 man/ac_qual_codebook_remove.Rd | 4 man/ac_qual_export_for_review.Rd | 4 man/ac_qual_import_human.Rd | 2 man/ac_qual_irr.Rd | 92 - man/ac_qual_list_models.Rd | 2 man/ac_qual_load_codebook.Rd | 8 man/ac_qual_recommend_model.Rd | 2 man/ac_qual_reliability.Rd | 297 ++-- man/ac_qual_report.Rd | 12 man/ac_qual_report_full.Rd | 8 man/ac_qual_sample.Rd | 56 man/ac_qual_save_codebook.Rd | 6 man/ac_qual_search_literature.Rd | 20 man/ac_readability.Rd |only man/ac_sentiment.Rd | 72 - man/ac_temporal.Rd |only man/ac_tf_idf.Rd | 30 man/ac_tokenize.Rd | 20 man/ac_top_terms.Rd | 24 man/ac_wordcloud.Rd | 8 man/ac_wordscores.Rd |only man/as_prompt.Rd | 2 man/figures/pipeline.svg | 13 man/is_ac_corpus.Rd | 2 tests/testthat/test-ac_ca.R |only tests/testthat/test-ac_cluster.R | 7 tests/testthat/test-ac_collocations.R |only tests/testthat/test-ac_cooccurrence.R | 19 tests/testthat/test-ac_dictionary.R |only tests/testthat/test-ac_dictionary_validate.R |only tests/testthat/test-ac_emotion.R |only tests/testthat/test-ac_kwic.R |only tests/testthat/test-ac_lda.R | 40 tests/testthat/test-ac_lexical_diversity.R |only tests/testthat/test-ac_plot_keyness.R | 11 tests/testthat/test-ac_plot_zipf.R |only tests/testthat/test-ac_qual_code.R | 2 tests/testthat/test-ac_qual_irr_export.R | 528 +++---- tests/testthat/test-ac_qual_reliability.R | 26 tests/testthat/test-ac_qual_search_literature.R | 1 tests/testthat/test-ac_readability.R |only tests/testthat/test-ac_sentiment.R | 509 +++---- tests/testthat/test-ac_temporal.R |only tests/testthat/test-ac_tokenize.R | 7 tests/testthat/test-ac_top_terms.R | 13 tests/testthat/test-ac_wordcloud.R | 9 tests/testthat/test-ac_wordscores.R |only vignettes/analise-proposicoes.Rmd | 952 +++++++------ vignettes/cluster.Rmd | 949 ++++++++----- vignettes/introducao-acR.Rmd | 525 ++++--- vignettes/lda.Rmd | 891 +++++++----- vignettes/llm-local-em-escala.Rmd | 428 ++--- vignettes/qualitativo-llm.Rmd | 1331 +++++++++--------- vignettes/quantitativo.Rmd | 1672 ++++++++++++++++++----- vignettes/quickstart.Rmd | 193 +- vignettes/replicabilidade.Rmd | 666 ++++----- vignettes/sentimento.Rmd | 774 ++++++---- 188 files changed, 22671 insertions(+), 15345 deletions(-)
Title: Simple Definition Of Time Intervals
Description: Simple definition of time intervals for the current, previous, and next week, month, quarter and year.
Author: Alexey Seleznev [aut, cre]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between timeperiodsR versions 0.7.7 dated 2026-05-12 and 0.7.9 dated 2026-10-16
DESCRIPTION | 9 ++- MD5 | 32 ++++++++----- NEWS.md | 15 +++++- R/check_dayoffs.R | 111 ++++++++++++++++++++++++------------------------ R/custom_period.R | 21 ++++++--- R/methods.R | 59 ++++++++++--------------- R/operators.R | 2 build/partial.rdb |binary inst/doc/tpr_intro.R | 8 +-- inst/doc/tpr_intro.Rmd | 4 - inst/doc/tpr_intro.html | 80 +++++++++++++++++----------------- man/check_dayoffs.Rd | 4 + tests |only vignettes/tpr_intro.Rmd | 4 - 14 files changed, 185 insertions(+), 164 deletions(-)
Title: Use Images in 'ggplot2'
Description: Supports image files and graphic objects to be visualized in
'ggplot2' graphic system. Images can be drawn at data points, used as the
background of a plot, or embedded as a sub-plot, and can be read from local
files or downloaded from remote services such as 'Pokemon', 'PhyloPic', and
emoji and icon collections. An interactive geom is provided for 'HTML'
output.
Author: Guangchuang Yu [aut, cre, cph] ,
Shuangbin Xu [ctb] ,
Yonghe Xia [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggimage versions 0.3.7 dated 2026-10-14 and 0.3.8 dated 2026-10-16
DESCRIPTION | 6 - MD5 | 25 ++--- NAMESPACE | 1 R/draw_key.R | 48 ++++++++-- R/geom_image.R | 143 +++++++++++++++++++++++++++---- R/ggpreview.R | 21 ++++ R/image_read2.R | 4 tests/testthat/helper-delegates.R |only tests/testthat/test-draw-key.R | 32 ++++++ tests/testthat/test-geom-image-cache.R | 62 +++++++++++++ tests/testthat/test-geom-subview-cache.R | 24 +++++ tests/testthat/test-ggpreview.R | 38 +++++++- tests/testthat/test-image-file-readers.R | 18 ++- tests/testthat/test-image-read2.R | 8 - 14 files changed, 377 insertions(+), 53 deletions(-)
Title: Ethnobotanical Analysis, Decision-Framing, and TEK Modeling
Description: Tools for quantifying Traditional Ecological Knowledge (TEK), modeling TEK in decision frameworks, and designing structured decision-framing exercises in conservation and development contexts. The package implements quantitative ethnobotany indices (Use Value, Relative Frequency of Citation, etc.) but positions them within a larger framework of Bayesian modeling and participatory decision analysis. Includes critical assessment of indices' limitations and case studies of participatory workshops.
Author: Cory Whitney [aut, cre]
Maintainer: Cory Whitney <whitney.cory@gmail.com>
Diff between ethnobotanyR versions 0.2.0 dated 2026-02-25 and 0.3.0 dated 2026-10-16
DESCRIPTION | 18 MD5 | 79 + NAMESPACE | 3 NEWS.md | 149 +-- R/ethno_bayes_consensus.R | 130 +- R/ethno_beta.R |only R/ethno_boot.R | 20 R/ethno_consensus.R |only R/ethno_saturation.R |only R/homegardens.R |only README.md | 48 - build/partial.rdb |binary build/vignette.rds |binary data/homegardens.rda |only data/homegardens_info.rda |only data/homegardens_species.rda |only inst/doc/TEK_modeling_vignette.R | 180 ++-- inst/doc/TEK_modeling_vignette.Rmd | 209 ++-- inst/doc/TEK_modeling_vignette.html | 805 +++++++++--------- inst/doc/benin_case_study.html | 4 inst/doc/decision_framing_guide.html | 4 inst/doc/ethnobotanyR_modeling_vignette.R | 200 ++-- inst/doc/ethnobotanyR_modeling_vignette.Rmd | 263 ++--- inst/doc/ethnobotanyR_modeling_vignette.html | 681 ++++++--------- inst/doc/ethnobotanyr_decision_framing_practical.html | 16 inst/doc/ethnobotanyr_vignette.R | 41 inst/doc/ethnobotanyr_vignette.Rmd | 41 inst/doc/ethnobotanyr_vignette.html | 98 +- inst/doc/honest_ethnobotany.R | 4 inst/doc/honest_ethnobotany.Rmd | 6 inst/doc/honest_ethnobotany.html | 14 man/ethno_bayes_consensus.Rd | 8 man/ethno_beta.Rd |only man/ethno_boot.Rd | 11 man/ethno_consensus.Rd |only man/ethno_saturation.Rd |only man/homegardens.Rd |only man/homegardens_info.Rd |only man/homegardens_species.Rd |only tests |only vignettes/TEK_modeling_vignette.Rmd | 209 ++-- vignettes/ethnobotanyR_modeling_vignette.Rmd | 263 ++--- vignettes/ethnobotanyr_vignette.Rmd | 41 vignettes/honest_ethnobotany.Rmd | 6 vignettes/references/ethnobotanyR.bib | 14 vignettes/references/model_packages.bib | 104 -- vignettes/references/packages.bib | 99 -- 47 files changed, 1827 insertions(+), 1941 deletions(-)
Title: Fitting Tails by the Empirical Residual Coefficient of Variation
Description: Provides a methodology simple and trustworthy for the analysis of extreme values and multiple threshold tests for a generalized Pareto distribution, together
with an automatic threshold selection algorithm. See del Castillo, J, Daoudi, J and Lockhart, R (2014) <doi:10.1111/sjos.12037>.
Author: Joan del Castillo [aut],
David Morina Soler [aut],
Isabel Serra [aut],
Sergi Vilardell [cre]
Maintainer: Sergi Vilardell <sergi.vilardell13@gmail.com>
Diff between ercv versions 1.0.1 dated 2019-10-15 and 1.0.2 dated 2026-10-16
DESCRIPTION | 23 ++++- MD5 | 26 +++--- R/ccdfplot.R | 2 R/confint.fitpot.R | 2 R/cvplot.R | 2 R/egpd.R | 4 - R/fitpot.R | 2 R/print.fitpot.R | 2 R/thrselect.R | 2 man/Tm.Rd | 176 ++++++++++++++++++++++---------------------- man/cvplot.Rd | 179 ++++++++++++++++++++++---------------------- man/fitpot.Rd | 154 +++++++++++++++++++------------------- man/tdata.Rd | 120 +++++++++++++++--------------- man/thrselect.Rd | 211 ++++++++++++++++++++++++++--------------------------- 14 files changed, 460 insertions(+), 445 deletions(-)
Title: Embedded Conic Solver in R
Description: R interface to the Embedded COnic Solver (ECOS), an efficient
and robust C library for convex problems. Conic and equality
constraints can be specified in addition to integer and
boolean variable constraints for mixed-integer problems. This
R interface is inspired by the python interface and has
similar calling conventions.
Author: Anqi Fu [aut],
Balasubramanian Narasimhan [aut, cre],
Florian Schwendinger [ctb],
Martin Maechler [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between ECOSolveR versions 0.6 dated 2026-02-18 and 0.6.2 dated 2026-10-16
DESCRIPTION | 10 ++++----- MD5 | 28 ++++++++++++------------- NAMESPACE | 2 + NEWS.md | 14 +++++++++--- R/ecos.R | 2 + README.md | 41 ++++++++++++++++++------------------- build/vignette.rds |binary inst/doc/examples.Rmd | 24 ++++++++++++++------- inst/doc/examples.html | 33 ++++++++++++++++++----------- man/ECOSolveR-package.Rd | 1 src/ecos/ecos_bb/ecos_bb.c | 4 +-- src/ecos/ecos_bb/ecos_bb_preproc.c | 4 +-- src/ecos/include/ecos_bb.h | 6 ++--- src/ecosolve.c | 13 +++++++---- vignettes/examples.Rmd | 24 ++++++++++++++------- 15 files changed, 122 insertions(+), 84 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-03-30 0.1.1
2026-01-27 0.1.0
Title: Visualize Probability Distributions
Description: Visualize and compute percentiles/probabilities of normal, t, f, chi square
and binomial distributions.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between vistributions versions 0.2.0 dated 2024-11-07 and 0.2.1 dated 2026-10-16
vistributions-0.2.0/vistributions/man/figures/README-binom-1.png |only vistributions-0.2.0/vistributions/man/figures/README-normal-1.png |only vistributions-0.2.0/vistributions/man/figures/README-normal-2.png |only vistributions-0.2.0/vistributions/man/figures/README-normal-3.png |only vistributions-0.2.0/vistributions/man/vdist_t.Rd |only vistributions-0.2.0/vistributions/tests/figs |only vistributions-0.2.1/vistributions/DESCRIPTION | 13 vistributions-0.2.1/vistributions/MD5 | 155 -- vistributions-0.2.1/vistributions/NAMESPACE | 5 vistributions-0.2.1/vistributions/NEWS.md | 44 vistributions-0.2.1/vistributions/R/vdist-app.R | 7 vistributions-0.2.1/vistributions/R/vdist-binomial.R | 14 vistributions-0.2.1/vistributions/R/vdist-chisquare.R | 12 vistributions-0.2.1/vistributions/R/vdist-data-prep.R | 84 - vistributions-0.2.1/vistributions/R/vdist-f.R | 15 vistributions-0.2.1/vistributions/R/vdist-normal.R | 6 vistributions-0.2.1/vistributions/R/vdist-plots.R | 30 vistributions-0.2.1/vistributions/R/vdist-t.R | 16 vistributions-0.2.1/vistributions/R/vdist-utils.R | 14 vistributions-0.2.1/vistributions/R/zzz.R | 29 vistributions-0.2.1/vistributions/README.md | 171 ++ vistributions-0.2.1/vistributions/build/vignette.rds |binary vistributions-0.2.1/vistributions/inst/doc/introduction-to-vistributions.R | 72 vistributions-0.2.1/vistributions/inst/doc/introduction-to-vistributions.Rmd | 744 +++++----- vistributions-0.2.1/vistributions/inst/doc/introduction-to-vistributions.html | 93 - 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vistributions-0.2.1/vistributions/vignettes/introduction-to-vistributions.Rmd | 744 +++++----- 72 files changed, 1402 insertions(+), 1218 deletions(-)
Title: Simplified Vertex-Wise Analyses of Whole-Brain and Subcortical
Surface
Description: Provides functions to run statistical analyses on
surface-based neuroimaging data, computing measures including cortical
thickness and surface area of the whole-brain and of the hippocampi.
It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12'
preprocessed datasets, 'HippUnfold' hippocampal outputs and
'SubCortexMesh' subcortical outputs for a given sample by
restructuring the data values into a single file. The single file can
then be used by the package for analyses independently from its base
dataset and without need for its access.
Author: Junhong Yu [aut] ,
Charly Billaud [aut, cre]
Maintainer: Charly Billaud <charly.billaud@ntu.edu.sg>
Diff between VertexWiseR versions 1.5.4 dated 2026-09-16 and 1.5.5 dated 2026-10-16
VertexWiseR-1.5.4/VertexWiseR/vignettes/allaseg_plotsurf3d.jpg |only VertexWiseR-1.5.5/VertexWiseR/DESCRIPTION | 10 VertexWiseR-1.5.5/VertexWiseR/MD5 | 40 +- VertexWiseR-1.5.5/VertexWiseR/NAMESPACE | 1 VertexWiseR-1.5.5/VertexWiseR/NEWS.md | 14 VertexWiseR-1.5.5/VertexWiseR/R/CAT12vextract.R | 3 VertexWiseR-1.5.5/VertexWiseR/R/DTSERIESvextract.R | 3 VertexWiseR-1.5.5/VertexWiseR/R/FSLRvextract.R | 1 VertexWiseR-1.5.5/VertexWiseR/R/HIPvextract.R | 10 VertexWiseR-1.5.5/VertexWiseR/R/SCMvextract.R | 78 ++-- VertexWiseR-1.5.5/VertexWiseR/R/SURFvextract.R | 1 VertexWiseR-1.5.5/VertexWiseR/R/VWRfirstrun.R | 14 VertexWiseR-1.5.5/VertexWiseR/R/decode_surf_data.R | 173 +++++++++- VertexWiseR-1.5.5/VertexWiseR/README.md | 2 VertexWiseR-1.5.5/VertexWiseR/inst/doc/VertexWiseR_Example_3.html | 14 VertexWiseR-1.5.5/VertexWiseR/inst/doc/VertexWiseR_surface_extraction.html | 118 +++--- VertexWiseR-1.5.5/VertexWiseR/man/HIPvextract.Rd | 12 VertexWiseR-1.5.5/VertexWiseR/man/SCMvextract.Rd | 7 VertexWiseR-1.5.5/VertexWiseR/man/decode_surf_data.Rd | 2 VertexWiseR-1.5.5/VertexWiseR/vignettes/VertexWiseR_Example_3.Rmd | 2 VertexWiseR-1.5.5/VertexWiseR/vignettes/VertexWiseR_surface_extraction.Rmd | 2 VertexWiseR-1.5.5/VertexWiseR/vignettes/allaseg_plotsurf3d.png |only 22 files changed, 350 insertions(+), 157 deletions(-)
Title: Recency, Frequency and Monetary Value Analysis
Description: Tools for RFM (recency, frequency and monetary value) analysis.
Generate RFM score from both transaction and customer level data. Visualize the
relationship between recency, frequency and monetary value using heatmap,
histograms, bar charts and scatter plots. Includes a 'shiny' app for
interactive segmentation. References:
i. Blattberg R.C., Kim BD., Neslin S.A (2008) <doi:10.1007/978-0-387-72579-6_12>.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between rfm versions 0.4.0 dated 2026-04-30 and 0.5.0 dated 2026-10-16
rfm-0.4.0/rfm/tests/figs |only rfm-0.4.0/rfm/tests/testthat/Rplots.pdf |only rfm-0.5.0/rfm/DESCRIPTION | 15 rfm-0.5.0/rfm/MD5 | 64 rfm-0.5.0/rfm/NAMESPACE | 7 rfm-0.5.0/rfm/NEWS.md | 18 rfm-0.5.0/rfm/R/rfm-ggplot.R | 7 rfm-0.5.0/rfm/R/rfm-plots.R | 13 rfm-0.5.0/rfm/R/rfm-report.R | 108 rfm-0.5.0/rfm/R/rfm-segment.R | 46 rfm-0.5.0/rfm/R/rfm-shiny-app.R | 33 rfm-0.5.0/rfm/R/utils.R | 30 rfm-0.5.0/rfm/R/zzz.R | 40 rfm-0.5.0/rfm/README.md | 6 rfm-0.5.0/rfm/inst/doc/rfm-introduction.html | 42 rfm-0.5.0/rfm/man/rfm_create_report.Rd | 134 rfm-0.5.0/rfm/man/rfm_plot_bar_chart.Rd | 118 rfm-0.5.0/rfm/man/rfm_plot_heatmap.Rd | 160 rfm-0.5.0/rfm/man/rfm_plot_histogram.Rd | 166 rfm-0.5.0/rfm/man/rfm_plot_order_dist.Rd | 172 rfm-0.5.0/rfm/man/rfm_plot_revenue_dist.Rd | 196 rfm-0.5.0/rfm/man/rfm_plot_segment.Rd | 146 rfm-0.5.0/rfm/man/rfm_plot_segment_scatter.Rd | 166 rfm-0.5.0/rfm/man/rfm_plot_segment_summary.Rd | 240 - rfm-0.5.0/rfm/man/rfm_segment_summary.Rd | 88 rfm-0.5.0/rfm/tests/testthat.R | 24 rfm-0.5.0/rfm/tests/testthat/_snaps/rfm-plotly.md | 4670 +++++++++++----------- rfm-0.5.0/rfm/tests/testthat/test-guards.R |only rfm-0.5.0/rfm/tests/testthat/test-rfm-report.R |only rfm-0.5.0/rfm/tests/testthat/test-rfm-shiny.R |only rfm-0.5.0/rfm/tests/testthat/test-zzz.R |only 31 files changed, 3346 insertions(+), 3363 deletions(-)
Title: Population Fisher Information Matrix
Description: Evaluate or optimize designs for nonlinear mixed effects models
using the Fisher Information matrix; see <doi:10.1093/biomet/84.2.429> and
<doi:10.1016/S0169-2607(00)00117-6>. Supports population, individual, and
Bayesian 'FIMs', covariates, inter-occasion variability, and D-optimal search
('Fedorov-Wynn', multiplicative, simplex, 'PSO', 'PGBO').
Author: Romain Leroux [aut] ,
France Mentre [cre] ,
Lucie Fayette [ctb] ,
Antoine Croxo [ctb] ,
Jeremy Seurat [ctb]
Maintainer: France Mentre <pfim@inserm.fr>
Diff between PFIM versions 8.0 dated 2026-09-28 and 8.0.1 dated 2026-10-16
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Title: Client for the 'enviPath' 'RESTful' API
Description: The environmental pathway database ('enviPath') is a key resource for the
functional annotation and pathway prediction of microbial communities,
providing knowledge on biotransformation pathways along with the chemical
reactions and produced compounds. This package enables the programmatic
access to 'enviPath' by porting the database 'RESTful' API from R. This
includes methods to both retrieve entries and predict pathways for custom
compounds.
Author: Giulio Benedetti [aut, cre, cph]
Maintainer: Giulio Benedetti <giulio.benedetti@utu.fi>
Diff between enviPathR versions 1.0.0 dated 2026-10-14 and 1.0.1 dated 2026-10-16
DESCRIPTION | 6 - MD5 | 26 ++--- README.md | 1 inst/doc/enviPathR.R | 6 - inst/doc/enviPathR.html | 26 +++-- tests/httptest/get/package_reaction/wrong.R | 10 +- tests/httptest/link/package_compound/wrong.R | 10 +- tests/httptest/list/package.json | 120 +++++++++++++-------------- tests/httptest/list/package/wrong/reaction.R | 10 +- tests/httptest/login/NA-2f7c1a-POST.R | 12 +- tests/httptest/model/util-e1f28b-POST.R | 6 - tests/testthat/setup.R | 2 tests/testthat/test-get.R | 8 - tests/testthat/test-link.R | 6 - 14 files changed, 127 insertions(+), 122 deletions(-)
Title: Easy and Accessible Bayesian Measurement Models Using 'brms'
Description: Fit computational and measurement models using full Bayesian
inference. The package provides a simple and accessible interface by
translating complex domain-specific models into 'brms' syntax, a
powerful and flexible framework for fitting Bayesian regression models
using 'Stan'. The package is designed so that users can easily apply
state-of-the-art models in various research fields, and so that
researchers can use it as a new model development framework.
References: Frischkorn and Popov (2025) <doi:10.3758/s13428-025-02643-0>.
Author: Vencislav Popov [aut, cph] ,
Gidon T. Frischkorn [aut, cre, cph] ,
Chenyu Li [ctb],
Paul-Christian Buerkner [cph]
Maintainer: Gidon T. Frischkorn <gfrischkorn@icloud.com>
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|only bmm-1.4.1/bmm/man/roc_sdt.Rd |only bmm-1.4.1/bmm/man/sdm.Rd | 10 bmm-1.4.1/bmm/man/sdt_cdp.Rd |only bmm-1.4.1/bmm/man/sdt_cdp_dist.Rd |only bmm-1.4.1/bmm/man/sdt_cdp_logmu.Rd |only bmm-1.4.1/bmm/man/sdt_dpsdt_dist.Rd |only bmm-1.4.1/bmm/man/sdt_mafc.Rd |only bmm-1.4.1/bmm/man/sdt_mafc_dist.Rd |only bmm-1.4.1/bmm/man/sdt_metad_dist.Rd |only bmm-1.4.1/bmm/man/sdt_ranking.Rd |only bmm-1.4.1/bmm/man/sdt_ranking_dist.Rd |only bmm-1.4.1/bmm/man/sdt_ranking_logmu.Rd |only bmm-1.4.1/bmm/man/sdt_rating.Rd |only bmm-1.4.1/bmm/man/sdt_rating_dist.Rd |only bmm-1.4.1/bmm/man/sdt_rating_logmu.Rd |only bmm-1.4.1/bmm/man/sdt_sensitivity.Rd |only bmm-1.4.1/bmm/man/sdt_thresholds.Rd |only bmm-1.4.1/bmm/man/sdt_yn.Rd |only bmm-1.4.1/bmm/man/sdt_yn_dist.Rd |only bmm-1.4.1/bmm/man/stancode.bmmformula.Rd | 6 bmm-1.4.1/bmm/man/standata.bmmformula.Rd | 6 bmm-1.4.1/bmm/man/summary.bmmfit.Rd | 2 bmm-1.4.1/bmm/man/supported_models.Rd | 27 bmm-1.4.1/bmm/man/update.bmmfit.Rd | 32 bmm-1.4.1/bmm/man/use_model_template.Rd | 2 bmm-1.4.1/bmm/tests/testthat/helper-epred.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-cases.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-cswald.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-data.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-ddm.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-ezdm.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-imm.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-m3.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-mixture2p.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-mixture3p.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-mpt.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-sdm.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-sdt_cdp.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-sdt_mafc.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-sdt_ranking.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-sdt_rating.R |only bmm-1.4.1/bmm/tests/testthat/helper-model-sdt_yn.R |only bmm-1.4.1/bmm/tests/testthat/helper-mpt.R |only bmm-1.4.1/bmm/tests/testthat/helper-sdt-analysis.R |only bmm-1.4.1/bmm/tests/testthat/helper-tiers.R |only bmm-1.4.1/bmm/tests/testthat/helper-warnings.R |only bmm-1.4.1/bmm/tests/testthat/setup.R |only bmm-1.4.1/bmm/tests/testthat/test-bmm.R | 144 bmm-1.4.1/bmm/tests/testthat/test-bmm_setup.R |only bmm-1.4.1/bmm/tests/testthat/test-conditional_effects.R | 1692 ++++++ bmm-1.4.1/bmm/tests/testthat/test-conventions.R |only bmm-1.4.1/bmm/tests/testthat/test-data_check.R |only bmm-1.4.1/bmm/tests/testthat/test-default-priors.R | 357 + bmm-1.4.1/bmm/tests/testthat/test-distributions.R | 759 ++- bmm-1.4.1/bmm/tests/testthat/test-emmeans.R | 44 bmm-1.4.1/bmm/tests/testthat/test-helpers-analysis.R |only bmm-1.4.1/bmm/tests/testthat/test-helpers-data-coercion.R |only bmm-1.4.1/bmm/tests/testthat/test-helpers-data.R | 508 +- bmm-1.4.1/bmm/tests/testthat/test-helpers-formula.R | 28 bmm-1.4.1/bmm/tests/testthat/test-helpers-init.R | 691 ++ bmm-1.4.1/bmm/tests/testthat/test-helpers-model.R | 445 + bmm-1.4.1/bmm/tests/testthat/test-helpers-parameters.R | 757 ++ bmm-1.4.1/bmm/tests/testthat/test-helpers-postprocess.R | 56 bmm-1.4.1/bmm/tests/testthat/test-helpers-prior.R | 577 ++ bmm-1.4.1/bmm/tests/testthat/test-links.R |only bmm-1.4.1/bmm/tests/testthat/test-model_cswald.R | 428 + bmm-1.4.1/bmm/tests/testthat/test-model_ddm.R | 177 bmm-1.4.1/bmm/tests/testthat/test-model_ezdm.R | 826 +++ bmm-1.4.1/bmm/tests/testthat/test-model_imm.R | 38 bmm-1.4.1/bmm/tests/testthat/test-model_m3.R | 436 + bmm-1.4.1/bmm/tests/testthat/test-model_mixture3p.R | 4 bmm-1.4.1/bmm/tests/testthat/test-model_mpt-stancode.R |only bmm-1.4.1/bmm/tests/testthat/test-model_mpt.R |only bmm-1.4.1/bmm/tests/testthat/test-model_mpt_data.R |only bmm-1.4.1/bmm/tests/testthat/test-model_mpt_expressions.R |only bmm-1.4.1/bmm/tests/testthat/test-model_mpt_import.R |only bmm-1.4.1/bmm/tests/testthat/test-model_mpt_plot.R |only 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|only bmm-1.4.1/bmm/tests/testthat/test-summary.R | 58 bmm-1.4.1/bmm/tests/testthat/test-update.R | 760 ++- bmm-1.4.1/bmm/tests/testthat/test-utils.R | 292 + 237 files changed, 18873 insertions(+), 2544 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior
distributions and Bayesian models. It includes point-estimates such as
Maximum A Posteriori (MAP), measures of dispersion (Highest Density
Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and
indices used for null-hypothesis testing (such as ROPE percentage, pd
and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Micah K. Wilson [aut] ,
Brenton M. Wiernik [aut] ,
Paul-Christian Buerkner [rev],
Tristan Mahr [rev] ,
Henrik Singmann [ctb] ,
Quentin F. Gron [...truncated...]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between bayestestR versions 0.19.0 dated 2026-09-09 and 0.20.0 dated 2026-10-16
bayestestR-0.19.0/bayestestR/R/p_rope.R |only bayestestR-0.19.0/bayestestR/man/p_rope.Rd |only bayestestR-0.19.0/bayestestR/tests/testthat/test-p_rope.R |only bayestestR-0.20.0/bayestestR/DESCRIPTION | 8 bayestestR-0.20.0/bayestestR/MD5 | 86 ++- bayestestR-0.20.0/bayestestR/NAMESPACE | 32 - bayestestR-0.20.0/bayestestR/NEWS.md | 51 ++ bayestestR-0.20.0/bayestestR/R/check_prior.R | 9 bayestestR-0.20.0/bayestestR/R/convert_bayesian_to_frequentist.R | 100 ++++ bayestestR-0.20.0/bayestestR/R/describe_posterior.R | 25 + bayestestR-0.20.0/bayestestR/R/display.R | 2 bayestestR-0.20.0/bayestestR/R/equivalence_test.R | 93 +++- bayestestR-0.20.0/bayestestR/R/format.R | 3 bayestestR-0.20.0/bayestestR/R/mediation.R | 69 ++- bayestestR-0.20.0/bayestestR/R/print.R | 25 - bayestestR-0.20.0/bayestestR/R/print.equivalence_test.R | 22 bayestestR-0.20.0/bayestestR/R/print_html.R | 19 bayestestR-0.20.0/bayestestR/R/print_md.R | 19 bayestestR-0.20.0/bayestestR/R/rope.R | 80 ++- bayestestR-0.20.0/bayestestR/R/rope_range.R | 65 ++ bayestestR-0.20.0/bayestestR/R/sensitivity_to_prior.R | 230 +++++++++- bayestestR-0.20.0/bayestestR/R/simulate_priors.R | 33 + bayestestR-0.20.0/bayestestR/man/convert_bayesian_as_frequentist.Rd | 14 bayestestR-0.20.0/bayestestR/man/dot-brms_cauchy_priors.Rd |only bayestestR-0.20.0/bayestestR/man/dot-brms_check_refit_priors.Rd |only bayestestR-0.20.0/bayestestR/man/dot-brms_priors.Rd |only bayestestR-0.20.0/bayestestR/man/dot-brms_slope_info.Rd |only bayestestR-0.20.0/bayestestR/man/dot-refit_brms.Rd |only bayestestR-0.20.0/bayestestR/man/equivalence_test.Rd | 26 - bayestestR-0.20.0/bayestestR/man/mediation.Rd | 5 bayestestR-0.20.0/bayestestR/man/rope.Rd | 22 bayestestR-0.20.0/bayestestR/man/sensitivity_to_prior.Rd | 35 + bayestestR-0.20.0/bayestestR/tests/testthat/helper.R | 14 bayestestR-0.20.0/bayestestR/tests/testthat/test-bayesfactor_models.R | 4 bayestestR-0.20.0/bayestestR/tests/testthat/test-bayesian_as_frequentist.R | 65 ++ bayestestR-0.20.0/bayestestR/tests/testthat/test-bayesian_as_frequentist_BayesFactor.R |only bayestestR-0.20.0/bayestestR/tests/testthat/test-blavaan.R | 3 bayestestR-0.20.0/bayestestR/tests/testthat/test-check_prior.R | 86 ++- bayestestR-0.20.0/bayestestR/tests/testthat/test-describe_posterior.R | 38 + bayestestR-0.20.0/bayestestR/tests/testthat/test-emmGrid.R | 37 - bayestestR-0.20.0/bayestestR/tests/testthat/test-equivalence_test.R | 14 bayestestR-0.20.0/bayestestR/tests/testthat/test-format.R | 20 bayestestR-0.20.0/bayestestR/tests/testthat/test-marginaleffects.R | 52 +- bayestestR-0.20.0/bayestestR/tests/testthat/test-mediation.R |only bayestestR-0.20.0/bayestestR/tests/testthat/test-rope.R | 63 ++ bayestestR-0.20.0/bayestestR/tests/testthat/test-rope_range.R | 83 +++ bayestestR-0.20.0/bayestestR/tests/testthat/test-sensitivity_to_prior.R |only bayestestR-0.20.0/bayestestR/tests/testthat/test-si.R | 7 bayestestR-0.20.0/bayestestR/tests/testthat/test-simulate_prior.R |only bayestestR-0.20.0/bayestestR/tests/testthat/test-weighted_posteriors.R | 44 + 50 files changed, 1257 insertions(+), 346 deletions(-)
Title: 'ggplot2'-Based Tools for Visualising DNA Sequences and
Modifications
Description: Uses 'ggplot2' to visualise either (a) a single DNA/RNA sequence split across multiple lines, (b) multiple DNA/RNA sequences, each occupying a whole line, or (c) base modifications such as DNA methylation called by modified bases models in Dorado or Guppy. Functions starting with visualise_<>() are the main plotting functions, and functions starting with extract_and_sort_<>() are key helper functions for reading files and reformatting data. Source code is available at <https://github.com/ejade42/ggDNAvis>, a full non-expert user guide is available at <https://ejade42.github.io/ggDNAvis/>, and an interactive web-app version of the software is available at <https://ejade42.github.io/ggDNAvis/articles/interactive_app.html>.
Author: Evelyn Jade [aut, cre, cph]
Maintainer: Evelyn Jade <evelynjade42@gmail.com>
Diff between ggDNAvis versions 1.0.1 dated 2026-06-22 and 1.1.0 dated 2026-10-16
DESCRIPTION | 6 MD5 | 62 +++--- NAMESPACE | 3 NEWS.md | 32 +++ R/alias_maps.R | 6 R/dna_tools.R | 40 ++++ R/merge_with_metadata.R | 92 +++++++++- R/visualise_many_sequences.R | 46 ++++- R/visualise_methylation.R | 35 ++- R/visualise_single_sequence.R | 14 - build/partial.rdb |binary build/vignette.rds |binary inst/shinyapp/mod_visualise_many_sequences.R | 2 inst/shinyapp/mod_visualise_methylation.R | 2 inst/shinyapp/mod_visualise_single_sequence.R | 2 man/extract_and_sort_methylation.Rd | 13 - man/invert_direction_vector.Rd |only man/merge_fastq_with_metadata.Rd | 7 man/merge_methylation_with_metadata.Rd | 9 man/sanitise_sequences_vector.Rd |only man/visualise_many_sequences.Rd | 29 +++ man/visualise_methylation.Rd | 7 man/visualise_single_sequence.Rd | 3 tests/testthat/reference_images/sone_2019_f1_1_expanded_test_33.png |binary tests/testthat/reference_images/sone_2019_f1_1_expanded_test_40.png |only tests/testthat/reference_images/visualise_many_sequences_test_29.png |only tests/testthat/reference_images/visualise_methylation_test_25.png |only tests/testthat/test-dna_tools.R | 22 ++ tests/testthat/test-merge_with_metadata.R | 36 +++ tests/testthat/test-visualise_many_sequences.R | 14 + tests/testthat/test-visualise_methylation.R | 28 +++ tests/testthat/test-visualise_single_sequence.R | 13 + tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_33.png |binary tests/testthat/test_plot_images/sone_2019_f1_1_expanded_test_40.png |only tests/testthat/test_plot_images/visualise_many_sequences_test_29.png |only tests/testthat/test_plot_images/visualise_methylation_test_25.png |only 36 files changed, 450 insertions(+), 73 deletions(-)