Title: Vertex Pool Topology for Well-Known Geometry
Description: Establishes and maintains vertex pool topology for geometry
handled by 'wk'. Segments are the atomic unit, vertices are shared via
integer references into a pool. Topology is made discoverable via coincident
vertex detection while not requiring modification of the input data.
Topological data models follow principles described in Worboys and
Duckham (2004, ISBN:978-0415283755). The edge-based topology geometry decomposed
into vertices and directed edge pairs is a simplification of the quad-edge case in
Guibas & Stolfi (1985) <doi:10.1145/282918.282923>.
Author: Michael Sumner [aut, cre, cph]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between wkpool versions 0.3.0 dated 2026-03-05 and 0.4.0 dated 2026-10-12
wkpool-0.3.0/wkpool/man/hole_points.Rd |only wkpool-0.3.0/wkpool/tests/testthat/Rplots.pdf |only wkpool-0.4.0/wkpool/DESCRIPTION | 19 wkpool-0.4.0/wkpool/MD5 | 121 +- wkpool-0.4.0/wkpool/NAMESPACE | 49 wkpool-0.4.0/wkpool/NEWS.md | 253 ++++ wkpool-0.4.0/wkpool/R/arc_node.R | 251 ++-- wkpool-0.4.0/wkpool/R/cpp11.R |only wkpool-0.4.0/wkpool/R/establish_topology.R | 66 - wkpool-0.4.0/wkpool/R/merge_coincident.R | 659 ++++++++--- wkpool-0.4.0/wkpool/R/round_trip.R | 336 +++-- wkpool-0.4.0/wkpool/R/wk-handle.R |only wkpool-0.4.0/wkpool/R/wkpool-package.R | 1 wkpool-0.4.0/wkpool/R/wkpool.R | 326 ++++- wkpool-0.4.0/wkpool/R/wkpool_tri.R |only wkpool-0.4.0/wkpool/README.md | 115 + wkpool-0.4.0/wkpool/build/partial.rdb |binary wkpool-0.4.0/wkpool/build/vignette.rds |binary wkpool-0.4.0/wkpool/inst/WORDLIST | 49 wkpool-0.4.0/wkpool/inst/doc/triangulation.R |only wkpool-0.4.0/wkpool/inst/doc/triangulation.Rmd |only wkpool-0.4.0/wkpool/inst/doc/triangulation.html |only wkpool-0.4.0/wkpool/inst/doc/wkpool-vignette-segments.R | 7 wkpool-0.4.0/wkpool/inst/doc/wkpool-vignette-segments.Rmd | 30 wkpool-0.4.0/wkpool/inst/doc/wkpool-vignette-segments.html | 80 - wkpool-0.4.0/wkpool/inst/doc/wkpool.R | 43 wkpool-0.4.0/wkpool/inst/doc/wkpool.Rmd | 114 + wkpool-0.4.0/wkpool/inst/doc/wkpool.html | 222 ++- wkpool-0.4.0/wkpool/man/arc_node_summary.Rd | 10 wkpool-0.4.0/wkpool/man/arcs_to_wkt.Rd | 19 wkpool-0.4.0/wkpool/man/as_arcs.Rd | 10 wkpool-0.4.0/wkpool/man/as_pslg.Rd | 25 wkpool-0.4.0/wkpool/man/classify_cycles.Rd | 14 wkpool-0.4.0/wkpool/man/cycle_signed_area.Rd | 2 wkpool-0.4.0/wkpool/man/cycles_to_wkt.Rd | 22 wkpool-0.4.0/wkpool/man/establish_topology.Rd | 15 wkpool-0.4.0/wkpool/man/figures |only wkpool-0.4.0/wkpool/man/find_arcs.Rd | 10 wkpool-0.4.0/wkpool/man/find_cycles.Rd | 9 wkpool-0.4.0/wkpool/man/find_internal_boundaries.Rd | 4 wkpool-0.4.0/wkpool/man/find_nodes.Rd | 9 wkpool-0.4.0/wkpool/man/merge_coincident.Rd | 74 + wkpool-0.4.0/wkpool/man/new_wkpool.Rd |only wkpool-0.4.0/wkpool/man/new_wkpool_tri.Rd |only wkpool-0.4.0/wkpool/man/plot.wkpool_tri.Rd |only wkpool-0.4.0/wkpool/man/pool_holes.Rd |only wkpool-0.4.0/wkpool/man/pool_triangles.Rd |only wkpool-0.4.0/wkpool/man/pool_triangulate.Rd |only wkpool-0.4.0/wkpool/man/segments_to_wkt.Rd | 8 wkpool-0.4.0/wkpool/man/topology_report.Rd | 5 wkpool-0.4.0/wkpool/man/vertex_degree.Rd | 9 wkpool-0.4.0/wkpool/man/wk_handle.wkpool.Rd |only wkpool-0.4.0/wkpool/man/wkpool-accessors.Rd | 13 wkpool-0.4.0/wkpool/man/wkpool-crs.Rd |only wkpool-0.4.0/wkpool/man/wkpool-package.Rd | 8 wkpool-0.4.0/wkpool/man/wkpool.Rd |only wkpool-0.4.0/wkpool/src |only wkpool-0.4.0/wkpool/tests/testthat/test-arcs-kernel.R |only wkpool-0.4.0/wkpool/tests/testthat/test-crs.R |only wkpool-0.4.0/wkpool/tests/testthat/test-cycles.R | 91 + wkpool-0.4.0/wkpool/tests/testthat/test-emit.R |only wkpool-0.4.0/wkpool/tests/testthat/test-exact.R |only wkpool-0.4.0/wkpool/tests/testthat/test-guard-boundaries.R |only wkpool-0.4.0/wkpool/tests/testthat/test-handle.R |only wkpool-0.4.0/wkpool/tests/testthat/test-path.R |only wkpool-0.4.0/wkpool/tests/testthat/test-period-x.R |only wkpool-0.4.0/wkpool/tests/testthat/test-quotient.R |only wkpool-0.4.0/wkpool/tests/testthat/test-roundtrip-coverage.R | 2 wkpool-0.4.0/wkpool/tests/testthat/test-roundtrip.R | 16 wkpool-0.4.0/wkpool/tests/testthat/test-verbs-vectorised.R |only wkpool-0.4.0/wkpool/tests/testthat/test-vx-match.R |only wkpool-0.4.0/wkpool/tests/testthat/test-wkpool-class.R | 16 wkpool-0.4.0/wkpool/tests/testthat/test-wkpool-tri.R |only wkpool-0.4.0/wkpool/vignettes/triangulation.Rmd |only wkpool-0.4.0/wkpool/vignettes/wkpool-vignette-segments.Rmd | 30 wkpool-0.4.0/wkpool/vignettes/wkpool.Rmd | 114 + 76 files changed, 2391 insertions(+), 885 deletions(-)
Title: Construct Mixed Type Data Structures with Vectors of Vectors
Description: Mixed type vectors are useful for combining semantically similar
classes. Some examples of semantically related classes include time across
different granularities (e.g. daily, monthly, annual) and probability
distributions (e.g. Normal, Uniform, Poisson). These groups of vector types
typically share common statistical operations which vary in results with the
attributes of each vector. The 'vecvec' data structure facilitates efficient
storage and computation across multiple vectors within the same object.
Author: Mitchell O'Hara-Wild [aut, cre]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between vecvec versions 1.3.0 dated 2026-08-20 and 1.4.0 dated 2026-10-12
DESCRIPTION | 6 +- MD5 | 31 +++++++----- NAMESPACE | 3 + NEWS.md | 22 +++++++++ R/apply.R | 23 +++++++-- R/array.R |only R/hook.R | 15 ++++++ R/predicates.R | 94 +++++++++++++++------------------------ R/utils.R | 3 + R/vctrs.R | 23 ++++++--- R/vecvec.R | 6 +- man/vecvec_abind.Rd |only tests/testthat/test-apply.R | 25 ++++++++++ tests/testthat/test-bind.R |only tests/testthat/test-format.R | 4 + tests/testthat/test-predicates.R | 40 ++++++++++++++++ tests/testthat/test-vctrs.R | 41 +++++++++++++++++ tests/testthat/test-vecvec.R | 12 ++++ 18 files changed, 261 insertions(+), 87 deletions(-)
Title: Imputing Responder Proportions from Continuous Outcomes
Description: Express meta-analyses of continuous trial outcomes in terms of
responder risks, following the interpretability tutorial of Thorlund,
Walter, Johnston, Furukawa and Guyatt (2011) <doi:10.1002/jrsm.46>. Given
the mean change, standard deviation and sample size per arm across studies,
respondeR estimates the proportion of patients who cross a minimal important
difference (MID) threshold under a parametric model for the change scores,
and contrasts the arms as a risk difference, risk ratio, odds ratio or
number needed to treat. It provides per-study (fixed- or random-effects)
pooling with exact tail probabilities, a pooled-summary method anchored on
the within-study mean difference, median and unweighted-mean summaries, the
standardized-mean-difference to odds-ratio bridge of Anzures-Cabrera,
Sarpatwari and Higgins (2011) <doi:10.1002/sim.4298>, a threshold-free
common-language effect size, results across a range of thresholds, GRADE
summary-of-findings rows, change-score stand [...truncated...]
Author: Ahmad Sofi-Mahmudi [aut, cre]
Maintainer: Ahmad Sofi-Mahmudi <a.sofimahmudi@gmail.com>
Diff between respondeR versions 0.1.0 dated 2026-06-19 and 0.2.0 dated 2026-10-12
DESCRIPTION | 29 - MD5 | 98 ++-- NAMESPACE | 30 + NEWS.md | 118 +++++ R/data.R | 27 - R/impute-change-sd.R |only R/measures.R | 219 +++++----- R/respondeR-package.R | 16 R/responder-adapters.R |only R/responder-analysis.R | 600 +++++++++++++++++++--------- R/responder-cles.R | 29 - R/responder-core.R | 520 +++++++++++++++++------- R/responder-curve.R |only R/responder-from-effect.R |only R/responder-rd.R | 172 +++++--- R/responder-result.R |only R/responder-sof.R |only R/validate.R | 162 ++++++- R/zzz.R |only README.md | 168 +++++-- build/vignette.rds |binary data/vas_pain.rda |binary inst/CITATION | 2 inst/doc/meta-analysis-objects.R |only inst/doc/meta-analysis-objects.Rmd |only inst/doc/meta-analysis-objects.html |only inst/doc/methodology.R | 57 +- inst/doc/methodology.Rmd | 509 ++++++++++++++++------- inst/doc/methodology.html | 662 ++++++++++++++++++++----------- inst/doc/respondeR.R | 61 +- inst/doc/respondeR.Rmd | 185 ++++---- inst/doc/respondeR.html | 315 ++++++++------ inst/shiny-apps/ResponderAnalysis/app.R | 200 ++++++--- man/as_responder_data.Rd |only man/estimate_change_cor.Rd |only man/format_responder_results.Rd | 17 man/impute_change_sd.Rd |only man/plot.responder_curve.Rd |only man/respondeR-package.Rd | 20 man/responder_analysis.Rd | 258 ++++++++---- man/responder_cles.Rd | 10 man/responder_curve.Rd |only man/responder_from_effect.Rd |only man/responder_proportions.Rd | 12 man/responder_rd_individual.Rd | 47 +- man/responder_result.Rd |only man/responder_sof.Rd |only man/vas_pain.Rd | 28 - tests/testthat/test-adapters.R |only tests/testthat/test-core.R | 180 ++++++-- tests/testthat/test-data.R | 2 tests/testthat/test-features.R |only tests/testthat/test-format.R | 11 tests/testthat/test-from-effect.R |only tests/testthat/test-measures.R | 80 ++- tests/testthat/test-responder-analysis.R | 373 +++++++++++++---- tests/testthat/test-robustness.R | 135 +++++- tests/testthat/test-validate.R | 34 + vignettes/meta-analysis-objects.Rmd |only vignettes/methodology.Rmd | 509 ++++++++++++++++------- vignettes/respondeR.Rmd | 185 ++++---- 61 files changed, 4169 insertions(+), 1911 deletions(-)
Title: Automatic Generation of Qualitative Color Palettes
Description: Automatic generation of maximally distinct qualitative color palettes,
optionally tailored to color deficiency. A set of colors or a subspace of a
color space is used as input and a final palette of specified size is
generated by picking colors that maximize the minimum pairwise difference
among the chosen colors. Adaptations to color vision deficiency,
background colors, and white points are supported.
Author: Johan Larsson [aut, cre]
Maintainer: Johan Larsson <johan@jolars.co>
Diff between qualpalr versions 2.0.0 dated 2026-01-29 and 2.1.0 dated 2026-10-12
qualpalr-2.0.0/qualpalr/R/RcppExports.R |only qualpalr-2.0.0/qualpalr/src/RcppExports.cpp |only qualpalr-2.1.0/qualpalr/DESCRIPTION | 10 qualpalr-2.1.0/qualpalr/MD5 | 43 - qualpalr-2.1.0/qualpalr/NAMESPACE | 2 qualpalr-2.1.0/qualpalr/NEWS.md | 16 qualpalr-2.1.0/qualpalr/R/convert_colors.R |only qualpalr-2.1.0/qualpalr/R/cpp11.R |only qualpalr-2.1.0/qualpalr/R/qualpal.R | 17 qualpalr-2.1.0/qualpalr/R/qualpalr.R | 1 qualpalr-2.1.0/qualpalr/R/utils.R | 21 qualpalr-2.1.0/qualpalr/build/vignette.rds |binary qualpalr-2.1.0/qualpalr/inst/doc/comparisons.html | 72 +- qualpalr-2.1.0/qualpalr/inst/doc/introduction.html | 151 +++-- qualpalr-2.1.0/qualpalr/inst/include/qualpal/qualpal.h | 23 qualpalr-2.1.0/qualpalr/man/convert_colors.Rd | 2 qualpalr-2.1.0/qualpalr/man/qualpal.Rd | 17 qualpalr-2.1.0/qualpalr/src/Makevars | 3 qualpalr-2.1.0/qualpalr/src/convert.h | 4 qualpalr-2.1.0/qualpalr/src/cpp11.cpp |only qualpalr-2.1.0/qualpalr/src/qualpal/color_grid.h | 115 ++++ qualpalr-2.1.0/qualpalr/src/qualpal/continuous_refinement.cpp |only qualpalr-2.1.0/qualpalr/src/qualpal/continuous_refinement.h |only qualpalr-2.1.0/qualpalr/src/qualpal/qualpal.cpp | 256 +++++++++- qualpalr-2.1.0/qualpalr/src/qualpalr.cpp | 230 ++++---- qualpalr-2.1.0/qualpalr/tests/testthat/test_qualpal.R | 50 + 26 files changed, 761 insertions(+), 272 deletions(-)
Title: Missingness Alleviation for Network Analysis
Description: Provides functionality for estimating cross-sectional network structures representing partial correlations while accounting for missing data. Networks are estimated via neighborhood selection or regularization, with model selection guided by information criteria. Missing data can be handled primarily via multiple imputation or a maximum likelihood-based approach, as demonstrated by Nehler and Schultze (2025) <doi:10.1080/00273171.2025.2503833> and Nehler and Schultze (2026) <doi:10.1037/met0000828>. Deletion-based approaches are also available but play a secondary role.
Author: Kai Jannik Nehler [aut, cre]
Maintainer: Kai Jannik Nehler <nehler@psych.uni-frankfurt.de>
Diff between mantar versions 0.3.1 dated 2026-07-08 and 0.3.2 dated 2026-10-12
DESCRIPTION | 8 - MD5 | 18 +- NEWS.md | 5 build/partial.rdb |binary build/stage23.rdb |binary build/vignette.rds |binary inst/doc/mantar.R | 27 +++- inst/doc/mantar.Rmd | 35 ++++- inst/doc/mantar.html | 317 +++++++++++++++++++++++++++------------------------ vignettes/mantar.Rmd | 35 ++++- 10 files changed, 265 insertions(+), 180 deletions(-)
Title: Grammar of Graphics and Plot Helpers for Time Series
Visualization
Description: Extends the capabilities of 'ggplot2' by providing grammatical
elements and plot helpers designed for visualizing temporal patterns. The
package implements a grammar of temporal graphics, which leverages calendar
structures to highlight changes over time. The package also provides plot
helper functions to quickly produce commonly used time series graphics,
including time plots, season plots, and seasonal sub-series plots.
Author: Mitchell O'Hara-Wild [aut, cre] ,
Cynthia A. Huang [aut] ,
Matthew Kay [aut] ,
Rob Hyndman [aut] ,
Earo Wang [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between ggtime versions 1.0.0 dated 2026-09-01 and 1.1.0 dated 2026-10-12
DESCRIPTION | 16 MD5 | 71 +- NAMESPACE | 15 NEWS.md | 56 + R/coord-calendar.R | 121 +++- R/coord-loop.R | 136 ++++ R/geom-candlestick.R |only R/loop-cut.R | 16 R/plot-helpers.R | 471 ++++------------ R/plot-mixtime.R |only R/plot-tsibble.R | 2 R/scale-time.R | 34 - R/transform.R | 2 R/utils.R | 144 ---- man/coord_calendar.Rd | 19 man/coord_loop.Rd | 3 man/draw_key_candlestick.Rd |only man/figures/README-coordloop-1.png |binary man/figures/README-scalemixtime-1.png |binary man/figures/README-seasonplot-1.png |binary man/geom_candlestick.Rd |only man/gg_lag.Rd | 11 man/gg_season.Rd | 20 man/gg_subseries.Rd | 14 man/gg_tsdisplay.Rd | 2 man/gg_tsresiduals.Rd | 2 man/scale_candlestick.Rd |only man/scale_mixtime.Rd | 11 man/transform_warp.Rd | 3 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/coord-calendar/granule-labels.svg | 70 +- tests/testthat/helper-mixtime.R |only tests/testthat/test-coord-calendar.R | 128 ++++ tests/testthat/test-coord-loop.R | 68 +- tests/testthat/test-geom-candlestick.R |only tests/testthat/test-geom-time-line.R | 1 tests/testthat/test-gg-lag.R |only tests/testthat/test-gg-subseries.R |only tests/testthat/test-loop-cut.R | 5 tests/testthat/test-plot-helpers.R | 381 ++++++++++++ tests/testthat/test-scale-time.R | 43 + 41 files changed, 1192 insertions(+), 673 deletions(-)
Title: Distributed Online Goodness-of-Fit Tests for Distributed
Datasets
Description: Distributed Online Goodness-of-Fit Test can process the distributed datasets. The philosophy of the package is described in Guo G.(2024) <doi:10.1016/j.apm.2024.115709>.
Author: Guangbao Guo [aut, cre] ,
Di Chang [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between Dogoftest versions 0.3 dated 2025-07-29 and 0.4.2 dated 2026-10-12
Dogoftest-0.3/Dogoftest/R/CVMgof2.R |only Dogoftest-0.3/Dogoftest/R/KSgof2.R |only Dogoftest-0.3/Dogoftest/R/cvmgof.R |only Dogoftest-0.3/Dogoftest/R/ksgof.R |only Dogoftest-0.3/Dogoftest/man/CVMgof2.Rd |only Dogoftest-0.3/Dogoftest/man/KSgof2.Rd |only Dogoftest-0.3/Dogoftest/man/cvmgof.Rd |only Dogoftest-0.3/Dogoftest/man/ksgof.Rd |only Dogoftest-0.4.2/Dogoftest/DESCRIPTION | 9 - Dogoftest-0.4.2/Dogoftest/MD5 | 72 ++++++++--- Dogoftest-0.4.2/Dogoftest/NAMESPACE | 25 +++- Dogoftest-0.4.2/Dogoftest/R/AD2gof.R | 103 ++++++++-------- Dogoftest-0.4.2/Dogoftest/R/ADgof.R | 135 +++++++++++----------- Dogoftest-0.4.2/Dogoftest/R/CVM2gof.R | 103 ++++++++-------- Dogoftest-0.4.2/Dogoftest/R/CVMgof.R |only Dogoftest-0.4.2/Dogoftest/R/DAD.R |only Dogoftest-0.4.2/Dogoftest/R/DAD2.R |only Dogoftest-0.4.2/Dogoftest/R/DCVM.R |only Dogoftest-0.4.2/Dogoftest/R/DCvM2.R |only Dogoftest-0.4.2/Dogoftest/R/DKS.R |only Dogoftest-0.4.2/Dogoftest/R/DKS2.R |only Dogoftest-0.4.2/Dogoftest/R/DPECVM.R |only Dogoftest-0.4.2/Dogoftest/R/DPECVM2.R |only Dogoftest-0.4.2/Dogoftest/R/KS2gof.R | 78 +++++------- Dogoftest-0.4.2/Dogoftest/R/KSgof.R |only Dogoftest-0.4.2/Dogoftest/R/PE2AD.R |only Dogoftest-0.4.2/Dogoftest/R/PE2CVM.R |only Dogoftest-0.4.2/Dogoftest/R/PE2KS.R |only Dogoftest-0.4.2/Dogoftest/R/PEAD.R |only Dogoftest-0.4.2/Dogoftest/R/PECVM.R |only Dogoftest-0.4.2/Dogoftest/R/PEKS.R |only Dogoftest-0.4.2/Dogoftest/R/Wgof.R | 2 Dogoftest-0.4.2/Dogoftest/R/data.R |only Dogoftest-0.4.2/Dogoftest/R/run_FDP_sim.R |only Dogoftest-0.4.2/Dogoftest/R/run_custom_tests.R |only Dogoftest-0.4.2/Dogoftest/R/simpleCvMgof.R | 50 +++++--- Dogoftest-0.4.2/Dogoftest/man/AD2gof.Rd | 49 +++---- Dogoftest-0.4.2/Dogoftest/man/ADgof.Rd | 70 +++++------ Dogoftest-0.4.2/Dogoftest/man/CVM2gof.Rd | 52 +++----- Dogoftest-0.4.2/Dogoftest/man/CVMgof.Rd |only Dogoftest-0.4.2/Dogoftest/man/DAD.Rd |only Dogoftest-0.4.2/Dogoftest/man/DAD2.Rd |only Dogoftest-0.4.2/Dogoftest/man/DCVM.Rd |only Dogoftest-0.4.2/Dogoftest/man/DCVM2.Rd |only Dogoftest-0.4.2/Dogoftest/man/DKS.Rd |only Dogoftest-0.4.2/Dogoftest/man/DKS2.Rd |only Dogoftest-0.4.2/Dogoftest/man/DPECVM.Rd |only Dogoftest-0.4.2/Dogoftest/man/DPECVM2.Rd |only Dogoftest-0.4.2/Dogoftest/man/KS2gof.Rd | 48 +++---- Dogoftest-0.4.2/Dogoftest/man/KSgof.Rd |only Dogoftest-0.4.2/Dogoftest/man/PE2AD.Rd |only Dogoftest-0.4.2/Dogoftest/man/PE2CVM.Rd |only Dogoftest-0.4.2/Dogoftest/man/PE2KS.Rd |only Dogoftest-0.4.2/Dogoftest/man/PECVM.Rd |only Dogoftest-0.4.2/Dogoftest/man/PEKS.Rd |only Dogoftest-0.4.2/Dogoftest/man/WhiteWine.Rd | 82 ++++++------- Dogoftest-0.4.2/Dogoftest/man/run_FDP_sim.Rd |only Dogoftest-0.4.2/Dogoftest/man/run_custom_tests.Rd |only Dogoftest-0.4.2/Dogoftest/man/simpleCvMgof.Rd | 28 ++-- 59 files changed, 470 insertions(+), 436 deletions(-)
Title: Changepoints for a Range of Penalties (CROPS)
Description: Implements the Changepoints for a Range of Penalties (CROPS) algorithm of Haynes et al. (2017) <doi:10.1080/10618600.2015.1116445> for finding all of the optimal segmentations for multiple penalty values over a continuous range.
Author: Daniel Grose [aut, cre],
Paul Fearnhead [aut],
Idris Eckley [ctb]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between crops versions 1.0.4 dated 2026-09-04 and 1.0.5 dated 2026-10-12
crops-1.0.4/crops/man/plot-methods.Rd |only crops-1.0.4/crops/man/print-methods.Rd |only crops-1.0.4/crops/man/segmentations-methods.Rd |only crops-1.0.4/crops/man/subset-methods.Rd |only crops-1.0.4/crops/man/summary-methods.Rd |only crops-1.0.4/crops/man/unique-methods.Rd |only crops-1.0.5/crops/DESCRIPTION | 12 - crops-1.0.5/crops/MD5 | 23 -- crops-1.0.5/crops/NAMESPACE | 11 crops-1.0.5/crops/NEWS.md |only crops-1.0.5/crops/R/crops.R | 98 +++----- crops-1.0.5/crops/R/crops.class.R | 282 +------------------------ crops-1.0.5/crops/R/utils.R | 8 crops-1.0.5/crops/build/partial.rdb |binary crops-1.0.5/crops/man/crops.Rd | 81 ++----- crops-1.0.5/crops/man/crops.class-class.Rd |only crops-1.0.5/crops/man/crops.class.Rd |only 17 files changed, 109 insertions(+), 406 deletions(-)
Title: Physics-Based Models for Acoustic Target Strength
Description: Acoustic target strength (TS) represents the intensity of an
echo returning from an individual scatterer such as bubbles, fish, or
zooplankton. TS can be used to convert integrated or volumetric
backscatter collected from fisheries acoustic surveys into units of
number density (e.g. animals per m^3), abundance (e.g. number of
animals), and biomass (e.g. kg). This parameter can also be used to
aid in classifying backscatter, such as separating likely echoes of
large predatory fish (e.g. adult cod) from smaller prey (e.g. shrimp).
One way to estimate TS is to use physics-based models to calculate
theoretical TS that comprise exact and approximate solutions as well
as analytical approaches. The models provided can help provide TS
estimates over broad statistical distributions of model parameters.
Applications are described by Lucca et al. (2023)
<doi:10.1121/10.0022459>, with fisheries-acoustics principles from
Simmonds and MacLennan (2005) <doi:10.1002/9780470995303>.
Author: Brandyn Lucca [aut, cre, cph] ,
Arnie Lee Van Buren [ctb, cph] ,
Jeffrey E. Boisvert [ctb]
Maintainer: Brandyn Lucca <brandyn.lucca@gmail.com>
Diff between acousticTS versions 2.0.6 dated 2026-09-26 and 2.0.8 dated 2026-10-12
DESCRIPTION | 8 MD5 | 103 ++++---- NEWS.md | 20 - R/RcppExports.R | 4 R/bessel-cylindrical.R | 17 - R/model-krm.R | 24 - R/model-sdwba.R | 56 ++-- R/model-sphms.R | 12 R/scatterer_reforge.R | 43 --- R/spheroidal.R | 4 R/utilities-geometry.R | 96 ++++--- R/validation.R | 14 - README.md | 27 +- man/KRM.Rd | 8 man/SDWBA.Rd | 32 +- man/Smn.Rd | 4 man/jc.Rd | 4 man/yc.Rd | 13 - src/Makevars.in | 5 src/Makevars.win.in | 5 src/RcppExports.cpp | 11 src/bessel.cpp | 35 +- src/goodman_stern.cpp | 49 ---- src/legendre.cpp | 44 --- src/precision.h | 7 src/prolate_swf.f90 | 18 - src/psms.cpp | 2 src/psms_backscatter.h | 68 ++--- src/psms_linear_systems.h | 89 ++++--- src/psms_rmn.h | 64 ++--- src/psms_smn.h | 34 +- src/psms_support.h | 4 src/svd_solve.h | 2 src/test-runner.cpp |only tests/testthat/native-solvers.h |only tests/testthat/test-bbfm.R | 5 tests/testthat/test-bessel_functions.R | 200 ++++++++++++++++ tests/testthat/test-dwba_profiles.R | 201 +++++++++++++--- tests/testthat/test-essms.R | 45 +++ tests/testthat/test-harmonics.R | 37 +++ tests/testthat/test-krm_modal_reference.R |only tests/testthat/test-model_helper_branches.R | 176 ++++++++++++++ tests/testthat/test-model_registry.R | 110 ++++++++ tests/testthat/test-native_kernels.R |only tests/testthat/test-psms_helpers.R | 181 ++++++++++++++ tests/testthat/test-scatterer_reforge.R | 123 ++++++++++ tests/testthat/test-sdwba_pipeline.R |only tests/testthat/test-shape_creation.R | 33 ++ tests/testthat/test-shape_manipulation.R | 208 ++++++++++++++++ tests/testthat/test-simulation.R | 173 +++++++++++++- tests/testthat/test-spheroidal.R | 343 ++++++++++++++++++++++++++++ tests/testthat/test-target_strength.R | 49 +++- tests/testthat/test-tmm.R | 95 +++++++ tests/testthat/test-tmm_internal_helpers.R | 229 ++++++++++++++++++ tests/testthat/test-utilities_validation.R | 113 +++++++++ 55 files changed, 2706 insertions(+), 541 deletions(-)
Title: Price Index Aggregation
Description: Most price indexes are made with a two-step procedure, where
period-over-period elementary indexes are first calculated for a collection
of elementary aggregates at each point in time, and then aggregated according
to a price index aggregation structure. These indexes can then be chained
together to form a time series that gives the evolution of prices with
respect to a fixed base period. This package contains a collection of
functions that revolve around this work flow, making it easy to build
standard price indexes, and implement the methods described by
Balk (2008, <doi:10.1017/CBO9780511720758>), von der Lippe (2007,
<doi:10.3726/978-3-653-01120-3>), and the CPI manual (2020,
<doi:10.5089/9781484354841.069>) and PPI manual
(2004, <doi:10.5089/9781589063044.069>) for bilateral price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between piar versions 0.10.1 dated 2026-07-30 and 0.11.0 dated 2026-10-12
piar-0.10.1/piar/LICENSE |only piar-0.11.0/piar/DESCRIPTION | 21 piar-0.11.0/piar/MD5 | 323 ++++---- piar-0.11.0/piar/NAMESPACE | 35 piar-0.11.0/piar/NEWS.md | 26 piar-0.11.0/piar/R/aggregate.piar_index.R | 45 - piar-0.11.0/piar/R/aggregation_structure.R | 6 piar-0.11.0/piar/R/as_aggregation_structure.R | 2 piar-0.11.0/piar/R/as_index.R | 3 piar-0.11.0/piar/R/back_period.R | 9 piar-0.11.0/piar/R/chain.R | 4 piar-0.11.0/piar/R/coerce-aggregation_structure.R | 23 piar-0.11.0/piar/R/coerce-index.R | 25 piar-0.11.0/piar/R/combine_classifications.R | 2 piar-0.11.0/piar/R/contrib.R | 2 piar-0.11.0/piar/R/cut.piar_aggregation_structure.R | 2 piar-0.11.0/piar/R/elementary_index.R | 44 - piar-0.11.0/piar/R/emean.R | 11 piar-0.11.0/piar/R/expand_classification.R | 6 piar-0.11.0/piar/R/extract.piar_index.R | 54 + piar-0.11.0/piar/R/geks_index.R | 15 piar-0.11.0/piar/R/gmean.R | 26 piar-0.11.0/piar/R/head.piar_index.R | 10 piar-0.11.0/piar/R/impute_prices.R | 20 piar-0.11.0/piar/R/index-class.R | 18 piar-0.11.0/piar/R/is.na.piar_index.R | 2 piar-0.11.0/piar/R/lag.piar_index.R |only piar-0.11.0/piar/R/levels.piar_aggregation_structure.R | 2 piar-0.11.0/piar/R/levels.piar_index.R | 2 piar-0.11.0/piar/R/mean.piar_index.R | 13 piar-0.11.0/piar/R/merge.piar_index.R | 2 piar-0.11.0/piar/R/outliers.R | 32 piar-0.11.0/piar/R/price_relative.R | 8 piar-0.11.0/piar/R/splice_index.R | 8 piar-0.11.0/piar/R/split.piar_index.R | 4 piar-0.11.0/piar/R/split_classification.R | 10 piar-0.11.0/piar/R/stack.piar_index.R | 2 piar-0.11.0/piar/R/time.piar_index.R | 2 piar-0.11.0/piar/R/transmute_weights.R | 46 - piar-0.11.0/piar/R/update.aggregation_structure.R | 2 piar-0.11.0/piar/R/update_weights.R | 11 piar-0.11.0/piar/R/utils.R | 99 -- piar-0.11.0/piar/R/weights.piar_aggregation_structure.R | 2 piar-0.11.0/piar/R/window.piar_index.R | 10 piar-0.11.0/piar/README.md | 117 +-- piar-0.11.0/piar/build/partial.rdb |binary piar-0.11.0/piar/build/vignette.rds |binary piar-0.11.0/piar/inst/REFERENCES.R |only piar-0.11.0/piar/inst/WORDLIST | 1 piar-0.11.0/piar/inst/doc/adjust-weights.R | 2 piar-0.11.0/piar/inst/doc/adjust-weights.Rmd | 5 piar-0.11.0/piar/inst/doc/adjust-weights.html | 2 piar-0.11.0/piar/inst/doc/contributions.R | 2 piar-0.11.0/piar/inst/doc/contributions.Rmd | 5 piar-0.11.0/piar/inst/doc/contributions.html | 259 +------ piar-0.11.0/piar/inst/doc/decomposing-indexes.R | 2 piar-0.11.0/piar/inst/doc/decomposing-indexes.Rmd | 63 - piar-0.11.0/piar/inst/doc/decomposing-indexes.html | 108 ++- piar-0.11.0/piar/inst/doc/imputation.R | 2 piar-0.11.0/piar/inst/doc/imputation.Rmd | 5 piar-0.11.0/piar/inst/doc/imputation.html | 2 piar-0.11.0/piar/inst/doc/index-number-formulas.R | 6 piar-0.11.0/piar/inst/doc/index-number-formulas.Rmd | 15 piar-0.11.0/piar/inst/doc/index-number-formulas.html | 157 ---- piar-0.11.0/piar/inst/doc/matrix-aggregation.R | 2 piar-0.11.0/piar/inst/doc/matrix-aggregation.Rmd | 5 piar-0.11.0/piar/inst/doc/matrix-aggregation.html | 114 --- piar-0.11.0/piar/inst/doc/multiple-baskets.R | 2 piar-0.11.0/piar/inst/doc/multiple-baskets.Rmd | 5 piar-0.11.0/piar/inst/doc/multiple-baskets.html | 2 piar-0.11.0/piar/inst/doc/multiple-data-sources.R | 2 piar-0.11.0/piar/inst/doc/multiple-data-sources.Rmd | 5 piar-0.11.0/piar/inst/doc/multiple-data-sources.html | 58 - piar-0.11.0/piar/inst/doc/multiple-dimensions.R | 23 piar-0.11.0/piar/inst/doc/multiple-dimensions.Rmd | 58 + piar-0.11.0/piar/inst/doc/multiple-dimensions.html | 126 +-- piar-0.11.0/piar/inst/doc/piar.R | 2 piar-0.11.0/piar/inst/doc/piar.Rmd | 16 piar-0.11.0/piar/inst/doc/piar.html | 359 ++-------- piar-0.11.0/piar/inst/doc/spatial-price-index.R | 2 piar-0.11.0/piar/inst/doc/spatial-price-index.Rmd | 5 piar-0.11.0/piar/inst/doc/spatial-price-index.html | 98 -- piar-0.11.0/piar/inst/doc/subperiods.R | 2 piar-0.11.0/piar/inst/doc/subperiods.Rmd | 5 piar-0.11.0/piar/inst/doc/subperiods.html | 34 piar-0.11.0/piar/inst/doc/superlative-aggregation.R | 2 piar-0.11.0/piar/inst/doc/superlative-aggregation.Rmd | 11 piar-0.11.0/piar/inst/doc/superlative-aggregation.html | 112 --- piar-0.11.0/piar/inst/tinytest/test-aggregate.R | 50 - piar-0.11.0/piar/inst/tinytest/test-aggregation-structure-attributes.R | 8 piar-0.11.0/piar/inst/tinytest/test-aggregation_structure.R | 8 piar-0.11.0/piar/inst/tinytest/test-as.ts.R | 2 piar-0.11.0/piar/inst/tinytest/test-as_index.R | 12 piar-0.11.0/piar/inst/tinytest/test-back_period.R | 6 piar-0.11.0/piar/inst/tinytest/test-chain.R | 22 piar-0.11.0/piar/inst/tinytest/test-coerce-aggregation-structure.R | 9 piar-0.11.0/piar/inst/tinytest/test-coerce-index.R | 6 piar-0.11.0/piar/inst/tinytest/test-combine_classifications.R | 6 piar-0.11.0/piar/inst/tinytest/test-contrib.R | 14 piar-0.11.0/piar/inst/tinytest/test-cut.R | 12 piar-0.11.0/piar/inst/tinytest/test-elemental_index.R | 10 piar-0.11.0/piar/inst/tinytest/test-expand_classification.R | 10 piar-0.11.0/piar/inst/tinytest/test-extract-index.R | 49 + piar-0.11.0/piar/inst/tinytest/test-geks_index.R | 12 piar-0.11.0/piar/inst/tinytest/test-gmean.R | 4 piar-0.11.0/piar/inst/tinytest/test-impute-prices.R | 18 piar-0.11.0/piar/inst/tinytest/test-index-attributes.R | 6 piar-0.11.0/piar/inst/tinytest/test-is.na.R | 4 piar-0.11.0/piar/inst/tinytest/test-known-values.R | 6 piar-0.11.0/piar/inst/tinytest/test-lag.R |only piar-0.11.0/piar/inst/tinytest/test-mean.R | 8 piar-0.11.0/piar/inst/tinytest/test-merge.R | 10 piar-0.11.0/piar/inst/tinytest/test-outliers.R | 8 piar-0.11.0/piar/inst/tinytest/test-splice_index.R | 18 piar-0.11.0/piar/inst/tinytest/test-split.R | 4 piar-0.11.0/piar/inst/tinytest/test-split_classification.R | 6 piar-0.11.0/piar/inst/tinytest/test-stack.R | 14 piar-0.11.0/piar/inst/tinytest/test-transmute_weights.R | 4 piar-0.11.0/piar/inst/tinytest/test-update.R | 6 piar-0.11.0/piar/inst/tinytest/test-window.R | 6 piar-0.11.0/piar/man/aggregate.piar_index.Rd | 36 - piar-0.11.0/piar/man/aggregation_structure.Rd | 2 piar-0.11.0/piar/man/as.data.frame.piar_index.Rd | 5 piar-0.11.0/piar/man/as.matrix.piar_aggregation_structure.Rd | 14 piar-0.11.0/piar/man/as.ts.piar_index.Rd | 7 piar-0.11.0/piar/man/back_period.Rd | 9 piar-0.11.0/piar/man/chain.Rd | 1 piar-0.11.0/piar/man/contrib.Rd | 1 piar-0.11.0/piar/man/elementary_index.Rd | 26 piar-0.11.0/piar/man/emean.Rd | 7 piar-0.11.0/piar/man/geks_index.Rd | 13 piar-0.11.0/piar/man/gmean.Rd | 18 piar-0.11.0/piar/man/head.piar_index.Rd | 5 piar-0.11.0/piar/man/impute_prices.Rd | 14 piar-0.11.0/piar/man/is.na.piar_index.Rd | 1 piar-0.11.0/piar/man/lag.piar_index.Rd |only piar-0.11.0/piar/man/levels.piar_index.Rd | 1 piar-0.11.0/piar/man/mean.piar_index.Rd | 10 piar-0.11.0/piar/man/merge.piar_index.Rd | 1 piar-0.11.0/piar/man/outliers.Rd | 28 piar-0.11.0/piar/man/piar-package.Rd | 4 piar-0.11.0/piar/man/price_relative.Rd | 2 piar-0.11.0/piar/man/splice_index.Rd | 8 piar-0.11.0/piar/man/split.piar_index.Rd | 3 piar-0.11.0/piar/man/split_classification.Rd | 4 piar-0.11.0/piar/man/stack.piar_index.Rd | 3 piar-0.11.0/piar/man/sub-.piar_index.Rd | 10 piar-0.11.0/piar/man/time.piar_index.Rd | 1 piar-0.11.0/piar/man/transmute_weights.Rd | 7 piar-0.11.0/piar/man/transmute_weights2.Rd | 17 piar-0.11.0/piar/man/update_weights.Rd | 11 piar-0.11.0/piar/man/window.piar_index.Rd | 2 piar-0.11.0/piar/vignettes/adjust-weights.Rmd | 5 piar-0.11.0/piar/vignettes/contributions.Rmd | 5 piar-0.11.0/piar/vignettes/decomposing-indexes.Rmd | 63 - piar-0.11.0/piar/vignettes/imputation.Rmd | 5 piar-0.11.0/piar/vignettes/index-number-formulas.Rmd | 15 piar-0.11.0/piar/vignettes/matrix-aggregation.Rmd | 5 piar-0.11.0/piar/vignettes/multiple-baskets.Rmd | 5 piar-0.11.0/piar/vignettes/multiple-data-sources.Rmd | 5 piar-0.11.0/piar/vignettes/multiple-dimensions.Rmd | 58 + piar-0.11.0/piar/vignettes/piar.Rmd | 16 piar-0.11.0/piar/vignettes/spatial-price-index.Rmd | 5 piar-0.11.0/piar/vignettes/subperiods.Rmd | 5 piar-0.11.0/piar/vignettes/superlative-aggregation.Rmd | 11 165 files changed, 1544 insertions(+), 2080 deletions(-)
Title: Read and Write 'Apache Iceberg' Tables
Description: A native client for 'Apache Iceberg', the open table format used by
'Snowflake', 'Databricks', 'BigQuery', 'AWS' and 'Dremio'. Rather than
reaching 'Iceberg' through a query engine such as 'DuckDB', this package
talks to it directly: it connects to REST and 'AWS Glue' catalogs, lists
namespaces and tables, reads the schema and partition specification of a
table, scans data with predicates and projections pushed down, travels back
through snapshot history, and appends new data. 'Apache Arrow' is the
interchange layer throughout, so scan results arrive in R without a
serialisation round trip. Built on 'iceberg-rust', the Apache-governed
'Rust' implementation, via 'extendr'.
Supports table spec versions 1 and 2; see the 'README' for the full matrix
of supported and unsupported features. This is a community package, not
affiliated with or endorsed by The Apache Software Foundation; 'Apache',
'Apache Iceberg' and 'Iceberg' are trademarks of The Apache Software
Foundation.
Author: Youzhi Yu [aut, cre],
The Apache Software Foundation [cph]
Maintainer: Youzhi Yu <yuyouzhi666@icloud.com>
Diff between icebergr versions 0.1.0 dated 2026-09-10 and 0.2.0 dated 2026-10-12
DESCRIPTION | 31 - LICENSE.note | 51 -- MD5 | 148 +++--- NEWS.md | 225 +++++++++ R/catalog.R | 226 ++++++++- R/extendr-wrappers.R | 4 R/filter.R | 172 ++++++ R/icebergr-package.R | 7 R/scan.R | 56 +- R/snapshots.R | 14 R/spec-support.R | 22 R/table.R | 22 R/utils.R | 70 ++ R/write.R | 174 ++++++- README.md | 347 ++------------ build/vignette.rds |binary inst/NOTICE | 4 inst/doc/catalog-configuration.R | 6 inst/doc/catalog-configuration.Rmd | 93 ++- inst/doc/catalog-configuration.html | 130 ++++- inst/doc/getting-started.R | 8 inst/doc/getting-started.Rmd | 48 + inst/doc/getting-started.html | 135 ++++- inst/doc/pushdown.R |only inst/doc/pushdown.Rmd |only inst/doc/pushdown.html |only inst/doc/table-format.R |only inst/doc/table-format.Rmd |only inst/doc/table-format.html |only inst/doc/time-travel.R |only inst/doc/time-travel.Rmd |only inst/doc/time-travel.html |only inst/doc/types.R |only inst/doc/types.Rmd |only inst/doc/types.html |only inst/doc/writing.R |only inst/doc/writing.Rmd |only inst/doc/writing.html |only man/figures |only man/icebergr-package.Rd | 8 man/icebergr_append.Rd | 13 man/icebergr_catalog.Rd | 44 + man/icebergr_create_table.Rd | 3 man/icebergr_properties.Rd | 2 man/icebergr_register_table.Rd | 28 + man/icebergr_scan.Rd | 32 - man/icebergr_table_exists.Rd | 6 src/Makevars.in | 6 src/rust/Cargo.lock | 813 ++++++++++++++++----------------- src/rust/Cargo.toml | 38 + src/rust/build.rs |only src/rust/src/arrow_bridge.rs | 12 src/rust/src/catalog.rs | 72 ++ src/rust/src/errors.rs | 258 ++++++++++ src/rust/src/lib.rs | 5 src/rust/src/panic.rs | 86 +++ src/rust/src/predicate.rs | 405 ++++++++++++---- src/rust/src/runtime.rs | 330 +++++++++++++ src/rust/src/scan.rs | 85 ++- src/rust/src/table.rs | 34 + src/rust/src/write.rs | 246 +++++++-- src/rust/vendor.tar.xz |binary tests/testthat/helper-icebergr.R | 47 + tests/testthat/test-case-sensitivity.R | 37 + tests/testthat/test-catalog.R | 19 tests/testthat/test-conditions.R | 26 + tests/testthat/test-confine.R |only tests/testthat/test-credentials.R |only tests/testthat/test-errors.R | 49 + tests/testthat/test-filter.R | 80 +++ tests/testthat/test-pushdown.R | 325 +++++++++++++ tests/testthat/test-roundtrip.R | 46 + tests/testthat/test-spec-support.R | 17 tests/testthat/test-time-travel.R | 72 ++ tests/testthat/test-types.R | 5 tools/config.R | 46 + tools/msrv.R | 61 ++ tools/vendor.R | 114 +++- vignettes/catalog-configuration.Rmd | 93 ++- vignettes/getting-started.Rmd | 48 + vignettes/pushdown.Rmd |only vignettes/table-format.Rmd |only vignettes/time-travel.Rmd |only vignettes/types.Rmd |only vignettes/vignette_reference.bib |only vignettes/writing.Rmd |only 86 files changed, 4274 insertions(+), 1330 deletions(-)
Title: Iterative Extrapolation of Species' Haplotype Accumulation
Curves for Genetic Diversity Assessment
Description: Performs iterative extrapolation of species' haplotype accumulation curves using a nonparametric stochastic (Monte Carlo) optimization method for assessment of specimen sampling completeness based on the approach of Phillips et al. (2015) <doi:10.1515/dna-2015-0008>, Phillips et al. (2019) <doi:10.1002/ece3.4757> and Phillips et al. (2020) <doi: 10.7717/peerj-cs.243>. 'HACSim' outputs a number of useful summary statistics of sampling coverage ("Measures of Sampling Closeness"), including an estimate of the likely required sample size (along with desired level confidence intervals) necessary to recover a given number/proportion of observed unique species' haplotypes. Any genomic marker can be targeted to assess likely required specimen sample sizes for genetic diversity assessment. The method is particularly well-suited to assess sampling sufficiency for DNA barcoding initiatives. Users can also simulate their own DNA sequences according to various models of nucleotide [...truncated...]
Author: Jarrett D. Phillips [aut, cre],
Steven H. French [ctb],
Navdeep Singh [ctb]
Maintainer: Jarrett D. Phillips <phillipsjarrett1@gmail.com>
Diff between HACSim versions 1.0.7-1 dated 2025-09-19 and 1.0.7-2 dated 2026-10-12
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Efficient Spatial Thinning of Species Occurrences
Description: Provides efficient geospatial thinning algorithms to reduce
the density of coordinate data while maintaining spatial
relationships. Implements K-D Tree and brute-force distance-based
thinning, as well as grid-based and precision-based thinning methods.
For more information on the methods, see Elseberg et al. (2012)
<https://hdl.handle.net/10446/86202>.
Author: Jorge Mestre-Tomas [aut, cre]
Maintainer: Jorge Mestre-Tomas <jorge.mestre.tomas@csic.es>
Diff between GeoThinneR versions 2.1.2 dated 2026-08-25 and 2.1.3 dated 2026-10-12
DESCRIPTION | 8 MD5 | 69 ++-- NAMESPACE | 63 +--- NEWS.md | 17 + R/GeoThinned_class.R | 9 R/distance_thinning.R | 78 ++++- R/grid_thinning.R | 2 R/precision_thinning.R | 2 R/thin_points.R | 1 R/thinning_algorithm.R | 15 - R/utils.R | 45 +-- build/vignette.rds |binary inst/CITATION | 28 - inst/doc/GeoThinneR.R | 23 + inst/doc/GeoThinneR.Rmd | 28 + inst/doc/GeoThinneR.html | 430 ++++++++++++++++-------------- man/GeoThinned.Rd | 203 ++++++-------- man/calculate_spatial_coverage.Rd | 69 ++-- man/caretta.Rd | 92 +++--- man/compute_nearest_neighbor_distances.Rd | 79 ++--- man/compute_neighbors_brute.Rd | 77 ++--- man/compute_neighbors_kdtree.Rd | 89 +++--- man/compute_neighbors_local_kdtree.Rd | 83 ++--- man/distance_thinning.Rd | 149 +++++----- man/estimate_k_max.Rd | 81 ++--- man/grid_thinning.Rd | 132 ++++----- man/is_lonlat.Rd | 61 ++-- man/lon_lat_to_cartesian.Rd | 53 +-- man/max_thinning_algorithm.Rd | 81 ++--- man/new_GeoThinned.Rd |only man/precision_thinning.Rd | 96 +++--- man/select_target_points.Rd | 88 +++--- man/thin_points.Rd | 255 ++++++++--------- man/thunnus.Rd | 72 ++--- tests/testthat/test-distance_thinning.R | 53 +++ vignettes/GeoThinneR.Rmd | 28 + 36 files changed, 1459 insertions(+), 1200 deletions(-)
Title: Local Large Language Model Inference Engine
Description: Enables R users to run large language models locally using 'GGUF' model files
and the 'llama.cpp' inference engine. Provides a complete R interface for loading models,
generating text completions, extracting vector representations, and streaming responses in real-time.
Includes grammar-constrained generation for structured output, text classification,
and retrieval-augmented generation (RAG) pipelines. Supports local inference without
requiring cloud APIs or internet connectivity, ensuring complete data privacy and
control. Based on the 'llama.cpp' project by Georgi Gerganov (2023) <https://github.com/ggml-org/llama.cpp>.
Author: Pawan Rama Mali [aut, cre, cph],
Georgi Gerganov [aut, cph] ,
The ggml authors [cph] ,
Jeffrey Quesnelle [ctb, cph] ,
Bowen Peng [ctb, cph] ,
pi6am [ctb] ,
Ivan Yurchenko [ctb] ,
Dirk Eddelbuettel [ctb, rev]
Maintainer: Pawan Rama Mali <prm@outlook.in>
Diff between edgemodelr versions 0.4.3 dated 2026-09-08 and 0.4.5 dated 2026-10-12
DESCRIPTION | 13 MD5 | 81 NEWS.md | 1003 ++- R/RcppExports.R | 8 R/api.R | 7316 ++++++++++++++-------------- R/edgemodelr-package.R | 42 R/ollama.R | 2 R/zzz.R | 2 inst/CITATION | 28 inst/examples/08_rag_pipeline.R | 650 +- man/edge_ask.Rd | 118 man/edge_chat_completion.Rd | 100 man/edge_classify.Rd | 102 man/edge_clean_cache.Rd | 90 man/edge_embeddings.Rd | 106 man/edge_extract.Rd | 102 man/edge_extract_batch.Rd | 102 man/edge_grammar_completion.Rd | 140 man/edge_index_documents.Rd | 112 man/edge_json_grammar.Rd | 70 man/edge_map.Rd | 102 man/edge_model_n_embd.Rd | 50 man/edge_search.Rd | 66 man/edge_serve.Rd | 108 man/edge_similarity.Rd | 58 man/edge_similarity_matrix.Rd | 56 src/Makevars | 14 src/Makevars.win | 8 src/RcppExports.cpp | 19 src/bindings.cpp | 152 src/ggml/ggml-common.h | 7 src/ggml/ggml.c | 10 tests/testthat.R | 8 tests/testthat/test-e2e-integration.R | 95 tests/testthat/test-error-handling.R | 27 tests/testthat/test-integration.R | 8 tests/testthat/test-malformed-model-files.R |only tests/testthat/test-model-loading.R | 13 tests/testthat/test-model-management.R | 16 tests/testthat/test-streaming.R | 22 tests/testthat/test-text-completion.R | 8 tests/testthat/test-utility-functions.R | 96 42 files changed, 5765 insertions(+), 5365 deletions(-)
Title: Data Science Infrastructure for Global Health
Description: Supports global health data analysis, including a
publication-ready 'ggplot2' theme, a 'flextable' defaults helper,
a thin pie chart wrapper, built-in regional country-code datasets
with a WHO region lookup helper, a geometric mean function for
indicator aggregation, an average annual rate of reduction function
for indicator progress tracking, direct age standardization against
the bundled WHO 2026 Standard Population, period life-table
construction, a snapshot helper for reproducible data pulls, and
convenience clients for the World Health Organization Global Health
Observatory (GHO) through its legacy OData API
<https://ghoapi.azureedge.net/api/> or the public WHO xMart OData API
<https://xmart-api-public.who.int/DATA_>, Global Health Estimates (GHE)
through WHO xMart, and
the United Nations Sustainable Development Goals (SDG) API
<https://unstats.un.org/SDGAPI/swagger/>.
Author: Shanlong Ding [aut, cre]
Maintainer: Shanlong Ding <dings@who.int>
Diff between DSIR versions 0.10.0 dated 2026-10-01 and 0.11.0 dated 2026-10-12
DESCRIPTION | 13 MD5 | 106 ++-- NAMESPACE | 85 +-- NEWS.md | 176 ++++--- R/DSIR-package.R | 69 +- R/age_standardize.R | 329 ++++++------- R/bind_indicators.R | 138 ++--- R/clean_metadata.R | 146 +++-- R/clean_schema.R | 126 ++--- R/data.R | 450 ++++++++---------- R/ghe.R |only R/gho.R | 507 +++++--------------- R/http.R | 45 + R/who_backend.R |only R/who_gho.R |only R/who_legacy.R |only README.md | 445 +++++++++++------ build/vignette.rds |binary data/who_std_pop.rda |binary inst/CITATION | 36 - inst/WORDLIST | 99 ++- inst/doc/DSIR.R | 350 ++++++-------- inst/doc/DSIR.Rmd | 273 +++++----- inst/doc/DSIR.html | 506 ++------------------ inst/doc/ghe-xmart.R |only inst/doc/ghe-xmart.Rmd |only inst/doc/ghe-xmart.html |only man/DSIR-package.Rd | 7 man/age_standardize.Rd | 209 ++++---- man/bind_indicators.Rd | 102 ++-- man/ghe_causes.Rd |only man/ghe_clean.Rd |only man/ghe_coverage.Rd |only man/ghe_data.Rd |only man/ghe_dimensions.Rd |only man/gho_clean.Rd | 185 +++---- man/gho_count.Rd | 148 +++-- man/gho_coverage.Rd | 170 +++--- man/gho_data.Rd | 171 ++++-- man/gho_dimensions.Rd | 98 ++- man/gho_has_data.Rd | 160 +++--- man/gho_indicators.Rd | 11 man/who_std_pop.Rd | 113 ++-- tests/testthat/helper-gho-cache.R | 27 - tests/testthat/helper-who-mock.R |only tests/testthat/test-age_standardize.R | 268 +++++----- tests/testthat/test-clean.R | 749 +++++++++++++++--------------- tests/testthat/test-ghe.R |only tests/testthat/test-gho-availability.R | 206 ++++---- tests/testthat/test-gho-backend.R |only tests/testthat/test-gho-catalog-cache.R | 150 +++--- tests/testthat/test-gho-dimensions.R | 219 ++++---- tests/testthat/test-gho-get-mock.R | 445 +++++++++-------- tests/testthat/test-gho.R | 4 tests/testthat/test-sdg-area-resolution.R | 145 ++--- tests/testthat/test-sdg-coverage.R | 258 +++++----- tests/testthat/test-sdg-indicators.R | 193 ++++--- tests/testthat/test-sdg-year-filter.R | 136 ++--- tests/testthat/test-who-html.R |only tests/testthat/test-who-xmart.R |only tests/testthat/test-who_std_pop.R | 75 +-- vignettes/DSIR.Rmd | 273 +++++----- vignettes/ghe-xmart.Rmd |only 63 files changed, 4087 insertions(+), 4334 deletions(-)
Title: Port of 'Dparser' Package
Description: A Scannerless GLR parser/parser generator. Note that GLR standing for "generalized LR", where L stands for "left-to-right" and
R stands for "rightmost (derivation)". For more information see <https://en.wikipedia.org/wiki/GLR_parser>. This parser is based on the Tomita
(1987) algorithm. (Paper can be found at <https://aclanthology.org/P84-1073.pdf>).
The original 'dparser' package documentation can be found at <https://dparser.sourceforge.net/>. This allows you to add mini-languages to R (like
rxode2's ODE mini-language Wang, Hallow, and James 2015 <DOI:10.1002/psp4.12052>) or to parse other languages like 'NONMEM' to automatically translate
them to R code. To use this in your code, add a LinkingTo dparser in your DESCRIPTION file and instead of using #include <dparse.h> use
#include <dparser.h>. This also provides a R-based port of the make_dparser <https://dparser.sourceforge.net/d/make_dparser.cat> command called
mkdparser(). Addition [...truncated...]
Author: Matthew Fidler [aut, cre],
John Plevyak [aut, cph]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between dparser versions 1.3.1-13 dated 2024-10-22 and 1.3.1-14 dated 2026-10-12
DESCRIPTION | 8 - MD5 | 40 +++++--- NAMESPACE | 6 - NEWS.md | 108 ++++++++++++++++++++++++ inst/ansic.test.g.d_parser.c |only man/dparser-package.Rd | 12 +- man/mkdparse.Rd | 12 +- src/dparse.h | 1 src/dparser.c | 2 src/dparser.h | 6 + src/dparser2.h | 1 src/dparserPtr.h | 3 src/lex.c | 9 +- src/parse.c | 57 ++++++++---- src/rdparse.c | 7 + src/util.c | 28 ++++-- src/write_tables.c | 45 ++++++---- tests/testthat/concurrent_parser.c |only tests/testthat/helper-concurrent.R |only tests/testthat/test-concurrent-dparse.R |only tests/testthat/test-mem-buf-read-large.R |only tests/testthat/test-mem-d-pass-negative.R |only tests/testthat/test-mem-dparse-unsigned.R |only tests/testthat/test-mem-new-D-Parser-negative.R |only tests/testthat/test-mem-rdparse-bad-file.R |only tests/testthat/test-mem-udparse-null.R |only 26 files changed, 268 insertions(+), 77 deletions(-)
Title: 'AV1' Video Encoding for Biological Microscopy Data
Description: Converts microscopy video and image data (H.264/H.265,
AVI/MJPEG, TIFF stacks) to the 'AV1' codec for compact storage, and
archives 16-bit image stacks and videos losslessly in the 'FFV1'
format. Encoding runs on the GPU via 'Vulkan' or 'VAAPI' when
available and falls back to the CPU through 'FFmpeg' and 'SVT-AV1'.
Whole experiment folders can be converted at once.
Author: Yuri Baramykov [aut, cre] ,
The Khronos Group Inc. [cph],
FFmpeg developers [cph]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
This is a re-admission after prior archival of version 0.1.3 dated 2026-03-23
Diff between AV1R versions 0.1.3 dated 2026-03-23 and 0.1.4 dated 2026-10-12
DESCRIPTION | 53 ++++------ MD5 | 98 ++++++++++++------ NAMESPACE | 2 NEWS.md | 11 ++ R/archive.R |only R/archive_video.R |only R/backend.R | 16 ++- R/convert.R | 57 ++++++---- R/quality.R | 17 ++- R/utils.R | 9 + README.md | 174 ++++++++++++++++++++++++++++++++- cleanup | 13 ++ cleanup.win |only configure | 29 +++++ configure.win | 26 ++++ inst/examples/benchmark_ffv1.R |only inst/examples/calibrate_vaapi_cqp.R | 17 --- inst/examples/profile_ffv1_shader.R |only man/AV1R-package.Rd | 10 + man/archive_tiff.Rd |only man/archive_video.Rd |only man/av1r_status.Rd | 3 man/detect_backend.Rd | 4 man/vulkan_available.Rd | 6 - man/vulkan_devices.Rd | 3 src/Makevars.in | 8 + src/Makevars.win.in | 8 + src/av1r_bindings.cpp | 62 +++++++++-- src/av1r_encode_vulkan.cpp | 14 +- src/av1r_ffv1_bindings.cpp |only src/av1r_ffv1_encoder.cpp |only src/av1r_ffv1_encoder.h |only src/av1r_ffv1_gpu.cpp |only src/av1r_ffv1_gpu.h |only src/av1r_ffv1_gpu_encoder.cpp |only src/av1r_ffv1_gpu_encoder.h |only src/av1r_ffv1_rangecoder.cpp |only src/av1r_ffv1_rangecoder.h |only src/av1r_ffv1_tables.h |only src/av1r_init.cpp | 11 +- src/av1r_memory.cpp | 7 + src/av1r_mkv_writer.cpp |only src/av1r_mkv_writer.h |only src/av1r_stderr_suppress.h | 7 + src/av1r_stream_encoder.h | 3 src/av1r_vk_instance.h |only src/av1r_vulkan_ctx.h | 5 src/ffv1_shaders |only tests/testthat/helper-device.R |only tests/testthat/test-archive-internal.R |only tests/testthat/test-archive-video.R |only tests/testthat/test-archive.R |only tests/testthat/test-backend.R | 8 - tests/testthat/test-batch-internal.R |only tests/testthat/test-compute-size.R | 4 tests/testthat/test-convert.R | 2 tests/testthat/test-ffmpeg.R | 21 +++ tests/testthat/test-ffv1.R |only tests/testthat/test-mkv.R |only tests/testthat/test-quality-internal.R | 2 tests/testthat/test-tiff.R | 42 ++++--- tests/testthat/test-utils.R | 8 + tools |only 63 files changed, 586 insertions(+), 174 deletions(-)
Title: Arc-Length Statistics: Goodness of Fit, Distributions and a
Bayesian Test
Description: Inference from the arc length of statistical functions. Three tools share one pure-C
back-end: a goodness-of-fit test based on the arc length of the probability plot, with an analytic
saddlepoint null and sensitivity to local density structure that the empirical-distribution tests
miss; two constructions that build a distribution from the arc length of its defining curve, the
arc-length generator and the quantile arc-length family estimated by L-moments; and a Bayesian
nonparametric arc-length goodness-of-fit test on the Dirichlet-process posterior. The same C sources
back the 'Python' package 'arcstat'.
Author: M. Theodor Loots [aut, cre]
Maintainer: M. Theodor Loots <theo.loots@gmail.com>
Diff between arcstat versions 0.3.0 dated 2026-09-14 and 0.3.1 dated 2026-10-12
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 11 +++++++++++ README.md | 12 ++++++++++++ src/arclen.c | 6 ++++++ tests/testthat/test-arclen.R | 13 +++++++++++++ 6 files changed, 50 insertions(+), 8 deletions(-)