Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Originally described in Kamvar, Tabima, and Grünwald (2014)
<doi:10.7717/peerj.281> with version 2.0 described in Kamvar, Brooks, and
Grünwald (2015) <doi:10.3389/fgene.2015.00208>.
Author: Zhian N. Kamvar [cre, aut] ,
Javier F. Tabima [aut] ,
Sydney E. Everhart [ctb, dtc] ,
Jonah C. Brooks [aut],
Stacy A. Krueger-Hadfield [ctb] ,
Erik Sotka [ctb],
Brian J. Knaus [ctb] ,
Patrick G. Meirmans [ctb] ,
Frederic D. Chevalier [ctb] ,
David Fo [...truncated...]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between poppr versions 2.9.7 dated 2025-06-18 and 2.9.8 dated 2025-08-23
DESCRIPTION | 6 MD5 | 260 ++-- NEWS.md | 275 ++-- R/Index_calculations.r | 901 ++++++++----- R/aaaMLGclass.R | 105 - R/aaaMLGmethods.R | 302 ++-- R/amova.r | 289 ++-- R/bitwise.r | 455 +++---- R/bootstraping.R | 575 +++++--- R/bruvo.r | 697 ++++++---- R/check_data.R | 54 R/classes.r | 160 +- R/data_subset.r | 745 ++++++----- R/distances.r | 342 ++--- R/file_handling.r | 640 +++++---- R/filter_stats.R | 304 ++-- R/global_memory.r | 42 R/ia_jackknife.R | 150 +- R/imsn.R | 92 - R/internal.r | 2191 +++++++++++++++++++--------------- R/internal_methods.R | 304 ++-- R/messages.r | 334 +++-- R/methods.r | 1537 ++++++++++++++--------- R/mlg.r | 382 +++-- R/msn_handlers.R | 337 ++--- R/poppr.R | 282 ++-- R/print_methods.r | 107 + R/round_robin.R | 596 ++++----- R/sample_schemes.r | 291 ++-- R/visualizations.r | 1425 ++++++++++++---------- R/zzz.r | 59 inst/doc/algo.pdf |binary inst/shiny/msn_explorer/server.R | 462 ++++--- inst/shiny/msn_explorer/ui.R | 357 +++-- inst/shiny/utils.R | 44 man/Aeut.Rd | 6 man/MLG-accessors.Rd | 10 man/MLG-class.Rd | 20 man/MLG-method.Rd | 6 man/Pinf.Rd | 16 man/Pram.Rd | 34 man/aboot.Rd | 4 man/bitwise.dist.Rd | 8 man/bootgen-class.Rd | 2 man/bootgen-methods.Rd | 4 man/bruvo.boot.Rd | 20 man/bruvo.dist.Rd | 66 - man/bruvo.msn.Rd | 100 - man/bruvomat-class.Rd | 2 man/bruvomat-methods.Rd | 2 man/clonecorrect.Rd | 20 man/coercion-methods.Rd | 6 man/cutoff_predictor.Rd | 18 man/diss.dist.Rd | 12 man/diversity_boot.Rd | 2 man/diversity_ci.Rd | 10 man/diversity_stats.Rd | 2 man/filter_stats.Rd | 34 man/fix_replen.Rd | 16 man/genclone-class.Rd | 38 man/genclone-method.Rd | 4 man/genetic_distance.Rd | 38 man/genotype_curve.Rd | 34 man/getfile.Rd | 4 man/greycurve.Rd | 6 man/ia.Rd | 20 man/imsn.Rd | 16 man/incomp.Rd | 2 man/info_table.Rd | 14 man/informloci.Rd | 29 man/is.clone.Rd | 4 man/levels-methods.Rd | 4 man/make_haplotypes-method.Rd | 8 man/missingno.Rd | 38 man/mlg.Rd | 8 man/mlg.filter.Rd | 44 man/mll-method.Rd | 2 man/mll.custom.Rd | 2 man/mll.reset-method.Rd | 2 man/monpop.Rd | 12 man/partial_clone.Rd | 6 man/pgen.Rd | 48 man/plot_filter_stats.Rd | 6 man/plot_poppr_msn.Rd | 94 - man/poppr.Rd | 6 man/poppr.amova.Rd | 4 man/poppr.msn.Rd | 68 - man/psex.Rd | 66 - man/rare_allele_correction.Rd | 40 man/read.genalex.Rd | 4 man/recode_polyploids.Rd | 48 man/rraf.Rd | 34 man/rrmlg.Rd | 2 man/samp.ia.Rd | 16 man/shufflepop.Rd | 20 man/snpclone-coercion-methods.Rd | 4 man/test_replen.Rd | 12 man/unique-methods.Rd | 4 man/win.ia.Rd | 4 tests/test-all.R | 2 tests/testthat/test-MLG-class.R | 7 tests/testthat/test-amova.R | 614 ++++++--- tests/testthat/test-bitwise.R | 264 +++- tests/testthat/test-bootclass.R | 27 tests/testthat/test-distpop.R | 62 tests/testthat/test-errors.R | 44 tests/testthat/test-filter.R | 238 ++- tests/testthat/test-genclone.R | 84 - tests/testthat/test-genotype_curve.R | 36 tests/testthat/test-greyscale.R | 14 tests/testthat/test-import.R | 473 ++++--- tests/testthat/test-incomp.R | 2 tests/testthat/test-informloci.R | 33 tests/testthat/test-jackia.R | 7 tests/testthat/test-locustable.R | 61 tests/testthat/test-make_haplotypes.R | 4 tests/testthat/test-missing.R | 12 tests/testthat/test-mlg.R | 738 ++++++++--- tests/testthat/test-msn.R | 392 +++--- tests/testthat/test-plots.R | 335 ++--- tests/testthat/test-polyploids.R | 56 tests/testthat/test-poppr.R | 214 ++- tests/testthat/test-popsub.R | 86 - tests/testthat/test-private.R | 25 tests/testthat/test-replen.R | 45 tests/testthat/test-round-robin.R | 206 +-- tests/testthat/test-sampling.R | 113 + tests/testthat/test-snpclone.R | 37 tests/testthat/test-trees.R | 144 +- tests/testthat/test-values.R | 953 ++++++++++++-- tests/testthat/test-winia.R | 44 131 files changed, 13057 insertions(+), 8652 deletions(-)
Title: Tools for Plant Image Analysis
Description: Tools for both single and batch image manipulation and
analysis (Olivoto, 2022 <doi:10.1111/2041-210X.13803>) and
phytopathometry (Olivoto et al., 2022 <doi:10.1007/S40858-021-00487-5>).
The tools can be used for the quantification of leaf area, object
counting, extraction of image indexes, shape measurement, object
landmark identification, and Elliptical Fourier Analysis of object
outlines (Claude (2008) <doi:10.1007/978-0-387-77789-4>). The package
also provides a comprehensive pipeline for generating shapefiles with
complex layouts and supports high-throughput phenotyping of RGB,
multispectral, and hyperspectral orthomosaics. This functionality
facilitates field phenotyping using UAV- or satellite-based imagery.
Author: Tiago Olivoto [aut, cre]
Maintainer: Tiago Olivoto <tiagoolivoto@gmail.com>
Diff between pliman versions 3.1.0 dated 2025-08-19 and 3.1.1 dated 2025-08-23
DESCRIPTION | 6 - MD5 | 18 +-- NAMESPACE | 4 NEWS.md | 7 + R/analyze_objects.R | 17 ++- R/utilities.R | 47 ++++++++ R/utils_objects.R | 254 ++++++++++++++++++++++++++++++++++++++++++++++ man/clear_pliman_cache.Rd |only man/object_scatter.Rd |only src/Makevars | 5 src/Makevars.win | 3 11 files changed, 348 insertions(+), 13 deletions(-)
Title: Import 'OpenStreetMap' Data as Simple Features or Spatial
Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf'
or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web
server (<https://overpass-api.de/>) and processed with very fast 'C++'
routines for return to 'R'.
Author: Joan Maspons [aut, cre] ,
Mark Padgham [aut],
Bob Rudis [aut],
Robin Lovelace [aut],
Maelle Salmon [aut],
Andrew Smith [ctb],
James Smith [ctb],
Andrea Gilardi [ctb],
Enrico Spinielli [ctb],
Anthony North [ctb],
Martin Machyna [ctb],
Marcin Kalicinsk [...truncated...]
Maintainer: Joan Maspons <joanmaspons@gmail.com>
Diff between osmdata versions 0.2.5 dated 2023-08-14 and 0.3.0 dated 2025-08-23
osmdata-0.2.5/osmdata/man/pipe.Rd |only osmdata-0.2.5/osmdata/tests/testthat/mock_bb_poly/nominatim/search-c1f6d2.json |only osmdata-0.2.5/osmdata/tests/testthat/mock_bb_sf |only osmdata-0.2.5/osmdata/tests/valgrind-test.R |only osmdata-0.3.0/osmdata/DESCRIPTION | 39 osmdata-0.3.0/osmdata/MD5 | 172 +-- osmdata-0.3.0/osmdata/NAMESPACE | 13 osmdata-0.3.0/osmdata/NEWS.md | 133 +- osmdata-0.3.0/osmdata/R/deprecated.R |only osmdata-0.3.0/osmdata/R/elevation.R | 30 osmdata-0.3.0/osmdata/R/features.R | 13 osmdata-0.3.0/osmdata/R/get-osmdata-df.R | 61 - osmdata-0.3.0/osmdata/R/get-osmdata-sc.R | 47 osmdata-0.3.0/osmdata/R/get-osmdata-sf.R | 88 + osmdata-0.3.0/osmdata/R/get-osmdata-sp.R | 52 osmdata-0.3.0/osmdata/R/get-osmdata-xml.R | 30 osmdata-0.3.0/osmdata/R/get-osmdata.R | 44 osmdata-0.3.0/osmdata/R/getbb.R | 279 +++-- osmdata-0.3.0/osmdata/R/opq.R | 234 ++-- osmdata-0.3.0/osmdata/R/osm-extract.R | 52 osmdata-0.3.0/osmdata/R/osmdata-class.R | 7 osmdata-0.3.0/osmdata/R/osmdata-methods.R | 16 osmdata-0.3.0/osmdata/R/osmdata-package.R | 19 osmdata-0.3.0/osmdata/R/overpass-query.R | 24 osmdata-0.3.0/osmdata/R/poly2line.R | 15 osmdata-0.3.0/osmdata/R/trim-osmdata.R | 395 +++---- osmdata-0.3.0/osmdata/R/unique-osmdata.R | 21 osmdata-0.3.0/osmdata/R/utils.R | 10 osmdata-0.3.0/osmdata/R/zzz.R | 2 osmdata-0.3.0/osmdata/README.md |only osmdata-0.3.0/osmdata/build/vignette.rds |binary osmdata-0.3.0/osmdata/inst/doc/osm-sf-translation.R | 64 - osmdata-0.3.0/osmdata/inst/doc/osm-sf-translation.Rmd | 45 osmdata-0.3.0/osmdata/inst/doc/osm-sf-translation.html | 26 osmdata-0.3.0/osmdata/inst/doc/osmdata-sc.R | 48 osmdata-0.3.0/osmdata/inst/doc/osmdata-sc.Rmd | 18 osmdata-0.3.0/osmdata/inst/doc/osmdata-sc.html | 22 osmdata-0.3.0/osmdata/inst/doc/osmdata.R | 534 +++++----- osmdata-0.3.0/osmdata/inst/doc/osmdata.Rmd | 245 ++-- osmdata-0.3.0/osmdata/inst/doc/osmdata.html | 241 ++-- osmdata-0.3.0/osmdata/inst/doc/query-split.R | 162 +-- osmdata-0.3.0/osmdata/inst/doc/query-split.html | 4 osmdata-0.3.0/osmdata/man/add_osm_feature.Rd | 29 osmdata-0.3.0/osmdata/man/add_osm_features.Rd | 17 osmdata-0.3.0/osmdata/man/bbox_to_string.Rd | 9 osmdata-0.3.0/osmdata/man/get_overpass_url.Rd | 3 osmdata-0.3.0/osmdata/man/getbb.Rd | 54 - osmdata-0.3.0/osmdata/man/opq.Rd | 49 osmdata-0.3.0/osmdata/man/opq_around.Rd | 6 osmdata-0.3.0/osmdata/man/opq_csv.Rd | 18 osmdata-0.3.0/osmdata/man/opq_enclosing.Rd | 8 osmdata-0.3.0/osmdata/man/opq_osm_id.Rd | 20 osmdata-0.3.0/osmdata/man/opq_string.Rd | 4 osmdata-0.3.0/osmdata/man/osm_elevation.Rd | 16 osmdata-0.3.0/osmdata/man/osm_lines.Rd | 14 osmdata-0.3.0/osmdata/man/osm_multilines.Rd | 8 osmdata-0.3.0/osmdata/man/osm_multipolygons.Rd | 10 osmdata-0.3.0/osmdata/man/osm_points.Rd | 8 osmdata-0.3.0/osmdata/man/osm_poly2line.Rd | 11 osmdata-0.3.0/osmdata/man/osm_polygons.Rd | 10 osmdata-0.3.0/osmdata/man/osmdata-deprecated.Rd |only osmdata-0.3.0/osmdata/man/osmdata-package.Rd |only osmdata-0.3.0/osmdata/man/osmdata.Rd | 64 - osmdata-0.3.0/osmdata/man/osmdata_data_frame.Rd | 41 osmdata-0.3.0/osmdata/man/osmdata_sc.Rd | 47 osmdata-0.3.0/osmdata/man/osmdata_sf.Rd | 46 osmdata-0.3.0/osmdata/man/osmdata_sp.Rd | 43 osmdata-0.3.0/osmdata/man/osmdata_xml.Rd | 30 osmdata-0.3.0/osmdata/man/overpass_status.Rd | 11 osmdata-0.3.0/osmdata/man/trim_osmdata.Rd | 51 osmdata-0.3.0/osmdata/man/unique_osmdata.Rd | 21 osmdata-0.3.0/osmdata/man/unname_osmdata_sf.Rd | 8 osmdata-0.3.0/osmdata/src/osmdata-sf.cpp | 4 osmdata-0.3.0/osmdata/tests/testthat/mock_bb_poly/nominatim/search-5fa35a.json |only osmdata-0.3.0/osmdata/tests/testthat/mock_bb_poly_no |only osmdata-0.3.0/osmdata/tests/testthat/test-c.R | 15 osmdata-0.3.0/osmdata/tests/testthat/test-data_frame-osm.R | 65 - osmdata-0.3.0/osmdata/tests/testthat/test-elevation.R | 4 osmdata-0.3.0/osmdata/tests/testthat/test-extract.R | 10 osmdata-0.3.0/osmdata/tests/testthat/test-getbb.R | 91 + osmdata-0.3.0/osmdata/tests/testthat/test-opq.R | 38 osmdata-0.3.0/osmdata/tests/testthat/test-osmdata.R | 140 +- osmdata-0.3.0/osmdata/tests/testthat/test-sc-osm.R | 5 osmdata-0.3.0/osmdata/tests/testthat/test-sf-construction.R | 21 osmdata-0.3.0/osmdata/tests/testthat/test-sf-osm.R | 40 osmdata-0.3.0/osmdata/tests/testthat/test-sp-osm.R | 30 osmdata-0.3.0/osmdata/tests/testthat/test-trim.R | 17 osmdata-0.3.0/osmdata/tests/testthat/test-unique.R | 10 osmdata-0.3.0/osmdata/tests/testthat/test-unname.R | 2 osmdata-0.3.0/osmdata/vignettes/osm-sf-translation.Rmd | 45 osmdata-0.3.0/osmdata/vignettes/osmdata-sc.Rmd | 18 osmdata-0.3.0/osmdata/vignettes/osmdata.Rmd | 245 ++-- 92 files changed, 2669 insertions(+), 1992 deletions(-)
Title: An R Package to Extend 'ACER ConQuest'
Description: Extends 'ACER ConQuest' through a family of functions
designed to improve graphical outputs and help with advanced analysis
(e.g., differential item functioning). Allows R users to call
'ACER ConQuest' from within R and read 'ACER ConQuest' System Files
(generated by the command `put` <https://conquestmanual.acer.org/s4-00.html#put>).
Requires 'ACER ConQuest' version 5.40 or later.
A demonstration version can be downloaded from <https://shop.acer.org/acer-conquest-5.html>.
Author: Dan Cloney [aut, cre] ,
Ray Adams [aut]
Maintainer: Dan Cloney <dan.cloney@acer.org>
Diff between conquestr versions 1.5.1 dated 2025-05-18 and 1.5.5 dated 2025-08-23
conquestr-1.5.1/conquestr/man/postProcessGncases.Rd |only conquestr-1.5.5/conquestr/DESCRIPTION | 6 conquestr-1.5.5/conquestr/MD5 | 61 ++++--- conquestr-1.5.5/conquestr/NEWS.md | 17 ++ conquestr-1.5.5/conquestr/R/ReadConQuestLibrary.R | 56 ++++--- conquestr-1.5.5/conquestr/R/ReadConQuestRout_createDF.R | 8 - conquestr-1.5.5/conquestr/R/ReadConQuestState.R | 71 ++++----- conquestr-1.5.5/conquestr/R/conquestr.R | 2 conquestr-1.5.5/conquestr/R/conquestrFunc.R | 77 +++++++--- conquestr-1.5.5/conquestr/R/generateHelpers.R | 2 conquestr-1.5.5/conquestr/R/itanalHelpers.R | 34 ++-- conquestr-1.5.5/conquestr/R/postProcessCqSysfile.R | 68 ++++++-- conquestr-1.5.5/conquestr/build/vignette.rds |binary conquestr-1.5.5/conquestr/inst/doc/data-cleaning-functions-in-conquestr.html | 9 - conquestr-1.5.5/conquestr/inst/doc/generateResponses.html | 53 +++--- conquestr-1.5.5/conquestr/inst/doc/intro-to-conquestr.html | 22 +- conquestr-1.5.5/conquestr/inst/doc/itanal-in-conquestr.html | 9 - conquestr-1.5.5/conquestr/inst/doc/plotting.html | 11 - conquestr-1.5.5/conquestr/inst/doc/responseProbs.html | 9 - conquestr-1.5.5/conquestr/inst/doc/test_item_review_sheet_markdown.html | 11 + conquestr-1.5.5/conquestr/man/ReadAllCaseEstimates.Rd | 2 conquestr-1.5.5/conquestr/man/ReadEstimatesRecord.Rd | 4 conquestr-1.5.5/conquestr/man/ReadSysMini.Rd | 19 +- conquestr-1.5.5/conquestr/man/genResponses.Rd | 4 conquestr-1.5.5/conquestr/man/getCqChain.Rd | 6 conquestr-1.5.5/conquestr/man/getCqFit.Rd | 2 conquestr-1.5.5/conquestr/man/postProcess_gLConstraint.Rd |only conquestr-1.5.5/conquestr/man/postProcess_gNCases.Rd |only conquestr-1.5.5/conquestr/man/searchConQuestSys.Rd | 2 conquestr-1.5.5/conquestr/man/summariseCqChain.Rd | 3 conquestr-1.5.5/conquestr/tests/testthat.R | 1 conquestr-1.5.5/conquestr/tests/testthat/test-ConQuestRout.R | 2 conquestr-1.5.5/conquestr/tests/testthat/test-plotItemMap.R | 2 33 files changed, 361 insertions(+), 212 deletions(-)
Title: 'Stata' Markdown
Description: Settings and functions to extend the 'knitr' 'Stata' engine.
Author: Doug Hemken [aut, cre] ),
Tom Palmer [ctb] ,
Philipp Lepert [ctb]
Maintainer: Doug Hemken <d_hemken@yahoo.com>
This is a re-admission after prior archival of version 0.9.2 dated 2023-12-04
Diff between Statamarkdown versions 0.9.2 dated 2023-12-04 and 0.9.4 dated 2025-08-23
DESCRIPTION | 16 +-- MD5 | 10 - R/find_stata.r | 28 ++--- R/misc.r | 1 man/Statamarkdown-package.rd | 216 +++++++++++++++++++++---------------------- man/stata_engine.rd | 140 +++++++++++++-------------- 6 files changed, 207 insertions(+), 204 deletions(-)
Title: Analysis and Manipulation of Data from Minecraft Bedrock Edition
Description: Implements an interface to Minecraft (Bedrock Edition) worlds. Supports the analysis and management of these worlds and game saves.
Author: Reed Cartwright [aut, cre] ,
Rich FitzJohn [ctb],
Christian Stigen Larsen [ctb],
The LevelDB Authors [cph]
Maintainer: Reed Cartwright <racartwright@gmail.com>
Diff between rbedrock versions 0.3.3 dated 2025-03-25 and 0.4.0 dated 2025-08-23
rbedrock-0.3.3/rbedrock/R/checksums.R |only rbedrock-0.3.3/rbedrock/R/data2d.R |only rbedrock-0.3.3/rbedrock/R/entity.R |only rbedrock-0.3.3/rbedrock/R/hsa.R |only rbedrock-0.3.3/rbedrock/inst/extdata/block_states.csv |only rbedrock-0.3.3/rbedrock/man/HSA.Rd |only rbedrock-0.3.3/rbedrock/man/SubchunkBlocks.Rd |only rbedrock-0.3.3/rbedrock/man/get_chunk_blocks_data.Rd |only rbedrock-0.3.3/rbedrock/man/get_subchunk_layers_data.Rd |only rbedrock-0.3.3/rbedrock/man/get_values.Rd |only rbedrock-0.3.3/rbedrock/man/list_biomes.Rd |only rbedrock-0.3.3/rbedrock/man/new_nbt.Rd |only rbedrock-0.3.3/rbedrock/man/op-pipe.Rd |only rbedrock-0.3.3/rbedrock/man/put_values.Rd |only rbedrock-0.3.3/rbedrock/tests/testthat/test_1nbt.R |only rbedrock-0.3.3/rbedrock/tests/testthat/test_2example.R |only rbedrock-0.3.3/rbedrock/tests/testthat/test_3bedrockdb.R |only rbedrock-0.3.3/rbedrock/tests/testthat/test_4keys.R |only rbedrock-0.3.3/rbedrock/tests/testthat/test_checksums.R |only rbedrock-0.3.3/rbedrock/tests/testthat/test_data2d.R |only rbedrock-0.3.3/rbedrock/tests/testthat/test_entity.R |only rbedrock-0.3.3/rbedrock/tests/testthat/test_hsa.R |only rbedrock-0.4.0/rbedrock/DESCRIPTION | 21 rbedrock-0.4.0/rbedrock/MD5 | 236 +- rbedrock-0.4.0/rbedrock/NAMESPACE | 434 +-- rbedrock-0.4.0/rbedrock/NEWS.md | 68 rbedrock-0.4.0/rbedrock/R/R6.R | 254 +- rbedrock-0.4.0/rbedrock/R/aaa.R |only rbedrock-0.4.0/rbedrock/R/actor.R | 316 +- rbedrock-0.4.0/rbedrock/R/bedrock_leveldb.R | 291 +- rbedrock-0.4.0/rbedrock/R/biomes.R | 457 ---- rbedrock-0.4.0/rbedrock/R/block_entity.R | 64 rbedrock-0.4.0/rbedrock/R/blocks-str.R |only rbedrock-0.4.0/rbedrock/R/blocks-subchunk.R |only rbedrock-0.4.0/rbedrock/R/blocks.R | 1095 ++------- rbedrock-0.4.0/rbedrock/R/chunk_version.R | 134 - 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rbedrock-0.4.0/rbedrock/tests/testthat/test_worlds.R | 68 156 files changed, 4850 insertions(+), 6604 deletions(-)
Title: Principal Coordinates of Phylogenetic Structure
Description: Set of functions for analysis of Principal Coordinates of Phylogenetic Structure (PCPS).
Author: Vanderlei Julio Debastiani [aut, cre]
Maintainer: Vanderlei Julio Debastiani <vanderleidebastiani@yahoo.com.br>
This is a re-admission after prior archival of version 1.0.7 dated 2020-01-15
Diff between PCPS versions 1.0.7 dated 2020-01-15 and 1.0.8 dated 2025-08-23
DESCRIPTION | 16 ++++++++++------ MD5 | 38 +++++++++++++++++++------------------- R/define.clade.R | 4 ++-- R/matrix.p.null.R | 4 ++-- R/organize.pcps.R | 8 ++++---- R/pcoa.sig.R | 4 ++-- R/pcps.R | 8 ++++---- R/pcps.curve.R | 4 ++-- R/pcps.sig.R | 48 ++++++++++++++++++++++++------------------------ R/self.belonging.R | 2 +- R/wcmdscale.org.R | 10 +++++----- man/define.clade.Rd | 4 ++-- man/matrix.p.null.Rd | 4 ++-- man/organize.pcps.Rd | 8 ++++---- man/pcoa.sig.Rd | 4 ++-- man/pcps.Rd | 8 ++++---- man/pcps.curve.Rd | 4 ++-- man/pcps.sig.Rd | 48 ++++++++++++++++++++++++------------------------ man/self.belonging.Rd | 2 +- man/wcmdscale.org.Rd | 10 +++++----- 20 files changed, 121 insertions(+), 117 deletions(-)
Title: Nonparametric Failure Time Bayesian Additive Regression Trees
Description: Nonparametric Failure Time (NFT) Bayesian Additive Regression Trees (BART): Time-to-event Machine Learning with Heteroskedastic Bayesian Additive Regression Trees (HBART) and Low Information Omnibus (LIO) Dirichlet Process Mixtures (DPM). An NFT BART model is of the form Y = mu + f(x) + sd(x) E where functions f and sd have BART and HBART priors, respectively, while E is a nonparametric error distribution due to a DPM LIO prior hierarchy. See the following for a description of the model at <doi:10.1111/biom.13857>.
Author: Rodney Sparapani [aut, cre],
Robert McCulloch [aut],
Matthew Pratola [ctb],
Hugh Chipman [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between nftbart versions 2.1 dated 2023-11-27 and 2.2 dated 2025-08-23
DESCRIPTION | 12 ++--- MD5 | 36 +++++++++------- NAMESPACE | 17 +++++-- NEWS | 12 +++++ R/mi.nft.R |only R/mi.nft2.R |only R/nft.R | 7 --- R/nft2.R | 113 +++++++++++++++++++++++++++++++++++++---------------- R/predict.nft2.R | 45 ++++++++++++--------- R/predict.nft2mi.R |only R/predict.nftmi.R |only R/tsvs.R | 19 +++++--- R/tsvs2.R | 35 +++++++++------- R/xicuts.R | 34 +++++++++------ cleanup | 3 - cleanup.win | 3 - demo/lung.R | 12 ++--- man/nft2.Rd | 5 +- man/tsvs2.Rd | 5 +- src/cnft2.h | 13 +++--- src/init.c | 4 - 21 files changed, 238 insertions(+), 137 deletions(-)
Title: Visualising and Interpreting Statistical Models Fit to
Compositional Data
Description: Statistical models fit to compositional data are often difficult to interpret due to the sum to 1 constraint on data variables. 'DImodelsVis' provides novel visualisations tools to aid with the interpretation of models fit to compositional data. All visualisations in the package are created using the 'ggplot2' plotting framework and can be extended like every other 'ggplot' object.
Author: Rishabh Vishwakarma [aut, cre] ,
Caroline Brophy [aut],
Laura Byrne [aut],
Catherine Hurley [aut]
Maintainer: Rishabh Vishwakarma <vishwakr@tcd.ie>
Diff between DImodelsVis versions 1.0.2 dated 2025-08-21 and 1.0.3 dated 2025-08-23
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Title: Artificial Intelligence for Education
Description: In social and educational settings, the use of Artificial
Intelligence (AI) is a challenging task. Relevant data is often only
available in handwritten forms, or the use of data is restricted by
privacy policies. This often leads to small data sets. Furthermore, in
the educational and social sciences, data is often unbalanced in terms
of frequencies. To support educators as well as educational and social
researchers in using the potentials of AI for their work, this package
provides a unified interface for neural nets in 'PyTorch' to deal with
natural language problems. In addition, the package ships with a shiny
app, providing a graphical user interface. This allows the usage of
AI for people without skills in writing python/R scripts. The tools
integrate existing mathematical and statistical methods for dealing
with small data sets via pseudo-labeling (e.g. Cascante-Bonilla et al.
(2020) <doi:10.48550/arXiv.2001.06001>) and imbalanced data via the
creation of synthetic cases [...truncated...]
Author: Berding Florian [aut, cre] ,
Tykhonova Yuliia [aut] ,
Pargmann Julia [ctb] ,
Leube Anna [ctb] ,
Riebenbauer Elisabeth [ctb] ,
Rebmann Karin [ctb],
Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
This is a re-admission after prior archival of version 1.1.0 dated 2025-08-19
Diff between aifeducation versions 1.1.0 dated 2025-08-19 and 1.1.1 dated 2025-08-23
DESCRIPTION | 6 MD5 | 146 +-- NEWS.md | 4 R/RcppExports.R | 23 R/onLoad.R | 2 R/utils_general.R | 27 man/ClassifiersBasedOnTextEmbeddings.Rd | 748 ++++++++-------- man/DataManagerClassifier.Rd | 802 +++++++++--------- man/EmbeddedText.Rd | 866 +++++++++---------- man/LargeDataSetBase.Rd | 534 ++++++------ man/LargeDataSetForTextEmbeddings.Rd | 886 ++++++++++---------- man/ModelsBasedOnTextEmbeddings.Rd | 408 ++++----- man/TEClassifiersBasedOnRegular.Rd | 446 +++++----- man/add_missing_args.Rd | 66 - man/build_documentation_for_model.Rd | 86 - man/build_layer_stack_documentation_for_vignette.Rd | 60 - man/calc_tokenizer_statistics.Rd | 80 - man/cat_message.Rd | 62 - man/check_adjust_n_samples_on_CI.Rd | 62 - man/check_all_args.Rd | 48 - man/check_class_and_type.Rd | 96 +- man/class_vector_to_py_dataset.Rd | 56 - man/clean_pytorch_log_transformers.Rd | 60 - man/create_dir.Rd | 58 - man/create_object.Rd | 58 - man/data.frame_to_py_dataset.Rd | 56 - man/generate_args_for_tests.Rd | 104 +- man/generate_embeddings.Rd | 82 - man/generate_tensors.Rd | 82 - man/get_TEClassifiers_class_names.Rd | 58 - man/get_batches_index.Rd | 66 - man/get_called_args.Rd | 54 - man/get_current_args_for_print.Rd | 58 - man/get_depr_obj_names.Rd | 48 - man/get_desc_for_core_model_architecture.Rd | 74 - man/get_dict_cls_type.Rd | 62 - man/get_dict_core_models.Rd | 74 - man/get_dict_input_types.Rd | 62 - man/get_file_extension.Rd | 44 man/get_fixed_test_tensor.Rd | 58 - man/get_layer_dict.Rd | 78 - man/get_layer_documentation.Rd | 92 +- man/get_magnitude_values.Rd | 72 - man/get_n_chunks.Rd | 74 - man/get_param_def.Rd | 60 - man/get_param_dict.Rd | 90 +- man/get_param_doc_desc.Rd | 58 - man/get_parameter_documentation.Rd | 80 - man/get_py_package_version.Rd | 50 - man/get_test_data_for_classifiers.Rd | 60 - man/gwet_ac.Rd | 94 +- man/install_aifeducation_studio.Rd | 50 - man/load_all_py_scripts.Rd | 44 man/load_py_scripts.Rd | 50 - man/matrix_to_array_c.Rd | 4 man/output_message.Rd | 70 - man/prepare_r_array_for_dataset.Rd | 58 - man/prepare_session.Rd | 68 - man/print_message.Rd | 62 - man/py_dataset_to_embeddings.Rd | 60 - man/random_bool_on_CI.Rd | 52 - man/read_log.Rd | 60 - man/read_loss_log.Rd | 76 - man/reduce_to_unique.Rd | 62 - man/reset_log.Rd | 60 - man/reset_loss_log.Rd | 68 - man/summarize_args_for_long_task.Rd | 140 +-- man/tensor_list_to_numpy.Rd | 60 - man/tensor_to_numpy.Rd | 60 - man/to_categorical_c.Rd | 4 man/update_aifeducation.Rd | 106 +- man/write_log.Rd | 150 +-- src/RcppExports.cpp | 25 src/aux_fcts.cpp | 54 - 74 files changed, 4448 insertions(+), 4475 deletions(-)
Title: Variable Importance and Variable Interaction Displays
Description: A suite of plots for displaying variable importance and two-way variable interaction jointly. Can also display partial dependence plots laid out in a pairs plot or 'zenplots' style.
Author: Alan Inglis [aut, cre],
Andrew Parnell [aut],
Catherine Hurley [aut]
Maintainer: Alan Inglis <alan.n.inglis@gmail.com>
This is a re-admission after prior archival of version 0.2.9 dated 2024-07-31
Diff between vivid versions 0.2.9 dated 2024-07-31 and 0.3.0 dated 2025-08-23
vivid-0.2.9/vivid/build |only vivid-0.2.9/vivid/inst/doc |only vivid-0.2.9/vivid/vignettes |only vivid-0.3.0/vivid/DESCRIPTION | 19 +++++++++---------- vivid-0.3.0/vivid/MD5 | 27 ++++++++++++++------------- vivid-0.3.0/vivid/NAMESPACE | 7 ++++++- vivid-0.3.0/vivid/NEWS.md | 8 +++++--- vivid-0.3.0/vivid/R/geom_encircle.R |only vivid-0.3.0/vivid/R/pdpPairs.R | 2 +- vivid-0.3.0/vivid/R/pdpVars.R | 11 +++++++++-- vivid-0.3.0/vivid/R/pdpZen.R | 2 +- vivid-0.3.0/vivid/R/vimp_vint.R |only vivid-0.3.0/vivid/R/viviNetwork.R | 20 +++++++++++++++++--- vivid-0.3.0/vivid/inst/CITATION | 17 +++++++++++++++++ vivid-0.3.0/vivid/man/GeomEncircle.Rd |only vivid-0.3.0/vivid/man/geom_encircle_vivi.Rd |only vivid-0.3.0/vivid/man/vivi_importance.Rd |only vivid-0.3.0/vivid/man/vivi_interaction.Rd |only 18 files changed, 79 insertions(+), 34 deletions(-)
Title: Van Westendorp Price Sensitivity Meter Analysis
Description: An implementation of the van Westendorp Price
Sensitivity Meter in R, which is a survey-based approach
to analyze consumer price preferences and sensitivity
(van Westendorp 1976, isbn:9789283100386).
Author: Max Alletsee [aut, cre]
Maintainer: Max Alletsee <max.alletsee@gmail.com>
Diff between pricesensitivitymeter versions 1.3.0 dated 2024-02-25 and 1.3.1 dated 2025-08-23
pricesensitivitymeter-1.3.0/pricesensitivitymeter/man/pricesensitivitymeter.rd |only pricesensitivitymeter-1.3.0/pricesensitivitymeter/man/psm_analysis.rd |only pricesensitivitymeter-1.3.0/pricesensitivitymeter/man/psm_analysis_weighted.rd |only pricesensitivitymeter-1.3.0/pricesensitivitymeter/man/psm_plot.rd |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/DESCRIPTION | 6 pricesensitivitymeter-1.3.1/pricesensitivitymeter/MD5 | 88 + pricesensitivitymeter-1.3.1/pricesensitivitymeter/NAMESPACE | 1 pricesensitivitymeter-1.3.1/pricesensitivitymeter/NEWS.md | 10 pricesensitivitymeter-1.3.1/pricesensitivitymeter/R/psm-utils.R | 90 + pricesensitivitymeter-1.3.1/pricesensitivitymeter/R/psm_constants.R |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/R/psm_data_processing.R |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/R/psm_functions.R | 496 +--------- pricesensitivitymeter-1.3.1/pricesensitivitymeter/R/psm_plot.R | 126 +- pricesensitivitymeter-1.3.1/pricesensitivitymeter/R/psm_utils.R |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/R/psm_validation.R |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/R/psm_weighted_functions.R | 474 +-------- pricesensitivitymeter-1.3.1/pricesensitivitymeter/README.md | 33 pricesensitivitymeter-1.3.1/pricesensitivitymeter/build/vignette.rds |binary pricesensitivitymeter-1.3.1/pricesensitivitymeter/inst/doc/interpolation-in-small-samples.R | 16 pricesensitivitymeter-1.3.1/pricesensitivitymeter/inst/doc/interpolation-in-small-samples.Rmd | 16 pricesensitivitymeter-1.3.1/pricesensitivitymeter/inst/doc/interpolation-in-small-samples.html | 84 - pricesensitivitymeter-1.3.1/pricesensitivitymeter/inst/doc/visualizing-psm-results.R | 32 pricesensitivitymeter-1.3.1/pricesensitivitymeter/inst/doc/visualizing-psm-results.Rmd | 33 pricesensitivitymeter-1.3.1/pricesensitivitymeter/inst/doc/visualizing-psm-results.html | 140 +- pricesensitivitymeter-1.3.1/pricesensitivitymeter/inst/doc/weighted-data.R | 2 pricesensitivitymeter-1.3.1/pricesensitivitymeter/inst/doc/weighted-data.Rmd | 2 pricesensitivitymeter-1.3.1/pricesensitivitymeter/inst/doc/weighted-data.html | 117 +- pricesensitivitymeter-1.3.1/pricesensitivitymeter/man/figures/example_plot-1.png |binary pricesensitivitymeter-1.3.1/pricesensitivitymeter/man/pricesensitivitymeter.Rd |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/man/psm_analysis.Rd |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/man/psm_analysis_weighted.Rd |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/man/psm_plot.Rd |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/tests/testthat.R | 7 pricesensitivitymeter-1.3.1/pricesensitivitymeter/tests/testthat/helper-setup.R |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/tests/testthat/test_constants.R |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/tests/testthat/test_data_input.R | 54 - pricesensitivitymeter-1.3.1/pricesensitivitymeter/tests/testthat/test_data_input_fixed.R |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/tests/testthat/test_data_input_weighted.R | 34 pricesensitivitymeter-1.3.1/pricesensitivitymeter/tests/testthat/test_data_output_weighted.R | 5 pricesensitivitymeter-1.3.1/pricesensitivitymeter/tests/testthat/test_data_processing.R |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/tests/testthat/test_ecdf_bug_fix.R |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/tests/testthat/test_integration_new_modules.R |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/tests/testthat/test_validation.R |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/tests/testthat/testthat-problems.rds |only pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/interpolation-in-small-samples.Rmd | 16 pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/visualizing-psm-results.Rmd | 33 pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data.Rmd | 2 pricesensitivitymeter-1.3.1/pricesensitivitymeter/vignettes/weighted-data_cache |only 48 files changed, 636 insertions(+), 1281 deletions(-)
More information about pricesensitivitymeter at CRAN
Permanent link
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.7.3 dated 2025-07-30 and 0.7.4 dated 2025-08-23
DESCRIPTION | 6 +- MD5 | 28 ++++++------ NAMESPACE | 1 R/boxviolinplot.R | 91 +++++++++++++++++++++++++++++++++++------- R/heatmap.R | 2 R/manhattanplot.R | 6 +- R/theming.R | 10 ++++ R/utils.R | 7 ++- data/palette_list.rda |binary man/BoxViolinPlot-internal.Rd | 13 +++++- man/BoxViolinPlotAtomic.Rd | 13 +++++- man/ManhattanPlot.Rd | 4 - man/ManhattanPlotAtomic.Rd | 4 - man/boxviolinplot.Rd | 15 +++++- man/theme_this.Rd | 12 ++++- 15 files changed, 160 insertions(+), 52 deletions(-)
Title: An Interface to the Reptile Database
Description: Provides tools to retrieve and summarize taxonomic information and synonymy data for reptile species using data scraped from The Reptile Database website (<https://reptile-database.reptarium.cz/>). Outputs include clean and structured data frames useful for ecological, evolutionary, and conservation research.
Author: Joao Paulo dos Santos Vieira-Alencar [aut, cre] ,
Christoph Liedtke [aut]
Maintainer: Joao Paulo dos Santos Vieira-Alencar <joaopaulo.valencar@gmail.com>
Diff between letsRept versions 1.0.0 dated 2025-08-22 and 1.0.1 dated 2025-08-23
DESCRIPTION | 6 ++--- MD5 | 28 ++++++++++++------------- NEWS.md | 7 +++++- R/internal_functions.R | 38 +++++++++++++++++++++++++++-------- R/reptSync.R | 2 - README.md | 12 +++++++---- inst/CITATION | 2 - tests/testthat/test-reptCompare.R | 8 ++++--- tests/testthat/test-reptRefs.R | 2 - tests/testthat/test-reptSearch.R | 2 - tests/testthat/test-reptSpecies.R | 4 +-- tests/testthat/test-reptSplitCheck.R | 13 +++++++---- tests/testthat/test-reptStats.R | 2 - tests/testthat/test-reptSync.R | 12 ++++++++--- tests/testthat/test-reptSynonyms.R | 5 ++-- 15 files changed, 93 insertions(+), 50 deletions(-)
Title: Functions for Common Chart Types
Description: Wrapper for the 'ggplot2' package that creates a variety of common
charts (e.g. bar, line, area, ROC, waterfall, pie) while aiming to reduce
typing.
Author: Wojtek Kostelecki [aut, cre]
Maintainer: Wojtek Kostelecki <wojtek.kostelecki@gmail.com>
Diff between ezplot versions 0.7.13 dated 2024-01-28 and 0.8.2 dated 2025-08-23
DESCRIPTION | 18 ++++++-- MD5 | 62 +++++++++++++++--------------- NEWS.md | 8 +++ R/ez_labels.R | 12 ++++- R/variable_plot.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/bar_plot.html | 50 ++++++++++++------------ inst/doc/basics.html | 16 +++---- inst/doc/line_plot.html | 24 +++++------ inst/doc/overview.html | 24 +++++------ inst/doc/variable_plot.html | 24 ++++++----- man/ez_labels.Rd | 7 ++- man/figures/README-area_plot-1-1.png |binary man/figures/README-area_plot-2-1.png |binary man/figures/README-area_plot-3-1.png |binary man/figures/README-bar_plot-1-1.png |binary man/figures/README-bar_plot-2-1.png |binary man/figures/README-bar_plot-3-1.png |binary man/figures/README-density_plot-1-1.png |binary man/figures/README-histogram_plot-1-1.png |binary man/figures/README-lift_plot-1-1.png |binary man/figures/README-line_plot-1-1.png |binary man/figures/README-line_plot-2-1.png |binary man/figures/README-line_plot-3-1.png |binary man/figures/README-line_plot-4-1.png |binary man/figures/README-line_plot-5-1.png |binary man/figures/README-pr_plot-1-1.png |binary man/figures/README-roc_plot-1-1.png |binary man/figures/README-secondary_plot-1-1.png |binary man/figures/README-tile_plot-2-1.png |binary man/figures/README-waterfall_plot-1-1.png |binary 32 files changed, 139 insertions(+), 110 deletions(-)
Title: Fetching Data from the 'Displacement Tracking Matrix'
Description: Allows humanitarian community, academia, media, government, and non-governmental organizations to utilize the data collected by the 'Displacement Tracking Matrix' (<https://dtm.iom.int>), a unit in the International Organization for Migration. This also provides non-sensitive Internally Displaced Person figures, aggregated at the country, Admin 1 (states, provinces, or equivalent), and Admin 2 (smaller administrative areas) levels.
Author: Luong Bang Tran [aut],
Assad Asil Companioni [aut, cre],
Displacement Tracking Matrix [cph]
Maintainer: Assad Asil Companioni <aasil@iom.int>
This is a re-admission after prior archival of version 0.0.3 dated 2025-06-23
Diff between dtmapi versions 0.0.3 dated 2025-06-23 and 0.1.0 dated 2025-08-23
dtmapi-0.0.3/dtmapi/inst/doc/introduction.R |only dtmapi-0.0.3/dtmapi/inst/doc/introduction.Rmd |only dtmapi-0.0.3/dtmapi/inst/doc/introduction.html |only dtmapi-0.0.3/dtmapi/vignettes/introduction.Rmd |only dtmapi-0.1.0/dtmapi/DESCRIPTION | 25 - dtmapi-0.1.0/dtmapi/LICENSE | 4 dtmapi-0.1.0/dtmapi/MD5 | 55 +- dtmapi-0.1.0/dtmapi/NAMESPACE | 33 - dtmapi-0.1.0/dtmapi/NEWS.md |only dtmapi-0.1.0/dtmapi/R/get_all_countries.R | 81 +-- dtmapi-0.1.0/dtmapi/R/get_all_operations.R | 84 +-- dtmapi-0.1.0/dtmapi/R/get_idp_admin0_data.R | 148 ++---- dtmapi-0.1.0/dtmapi/R/get_idp_admin1_data.R | 158 +++--- dtmapi-0.1.0/dtmapi/R/get_idp_admin2_data.R | 173 +++---- dtmapi-0.1.0/dtmapi/R/get_subscription_key.R |only dtmapi-0.1.0/dtmapi/R/set_subscription_key.R |only dtmapi-0.1.0/dtmapi/README.md | 246 +++++++--- dtmapi-0.1.0/dtmapi/build/vignette.rds |binary dtmapi-0.1.0/dtmapi/inst/doc/user_guide.R |only dtmapi-0.1.0/dtmapi/inst/doc/user_guide.Rmd |only dtmapi-0.1.0/dtmapi/inst/doc/user_guide.html |only dtmapi-0.1.0/dtmapi/man/figures |only dtmapi-0.1.0/dtmapi/man/get_all_countries.Rd | 41 - dtmapi-0.1.0/dtmapi/man/get_all_operations.Rd | 42 - dtmapi-0.1.0/dtmapi/man/get_idp_admin0_data.Rd | 92 +-- dtmapi-0.1.0/dtmapi/man/get_idp_admin1_data.Rd | 102 ++-- dtmapi-0.1.0/dtmapi/man/get_idp_admin2_data.Rd | 114 ++-- dtmapi-0.1.0/dtmapi/man/get_subscription_key.Rd |only dtmapi-0.1.0/dtmapi/man/set_subscription_key.Rd |only dtmapi-0.1.0/dtmapi/tests/testthat/test-get_all_countries.R | 19 dtmapi-0.1.0/dtmapi/tests/testthat/test-get_all_operations.R | 19 dtmapi-0.1.0/dtmapi/tests/testthat/test-get_idp_admin0_data.R | 21 dtmapi-0.1.0/dtmapi/tests/testthat/test-get_idp_admin1_data.R | 22 dtmapi-0.1.0/dtmapi/tests/testthat/test-get_idp_admin2_data.R | 17 dtmapi-0.1.0/dtmapi/tests/testthat/test-set_subscription_key.R |only dtmapi-0.1.0/dtmapi/vignettes/user_guide.Rmd |only 36 files changed, 804 insertions(+), 692 deletions(-)
Title: Using CF-Compliant Calendars with Climate Projection Data
Description: Support for all calendars as specified in the Climate and Forecast
(CF) Metadata Conventions for climate and forecasting data. The CF Metadata
Conventions is widely used for distributing files with climate observations
or projections, including the Coupled Model Intercomparison Project (CMIP)
data used by climate change scientists and the Intergovernmental Panel on
Climate Change (IPCC). This package specifically allows the user to work
with any of the CF-compliant calendars (many of which are not compliant with
POSIXt). The CF time coordinate is formally defined in the CF Metadata
Conventions document available at <https://cfconventions.org/Data/cf-conventions/cf-conventions-1.12/cf-conventions.html#time-coordinate>.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between CFtime versions 1.6.2 dated 2025-05-18 and 1.7.0 dated 2025-08-23
DESCRIPTION | 13 - MD5 | 62 ++++---- NAMESPACE | 5 NEWS.md | 7 R/CFCalendar360.R | 2 R/CFCalendar365.R | 2 R/CFCalendar366.R | 2 R/CFCalendarNone.R | 1 R/CFCalendarProleptic.R | 2 R/CFClimatology.R | 6 R/CFtime-package.R | 2 R/CFtime.R | 53 +++++-- R/api.R | 84 ++++++++++- R/deprecated.R | 44 +----- README.md | 10 - inst/doc/CFtime.Rmd | 2 inst/doc/CFtime.html | 290 +++++++++++++++++++---------------------- inst/doc/Conformance.Rmd | 6 inst/doc/Conformance.html | 12 - inst/doc/Processing.Rmd | 4 inst/doc/Processing.html | 262 +++++++++++++++++-------------------- man/CFClimatology.Rd | 8 - man/CFTime.Rd | 39 +++++ man/CFtime-function.Rd | 43 +++++- man/CFtime-package.Rd | 6 man/deprecated_functions.Rd | 26 +-- tests/testthat/test-CFbounds.R | 6 tests/testthat/test-CFformat.R | 46 +++--- tests/testthat/test-CFtime.R | 6 vignettes/CFtime.Rmd | 2 vignettes/Conformance.Rmd | 6 vignettes/Processing.Rmd | 4 32 files changed, 591 insertions(+), 472 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-19 1.1.0
2025-02-05 1.0.2
2025-01-28 1.0.1
2024-12-20 1.0.0
2024-04-22 0.3.3
Title: Query the USDA NWCC Air and Water Database REST API
Description: Query the four endpoints of the 'Air and Water Database (AWDB) REST
API' maintained by the National Water and Climate Center (NWCC) at the
United States Department of Agriculture (USDA). Endpoints include data,
forecast, reference-data, and metadata. The package is extremely light
weight, with 'Rust' via 'extendr' doing most of the heavy lifting to
deserialize and flatten deeply nested 'JSON' responses. The AWDB can be
found at <https://wcc.sc.egov.usda.gov/awdbRestApi/swagger-ui/index.html>.
Author: Kenneth Blake Vernon [aut, cre, cph]
Maintainer: Kenneth Blake Vernon <kenneth.b.vernon@gmail.com>
Diff between awdb versions 0.1.2 dated 2025-04-14 and 0.1.3 dated 2025-08-23
DESCRIPTION | 12 LICENSE | 4 MD5 | 52 - NAMESPACE | 20 NEWS.md | 4 R/get-elements.R | 4 R/get-forecasts.R | 4 R/get-references.R | 2 R/get-stations.R | 4 R/import-standalone-obj-type.R | 752 ++++++++++---------- R/import-standalone-types-check.R | 1070 ++++++++++++++-------------- R/set-options.R | 93 +- README.md | 33 man/awdb.Rd | 50 - man/awdb_options.Rd | 257 +++--- man/datasets.Rd | 64 - man/figures/README-stations-1.svg | 79 +- man/get_elements.Rd | 175 ++-- man/get_forecasts.Rd | 203 ++--- man/get_references.Rd | 53 - man/get_stations.Rd | 161 ++-- src/Makevars.in | 18 src/Makevars.win.in | 12 src/awdb-win.def | 4 src/rust/src/lib.rs | 1416 +++++++++++++++++++------------------- src/rust/vendor.tar.xz |binary tools/config.R | 35 27 files changed, 2311 insertions(+), 2270 deletions(-)
Title: Complete Stochastic Modelling Solution
Description: Makes univariate, multivariate, or random fields simulations precise and simple. Just select the desired time series or random fields’ properties and it will do the rest. CoSMoS is based on the framework described in Papalexiou (2018, <doi:10.1016/j.advwatres.2018.02.013>), extended for random fields in Papalexiou and Serinaldi (2020, <doi:10.1029/2019WR026331>), and further advanced in Papalexiou et al. (2021, <doi:10.1029/2020WR029466>) to allow fine-scale space-time simulation of storms (or even cyclone-mimicking fields).
Author: Simon Michael Papalexiou [aut],
Francesco Serinaldi [aut],
Filip Strnad [aut],
Yannis Markonis [aut],
Kevin Shook [ctb, cre]
Maintainer: Kevin Shook <kevin.shook@usask.ca>
Diff between CoSMoS versions 2.1.0 dated 2021-05-29 and 2.1.1 dated 2025-08-23
DESCRIPTION | 20 MD5 | 50 - NEWS.md | 16 R/CoSMoS.R | 4 R/acs.R | 3 R/advectionF.R | 2 R/analyzeTS.R | 1 R/checkRF.r | 2 R/checkTS.R | 2 R/ecdf.R | 2 R/seasonalACF.R | 2 R/seasonalAR.R | 2 README.md | 1 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 inst/doc/vignette.R | 47 - inst/doc/vignette.Rmd | 9 inst/doc/vignette.html | 1548 +++++++++++++++++++++++++++++++--------------- man/CoSMoS-package.Rd | 9 man/acs.Rd | 1 man/advectionFspiralCE.Rd | 2 man/analyzeTS.Rd | 1 man/seasonalACF.Rd | 2 man/seasonalAR.Rd | 2 vignettes/vignette.Rmd | 9 26 files changed, 1176 insertions(+), 567 deletions(-)
Title: Animal Movement Tools
Description: Manage and analyze animal movement data. The functionality of
'amt' includes methods to calculate home ranges, track statistics
(e.g. step lengths, speed, or turning angles), prepare data for
fitting habitat selection analyses, and simulation of space-use from
fitted step-selection functions.
Author: Johannes Signer [aut, cre],
Brian Smith [ctb],
Bjoern Reineking [ctb],
Ulrike Schlaegel [ctb],
John Fieberg [ctb],
Josh O'Brien [ctb],
Bernardo Niebuhr [ctb],
Alec Robitaille [ctb],
Tal Avgar [ctb],
Gerben IJntema [ctb],
Scott LaPoint [dtc]
Maintainer: Johannes Signer <jsigner@gwdg.de>
Diff between amt versions 0.2.2.0 dated 2024-04-01 and 0.3.0.0 dated 2025-08-23
amt-0.2.2.0/amt/inst/tinytest/test_hr_isopleth.R |only amt-0.3.0.0/amt/DESCRIPTION | 14 - amt-0.3.0.0/amt/MD5 | 82 +++---- amt-0.3.0.0/amt/NAMESPACE | 4 amt-0.3.0.0/amt/NEWS.md | 14 + amt-0.3.0.0/amt/R/bbox.R | 2 amt-0.3.0.0/amt/R/cleaning.R | 2 amt-0.3.0.0/amt/R/distance_to_feature.R |only amt-0.3.0.0/amt/R/distributions.R | 4 amt-0.3.0.0/amt/R/hr_area.R | 2 amt-0.3.0.0/amt/R/hr_documentation.R | 2 amt-0.3.0.0/amt/R/hr_kde.R | 2 amt-0.3.0.0/amt/R/movement_metrics.R | 4 amt-0.3.0.0/amt/R/random_points.R | 2 amt-0.3.0.0/amt/R/random_steps.R | 11 - amt-0.3.0.0/amt/R/steps.R | 6 amt-0.3.0.0/amt/R/track_align.R | 101 ++++++--- amt-0.3.0.0/amt/build/partial.rdb |binary amt-0.3.0.0/amt/build/vignette.rds |binary amt-0.3.0.0/amt/inst/doc/p1_getting_started.html | 145 ++++++------- amt-0.3.0.0/amt/inst/doc/p2_hr.R | 44 ++-- amt-0.3.0.0/amt/inst/doc/p2_hr.Rmd | 2 amt-0.3.0.0/amt/inst/doc/p2_hr.html | 186 ++++++++-------- amt-0.3.0.0/amt/inst/doc/p3_rsf.html | 192 ++++++++--------- amt-0.3.0.0/amt/inst/doc/p4_SSF.html | 184 ++++++++-------- amt-0.3.0.0/amt/inst/doc/p5_other_packages.R | 6 amt-0.3.0.0/amt/inst/doc/p5_other_packages.Rmd | 17 + amt-0.3.0.0/amt/inst/doc/p5_other_packages.html | 242 ++++++++++++---------- amt-0.3.0.0/amt/inst/doc/p6_uhc_plots.Rmd | 4 amt-0.3.0.0/amt/inst/doc/p6_uhc_plots.html | 44 ++-- amt-0.3.0.0/amt/inst/tinytest/test_random_steps.R | 13 + amt-0.3.0.0/amt/inst/tinytest/test_steps.R | 4 amt-0.3.0.0/amt/inst/tinytest/test_track_align.R |only amt-0.3.0.0/amt/man/bandwidth_pi.Rd | 2 amt-0.3.0.0/amt/man/bbox.Rd | 2 amt-0.3.0.0/amt/man/flag_duplicates.Rd | 2 amt-0.3.0.0/amt/man/hr_area.Rd | 4 amt-0.3.0.0/amt/man/hrest.Rd | 2 amt-0.3.0.0/amt/man/random_numbers.Rd | 4 amt-0.3.0.0/amt/man/random_points.Rd | 2 amt-0.3.0.0/amt/man/track_align.Rd |only amt-0.3.0.0/amt/vignettes/p2_hr.Rmd | 2 amt-0.3.0.0/amt/vignettes/p5_other_packages.Rmd | 17 + amt-0.3.0.0/amt/vignettes/p6_uhc_plots.Rmd | 4 44 files changed, 760 insertions(+), 616 deletions(-)
Title: A 'ggplot2' Extension Inspired by 'GraphPad Prism'
Description: Provides various themes, palettes, and other functions
that are used to customise ggplots to look like they were made in 'GraphPad
Prism'. The 'Prism'-look is achieved with theme_prism() and
scale_fill|colour_prism(), axes can be changed with custom guides like
guide_prism_minor(), and significance indicators added with add_pvalue().
Author: Charlotte Dawson [aut, cre]
Maintainer: Charlotte Dawson <csdaw@outlook.com>
Diff between ggprism versions 1.0.6 dated 2025-05-17 and 1.0.7 dated 2025-08-23
DESCRIPTION | 8 ++--- MD5 | 34 ++++++++++++------------ NEWS.md | 7 +++++ R/add_pvalue.R | 5 ++- R/theme_prism.R | 6 ++-- README.md | 4 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/axes.html | 54 +++++++++++++++++++-------------------- inst/doc/colours.html | 20 +++++++------- inst/doc/ggprism.html | 14 +++++----- inst/doc/pvalues.html | 38 +++++++++++++-------------- inst/doc/themes.html | 22 +++++++-------- inst/tinytest/test-theme_prism.R | 2 - man/figures/README-ex-2.png |binary man/figures/README-ex2-1.png |binary man/figures/README-ex2-2.png |binary man/figures/README-ex3-2.png |binary 18 files changed, 112 insertions(+), 102 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with [...truncated...]
Author: Mary Meyer [aut],
Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>
Diff between cgam versions 1.28 dated 2025-07-05 and 1.29 dated 2025-08-23
ChangeLog | 7 + DESCRIPTION | 8 - MD5 | 10 +- NAMESPACE | 6 - R/cgam.R | 274 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++- man/cgam.Rd | 2 6 files changed, 292 insertions(+), 15 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-06 1.1.5
2024-07-31 1.1.4
Title: Generalized Latent Markov Models
Description: Latent Markov models for longitudinal continuous and categorical data. See Bartolucci, Pandolfi, Pennoni (2017)<doi:10.18637/jss.v081.i04>.
Author: Francesco Bartolucci [aut, cre],
Silvia Pandolfi [aut],
Fulvia Pennoni [aut],
Alessio Farcomeni [ctb],
Alessio Serafini [ctb]
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between LMest versions 3.2.6 dated 2025-06-28 and 3.2.7 dated 2025-08-23
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/est_old.R | 26 ++++++++++++++++---------- R/lmcovlatent.R | 6 ++++-- R/lmcovlatent.cont.R | 6 ++++-- R/mccov.R | 8 ++++---- R/se.R | 12 ++++++++---- inst/doc/vignetteLMest.html | 6 +++--- man/lmest.Rd | 3 ++- man/lmestMc.Rd | 2 +- 10 files changed, 55 insertions(+), 40 deletions(-)
Title: Calculating Optimum Sampling Effort in Community Ecology
Description: A system for calculating the optimal sampling effort, based on the ideas of
"Ecological cost-benefit optimization" as developed by A. Underwood (1997,
ISBN 0 521 55696 1). Data is obtained from simulated ecological communities with
prep_data() which formats and arranges the initial data, and then the
optimization follows the following procedure of four functions: (1) prep_data()
takes the original dataset and creates simulated sets that can be used as a
basis for estimating statistical power and type II error. (2) sim_beta() is used
to estimate the statistical power for the different sampling efforts specified
by the user. (3) sim_cbo() calculates then the optimal sampling effort, based
on the statistical power and the sampling costs. Additionally, (4) scompvar()
calculates the variation components necessary for (5) Underwood_cbo() to calculate
the optimal combination of number of sites and samples depending on either
an economic budget or on a desired statistical accuracy. Lastly, (6) [...truncated...]
Author: Edlin Guerra-Castro [aut, cph] ,
Arturo Sanchez-Porras [aut, cre]
Maintainer: Arturo Sanchez-Porras <sp.arturo@gmail.com>
Diff between ecocbo versions 0.12.0 dated 2024-08-21 and 0.13.0 dated 2025-08-23
ecocbo-0.12.0/ecocbo/man/SS.Rd |only ecocbo-0.12.0/ecocbo/man/balanced_sampling.Rd |only ecocbo-0.12.0/ecocbo/man/balanced_sampling2.Rd |only ecocbo-0.12.0/ecocbo/man/permanova_oneway.Rd |only ecocbo-0.12.0/ecocbo/man/permanova_twoway.Rd |only ecocbo-0.12.0/ecocbo/man/prep_data_nestedsymmetric.Rd |only ecocbo-0.12.0/ecocbo/man/prep_data_single.Rd |only ecocbo-0.12.0/ecocbo/man/prints.Rd |only ecocbo-0.13.0/ecocbo/DESCRIPTION | 51 ecocbo-0.13.0/ecocbo/MD5 | 90 - ecocbo-0.13.0/ecocbo/NAMESPACE | 40 ecocbo-0.13.0/ecocbo/NEWS.md | 19 ecocbo-0.13.0/ecocbo/R/data.R |only ecocbo-0.13.0/ecocbo/R/plot_power.R | 267 +--- ecocbo-0.13.0/ecocbo/R/plot_power0.R |only ecocbo-0.13.0/ecocbo/R/prep_data.R | 104 - ecocbo-0.13.0/ecocbo/R/prep_data0.R | 367 ++++-- ecocbo-0.13.0/ecocbo/R/scompvar.R | 85 - ecocbo-0.13.0/ecocbo/R/sim_beta.R | 192 ++- ecocbo-0.13.0/ecocbo/R/sim_cbo.R | 211 ++- ecocbo-0.13.0/ecocbo/R/underwood_cbo.R |only ecocbo-0.13.0/ecocbo/R/utils-globals.R |only ecocbo-0.13.0/ecocbo/R/utils.R | 583 +++++++--- ecocbo-0.13.0/ecocbo/README.md | 54 ecocbo-0.13.0/ecocbo/build/partial.rdb |only ecocbo-0.13.0/ecocbo/build/vignette.rds |binary ecocbo-0.13.0/ecocbo/data/betaNested.rda |only ecocbo-0.13.0/ecocbo/data/epiBetaR.rda |only ecocbo-0.13.0/ecocbo/data/macrofDat.rda |only ecocbo-0.13.0/ecocbo/data/simResults.rda |binary ecocbo-0.13.0/ecocbo/data/simResultsNested.rda |only ecocbo-0.13.0/ecocbo/inst/doc/ecocbo-guide.R | 34 ecocbo-0.13.0/ecocbo/inst/doc/ecocbo-guide.Rmd | 88 - ecocbo-0.13.0/ecocbo/inst/doc/ecocbo-guide.html | 231 +-- ecocbo-0.13.0/ecocbo/man/Underwood_cbo.Rd |only ecocbo-0.13.0/ecocbo/man/betaNested.Rd |only ecocbo-0.13.0/ecocbo/man/density_plot.Rd |only ecocbo-0.13.0/ecocbo/man/ecocbo-package.Rd | 15 ecocbo-0.13.0/ecocbo/man/epiBetaR.Rd |only ecocbo-0.13.0/ecocbo/man/epiDat.Rd | 24 ecocbo-0.13.0/ecocbo/man/figures/README-unnamed-chunk-3-1.png |binary ecocbo-0.13.0/ecocbo/man/macrofDat.Rd |only ecocbo-0.13.0/ecocbo/man/plot_power.Rd | 85 - ecocbo-0.13.0/ecocbo/man/power_curve.Rd |only ecocbo-0.13.0/ecocbo/man/prep_data.Rd | 94 - ecocbo-0.13.0/ecocbo/man/print.cbo_result.Rd |only ecocbo-0.13.0/ecocbo/man/print.ecocbo_beta.Rd |only ecocbo-0.13.0/ecocbo/man/scompvar.Rd | 30 ecocbo-0.13.0/ecocbo/man/simResults.Rd | 63 - ecocbo-0.13.0/ecocbo/man/simResultsNested.Rd |only ecocbo-0.13.0/ecocbo/man/sim_beta.Rd | 51 ecocbo-0.13.0/ecocbo/man/sim_cbo.Rd | 46 ecocbo-0.13.0/ecocbo/man/surface_plot.Rd |only ecocbo-0.13.0/ecocbo/tests/testthat/test-Underwood_cbo.R |only ecocbo-0.13.0/ecocbo/tests/testthat/test-plot_power.R | 12 ecocbo-0.13.0/ecocbo/tests/testthat/test-prep_data.R | 8 ecocbo-0.13.0/ecocbo/tests/testthat/test-scompvar.R | 5 ecocbo-0.13.0/ecocbo/tests/testthat/test-sim_beta.R | 3 ecocbo-0.13.0/ecocbo/tests/testthat/test-sim_cbo.R | 13 ecocbo-0.13.0/ecocbo/vignettes/ecocbo-guide.Rmd | 88 - 60 files changed, 1742 insertions(+), 1211 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-12-12 0.3.1
2024-10-29 0.3.0
Title: Interactive 'OpenAI' Model Integration in 'RStudio'
Description: Offers an interactive 'RStudio' gadget interface for communicating
with 'OpenAI' large language models (e.g., 'gpt-5', 'gpt-5-mini', 'gpt-5-nano')
(<https://platform.openai.com/docs/api-reference>).
Enables users to conduct multiple chat conversations simultaneously in
separate tabs. Supports uploading local files (R, PDF, DOCX) to provide
context for the models. Allows per-conversation configuration of system
messages (where supported by the model). API interactions via the 'httr'
package are performed asynchronously using 'promises' and 'future' to avoid
blocking the R console. Useful for tasks like code generation, text
summarization, and document analysis directly within the 'RStudio' environment.
Requires an 'OpenAI' API key set as an environment variable.
Author: Antoni Czolgowski [aut, cre]
Maintainer: Antoni Czolgowski <antoni.czolgowski@gmail.com>
Diff between PacketLLM versions 0.1.0 dated 2025-04-24 and 0.1.1 dated 2025-08-23
PacketLLM-0.1.0/PacketLLM/man/set_conversation_temperature.Rd |only PacketLLM-0.1.1/PacketLLM/DESCRIPTION | 22 PacketLLM-0.1.1/PacketLLM/MD5 | 83 PacketLLM-0.1.1/PacketLLM/NAMESPACE | 1 PacketLLM-0.1.1/PacketLLM/NEWS.md | 6 PacketLLM-0.1.1/PacketLLM/R/advanced_settings.R | 93 PacketLLM-0.1.1/PacketLLM/R/chat_logic.R | 253 -- PacketLLM-0.1.1/PacketLLM/R/history_menager.R | 1049 +--------- PacketLLM-0.1.1/PacketLLM/R/llm_chat_app.R | 409 +-- PacketLLM-0.1.1/PacketLLM/R/openai_api.R | 169 - PacketLLM-0.1.1/PacketLLM/README.md | 11 PacketLLM-0.1.1/PacketLLM/build/vignette.rds |binary PacketLLM-0.1.1/PacketLLM/inst/doc/PacketLLM-introduction.Rmd | 7 PacketLLM-0.1.1/PacketLLM/inst/doc/PacketLLM-introduction.html | 17 PacketLLM-0.1.1/PacketLLM/man/add_attachment_to_active_conversation.Rd | 47 PacketLLM-0.1.1/PacketLLM/man/add_message_to_active_history.Rd | 56 PacketLLM-0.1.1/PacketLLM/man/add_user_message.Rd | 34 PacketLLM-0.1.1/PacketLLM/man/available_openai_models.Rd | 2 PacketLLM-0.1.1/PacketLLM/man/call_openai_chat.Rd | 67 PacketLLM-0.1.1/PacketLLM/man/check_api_key.Rd | 23 PacketLLM-0.1.1/PacketLLM/man/create_new_conversation.Rd | 40 PacketLLM-0.1.1/PacketLLM/man/delete_conversation.Rd | 42 PacketLLM-0.1.1/PacketLLM/man/get_active_chat_history.Rd | 34 PacketLLM-0.1.1/PacketLLM/man/get_active_conversation.Rd | 32 PacketLLM-0.1.1/PacketLLM/man/get_active_conversation_attachments.Rd | 37 PacketLLM-0.1.1/PacketLLM/man/get_active_conversation_id.Rd | 29 PacketLLM-0.1.1/PacketLLM/man/get_all_conversation_ids.Rd | 32 PacketLLM-0.1.1/PacketLLM/man/get_assistant_response.Rd | 42 PacketLLM-0.1.1/PacketLLM/man/get_conversation_attachments.Rd | 36 PacketLLM-0.1.1/PacketLLM/man/get_conversation_data.Rd | 31 PacketLLM-0.1.1/PacketLLM/man/get_conversation_history.Rd | 35 PacketLLM-0.1.1/PacketLLM/man/get_conversation_model.Rd | 26 PacketLLM-0.1.1/PacketLLM/man/get_conversation_title.Rd | 27 PacketLLM-0.1.1/PacketLLM/man/initialize_history_manager.Rd | 23 PacketLLM-0.1.1/PacketLLM/man/is_conversation_started.Rd | 36 PacketLLM-0.1.1/PacketLLM/man/reset_history_manager.Rd | 31 PacketLLM-0.1.1/PacketLLM/man/run_llm_chat_app.Rd | 21 PacketLLM-0.1.1/PacketLLM/man/set_active_conversation.Rd | 38 PacketLLM-0.1.1/PacketLLM/man/set_conversation_model.Rd | 52 PacketLLM-0.1.1/PacketLLM/man/set_conversation_system_message.Rd | 42 PacketLLM-0.1.1/PacketLLM/tests/testthat/test-chat_logic_formatting.R | 169 - PacketLLM-0.1.1/PacketLLM/tests/testthat/test-history_manager.R | 121 - PacketLLM-0.1.1/PacketLLM/vignettes/PacketLLM-introduction.Rmd | 7 43 files changed, 733 insertions(+), 2599 deletions(-)
Title: Date/Time Classes Based on Jalali Calendar
Description: Implements S3 classes for storing dates and date-times based on the Jalali calendar.
The main design goal of 'shide' is consistency with base R's 'Date' and 'POSIXct'.
It provide features such as: date-time parsing, formatting and arithmetic.
Author: Mohsen Mollayi [aut, cre, cph]
Maintainer: Mohsen Mollayi <mmollayi@gmail.com>
Diff between shide versions 0.2.1 dated 2024-07-19 and 0.3.0 dated 2025-08-23
shide-0.2.1/shide/src/jalali.cpp |only shide-0.2.1/shide/src/jalali.h |only shide-0.2.1/shide/src/sh_year_month_day.h |only shide-0.3.0/shide/DESCRIPTION | 14 - shide-0.3.0/shide/MD5 | 70 ++--- shide-0.3.0/shide/NAMESPACE | 4 shide-0.3.0/shide/NEWS.md | 12 shide-0.3.0/shide/R/cpp11.R | 8 shide-0.3.0/shide/R/round.R | 83 ++++-- shide-0.3.0/shide/R/seq.R | 290 +++++++++++++++------- shide-0.3.0/shide/R/update.R | 4 shide-0.3.0/shide/R/utils.R | 4 shide-0.3.0/shide/README.md | 19 - shide-0.3.0/shide/inst |only shide-0.3.0/shide/man/seq.jdate.Rd | 152 +++++------ shide-0.3.0/shide/man/seq.jdatetime.Rd |only shide-0.3.0/shide/man/sh_round.Rd | 102 ++++--- shide-0.3.0/shide/src/Makevars |only shide-0.3.0/shide/src/Makevars.win |only shide-0.3.0/shide/src/accessors.cpp | 62 +--- shide-0.3.0/shide/src/cpp11.cpp | 16 + shide-0.3.0/shide/src/format.cpp | 17 - shide-0.3.0/shide/src/leap_years.cpp | 13 shide-0.3.0/shide/src/make.cpp | 209 ++------------- shide-0.3.0/shide/src/parse.cpp | 41 +-- shide-0.3.0/shide/src/round.cpp | 209 ++++++--------- shide-0.3.0/shide/src/seq.cpp | 49 --- shide-0.3.0/shide/src/shide.h | 9 shide-0.3.0/shide/src/utils.cpp | 34 -- shide-0.3.0/shide/src/zone.cpp | 8 shide-0.3.0/shide/tests/testthat/test-jdate.R | 7 shide-0.3.0/shide/tests/testthat/test-jdatetime.R | 11 shide-0.3.0/shide/tests/testthat/test-round.R | 251 +++++++++++++++++-- shide-0.3.0/shide/tests/testthat/test-seq.R | 75 +++++ shide-0.3.0/shide/tests/testthat/test-setters.R | 5 shide-0.3.0/shide/tests/testthat/test-update.R | 38 ++ 36 files changed, 1049 insertions(+), 767 deletions(-)
Title: Occurrence Data Cleaning
Description: Flags and checks occurrence data that are in Darwin Core
format. The package includes generic functions and data as well as
some that are specific to bees. This package is meant to build upon
and be complimentary to other excellent occurrence cleaning packages,
including 'bdc' and 'CoordinateCleaner'. This package uses datasets
from several sources and particularly from the Discover Life Website,
created by Ascher and Pickering (2020). For further information,
please see the original publication and package website. Publication
- Dorey et al. (2023) <doi:10.1101/2023.06.30.547152> and package
website - Dorey et al. (2023) <https://github.com/jbdorey/BeeBDC>.
Author: James B. Dorey [aut, cre, cph] ,
Robert L. O'Reilly [aut] ,
Silas Bossert [aut] ,
Erica E. Fischer [aut]
Maintainer: James B. Dorey <jbdorey@me.com>
Diff between BeeBDC versions 1.2.1 dated 2024-11-03 and 1.3.0 dated 2025-08-23
BeeBDC-1.2.1/BeeBDC/R/continentOutliers.R |only BeeBDC-1.2.1/BeeBDC/R/testChecklist.R |only BeeBDC-1.2.1/BeeBDC/R/testTaxonomy.R |only BeeBDC-1.2.1/BeeBDC/build |only BeeBDC-1.2.1/BeeBDC/data/testChecklist.rda |only BeeBDC-1.2.1/BeeBDC/data/testTaxonomy.rda |only BeeBDC-1.2.1/BeeBDC/inst/doc |only BeeBDC-1.2.1/BeeBDC/man/continentOutlieRs.Rd |only BeeBDC-1.2.1/BeeBDC/man/testChecklist.Rd |only BeeBDC-1.2.1/BeeBDC/man/testTaxonomy.Rd |only BeeBDC-1.2.1/BeeBDC/tests/testthat/test-continentOutlieRs.R |only BeeBDC-1.2.1/BeeBDC/vignettes |only BeeBDC-1.3.0/BeeBDC/DESCRIPTION | 30 BeeBDC-1.3.0/BeeBDC/MD5 | 181 +-- BeeBDC-1.3.0/BeeBDC/NAMESPACE | 8 BeeBDC-1.3.0/BeeBDC/NEWS.md | 22 BeeBDC-1.3.0/BeeBDC/R/ChaoWrapper.R |only BeeBDC-1.3.0/BeeBDC/R/ColTypeR.R | 128 +- BeeBDC-1.3.0/BeeBDC/R/HarmoniseR.R | 16 BeeBDC-1.3.0/BeeBDC/R/additionalData_readRs.R | 100 - BeeBDC-1.3.0/BeeBDC/R/atlasDownloader.R | 7 BeeBDC-1.3.0/BeeBDC/R/beesChecklist.R | 14 BeeBDC-1.3.0/BeeBDC/R/beesCountrySubset.R |only BeeBDC-1.3.0/BeeBDC/R/beesTaxonomy.R | 11 BeeBDC-1.3.0/BeeBDC/R/countryHarmoniseR.R |only BeeBDC-1.3.0/BeeBDC/R/countryOutliers.R | 29 BeeBDC-1.3.0/BeeBDC/R/dateFindR.R | 635 ++++++++--- BeeBDC-1.3.0/BeeBDC/R/dupePlotR.R | 8 BeeBDC-1.3.0/BeeBDC/R/dupeSummary.R | 2 BeeBDC-1.3.0/BeeBDC/R/flagAbsent.R | 11 BeeBDC-1.3.0/BeeBDC/R/flagLicense.R | 6 BeeBDC-1.3.0/BeeBDC/R/formattedCombiner.R | 6 BeeBDC-1.3.0/BeeBDC/R/ggRichnessWrapper.R |only BeeBDC-1.3.0/BeeBDC/R/iNEXTwrapper.R |only BeeBDC-1.3.0/BeeBDC/R/interactiveMapR.R | 133 +- BeeBDC-1.3.0/BeeBDC/R/jbd_CfC_chunker.R | 6 BeeBDC-1.3.0/BeeBDC/R/jbd_Ctrans_chunker.R | 3 BeeBDC-1.3.0/BeeBDC/R/jbd_coordCountryInconsistent.R | 54 BeeBDC-1.3.0/BeeBDC/R/jbd_coordinates_transposed.R | 4 BeeBDC-1.3.0/BeeBDC/R/jbd_correct_coordinates.R | 6 BeeBDC-1.3.0/BeeBDC/R/jbd_create_figures.R | 1 BeeBDC-1.3.0/BeeBDC/R/plotFlagSummary.R | 3 BeeBDC-1.3.0/BeeBDC/R/richnessEstimateR.R |only BeeBDC-1.3.0/BeeBDC/R/richnessPrepR.R |only BeeBDC-1.3.0/BeeBDC/R/summaryFun.R | 18 BeeBDC-1.3.0/BeeBDC/R/summaryMaps.R | 19 BeeBDC-1.3.0/BeeBDC/R/taxadbToBeeBDC.R | 51 BeeBDC-1.3.0/BeeBDC/R/taxoDuplicator.R | 4 BeeBDC-1.3.0/BeeBDC/R/tibble_utils.R |only BeeBDC-1.3.0/BeeBDC/R/toyData_bees3sp.R | 4 BeeBDC-1.3.0/BeeBDC/R/toyData_beesFlagged.R | 5 BeeBDC-1.3.0/BeeBDC/R/toyData_beesRaw.R | 4 BeeBDC-1.3.0/BeeBDC/README.md | 103 + BeeBDC-1.3.0/BeeBDC/data/beesCountrySubset.rda |only BeeBDC-1.3.0/BeeBDC/inst/BeeBDC_basicWorkflow.R | 18 BeeBDC-1.3.0/BeeBDC/inst/BeeBDC_fullWorkflow.R | 54 BeeBDC-1.3.0/BeeBDC/inst/CITATION | 12 BeeBDC-1.3.0/BeeBDC/inst/extdata/testChecklist.rda |binary BeeBDC-1.3.0/BeeBDC/inst/extdata/testTaxonomy.rda |binary BeeBDC-1.3.0/BeeBDC/man/ChaoWrapper.Rd |only BeeBDC-1.3.0/BeeBDC/man/ColTypeR.Rd | 15 BeeBDC-1.3.0/BeeBDC/man/atlasDownloader.Rd | 4 BeeBDC-1.3.0/BeeBDC/man/bees3sp.Rd | 4 BeeBDC-1.3.0/BeeBDC/man/beesChecklist.Rd | 21 BeeBDC-1.3.0/BeeBDC/man/beesCountrySubset.Rd |only BeeBDC-1.3.0/BeeBDC/man/beesFlagged.Rd | 4 BeeBDC-1.3.0/BeeBDC/man/beesRaw.Rd | 4 BeeBDC-1.3.0/BeeBDC/man/beesTaxonomy.Rd | 11 BeeBDC-1.3.0/BeeBDC/man/countryHarmoniseR.Rd |only BeeBDC-1.3.0/BeeBDC/man/countryOutlieRs.Rd | 9 BeeBDC-1.3.0/BeeBDC/man/dateFindR.Rd | 7 BeeBDC-1.3.0/BeeBDC/man/dupePlotR.Rd | 6 BeeBDC-1.3.0/BeeBDC/man/ggRichnessWrapper.Rd |only BeeBDC-1.3.0/BeeBDC/man/harmoniseR.Rd | 16 BeeBDC-1.3.0/BeeBDC/man/iNEXTwrapper.Rd |only BeeBDC-1.3.0/BeeBDC/man/interactiveMapR.Rd | 28 BeeBDC-1.3.0/BeeBDC/man/jbd_CfC_chunker.Rd | 2 BeeBDC-1.3.0/BeeBDC/man/jbd_Ctrans_chunker.Rd | 2 BeeBDC-1.3.0/BeeBDC/man/jbd_coordCountryInconsistent.Rd | 7 BeeBDC-1.3.0/BeeBDC/man/jbd_coordinates_transposed.Rd | 4 BeeBDC-1.3.0/BeeBDC/man/readr_BeeBDC.Rd | 55 BeeBDC-1.3.0/BeeBDC/man/richnessEstimateR.Rd |only BeeBDC-1.3.0/BeeBDC/man/richnessPrepR.Rd |only BeeBDC-1.3.0/BeeBDC/man/summaryFun.Rd | 6 BeeBDC-1.3.0/BeeBDC/man/summaryMaps.Rd | 11 BeeBDC-1.3.0/BeeBDC/man/taxadbToBeeBDC.Rd | 8 BeeBDC-1.3.0/BeeBDC/tests/testthat/test-HarmoniseR.R | 8 BeeBDC-1.3.0/BeeBDC/tests/testthat/test-beesChecklist.R | 8 BeeBDC-1.3.0/BeeBDC/tests/testthat/test-countryOutlieRs.R | 11 BeeBDC-1.3.0/BeeBDC/tests/testthat/test-dateFindR.R | 115 + BeeBDC-1.3.0/BeeBDC/tests/testthat/test-dupePlotR.R | 20 BeeBDC-1.3.0/BeeBDC/tests/testthat/test-flagAbsent.R | 92 - BeeBDC-1.3.0/BeeBDC/tests/testthat/test-formattedCombiner.R | 17 BeeBDC-1.3.0/BeeBDC/tests/testthat/test-idMatchR.R | 3 BeeBDC-1.3.0/BeeBDC/tests/testthat/test-interactiveMapR.R | 6 BeeBDC-1.3.0/BeeBDC/tests/testthat/test-jbd_CfC_chunker.R | 5 BeeBDC-1.3.0/BeeBDC/tests/testthat/test-jbd_Ctrans_chunker.R | 10 BeeBDC-1.3.0/BeeBDC/tests/testthat/test-jbd_create_figures.R | 36 BeeBDC-1.3.0/BeeBDC/tests/testthat/test-plotFlagSummary.R | 18 BeeBDC-1.3.0/BeeBDC/tests/testthat/test-readr_BeeBDC.R | 18 BeeBDC-1.3.0/BeeBDC/tests/testthat/test-richnessPrepR.R |only BeeBDC-1.3.0/BeeBDC/tests/testthat/test-summaryMaps.R | 20 BeeBDC-1.3.0/BeeBDC/tests/testthat/test-taxadbToBeeBDC.R | 12 103 files changed, 1375 insertions(+), 964 deletions(-)
Title: Vertical and Horizontal Inheritance Consistence Analysis
Description: The "Vertical and Horizontal Inheritance Consistence Analysis" method is described in the following publication: "VHICA: a new method to discriminate between vertical and horizontal transposon transfer: application to the mariner family within Drosophila" by G. Wallau. et al. (2016) <DOI:10.1093/molbev/msv341>. The purpose of the method is to detect horizontal transfers of transposable elements, by contrasting the divergence of transposable element sequences with that of regular genes.
Author: Arnaud Le Rouzic [aut, cre]
Maintainer: Arnaud Le Rouzic <arnaud.le-rouzic@universite-paris-saclay.fr>
Diff between vhica versions 0.2.8 dated 2023-03-08 and 0.2.9 dated 2025-08-23
DESCRIPTION | 14 +++++++++----- MD5 | 16 ++++++++-------- R/vhica-internal.R | 2 +- man/div.Rd | 6 +++--- man/image.vhica.Rd | 4 ++-- man/plot.vhica.Rd | 2 +- man/read.vhica.Rd | 37 +++++++++++++++++++------------------ man/summary.vhicaimage.Rd | 2 +- man/vhica-package.Rd | 8 ++++---- 9 files changed, 48 insertions(+), 43 deletions(-)
Title: Meteorological Data Processing
Description: Set of tools aimed at processing meteorological data, converting hourly recorded data to daily, monthly and annual data.
Author: Wagner Martins dos Santos [aut, cre] ,
Hoi Leong Lee [aut],
Edimir Xavier Leal Ferraz [aut] ,
Abelardo Antonio de Assuncao Montenegro [aut],
Lady Daiane Costa de Sousa Martins [aut] ,
Alan Cezar Bezerra [aut],
Ênio Farias de Franca e Silva [aut],
Thi [...truncated...]
Maintainer: Wagner Martins dos Santos <wagnnerms97@gmail.com>
Diff between DataMetProcess versions 1.0.5 dated 2025-05-12 and 1.0.6 dated 2025-08-23
DESCRIPTION | 16 +++++++++------- MD5 | 8 ++++---- R/adjustDate.R | 14 ++++++++++++++ R/list_inmet.R | 32 ++++++++++++++++++++++++-------- inst/doc/DataMetProcess-vignette.html | 2 +- 5 files changed, 52 insertions(+), 20 deletions(-)
More information about DataMetProcess at CRAN
Permanent link
Title: Complementary Genomic Functions
Description: Presents a series of molecular and genetic routines in the R
environment with the aim of assisting in analytical pipelines before
and after the use of 'asreml' or another library to perform analyses such
as Genomic Selection or Genome-Wide Association Analyses.
Methods and examples are described in Gezan, Oliveira, Galli, and Murray (2022)
<https://asreml.kb.vsni.co.uk/wp-content/uploads/sites/3/ASRgenomics_Manual.pdf>.
Author: Salvador Gezan [aut, cre],
Darren Murray [aut],
Amanda Avelar de Oliveira [aut],
Giovanni Galli [aut],
VSN International [cph]
Maintainer: Salvador Gezan <salvador.gezan@vsni.co.uk>
Diff between ASRgenomics versions 1.1.4 dated 2024-01-29 and 1.1.5 dated 2025-08-23
DESCRIPTION | 10 MD5 | 42 - NEWS.md | 176 +++---- R/ASRgenomics-package.R | 91 ++- R/G_tuneup.R | 566 +++++++++++----------- R/Kinship_pca.R | 364 +++++++------- R/auxiliar.R | 29 - R/check_args.R | 288 +++++------ R/kinship_diagnostics.R | 548 +++++++++++----------- R/snp_pca.R | 348 +++++++------- R/snp_pruning.R | 908 ++++++++++++++++++------------------ R/snp_recode.R | 630 ++++++++++++------------- R/synthetic_cross.R | 960 +++++++++++++++++++-------------------- README.md | 75 +-- inst/CITATION | 22 inst/WORDLIST | 220 ++++---- man/G.inverse.Rd | 2 man/G.tuneup.Rd | 2 tests/testthat/test-checkargs.R | 90 +-- tests/testthat/test-kinshippca.R | 29 - tests/testthat/test-qc.R | 106 ++-- tests/testthat/test-snpPCA.R | 10 22 files changed, 2772 insertions(+), 2744 deletions(-)
Title: Boosting Functional Regression Models
Description: Regression models for functional data, i.e.,
scalar-on-function, function-on-scalar and function-on-function
regression models, are fitted by a component-wise gradient boosting
algorithm. For a manual on how to use 'FDboost', see Brockhaus,
Ruegamer, Greven (2017) <doi:10.18637/jss.v094.i10>.
Author: Sarah Brockhaus [aut] ,
David Ruegamer [aut, cre] ,
Almond Stoecker [aut] ,
Torsten Hothorn [ctb] ,
with contributions by many others [ctb]
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Diff between FDboost versions 1.1-2 dated 2023-08-12 and 1.1-3 dated 2025-08-23
FDboost-1.1-2/FDboost/inst/NEWS.Rd |only FDboost-1.1-2/FDboost/vignettes/density-on-scalar_birth-concordance.tex |only FDboost-1.1-3/FDboost/DESCRIPTION | 67 +-- FDboost-1.1-3/FDboost/MD5 | 79 +-- FDboost-1.1-3/FDboost/NEWS.md |only FDboost-1.1-3/FDboost/R/FDboost-package.R | 128 +++--- FDboost-1.1-3/FDboost/R/FDboost.R | 132 +++--- FDboost-1.1-3/FDboost/R/FDboostLSS.R | 20 FDboost-1.1-3/FDboost/R/baselearners.R | 100 ++-- FDboost-1.1-3/FDboost/R/baselearnersX.R | 12 FDboost-1.1-3/FDboost/R/bootstrapCIs.R | 46 +- FDboost-1.1-3/FDboost/R/constrainedX.R | 60 +- FDboost-1.1-3/FDboost/R/crossvalidation.R | 162 +++---- FDboost-1.1-3/FDboost/R/factorize.R | 10 FDboost-1.1-3/FDboost/R/hmatrix.R | 16 FDboost-1.1-3/FDboost/R/methods.R | 208 +++++----- FDboost-1.1-3/FDboost/R/stabsel.R | 6 FDboost-1.1-3/FDboost/R/utilityFunctions.R | 98 ++-- FDboost-1.1-3/FDboost/build/vignette.rds |binary FDboost-1.1-3/FDboost/inst/CITATION | 13 FDboost-1.1-3/FDboost/inst/doc/FLAM_canada.R | 28 - FDboost-1.1-3/FDboost/inst/doc/FLAM_canada.pdf |binary FDboost-1.1-3/FDboost/inst/doc/FLAM_fuel.R | 66 +-- FDboost-1.1-3/FDboost/inst/doc/FLAM_fuel.pdf |binary FDboost-1.1-3/FDboost/inst/doc/FLAM_viscosity.R | 94 ++-- FDboost-1.1-3/FDboost/inst/doc/FLAM_viscosity.pdf |binary FDboost-1.1-3/FDboost/inst/doc/density-on-scalar_birth.pdf |binary FDboost-1.1-3/FDboost/man/FDboost-package.Rd | 79 +-- FDboost-1.1-3/FDboost/man/FDboost.Rd | 14 FDboost-1.1-3/FDboost/man/FDboostLSS.Rd | 6 FDboost-1.1-3/FDboost/man/applyFolds.Rd | 2 FDboost-1.1-3/FDboost/man/bootstrapCI.Rd | 2 FDboost-1.1-3/FDboost/man/coef.FDboost.Rd | 2 FDboost-1.1-3/FDboost/man/cvrisk.FDboostLSS.Rd | 12 FDboost-1.1-3/FDboost/man/factorize.Rd | 8 FDboost-1.1-3/FDboost/man/hmatrix.Rd | 6 FDboost-1.1-3/FDboost/man/predict.FDboost.Rd | 4 FDboost-1.1-3/FDboost/man/predict.FDboost_fac.Rd | 2 FDboost-1.1-3/FDboost/man/validateFDboost.Rd | 2 FDboost-1.1-3/FDboost/tests/factorize_test_irregular.R | 4 FDboost-1.1-3/FDboost/tests/factorize_test_regular.R | 4 FDboost-1.1-3/FDboost/tests/general_tests.R | 2 42 files changed, 752 insertions(+), 742 deletions(-)
Title: Estimating and Mapping Disaggregated Indicators
Description: Functions that support estimating, assessing and mapping regional
disaggregated indicators. So far, estimation methods comprise direct estimation,
the model-based unit-level approach Empirical Best Prediction (see "Small area
estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>),
the area-level model (see "Estimates of income for small places: An
application of James-Stein procedures to Census Data" by Fay and Herriot (1979)
<doi:10.1080/01621459.1979.10482505>) and various extensions of it (adjusted variance
estimation methods, log and arcsin transformation, spatial, robust and measurement
error models), as well as their precision estimates. The assessment of the used model
is supported by a summary and diagnostic plots. For a suitable presentation of
estimates, map plots can be easily created. Furthermore, results can easily be
exported to excel. For a detailed description of the package and the methods used
see "The R Package emdi for Estima [...truncated...]
Author: Sylvia Harmening [aut],
Ann-Kristin Kreutzmann [aut],
Soeren Pannier [aut, cre],
Felix Skarke [aut],
Natalia Rojas-Perilla [aut],
Nicola Salvati [aut],
Timo Schmid [aut],
Matthias Templ [aut],
Nikos Tzavidis [aut],
Nora Wuerz [aut]
Maintainer: Soeren Pannier <soeren.pannier@fu-berlin.de>
Diff between emdi versions 2.2.2 dated 2024-06-11 and 2.2.3 dated 2025-08-23
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 8 +++++++- R/eblup_robust.R | 3 ++- R/emdi.R | 1 + R/write.excel.emdi.R | 4 ++-- build/vignette.rds |binary inst/CITATION | 27 ++++++++++++++++++++++++++- man/emdi.Rd | 26 ++++++++++++++++++++++++++ man/write.excel.Rd | 4 ++-- 10 files changed, 80 insertions(+), 21 deletions(-)
Title: Selecting General Circulation Models for Species Distribution
Modeling
Description: Methods to help selecting General Circulation Models (GCMs)
in the context of projecting models to future scenarios. It is provided
clusterization algorithms, distance and correlation metrics, as well as
a tailor-made algorithm to detect the optimum subset of GCMs that recreate
the environment of all GCMs as proposed in Esser et al. (2025) <doi:10.1111/gcb.70008>.
Author: Dayani Bailly [aut] ,
Reginaldo Re [aut] ,
Marcos R. Lima [aut] ,
Luiz Esser [aut, cre, cph]
Maintainer: Luiz Esser <luizesser@gmail.com>
Diff between chooseGCM versions 1.1 dated 2025-08-18 and 1.2 dated 2025-08-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 ++++- tests/testthat/test-env_gcms.R | 18 +++++++++--------- tests/testthat/test-optk_gcms.R | 8 +++----- 5 files changed, 23 insertions(+), 22 deletions(-)
Title: Extra Functionality for the 'xpose' Package
Description: Adding some at-present missing functionality, or functions
unlikely to be added to the base 'xpose' package. This includes some
diagnostic plots that have been missing in translation from 'xpose4',
but also some useful features that truly extend the capabilities of what
can be done with 'xpose'. These extensions include the concept of a set of
'xpose' objects, and diagnostics for likelihood-based models.
Author: John Prybylski [aut, cre, cph]
Maintainer: John Prybylski <jprybylski@gmail.com>
Diff between xpose.xtras versions 0.0.2 dated 2024-11-21 and 0.0.3 dated 2025-08-23
DESCRIPTION | 15 MD5 | 99 - NEWS.md | 7 R/categorical.R | 939 ++++++------ R/covariates.R | 1396 ++++++++--------- R/fixes.R | 874 +++++++---- R/modavg_xpdb.R | 582 +++---- R/utils.R | 844 +++++----- R/xp_xtras.R | 1508 +++++++++---------- R/xplot_boxplot.R | 453 ++--- R/xplot_pairs.R | 249 ++- R/xpose_set.R | 2566 ++++++++++++++++----------------- R/xset_diagram.R | 100 - R/xset_features.R | 488 +++--- R/xset_plots.R | 2350 +++++++++++++++--------------- R/xset_shark.R | 910 +++++------ R/xset_waterfall.R | 750 ++++----- R/xtra_pars.R | 2142 +++++++++++++-------------- R/xtra_plots.R | 697 ++++---- R/zzz.R | 14 README.md | 18 build/vignette.rds |binary data/pheno_base.rda |binary data/pheno_final.rda |binary data/pheno_saem.rda |binary data/pheno_set.rda |binary data/pkpd_m3_df.rda |binary data/vismo_dtmm.rda |binary data/vismo_pomod.rda |binary data/vismodegib.rda |binary data/xpdb_set.rda |binary data/xpdb_x.rda |binary inst/doc/a01-the-xp_xtra-object.R | 4 inst/doc/a01-the-xp_xtra-object.Rmd | 318 ++-- inst/doc/a01-the-xp_xtra-object.html | 9 inst/doc/a02-xpose-sets.Rmd | 348 ++-- inst/doc/a02-xpose-sets.html | 18 inst/doc/a03-useful_plots.Rmd | 200 +- inst/doc/a03-useful_plots.html | 31 man/catdv_vs_dvprobs.Rd | 1 man/convenience.Rd | 34 man/figures/README-m3-1.png |binary man/figures/README-shark-1.png |binary man/print.xpose_plot.Rd |only man/xpose.xtras-package.Rd | 2 tests/testthat/_snaps/xset_features.md | 56 tests/testthat/test-xp_xtras.R | 18 tests/testthat/test-xplot_boxplot.R | 25 vignettes/a01-the-xp_xtra-object.Rmd | 318 ++-- vignettes/a02-xpose-sets.Rmd | 348 ++-- vignettes/a03-useful_plots.Rmd | 200 +- 51 files changed, 9655 insertions(+), 9276 deletions(-)
Title: R Interface to W3C Markup Validation Services
Description: R interface to a W3C Markup Validation service.
See <https://validator.w3.org/> for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between W3CMarkupValidator versions 0.2-0 dated 2025-08-21 and 0.2-1 dated 2025-08-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/w3c.R | 27 ++++++++++++++++++++------- 3 files changed, 25 insertions(+), 12 deletions(-)
More information about W3CMarkupValidator at CRAN
Permanent link
Title: Mander and Thompson Designs
Description: Implements Mander & Thompson's (2010)
<doi:10.1016/j.cct.2010.07.008> methods for two-stage designs
optimal under the alternative hypothesis for phase II [cancer] trials. Also
provides an implementation of Simon's (1989)
<doi:10.1016/0197-2456(89)90015-9> original methodology and
allows exploration of the operating characteristics of sub-optimal designs.
Author: John Kirkpatrick [aut, cre]
Maintainer: John Kirkpatrick <mtdesign@puzzledface.net>
Diff between mtdesign versions 0.1.2 dated 2024-11-05 and 0.1.3 dated 2025-08-23
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NEWS.md | 3 +++ R/RcppExports.R | 7 ++++--- tests/testthat/test-powerPlot.R | 21 +++++++++++++++++---- 5 files changed, 34 insertions(+), 16 deletions(-)
Title: Plot Positive and Negative Predictive Values for Medical Tests
Description: Functions to plot and help understand positive and negative
predictive values (PPV and NPV), and their relationship with
sensitivity, specificity, and prevalence. See Akobeng, A.K. (2007)
<doi:10.1111/j.1651-2227.2006.00180.x> for a theoretical overview of
the technical concepts and Navarrete et al. (2015) for a practical
explanation about the importance of their understanding
<doi:10.3389/fpsyg.2015.01327>.
Author: Gorka Navarrete [aut, cre]
Maintainer: Gorka Navarrete <gorkang@gmail.com>
Diff between BayesianReasoning versions 0.4.2 dated 2023-11-14 and 0.4.3 dated 2025-08-23
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Title: Phylogenetic Analysis with Discrete Character Data
Description: Reconstruct phylogenetic trees from discrete data.
Inapplicable character states are handled using the algorithm of Brazeau,
Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy"
library, under equal or implied step weights.
Contains a "shiny" user interface for interactive tree search and exploration
of results, including character visualization, rogue taxon detection,
tree space mapping, and cluster consensus trees (Smith 2022a, b)
<doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>.
Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>,
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>
and custom optimality criteria are implemented.
Author: Martin R. Smith [aut, cre, cph] ,
Martin Brazeau [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeSearch versions 1.6.1 dated 2025-06-10 and 1.7.0 dated 2025-08-23
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TreeSearch-1.7.0/TreeSearch/tests/testthat/test-iw-scoring.R | 120 TreeSearch-1.7.0/TreeSearch/tests/testthat/test-length_range.R | 306 TreeSearch-1.7.0/TreeSearch/tests/testthat/test-mpl_morphy_objects.R | 82 TreeSearch-1.7.0/TreeSearch/tests/testthat/test-pp-fitch.R | 184 TreeSearch-1.7.0/TreeSearch/tests/testthat/test-pp-random-tree.R | 276 TreeSearch-1.7.0/TreeSearch/tests/testthat/test-tree_length.R | 623 TreeSearch-1.7.0/TreeSearch/tests/testthat/test-zzz-tree-rearrange.R | 540 TreeSearch-1.7.0/TreeSearch/vignettes/custom.Rmd | 537 TreeSearch-1.7.0/TreeSearch/vignettes/getting-started.Rmd | 136 TreeSearch-1.7.0/TreeSearch/vignettes/profile-scores.Rmd | 556 TreeSearch-1.7.0/TreeSearch/vignettes/profile.Rmd | 294 TreeSearch-1.7.0/TreeSearch/vignettes/tree-search.Rmd | 722 TreeSearch-1.7.0/TreeSearch/vignettes/tree-space.Rmd | 866 - 251 files changed, 44878 insertions(+), 44405 deletions(-)
Title: Extension to 'ggplot2'
Description: The R package 'ggplot2' is a plotting system based on the
grammar of graphics. 'GGally' extends 'ggplot2' by adding several
functions to reduce the complexity of combining geometric objects with
transformed data. Some of these functions include a pairwise plot
matrix, a two group pairwise plot matrix, a parallel coordinates plot,
a survival plot, and several functions to plot networks.
Author: Barret Schloerke [aut, cre] ,
Di Cook [aut, ths] ,
Joseph Larmarange [aut] ,
Francois Briatte [aut],
Moritz Marbach [aut],
Edwin Thoen [aut],
Amos Elberg [aut],
Ott Toomet [ctb],
Jason Crowley [aut],
Heike Hofmann [ths] ,
Hadley Wickham [ths]
Maintainer: Barret Schloerke <schloerke@gmail.com>
Diff between GGally versions 2.3.0 dated 2025-07-18 and 2.4.0 dated 2025-08-23
DESCRIPTION | 31 ++-- MD5 | 87 ++++++------- NEWS.md | 11 + R/data-nba_ppg_2008.R |only R/deprecated.R | 34 +++-- R/gg-plots.R | 38 +++-- R/ggally_colbar.R | 4 R/ggaly_trends.R | 4 R/ggbivariate.R | 2 R/ggcoef.R | 4 R/ggcorr.R | 39 ++--- R/ggfacet.R | 20 +-- R/gglyph.R | 10 - R/ggmatrix.R | 6 R/ggmatrix_gtable.R | 22 +-- R/ggmatrix_progress.R | 8 - R/ggnet.R | 80 ++++++------ R/ggnet2.R | 123 +++++++++--------- R/ggnetworkmap.R | 224 ++++++++++++++++++---------------- R/ggnostic.R | 42 +----- R/ggpairs.R | 158 +++++++---------------- R/ggpairs_add.R | 94 +++++--------- R/ggpairs_getput.R | 17 +- R/ggpairs_internal_plots.R | 29 ++-- R/ggparcoord.R | 106 ++++++++-------- R/ggscatmat.R | 26 ++- R/ggsurv.R | 10 - R/vig_ggally.R | 4 build/stage23.rdb |binary data/nba_ppg_2008.rda |only inst/WORDLIST | 12 + man/ggcorr.Rd | 11 - man/ggnetworkmap.Rd | 208 +++++++++++++++++-------------- man/nba_ppg_2008.Rd |only tests/testthat/test-crosstalk.R | 8 - tests/testthat/test-ggcorr.R | 4 tests/testthat/test-ggmatrix.R | 13 + tests/testthat/test-ggmatrix_add.R | 2 tests/testthat/test-ggmatrix_getput.R | 16 +- tests/testthat/test-ggnet.R | 32 ++-- tests/testthat/test-ggnet2.R | 63 +++++---- tests/testthat/test-ggnetworkmap.R | 4 tests/testthat/test-ggnostic.R | 2 tests/testthat/test-ggparcoord.R | 38 ++--- tests/testthat/test-wrap.R | 6 tests/testthat/test-zzz_ggpairs.R | 67 ++++------ 46 files changed, 858 insertions(+), 861 deletions(-)