Title: Compute Standardized Mean Differences
Description: Computes standardized mean differences and confidence intervals for
multiple data types based on Yang, D., & Dalton, J. E. (2012)
<http://www.lerner.ccf.org/qhs/software/lib/stddiff.pdf>.
Author: Bradley Saul [aut, cre],
Alex Breskin [ctb],
Catie Wiener [ctb],
Matt Phelan [ctb],
Daniel Sjoberg [ctb]
Maintainer: Bradley Saul <bradleysaul@fastmail.com>
Diff between smd versions 0.6.6 dated 2020-10-22 and 0.6.7 dated 2024-03-28
DESCRIPTION | 29 ++- LICENSE | 4 MD5 | 18 +- NAMESPACE | 2 R/mean_var.R | 2 R/smd.R | 1 README.md | 17 +- build/vignette.rds |binary inst/doc/smd_usage.html | 367 ++++++++++++++++++++++++++-------------------- tests/testthat/test_smd.R | 67 ++++++++ 10 files changed, 321 insertions(+), 186 deletions(-)
Title: Estimating Hidden Population Size using Respondent Driven
Sampling Data
Description: Estimate the size of a networked population based on
respondent-driven sampling data. The package is part of the "RDS Analyst"
suite of packages for the analysis of respondent-driven sampling data.
See Handcock, Gile and Mar (2014) <doi:10.1214/14-EJS923>,
Handcock, Gile and Mar (2015) <doi:10.1111/biom.12255>,
Kim and Handcock (2021) <doi:10.1093/jssam/smz055>, and
McLaughlin, et. al. (2023) <doi:10.1214/23-AOAS1807>.
Author: Mark S. Handcock [aut, cre, cph]
,
Krista J. Gile [aut, cph],
Brian Kim [ctb],
Katherine R. McLaughlin [ctb]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between sspse versions 1.1.0 dated 2023-08-08 and 1.1.0-1 dated 2024-03-28
DESCRIPTION | 18 +++++---- MD5 | 24 +++++++------ R/impute.visibility.R | 86 ++++++++++++++++++++++++++--------------------- R/plot.sspse.R | 2 + R/pospreddeg.R | 4 ++ R/posteriorsize.R | 4 +- R/sspse-doc.R |only build |only data |only man/fauxmadrona2.Rd |only man/impute.visibility.Rd | 71 ++++++++++++++++++++++---------------- man/plot.pospreddeg.Rd | 4 +- man/plot.sspse.Rd | 8 ++-- man/pospreddeg.Rd | 2 + man/sspse-package.Rd | 8 ++++ 15 files changed, 139 insertions(+), 92 deletions(-)
Title: A MediaWiki API Wrapper
Description: A wrapper for the MediaWiki API, aimed particularly at the
Wikimedia 'production' wikis, such as Wikipedia. It can be used to retrieve
page text, information about users or the history of pages, and elements of
the category tree.
Author: Os Keyes [aut, cre], Brock Tilbert [ctb], Clemens Schmid [aut]
Maintainer: Os Keyes <ironholds@gmail.com>
Diff between WikipediR versions 1.5.0 dated 2017-02-05 and 1.7.0 dated 2024-03-28
WikipediR-1.5.0/WikipediR/vignettes/WikipediR.md |only WikipediR-1.7.0/WikipediR/DESCRIPTION | 17 +- WikipediR-1.7.0/WikipediR/MD5 | 61 +++++----- WikipediR-1.7.0/WikipediR/NAMESPACE | 20 +++ WikipediR-1.7.0/WikipediR/R/WikipediR.R | 3 WikipediR-1.7.0/WikipediR/R/content.R | 2 WikipediR-1.7.0/WikipediR/R/create_content.R |only WikipediR-1.7.0/WikipediR/R/login.R |only WikipediR-1.7.0/WikipediR/R/parse.R | 55 +++++++++ WikipediR-1.7.0/WikipediR/README.md | 8 - WikipediR-1.7.0/WikipediR/build/vignette.rds |binary WikipediR-1.7.0/WikipediR/man/WikipediR.Rd | 1 WikipediR-1.7.0/WikipediR/man/categories_in_page.Rd | 15 +- WikipediR-1.7.0/WikipediR/man/create_page.Rd |only WikipediR-1.7.0/WikipediR/man/create_pages.Rd |only WikipediR-1.7.0/WikipediR/man/get_action_token.Rd |only WikipediR-1.7.0/WikipediR/man/get_prelogin_token.Rd |only WikipediR-1.7.0/WikipediR/man/login.Rd |only WikipediR-1.7.0/WikipediR/man/page_backlinks.Rd | 16 +- WikipediR-1.7.0/WikipediR/man/page_content.Rd | 13 +- WikipediR-1.7.0/WikipediR/man/page_external_links.Rd | 12 + WikipediR-1.7.0/WikipediR/man/page_info.Rd | 11 + WikipediR-1.7.0/WikipediR/man/page_links.Rd | 15 +- WikipediR-1.7.0/WikipediR/man/pages_in_category.Rd | 17 +- WikipediR-1.7.0/WikipediR/man/parse_response.Rd |only WikipediR-1.7.0/WikipediR/man/query.Rd | 1 WikipediR-1.7.0/WikipediR/man/random_page.Rd | 14 +- WikipediR-1.7.0/WikipediR/man/recent_changes.Rd | 20 ++- WikipediR-1.7.0/WikipediR/man/revision_content.Rd | 15 +- WikipediR-1.7.0/WikipediR/man/revision_diff.Rd | 17 +- WikipediR-1.7.0/WikipediR/man/user_contributions.Rd | 17 +- WikipediR-1.7.0/WikipediR/man/user_information.Rd | 16 +- WikipediR-1.7.0/WikipediR/tests/testthat/test_category_retrieval.R | 5 WikipediR-1.7.0/WikipediR/tests/testthat/test_content_retrieval.R | 5 WikipediR-1.7.0/WikipediR/tests/testthat/test_metadata_retrieval.R | 7 + WikipediR-1.7.0/WikipediR/tests/testthat/test_recent_changes.R | 4 36 files changed, 286 insertions(+), 101 deletions(-)
Title: A Suite of Routines for Working with Jordan Algebras
Description: A Jordan algebra is an algebraic object originally
designed to study observables in quantum mechanics. Jordan
algebras are commutative but non-associative; they satisfy the
Jordan identity. The package follows the ideas and notation of
K. McCrimmon (2004, ISBN:0-387-95447-3) "A Taste of Jordan
Algebras". To cite in publications please use Hankin (2023)
<arXiv:2303.06062v1>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between jordan versions 1.0-1 dated 2021-04-08 and 1.0-5 dated 2024-03-28
jordan-1.0-1/jordan/inst/doc/jordan.pdf |only jordan-1.0-1/jordan/inst/non_jordan.Rmd |only jordan-1.0-5/jordan/DESCRIPTION | 11 +-- jordan-1.0-5/jordan/MD5 | 54 +++++++++-------- jordan-1.0-5/jordan/NAMESPACE | 2 jordan-1.0-5/jordan/R/aaa_allclasses.R | 71 ++++++++++++++-------- jordan-1.0-5/jordan/R/type_1.R | 9 +- jordan-1.0-5/jordan/R/type_2.R | 9 +- jordan-1.0-5/jordan/R/type_3.R | 11 +-- jordan-1.0-5/jordan/R/type_4.R | 18 ++++- jordan-1.0-5/jordan/R/type_5.R | 20 ++++-- jordan-1.0-5/jordan/README.md | 9 ++ jordan-1.0-5/jordan/build/jordan.pdf |binary jordan-1.0-5/jordan/build/partial.rdb |binary jordan-1.0-5/jordan/build/stage23.rdb |only jordan-1.0-5/jordan/build/vignette.rds |binary jordan-1.0-5/jordan/inst/CITATION |only jordan-1.0-5/jordan/inst/doc/jordan.Rmd | 93 ++++++++++++++++++------------ jordan-1.0-5/jordan/inst/doc/jordan.html |only jordan-1.0-5/jordan/inst/read.me |only jordan-1.0-5/jordan/man/Arith.Rd | 12 ++- jordan-1.0-5/jordan/man/c.Rd | 2 jordan-1.0-5/jordan/man/figures |only jordan-1.0-5/jordan/man/id.Rd | 23 +++++-- jordan-1.0-5/jordan/man/jordan-package.Rd | 2 jordan-1.0-5/jordan/man/jordan.Rd | 45 ++++++++++---- jordan-1.0-5/jordan/man/r_to_n.Rd | 2 jordan-1.0-5/jordan/man/random.Rd | 4 - jordan-1.0-5/jordan/man/show.Rd | 22 +++---- jordan-1.0-5/jordan/man/zero.Rd | 10 ++- jordan-1.0-5/jordan/vignettes/jordan.Rmd | 93 ++++++++++++++++++------------ jordan-1.0-5/jordan/vignettes/jordan.bib |only 32 files changed, 330 insertions(+), 192 deletions(-)
Title: Tools to Create, Modify and Manage 'CWB' Corpora
Description: The 'Corpus Workbench' ('CWB', <https://cwb.sourceforge.io/>) offers a classic and mature
approach for working with large, linguistically and structurally annotated corpora. The 'CWB'
is memory efficient and its design makes running queries fast, see Evert (2011)
<https://eprints.lancs.ac.uk/id/eprint/62721>. The 'cwbtools' package offers
pure 'R' tools to create indexed corpus files as well as high-level wrappers for the original 'C'
implementation of 'CWB' as exposed by the 'RcppCWB' package
(<https://CRAN.R-project.org/package=RcppCWB>). Additional functionality to add and
modify annotations of corpora from within 'R' makes working with 'CWB' indexed corpora
much more flexible and convenient. The 'cwbtools' package in combination with the 'R' packages
'RcppCWB' (<https://CRAN.R-project.org/package=RcppCWB>) and 'polmineR'
(<https://CRAN.R-project.org/package=polmineR>) offers a lightweight infrastructure
to support the combination of quantitative and qu [...truncated...]
Author: Andreas Blaette [aut, cre],
Christoph Leonhardt [aut]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between cwbtools versions 0.4.0 dated 2024-02-26 and 0.4.1 dated 2024-03-28
DESCRIPTION | 8 ++-- MD5 | 14 +++---- NEWS.md | 36 ++++++++++++++----- R/corpus.R | 77 +++++++++++++++++++++++++++++++++--------- R/zenodo.R | 21 ++++++++--- build/vignette.rds |binary inst/doc/vignette.html | 10 ++--- tests/testthat/test_install.R | 2 - 8 files changed, 119 insertions(+), 49 deletions(-)
Title: Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'
Description: Simplifies custom 'CSS' styling of both 'shiny' and
'rmarkdown' via 'Bootstrap' 'Sass'. Supports 'Bootstrap' 3, 4 and 5 as
well as their various 'Bootswatch' themes. An interactive widget is
also provided for previewing themes in real time.
Author: Carson Sievert [aut, cre] ,
Joe Cheng [aut],
Garrick Aden-Buie [aut] ,
Posit Software, PBC [cph, fnd],
Bootstrap contributors [ctb] ,
Twitter, Inc [cph] ,
Javi Aguilar [ctb, cph] ,
Thomas Park [ctb, cph] ,
PayPal [ctb, cph]
Maintainer: Carson Sievert <carson@posit.co>
Diff between bslib versions 0.6.2 dated 2024-03-22 and 0.7.0 dated 2024-03-28
bslib-0.6.2/bslib/inst/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVs9pbCIPrc.woff |only bslib-0.6.2/bslib/inst/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVvaorCIPrc.woff |only bslib-0.6.2/bslib/inst/fonts/1adeadb2fe618c5ed46221f15e12b9c8.woff |only bslib-0.6.2/bslib/inst/fonts/4iCs6KVjbNBYlgo6ew.woff |only bslib-0.6.2/bslib/inst/fonts/4iCs6KVjbNBYlgoKfw7w.woff |only bslib-0.6.2/bslib/inst/fonts/4iCv6KVjbNBYlgoCxCvTtA.woff |only bslib-0.6.2/bslib/inst/fonts/4iCv6KVjbNBYlgoCxCvjsGyL.woff |only bslib-0.6.2/bslib/inst/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDQ.woff |only bslib-0.6.2/bslib/inst/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPa7j.woff |only bslib-0.6.2/bslib/inst/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3aPA.woff |only bslib-0.6.2/bslib/inst/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7j.woff |only bslib-0.6.2/bslib/inst/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3i54rAkw.woff |only bslib-0.6.2/bslib/inst/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vAkw.woff |only bslib-0.6.2/bslib/inst/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdo.woff |only 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bslib-0.7.0/bslib/tools/download_preset_fonts.R | 30 363 files changed, 11136 insertions(+), 1349 deletions(-)
Title: Explore 'Wikidata' Through Tidy Data Frames
Description: Query 'Wikidata' API <https://www.wikidata.org/wiki/Wikidata:Main_Page> with ease, get tidy data frames in response, and cache data in a local database.
Author: Giorgio Comai [aut, cre, cph] ,
EDJNet [fnd]
Maintainer: Giorgio Comai <giorgio.comai@cci.tn.it>
Diff between tidywikidatar versions 0.5.7 dated 2023-03-10 and 0.5.8 dated 2024-03-28
DESCRIPTION | 19 - MD5 | 70 ++--- NAMESPACE | 1 NEWS.md | 159 +++++++------ R/tw_cache_indexing.R | 41 +-- R/tw_caching.R | 66 ++--- R/tw_check.R | 4 R/tw_check_pid.R |only R/tw_check_qid.R | 6 R/tw_connect_to_cache.R | 16 - R/tw_extract.R | 10 R/tw_filter.R | 6 R/tw_get.R | 19 - R/tw_get_all_with_p.R | 4 R/tw_get_cached_item.R | 17 - R/tw_get_field.R | 6 R/tw_get_image.R | 9 R/tw_get_p_wide.R | 16 - R/tw_get_property_label_description.R | 10 R/tw_get_property_with_details.R | 7 R/tw_get_qualifiers.R | 31 +- R/tw_get_wikipedia_category_members.R | 17 - R/tw_get_wikipedia_page_links.R | 24 + R/tw_get_wikipedia_page_qid.R | 36 +- R/tw_get_wikipedia_page_section_links.R | 18 - R/tw_get_wikipedia_page_sections.R | 11 R/tw_search.R | 34 ++ R/tw_write_search_to_cache.R | 9 README.md | 275 ++++++++++------------ build/vignette.rds |binary inst/doc/caching.R | 2 inst/doc/caching.html | 86 +++---- inst/doc/wikipedia_start.html | 388 ++++++++++++++++---------------- man/tw_check_pid.Rd |only man/tw_filter_people.Rd | 3 man/tw_get_property_with_details.Rd | 2 man/tw_index_cache_item.Rd | 4 37 files changed, 746 insertions(+), 680 deletions(-)
Title: Construction and Analysis of Matrix Population Models
Description: Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).
Author: Chris Stubben, Brook Milligan, Patrick Nantel
Maintainer: Chris Stubben <chris.stubben@hci.utah.edu>
Diff between popbio versions 2.7 dated 2020-02-01 and 2.8 dated 2024-03-28
DESCRIPTION | 8 ++-- MD5 | 80 +++++++++++++++++++++++------------------------ NAMESPACE | 50 +++++++++++++++++++++++++---- R/Kendall.R | 14 ++++---- R/boot.transitions.R | 2 - R/countCDFxt.R | 2 - R/data.R | 6 +-- R/logi.hist.plot.R | 2 - R/matplot2.R | 4 +- R/stage.vector.plot.R | 4 +- R/stoch.quasi.ext.R | 2 - inst/CITATION | 11 +----- inst/ChangeLog | 3 + man/01Introduction.Rd | 14 ++++---- man/Kendall.Rd | 24 ++++++++------ man/aq.census.Rd | 6 ++- man/aq.matrix.Rd | 11 +++++- man/aq.trans.Rd | 10 +++-- man/boot.transitions.Rd | 2 - man/calathea.Rd | 6 ++- man/countCDFxt.Rd | 5 +- man/grizzly.Rd | 6 ++- man/hudcorrs.Rd | 6 ++- man/hudsonia.Rd | 4 +- man/hudvrs.Rd | 6 ++- man/image2.Rd | 21 +++++++++--- man/logi.hist.plot.Rd | 19 ++++++++--- man/matplot2.Rd | 23 +++++++++++-- man/monkeyflower.Rd | 6 ++- man/nematode.Rd | 4 +- man/projection.matrix.Rd | 11 +++++- man/stage.vector.plot.Rd | 15 ++++++-- man/stoch.growth.rate.Rd | 3 - man/stoch.projection.Rd | 12 +++++-- man/stoch.quasi.ext.Rd | 15 +++++++- man/teasel.Rd | 4 +- man/test.census.Rd | 6 ++- man/tortoise.Rd | 4 +- man/vitalsim.Rd | 19 +++++++++-- man/whale.Rd | 4 +- man/woodpecker.Rd | 6 ++- 41 files changed, 308 insertions(+), 152 deletions(-)
Title: A Shiny App to Visualize Genetic Maps and QTL Analysis in
Polyploid Species
Description: Provides a graphical user interface to integrate, visualize and explore results
from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid
species. The app is meant for interactive use and allows users to optionally upload different sources
of information, including gene annotation and alignment files, enabling the exploitation and search for
candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly',
'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages.
Author: Cristiane Taniguti [aut, cre],
Gabriel de Siqueira Gesteira [aut],
Jeekin Lau [aut],
Olivia Angelin-Bonnet [aut],
Susan Thomson [ctb],
Guilherme da Silva Pereira [ctb],
David Byrne [ctb],
Zhao-Bang Zeng [ctb],
Oscar Riera-Lizarazu [ctb],
Marcelo Moll [...truncated...]
Maintainer: Cristiane Taniguti <chtaniguti@tamu.edu>
Diff between viewpoly versions 0.3.2 dated 2022-11-01 and 0.4.1 dated 2024-03-28
viewpoly-0.3.2/viewpoly/inst/ext/include.html |only viewpoly-0.3.2/viewpoly/inst/ext/viewmap_tetra.rda |only viewpoly-0.3.2/viewpoly/inst/ext/viewqtl_tetra.rda |only viewpoly-0.3.2/viewpoly/tests/testthat/_snaps |only viewpoly-0.3.2/viewpoly/tests/testthat/test-custom_files.R |only viewpoly-0.3.2/viewpoly/tests/testthat/test-golem-recommended.R |only viewpoly-0.4.1/viewpoly/DESCRIPTION | 22 - viewpoly-0.4.1/viewpoly/MD5 | 61 +-- viewpoly-0.4.1/viewpoly/NAMESPACE | 12 viewpoly-0.4.1/viewpoly/NEWS.md | 10 viewpoly-0.4.1/viewpoly/R/app_server.R | 8 viewpoly-0.4.1/viewpoly/R/app_ui.R | 4 viewpoly-0.4.1/viewpoly/R/functions_map.R | 179 ++++++--- viewpoly-0.4.1/viewpoly/R/functions_qtl.R | 175 ++++----- viewpoly-0.4.1/viewpoly/R/functions_upload.R | 88 ++++ viewpoly-0.4.1/viewpoly/R/mod_genes_view.R | 16 viewpoly-0.4.1/viewpoly/R/mod_hidecan.R |only viewpoly-0.4.1/viewpoly/R/mod_map_view.R | 36 + viewpoly-0.4.1/viewpoly/R/mod_qtl_view.R | 17 viewpoly-0.4.1/viewpoly/R/mod_upload.R | 154 +++++++- viewpoly-0.4.1/viewpoly/R/utils_helpers.R | 13 viewpoly-0.4.1/viewpoly/README.md | 15 viewpoly-0.4.1/viewpoly/build/partial.rdb |binary viewpoly-0.4.1/viewpoly/inst/app/www/flow_chart.png |only viewpoly-0.4.1/viewpoly/inst/app/www/include.html |only viewpoly-0.4.1/viewpoly/inst/ext/about.Rmd | 6 viewpoly-0.4.1/viewpoly/inst/ext/viewmap_tetra.rds |only viewpoly-0.4.1/viewpoly/inst/ext/viewqtl_tetra.rds |only viewpoly-0.4.1/viewpoly/man/draw_map_shiny.Rd | 105 ++--- viewpoly-0.4.1/viewpoly/man/map_summary.Rd | 4 viewpoly-0.4.1/viewpoly/man/prepare_hidecan_examples.Rd |only viewpoly-0.4.1/viewpoly/man/read_input_hidecan.Rd |only viewpoly-0.4.1/viewpoly/man/summary_maps.Rd | 48 +- viewpoly-0.4.1/viewpoly/tests/testthat.R | 2 viewpoly-0.4.1/viewpoly/tests/testthat/test-tetra_example.R | 189 ---------- 35 files changed, 668 insertions(+), 496 deletions(-)
Title: ExifTool Functionality from R
Description: Reads, writes, and edits EXIF and other file metadata using
ExifTool <https://exiftool.org/>, returning read results as a data
frame. ExifTool supports many different metadata formats including EXIF,
GPS, IPTC, XMP, JFIF, GeoTIFF, ICC Profile, Photoshop IRB, FlashPix, AFCP
and ID3, Lyrics3, as well as the maker notes of many digital cameras by
Canon, Casio, DJI, FLIR, FujiFilm, GE, GoPro, HP, JVC/Victor, Kodak, Leaf,
Minolta/Konica-Minolta, Motorola, Nikon, Nintendo, Olympus/Epson,
Panasonic/Leica, Pentax/Asahi, Phase One, Reconyx, Ricoh, Samsung, Sanyo,
Sigma/Foveon and Sony.
Author: Joshua O'Brien [aut, cre]
Maintainer: Joshua O'Brien <joshmobrien@gmail.com>
Diff between exiftoolr versions 0.2.3 dated 2023-10-17 and 0.2.4 dated 2024-03-28
DESCRIPTION | 27 ++++----- MD5 | 6 +- NEWS.md | 165 +++++++++++++++++++++++++++++----------------------------- R/exif_read.R | 36 +++++++++++- 4 files changed, 135 insertions(+), 99 deletions(-)
Title: Single-Species, Multi-Species, and Integrated Spatial Occupancy
Models
Description: Fits single-species, multi-species, and integrated non-spatial and spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models are fit using Polya-Gamma data augmentation detailed in Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2020) <arXiv:2001.09111>. Provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. Details on data integration are given in Miller, Pacifici, Sanderlin, and Reich (2019) <doi:10.1111/2041-210X.13110>. Details on single-species and multi-species models are found in MacKenzie, Nichols, Lachman, Droege, Royle, and Langtimm (2002) <doi:10.1890/0012-9658(2002)083[2 [...truncated...]
Author: Jeffrey Doser [aut, cre],
Andrew Finley [aut],
Marc Kery [ctb]
Maintainer: Jeffrey Doser <doserjef@msu.edu>
Diff between spOccupancy versions 0.7.2 dated 2023-11-01 and 0.7.3 dated 2024-03-28
DESCRIPTION | 9 MD5 | 167 ++++++------- NAMESPACE | 2 NEWS.md | 12 R/PGOcc.R | 12 R/generics.R | 520 ++++++++++++++++++++--------------------- R/getSVCSamples.R | 4 R/intMsPGOcc.R | 24 + R/intPGOcc.R | 10 R/lfJSDM.R | 15 - R/lfMsPGOcc.R | 23 + R/msPGOcc.R | 21 + R/postHocLM.R | 6 R/ppcOcc.R | 1 R/sfJSDM.R | 18 - R/sfMsPGOcc.R | 133 +++++++--- R/simIntMsOcc.R | 29 -- R/simMsOcc.R | 50 ++- R/simOcc.R | 59 +--- R/simTMsOcc.R | 44 ++- R/simTOcc.R | 39 ++- R/spIntPGOcc.R | 195 +++++++-------- R/spMsPGOcc.R | 503 ++++++++++++++++++++------------------- R/spPGOcc.R | 206 +++++++--------- R/stMsPGOcc.R | 101 ++++--- R/stPGOcc.R | 121 ++++++--- R/svcMsPGOcc.R | 25 + R/svcPGBinom.R | 15 - R/svcPGOcc.R | 148 ++++++----- R/svcTMsPGOcc.R | 154 ++++++++---- R/svcTPGBinom.R | 11 R/svcTPGOcc.R | 131 ++++++---- R/tMsPGOcc.R | 67 +++-- R/tPGOcc.R | 14 - R/updateMCMC.R | 198 ++++++++++++++- R/waicOcc.R | 10 README.md | 45 ++- build/partial.rdb |binary inst/CITATION | 12 man/intMsPGOcc.Rd | 2 man/postHocLM.Rd | 21 - man/predict.sfMsPGOcc.Rd | 4 man/predict.spPGOcc.Rd | 4 man/predict.stMsPGOcc.Rd | 4 man/predict.stPGOcc.Rd | 4 man/predict.svcPGOcc.Rd | 4 man/predict.svcTMsPGOcc.Rd | 4 man/predict.svcTPGOcc.Rd | 9 man/sfJSDM.Rd | 32 +- man/sfMsPGOcc.Rd | 19 + man/simMsOcc.Rd | 4 man/simOcc.Rd | 2 man/simTMsOcc.Rd | 4 man/simTOcc.Rd | 4 man/spOccupancy-package.Rd | 29 +- man/spPGOcc.Rd | 16 + man/stMsPGOcc.Rd | 19 + man/stPGOcc.Rd | 18 + man/svcMsPGOcc.Rd | 5 man/svcPGOcc.Rd | 15 - man/svcTMsPGOcc.Rd | 30 +- man/svcTPGOcc.Rd | 18 + man/updateMCMC.Rd |only man/waicOcc.Rd | 6 src/init.cpp | 32 +- src/sfJSDMNNGP.cpp | 109 ++++---- src/sfMsPGOccNNGP.cpp | 126 +++++---- src/sfMsPGOccNNGPPredict.cpp | 98 ++++--- src/spMsPGOccNNGPPredict.cpp | 82 +++--- src/spMsPGOccPredict.cpp | 14 - src/spOccupancy.h | 63 ++-- src/spPGOccNNGP.cpp | 83 +++--- src/spPGOccNNGPPredict.cpp | 87 +++--- src/spPGOccPredict.cpp | 30 +- src/stMsPGOccNNGP.cpp | 145 ++++++----- src/stPGOccNNGP.cpp | 90 +++---- src/stPGOccNNGPPredict.cpp | 31 +- src/svcMsPGOccNNGPPredict.cpp | 9 src/svcPGOccNNGP.cpp | 120 +++++---- src/svcPGOccNNGPPredict.cpp | 89 +++---- src/svcTMsPGOccNNGP.cpp | 469 +++++++++++++++++++----------------- src/svcTMsPGOccNNGPPredict.cpp | 39 +-- src/svcTPGOccNNGP.cpp | 132 +++++----- src/svcTPGOccNNGPPredict.cpp | 36 +- src/tMsPGOcc.cpp | 180 +++++++------- 85 files changed, 3180 insertions(+), 2315 deletions(-)
Title: Fast Time Series Modeling for Seasonal Series with Exogenous
Variables
Description: An implementation of sparsity-ranked lasso and related methods
for time series data. This methodology is especially useful for
large time series with exogenous features and/or complex
seasonality. Originally described in Peterson and Cavanaugh
(2022) <doi:10.1007/s10182-021-00431-7> in the context of variable
selection with interactions and/or polynomials, ranked sparsity is
a philosophy with methods useful for variable selection in the
presence of prior informational asymmetry. This situation exists for time
series data with complex seasonality, as shown in Peterson and Cavanaugh
(2024) <doi:10.1177/1471082X231225307>, which also describes this package
in greater detail. The sparsity-ranked penalization methods for time series
implemented in 'fastTS' can fit large/complex/high-frequency time series
quickly, even with a high-dimensional exogenous feature set. The method is
considerably faster than its competitors, while often producing more
accurate predictions. Also includ [...truncated...]
Author: Ryan Andrew Peterson [aut, cre, cph]
Maintainer: Ryan Andrew Peterson <ryan.a.peterson@cuanschutz.edu>
Diff between fastTS versions 1.0.0 dated 2024-03-07 and 1.0.1 dated 2024-03-28
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NEWS.md | 4 ++++ README.md | 18 ++++++++++++------ inst/CITATION | 12 ++++++------ 5 files changed, 32 insertions(+), 22 deletions(-)
Title: Identifying Unique Multilocus Genotypes where Genotyping Error
and Missing Data may be Present
Description: Tools for the identification of unique of multilocus genotypes when both genotyping error and missing data may be present; targeted for use with large datasets and databases containing multiple samples of each individual (a common situation in conservation genetics, particularly in non-invasive wildlife sampling applications). Functions explicitly incorporate missing data and can tolerate allele mismatches created by genotyping error. If you use this package, please cite the original publication in Molecular Ecology Resources (Galpern et al., 2012), the details for which can be generated using citation('allelematch'). For a complete vignette, please access via the Data S1 Supplementary documentation and tutorials (PDF) located at <doi:10.1111/j.1755-0998.2012.03137.x>.
Author: Paul Galpern <pgalpern@gmail.com>
Maintainer: Todd Cross <todd.cross@gmail.com>
Diff between allelematch versions 2.5.3 dated 2023-08-24 and 2.5.4 dated 2024-03-28
DESCRIPTION | 8 MD5 | 16 NAMESPACE | 10 R/allelematch.r | 6088 ++++++++++++++++++++++++++++++++++-------------------- build/partial.rdb |binary man/amCluster.Rd | 487 ++-- man/amDataset.Rd | 2 man/amPairwise.Rd | 414 +-- man/amUnique.Rd | 570 ++--- 9 files changed, 4653 insertions(+), 2942 deletions(-)
Title: Create a Mini Version of CRAN Containing Only Selected Packages
Description: Makes it possible to create an internally consistent
repository consisting of selected packages from CRAN-like repositories.
The user specifies a set of desired packages, and 'miniCRAN' recursively
reads the dependency tree for these packages, then downloads only this
subset. The user can then install packages from this repository directly,
rather than from CRAN. This is useful in production settings, e.g. server
behind a firewall, or remote locations with slow (or zero) Internet access.
Author: Andrie de Vries [aut, cre, cph],
Alex Chubaty [ctb],
Microsoft Corporation [cph]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between miniCRAN versions 0.2.16 dated 2022-02-14 and 0.3.0 dated 2024-03-28
miniCRAN-0.2.16/miniCRAN/R/MRAN.R |only miniCRAN-0.3.0/miniCRAN/DESCRIPTION | 8 miniCRAN-0.3.0/miniCRAN/MD5 | 99 - miniCRAN-0.3.0/miniCRAN/NAMESPACE | 2 miniCRAN-0.3.0/miniCRAN/NEWS | 16 miniCRAN-0.3.0/miniCRAN/R/P3M.R |only miniCRAN-0.3.0/miniCRAN/R/github-functions.R | 2 miniCRAN-0.3.0/miniCRAN/R/internal.R | 2 miniCRAN-0.3.0/miniCRAN/R/makeDepGraph.R | 3 miniCRAN-0.3.0/miniCRAN/R/makeRepo.R | 8 miniCRAN-0.3.0/miniCRAN/R/minicran-package.R | 4 miniCRAN-0.3.0/miniCRAN/R/pkgDep.R | 28 miniCRAN-0.3.0/miniCRAN/R/pkgDepTools.R | 4 miniCRAN-0.3.0/miniCRAN/R/plot.pkgDepGraph.R | 8 miniCRAN-0.3.0/miniCRAN/R/utils.R | 10 miniCRAN-0.3.0/miniCRAN/R/zzz.R | 4 miniCRAN-0.3.0/miniCRAN/build/vignette.rds |binary miniCRAN-0.3.0/miniCRAN/inst/doc/miniCRAN-dependency-graph.html | 159 + miniCRAN-0.3.0/miniCRAN/inst/doc/miniCRAN-introduction.R | 20 miniCRAN-0.3.0/miniCRAN/inst/doc/miniCRAN-introduction.html | 241 +- miniCRAN-0.3.0/miniCRAN/inst/doc/miniCRAN-introduction.rmd | 20 miniCRAN-0.3.0/miniCRAN/inst/doc/miniCRAN-non-CRAN-repos.R | 30 miniCRAN-0.3.0/miniCRAN/inst/doc/miniCRAN-non-CRAN-repos.html | 192 +- miniCRAN-0.3.0/miniCRAN/inst/doc/miniCRAN-non-CRAN-repos.rmd | 47 miniCRAN-0.3.0/miniCRAN/inst/examples/example_checkVersions.R | 20 miniCRAN-0.3.0/miniCRAN/inst/examples/example_makeRepo.R | 8 miniCRAN-0.3.0/miniCRAN/inst/examples/example_updatePackages.R | 20 miniCRAN-0.3.0/miniCRAN/man/addOldPackage.Rd | 22 miniCRAN-0.3.0/miniCRAN/man/addPackage.Rd | 22 miniCRAN-0.3.0/miniCRAN/man/checkVersions.Rd | 20 miniCRAN-0.3.0/miniCRAN/man/figures/logo.svg | 828 +++++----- miniCRAN-0.3.0/miniCRAN/man/getCranDescription.Rd | 2 miniCRAN-0.3.0/miniCRAN/man/is.online.Rd | 32 miniCRAN-0.3.0/miniCRAN/man/makeDepGraph.Rd | 2 miniCRAN-0.3.0/miniCRAN/man/makeRepo.Rd | 10 miniCRAN-0.3.0/miniCRAN/man/miniCRAN-package.Rd | 5 miniCRAN-0.3.0/miniCRAN/man/pkgAvail.Rd | 7 miniCRAN-0.3.0/miniCRAN/man/pkgDep.Rd | 2 miniCRAN-0.3.0/miniCRAN/man/updatePackages.Rd | 22 miniCRAN-0.3.0/miniCRAN/tests/testthat/helpers.R | 71 miniCRAN-0.3.0/miniCRAN/tests/testthat/test-1-pkgAvail.R | 12 miniCRAN-0.3.0/miniCRAN/tests/testthat/test-2-makeDepGraph.R | 2 miniCRAN-0.3.0/miniCRAN/tests/testthat/test-3-makeRepo.R | 95 - miniCRAN-0.3.0/miniCRAN/tests/testthat/test-4-makeRepo-from-localCRAN.R | 26 miniCRAN-0.3.0/miniCRAN/tests/testthat/test-5-ask-for-confirmation.R | 10 miniCRAN-0.3.0/miniCRAN/tests/testthat/test-5-updateRepo.R | 84 - miniCRAN-0.3.0/miniCRAN/tests/testthat/test-6-getCranDescription.R | 20 miniCRAN-0.3.0/miniCRAN/tests/testthat/test-7-addGithubPackage.R | 2 miniCRAN-0.3.0/miniCRAN/tests/testthat/test-9-is-online.R | 3 miniCRAN-0.3.0/miniCRAN/tests/testthat/test-r-version.R |only miniCRAN-0.3.0/miniCRAN/vignettes/miniCRAN-introduction.rmd | 20 miniCRAN-0.3.0/miniCRAN/vignettes/miniCRAN-non-CRAN-repos.rmd | 47 52 files changed, 1155 insertions(+), 1166 deletions(-)
Title: Kinship Ties in (Virtual) Multi-Generation Populations
Description: Tools to study lineages, grandparenthood, loss of close relatives, kinship networks and other topics in multi-generation populations.
Author: Frans Willekens [aut, cre]
Maintainer: Frans Willekens <willekens@nidi.nl>
Diff between Families versions 2.0.0 dated 2024-03-21 and 2.0.1 dated 2024-03-28
DESCRIPTION | 8 +-- MD5 | 24 +++++------ NEWS.md | 17 ++++++-- R/Age.R | 4 + R/IDch.R | 123 ++++++++++++++++++++++++---------------------------------- R/IDfather.R | 15 +++---- R/IDgch.R | 119 ++++++++++++++++++++++++++++++++++---------------------- R/IDpartner.R | 4 + R/Tests.R | 35 ++++++++++++---- man/Age.Rd | 2 man/IDch.Rd | 16 ++++--- man/IDgch.Rd | 9 ++-- man/Tests.Rd | 19 ++++++-- 13 files changed, 226 insertions(+), 169 deletions(-)
Title: Clustering of Functional Data Based on Measures of Change
Description: Implements a three-step procedure in the spirit of Leffondree et al. (2004) to identify clusters of individual longitudinal trajectories. The procedure involves (1) computing a number of "measures of change"" capturing various features of the trajectories; (2) using a Principal Component Analysis based dimension reduction algorithm to select a subset of measures and (3) using the k-means clustering algorithm to identify clusters of trajectories.
Author: Marie-Pierre Sylvestre [aut],
Laurence Boulanger [aut, cre],
Gillis Delmas Tchouangue Dinkou [ctb],
Dan Vatnik [ctb]
Maintainer: Laurence Boulanger <laurence.boulanger@umontreal.ca>
Diff between traj versions 2.0.1 dated 2023-12-07 and 2.1.0 dated 2024-03-28
traj-2.0.1/traj/man/figures |only traj-2.1.0/traj/DESCRIPTION | 14 traj-2.1.0/traj/LICENSE | 4 traj-2.1.0/traj/MD5 | 39 - traj-2.1.0/traj/NEWS.md | 28 - traj-2.1.0/traj/R/Der.R | 11 traj-2.1.0/traj/R/Step1Measures.R | 698 +++++++++++++++---------------- traj-2.1.0/traj/R/Step2Selection.R | 262 +++++++---- traj-2.1.0/traj/R/Step3Clusters.R | 17 traj-2.1.0/traj/R/data.R |only traj-2.1.0/traj/R/plot.trajClusters.R | 29 - traj-2.1.0/traj/README.md | 25 - traj-2.1.0/traj/build |only traj-2.1.0/traj/data/trajdata.rda |binary traj-2.1.0/traj/inst |only traj-2.1.0/traj/man/Step1Measures.Rd | 88 ++- traj-2.1.0/traj/man/Step2Selection.Rd | 45 - traj-2.1.0/traj/man/Step3Clusters.Rd | 13 traj-2.1.0/traj/man/plot.trajClusters.Rd | 21 traj-2.1.0/traj/man/traj-package.Rd | 2 traj-2.1.0/traj/man/trajdata.Rd | 40 + traj-2.1.0/traj/vignettes |only 22 files changed, 736 insertions(+), 600 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [ctb] ,
Xintong Li [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 0.6.2 dated 2024-03-05 and 0.7.0 dated 2024-03-28
PatientProfiles-0.6.2/PatientProfiles/R/formattedTables.R |only PatientProfiles-0.6.2/PatientProfiles/R/tidyTables.R |only PatientProfiles-0.6.2/PatientProfiles/build |only PatientProfiles-0.6.2/PatientProfiles/inst/doc |only PatientProfiles-0.6.2/PatientProfiles/man/detectVariables.Rd |only PatientProfiles-0.6.2/PatientProfiles/man/figures/Hex.png |only PatientProfiles-0.6.2/PatientProfiles/man/tidyCharacteristics.Rd |only PatientProfiles-0.6.2/PatientProfiles/tests/testthat/test-tableSummary.R |only PatientProfiles-0.6.2/PatientProfiles/vignettes |only PatientProfiles-0.7.0/PatientProfiles/DESCRIPTION | 15 PatientProfiles-0.7.0/PatientProfiles/MD5 | 210 +- PatientProfiles-0.7.0/PatientProfiles/NAMESPACE | 26 PatientProfiles-0.7.0/PatientProfiles/R/addCategories.R | 19 PatientProfiles-0.7.0/PatientProfiles/R/addCohortIntersect.R | 103 - PatientProfiles-0.7.0/PatientProfiles/R/addConceptIntersect.R | 471 ++-- PatientProfiles-0.7.0/PatientProfiles/R/addDateOfBirth.R | 15 PatientProfiles-0.7.0/PatientProfiles/R/addDemographics.R | 290 ++ PatientProfiles-0.7.0/PatientProfiles/R/addIntersect.R | 275 +- PatientProfiles-0.7.0/PatientProfiles/R/addTableIntersect.R | 117 - PatientProfiles-0.7.0/PatientProfiles/R/checks.R | 791 ++++++- PatientProfiles-0.7.0/PatientProfiles/R/formats.R | 425 +++- PatientProfiles-0.7.0/PatientProfiles/R/gtResult.R | 496 ---- PatientProfiles-0.7.0/PatientProfiles/R/mockPatientProfiles.R | 75 PatientProfiles-0.7.0/PatientProfiles/R/plotCharacteristics.R |only PatientProfiles-0.7.0/PatientProfiles/R/plotLargeScaleCharacteristics.R |only PatientProfiles-0.7.0/PatientProfiles/R/plotSummarised.R |only PatientProfiles-0.7.0/PatientProfiles/R/reexports-omopgenerics.R | 4 PatientProfiles-0.7.0/PatientProfiles/R/summariseCharacteristics.R | 162 - PatientProfiles-0.7.0/PatientProfiles/R/summariseCohortIntersect.R |only PatientProfiles-0.7.0/PatientProfiles/R/summariseCohortOverlap.R |only PatientProfiles-0.7.0/PatientProfiles/R/summariseCohortTiming.R |only PatientProfiles-0.7.0/PatientProfiles/R/summariseDemographics.R |only PatientProfiles-0.7.0/PatientProfiles/R/summariseLargeScaleCharacteristics.R | 123 + PatientProfiles-0.7.0/PatientProfiles/R/summariseResult.R | 1024 ++++------ PatientProfiles-0.7.0/PatientProfiles/R/summariseTableIntersect.R |only PatientProfiles-0.7.0/PatientProfiles/R/sysdata.rda |binary PatientProfiles-0.7.0/PatientProfiles/R/tableSummarised.R |only PatientProfiles-0.7.0/PatientProfiles/R/utilities.R | 5 PatientProfiles-0.7.0/PatientProfiles/README.md | 260 +- PatientProfiles-0.7.0/PatientProfiles/inst/WORDLIST | 52 PatientProfiles-0.7.0/PatientProfiles/man/PatientProfiles-package.Rd | 3 PatientProfiles-0.7.0/PatientProfiles/man/addAge.Rd | 3 PatientProfiles-0.7.0/PatientProfiles/man/addCategories.Rd | 7 PatientProfiles-0.7.0/PatientProfiles/man/addCohortIntersect.Rd | 29 PatientProfiles-0.7.0/PatientProfiles/man/addCohortIntersectCount.Rd | 19 PatientProfiles-0.7.0/PatientProfiles/man/addCohortIntersectDate.Rd | 13 PatientProfiles-0.7.0/PatientProfiles/man/addCohortIntersectDays.Rd | 13 PatientProfiles-0.7.0/PatientProfiles/man/addCohortIntersectFlag.Rd | 19 PatientProfiles-0.7.0/PatientProfiles/man/addConceptIntersect.Rd | 61 PatientProfiles-0.7.0/PatientProfiles/man/addConceptIntersectCount.Rd | 45 PatientProfiles-0.7.0/PatientProfiles/man/addConceptIntersectDate.Rd | 38 PatientProfiles-0.7.0/PatientProfiles/man/addConceptIntersectDays.Rd | 38 PatientProfiles-0.7.0/PatientProfiles/man/addConceptIntersectFlag.Rd | 45 PatientProfiles-0.7.0/PatientProfiles/man/addDateOfBirth.Rd | 15 PatientProfiles-0.7.0/PatientProfiles/man/addDemographics.Rd | 37 PatientProfiles-0.7.0/PatientProfiles/man/addFutureObservation.Rd | 11 PatientProfiles-0.7.0/PatientProfiles/man/addInObservation.Rd | 18 PatientProfiles-0.7.0/PatientProfiles/man/addIntersect.Rd | 34 PatientProfiles-0.7.0/PatientProfiles/man/addLargeScaleCharacteristics.Rd | 17 PatientProfiles-0.7.0/PatientProfiles/man/addPriorObservation.Rd | 13 PatientProfiles-0.7.0/PatientProfiles/man/addSex.Rd | 73 PatientProfiles-0.7.0/PatientProfiles/man/addTableIntersect.Rd | 19 PatientProfiles-0.7.0/PatientProfiles/man/addTableIntersectCount.Rd | 12 PatientProfiles-0.7.0/PatientProfiles/man/addTableIntersectDate.Rd | 4 PatientProfiles-0.7.0/PatientProfiles/man/addTableIntersectDays.Rd | 4 PatientProfiles-0.7.0/PatientProfiles/man/addTableIntersectField.Rd | 30 PatientProfiles-0.7.0/PatientProfiles/man/addTableIntersectFlag.Rd | 11 PatientProfiles-0.7.0/PatientProfiles/man/assertNameStyle.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/availableEstimates.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/availableFunctions.Rd | 5 PatientProfiles-0.7.0/PatientProfiles/man/endDateColumn.Rd | 4 PatientProfiles-0.7.0/PatientProfiles/man/figures/logo.png |only PatientProfiles-0.7.0/PatientProfiles/man/formatCharacteristics.Rd | 25 PatientProfiles-0.7.0/PatientProfiles/man/gtCharacteristics.Rd | 15 PatientProfiles-0.7.0/PatientProfiles/man/gtResult.Rd | 15 PatientProfiles-0.7.0/PatientProfiles/man/mockPatientProfiles.Rd | 75 PatientProfiles-0.7.0/PatientProfiles/man/optionsTableCharacteristics.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/optionsTableCohortOverlap.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/optionsTableCohortTiming.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/plotCharacteristics.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/plotCohortIntersect.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/plotCohortOverlap.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/plotCohortTiming.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/plotDemographics.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/plotLargeScaleCharacteristics.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/plotTableIntersect.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/reexports.Rd | 3 PatientProfiles-0.7.0/PatientProfiles/man/sourceConceptIdColumn.Rd | 4 PatientProfiles-0.7.0/PatientProfiles/man/standardConceptIdColumn.Rd | 4 PatientProfiles-0.7.0/PatientProfiles/man/startDateColumn.Rd | 4 PatientProfiles-0.7.0/PatientProfiles/man/summariseCharacteristics.Rd | 20 PatientProfiles-0.7.0/PatientProfiles/man/summariseCohortIntersect.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/summariseCohortOverlap.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/summariseCohortTiming.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/summariseConceptIntersect.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/summariseDemographics.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/summariseLargeScaleCharacteristics.Rd | 26 PatientProfiles-0.7.0/PatientProfiles/man/summariseResult.Rd | 36 PatientProfiles-0.7.0/PatientProfiles/man/summariseTableIntersect.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/tableCharacteristics.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/tableCohortIntersect.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/tableCohortOverlap.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/tableCohortTiming.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/tableDemographics.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/tableLargeScaleCharacteristics.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/tableTableIntersect.Rd |only PatientProfiles-0.7.0/PatientProfiles/man/variableTypes.Rd | 4 PatientProfiles-0.7.0/PatientProfiles/tests/testthat/setup.R | 15 PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-addCohortIntersect.R | 53 PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-addConceptIntersect.R | 108 + PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-addDemographics.R | 16 PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-addFutureObservation.R | 22 PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-addInObservation.R | 20 PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-addIntersect.R | 130 - PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-addPriorObservation.R | 22 PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-checks.R | 82 PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-format.R | 49 PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-mockPatientProfiles.R | 5 PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-plotCharacteristics.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-plotLargeScaleCharacteristics.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-plotSummarised.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-summariseCharacteristics.R | 21 PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-summariseCohortIntersect.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-summariseCohortOverlap.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-summariseCohortTiming.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-summariseDemographics.R |only PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-summariseLargeScaleCharacteristics.R | 15 PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-summariseResult.R | 73 PatientProfiles-0.7.0/PatientProfiles/tests/testthat/test-tableSummarised.R |only 129 files changed, 3885 insertions(+), 2575 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: Mast Inference and Forecasting
Description: Analyzes production and dispersal of seeds dispersed from trees and recovered in seed traps. Motivated by long-term inventory plots where seed collections are used to infer seed production by each individual plant.
Author: James S. Clark
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between mastif versions 2.2 dated 2024-02-16 and 2.3 dated 2024-03-28
DESCRIPTION | 8 MD5 | 10 R/mastifFunctions.R | 263 +++++++----- build/vignette.rds |binary inst/doc/mastifVignette.html | 922 +++++++++++++++++++++---------------------- man/mastif-package.Rd | 4 6 files changed, 640 insertions(+), 567 deletions(-)
Title: Analyze, Summarize, and Visualize Daily Streamflow Data
Description: The Flow Analysis Summary Statistics Tool for R, 'fasstr', provides various functions to tidy and screen daily stream discharge data, calculate and visualize various summary statistics and metrics, and compute annual trending and volume frequency analyses.
It features useful function arguments for filtering of and handling dates, customizing data and metrics, and the ability to pull daily data directly from the Water Survey of Canada hydrometric database (<https://collaboration.cmc.ec.gc.ca/cmc/hydrometrics/www/>).
Author: Jon Goetz [aut, cre] ,
Carl James Schwarz [aut],
Sam Albers [ctb] ,
Robin Pike [ctb],
Province of British Columbia [cph]
Maintainer: Jon Goetz <jon.goetz@gov.bc.ca>
Diff between fasstr versions 0.5.1 dated 2023-03-22 and 0.5.2 dated 2024-03-28
DESCRIPTION | 8 MD5 | 78 +- NEWS.md | 11 R/compute_annual_trends.R | 2 R/compute_frequency_analysis.R | 4 R/plot_annual_cumulative_stats.R | 12 R/plot_annual_extremes.R | 2 R/plot_annual_extremes_year.R | 4 R/plot_annual_flow_timing_year.R | 4 R/plot_annual_highflows.R | 2 R/plot_annual_lowflows.R | 2 R/plot_annual_normal_days_year.R | 4 R/plot_annual_stats.R | 4 R/plot_annual_stats2.R | 4 R/plot_daily_cumulative_stats.R | 4 R/plot_daily_stats.R | 4 R/plot_data_screening.R | 2 R/plot_flow_data.R | 4 R/plot_flow_duration.R | 4 R/plot_longterm_daily_stats.R | 4 R/plot_longterm_monthly_stats.R | 4 R/plot_monthly_cumulative_stats.R | 4 R/plot_monthly_stats.R | 4 R/plot_monthly_stats2.R | 4 build/vignette.rds |binary inst/doc/fasstr.R | 6 inst/doc/fasstr.html | 64 +- inst/doc/fasstr_frequency_analysis.R | 32 - inst/doc/fasstr_frequency_analysis.html | 80 +- inst/doc/fasstr_full_analysis.R | 112 ++-- inst/doc/fasstr_full_analysis.html | 56 +- inst/doc/fasstr_trending_analysis.R | 26 inst/doc/fasstr_trending_analysis.html | 46 - inst/doc/fasstr_under_the_hood.R | 14 inst/doc/fasstr_under_the_hood.html | 292 +++++----- inst/doc/fasstr_users_guide.R | 232 ++++---- inst/doc/fasstr_users_guide.html | 892 ++++++++++++++++---------------- man/figures/plot1-1.png |binary man/figures/plot2-1.png |binary man/figures/plot3-1.png |binary 40 files changed, 1022 insertions(+), 1009 deletions(-)
Title: Boundary Adaptive Local Polynomial Conditional Density Estimator
Description: Tools for estimation and inference of conditional densities, derivatives and functions. This is the companion software for Cattaneo, Chandak, Jansson and Ma (2024) <arXiv:2204.10359>.
Author: Rajita Chandak [aut, cre]
Maintainer: Rajita Chandak <rchandak@princeton.edu>
Diff between lpcde versions 0.1.2 dated 2024-02-29 and 0.1.3 dated 2024-03-28
lpcde-0.1.2/lpcde/man/bw_imse.Rd |only lpcde-0.1.2/lpcde/man/bw_mse.Rd |only lpcde-0.1.3/lpcde/DESCRIPTION | 11 lpcde-0.1.3/lpcde/MD5 | 84 +-- lpcde-0.1.3/lpcde/NAMESPACE | 1 lpcde-0.1.3/lpcde/NEWS.md | 5 lpcde-0.1.3/lpcde/R/RcppExports.R | 4 lpcde-0.1.3/lpcde/R/lpbwcde.R | 36 - lpcde-0.1.3/lpcde/R/lpbwcde_fns.R | 638 ++++++++++++------------ lpcde-0.1.3/lpcde/R/lpbwcde_methods.R | 6 lpcde-0.1.3/lpcde/R/lpcde.R | 44 + lpcde-0.1.3/lpcde/R/lpcde_fns.R | 81 +-- lpcde-0.1.3/lpcde/R/lpcde_methods.R | 46 + lpcde-0.1.3/lpcde/R/matrices.R | 44 - lpcde-0.1.3/lpcde/R/utils.R | 44 - lpcde-0.1.3/lpcde/build |only lpcde-0.1.3/lpcde/inst |only lpcde-0.1.3/lpcde/man/S_x.Rd | 8 lpcde-0.1.3/lpcde/man/T_x.Rd | 14 lpcde-0.1.3/lpcde/man/T_y.Rd | 10 lpcde-0.1.3/lpcde/man/b_x.Rd | 12 lpcde-0.1.3/lpcde/man/basis_vec.Rd | 6 lpcde-0.1.3/lpcde/man/c_x.Rd | 12 lpcde-0.1.3/lpcde/man/check_inv.Rd | 4 lpcde-0.1.3/lpcde/man/coef.lpbwcde.Rd | 2 lpcde-0.1.3/lpcde/man/coef.lpcde.Rd | 5 lpcde-0.1.3/lpcde/man/confint.lpcde.Rd | 4 lpcde-0.1.3/lpcde/man/cov_hat.Rd | 16 lpcde-0.1.3/lpcde/man/fhat.Rd | 18 lpcde-0.1.3/lpcde/man/int_val.Rd | 14 lpcde-0.1.3/lpcde/man/kernel_eval.Rd | 6 lpcde-0.1.3/lpcde/man/lpbwcde.Rd | 15 lpcde-0.1.3/lpcde/man/lpcde.Rd | 38 + lpcde-0.1.3/lpcde/man/lpcde_fn.Rd | 18 lpcde-0.1.3/lpcde/man/mvec.Rd | 8 lpcde-0.1.3/lpcde/man/plot.lpcde.Rd | 8 lpcde-0.1.3/lpcde/man/poly_base.Rd | 6 lpcde-0.1.3/lpcde/man/print.lpbwcde.Rd | 2 lpcde-0.1.3/lpcde/man/print.lpcde.Rd | 2 lpcde-0.1.3/lpcde/man/print_all_sumC.Rd | 4 lpcde-0.1.3/lpcde/man/summary.lpbwcde.Rd | 2 lpcde-0.1.3/lpcde/man/summary.lpcde.Rd | 2 lpcde-0.1.3/lpcde/man/vcov.lpcde.Rd | 4 lpcde-0.1.3/lpcde/src/utilsC.cpp | 4 lpcde-0.1.3/lpcde/tests/testthat/test-lpbwcde.R | 7 45 files changed, 674 insertions(+), 621 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] ,
Martin Maechler [aut] ,
Ben Bolker [aut, cre] ,
Steven Walker [aut] ,
Rune Haubo Bojesen Christensen [ctb]
,
Henrik Singmann [ctb] ,
Bin Dai [ctb],
Fabian Scheipl [ctb] ,
Gabor Grothendieck [ctb],
Peter Green [ctb] ,
John Fox [c [...truncated...]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-35.1 dated 2023-11-05 and 1.1-35.2 dated 2024-03-28
lme4-1.1-35.1/lme4/R/hooks.R |only lme4-1.1-35.2/lme4/DESCRIPTION | 6 ++-- lme4-1.1-35.2/lme4/MD5 | 18 +++++++------- lme4-1.1-35.2/lme4/R/predict.R | 3 ++ lme4-1.1-35.2/lme4/R/zzz.R |only lme4-1.1-35.2/lme4/inst/NEWS.Rd | 29 +++++++++++++++++++---- lme4-1.1-35.2/lme4/inst/doc/PLSvGLS.pdf |binary lme4-1.1-35.2/lme4/inst/doc/Theory.pdf |binary lme4-1.1-35.2/lme4/inst/doc/lmer.pdf |binary lme4-1.1-35.2/lme4/man/nlmer.Rd | 2 - lme4-1.1-35.2/lme4/tests/testthat/test-predict.R | 19 +++++++++++++++ 11 files changed, 60 insertions(+), 17 deletions(-)
Title: Generalized Partially Linear Tree-Based Regression Model
Description: Combining a generalized linear model with an additional tree part
on the same scale. A four-step procedure is proposed to fit the model and test
the joint effect of the selected tree part while adjusting on confounding factors.
We also proposed an ensemble procedure based on the bagging to improve prediction
accuracy and computed several scores of importance for variable selection.
See 'Cyprien Mbogning et al.'(2014)<doi:10.1186/2043-9113-4-6> and
'Cyprien Mbogning et al.'(2015)<doi:10.1159/000380850>
for an overview of all the methods implemented in this package.
Author: Cyprien Mbogning <cyprien.mbogning@inserm.fr> and Wilson Toussile
Maintainer: Cyprien Mbogning <cyprien.mbogning@gmail.com>
Diff between GPLTR versions 1.4 dated 2023-08-26 and 1.5 dated 2024-03-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/doc/GPLTR-manual.pdf |binary inst/doc/intro.pdf |binary man/GPLTR-package.Rd | 4 ++-- man/best.tree.permute.Rd | 3 ++- 6 files changed, 13 insertions(+), 12 deletions(-)
Title: Admissible Exact Intervals for One-Dimensional Discrete
Distributions
Description: Construct the admissible exact intervals for the binomial proportion, the Poisson mean and the total number of subjects with a certain attribute or the total number of the subjects for the hypergeometric distribution. Both one-sided and two-sided intervals are of interest. This package can be used to calculate the intervals constructed methods developed by Wang (2014) <doi:10.5705/ss.2012.257> and Wang (2015) <doi:10.1111/biom.12360>.
Author: Chongxiu Yu [aut, cre],
Weizhen Wang [aut],
Zhongzhan Zhang [aut]
Maintainer: Chongxiu Yu <yuchongxiu@163.com>
Diff between ExactCIone versions 1.0.0 dated 2024-02-17 and 1.0.5 dated 2024-03-28
DESCRIPTION | 6 MD5 | 6 R/WbinoCI.R | 588 +++++++++++++++++++------------------- inst/doc/ExactCIone_vignette.html | 28 - 4 files changed, 314 insertions(+), 314 deletions(-)
Title: Simple Presentation of Estimated Exponential Semi-Variograms
Description: User friendly interface based on the R package 'gstat' to fit
exponential parametric models to empirical semi-variograms in order to
model the spatial correlation structure of health data. Geo-located
health outcomes of survey participants may be used to model spatial
effects on health in an ego-centred approach. The package contains a
range of functions to help explore the spatial structure of the data
as well as visualize the fit of exponential models for various
metaparameter combinations with respect to the number of lag intervals
and maximal distance. Furthermore, the outcome of interest can be
adjusted for covariates by fitting a linear regression in a
preliminary step before the semi-variogram fitting process.
Author: Julia Dyck [aut, cre],
Odile Sauzet [aut],
Jan-Ole Koslik [aut]
Maintainer: Julia Dyck <j.dyck@uni-bielefeld.de>
Diff between EgoCor versions 1.1.0 dated 2023-08-08 and 1.2.0 dated 2024-03-28
DESCRIPTION | 6 +- MD5 | 40 +++++++-------- R/birth.R | 2 R/coords.plot.function.R | 61 +++++++++++----------- R/distance.info.function.R | 17 +++--- R/par.uncertainty.function.R | 2 R/vario.mod.function.gstat.R | 24 ++++----- R/vario.reg.prep.function.R | 18 +++--- build/partial.rdb |binary data/birth.rda |binary inst/REFERENCES.bib | 6 +- inst/doc/Intro_to_EgoCor.Rmd | 23 ++++---- inst/doc/Intro_to_EgoCor.html | 112 ++++++++++++++++++++++-------------------- man/birth.Rd | 2 man/coords.plot.Rd | 8 --- man/distance.info.Rd | 2 man/par.uncertainty.Rd | 2 man/vario.mod.Rd | 2 man/vario.reg.prep.Rd | 18 +++--- vignettes/Intro_to_EgoCor.Rmd | 23 ++++---- vignettes/REFERENCES.bib | 6 +- 21 files changed, 192 insertions(+), 182 deletions(-)
Title: Interactive Tables, Calendars and Charts for the Web
Description: Create interactive tables, calendars and charts with 'TOAST UI' <https://ui.toast.com/> libraries to
integrate in 'shiny' applications or 'rmarkdown' 'HTML' documents.
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
NHN FE Development Lab [cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between toastui versions 0.3.2 dated 2024-03-02 and 0.3.3 dated 2024-03-28
DESCRIPTION | 8 MD5 | 45 - NAMESPACE | 4 NEWS.md | 120 ++-- R/chart.R | 174 +++--- R/datagrid.R | 34 + R/grid-column-renderer.R |only R/grid-columns.R | 56 -- R/grid-editor.R | 422 ++++++++-------- R/grid-proxy.R | 6 R/onLoad.R | 122 ++-- R/shiny.R | 242 ++++----- R/utils.R | 6 README.md | 156 +++--- build/vignette.rds |binary inst/doc/toastui.R | 38 - inst/doc/toastui.html | 790 +++++++++++++++---------------- inst/examples/calendar-edit-schedules.R | 284 +++++------ inst/htmlwidgets/datagrid.js | 2 inst/htmlwidgets/datagrid.js.LICENSE.txt | 4 man/datagrid-shiny.Rd | 6 man/datagrid.Rd | 3 man/grid_col_button.Rd | 2 man/grid_col_checkbox.Rd |only man/guess_colwidths_options.Rd |only 25 files changed, 1265 insertions(+), 1259 deletions(-)
Title: Simple and Configurable Tables in 'HTML', 'LaTeX', 'Markdown',
'Word', 'PNG', 'PDF', and 'Typst' Formats
Description: Create highly customized tables with this simple and dependency-free package. Data frames can be converted to 'HTML', 'LaTeX', 'Markdown', 'Word', 'PNG', 'PDF', or 'Typst' tables. The user interface is minimalist and easy to learn. The syntax concise. 'HTML' tables can be customized using the flexible 'Bootstrap' framework, and 'LaTeX' code with the 'tabularray' package.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinytable versions 0.2.0 dated 2024-03-20 and 0.2.1 dated 2024-03-28
DESCRIPTION | 14 +++++++------- MD5 | 22 ++++++++++++---------- NAMESPACE | 2 ++ NEWS.md | 8 ++++++++ R/build_tt.R | 9 +++++---- R/class.R | 4 +++- R/print.R | 13 ++++++++----- R/sanity.R | 8 ++------ R/tt.R | 4 ++-- build/partial.rdb |binary inst/tinytest/helpers.R | 1 + inst/tinytest/test-misc.R |only inst/tinytest/test-print.R |only 13 files changed, 50 insertions(+), 35 deletions(-)
Title: Retrieve, Harmonise and Map Open Data Regarding the Italian
School System
Description: Compiles and displays the available data sets regarding the Italian school system, with a focus on the infrastructural aspects.
Input datasets are downloaded from the web, with the aim of updating everything to real time.
The functions are divided in four main modules, namely
'Get', to scrape raw data from the web
'Util', various utilities needed to process raw data
'Group', to aggregate data at the municipality or province level
'Map', to visualize the output datasets.
Author: Leonardo Cefalo [aut, cre] ,
Alessio Pollice [ctb, ths] ,
Paolo Maranzano [ctb]
Maintainer: Leonardo Cefalo <leonardo.cefalo@uniba.it>
Diff between SchoolDataIT versions 0.1.0 dated 2024-03-21 and 0.1.1 dated 2024-03-28
SchoolDataIT-0.1.0/SchoolDataIT/R/Get_invalsi_IS.R |only SchoolDataIT-0.1.1/SchoolDataIT/DESCRIPTION | 6 SchoolDataIT-0.1.1/SchoolDataIT/MD5 | 118 ++-- SchoolDataIT-0.1.1/SchoolDataIT/NEWS.md | 5 SchoolDataIT-0.1.1/SchoolDataIT/R/Check_connection.R | 38 - SchoolDataIT-0.1.1/SchoolDataIT/R/Get_AdmUnNames.R | 22 SchoolDataIT-0.1.1/SchoolDataIT/R/Get_BroadBand.R | 38 - SchoolDataIT-0.1.1/SchoolDataIT/R/Get_DB_MIUR.R | 37 + SchoolDataIT-0.1.1/SchoolDataIT/R/Get_InnerAreas.R | 29 - SchoolDataIT-0.1.1/SchoolDataIT/R/Get_Invalsi_IS.R |only SchoolDataIT-0.1.1/SchoolDataIT/R/Get_Registry.R | 32 - SchoolDataIT-0.1.1/SchoolDataIT/R/Get_RiskMap.R | 20 SchoolDataIT-0.1.1/SchoolDataIT/R/Get_School2mun.R | 51 + SchoolDataIT-0.1.1/SchoolDataIT/R/Get_Shapefile.R | 21 SchoolDataIT-0.1.1/SchoolDataIT/R/Get_nstud.R | 32 - SchoolDataIT-0.1.1/SchoolDataIT/R/Get_nteachers_prov.R | 39 + SchoolDataIT-0.1.1/SchoolDataIT/R/Group_BroadBand.R | 5 SchoolDataIT-0.1.1/SchoolDataIT/R/Group_DB_MIUR.R | 34 - SchoolDataIT-0.1.1/SchoolDataIT/R/Group_nstud.R | 72 +- SchoolDataIT-0.1.1/SchoolDataIT/R/Group_teachers4stud.R | 75 +- SchoolDataIT-0.1.1/SchoolDataIT/R/Map_DB.R | 56 + SchoolDataIT-0.1.1/SchoolDataIT/R/Map_Invalsi.R | 55 + SchoolDataIT-0.1.1/SchoolDataIT/R/Map_School_Buildings.R | 55 + SchoolDataIT-0.1.1/SchoolDataIT/R/Set_DB.R | 289 +++++----- SchoolDataIT-0.1.1/SchoolDataIT/R/Util_Check_nstud_availability.R | 82 +- SchoolDataIT-0.1.1/SchoolDataIT/R/Util_DB_MIUR_bool.R | 7 SchoolDataIT-0.1.1/SchoolDataIT/R/Util_DB_MIUR_num.R | 31 - SchoolDataIT-0.1.1/SchoolDataIT/R/Util_Invalsi_filter.R | 36 - SchoolDataIT-0.1.1/SchoolDataIT/R/Util_nstud_wide.R | 35 - SchoolDataIT-0.1.1/SchoolDataIT/R/example_AdmUnNames20220630.R | 2 SchoolDataIT-0.1.1/SchoolDataIT/R/example_InnerAreas.R | 3 SchoolDataIT-0.1.1/SchoolDataIT/R/example_input_DB23_MIUR.R | 3 SchoolDataIT-0.1.1/SchoolDataIT/data/example_AdmUnNames20220630.rda |binary SchoolDataIT-0.1.1/SchoolDataIT/data/example_InnerAreas.rda |binary SchoolDataIT-0.1.1/SchoolDataIT/data/example_input_DB23_MIUR.rda |binary SchoolDataIT-0.1.1/SchoolDataIT/man/Get_AdmUnNames.Rd | 6 SchoolDataIT-0.1.1/SchoolDataIT/man/Get_BroadBand.Rd | 11 SchoolDataIT-0.1.1/SchoolDataIT/man/Get_DB_MIUR.Rd | 8 SchoolDataIT-0.1.1/SchoolDataIT/man/Get_InnerAreas.Rd | 7 SchoolDataIT-0.1.1/SchoolDataIT/man/Get_Invalsi_IS.Rd | 13 SchoolDataIT-0.1.1/SchoolDataIT/man/Get_Registry.Rd | 7 SchoolDataIT-0.1.1/SchoolDataIT/man/Get_RiskMap.Rd | 6 SchoolDataIT-0.1.1/SchoolDataIT/man/Get_School2mun.Rd | 11 SchoolDataIT-0.1.1/SchoolDataIT/man/Get_Shapefile.Rd | 6 SchoolDataIT-0.1.1/SchoolDataIT/man/Get_nstud.Rd | 7 SchoolDataIT-0.1.1/SchoolDataIT/man/Get_nteachers_prov.Rd | 8 SchoolDataIT-0.1.1/SchoolDataIT/man/Group_DB_MIUR.Rd | 6 SchoolDataIT-0.1.1/SchoolDataIT/man/Group_nstud.Rd | 12 SchoolDataIT-0.1.1/SchoolDataIT/man/Group_teachers4stud.Rd | 22 SchoolDataIT-0.1.1/SchoolDataIT/man/Map_DB.Rd | 3 SchoolDataIT-0.1.1/SchoolDataIT/man/Map_Invalsi.Rd | 5 SchoolDataIT-0.1.1/SchoolDataIT/man/Map_School_Buildings.Rd | 3 SchoolDataIT-0.1.1/SchoolDataIT/man/Set_DB.Rd | 29 - SchoolDataIT-0.1.1/SchoolDataIT/man/Util_Check_nstud_availability.Rd | 5 SchoolDataIT-0.1.1/SchoolDataIT/man/Util_DB_MIUR_bool.Rd | 3 SchoolDataIT-0.1.1/SchoolDataIT/man/Util_DB_MIUR_num.Rd | 5 SchoolDataIT-0.1.1/SchoolDataIT/man/Util_Invalsi_filter.Rd | 12 SchoolDataIT-0.1.1/SchoolDataIT/man/Util_nstud_wide.Rd | 9 SchoolDataIT-0.1.1/SchoolDataIT/man/example_AdmUnNames20220630.Rd | 2 SchoolDataIT-0.1.1/SchoolDataIT/man/example_InnerAreas.Rd | 3 SchoolDataIT-0.1.1/SchoolDataIT/man/example_input_DB23_MIUR.Rd | 3 61 files changed, 959 insertions(+), 581 deletions(-)
Title: Tools for Type S (Sign) and Type M (Magnitude) Errors
Description: Provides tools for working with Type S (Sign) and
Type M (Magnitude) errors, as proposed in Gelman and Tuerlinckx (2000)
<doi:10.1007/s001800000040> and
Gelman & Carlin (2014) <doi:10.1177/1745691614551642>.
In addition to simply calculating the probability of
Type S/M error, the package includes functions for calculating these errors
across a variety of effect sizes for comparison, and recommended sample size
given "tolerances" for Type S/M errors. To improve the speed of these
calculations, closed forms solutions for the probability of a Type S/M error
from Lu, Qiu, and Deng (2018) <doi:10.1111/bmsp.12132>
are implemented. As of 1.0.0, this includes
support only for simple research designs. See the
package vignette for a fuller exposition on how Type S/M errors arise in
research, and how to analyze them using the type of design analysis proposed
in the above papers.
Author: Andrew Timm [cre, aut],
Andrew Gelman [ctb, cph],
John Carlin [ctb, cph],
Martijn Weterings [ctb]
Maintainer: Andrew Timm <timmandrew1@gmail.com>
Diff between retrodesign versions 0.2.1 dated 2023-11-02 and 0.2.2 dated 2024-03-28
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 10 ++++++++++ R/simple_hypothesis_tests.R | 4 ++-- inst/doc/Intro_To_retrodesign.R | 2 +- inst/doc/Intro_To_retrodesign.html | 22 ++++++++++++++-------- tests/testthat/test_sim_precision.R | 27 ++++++++++++++++++++------- 7 files changed, 56 insertions(+), 27 deletions(-)
Title: Interpolation and Extrapolation for Three Dimensions of
Biodiversity
Description: Biodiversity is a multifaceted concept covering different levels of organization from
genes to ecosystems. 'iNEXT.3D' extends 'iNEXT' to include three dimensions (3D)
of biodiversity, i.e., taxonomic diversity (TD), phylogenetic diversity (PD) and functional
diversity (FD). This package provides functions to compute standardized 3D diversity estimates
with a common sample size or sample coverage. A unified framework based on Hill numbers
and their generalizations (Hill-Chao numbers) are used to quantify 3D. All 3D estimates
are in the same units of species/lineage equivalents and can be meaningfully compared.
The package features size- and coverage-based rarefaction and extrapolation sampling
curves to facilitate rigorous comparison of 3D diversity across individual assemblages.
Asymptotic 3D diversity estimates are also provided. See Chao et al. (2021)
<doi:10.1111/2041-210X.13682> for more details.
Author: Anne Chao [aut, cre],
KaiHsiang Hu [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between iNEXT.3D versions 1.0.3 dated 2024-03-25 and 1.0.4 dated 2024-03-28
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS | 8 +++++++- R/CommonFun.R | 5 ++++- R/FD_Fun.R | 46 ++++++++++++++++++++++++++++------------------ R/PD_Fun.R | 7 +++++-- R/TD_Fun.R | 8 ++++---- inst/doc/Introduction.pdf |binary 8 files changed, 58 insertions(+), 36 deletions(-)
Title: Interface to the 'OpenGWAS' Database API
Description: Interface to the 'OpenGWAS' database API <https://gwas-api.mrcieu.ac.uk/>. Includes a wrapper
to make generic calls to the API, plus convenience functions for
specific queries.
Author: Gibran Hemani [aut, cre, cph] ,
Ben Elsworth [aut] ,
Tom Palmer [aut] ,
Rita Rasteiro [aut]
Maintainer: Gibran Hemani <g.hemani@bristol.ac.uk>
Diff between ieugwasr versions 0.2.0 dated 2024-03-25 and 0.2.2 dated 2024-03-28
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 9 +++++++++ R/query.R | 2 +- R/zzz.R | 11 +++++++++-- tests/testthat/test_afl2.r | 5 ++++- tests/testthat/test_api.r | 8 ++++++-- tests/testthat/test_backwards.r | 2 -- tests/testthat/test_ld.r | 6 +++++- tests/testthat/test_query.r | 12 +++++++++++- tests/testthat/test_variants.r | 6 +++++- 11 files changed, 63 insertions(+), 24 deletions(-)
Title: 'GitHub' 'API'
Description: Minimal client to access the 'GitHub' 'API'.
Author: Gabor Csardi [cre, ctb],
Jennifer Bryan [aut],
Hadley Wickham [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between gh versions 1.4.0 dated 2023-02-22 and 1.4.1 dated 2024-03-28
DESCRIPTION | 22 +++++----- LICENSE | 4 - MD5 | 57 +++++++++++++++----------- NAMESPACE | 2 NEWS.md | 21 ++++++--- R/gh-package.R | 2 R/gh.R | 55 +++++++++++++++++-------- R/gh_request.R | 12 +++++ R/gh_response.R | 2 R/import-standalone-purrr.R |only R/pagination.R | 46 ++------------------ README.md | 8 +++ build/vignette.rds |binary inst/WORDLIST | 3 - inst/doc/managing-personal-access-tokens.R | 4 - inst/doc/managing-personal-access-tokens.html | 26 +++++------ man/figures |only man/gh-package.Rd | 3 - man/gh.Rd | 23 +++++++++- tests/testthat.R | 4 + tests/testthat/_snaps/gh.md | 8 +++ tests/testthat/_snaps/gh_whoami.md | 2 tests/testthat/_snaps/pagination.md |only tests/testthat/test-gh.R | 34 +++++++++++++++ tests/testthat/test-gh_response.R | 18 +++++++- tests/testthat/test-pagination.R | 24 ++++++++++ tests/testthat/test-print.R | 1 27 files changed, 254 insertions(+), 127 deletions(-)
Title: Retrieve ESPN Fantasy Football Data
Description: Format the raw data from the ESPN fantasy football API
<https://fantasy.espn.com/apis/v3/games/ffl/> as data frames.
Retrieve data on public leagues, rosters, athletes, and matches.
Author: Kiernan Nicholls [aut, cre, cph]
Maintainer: Kiernan Nicholls <k5cents@gmail.com>
Diff between fflr versions 2.2.3 dated 2024-03-11 and 2.2.4 dated 2024-03-28
DESCRIPTION | 6 +-- MD5 | 20 +++++------ NEWS.md | 4 ++ R/live.R | 14 ++++++++ README.md | 18 +++++----- build/vignette.rds |binary inst/doc/fantasy-football.R | 2 - inst/doc/fantasy-football.html | 71 +++++++++++++++-------------------------- tests/testthat/test-best.R | 4 +- tests/testthat/test-live.R | 6 +-- tests/testthat/test-outlook.R | 6 ++- 11 files changed, 79 insertions(+), 72 deletions(-)
Title: Network Analysis of Dependencies of CRAN Packages
Description: The dependencies of CRAN packages can be analysed in a network fashion. For each package we can obtain the packages that it depends, imports, suggests, etc. By iterating this procedure over a number of packages, we can build, visualise, and analyse the dependency network, enabling us to have a bird's-eye view of the CRAN ecosystem. One aspect of interest is the number of reverse dependencies of the packages, or equivalently the in-degree distribution of the dependency network. This can be fitted by the power law and/or an extreme value mixture distribution <arXiv:2008.03073>, of which functions are provided.
Author: Clement Lee [aut, cre]
Maintainer: Clement Lee <clement.lee.tm@outlook.com>
Diff between crandep versions 0.3.6 dated 2024-02-26 and 0.3.7 dated 2024-03-28
DESCRIPTION | 6 MD5 | 44 +- NEWS.md | 6 R/RcppExports.R | 43 +- R/optim.R | 69 +++- build/vignette.rds |binary inst/doc/cran.html | 46 +- inst/doc/degree.R | 4 inst/doc/degree.Rmd | 4 inst/doc/degree.html | 58 +-- inst/doc/introduction.html | 4 man/marg_pow.Rd | 2 man/mcmc_mix1.Rd | 10 man/mcmc_mix1_wrapper.Rd | 6 man/mcmc_mix2.Rd | 7 man/mcmc_mix2_wrapper.Rd | 8 man/mcmc_mix3.Rd | 7 man/mcmc_mix3_wrapper.Rd | 8 man/mcmc_pol.Rd | 9 man/mcmc_pol_wrapper.Rd | 11 src/RcppExports.cpp | 67 ++-- src/algo.cpp | 700 +++++++++++++++++++++++++++++---------------- vignettes/degree.Rmd | 4 23 files changed, 703 insertions(+), 420 deletions(-)
Title: Utilities for 'big.matrix' Objects from Package 'bigmemory'
Description: Extend the 'bigmemory' package with various analytics.
Functions 'bigkmeans' and 'binit' may also be used with native R objects.
For 'tapply'-like functions, the bigtabulate package may also be helpful.
For linear algebra support, see 'bigalgebra'. For mutex (locking) support
for advanced shared-memory usage, see 'synchronicity'.
Author: John W. Emerson [aut],
Michael J. Kane [cre, aut] ,
Saksham Chandra [ctb]
Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>
Diff between biganalytics versions 1.1.21 dated 2020-06-09 and 1.1.22 dated 2024-03-28
DESCRIPTION | 22 +++++++++++----------- MD5 | 12 ++++++------ NAMESPACE | 1 + R/apply.R | 2 +- R/hello-biganalytics.R | 2 +- man/apply-methods.Rd | 3 +-- man/biganalytics-package.Rd | 2 +- 7 files changed, 22 insertions(+), 22 deletions(-)
Title: S3 Classes and Methods for Tidy Functional Data
Description: Defines S3 vector data types for vectors of functional data
(grid-based, spline-based or functional principal components-based) with all
arithmetic and summary methods, derivation, integration and smoothing,
plotting, data import and export, and data wrangling, such as re-evaluating,
subsetting, sub-assigning, zooming into sub-domains, or extracting functional
features like minima/maxima and their locations.
The implementation allows including such vectors in data frames for joint
analysis of functional and scalar variables.
Author: Fabian Scheipl [aut, cre] ,
Jeff Goldsmith [aut],
Julia Wrobel [ctb] ,
Maximilian Muecke [ctb] ,
Sebastian Fischer [ctb] ,
Trevor Hastie [ctb] ,
Rahul Mazumder [ctb] ,
Chen Meng [ctb]
Maintainer: Fabian Scheipl <fabian.scheipl@googlemail.com>
Diff between tf versions 0.3.2 dated 2024-03-18 and 0.3.3 dated 2024-03-28
DESCRIPTION | 6 - MD5 | 19 ++-- NEWS.md |only R/ops.R | 6 - R/rebase.R | 23 +++++ R/tfb-fpc.R | 16 +++ R/utils.R | 15 +++ R/vctrs-ptype2.R | 63 ++++++--------- man/tfb_fpc.Rd | 16 +++ tests/testthat/test-concatenation.R | 5 - tests/testthat/test-rebase.R | 150 ++++++++++++++++++------------------ 11 files changed, 184 insertions(+), 135 deletions(-)
Title: Penalized Synthetic Control Estimation
Description: Estimate penalized synthetic control models
and perform hold-out validation to determine their
penalty parameter. This method is based on the work by
Abadie & L'Hour (2021) <doi:10.1080/01621459.2021.1971535>.
Penalized synthetic controls smoothly interpolate between
one-to-one matching and the synthetic control method.
Author: Erik-Jan van Kesteren [cre, aut]
,
Isaac Slaughter [ctb]
Maintainer: Erik-Jan van Kesteren <e.vankesteren1@uu.nl>
Diff between pensynth versions 0.3.0 dated 2024-03-15 and 0.5.1 dated 2024-03-28
pensynth-0.3.0/pensynth/man/plot_path.Rd |only pensynth-0.5.1/pensynth/DESCRIPTION | 16 - pensynth-0.5.1/pensynth/MD5 | 42 ++- pensynth-0.5.1/pensynth/NAMESPACE | 39 ++- pensynth-0.5.1/pensynth/R/convex_hull.R | 94 ++++++- pensynth-0.5.1/pensynth/R/cv_pensynth.R | 156 ++++++++---- pensynth-0.5.1/pensynth/R/examples |only pensynth-0.5.1/pensynth/R/pensynth.R | 107 +++++--- pensynth-0.5.1/pensynth/R/placebo_test.R |only pensynth-0.5.1/pensynth/R/simulate_data.R |only pensynth-0.5.1/pensynth/R/standardization.R | 2 pensynth-0.5.1/pensynth/man/cv_pensynth.Rd | 33 -- pensynth-0.5.1/pensynth/man/in_convex_hull.Rd | 77 ++++- pensynth-0.5.1/pensynth/man/lambda_sequence.Rd |only pensynth-0.5.1/pensynth/man/pensynth.Rd | 27 +- pensynth-0.5.1/pensynth/man/placebo_test.Rd |only pensynth-0.5.1/pensynth/man/plot.cvpensynth.Rd |only pensynth-0.5.1/pensynth/man/plot.pensynthtest.Rd |only pensynth-0.5.1/pensynth/man/predict.cvpensynth.Rd |only pensynth-0.5.1/pensynth/man/predict.pensynth.Rd |only pensynth-0.5.1/pensynth/man/print.cvpensynth.Rd |only pensynth-0.5.1/pensynth/man/print.pensynth.Rd |only pensynth-0.5.1/pensynth/man/simulate_data.Rd |only pensynth-0.5.1/pensynth/man/standardize_X.Rd | 3 pensynth-0.5.1/pensynth/tests/testthat/test-convexhull.R |only pensynth-0.5.1/pensynth/tests/testthat/test-cvpensynth.R | 2 pensynth-0.5.1/pensynth/tests/testthat/test-placebo_test.R |only pensynth-0.5.1/pensynth/tests/testthat/test-simulate_data.R |only 28 files changed, 424 insertions(+), 174 deletions(-)
Title: Next Generation Clustered Heat Maps
Description: Next-Generation Clustered Heat Maps (NG-CHMs) allow for
dynamic exploration of heat map data in a web browser. 'NGCHM' allows
users to create both stand-alone HTML files containing a
Next-Generation Clustered Heat Map, and .ngchm files to view in the
NG-CHM viewer. See Ryan MC, Stucky M, et al (2020)
<doi:10.12688/f1000research.20590.2> for more details.
Author: Bradley M Broom [aut] ,
Mary A Rohrdanz [ctb, cre],
Chris Wakefield [ctb],
James Melott [ctb],
MD Anderson Cancer Center [cph]
Maintainer: Mary A Rohrdanz <marohrdanz@mdanderson.org>
Diff between NGCHM versions 1.0.1 dated 2024-01-16 and 1.0.2 dated 2024-03-28
DESCRIPTION | 15 ++++--- MD5 | 19 +++++----- R/functions.R | 79 +++++++++++++++++++++++++++++------------- R/internalFunctions.R |only R/package.R | 10 +++++ R/zzz.R | 7 ++- man/NGCHM-package.Rd | 12 ++++++ man/chmExportToFile-method.Rd | 8 ++++ man/chmExportToHTML-method.Rd | 8 ++++ man/chmExportToPDF-method.Rd | 8 ++++ man/chmNew.Rd | 1 11 files changed, 126 insertions(+), 41 deletions(-)
Title: Meta-Analysis Package for R
Description: A comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit equal-, fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat, bubble, and GOSH plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta [...truncated...]
Author: Wolfgang Viechtbauer [aut, cre]
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>
Diff between metafor versions 4.4-0 dated 2023-09-27 and 4.6-0 dated 2024-03-28
DESCRIPTION | 18 MD5 | 434 ++++++++-------- NAMESPACE | 1 NEWS.md | 30 + R/AIC.rma.r | 2 R/BIC.rma.r | 2 R/addpoly.default.r | 22 R/addpoly.predict.rma.r | 2 R/addpoly.rma.r | 8 R/aggregate.escalc.r | 4 R/anova.rma.r | 62 +- R/baujat.rma.r | 2 R/bldiag.r | 8 R/blsplit.r | 2 R/blup.rma.uni.r | 15 R/coef.matreg.r | 2 R/coef.permutest.rma.uni.r | 2 R/coef.rma.r | 2 R/coef.summary.rma.r | 2 R/confint.rma.glmm.r | 2 R/confint.rma.ls.r | 20 R/confint.rma.mh.r | 4 R/confint.rma.mv.r | 38 - R/confint.rma.peto.r | 4 R/confint.rma.uni.r | 20 R/confint.rma.uni.selmodel.r | 23 R/contrmat.r | 2 R/conv.2x2.r | 2 R/conv.delta.r | 2 R/conv.fivenum.r | 8 R/conv.wald.r | 4 R/cooks.distance.rma.mv.r | 11 R/cumul.rma.mh.r | 16 R/cumul.rma.peto.r | 16 R/cumul.rma.uni.r | 14 R/deviance.rma.r | 2 R/df.residual.rma.r | 2 R/dfbetas.rma.mv.r | 9 R/dfround.r | 2 R/emmprep.r | 4 R/escalc.r | 389 +++++++++----- R/fitstats.rma.r | 2 R/fitted.rma.r | 2 R/forest.cumul.rma.r | 71 +- R/forest.default.r | 81 +- R/forest.rma.r | 149 ++--- R/formatters.r | 32 - R/formula.rma.r | 2 R/fsn.r | 42 - R/funnel.default.r | 107 +-- R/funnel.rma.r | 107 +-- R/gosh.rma.r | 6 R/hatvalues.rma.mv.r | 6 R/hatvalues.rma.uni.r | 6 R/hc.rma.uni.r | 4 R/influence.rma.uni.r | 19 R/labbe.rma.r | 16 R/leave1out.rma.mh.r | 4 R/leave1out.rma.peto.r | 4 R/leave1out.rma.uni.r | 2 R/llplot.r | 16 R/logLik.rma.r | 2 R/matreg.r | 2 R/methods.confint.rma.r | 13 R/methods.list.rma.r | 2 R/mfopt.r | 10 R/misc.func.hidden.escalc.r | 15 R/misc.func.hidden.funnel.r | 4 R/misc.func.hidden.glmm.r | 12 R/misc.func.hidden.mv.r | 68 +- R/misc.func.hidden.profile.r | 35 - R/misc.func.hidden.r | 242 ++++++-- R/misc.func.hidden.selmodel.r | 105 +++ R/misc.func.hidden.uni.r | 24 R/model.matrix.rma.r | 2 R/nobs.rma.r | 2 R/permutest.rma.ls.r | 2 R/permutest.rma.uni.r | 2 R/plot.cumul.rma.r | 26 R/plot.gosh.rma.r | 29 - R/plot.infl.rma.uni.r | 5 R/plot.permutest.rma.uni.r | 24 R/plot.profile.rma.r | 45 + R/plot.rma.glmm.r | 2 R/plot.rma.mh.r | 2 R/plot.rma.peto.r | 2 R/plot.rma.uni.r | 2 R/plot.rma.uni.selmodel.r | 8 R/plot.vif.rma.r | 30 - R/predict.rma.ls.r | 84 +-- R/predict.rma.r | 27 R/print.anova.rma.r | 4 R/print.confint.rma.r | 2 R/print.escalc.r | 2 R/print.fsn.r | 2 R/print.gosh.rma.r | 2 R/print.hc.rma.uni.r | 2 R/print.infl.rma.uni.r | 2 R/print.list.anova.rma.r | 2 R/print.list.confint.rma.r | 2 R/print.list.rma.r | 4 R/print.matreg.r | 2 R/print.permutest.rma.uni.r | 2 R/print.profile.rma.r | 2 R/print.ranktest.r | 2 R/print.regtest.r | 2 R/print.rma.glmm.r | 2 R/print.rma.mh.r | 2 R/print.rma.mv.r | 16 R/print.rma.peto.r | 2 R/print.rma.uni.r | 8 R/print.summary.matreg.r | 2 R/print.summary.rma.r | 2 R/print.tes.r | 2 R/print.vif.rma.r | 2 R/profile.rma.ls.r | 95 ++- R/profile.rma.mv.r | 147 +++-- R/profile.rma.uni.r | 181 +++++- R/profile.rma.uni.selmodel.r | 103 ++- R/qqnorm.rma.glmm.r | 2 R/qqnorm.rma.mh.r | 2 R/qqnorm.rma.mv.r | 2 R/qqnorm.rma.peto.r | 2 R/qqnorm.rma.uni.r | 12 R/radial.rma.r | 12 R/ranef.rma.mv.r | 4 R/ranef.rma.uni.r | 9 R/ranktest.r | 8 R/rcalc.r | 15 R/regplot.rma.r | 98 +-- R/regtest.r | 22 R/replmiss.r | 2 R/reporter.rma.uni.r | 2 R/residuals.rma.r | 2 R/rma.glmm.r | 26 R/rma.mh.r | 48 - R/rma.mv.r | 178 +++--- R/rma.peto.r | 34 - R/rma.uni.r | 354 ++++++------- R/robust.rma.mv.r | 33 - R/robust.rma.uni.r | 33 - R/rstandard.rma.mh.r | 4 R/rstandard.rma.mv.r | 11 R/rstandard.rma.peto.r | 4 R/rstandard.rma.uni.r | 4 R/rstudent.rma.mh.r | 4 R/rstudent.rma.mv.r | 9 R/rstudent.rma.peto.r | 4 R/selmodel.rma.uni.r | 379 ++++++++++--- R/simulate.rma.r | 5 R/summary.escalc.r | 9 R/summary.matreg.r | 2 R/summary.rma.r | 2 R/tes.r | 37 - R/to.long.r | 46 - R/to.table.r | 46 - R/to.wide.r | 2 R/trimfill.rma.uni.r | 14 R/update.rma.r | 2 R/vcalc.r | 43 + R/vcov.matreg.r | 2 R/vcov.rma.r | 2 R/vec2mat.r | 2 R/vif.rma.r | 32 - R/weights.rma.glmm.r | 2 R/weights.rma.mh.r | 2 R/weights.rma.mv.r | 2 R/weights.rma.peto.r | 2 R/weights.rma.uni.r | 2 R/zzz.r | 2 README.md | 2 build/metafor.pdf |binary build/stage23.rdb |binary build/vignette.rds |binary man/addpoly.default.Rd | 2 man/addpoly.predict.rma.Rd | 2 man/addpoly.rma.Rd | 2 man/blup.Rd | 2 man/coef.permutest.rma.uni.Rd | 2 man/coef.rma.Rd | 2 man/confint.rma.Rd | 6 man/conv.delta.Rd | 4 man/conv.fivenum.Rd | 6 man/conv.wald.Rd | 4 man/cumul.Rd | 2 man/emmprep.Rd | 2 man/escalc.Rd | 39 - man/forest.cumul.rma.Rd | 2 man/forest.default.Rd | 8 man/forest.rma.Rd | 14 man/fsn.Rd | 2 man/gosh.Rd | 4 man/leave1out.Rd | 2 man/metafor-package.Rd | 2 man/methods.confint.rma.Rd | 4 man/mfopt.Rd | 2 man/misc-models.Rd | 12 man/misc-options.Rd | 17 man/misc-recs.Rd | 4 man/plot.gosh.rma.Rd | 4 man/plot.infl.rma.uni.Rd | 2 man/predict.rma.Rd | 13 man/print.escalc.Rd | 2 man/profile.rma.Rd | 75 +- man/ranef.Rd | 2 man/rma.glmm.Rd | 2 man/rma.mv.Rd | 2 man/rma.uni.Rd | 8 man/selmodel.Rd | 28 - man/to.table.Rd | 4 man/transf.Rd | 6 man/weights.rma.Rd | 2 tests/testthat/test_analysis_example_viechtbauer2007b.r | 4 tests/testthat/test_misc_escalc.r | 4 tests/testthat/test_misc_rma_uni.r | 4 tests/testthat/test_misc_selmodel.r | 14 tests/testthat/test_plots_baujat_plot.r | 2 tests/testthat/test_plots_labbe_plot.r | 2 218 files changed, 2919 insertions(+), 2306 deletions(-)
Title: Simplify 'ggplot2' Visualisation
Description: Simplify 'ggplot2' visualisation with 'ggblanket' wrapper
functions.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggblanket versions 6.0.0 dated 2024-02-23 and 7.0.0 dated 2024-03-28
ggblanket-6.0.0/ggblanket/R/col_pals.R |only ggblanket-6.0.0/ggblanket/R/mode_set.R |only ggblanket-6.0.0/ggblanket/man/greys.Rd |only ggblanket-6.0.0/ggblanket/man/mode_set.Rd |only ggblanket-6.0.0/ggblanket/man/plum.Rd |only ggblanket-7.0.0/ggblanket/DESCRIPTION | 15 ggblanket-7.0.0/ggblanket/MD5 | 436 +-- ggblanket-7.0.0/ggblanket/NAMESPACE | 7 ggblanket-7.0.0/ggblanket/NEWS.md | 16 ggblanket-7.0.0/ggblanket/R/aes_contrast.R | 38 ggblanket-7.0.0/ggblanket/R/base_mode.R | 110 ggblanket-7.0.0/ggblanket/R/colours.R |only ggblanket-7.0.0/ggblanket/R/dark_mode.R | 82 ggblanket-7.0.0/ggblanket/R/gg_area.R | 33 ggblanket-7.0.0/ggblanket/R/gg_bar.R | 33 ggblanket-7.0.0/ggblanket/R/gg_bin_2d.R | 33 ggblanket-7.0.0/ggblanket/R/gg_blanket.R | 896 +----- ggblanket-7.0.0/ggblanket/R/gg_boxplot.R | 33 ggblanket-7.0.0/ggblanket/R/gg_col.R | 33 ggblanket-7.0.0/ggblanket/R/gg_contour.R | 33 ggblanket-7.0.0/ggblanket/R/gg_contour_filled.R | 33 ggblanket-7.0.0/ggblanket/R/gg_crossbar.R | 33 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Title: Apply Function to Elements in Parallel using Futures
Description: Implementations of apply(), by(), eapply(), lapply(), Map(), .mapply(), mapply(), replicate(), sapply(), tapply(), and vapply() that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster. These future_*apply() functions come with the same pros and cons as the corresponding base-R *apply() functions but with the additional feature of being able to be processed via the future framework.
Author: Henrik Bengtsson [aut, cre, cph]
,
R Core Team [cph, ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.apply versions 1.11.1 dated 2023-12-21 and 1.11.2 dated 2024-03-28
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NEWS.md | 7 +++++++ R/future_lapply.R | 3 +-- R/options.R | 3 +-- build/vignette.rds |binary man/future.apply.Rd | 9 +++++++++ man/future.apply.options.Rd | 3 +-- man/future_lapply.Rd | 3 +-- tests/future_mapply,globals.R | 2 +- tests/startup.Rs |only 11 files changed, 35 insertions(+), 22 deletions(-)
Title: Area-Proportional Euler and Venn Diagrams with Ellipses
Description: Generate area-proportional Euler diagrams
using numerical optimization. An Euler diagram is a generalization of a Venn
diagram, relaxing the criterion that all interactions need to be
represented. Diagrams may be fit with ellipses and circles via
a wide range of inputs and can be visualized in numerous ways.
Author: Johan Larsson [aut, cre] ,
A. Jonathan R. Godfrey [ctb],
Peter Gustafsson [ctb],
David H. Eberly [ctb] ,
Emanuel Huber [ctb] ,
Florian Prive [ctb]
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between eulerr versions 7.0.1 dated 2024-02-16 and 7.0.2 dated 2024-03-28
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 8 +++++++- R/plot.euler.R | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/gallery.html | 22 +++++++++++----------- inst/doc/introduction.html | 4 ++-- inst/doc/under-the-hood.html | 4 ++-- inst/doc/venn-diagrams.html | 4 ++-- inst/doc/visualization.html | 4 ++-- 11 files changed, 41 insertions(+), 35 deletions(-)
Title: Model Transport of Environmental DNA in River Networks
Description: Runs the eDITH (environmental DNA Integrating Transport
and Hydrology) model, which implements a mass balance of environmental DNA (eDNA)
transport at a river network scale coupled with a species distribution model
to obtain maps of species distribution. eDITH can work with both eDNA concentration
(e.g., obtained via quantitative polymerase chain reaction) or metabarcoding
(read count) data. Parameter estimation can be performed via Bayesian techniques
(via the 'BayesianTools' package) or optimization algorithms. An interface to the
'DHARMa' package for posterior predictive checks is provided. See Carraro and
Altermatt (2024) <doi:10.1111/2041-210X.14317> for a package introduction;
Carraro et al. (2018) <doi:10.1073/pnas.1813843115> and Carraro et al. (2020)
<doi:10.1038/s41467-020-17337-8> for methodological details.
Author: Luca Carraro [cre, aut],
Florian Altermatt [aut],
University of Zurich [cph, fnd]
Maintainer: Luca Carraro <luca.carraro@hotmail.it>
Diff between eDITH versions 0.2.0 dated 2024-01-16 and 0.3.0 dated 2024-03-28
DESCRIPTION | 11 ++++++----- MD5 | 11 ++++++----- NEWS.md | 11 +++++++++++ R/run_eDITH_optim.R | 20 +++++++++++--------- inst/CITATION |only inst/doc/eDITH.R | 28 ++++++++++++++-------------- man/run_eDITH_optim.Rd | 11 ++++++++--- 7 files changed, 56 insertions(+), 36 deletions(-)
Title: Chemical Analysis of Proteins
Description: Chemical analysis of proteins based on their amino acid
compositions. Amino acid compositions can be read from FASTA files and used to
calculate chemical metrics including carbon oxidation state and stoichiometric
hydration state, as described in Dick et al. (2020) <doi:10.5194/bg-17-6145-2020>.
Other properties that can be calculated include protein length, grand average of
hydropathy (GRAVY), isoelectric point (pI), molecular weight (MW), standard
molal volume (V0), and metabolic costs (Akashi and Gojobori, 2002
<doi:10.1073/pnas.062526999>; Wagner, 2005 <doi:10.1093/molbev/msi126>;
Zhang et al., 2018 <doi:10.1038/s41467-018-06461-1>). A database of amino acid
compositions of human proteins derived from UniProt is provided.
Author: Jeffrey Dick [aut, cre]
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Diff between canprot versions 1.1.2 dated 2022-01-17 and 2.0.0 dated 2024-03-28
canprot-1.1.2/canprot/R/check_IDs.R |only canprot-1.1.2/canprot/R/cleanup.R |only canprot-1.1.2/canprot/R/diffplot.R |only canprot-1.1.2/canprot/R/get_comptab.R |only canprot-1.1.2/canprot/R/mkvig.R |only canprot-1.1.2/canprot/R/pdat_3D.R |only canprot-1.1.2/canprot/R/pdat_breast.R |only canprot-1.1.2/canprot/R/pdat_colorectal.R |only canprot-1.1.2/canprot/R/pdat_glucose.R |only canprot-1.1.2/canprot/R/pdat_hypoxia.R |only canprot-1.1.2/canprot/R/pdat_liver.R |only canprot-1.1.2/canprot/R/pdat_lung.R |only canprot-1.1.2/canprot/R/pdat_multi.R |only canprot-1.1.2/canprot/R/pdat_osmotic.R |only canprot-1.1.2/canprot/R/pdat_osmotic_bact.R |only canprot-1.1.2/canprot/R/pdat_osmotic_euk.R |only canprot-1.1.2/canprot/R/pdat_osmotic_halo.R |only canprot-1.1.2/canprot/R/pdat_pancreatic.R |only canprot-1.1.2/canprot/R/pdat_prostate.R |only canprot-1.1.2/canprot/R/pdat_secreted.R |only canprot-1.1.2/canprot/R/protcomp.R |only canprot-1.1.2/canprot/R/qdist.R |only canprot-1.1.2/canprot/R/xsummary.R |only canprot-1.1.2/canprot/R/xsummary2.R |only canprot-1.1.2/canprot/R/xsummary3.R |only canprot-1.1.2/canprot/demo/X3D.R |only canprot-1.1.2/canprot/demo/breast.R |only canprot-1.1.2/canprot/demo/colorectal.R |only canprot-1.1.2/canprot/demo/glucose.R |only canprot-1.1.2/canprot/demo/hypoxia.R |only canprot-1.1.2/canprot/demo/liver.R |only canprot-1.1.2/canprot/demo/lung.R |only canprot-1.1.2/canprot/demo/osmotic_bact.R |only canprot-1.1.2/canprot/demo/osmotic_euk.R |only canprot-1.1.2/canprot/demo/osmotic_halo.R |only canprot-1.1.2/canprot/demo/pancreatic.R |only canprot-1.1.2/canprot/demo/prostate.R |only canprot-1.1.2/canprot/demo/secreted.R |only canprot-1.1.2/canprot/inst/NEWS |only canprot-1.1.2/canprot/inst/doc/canprot.R |only canprot-1.1.2/canprot/inst/doc/canprot.Rmd |only canprot-1.1.2/canprot/inst/doc/canprot.html |only canprot-1.1.2/canprot/inst/extdata/aa/archaea |only canprot-1.1.2/canprot/inst/extdata/aa/bacteria |only canprot-1.1.2/canprot/inst/extdata/aa/cow |only canprot-1.1.2/canprot/inst/extdata/aa/dog |only canprot-1.1.2/canprot/inst/extdata/aa/human |only canprot-1.1.2/canprot/inst/extdata/aa/mouse |only canprot-1.1.2/canprot/inst/extdata/aa/rat |only canprot-1.1.2/canprot/inst/extdata/aa/yeast |only canprot-1.1.2/canprot/inst/extdata/expression |only canprot-1.1.2/canprot/inst/extdata/misc |only canprot-1.1.2/canprot/inst/extdata/protein/human_additional.rds |only canprot-1.1.2/canprot/inst/extdata/protein/human_base.rds |only canprot-1.1.2/canprot/inst/extdata/protein/human_extra.csv |only canprot-1.1.2/canprot/inst/extdata/protein/uniprot_updates.csv |only canprot-1.1.2/canprot/inst/vignettes |only canprot-1.1.2/canprot/man/check_IDs.Rd |only canprot-1.1.2/canprot/man/cleanup.Rd |only canprot-1.1.2/canprot/man/diffplot.Rd |only canprot-1.1.2/canprot/man/get_comptab.Rd |only canprot-1.1.2/canprot/man/mkvig.Rd |only canprot-1.1.2/canprot/man/pdat_.Rd |only canprot-1.1.2/canprot/man/protcomp.Rd |only canprot-1.1.2/canprot/man/qdist.Rd |only canprot-1.1.2/canprot/man/xsummary.Rd |only canprot-1.1.2/canprot/tests/testthat |only canprot-1.1.2/canprot/tests/testthat.R |only canprot-1.1.2/canprot/vignettes/canprot.Rmd |only canprot-1.1.2/canprot/vignettes/mkall.R |only canprot-2.0.0/canprot/DESCRIPTION | 45 canprot-2.0.0/canprot/MD5 | 495 +-------- canprot-2.0.0/canprot/NAMESPACE | 74 - canprot-2.0.0/canprot/R/CLES.R | 2 canprot-2.0.0/canprot/R/add_cld.R |only canprot-2.0.0/canprot/R/add_hull.R |only canprot-2.0.0/canprot/R/calc_metrics.R |only canprot-2.0.0/canprot/R/cplab.R |only canprot-2.0.0/canprot/R/human_aa.R |only canprot-2.0.0/canprot/R/metrics.R | 548 ++++++++-- canprot-2.0.0/canprot/R/read_fasta.R |only canprot-2.0.0/canprot/R/zzz.R | 50 canprot-2.0.0/canprot/README.md | 73 - canprot-2.0.0/canprot/build/partial.rdb |binary canprot-2.0.0/canprot/build/vignette.rds |binary canprot-2.0.0/canprot/demo/00Index | 16 canprot-2.0.0/canprot/demo/locations.R |only canprot-2.0.0/canprot/demo/redoxins.R |only canprot-2.0.0/canprot/demo/thermophiles.R |only canprot-2.0.0/canprot/inst/CITATION | 10 canprot-2.0.0/canprot/inst/NEWS.Rd |only canprot-2.0.0/canprot/inst/ONEWS |only canprot-2.0.0/canprot/inst/doc/demos.R |only canprot-2.0.0/canprot/inst/doc/demos.Rmd |only canprot-2.0.0/canprot/inst/doc/demos.html |only canprot-2.0.0/canprot/inst/doc/introduction.R |only canprot-2.0.0/canprot/inst/doc/introduction.Rmd |only canprot-2.0.0/canprot/inst/doc/introduction.html |only canprot-2.0.0/canprot/inst/doc/metrics.R |only canprot-2.0.0/canprot/inst/doc/metrics.Rmd |only canprot-2.0.0/canprot/inst/doc/metrics.html |only canprot-2.0.0/canprot/inst/extdata/aa/dates.dat |only canprot-2.0.0/canprot/inst/extdata/aa/methanogen_aa.csv |only canprot-2.0.0/canprot/inst/extdata/aa/nitrososphaeria_MAGs.csv |only canprot-2.0.0/canprot/inst/extdata/aa/nitrososphaeria_aa.csv |only canprot-2.0.0/canprot/inst/extdata/aa/prepare.R |only canprot-2.0.0/canprot/inst/extdata/fasta |only canprot-2.0.0/canprot/inst/extdata/human |only canprot-2.0.0/canprot/inst/extdata/protein/TAW+17_Table_S6_Validated.csv |only canprot-2.0.0/canprot/inst/images |only canprot-2.0.0/canprot/inst/tinytest |only canprot-2.0.0/canprot/man/CLES.Rd | 7 canprot-2.0.0/canprot/man/add_cld.Rd |only canprot-2.0.0/canprot/man/add_hull.Rd |only canprot-2.0.0/canprot/man/calc_metrics.Rd |only canprot-2.0.0/canprot/man/canprot-package.Rd | 71 - canprot-2.0.0/canprot/man/human.Rd | 37 canprot-2.0.0/canprot/man/human_aa.Rd |only canprot-2.0.0/canprot/man/macros/macros.Rd | 18 canprot-2.0.0/canprot/man/metrics.Rd | 234 ++-- canprot-2.0.0/canprot/man/read_fasta.Rd |only canprot-2.0.0/canprot/tests/tinytest.R |only canprot-2.0.0/canprot/vignettes/canprot.bib | 119 +- canprot-2.0.0/canprot/vignettes/demos.Rmd |only canprot-2.0.0/canprot/vignettes/example.R |only canprot-2.0.0/canprot/vignettes/introduction.Rmd |only canprot-2.0.0/canprot/vignettes/metrics.Rmd |only canprot-2.0.0/canprot/vignettes/mkdoc.R |only 128 files changed, 963 insertions(+), 836 deletions(-)
Title: A Bayesian No-Effect- Concentration (NEC) Algorithm
Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>), 'NSEC' (see Fisher and Fox (2023)<doi:10.1002/etc.5610>), and 'N(S)EC (see Fisher et al. 2023<doi:10.1002/ieam.4809>). This package expands and supersedes an original version implemented in R2jags, see Fisher, Ricardo and Fox (2020)<doi:10.5281/ZENODO.3966864>.
Author: Rebecca Fisher [aut, cre],
Diego Barneche [aut],
Gerard Ricardo [aut],
David Fox [aut]
Maintainer: Rebecca Fisher <r.fisher@aims.gov.au>
Diff between bayesnec versions 2.1.1.0 dated 2023-09-26 and 2.1.2.0 dated 2024-03-28
DESCRIPTION | 6 MD5 | 96 +- NAMESPACE | 1 R/helpers.R | 12 R/sysdata.rda |binary README.md | 2 build/vignette.rds |binary data/manec_example.rda |binary inst/doc/example1.Rmd | 927 +++++++++++------------ inst/doc/example1.html | 73 - inst/doc/example2.Rmd | 623 +++++++-------- inst/doc/example2.html | 63 - inst/doc/example2b.Rmd | 977 ++++++++++++------------- inst/doc/example2b.html | 47 - inst/doc/example3.Rmd | 402 +++++----- inst/doc/example3.html | 14 inst/doc/example4.Rmd | 425 +++++----- inst/doc/example4.html | 51 - inst/doc/example5.Rmd | 53 - inst/doc/example5.html | 53 - man/figures |only man/step.Rd |only vignettes/example1.Rmd | 927 +++++++++++------------ vignettes/example1.Rmd.orig | 15 vignettes/example2.Rmd | 623 +++++++-------- vignettes/example2.Rmd.orig | 3 vignettes/example2b.Rmd | 977 ++++++++++++------------- vignettes/example3.Rmd | 402 +++++----- vignettes/example3.Rmd.orig | 15 vignettes/example4.Rmd | 425 +++++----- vignettes/example4.Rmd.orig | 3 vignettes/example5.Rmd | 53 - vignettes/vignette-fig-exmp1-bbinom-1.pdf |binary vignettes/vignette-fig-exmp1-beta-1.pdf |binary vignettes/vignette-fig-exmp1-binom-1.pdf |binary vignettes/vignette-fig-exmp1-gammabase-1.pdf |binary vignettes/vignette-fig-exmp1-negbinbase-1.pdf |binary vignettes/vignette-fig-exmp1-poisson-1.pdf |binary vignettes/vignette-fig-exmp2-allmods-1.pdf |binary vignettes/vignette-fig-exmp2-checkpriors-1.pdf |binary vignettes/vignette-fig-exmp2-decline-1.pdf |binary vignettes/vignette-fig-exmp2-ecx4param-1.pdf |binary vignettes/vignette-fig-exmp2-goodmod-1.pdf |binary vignettes/vignette-fig-exmp2-pretty-1.pdf |binary vignettes/vignette-fig-exmp3-checkpriors-1.pdf |binary vignettes/vignette-fig-exmp4-differences-1.pdf |binary vignettes/vignette-fig-exmp4-fitted-1.pdf |binary vignettes/vignette-fig-exmp4-fitteddiff-1.pdf |binary vignettes/vignette-fig-exmp4-posterior-1.pdf |binary vignettes/vignette-fig-exmp4-probplot-1.pdf |binary 50 files changed, 3673 insertions(+), 3595 deletions(-)
Title: Optimized Automated Gaussian Mixture Assessment
Description: Necessary functions for optimized automated evaluation of the number and parameters of Gaussian mixtures in one-dimensional data. Various methods are available for parameter estimation and for determining the number of modes in the mixture. A detailed description of the methods ca ben found in Lotsch, J., Malkusch, S. and A. Ultsch. (2022) <doi:10.1016/j.imu.2022.101113>.
Author: Jorn Lotsch [aut,cre] ,
Sebastian Malkusch [aut] ,
Martin Maechler [ctb],
Peter Rousseeuw [ctb],
Anja Struyf [ctb],
Mia Hubert [ctb],
Kurt Hornik [ctb]
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>
Diff between opGMMassessment versions 0.3.5 dated 2023-02-12 and 0.3.6 dated 2024-03-28
DESCRIPTION | 6 - MD5 | 18 ++--- NAMESPACE | 2 R/CreateGMM.R | 40 +++++------ R/DetermineBestGMM.R | 167 ++++++++++++++++++++++++----------------------- R/GMMplotGG.R | 133 +++++++++++++++++++------------------ R/PerformGMMfit.R | 112 +++++++++++++++---------------- R/clusGapP.R | 102 ++++++++++++++--------------- R/cutGMM.R | 51 +++++++------- R/opGMMassessment.R | 179 +++++++++++++++++++++++++-------------------------- 10 files changed, 414 insertions(+), 396 deletions(-)
More information about opGMMassessment at CRAN
Permanent link
Title: Small Area Estimation for Continuous Zero Inflated Data
Description: Provides functionality to fit a zero-inflated estimator for small area estimation.
This estimator is a combines a linear mixed effects regression model and a logistic
mixed effects regression model via a two-stage modeling approach. The estimator's mean
squared error is estimated via a parametric bootstrap method. Chandra and others
(2012, <doi:10.1080/03610918.2011.598991>) introduce and describe this estimator and mean
squared error estimator. White and others (2024+, <arXiv:2402.03263>) describe the
applicability of this estimator to estimation of forest attributes and further assess the
estimator's properties.
Author: Josh Yamamoto [aut, cre],
Dinan Elsyad [aut],
Grayson White [aut],
Julian Schmitt [aut],
Niels Korsgaard [aut],
Kelly McConville [aut],
Kate Hu [aut]
Maintainer: Josh Yamamoto <joshuayamamoto5@gmail.com>
Diff between saeczi versions 0.1.1 dated 2024-03-13 and 0.1.2 dated 2024-03-28
DESCRIPTION | 6 - MD5 | 18 +-- NEWS.md | 2 R/saeczi.R | 121 ++++------------------ R/utils.R | 203 +++++++++++++++++++++++++++++--------- README.md | 41 +++---- man/saeczi.Rd | 2 src/helpers.cpp | 1 tests/testthat/_snaps |only tests/testthat/test-saeczi.R | 26 +++- tests/testthat/test-samp_by_grp.R |only 11 files changed, 237 insertions(+), 183 deletions(-)
Title: Bottom-Up Proteomics and LiP-MS Quality Control and Data
Analysis Tools
Description: Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
Author: Jan-Philipp Quast [aut, cre] ,
Dina Schuster [aut] ,
ETH Zurich [cph, fnd]
Maintainer: Jan-Philipp Quast <quast@imsb.biol.ethz.ch>
Diff between protti versions 0.7.0 dated 2024-02-17 and 0.8.0 dated 2024-03-28
DESCRIPTION | 11 MD5 | 98 +- NEWS.md | 58 + R/barcode_plot.R | 49 - R/calculate_diff_abundance.R | 187 ++-- R/calculate_go_enrichment.R | 575 ++++++++----- R/calculate_sequence_coverage.R | 11 R/calculate_treatment_enrichment.R | 74 + R/data.R | 14 R/drc_4p_plot.R | 231 +---- R/fetch_chebi.R | 6 R/fetch_pdb.R | 2 R/fetch_uniprot.R | 58 - R/fetch_uniprot_proteome.R | 1 R/find_peptide.R | 8 R/fit_drc_4p.R | 316 ++++--- R/normalise.R | 12 R/parallel_fit_drc_4p.R | 151 ++- R/qc_charge_states.R | 55 - R/qc_data_completeness.R | 2 R/qc_missed_cleavages.R | 69 - R/qc_peptide_type.R | 40 R/qc_proteome_coverage.R | 2 R/qc_sequence_coverage.R | 21 data/mako_colours.rda |only data/metal_chebi_uniprot.rda |binary data/metal_go_slim_subset.rda |binary inst/doc/data_analysis_dose_response_workflow.html | 4 inst/doc/data_analysis_single_dose_treatment_workflow.html | 4 inst/doc/input_preparation_workflow.html | 4 inst/doc/protein_structure_workflow.html | 4 inst/doc/quality_control_workflow.Rmd | 4 inst/doc/quality_control_workflow.html | 8 man/barcode_plot.Rd | 30 man/calculate_diff_abundance.Rd | 2 man/calculate_go_enrichment.Rd | 94 +- man/calculate_treatment_enrichment.Rd | 35 man/drc_4p_plot.Rd | 20 man/fetch_uniprot.Rd | 9 man/fit_drc_4p.Rd | 112 +- man/go_enrichment.Rd | 5 man/mako_colours.Rd |only man/metal_chebi_uniprot.Rd | 2 man/metal_go_slim_subset.Rd | 2 man/normalise.Rd | 3 man/parallel_fit_drc_4p.Rd | 111 +- man/qc_missed_cleavages.Rd | 9 man/qc_sequence_coverage.Rd | 2 man/viridis_colours.Rd | 2 tests/testthat/test-workflow.R | 82 - vignettes/quality_control_workflow.Rmd | 4 51 files changed, 1651 insertions(+), 952 deletions(-)
Title: Geographical Risk Analysis Based on Habitat Connectivity
Description: The geohabnet package is designed to perform a geographically or spatially explicit risk analysis of habitat connectivity. Xing et al (2021) <doi:10.1093/biosci/biaa067> proposed the concept of cropland connectivity as a risk factor for plant pathogen or pest invasions. As the functions in geohabnet were initially developed thinking on cropland connectivity, users are recommended to first be familiar with the concept by looking at the Xing et al paper. In a nutshell, a habitat connectivity analysis combines information from maps of host density, estimates the relative likelihood of pathogen movement between habitat locations in the area of interest, and applies network analysis to calculate the connectivity of habitat locations.
The functions of geohabnet are built to conduct a habitat connectivity analysis relying on geographic parameters (spatial resolution and spatial extent), dispersal parameters (in two commonly used dispersal kernels: inverse power law and negative exponent [...truncated...]
Author: Krishna Keshav [aut, cre],
Aaron Plex [aut] ,
Garrett Lab [ctb] ,
Karen Garrett [aut] ,
University of Florida [cph, fnd]
Maintainer: Krishna Keshav <kkeshav@ufl.edu>
Diff between geohabnet versions 2.0.0 dated 2024-02-27 and 2.1.0 dated 2024-03-28
geohabnet-2.0.0/geohabnet/man/ccri_diff.Rd |only geohabnet-2.0.0/geohabnet/man/ccri_mean.Rd |only geohabnet-2.0.0/geohabnet/man/ccri_variance.Rd |only geohabnet-2.1.0/geohabnet/DESCRIPTION | 14 geohabnet-2.1.0/geohabnet/MD5 | 59 +-- geohabnet-2.1.0/geohabnet/NAMESPACE | 6 geohabnet-2.1.0/geohabnet/NEWS.md | 4 geohabnet-2.1.0/geohabnet/R/ccri_helper.R | 5 geohabnet-2.1.0/geohabnet/R/connectivity.R | 32 +- geohabnet-2.1.0/geohabnet/R/geo_network.R | 80 ++--- geohabnet-2.1.0/geohabnet/R/hci_helper.R |only geohabnet-2.1.0/geohabnet/R/maps.R | 56 +-- geohabnet-2.1.0/geohabnet/R/models.R | 14 geohabnet-2.1.0/geohabnet/R/params.R | 45 ++ geohabnet-2.1.0/geohabnet/R/sean.R | 182 +++++++----- geohabnet-2.1.0/geohabnet/README.md | 52 +-- geohabnet-2.1.0/geohabnet/inst/doc/LinkWeightsAnalysis.html | 4 geohabnet-2.1.0/geohabnet/inst/doc/analysis.R | 1 geohabnet-2.1.0/geohabnet/inst/doc/analysis.Rmd | 5 geohabnet-2.1.0/geohabnet/inst/doc/analysis.html | 30 - geohabnet-2.1.0/geohabnet/man/Dispersal-kernels.Rd | 34 +- geohabnet-2.1.0/geohabnet/man/connectivity.Rd | 2 geohabnet-2.1.0/geohabnet/man/dist_methods.Rd | 11 geohabnet-2.1.0/geohabnet/man/geohabnet-package.Rd | 2 geohabnet-2.1.0/geohabnet/man/hci_diff.Rd |only geohabnet-2.1.0/geohabnet/man/hci_mean.Rd |only geohabnet-2.1.0/geohabnet/man/hci_variance.Rd |only geohabnet-2.1.0/geohabnet/man/mapspam.Rd | 6 geohabnet-2.1.0/geohabnet/man/monfreda.Rd | 6 geohabnet-2.1.0/geohabnet/man/risk_indices.Rd | 12 geohabnet-2.1.0/geohabnet/man/sean.Rd | 19 - geohabnet-2.1.0/geohabnet/man/search_crop.Rd | 17 + geohabnet-2.1.0/geohabnet/man/supported_sources.Rd | 12 geohabnet-2.1.0/geohabnet/vignettes/analysis.Rmd | 5 34 files changed, 440 insertions(+), 275 deletions(-)
Title: Mobility Oriented-Parity Metric
Description: A set of tools to perform multiple versions of the Mobility
Oriented-Parity metric. This multivariate analysis helps to characterize
levels of dissimilarity between a set of conditions of reference and another
set of conditions of interest. If predictive models are transferred to
conditions different from those over which models were calibrated (trained),
this metric helps to identify transfer conditions that differ
substantially from those of calibration. These tools are implemented
following principles proposed in Owens et al. (2013)
<doi:10.1016/j.ecolmodel.2013.04.011>, and expanded to obtain more detailed
results that aid in interpretation.
Author: Marlon E. Cobos [aut, cre] ,
Hannah L. Owens [aut] ,
Jorge Soberon [aut] ,
A. Townsend Peterson [aut]
Maintainer: Marlon E. Cobos <manubio13@gmail.com>
Diff between mop versions 0.1.1 dated 2023-06-12 and 0.1.2 dated 2024-03-28
mop-0.1.1/mop/man/mop_package.Rd |only mop-0.1.2/mop/DESCRIPTION | 10 +++--- mop-0.1.2/mop/MD5 | 22 +++++++------- mop-0.1.2/mop/NAMESPACE | 1 mop-0.1.2/mop/NEWS.md | 6 ++++ mop-0.1.2/mop/R/methods.R | 2 - mop-0.1.2/mop/R/mop.R | 12 ++++---- mop-0.1.2/mop/R/mop_distance.R | 20 ++++++++----- mop-0.1.2/mop/R/mop_doc.R | 4 -- mop-0.1.2/mop/README.md | 56 +++++++++++++++++++++----------------- mop-0.1.2/mop/man/mop-package.Rd |only mop-0.1.2/mop/man/mop.Rd | 7 +++- mop-0.1.2/mop/man/mop_distance.Rd | 5 ++- 13 files changed, 84 insertions(+), 61 deletions(-)
Title: Flexible Segment Geoms with Arrows for 'ggplot2'
Description: Geoms for placing arrowheads at multiple points along a segment, not just at the end; position function to shift starts and ends of arrows to avoid exactly intersecting points.
Author: Matthew Hall [aut, cre]
Maintainer: Matthew Hall <matthew.hall@bdi.ox.ac.uk>
Diff between ggarchery versions 0.4.2 dated 2023-01-24 and 0.4.3 dated 2024-03-28
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- R/position-attractsegment.R | 2 +- man/attract_by_distance.Rd | 2 +- man/geom_arrowsegment.Rd | 20 ++++++++++++-------- man/position_attractsegment.Rd | 8 ++++---- 6 files changed, 28 insertions(+), 23 deletions(-)
Title: Utilities to Output CDISC SDTM/ADaM XPT Files
Description: Tools to build CDISC compliant data sets and check for CDISC
compliance.
Author: Eli Miller [aut, cre] ,
Ben Straub [aut],
Zelos Zhu [aut],
Ethan Brockmann [aut],
Vedha Viyash [aut],
Andre Verissimo [aut],
Sophie Shapcott [aut],
Celine Piraux [aut],
Kangjie Zhang [aut],
Adrian Chan [aut],
Sadchla Mascary [aut],
Atorus/GSK JPT [cp [...truncated...]
Maintainer: Eli Miller <Eli.Miller@AtorusResearch.com>
Diff between xportr versions 0.3.2 dated 2024-02-19 and 0.4.0 dated 2024-03-28
xportr-0.3.2/xportr/data/adsl.rda |only xportr-0.3.2/xportr/inst/specs/ADaM_admiral_spec.xlsx |only xportr-0.3.2/xportr/inst/specs/SDTM_spec.xlsx |only xportr-0.3.2/xportr/man/adsl.Rd |only xportr-0.3.2/xportr/man/label_log.Rd |only xportr-0.3.2/xportr/man/length_log.Rd |only xportr-0.3.2/xportr/man/type_log.Rd |only xportr-0.3.2/xportr/man/var_names_log.Rd |only xportr-0.3.2/xportr/man/var_ord_msg.Rd |only xportr-0.3.2/xportr/man/xportr_logger.Rd |only xportr-0.3.2/xportr/man/xportr_metadata.Rd |only xportr-0.3.2/xportr/tests/testthat/test-depreciation.R |only xportr-0.3.2/xportr/tests/testthat/test-pipe.R |only xportr-0.4.0/xportr/DESCRIPTION | 89 xportr-0.4.0/xportr/MD5 | 140 - xportr-0.4.0/xportr/NAMESPACE | 41 xportr-0.4.0/xportr/NEWS.md | 50 xportr-0.4.0/xportr/R/data.R | 110 - xportr-0.4.0/xportr/R/df_label.R | 42 xportr-0.4.0/xportr/R/format.R | 201 + xportr-0.4.0/xportr/R/label.R | 50 xportr-0.4.0/xportr/R/length.R | 131 - xportr-0.4.0/xportr/R/messages.R | 71 xportr-0.4.0/xportr/R/metadata.R | 47 xportr-0.4.0/xportr/R/options.R |only xportr-0.4.0/xportr/R/order.R | 48 xportr-0.4.0/xportr/R/split.R |only xportr-0.4.0/xportr/R/support-test.R | 31 xportr-0.4.0/xportr/R/type.R | 94 xportr-0.4.0/xportr/R/utils-xportr.R | 275 +- xportr-0.4.0/xportr/R/write.R | 121 - xportr-0.4.0/xportr/R/xportr-package.R | 47 xportr-0.4.0/xportr/R/xportr.R |only xportr-0.4.0/xportr/R/zzz.R | 58 xportr-0.4.0/xportr/README.md | 63 xportr-0.4.0/xportr/build/vignette.rds |binary xportr-0.4.0/xportr/data/adsl_xportr.rda |only xportr-0.4.0/xportr/data/dataset_spec.rda |only xportr-0.4.0/xportr/inst/WORDLIST | 50 xportr-0.4.0/xportr/inst/doc/agency_standards.Rmd |only xportr-0.4.0/xportr/inst/doc/agency_standards.html |only xportr-0.4.0/xportr/inst/doc/deepdive.R | 124 - xportr-0.4.0/xportr/inst/doc/deepdive.Rmd | 161 + xportr-0.4.0/xportr/inst/doc/deepdive.html | 1251 ++++++------ xportr-0.4.0/xportr/inst/doc/xportr.R | 34 xportr-0.4.0/xportr/inst/doc/xportr.Rmd | 47 xportr-0.4.0/xportr/inst/doc/xportr.html | 200 - xportr-0.4.0/xportr/inst/specs/ADaM_spec.xlsx |binary xportr-0.4.0/xportr/man/adsl_xportr.Rd |only xportr-0.4.0/xportr/man/dataset_spec.Rd |only xportr-0.4.0/xportr/man/figures/fda.jpg |only xportr-0.4.0/xportr/man/figures/nmpa.png |only xportr-0.4.0/xportr/man/figures/pmda.png |only xportr-0.4.0/xportr/man/figures/xpt.png |only xportr-0.4.0/xportr/man/metadata.Rd |only xportr-0.4.0/xportr/man/multiple_vars_in_spec_helper.Rd | 2 xportr-0.4.0/xportr/man/multiple_vars_in_spec_helper2.Rd | 2 xportr-0.4.0/xportr/man/var_spec.Rd | 6 xportr-0.4.0/xportr/man/xportr-package.Rd | 31 xportr-0.4.0/xportr/man/xportr.Rd |only xportr-0.4.0/xportr/man/xportr_df_label.Rd | 9 xportr-0.4.0/xportr/man/xportr_format.Rd | 82 xportr-0.4.0/xportr/man/xportr_label.Rd | 9 xportr-0.4.0/xportr/man/xportr_length.Rd | 27 xportr-0.4.0/xportr/man/xportr_options.Rd |only xportr-0.4.0/xportr/man/xportr_options_list.Rd |only xportr-0.4.0/xportr/man/xportr_order.Rd | 13 xportr-0.4.0/xportr/man/xportr_split.Rd |only xportr-0.4.0/xportr/man/xportr_type.Rd | 21 xportr-0.4.0/xportr/man/xportr_write.Rd | 53 xportr-0.4.0/xportr/tests/testthat/test-deprecation.R |only xportr-0.4.0/xportr/tests/testthat/test-df_label.R | 13 xportr-0.4.0/xportr/tests/testthat/test-format.R | 286 ++ xportr-0.4.0/xportr/tests/testthat/test-label.R | 45 xportr-0.4.0/xportr/tests/testthat/test-length.R | 256 +- xportr-0.4.0/xportr/tests/testthat/test-messages.R | 35 xportr-0.4.0/xportr/tests/testthat/test-metadata.R | 406 ++- xportr-0.4.0/xportr/tests/testthat/test-options.R | 35 xportr-0.4.0/xportr/tests/testthat/test-order.R | 87 xportr-0.4.0/xportr/tests/testthat/test-pkg-load.R | 18 xportr-0.4.0/xportr/tests/testthat/test-support-for-tests.R | 11 xportr-0.4.0/xportr/tests/testthat/test-type.R | 171 + xportr-0.4.0/xportr/tests/testthat/test-utils-xportr.R | 73 xportr-0.4.0/xportr/tests/testthat/test-write.R | 307 ++ xportr-0.4.0/xportr/tests/testthat/test-xportr.R |only xportr-0.4.0/xportr/vignettes/agency_standards.Rmd |only xportr-0.4.0/xportr/vignettes/deepdive.Rmd | 161 + xportr-0.4.0/xportr/vignettes/xportr.Rmd | 47 88 files changed, 3791 insertions(+), 1991 deletions(-)
Title: Automating the Creation of Stan Code for TDCMs
Description: A collection of functions for automatically creating 'Stan'
code for transition diagnostic classification models (TDCMs) as they are
defined by Madison and Bradshaw (2018) <DOI:10.1007/s11336-018-9638-5>.
This package supports automating the creation of 'Stan' code for TDCMs,
fungible TDCMs (i.e., TDCMs with item parameters constrained to be equal
across all items), and multi-threaded TDCMs.
Author: Jeffrey Hoover [aut, cre, cph]
,
W. Jake Thompson [aut]
Maintainer: Jeffrey Hoover <jeffrey.c.hoover@gmail.com>
Diff between tdcmStan versions 2.0.0 dated 2023-03-03 and 3.0.0 dated 2024-03-28
DESCRIPTION | 10 + MD5 | 24 ++-- R/create-fng-tdcm-no-common-items-stan.R | 42 ++++---- R/create-fng-tdcm-stan.R | 42 ++++---- R/create-tdcm-stan.R | 42 ++++---- R/create-threaded-tdcm-stan.R | 126 ++++++++++++------------ inst |only tests/testthat/data/automated-madison-tdcm.stan | 122 +++++++++++------------ tests/testthat/data/dlm-fng-tdcm.stan | 36 +++--- tests/testthat/data/madison-tdcm.stan | 36 +++--- tests/testthat/data/multi-tdcm-stan.stan | 122 +++++++++++------------ tests/testthat/data/tdcm-stan.stan | 1 12 files changed, 304 insertions(+), 299 deletions(-)
Title: Data from all Seasons of Survivor (US) TV Series in Tidy Format
Description: Several datasets which detail the results and events of each season of Survivor. This includes
details on the cast, voting history, immunity and reward challenges, jury votes and viewers. This data is
useful for practicing data wrangling, graph analytics and analysing how each season of Survivor played out.
Includes 'ggplot2' scales and colour palettes for visualisation.
Author: Daniel Oehm [aut, cre],
Carly Levitz [ctb],
Dario Mavec [ctb]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between survivoR versions 2.3.1 dated 2024-02-15 and 2.3.2 dated 2024-03-28
DESCRIPTION | 6 +-- MD5 | 48 ++++++++++++------------- NEWS.md | 6 +++ R/datasets.R | 2 + README.md | 74 +++++++++++++++++++++++---------------- data/advantage_details.rda |binary data/advantage_movement.rda |binary data/auction_details.rda |binary data/boot_mapping.rda |binary data/castaway_details.rda |binary data/castaways.rda |binary data/challenge_description.rda |binary data/challenge_results.rda |binary data/confessionals.rda |binary data/episodes.rda |binary data/jury_votes.rda |binary data/season_palettes.rda |binary data/season_summary.rda |binary data/survivor_auction.rda |binary data/tribe_colours.rda |binary data/tribe_mapping.rda |binary data/viewers.rda |binary data/vote_history.rda |binary man/season_summary.Rd | 2 + tests/testthat/tests.R | 77 +++++++++++++++++++++++++++++++++++++++++ 25 files changed, 159 insertions(+), 56 deletions(-)
Title: Aid Querying 'nomis' and 'Office for National Statistics Open
Geography' APIs
Description: Facilitates extraction of geospatial data from the 'Office for National Statistics Open Geography' and 'nomis' Application Programming Interfaces (APIs). Simplifies process of querying 'nomis' datasets <https://www.nomisweb.co.uk/> and extracting desired datasets in dataframe format. Extracts area shapefiles at chosen resolution from 'Office for National Statistics Open Geography' <https://geoportal.statistics.gov.uk/>.
Author: Andrew Christy [aut, cre],
James Macpherson [aut],
Hadyn Jenkins [aut],
Crown Copyright
[cph]
Maintainer: Andrew Christy <OR_Hub@defra.gov.uk>
Diff between sgapi versions 1.0.1 dated 2024-03-20 and 1.0.2 dated 2024-03-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- tests/testthat/test-get_boundaries.R | 15 ++++----------- tests/testthat/test-get_table_dimensions.R | 8 ++++---- tests/testthat/test-list_data_sources.R | 6 +++--- 5 files changed, 18 insertions(+), 25 deletions(-)
Title: Query 'SWI'-'Prolog' from R
Description: This R package connects to SWI-Prolog, <https://www.swi-prolog.org/>, so that R can send deterministic and non-deterministic queries to prolog (consult, query/submit, once, findall).
Author: Matthias Gondan [aut, com, cre] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rolog versions 0.9.15 dated 2024-03-18 and 0.9.16 dated 2024-03-28
DESCRIPTION | 8 - MD5 | 10 - NEWS.md | 4 R/plbase.R | 231 +++++++++++++++++++++++++++++++++++++-- R/rolog.R | 304 ++-------------------------------------------------- inst/doc/rolog.html | 7 - 6 files changed, 253 insertions(+), 311 deletions(-)
Title: Extract 'REDCap' Databases into Tidy 'Tibble's
Description: Convert 'REDCap' exports into tidy tables for easy handling of 'REDCap' repeat instruments and event arms.
Author: Richard Hanna [aut, cre] ,
Stephan Kadauke [aut] ,
Ezra Porter [aut]
Maintainer: Richard Hanna <richardshanna91@gmail.com>
Diff between REDCapTidieR versions 1.0.0 dated 2023-11-08 and 1.1.0 dated 2024-03-28
DESCRIPTION | 13 - MD5 | 78 ++++---- NAMESPACE | 19 + NEWS.md | 23 +- R/REDCapTidieR-package.R | 11 - R/checks.R | 131 +++++++++---- R/clean_redcap_long.R | 168 +++++++++++++++-- R/read_redcap.R | 49 ++--- R/supertibble.R |only R/utils.R | 219 +++++++++++++++++++---- R/write.R | 2 README.md | 1 build/vignette.rds |binary inst/WORDLIST | 5 inst/doc/REDCapTidieR.Rmd | 18 + inst/doc/REDCapTidieR.html | 118 ++++++++---- inst/doc/glossary.Rmd | 2 inst/doc/glossary.html | 6 inst/testdata/db_metadata_mixed_structure.RDS |only inst/testdata/db_mixed_structure.RDS |only inst/testdata/db_mixed_structure_linked_arms.RDS |only man/REDCapTidieR-package.Rd | 2 man/apply_labs_factor.Rd |only man/apply_labs_haven.Rd |only man/as_supertbl.Rd | 2 man/check_extra_field_values.Rd |only man/check_field_is_logical.Rd |only man/clean_redcap_long.Rd | 12 + man/convert_mixed_instrument.Rd |only man/distill_repeat_table_long.Rd | 10 - man/figures/write_xlsx_default.png |binary man/get_mixed_structure_fields.Rd |only man/invert_vec.Rd |only man/multi_choice_to_labels.Rd | 14 + man/parse_logical_cols.Rd |only man/read_redcap.Rd | 13 + man/tbl_sum.redcap_supertbl.Rd |only man/vec_ptype_abbr.redcap_supertbl.Rd |only tests/testthat/_snaps/supertibble.md |only tests/testthat/_snaps/write.md | 162 ++++++++--------- tests/testthat/test-checks.R | 23 ++ tests/testthat/test-clean_redcap_long.R | 106 +++++++++++ tests/testthat/test-read_redcap.R | 23 ++ tests/testthat/test-supertibble.R |only tests/testthat/test-utils.R | 99 ++++++++++ tests/testthat/test-write.R | 1 vignettes/REDCapTidieR.Rmd | 18 + vignettes/glossary.Rmd | 2 48 files changed, 1057 insertions(+), 293 deletions(-)
Title: PLS Analyses for Genomics
Description: Routines for PLS-based genomic analyses,
implementing PLS methods for classification with
microarray data and prediction of transcription factor
activities from combined ChIP-chip analysis. The >=1.2-1
versions include two new classification methods for microarray
data: GSIM and Ridge PLS. The >=1.3 versions includes a
new classification method combining variable selection and
compression in logistic regression context: logit-SPLS; and
an adaptive version of the sparse PLS.
Author: Anne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>,
Ghislain Durif <gd.dev@libertymail.net>,
Sophie Lambert-Lacroix
<sophie.lambert-lacroix@univ-grenoble-alpes.fr>, Julie Peyre
<Julie.Peyre@univ-grenoble-alpes.fr>, and Korbinian Strimmer
<k.s [...truncated...]
Maintainer: Ghislain Durif <gd.dev@libertymail.net>
Diff between plsgenomics versions 1.5-2.1 dated 2023-11-27 and 1.5-3 dated 2024-03-28
DESCRIPTION | 17 ++-- MD5 | 113 +++++++++++++------------- R/deprecated.R | 4 R/gsim.aux.R | 2 R/internal.R | 33 ------- R/logit.spls.R | 15 +-- R/logit.spls.cv.R | 15 +-- R/logit.spls.stab.R | 17 ++-- R/matrix.heatmap.R | 2 R/multinom.spls.R | 23 ++--- R/multinom.spls.cv.R | 15 +-- R/multinom.spls.stab.R | 17 ++-- R/pls.regression.R | 1 R/pls.regression.cv.R | 156 ++++++++++++++++++------------------- R/sample.bin.R | 20 ++-- R/sample.multinom.R | 16 ++- R/spls.R | 15 +-- R/spls.cv.R | 21 ++-- R/spls.stab.R | 19 ++-- R/stability.selection.R | 31 ++++--- R/zzz.R | 4 build |only data/Colon.rda |binary data/Ecoli.rda |binary data/SRBCT.rda |binary data/leukemia.rda |binary man/Colon.Rd | 6 - man/Ecoli.Rd | 8 + man/SRBCT.Rd | 7 - man/TFA.estimate.Rd | 4 man/gsim.Rd | 2 man/gsim.cv.Rd | 2 man/leukemia.Rd | 8 + man/logit.spls.Rd | 32 +++++-- man/logit.spls.cv.Rd | 39 ++++++--- man/logit.spls.stab.Rd | 38 ++++++--- man/matrix.heatmap.Rd | 2 man/mgsim.Rd | 2 man/mgsim.cv.Rd | 2 man/multinom.spls.Rd | 40 ++++++--- man/multinom.spls.cv.Rd | 39 ++++++--- man/multinom.spls.stab.Rd | 38 ++++++--- man/pls.lda.Rd | 2 man/pls.lda.cv.Rd | 2 man/pls.regression.Rd | 4 man/pls.regression.cv.Rd | 4 man/plsgenomics-deprecated.Rd | 4 man/plsgenomics-internal.Rd | 2 man/preprocess.Rd | 2 man/sample.bin.Rd | 27 ++++-- man/sample.cont.Rd | 11 +- man/sample.multinom.Rd | 28 ++++-- man/spls.Rd | 32 +++++-- man/spls.cv.Rd | 45 +++++++--- man/spls.stab.Rd | 46 +++++++--- man/stability.selection.Rd | 23 ++++- man/stability.selection.heatmap.Rd | 8 - man/variable.selection.Rd | 2 58 files changed, 616 insertions(+), 451 deletions(-)
Title: Sample Size Calculation under Non-Proportional Hazards
Description: Performs combination tests and sample size calculation for
fixed design with survival endpoints using combination tests under either
proportional hazards or non-proportional hazards. The combination tests
include maximum weighted log-rank test and projection test. The sample
size calculation procedure is very flexible, allowing for user-defined
hazard ratio function and considering various trial conditions like
staggered entry, drop-out etc. The sample size calculation also applies to
various cure models such as proportional hazards cure model, cure model with
(random) delayed treatments effects. Trial simulation function is also provided
to facilitate the empirical power calculation. The references for
projection test and maximum weighted logrank test include Brendel et al. (2014)
<doi:10.1111/sjos.12059> and Cheng and He (2021) <arXiv:2110.03833>. The
references for sample size calculation under proportional hazard include
Schoenfeld (1981) <doi:10.1093/biomet/68.1.316 [...truncated...]
Author: Huan Cheng [aut, cre]
Maintainer: Huan Cheng <hcheng1118@hotmail.com>
Diff between nphPower versions 1.0.0 dated 2021-12-01 and 1.1.0 dated 2024-03-28
nphPower-1.0.0/nphPower/R/pwr2n.prj.R |only nphPower-1.1.0/nphPower/DESCRIPTION | 14 nphPower-1.1.0/nphPower/MD5 | 42 - nphPower-1.1.0/nphPower/NAMESPACE | 3 nphPower-1.1.0/nphPower/NEWS.md | 16 nphPower-1.1.0/nphPower/R/MaxLRtest.R | 4 nphPower-1.1.0/nphPower/R/cureHR.R |only nphPower-1.1.0/nphPower/R/n2pwr.NPH.R | 16 nphPower-1.1.0/nphPower/R/oxy-MaxLRtest.R | 5 nphPower-1.1.0/nphPower/R/oxy-cureHR.R |only nphPower-1.1.0/nphPower/R/oxy-n2pwr.NPH.R | 453 +++++------ nphPower-1.1.0/nphPower/R/oxy-plotHazSurv.R | 32 nphPower-1.1.0/nphPower/R/oxy-pwr2n.NPH.R | 1086 +++++++++++++++------------- nphPower-1.1.0/nphPower/R/oxy-simu.trial.R | 684 ++++++++++------- nphPower-1.1.0/nphPower/R/plotHazSurv.R | 15 nphPower-1.1.0/nphPower/R/pwr2n.LR.R | 285 +++---- nphPower-1.1.0/nphPower/R/pwr2n.NPH.R | 643 ++++++++-------- nphPower-1.1.0/nphPower/R/simu.trial.R | 432 +++++++---- nphPower-1.1.0/nphPower/R/trans.mat.R | 85 +- nphPower-1.1.0/nphPower/man/cureHR.Rd |only nphPower-1.1.0/nphPower/man/n2pwr.NPH.Rd | 18 nphPower-1.1.0/nphPower/man/plotHazSurv.Rd | 6 nphPower-1.1.0/nphPower/man/pwr2n.NPH.Rd | 413 +++++----- nphPower-1.1.0/nphPower/man/simu.trial.Rd | 39 - 24 files changed, 2408 insertions(+), 1883 deletions(-)
Title: Inference in Graphical Gaussian Models with Edge and Vertex
Symmetries
Description: Estimation, model selection and other aspects of
statistical inference in Graphical Gaussian models with edge and
vertex symmetries (Graphical Gaussian models with colours).
Documentation about 'gRc' is provided in the paper by Hojsgaard and
Lauritzen (2007, <doi:10.18637/jss.v023.i06>) and the paper by
Hojsgaard and Lauritzen (2008, <doi:10.1111/j.1467-9868.2008.00666.x>).
Author: Soeren Hoejsgaard <sorenh@math.aau.dk>, Steffen L. Lauritzen <lauritzen@math.ku.dk>
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between gRc versions 0.4.6 dated 2023-11-29 and 0.5.0 dated 2024-03-28
gRc-0.4.6/gRc/man/set-op.Rd |only gRc-0.5.0/gRc/DESCRIPTION | 14 +- gRc-0.5.0/gRc/MD5 | 33 +++--- gRc-0.5.0/gRc/NAMESPACE | 33 +++++- gRc-0.5.0/gRc/NEWS | 10 + gRc-0.5.0/gRc/R/NAMESPACE.R | 31 ----- gRc-0.5.0/gRc/R/display.R | 179 ++++++++++----------------------- gRc-0.5.0/gRc/R/repair_K.R | 1 gRc-0.5.0/gRc/R/set_op.R | 61 ++++++----- gRc-0.5.0/gRc/R/testing_stepwise.R | 4 gRc-0.5.0/gRc/R/update.R | 12 +- gRc-0.5.0/gRc/R/utility4.R | 25 ++-- gRc-0.5.0/gRc/R/vcov.R | 98 +++++++++--------- gRc-0.5.0/gRc/R/xxx2yyy.R | 15 +- gRc-0.5.0/gRc/R/zzz_generating_class.R | 149 +++++++++++++-------------- gRc-0.5.0/gRc/man/generating-class.Rd | 32 ----- gRc-0.5.0/gRc/man/internal.Rd | 1 gRc-0.5.0/gRc/man/plot.rcox.Rd |only gRc-0.5.0/gRc/man/toLisp.Rd |only 19 files changed, 312 insertions(+), 386 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.3.0 dated 2024-02-28 and 1.3.1 dated 2024-03-28
DESCRIPTION | 8 MD5 | 66 R/GPModel.R | 187 - R/gpb.Booster.R | 6 R/gpb.cv.R | 2 configure.ac | 2 demo/generalized_linear_Gaussian_process_mixed_effects_models.R | 39 man/GPModel.Rd | 6 man/GPModel_shared_params.Rd | 18 man/fit.GPModel.Rd | 14 man/fit.Rd | 14 man/fitGPModel.Rd | 20 man/neg_log_likelihood.GPModel.Rd | 3 man/neg_log_likelihood.Rd | 3 man/predict.GPModel.Rd | 17 man/set_optim_params.GPModel.Rd | 6 man/set_optim_params.Rd | 6 src/CG_utils.cpp | 156 + src/include/GPBoost/CG_utils.h | 28 src/include/GPBoost/GP_utils.h | 1 src/include/GPBoost/Vecchia_utils.h | 29 src/include/GPBoost/cov_fcts.h | 1339 +++++++--- src/include/GPBoost/likelihoods.h | 698 ++++- src/include/GPBoost/re_comp.h | 178 + src/include/GPBoost/re_model_template.h | 541 ++-- src/include/LBFGS.h | 3 src/objective/regression_objective.hpp | 3 src/re_model.cpp | 2 tests/testthat/test_GPModel_combined_GP_random_effects.R | 12 tests/testthat/test_GPModel_gaussian_process.R | 915 +++++- tests/testthat/test_GPModel_grouped_random_effects.R | 10 tests/testthat/test_GPModel_non_Gaussian_data.R | 744 ++++- tests/testthat/test_z_GPBoost_algorithm.R | 40 tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data.R | 435 +-- 34 files changed, 4185 insertions(+), 1366 deletions(-)
Title: Wearable Accelerometer Data File Readers
Description: Reads data collected from wearable acceleratometers as used in sleep and physical activity research. Currently supports file formats: binary data from 'GENEActiv' <https://activinsights.com/>, .bin-format from GENEA devices (not for sale), and .cwa-format from 'Axivity' <https://axivity.com>. Primarily designed to complement R package GGIR <https://CRAN.R-project.org/package=GGIR>.
Author: Vincent T van Hees [aut, cre],
Patrick Bos [aut] ,
Lena Kushleyeva [ctb],
Jing Hua Zhao [ctb],
Evgeny Mirkes [ctb],
Dan Jackson [ctb],
Jairo H Migueles [ctb],
Medical Research Council UK [cph, fnd],
Accelting [cph, fnd]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIRread versions 0.3.3 dated 2024-01-24 and 1.0.0 dated 2024-03-28
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/readGENEActiv.R | 6 +++++- inst/NEWS.Rd | 8 ++++++++ man/GGIRread-package.Rd | 4 ++-- src/GENEActivReader.cpp | 19 +++++++++---------- tests/testthat/test_readGENEActiv.R | 16 +++++++++------- 7 files changed, 43 insertions(+), 30 deletions(-)
Title: Extra Additive Terms for Generalized Additive Models for
Location Scale and Shape
Description: Interface for extra smooth functions including tensor products,
neural networks and decision trees.
Author: Mikis Stasinopoulos [aut, cre]
,
Robert Rigby [aut] ,
Vlasios Voudouris [ctb],
Daniil Kiose [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@gre.ac.uk>
Diff between gamlss.add versions 5.1-12 dated 2024-01-27 and 5.1-13 dated 2024-03-28
DESCRIPTION | 33 ++++++++++++++++++++++----------- MD5 | 28 +++++++++++++++------------- NEWS.md |only README.md |only build/partial.rdb |binary man/centilesTwo.Rd | 2 +- man/fitFixedKnots.Rd | 2 +- man/fk.Rd | 2 +- man/ga.Rd | 2 +- man/gamlss.add-package.Rd | 2 +- man/gamlss.fk.Rd | 2 +- man/gamlss.ga.Rd | 4 ++-- man/gamlss.nn.Rd | 2 +- man/nn.Rd | 2 +- man/plotNN.Rd | 2 +- man/tr.Rd | 7 ++----- 16 files changed, 50 insertions(+), 40 deletions(-)
Title: Framework for Easy Statistical Modeling, Visualization, and
Reporting
Description: A meta-package that installs and loads a set of packages from
'easystats' ecosystem in a single step. This collection of packages provide
a unifying and consistent framework for statistical modeling, visualization,
and reporting. Additionally, it provides articles targeted at instructors for
teaching 'easystats', and a dashboard targeted at new R users for easily
conducting statistical analysis by accessing summary results, model fit indices,
and visualizations with minimal programming.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Brenton M. Wiernik [aut] ,
Etienne Bacher [aut] ,
Remi Theriault [aut]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between easystats versions 0.7.0 dated 2023-11-05 and 0.7.1 dated 2024-03-28
DESCRIPTION | 18 +++++++++--------- MD5 | 36 ++++++++++++++++++------------------ NEWS.md | 7 +++++++ R/easystats_update.R | 2 +- R/install_easystats.R | 2 +- R/install_suggested.R | 8 ++++---- R/utils.R | 22 +++++++++++----------- R/zen.R | 2 +- R/zzz.R | 6 +++--- README.md | 6 +++--- build/vignette.rds |binary inst/doc/list_of_functions.R | 2 +- inst/doc/list_of_functions.Rmd | 2 +- inst/doc/list_of_functions.html | 18 ++++++++++++++++++ inst/templates/easydashboard.Rmd | 6 +++--- man/easystats-package.Rd | 1 - man/figures/depnetwork-1.png |binary man/figures/unnamed-chunk-7-1.png |binary vignettes/list_of_functions.Rmd | 2 +- 19 files changed, 82 insertions(+), 58 deletions(-)
Title: Modify Data Using Externally Defined Modification Rules
Description: Data cleaning scripts typically contain a lot of 'if this change that'
type of statements. Such statements are typically condensed expert knowledge.
With this package, such 'data modifying rules' are taken out of the code and
become in stead parameters to the work flow. This allows one to maintain, document,
and reason about data modification rules as separate entities.
Author: Mark van der Loo [cre, aut] ,
Edwin de Jonge [aut] ,
Sjabbo Schaveling [ctb],
Floris Ruijter [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between dcmodify versions 0.8.0 dated 2023-04-07 and 0.9.0 dated 2024-03-28
DESCRIPTION | 9 +- MD5 | 26 ++--- NAMESPACE | 13 ++ NEWS | 4 R/modifier.R | 3 R/modify.R | 93 +++++++++++++++++---- build/vignette.rds |binary inst/doc/introduction.R | 18 ++++ inst/doc/introduction.html | 185 ++++++++++++++++++++++++------------------ inst/doc/introduction.md | 29 ++++++ inst/tinytest/test_modifier.R | 19 +++- man/dcmodify.Rd | 23 +++++ man/modify.Rd | 17 +++ vignettes/introduction.md | 29 ++++++ 14 files changed, 352 insertions(+), 116 deletions(-)
Title: Business Process Analysis in R
Description: Comprehensive Business Process Analysis toolkit. Creates S3-class for event log objects, and related handler functions. Imports related packages for filtering event data, computation of descriptive statistics, handling of 'Petri Net' objects and visualization of process maps. See also packages 'edeaR','processmapR', 'eventdataR' and 'processmonitR'.
Author: Gert Janssenswillen [aut, cre],
Gerard van Hulzen [ctb],
Felix Mannhardt [ctb],
Niels Martin [ctb],
Greg Van Houdt [ctb]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between bupaR versions 0.5.3 dated 2023-04-02 and 0.5.4 dated 2024-03-28
DESCRIPTION | 6 MD5 | 19 +- R/act_collapse.R | 281 ++++++++++++++++++------------------ R/detect_resource_inconsistencies.R | 2 R/rename.R | 31 +++ R/to_eventlog.R | 2 R/unite.eventlog.R | 2 README.md | 22 +- man/count.Rd | 9 - man/rename.Rd |only man/unite.Rd | 4 11 files changed, 200 insertions(+), 178 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-22 3.0.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-08 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-29 1.0.4
2023-07-05 1.0.3
2023-05-18 1.0.2
2023-01-31 1.0.1
2023-01-27 1.0.0
2022-11-16 0.9.0
2022-09-16 0.8.0
Title: A Shiny App for Design of Experiments in Life Sciences
Description: A shiny design of experiments (DOE) app that aids in the creation of traditional,
un-replicated, augmented and partially-replicated designs applied to agriculture,
plant breeding, forestry, animal and biological sciences.
Author: Didier Murillo [cre, aut],
Salvador Gezan [aut],
Ana Heilman [ctb],
Thomas Walk [ctb],
Johan Aparicio [ctb],
Matthew Seefeldt [ctb],
Jean-Marc Montpetit [ctb],
Richard Horsley [ctb],
North Dakota State University [cph]
Maintainer: Didier Murillo <didier.murilloflorez@ndsu.edu>
Diff between FielDHub versions 1.3.4 dated 2023-10-19 and 1.3.7 dated 2024-03-28
FielDHub-1.3.4/FielDHub/R/utils-pipe.R |only FielDHub-1.3.4/FielDHub/man/pipe.Rd |only FielDHub-1.3.7/FielDHub/DESCRIPTION | 13 FielDHub-1.3.7/FielDHub/MD5 | 124 ++--- FielDHub-1.3.7/FielDHub/NAMESPACE | 3 FielDHub-1.3.7/FielDHub/R/app_ui.R | 16 FielDHub-1.3.7/FielDHub/R/fct_diagonal_arrangement.R | 6 FielDHub-1.3.7/FielDHub/R/fct_do_optim.R | 71 +- FielDHub-1.3.7/FielDHub/R/fct_incomplete_blocks.R | 55 +- FielDHub-1.3.7/FielDHub/R/fct_partially_replicated.R | 8 FielDHub-1.3.7/FielDHub/R/globals.R | 5 FielDHub-1.3.7/FielDHub/R/mod_Alpha_Lattice.R | 24 FielDHub-1.3.7/FielDHub/R/mod_CRD.R | 24 FielDHub-1.3.7/FielDHub/R/mod_Diagonal.R | 14 FielDHub-1.3.7/FielDHub/R/mod_FD.R | 26 - FielDHub-1.3.7/FielDHub/R/mod_IBD.R | 24 FielDHub-1.3.7/FielDHub/R/mod_LSD.R | 24 FielDHub-1.3.7/FielDHub/R/mod_Optim.R | 16 FielDHub-1.3.7/FielDHub/R/mod_RCBD.R | 24 FielDHub-1.3.7/FielDHub/R/mod_RCBD_augmented.R | 20 FielDHub-1.3.7/FielDHub/R/mod_Rectangular_Lattice.R | 26 - FielDHub-1.3.7/FielDHub/R/mod_RowCol.R | 26 - FielDHub-1.3.7/FielDHub/R/mod_SPD.R | 24 FielDHub-1.3.7/FielDHub/R/mod_SSPD.R | 24 FielDHub-1.3.7/FielDHub/R/mod_STRIPD.R | 26 - FielDHub-1.3.7/FielDHub/R/mod_Square_Lattice.R | 22 FielDHub-1.3.7/FielDHub/R/mod_diagonal_multiple.R | 18 FielDHub-1.3.7/FielDHub/R/mod_multi_loc_prep.R | 43 - FielDHub-1.3.7/FielDHub/R/mod_pREPS.R | 18 FielDHub-1.3.7/FielDHub/R/mod_sparse_allocation.R | 39 - FielDHub-1.3.7/FielDHub/R/utils_AR1xAR1_simulation.R | 2 FielDHub-1.3.7/FielDHub/R/utils_S3_methods.R | 2 FielDHub-1.3.7/FielDHub/R/utils_available_percent.R | 6 FielDHub-1.3.7/FielDHub/R/utils_diagonals_checks.R | 115 ++++ FielDHub-1.3.7/FielDHub/R/utils_export_design.R | 2 FielDHub-1.3.7/FielDHub/R/utils_get_random.R | 8 FielDHub-1.3.7/FielDHub/R/utils_names_layout.R | 6 FielDHub-1.3.7/FielDHub/R/utils_pREP.R | 4 FielDHub-1.3.7/FielDHub/R/utils_plot_RCBD.R | 10 FielDHub-1.3.7/FielDHub/R/utils_plot_diagonal_arrangement.R | 18 FielDHub-1.3.7/FielDHub/R/utils_plot_iblocks_1.R | 24 FielDHub-1.3.7/FielDHub/R/utils_plot_latinSQ.R | 6 FielDHub-1.3.7/FielDHub/R/utils_plot_splitPlots.R | 16 FielDHub-1.3.7/FielDHub/R/utils_swap_functions.R | 4 FielDHub-1.3.7/FielDHub/R/utils_validateTreatments.R |only FielDHub-1.3.7/FielDHub/inst/app/www/home.html | 2 FielDHub-1.3.7/FielDHub/inst/doc/RCBD_augmented.html | 40 - FielDHub-1.3.7/FielDHub/inst/doc/diagonal_arrangement.html | 80 +-- FielDHub-1.3.7/FielDHub/inst/doc/multi_location_prep.R | 24 FielDHub-1.3.7/FielDHub/inst/doc/multi_location_prep.Rmd | 24 FielDHub-1.3.7/FielDHub/inst/doc/multi_location_prep.html | 48 - FielDHub-1.3.7/FielDHub/inst/doc/optimized_arrangement.html | 248 +++------- FielDHub-1.3.7/FielDHub/inst/doc/partially_replicated.html | 248 +++------- FielDHub-1.3.7/FielDHub/inst/doc/rcbd.html | 84 +-- FielDHub-1.3.7/FielDHub/inst/doc/rectangular_lattice.html | 152 ++---- FielDHub-1.3.7/FielDHub/inst/doc/row_column.html | 152 ++---- FielDHub-1.3.7/FielDHub/inst/doc/sparse_allocation.R | 9 FielDHub-1.3.7/FielDHub/inst/doc/sparse_allocation.Rmd | 9 FielDHub-1.3.7/FielDHub/inst/doc/sparse_allocation.html | 40 - FielDHub-1.3.7/FielDHub/inst/doc/split_plot.html | 66 -- FielDHub-1.3.7/FielDHub/inst/doc/square_lattice.html | 152 ++---- FielDHub-1.3.7/FielDHub/man/do_optim.Rd | 3 FielDHub-1.3.7/FielDHub/tests/testthat/test_compute_index_ranges.R |only FielDHub-1.3.7/FielDHub/vignettes/multi_location_prep.Rmd | 24 FielDHub-1.3.7/FielDHub/vignettes/sparse_allocation.Rmd | 9 65 files changed, 1017 insertions(+), 1383 deletions(-)
Title: Global Surface Summary of the Day ('GSOD') Weather Data Client
Description: Provides automated downloading, parsing, cleaning, unit conversion
and formatting of Global Surface Summary of the Day ('GSOD') weather data
from the from the USA National Centers for Environmental Information
('NCEI'). Units are converted from from United States Customary System
('USCS') units to International System of Units ('SI'). Stations may be
individually checked for number of missing days defined by the user, where
stations with too many missing observations are omitted. Only stations with
valid reported latitude and longitude values are permitted in the final
data. Additional useful elements, saturation vapour pressure ('es'), actual
vapour pressure ('ea') and relative humidity ('RH') are calculated from the
original data using the improved August-Roche-Magnus approximation (Alduchov
& Eskridge 1996) and included in the final data set. The resulting metadata
include station identification information, country, state, latitude,
longitude, elevation, weather observatio [...truncated...]
Author: Adam H. Sparks [aut, cre] ,
Tomislav Hengl [aut] ,
Andrew Nelson [aut] ,
Hugh Parsonage [cph, ctb] ,
Taras Kaduk [ctb] ,
Gwenael Giboire [ctb] ,
Lukasz Pawlik [ctb] ,
Ross Darnell [ctb] ,
Tyler Widdison [ctb] ` did not
return stations in order of nea [...truncated...]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Diff between GSODR versions 3.1.10 dated 2024-02-05 and 4.0.0 dated 2024-03-28
DESCRIPTION | 8 +- MD5 | 28 +++++----- NEWS.md | 16 +++++ R/nearest_stations.R | 33 ++++++------ README.md | 5 + build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/GSODR.html | 6 +- inst/extdata/isd_diff.rda |binary inst/extdata/isd_history.rda |binary man/nearest_stations.Rd | 8 -- tests/testthat/test-get_inventory.R | 52 +++++++++---------- tests/testthat/test-nearest_stations.R | 6 +- tests/testthat/test-process_csv.R | 90 ++++++++++++++++----------------- tests/testthat/test-reformat_GSOD.R | 5 - 15 files changed, 137 insertions(+), 122 deletions(-)