Title: Create and Evaluate Stopping Rules for Safety Monitoring
Description: Provides functions for creating, displaying, and evaluating stopping rules for safety monitoring in clinical studies.
Author: Michael J. Martens [aut, cre],
Qinghua Lian [aut],
Brent R. Logan [ctb]
Maintainer: Michael J. Martens <mmartens@mcw.edu>
Diff between stoppingrule versions 0.5.1 dated 2024-12-05 and 0.5.2 dated 2025-02-06
DESCRIPTION | 8 +++---- MD5 | 54 ++++++++++++++++++++++++------------------------- R/OC.rule.R | 3 +- R/OC.rule.bin.R | 3 +- R/OC.rule.surv.R | 6 ++--- R/calc.rule.R | 3 +- R/calc.rule.bin.R | 4 +-- R/calc.rule.surv.R | 5 ++-- R/lines.rule.bin.R | 3 +- R/lines.rule.surv.R | 4 +-- R/plot.rule.bin.R | 3 +- R/plot.rule.surv.R | 3 +- R/simtrials.surv.R | 3 +- R/table.rule.bin.R | 3 +- R/table.rule.surv.R | 3 +- man/OC.rule.Rd | 3 +- man/OC.rule.bin.Rd | 3 +- man/OC.rule.surv.Rd | 4 +-- man/calc.rule.Rd | 3 +- man/calc.rule.bin.Rd | 4 +-- man/calc.rule.surv.Rd | 6 +++-- man/lines.rule.bin.Rd | 3 +- man/lines.rule.surv.Rd | 4 +-- man/plot.rule.bin.Rd | 3 +- man/plot.rule.surv.Rd | 3 +- man/simtrials.surv.Rd | 3 +- man/table.rule.bin.Rd | 3 +- man/table.rule.surv.Rd | 3 +- 28 files changed, 87 insertions(+), 66 deletions(-)
Title: Biodiversity Data from the GBIF Node Network
Description: The Global Biodiversity Information Facility
('GBIF', <https://www.gbif.org>) sources data from an international network
of data providers, known as 'nodes'. Several of these nodes - the "living
atlases" (<https://living-atlases.gbif.org>) - maintain their own web
services using software originally developed by the Atlas of Living
Australia ('ALA', <https://www.ala.org.au>). 'galah' enables the R community
to directly access data and resources hosted by 'GBIF' and its partner nodes.
Author: Martin Westgate [aut, cre],
Dax Kellie [aut],
Matilda Stevenson [aut],
Peggy Newman [aut]
Maintainer: Martin Westgate <martin.westgate@csiro.au>
Diff between galah versions 2.1.0 dated 2024-11-18 and 2.1.1 dated 2025-02-06
DESCRIPTION | 8 - MD5 | 144 +++++++++++++------------- NAMESPACE | 11 - NEWS.md | 16 ++ R/atlas_citation.R | 130 +++++++++++++++++------ R/atlas_media.R | 3 R/atlas_occurrences.R | 18 +-- R/build.R | 13 +- R/build_query_set.R | 8 + R/check.R | 10 - R/collapse_metadata.R | 2 R/collapse_species.R | 10 + R/collapse_unnest.R | 1 R/collect_metadata.R | 28 +++-- R/collect_occurrences.R | 64 +---------- R/collect_species.R | 30 ++++- R/collect_taxa.R | 3 R/galah-package.R | 1 R/galah_config.R | 2 R/galah_group_by.R | 22 +++ R/parse_checks.R | 3 R/parse_occurrences_count.R | 6 - R/quosure_handling.R | 8 + R/read_zip.R |only R/search_all.R | 3 R/sysdata.rda |binary R/url_lookup.R | 6 - build/vignette.rds |binary inst/CITATION | 2 inst/doc/choosing_an_atlas.html | 6 - inst/doc/download-data-reproducibly.Rmd |only inst/doc/download-data-reproducibly.html |only inst/doc/download_data.html | 2 inst/doc/look_up_information.html | 2 inst/doc/object_oriented_programming.html | 2 inst/doc/quick_start_guide.html | 2 inst/doc/spatial_filtering.html | 2 inst/doc/taxonomic_filtering.html | 2 inst/doc/temporal_filtering.html | 2 man/atlas_.Rd | 18 +-- man/atlas_citation.Rd | 24 ++-- man/figures/doi-web-example.png |only man/galah.Rd | 1 man/group_by.data_request.Rd | 22 +++ man/read_zip.Rd |only tests/testthat/test-atlas_citation.R | 43 ++++++- tests/testthat/test-atlas_counts.R | 32 ++--- tests/testthat/test-atlas_distributions.R | 12 +- tests/testthat/test-atlas_media.R | 14 +- tests/testthat/test-atlas_occurrences.R | 43 +++++-- tests/testthat/test-atlas_species.R | 35 ++++-- tests/testthat/test-atlas_taxonomy.R | 6 - tests/testthat/test-count_arrange_slice.R | 18 +-- tests/testthat/test-galah_apply_profile.R | 14 +- tests/testthat/test-galah_call.R | 6 - tests/testthat/test-galah_config.R | 6 - tests/testthat/test-galah_filter.R | 46 ++++---- tests/testthat/test-galah_group_by.R | 30 +++-- tests/testthat/test-galah_identify.R | 10 - tests/testthat/test-galah_select.R | 40 +++---- tests/testthat/test-international-Austria.R | 40 +++---- tests/testthat/test-international-Brazil.R | 34 +++--- tests/testthat/test-international-France.R | 30 ++--- tests/testthat/test-international-GBIF.R | 43 +++---- tests/testthat/test-international-Guatemala.R | 48 +++++--- tests/testthat/test-international-Portugal.R | 32 ++--- tests/testthat/test-international-Spain.R | 50 ++++----- tests/testthat/test-international-Sweden.R | 54 ++++----- tests/testthat/test-international-UK.R | 48 ++++---- tests/testthat/test-masked-functions.R | 8 - tests/testthat/test-request_metadata_unnest.R | 12 +- tests/testthat/test-search_all.R | 58 +++++----- tests/testthat/test-search_taxa.R | 30 ++--- tests/testthat/test-show_all.R | 2 tests/testthat/test-show_values.R | 24 ++-- vignettes/download-data-reproducibly.Rmd |only 76 files changed, 869 insertions(+), 636 deletions(-)
Title: Access Data from the Brazilian Development Bank (BNDES)
Description: Allows access to data on BNDES disbursements and contracts since 1995. The package makes it easy to import data from the bank into R.<https://www.bndes.gov.br/SiteBNDES/bndes/bndes_en>.
Author: Igor Laltuf [aut, cre]
Maintainer: Igor Laltuf <igorlaltuf@gmail.com>
Diff between bndesr versions 1.0.3 dated 2023-06-06 and 1.0.4 dated 2025-02-06
bndesr-1.0.3/bndesr/README.md |only bndesr-1.0.4/bndesr/DESCRIPTION | 11 ++--- bndesr-1.0.4/bndesr/MD5 | 13 ++---- bndesr-1.0.4/bndesr/NAMESPACE | 16 +++---- bndesr-1.0.4/bndesr/R/query_bndespar_desimbursements.R | 31 ++++++++++---- bndesr-1.0.4/bndesr/R/query_bndespar_portfolio.R | 26 ++++++++---- bndesr-1.0.4/bndesr/R/query_contracts.R | 25 +++++++---- bndesr-1.0.4/bndesr/R/query_desimbursements.R | 36 ++++++++++++++++- 8 files changed, 108 insertions(+), 50 deletions(-)
Title: Input/Output 'SomaScan' Data
Description: Load and export 'SomaScan' data via the
'Standard BioTools, Inc.' structured text file
called an ADAT ('*.adat'). For file format see
<https://github.com/SomaLogic/SomaLogic-Data/blob/main/README.md>.
The package also exports auxiliary functions for
manipulating, wrangling, and extracting relevant
information from an ADAT object once in memory.
Author: Stu Field [aut] ,
Caleb Scheidel [cre],
Standard BioTools, Inc. [cph, fnd]
Maintainer: Caleb Scheidel <calebjscheidel@gmail.com>
Diff between SomaDataIO versions 6.1.0 dated 2024-03-26 and 6.2.0 dated 2025-02-06
DESCRIPTION | 39 +++++---- LICENSE | 4 MD5 | 112 +++++++++++++++------------ NAMESPACE | 6 + NEWS.md | 91 ++++++++++++++++++++++ R/0-declare-global-variables.R | 1 R/adat2eSet.R | 8 + R/calc_eLOD.R |only R/data.R | 2 R/diffAdats.R | 2 R/groupGenerics.R | 25 ++++-- R/is-intact-attr.R | 10 +- R/loadAdatsAsList.R | 59 +++++++++++--- R/parseCheck.R | 12 +- R/parseHeader.R | 10 ++ R/pivotExpressionSet.R | 6 - R/prepHeaderMeta.R | 2 R/read-annotations.R | 55 +++++-------- R/s3-print-soma-adat.R | 5 - R/sysdata.rda |binary R/utils-read-adat.R | 2 R/utils-release.R | 85 +++++++++++--------- R/utils.R | 24 ++--- R/write-adat.R | 6 - R/zzz.R | 6 - README.md | 60 +++++++------- build/vignette.rds |binary inst/WORDLIST | 37 ++++++--- inst/cli/merge/merge_clin.R | 2 inst/doc/SomaDataIO.Rmd | 21 ++--- inst/doc/SomaDataIO.html | 36 ++++---- man/SomaDataIO-package.Rd | 11 +- man/SomaScanObjects.Rd | 2 man/adat2eSet.Rd | 2 man/calc_eLOD.Rd |only man/loadAdatsAsList.Rd | 2 man/parseHeader.Rd | 10 ++ man/pivotExpressionSet.Rd | 4 man/read_annotations.Rd | 4 man/soma_adat.Rd | 5 - tests/testthat/_snaps/S3-print.md | 10 +- tests/testthat/_snaps/diffAdats.md | 126 +++++++++++++++---------------- tests/testthat/_snaps/groupGenerics.md | 26 ++++-- tests/testthat/_snaps/is-intact-attr.md | 4 tests/testthat/_snaps/loadAdatsAsList.md | 6 - tests/testthat/_snaps/parseCheck.md |only tests/testthat/_snaps/utils-read-adat.md |only tests/testthat/_snaps/utils-release.md |only tests/testthat/helper.R | 9 ++ tests/testthat/test-S3-print.R | 16 ++- tests/testthat/test-S3-transform.R | 12 ++ tests/testthat/test-adat2eSet.R | 12 +- tests/testthat/test-calc_eLOD.R |only tests/testthat/test-getSomaScanLiftCCC.R |only tests/testthat/test-groupGenerics.R | 67 +++++++++++++++- tests/testthat/test-lift-adat.R | 13 +-- tests/testthat/test-parseCheck.R |only tests/testthat/test-pivotExpressionSet.R | 22 ++++- tests/testthat/test-read-annotations.R | 25 +++++- tests/testthat/test-utils-read-adat.R |only tests/testthat/test-utils-release.R |only vignettes/SomaDataIO.Rmd | 21 ++--- 62 files changed, 747 insertions(+), 390 deletions(-)
Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using 'SpatRaster' and 'SpatVector'
objects are provided. Non-Gaussian models are fit using 'INLA', and Gaussian
geostatistical models use Maximum Likelihood Estimation. For details see Brown (2015) <doi:10.18637/jss.v063.i12>. The 'RandomFields' package is available at <https://www.wim.uni-mannheim.de/schlather/publications/software>.
Author: Patrick Brown [aut, cre, cph]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between geostatsp versions 2.0.6 dated 2024-02-20 and 2.0.8 dated 2025-02-06
geostatsp-2.0.6/geostatsp/build/geostatsp.pdf |only geostatsp-2.0.6/geostatsp/inst/extR/murder.R |only geostatsp-2.0.8/geostatsp/DESCRIPTION | 8 geostatsp-2.0.8/geostatsp/MD5 | 62 - geostatsp-2.0.8/geostatsp/R/0gm.R | 740 +++++++++++------------ geostatsp-2.0.8/geostatsp/R/glgm.R | 8 geostatsp-2.0.8/geostatsp/R/krige.R | 16 geostatsp-2.0.8/geostatsp/R/lgcp.R | 9 geostatsp-2.0.8/geostatsp/R/lgm.R | 716 +++++++++++----------- geostatsp-2.0.8/geostatsp/R/maternCholSolve.R | 20 geostatsp-2.0.8/geostatsp/R/simLgcp.R | 1 geostatsp-2.0.8/geostatsp/R/stackRasterList.R | 5 geostatsp-2.0.8/geostatsp/build/stage23.rdb |binary geostatsp-2.0.8/geostatsp/build/vignette.rds |binary geostatsp-2.0.8/geostatsp/inst/doc/glgm.pdf |binary geostatsp-2.0.8/geostatsp/inst/doc/lgcp.R | 9 geostatsp-2.0.8/geostatsp/inst/doc/lgcp.Rnw | 9 geostatsp-2.0.8/geostatsp/inst/doc/lgcp.pdf |binary geostatsp-2.0.8/geostatsp/man/gambiaUTM.Rd | 2 geostatsp-2.0.8/geostatsp/man/glgm.Rd | 21 geostatsp-2.0.8/geostatsp/man/loaloa.Rd | 4 geostatsp-2.0.8/geostatsp/man/murder.Rd | 2 geostatsp-2.0.8/geostatsp/man/rongelapUTM.Rd | 2 geostatsp-2.0.8/geostatsp/man/swissRain.Rd | 4 geostatsp-2.0.8/geostatsp/src/gmrfEdge.c | 30 geostatsp-2.0.8/geostatsp/src/gmrfLik.c | 5 geostatsp-2.0.8/geostatsp/src/matern.c | 76 +- geostatsp-2.0.8/geostatsp/src/maternLogL.c | 18 geostatsp-2.0.8/geostatsp/src/maternLogLopt.c | 30 geostatsp-2.0.8/geostatsp/tests/lgcp.R | 18 geostatsp-2.0.8/geostatsp/tests/lgm.R | 14 geostatsp-2.0.8/geostatsp/tests/maternGmrfPrec.R | 4 geostatsp-2.0.8/geostatsp/vignettes/lgcp.Rnw | 9 33 files changed, 931 insertions(+), 911 deletions(-)
Title: Chat with Large Language Models
Description: Chat with large language models from a range of providers
including 'Claude' <https://claude.ai>, 'OpenAI'
<https://chatgpt.com>, and more. Supports streaming, asynchronous
calls, tool calling, and structured data extraction.
Author: Hadley Wickham [aut, cre] ,
Joe Cheng [aut],
Aaron Jacobs [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between ellmer versions 0.1.0 dated 2025-01-09 and 0.1.1 dated 2025-02-06
DESCRIPTION | 58 +++--- MD5 | 145 ++++++++++------- NAMESPACE | 8 NEWS.md | 64 +++++++ R/chat.R | 5 R/content-image.R | 28 ++- R/content-pdf.R |only R/content.R | 17 +- R/ellmer-package.R | 4 R/httr2.R | 87 ---------- R/provider-azure.R | 226 +++++++++++++++++++++++---- R/provider-bedrock.R | 115 ++++++++++--- R/provider-claude.R | 40 +++- R/provider-cortex.R | 182 ++++++++------------- R/provider-databricks.R | 185 +++++++++++++--------- R/provider-deepseek.R |only R/provider-gemini.R | 28 ++- R/provider-groq.R | 4 R/provider-ollama.R | 17 +- R/provider-openai.R | 16 + R/provider-openrouter.R |only R/provider-snowflake.R |only R/provider.R | 4 R/utils.R | 30 +++ README.md | 45 ++++- build/vignette.rds |binary inst/doc/ellmer.Rmd | 8 inst/doc/ellmer.html | 48 +++-- inst/doc/prompt-design.html | 92 +++++----- inst/doc/streaming-async.Rmd | 18 +- inst/doc/streaming-async.html | 67 +++----- inst/doc/structured-data.Rmd | 2 inst/doc/structured-data.html | 81 ++++----- inst/doc/tool-calling.html | 6 man/Chat.Rd | 11 + man/Content.Rd | 3 man/chat_azure.Rd | 37 +++- man/chat_bedrock.Rd | 39 +++- man/chat_claude.Rd | 6 man/chat_cortex.Rd | 60 +------ man/chat_cortex_analyst.Rd |only man/chat_databricks.Rd | 17 +- man/chat_deepseek.Rd |only man/chat_gemini.Rd | 7 man/chat_github.Rd | 4 man/chat_groq.Rd | 8 man/chat_ollama.Rd | 13 + man/chat_openai.Rd | 4 man/chat_openrouter.Rd |only man/chat_perplexity.Rd | 6 man/chat_snowflake.Rd |only man/content_image_url.Rd | 2 man/content_pdf_file.Rd |only man/ellmer-package.Rd | 5 man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only tests/testthat/_snaps/chat.md | 3 tests/testthat/_snaps/provider-azure.md |only tests/testthat/_snaps/provider-bedrock.md | 17 +- tests/testthat/_snaps/provider-cortex.md | 12 - tests/testthat/_snaps/provider-deepseek.md |only tests/testthat/_snaps/provider-gemini.md | 2 tests/testthat/_snaps/provider-openrouter.md |only tests/testthat/_snaps/provider-snowflake.md |only tests/testthat/apples.pdf |only tests/testthat/helper-provider.R | 19 ++ tests/testthat/test-chat.R | 7 tests/testthat/test-content-pdf.R |only tests/testthat/test-provider-azure.R | 125 +++++++++++++- tests/testthat/test-provider-bedrock.R | 74 ++++++++ tests/testthat/test-provider-claude.R | 18 +- tests/testthat/test-provider-cortex.R | 4 tests/testthat/test-provider-databricks.R | 63 ++++++- tests/testthat/test-provider-deepseek.R |only tests/testthat/test-provider-gemini.R | 17 +- tests/testthat/test-provider-ollama.R |only tests/testthat/test-provider-openai.R | 2 tests/testthat/test-provider-openrouter.R |only tests/testthat/test-provider-snowflake.R |only tests/testthat/test-provider-vllm.R | 2 vignettes/ellmer.Rmd | 8 vignettes/streaming-async.Rmd | 18 +- vignettes/structured-data.Rmd | 2 85 files changed, 1484 insertions(+), 761 deletions(-)
Title: Stratified Randomized Experiments
Description: Estimate average treatment effects (ATEs) in stratified randomized experiments. 'sreg' is designed to accommodate scenarios with multiple treatments and cluster-level treatment assignments, and accommodates optimal linear covariate adjustment based on baseline observable characteristics. 'sreg' computes estimators and standard errors based on Bugni, Canay, Shaikh (2018) <doi:10.1080/01621459.2017.1375934>; Bugni, Canay, Shaikh, Tabord-Meehan (2024+) <doi:10.48550/arXiv.2204.08356>; and Jiang, Linton, Tang, Zhang (2023+) <doi:10.48550/arXiv.2201.13004>.
Author: Juri Trifonov [aut, cre, cph],
Yuehao Bai [aut],
Azeem Shaikh [aut],
Max Tabord-Meehan [aut]
Maintainer: Juri Trifonov <jutrifonov@uchicago.edu>
Diff between sreg versions 1.0.0 dated 2024-06-25 and 1.0.1 dated 2025-02-06
DESCRIPTION | 10 +++---- MD5 | 18 +++++++------- NEWS.md | 16 ++++-------- R/core.R | 32 ++++++++++++++++++++++--- R/data_check.r | 31 ++++++++++++++++++++++++ README.md | 56 +++++++++++++++++++++++++++++++++++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/intro-to-sreg.html | 28 +++++++++++----------- tests/testthat/test-core.R | 11 ++++---- 10 files changed, 149 insertions(+), 53 deletions(-)
Title: Data Processing of SMN Hi-Res Weather Forecast from 'AWS'
Description: Exploration of Weather Research & Forecasting ('WRF') Model data
of Servicio Meteorologico Nacional (SMN) from Amazon Web Services
(<https://registry.opendata.aws/smn-ar-wrf-dataset/>) cloud. The package
provides the possibility of data downloading, processing and correction
methods. It also has map management and series exploration of available
meteorological variables of 'WRF' forecast.
Author: Gonzalo Diaz [cre, aut]
Maintainer: Gonzalo Diaz <gonzalomartindiaz22@gmail.com>
Diff between aws.wrfsmn versions 0.0.4 dated 2025-01-10 and 0.0.5 dated 2025-02-06
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NAMESPACE | 3 +++ NEWS.md | 6 ++++++ R/daily_data_fields.R |only man/daily.data.fields.Rd |only 6 files changed, 17 insertions(+), 6 deletions(-)
Title: Static Analysis of R-Code Dependencies
Description: A minimal R-package to approximately detect global and imported functions or variables from R-source code or R-packages by static code analysis.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between checkglobals versions 0.1.0 dated 2023-06-02 and 0.1.3 dated 2025-02-06
DESCRIPTION | 12 - LICENSE | 2 MD5 | 46 +++--- NEWS.md | 11 + R/as.R | 4 R/check_internal.R | 56 ++++---- R/check_pkg.R | 22 ++- R/check_source.R | 28 +++- R/print.R | 106 +++++++++++---- inst/unit_tests/pkg/testpkg/DESCRIPTION | 1 inst/unit_tests/pkg/testpkg/NAMESPACE | 4 inst/unit_tests/pkg/testpkg/R/aaa.R | 11 + inst/unit_tests/pkg/testpkg/R/functions1.R | 42 +++++- inst/unit_tests/unit_tests_checkglobals.R | 105 +++++++++------ man/as.data.frame.checkglobals.Rd | 2 man/as.matrix.checkglobals.Rd | 2 man/check_pkg.Rd | 3 man/print.checkglobals.Rd | 2 man/print.checkglobalsg.Rd | 2 man/print.checkglobalsi.Rd | 2 src/checkglobals.h | 23 ++- src/handlers.c | 193 +++++++++++++++++++++++------ src/utils.c | 60 +++++++-- src/walk_expr.c | 146 ++++++++++++++------- 24 files changed, 632 insertions(+), 253 deletions(-)
Title: Exploratory Analysis of Genetic and Genomic Data
Description: Toolset for the exploration of genetic and genomic
data. Adegenet provides formal (S4) classes for storing and handling
various genetic data, including genetic markers with varying ploidy
and hierarchical population structure ('genind' class), alleles counts
by populations ('genpop'), and genome-wide SNP data ('genlight'). It
also implements original multivariate methods (DAPC, sPCA), graphics,
statistical tests, simulation tools, distance and similarity measures,
and several spatial methods. A range of both empirical and simulated
datasets is also provided to illustrate various methods.
Author: Thibaut Jombart [aut] ,
Zhian N. Kamvar [aut, cre] ,
Caitlin Collins [ctb],
Roman Lustrik [ctb],
Marie-Pauline Beugin [ctb],
Brian J. Knaus [ctb],
Peter Solymos [ctb],
Vladimir Mikryukov [ctb],
Klaus Schliep [ctb],
Tiago Maie [ctb],
Libor Morkovsky [ [...truncated...]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between adegenet versions 2.1.10 dated 2023-01-26 and 2.1.11 dated 2025-02-06
ChangeLog | 17 ++++++++++ DESCRIPTION | 20 ++++++++---- MD5 | 66 ++++++++++++++++++++--------------------- NAMESPACE | 6 +-- R/basicMethods.R | 2 - R/find.clust.R | 2 - R/glHandle.R | 5 ++- R/haploGen.R | 1 R/import.R | 2 - R/spca.R | 2 - R/spca_randtest.R | 60 ++++++++++++++++++++++--------------- R/strataMethods.R | 2 - build/partial.rdb |binary data/H3N2.rda |binary data/dapcIllus.rda |binary data/eHGDP.rda |binary data/hybridtoy.RData |binary data/microbov.rda |binary data/nancycats.rda |binary data/rupica.RData |binary data/sim2pop.rda |binary data/spcaIllus.rda |binary data/swallowtails.rda |binary inst/CITATION | 8 ++-- man/adegenet.package.Rd | 1 man/auxil.Rd | 2 + man/df2genind.Rd | 2 - man/find.clusters.Rd | 2 - man/pairDist.Rd | 2 - man/spca.Rd | 5 +-- man/spca_randtest.Rd | 4 +- man/strata-methods.Rd | 2 - src/snpbin.c | 48 +++++++++++++++-------------- tests/testthat/test_genlight.R | 18 +++++++++++ 34 files changed, 170 insertions(+), 109 deletions(-)
Title: Two One-Sided Tests (TOST) Equivalence Testing
Description: Two one-sided tests (TOST) procedure to test equivalence for t-tests, correlations, differences between proportions, and meta-analyses, including power analysis for t-tests and correlations. Allows you to specify equivalence bounds in raw scale units or in terms of effect sizes. See: Lakens (2017) <doi:10.1177/1948550617697177>.
Author: Daniel Lakens [aut],
Aaron Caldwell [aut, cre]
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>
Diff between TOSTER versions 0.8.3 dated 2024-05-08 and 0.8.4 dated 2025-02-06
DESCRIPTION | 6 MD5 | 58 - NEWS.md | 5 R/00jmv.R | 36 R/datatostone.h.R | 993 +++++++++++++-------------- R/datatostpaired.h.R | 973 +++++++++++++-------------- R/datatostr.h.R | 657 +++++++++--------- R/datatosttwo.h.R | 1153 ++++++++++++++++---------------- R/datatosttwoprop.b.R | 54 + R/datatosttwoprop.h.R | 711 +++++++++---------- R/globals.R | 3 R/methods.TOSTt.R | 106 ++ R/power_correlations.R | 16 R/t_TOST.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/IntroTOSTt.R | 15 inst/doc/IntroTOSTt.Rmd | 25 inst/doc/IntroTOSTt.html | 447 ++++++------ inst/doc/IntroductionToTOSTER.html | 16 inst/doc/SMD_calcs.html | 18 inst/doc/correlations.html | 6 inst/doc/robustTOST.html | 20 inst/doc/the_ftestTOSTER.html | 8 man/TOSTt-methods.Rd | 2 man/dataTOSTpaired.Rd | 2 tests/testthat/test-jamovi.R | 8 tests/testthat/test-power_correlation.R | 6 tests/testthat/test-tTOST.R | 4 vignettes/IntroTOSTt.Rmd | 25 30 files changed, 2775 insertions(+), 2600 deletions(-)
Title: Interactive Scatter Plot and Volcano Plot Labels
Description: Interactive labelling of scatter plots, volcano plots and
Manhattan plots using a 'shiny' and 'plotly' interface. Users can hover
over points to see where specific points are located and click points
on/off to easily label them. Labels can be dragged around the plot to place
them optimally. Plots can be exported directly to PDF for publication. For
plots with large numbers of points, points can optionally be rasterized as a
bitmap, while all other elements (axes, text, labels & lines) are preserved
as vector objects. This can dramatically reduce file size for plots with
millions of points such as Manhattan plots, and is ideal for publication.
Author: Myles Lewis [aut, cre] ,
Katriona Goldmann [aut] ,
Cankut Cubuk [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between easylabel versions 0.3.2 dated 2025-01-09 and 0.3.3 dated 2025-02-06
DESCRIPTION | 6 MD5 | 15 + NAMESPACE | 2 NEWS.md | 8 R/add_labels.R |only R/easylabel.R | 16 - R/utils.R | 5 inst/doc/easylabel.R | 450 +++++++++++++++++++++++++-------------------------- man/add_labels.Rd |only man/arial.Rd |only 10 files changed, 258 insertions(+), 244 deletions(-)
Title: Treatment Switching
Description: Implements rank-preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), and two-stage estimation (TSE) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between trtswitch versions 0.1.2 dated 2024-12-05 and 0.1.3 dated 2025-02-06
DESCRIPTION | 8 MD5 | 57 ++-- NAMESPACE | 1 NEWS.md | 4 R/RcppExports.R | 199 ++++++++------ R/ipcw.R | 14 - R/ipe.R | 8 R/logisregr.R | 16 + R/rpsftm.R | 4 R/trtswitch-package.R | 10 R/tsegest.R | 9 R/tsesimp.R | 17 - man/ipcw.Rd | 14 - man/ipe.Rd | 8 man/kmdiff.Rd |only man/logisregr.Rd | 10 man/qrcpp.Rd | 10 man/rpsftm.Rd | 4 man/trtswitch-package.Rd | 10 man/tsegest.Rd | 9 man/tsesimp.Rd | 17 - src/RcppExports.cpp | 228 ++--------------- src/ipcw.cpp | 4 src/logistic_regression.cpp | 249 +++++++++++++++--- src/logistic_regression.h | 10 src/survival_analysis.cpp | 589 +++++++++++++++++++++++++++++++++++++++++++- src/survival_analysis.h | 10 src/tsegest.cpp | 2 src/utilities.cpp | 135 ++++------ src/utilities.h | 7 30 files changed, 1143 insertions(+), 520 deletions(-)
Title: Pull Data from an 'ArcGIS REST' API
Description: Functions to efficiently query 'ArcGIS REST' APIs
<https://developers.arcgis.com/rest/>.
Both spatial and SQL queries can be used to retrieve data.
Simple Feature (sf) objects are utilized to perform spatial queries.
This package was neither produced nor is maintained by Esri.
Author: Paul Frater [aut, cre] ,
Zac Driscoll [aut]
Maintainer: Paul Frater <paul.frater@wisconsin.gov>
Diff between arcpullr versions 0.2.9 dated 2024-03-11 and 0.3.0 dated 2025-02-06
arcpullr-0.2.9/arcpullr/data/wi_aerial_imagery.rda |only arcpullr-0.2.9/arcpullr/data/wi_landcover.rda |only arcpullr-0.2.9/arcpullr/man/match_raster_colors.Rd |only arcpullr-0.2.9/arcpullr/man/sf_example_raster.Rd |only arcpullr-0.2.9/arcpullr/tests/testthat/test_process_rasters.R |only arcpullr-0.3.0/arcpullr/DESCRIPTION | 17 arcpullr-0.3.0/arcpullr/MD5 | 57 +-- arcpullr-0.3.0/arcpullr/NAMESPACE | 7 arcpullr-0.3.0/arcpullr/R/arcpullr-package.R | 30 + arcpullr-0.3.0/arcpullr/R/data.R | 20 - arcpullr-0.3.0/arcpullr/R/imports.R | 14 arcpullr-0.3.0/arcpullr/R/plot_layers.R | 160 +++++++- arcpullr-0.3.0/arcpullr/R/process_raster.R | 149 +++++--- arcpullr-0.3.0/arcpullr/R/retrieve_layer_properties.R | 34 - arcpullr-0.3.0/arcpullr/R/retrieve_layers.R | 74 +--- arcpullr-0.3.0/arcpullr/R/utilities.R | 74 ++-- arcpullr-0.3.0/arcpullr/build/vignette.rds |binary arcpullr-0.3.0/arcpullr/inst/doc/intro_to_arcpullr.html | 2 arcpullr-0.3.0/arcpullr/inst/doc/raster_layers.R | 15 arcpullr-0.3.0/arcpullr/inst/doc/raster_layers.Rmd | 16 arcpullr-0.3.0/arcpullr/inst/doc/raster_layers.html | 20 - arcpullr-0.3.0/arcpullr/inst/doc/spatial_queries.html | 185 +++------- arcpullr-0.3.0/arcpullr/inst/wi_aerial_imagery.png |only arcpullr-0.3.0/arcpullr/inst/wi_aerial_imagery.png.aux.xml |only arcpullr-0.3.0/arcpullr/inst/wi_landcover.png |only arcpullr-0.3.0/arcpullr/inst/wi_landcover.png.aux.xml |only arcpullr-0.3.0/arcpullr/man/arcpullr-package.Rd | 10 arcpullr-0.3.0/arcpullr/man/get_image_layer.Rd | 2 arcpullr-0.3.0/arcpullr/man/get_map_layer.Rd | 2 arcpullr-0.3.0/arcpullr/man/get_raster_layer.Rd | 3 arcpullr-0.3.0/arcpullr/man/match_legend_colors.Rd |only arcpullr-0.3.0/arcpullr/man/plot_layer-SpatRaster-method.Rd |only arcpullr-0.3.0/arcpullr/man/raster_colors-SpatRaster-method.Rd |only arcpullr-0.3.0/arcpullr/tests/testthat/test_layer_properties.R | 6 arcpullr-0.3.0/arcpullr/tests/testthat/test_process_terra_rasters.R |only arcpullr-0.3.0/arcpullr/vignettes/raster_layers.Rmd | 16 36 files changed, 519 insertions(+), 394 deletions(-)
Title: Scientific Analysis of Trial Errors (SATE)
Description: Bundles functions used to analyze the harmfulness of trial errors in criminal trials.
Functions in the Scientific Analysis of Trial Errors ('SATE') package help users estimate the
probability that a jury will find a defendant guilty given jurors' preferences for a guilty
verdict and the uncertainty of that estimate. Users can also compare actual and hypothetical
trial conditions to conduct harmful error analysis. The relationship between individual jurors'
verdict preferences and the probability that a jury returns a guilty verdict has been studied
by Davis (1973) <doi:10.1037/h0033951>; MacCoun & Kerr (1988) <doi:10.1037/0022-3514.54.1.21>,
and Devine et el. (2001) <doi:10.1037/1076-8971.7.3.622>, among others.
Author: Barry Edwards [aut, cre]
Maintainer: Barry Edwards <bce@uga.edu>
Diff between sate versions 2.2.1 dated 2024-12-05 and 2.3.0 dated 2025-02-06
DESCRIPTION | 11 +- MD5 | 43 +++++--- NAMESPACE | 12 ++ NEWS.md | 17 +++ R/as.jury.point.r | 1 R/as.jury.stats.r | 1 R/basic.plot.grid.R |only R/compare.juror.stats.R |only R/compare.jury.stats.r | 9 + R/data.R |only R/deliberate.civil.r | 1 R/deliberate.r | 1 R/encode.cloud.respondent.variables.R |only R/graph.effect.defendant.r | 5 R/graph.estimate.r | 1 R/helper.functions.r | 156 ++++++++++++++++++------------- R/select.with.strikes.r | 1 R/sim.as.jury.stats.r | 1 R/sim.compare.jury.stats.r | 1 R/sysdata.rda |only R/target.population.demographics.R |only R/weights_for_population.R |only data |only man/basic.plot.grid.Rd |only man/compact_harm_plot.Rd |only man/compare.juror.stats.Rd |only man/encode.cloud.respondent.variables.Rd |only man/state.demographic.info.Rd |only man/target.population.demographics.Rd |only man/weights_for_population.Rd |only 30 files changed, 166 insertions(+), 95 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 0.7.3 dated 2024-07-22 and 0.7.4 dated 2025-02-06
easystats-0.7.3/easystats/inst/doc/citation.R |only easystats-0.7.3/easystats/inst/doc/citation.Rmd |only easystats-0.7.3/easystats/inst/doc/citation.html |only easystats-0.7.3/easystats/inst/doc/conventions.R |only easystats-0.7.3/easystats/inst/doc/conventions.Rmd |only easystats-0.7.3/easystats/inst/doc/conventions.html |only easystats-0.7.3/easystats/inst/doc/list_of_functions.R |only easystats-0.7.3/easystats/inst/doc/list_of_functions.Rmd |only easystats-0.7.3/easystats/inst/doc/list_of_functions.html |only easystats-0.7.3/easystats/inst/doc/resources.R |only easystats-0.7.3/easystats/inst/doc/resources.Rmd |only easystats-0.7.3/easystats/inst/doc/resources.html |only easystats-0.7.3/easystats/inst/doc/workflow_performance.R |only easystats-0.7.3/easystats/inst/doc/workflow_performance.html |only easystats-0.7.3/easystats/inst/doc/workflow_performance.rmd |only easystats-0.7.3/easystats/man/figures/unnamed-chunk-7-1.png |only easystats-0.7.3/easystats/vignettes/citation.Rmd |only easystats-0.7.3/easystats/vignettes/conventions.Rmd |only easystats-0.7.3/easystats/vignettes/images |only easystats-0.7.3/easystats/vignettes/list_of_functions.Rmd |only easystats-0.7.3/easystats/vignettes/resources.Rmd |only easystats-0.7.3/easystats/vignettes/workflow_performance.rmd |only easystats-0.7.4/easystats/DESCRIPTION | 44 ++++---- easystats-0.7.4/easystats/MD5 | 49 +++------- easystats-0.7.4/easystats/NEWS.md | 9 + easystats-0.7.4/easystats/R/install_easystats.R | 4 easystats-0.7.4/easystats/R/install_suggested.R | 2 easystats-0.7.4/easystats/R/utils.R | 1 easystats-0.7.4/easystats/README.md | 45 +++++++-- easystats-0.7.4/easystats/build/vignette.rds |binary easystats-0.7.4/easystats/inst/WORDLIST | 11 +- easystats-0.7.4/easystats/inst/doc/overview_of_vignettes.R |only easystats-0.7.4/easystats/inst/doc/overview_of_vignettes.Rmd |only easystats-0.7.4/easystats/inst/doc/overview_of_vignettes.html |only easystats-0.7.4/easystats/inst/templates/easydashboard.Rmd | 16 --- easystats-0.7.4/easystats/man/easystats-package.Rd | 10 +- easystats-0.7.4/easystats/man/figures/README-6-1.png |only easystats-0.7.4/easystats/man/figures/depnetwork-1.png |binary easystats-0.7.4/easystats/vignettes/overview_of_vignettes.Rmd |only 39 files changed, 97 insertions(+), 94 deletions(-)
Title: Simulate, Evaluate, and Analyze Dose Finding Trials with
Bayesian MCPMod
Description: Bayesian MCPMod (Fleischer et al. (2022)
<doi:10.1002/pst.2193>) is an innovative method that improves the
traditional MCPMod by systematically incorporating historical data,
such as previous placebo group data. This R package offers functions
for simulating, analyzing, and evaluating Bayesian MCPMod trials with
normally distributed endpoints. It enables the assessment of trial
designs incorporating historical data across various true
dose-response relationships and sample sizes. Robust mixture prior
distributions, such as those derived with the Meta-Analytic-Predictive
approach (Schmidli et al. (2014) <doi:10.1111/biom.12242>), can be
specified for each dose group. Resulting mixture posterior
distributions are used in the Bayesian Multiple Comparison Procedure
and modeling steps. The modeling step also includes a weighted model
averaging approach (Pinheiro et al. (2014) <doi:10.1002/sim.6052>).
Estimated dose-response relationships can be bootstrapped and
visualiz [...truncated...]
Author: Boehringer Ingelheim Pharma GmbH & Co. KG [cph, fnd],
Stephan Wojciekowski [aut, cre],
Lars Andersen [aut],
Jonas Schick [ctb],
Sebastian Bossert [aut]
Maintainer: Stephan Wojciekowski <stephan.wojciekowski@boehringer-ingelheim.com>
Diff between BayesianMCPMod versions 1.0.1 dated 2024-04-05 and 1.0.2 dated 2025-02-06
BayesianMCPMod-1.0.1/BayesianMCPMod/R/modelling.R |only BayesianMCPMod-1.0.1/BayesianMCPMod/man/getBootstrapSamples.Rd |only BayesianMCPMod-1.0.1/BayesianMCPMod/tests/testthat/test-global.R |only BayesianMCPMod-1.0.2/BayesianMCPMod/DESCRIPTION | 24 BayesianMCPMod-1.0.2/BayesianMCPMod/MD5 | 111 BayesianMCPMod-1.0.2/BayesianMCPMod/NAMESPACE | 1 BayesianMCPMod-1.0.2/BayesianMCPMod/NEWS.md | 12 BayesianMCPMod-1.0.2/BayesianMCPMod/R/BMCPMod.R | 402 - BayesianMCPMod-1.0.2/BayesianMCPMod/R/Quarto |only BayesianMCPMod-1.0.2/BayesianMCPMod/R/bootstrapping.R | 150 BayesianMCPMod-1.0.2/BayesianMCPMod/R/modeling.R |only BayesianMCPMod-1.0.2/BayesianMCPMod/R/plot.R | 128 BayesianMCPMod-1.0.2/BayesianMCPMod/R/posterior.R | 254 BayesianMCPMod-1.0.2/BayesianMCPMod/R/s3methods.R | 217 BayesianMCPMod-1.0.2/BayesianMCPMod/R/simulation.R | 2 BayesianMCPMod-1.0.2/BayesianMCPMod/README.md | 6 BayesianMCPMod-1.0.2/BayesianMCPMod/build/vignette.rds |binary BayesianMCPMod-1.0.2/BayesianMCPMod/inst/WORDLIST | 75 BayesianMCPMod-1.0.2/BayesianMCPMod/inst/doc/Simulation_Comparison.R |only BayesianMCPMod-1.0.2/BayesianMCPMod/inst/doc/Simulation_Comparison.Rmd |only BayesianMCPMod-1.0.2/BayesianMCPMod/inst/doc/Simulation_Comparison.html |only BayesianMCPMod-1.0.2/BayesianMCPMod/inst/doc/Simulation_Example.R | 15 BayesianMCPMod-1.0.2/BayesianMCPMod/inst/doc/Simulation_Example.Rmd | 25 BayesianMCPMod-1.0.2/BayesianMCPMod/inst/doc/Simulation_Example.html | 1002 +-- BayesianMCPMod-1.0.2/BayesianMCPMod/inst/doc/analysis_normal.R | 257 BayesianMCPMod-1.0.2/BayesianMCPMod/inst/doc/analysis_normal.Rmd | 408 + BayesianMCPMod-1.0.2/BayesianMCPMod/inst/doc/analysis_normal.html | 2718 +++++++--- BayesianMCPMod-1.0.2/BayesianMCPMod/man/assessDesign.Rd | 10 BayesianMCPMod-1.0.2/BayesianMCPMod/man/getBootstrapQuantiles.Rd | 43 BayesianMCPMod-1.0.2/BayesianMCPMod/man/getContr.Rd | 4 BayesianMCPMod-1.0.2/BayesianMCPMod/man/getCritProb.Rd | 2 BayesianMCPMod-1.0.2/BayesianMCPMod/man/getModelFits.Rd | 6 BayesianMCPMod-1.0.2/BayesianMCPMod/man/getPosterior.Rd | 24 BayesianMCPMod-1.0.2/BayesianMCPMod/man/performBayesianMCP.Rd | 8 BayesianMCPMod-1.0.2/BayesianMCPMod/man/performBayesianMCPMod.Rd | 10 BayesianMCPMod-1.0.2/BayesianMCPMod/man/plot.modelFits.Rd | 6 BayesianMCPMod-1.0.2/BayesianMCPMod/man/predict.modelFits.Rd | 4 BayesianMCPMod-1.0.2/BayesianMCPMod/man/simulateData.Rd | 2 BayesianMCPMod-1.0.2/BayesianMCPMod/tests/testthat/data |only BayesianMCPMod-1.0.2/BayesianMCPMod/tests/testthat/setup.R | 124 BayesianMCPMod-1.0.2/BayesianMCPMod/tests/testthat/test-BMCPMod.R | 305 - BayesianMCPMod-1.0.2/BayesianMCPMod/tests/testthat/test-bootstrapping.R | 41 BayesianMCPMod-1.0.2/BayesianMCPMod/tests/testthat/test-modelling.R | 113 BayesianMCPMod-1.0.2/BayesianMCPMod/tests/testthat/test-plot.R | 76 BayesianMCPMod-1.0.2/BayesianMCPMod/tests/testthat/test-posterior.R | 175 BayesianMCPMod-1.0.2/BayesianMCPMod/tests/testthat/test-s3methods.R | 65 BayesianMCPMod-1.0.2/BayesianMCPMod/tests/testthat/test-simulation.R | 114 BayesianMCPMod-1.0.2/BayesianMCPMod/vignettes/Simulation_Comparison.Rmd |only BayesianMCPMod-1.0.2/BayesianMCPMod/vignettes/Simulation_Example.Rmd | 25 BayesianMCPMod-1.0.2/BayesianMCPMod/vignettes/analysis_normal.Rmd | 408 + BayesianMCPMod-1.0.2/BayesianMCPMod/vignettes/data |only BayesianMCPMod-1.0.2/BayesianMCPMod/vignettes/references.bib |only 52 files changed, 5148 insertions(+), 2224 deletions(-)
More information about BayesianMCPMod at CRAN
Permanent link
Title: Detecting Influence Paths with Information Theory
Description: Traces information spread through interactions between features, utilising information theory measures and a higher-order generalisation of the concept of widest paths in graphs.
In particular, 'vistla' can be used to better understand the results of high-throughput biomedical experiments, by organising the effects of the investigated intervention in a tree-like hierarchy from direct to indirect ones, following the plausible information relay circuits.
Due to its higher-order nature, 'vistla' can handle multi-modality and assign multiple roles to a single feature.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>
Diff between vistla versions 2.0.4 dated 2025-01-25 and 2.1.0 dated 2025-02-06
vistla-2.0.4/vistla/man/leaf_scores.Rd |only vistla-2.1.0/vistla/DESCRIPTION | 6 +++--- vistla-2.1.0/vistla/MD5 | 30 +++++++++++++++++++----------- vistla-2.1.0/vistla/NAMESPACE | 2 +- vistla-2.1.0/vistla/R/collapse.R |only vistla-2.1.0/vistla/R/ensemble.R | 6 +++--- vistla-2.1.0/vistla/R/vistla.R | 23 ++--------------------- vistla-2.1.0/vistla/build |only vistla-2.1.0/vistla/inst/NEWS | 20 ++++++++++++++++++++ vistla-2.1.0/vistla/inst/doc |only vistla-2.1.0/vistla/man/collapse.Rd |only vistla-2.1.0/vistla/man/ensemble.Rd | 6 +++--- vistla-2.1.0/vistla/man/vistla.Rd | 5 ++--- vistla-2.1.0/vistla/src/ensemble.h | 6 +++--- vistla-2.1.0/vistla/src/interface.h | 6 +++--- vistla-2.1.0/vistla/src/vistla.h | 1 + vistla-2.1.0/vistla/vignettes |only 17 files changed, 60 insertions(+), 51 deletions(-)
Title: Dimensional Data Frames
Description: Provides a 'dibble' that implements data cubes (derived from
'dimensional tibble'), and allows broadcasting by dimensional names.
Author: Mizuki Uchida [aut, cre]
Maintainer: Mizuki Uchida <uchidamizuki@vivaldi.net>
Diff between dibble versions 0.3.0 dated 2024-06-23 and 0.3.1 dated 2025-02-06
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 3 +++ NEWS.md | 7 +++++++ R/ddf_col.R | 10 ++++++++++ R/dibble-package.R | 1 + R/dibble.R | 26 ++++---------------------- R/dim_names.R | 11 ++++++----- R/methods.R | 28 +++++++++++++++++++--------- R/tbl_ddf.R | 14 ++++++++++++++ R/utils.R | 2 +- README.md | 4 ++-- tests/testthat/test-broadcast.R | 9 +++++++++ tests/testthat/test-matrix.R | 16 ++++++++++++++++ tests/testthat/test-rbind.R | 26 ++++++++++++++++++++++++++ 15 files changed, 137 insertions(+), 58 deletions(-)
Title: Analyzes Real-World Treatment Patterns of a Study Population of
Interest
Description: Computes treatment patterns within a given cohort using the Observational
Medical Outcomes Partnership (OMOP) common data model (CDM). As described
in Markus, Verhamme, Kors, and Rijnbeek (2022) <doi:10.1016/j.cmpb.2022.107081>.
Author: Aniek Markus [aut] ,
Maarten van Kessel [cre]
Maintainer: Maarten van Kessel <m.l.vankessel@erasmusmc.nl>
Diff between TreatmentPatterns versions 2.7.0 dated 2024-11-27 and 3.0.0 dated 2025-02-06
TreatmentPatterns-2.7.0/TreatmentPatterns/inst/DummyOutput/countsAge.csv |only TreatmentPatterns-2.7.0/TreatmentPatterns/inst/DummyOutput/countsSex.csv |only TreatmentPatterns-2.7.0/TreatmentPatterns/inst/DummyOutput/countsYear.csv |only TreatmentPatterns-2.7.0/TreatmentPatterns/inst/DummyOutput/summaryEventDuration.csv |only TreatmentPatterns-2.7.0/TreatmentPatterns/inst/DummyOutput/treatmentPathways.csv |only TreatmentPatterns-2.7.0/TreatmentPatterns/vignettes/articles/PareReport.Rmd |only TreatmentPatterns-2.7.0/TreatmentPatterns/vignettes/articles/bestPractices.html |only TreatmentPatterns-2.7.0/TreatmentPatterns/vignettes/articles/latestChanges.Rmd |only TreatmentPatterns-3.0.0/TreatmentPatterns/DESCRIPTION | 25 TreatmentPatterns-3.0.0/TreatmentPatterns/MD5 | 116 - TreatmentPatterns-3.0.0/TreatmentPatterns/NAMESPACE | 5 TreatmentPatterns-3.0.0/TreatmentPatterns/NEWS.md | 17 TreatmentPatterns-3.0.0/TreatmentPatterns/R/CDMInterface.R | 302 ++-- TreatmentPatterns-3.0.0/TreatmentPatterns/R/CharacterizationPlots.R | 2 TreatmentPatterns-3.0.0/TreatmentPatterns/R/InputHandler.R | 42 TreatmentPatterns-3.0.0/TreatmentPatterns/R/InteractivePlots.R | 8 TreatmentPatterns-3.0.0/TreatmentPatterns/R/TreatmentPatterns-package.R | 14 TreatmentPatterns-3.0.0/TreatmentPatterns/R/TreatmentPatternsResults.R |only TreatmentPatterns-3.0.0/TreatmentPatterns/R/attrition.R | 10 TreatmentPatterns-3.0.0/TreatmentPatterns/R/computePathways.R | 37 TreatmentPatterns-3.0.0/TreatmentPatterns/R/constructPathways.R | 333 ++-- TreatmentPatterns-3.0.0/TreatmentPatterns/R/createSankeyDiagram.R | 12 TreatmentPatterns-3.0.0/TreatmentPatterns/R/createSunburstPlot.R | 4 TreatmentPatterns-3.0.0/TreatmentPatterns/R/executeTreatmentPatterns.R | 18 TreatmentPatterns-3.0.0/TreatmentPatterns/R/export.R | 358 +++-- TreatmentPatterns-3.0.0/TreatmentPatterns/R/getResultsDataModelSpecification.R |only TreatmentPatterns-3.0.0/TreatmentPatterns/R/plotEventDuration.R | 37 TreatmentPatterns-3.0.0/TreatmentPatterns/README.md | 3 TreatmentPatterns-3.0.0/TreatmentPatterns/build/partial.rdb |binary TreatmentPatterns-3.0.0/TreatmentPatterns/build/vignette.rds |binary TreatmentPatterns-3.0.0/TreatmentPatterns/inst/DummyOutput/analyses.csv |only TreatmentPatterns-3.0.0/TreatmentPatterns/inst/DummyOutput/arguments.csv |only TreatmentPatterns-3.0.0/TreatmentPatterns/inst/DummyOutput/attrition.csv |only TreatmentPatterns-3.0.0/TreatmentPatterns/inst/DummyOutput/cdm_source_info.csv |only TreatmentPatterns-3.0.0/TreatmentPatterns/inst/DummyOutput/counts_age.csv |only TreatmentPatterns-3.0.0/TreatmentPatterns/inst/DummyOutput/counts_sex.csv |only TreatmentPatterns-3.0.0/TreatmentPatterns/inst/DummyOutput/counts_year.csv |only TreatmentPatterns-3.0.0/TreatmentPatterns/inst/DummyOutput/metadata.csv | 4 TreatmentPatterns-3.0.0/TreatmentPatterns/inst/DummyOutput/output.zip |binary TreatmentPatterns-3.0.0/TreatmentPatterns/inst/DummyOutput/summary_event_duration.csv |only TreatmentPatterns-3.0.0/TreatmentPatterns/inst/DummyOutput/treatment_pathways.csv |only TreatmentPatterns-3.0.0/TreatmentPatterns/inst/doc/DefiningCohorts.R | 38 TreatmentPatterns-3.0.0/TreatmentPatterns/inst/doc/DefiningCohorts.html | 16 TreatmentPatterns-3.0.0/TreatmentPatterns/inst/resultsDataModelSpecifications.csv |only TreatmentPatterns-3.0.0/TreatmentPatterns/inst/sql/selectData.sql | 13 TreatmentPatterns-3.0.0/TreatmentPatterns/man/TreatmentPatterns-package.Rd | 1 TreatmentPatterns-3.0.0/TreatmentPatterns/man/TreatmentPatternsResults.Rd |only TreatmentPatterns-3.0.0/TreatmentPatterns/man/computePathways.Rd | 6 TreatmentPatterns-3.0.0/TreatmentPatterns/man/createSankeyDiagram.Rd | 2 TreatmentPatterns-3.0.0/TreatmentPatterns/man/createSunburstPlot.Rd | 2 TreatmentPatterns-3.0.0/TreatmentPatterns/man/executeTreatmentPatterns.Rd | 8 TreatmentPatterns-3.0.0/TreatmentPatterns/man/export.Rd | 25 TreatmentPatterns-3.0.0/TreatmentPatterns/man/getResultsDataModelSpecifications.Rd |only TreatmentPatterns-3.0.0/TreatmentPatterns/man/plotEventDuration.Rd | 9 TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-CDMInterfaceCDMC.R | 14 TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-CharacterizationPlots.R | 110 - TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-InputHandler.R | 306 ++-- TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-InteractivePlots.R | 184 +- TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-ShinyApp.R | 46 TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-TreatmentPatternsResults.R |only TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-computePathways.R | 113 - TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-createSankeyDiagram.R | 10 TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-createSunburstPlot.R | 3 TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-executeTreatmentPatterns.R | 61 TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-export.R | 425 ++++-- TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-getResultsDataModelSpecifications.R |only TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-launchResultsExplorer.R | 22 TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-multipleCohortTables.R |only TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-pathwaysLogical.R | 683 ++++------ TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-pathwaysMultipleTargetsLogical.R |only TreatmentPatterns-3.0.0/TreatmentPatterns/tests/testthat/test-plotEventDuration.R | 16 TreatmentPatterns-3.0.0/TreatmentPatterns/vignettes/articles/ComputingTreatmentPathways.Rmd | 76 - 72 files changed, 1884 insertions(+), 1652 deletions(-)
More information about TreatmentPatterns at CRAN
Permanent link
Title: ICU Length of Stay Prediction and Efficiency Evaluation
Description: Provides tools for predicting ICU length of stay and assessing ICU efficiency.
It is based on the methodologies proposed by Peres et al. (2022, 2023), which utilize data-driven approaches for modeling and validation, offering insights into ICU performance and patient outcomes. References: Peres et al. (2022)<https://pubmed.ncbi.nlm.nih.gov/35988701/>, Peres et al. (2023)<https://pubmed.ncbi.nlm.nih.gov/37922007/>.
More information: <https://github.com/igor-peres/ICU-Length-of-Stay-Prediction>.
Author: Igor Peres [aut],
Joana da Matta [cre]
Maintainer: Joana da Matta <joana.damatta02@gmail.com>
Diff between SLOS versions 1.0.0 dated 2025-01-20 and 1.0.1 dated 2025-02-06
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NAMESPACE | 2 +- NEWS.md |only R/01-Prediction.R | 10 +++++++--- 5 files changed, 15 insertions(+), 10 deletions(-)
Title: Fast Simple URL Parser
Description: A fast and simple 'URL' parser package for 'R'. This package provides
functions to parse 'URLs' into their components, such as scheme, user, password, host, port,
path, query, and fragment.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between urlparse versions 0.1.0 dated 2025-01-13 and 0.2.0 dated 2025-02-06
DESCRIPTION | 6 MD5 | 24 +-- NAMESPACE | 2 NEWS.md | 4 R/RcppExports.R | 31 ++++ README.md | 171 ++++++++++++++++++++---- man/figures/README-benchmark-1.png |binary man/figures/README-benchmark_encode_large-1.png |binary man/figures/README-benchmark_encode_small-1.png |binary man/figures/README-benchmark_vectorise-1.png |only man/url_parse_v2.Rd |only src/RcppExports.cpp | 12 + src/url_parse.cpp | 86 ++++++++++++ tests/testthat/test-url_parse.R | 45 ++++++ 14 files changed, 341 insertions(+), 40 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [aut, ctb]
,
Etienne Bacher [aut, ctb] ,
Ale [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between insight versions 1.0.1 dated 2025-01-09 and 1.0.2 dated 2025-02-06
insight-1.0.1/insight/tests/testthat/_snaps |only insight-1.0.2/insight/DESCRIPTION | 34 +- insight-1.0.2/insight/MD5 | 32 -- insight-1.0.2/insight/NEWS.md | 22 + insight-1.0.2/insight/R/get_datagrid.R | 93 ++++-- insight-1.0.2/insight/R/get_parameters_others.R | 3 insight-1.0.2/insight/R/get_predicted_args.R | 2 insight-1.0.2/insight/R/get_statistic.R | 6 insight-1.0.2/insight/R/get_varcov.R | 10 insight-1.0.2/insight/R/standardize_names.R | 1 insight-1.0.2/insight/inst/doc/display.html | 220 +++++++-------- insight-1.0.2/insight/man/get_datagrid.Rd | 9 insight-1.0.2/insight/tests/testthat/test-get_datagrid.R | 75 +++++ insight-1.0.2/insight/tests/testthat/test-ggeffects.R | 88 +----- insight-1.0.2/insight/tests/testthat/test-lmer.R | 4 15 files changed, 343 insertions(+), 256 deletions(-)
Title: Cox MultiBlock Survival
Description: This software package provides Cox survival analysis for high-dimensional and multiblock datasets.
It encompasses a suite of functions dedicated from the classical Cox regression to newest analysis,
including Cox proportional hazards model, Stepwise Cox regression, and Elastic-Net Cox regression,
Sparse Partial Least Squares Cox regression (sPLS-COX) incorporating three distinct strategies,
and two Multiblock-PLS Cox regression (MB-sPLS-COX) methods. This tool is designed to adeptly handle
high-dimensional data, and provides tools for cross-validation, plot generation, and additional resources
for interpreting results. While references are available within the corresponding functions,
key literature is mentioned below.
Terry M Therneau (2024) <https://CRAN.R-project.org/package=survival>,
Noah Simon et al. (2011) <doi:10.18637/jss.v039.i05>,
Philippe Bastien et al. (2005) <doi:10.1016/j.csda.2004.02.005>,
Philippe Bastien (2008) <doi:10.1016/j.chemolab.2007.09.009& [...truncated...]
Author: Pedro Salguero Garcia [aut, cre, rev]
,
Sonia Tarazona Campos [ths],
Ana Conesa Cegarra [ths],
Kassu Mehari Beyene [ctb],
Luis Meira Machado [ctb],
Marta Sestelo [ctb],
Artur Araujo [ctb]
Maintainer: Pedro Salguero Garcia <pedrosalguerog@gmail.com>
Diff between Coxmos versions 1.1.0 dated 2025-01-18 and 1.1.1 dated 2025-02-06
DESCRIPTION | 6 MD5 | 18 R/Coxmos_common_functions.R |12480 +++++++++++++++++++-------------------- R/Coxmos_isb_splsdacox_dynamic.R | 16 R/Coxmos_isb_splsdrcox.R | 16 R/Coxmos_isb_splsdrcox_dynamic.R | 16 R/Coxmos_isb_splsicox.R | 14 build/partial.rdb |binary inst/doc/Coxmos-MO-pipeline.html | 20 inst/doc/Coxmos-pipeline.html | 24 10 files changed, 6349 insertions(+), 6261 deletions(-)
Title: Bayesian Vector Heterogeneous Autoregressive Modeling
Description: Tools to model and forecast multivariate time series
including Bayesian Vector heterogeneous autoregressive (VHAR) model
by Kim & Baek (2023) (<doi:10.1080/00949655.2023.2281644>).
'bvhar' can model Vector Autoregressive (VAR), VHAR, Bayesian VAR (BVAR), and Bayesian VHAR (BVHAR) models.
Author: Young Geun Kim [aut, cre, cph]
,
Changryong Baek [ctb]
Maintainer: Young Geun Kim <ygeunkimstat@gmail.com>
Diff between bvhar versions 2.1.2 dated 2024-10-11 and 2.2.0 dated 2025-02-06
bvhar-2.1.2/bvhar/R/bvar-horseshoe.R |only bvhar-2.1.2/bvhar/R/bvar-ssvs.R |only bvhar-2.1.2/bvhar/R/bvar-sv.R |only bvhar-2.1.2/bvhar/R/bvhar-horseshoe.R |only bvhar-2.1.2/bvhar/R/bvhar-ssvs.R |only bvhar-2.1.2/bvhar/R/bvhar-sv.R |only bvhar-2.1.2/bvhar/R/utils-pipe.R |only bvhar-2.1.2/bvhar/inst/doc/linking.R |only bvhar-2.1.2/bvhar/inst/doc/linking.Rmd |only bvhar-2.1.2/bvhar/inst/doc/linking.html |only bvhar-2.1.2/bvhar/inst/include/bvharcommon.h |only bvhar-2.1.2/bvhar/inst/include/bvhardesign.h |only bvhar-2.1.2/bvhar/inst/include/bvhardraw.h |only bvhar-2.1.2/bvhar/inst/include/bvharinterrupt.h |only bvhar-2.1.2/bvhar/inst/include/bvharomp.h |only bvhar-2.1.2/bvhar/inst/include/bvharprogress.h |only bvhar-2.1.2/bvhar/inst/include/bvharsim.h |only bvhar-2.1.2/bvhar/inst/include/bvharstructural.h |only bvhar-2.1.2/bvhar/inst/include/commondefs.h |only bvhar-2.1.2/bvhar/inst/include/mcmchs.h |only bvhar-2.1.2/bvhar/inst/include/mcmcreg.h |only bvhar-2.1.2/bvhar/inst/include/mcmcssvs.h |only bvhar-2.1.2/bvhar/inst/include/mcmcsv.h |only bvhar-2.1.2/bvhar/inst/include/minnesota.h |only bvhar-2.1.2/bvhar/inst/include/minnforecaster.h |only bvhar-2.1.2/bvhar/inst/include/minnspillover.h |only bvhar-2.1.2/bvhar/inst/include/ols.h |only bvhar-2.1.2/bvhar/inst/include/olsforecaster.h |only bvhar-2.1.2/bvhar/inst/include/olsspillover.h |only bvhar-2.1.2/bvhar/inst/include/regforecaster.h |only bvhar-2.1.2/bvhar/inst/include/regspillover.h |only bvhar-2.1.2/bvhar/inst/include/svforecaster.h |only bvhar-2.1.2/bvhar/inst/include/svspillover.h |only bvhar-2.1.2/bvhar/man/bvar_horseshoe.Rd |only bvhar-2.1.2/bvhar/man/bvar_ssvs.Rd |only bvhar-2.1.2/bvhar/man/bvar_sv.Rd |only bvhar-2.1.2/bvhar/man/bvhar_horseshoe.Rd |only bvhar-2.1.2/bvhar/man/bvhar_ssvs.Rd |only bvhar-2.1.2/bvhar/man/bvhar_sv.Rd |only bvhar-2.1.2/bvhar/man/choose_ssvs.Rd |only bvhar-2.1.2/bvhar/man/init_ssvs.Rd |only bvhar-2.1.2/bvhar/man/pipe.Rd |only bvhar-2.1.2/bvhar/man/sim_gig.Rd |only bvhar-2.1.2/bvhar/man/sim_horseshoe_var.Rd |only bvhar-2.1.2/bvhar/man/sim_ssvs_var.Rd |only bvhar-2.1.2/bvhar/src/bvhardesign.cpp |only bvhar-2.1.2/bvhar/src/bvharomp.cpp |only bvhar-2.1.2/bvhar/src/bvharsim.cpp |only bvhar-2.1.2/bvhar/src/bvharstructural.cpp |only bvhar-2.1.2/bvhar/src/estimate-bvar.cpp |only bvhar-2.1.2/bvhar/src/estimate-hierarchical.cpp |only bvhar-2.1.2/bvhar/src/estimate-horseshoe.cpp |only bvhar-2.1.2/bvhar/src/estimate-ssvs.cpp |only bvhar-2.1.2/bvhar/src/estimate-sur.cpp |only bvhar-2.1.2/bvhar/src/estimate-sv.cpp |only bvhar-2.1.2/bvhar/src/estimate-var.cpp |only bvhar-2.1.2/bvhar/src/estimate-vhar.cpp |only bvhar-2.1.2/bvhar/src/forecast-bvar.cpp |only bvhar-2.1.2/bvhar/src/forecast-bvhar.cpp |only bvhar-2.1.2/bvhar/src/forecast-ldlt.cpp |only bvhar-2.1.2/bvhar/src/forecast-minn.cpp |only bvhar-2.1.2/bvhar/src/forecast-ols.cpp |only bvhar-2.1.2/bvhar/src/forecast-sv.cpp |only bvhar-2.1.2/bvhar/src/is-stable.cpp |only bvhar-2.1.2/bvhar/src/simulate-data.cpp |only bvhar-2.1.2/bvhar/src/spillover-ldlt.cpp |only bvhar-2.1.2/bvhar/src/spillover-minn.cpp |only bvhar-2.1.2/bvhar/src/spillover-ols.cpp |only bvhar-2.1.2/bvhar/src/spillover-sv.cpp |only bvhar-2.1.2/bvhar/src/tuning-models.cpp |only bvhar-2.1.2/bvhar/vignettes/linking.Rmd |only bvhar-2.2.0/bvhar/DESCRIPTION | 19 bvhar-2.2.0/bvhar/MD5 | 265 -- bvhar-2.2.0/bvhar/NAMESPACE | 40 bvhar-2.2.0/bvhar/NEWS.md | 52 bvhar-2.2.0/bvhar/R/RcppExports.R | 1887 ++++++-------- bvhar-2.2.0/bvhar/R/criteria.R | 66 bvhar-2.2.0/bvhar/R/forecast.R | 492 --- bvhar-2.2.0/bvhar/R/generate-process.R | 40 bvhar-2.2.0/bvhar/R/globals.R | 1 bvhar-2.2.0/bvhar/R/hyperparam.R | 259 -- bvhar-2.2.0/bvhar/R/irf.R | 16 bvhar-2.2.0/bvhar/R/member.R | 35 bvhar-2.2.0/bvhar/R/misc-r.R | 268 +- bvhar-2.2.0/bvhar/R/plot-spillover.R | 14 bvhar-2.2.0/bvhar/R/plot.R | 113 bvhar-2.2.0/bvhar/R/print-bvharsp.R | 156 - bvhar-2.2.0/bvhar/R/print-bvharspec.R | 165 - bvhar-2.2.0/bvhar/R/print-spillover.R | 64 bvhar-2.2.0/bvhar/R/print-varlse.R | 4 bvhar-2.2.0/bvhar/R/print-vharlse.R | 8 bvhar-2.2.0/bvhar/R/simulate-param.R | 443 --- bvhar-2.2.0/bvhar/R/spillover.R | 328 +- bvhar-2.2.0/bvhar/R/stable-process.R | 40 bvhar-2.2.0/bvhar/R/summary-bayes.R | 12 bvhar-2.2.0/bvhar/R/summary-forecast.R | 564 +--- bvhar-2.2.0/bvhar/R/summary-sparse.R | 14 bvhar-2.2.0/bvhar/R/summary-varlse.R | 8 bvhar-2.2.0/bvhar/R/summary-vharlse.R | 8 bvhar-2.2.0/bvhar/R/tuning.R | 116 bvhar-2.2.0/bvhar/R/var-bayes.R | 133 - bvhar-2.2.0/bvhar/R/vhar-bayes.R | 133 - bvhar-2.2.0/bvhar/README.md | 22 bvhar-2.2.0/bvhar/build/partial.rdb |binary bvhar-2.2.0/bvhar/build/vignette.rds |binary bvhar-2.2.0/bvhar/inst/doc/bvhar.R | 2 bvhar-2.2.0/bvhar/inst/doc/bvhar.Rmd | 2 bvhar-2.2.0/bvhar/inst/doc/bvhar.html | 7 bvhar-2.2.0/bvhar/inst/doc/forecasting.R | 24 bvhar-2.2.0/bvhar/inst/doc/forecasting.Rmd | 24 bvhar-2.2.0/bvhar/inst/doc/forecasting.html | 27 bvhar-2.2.0/bvhar/inst/doc/minnesota.html | 5 bvhar-2.2.0/bvhar/inst/doc/shrinkage.html | 138 - bvhar-2.2.0/bvhar/inst/doc/stochastic-volatility.html | 127 - bvhar-2.2.0/bvhar/inst/include/bvhar |only bvhar-2.2.0/bvhar/man/alpl.Rd |only bvhar-2.2.0/bvhar/man/bound_bvhar.Rd | 2 bvhar-2.2.0/bvhar/man/bvar_flat.Rd | 2 bvhar-2.2.0/bvhar/man/bvar_minnesota.Rd | 2 bvhar-2.2.0/bvhar/man/bvhar_minnesota.Rd | 2 bvhar-2.2.0/bvhar/man/choose_bvar.Rd | 2 bvhar-2.2.0/bvhar/man/dynamic_spillover.Rd | 12 bvhar-2.2.0/bvhar/man/figures/logo.png |binary bvhar-2.2.0/bvhar/man/forecast_expand.Rd | 12 bvhar-2.2.0/bvhar/man/forecast_roll.Rd | 14 bvhar-2.2.0/bvhar/man/irf.Rd | 2 bvhar-2.2.0/bvhar/man/predict.Rd | 48 bvhar-2.2.0/bvhar/man/set_bvar.Rd | 2 bvhar-2.2.0/bvhar/man/set_dl.Rd | 8 bvhar-2.2.0/bvhar/man/set_gdp.Rd |only bvhar-2.2.0/bvhar/man/set_horseshoe.Rd | 2 bvhar-2.2.0/bvhar/man/set_intercept.Rd | 2 bvhar-2.2.0/bvhar/man/set_lambda.Rd | 13 bvhar-2.2.0/bvhar/man/set_ldlt.Rd | 2 bvhar-2.2.0/bvhar/man/set_ng.Rd | 2 bvhar-2.2.0/bvhar/man/set_ssvs.Rd | 42 bvhar-2.2.0/bvhar/man/spillover.Rd | 6 bvhar-2.2.0/bvhar/man/var_bayes.Rd | 11 bvhar-2.2.0/bvhar/man/var_lm.Rd | 2 bvhar-2.2.0/bvhar/man/vhar_bayes.Rd | 11 bvhar-2.2.0/bvhar/man/vhar_lm.Rd | 2 bvhar-2.2.0/bvhar/src/Makevars | 2 bvhar-2.2.0/bvhar/src/Makevars.ucrt | 2 bvhar-2.2.0/bvhar/src/Makevars.win | 2 bvhar-2.2.0/bvhar/src/RcppExports.cpp | 1903 ++++++--------- bvhar-2.2.0/bvhar/src/mniw.cpp |only bvhar-2.2.0/bvhar/src/ols.cpp |only bvhar-2.2.0/bvhar/src/triangular.cpp |only bvhar-2.2.0/bvhar/src/utils.cpp |only bvhar-2.2.0/bvhar/tests/testthat/test-generate-process.R | 86 bvhar-2.2.0/bvhar/tests/testthat/test-misc-r.R |only bvhar-2.2.0/bvhar/tests/testthat/test-spillover.R | 30 bvhar-2.2.0/bvhar/tests/testthat/test-summary-forecast.R | 776 ++++++ bvhar-2.2.0/bvhar/tests/testthat/test-var-bayes.R | 60 bvhar-2.2.0/bvhar/tests/testthat/test-vhar-bayes.R | 58 bvhar-2.2.0/bvhar/vignettes/bvhar.Rmd | 2 bvhar-2.2.0/bvhar/vignettes/forecasting.Rmd | 24 157 files changed, 4362 insertions(+), 4927 deletions(-)
Title: A 'ggplot2' Extension for Consistent Axis Alignment
Description: A 'ggplot2' extension offers various tools for organizing and arranging plots.
It is designed to consistently align a specific axis across multiple 'ggplot' objects,
making it especially useful for plots requiring data order manipulation. A typical use
case includes organizing combinations like a dendrogram and a heatmap.
Author: Yun Peng [aut, cre] ,
Shixiang Wang [aut] ,
Guangchuang Yu [aut]
Maintainer: Yun Peng <yunyunp96@163.com>
Diff between ggalign versions 0.0.5 dated 2024-11-14 and 0.1.0 dated 2025-02-06
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Title: Convert Gene IDs Between Each Other and Fetch Annotations from
Biomart
Description: Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() but
that function is only provided as fallback mechanism for the most common use cases in data analysis. The main function
in the package is convert.bm() which queries BioMart using the full capacity of the API provided through the
'biomaRt' package. Presets and defaults are provided for convenience but all "marts", "filters" and "attributes"
can be set by the user. Function convert.alias() converts Gene Symbols to Aliases and vice versa and function likely_symbol()
attempts to determine the most likely current Gene Symbol.
Author: Vidal Fey [aut, cre],
Henrik Edgren [aut]
Maintainer: Vidal Fey <vidal.fey@gmail.com>
Diff between convertid versions 0.1.8 dated 2023-11-29 and 0.1.10 dated 2025-02-06
DESCRIPTION | 10 +++++----- MD5 | 11 +++++++---- R/biomart.R | 5 +++++ R/convertId2.R | 5 +++-- man/convertid.Rd | 2 ++ man/dot-addToCache.Rd |only man/dot-checkInCache.Rd |only man/dot-readFromCache.Rd |only 8 files changed, 22 insertions(+), 11 deletions(-)
Title: Data Supporting the 'VGAM' Package
Description: Mainly data sets to accompany the VGAM package and
the book "Vector Generalized Linear and
Additive Models: With an Implementation in R" (Yee, 2015)
<DOI:10.1007/978-1-4939-2818-7>.
These are used to illustrate vector generalized
linear and additive models (VGLMs/VGAMs), and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column
Interaction Models, and constrained and unconstrained ordination
models in ecology). This package now contains some
old VGAM family functions which have been replaced by newer
ones (often because they are now special cases).
Author: Thomas Yee [aut, cre, cph] ,
James Gray [dtc]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAMdata versions 1.1-12 dated 2024-09-17 and 1.1-13 dated 2025-02-06
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Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] ,
Edward Burn [aut] ,
Theresa Burkard [aut] ,
Yuchen Guo [ctb] ,
Marti Catala [ctb] ,
Mike Du [ctb] ,
Xintong Li [ctb] ,
Ross Williams [ctb] ,
Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between DrugExposureDiagnostics versions 1.1.0 dated 2024-12-22 and 1.1.1 dated 2025-02-06
DrugExposureDiagnostics-1.1.0/DrugExposureDiagnostics/R/getDrugStrength.R |only DrugExposureDiagnostics-1.1.0/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/data2/Local_PG |only DrugExposureDiagnostics-1.1.0/DrugExposureDiagnostics/man/getDrugStrength.Rd |only DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/DESCRIPTION | 18 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/MD5 | 158 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/NAMESPACE | 3 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/NEWS.md | 5 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/R/DrugExposureDiagnostics-package.R | 1 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/R/dataPlotPanel.R |only DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/R/executeChecks.R | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/R/metaDataPanel.R |only DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/R/mockDrugExposure.R | 8 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/R/shinyApp.R |only DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/R/shinyModule.R |only DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DaysSupply.R | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DaysSupply.Rmd | 18 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DaysSupply.html | 24 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DiagnosticsSummary.R | 8 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DiagnosticsSummary.Rmd | 8 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DiagnosticsSummary.html | 22 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugDose.R | 8 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugDose.Rmd | 8 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugDose.html | 22 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugDuration.R | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugDuration.Rmd | 19 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugDuration.html | 28 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugSig.R | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugSig.Rmd | 17 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugSig.html | 28 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugSourceConcepts.R | 14 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugSourceConcepts.Rmd | 14 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugSourceConcepts.html | 2525 ---------- DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugTypes.R | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugTypes.Rmd | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/DrugTypes.html | 28 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.R | 5 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.Rmd | 5 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.html | 15 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/Missingness.R | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/Missingness.Rmd | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/Missingness.html | 28 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/Quantity.R | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/Quantity.Rmd | 18 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/Quantity.html | 28 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/Routes.R | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/Routes.Rmd | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/Routes.html | 28 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/VerbatimEndDate.R | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/VerbatimEndDate.Rmd | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/doc/VerbatimEndDate.html | 28 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/ShinyApp.R |only DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/ShinyModule.R |only DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/data2/Local_PG.zip |binary DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/data3 |only DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/dataPlotPanel.R | 178 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/global-new.R |only DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/global.R | 2 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/ui.R | 8 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/utils.R | 6 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/man/ShinyModule.Rd |only DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/man/dataPlotPanel.Rd |only DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/man/executeChecks.Rd | 4 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/man/metaDataPanel.Rd |only DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/tests/testthat/helper-ableToRun.R |only DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/tests/testthat/test-ShinyApp.R |only DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/tests/testthat/test-SyntheaSqlServer.R | 2 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/vignettes/DaysSupply.Rmd | 18 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/vignettes/DiagnosticsSummary.Rmd | 8 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/vignettes/DrugDose.Rmd | 8 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/vignettes/DrugDuration.Rmd | 19 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/vignettes/DrugSig.Rmd | 17 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/vignettes/DrugSourceConcepts.Rmd | 14 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/vignettes/DrugTypes.Rmd | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/vignettes/IntroductionToDrugExposureDiagnostics.Rmd | 5 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/vignettes/Missingness.Rmd | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/vignettes/Quantity.Rmd | 18 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/vignettes/Routes.Rmd | 16 DrugExposureDiagnostics-1.1.1/DrugExposureDiagnostics/vignettes/VerbatimEndDate.Rmd | 16 78 files changed, 457 insertions(+), 3261 deletions(-)
More information about DrugExposureDiagnostics at CRAN
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Title: Statistical Methods and Models for Claims Reserving in General
Insurance
Description: Various statistical methods and models which are
typically used for the estimation of outstanding claims reserves
in general insurance, including those to estimate the claims
development result as required under Solvency II.
Author: Markus Gesmann [aut, cre],
Daniel Murphy [aut],
Yanwei Zhang [aut],
Alessandro Carrato [aut],
Giuseppe Crupi [ctb],
Christophe Dutang [ctb],
Arnaud Lacoume [ctb],
Arthur Charpentier [ctb],
Mario Wuthrich [aut],
Fabio Concina [aut],
Eric Dal Moro [au [...truncated...]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>
Diff between ChainLadder versions 0.2.19 dated 2024-07-21 and 0.2.20 dated 2025-02-06
ChainLadder-0.2.19/ChainLadder/demo/DatabaseExamples.R |only ChainLadder-0.2.20/ChainLadder/DESCRIPTION | 8 ChainLadder-0.2.20/ChainLadder/MD5 | 21 ChainLadder-0.2.20/ChainLadder/NEWS.md | 6 ChainLadder-0.2.20/ChainLadder/build/vignette.rds |binary ChainLadder-0.2.20/ChainLadder/demo/00Index | 11 ChainLadder-0.2.20/ChainLadder/demo/ChainLadder.R | 21 ChainLadder-0.2.20/ChainLadder/inst/doc/ChainLadder.R | 125 +-- ChainLadder-0.2.20/ChainLadder/inst/doc/ChainLadder.Rmd | 6 ChainLadder-0.2.20/ChainLadder/inst/doc/ChainLadder.html | 556 +++++++-------- ChainLadder-0.2.20/ChainLadder/man/USAA.Rd | 4 ChainLadder-0.2.20/ChainLadder/vignettes/ChainLadder.Rmd | 6 12 files changed, 364 insertions(+), 400 deletions(-)
Title: Analysing Convergent Evolution using the Wheatsheaf Index
Description: Analysing convergent evolution using the Wheatsheaf index, described in Arbuckle et al. (2014) <doi: 10.1111/2041-210X.12195>, and some other unrelated but perhaps useful functions.
Author: Kevin Arbuckle [aut, cre],
Amanda Minter [aut]
Maintainer: Kevin Arbuckle <kevin.arbuckle@swansea.ac.uk>
Diff between windex versions 2.0.8 dated 2024-04-26 and 2.1.0 dated 2025-02-06
DESCRIPTION | 18 +++++++++++++----- MD5 | 26 ++++++++++++++------------ NAMESPACE | 2 +- R/LRbarplot.R |only R/nodeDist.R | 2 +- R/test.windex.R | 6 +++--- R/windex.R | 6 +++--- R/windex.sim.test.R | 8 ++++---- man/LRbarplot.Rd |only man/mark.dist.Rd | 2 +- man/pir.Rd | 2 +- man/richYuleInputs.Rd | 2 +- man/test.windex.Rd | 8 ++++++-- man/windex.Rd | 8 ++++++-- man/windex.sim.test.Rd | 8 ++++++-- 15 files changed, 60 insertions(+), 38 deletions(-)
Title: Sparse-Group SLOPE: Adaptive Bi-Level Selection with FDR Control
Description: Implementation of Sparse-group SLOPE (SGS) (Feser and Evangelou (2023) <doi:10.48550/arXiv.2305.09467>) models. Linear and logistic regression models are supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported. In addition, a general Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) implementation is provided. Group SLOPE (gSLOPE) (Brzyski et al. (2019) <doi:10.1080/01621459.2017.1411269>) and group-based OSCAR models (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) are also implemented. All models are available with strong screening rules (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) for computational speed-up.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>
Diff between sgs versions 0.3.3 dated 2025-02-03 and 0.3.4 dated 2025-02-06
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/global_wrapper_code.R | 1 + inst/doc/reproducible_example.html | 12 ++++++------ 4 files changed, 14 insertions(+), 13 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis (Balduzzi et al., 2023) <doi:10.18637/jss.v106.i02> and supporting Schwarzer et al. (2015) <doi:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <doi:10.1002/jrsm.1058>;
- additive network meta-analysis for combinations of treatments (Rücker et al., 2020) <doi:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <doi:10.1002/sim.8158>, or penalised logistic regression (Evrenoglou et al., 2022) <doi:10.1002/sim.9562>;
- rankograms and ranking of treatments by the Surface under the cumulative ranking curve (SUCRA) (Salanti et al., 2013) <doi:10.1016/j.jclinepi.2010.03.016>;
- ranking of treatments using P-scores (frequentist analogue of SUCRAs without resampling) according to [...truncated...]
Author: Gerta Ruecker [aut] ,
Ulrike Krahn [aut],
Jochem Koenig [aut] ,
Orestis Efthimiou [aut] ,
Annabel Davies [aut] ,
Theodoros Papakonstantinou [aut]
,
Theodoros Evrenoglou [ctb] ,
Krzysztof Ciomek [ctb] ,
Guido Schwarzer [aut, cre]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between netmeta versions 3.1-0 dated 2025-02-04 and 3.1-1 dated 2025-02-06
DESCRIPTION | 15 +- MD5 | 276 ++++++++++++++++++++--------------------- NAMESPACE | 15 -- NEWS.md | 15 ++ R/Baker2009.R | 19 +- R/Dogliotti2014.R | 19 +- R/Dong2013.R | 25 +-- R/Franchini2012.R | 17 +- R/Gurusamy2011.R | 29 +--- R/Linde2015.R | 20 +- R/Linde2016.R | 19 -- R/Senn2013.R | 3 R/Stowe2010.R | 6 R/Woods2010.R | 24 ++- R/as.data.frame.netmeta.R | 6 R/createC.R | 30 ---- R/decomp.design.R | 2 R/dietaryfat.R | 14 +- R/discomb.R | 2 R/forest.netbind.R | 2 R/forest.netcomb.R | 28 ---- R/forest.netcomparison.R | 2 R/forest.netcomplex.R | 2 R/forest.netmeta.R | 6 R/forest.netsplit.R | 10 - R/forest.subgroup.netmeta.R | 19 ++ R/funnel.netmeta.R | 2 R/hasse-internal.R | 46 +++--- R/hasse.R | 24 ++- R/hatmatrix.R | 4 R/invmat.R | 9 - R/merge.pairwise.R | 10 - R/metabias.netmeta.R | 2 R/netbind.R | 2 R/netcomb.R | 5 R/netcomparison.R | 2 R/netcomplex.R | 2 R/netconnection.R | 2 R/netcontrib.R | 6 R/netdistance.R | 6 R/netgraph.R | 28 +--- R/netgraph.netimpact.R | 11 - R/netgraph.netmeta.R | 6 R/netheat.R | 13 + R/netimpact.R | 4 R/netleague.R | 37 ++--- R/netmatrix.R | 17 +- R/netmeasures.R | 6 R/netmeta-package.R | 5 R/netmeta.R | 6 R/netmetabin.R | 24 +-- R/netpairwise.R | 6 R/netposet.R | 41 ++++-- R/netrank.R | 6 R/netsplit.R | 10 - R/nettable.R | 7 - R/plot.netposet.R | 19 +- R/plot.netrank.R | 22 +-- R/plot.rankogram.R | 4 R/print.netcomb.R | 3 R/print.netimpact.R | 4 R/print.rankogram.R | 4 R/print.summary.netmeta.R | 6 R/radial.netmeta.R | 2 R/rankogram.R | 4 R/rankogram.default.R | 13 + R/rankogram.netmeta.R | 4 R/smokingcessation.R | 6 R/subgroup.netmeta.R | 2 R/summary.netcomb.R | 3 R/summary.netmeta.R | 6 R/treats.R | 6 inst/doc/netmeta.pdf |binary man/Baker2009.Rd | 18 +- man/Dogliotti2014.Rd | 18 +- man/Dong2013.Rd | 25 +-- man/Franchini2012.Rd | 16 +- man/Gurusamy2011.Rd | 28 +--- man/Linde2015.Rd | 19 +- man/Linde2016.Rd | 18 -- man/Senn2013.Rd | 2 man/Stowe2010.Rd | 6 man/Woods2010.Rd | 23 ++- man/as.data.frame.netmeta.Rd | 6 man/createC.Rd | 30 ---- man/decomp.design.Rd | 2 man/dietaryfat.Rd | 13 + man/discomb.Rd | 2 man/forest.netbind.Rd | 2 man/forest.netcomb.Rd | 28 ---- man/forest.netcomparison.Rd | 2 man/forest.netcomplex.Rd | 2 man/forest.netmeta.Rd | 6 man/forest.netsplit.Rd | 10 - man/forest.subgroup.netmeta.Rd | 19 ++ man/funnel.netmeta.Rd | 2 man/hasse.netposet.Rd | 12 + man/hatmatrix.Rd | 4 man/invmat.Rd | 9 - man/merge.pairwise.Rd | 10 - man/metabias.netmeta.Rd | 2 man/netbind.Rd | 2 man/netcomb.Rd | 5 man/netcomparison.Rd | 2 man/netcomplex.Rd | 2 man/netconnection.Rd | 2 man/netcontrib.Rd | 6 man/netdistance.Rd | 6 man/netgraph.Rd | 28 +--- man/netgraph.netimpact.Rd | 11 - man/netgraph.netmeta.Rd | 6 man/netheat.Rd | 13 + man/netimpact.Rd | 4 man/netleague.Rd | 35 ++--- man/netmatrix.Rd | 17 +- man/netmeasures.Rd | 6 man/netmeta.Rd | 6 man/netmetabin.Rd | 24 +-- man/netpairwise.Rd | 6 man/netposet.Rd | 41 ++++-- man/netrank.Rd | 6 man/netsplit.Rd | 10 - man/nettable.Rd | 7 - man/plot.netposet.Rd | 19 +- man/plot.netrank.Rd | 22 +-- man/plot.rankogram.Rd | 4 man/print.netcomb.Rd | 3 man/print.netimpact.Rd | 4 man/print.rankogram.Rd | 4 man/print.summary.netmeta.Rd | 6 man/radial.netmeta.Rd | 2 man/rankogram.Rd | 4 man/rankogram.default.Rd | 13 + man/rankogram.netmeta.Rd | 4 man/smokingcessation.Rd | 6 man/subgroup.netmeta.Rd | 2 man/summary.netcomb.Rd | 3 man/summary.netmeta.Rd | 6 man/treats.Rd | 6 139 files changed, 889 insertions(+), 880 deletions(-)
Title: Dual Feature Reduction for SGL
Description: Implementation of the Dual Feature Reduction (DFR) approach for the Sparse Group Lasso (SGL) and the Adaptive Sparse Group Lasso (aSGL) (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.17094>). The DFR approach is a feature reduction approach that applies strong screening to reduce the feature space before optimisation, leading to speed-up improvements for fitting SGL (Simon et al. (2013) <doi:10.1080/10618600.2012.681250>) and aSGL (Mendez-Civieta et al. (2020) <doi:10.1007/s11634-020-00413-8> and Poignard (2020) <doi:10.1007/s10463-018-0692-7>) models. DFR is implemented using the Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) algorithm, with linear and logistic SGL models supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported.
Author: Fabio Feser [aut, cre]
Maintainer: Fabio Feser <ff120@ic.ac.uk>
Diff between dfr versions 0.1.3 dated 2025-02-03 and 0.1.4 dated 2025-02-06
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Cross-Validation for Multi-Population Mortality Models
Description: Implementation of cross-validation method for testing the forecasting accuracy of several multi-population mortality models. The family of multi-population includes several multi-population mortality models proposed through the actuarial and demography literature. The package includes functions for fitting and forecast the mortality rates of several populations. Additionally, we include functions for testing the forecasting accuracy of different multi-population models.
References.
Atance, D., Debon, A., and Navarro, E. (2020) <doi:10.3390/math8091550>.
Bergmeir, C. & Benitez, J.M. (2012) <doi:10.1016/j.ins.2011.12.028>.
Debon, A., Montes, F., & Martinez-Ruiz, F. (2011) <doi:10.1007/s13385-011-0043-z>.
Lee, R.D. & Carter, L.R. (1992) <doi:10.1080/01621459.1992.10475265>.
Russolillo, M., Giordano, G., & Haberman, S. (2011) <doi:10.1080/03461231003611933>.
Santolino, M. (2023) <doi:10.3390/risks11100170>.
Author: David Atance [aut, cre] ,
Ana Debon [aut]
Maintainer: David Atance <david.atance@uah.es>
Diff between CvmortalityMult versions 1.0.7 dated 2024-08-31 and 1.0.8 dated 2025-02-06
CvmortalityMult-1.0.7/CvmortalityMult/R/multipopulation_loocv.R |only CvmortalityMult-1.0.7/CvmortalityMult/man/multipopulation_loocv.Rd |only CvmortalityMult-1.0.8/CvmortalityMult/DESCRIPTION | 8 CvmortalityMult-1.0.8/CvmortalityMult/MD5 | 58 CvmortalityMult-1.0.8/CvmortalityMult/NAMESPACE | 3 CvmortalityMult-1.0.8/CvmortalityMult/R/MeasureAccuracy.R | 68 CvmortalityMult-1.0.8/CvmortalityMult/R/SpainMap.R | 20 CvmortalityMult-1.0.8/CvmortalityMult/R/SpainNat.R | 3 CvmortalityMult-1.0.8/CvmortalityMult/R/SpainRegions.R | 2 CvmortalityMult-1.0.8/CvmortalityMult/R/fitLCmulti.R | 352 + CvmortalityMult-1.0.8/CvmortalityMult/R/forecast.fitLCmulti.R | 283 - CvmortalityMult-1.0.8/CvmortalityMult/R/multipopulation_cv.R | 2459 +++++++--- CvmortalityMult-1.0.8/CvmortalityMult/R/plot.fitLCmulti.R | 241 CvmortalityMult-1.0.8/CvmortalityMult/R/plot.forLCmulti.R | 172 CvmortalityMult-1.0.8/CvmortalityMult/R/residSVD2.R | 5 CvmortalityMult-1.0.8/CvmortalityMult/README.md | 7 CvmortalityMult-1.0.8/CvmortalityMult/data/SpainNat.rda |binary CvmortalityMult-1.0.8/CvmortalityMult/data/SpainRegions.rda |binary CvmortalityMult-1.0.8/CvmortalityMult/man/MeasureAccuracy.Rd | 40 CvmortalityMult-1.0.8/CvmortalityMult/man/SpainMap.Rd | 4 CvmortalityMult-1.0.8/CvmortalityMult/man/SpainNat.Rd | 1 CvmortalityMult-1.0.8/CvmortalityMult/man/SpainRegions.Rd | 2 CvmortalityMult-1.0.8/CvmortalityMult/man/figures/FIXED-ORIGIN.jpg |only CvmortalityMult-1.0.8/CvmortalityMult/man/figures/FIXED-ORIGIN.png |only CvmortalityMult-1.0.8/CvmortalityMult/man/figures/RO_RECALIBRATION.jpg |only CvmortalityMult-1.0.8/CvmortalityMult/man/figures/RO_RECALIBRATION.png |only CvmortalityMult-1.0.8/CvmortalityMult/man/figures/RW_RECALIBRATION.jpg |only CvmortalityMult-1.0.8/CvmortalityMult/man/figures/RW_RECALIBRATION.png |only CvmortalityMult-1.0.8/CvmortalityMult/man/fitLCmulti.Rd | 90 CvmortalityMult-1.0.8/CvmortalityMult/man/forecast.fitLCmulti.Rd | 127 CvmortalityMult-1.0.8/CvmortalityMult/man/multipopulation_cv.Rd | 248 - CvmortalityMult-1.0.8/CvmortalityMult/man/plot.fitLCmulti.Rd | 65 CvmortalityMult-1.0.8/CvmortalityMult/man/plot.forLCmulti.Rd | 96 CvmortalityMult-1.0.8/CvmortalityMult/man/residSVD2.Rd | 4 34 files changed, 3369 insertions(+), 989 deletions(-)
More information about CvmortalityMult at CRAN
Permanent link
Title: Bayesian Meta-Analysis of Diagnostic Test Data
Description: Provides a new class of Bayesian meta-analysis models that incorporates a model for internal and external validity bias. In this way, it is possible to combine studies of diverse quality and different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS).
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>
Diff between bamdit versions 3.4.3 dated 2024-11-22 and 3.4.4 dated 2025-02-06
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/metadiag.R | 5 +++-- 4 files changed, 16 insertions(+), 9 deletions(-)
Title: Data Correction and Imputation Using Deductive Methods
Description: Attempt to repair inconsistencies and missing values in
data records by using information from valid values and
validation rules restricting the data.
Author: Mark van der Loo [cre, aut] ,
Edwin de Jonge [aut] ,
Reijer Idema [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between deductive versions 1.0.0 dated 2021-03-29 and 1.0.1 dated 2025-02-06
DESCRIPTION | 25 +++--- MD5 | 22 +++-- NEWS | 8 ++ R/deductive-pkg.R | 3 R/linimpute.R | 148 ++++++++++++++++++++++++------------- R/typocorr.R | 8 +- inst/tinytest/lr_fm_data.csv |only inst/tinytest/lr_fm_rules.yml |only inst/tinytest/lr_implied_data.csv |only inst/tinytest/lr_implied_rules.yml |only inst/tinytest/test_correct_typos.R | 8 +- inst/tinytest/test_linimpute.R | 35 ++++++-- man/deductive.Rd | 23 +++++ src/imputezero.c | 10 +- 14 files changed, 202 insertions(+), 88 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Doug Bates [aut] ,
Binxiang Ni [aut],
Conrad Sanderson [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 14.2.2-1 dated 2024-12-06 and 14.2.3-1 dated 2025-02-06
ChangeLog | 9 DESCRIPTION | 8 MD5 | 36 - configure | 576 ++++++++++++----------- configure.ac | 4 inst/NEWS.Rd | 10 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo_bits/Cube_meat.hpp | 8 inst/include/armadillo_bits/Mat_meat.hpp | 8 inst/include/armadillo_bits/arma_version.hpp | 2 inst/include/armadillo_bits/compiler_setup.hpp | 5 inst/include/armadillo_bits/config.hpp | 3 inst/include/armadillo_bits/def_lapack.hpp | 16 inst/include/armadillo_bits/field_meat.hpp | 12 inst/include/armadillo_bits/fn_accu.hpp | 2 inst/include/armadillo_bits/gmm_full_meat.hpp | 2 inst/include/armadillo_bits/op_reshape_meat.hpp | 22 inst/include/armadillo_bits/translate_lapack.hpp | 16 19 files changed, 405 insertions(+), 334 deletions(-)
Title: Stratified-Petersen Analysis System
Description: The Stratified-Petersen Analysis System (SPAS) is designed
to estimate abundance in two-sample capture-recapture experiments
where the capture and recaptures are stratified. This is a generalization
of the simple Lincoln-Petersen estimator.
Strata may be defined in time or in space or both,
and the s strata in which marking takes place
may differ from the t strata in which recoveries take place.
When s=t, SPAS reduces to the method described by
Darroch (1961) <doi:10.2307/2332748>.
When s<t, SPAS implements the methods described in
Plante, Rivest, and Tremblay (1988) <doi:10.2307/2533994>.
Schwarz and Taylor (1998) <doi:10.1139/f97-238> describe
the use of SPAS in estimating return of salmon stratified by
time and geography.
A related package, BTSPAS, deals with temporal stratification where
a spline is used to model the distribution of the population
over time as it passes the second capture location.
This is the R-version of the (now obsolete) standalone Windows
[...truncated...]
Author: Carl James Schwarz [aut, cre]
Maintainer: Carl James Schwarz <cschwarz.stat.sfu.ca@gmail.com>
Diff between SPAS versions 2024.1.31 dated 2024-01-25 and 2025.2.1 dated 2025-02-06
DESCRIPTION | 23 +++--- MD5 | 30 +++---- NAMESPACE | 2 NEWS.md | 7 + R/SPAS.fit.model.R | 3 R/SPAS.print.model.R | 136 +++++++++++++++++++++++++++--------- R/zzz.R | 3 build/vignette.rds |binary inst/doc/AutomaticPooling.html | 14 +-- inst/doc/Conne1991.html | 28 +++---- inst/doc/Conne1992.html | 24 +++--- inst/doc/HarrisonF2011.html | 64 ++++++++-------- inst/doc/PoolingColumns.html | 64 ++++++++-------- inst/doc/TestingPooledPetersen.html | 38 +++++----- inst/doc/ThingsThatGoWrong.html | 24 +++--- man/SPAS.print.model.Rd | 16 ++-- 16 files changed, 284 insertions(+), 192 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-15 1.0.4
2025-01-09 1.0.3
2024-11-14 1.0.1
2024-11-13 1.0.0