Title: Weighted and Unweighted Spatial Centers
Description: Generate mean and median weighted or unweighted spatial centers.
Functions are analogous to their identically named counterparts within
'ArcGIS Pro'. Median center methodology based off of Kuhn and Kuenne
(1962) <doi:10.1111/j.1467-9787.1962.tb00902.x>.
Author: Ryan Zomorrodi [aut, cre, cph]
Maintainer: Ryan Zomorrodi <rzomor2@uic.edu>
Diff between centr versions 0.2.1 dated 2024-12-22 and 0.2.2 dated 2025-02-07
DESCRIPTION | 7 ++++--- MD5 | 6 +++--- NEWS.md | 12 ++++++++---- build/vignette.rds |binary 4 files changed, 15 insertions(+), 10 deletions(-)
Title: Bayesian Super Imposition by Translation and Rotation Growth
Curve Analysis
Description: The Super Imposition by Translation and Rotation (SITAR) model
is a shape-invariant nonlinear mixed effect model that fits a natural cubic
spline mean curve to the growth data and aligns individual-specific growth
curves to the underlying mean curve via a set of random effects (see Cole,
2010 <doi:10.1093/ije/dyq115> for details). The non-Bayesian version of the
SITAR model can be fit by using the already available R package 'sitar'. While
the 'sitar' package allows modelling of a single outcome only, the 'bsitar'
package offers great flexibility in fitting models of varying complexities,
including joint modelling of multiple outcomes such as height and weight
(multivariate model). Additionally, the 'bsitar' package allows for the simultaneous
analysis of an outcome separately for subgroups defined by a factor variable such
as gender. This is achieved by fitting separate models for each subgroup
(for example males and females for gender variable). An advantage of this approach
is [...truncated...]
Author: Satpal Sandhu [aut, cre, cph]
Maintainer: Satpal Sandhu <satpal.sandhu@bristol.ac.uk>
Diff between bsitar versions 0.2.1 dated 2024-03-19 and 0.3.2 dated 2025-02-07
bsitar-0.2.1/bsitar/man/figures/README-conditional_effects-1.png |only bsitar-0.2.1/bsitar/man/figures/README-plot-1.png |only bsitar-0.2.1/bsitar/vignettes/during |only bsitar-0.3.2/bsitar/DESCRIPTION | 59 bsitar-0.3.2/bsitar/MD5 | 139 bsitar-0.3.2/bsitar/NAMESPACE | 1 bsitar-0.3.2/bsitar/NEWS.md | 90 bsitar-0.3.2/bsitar/R/add_model_criterion.R | 36 bsitar-0.3.2/bsitar/R/berkeley.R | 97 bsitar-0.3.2/bsitar/R/berkeley_exdata.R | 48 bsitar-0.3.2/bsitar/R/berkeley_exfit.R | 38 bsitar-0.3.2/bsitar/R/bsitar.R | 4998 ++++-- bsitar-0.3.2/bsitar/R/check_and_get_object.R | 117 bsitar-0.3.2/bsitar/R/datasets.R | 104 bsitar-0.3.2/bsitar/R/expose_model_functions.R | 239 bsitar-0.3.2/bsitar/R/fitted_draws.R | 95 bsitar-0.3.2/bsitar/R/growthparameters.R | 596 bsitar-0.3.2/bsitar/R/growthparameters_comparison.R | 2189 ++ bsitar-0.3.2/bsitar/R/loo_validation.R | 59 bsitar-0.3.2/bsitar/R/marginal_comparison.R | 1229 + bsitar-0.3.2/bsitar/R/marginal_draws.R | 1529 +- bsitar-0.3.2/bsitar/R/optimize_model.R | 578 bsitar-0.3.2/bsitar/R/plot_conditional_effects.R | 41 bsitar-0.3.2/bsitar/R/plot_curves.R | 370 bsitar-0.3.2/bsitar/R/plot_ppc.R | 30 bsitar-0.3.2/bsitar/R/predict_draws.R | 113 bsitar-0.3.2/bsitar/R/update_model.R | 63 bsitar-0.3.2/bsitar/R/utils-helper-1.R | 1721 ++ bsitar-0.3.2/bsitar/R/utils-helper-10.R |only bsitar-0.3.2/bsitar/R/utils-helper-2.R | 248 bsitar-0.3.2/bsitar/R/utils-helper-3.R | 489 bsitar-0.3.2/bsitar/R/utils-helper-4.R | 525 bsitar-0.3.2/bsitar/R/utils-helper-44.R |only bsitar-0.3.2/bsitar/R/utils-helper-5.R | 4667 +++--- bsitar-0.3.2/bsitar/R/utils-helper-55.R |only bsitar-0.3.2/bsitar/R/utils-helper-555.R |only bsitar-0.3.2/bsitar/R/utils-helper-6.R | 7332 +++++----- bsitar-0.3.2/bsitar/R/utils-helper-7.R | 17 bsitar-0.3.2/bsitar/R/utils-helper-8.R | 3792 ++--- bsitar-0.3.2/bsitar/R/utils-helper-9.R |only bsitar-0.3.2/bsitar/README.md | 27 bsitar-0.3.2/bsitar/build/partial.rdb |binary bsitar-0.3.2/bsitar/build/vignette.rds |binary bsitar-0.3.2/bsitar/data/berkeley.rda |binary bsitar-0.3.2/bsitar/data/berkeley_exdata.rda |binary bsitar-0.3.2/bsitar/data/berkeley_exfit.rda |binary bsitar-0.3.2/bsitar/inst/WORDLIST | 38 bsitar-0.3.2/bsitar/inst/doc/Bayesian_SITAR_model_An_Introduction.Rmd | 320 bsitar-0.3.2/bsitar/inst/doc/Bayesian_SITAR_model_An_Introduction.html | 703 bsitar-0.3.2/bsitar/inst/doc/Bayesian_SITAR_model_fit.R |only bsitar-0.3.2/bsitar/inst/doc/Bayesian_SITAR_model_fit.Rmd |only bsitar-0.3.2/bsitar/inst/doc/Bayesian_SITAR_model_fit.html |only bsitar-0.3.2/bsitar/inst/stanhelper |only bsitar-0.3.2/bsitar/man/add_model_criterion.bgmfit.Rd | 168 bsitar-0.3.2/bsitar/man/berkeley.Rd | 59 bsitar-0.3.2/bsitar/man/berkeley_exdata.Rd | 16 bsitar-0.3.2/bsitar/man/berkeley_exfit.Rd | 11 bsitar-0.3.2/bsitar/man/bsitar.Rd | 2731 ++- bsitar-0.3.2/bsitar/man/expose_model_functions.bgmfit.Rd | 71 bsitar-0.3.2/bsitar/man/fitted_draws.bgmfit.Rd | 409 bsitar-0.3.2/bsitar/man/getNsObject.Rd | 24 bsitar-0.3.2/bsitar/man/growthparameters.bgmfit.Rd | 549 bsitar-0.3.2/bsitar/man/growthparameters_comparison.bgmfit.Rd | 847 - bsitar-0.3.2/bsitar/man/loo_validation.bgmfit.Rd | 197 bsitar-0.3.2/bsitar/man/marginal_comparison.bgmfit.Rd | 707 bsitar-0.3.2/bsitar/man/marginal_draws.bgmfit.Rd | 738 - bsitar-0.3.2/bsitar/man/optimize_model.bgmfit.Rd | 329 bsitar-0.3.2/bsitar/man/plot_conditional_effects.bgmfit.Rd | 255 bsitar-0.3.2/bsitar/man/plot_curves.bgmfit.Rd | 772 - bsitar-0.3.2/bsitar/man/plot_ppc.bgmfit.Rd | 162 bsitar-0.3.2/bsitar/man/predict_draws.bgmfit.Rd | 406 bsitar-0.3.2/bsitar/man/update_model.bgmfit.Rd | 78 bsitar-0.3.2/bsitar/vignettes/Bayesian_SITAR_model_An_Introduction.Rmd | 320 bsitar-0.3.2/bsitar/vignettes/Bayesian_SITAR_model_fit.Rmd |only 74 files changed, 25215 insertions(+), 16371 deletions(-)
Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre, cph],
Matt Dennis [ctb],
Antoine Bichat [ctb] ,
Daniel Fahey [ctb],
Johann R. Kleinbub [ctb],
Panagiotis Moulos [ctb],
Swechhya Bista [ctb],
Colin Fay [ctb]
Maintainer: Andrew B. Collier <andrew.b.collier@gmail.com>
Diff between emayili versions 0.9.2 dated 2025-01-28 and 0.9.3 dated 2025-02-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/envelope.R | 28 ++++++++++++++++++++++++---- R/mime.R | 8 ++++---- README.md | 14 +++++++------- 5 files changed, 42 insertions(+), 22 deletions(-)
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 - 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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
VGAMdata-1.1-12/VGAMdata/man/laplace.Rd |only VGAMdata-1.1-12/VGAMdata/man/laplaceUC.Rd |only VGAMdata-1.1-12/VGAMdata/man/triangleUC.Rd |only VGAMdata-1.1-13/VGAMdata/DESCRIPTION | 8 VGAMdata-1.1-13/VGAMdata/MD5 | 34 - VGAMdata-1.1-13/VGAMdata/NAMESPACE | 6 VGAMdata-1.1-13/VGAMdata/NEWS | 14 VGAMdata-1.1-13/VGAMdata/R/family.fishing.R | 7 VGAMdata-1.1-13/VGAMdata/R/family.laplace.R | 662 +++-------------------- VGAMdata-1.1-13/VGAMdata/R/family.vd1.R | 299 ++++++---- VGAMdata-1.1-13/VGAMdata/R/family.vd2.R | 38 - VGAMdata-1.1-13/VGAMdata/data/T101.rda |only VGAMdata-1.1-13/VGAMdata/data/birds.df.rda |only VGAMdata-1.1-13/VGAMdata/data/tb101.rda |only VGAMdata-1.1-13/VGAMdata/man/T101.Rd |only VGAMdata-1.1-13/VGAMdata/man/alaplace3.Rd | 4 VGAMdata-1.1-13/VGAMdata/man/alaplaceUC.Rd | 3 VGAMdata-1.1-13/VGAMdata/man/birds.df.Rd |only VGAMdata-1.1-13/VGAMdata/man/genpoisson.Rd | 4 VGAMdata-1.1-13/VGAMdata/man/loglapUC.Rd |only VGAMdata-1.1-13/VGAMdata/man/notdocumentedyet.Rd | 8 VGAMdata-1.1-13/VGAMdata/man/tb101.Rd |only VGAMdata-1.1-13/VGAMdata/man/triangle.Rd | 10 23 files changed, 361 insertions(+), 736 deletions(-)
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 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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
Permanent link
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
Title: Interface for 'Google Gemini' API
Description: Provides a comprehensive interface for Google Gemini API,
enabling users to access and utilize Gemini Large Language Model (LLM) functionalities directly from R.
This package facilitates seamless integration with Google Gemini, allowing for advanced language processing,
text generation, and other AI-driven capabilities within the R environment.
For more information, please visit <https://ai.google.dev/docs/gemini_api_overview>.
Author: Jinhwan Kim [aut, cre, cph] ,
Maciej Nasinski [ctb]
Maintainer: Jinhwan Kim <hwanistic@gmail.com>
Diff between gemini.R versions 0.6.1 dated 2024-12-10 and 0.8.0 dated 2025-02-05
DESCRIPTION | 10 ++--- MD5 | 38 +++++++++++++------ NAMESPACE | 14 +++++++ NEWS.md | 21 +++++++++- R/Urrecipe.R |only R/gemini.R | 70 ++++++++++++++++++++++++++++++++++-- R/gemini_audio.R |only R/gemini_chat.R | 15 +++++-- R/gemini_image.R | 75 ++++++++++++++++++++++++++++++++++++-- R/gen_tests.R |only R/vertex.R |only README.md | 83 +++++++++++++++++++++++++++++++++++++++---- inst/quarto |only inst/rstudio/addins.dcf | 5 ++ man/figures/testing.gif |only man/figures/vertex_audio.png |only man/figures/vertex_image.png |only man/figures/vertex_text.png |only man/gemini.Rd | 2 - man/gemini.vertex.Rd |only man/gemini_audio.Rd |only man/gemini_audio.vertex.Rd |only man/gemini_chat.Rd | 2 - man/gemini_image.Rd | 2 - man/gemini_image.vertex.Rd |only man/gen_tests.Rd |only man/token.vertex.Rd |only 27 files changed, 295 insertions(+), 42 deletions(-)
Title: R and C/C++ Wrappers to Run the Leiden find_partition() Function
Description: An R to C/C++ interface that runs the Leiden community
detection algorithm to find a basic partition (). It runs the
equivalent of the 'leidenalg' find_partition() function, which is
given in the 'leidenalg' distribution file
'leiden/src/functions.py'. This package includes the
required source code files from the official 'leidenalg'
distribution and functions from the R 'igraph'
package. The 'leidenalg' distribution is available from
<https://github.com/vtraag/leidenalg/>
and the R 'igraph' package is available from
<https://igraph.org/r/>.
The Leiden algorithm is described in the article by
Traag et al. (2019) <doi:10.1038/s41598-019-41695-z>.
Leidenbase includes code from the packages:
igraph version 0.9.8 with license GPL (>= 2),
leidenalg version 0.8.10 with license GPL 3.
Author: Brent Ewing [aut, cre],
Vincent Traag [ctb],
Gabor Csardi [ctb],
Tamas Nepusz [ctb],
Szabolcs Horvat [ctb],
Fabio Zanini [ctb]
Maintainer: Brent Ewing <bge@uw.edu>
Diff between leidenbase versions 0.1.31 dated 2024-09-25 and 0.1.32 dated 2025-02-05
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/vignette.rds |binary src/Makevars.ucrt | 43 +++++++++++++++++++++++++++++++++++-------- 4 files changed, 41 insertions(+), 14 deletions(-)
Title: Life and Fertility Tables Specially for Insects
Description: Life and Fertility Tables are appropriate to study the dynamics of
arthropods populations. This package provides utilities for constructing
Life Tables and Fertility Tables, related demographic parameters, and some
simple graphs of interest. It also offers functions to transform the
obtained data into a known format for better manipulation. This document is
based on the article by Maia, Luiz, and Campanhola "Statistical Inference on
Associated Fertility Life Table Parameters Using Jackknife Technique
Computational Aspects" (April 2000, Journal of Economic Entomology, Volume
93, Issue 2) <doi:10.1603/0022-0493-93.2.511>.
Author: Carlos Abimael Sarmiento Sanchez [aut, cre],
Lauro Soto Rojas [ctb],
Alejandro Corona Ambriz [ctb],
Gabriel Arcangel Rodriguez Yam [ctb],
Yolanda Franco Islas [ctb],
Noe Ramirez Negrete [ctb]
Maintainer: Carlos Abimael Sarmiento Sanchez <cass9918@hotmail.com>
Diff between Lifertable versions 0.0.1 dated 2024-02-29 and 0.1.0 dated 2025-02-05
DESCRIPTION | 31 ++- MD5 | 53 +++--- NEWS.md |only R/Insects.R | 23 +- R/PlotPseudoVals.R | 135 ++++++++--------- R/as.data.frame.lifertableCI.R | 8 - R/as.data.frame.lifertableLFT.R | 18 +- R/as.data.frame.lifertableParmEst.R | 76 +++++---- R/as.data.frame.lifertableTotEggs.R | 8 - R/lifertable.R | 162 +++++++++++++------- R/lifertable.groups.R | 258 +++++++++++++++++---------------- R/lifertable.individual.R | 156 ++++++++++--------- R/lifertable.jackknife.R | 5 R/plotDistrOvipos.R | 172 ++++++++++++---------- R/plotEggs.R | 18 +- R/plotSurvivalCurve.R | 150 +++++++++---------- build/partial.rdb |binary data/Insects.rda |binary man/Insects.Rd | 22 +- man/PlotPseudoVals.Rd | 9 - man/as.data.frame.lifertableCI.Rd | 8 - man/as.data.frame.lifertableLFT.Rd | 8 - man/as.data.frame.lifertableParmEst.Rd | 8 - man/as.data.frame.lifertableTotEggs.Rd | 8 - man/lifertable.Rd | 109 ++++++++----- man/plotDistrOvipos.Rd | 17 +- man/plotEggs.Rd | 18 +- man/plotSurvivalCurve.Rd | 6 28 files changed, 857 insertions(+), 629 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects and adjusted predictions from statistical
models and returns the result as tidy data frames. These data frames are
ready to use with the 'ggplot2'-package. Effects and predictions can be
calculated for many different models. Interaction terms, splines and
polynomial terms are also supported. The main functions are ggpredict(),
ggemmeans() and ggeffect(). There is a generic plot()-method to plot the
results using 'ggplot2'.
Author: Daniel Luedecke [aut, cre] ,
Frederik Aust [ctb] ,
Sam Crawley [ctb] ,
Mattan S. Ben-Shachar [ctb] ,
Sean C. Anderson [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between ggeffects versions 2.1.0 dated 2025-01-20 and 2.2.0 dated 2025-02-05
ggeffects-2.1.0/ggeffects/R/johnson_neyman_numcat.R |only ggeffects-2.1.0/ggeffects/R/tp_label_hypothesis_categorical.R |only ggeffects-2.1.0/ggeffects/R/tp_label_hypothesis_formula.R |only ggeffects-2.1.0/ggeffects/R/tp_label_hypothesis_slopes.R |only ggeffects-2.1.0/ggeffects/R/tp_label_pairwise_categorical.R |only ggeffects-2.1.0/ggeffects/R/tp_label_pairwise_slopes.R |only ggeffects-2.1.0/ggeffects/tests/testthat/test-johnson_neyman_numcat.R |only ggeffects-2.1.0/ggeffects/tests/testthat/test-test_predictions.R |only ggeffects-2.2.0/ggeffects/DESCRIPTION | 25 ggeffects-2.2.0/ggeffects/LICENSE | 4 ggeffects-2.2.0/ggeffects/MD5 | 86 - ggeffects-2.2.0/ggeffects/NAMESPACE | 3 ggeffects-2.2.0/ggeffects/NEWS.md | 10 ggeffects-2.2.0/ggeffects/R/format.R | 12 ggeffects-2.2.0/ggeffects/R/ggemmeans_zi_predictions.R | 10 ggeffects-2.2.0/ggeffects/R/johnson_neyman.R | 484 ++------- ggeffects-2.2.0/ggeffects/R/pool_comparisons.R | 39 ggeffects-2.2.0/ggeffects/R/predict_response.R | 4 ggeffects-2.2.0/ggeffects/R/predict_zero_inflation.R | 9 ggeffects-2.2.0/ggeffects/R/print.R | 69 - ggeffects-2.2.0/ggeffects/R/test_predictions.R | 506 ---------- ggeffects-2.2.0/ggeffects/R/utils_test_predictions.R | 17 ggeffects-2.2.0/ggeffects/README.md | 35 ggeffects-2.2.0/ggeffects/inst/doc/content.Rmd | 9 ggeffects-2.2.0/ggeffects/inst/doc/content.html | 17 ggeffects-2.2.0/ggeffects/man/ggpredict.Rd | 4 ggeffects-2.2.0/ggeffects/man/install_latest.Rd | 80 - ggeffects-2.2.0/ggeffects/man/johnson_neyman.Rd | 30 ggeffects-2.2.0/ggeffects/man/predict_response.Rd | 4 ggeffects-2.2.0/ggeffects/man/print.Rd | 2 ggeffects-2.2.0/ggeffects/man/test_predictions.Rd | 23 ggeffects-2.2.0/ggeffects/tests/testthat/test-betareg.R | 2 ggeffects-2.2.0/ggeffects/tests/testthat/test-fixest.R | 6 ggeffects-2.2.0/ggeffects/tests/testthat/test-focal_only_random.R | 4 ggeffects-2.2.0/ggeffects/tests/testthat/test-ggaverage.R | 13 ggeffects-2.2.0/ggeffects/tests/testthat/test-glmmTMB.R | 1 ggeffects-2.2.0/ggeffects/tests/testthat/test-johnson_neyman.R | 177 --- ggeffects-2.2.0/ggeffects/tests/testthat/test-mgcv.R | 4 ggeffects-2.2.0/ggeffects/tests/testthat/test-parsnip.R | 7 ggeffects-2.2.0/ggeffects/tests/testthat/test-pool_comparisons.R | 4 ggeffects-2.2.0/ggeffects/tests/testthat/test-print_md.R | 2 ggeffects-2.2.0/ggeffects/tests/testthat/test-print_test_predictions-ordinal.R | 2 ggeffects-2.2.0/ggeffects/tests/testthat/test-print_test_predictions.R | 158 +-- ggeffects-2.2.0/ggeffects/tests/testthat/test-test_predictions-formula.R | 4 ggeffects-2.2.0/ggeffects/tests/testthat/test-test_predictions-mixed.R | 7 ggeffects-2.2.0/ggeffects/tests/testthat/test-test_predictions_emmeans.R | 68 - ggeffects-2.2.0/ggeffects/tests/testthat/test-vcov.R | 27 ggeffects-2.2.0/ggeffects/vignettes/content.Rmd | 9 48 files changed, 536 insertions(+), 1441 deletions(-)
Title: Methods to Analyse Signed Networks
Description: Methods for the analysis of signed networks. This includes
several measures for structural balance as introduced by Cartwright
and Harary (1956) <doi:10.1037/h0046049>, blockmodeling algorithms
from Doreian (2008) <doi:10.1016/j.socnet.2008.03.005>, various
centrality indices, and projections of signed two-mode networks
introduced by Schoch (2020) <doi:10.1080/0022250X.2019.1711376>.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between signnet versions 1.0.4 dated 2024-01-08 and 1.0.5 dated 2025-02-05
DESCRIPTION | 8 MD5 | 46 NEWS.md | 4 R/blockmodel.R | 127 +- R/centrality_indices.R | 176 +-- R/complex_matrices.R | 400 +++---- R/laplace_matrix.R | 26 R/random_graphs.R | 190 ++- R/signed_triangles.R | 2154 ++++++++++++++++++++++++++++++++------- build/vignette.rds |binary inst/doc/blockmodeling.R | 2 inst/doc/blockmodeling.html | 221 +--- inst/doc/centrality.R | 2 inst/doc/centrality.html | 191 +-- inst/doc/complex_matrices.R | 4 inst/doc/complex_matrices.html | 175 +-- inst/doc/signed_2mode.html | 191 +-- inst/doc/signed_networks.html | 163 +- inst/doc/structural_balance.html | 173 +-- man/count_complex_triangles.Rd | 2 man/count_signed_triangles.Rd | 2 man/signed_blockmodel_general.Rd | 8 man/signed_triangles.Rd | 2 man/triad_census_signed.Rd | 2 24 files changed, 2886 insertions(+), 1383 deletions(-)
Title: Emax Model Analysis with 'Stan'
Description: Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.
Author: Kenta Yoshida [aut, cre] ,
Danielle Navarro [aut] ,
Trustees of Columbia University [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between rstanemax versions 0.1.7 dated 2024-12-06 and 0.1.8 dated 2025-02-05
rstanemax-0.1.7/rstanemax/src/Makevars.win |only rstanemax-0.1.8/rstanemax/DESCRIPTION | 16 rstanemax-0.1.8/rstanemax/MD5 | 22 rstanemax-0.1.8/rstanemax/NAMESPACE | 6 rstanemax-0.1.8/rstanemax/NEWS.md | 9 rstanemax-0.1.8/rstanemax/R/posterior_predict.R | 428 ++++++---- rstanemax-0.1.8/rstanemax/build/vignette.rds |binary rstanemax-0.1.8/rstanemax/inst/doc/emaxmodel.html | 129 +-- rstanemax-0.1.8/rstanemax/man/posterior_predict.Rd | 101 +- rstanemax-0.1.8/rstanemax/man/rstanemax-package.Rd | 2 rstanemax-0.1.8/rstanemax/tests/testthat/test-posterior_predict.R | 44 - rstanemax-0.1.8/rstanemax/tests/testthat/test-stan_emax_binary.R | 4 rstanemax-0.1.8/rstanemax/tests/testthat/test-tidybayes_integration.R |only 13 files changed, 488 insertions(+), 273 deletions(-)
Title: Lightweight Extension of the Base R Graphics System
Description: Lightweight extension of the base R graphics system, with support
for automatic legends, facets, themes, and various other enhancements.
Author: Grant McDermott [aut, cre] ,
Vincent Arel-Bundock [aut] ,
Achim Zeileis [aut] ,
Etienne Bacher [ctb]
Maintainer: Grant McDermott <gmcd@amazon.com>
Diff between tinyplot versions 0.2.1 dated 2024-08-26 and 0.3.0 dated 2025-02-05
tinyplot-0.2.1/tinyplot/R/aesthetics.R |only tinyplot-0.2.1/tinyplot/R/draw_elements.R |only tinyplot-0.3.0/tinyplot/DESCRIPTION | 21 tinyplot-0.3.0/tinyplot/MD5 | 114 + tinyplot-0.3.0/tinyplot/NAMESPACE | 61 tinyplot-0.3.0/tinyplot/NEWS.md | 178 ++ tinyplot-0.3.0/tinyplot/R/assertions.R | 17 tinyplot-0.3.0/tinyplot/R/by_aesthetics.R | 144 + tinyplot-0.3.0/tinyplot/R/draw_legend.R | 76 tinyplot-0.3.0/tinyplot/R/facet.R | 227 ++ tinyplot-0.3.0/tinyplot/R/get_saved_par.R | 4 tinyplot-0.3.0/tinyplot/R/lim.R | 32 tinyplot-0.3.0/tinyplot/R/sanitize.R | 89 - tinyplot-0.3.0/tinyplot/R/tinyAxis.R | 4 tinyplot-0.3.0/tinyplot/R/tinyplot.R | 782 ++++++---- tinyplot-0.3.0/tinyplot/R/tinyplot_add.R |only tinyplot-0.3.0/tinyplot/R/tinytheme.R |only tinyplot-0.3.0/tinyplot/R/tpar.R | 419 +++-- tinyplot-0.3.0/tinyplot/R/type_abline.R |only tinyplot-0.3.0/tinyplot/R/type_area.R | 34 tinyplot-0.3.0/tinyplot/R/type_boxplot.R | 185 +- tinyplot-0.3.0/tinyplot/R/type_density.R | 385 ++-- tinyplot-0.3.0/tinyplot/R/type_errorbar.R |only tinyplot-0.3.0/tinyplot/R/type_function.R |only tinyplot-0.3.0/tinyplot/R/type_glm.R |only tinyplot-0.3.0/tinyplot/R/type_histogram.R | 205 ++ tinyplot-0.3.0/tinyplot/R/type_hline.R |only tinyplot-0.3.0/tinyplot/R/type_jitter.R | 93 - tinyplot-0.3.0/tinyplot/R/type_lines.R |only tinyplot-0.3.0/tinyplot/R/type_lm.R |only tinyplot-0.3.0/tinyplot/R/type_loess.R |only tinyplot-0.3.0/tinyplot/R/type_pointrange.R | 65 tinyplot-0.3.0/tinyplot/R/type_points.R |only tinyplot-0.3.0/tinyplot/R/type_polygon.R |only tinyplot-0.3.0/tinyplot/R/type_polypath.R |only tinyplot-0.3.0/tinyplot/R/type_qq.R |only tinyplot-0.3.0/tinyplot/R/type_rect.R |only tinyplot-0.3.0/tinyplot/R/type_ribbon.R | 157 +- tinyplot-0.3.0/tinyplot/R/type_ridge.R |only tinyplot-0.3.0/tinyplot/R/type_rug.R |only tinyplot-0.3.0/tinyplot/R/type_segments.R |only tinyplot-0.3.0/tinyplot/R/type_spineplot.R |only tinyplot-0.3.0/tinyplot/R/type_spline.R |only tinyplot-0.3.0/tinyplot/R/type_summary.R |only tinyplot-0.3.0/tinyplot/R/type_text.R |only tinyplot-0.3.0/tinyplot/R/type_vline.R |only tinyplot-0.3.0/tinyplot/R/utils.R | 15 tinyplot-0.3.0/tinyplot/R/zzz.R | 41 tinyplot-0.3.0/tinyplot/README.md | 55 tinyplot-0.3.0/tinyplot/man/ci.Rd |only tinyplot-0.3.0/tinyplot/man/figures/README-quickstart4-1.png |binary tinyplot-0.3.0/tinyplot/man/figures/README-quickstart5-1.png |binary tinyplot-0.3.0/tinyplot/man/figures/README-quickstart_theme-1.png |only tinyplot-0.3.0/tinyplot/man/get_saved_par.Rd | 2 tinyplot-0.3.0/tinyplot/man/tinyAxis.Rd |only tinyplot-0.3.0/tinyplot/man/tinyplot-package.Rd | 2 tinyplot-0.3.0/tinyplot/man/tinyplot.Rd | 237 +-- tinyplot-0.3.0/tinyplot/man/tinyplot_add.Rd |only tinyplot-0.3.0/tinyplot/man/tinytheme.Rd |only tinyplot-0.3.0/tinyplot/man/tpar.Rd | 79 - tinyplot-0.3.0/tinyplot/man/type_abline.Rd |only tinyplot-0.3.0/tinyplot/man/type_boxplot.Rd |only tinyplot-0.3.0/tinyplot/man/type_density.Rd |only tinyplot-0.3.0/tinyplot/man/type_errorbar.Rd |only tinyplot-0.3.0/tinyplot/man/type_function.Rd |only tinyplot-0.3.0/tinyplot/man/type_glm.Rd |only tinyplot-0.3.0/tinyplot/man/type_histogram.Rd |only tinyplot-0.3.0/tinyplot/man/type_hline.Rd |only tinyplot-0.3.0/tinyplot/man/type_jitter.Rd |only tinyplot-0.3.0/tinyplot/man/type_lines.Rd |only tinyplot-0.3.0/tinyplot/man/type_lm.Rd |only tinyplot-0.3.0/tinyplot/man/type_loess.Rd |only tinyplot-0.3.0/tinyplot/man/type_points.Rd |only tinyplot-0.3.0/tinyplot/man/type_polygon.Rd |only tinyplot-0.3.0/tinyplot/man/type_polypath.Rd |only tinyplot-0.3.0/tinyplot/man/type_qq.Rd |only tinyplot-0.3.0/tinyplot/man/type_rect.Rd |only tinyplot-0.3.0/tinyplot/man/type_ribbon.Rd |only tinyplot-0.3.0/tinyplot/man/type_ridge.Rd |only tinyplot-0.3.0/tinyplot/man/type_rug.Rd |only tinyplot-0.3.0/tinyplot/man/type_segments.Rd |only tinyplot-0.3.0/tinyplot/man/type_spineplot.Rd |only tinyplot-0.3.0/tinyplot/man/type_spline.Rd |only tinyplot-0.3.0/tinyplot/man/type_summary.Rd |only tinyplot-0.3.0/tinyplot/man/type_text.Rd |only tinyplot-0.3.0/tinyplot/man/type_vline.Rd |only 86 files changed, 2538 insertions(+), 1185 deletions(-)
Title: Geometric Morphometric Analyses of 2D and 3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams [aut, cre],
Michael Collyer [aut],
Antigoni Kaliontzopoulou [aut],
Erica Baken [aut]
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 4.0.9 dated 2024-11-15 and 4.0.10 dated 2025-02-05
geomorph-4.0.10/geomorph/DESCRIPTION | 8 geomorph-4.0.10/geomorph/MD5 | 23 - geomorph-4.0.10/geomorph/NEWS.md | 17 geomorph-4.0.10/geomorph/R/extended.pgls.r | 2 geomorph-4.0.10/geomorph/R/physignal.eigen.R | 38 +- geomorph-4.0.10/geomorph/build/vignette.rds |binary geomorph-4.0.10/geomorph/data/pupfish.ws.rda |binary geomorph-4.0.10/geomorph/inst/CITATION | 4 geomorph-4.0.10/geomorph/inst/doc/geomorph.digitize3D.html | 4 geomorph-4.0.10/geomorph/man/extended.pgls.Rd | 2 geomorph-4.0.10/geomorph/man/physignal.eigen.Rd | 18 geomorph-4.0.10/geomorph/tests/testthat/test-geomorph.R | 245 ++++++------- geomorph-4.0.9/geomorph/vignettes/cran-comments.md |only 13 files changed, 205 insertions(+), 156 deletions(-)
Title: Easy Study of Patient DICOM Data in Oncology
Description: Exploitation, processing and 2D-3D visualization of DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, in a patient-oriented perspective.
Author: Cathy Fontbonne [aut, cre] ,
Jean-Marc Fontbonne [aut] ,
Nathan Azemar [ctb]
Maintainer: Cathy Fontbonne <contact.espadon@lpccaen.in2p3.fr>
Diff between espadon versions 1.9.0 dated 2024-11-25 and 1.10.0 dated 2025-02-05
espadon-1.10.0/espadon/DESCRIPTION | 6 espadon-1.10.0/espadon/MD5 | 111 ++-- espadon-1.10.0/espadon/NAMESPACE | 3 espadon-1.10.0/espadon/R/RcppExports.R | 4 espadon-1.10.0/espadon/R/bin_from_roi.R | 31 - espadon-1.10.0/espadon/R/contour.R |only espadon-1.10.0/espadon/R/dicom_set_tag_value.R | 129 ----- espadon-1.10.0/espadon/R/display_3D_contour.R | 5 espadon-1.10.0/espadon/R/display_3D_mesh.R | 3 espadon-1.10.0/espadon/R/display_3D_sections.R | 3 espadon-1.10.0/espadon/R/display_3D_stack.R | 3 espadon-1.10.0/espadon/R/err_metrics_from_roi.R |only espadon-1.10.0/espadon/R/espadon_hidden.R | 5 espadon-1.10.0/espadon/R/export.R | 2 espadon-1.10.0/espadon/R/fan_beam.R | 8 espadon-1.10.0/espadon/R/fan_planar.R | 8 espadon-1.10.0/espadon/R/fan_sphere.R | 12 espadon-1.10.0/espadon/R/get_value_from_mesh.R | 25 espadon-1.10.0/espadon/R/histo_vol.R | 1 espadon-1.10.0/espadon/R/mesh_spheric_proj.R | 34 - espadon-1.10.0/espadon/R/nesting_bin.R | 6 espadon-1.10.0/espadon/R/nesting_cube.R | 15 espadon-1.10.0/espadon/R/orientation_create.R | 7 espadon-1.10.0/espadon/R/plot.R | 18 espadon-1.10.0/espadon/R/polyg.R | 234 --------- espadon-1.10.0/espadon/R/rt_chi_index.R | 2 espadon-1.10.0/espadon/R/rt_gamma_index.R | 2 espadon-1.10.0/espadon/R/rt_indices_from_roi.R | 4 espadon-1.10.0/espadon/R/struct_create.R | 6 espadon-1.10.0/espadon/R/toy_load_patient.R | 65 +- espadon-1.10.0/espadon/R/vol_abserror.R |only espadon-1.10.0/espadon/R/vol_error.R |only espadon-1.10.0/espadon/build/partial.rdb |binary espadon-1.10.0/espadon/build/stage23.rdb |binary espadon-1.10.0/espadon/inst/doc/espadon_overview.R | 317 ++++++------ espadon-1.10.0/espadon/inst/doc/espadon_overview.Rmd | 362 ++++++++------ espadon-1.10.0/espadon/inst/doc/espadon_overview.html | 462 ++++++++++-------- espadon-1.10.0/espadon/man/bin.from.roi.Rd | 6 espadon-1.10.0/espadon/man/display.3D.contour.Rd | 5 espadon-1.10.0/espadon/man/display.3D.mesh.Rd | 3 espadon-1.10.0/espadon/man/display.3D.sections.Rd | 3 espadon-1.10.0/espadon/man/display.3D.stack.Rd | 3 espadon-1.10.0/espadon/man/err.metrics.from.roi.Rd |only espadon-1.10.0/espadon/man/export.Rd | 2 espadon-1.10.0/espadon/man/fan.beam.Rd | 7 espadon-1.10.0/espadon/man/fan.planar.Rd | 7 espadon-1.10.0/espadon/man/fan.sphere.Rd | 11 espadon-1.10.0/espadon/man/get.value.from.mesh.Rd | 19 espadon-1.10.0/espadon/man/mesh.spheric.proj.Rd | 30 - espadon-1.10.0/espadon/man/rt.chi.index.Rd | 2 espadon-1.10.0/espadon/man/rt.gamma.index.Rd | 2 espadon-1.10.0/espadon/man/struct.create.Rd | 6 espadon-1.10.0/espadon/man/toy.load.patient.Rd | 2 espadon-1.10.0/espadon/man/vol.abserror.Rd |only espadon-1.10.0/espadon/man/vol.error.Rd |only espadon-1.10.0/espadon/src/RcppExports.cpp | 22 espadon-1.10.0/espadon/src/esplib.h | 1 espadon-1.10.0/espadon/src/getvaluefromijkC.cpp | 25 espadon-1.10.0/espadon/vignettes/espadon_overview.Rmd | 362 ++++++++------ espadon-1.9.0/espadon/R/roidata.R |only espadon-1.9.0/espadon/src/addcommonptC.cpp |only 61 files changed, 1150 insertions(+), 1261 deletions(-)
More information about CircNNTSRSymmetric at CRAN
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Title: Bayesian Knowledge Tracing Model
Description: Fitting, cross-validating, and predicting with Bayesian Knowledge Tracing (BKT) models. It is designed for analyzing educational datasets to trace student knowledge over time. The package includes functions for fitting BKT models, evaluating their performance using various metrics, and making predictions on new data. It provides the similar functionality as the Python package pyBKT authored by Zachary A. Pardos (zp@berkeley.edu) at <https://github.com/CAHLR/pyBKT>.
Author: Yuhao Yuan [aut, cre],
Biying Zhou [aut],
Feng Ji [aut]
Maintainer: Yuhao Yuan <yuanyuhaoapply@163.com>
Diff between BKT versions 0.0.1 dated 2025-01-30 and 0.1.0 dated 2025-02-05
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Estimation of Return Curves
Description: Estimates the p-probability return curve proposed by Murphy-Barltrop et al. (2023) <doi:10.1002/env.2797>. Implements pointwise and smooth estimation of the angular dependence function introduced by Wadsworth and Tawn (2013) <doi:10.3150/12-BEJ471>.
Author: Lidia Andre [aut, cre],
Callum Murphy-Barltrop [aut]
Maintainer: Lidia Andre <lidia.andre@unamur.be>
Diff between ReturnCurves versions 1.0 dated 2024-07-04 and 1.0.1 dated 2025-02-05
ReturnCurves-1.0.1/ReturnCurves/DESCRIPTION | 13 +++++++------ ReturnCurves-1.0.1/ReturnCurves/MD5 | 13 ++++++------- ReturnCurves-1.0.1/ReturnCurves/README.md | 5 ++++- ReturnCurves-1.0.1/ReturnCurves/build/partial.rdb |binary ReturnCurves-1.0.1/ReturnCurves/build/stage23.rdb |binary ReturnCurves-1.0.1/ReturnCurves/build/vignette.rds |binary ReturnCurves-1.0.1/ReturnCurves/inst/doc/ReturnCurves.pdf |binary ReturnCurves-1.0/ReturnCurves/build/ReturnCurves.pdf |only 8 files changed, 17 insertions(+), 14 deletions(-)
Title: Functional Programming Tools
Description: A complete and consistent functional programming toolkit for
R.
Author: Hadley Wickham [aut, cre] ,
Lionel Henry [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between purrr versions 1.0.2 dated 2023-08-10 and 1.0.4 dated 2025-02-05
DESCRIPTION | 23 ++-- LICENSE | 2 MD5 | 153 +++++++++++++++---------------- NAMESPACE | 33 ++++++ NEWS.md | 92 ++++++++++-------- R/deprec-when.R | 2 R/imap.R | 7 + R/keep.R | 8 - R/list-combine.R | 4 R/list-flatten.R | 4 R/list-modify.R | 5 - R/list-simplify.R | 8 - R/list-transpose.R | 25 +++-- R/modify-tree.R | 4 R/modify.R | 6 - R/pmap.R | 20 +++- R/progress-bars.R | 2 R/reduce.R | 68 +++++++------ R/superseded-map-df.R | 17 +++ R/superseded-transpose.R | 6 + R/utils.R | 2 README.md | 11 +- build/vignette.rds |binary inst/doc/base.R | 20 ++-- inst/doc/base.Rmd | 8 - inst/doc/base.html | 12 +- inst/doc/other-langs.Rmd | 2 inst/doc/other-langs.html | 2 man/accumulate.Rd | 2 man/figures/logo.png |binary man/imap.Rd | 5 - man/keep_at.Rd | 8 - man/list_assign.Rd | 7 - man/list_simplify.Rd | 6 - man/list_transpose.Rd | 6 - man/lmap.Rd | 2 man/map2.Rd | 2 man/map_depth.Rd | 8 - man/map_dfr.Rd | 17 +++ man/map_if.Rd | 2 man/modify.Rd | 2 man/modify_tree.Rd | 2 man/pmap.Rd | 10 +- man/progress_bars.Rd | 2 man/purrr-package.Rd | 6 - man/reduce.Rd | 33 ------ man/reduce_right.Rd | 31 ++++-- man/when.Rd | 2 src/backports.c | 10 ++ src/backports.h | 6 + src/conditions.c | 6 - src/map.c | 5 - src/pluck.c | 2 tests/testthat/_snaps/coerce.md | 56 +++++++++++ tests/testthat/_snaps/deprec-cross.md | 8 + tests/testthat/_snaps/deprec-prepend.md | 24 ++++ tests/testthat/_snaps/deprec-utils.md | 32 ++++++ tests/testthat/_snaps/deprec-when.md | 8 + tests/testthat/_snaps/every-some-none.md |only tests/testthat/_snaps/list-transpose.md | 16 +++ tests/testthat/_snaps/map-depth.md | 24 ++++ tests/testthat/_snaps/pluck.md | 16 +++ tests/testthat/test-adverb-auto-browse.R | 2 tests/testthat/test-coerce.R | 14 +- tests/testthat/test-deprec-cross.R | 2 tests/testthat/test-deprec-prepend.R | 15 --- tests/testthat/test-deprec-utils.R | 8 - tests/testthat/test-deprec-when.R | 2 tests/testthat/test-every-some-none.R | 4 tests/testthat/test-imap.R | 1 tests/testthat/test-list-transpose.R | 19 +++ tests/testthat/test-lmap.R | 1 tests/testthat/test-map-depth.R | 4 tests/testthat/test-modify.R | 1 tests/testthat/test-pluck.R | 4 tests/testthat/test-utils.R | 2 vignettes/base.Rmd | 8 - vignettes/other-langs.Rmd | 2 78 files changed, 669 insertions(+), 332 deletions(-)
Title: Simulating Diversification Dynamics
Description: Simulation of species diversification, fossil records, and phylogenies. While the literature on species birth-death simulators is extensive, including important software like 'paleotree' and 'APE', we concluded there were interesting gaps to be filled regarding possible diversification scenarios. Here we strove for flexibility over focus, implementing a large array of regimens for users to experiment with and combine. In this way, 'paleobuddy' can be used in complement to other simulators as a flexible jack of all trades, or, in the case of scenarios implemented only here, can allow for robust and easy simulations for novel situations. Environmental data modified from that in 'RPANDA': Morlon H. et al (2016) <doi:10.1111/2041-210X.12526>.
Author: Bruno do Rosario Petrucci [aut, cre]
,
Matheus Januario [aut] ,
Tiago Quental [aut]
Maintainer: Bruno do Rosario Petrucci <petrucci@iastate.edu>
Diff between paleobuddy versions 1.0.0 dated 2021-12-21 and 1.1.0 dated 2025-02-05
DESCRIPTION | 10 MD5 | 64 - NAMESPACE | 6 NEWS.md | 232 ++-- R/bd.sim.R | 58 - R/bd.sim.constant.R | 100 + R/bd.sim.general.R | 107 + R/bd.sim.traits.R |only R/bin.occurrences.R |only R/draw.sim.R | 391 ++++++- R/make.phylo.R | 507 ++++++++- R/paleobuddy.R | 8 R/phylo.to.sim.R | 4 R/rexp.musse.R |only R/sample.age.time.R | 8 R/sample.clade.R | 57 - R/sample.clade.traits.R |only R/sim.R | 12 R/traits.summary.R |only README.md | 8 build/vignette.rds |binary inst/CITATION |only inst/doc/overview.R | 245 +++- inst/doc/overview.Rmd | 220 +++ inst/doc/overview.html | 1713 ++++++++++++++++++++++++------- man/bd.sim.Rd | 43 man/bd.sim.traits.Rd |only man/bin.occurrences.Rd |only man/draw.sim.Rd | 146 ++ man/figures/README-unnamed-chunk-6-1.png |binary man/find.lineages.Rd | 6 man/make.phylo.Rd | 218 +++ man/paleobuddy.Rd | 17 man/sample.clade.Rd | 49 man/sample.clade.traits.Rd |only man/sim.Rd | 6 man/traits.summary.Rd |only vignettes/overview.Rmd | 220 +++ 38 files changed, 3707 insertions(+), 748 deletions(-)
Title: A Crew Launcher Plugin for AWS Batch
Description: In computationally demanding analysis projects,
statisticians and data scientists asynchronously
deploy long-running tasks to distributed systems,
ranging from traditional clusters to cloud services.
The 'crew.aws.batch' package extends the 'mirai'-powered
'crew' package with a worker launcher plugin for AWS Batch.
Inspiration also comes from packages 'mirai' by Gao (2023)
<https://github.com/shikokuchuo/mirai>,
'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>,
'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>,
'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
and 'batchtools' by Lang, Bischl, and Surmann (2017).
<doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre]
,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between crew.aws.batch versions 0.0.7 dated 2024-11-17 and 0.0.8 dated 2025-02-05
crew.aws.batch-0.0.7/crew.aws.batch/R/utils_options.R |only crew.aws.batch-0.0.7/crew.aws.batch/tests/testthat/test-utils_options.R |only crew.aws.batch-0.0.8/crew.aws.batch/DESCRIPTION | 8 crew.aws.batch-0.0.8/crew.aws.batch/MD5 | 38 +- crew.aws.batch-0.0.8/crew.aws.batch/NEWS.md | 7 crew.aws.batch-0.0.8/crew.aws.batch/R/crew_controller_aws_batch.R | 36 +- crew.aws.batch-0.0.8/crew.aws.batch/R/crew_launcher_aws_batch.R | 54 +-- crew.aws.batch-0.0.8/crew.aws.batch/R/crew_monitor_aws_batch.R | 160 ++++++---- crew.aws.batch-0.0.8/crew.aws.batch/R/crew_options_aws_batch.R | 61 ++- crew.aws.batch-0.0.8/crew.aws.batch/R/utils_time.R |only crew.aws.batch-0.0.8/crew.aws.batch/inst/WORDLIST | 1 crew.aws.batch-0.0.8/crew.aws.batch/man/crew_class_launcher_aws_batch.Rd | 41 -- crew.aws.batch-0.0.8/crew.aws.batch/man/crew_class_monitor_aws_batch.Rd | 12 crew.aws.batch-0.0.8/crew.aws.batch/man/crew_controller_aws_batch.Rd | 64 ++-- crew.aws.batch-0.0.8/crew.aws.batch/man/crew_definition_aws_batch.Rd | 6 crew.aws.batch-0.0.8/crew.aws.batch/man/crew_launcher_aws_batch.Rd | 28 + crew.aws.batch-0.0.8/crew.aws.batch/man/crew_monitor_aws_batch.Rd | 8 crew.aws.batch-0.0.8/crew.aws.batch/man/crew_options_aws_batch.Rd | 32 -- crew.aws.batch-0.0.8/crew.aws.batch/tests/monitor/test-monitor.R | 6 crew.aws.batch-0.0.8/crew.aws.batch/tests/testthat/test-crew_controller_aws_batch.R | 40 -- crew.aws.batch-0.0.8/crew.aws.batch/tests/testthat/test-crew_launcher_aws_batch.R | 20 - crew.aws.batch-0.0.8/crew.aws.batch/tests/testthat/test-utils_time.R |only 22 files changed, 327 insertions(+), 295 deletions(-)
More information about crew.aws.batch at CRAN
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Title: Targeted Maximum Likelihood Estimation for Two-Stage Study
Design
Description: An inverse probability of censoring weighted (IPCW) targeted maximum likelihood estimator (TMLE) for evaluating a marginal point treatment effect from data where some variables were collected on only a subset of participants using a two-stage design (or marginal mean outcome for a single arm study). A TMLE for conditional parameters defined by a marginal structural model (MSM) is also available.
Author: Susan Gruber [aut, cre],
Mark van der Laan [aut]
Maintainer: Susan Gruber <sgruber@TLrevolution.com>
Diff between twoStageDesignTMLE versions 1.0 dated 2024-09-05 and 1.0.1.2 dated 2025-02-05
DESCRIPTION | 8 +- MD5 | 22 ++++---- NAMESPACE | 3 + NEWS | 5 + R/Utils.R | 12 ++-- R/estimatePi.R |only R/twoStageTMLE.R | 111 ++++++++++++++++++++++++++++------------- R/twoStageTMLEMSM.R | 131 ++++++++++++++++++++++++++++++++----------------- build/partial.rdb |binary inst/CITATION | 2 man/estimatePi.Rd |only man/twoStageTMLE.Rd | 17 ++++-- man/twoStageTMLEmsm.Rd | 22 +++++--- 13 files changed, 222 insertions(+), 111 deletions(-)
More information about twoStageDesignTMLE at CRAN
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Title: Transfer of Hydrograph from Gauged to Ungauged Catchments
Description: A geomorphology-based hydrological modelling for transferring
streamflow measurements from gauged to ungauged catchments. Inverse
modelling enables to estimate net rainfall from streamflow measurements
following Boudhraâ et al. (2018) <doi:10.1080/02626667.2018.1425801>.
Resulting net rainfall is then estimated on the ungauged catchments
by spatial interpolation in order to finally simulate streamflow
following de Lavenne et al. (2016) <doi:10.1002/2016WR018716>.
Author: Alban de Lavenne [aut, cre] ,
Christophe Cudennec [ths] ,
Tom Loree [ctb],
Herve Squividant [ctb]
Maintainer: Alban de Lavenne <alban.delavenne@inrae.fr>
Diff between transfR versions 1.0.11 dated 2023-10-02 and 1.1.0 dated 2025-02-05
DESCRIPTION | 12 +-- MD5 | 50 +++++++------ NAMESPACE | 8 ++ R/as_transfr.R | 2 R/hdist.R | 96 ++++++++++++++++---------- R/mixr.R | 80 +++++++++++++-------- R/rsimilarity.R |only R/utils.R | 7 + R/weightr.R | 67 +++++++++--------- build/partial.rdb |binary build/vignette.rds |binary data/Blavet.rda |binary data/Oudon.rda |binary inst/doc/V01_get_started.html | 13 +-- inst/doc/V02_inputs_preparation_stars.html | 13 +-- inst/doc/V03_inputs_preparation_whitebox.Rmd | 2 inst/doc/V03_inputs_preparation_whitebox.html | 25 +++--- man/Blavet.Rd | 18 ++-- man/Oudon.Rd | 16 ++-- man/hdist.Rd | 13 ++- man/mixr.Rd | 19 +++-- man/rsimilarity.Rd |only man/weightr.Rd | 15 +++- src/Makevars |only src/Makevars.win |only src/gdist.f90 | 19 ++++- src/transfR.c | 4 - vignettes/V03_inputs_preparation_whitebox.Rmd | 2 28 files changed, 291 insertions(+), 190 deletions(-)
Title: Plot FTIR Spectra
Description: The goal of 'PlotFTIR' is to easily and quickly kick-start the production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using 'ggplot2'. The produced plots can be published directly or further modified by 'ggplot2' functions.
L'objectif de 'PlotFTIR' est de démarrer facilement et rapidement la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de 'ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions 'ggplot2'.
Author: Philip Bulsink [aut, cre] ,
Ulrich Makanda [trl] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources [cph]
Maintainer: Philip Bulsink <philip.bulsink@nrcan-rncan.gc.ca>
Diff between PlotFTIR versions 1.0.0 dated 2024-11-13 and 1.1.0 dated 2025-02-05
DESCRIPTION | 12 - MD5 | 69 ++++---- NAMESPACE | 2 NEWS.md | 15 + R/io.R | 53 ++++-- R/manipulations.R | 212 +++++++++++++++++++++++-- R/maths.R | 136 ++++++++++++++-- R/plot_ftir.R | 78 ++++++--- R/utils.R | 140 +++++----------- R/zzz.R |only README.md | 61 +++++-- inst/doc/plotting_ftir_spectra.R | 24 +- inst/doc/plotting_ftir_spectra.html | 48 ++--- man/add_band.Rd |only man/add_wavenumber_marker.Rd | 10 - man/check_ftir_data.Rd | 11 - man/conversion.Rd | 2 man/figures/README-basic_plot_en-1.png |binary man/figures/README-basic_plot_fr-1.png |binary man/figures/README-biodiesel_compress_en-1.png |binary man/figures/README-biodiesel_compress_fr-1.png |binary man/figures/README-biodiesel_labelled_en-1.png |binary man/figures/README-biodiesel_labelled_fr-1.png |binary man/figures/README-biodiesel_zoom_en-1.png |binary man/figures/README-biodiesel_zoom_fr-1.png |binary man/figures/README-stack_plot_en-1.png |binary man/figures/README-stack_plot_fr-1.png |binary man/highlight_sample.Rd |only man/intensity_type.Rd |only man/normalize_spectra.Rd | 3 man/plot_ftir.Rd | 15 + man/plot_ftir_core.Rd | 15 + man/plot_ftir_stacked.Rd | 15 + tests/testthat/test-manipulations.R | 149 +++++++++++++++++ tests/testthat/test-maths.R | 167 +++++++++++++++++-- tests/testthat/test-plot_ftir.R | 16 + tests/testthat/test-utils.R | 77 ++------- vignettes/peak_fitting.Rbak |only 38 files changed, 964 insertions(+), 366 deletions(-)
Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating manual work and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre],
Brian Reilly [ctb],
Sanaya Shroff [ctb],
Boris Grinshpun [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.1.5 dated 2024-11-14 and 0.1.6 dated 2025-02-05
NMsim-0.1.5/NMsim/tests/testthat/testReference/NMsim_03.rds |only NMsim-0.1.5/NMsim/tests/testthat/testReference/fnAppend_02.rds |only NMsim-0.1.5/NMsim/tests/testthat/testReference/fnAppend_03.rds |only NMsim-0.1.5/NMsim/tests/testthat/testReference/fnAppend_1.rds |only NMsim-0.1.6/NMsim/DESCRIPTION | 12 NMsim-0.1.6/NMsim/MD5 | 155 ++-- NMsim-0.1.6/NMsim/NAMESPACE | 3 NMsim-0.1.6/NMsim/NEWS.md | 58 + NMsim-0.1.6/NMsim/R/NMcreateMatLines.R | 104 +- NMsim-0.1.6/NMsim/R/NMexec.R | 95 -- NMsim-0.1.6/NMsim/R/NMexecDirectory.R | 8 NMsim-0.1.6/NMsim/R/NMreadSimModTab.R | 13 NMsim-0.1.6/NMsim/R/NMreplaceInits.R | 37 - NMsim-0.1.6/NMsim/R/NMrunWin.R | 93 +- NMsim-0.1.6/NMsim/R/NMsim.R | 356 +++++----- NMsim-0.1.6/NMsim/R/NMsimTestConf.R | 2 NMsim-0.1.6/NMsim/R/NMsim_EBE.R | 8 NMsim-0.1.6/NMsim/R/NMsim_NWPRI.R | 81 +- NMsim-0.1.6/NMsim/R/NMsim_VarCov.R | 1 NMsim-0.1.6/NMsim/R/NMsim_default.R | 9 NMsim-0.1.6/NMsim/R/NMsim_helpers.R | 56 + NMsim-0.1.6/NMsim/R/NMupdateInits.R | 6 NMsim-0.1.6/NMsim/R/NMupdateSizes.R |only NMsim-0.1.6/NMsim/R/NMwriteInits.R |only NMsim-0.1.6/NMsim/R/NWPRI_df.R | 1 NMsim-0.1.6/NMsim/R/modifyHelpers.R | 11 NMsim-0.1.6/NMsim/R/modifyModel.R |only NMsim-0.1.6/NMsim/R/pasteFuns.R |only NMsim-0.1.6/NMsim/R/prettyMatLines.R | 11 NMsim-0.1.6/NMsim/R/sampleParsSimpar.R | 2 NMsim-0.1.6/NMsim/R/simPopEtas.R | 21 NMsim-0.1.6/NMsim/R/zzz.R | 2 NMsim-0.1.6/NMsim/README.md | 5 NMsim-0.1.6/NMsim/inst/bash |only NMsim-0.1.6/NMsim/man/NMcreateMatLines.Rd | 23 NMsim-0.1.6/NMsim/man/NMexec.Rd | 53 - 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NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/xgxr021_nmtranfail_input.rds |binary NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail_MetaData.rds |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/example1.csv |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.cov |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.ctl |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.ext |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.phi |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.res |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.tab |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.vpd |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/predu.vpt |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/xgxr021.mod | 1 NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/xgxr021com.mod |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/xgxr032.mod | 36 - NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/xgxr051.mod |only NMsim-0.1.6/NMsim/tests/testthat/testData/nonmem/xgxr133.mod |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMcreateMatLines_01.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMcreateMatLines_02.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMcreateMatLines_03.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMseed_04.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_02.rds |binary NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_02b.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_07.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_EBE_03.rds |binary NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_01.rds |binary NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_01_OMEGAP.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_01_THETAPV.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_02.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_02_OMEGAP.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_NWPRI_02_THETAPV.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_inits_06.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMsim_sizes_05.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMupdateSizes_01.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMupdateSizes_02.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMwriteInits_01.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMwriteInits_02.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMwriteInits_03.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMwriteInits_04.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMwriteInits_05.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/NMwriteInits_06.rds |only NMsim-0.1.6/NMsim/tests/testthat/testReference/genPhiFile_01.rds |only NMsim-0.1.6/NMsim/tests/testthat/test_NMcreateMatLines.R |only NMsim-0.1.6/NMsim/tests/testthat/test_NMreadParsWide.R | 2 NMsim-0.1.6/NMsim/tests/testthat/test_NMreplaceInits.R |only NMsim-0.1.6/NMsim/tests/testthat/test_NMseed.R | 15 NMsim-0.1.6/NMsim/tests/testthat/test_NMsim.R | 150 ++++ NMsim-0.1.6/NMsim/tests/testthat/test_NMsim_NWPRI.R | 159 +++- NMsim-0.1.6/NMsim/tests/testthat/test_NMupdateSizes.R |only NMsim-0.1.6/NMsim/tests/testthat/test_NMwriteInits.R |only NMsim-0.1.6/NMsim/tests/testthat/test_genPhiFile.R |only 106 files changed, 1157 insertions(+), 589 deletions(-)
Title: Inference, Goodness-of-Fit and Forecast for Univariate Gaussian
Hidden Markov Models
Description: Inference, goodness-of-fit test, and prediction densities and intervals for univariate Gaussian Hidden Markov Models (HMM). The goodness-of-fit is based on a Cramer-von Mises statistic and uses parametric bootstrap to estimate the p-value. The description of the methodology is taken from Chapter 10.2 of Remillard (2013) <doi:10.1201/b14285>.
Author: Bouchra R. Nasri [aut, cre, cph],
Bruno N Remillard [aut, ctb, cph]
Maintainer: Bouchra R. Nasri <bouchra.nasri@umontreal.ca>
Diff between GaussianHMM1d versions 1.1.1 dated 2023-07-08 and 1.1.2 dated 2025-02-05
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/Sim.Markov.Chain.R | 9 +++++---- R/bootstrapfun.R | 6 +++--- man/Sim.Markov.Chain.Rd | 6 +++--- man/bootstrapfun.Rd | 3 +-- src/HMM_est_1d_new.c | 4 ++-- 7 files changed, 24 insertions(+), 24 deletions(-)
Title: Crew Launcher Plugins for Traditional High-Performance Computing
Clusters
Description: In computationally demanding analysis projects,
statisticians and data scientists asynchronously
deploy long-running tasks to distributed systems,
ranging from traditional clusters to cloud services.
The 'crew.cluster' package extends the 'mirai'-powered
'crew' package with worker launcher plugins for traditional
high-performance computing systems.
Inspiration also comes from packages 'mirai' by Gao (2023)
<https://github.com/shikokuchuo/mirai>,
'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>,
'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>,
'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
and 'batchtools' by Lang, Bischl, and Surmann (2017).
<doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre]
,
Michael Gilbert Levin [aut] ,
Brendan Furneaux [aut] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between crew.cluster versions 0.3.3 dated 2024-11-17 and 0.3.4 dated 2025-02-05
crew.cluster-0.3.3/crew.cluster/tests/sge/retries.R |only crew.cluster-0.3.4/crew.cluster/DESCRIPTION | 10 crew.cluster-0.3.4/crew.cluster/MD5 | 103 ++++------ crew.cluster-0.3.4/crew.cluster/NEWS.md | 4 crew.cluster-0.3.4/crew.cluster/R/crew_controller_lsf.R | 36 ++- crew.cluster-0.3.4/crew.cluster/R/crew_controller_pbs.R | 36 ++- crew.cluster-0.3.4/crew.cluster/R/crew_controller_sge.R | 36 ++- crew.cluster-0.3.4/crew.cluster/R/crew_controller_slurm.R | 36 ++- crew.cluster-0.3.4/crew.cluster/R/crew_launcher_cluster.R | 52 ++--- crew.cluster-0.3.4/crew.cluster/R/crew_launcher_lsf.R | 25 +- crew.cluster-0.3.4/crew.cluster/R/crew_launcher_pbs.R | 27 +- crew.cluster-0.3.4/crew.cluster/R/crew_launcher_sge.R | 25 +- crew.cluster-0.3.4/crew.cluster/R/crew_launcher_slurm.R | 25 +- crew.cluster-0.3.4/crew.cluster/R/crew_options_lsf.R | 61 +++-- crew.cluster-0.3.4/crew.cluster/R/crew_options_pbs.R | 62 +++--- crew.cluster-0.3.4/crew.cluster/R/crew_options_sge.R | 74 +++---- crew.cluster-0.3.4/crew.cluster/R/crew_options_slurm.R | 86 ++++---- crew.cluster-0.3.4/crew.cluster/R/utils_options.R | 12 - crew.cluster-0.3.4/crew.cluster/inst/WORDLIST | 1 crew.cluster-0.3.4/crew.cluster/man/crew_class_launcher_cluster.Rd | 35 +-- crew.cluster-0.3.4/crew.cluster/man/crew_class_launcher_lsf.Rd | 24 -- crew.cluster-0.3.4/crew.cluster/man/crew_class_launcher_pbs.Rd | 26 -- crew.cluster-0.3.4/crew.cluster/man/crew_class_launcher_sge.Rd | 24 -- crew.cluster-0.3.4/crew.cluster/man/crew_class_launcher_slurm.Rd | 24 -- crew.cluster-0.3.4/crew.cluster/man/crew_controller_lsf.Rd | 64 ++++-- crew.cluster-0.3.4/crew.cluster/man/crew_controller_pbs.Rd | 64 ++++-- crew.cluster-0.3.4/crew.cluster/man/crew_controller_sge.Rd | 64 ++++-- crew.cluster-0.3.4/crew.cluster/man/crew_controller_slurm.Rd | 64 ++++-- crew.cluster-0.3.4/crew.cluster/man/crew_launcher_cluster.Rd | 28 +- crew.cluster-0.3.4/crew.cluster/man/crew_launcher_lsf.Rd | 28 +- crew.cluster-0.3.4/crew.cluster/man/crew_launcher_pbs.Rd | 28 +- crew.cluster-0.3.4/crew.cluster/man/crew_launcher_sge.Rd | 28 +- crew.cluster-0.3.4/crew.cluster/man/crew_launcher_slurm.Rd | 28 +- crew.cluster-0.3.4/crew.cluster/man/crew_options_lsf.Rd | 34 --- crew.cluster-0.3.4/crew.cluster/man/crew_options_pbs.Rd | 35 --- crew.cluster-0.3.4/crew.cluster/man/crew_options_sge.Rd | 43 ---- crew.cluster-0.3.4/crew.cluster/man/crew_options_slurm.Rd | 50 +--- crew.cluster-0.3.4/crew.cluster/tests/sge/monitor.R | 4 crew.cluster-0.3.4/crew.cluster/tests/slurm/monitor.R | 4 crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_controller_lsf.R | 48 ---- crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_controller_pbs.R | 45 ---- crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_controller_sge.R | 51 ---- crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_controller_slurm.R | 46 ---- crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_launcher_cluster.R | 83 +------- crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_launcher_lsf.R | 11 - crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_launcher_pbs.R | 11 - crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_launcher_sge.R | 11 - crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_launcher_slurm.R | 11 - crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_options_lsf.R | 66 ------ crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_options_pbs.R | 70 ------ crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_options_sge.R | 78 ------- crew.cluster-0.3.4/crew.cluster/tests/testthat/test-crew_options_slurm.R | 70 ------ crew.cluster-0.3.4/crew.cluster/tests/testthat/test-utils_options.R | 39 --- 53 files changed, 753 insertions(+), 1297 deletions(-)
Title: B-Spline Interpolation and Regression
Description: Build and use B-splines for interpolation and regression.
In case of regression, equality constraints as well as monotonicity
and/or positivity of B-spline weights can be imposed. Moreover,
knot positions (not only spline weights) can be part of
optimized parameters too. For this end, 'bspline' is able to calculate
Jacobian of basis vectors as function of knot positions. User is provided with
functions calculating spline values at arbitrary points. These
functions can be differentiated and integrated to obtain B-splines calculating
derivatives/integrals at any point. B-splines of this package can
simultaneously operate on a series of curves sharing the same set of
knots. 'bspline' is written with concern about computing
performance that's why the basis and Jacobian calculation is implemented in C++.
The rest is implemented in R but without notable impact on computing speed.
Author: Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between bspline versions 2.2.2 dated 2024-07-02 and 2.3.0 dated 2025-02-05
DESCRIPTION | 16 +++--- MD5 | 19 +++---- NAMESPACE | 1 NEWS.md | 9 +++ R/bspline.R | 103 ++++++++++++++++++++++++++++++----------- inst/unitTests/runit.bspline.R | 2 man/bspline.Rd | 16 +++--- man/dmat.Rd | 2 man/ibsp.Rd | 6 +- man/iknots.Rd | 4 + man/imat.Rd |only 11 files changed, 122 insertions(+), 56 deletions(-)
Title: R Session Information
Description: Query and print information about the current R session. It
is similar to 'utils::sessionInfo()', but includes more information
about packages, and where they were installed from.
Author: Gabor Csardi [cre],
Hadley Wickham [aut],
Winston Chang [aut],
Robert Flight [aut],
Kirill Mueller [aut],
Jim Hester [aut],
R Core team [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between sessioninfo versions 1.2.2 dated 2021-12-06 and 1.2.3 dated 2025-02-05
DESCRIPTION | 60 +++++++----------- MD5 | 39 ++++++------ NEWS.md | 34 ++++++++-- R/compare.R | 98 ++++++++++++++++++++++++++++--- R/github-actions.R |only R/mocks.r |only R/package-info.R | 8 ++ R/platform-info.R | 25 +++++++ R/printing.R | 2 R/session-info.R | 7 -- R/sessioninfo-package.R |only README.md | 24 ++++++- man/platform_info.Rd | 4 + man/session_diff.Rd | 28 +++++++- man/sessioninfo-package.Rd |only tests/testthat/_snaps/platform-info.md |only tests/testthat/test-dependent-packages.R | 32 ++-------- tests/testthat/test-diff.R | 57 +++++++----------- tests/testthat/test-os-name.R | 4 - tests/testthat/test-package-info.R | 20 +----- tests/testthat/test-platform-info.R | 21 +++++- tests/testthat/test-session-info.R | 38 +++++++++++- tests/testthat/test-warnings.R | 4 + 23 files changed, 345 insertions(+), 160 deletions(-)
Title: Geographically Weighted Non-Negative Principal Components
Analysis
Description: Implements a geographically weighted non-negative principal
components analysis, which consists of the fusion of geographically
weighted and sparse non-negative principal components analyses
<doi:10.17608/k6.auckland.9850826.v1>.
Author: Narumasa Tsutsumida [aut, cre]
Maintainer: Narumasa Tsutsumida <rsnaru.jp@gmail.com>
Diff between GWnnegPCA versions 0.0.4 dated 2020-11-18 and 0.0.5 dated 2025-02-05
DESCRIPTION | 32 ++++--- MD5 | 10 +- NAMESPACE | 19 ++-- R/gw_nsprcomp.R | 221 ++++++++++++++++++++++++++++++++++++----------------- man/gw_nsprcomp.Rd | 195 +++++++++++++++------------------------------- tests |only 6 files changed, 254 insertions(+), 223 deletions(-)
Title: Fishery Science Methods and Models
Description: Functions for applying a wide range of fisheries stock assessment methods.
Author: Gary A. Nelson [aut, cre]
Maintainer: Gary A. Nelson <gary.nelson@mass.gov>
Diff between fishmethods versions 1.12-1 dated 2023-04-27 and 1.13-1 dated 2025-02-05
DESCRIPTION | 13 ++- MD5 | 31 +++++---- NAMESPACE | 3 R/fm_telemetry.R | 5 + R/growth_LEP.R |only R/inverse_alk.R |only R/sbpr.R | 125 ++++++++++++++++++++++++++----------- R/ypr.R | 98 +++++++++++++++++++---------- data/hohe.rda |only data/lepdata.rda |only man/grotag.Rd | 7 +- man/growth_LEP.Rd |only man/hohe.Rd |only man/inverse_alk.Rd |only man/irm_cr.Rd | 4 - man/irm_h.Rd | 4 - man/lepdata.Rd |only man/sbpr.Rd | 53 ++++++++------- man/ypr.Rd | 21 +++--- src/TMB/fishmethods_TMBExports.cpp | 3 src/TMB/grow_LEP.hpp |only 21 files changed, 245 insertions(+), 122 deletions(-)
Title: Dynamical Assembly of Islands by Speciation, Immigration and
Extinction
Description: Simulates and computes the (maximum) likelihood of a dynamical
model of island biota assembly through speciation, immigration and
extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.
Author: Rampal S. Etienne [aut, cre] ,
Luis Valente [aut] ,
Albert B. Phillimore [aut] ,
Bart Haegeman [aut] ,
Joshua W. Lambert [aut] ,
Pedro Santos Neves [aut] ,
Shu Xie [aut] ,
Richel J.C. Bilderbeek [aut] ,
Hanno Hildenbrandt [aut] ,
Torsten Hauffe [ctb] [...truncated...]
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DAISIE versions 4.4.1 dated 2023-10-21 and 4.5.0 dated 2025-02-05
DESCRIPTION | 10 - MD5 | 112 +++++++++++---------- NAMESPACE | 1 NEWS.md | 9 + R/DAISIE_ML1.R | 32 ++++-- R/DAISIE_ML_CS.R | 6 - R/DAISIE_ML_IW.R | 14 ++ R/DAISIE_SR_sim_core.R | 11 +- R/DAISIE_data.R | 40 +++++++ R/DAISIE_format_IW.R | 89 ++++++++++++++++ R/DAISIE_loglik_CS.R | 44 +++++++- R/DAISIE_loglik_IW.R | 11 +- R/DAISIE_loglik_high_lambda.R | 39 +++---- R/DAISIE_rates.R | 21 ++- R/DAISIE_sim_core_cr.R | 5 R/DAISIE_sim_core_cr_shift.R | 3 R/DAISIE_sim_core_time_dep.R | 3 R/DAISIE_sim_core_trait_dep.R | 3 R/DAISIE_sim_trait_dep.R | 6 - R/DAISIE_utils.R | 2 R/default_params_doc.R | 7 + build/partial.rdb |binary build/vignette.rds |binary data/frogs_sim_datalist.RData |only inst/doc/DAISIE_FAQs.Rmd |only inst/doc/DAISIE_FAQs.html |only man/DAISIE_ML.Rd | 10 + man/DAISIE_ML1.Rd | 29 +++-- man/DAISIE_ML2.Rd | 2 man/DAISIE_ML4.Rd | 2 man/DAISIE_ML_IW.Rd | 2 man/DAISIE_loglik_integrand.Rd | 2 man/DAISIE_loglik_integrate.Rd | 2 man/DAISIE_logp0.Rd |only man/DAISIE_plot_area.Rd | 2 man/DAISIE_sim_cr_shift.Rd | 4 man/DAISIE_sim_relaxed_rate.Rd | 4 man/DAISIE_sim_time_dep.Rd | 4 man/DAISIE_sim_trait_dep.Rd | 4 man/calc_next_timeval.Rd | 2 man/calc_next_timeval_shift.Rd | 2 man/default_params_doc.Rd | 8 + man/frogs_sim_datalist.Rd |only man/get_ana_rate.Rd | 2 man/get_ext_rate.Rd | 2 man/get_immig_rate.Rd | 2 man/update_max_rates.Rd | 2 man/update_rates.Rd | 2 src/DAISIE_loglik_rhs_FORTRAN.f95 | 22 ++-- src/Makevars | 1 src/Makevars.win | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test-DAISIE_ML1.R | 72 +++++++++---- tests/testthat/test-DAISIE_ML2.R | 37 ++---- tests/testthat/test-DAISIE_format_IW.R | 32 +++--- tests/testthat/test-DAISIE_format_IW_full_stt.R | 6 - tests/testthat/test-DAISIE_format_IW_sampled_stt.R | 6 - tests/testthat/test-DAISIE_logp0.R |only tests/testthat/test-integration_DAISIE.R | 112 +++++++++++++++++++++ vignettes/DAISIE_FAQs.Rmd |only vignettes/Figure1.png |only 61 files changed, 625 insertions(+), 221 deletions(-)
Title: Collection of Helper Functions
Description: Provides a collection of lightweight helper functions (imps) both
for interactive use and for inclusion within other packages. These include
functions for minimal input assertions, visualising colour palettes,
quoting user input, searching rows of a data frame and capturing string
tokens.
Author: Tim Taylor [aut, cre, cph] ,
R Core Team [cph] ,
Toby Hocking [cph]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ympes versions 1.7.0 dated 2024-11-27 and 1.8.0 dated 2025-02-05
DESCRIPTION | 6 +-- MD5 | 18 +++++----- NAMESPACE | 1 NEWS.md | 6 +++ R/fstrcapture.R | 78 +++++++++++++++++++++++++++++++++++++++++--- build/vignette.rds |binary inst/doc/ympes.Rmd | 6 +-- inst/doc/ympes.html | 91 +++++++++++++++++++++++++--------------------------- man/fstrcapture.Rd | 15 ++++++-- vignettes/ympes.Rmd | 6 +-- 10 files changed, 152 insertions(+), 75 deletions(-)
Title: Assess Study Cohorts Using a Common Data Model
Description: Phenotype study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model. Diagnostics
are run at the database, code list, cohort, and population level to assess
whether study cohorts are ready for research.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Xihang Chen [aut] ,
Marta Alcalde-Herraiz [aut] ,
Albert Prats-Uribe [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between PhenotypeR versions 0.1.1 dated 2025-01-17 and 0.1.2 dated 2025-02-05
DESCRIPTION | 21 MD5 | 80 R/cohortDiagnostics.R | 2 R/matchedDiagnostics.R | 28 R/phenotypeR-package.R | 16 R/populationDiagnostics.R | 2 R/shinyDiagnostics.R | 4 R/utils-pipe.R | 28 README.md | 106 build/vignette.rds |binary inst/doc/a01_DatabaseDiagnostics.R | 38 inst/doc/a01_DatabaseDiagnostics.Rmd | 55 inst/doc/a01_DatabaseDiagnostics.html | 1125 ++++++ inst/doc/a02_CodelistDiagnostics.R | 24 inst/doc/a02_CodelistDiagnostics.Rmd | 31 inst/doc/a02_CodelistDiagnostics.html | 1811 ++++++++++ inst/doc/a03_CohortDiagnostics.R | 17 inst/doc/a03_CohortDiagnostics.Rmd | 17 inst/doc/a03_CohortDiagnostics.html | 4839 +++-------------------------- inst/doc/a04_MatchedDiagnostics.R | 43 inst/doc/a04_MatchedDiagnostics.Rmd | 51 inst/doc/a04_MatchedDiagnostics.html | 46 inst/doc/a05_PopulationDiagnostics.R | 51 inst/doc/a05_PopulationDiagnostics.Rmd | 63 inst/doc/a05_PopulationDiagnostics.html | 2040 ++++++++++-- inst/shiny/background.md | 8 inst/shiny/global.R | 139 inst/shiny/scripts/preprocess.R | 49 inst/shiny/server.R | 2004 ++++++------ inst/shiny/ui.R | 1287 +++---- man/pipe.Rd | 40 man/shinyDiagnostics.Rd | 9 tests/testthat/test-addCodelistAttribute.R | 2 tests/testthat/test-codelistDiagnostics.R | 2 tests/testthat/test-phenotypeDiagnostics.R | 2 tests/testthat/test-shinyDiagnostics.R | 6 vignettes/a01_DatabaseDiagnostics.Rmd | 55 vignettes/a02_CodelistDiagnostics.Rmd | 31 vignettes/a03_CohortDiagnostics.Rmd | 17 vignettes/a04_MatchedDiagnostics.Rmd | 51 vignettes/a05_PopulationDiagnostics.Rmd | 63 41 files changed, 7744 insertions(+), 6559 deletions(-)
Title: Constructing Hierarchical Voronoi Tessellations and Overlay
Heatmaps for Data Analysis
Description: Facilitates building topology preserving maps for data analysis.
Author: Zubin Dowlaty [aut],
Mu Sigma, Inc. [cre]
Maintainer: "Mu Sigma, Inc." <ird.experiencelab@mu-sigma.com>
Diff between HVT versions 25.2.1 dated 2025-02-04 and 25.2.2 dated 2025-02-05
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ README.md | 12 ++++++------ inst/doc/HVT.R | 3 ++- inst/doc/HVT.Rmd | 15 +++++++++------ inst/doc/HVT.html | 37 +++++++++++++++++++++---------------- vignettes/HVT.Rmd | 15 +++++++++------ 7 files changed, 57 insertions(+), 45 deletions(-)
Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating
grouped date classes. This package is part of the RECON
(<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between grates versions 1.4.0 dated 2025-01-17 and 1.4.1 dated 2025-02-05
DESCRIPTION | 12 - MD5 | 14 - NEWS.md | 4 README.md | 27 --- inst/doc/grates.R | 35 ---- inst/doc/grates.Rmd | 23 +- inst/doc/grates.html | 406 +++++++++++++++++++++++---------------------------- vignettes/grates.Rmd | 23 +- 8 files changed, 238 insertions(+), 306 deletions(-)
Title: Seasonal Adjustment of Weekly Data
Description: Perform seasonal adjustment of weekly data. The package provides a user-friendly interface for computing seasonally adjusted estimates of weekly data and includes functions for the creation of country-specific prior adjustment variables, as well as diagnostic tools to assess the quality of the adjustments. The method is described in more detail in Ginker (2023) <doi:10.13140/RG.2.2.12221.44000>.
Author: Tim Ginker [aut, cre, cph] ,
Jon Lachman [ctb]
Maintainer: Tim Ginker <tim.ginker@gmail.com>
Diff between boiwsa versions 1.1.2 dated 2024-09-23 and 1.1.3 dated 2025-02-05
DESCRIPTION | 20 + LICENSE | 4 MD5 | 73 +++--- NAMESPACE | 75 +++--- NEWS.md | 4 R/boiwsa.R | 71 ++++-- R/data.R | 96 ++++---- R/find_opt.R | 35 ++- R/find_outliers.R | 37 ++- R/fourier_vars.R | 182 ++++++++-------- R/generic_functions.R | 104 +++++++++ R/genhol.R | 146 ++++++------- R/my_ao.R | 94 ++++---- R/my_rosh.R | 138 ++++++------ R/plot_spec.R | 88 ++++---- R/simple_td.R | 138 ++++++------ README.md | 324 ++++++++++++++++++++++++++---- man/boiwsa.Rd | 136 ++++++------ man/dates_il.Rd | 50 ++-- man/figures/README-unnamed-chunk-10-1.png |only man/figures/README-unnamed-chunk-11-1.png |only man/figures/README-unnamed-chunk-12-1.png |only man/figures/README-unnamed-chunk-8-1.png |only man/find_opt.Rd | 96 ++++---- man/find_outliers.Rd | 104 ++++----- man/fourier_vars.Rd | 58 ++--- man/gasoline.data.Rd | 52 ++-- man/genhol.Rd | 74 +++--- man/holiday_dates_il.Rd | 48 ++-- man/lbm.Rd | 52 ++-- man/my_ao.Rd | 62 ++--- man/my_rosh.Rd | 62 ++--- man/plot.boiwsa.Rd | 34 +-- man/plot_spec.Rd | 50 ++-- man/predict.boiwsa.Rd |only man/print.Rd | 32 +- man/print.boiwsa.Rd | 34 +-- man/simple_td.Rd | 72 +++--- man/summary.Rd | 32 +- man/summary.boiwsa.Rd | 32 +- 40 files changed, 1560 insertions(+), 1149 deletions(-)
Title: Artificial Intelligence for Education
Description: In social and educational settings, the use of Artificial
Intelligence (AI) is a challenging task. Relevant data is often only
available in handwritten forms, or the use of data is restricted by
privacy policies. This often leads to small data sets. Furthermore, in
the educational and social sciences, data is often unbalanced in terms
of frequencies. To support educators as well as educational and social
researchers in using the potentials of AI for their work, this package
provides a unified interface for neural nets in 'PyTorch' to deal with
natural language problems. In addition, the package ships with a shiny
app, providing a graphical user interface. This allows the usage of
AI for people without skills in writing python/R scripts. The tools
integrate existing mathematical and statistical methods for dealing
with small data sets via pseudo-labeling (e.g. Cascante-Bonilla et al.
(2020) <doi:10.48550/arXiv.2001.06001>) and imbalanced data via the
creation of synthetic cases [...truncated...]
Author: Berding Florian [aut, cre] ,
Tykhonova Yuliia [aut] ,
Pargmann Julia [ctb] ,
Leube Anna [ctb] ,
Riebenbauer Elisabeth [ctb] ,
Rebmann Karin [ctb],
Slopinski Andreas [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Diff between aifeducation versions 1.0.1 dated 2025-01-28 and 1.0.2 dated 2025-02-05
aifeducation-1.0.1/aifeducation/R/sysdata.rda |only aifeducation-1.0.2/aifeducation/DESCRIPTION | 6 aifeducation-1.0.2/aifeducation/MD5 | 30 - aifeducation-1.0.2/aifeducation/NAMESPACE | 1 aifeducation-1.0.2/aifeducation/NEWS.md | 7 aifeducation-1.0.2/aifeducation/R/Studio_Classifier_Create.R | 2 aifeducation-1.0.2/aifeducation/R/Studio_FeatureExtractor_Create.R | 2 aifeducation-1.0.2/aifeducation/R/Studio_Tabs_DM_DataSetEditor.R | 2 aifeducation-1.0.2/aifeducation/R/data.R | 2 aifeducation-1.0.2/aifeducation/R/onLoad.R | 2 aifeducation-1.0.2/aifeducation/R/sustainability.R | 264 ++++++++++ aifeducation-1.0.2/aifeducation/README.md | 15 aifeducation-1.0.2/aifeducation/inst/studio_app/app.r | 2 aifeducation-1.0.2/aifeducation/man/get_alpha_3_codes.Rd |only aifeducation-1.0.2/aifeducation/man/matrix_to_array_c.Rd | 1 aifeducation-1.0.2/aifeducation/man/summarize_tracked_sustainability.Rd | 1 aifeducation-1.0.2/aifeducation/man/to_categorical_c.Rd | 1 17 files changed, 308 insertions(+), 30 deletions(-)
Title: Interpreted String Literals
Description: An implementation of interpreted string literals. Based on the
'glue' package by Hester & Bryan (2024) <doi:10.32614/CRAN.package.glue> but
with a focus on efficiency and simplicity at a cost of flexibility.
Author: Tim Taylor [aut, cre] ,
Jim Hester [aut] ,
Jennifer Bryan [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between super versions 0.0.4 dated 2024-12-16 and 0.0.5 dated 2025-02-05
DESCRIPTION | 6 MD5 | 26 +-- NEWS.md | 6 R/glue.R | 64 ++++---- R/trim.R | 12 - README.md | 32 +--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/super.R | 2 inst/doc/super.Rmd | 17 -- inst/doc/super.html | 101 ++++++-------- src/glue.c | 113 +++++++-------- src/trim.c | 370 ++++++++++++++++++++++++++-------------------------- vignettes/super.Rmd | 17 -- 14 files changed, 371 insertions(+), 395 deletions(-)
Title: Calculation of IBD Probabilities
Description: For biparental, three and four-way crosses Identity by Descent
(IBD) probabilities can be calculated using Hidden Markov Models and
inheritance vectors following Lander and Green
(<https://www.jstor.org/stable/29713>) and Huang
(<doi:10.1073/pnas.1100465108>). One of a series of statistical genetic
packages for streamlining the analysis of typical plant breeding experiments
developed by Biometris.
Author: Martin Boer [aut] ,
Bart-Jan van Rossum [aut, cre]
,
Wenhao Li [ctb] ,
Johannes Kruisselbrink [ctb]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenIBD versions 1.0.7 dated 2024-02-02 and 1.0.8 dated 2025-02-05
statgenIBD-1.0.7/statgenIBD/R/redundant |only statgenIBD-1.0.8/statgenIBD/DESCRIPTION | 12 statgenIBD-1.0.8/statgenIBD/MD5 | 90 ++++-- statgenIBD-1.0.8/statgenIBD/NEWS.md | 40 +-- statgenIBD-1.0.8/statgenIBD/R/IBDprob.R | 6 statgenIBD-1.0.8/statgenIBD/R/RcppExports.R | 2 statgenIBD-1.0.8/statgenIBD/R/getProbs.R | 2 statgenIBD-1.0.8/statgenIBD/R/readIBDs.R | 2 statgenIBD-1.0.8/statgenIBD/R/readRABBIT.R | 80 +----- statgenIBD-1.0.8/statgenIBD/R/writeFlapjack.R | 2 statgenIBD-1.0.8/statgenIBD/R/writeIBDs.R | 2 statgenIBD-1.0.8/statgenIBD/README.md | 21 - statgenIBD-1.0.8/statgenIBD/build/partial.rdb |binary statgenIBD-1.0.8/statgenIBD/build/vignette.rds |binary statgenIBD-1.0.8/statgenIBD/inst/doc/IBDCalculations.R | 22 - statgenIBD-1.0.8/statgenIBD/inst/doc/IBDCalculations.Rmd | 9 statgenIBD-1.0.8/statgenIBD/inst/doc/IBDCalculations.html | 132 ++++------ statgenIBD-1.0.8/statgenIBD/inst/doc/IBDFileFormat.R | 6 statgenIBD-1.0.8/statgenIBD/inst/doc/IBDFileFormat.html | 24 - statgenIBD-1.0.8/statgenIBD/inst/tinytest/example_magicreconstruct_ancestry.csv.gz |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/example_ped.csv |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popBC1S2 |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popBC1S2DH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popBC3 |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popBC3DH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC3 |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC3DH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC3S4 |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC3S4DH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC4 |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC4DH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC4S3 |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popC4S3DH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popDH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popF4 |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/popF4DH |only statgenIBD-1.0.8/statgenIBD/inst/tinytest/test_calcIBD.R | 11 statgenIBD-1.0.8/statgenIBD/inst/tinytest/test_readRABBIT.R | 31 ++ statgenIBD-1.0.8/statgenIBD/man/allGenoPlot.Rd | 24 - statgenIBD-1.0.8/statgenIBD/man/figures |only statgenIBD-1.0.8/statgenIBD/man/getProbs.Rd | 90 +++--- statgenIBD-1.0.8/statgenIBD/man/readRABBIT.Rd | 3 statgenIBD-1.0.8/statgenIBD/man/singleGenoPlot.Rd | 24 - statgenIBD-1.0.8/statgenIBD/man/statgenIBD-package.Rd | 2 statgenIBD-1.0.8/statgenIBD/man/summary.IBDprob.Rd | 66 ++--- statgenIBD-1.0.8/statgenIBD/man/writeFlapjack.Rd | 82 +++--- statgenIBD-1.0.8/statgenIBD/src/calcIBD.cpp | 2 statgenIBD-1.0.8/statgenIBD/vignettes/IBDCalculations.Rmd | 9 48 files changed, 410 insertions(+), 386 deletions(-)
Title: Small Count Rounding of Tabular Data
Description: A statistical disclosure control tool to protect frequency tables in cases where small values are sensitive. The function PLSrounding() performs small count rounding of necessary inner cells so that all small frequencies of cross-classifications to be published (publishable cells) are rounded. This is equivalent to changing micro data since frequencies of unique combinations are changed. Thus, additivity and consistency are guaranteed. The methodology is described in Langsrud and Heldal (2018) <https://www.researchgate.net/publication/327768398_An_Algorithm_for_Small_Count_Rounding_of_Tabular_Data>.
Author: Oeyvind Langsrud [aut, cre],
Johan Heldal [aut]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between SmallCountRounding versions 1.1.0 dated 2024-12-09 and 1.2.0 dated 2025-02-05
SmallCountRounding-1.1.0/SmallCountRounding/R/Extend0fromModelMatrixInput.R |only SmallCountRounding-1.2.0/SmallCountRounding/DESCRIPTION | 16 +++--- SmallCountRounding-1.2.0/SmallCountRounding/MD5 | 25 +++++----- SmallCountRounding-1.2.0/SmallCountRounding/NAMESPACE | 10 +++- SmallCountRounding-1.2.0/SmallCountRounding/NEWS.md | 11 ++++ SmallCountRounding-1.2.0/SmallCountRounding/R/PLSrounding.R | 22 ++++++++ SmallCountRounding-1.2.0/SmallCountRounding/R/reexport.R |only SmallCountRounding-1.2.0/SmallCountRounding/inst/doc/Introduction_to_SmallCountRounding.R | 16 +++--- SmallCountRounding-1.2.0/SmallCountRounding/inst/doc/Introduction_to_SmallCountRounding.Rmd | 2 SmallCountRounding-1.2.0/SmallCountRounding/inst/doc/Introduction_to_SmallCountRounding.html | 4 - SmallCountRounding-1.2.0/SmallCountRounding/man/PLSrounding.Rd | 20 ++++++++ SmallCountRounding-1.2.0/SmallCountRounding/man/SmallCountRounding-package.Rd | 1 SmallCountRounding-1.2.0/SmallCountRounding/man/reexports.Rd |only SmallCountRounding-1.2.0/SmallCountRounding/tests/testthat/test-PLSrounding.R | 2 SmallCountRounding-1.2.0/SmallCountRounding/vignettes/Introduction_to_SmallCountRounding.Rmd | 2 15 files changed, 95 insertions(+), 36 deletions(-)
More information about SmallCountRounding at CRAN
Permanent link
Title: A Template for Creating Reproducible 'shiny' Applications
Description: Create a skeleton 'shiny' application with create_template() that is
reproducible, can be saved and meets academic standards for attribution.
Forked from 'wallace'. Code is split into modules that are loaded and linked
together automatically and each call one function. Guidance pages explain
modules to users and flexible logging informs them of any errors. Options
enable asynchronous operations, viewing of source code, interactive maps and
data tables. Use to create complex analytical applications, following best
practices in open science and software development. Includes functions for
automating repetitive development tasks and an example application at
run_shinyscholar() that requires
install.packages("shinyscholar", dependencies = TRUE). A guide to developing
applications can be found on the package website.
Author: Simon E. H. Smart [aut, cre, cph],
Tim Lucas [aut] ,
Jamie M. Kass [ctb],
Gonzalo E. Pinilla-Buitrago [ctb],
Andrea Paz [ctb],
Bethany A. Johnson [ctb],
Valentina Grisales-Betancur [ctb],
Dean Attali [ctb],
Matthew E. Aiello-Lammens [ctb],
Cory Merow [...truncated...]
Maintainer: Simon E. H. Smart <simon.smart@cantab.net>
Diff between shinyscholar versions 0.2.4 dated 2025-01-29 and 0.2.5 dated 2025-02-05
DESCRIPTION | 6 ++-- MD5 | 44 +++++++++++++++++------------------ NEWS.md | 6 ++++ R/helper_functions.R | 2 - README.md | 2 - inst/app_skeleton/helper_functions.R | 2 - inst/app_skeleton/intro.Rmd | 8 +++--- inst/app_skeleton/server.Rmd | 10 +++++++ inst/app_skeleton/ui.Rmd | 10 ++++++- inst/shiny/Rmd/text_intro_tab.Rmd | 2 - inst/shiny/Rmd/userReport_intro.Rmd | 2 - inst/shiny/modules/core_intro.R | 2 - inst/shiny/modules/select_user.R | 4 ++- inst/shiny/server.R | 9 +++++++ inst/shiny/ui.R | 10 ++++++- tests/testthat/helper_data.R | 21 ++++++++++++++++ tests/testthat/helper_select_user.R | 16 ++++++++++++ tests/testthat/test-downloads.R | 7 +++++ tests/testthat/test-metadata.R | 3 ++ tests/testthat/test-plot_hist.R | 3 ++ tests/testthat/test-plot_scatter.R | 3 ++ tests/testthat/test-save_load.R | 12 +++++++++ tests/testthat/test-select_user.R | 14 +++++++++++ 23 files changed, 158 insertions(+), 40 deletions(-)
Title: Plot Function for Single-Case Data Frames
Description: Add-on for the 'scan' package that creates plots
from single-case data frames ('scdf'). It includes functions for styling
single-case plots, adding phase-based lines to indicate various statistical
parameters, and predefined themes for presentations and publications. More
information and in depth examples can be found in the online book
"Analyzing Single-Case Data with R and 'scan"
Jürgen Wilbert (2025) <https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [aut, cre]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>
Diff between scplot versions 0.4.0 dated 2024-06-29 and 0.5.0 dated 2025-02-05
scplot-0.4.0/scplot/R/forestplots.R |only scplot-0.4.0/scplot/R/private_scplot.R |only scplot-0.4.0/scplot/R/private_statline.R |only scplot-0.4.0/scplot/R/private_themes.R |only scplot-0.4.0/scplot/man/plot.sc_hplm.Rd |only scplot-0.4.0/scplot/man/plot.sc_tauu.Rd |only scplot-0.4.0/scplot/man/scplot.Rd |only scplot-0.5.0/scplot/DESCRIPTION | 16 +++--- scplot-0.5.0/scplot/MD5 | 44 ++++++++++-------- scplot-0.5.0/scplot/NAMESPACE | 7 ++ scplot-0.5.0/scplot/NEWS.md | 10 +++- scplot-0.5.0/scplot/R/add_legend.R | 29 +++++++++++- scplot-0.5.0/scplot/R/add_statline.R | 7 ++ scplot-0.5.0/scplot/R/as_ggplot.R | 68 +++++++++++++++-------------- scplot-0.5.0/scplot/R/private-forestplot.R |only scplot-0.5.0/scplot/R/private-scplot.R |only scplot-0.5.0/scplot/R/private-statline.R |only scplot-0.5.0/scplot/R/private-themes.R |only scplot-0.5.0/scplot/R/scplot-generic.R |only scplot-0.5.0/scplot/R/scplot-package.R | 2 scplot-0.5.0/scplot/R/scplot.R | 34 ++++++-------- scplot-0.5.0/scplot/R/scplot.sc_hplm.R |only scplot-0.5.0/scplot/R/scplot.sc_rand.R |only scplot-0.5.0/scplot/R/scplot.sc_tauu.R |only scplot-0.5.0/scplot/R/set_dataline.R | 24 +++++----- scplot-0.5.0/scplot/R/startup.R |only scplot-0.5.0/scplot/man/add_legend.Rd | 30 +++++++++++- scplot-0.5.0/scplot/man/add_statline.Rd | 5 +- scplot-0.5.0/scplot/man/scplot.sc_hplm.Rd |only scplot-0.5.0/scplot/man/scplot.sc_rand.Rd |only scplot-0.5.0/scplot/man/scplot.sc_tauu.Rd |only scplot-0.5.0/scplot/man/scplot.scdf.Rd |only scplot-0.5.0/scplot/man/set_dataline.Rd | 14 +++++ 33 files changed, 188 insertions(+), 102 deletions(-)
Title: Single-Case Data Analyses for Single and Multiple Baseline
Designs
Description: A collection of procedures for analysing, visualising,
and managing single-case data. These include piecewise linear regression
models, multilevel models, overlap indices ('PND', 'PEM', 'PAND', 'PET', 'tau-u',
'baseline corrected tau', 'CDC'), and randomization tests. Data preparation functions
support outlier detection, handling missing values, scaling, and custom transformations.
An export function helps to generate
html, word, and latex tables in a publication friendly style. More details can be
found in the online book 'Analyzing single-case data with R and scan', Juergen Wilbert (2025)
<https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [cre, aut] ,
Timo Lueke [aut]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>
Diff between scan versions 0.61.0 dated 2024-07-01 and 0.62.0 dated 2025-02-05
scan-0.61.0/scan/R/private_kendall_meta.R |only scan-0.61.0/scan/R/private_prepare_scdf.R |only scan-0.61.0/scan/R/private_regression.R |only scan-0.61.0/scan/R/private_utilities.R |only scan-0.62.0/scan/DESCRIPTION | 20 +- scan-0.62.0/scan/MD5 | 198 ++++++++++++----------- scan-0.62.0/scan/NAMESPACE | 17 - scan-0.62.0/scan/NEWS.md | 54 +++++- scan-0.62.0/scan/R/add_l2.R | 2 scan-0.62.0/scan/R/as_scdf.R | 20 +- scan-0.62.0/scan/R/between_smd.R |only scan-0.62.0/scan/R/cdc.R | 24 +- scan-0.62.0/scan/R/corrected_tau.R | 9 - scan-0.62.0/scan/R/deprec-ranks.R | 11 + scan-0.62.0/scan/R/deprec-shift.R | 4 scan-0.62.0/scan/R/deprec-smooth_cases.R | 2 scan-0.62.0/scan/R/deprec-standardize.R | 8 scan-0.62.0/scan/R/deprecated.R | 87 ---------- scan-0.62.0/scan/R/design.R | 32 +-- scan-0.62.0/scan/R/export.R | 31 ++- scan-0.62.0/scan/R/export.sc_hplm.R | 4 scan-0.62.0/scan/R/export.sc_pet.R | 19 +- scan-0.62.0/scan/R/export.sc_trend.R | 8 scan-0.62.0/scan/R/hplm.R | 56 +++--- scan-0.62.0/scan/R/ird.R | 7 scan-0.62.0/scan/R/mplm.R | 17 + scan-0.62.0/scan/R/nap.R | 8 scan-0.62.0/scan/R/outlier.R | 41 ++-- scan-0.62.0/scan/R/overlap.R | 13 - scan-0.62.0/scan/R/pand.R | 29 ++- scan-0.62.0/scan/R/pet.R | 25 +- scan-0.62.0/scan/R/plm.R | 20 +- scan-0.62.0/scan/R/plot.scdf.R | 5 scan-0.62.0/scan/R/plot_rand.R | 79 ++++++--- scan-0.62.0/scan/R/print.sc_bcsmd.R |only scan-0.62.0/scan/R/print.sc_hplm.R | 25 +- scan-0.62.0/scan/R/print.sc_pet.R | 11 + scan-0.62.0/scan/R/print.sc_tauu.R | 1 scan-0.62.0/scan/R/print.sc_trend.R | 2 scan-0.62.0/scan/R/private-kendall-meta.R |only scan-0.62.0/scan/R/private-prepare_scdf.R |only scan-0.62.0/scan/R/private-regression.R |only scan-0.62.0/scan/R/private-utilities.R |only scan-0.62.0/scan/R/private_check.R | 91 ++++++++-- scan-0.62.0/scan/R/private_kendall.R | 85 --------- scan-0.62.0/scan/R/private_options.R | 8 scan-0.62.0/scan/R/private_options_mc.R | 10 - scan-0.62.0/scan/R/rand_test.R | 96 ++++++++--- scan-0.62.0/scan/R/random_scdf.R | 7 scan-0.62.0/scan/R/rescale.R |only scan-0.62.0/scan/R/scan.R | 1 scan-0.62.0/scan/R/scdf-functions.R | 12 + scan-0.62.0/scan/R/scdf.R | 14 + scan-0.62.0/scan/R/scdf_attr.R | 5 scan-0.62.0/scan/R/select_phases.R | 6 scan-0.62.0/scan/R/set_vars.R | 4 scan-0.62.0/scan/R/smd.R | 2 scan-0.62.0/scan/R/style_plot.R | 5 scan-0.62.0/scan/R/subset.scdf.R | 2 scan-0.62.0/scan/R/tau_u.R | 159 ++++++++++-------- scan-0.62.0/scan/R/transform.scdf.R | 14 - scan-0.62.0/scan/R/trend.R | 49 ++--- scan-0.62.0/scan/inst/CITATION | 6 scan-0.62.0/scan/inst/shiny/server.R | 26 ++- scan-0.62.0/scan/inst/shiny/ui.R | 2 scan-0.62.0/scan/man/add_l2.Rd | 3 scan-0.62.0/scan/man/as.data.frame.scdf.Rd | 1 scan-0.62.0/scan/man/as_scdf.Rd | 1 scan-0.62.0/scan/man/between_smd.Rd |only scan-0.62.0/scan/man/cdc.Rd | 23 +- scan-0.62.0/scan/man/deprecated-functions.Rd | 42 ---- scan-0.62.0/scan/man/design.Rd | 4 scan-0.62.0/scan/man/export.Rd | 2 scan-0.62.0/scan/man/fill_missing.Rd | 1 scan-0.62.0/scan/man/hplm.Rd | 29 ++- scan-0.62.0/scan/man/ird.Rd | 12 + scan-0.62.0/scan/man/mplm.Rd | 9 - scan-0.62.0/scan/man/na.omit.scdf.Rd |only scan-0.62.0/scan/man/nap.Rd | 8 scan-0.62.0/scan/man/outlier.Rd | 39 ++-- scan-0.62.0/scan/man/overlap.Rd | 13 - scan-0.62.0/scan/man/pand.Rd | 27 +-- scan-0.62.0/scan/man/pem.Rd | 1 scan-0.62.0/scan/man/pet.Rd | 13 - scan-0.62.0/scan/man/plm.Rd | 10 - scan-0.62.0/scan/man/plot.scdf.Rd | 6 scan-0.62.0/scan/man/plot_rand.Rd | 9 - scan-0.62.0/scan/man/pnd.Rd | 1 scan-0.62.0/scan/man/rand_test.Rd | 49 ++++- scan-0.62.0/scan/man/ranks.Rd | 12 + scan-0.62.0/scan/man/rescale.Rd |only scan-0.62.0/scan/man/scdf.Rd | 7 scan-0.62.0/scan/man/select_cases.Rd | 1 scan-0.62.0/scan/man/select_phases.Rd | 6 scan-0.62.0/scan/man/set_vars.Rd | 5 scan-0.62.0/scan/man/shift.Rd | 5 scan-0.62.0/scan/man/smd.Rd | 2 scan-0.62.0/scan/man/smooth_cases.Rd | 3 scan-0.62.0/scan/man/standardize.Rd | 9 - scan-0.62.0/scan/man/style_plot.Rd | 2 scan-0.62.0/scan/man/subset.scdf.Rd | 2 scan-0.62.0/scan/man/tau_u.Rd | 36 ++-- scan-0.62.0/scan/man/transform.scdf.Rd | 13 - scan-0.62.0/scan/man/trend.Rd | 11 - scan-0.62.0/scan/man/truncate_phase.Rd | 1 scan-0.62.0/scan/tests/testthat/test-rand_test.R |only scan-0.62.0/scan/tests/testthat/test-scdf.R |only scan-0.62.0/scan/tests/testthat/test-tau.R |only scan-0.62.0/scan/tests/testthat/test-trend.R |only 109 files changed, 1065 insertions(+), 846 deletions(-)
Title: Analyzing Partial Rankings in Networks
Description: Implements methods for centrality related analyses of networks.
While the package includes the possibility to build more than 20 indices,
its main focus lies on index-free assessment of centrality via partial
rankings obtained by neighborhood-inclusion or positional dominance. These
partial rankings can be analyzed with different methods, including
probabilistic methods like computing expected node ranks and relative
rank probabilities (how likely is it that a node is more central than another?).
The methodology is described in depth in the vignettes and in
Schoch (2018) <doi:10.1016/j.socnet.2017.12.003>.
Author: David Schoch [aut, cre] ,
Julian Mueller [ctb]
Maintainer: David Schoch <david@schochastics.net>
Diff between netrankr versions 1.2.3 dated 2023-12-19 and 1.2.4 dated 2025-02-05
DESCRIPTION | 8 MD5 | 71 ++--- NAMESPACE | 4 NEWS.md | 5 R/approximate.ranks.R | 20 - R/comparable.pairs.R | 4 R/hyperbolic.index.R | 12 R/indirect.relations.R | 36 +- R/majorization.gap.R | 2 R/mcmc.rank.R | 12 R/neighborhood.inclusion.R | 2 R/netswan.R |only R/rank.analysis.R | 16 - R/spectral.gap.R | 2 README.md | 131 +++++----- build/vignette.rds |binary inst/doc/benchmarks.html | 53 +--- inst/doc/centrality_indices.R | 136 +++++----- inst/doc/centrality_indices.html | 267 ++++++++++---------- inst/doc/indirect_relations.html | 181 +++++++------- inst/doc/neighborhood_inclusion.html | 197 +++++++-------- inst/doc/partial_centrality.html | 197 +++++++-------- inst/doc/positional_dominance.html | 171 ++++++------- inst/doc/probabilistic_cent.html | 175 ++++++------- inst/doc/threshold_graph.html | 216 ++++++++-------- inst/doc/use_case.html | 398 +++++++++++++++---------------- man/majorization_gap.Rd | 2 man/neighborhood_inclusion.Rd | 2 man/netrankr-package.Rd | 2 man/swan_closeness.Rd |only man/swan_combinatory.Rd |only man/swan_connectivity.Rd |only man/swan_efficiency.Rd |only tests/testthat/test-hyperbolic.index.R | 10 tests/testthat/test_dominance.R | 4 tests/testthat/test_helpers.R | 10 tests/testthat/test_indices.R | 18 - tests/testthat/test_indirect_relations.R | 22 - tests/testthat/test_threshold_graph.R | 6 39 files changed, 1201 insertions(+), 1191 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models, used in the computation of
marginal means, contrast analysis and predictions. For a list of supported models,
see 'insight::supported_models()'.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut]
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between modelbased versions 0.8.9 dated 2024-10-26 and 0.9.0 dated 2025-02-05
modelbased-0.8.9/modelbased/R/get_marginaleffects.R |only modelbased-0.8.9/modelbased/R/visualisation_recipe.estimate_grouplevel.R |only modelbased-0.8.9/modelbased/R/visualisation_recipe.estimate_means.R |only modelbased-0.8.9/modelbased/R/visualisation_recipe.estimate_predicted.R |only modelbased-0.8.9/modelbased/R/visualisation_recipe.estimate_slopes.R |only modelbased-0.8.9/modelbased/man/figures/gganimate_figure.gif |only modelbased-0.8.9/modelbased/man/figures/unnamed-chunk-17-1.png |only modelbased-0.8.9/modelbased/man/figures/unnamed-chunk-18-1.png |only modelbased-0.8.9/modelbased/man/figures/unnamed-chunk-4-1.png |only modelbased-0.8.9/modelbased/man/figures/unnamed-chunk-6-1.png |only modelbased-0.8.9/modelbased/man/find_inversions.Rd |only modelbased-0.8.9/modelbased/man/get_marginaleffects.Rd |only modelbased-0.8.9/modelbased/tests/testthat/test-get_marginaleffects.R |only modelbased-0.9.0/modelbased/DESCRIPTION | 24 modelbased-0.9.0/modelbased/MD5 | 172 +- modelbased-0.9.0/modelbased/NAMESPACE | 22 modelbased-0.9.0/modelbased/NEWS.md | 62 modelbased-0.9.0/modelbased/R/clean_names.R | 15 modelbased-0.9.0/modelbased/R/data.R |only modelbased-0.9.0/modelbased/R/describe_nonlinear.R | 8 modelbased-0.9.0/modelbased/R/estimate_contrast_methods.R |only modelbased-0.9.0/modelbased/R/estimate_contrasts.R | 190 +- modelbased-0.9.0/modelbased/R/estimate_grouplevel.R | 6 modelbased-0.9.0/modelbased/R/estimate_means.R | 259 +++- modelbased-0.9.0/modelbased/R/estimate_predicted.R | 269 ++-- modelbased-0.9.0/modelbased/R/estimate_slopes.R | 186 -- modelbased-0.9.0/modelbased/R/format.R |only modelbased-0.9.0/modelbased/R/get_emcontrasts.R | 140 +- modelbased-0.9.0/modelbased/R/get_emmeans.R | 251 +-- modelbased-0.9.0/modelbased/R/get_emtrends.R | 98 - modelbased-0.9.0/modelbased/R/get_marginalcontrasts.R | 399 +++++- modelbased-0.9.0/modelbased/R/get_marginaleffects_type.R |only modelbased-0.9.0/modelbased/R/get_marginalmeans.R | 343 ++++- modelbased-0.9.0/modelbased/R/get_marginaltrends.R |only modelbased-0.9.0/modelbased/R/print.R | 77 - modelbased-0.9.0/modelbased/R/print_html.R |only modelbased-0.9.0/modelbased/R/print_md.R | 10 modelbased-0.9.0/modelbased/R/reexports.R | 4 modelbased-0.9.0/modelbased/R/reshape_grouplevel.R | 14 modelbased-0.9.0/modelbased/R/smoothing.R | 5 modelbased-0.9.0/modelbased/R/standardize_methods.R | 6 modelbased-0.9.0/modelbased/R/summary.R |only modelbased-0.9.0/modelbased/R/table_footer.R |only modelbased-0.9.0/modelbased/R/utils.R | 29 modelbased-0.9.0/modelbased/R/visualisation_matrix.R | 42 modelbased-0.9.0/modelbased/R/visualisation_recipe.R |only modelbased-0.9.0/modelbased/R/visualisation_recipe_internal.R |only modelbased-0.9.0/modelbased/R/zero_crossings.R | 36 modelbased-0.9.0/modelbased/R/zzz.R |only modelbased-0.9.0/modelbased/README.md | 374 +++-- modelbased-0.9.0/modelbased/build/partial.rdb |only modelbased-0.9.0/modelbased/build/vignette.rds |binary modelbased-0.9.0/modelbased/data |only modelbased-0.9.0/modelbased/inst/WORDLIST | 21 modelbased-0.9.0/modelbased/inst/doc/overview_of_vignettes.Rmd | 18 modelbased-0.9.0/modelbased/inst/doc/overview_of_vignettes.html | 25 modelbased-0.9.0/modelbased/man/coffee_data.Rd |only modelbased-0.9.0/modelbased/man/describe_nonlinear.Rd | 2 modelbased-0.9.0/modelbased/man/efc.Rd |only modelbased-0.9.0/modelbased/man/estimate_contrasts.Rd | 230 ++- modelbased-0.9.0/modelbased/man/estimate_expectation.Rd | 129 +- modelbased-0.9.0/modelbased/man/estimate_grouplevel.Rd | 2 modelbased-0.9.0/modelbased/man/estimate_means.Rd | 218 ++- modelbased-0.9.0/modelbased/man/estimate_slopes.Rd | 97 + modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-10-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-11-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-13-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-14-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-15-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-16-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-3-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-5-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-7-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-8-1.png |binary modelbased-0.9.0/modelbased/man/figures/unnamed-chunk-9-1.png |binary modelbased-0.9.0/modelbased/man/fish.Rd |only modelbased-0.9.0/modelbased/man/get_emmeans.Rd | 383 ++++-- modelbased-0.9.0/modelbased/man/reexports.Rd | 3 modelbased-0.9.0/modelbased/man/visualisation_matrix.Rd | 33 modelbased-0.9.0/modelbased/man/visualisation_recipe.estimate_predicted.Rd | 332 ++--- modelbased-0.9.0/modelbased/man/zero_crossings.Rd | 14 modelbased-0.9.0/modelbased/tests/testthat/test-attributes_estimatefun.R |only modelbased-0.9.0/modelbased/tests/testthat/test-attributes_visualisation.R | 18 modelbased-0.9.0/modelbased/tests/testthat/test-brms-marginaleffects.R |only modelbased-0.9.0/modelbased/tests/testthat/test-brms.R | 15 modelbased-0.9.0/modelbased/tests/testthat/test-estimate_contrasts.R | 637 +++++++++- modelbased-0.9.0/modelbased/tests/testthat/test-estimate_contrasts_methods.R |only modelbased-0.9.0/modelbased/tests/testthat/test-estimate_expectation.R | 65 - modelbased-0.9.0/modelbased/tests/testthat/test-estimate_grouplevel.R | 2 modelbased-0.9.0/modelbased/tests/testthat/test-estimate_means.R | 426 +++++- modelbased-0.9.0/modelbased/tests/testthat/test-estimate_means_counterfactuals.R |only modelbased-0.9.0/modelbased/tests/testthat/test-estimate_means_mixed.R |only modelbased-0.9.0/modelbased/tests/testthat/test-estimate_predicted.R | 47 modelbased-0.9.0/modelbased/tests/testthat/test-estimate_slopes.R | 57 modelbased-0.9.0/modelbased/tests/testthat/test-g_computation.R |only modelbased-0.9.0/modelbased/tests/testthat/test-get_marginaltrends.R |only modelbased-0.9.0/modelbased/tests/testthat/test-glmmTMB.R | 95 + modelbased-0.9.0/modelbased/tests/testthat/test-mgcv.R | 67 - modelbased-0.9.0/modelbased/tests/testthat/test-ordinal.R |only modelbased-0.9.0/modelbased/tests/testthat/test-plot-facet.R |only modelbased-0.9.0/modelbased/tests/testthat/test-plot.R |only modelbased-0.9.0/modelbased/tests/testthat/test-predict-dpar.R |only modelbased-0.9.0/modelbased/tests/testthat/test-print.R |only modelbased-0.9.0/modelbased/tests/testthat/test-table_footer.R |only modelbased-0.9.0/modelbased/tests/testthat/test-transform_response.R |only modelbased-0.9.0/modelbased/tests/testthat/test-vcov.R |only modelbased-0.9.0/modelbased/tests/testthat/test-verbose.R |only modelbased-0.9.0/modelbased/tests/testthat/test-visualisation_recipe.R |only modelbased-0.9.0/modelbased/vignettes/overview_of_vignettes.Rmd | 18 109 files changed, 4017 insertions(+), 1978 deletions(-)
Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the
Multi-format archive and compression library. Offers R connections and
direct extraction for many archive formats including 'tar', 'ZIP',
'7-zip', 'RAR', 'CAB' and compression formats including 'gzip',
'bzip2', 'compress', 'lzma' and 'xz'.
Author: Jim Hester [aut] ,
Gabor Csardi [aut, cre],
Ondrej Holy [cph] ,
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between archive versions 1.1.10 dated 2024-11-08 and 1.1.11 dated 2025-02-05
DESCRIPTION | 8 ++-- MD5 | 60 +++++++++++++++++----------------- NEWS.md | 4 ++ R/archive.R | 14 +++++-- R/archive_extract.R | 4 +- R/archive_read.R | 4 +- R/archive_write.R | 6 +-- R/archive_write_dir.R | 4 +- R/archive_write_files.R | 4 +- R/cpp11.R | 24 ++++++------- R/file_read.R | 4 +- R/file_write.R | 4 +- man/archive.Rd | 4 +- man/archive_extract.Rd | 5 ++ man/archive_read.Rd | 5 ++ man/archive_write.Rd | 5 ++ man/archive_write_files.Rd | 6 ++- man/file_connections.Rd | 18 +++++++++- src/archive.cpp | 6 ++- src/archive_extract.cpp | 5 ++ src/archive_read.cpp | 6 +++ src/archive_write.cpp | 6 +++ src/archive_write_direct.cpp | 6 +++ src/archive_write_files.cpp | 5 ++ src/cpp11.cpp | 48 +++++++++++++-------------- src/r_archive.h | 1 tests/testthat/helper-mock.R |only tests/testthat/helpers.R |only tests/testthat/test-archive.R | 20 +++++++++++ tests/testthat/test-archive_extract.R | 17 +++++++++ tests/testthat/test-archive_read.R | 1 tests/testthat/test-archive_write.R | 2 + 32 files changed, 209 insertions(+), 97 deletions(-)
Title: Bayesian Penalized Quantile Regression
Description: The quantile varying coefficient model is robust to data heterogeneity,
outliers and heavy-tailed distributions in the response variable. In addition,
it can flexibly model dynamic patterns of regression coefficients through
nonparametric varying coefficient functions. In this package, we have implemented
the Gibbs samplers of the penalized Bayesian quantile varying coefficient model with
spike-and-slab priors [Zhou et al.(2023)]<doi:10.1016/j.csda.2023.107808> for efficient
Bayesian shrinkage estimation, variable selection and statistical inference. In particular,
valid Bayesian inferences on sparse quantile varying coefficient functions can be validated
on finite samples. The Markov Chain Monte Carlo (MCMC) algorithms of the proposed
and alternative models can be efficiently performed by using the package.
Author: Kun Fan [aut],
Cen Wu [aut, cre],
Jie Ren [aut],
Fei Zhou [aut]
Maintainer: Cen Wu <wucen@ksu.edu>
Diff between pqrBayes versions 1.0.4 dated 2025-01-24 and 1.0.5 dated 2025-02-05
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- README.md | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Performs Quality Control, Data Normalization, and Batch Effect
Correction for 'NanoString nCounter' Data
Description: Provides quality control (QC), normalization, and batch
effect correction operations for 'NanoString nCounter' data, Talhouk
et al. (2016) <doi:10.1371/journal.pone.0153844>. Various metrics are
used to determine which samples passed or failed QC. Gene expression
should first be normalized to housekeeping genes, before a
reference-based approach is used to adjust for batch effects. Raw
NanoString data can be imported in the form of Reporter Code Count
(RCC) files.
Author: Derek Chiu [aut, cre] ,
Aline Talhouk [aut] ,
Samuel Leung [aut]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between nanostringr versions 0.4.2 dated 2024-06-11 and 0.5.0 dated 2025-02-05
DESCRIPTION | 10 ++-- MD5 | 32 ++++++------- NEWS.md | 6 ++ R/NanoStringQC.R | 2 R/normalize_pools.R | 36 ++++++++------ R/normalize_random.R | 20 ++++---- R/read_rcc.R | 2 R/utils.R | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview.R | 2 inst/doc/Overview.Rmd | 102 ------------------------------------------ inst/doc/Overview.html | 106 ++++++-------------------------------------- man/normalize_pools.Rd | 4 - man/normalize_random.Rd | 10 ++-- tests/testthat/test-order.R | 5 -- vignettes/Overview.Rmd | 102 ------------------------------------------ 17 files changed, 87 insertions(+), 353 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] ,
yoonkyoung Chun [aut],
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.5.8 dated 2025-01-08 and 0.5.10 dated 2025-02-05
DESCRIPTION | 11 - MD5 | 22 +-- NAMESPACE | 2 NEWS.md | 10 + R/adjustedLR.R |only R/jskm.R | 366 +++++++++++++++++++++++++++++++++-------------------- R/svyjskm.R | 4 inst/doc/jskm.R | 2 inst/doc/jskm.Rmd | 2 inst/doc/jskm.html | 175 ++----------------------- man/adjusted.LR.Rd |only man/jskm.Rd | 2 vignettes/jskm.Rmd | 2 13 files changed, 284 insertions(+), 314 deletions(-)
Title: Corrected Test Statistics for Comparing Machine Learning Models
on Correlated Samples
Description: Calculate a set of corrected test statistics for cases when samples
are not independent, such as when classification accuracy values are obtained
over resamples or through k-fold cross-validation, as proposed by Nadeau and Bengio (2003) <doi:10.1023/A:1024068626366>
and presented in Bouckaert and Frank (2004) <doi:10.1007/978-3-540-24775-3_3>.
Author: Trent Henderson [cre, aut]
Maintainer: Trent Henderson <then6675@uni.sydney.edu.au>
Diff between correctR versions 0.2.1 dated 2024-03-13 and 0.3.1 dated 2025-02-05
DESCRIPTION | 10 LICENSE | 2 MD5 | 42 - NAMESPACE | 14 R/correctR.R | 20 R/kfold_ttest.R | 152 ++--- R/repkfold_ttest.R | 198 +++--- R/resampled_ttest.R | 158 ++--- R/zzz.R | 10 README.md | 101 +-- build/vignette.rds |binary inst/doc/correctR.R | 92 +-- inst/doc/correctR.Rmd | 252 ++++---- inst/doc/correctR.html | 1100 +++++++++++++++++++------------------- man/correctR.Rd | 20 man/kfold_ttest.Rd | 82 +- man/repkfold_ttest.Rd | 94 +-- man/resampled_ttest.Rd | 86 +- tests/testthat.R | 24 tests/testthat/helper-core_data.R | 24 tests/testthat/test-correctR.R | 30 - vignettes/correctR.Rmd | 252 ++++---- 22 files changed, 1377 insertions(+), 1386 deletions(-)
Title: Diverse Cluster Ensemble in R
Description: Performs cluster analysis using an ensemble clustering
framework, Chiu & Talhouk (2018) <doi:10.1186/s12859-017-1996-y>.
Results from a diverse set of algorithms are pooled together using
methods such as majority voting, K-Modes, LinkCluE, and CSPA. There
are options to compare cluster assignments across algorithms using
internal and external indices, visualizations such as heatmaps, and
significance testing for the existence of clusters.
Author: Derek Chiu [aut, cre],
Aline Talhouk [aut],
Johnson Liu [ctb, com]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between diceR versions 2.2.0 dated 2024-01-22 and 3.0.0 dated 2025-02-05
DESCRIPTION | 24 ++-- MD5 | 46 ++++---- NEWS.md | 7 + R/algorithms.R | 35 ++++-- R/consensus_cluster.R | 7 + R/consensus_evaluate.R | 78 ++++++-------- R/dice.R | 21 ++- R/graphs.R | 136 ++++++++++++++++++------ R/utils.R | 9 + README.md | 33 ++++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/overview.R | 28 +++-- inst/doc/overview.Rmd | 25 +++- inst/doc/overview.html | 175 ++++++++++++++++++++++---------- man/dice.Rd | 15 +- man/min_fnorm.Rd | 1 tests/testthat.R | 8 + tests/testthat/test-consensus_cluster.R | 18 +-- tests/testthat/test-consensus_funs.R | 6 - tests/testthat/test-dice.R | 100 ++++++++++++++---- tests/testthat/test-graphs.R | 19 ++- tests/testthat/test-utils.R | 2 vignettes/overview.Rmd | 25 +++- 24 files changed, 555 insertions(+), 263 deletions(-)
Title: Estimate Real-Time Case Counts and Time-Varying Epidemiological
Parameters
Description: Estimates the time-varying reproduction number,
rate of spread, and doubling time using a range of open-source tools
(Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and
current best practices (Gostic et al. (2020)
<doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some
of the limitations of naive implementations in a framework that is
informed by community feedback and is actively supported.
Author: Sam Abbott [aut] ,
Joel Hellewell [aut] ,
Katharine Sherratt [aut],
Katelyn Gostic [aut],
Joe Hickson [aut],
Hamada S. Badr [aut] ,
Michael DeWitt [aut] ,
James M. Azam [aut] ,
Robin Thompson [ctb],
Sophie Meakin [ctb],
James Munday [ctb],
Nikos Boss [...truncated...]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between EpiNow2 versions 1.6.1 dated 2024-10-31 and 1.7.0 dated 2025-02-05
EpiNow2-1.6.1/EpiNow2/inst/stan/data/generation_time.stan |only EpiNow2-1.6.1/EpiNow2/man/create_complete_cases.Rd |only EpiNow2-1.7.0/EpiNow2/DESCRIPTION | 6 EpiNow2-1.7.0/EpiNow2/MD5 | 386 EpiNow2-1.7.0/EpiNow2/NAMESPACE | 7 EpiNow2-1.7.0/EpiNow2/NEWS.md | 45 EpiNow2-1.7.0/EpiNow2/R/checks.R | 38 EpiNow2-1.7.0/EpiNow2/R/create.R | 417 EpiNow2-1.7.0/EpiNow2/R/deprecated.R | 12 EpiNow2-1.7.0/EpiNow2/R/dist_spec.R | 228 EpiNow2-1.7.0/EpiNow2/R/epinow-internal.R | 10 EpiNow2-1.7.0/EpiNow2/R/epinow.R | 64 EpiNow2-1.7.0/EpiNow2/R/estimate_infections.R | 114 EpiNow2-1.7.0/EpiNow2/R/estimate_secondary.R | 101 EpiNow2-1.7.0/EpiNow2/R/estimate_truncation.R | 17 EpiNow2-1.7.0/EpiNow2/R/extract.R | 55 EpiNow2-1.7.0/EpiNow2/R/fit.R | 6 EpiNow2-1.7.0/EpiNow2/R/get.R | 17 EpiNow2-1.7.0/EpiNow2/R/opts.R | 342 EpiNow2-1.7.0/EpiNow2/R/plot.R | 23 EpiNow2-1.7.0/EpiNow2/R/preprocessing.R |only EpiNow2-1.7.0/EpiNow2/R/regional_epinow.R | 36 EpiNow2-1.7.0/EpiNow2/R/report.R | 34 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Title: Classes and Methods for "Class Comparison" Problems on
Microarrays
Description: Defines the classes used for "class comparison" problems
in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class
comparison includes tests for differential expression; see Simon's
book for details on typical problem types.
Author: Kevin R. Coombes [aut, cre]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between ClassComparison versions 3.3.2 dated 2024-08-17 and 3.3.5 dated 2025-02-05
ClassComparison-3.3.2/ClassComparison/tests/testDiff.R |only ClassComparison-3.3.2/ClassComparison/tests/testDiff.Rout.save |only ClassComparison-3.3.5/ClassComparison/DESCRIPTION | 8 ++++---- ClassComparison-3.3.5/ClassComparison/MD5 | 10 ++++------ ClassComparison-3.3.5/ClassComparison/R/cc01-ttest.R | 4 ++-- ClassComparison-3.3.5/ClassComparison/R/cc03-fastlm.R | 4 ++-- ClassComparison-3.3.5/ClassComparison/inst/doc/oompa-cc.pdf |binary 7 files changed, 12 insertions(+), 14 deletions(-)
More information about ClassComparison at CRAN
Permanent link
Title: Fast Searching for Multiple Keywords in Multiple Texts
Description: Aho-Corasick is an optimal algorithm for finding many
keywords in a text. It can locate all matches in a text in O(N+M) time; i.e.,
the time needed scales linearly with the number of keywords (N) and the size of
the text (M). Compare this to the naive approach which takes O(N*M) time to loop
through each pattern and scan for it in the text. This implementation builds the
trie (the generic name of the data structure) and runs the search in a single
function call. If you want to search multiple texts with the same trie, the
function will take a list or vector of texts and return a list of matches to
each text. By default, all 128 ASCII characters are allowed in both the keywords
and the text. A more efficient trie is possible if the alphabet size can be
reduced. For example, DNA sequences use at most 19 distinct characters and
usually only 4; protein sequences use at most 26 distinct characters and usually
only 20. UTF-8 (Unicode) matching is not currently supported.
Author: Matt Chambers [aut, cre],
Tomas Petricek [aut, cph],
Vanderbilt University [cph]
Maintainer: Matt Chambers <matt.chambers42@gmail.com>
Diff between AhoCorasickTrie versions 0.1.2 dated 2020-09-29 and 0.1.3 dated 2025-02-04
DESCRIPTION | 12 +++----- MD5 | 20 +++++++------- R/AhoCorasickTrie.R | 2 - R/RcppExports.R | 4 +- man/AhoCorasickSearch.Rd | 2 - man/AhoCorasickSearchList.Rd | 2 - man/AhoCorasickTrie.Rd | 23 ++++++++++++++++ src/AhoCorasickTrie.cpp | 60 +++++++++++++++++++++---------------------- src/RcppExports.cpp | 5 +++ tests/AhoCorasickTrieTests.R | 16 +++++------ tests/benchmark.R | 16 +++++------ 11 files changed, 94 insertions(+), 68 deletions(-)
More information about AhoCorasickTrie at CRAN
Permanent link
Title: Simulating Realistic Gene Expression and Clinical Data
Description: The Ultimate Microrray Prediction, Reality and Inference
Engine (UMPIRE) is a package to facilitate the simulation of realistic
microarray data sets with links to associated outcomes. See Zhang and
Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>. Version 2.0 adds the
ability to simulate realistic mixed-typed clinical data.
Author: Kevin R. Coombes [aut, cre],
Jiexin Zhang [aut],
Caitlin E. Coombes [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Umpire versions 2.0.10 dated 2020-11-10 and 2.0.11 dated 2025-02-04
Umpire-2.0.10/Umpire/tests/t02-indLogNorm.R |only Umpire-2.0.10/Umpire/tests/t02-indLogNorm.Rout.save |only Umpire-2.0.11/Umpire/DESCRIPTION | 18 Umpire-2.0.11/Umpire/MD5 | 16 Umpire-2.0.11/Umpire/build/vignette.rds |binary Umpire-2.0.11/Umpire/inst/doc/Umpire.pdf |binary Umpire-2.0.11/Umpire/inst/doc/Umpire2.R | 2 Umpire-2.0.11/Umpire/inst/doc/Umpire2.html | 441 +++++++++--------- Umpire-2.0.11/Umpire/inst/doc/surv.html | 470 +++++++++----------- Umpire-2.0.11/Umpire/man/e31-setDataTypes.Rd | 2 10 files changed, 471 insertions(+), 478 deletions(-)
Title: Estimates and Plots Single-Level and Multilevel Latent Class
Models
Description: Efficiently estimates single- and multilevel latent class models with covariates, allowing for output visualization in all specifications. For more technical details, see Lyrvall et al (2023) <doi:10.48550/arXiv.2305.07276>.
Author: Roberto Di Mari [aut, cre],
Johan Lyrvall [aut],
Zsuzsa Bakk [ctb],
Jennifer Oser [ctb],
Jouni Kuha [ctb]
Maintainer: Roberto Di Mari <roberto.dimari@unict.it>
Diff between multilevLCA versions 1.5.2 dated 2024-10-12 and 2.0.0 dated 2025-02-04
DESCRIPTION | 10 MD5 | 24 NAMESPACE | 7 R/MLCAfunctions.R | 7078 ++++++++++++++++++++++++++------------------------ R/RcppExports.R | 44 build/partial.rdb |binary data/dataIEA.rda |binary data/dataTOY.rda |binary man/multiLCA.Rd | 47 src/LCAfit.cpp | 845 +++-- src/Makevars | 1 src/RcppExports.cpp | 233 + src/multilevLC_EM.cpp | 3450 +++++++++++++++++++++++- 13 files changed, 7985 insertions(+), 3754 deletions(-)
Title: Meta-Analysis Datasets
Description: A collection of meta-analysis datasets for teaching purposes, illustrating/testing meta-analytic methods, and validating published analyses.
Author: Wolfgang Viechtbauer [aut, cre]
,
Thomas White [aut] ,
Daniel Noble [aut] ,
Alistair Senior [aut] ,
W. Kyle Hamilton [aut] ,
Guido Schwarzer [dtc]
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>
Diff between metadat versions 1.2-0 dated 2022-04-06 and 1.4-0 dated 2025-02-04
DESCRIPTION | 28 ++-- MD5 | 216 +++++++++++++++++-------------- NEWS.md | 6 R/datsearch.r | 10 + README.md | 2 build/metadat.pdf |binary build/stage23.rdb |only data/dat.assink2016.rda |binary data/dat.bartos2023.rda |only data/dat.bassler2004.rda |only data/dat.crisafulli2020.rda |only data/dat.curtin2002.rda |only data/dat.dumouchel1994.rda |only data/dat.furukawa2003.rda |only data/dat.kalaian1996.rda |binary data/dat.roever2022.rda |only data/dat.spooner2002.rda |only data/dat.ursino2021.rda |only inst/help.rdata |binary man/dat.aloe2013.Rd | 2 man/dat.anand1999.Rd | 5 man/dat.assink2016.Rd | 19 ++ man/dat.axfors2021.Rd | 5 man/dat.bakdash2021.Rd | 7 - man/dat.baker2009.Rd | 16 -- man/dat.bangertdrowns2004.Rd | 5 man/dat.bartos2023.Rd |only man/dat.baskerville2012.Rd | 5 man/dat.bassler2004.Rd |only man/dat.bcg.Rd | 9 - man/dat.begg1989.Rd | 5 man/dat.berkey1998.Rd | 9 - man/dat.besson2016.Rd | 2 man/dat.bonett2010.Rd | 8 - man/dat.bornmann2007.Rd | 5 man/dat.bourassa1996.Rd | 33 ++++ man/dat.cannon2006.Rd | 9 - man/dat.cohen1981.Rd | 7 - man/dat.colditz1994.Rd | 9 - man/dat.collins1985a.Rd | 5 man/dat.collins1985b.Rd | 5 man/dat.craft2003.Rd | 7 - man/dat.crede2010.Rd | 5 man/dat.crisafulli2020.Rd |only man/dat.curtin2002.Rd |only man/dat.curtis1998.Rd | 7 - man/dat.dagostino1998.Rd | 7 - man/dat.damico2009.Rd | 5 man/dat.debruin2009.Rd | 5 man/dat.dogliotti2014.Rd | 14 -- man/dat.dong2013.Rd | 14 -- man/dat.dorn2007.Rd | 9 - man/dat.dumouchel1994.Rd |only man/dat.egger2001.Rd | 5 man/dat.fine1993.Rd | 23 +-- man/dat.franchini2012.Rd | 11 - man/dat.frank2008.Rd | 9 - man/dat.furukawa2003.Rd |only man/dat.gibson2002.Rd | 5 man/dat.graves2010.Rd | 5 man/dat.gurusamy2011.Rd | 14 -- man/dat.hackshaw1998.Rd | 15 +- man/dat.hahn2001.Rd | 7 - man/dat.hannum2020.Rd | 5 man/dat.hart1999.Rd | 11 - man/dat.hartmannboyce2018.Rd | 5 man/dat.hasselblad1998.Rd | 15 -- man/dat.hine1989.Rd | 5 man/dat.ishak2007.Rd | 7 - man/dat.kalaian1996.Rd | 17 +- man/dat.kearon1998.Rd | 16 +- man/dat.knapp2017.Rd | 7 - man/dat.konstantopoulos2011.Rd | 21 +-- man/dat.landenberger2005.Rd | 5 man/dat.laopaiboon2015.Rd | 5 man/dat.lau1992.Rd | 17 +- man/dat.lee2004.Rd | 5 man/dat.lehmann2018.Rd | 14 -- man/dat.li2007.Rd | 5 man/dat.lim2014.Rd | 5 man/dat.linde2005.Rd | 7 - man/dat.linde2015.Rd | 16 +- man/dat.linde2016.Rd | 16 +- man/dat.lopez2019.Rd | 14 +- man/dat.maire2019.Rd | 7 - man/dat.mccurdy2020.Rd | 13 - man/dat.mcdaniel1994.Rd | 21 ++- man/dat.michael2013.Rd | 2 man/dat.molloy2014.Rd | 7 - man/dat.moura2021.Rd | 5 man/dat.nakagawa2007.Rd | 4 man/dat.nielweise2007.Rd | 5 man/dat.nielweise2008.Rd | 5 man/dat.normand1999.Rd | 5 man/dat.obrien2003.Rd | 9 - man/dat.pagliaro1992.Rd | 7 - man/dat.pignon2000.Rd | 5 man/dat.pritz1997.Rd | 28 +++- man/dat.raudenbush1985.Rd | 5 man/dat.riley2003.Rd | 5 man/dat.roever2022.Rd |only man/dat.senn2013.Rd | 21 +-- man/dat.spooner2002.Rd |only man/dat.stowe2010.Rd | 14 -- man/dat.tannersmith2016.Rd | 5 man/dat.ursino2021.Rd |only man/dat.vanhowe1999.Rd | 5 man/dat.viechtbauer2021.Rd | 22 +-- man/dat.white2020.Rd | 2 man/dat.woods2010.Rd | 11 - man/dat.yusuf1985.Rd | 5 man/datsearch.Rd | 4 tests/testthat/test_dat.assink2016.r | 2 tests/testthat/test_dat.bartos2023.r |only tests/testthat/test_dat.bassler2004.r |only tests/testthat/test_dat.crisafulli2020.r |only tests/testthat/test_dat.curtin2002.r |only tests/testthat/test_dat.dumouchel1994.r |only tests/testthat/test_dat.furukawa2003.r |only tests/testthat/test_dat.kalaian1996.r | 2 tests/testthat/test_dat.roever2022.r |only tests/testthat/test_dat.spooner2002.r |only tests/testthat/test_dat.ursino2021.r |only 123 files changed, 530 insertions(+), 513 deletions(-)
Title: Individual Dose Optimization using Population Pharmacokinetics
Description: Personalize drug regimens using individual pharmacokinetic (PK) and
pharmacokinetic-pharmacodynamic (PK-PD) profiles. By combining therapeutic
drug monitoring (TDM) data with a population model, 'posologyr' offers
accurate posterior estimates and helps compute optimal individualized dosing
regimens. The empirical Bayes estimates are computed following the method
described by Kang et al. (2012) <doi:10.4196/kjpp.2012.16.2.97>.
Author: Cyril Leven [aut, cre, cph] ,
Matthew Fidler [ctb] ,
Emmanuelle Comets [ctb],
Audrey Lavenu [ctb],
Marc Lavielle [ctb]
Maintainer: Cyril Leven <cyril.leven@chu-brest.fr>
Diff between posologyr versions 1.2.7 dated 2024-09-13 and 1.2.8 dated 2025-02-04
DESCRIPTION | 19 +++++++++---------- MD5 | 6 +++--- NEWS.md | 5 ++++- tests/testthat/test_doseoptim_tdm.R | 2 +- 4 files changed, 17 insertions(+), 15 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.5.0 dated 2025-01-09 and 0.5.1 dated 2025-02-04
DESCRIPTION | 6 - MD5 | 20 ++-- NAMESPACE | 2 R/heatmap.R | 16 +-- R/sankeyplot.R | 218 +++++++++++++++++++++++++++++++++++------------ R/volcanoplot.R | 29 ++++-- README.md | 32 +++--- man/SankeyPlotAtomic.Rd | 24 ++--- man/VolcanoPlot.Rd | 9 + man/VolcanoPlotAtomic.Rd | 9 + man/sankeyplot.Rd | 78 +++++++++------- 11 files changed, 297 insertions(+), 146 deletions(-)
Title: Robust and Flexible Model-Based Clustering for Data Sets with
Missing Values at Random
Description: Implementations of various robust and flexible model-based clustering methods for data sets with missing values at random.
Two main models are: Multivariate Contaminated Normal Mixture (MCNM, Tong and Tortora, 2022, <doi:10.1007/s11634-021-00476-1>) and
Multivariate Generalized Hyperbolic Mixture (MGHM, Wei et al., 2019, <doi:10.1016/j.csda.2018.08.016>). Mixtures via some special or limiting
cases of the multivariate generalized hyperbolic distribution are also included: Normal-Inverse Gaussian, Symmetric Normal-Inverse Gaussian,
Skew-Cauchy, Cauchy, Skew-t, Student's t, Normal, Symmetric Generalized Hyperbolic, Hyperbolic Univariate Marginals,
Hyperbolic, and Symmetric Hyperbolic.
Author: Hung Tong [aut, cre],
Cristina Tortora [aut, ths, dgs]
Maintainer: Hung Tong <hungtongmx@gmail.com>
Diff between MixtureMissing versions 3.0.3 dated 2024-10-15 and 3.0.4 dated 2025-02-04
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/dist_Norm.R | 32 -------------------------------- R/dist_Skew_t.R | 32 -------------------------------- 4 files changed, 6 insertions(+), 70 deletions(-)
More information about MixtureMissing at CRAN
Permanent link
Title: Get and Modify 'oTree' Data
Description: Efficiently manage and process data from 'oTree' experiments.
Import 'oTree' data and clean them by using functions that handle
messy data, dropouts, and other problematic cases. Create IDs,
calculate the time, transfer variables between app data frames, and
delete sensitive information. Review your experimental data prior to
running the experiment and automatically generate a detailed summary
of the variables used in your 'oTree' code. Information on 'oTree' is
found in Chen, D. L., Schonger, M., & Wickens, C. (2016)
<doi:10.1016/j.jbef.2015.12.001>.
Author: Patricia F. Zauchner [aut, trl, cre, cph]
Maintainer: Patricia F. Zauchner <patricia.zauchner@gmx.at>
Diff between gmoTree versions 1.4.0 dated 2025-02-04 and 1.4.1 dated 2025-02-04
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------- NEWS.md | 5 ++++ R/codebook.R | 2 - inst/CITATION | 6 ++--- inst/doc/intro_to_gmoTree.html | 18 ++++++++--------- inst/pkgdown.yml | 2 - tests/testthat/tests_codebook.R | 41 +++++++++++++++++++++++++++++----------- 8 files changed, 59 insertions(+), 35 deletions(-)
Title: Constrained, Covariance-Matching Constrained and Universal Point
or Block Kriging
Description: Provides functions for efficient computation of non-linear spatial predictions with local change of support (Hofer, C. and Papritz, A. (2011) "constrainedKriging: An R-package for customary, constrained and covariance-matching constrained point or block kriging" <doi:10.1016/j.cageo.2011.02.009>). This package supplies functions for two-dimensional spatial interpolation by constrained (Cressie, N. (1993) "Aggregation in geostatistical problems" <doi:10.1007/978-94-011-1739-5_3>), covariance-matching constrained (Aldworth, J. and Cressie, N. (2003) "Prediction of nonlinear spatial functionals" <doi:10.1016/S0378-3758(02)00321-X>) and universal (external drift) Kriging for points or blocks of any shape from data with a non-stationary mean function and an isotropic weakly stationary covariance function. The linear spatial interpolation methods, constrained and covariance-matching constrained Kriging, provide approximately unbiased prediction for non-linear target value [...truncated...]
Author: Christoph Hofer [aut],
Andreas Papritz [ctb, cre]
Maintainer: Andreas Papritz <papritz@retired.ethz.ch>
Diff between constrainedKriging versions 0.2-10 dated 2025-02-01 and 0.2-11 dated 2025-02-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/ChangeLog.txt | 6 +++++- src/point_block_cov.c | 13 +++++++------ 4 files changed, 19 insertions(+), 14 deletions(-)
More information about constrainedKriging at CRAN
Permanent link
Title: Collection of Methods Constructed using Kernel-Based Quadratic
Distances
Description: It includes test for multivariate normality, test for uniformity on the d-dimensional
Sphere, non-parametric two- and k-sample tests, random generation of points from the Poisson
kernel-based density and clustering algorithm for spherical data. For more information see
Saraceno G., Markatou M., Mukhopadhyay R. and Golzy M. (2024)
<doi:10.48550/arXiv.2402.02290>
Markatou, M. and Saraceno, G. (2024) <doi:10.48550/arXiv.2407.16374>,
Ding, Y., Markatou, M. and Saraceno, G. (2023) <doi:10.5705/ss.202022.0347>,
and Golzy, M. and Markatou, M. (2020) <doi:10.1080/10618600.2020.1740713>.
Author: Giovanni Saraceno [aut, cre] ,
Marianthi Markatou [aut],
Raktim Mukhopadhyay [aut],
Mojgan Golzy [aut],
Hingee Kassel [rev],
Emi Tanaka [rev]
Maintainer: Giovanni Saraceno <giovanni.saraceno@unipd.it>
Diff between QuadratiK versions 1.1.2 dated 2024-10-29 and 1.1.3 dated 2025-02-04
QuadratiK-1.1.2/QuadratiK/tests/testthat/Rplots.pdf |only QuadratiK-1.1.3/QuadratiK/DESCRIPTION | 26 - QuadratiK-1.1.3/QuadratiK/MD5 | 127 +++---- QuadratiK-1.1.3/QuadratiK/NAMESPACE | 130 ++++--- QuadratiK-1.1.3/QuadratiK/NEWS.md | 41 ++ QuadratiK-1.1.3/QuadratiK/R/QuadratiK-package.R | 5 QuadratiK-1.1.3/QuadratiK/R/RcppExports.R | 20 - QuadratiK-1.1.3/QuadratiK/R/breast_cancer.R | 2 QuadratiK-1.1.3/QuadratiK/R/classes.R | 10 QuadratiK-1.1.3/QuadratiK/R/clustering_functions.R | 137 ++++---- QuadratiK-1.1.3/QuadratiK/R/critical_value.R | 12 QuadratiK-1.1.3/QuadratiK/R/h_selection.R | 16 QuadratiK-1.1.3/QuadratiK/R/kb.test.R | 29 - QuadratiK-1.1.3/QuadratiK/R/pk.test.R | 32 + QuadratiK-1.1.3/QuadratiK/R/pkbd_functions.R | 29 - QuadratiK-1.1.3/QuadratiK/R/srr-stats-standards.R | 1 QuadratiK-1.1.3/QuadratiK/R/utility.R | 19 - QuadratiK-1.1.3/QuadratiK/R/wine.R | 2 QuadratiK-1.1.3/QuadratiK/R/wireless.R | 2 QuadratiK-1.1.3/QuadratiK/README.md | 21 - QuadratiK-1.1.3/QuadratiK/inst/CITATION | 2 QuadratiK-1.1.3/QuadratiK/inst/doc/Introduction.R | 30 - QuadratiK-1.1.3/QuadratiK/inst/doc/Introduction.Rmd | 38 +- QuadratiK-1.1.3/QuadratiK/inst/doc/Introduction.html | 124 +++---- QuadratiK-1.1.3/QuadratiK/inst/doc/TwoSample_test.R | 28 - QuadratiK-1.1.3/QuadratiK/inst/doc/TwoSample_test.Rmd | 14 QuadratiK-1.1.3/QuadratiK/inst/doc/TwoSample_test.html | 16 QuadratiK-1.1.3/QuadratiK/inst/doc/generate_rpkb.R | 34 -- QuadratiK-1.1.3/QuadratiK/inst/doc/generate_rpkb.Rmd | 26 - QuadratiK-1.1.3/QuadratiK/inst/doc/generate_rpkb.html | 203 +++++++----- QuadratiK-1.1.3/QuadratiK/inst/doc/kSample_test.R | 22 - QuadratiK-1.1.3/QuadratiK/inst/doc/kSample_test.Rmd | 10 QuadratiK-1.1.3/QuadratiK/inst/doc/kSample_test.html | 12 QuadratiK-1.1.3/QuadratiK/inst/doc/uniformity.R | 16 QuadratiK-1.1.3/QuadratiK/inst/doc/uniformity.Rmd | 8 QuadratiK-1.1.3/QuadratiK/inst/doc/uniformity.html | 8 QuadratiK-1.1.3/QuadratiK/inst/doc/wireless_clustering.R | 16 QuadratiK-1.1.3/QuadratiK/inst/doc/wireless_clustering.Rmd | 8 QuadratiK-1.1.3/QuadratiK/inst/doc/wireless_clustering.html | 26 - QuadratiK-1.1.3/QuadratiK/man/QuadratiK-package.Rd | 11 QuadratiK-1.1.3/QuadratiK/man/dpkb.Rd | 23 - QuadratiK-1.1.3/QuadratiK/man/kb.test-class.Rd | 10 QuadratiK-1.1.3/QuadratiK/man/kb.test.Rd | 16 QuadratiK-1.1.3/QuadratiK/man/pk.test.Rd | 22 - QuadratiK-1.1.3/QuadratiK/man/pkbc.Rd | 34 +- QuadratiK-1.1.3/QuadratiK/man/pkbc_validation.Rd | 30 - QuadratiK-1.1.3/QuadratiK/man/plot.pkbc.Rd | 132 +++---- QuadratiK-1.1.3/QuadratiK/man/predict.pkbc.Rd | 10 QuadratiK-1.1.3/QuadratiK/man/select_h.Rd | 6 QuadratiK-1.1.3/QuadratiK/man/summary.kb.test.Rd | 72 ++-- QuadratiK-1.1.3/QuadratiK/man/summary.pk.test.Rd | 72 ++-- QuadratiK-1.1.3/QuadratiK/man/summary.pkbc.Rd | 4 QuadratiK-1.1.3/QuadratiK/tests/testthat/test-dpkb.R | 26 - QuadratiK-1.1.3/QuadratiK/tests/testthat/test-kb.test.R | 3 QuadratiK-1.1.3/QuadratiK/tests/testthat/test-pk.test.R | 2 QuadratiK-1.1.3/QuadratiK/tests/testthat/test-pkbc.R | 36 +- QuadratiK-1.1.3/QuadratiK/tests/testthat/test-rpkb.R | 42 +- QuadratiK-1.1.3/QuadratiK/tests/testthat/test-select_h.R | 3 QuadratiK-1.1.3/QuadratiK/tests/testthat/test-validation.R | 2 QuadratiK-1.1.3/QuadratiK/vignettes/Introduction.Rmd | 38 +- QuadratiK-1.1.3/QuadratiK/vignettes/TwoSample_test.Rmd | 14 QuadratiK-1.1.3/QuadratiK/vignettes/generate_rpkb.Rmd | 26 - QuadratiK-1.1.3/QuadratiK/vignettes/kSample_test.Rmd | 10 QuadratiK-1.1.3/QuadratiK/vignettes/uniformity.Rmd | 8 QuadratiK-1.1.3/QuadratiK/vignettes/wireless_clustering.Rmd | 8 65 files changed, 1042 insertions(+), 920 deletions(-)
Title: Meta Clustering with Similarity Network Fusion
Description: Framework to facilitate patient subtyping with similarity network fusion and meta clustering. The similarity network fusion (SNF) algorithm was introduced by Wang et al. (2014) in <doi:10.1038/nmeth.2810>. SNF is a data integration approach that can transform high-dimensional and diverse data types into a single similarity network suitable for clustering with minimal loss of information from each initial data source. The meta clustering approach was introduced by Caruana et al. (2006) in <doi:10.1109/ICDM.2006.103>. Meta clustering involves generating a wide range of cluster solutions by adjusting clustering hyperparameters, then clustering the solutions themselves into a manageable number of qualitatively similar solutions, and finally characterizing representative solutions to find ones that are best for the user's specific context. This package provides a framework to easily transform multi-modal data into a wide range of similarity network fusion-derived cluster solutio [...truncated...]
Author: Prashanth S Velayudhan [aut, cre],
Xiaoqiao Xu [aut],
Prajkta Kallurkar [aut],
Ana Patricia Balbon [aut],
Maria T Secara [aut],
Adam Taback [aut],
Denise Sabac [aut],
Nicholas Chan [aut],
Shihao Ma [aut],
Bo Wang [aut],
Daniel Felsky [aut],
Stephanie [...truncated...]
Maintainer: Prashanth S Velayudhan <psvelayu@gmail.com>
Diff between metasnf versions 1.1.1 dated 2024-11-08 and 2.0.0 dated 2025-02-04
metasnf-1.1.1/metasnf/R/clust_algs_list.R |only metasnf-1.1.1/metasnf/R/cluster_extraction.R |only metasnf-1.1.1/metasnf/R/distance_metrics_list.R |only metasnf-1.1.1/metasnf/R/meta_cluster.R |only metasnf-1.1.1/metasnf/R/settings_matrix.R |only metasnf-1.1.1/metasnf/R/solutions_matrix.R |only metasnf-1.1.1/metasnf/inst/doc/settings_matrix.R |only metasnf-1.1.1/metasnf/inst/doc/settings_matrix.Rmd |only metasnf-1.1.1/metasnf/inst/doc/settings_matrix.html |only metasnf-1.1.1/metasnf/man/add_settings_matrix_rows.Rd |only metasnf-1.1.1/metasnf/man/arrange_dl.Rd |only metasnf-1.1.1/metasnf/man/batch_nmi.Rd |only metasnf-1.1.1/metasnf/man/calculate_db_indices.Rd |only metasnf-1.1.1/metasnf/man/calculate_dunn_indices.Rd |only metasnf-1.1.1/metasnf/man/calculate_silhouettes.Rd |only metasnf-1.1.1/metasnf/man/dl_has_duplicates.Rd |only metasnf-1.1.1/metasnf/man/dl_uid_first_col.Rd |only metasnf-1.1.1/metasnf/man/domain_merge.Rd |only metasnf-1.1.1/metasnf/man/euclidean_distance.Rd |only metasnf-1.1.1/metasnf/man/generate_data_list.Rd |only metasnf-1.1.1/metasnf/man/generate_weights_matrix.Rd |only metasnf-1.1.1/metasnf/man/get_dl_subjects.Rd |only metasnf-1.1.1/metasnf/man/gower_distance.Rd |only metasnf-1.1.1/metasnf/man/hamming_distance.Rd |only metasnf-1.1.1/metasnf/man/individual.Rd |only metasnf-1.1.1/metasnf/man/list_remove.Rd |only metasnf-1.1.1/metasnf/man/lp_solutions_matrix.Rd |only metasnf-1.1.1/metasnf/man/merge_data_lists.Rd |only metasnf-1.1.1/metasnf/man/no_subs.Rd |only metasnf-1.1.1/metasnf/man/prefix_dl_sk.Rd |only metasnf-1.1.1/metasnf/man/reduce_dl_to_common.Rd |only metasnf-1.1.1/metasnf/man/remove_dl_na.Rd |only metasnf-1.1.1/metasnf/man/reorder_dl_subs.Rd |only metasnf-1.1.1/metasnf/man/settings_matrix_heatmap.Rd |only metasnf-1.1.1/metasnf/man/sew_euclidean_distance.Rd |only metasnf-1.1.1/metasnf/man/sn_euclidean_distance.Rd |only metasnf-1.1.1/metasnf/man/spectral_eigen.Rd |only metasnf-1.1.1/metasnf/man/spectral_eigen_classic.Rd |only metasnf-1.1.1/metasnf/man/spectral_eight.Rd |only metasnf-1.1.1/metasnf/man/spectral_five.Rd |only metasnf-1.1.1/metasnf/man/spectral_four.Rd |only metasnf-1.1.1/metasnf/man/spectral_nine.Rd |only metasnf-1.1.1/metasnf/man/spectral_rot.Rd |only metasnf-1.1.1/metasnf/man/spectral_rot_classic.Rd |only metasnf-1.1.1/metasnf/man/spectral_seven.Rd |only metasnf-1.1.1/metasnf/man/spectral_six.Rd |only metasnf-1.1.1/metasnf/man/spectral_ten.Rd |only metasnf-1.1.1/metasnf/man/spectral_three.Rd |only metasnf-1.1.1/metasnf/man/spectral_two.Rd |only metasnf-1.1.1/metasnf/man/subs.Rd |only metasnf-1.1.1/metasnf/man/subsample_data_list.Rd |only metasnf-1.1.1/metasnf/man/summarize_clust_algs_list.Rd |only metasnf-1.1.1/metasnf/man/summarize_dml.Rd |only metasnf-1.1.1/metasnf/man/two_step_merge.Rd |only metasnf-1.1.1/metasnf/tests/testthat/test-settings_matrix.R |only metasnf-1.1.1/metasnf/vignettes/clust_esm_manhattan_l.png |only metasnf-1.1.1/metasnf/vignettes/settings_matrix.Rmd |only 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Title: Forest Inventory Estimation and Analysis
Description: A research estimation tool for analysts that work with sample-based
inventory data from the U.S. Department of Agriculture, Forest Service,
Forest Inventory and Analysis (FIA) Program.
Author: Tracey Frescino [aut],
Gretchen Moisen [aut],
Paul Patterson [aut],
Chris Toney [aut],
Grayson White [aut, cre] ,
Joshua Yamamoto [aut]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Diff between FIESTA versions 3.6.4 dated 2024-06-07 and 3.7.0 dated 2025-02-04
FIESTA-3.6.4/FIESTA/R/check.pltcnt.R |only FIESTA-3.6.4/FIESTA/R/check.popdataDWM.R |only FIESTA-3.6.4/FIESTA/R/getpse.R |only FIESTA-3.6.4/FIESTA/R/modGBdwm.R |only FIESTA-3.6.4/FIESTA/R/modWFarea.R |only FIESTA-3.6.4/FIESTA/R/modWFpop.R |only FIESTA-3.6.4/FIESTA/R/modWFtree.R |only FIESTA-3.6.4/FIESTA/R/popFilters.R |only FIESTA-3.6.4/FIESTA/R/popTableIDs.R |only FIESTA-3.6.4/FIESTA/R/popTables.R |only FIESTA-3.6.4/FIESTA/man/modGBdwm.Rd |only FIESTA-3.6.4/FIESTA/man/modWFarea.Rd |only FIESTA-3.6.4/FIESTA/man/modWFpop.Rd |only FIESTA-3.6.4/FIESTA/man/modWFtree.Rd |only FIESTA-3.6.4/FIESTA/man/popFilters.Rd |only FIESTA-3.6.4/FIESTA/man/popTableIDs.Rd |only FIESTA-3.6.4/FIESTA/man/popTables.Rd |only FIESTA-3.7.0/FIESTA/DESCRIPTION | 12 FIESTA-3.7.0/FIESTA/MD5 | 336 FIESTA-3.7.0/FIESTA/NAMESPACE | 16 FIESTA-3.7.0/FIESTA/NEWS.md | 95 FIESTA-3.7.0/FIESTA/R/DBgetCSV.R | 21 FIESTA-3.7.0/FIESTA/R/DBgetEvalid.R | 796 - FIESTA-3.7.0/FIESTA/R/DBgetPlots.R | 1553 +-- FIESTA-3.7.0/FIESTA/R/DBgetXY.R | 310 FIESTA-3.7.0/FIESTA/R/FIESTA-package.R | 52 FIESTA-3.7.0/FIESTA/R/ISAinternal.R | 31 FIESTA-3.7.0/FIESTA/R/SQLite_FIADB_ENTIRE_create_indices.R |only FIESTA-3.7.0/FIESTA/R/check.PROPvars.R | 13 FIESTA-3.7.0/FIESTA/R/check.auxiliary.R | 295 FIESTA-3.7.0/FIESTA/R/check.cond.R |only FIESTA-3.7.0/FIESTA/R/check.condCHNG.R |only FIESTA-3.7.0/FIESTA/R/check.estdata.R | 527 - FIESTA-3.7.0/FIESTA/R/check.estdataP2VEG.R |only FIESTA-3.7.0/FIESTA/R/check.estdataVOL.R |only FIESTA-3.7.0/FIESTA/R/check.outparams.R | 54 FIESTA-3.7.0/FIESTA/R/check.popdataCHNG.R | 2390 +++- FIESTA-3.7.0/FIESTA/R/check.popdataP2VEG.R | 2394 +++- FIESTA-3.7.0/FIESTA/R/check.popdataPLT.R | 1995 ++-- FIESTA-3.7.0/FIESTA/R/check.popdataVOL.R | 1586 ++- FIESTA-3.7.0/FIESTA/R/check.rowcol.R | 2424 ++-- FIESTA-3.7.0/FIESTA/R/check.titles.R | 103 FIESTA-3.7.0/FIESTA/R/check.tree.R | 396 FIESTA-3.7.0/FIESTA/R/datLUTclass.R | 145 FIESTA-3.7.0/FIESTA/R/datLUTnm.R | 32 FIESTA-3.7.0/FIESTA/R/datLUTspp.R | 204 FIESTA-3.7.0/FIESTA/R/datPivot.R | 374 FIESTA-3.7.0/FIESTA/R/datSumCond.R | 79 FIESTA-3.7.0/FIESTA/R/datSumTree.R | 3068 ++++-- FIESTA-3.7.0/FIESTA/R/datSumTreeDom.R | 1817 --- FIESTA-3.7.0/FIESTA/R/dbTables.R | 12 FIESTA-3.7.0/FIESTA/R/est.outtabs.R | 320 FIESTA-3.7.0/FIESTA/R/getADJqry.R |only FIESTA-3.7.0/FIESTA/R/getADJwhereqry.R |only FIESTA-3.7.0/FIESTA/R/getGBestimates.R |only FIESTA-3.7.0/FIESTA/R/getMAestimates.R |only FIESTA-3.7.0/FIESTA/R/getSAestimates.R |only FIESTA-3.7.0/FIESTA/R/getpopFilterqry.R |only FIESTA-3.7.0/FIESTA/R/modGBarea.R | 620 - 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Title: Iteratively Reweighted Boosting for Robust Analysis
Description: Fit a predictive model using iteratively reweighted boosting (IRBoost) to minimize robust loss functions within the CC-family (concave-convex). This constitutes an application of iteratively reweighted convex optimization (IRCO), where convex optimization is performed using the functional descent boosting algorithm. IRBoost assigns weights to facilitate outlier identification. Applications include robust generalized linear models and robust accelerated failure time models. Wang (2025) <doi:10.6339/24-JDS1138>.
Author: Zhu Wang [aut, cre]
Maintainer: Zhu Wang <zhuwang@gmail.com>
Diff between irboost versions 0.1-1.5 dated 2024-04-18 and 0.2-1.0 dated 2025-02-04
irboost-0.1-1.5/irboost/vignettes/irbst_code.pdf |only irboost-0.2-1.0/irboost/DESCRIPTION | 10 +++---- irboost-0.2-1.0/irboost/MD5 | 28 +++++++++++++------- irboost-0.2-1.0/irboost/NEWS | 6 ++++ irboost-0.2-1.0/irboost/R/irb.train.R | 2 - irboost-0.2-1.0/irboost/R/irb.train_aft.R | 2 - irboost-0.2-1.0/irboost/R/irboost.R | 2 - irboost-0.2-1.0/irboost/build/vignette.rds |binary irboost-0.2-1.0/irboost/inst/doc/static_irbst.pdf |binary irboost-0.2-1.0/irboost/vignettes/irbst.bib | 29 +++++++++++++-------- irboost-0.2-1.0/irboost/vignettes/irbst_code_files |only 11 files changed, 51 insertions(+), 28 deletions(-)
Title: Statistics Norway's Miscellaneous Tools
Description: Functions used by other packages from Statistics Norway are gathered. General data manipulation functions, algorithms for statistical disclosure control (Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6> and functions for hierarchical computations by sparse model matrices are included (Langsrud, 2023) <doi:10.32614/RJ-2023-088>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Bjoern-Helge Mevik [ctb],
Vidar Norstein Klungre [rev] ,
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between SSBtools versions 1.6.0 dated 2024-12-04 and 1.7.0 dated 2025-02-04
DESCRIPTION | 11 + MD5 | 38 +++--- NAMESPACE | 5 NEWS.md | 44 +++++++ R/Extend0fromModelMatrixInput.R |only R/GaussSuppression.R | 208 +++++++++++++++++++++++++++++++++++-- R/filter_by_variable.R |only R/formula_utils.R | 25 +++- R/hierarchies_as_vars.R | 27 ++++ R/map_hierarchies_to_data.R | 40 ++++++- R/model_aggregate.R | 63 ++++++++++- R/tables_by_formulas.R |only R/total_collapse.R | 2 man/Extend0fromModelMatrixInput.Rd |only man/GaussSuppression.Rd | 24 ++++ man/combine_formulas.Rd | 7 + man/filter_by_variable.Rd |only man/hierarchies_as_vars.Rd | 15 ++ man/map_hierarchies_to_data.Rd | 25 ++++ man/model_aggregate.Rd | 29 ++++- man/tables_by_formulas.Rd |only man/total_collapse.Rd | 2 tests/testthat/test-ModelMatrix.R | 3 23 files changed, 521 insertions(+), 47 deletions(-)
Title: Get and Modify 'oTree' Data
Description: Efficiently manage and process data from 'oTree' experiments.
Import 'oTree' data and clean them by using functions that handle
messy data, dropouts, and other problematic cases. Create IDs,
calculate the time, transfer variables between app data frames, and
delete sensitive information. Review your experimental data prior to
running the experiment and automatically generate a detailed summary
of the variables used in your 'oTree' code. Information on 'oTree' is
found in Chen, D. L., Schonger, M., & Wickens, C. (2016)
<doi:10.1016/j.jbef.2015.12.001>.
Author: Patricia F. Zauchner [aut, trl, cre, cph]
Maintainer: Patricia F. Zauchner <patricia.zauchner@gmx.at>
Diff between gmoTree versions 1.3.0 dated 2024-12-06 and 1.4.0 dated 2025-02-04
gmoTree-1.3.0/gmoTree/tests/testthat/tessts.R |only gmoTree-1.3.0/gmoTree/vignettes/intro.png |only gmoTree-1.3.0/gmoTree/vignettes/title.PNG |only gmoTree-1.4.0/gmoTree/DESCRIPTION | 14 gmoTree-1.4.0/gmoTree/MD5 | 142 gmoTree-1.4.0/gmoTree/NEWS.md | 82 gmoTree-1.4.0/gmoTree/R/apptime.R | 423 +- gmoTree-1.4.0/gmoTree/R/assignv.R | 19 gmoTree-1.4.0/gmoTree/R/assignv_to_aaw.R | 23 gmoTree-1.4.0/gmoTree/R/codebook.R | 237 - gmoTree-1.4.0/gmoTree/R/constant_col.R | 11 gmoTree-1.4.0/gmoTree/R/delete_cases.R | 93 gmoTree-1.4.0/gmoTree/R/delete_dropouts.R | 27 gmoTree-1.4.0/gmoTree/R/delete_duplicate.R | 15 gmoTree-1.4.0/gmoTree/R/delete_plabels.R | 5 gmoTree-1.4.0/gmoTree/R/delete_sessions.R | 47 gmoTree-1.4.0/gmoTree/R/extime.R | 87 gmoTree-1.4.0/gmoTree/R/import_otree.R | 141 gmoTree-1.4.0/gmoTree/R/make_ids.R | 76 gmoTree-1.4.0/gmoTree/R/messy_chat.R | 3 gmoTree-1.4.0/gmoTree/R/messy_time.R | 3 gmoTree-1.4.0/gmoTree/R/pagesec.R | 7 gmoTree-1.4.0/gmoTree/R/show_constant.R | 19 gmoTree-1.4.0/gmoTree/R/show_dropouts.R | 12 gmoTree-1.4.0/gmoTree/README.md | 14 gmoTree-1.4.0/gmoTree/inst/CITATION | 4 gmoTree-1.4.0/gmoTree/inst/doc/codebook.R | 11 gmoTree-1.4.0/gmoTree/inst/doc/codebook.Rmd | 67 gmoTree-1.4.0/gmoTree/inst/doc/codebook.html | 204 - gmoTree-1.4.0/gmoTree/inst/doc/intro_to_gmoTree.R | 2 gmoTree-1.4.0/gmoTree/inst/doc/intro_to_gmoTree.Rmd | 21 gmoTree-1.4.0/gmoTree/inst/doc/intro_to_gmoTree.html | 55 gmoTree-1.4.0/gmoTree/inst/extdata/ocode_z/settings.py | 2 gmoTree-1.4.0/gmoTree/inst/pkgdown.yml |only gmoTree-1.4.0/gmoTree/inst/rmd/codebook.Rmd | 259 - gmoTree-1.4.0/gmoTree/man/apptime.Rd | 15 gmoTree-1.4.0/gmoTree/man/assignv.Rd | 10 gmoTree-1.4.0/gmoTree/man/assignv_to_aaw.Rd | 14 gmoTree-1.4.0/gmoTree/man/codebook.Rd | 87 gmoTree-1.4.0/gmoTree/man/delete_cases.Rd | 80 gmoTree-1.4.0/gmoTree/man/delete_dropouts.Rd | 42 gmoTree-1.4.0/gmoTree/man/delete_duplicate.Rd | 15 gmoTree-1.4.0/gmoTree/man/delete_plabels.Rd | 6 gmoTree-1.4.0/gmoTree/man/delete_sessions.Rd | 49 gmoTree-1.4.0/gmoTree/man/extime.Rd | 38 gmoTree-1.4.0/gmoTree/man/import_otree.Rd | 28 gmoTree-1.4.0/gmoTree/man/make_ids.Rd | 15 gmoTree-1.4.0/gmoTree/man/messy_chat.Rd | 4 gmoTree-1.4.0/gmoTree/man/messy_time.Rd | 4 gmoTree-1.4.0/gmoTree/man/pagesec.Rd | 6 gmoTree-1.4.0/gmoTree/man/show_constant.Rd | 16 gmoTree-1.4.0/gmoTree/man/show_dropouts.Rd | 30 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/exp_cust_data_rename |only gmoTree-1.4.0/gmoTree/tests/testthat/testdata/exp_data_2.1.0.w |only gmoTree-1.4.0/gmoTree/tests/testthat/testdata/exp_data_5.4.0/custexp_dictator_2025-01-10.csv |only gmoTree-1.4.0/gmoTree/tests/testthat/testdata/exp_data_5.4.0subapp/custexp_dictator_2025-01-10.csv |only gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_f1/MIG1/models.py | 10 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_f2/MIG1/models.py | 10 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_f3/MIG1/models.py | 6 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_f4/MIG1/models.py | 14 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_f5/MIG1/models.py | 6 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_f6 |only gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_new4 |only gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_y1/test/models.py | 5 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_z2/rankaversion/models.py | 13 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_z3/rankaversion/models.py | 1 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_z3/settings.py | 2 gmoTree-1.4.0/gmoTree/tests/testthat/tests.R |only gmoTree-1.4.0/gmoTree/tests/testthat/tests_codebook.R | 1667 +++++----- gmoTree-1.4.0/gmoTree/vignettes/codebook.Rmd | 67 gmoTree-1.4.0/gmoTree/vignettes/intro_to_gmoTree.Rmd | 21 gmoTree-1.4.0/gmoTree/vignettes/title.png |only 72 files changed, 2421 insertions(+), 1985 deletions(-)
Title: Set Axis Break for 'ggplot2'
Description: An implementation of scale functions for setting axis breaks of a 'gg' plot (S Xu (2021) <doi:10.3389/fgene.2021.774846>).
Author: Guangchuang Yu [aut, cre, cph]
,
Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggbreak versions 0.1.3 dated 2025-01-08 and 0.1.4 dated 2025-02-04
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/method-ggplot-add.R | 1 + R/scales.R | 37 ++----------------------------------- R/utilities.R | 2 ++ R/zzz.R | 16 ++++++++++++++++ inst/doc/ggbreak.html | 38 +++++++++++++++++++------------------- 7 files changed, 49 insertions(+), 63 deletions(-)
Title: Perform Recursive Computations
Description: Mass rollup for a Bill of Materials is an example of a class of computations in which elements are arranged in a tree structure and some property of each element is a computed function of the corresponding values of its child elements. Leaf elements, i.e., those with no children, have values assigned. In many cases, the combining function is simple arithmetic sum; in other cases (e.g., mass properties), the combiner may involve other information such as the geometric relationship between parent and child, or statistical relations such as root-sum-of-squares (RSS). This package implements a general function for such problems. It is adapted to specific recursive computations by functional programming techniques; the caller passes a function as the update parameter to rollup() (or, at a lower level, passes functions as the get, set, combine, and override parameters to update_prop()) at runtime to specify the desired operations. The implementation relies on graph-theoretic algorithms from [...truncated...]
Author: James Steven Jenkins [aut, cre, cph]
Maintainer: James Steven Jenkins <sjenkins@studioj.us>
Diff between rollupTree versions 0.1.0 dated 2025-01-20 and 0.2.0 dated 2025-02-04
DESCRIPTION | 6 - MD5 | 58 +++++++++------ NAMESPACE | 1 NEWS.md | 11 +++ R/fault_table.R |only R/fault_tree.R |only R/rollup.R | 36 +++++++++ R/update_prop.R | 118 ++++++++++++++++---------------- R/wbs_table.R | 2 README.md | 1 data/fault_table.rda |only data/fault_tree.rda |only inst/doc/rollupTree.R | 64 ++++++++++++++++- inst/doc/rollupTree.Rmd | 96 ++++++++++++++++++++++++-- inst/doc/rollupTree.html | 157 +++++++++++++++++++++++++++++++++++-------- man/create_rollup_tree.Rd |only man/df_get_by_id.Rd | 6 - man/df_get_by_key.Rd | 10 +- man/df_get_ids.Rd | 4 - man/df_get_keys.Rd | 4 - man/df_set_by_id.Rd | 10 +- man/df_set_by_key.Rd | 10 +- man/fault_table.Rd |only man/fault_tree.Rd |only man/update_df_prop_by_id.Rd | 14 +-- man/update_df_prop_by_key.Rd | 18 ++-- man/update_prop.Rd | 18 ++-- man/validate_df_by_id.Rd | 12 +-- man/validate_df_by_key.Rd | 12 +-- man/wbs_table.Rd | 4 - tests/testthat/test-rollup.R | 20 +++++ vignettes/fta-example.jpg |only vignettes/references.bib | 8 ++ vignettes/rollupTree.Rmd | 96 ++++++++++++++++++++++++-- 34 files changed, 604 insertions(+), 192 deletions(-)
Title: Joint Modelling of Multivariate Longitudinal Data and
Time-to-Event Outcomes
Description: Fits the joint model proposed by Henderson and colleagues (2000)
<doi:10.1093/biostatistics/1.4.465>, but extended to the case of multiple
continuous longitudinal measures. The time-to-event data is modelled using a
Cox proportional hazards regression model with time-varying covariates. The
multiple longitudinal outcomes are modelled using a multivariate version of the
Laird and Ware linear mixed model. The association is captured by a multivariate
latent Gaussian process. The model is estimated using a Monte Carlo Expectation
Maximization algorithm. This project was funded by the Medical Research Council
(Grant number MR/M013227/1).
Author: Graeme L. Hickey [cre, aut] ,
Pete Philipson [aut] ,
Andrea Jorgensen [ctb] ,
Ruwanthi Kolamunnage-Dona [aut]
,
Paula Williamson [ctb] ,
Dimitris Rizopoulos [ctb, dtc] ,
Alessandro Gasparini [aut] ,
Medical Research Council [fnd]
Maintainer: Graeme L. Hickey <graemeleehickey@gmail.com>
Diff between joineRML versions 0.4.6 dated 2023-01-19 and 0.4.7 dated 2025-02-04
joineRML-0.4.6/joineRML/src/init.c |only joineRML-0.4.7/joineRML/DESCRIPTION | 10 joineRML-0.4.7/joineRML/MD5 | 77 +- joineRML-0.4.7/joineRML/NAMESPACE | 4 joineRML-0.4.7/joineRML/NEWS.md | 28 joineRML-0.4.7/joineRML/R/bootSE.R | 11 joineRML-0.4.7/joineRML/R/confint.mjoint.R | 2 joineRML-0.4.7/joineRML/R/fixef.mjoint.R | 2 joineRML-0.4.7/joineRML/R/joineRML.R | 16 joineRML-0.4.7/joineRML/R/mjoint.R | 2 joineRML-0.4.7/joineRML/R/plot.mjoint.R | 2 joineRML-0.4.7/joineRML/R/plot.ranef.mjoint.R | 8 joineRML-0.4.7/joineRML/R/tidiers.R | 18 joineRML-0.4.7/joineRML/R/vcov.mjoint.R | 8 joineRML-0.4.7/joineRML/README.md | 14 joineRML-0.4.7/joineRML/build/partial.rdb |only joineRML-0.4.7/joineRML/build/vignette.rds |binary joineRML-0.4.7/joineRML/inst/CITATION | 6 joineRML-0.4.7/joineRML/inst/doc/joineRML-tidy.R | 26 joineRML-0.4.7/joineRML/inst/doc/joineRML-tidy.Rmd | 33 joineRML-0.4.7/joineRML/inst/doc/joineRML-tidy.html | 259 +++---- joineRML-0.4.7/joineRML/inst/doc/joineRML.R | 43 - joineRML-0.4.7/joineRML/inst/doc/joineRML.Rmd | 46 - joineRML-0.4.7/joineRML/inst/doc/joineRML.html | 731 ++++++++++---------- joineRML-0.4.7/joineRML/inst/doc/technical.pdf |binary joineRML-0.4.7/joineRML/man/bootSE.Rd | 4 joineRML-0.4.7/joineRML/man/confint.mjoint.Rd | 2 joineRML-0.4.7/joineRML/man/fixef.mjoint.Rd | 2 joineRML-0.4.7/joineRML/man/joineRML-package.Rd |only joineRML-0.4.7/joineRML/man/joineRML.Rd | 1 joineRML-0.4.7/joineRML/man/mjoint.Rd | 2 joineRML-0.4.7/joineRML/man/mjoint_tidiers.Rd | 7 joineRML-0.4.7/joineRML/man/plot.mjoint.Rd | 2 joineRML-0.4.7/joineRML/man/plot.ranef.mjoint.Rd | 4 joineRML-0.4.7/joineRML/man/vcov.mjoint.Rd | 8 joineRML-0.4.7/joineRML/src/Makevars | 1 joineRML-0.4.7/joineRML/src/Makevars.win | 1 joineRML-0.4.7/joineRML/src/RcppExports.cpp | 16 joineRML-0.4.7/joineRML/tests/testthat/Rplots.pdf |binary joineRML-0.4.7/joineRML/vignettes/joineRML-tidy.Rmd | 33 joineRML-0.4.7/joineRML/vignettes/joineRML.Rmd | 46 - 41 files changed, 826 insertions(+), 649 deletions(-)
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions; supports sf and stars.
Author: Edzer Pebesma [aut, cre] ,
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 2.1-2 dated 2024-09-05 and 2.1-3 dated 2025-02-04
DESCRIPTION | 9 - MD5 | 56 ++++----- R/predict.gstat.R | 2 build/vignette.rds |binary data/DE_RB_2005.rda |binary data/coalash.rda |binary data/fulmar.rda |binary data/jura.rda |binary data/meuse.all.rda |binary data/meuse.alt.rda |binary data/ncp.grid.rda |binary data/oxford.rda |binary data/pcb.rda |binary data/sic2004.rda |binary data/sic97.rda |binary data/tull.rda |binary data/vv.rda |binary data/walker.rda |binary data/wind.rda |binary inst/doc/gstat.pdf |binary inst/doc/prs.pdf |binary inst/doc/spatio-temporal-kriging.pdf |binary inst/doc/st.pdf |binary man/sic2004.Rd | 4 man/sic97.Rd | 5 man/walker.Rd | 7 - tests/cv.Rout.save | 204 +++++++++++++++++------------------ tests/cv3d.Rout.save | 96 ++++++++-------- tests/stars.Rout.save | 84 +++++++------- 29 files changed, 229 insertions(+), 238 deletions(-)
Title: Forensic Bayesian Networks
Description: Open-source package for computing likelihood ratios in kinship testing and human identification cases. It has the core function of the software GENis, developed by Fundación Sadosky. It relies on a Bayesian Networks framework and is particularly well suited to efficiently perform large-size queries against databases of missing individuals.
Author: Franco Marsico [aut, cre],
Ariel Chernomoretz [aut]
Maintainer: Franco Marsico <franco.lmarsico@gmail.com>
Diff between fbnet versions 1.0.3 dated 2023-07-01 and 1.0.4 dated 2025-02-04
fbnet-1.0.3/fbnet/R/FamiliasLocus.R |only fbnet-1.0.3/fbnet/R/FamiliasPedigree.R |only fbnet-1.0.3/fbnet/R/convertPedformat.R |only fbnet-1.0.3/fbnet/R/preparePed.R |only fbnet-1.0.3/fbnet/man/FamiliasLocus.Rd |only fbnet-1.0.3/fbnet/man/FamiliasPedigree.Rd |only fbnet-1.0.3/fbnet/man/convertPedformat.Rd |only fbnet-1.0.3/fbnet/man/preparePed.Rd |only fbnet-1.0.4/fbnet/DESCRIPTION | 17 ++--- fbnet-1.0.4/fbnet/MD5 | 92 ++++++++++++++-------------- fbnet-1.0.4/fbnet/NAMESPACE | 6 - fbnet-1.0.4/fbnet/R/bnet.R |only fbnet-1.0.4/fbnet/R/buildBN.R | 4 - fbnet-1.0.4/fbnet/R/buildCPTs.R | 5 - fbnet-1.0.4/fbnet/R/evidencePrunning.R | 1 fbnet-1.0.4/fbnet/R/factorHeteroFounders.R | 1 fbnet-1.0.4/fbnet/R/fbnet.R | 1 fbnet-1.0.4/fbnet/R/getGenotypeTables.R | 1 fbnet-1.0.4/fbnet/R/getLocusCPT.R | 6 - fbnet-1.0.4/fbnet/R/getMAP.R | 1 fbnet-1.0.4/fbnet/R/getQSetRMP.R | 1 fbnet-1.0.4/fbnet/R/getValuesOut.R | 1 fbnet-1.0.4/fbnet/R/imposeEvidence.R | 1 fbnet-1.0.4/fbnet/R/initBN.R | 18 ++++- fbnet-1.0.4/fbnet/R/initBN.fromPed.R | 8 -- fbnet-1.0.4/fbnet/R/initBN.fromVars.R | 13 --- fbnet-1.0.4/fbnet/R/minOrdering.R | 1 fbnet-1.0.4/fbnet/R/pbn.R |only fbnet-1.0.4/fbnet/R/prodFactor.R | 1 fbnet-1.0.4/fbnet/R/pruneNodes.R | 1 fbnet-1.0.4/fbnet/R/removeEvidenceFromPed.R | 1 fbnet-1.0.4/fbnet/R/reportLR.R | 1 fbnet-1.0.4/fbnet/R/reportPQ.R | 1 fbnet-1.0.4/fbnet/R/reverseSplit.R | 1 fbnet-1.0.4/fbnet/R/setOrdering.R | 1 fbnet-1.0.4/fbnet/R/stateRemoval.R | 1 fbnet-1.0.4/fbnet/R/stateRemoval2.R | 1 fbnet-1.0.4/fbnet/R/stateRemovalSubnucs.R | 1 fbnet-1.0.4/fbnet/R/sumFactor.R | 1 fbnet-1.0.4/fbnet/R/velim.bn.R | 6 - fbnet-1.0.4/fbnet/README.md | 13 --- fbnet-1.0.4/fbnet/build/partial.rdb |binary fbnet-1.0.4/fbnet/data/bnet.rda |only fbnet-1.0.4/fbnet/data/pbn.rda |only fbnet-1.0.4/fbnet/man/bnet.Rd |only fbnet-1.0.4/fbnet/man/buildBN.Rd | 4 - fbnet-1.0.4/fbnet/man/buildCPTs.Rd | 5 - fbnet-1.0.4/fbnet/man/fbnet.Rd | 19 +++++ fbnet-1.0.4/fbnet/man/figures |only fbnet-1.0.4/fbnet/man/getLocusCPT.Rd | 6 - fbnet-1.0.4/fbnet/man/initBN.Rd | 15 ++++ fbnet-1.0.4/fbnet/man/pbn.Rd |only fbnet-1.0.4/fbnet/man/velim.bn.Rd | 6 - 53 files changed, 109 insertions(+), 154 deletions(-)
Title: SAGA Geoprocessing and Terrain Analysis
Description: Provides access to geocomputing and terrain analysis
functions of the geographical information system (GIS) 'SAGA' (System
for Automated Geoscientific Analyses) from within R by running the
command line version of SAGA. This package furthermore provides
several R functions for handling ASCII grids, including a flexible
framework for applying local functions (including predict methods of
fitted models) and focal functions to multiple grids. SAGA GIS is
available under GPL-2 / LGPL-2 licences from
<https://sourceforge.net/projects/saga-gis/>.
Author: Alexander Brenning [aut, cre] ,
Donovan Bangs [aut],
Marc Becker [aut],
Patrick Schratz [ctb] ,
Fabian Polakowski [ctb]
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>
Diff between RSAGA versions 1.4.0 dated 2022-12-09 and 1.4.2 dated 2025-02-04
DESCRIPTION | 66 ++-- MD5 | 142 +++++----- R/RSAGA-core.R | 57 ++-- R/RSAGA-modules.R | 460 ++++++++++++++++++--------------- R/RSAGA-package.R | 7 R/RSAGA-utils.R | 10 R/dem.R |only R/gridtools.R | 24 + R/landslides.R | 57 +--- R/study_area.R |only build/vignette.rds |binary data/dem.rda |only data/landslides.rda |binary data/study_area.rda |only inst/doc/RSAGA.R | 194 +++++++------ inst/doc/RSAGA.Rmd | 10 inst/doc/RSAGA.html | 257 +++++++++--------- man/RSAGA-package.Rd | 134 +++++---- man/centervalue.Rd | 53 ++- man/create.variable.name.Rd | 52 ++- man/dem.Rd |only man/focal.function.Rd | 292 ++++++++++---------- man/grid.predict.Rd | 174 ++++++------ man/grid.to.xyz.Rd | 68 ++-- man/landslides.Rd | 159 +++++------ man/match.arg.ext.Rd | 138 ++++----- man/multi.focal.function.Rd | 364 +++++++++++++------------- man/pick.from.points.Rd | 447 ++++++++++++++++---------------- man/read.ascii.grid.Rd | 262 +++++++++--------- man/relative.position.Rd | 84 +++--- man/resid.median.Rd | 78 ++--- man/rsaga.add.grid.values.to.points.Rd | 87 +++--- man/rsaga.close.gaps.Rd | 110 +++---- man/rsaga.contour.Rd | 96 +++--- man/rsaga.copy.sgrd.Rd | 53 ++- man/rsaga.env.Rd | 202 +++++++------- man/rsaga.esri.to.sgrd.Rd | 84 +++--- man/rsaga.esri.wrapper.Rd | 158 +++++------ man/rsaga.fill.sinks.Rd | 132 ++++----- man/rsaga.filter.gauss.Rd | 84 +++--- man/rsaga.filter.simple.Rd | 96 +++--- man/rsaga.geoprocessor.Rd | 216 +++++++-------- man/rsaga.get.modules.Rd | 204 +++++++------- man/rsaga.get.modules.path.Rd | 43 +-- man/rsaga.get.usage.Rd | 90 +++--- man/rsaga.get.version.Rd | 80 ++--- man/rsaga.grid.calculus.Rd | 188 ++++++------- man/rsaga.grid.to.points.Rd | 129 ++++----- man/rsaga.hillshade.Rd | 112 ++++---- man/rsaga.html.help.Rd | 91 +++--- man/rsaga.import.gdal.Rd | 115 ++++---- man/rsaga.insolation.Rd | 210 +++++++-------- man/rsaga.intersect.polygons.Rd | 112 ++++---- man/rsaga.inverse.distance.Rd | 197 +++++++------- man/rsaga.lib.prefix.Rd | 70 ++--- man/rsaga.local.morphometry.Rd | 232 ++++++++-------- man/rsaga.parallel.processing.Rd | 238 ++++++++--------- man/rsaga.pisr.Rd | 295 ++++++++++----------- man/rsaga.pisr2.Rd | 268 +++++++++---------- man/rsaga.set.env.Rd | 71 ++--- man/rsaga.sgrd.to.esri.Rd | 138 ++++----- man/rsaga.sink.removal.Rd | 84 +++--- man/rsaga.sink.route.Rd | 80 ++--- man/rsaga.slope.asp.curv.Rd | 306 ++++++++++----------- man/rsaga.solar.radiation.Rd | 189 ++++++------- man/rsaga.target.Rd | 135 ++++----- man/rsaga.topdown.processing.Rd | 272 +++++++++---------- man/rsaga.union.polygons.Rd | 116 ++++---- man/rsaga.wetness.index.Rd | 164 +++++------ man/set.file.extension.Rd | 74 ++--- man/study_area.Rd |only man/wind.shelter.Rd | 140 +++++----- tests/testthat/test-core.R | 17 + tests/testthat/test-modules.R | 50 +++ vignettes/RSAGA.Rmd | 10 75 files changed, 4785 insertions(+), 4642 deletions(-)
Title: Information Theory Tools for Forensic Analysis
Description: The 'forensIT' package is a comprehensive statistical toolkit tailored for handling missing person cases. By leveraging information theory metrics, it enables accurate assessment of kinship, particularly when limited genetic evidence is available. With a focus on optimizing statistical power, 'forensIT' empowers investigators to effectively prioritize family members, enhancing the reliability and efficiency of missing person investigations.
Author: Franco Marsico [aut, cre],
Ariel Chernomoretz [aut]
Maintainer: Franco Marsico <franco.lmarsico@gmail.com>
Diff between forensIT versions 1.0.0 dated 2023-06-22 and 1.1.1 dated 2025-02-04
forensIT-1.0.0/forensIT/R/convertPed.R |only forensIT-1.0.0/forensIT/man/convertPed.Rd |only forensIT-1.1.1/forensIT/DESCRIPTION | 12 +- forensIT-1.1.1/forensIT/MD5 | 16 +-- forensIT-1.1.1/forensIT/NAMESPACE | 2 forensIT-1.1.1/forensIT/R/run-it.R | 3 forensIT-1.1.1/forensIT/R/simMinimalEnsemble.R | 4 forensIT-1.1.1/forensIT/R/simTestIDMarkers.R | 1 forensIT-1.1.1/forensIT/README.md | 104 ++++++++++--------------- forensIT-1.1.1/forensIT/man/forensIT.Rd | 10 ++ 10 files changed, 69 insertions(+), 83 deletions(-)
Title: Miscellaneous Functions for Panel Data, Quantiles, and Printing
Results
Description: These are miscellaneous functions for working with panel data, quantiles, and printing results. For panel data, the package includes functions for making a panel data balanced (that is, dropping missing individuals that have missing observations in any time period), converting id numbers to row numbers, and to treat repeated cross sections as panel data under the assumption of rank invariance. For quantiles, there are functions to make distribution functions from a set of data points (this is particularly useful when a distribution function is created in several steps), to combine distribution functions based on some external weights, and to invert distribution functions. Finally, there are several other miscellaneous functions for obtaining weighted means, weighted distribution functions, and weighted quantiles; to generate summary statistics and their differences for two groups; and to add or drop covariates from formulas.
Author: Brantly Callaway [aut, cre]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>
Diff between BMisc versions 1.4.7 dated 2025-01-10 and 1.4.8 dated 2025-02-04
BMisc-1.4.7/BMisc/man/compareSingleBinary.Rd |only BMisc-1.4.7/BMisc/man/getWeightedQuantile.Rd |only BMisc-1.4.8/BMisc/DESCRIPTION | 9 BMisc-1.4.8/BMisc/MD5 | 65 ++- BMisc-1.4.8/BMisc/NAMESPACE | 19 BMisc-1.4.8/BMisc/NEWS.md | 8 BMisc-1.4.8/BMisc/R/BMisc.R | 457 ++++++++++++++++++----- BMisc-1.4.8/BMisc/README.md | 33 - BMisc-1.4.8/BMisc/inst |only BMisc-1.4.8/BMisc/man/BMisc.Rd | 1 BMisc-1.4.8/BMisc/man/addCovToFormla.Rd | 21 - BMisc-1.4.8/BMisc/man/add_cov_to_formula.Rd |only BMisc-1.4.8/BMisc/man/blockBootSample.Rd | 28 - BMisc-1.4.8/BMisc/man/block_boot_sample.Rd |only BMisc-1.4.8/BMisc/man/combineDfs.Rd | 26 - BMisc-1.4.8/BMisc/man/combine_ecdfs.Rd |only BMisc-1.4.8/BMisc/man/compareBinary.Rd | 10 BMisc-1.4.8/BMisc/man/compare_binary.Rd |only BMisc-1.4.8/BMisc/man/compare_binary_inner.Rd |only BMisc-1.4.8/BMisc/man/dropCovFromFormla.Rd | 19 BMisc-1.4.8/BMisc/man/drop_cov_from_formula.Rd |only BMisc-1.4.8/BMisc/man/getListElement.Rd | 17 BMisc-1.4.8/BMisc/man/getWeightedDf.Rd | 10 BMisc-1.4.8/BMisc/man/getWeightedMean.Rd | 9 BMisc-1.4.8/BMisc/man/getWeightedQuantiles.Rd | 10 BMisc-1.4.8/BMisc/man/get_list_element.Rd |only BMisc-1.4.8/BMisc/man/invertEcdf.Rd | 10 BMisc-1.4.8/BMisc/man/invert_ecdf.Rd |only BMisc-1.4.8/BMisc/man/lhs.vars.Rd | 17 BMisc-1.4.8/BMisc/man/lhs_vars.Rd |only BMisc-1.4.8/BMisc/man/makeBalancedPanel.Rd | 22 - BMisc-1.4.8/BMisc/man/makeDist.Rd | 19 BMisc-1.4.8/BMisc/man/make_balanced_panel.Rd |only BMisc-1.4.8/BMisc/man/make_dist.Rd |only BMisc-1.4.8/BMisc/man/rhs.Rd | 4 BMisc-1.4.8/BMisc/man/rhs.vars.Rd | 18 BMisc-1.4.8/BMisc/man/rhs_vars.Rd |only BMisc-1.4.8/BMisc/man/weighted.checkfun.Rd | 9 BMisc-1.4.8/BMisc/man/weighted_checkfun.Rd |only BMisc-1.4.8/BMisc/man/weighted_combine_list.Rd |only BMisc-1.4.8/BMisc/man/weighted_ecdf.Rd |only BMisc-1.4.8/BMisc/man/weighted_mean.Rd |only BMisc-1.4.8/BMisc/man/weighted_quantile.Rd |only BMisc-1.4.8/BMisc/man/weighted_quantile_inner.Rd |only 44 files changed, 533 insertions(+), 308 deletions(-)
Title: Stochastic Search Inconsistency Factor Selection
Description: Evaluating the consistency assumption of Network Meta-Analysis both globally and locally in the Bayesian framework. Inconsistencies are located by applying Bayesian variable selection to the inconsistency factors. The implementation of the method is described by Seitidis et al. (2023) <doi:10.1002/sim.9891>.
Author: Georgios Seitidis [aut, cre] ,
Stavros Nikolakopoulos [aut] ,
Ioannis Ntzoufras [aut] ,
Dimitris Mavridis [aut]
Maintainer: Georgios Seitidis <g.seitidis@uoi.gr>
Diff between ssifs versions 1.0.2 dated 2023-05-12 and 1.0.4 dated 2025-02-04
DESCRIPTION | 15 ++++++++------- MD5 | 26 +++++++++++++------------- NAMESPACE | 2 ++ NEWS.md | 2 ++ R/higgdes.R | 6 ++++-- R/smokingcessation.R | 3 ++- R/ssifs.R | 8 ++++---- README.md | 11 +++++++++-- inst/doc/An_introduction_to_ssifs.Rmd | 2 +- inst/doc/An_introduction_to_ssifs.html | 8 +++++++- man/smokingcessation.Rd | 2 +- man/ssifs.Rd | 8 ++++---- vignettes/An_introduction_to_ssifs.Rmd | 2 +- vignettes/references.bib | 11 +++++++++++ 14 files changed, 69 insertions(+), 37 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 3.0-2 dated 2025-01-22 and 3.1-0 dated 2025-02-04
DESCRIPTION | 26 ++++++---- LICENSE |only MD5 | 43 +++++++++-------- NAMESPACE | 48 +++++++++++++++++++ NEWS.md | 56 +++++++++++++++++++--- R/contribution.matrix.R | 59 ++++++++++------------- R/hasse-internal.R |only R/hasse.R | 63 +++++++++++------------- R/netconnection.R | 16 +++++- R/netcontrib.R | 21 +++----- R/netleague.R | 8 +-- R/netmeta-package.R | 41 ++++++++++------ R/netmeta.R | 58 +++++++++++++---------- R/netmetabin.R | 121 +++++++++++++++++++++++------------------------- R/netposet.R | 17 ++---- R/plot.netposet.R | 3 - inst/MIT_LICENSE |only inst/doc/netmeta.pdf |binary man/hasse.netposet.Rd | 30 +++++++++-- man/netcontrib.Rd | 19 +++---- man/netleague.Rd | 8 +-- man/netmetabin.Rd | 3 - man/netposet.Rd | 15 +---- man/plot.netposet.Rd | 3 - 24 files changed, 388 insertions(+), 270 deletions(-)
Title: Constructing Hierarchical Voronoi Tessellations and Overlay
Heatmaps for Data Analysis
Description: Facilitates building topology preserving maps for data analysis.
Author: Zubin Dowlaty [aut],
Mu Sigma, Inc. [cre]
Maintainer: "Mu Sigma, Inc." <ird.experiencelab@mu-sigma.com>
Diff between HVT versions 24.9.1 dated 2024-09-11 and 25.2.1 dated 2025-02-04
HVT-24.9.1/HVT/man/getCellId.Rd |only HVT-24.9.1/HVT/man/hvq.Rd |only HVT-24.9.1/HVT/man/madPlot.Rd |only HVT-24.9.1/HVT/vignettes/scoreLayeredHVT_function.png |only HVT-24.9.1/HVT/vignettes/torus2.png |only HVT-25.2.1/HVT/DESCRIPTION | 29 HVT-25.2.1/HVT/MD5 | 110 +- HVT-25.2.1/HVT/NAMESPACE | 12 HVT-25.2.1/HVT/R/clustHVT.R | 46 - HVT-25.2.1/HVT/R/clusterPlot.R | 187 ++-- HVT-25.2.1/HVT/R/diagPlot.R | 5 HVT-25.2.1/HVT/R/diagSuggestion.R | 2 HVT-25.2.1/HVT/R/displayTable.R | 127 -- HVT-25.2.1/HVT/R/edaPlots.R | 203 +++- HVT-25.2.1/HVT/R/getCellId.R | 20 HVT-25.2.1/HVT/R/getOptimalCentroids.R | 1 HVT-25.2.1/HVT/R/getTransitionProbability.R | 113 +- HVT-25.2.1/HVT/R/hvq.R | 63 - HVT-25.2.1/HVT/R/madPlot.R | 53 - HVT-25.2.1/HVT/R/msm.R |only HVT-25.2.1/HVT/R/msm_plots.R |only HVT-25.2.1/HVT/R/plotAnimatedFlowmap.R | 723 ++++++++-------- HVT-25.2.1/HVT/R/plotHVT.R | 204 ++-- HVT-25.2.1/HVT/R/plotModelDiagnostics.R | 1 HVT-25.2.1/HVT/R/plotNovelCells.R | 4 HVT-25.2.1/HVT/R/plotQuantErrorHistogram.R | 3 HVT-25.2.1/HVT/R/plotStateTransition.R | 226 ++++- HVT-25.2.1/HVT/R/plotZscore.R |only HVT-25.2.1/HVT/R/reconcileTransitionProbability.R | 20 HVT-25.2.1/HVT/R/removeNovelty.R | 2 HVT-25.2.1/HVT/R/scoreHVT.R | 48 - HVT-25.2.1/HVT/R/scoreLayeredHVT.R | 11 HVT-25.2.1/HVT/R/summary.R |only HVT-25.2.1/HVT/R/trainHVT.R | 52 - HVT-25.2.1/HVT/README.md | 118 +- HVT-25.2.1/HVT/build/vignette.rds |binary HVT-25.2.1/HVT/inst/doc/HVT.R | 42 HVT-25.2.1/HVT/inst/doc/HVT.Rmd | 90 +- HVT-25.2.1/HVT/inst/doc/HVT.html | 769 ++++++++++++++---- HVT-25.2.1/HVT/man/clustHVT.Rd | 20 HVT-25.2.1/HVT/man/displayTable.Rd | 46 - HVT-25.2.1/HVT/man/edaPlots.Rd | 28 HVT-25.2.1/HVT/man/getTransitionProbability.Rd | 31 HVT-25.2.1/HVT/man/msm.Rd |only HVT-25.2.1/HVT/man/plotAnimatedFlowmap.Rd | 13 HVT-25.2.1/HVT/man/plotHVT.Rd | 65 - HVT-25.2.1/HVT/man/plotNovelCells.Rd | 2 HVT-25.2.1/HVT/man/plotStateTransition.Rd | 16 HVT-25.2.1/HVT/man/plotZscore.Rd |only HVT-25.2.1/HVT/man/reconcileTransitionProbability.Rd | 7 HVT-25.2.1/HVT/man/scoreHVT.Rd | 3 HVT-25.2.1/HVT/man/summary.Rd |only HVT-25.2.1/HVT/man/trainHVT.Rd | 11 HVT-25.2.1/HVT/vignettes/HVT.Rmd | 90 +- HVT-25.2.1/HVT/vignettes/pngs |only 55 files changed, 2188 insertions(+), 1428 deletions(-)
Title: Robust Bayesian Meta-Analyses
Description: A framework for estimating ensembles of meta-analytic and meta-regression models
(assuming either presence or absence of the effect, heterogeneity,
publication bias, and moderators). The RoBMA framework uses Bayesian model-averaging to
combine the competing meta-analytic models into a model ensemble, weights
the posterior parameter distributions based on posterior model probabilities
and uses Bayes factors to test for the presence or absence of the
individual components (e.g., effect vs. no effect; Bartoš et al., 2022,
<doi:10.1002/jrsm.1594>; Maier, Bartoš & Wagenmakers, 2022,
<doi:10.1037/met0000405>). Users can define a wide range of prior distributions for +
the effect size, heterogeneity, publication bias (including selection models and PET-PEESE),
and moderator components. The package provides convenient functions for summary, visualizations, and
fit diagnostics.
Author: Frantisek Bartos [aut, cre] ,
Maximilian Maier [aut] ,
Eric-Jan Wagenmakers [ths] ,
Joris Goosen [ctb],
Matthew Denwood [cph] ,
Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between RoBMA versions 3.3.0 dated 2025-01-15 and 3.4.0 dated 2025-02-04
DESCRIPTION | 6 MD5 | 87 +++--- NAMESPACE | 2 NEWS.md | 12 R/BiBMA-reg.R |only R/BiBMA.R | 182 ++++++++------ R/RoBMA-reg.R | 126 ---------- R/RoBMA.R | 28 +- R/check-priors-and-models.R | 450 ++++++++++++++++++------------------ R/fit-and-marglik.R | 150 +++++++++++- R/plots.R | 2 R/priors.R | 81 ++++++ R/tools.R | 23 - R/transformations.R | 164 +++++++++++++ R/utilities.R | 1 build/partial.rdb |binary inst/REFERENCES.bib | 2 inst/doc/CustomEnsembles.html | 4 inst/doc/FastRoBMA.html | 10 inst/doc/HierarchicalBMA.html | 4 inst/doc/MedicineBMA.html | 4 inst/doc/MedicineBiBMA.html | 4 inst/doc/MetaRegression.html | 10 inst/doc/ReproducingBMA.html | 4 man/BiBMA.Rd | 28 +- man/BiBMA.reg.Rd |only man/RoBMA-package.Rd | 84 +++--- man/RoBMA_options.Rd | 54 ++-- man/effect_sizes.Rd | 186 +++++++------- man/forest.Rd | 144 +++++------ man/interpret.Rd | 42 +-- man/plot.RoBMA.Rd | 218 ++++++++--------- man/plot_models.Rd | 164 ++++++------- man/print.RoBMA.Rd | 44 +-- man/print.summary.RoBMA.Rd | 44 +-- man/prior.Rd | 170 ++++++------- man/prior_PEESE.Rd | 156 ++++++------ man/prior_PET.Rd | 156 ++++++------ man/prior_none.Rd | 80 +++--- man/prior_weightfunction.Rd | 124 ++++----- man/sample_sizes.Rd | 120 ++++----- man/set_default_binomial_priors.Rd |only man/set_default_priors.Rd | 150 ++++++------ man/standard_errors.Rd | 190 +++++++-------- man/weighted_multivariate_normal.Rd | 72 ++--- man/weighted_normal.Rd | 206 ++++++++-------- 46 files changed, 2062 insertions(+), 1726 deletions(-)
Title: Download and Display Map Tiles
Description: To create maps from tiles, 'maptiles' downloads, composes and
displays tiles from a large number of providers (e.g. 'OpenStreetMap',
'Stadia', 'Esri', 'CARTO', or 'Thunderforest').
Author: Timothee Giraud [cre, aut] ,
Diego Hernangomez [ctb] ,
Robert J. Hijmans [ctb] ,
Hugh A. Graham [ctb]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between maptiles versions 0.8.0 dated 2024-10-22 and 0.9.0 dated 2025-02-04
maptiles-0.8.0/maptiles/R/sysdata.rda |only maptiles-0.9.0/maptiles/DESCRIPTION | 10 +- maptiles-0.9.0/maptiles/MD5 | 23 ++--- maptiles-0.9.0/maptiles/NEWS.md | 13 ++ maptiles-0.9.0/maptiles/R/get_tiles.R | 60 +++++++------ maptiles-0.9.0/maptiles/R/providers.R | 62 +++++++++----- maptiles-0.9.0/maptiles/R/utils.R | 42 ++++++++- maptiles-0.9.0/maptiles/README.md | 9 +- maptiles-0.9.0/maptiles/inst/tinytest/test_maptiles.R | 13 +- maptiles-0.9.0/maptiles/man/figures/README-example-1.png |binary maptiles-0.9.0/maptiles/man/figures/README-example2-1.png |binary maptiles-0.9.0/maptiles/man/figures/README-front.png |binary maptiles-0.9.0/maptiles/man/get_tiles.Rd | 55 +++++++----- 13 files changed, 189 insertions(+), 98 deletions(-)
Title: Fast Functions for Prime Numbers
Description: Fast functions for dealing with prime numbers, such as testing
whether a number is prime and generating a sequence prime numbers.
Additional functions include finding prime factors and Ruth-Aaron pairs,
finding next and previous prime numbers in the series, finding or estimating
the nth prime, estimating the number of primes less than or equal to an
arbitrary number, computing primorials, prime k-tuples (e.g., twin primes),
finding the greatest common divisor and smallest (least) common multiple,
testing whether two numbers are coprime, and computing Euler's totient
function. Most functions are vectorized for speed and convenience.
Author: Os Keyes [aut],
Paul Egeler [aut, cre]
Maintainer: Paul Egeler <paulegeler@gmail.com>
Diff between primes versions 1.6.0 dated 2024-01-08 and 1.6.1 dated 2025-02-04
primes-1.6.0/primes/tests/failures |only primes-1.6.1/primes/DESCRIPTION | 18 +++++++++--------- primes-1.6.1/primes/MD5 | 7 +++---- primes-1.6.1/primes/R/phi.R | 2 +- primes-1.6.1/primes/README.md | 2 +- 5 files changed, 14 insertions(+), 15 deletions(-)
Title: Single-Source Capture-Recapture Models
Description: Implementation of single-source capture-recapture methods for population size estimation using zero-truncated, zero-one truncated and zero-truncated one-inflated Poisson, Geometric and Negative Binomial regression as well as Zelterman's and Chao's regression. Package includes point and interval estimators for the population size with variances estimated using analytical or bootstrap method. Details can be found in: van der Heijden et all. (2003) <doi:10.1191/1471082X03st057oa>, Böhning and van der Heijden (2019) <doi:10.1214/18-AOAS1232>, Böhning et al. (2020) Capture-Recapture Methods for the Social and Medical Sciences or Böhning and Friedl (2021) <doi:10.1007/s10260-021-00556-8>.
Author: Piotr Chlebicki [aut, ctb] ,
Maciej Beresewicz [aut, cre]
Maintainer: Maciej Beresewicz <maciej.beresewicz@ue.poznan.pl>
Diff between singleRcapture versions 0.2.1.4 dated 2025-01-07 and 0.2.2 dated 2025-02-04
singleRcapture-0.2.1.4/singleRcapture/R/methodsNotWorking.R |only singleRcapture-0.2.2/singleRcapture/DESCRIPTION | 22 - singleRcapture-0.2.2/singleRcapture/MD5 | 132 +++++----- singleRcapture-0.2.2/singleRcapture/NAMESPACE | 8 singleRcapture-0.2.2/singleRcapture/NEWS.md | 10 singleRcapture-0.2.2/singleRcapture/R/Chao.R | 12 singleRcapture-0.2.2/singleRcapture/R/Hurdleztgeom.R | 79 +++-- singleRcapture-0.2.2/singleRcapture/R/Hurdleztnegbin.R | 66 ++--- singleRcapture-0.2.2/singleRcapture/R/Hurdleztpoisson.R | 31 +- singleRcapture-0.2.2/singleRcapture/R/Internals.R | 71 +---- singleRcapture-0.2.2/singleRcapture/R/control.R | 10 singleRcapture-0.2.2/singleRcapture/R/data.R | 2 singleRcapture-0.2.2/singleRcapture/R/estimatePopsize.R | 123 +-------- singleRcapture-0.2.2/singleRcapture/R/estimatePopsizeFit.R | 32 -- singleRcapture-0.2.2/singleRcapture/R/leave-one-out.R | 5 singleRcapture-0.2.2/singleRcapture/R/linkFunctions.R | 99 +++---- singleRcapture-0.2.2/singleRcapture/R/marginal.R | 8 singleRcapture-0.2.2/singleRcapture/R/miscDiagnostics.R | 5 singleRcapture-0.2.2/singleRcapture/R/nonparametricBootstrap.R | 35 -- singleRcapture-0.2.2/singleRcapture/R/oiztgeom.R | 37 +- singleRcapture-0.2.2/singleRcapture/R/oiztnegbin.R | 18 - singleRcapture-0.2.2/singleRcapture/R/oiztpoisson.R | 17 - singleRcapture-0.2.2/singleRcapture/R/parametricBootstrap.R | 8 singleRcapture-0.2.2/singleRcapture/R/plots.R | 63 +--- singleRcapture-0.2.2/singleRcapture/R/predict.R | 2 singleRcapture-0.2.2/singleRcapture/R/sandwichMethods.R | 23 + singleRcapture-0.2.2/singleRcapture/R/semiparametricBootstrap.R | 3 singleRcapture-0.2.2/singleRcapture/R/simulate.R | 1 singleRcapture-0.2.2/singleRcapture/R/smallMethods.R | 9 singleRcapture-0.2.2/singleRcapture/R/strataEstimation.R | 19 - singleRcapture-0.2.2/singleRcapture/R/summary.R | 4 singleRcapture-0.2.2/singleRcapture/R/updates.R | 3 singleRcapture-0.2.2/singleRcapture/R/zelterman.R | 10 singleRcapture-0.2.2/singleRcapture/R/zotgeom.R | 7 singleRcapture-0.2.2/singleRcapture/R/zotnegbin.R | 39 +- singleRcapture-0.2.2/singleRcapture/R/zotpoisson.R | 16 - singleRcapture-0.2.2/singleRcapture/R/ztHurdlegeom.R | 24 + singleRcapture-0.2.2/singleRcapture/R/ztHurdlenegbin.R | 29 -- singleRcapture-0.2.2/singleRcapture/R/ztHurdlepoisson.R | 32 +- singleRcapture-0.2.2/singleRcapture/R/ztgeom.R | 15 - singleRcapture-0.2.2/singleRcapture/R/ztnegbin.R | 84 +----- singleRcapture-0.2.2/singleRcapture/R/ztoigeom.R | 26 - singleRcapture-0.2.2/singleRcapture/R/ztoinegbin.R | 18 - singleRcapture-0.2.2/singleRcapture/R/ztoipoisson.R | 33 +- singleRcapture-0.2.2/singleRcapture/R/ztpoisson.R | 8 singleRcapture-0.2.2/singleRcapture/README.md | 67 ++--- singleRcapture-0.2.2/singleRcapture/build/singleRcapture.pdf |binary singleRcapture-0.2.2/singleRcapture/build/stage23.rdb |binary singleRcapture-0.2.2/singleRcapture/build/vignette.rds |only singleRcapture-0.2.2/singleRcapture/inst/doc |only singleRcapture-0.2.2/singleRcapture/inst/tinytest/test_developer_only.R | 1 singleRcapture-0.2.2/singleRcapture/inst/tinytest/test_inflated_hurdle.R | 2 singleRcapture-0.2.2/singleRcapture/inst/tinytest/test_singleRcapture.R | 1 singleRcapture-0.2.2/singleRcapture/inst/tinytest/test_zerotruncated.R | 1 singleRcapture-0.2.2/singleRcapture/man/estimatePopsize.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/estimatePopsizeFit.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/figures/README-plot-example-1.png |only singleRcapture-0.2.2/singleRcapture/man/figures/README-plot-inflated-1.png |only singleRcapture-0.2.2/singleRcapture/man/figures/README-unnamed-chunk-5-1.png |binary singleRcapture-0.2.2/singleRcapture/man/marginalFreq.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/netherlandsimmigrant.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/plot.singleRStaticCountData.Rd | 4 singleRcapture-0.2.2/singleRcapture/man/popSizeEst.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/predict.singleRStaticCountData.Rd | 5 singleRcapture-0.2.2/singleRcapture/man/redoPopEstimation.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/summary.singleRmargin.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/vcov.singleRStaticCountData.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/vcovHC.singleRStaticCountData.Rd | 2 singleRcapture-0.2.2/singleRcapture/vignettes |only 69 files changed, 563 insertions(+), 834 deletions(-)
More information about singleRcapture at CRAN
Permanent link
Title: Tools for Analyzing Remote Sensing Forest Data
Description: Tools for analyzing remote sensing forest data, including functions for detecting treetops from canopy models, outlining tree crowns, and calculating textural metrics.
Author: Andrew Plowright [aut, cre],
Jean-Romain Roussel [ctb]
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>
Diff between ForestTools versions 1.0.2 dated 2024-04-28 and 1.0.3 dated 2025-02-03
ForestTools-1.0.2/ForestTools/README.md |only ForestTools-1.0.3/ForestTools/DESCRIPTION | 10 ForestTools-1.0.3/ForestTools/MD5 | 15 ForestTools-1.0.3/ForestTools/NEWS.md | 246 ++--- ForestTools-1.0.3/ForestTools/R/vwf.R | 419 +++++----- ForestTools-1.0.3/ForestTools/man/vwf.Rd | 7 ForestTools-1.0.3/ForestTools/tests/testthat/test_data/ttops_orphans.gpkg |only ForestTools-1.0.3/ForestTools/tests/testthat/test_data/ttops_test.gpkg |only ForestTools-1.0.3/ForestTools/tests/testthat/test_glcm_internal.R | 236 ++--- ForestTools-1.0.3/ForestTools/tests/testthat/test_mcws.R | 109 +- 10 files changed, 529 insertions(+), 513 deletions(-)
Title: Publication-Ready PCA, t-SNE, and UMAP Plots
Description: Provides tools for creating publication-ready dimensionality reduction plots, including Principal Component Analysis (PCA), t-Distributed Stochastic Neighbor Embedding (t-SNE), and Uniform Manifold Approximation and Projection (UMAP). This package helps visualize high-dimensional data with options for custom labels, density plots, and faceting, using the 'ggplot2' framework Wickham (2016) <doi:10.1007/978-3-319-24277-4>.
Author: Yaoxiang Li [cre, aut]
Maintainer: Yaoxiang Li <liyaoxiang@outlook.com>
Diff between ggpca versions 0.1.2 dated 2024-10-28 and 0.1.3 dated 2025-02-03
DESCRIPTION | 6 MD5 | 17 - NAMESPACE | 3 R/utils.R | 187 +++++++++++++++---- build/vignette.rds |binary inst/doc/ggpca-examples.Rmd | 420 +++++++++++++++++++++---------------------- inst/doc/ggpca-examples.html | 38 +-- man/ggpca.Rd | 11 - man/process_missing_value.Rd |only vignettes/ggpca-examples.Rmd | 420 +++++++++++++++++++++---------------------- 10 files changed, 612 insertions(+), 490 deletions(-)
Title: Database Queries Using 'data.table' Syntax
Description: Query database tables over a 'DBI' connection using 'data.table' syntax.
Attach database schemas to the search path. Automatically merge using foreign
key constraints.
Author: Kjell P. Konis [aut, cre],
Luis Rocha [ctb]
Maintainer: Kjell P. Konis <kjellk@gmail.com>
Diff between dbi.table versions 1.0.1 dated 2024-12-10 and 1.0.3 dated 2025-02-03
dbi.table-1.0.1/dbi.table/inst/example_files/LICENSE |only dbi.table-1.0.1/dbi.table/inst/example_files/chinook_export/album.csv.bz2 |only dbi.table-1.0.1/dbi.table/inst/example_files/chinook_export/artist.csv.bz2 |only dbi.table-1.0.1/dbi.table/inst/example_files/chinook_export/customer.csv.bz2 |only dbi.table-1.0.1/dbi.table/inst/example_files/chinook_export/employee.csv.bz2 |only dbi.table-1.0.1/dbi.table/inst/example_files/chinook_export/genre.csv.bz2 |only dbi.table-1.0.1/dbi.table/inst/example_files/chinook_export/invoice.csv.bz2 |only dbi.table-1.0.1/dbi.table/inst/example_files/chinook_export/invoiceline.csv.bz2 |only dbi.table-1.0.1/dbi.table/inst/example_files/chinook_export/mediatype.csv.bz2 |only dbi.table-1.0.1/dbi.table/inst/example_files/chinook_export/playlist.csv.bz2 |only dbi.table-1.0.1/dbi.table/inst/example_files/chinook_export/playlisttrack.csv.bz2 |only dbi.table-1.0.1/dbi.table/inst/example_files/chinook_export/track.csv.bz2 |only dbi.table-1.0.1/dbi.table/man/as.data.table.Rd |only dbi.table-1.0.3/dbi.table/DESCRIPTION | 22 dbi.table-1.0.3/dbi.table/MD5 | 98 ++-- dbi.table-1.0.3/dbi.table/NAMESPACE | 6 dbi.table-1.0.3/dbi.table/NEWS.md |only dbi.table-1.0.3/dbi.table/R/DBI_methods.R | 19 dbi.table-1.0.3/dbi.table/R/as.data.table.R |only dbi.table-1.0.3/dbi.table/R/attach.R | 65 +- dbi.table-1.0.3/dbi.table/R/calls.R | 10 dbi.table-1.0.3/dbi.table/R/catalog.R | 140 +++--- dbi.table-1.0.3/dbi.table/R/connection.R | 4 dbi.table-1.0.3/dbi.table/R/dbi.table.R | 84 +-- dbi.table-1.0.3/dbi.table/R/examples.R | 14 dbi.table-1.0.3/dbi.table/R/extract.R | 31 - dbi.table-1.0.3/dbi.table/R/information_schema.R | 111 ++--- dbi.table-1.0.3/dbi.table/R/merge.R | 146 ++++-- dbi.table-1.0.3/dbi.table/R/onLoad.R | 13 dbi.table-1.0.3/dbi.table/R/reference.test.R | 22 dbi.table-1.0.3/dbi.table/R/relational.R | 221 +++------- dbi.table-1.0.3/dbi.table/R/sql.join.R | 155 +++---- dbi.table-1.0.3/dbi.table/R/utilities.R | 86 +++ dbi.table-1.0.3/dbi.table/inst/doc/introduction_to_dbi_table.R | 1 dbi.table-1.0.3/dbi.table/inst/doc/introduction_to_dbi_table.Rmd | 3 dbi.table-1.0.3/dbi.table/inst/doc/introduction_to_dbi_table.html | 21 dbi.table-1.0.3/dbi.table/inst/example_files/chinook_export/LICENSE |only dbi.table-1.0.3/dbi.table/inst/example_files/chinook_export/album.csv |only dbi.table-1.0.3/dbi.table/inst/example_files/chinook_export/artist.csv |only dbi.table-1.0.3/dbi.table/inst/example_files/chinook_export/customer.csv |only dbi.table-1.0.3/dbi.table/inst/example_files/chinook_export/employee.csv |only dbi.table-1.0.3/dbi.table/inst/example_files/chinook_export/genre.csv |only dbi.table-1.0.3/dbi.table/inst/example_files/chinook_export/invoice.csv |only dbi.table-1.0.3/dbi.table/inst/example_files/chinook_export/invoiceline.csv |only dbi.table-1.0.3/dbi.table/inst/example_files/chinook_export/mediatype.csv |only dbi.table-1.0.3/dbi.table/inst/example_files/chinook_export/playlist.csv |only dbi.table-1.0.3/dbi.table/inst/example_files/chinook_export/playlisttrack.csv |only dbi.table-1.0.3/dbi.table/inst/example_files/chinook_export/track.csv |only dbi.table-1.0.3/dbi.table/man/DBI-methods.Rd | 3 dbi.table-1.0.3/dbi.table/man/as.data.frame.Rd |only dbi.table-1.0.3/dbi.table/man/dbi.attach.Rd | 6 dbi.table-1.0.3/dbi.table/man/dbi.catalog.Rd | 12 dbi.table-1.0.3/dbi.table/man/dbi.table-package.Rd | 4 dbi.table-1.0.3/dbi.table/man/merge.Rd | 24 - dbi.table-1.0.3/dbi.table/man/reference.test.Rd | 1 dbi.table-1.0.3/dbi.table/man/sql.join.Rd | 8 dbi.table-1.0.3/dbi.table/tests/testthat/helper-library(data.table).R |only dbi.table-1.0.3/dbi.table/tests/testthat/test-DBI_methods.R |only dbi.table-1.0.3/dbi.table/tests/testthat/test-assumptions.R | 10 dbi.table-1.0.3/dbi.table/tests/testthat/test-attach.R | 47 ++ dbi.table-1.0.3/dbi.table/tests/testthat/test-data.table-set-functions.R |only dbi.table-1.0.3/dbi.table/tests/testthat/test-dbi.table.R | 1 dbi.table-1.0.3/dbi.table/tests/testthat/test-merge.R | 4 dbi.table-1.0.3/dbi.table/tests/testthat/test-relational.R |only dbi.table-1.0.3/dbi.table/tests/testthat/test-sql.join.R | 3 dbi.table-1.0.3/dbi.table/vignettes/introduction_to_dbi_table.Rmd | 3 66 files changed, 775 insertions(+), 623 deletions(-)
Title: Access, Retrieve, and Work with CMHC Data
Description: Wrapper around the Canadian Mortgage and Housing Corporation (CMHC) web interface. It enables programmatic and reproducible access to a wide variety of housing data from CMHC.
Author: Jens von Bergmann [aut, cre]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between cmhc versions 0.2.9 dated 2024-11-05 and 0.2.10 dated 2025-02-03
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/cmhc_tables.R | 3 ++- README.md | 6 +++--- build/vignette.rds |binary inst/doc/basic_usage.html | 6 +++--- inst/doc/rental_universe.html | 4 ++-- 8 files changed, 25 insertions(+), 19 deletions(-)
Title: Plot Stacked Areas and Confidence Bands as Filled Polygons
Description: Plot stacked areas and confidence bands as filled polygons, or add
polygons to existing plots. A variety of input formats are supported,
including vectors, matrices, data frames, formulas, etc.
Author: Arni Magnusson [aut, cre]
Maintainer: Arni Magnusson <thisisarni@gmail.com>
Diff between areaplot versions 2.1.2 dated 2024-01-14 and 2.1.3 dated 2025-02-03
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS.md | 14 ++++++++++++++ R/areaplot-package.R | 6 ++---- R/areaplot.R | 38 +++++++++++++++++++++++++++----------- R/confplot.R | 8 +++++--- man/areaplot-package.Rd | 9 ++++++++- man/areaplot.Rd | 19 ++++++++++++++++--- man/confplot.Rd | 6 +++--- 9 files changed, 88 insertions(+), 38 deletions(-)
Title: Filter Module for 'teal' Applications
Description: Data filtering module for 'teal' applications. Allows for
interactive filtering of data stored in 'data.frame' and
'MultiAssayExperiment' objects. Also displays filtered and unfiltered
observation counts.
Author: Dawid Kaledkowski [aut, cre] ,
Pawel Rucki [aut],
Aleksander Chlebowski [aut] ,
Andre Verissimo [aut] ,
Kartikeya Kirar [aut],
Marcin Kosinski [aut],
Chendi Liao [rev],
Dony Unardi [rev],
Andrew Bates [aut],
Mahmoud Hallal [aut],
Nikolas Burkoff [aut [...truncated...]
Maintainer: Dawid Kaledkowski <dawid.kaledkowski@roche.com>
Diff between teal.slice versions 0.5.1 dated 2024-04-30 and 0.6.0 dated 2025-02-03
teal.slice-0.5.1/teal.slice/man/check_simple_name.Rd |only teal.slice-0.6.0/teal.slice/DESCRIPTION | 27 teal.slice-0.6.0/teal.slice/MD5 | 130 +-- teal.slice-0.6.0/teal.slice/NEWS.md | 19 teal.slice-0.6.0/teal.slice/R/FilterState.R | 76 +- teal.slice-0.6.0/teal.slice/R/FilterStateChoices.R | 60 - teal.slice-0.6.0/teal.slice/R/FilterStateDate.R | 22 teal.slice-0.6.0/teal.slice/R/FilterStateDatettime.R | 26 teal.slice-0.6.0/teal.slice/R/FilterStateExpr.R | 38 - teal.slice-0.6.0/teal.slice/R/FilterStateLogical.R | 14 teal.slice-0.6.0/teal.slice/R/FilterStateRange.R | 116 +-- teal.slice-0.6.0/teal.slice/R/FilterStates.R | 98 +- teal.slice-0.6.0/teal.slice/R/FilterStatesMatrix.R | 5 teal.slice-0.6.0/teal.slice/R/FilterStatesSE.R | 41 - teal.slice-0.6.0/teal.slice/R/FilteredData-utils.R | 18 teal.slice-0.6.0/teal.slice/R/FilteredData.R | 354 ++++------ teal.slice-0.6.0/teal.slice/R/FilteredDataset.R | 199 +++-- teal.slice-0.6.0/teal.slice/R/FilteredDatasetDataframe.R | 15 teal.slice-0.6.0/teal.slice/R/FilteredDatasetDefault.R | 3 teal.slice-0.6.0/teal.slice/R/FilteredDatasetMAE.R | 8 teal.slice-0.6.0/teal.slice/R/count_labels.R | 14 teal.slice-0.6.0/teal.slice/R/filter_panel_api.R | 9 teal.slice-0.6.0/teal.slice/R/teal_slice.R | 1 teal.slice-0.6.0/teal.slice/R/teal_slices.R | 3 teal.slice-0.6.0/teal.slice/R/utils.R | 99 ++ teal.slice-0.6.0/teal.slice/R/zzz.R | 2 teal.slice-0.6.0/teal.slice/README.md | 11 teal.slice-0.6.0/teal.slice/build/vignette.rds |binary teal.slice-0.6.0/teal.slice/inst/css/filter-panel.css | 95 ++ teal.slice-0.6.0/teal.slice/inst/doc/filter-panel-for-developers.R | 2 teal.slice-0.6.0/teal.slice/inst/doc/filter-panel-for-developers.Rmd | 2 teal.slice-0.6.0/teal.slice/inst/doc/filter-panel-for-developers.html | 259 +++---- teal.slice-0.6.0/teal.slice/inst/doc/teal-slice-classes.html | 22 teal.slice-0.6.0/teal.slice/inst/doc/teal-slice.R | 2 teal.slice-0.6.0/teal.slice/inst/doc/teal-slice.Rmd | 30 teal.slice-0.6.0/teal.slice/inst/doc/teal-slice.html | 118 +-- teal.slice-0.6.0/teal.slice/inst/js/icons.js |only teal.slice-0.6.0/teal.slice/inst/js/togglePanelItems.js |only teal.slice-0.6.0/teal.slice/man/ChoicesFilterState.Rd | 2 teal.slice-0.6.0/teal.slice/man/DFFilterStates.Rd | 1 teal.slice-0.6.0/teal.slice/man/DataframeFilteredDataset.Rd | 2 teal.slice-0.6.0/teal.slice/man/DateFilterState.Rd | 2 teal.slice-0.6.0/teal.slice/man/DatetimeFilterState.Rd | 2 teal.slice-0.6.0/teal.slice/man/DefaultFilteredDataset.Rd | 6 teal.slice-0.6.0/teal.slice/man/EmptyFilterState.Rd | 2 teal.slice-0.6.0/teal.slice/man/FilterState.Rd | 17 teal.slice-0.6.0/teal.slice/man/FilterStateExpr.Rd | 17 teal.slice-0.6.0/teal.slice/man/FilterStates.Rd | 18 teal.slice-0.6.0/teal.slice/man/FilteredData.Rd | 76 -- teal.slice-0.6.0/teal.slice/man/FilteredDataset.Rd | 37 - teal.slice-0.6.0/teal.slice/man/LogicalFilterState.Rd | 2 teal.slice-0.6.0/teal.slice/man/MAEFilterStates.Rd | 1 teal.slice-0.6.0/teal.slice/man/MAEFilteredDataset.Rd | 2 teal.slice-0.6.0/teal.slice/man/MatrixFilterStates.Rd | 1 teal.slice-0.6.0/teal.slice/man/RangeFilterState.Rd | 2 teal.slice-0.6.0/teal.slice/man/SEFilterStates.Rd | 1 teal.slice-0.6.0/teal.slice/man/dot-finalize_session_bindings.Rd |only teal.slice-0.6.0/teal.slice/man/init_filtered_data.Rd | 6 teal.slice-0.6.0/teal.slice/man/pair_counts.Rd |only teal.slice-0.6.0/teal.slice/man/sanitize_id.Rd |only teal.slice-0.6.0/teal.slice/man/teal_slices.Rd | 2 teal.slice-0.6.0/teal.slice/tests/testthat/test-ChoicesFilterState.R | 82 ++ teal.slice-0.6.0/teal.slice/tests/testthat/test-DataframeFilteredDataset.R | 4 teal.slice-0.6.0/teal.slice/tests/testthat/test-FilteredData.R | 53 - teal.slice-0.6.0/teal.slice/tests/testthat/test-teal_slice.R | 5 teal.slice-0.6.0/teal.slice/tests/testthat/test-teal_slices.R | 7 teal.slice-0.6.0/teal.slice/tests/testthat/test-utils.R | 111 ++- teal.slice-0.6.0/teal.slice/vignettes/filter-panel-for-developers.Rmd | 2 teal.slice-0.6.0/teal.slice/vignettes/teal-slice.Rmd | 30 69 files changed, 1373 insertions(+), 1058 deletions(-)
Title: Fast Imputations Using 'Rcpp' and 'Armadillo'
Description: Fast imputations under the object-oriented programming paradigm.
Moreover there are offered a few functions built to work with popular R packages such as 'data.table' or 'dplyr'.
The biggest improvement in time performance could be achieve for a calculation where a grouping variable have to be used.
A single evaluation of a quantitative model for the multiple imputations is another major enhancement.
A new major improvement is one of the fastest predictive mean matching in the R world because of presorting and binary search.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>
Diff between miceFast versions 0.8.2 dated 2022-11-17 and 0.8.5 dated 2025-02-03
miceFast-0.8.2/miceFast/tests/testthat/Rplots.pdf |only miceFast-0.8.5/miceFast/DESCRIPTION | 9 miceFast-0.8.5/miceFast/MD5 | 41 miceFast-0.8.5/miceFast/NEWS.md | 10 miceFast-0.8.5/miceFast/R/VIF.R | 9 miceFast-0.8.5/miceFast/README.md | 118 +- miceFast-0.8.5/miceFast/build/vignette.rds |binary miceFast-0.8.5/miceFast/inst/doc/miceFast-intro.R | 340 ++---- miceFast-0.8.5/miceFast/inst/doc/miceFast-intro.Rmd | 587 ++++------- miceFast-0.8.5/miceFast/inst/doc/miceFast-intro.html | 925 +++++++---------- miceFast-0.8.5/miceFast/man/Rcpp_corrData-class.Rd | 13 miceFast-0.8.5/miceFast/man/Rcpp_miceFast-class.Rd | 9 miceFast-0.8.5/miceFast/man/VIF.Rd | 2 miceFast-0.8.5/miceFast/src/Makevars | 2 miceFast-0.8.5/miceFast/src/Makevars.win | 3 miceFast-0.8.5/miceFast/src/R_funs.cpp | 176 +-- miceFast-0.8.5/miceFast/src/corrData.cpp | 95 - miceFast-0.8.5/miceFast/src/miceFast.h | 84 - miceFast-0.8.5/miceFast/src/miceFast_class.cpp | 1006 ++++++++----------- miceFast-0.8.5/miceFast/src/miceFast_quantmodels.cpp | 358 +++--- miceFast-0.8.5/miceFast/tests/testthat.R | 2 miceFast-0.8.5/miceFast/vignettes/miceFast-intro.Rmd | 587 ++++------- 22 files changed, 1847 insertions(+), 2529 deletions(-)
Title: Simple Framework for Simple Automation
Description: Build a project framework for users with
access to only the most basic of automation tools.
Author: Alexander Senetcky [aut, cre, cph]
Maintainer: Alexander Senetcky <asenetcky@gmail.com>
Diff between strata versions 1.0.1 dated 2024-11-27 and 1.4.0 dated 2025-02-03
strata-1.0.1/strata/R/adhoc.R |only strata-1.0.1/strata/R/builders.R |only strata-1.0.1/strata/R/execution_plan.R |only strata-1.0.1/strata/R/logging.R |only strata-1.0.1/strata/R/main.R |only strata-1.0.1/strata/R/manage_tomls.R |only strata-1.0.1/strata/R/quick_build.R |only strata-1.0.1/strata/R/read_write_toml.R |only strata-1.0.1/strata/R/survey_strata.R |only strata-1.0.1/strata/R/user_toml_interaction.R |only strata-1.0.1/strata/tests/testthat/test-adhoc.R |only strata-1.0.1/strata/tests/testthat/test-builders.R |only strata-1.0.1/strata/tests/testthat/test-execution_plan.R |only strata-1.0.1/strata/tests/testthat/test-logging.R |only strata-1.0.1/strata/tests/testthat/test-main.R |only strata-1.0.1/strata/tests/testthat/test-manage_tomls.R |only strata-1.0.1/strata/tests/testthat/test-quick_build.R |only strata-1.0.1/strata/tests/testthat/test-survey_strata.R |only strata-1.0.1/strata/tests/testthat/test-user_toml_interaction.R |only strata-1.4.0/strata/DESCRIPTION | 9 strata-1.4.0/strata/LICENSE | 4 strata-1.4.0/strata/MD5 | 96 strata-1.4.0/strata/NAMESPACE | 42 strata-1.4.0/strata/NEWS.md | 128 - strata-1.4.0/strata/R/adhoc-core.R |only strata-1.4.0/strata/R/adhoc-utils.R |only strata-1.4.0/strata/R/build-core.R |only strata-1.4.0/strata/R/build-quick.R |only strata-1.4.0/strata/R/log-core.R |only strata-1.4.0/strata/R/main-core.R |only strata-1.4.0/strata/R/main-utils.R |only strata-1.4.0/strata/R/strata-package.R | 18 strata-1.4.0/strata/R/survey-core.R |only strata-1.4.0/strata/R/survey-utils.R |only strata-1.4.0/strata/R/toml-core.R |only strata-1.4.0/strata/R/toml-io.R |only strata-1.4.0/strata/R/toml-utils.R |only strata-1.4.0/strata/README.md | 1085 ++++++++-- strata-1.4.0/strata/man/adhoc.Rd |only strata-1.4.0/strata/man/adhoc_lamina.Rd | 66 strata-1.4.0/strata/man/adhoc_stratum.Rd | 66 strata-1.4.0/strata/man/build_lamina.Rd | 60 strata-1.4.0/strata/man/build_outlined_strata_project.Rd | 116 - strata-1.4.0/strata/man/build_quick_strata_project.Rd | 66 strata-1.4.0/strata/man/build_stratum.Rd | 54 strata-1.4.0/strata/man/edit_toml.Rd | 146 - strata-1.4.0/strata/man/figures/lifecycle-deprecated.svg | 42 strata-1.4.0/strata/man/figures/lifecycle-experimental.svg | 42 strata-1.4.0/strata/man/figures/lifecycle-stable.svg | 58 strata-1.4.0/strata/man/figures/lifecycle-superseded.svg | 42 strata-1.4.0/strata/man/log_error.Rd | 50 strata-1.4.0/strata/man/log_message.Rd | 66 strata-1.4.0/strata/man/log_total_time.Rd | 57 strata-1.4.0/strata/man/main.Rd | 114 - strata-1.4.0/strata/man/strata-package.Rd | 48 strata-1.4.0/strata/man/survey_log.Rd |only strata-1.4.0/strata/man/survey_strata.Rd | 76 strata-1.4.0/strata/man/survey_tomls.Rd | 52 strata-1.4.0/strata/man/view_toml.Rd | 48 strata-1.4.0/strata/tests/testthat.R | 24 strata-1.4.0/strata/tests/testthat/test-adhoc-core.R |only strata-1.4.0/strata/tests/testthat/test-adhoc-utils.R |only strata-1.4.0/strata/tests/testthat/test-build-core.R |only strata-1.4.0/strata/tests/testthat/test-build-quick.R |only strata-1.4.0/strata/tests/testthat/test-log-core.R |only strata-1.4.0/strata/tests/testthat/test-main-core.R |only strata-1.4.0/strata/tests/testthat/test-main-utils.R |only strata-1.4.0/strata/tests/testthat/test-survey-core.R |only strata-1.4.0/strata/tests/testthat/test-survey-utils.R |only strata-1.4.0/strata/tests/testthat/test-toml-core.R |only strata-1.4.0/strata/tests/testthat/test-toml-utils.R |only 71 files changed, 1780 insertions(+), 895 deletions(-)
Title: 'tidyverse' Methods and 'ggplot2' Helpers for 'terra' Objects
Description: Extension of the 'tidyverse' for 'SpatRaster' and
'SpatVector' objects of the 'terra' package. It includes also new
'geom_' functions that provide a convenient way of visualizing 'terra'
objects with 'ggplot2'.
Author: Diego Hernangomez [aut, cre, cph]
,
Dewey Dunnington [ctb] ,
ggplot2 authors [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between tidyterra versions 0.6.2 dated 2025-01-08 and 0.7.0 dated 2025-02-03
DESCRIPTION | 14 MD5 | 42 NEWS.md | 18 R/fortify-Spat.R | 24 R/geom_spat_contour.R | 970 +++++++-------- R/geom_spatraster.R | 23 R/scales_cross_blended.R | 1494 +++++++++++------------- R/scales_grass.R | 13 R/scales_hypso.R | 35 inst/schemaorg.json | 2 man/fortify.Spat.Rd | 24 man/geom_spat_contour.Rd | 6 man/scale_cross_blended.Rd | 26 man/scale_grass.Rd | 5 man/scale_hypso.Rd | 26 tests/testthat/test-fortify-Spat.R | 94 + tests/testthat/test-geom_spatraster_3lyr.R | 46 tests/testthat/test-scales_col_cross_blended.R | 37 tests/testthat/test-scales_col_hypso.R | 4 tests/testthat/test-scales_fill_cross_blended.R | 4 tests/testthat/test-scales_fill_hypso.R | 40 tests/testthat/test-scales_grass.R | 41 22 files changed, 1599 insertions(+), 1389 deletions(-)
Title: Interface Between 'GRASS' Geographical Information System and
'R'
Description: An interface between the 'GRASS' geographical information system ('GIS') and 'R', based on starting 'R' from within the 'GRASS' 'GIS' environment, or running a free-standing 'R' session in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the 'R' command line. The original interface package for 'GRASS 5' (2000-2010) is described in Bivand (2000) <doi:10.1016/S0098-3004(00)00057-1> and Bivand (2001) <https://www.r-project.org/conferences/DSC-2001/Proceedings/Bivand.pdf>. This was succeeded by 'spgrass6' for 'GRASS 6' (2006-2016) and 'rgrass7' for 'GRASS 7' (2015-present). The 'rgrass' package modernizes the interface for 'GRASS 8' while still permitting the use of 'GRASS 7'.
Author: Roger Bivand [aut] ,
Sebastian Jeworutzki [ctb] ,
Rainer Krug [ctb] ,
Robin Lovelace [ctb] ,
Markus Neteler [ctb] ,
Steven Pawley [cre, aut] ,
Floris Vanderhaeghe [ctb]
Maintainer: Steven Pawley <dr.stevenpawley@gmail.com>
Diff between rgrass versions 0.4-4 dated 2024-09-03 and 0.5-1 dated 2025-02-03
rgrass-0.4-4/rgrass/R/rgrass.R |only rgrass-0.4-4/rgrass/man/readRAST.Rd |only rgrass-0.4-4/rgrass/man/readVECT.Rd |only rgrass-0.4-4/rgrass/tests/test_XML_xml2.R |only rgrass-0.4-4/rgrass/tests/test_XML_xml2.Rout.save |only rgrass-0.4-4/rgrass/tests/test_terra_ptr.R |only rgrass-0.4-4/rgrass/tests/test_terra_ptr.Rout.save |only rgrass-0.5-1/rgrass/DESCRIPTION | 35 - rgrass-0.5-1/rgrass/MD5 | 59 - rgrass-0.5-1/rgrass/NAMESPACE | 71 +- rgrass-0.5-1/rgrass/NEWS.md | 16 rgrass-0.5-1/rgrass/R/gmeta.R |only rgrass-0.5-1/rgrass/R/initGRASS.R | 685 ++++++++++++++------- rgrass-0.5-1/rgrass/R/options.R | 56 + rgrass-0.5-1/rgrass/R/rast_link.R | 204 ++++++ rgrass-0.5-1/rgrass/R/rgrass-package.R |only rgrass-0.5-1/rgrass/R/vect_link.R | 19 rgrass-0.5-1/rgrass/R/vect_link_ng.R | 168 +++++ rgrass-0.5-1/rgrass/R/xml1.R | 231 +++++++ rgrass-0.5-1/rgrass/build/vignette.rds |binary rgrass-0.5-1/rgrass/inst/doc/coerce.Rmd | 4 rgrass-0.5-1/rgrass/inst/doc/coerce.html | 40 - rgrass-0.5-1/rgrass/inst/doc/use.Rmd | 6 rgrass-0.5-1/rgrass/inst/doc/use.html | 21 rgrass-0.5-1/rgrass/man/execGRASS.Rd | 317 +++++++-- rgrass-0.5-1/rgrass/man/gmeta.Rd | 87 +- rgrass-0.5-1/rgrass/man/initGRASS.Rd | 224 +++++- rgrass-0.5-1/rgrass/man/read_RAST.Rd |only rgrass-0.5-1/rgrass/man/read_VECT.Rd |only rgrass-0.5-1/rgrass/man/rgrass.Rd | 97 +- rgrass-0.5-1/rgrass/tests/testthat |only rgrass-0.5-1/rgrass/tests/testthat.R |only rgrass-0.5-1/rgrass/vignettes/coerce.Rmd | 4 rgrass-0.5-1/rgrass/vignettes/use.Rmd | 6 34 files changed, 1805 insertions(+), 545 deletions(-)
Title: Ordered Beta Regression Models with 'brms'
Description: Implements ordered beta regression models, which are for modeling continuous variables with upper and lower bounds, such as
survey sliders, dose-response relationships and indexes. For more information, see
Kubinec (2023) <doi:10.31235/osf.io/2sx6y>. The package is a front-end to the R package 'brms', which
facilitates a range of regression specifications, including hierarchical, dynamic and
multivariate modeling.
Author: Robert Kubinec [aut, cre]
Maintainer: Robert Kubinec <bobkubinec@gmail.com>
Diff between ordbetareg versions 0.7.2 dated 2023-08-10 and 0.8 dated 2025-02-03
ordbetareg-0.7.2/ordbetareg/data/fit_imputed.rda |only ordbetareg-0.7.2/ordbetareg/inst/doc/package_introduction.Rmd |only ordbetareg-0.7.2/ordbetareg/man/fit_imputed.Rd |only ordbetareg-0.7.2/ordbetareg/vignettes/package_introduction.Rmd |only ordbetareg-0.8/ordbetareg/DESCRIPTION | 25 ordbetareg-0.8/ordbetareg/MD5 | 39 ordbetareg-0.8/ordbetareg/NAMESPACE | 18 ordbetareg-0.8/ordbetareg/NEWS.md | 18 ordbetareg-0.8/ordbetareg/R/distribution.R | 5 ordbetareg-0.8/ordbetareg/R/modeling.R | 685 ++ ordbetareg-0.8/ordbetareg/R/package_info.R | 27 ordbetareg-0.8/ordbetareg/R/plot.R | 362 + ordbetareg-0.8/ordbetareg/build/vignette.rds |binary ordbetareg-0.8/ordbetareg/data/fit_multivariate.rda |binary ordbetareg-0.8/ordbetareg/data/ord_fit_mean.rda |binary ordbetareg-0.8/ordbetareg/data/ord_fit_phi.rda |binary ordbetareg-0.8/ordbetareg/inst/doc/package_introduction.R | 194 ordbetareg-0.8/ordbetareg/inst/doc/package_introduction.html | 2779 +++------- ordbetareg-0.8/ordbetareg/inst/doc/package_introduction.qmd |only ordbetareg-0.8/ordbetareg/man/ordbetareg-package.Rd |only ordbetareg-0.8/ordbetareg/man/ordbetareg.Rd | 36 ordbetareg-0.8/ordbetareg/man/plot_heiss.Rd |only ordbetareg-0.8/ordbetareg/man/posterior_epred_ordbeta.brmsfit.Rd |only ordbetareg-0.8/ordbetareg/man/pp_check_ordbeta.Rd | 9 ordbetareg-0.8/ordbetareg/vignettes/package_introduction.qmd |only 25 files changed, 2312 insertions(+), 1885 deletions(-)
Title: Clean and Analyze Continuous Glucose Monitor Data
Description: This code provides several different functions for cleaning and analyzing continuous glucose monitor data. Currently it works with 'Dexcom', 'iPro 2', 'Diasend', 'Libre', or 'Carelink' data. The cleandata() function takes a directory of CGM data files and prepares them for analysis. cgmvariables() iterates through a directory of cleaned CGM data files and produces a single spreadsheet with data for each file in either rows or columns. The column format of this spreadsheet is compatible with REDCap data upload. cgmreport() also iterates through a directory of cleaned data, and produces PDFs of individual and aggregate AGP plots. Please visit <https://github.com/childhealthbiostatscore/R-Packages/> to download the new-user guide.
Author: Tim Vigers [aut, cre]
Maintainer: Tim Vigers <timothy.vigers@cuanschutz.edu>
Diff between cgmanalysis versions 3.0.1 dated 2025-02-01 and 3.0.2 dated 2025-02-03
DESCRIPTION | 6 - MD5 | 6 - R/cgmvariables.R | 221 +++++++++++++++++++++++++++++----------------------- man/cgmvariables.Rd | 5 - 4 files changed, 135 insertions(+), 103 deletions(-)
More information about tmap.cartogram at CRAN
Permanent link
Title: Retrieving, Organizing, and Analyzing Estuary Monitoring Data
Description: Tools for retrieving, organizing, and analyzing environmental
data from the System Wide Monitoring Program of the National Estuarine
Research Reserve System <https://cdmo.baruch.sc.edu/>. These tools
address common challenges associated with continuous time series data
for environmental decision making.
Author: Marcus W. Beck [aut, cre],
Kimberly Cressman [ctb]
Maintainer: Marcus W. Beck <mbeck@tbep.org>
Diff between SWMPr versions 2.5.1 dated 2024-06-24 and 2.5.2 dated 2025-02-03
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/decomp.R | 2 +- inst/doc/Overview.R | 18 +++++++++--------- inst/doc/Overview.html | 2 +- 6 files changed, 24 insertions(+), 20 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 4.3.6 dated 2024-10-20 and 4.3.7 dated 2025-02-03
sommer-4.3.6/sommer/inst/doc/rice_example.R |only sommer-4.3.7/sommer/CHANGELOG | 2 sommer-4.3.7/sommer/DESCRIPTION | 8 sommer-4.3.7/sommer/MD5 | 33 +-- sommer-4.3.7/sommer/R/FUN_utils.R | 2 sommer-4.3.7/sommer/R/GWAS.R | 16 + sommer-4.3.7/sommer/R/mmec.R | 11 - sommer-4.3.7/sommer/R/mmer.R | 18 + sommer-4.3.7/sommer/man/mmec.Rd | 7 sommer-4.3.7/sommer/man/mmer.Rd | 3 sommer-4.3.7/sommer/src/MNR.cpp | 93 +++++----- sommer-4.3.7/sommer/src/RcppExports.cpp | 4 sommer-4.3.7/sommer/vignettes/v1.sommer.quick.start.html | 11 - sommer-4.3.7/sommer/vignettes/v2.sommer.changes.and.faqs.html | 5 sommer-4.3.7/sommer/vignettes/v3.sommer.qg.html | 11 - sommer-4.3.7/sommer/vignettes/v4.sommer.gxe.html | 9 sommer-4.3.7/sommer/vignettes/v5.sommer.vs.lme4.html | 5 sommer-4.3.7/sommer/vignettes/v6.sommer.spatial.html | 5 18 files changed, 135 insertions(+), 108 deletions(-)
Title: High Performance Tools for Combinatorics and Computational
Mathematics
Description: Provides optimized functions and flexible iterators implemented in
C++ for solving problems in combinatorics and computational mathematics.
Handles various combinatorial objects including combinations, permutations,
integer partitions and compositions, Cartesian products, unordered
Cartesian products, and partition of groups. Utilizes the RMatrix class
from 'RcppParallel' for thread safety. The combination and permutation
functions contain constraint parameters that allow for generation of all
results of a vector meeting specific criteria (e.g. finding all
combinations such that the sum is between two bounds). Capable of
ranking/unranking combinatorial objects efficiently (e.g. retrieve only the
nth lexicographical result) which sets up nicely for parallelization as
well as random sampling. Gmp support permits exploration where the total
number of results is large (e.g. comboSample(10000, 500, n = 4)).
Additionally, there are several high performance number theoretic
functions that are [...truncated...]
Author: Joseph Wood [aut, cre]
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between RcppAlgos versions 2.9.1 dated 2025-01-27 and 2.9.3 dated 2025-02-03
DESCRIPTION | 8 +- MD5 | 64 +++++++++---------- NEWS.md | 12 +++ inst/NEWS.Rd | 18 +++++ inst/doc/CombPermConstraints.Rmd | 44 ++++++------- inst/doc/CombPermConstraints.html | 46 ++++++------- inst/doc/CombinatorialSampling.Rmd | 20 ++--- inst/doc/CombinatorialSampling.html | 22 +++--- inst/doc/CombinatoricsIterators.Rmd | 81 +++++++++++------------- inst/doc/CombinatoricsIterators.html | 107 +++++++++++++++----------------- inst/doc/ComputationalMathematics.Rmd | 38 +++++------ inst/doc/ComputationalMathematics.html | 40 +++++------ inst/doc/GeneralCombinatorics.Rmd | 28 ++++---- inst/doc/GeneralCombinatorics.html | 30 ++++---- inst/doc/HighPerformanceBenchmarks.Rmd | 102 +++++++++++++++--------------- inst/doc/HighPerformanceBenchmarks.html | 104 +++++++++++++++---------------- inst/doc/OtherCombinatorics.Rmd | 22 +++--- inst/doc/OtherCombinatorics.html | 24 +++---- inst/doc/SubsetSum.Rmd | 32 ++++----- inst/doc/SubsetSum.html | 36 +++++----- inst/include/Combinations/ComboCount.h | 4 + src/ComboCount.cpp | 37 ++++++++--- src/ComboGroupsGeneral.cpp | 13 ++- src/NthCombination.cpp | 28 +------- src/RankCombination.cpp | 28 +------- vignettes/CombPermConstraints.Rmd | 44 ++++++------- vignettes/CombinatorialSampling.Rmd | 20 ++--- vignettes/CombinatoricsIterators.Rmd | 81 +++++++++++------------- vignettes/ComputationalMathematics.Rmd | 38 +++++------ vignettes/GeneralCombinatorics.Rmd | 28 ++++---- vignettes/HighPerformanceBenchmarks.Rmd | 102 +++++++++++++++--------------- vignettes/OtherCombinatorics.Rmd | 22 +++--- vignettes/SubsetSum.Rmd | 32 ++++----- 33 files changed, 684 insertions(+), 671 deletions(-)
Title: Define and Enforce Contracts for Dataframes as Function
Parameters
Description: A dataframe validation framework for package builders who use
dataframes as function parameters. It performs checks on column names, coerces
data-types, and checks grouping to make sure user inputs conform to a
specification provided by the package author. It provides a mechanism for
package authors to automatically document supported dataframe inputs and
selectively dispatch to functions depending on the format of a dataframe much
like S3 does for classes. It also contains some developer tools to make
working with and documenting dataframe specifications easier. It helps package
developers to improve their documentation and simplifies parameter validation
where dataframes are used as function parameters.
Author: Robert Challen [aut, cre, cph]
Maintainer: Robert Challen <rob.challen@bristol.ac.uk>
Diff between interfacer versions 0.3.2 dated 2024-11-14 and 0.3.3 dated 2025-02-03
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS.md | 7 ++++++- R/type-coerce.R | 4 +++- R/utils-functions.R | 7 ++++--- README.md | 19 +++++++++---------- build/vignette.rds |binary inst/doc/nesting.html | 2 +- 8 files changed, 36 insertions(+), 29 deletions(-)
Title: Access Data from the Atlas do Estado Brasileiro
Description: Facilitates access to the data from the Atlas do Estado Brasileiro
(<https://www.ipea.gov.br/atlasestado/>), maintained by the Instituto de
Pesquisa Econômica Aplicada (Ipea). It allows users to search for specific
series, list series or themes, and download data when available.
Author: Hugo Macedo [aut, cre, cph]
Maintainer: Hugo Macedo <aebdata@hhmace.do>
Diff between aebdata versions 0.1.3 dated 2025-01-12 and 0.1.4 dated 2025-02-03
DESCRIPTION | 6 +- MD5 | 8 +-- NEWS.md | 8 +++ inst/doc/exploring-data.html | 90 +++++++++++++++++++++++++++++++++++++++- tests/testthat/_data/search.rds |binary 5 files changed, 104 insertions(+), 8 deletions(-)
Title: Tensors and Neural Networks with 'GPU' Acceleration
Description: Provides functionality to define and train neural networks similar to
'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R
using the 'libtorch' library. Also supports low-level tensor operations and
'GPU' acceleration.
Author: Daniel Falbel [aut, cre, cph],
Javier Luraschi [aut],
Dmitriy Selivanov [ctb],
Athos Damiani [ctb],
Christophe Regouby [ctb],
Krzysztof Joachimiak [ctb],
Hamada S. Badr [ctb],
Sebastian Fischer [ctb],
Maximilian Pichler [ctb],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between torch versions 0.14.0 dated 2025-01-30 and 0.14.1 dated 2025-02-03
DESCRIPTION | 6 MD5 | 18 - NEWS.md | 6 R/install.R | 2 build/partial.rdb |binary inst/doc/tensor-creation.html | 8 inst/doc/torchscript.html | 112 +++++----- inst/include/lantern/lantern.h | 5 inst/po/fr/LC_MESSAGES/R-torch.mo |binary po/R-fr.po | 400 +++++++++++++++++++++++++++++--------- 10 files changed, 393 insertions(+), 164 deletions(-)
Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting.
The package includes ADAM (Svetunkov, 2023, <https://openforecast.org/adam/>),
Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>),
SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>),
Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>),
Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>)
and several simulation functions. It also allows dealing with intermittent demand based on the
iETS framework (Svetunkov & Boylan, 2019, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>
Diff between smooth versions 4.1.0 dated 2024-10-01 and 4.1.1 dated 2025-02-03
DESCRIPTION | 10 - MD5 | 112 ++++++++-------- NAMESPACE | 1 NEWS | 15 ++ R/adam-sma.R | 2 R/adam.R | 52 +++++-- R/adamGeneral.R | 22 ++- R/methods.R | 6 R/msdecompose.R | 189 +++++++++++++++++++-------- R/smooth-package.R | 3 R/sowhat.R | 2 R/zzz.R | 8 - README.md | 2 inst/doc/adam.R | 70 +++++----- inst/doc/adam.Rmd | 74 +++++----- inst/doc/adam.html | 333 ++++++++++++++++++++++++------------------------- inst/doc/ces.html | 8 - inst/doc/es.html | 14 +- inst/doc/gum.html | 10 - inst/doc/oes.html | 116 ++++++++--------- inst/doc/simulate.html | 78 +++++------ inst/doc/sma.html | 12 - inst/doc/smooth.html | 4 inst/doc/ssarima.html | 26 +-- man/accuracy.Rd | 2 man/adam.Rd | 4 man/auto.ces.Rd | 2 man/auto.gum.Rd | 2 man/auto.ssarima.Rd | 2 man/ces.Rd | 2 man/cma.Rd | 2 man/es.Rd | 2 man/forecast.smooth.Rd | 2 man/gum.Rd | 2 man/isFunctions.Rd | 2 man/msarima.Rd | 2 man/msdecompose.Rd | 16 ++ man/multicov.Rd | 8 - man/oes.Rd | 2 man/oesg.Rd | 2 man/orders.Rd | 2 man/plot.smooth.Rd | 2 man/pls.Rd | 2 man/reapply.Rd | 2 man/rmultistep.Rd | 2 man/sim.ces.Rd | 2 man/sim.es.Rd | 2 man/sim.gum.Rd | 2 man/sim.oes.Rd | 2 man/sim.sma.Rd | 2 man/sim.ssarima.Rd | 2 man/sma.Rd | 2 man/smooth.Rd | 4 man/smoothCombine.Rd | 2 man/sowhat.Rd | 4 man/ssarima.Rd | 2 vignettes/adam.Rmd | 74 +++++----- 57 files changed, 732 insertions(+), 601 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 0.3.2 dated 2024-11-28 and 0.3.3 dated 2025-02-03
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/atos.R | 4 ++-- R/fit_sgs.R | 2 +- R/run_algorithm.R | 8 ++++---- R/utils.R | 8 ++++---- inst/doc/reproducible_example.html | 12 ++++++------ man/fit_sgs.Rd | 2 +- 8 files changed, 29 insertions(+), 29 deletions(-)
Title: Information Preserving Regression-Based Tools for Statistical
Disclosure Control
Description: Implementation of the methods described in the paper with the above title: Langsrud, Ø. (2019) <doi:10.1007/s11222-018-9848-9>. The package can be used to generate synthetic or hybrid continuous microdata, and the relationship to the original data can be controlled in several ways. A function for replacing suppressed tabular cell frequencies with decimal numbers is included.
Author: Oeyvind Langsrud [aut, cre]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between RegSDC versions 0.7.0 dated 2022-08-19 and 1.0.0 dated 2025-02-03
DESCRIPTION | 17 +++++++++-------- MD5 | 10 +++++----- R/SuppressDec.R | 10 +++++----- man/ReduceX.Rd | 2 +- man/SuppressDec.Rd | 2 +- man/Z2Yhat.Rd | 4 ++-- 6 files changed, 23 insertions(+), 22 deletions(-)
Title: Local Regression, Likelihood and Density Estimation
Description: Local regression, likelihood and density estimation methods as described in the 1999 book by Loader.
Author: Catherine Loader [aut],
Jiayang Sun [ctb],
Lucent Technologies [cph],
Andy Liaw [cre]
Maintainer: Andy Liaw <andy_liaw@merck.com>
Diff between locfit versions 1.5-9.10 dated 2024-06-24 and 1.5-9.11 dated 2025-02-03
DESCRIPTION | 8 +-- MD5 | 108 ++++++++++++++++++++++++++--------------------------- src/S_enter.c | 71 ++++++++++++++++++++-------------- src/band.c | 64 +++++++++++++++---------------- src/dbinom.c | 52 +++++++------------------ src/dens_haz.c | 23 ++++------- src/dens_int.c | 27 ++++--------- src/dens_odi.c | 88 +++++++++++++++++++++---------------------- src/density.c | 50 +++++++----------------- src/ev_atree.c | 30 ++++---------- src/ev_interp.c | 57 ++++++++++------------------ src/ev_kdtre.c | 46 +++++++--------------- src/ev_main.c | 62 ++++++++++++------------------ src/ev_sphere.c | 15 ++----- src/ev_trian.c | 78 ++++++++++++++------------------------ src/family.c | 104 ++++++++++++++++++++------------------------------- src/fitted.c | 16 ++----- src/frend.c | 15 ++----- src/lf_adap.c | 41 +++++--------------- src/lf_dercor.c | 7 --- src/lf_fitfun.c | 35 +++++------------ src/lf_nbhd.c | 44 ++++++++++----------- src/lf_robust.c | 28 ++++++------- src/lf_vari.c | 24 +++++------ src/lf_wdiag.c | 31 ++++++--------- src/lffuns.h | 6 +- src/lfstr.c | 28 ++++++++----- src/locfit.c | 75 ++++++++++++++++++------------------ src/m_chol.c | 24 +++++------ src/m_eigen.c | 30 +++++++------- src/m_icirc.c | 18 ++++---- src/m_imont.c | 6 +- src/m_isimp.c | 36 ++++++++--------- src/m_isphr.c | 34 ++++++++-------- src/m_jacob.c | 30 +++++++------- src/m_max.c | 27 +++++++------ src/m_qr.c | 24 +++++------ src/m_solve.c | 23 ++++++----- src/m_svd.c | 26 ++++++++---- src/m_vector.c | 49 +++++++++++++----------- src/math.c | 38 +++++++++--------- src/minmax.c | 70 ++++++++++++++++++++-------------- src/mutil.h | 55 ++++++++++++++++++++------- src/pcomp.c | 62 +++++++++++++++++------------- src/preplot.c | 34 ++++++++-------- src/prob.c | 20 ++++----- src/procv.c | 40 +++++++++---------- src/scb.c | 44 ++++++++------------- src/scb_cons.c | 56 +++++++-------------------- src/scb_crit.c | 49 +++++++++--------------- src/scb_iface.c | 15 ++++--- src/simul.c | 48 +++++++---------------- src/smisc.c | 15 ++----- src/startlf.c | 41 ++++++++------------ src/weight.c | 114 +++++++++++++++++++++++--------------------------------- 55 files changed, 1045 insertions(+), 1216 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 0.1.2 dated 2024-11-28 and 0.1.3 dated 2025-02-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/dfr_sgl.R | 2 +- man/dfr_sgl.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, encryption,
enterprise authentication, and GridFS. The online user manual provides an overview
of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] ,
MongoDB, Inc [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between mongolite versions 3.0.0 dated 2025-01-27 and 3.0.1 dated 2025-02-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ configure | 11 ++--------- src/bson/bson-memory.c | 2 +- 5 files changed, 13 insertions(+), 17 deletions(-)
Title: Less Code, More Results
Description: Each function replaces multiple standard R functions. For example, two function calls, Read() and CountAll(), generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for summary statistics via pivot tables, a comprehensive regression analysis, ANOVA and t-test, visualizations including the Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, time series with aggregation and forecasting, color themes, and Trellis (facet) graphics. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, generation and rendering of regression instructions for interpretative output, and interactive visualizations.
Author: David W. Gerbing [aut, cre]
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 4.4.0 dated 2025-01-12 and 4.4.1 dated 2025-02-03
DESCRIPTION | 8 MD5 | 52 ++-- NEWS.md | 67 ++++- R/BarChart.R | 2 R/Density.R | 1 R/Histogram.R | 6 R/PieChart.R | 12 R/Plot.R | 297 ++++++++++++++---------- R/Regression.R | 22 + R/bc.data.frame.R | 14 - R/bc.main.R | 20 + R/dn.main.R | 15 - R/dpmat.main.R | 42 +-- R/hst.main.R | 61 ++--- R/plt.add.R | 3 R/plt.fit.R | 48 ++- R/plt.lattice.R | 154 +++++++++--- R/plt.main.R | 104 ++++---- R/plt.txt.R | 632 +++++++++++++++++++++------------------------------- R/print.outall.R | 16 - R/reg.5Plot.R | 75 +++--- R/regPlot.R | 12 R/zzz.R | 87 ++++--- inst/doc/intro.html | 38 +-- man/PieChart.Rd | 8 man/Plot.Rd | 58 ++-- man/Regression.Rd | 35 +- 27 files changed, 1025 insertions(+), 864 deletions(-)
Title: A Distributed Worker Launcher Framework
Description: In computationally demanding analysis projects,
statisticians and data scientists asynchronously
deploy long-running tasks to distributed systems,
ranging from traditional clusters to cloud services.
The 'NNG'-powered 'mirai' R package by Gao (2023)
<doi:10.5281/zenodo.7912722> is a sleek
and sophisticated scheduler that
efficiently processes these intense workloads.
The 'crew' package extends 'mirai' with a unifying
interface for third-party worker launchers.
Inspiration also comes from packages.
'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>,
'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>,
'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
and 'batchtools' by Lang, Bischel, and Surmann (2017)
<doi:10.21105/joss.00135>.
Author: William Michael Landau [aut, cre]
,
Daniel Woodie [ctb],
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between crew versions 0.10.2 dated 2024-11-15 and 1.0.0 dated 2025-02-03
crew-0.10.2/crew/tests/local/test-backlog_crash.R |only crew-0.10.2/crew/tests/local/test-backlog_seconds_idle.R |only crew-0.10.2/crew/tests/local/test-backlog_tasks_max.R |only crew-0.10.2/crew/tests/local/test-crashes_error.R |only crew-1.0.0/crew/DESCRIPTION | 10 crew-1.0.0/crew/MD5 | 169 +- crew-1.0.0/crew/NAMESPACE | 6 crew-1.0.0/crew/NEWS.md | 15 crew-1.0.0/crew/R/class_monad.R | 126 - crew-1.0.0/crew/R/crew_assert.R | 11 crew-1.0.0/crew/R/crew_clean.R | 2 crew-1.0.0/crew/R/crew_client.R | 189 +- crew-1.0.0/crew/R/crew_controller.R | 906 +++++++----- crew-1.0.0/crew/R/crew_controller_group.R | 202 +- crew-1.0.0/crew/R/crew_controller_local.R | 40 crew-1.0.0/crew/R/crew_eval.R | 54 crew-1.0.0/crew/R/crew_launcher.R | 759 +++------- crew-1.0.0/crew/R/crew_launcher_local.R | 37 crew-1.0.0/crew/R/crew_options_metrics.R | 2 crew-1.0.0/crew/R/crew_package.R | 4 crew-1.0.0/crew/R/crew_queue.R |only crew-1.0.0/crew/R/crew_relay.R | 14 crew-1.0.0/crew/R/crew_retry.R | 65 crew-1.0.0/crew/R/crew_throttle.R | 180 ++ crew-1.0.0/crew/R/crew_tls.R | 17 crew-1.0.0/crew/R/crew_worker.R | 27 crew-1.0.0/crew/R/utils_logic.R | 2 crew-1.0.0/crew/R/utils_mirai.R | 83 - crew-1.0.0/crew/R/utils_names.R | 13 crew-1.0.0/crew/R/utils_nanonext.R |only crew-1.0.0/crew/inst/WORDLIST | 1 crew-1.0.0/crew/inst/doc/groups.Rmd | 121 + crew-1.0.0/crew/inst/doc/groups.html | 126 + crew-1.0.0/crew/inst/doc/introduction.Rmd | 169 +- crew-1.0.0/crew/inst/doc/introduction.html | 224 +- crew-1.0.0/crew/inst/doc/plugins.Rmd | 110 - crew-1.0.0/crew/inst/doc/plugins.html | 602 +++---- crew-1.0.0/crew/man/crew_class_client.Rd | 54 crew-1.0.0/crew/man/crew_class_controller.Rd | 214 +- crew-1.0.0/crew/man/crew_class_controller_group.Rd | 101 + crew-1.0.0/crew/man/crew_class_launcher.Rd | 470 +----- crew-1.0.0/crew/man/crew_class_launcher_local.Rd | 46 crew-1.0.0/crew/man/crew_class_queue.Rd |only crew-1.0.0/crew/man/crew_class_relay.Rd | 8 crew-1.0.0/crew/man/crew_class_throttle.Rd | 86 + crew-1.0.0/crew/man/crew_class_tls.Rd | 28 crew-1.0.0/crew/man/crew_clean.Rd | 2 crew-1.0.0/crew/man/crew_client.Rd | 24 crew-1.0.0/crew/man/crew_controller.Rd | 41 crew-1.0.0/crew/man/crew_controller_group.Rd | 7 crew-1.0.0/crew/man/crew_controller_local.Rd | 68 crew-1.0.0/crew/man/crew_eval.Rd | 7 crew-1.0.0/crew/man/crew_launcher.Rd | 40 crew-1.0.0/crew/man/crew_launcher_local.Rd | 36 crew-1.0.0/crew/man/crew_options_metrics.Rd | 2 crew-1.0.0/crew/man/crew_queue.Rd |only crew-1.0.0/crew/man/crew_retry.Rd | 6 crew-1.0.0/crew/man/crew_throttle.Rd | 41 crew-1.0.0/crew/man/crew_worker.Rd | 10 crew-1.0.0/crew/tests/local/test-cleanup.R | 2 crew-1.0.0/crew/tests/local/test-crew_clean.R | 2 crew-1.0.0/crew/tests/local/test-crew_relay.R | 8 crew-1.0.0/crew/tests/local/test-crew_throttle.R | 4 crew-1.0.0/crew/tests/local/test-launcher-system2.R | 38 crew-1.0.0/crew/tests/local/test-long_seconds_idle.R |only crew-1.0.0/crew/tests/local/test-long_tasks_max.R |only crew-1.0.0/crew/tests/local/test-map.R | 14 crew-1.0.0/crew/tests/local/test-persistent-autoscale.R | 11 crew-1.0.0/crew/tests/local/test-transient.R | 22 crew-1.0.0/crew/tests/local/test-wait.R | 5 crew-1.0.0/crew/tests/testthat.R | 4 crew-1.0.0/crew/tests/testthat/test-class_monad.R | 35 crew-1.0.0/crew/tests/testthat/test-crew_async.R | 2 crew-1.0.0/crew/tests/testthat/test-crew_client.R | 56 crew-1.0.0/crew/tests/testthat/test-crew_controller.R | 364 +++- crew-1.0.0/crew/tests/testthat/test-crew_controller_group.R | 314 +++- crew-1.0.0/crew/tests/testthat/test-crew_controller_local.R | 140 + crew-1.0.0/crew/tests/testthat/test-crew_eval.R | 73 crew-1.0.0/crew/tests/testthat/test-crew_launcher.R | 361 ++-- crew-1.0.0/crew/tests/testthat/test-crew_launcher_local.R | 203 -- crew-1.0.0/crew/tests/testthat/test-crew_queue.R |only crew-1.0.0/crew/tests/testthat/test-crew_relay.R | 5 crew-1.0.0/crew/tests/testthat/test-crew_throttle.R | 93 + crew-1.0.0/crew/tests/testthat/test-crew_tls.R | 33 crew-1.0.0/crew/tests/testthat/test-crew_worker.R | 104 - crew-1.0.0/crew/tests/testthat/test-plugins.R | 305 +++- crew-1.0.0/crew/tests/testthat/test-utils_mirai.R | 85 + crew-1.0.0/crew/tests/testthat/test-utils_names.R | 20 crew-1.0.0/crew/vignettes/groups.Rmd | 121 + crew-1.0.0/crew/vignettes/introduction.Rmd | 169 +- crew-1.0.0/crew/vignettes/plugins.Rmd | 110 - 91 files changed, 4765 insertions(+), 3515 deletions(-)
Title: Long-Short Term Memory for Time-Series Forecasting, Enhanced
Description: The LSTM (Long Short-Term Memory) model is a Recurrent Neural Network (RNN) based architecture that is widely used for time series forecasting. Customizable configurations for the model are allowed, improving the capabilities and usability of this model compared to other packages. This package is based on 'keras' and 'tensorflow' modules and the algorithm of Paul and Garai (2021) <doi:10.1007/s00500-021-06087-4>.
Author: Jaime Pizarroso Gonzalo [aut, ctb, cre],
Antonio Munoz San Roque [aut]
Maintainer: Jaime Pizarroso Gonzalo <jpizarroso@comillas.edu>
Diff between TSLSTMplus versions 1.0.5 dated 2024-09-06 and 1.0.6 dated 2025-02-03
DESCRIPTION | 12 ++++++------ MD5 | 7 ++++--- NAMESPACE | 2 +- R/TSLSTM.R | 44 +++++++++++++++++++++++++++++++++++++++++++- man/lagmatrix.Rd |only 5 files changed, 54 insertions(+), 11 deletions(-)
Title: Optimising Random Forest Stability by Determining the Optimal
Number of Trees
Description: Calculating the stability of random forest with certain numbers of trees. The non-linear relationship between stability and numbers of trees is described using a logistic regression model and used to estimate the optimal number of trees.
Author: Thomas Martin Lange [cre, aut]
,
Felix Heinrich [ctb]
Maintainer: Thomas Martin Lange <thomas.lange@uni-goettingen.de>
Diff between optRF versions 1.0.1 dated 2024-09-23 and 1.1.0 dated 2025-02-03
DESCRIPTION | 39 - MD5 | 59 +- NEWS.md |only R/SNPdata.R | 46 - R/estimate_numtrees.R | 251 ++++------ R/estimate_stability.R | 179 +++---- R/opt_importance.R | 797 +++++++++++++------------------- R/opt_prediction.R | 941 ++++++++++++++++---------------------- R/plot.opt_importance_object.R | 5 R/plot.opt_prediction_object.R | 5 R/plot_stability.R | 261 +++++----- R/summary.opt_importance_object.R | 6 R/summary.opt_prediction_object.R | 7 R/utils.R |only README.md |only build |only data/SNPdata.rda |binary inst |only man/SNPdata.Rd | 4 man/estimate_numtrees.Rd | 2 man/estimate_stability.Rd | 2 man/opt_importance.Rd | 18 man/opt_prediction.Rd | 15 man/plot_stability.Rd | 2 vignettes |only 25 files changed, 1207 insertions(+), 1432 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] ,
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between openssl versions 2.3.1 dated 2025-01-09 and 2.3.2 dated 2025-02-03
DESCRIPTION | 6 ++--- MD5 | 18 ++++++++-------- NEWS | 4 +++ inst/doc/bignum.html | 32 ++++++++++++++-------------- inst/doc/crypto_hashing.html | 4 +-- inst/doc/keys.html | 48 +++++++++++++++++++++---------------------- inst/doc/secure_rng.html | 18 ++++++++-------- src/Makevars.win | 2 - src/onload.c | 5 ---- tools/winlibs.R | 6 ++--- 10 files changed, 71 insertions(+), 72 deletions(-)
Title: Easily Access and Maintain Time-Based Versioned Data
(Slowly-Changing-Dimension)
Description: A collection of functions that enable easy access and updating of a database of data over time.
More specifically, the package facilitates type-2 history for data-warehouses and provides a number
of Quality of life improvements for working on SQL databases with R.
For reference see Ralph Kimball and Margy Ross (2013, ISBN 9781118530801).
Author: Rasmus Skytte Randloev [aut, cre, rev]
,
Marcus Munch Gruenewald [aut] ,
Lasse Engbo Christiansen [rev]
,
Sofia Myrup Otero [rev],
Statens Serum Institut [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>
Diff between SCDB versions 0.4.1 dated 2024-10-03 and 0.5.0 dated 2025-02-03
SCDB-0.4.1/SCDB/R/0_linters.R |only SCDB-0.4.1/SCDB/tests/testthat/test-0_linters.R |only SCDB-0.4.1/SCDB/tests/testthat/test-0_rd_files.R |only SCDB-0.5.0/SCDB/DESCRIPTION | 18 SCDB-0.5.0/SCDB/MD5 | 123 +- SCDB-0.5.0/SCDB/NAMESPACE | 7 SCDB-0.5.0/SCDB/NEWS.md | 29 SCDB-0.5.0/SCDB/R/0_miscellaneous.R |only SCDB-0.5.0/SCDB/R/Logger.R | 33 SCDB-0.5.0/SCDB/R/connection.R | 32 SCDB-0.5.0/SCDB/R/create_index.R |only SCDB-0.5.0/SCDB/R/create_table.R | 14 SCDB-0.5.0/SCDB/R/db_joins.R | 134 +- SCDB-0.5.0/SCDB/R/digest_to_checksum.R | 34 SCDB-0.5.0/SCDB/R/filter_keys.R | 10 SCDB-0.5.0/SCDB/R/get_tables.R | 64 - SCDB-0.5.0/SCDB/R/helpers.R | 18 SCDB-0.5.0/SCDB/R/id.R | 10 SCDB-0.5.0/SCDB/R/interlace.R | 86 - SCDB-0.5.0/SCDB/R/locks.R | 2 SCDB-0.5.0/SCDB/R/schema_exists.R | 4 SCDB-0.5.0/SCDB/R/slice_time.R | 4 SCDB-0.5.0/SCDB/R/table_exists.R | 10 SCDB-0.5.0/SCDB/R/unite.tbl_dbi.R | 10 SCDB-0.5.0/SCDB/R/update_snapshot.R | 271 +++-- SCDB-0.5.0/SCDB/R/utils-pipe.R |only SCDB-0.5.0/SCDB/build/vignette.rds |binary SCDB-0.5.0/SCDB/inst/WORDLIST | 6 SCDB-0.5.0/SCDB/inst/doc/SCDB.R | 44 SCDB-0.5.0/SCDB/inst/doc/SCDB.Rmd | 74 - SCDB-0.5.0/SCDB/inst/doc/SCDB.html | 249 ++--- SCDB-0.5.0/SCDB/inst/doc/benchmarks.R |only SCDB-0.5.0/SCDB/inst/doc/benchmarks.Rmd |only SCDB-0.5.0/SCDB/inst/doc/benchmarks.html |only SCDB-0.5.0/SCDB/inst/doc/slowly-changing-dimension.R | 277 +++--- SCDB-0.5.0/SCDB/inst/doc/slowly-changing-dimension.Rmd | 506 +++++------ SCDB-0.5.0/SCDB/inst/doc/slowly-changing-dimension.html | 145 ++- SCDB-0.5.0/SCDB/inst/extdata |only SCDB-0.5.0/SCDB/man/SCDB-package.Rd | 1 SCDB-0.5.0/SCDB/man/create_index.Rd |only SCDB-0.5.0/SCDB/man/interlace.Rd | 13 SCDB-0.5.0/SCDB/man/joins.Rd | 6 SCDB-0.5.0/SCDB/man/pipe.Rd |only SCDB-0.5.0/SCDB/man/slice_time.Rd | 2 SCDB-0.5.0/SCDB/man/unique_table_name.Rd | 8 SCDB-0.5.0/SCDB/man/unite.tbl_dbi.Rd | 4 SCDB-0.5.0/SCDB/tests/spelling.R | 10 SCDB-0.5.0/SCDB/tests/testthat/helper-setup.R | 101 +- SCDB-0.5.0/SCDB/tests/testthat/setup.R | 16 SCDB-0.5.0/SCDB/tests/testthat/test-Logger.R | 50 - SCDB-0.5.0/SCDB/tests/testthat/test-connection.R | 6 SCDB-0.5.0/SCDB/tests/testthat/test-create_logs_if_missing.R | 8 SCDB-0.5.0/SCDB/tests/testthat/test-create_table.R | 16 SCDB-0.5.0/SCDB/tests/testthat/test-db_joins.R | 187 ++-- SCDB-0.5.0/SCDB/tests/testthat/test-digest_to_checksum.R | 32 SCDB-0.5.0/SCDB/tests/testthat/test-filter_keys.R | 64 - SCDB-0.5.0/SCDB/tests/testthat/test-getTableSignature.R | 2 SCDB-0.5.0/SCDB/tests/testthat/test-get_table.R | 20 SCDB-0.5.0/SCDB/tests/testthat/test-get_tables.R | 16 SCDB-0.5.0/SCDB/tests/testthat/test-helpers.R | 28 SCDB-0.5.0/SCDB/tests/testthat/test-id.R | 4 SCDB-0.5.0/SCDB/tests/testthat/test-interlace.R | 16 SCDB-0.5.0/SCDB/tests/testthat/test-locks.R | 10 SCDB-0.5.0/SCDB/tests/testthat/test-slice_time.R | 16 SCDB-0.5.0/SCDB/tests/testthat/test-unite.tbl_dbi.R | 58 - SCDB-0.5.0/SCDB/tests/testthat/test-update_snapshot.R | 475 +++++++--- SCDB-0.5.0/SCDB/vignettes/SCDB.Rmd | 74 - SCDB-0.5.0/SCDB/vignettes/benchmarks.Rmd |only SCDB-0.5.0/SCDB/vignettes/slowly-changing-dimension.Rmd | 506 +++++------ 69 files changed, 2297 insertions(+), 1666 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent class mixed models, mixed models for curvilinear outcomes, mixed models for multivariate longitudinal outcomes using a maximum likelihood estimation method (Proust-Lima, Philipps, Liquet (2017) <doi:10.18637/jss.v078.i02>).
Author: Cecile Proust-Lima [aut, cre],
Viviane Philipps [aut],
Amadou Diakite [ctb],
Benoit Liquet [ctb],
Alan Genz [ctb] ,
John Burkardt [ctb]
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>
Diff between lcmm versions 2.1.0 dated 2023-10-06 and 2.2.0 dated 2025-02-03
DESCRIPTION | 20 MD5 | 82 +- NAMESPACE | 3 NEWS.md | 7 R/Jointlcmm.R | 20 R/externVar.R | 1515 +++++++++++++++++++++++++------------------------ R/hlme.R | 7 R/lcmm-package.R | 6 R/lcmm.R | 14 R/mpjlcmm.R | 5 R/multlcmm.R | 34 - R/permut.R | 32 + R/predictClass.R | 3 R/predictYback.R |only R/print.lcmm.R | 2 R/summary.externSurv.R | 229 +++---- R/summary.externX.R | 20 R/summary.hlme.R | 649 ++++++++++---------- R/summary.lcmm.R | 15 R/summary.multlcmm.R | 12 R/summaryplot.R | 4 R/summarytable.R | 4 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/COPYRIGHTS |only inst/doc/lcmm.R | 2 man/Jointlcmm.Rd | 18 man/externVar.Rd | 195 +++--- man/hlme.Rd | 7 man/lcmm-package.Rd | 9 man/lcmm.Rd | 14 man/mpjlcmm.Rd | 2 man/multlcmm.Rd | 22 man/predictYback.Rd |only man/print.lcmm.Rd | 2 man/summary.lcmm.Rd | 2 man/summaryplot.Rd | 4 man/summarytable.Rd | 4 src/Integ.f90 |only src/Makevars | 3 src/init.c | 1 src/lcmm.h | 19 src/mpjhet.f90 | 4 44 files changed, 1609 insertions(+), 1384 deletions(-)
Title: Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as
calculating spectral indexes, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [aut] ,
Ned Horning [aut],
Jakob Schwalb-Willmann [aut] ,
Robert J. Hijmans [ctb] ,
Konstantin Mueller [aut, cre]
Maintainer: Konstantin Mueller <konstantinfinn.mueller@gmx.de>
Diff between RStoolbox versions 1.0.1 dated 2025-02-01 and 1.0.2.1 dated 2025-02-03
RStoolbox-1.0.1/RStoolbox/src/tinyexpr.c |only RStoolbox-1.0.1/RStoolbox/src/tinyexpr.h |only RStoolbox-1.0.2.1/RStoolbox/DESCRIPTION | 8 RStoolbox-1.0.2.1/RStoolbox/MD5 | 14 RStoolbox-1.0.2.1/RStoolbox/NEWS.md | 6 RStoolbox-1.0.2.1/RStoolbox/R/spectralIndices.R | 7 RStoolbox-1.0.2.1/RStoolbox/man/spectralIndices.Rd | 27 + RStoolbox-1.0.2.1/RStoolbox/src/spectralIndices.cpp | 188 +++++++--- RStoolbox-1.0.2.1/RStoolbox/tests/testthat/test-spectralIndices.R | 19 + 9 files changed, 214 insertions(+), 55 deletions(-)
Title: Analysis of Heavy Tailed Distributions
Description: An implementation of maximum likelihood estimators for a
variety of heavy tailed distributions, including both the discrete and
continuous power law distributions. Additionally, a goodness-of-fit
based approach is used to estimate the lower cut-off for the scaling
region.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie <csgillespie@gmail.com>
Diff between poweRlaw versions 0.80.0 dated 2024-01-25 and 1.0.0 dated 2025-02-03
DESCRIPTION | 27 ++++----- MD5 | 83 ++++++++++++++------------- NAMESPACE | 15 ----- NEWS.md | 13 ++-- R/bootstrap.R | 4 - R/bootstrap_p.R | 18 +++--- R/compare_distributions.R | 7 +- R/conlnorm.R | 6 +- R/data_help_files.R | 2 R/def_conweibull.R | 2 R/def_dislnorm.R | 3 + R/def_displ.R | 5 - R/def_dispois.R | 17 ++--- R/estimate_xmin.R | 6 -- R/lines_methods.R | 6 -- R/plcon.R | 4 - R/pldis.R | 6 +- R/plot_methods.R | 18 ++---- R/powerlaw-package.R | 1 R/show_methods.R | 4 - README.md | 13 +++- build/vignette.rds |binary demo/moby.R | 6 +- inst/WORDLIST |only inst/doc/a_introduction.pdf |binary inst/doc/b_powerlaw_examples.pdf |binary inst/doc/c_comparing_distributions.pdf |binary inst/doc/d_jss_paper.pdf |binary man/bootstrap_moby.Rd | 2 man/compare_distributions.Rd | 2 man/displ.Rd | 3 + man/dplcon.Rd | 4 - man/estimate_xmin.Rd | 4 - man/plot-distribution-method.Rd | 2 man/poweRlaw-package.Rd | 1 tests/testthat/test_compare_distributions.R | 16 ++--- tests/testthat/test_dist_cdf.R | 84 ++++++++++++++-------------- tests/testthat/test_dist_data_cdf.R | 29 ++++----- tests/testthat/test_dist_ll.R | 26 ++++---- tests/testthat/test_estimate_pars.R | 24 ++++---- tests/testthat/test_estimate_xmin.R | 32 +++++----- tests/testthat/test_get_sims.R | 8 +- tests/testthat/test_plot.R | 36 ++++++------ 43 files changed, 263 insertions(+), 276 deletions(-)
Title: Classification Evaluation Metrics
Description: A fast, robust and easy-to-use calculation
of multi-class classification evaluation metrics based on confusion matrix.
Author: G. Dudnik [aut, cre, cph]
Maintainer: G. Dudnik <gl.dudnik@gmail.com>
Diff between mltest versions 1.0.2 dated 2025-02-02 and 1.0.3 dated 2025-02-03
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 10 +++++++++- R/ml_test.R | 50 +++++++++++++++++++++++++------------------------- build/partial.rdb |binary inst/CITATION | 3 ++- man/ml_test.Rd | 50 +++++++++++++++++++++++++------------------------- 7 files changed, 70 insertions(+), 61 deletions(-)
Title: SDTM Datacut
Description: Supports the process of applying a cut to Standard Data Tabulation Model (SDTM),
as part of the analysis of specific points in time of the data, normally as part of
investigation into clinical trials. The functions support different approaches of
cutting to the different domains of SDTM normally observed.
Author: Tim Barnett [cph, aut, cre],
Nathan Rees [aut],
Alana Harris [aut],
Cara Andrews [aut]
Maintainer: Tim Barnett <timothy.barnett@roche.com>
Diff between datacutr versions 0.2.2 dated 2025-01-10 and 0.2.3 dated 2025-02-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/read_out.R | 4 +++- inst/doc/variable_cut.html | 24 ++++++++++++------------ 5 files changed, 27 insertions(+), 20 deletions(-)
Title: 3D Software Rasterizer
Description: Rasterize images using a 3D software renderer. 3D scenes are created either by importing external files, building scenes out of the included objects, or by constructing meshes manually. Supports point and directional lights, anti-aliased lines, shadow mapping, transparent objects, translucent objects, multiple materials types, reflection, refraction, environment maps, multicore rendering, bloom, tone-mapping, and screen-space ambient occlusion.
Author: Tyler Morgan-Wall [aut, cph, cre]
,
Syoyo Fujita [ctb, cph],
Vilya Harvey [ctb, cph],
G-Truc Creation [ctb, cph],
Sean Barrett [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayvertex versions 0.11.4 dated 2024-07-22 and 0.12.0 dated 2025-02-03
DESCRIPTION | 14 ++--- MD5 | 20 +++---- R/objects.R | 118 ++++++++++++++++++++++++++-------------------- R/zzz.R | 2 inst/extdata/xy_plane.txt | 6 +- inst/extdata/yz_plane.txt | 2 man/text3d_mesh.Rd | 66 +++++++++++++++++++------ src/glm/detail/glm.cpp | 23 ++++++++ src/glm/glm.hpp | 23 ++++++++ src/load_obj.cpp | 17 +++++- src/load_ply.cpp | 17 +++++- 11 files changed, 214 insertions(+), 94 deletions(-)
Title: A Collection of R Functions by the Petersen Lab
Description: A collection of R functions that are widely used by the Petersen
Lab. Included are functions for various purposes, including evaluating the
accuracy of judgments and predictions, performing scoring of assessments,
generating correlation matrices, conversion of data between various types,
data management, psychometric evaluation, extensions related to latent
variable modeling, various plotting capabilities, and other miscellaneous
useful functions. By making the package available, we hope to make our
methods reproducible and replicable by others and to help others perform
their data processing and analysis methods more easily and efficiently. The
codebase is provided in Petersen (2024) <doi:10.5281/zenodo.7602890> and on
CRAN: <doi: 10.32614/CRAN.package.petersenlab>. The package is described in
"Principles of Psychological Assessment: With Applied Examples in R"
(Petersen, 2024, 2025) <doi:10.1201/9781003357421>,
<doi:10.25820/work.007199>, <doi:10.5281/zenod [...truncated...]
Author: Isaac T. Petersen [aut, cre] ,
Developmental Psychopathology Lab at the University of Iowa [ctb],
Angela D. Staples [ctb] ,
Johanna Caskey [ctb] ,
Philipp Doebler [ctb] ,
Loreen Sabel [ctb]
Maintainer: Isaac T. Petersen <isaac-t-petersen@uiowa.edu>
Diff between petersenlab versions 1.0.0 dated 2024-04-30 and 1.1.0 dated 2025-02-03
DESCRIPTION | 41 +- MD5 | 109 +++-- NAMESPACE | 42 ++ R/accuracyOverall.R | 52 ++ R/apa.R |only R/cleanUpNames.R |only R/convert.magic.R | 2 R/frequencyPerDuration.R | 18 R/itemInformationZINB.R |only R/my_loadings_sorter.R |only R/nomogrammer.R | 104 ++++- R/pValues.R | 2 R/posttestOddsProbability.R |only R/recodeIntensity.R | 5 R/semPlotInteraction.R |only R/specifyDecimals.R | 2 R/suppressLeadingZero.R | 2 R/testInformation.R |only R/varsDifferentTypes.R |only R/weightedQuantile.R |only README.md | 20 - inst/CITATION | 6 man/Mode.Rd | 93 ++--- man/accuracyAtCutoff.Rd | 3 man/accuracyAtEachCutoff.Rd | 3 man/accuracyOverall.Rd | 7 man/addText.Rd | 1 man/apa.Rd |only man/bayesTheorem.Rd | 4 man/cleanUpNames.Rd |only man/columnBindFill.Rd | 3 man/convert.magic.Rd | 5 man/discriminationToFactorLoading.Rd | 4 man/dropColsWithAllNA.Rd | 109 ++--- man/dropRowsWithAllNA.Rd | 105 ++--- man/equiv_chi.Rd | 3 man/figures |only man/fourPL.Rd | 4 man/frequencyPerDuration.Rd | 20 - man/itemInformation.Rd | 4 man/itemInformationZINB.Rd |only man/lmCombine.Rd | 1 man/make_esem_model.Rd | 3 man/meanSum.Rd | 71 +-- man/mySum.Rd | 75 ++-- man/my_loadings_sorter.Rd |only man/nomogrammer.Rd | 221 ++++++------ man/optimalCutoff.Rd | 3 man/pValue.Rd | 7 man/plot2WayInteraction.Rd | 2 man/posttest.Rd |only man/ppPlot.Rd | 2 man/puc.Rd | 3 man/recodeBehaviorIntensity.Rd | 5 man/reliabilityIRT.Rd | 4 man/satorraBentlerScaledChiSquareDifferenceTestStatistic.Rd | 3 man/semPlotInteraction.Rd |only man/specify_decimal.Rd | 7 man/standardErrorIRT.Rd | 4 man/suppressLeadingZero.Rd | 7 man/testInformation.Rd |only man/update_nested.Rd | 3 man/varsDifferentTypes.Rd |only man/vwReg.Rd | 3 man/weightedQuantile.Rd |only 65 files changed, 754 insertions(+), 443 deletions(-)