Title: A Comprehensive Collection of Cardiovascular and Heart Disease
Datasets
Description: Offers a diverse collection of datasets focused on cardiovascular and heart disease research, including heart failure, myocardial infarction, aortic dissection, transplant outcomes, cardiovascular risk factors, drug efficacy, and mortality trends.
Designed for researchers, clinicians, epidemiologists, and data scientists, the package features clinical, epidemiological, and simulated datasets covering a wide range of conditions and treatments such as statins, anticoagulants, and beta blockers.
It supports analyses related to disease progression, treatment effects, rehospitalization, and public health outcomes across various cardiovascular patient populations.
Author: Renzo Caceres Rossi [aut, cre]
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Diff between CardioDataSets versions 0.1.0 dated 2025-05-13 and 0.2.0 dated 2025-09-05
CardioDataSets-0.1.0/CardioDataSets/R/view_datasets.R |only CardioDataSets-0.1.0/CardioDataSets/man/view_datasets.Rd |only CardioDataSets-0.1.0/CardioDataSets/tests/testthat/test-view_datasets.R |only CardioDataSets-0.2.0/CardioDataSets/DESCRIPTION | 15 - CardioDataSets-0.2.0/CardioDataSets/MD5 | 25 +- CardioDataSets-0.2.0/CardioDataSets/NAMESPACE | 2 CardioDataSets-0.2.0/CardioDataSets/NEWS.md |only CardioDataSets-0.2.0/CardioDataSets/R/view_datasets_CardioDataSets.R |only CardioDataSets-0.2.0/CardioDataSets/README.md | 10 - CardioDataSets-0.2.0/CardioDataSets/build/vignette.rds |binary CardioDataSets-0.2.0/CardioDataSets/inst/CITATION | 6 CardioDataSets-0.2.0/CardioDataSets/inst/doc/Introduction_to_CardioDataSets.R | 7 CardioDataSets-0.2.0/CardioDataSets/inst/doc/Introduction_to_CardioDataSets.Rmd | 14 + CardioDataSets-0.2.0/CardioDataSets/inst/doc/Introduction_to_CardioDataSets.html | 96 ++++++---- CardioDataSets-0.2.0/CardioDataSets/man/view_datasets_CardioDataSets.Rd |only CardioDataSets-0.2.0/CardioDataSets/tests/testthat/test-view_datasets_CardioDataSets.R |only CardioDataSets-0.2.0/CardioDataSets/vignettes/Introduction_to_CardioDataSets.Rmd | 14 + 17 files changed, 126 insertions(+), 63 deletions(-)
More information about CardioDataSets at CRAN
Permanent link
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 0.2.4 dated 2025-07-15 and 0.2.5 dated 2025-09-05
NMsim-0.2.4/NMsim/R/dtapply.R |only NMsim-0.2.4/NMsim/man/dtapply.Rd |only NMsim-0.2.5/NMsim/DESCRIPTION | 6 NMsim-0.2.5/NMsim/MD5 | 101 +++-- NMsim-0.2.5/NMsim/NAMESPACE | 1 NMsim-0.2.5/NMsim/NEWS.md | 31 + NMsim-0.2.5/NMsim/R/NMcreateDoses.R | 23 + NMsim-0.2.5/NMsim/R/NMexec.R | 9 NMsim-0.2.5/NMsim/R/NMextractText.R | 11 NMsim-0.2.5/NMsim/R/NMreadInits.R | 63 +-- NMsim-0.2.5/NMsim/R/NMreadSection.R | 8 NMsim-0.2.5/NMsim/R/NMreadSim.R | 8 NMsim-0.2.5/NMsim/R/NMreadSimOne.R | 4 NMsim-0.2.5/NMsim/R/NMsim.R | 95 +++-- NMsim-0.2.5/NMsim/R/NMsimRes_utils.R | 3 NMsim-0.2.5/NMsim/R/NMsim_helpers.R | 2 NMsim-0.2.5/NMsim/R/NMwriteInits.R | 162 +++++++- NMsim-0.2.5/NMsim/R/NMwriteInitsOne.R | 39 +- NMsim-0.2.5/NMsim/R/NMwriteSectionOne.R | 13 NMsim-0.2.5/NMsim/R/addParType.R | 142 ++++++- NMsim-0.2.5/NMsim/R/checkTimes.R | 10 NMsim-0.2.5/NMsim/R/deleteTmpDirs.R |only NMsim-0.2.5/NMsim/R/fnAppend.R | 60 ++- NMsim-0.2.5/NMsim/R/sampleCovs.R | 10 NMsim-0.2.5/NMsim/R/seedFunDefault.R | 1 NMsim-0.2.5/NMsim/R/typicalize.R | 84 ++-- NMsim-0.2.5/NMsim/README.md | 10 NMsim-0.2.5/NMsim/man/NMcreateDoses.Rd | 10 NMsim-0.2.5/NMsim/man/NMreadInits.Rd | 1 NMsim-0.2.5/NMsim/man/NMsim.Rd | 70 ++- NMsim-0.2.5/NMsim/man/NMwriteInits.Rd | 11 NMsim-0.2.5/NMsim/man/addParType.Rd |only NMsim-0.2.5/NMsim/man/addParameter.Rd |only NMsim-0.2.5/NMsim/man/count_ij.Rd | 2 NMsim-0.2.5/NMsim/man/deleteTmpDirs.Rd |only NMsim-0.2.5/NMsim/man/fnAppend.Rd | 16 NMsim-0.2.5/NMsim/man/initsToExt.Rd |only NMsim-0.2.5/NMsim/man/triagSize.Rd | 4 NMsim-0.2.5/NMsim/man/typicalize.Rd |only NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/xgxr021_nmtranfail.lst | 2 NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail_MetaData.rds |binary NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/xgxr011.ext |only NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/xgxr011.lst |only NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/xgxr011.mod |only NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/xgxr011.phi |only NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/xgxr011_fo1.txt |only NMsim-0.2.5/NMsim/tests/testthat/testData/nonmem/xgxr032_sd1_NWPRI.mod |only NMsim-0.2.5/NMsim/tests/testthat/testReference/NMcreateDoses_17.rds |only NMsim-0.2.5/NMsim/tests/testthat/testReference/NMsim_04.rds |binary NMsim-0.2.5/NMsim/tests/testthat/testReference/NMsim_04b.rds |only NMsim-0.2.5/NMsim/tests/testthat/testReference/NMsim_NWPRI_03.rds |only NMsim-0.2.5/NMsim/tests/testthat/testReference/NMsim_NWPRI_03_OMEGAP.rds |only NMsim-0.2.5/NMsim/tests/testthat/testReference/NMsim_NWPRI_03_OMEGAPD.rds |only NMsim-0.2.5/NMsim/tests/testthat/testReference/NMwriteInits_07.rds |binary NMsim-0.2.5/NMsim/tests/testthat/testReference/typicalize_01.rds |only NMsim-0.2.5/NMsim/tests/testthat/testReference/typicalize_02.rds |only NMsim-0.2.5/NMsim/tests/testthat/testReference/typicalize_03.rds |only NMsim-0.2.5/NMsim/tests/testthat/test_NMcreateDoses.R | 9 NMsim-0.2.5/NMsim/tests/testthat/test_NMsim.R | 67 ++- NMsim-0.2.5/NMsim/tests/testthat/test_NMsim_NWPRI.R | 189 ++++++---- NMsim-0.2.5/NMsim/tests/testthat/test_NMsim_default.R | 2 NMsim-0.2.5/NMsim/tests/testthat/test_NMwriteInits.R | 17 NMsim-0.2.5/NMsim/tests/testthat/test_typicalize.R |only 63 files changed, 924 insertions(+), 372 deletions(-)
Title: Optimal Estimation of Function Parameters by Iterated
Linearization
Description: Package for estimating the parameters of a nonlinear function using iterated linearization via Taylor series. Method is based on Kubáček (2000) ISBN: 80-244-0093-6. The algorithm is a generalization of the procedure given in Köning, R., Wimmer, G.
and Witkovský, V. (2014) <doi:10.1088/0957-0233/25/11/115001>.
Author: Stanislav Zamecnik [aut, cre],
Vojtech Sindlar [aut] ,
Zdenka Gerslova [aut] ,
Gejza Wimmer [aut] ,
Technology Agency of the Czech Republic [fnd] ,
Masaryk University, a public university, ID: 00216224 [cph]
Maintainer: Stanislav Zamecnik <zamecnik@math.muni.cz>
This is a re-admission after prior archival of version 0.1.1 dated 2021-11-04
Diff between OEFPIL versions 0.1.1 dated 2021-11-04 and 0.1.2 dated 2025-09-05
DESCRIPTION | 8 MD5 | 66 +- NAMESPACE | 46 - NEWS.md | 24 R/NanoIndent.OEFPIL.R | 488 +++++++-------- R/OEFPIL.R | 1460 ++++++++++++++++++++++----------------------- R/coef.OEFPIL.R | 80 +- R/confBands.OEFPIL.R | 238 +++---- R/confInt.OEFPIL.R | 162 ++-- R/curvplot.OEFPIL.R | 238 +++---- R/ortresiduals.OEFPIL.R | 210 +++--- R/paramplot.OEFPIL.R | 194 ++--- R/plot.OEFPIL.R | 226 +++--- R/print.OEFPIL.R | 72 +- R/silica2098-data.R | 60 - R/silicaBerk-data.R | 54 - R/summary.OEFPIL.R | 202 +++--- R/vcov.OEFPIL.R | 52 - README.md | 240 +++---- build/partial.rdb |binary man/NanoIndent.OEFPIL.Rd | 200 +++--- man/OEFPIL.Rd | 240 +++---- man/coef.OEFPIL.Rd | 78 +- man/confBands.OEFPIL.Rd | 104 +-- man/confInt.OEFPIL.Rd | 86 +- man/curvplot.OEFPIL.Rd | 106 +-- man/ortresiduals.OEFPIL.Rd | 86 +- man/paramplot.OEFPIL.Rd | 88 +- man/plot.OEFPIL.Rd | 130 ++-- man/print.OEFPIL.Rd | 62 - man/silica2098.Rd | 72 +- man/silicaBerk.Rd | 64 - man/summary.OEFPIL.Rd | 88 +- man/vcov.OEFPIL.Rd | 62 - 34 files changed, 2793 insertions(+), 2793 deletions(-)
Title: Identify Text Written by Large Language Models using 'GPTZero'
Description: An R interface to the 'GPTZero' API (<https://gptzero.me/docs>). Allows
users to classify text into human and computer written with probabilities. Formats
the data into data frames where each sentence is an observation. Paragraph-level
and document-level predictions are organized to align with the sentences.
Author: Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
Diff between gptzeror versions 0.0.1 dated 2023-06-05 and 0.0.2 dated 2025-09-05
gptzeror-0.0.1/gptzeror/R/gptzeror-package.R |only gptzeror-0.0.2/gptzeror/DESCRIPTION | 17 gptzeror-0.0.2/gptzeror/MD5 | 34 - gptzeror-0.0.2/gptzeror/NAMESPACE | 18 gptzeror-0.0.2/gptzeror/NEWS.md | 4 gptzeror-0.0.2/gptzeror/R/GPTZeroR-package.R |only gptzeror-0.0.2/gptzeror/R/api_url.R | 6 gptzeror-0.0.2/gptzeror/R/key.R | 180 +++--- gptzeror-0.0.2/gptzeror/R/predict.R | 276 +++++----- gptzeror-0.0.2/gptzeror/R/utils.R | 38 - gptzeror-0.0.2/gptzeror/inst/httptest2/redact.R | 8 gptzeror-0.0.2/gptzeror/man/gptzero_set_key.Rd | 56 +- gptzeror-0.0.2/gptzeror/man/gptzeror-package.Rd | 4 gptzeror-0.0.2/gptzeror/man/key.Rd | 44 - gptzeror-0.0.2/gptzeror/tests/testthat.R | 24 gptzeror-0.0.2/gptzeror/tests/testthat/httptest2/predict/api.gptzero.me/v2/predict/files-8c5839-POST.json | 86 +-- gptzeror-0.0.2/gptzeror/tests/testthat/httptest2/predict/api.gptzero.me/v2/predict/text-6834ac-POST.json | 86 +-- gptzeror-0.0.2/gptzeror/tests/testthat/setup.R | 72 +- gptzeror-0.0.2/gptzeror/tests/testthat/test-predict.R | 26 19 files changed, 492 insertions(+), 487 deletions(-)
Title: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME
Models
Description: At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling
activities in order to reduce the overall effort required for generating such plots.
For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox,
called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient
for publication and submissions using few lines of code. This package focuses on plots recommended by ISoP
<doi:10.1002/psp4.12161>. While not required, you can get/install the 'R' 'lixoftConnectors'
package in the 'Monolix' installation, as described at the following url
<https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>.
When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required
Chart Data instead of exporting it from the 'Monolix' gui.
Author: Amine Gassem [aut],
Bruno Bieth [aut],
Irina Baltcheva [aut],
Thomas Dumortier [aut],
Christian Bartels [aut],
Souvik Bhattacharya [aut],
Inga Ludwig [aut],
Ines Paule [aut],
Didier Renard [aut],
Matthew Fidler [aut] ,
Seid Hamzic [aut],
Benjamin Gui [...truncated...]
Maintainer: Aleksandr Pogodaev <alex.pogodaev@novartis.com>
Diff between ggPMX versions 1.3.1 dated 2025-08-27 and 1.3.2 dated 2025-09-05
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS.md | 4 ++++ R/plot-individual.R | 16 ++++++++-------- R/pmx-reader.R | 24 +++++++++++++++++++++--- R/pmxClass.R | 2 +- inst/doc/ggPMX-guide.pdf |binary tests/testthat/setup.R |only tests/testthat/test-reader.R | 40 ++++++++++++++++++++++++++++++++++++++++ 9 files changed, 85 insertions(+), 22 deletions(-)
Title: Accesses Brazilian Public Security Data from SINESP Since 2015
Description: Allows access to data from the Brazilian Public Security Information System (SINESP) by state and municipality. It should be emphasized that the package only extracts the data and facilitates its manipulation in R. Therefore, its sole purpose is to support empirical research. All data credits belong to SINESP, an integrated information platform developed and maintained by the National Secretariat of Public Security (SENASP) of the Ministry of Justice and Public Security. <https://www.gov.br/mj/pt-br/assuntos/sua-seguranca/seguranca-publica/sinesp-1>.
Author: Giovanni Vargette [aut, cre] ,
Igor Laltuf [aut] ,
Marcelo Justus [aut]
Maintainer: Giovanni Vargette <g216978@dac.unicamp.br>
Diff between BrazilCrime versions 0.2.1 dated 2024-09-14 and 0.3.0 dated 2025-09-05
BrazilCrime-0.2.1/BrazilCrime/R/get_sinesp_data.R |only BrazilCrime-0.2.1/BrazilCrime/man/get_sinesp_data.Rd |only BrazilCrime-0.3.0/BrazilCrime/DESCRIPTION | 23 BrazilCrime-0.3.0/BrazilCrime/LICENSE | 4 BrazilCrime-0.3.0/BrazilCrime/MD5 | 37 BrazilCrime-0.3.0/BrazilCrime/NAMESPACE | 10 BrazilCrime-0.3.0/BrazilCrime/R/br_crime_predict.R |only BrazilCrime-0.3.0/BrazilCrime/R/get_sinesp_vde_data.R | 166 +-- BrazilCrime-0.3.0/BrazilCrime/R/sysdata.rda |binary BrazilCrime-0.3.0/BrazilCrime/README.md | 454 +++++----- BrazilCrime-0.3.0/BrazilCrime/build |only BrazilCrime-0.3.0/BrazilCrime/inst/THANKS |only BrazilCrime-0.3.0/BrazilCrime/inst/doc |only BrazilCrime-0.3.0/BrazilCrime/inst/extdata/ufs.csv | 56 - BrazilCrime-0.3.0/BrazilCrime/man/br_crime_predict.Rd |only BrazilCrime-0.3.0/BrazilCrime/man/get_sinesp_vde_data.Rd | 85 - BrazilCrime-0.3.0/BrazilCrime/tests/testthat.R | 24 BrazilCrime-0.3.0/BrazilCrime/tests/testthat/test-get_sinesp_data.R | 68 - BrazilCrime-0.3.0/BrazilCrime/tests/testthat/test-get_sinesp_vde_data.R | 94 +- BrazilCrime-0.3.0/BrazilCrime/vignettes |only 20 files changed, 506 insertions(+), 515 deletions(-)
Title: Markdown Parser and Renderer for R Graphics
Description: Provides the mean to parse and render markdown text with grid
along with facilities to define the styling of the text.
Author: Thomas Lin Pedersen [aut, cre] ,
Martin Mitas [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between marquee versions 1.1.1 dated 2025-08-27 and 1.2.0 dated 2025-09-05
DESCRIPTION | 11 - MD5 | 54 +++--- NAMESPACE | 3 NEWS.md | 9 + R/classic_style.R | 238 ++++++++++++++++------------ R/geom_marquee.R | 13 - R/grob.R | 82 ++++++--- R/guide_marquee.R | 2 R/marquee-package.R | 5 R/style.R | 106 ++++++++++-- R/style_set.R | 77 +++++---- inst/doc/marquee.html | 18 +- inst/doc/marquee_style.Rmd | 2 inst/doc/marquee_style.html | 25 +- man/classic_style.Rd | 10 + man/figures/README-unnamed-chunk-2-1.png |binary man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/geom_marquee.Rd | 2 man/guide_marquee.Rd | 2 man/marquee_grob.Rd | 7 man/style.Rd | 27 ++- tests/testthat/_snaps/grob/marquee_grob.png |binary tests/testthat/_snaps/parse/parsed.csv | 122 +++++++------- tests/testthat/_snaps/style.md | 4 tests/testthat/_snaps/style_set.md | 2 tests/testthat/test-style.R | 14 - vignettes/marquee_style.Rmd | 2 30 files changed, 512 insertions(+), 325 deletions(-)
Title: Evolutionary Quantitative Genetics
Description: Provides functions for covariance matrix comparisons, estimation of repeatabilities in measurements and matrices, and general evolutionary quantitative genetics tools. Melo D, Garcia G, Hubbe A, Assis A P, Marroig G. (2016) <doi:10.12688/f1000research.7082.3>.
Author: Diogo Melo [aut, cre] ,
Ana Paula Assis [aut],
Edgar Zanella [ctb],
Fabio Andrade Machado [aut] ,
Guilherme Garcia [aut],
Alex Hubbe [rev] ,
Gabriel Marroig [ths]
Maintainer: Diogo Melo <diogro@gmail.com>
Diff between evolqg versions 0.3-4 dated 2023-12-05 and 0.3-6 dated 2025-09-05
DESCRIPTION | 19 ++++++++++--------- MD5 | 24 ++++++++++++------------ R/EigenTensorDecomposition.R | 2 +- R/EvolQG.R | 4 ++-- R/MantelCor.R | 2 +- R/MantelModTest.R | 2 +- man/MantelCor.Rd | 2 +- man/MantelModTest.Rd | 2 +- man/evolqg.Rd | 25 +++++++++++++++++++++++++ man/ratones.Rd | 2 +- src/Makevars | 1 + src/Makevars.win | 1 + tests/testthat/test.TestModularity.r | 3 ++- 13 files changed, 59 insertions(+), 30 deletions(-)
Title: Power Analyses using Monte Carlo Simulations
Description: Provides a general purpose simulation-based power analysis
API for routine and customized simulation experimental designs.
The package focuses exclusively on Monte Carlo simulation experiment variants of
(expected) prospective power analyses,
criterion analyses, compromise analyses, sensitivity analyses, and
a priori/post-hoc analyses. The default simulation experiment functions defined within the package
provide stochastic variants of the power analysis subroutines in
G*Power 3.1 (Faul, Erdfelder, Buchner, and Lang, 2009) <doi:10.3758/brm.41.4.1149>,
along with various other parametric and non-parametric power analysis
applications (e.g., mediation analyses) and support for Bayesian power analysis
by way of Bayes factors or posterior probability evaluations.
Additional functions for building
empirical power curves, reanalyzing simulation information, and
for increasing the precision of the resulting power
estimates are also included, each of which utilize similar API structures.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between Spower versions 0.3.1 dated 2025-07-17 and 0.4.0 dated 2025-09-05
Spower-0.3.1/Spower/man/SpowerCurve.Rd |only Spower-0.4.0/Spower/DESCRIPTION | 10 Spower-0.4.0/Spower/MD5 | 28 + Spower-0.4.0/Spower/NAMESPACE | 4 Spower-0.4.0/Spower/R/Spower.R | 114 ++++-- Spower-0.4.0/Spower/R/SpowerBatch.R |only Spower-0.4.0/Spower/R/SpowerCurve.R | 170 ++++----- Spower-0.4.0/Spower/R/util.R | 19 - Spower-0.4.0/Spower/build/vignette.rds |binary Spower-0.4.0/Spower/inst/doc/SpowerIntro.R |only Spower-0.4.0/Spower/inst/doc/SpowerIntro.Rmd |only Spower-0.4.0/Spower/inst/doc/SpowerIntro.html |only Spower-0.4.0/Spower/inst/doc/SpowerIntro_logicals.R |only Spower-0.4.0/Spower/inst/doc/SpowerIntro_logicals.Rmd |only Spower-0.4.0/Spower/inst/doc/SpowerIntro_logicals.html |only Spower-0.4.0/Spower/inst/intro.rds |only Spower-0.4.0/Spower/inst/intro2.rds |only Spower-0.4.0/Spower/man/Spower.Rd | 306 ++++++++++++++--- Spower-0.4.0/Spower/man/getLastSpower.Rd | 7 Spower-0.4.0/Spower/vignettes/SpowerIntro.Rmd |only Spower-0.4.0/Spower/vignettes/SpowerIntro_logicals.Rmd |only 21 files changed, 462 insertions(+), 196 deletions(-)
Title: Sensitivity Analysis for Irregular Assessment Times
Description: Sensitivity analysis for trials with irregular and informative
assessment times, based on a new influence function-based, augmented
inverse intensity-weighted estimator.
Author: Andrew Redd [aut, cre] ,
Yujing Gao [aut],
Shu Yang [aut],
Bonnie Smith [aut],
Ravi Varadhan [aut],
Agatha Mallett [ctb, ctr],
Daniel Scharfstein [pdr, aut] ,
University of Utah [cph]
Maintainer: Andrew Redd <andrew.redd@hsc.utah.edu>
Diff between SensIAT versions 0.2.0 dated 2025-08-18 and 0.3.0 dated 2025-09-05
SensIAT-0.2.0/SensIAT/R/Cond_mean_fn.R |only SensIAT-0.2.0/SensIAT/R/PCORI_example_data.R |only SensIAT-0.2.0/SensIAT/R/PCORI_fulldata_model.R |only SensIAT-0.2.0/SensIAT/R/PCORI_within_group_model.R |only SensIAT-0.2.0/SensIAT/R/SensIAT_prepare_data.R |only SensIAT-0.2.0/SensIAT/R/Y_draw_fn.R |only SensIAT-0.2.0/SensIAT/R/compute_influence_term_2_quadv.R |only SensIAT-0.2.0/SensIAT/R/data_transform.R |only SensIAT-0.2.0/SensIAT/man/Cond_mean_fn.Rd |only SensIAT-0.2.0/SensIAT/man/SensIAT_fit_marginal_model.Rd |only SensIAT-0.2.0/SensIAT/man/SensIAT_jackknife.Rd |only SensIAT-0.2.0/SensIAT/man/SensIAT_prepare_data.Rd |only SensIAT-0.2.0/SensIAT/man/SensIAT_sim_outcome_modeler.Rd |only SensIAT-0.2.0/SensIAT/man/SensIAT_sim_outcome_modeler_mave.Rd |only SensIAT-0.2.0/SensIAT/man/sensitivity_expected_values.Rd |only SensIAT-0.3.0/SensIAT/DESCRIPTION | 6 SensIAT-0.3.0/SensIAT/MD5 | 92 +-- SensIAT-0.3.0/SensIAT/NAMESPACE | 22 SensIAT-0.3.0/SensIAT/NEWS.md | 10 SensIAT-0.3.0/SensIAT/R/RcppExports.R | 4 SensIAT-0.3.0/SensIAT/R/SensIAT_sim_outcome_modeler_mave.R | 242 +++++----- SensIAT-0.3.0/SensIAT/R/add_class.R | 3 SensIAT-0.3.0/SensIAT/R/autoplot.R | 18 SensIAT-0.3.0/SensIAT/R/compute_influence_for_one_alpha_and_one_patient.R | 4 SensIAT-0.3.0/SensIAT/R/compute_influence_term_2_quadv_sim.R | 174 +++---- SensIAT-0.3.0/SensIAT/R/example_data.R |only SensIAT-0.3.0/SensIAT/R/fit_marginal_model.R | 8 SensIAT-0.3.0/SensIAT/R/fulldata_model.R |only SensIAT-0.3.0/SensIAT/R/jackknife.R | 67 +- SensIAT-0.3.0/SensIAT/R/predict_within_group.R | 7 SensIAT-0.3.0/SensIAT/R/prepare_data.R |only SensIAT-0.3.0/SensIAT/R/sensitivity_expected_values.R | 42 - SensIAT-0.3.0/SensIAT/R/sim_outcome_modeler.R | 14 SensIAT-0.3.0/SensIAT/R/within_group_model.R |only SensIAT-0.3.0/SensIAT/inst/examples/basic.R | 4 SensIAT-0.3.0/SensIAT/inst/examples/recreate_original.R | 2 SensIAT-0.3.0/SensIAT/man/SensIAT_example_data.Rd | 8 SensIAT-0.3.0/SensIAT/man/add_class.Rd | 2 SensIAT-0.3.0/SensIAT/man/autoplot.SensIAT_fulldata_jackknife_results.Rd | 4 SensIAT-0.3.0/SensIAT/man/autoplot.SensIAT_fulldata_model.Rd | 4 SensIAT-0.3.0/SensIAT/man/autoplot.SensIAT_within_group_model.Rd | 6 SensIAT-0.3.0/SensIAT/man/autoplot.SensIAT_withingroup_jackknife_results.Rd | 4 SensIAT-0.3.0/SensIAT/man/compute_SensIAT_expected_values.Rd |only SensIAT-0.3.0/SensIAT/man/fit_SensIAT_marginal_mean_model.Rd |only SensIAT-0.3.0/SensIAT/man/fit_SensIAT_single_index_fixed_coef_model.Rd |only SensIAT-0.3.0/SensIAT/man/fit_SensIAT_single_index_norm1coef_model.Rd |only SensIAT-0.3.0/SensIAT/man/fit_SensIAT_within_group_model.Rd | 10 SensIAT-0.3.0/SensIAT/man/jackknife.Rd | 34 + SensIAT-0.3.0/SensIAT/man/pcoriaccel_estimate_pmf.Rd | 1 SensIAT-0.3.0/SensIAT/man/pcoriaccel_evaluate_basis.Rd | 1 SensIAT-0.3.0/SensIAT/man/pcoriaccel_evaluate_basis_mat.Rd | 1 SensIAT-0.3.0/SensIAT/man/predict.SensIAT_within_group_model.Rd | 9 SensIAT-0.3.0/SensIAT/man/prepare_SensIAT_data.Rd |only SensIAT-0.3.0/SensIAT/src/estimate_pmf.cpp | 1 SensIAT-0.3.0/SensIAT/src/spline_basis.h | 3 SensIAT-0.3.0/SensIAT/tests/testthat/test-PCORI_within_group_model.R | 10 SensIAT-0.3.0/SensIAT/tests/testthat/test-SensIAT_sim_outcome_modeler_mave.R | 140 ++++- SensIAT-0.3.0/SensIAT/tests/testthat/test-influence_term1.R | 2 SensIAT-0.3.0/SensIAT/tests/testthat/test-influence_term2.R | 2 59 files changed, 521 insertions(+), 440 deletions(-)
Title: Tools for Analyzing Mixed Effect Regression Models
Description: Provides methods for extracting results from mixed-effect model
objects fit with the 'lme4' package. Allows construction of prediction intervals
efficiently from large scale linear and generalized linear mixed-effects models.
This method draws from the simulation framework used in the Gelman and Hill (2007) textbook:
Data Analysis Using Regression and Multilevel/Hierarchical Models.
Author: Jared E. Knowles [aut, cre],
Carl Frederick [aut],
Alex Whitworth [ctb]
Maintainer: Jared E. Knowles <jared@civilytics.com>
Diff between merTools versions 0.6.2 dated 2024-02-08 and 0.6.3 dated 2025-09-05
DESCRIPTION | 10 +- MD5 | 45 +++++------ NEWS.md | 4 + R/helpers.R | 2 R/merList.R | 17 +++- R/merPlots.R | 6 - R/subBoot.R | 4 - build/vignette.rds |binary inst/doc/Using_predictInterval.html | 16 ++-- inst/doc/imputation.html | 4 - inst/doc/marginal_effects.html | 6 - inst/doc/merToolsIntro.html | 22 ++--- man/VarCorr.merModList.Rd | 4 - man/merModList-class.Rd |only man/merTools-package.Rd | 142 ++++++++++++++++++------------------ man/mkNewReTrms.Rd | 66 ++++++++-------- man/modelFixedEff.Rd | 66 ++++++++-------- man/plotFEsim.Rd | 94 +++++++++++------------ man/plotREsim.Rd | 118 ++++++++++++++--------------- man/ranef.merModList.Rd | 72 ++++++++---------- man/thetaExtract.Rd | 50 ++++++------ tests/testthat/_snaps/predict2.md | 20 ++--- tests/testthat/test-predict1.R | 8 +- tests/testthat/test-predict2.R | 8 +- 24 files changed, 399 insertions(+), 385 deletions(-)
Title: Process and Report 'GreenFeed' Data
Description: Provides tools for downloading, processing, and reporting daily and finalized 'GreenFeed' data.
Author: Guillermo Martinez-Boggio [cre, aut, cph] ,
Meredith Harrison [ctb],
Patrick Lutz [ctb]
Maintainer: Guillermo Martinez-Boggio <gmartinezboggio@ucdavis.edu>
Diff between greenfeedr versions 1.3.0 dated 2025-08-18 and 1.3.1 dated 2025-09-05
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/viseat.R | 8 ++++++++ README.md | 7 +------ inst/doc/greenfeedr.html | 2 +- inst/shinyapp/app_server.R | 2 +- 7 files changed, 24 insertions(+), 17 deletions(-)
Title: Fairness Evaluation Metrics with Confidence Intervals for Binary
Protected Attributes
Description: A collection of functions for computing fairness metrics for machine learning and statistical models, including confidence intervals for each metric. The package supports the evaluation of group-level fairness criterion commonly used in fairness research, particularly in healthcare for binary protected attributes. It is based on the overview of fairness in machine learning written by Gao et al (2024) <doi:10.48550/arXiv.2406.09307>.
Author: Jianhui Gao [aut] ,
Benjamin Smith [aut, cre] ,
Benson Chou [aut] ,
Jessica Gronsbell [aut]
Maintainer: Benjamin Smith <benyamin.smith@mail.utoronto.ca>
Diff between fairmetrics versions 1.0.4 dated 2025-07-22 and 1.0.5 dated 2025-09-05
fairmetrics-1.0.4/fairmetrics/R/Fairness.R |only fairmetrics-1.0.4/fairmetrics/R/Helper.R |only fairmetrics-1.0.4/fairmetrics/man/eval_cond_stats_parity.Rd |only fairmetrics-1.0.5/fairmetrics/DESCRIPTION | 11 fairmetrics-1.0.5/fairmetrics/MD5 | 61 fairmetrics-1.0.5/fairmetrics/NAMESPACE | 1 fairmetrics-1.0.5/fairmetrics/R/ModelPerformance.R | 76 fairmetrics-1.0.5/fairmetrics/R/eval_acc_parity.R |only fairmetrics-1.0.5/fairmetrics/R/eval_bs_parity.R |only fairmetrics-1.0.5/fairmetrics/R/eval_cond_acc_equality.R |only fairmetrics-1.0.5/fairmetrics/R/eval_eq_odds.R |only fairmetrics-1.0.5/fairmetrics/R/eval_eq_opp.R |only fairmetrics-1.0.5/fairmetrics/R/eval_neg_class_bal.R |only fairmetrics-1.0.5/fairmetrics/R/eval_neg_pred_parity.R |only fairmetrics-1.0.5/fairmetrics/R/eval_pos_class_bal.R |only fairmetrics-1.0.5/fairmetrics/R/eval_pos_pred_parity.R |only fairmetrics-1.0.5/fairmetrics/R/eval_pred_equality.R |only fairmetrics-1.0.5/fairmetrics/R/eval_stats_parity.R |only fairmetrics-1.0.5/fairmetrics/R/eval_treatment_equality.R |only fairmetrics-1.0.5/fairmetrics/R/get_fairness_metrics.R | 469 ++- fairmetrics-1.0.5/fairmetrics/build/vignette.rds |binary fairmetrics-1.0.5/fairmetrics/inst/CITATION | 2 fairmetrics-1.0.5/fairmetrics/inst/doc/fairmetrics.R | 144 - fairmetrics-1.0.5/fairmetrics/inst/doc/fairmetrics.Rmd | 465 +-- fairmetrics-1.0.5/fairmetrics/inst/doc/fairmetrics.html | 1434 +---------- fairmetrics-1.0.5/fairmetrics/man/eval_acc_parity.Rd | 11 fairmetrics-1.0.5/fairmetrics/man/eval_bs_parity.Rd | 12 fairmetrics-1.0.5/fairmetrics/man/eval_cond_acc_equality.Rd | 12 fairmetrics-1.0.5/fairmetrics/man/eval_eq_odds.Rd | 11 fairmetrics-1.0.5/fairmetrics/man/eval_eq_opp.Rd | 15 fairmetrics-1.0.5/fairmetrics/man/eval_neg_class_bal.Rd | 11 fairmetrics-1.0.5/fairmetrics/man/eval_neg_pred_parity.Rd | 10 fairmetrics-1.0.5/fairmetrics/man/eval_pos_class_bal.Rd | 11 fairmetrics-1.0.5/fairmetrics/man/eval_pos_pred_parity.Rd | 10 fairmetrics-1.0.5/fairmetrics/man/eval_pred_equality.Rd | 10 fairmetrics-1.0.5/fairmetrics/man/eval_stats_parity.Rd | 13 fairmetrics-1.0.5/fairmetrics/man/eval_treatment_equality.Rd | 10 fairmetrics-1.0.5/fairmetrics/man/get_fairness_metrics.Rd | 28 fairmetrics-1.0.5/fairmetrics/vignettes/fairmetrics.Rmd | 465 +-- 39 files changed, 1104 insertions(+), 2188 deletions(-)
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 0.4.2 dated 2025-06-01 and 0.4.3 dated 2025-09-05
DESCRIPTION | 6 - MD5 | 27 ++-- NEWS.md | 7 + R/create_template.R | 11 + R/custom_modules.R | 8 + README.md | 206 ++++++++++++++++++++++++++---------- inst/app_skeleton/load.Rmd | 6 - inst/app_skeleton/save.Rmd | 25 +++- inst/app_skeleton/testthat.Rmd |only inst/shiny/Rmd/text_intro_tab.Rmd | 2 inst/shiny/Rmd/userReport_intro.Rmd | 2 inst/shiny/modules/core_load.R | 6 - inst/shiny/modules/core_save.R | 33 +++-- inst/shiny/modules/rep_markdown.R | 4 tests/testthat/test-save_load.R | 13 +- 15 files changed, 257 insertions(+), 99 deletions(-)
Title: 'shiny' Applications for the 'tesselle' Packages
Description: A collection of 'shiny' applications for the 'tesselle'
packages <https://www.tesselle.org/>. This package provides
applications for archaeological data analysis and visualization. These
mainly, but not exclusively, include applications for chronological
modelling (e.g. matrix seriation, aoristic analysis) and count data
analysis (e.g. diversity measures, compositional data analysis).
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between kinesis versions 0.2.1 dated 2025-07-15 and 0.3.0 dated 2025-09-05
kinesis-0.2.1/kinesis/inst/tinytest/_tinysnapshot |only kinesis-0.2.1/kinesis/inst/tinytest/helpers.R |only kinesis-0.2.1/kinesis/man/update_selectize_values.Rd |only kinesis-0.2.1/kinesis/man/update_selectize_variables.Rd |only kinesis-0.3.0/kinesis/DESCRIPTION | 19 kinesis-0.3.0/kinesis/MD5 | 181 +-- kinesis-0.3.0/kinesis/NAMESPACE | 6 kinesis-0.3.0/kinesis/NEWS.md | 8 kinesis-0.3.0/kinesis/R/bertin.R | 16 kinesis-0.3.0/kinesis/R/ca.R | 16 kinesis-0.3.0/kinesis/R/coda.R | 104 - kinesis-0.3.0/kinesis/R/coda_barplot.R | 2 kinesis-0.3.0/kinesis/R/coda_hist.R | 2 kinesis-0.3.0/kinesis/R/coda_statistics.R | 3 kinesis-0.3.0/kinesis/R/count.R |only kinesis-0.3.0/kinesis/R/count_diversity_alpha.R | 26 kinesis-0.3.0/kinesis/R/count_diversity_beta.R | 69 - kinesis-0.3.0/kinesis/R/count_occurrence.R | 29 kinesis-0.3.0/kinesis/R/diversity.R |only kinesis-0.3.0/kinesis/R/graphics.R | 3 kinesis-0.3.0/kinesis/R/help.R | 4 kinesis-0.3.0/kinesis/R/home.R | 49 kinesis-0.3.0/kinesis/R/import.R | 117 +- kinesis-0.3.0/kinesis/R/kinesis-internal.R | 177 --- kinesis-0.3.0/kinesis/R/kinesis-package.R | 6 kinesis-0.3.0/kinesis/R/lm.R |only kinesis-0.3.0/kinesis/R/multivariate.R | 79 - kinesis-0.3.0/kinesis/R/pca.R | 14 kinesis-0.3.0/kinesis/R/plot.R | 2 kinesis-0.3.0/kinesis/R/prepare.R | 213 +--- kinesis-0.3.0/kinesis/R/run.R | 12 kinesis-0.3.0/kinesis/R/scatter.R | 111 -- kinesis-0.3.0/kinesis/R/table.R | 2 kinesis-0.3.0/kinesis/R/ternary.R | 110 +- kinesis-0.3.0/kinesis/R/time_interval.R | 46 kinesis-0.3.0/kinesis/R/variables.R |only kinesis-0.3.0/kinesis/README.md | 5 kinesis-0.3.0/kinesis/build/partial.rdb |binary kinesis-0.3.0/kinesis/inst/app/aoristic/server.R | 1 kinesis-0.3.0/kinesis/inst/app/aoristic/ui.R | 2 kinesis-0.3.0/kinesis/inst/app/ca/server.R | 3 kinesis-0.3.0/kinesis/inst/app/ca/ui.R | 4 kinesis-0.3.0/kinesis/inst/app/diversity/server.R | 10 kinesis-0.3.0/kinesis/inst/app/diversity/ui.R | 7 kinesis-0.3.0/kinesis/inst/app/mcd/server.R | 3 kinesis-0.3.0/kinesis/inst/app/mcd/ui.R | 4 kinesis-0.3.0/kinesis/inst/app/pca/server.R | 1 kinesis-0.3.0/kinesis/inst/app/pca/ui.R | 2 kinesis-0.3.0/kinesis/inst/app/scatter/config.yml | 4 kinesis-0.3.0/kinesis/inst/app/scatter/server.R | 6 kinesis-0.3.0/kinesis/inst/app/scatter/ui.R | 3 kinesis-0.3.0/kinesis/inst/app/seriation/server.R | 3 kinesis-0.3.0/kinesis/inst/app/seriation/ui.R | 4 kinesis-0.3.0/kinesis/inst/app/source/server.R | 1 kinesis-0.3.0/kinesis/inst/app/source/ui.R | 2 kinesis-0.3.0/kinesis/inst/app/ternary/server.R | 1 kinesis-0.3.0/kinesis/inst/app/ternary/ui.R | 2 kinesis-0.3.0/kinesis/inst/extdata |only kinesis-0.3.0/kinesis/inst/po/fr/LC_MESSAGES/R-kinesis.mo |binary kinesis-0.3.0/kinesis/inst/tinytest/bronze.csv | 740 +++++++------- kinesis-0.3.0/kinesis/inst/tinytest/fake.csv |only kinesis-0.3.0/kinesis/inst/tinytest/test_coda.R | 33 kinesis-0.3.0/kinesis/inst/tinytest/test_coda_logratio.R | 15 kinesis-0.3.0/kinesis/inst/tinytest/test_coda_plot.R | 44 kinesis-0.3.0/kinesis/inst/tinytest/test_import.R | 20 kinesis-0.3.0/kinesis/inst/tinytest/test_inputs.R | 25 kinesis-0.3.0/kinesis/inst/tinytest/test_prepare.R | 45 kinesis-0.3.0/kinesis/inst/tinytest/test_ternary.R | 52 kinesis-0.3.0/kinesis/man/bertin_server.Rd | 4 kinesis-0.3.0/kinesis/man/bertin_ui.Rd | 4 kinesis-0.3.0/kinesis/man/checkbox_ui.Rd |only kinesis-0.3.0/kinesis/man/count_server.Rd |only kinesis-0.3.0/kinesis/man/count_ui.Rd |only kinesis-0.3.0/kinesis/man/diversity_alpha_server.Rd | 6 kinesis-0.3.0/kinesis/man/diversity_alpha_ui.Rd | 4 kinesis-0.3.0/kinesis/man/diversity_beta_server.Rd | 13 kinesis-0.3.0/kinesis/man/diversity_beta_ui.Rd | 4 kinesis-0.3.0/kinesis/man/diversity_docs_ui.Rd | 4 kinesis-0.3.0/kinesis/man/diversity_server.Rd |only kinesis-0.3.0/kinesis/man/diversity_ui.Rd |only kinesis-0.3.0/kinesis/man/falsy.Rd |only kinesis-0.3.0/kinesis/man/home_ui.Rd | 2 kinesis-0.3.0/kinesis/man/kinesis-package.Rd | 4 kinesis-0.3.0/kinesis/man/lm_server.Rd |only kinesis-0.3.0/kinesis/man/lm_ui.Rd |only kinesis-0.3.0/kinesis/man/occurrence_server.Rd | 6 kinesis-0.3.0/kinesis/man/occurrence_ui.Rd | 4 kinesis-0.3.0/kinesis/man/prepare_server.Rd | 11 kinesis-0.3.0/kinesis/man/run_app.Rd | 4 kinesis-0.3.0/kinesis/man/selectize_ui.Rd | 5 kinesis-0.3.0/kinesis/man/update_checkbox_colnames.Rd |only kinesis-0.3.0/kinesis/man/update_input.Rd |only kinesis-0.3.0/kinesis/man/update_selectize_colnames.Rd |only kinesis-0.3.0/kinesis/man/update_selectize_rownames.Rd |only kinesis-0.3.0/kinesis/po/R-fr.po | 479 +++++---- kinesis-0.3.0/kinesis/po/R-kinesis.pot | 462 ++++---- kinesis-0.3.0/kinesis/tests/tinytest.R | 6 97 files changed, 1619 insertions(+), 1871 deletions(-)
Title: Supervised Feature Selection
Description: Interfaces for choosing important predictors in supervised
regression, classification, and censored regression models. Permuted
importance scores (Biecek and Burzykowski (2021)
<doi:10.1201/9780429027192>) can be computed for 'tidymodels' model
fits.
Author: Max Kuhn [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between important versions 0.0.1 dated 2025-08-20 and 0.2.0 dated 2025-09-05
DESCRIPTION | 15 +- MD5 | 37 +++++- NAMESPACE | 25 ++++ NEWS.md | 10 + R/import-standalone-obj-type.R |only R/import-standalone-types-check.R |only R/importance_perm.R | 18 ++- R/important-package.R | 26 +++- R/recipe_utils.R |only R/step_predictor_best.R |only R/step_predictor_desirability.R |only R/step_predictor_retain.R |only README.md | 103 ++++++++++++++++++- build/partial.rdb |binary inst/WORDLIST | 3 man/required_pkgs.important.Rd |only man/rmd |only man/step_predictor_best.Rd |only man/step_predictor_desirability.Rd |only man/step_predictor_retain.Rd |only tests/testthat/_snaps/recipes_utils.md |only tests/testthat/_snaps/step_predictor_best.md |only tests/testthat/_snaps/step_predictor_desirability.md |only tests/testthat/_snaps/step_predictor_retain.md |only tests/testthat/helper-objects.R | 49 ++++++--- tests/testthat/test-recipes_utils.R |only tests/testthat/test-step_predictor_best.R |only tests/testthat/test-step_predictor_desirability.R |only tests/testthat/test-step_predictor_retain.R |only 29 files changed, 242 insertions(+), 44 deletions(-)
Title: Cohort Generation for the OMOP Common Data Model
Description: Generate cohorts and subsets using an Observational
Medical Outcomes Partnership (OMOP) Common Data Model (CDM) Database.
Cohorts are defined using 'CIRCE' (<https://github.com/ohdsi/circe-be>) or
SQL compatible with 'SqlRender' (<https://github.com/OHDSI/SqlRender>).
Author: Anthony Sena [aut, cre],
Jamie Gilbert [aut],
Gowtham Rao [aut],
Freddy Avila Cruz [aut],
Martijn Schuemie [aut],
Observational Health Data Science and Informatics [cph]
Maintainer: Anthony Sena <sena@ohdsi.org>
Diff between CohortGenerator versions 0.12.0 dated 2025-07-31 and 0.12.1 dated 2025-09-05
DESCRIPTION | 8 +- MD5 | 18 ++--- NEWS.md | 6 + R/SubsetQueryBuilders.R | 2 build/vignette.rds |binary inst/doc/CreatingCohortSubsetDefinitions.R | 18 ++--- inst/doc/CreatingCohortSubsetDefinitions.html | 4 - inst/doc/GeneratingCohorts.pdf |binary inst/doc/SamplingCohorts.R | 92 +++++++++++++------------- inst/doc/SamplingCohorts.pdf |binary 10 files changed, 77 insertions(+), 71 deletions(-)
More information about CohortGenerator at CRAN
Permanent link
Title: Package Admix for Admixture (aka Contamination) Models
Description: Implements techniques to estimate the unknown quantities
related to two-component admixture models, where the two components
can belong to any distribution (note that in the case of multinomial
mixtures, the two components must belong to the same family).
Estimation methods depend on the assumptions made on the unknown
component density; see Bordes and Vandekerkhove (2010)
<doi:10.3103/S1066530710010023>, Patra and Sen (2016)
<doi:10.1111/rssb.12148>, and Milhaud, Pommeret, Salhi, Vandekerkhove
(2024) <doi:10.3150/23-BEJ1593>. In practice, one can estimate both
the mixture weight and the unknown component density in a wide variety
of frameworks. On top of that, hypothesis tests can be performed in
one and two-sample contexts to test the unknown component density (see
Milhaud, Pommeret, Salhi and Vandekerkhove (2022)
<doi:10.1016/j.jspi.2021.05.010>, and Milhaud, Pommeret, Salhi,
Vandekerkhove (2024) <doi:10.3150/23-BEJ1593>). Finally, clustering of
unknown [...truncated...]
Author: Xavier Milhaud [aut, cre],
Pierre Vandekerkhove [ctb],
Denys Pommeret [ctb],
Yahia Salhi [ctb]
Maintainer: Xavier Milhaud <xavier.milhaud.research@gmail.com>
Diff between admix versions 2.4.3 dated 2025-08-21 and 2.5.1 dated 2025-09-05
DESCRIPTION | 6 MD5 | 45 ++-- NAMESPACE | 15 + R/IBM_k_samples_test.R | 92 +++++--- R/admix_estim.R | 24 +- R/admix_test.R | 10 R/decontaminated_dist.R | 51 +++- R/extractors.R | 309 +++++++++++++++++++++++----- R/gaussianity_test.R | 14 - R/orthobasis_test.R | 13 - R/utils.R | 88 +++++-- build/partial.rdb |binary inst/doc/admixture-weight-estimation.html | 18 - man/admix_estim.Rd | 21 + man/decontaminated_density.Rd | 13 - man/get_cluster_members.admix_cluster.Rd |only man/get_cluster_sizes.admix_cluster.Rd |only man/get_discrepancy_id.IBM_test.Rd |only man/get_discrepancy_matrix.IBM_test.Rd |only man/get_discrepancy_matrix.admix_cluster.Rd |only man/get_discrepancy_rank.IBM_test.Rd |only man/get_known_component.admix_cluster.Rd |only man/get_known_component.admix_estim.Rd |only man/get_known_component.htest.Rd |only man/get_mixing_weights.admix_estim.Rd |only man/get_mixing_weights.htest.Rd |only man/get_statistic_components.IBM_test.Rd |only man/get_tabulated_dist.IBM_test.Rd |only man/plot.decontaminated_density.Rd | 14 - man/reject_nullHyp.htest.Rd |only man/which_rank.htest.Rd |only 31 files changed, 550 insertions(+), 183 deletions(-)
Title: 'Canvas' LMS API Integration
Description: Allow R users to interact with the 'Canvas' Learning Management System (LMS) API (see
<https://canvas.instructure.com/doc/api/all_resources.html> for details).
It provides a set of functions to access and manipulate course data, assignments, grades, users,
and other resources available through the 'Canvas' API.
Author: Tomer Iwan [aut, cre],
Niels Smits [ctb] ,
VU Analytics [cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Diff between vvcanvas versions 0.0.5 dated 2025-03-31 and 0.0.6 dated 2025-09-05
DESCRIPTION | 8 - MD5 | 144 ++++++++++++++++------------ NAMESPACE | 16 +++ NEWS.md | 5 R/create_assignment_group.R | 7 - R/create_conversation.R |only R/create_course_section.R | 7 - R/create_folder.R | 7 - R/create_group_category.R | 7 - R/create_module.R | 15 +- R/create_module_item.R | 20 +-- R/create_page.R | 7 - R/delete_course_section.R | 6 - R/delete_page.R | 19 +-- R/edit_section.R | 7 - R/get_all_courses.R | 49 ++------- R/get_assignment_details.R | 6 - R/get_assignment_groups.R | 18 +-- R/get_assignment_submissions.R | 17 +-- R/get_assignments.R | 17 +-- R/get_calendar_events.R | 20 ++- R/get_conversations.R |only R/get_course_enrollments.R | 16 +-- R/get_course_files.R | 17 +-- R/get_course_folders.R | 21 ++-- R/get_course_gradebook.R |only R/get_course_groups.R | 16 +-- R/get_course_media_objects.R | 18 +-- R/get_course_pages.R | 18 +-- R/get_course_quizzes.R | 17 +-- R/get_course_root_folder.R |only R/get_course_sections.R | 16 +-- R/get_course_students.R | 17 +-- R/get_course_users.R | 17 +-- R/get_courses.R | 2 R/get_department_statistics.R | 16 +-- R/get_department_statistics_by_subaccount.R | 16 +-- R/get_discussions.R | 17 +-- R/get_favorite_courses.R | 6 - R/get_folder_files.R |only R/get_group_categories.R | 16 +-- R/get_group_memberships.R | 16 +-- R/get_group_users.R | 16 +-- R/get_module_items.R | 16 +-- R/get_modules.R | 17 +-- R/get_quiz_submissions.R |only R/get_roles.R | 1 R/get_section_information.R | 6 - R/get_single_conversation.R |only R/get_user_folders.R |only R/paginate.R |only R/post_new_discussion.R | 7 - R/query_progress.R |only R/update_course_grades.R |only R/update_page.R | 25 ++-- R/update_quiz.R | 9 - R/update_section_grades.R |only R/upload_file.R | 21 ++-- R/upload_folder_file.R |only R/upload_qti_file_with_migration.R | 49 +++++---- inst/doc/QTI_quiz.R | 7 - inst/doc/QTI_quiz.Rmd | 7 - inst/doc/QTI_quiz.html | 6 - inst/doc/getting_started.R | 3 inst/doc/getting_started.Rmd | 3 inst/doc/groups_use_case.R | 15 +- inst/doc/groups_use_case.Rmd | 21 +--- inst/doc/groups_use_case.html | 37 +++---- man/append_access_token.Rd |only man/create_conversation.Rd |only man/extract_next_url.Rd |only man/get_conversations.Rd |only man/get_course_folders.Rd | 7 + man/get_course_gradebook.Rd |only man/get_course_root_folder.Rd |only man/get_folder_files.Rd |only man/get_quiz_submissions.Rd |only man/get_single_conversation.Rd |only man/get_user_folders.Rd |only man/paginate.Rd |only man/query_progress.Rd |only man/update_course_grades.Rd |only man/update_section_grades.Rd |only man/upload_folder_file.Rd |only vignettes/QTI_quiz.Rmd | 7 - vignettes/getting_started.Rmd | 3 vignettes/groups_use_case.Rmd | 21 +--- 87 files changed, 519 insertions(+), 449 deletions(-)
Title: Byte Pair Encoding Text Tokenization
Description: Unsupervised text tokenizer focused on computational efficiency. Wraps the 'YouTokenToMe' library <https://github.com/VKCOM/YouTokenToMe> which is an implementation of fast Byte Pair Encoding (BPE) <https://aclanthology.org/P16-1162/>.
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
VK.com [cph],
Gregory Popovitch [ctb, cph] ,
The Abseil Authors [ctb, cph] ,
Ivan Belonogov [ctb, cph] )
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between tokenizers.bpe versions 0.1.3 dated 2023-09-15 and 0.1.4 dated 2025-09-05
DESCRIPTION | 8 LICENSE.note | 2 MD5 | 20 - NEWS.md | 4 src/parallel_hashmap/btree.h | 52 +-- src/parallel_hashmap/phmap.h | 522 +++++++++++++++++++++--------------- src/parallel_hashmap/phmap_base.h | 476 +++++++++++++++----------------- src/parallel_hashmap/phmap_bits.h | 83 ++--- src/parallel_hashmap/phmap_config.h | 66 +++- src/parallel_hashmap/phmap_dump.h | 67 +++- src/parallel_hashmap/phmap_utils.h | 2 11 files changed, 724 insertions(+), 578 deletions(-)
More information about tokenizers.bpe at CRAN
Permanent link
Title: Species Distribution Models with Tidymodels
Description: Fit species distribution models (SDMs) using the 'tidymodels' framework,
which provides a standardised interface to define models and process their
outputs. 'tidysdm' expands 'tidymodels' by providing methods for spatial objects,
models and metrics specific to SDMs,
as well as a number of specialised functions to process occurrences
for contemporary and palaeo datasets. The full
functionalities of the package are described
in Leonardi et al. (2023) <doi:10.1101/2023.07.24.550358>.
Author: Michela Leonardi [aut],
Margherita Colucci [aut],
Andrea Vittorio Pozzi [aut],
Eleanor M.L. Scerri [aut],
Ben Tupper [ctb],
Andrea Manica [aut, cre]
Maintainer: Andrea Manica <am315@cam.ac.uk>
Diff between tidysdm versions 1.0.2 dated 2025-08-22 and 1.0.3 dated 2025-09-05
DESCRIPTION | 8 +- MD5 | 22 +++--- NEWS.md | 3 R/tidysdm-package.R | 1 R/zzz.R | 5 + inst/doc/a0_tidysdm_overview.html | 112 ++++++++++++++++---------------- inst/doc/a1_palaeodata_application.html | 26 +++---- inst/doc/a2_tidymodels_additions.html | 81 ++++++++++++++--------- inst/doc/a3_troubleshooting.html | 67 ++++++++----------- man/geom_split_violin.Rd | 10 +- tests/spelling.R | 9 +- tests/testthat/Rplots.pdf |binary 12 files changed, 185 insertions(+), 159 deletions(-)
Title: Stock Assessment Methods Toolkit
Description: Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries.
'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting,
model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Author: Quang Huynh [aut, cre],
Tom Carruthers [aut],
Adrian Hordyk [aut]
Maintainer: Quang Huynh <quang@bluematterscience.com>
Diff between SAMtool versions 1.8.1 dated 2025-04-28 and 1.8.2 dated 2025-09-05
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS.md | 6 +++++- R/RCM_est.R | 7 +++++-- R/RCM_int.R | 12 ++++++++---- R/RCM_rmd.R | 4 ++-- R/define_S4_class_RCModel.R | 6 +++++- build/partial.rdb |binary 8 files changed, 37 insertions(+), 22 deletions(-)
Title: Exploratory Analysis of Temporal and Spatio-Temporal Health Data
Description: A collection of commonly used visualizations of temporal and
spatio-temporal health data including case counts, incidence rates, and
covariates. The available plot types include time series, heatmaps,
seasonality plots, maps and more. The package supports standard data
transformations such as temporal and spatial aggregations, while
offering extensive customization options for the resulting figures.
Author: Carles Mila [aut, cre] ,
Giovenale Moirano [aut] ,
Anna B. Kawiecki [aut] ,
Rachel Lowe [aut, cph]
Maintainer: Carles Mila <carles.milagarcia@bsc.es>
Diff between GHRexplore versions 0.1.1 dated 2025-07-10 and 0.2.0 dated 2025-09-05
DESCRIPTION | 6 - MD5 | 45 ++++---- NAMESPACE | 1 NEWS.md | 8 + R/dengue_MS.R | 19 ++- R/dengue_SP.R | 4 R/map_MS.R | 6 - R/plot_compare.R | 2 R/plot_map.R | 79 +++++++++------ R/plot_timeseries.R | 4 R/plot_timeseries2.R |only README.md | 2 inst/doc/GHRexplore.R | 47 ++++++++- inst/doc/GHRexplore.Rmd | 65 +++++++++++- inst/doc/GHRexplore.html | 166 ++++++++++++++++++++------------- man/dengue_MS.Rd | 16 +-- man/dengue_SP.Rd | 2 man/map_MS.Rd | 2 man/plot_compare.Rd | 2 man/plot_map.Rd | 19 ++- man/plot_timeseries.Rd | 3 man/plot_timeseries2.Rd |only tests/testthat/test-plot_map.R | 6 - tests/testthat/test-plot_timeseries2.R |only vignettes/GHRexplore.Rmd | 65 +++++++++++- 25 files changed, 402 insertions(+), 167 deletions(-)
Title: Fast and Robust Multi-Scale Graph Clustering
Description: A graph community detection algorithm that aims to be performant
on large graphs and robust, returning consistent results across runs.
SpeakEasy 2 (SE2), the underlying algorithm, is described in Chris Gaiteri,
David R. Connell & Faraz A. Sultan et al. (2023)
<doi:10.1186/s13059-023-03062-0>. The core algorithm is written in 'C',
providing speed and keeping the memory requirements low. This implementation
can take advantage of multiple computing cores without increasing memory
usage. SE2 can detect community structure across scales, making it a good
choice for biological data, which often has hierarchical structure. Graphs
can be passed to the algorithm as adjacency matrices using base 'R'
matrices, the 'Matrix' library, 'igraph' graphs, or any data that can be
coerced into a matrix.
Author: David Connell [aut, cre, cph] ,
Chris Gaiteri [cph] ,
Gabor Csardi [cph, ctb] ,
Tamas Nepusz [cph, ctb] ,
Szabolcs Horvat [cph, ctb] ,
Vincent Traag [cph, ctb] ,
Fabio Zanini [cph, ctb] ,
Daniel Noom [cph, ctb] ,
The igraph development team [cph] ,
F [...truncated...]
Maintainer: David Connell <david32@dcon.addy.io>
Diff between speakeasyR versions 0.1.6 dated 2025-08-28 and 0.1.7 dated 2025-09-05
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ configure | 18 +++++++++--------- configure.ac | 2 +- inst/doc/speakeasyR.html | 10 +++++----- src/se2/src/speakeasy2/se2_core.c | 5 +++-- 7 files changed, 33 insertions(+), 26 deletions(-)
Title: Nearest Neighbor Descent Method for Approximate Nearest
Neighbors
Description: The Nearest Neighbor Descent method for finding approximate
nearest neighbors by Dong and co-workers (2010)
<doi:10.1145/1963405.1963487>. Based on the 'Python' package
'PyNNDescent' <https://github.com/lmcinnes/pynndescent>.
Author: James Melville [aut, cre, cph],
Vitalie Spinu [ctb],
Ralf Stubner [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between rnndescent versions 0.1.6 dated 2024-05-14 and 0.1.8 dated 2025-09-05
DESCRIPTION | 8 +++--- MD5 | 30 ++++++++++++------------ NEWS.md | 5 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/brute-force.html | 2 - inst/doc/hubness.html | 40 ++++++++++++++++---------------- inst/doc/metrics.html | 2 - inst/doc/nearest-neighbor-descent.html | 2 - inst/doc/querying-data.html | 4 +-- inst/doc/random-partition-forests.html | 2 - inst/doc/rnndescent.html | 2 - tests/testthat/test_brute_force.R | 4 +-- tests/testthat/test_descent_euclidean.R | 2 - tests/testthat/test_random_nbrs.R | 4 +-- tests/testthat/test_rptree.R | 8 +++--- 16 files changed, 60 insertions(+), 55 deletions(-)
Title: Quantile-Quantile Plot Extensions for 'ggplot2'
Description: Extensions of 'ggplot2' Q-Q plot functionalities.
Author: Alexandre Almeida [aut],
Adam Loy [aut, cre],
Heike Hofmann [aut]
Maintainer: Adam Loy <loyad01@gmail.com>
Diff between qqplotr versions 0.0.6 dated 2023-01-25 and 0.0.7 dated 2025-09-05
DESCRIPTION | 8 - MD5 | 69 +++++----- NEWS.md | 4 R/data.R | 2 R/geom_qq_band.R | 4 R/qqplotr.R | 3 R/stat_pp_band.R | 8 - R/stat_pp_line.R | 6 R/stat_pp_point.R | 5 R/stat_qq_band.R | 8 - R/stat_qq_line.R | 4 R/stat_qq_point.R | 4 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 28 +--- inst/doc/introduction.R | 10 - inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 196 +++++++++++++++--------------- man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/longjump.Rd | 2 man/qqplotr.Rd | 19 ++ man/stat_pp_band.Rd | 82 +++++++++--- man/stat_pp_line.Rd | 78 +++++++++-- man/stat_pp_point.Rd | 78 +++++++++-- man/stat_qq_band.Rd | 82 +++++++++--- man/stat_qq_line.Rd | 78 +++++++++-- man/stat_qq_point.Rd | 78 +++++++++-- vignettes/introduction.Rmd | 2 36 files changed, 572 insertions(+), 288 deletions(-)
Title: Connect to ODBC Compatible Databases (using the DBI Interface)
Description: A DBI-compatible interface to ODBC databases.
Author: Jim Hester [aut],
Hadley Wickham [aut, cre],
Oliver Gjoneski [aut],
Simon Couch [aut],
lexicalunit [cph] ,
Google Inc. [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between odbc versions 1.6.2 dated 2025-08-28 and 1.6.3 dated 2025-09-05
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/nanodbc/nanodbc.cpp | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Neighborhood Deprivation Indices
Description: Computes various geospatial indices of socioeconomic deprivation and disparity
in the United States. Some indices are considered "spatial" because they
consider the values of neighboring (i.e., adjacent) census geographies in
their computation, while other indices are "aspatial" because they only
consider the value within each census geography. Two types of aspatial
neighborhood deprivation indices (NDI) are available: including:
(1) based on Messer et al. (2006) <doi:10.1007/s11524-006-9094-x>
and (2) based on Andrews et al. (2020) <doi:10.1080/17445647.2020.1750066>
and Slotman et al. (2022) <doi:10.1016/j.dib.2022.108002>
who use variables chosen by Roux and Mair (2010)
<doi:10.1111/j.1749-6632.2009.05333.x>. Both are a decomposition of multiple
demographic characteristics from the U.S. Census Bureau American Community
Survey 5-year estimates (ACS-5; 2006-2010 onward). Using data from the ACS-5
(2005-2009 onward), the package can also compute indices of racia [...truncated...]
Author: Ian D. Buller [aut, cre, cph] ,
NCI [cph, fnd]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>
Diff between ndi versions 0.1.5 dated 2024-01-23 and 0.2.1 dated 2025-09-05
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Title: Multivariate (Dynamic) Generalized Additive Models
Description: Fit Bayesian Dynamic Generalized Additive Models to multivariate observations. Users can build nonlinear State-Space models that can incorporate semiparametric effects in observation and process components, using a wide range of observation families. Estimation is performed using Markov Chain Monte Carlo with Hamiltonian Monte Carlo in the software 'Stan'. References: Clark & Wells (2023) <doi:10.1111/2041-210X.13974>.
Author: Nicholas J Clark [aut, cre] ,
KANK Karunarathna [ctb] ,
Sarah Heaps [ctb] ,
Scott Pease [ctb] ,
Matthijs Hollanders [ctb]
Maintainer: Nicholas J Clark <nicholas.j.clark1214@gmail.com>
Diff between mvgam versions 1.1.51 dated 2025-03-14 and 1.1.593 dated 2025-09-05
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Title: Power Analysis and Sample Size Calculation
Description: Power analysis and sample size calculation for Welch and Hsu (Hedderich and Sachs (2018), ISBN:978-3-662-56657-2) t-tests including Monte-Carlo simulations of empirical power and type-I-error. Power and sample size calculation for Wilcoxon rank sum and signed rank tests via Monte-Carlo simulations. Power and sample size required for the evaluation of a diagnostic test(-system) (Flahault et al. (2005), <doi:10.1016/j.jclinepi.2004.12.009>; Dobbin and Simon (2007), <doi:10.1093/biostatistics/kxj036>) as well as for a single proportion (Fleiss et al. (2003), ISBN:978-0-471-52629-2; Piegorsch (2004), <doi:10.1016/j.csda.2003.10.002>; Thulin (2014), <doi:10.1214/14-ejs909>), comparing two negative binomial rates (Zhu and Lakkis (2014), <doi:10.1002/sim.5947>), ANCOVA (Shieh (2020), <doi:10.1007/s11336-019-09692-3>), reference ranges (Jennen-Steinmetz and Wellek (2005), <doi:10.1002/sim.2177>), multiple primary endpoints (Sozu et al. (2015), ISBN:978 [...truncated...]
Author: Matthias Kohl [aut, cre]
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKpower versions 1.0 dated 2024-09-23 and 1.1 dated 2025-09-05
DESCRIPTION | 15 ++- MD5 | 24 +++--- NAMESPACE | 3 NEWS | 8 ++ R/histSimPower.R | 24 +++--- R/powerDiagnosticTest.R | 4 - R/qqunifSimPower.R | 18 ++-- R/ssizeAUCCI.R | 2 R/volcanoSimPower.R | 40 +++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/MKpower.html | 183 +++++++++++++++++++++++------------------------- man/ssize.auc.ci.Rd | 13 +-- 13 files changed, 168 insertions(+), 166 deletions(-)
Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing with
meteorological data in the tidy data framework. Extends 'ggplot2' for
better plotting of scalar and vector fields and provides commonly used
analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut]
Maintainer: Elio Campitelli <eliocampitelli@gmail.com>
Diff between metR versions 0.18.1 dated 2025-05-13 and 0.18.2 dated 2025-09-05
DESCRIPTION | 38 +- MD5 | 75 ++-- NAMESPACE | 2 NEWS.md | 24 + R/Derivate.R | 2 R/FitLm.R | 4 R/GetTopography.R | 4 R/MaskLand.R | 2 R/ReadNetCDF.R | 104 +++++- R/Smooth2D.R | 2 R/WriteNetCDF.R | 8 R/arrowGrob.R | 12 R/geom_contour_tanaka.R | 1 R/geom_text_contour.R | 3 R/guide_colorstrip.R | 10 R/helpfunctions.R | 23 - R/scale-unbinned.R | 18 - R/scale_vector.R | 1 R/standard_atmosphere.R | 2 R/stat_contour2.r | 479 +++++++++++++++-------------- R/stat_contour_fill.R | 11 R/textContourGrob.R | 2 README.md | 8 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/Visualization-tools.html | 298 +++++++++--------- inst/doc/Working-with-data.html | 239 ++++++++------ man/ReadNetCDF.Rd | 28 + man/figures/field-1.png |binary man/figures/timeseries-1.png |binary man/metR.Rd | 1 man/standard_atmosphere.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/era5 |only tests/testthat/test-ReadNetCDF.R | 25 + tests/testthat/test-fitlm.R | 4 tests/testthat/test-vis-guide_colorstrip.R | 17 - 38 files changed, 835 insertions(+), 616 deletions(-)
Title: Individual-Level, Summary-Level and Single-Step Bayesian
Regression Model
Description: A user-friendly tool to fit Bayesian regression models. It can fit 3 types of Bayesian models using individual-level, summary-level, and individual plus pedigree-level (single-step) data for both Genomic prediction/selection (GS) and Genome-Wide Association Study (GWAS), it was designed to estimate joint effects and genetic parameters for a complex trait, including:
(1) fixed effects and coefficients of covariates,
(2) environmental random effects, and its corresponding variance,
(3) genetic variance,
(4) residual variance,
(5) heritability,
(6) genomic estimated breeding values (GEBV) for both genotyped and non-genotyped individuals,
(7) SNP effect size,
(8) phenotype/genetic variance explained (PVE) for single or multiple SNPs,
(9) posterior probability of association of the genomic window (WPPA),
(10) posterior inclusive probability (PIP).
The functions are not limited, we will keep on going in enriching it with more features.
References: Lilin Yin et al. (2025) <doi:10.18637/jss [...truncated...]
Author: Lilin Yin [aut, cre, cph] ,
Haohao Zhang [aut, cph] ,
Xiaolei Liu [aut, cph]
Maintainer: Lilin Yin <ylilin@163.com>
Diff between hibayes versions 3.0.3 dated 2024-02-20 and 3.1.0 dated 2025-09-05
DESCRIPTION | 27 ++++++++++++++++----------- MD5 | 13 +++++++------ inst/CITATION |only src/Makevars | 2 +- src/Makevars.win | 2 +- src/omp_set.h | 2 -- src/rm.cpp | 4 ++-- src/solver.cpp | 28 ++++++++++++++-------------- 8 files changed, 41 insertions(+), 37 deletions(-)
Title: Plotting Decision Curve Analysis with Coloured Bars
Description: Decision curve analysis is a method for evaluating and comparing prediction models that incorporates clinical consequences, requires only the data set on which the models are tested, and can be applied to models that have either continuous or dichotomous results. The 'ggscidca' package adds coloured bars of discriminant relevance to the traditional decision curve. Improved practicality and aesthetics. This method was described by Balachandran VP (2015) <doi:10.1016/S1470-2045(14)71116-7>.
Author: Qiang Liu [aut, cre]
Maintainer: Qiang Liu <dege857@163.com>
Diff between ggscidca versions 0.2.3 dated 2024-05-19 and 0.2.5 dated 2025-09-05
DESCRIPTION | 10 - MD5 | 54 +++++---- NAMESPACE | 10 + R/cox.tcdca.R | 47 +++++++- R/getplot.R | 27 ++-- R/modeldata.R | 9 + R/netdata.R | 251 ++++++++++++++++++++++++++++++++++++++++++++- R/randomForest.R | 9 + R/scidca.R | 23 ---- R/scidca.coxph.R | 11 + R/scidca.glm.R | 11 + R/scidca.scixgboot.R |only R/scidca.svm.R | 7 - R/scidcacrr.R | 11 + R/scidcaksvm.R | 7 - R/tcdca.R | 27 +++- man/cox.tcdca.Rd | 42 +++++++ man/netdata.coxph.Rd |only man/netdata.crr.Rd |only man/netdata.glm.Rd |only man/netdata.randomFores.Rd |only man/netdata.scixgboot.Rd |only man/netdata.svm.Rd |only man/scidca.Rd | 24 ---- man/scidca.coxph.Rd | 5 man/scidca.crr.Rd | 5 man/scidca.glm.Rd | 5 man/scidca.ksvm.Rd | 5 man/scidca.randomForest.Rd | 5 man/scidca.scixgboot.Rd |only man/scidca.svm.Rd | 5 man/tcdca.Rd | 41 ++++++- 32 files changed, 533 insertions(+), 118 deletions(-)
Title: More Miscellaneous Steps for the 'recipes' Package
Description: Contains additional miscellaneous steps for the 'recipes' package.
These steps are useful, but doesn't have a good home in other 'recipes'
packages or its extensions.
Author: Emil Hvitfeldt [aut, cre]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between extrasteps versions 0.1.0 dated 2024-10-03 and 0.3.0 dated 2025-09-05
extrasteps-0.1.0/extrasteps/tests/testthat/_snaps/combine_stringdist.md |only extrasteps-0.1.0/extrasteps/tests/testthat/_snaps/yeet.md |only extrasteps-0.3.0/extrasteps/DESCRIPTION | 9 extrasteps-0.3.0/extrasteps/MD5 | 92 ++++------ extrasteps-0.3.0/extrasteps/NAMESPACE | 2 extrasteps-0.3.0/extrasteps/NEWS.md | 6 extrasteps-0.3.0/extrasteps/R/0_imports.R | 2 extrasteps-0.3.0/extrasteps/R/aaa.R | 6 extrasteps-0.3.0/extrasteps/R/date_after.R | 82 +++++--- extrasteps-0.3.0/extrasteps/R/date_before.R | 80 +++++--- extrasteps-0.3.0/extrasteps/R/date_nearest.R | 88 ++++++--- extrasteps-0.3.0/extrasteps/R/difftime.R | 44 ++-- extrasteps-0.3.0/extrasteps/R/encoding_binary.R | 30 +-- extrasteps-0.3.0/extrasteps/R/encoding_frequency.R | 22 +- extrasteps-0.3.0/extrasteps/R/maxabs.R | 22 +- extrasteps-0.3.0/extrasteps/R/minmax.R | 22 +- extrasteps-0.3.0/extrasteps/R/robust.R | 24 +- extrasteps-0.3.0/extrasteps/R/time_event.R | 47 ++--- extrasteps-0.3.0/extrasteps/R/unit_normalize.R | 24 +- extrasteps-0.3.0/extrasteps/README.md | 4 extrasteps-0.3.0/extrasteps/man/step_date_after.Rd | 30 +-- extrasteps-0.3.0/extrasteps/man/step_date_before.Rd | 30 +-- extrasteps-0.3.0/extrasteps/man/step_date_nearest.Rd | 30 +-- extrasteps-0.3.0/extrasteps/man/step_difftime.Rd | 19 -- extrasteps-0.3.0/extrasteps/man/step_encoding_binary.Rd | 22 +- extrasteps-0.3.0/extrasteps/man/step_encoding_frequency.Rd | 22 +- extrasteps-0.3.0/extrasteps/man/step_maxabs.Rd | 22 +- extrasteps-0.3.0/extrasteps/man/step_minmax.Rd | 22 +- extrasteps-0.3.0/extrasteps/man/step_robust.Rd | 22 +- extrasteps-0.3.0/extrasteps/man/step_time_event.Rd | 34 +-- extrasteps-0.3.0/extrasteps/man/step_unit_normalize.Rd | 22 +- extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/date_after.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/date_before.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/date_nearest.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/difftime.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/maxabs.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/minmax.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/robust.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/time_event.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/_snaps/unit_normalize.md | 12 - extrasteps-0.3.0/extrasteps/tests/testthat/test-date_after.R | 38 ++-- extrasteps-0.3.0/extrasteps/tests/testthat/test-date_before.R | 38 ++-- extrasteps-0.3.0/extrasteps/tests/testthat/test-date_nearest.R | 38 ++-- extrasteps-0.3.0/extrasteps/tests/testthat/test-maxabs.R | 4 extrasteps-0.3.0/extrasteps/tests/testthat/test-minmax.R | 4 extrasteps-0.3.0/extrasteps/tests/testthat/test-robust.R | 53 ++++- extrasteps-0.3.0/extrasteps/tests/testthat/test-time_event.R | 25 +- extrasteps-0.3.0/extrasteps/tests/testthat/test-unit_normalize.R | 36 ++- 48 files changed, 676 insertions(+), 549 deletions(-)
Title: Bayesian Structural Time Series
Description: Time series regression using dynamic linear models fit using
MCMC. See Scott and Varian (2014) <DOI:10.1504/IJMMNO.2014.059942>, among many
other sources.
Author: Steven L. Scott [aut, cre]
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>
Diff between bsts versions 0.9.10 dated 2024-01-17 and 0.9.11 dated 2025-09-05
DESCRIPTION | 23 ++++--- MD5 | 58 ++++++++++---------- inst/tests/tests/testthat/test-dirm.R | 4 - inst/tests/tests/testthat/test-dynamic-regression.R | 14 +++- inst/tests/tests/testthat/test-goog.R | 4 - inst/tests/tests/testthat/test-multivariate.R | 2 inst/tests/tests/testthat/test-plot-components.R | 3 - inst/tests/tests/testthat/test-poisson.R | 14 ++-- inst/tests/tests/testthat/test-prediction.R | 6 +- inst/tests/tests/testthat/test-regressionholiday.R | 6 +- inst/tests/tests/testthat/test-student.R | 10 +-- inst/tests/tests/testthat/test-trig.R | 2 inst/tests/testthat/test-dirm.R | 4 - inst/tests/testthat/test-dynamic-regression.R | 14 +++- inst/tests/testthat/test-goog.R | 4 - inst/tests/testthat/test-multivariate.R | 2 inst/tests/testthat/test-plot-components.R | 3 - inst/tests/testthat/test-poisson.R | 14 ++-- inst/tests/testthat/test-prediction.R | 6 +- inst/tests/testthat/test-regressionholiday.R | 6 +- inst/tests/testthat/test-student.R | 10 +-- inst/tests/testthat/test-trig.R | 2 man/add.dynamic.regression.Rd | 21 +++---- man/add.monthly.annual.cycle.Rd | 2 man/bsts.Rd | 4 - man/descriptive-plots.Rd | 12 ++-- man/mbsts.Rd | 9 +-- man/plot.bsts.mixed.Rd | 3 - man/to.posixt.Rd | 6 +- man/wide.to.long.Rd | 7 +- 30 files changed, 142 insertions(+), 133 deletions(-)
Title: A Minimalist Web Framework for R
Description: A minimalist web framework for developing application programming
interfaces in R that provides a flexible framework for handling common
HTTP-requests, errors, logging, and an ability to integrate any R code as
server middle-ware.
Author: Hans Martin [aut],
Jonathan Callahan [aut, cre]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between beakr versions 0.4.3 dated 2021-04-06 and 0.4.4 dated 2025-09-05
DESCRIPTION | 8 - MD5 | 36 ++++---- NEWS.md | 6 + R/Beakr.R | 102 +++++++++--------------- R/Error.R | 45 ++++------ R/Listener.R | 50 +++++------- R/Middleware.R | 68 ++++++---------- R/Request.R | 125 +++++++++++------------------- R/Response.R | 134 +++++++++++++++----------------- R/Router.R | 146 ++++++++++++++--------------------- README.md | 31 ++++--- man/Beakr.Rd | 105 +++++++++++-------------- man/Error.Rd | 63 ++++++++------- man/Listener.Rd | 65 ++++++++------- man/Middleware.Rd | 73 +++++++++-------- man/Request.Rd | 162 +++++++++++++++++++++------------------ man/Response.Rd | 210 ++++++++++++++++++++++++++++++--------------------- man/Router.Rd | 120 ++++++++++++++++------------- man/beakr-package.Rd | 21 ++++- 19 files changed, 778 insertions(+), 792 deletions(-)
Title: Tools for Antitrust Practitioners
Description: A collection of tools for antitrust practitioners, including the ability to calibrate different consumer demand systems and simulate the effects of mergers under different competitive regimes.
Author: Charles Taragin [aut, cre],
Michael Sandfort [aut],
Shlok Goyal [ctb]
Maintainer: Charles Taragin <ctaragin+antitrustr@gmail.com>
Diff between antitrust versions 0.99.26 dated 2022-08-24 and 0.99.29 dated 2025-09-05
DESCRIPTION | 13 MD5 | 112 NAMESPACE | 202 R/AIDSFunctions.R | 918 ++-- R/AggregateGamesMethods.R |only R/AntitrustClasses.R | 230 - R/Auction2ndLogitFunctions.R | 706 +-- R/AuctionClasses.R | 662 +-- R/BargainingLogitFunctions.R | 463 +- R/BertrandClasses.R | 720 +-- R/BertrandRUMClasses.R | 1096 ++--- R/CESFunctions.R | 786 +-- R/CMCRBertrandFunctions.R | 618 +- R/CMCRMethods.R | 514 +- R/CVMethods.R | 787 +-- R/CostMethods.R | 805 +-- R/CournotFunctions.R | 821 +-- R/HypoMonMethods.R | 1274 +++-- R/LogitFunctions.R | 1458 +++--- R/MarginsMethods.R | 1272 +++-- R/OutputMethods.R | 1872 ++++---- R/OwnershipMethods.R | 410 - R/PSMethods.R | 630 +- R/ParamsMethods.R | 5872 ++++++++++++++------------- R/PlotMethods.R | 254 - R/PriceDeltaMethods.R | 642 +- R/PricesMethods.R | 1680 ++++--- R/SimFunctions.R | 1062 ++-- R/SummaryMethods.R | 1299 +++--- R/UPPMethods.R | 242 - R/VerticalClasses.R | 200 R/VerticalFunctions.R | 727 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Reference.R | 8 inst/doc/Reference.Rmd | 4639 ++++++++++----------- inst/doc/Reference.html | 8428 +++++++++++++++++++-------------------- man/Antitrust-Class.Rd | 3 man/Auction2ndLogit-Functions.Rd | 4 man/Bargaining-Classes.Rd | 76 man/BargainingLogit-Functions.Rd | 4 man/BertrandRUM-Classes.Rd | 3 man/CES-Functions.Rd | 4 man/CMCRBertrand-Functions.Rd | 7 man/Cournot-Functions.Rd | 5 man/Logit-Functions.Rd | 36 man/Margins-Methods.Rd | 8 man/MarginsAG-Methods.Rd |only man/Output-Methods.Rd | 2 man/PS-methods.Rd | 2 man/Params-Methods.Rd | 3 man/PriceDelta-Methods.Rd | 36 man/Sim-Functions.Rd | 53 man/SupplyChain-Functions.Rd | 28 man/Vertical-Classes.Rd | 3 man/defineMarketTools-methods.Rd | 34 man/summary-methods.Rd | 13 vignettes/Reference.Rmd | 4639 ++++++++++----------- 58 files changed, 23671 insertions(+), 22714 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-12-10 0.1.0
Title: Collinearity Detection using Redefined Variance Inflation Factor
and Graphical Methods
Description: The detection of troubling approximate collinearity in a multiple linear regression model is a classical problem in Econometrics. The objective of this package is to detect it using the variance inflation factor redefined and the scatterplot between the variance inflation factor and the coefficient of variation. For more details see Salmerón R., García C.B. and García J. (2018) <doi:10.1080/00949655.2018.1463376>, Salmerón, R., Rodríguez, A. and García C. (2020) <doi:10.1007/s00180-019-00922-x>, Salmerón, R., García, C.B, Rodríguez, A. and García, C. (2022) <doi:10.32614/RJ-2023-010>, Salmerón, R., García, C.B. and García, J. (2025) <doi:10.1007/s10614-024-10575-8> and Salmerón, R., García, C.B, García J. (2023, working paper) <doi:10.48550/arXiv.2005.02245>. You can also view the package vignette using 'browseVignettes("rvif")', the package website using 'browseURL(system.file("docs/index.html", package = "rvif"))' or version control on GitHub (<https: [...truncated...]
Author: R. Salmeron [aut, cre],
C.B. Garcia [aut]
Maintainer: R. Salmeron <romansg@ugr.es>
This is a re-admission after prior archival of version 3.0 dated 2025-07-29
Diff between rvif versions 3.0 dated 2025-07-29 and 3.1 dated 2025-09-05
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- inst/docs/index.html | 6 +++--- inst/docs/pkgdown.yml | 2 +- tests/testthat/test-cv_vif.R | 23 ++++++----------------- tests/testthat/test-cv_vif_plot.R | 6 ++---- tests/testthat/test-multicollinearity.R | 13 ------------- tests/testthat/test-rvifs.R | 20 ++++++++------------ 8 files changed, 31 insertions(+), 61 deletions(-)
Title: Visualization of Patient Profiles
Description: Creation of patient profile visualizations for
exploration, diagnostic or monitoring purposes during a clinical trial.
These static visualizations display a patient-specific overview
of the evolution during the trial time frame of
parameters of interest (as laboratory, ECG, vital signs),
presence of adverse events, exposure to a treatment;
associated with metadata patient information,
as demography, concomitant medication.
The visualizations can be tailored for specific domain(s) or endpoint(s) of interest.
Visualizations are exported into patient profile report(s)
or can be embedded in custom report(s).
Author: Laure Cougnaud [aut, cre],
Margaux Faes [rev] ,
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between patientProfilesVis versions 2.0.9 dated 2024-06-18 and 2.0.10 dated 2025-09-05
DESCRIPTION | 10 MD5 | 18 R/report_combineVerticallyGGplot.R | 2 R/subjectProfileTextPlot.R | 4 build/vignette.rds |binary inst/NEWS | 2 inst/doc/patientProfiles-template-SDTM.R | 94 +- inst/doc/patientProfiles-template-SDTM.html | 261 ++++--- inst/doc/patientProfilesVis-introduction.R | 504 +++++++------- inst/doc/patientProfilesVis-introduction.html | 921 ++++++++++++++++---------- 10 files changed, 1063 insertions(+), 753 deletions(-)
More information about patientProfilesVis at CRAN
Permanent link
Title: Mosquito Gene Drive Explorer
Description: Provides a model designed to be a reliable testbed where various gene
drive interventions for mosquito-borne diseases control. It is being developed to
accommodate the use of various mosquito-specific gene drive systems within a
population dynamics framework that allows migration of individuals between patches
in landscape. Previous work developing the population dynamics can be found in Deredec et al.
(2001) <doi:10.1073/pnas.1110717108> and Hancock & Godfray (2007) <doi:10.1186/1475-2875-6-98>,
and extensions to accommodate CRISPR homing dynamics in Marshall et al. (2017)
<doi:10.1038/s41598-017-02744-7>.
Author: Hector Manuel Sanchez Castellanos [aut, cre],
Jared Bennett [aut],
Sean Wu [aut],
John M. Marshall [aut]
Maintainer: Hector Manuel Sanchez Castellanos <sanchez.hmsc@berkeley.edu>
This is a re-admission after prior archival of version 1.6.0 dated 2020-10-05
Diff between MGDrivE versions 1.6.0 dated 2020-10-05 and 1.6.2 dated 2025-09-05
MGDrivE-1.6.0/MGDrivE/R/Cube-SplitDrive.R |only MGDrivE-1.6.2/MGDrivE/DESCRIPTION | 14 MGDrivE-1.6.2/MGDrivE/MD5 | 265 MGDrivE-1.6.2/MGDrivE/NAMESPACE | 16 MGDrivE-1.6.2/MGDrivE/NEWS.md | 35 MGDrivE-1.6.2/MGDrivE/R/Cube-ASmidler.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-AlleleSail.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-Auxiliary.R | 26 MGDrivE-1.6.2/MGDrivE/R/Cube-CLEAVRMF.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-CLEAVRX.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-CRISPR2MF_SM.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-CRISPR2X.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-ClvR.R | 2 MGDrivE-1.6.2/MGDrivE/R/Cube-ClvR2.R | 18 MGDrivE-1.6.2/MGDrivE/R/Cube-ConfinableHoming.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-ConfinableHomingX.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-ECHACR.R | 2 MGDrivE-1.6.2/MGDrivE/R/Cube-ECHACRX.R | 2 MGDrivE-1.6.2/MGDrivE/R/Cube-ImmunizingReversalMF.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-ImmunizingReversalX.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-JOHNConfineableHomingWithRandB.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-ShredderMF.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-ShredderY.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-SplitDriveMF.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-SplitDriveX.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-SplitDriveY.R |only MGDrivE-1.6.2/MGDrivE/R/Cube-tGD.R | 11 MGDrivE-1.6.2/MGDrivE/R/MGDrivE-Auxiliary.R | 36 MGDrivE-1.6.2/MGDrivE/R/MGDrivE-Graphics.R | 2 MGDrivE-1.6.2/MGDrivE/R/MGDrivE-Releases.R | 3 MGDrivE-1.6.2/MGDrivE/R/MGDrivE.R | 4 MGDrivE-1.6.2/MGDrivE/R/Network-Class.R | 42 MGDrivE-1.6.2/MGDrivE/R/Network-Migration.R | 4 MGDrivE-1.6.2/MGDrivE/R/Network-Parameters.R | 12 MGDrivE-1.6.2/MGDrivE/R/Network-Simulation.R | 2 MGDrivE-1.6.2/MGDrivE/R/Patch-Class.R | 8 MGDrivE-1.6.2/MGDrivE/R/Patch-Methods.R | 14 MGDrivE-1.6.2/MGDrivE/R/Patch-Migration.R | 2 MGDrivE-1.6.2/MGDrivE/R/Patch-Simulation.R | 122 MGDrivE-1.6.2/MGDrivE/R/RcppExports.R | 11 MGDrivE-1.6.2/MGDrivE/README.md | 2 MGDrivE-1.6.2/MGDrivE/build/partial.rdb |binary MGDrivE-1.6.2/MGDrivE/build/vignette.rds |binary MGDrivE-1.6.2/MGDrivE/inst/CITATION | 4 MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_examples.R | 86 MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_examples.Rmd | 71 MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_examples.html | 3555 +++++----- MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_math.R | 6 MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_math.Rmd | 56 MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_math.html | 784 +- MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_run.R | 296 MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_run.Rmd | 12 MGDrivE-1.6.2/MGDrivE/inst/doc/mgdrive_run.html | 1554 ++-- MGDrivE-1.6.2/MGDrivE/man/MGDrivE-Cube.Rd | 21 MGDrivE-1.6.2/MGDrivE/man/MGDrivE-Model.Rd | 3 MGDrivE-1.6.2/MGDrivE/man/Network.Rd | 2 MGDrivE-1.6.2/MGDrivE/man/Patch.Rd | 2 MGDrivE-1.6.2/MGDrivE/man/basicRepeatedReleases.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcAquaticStageSurvivalProbability.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcAverageGenerationTime.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcDensityDependentDeathRate.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcHurdleExpKernel.Rd | 4 MGDrivE-1.6.2/MGDrivE/man/calcLarvalDist.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcLarvalPopEquilibrium.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcLarvalStageMortalityRate.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcPopulationGrowthRate.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/calcQuantiles.Rd | 2 MGDrivE-1.6.2/MGDrivE/man/cubeASmidler.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeAlleleSail.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeCLEAVRMF.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeCLEAVRX.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeClvR.Rd | 2 MGDrivE-1.6.2/MGDrivE/man/cubeClvR2.Rd | 2 MGDrivE-1.6.2/MGDrivE/man/cubeConfinableHoming.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeConfinableHomingJOHN.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeConfinableHomingX.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeECHACR.Rd | 2 MGDrivE-1.6.2/MGDrivE/man/cubeECHACRX.Rd | 2 MGDrivE-1.6.2/MGDrivE/man/cubeHomingDriveSM.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeImmunizingReversalMF.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeImmunizingReversalX.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeModifiers.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/cubeSplitDrive.Rd | 4 MGDrivE-1.6.2/MGDrivE/man/cubeSplitDriveX.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeSplitDriveY.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeXHomingDeposition.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeXShredderMF.Rd |only MGDrivE-1.6.2/MGDrivE/man/cubeXShredderY.Rd |only MGDrivE-1.6.2/MGDrivE/man/get_alpha_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_beta_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_conF_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_conM_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_drivecubeindex_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_eta_Network.Rd | 9 MGDrivE-1.6.2/MGDrivE/man/get_femalePop_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_genotypesID_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_genotypesN_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_malePop_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_muAd_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_muAq_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_nPatch_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_omega_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_patchReleases_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_phi_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_s_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_tNow_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_tau_Network.Rd | 7 MGDrivE-1.6.2/MGDrivE/man/get_timeAq_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_xiF_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/get_xiM_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/ggColUtility.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/normalise.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_Migration_Deterministic_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_Migration_Stochastic_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_Network.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_PopDynamics_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_adultDeath_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_adultDeath_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_eggDM_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_eggDM_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_eggReleases_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_initOutput_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_larvaDM_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_larvaDM_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_mating_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_mating_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_migrationIn_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_oviposit_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_oviposit_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_pupaDM_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_pupaDM_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_pupation_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_pupation_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_releases_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/oneDay_writeOutput_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/quantileC.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/rDirichlet.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/reset_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/set_NetworkPointer_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/set_initialPopulation_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/set_population_deterministic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/man/set_population_stochastic_Patch.Rd | 1 MGDrivE-1.6.2/MGDrivE/src/MGDrivE-Auxilary.cpp | 8 MGDrivE-1.6.2/MGDrivE/src/MGDrivE-DistanceFunctions.cpp | 1 MGDrivE-1.6.2/MGDrivE/src/MGDrivE-Kernels.cpp | 130 MGDrivE-1.6.2/MGDrivE/src/RcppExports.cpp | 14 MGDrivE-1.6.2/MGDrivE/vignettes/diagram.png |only MGDrivE-1.6.2/MGDrivE/vignettes/mgdrive_examples.Rmd | 71 MGDrivE-1.6.2/MGDrivE/vignettes/mgdrive_math.Rmd | 56 MGDrivE-1.6.2/MGDrivE/vignettes/mgdrive_run.Rmd | 12 150 files changed, 4139 insertions(+), 3355 deletions(-)
Title: Convenience Functions for Education Data
Description: Collection of convenience functions to make working with
administrative records easier and more consistent. Includes functions to
clean strings, and identify cut points. Also includes three example data
sets of administrative education records for learning how to process records
with errors.
Author: Jason P. Becker [ctb],
Jared E. Knowles [aut, cre]
Maintainer: Jared E. Knowles <jared@civilytics.com>
Diff between eeptools versions 1.2.5 dated 2023-06-01 and 1.2.7 dated 2025-09-05
DESCRIPTION | 8 - MD5 | 47 +++--- NEWS.md | 9 + R/eeptools-data.R |only R/eeptools-package.r | 121 ---------------- R/eeptools.R | 2 R/modsims.R | 4 R/moves_calc.R | 2 R/proficiency_tools.R | 6 R/theme_dpi.R | 16 +- build/vignette.rds |binary inst/doc/intro.html | 357 +++++++++++++++++++++++------------------------- man/crosstabplot.Rd | 2 man/eeptools.Rd | 19 +- man/gelmansim.Rd | 4 man/midsch.Rd | 2 man/moves_calc.Rd | 2 man/profpoly.Rd | 2 man/profpoly.data.Rd | 2 man/stuatt.Rd | 2 man/stulevel.Rd | 2 man/theme_dpi.Rd | 4 man/theme_dpi_map.Rd | 4 man/theme_dpi_map2.Rd | 4 man/theme_dpi_mapPNG.Rd | 4 25 files changed, 262 insertions(+), 363 deletions(-)
Title: Solve the Empirical Bayes Normal Means Problem
Description: Provides simple, fast, and stable functions to fit the normal
means model using empirical Bayes. For available models and details, see
function ebnm(). Our JSS article,
Willwerscheid, Carbonetto, and Stephens (2025) <doi:10.18637/jss.v114.i03>,
provides a detailed introduction to the package.
Author: Jason Willwerscheid [aut],
Matthew Stephens [aut],
Peter Carbonetto [aut, cre],
Andrew Goldstein [ctb],
Yusha Liu [ctb]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between ebnm versions 1.1-2 dated 2023-10-12 and 1.1-38 dated 2025-09-05
ebnm-1.1-2/ebnm/inst/doc/ebnm.R |only ebnm-1.1-2/ebnm/inst/doc/ebnm.Rmd |only ebnm-1.1-2/ebnm/inst/doc/ebnm.html |only ebnm-1.1-2/ebnm/vignettes/ebnm.Rmd |only ebnm-1.1-38/ebnm/DESCRIPTION | 17 - ebnm-1.1-38/ebnm/MD5 | 86 +++-- ebnm-1.1-38/ebnm/NAMESPACE | 3 ebnm-1.1-38/ebnm/R/check_fn.R |only ebnm-1.1-38/ebnm/R/ebnm.R | 159 +++++++--- ebnm-1.1-38/ebnm/R/ebnm_fns.R | 90 +++-- ebnm-1.1-38/ebnm/R/ebnm_methods.R | 45 +- ebnm-1.1-38/ebnm/R/generalized_binary.R | 34 +- ebnm-1.1-38/ebnm/R/grid_selection.R | 2 ebnm-1.1-38/ebnm/R/infer_prior_family.R | 1 ebnm-1.1-38/ebnm/R/point_exponential.R | 1 ebnm-1.1-38/ebnm/R/point_laplace.R | 3 ebnm-1.1-38/ebnm/R/point_normal.R | 1 ebnm-1.1-38/ebnm/R/rebayes.R | 13 ebnm-1.1-38/ebnm/R/workhorse_parametric.R | 7 ebnm-1.1-38/ebnm/build/partial.rdb |only ebnm-1.1-38/ebnm/build/vignette.rds |binary ebnm-1.1-38/ebnm/inst/CITATION | 35 +- ebnm-1.1-38/ebnm/inst/code |only ebnm-1.1-38/ebnm/inst/doc/baseball.R |only ebnm-1.1-38/ebnm/inst/doc/baseball.Rmd |only ebnm-1.1-38/ebnm/inst/doc/baseball.html |only ebnm-1.1-38/ebnm/inst/doc/extending_ebnm.R |only ebnm-1.1-38/ebnm/inst/doc/extending_ebnm.Rmd |only ebnm-1.1-38/ebnm/inst/doc/extending_ebnm.html |only ebnm-1.1-38/ebnm/inst/doc/shrink_intro.R |only ebnm-1.1-38/ebnm/inst/doc/shrink_intro.Rmd |only ebnm-1.1-38/ebnm/inst/doc/shrink_intro.html |only ebnm-1.1-38/ebnm/man/confint.ebnm.Rd | 13 ebnm-1.1-38/ebnm/man/ebnm.Rd | 76 +++- ebnm-1.1-38/ebnm/man/ebnm_check_fn.Rd |only ebnm-1.1-38/ebnm/man/ebnm_generalized_binary.Rd | 12 ebnm-1.1-38/ebnm/man/ebnm_normal.Rd | 13 ebnm-1.1-38/ebnm/man/ebnm_normal_scale_mixture.Rd | 11 ebnm-1.1-38/ebnm/man/ebnm_npmle.Rd | 16 - ebnm-1.1-38/ebnm/man/ebnm_point_exponential.Rd | 33 +- ebnm-1.1-38/ebnm/man/ebnm_point_laplace.Rd | 13 ebnm-1.1-38/ebnm/man/ebnm_point_mass.Rd | 6 ebnm-1.1-38/ebnm/man/ebnm_point_normal.Rd | 13 ebnm-1.1-38/ebnm/man/ebnm_unimodal.Rd | 11 ebnm-1.1-38/ebnm/man/ebnm_unimodal_nonnegative.Rd | 11 ebnm-1.1-38/ebnm/man/ebnm_unimodal_nonpositive.Rd | 11 ebnm-1.1-38/ebnm/man/ebnm_unimodal_symmetric.Rd | 11 ebnm-1.1-38/ebnm/tests/testthat/test_optmethod.R | 108 ++++-- ebnm-1.1-38/ebnm/tests/testthat/test_point_mass.R | 4 ebnm-1.1-38/ebnm/tests/testthat/test_prior_family_inference.R | 3 ebnm-1.1-38/ebnm/vignettes/baseball.Rmd |only ebnm-1.1-38/ebnm/vignettes/ebnm.bib | 18 + ebnm-1.1-38/ebnm/vignettes/extending_ebnm.Rmd |only ebnm-1.1-38/ebnm/vignettes/shrink_intro.Rmd |only 54 files changed, 588 insertions(+), 292 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-18 1.1.0
2019-05-08 1.0.0
More information about connector.databricks at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-08-18 1.0.0
2023-10-15 0.1.8
2023-09-05 0.1.7
2023-07-04 0.1.6
2023-05-08 0.1.5
2022-03-30 0.1.4
2021-10-24 0.1.3
2021-10-17 0.1.3
2021-10-08 0.1.2
2020-11-24 0.1.1
2020-09-29 0.1.0
Title: An Implementation of Z-Curves
Description: An implementation of z-curves - a method for estimating expected discovery
and replicability rates on the bases of test-statistics of published studies. The package
provides functions for fitting the density, EM, and censored EM version (Bartoš & Schimmack, 2022,
<doi:10.15626/MP.2021.2720>; Schimmack & Bartoš, 2023, <doi: 10.1371/journal.pone.0290084>),
as well as the original density z-curve (Brunner & Schimmack, 2020, <doi:10.15626/MP.2018.874>).
Furthermore, the package provides summarizing and plotting functions for the fitted z-curve objects.
See the aforementioned articles for more information about the z-curves, expected discovery
and replicability rates, validation studies, and limitations.
Author: Frantisek Bartos [aut, cre],
Ulrich Schimmack [aut]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between zcurve versions 2.4.4 dated 2025-08-20 and 2.4.5 dated 2025-09-05
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/tools.R | 4 +++- build/partial.rdb |binary tests/testthat/test-zcurve.R | 6 +++--- 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Easily Install and Load the 'Tidymodels' Packages
Description: The tidy modeling "verse" is a collection of packages for
modeling and statistical analysis that share the underlying design
philosophy, grammar, and data structures of the tidyverse.
Author: Max Kuhn [aut, cre] ,
Hadley Wickham [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between tidymodels versions 1.3.0 dated 2025-02-21 and 1.4.0 dated 2025-09-05
DESCRIPTION | 30 +- LICENSE | 2 MD5 | 36 +- NAMESPACE | 2 NEWS.md | 8 R/attach.R | 28 +- R/conflicts.R | 44 +-- R/emails.R | 9 R/imports.R | 1 R/tags.R | 23 + R/tidymodels_prefer.R | 138 ++++++---- R/update.R | 54 +++ README.md | 18 - build/vignette.rds |binary inst/doc/Tags.R | 4 inst/doc/Tags.Rmd | 7 inst/rmarkdown/templates/model-analysis/skeleton/skeleton.Rmd | 22 - man/tidymodels-package.Rd | 2 vignettes/Tags.Rmd | 7 19 files changed, 288 insertions(+), 147 deletions(-)