Title: Methods for ''A Fast Alternative for the R x C Ecological
Inference Case''
Description: Estimates the probability matrix for the R×C Ecological Inference problem using the Expectation-Maximization Algorithm with four approximation methods for the E-Step, and an exact method as well. It also provides a bootstrap function to estimate the standard deviation of the estimated probabilities. In addition, it has functions that aggregate rows optimally to have more reliable estimates in cases of having few data points. For comparing the probability estimates of two groups, a Wald test routine is implemented. The library has data from the first round of the Chilean Presidential Election 2021 and can also generate synthetic election data. Methods described in Thraves, Charles; Ubilla, Pablo; Hermosilla, Daniel (2024) ''A Fast Ecological Inference Algorithm for the R×C case'' <doi:10.2139/ssrn.4832834>.
Author: Charles Thraves [aut],
Pablo Ubilla [aut],
Daniel Hermosilla [aut, cre],
Hanson Troy [ctb, cph]
Maintainer: Daniel Hermosilla <daniel.hermosilla.r@ug.uchile.cl>
Diff between fastei versions 0.0.0.7 dated 2025-05-20 and 0.0.0.9 dated 2025-07-18
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 2 +- R/data-utils.R | 11 +++++++++-- R/data.R | 2 ++ R/eim-class.R | 18 +++++++++++++++--- R/fastei-package.R | 2 +- README.md | 3 +-- build/vignette.rds |binary data/chile_election_2021.rda |binary inst/doc/demonstration.html | 4 ++-- man/chile_election_2021.Rd | 2 ++ man/get_eim_chile.Rd | 5 ++++- src/main.c | 3 +++ src/multinomial.c | 16 ++++++++-------- src/multinomial.h | 1 + src/wrapper.cpp | 25 ++++++++++++++++++------- 17 files changed, 86 insertions(+), 46 deletions(-)
Title: An R Package for Extended Behavior Genetics Analysis
Description: Provides functions for behavior genetics analysis,
including variance component model identification [Hunter et al. (2021) <doi:10.1007/s10519-021-10055-x>],
calculation of relatedness coefficients using path-tracing methods
[Wright (1922) <doi:10.1086/279872>; McArdle & McDonald (1984) <doi:10.1111/j.2044-8317.1984.tb00802.x>],
inference of relatedness, pedigree conversion, and simulation of multi-generational family data
[Lyu et al. (2024) <doi:10.1101/2024.12.19.629449>]. For a full overview,
see [Garrison et al. (2024) <doi:10.21105/joss.06203>].
Author: S. Mason Garrison [aut, cre] ,
Michael D. Hunter [aut] ,
Xuanyu Lyu [aut] ,
Rachel N. Good [ctb],
Jonathan D. Trattner [aut] ,
S. Alexandra Burt [aut]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>
Diff between BGmisc versions 1.4.3.1 dated 2025-06-10 and 1.5.0 dated 2025-07-18
BGmisc-1.4.3.1/BGmisc/data/ASOIAF.rda |only BGmisc-1.4.3.1/BGmisc/man/ASOIAF.Rd |only BGmisc-1.4.3.1/BGmisc/tests/testthat/Rplots.pdf |only BGmisc-1.4.3.1/BGmisc/tests/testthat/test-plotPedigree.X |only BGmisc-1.5.0/BGmisc/DESCRIPTION | 12 BGmisc-1.5.0/BGmisc/MD5 | 158 +++--- BGmisc-1.5.0/BGmisc/NAMESPACE | 2 BGmisc-1.5.0/BGmisc/NEWS.md | 24 BGmisc-1.5.0/BGmisc/R/buildComponent.R | 208 ++++---- BGmisc-1.5.0/BGmisc/R/checkIDs.R | 18 BGmisc-1.5.0/BGmisc/R/checkParents.R | 72 +- BGmisc-1.5.0/BGmisc/R/checkPedigreeNetwork.R | 8 BGmisc-1.5.0/BGmisc/R/checkSex.R | 14 BGmisc-1.5.0/BGmisc/R/cleanPedigree.R | 12 BGmisc-1.5.0/BGmisc/R/constructAdjacency.R | 38 + BGmisc-1.5.0/BGmisc/R/documentData.R | 252 ++++------ BGmisc-1.5.0/BGmisc/R/estimateCIs.R | 41 + BGmisc-1.5.0/BGmisc/R/helpGeneric.R | 2 BGmisc-1.5.0/BGmisc/R/identifyModel.R | 6 BGmisc-1.5.0/BGmisc/R/insertEven.R | 4 BGmisc-1.5.0/BGmisc/R/makeLinks.R | 2 BGmisc-1.5.0/BGmisc/R/makeLinkslegacy.R | 8 BGmisc-1.5.0/BGmisc/R/readGedcom.R | 18 BGmisc-1.5.0/BGmisc/R/readGedcomlegacy.R | 18 BGmisc-1.5.0/BGmisc/R/readWikifamilytree.R | 4 BGmisc-1.5.0/BGmisc/R/simulatePedigree.R | 39 + BGmisc-1.5.0/BGmisc/R/sliceFamilies.R |only BGmisc-1.5.0/BGmisc/R/summarizePedigree.R | 186 ++++--- BGmisc-1.5.0/BGmisc/R/tweakPedigree.R | 85 ++- BGmisc-1.5.0/BGmisc/build/partial.rdb |binary BGmisc-1.5.0/BGmisc/build/vignette.rds |binary BGmisc-1.5.0/BGmisc/data/hazard.rda |binary BGmisc-1.5.0/BGmisc/data/inbreeding.rda |binary BGmisc-1.5.0/BGmisc/data/potter.rda |binary BGmisc-1.5.0/BGmisc/data/royal92.rda |binary BGmisc-1.5.0/BGmisc/inst/doc/v0_network.html | 6 BGmisc-1.5.0/BGmisc/inst/doc/v1_modelingvariancecomponents.html | 8 BGmisc-1.5.0/BGmisc/inst/doc/v2_pedigree.html | 4 BGmisc-1.5.0/BGmisc/inst/doc/v3_analyticrelatedness.R | 4 BGmisc-1.5.0/BGmisc/inst/doc/v3_analyticrelatedness.Rmd | 4 BGmisc-1.5.0/BGmisc/inst/doc/v3_analyticrelatedness.html | 52 +- BGmisc-1.5.0/BGmisc/inst/doc/v4_validation.html | 194 ++++--- BGmisc-1.5.0/BGmisc/inst/doc/v5_ASOIAF.R | 60 +- BGmisc-1.5.0/BGmisc/inst/doc/v5_ASOIAF.Rmd | 67 +- BGmisc-1.5.0/BGmisc/inst/doc/v5_ASOIAF.html | 77 +-- BGmisc-1.5.0/BGmisc/man/addParentRow.Rd | 4 BGmisc-1.5.0/BGmisc/man/addPersonToPed.Rd | 34 + BGmisc-1.5.0/BGmisc/man/adjustKidsPerCouple.Rd | 8 BGmisc-1.5.0/BGmisc/man/buildBetweenGenerations.Rd | 27 - BGmisc-1.5.0/BGmisc/man/buildWithinGenerations.Rd | 13 BGmisc-1.5.0/BGmisc/man/checkParentIDs.Rd | 14 BGmisc-1.5.0/BGmisc/man/dot-adjBeta.Rd |only BGmisc-1.5.0/BGmisc/man/dot-adjDirect.Rd |only BGmisc-1.5.0/BGmisc/man/dot-adjIndexed.Rd |only BGmisc-1.5.0/BGmisc/man/dot-adjLoop.Rd |only BGmisc-1.5.0/BGmisc/man/dot-loadOrComputeParList.Rd | 3 BGmisc-1.5.0/BGmisc/man/figures/hex.png |binary BGmisc-1.5.0/BGmisc/man/findBiggest.Rd | 9 BGmisc-1.5.0/BGmisc/man/findOldest.Rd | 5 BGmisc-1.5.0/BGmisc/man/ped2add.Rd | 12 BGmisc-1.5.0/BGmisc/man/ped2cn.Rd | 16 BGmisc-1.5.0/BGmisc/man/ped2com.Rd | 12 BGmisc-1.5.0/BGmisc/man/ped2mit.Rd | 12 BGmisc-1.5.0/BGmisc/man/potter.Rd | 6 BGmisc-1.5.0/BGmisc/man/prepSummarizePedigrees.Rd |only BGmisc-1.5.0/BGmisc/man/repairParentIDs.Rd | 17 BGmisc-1.5.0/BGmisc/man/resample.Rd | 1 BGmisc-1.5.0/BGmisc/man/simulatePedigree.Rd | 35 - BGmisc-1.5.0/BGmisc/man/sliceFamilies.Rd |only BGmisc-1.5.0/BGmisc/man/summarizeFamilies.Rd | 22 BGmisc-1.5.0/BGmisc/man/summarizeFounder.Rd | 2 BGmisc-1.5.0/BGmisc/man/summarizeMatrilines.Rd | 22 BGmisc-1.5.0/BGmisc/man/summarizePatrilines.Rd | 22 BGmisc-1.5.0/BGmisc/man/summarizePedigrees.Rd | 22 BGmisc-1.5.0/BGmisc/tests/testthat/test-checkParents.R | 7 BGmisc-1.5.0/BGmisc/tests/testthat/test-checkPedigreeNetwork.R | 2 BGmisc-1.5.0/BGmisc/tests/testthat/test-constructAdjacency.R | 113 ++++ BGmisc-1.5.0/BGmisc/tests/testthat/test-convertPedigree.R | 2 BGmisc-1.5.0/BGmisc/tests/testthat/test-documentData.R | 48 + BGmisc-1.5.0/BGmisc/tests/testthat/test-helpPedigree.R | 105 ---- BGmisc-1.5.0/BGmisc/tests/testthat/test-makeLinks.R | 2 BGmisc-1.5.0/BGmisc/tests/testthat/test-sliceFamilies.R |only BGmisc-1.5.0/BGmisc/tests/testthat/test-summarizePedigree.R | 86 ++- BGmisc-1.5.0/BGmisc/tests/testthat/test-tweakPedigree.R | 128 +++++ BGmisc-1.5.0/BGmisc/vignettes/v3_analyticrelatedness.Rmd | 4 BGmisc-1.5.0/BGmisc/vignettes/v5_ASOIAF.Rmd | 67 +- 86 files changed, 1605 insertions(+), 984 deletions(-)
Title: Visualization of BART and BARP using SHAP
Description: Complex machine learning models are often difficult to interpret. Shapley values serve as a powerful tool to understand and explain why a model makes a particular prediction. This package computes variable contributions using permutation-based Shapley values for Bayesian Additive Regression Trees (BART) and its extension with Post-Stratification (BARP). The permutation-based SHAP method proposed by Strumbel and Kononenko (2014) <doi:10.1007/s10115-013-0679-x> is grounded in data obtained via MCMC sampling. Similar to the BART model introduced by Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>, this package leverages Bayesian posterior samples generated during model estimation, allowing variable contributions to be computed without requiring additional sampling. For XGBoost and baseline adjustments, the approach by Lundberg et al. (2020) <doi:10.1038/s42256-019-0138-9> is also considered.The BARP model proposed by Bisbee (2019) <doi:10.1017/S000305541 [...truncated...]
Author: Dong-eun Lee [aut, cre],
Eun-Kyung Lee [aut]
Maintainer: Dong-eun Lee <ldongeun.leel@gmail.com>
Diff between bartXViz versions 1.0.5 dated 2025-06-24 and 1.0.6 dated 2025-07-18
DESCRIPTION | 13 ++++++------- MD5 | 2 +- 2 files changed, 7 insertions(+), 8 deletions(-)
Title: Modeling Species Distributions in Three Dimensions
Description: Facilitates modeling species' ecological niches and
geographic distributions based on occurrences and environments that
have a vertical as well as horizontal component, and projecting models
into three-dimensional geographic space. Working in three dimensions is
useful in an aquatic context when the organisms one wishes to model can
be found across a wide range of depths in the water column. The package
also contains functions to automatically generate marine training
model training regions using machine learning, and interpolate and smooth
patchily sampled environmental rasters using thin plate splines.
Davis Rabosky AR, Cox CL, Rabosky DL, Title PO, Holmes IA, Feldman A, McGuire JA (2016) <doi:10.1038/ncomms11484>.
Nychka D, Furrer R, Paige J, Sain S (2021) <doi:10.5065/D6W957CT>.
Pateiro-Lopez B, Rodriguez-Casal A (2022) <https://CRAN.R-project.org/package=alphahull>.
Author: Hannah L. Owens [aut, cre] ,
Emmaline Sheahan [aut] ,
Carsten Rahbek [aut]
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
Diff between voluModel versions 0.2.2 dated 2024-08-20 and 0.2.3 dated 2025-07-18
voluModel-0.2.2/voluModel/inst/extdata/backgroundSamplingRegions.cpg |only voluModel-0.2.2/voluModel/inst/extdata/backgroundSamplingRegions.dbf |only voluModel-0.2.2/voluModel/inst/extdata/backgroundSamplingRegions.prj |only voluModel-0.2.2/voluModel/inst/extdata/backgroundSamplingRegions.shp |only voluModel-0.2.2/voluModel/inst/extdata/backgroundSamplingRegions.shx |only voluModel-0.2.2/voluModel/inst/extdata/smallLand.rds |only voluModel-0.2.2/voluModel/man/figures/vmHex.ai |only voluModel-0.2.2/voluModel/vignettes/AOUInterpAndSmooth.png |only voluModel-0.2.2/voluModel/vignettes/OxygenTopBottom.png |only voluModel-0.2.2/voluModel/vignettes/PointsAndTrainingRegion.png |only voluModel-0.2.2/voluModel/vignettes/TemperatureTopBottom.png |only voluModel-0.2.2/voluModel/vignettes/alphaHullDemonstration-1.png |only voluModel-0.2.2/voluModel/vignettes/clipToOceanDemo-1.png |only voluModel-0.2.2/voluModel/vignettes/meridianWrapDemo-1.png |only voluModel-0.2.3/voluModel/DESCRIPTION | 22 voluModel-0.2.3/voluModel/MD5 | 78 -- voluModel-0.2.3/voluModel/NAMESPACE | 1 voluModel-0.2.3/voluModel/NEWS.md | 6 voluModel-0.2.3/voluModel/R/interpolateRaster.R | 19 voluModel-0.2.3/voluModel/R/marineBackground.R | 23 voluModel-0.2.3/voluModel/R/visualizations.R | 12 voluModel-0.2.3/voluModel/inst/doc/a_Introduction.R | 69 -- voluModel-0.2.3/voluModel/inst/doc/a_Introduction.Rmd | 39 - voluModel-0.2.3/voluModel/inst/doc/a_Introduction.html | 51 - voluModel-0.2.3/voluModel/inst/doc/b_RasterProcessing.R | 119 +-- voluModel-0.2.3/voluModel/inst/doc/b_RasterProcessing.Rmd | 39 - voluModel-0.2.3/voluModel/inst/doc/b_RasterProcessing.html | 191 ++--- voluModel-0.2.3/voluModel/inst/doc/c_DataSampling.R | 113 +-- voluModel-0.2.3/voluModel/inst/doc/c_DataSampling.Rmd | 59 - voluModel-0.2.3/voluModel/inst/doc/c_DataSampling.html | 341 ++++------ voluModel-0.2.3/voluModel/inst/doc/d_Visualization.R | 2 voluModel-0.2.3/voluModel/inst/doc/d_Visualization.Rmd | 6 voluModel-0.2.3/voluModel/inst/doc/d_Visualization.html | 114 +-- voluModel-0.2.3/voluModel/inst/doc/e_GLMWorkflow.R | 31 voluModel-0.2.3/voluModel/inst/doc/e_GLMWorkflow.Rmd | 20 voluModel-0.2.3/voluModel/inst/doc/e_GLMWorkflow.html | 259 +++---- voluModel-0.2.3/voluModel/inst/extdata/oxygenBottom.tif |binary voluModel-0.2.3/voluModel/inst/extdata/oxygenSmooth.tif |binary voluModel-0.2.3/voluModel/inst/extdata/woa18_all_A00mn01_cropped.zip |binary voluModel-0.2.3/voluModel/inst/extdata/woa18_decav_t00mn01_cropped.zip |binary voluModel-0.2.3/voluModel/tests/testthat/test-marineBackground.R | 28 voluModel-0.2.3/voluModel/tests/testthat/test-visualizations.R | 37 - voluModel-0.2.3/voluModel/vignettes/a_Introduction.Rmd | 39 - voluModel-0.2.3/voluModel/vignettes/b_RasterProcessing.Rmd | 39 - voluModel-0.2.3/voluModel/vignettes/c_DataSampling.Rmd | 59 - voluModel-0.2.3/voluModel/vignettes/d_Visualization.Rmd | 6 voluModel-0.2.3/voluModel/vignettes/e_GLMWorkflow.Rmd | 20 47 files changed, 812 insertions(+), 1030 deletions(-)
Title: SQLite Interface for R
Description: Embeds the SQLite database engine in R and provides an
interface compliant with the DBI package. The source for the SQLite
engine (version 3.50.3) and for various extensions is included.
System libraries will never be consulted because this package relies
on static linking for the plugins it includes; this also ensures a
consistent experience across all installations.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
D. Richard Hipp [ctb] ,
Dan Kennedy [ctb] ,
Joe Mistachkin [ctb] ,
SQLite Authors [ctb] ,
Liam Healy [ctb] ,
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RSQLite versions 2.4.1 dated 2025-06-08 and 2.4.2 dated 2025-07-18
DESCRIPTION | 10 - MD5 | 10 - NEWS.md | 11 + build/vignette.rds |binary src/vendor/sqlite3/sqlite3.c | 361 +++++++++++++++++++++++++------------------ src/vendor/sqlite3/sqlite3.h | 176 ++++++++++---------- 6 files changed, 322 insertions(+), 246 deletions(-)
Title: Bayesian Heteroskedastic Gaussian Processes
Description: Performs Bayesian posterior inference for heteroskedastic Gaussian processes.
Models are trained through MCMC including elliptical slice sampling (ESS) of
latent noise processes and Metropolis-Hastings sampling of
kernel hyperparameters. Replicates are handled efficientyly through a
Woodbury formulation of the joint likelihood for the mean and noise process
(Binois, M., Gramacy, R., Ludkovski, M. (2018) <doi:10.1080/10618600.2018.1458625>)
For large data, Vecchia-approximation for faster
computation is leveraged (Sauer, A., Cooper, A., and Gramacy, R.,
(2023), <doi:10.1080/10618600.2022.2129662>). Incorporates 'OpenMP' and
SNOW parallelization and utilizes 'C'/'C++' under the hood.
Author: Parul V. Patil [aut, cre]
Maintainer: Parul V. Patil <parulvijay@vt.edu>
Diff between bhetGP versions 1.0 dated 2025-07-14 and 1.0.1 dated 2025-07-18
bhetGP-1.0.1/bhetGP/DESCRIPTION | 6 - bhetGP-1.0.1/bhetGP/MD5 | 32 +++---- bhetGP-1.0.1/bhetGP/NAMESPACE | 1 bhetGP-1.0.1/bhetGP/R/RcppExports.R | 4 bhetGP-1.0.1/bhetGP/R/bhetGP-package.R | 12 +- bhetGP-1.0.1/bhetGP/R/checks.R | 9 - bhetGP-1.0.1/bhetGP/R/fit.R | 136 +++++++++++++++++++++--------- bhetGP-1.0.1/bhetGP/R/plots.R | 70 +++++++++------ bhetGP-1.0.1/bhetGP/R/predict.R | 15 ++- bhetGP-1.0.1/bhetGP/R/vecchia.R | 33 +++++-- bhetGP-1.0.1/bhetGP/man/bhetGP-package.Rd |only bhetGP-1.0.1/bhetGP/man/bhetGP.Rd | 69 +++++++++++---- bhetGP-1.0.1/bhetGP/man/bhomGP.Rd | 43 +++++++-- bhetGP-1.0.1/bhetGP/man/predict.Rd | 5 + bhetGP-1.0.1/bhetGP/src/Makevars | 3 bhetGP-1.0.1/bhetGP/src/RcppExports.cpp | 52 +++++++---- bhetGP-1.0.1/bhetGP/src/vecchia.cpp | 68 ++++++++++----- bhetGP-1.0/bhetGP/man/bhetgp-package.Rd |only 18 files changed, 377 insertions(+), 181 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 0.5.2 dated 2025-02-06 and 0.6 dated 2025-07-18
DESCRIPTION | 6 ++-- MD5 | 42 ++++++++++++++++++++++++---------- NAMESPACE | 55 +++++++++++++++++++++++++-------------------- R/OC.rule.R | 55 ++++++++++++++++++++++++--------------------- R/OC.rule.tite.R |only R/bdryfcn.R | 37 +++++++++++++++--------------- R/bdryfcn.bin.inverse.R |only R/calc.rule.R | 8 ++++-- R/calc.rule.surv.R | 5 ++-- R/calc.rule.tite.R |only R/lines.rule.tite.R |only R/opchars.tite.R |only R/plot.rule.bin.R | 4 +-- R/plot.rule.surv.R | 2 - R/plot.rule.tite.R |only R/sim_tite_data.R |only R/simtrials.tite.R |only R/table.rule.tite.R |only man/Internal.Rd |only man/OC.rule.Rd | 5 +++- man/OC.rule.tite.Rd |only man/bdryfcn.Rd | 4 +-- man/bdryfcn.bin.inverse.Rd |only man/calc.rule.Rd | 3 +- man/calc.rule.surv.Rd | 6 +++- man/calc.rule.tite.Rd |only man/lines.rule.tite.Rd |only man/opchars.tite.Rd |only man/plot.rule.tite.Rd |only man/simtrials.tite.Rd |only man/table.rule.tite.Rd |only 31 files changed, 136 insertions(+), 96 deletions(-)
Title: Heterogeneous Treatment Effects in Regression Discontinuity
Designs
Description: Understanding heterogeneous causal effects based on pretreatment covariates is a crucial step in modern empirical work in data science. Building on the recent developments in Calonico et al (2025) <https://rdpackages.github.io/references/Calonico-Cattaneo-Farrell-Palomba-Titiunik_2025_HTERD.pdf>, this package provides tools for estimation and inference of heterogeneous treatment effects in Regression Discontinuity (RD) Designs. The package includes two main commands: 'rdhte' to conduct estimation and robust bias-corrected inference for conditional RD treatment effects (given choice of bandwidth parameter); 'rdbwhte', which implements automatic bandwidth selection methods; and 'rdhte_lincom' to test linear combinations of parameters.
Author: Sebastian Calonico [aut, cre],
Matias D. Cattaneo [aut],
Max H. Farrell [aut],
Filippo Palomba [aut],
Rocio Titiunik [aut]
Maintainer: Sebastian Calonico <scalonico@ucdavis.edu>
Diff between rdhte versions 0.0.2 dated 2025-04-03 and 0.1.0 dated 2025-07-18
DESCRIPTION | 15 - MD5 | 21 + NAMESPACE | 9 R/rdbwhte.R | 261 ++++++++++++------ R/rdhte-package.R | 9 R/rdhte.R | 726 +++++++++++++++++++++++++++++++++++++--------------- R/rdhte_lincom.R |only build |only inst |only man/rdbwhte.Rd | 50 ++- man/rdhte.Rd | 107 +++++-- man/rdhte_lincom.Rd |only vignettes |only 13 files changed, 851 insertions(+), 347 deletions(-)
Title: Acceptance Sampling Plans Design
Description: Provides tools for designing and analyzing Acceptance Sampling plans.
Supports both Attributes Sampling (Binomial and Poisson distributions) and
Variables Sampling (Normal and Beta distributions), enabling quality control
for fractional and compositional data. Uses nonlinear programming for sampling
plan optimization, minimizing sample size while controlling producer's and
consumer's risks. Operating Characteristic curves are available for plan visualization.
Author: Ha Truong [aut, cre, cph],
Victor Miranda [ths, rev],
Roger Kissling [ths, rev]
Maintainer: Ha Truong <truongvietha87@gmail.com>
Diff between AccSamplingDesign versions 0.0.5 dated 2025-07-11 and 0.0.6 dated 2025-07-18
DESCRIPTION | 6 MD5 | 16 - R/manualPlan.R | 7 README.md | 449 +++++++++----------------------- inst/doc/introduction.R | 227 +++++----------- inst/doc/introduction.Rmd | 402 +++++++---------------------- inst/doc/introduction.html | 617 ++++++++++++--------------------------------- man/manualPlan.Rd | 9 vignettes/introduction.Rmd | 402 +++++++---------------------- 9 files changed, 588 insertions(+), 1547 deletions(-)
More information about AccSamplingDesign at CRAN
Permanent link
Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Author: A. Marcia Barbosa [aut, cre],
Jennifer A. Brown [aut],
Alberto Jimenez-Valverde [aut],
Raimundo Real [aut],
Oswald van Ginkel [ctb],
Jurica Levatic [ctb],
Victoria Formoso-Freire [ctb],
Andres Baselga [ctb],
Carola Gomez-Rodriguez [ctb],
Jose Carlos [...truncated...]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between modEvA versions 3.34 dated 2025-04-29 and 3.39 dated 2025-07-18
DESCRIPTION | 10 +- MD5 | 42 ++++----- NAMESPACE | 3 NEWS.md | 109 ++++++++++++++++++++++- R/Dsquared.R | 230 +++++++++++++++++++++++++------------------------- R/MillerCalib.R | 7 - R/RsqGLM.R | 86 ------------------ R/confusionLabel.R | 62 ++++++------- R/mod2obspred.R | 18 +-- R/optiThresh.R | 2 R/prevalence.R | 3 R/pseudoRsq.R |only R/quantReclass.R | 6 - R/varImp.R | 62 +++++++------ data/rotif.mods.rda |binary man/AUC.Rd | 8 + man/MillerCalib.Rd | 12 +- man/RsqGLM.Rd | 65 +++----------- man/confusionLabel.Rd | 112 ++++++++++++------------ man/modEvA-package.Rd | 4 man/pseudoRsq.Rd |only man/threshMeasures.Rd | 8 + man/varImp.Rd | 18 ++- 23 files changed, 437 insertions(+), 430 deletions(-)
Title: A Shiny App for Network Modeling with 'statnet'
Description: A graphical user interface for cross-sectional network modeling
with the 'statnet' software suite <https://github.com/statnet>.
Author: Martina Morris [cre, aut],
Emily Beylerian [aut],
Kirk Li [ctb],
Samuel Jenness [ctb],
Michal Bojanowski [ctb]
Maintainer: Martina Morris <morrism@uw.edu>
Diff between statnetWeb versions 0.5.8 dated 2024-07-17 and 0.6.1 dated 2025-07-18
statnetWeb-0.5.8/statnetWeb/inst/shiny/statnetWeb/rsconnect |only statnetWeb-0.6.1/statnetWeb/DESCRIPTION | 11 - statnetWeb-0.6.1/statnetWeb/MD5 | 17 +- statnetWeb-0.6.1/statnetWeb/NAMESPACE | 1 statnetWeb-0.6.1/statnetWeb/NEWS.md | 61 +++++--- statnetWeb-0.6.1/statnetWeb/R/statnetWeb-package.R | 1 statnetWeb-0.6.1/statnetWeb/README.md | 2 statnetWeb-0.6.1/statnetWeb/inst/shiny/statnetWeb/global.R | 16 +- statnetWeb-0.6.1/statnetWeb/inst/shiny/statnetWeb/server.R | 17 +- statnetWeb-0.6.1/statnetWeb/man/statnetWeb.Rd | 82 ++++++------ 10 files changed, 116 insertions(+), 92 deletions(-)
Title: Iota Inter Coder Reliability for Content Analysis
Description: Routines and tools for assessing the quality of content
analysis on the basis of the Iota Reliability Concept. The concept is
inspired by item response theory and can be applied to any kind of
content analysis which uses a standardized coding scheme and discrete
categories. It is also applicable for content analysis conducted by
artificial intelligence. The package provides reliability measures
for a complete scale as well as for every single category. Analysis of
subgroup-invariance and error corrections are implemented. This
information can support the development process of a coding scheme and
allows a detailed inspection of the quality of the generated data.
Equations and formulas working in this package are part of Berding et
al. (2022)<doi:10.3389/feduc.2022.818365> and Berding and Pargmann
(2022) <doi:10.30819/5581>.
Author: Berding Florian [aut, cre] ,
Pargmann Julia [ctb]
Maintainer: Berding Florian <florian.berding@uni-hamburg.de>
Diff between iotarelr versions 0.1.5 dated 2024-01-25 and 0.1.6 dated 2025-07-18
DESCRIPTION | 18 ++-- MD5 | 40 ++++----- R/additional_functions.R | 14 +++ R/data_new_rater.R | 14 +++ R/iota_version_1.R | 16 +++ R/iota_version_2.R | 14 +++ R/plots.R | 22 ++++- R/writtenexams.R | 14 +++ README.md | 30 +++++-- build/vignette.rds |binary inst/doc/Old_01_How_to_use_Iota1.html | 8 - inst/doc/V_02_Estimating_Consequences_for_Subsequent_Analyses.html | 10 +- inst/doc/V_03_Different_Guidance_Functioning.html | 42 +++++----- inst/doc/V_04_Error_Correction.html | 20 ++-- inst/doc/V_05_Test_New_Raters.html | 12 +- inst/doc/iotarelr.html | 20 ++-- man/compute_iota2.Rd | 42 +++++----- man/get_iota2_measures.Rd | 22 ++--- man/plot_iota.Rd | 2 man/plot_iota2_alluvial.Rd | 4 src/estimation.cpp | 14 +++ 21 files changed, 247 insertions(+), 131 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) (fast) simulation of random fields, b) inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Flexible covariance models for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. Se [...truncated...]
Author: Moreno Bevilacqua [aut, cre, cph],
Victor Morales-Onate [ctb],
Francisco Cuevas-Pacheco [ctb],
Christian Caamano-Carrillo [ctb]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 2.1.6 dated 2025-06-25 and 2.1.7 dated 2025-07-18
GeoModels-2.1.6/GeoModels/src/Gradient.c |only GeoModels-2.1.6/GeoModels/src/specfun.f |only GeoModels-2.1.7/GeoModels/DESCRIPTION | 16 GeoModels-2.1.7/GeoModels/MD5 | 134 - GeoModels-2.1.7/GeoModels/NAMESPACE | 3 GeoModels-2.1.7/GeoModels/R/GeoCV.R | 585 +++--- GeoModels-2.1.7/GeoModels/R/GeoCompositeLik.r | 161 - GeoModels-2.1.7/GeoModels/R/GeoCompositeLik2.R | 190 -- GeoModels-2.1.7/GeoModels/R/GeoCovariogram.r | 20 GeoModels-2.1.7/GeoModels/R/GeoCovmatrix.r | 39 GeoModels-2.1.7/GeoModels/R/GeoDoScores.R | 300 +-- GeoModels-2.1.7/GeoModels/R/GeoFit.r | 53 GeoModels-2.1.7/GeoModels/R/GeoFit2.R | 52 GeoModels-2.1.7/GeoModels/R/GeoIndCompositeLik2.R | 104 - GeoModels-2.1.7/GeoModels/R/GeoKrig.r | 196 -- GeoModels-2.1.7/GeoModels/R/GeoKrigloc.R | 494 +++-- GeoModels-2.1.7/GeoModels/R/GeoLik.r | 20 GeoModels-2.1.7/GeoModels/R/GeoNA.R | 401 +++- GeoModels-2.1.7/GeoModels/R/GeoNeighIndex.R | 6 GeoModels-2.1.7/GeoModels/R/GeoNeighbSelect.R | 3 GeoModels-2.1.7/GeoModels/R/GeoNeighborhood.R | 671 ++++--- GeoModels-2.1.7/GeoModels/R/GeoPit.R | 5 GeoModels-2.1.7/GeoModels/R/GeoScatterplot.R | 2 GeoModels-2.1.7/GeoModels/R/GeoScores.R | 145 + GeoModels-2.1.7/GeoModels/R/GeoSim.r | 14 GeoModels-2.1.7/GeoModels/R/GeoSimCopula.R | 25 GeoModels-2.1.7/GeoModels/R/GeoSimapprox.r | 2 GeoModels-2.1.7/GeoModels/R/GeoSimcond.R | 58 GeoModels-2.1.7/GeoModels/R/GeoSpoutlier.R | 2 GeoModels-2.1.7/GeoModels/R/GeoTest.r | 18 GeoModels-2.1.7/GeoModels/R/GeoVariogram.r | 19 GeoModels-2.1.7/GeoModels/R/GeoWls.r | 2 GeoModels-2.1.7/GeoModels/R/Geovarestbootstrap.R | 329 +-- GeoModels-2.1.7/GeoModels/R/SimCE.R | 2 GeoModels-2.1.7/GeoModels/R/Utility.r | 310 +-- GeoModels-2.1.7/GeoModels/R/Utility_cov.R | 79 GeoModels-2.1.7/GeoModels/man/CompIndLik2.Rd | 5 GeoModels-2.1.7/GeoModels/man/CompLik.Rd | 9 GeoModels-2.1.7/GeoModels/man/CompLik2.Rd | 13 GeoModels-2.1.7/GeoModels/man/GeoCorrFct.Rd | 2 GeoModels-2.1.7/GeoModels/man/GeoCovmatrix.Rd | 4 GeoModels-2.1.7/GeoModels/man/GeoFit.Rd | 17 GeoModels-2.1.7/GeoModels/man/GeoFit2.Rd | 17 GeoModels-2.1.7/GeoModels/man/GeoKrig.Rd | 4 GeoModels-2.1.7/GeoModels/man/GeoKrigloc.Rd | 4 GeoModels-2.1.7/GeoModels/man/GeoNeighIndex.Rd | 4 GeoModels-2.1.7/GeoModels/man/GeoNeighbSelect.Rd | 6 GeoModels-2.1.7/GeoModels/man/GeoNeighborhood.Rd | 4 GeoModels-2.1.7/GeoModels/man/GeoOutlier.Rd | 4 GeoModels-2.1.7/GeoModels/man/GeoScatterplot.Rd | 4 GeoModels-2.1.7/GeoModels/man/GeoScores.Rd | 16 GeoModels-2.1.7/GeoModels/man/GeoSim.Rd | 9 GeoModels-2.1.7/GeoModels/man/GeoSimCopula.Rd | 11 GeoModels-2.1.7/GeoModels/man/GeoSimapprox.Rd | 3 GeoModels-2.1.7/GeoModels/man/GeoSimcond.Rd | 8 GeoModels-2.1.7/GeoModels/man/GeoVarestbootstrap.Rd | 5 GeoModels-2.1.7/GeoModels/man/GeoVariogram.Rd | 4 GeoModels-2.1.7/GeoModels/man/GeoWls.Rd | 5 GeoModels-2.1.7/GeoModels/man/Lik.Rd | 5 GeoModels-2.1.7/GeoModels/src/2kummer.c | 695 +++++++ GeoModels-2.1.7/GeoModels/src/CompositeLikelihood2.c | 186 +- GeoModels-2.1.7/GeoModels/src/CompositeLikelihood2_ani.c | 113 - GeoModels-2.1.7/GeoModels/src/CompositeLikelihoodCond2.c | 142 - GeoModels-2.1.7/GeoModels/src/CompositeLikelihoodCond2_ani.c | 90 GeoModels-2.1.7/GeoModels/src/CorrelationFunction.c | 316 ++- GeoModels-2.1.7/GeoModels/src/Distributions.c | 1007 ++++++++++- GeoModels-2.1.7/GeoModels/src/GeoModels_init.c | 938 +++++----- GeoModels-2.1.7/GeoModels/src/Utility.c | 1 GeoModels-2.1.7/GeoModels/src/header.h | 468 ----- 69 files changed, 4890 insertions(+), 3689 deletions(-)
Title: Models, Datasets and Transformations for Images
Description: Provides access to datasets, models and preprocessing
facilities for deep learning with images. Integrates seamlessly
with the 'torch' package and it's 'API' borrows heavily from
'PyTorch' vision package.
Author: Daniel Falbel [aut, cre],
Christophe Regouby [ctb],
Akanksha Koshti [ctb],
Derrick Richard [ctb],
RStudio [cph]
Maintainer: Daniel Falbel <daniel@posit.co>
Diff between torchvision versions 0.6.0 dated 2024-06-14 and 0.7.0 dated 2025-07-18
torchvision-0.6.0/torchvision/man/cifar10_dataset.Rd |only torchvision-0.6.0/torchvision/man/kmnist_dataset.Rd |only torchvision-0.7.0/torchvision/DESCRIPTION | 28 torchvision-0.7.0/torchvision/MD5 | 150 +- torchvision-0.7.0/torchvision/NAMESPACE | 37 torchvision-0.7.0/torchvision/NEWS.md | 31 torchvision-0.7.0/torchvision/R/conditions.R | 42 torchvision-0.7.0/torchvision/R/dataset-caltech.R |only torchvision-0.7.0/torchvision/R/dataset-cifar.R | 75 - torchvision-0.7.0/torchvision/R/dataset-coco.R |only torchvision-0.7.0/torchvision/R/dataset-eurosat.R |only torchvision-0.7.0/torchvision/R/dataset-fer.R |only torchvision-0.7.0/torchvision/R/dataset-fgvc.R |only torchvision-0.7.0/torchvision/R/dataset-flickr.R |only torchvision-0.7.0/torchvision/R/dataset-flowers.R |only torchvision-0.7.0/torchvision/R/dataset-mnist.R | 462 +++++++- torchvision-0.7.0/torchvision/R/dataset-oxfordiiitpet.R |only torchvision-0.7.0/torchvision/R/extension.R |only torchvision-0.7.0/torchvision/R/folder-dataset.R | 8 torchvision-0.7.0/torchvision/R/globals.R | 2 torchvision-0.7.0/torchvision/R/models-inception.R | 20 torchvision-0.7.0/torchvision/R/models-mobilenetv2.R | 3 torchvision-0.7.0/torchvision/R/models-vgg.R | 2 torchvision-0.7.0/torchvision/R/ops-box_convert.R |only torchvision-0.7.0/torchvision/R/ops-boxes.R |only torchvision-0.7.0/torchvision/R/tiny-imagenet-dataset.R | 8 torchvision-0.7.0/torchvision/R/transforms-defaults.R | 4 torchvision-0.7.0/torchvision/R/transforms-generics.R | 23 torchvision-0.7.0/torchvision/R/transforms-tensor.R | 14 torchvision-0.7.0/torchvision/R/utils.R | 2 torchvision-0.7.0/torchvision/R/vision_utils.R | 537 ++++++---- torchvision-0.7.0/torchvision/inst |only torchvision-0.7.0/torchvision/man/base_loader.Rd | 2 torchvision-0.7.0/torchvision/man/batched_nms.Rd |only torchvision-0.7.0/torchvision/man/box_area.Rd |only torchvision-0.7.0/torchvision/man/box_convert.Rd |only torchvision-0.7.0/torchvision/man/box_cxcywh_to_xyxy.Rd |only torchvision-0.7.0/torchvision/man/box_iou.Rd |only torchvision-0.7.0/torchvision/man/box_xywh_to_xyxy.Rd |only torchvision-0.7.0/torchvision/man/box_xyxy_to_cxcywh.Rd |only torchvision-0.7.0/torchvision/man/box_xyxy_to_xywh.Rd |only torchvision-0.7.0/torchvision/man/caltech_dataset.Rd |only torchvision-0.7.0/torchvision/man/cifar_datasets.Rd |only torchvision-0.7.0/torchvision/man/clip_boxes_to_image.Rd |only torchvision-0.7.0/torchvision/man/coco_caption_dataset.Rd |only torchvision-0.7.0/torchvision/man/coco_detection_dataset.Rd |only torchvision-0.7.0/torchvision/man/coco_polygon_to_mask.Rd |only torchvision-0.7.0/torchvision/man/draw_bounding_boxes.Rd | 55 - torchvision-0.7.0/torchvision/man/draw_keypoints.Rd | 22 torchvision-0.7.0/torchvision/man/draw_segmentation_masks.Rd | 36 torchvision-0.7.0/torchvision/man/eurosat_dataset.Rd |only torchvision-0.7.0/torchvision/man/fer_dataset.Rd |only torchvision-0.7.0/torchvision/man/fgvc_aircraft_dataset.Rd |only torchvision-0.7.0/torchvision/man/flickr_caption_dataset.Rd |only torchvision-0.7.0/torchvision/man/flowers102_dataset.Rd |only torchvision-0.7.0/torchvision/man/generalized_box_iou.Rd |only torchvision-0.7.0/torchvision/man/mnist_dataset.Rd | 144 ++ torchvision-0.7.0/torchvision/man/model_alexnet.Rd | 4 torchvision-0.7.0/torchvision/man/model_inception_v3.Rd | 20 torchvision-0.7.0/torchvision/man/model_mobilenet_v2.Rd | 4 torchvision-0.7.0/torchvision/man/model_resnet.Rd | 4 torchvision-0.7.0/torchvision/man/model_vgg.Rd | 8 torchvision-0.7.0/torchvision/man/nms.Rd |only torchvision-0.7.0/torchvision/man/oxfordiiitpet_dataset.Rd |only torchvision-0.7.0/torchvision/man/oxfordiiitpet_segmentation_dataset.Rd |only torchvision-0.7.0/torchvision/man/remove_small_boxes.Rd |only torchvision-0.7.0/torchvision/man/tensor_image_browse.Rd | 13 torchvision-0.7.0/torchvision/man/tensor_image_display.Rd | 13 torchvision-0.7.0/torchvision/man/tiny_imagenet_dataset.Rd | 13 torchvision-0.7.0/torchvision/man/transform_affine.Rd | 23 torchvision-0.7.0/torchvision/man/transform_center_crop.Rd | 4 torchvision-0.7.0/torchvision/man/transform_five_crop.Rd | 2 torchvision-0.7.0/torchvision/man/transform_random_affine.Rd | 6 torchvision-0.7.0/torchvision/man/transform_random_crop.Rd | 2 torchvision-0.7.0/torchvision/man/transform_random_resized_crop.Rd | 2 torchvision-0.7.0/torchvision/man/transform_random_rotation.Rd | 4 torchvision-0.7.0/torchvision/man/transform_resize.Rd | 2 torchvision-0.7.0/torchvision/man/transform_resized_crop.Rd | 2 torchvision-0.7.0/torchvision/man/transform_rotate.Rd | 2 torchvision-0.7.0/torchvision/man/transform_ten_crop.Rd | 2 torchvision-0.7.0/torchvision/man/vision_make_grid.Rd | 16 torchvision-0.7.0/torchvision/po |only torchvision-0.7.0/torchvision/tests/testthat/assets/class/horse |only torchvision-0.7.0/torchvision/tests/testthat/test-dataset-caltech.R |only torchvision-0.7.0/torchvision/tests/testthat/test-dataset-cifar.R | 12 torchvision-0.7.0/torchvision/tests/testthat/test-dataset-coco.R |only torchvision-0.7.0/torchvision/tests/testthat/test-dataset-eurosat.R |only torchvision-0.7.0/torchvision/tests/testthat/test-dataset-fer.R |only torchvision-0.7.0/torchvision/tests/testthat/test-dataset-fgvc.R |only torchvision-0.7.0/torchvision/tests/testthat/test-dataset-flickr.R |only torchvision-0.7.0/torchvision/tests/testthat/test-dataset-flowers.R |only torchvision-0.7.0/torchvision/tests/testthat/test-dataset-mnist.R | 132 ++ torchvision-0.7.0/torchvision/tests/testthat/test-dataset-oxfordiiitpet.R |only torchvision-0.7.0/torchvision/tests/testthat/test-folder-dataset.R | 2 torchvision-0.7.0/torchvision/tests/testthat/test-message-translations.R |only torchvision-0.7.0/torchvision/tests/testthat/test-ops-box_convert.R |only torchvision-0.7.0/torchvision/tests/testthat/test-ops-boxes.R |only torchvision-0.7.0/torchvision/tests/testthat/test-transforms.R | 21 torchvision-0.7.0/torchvision/tests/testthat/test-vision-utils.R | 104 + torchvision-0.7.0/torchvision/tools/convert-models.py | 83 + 100 files changed, 1708 insertions(+), 499 deletions(-)
Title: Distribution Comparison Through Density Ratio Estimation
Description: Fast, flexible and user-friendly tools for distribution comparison
through direct density ratio estimation. The estimated density ratio can be
used for covariate shift adjustment, outlier-detection, change-point detection,
classification and evaluation of synthetic data quality. The package implements
multiple non-parametric estimation techniques (unconstrained least-squares
importance fitting, ulsif(), Kullback-Leibler importance estimation procedure,
kliep(), spectral density ratio estimation, spectral(), kernel mean matching,
kmm(), and least-squares hetero-distributional subspace search, lhss()).
with automatic tuning of hyperparameters. Helper functions are available for
two-sample testing and visualizing the density ratios. For an overview on
density ratio estimation, see Sugiyama et al. (2012) <doi:10.1017/CBO9781139035613>
for a general overview, and the help files for references on the specific
estimation techniques.
Author: Thom Volker [aut, cre] ,
Carlos Gonzalez Poses [ctb],
Erik-Jan van Kesteren [ctb]
Maintainer: Thom Volker <thombenjaminvolker@gmail.com>
Diff between densityratio versions 0.2.1 dated 2025-06-18 and 0.2.2 dated 2025-07-18
DESCRIPTION | 8 +++--- MD5 | 38 ++++++++++++++--------------- NAMESPACE | 5 --- NEWS.md | 6 ++++ R/plot.R | 38 ++++++----------------------- README.md | 8 +++--- inst/doc/covariate-shift.Rmd | 4 +-- inst/doc/covariate-shift.html | 8 +++--- inst/doc/densityratio.Rmd | 2 - inst/doc/densityratio.html | 4 +-- man/figures/README-densities-1.png |binary man/figures/README-plot-methods-1.png |binary man/figures/README-plot-univ-1.png |binary man/figures/logo.png |binary tests/testthat/test-ulsif.R | 12 ++++++--- vignettes/covariate-shift-plot-dr-cs-1.png |binary vignettes/covariate-shift-plot-dr-rs-1.png |binary vignettes/covariate-shift.Rmd | 4 +-- vignettes/densityratio-plot-dr-1.png |binary vignettes/densityratio.Rmd | 2 - 20 files changed, 64 insertions(+), 75 deletions(-)
Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival
Analysis
Description: This model fitting tool incorporates cyclic coordinate descent and
majorization-minimization approaches to fit a variety of regression models
found in large-scale observational healthcare data. Implementations focus
on computational optimization and fine-scale parallelization to yield
efficient inference in massive datasets. Please see:
Suchard, Simpson, Zorych, Ryan and Madigan (2013) <doi:10.1145/2414416.2414791>.
Author: Marc A. Suchard [aut, cre],
Martijn J. Schuemie [aut],
Trevor R. Shaddox [aut],
Yuxi Tian [aut],
Jianxiao Yang [aut],
Eric Kawaguchi [aut],
Sushil Mittal [ctb],
Observational Health Data Sciences and Informatics [cph],
Marcus Geelnard [cph, ctb] ,
Ru [...truncated...]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between Cyclops versions 3.5.2 dated 2025-06-24 and 3.6.0 dated 2025-07-18
DESCRIPTION | 15 +- MD5 | 65 +++++++----- NAMESPACE | 3 NEWS.md | 14 ++ R/ModelFit.R | 161 +++++++++++++++++++++++++----- R/NewDataConversion.R | 12 +- R/RcppExports.R | 16 ++ man/cacheCyclopsModelForJava.Rd |only man/clearCyclopsModelCache.Rd |only man/cyclopsLibraryFileName.Rd |only man/getCyclopsProfileLogLikelihood.Rd | 5 man/gradient.Rd |only man/runBootstrap.Rd | 12 +- src/RcppCyclopsInterface.cpp | 98 ++++++++++++++++-- src/RcppCyclopsInterface.h | 11 -- src/RcppExports.cpp | 43 +++++++- src/cyclops/CcdInterface.cpp | 47 +++++++- src/cyclops/CcdInterface.h | 1 src/cyclops/CyclicCoordinateDescent.cpp | 44 ++++++++ src/cyclops/CyclicCoordinateDescent.h | 14 ++ src/cyclops/drivers/BootstrapDriver.cpp | 69 +++++++++++- src/cyclops/drivers/BootstrapDriver.h | 5 src/cyclops/drivers/BootstrapSelector.cpp | 13 +- src/cyclops/drivers/BootstrapSelector.h | 4 src/cyclops/io/OutputWriter.h | 3 src/cyclops/jni |only tests/testthat/test-JNI.R |only tests/testthat/test-bootstrap.R |only tests/testthat/test-gradient.R |only tests/testthat/test-profileLikelihood.R | 25 ++++ tests/testthat/test-residuals.R | 4 tests/testthat/test-smallCox.R | 8 - tests/testthat/test-sqlConstructor.R | 6 - tests/testthat/test-weighting.R | 1 tools/configure.R | 44 +++++++- tools/jvm-w32 |only 36 files changed, 627 insertions(+), 116 deletions(-)
Title: Sparse Projected Averaged Regression
Description: A flexible framework combining
variable screening and random projection techniques for fitting ensembles of
predictive generalized linear models to high-dimensional data.
Designed for extensibility, the package implements
key techniques as S3 classes with user-friendly constructors,
enabling easy integration and development of new procedures for
high-dimensional applications. For more details see
Parzer et al (2024a) <doi:10.48550/arXiv.2312.00130> and
Parzer et al (2024b) <doi:10.48550/arXiv.2410.00971>.
Author: Laura Vana-Guer [aut, cre] ,
Roman Parzer [aut] ,
Peter Filzmoser [aut]
Maintainer: Laura Vana-Guer <laura.vana.guer@tuwien.ac.at>
Diff between spareg versions 1.0.0 dated 2025-05-06 and 1.1.0 dated 2025-07-18
DESCRIPTION | 10 MD5 | 58 +-- NAMESPACE | 10 NEWS.md | 23 + R/rp_classes.R | 3 R/simulate.R | 7 R/spareg.R | 644 ++++++++++++++++++++++++++++++-------- R/sparegcv.R | 427 +++++++++++++++---------- R/utilities.R | 60 +++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/spareg.R | 353 ++++++++++++--------- inst/doc/spareg.Rnw | 682 ++++++++++++++++++++++++++--------------- inst/doc/spareg.pdf |binary man/coef.spar.Rd | 22 + man/coef.spar.cv.Rd | 25 + man/get_coef.Rd |only man/get_intercept.Rd |only man/get_measure.Rd |only man/get_model.Rd |only man/plot.spar.Rd | 16 man/plot.spar.cv.Rd | 18 - man/predict.spar.Rd | 12 man/predict.spar.cv.Rd | 12 man/print.coefspar.Rd |only man/simulate_spareg_data.Rd | 4 man/spar.Rd | 31 + man/spar.cv.Rd | 41 +- man/summary.coefspar.Rd |only tests/testthat/test-spareg.R | 126 +++++-- tests/testthat/test-sparegcv.R | 59 +++ vignettes/spareg.Rnw | 682 ++++++++++++++++++++++++++--------------- vignettes/spareg.bib | 78 ++++ 33 files changed, 2306 insertions(+), 1097 deletions(-)
Title: Data on Base and Recommended Packages for Current and Previous
Versions of R
Description: Provides a dataset of functions in all base and recommended packages of R versions 0.50 onwards.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between rcheology versions 4.5.0.0 dated 2025-04-12 and 4.5.1.0 dated 2025-07-18
DESCRIPTION | 6 +-- MD5 | 14 +++---- NEWS.md | 5 ++ README.md | 61 ++++++++++++++----------------- data/Rversions.rda |binary data/rcheology.rda |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary 8 files changed, 43 insertions(+), 43 deletions(-)
Title: Infinitesimal Jackknife Standard Errors for 'brms' Models
Description: Provides a function to calculate infinite-jackknife-based
standard errors for fixed effects parameters in 'brms' models, handling
both clustered and independent data.
References: Ji et al. (2024) <doi:10.48550/arXiv.2407.09772>; Giordano et al. (2024) <doi:10.48550/arXiv.2305.06466>.
Author: Feng Ji [aut, cre] ,
JoonHo Lee [aut],
Sophia Rabe-Hesketh [aut]
Maintainer: Feng Ji <f.ji@utoronto.ca>
Diff between IJSE versions 0.1.1 dated 2024-09-26 and 0.1.2 dated 2025-07-18
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NEWS.md | 5 +++++ 3 files changed, 12 insertions(+), 7 deletions(-)
Title: Interface R to MPFR - Multiple Precision Floating-Point Reliable
Description: Arithmetic (via S4 classes and methods) for
arbitrary precision floating point numbers, including transcendental
("special") functions. To this end, the package interfaces to
the 'LGPL' licensed 'MPFR' (Multiple Precision Floating-Point Reliable) Library
which itself is based on the 'GMP' (GNU Multiple Precision) Library.
Author: Martin Maechler [aut, cre] ,
Richard M. Heiberger [ctb] , *Bin, *Dec),
John C. Nash [ctb] , origin of unirootR),
Hans W. Borchers [ctb] ; origin of
hjkMpfr),
Mikael Jagan [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between Rmpfr versions 1.1-0 dated 2025-05-13 and 1.1-1 dated 2025-07-18
DESCRIPTION | 11 ++++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + R/special-fun.R | 16 +++++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 15 +++++++++++++++ inst/doc/Maechler_useR_2011-abstr.pdf |binary inst/doc/Rmpfr-pkg.pdf |binary inst/doc/log1mexp-note.pdf |binary man/distr-etc.Rd | 4 +++- 11 files changed, 44 insertions(+), 23 deletions(-)
More information about easyScieloPack at CRAN
Permanent link
Title: Generate Analysis Results Programmes Using ARS Metadata
Description: Analysis Results Standard (ARS), a foundational standard by CDISC
(Clinical Data Interchange Standards Consortium), provides a logical
data model for metadata describing all components to calculate Analysis Results.
<https://www.cdisc.org/standards/foundational/analysis-results-standard>
Using 'siera' package, ARS metadata is ingested (JSON or Excel format),
producing programmes to generate Analysis Results Datasets (ARDs).
Author: Malan Bosman [aut, cre],
Clymb Clinical [cph, fnd]
Maintainer: Malan Bosman <malanbos@gmail.com>
Diff between siera versions 0.3.0 dated 2025-03-03 and 0.4.0 dated 2025-07-18
DESCRIPTION | 12 ++- MD5 | 29 +++++-- NAMESPACE | 3 NEWS.md | 5 + R/ARD_script_example.R |only R/ARS_example.R | 2 R/globals.R | 5 + R/readARS.R | 94 +++++++++++++------------ R/readARS_xl.R |only README.md | 87 +++++++++++++++-------- build |only inst/doc |only inst/extdata/Common_Safety_Displays_cards.xlsx |only inst/extdata/cards_constructs.xlsx |only inst/script |only man/ARD_script_example.Rd |only man/ARS_example.Rd | 2 man/figures/logo.png |only man/readARS_xl.Rd |only vignettes |only 20 files changed, 155 insertions(+), 84 deletions(-)
Title: Client for 'GoFigr.io'
Description: Integrates with your 'RMarkdown' documents to automatically publish
figures to the <https://GoFigr.io> service. Supports both 'knitr' and interactive
execution within 'RStudio'.
Author: Maciej Pacula [cre, aut],
Flagstaff Solutions, LLC [cph]
Maintainer: Maciej Pacula <maciej@gofigr.io>
Diff between gofigR versions 0.3.1 dated 2025-03-19 and 1.1.0 dated 2025-07-18
DESCRIPTION | 13 +- MD5 | 58 ++++++++++--- NAMESPACE | 20 ++++ R/analysis.R | 13 ++ R/api.R | 42 ++++++++- R/asset.R |only R/data.R | 12 ++ R/integrations.R | 158 ++++++++++++++++++++++++++++++++---- R/revision.R | 19 +++- R/shiny_components.R |only README.md | 94 +++++++++++++++------ man/CONFIG_PATH.Rd | 7 + man/asset_linked_to_figure.Rd |only man/calc_checksum.Rd |only man/cat.gofigr_revision.Rd |only man/create_asset.Rd |only man/create_asset_revision.Rd |only man/create_revision.Rd | 2 man/delete_analysis.Rd |only man/enable.Rd | 7 + man/find_asset_by_name.Rd |only man/find_asset_revision_by_hash.Rd |only man/find_config.Rd |only man/get_asset.Rd |only man/get_asset_revision.Rd |only man/get_client.Rd |only man/get_data.Rd |only man/get_qr_png.Rd |only man/gfContainer.Rd |only man/gfPlot.Rd |only man/gfPlotServer.Rd |only man/new_asset_revision_from_file.Rd |only man/print.gofigr_revision.Rd |only man/publish.Rd | 5 - man/read_config.Rd | 4 man/sync_file.Rd |only man/sync_workspace_asset.Rd |only man/try_base2grob.Rd |only man/update_revision_data.Rd | 4 man/with_isolated_devices.Rd |only tests |only 41 files changed, 377 insertions(+), 81 deletions(-)
Title: Decorrelation Projection Scalable to High Dimensional Data
Description: Data whitening is a widely used preprocessing step to remove correlation structure since statistical models often assume independence. Here we use a probabilistic model of the observed data to apply a whitening transformation. This Gaussian Inverse Wishart Empirical Bayes model substantially reduces computational complexity, and regularizes the eigen-values of the sample covariance matrix to improve out-of-sample performance.
Author: Gabriel Hoffman [aut, cre]
Maintainer: Gabriel Hoffman <gabriel.hoffman@mssm.edu>
Diff between decorrelate versions 0.1.6.3 dated 2025-07-17 and 0.1.6.4 dated 2025-07-18
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/doc/decorrelate.html | 12 ++++++------ inst/unitTests/test_eclairs.R | 2 +- 4 files changed, 15 insertions(+), 15 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.6.0 dated 2025-05-13 and 0.6.1 dated 2025-07-18
DESCRIPTION | 6 +- MD5 | 35 ++++++----- NEWS.md | 12 ++++ R/MaestroPipeline.R | 2 R/MaestroPipelineList.R | 9 ++- R/invoke.R | 26 +++++++- inst/doc/maestro-1-quick-start.html | 6 +- inst/doc/maestro-3-advanced-scheduling.html | 12 ++-- inst/doc/maestro-4-directed-acyclic-graphs.html | 22 +++---- inst/doc/maestro-5-logging.html | 54 +++++++++--------- inst/doc/maestro-7-tag-reference.html | 9 +++ inst/doc/maestro-7-tag-reference.qmd | 12 ++++ man/MaestroPipelineList.Rd | 4 + man/invoke.Rd | 3 - tests/testthat/_snaps/MaestroPipeline.md | 2 tests/testthat/_snaps/invoke.md |only tests/testthat/test-invoke.R | 72 ++++++++++++++++++++++++ tests/testthat/test-run_schedule.R | 5 + vignettes/maestro-7-tag-reference.qmd | 12 ++++ 19 files changed, 224 insertions(+), 79 deletions(-)
Title: Support for Spatial Objects Within the 'mlr3' Ecosystem
Description: Extends the 'mlr3' ML framework with methods for spatial
objects. Data storage and prediction are supported for packages
'terra', 'raster' and 'stars'.
Author: Marc Becker [aut, cre] ,
Patrick Schratz [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3spatial versions 0.5.0 dated 2024-03-09 and 0.6.0 dated 2025-07-18
DESCRIPTION | 14 - MD5 | 42 ++--- NEWS.md | 4 R/DataBackendRaster.R | 4 R/TaskClassifST.R | 4 R/TaskRegrST.R | 2 R/as_task_classif_st.R | 9 - R/as_task_regr_st.R | 8 - R/data.R | 2 R/predict_spatial.R | 4 README.md | 31 ++-- build/vignette.rds |binary inst/doc/benchmark.html | 231 +++++++++++++++---------------- man/TaskClassifST.Rd | 16 +- man/TaskRegrST.Rd | 14 + man/as_data_backend.Rd | 4 man/as_task_classif_st.Rd | 7 man/as_task_regr_st.Rd | 7 man/mlr3spatial-package.Rd | 3 man/predict_spatial.Rd | 2 tests/testthat/test_as_task_classif_st.R | 12 + tests/testthat/test_as_task_regr_st.R | 12 + 22 files changed, 238 insertions(+), 194 deletions(-)
Title: Unbiased Distances for Mixed-Type Data
Description: A comprehensive framework for calculating unbiased distances in datasets
containing mixed-type variables (numerical and categorical). The package implements
a general formulation that ensures multivariate additivity and commensurability,
meaning that variables contribute equally to the overall distance regardless of
their type, scale, or distribution. Supports multiple distance measures including
Gower's distance, Euclidean distance, Manhattan distance, and various categorical
variable distances such as simple matching, Eskin, occurrence frequency, and
association-based distances. Provides tools for variable scaling (standard
deviation, range, robust range, and principal component scaling), and handles
both independent and association-based category dissimilarities. Implements
methods to correct for biases that typically arise from different variable types,
distributions, and number of categories. Particularly useful for cluster analysis,
data visualization, and other distance-based me [...truncated...]
Author: Alfonso Iodice D'Enza [aut],
Angelos Markos [aut, cre],
Michel van de Velden [aut],
Carlo Cavicchia [aut]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between manydist versions 0.4.7 dated 2025-07-08 and 0.4.8 dated 2025-07-18
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/mdist.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Interactive 'shiny' Dashboard for 'nlmixr2'
Description: An R shiny user interface for the 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>) package,
designed to simplify the modeling process for users. Additionally, this package includes supplementary functions
to further enhances the usage of 'nlmixr2'.
Author: Richard Hooijmaijers [aut, cre, cph],
Teun Post [aut, cph],
LAPP Consultants [fnd, cph],
Matthew Fidler [ctb],
Veerle van Leemput [ctb]
Maintainer: Richard Hooijmaijers <richardhooijmaijers@gmail.com>
Diff between shinyMixR versions 0.5.0 dated 2024-11-14 and 0.5.1 dated 2025-07-18
DESCRIPTION | 20 +- MD5 | 64 ++++---- NAMESPACE | 2 NEWS.md | 6 R/fit_plot.r | 6 R/gof_plot.r | 8 - R/module_run.R | 54 +++---- R/run_nmx.r | 22 +-- R/shinyMixR-package.R | 4 R/update_inits.r | 8 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/getting_started.R | 46 +++--- inst/doc/getting_started.html | 2 inst/other/combined.results.html.r | 6 inst/other/run_nmx.tmp | 6 inst/other/vpc.plot.r | 4 man/adpt_meta.Rd | 58 ++++---- man/create_proj.Rd | 58 ++++---- man/exploreplot.Rd | 52 +++---- man/fit_plot.Rd | 152 ++++++++++----------- man/get_meta.Rd | 46 +++--- man/get_proj.Rd | 52 +++---- man/gof_plot.Rd | 130 ++++++++--------- man/incr_mdl.Rd | 56 +++---- man/numfmt.Rd | 56 +++---- man/par_table.Rd | 124 ++++++++--------- man/run_nmx.Rd | 112 +++++++-------- man/shinyMixR-package.Rd | 9 + man/sigdigs.Rd | 38 ++--- man/theme_shinyMixR.Rd | 34 ++-- man/update_inits.Rd | 64 ++++---- tests/testthat/test-shinymixr-03-create-newmodel.R | 42 ++--- 33 files changed, 679 insertions(+), 662 deletions(-)
Title: Construct Parsers for Structured Text Files
Description: Construct parser combinator functions, higher order functions that
parse input. Construction of such parsers is transparent and easy. Their main
application is the parsing of structured text files like those generated by
laboratory instruments. Based on a paper by Hutton (1992)
<doi:10.1017/S0956796800000411>.
Author: Douwe Molenaar [aut, cre, cph]
Maintainer: Douwe Molenaar <d.molenaar@vu.nl>
Diff between parcr versions 0.5.2 dated 2024-06-07 and 0.5.3 dated 2025-07-18
DESCRIPTION | 12 ++-- MD5 | 27 ++++++---- NAMESPACE | 1 NEWS.md | 7 ++ R/parsers_basic.R | 2 R/stringparser_constructor.R |only README.md | 62 +++++-------------------- build/vignette.rds |binary inst/doc/Creating_parser_combinators.R | 2 inst/doc/Creating_parser_combinators.Rmd | 2 inst/doc/Creating_parser_combinators.html | 4 - inst/doc/Design_details.html | 4 - man/stringparser.Rd |only man/zero_or_more.Rd | 4 - tests/testthat/test-stringparser_constructor.R |only vignettes/Creating_parser_combinators.Rmd | 2 16 files changed, 52 insertions(+), 77 deletions(-)
Title: Compute Global Sensitivity Analysis Indices Using Optimal
Transport
Description: Computing Global Sensitivity Indices from given data using Optimal Transport, as defined in Borgonovo et al (2024) <doi:10.1287/mnsc.2023.01796>. You provide an input sample, an output sample, decide the algorithm, and compute the indices.
Author: Leonardo Chiani [aut, cre, cph] ,
Emanuele Borgonovo [rev],
Elmar Plischke [rev],
Massimo Tavoni [rev]
Maintainer: Leonardo Chiani <leonardo.chiani@polimi.it>
Diff between gsaot versions 1.0.0 dated 2025-06-17 and 1.1.0 dated 2025-07-18
gsaot-1.0.0/gsaot/R/ot_indices_divergence.R |only gsaot-1.1.0/gsaot/DESCRIPTION | 6 gsaot-1.1.0/gsaot/MD5 | 51 ++--- gsaot-1.1.0/gsaot/NAMESPACE | 2 gsaot-1.1.0/gsaot/NEWS.md | 14 + gsaot-1.1.0/gsaot/R/gsaot_indices.R | 247 ++++++++++++++++++++++++- gsaot-1.1.0/gsaot/R/ot_indices.R | 53 +++-- gsaot-1.1.0/gsaot/R/ot_indices_1d.R | 25 +- gsaot-1.1.0/gsaot/R/ot_indices_bw.R | 25 +- gsaot-1.1.0/gsaot/R/ot_indices_smap.R | 2 gsaot-1.1.0/gsaot/R/plot_functions.R | 18 + gsaot-1.1.0/gsaot/R/test_functions.R | 4 gsaot-1.1.0/gsaot/R/utils.R | 4 gsaot-1.1.0/gsaot/README.md | 36 +-- gsaot-1.1.0/gsaot/build/partial.rdb |binary gsaot-1.1.0/gsaot/man/confint.gsaot_indices.Rd |only gsaot-1.1.0/gsaot/man/entropic_bound.Rd | 2 gsaot-1.1.0/gsaot/man/irrelevance_threshold.Rd | 2 gsaot-1.1.0/gsaot/man/ishi_homma_fun.Rd | 2 gsaot-1.1.0/gsaot/man/ot_indices.Rd | 22 +- gsaot-1.1.0/gsaot/man/ot_indices_1d.Rd | 26 +- gsaot-1.1.0/gsaot/man/ot_indices_smap.Rd | 4 gsaot-1.1.0/gsaot/man/ot_indices_wb.Rd | 26 +- gsaot-1.1.0/gsaot/man/plot.gsaot_indices.Rd | 2 gsaot-1.1.0/gsaot/man/plot_separations.Rd | 2 gsaot-1.1.0/gsaot/man/print.gsaot_indices.Rd | 4 gsaot-1.1.0/gsaot/man/sobol_fun.Rd | 2 gsaot-1.1.0/gsaot/man/summary.gsaot_indices.Rd |only 28 files changed, 446 insertions(+), 135 deletions(-)
Title: Linear and Nonlinear Methods for Analyzing Daily and Monthly
Dendroclimatological Data
Description: Provides novel dendroclimatological methods, primarily used by the
Tree-ring research community. There are four core functions. The first one is
daily_response(), which finds the optimal sequence of days that are related
to one or more tree-ring proxy records. Similar function is daily_response_seascorr(),
which implements partial correlations in the analysis of daily response functions.
For the enthusiast of monthly data, there is monthly_response() function.
The last core function is compare_methods(), which effectively compares several
linear and nonlinear regression algorithms on the task of climate reconstruction.
Author: Jernej Jevsenak [aut, cre]
Maintainer: Jernej Jevsenak <jernej.jevsenak@gmail.com>
Diff between dendroTools versions 1.2.14 dated 2025-06-03 and 1.2.15 dated 2025-07-18
DESCRIPTION | 6 - MD5 | 20 ++--- NEWS.md | 3 R/daily_response.R | 24 +++--- R/daily_response_seascorr.R | 16 ++-- R/monthly_response.R | 76 ++++++++++++++------- R/monthly_response_seascorr.R | 72 ++++++++++++++----- inst/doc/Compare_different_regression_methods.html | 4 - inst/doc/Examples_with_daily_climate_data.html | 4 - man/monthly_response.Rd | 4 - man/monthly_response_seascorr.Rd | 6 - 11 files changed, 151 insertions(+), 84 deletions(-)
Title: Reading, Quality Control and Preprocessing of MBA (Multiplex
Bead Assay) Data
Description: Speeds up the process of loading raw data from MBA (Multiplex Bead Assay) examinations, performs quality control checks, and automatically normalises the data, preparing it for more advanced, downstream tasks. The main objective of the package is to create a simple environment for a user, who does not necessarily have experience with R language. The package is developed within the project 'PvSTATEM', which is an international project aiming for malaria elimination.
Author: Tymoteusz Kwiecinski [aut, cre] ,
Jakub Grzywaczewski [aut],
Mateusz Nizwantowski [aut],
Przemyslaw Biecek [ths] ,
Nuno Sepulveda [ths]
Maintainer: Tymoteusz Kwiecinski <tymoteuszkwiecinski@gmail.com>
Diff between SerolyzeR versions 1.2.0 dated 2025-05-06 and 1.3.0 dated 2025-07-18
DESCRIPTION | 8 MD5 | 110 ++++++----- NAMESPACE | 2 R/classes-model.R | 20 +- R/classes-plate.R | 31 +-- R/classes-plate_builder.R | 29 ++- R/config.R | 5 R/generate_report.R | 42 +++- R/get-nmfi.R | 52 ++++- R/helpers.R | 49 +++++ R/merge-plate-outputs.R |only R/parser.R | 128 ++++++++++++- R/plots-levey_jennings.R | 103 +++++++++- R/plots-mfi.R | 3 R/plots-standard_curve.R | 118 +++++++++--- R/process-dir.R | 85 ++++---- R/process-file.R | 11 - R/process-plate.R | 149 ++++++++------- build/partial.rdb |only build/vignette.rds |binary inst/doc/example_script.Rmd | 28 +- inst/doc/example_script.html | 182 +++++++++---------- inst/extdata/CovidOISExPONTENT_CO_layout.xlsx |binary inst/extdata/CovidOISExPONTENT_layout_duplicates.csv |only inst/extdata/random.csv | 2 inst/templates/levey_jennings_report_template.Rmd | 49 ++++- inst/templates/plate_report_template.Rmd | 49 ++++- man/Model.Rd | 16 + man/Plate.Rd | 18 + man/PlateBuilder.Rd | 5 man/extract_xponent_experiment_date.Rd |only man/filter_sample_types.Rd |only man/generate_levey_jennings_report.Rd | 12 + man/generate_plate_report.Rd | 10 - man/get_nmfi.Rd | 44 +++- man/handle_high_dose_hook.Rd | 6 man/macros |only man/merge_plate_outputs.Rd |only man/plot_levey_jennings.Rd | 34 +++ man/plot_mfi_for_analyte.Rd | 5 man/plot_standard_curve_analyte.Rd | 8 man/plot_standard_curve_analyte_with_model.Rd | 3 man/plot_standard_curve_stacked.Rd | 37 +++ man/process_dir.Rd | 11 - man/process_file.Rd | 10 - man/process_plate.Rd | 135 +++++++------- man/read_luminex_data.Rd | 36 ++- man/translate_sample_names_to_sample_types.Rd | 5 tests/testthat/Rplots.pdf |only tests/testthat/normalised_data |only tests/testthat/test-get-nmfi.R | 2 tests/testthat/test-helpers.R | 58 ++++++ tests/testthat/test-integration.R | 35 +++ tests/testthat/test-merge-plate-outputs.R |only tests/testthat/test-parser.R | 38 +++ tests/testthat/test-plate.R | 7 tests/testthat/test-plots-levey_jennings.R | 116 ++++++++++++ tests/testthat/test-plots-standard_curve.R | 44 ++++ tests/testthat/test-process-plate.R | 11 - vignettes/example_script.Rmd | 28 +- 60 files changed, 1452 insertions(+), 537 deletions(-)
Title: Data Base Backend for 'mlr3'
Description: Extends the 'mlr3' package with a backend to transparently
work with databases such as 'SQLite', 'DuckDB', 'MySQL', 'MariaDB', or
'PostgreSQL'. The package provides three additional backends:
'DataBackendDplyr' relies on the abstraction of package 'dbplyr' to
interact with most DBMS. 'DataBackendDuckDB' operates on 'DuckDB' data
bases and also on Apache Parquet files. 'DataBackendPolars' operates on
'Polars' data frames.
Author: Michel Lang [aut] ,
Lona Koers [aut],
Marc Becker [cre, aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3db versions 0.5.2 dated 2023-11-04 and 0.6.0 dated 2025-07-18
DESCRIPTION | 48 +++++++++++++++-------------- MD5 | 33 ++++++++++++------- NAMESPACE | 6 +++ NEWS.md | 19 ++++++----- R/DataBackendDplyr.R | 21 ++++-------- R/DataBackendDuckDB.R | 19 ++++------- R/DataBackendPolars.R |only R/as_duckdb_backend.R | 8 ++-- R/as_polars_backend.R |only R/as_sqlite_backend.R | 8 ++-- README.md | 37 +++++++++++++++------- man/DataBackendDplyr.Rd | 7 +--- man/DataBackendDuckDB.Rd | 5 --- man/DataBackendPolars.Rd |only man/as_duckdb_backend.Rd | 10 +++--- man/as_polars_backend.Rd |only man/as_sqlite_backend.Rd | 10 +++--- man/mlr3db-package.Rd | 5 +++ tests/testthat/test_as_polars_backend.R |only tests/testthat/test_polars.R |only tests/testthat/test_train_predict_polars.R |only 21 files changed, 129 insertions(+), 107 deletions(-)
Title: Calculating Heat Stress
Description: Implements the simpler and faster heat index, which matches the values of the original 1979 heat index and its 2022 extension for air temperatures above 300 K (27 C, 80 F) and with only minor differences at lower temperatures. Also implements an algorithm for calculating the thermodynamic (and psychrometric) wet-bulb (and ice-bulb) temperature.
Author: Yi-Chuan Lu [aut] ,
David M. Romps [aut, cre]
Maintainer: David M. Romps <romps@berkeley.edu>
Diff between heatindex versions 0.0.1 dated 2025-04-15 and 0.0.2 dated 2025-07-18
heatindex-0.0.1/heatindex/src/r_binding.cpp |only heatindex-0.0.2/heatindex/DESCRIPTION | 15 +- heatindex-0.0.2/heatindex/MD5 | 30 ++-- heatindex-0.0.2/heatindex/NAMESPACE | 2 heatindex-0.0.2/heatindex/R/RcppExports.R | 48 ++++++- heatindex-0.0.2/heatindex/R/heatindex.R | 14 +- heatindex-0.0.2/heatindex/R/rh_from_wetbulb.R |only heatindex-0.0.2/heatindex/R/wetbulb.R |only heatindex-0.0.2/heatindex/build/partial.rdb |binary heatindex-0.0.2/heatindex/man/heatindex.Rd | 8 - heatindex-0.0.2/heatindex/man/rh_from_wetbulb.Rd |only heatindex-0.0.2/heatindex/man/wetbulb.Rd |only heatindex-0.0.2/heatindex/src/RcppExports.cpp | 157 ++++++++++++++++++++++- heatindex-0.0.2/heatindex/src/bindings.cpp |only heatindex-0.0.2/heatindex/src/heatindex.cpp | 95 +++---------- heatindex-0.0.2/heatindex/src/heatindex.h | 15 +- heatindex-0.0.2/heatindex/src/lambert_w.cpp |only heatindex-0.0.2/heatindex/src/lambert_w.h |only heatindex-0.0.2/heatindex/src/solve.cpp |only heatindex-0.0.2/heatindex/src/solve.h |only heatindex-0.0.2/heatindex/src/thermo.cpp |only heatindex-0.0.2/heatindex/src/thermo.h |only 22 files changed, 273 insertions(+), 111 deletions(-)
Title: Extension to 'ggplot2'
Description: The R package 'ggplot2' is a plotting system based on the
grammar of graphics. 'GGally' extends 'ggplot2' by adding several
functions to reduce the complexity of combining geometric objects with
transformed data. Some of these functions include a pairwise plot
matrix, a two group pairwise plot matrix, a parallel coordinates plot,
a survival plot, and several functions to plot networks.
Author: Barret Schloerke [aut, cre] ,
Di Cook [aut, ths] ,
Joseph Larmarange [aut] ,
Francois Briatte [aut],
Moritz Marbach [aut],
Edwin Thoen [aut],
Amos Elberg [aut],
Ott Toomet [ctb],
Jason Crowley [aut],
Heike Hofmann [ths] ,
Hadley Wickham [ths]
Maintainer: Barret Schloerke <schloerke@gmail.com>
Diff between GGally versions 2.2.1 dated 2024-02-13 and 2.3.0 dated 2025-07-18
GGally-2.2.1/GGally/build/GGally.pdf |only GGally-2.2.1/GGally/man/gg-add.Rd |only GGally-2.2.1/GGally/man/require_namespaces.Rd |only GGally-2.2.1/GGally/tests/testthat/test-utils.R |only GGally-2.3.0/GGally/DESCRIPTION | 112 +- GGally-2.3.0/GGally/MD5 | 170 +-- GGally-2.3.0/GGally/NAMESPACE | 32 GGally-2.3.0/GGally/NEWS.md | 38 GGally-2.3.0/GGally/R/GGally-package.R | 17 GGally-2.3.0/GGally/R/data-australia-pisa-2012.R | 2 GGally-2.3.0/GGally/R/deprecated.R | 133 +- GGally-2.3.0/GGally/R/find-combo.R | 18 GGally-2.3.0/GGally/R/gg-plots.R | 618 ++++++------ GGally-2.3.0/GGally/R/ggally_colbar.R | 44 GGally-2.3.0/GGally/R/ggally_cross.R | 79 + GGally-2.3.0/GGally/R/ggaly_trends.R | 64 - GGally-2.3.0/GGally/R/ggbivariate.R | 18 GGally-2.3.0/GGally/R/ggcoef.R | 58 - GGally-2.3.0/GGally/R/ggcorr.R | 185 ++- GGally-2.3.0/GGally/R/ggfacet.R | 79 - GGally-2.3.0/GGally/R/gglyph.R | 120 +- GGally-2.3.0/GGally/R/ggmatrix.R | 186 ++- GGally-2.3.0/GGally/R/ggmatrix_gtable.R | 117 +- GGally-2.3.0/GGally/R/ggmatrix_gtable_helpers.R | 56 - GGally-2.3.0/GGally/R/ggmatrix_legend.R | 9 GGally-2.3.0/GGally/R/ggmatrix_make_plot.R | 4 GGally-2.3.0/GGally/R/ggmatrix_print.R | 11 GGally-2.3.0/GGally/R/ggmatrix_progress.R | 9 GGally-2.3.0/GGally/R/ggnet.R | 308 ++--- GGally-2.3.0/GGally/R/ggnet2.R | 396 +++---- GGally-2.3.0/GGally/R/ggnetworkmap.R | 173 +-- GGally-2.3.0/GGally/R/ggnostic.R | 326 +++--- GGally-2.3.0/GGally/R/ggpairs.R | 377 ++++--- GGally-2.3.0/GGally/R/ggpairs_add.R | 270 +++-- GGally-2.3.0/GGally/R/ggpairs_getput.R | 25 GGally-2.3.0/GGally/R/ggpairs_internal_plots.R | 105 +- GGally-2.3.0/GGally/R/ggparcoord.R | 310 ++++-- GGally-2.3.0/GGally/R/ggscatmat.R | 195 ++- GGally-2.3.0/GGally/R/ggsurv.R | 285 +++-- GGally-2.3.0/GGally/R/ggtable.R | 23 GGally-2.3.0/GGally/R/utils.R | 25 GGally-2.3.0/GGally/R/zzz.R |only GGally-2.3.0/GGally/README.md | 9 GGally-2.3.0/GGally/build/stage23.rdb |binary GGally-2.3.0/GGally/inst/WORDLIST | 124 +- GGally-2.3.0/GGally/man/GGally-package.Rd | 10 GGally-2.3.0/GGally/man/add_to_ggmatrix.Rd |only GGally-2.3.0/GGally/man/australia_PISA2012.Rd | 2 GGally-2.3.0/GGally/man/ggally_cor.Rd | 15 GGally-2.3.0/GGally/man/ggally_cor_v1_5.Rd | 11 GGally-2.3.0/GGally/man/ggduo.Rd | 4 GGally-2.3.0/GGally/man/ggmatrix_gtable.Rd | 2 GGally-2.3.0/GGally/man/ggnet.Rd | 23 GGally-2.3.0/GGally/man/ggpairs.Rd | 10 GGally-2.3.0/GGally/man/ggsurv.Rd | 2 GGally-2.3.0/GGally/man/is_ggmatrix.Rd |only GGally-2.3.0/GGally/man/print.ggmatrix.Rd | 3 GGally-2.3.0/GGally/man/reexports.Rd | 2 GGally-2.3.0/GGally/man/str.ggmatrix.Rd | 3 GGally-2.3.0/GGally/man/v1_ggmatrix_theme.Rd | 30 GGally-2.3.0/GGally/tests/spelling.R | 3 GGally-2.3.0/GGally/tests/testthat.R | 16 GGally-2.3.0/GGally/tests/testthat/helper-doppelganger.R |only GGally-2.3.0/GGally/tests/testthat/test-crosstalk.R | 1 GGally-2.3.0/GGally/tests/testthat/test-deprecated.R | 35 GGally-2.3.0/GGally/tests/testthat/test-gg-plots.R | 213 +++- GGally-2.3.0/GGally/tests/testthat/test-ggally_colbar.R | 121 +- GGally-2.3.0/GGally/tests/testthat/test-ggally_cross.R | 120 +- GGally-2.3.0/GGally/tests/testthat/test-ggally_trends.R | 65 - GGally-2.3.0/GGally/tests/testthat/test-ggbivariate.R | 26 GGally-2.3.0/GGally/tests/testthat/test-ggcoef.R | 19 GGally-2.3.0/GGally/tests/testthat/test-ggcorr.R | 74 - GGally-2.3.0/GGally/tests/testthat/test-ggfacet.R | 31 GGally-2.3.0/GGally/tests/testthat/test-gglegend.R | 44 GGally-2.3.0/GGally/tests/testthat/test-gglyph.R | 44 GGally-2.3.0/GGally/tests/testthat/test-ggmatrix.R | 88 + GGally-2.3.0/GGally/tests/testthat/test-ggmatrix_add.R | 27 GGally-2.3.0/GGally/tests/testthat/test-ggmatrix_getput.R | 14 GGally-2.3.0/GGally/tests/testthat/test-ggmatrix_location.R | 6 GGally-2.3.0/GGally/tests/testthat/test-ggnet.R | 134 +- GGally-2.3.0/GGally/tests/testthat/test-ggnet2.R | 74 + GGally-2.3.0/GGally/tests/testthat/test-ggnetworkmap.R | 192 ++- GGally-2.3.0/GGally/tests/testthat/test-ggnostic.R | 33 GGally-2.3.0/GGally/tests/testthat/test-ggparcoord.R | 307 ++++- GGally-2.3.0/GGally/tests/testthat/test-ggsave.R | 1 GGally-2.3.0/GGally/tests/testthat/test-ggscatmat.R | 38 GGally-2.3.0/GGally/tests/testthat/test-ggsurv.R | 33 GGally-2.3.0/GGally/tests/testthat/test-ggtable.R | 35 GGally-2.3.0/GGally/tests/testthat/test-wrap.R | 9 GGally-2.3.0/GGally/tests/testthat/test-zzz_ggpairs.R | 594 +++++++---- 90 files changed, 4800 insertions(+), 2844 deletions(-)
Title: Steve's Toy Data for Teaching About a Variety of Methodological,
Social, and Political Topics
Description: This is a collection of various kinds of data with broad uses for teaching.
My students, and academics like me who teach the same topics I teach, should find
this useful if their teaching workflow is also built around the R programming
language. The applications are multiple but mostly cluster on topics of statistical
methodology, international relations, and political economy.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steve@svmiller.com>
Diff between stevedata versions 1.5.0 dated 2025-01-24 and 1.6.0 dated 2025-07-18
DESCRIPTION | 9 ++++--- MD5 | 57 ++++++++++++++++++++++++++++---------------------- NEWS.md | 12 ++++++++++ R/rd-AJR5.R |only R/rd-ESS9GB.R | 2 - R/rd-OODTPT.R | 2 - R/rd-PRDEG.R | 2 - R/rd-TV16.R | 2 - R/rd-USFAHR.R | 2 - R/rd-asn_stats.R | 9 +++++-- R/rd-fakeAPI.R | 5 +++- R/rd-gatt_members.R |only R/rd-illiteracy30.R | 2 - R/rd-inglehart03.R | 2 - R/rd-rok_unga.R |only R/rd-wvs_ccodes.R | 2 - README.md | 10 ++++---- build/partial.rdb |binary data/AJR5.rda |only data/gatt_members.rda |only data/rok_unga.rda |only man/AJR5.Rd |only man/ESS9GB.Rd | 2 - man/OODTPT.Rd | 2 - man/PRDEG.Rd | 2 - man/TV16.Rd | 2 - man/USFAHR.Rd | 2 - man/asn_stats.Rd | 6 ++--- man/fakeAPI.Rd | 3 +- man/gatt_members.Rd |only man/illiteracy30.Rd | 2 - man/inglehart03.Rd | 2 - man/rok_unga.Rd |only man/wvs_ccodes.Rd | 2 - 34 files changed, 86 insertions(+), 57 deletions(-)
Title: Interface to the 'JWSACruncher' of 'JDemetra+'
Description: 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>) is the seasonal adjustment software officially recommended
to the members of the European Statistical System and the European System of Central Banks. Seasonal adjustment models performed
with 'JDemetra+' can be stored into workspaces. 'JWSACruncher' (<https://github.com/jdemetra/jwsacruncher/releases> for v2 and <https://github.com/jdemetra/jdplus-main/releases> for v3) is a console tool that
re-estimates all the multi-processing defined in a workspace and to export the result. 'rjwsacruncher' allows to launch easily the 'JWSACruncher'.
Author: Alain Quartier-la-Tente [aut, cre] ,
Institut national de la statistique et des etudes economiques [cph]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between rjwsacruncher versions 0.2.1 dated 2025-02-07 and 0.2.2 dated 2025-07-18
DESCRIPTION | 15 ++++++----- MD5 | 16 ++++++------ NEWS.md | 10 +++++++ R/param_file.R | 54 +++++++++++++++++++++++++---------------- inst/doc/run_jwsacruncher.R | 2 - inst/doc/run_jwsacruncher.Rmd | 2 - inst/doc/run_jwsacruncher.html | 6 ++-- man/create_param_file.Rd | 6 +++- vignettes/run_jwsacruncher.Rmd | 2 - 9 files changed, 70 insertions(+), 43 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-06-22 2.3.11
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-04-02 1.2.6
2024-03-18 1.2.5
2022-03-17 1.2.4
2020-03-21 1.2.3
2019-07-29 1.2.2
2018-06-15 1.2.1
2018-06-10 1.2.0
2018-01-03 1.1.2
2017-11-26 1.1.1
2017-10-22 1.1.0
2017-08-06 1.0.1
2017-08-05 1.0
Title: Snapshots for Unit Tests using the 'tinytest' Framework
Description: Snapshots for unit tests using the 'tinytest' framework for R. Includes expectations to test base R and 'ggplot2' plots as well as console output from print().
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinysnapshot versions 0.1.0 dated 2025-03-16 and 0.2.0 dated 2025-07-18
tinysnapshot-0.1.0/tinysnapshot/inst/tinytest/_tinysnapshot/png-ggplot2_theme.png |only tinysnapshot-0.1.0/tinysnapshot/inst/tinytest/_tinysnapshot/ragg-ggplot2_theme.png |only tinysnapshot-0.1.0/tinysnapshot/inst/tinytest/_tinysnapshot/svg-ggplot2_theme.svg |only tinysnapshot-0.1.0/tinysnapshot/inst/tinytest/_tinysnapshot/svglite-ggplot2_theme.svg |only tinysnapshot-0.2.0/tinysnapshot/DESCRIPTION | 10 tinysnapshot-0.2.0/tinysnapshot/MD5 | 54 - tinysnapshot-0.2.0/tinysnapshot/NEWS.md | 13 tinysnapshot-0.2.0/tinysnapshot/R/expect_snapshot_plot.R | 392 +++++---- tinysnapshot-0.2.0/tinysnapshot/R/expect_snapshot_print.R | 174 ++-- tinysnapshot-0.2.0/tinysnapshot/R/utils.R | 108 +- tinysnapshot-0.2.0/tinysnapshot/R/zzz.R | 11 tinysnapshot-0.2.0/tinysnapshot/README.md | 2 tinysnapshot-0.2.0/tinysnapshot/build/partial.rdb |binary tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/_tinysnapshot/png-ggplot2_variable.png |binary tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/_tinysnapshot/print-sub_label_fn.txt | 2 tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/_tinysnapshot/ragg-base.png |binary tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/_tinysnapshot/ragg-ggplot2_variable.png |binary tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/_tinysnapshot/svg-base.svg | 420 ++++------ tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/_tinysnapshot/svg-ggplot2_variable.svg | 284 +++--- tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/_tinysnapshot/svglite-base.svg | 34 tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/_tinysnapshot/svglite-ggplot2_variable.svg | 122 +- tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/helpers.R | 14 tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/test-options.R | 14 tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/test-png.R | 47 - tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/test-print.R | 15 tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/test-ragg.R | 31 tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/test-svg.R | 19 tinysnapshot-0.2.0/tinysnapshot/inst/tinytest/test-svglite.R | 26 tinysnapshot-0.2.0/tinysnapshot/man/expect_snapshot_plot.Rd | 9 tinysnapshot-0.2.0/tinysnapshot/tests/tinytest.R | 9 30 files changed, 978 insertions(+), 832 deletions(-)
Title: A Simple Way to Specify Symmetric, Block Diagonal Matrices
Description: Provides a simple mechanism to specify a symmetric block
diagonal matrices (often used for covariance matrices). This is based
on the domain specific language implemented in 'nlmixr2' but expanded
to create matrices in R generally instead of specifying parts of
matrices to estimate. It has expanded to include some matrix manipulation
functions that are generally useful for 'rxode2' and 'nlmixr2'.
Author: Matthew L. Fidler [aut, cre] ,
Bill Denney [ctb]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between lotri versions 1.0.0 dated 2024-09-18 and 1.0.1 dated 2025-07-18
DESCRIPTION | 11 +- MD5 | 34 +++--- NEWS.md | 4 R/as.data.frame.R | 6 + R/as.expression.R | 35 ++++++- R/as.lotri.R | 18 +++ R/lotri.R | 48 +++++++++ R/lotriMatInv.R | 16 +++ R/print.R | 8 + build/vignette.rds |binary inst/doc/lotri-motivation.html | 17 +-- src/matlist.h | 12 +- src/nearPD.cpp | 26 ++--- src/rcm.cpp | 129 +++++++++++++------------- tests/testthat/_snaps/as.data.frame.md | 35 +++++++ tests/testthat/test-as.data.frame.R | 47 ++++++--- tests/testthat/test-label.R | 46 +++++++++ tests/testthat/test-theta-lhs-as.expression.R | 114 ++++++++++++++++++++++ 18 files changed, 465 insertions(+), 141 deletions(-)