Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Tyson Barrett [aut, cre] ,
Matt Dowle [aut],
Arun Srinivasan [aut],
Jan Gorecki [aut],
Michael Chirico [aut] ,
Toby Hocking [aut] ,
Benjamin Schwendinger [aut] ,
Ivan Krylov [aut] ,
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduar [...truncated...]
Maintainer: Tyson Barrett <t.barrett88@gmail.com>
Diff between data.table versions 1.17.4 dated 2025-05-26 and 1.17.6 dated 2025-06-16
DESCRIPTION | 6 +- MD5 | 30 ++++++------ NEWS.md | 4 + inst/doc/datatable-benchmarking.html | 2 inst/doc/datatable-faq.html | 2 inst/doc/datatable-importing.html | 2 inst/doc/datatable-intro.html | 2 inst/doc/datatable-joins.html | 2 inst/doc/datatable-keys-fast-subset.html | 8 +-- inst/doc/datatable-programming.html | 2 inst/doc/datatable-reference-semantics.html | 2 inst/doc/datatable-reshape.html | 2 inst/doc/datatable-sd-usage.html | 2 inst/doc/datatable-secondary-indices-and-auto-indexing.html | 10 ++-- src/forder.c | 2 src/init.c | 2 16 files changed, 43 insertions(+), 37 deletions(-)
Title: Semiparametric Bayesian Regression Analysis
Description: Monte Carlo sampling algorithms for semiparametric
Bayesian regression analysis. These models feature a nonparametric
(unknown) transformation of the data paired with widely-used
regression models including linear regression, spline regression,
quantile regression, and Gaussian processes. The transformation
enables broader applicability of these key models, including for
real-valued, positive, and compactly-supported data with challenging
distributional features. The samplers prioritize computational
scalability and, for most cases, Monte Carlo (not MCMC) sampling for
greater efficiency. Details of the methods and algorithms are provided
in Kowal and Wu (2024) <doi:10.1080/01621459.2024.2395586>.
Author: Dan Kowal [aut, cre, cph]
Maintainer: Dan Kowal <daniel.r.kowal@gmail.com>
Diff between SeBR versions 1.0.0 dated 2023-07-03 and 1.1.0 dated 2025-06-16
DESCRIPTION | 18 - MD5 | 60 ++-- NAMESPACE | 20 + NEWS.md | 24 + R/helper_funs.R | 467 +++++++++++++++++++++++++++++++-- R/source_compete.R | 468 +++++++++++++++++++++++++++++---- R/source_sba.R | 611 ++++++++++++++++++++++++++++---------------- R/source_varsel.R |only README.md | 44 +-- build/vignette.rds |binary inst/doc/SeBR.R | 23 + inst/doc/SeBR.Rmd | 62 +++- inst/doc/SeBR.html | 465 +++++++++++++++++---------------- man/SSR_gprior.Rd |only man/all_subsets.Rd |only man/bb.Rd |only man/bgp_bc.Rd | 3 man/blm_bc.Rd | 7 man/blm_bc_hs.Rd |only man/bqr.Rd | 7 man/bsm_bc.Rd | 2 man/computeTimeRemaining.Rd | 16 - man/concen_hbb.Rd |only man/g_inv_bc.Rd | 5 man/hbb.Rd |only man/sampleFastGaussian.Rd |only man/sbgp.Rd | 20 + man/sblm.Rd | 28 +- man/sblm_hs.Rd |only man/sblm_modelsel.Rd |only man/sblm_ssvs.Rd |only man/sbqr.Rd | 16 + man/sbsm.Rd | 24 + man/simulate_tlm.Rd | 20 + man/sir_adjust.Rd | 21 + man/square_stabilize.Rd |only vignettes/SeBR.Rmd | 62 +++- 37 files changed, 1828 insertions(+), 665 deletions(-)
Title: N-Factor Commodity Pricing Through Term Structure Estimation
Description: Commodity pricing models are (systems of) stochastic differential equations that are utilized for the valuation and hedging of commodity contingent claims (i.e. derivative products on the commodity) and other commodity related investments. Commodity pricing models that capture market dynamics are of great importance to commodity market participants in order to exercise sound investment and risk-management strategies. Parameters of commodity pricing models are estimated through maximum likelihood estimation, using available term structure futures data of a commodity. 'NFCP' (n-factor commodity pricing) provides a framework for the modeling, parameter estimation, probabilistic forecasting, option valuation and simulation of commodity prices through state space and Monte Carlo methods, risk-neutral valuation and Kalman filtering. 'NFCP' allows the commodity pricing model to consist of n correlated factors, with both random walk and mean-reverting elements. The n-factor commodity pricing m [...truncated...]
Author: Thomas Aspinall [aut, cre] ,
Adrian Gepp [aut] ,
Geoff Harris [aut] ,
Simone Kelly [aut] ,
Colette Southam [aut] ,
Bruce Vanstone [aut]
Maintainer: Thomas Aspinall <tomaspinall2512@gmail.com>
Diff between NFCP versions 1.2.1 dated 2022-02-17 and 1.2.2 dated 2025-06-16
NFCP-1.2.1/NFCP/build/NFCP.pdf |only NFCP-1.2.2/NFCP/DESCRIPTION | 23 NFCP-1.2.2/NFCP/MD5 | 32 NFCP-1.2.2/NFCP/NAMESPACE | 2 NFCP-1.2.2/NFCP/NEWS.md | 120 +-- NFCP-1.2.2/NFCP/R/Kalman_filter.R | 1258 ++++++++++++++++----------------- NFCP-1.2.2/NFCP/R/NFCP-package.R |only NFCP-1.2.2/NFCP/R/NFCPdescription.R | 58 - NFCP-1.2.2/NFCP/R/analysis.R | 190 ++--- NFCP-1.2.2/NFCP/R/data_description.R | 102 +- NFCP-1.2.2/NFCP/R/dependencies.R | 1206 +++++++++++++++---------------- NFCP-1.2.2/NFCP/R/option_valuation.R | 806 ++++++++++----------- NFCP-1.2.2/NFCP/R/simulations.R | 1330 +++++++++++++++++------------------ NFCP-1.2.2/NFCP/README.md | 64 - NFCP-1.2.2/NFCP/build/stage23.rdb |only NFCP-1.2.2/NFCP/build/vignette.rds |binary NFCP-1.2.2/NFCP/inst/doc/NFCP.R | 4 NFCP-1.2.2/NFCP/inst/doc/NFCP.html | 836 ++++++++++------------ NFCP-1.2.2/NFCP/man/NFCP-package.Rd |only 19 files changed, 3010 insertions(+), 3021 deletions(-)
Title: Marginal Structural Models with Latent Class Growth Analysis of
Treatment Trajectories
Description: Implements marginal structural models combined with a latent class growth analysis framework for assessing the causal effect of treatment trajectories. Based on the approach described in "Marginal Structural Models with Latent Class Growth Analysis of Treatment Trajectories" Diop, A., Sirois, C., Guertin, J.R., Schnitzer, M.E., Candas, B., Cossette, B., Poirier, P., Brophy, J., Mésidor, M., Blais, C. and Hamel, D., (2023) <doi:10.1177/09622802231202384>.
Author: Awa Diop [aut, cre],
Denis Talbot [aut]
Maintainer: Awa Diop <awa.diop.2@ulaval.ca>
Diff between trajmsm versions 0.1.3 dated 2024-10-05 and 0.1.4 dated 2025-06-16
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NAMESPACE | 11 ++++++++++- R/ggtraj.R | 3 ++- R/split_data.R | 2 ++ R/trajmsm_ipw.R | 3 ++- README.md | 6 +++--- man/split_data.Rd | 2 ++ 8 files changed, 31 insertions(+), 16 deletions(-)
Title: Bayesian Exposure-Response Analysis Tools
Description: Suite of tools that facilitate
exposure-response analysis using Bayesian methods. The package
provides a streamlined workflow for fitting types of models that are
commonly used in exposure-response analysis - linear and Emax for continuous
endpoints, logistic linear and logistic Emax for binary endpoints, as well
as performing simulation and visualization. Learn more about the workflow
at <https://genentech.github.io/BayesERbook/>.
Author: Kenta Yoshida [aut, cre] ,
Francois Mercier [aut] ,
Danielle Navarro [aut] ,
Genentech, Inc. [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between BayesERtools versions 0.2.2 dated 2025-06-06 and 0.2.3 dated 2025-06-16
DESCRIPTION | 9 ++++++--- MD5 | 28 ++++++++++++++-------------- NEWS.md | 8 ++++++++ R/coveff.R | 7 ++++--- R/plot_ermod.R | 9 ++++++--- R/plot_ermod_exp_cov_sel.R | 3 ++- README.md | 2 +- man/BayesERtools-package.Rd | 1 + man/figures/README-ermod_bin-1.png |binary man/figures/README-ermod_bin_cov_sel-1.png |binary man/figures/README-plot_coveff-1.png |binary man/plot_er.Rd | 3 ++- man/plot_er_exp_sel.Rd | 3 ++- man/plot_er_gof.Rd | 4 +++- tests/testthat/Rplots.pdf |binary 15 files changed, 49 insertions(+), 28 deletions(-)
Title: Simulation of Sediment Archived Climate Proxy Records
Description: Proxy forward modelling for sediment archived climate proxies such
as Mg/Ca, d18O or Alkenones. The user provides a hypothesised "true" past climate,
such as output from a climate model, and details of the sedimentation rate and
sampling scheme of a sediment core. Sedproxy returns simulated proxy records.
Implements the methods described in Dolman and Laepple (2018)
<doi:10.5194/cp-14-1851-2018>.
Author: Thomas Laepple [aut],
Andrew Dolman [aut, cre]
Maintainer: Andrew Dolman <andrew.dolman@awi.de>
Diff between sedproxy versions 0.7.5 dated 2023-02-26 and 0.7.6 dated 2025-06-16
DESCRIPTION | 8 LICENSE | 4 MD5 | 88 - NAMESPACE | 28 NEWS.md | 160 + R/BioturbationWeights.R | 120 - R/ClimToProxyClim.R | 2020 ++++++++++++------------- R/GrowthfT.R | 150 - R/PlotPFMs.R | 370 ++-- R/calib.functions.R | 474 ++--- R/document-example-data.R | 258 +-- R/sedproxy.R | 51 build/partial.rdb |binary build/vignette.rds |binary inst/doc/effect-of-climate-dependent-flux.R | 348 ++-- inst/doc/effect-of-climate-dependent-flux.Rmd | 496 +++--- inst/doc/effect-of-climate-dependent-flux.html | 1191 +++++++------- inst/doc/introduction-to-sedproxy.R | 376 ++-- inst/doc/introduction-to-sedproxy.Rmd | 630 +++---- inst/doc/introduction-to-sedproxy.html | 1413 ++++++++--------- man/BioturbationWeights.Rd | 114 - man/ClimToProxyClim.Rd | 448 ++--- man/ForamGrowthfT.Rd | 96 - man/MakePFMDataframe.Rd | 40 man/N41.G.ruber.seasonality.Rd | 44 man/N41.proxy.Rd | 76 man/N41.proxy.details.Rd | 82 - man/N41.t21k.climate.Rd | 48 man/PlotPFMs.Rd | 124 - man/ProxyConversion.Rd | 200 +- man/example.data.Rd | 38 man/figures/README-MgCa_plot-1.svg | 1369 ++++++++-------- man/figures/README-default_plot-1.svg | 881 +++++----- man/figures/README-plot_reps-1.svg | 627 +++---- man/gisp2.ann.Rd | 66 man/param.tab.Rd | 44 man/scussolini.tab1.Rd | 44 man/sedproxy.Rd | 36 man/stages.key.Rd | 50 tests/testthat.R | 8 tests/testthat/test-ClimToProxyClim.R | 677 ++++---- tests/testthat/test-ProxyConversion.R | 108 - tests/testthat/test-growth_rate_l09_R.R | 116 - vignettes/effect-of-climate-dependent-flux.Rmd | 496 +++--- vignettes/introduction-to-sedproxy.Rmd | 630 +++---- 45 files changed, 7325 insertions(+), 7322 deletions(-)
Title: A Dependency Management System for Projects and their R Package
Dependencies
Description: Manage the R packages your project depends on in an isolated,
portable, and reproducible way.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Kevin Ushey [aut],
Jonathan McPherson [aut],
Joe Cheng [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between packrat versions 0.9.2 dated 2023-09-05 and 0.9.3 dated 2025-06-16
DESCRIPTION | 10 MD5 | 28 - R/downloader.R | 4 R/pkg.R | 14 R/renv.R | 6 R/restore.R | 167 ++++--- R/update.R | 9 README.md | 6 inst/resources/init-rprofile.R | 2 inst/resources/init.R | 2 inst/vendor/renv.R | 623 ++++++++++++++++++---------- tests/test-cranlike-repositories.R | 17 tests/testthat/packages/packrat/DESCRIPTION | 8 tests/testthat/test-packrat.R | 25 - tests/testthat/test-restore.R | 29 + 15 files changed, 601 insertions(+), 349 deletions(-)
Title: Composable Preprocessing Operators and Pipelines for Machine
Learning
Description: Toolset that enriches 'mlr' with a diverse set of preprocessing
operators. Composable Preprocessing Operators ("CPO"s) are first-class
R objects that can be applied to data.frames and 'mlr' "Task"s to modify
data, can be attached to 'mlr' "Learner"s to add preprocessing to machine
learning algorithms, and can be composed to form preprocessing pipelines.
Author: Martin Binder [aut, cre],
Bernd Bischl [ctb],
Michel Lang [ctb],
Lars Kotthoff [ctb]
Maintainer: Martin Binder <developer.mb706@doublecaret.com>
Diff between mlrCPO versions 0.3.7-7 dated 2024-02-20 and 0.3.8 dated 2025-06-16
mlrCPO-0.3.7-7/mlrCPO/man/cpoFilterRfSRCMinDepth.Rd |only mlrCPO-0.3.8/mlrCPO/DESCRIPTION | 8 mlrCPO-0.3.8/mlrCPO/MD5 | 211 - mlrCPO-0.3.8/mlrCPO/NAMESPACE | 1 mlrCPO-0.3.8/mlrCPO/NEWS | 3 mlrCPO-0.3.8/mlrCPO/R/CPO_applyFun.R | 2 mlrCPO-0.3.8/mlrCPO/R/CPO_filterFeatures.R | 23 mlrCPO-0.3.8/mlrCPO/R/CPO_impute.R | 8 mlrCPO-0.3.8/mlrCPO/R/ParamSetSugar.R | 14 mlrCPO-0.3.8/mlrCPO/R/RandomForestSRC.R | 48 mlrCPO-0.3.8/mlrCPO/R/inverter.R | 2 mlrCPO-0.3.8/mlrCPO/R/makeCPOHelp.R | 2 mlrCPO-0.3.8/mlrCPO/README.md | 2 mlrCPO-0.3.8/mlrCPO/inst/doc/a_1_getting_started.html | 1082 ++++------ mlrCPO-0.3.8/mlrCPO/inst/doc/a_2_mlrCPO_core.R | 10 mlrCPO-0.3.8/mlrCPO/inst/doc/a_2_mlrCPO_core.html | 4 mlrCPO-0.3.8/mlrCPO/inst/doc/a_3_all_CPOs.R | 6 mlrCPO-0.3.8/mlrCPO/inst/doc/a_3_all_CPOs.html | 140 - mlrCPO-0.3.8/mlrCPO/inst/doc/a_4_custom_CPOs.R | 2 mlrCPO-0.3.8/mlrCPO/inst/doc/a_4_custom_CPOs.html | 18 mlrCPO-0.3.8/mlrCPO/inst/doc/z_1_getting_started_terse.R | 262 +- mlrCPO-0.3.8/mlrCPO/inst/doc/z_1_getting_started_terse.html | 4 mlrCPO-0.3.8/mlrCPO/inst/doc/z_2_mlrCPO_core_terse.R | 352 +-- mlrCPO-0.3.8/mlrCPO/inst/doc/z_2_mlrCPO_core_terse.html | 4 mlrCPO-0.3.8/mlrCPO/inst/doc/z_3_all_CPOs_terse.R | 250 +- mlrCPO-0.3.8/mlrCPO/inst/doc/z_3_all_CPOs_terse.html | 4 mlrCPO-0.3.8/mlrCPO/inst/doc/z_4_custom_CPOs_terse.R | 720 +++--- mlrCPO-0.3.8/mlrCPO/inst/doc/z_4_custom_CPOs_terse.html | 4 mlrCPO-0.3.8/mlrCPO/man/CPOConstructor.Rd | 2 mlrCPO-0.3.8/mlrCPO/man/CPOLearner.Rd | 2 mlrCPO-0.3.8/mlrCPO/man/CPOTrained.Rd | 2 mlrCPO-0.3.8/mlrCPO/man/NULLCPO.Rd | 2 mlrCPO-0.3.8/mlrCPO/man/attachCPO.Rd | 2 mlrCPO-0.3.8/mlrCPO/man/composeCPO.Rd | 2 mlrCPO-0.3.8/mlrCPO/man/cpoApplyFun.Rd | 13 mlrCPO-0.3.8/mlrCPO/man/cpoApplyFunRegrTarget.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoAsNumeric.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoCache.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoCbind.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoCollapseFact.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoDropConstants.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoDropMostlyConstants.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoDummyEncode.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoFilterAnova.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterCarscore.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterChiSquared.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterFeatures.Rd | 25 mlrCPO-0.3.8/mlrCPO/man/cpoFilterGainRatio.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterInformationGain.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterKruskal.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterLinearCorrelation.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterMrmr.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterOneR.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterPermutationImportance.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterRankCorrelation.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterRelief.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterRfCImportance.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterRfImportance.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterRfSRCImportance.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterSymmetricalUncertainty.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterUnivariate.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFilterVariance.Rd | 16 mlrCPO-0.3.8/mlrCPO/man/cpoFixFactors.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoIca.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoImpactEncodeClassif.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoImpactEncodeRegr.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoImpute.Rd | 17 mlrCPO-0.3.8/mlrCPO/man/cpoImputeConstant.Rd | 19 mlrCPO-0.3.8/mlrCPO/man/cpoImputeHist.Rd | 19 mlrCPO-0.3.8/mlrCPO/man/cpoImputeLearner.Rd | 23 mlrCPO-0.3.8/mlrCPO/man/cpoImputeMax.Rd | 19 mlrCPO-0.3.8/mlrCPO/man/cpoImputeMean.Rd | 19 mlrCPO-0.3.8/mlrCPO/man/cpoImputeMedian.Rd | 19 mlrCPO-0.3.8/mlrCPO/man/cpoImputeMin.Rd | 19 mlrCPO-0.3.8/mlrCPO/man/cpoImputeMode.Rd | 19 mlrCPO-0.3.8/mlrCPO/man/cpoImputeNormal.Rd | 19 mlrCPO-0.3.8/mlrCPO/man/cpoImputeUniform.Rd | 19 mlrCPO-0.3.8/mlrCPO/man/cpoLogTrafoRegr.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoMakeCols.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoMissingIndicators.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoModelMatrix.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoOversample.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoPca.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoProbEncode.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoQuantileBinNumerics.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoRegrResiduals.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoResponseFromSE.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoSample.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoScale.Rd | 13 mlrCPO-0.3.8/mlrCPO/man/cpoScaleMaxAbs.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoScaleRange.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoSelect.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoSmote.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoSpatialSign.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoTransformParams.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/cpoWrap.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/getCPOClass.Rd | 2 mlrCPO-0.3.8/mlrCPO/man/getCPOConstructor.Rd | 2 mlrCPO-0.3.8/mlrCPO/man/getCPOTrainedCPO.Rd | 2 mlrCPO-0.3.8/mlrCPO/man/grapes-greater-than-greater-than-grapes.Rd | 2 mlrCPO-0.3.8/mlrCPO/man/identicalCPO.Rd | 2 mlrCPO-0.3.8/mlrCPO/man/invert.Rd | 2 mlrCPO-0.3.8/mlrCPO/man/makeCPO.Rd | 2 mlrCPO-0.3.8/mlrCPO/man/makeCPOCase.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/makeCPOMultiplex.Rd | 15 mlrCPO-0.3.8/mlrCPO/man/pSS.Rd | 14 mlrCPO-0.3.8/mlrCPO/man/randomForestSRC_filters.Rd | 28 107 files changed, 2051 insertions(+), 2233 deletions(-)
Title: Biological Analysis and Visualization of Weather Radar Data
Description: Extract, visualize and summarize aerial movements of birds and
insects from weather radar data. See Dokter, A. M. et al. (2018)
"bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028>
for a software paper describing package and methodologies.
Author: Adriaan M. Dokter [aut, cre] ,
Peter Desmet [aut] ,
Bart Kranstauber [aut] ,
Cecilia Nilsson [aut] ,
Stijn Van Hoey [aut] ,
Bart Hoekstra [ctb] ,
Pieter Huybrechts [ctb] ,
Hidde Leijnse [ctb] ,
Nicolas Noe [ctb] ,
Raphael Nussbaumer [ctb] ,
Jurriaan [...truncated...]
Maintainer: Adriaan M. Dokter <biorad@cornell.edu>
Diff between bioRad versions 0.9.1 dated 2025-04-05 and 0.10.0 dated 2025-06-16
bioRad-0.10.0/bioRad/DESCRIPTION | 43 ++++---- bioRad-0.10.0/bioRad/MD5 | 49 +++++----- bioRad-0.10.0/bioRad/NAMESPACE | 1 bioRad-0.10.0/bioRad/NEWS.md | 35 +++++-- bioRad-0.10.0/bioRad/R/bioRad-package.R |only bioRad-0.10.0/bioRad/R/calculate_vp.R | 20 ++-- bioRad-0.10.0/bioRad/R/download_pvolfiles.R | 25 ++++- bioRad-0.10.0/bioRad/R/download_vpfiles.R | 11 +- bioRad-0.10.0/bioRad/R/integrate_to_ppi.R | 26 ++--- bioRad-0.10.0/bioRad/R/list_vpts_aloft.R | 8 + bioRad-0.10.0/bioRad/R/project_as_ppi.R | 6 - bioRad-0.10.0/bioRad/README.md | 4 bioRad-0.10.0/bioRad/inst/doc/bioRad.html | 2 bioRad-0.10.0/bioRad/inst/doc/range_correction.html | 15 +-- bioRad-0.10.0/bioRad/man/bioRad-package.Rd | 2 bioRad-0.10.0/bioRad/man/download_pvolfiles.Rd | 8 + bioRad-0.10.0/bioRad/man/download_vpfiles.Rd | 8 + bioRad-0.10.0/bioRad/man/figures/lifecycle-archived.svg |only bioRad-0.10.0/bioRad/man/figures/lifecycle-defunct.svg |only bioRad-0.10.0/bioRad/man/figures/lifecycle-deprecated.svg |only bioRad-0.10.0/bioRad/man/figures/lifecycle-experimental.svg |only bioRad-0.10.0/bioRad/man/figures/lifecycle-maturing.svg |only bioRad-0.10.0/bioRad/man/figures/lifecycle-questioning.svg |only bioRad-0.10.0/bioRad/man/figures/lifecycle-soft-deprecated.svg |only bioRad-0.10.0/bioRad/man/figures/lifecycle-stable.svg |only bioRad-0.10.0/bioRad/man/figures/lifecycle-superseded.svg |only bioRad-0.10.0/bioRad/man/integrate_to_ppi.Rd | 41 ++++---- bioRad-0.10.0/bioRad/man/list_vpts_aloft.Rd | 6 - bioRad-0.10.0/bioRad/tests/testthat/test-download_vpfiles.R | 1 bioRad-0.10.0/bioRad/tests/testthat/test-list_vpts_aloft.R | 9 + bioRad-0.9.1/bioRad/R/bioRad.R |only 31 files changed, 206 insertions(+), 114 deletions(-)
Title: 1d Goodness of Fit Tests
Description: Routines that allow the user to run a large number of goodness-of-fit tests.
It allows for data to be continuous or discrete. It includes routines to estimate
the power of the tests and display them as a power graph.
The routine run.studies allows a user to quickly study the power of a new method and
how it compares to some of the standard ones.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between Rgof versions 3.2.0 dated 2025-04-27 and 3.3.0 dated 2025-06-16
DESCRIPTION | 12 - MD5 | 40 +-- NAMESPACE | 1 NEWS.md | 3 R/gof_power.R | 91 +++++-- R/gof_test.R | 19 + R/gof_test_adjusted_pvalue.R | 13 - R/power_newtest.R | 20 - R/run.studies.R | 40 ++- R/signif.digits.R | 2 R/test_methods.R |only inst/doc/Rgof.R | 44 ++- inst/doc/Rgof.Rmd | 59 +++-- inst/doc/Rgof.html | 464 +++++++++++----------------------------- man/gof_power.Rd | 32 ++ man/gof_test.Rd | 9 man/gof_test_adjusted_pvalue.Rd | 9 man/power_newtest.Rd | 2 man/run.studies.Rd | 10 man/signif.digits.Rd | 2 man/test_methods.Rd |only vignettes/Rgof.Rmd | 59 +++-- 22 files changed, 440 insertions(+), 491 deletions(-)
Title: Various Methods for the Two Sample Problem
Description: The routine twosample_test() in this package runs the
two sample test using various test statistic. The p values are
found via permutation or large sample theory. The routine twosample_power() allows the
calculation of the power in various cases, and plot_power() draws the corresponding power graphs.
The routine run.studies allows a user to quickly study the power of a new method and
how it compares to some of the standard ones.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between R2sample versions 4.0.1 dated 2025-04-30 and 4.1.0 dated 2025-06-16
R2sample-4.0.1/R2sample/src/test.cpp |only R2sample-4.1.0/R2sample/DESCRIPTION | 6 R2sample-4.1.0/R2sample/MD5 | 49 +++--- R2sample-4.1.0/R2sample/NAMESPACE | 1 R2sample-4.1.0/R2sample/NEWS.md | 12 + R2sample-4.1.0/R2sample/R/RcppExports.R | 12 - R2sample-4.1.0/R2sample/R/powerR.R | 2 R2sample-4.1.0/R2sample/R/power_cont_LS.R | 2 R2sample-4.1.0/R2sample/R/power_newtest.R | 12 - R2sample-4.1.0/R2sample/R/run.studies.R | 12 + R2sample-4.1.0/R2sample/R/test_methods.R |only R2sample-4.1.0/R2sample/R/twosample_power.R | 51 +++++-- R2sample-4.1.0/R2sample/R/twosample_test.R | 18 +- R2sample-4.1.0/R2sample/R/twosample_test_adjusted_pvalue.R | 13 + R2sample-4.1.0/R2sample/inst/doc/R2sample.R | 2 R2sample-4.1.0/R2sample/inst/doc/R2sample.Rmd | 14 - R2sample-4.1.0/R2sample/inst/doc/R2sample.html | 53 +++---- R2sample-4.1.0/R2sample/man/power_newtest.Rd | 2 R2sample-4.1.0/R2sample/man/run.studies.Rd | 10 - R2sample-4.1.0/R2sample/man/test_methods.Rd |only R2sample-4.1.0/R2sample/man/twosample_power.Rd | 33 +++- R2sample-4.1.0/R2sample/man/twosample_test.Rd | 11 - R2sample-4.1.0/R2sample/man/twosample_test_adjusted_pvalue.Rd | 9 - R2sample-4.1.0/R2sample/src/RcppExports.cpp | 39 ++--- R2sample-4.1.0/R2sample/src/gen_sim_data.cpp | 71 +++++----- R2sample-4.1.0/R2sample/src/gen_sim_data.h | 4 R2sample-4.1.0/R2sample/vignettes/R2sample.Rmd | 14 - 27 files changed, 262 insertions(+), 190 deletions(-)
Title: Cross-Validating Regression Models
Description: Cross-validation methods of regression models that exploit features of various
modeling functions to improve speed. Some of the methods implemented in the package are
novel, as described in the package vignettes; for general introductions to cross-validation,
see, for example, Gareth James, Daniela Witten, Trevor Hastie, and Robert Tibshirani
(2021, ISBN 978-1-0716-1417-4, Secs. 5.1, 5.3), "An Introduction to Statistical Learning with
Applications in R, Second Edition", and Trevor Hastie, Robert Tibshirani,
and Jerome Friedman (2009, ISBN 978-0-387-84857-0, Sec. 7.10), "The Elements of Statistical
Learning, Second Edition".
Author: John Fox [aut] ,
Georges Monette [aut, cre]
Maintainer: Georges Monette <georges+cv@yorku.ca>
Diff between cv versions 2.0.3 dated 2024-09-22 and 2.0.4 dated 2025-06-16
DESCRIPTION | 10 MD5 | 66 NAMESPACE | 1 NEWS.md | 6 R/cv-mixed-models.R | 5 R/cv-utilities.R | 170 + R/cv.R | 39 R/cv.modList.R | 44 build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/cv-extend.R | 14 inst/doc/cv-extend.html | 27 inst/doc/cv-mixed.html | 27 inst/doc/cv-notes.html | 48 inst/doc/cv-selection.R | 11 inst/doc/cv-selection.html | 31 inst/doc/cv.R | 13 inst/doc/cv.Rmd | 18 inst/doc/cv.html | 956 +++++----- man/cv.Rd | 22 man/cv.merMod.Rd | 5 man/cvCompute.Rd | 21 vignettes/cv-notes_cache/html/__packages | 10 vignettes/cv-notes_cache/html/cv.lm.timings_e03718670033c66a4f3c39e76a71dbfc.RData |binary vignettes/cv-notes_cache/html/cv.lm.timings_e03718670033c66a4f3c39e76a71dbfc.rdb |binary vignettes/cv-notes_cache/html/cv.lm.timings_e03718670033c66a4f3c39e76a71dbfc.rdx |binary vignettes/cv-notes_cache/html/glm.timings_2b7c8d05fe831884caced4b0ec3053df.RData |binary vignettes/cv-notes_cache/html/glm.timings_2b7c8d05fe831884caced4b0ec3053df.rdx |binary vignettes/cv-selection_cache/html/__packages | 10 vignettes/cv-selection_cache/html/cvSelect-artificial-data_9ad06ef148cf54d6b84209620167407e.RData |binary vignettes/cv-selection_cache/html/cvSelect-artificial-data_9ad06ef148cf54d6b84209620167407e.rdb |binary vignettes/cv-selection_cache/html/cvSelect-artificial-data_9ad06ef148cf54d6b84209620167407e.rdx |binary vignettes/cv.Rmd | 18 vignettes/cv.bib | 2 34 files changed, 891 insertions(+), 685 deletions(-)
Title: Contextual Importance and Utility
Description: Implementation of the Contextual Importance and Utility
(CIU) concepts for Explainable AI (XAI). A description of CIU
can be found in e.g. Främling (2020) <doi:10.1007/978-3-030-51924-7_4>.
Author: Kary Fraemling [aut, cre]
Maintainer: Kary Fraemling <Kary.Framling@umu.se>
Diff between ciu versions 0.6.0 dated 2022-11-29 and 0.8 dated 2025-06-16
DESCRIPTION | 21 ++++++--- MD5 | 44 ++++++++++++-------- NAMESPACE | 5 ++ NEWS.md | 21 +++++++++ R/ContextualImportanceUtility.R | 78 ++++++++++++++++++++++++------------- R/ContextualInfluence.R |only R/MetaExplain.R | 2 R/ciu-package.r | 4 - R/ciu.R | 7 ++- R/ciu.ggplot.col.R | 56 +++++++++++--------------- R/ciu.plots.R |only R/ciu.result.R | 2 build |only inst/CITATION | 2 man/ciu-package.Rd | 11 ++--- man/ciu.contextual.influence.Rd |only man/ciu.contrastive.Rd |only man/ciu.explain.long.data.frame.Rd |only man/ciu.ggplot.Rd | 6 ++ man/ciu.ggplot.col.Rd | 5 +- man/ciu.ggplot.contrastive.Rd |only man/ciu.meta.explain.Rd | 2 man/ciu.meta.result.new.Rd | 2 man/ciu.new.Rd | 9 ---- man/ciu.plots.beeswarm.Rd |only man/ciu.result.new.Rd | 2 man/ciu.textual.Rd | 2 27 files changed, 169 insertions(+), 112 deletions(-)
Title: Automating Choosing Statistical Tests
Description: Automatically selects and runs the most appropriate statistical test for your data, returning clear, easy-to-read results. Ideal for all experience levels.
Author: Wouter Zeevat [aut, cre]
Maintainer: Wouter Zeevat <wouterzeevat@gmail.com>
Diff between automatedtests versions 0.1.1 dated 2025-05-21 and 0.1.2 dated 2025-06-16
DESCRIPTION | 6 MD5 | 31 ++-- NAMESPACE | 1 NEWS.md | 8 + R/automatical_test.R | 21 ++- R/class-AutomatedTest.R | 107 ++++++++++------ R/test-picker.R | 40 +++--- R/utils.R | 28 ++-- README.md | 27 ++-- inst/doc/automatical_test_vignette.R | 6 inst/doc/automatical_test_vignette.Rmd | 55 ++++---- inst/doc/automatical_test_vignette.html | 78 ++++++++--- man/AutomatedTest.Rd | 124 +++++++++---------- man/automatical_test.Rd | 17 +- man/figures/overview-statistical-tests-statsandr.jpg |only man/get_strength_from_test.Rd | 2 vignettes/automatical_test_vignette.Rmd | 55 ++++---- 17 files changed, 357 insertions(+), 249 deletions(-)
More information about automatedtests at CRAN
Permanent link
Title: Fit the Semiparametric Accelerated Failure Time Model with
Elastic Net and Sparse Group Lasso Penalties
Description: The semiparametric accelerated failure time (AFT) model is an attractive alternative to the Cox proportional hazards model. This package provides a suite of functions for fitting one popular rank-based estimator of the semiparametric AFT model, the regularized Gehan estimator. Specifically, we provide functions for cross-validation, prediction, coefficient extraction, and visualizing both trace plots and cross-validation curves. For further details, please see Suder, P. M. and Molstad, A. J., (2022) Scalable algorithms for semiparametric accelerated failure time models in high dimensions, Statistics in Medicine <doi:10.1002/sim.9264>.
Author: Aaron J. Molstad [aut, cre] ,
Piotr M. Suder [aut]
Maintainer: Aaron J. Molstad <amolstad@ufl.edu>
Diff between penAFT versions 0.3.0 dated 2023-04-17 and 0.3.2 dated 2025-06-16
penAFT-0.3.0/penAFT/README.md |only penAFT-0.3.2/penAFT/DESCRIPTION | 18 ++++++++++-------- penAFT-0.3.2/penAFT/MD5 | 13 ++++++------- penAFT-0.3.2/penAFT/man/penAFT-package.Rd | 6 +++--- penAFT-0.3.2/penAFT/man/penAFT.Rd | 4 ++-- penAFT-0.3.2/penAFT/man/penAFT.coef.Rd | 2 +- penAFT-0.3.2/penAFT/man/penAFT.cv.Rd | 6 +++--- penAFT-0.3.2/penAFT/man/penAFT.trace.Rd | 4 ++-- 8 files changed, 27 insertions(+), 26 deletions(-)
Title: Interactive Maps with 'Mapbox GL JS' and 'MapLibre GL JS'
Description: Provides an interface to the 'Mapbox GL JS' (<https://docs.mapbox.com/mapbox-gl-js/guides>)
and the 'MapLibre GL JS' (<https://maplibre.org/maplibre-gl-js/docs/>) interactive mapping libraries to help users
create custom interactive maps in R. Users can create interactive globe visualizations; layer 'sf' objects to create
filled maps, circle maps, 'heatmaps', and three-dimensional graphics; and customize map styles and views. The package
also includes utilities to use 'Mapbox' and 'MapLibre' maps in 'Shiny' web applications.
Author: Kyle Walker [aut, cre]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between mapgl versions 0.2.2 dated 2025-05-23 and 0.3 dated 2025-06-16
mapgl-0.2.2/mapgl/man/add_categorical_legend.Rd |only mapgl-0.2.2/mapgl/man/add_continuous_legend.Rd |only mapgl-0.2.2/mapgl/man/add_legend.Rd |only mapgl-0.2.2/mapgl/man/clear_legend.Rd |only mapgl-0.3/mapgl/DESCRIPTION | 8 mapgl-0.3/mapgl/MD5 | 78 mapgl-0.3/mapgl/NAMESPACE | 16 mapgl-0.3/mapgl/NEWS.md | 64 mapgl-0.3/mapgl/R/controls.R | 1579 ++- mapgl-0.3/mapgl/R/hover.R |only mapgl-0.3/mapgl/R/legends.R | 436 mapgl-0.3/mapgl/R/quickview.R | 1582 +-- mapgl-0.3/mapgl/R/shiny.R | 190 mapgl-0.3/mapgl/R/sources.R | 747 - mapgl-0.3/mapgl/R/style_helpers.R | 1451 ++ mapgl-0.3/mapgl/inst/htmlwidgets/lib/mapbox-gl-draw/mapbox-gl-draw.js | 2 mapgl-0.3/mapgl/inst/htmlwidgets/lib/maplibre-gl/maplibre-gl.js | 8 mapgl-0.3/mapgl/inst/htmlwidgets/lib/pmtiles/pmtiles.js | 1740 --- mapgl-0.3/mapgl/inst/htmlwidgets/mapboxgl.js | 5006 +++++----- mapgl-0.3/mapgl/inst/htmlwidgets/mapboxgl.yaml | 68 mapgl-0.3/mapgl/inst/htmlwidgets/mapboxgl_compare.js | 4705 ++++----- mapgl-0.3/mapgl/inst/htmlwidgets/maplibregl.js | 1465 ++ mapgl-0.3/mapgl/inst/htmlwidgets/maplibregl.yaml | 82 mapgl-0.3/mapgl/inst/htmlwidgets/maplibregl_compare.js | 976 + mapgl-0.3/mapgl/inst/htmlwidgets/maplibregl_compare.yaml | 92 mapgl-0.3/mapgl/man/add_draw_control.Rd | 44 mapgl-0.3/mapgl/man/add_features_to_draw.Rd |only mapgl-0.3/mapgl/man/add_raster_dem_source.Rd | 4 mapgl-0.3/mapgl/man/add_raster_source.Rd | 5 mapgl-0.3/mapgl/man/add_vector_source.Rd | 6 mapgl-0.3/mapgl/man/classification_helpers.Rd |only mapgl-0.3/mapgl/man/clear_drawn_features.Rd |only mapgl-0.3/mapgl/man/clear_layer.Rd | 6 mapgl-0.3/mapgl/man/concat.Rd |only mapgl-0.3/mapgl/man/enable_shiny_hover.Rd |only mapgl-0.3/mapgl/man/format_numbers.Rd |only mapgl-0.3/mapgl/man/interpolate_palette.Rd |only mapgl-0.3/mapgl/man/map_legends.Rd |only mapgl-0.3/mapgl/man/mapboxgl_view.Rd | 11 mapgl-0.3/mapgl/man/maplibre_view.Rd | 11 mapgl-0.3/mapgl/man/maptiler_style.Rd | 6 mapgl-0.3/mapgl/man/number_format.Rd |only mapgl-0.3/mapgl/man/set_layout_property.Rd | 6 mapgl-0.3/mapgl/man/set_paint_property.Rd | 6 mapgl-0.3/mapgl/man/set_popup.Rd |only mapgl-0.3/mapgl/man/set_source.Rd | 6 mapgl-0.3/mapgl/man/set_tooltip.Rd | 6 mapgl-0.3/mapgl/man/step_classification.Rd |only 48 files changed, 11837 insertions(+), 8575 deletions(-)
Title: Distribution of Gaussian Ratios
Description: It is well known that the distribution of a Gaussian ratio
does not follow a Gaussian distribution.
The lack of awareness among users of vegetation indices about this
non-Gaussian nature could lead to incorrect statistical modeling
and interpretation.
This package provides tools to accurately handle and analyse such
ratios: density function, parameter estimation, simulation.
An example on the study of chlorophyll fluorescence can be found in
A. El Ghaziri et al. (2023) <doi:10.3390/rs15020528>
and another method for parameter estimation is given in Bouhlel et al. (2023)
<doi:10.23919/EUSIPCO58844.2023.10290111>.
Author: Pierre Santagostini [aut, cre],
Angelina El Ghaziri [aut],
Nizar Bouhlel [aut],
David Rousseau [ctb]
Maintainer: Pierre Santagostini <pierre.santagostini@institut-agro.fr>
Diff between gaussratiovegind versions 2.0.1 dated 2025-05-15 and 2.0.3 dated 2025-06-16
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/estparnormratio.R | 31 ++++++++++++++++++++++++------- R/kummer.R | 3 +++ README.md | 2 +- man/gaussratiovegind-package.Rd | 4 ++-- tests/manual/test-estparVB_1.R | 2 +- tests/testthat/Rplots.pdf |binary tests/testthat/test-estparEM.R | 26 ++++++++++++++++++++++++++ tests/testthat/test-estparVB.R | 14 ++++++++++++++ 10 files changed, 85 insertions(+), 25 deletions(-)
More information about gaussratiovegind at CRAN
Permanent link
Title: Less Code, More Results
Description: Each function replaces multiple standard R functions. For example, two function calls, Read() and CountAll(), generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for summary statistics via pivot tables, a comprehensive regression analysis, ANOVA and t-test, visualizations including the Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, time series with aggregation and forecasting, color themes, and Trellis (facet) graphics. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, generation and rendering of regression instructions for interpretative output, and interactive visualizations.
Author: David W. Gerbing [aut, cre]
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 4.4.3 dated 2025-05-08 and 4.4.4 dated 2025-06-16
lessR-4.4.3/lessR/R/Density.R |only lessR-4.4.3/lessR/R/dn.R |only lessR-4.4.3/lessR/man/Density.Rd |only lessR-4.4.4/lessR/DESCRIPTION | 10 lessR-4.4.4/lessR/MD5 | 50 +- lessR-4.4.4/lessR/NAMESPACE | 3 lessR-4.4.4/lessR/NEWS.md | 61 ++ lessR-4.4.4/lessR/R/Histogram.R | 24 - lessR-4.4.4/lessR/R/Plot.R | 180 +++++++- lessR-4.4.4/lessR/R/dn.main.R | 174 ++++---- lessR-4.4.4/lessR/R/param.VBS.R | 603 ++++++++++++++--------------- lessR-4.4.4/lessR/R/pivot.R | 30 + lessR-4.4.4/lessR/R/plt.bubble.R | 7 lessR-4.4.4/lessR/R/plt.by.legend.R | 9 lessR-4.4.4/lessR/R/plt.contour.R | 40 + lessR-4.4.4/lessR/R/plt.lattice.R | 163 ++++--- lessR-4.4.4/lessR/R/plt.main.R | 84 ++-- lessR-4.4.4/lessR/R/plt.marg.R | 2 lessR-4.4.4/lessR/R/plt.panel.R | 10 lessR-4.4.4/lessR/R/plt.shapes.R | 63 +-- lessR-4.4.4/lessR/R/plt.sym.legend.R |only lessR-4.4.4/lessR/R/reshape_wide.R | 4 lessR-4.4.4/lessR/R/zzz.R | 167 ++++++-- lessR-4.4.4/lessR/inst/doc/intro.html | 701 ++++++++++++++++------------------ lessR-4.4.4/lessR/man/Histogram.Rd | 42 +- lessR-4.4.4/lessR/man/Plot.Rd | 80 ++- lessR-4.4.4/lessR/man/Regression.Rd | 6 lessR-4.4.4/lessR/man/reshape_wide.Rd | 7 28 files changed, 1458 insertions(+), 1062 deletions(-)
Title: Fast PCA for Large Pedigrees
Description: Carry out principal component analysis (PCA) of very large pedigrees such as found
in breeding populations! This package exploits sparse matrices and randomised
linear algebra to deliver a gazillion-times speed-up compared to naive singular value decoposition (SVD)
(and eigen decomposition).
Author: Hanbin Lee [aut],
Hannes Becher [cre],
Ros Craddock [aut],
Gregor Gorjanc [aut]
Maintainer: Hannes Becher <h.becher@ed.ac.uk>
Diff between randPedPCA versions 1.0.0 dated 2025-04-24 and 1.1.2 dated 2025-06-16
randPedPCA-1.0.0/randPedPCA/data/pedLinv.rda |only randPedPCA-1.1.2/randPedPCA/DESCRIPTION | 14 randPedPCA-1.1.2/randPedPCA/MD5 | 47 +- randPedPCA-1.1.2/randPedPCA/NAMESPACE | 1 randPedPCA-1.1.2/randPedPCA/R/data.R | 57 --- randPedPCA-1.1.2/randPedPCA/R/hutchpp.R | 14 randPedPCA-1.1.2/randPedPCA/R/rppca.R | 129 ++++--- randPedPCA-1.1.2/randPedPCA/R/utils.R | 18 randPedPCA-1.1.2/randPedPCA/build/vignette.rds |binary randPedPCA-1.1.2/randPedPCA/data/pedLInv.rda |only randPedPCA-1.1.2/randPedPCA/data/pedMeta.rda |binary randPedPCA-1.1.2/randPedPCA/inst/doc/pedigree-pca.R | 42 +- randPedPCA-1.1.2/randPedPCA/inst/doc/pedigree-pca.Rmd | 64 ++- randPedPCA-1.1.2/randPedPCA/inst/doc/pedigree-pca.html | 183 +++++----- randPedPCA-1.1.2/randPedPCA/man/hutchpp.Rd | 2 randPedPCA-1.1.2/randPedPCA/man/pedLInv.Rd | 12 randPedPCA-1.1.2/randPedPCA/man/pedLInv2.Rd | 2 randPedPCA-1.1.2/randPedPCA/man/pedLInv4.Rd | 2 randPedPCA-1.1.2/randPedPCA/man/pedMeta.Rd | 7 randPedPCA-1.1.2/randPedPCA/man/pedMeta2.Rd | 13 randPedPCA-1.1.2/randPedPCA/man/pedMeta4.Rd | 13 randPedPCA-1.1.2/randPedPCA/man/rppca.Rd | 22 - randPedPCA-1.1.2/randPedPCA/tests/testthat/Rplots.pdf |binary randPedPCA-1.1.2/randPedPCA/tests/testthat/test_rppca.R | 22 - randPedPCA-1.1.2/randPedPCA/tests/testthat/testthat-problems.rds |only randPedPCA-1.1.2/randPedPCA/vignettes/pedigree-pca.Rmd | 64 ++- 26 files changed, 375 insertions(+), 353 deletions(-)
Title: Tools for Environmental Analyses, Ecotoxicology and Various R
Functions
Description: Contains miscellaneous functions useful for managing 'NetCDF' files (see <https://en.wikipedia.org/wiki/NetCDF>), get moon phase and time for sun rise and fall, tide level, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between HelpersMG versions 6.5 dated 2025-05-09 and 6.6 dated 2025-06-16
HelpersMG-6.5/HelpersMG/R/sd_from_min_max.R |only HelpersMG-6.5/HelpersMG/man/sd_from_min_max.Rd |only HelpersMG-6.6/HelpersMG/DESCRIPTION | 8 ++++---- HelpersMG-6.6/HelpersMG/MD5 | 22 +++++++++++----------- HelpersMG-6.6/HelpersMG/NAMESPACE | 2 +- HelpersMG-6.6/HelpersMG/NEWS | 5 +++-- HelpersMG-6.6/HelpersMG/R/HelpersMG-package.R | 8 ++++---- HelpersMG-6.6/HelpersMG/R/MHalgoGen.R | 2 +- HelpersMG-6.6/HelpersMG/R/from_min_max.R |only HelpersMG-6.6/HelpersMG/R/sysdata.rda |binary HelpersMG-6.6/HelpersMG/inst/shiny/cutter/ui.R | 2 +- HelpersMG-6.6/HelpersMG/man/HelpersMG-package.Rd | 6 +++--- HelpersMG-6.6/HelpersMG/man/MHalgoGen.Rd | 2 +- HelpersMG-6.6/HelpersMG/man/from_min_max.Rd |only 14 files changed, 29 insertions(+), 28 deletions(-)
Title: Markov Models for Health Economic Evaluations
Description: An implementation of the modelling and reporting features described
in reference textbook and guidelines (Briggs, Andrew, et al. Decision
Modelling for Health Economic Evaluation. Oxford Univ. Press, 2011;
Siebert, U. et al. State-Transition Modeling. Medical Decision Making
32, 690-700 (2012).): deterministic and probabilistic sensitivity analysis,
heterogeneity analysis, time dependency on state-time and model-time
(semi-Markov and non-homogeneous Markov models), etc.
Author: Kevin Zarca [aut, cre],
Antoine Filipovic-Pierucci [aut],
Matthew Wiener [ctb],
Zdenek Kabat [ctb],
Vojtech Filipec [ctb],
Jordan Amdahl [ctb],
Yonatan Carranza Alarcon [ctb],
Vince Daniels [ctb]
Maintainer: Kevin Zarca <kevin.zarca@gmail.com>
Diff between heemod versions 1.0.2 dated 2024-09-11 and 1.1.0 dated 2025-06-16
DESCRIPTION | 17 - MD5 | 68 ++--- NAMESPACE | 3 NEWS.md | 4 R/gho_mortality.R | 169 ------------- R/heemod.R | 3 R/survival_eval.R | 4 build/vignette.rds |binary inst/doc/a_introduction.Rmd | 2 inst/doc/a_introduction.html | 30 +- inst/doc/b_time_dependency.html | 8 inst/doc/c_homogeneous.html | 18 - inst/doc/d_non_homogeneous.R | 2 inst/doc/d_non_homogeneous.Rmd | 2 inst/doc/d_non_homogeneous.html | 32 +- inst/doc/e_probabilistic.html | 8 inst/doc/f_sensitivity.html | 20 - inst/doc/g_heterogeneity.R | 2 inst/doc/g_heterogeneity.Rmd | 2 inst/doc/g_heterogeneity.html | 152 ++++++------ inst/doc/h_tabular.html | 116 ++++----- inst/doc/i_reproduction.html | 8 inst/doc/j_survival.html | 22 - inst/doc/j_survival_2_psa.html | 16 - inst/doc/k_calibration.R | 2 inst/doc/k_calibration.Rmd | 2 inst/doc/k_calibration.html | 464 ++++++++++++++++++++++++++++++++++++-- man/compute_surv.Rd | 5 man/eval_surv.Rd | 5 man/who_mortality.Rd | 39 --- tests/testthat/test_calibration.R | 2 vignettes/a_introduction.Rmd | 2 vignettes/d_non_homogeneous.Rmd | 2 vignettes/g_heterogeneity.Rmd | 2 vignettes/k_calibration.Rmd | 2 35 files changed, 734 insertions(+), 501 deletions(-)
Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms. See <doi:10.7717/peerj.8451> for tsd functions; see <doi:10.1016/j.jtherbio.2014.08.005> for thermal reaction norm of embryo growth.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between embryogrowth versions 9.5 dated 2024-08-23 and 10.2 dated 2025-06-16
embryogrowth-10.2/embryogrowth/DESCRIPTION | 13 embryogrowth-10.2/embryogrowth/MD5 | 138 +- embryogrowth-10.2/embryogrowth/NAMESPACE | 7 embryogrowth-10.2/embryogrowth/NEWS | 38 embryogrowth-10.2/embryogrowth/R/DatabaseTSD.R | 2 embryogrowth-10.2/embryogrowth/R/FormatNests.R | 291 ++++- embryogrowth-10.2/embryogrowth/R/GRTRN_MHmcmc.R | 89 + embryogrowth-10.2/embryogrowth/R/Generate_hatchling_metric.R | 85 - embryogrowth-10.2/embryogrowth/R/HeterogeneityNests.R |only embryogrowth-10.2/embryogrowth/R/P_TRT.R | 124 ++ embryogrowth-10.2/embryogrowth/R/ROSIE.version.R | 5 embryogrowth-10.2/embryogrowth/R/SSM.R | 18 embryogrowth-10.2/embryogrowth/R/STRN.R | 19 embryogrowth-10.2/embryogrowth/R/STRN_MHmcmc.R | 21 embryogrowth-10.2/embryogrowth/R/STRN_fit.R | 23 embryogrowth-10.2/embryogrowth/R/UpdateNests.R |only embryogrowth-10.2/embryogrowth/R/embryogrowth-package.R | 19 embryogrowth-10.2/embryogrowth/R/gradientRichardson.R | 2 embryogrowth-10.2/embryogrowth/R/hist.Nests.R | 151 +- embryogrowth-10.2/embryogrowth/R/hist.NestsResult.R | 15 embryogrowth-10.2/embryogrowth/R/info.nests.R | 149 ++ embryogrowth-10.2/embryogrowth/R/likelihoodR.R | 341 +++--- embryogrowth-10.2/embryogrowth/R/modelTSD.R | 74 + embryogrowth-10.2/embryogrowth/R/movement.R | 125 ++ embryogrowth-10.2/embryogrowth/R/plot.Nests.R |only embryogrowth-10.2/embryogrowth/R/plot.NestsResult.R | 61 - embryogrowth-10.2/embryogrowth/R/plot.tsd.R | 84 + embryogrowth-10.2/embryogrowth/R/plotR.R | 13 embryogrowth-10.2/embryogrowth/R/predict.tsd.R | 4 embryogrowth-10.2/embryogrowth/R/resultNest_mcmc_4p_SSM.R | 9 embryogrowth-10.2/embryogrowth/R/resultNest_mcmc_4p_SSM_Linear.R | 9 embryogrowth-10.2/embryogrowth/R/searchR.R | 126 +- embryogrowth-10.2/embryogrowth/R/summary.Nests.R | 28 embryogrowth-10.2/embryogrowth/R/tsd.R | 229 +++- embryogrowth-10.2/embryogrowth/R/tsd_MHmcmc.R | 23 embryogrowth-10.2/embryogrowth/R/tsd_MHmcmc_p.R | 179 +-- embryogrowth-10.2/embryogrowth/R/tsd_fit.R | 4 embryogrowth-10.2/embryogrowth/R/weightmaxentropy.R | 278 ++--- embryogrowth-10.2/embryogrowth/build/partial.rdb |binary embryogrowth-10.2/embryogrowth/data/DatabaseNestingArea.rda |binary embryogrowth-10.2/embryogrowth/data/DatabaseTSD.rda |binary embryogrowth-10.2/embryogrowth/data/ROSIE.rda |binary embryogrowth-10.2/embryogrowth/data/TSP.list.rda |binary embryogrowth-10.2/embryogrowth/data/resultNest_4p_SSM.rda |binary embryogrowth-10.2/embryogrowth/data/resultNest_4p_SSM_Linear.rda |binary embryogrowth-10.2/embryogrowth/data/resultNest_6p_SSM.rda |binary embryogrowth-10.2/embryogrowth/data/resultNest_mcmc_4p_SSM.rda |binary embryogrowth-10.2/embryogrowth/data/stages.rda |binary embryogrowth-10.2/embryogrowth/inst/REFERENCES.bib | 526 +++++----- embryogrowth-10.2/embryogrowth/man/DatabaseTSD.Rd | 2 embryogrowth-10.2/embryogrowth/man/FormatNests.Rd | 112 +- embryogrowth-10.2/embryogrowth/man/GRTRN_MHmcmc.Rd | 26 embryogrowth-10.2/embryogrowth/man/Generate_hatchling_metric.Rd | 4 embryogrowth-10.2/embryogrowth/man/HeterogeneityNests.Rd |only embryogrowth-10.2/embryogrowth/man/ROSIE.version.Rd | 2 embryogrowth-10.2/embryogrowth/man/STRN_MHmcmc.Rd | 3 embryogrowth-10.2/embryogrowth/man/UpdateNests.Rd |only embryogrowth-10.2/embryogrowth/man/embryogrowth-package.Rd | 19 embryogrowth-10.2/embryogrowth/man/hist.Nests2.Rd |only embryogrowth-10.2/embryogrowth/man/info.nests.Rd | 12 embryogrowth-10.2/embryogrowth/man/movement.Rd | 18 embryogrowth-10.2/embryogrowth/man/plot.Nests2.Rd |only embryogrowth-10.2/embryogrowth/man/plot.NestsResult.Rd | 18 embryogrowth-10.2/embryogrowth/man/plot.tsd.Rd | 5 embryogrowth-10.2/embryogrowth/man/plotR.Rd | 3 embryogrowth-10.2/embryogrowth/man/predict.tsd.Rd | 3 embryogrowth-10.2/embryogrowth/man/resultNest_mcmc_4p_SSM.Rd | 9 embryogrowth-10.2/embryogrowth/man/resultNest_mcmc_4p_SSM_Linear.Rd | 9 embryogrowth-10.2/embryogrowth/man/searchR.Rd | 86 + embryogrowth-10.2/embryogrowth/man/summary.Nests2.Rd |only embryogrowth-10.2/embryogrowth/man/tsd.Rd | 70 + embryogrowth-10.2/embryogrowth/man/tsd_MHmcmc_p.Rd | 2 embryogrowth-10.2/embryogrowth/man/weightmaxentropy.Rd | 2 embryogrowth-9.5/embryogrowth/man/hist.Nests.Rd |only embryogrowth-9.5/embryogrowth/man/summary.Nests.Rd |only 75 files changed, 2421 insertions(+), 1306 deletions(-)
Title: Network Analysis of Dependencies of CRAN Packages
Description: The dependencies of CRAN packages can be analysed in a network fashion. For each package we can obtain the packages that it depends, imports, suggests, etc. By iterating this procedure over a number of packages, we can build, visualise, and analyse the dependency network, enabling us to have a bird's-eye view of the CRAN ecosystem. One aspect of interest is the number of reverse dependencies of the packages, or equivalently the in-degree distribution of the dependency network. This can be fitted by the power law and/or an extreme value mixture distribution <doi:10.1111/stan.12355>, of which functions are provided.
Author: Clement Lee [aut, cre]
Maintainer: Clement Lee <clement.lee.tm@outlook.com>
Diff between crandep versions 0.3.12 dated 2025-05-02 and 0.3.13 dated 2025-06-16
DESCRIPTION | 6 +- MD5 | 28 +++++------ NEWS.md | 5 ++ R/cleaning.R | 2 R/get_dep.R | 14 ++--- R/graph.R | 19 +++---- inst/doc/cran.R | 2 inst/doc/cran.Rmd | 2 inst/doc/cran.html | 104 +++++++++++++++++++++--------------------- inst/doc/degree.html | 32 ++++++------ inst/doc/introduction.html | 10 ++-- man/get_dep.Rd | 2 man/get_dep_all_packages.Rd | 4 - man/get_graph_all_packages.Rd | 2 vignettes/cran.Rmd | 2 15 files changed, 119 insertions(+), 115 deletions(-)
Title: Querying and Managing Large Biodiversity Occurrence Datasets
Description: Facilitates the gathering of biodiversity occurrence data
from disparate sources. Metadata is managed throughout the process to facilitate
reporting and enhanced ability to repeat analyses.
Author: Hannah L. Owens [aut, cre] ,
Cory Merow [aut] ,
Brian Maitner [aut] ,
Jamie M. Kass [aut] ,
Vijay Barve [aut] ,
Robert P. Guralnick [aut] ,
Damiano Oldoni [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/407>)
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
Diff between occCite versions 0.5.9 dated 2024-10-28 and 0.6.0 dated 2025-06-16
DESCRIPTION | 33 +++-- MD5 | 35 +++-- NAMESPACE | 1 NEWS.md | 6 + R/occCite_plotting.R | 14 ++ R/studyTaxonList.R | 1 R/taxonRectification.R | 163 +++++++++++++-------------- inst/doc/a_Simple.R | 36 +++--- inst/doc/a_Simple.html | 29 ++-- inst/doc/b_Advanced.R | 14 +- inst/doc/b_Advanced.html | 185 +++++++++++++++++++++---------- inst/extdata/0169441-210914110416597.zip |only man/studyTaxonList.Rd | 1 man/taxonRectification.Rd | 11 - tests/testthat/test-GBIFLoginManager.R | 15 +- tests/testthat/test-occCitePrint.R | 17 +- tests/testthat/test-studyTaxonList.R | 9 + tests/testthat/test-sumFig.R | 21 ++- tests/testthat/test-taxonRectification.R | 91 +++++++-------- 19 files changed, 399 insertions(+), 283 deletions(-)
Title: Calculate Expertise Indices
Description: Institutional performance assessment remains a key challenge to a multitude of stakeholders. Existing indicators such as h-type indicators, g-type indicators, and many others do not reflect expertise of institutions that defines their research portfolio. The package offers functionality to compute and visualise two novel indices: the x-index and the xd-index. The x-index evaluates an institution's scholarly expertise within a specific discipline or field, while the xd-index provides a broader assessment of overall scholarly expertise considering an institution's publication pattern and strengths across coarse thematic areas. These indices offer a nuanced understanding of institutional research capabilities, aiding stakeholders in research management and resource allocation decisions. Lathabai, H.H., Nandy, A., and Singh, V.K. (2021) <doi:10.1007/s11192-021-04188-3>. Nandy, A., Lathabai, H.H., and Singh, V.K. (2023) <doi:10.5281/zenodo.8305585>. This package provides the h, [...truncated...]
Author: Nilabhra Rohan Das [cre, aut] ,
Abhirup Nandy [aut]
Maintainer: Nilabhra Rohan Das <nr.das@yahoo.com>
Diff between xxdi versions 1.2.3 dated 2024-08-16 and 1.2.4 dated 2025-06-16
xxdi-1.2.3/xxdi/R/xc_index.R |only xxdi-1.2.3/xxdi/R/xdc_index.R |only xxdi-1.2.3/xxdi/man/xc_index.Rd |only xxdi-1.2.3/xxdi/man/xdc_index.Rd |only xxdi-1.2.4/xxdi/DESCRIPTION | 15 +++--- xxdi-1.2.4/xxdi/MD5 | 26 ++++------ xxdi-1.2.4/xxdi/NAMESPACE | 2 xxdi-1.2.4/xxdi/NEWS.md | 14 +++++ xxdi-1.2.4/xxdi/R/g_index.R | 78 ++++++++++++++----------------- xxdi-1.2.4/xxdi/R/h_index.R | 76 ++++++++++++++---------------- xxdi-1.2.4/xxdi/R/x_index.R | 96 +++++++++++++++++---------------------- xxdi-1.2.4/xxdi/R/xd_index.R | 96 +++++++++++++++++---------------------- xxdi-1.2.4/xxdi/man/g_index.Rd | 21 ++++---- xxdi-1.2.4/xxdi/man/h_index.Rd | 22 +++++--- xxdi-1.2.4/xxdi/man/x_index.Rd | 20 ++++---- xxdi-1.2.4/xxdi/man/xd_index.Rd | 20 ++++---- 16 files changed, 238 insertions(+), 248 deletions(-)
Title: Utilities and Design Aids for Up-and-Down Dose-Finding Studies
Description: Up-and-Down (UD) is the most popular design approach for dose-finding, but it has been severely under-served by the statistical and computing communities. This is the first package that comprehensively addresses UD's needs. Recent applied UD tutorial: Oron et al., 2022 <doi:10.1097/ALN.0000000000004282>. Recent methodological overview: Oron and Flournoy, 2024 <doi:10.51387/24-NEJSDS74>.
Author: Assaf P. Oron [cre, aut]
Maintainer: Assaf P. Oron <assaf.oron@gmail.com>
Diff between upndown versions 0.2.0 dated 2024-12-10 and 0.3.0 dated 2025-06-16
DESCRIPTION | 12 ++-- MD5 | 40 ++++++------- R/cirWrappers.r | 6 +- R/genutils.r | 111 +++++++++++++++++-------------------- R/matrixFunctions.r | 20 +++--- R/simulate.r | 3 - R/vectorFunctions.r | 15 ++--- build/vignette.rds |binary inst/doc/upndown_basics.R | 4 - inst/doc/upndown_basics.Rmd | 15 ++--- inst/doc/upndown_basics.html | 127 ++++++++++++++++++++++--------------------- inst/examples/simExample.r | 3 - man/bcdmat.Rd | 20 +++--- man/dfsim.Rd | 3 - man/drplot.Rd | 2 man/k2targ.Rd | 30 ++++------ man/krow.Rd | 2 man/pivec.Rd | 12 ++-- man/udest.Rd | 5 + man/validUDinput.Rd | 2 vignettes/upndown_basics.Rmd | 15 ++--- 21 files changed, 226 insertions(+), 221 deletions(-)
Title: Apply a PCA Like Procedure Suited for Multivariate Extreme Value
Distributions
Description: Dimension reduction for multivariate data of extreme events with a PCA like procedure as described in Reinbott, Janßen, (2024), <doi:10.48550/arXiv.2408.10650>. Tools for necessary transformations of the data are provided.
Author: Felix Reinbott [aut, cre]
Maintainer: Felix Reinbott <felix.reinbott@ovgu.de>
Diff between maxstablePCA versions 0.1.1 dated 2024-09-06 and 0.1.2 dated 2025-06-16
DESCRIPTION | 9 +++-- MD5 | 13 +++++--- R/data.R |only R/maxstablePCA.R | 2 - R/pca.R | 73 ++++++++++++++++++++++++++++++++++++++--------- README.md | 4 +- data |only man/elbe.Rd |only man/max_stable_prcomp.Rd | 20 ++++++++++-- 9 files changed, 92 insertions(+), 29 deletions(-)
Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] ,
Edward Burn [aut] ,
Theresa Burkard [aut] ,
Yuchen Guo [ctb] ,
Marti Catala [ctb] ,
Mike Du [ctb] ,
Xintong Li [ctb] ,
Ross Williams [ctb] ,
Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between DrugExposureDiagnostics versions 1.1.3 dated 2025-05-28 and 1.1.4 dated 2025-06-16
DrugExposureDiagnostics-1.1.3/DrugExposureDiagnostics/tests/testthat/test-checkDrugSig.R |only DrugExposureDiagnostics-1.1.3/DrugExposureDiagnostics/tests/testthat/test-checkVerbatimEndDate.R |only DrugExposureDiagnostics-1.1.4/DrugExposureDiagnostics/DESCRIPTION | 8 DrugExposureDiagnostics-1.1.4/DrugExposureDiagnostics/MD5 | 24 +- DrugExposureDiagnostics-1.1.4/DrugExposureDiagnostics/NEWS.md | 5 DrugExposureDiagnostics-1.1.4/DrugExposureDiagnostics/R/checkTimeBetween.R | 8 DrugExposureDiagnostics-1.1.4/DrugExposureDiagnostics/R/executeChecks.R | 8 DrugExposureDiagnostics-1.1.4/DrugExposureDiagnostics/R/summariseChecks.R | 9 DrugExposureDiagnostics-1.1.4/DrugExposureDiagnostics/inst/doc/DrugSig.html | 2 DrugExposureDiagnostics-1.1.4/DrugExposureDiagnostics/inst/doc/IntroductionToDrugExposureDiagnostics.html | 6 DrugExposureDiagnostics-1.1.4/DrugExposureDiagnostics/inst/shiny/ResultsExplorer/utils.R | 118 +++++----- DrugExposureDiagnostics-1.1.4/DrugExposureDiagnostics/tests/testthat/test-CheckDrugSig.R |only DrugExposureDiagnostics-1.1.4/DrugExposureDiagnostics/tests/testthat/test-CheckVerbatimEndDate.R |only DrugExposureDiagnostics-1.1.4/DrugExposureDiagnostics/tests/testthat/test-SummariseChecks.R | 5 DrugExposureDiagnostics-1.1.4/DrugExposureDiagnostics/tests/testthat/test-SyntheaSqlServer.R | 8 15 files changed, 113 insertions(+), 88 deletions(-)
More information about DrugExposureDiagnostics at CRAN
Permanent link
Title: Quantifying Similarity of Datasets and Multivariate Two- And
k-Sample Testing
Description: A collection of methods for quantifying the similarity of two or more datasets, many of which can be used for two- or k-sample testing. It provides newly implemented methods as well as wrapper functions for existing methods that enable calling many different methods in a unified framework. The methods were selected from the review and comparison of Stolte et al. (2024) <doi:10.1214/24-SS149>.
Author: Marieke Stolte [aut, cre, cph] ,
Luca Sauer [aut] ,
David Alvarez-Melis [ctb] ,
Nabarun Deb [ctb] , <https://github.com/NabarunD/MultiDistFree.git>),
Bodhisattva Sen [ctb] , <https://github.com/NabarunD/MultiDistFree.git>)
Maintainer: Marieke Stolte <stolte@statistik.tu-dortmund.de>
Diff between DataSimilarity versions 0.1.1 dated 2025-03-18 and 0.2.0 dated 2025-06-16
DataSimilarity-0.1.1/DataSimilarity/inst/doc/vignette.R |only DataSimilarity-0.1.1/DataSimilarity/inst/doc/vignette.Rnw |only DataSimilarity-0.1.1/DataSimilarity/inst/doc/vignette.pdf |only DataSimilarity-0.1.1/DataSimilarity/vignettes/vignette.Rnw |only DataSimilarity-0.2.0/DataSimilarity/ChangeLog |only DataSimilarity-0.2.0/DataSimilarity/DESCRIPTION | 20 DataSimilarity-0.2.0/DataSimilarity/MD5 | 229 +++++----- DataSimilarity-0.2.0/DataSimilarity/NAMESPACE | 16 DataSimilarity-0.2.0/DataSimilarity/R/BF.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/BG.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/BG2.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/BMG.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/BQS.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/BallDivergence.R | 15 DataSimilarity-0.2.0/DataSimilarity/R/C2ST.R | 16 DataSimilarity-0.2.0/DataSimilarity/R/CCS.R | 4 DataSimilarity-0.2.0/DataSimilarity/R/CF.R | 4 DataSimilarity-0.2.0/DataSimilarity/R/CMDistance.R | 29 - DataSimilarity-0.2.0/DataSimilarity/R/DISCO.R | 4 DataSimilarity-0.2.0/DataSimilarity/R/DS.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/DataSimilarity.R |only DataSimilarity-0.2.0/DataSimilarity/R/DiProPerm.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/Energy.R | 2 DataSimilarity-0.2.0/DataSimilarity/R/FR.R | 4 DataSimilarity-0.2.0/DataSimilarity/R/FStest.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/GGRL.R | 14 DataSimilarity-0.2.0/DataSimilarity/R/GPK.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/HMN.R | 2 DataSimilarity-0.2.0/DataSimilarity/R/HamiltonPath.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/Jeffreys.R | 10 DataSimilarity-0.2.0/DataSimilarity/R/KMD.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/LHZ.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/MMCM.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/MMD.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/MW.R | 6 DataSimilarity-0.2.0/DataSimilarity/R/NKT.R | 20 DataSimilarity-0.2.0/DataSimilarity/R/OTDD.R | 6 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More information about DataSimilarity at CRAN
Permanent link
Title: Estimate Survival from Common Data Model Cohorts
Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
Author: Kim Lopez-Gueell [aut, cre] ,
Edward Burn [aut] ,
Marti Catala [aut] ,
Xintong Li [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut]
Maintainer: Kim Lopez-Gueell <kim.lopez@spc.ox.ac.uk>
Diff between CohortSurvival versions 1.0.1 dated 2025-04-02 and 1.0.2 dated 2025-06-16
DESCRIPTION | 20 MD5 | 91 NEWS.md |only R/CohortSurvival-package.R | 16 R/addCohortSurvival.R | 522 - R/asSurvivalResult.R | 244 R/estimateSurvival.R | 27 R/inputValidation.R | 104 R/mockMGUS2cdm.R | 450 - R/plotSurvival.R | 595 - R/reexport-omopgenerics.R | 94 R/tableSurvival.R | 872 +- R/utils-pipe.R | 28 R/utils-tidy-eval.R | 216 README.md | 1294 +-- build/vignette.rds |binary inst/WORDLIST | 66 inst/doc/a01_Single_event_of_interest.R | 349 inst/doc/a01_Single_event_of_interest.Rmd | 692 - inst/doc/a01_Single_event_of_interest.html |10673 ++++++++++++++------------- inst/doc/a02_Competing_risk_survival.R | 134 inst/doc/a02_Competing_risk_survival.Rmd | 236 inst/doc/a02_Competing_risk_survival.html | 2842 +++---- inst/doc/a03_Further_survival_analyses.R | 186 inst/doc/a03_Further_survival_analyses.Rmd | 272 inst/doc/a03_Further_survival_analyses.html | 1124 +- man/CohortSurvival-package.Rd | 66 man/addCohortSurvival.Rd | 132 man/asSurvivalResult.Rd | 66 man/estimateCompetingRiskSurvival.Rd | 210 man/estimateSingleEventSurvival.Rd | 176 man/mockMGUS2cdm.Rd | 40 man/optionsTableSurvival.Rd | 44 man/pipe.Rd | 40 man/plotSurvival.Rd | 102 man/reexports.Rd | 46 man/tableSurvival.Rd | 102 man/tidyeval.Rd | 202 tests/testthat.R | 24 tests/testthat/test-addCohortSurvival.R | 1756 ++-- tests/testthat/test-estimateSurvival.R | 5030 ++++++------ tests/testthat/test-plotSurvival.R | 299 tests/testthat/test-reexports-omopgenerics.R | 151 tests/testthat/test-tableSurvival.R | 270 vignettes/a01_Single_event_of_interest.Rmd | 692 - vignettes/a02_Competing_risk_survival.Rmd | 236 vignettes/a03_Further_survival_analyses.Rmd | 272 47 files changed, 15896 insertions(+), 15207 deletions(-)
More information about CohortSurvival at CRAN
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Title: Analysis and Visualization of Multi-Omics Data
Description: A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10. [...truncated...]
Author: Dongyue Yu [aut, cre, cph]
Maintainer: Dongyue Yu <yudongyue@mail.nankai.edu.cn>
Diff between TransProR versions 1.0.3 dated 2025-02-18 and 1.0.5 dated 2025-06-16
DESCRIPTION | 15 ++++++++------- MD5 | 20 +++++++++++--------- NAMESPACE | 10 +++++++++- R/EnrichPolarBubble.R | 5 ++--- R/EnrichmentSpiralize.R | 5 +++++ R/GeneHighlights.R | 4 ++++ R/HighlightByNode.R | 4 ++++ R/HighlightGenes.R | 4 ++++ R/spline.R |only README.md | 3 ++- inst/doc/TransProR.html | 4 ++-- man/stat_xspline.Rd |only 12 files changed, 51 insertions(+), 23 deletions(-)
Title: Extended Joint Models for Longitudinal and Time-to-Event Data
Description: Fit joint models for longitudinal and time-to-event data under the Bayesian approach. Multiple longitudinal outcomes of mixed type (continuous/categorical) and multiple event times (competing risks and multi-state processes) are accommodated. Rizopoulos (2012, ISBN:9781439872864).
Author: Dimitris Rizopoulos [aut, cre] ,
Pedro Miranda Afonso [aut],
Grigorios Papageorgiou [aut]
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes2 versions 0.5-2 dated 2025-02-28 and 0.5-7 dated 2025-06-16
DESCRIPTION | 14 MD5 | 18 NAMESPACE | 7 R/accuracy_measures.R | 1005 +++++++++++++++++++++------------------------- R/accuracy_measures_Cox.R | 81 +++ R/basic_methods.R | 70 +++ R/help_functions.R | 42 + README.md | 2 man/JMbayes2.Rd | 4 man/accuracy.Rd | 24 - 10 files changed, 694 insertions(+), 573 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-11 2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-27 0.3-21
2023-07-20 0.3-20
2020-01-31 0.3-19
2018-04-22 0.3-18
2018-04-13 0.3-17
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-15 0.9-1
Title: Functionalities for the 'INLA' Package
Description: Contain code to work with latent Gaussian
Markov random field (GMRF) models. Queries for the
'cgeneric' interface, specified as a way to implement
new GMRF models to be fitted as model components
in the 'INLA' package (<https://www.r-inla.org>).
The implemented functionalities leverage the use
of 'cgeneric' models and provide a way to debug
the code as well to work with the prior for the
model parameters and to sample from it.
A Kronecker product method is also implemented to
work with the four possible combinations between
a 'cgeneric' and a 'rgeneric' model.
Author: Elias Teixeira Krainski [cre, aut, cph] ,
Haavard Rue’ [aut]
Maintainer: Elias Teixeira Krainski <eliaskrainski@gmail.com>
Diff between INLAtools versions 0.0.2 dated 2025-06-04 and 0.0.3 dated 2025-06-16
DESCRIPTION | 6 MD5 | 38 ++-- NAMESPACE | 13 + R/aaa_methods.R | 63 +++++++ R/cgeneric.R | 68 ++++++-- R/inla_methods.R |only R/kronecker.R | 18 -- R/rgeneric.R |only man/cgeneric-class.Rd | 12 + man/cgeneric.Rd | 3 man/is.zero.Rd |only man/kronecker.Rd | 24 -- man/methods.Rd | 23 ++ man/rgeneric-class.Rd | 39 ++++ man/rgeneric.Rd |only src/INLAtools.h | 9 - src/INLAtools_init.c | 14 - src/Makevars | 2 src/cgeneric.h | 10 - src/cgeneric_generic0.c | 153 +++++++++--------- src/cgeneric_get.c | 109 +++++++------ src/cgeneric_kronecker.c | 392 ++++++++++++++++++++++++++--------------------- 22 files changed, 625 insertions(+), 371 deletions(-)
Title: Causal Decomposition of Group Disparities
Description: The framework of causal decomposition of group disparities developed by
Yu and Elwert (2025)
<doi:10.1214/24-AOAS1990>.
This package implements the decomposition estimators
that are based on efficient influence functions. For the
nuisance functions of the estimators, both parametric and
nonparametric options are provided, as well as manual options in case
the default models are not satisfying.
Author: Ang Yu [aut, cre, cph]
Maintainer: Ang Yu <ang_yu@outlook.com>
Diff between cdgd versions 0.3.5 dated 2024-04-15 and 1.0.0 dated 2025-06-16
DESCRIPTION | 14 ++-- MD5 | 30 +++++----- NEWS.md | 3 + R/cdgd0_manual.R | 85 +++++++++++++++++------------ R/cdgd0_ml.R | 85 +++++++++++++++++------------ R/cdgd0_pa.R | 85 +++++++++++++++++------------ R/cdgd1_manual.R | 62 +++++++++++++-------- R/cdgd1_ml.R | 151 +++++++++++++++++++++++++++++++++++----------------- R/cdgd1_pa.R | 87 ++++++++++++++++++++--------- README.md | 5 + man/cdgd0_manual.Rd | 5 + man/cdgd0_ml.Rd | 4 + man/cdgd0_pa.Rd | 4 + man/cdgd1_manual.Rd | 17 +++-- man/cdgd1_ml.Rd | 16 +++++ man/cdgd1_pa.Rd | 15 ++++- 16 files changed, 428 insertions(+), 240 deletions(-)
Title: Linear Model with Tree-Based Lasso Regularization for Rare
Features
Description: Implementation of an alternating direction method of multipliers
algorithm for fitting a linear model with tree-based lasso regularization,
which is proposed in Algorithm 1 of Yan and Bien (2020) <doi:10.1080/01621459.2020.1796677>.
The package allows efficient model fitting on the entire 2-dimensional
regularization path for large datasets. The complete set of functions
also makes the entire process of tuning regularization parameters and
visualizing results hassle-free.
Author: Xiaohan Yan [aut, cre],
Jacob Bien [aut]
Maintainer: Xiaohan Yan <xy257@cornell.edu>
Diff between rare versions 0.1.1 dated 2018-08-03 and 0.1.2 dated 2025-06-16
DESCRIPTION | 20 + MD5 | 11 R/rare.fit.R | 4 README.md |only build/vignette.rds |binary inst/doc/rare-vignette.R | 22 - inst/doc/rare-vignette.html | 564 ++++++++++++++++++++++++++++---------------- 7 files changed, 404 insertions(+), 217 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-26 1.5.3
2024-05-02 1.5.2
2024-02-05 1.5.1
2023-09-19 1.5.0
Title: Univariate Feature Selection and Compound Covariate for
Predicting Survival, Including Copula-Based Analyses for
Dependent Censoring
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (e.g., gene expressions).
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>,
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al (2019)<DOI:10.1016/j.cmpb.2018.10.020>.
Algorithms for generating correlated gene expressions are also available.
Estimation of survival functions via copula-graphic (CG) estimators is also implemented, which is useful for
sensitivity analyses under dependent censoring (Yeh et al 2023 Biomedicines) <DOI:10.3390/biomedicines11030797> and
factorial survival analyses (Emura et al 2024 Stat Methods Med Res) <DOI:10.1177/09622802231215805>.
Author: Takeshi Emura [aut, cre],
Hsuan-Yu Chen [aut],
Shigeyuki Matsui [aut],
Yi-Hau Chen [aut]
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.32 dated 2025-01-11 and 3.33 dated 2025-06-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/CG.Clayton.R | 3 ++- R/CG.Frank.R | 4 +++- R/CG.Gumbel.R | 3 ++- man/compound.Cox-package.Rd | 4 ++-- 6 files changed, 18 insertions(+), 14 deletions(-)