Title: Evolutionary Algorithm
Description: Runs an evolutionary algorithm using the 'AlphaSimR' machinery <doi:10.1093/g3journal/jkaa017> .
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between evola versions 1.0.5 dated 2025-04-25 and 1.0.6 dated 2025-07-30
ChangeLog | 13 +- DESCRIPTION | 14 +- MD5 | 38 ++++--- NAMESPACE | 14 +- R/evolafit.R | 208 ++++++++++++++++++++++------------------ R/methods.R | 35 +++++- R/utlis.R | 53 +++++++++- data/DT_envs.RData |only data/datalist | 1 inst/doc/evola_intro.R | 18 +-- inst/doc/evola_intro.Rmd | 18 +-- inst/doc/evola_intro.html | 82 +++++++-------- man/DT_cpdata.Rd | 6 - man/DT_envs.Rd |only man/DT_technow.Rd | 6 - man/DT_wheat.Rd | 6 - man/bestSol.Rd | 2 man/drift.Rd |only man/evolafit.Rd | 238 +++++++++++++++++++++++++++++++++------------- man/summary.method.Rd |only man/varQ.Rd | 2 vignettes/evola_intro.Rmd | 18 +-- 22 files changed, 490 insertions(+), 282 deletions(-)
Title: A Companion to the e-Book "YaRrr!: The Pirate's Guide to R"
Description: Contains a mixture of functions and data sets referred to in the introductory e-book "YaRrr!: The Pirate's Guide to R". The latest version of the e-book is available for free at <https://bookdown.org/ndphillips/YaRrr/>.
Author: Nathaniel Phillips [aut, cre]
Maintainer: Nathaniel Phillips <nathaniel.d.phillips.is@gmail.com>
This is a re-admission after prior archival of version 0.1.5 dated 2017-04-19
Diff between yarrr versions 0.1.5 dated 2017-04-19 and 0.1.14 dated 2025-07-30
DESCRIPTION | 18 MD5 | 92 - NAMESPACE | 1 NEWS.md | 14 R/apa_function.R | 51 R/geom_pirate.R |only R/guide_function.R | 12 R/hdi_function.R | 99 - R/helper_fun.R | 2 R/piratepal_function.R | 463 +++--- R/pirateplot_function.R | 3207 +++++++++++++++++++++++++---------------------- R/pirates_doc.R | 10 R/pirateserrors_doc.R | 10 R/recodev_function.R | 44 R/transparent_function.R | 102 - R/zzz.R | 5 README.md | 142 +- build/vignette.rds |binary inst/doc/guide.R | 33 inst/doc/guide.Rmd | 32 inst/doc/guide.html | 433 +++++- inst/doc/piratepal.R | 94 - inst/doc/piratepal.Rmd | 76 - inst/doc/piratepal.html | 550 ++++++-- inst/doc/pirateplot.R | 431 +++--- inst/doc/pirateplot.Rmd | 402 +++-- inst/doc/pirateplot.html | 828 +++++++++--- inst/ppelements.png |only man/BeardLengths.Rd | 6 man/apa.Rd | 2 man/auction.Rd | 6 man/capture.Rd | 6 man/diamonds.Rd | 6 man/examscores.Rd | 6 man/figures |only man/movies.Rd | 6 man/piratepal.Rd | 23 man/pirateplot.Rd | 245 ++- man/pirates.Rd | 6 man/pirateserrors.Rd | 6 man/pircharter.Rd | 6 man/poopdeck.Rd | 6 man/recodev.Rd | 17 man/transparent.Rd | 42 vignettes/guide.Rmd | 32 vignettes/piratepal.Rmd | 76 - vignettes/pirateplot.Rmd | 402 +++-- 47 files changed, 4951 insertions(+), 3099 deletions(-)
Title: Scopus Database 'API' Interface
Description: Uses Elsevier 'Scopus' API
<https://dev.elsevier.com/sc_apis.html> to download
information about authors and their citations.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between rscopus versions 0.8.1 dated 2025-04-02 and 0.9.0 dated 2025-07-30
rscopus-0.8.1/rscopus/R/read_cto.r |only rscopus-0.9.0/rscopus/DESCRIPTION | 6 rscopus-0.9.0/rscopus/MD5 | 16 rscopus-0.9.0/rscopus/NEWS.md | 4 rscopus-0.9.0/rscopus/R/author_retrieval.R | 15 rscopus-0.9.0/rscopus/R/read_cto.R |only rscopus-0.9.0/rscopus/build/vignette.rds |binary rscopus-0.9.0/rscopus/inst/doc/api_key.html | 35 rscopus-0.9.0/rscopus/inst/doc/multi_author.html | 1367 ++++++++++++++++++++++- rscopus-0.9.0/rscopus/man/author_retrieval.Rd | 7 10 files changed, 1419 insertions(+), 31 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 2.1.7 dated 2025-07-18 and 2.1.8 dated 2025-07-30
DESCRIPTION | 14 MD5 | 72 +- NAMESPACE | 5 R/GeoCV.R | 1129 +++++++++++++++------------------------------- R/GeoCompositeLik2.R | 112 +++- R/GeoCovmatrix.r | 10 R/GeoFit.r | 58 -- R/GeoFit2.R | 18 R/GeoIndCompositeLik2.R | 199 ++++---- R/GeoKrig.r | 230 ++++----- R/GeoKrigloc.R | 31 - R/GeoLik.r | 203 ++------ R/GeoNeighIndex.R | 2 R/GeoNeighbSelect.R | 356 +++++++------- R/GeoPit.R | 22 R/GeoQQ.R | 67 +- R/GeoScores.R | 2 R/GeoSim.r | 4 R/GeoSimCopula.R | 57 +- R/GeoSimapprox.r | 4 R/GeoSimcond.R | 6 R/Geovarestbootstrap.R | 333 ++++++++----- R/TB.R | 51 +- R/Utility.r | 407 +++++----------- R/Utility_cov.R | 139 ++--- man/GeoCV.Rd | 3 man/GeoCovmatrix.Rd | 765 +++++++++++++------------------ man/GeoKrig.Rd | 40 - man/GeoKrigloc.Rd | 15 man/GeoNeighbSelect.Rd | 3 man/GeoVarestbootstrap.Rd | 3 src/1F1.c | 458 +++--------------- src/2F1_v2.c | 32 - src/2gammainc.c | 35 - src/2kummer.c | 1 src/Distributions.c | 708 +++++++++++++++++++++------- src/header.h | 9 37 files changed, 2580 insertions(+), 3023 deletions(-)
Title: Process Text and Compute Linguistic Alignment in Conversation
Transcripts
Description: Imports conversation transcripts into R, concatenates them into a single dataframe appending event identifiers, cleans and formats the text, then yokes user-specified psycholinguistic database values to each word. 'ConversationAlign' then computes alignment indices between two interlocutors across each transcript for >40 possible semantic, lexical, and affective dimensions. In addition to alignment, 'ConversationAlign' also produces a table of analytics (e.g., token count, type-token-ratio) in a summary table describing your particular text corpus.
Author: Jamie Reilly [aut, cre] ,
Virginia Ulichney [aut],
Ben Sacks [aut],
Sarah Weinstein [ctb],
Chelsea Helion [ctb],
Gus Cooney [ctb]
Maintainer: Jamie Reilly <jamie_reilly@temple.edu>
Diff between ConversationAlign versions 0.2.0 dated 2025-07-22 and 0.3.2 dated 2025-07-30
ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Intro.R |only ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Intro.Rmd |only ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Intro.html |only ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Step1_Read.R |only ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Step1_Read.Rmd |only ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Step1_Read.html |only ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Step2_Prep.R |only ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Step2_Prep.Rmd |only ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Step2_Prep.html |only ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Step3_Summarize.R |only ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Step3_Summarize.Rmd |only ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Step3_Summarize.html |only ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Step4_Analytics.R |only ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Step4_Analytics.Rmd |only ConversationAlign-0.2.0/ConversationAlign/inst/doc/CA_Step4_Analytics.html |only ConversationAlign-0.2.0/ConversationAlign/vignettes/CA_Intro.Rmd |only ConversationAlign-0.2.0/ConversationAlign/vignettes/CA_Step1_Read.Rmd |only ConversationAlign-0.2.0/ConversationAlign/vignettes/CA_Step2_Prep.Rmd |only ConversationAlign-0.2.0/ConversationAlign/vignettes/CA_Step3_Summarize.Rmd |only ConversationAlign-0.2.0/ConversationAlign/vignettes/CA_Step4_Analytics.Rmd |only ConversationAlign-0.3.2/ConversationAlign/DESCRIPTION | 8 - ConversationAlign-0.3.2/ConversationAlign/MD5 | 52 +++++----- ConversationAlign-0.3.2/ConversationAlign/R/prep_dyads.R | 45 ++++++++ ConversationAlign-0.3.2/ConversationAlign/README.md | 22 ++-- ConversationAlign-0.3.2/ConversationAlign/build/vignette.rds |binary ConversationAlign-0.3.2/ConversationAlign/inst/NEWS.md | 31 +++++ ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Introduction.R |only ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Introduction.Rmd |only ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Introduction.html |only ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Step1_Read.R |only ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Step1_Read.Rmd |only ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Step1_Read.html |only ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Step2_Prep.R |only ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Step2_Prep.Rmd |only ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Step2_Prep.html |only ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Step3_Summarize.R |only ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Step3_Summarize.Rmd |only ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Step3_Summarize.html |only ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Step4_Analytics.R |only ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Step4_Analytics.Rmd |only ConversationAlign-0.3.2/ConversationAlign/inst/doc/ConversationAlign_Step4_Analytics.html |only ConversationAlign-0.3.2/ConversationAlign/man/figures/logo.png |binary ConversationAlign-0.3.2/ConversationAlign/vignettes/ConversationAlign_Introduction.Rmd |only ConversationAlign-0.3.2/ConversationAlign/vignettes/ConversationAlign_Step1_Read.Rmd |only ConversationAlign-0.3.2/ConversationAlign/vignettes/ConversationAlign_Step2_Prep.Rmd |only ConversationAlign-0.3.2/ConversationAlign/vignettes/ConversationAlign_Step3_Summarize.Rmd |only ConversationAlign-0.3.2/ConversationAlign/vignettes/ConversationAlign_Step4_Analytics.Rmd |only 47 files changed, 119 insertions(+), 39 deletions(-)
More information about ConversationAlign at CRAN
Permanent link
Title: Bootstrapped Differences of Time Series
Description: Analyze differences among time series curves with p-value
adjustment for multiple comparisons introduced in Oleson et al
(2015) <DOI:10.1177/0962280215607411>.
Author: Collin Nolte [aut, cre],
Michael Seedorff [aut],
Jacob Oleson [aut],
Grant Brown [aut],
Joseph Cavanaugh [aut],
Bob McMurray [aut]
Maintainer: Collin Nolte <noltecollin@grinnell.edu>
Diff between bdots versions 1.2.5 dated 2023-01-06 and 2.0.0 dated 2025-07-30
bdots-1.2.5/bdots/LICENSE |only bdots-1.2.5/bdots/R/curveBooter.R |only bdots-1.2.5/bdots/man/rbindlist.bdObjList.Rd |only bdots-2.0.0/bdots/DESCRIPTION | 33 + bdots-2.0.0/bdots/MD5 | 98 ++-- bdots-2.0.0/bdots/NAMESPACE | 8 bdots-2.0.0/bdots/NEWS.md | 17 bdots-2.0.0/bdots/R/DEPRECATED.R |only bdots-2.0.0/bdots/R/bdotsBoot.R | 153 +++++-- bdots-2.0.0/bdots/R/bdotsCorr.R | 2 bdots-2.0.0/bdots/R/bdotsFit.R | 119 ++--- bdots-2.0.0/bdots/R/bdotsFitter.R | 27 - bdots-2.0.0/bdots/R/bdotsRefit.R | 201 +++++++++ bdots-2.0.0/bdots/R/bootHelper.R | 159 +++++-- bdots-2.0.0/bdots/R/bootstrapping.R |only bdots-2.0.0/bdots/R/coefMerge.R | 4 bdots-2.0.0/bdots/R/curveBooter_SINGLEMEAN.R |only bdots-2.0.0/bdots/R/curveFunctions.R | 264 +++++++++---- bdots-2.0.0/bdots/R/methods.R | 72 ++- bdots-2.0.0/bdots/R/modifiedAlphaFunctions.R | 1 bdots-2.0.0/bdots/R/permutation.R |only bdots-2.0.0/bdots/R/plotFunctions.R | 21 - bdots-2.0.0/bdots/R/summaryFunctions.R | 66 ++- bdots-2.0.0/bdots/build/vignette.rds |binary bdots-2.0.0/bdots/inst/doc/bdots.R | 101 ++--- bdots-2.0.0/bdots/inst/doc/bdots.Rmd | 59 +- bdots-2.0.0/bdots/inst/doc/bdots.html | 529 +++++++++++++++++++------- bdots-2.0.0/bdots/inst/doc/correlations.R | 23 - bdots-2.0.0/bdots/inst/doc/correlations.Rmd | 29 - bdots-2.0.0/bdots/inst/doc/correlations.html | 433 ++++++++++++++++----- bdots-2.0.0/bdots/inst/doc/customCurves.R | 31 - bdots-2.0.0/bdots/inst/doc/customCurves.Rmd | 33 - bdots-2.0.0/bdots/inst/doc/customCurves.html | 543 +++++++++++++++++++-------- bdots-2.0.0/bdots/inst/doc/refitCoef.R | 35 - bdots-2.0.0/bdots/inst/doc/refitCoef.Rmd | 33 - bdots-2.0.0/bdots/inst/doc/refitCoef.html | 432 ++++++++++++++++----- bdots-2.0.0/bdots/man/bboot.Rd |only bdots-2.0.0/bdots/man/bcorr.Rd |only bdots-2.0.0/bdots/man/bdotsBoot.Rd | 108 ----- bdots-2.0.0/bdots/man/bdotsCorr.Rd | 5 bdots-2.0.0/bdots/man/bdotsFit.Rd | 15 bdots-2.0.0/bdots/man/bdotsFitter.Rd | 4 bdots-2.0.0/bdots/man/bdotsRefit.Rd | 15 bdots-2.0.0/bdots/man/bfit.Rd |only bdots-2.0.0/bdots/man/bool2idx.Rd |only bdots-2.0.0/bdots/man/brbindlist.Rd |only bdots-2.0.0/bdots/man/brefit.Rd |only bdots-2.0.0/bdots/man/createCurveList.Rd |only bdots-2.0.0/bdots/man/createGroupDists.Rd |only bdots-2.0.0/bdots/man/doubleGauss_sac.Rd |only bdots-2.0.0/bdots/man/getBootDistPaired.Rd |only bdots-2.0.0/bdots/man/getBootDistUnpaired.Rd |only bdots-2.0.0/bdots/man/getT.Rd |only bdots-2.0.0/bdots/man/getTDist.Rd |only bdots-2.0.0/bdots/man/isDODpaired.Rd |only bdots-2.0.0/bdots/man/logistic_sac.Rd |only bdots-2.0.0/bdots/man/permTest.Rd |only bdots-2.0.0/bdots/tests/formula_test.R |only bdots-2.0.0/bdots/vignettes/bdots.Rmd | 59 +- bdots-2.0.0/bdots/vignettes/correlations.Rmd | 29 - bdots-2.0.0/bdots/vignettes/customCurves.Rmd | 33 - bdots-2.0.0/bdots/vignettes/refitCoef.Rmd | 33 - 62 files changed, 2629 insertions(+), 1198 deletions(-)
Title: Just Another Latent Space Network Clustering Algorithm
Description: Fit latent space network cluster models using an expectation-maximization algorithm. Enables flexible modeling of unweighted or weighted network data (with or without noise edges), supporting both directed and undirected networks (with or without degree and strength heterogeneity). Designed to handle large networks efficiently, it allows users to explore network structure through latent space representations, identify clusters (i.e., community detection) within network data, and simulate networks with varying clustering, connectivity patterns, and noise edges. Methodology for the implementation is described in Arakkal and Sewell (2025) <doi:10.1016/j.csda.2025.108228>.
Author: Alan Arakkal [aut, cre, cph] ,
Daniel Sewell [aut]
Maintainer: Alan Arakkal <alan-arakkal@uiowa.edu>
Diff between JANE versions 1.1.0 dated 2025-06-06 and 2.0.0 dated 2025-07-30
DESCRIPTION | 11 - MD5 | 36 +++-- NAMESPACE | 1 NEWS.md | 8 + R/JANE.R | 282 ++++++++++++++++++++++++++++++++++++------ R/check_initial_values.R | 29 +++- R/generics.R | 9 - R/imports.R | 2 R/sim_A.R | 14 +- R/specify_initial_values.R | 15 +- R/specify_priors.R | 131 ++++++++++++++----- build |only inst/doc |only man/JANE.Rd | 24 +-- man/sim_A.Rd | 12 - man/specify_initial_values.Rd | 10 - man/specify_priors.Rd | 76 ++++++++--- tests/testthat/test-JANE.R | 4 vignettes |only 19 files changed, 498 insertions(+), 166 deletions(-)
Title: Cone Constrained Convex Problems
Description: Routines for solving convex optimization problems with cone constraints by means of interior-point methods. The implemented algorithms are partially ported from CVXOPT, a Python module for convex optimization (see <https://cvxopt.org> for more information).
Author: Bernhard Pfaff [aut, cre],
Lieven Vandenberghe [cph] ,
Martin Andersen [cph] ,
Joachim Dahl [cph]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between cccp versions 0.3-1 dated 2023-12-09 and 0.3-2 dated 2025-07-30
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- man/Rcpp_CONEC-class.Rd | 4 ++-- man/Rcpp_CPS-class.Rd | 4 ++-- man/Rcpp_CTRL-class.Rd | 4 ++-- man/Rcpp_DCP-class.Rd | 4 ++-- man/Rcpp_DLP-class.Rd | 4 ++-- man/Rcpp_DNL-class.Rd | 4 ++-- man/Rcpp_DQP-class.Rd | 4 ++-- man/Rcpp_PDV-class.Rd | 4 ++-- 10 files changed, 29 insertions(+), 29 deletions(-)
Title: Analyze Shot Group Data
Description: Analyzes shooting data with respect to group shape,
precision, and accuracy. This includes graphical methods,
descriptive statistics, and inference tests using standard,
but also non-parametric and robust statistical methods.
Implements distributions for radial error in bivariate normal
variables. Works with files exported by 'OnTarget PC/TDS',
'Silver Mountain' e-target, 'ShotMarker' e-target, 'SIUS'
e-target, or 'Taran', as well as with custom data files in
text format. Supports inference from range statistics such as
extreme spread. Includes a set of web-based graphical user
interfaces.
Author: Daniel Wollschlaeger [aut, cre]
Maintainer: Daniel Wollschlaeger <dwoll@kuci.org>
Diff between shotGroups versions 0.8.2 dated 2022-09-17 and 0.8.4 dated 2025-07-30
DESCRIPTION | 28 +-- MD5 | 132 ++++++++-------- NAMESPACE | 11 - R/CEPs.R | 1 R/aaa.R |only R/compareGroups.R | 61 ++++--- R/drawGroup.R | 32 ++- R/efficiency.R | 148 +++++++++--------- R/getCEP.R | 23 +- R/getConfEll.R | 41 +++- R/getDistToCtr.R | 2 R/getMinEllipse.R | 9 - R/getRangeStat.R | 29 ++- R/getRangeStatCI.R |only R/getRangeStatEff.R |only R/getXYmat.R | 2 R/groupLocation.R | 21 +- R/groupShape.R | 55 ++++-- R/groupSpread.R | 57 ++++-- R/hoyt.R | 2 R/mvnEll.R | 21 -- R/range2CEP.R |only R/range2sigma.R | 96 +++-------- R/rangeStat.R | 8 R/rayleigh.R | 40 ++-- R/readData.R | 189 ++++++++++++++++++++++- R/readDataSM.R | 14 - R/runGUI.R | 2 R/saddlepoint.R | 4 R/scaleGroup.R |only R/unitConversion.R | 6 R/unix/getFileNames.R | 8 R/windows/getFileNames.R | 8 build/vignette.rds |binary data/DF300BLK.rda |binary data/DF300BLKhl.rda |binary data/DFcciHV.rda |binary data/DFcm.rda |binary data/DFdistr.rda |binary data/DFinch.rda |binary data/DFlandy01.rda |binary data/DFlandy02.rda |binary data/DFlandy03.rda |binary data/DFlandy04.rda |binary data/DFlistCm.rda |binary data/DFsavage.rda |binary data/DFscar17.rda |binary data/DFtalon.rda |binary data/targets.rda |binary inst/ChangeLog | 34 ++++ inst/doc/shotGroups.R | 22 +- inst/doc/shotGroups.Rnw | 13 - inst/doc/shotGroups.pdf |binary inst/shotGroups_AnalyzeGroups/app.R | 14 + inst/shotGroups_AnalyzeGroups/app_ui_tab_about.R | 26 +-- inst/shotGroups_AnalyzeGroups/app_ui_tab_data.R | 4 inst/shotGroups_HitProb/app.R | 8 inst/shotGroups_HitProb/app_ui_tab_about.R | 15 - inst/shotGroups_HitProb/app_ui_tab_data.R | 3 man/compareGroups.Rd | 6 man/getRangeStat.Rd | 14 + man/getRangeStatCI.Rd |only man/getRangeStatEff.Rd |only man/getRayParam.Rd | 7 man/range2CEP.Rd | 2 man/range2sigma.Rd | 6 man/readDataArcheryWC.Rd |only man/readDataSIUS.Rd |only man/scaleGroup.Rd |only man/shotGroups-package.Rd | 10 - vignettes/lit.bib | 36 ++-- vignettes/shotGroups.Rnw | 13 - 72 files changed, 817 insertions(+), 466 deletions(-)
Title: Utilities for Interacting with the 'Posit Connect' Server API
Description: Provides a helpful 'R6' class and methods for interacting with
the 'Posit Connect' Server API along with some meaningful utility functions
for regular tasks. API documentation varies by 'Posit Connect' installation
and version, but the latest documentation is also hosted publicly at
<https://docs.posit.co/connect/api/>.
Author: Toph Allen [aut, cre],
Neal Richardson [aut],
Sean Lopp [aut],
Cole Arendt [aut],
Posit, PBC [cph, fnd]
Maintainer: Toph Allen <toph@posit.co>
Diff between connectapi versions 0.7.0 dated 2025-03-27 and 0.8.0 dated 2025-07-30
connectapi-0.7.0/connectapi/man/dashboard_url_chr.Rd |only connectapi-0.7.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/01234567.json |only connectapi-0.7.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/12345678.json |only connectapi-0.7.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/23456789.json |only connectapi-0.7.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/34567890.json |only connectapi-0.7.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/8f37d6e0.json |only connectapi-0.7.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/951bf3ad.json |only connectapi-0.7.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/c3426b0b.json |only connectapi-0.7.0/connectapi/tests/testthat/2024.08.0/__api__/v1/content/f2f37341.json |only connectapi-0.7.0/connectapi/tests/testthat/2024.08.0/__api__/v1/oauth/integrations/credentials-8dea8e-POST.json |only 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Title: Network-Based Gene Set Analysis
Description: Carry out network-based gene set analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data. Implements methods described in Shojaie A, Michailidis G (2010) <doi:10.1093/biomet/asq038>, Shojaie A, Michailidis G (2009) <doi:10.1089/cmb.2008.0081>, and Ma J, Shojaie A, Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.
Author: Michael Hellstern [aut, cre],
Ali Shojaie [aut],
Jing Ma [aut],
Kun Yue [aut]
Maintainer: Michael Hellstern <mikeh1@uw.edu>
Diff between netgsa versions 4.0.5 dated 2023-11-14 and 4.0.6 dated 2025-07-30
DESCRIPTION | 8 MD5 | 16 - NEWS.md | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/netgsa.html | 565 +++++++++++++++++++++++++++++++++++--------------- man/netEst.dir.Rd | 2 man/netEst.undir.Rd | 2 man/netgsa-package.Rd | 2 9 files changed, 420 insertions(+), 178 deletions(-)
Title: Analysis and Visualisation of Musical Audio and Video Movement
Synchrony Data
Description: Analysis and visualisation of synchrony, interaction, and joint
movements from audio and video movement data of a group of music performers. The demo is data described in Clayton, Leante, and
Tarsitani (2021) <doi:10.17605/OSF.IO/KS325>, while example analyses
can be found in Clayton, Jakubowski, and Eerola (2019)
<doi:10.1177/1029864919844809>. Additionally, wavelet analysis
techniques have been applied to examine movement-related
musical interactions, as shown in Eerola et al. (2018)
<doi:10.1098/rsos.171520>.
Author: Tuomas Eerola [aut, cre, cph] ,
Martin Clayton [aut] ,
Paul Emms [aut]
Maintainer: Tuomas Eerola <tuomas.eerola@durham.ac.uk>
Diff between movementsync versions 0.1.4 dated 2023-06-09 and 0.1.5 dated 2025-07-30
DESCRIPTION | 13 ++++--- MD5 | 62 ++++++++++++++++++------------------ NEWS.md | 4 ++ R/granger.R | 2 - R/plot_diagnostics.R | 2 - man/apply_filter_sgolay.Rd | 4 +- man/clip_splice.Rd | 2 - man/get_data_points.Rd | 4 +- man/get_duration_annotation_data.Rd | 4 +- man/get_feature_data.Rd | 4 +- man/get_filtered_views.Rd | 4 +- man/get_joined_view.Rd | 4 +- man/get_metre_data.Rd | 4 +- man/get_onsets_selected_data.Rd | 4 +- man/get_processed_view.Rd | 2 - man/get_processed_views.Rd | 2 - man/get_raw_optflow_view.Rd | 4 +- man/get_raw_view.Rd | 2 - man/get_raw_views.Rd | 2 - man/get_recording.Rd | 4 +- man/get_sample_recording.Rd | 4 +- man/get_spliced_view.Rd | 2 - man/is_splice_overlapping.Rd | 2 - man/merge_splice.Rd | 2 - man/plot.GrangerInteraction.Rd | 2 - man/plot.View.Rd | 2 - man/splice_time.Duration.Rd | 2 - man/splice_time.Metre.Rd | 2 - man/splice_time.OnsetsDifference.Rd | 2 - man/splice_time.View.Rd | 2 - man/splice_time.list.Rd | 2 - man/split.SplicedView.Rd | 4 +- 32 files changed, 83 insertions(+), 78 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Patrick Schratz [aut] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [aut],
Florian Pfisterer [aut] ,
Raphael Sonabend [aut] ,
Lennart Schneider [ctb] , [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3 versions 1.0.1 dated 2025-07-03 and 1.1.0 dated 2025-07-30
DESCRIPTION | 21 ++++---- MD5 | 77 ++++++++++++++++--------------- NAMESPACE | 2 NEWS.md | 7 ++ R/LearnerClassif.R | 65 ++++++++++++++++++++++++++ R/LearnerRegr.R | 70 ++++++++++++++++++++++++++++ R/LearnerRegrDebug.R | 42 ++++++++++++++++ R/MeasureRegrPinball.R | 4 - R/MeasureRegrRQR.R |only R/assertions.R | 3 + R/bibentries.R | 12 ++++ build/partial.rdb |binary inst/testthat/helper_autotest.R | 27 ++++++++++ man/LearnerClassif.Rd | 34 +++++++++++++ man/LearnerRegr.Rd | 34 +++++++++++++ man/Measure.Rd | 1 man/MeasureClassif.Rd | 1 man/MeasureRegr.Rd | 1 man/MeasureSimilarity.Rd | 1 man/mlr_assertions.Rd | 6 +- man/mlr_learners_classif.debug.Rd | 1 man/mlr_learners_classif.featureless.Rd | 1 man/mlr_learners_classif.rpart.Rd | 1 man/mlr_learners_regr.debug.Rd | 9 +++ man/mlr_learners_regr.featureless.Rd | 1 man/mlr_learners_regr.rpart.Rd | 1 man/mlr_measures.Rd | 1 man/mlr_measures_aic.Rd | 1 man/mlr_measures_bic.Rd | 1 man/mlr_measures_classif.costs.Rd | 1 man/mlr_measures_debug_classif.Rd | 1 man/mlr_measures_elapsed_time.Rd | 1 man/mlr_measures_internal_valid_score.Rd | 1 man/mlr_measures_oob_error.Rd | 1 man/mlr_measures_regr.pinball.Rd | 15 +++--- man/mlr_measures_regr.rqr.Rd |only man/mlr_measures_regr.rsq.Rd | 1 man/mlr_measures_selected_features.Rd | 1 tests/testthat/test_LearnerClassif.R |only tests/testthat/test_LearnerRegr.R |only tests/testthat/test_MeasureRegrRQR.R |only tests/testthat/test_autotest.R | 21 ++++++++ 42 files changed, 408 insertions(+), 60 deletions(-)
Title: Extended Evolutionary and Genetic Algorithms
Description: Implementation of a scalable, highly configurable, and
e(x)tended architecture for (e)volutionary and (g)enetic (a)lgorithms.
Multiple representations (binary, real-coded, permutation, and
derivation-tree), a rich collection of genetic operators,
as well as an extended processing pipeline are provided
for genetic algorithms (Goldberg, D. E. (1989, ISBN:0-201-15767-5)),
differential evolution (Price, Kenneth V., Storn, Rainer M. and Lampinen, Jouni A. (2005)
<doi:10.1007/3-540-31306-0>), simulated annealing (Aarts, E., and Korst, J.
(1989, ISBN:0-471-92146-7)), grammar-based genetic programming
(Geyer-Schulz (1997, ISBN:978-3-7908-0830-X)), and grammatical evolution
(Ryan, C., O'Neill, M., and Collins, J. J. (2018) <doi:10.1007/978-3-319-78717-6>).
All algorithms reuse basic adaptive mechanisms for performance optimization.
Sequential or parallel execution (on multi-core machines,
local clusters, and high-performance computing environments)
is available for all algorithms. S [...truncated...]
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xega versions 0.9.0.8 dated 2025-04-17 and 0.9.0.12 dated 2025-07-30
DESCRIPTION | 10 +- MD5 | 22 ++-- NAMESPACE | 3 NEWS | 28 +++++ R/sgXReplicationFactory.R | 4 R/xega-package.R | 37 +++++++ R/xegaResult.R |only R/xegaRun.R | 207 +++++++++++++++++++++++++++++++++++++------ R/xegaVersion.R | 4 man/sgXReplicationFactory.Rd | 4 man/xega.Rd | 39 ++++++++ man/xegaAnyTimeResult.Rd |only man/xegaRun.Rd | 169 ++++++++++++++++++++++++++++++----- 13 files changed, 461 insertions(+), 66 deletions(-)
Title: Adaptation of the Coloc Method for PheWAS
Description: A Bayesian method for Phenome-wide association studies (PheWAS) that identifies causal associations between genetic variants and traits, while simultaneously addressing confounding due to linkage disequilibrium. For details see
Manipur et al (2024, Nature Communications) <doi:10.1038/s41467-024-49990-8>.
Author: Ichcha Manipur [aut, cre],
Chris Wallace [aut]
Maintainer: Ichcha Manipur <im504@cam.ac.uk>
Diff between cophescan versions 1.4.1 dated 2024-06-11 and 1.4.2 dated 2025-07-30
DESCRIPTION | 8 - MD5 | 32 +++---- NEWS.md | 12 +- R/copheplots.R | 2 R/multivarsusie.R | 17 ++-- R/singlevar.R | 14 ++- README.md | 16 +++ inst/doc/FixedPriors_03.html | 31 ++++--- inst/doc/HierarchicalPriors_04.html | 140 ++++++++++++++++----------------- inst/doc/InputData_02.html | 6 - inst/doc/IntroductionCoPheScan_01.Rmd | 4 inst/doc/IntroductionCoPheScan_01.html | 30 +++---- man/cophe.prepare.dat.susie.Rd | 2 man/cophe.susie.Rd | 4 man/cophe.susie.lbf.Rd | 2 man/cophe_heatmap.Rd | 2 vignettes/IntroductionCoPheScan_01.Rmd | 4 17 files changed, 176 insertions(+), 150 deletions(-)
Title: Tidy Structural Equation Modeling
Description: A tidy workflow for generating, estimating, reporting,
and plotting structural equation models using 'lavaan', 'OpenMx', or
'Mplus'. Throughout this workflow, elements of syntax, results, and graphs
are represented as 'tidy' data, making them easy to customize.
Includes functionality to estimate latent class analyses, and to plot
'dagitty' and 'igraph' objects.
Author: Caspar J. van Lissa [aut, cre] ,
Mauricio Garnier-Villarreal [ctb] ,
Frank C Gootjes [ctb]
Maintainer: Caspar J. van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between tidySEM versions 0.2.8 dated 2025-03-04 and 0.2.9 dated 2025-07-30
DESCRIPTION | 27 MD5 | 84 - NAMESPACE | 10 R/data-mac.R | 2 R/empathy.R | 2 R/igraph.R |only R/lr_vml.R | 3 R/maene_identity.R | 2 R/mixture-3step.R | 4 R/mixture-pseudo_class.R | 6 R/mx_mixture.R | 2 R/mx_temp_start.R | 206 +-- R/plot-bivariate.R | 13 R/plot-plot_sem.R | 6 R/results-table_results.R | 1463 +++++++++++++-------------- R/syntax-create_scales.R | 2 R/syntax-run.R | 344 +++--- R/wald_test.R | 68 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/Generating_syntax.html | 8 inst/doc/SMART_LCA_checklist.html | 2 inst/doc/Tabulating_results.R | 2 inst/doc/Tabulating_results.Rmd | 6 inst/doc/Tabulating_results.html | 12 man/BCH.Rd | 3 man/append_class_draws.Rd | 1 man/create_scales.Rd | 2 man/curry_mac.Rd | 2 man/empathy.Rd | 2 man/get_estimates.Rd |only man/graph_sem.Rd | 3 man/lr_lmr.Rd | 3 man/lr_test.Rd | 1 man/maene_identity.Rd | 2 man/mixture_starts.Rd | 2 man/plot_bivariate.Rd | 1 man/pseudo_class.Rd | 1 tests/testthat.R | 1 tests/testthat/data_mix_ordinal.csv |only tests/testthat/fit.testdata |only tests/testthat/test-blavaan_suggest.R |only tests/testthat/test-dagitty_nodes_edges.R | 135 +- tests/testthat/test-plot_igraph.R |only tests/testthat/test-pseudo_class_technique.R | 1 vignettes/Tabulating_results.Rmd | 6 46 files changed, 1268 insertions(+), 1172 deletions(-)
Title: Build and Manipulate Study Cohorts Using a Common Data Model
Description: Create and manipulate study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Nuria Mercade-Besora [aut] ,
Marta Alcalde-Herraiz [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Xihang Chen [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CohortConstructor versions 0.4.0 dated 2025-05-08 and 0.5.0 dated 2025-07-30
DESCRIPTION | 6 MD5 | 350 +- NAMESPACE | 128 NEWS.md |only R/CohortConstructor-package.R | 24 R/addIndex.R | 148 - R/benchmark.R | 1534 +++++------ R/collapseCohorts.R | 189 - R/conceptCohort.R | 38 R/copyCohorts.R | 198 - R/deathCohort.R | 265 + R/documentationHelper.R | 389 +- R/entryAtColumnDate.R | 208 - R/exitAtDate.R | 490 +-- R/intersectCohorts.R | 1111 ++++---- R/matchCohorts.R | 882 +++--- R/measurementCohort.R | 592 ++-- R/mockCohortConstructor.R | 222 - R/padCohortDate.R | 704 ++--- R/reexports.R | 62 R/renameCohort.R | 116 R/requireCohortIntersect.R | 440 +-- R/requireConceptIntersect.R | 401 +- R/requireDateRange.R | 606 ++-- R/requireDemographics.R | 1140 ++++---- R/requireIsEntry.R | 552 ++-- R/requireMinCohortCount.R | 166 - R/requireTableIntersect.R | 303 +- R/sampleCohorts.R | 242 - R/stratifyCohorts.R | 510 +-- R/subsetCohorts.R | 132 R/sysdata.rda |binary R/trimDemographics.R | 848 +++--- R/unionCohorts.R | 245 - R/utilities.R | 24 R/validateFunctions.R | 346 +- R/yearCohorts.R | 412 +-- README.md | 614 ++-- build/vignette.rds |binary data/benchmarkData.rda |binary inst/WORDLIST | 34 inst/doc/a00_introduction.R | 12 inst/doc/a00_introduction.Rmd | 78 inst/doc/a00_introduction.html | 624 ++-- inst/doc/a01_building_base_cohorts.R | 420 +-- inst/doc/a01_building_base_cohorts.Rmd | 560 ++-- inst/doc/a01_building_base_cohorts.html | 1574 +++++------ inst/doc/a02_cohort_table_requirements.R | 280 +- inst/doc/a02_cohort_table_requirements.Rmd | 416 +-- inst/doc/a02_cohort_table_requirements.html | 3556 +++++++++++++------------- inst/doc/a03_require_demographics.R | 158 - inst/doc/a03_require_demographics.Rmd | 240 - inst/doc/a03_require_demographics.html | 3364 ++++++++++++------------ inst/doc/a04_require_intersections.R | 215 - inst/doc/a04_require_intersections.Rmd | 305 +- inst/doc/a04_require_intersections.html | 2188 +++------------ inst/doc/a05_update_cohort_start_end.R | 232 - inst/doc/a05_update_cohort_start_end.Rmd | 494 +-- inst/doc/a05_update_cohort_start_end.html | 1370 +++++----- inst/doc/a06_concatanate_cohorts.R | 123 inst/doc/a06_concatanate_cohorts.Rmd | 182 - inst/doc/a06_concatanate_cohorts.html | 1299 ++------- inst/doc/a07_filter_cohorts.R | 165 - inst/doc/a07_filter_cohorts.Rmd | 230 - inst/doc/a07_filter_cohorts.html | 846 ++---- inst/doc/a08_split_cohorts.R | 222 - inst/doc/a08_split_cohorts.Rmd | 351 +- inst/doc/a08_split_cohorts.html | 1088 +++---- inst/doc/a09_combine_cohorts.R | 214 - inst/doc/a09_combine_cohorts.html | 850 +++--- inst/doc/a10_match_cohorts.R | 106 inst/doc/a10_match_cohorts.Rmd | 206 - inst/doc/a10_match_cohorts.html | 949 +++--- inst/doc/a11_benchmark.R | 428 +-- inst/doc/a11_benchmark.Rmd | 93 inst/doc/a11_benchmark.html | 1005 +++---- inst/doc/a12_behind_the_scenes.R | 146 - inst/doc/a12_behind_the_scenes.html | 846 +++--- man/CohortConstructor-package.Rd | 74 man/atFirstDoc.Rd |only man/benchmarkCohortConstructor.Rd | 68 man/cdmDoc.Rd | 24 man/cohortDoc.Rd | 24 man/cohortIdModifyDoc.Rd | 30 man/cohortIdSubsetDoc.Rd | 28 man/collapseCohorts.Rd | 82 man/collapseDoc.Rd | 26 man/columnDateDoc.Rd | 38 man/conceptCohort.Rd | 232 - man/conceptSetDoc.Rd | 26 man/copyCohorts.Rd | 78 man/daysDoc.Rd | 26 man/deathCohort.Rd | 96 man/demographicsCohort.Rd | 130 man/entryAtFirstDate.Rd | 130 man/entryAtLastDate.Rd | 130 man/exitAtDeath.Rd | 100 man/exitAtFirstDate.Rd | 130 man/exitAtLastDate.Rd | 130 man/exitAtObservationEnd.Rd | 108 man/gapDoc.Rd | 26 man/intersectCohorts.Rd | 130 man/keepOriginalCohortsDoc.Rd | 26 man/matchCohorts.Rd | 146 - man/measurementCohort.Rd | 252 - man/mockCohortConstructor.Rd | 132 man/nameDoc.Rd | 24 man/padCohortDate.Rd | 132 man/padCohortEnd.Rd | 136 man/padCohortStart.Rd | 130 man/padObservationDoc.Rd | 28 man/reexports.Rd | 50 man/renameCohort.Rd | 90 man/requireAge.Rd | 112 man/requireCohortIntersect.Rd | 168 - man/requireConceptIntersect.Rd | 171 - man/requireDemographics.Rd | 138 - man/requireDemographicsDoc.Rd | 56 man/requireFutureObservation.Rd | 114 man/requireInDateRange.Rd | 116 man/requireIntersectDoc.Rd | 78 man/requireIsEntry.Rd | 96 man/requireIsFirstEntry.Rd | 90 man/requireIsLastEntry.Rd | 90 man/requireMinCohortCount.Rd | 92 man/requirePriorObservation.Rd | 114 man/requireSex.Rd | 102 man/requireTableIntersect.Rd | 167 - man/sampleCohorts.Rd | 72 man/softValidationDoc.Rd | 34 man/stratifyCohorts.Rd | 126 man/subsetCohorts.Rd | 90 man/trimDemographics.Rd | 122 man/trimToDateRange.Rd | 120 man/unionCohorts.Rd | 120 man/windowDoc.Rd | 26 man/yearCohorts.Rd | 96 tests/testthat.R | 24 tests/testthat/setup.R | 138 - tests/testthat/test-addIndex.R | 136 tests/testthat/test-benchmark.R | 182 - tests/testthat/test-collapseCohorts.R | 584 ++-- tests/testthat/test-conceptCohort.R | 2538 +++++++++--------- tests/testthat/test-copyCohorts.R | 281 +- tests/testthat/test-deathCohort.R | 945 +++--- tests/testthat/test-demographicsCohort.R | 494 +-- tests/testthat/test-entryAtColumnDate.R | 544 +-- tests/testthat/test-exitAtColumnDate.R | 688 ++--- tests/testthat/test-exitAtDate.R | 524 ++- tests/testthat/test-intersectCohorts.R | 1431 +++++----- tests/testthat/test-matchCohorts.R | 708 ++--- tests/testthat/test-measurementCohort.R | 1374 +++++----- tests/testthat/test-padCohortDate.R | 822 +++--- tests/testthat/test-requireCohortIntersect.R | 864 +++--- tests/testthat/test-requireConceptIntersect.R | 905 +++--- tests/testthat/test-requireDateRange.R | 580 ++-- tests/testthat/test-requireDemographics.R | 872 +++--- tests/testthat/test-requireIsEntry.R | 674 ++-- tests/testthat/test-requireMinCohortCount.R | 304 +- tests/testthat/test-requireTableIntersect.R | 823 +++--- tests/testthat/test-sampleCohorts.R | 336 +- tests/testthat/test-stratifyCohorts.R | 328 +- tests/testthat/test-subsetCohorts.R | 343 +- tests/testthat/test-trimDemographics.R | 907 +++--- tests/testthat/test-unionCohorts.R | 941 ++++-- tests/testthat/test-yearCohorts.R | 511 ++- vignettes/a00_introduction.Rmd | 78 vignettes/a01_building_base_cohorts.Rmd | 560 ++-- vignettes/a02_cohort_table_requirements.Rmd | 416 +-- vignettes/a03_require_demographics.Rmd | 240 - vignettes/a04_require_intersections.Rmd | 305 +- vignettes/a05_update_cohort_start_end.Rmd | 494 +-- vignettes/a06_concatanate_cohorts.Rmd | 182 - vignettes/a07_filter_cohorts.Rmd | 230 - vignettes/a08_split_cohorts.Rmd | 351 +- vignettes/a10_match_cohorts.Rmd | 206 - vignettes/a11_benchmark.Rmd | 93 177 files changed, 34308 insertions(+), 34276 deletions(-)
More information about CohortConstructor at CRAN
Permanent link
Title: Project MOSAIC Statistics and Mathematics Teaching Utilities
Description: Data sets and utilities from Project MOSAIC (<http://www.mosaic-web.org>) used
to teach mathematics, statistics, computation and modeling. Funded by the
NSF, Project MOSAIC is a community of educators working to tie together
aspects of quantitative work that students in science, technology,
engineering and mathematics will need in their professional lives, but
which are usually taught in isolation, if at all.
Author: Randall Pruim [aut, cre],
Daniel T. Kaplan [aut],
Nicholas J. Horton [aut]
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between mosaic versions 1.9.1 dated 2024-02-23 and 1.9.2 dated 2025-07-30
mosaic-1.9.1/mosaic/tests/testthat/Rplots.pdf |only mosaic-1.9.1/mosaic/tests/testthat/_snaps |only mosaic-1.9.2/mosaic/DESCRIPTION | 8 mosaic-1.9.2/mosaic/MD5 | 129 ++---------- mosaic-1.9.2/mosaic/NAMESPACE | 1 mosaic-1.9.2/mosaic/NEWS.md | 4 mosaic-1.9.2/mosaic/R/chisq.R | 2 mosaic-1.9.2/mosaic/R/confint.R | 1 mosaic-1.9.2/mosaic/R/frequencyPolygon.R | 2 mosaic-1.9.2/mosaic/R/mosaic-package.R | 4 mosaic-1.9.2/mosaic/R/plotCumfreq.R | 2 mosaic-1.9.2/mosaic/R/plotModel.R | 2 mosaic-1.9.2/mosaic/R/themes.R | 6 mosaic-1.9.2/mosaic/R/xpnorm.R | 4 mosaic-1.9.2/mosaic/build/vignette.rds |binary mosaic-1.9.2/mosaic/inst/doc/MinimalRgg.R | 218 ++++++++++----------- mosaic-1.9.2/mosaic/inst/doc/MinimalRgg.pdf |binary mosaic-1.9.2/mosaic/inst/doc/Resampling.R | 6 mosaic-1.9.2/mosaic/inst/doc/Resampling.html | 33 +-- mosaic-1.9.2/mosaic/inst/doc/mosaic-resources.html | 4 mosaic-1.9.2/mosaic/man/cdist.Rd | 2 mosaic-1.9.2/mosaic/man/chisq.Rd | 2 mosaic-1.9.2/mosaic/man/cnorm.Rd | 2 mosaic-1.9.2/mosaic/man/freqpolygon.Rd | 2 mosaic-1.9.2/mosaic/man/pdist.Rd | 2 mosaic-1.9.2/mosaic/man/plotCumfreq.Rd | 2 mosaic-1.9.2/mosaic/man/plotModel.Rd | 2 mosaic-1.9.2/mosaic/man/qdist.Rd | 2 mosaic-1.9.2/mosaic/man/themes.Rd | 6 mosaic-1.9.2/mosaic/man/ttest.Rd | 7 mosaic-1.9.2/mosaic/man/xpnorm.Rd | 4 31 files changed, 198 insertions(+), 261 deletions(-)
Title: Exploring Heterogeneity in Meta-Analysis using Random Forests
Description: Conduct random forests-based meta-analysis, obtain partial dependence plots for metaforest and classic meta-analyses, and cross-validate and tune metaforest- and classic meta-analyses in conjunction with the caret package. A requirement of classic meta-analysis is that the studies being aggregated are conceptually similar, and ideally, close replications. However, in many fields, there is substantial heterogeneity between studies on the same topic. Classic meta-analysis lacks the power to assess more than a handful of univariate moderators. MetaForest, by contrast, has substantial power to explore heterogeneity in meta-analysis. It can identify important moderators from a larger set of potential candidates (Van Lissa, 2020). This is an appealing quality, because many meta-analyses have small sample sizes. Moreover, MetaForest yields a measure of variable importance which can be used to identify important moderators, and offers partial prediction plots to explore the shape of the margin [...truncated...]
Author: Caspar J. Van Lissa [aut, cre]
Maintainer: Caspar J. Van Lissa <c.j.vanlissa@gmail.com>
Diff between metaforest versions 0.1.4 dated 2024-01-26 and 0.1.5 dated 2025-07-30
DESCRIPTION | 29 +++-- MD5 | 67 ++++++------ NAMESPACE | 5 NEWS.md | 1 R/MF.R | 24 ++-- R/MF_cluster.R | 141 ++++++++++++++------------ R/MetaForest.R | 14 +- R/ModelInfo_mf.R | 17 +-- R/ModelInfo_rma.R | 5 R/PartialDependence.R | 75 ++++++------- R/VarImpPlot.R | 6 - R/WeightedScatter.R | 10 - R/coef_test.R | 5 R/marginal_predictions.R | 17 ++- R/plot.MetaForest.R | 5 R/preselect.R | 34 +++--- R/rma_dl.R |only R/summary.MetaForest.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction_to_metaforest.R | 167 +++++++++++++++---------------- inst/doc/Introduction_to_metaforest.Rmd | 1 inst/doc/Introduction_to_metaforest.html | 8 - man/MetaForest.Rd | 11 +- man/ModelInfo_mf.Rd | 17 +-- man/ModelInfo_rma.Rd | 3 man/PartialDependence.Rd | 5 man/coef_test.Rd | 5 man/preselect.Rd | 15 +- man/preselect_vars.Rd | 15 +- tests/testthat.R | 1 tests/testthat/test-clusterMF.R | 15 +- tests/testthat/test-s4.R | 5 tests/testthat/test-summary.R | 15 +- vignettes/Introduction_to_metaforest.Rmd | 1 35 files changed, 398 insertions(+), 345 deletions(-)
Title: MedPC Text Parser
Description: Parses information from text files with specific utility aimed at pulling information from Med Associate's (MPC) files. These functions allow for further analysis of MPC files.
Author: Olivia Ortelli [aut, cre],
Tony Colarusso [aut]
Maintainer: Olivia Ortelli <oortelli@wakehealth.edu>
Diff between medparser versions 0.1.0 dated 2024-04-27 and 0.2.0 dated 2025-07-30
DESCRIPTION | 12 +++++++----- MD5 | 2 +- 2 files changed, 8 insertions(+), 6 deletions(-)
Title: Utility Functions for Large-scale Data
Description: Utility functions for large-scale data. For now, package 'bigutilsr'
mainly includes functions for outlier detection and unbiased PCA projection.
Author: Florian Prive [aut, cre]
Maintainer: Florian Prive <florian.prive.21@gmail.com>
Diff between bigutilsr versions 0.3.4 dated 2021-04-13 and 0.3.11 dated 2025-07-30
DESCRIPTION | 12 ++-- MD5 | 59 ++++++++++++-------- NAMESPACE | 3 + R/KNN.R | 2 R/OGK.R | 2 R/RcppExports.R | 25 ++++++++ R/glasso.R |only R/outlier-tukey.R | 9 +-- R/varimax.R |only README.md | 11 ++- man/LOF.Rd | 120 +++++++++++++++++++++--------------------- man/as_model_matrix.Rd | 46 ++++++++-------- man/bigutilsr-package.Rd | 47 ++++++++-------- man/covRob.Rd | 38 ++++++------- man/covrob_ogk.Rd | 20 ------- man/geometric_median.Rd | 84 ++++++++++++++--------------- man/hist_out.Rd | 98 +++++++++++++++++----------------- man/knn_parallel.Rd | 84 ++++++++++++++--------------- man/maha_trans.Rd | 62 ++++++++++----------- man/nclass.scottRob.Rd | 64 +++++++++++----------- man/pca_OADP_proj.Rd | 112 +++++++++++++++++++-------------------- man/pca_nspike.Rd | 70 ++++++++++++------------ man/prob_dist.Rd | 82 ++++++++++++++-------------- man/procrustes.Rd | 82 ++++++++++++++-------------- man/regul_glasso.Rd |only man/solve_linear_system.Rd |only man/tukey_mc_up.Rd | 89 +++++++++++++++---------------- man/varimax2.Rd |only src/Makevars |only src/RcppExports.cpp | 38 +++++++++++++ src/glasso.cpp |only src/linear-system.cpp |only tests/testthat/test-OGK.R | 16 +++++ tests/testthat/test-glasso.R |only tests/testthat/test-solve.R |only tests/testthat/test-varimax.R |only 36 files changed, 677 insertions(+), 598 deletions(-)
Title: Tools to Generate Daily-Precipitation Time Series
Description: The method 'generate()' is extended for spatial multi-site
stochastic generation of daily precipitation. It generates precipitation
occurrence in several sites using logit regression (Generalized Linear
Models) and the approach by D.S. Wilks (1998) <doi:10.1016/S0022-1694(98)00186-3> .
Author: Emanuele Cordano [aut, cre, ctb]
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>
Diff between RGENERATEPREC versions 1.2.9 dated 2022-01-20 and 1.3.2 dated 2025-07-30
RGENERATEPREC-1.2.9/RGENERATEPREC/README.md |only RGENERATEPREC-1.2.9/RGENERATEPREC/inst/doc_copy |only RGENERATEPREC-1.3.2/RGENERATEPREC/DESCRIPTION | 24 RGENERATEPREC-1.3.2/RGENERATEPREC/MD5 | 55 RGENERATEPREC-1.3.2/RGENERATEPREC/NAMESPACE | 3 RGENERATEPREC-1.3.2/RGENERATEPREC/R/Gamma.R | 6 RGENERATEPREC-1.3.2/RGENERATEPREC/R/GammaBlockmatrix.R | 6 RGENERATEPREC-1.3.2/RGENERATEPREC/R/PrecipitationOccurenceMultiSiteModel.R | 3 RGENERATEPREC-1.3.2/RGENERATEPREC/R/dw.spell.R | 14 RGENERATEPREC-1.3.2/RGENERATEPREC/R/generate.PrecipitationAmountModel.R |only RGENERATEPREC-1.3.2/RGENERATEPREC/R/generate.PrecipitationOccurenceModel.R | 44 RGENERATEPREC-1.3.2/RGENERATEPREC/R/omega.R | 14 RGENERATEPREC-1.3.2/RGENERATEPREC/R/omega_inv.R | 6 RGENERATEPREC-1.3.2/RGENERATEPREC/R/omega_root.R | 4 RGENERATEPREC-1.3.2/RGENERATEPREC/R/predict.PrecipitationOccurenceModel.R | 6 RGENERATEPREC-1.3.2/RGENERATEPREC/build/partial.rdb |binary RGENERATEPREC-1.3.2/RGENERATEPREC/build/vignette.rds |binary RGENERATEPREC-1.3.2/RGENERATEPREC/inst/CITATION | 43 RGENERATEPREC-1.3.2/RGENERATEPREC/inst/build_website.R |only RGENERATEPREC-1.3.2/RGENERATEPREC/inst/doc/precipitation_stochastic_generation_v8.html | 7837 ++++++++-- RGENERATEPREC-1.3.2/RGENERATEPREC/inst/example.generate_v20130120.R |only RGENERATEPREC-1.3.2/RGENERATEPREC/inst/example.generate_with_null_exogen_v20130120.R |only RGENERATEPREC-1.3.2/RGENERATEPREC/inst/tools_for_stochastic_weather_series_generation_in_r_environment.pdf |only RGENERATEPREC-1.3.2/RGENERATEPREC/man/CCGamma.Rd | 4 RGENERATEPREC-1.3.2/RGENERATEPREC/man/CCGammaToBlockmatrix.Rd | 8 RGENERATEPREC-1.3.2/RGENERATEPREC/man/dw.spell.Rd | 2 RGENERATEPREC-1.3.2/RGENERATEPREC/man/generate.Rd | 27 RGENERATEPREC-1.3.2/RGENERATEPREC/man/omega.Rd | 12 RGENERATEPREC-1.3.2/RGENERATEPREC/man/omega_inv.Rd | 4 RGENERATEPREC-1.3.2/RGENERATEPREC/man/omega_root.Rd | 2 RGENERATEPREC-1.3.2/RGENERATEPREC/vignettes/bibliography.bib | 41 31 files changed, 7063 insertions(+), 1102 deletions(-)
Title: Tools for Post-Processing Predicted Values
Description: Models can be improved by post-processing class
probabilities, by: recalibration, conversion to hard probabilities,
assessment of equivocal zones, and other activities. 'probably'
contains tools for conducting these operations as well as calibration
tools and conformal inference techniques for regression models.
Author: Max Kuhn [aut, cre],
Davis Vaughan [aut],
Edgar Ruiz [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between probably versions 1.1.0 dated 2025-05-21 and 1.1.1 dated 2025-07-30
DESCRIPTION | 12 - MD5 | 32 +-- NEWS.md | 6 R/cal-estimate-utils.R | 2 R/cal-validate.R | 65 ++++++ build/vignette.rds |binary inst/doc/equivocal-zones.html | 4 inst/doc/where-to-use.html | 4 man/int_conformal_full.Rd | 92 --------- tests/testthat/_snaps/cal-estimate.md | 53 +++++ tests/testthat/_snaps/cal-plot.md | 243 ++++++++++++++++++++++++++ tests/testthat/_snaps/cal-validate.md | 56 +++++ tests/testthat/test-cal-estimate.R | 18 - tests/testthat/test-cal-plot.R | 50 +---- tests/testthat/test-cal-validate-multiclass.R | 4 tests/testthat/test-cal-validate.R | 61 ++++-- tests/testthat/test-conformal-intervals.R | 4 17 files changed, 513 insertions(+), 193 deletions(-)
Title: Study Design Toolbox for Movement Ecology Studies
Description: Toolbox and 'shiny' application to help researchers design
movement ecology studies, focusing on two key objectives: estimating
home range areas, and estimating fine-scale movement behavior,
specifically speed and distance traveled. It provides interactive
simulations and methodological guidance to support study planning and
decision-making. The application is described in Silva et al. (2023)
<doi:10.1111/2041-210X.14153>.
Author: Ines Silva [cre, aut, cph]
Maintainer: Ines Silva <i.simoes-silva@hzdr.de>
Diff between movedesign versions 0.3.1 dated 2025-06-24 and 0.3.2 dated 2025-07-30
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Title: Analyze Interconnection Structure of Tripartite Interaction
Networks
Description: In view of the analysis of the structural characteristics of the tripartite
network has been complete, however, there is still a lack of a unified
operation that can quickly obtain the corresponding characteristics of the
tripartite network.
To solve this insufficiency, 'ILSM' was designed for supporting calculating
such metrics of tripartite networks by functions of this R package.
Author: Weicheng Sun [aut, cre],
Chuan Yan [aut],
Yangyang Zhao [aut]
Maintainer: Weicheng Sun <sunwch2023@lzu.edu.cn>
Diff between ILSM versions 1.0.3.2 dated 2024-09-04 and 1.1.0.1 dated 2025-07-30
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Title: Map User-Created Functions
Description: Create an interactive function map by analyzing a specified
R script. It uses the find_dependencies() function from the
'functiondepends' package to recursively trace all user-defined
function dependencies.
Author: Antonio Fratamico [aut, cre]
Maintainer: Antonio Fratamico <fratamicoa@outlook.com>
Diff between funcMapper versions 1.0.1 dated 2025-07-24 and 1.0.2 dated 2025-07-30
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NAMESPACE | 4 ++++ NEWS.md | 4 ++++ R/build_dependency_map.R | 3 ++- R/funcMapper.R | 1 + R/get_edges_from_map.R | 1 + R/plot_dependency_graph.R | 1 + inst/doc/funcMapper-guidance.Rmd | 2 +- inst/doc/funcMapper-guidance.html | 4 +++- vignettes/funcMapper-guidance.Rmd | 2 +- 11 files changed, 31 insertions(+), 17 deletions(-)
Title: Foundations and Applications of Statistics Using R (2nd Edition)
Description: Data sets and utilities to accompany the second edition of
"Foundations and Applications of Statistics: an Introduction
using R" (R Pruim, published by AMS, 2017), a text covering
topics from probability and mathematical statistics at an advanced
undergraduate level. R is integrated throughout, and access to all
the R code in the book is provided via the snippet() function.
Author: Randall Pruim [aut, cre]
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between fastR2 versions 1.2.4 dated 2023-11-09 and 1.2.5 dated 2025-07-30
DESCRIPTION | 8 - MD5 | 28 ++--- R/SSplot.R | 2 R/col.fastR.R | 4 R/datasets.R | 2 R/fastR2-package.R | 3 R/maxLik2.R | 8 - build/vignette.rds |binary inst/doc/Errata2e.html | 243 ------------------------------------------------- man/MIAA05.Rd | 2 man/SSplot.Rd | 2 man/col.fastR.Rd | 4 man/fastR2-package.Rd | 9 + man/maxLik2.Rd | 6 - man/plot.maxLik2.Rd | 2 15 files changed, 47 insertions(+), 276 deletions(-)
Title: Genetic Population Level Functions
Description: This collection of gene representation-independent functions
implements the population layer of extended evolutionary and genetic
algorithms and its support. The population layer consists of functions
for initializing, logging, observing, evaluating a population of genes,
as well as of computing the next population. For parallel evaluation of a
population of genes 4 execution models - named Sequential, MultiCore,
FutureApply, and Cluster - are provided. They are implemented by
configuring the lapply() function. The execution model FutureApply can be
externally configured as recommended by Bengtsson (2021)
<doi:10.32614/RJ-2021-048>. Configurable acceptance rules and cooling
schedules (see Kirkpatrick, S., Gelatt, C. D. J, and Vecchi, M. P. (1983)
<doi:10.1126/science.220.4598.671>, and Aarts, E., and Korst, J.
(1989, ISBN:0-471-92146-7) offer simulated annealing or greedy randomized
approximate search procedure elements. Adaptive crossover and mutation
rates depending on po [...truncated...]
Author: Andreas Geyer-Schulz [aut, cre]
Maintainer: Andreas Geyer-Schulz <Andreas.Geyer-Schulz@kit.edu>
Diff between xegaPopulation versions 1.0.0.7 dated 2025-04-16 and 1.0.0.8 dated 2025-07-30
DESCRIPTION | 10 ++--- MD5 | 24 ++++++------ NAMESPACE | 3 + NEWS | 12 ++++++ R/xegaEvalPopulation.R | 73 +++++++++++++++++++++++++++++++++++---- R/xegaNextPopulation.R | 29 +++++++++------ man/asPipeline.Rd |only man/lFxegaGaGene.Rd | 4 +- man/xegaEvalPopulation.Rd | 11 ++++- man/xegaNextPopulation.Rd | 19 ++++++---- man/xegaRepEvalPopulation.Rd | 9 ++++ man/xegaRepairPop.Rd |only tests/testthat/test-replicate.R | 4 ++ tests/testthat/test-replicate2.R | 4 ++ 14 files changed, 157 insertions(+), 45 deletions(-)
More information about xegaPopulation at CRAN
Permanent link
Title: Response Item Networks
Description: Contains various tools to perform and visualize Response Item Networks ('ResIN's'). 'ResIN' binarizes ordered-categorical and qualitative response choices from (survey) data, calculates pairwise associations and maps the location of each item response as a node in a force-directed network. Please refer to <https://www.resinmethod.net/> for more details.
Author: Philip Warncke [cre, aut],
Dino Carpentras [aut],
Adrian Lueders [aut]
Maintainer: Philip Warncke <philip.warncke@ul.ie>
Diff between ResIN versions 2.2.0 dated 2025-07-11 and 2.2.1 dated 2025-07-30
ResIN-2.2.0/ResIN/vignettes/--find-assets.html |only ResIN-2.2.1/ResIN/DESCRIPTION | 18 +++++++++--------- ResIN-2.2.1/ResIN/MD5 | 24 ++++++++++++++---------- ResIN-2.2.1/ResIN/NAMESPACE | 12 ++++++++++++ ResIN-2.2.1/ResIN/R/ResIN.R | 16 ++++++++++++---- ResIN-2.2.1/ResIN/R/ResIN_boots_execute.R | 2 +- ResIN-2.2.1/ResIN/R/ResIN_boots_prepare.R | 4 ++-- ResIN-2.2.1/ResIN/R/ResIN_to_gephi.R | 2 +- ResIN-2.2.1/ResIN/R/ResIN_to_igraph.R | 2 +- ResIN-2.2.1/ResIN/R/ResIN_to_qgraph.R | 2 +- ResIN-2.2.1/ResIN/R/methods-ResIN.R |only ResIN-2.2.1/ResIN/inst/doc/ResIN-VIGNETTE.html | 2 +- ResIN-2.2.1/ResIN/man/autoplot.ResIN.Rd |only ResIN-2.2.1/ResIN/man/plot.ResIN.Rd |only ResIN-2.2.1/ResIN/man/print.ResIN.Rd |only ResIN-2.2.1/ResIN/man/summary.ResIN.Rd |only 16 files changed, 54 insertions(+), 30 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington', 'Ludwig' and Omnivariant Generalised Least-Squares ('OGLS') approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Th-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isoch [...truncated...]
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 6.6 dated 2025-05-08 and 6.7 dated 2025-07-30
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/bayes.R | 49 ++++++++++++++++++++++++++----------------------- R/ci.R | 32 ++++++++++++++++++-------------- R/diseq.R | 1 + R/isochron.R | 13 +++++++++---- R/ludwig.R | 8 ++++++-- R/weightedmean.R | 27 ++++++++++++++++----------- R/york2ludwig.R | 22 ++++++++++++---------- man/isochron.Rd | 5 +++++ man/ludwig.Rd | 6 ++++++ man/weightedmean.Rd | 3 +++ 12 files changed, 117 insertions(+), 79 deletions(-)
Title: Interpolation and Extrapolation for Species Diversity
Description: Provides simple functions to compute and plot two types
(sample-size- and coverage-based) rarefaction and extrapolation curves for species
diversity (Hill numbers) based on individual-based abundance data or sampling-unit-
based incidence data; see Chao and others (2014, Ecological Monographs) for pertinent
theory and methodologies, and Hsieh, Ma and Chao (2016, Methods in Ecology and Evolution)
for an introduction of the R package.
Author: T. C. Hsieh [aut],
K. H. Ma [aut],
Anne Chao [aut, cre]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between iNEXT versions 3.0.1 dated 2024-03-24 and 3.0.2 dated 2025-07-30
DESCRIPTION | 27 +++++- MD5 | 8 +- NEWS | 184 +++++++++++++++++++++++----------------------- R/iNEXT.r | 57 +++++++++++--- inst/doc/Introduction.pdf |binary 5 files changed, 161 insertions(+), 115 deletions(-)
Title: Open-Source Software for 'Omic' Data Analysis and Visualization
Description: A tool for interactive exploration of the results from 'omics'
experiments to facilitate novel discoveries from high-throughput biology. The
software includes R functions for the 'bioinformatician' to deposit study
metadata and the outputs from statistical analyses (e.g. differential
expression, enrichment). These results are then exported to an interactive
JavaScript dashboard that can be interrogated on the user's local machine or
deployed online to be explored by collaborators. The dashboard includes
'sortable' tables, interactive plots including network visualization, and
fine-grained filtering based on statistical significance.
Author: Terrence Ernst [aut] ,
John Blischak [aut, cre] ,
Paul Nordlund [aut] ,
Justin Moore [aut] ,
Joe Dalen [aut] ,
Akshay Bhamidipati [aut] ,
Brett Engelmann [aut],
Marco Curado [aut] ,
Joe LoGrasso [aut] ,
Elyse Geoffroy [ctb],
AbbVie Inc. [cph, fnd]
Maintainer: John Blischak <jdblischak@gmail.com>
Diff between OmicNavigator versions 1.15.0 dated 2025-05-28 and 1.16.0 dated 2025-07-30
DESCRIPTION | 6 +-- MD5 | 30 ++++++++-------- NEWS.md | 18 ++++++++++ R/add.R | 18 ++++++++-- R/export.R | 30 ++++++++++++---- R/get.R | 6 +-- R/tests.R | 12 ++++-- R/zzz.R | 19 +++++++--- inst/doc/OmicNavigatorAPI.pdf |binary inst/doc/OmicNavigatorUsersGuide.pdf |binary inst/tinytest/testExport.R | 62 ++++++++++++++++++++++++++++++++++- inst/tinytest/testPlot.R | 1 man/addPlots.Rd | 18 ++++++++-- man/createStudy.Rd | 10 +++-- man/exportStudy.Rd | 3 + man/installStudy.Rd | 17 +++++++++ 16 files changed, 199 insertions(+), 51 deletions(-)
Title: Procedures for Automated Interpolation
Description: Geostatistical interpolation has traditionally been done by manually fitting a variogram and then interpolating. Here, we introduce classes and methods that can do this interpolation automatically. Pebesma et al (2010) gives an overview of the methods behind and possible usage <doi:10.1016/j.cageo.2010.03.019>.
Author: Edzer Pebesma [aut],
Jon Olav Skoien [aut, cre],
Olivier Baume [ctb],
A Chorti [ctb],
Dionisis Hristopulos [ctb],
Hannes Kazianka [ctb],
Stepahnie Melles [ctb],
Giannis Spiliopoulos [ctb]
Maintainer: Jon Olav Skoien <jon.skoien@gmail.com>
Diff between intamap versions 1.5-10 dated 2025-07-17 and 1.5-11 dated 2025-07-30
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Fast and Flexible Implementations of Exploratory Factor Analysis
Tools
Description: Provides functions to perform exploratory factor analysis (EFA) procedures and compare their solutions. The goal is to provide state-of-the-art factor retention methods and a high degree of flexibility in the EFA procedures. This way, for example, implementations from R 'psych' and 'SPSS' can be compared. Moreover, functions for Schmid-Leiman transformation and the computation of omegas are provided. To speed up the analyses, some of the iterative procedures, like principal axis factoring (PAF), are implemented in C++.
Author: Markus Steiner [aut, cre],
Silvia Grieder [aut],
William Revelle [ctb],
Max Auerswald [ctb],
Morten Moshagen [ctb],
John Ruscio [ctb],
Brendan Roche [ctb],
Urbano Lorenzo-Seva [ctb],
David Navarro-Gonzalez [ctb],
Johan Braeken [ctb]
Maintainer: Markus Steiner <markus.d.steiner@gmail.com>
Diff between EFAtools versions 0.6.0 dated 2025-06-19 and 0.6.1 dated 2025-07-30
DESCRIPTION | 6 - MD5 | 12 +-- NEWS.md | 6 + R/EKC.R | 12 +-- inst/doc/EFAtools.html | 130 ++++++++++++++++++------------------- inst/doc/Replicate_SPSS_psych.html | 18 ++--- man/EKC.Rd | 3 7 files changed, 96 insertions(+), 91 deletions(-)
Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
Corrections
Description: Provides several cluster-robust variance estimators (i.e.,
sandwich estimators) for ordinary and weighted least squares linear regression
models, including the bias-reduced linearization estimator introduced by Bell
and McCaffrey (2002)
<https://www150.statcan.gc.ca/n1/pub/12-001-x/2002002/article/9058-eng.pdf> and
developed further by Pustejovsky and Tipton (2017)
<DOI:10.1080/07350015.2016.1247004>. The package includes functions for estimating
the variance- covariance matrix and for testing single- and multiple-
contrast hypotheses based on Wald test statistics. Tests of single regression
coefficients use Satterthwaite or saddle-point corrections. Tests of multiple-
contrast hypotheses use an approximation to Hotelling's T-squared distribution.
Methods are provided for a variety of fitted models, including lm() and mlm
objects, glm(), geeglm() (from package 'geepack'), lm_robust() and lm_lin()
(from package 'estimatr'), ivreg() (from package 'AER'), ivreg() (from package [...truncated...]
Author: James E. Pustejovsky [aut, cre] ,
Samuel Pekofsky [ctb],
Jingru Zhang [ctb]
Maintainer: James E. Pustejovsky <jepusto@gmail.com>
Diff between clubSandwich versions 0.6.0 dated 2025-04-01 and 0.6.1 dated 2025-07-30
DESCRIPTION | 15 MD5 | 21 NAMESPACE | 7 NEWS.md | 4 R/clubSandwich.R | 8 R/lm_robust.R |only inst/doc/Wald-tests-in-clubSandwich.html | 9 inst/doc/meta-analysis-with-CRVE.html | 9 inst/doc/panel-data-CRVE.html | 9 man/vcovCR.Rd | 8 man/vcovCR.lm_robust.Rd |only tests/testthat/test_lm_lin.R |only tests/testthat/test_lm_robust.R | 907 +++++++++++++++++++++++++++++++ 13 files changed, 963 insertions(+), 34 deletions(-)
Title: Visualizations for 'mice' with 'ggplot2'
Description: Enhance a 'mice' imputation workflow with visualizations for
incomplete and/or imputed data. The plotting functions produce
'ggplot' objects which may be easily manipulated or extended. Use
'ggmice' to inspect missing data, develop imputation models, evaluate
algorithmic convergence, or compare observed versus imputed data.
Author: Hanne Oberman [aut, cre] ,
Utrecht University [fnd],
University Medical Centre Utrecht [fnd],
Thom Volker [ctb] ,
Gerko Vink [ctb] ,
Pepijn Vink [ctb] ,
Jamie Wallis [ctb] ,
Kyle Lang [ctb]
Maintainer: Hanne Oberman <h.i.oberman@uu.nl>
Diff between ggmice versions 0.1.0 dated 2023-08-07 and 0.1.1 dated 2025-07-30
DESCRIPTION | 36 MD5 | 90 NAMESPACE | 31 NEWS.md | 90 R/ggmice.R | 20 R/old_friends.R | 200 - R/plot_corr.R | 245 - R/plot_flux.R | 178 - R/plot_miss.R |only R/plot_pattern.R | 468 +-- R/plot_pred.R | 271 + R/plot_trace.R | 221 - R/theme.R | 57 R/utils.R | 56 README.md | 204 - build/vignette.rds |binary inst/doc/ggmice.R | 288 +- inst/doc/ggmice.Rmd | 586 ++-- inst/doc/ggmice.html | 1501 +++++----- inst/doc/old_friends.R | 326 +- inst/doc/old_friends.html | 5104 ++++++++++++++++++------------------- man/bwplot.Rd | 42 man/densityplot.Rd | 42 man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/ggmice.Rd | 65 man/pipe.Rd | 40 man/plot_corr.Rd | 95 man/plot_flux.Rd | 67 man/plot_miss.Rd |only man/plot_pattern.Rd | 95 man/plot_pred.Rd | 113 man/plot_trace.Rd | 78 man/stripplot.Rd | 42 man/theme_mice.Rd | 29 man/theme_minimice.Rd | 29 man/xyplot.Rd | 42 tests/testthat.R | 12 tests/testthat/Rplots.pdf |only tests/testthat/test-ggmice.R | 118 tests/testthat/test-old_friends.R | 34 tests/testthat/test-plot_corr.R | 58 tests/testthat/test-plot_flux.R | 36 tests/testthat/test-plot_miss.R |only tests/testthat/test-plot_pattern.R | 52 tests/testthat/test-plot_pred.R | 52 tests/testthat/test-plot_trace.R | 5 vignettes/ggmice.Rmd | 586 ++-- 48 files changed, 6027 insertions(+), 5677 deletions(-)
Title: Inference About Relationships from DNA Mixtures
Description: Methods for inference about/under complex relationships using
peak height data from DNA mixtures: the most basic example would be testing whether a contributor to
a mixture is the father of a child of known genotype. This provides most of the functionality
of the 'KinMix' package, but with some loss of efficiency and restriction on problem size,
as the latter uses 'RHugin' as the Bayes net engine, while this package uses 'gRain'.
The package implements the methods introduced in
Green, P. J. and Mortera, J. (2017) <doi:10.1016/j.fsigen.2017.02.001> and
Green, P. J. and Mortera, J. (2021) <doi:10.1111/rssc.12498>.
Author: Peter Green [aut, cre]
Maintainer: Peter Green <P.J.Green@bristol.ac.uk>
Diff between KinMixLite versions 2.2.0 dated 2025-07-15 and 2.2.1 dated 2025-07-30
DESCRIPTION | 8 ++--- MD5 | 33 ++++++++++++---------- NAMESPACE | 3 +- R/KMmodel.R |only R/KinMix.R | 30 +++++++++++++------- R/KinMixsubs.R | 78 +++++++++++++++++++++++++++++++++++++++++++--------- R/bymarker.R |only build/partial.rdb |binary demo/KMdemo.R | 69 ++++++++++++++++++++++++++++++++++------------ man/KinMix.Rd | 7 +++- man/checkdata.Rd | 2 - man/logL.UKX.Rd | 2 - man/logLX.Rd | 2 - man/logLm.Rd |only man/loop.rpt.IBD.Rd | 2 - man/mixMLX.Rd | 2 - man/rpt.IBD.Rd | 8 +++-- man/rpt.UAF.Rd | 2 - man/test2data.Rd | 4 +- 19 files changed, 179 insertions(+), 73 deletions(-)
Title: Import Surface Meteorological Data from NOAA Integrated Surface
Database (ISD)
Description: Functions to import data from more than 30,000 surface
meteorological sites around the world managed by the National Oceanic
and Atmospheric Administration (NOAA) Integrated Surface Database
(ISD, see
<https://www.ncei.noaa.gov/products/land-based-station/integrated-surface-database>).
Author: David Carslaw [aut, cre] ,
Jack Davison [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between worldmet versions 0.9.9 dated 2025-01-14 and 0.10.0 dated 2025-07-30
worldmet-0.10.0/worldmet/DESCRIPTION | 25 worldmet-0.10.0/worldmet/LICENSE | 4 worldmet-0.10.0/worldmet/MD5 | 35 - worldmet-0.10.0/worldmet/NAMESPACE | 20 worldmet-0.10.0/worldmet/NEWS.md | 22 worldmet-0.10.0/worldmet/R/exportADMS.R | 339 +++++++------ worldmet-0.10.0/worldmet/R/getMeta.R | 584 +++++++++++------------ worldmet-0.10.0/worldmet/R/importNOAA.R |only worldmet-0.10.0/worldmet/R/importNOAAlite.R |only worldmet-0.10.0/worldmet/R/weatherCodes.R | 24 worldmet-0.10.0/worldmet/R/worldmet-package.R | 50 - worldmet-0.10.0/worldmet/README.md | 184 +++---- worldmet-0.10.0/worldmet/man/exportADMS.Rd | 72 +- worldmet-0.10.0/worldmet/man/getMeta.Rd | 188 +++---- worldmet-0.10.0/worldmet/man/getMetaLive.Rd | 53 +- worldmet-0.10.0/worldmet/man/importNOAA.Rd | 274 +++++----- worldmet-0.10.0/worldmet/man/importNOAAlite.Rd |only worldmet-0.10.0/worldmet/man/weatherCodes.Rd | 52 +- worldmet-0.10.0/worldmet/man/worldmet-package.Rd | 81 +-- worldmet-0.9.9/worldmet/R/metNOAA.R |only worldmet-0.9.9/worldmet/R/zzz.R |only 21 files changed, 1055 insertions(+), 952 deletions(-)
Title: Data and Variable Transformation Functions
Description: Collection of miscellaneous utility functions, supporting data
transformation tasks like recoding, dichotomizing or grouping variables,
setting and replacing missing values. The data transformation functions
also support labelled data, and all integrate seamlessly into a
'tidyverse'-workflow.
Author: Daniel Luedecke [aut, cre] ,
Iago Gine-Vazquez [ctb],
Alexander Bartel [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between sjmisc versions 2.8.10 dated 2024-05-13 and 2.8.11 dated 2025-07-30
DESCRIPTION | 21 +- MD5 | 48 +++--- NEWS.md | 8 - R/add_columns.R | 2 R/to_value.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/design_philosophy.html | 9 - inst/doc/exploringdatasets.html | 9 - inst/doc/recodingvariables.html | 9 - man/add_columns.Rd | 292 ++++++++++++++++++++-------------------- man/empty_cols.Rd | 98 ++++++------- man/grapes-nin-grapes.Rd | 68 ++++----- man/is_even.Rd | 68 ++++----- man/is_float.Rd | 84 +++++------ man/is_num_fac.Rd | 82 +++++------ man/merge_imputations.Rd | 206 ++++++++++++++-------------- man/rec_pattern.Rd | 108 +++++++------- man/round_num.Rd | 52 +++---- man/seq_col.Rd | 54 +++---- man/shorten_string.Rd | 84 +++++------ man/to_long.Rd | 270 ++++++++++++++++++------------------ man/to_value.Rd | 3 man/trim.Rd | 64 ++++---- man/typical_value.Rd | 148 ++++++++++---------- 25 files changed, 901 insertions(+), 889 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.7.2 dated 2025-07-12 and 0.7.3 dated 2025-07-30
DESCRIPTION | 6 ++--- MD5 | 28 ++++++++++++------------ R/densityplot.R | 57 ++++++++++++++++++++++++++++++++++++++++++++----- R/heatmap.R | 42 +++++++++++++++++++++++++++++++----- R/lineplot.R | 48 +++++++++++++++++++++++++++++++++++++++++ R/theming.R | 2 - man/Heatmap.Rd | 21 ++++++++++++++++-- man/HeatmapAtomic.Rd | 8 +++++- man/LinePlot.Rd | 19 ++++++++++++++++ man/LinePlotAtomic.Rd | 17 ++++++++++++++ man/LinePlotGrouped.Rd | 17 ++++++++++++++ man/LinePlotSingle.Rd | 17 ++++++++++++++ man/RidgePlot.Rd | 24 +++++++++++++++++++- man/RidgePlotAtomic.Rd | 20 ++++++++++++++++- man/show_palettes.Rd | 2 - 15 files changed, 293 insertions(+), 35 deletions(-)
Title: Predictor-Assisted Graphical Models under Error-in-Variables
Description: We consider the network structure detection for variables Y with auxiliary variables X accommodated, which are possibly subject to measurement error. The following three functions are designed to address various structures by different methods : one is NP_Graph() that is used for handling the nonlinear relationship between the responses and the covariates, another is Joint_Gaussian() that is used for correction in linear regression models via the Gaussian maximum likelihood, and the other Cond_Gaussian() is for linear regression models via conditional likelihood function.
Author: Wan-Yi Chang [aut, cre],
Li-Pang Chen [aut]
Maintainer: Wan-Yi Chang <jessica306a@gmail.com>
Diff between PAGE versions 0.2.0 dated 2025-07-29 and 0.3.0 dated 2025-07-30
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/Con_Gaussian.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Calculate the Open Bodem Index (OBI) Score
Description: The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in The Netherlands and the sustainability of the current agricultural practices.
The OBI score is based on four main criteria: chemical, physical, biological and management, which consist of more than 21 indicators.
By providing results of a soil analysis and management info the 'OBIC' package can be use to calculate he scores, indicators and derivatives that are used by the OBI.
More information about the Open Bodem Index can be found at <https://openbodemindex.nl/>.
Author: Sven Verweij [aut, cre] ,
Gerard Ros [aut] ,
Yuki Fujita [aut] ,
Wilbrand Hendrik Riechelman [aut] ,
Kees van den Dool [aut] ,
Job de Pater [ctb],
Nutrienten Managment Instituut [cph]
Maintainer: Sven Verweij <sven.verweij@nmi-agro.nl>
Diff between OBIC versions 3.0.3 dated 2024-09-09 and 4.0.0 dated 2025-07-30
OBIC-3.0.3/OBIC/man/format_gwt.Rd |only OBIC-3.0.3/OBIC/tests/testthat/test-format_gwt.R |only OBIC-3.0.3/OBIC/tests/testthat/test-obic_field.R |only OBIC-4.0.0/OBIC/DESCRIPTION | 22 OBIC-4.0.0/OBIC/MD5 | 80 +- OBIC-4.0.0/OBIC/NAMESPACE | 1 OBIC-4.0.0/OBIC/NEWS.md | 40 + OBIC-4.0.0/OBIC/R/groundwater_recharge.R | 15 OBIC-4.0.0/OBIC/R/management.R | 14 OBIC-4.0.0/OBIC/R/nitrogen_efficiency.R | 17 OBIC-4.0.0/OBIC/R/nretention.r | 18 OBIC-4.0.0/OBIC/R/obic.R | 11 OBIC-4.0.0/OBIC/R/obic_format_inputs.R | 41 - OBIC-4.0.0/OBIC/R/tables.R | 4 OBIC-4.0.0/OBIC/R/wateravailability.R | 19 OBIC-4.0.0/OBIC/build/vignette.rds |binary OBIC-4.0.0/OBIC/data/crops.obic.rda |binary OBIC-4.0.0/OBIC/data/nleach_table.rda |binary OBIC-4.0.0/OBIC/data/waterstress.obic.rda |binary OBIC-4.0.0/OBIC/inst/doc/description-of-the-columns.html | 6 OBIC-4.0.0/OBIC/inst/doc/obic_introduction.R | 410 ++++++------- OBIC-4.0.0/OBIC/inst/doc/obic_introduction.Rmd | 10 OBIC-4.0.0/OBIC/inst/doc/obic_introduction.html | 80 +- OBIC-4.0.0/OBIC/inst/doc/obic_score_aggregation.R | 186 ++--- OBIC-4.0.0/OBIC/inst/doc/obic_score_aggregation.html | 22 OBIC-4.0.0/OBIC/inst/doc/obic_water_functions.html | 14 OBIC-4.0.0/OBIC/inst/doc/obic_workability.html | 16 OBIC-4.0.0/OBIC/man/calc_man_ess.Rd | 2 OBIC-4.0.0/OBIC/man/calc_management.Rd | 2 OBIC-4.0.0/OBIC/man/calc_n_efficiency.Rd | 4 OBIC-4.0.0/OBIC/man/calc_nleach.Rd | 4 OBIC-4.0.0/OBIC/man/calc_waterstressindex.Rd | 2 OBIC-4.0.0/OBIC/man/ind_gw_recharge.Rd | 4 OBIC-4.0.0/OBIC/man/nleach_table.Rd | 4 OBIC-4.0.0/OBIC/man/waterstress.obic.Rd | 4 OBIC-4.0.0/OBIC/tests/testthat/test-groundwater_recharge.R | 27 OBIC-4.0.0/OBIC/tests/testthat/test-management.R | 14 OBIC-4.0.0/OBIC/tests/testthat/test-nitrogen_efficiency.R | 6 OBIC-4.0.0/OBIC/tests/testthat/test-nretention.R | 10 OBIC-4.0.0/OBIC/tests/testthat/test-obic_farm.R | 4 OBIC-4.0.0/OBIC/tests/testthat/test-table-contents.R |only OBIC-4.0.0/OBIC/tests/testthat/test-waterstress.R | 14 OBIC-4.0.0/OBIC/vignettes/obic_introduction.Rmd | 10 43 files changed, 593 insertions(+), 544 deletions(-)
Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import bathymetric and hypsometric data from the NOAA (National Oceanic and Atmospheric Administration, <https://www.ncei.noaa.gov/products/etopo-global-relief-model>), GEBCO (General Bathymetric Chart of the Oceans, <https://www.gebco.net>) and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante [aut],
Benoit Simon-Bouhet [aut, cre],
Jean-Olivier Irisson [aut]
Maintainer: Benoit Simon-Bouhet <besibo@gmail.com>
Diff between marmap versions 1.0.10 dated 2023-03-24 and 1.0.12 dated 2025-07-30
DESCRIPTION | 24 +++++++++++++----- MD5 | 58 +++++++++++++++++++++++---------------------- R/autoplot.bathy.R | 4 +-- R/lc.dist2.R |only build/partial.rdb |binary build/vignette.rds |binary data/aleutians.rda |binary data/celt.rda |binary data/florida.rda |binary data/hawaii.rda |binary data/hawaii.sites.rda |binary data/irregular.rda |binary data/metallo.rda |binary data/nw.atlantic.coast.rda |binary data/nw.atlantic.rda |binary man/aleutians.Rd | 8 +++--- man/as.xyz.Rd | 2 - man/autoplot.bathy.Rd | 14 +++++----- man/celt.Rd | 4 +-- man/florida.Rd | 4 +-- man/get.area.Rd | 46 +++++++++++++++++------------------ man/getNOAA.bathy.Rd | 2 - man/hawaii.Rd | 4 +-- man/lc.dist2.Rd |only man/marmap.Rd | 6 ++-- man/metallo.Rd | 2 - man/nw.atlantic.Rd | 4 +-- man/nw.atlantic.coast.Rd | 14 +++++----- man/plotArea.Rd | 2 - man/read.bathy.Rd | 5 --- man/subsetSQL.Rd | 2 - 31 files changed, 108 insertions(+), 97 deletions(-)
Title: Tools for Bayesian Analyses
Description: Provides tools for conducting Bayesian analyses and Bayesian model averaging
(Kass and Raftery, 1995, <doi:10.1080/01621459.1995.10476572>,
Hoeting et al., 1999, <doi:10.1214/ss/1009212519>). The package contains
functions for creating a wide range of prior distribution objects, mixing posterior
samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc...
The tools for working with prior distribution span from visualization, generating 'JAGS'
and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.
Author: Frantisek Bartos [aut, cre]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between BayesTools versions 0.2.19 dated 2025-06-08 and 0.2.20 dated 2025-07-30
DESCRIPTION | 6 MD5 | 30 +- NEWS.md | 9 R/JAGS-fit.R | 87 ++++--- R/JAGS-formula.R | 472 ++++++++++++++++++++++++++++++++++++++- R/priors-print.R | 10 R/priors-tools.R | 56 ++++ R/priors.R | 6 R/summary-tables.R | 7 build/partial.rdb |binary build/vignette.rds |binary inst/doc/ComparisonR.html | 13 - inst/doc/SpikeAndSlab.html | 9 man/parameter_names.Rd | 3 man/transform_factor_samples.Rd | 48 +-- man/transform_meandif_samples.Rd | 48 +-- 16 files changed, 670 insertions(+), 134 deletions(-)
Title: ARAchnid KNowledge Online
Description: Allows the user to connect with the World Spider Catalogue (WSC; <https://wsc.nmbe.ch/>) and the World Spider Trait (WST; <https://spidertraits.sci.muni.cz/>) databases. Also performs several basic functions such as checking names validity, retrieving coordinate data from the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/>), and mapping.
Author: Pedro Cardoso [aut, cre]
Maintainer: Pedro Cardoso <pmcardoso@ciencias.ulisboa.pt>
Diff between arakno versions 1.3.0 dated 2022-08-23 and 1.3.1 dated 2025-07-30
DESCRIPTION | 14 +++---- MD5 | 30 +++++++-------- R/arakno.R | 102 ++++++++++++++++++++++++++++------------------------ data/globalTree.rda |binary data/wscmap.rda |binary man/authors.Rd | 4 +- man/buildtree.Rd | 4 +- man/checknames.Rd | 4 +- man/countries.Rd | 4 +- man/distribution.Rd | 4 +- man/endemics.Rd | 12 +++--- man/lsid.Rd | 4 +- man/map.Rd | 4 +- man/species.Rd | 4 +- man/taxonomy.Rd | 4 +- man/wsc.Rd | 4 +- 16 files changed, 104 insertions(+), 94 deletions(-)
Title: Design of Experiments and Factorial Plans Utilities
Description: A number of functions to create and analyze factorial plans according to the Design of Experiments (DoE) approach, with the addition of some utility function to perform some statistical analyses. DoE approach follows the approach in "Design and Analysis of Experiments" by Douglas C. Montgomery (2019, ISBN:978-1-119-49244-3). The package also provides utilities used in the course "Analysis of Data and Statistics" at the University of Trento, Italy.
Author: Paolo Bosetti [aut, cre]
Maintainer: Paolo Bosetti <paolo.bosetti@unitn.it>
Diff between adas.utils versions 1.2.0 dated 2025-05-06 and 1.2.1 dated 2025-07-30
DESCRIPTION | 6 - MD5 | 17 ++-- NEWS.md | 4 + R/factorial_plan.R | 14 ++-- README.md | 3 inst/doc/adas.utils.html | 106 +++++++++++++++---------------- man/figures/README-unnamed-chunk-5-1.png |binary tools/aberration.Rmd |only tools/setup.Rmd | 13 +++ tools/setup.nb.html | 74 ++++++++++++++++++++- 10 files changed, 161 insertions(+), 76 deletions(-)
Title: Run Once and Save Result
Description: Package 'runonce' helps automating the saving of long-running code
to help running the same code multiple times. If you run some long-running
code once, it saves the result in a file on disk. Then, if the result
already exists, i.e. if the code has already been run and its output has
already been saved, it just reads the result from the stored file instead
of running the code again.
Author: Florian Prive [aut, cre]
Maintainer: Florian Prive <florian.prive.21@gmail.com>
Diff between runonce versions 0.2.3 dated 2021-10-02 and 0.3.2 dated 2025-07-30
DESCRIPTION | 11 +-- MD5 | 20 +++--- R/download-file.R | 9 ++ R/save-run.R | 28 ++++----- R/skip-run.R | 4 - README.md | 4 - man/download_file.Rd | 126 +++++++++++++++++++++-------------------- man/runonce-package.Rd | 58 ++++++++---------- man/save_run.Rd | 76 +++++++++++------------- man/skip_run_if.Rd | 102 ++++++++++++++++----------------- tests/testthat/test-save-run.R | 37 ++++++------ 11 files changed, 239 insertions(+), 236 deletions(-)
Title: Post Processing of (Half-)Hourly Eddy-Covariance Measurements
Description: Standard and extensible Eddy-Covariance data post-processing
(Wutzler et al. (2018) <doi:10.5194/bg-15-5015-2018>)
includes
uStar-filtering, gap-filling, and flux-partitioning.
The Eddy-Covariance (EC) micrometeorological technique quantifies continuous
exchange fluxes of gases, energy, and momentum between an ecosystem and the atmosphere.
It is important for understanding ecosystem dynamics and upscaling exchange fluxes.
(Aubinet et al. (2012) <doi:10.1007/978-94-007-2351-1>).
This package inputs pre-processed (half-)hourly data and supports further processing.
First, a quality-check and filtering is performed based on the relationship between
measured flux and friction
velocity (uStar) to discard biased data
(Papale et al. (2006) <doi:10.5194/bg-3-571-2006>).
Second, gaps in the data are filled based on information from environmental conditions
(Reichstein et al. (2005) <doi:10.1111/j.1365-2486.2005.001002.x>).
Third, the net flux of carbon dioxide is partiti [...truncated...]
Author: Department for Biogeochemical Integration at MPI-BGC, Jena, Germany
[cph],
Thomas Wutzler [aut, cre],
Markus Reichstein [aut],
Antje Maria Moffat [aut, trl],
Olaf Menzer [ctb],
Mirco Migliavacca [aut],
Kerstin Sickel [ctb, trl],
Ladislav <U+0160>igut [...truncated...]
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>
Diff between REddyProc versions 1.3.3 dated 2024-01-25 and 1.3.4 dated 2025-07-30
REddyProc-1.3.3/REddyProc/vignettes/plots |only REddyProc-1.3.4/REddyProc/DESCRIPTION | 10 - REddyProc-1.3.4/REddyProc/MD5 | 41 ++---- REddyProc-1.3.4/REddyProc/NEWS.md | 13 + REddyProc-1.3.4/REddyProc/R/EddyUStarFilterDP.R | 9 - REddyProc-1.3.4/REddyProc/R/Example.R | 2 REddyProc-1.3.4/REddyProc/R/FileHandling.R | 2 REddyProc-1.3.4/REddyProc/R/FileHandlingFormats.R | 6 REddyProc-1.3.4/REddyProc/R/PartitioningLasslop10Nighttime.R | 7 + REddyProc-1.3.4/REddyProc/build/vignette.rds |binary REddyProc-1.3.4/REddyProc/inst/WORDLIST | 74 ++++++----- REddyProc-1.3.4/REddyProc/inst/doc/DEGebExample.html | 18 +- REddyProc-1.3.4/REddyProc/inst/doc/aggUncertainty.html | 18 +- REddyProc-1.3.4/REddyProc/inst/doc/bigleaf.html | 4 REddyProc-1.3.4/REddyProc/inst/doc/gapFilling.html | 8 - REddyProc-1.3.4/REddyProc/inst/doc/uStarCases.html | 42 ++---- REddyProc-1.3.4/REddyProc/inst/doc/useCase.html | 49 +++---- REddyProc-1.3.4/REddyProc/man/fLoadAmeriflux22.Rd | 2 REddyProc-1.3.4/REddyProc/man/fLoadFluxnet15.Rd | 4 REddyProc-1.3.4/REddyProc/man/help_export.Rd | 2 REddyProc-1.3.4/REddyProc/tests/testthat/Rplots.pdf |binary REddyProc-1.3.4/REddyProc/tests/testthat/test_UStarFilter.R | 3 22 files changed, 164 insertions(+), 150 deletions(-)
Title: Plot Null Hypothesis Significance Tests
Description: Illustrate graphically the most common Null Hypothesis Significance Testing procedures. More specifically, this package provides functions to plot Chi-Squared, F, t (one- and two-tailed) and z (one- and two-tailed) tests, by plotting the probability density under the null hypothesis as a function of the different test statistic values. Although highly flexible (color theme, fonts, etc.), only the minimal number of arguments (observed test statistic, degrees of freedom) are necessary for a clear and useful graph to be plotted, with the observed test statistic and the p value, as well as their corresponding value labels. The axes are automatically scaled to present the relevant part and the overall shape of the probability density function. This package is especially intended for education purposes, as it provides a helpful support to help explain the Null Hypothesis Significance Testing process, its use and/or shortcomings.
Author: Nils Myszkowski [aut, cre]
Maintainer: Nils Myszkowski <nilsmyszkowskiscience@gmail.com>
Diff between nhstplot versions 1.3.0 dated 2024-03-01 and 1.4.0 dated 2025-07-30
DESCRIPTION | 13 +++++---- MD5 | 26 +++++++++---------- NEWS.md | 5 +++ R/plot.chisqtest.R | 42 ++++++++++++++++++++++++++++++-- R/plot.ftest.R | 24 ++++++++++++++---- R/plot.ttest.R | 9 ++++++ R/plot.ztest.R | 4 +++ build/vignette.rds |binary inst/doc/nhstplot.R | 4 +++ inst/doc/nhstplot.Rmd | 9 ++++++ inst/doc/nhstplot.html | 64 ++++++++++++++++++++++++++----------------------- man/plotchisqtest.Rd | 8 +++++- man/plotttest.Rd | 2 - vignettes/nhstplot.Rmd | 9 ++++++ 14 files changed, 161 insertions(+), 58 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] ,
yoonkyoung Chun [aut],
Zarathu [cph, fnd],
sungho Choi [aut],
Mingu Jee [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.5.13 dated 2025-06-12 and 0.5.14 dated 2025-07-30
DESCRIPTION | 14 +++--- MD5 | 16 +++---- NEWS.md | 4 + R/jskm.R | 117 +++++++++++++++++++++++++++++++++++++++++++++++------ R/svyjskm.R | 114 +++++++++++++++++++++++++++++++++++++++++++++++---- build/vignette.rds |binary inst/doc/jskm.html | 12 +++-- man/jskm.Rd | 3 + man/svyjskm.Rd | 3 + 9 files changed, 242 insertions(+), 41 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-23 0.0.3
2024-09-17 0.0.2
2024-09-16 0.0.1
Title: Inference for Functions of Multinomial Parameters
Description: We consider the problem where we observe k vectors (possibly of different lengths), each representing an independent multinomial random vector. For a given function that takes in the concatenated vector of multinomial probabilities and outputs a real number, this is a Monte Carlo estimation procedure of an exact p-value and confidence interval. The resulting inference is valid even in small samples, when the parameter is on the boundary, and when the function is not differentiable at the parameter value, all situations where asymptotic methods and the bootstrap would fail. For more details see Sachs, Fay, and Gabriel (2025) <doi:10.48550/arXiv.2406.19141>.
Author: Michael C Sachs [aut, cre],
Michael P Fay [aut],
Erin E Gabriel [aut],
David B Dahl [ctb] )
Maintainer: Michael C Sachs <sachsmc@gmail.com>
Diff between xactonomial versions 1.0.3 dated 2025-04-28 and 1.2.0 dated 2025-07-30
DESCRIPTION | 8 - MD5 | 33 +++--- NEWS.md | 11 ++ R/calculate-pvalues.R | 8 - R/utils.R | 3 R/xactonomial.R | 207 +++++++++++++++++++++++++++-------------- README.md | 4 inst/CITATION |only inst/doc/example.R | 24 ++-- inst/doc/example.Rmd | 26 ++--- inst/doc/example.html | 95 +++++++++--------- man/calc_prob_null.Rd | 4 man/calc_prob_null_fast.Rd | 4 man/calc_prob_null_gradient.Rd | 4 man/pvalue_psi0.Rd | 18 +-- man/xactonomial.Rd | 66 +++++++------ tests/testthat/test-boundary.R | 2 vignettes/example.Rmd | 26 ++--- 18 files changed, 323 insertions(+), 220 deletions(-)
More information about ggdmcLikelihood at CRAN
Permanent link
Title: Physical Activity with Accelerometers
Description: Functions to process, format and store ActiGraph GT1M and GT3X accelerometer data.
Author: Marco Geraci [aut, cph, cre]
Maintainer: Marco Geraci <marco.geraci@uniroma1.it>
Diff between pawacc versions 1.2.3 dated 2024-02-12 and 1.2.4 dated 2025-07-30
DESCRIPTION | 12 +++++++----- MD5 | 10 +++++----- inst/ChangeLog | 11 +++++++++++ man/gt1mAccFile.Rd | 2 +- man/gt3xAccFile.Rd | 2 +- man/pawacc-package.Rd | 4 ++-- 6 files changed, 27 insertions(+), 14 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-23 1.4.3
2024-04-16 1.4.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-02 0.2.0
2021-03-12 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-13 2.1.1
2024-08-21 2.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-06-23 3.1-6
2024-11-01 3.1-5
2024-05-23 3.1-4
2023-06-04 3.1-3
2023-05-20 3.1-2
2023-04-08 3.1-1
2023-02-06 3.0-0
2021-06-17 2.1.4
2020-02-23 2.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-15 1.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-21 5.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-13 2.1.3
2024-08-21 2.1.2
2024-07-08 2.1.0
2024-02-02 1.3.2
2023-10-10 1.3.1
2023-08-09 1.3
2023-02-07 1.2.1
2023-01-16 1.2.0
2022-09-05 1.1.1
2022-08-31 1.1.0
2022-06-15 1.0.6
2022-06-14 1.0.5
Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 4.4.2 dated 2025-05-26 and 4.4.3 dated 2025-07-30
sommer-4.4.2/sommer/man/stackTrait.Rd |only sommer-4.4.3/sommer/CHANGELOG | 7 +++ sommer-4.4.3/sommer/DESCRIPTION | 8 ++-- sommer-4.4.3/sommer/MD5 | 43 +++++++++++------------ sommer-4.4.3/sommer/NAMESPACE | 2 - sommer-4.4.3/sommer/R/FUN_methods_mmes.R | 2 - sommer-4.4.3/sommer/R/FUN_special.R | 26 ------------- sommer-4.4.3/sommer/R/FUN_vsm.R | 7 ++- sommer-4.4.3/sommer/R/mmes.R | 2 - sommer-4.4.3/sommer/inst/doc/sommer.gxe.html | 2 - sommer-4.4.3/sommer/inst/doc/sommer.qg.R | 22 ++++++++--- sommer-4.4.3/sommer/inst/doc/sommer.qg.Rmd | 26 +++++++++---- sommer-4.4.3/sommer/inst/doc/sommer.qg.html | 28 +++++++++----- sommer-4.4.3/sommer/inst/doc/sommer.spatial.html | 2 - sommer-4.4.3/sommer/inst/doc/sommer.vs.lme4.html | 2 - sommer-4.4.3/sommer/man/DT_btdata.Rd | 25 ++++++++----- sommer-4.4.3/sommer/man/DT_cpdata.Rd | 21 +++++++---- sommer-4.4.3/sommer/man/DT_example.Rd | 23 ++++++++++++ sommer-4.4.3/sommer/man/DT_gryphon.Rd | 19 +++++++--- sommer-4.4.3/sommer/man/DT_rice.Rd | 20 ++++++++++ sommer-4.4.3/sommer/man/DT_technow.Rd | 23 ++++++++---- sommer-4.4.3/sommer/src/MNR.cpp | 2 - sommer-4.4.3/sommer/vignettes/sommer.qg.Rmd | 26 +++++++++---- 23 files changed, 212 insertions(+), 126 deletions(-)
Title: Common Utilities for Other MOSAIC-Family Packages
Description: Common utilities used in other MOSAIC-family packages are
collected here.
Author: Randall Pruim [aut, cre],
Daniel T. Kaplan [aut],
Nicholas J. Horton [aut]
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between mosaicCore versions 0.9.4.0 dated 2023-11-04 and 0.9.5 dated 2025-07-30
DESCRIPTION | 27 ++++++++++++++++++++------- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/vector2df.R | 2 +- man/make_df.Rd | 2 +- 5 files changed, 30 insertions(+), 13 deletions(-)
Title: A 'DuckDB'-Backed Version of 'dplyr'
Description: A drop-in replacement for 'dplyr', powered by 'DuckDB' for
performance. Offers convenient utilities for working with in-memory and
larger-than-memory data while retaining full 'dplyr' compatibility.
Author: Hannes Muehleisen [aut] ,
Kirill Mueller [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckplyr versions 1.1.0 dated 2025-05-08 and 1.1.1 dated 2025-07-30
DESCRIPTION | 6 MD5 | 40 ++-- NEWS.md | 7 R/telemetry.R | 6 build/vignette.rds |binary inst/doc/developers.R | 64 +++---- inst/doc/developers.html | 97 +++++++++-- inst/doc/duckdb.R | 42 ++-- inst/doc/duckdb.html | 55 +++++- inst/doc/extend.R | 218 ++++++++++++------------ inst/doc/extend.html | 271 +++++++++++++++++++----------- inst/doc/fallback.R | 58 +++--- inst/doc/fallback.html | 113 +++++++++++- inst/doc/large.R | 170 +++++++++---------- inst/doc/large.html | 269 ++++++++++++++++++++++++++---- inst/doc/limits.R | 358 ++++++++++++++++++++-------------------- inst/doc/limits.html | 413 ++++++++++++++++++++++++++++++++++++++--------- inst/doc/prudence.R | 222 ++++++++++++------------- inst/doc/prudence.html | 213 ++++++++++++++++++++---- inst/doc/telemetry.R | 22 +- inst/doc/telemetry.html | 19 +- 21 files changed, 1792 insertions(+), 871 deletions(-)