Title: Toolkit for Reduced Form and Structural Smooth Transition Vector
Autoregressive Models
Description: Maximum likelihood estimation of smooth transition vector
autoregressive models with various types of transition weight functions,
conditional distributions, and identification methods. Constrained
estimation with various types of constraints is available. Residual based
model diagnostics, forecasting, simulations, and calculation of impulse
response functions, generalized impulse response functions, and generalized
forecast error variance decompositions. See
Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>,
Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>,
Markku Lanne, Savi Virolainen (2024) <doi:10.48550/arXiv.2403.14216>,
Savi Virolainen (2024) <doi:10.48550/arXiv.2404.19707>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between sstvars versions 1.1.1 dated 2024-12-07 and 1.1.2 dated 2025-01-07
DESCRIPTION | 6 MD5 | 34 +-- NEWS.md | 13 + R/GIRFandGFEVD.R | 351 ++++++++++++++++++++++++++++++----------- R/MAINest.R | 9 - R/STVARconstruction.R | 11 - R/moreEst.R | 2 R/plotMethods.R | 2 R/printMethods.R | 2 R/simulate.R | 2 inst/doc/sstvars-vignette.Rnw | 20 +- inst/doc/sstvars-vignette.pdf |binary man/GFEVD.Rd | 77 +++++--- man/GIRF.Rd | 53 +++++- man/iterate_more.Rd | 2 man/stvar_to_sstvars110.Rd | 2 vignettes/refs.bib | 7 vignettes/sstvars-vignette.Rnw | 20 +- 18 files changed, 432 insertions(+), 181 deletions(-)
Title: Slide Automation for Tables, Listings and Figures
Description: The normal process of creating clinical study slides is that
a statistician manually type in the numbers from outputs and a
separate statistician to double check the typed in numbers. This
process is time consuming, resource intensive, and error prone.
Automatic slide generation is a solution to address these issues. It
reduces the amount of work and the required time when creating slides,
and reduces the risk of errors from manually typing or copying numbers
from the output to slides. It also helps users to avoid unnecessary
stress when creating large amounts of slide decks in a short time
window.
Author: Joe Zhu [cre, aut] ,
Heng Wang [aut],
Yinqi Zhao [aut],
Bo Ci [aut],
Liming Li [aut],
Laura Wang [ctb],
Xiaoli Duan [aut],
Stefan Pascal Thoma [aut],
Thomas Neitmann [ctb],
Miles Almond [aut],
Mahdi About [ctb],
Kai Lim [ctb],
Nolan Steed [ctb],
Daol [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between autoslider.core versions 0.2.1 dated 2024-12-23 and 0.2.2 dated 2025-01-07
autoslider.core-0.2.1/autoslider.core/man/s_proportion_1.Rd |only autoslider.core-0.2.2/autoslider.core/DESCRIPTION | 29 autoslider.core-0.2.2/autoslider.core/MD5 | 69 + autoslider.core-0.2.2/autoslider.core/NAMESPACE | 4 autoslider.core-0.2.2/autoslider.core/NEWS.md | 8 autoslider.core-0.2.2/autoslider.core/R/decorate.R | 21 autoslider.core-0.2.2/autoslider.core/R/ft_formats.R | 48 + autoslider.core-0.2.2/autoslider.core/R/g_mean_slides.R | 24 autoslider.core-0.2.2/autoslider.core/R/package.R | 3 autoslider.core-0.2.2/autoslider.core/R/t_aesi_slide.R | 3 autoslider.core-0.2.2/autoslider.core/R/to_ft_funs.R | 10 autoslider.core-0.2.2/autoslider.core/R/to_slides.R | 63 + autoslider.core-0.2.2/autoslider.core/R/util.R | 47 - autoslider.core-0.2.2/autoslider.core/build/vignette.rds |binary autoslider.core-0.2.2/autoslider.core/inst/WORDLIST | 1 autoslider.core-0.2.2/autoslider.core/inst/doc/autoslideR.R | 33 autoslider.core-0.2.2/autoslider.core/inst/doc/autoslideR.Rmd | 66 - autoslider.core-0.2.2/autoslider.core/inst/doc/autoslideR.html | 352 ++++------ autoslider.core-0.2.2/autoslider.core/inst/doc/downstream.R |only autoslider.core-0.2.2/autoslider.core/inst/doc/downstream.Rmd |only autoslider.core-0.2.2/autoslider.core/inst/doc/downstream.html |only autoslider.core-0.2.2/autoslider.core/inst/doc/opensource.R |only autoslider.core-0.2.2/autoslider.core/inst/doc/opensource.Rmd |only autoslider.core-0.2.2/autoslider.core/inst/doc/opensource.html |only autoslider.core-0.2.2/autoslider.core/man/autoslider.core-package.Rd | 2 autoslider.core-0.2.2/autoslider.core/man/autoslider_format.Rd | 13 autoslider.core-0.2.2/autoslider.core/man/decorate.grob.Rd | 9 autoslider.core-0.2.2/autoslider.core/man/g_eg_slide.Rd | 7 autoslider.core-0.2.2/autoslider.core/man/g_lb_slide.Rd | 7 autoslider.core-0.2.2/autoslider.core/man/g_mean_general.Rd | 3 autoslider.core-0.2.2/autoslider.core/man/g_vs_slide.Rd | 7 autoslider.core-0.2.2/autoslider.core/tests/testthat/_snaps/slides_preview.md | 32 autoslider.core-0.2.2/autoslider.core/tests/testthat/t_dm_output.rds |binary autoslider.core-0.2.2/autoslider.core/tests/testthat/test-bad_filters.R | 6 autoslider.core-0.2.2/autoslider.core/tests/testthat/test-decorate.R | 21 autoslider.core-0.2.2/autoslider.core/tests/testthat/test-srep_outputs.R | 7 autoslider.core-0.2.2/autoslider.core/tests/testthat/test-t_dm_slide.R | 5 autoslider.core-0.2.2/autoslider.core/vignettes/autoslideR.Rmd | 66 - autoslider.core-0.2.2/autoslider.core/vignettes/downstream.Rmd |only autoslider.core-0.2.2/autoslider.core/vignettes/opensource.Rmd |only 40 files changed, 449 insertions(+), 517 deletions(-)
More information about autoslider.core at CRAN
Permanent link
Title: Creating, Manipulating and Annotating Matrix Ensemble
Description: Creates an object that stores a matrix ensemble, matrices
that share the same common properties, where rows and columns can be
annotated. Matrices must have the same dimension and dimnames. Operators to
manipulate these objects are provided as well as mechanisms to apply
functions to these objects.
Author: Pascal Croteau [aut, cre, cph]
Maintainer: Pascal Croteau <croteaupascl@gmail.com>
Diff between matrixset versions 0.3.0 dated 2024-01-14 and 0.4.0 dated 2025-01-07
DESCRIPTION | 14 MD5 | 89 NAMESPACE | 40 NEWS.md | 51 R/aaa.R | 6 R/context.R | 32 R/fn.R | 3607 +++++++++++++++--------------- R/fn_back.R |only R/group.R | 4 R/join.R | 621 ++++- R/matrixset-package.R | 3 R/mutate.R | 208 - R/properties.R | 4 R/replace.R | 1 R/scope.R |only R/utils.R | 87 build/vignette.rds |binary inst/doc/annotation.R | 6 inst/doc/annotation.html | 41 inst/doc/apply.R | 34 inst/doc/apply.Rmd | 28 inst/doc/apply.html | 132 - inst/doc/example.R | 38 inst/doc/example.Rmd | 18 inst/doc/example.html | 38 inst/doc/introduction.R | 12 inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 6 man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-soft-deprecated.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/join.Rd | 100 man/loop.Rd | 48 tests/testthat/test-construct-Matrix.R | 178 - tests/testthat/test-context.R | 194 - tests/testthat/test-extract-Matrix.R | 24 tests/testthat/test-fn-Matrix.R | 262 +- tests/testthat/test-fn-mult-Matrix.R | 163 - tests/testthat/test-fn-mult.R | 232 + tests/testthat/test-fn.R | 1073 +++++--- tests/testthat/test-join-Matrix.R | 6 tests/testthat/test-join.R | 277 ++ vignettes/apply.Rmd | 28 vignettes/example.Rmd | 18 vignettes/introduction.Rmd | 2 51 files changed, 4730 insertions(+), 2997 deletions(-)
Title: 'CDsampling': Constraint Sampling in Paid Research Studies
Description: In the context of paid research studies and clinical trials, budget considerations and patient sampling from available populations are subject to inherent constraints. We introduce the 'CDsampling' package, which integrates optimal design theories within the framework of constrained sampling. This package offers the possibility to find both D-optimal approximate and exact allocations for samplings with or without constraints. Additionally, it provides functions to find constrained uniform sampling as a robust sampling strategy with limited model information. Our package offers functions for the computation of the Fisher information matrix under generalized linear models (including regular linear regression model) and multinomial logistic models.To demonstrate the applications, we also provide a simulated dataset and a real dataset embedded in the package. Yifei Huang, Liping Tong, and Jie Yang (2025)<doi:10.5705/ss.202022.0414>.
Author: Yifei Huang [aut, cre],
Liping Tong [aut],
Jie Yang [aut]
Maintainer: Yifei Huang <yhuan39@uic.edu>
Diff between CDsampling versions 0.1.2 dated 2024-11-19 and 0.1.3 dated 2025-01-07
DESCRIPTION | 6 MD5 | 18 +- R/liftone_constrained_GLM.R | 1 R/print.list_output.R | 34 +++- R/print.matrix_list.R | 4 R/print.matrix_output.R | 2 inst/doc/Intro_to_CDsampling.R | 1 inst/doc/Intro_to_CDsampling.Rmd | 1 inst/doc/Intro_to_CDsampling.html | 288 ++++++++++++++++---------------------- vignettes/Intro_to_CDsampling.Rmd | 1 10 files changed, 170 insertions(+), 186 deletions(-)
Title: Utility Functions for 'spatstat'
Description: Contains utility functions for the 'spatstat' family of packages
which may also be useful for other purposes.
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.utils versions 3.1-1 dated 2024-11-03 and 3.1-2 dated 2025-01-07
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 7 +++++++ R/resolve.defaults.R | 43 +++++++++++++++++++++++++++---------------- inst/doc/packagesizes.txt | 1 + inst/info/packagesizes.txt | 1 + man/primefactors.Rd | 4 ++++ tests/numerical.R | 1 + 8 files changed, 52 insertions(+), 27 deletions(-)
More information about spatstat.utils at CRAN
Permanent link
Title: Interactively Visualize Structural Equation Modeling Diagrams
Description: It is an R package and web-based application, allowing users to perform interactive and reproducible visualizations of path diagrams for structural equation modeling (SEM) and networks using the 'ggplot2' engine. Its app (built with 'shiny') provides an interface that allows extensive customization, and creates CSV outputs, which can then be used to recreate the figures either using the web app or script-based workflow.
Author: Seung Hyun Min [aut, cre]
Maintainer: Seung Hyun Min <seung.min@mail.mcgill.ca>
Diff between ggsem versions 0.1.2 dated 2024-12-20 and 0.2.0 dated 2025-01-07
DESCRIPTION | 12 MD5 | 40 NAMESPACE | 6 R/adjust_axis_range.R |only R/adjust_axis_space.R |only R/csv_to_ggplot.R | 94 R/draw_annotations.R | 86 R/draw_lines.R | 122 R/draw_loops.R | 101 R/draw_points.R | 253 R/launch.R | 2 R/save_fig.R |only R/utils.R | 142 README.md | 31 inst/shiny/app.R | 6700 +++++++++++++++++---- inst/shiny/rsconnect/shinyapps.io/smin95/ggsem.dcf | 4 man/adjust_axis_range.Rd |only man/adjust_axis_space.Rd |only man/csv_to_ggplot.Rd | 54 man/draw_annotations.Rd | 27 man/draw_lines.Rd | 41 man/draw_loops.Rd | 27 man/draw_points.Rd | 36 man/save_figure.Rd |only 24 files changed, 6267 insertions(+), 1511 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, [...truncated...]
Author: Liam J. Revell [aut, cre]
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between phytools versions 2.3-0 dated 2024-06-13 and 2.4-4 dated 2025-01-07
DESCRIPTION | 16 +- MD5 | 280 +++++++++++++++++++++---------------------- NAMESPACE | 4 R/anc.ML.R | 3 R/asr.R | 169 +++++++++++++++++++++---- R/cophylo.R | 8 + R/densityMap.R | 3 R/drop.tip.simmap.R | 154 +++++++++++++---------- R/fancyTree.R | 9 - R/fitMk.R | 22 ++- R/fitMk.parallel.R | 10 + R/fitPagel.R | 2 R/fitThresh.R | 69 +++++++++- R/fitfnMk.R | 120 +++++++++++++++--- R/fitgammaMk.R | 45 ++++-- R/fitmultiBM.R | 68 +++++++--- R/fitpolyMk.R | 29 ++-- R/make.simmap.R | 6 R/phenogram.R | 16 +- R/phylo.to.map.R | 28 ++-- R/plotFanTree.wTraits.R | 2 R/plotTree.wBars.R | 5 R/rateshift.R | 110 ++++++++++++---- man/add.arrow.Rd | 14 +- man/add.random.Rd | 2 man/allFurcTrees.Rd | 4 man/anc.Bayes.Rd | 15 +- man/anc.ML.Rd | 6 man/anc.trend.Rd | 7 - man/ancThresh.Rd | 8 + man/ancr.Rd | 47 ++++--- man/ansi_phylo.Rd | 12 + man/bd.Rd | 6 man/bind.tip.Rd | 29 +++- man/bind.tree.simmap.Rd | 2 man/bmPlot.Rd | 5 man/bounded_bm.Rd | 25 +++ man/brownie.lite.Rd | 4 man/brownieREML.Rd | 8 - man/cladelabels.Rd | 2 man/collapseTree.Rd | 8 + man/contMap.Rd | 11 + man/cophylo.Rd | 10 + man/cospeciation.Rd | 5 man/countSimmap.Rd | 4 man/densityMap.Rd | 22 ++- man/describe.simmap.Rd | 2 man/di2multi.simmap.Rd | 6 man/dotTree.Rd | 6 man/drop.tip.contMap.Rd | 4 man/drop.tip.multiSimmap.Rd | 4 man/drop.tip.simmap.Rd | 8 - man/edge.widthMap.Rd | 10 + man/estDiversity.Rd | 2 man/evol.vcv.Rd | 3 man/evolvcv.lite.Rd | 7 - man/exhaustiveMP.Rd | 6 man/export.as.xml.Rd | 2 man/fancyTree.Rd | 19 +- man/fastAnc.Rd | 4 man/fastBM.Rd | 8 + man/fastMRCA.Rd | 10 + man/findMRCA.Rd | 28 ++-- man/fit.bd.Rd | 8 + man/fitMk.Rd | 28 +++- man/fitPagel.Rd | 14 +- man/fitThresh.Rd | 40 +++++- man/fitmultiBM.Rd | 42 +++++- man/force.ultrametric.Rd | 8 - man/gamma_pruning.Rd | 4 man/gammatest.Rd | 5 man/genSeq.Rd | 8 + man/geo.legend.Rd | 8 + man/getCladesofSize.Rd | 2 man/getDescendants.Rd | 2 man/getSisters.Rd | 2 man/labelnodes.Rd | 2 man/ladderize.simmap.Rd | 23 +++ man/lambda.transform.Rd | 4 man/likMlambda.Rd | 2 man/linklabels.Rd | 2 man/ltt.Rd | 19 ++ man/make.era.map.Rd | 9 + man/make.simmap.Rd | 24 ++- man/map.to.singleton.Rd | 4 man/markChanges.Rd | 10 + man/midpoint.root.Rd | 10 - man/modified.Grafen.Rd | 2 man/mrp.supertree.Rd | 10 - man/multiC.Rd | 4 man/multiRF.Rd | 2 man/multirateBM.Rd | 5 man/nodeHeights.Rd | 2 man/nodelabels.cophylo.Rd | 4 man/optim.phylo.ls.Rd | 4 man/orderMappedEdge.Rd | 6 man/paste.tree.Rd | 29 ++++ man/pbtree.Rd | 3 man/pgls.Ives.Rd | 4 man/phenogram.Rd | 8 - man/phyl.RMA.Rd | 9 - man/phyl.pca.Rd | 2 man/phyl.resid.Rd | 2 man/phyl.vcv.Rd | 4 man/phylo.heatmap.Rd | 14 +- man/phylo.to.map.Rd | 23 ++- man/phylomorphospace.Rd | 5 man/phylomorphospace3d.Rd | 13 + man/phylosig.Rd | 3 man/plot.backbonePhylo.Rd | 11 + man/plotBranchbyTrait.Rd | 4 man/plotSimmap.Rd | 13 + man/plotThresh.Rd | 4 man/plotTree.Rd | 9 + man/plotTree.datamatrix.Rd | 53 ++++---- man/plotTree.lollipop.Rd | 22 ++- man/plotTree.wBars.Rd | 4 man/pscore.Rd | 2 man/ratebystate.Rd | 2 man/ratebytree.Rd | 4 man/rateshift.Rd | 2 man/read.newick.Rd | 22 ++- man/read.simmap.Rd | 4 man/reorder.backbonePhylo.Rd | 2 man/reorderSimmap.Rd | 4 man/rep.phylo.Rd | 5 man/reroot.Rd | 4 man/rerootingMethod.Rd | 2 man/rescaleSimmap.Rd | 8 - man/resolveNode.Rd | 2 man/rotateNodes.Rd | 6 man/roundPhylogram.Rd | 7 - man/simBMphylo.Rd | 7 - man/starTree.Rd | 2 man/threshBayes.Rd | 4 man/tree.grow.Rd | 8 - man/treeSlice.Rd | 4 man/untangle.Rd | 4 man/vcvPhylo.Rd | 2 man/writeAncestors.Rd | 4 man/writeNexus.Rd | 4 141 files changed, 1566 insertions(+), 670 deletions(-)
Title: Graph/Network Analysis Based on L1 Centrality
Description: Analyze graph/network data using L1 centrality and prestige. Functions for deriving global, local, and group L1 centrality/prestige are provided. Routines for visual inspection of a graph/network are also provided. Details are in Kang and Oh (2024a) <doi:10.48550/arXiv.2404.13233> and Kang and Oh (2024b) <doi:10.48550/arXiv.2408.12078>.
Author: Seungwoo Kang [aut, cre] ,
Hee-Seok Oh [aut]
Maintainer: Seungwoo Kang <kangsw0401@snu.ac.kr>
Diff between L1centrality versions 0.3.0 dated 2024-10-06 and 0.3.1 dated 2025-01-07
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/L1centEDGE.R | 4 ++-- R/L1centLOC.R | 4 ++-- R/L1centNB.R | 1 + 6 files changed, 19 insertions(+), 12 deletions(-)
Title: Seeded Sequential LDA for Topic Modeling
Description: Seeded Sequential LDA can classify sentences of texts into pre-define topics with a small number of seed words (Watanabe & Baturo, 2023) <doi:10.1177/08944393231178605>.
Implements Seeded LDA (Lu et al., 2010) <doi:10.1109/ICDMW.2011.125> and Sequential LDA (Du et al., 2012) <doi:10.1007/s10115-011-0425-1> with the distributed LDA algorithm (Newman, et al., 2009) for parallel computing.
Author: Kohei Watanabe [aut, cre, cph],
Phan Xuan-Hieu [aut, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between seededlda versions 1.4.1 dated 2024-09-06 and 1.4.2 dated 2025-01-07
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test-internal.R | 7 ++++--- 4 files changed, 16 insertions(+), 11 deletions(-)
Title: Word and Document Vector Models
Description: Create dense vector representation of words and documents using 'quanteda'. Currently implements Word2vec (Mikolov et al., 2013) <doi:10.48550/arXiv.1310.4546> and Latent Semantic Analysis (Deerwester et al., 1990) <doi:10.1002/(SICI)1097-4571(199009)41:6%3C391::AID-ASI1%3E3.0.CO;2-9>.
Author: Kohei Watanabe [aut, cre, cph]
,
Jan Wijffels [aut] ,
BNOSAC [cph] ,
Max Fomichev [ctb, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between wordvector versions 0.1.0 dated 2024-12-11 and 0.2.0 dated 2025-01-07
wordvector-0.1.0/wordvector/man/doc2vec.Rd |only wordvector-0.1.0/wordvector/man/lsa.Rd |only wordvector-0.1.0/wordvector/man/word2vec.Rd |only wordvector-0.1.0/wordvector/src/word2vec/trainer.cpp |only wordvector-0.1.0/wordvector/src/word2vec/trainer.hpp |only wordvector-0.2.0/wordvector/DESCRIPTION | 6 wordvector-0.2.0/wordvector/MD5 | 55 +-- wordvector-0.2.0/wordvector/NAMESPACE | 13 wordvector-0.2.0/wordvector/NEWS.md | 11 wordvector-0.2.0/wordvector/R/doc2vec.R | 25 + wordvector-0.2.0/wordvector/R/lsa.R | 33 +- wordvector-0.2.0/wordvector/R/utils.R | 129 ++++---- wordvector-0.2.0/wordvector/R/word2vec.R | 48 +-- wordvector-0.2.0/wordvector/inst/WORDLIST | 21 - wordvector-0.2.0/wordvector/man/analogy.Rd | 65 +--- wordvector-0.2.0/wordvector/man/similarity.Rd | 49 +-- wordvector-0.2.0/wordvector/man/textmodel_doc2vec.Rd |only wordvector-0.2.0/wordvector/man/textmodel_lsa.Rd |only wordvector-0.2.0/wordvector/man/textmodel_word2vec.Rd |only wordvector-0.2.0/wordvector/man/weights.Rd |only wordvector-0.2.0/wordvector/src/Makevars | 1 wordvector-0.2.0/wordvector/src/Makevars.win | 1 wordvector-0.2.0/wordvector/src/word2vec/trainThread.cpp | 208 +++---------- wordvector-0.2.0/wordvector/src/word2vec/trainThread.hpp | 35 -- wordvector-0.2.0/wordvector/src/word2vec/word2vec.cpp | 115 +++++-- wordvector-0.2.0/wordvector/src/word2vec/word2vec.hpp | 89 ++--- wordvector-0.2.0/wordvector/src/wordvector.cpp | 78 +--- wordvector-0.2.0/wordvector/tests/misc/test_large.R | 6 wordvector-0.2.0/wordvector/tests/misc/test_small.R | 22 - wordvector-0.2.0/wordvector/tests/testthat/replication.R | 22 - wordvector-0.2.0/wordvector/tests/testthat/test-lsa.R | 16 - wordvector-0.2.0/wordvector/tests/testthat/test-utils.R | 101 ++---- wordvector-0.2.0/wordvector/tests/testthat/test-word2vec.R | 88 ++++- 33 files changed, 610 insertions(+), 627 deletions(-)
Title: Feature Extraction and Document Classification with Noisy Labels
Description: Extract features and classify documents with noisy labels given by document-meta data or keyword matching Watanabe & Zhou (2020) <doi:10.1177/0894439320907027>.
Author: Kohei Watanabe [aut, cre, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between wordmap versions 0.9.1 dated 2024-10-20 and 0.9.2 dated 2025-01-07
DESCRIPTION | 6 ++--- MD5 | 13 ++++++------ NEWS.md | 4 +++ R/textmodel.R | 24 +++++++++++++++------- man/textmodel_wordmap.Rd | 7 +++--- tests/testthat/Rplots.pdf |only tests/testthat/test-predict.R | 10 ++++----- tests/testthat/test-textmodel.R | 43 ++++++++++++++++++++++++++++++++++++++++ 8 files changed, 83 insertions(+), 24 deletions(-)
Title: Treatment-Specific Subgroup Detection Tool
Description: Implements a method for identifying subgroups with superior response relative to the overall sample.
Author: Chakib Battioui [aut],
Brian Denton [aut, cre],
Lei Shen [ctb],
Eli Lilly and Company [cph]
Maintainer: Brian Denton <denton_brian_david@lilly.com>
Diff between TSDT versions 1.0.7 dated 2022-04-06 and 1.0.8 dated 2025-01-07
CHANGELOG | 7 +++++++ DESCRIPTION | 10 +++++----- MD5 | 23 ++++++++++++----------- R/TSDT.R | 2 +- R/TSDT_CutpointDistribution.ClassDefinition.R | 2 +- R/TSDT_helper_functions.R | 4 ++-- R/TSDT_scoring_functions.R | 13 ++++++------- R/tree_functions.R | 2 +- R/utility_functions.R | 6 +++--- build |only man/TSDT.Rd | 2 +- man/binary_transform.Rd | 4 ++-- man/mean_deviance_residuals.Rd | 3 +-- 13 files changed, 42 insertions(+), 36 deletions(-)
Title: Small-Area-Estimation Unit/Area Models and Methods for
Estimation in R
Description: Provides methods for spatial and spatio-temporal smoothing of demographic and health indicators using survey data, with particular focus on estimating and projecting under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>, Li et al. (2019) <doi:10.1371/journal.pone.0210645>, Wu et al. (DHS Spatial Analysis Reports No. 21, 2021), and Li et al. (2023) <doi:10.48550/arXiv.2007.05117>.
Author: Zehang R Li [cre, aut],
Bryan D Martin [aut],
Yuan Hsiao [aut],
Jessica Godwin [aut],
John Paige [aut],
Peter Gao [aut],
Jon Wakefield [aut],
Samuel J Clark [aut],
Geir-Arne Fuglstad [aut],
Andrea Riebler [aut]
Maintainer: Zehang R Li <lizehang@gmail.com>
Diff between SUMMER versions 1.4.0 dated 2024-03-01 and 2.0.0 dated 2025-01-07
SUMMER-1.4.0/SUMMER/R/ChangeRegion.R |only SUMMER-1.4.0/SUMMER/R/Kendata.R |only SUMMER-1.4.0/SUMMER/R/countrySummary.R |only SUMMER-1.4.0/SUMMER/R/countrySummary_mult.R |only SUMMER-1.4.0/SUMMER/R/fitINLA.R |only SUMMER-1.4.0/SUMMER/R/fitINLA2.R |only SUMMER-1.4.0/SUMMER/R/fitspace.R |only SUMMER-1.4.0/SUMMER/R/getSmoothedDensity.R |only SUMMER-1.4.0/SUMMER/R/projINLA.R |only SUMMER-1.4.0/SUMMER/R/simRandom.R |only SUMMER-1.4.0/SUMMER/man/ChangeRegion.Rd |only SUMMER-2.0.0/SUMMER/DESCRIPTION | 20 SUMMER-2.0.0/SUMMER/MD5 | 187 - SUMMER-2.0.0/SUMMER/NAMESPACE | 5 SUMMER-2.0.0/SUMMER/NEWS.md | 6 SUMMER-2.0.0/SUMMER/R/INLA-internal-pc.R | 12 SUMMER-2.0.0/SUMMER/R/INLA-internals.R | 12 SUMMER-2.0.0/SUMMER/R/KenData.R |only SUMMER-2.0.0/SUMMER/R/SUMMER-package.R |only SUMMER-2.0.0/SUMMER/R/benchmark.R | 9 SUMMER-2.0.0/SUMMER/R/changeRegion.R |only SUMMER-2.0.0/SUMMER/R/compareEstimates.R |only SUMMER-2.0.0/SUMMER/R/getAdjusted.R | 8 SUMMER-2.0.0/SUMMER/R/getAreaName.R | 10 SUMMER-2.0.0/SUMMER/R/getBirths.R | 4 SUMMER-2.0.0/SUMMER/R/getDiag.R | 152 - SUMMER-2.0.0/SUMMER/R/getDirect.R |only SUMMER-2.0.0/SUMMER/R/getDirectList.R |only SUMMER-2.0.0/SUMMER/R/getSmoothed.R |only SUMMER-2.0.0/SUMMER/R/hatchPlot.R | 2 SUMMER-2.0.0/SUMMER/R/kenyaPopulationData.R | 2 SUMMER-2.0.0/SUMMER/R/logitNormMean.R | 4 SUMMER-2.0.0/SUMMER/R/mapEstimates.R |only SUMMER-2.0.0/SUMMER/R/mapPlot.R | 4 SUMMER-2.0.0/SUMMER/R/plot_projINLA.R | 88 SUMMER-2.0.0/SUMMER/R/popGrid.R | 475 ++-- SUMMER-2.0.0/SUMMER/R/projKenya.R | 3 SUMMER-2.0.0/SUMMER/R/ridgePlot.R |only SUMMER-2.0.0/SUMMER/R/rst.R |only SUMMER-2.0.0/SUMMER/R/simPop.R | 1135 +++++----- SUMMER-2.0.0/SUMMER/R/simSPDE.R | 20 SUMMER-2.0.0/SUMMER/R/simhyper.R | 2 SUMMER-2.0.0/SUMMER/R/smoothArea.R | 155 - SUMMER-2.0.0/SUMMER/R/smoothCluster.R |only SUMMER-2.0.0/SUMMER/R/smoothDirect.R |only SUMMER-2.0.0/SUMMER/R/smoothSurvey.R |only SUMMER-2.0.0/SUMMER/R/summary.R | 26 SUMMER-2.0.0/SUMMER/R/tcpPlot.R | 20 SUMMER-2.0.0/SUMMER/README.md | 37 SUMMER-2.0.0/SUMMER/build/partial.rdb |only SUMMER-2.0.0/SUMMER/build/vignette.rds |binary SUMMER-2.0.0/SUMMER/data/kenyaPopulationData.rda |binary SUMMER-2.0.0/SUMMER/inst/doc/cluster-model-vignette.html |only SUMMER-2.0.0/SUMMER/inst/doc/cluster-model-vignette.html.asis |only SUMMER-2.0.0/SUMMER/inst/doc/small-area-estimation.html | 124 - 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Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating
random and regular graphs, graph visualization, centrality methods and
much more.
Author: Gabor Csardi [aut] ,
Tamas Nepusz [aut] ,
Vincent Traag [aut] ,
Szabolcs Horvat [aut] ,
Fabio Zanini [aut] ,
Daniel Noom [aut],
Kirill Mueller [aut, cre] ,
Maelle Salmon [ctb],
Michael Antonov [ctb],
Chan Zuckerberg Initiative [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between igraph versions 2.1.2 dated 2024-12-07 and 2.1.3 dated 2025-01-07
DESCRIPTION | 6 MD5 | 60 - NEWS.md | 25 R/bipartite.R | 4 R/conversion.R | 4 R/foreign.R | 44 - R/operators.R | 9 R/plot.common.R | 460 +++++++++++++++ R/topology.R | 6 inst/doc/igraph.html | 48 - inst/doc/igraph_ES.html | 48 - man/bipartite_projection.Rd | 4 man/canonical_permutation.Rd | 2 man/closeness.Rd | 2 man/complementer.Rd | 2 man/disjoint_union.Rd | 7 man/graph_from_adj_list.Rd | 4 man/graph_from_graphdb.Rd | 17 man/permute.Rd | 4 man/plot.common.Rd | 822 ++++++++++++--------------- man/read_graph.Rd | 31 - man/vertex.shape.pie.Rd | 51 - src/rinterface.c | 2 src/rinterface.h | 22 src/rinterface_extra.c | 223 ++++--- src/vendor/cigraph/interfaces/functions.yaml | 2 src/vendor/cigraph/interfaces/types.yaml | 7 tests/testthat/helper.R | 2 tests/testthat/test-correlated.R | 2 tests/testthat/test-get.adjlist.R | 10 tests/testthat/test-graphNEL.R | 4 31 files changed, 1249 insertions(+), 685 deletions(-)
Title: Dyadic Structural Equation Modeling
Description: Scripting of structural equation models via 'lavaan' for
Dyadic Data Analysis, and helper functions for supplemental
calculations, tabling, and model visualization. Current models
supported include Dyadic Confirmatory Factor Analysis, the Actor–Partner
Interdependence Model (observed and latent), the Common Fate Model
(observed and latent), Mutual Influence Model (latent), and the Bifactor
Dyadic Model (latent).
Author: John Sakaluk [aut, cre, cph] ,
Omar Camanto [aut],
Robyn Kilshaw [ctb],
Alexandra Fisher [ctb]
Maintainer: John Sakaluk <jksakaluk@gmail.com>
Diff between dySEM versions 1.0.0 dated 2024-03-15 and 1.1.1 dated 2025-01-07
DESCRIPTION | 8 - MD5 | 68 +++++---- NAMESPACE | 5 NEWS.md | 16 +- R/esHelpers.R | 4 R/getConstraintTests.R | 3 R/getInvarCompTable.R | 3 R/outHelpers.R | 73 ++++++++- R/outputConstraintTab.R |only R/outputInvarCompTab.R |only R/outputModel.R | 2 R/outputParamFig.R |only R/outputParamTab.R |only R/scrapeVarCross.R | 11 + R/scriptCFA.R | 2 R/scriptDyEFA.R |only R/semHelpers.R | 1 README.md | 77 ++++++---- build/vignette.rds |binary inst/doc/dySEM.R | 13 + inst/doc/dySEM.Rmd | 21 +- inst/doc/dySEM.html | 70 ++++----- inst/doc/varnames.html | 26 +-- man/outputConstraintTab.Rd |only man/outputInvarCompTab.Rd |only man/outputParamFig.Rd |only man/outputParamTab.Rd |only man/scrapeVarCross.Rd | 16 ++ man/scriptAPIM.Rd | 1 man/scriptBiDy.Rd | 1 man/scriptCFA.Rd | 3 man/scriptCFM.Rd | 1 man/scriptDyEFA.Rd |only man/scriptINULL.Rd | 1 man/scriptISAT.Rd | 1 man/scriptMIM.Rd | 1 tests/testthat/test-outputModel.R |only tests/testthat/test-scriptAPIM.R | 32 ---- tests/testthat/test-scriptDyEFA.R |only tests/testthat/test-scriptMIM.R | 284 ++++++++++++++++++++++++++++++++++++++ vignettes/dySEM.Rmd | 21 +- 41 files changed, 579 insertions(+), 186 deletions(-)
Title: Tidy Processing and Analysis of Biological Sequences
Description: A tidy approach to analysis of biological sequences. All processing and data-storage functions are heavily optimized to allow the fastest and most efficient data storage.
Author: Dominik Rafacz [cre, aut] ,
Michal Burdukiewicz [aut] ,
Laura Bakala [aut],
Leon Eyrich Jessen [ctb] ,
Stefan Roediger [ctb] ,
Jadwiga Slowik [ctb] ,
Weronika Puchala [ctb] ,
Katarzyna Sidorczuk [ctb],
Filip Pietluch [ctb],
Jaroslaw Chilimoniuk [ctb] [...truncated...]
Maintainer: Dominik Rafacz <dominikrafacz@gmail.com>
Diff between tidysq versions 1.2.2 dated 2024-10-24 and 1.2.3 dated 2025-01-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/alphabet.R | 6 +++++- inst/doc/advanced-alphabet.R | 2 ++ inst/doc/quick-start.R | 12 ++++++------ 6 files changed, 27 insertions(+), 16 deletions(-)
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Complete analytical environment for the construction and analysis
of matrix population models and integral projection models.
Includes the ability to construct historical matrices, which are
2d matrices comprising 3 consecutive times of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. It also estimates
function-based age-by-stage matrices and raw and function-based
Leslie matrices.
Author: Richard P. Shefferson [aut, cre]
,
Johan Ehrlen [aut]
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 6.3.1 dated 2024-08-20 and 6.3.2 dated 2025-01-07
DESCRIPTION | 8 MD5 | 30 +- NEWS.md | 18 + R/modelselection.R | 2 R/popchar.R | 353 +++++++++++++++-------------- build/vignette.rds |binary inst/doc/Chapter1.html | 4 inst/doc/Chapter2.html | 14 - inst/doc/Chapter5.html | 22 - inst/doc/Chapter6.html | 14 - inst/doc/Chapter8.html | 22 - inst/doc/Chapter9.html | 10 inst/include/basic_funcs/main_utils.h | 33 ++ man/hfv_qc.Rd | 5 src/MatsNProj.cpp | 8 src/PopChar.cpp | 413 ++++++++++++++++++++++++++-------- 16 files changed, 633 insertions(+), 323 deletions(-)
Title: An Interface to Google's 'BigQuery Storage' API
Description: Easily talk to Google's 'BigQuery Storage' API from R
(<https://cloud.google.com/bigquery/docs/reference/storage/rpc>).
Author: Bruno Tremblay [aut, cre],
Google LLC [cph, fnd]
Maintainer: Bruno Tremblay <openr@neoxone.com>
Diff between bigrquerystorage versions 1.2.1 dated 2024-10-17 and 1.2.2 dated 2025-01-07
DESCRIPTION | 6 MD5 | 24 NEWS.md | 48 R/RcppExports.R | 46 R/bqs_download.R | 676 +++++++------- README.md | 4 cleanup | 2 src/Makevars.win.withgrpc | 56 - src/Makevars.win.withoutgrpc | 94 - src/bqs.cpp | 55 + src/protos/google/api/client.proto | 27 src/protos/google/cloud/bigquery/storage/v1/storage.proto | 15 tests/testthat/test-integration.R | 437 ++++----- 13 files changed, 801 insertions(+), 689 deletions(-)
More information about bigrquerystorage at CRAN
Permanent link
Title: Weighted Dependence Measures
Description: Provides efficient implementations of weighted dependence measures
and related asymptotic tests for independence. Implemented measures are
the Pearson correlation, Spearman's rho, Kendall's tau, Blomqvist's beta, and
Hoeffding's D; see, e.g., Nelsen (2006) <doi:10.1007/0-387-28678-0> and
Hollander et al. (2015, ISBN:9780470387375).
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between wdm versions 0.2.4 dated 2023-08-10 and 0.2.6 dated 2025-01-07
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- R/wdm-package.R | 2 +- build/partial.rdb |binary inst/CMakeLists.txt | 4 ++-- inst/include/wdm/random.hpp |only inst/include/wdm/ranks.hpp | 36 +++++++++++++++++++----------------- inst/test/CMakeLists.txt | 4 ++-- man/wdm-package.Rd | 12 ++++++++++++ src/wrappers.cpp | 2 +- 10 files changed, 50 insertions(+), 35 deletions(-)
Title: Lyrics and Song Data for Taylor Swift's Discography
Description: A comprehensive resource for data on Taylor Swift songs. Data
is included for all officially released studio albums, extended plays
(EPs), and individual singles are included. Data comes from 'Genius'
(lyrics) and 'Spotify' (song characteristics). Additional functions
are included for easily creating data visualizations with color
palettes inspired by Taylor Swift's album covers.
Author: W. Jake Thompson [aut, cre, cph]
Maintainer: W. Jake Thompson <wjakethompson@gmail.com>
Diff between taylor versions 3.1.0 dated 2024-05-08 and 3.2.0 dated 2025-01-07
DESCRIPTION | 18 - MD5 | 82 +++---- NEWS.md | 32 ++ R/data-checks.R | 103 +++++--- R/lyric-abbreviation.R | 2 R/misc.R | 2 R/palette.R | 6 R/taylor-album-palettes.R | 6 R/taylor-package.R | 18 - README.md | 16 - build/vignette.rds |binary data/eras_tour_surprise.rda |binary data/taylor_album_songs.rda |binary data/taylor_all_songs.rda |binary inst/WORDLIST | 9 inst/doc/lyrics.R | 10 inst/doc/lyrics.Rmd | 6 inst/doc/lyrics.html | 8 inst/doc/palettes.R | 6 inst/doc/plotting.R | 6 inst/doc/plotting.html | 4 inst/doc/taylor.R | 292 ++++++++++++++++--------- inst/doc/taylor.Rmd | 67 ++++- inst/doc/taylor.html | 79 +++++- man/eras_tour_surprise.Rd | 2 man/figures/lifecycle-deprecated.svg | 22 + man/figures/lifecycle-experimental.svg | 22 + man/figures/lifecycle-stable.svg | 30 ++ man/figures/lifecycle-superseded.svg | 22 + man/figures/logo.png |binary man/taylor-package.Rd |only man/taylor_songs.Rd | 2 tests/testthat/_snaps/data-checks.md |only tests/testthat/_snaps/misc.md |only tests/testthat/_snaps/palette.md | 48 ++-- tests/testthat/_snaps/taylor-album-palettes.md |only tests/testthat/test-data-checks.R | 255 +++++++++------------ tests/testthat/test-data.R | 6 tests/testthat/test-misc.R | 6 tests/testthat/test-palette.R | 46 +-- tests/testthat/test-taylor-album-palettes.R | 18 - vignettes/children/chunk-options.txt | 6 vignettes/lyrics.Rmd | 6 vignettes/taylor.Rmd | 67 ++++- 44 files changed, 835 insertions(+), 495 deletions(-)
Title: Pediatric Blood Pressure
Description: Data and utilities for estimating pediatric blood pressure
percentiles by sex, age, and optionally height (stature) as described in
Martin et.al. (2022) <doi:10.1001/jamanetworkopen.2022.36918>.
Blood pressure percentiles for children under one year of age come from Gemelli
et.al. (1990) <doi:10.1007/BF02171556>. Estimates of blood pressure
percentiles for children at least one year of age are informed by
data from the National Heart, Lung, and Blood Institute (NHLBI) and the
Centers for Disease Control and Prevention (CDC)
<doi:10.1542/peds.2009-2107C> or from Lo et.al. (2013)
<doi:10.1542/peds.2012-1292>. The flowchart for selecting the informing
data source comes from Martin et.al. (2022)
<doi:10.1542/hpeds.2021-005998>.
Author: Peter DeWitt [aut, cre] ,
Blake Martin [ctb] ,
David Albers [ctb] ,
Tell Bennett [ctb]
Maintainer: Peter DeWitt <peter.dewitt@cuanschutz.edu>
Diff between pedbp versions 2.0.1 dated 2024-09-16 and 2.0.2 dated 2025-01-07
DESCRIPTION | 6 ++-- MD5 | 42 ++++++++++++++++---------------- NEWS.md | 4 +++ R/sysdata.rda |binary data/bp_parameters.rda |binary data/flynn2017.rda |binary data/gemelli1990.rda |binary data/lo2013.rda |binary data/nhlbi_bp_norms.rda |binary tests/test-bmi_for_age.R | 1 tests/test-bp-by-source.R | 8 ------ tests/test-bp_chart.R | 9 ------ tests/test-bp_distributions.R | 10 ------- tests/test-cppPGSF.R | 1 tests/test-gs_chart.R | 8 ------ tests/test-head_circumference_for_age.R | 1 tests/test-height_for_age.R | 1 tests/test-internal-data.R | 2 + tests/test-length_for_age.R | 1 tests/test-weight_for_age.R | 1 tests/test-weight_for_height.R | 1 tests/test-weight_for_length.R | 1 22 files changed, 38 insertions(+), 59 deletions(-)
Title: Diagnostics for Pharmacometric Models
Description: Diagnostics for non-linear mixed-effects (population)
models from 'NONMEM' <https://www.iconplc.com/solutions/technologies/nonmem/>.
'xpose' facilitates data import, creation of numerical run summary
and provide 'ggplot2'-based graphics for data exploration and model
diagnostics.
Author: Benjamin Guiastrennec [aut, cre, cph],
Andrew C. Hooker [aut, cph],
Sebastian Ueckert [aut, cph],
Mike K. Smith [ctb],
Mats O. Karlsson [aut, cph]
Maintainer: Benjamin Guiastrennec <guiastrennec@gmail.com>
Diff between xpose versions 0.4.18 dated 2024-02-01 and 0.4.19 dated 2025-01-07
DESCRIPTION | 8 +- MD5 | 36 ++++++------ NEWS.md | 3 + R/summarise_nm_model.R | 58 ++++++++++++++----- build/vignette.rds |binary inst/doc/access_xpdb_data.html | 6 +- inst/doc/customize_plots.R | 20 +++--- inst/doc/customize_plots.html | 38 ++++++------ inst/doc/import_model_outputs.html | 6 +- inst/doc/introduction.R | 22 +++---- inst/doc/introduction.html | 14 ++-- inst/doc/multiple_pages.R | 18 +++--- inst/doc/multiple_pages.html | 18 +++--- inst/doc/vpc.R | 26 ++++---- inst/doc/vpc.html | 12 ++-- tests/testthat/_snaps/xpose_save.md | 8 -- tests/testthat/helper-test_that_for_all.R | 18 +++--- tests/testthat/test-model-summary.R | 90 +++++++++++++++++++++++++++++- tests/testthat/test-xpose_save.R | 7 +- 19 files changed, 258 insertions(+), 150 deletions(-)
Title: Nonparametric Comparison of Multivariate Samples
Description: Performs analysis of one-way multivariate data, for small samples using Nonparametric techniques. Using approximations for ANOVA Type, Wilks' Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package compares the multivariate distributions for a single explanatory variable. The comparison is also performed using a permutation test for each of the four test statistics. The package also performs an all-subsets algorithm regarding variables and regarding factor levels.
Author: Woodrow Burchett [aut],
Amanda Ellis [aut, cre]
Maintainer: Amanda Ellis <arelli4@uky.edu>
Diff between npmv versions 2.4.0 dated 2017-01-09 and 2.4.1 dated 2025-01-07
DESCRIPTION | 19 +++++++++++---- MD5 | 8 +++--- man/nonpartest.Rd | 65 ++++++++++++++++++++++++++++++++-------------------- man/npmv-package.Rd | 8 ------ man/ssnonpartest.Rd | 65 ++++++++++++++++++++++++++++++++-------------------- 5 files changed, 101 insertions(+), 64 deletions(-)
Title: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
Author: Henrik Bengtsson [aut, cre, cph],
Constantin Ahlmann-Eltze [ctb],
Hector Corrada Bravo [ctb],
Robert Gentleman [ctb],
Jan Gleixner [ctb],
Peter Hickey [ctb],
Ola Hossjer [ctb],
Harris Jaffee [ctb],
Dongcan Jiang [ctb],
Peter Langfelder [ctb],
Brian M [...truncated...]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 1.4.1 dated 2024-09-08 and 1.5.0 dated 2025-01-07
DESCRIPTION | 8 - MD5 | 224 ++++++++++++++++---------------- NEWS.md | 37 ++++- R/000.DEPRECATION.R | 50 +++---- R/options.R | 25 --- R/rowAlls.R | 58 +++----- R/rowCollapse.R | 30 +--- R/rowCounts.R | 46 ++---- R/rowCumsums.R | 8 - R/rowDiffs.R | 2 R/rowIQRs.R | 12 - R/rowLogSumExps.R | 2 R/rowMads.R | 32 +--- R/rowMeans2.R | 2 R/rowMedians.R | 2 R/rowOrderStats.R | 2 R/rowProds.R | 24 +-- R/rowQuantiles.R | 20 -- R/rowRanges.R | 6 R/rowRanks.R | 4 R/rowSums2.R | 2 R/rowTabulates.R | 28 +--- R/rowVars.R | 46 ++---- R/rowWeightedMeans.R | 54 +++---- R/rowWeightedMedians.R | 8 - R/sum2.R | 10 - R/varDiff.R | 32 +--- R/weightedMad.R | 10 - R/weightedVar.R | 8 - build/vignette.rds |binary inst/doc/matrixStats-methods.html | 2 man/matrixStats.options.Rd | 19 -- man/rowQuantiles.Rd | 2 man/sum2.Rd | 10 - src/000.types.h | 36 ----- src/colCounts.c | 4 src/colOrderStats.c | 6 src/colRanges.c | 6 src/diff2.c | 4 src/diff2_lowlevel_template.h | 6 src/rowCounts.c | 4 src/rowCummaxs.c | 6 src/rowCummins.c | 6 src/rowCumprods.c | 6 src/rowCumsums.c | 6 src/rowDiffs.c | 6 src/rowDiffs_lowlevel_template.h | 4 src/rowLogSumExp.c | 4 src/rowMads.c | 4 src/rowMeans2.c | 4 src/rowMedians.c | 4 src/rowOrderStats.c | 6 src/rowRanges.c | 6 src/rowRanksWithTies.c | 4 src/rowSums2.c | 4 src/rowVars.c | 4 src/validateIndices_lowlevel_template.h | 6 src/weightedMedian_lowlevel_template.h | 42 +++--- tests/benchmark.R | 5 tests/diff2.R | 6 tests/diff2_subset.R | 6 tests/rowAllAnys.R | 28 ++-- tests/rowAllAnys_subset.R | 16 +- tests/rowCollapse.R | 20 +- tests/rowCollapse_subset.R | 6 tests/rowCounts.R | 10 - tests/rowCounts_subset.R | 8 - tests/rowCumMinMaxs.R | 18 +- tests/rowCumMinMaxs_subset.R | 10 - tests/rowCumprods.R | 16 +- tests/rowCumprods_subset.R | 6 tests/rowCumsums.R | 12 - tests/rowCumsums_subset.R | 6 tests/rowDiffs.R | 12 - tests/rowDiffs_subset.R | 8 - tests/rowIQRs.R | 8 - tests/rowIQRs_subset.R | 6 tests/rowLogSumExps.R | 4 tests/rowLogSumExps_subset.R | 4 tests/rowMads.R | 24 +-- tests/rowMads_subset.R | 14 +- tests/rowMeans2.R | 26 +-- tests/rowMeans2_subset.R | 6 tests/rowMedians.R | 26 +-- tests/rowMedians_subset.R | 10 - tests/rowOrderStats.R | 6 tests/rowOrderStats_subset.R | 6 tests/rowProds.R | 6 tests/rowProds_subset.R | 6 tests/rowQuantiles.R | 22 --- tests/rowQuantiles_subset.R | 4 tests/rowRanges.R | 18 +- tests/rowRanges_subset.R | 14 +- tests/rowRanks.R | 40 ++--- tests/rowRanks_subset.R | 12 - tests/rowSds.R | 18 +- tests/rowSds_subset.R | 14 +- tests/rowSums2.R | 24 +-- tests/rowSums2_subset.R | 10 - tests/rowTabulates.R | 24 --- tests/rowTabulates_subset.R | 2 tests/rowVarDiffs.R | 6 tests/rowVarDiffs_mad,iqr_subset.R | 2 tests/rowVarDiffs_var,sd_subset.R | 2 tests/rowVars.R | 22 +-- tests/rowVars_subset.R | 14 +- tests/rowWeightedMeans.R | 26 +-- tests/rowWeightedMeans_subset.R | 10 - tests/rowWeightedMedians.R | 26 +-- tests/rowWeightedMedians_subset.R | 6 tests/rowWeightedVars.R | 48 ------ tests/rowWeightedVars_subset.R | 2 tests/sum2.R | 1 113 files changed, 714 insertions(+), 1011 deletions(-)
Title: Simulate Data from a DAG and Associated Node Information
Description: Simulate complex data from a given directed acyclic graph and information about each individual node.
Root nodes are simply sampled from the specified distribution. Child Nodes are simulated according to
one of many implemented regressions, such as logistic regression, linear
regression, poisson regression and more. Also includes a comprehensive framework for discrete-time
simulation, which can generate even more complex longitudinal data.
Author: Robin Denz [aut, cre],
Katharina Meiszl [aut]
Maintainer: Robin Denz <robin.denz@rub.de>
Diff between simDAG versions 0.2.0 dated 2024-09-03 and 0.2.1 dated 2025-01-07
DESCRIPTION | 8 - MD5 | 95 ++++++++++---------- NAMESPACE | 3 NEWS.md | 21 ++++ R/dag.r | 7 + R/formula_interface.r | 38 ++++++-- R/input_checks.r | 13 ++ R/long2start_stop.r | 38 ++++---- R/node.r | 22 +++- R/node_identity.r |only R/node_time_to_event.r | 8 + R/sim2data.r | 17 ++- R/sim2long.r | 2 R/sim2start_stop.r | 54 +++++++++-- R/sim2start_stop_collapse.r | 45 +++++++++ R/sim_discrete_time.r | 2 R/sim_from_dag.r | 3 R/sim_n_datasets.r | 12 ++ R/structural_equations.r | 47 +++++++++- README.md | 130 +++++++++++++++++++++------- inst/doc/v_covid_example.html | 2 inst/doc/v_sim_from_dag.Rmd | 1 inst/doc/v_sim_from_dag.html | 2 inst/doc/v_using_formulas.R | 11 ++ inst/doc/v_using_formulas.Rmd | 29 +++++- inst/doc/v_using_formulas.html | 41 ++++++++ man/node.Rd | 3 man/node_identity.Rd |only man/node_multinomial.Rd | 2 man/node_time_to_event.Rd | 7 + man/sim2data.Rd | 12 +- man/simDAG.Rd | 2 man/sim_discrete_time.Rd | 4 tests/testthat.R | 2 tests/testthat/_snaps/dag.md | 3 tests/testthat/test_add_line_breaks.r |only tests/testthat/test_dag_from_data.r | 18 +-- tests/testthat/test_get_event_duration.r | 17 +++ tests/testthat/test_input_checks_sim2data.r | 5 + tests/testthat/test_is_valid_number.r |only tests/testthat/test_long2start_stop.r | 47 +++++++++- tests/testthat/test_node_gaussian.r | 58 ++++++++++++ tests/testthat/test_node_identity.r |only tests/testthat/test_node_time_to_event.r | 16 +++ tests/testthat/test_remove_not_at_risk.r |only tests/testthat/test_sim2long.all.r | 53 +++++++++++ tests/testthat/test_sim2start_stop.all.r | 17 +++ tests/testthat/test_sim_from_dag.r | 63 +++++++------ tests/testthat/test_sim_n_datasets.r | 36 +++++-- tests/testthat/test_str_eq_identity.r |only vignettes/v_sim_from_dag.Rmd | 1 vignettes/v_using_formulas.Rmd | 29 +++++- 52 files changed, 844 insertions(+), 202 deletions(-)
Title: Radiocarbon Equations
Description: Provides functions for the calibration of radiocarbon dates, as well as options to calculate different radiocarbon realms (C14 age, F14C, pMC, D14C) and estimating the effects of contamination or local reservoir offsets (Reimer and Reimer 2001 <doi:10.1017/S0033822200038339>). The methods follow long-established recommendations such as Stuiver and Polach (1977) <doi:10.1017/S0033822200003672> and Reimer et al. (2004) <doi:10.1017/S0033822200033154>. This package complements the data package 'rintcal'.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rice versions 0.4.0 dated 2024-10-29 and 1.0.0 dated 2025-01-07
DESCRIPTION | 18 - MD5 | 88 ++++---- NAMESPACE | 20 + NEWS.md | 11 + R/calc.R | 528 +++++++++++++++++++++++++++++++++++++++++++------- R/calibrate.R | 156 +++++++++----- R/marine.R | 148 +++++++++----- R/plots.R | 362 +++++++++++++++++----------------- R/realms.R | 120 +++++------ R/rice-package.R | 21 + R/rice.R | 7 R/sets.R | 210 +++++++++++++++---- README.md |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/rice.R | 69 ++++-- inst/doc/rice.Rmd | 125 ++++++++--- inst/doc/rice.html | 408 ++++++++++++++++++++++---------------- man/C14topMC.Rd | 4 man/as.bin.Rd | 17 + man/as.one.Rd | 9 man/caldist.Rd | 14 - man/calib.t.Rd | 10 man/calibrate.Rd | 12 - man/clean.Rd | 43 +++- man/contaminate.Rd | 44 +++- man/draw.dates.Rd | 23 +- man/find.shells.Rd | 13 - man/hpd.Rd | 18 + man/l.calib.Rd | 6 man/map.shells.Rd | 10 man/muck.Rd | 38 +++ man/older.Rd | 6 man/overlap.Rd |only man/p.range.Rd | 6 man/pMCtoC14.Rd | 6 man/pool.Rd | 6 man/push.gamma.Rd |only man/push.normal.Rd |only man/r.calib.Rd | 8 man/rice-package.Rd | 2 man/rice.Rd | 2 man/shells.mean.Rd | 2 man/spread.Rd | 9 man/weighted_means.Rd | 2 man/younger.Rd | 6 vignettes/rice.Rmd | 125 ++++++++--- 47 files changed, 1873 insertions(+), 859 deletions(-)
Title: Server-Side Syntax Highlighting
Description: Prism <https://prismjs.com/> is a lightweight, extensible syntax
highlighter, built with modern web standards in mind. This package provides
server-side rendering in R using 'V8' such that no JavaScript library is
required in the resulting HTML documents. Over 400 languages are supported.
Author: Jeroen Ooms [aut, cre] ,
Lea Verou [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between prismjs versions 2.0.1 dated 2024-10-04 and 2.1.0 dated 2025-01-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ R/highlight.R | 4 ++-- 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Design and Analysis of Hierarchical Composite Endpoints
Description: Simulate and analyze hierarchical composite endpoints. Win odds is the main analysis method, but other win statistics (win ratio, net benefit) are also implemented, provided there is no censoring. See Gasparyan SB et al (2023) "Hierarchical Composite Endpoints in COVID-19: The DARE-19 Trial." Case Studies in Innovative Clinical Trials, 95-148. Chapman; Hall/CRC. <doi:10.1201/9781003288640-7>.
Author: Samvel B. Gasparyan [aut, cre]
Maintainer: Samvel B. Gasparyan <gasparyan.co@gmail.com>
Diff between hce versions 0.6.5 dated 2024-10-16 and 0.6.7 dated 2025-01-07
DESCRIPTION | 6 ++-- MD5 | 63 +++++++++++++++++++++++---------------------- NAMESPACE | 1 NEWS.md | 8 +++++ R/calcWO_data_frame.R | 13 +++++---- R/calcWO_formula.R | 6 ++-- R/calcWO_hce.R | 6 ++-- R/plot_hce.R |only R/simHCE.R | 56 +++++++++++++++++++++++++++++++++------- README.md | 5 ++- build/vignette.rds |binary inst/doc/Introduction.R | 6 ++-- inst/doc/Introduction.Rmd | 10 ++----- inst/doc/Introduction.html | 29 ++++++++++---------- inst/doc/Wins.R | 4 +- inst/doc/Wins.Rmd | 4 +- inst/doc/Wins.html | 10 +++---- inst/doc/hce.R | 4 +- inst/doc/hce.Rmd | 4 +- inst/doc/hce.html | 10 +++---- inst/doc/maraca.R | 16 +++++------ inst/doc/maraca.Rmd | 4 +- inst/doc/maraca.html | 10 +++---- man/calcWO.data.frame.Rd | 6 ++-- man/calcWO.formula.Rd | 6 ++-- man/calcWO.hce.Rd | 6 ++-- man/figures/logo.png |only man/plot.hce.Rd |only man/simHCE.Rd | 13 +++++++++ vignettes/Introduction.Rmd | 10 ++----- vignettes/REFERENCES.bib | 4 +- vignettes/Wins.Rmd | 4 +- vignettes/hce.Rmd | 4 +- vignettes/maraca.Rmd | 4 +- 34 files changed, 202 insertions(+), 130 deletions(-)
Title: Diagnostic Analysis Using Forward Search Procedure for Various
Models
Description: Identifies potential data outliers and their impact on estimates and
analyses. Tool for evaluation of study credibility. Uses the forward
search approach of Atkinson and Riani, "Robust Diagnostic Regression
Analysis", 2000,<ISBN: o-387-95017-6> to prepare descriptive statistics
of a dataset that is to be analyzed by functions lm {stats}, glm {stats},
nls {stats}, lme {nlme}, or coxph {survival}, or their equivalent in
another language. Includes graphics functions to display the
descriptive statistics.
Author: William Fairweather [aut, cre]
Maintainer: William Fairweather <wrf343@flowervalleyconsulting.com>
Diff between forsearch versions 6.3.0 dated 2024-11-16 and 6.4.0 dated 2025-01-07
forsearch-6.3.0/forsearch/vignettes/Study-Credibility.RMD |only forsearch-6.4.0/forsearch/DESCRIPTION | 16 forsearch-6.4.0/forsearch/MD5 | 94 ++-- forsearch-6.4.0/forsearch/NAMESPACE | 2 forsearch-6.4.0/forsearch/NEWS.md | 18 forsearch-6.4.0/forsearch/R/aStep1.R | 2 forsearch-6.4.0/forsearch/R/aStep2.R | 3 forsearch-6.4.0/forsearch/R/bStep1.R | 34 - forsearch-6.4.0/forsearch/R/bStep2.R | 170 +++---- forsearch-6.4.0/forsearch/R/baseExport |only forsearch-6.4.0/forsearch/R/cStep1.R | 6 forsearch-6.4.0/forsearch/R/cStep2.R | 14 forsearch-6.4.0/forsearch/R/candprep.R | 3 forsearch-6.4.0/forsearch/R/dStep2.R | 1 forsearch-6.4.0/forsearch/R/eStep1.R |only forsearch-6.4.0/forsearch/R/eStep2.R |only forsearch-6.4.0/forsearch/R/forsearch_cph.R | 5 forsearch-6.4.0/forsearch/R/forsearch_lme.R | 223 +++++----- forsearch-6.4.0/forsearch/R/forsearch_nls.R |only forsearch-6.4.0/forsearch/R/logist3.R |only forsearch-6.4.0/forsearch/R/my.transfer.R |only forsearch-6.4.0/forsearch/build/partial.rdb |binary forsearch-6.4.0/forsearch/build/vignette.rds |binary forsearch-6.4.0/forsearch/inst/doc/How-many-observations-are-needed-and-where-do-we-get-them.Rmd | 12 forsearch-6.4.0/forsearch/inst/doc/How-many-observations-are-needed-and-where-do-we-get-them.html | 9 forsearch-6.4.0/forsearch/inst/doc/Quality-control-of-the-dataset-using-the-forward-search.Rmd | 2 forsearch-6.4.0/forsearch/inst/doc/Quality-control-of-the-dataset-using-the-forward-search.html | 2 forsearch-6.4.0/forsearch/inst/doc/StudyCredibility.R |only forsearch-6.4.0/forsearch/inst/doc/StudyCredibility.Rmd |only forsearch-6.4.0/forsearch/inst/doc/StudyCredibility.html |only forsearch-6.4.0/forsearch/man/bStep1.rd | 8 forsearch-6.4.0/forsearch/man/bStep2.rd | 3 forsearch-6.4.0/forsearch/man/forsearch_cph.Rd | 83 +-- forsearch-6.4.0/forsearch/man/forsearch_glm.Rd | 5 forsearch-6.4.0/forsearch/man/forsearch_lm.Rd | 14 forsearch-6.4.0/forsearch/man/forsearch_lme.Rd | 34 - forsearch-6.4.0/forsearch/man/forsearch_nls.rd |only forsearch-6.4.0/forsearch/man/logist3.Rd |only forsearch-6.4.0/forsearch/vignettes/How-many-observations-are-needed-and-where-do-we-get-them.Rmd | 12 forsearch-6.4.0/forsearch/vignettes/Quality-control-of-the-dataset-using-the-forward-search.Rmd | 2 forsearch-6.4.0/forsearch/vignettes/StudyCredibility.Rmd |only 41 files changed, 410 insertions(+), 367 deletions(-)
Title: Statistical Tools for Immune Correlates Analysis of Vaccine
Clinical Trial Data
Description: Various semiparametric and nonparametric statistical tools for
immune correlates analysis of vaccine clinical trial data. This includes
calculation of summary statistics and estimation of risk, vaccine efficacy,
controlled effects (controlled risk and controlled vaccine efficacy), and
mediation effects (natural direct effect, natural indirect effect,
proportion mediated). See Gilbert P, Fong Y, Kenny A, and Carone, M (2022)
<doi:10.1093/biostatistics/kxac024> and Fay MP and Follmann DA (2023)
<doi:10.48550/arXiv.2208.06465>.
Author: Avi Kenny [aut, cre]
Maintainer: Avi Kenny <avi.kenny@gmail.com>
Diff between vaccine versions 1.2.1 dated 2024-02-16 and 1.3.0 dated 2025-01-07
vaccine-1.2.1/vaccine/inst/doc/basic.R |only vaccine-1.2.1/vaccine/inst/doc/basic.Rmd |only vaccine-1.2.1/vaccine/inst/doc/basic.html |only vaccine-1.2.1/vaccine/vignettes/basic.Rmd |only vaccine-1.3.0/vaccine/DESCRIPTION | 24 vaccine-1.3.0/vaccine/MD5 | 46 - vaccine-1.3.0/vaccine/NEWS.md | 16 vaccine-1.3.0/vaccine/R/est_ce.R | 25 vaccine-1.3.0/vaccine/R/est_np.R | 27 vaccine-1.3.0/vaccine/R/load_data.R | 9 vaccine-1.3.0/vaccine/R/nuisance_estimators.R | 5 vaccine-1.3.0/vaccine/R/plots.R | 297 ++++++---- vaccine-1.3.0/vaccine/R/vaccine-package.R | 2 vaccine-1.3.0/vaccine/README.md | 4 vaccine-1.3.0/vaccine/build/partial.rdb |binary vaccine-1.3.0/vaccine/build/vignette.rds |binary vaccine-1.3.0/vaccine/inst/doc/vaccine.R |only vaccine-1.3.0/vaccine/inst/doc/vaccine.Rmd |only vaccine-1.3.0/vaccine/inst/doc/vaccine.html |only vaccine-1.3.0/vaccine/man/as_table.Rd | 5 vaccine-1.3.0/vaccine/man/est_ce.Rd | 4 vaccine-1.3.0/vaccine/man/figures/logo.png |binary vaccine-1.3.0/vaccine/man/hvtn505.Rd | 2 vaccine-1.3.0/vaccine/man/plot_ce.Rd | 45 + vaccine-1.3.0/vaccine/man/trim.Rd | 11 vaccine-1.3.0/vaccine/man/vaccine-package.Rd | 4 vaccine-1.3.0/vaccine/tests/testthat/test-test-core-functions.R | 87 ++ vaccine-1.3.0/vaccine/vignettes/vaccine.Rmd |only 28 files changed, 426 insertions(+), 187 deletions(-)
Title: Read Markdown Tables into Tibbles
Description: Efficient reading of raw markdown tables into tibbles. Designed to
accept content from strings, files, and URLs with the ability to extract
and read multiple tables from markdown for analysis.
Author: Jordan Bradford [aut, cre, cph]
Maintainer: Jordan Bradford <jrdnbradford@gmail.com>
Diff between readMDTable versions 0.2.0 dated 2024-09-25 and 0.3.0 dated 2025-01-07
readMDTable-0.2.0/readMDTable/R/warn_md_table.R |only readMDTable-0.3.0/readMDTable/DESCRIPTION | 8 readMDTable-0.3.0/readMDTable/MD5 | 45 - readMDTable-0.3.0/readMDTable/NAMESPACE | 1 readMDTable-0.3.0/readMDTable/NEWS.md | 10 readMDTable-0.3.0/readMDTable/R/extract_md_tables.R | 44 + readMDTable-0.3.0/readMDTable/R/match_md_tables.R |only readMDTable-0.3.0/readMDTable/R/read_md_table.R | 74 ++ readMDTable-0.3.0/readMDTable/R/read_md_table_content.R | 6 readMDTable-0.3.0/readMDTable/README.md | 41 - readMDTable-0.3.0/readMDTable/inst/doc/rvest-benchmarks.R | 22 readMDTable-0.3.0/readMDTable/inst/doc/rvest-benchmarks.Rmd | 27 - readMDTable-0.3.0/readMDTable/inst/doc/rvest-benchmarks.html | 269 +++++----- readMDTable-0.3.0/readMDTable/man/extract_md_tables.Rd | 14 readMDTable-0.3.0/readMDTable/man/read_md_table.Rd | 36 - readMDTable-0.3.0/readMDTable/tests/testthat/_snaps/read_md_table.md | 105 --- readMDTable-0.3.0/readMDTable/tests/testthat/helper-tibbles.R |only readMDTable-0.3.0/readMDTable/tests/testthat/test-extract_md_tables.R | 32 - readMDTable-0.3.0/readMDTable/tests/testthat/test-read_md_table.R | 98 +-- readMDTable-0.3.0/readMDTable/tests/testthat/test-read_md_table_example.R | 12 readMDTable-0.3.0/readMDTable/tests/testthat/testmd/aligned.md |only readMDTable-0.3.0/readMDTable/tests/testthat/testmd/gke-terraform.md |only readMDTable-0.3.0/readMDTable/tests/testthat/testmd/gutenberg.md |only readMDTable-0.3.0/readMDTable/tests/testthat/testmd/messy-multiple-tables.md | 6 readMDTable-0.3.0/readMDTable/tests/testthat/testmd/messy.md | 2 readMDTable-0.3.0/readMDTable/tests/testthat/testmd/no-table.md |only readMDTable-0.3.0/readMDTable/vignettes/rvest-benchmarks.Rmd | 27 - 27 files changed, 425 insertions(+), 454 deletions(-)
Title: Irish Grid Reference Utilities
Description: Convert between Irish grid references and Irish Grid coordinates. Irish grid
references can also be converted to or from an 'sf' object in any coordinate reference
system. Precisions from 1 m to 100 km including 2 km (tetrads) are supported, as are
datasets with mixed precision. Conversion to 'sf' polygons is precision-aware.
Author: John Kennedy [aut, cre, cph] ,
Digital Nature [fnd]
Maintainer: John Kennedy <john@digitalnature.ie>
Diff between igr versions 0.2.0 dated 2024-08-24 and 1.0.0 dated 2025-01-07
DESCRIPTION | 6 MD5 | 36 +- NEWS.md | 6 R/ig_to_igr.R | 55 +-- R/igr_is_valid.R | 2 R/st_igr_as_sf.R | 2 README.md | 55 ++- build/vignette.rds |binary inst/doc/igr.R | 15 - inst/doc/igr.Rmd | 11 inst/doc/igr.html | 384 +++++++++++++------------- man/figures/README-example-igr-points-1.png |binary man/figures/README-example-igr-polygons-1.png |binary man/ig_to_igr.Rd | 4 man/igr-package.Rd | 2 man/igr_is_valid.Rd | 2 man/st_igr_as_sf.Rd | 2 tests/testthat/test-ig_to_igr.R | 2 vignettes/igr.Rmd | 11 19 files changed, 334 insertions(+), 261 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],
Christian Caamano-Carrillo [cph]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 2.0.8 dated 2024-11-10 and 2.0.9 dated 2025-01-07
GeoModels-2.0.8/GeoModels/man/CkVarType.Rd |only GeoModels-2.0.8/GeoModels/src/Godambe.c |only GeoModels-2.0.9/GeoModels/DESCRIPTION | 33 +- GeoModels-2.0.9/GeoModels/MD5 | 122 +++++----- GeoModels-2.0.9/GeoModels/NAMESPACE | 3 GeoModels-2.0.9/GeoModels/R/GeoAniso.R | 46 +++ GeoModels-2.0.9/GeoModels/R/GeoCompositeLik.r | 208 ++++------------- GeoModels-2.0.9/GeoModels/R/GeoCompositeLik2.R | 100 -------- GeoModels-2.0.9/GeoModels/R/GeoCovariogram.r | 5 GeoModels-2.0.9/GeoModels/R/GeoCovmatrix.r | 114 +++++---- GeoModels-2.0.9/GeoModels/R/GeoFit.r | 87 ++++--- GeoModels-2.0.9/GeoModels/R/GeoFit2.R | 44 +-- GeoModels-2.0.9/GeoModels/R/GeoIndCompositeLik2.R | 2 GeoModels-2.0.9/GeoModels/R/GeoKrig.r | 233 +++++++++++++------- GeoModels-2.0.9/GeoModels/R/GeoKrigloc.R | 60 +++-- GeoModels-2.0.9/GeoModels/R/GeoLik.r | 173 ++++++++------ GeoModels-2.0.9/GeoModels/R/GeoNA.R | 15 - GeoModels-2.0.9/GeoModels/R/GeoNeighIndex.R | 37 +-- GeoModels-2.0.9/GeoModels/R/GeoNeighbSelect.R | 59 ++--- GeoModels-2.0.9/GeoModels/R/GeoNeighborhood.R | 14 - GeoModels-2.0.9/GeoModels/R/GeoResiduals.r | 26 -- GeoModels-2.0.9/GeoModels/R/GeoScatterplot.R | 51 ++-- GeoModels-2.0.9/GeoModels/R/GeoScores.R | 3 GeoModels-2.0.9/GeoModels/R/GeoSim.r | 55 +++- GeoModels-2.0.9/GeoModels/R/GeoSimCopula.R | 13 - GeoModels-2.0.9/GeoModels/R/GeoSimapprox.r | 41 ++- GeoModels-2.0.9/GeoModels/R/GeoSpoutlier.R | 36 ++- GeoModels-2.0.9/GeoModels/R/GeoTest.r | 79 ------ GeoModels-2.0.9/GeoModels/R/GeoVariogram.r | 92 ++++--- GeoModels-2.0.9/GeoModels/R/GeoWls.r | 46 ++- GeoModels-2.0.9/GeoModels/R/SimCE.R | 2 GeoModels-2.0.9/GeoModels/R/Utility.r | 153 +++++++------ GeoModels-2.0.9/GeoModels/man/CkInput.Rd | 20 - GeoModels-2.0.9/GeoModels/man/CompIndLik2.Rd | 17 - GeoModels-2.0.9/GeoModels/man/CompLik.Rd | 34 -- GeoModels-2.0.9/GeoModels/man/CompLik2.Rd | 33 -- GeoModels-2.0.9/GeoModels/man/GeoCorrFct.Rd | 2 GeoModels-2.0.9/GeoModels/man/GeoCovmatrix.Rd | 25 +- GeoModels-2.0.9/GeoModels/man/GeoFit.Rd | 44 --- GeoModels-2.0.9/GeoModels/man/GeoFit2.Rd | 40 --- GeoModels-2.0.9/GeoModels/man/GeoKrig.Rd | 12 - GeoModels-2.0.9/GeoModels/man/GeoKrigloc.Rd | 15 - GeoModels-2.0.9/GeoModels/man/GeoNA.Rd | 14 - GeoModels-2.0.9/GeoModels/man/GeoNeighIndex.Rd | 22 - GeoModels-2.0.9/GeoModels/man/GeoNeighbSelect.Rd | 18 - GeoModels-2.0.9/GeoModels/man/GeoNeighborhood.Rd | 14 - GeoModels-2.0.9/GeoModels/man/GeoOutlier.Rd | 14 - GeoModels-2.0.9/GeoModels/man/GeoResiduals.Rd | 18 - GeoModels-2.0.9/GeoModels/man/GeoScatterplot.Rd | 18 - GeoModels-2.0.9/GeoModels/man/GeoSim.Rd | 68 +++-- GeoModels-2.0.9/GeoModels/man/GeoSimCopula.Rd | 15 - GeoModels-2.0.9/GeoModels/man/GeoSimapprox.Rd | 13 - GeoModels-2.0.9/GeoModels/man/GeoVariogram.Rd | 20 - GeoModels-2.0.9/GeoModels/man/GeoWls.Rd | 14 - GeoModels-2.0.9/GeoModels/man/Lik.Rd | 21 - GeoModels-2.0.9/GeoModels/man/SimCE.Rd | 3 GeoModels-2.0.9/GeoModels/man/StartParam.Rd | 42 +-- GeoModels-2.0.9/GeoModels/man/WlsStart.Rd | 30 -- GeoModels-2.0.9/GeoModels/src/CorrelationFunction.c | 187 +++++++--------- GeoModels-2.0.9/GeoModels/src/GeoModels_init.c | 73 ++---- GeoModels-2.0.9/GeoModels/src/Utility.c | 89 +++++-- GeoModels-2.0.9/GeoModels/src/header.h | 11 GeoModels-2.0.9/GeoModels/src/weightedleastsquare.c | 59 ++--- 63 files changed, 1468 insertions(+), 1489 deletions(-)
Title: Constrained, Covariance-Matching Constrained and Universal Point
or Block Kriging
Description: Provides functions for efficient computation of non-linear spatial predictions with local change of support (Hofer, C. and Papritz, A. (2011) "constrainedKriging: An R-package for customary, constrained and covariance-matching constrained point or block kriging" <doi:10.1016/j.cageo.2011.02.009>). This package supplies functions for two-dimensional spatial interpolation by constrained (Cressie, N. (1993) "Aggregation in geostatistical problems" <doi:10.1007/978-94-011-1739-5_3>), covariance-matching constrained (Aldworth, J. and Cressie, N. (2003) "Prediction of nonlinear spatial functionals" <doi:10.1016/S0378-3758(02)00321-X>) and universal (external drift) Kriging for points or blocks of any shape from data with a non-stationary mean function and an isotropic weakly stationary covariance function. The linear spatial interpolation methods, constrained and covariance-matching constrained Kriging, provide approximately unbiased prediction for non-linear target value [...truncated...]
Author: Christoph Hofer [aut],
Andreas Papritz [ctb, cre]
Maintainer: Andreas Papritz <papritz@retired.ethz.ch>
Diff between constrainedKriging versions 0.2-8 dated 2024-08-24 and 0.2-9 dated 2025-01-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/f.pixelgrid.sfc.R | 6 ++++++ build/partial.rdb |binary inst/ChangeLog.txt | 6 ++++++ 5 files changed, 20 insertions(+), 8 deletions(-)
More information about constrainedKriging at CRAN
Permanent link
Title: Data Access and Analytical Tools for 'VectorSurv' Users
Description: Allows registered 'VectorSurv' <https://vectorsurv.org/> users access to data through the 'VectorSurv API' <https://api.vectorsurv.org/>. Additionally provides functions for analysis and visualization.
Author: Christina De Cesaris [aut, cre]
Maintainer: Christina De Cesaris <cmdecesaris@ucdavis.edu>
Diff between vectorsurvR versions 1.2.1 dated 2024-09-30 and 1.3.0 dated 2025-01-07
vectorsurvR-1.2.1/vectorsurvR/R/plotInfectionRate.R |only vectorsurvR-1.2.1/vectorsurvR/man/plotInfectionRate.Rd |only vectorsurvR-1.2.1/vectorsurvR/tests/testthat/test-ProcessAbunAnom.R |only vectorsurvR-1.3.0/vectorsurvR/DESCRIPTION | 8 vectorsurvR-1.3.0/vectorsurvR/MD5 | 67 vectorsurvR-1.3.0/vectorsurvR/NAMESPACE | 26 vectorsurvR-1.3.0/vectorsurvR/R/data.R | 2 vectorsurvR-1.3.0/vectorsurvR/R/getAbundance.R | 208 vectorsurvR-1.3.0/vectorsurvR/R/getAbundanceAnomaly.R | 87 vectorsurvR-1.3.0/vectorsurvR/R/getArthroCollections.R | 90 vectorsurvR-1.3.0/vectorsurvR/R/getInfectionRate.R | 348 vectorsurvR-1.3.0/vectorsurvR/R/getPools.R | 25 vectorsurvR-1.3.0/vectorsurvR/R/getPoolsComparisonTable.R | 35 vectorsurvR-1.3.0/vectorsurvR/R/getVectorIndex.R | 87 vectorsurvR-1.3.0/vectorsurvR/R/globals.R | 14 vectorsurvR-1.3.0/vectorsurvR/R/processAbunAnom.R | 21 vectorsurvR-1.3.0/vectorsurvR/R/sysdata.rda |only vectorsurvR-1.3.0/vectorsurvR/R/utils-dplyr-aliases.R |only vectorsurvR-1.3.0/vectorsurvR/README.md | 8 vectorsurvR-1.3.0/vectorsurvR/data/sample_collections.rda |binary vectorsurvR-1.3.0/vectorsurvR/data/sample_pools.rda |binary vectorsurvR-1.3.0/vectorsurvR/inst/doc/vectorsurvR.R | 175 vectorsurvR-1.3.0/vectorsurvR/inst/doc/vectorsurvR.Rmd | 277 vectorsurvR-1.3.0/vectorsurvR/inst/doc/vectorsurvR.html | 3698 ++++++---- vectorsurvR-1.3.0/vectorsurvR/man/getAbundance.Rd | 25 vectorsurvR-1.3.0/vectorsurvR/man/getAbundanceAnomaly.Rd | 17 vectorsurvR-1.3.0/vectorsurvR/man/getInfectionRate.Rd | 26 vectorsurvR-1.3.0/vectorsurvR/man/getPoolsComparisionTable.Rd | 11 vectorsurvR-1.3.0/vectorsurvR/man/getVectorIndex.Rd | 19 vectorsurvR-1.3.0/vectorsurvR/man/processAbunAnom.Rd | 10 vectorsurvR-1.3.0/vectorsurvR/man/sample_collections.Rd | 1 vectorsurvR-1.3.0/vectorsurvR/man/sample_pools.Rd | 1 vectorsurvR-1.3.0/vectorsurvR/tests/testthat/test-getAbundance.R | 70 vectorsurvR-1.3.0/vectorsurvR/tests/testthat/test-getAbundanceAnomaly.R | 36 vectorsurvR-1.3.0/vectorsurvR/tests/testthat/test-getInfectionRate.R | 22 vectorsurvR-1.3.0/vectorsurvR/tests/testthat/test-getVectorIndex.R | 14 vectorsurvR-1.3.0/vectorsurvR/vignettes/vectorsurvR.Rmd | 277 37 files changed, 3443 insertions(+), 2262 deletions(-)
Title: Pattern-Oriented Modeling Framework for Coupled Niche-Population
Paleo-Climatic Models
Description: This extension of the poems pattern-oriented modeling (POM) framework
provides a collection of modules and functions customized for paleontological
time-scales, and optimized for single-generation transitions and large populations,
across multiple generations.
Author: Sean Haythorne [aut],
July Pilowsky [aut, cre] ,
Stuart Brown [aut] ,
Damien Fordham [aut]
Maintainer: July Pilowsky <pilowskyj@caryinstitute.org>
Diff between paleopop versions 2.1.6 dated 2024-09-24 and 2.1.7 dated 2025-01-07
DESCRIPTION | 10 +++--- MD5 | 10 +++--- NEWS.md | 4 ++ README.md | 38 ++++++++++++++---------- inst/doc/bison_example.html | 19 ++++++------ man/figures/README-paleosimulator_example-1.png |binary 6 files changed, 47 insertions(+), 34 deletions(-)
Title: Bayesian Longitudinal Regularized Quantile Mixed Model
Description: In longitudinal studies, the same subjects are measured repeatedly over time, leading to correlations among the repeated measurements. Properly accounting for the intra-cluster correlations in the presence of data heterogeneity and long tailed distributions of the disease phenotype is challenging, especially in the context of high dimensional regressions. In this package, we developed a Bayesian quantile mixed effects model with spike- and -slab priors dissect important gene - environment interactions under longitudinal genomics studies. An efficient Gibbs sampler has been developed to facilitate fast computation. The Markov chain Monte Carlo algorithms of the proposed and alternative methods are efficiently implemented in 'C++'. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Kun Fan [aut, cre],
Cen Wu [aut]
Maintainer: Kun Fan <kfan@ksu.edu>
Diff between mixedBayes versions 0.1.3 dated 2024-09-27 and 0.1.4 dated 2025-01-07
DESCRIPTION | 10 - MD5 | 23 ++-- R/LONBGLSS.R | 108 ++++++++++----------- R/LONRBGLSS.R | 122 ++++++++++++------------ R/RcppExports.R | 70 ++++++------- R/data.R | 64 ++++++------ R/mixedBayes-package.R | 124 ++++++++++++------------ R/mixedBayes.R | 232 +++++++++++++++++++++++----------------------- R/selection.R | 96 +++++++++---------- README.md |only build/partial.rdb |binary man/mixedBayes-package.Rd | 2 man/mixedBayes.Rd | 226 ++++++++++++++++++++++---------------------- 13 files changed, 539 insertions(+), 538 deletions(-)
Title: Inference on Predicted Data
Description: Performs valid statistical inference on predicted data (IPD) using recent methods, where for a subset of the data, the outcomes have been predicted by an algorithm. Provides a wrapper function with specified defaults for the type of model and method to be used for estimation and inference. Further provides methods for tidying and summarizing results. Salerno et al., (2024) <doi:10.48550/arXiv.2410.09665>.
Author: Stephen Salerno [aut, cre, cph]
,
Jiacheng Miao [aut],
Awan Afiaz [aut],
Kentaro Hoffman [aut],
Anna Neufeld [aut],
Qiongshi Lu [aut],
Tyler H McCormick [aut],
Jeffrey T Leek [aut]
Maintainer: Stephen Salerno <ssalerno@fredhutch.org>
Diff between ipd versions 0.1.3 dated 2024-12-03 and 0.1.4 dated 2025-01-07
DESCRIPTION | 6 MD5 | 123 - NEWS.md | 14 R/helpers.R | 3506 +++++++++++++++++++-------------------- R/ipd-package.R |only R/ipd.R | 74 R/methods.R | 760 ++++---- R/postpi_analytic_ols.R | 198 +- R/postpi_boot_logistic.R | 10 R/postpi_boot_ols.R | 440 ++-- R/ppi_logistic.R | 212 +- R/ppi_mean.R | 140 - R/ppi_ols.R | 250 +- R/ppi_plusplus_logistic.R | 570 +++--- R/ppi_plusplus_mean.R | 416 ++-- R/ppi_plusplus_ols.R | 484 ++--- R/ppi_plusplus_quantile.R | 370 ++-- R/ppi_quantile.R | 184 +- R/pspa_logistic.R | 152 - R/pspa_mean.R | 128 - R/pspa_ols.R | 152 - R/pspa_poisson.R | 10 R/pspa_quantile.R | 144 - R/simdat.R | 532 +++-- README.md | 61 build/partial.rdb |only inst/WORDLIST | 8 inst/doc/ipd.R | 44 inst/doc/ipd.Rmd | 44 inst/doc/ipd.html | 110 - inst/paper.R | 22 man/augment.ipd.Rd | 2 man/calc_lhat_glm.Rd | 10 man/glance.ipd.Rd | 2 man/ipd-package.Rd |only man/ipd.Rd | 72 man/logistic_get_stats.Rd | 10 man/ols_get_stats.Rd | 10 man/postpi_analytic_ols.Rd | 10 man/postpi_boot_logistic.Rd | 10 man/postpi_boot_ols.Rd | 10 man/ppi_logistic.Rd | 10 man/ppi_mean.Rd | 6 man/ppi_ols.Rd | 10 man/ppi_plusplus_logistic.Rd | 10 man/ppi_plusplus_logistic_est.Rd | 10 man/ppi_plusplus_mean.Rd | 6 man/ppi_plusplus_mean_est.Rd | 6 man/ppi_plusplus_ols.Rd | 10 man/ppi_plusplus_ols_est.Rd | 10 man/ppi_plusplus_quantile.Rd | 6 man/ppi_plusplus_quantile_est.Rd | 6 man/ppi_quantile.Rd | 6 man/print.ipd.Rd | 2 man/print.summary.ipd.Rd | 2 man/pspa_logistic.Rd | 10 man/pspa_mean.Rd | 6 man/pspa_ols.Rd | 10 man/pspa_poisson.Rd | 10 man/pspa_quantile.Rd | 6 man/simdat.Rd | 155 + man/summary.ipd.Rd | 2 man/tidy.ipd.Rd | 2 vignettes/ipd.Rmd | 44 64 files changed, 5006 insertions(+), 4639 deletions(-)
Title: Simple Fisheries Stock Assessment Methods
Description: A variety of simple fish stock assessment methods.
Author: Derek H. Ogle [aut, cre] ,
Jason C. Doll [aut],
A. Powell Wheeler [aut],
Alexis Dinno [aut] )
Maintainer: Derek H. Ogle <DerekOgle51@gmail.com>
Diff between FSA versions 0.9.5 dated 2023-08-26 and 0.9.6 dated 2025-01-07
FSA-0.9.5/FSA/tests/test-all.R |only FSA-0.9.6/FSA/DESCRIPTION | 15 FSA-0.9.6/FSA/MD5 | 116 +- FSA-0.9.6/FSA/NAMESPACE | 6 FSA-0.9.6/FSA/NEWS.md | 35 FSA-0.9.6/FSA/R/FSAUtils.R | 12 FSA-0.9.6/FSA/R/alkPlot.R | 3 FSA-0.9.6/FSA/R/bootstrap.R | 4 FSA-0.9.6/FSA/R/catchCurve.R | 148 ++- FSA-0.9.6/FSA/R/chapmanRobson.R | 112 ++ FSA-0.9.6/FSA/R/depletion.R | 178 +++- FSA-0.9.6/FSA/R/growthModels.R | 706 ++++++++-------- FSA-0.9.6/FSA/R/knitUtil.R | 6 FSA-0.9.6/FSA/R/metaM.R | 163 ++- FSA-0.9.6/FSA/R/psdCI.R | 2 FSA-0.9.6/FSA/R/removal.R | 321 ++++--- FSA-0.9.6/FSA/man/FSA.Rd | 2 FSA-0.9.6/FSA/man/alkPlot.Rd | 4 FSA-0.9.6/FSA/man/boot.Rd | 2 FSA-0.9.6/FSA/man/catchCurve.Rd | 52 + FSA-0.9.6/FSA/man/chapmanRobson.Rd | 55 + FSA-0.9.6/FSA/man/depletion.Rd | 87 +- FSA-0.9.6/FSA/man/growthModels.Rd | 30 FSA-0.9.6/FSA/man/knitUtil.Rd | 6 FSA-0.9.6/FSA/man/metaM.Rd | 67 - FSA-0.9.6/FSA/man/nlsBoot.Rd | 2 FSA-0.9.6/FSA/man/psdCI.Rd | 2 FSA-0.9.6/FSA/man/removal.Rd | 152 ++- FSA-0.9.6/FSA/man/se.Rd | 12 FSA-0.9.6/FSA/tests/testthat.R |only FSA-0.9.6/FSA/tests/testthat/Rplots.pdf |binary FSA-0.9.6/FSA/tests/testthat/testthat_AgeComparisons.R | 101 +- FSA-0.9.6/FSA/tests/testthat/testthat_AgeLengthKey.R | 89 +- FSA-0.9.6/FSA/tests/testthat/testthat_FSAUtils.R | 84 - FSA-0.9.6/FSA/tests/testthat/testthat_Internals.R | 118 +- FSA-0.9.6/FSA/tests/testthat/testthat_LWCompPreds.R | 6 FSA-0.9.6/FSA/tests/testthat/testthat_PSD.R | 102 +- FSA-0.9.6/FSA/tests/testthat/testthat_StockRecruit.R | 84 - FSA-0.9.6/FSA/tests/testthat/testthat_Summarize.R | 62 - FSA-0.9.6/FSA/tests/testthat/testthat_VonBertalanffy.R | 733 ++++++++--------- FSA-0.9.6/FSA/tests/testthat/testthat_WSWR.R | 12 FSA-0.9.6/FSA/tests/testthat/testthat_addZeroCatch.R | 10 FSA-0.9.6/FSA/tests/testthat/testthat_bootstrap.R | 32 FSA-0.9.6/FSA/tests/testthat/testthat_capHist.R | 76 - FSA-0.9.6/FSA/tests/testthat/testthat_catchCurve.R | 248 ++++- FSA-0.9.6/FSA/tests/testthat/testthat_ciDists.R | 53 - FSA-0.9.6/FSA/tests/testthat/testthat_depletion.R | 416 +++++---- FSA-0.9.6/FSA/tests/testthat/testthat_dunnTest.R | 177 +--- FSA-0.9.6/FSA/tests/testthat/testthat_expandCounts.R | 92 +- FSA-0.9.6/FSA/tests/testthat/testthat_expandLenFreq.R | 16 FSA-0.9.6/FSA/tests/testthat/testthat_extraTests.R | 85 - FSA-0.9.6/FSA/tests/testthat/testthat_growthFuns.R | 44 - FSA-0.9.6/FSA/tests/testthat/testthat_ksTest.R | 6 FSA-0.9.6/FSA/tests/testthat/testthat_lencat.R | 62 - FSA-0.9.6/FSA/tests/testthat/testthat_metaM.R | 114 +- FSA-0.9.6/FSA/tests/testthat/testthat_mrClosed.R | 288 +++--- FSA-0.9.6/FSA/tests/testthat/testthat_mrOpen.R | 33 FSA-0.9.6/FSA/tests/testthat/testthat_nlsTracePlot.R | 28 FSA-0.9.6/FSA/tests/testthat/testthat_removal.R | 289 ++++-- FSA-0.9.6/FSA/tests/testthat/testthat_sumTable.R | 29 60 files changed, 3327 insertions(+), 2462 deletions(-)
Title: 'Shiny' Modules for General Tasks
Description: 'Shiny' apps can often make use of the same key elements, this package provides modules for common tasks (data upload, wrangling data, figure generation and saving the app state), and also a framework for developing. These modules can react and interact as well as generate code to create reproducible analyses.
Author: John Harrold [aut, cre]
Maintainer: John Harrold <john.m.harrold@gmail.com>
Diff between formods versions 0.1.7 dated 2024-09-20 and 0.2.0 dated 2025-01-07
formods-0.1.7/formods/man/ASM_write_state.Rd |only formods-0.2.0/formods/DESCRIPTION | 8 formods-0.2.0/formods/MD5 | 203 +- formods-0.2.0/formods/NAMESPACE | 19 formods-0.2.0/formods/NEWS.md | 16 formods-0.2.0/formods/R/ASM_Server.R | 982 ++++++++---- formods-0.2.0/formods/R/DW_Server.R | 820 ++++------ formods-0.2.0/formods/R/FG_Server.R | 854 +++++++--- formods-0.2.0/formods/R/UD_Server.R | 494 +++++- formods-0.2.0/formods/R/formods.R | 455 ++++- formods-0.2.0/formods/README.md | 27 formods-0.2.0/formods/build/vignette.rds |binary formods-0.2.0/formods/inst/doc/included_modules.html | 15 formods-0.2.0/formods/inst/doc/making_modules.Rmd | 89 - formods-0.2.0/formods/inst/doc/making_modules.html | 208 +- formods-0.2.0/formods/inst/doc/preload.R |only formods-0.2.0/formods/inst/doc/preload.Rmd |only formods-0.2.0/formods/inst/doc/preload.html |only formods-0.2.0/formods/inst/preload |only formods-0.2.0/formods/inst/templates/ASM.yaml | 5 formods-0.2.0/formods/inst/templates/DW.yaml | 103 - formods-0.2.0/formods/inst/templates/FG.yaml | 7 formods-0.2.0/formods/inst/templates/FM_compact.R | 56 formods-0.2.0/formods/inst/templates/UD.yaml | 32 formods-0.2.0/formods/inst/templates/UD_module_components.R | 15 formods-0.2.0/formods/inst/templates/ZZ.yaml | 8 formods-0.2.0/formods/inst/templates/ZZ_Server.R | 320 +++ formods-0.2.0/formods/inst/templates/formods.yaml | 30 formods-0.2.0/formods/inst/test_apps/DW_funcs.R | 2 formods-0.2.0/formods/inst/test_apps/FG_funcs.R | 6 formods-0.2.0/formods/inst/test_apps/FM_compact.R | 56 formods-0.2.0/formods/man/ASM_Server.Rd | 56 formods-0.2.0/formods/man/ASM_fetch_code.Rd | 2 formods-0.2.0/formods/man/ASM_fetch_dlfn.Rd | 2 formods-0.2.0/formods/man/ASM_fetch_state.Rd | 2 formods-0.2.0/formods/man/ASM_init_state.Rd | 2 formods-0.2.0/formods/man/ASM_load_state.Rd |only formods-0.2.0/formods/man/ASM_mk_preload.Rd |only formods-0.2.0/formods/man/ASM_onload.Rd | 2 formods-0.2.0/formods/man/ASM_preload.Rd |only formods-0.2.0/formods/man/ASM_read_app_state.Rd |only formods-0.2.0/formods/man/ASM_save_state.Rd |only formods-0.2.0/formods/man/ASM_test_mksession.Rd | 31 formods-0.2.0/formods/man/DW_Server.Rd | 56 formods-0.2.0/formods/man/DW_add_wrangling_element.Rd | 2 formods-0.2.0/formods/man/DW_append_report.Rd | 6 formods-0.2.0/formods/man/DW_attach_ds.Rd | 2 formods-0.2.0/formods/man/DW_fetch_code.Rd | 2 formods-0.2.0/formods/man/DW_fetch_current_view.Rd | 2 formods-0.2.0/formods/man/DW_fetch_ds.Rd | 3 formods-0.2.0/formods/man/DW_fetch_state.Rd | 2 formods-0.2.0/formods/man/DW_hasds.Rd |only formods-0.2.0/formods/man/DW_init_state.Rd | 2 formods-0.2.0/formods/man/DW_mk_preload.Rd |only formods-0.2.0/formods/man/DW_new_view.Rd | 2 formods-0.2.0/formods/man/DW_preload.Rd |only formods-0.2.0/formods/man/DW_set_current_view.Rd | 2 formods-0.2.0/formods/man/DW_test_mksession.Rd | 21 formods-0.2.0/formods/man/DW_update_checksum.Rd | 2 formods-0.2.0/formods/man/FG_Server.Rd | 56 formods-0.2.0/formods/man/FG_append_report.Rd | 2 formods-0.2.0/formods/man/FG_build.Rd | 10 formods-0.2.0/formods/man/FG_extract_page.Rd | 6 formods-0.2.0/formods/man/FG_fetch_code.Rd | 2 formods-0.2.0/formods/man/FG_fetch_current_fig.Rd | 6 formods-0.2.0/formods/man/FG_fetch_state.Rd | 13 formods-0.2.0/formods/man/FG_mk_preload.Rd |only formods-0.2.0/formods/man/FG_new_fig.Rd | 6 formods-0.2.0/formods/man/FG_preload.Rd |only formods-0.2.0/formods/man/FG_set_current_fig.Rd | 6 formods-0.2.0/formods/man/FG_test_mksession.Rd | 34 formods-0.2.0/formods/man/FG_update_checksum.Rd | 2 formods-0.2.0/formods/man/FM_add_ui_tooltip.Rd | 3 formods-0.2.0/formods/man/FM_app_preload.Rd |only formods-0.2.0/formods/man/FM_fetch_app_code.Rd | 2 formods-0.2.0/formods/man/FM_fetch_app_info.Rd | 4 formods-0.2.0/formods/man/FM_fetch_app_state.Rd | 3 formods-0.2.0/formods/man/FM_fetch_data_format.Rd | 2 formods-0.2.0/formods/man/FM_fetch_deps.Rd | 3 formods-0.2.0/formods/man/FM_fetch_ds.Rd | 4 formods-0.2.0/formods/man/FM_fetch_log_path.Rd | 13 formods-0.2.0/formods/man/FM_fetch_mdl.Rd | 3 formods-0.2.0/formods/man/FM_fetch_mod_state.Rd | 5 formods-0.2.0/formods/man/FM_fetch_user_files_path.Rd | 3 formods-0.2.0/formods/man/FM_init_state.Rd | 2 formods-0.2.0/formods/man/FM_le.Rd | 3 formods-0.2.0/formods/man/FM_mk_app_preload.Rd |only formods-0.2.0/formods/man/FM_pause_screen.Rd | 4 formods-0.2.0/formods/man/FM_proc_include.Rd | 3 formods-0.2.0/formods/man/FM_reset_app.Rd |only formods-0.2.0/formods/man/FM_resume_screen.Rd | 4 formods-0.2.0/formods/man/FM_set_app_state.Rd | 3 formods-0.2.0/formods/man/FM_set_mod_state.Rd | 5 formods-0.2.0/formods/man/FM_set_ui_msg.Rd | 3 formods-0.2.0/formods/man/UD_Server.Rd | 56 formods-0.2.0/formods/man/UD_fetch_ds.Rd | 5 formods-0.2.0/formods/man/UD_mk_preload.Rd |only formods-0.2.0/formods/man/UD_preload.Rd |only formods-0.2.0/formods/man/UD_test_mksession.Rd | 19 formods-0.2.0/formods/man/dw_eval_element.Rd | 2 formods-0.2.0/formods/man/dwrs_builder.Rd | 4 formods-0.2.0/formods/man/fers_builder.Rd | 4 formods-0.2.0/formods/man/is_shiny.Rd |only formods-0.2.0/formods/man/render_str.Rd |only formods-0.2.0/formods/man/run_formods.Rd |only formods-0.2.0/formods/tests/testthat/test-ASM_module.R |only formods-0.2.0/formods/tests/testthat/test-DW_module.R | 1 formods-0.2.0/formods/tests/testthat/test-FG_module.R | 1 formods-0.2.0/formods/tests/testthat/test-UD_module.R | 1 formods-0.2.0/formods/tests/testthat/test-formods.R | 47 formods-0.2.0/formods/vignettes/making_modules.Rmd | 89 - formods-0.2.0/formods/vignettes/preload.Rmd |only formods-0.2.0/formods/vignettes/run_workflow.png |only 113 files changed, 3739 insertions(+), 1736 deletions(-)
Title: Extract Tox Info from Various Databases
Description: Extract toxicological and chemical information from databases
maintained by scientific agencies and resources, including the
Comparative Toxicogenomics Database <https://ctdbase.org/>, the
Integrated Chemical Environment <https://ice.ntp.niehs.nih.gov/>, the
Integrated Risk Information System <https://cfpub.epa.gov/ncea/iris/>,
Provisional Peer-Reviewed Toxicity Values
<https://www.epa.gov/pprtv/provisional-peer-reviewed-toxicity-values-pprtvs-assessments>,
the CompTox Chemicals Dashboard Resource Hub
<https://www.epa.gov/comptox-tools/comptox-chemicals-dashboard-resource-hub>,
PubChem <https://pubchem.ncbi.nlm.nih.gov/>, and others.
Author: Claudio Zanettini [aut, cre, cph]
,
Lucio Queiroz [aut]
Maintainer: Claudio Zanettini <claudio.zanettini@gmail.com>
Diff between extractox versions 0.1.0 dated 2024-12-03 and 1.0.0 dated 2025-01-07
extractox-0.1.0/extractox/tests/testthat/_snaps |only extractox-1.0.0/extractox/DESCRIPTION | 14 extractox-1.0.0/extractox/MD5 | 74 +- extractox-1.0.0/extractox/NAMESPACE | 5 extractox-1.0.0/extractox/NEWS.md | 47 + extractox-1.0.0/extractox/R/cache.R |only extractox-1.0.0/extractox/R/checks.R |only extractox-1.0.0/extractox/R/extr_comptox.R | 198 +++-- extractox-1.0.0/extractox/R/extr_ctd.R | 129 ++- extractox-1.0.0/extractox/R/extr_ice.R |only extractox-1.0.0/extractox/R/extr_iris.R |only extractox-1.0.0/extractox/R/extr_monograph.R |only extractox-1.0.0/extractox/R/extr_pprtv.R |only extractox-1.0.0/extractox/R/extr_pubchem.R | 348 +++++----- extractox-1.0.0/extractox/R/extr_tox.R | 270 +------- extractox-1.0.0/extractox/R/other.R |only extractox-1.0.0/extractox/R/sysdata.rda |only extractox-1.0.0/extractox/R/utils.R | 234 +++--- extractox-1.0.0/extractox/README.md | 471 ++++++-------- extractox-1.0.0/extractox/inst |only extractox-1.0.0/extractox/man/extr_casrn_from_cid.Rd | 15 extractox-1.0.0/extractox/man/extr_chem_info.Rd | 17 extractox-1.0.0/extractox/man/extr_comptox.Rd | 180 +++-- extractox-1.0.0/extractox/man/extr_ctd.Rd | 43 - extractox-1.0.0/extractox/man/extr_ice.Rd | 21 extractox-1.0.0/extractox/man/extr_ice_assay_names.Rd |only extractox-1.0.0/extractox/man/extr_iris.Rd | 16 extractox-1.0.0/extractox/man/extr_monograph.Rd |only extractox-1.0.0/extractox/man/extr_pprtv.Rd |only extractox-1.0.0/extractox/man/extr_pubchem_fema.Rd | 14 extractox-1.0.0/extractox/man/extr_pubchem_ghs.Rd | 4 extractox-1.0.0/extractox/man/extr_tetramer.Rd | 34 - extractox-1.0.0/extractox/man/extr_tox.Rd | 47 - extractox-1.0.0/extractox/man/search_and_match.Rd |only extractox-1.0.0/extractox/man/with_extr_sandbox.Rd |only extractox-1.0.0/extractox/tests/testthat/setup.R |only extractox-1.0.0/extractox/tests/testthat/test-cache.R |only extractox-1.0.0/extractox/tests/testthat/test-comptox.R | 70 +- extractox-1.0.0/extractox/tests/testthat/test-ctd.R | 190 ++++- extractox-1.0.0/extractox/tests/testthat/test-ice.R | 75 ++ extractox-1.0.0/extractox/tests/testthat/test-iris.R | 57 + extractox-1.0.0/extractox/tests/testthat/test-pubchem.R | 192 +++++ extractox-1.0.0/extractox/tests/testthat/test-tox.R | 25 extractox-1.0.0/extractox/tests/testthat/test_monograph.R |only extractox-1.0.0/extractox/tests/testthat/test_pprtv.R |only 45 files changed, 1709 insertions(+), 1081 deletions(-)
More information about Certara.RsNLME.ModelExecutor at CRAN
Permanent link
Title: Utilities to Output CDISC SDTM/ADaM XPT Files
Description: Tools to build CDISC compliant data sets and check for CDISC
compliance.
Author: Eli Miller [aut, cre] ,
Ben Straub [aut],
Zelos Zhu [aut],
Ethan Brockmann [aut],
Vedha Viyash [aut],
Andre Verissimo [aut],
Sophie Shapcott [aut],
Celine Piraux [aut],
Kangjie Zhang [aut],
Adrian Chan [aut],
Sadchla Mascary [aut],
Atorus/GSK JPT [cp [...truncated...]
Maintainer: Eli Miller <Eli.Miller@AtorusResearch.com>
Diff between xportr versions 0.4.1 dated 2024-10-07 and 0.4.2 dated 2025-01-07
DESCRIPTION | 6 MD5 | 52 ++-- NEWS.md | 14 + R/format.R | 3 R/label.R | 3 R/length.R | 3 R/messages.R | 52 ++++ R/options.R | 68 +++--- R/order.R | 3 R/split.R | 2 R/type.R | 24 +- R/xportr-package.R | 38 +-- R/zzz.R | 2 build/vignette.rds |binary inst/doc/agency_standards.html | 88 ++++---- inst/doc/deepdive.R | 60 ++--- inst/doc/deepdive.html | 433 ++++++++++++----------------------------- inst/doc/xportr.R | 36 +-- inst/doc/xportr.html | 383 +++++++++++------------------------- man/xportr-package.Rd | 41 +-- man/xportr_options.Rd | 68 +++--- man/xportr_type.Rd | 11 - tests/testthat/test-messages.R | 29 ++ tests/testthat/test-metadata.R | 2 tests/testthat/test-order.R | 6 tests/testthat/test-type.R | 26 ++ tests/testthat/test-write.R | 9 27 files changed, 647 insertions(+), 815 deletions(-)
Title: Supporting Functions for Packages Maintained by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] ,
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brueggemann [ctb] ,
Christophe Dervieux [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.49 dated 2024-10-31 and 0.50 dated 2025-01-07
xfun-0.49/xfun/man/isFALSE.Rd |only xfun-0.50/xfun/DESCRIPTION | 12 +- xfun-0.50/xfun/MD5 | 59 ++++++----- xfun-0.50/xfun/NAMESPACE | 11 ++ xfun-0.50/xfun/NEWS.md | 42 ++++++++ xfun-0.50/xfun/R/base64.R | 3 xfun-0.50/xfun/R/cache.R | 51 ++++++++-- xfun-0.50/xfun/R/citation.R |only xfun-0.50/xfun/R/image.R | 4 xfun-0.50/xfun/R/knitr.R | 42 +++++--- xfun-0.50/xfun/R/markdown.R | 73 ++++++++++++++ xfun-0.50/xfun/R/packages.R | 93 ++++-------------- xfun-0.50/xfun/R/record.R | 50 +++++++--- xfun-0.50/xfun/R/revcheck.R | 60 ------------ xfun-0.50/xfun/R/string.R | 99 ++++++++++++++++--- xfun-0.50/xfun/R/utils.R | 35 ------- xfun-0.50/xfun/R/yaml.R | 124 +++++++++++++++++++------ xfun-0.50/xfun/build/vignette.rds |binary xfun-0.50/xfun/inst/doc/xfun.html | 22 ++-- xfun-0.50/xfun/man/cache_exec.Rd | 12 +- xfun-0.50/xfun/man/find_globals.Rd |only xfun-0.50/xfun/man/install_dir.Rd | 2 xfun-0.50/xfun/man/join_words.Rd |only xfun-0.50/xfun/man/pkg_bib.Rd |only xfun-0.50/xfun/man/record.Rd | 14 ++ xfun-0.50/xfun/man/str_wrap.Rd |only xfun-0.50/xfun/man/tabset.Rd |only xfun-0.50/xfun/man/taml_load.Rd |only xfun-0.50/xfun/man/tinify.Rd | 5 - xfun-0.50/xfun/man/yaml_body.Rd | 12 +- xfun-0.50/xfun/man/yaml_load.Rd | 20 ---- xfun-0.50/xfun/tests/test-cran/test-citation.R |only xfun-0.50/xfun/tests/test-cran/test-packages.R | 5 - xfun-0.50/xfun/tests/test-cran/test-string.R | 15 +++ xfun-0.50/xfun/tests/test-cran/test-yaml.R | 62 +++++++++++- 35 files changed, 578 insertions(+), 349 deletions(-)
Title: The Q-Matrix Validation Methods Framework
Description: Provide a variety of Q-matrix validation methods for the generalized cognitive diagnosis models, including the method based on the generalized deterministic input, noisy, and gate model (G-DINA) by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> discrimination index (the GDI method) by de la Torre and Chiu (2016) <DOI:10.1007/s11336-015-9467-8>, the step-wise Wald test method (the Wald method) by Ma and de la Torre (2020) <DOI:10.1111/bmsp.12156>, the Hull method by Najera et al. (2021) <DOI:10.1111/bmsp.12228>, the multiple logistic regression‑based Q‑matrix validation method (the MLR-B method) by Tu et al. (2022) <DOI:10.3758/s13428-022-01880-x>, the beta method based on signal detection theory by Li and Chen (2024) <DOI:10.1111/bmsp.12371> and Q-matrix validation based on relative fit index by Chen et la. (2013) <DOI:10.1111/j.1745-3984.2012.00185.x>. Different research methods and iterative procedures during Q-matrix validating are avai [...truncated...]
Author: Haijiang Qin [aut, cre, cph] ,
Lei Guo [aut, cph]
Maintainer: Haijiang Qin <haijiang133@outlook.com>
Diff between Qval versions 1.0.0 dated 2024-09-20 and 1.1.0 dated 2025-01-07
DESCRIPTION | 43 ++++--- MD5 | 56 ++++++---- NAMESPACE | 4 NEWS.md | 29 +++-- R/CDM.R | 12 +- R/GDI.R | 63 +++++++---- R/Hull.R | 94 +++++++++-------- R/MLR-B.R | 39 ++++--- R/PVAF.R | 6 - R/R2.R | 18 +-- R/RcppExports.R |only R/Wald.R | 160 ++++++++++++++++++++++------- R/Wald.test.R | 10 + R/beta.R |only R/cov.R | 2 R/fit.R | 1 R/utils.R |only R/validation.R | 226 +++++++++++++++++++++++++++++++---------- R/zzz.R | 2 man/CDM.Rd | 6 - man/Wald.test.Rd | 4 man/parallel_iter.Rd |only man/validation.Rd | 156 ++++++++++++++++++++++------ src |only tests/building.R | 11 - tests/demo.R | 55 +++++---- tests/realdata_analysis.R | 60 +++++----- tests/realdata_analysis_beta.R |only tests/repeat.R | 37 +++--- tests/test.JSS.R |only 30 files changed, 745 insertions(+), 349 deletions(-)
Title: Explore Your Data with Interactive Figures
Description: A framework for creating interactive figures for data exploration.
All plots are automatically linked and support several kinds of interactive features,
including selection, zooming, panning, and parameter manipulation. The figures
can be interacted with either manually, using a mouse and a keyboard,
or by running code from inside an active R session.
Author: Adam Bartonicek [aut, cre, cph]
Maintainer: Adam Bartonicek <bartonicek@gmail.com>
Diff between plotscaper versions 0.2.5 dated 2024-12-22 and 0.2.6 dated 2025-01-07
DESCRIPTION | 6 +- MD5 | 28 +++++------ NEWS.md | 2 inst/doc/algebra.R | 4 - inst/doc/algebra.html | 12 ++--- inst/doc/available-interactions.R | 4 - inst/doc/available-interactions.html | 64 +++++++++++++-------------- inst/doc/layout.R | 22 ++++----- inst/doc/layout.html | 16 +++--- inst/doc/performance.R | 40 ++++++++-------- inst/doc/performance.html | 8 +-- inst/doc/plotscaper.R | 42 +++++++++-------- inst/doc/plotscaper.html | 16 +++--- inst/htmlwidgets/plotscape/main.iife.js | 4 - man/figures/readme1.pngunnamed-chunk-3-1.png |binary 15 files changed, 136 insertions(+), 132 deletions(-)
Title: Graph the Relationship Between Functions in an R Package
Description: It is often useful when developing an R package to track the relationship between functions in order to appropriately test and track changes. This package generates a graph of the relationship between all R functions in a package. It can also be used on any directory containing .R files which can be very useful for 'shiny' apps or other non-package workflows.
Author: David Oliver [aut, cre, cph]
Maintainer: David Oliver <doliv071@gmail.com>
Diff between pkgGraphR versions 0.3.0 dated 2024-12-19 and 0.3.1 dated 2025-01-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/utils.r | 31 +++++++++++++++---------------- inst/doc/pkgGraphR.R | 40 ++++++++++++++++++++-------------------- 4 files changed, 41 insertions(+), 42 deletions(-)
Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript
library 'paged.js' to split the content of an HTML document into discrete
pages. Each page can have its page size, page numbers, margin boxes, and
running headers, etc. Applications of this package include books, letters,
reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] ,
Romain Lesur [aut, cph] ,
Christophe Dervieux [ctb] ,
Brent Thorne [aut] ,
Xianying Tan [aut] ,
Atsushi Yasumoto [ctb] ,
Posit Software, PBC [cph, fnd],
Adam Hyde [ctb] ,
Min-Zhong Lu [ctb] ,
Zulko [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between pagedown versions 0.21 dated 2024-10-11 and 0.22 dated 2025-01-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/chrome.R | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Description: Extends the fitdistr() function (of the MASS package) with several functions
to help the fit of a parametric distribution to non-censored or censored data.
Censored data may contain left censored, right censored and interval censored values,
with several lower and upper bounds. In addition to maximum likelihood estimation (MLE),
the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit
estimation (MGE) and maximum spacing estimation (MSE) methods (available only for
non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g.
Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction
to parametric estimation.
Author: Marie-Laure Delignette-Muller [aut]
,
Christophe Dutang [aut] ,
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between fitdistrplus versions 1.2-1 dated 2024-07-12 and 1.2-2 dated 2025-01-07
DESCRIPTION | 6 MD5 | 188 - NEWS.md | 178 - R/bootdist.R | 1 R/mgedist.R | 49 R/mledist.R | 98 R/mmedist.R | 4 R/qmedist.R | 4 R/util-mledist-vcov.R | 6 R/util-mmedist-vcov.R | 4 R/util-startarg.R | 2 README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/FAQ.R | 103 inst/doc/FAQ.Rmd | 134 inst/doc/FAQ.html | 4340 +++++++++++++++++++++++---- inst/doc/Optimalgo.R | 10 inst/doc/Optimalgo.Rmd | 50 inst/doc/Optimalgo.html | 518 +-- inst/doc/fitdistrplus_vignette.R | 8 inst/doc/fitdistrplus_vignette.Rmd | 42 inst/doc/fitdistrplus_vignette.html | 194 - inst/doc/starting-values.Rmd | 107 inst/doc/starting-values.html | 353 +- man/bootdist.Rd | 2 man/bootdistcens.Rd | 2 man/figures |only man/fitdist.Rd | 10 man/fitdistcens.Rd | 2 man/logLik-plot.Rd | 2 man/mgedist.Rd | 2 man/mmedist.Rd | 2 tests/t-CIcdfplot.R | 2 tests/t-Surv2fitdistcens.R | 2 tests/t-bootdist.R | 10 tests/t-bootdistcens.R | 2 tests/t-cdfcomp.R | 10 tests/t-cdfcompcens.R | 4 tests/t-cvg-algo.R | 4 tests/t-denscomp.R | 2 tests/t-descdist.R | 2 tests/t-detectbound.R | 4 tests/t-fitbench.R | 2 tests/t-fitdist-customoptim.R | 4 tests/t-fitdist-hessianpb.R | 4 tests/t-fitdist-test-arguments.R | 2 tests/t-fitdist.R | 10 tests/t-fitdistcens.R | 48 tests/t-gen-max-spacing-estim.R | 2 tests/t-getparam.R | 5 tests/t-gofstat.R | 3 tests/t-init-actuar.R | 5 tests/t-llplot.R | 132 tests/t-lnL-surf.R | 134 tests/t-logLik-vcov-coef.R | 70 tests/t-manageparam.R | 3 tests/t-mgedist.R | 77 tests/t-mledist-asymptotic-vcov.R | 33 tests/t-mledist-cens.R | 14 tests/t-mledist-nocens.R | 357 +- tests/t-mledist-paramsupport.R | 6 tests/t-mmedist-asymptotic-vcov.R | 13 tests/t-mmedist.R | 46 tests/t-msedist.R | 15 tests/t-parallel.R | 86 tests/t-plotdist.R | 2 tests/t-plotdistcens.R | 2 tests/t-ppcomp.R | 8 tests/t-ppcompcens.R | 2 tests/t-prefit.R | 4 tests/t-qme-discrete.R | 2 tests/t-qmedist.R | 41 tests/t-qqcomp.R | 10 tests/t-qqcompcens.R | 4 tests/t-quantiledist.R | 2 tests/t-startfixarg-overall.R | 2 tests/t-starting-value-scale-rate.R | 4 tests/t-startingvalues-fellerpareto-family.R | 25 tests/t-startingvalues-invtrgamma-family.R | 4 tests/t-startingvalues-othercont-family.R | 4 tests/t-startingvalues-trgamma-family.R | 10 tests/t-startingvalues-zeromod-family.R | 4 tests/t-startingvalues-zerotrunc-family.R | 8 tests/t-startingvalues.R | 7 tests/t-util-mmedist-vcov.R | 3 tests/t-util-npmle.R | 4 tests/t-util-npsurv-mainfunction.R | 8 tests/t-util-testdensity.R | 7 tests/t-weird-ppcomp-cens.R | 212 - tests/t-weird-qqcomp-cens.R | 206 - vignettes/FAQ.Rmd | 134 vignettes/Optimalgo.Rmd | 50 vignettes/fitdistrplus_vignette.Rmd | 42 vignettes/starting-values.Rmd | 107 95 files changed, 5883 insertions(+), 2575 deletions(-)
Title: Determining the Number of Factors in Exploratory Factor Analysis
Description: Provides a collection of standard factor retention methods in Exploratory Factor Analysis (EFA), making it easier to determine the number of factors. Traditional methods such as the scree plot by Cattell (1966) <doi:10.1207/s15327906mbr0102_10>, Kaiser-Guttman Criterion (KGC) by Guttman (1954) <doi:10.1007/BF02289162> and Kaiser (1960) <doi:10.1177/001316446002000116>, and flexible Parallel Analysis (PA) by Horn (1965) <doi:10.1007/BF02289447> based on eigenvalues form PCA or EFA are readily available. This package also implements several newer methods, such as the Empirical Kaiser Criterion (EKC) by Braeken and van Assen (2017) <doi:10.1037/met0000074>, Comparison Data (CD) by Ruscio and Roche (2012) <doi:10.1037/a0025697>, and Hull method by Lorenzo-Seva et al. (2011) <doi:10.1080/00273171.2011.564527>, as well as some AI-based methods like Comparison Data Forest (CDF) by Goretzko and Ruscio (2024) <doi:10.3758/s13428-023-02122-4> and F [...truncated...]
Author: Haijiang Qin [aut, cre, cph] ,
Lei Guo [aut, cph]
Maintainer: Haijiang Qin <haijiang133@outlook.com>
Diff between EFAfactors versions 1.1.1 dated 2024-11-19 and 1.2.0 dated 2025-01-07
DESCRIPTION | 41 +++++++++++++++++++++++++---------------- MD5 | 35 +++++++++++++++++++---------------- NAMESPACE | 25 +++++++++++++++++++------ NEWS.md | 6 ++++++ R/CD.R | 28 ++++++++++++++-------------- R/CDF.R | 2 +- R/DNN_predictor.R | 18 ++++++++++++------ R/EFAkmeans.R | 1 - R/EFAsim.data.R | 19 ++++--------------- R/EKC.R | 2 +- R/FF.R | 1 - R/ParamHelpers.R |only R/check_python_libraries.R |only man/CD.Rd | 28 ++++++++++++++-------------- man/DNN_predictor.Rd | 15 ++++++++++----- man/EFAsim.data.Rd | 8 ++------ man/EKC.Rd | 2 +- man/check_python_libraries.Rd |only tests/building.R | 5 +++-- tests/testthat/demo_realdata.R | 16 ++++++++-------- 20 files changed, 139 insertions(+), 113 deletions(-)
Title: Econometrics of Network Data
Description: Simulating and estimating peer effect models and network formation models. The class of peer effect models includes linear-in-means models (Lee, 2004; <doi:10.1111/j.1468-0262.2004.00558.x>), Tobit models (Xu and Lee, 2015; <doi:10.1016/j.jeconom.2015.05.004>), and discrete numerical data models (Houndetoungan, 2024; <doi:10.2139/ssrn.3721250>). The network formation models include pair-wise regressions with degree heterogeneity (Graham, 2017; <doi:10.3982/ECTA12679>) and exponential random graph models (Mele, 2017; <doi:10.3982/ECTA10400>).
Author: Aristide Houndetoungan [cre, aut]
Maintainer: Aristide Houndetoungan <ahoundetoungan@gmail.com>
Diff between CDatanet versions 2.2.0 dated 2024-05-14 and 2.2.1 dated 2025-01-07
DESCRIPTION | 10 MD5 | 74 - NAMESPACE | 1 NEWS.md | 3 R/CDatanet.R | 10 R/RcppExports.R | 44 + R/auxfunc.R | 135 +-- R/cdnet.R | 263 +++--- R/homophilidata.R | 14 R/homophily.fe.R | 292 ++++--- R/homophily.re.R | 23 R/sar.R | 77 +- R/sart.R | 208 +++-- build/partial.rdb |binary man/CDatanet-package.Rd | 10 man/cdnet.Rd | 78 -- man/homophili.data.Rd | 14 man/homophily.fe.Rd | 69 - man/homophily.re.Rd | 21 man/peer.avg.Rd | 32 man/print.simcdEy.Rd | 5 man/remove.ids.Rd | 21 man/sar.Rd | 16 man/sart.Rd | 89 +- man/simcdEy.Rd | 13 man/simcdnet.Rd | 131 +-- man/simnetwork.Rd | 16 man/simsar.Rd | 39 - man/simsart.Rd | 107 +- man/summary.cdnet.Rd | 10 man/summary.sar.Rd | 4 man/summary.sart.Rd | 2 man/vec.to.mat.Rd | 42 - src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 311 +++++++- src/homophily.cpp | 1805 +++++++++++++++++++++++++++++++++++++++++------- src/sar.cpp | 38 - 38 files changed, 2915 insertions(+), 1114 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] ,
Christophe Dervieux [ctb] ,
JJ Allaire [ctb],
Albert Kim [ctb],
Alessandro Samuel-Rosa [ctb],
Andrzej Oles [ctb],
Atsushi Yasumoto [ctb] ,
Aust Frederik [ctb] ,
Bastiaan Quast [ctb],
Ben Marwick [ctb],
Chester Ismay [ctb],
Clif [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.41 dated 2024-10-15 and 0.42 dated 2025-01-07
DESCRIPTION | 6 ++--- MD5 | 20 +++++++++--------- R/bs4_book.R | 2 - R/html.R | 2 - R/skeleton.R | 2 - R/utils.R | 9 ++++---- build/vignette.rds |binary inst/doc/bookdown.R | 22 ++++++++++---------- inst/doc/bookdown.html | 4 +-- inst/resources/gitbook/js/plugin-fontsettings.js | 25 ++++++++++++++++++++++- tests/testit/test-utils.R | 12 +++++++---- 11 files changed, 66 insertions(+), 38 deletions(-)
Title: Create Blogs and Websites with R Markdown
Description: Write blog posts and web pages in R Markdown. This package
supports the static site generator 'Hugo' (<https://gohugo.io>) best,
and it also supports 'Jekyll' (<https://jekyllrb.com>) and 'Hexo'
(<https://hexo.io>).
Author: Yihui Xie [aut, cre] ,
Christophe Dervieux [aut] ,
Alison Presmanes Hill [aut] ,
Amber Thomas [ctb],
Beilei Bian [ctb],
Brandon Greenwell [ctb],
Brian Barkley [ctb],
Deependra Dhakal [ctb],
Eric Nantz [ctb],
Forest Fang [ctb],
Garrick Aden-Buie [ctb] [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between blogdown versions 1.19 dated 2024-02-01 and 1.20 dated 2025-01-07
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 1 - R/format.R | 27 +++++++++++++-------------- R/hugo.R | 4 ++-- R/package.R | 2 +- R/render.R | 4 ++-- R/serve.R | 6 +++--- R/utils.R | 42 +++++++++++++++++++++++------------------- man/build_dir.Rd | 2 +- man/html_page.Rd | 28 +++++++++++++--------------- man/hugo_cmd.Rd | 2 +- man/read_toml.Rd | 34 +++++++++++++++++----------------- man/serve_site.Rd | 6 +++--- tests/test-ci/test-themes.R | 2 +- 15 files changed, 98 insertions(+), 98 deletions(-)
Title: Black Marble Data and Statistics
Description: Geographically referenced data and statistics of nighttime lights from NASA Black Marble <https://blackmarble.gsfc.nasa.gov/>.
Author: Robert Marty [aut, cre] ,
Gabriel Stefanini Vicente [aut]
Maintainer: Robert Marty <rmarty@worldbank.org>
Diff between blackmarbler versions 0.2.3 dated 2024-11-26 and 0.2.4 dated 2025-01-07
blackmarbler-0.2.3/blackmarbler/README.md |only blackmarbler-0.2.4/blackmarbler/DESCRIPTION | 10 blackmarbler-0.2.4/blackmarbler/MD5 | 12 blackmarbler-0.2.4/blackmarbler/NAMESPACE | 2 blackmarbler-0.2.4/blackmarbler/R/blackmarbler.R | 335 ++++++---- blackmarbler-0.2.4/blackmarbler/man/bm_extract.Rd | 5 blackmarbler-0.2.4/blackmarbler/man/bm_raster.Rd | 5 blackmarbler-0.2.4/blackmarbler/man/figures/nasa_profile_info.png |only 8 files changed, 220 insertions(+), 149 deletions(-)
Title: PKPD, PBPK, and Systems Pharmacology Modeling Tools
Description: Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'.
Author: John Harrold [aut, cre]
Maintainer: John Harrold <john.m.harrold@gmail.com>
Diff between ubiquity versions 2.0.3 dated 2024-03-08 and 2.1.0 dated 2025-01-07
ubiquity-2.0.3/ubiquity/inst/ubinc/templates/monolix.txt |only ubiquity-2.0.3/ubiquity/inst/ubinc/templates/nonmem.ctl |only ubiquity-2.0.3/ubiquity/vignettes/nca_reporting-md.png |only ubiquity-2.0.3/ubiquity/vignettes/nca_reporting-sd.png |only ubiquity-2.0.3/ubiquity/vignettes/nca_reporting-sparse.png |only ubiquity-2.1.0/ubiquity/DESCRIPTION | 22 ubiquity-2.1.0/ubiquity/MD5 | 73 ubiquity-2.1.0/ubiquity/NAMESPACE | 1 ubiquity-2.1.0/ubiquity/NEWS.md | 12 ubiquity-2.1.0/ubiquity/R/ubiquity.r | 199 +- ubiquity-2.1.0/ubiquity/build/partial.rdb |binary ubiquity-2.1.0/ubiquity/build/vignette.rds |binary ubiquity-2.1.0/ubiquity/inst/doc/Deployment.R | 64 ubiquity-2.1.0/ubiquity/inst/doc/Deployment.html | 108 - ubiquity-2.1.0/ubiquity/inst/doc/Estimation.R | 510 +++--- ubiquity-2.1.0/ubiquity/inst/doc/Estimation.Rmd | 2 ubiquity-2.1.0/ubiquity/inst/doc/Estimation.html | 488 +++--- ubiquity-2.1.0/ubiquity/inst/doc/Language.Rmd | 80 - ubiquity-2.1.0/ubiquity/inst/doc/Language.html | 124 - ubiquity-2.1.0/ubiquity/inst/doc/Reporting.R | 516 +++--- ubiquity-2.1.0/ubiquity/inst/doc/Reporting.html | 425 ++--- ubiquity-2.1.0/ubiquity/inst/doc/Simulation.R | 104 - ubiquity-2.1.0/ubiquity/inst/doc/Simulation.Rmd | 1 ubiquity-2.1.0/ubiquity/inst/doc/Simulation.html | 140 - ubiquity-2.1.0/ubiquity/inst/doc/Titration.R | 282 +-- ubiquity-2.1.0/ubiquity/inst/doc/Titration.html | 248 +-- ubiquity-2.1.0/ubiquity/inst/ubinc/csv/in_vitro_er_data.csv |only ubiquity-2.1.0/ubiquity/inst/ubinc/perl/build_system.pl | 789 +--------- ubiquity-2.1.0/ubiquity/inst/ubinc/scripts/analysis_in_vitro.R |only ubiquity-2.1.0/ubiquity/inst/ubinc/scripts/mk_data_in_vitro.R |only ubiquity-2.1.0/ubiquity/inst/ubinc/scripts/ubiquity_fcns.R | 199 +- ubiquity-2.1.0/ubiquity/inst/ubinc/systems/system-in_vitro.txt |only ubiquity-2.1.0/ubiquity/inst/ubinc/systems/system-mab_pk.txt | 2 ubiquity-2.1.0/ubiquity/inst/ubinc/templates/mrgsolve.cpp | 1 ubiquity-2.1.0/ubiquity/inst/ubinc/templates/r_components.R | 5 ubiquity-2.1.0/ubiquity/inst/ubinc/templates/r_nlmixr.R | 2 ubiquity-2.1.0/ubiquity/man/system_fetch_template.Rd | 5 ubiquity-2.1.0/ubiquity/man/system_set_option.Rd | 1 ubiquity-2.1.0/ubiquity/man/workshop_fetch.Rd | 2 ubiquity-2.1.0/ubiquity/vignettes/Estimation.Rmd | 2 ubiquity-2.1.0/ubiquity/vignettes/Language.Rmd | 80 - ubiquity-2.1.0/ubiquity/vignettes/Simulation.Rmd | 1 42 files changed, 2080 insertions(+), 2408 deletions(-)
Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more kernel density estimations from empirical data.
Author: Massimiliano Pastore [aut, cre],
Pierfrancesco Alaimo Di Loro [ctb],
Marco Mingione [ctb],
Antonio Calcagni' [ctb]
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between overlapping versions 2.1 dated 2022-12-14 and 2.2 dated 2025-01-07
DESCRIPTION | 29 +++++++++++++++++++++-------- MD5 | 10 +++++++--- NEWS.md | 9 ++++++++- R/perm.pairs.R |only R/perm.test.R |only build/partial.rdb |binary man/perm.pairs.Rd |only man/perm.test.Rd |only 8 files changed, 36 insertions(+), 12 deletions(-)
Title: Minimal Type Guesser
Description: Port the type guesser from 'readr' (so-called 'readr' first edition parsing engine, now superseded by 'vroom').
Author: Chung-hong Chan [aut, cre] ,
Hadley Wickham [aut] ,
Jim Hester [aut] ,
Romain Francois [ctb] ,
Jennifer Bryan [aut] ,
Shelby Bearrows [ctb] ,
Posit Software, PBC [cph] ,
David Olson [aut]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between minty versions 0.0.4 dated 2024-11-08 and 0.0.5 dated 2025-01-07
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- src/CollectorGuess.cpp | 12 +++++++++--- src/utils.h | 7 +++++-- tests/testthat/test-parsing.R | 10 ++++++++++ tests/testthat/test-type-convert.R | 12 ++++++++++++ 6 files changed, 44 insertions(+), 13 deletions(-)
Title: R Markdown and Bookdown Templates to Publish Documents
Description: Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem.
'memoiR' makes it easy.
It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Author: Eric Marcon [aut, cre]
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between memoiR versions 1.2-10 dated 2024-10-15 and 1.3-0 dated 2025-01-07
DESCRIPTION | 6 MD5 | 28 +- NEWS.md | 10 + R/memoiR.R | 17 - build/vignette.rds |binary inst/doc/memoiR.Rmd | 2 inst/doc/memoiR.html | 3 inst/rmarkdown/templates/beamer_presentation/skeleton/skeleton.Rmd | 30 +-- inst/rmarkdown/templates/memoir/skeleton/82-syntax.Rmd | 57 +++--- inst/rmarkdown/templates/memoir/skeleton/index.Rmd | 37 +-- inst/rmarkdown/templates/simple_article/skeleton/skeleton.Rmd | 55 ++--- inst/rmarkdown/templates/stylish_article/skeleton/latex/stylish_article.cls | 17 + inst/rmarkdown/templates/stylish_article/skeleton/latex/template.tex | 8 inst/rmarkdown/templates/stylish_article/skeleton/skeleton.Rmd | 94 +++++----- vignettes/memoiR.Rmd | 2 15 files changed, 207 insertions(+), 159 deletions(-)
Title: A Lightweight Version of R Markdown
Description: Render R Markdown to Markdown (without using 'knitr'), and Markdown
to lightweight HTML or 'LaTeX' documents with the 'commonmark' package (instead
of 'Pandoc'). Some missing Markdown features in 'commonmark' are also
supported, such as raw HTML or 'LaTeX' blocks, 'LaTeX' math, superscripts,
subscripts, footnotes, element attributes, and appendices,
but not all 'Pandoc' Markdown features are (or will be) supported. With
additional JavaScript and CSS, you can also create HTML slides and articles.
This package can be viewed as a trimmed-down version of R Markdown and
'knitr'. It does not aim at rich Markdown features or a large variety of
output formats (the primary formats are HTML and 'LaTeX'). Book and website
projects of multiple input documents are also supported.
Author: Yihui Xie [aut, cre] ,
Tim Taylor [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between litedown versions 0.4 dated 2024-11-06 and 0.5 dated 2025-01-07
DESCRIPTION | 20 +- MD5 | 64 ++++---- NAMESPACE | 17 ++ NEWS.md | 40 +++++ R/format.R | 112 ++++++--------- R/fuse.R | 276 +++++++++++++++++++++++++------------- R/mark.R | 99 +++++++------ R/package.R | 167 ++++++++++++++++++----- R/preview.R | 74 +++++++--- R/site.R | 60 +++----- R/utils.R | 288 ++++++++++++++++++++++++++++------------ README.md | 22 ++- inst/doc/markdown-examples.Rmd | 6 inst/doc/markdown-examples.html | 6 inst/doc/markdown-output.Rmd | 8 - inst/doc/markdown-output.html | 12 - inst/doc/slides.Rmd | 16 +- inst/doc/slides.html | 44 +++--- inst/resources/default.css | 51 +++---- inst/resources/listing.css | 9 + inst/resources/server.css | 4 inst/resources/server.js | 90 +++++++++--- inst/resources/snap.css | 4 man/fuse_book.Rd | 15 -- man/fuse_site.Rd | 4 man/html_format.Rd | 40 ++--- man/litedown-package.Rd | 7 man/mark.Rd | 10 - man/pkg_desc.Rd | 27 +++ man/vest.Rd |only tests/examples.R |only vignettes/markdown-examples.Rmd | 6 vignettes/markdown-output.Rmd | 8 - vignettes/slides.Rmd | 16 +- 34 files changed, 1058 insertions(+), 564 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.17.0 dated 2024-08-28 and 1.18.0 dated 2025-01-07
DESCRIPTION | 20 - MD5 | 64 ++-- NAMESPACE | 2 NEWS.md | 19 + R/broom.helpers-package.R | 2 R/model_compute_terms_contributions.R | 3 R/model_get_model_frame.R | 9 R/model_get_model_matrix.R | 10 R/model_get_terms.R | 28 +- R/model_identify_variables.R | 11 R/model_list_variables.R | 69 +++-- R/tidy_add_reference_rows.R | 16 + R/tidy_add_variable_labels.R | 10 R/tidy_identify_variables.R | 17 + R/tidy_plus_plus.R | 7 README.md | 4 data/supported_models.rda |binary inst/doc/tidy.R | 5 inst/doc/tidy.Rmd | 5 inst/doc/tidy.html | 455 +++++++++++++++++----------------- man/model_get_model_frame.Rd | 3 man/model_get_model_matrix.Rd | 9 man/model_get_terms.Rd | 9 man/model_identify_variables.Rd | 11 man/model_list_variables.Rd | 41 +-- man/supported_models.Rd | 3 man/tidy_add_variable_labels.Rd | 5 man/tidy_identify_variables.Rd | 3 man/tidy_plus_plus.Rd | 5 tests/testthat/test-add_n.R | 12 tests/testthat/test-add_term_labels.R | 6 tests/testthat/test-tidy_plus_plus.R | 48 +++ vignettes/tidy.Rmd | 5 33 files changed, 572 insertions(+), 344 deletions(-)
Title: Bayesian Network Structure Learning, Parameter Learning and
Inference
Description: Bayesian network structure learning, parameter learning and inference.
This package implements constraint-based (PC, GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC,
Hiton-PC, HPC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu
Search) and hybrid (MMHC, RSMAX2, H2PC) structure learning algorithms for discrete,
Gaussian and conditional Gaussian networks, along with many score functions and
conditional independence tests.
The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented.
Some utility functions (model comparison and manipulation, random data generation, arc
orientation testing, simple and advanced plots) are included, as well as support for
parameter estimation (maximum likelihood and Bayesian) and inference, conditional
probability queries, cross-validation, bootstrap and model averaging.
Development snapshots with the latest bugfixes are available from <https://www.bnlearn.com/>.
Author: Marco Scutari [aut, cre],
Tomi Silander [ctb]
Maintainer: Marco Scutari <scutari@bnlearn.com>
Diff between bnlearn versions 5.0.1 dated 2024-08-19 and 5.0.2 dated 2025-01-07
Changelog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 24 +++++++++++++----------- src/Makevars | 1 + src/arcs/hash.c | 5 +++-- src/bnlearn/bayesian.network.c | 7 ++++--- src/core/math.functions.c | 3 ++- src/core/sort.c |only src/core/sort.h |only src/graphs/topological.ordering.c | 3 ++- src/learning/averaging/averaging.c | 3 ++- src/learning/local/mi.matrix.c | 3 ++- src/preprocessing/discretize.c | 3 ++- src/scores/graph.priors.c | 3 ++- 14 files changed, 41 insertions(+), 26 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-02 0.1.1
Title: Systematic Comparison of Trip Distribution Laws and Models
Description: The main purpose of this package is to propose a rigorous framework to fairly compare trip distribution laws and models as described in Lenormand et al. (2016) <doi:10.1016/j.jtrangeo.2015.12.008>.
Author: Maxime Lenormand [aut, cre]
Maintainer: Maxime Lenormand <maxime.lenormand@inrae.fr>
Diff between TDLM versions 1.0.0 dated 2023-12-19 and 1.1.0 dated 2025-01-07
TDLM-1.0.0/TDLM/build/TDLM.pdf |only TDLM-1.0.0/TDLM/build/partial.rdb |only TDLM-1.0.0/TDLM/build/stage23.rdb |only TDLM-1.1.0/TDLM/DESCRIPTION | 8 TDLM-1.1.0/TDLM/MD5 | 84 +- TDLM-1.1.0/TDLM/NAMESPACE | 1 TDLM-1.1.0/TDLM/NEWS.md | 38 - TDLM-1.1.0/TDLM/R/calib_param.R | 68 +- TDLM-1.1.0/TDLM/R/check_format_names.R | 44 - TDLM-1.1.0/TDLM/R/data.R | 44 + TDLM-1.1.0/TDLM/R/extract_distances.R |only TDLM-1.1.0/TDLM/R/extract_opportunities.R | 78 +- TDLM-1.1.0/TDLM/R/extract_spatial_information.R | 70 +- TDLM-1.1.0/TDLM/R/gof.R | 225 +++---- TDLM-1.1.0/TDLM/R/package.R | 2 TDLM-1.1.0/TDLM/R/run_law.R | 149 ++-- TDLM-1.1.0/TDLM/R/run_law_model.R | 245 +++---- TDLM-1.1.0/TDLM/R/run_model.R | 126 ++- TDLM-1.1.0/TDLM/R/utils.R | 47 + TDLM-1.1.0/TDLM/README.md | 21 TDLM-1.1.0/TDLM/build/vignette.rds |binary TDLM-1.1.0/TDLM/data/coords.rda |only TDLM-1.1.0/TDLM/data/coords_xy.rda |only TDLM-1.1.0/TDLM/data/county.rda |binary TDLM-1.1.0/TDLM/data/distance.rda |binary TDLM-1.1.0/TDLM/data/mass.rda |binary TDLM-1.1.0/TDLM/data/od.rda |binary TDLM-1.1.0/TDLM/inst/REFERENCES.bib | 86 +- TDLM-1.1.0/TDLM/inst/doc/TDLM.R | 52 + TDLM-1.1.0/TDLM/inst/doc/TDLM.Rmd | 315 ++++++--- TDLM-1.1.0/TDLM/inst/doc/TDLM.html | 674 +++++++++++---------- TDLM-1.1.0/TDLM/man/calib_param.Rd | 34 - TDLM-1.1.0/TDLM/man/check_format_names.Rd | 25 TDLM-1.1.0/TDLM/man/coords.Rd |only TDLM-1.1.0/TDLM/man/coords_xy.Rd |only TDLM-1.1.0/TDLM/man/county.Rd | 2 TDLM-1.1.0/TDLM/man/distance.Rd | 6 TDLM-1.1.0/TDLM/man/extract_distances.Rd |only TDLM-1.1.0/TDLM/man/extract_opportunities.Rd | 49 - TDLM-1.1.0/TDLM/man/extract_spatial_information.Rd | 33 - TDLM-1.1.0/TDLM/man/gof.Rd | 183 ++--- TDLM-1.1.0/TDLM/man/mass.Rd | 4 TDLM-1.1.0/TDLM/man/od.Rd | 4 TDLM-1.1.0/TDLM/man/run_law.Rd | 117 +-- TDLM-1.1.0/TDLM/man/run_law_model.Rd | 202 +++--- TDLM-1.1.0/TDLM/man/run_model.Rd | 107 +-- TDLM-1.1.0/TDLM/vignettes/TDLM.Rmd | 315 ++++++--- TDLM-1.1.0/TDLM/vignettes/format_citation.csl |only 48 files changed, 1901 insertions(+), 1557 deletions(-)
Title: R-Friendly Threading in C++
Description: Provides a C++11-style thread class and thread pool that can safely
be interrupted from R. See Nagler (2021) <doi:10.18637/jss.v097.c01>.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between RcppThread versions 2.1.7 dated 2024-02-09 and 2.2.0 dated 2025-01-07
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- NEWS.md | 12 ++++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/include/RcppThread.h | 1 + inst/include/RcppThread/RMonitor.hpp | 2 ++ inst/include/RcppThread/SafeTypes.hpp |only man/RcppThread.Rd | 2 +- src/detectCores.cpp | 2 ++ 10 files changed, 31 insertions(+), 13 deletions(-)
Title: Life History Metrics from Matrix Population Models
Description: Functions for calculating life history metrics using matrix
population models ('MPMs'). Described in Jones et al. (2021)
<doi:10.1101/2021.04.26.441330>.
Author: Patrick Barks [aut] ,
Danny Buss [ctb],
Pol Capdevila [aut] ,
Hal Caswell [aut] ,
Judy P. Che-Castaldo [aut] ,
Richard A. Hinrichsen [aut] ,
John Jackson [aut] ,
Tamora James [aut] ,
Owen Jones [aut, cre] ,
Sam Levin [aut] ,
William K. Petry [aut] ,
[...truncated...]
Maintainer: Owen Jones <jones@biology.sdu.dk>
Diff between Rage versions 1.6.0 dated 2023-09-29 and 1.8.0 dated 2025-01-07
DESCRIPTION | 20 +++-- MD5 | 107 ++++++++++++++++-------------- NAMESPACE | 4 + NEWS.md | 95 ++++++++++++++------------ R/entropy_d.R | 79 +++++++++++++++------- R/entropy_k.R | 25 ++++++- R/entropy_k_age.R |only R/entropy_k_stage.R |only R/gen_time.R | 23 +++++- R/leslie_collapse.R | 2 R/life_elas.R |only R/life_expect.R | 6 - R/mature_.R | 35 +++++++-- R/mpm_to_.R | 30 ++++++-- R/mpm_to_table.R | 51 ++++++++++---- R/net_repro_rate.R | 30 +++++++- R/plot_life_cycle.R | 13 +++ R/shape_rep.R | 12 ++- R/shape_surv.R | 11 +++ R/utils.R | 36 ++++++++++ README.md | 27 ++----- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 15 +++- inst/doc/a01_GettingStarted.R | 11 +-- inst/doc/a01_GettingStarted.Rmd | 20 ++--- inst/doc/a01_GettingStarted.html | 68 ++++++++++++------- inst/doc/a02_VitalRates.html | 8 +- inst/doc/a03_LifeHistoryTraits.R | 14 +++ inst/doc/a03_LifeHistoryTraits.Rmd | 32 ++++++-- inst/doc/a03_LifeHistoryTraits.html | 85 +++++++++++++++-------- inst/doc/a04_AgeFromStage.html | 14 +-- inst/doc/a05_SuggestedQualityControl.html | 4 - man/Rage-package.Rd | 2 man/age_from_stage.Rd | 32 +++++++- man/entropy_d.Rd | 43 +++++++++--- man/entropy_k.Rd | 18 ++++- man/entropy_k_age.Rd |only man/entropy_k_stage.Rd |only man/gen_time.Rd | 28 ++++++- man/leslie_collapse.Rd | 2 man/life_elas.Rd |only man/life_expect.Rd | 3 man/longevity.Rd | 3 man/mpm_to_table.Rd | 26 ++++--- man/net_repro_rate.Rd | 37 +++++++++- man/plot_life_cycle.Rd | 13 +++ man/repro_maturity.Rd | 30 +++++--- man/shape_rep.Rd | 15 +++- man/shape_surv.Rd | 15 ++++ man/vital_rates.Rd | 4 - man/vr_mat.Rd | 4 - man/vr_vec.Rd | 4 - tests/testthat/test-entropy_k_age.R |only tests/testthat/test-entropy_k_stage.R |only tests/testthat/test-life_elas.R |only tests/testthat/test-mpm_to_table.R | 30 ++++---- vignettes/a01_GettingStarted.Rmd | 20 ++--- vignettes/a03_LifeHistoryTraits.Rmd | 32 ++++++-- 59 files changed, 860 insertions(+), 378 deletions(-)
Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 1.11.0 dated 2024-12-15 and 1.12.0 dated 2025-01-07
microeco-1.11.0/microeco/inst/extdata |only microeco-1.12.0/microeco/DESCRIPTION | 8 - microeco-1.12.0/microeco/MD5 | 44 ++++---- microeco-1.12.0/microeco/NAMESPACE | 1 microeco-1.12.0/microeco/R/import.R | 1 microeco-1.12.0/microeco/R/microtable.R | 15 ++ microeco-1.12.0/microeco/R/trans_abund.R | 17 +-- microeco-1.12.0/microeco/R/trans_alpha.R | 1 microeco-1.12.0/microeco/R/trans_beta.R | 39 +++++-- microeco-1.12.0/microeco/R/trans_classifier.R | 10 + microeco-1.12.0/microeco/R/trans_diff.R | 43 +++----- microeco-1.12.0/microeco/R/trans_env.R | 46 +++++---- microeco-1.12.0/microeco/R/trans_func.R | 25 +--- microeco-1.12.0/microeco/R/trans_network.R | 122 +++++++++++++----------- microeco-1.12.0/microeco/R/trans_nullmodel.R | 30 +++-- microeco-1.12.0/microeco/R/trans_venn.R | 3 microeco-1.12.0/microeco/data/dataset.RData |binary microeco-1.12.0/microeco/man/trans_abund.Rd | 8 - microeco-1.12.0/microeco/man/trans_beta.Rd | 12 ++ microeco-1.12.0/microeco/man/trans_diff.Rd | 24 +--- microeco-1.12.0/microeco/man/trans_func.Rd | 11 -- microeco-1.12.0/microeco/man/trans_network.Rd | 15 +- microeco-1.12.0/microeco/man/trans_nullmodel.Rd | 10 - 23 files changed, 270 insertions(+), 215 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.4.1 dated 2024-11-22 and 0.5.0 dated 2025-01-07
maestro-0.4.1/maestro/inst/doc/maestro-2-motivation-concepts.Rmd |only maestro-0.4.1/maestro/inst/doc/maestro-3-use-cases.Rmd |only maestro-0.4.1/maestro/inst/doc/maestro-4-advanced-scheduling.Rmd |only maestro-0.4.1/maestro/tests/testthat/test-workflow.R |only maestro-0.4.1/maestro/vignettes/maestro-2-motivation-concepts.Rmd |only maestro-0.4.1/maestro/vignettes/maestro-3-use-cases.Rmd |only maestro-0.4.1/maestro/vignettes/maestro-4-advanced-scheduling.Rmd |only maestro-0.5.0/maestro/DESCRIPTION | 12 maestro-0.5.0/maestro/MD5 | 94 - maestro-0.5.0/maestro/NEWS.md | 24 maestro-0.5.0/maestro/R/MaestroPipeline.R | 34 maestro-0.5.0/maestro/R/roxy_maestro.R | 40 maestro-0.5.0/maestro/R/run_schedule.R | 113 + maestro-0.5.0/maestro/R/utils.R | 21 maestro-0.5.0/maestro/README.md | 12 maestro-0.5.0/maestro/build/vignette.rds |binary maestro-0.5.0/maestro/inst/doc/maestro-1-quick-start.R | 74 - maestro-0.5.0/maestro/inst/doc/maestro-1-quick-start.Rmd | 54 maestro-0.5.0/maestro/inst/doc/maestro-1-quick-start.html | 17 maestro-0.5.0/maestro/inst/doc/maestro-2-motivation-concepts.R | 2 maestro-0.5.0/maestro/inst/doc/maestro-2-motivation-concepts.html | 520 +------ maestro-0.5.0/maestro/inst/doc/maestro-2-motivation-concepts.qmd |only maestro-0.5.0/maestro/inst/doc/maestro-3-use-cases.R | 1 maestro-0.5.0/maestro/inst/doc/maestro-3-use-cases.html | 486 +----- maestro-0.5.0/maestro/inst/doc/maestro-3-use-cases.qmd |only maestro-0.5.0/maestro/inst/doc/maestro-4-advanced-scheduling.R | 66 maestro-0.5.0/maestro/inst/doc/maestro-4-advanced-scheduling.html | 703 ++-------- maestro-0.5.0/maestro/inst/doc/maestro-4-advanced-scheduling.qmd |only maestro-0.5.0/maestro/inst/doc/maestro-5-directed-acyclic-graphs.R | 47 maestro-0.5.0/maestro/inst/doc/maestro-5-directed-acyclic-graphs.Rmd | 48 maestro-0.5.0/maestro/inst/doc/maestro-5-directed-acyclic-graphs.html | 193 +- maestro-0.5.0/maestro/inst/doc/maestro-6-logging.R |only maestro-0.5.0/maestro/inst/doc/maestro-6-logging.html |only maestro-0.5.0/maestro/inst/doc/maestro-6-logging.qmd |only maestro-0.5.0/maestro/man/MaestroPipeline.Rd | 3 maestro-0.5.0/maestro/man/figures/README-/unnamed-chunk-3-dark.svg | 2 maestro-0.5.0/maestro/man/figures/README-/unnamed-chunk-3.svg | 2 maestro-0.5.0/maestro/man/run_schedule.Rd | 34 maestro-0.5.0/maestro/tests/testthat/_snaps/MaestroPipeline.md | 77 - maestro-0.5.0/maestro/tests/testthat/_snaps/MaestroPipelineList.md | 11 maestro-0.5.0/maestro/tests/testthat/_snaps/get_schedule.md | 26 maestro-0.5.0/maestro/tests/testthat/_snaps/run_schedule.md | 6 maestro-0.5.0/maestro/tests/testthat/test-MaestroPipeline.R | 7 maestro-0.5.0/maestro/tests/testthat/test-MaestroPipelineList.R | 1 maestro-0.5.0/maestro/tests/testthat/test-get_schedule.R | 2 maestro-0.5.0/maestro/tests/testthat/test-get_status.R | 2 maestro-0.5.0/maestro/tests/testthat/test-roclets.R | 30 maestro-0.5.0/maestro/tests/testthat/test-run_schedule.R | 94 + maestro-0.5.0/maestro/tests/testthat/test_pipelines/test_pipeline_days_bad3.R |only maestro-0.5.0/maestro/tests/testthat/test_pipelines/test_pipeline_hours_bad2.R |only maestro-0.5.0/maestro/tests/testthat/test_pipelines/test_pipeline_months_bad2.R |only maestro-0.5.0/maestro/tests/testthat/test_pipelines_run_all_good/pipe1.R | 2 maestro-0.5.0/maestro/vignettes/maestro-1-quick-start.Rmd | 54 maestro-0.5.0/maestro/vignettes/maestro-2-motivation-concepts.qmd |only maestro-0.5.0/maestro/vignettes/maestro-3-use-cases.qmd |only maestro-0.5.0/maestro/vignettes/maestro-4-advanced-scheduling.qmd |only maestro-0.5.0/maestro/vignettes/maestro-5-directed-acyclic-graphs.Rmd | 48 maestro-0.5.0/maestro/vignettes/maestro-6-logging.qmd |only 58 files changed, 1169 insertions(+), 1793 deletions(-)
Title: Supporting Functions for Packages Maintained by 'YuLab-SMU'
Description: Miscellaneous functions commonly used by 'YuLab-SMU'.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between yulab.utils versions 0.1.8 dated 2024-11-07 and 0.1.9 dated 2025-01-07
yulab.utils-0.1.8/yulab.utils/inst/prototype/concat.r |only yulab.utils-0.1.9/yulab.utils/DESCRIPTION | 6 ++--- yulab.utils-0.1.9/yulab.utils/MD5 | 13 ++++++------ yulab.utils-0.1.9/yulab.utils/NAMESPACE | 7 ++++++ yulab.utils-0.1.9/yulab.utils/NEWS.md | 4 +++ yulab.utils-0.1.9/yulab.utils/R/bib-knownledge.R | 4 ++- yulab.utils-0.1.9/yulab.utils/R/concat.r |only yulab.utils-0.1.9/yulab.utils/R/utilities.R | 19 ++++++++++++++++++ yulab.utils-0.1.9/yulab.utils/man/c2.Rd |only 9 files changed, 43 insertions(+), 10 deletions(-)
Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rswipl versions 9.3.16 dated 2024-12-04 and 9.3.18 dated 2025-01-07
rswipl-9.3.16/rswipl/src/swipl-devel/library/dialect/sicstus/swipl-lfr.pl |only rswipl-9.3.18/rswipl/DESCRIPTION | 14 rswipl-9.3.18/rswipl/MD5 | 185 +- rswipl-9.3.18/rswipl/NEWS.md | 6 rswipl-9.3.18/rswipl/src/Makevars | 7 rswipl-9.3.18/rswipl/src/install.libs.R | 2 rswipl-9.3.18/rswipl/src/swipl-devel/CMakeLists.txt | 3 rswipl-9.3.18/rswipl/src/swipl-devel/VERSION | 2 rswipl-9.3.18/rswipl/src/swipl-devel/app/pack.pl | 75 - rswipl-9.3.18/rswipl/src/swipl-devel/app/splfr.pl |only rswipl-9.3.18/rswipl/src/swipl-devel/boot/packs.pl | 11 rswipl-9.3.18/rswipl/src/swipl-devel/boot/syspred.pl | 16 rswipl-9.3.18/rswipl/src/swipl-devel/cmake/TestSignalType.c | 3 rswipl-9.3.18/rswipl/src/swipl-devel/library/aggregate.pl | 162 +- rswipl-9.3.18/rswipl/src/swipl-devel/library/main.pl | 58 rswipl-9.3.18/rswipl/src/swipl-devel/library/option.pl | 4 rswipl-9.3.18/rswipl/src/swipl-devel/library/pairs.pl | 58 rswipl-9.3.18/rswipl/src/swipl-devel/library/pprint.pl | 58 rswipl-9.3.18/rswipl/src/swipl-devel/library/prolog_colour.pl | 11 rswipl-9.3.18/rswipl/src/swipl-devel/library/prolog_debug.pl | 14 rswipl-9.3.18/rswipl/src/swipl-devel/library/prolog_pack.pl | 111 + rswipl-9.3.18/rswipl/src/swipl-devel/library/prolog_xref.pl | 21 rswipl-9.3.18/rswipl/src/swipl-devel/library/qsave.pl | 1 rswipl-9.3.18/rswipl/src/swipl-devel/library/sandbox.pl | 4 rswipl-9.3.18/rswipl/src/swipl-devel/packages/clib/nonblockio.c | 2 rswipl-9.3.18/rswipl/src/swipl-devel/packages/cpp/test_cpp.cpp | 20 rswipl-9.3.18/rswipl/src/swipl-devel/packages/cpp/test_cpp.pl | 34 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/README.md | 2 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/ax.pl | 2 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/cgi_stream.c | 4 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/graphql.pl | 6 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/html_head.pl | 4 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/html_write.pl | 6 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/htmx.pl | 17 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http.doc | 10 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_authenticate.pl | 4 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_cookie.pl | 2 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_cors.pl | 4 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_digest.pl | 6 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_dirindex.pl | 2 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_dispatch.pl | 12 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_dyn_workers.pl | 2 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_error.pl | 2 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_files.pl | 2 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_header.pl | 10 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_multipart_plugin.pl | 2 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_open.pl | 4 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_openid.pl | 10 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_parameters.pl | 2 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_path.pl | 4 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_pwp.pl | 2 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_session.pl | 10 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_stream.pl | 16 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_unix_daemon.pl | 8 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/http_wrapper.pl | 6 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/hub.pl | 4 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/js_write.pl | 6 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/json.pl | 10 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/json_convert.pl | 6 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/mimetype.pl | 2 rswipl-9.3.18/rswipl/src/swipl-devel/packages/http/thread_httpd.pl | 4 rswipl-9.3.18/rswipl/src/swipl-devel/scripts/callgrind.sh |only rswipl-9.3.18/rswipl/src/swipl-devel/scripts/configure | 15 rswipl-9.3.18/rswipl/src/swipl-devel/src/CMakeLists.txt | 23 rswipl-9.3.18/rswipl/src/swipl-devel/src/SWI-Prolog.h | 2 rswipl-9.3.18/rswipl/src/swipl-devel/src/Tests/library/test_main.pl | 18 rswipl-9.3.18/rswipl/src/swipl-devel/src/compat/sicstus.h | 38 rswipl-9.3.18/rswipl/src/swipl-devel/src/os/README | 2 rswipl-9.3.18/rswipl/src/swipl-devel/src/os/dtoa.c | 6 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-comp.c | 18 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-comp.h | 4 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-copyterm.c | 168 +- rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-copyterm.h | 12 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-dict.c | 91 - rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-dict.h | 6 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-error.c | 14 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-error.h | 4 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-fli.c | 5 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-global.h | 4 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-gvar.c | 80 - rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-gvar.h | 2 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-incl.h | 21 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-index.c | 718 ++++++---- rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-init.c | 14 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-inline.h | 27 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-list.c | 2 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-modul.c | 5 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-prims.c | 62 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-prims.h | 7 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-pro.c | 2 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-proc.c | 2 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-supervisor.c | 32 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-supervisor.h | 8 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-termwalk.c | 55 rswipl-9.3.18/rswipl/src/swipl-devel/src/pl-wam.c | 27 95 files changed, 1581 insertions(+), 988 deletions(-)
Title: Compare Microbial Networks of 'trans_network' Class of
'microeco' Package
Description: Compare microbial co-occurrence networks created from 'trans_network' class of 'microeco' package <https://github.com/ChiLiubio/microeco>.
This package is the extension of 'trans_network' class of 'microeco' package and especially useful when different networks are constructed and analyzed simultaneously.
Author: Chi Liu [aut, cre],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between meconetcomp versions 0.5.1 dated 2024-06-22 and 0.6.0 dated 2025-01-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/cohesionclass.R | 1 + R/edge_node_distance.R | 26 ++++++++++++++++++++------ R/edge_tax_comp.R | 7 ++++--- man/edge_node_distance.Rd | 2 +- man/edge_tax_comp.Rd | 12 ++++++++++-- 7 files changed, 46 insertions(+), 22 deletions(-)
Title: Download Weather Station Data from GHCNd
Description: The goal of 'GHCNr' is to provide a fast and friendly interface with the Global Historical Climatology Network daily (GHCNd) database, which contains daily summaries of weather station data worldwide (<https://www.ncei.noaa.gov/products/land-based-station/global-historical-climatology-network-daily>). GHCNd is accessed through the web API <https://www.ncei.noaa.gov/access/services/data/v1>. 'GHCNr' main functionalities consist of downloading data from GHCNd, filter it, and to aggregate it at monthly and annual scales.
Author: Emilio Berti [aut, cre]
Maintainer: Emilio Berti <emilio.berti@idiv.de>
Diff between GHCNr versions 1.0.0 dated 2024-12-20 and 1.4.5 dated 2025-01-07
GHCNr-1.0.0/GHCNr/data/stations_elevation.rda |only GHCNr-1.0.0/GHCNr/man/stations_elevation.Rd |only GHCNr-1.4.5/GHCNr/DESCRIPTION | 8 GHCNr-1.4.5/GHCNr/MD5 | 47 + GHCNr-1.4.5/GHCNr/NAMESPACE | 12 GHCNr-1.4.5/GHCNr/R/annual.R | 6 GHCNr-1.4.5/GHCNr/R/anomaly.R |only GHCNr-1.4.5/GHCNr/R/daily.R | 18 GHCNr-1.4.5/GHCNr/R/data.R | 11 GHCNr-1.4.5/GHCNr/R/elevation.R |only GHCNr-1.4.5/GHCNr/R/monthly.R | 6 GHCNr-1.4.5/GHCNr/R/plotting.R | 115 ++++ GHCNr-1.4.5/GHCNr/R/quarterly.R |only GHCNr-1.4.5/GHCNr/R/s3_classes.R | 27 - GHCNr-1.4.5/GHCNr/R/stations.R | 6 GHCNr-1.4.5/GHCNr/build/vignette.rds |binary GHCNr-1.4.5/GHCNr/inst/doc/daily.R | 73 +- GHCNr-1.4.5/GHCNr/inst/doc/daily.Rmd | 85 +-- GHCNr-1.4.5/GHCNr/inst/doc/daily.html | 666 +++++++++++++++++--------- GHCNr-1.4.5/GHCNr/man/anomaly.Rd |only GHCNr-1.4.5/GHCNr/man/dot-elevation_url.Rd |only GHCNr-1.4.5/GHCNr/man/dot-s3_anomaly.Rd |only GHCNr-1.4.5/GHCNr/man/dot-s3_quarterly.Rd |only GHCNr-1.4.5/GHCNr/man/elevation_stations.Rd |only GHCNr-1.4.5/GHCNr/man/plot.ghcn_annual.Rd | 6 GHCNr-1.4.5/GHCNr/man/plot.ghcn_anomaly.Rd |only GHCNr-1.4.5/GHCNr/man/plot.ghcn_daily.Rd | 4 GHCNr-1.4.5/GHCNr/man/plot.ghcn_monthly.Rd | 6 GHCNr-1.4.5/GHCNr/man/plot.ghcn_quarterly.Rd |only GHCNr-1.4.5/GHCNr/man/quarterly.Rd |only GHCNr-1.4.5/GHCNr/vignettes/daily.Rmd | 85 +-- 31 files changed, 796 insertions(+), 385 deletions(-)
Title: Extension to 'ggplot2' for Plotting Stats
Description: Provides new statistics, new geometries and new positions for
'ggplot2' and a suite of functions to facilitate the creation of
statistical plots.
Author: Joseph Larmarange [aut, cre]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between ggstats versions 0.7.0 dated 2024-09-22 and 0.8.0 dated 2025-01-07
ggstats-0.7.0/ggstats/tests/spelling.R |only ggstats-0.8.0/ggstats/DESCRIPTION | 8 ggstats-0.8.0/ggstats/MD5 | 66 +- ggstats-0.8.0/ggstats/NAMESPACE | 7 ggstats-0.8.0/ggstats/NEWS.md | 16 ggstats-0.8.0/ggstats/R/geom_connector.R |only ggstats-0.8.0/ggstats/R/geom_diverging.R | 240 +++------- ggstats-0.8.0/ggstats/R/ggstats-package.R | 2 ggstats-0.8.0/ggstats/R/hex_bw.R | 32 + ggstats-0.8.0/ggstats/R/stat_prop.R | 206 +++++--- ggstats-0.8.0/ggstats/R/weighted_quantile.R | 8 ggstats-0.8.0/ggstats/README.md | 19 ggstats-0.8.0/ggstats/inst/WORDLIST | 1 ggstats-0.8.0/ggstats/inst/doc/geom_diverging.html | 28 - ggstats-0.8.0/ggstats/inst/doc/ggcoef_model.html | 132 ++--- ggstats-0.8.0/ggstats/inst/doc/gglikert.html | 76 +-- ggstats-0.8.0/ggstats/inst/doc/stat_cross.html | 10 ggstats-0.8.0/ggstats/inst/doc/stat_prop.html | 30 - ggstats-0.8.0/ggstats/inst/doc/stat_weighted_mean.html | 18 ggstats-0.8.0/ggstats/man/figures/README-unnamed-chunk-10-1.png |binary ggstats-0.8.0/ggstats/man/figures/README-unnamed-chunk-11-1.png |binary ggstats-0.8.0/ggstats/man/figures/README-unnamed-chunk-12-1.png |only ggstats-0.8.0/ggstats/man/figures/README-unnamed-chunk-4-2.png |binary ggstats-0.8.0/ggstats/man/figures/README-unnamed-chunk-5-1.png |binary ggstats-0.8.0/ggstats/man/figures/README-unnamed-chunk-6-1.png |binary ggstats-0.8.0/ggstats/man/figures/README-unnamed-chunk-7-1.png |binary ggstats-0.8.0/ggstats/man/figures/README-unnamed-chunk-9-1.png |binary ggstats-0.8.0/ggstats/man/geom_connector.Rd |only ggstats-0.8.0/ggstats/man/geom_diverging.Rd | 140 +---- ggstats-0.8.0/ggstats/man/geom_prop_bar.Rd |only ggstats-0.8.0/ggstats/man/hex_bw.Rd | 36 + ggstats-0.8.0/ggstats/man/stat_prop.Rd | 57 -- ggstats-0.8.0/ggstats/tests/testthat.R | 4 ggstats-0.8.0/ggstats/tests/testthat/test-geom_connector.R |only ggstats-0.8.0/ggstats/tests/testthat/test-ggcoef_model.R | 20 ggstats-0.8.0/ggstats/tests/testthat/test-gglikert.R | 5 ggstats-0.8.0/ggstats/tests/testthat/test-stat_prop.R | 26 - 37 files changed, 577 insertions(+), 610 deletions(-)
Title: Causal Batch Effects
Description: Software which provides numerous functionalities for detecting and removing group-level effects from high-dimensional scientific data which, when combined with additional assumptions, allow for causal conclusions, as-described in our manuscripts Bridgeford et al. (2024) <doi:10.1101/2021.09.03.458920> and Bridgeford et al. (2023) <doi:10.48550/arXiv.2307.13868>. Also provides a number of useful utilities for generating simulations and balancing covariates across multiple groups/batches of data via matching and propensity trimming for more than two groups.
Author: Eric W. Bridgeford [aut, cre],
Michael Powell [ctb],
Brian Caffo [ctb],
Joshua T. Vogelstein [ctb]
Maintainer: Eric W. Bridgeford <ericwb95@gmail.com>
Diff between causalBatch versions 1.2.0 dated 2024-03-01 and 1.3.0 dated 2025-01-07
causalBatch-1.2.0/causalBatch/LICENSE |only causalBatch-1.2.0/causalBatch/inst/doc/causal_ccombat.R |only causalBatch-1.2.0/causalBatch/inst/doc/causal_ccombat.Rmd |only causalBatch-1.2.0/causalBatch/inst/doc/causal_ccombat.html |only causalBatch-1.2.0/causalBatch/man/cb.correct.caus_cComBat.Rd |only causalBatch-1.2.0/causalBatch/man/cb.sims.covar_generator.Rd |only causalBatch-1.2.0/causalBatch/man/cb.sims.get_beta_overlap.Rd |only causalBatch-1.2.0/causalBatch/man/covariate.match.Rd |only causalBatch-1.2.0/causalBatch/man/ohe.Rd |only causalBatch-1.2.0/causalBatch/man/sigmoid.Rd |only causalBatch-1.2.0/causalBatch/man/zero_one_dist.Rd |only causalBatch-1.2.0/causalBatch/vignettes/causal_ccombat.Rmd |only causalBatch-1.3.0/causalBatch/DESCRIPTION | 19 - causalBatch-1.3.0/causalBatch/MD5 | 72 ++--- causalBatch-1.3.0/causalBatch/NAMESPACE | 25 + causalBatch-1.3.0/causalBatch/R/aipw_ccombat_helpers.R |only causalBatch-1.3.0/causalBatch/R/causal_ccombat.R | 141 ++++++++-- causalBatch-1.3.0/causalBatch/R/causal_cdcorr.R | 62 +++- causalBatch-1.3.0/causalBatch/R/combat_helpers.R |only causalBatch-1.3.0/causalBatch/R/sims.R | 106 +++++-- causalBatch-1.3.0/causalBatch/build/vignette.rds |binary causalBatch-1.3.0/causalBatch/inst/doc/aipw_ccombat.R |only causalBatch-1.3.0/causalBatch/inst/doc/aipw_ccombat.Rmd |only causalBatch-1.3.0/causalBatch/inst/doc/aipw_ccombat.html |only causalBatch-1.3.0/causalBatch/inst/doc/causal_balancing.R | 2 causalBatch-1.3.0/causalBatch/inst/doc/causal_balancing.Rmd | 2 causalBatch-1.3.0/causalBatch/inst/doc/causal_balancing.html | 21 - causalBatch-1.3.0/causalBatch/inst/doc/causal_cdcorr.html | 6 causalBatch-1.3.0/causalBatch/inst/doc/causal_simulations.html | 28 - causalBatch-1.3.0/causalBatch/inst/doc/matching_ccombat.R |only causalBatch-1.3.0/causalBatch/inst/doc/matching_ccombat.Rmd |only causalBatch-1.3.0/causalBatch/inst/doc/matching_ccombat.html |only causalBatch-1.3.0/causalBatch/man/cb.align.kway_match.Rd | 6 causalBatch-1.3.0/causalBatch/man/cb.align.vm_trim.Rd | 13 causalBatch-1.3.0/causalBatch/man/cb.correct.aipw_cComBat.Rd |only causalBatch-1.3.0/causalBatch/man/cb.correct.apply_aipw_cComBat.Rd |only causalBatch-1.3.0/causalBatch/man/cb.correct.apply_cComBat.Rd |only causalBatch-1.3.0/causalBatch/man/cb.correct.matching_cComBat.Rd |only causalBatch-1.3.0/causalBatch/man/cb.detect.caus_cdcorr.Rd | 3 causalBatch-1.3.0/causalBatch/man/cb.sims.sim_impulse.Rd | 2 causalBatch-1.3.0/causalBatch/man/cb.sims.sim_impulse_asycov.Rd | 2 causalBatch-1.3.0/causalBatch/man/cb.sims.sim_linear.Rd | 2 causalBatch-1.3.0/causalBatch/man/cb.sims.sim_sigmoid.Rd | 2 causalBatch-1.3.0/causalBatch/tests/testthat/test-causal_ccombat.R | 94 ++++++ causalBatch-1.3.0/causalBatch/tests/testthat/test-causal_cdcorr.R | 4 causalBatch-1.3.0/causalBatch/tests/testthat/test-kway_match.R | 12 causalBatch-1.3.0/causalBatch/tests/testthat/test-vector_matching.R | 29 +- causalBatch-1.3.0/causalBatch/vignettes/aipw_ccombat.Rmd |only causalBatch-1.3.0/causalBatch/vignettes/causal_balancing.Rmd | 2 causalBatch-1.3.0/causalBatch/vignettes/matching_ccombat.Rmd |only 50 files changed, 503 insertions(+), 152 deletions(-)
Title: Create Actuarial Experience Studies: Prepare Data, Summarize
Results, and Create Reports
Description: Experience studies are used by actuaries to explore historical
experience across blocks of business and to inform assumption setting
activities. This package provides functions for preparing data, creating
studies, visualizing results, and beginning assumption development.
Experience study methods, including exposure calculations, are described in:
Atkinson & McGarry (2016) "Experience Study Calculations"
<https://www.soa.org/49378a/globalassets/assets/files/research/experience-study-calculations.pdf>.
The limited fluctuation credibility method used by the 'exp_stats()'
function is described in: Herzog (1999, ISBN:1-56698-374-6)
"Introduction to Credibility Theory".
Author: Matt Heaphy [aut, cre]
Maintainer: Matt Heaphy <mattrmattrs@gmail.com>
Diff between actxps versions 1.5.0 dated 2024-06-25 and 1.6.0 dated 2025-01-07
DESCRIPTION | 10 MD5 | 84 +-- NEWS.md | 22 R/exp_df_helpers.R | 3 R/exp_shiny.R | 85 +-- R/exp_stats.R | 160 +++++- R/expose.R | 8 R/exposed_df_helpers.R | 37 - R/globals.R | 2 R/tables.R | 53 ++ R/transactions.R | 4 R/trx_stats.R | 21 README.md | 30 - build/vignette.rds |binary inst/doc/actxps.R | 8 inst/doc/actxps.Rmd | 2 inst/doc/actxps.html | 245 ++++----- inst/doc/exp_summary.R | 18 inst/doc/exp_summary.Rmd | 46 + inst/doc/exp_summary.html | 856 +++++++++++++++++++--------------- inst/doc/exposures.R | 22 inst/doc/exposures.Rmd | 2 inst/doc/exposures.html | 626 ++++++++++++------------ inst/doc/misc.R | 2 inst/doc/misc.Rmd | 2 inst/doc/misc.html | 89 +-- inst/doc/transactions.R | 16 inst/doc/transactions.html | 397 ++++++++------- man/autotable.Rd | 4 man/exp_shiny.Rd | 18 man/exp_stats.Rd | 49 + man/figures/exp_gt.png |binary man/trx_stats.Rd | 2 tests/testthat/test-add_predictions.R | 6 tests/testthat/test-exp_df_helpers.R | 2 tests/testthat/test-exp_stats.R | 39 + tests/testthat/test-expose.R | 506 ++++++++++---------- tests/testthat/test-tables.R | 5 tests/testthat/test-trx_df_helpers.R | 2 vignettes/actxps.Rmd | 2 vignettes/exp_summary.Rmd | 46 + vignettes/exposures.Rmd | 2 vignettes/misc.Rmd | 2 43 files changed, 2031 insertions(+), 1504 deletions(-)
Title: Workflow for Open Reproducible Code in Science
Description: Create reproducible and transparent research projects in 'R'.
This package is based on the Workflow for Open
Reproducible Code in Science (WORCS), a step-by-step procedure based on best
practices for
Open Science. It includes an 'RStudio' project template, several
convenience functions, and all dependencies required to make your project
reproducible and transparent. WORCS is explained in the tutorial paper
by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2021).
<doi:10.3233/DS-210031>.
Author: Caspar J. Van Lissa [aut, cre]
,
Aaron Peikert [aut] ,
Andreas M. Brandmaier [aut]
Maintainer: Caspar J. Van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between worcs versions 0.1.15 dated 2024-09-14 and 0.1.16 dated 2025-01-07
worcs-0.1.15/worcs/man/github_action_reproduce.Rd |only worcs-0.1.16/worcs/DESCRIPTION | 16 worcs-0.1.16/worcs/MD5 | 77 - worcs-0.1.16/worcs/NAMESPACE | 13 worcs-0.1.16/worcs/R/add_synthetic.R | 63 - worcs-0.1.16/worcs/R/check_installation.R | 2 worcs-0.1.16/worcs/R/codebook.R | 20 worcs-0.1.16/worcs/R/descriptives.R | 16 worcs-0.1.16/worcs/R/endpoint.R | 85 + worcs-0.1.16/worcs/R/github.R | 433 +++++++--- worcs-0.1.16/worcs/R/licenses.R |only worcs-0.1.16/worcs/R/misc.R | 12 worcs-0.1.16/worcs/R/recipes.R | 10 worcs-0.1.16/worcs/R/save_load.R | 78 + worcs-0.1.16/worcs/R/targets.R | 23 worcs-0.1.16/worcs/R/ui.R |only worcs-0.1.16/worcs/R/worcs_badge.R | 34 worcs-0.1.16/worcs/R/worcs_project.R | 65 - worcs-0.1.16/worcs/build/vignette.rds |binary worcs-0.1.16/worcs/inst/doc/citation.Rmd | 2 worcs-0.1.16/worcs/inst/doc/citation.html | 4 worcs-0.1.16/worcs/inst/doc/endpoints.html | 2 worcs-0.1.16/worcs/inst/doc/reproduce.html | 2 worcs-0.1.16/worcs/inst/doc/setup-docker.R | 4 worcs-0.1.16/worcs/inst/doc/setup-docker.html | 2 worcs-0.1.16/worcs/inst/doc/synthetic_data.R | 62 - worcs-0.1.16/worcs/inst/doc/synthetic_data.html | 73 - worcs-0.1.16/worcs/inst/doc/targets.R |only worcs-0.1.16/worcs/inst/doc/targets.Rmd |only worcs-0.1.16/worcs/inst/doc/targets.html |only worcs-0.1.16/worcs/inst/doc/workflow.Rmd | 9 worcs-0.1.16/worcs/inst/doc/workflow.html | 21 worcs-0.1.16/worcs/inst/rstudio/templates/project/resources/README.md | 6 worcs-0.1.16/worcs/inst/rstudio/templates/project/worcs.dcf | 6 worcs-0.1.16/worcs/man/add_license_file.Rd |only worcs-0.1.16/worcs/man/git_remote_connect.Rd |only worcs-0.1.16/worcs/man/git_remote_create.Rd |only worcs-0.1.16/worcs/man/github_action_check_endpoints.Rd | 13 worcs-0.1.16/worcs/man/worcs_project.Rd | 23 worcs-0.1.16/worcs/tests/testthat/test-github.R |only worcs-0.1.16/worcs/tests/testthat/test-worcs_project.R | 4 worcs-0.1.16/worcs/vignettes/citation.Rmd | 2 worcs-0.1.16/worcs/vignettes/targets.Rmd |only worcs-0.1.16/worcs/vignettes/vignettes.bib | 16 worcs-0.1.16/worcs/vignettes/workflow.Rmd | 9 45 files changed, 793 insertions(+), 414 deletions(-)
Title: Effects under Linear, Logistic and Poisson Regression Models
with Transformed Variables
Description: Computation of effects under linear, logistic and Poisson regression
models with transformed variables. Logarithm and power transformations are allowed.
Effects can be displayed both numerically and graphically in both the original
and the transformed space of the variables. The methods are described in Barrera-Gomez
and Basagana (2015) <doi:10.1097/EDE.0000000000000247>.
Author: Jose Barrera-Gomez [aut, cre] ,
Xavier Basagana [aut]
Maintainer: Jose Barrera-Gomez <jose.barrera@isglobal.org>
Diff between tlm versions 0.1.5 dated 2017-04-10 and 0.2.0 dated 2025-01-07
tlm-0.1.5/tlm/NEWS |only tlm-0.1.5/tlm/R/betaCIContinuousExactTrans.R |only tlm-0.1.5/tlm/R/bijectivityback.R |only tlm-0.1.5/tlm/R/bijectivityforward.R |only tlm-0.1.5/tlm/R/checkc.R |only tlm-0.1.5/tlm/R/checkfornumber.R |only tlm-0.1.5/tlm/R/checkfornumberorvector.R |only tlm-0.1.5/tlm/R/checkforvector.R |only tlm-0.1.5/tlm/R/checknbootseed.R |only tlm-0.1.5/tlm/R/checknpoints.R |only tlm-0.1.5/tlm/R/checkq.R |only tlm-0.1.5/tlm/R/checkr.R |only tlm-0.1.5/tlm/R/effectContinuous.R |only tlm-0.1.5/tlm/R/effectContinuousGeneral.R |only tlm-0.1.5/tlm/R/effectContinuousReduxmod1.R |only tlm-0.1.5/tlm/R/effectContinuousReduxmod10.R |only tlm-0.1.5/tlm/R/effectContinuousReduxmod12.R |only tlm-0.1.5/tlm/R/effectContinuousReduxmod3.R |only tlm-0.1.5/tlm/R/effectContinuousReduxmod5.R |only tlm-0.1.5/tlm/R/effectContinuousReduxmod6.R |only tlm-0.1.5/tlm/R/effectContinuousReduxmod7.R |only tlm-0.1.5/tlm/R/effectContinuousReduxmod9.R |only tlm-0.1.5/tlm/R/effectContinuousmod1.R |only tlm-0.1.5/tlm/R/effectContinuousmod10.R |only tlm-0.1.5/tlm/R/effectContinuousmod12.R |only tlm-0.1.5/tlm/R/effectContinuousmod3.R |only tlm-0.1.5/tlm/R/effectContinuousmod5.R |only tlm-0.1.5/tlm/R/effectContinuousmod6.R |only tlm-0.1.5/tlm/R/effectContinuousmod7.R |only tlm-0.1.5/tlm/R/effectContinuousmod9.R |only tlm-0.1.5/tlm/R/effectFactor.R |only tlm-0.1.5/tlm/R/effectFactorBoot.R |only tlm-0.1.5/tlm/R/effectFactorExactTrans.R |only tlm-0.1.5/tlm/R/effectFactormod11.R |only tlm-0.1.5/tlm/R/effectFactormod2.R |only tlm-0.1.5/tlm/R/effectFactormod4.R |only tlm-0.1.5/tlm/R/effectFactormod8.R |only tlm-0.1.5/tlm/R/effectInfomod0.R |only tlm-0.1.5/tlm/R/effectInfomod1.R |only tlm-0.1.5/tlm/R/effectInfomod10.R |only tlm-0.1.5/tlm/R/effectInfomod11.R |only tlm-0.1.5/tlm/R/effectInfomod12.R |only tlm-0.1.5/tlm/R/effectInfomod2.R |only tlm-0.1.5/tlm/R/effectInfomod3.R |only tlm-0.1.5/tlm/R/effectInfomod4.R |only tlm-0.1.5/tlm/R/effectInfomod5.R |only tlm-0.1.5/tlm/R/effectInfomod6.R |only tlm-0.1.5/tlm/R/effectInfomod7.R |only tlm-0.1.5/tlm/R/effectInfomod8.R |only tlm-0.1.5/tlm/R/effectInfomod9.R |only tlm-0.1.5/tlm/R/effectboot.R |only tlm-0.1.5/tlm/R/getL.R |only tlm-0.1.5/tlm/R/getM.R |only tlm-0.1.5/tlm/R/geteffectx1x2.R |only tlm-0.1.5/tlm/R/modelType.R |only tlm-0.1.5/tlm/R/plot.tlm.R |only tlm-0.1.5/tlm/R/powerTransform.R |only tlm-0.1.5/tlm/R/powerUntransform.R |only tlm-0.1.5/tlm/R/print.MY.R |only tlm-0.1.5/tlm/R/print.effect.R |only tlm-0.1.5/tlm/R/print.effectInfo.R |only tlm-0.1.5/tlm/R/print.summary.tlm.R |only tlm-0.1.5/tlm/R/print.tlm.R |only tlm-0.1.5/tlm/R/printPreamble.R |only tlm-0.1.5/tlm/inst/doc/tlm-manual.pdf |only tlm-0.1.5/tlm/man/tlm-internal.Rd |only tlm-0.1.5/tlm/vignettes/authblk.sty |only tlm-0.1.5/tlm/vignettes/framed.sty |only tlm-0.2.0/tlm/DESCRIPTION | 34 - tlm-0.2.0/tlm/MD5 | 140 +--- tlm-0.2.0/tlm/NAMESPACE | 114 +-- tlm-0.2.0/tlm/NEWS.md |only tlm-0.2.0/tlm/R/MY.R | 211 +++++-- tlm-0.2.0/tlm/R/cotinine.R |only tlm-0.2.0/tlm/R/effect.R | 160 ++++- tlm-0.2.0/tlm/R/effectInfo.R | 88 ++ tlm-0.2.0/tlm/R/feld1.R |only tlm-0.2.0/tlm/R/glucose.R |only tlm-0.2.0/tlm/R/imt.R |only tlm-0.2.0/tlm/R/internal_bijectivity.R |only tlm-0.2.0/tlm/R/internal_checkarguments.R |only tlm-0.2.0/tlm/R/internal_effectContinuous.R |only tlm-0.2.0/tlm/R/internal_effectContinuousReduxmodels.R |only tlm-0.2.0/tlm/R/internal_effectContinuousmodels.R |only tlm-0.2.0/tlm/R/internal_effectFactormodels.R |only tlm-0.2.0/tlm/R/internal_effectInfomodels.R |only tlm-0.2.0/tlm/R/internal_main.R |only tlm-0.2.0/tlm/R/internal_misc.R |only tlm-0.2.0/tlm/R/onAttach.R |only tlm-0.2.0/tlm/R/summary.tlm.R | 65 ++ tlm-0.2.0/tlm/R/tlm-package.R |only tlm-0.2.0/tlm/R/tlm.R | 500 ++++++++++++++--- tlm-0.2.0/tlm/README.md |only tlm-0.2.0/tlm/build/partial.rdb |only tlm-0.2.0/tlm/build/vignette.rds |binary tlm-0.2.0/tlm/data/cotinine.rda |binary tlm-0.2.0/tlm/data/feld1.rda |binary tlm-0.2.0/tlm/data/glucose.rda |binary tlm-0.2.0/tlm/data/imt.rda |binary tlm-0.2.0/tlm/inst/CITATION |only tlm-0.2.0/tlm/inst/doc/tlm.R | 199 ++---- tlm-0.2.0/tlm/inst/doc/tlm.Rnw | 412 +++++++------- tlm-0.2.0/tlm/inst/doc/tlm.pdf |binary tlm-0.2.0/tlm/man/MY.Rd | 92 ++- tlm-0.2.0/tlm/man/cotinine.Rd | 44 - tlm-0.2.0/tlm/man/effect.Rd | 122 ++-- tlm-0.2.0/tlm/man/effectInfo.Rd | 62 +- tlm-0.2.0/tlm/man/feld1.Rd | 45 - tlm-0.2.0/tlm/man/glucose.Rd | 42 - tlm-0.2.0/tlm/man/imt.Rd | 42 - tlm-0.2.0/tlm/man/summary.tlm.Rd | 48 + tlm-0.2.0/tlm/man/tlm-package.Rd | 63 -- tlm-0.2.0/tlm/man/tlm.Rd | 155 +++-- tlm-0.2.0/tlm/vignettes/bibliography.bib |only tlm-0.2.0/tlm/vignettes/tlm.Rnw | 412 +++++++------- 115 files changed, 1930 insertions(+), 1120 deletions(-)
Title: Presmoothed Estimation in Survival Analysis
Description: Presmoothed estimators of survival, density, cumulative and non-cumulative hazard functions with right-censored survival data. For details, see Lopez-de-Ullibarri and Jacome (2013) <doi:10.18637/jss.v054.i11>.
Author: Ignacio Lopez de Ullibarri [aut, cre],
Maria Amalia Jacome [aut]
Maintainer: Ignacio Lopez de Ullibarri <ilu@udc.es>
Diff between survPresmooth versions 1.1-11 dated 2021-10-06 and 1.1-12 dated 2025-01-07
ChangeLog | 10 DESCRIPTION | 8 MD5 | 14 R/presmooth.R | 999 ++++++++++++++++++++++++++++-------------------------- R/zzz.R | 6 build/partial.rdb |binary inst/CITATION | 29 - src/presmestim.c | 4 8 files changed, 562 insertions(+), 508 deletions(-)
Title: Single-Source Capture-Recapture Models
Description: Implementation of single-source capture-recapture methods for population size estimation using zero-truncated, zero-one truncated and zero-truncated one-inflated Poisson, Geometric and Negative Binomial regression as well as Zelterman's and Chao's regression. Package includes point and interval estimators for the population size with variances estimated using analytical or bootstrap method. Details can be found in: van der Heijden et all. (2003) <doi:10.1191/1471082X03st057oa>, Böhning and van der Heijden (2019) <doi:10.1214/18-AOAS1232>, Böhning et al. (2020) Capture-Recapture Methods for the Social and Medical Sciences or Böhning and Friedl (2021) <doi:10.1007/s10260-021-00556-8>.
Author: Piotr Chlebicki [aut, cre],
Maciej Beresewicz [aut, ctb]
Maintainer: Piotr Chlebicki <piotrek.pecet@gmail.com>
Diff between singleRcapture versions 0.2.1.3 dated 2024-11-10 and 0.2.1.4 dated 2025-01-07
DESCRIPTION | 6 +-- MD5 | 25 ++++++------ NAMESPACE | 18 ++++++++- R/documentationFiles.R | 9 +++- R/estimatePopsize.R | 2 - R/marginal.R | 6 ++- R/methodsNotWorking.R |only R/miscPrints.R | 1 R/plots.R | 19 ++++++++- R/smallMethods.R | 84 ++++++++++++++++++++++++++++++++++++------- build/singleRcapture.pdf |binary build/stage23.rdb |binary man/regDiagSingleR.Rd | 25 +++++++++++- man/summary.singleRmargin.Rd | 2 - 14 files changed, 158 insertions(+), 39 deletions(-)
More information about singleRcapture at CRAN
Permanent link
Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed
for formatting columns of data using the full range of colours
provided by modern terminals.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between pillar versions 1.10.0 dated 2024-12-17 and 1.10.1 dated 2025-01-07
DESCRIPTION | 6 MD5 | 12 NEWS.md | 7 R/type.R | 6 R/zzz.R | 12 inst/doc/printing.html | 3073 ++++++++++++++++++++++++++++++++++++++++++++----- man/format_type_sum.Rd | 6 7 files changed, 2844 insertions(+), 278 deletions(-)
Title: Causal Inference with Spatio-Temporal Data
Description: Spatio-temporal causal inference based on point process data.
You provide the raw data of locations and timings of treatment and
outcome events, specify counterfactual scenarios, and the package
estimates causal effects over specified spatial and temporal windows.
See Papadogeorgou, et al. (2022) <doi:10.1111/rssb.12548> and
Mukaigawara, et al. (2024) <doi:10.31219/osf.io/5kc6f>.
Author: Mitsuru Mukaigawara [cre, aut]
,
Lingxiao Zhou [aut],
Georgia Papadogeorgou [aut] ,
Jason Lyall [aut] ,
Kosuke Imai [aut]
Maintainer: Mitsuru Mukaigawara <mitsuru_mukaigawara@g.harvard.edu>
Diff between geocausal versions 0.3.3 dated 2024-12-03 and 0.3.4 dated 2025-01-07
DESCRIPTION | 6 +++--- MD5 | 32 +++++++++++++++++--------------- NAMESPACE | 17 +---------------- NEWS.md | 4 ++++ R/get_obs_dens.R | 9 +++++++-- R/plot.im.R | 19 +++++++++++++++++-- R/plot.imlist.R | 52 ++++++++++++++++++++++++++++++++++++++++++---------- R/plot.list.R |only R/plot.obs.R | 5 ++--- R/plot.ppplist.R | 11 ++++++----- R/smooth_ppp.R | 2 ++ README.md | 13 ++++++++----- man/get_obs_dens.Rd | 1 + man/plot.im.Rd | 3 +++ man/plot.imlist.Rd | 6 ++++++ man/plot.list.Rd |only man/plot.obs.Rd | 12 +----------- man/plot.ppplist.Rd | 8 +++++--- 18 files changed, 125 insertions(+), 75 deletions(-)
Title: Makes it Easier to Work with Daily 'netCDF' from EURO-CORDEX
RCMs
Description: Daily 'netCDF' data from e.g. regional climate models (RCMs) are not trivial
to work with. This package, which relies on 'data.table', makes it easier
to deal with large data from RCMs, such as from EURO-CORDEX
(<https://www.euro-cordex.net/>, <https://cordex.org/data-access/>). It has
functions to extract single grid cells from rotated pole grids as well as
the whole array in long format. Can handle non-standard calendars (360,
noleap) and interpolate them to a standard one. Potentially works with many
CF-conform 'netCDF' files.
Author: Michael Matiu [aut, cre]
Maintainer: Michael Matiu <michaelmatiu@gmail.com>
Diff between eurocordexr versions 0.2.4 dated 2023-08-24 and 0.2.5 dated 2025-01-07
DESCRIPTION | 17 ++-- MD5 | 32 +++++---- NAMESPACE | 1 NEWS.md | 7 ++ R/get_inventory.R | 6 + R/get_inventory_cmip5.R | 5 + R/map_non_standard_calendar.R | 2 R/nc_grid_to_dt_raw.R |only R/print.eurocordexr_inv.R | 10 -- README.md | 86 ++++++++++++++----------- inst/extdata/alps1.nc |only inst/extdata/alps1_regular.nc |only inst/extdata/alps2.nc |only inst/extdata/test3.nc |only man/eurocordexr-package.Rd | 3 man/figures |only man/map_non_standard_calendar.Rd | 2 man/nc_grid_to_dt_raw.Rd |only tests/testthat/_snaps/check_inventory.md | 3 tests/testthat/_snaps/check_inventory_cmip5.md | 6 + tests/testthat/test-nc_grid_to_dt_raw.R |only 21 files changed, 114 insertions(+), 66 deletions(-)
Title: Canonical Correlations and Tests of Independence
Description: A simple interface for multivariate correlation analysis that unifies various classical
statistical procedures including t-tests, tests in univariate and multivariate linear models,
parametric and nonparametric tests for correlation, Kruskal-Wallis tests, common approximate
versions of Wilcoxon rank-sum and signed rank tests, chi-squared tests of independence, score
tests of particular hypotheses in generalized linear models, canonical correlation analysis and
linear discriminant analysis.
Author: Robert Schlicht [aut, cre]
Maintainer: Robert Schlicht <robert.schlicht@tu-dresden.de>
Diff between cctest versions 1.1.0 dated 2024-10-02 and 1.2.0 dated 2025-01-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 2 +- R/cctest.R | 50 +++++++++++++++++++++++++------------------------- build/partial.rdb |binary 5 files changed, 33 insertions(+), 33 deletions(-)
Title: 'ROI' Optimization Problems Based on 'globalOptTests'
Description: A collection of non-linear optimization problems with box bounds
transformed into 'ROI' optimization problems.
This package provides a wrapper around the 'globalOptTests'
which provides a collection of global optimization problems.
More information can be found in the 'README' file.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.models.globalOptTests versions 1.1-1 dated 2020-08-29 and 1.1-2 dated 2025-01-07
DESCRIPTION | 13 +++++++------ MD5 | 6 +++--- R/globalopt.R | 9 ++++----- man/globopt.Rd | 4 ++-- 4 files changed, 16 insertions(+), 16 deletions(-)
More information about ROI.models.globalOptTests at CRAN
Permanent link
Title: Portable Emissions (and Other Mobile) Measurement System
Utilities
Description: Utility functions for the handling, analysis and visualisation of data
from portable emissions measurement systems ('PEMS') and other similar
mobile activity monitoring devices. The package includes a dedicated 'pems'
data class that manages many of the quality control, unit handling and data
archiving issues that can hinder efforts to standardise 'PEMS' research.
Author: Karl Ropkins [aut, cre],
Adrian Felipe Ortega Calle [ctb]
Maintainer: Karl Ropkins <karl.ropkins@gmail.com>
Diff between pems.utils versions 0.2.29.1 dated 2021-04-25 and 0.3.0.7 dated 2025-01-07
pems.utils-0.2.29.1/pems.utils/R/RcppExports.R |only pems.utils-0.2.29.1/pems.utils/src |only pems.utils-0.3.0.7/pems.utils/DESCRIPTION | 39 pems.utils-0.3.0.7/pems.utils/MD5 | 71 - pems.utils-0.3.0.7/pems.utils/NAMESPACE | 81 - pems.utils-0.3.0.7/pems.utils/NEWS | 22 pems.utils-0.3.0.7/pems.utils/R/0pts.R | 12 pems.utils-0.3.0.7/pems.utils/R/calcColdStart.R | 104 - pems.utils-0.3.0.7/pems.utils/R/calcSpeedEm.R | 73 - pems.utils-0.3.0.7/pems.utils/R/calcVSP.R | 177 +-- pems.utils-0.3.0.7/pems.utils/R/check.functions.R | 5 pems.utils-0.3.0.7/pems.utils/R/common.corrections.1.R | 42 pems.utils-0.3.0.7/pems.utils/R/export.pems.data.R | 10 pems.utils-0.3.0.7/pems.utils/R/generic.pems.element.handlers.R | 13 pems.utils-0.3.0.7/pems.utils/R/generic.pems.handlers.R | 88 - pems.utils-0.3.0.7/pems.utils/R/import.pems.main.R | 89 + pems.utils-0.3.0.7/pems.utils/R/import.pems.working2.R | 5 pems.utils-0.3.0.7/pems.utils/R/import.pems.working3.R | 7 pems.utils-0.3.0.7/pems.utils/R/make.pems.R | 30 pems.utils-0.3.0.7/pems.utils/R/merge.pems.R | 42 pems.utils-0.3.0.7/pems.utils/R/pems.plots.R | 540 ++++++---- pems.utils-0.3.0.7/pems.utils/R/pems.structure.R | 41 pems.utils-0.3.0.7/pems.utils/R/summaryReports.R | 2 pems.utils-0.3.0.7/pems.utils/R/tidyverse.tools.R | 88 - pems.utils-0.3.0.7/pems.utils/R/time.handlers.R | 80 + pems.utils-0.3.0.7/pems.utils/inst/CITATION | 12 pems.utils-0.3.0.7/pems.utils/man/4.1.merge.data.pems.Rd | 8 pems.utils-0.3.0.7/pems.utils/man/4.3.time.handlers.Rd | 34 pems.utils-0.3.0.7/pems.utils/man/5.1.pems.plots.Rd | 72 - pems.utils-0.3.0.7/pems.utils/man/6.2.check.functions.Rd | 2 pems.utils-0.3.0.7/pems.utils/man/6.3.corrections.Rd | 10 pems.utils-0.3.0.7/pems.utils/man/7.1.vsp.code.Rd | 14 pems.utils-0.3.0.7/pems.utils/man/7.2.emissions.code.Rd | 2 pems.utils-0.3.0.7/pems.utils/man/7.3.coldstart.code.Rd | 11 pems.utils-0.3.0.7/pems.utils/man/7.4.speed.em.code.Rd | 11 pems.utils-0.3.0.7/pems.utils/man/8.1.tidyverse.tools.Rd | 2 pems.utils-0.3.0.7/pems.utils/man/pems.utils-package.Rd | 4 37 files changed, 1116 insertions(+), 727 deletions(-)
Title: Pipeline Tools Inspired by 'GNU Make'
Description: A suite of tools for transforming an existing workflow into a
self-documenting pipeline with very minimal upfront costs. Segments of
the pipeline are specified in much the same way a 'Make' rule is, by
declaring an executable recipe (which might be an R script), along
with the corresponding targets and dependencies. When the entire
pipeline is run through, only those recipes that need to be executed
will be. Meanwhile, execution metadata is captured behind the scenes
for later inspection.
Author: Kinto Behr [aut, cre, cph]
Maintainer: Kinto Behr <kinto.behr@gmail.com>
Diff between makepipe versions 0.2.1 dated 2022-12-07 and 0.2.2 dated 2025-01-07
makepipe-0.2.1/makepipe/man/figures/archive |only makepipe-0.2.1/makepipe/tests/testthat/_snaps/Pipeline.md |only makepipe-0.2.1/makepipe/tests/testthat/_snaps/Pipeline/pipeline_png |only makepipe-0.2.2/makepipe/DESCRIPTION | 10 makepipe-0.2.2/makepipe/MD5 | 41 makepipe-0.2.2/makepipe/NEWS.md | 21 makepipe-0.2.2/makepipe/R/Pipeline.R | 1769 +++++----- makepipe-0.2.2/makepipe/R/make.R | 321 - makepipe-0.2.2/makepipe/R/make_with_dir.R | 416 +- makepipe-0.2.2/makepipe/R/out_of_date.R | 82 makepipe-0.2.2/makepipe/R/params.R | 42 makepipe-0.2.2/makepipe/inst/doc/makepipe.R | 2 makepipe-0.2.2/makepipe/inst/doc/makepipe.html | 362 +- makepipe-0.2.2/makepipe/man/Pipeline.Rd | 17 makepipe-0.2.2/makepipe/man/make_params.Rd | 3 makepipe-0.2.2/makepipe/man/make_with_dir.Rd | 5 makepipe-0.2.2/makepipe/man/make_with_recipe.Rd | 4 makepipe-0.2.2/makepipe/man/make_with_source.Rd | 4 makepipe-0.2.2/makepipe/tests/testthat/_snaps/Pipeline/pipeline.png |only makepipe-0.2.2/makepipe/tests/testthat/_snaps/make.md |only makepipe-0.2.2/makepipe/tests/testthat/test-Pipeline.R | 23 makepipe-0.2.2/makepipe/tests/testthat/test-Segment.R | 3 makepipe-0.2.2/makepipe/tests/testthat/test-make.R | 177 - 23 files changed, 1741 insertions(+), 1561 deletions(-)
Title: Recursive Partitioning and Regression Trees
Description: Recursive partitioning for classification,
regression and survival trees. An implementation of most of the
functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut],
Beth Atkinson [aut, cre],
Brian Ripley [trl]
Maintainer: Beth Atkinson <atkinson@mayo.edu>
Diff between rpart versions 4.1.23 dated 2023-12-05 and 4.1.24 dated 2025-01-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/rpart.R | 8 +++++++- man/rpart.control.Rd | 4 ++-- src/gini.c | 4 ++-- src/node.h | 5 +++-- 6 files changed, 23 insertions(+), 16 deletions(-)