Title: Interactive Data Tables Based on 'React Table'
Description: Interactive data tables for R, based on the 'React Table'
JavaScript library. Provides an HTML widget that can be used in 'R Markdown'
documents and 'Shiny' applications, or viewed from an R console.
Author: Greg Lin [aut, cre],
Tanner Linsley [ctb, cph] (React Table library),
Emotion team and other contributors [ctb, cph] (Emotion library)
Maintainer: Greg Lin <glin@glin.io>
Diff between reactable versions 0.2.1 dated 2020-09-01 and 0.2.2 dated 2020-09-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 7 +++++++ inst/htmlwidgets/reactable.js | 2 +- inst/htmlwidgets/reactable.js.map | 2 +- 5 files changed, 16 insertions(+), 9 deletions(-)
Title: Safety Diagnostics for Dose-Escalation Trial Designs
Description: Enhances various R packages that support the design and simulation
of phase 1 dose-escalation trials, adding diagnostics to examine
the safety characteristics of these designs in light of expected
inter-individual variation in pharmacokinetics and pharmacodynamics.
See Norris (2020), "Retrospective analysis of a fatal dose-finding
trial" <arXiv:2004.12755>.
Author: David C. Norris [aut, cre, cph]
(<https://orcid.org/0000-0001-9593-6343>)
Maintainer: David C. Norris <david@precisionmethods.guru>
Diff between precautionary versions 0.1-2 dated 2020-08-01 and 0.1-3 dated 2020-09-13
DESCRIPTION | 8 - MD5 | 50 +++++---- NAMESPACE | 2 NEWS.md | 6 + R/enhance.R | 20 +-- R/precautionary-package.R | 10 - R/simulate_trials.R | 16 +- R/toxicity_generators.R | 13 +- build/partial.rdb |binary demo |only exec |only inst/doc/Intro.Rmd | 29 ++--- inst/doc/Intro.html | 200 ++++++++++++++++++------------------ inst/shiny-apps |only man/cohorts_of_n.Rd | 4 man/format.safetytab.Rd | 2 man/phase1_sim.Rd | 6 - man/precautionary-package.Rd | 10 - man/print.hyper.Rd | 4 man/print.precautionary.Rd | 4 man/simulate_trials.Rd | 10 + man/simulation_function.u_i.Rd | 4 man/summary.precautionary.Rd | 2 vignettes/Intro.Rmd | 29 ++--- vignettes/precautionary-package.bib | 2 25 files changed, 235 insertions(+), 196 deletions(-)
Title: Preprocessing Operators and Pipelines for 'mlr3'
Description: Dataflow programming toolkit that enriches 'mlr3' with a diverse
set of pipelining operators ('PipeOps') that can be composed into graphs.
Operations exist for data preprocessing, model fitting, and ensemble
learning. Graphs can themselves be treated as 'mlr3' 'Learners' and can
therefore be resampled, benchmarked, and tuned.
Author: Martin Binder [aut, cre],
Florian Pfisterer [aut] (<https://orcid.org/0000-0001-8867-762X>),
Lennart Schneider [aut] (<https://orcid.org/0000-0003-4152-5308>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Susanne Dandl [aut]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between mlr3pipelines versions 0.2.1 dated 2020-08-18 and 0.3.0 dated 2020-09-13
mlr3pipelines-0.2.1/mlr3pipelines/R/convert_task.R |only mlr3pipelines-0.2.1/mlr3pipelines/inst/doc |only mlr3pipelines-0.2.1/mlr3pipelines/man/PipeOpProxy.Rd |only mlr3pipelines-0.2.1/mlr3pipelines/man/convert_task.Rd |only mlr3pipelines-0.2.1/mlr3pipelines/tests/testthat/test_convert_task.R |only mlr3pipelines-0.3.0/mlr3pipelines/DESCRIPTION | 44 - mlr3pipelines-0.3.0/mlr3pipelines/MD5 | 266 +++++----- mlr3pipelines-0.3.0/mlr3pipelines/NAMESPACE | 6 mlr3pipelines-0.3.0/mlr3pipelines/NEWS.md | 21 mlr3pipelines-0.3.0/mlr3pipelines/R/Graph.R | 104 ++- mlr3pipelines-0.3.0/mlr3pipelines/R/GraphLearner.R | 11 mlr3pipelines-0.3.0/mlr3pipelines/R/LearnerAvg.R | 173 ++++-- mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOp.R | 3 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpBoxCox.R | 2 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpClassBalancing.R | 2 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpClassifAvg.R | 2 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpColRoles.R |only mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpCollapseFactors.R | 6 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpEncodeImpact.R | 2 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpEncodeLmer.R | 4 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpFilter.R | 4 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpImputeHist.R | 2 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpImputeOOR.R | 15 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpKernelPCA.R | 2 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpLearner.R | 5 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpLearnerCV.R | 4 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpMultiplicity.R | 3 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpNMF.R |only mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpOVR.R | 8 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpPCA.R | 2 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpProxy.R | 1 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpQuantileBin.R | 4 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpRandomProjection.R |only mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpRandomResponse.R | 17 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpSmote.R | 9 mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpTextVectorizer.R | 94 ++- mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpTrafo.R | 31 - mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpTuneThreshold.R |only mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpVtreat.R |only mlr3pipelines-0.3.0/mlr3pipelines/R/PipeOpYeoJohnson.R | 2 mlr3pipelines-0.3.0/mlr3pipelines/R/mlr_graphs_elements.R | 10 mlr3pipelines-0.3.0/mlr3pipelines/R/typecheck.R | 11 mlr3pipelines-0.3.0/mlr3pipelines/R/utils.R | 21 mlr3pipelines-0.3.0/mlr3pipelines/R/zzz.R | 8 mlr3pipelines-0.3.0/mlr3pipelines/README.md | 13 mlr3pipelines-0.3.0/mlr3pipelines/build |only mlr3pipelines-0.3.0/mlr3pipelines/inst/references.bib |only mlr3pipelines-0.3.0/mlr3pipelines/man/Graph.Rd | 13 mlr3pipelines-0.3.0/mlr3pipelines/man/PipeOp.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/PipeOpEnsemble.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/PipeOpImpute.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/PipeOpTargetTrafo.Rd | 9 mlr3pipelines-0.3.0/mlr3pipelines/man/PipeOpTaskPreproc.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/PipeOpTaskPreprocSimple.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_graphs_bagging.Rd | 2 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_graphs_robustify.Rd | 2 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_graphs_targettrafo.Rd | 4 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_learners_avg.Rd | 35 - mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_boxcox.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_branch.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_chunk.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_classbalancing.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_classifavg.Rd | 9 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_classweights.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_colapply.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_collapsefactors.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_colroles.Rd |only mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_copy.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_datefeatures.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_encode.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_encodeimpact.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_encodelmer.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_featureunion.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_filter.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_fixfactors.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_histbin.Rd | 9 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_ica.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_imputeconstant.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_imputehist.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_imputelearner.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_imputemean.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_imputemedian.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_imputemode.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_imputeoor.Rd | 16 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_imputesample.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_kernelpca.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_learner.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_missind.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_modelmatrix.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_multiplicityexply.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_multiplicityimply.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_mutate.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_nmf.Rd |only mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_nop.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_ovrsplit.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_ovrunite.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_pca.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_proxy.Rd |only mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_quantilebin.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_randomprojection.Rd |only mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_randomresponse.Rd | 11 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_regravg.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_removeconstants.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_renamecolumns.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_replicate.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_scale.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_scalemaxabs.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_scalerange.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_select.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_smote.Rd | 18 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_spatialsign.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_subsample.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_targetinvert.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_targetmutate.Rd | 22 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_targettrafoscalerange.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_textvectorizer.Rd | 17 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_threshold.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_tunethreshold.Rd |only mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_unbranch.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_updatetarget.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_vtreat.Rd |only mlr3pipelines-0.3.0/mlr3pipelines/man/mlr_pipeops_yeojohnson.Rd | 7 mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_Graph.R | 52 + mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_PipeOp.R | 9 mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_conversion.R | 29 + mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_graphlearner.R | 18 mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_learner_weightedaverage.R | 16 mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_mlr_graphs_bagging.R | 1 mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_mlr_graphs_branching.R | 2 mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_mlr_graphs_robustify.R | 14 mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_multichannels.R | 3 mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_pipeop_colroles.R |only mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_pipeop_ensemble.R | 6 mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_pipeop_histbin.R | 22 mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_pipeop_missind.R | 2 mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_pipeop_multiplicityimply.R | 12 mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_pipeop_nmf.R |only mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_pipeop_ovr.R | 10 mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_pipeop_randomprojection.R |only mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_pipeop_randomresponse.R | 7 mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_pipeop_textvectorizer.R | 129 ++++ mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_pipeop_tunethreshold.R |only mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_pipeop_vtreat.R |only mlr3pipelines-0.3.0/mlr3pipelines/tests/testthat/test_typecheck.R | 51 + 145 files changed, 1380 insertions(+), 481 deletions(-)
Title: Create Dendrograms and Tree Diagrams Using 'ggplot2'
Description: This is a set of tools for dendrograms and
tree plots using 'ggplot2'. The 'ggplot2' philosophy is to
clearly separate data from the presentation.
Unfortunately the plot method for dendrograms plots
directly to a plot device without exposing the data.
The 'ggdendro' package resolves this by making available
functions that extract the dendrogram plot data. The package
provides implementations for 'tree', 'rpart', as well as diana and agnes
(from 'cluster') diagrams.
Author: Andrie de Vries [aut, cre],
Brian D. Ripley [aut] (author of package tree)
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between ggdendro versions 0.1.21 dated 2020-08-11 and 0.1.22 dated 2020-09-13
DESCRIPTION | 7 - MD5 | 18 ++-- NEWS | 7 + inst/doc/ggdendro.html | 142 +++++++++++++++-------------------- tests/testthat/test-1-dendrogram.R | 24 +---- tests/testthat/test-2-hclust.R | 7 - tests/testthat/test-3-rpart.R | 9 -- tests/testthat/test-3-tree.R | 9 -- tests/testthat/test-4-clusterplots.R | 4 tests/testthat/test-6-ggdendrogram.R | 8 - 10 files changed, 105 insertions(+), 130 deletions(-)
Title: Automating the Fitting of Double Linear Mixed Models in 'JAGS'
and 'nimble'
Description: Automates fitting of double GLM in 'JAGS'. Includes automatic
generation of 'JAGS' scripts, running 'JAGS' or 'nimble' via the 'rjags'
and 'nimble' package, and summarizing the resulting output.
Author: Simon Bonner [aut, cre] (<https://orcid.org/0000-0003-2063-4572>),
Hanna Kim [aut]
Maintainer: Simon Bonner <simon.bonner@uwo.ca>
Diff between dalmatian versions 0.3.0 dated 2018-01-29 and 0.6.1 dated 2020-09-13
dalmatian-0.3.0/dalmatian/R/fitted.R |only dalmatian-0.3.0/dalmatian/data/weights_data_1.RData |only dalmatian-0.3.0/dalmatian/inst/Pied_Flycatchers_1 |only dalmatian-0.3.0/dalmatian/inst/Pied_Flycatchers_2 |only dalmatian-0.3.0/dalmatian/man/fitted.dalmatian.Rd |only dalmatian-0.3.0/dalmatian/man/weights.df.Rd |only dalmatian-0.6.1/dalmatian/DESCRIPTION | 27 dalmatian-0.6.1/dalmatian/MD5 | 124 - dalmatian-0.6.1/dalmatian/NAMESPACE | 24 dalmatian-0.6.1/dalmatian/R/betabin_jags_code.R |only dalmatian-0.6.1/dalmatian/R/dalmatian.R | 1054 +++++++---- dalmatian-0.6.1/dalmatian/R/dalmatian_doc.R |only dalmatian-0.6.1/dalmatian/R/data_doc.R | 44 dalmatian-0.6.1/dalmatian/R/gamma_jags_code.R |only dalmatian-0.6.1/dalmatian/R/gaussian_jags_code.R |only dalmatian-0.6.1/dalmatian/R/generate_jags_code.R | 665 +++++-- dalmatian-0.6.1/dalmatian/R/generate_jags_data.R | 82 dalmatian-0.6.1/dalmatian/R/generate_jags_inits.R | 588 +++--- dalmatian-0.6.1/dalmatian/R/nbinom_jags_code.R |only dalmatian-0.6.1/dalmatian/R/post_processing.R | 1137 +++++++----- dalmatian-0.6.1/dalmatian/R/predict.R |only dalmatian-0.6.1/dalmatian/R/residuals.R |only dalmatian-0.6.1/dalmatian/R/run_jags.R |only dalmatian-0.6.1/dalmatian/R/run_nimble.R |only dalmatian-0.6.1/dalmatian/README.md |only dalmatian-0.6.1/dalmatian/build/vignette.rds |binary dalmatian-0.6.1/dalmatian/data/betabin_data_1.rda |only dalmatian-0.6.1/dalmatian/data/gamma_data_1.rda |only dalmatian-0.6.1/dalmatian/data/nbinom_data_1.rda |only dalmatian-0.6.1/dalmatian/data/pied_flycatchers_1.RData |binary dalmatian-0.6.1/dalmatian/data/weights_data_1.rda |only dalmatian-0.6.1/dalmatian/inst/bbresults.RData |only dalmatian-0.6.1/dalmatian/inst/doc/beta-binomial-1.R |only dalmatian-0.6.1/dalmatian/inst/doc/beta-binomial-1.Rmd |only dalmatian-0.6.1/dalmatian/inst/doc/beta-binomial-1.html |only dalmatian-0.6.1/dalmatian/inst/doc/gamma-1.R |only dalmatian-0.6.1/dalmatian/inst/doc/gamma-1.Rmd |only dalmatian-0.6.1/dalmatian/inst/doc/gamma-1.html |only dalmatian-0.6.1/dalmatian/inst/doc/negative-binomial-1.R |only dalmatian-0.6.1/dalmatian/inst/doc/negative-binomial-1.Rmd |only dalmatian-0.6.1/dalmatian/inst/doc/negative-binomial-1.html |only dalmatian-0.6.1/dalmatian/inst/doc/pied-flycatchers-1.R | 310 +-- dalmatian-0.6.1/dalmatian/inst/doc/pied-flycatchers-1.Rmd | 267 +- dalmatian-0.6.1/dalmatian/inst/doc/pied-flycatchers-1.html | 840 +++++--- dalmatian-0.6.1/dalmatian/inst/doc/pied-flycatchers-2.R | 161 - dalmatian-0.6.1/dalmatian/inst/doc/pied-flycatchers-2.Rmd | 370 ++- dalmatian-0.6.1/dalmatian/inst/doc/pied-flycatchers-2.html | 569 ++++-- dalmatian-0.6.1/dalmatian/inst/doc/pied-flycatchers-3.R |only dalmatian-0.6.1/dalmatian/inst/doc/pied-flycatchers-3.Rmd |only dalmatian-0.6.1/dalmatian/inst/doc/pied-flycatchers-3.html |only dalmatian-0.6.1/dalmatian/inst/doc/weights-1-simulate.R | 71 dalmatian-0.6.1/dalmatian/inst/doc/weights-1-simulate.Rmd | 225 +- dalmatian-0.6.1/dalmatian/inst/doc/weights-1-simulate.html | 540 ++++- dalmatian-0.6.1/dalmatian/inst/gresults.RData |only dalmatian-0.6.1/dalmatian/inst/nbresults.RData |only dalmatian-0.6.1/dalmatian/inst/pfresults1.RData |only dalmatian-0.6.1/dalmatian/inst/pfresults2.RData |only dalmatian-0.6.1/dalmatian/inst/pfresults3.RData |only dalmatian-0.6.1/dalmatian/inst/pfresults4.RData |only dalmatian-0.6.1/dalmatian/man/betabin_data_1.Rd |only dalmatian-0.6.1/dalmatian/man/caterpillar.Rd | 9 dalmatian-0.6.1/dalmatian/man/caterpillar.dalmatian.Rd | 26 dalmatian-0.6.1/dalmatian/man/coef.dalmatian.Rd |only dalmatian-0.6.1/dalmatian/man/convergence.Rd | 9 dalmatian-0.6.1/dalmatian/man/convergence.dalmatian.Rd | 23 dalmatian-0.6.1/dalmatian/man/dalmatian.Rd | 62 dalmatian-0.6.1/dalmatian/man/gamma_data_1.Rd |only dalmatian-0.6.1/dalmatian/man/nbinom_data_1.Rd |only dalmatian-0.6.1/dalmatian/man/pfdata.Rd | 4 dalmatian-0.6.1/dalmatian/man/plot.dalmatian.Rd |only dalmatian-0.6.1/dalmatian/man/predict.dalmatian.Rd |only dalmatian-0.6.1/dalmatian/man/print.dalmatian.Rd |only dalmatian-0.6.1/dalmatian/man/print.dalmatian.summary.Rd | 9 dalmatian-0.6.1/dalmatian/man/ranef.Rd | 9 dalmatian-0.6.1/dalmatian/man/ranef.dalmatian.Rd | 18 dalmatian-0.6.1/dalmatian/man/residuals.dalmatian.Rd |only dalmatian-0.6.1/dalmatian/man/setJAGSInits.Rd | 43 dalmatian-0.6.1/dalmatian/man/summary.dalmatian.Rd | 17 dalmatian-0.6.1/dalmatian/man/terms.dalmatian.Rd |only dalmatian-0.6.1/dalmatian/man/traceplots.Rd | 9 dalmatian-0.6.1/dalmatian/man/traceplots.dalmatian.Rd | 26 dalmatian-0.6.1/dalmatian/man/weights_data_1.Rd |only dalmatian-0.6.1/dalmatian/vignettes/beta-binomial-1.Rmd |only dalmatian-0.6.1/dalmatian/vignettes/gamma-1.Rmd |only dalmatian-0.6.1/dalmatian/vignettes/negative-binomial-1.Rmd |only dalmatian-0.6.1/dalmatian/vignettes/pied-flycatchers-1.Rmd | 267 +- dalmatian-0.6.1/dalmatian/vignettes/pied-flycatchers-2.Rmd | 370 ++- dalmatian-0.6.1/dalmatian/vignettes/pied-flycatchers-3.Rmd |only dalmatian-0.6.1/dalmatian/vignettes/weights-1-simulate.Rmd | 225 +- 89 files changed, 5086 insertions(+), 3138 deletions(-)
Title: 'RStudio' Addin for Network Analysis and Visualization
Description: 'RStudio' addin which provides a GUI to visualize and analyse networks.
After finishing a session, the code to produce the plot is inserted in the current script.
Alternatively, the function SNAhelperGadget() can be used directly from the console.
Additional addins include the Netreader() for reading network files, Netbuilder() to create
small networks via point and click, and the Componentlayouter() to layout networks with many components manually.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david.schoch@manchester.ac.uk>
Diff between snahelper versions 1.1.0 dated 2020-03-03 and 1.2.0 dated 2020-09-13
DESCRIPTION | 13 +++++++------ MD5 | 14 ++++++++------ NAMESPACE | 1 + NEWS.md | 4 ++++ R/Componentlayouter.R |only R/SNAhelper.R | 6 +----- README.md | 20 +++++++++++++++++--- inst/rstudio/addins.dcf | 5 +++++ man/Componentlayouter.Rd |only 9 files changed, 43 insertions(+), 20 deletions(-)
Title: Miscellaneous Functions for Data Cleaning and Analysis
Description: Provides functions needed for data cleaning and
formatting and forms data cleaning and wrangling backend for the
following packages: 'broomExtra', 'ggstatsplot', 'groupedstats',
'pairwiseComparisons', 'statsExpressions', and 'tidyBF'.
Author: Indrajeet Patil [aut, cre, cph]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ipmisc versions 3.1.0 dated 2020-06-19 and 3.2.0 dated 2020-09-13
DESCRIPTION | 10 ++--- MD5 | 19 +++++---- NAMESPACE | 3 + NEWS.md | 6 +++ R/easystats_to_tidy_names.R |only R/long_to_wide_converter.R | 7 --- R/outlier_df.R | 28 +++----------- R/p_value_formatter.R | 3 + R/signif_column.R | 19 ++++----- README.md | 51 ++++++++++++++------------ man/easystats_to_tidy_names.Rd |only tests/testthat/test-easystats_to_tidy_names.R |only 12 files changed, 72 insertions(+), 74 deletions(-)
Title: Dirichlet Process Weibull Mixture Model for Survival Data
Description: Use Dirichlet process Weibull mixture model and dependent Dirichlet process Weibull mixture model for survival data with and without competing risks. Dirichlet process Weibull mixture model is used for data without covariates and dependent Dirichlet process model is used for regression data. The package is designed to handle exact/right-censored/ interval-censored observations without competing risks and exact/right-censored observations for data with competing risks. Inside each cluster of Dirichlet process, we assume a multiplicative effect of covariates as in Cox model and Fine and Gray model. For wrapper of the DPdensity function from the R package DPpackage (already archived by CRAN) that uses the Low Information Omnibus prior, please check (<https://github.com/mjmartens/DPdensity-wrapper-with-LIO-prior>).
Author: Yushu Shi
Maintainer: Yushu Shi <shiyushu2006@gmail.com>
Diff between DPWeibull versions 1.5 dated 2020-01-08 and 1.6 dated 2020-09-13
DESCRIPTION | 14 - MD5 | 34 +- NAMESPACE | 3 R/RcppExports.R | 134 +++++----- R/dpm.R | 114 ++++----- R/plot.R | 598 +++++++++++++++++++++++++++---------------------- R/pred.R | 24 - R/reg.R | 138 +++++------ R/summary.R | 26 +- data/deterioration.rda |binary data/survmedian.rda |binary man/dpweib.Rd | 232 +++++++------------ man/predict.ddp.Rd | 4 man/predict.ddpcomp.Rd | 4 src/compnoreg.cpp | 4 src/compreg.cpp | 219 +++++++---------- src/noreg.cpp | 4 src/reg.cpp | 51 ++-- 18 files changed, 788 insertions(+), 815 deletions(-)
Title: Generate Random Data Sets
Description: Generates random data sets including: data.frames, lists,
and vectors.
Author: Tyler Rinker [aut, cre],
Josh O'Brien [ctb],
Ananda Mahto [ctb],
Matthew Sigal [ctb],
Jonathan Carroll [ctb],
Scott Westenberger [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between wakefield versions 0.3.3 dated 2018-05-19 and 0.3.6 dated 2020-09-13
DESCRIPTION | 10 MD5 | 216 ++++++++--------- NEWS | 6 R/color.R | 3 R/hair.R | 2 R/internet_browser.R | 4 R/lorem_ipsum.R | 7 R/r_data_frame.R | 2 R/r_list.R | 2 R/religion.R | 4 R/sex_inclusive.R | 2 R/table_heat.R | 2 R/wakefield-package.R | 18 - README.md | 439 ++++++++++++++++++------------------ data/animal_list.rda |binary data/grady_augmented.rda |binary data/languages.rda |binary data/name_neutral.rda |binary data/presidential_debates_2012.rda |binary data/state_populations.rda |binary man/age.Rd | 148 +++++++----- man/animal.Rd | 191 +++++++++------ man/animal_list.Rd | 36 +- man/answer.Rd | 144 ++++++----- man/area.Rd | 140 ++++++----- man/as_integer.Rd | 88 +++---- man/car.Rd | 140 ++++++----- man/children.Rd | 146 +++++++---- man/coin.Rd | 144 ++++++----- man/color.Rd | 171 ++++++++------ man/date_stamp.Rd | 190 +++++++++------ man/death.Rd | 150 +++++++----- man/dice.Rd | 141 ++++++----- man/dna.Rd | 147 +++++++----- man/dob.Rd | 201 +++++++++------- man/dummy.Rd | 139 ++++++----- man/education.Rd | 204 +++++++++------- man/employment.Rd | 173 ++++++++------ man/eye.Rd | 173 ++++++++------ man/grade.Rd | 225 ++++++++++-------- man/grade_level.Rd | 147 +++++++----- man/grady_augmented.Rd | 60 ++-- man/group.Rd | 149 +++++++----- man/hair.Rd | 173 ++++++++------ man/height.Rd | 214 ++++++++++------- man/hour.Rd | 77 +++--- man/id.Rd | 110 ++++----- man/income.Rd | 151 +++++++----- man/internet_browser.Rd | 182 ++++++++------ man/interval.Rd | 117 +++++---- man/iq.Rd | 164 +++++++------ man/language.Rd | 159 +++++++------ man/languages.Rd | 54 ++-- man/letter.Rd | 207 +++++++++------- man/level.Rd | 202 +++++++++------- man/likert.Rd | 185 +++++++++------ man/lorem_ipsum.Rd | 164 +++++++------ man/marital.Rd | 153 +++++++----- man/military.Rd | 183 ++++++++------- man/minute.Rd | 85 +++--- man/month.Rd | 141 ++++++----- man/name.Rd | 158 +++++++----- man/name_neutral.Rd | 38 +-- man/normal.Rd | 192 +++++++++------ man/peek.Rd | 110 ++++----- man/plot.tbl_df.Rd | 32 +- man/political.Rd | 182 ++++++++------ man/presidential_debates_2012.Rd | 32 +- man/print.available.Rd | 32 +- man/print.variable.Rd | 32 +- man/probs.Rd | 56 ++-- man/r_data.Rd | 128 +++++----- man/r_data_frame.Rd | 222 +++++++++--------- man/r_dummy.Rd | 82 +++--- man/r_insert.Rd | 90 +++---- man/r_list.Rd | 140 +++++------ man/r_na.Rd | 100 ++++---- man/r_sample.Rd | 70 ++--- man/r_sample_binary.Rd | 80 +++--- man/r_sample_factor.Rd | 68 ++--- man/r_sample_integer.Rd | 70 ++--- man/r_sample_logical.Rd | 64 ++--- man/r_sample_ordered.Rd | 86 +++---- man/r_sample_replace.Rd | 77 +++--- man/r_series.Rd | 204 ++++++++-------- man/race.Rd | 181 ++++++++------ man/relate.Rd | 146 ++++++----- man/religion.Rd | 190 ++++++++------- man/sat.Rd | 164 +++++++------ man/second.Rd | 85 +++--- man/sentence.Rd | 147 +++++++----- man/seriesname.Rd | 52 ++-- man/sex.Rd | 181 ++++++++------ man/sex_inclusive.Rd | 201 +++++++++------- man/smokes.Rd | 143 ++++++----- man/speed.Rd | 206 ++++++++++------ man/state.Rd | 261 +++++++++++---------- man/state_populations.Rd | 50 ++-- man/string.Rd | 147 +++++++----- man/table_heat.Rd | 152 ++++++------ man/time_stamp.Rd | 83 +++--- man/valid.Rd | 143 ++++++----- man/variables.Rd | 94 +++---- man/varname.Rd | 62 ++--- man/wakefield.Rd | 21 - man/year.Rd | 149 +++++++----- man/zip_code.Rd | 145 ++++++----- tools/figure/unnamed-chunk-17-1.png |binary tools/figure/unnamed-chunk-19-1.png |binary 109 files changed, 6846 insertions(+), 5387 deletions(-)
Title: A Pipeline for Microbiome Analysis and Visualization
Description: A reliable alternative to popular microbiome analysis R packages. We provide standard tools as well as novel extensions on standard analyses to improve interpretability and the analyst’s ability to communicate results, all while maintaining object malleability to encourage open source collaboration.
Author: Charlie Carpenter [aut, cre],
Dan Frank [aut],
Kayla Williamson [aut],
Rachel Johnson [ctb]
Maintainer: Charlie Carpenter <charles.carpenter@cuanschutz.edu>
Diff between tidyMicro versions 1.43 dated 2020-03-28 and 1.47 dated 2020-09-13
tidyMicro-1.43/tidyMicro/R/Data_Class.R |only tidyMicro-1.43/tidyMicro/R/Data_Clin.R |only tidyMicro-1.43/tidyMicro/R/Data_Family.R |only tidyMicro-1.43/tidyMicro/R/Data_Order.R |only tidyMicro-1.43/tidyMicro/R/Data_Phylum.R |only tidyMicro-1.43/tidyMicro/data/cla.rda |only tidyMicro-1.43/tidyMicro/data/clin.rda |only tidyMicro-1.43/tidyMicro/data/fam.rda |only tidyMicro-1.43/tidyMicro/data/ord.rda |only tidyMicro-1.43/tidyMicro/data/phy.rda |only tidyMicro-1.43/tidyMicro/inst/doc/tidyMicro_vignette.R |only tidyMicro-1.43/tidyMicro/inst/doc/tidyMicro_vignette.Rmd |only tidyMicro-1.43/tidyMicro/inst/doc/tidyMicro_vignette.html |only tidyMicro-1.43/tidyMicro/man/cla.Rd |only tidyMicro-1.43/tidyMicro/man/clin.Rd |only tidyMicro-1.43/tidyMicro/man/fam.Rd |only tidyMicro-1.43/tidyMicro/man/ord.Rd |only tidyMicro-1.43/tidyMicro/man/phy.Rd |only tidyMicro-1.43/tidyMicro/vignettes/tidyMicro_vignette.Rmd |only tidyMicro-1.47/tidyMicro/DESCRIPTION | 12 tidyMicro-1.47/tidyMicro/MD5 | 174 +++++++------ tidyMicro-1.47/tidyMicro/NAMESPACE | 1 tidyMicro-1.47/tidyMicro/R/Data_BPD_Class.R |only tidyMicro-1.47/tidyMicro/R/Data_BPD_Clin.R |only tidyMicro-1.47/tidyMicro/R/Data_BPD_Family.R |only tidyMicro-1.47/tidyMicro/R/Data_BPD_Order.R |only tidyMicro-1.47/tidyMicro/R/Data_BPD_Phylum.R |only tidyMicro-1.47/tidyMicro/R/Data_MRSA_Clin.R |only tidyMicro-1.47/tidyMicro/R/Data_MRSA_Gen.R |only tidyMicro-1.47/tidyMicro/R/alpha_div.R | 17 - tidyMicro-1.47/tidyMicro/R/alpha_div_helper.R | 1 tidyMicro-1.47/tidyMicro/R/bb_bars.R | 8 tidyMicro-1.47/tidyMicro/R/bb_mods.R | 14 - tidyMicro-1.47/tidyMicro/R/beta_divs.R | 7 tidyMicro-1.47/tidyMicro/R/beta_heatmap.R | 11 tidyMicro-1.47/tidyMicro/R/box_plot.R | 8 tidyMicro-1.47/tidyMicro/R/cor_heatmap.R | 15 - tidyMicro-1.47/tidyMicro/R/cor_rocky_mtn.R | 15 - tidyMicro-1.47/tidyMicro/R/filter_funs.R | 7 tidyMicro-1.47/tidyMicro/R/filter_funs_helper.R | 10 tidyMicro-1.47/tidyMicro/R/micro_PERMANOVA.R | 8 tidyMicro-1.47/tidyMicro/R/micro_alpha_reg.R | 10 tidyMicro-1.47/tidyMicro/R/micro_chisq.R | 12 tidyMicro-1.47/tidyMicro/R/micro_forest.R | 13 tidyMicro-1.47/tidyMicro/R/micro_heatmap.R | 11 tidyMicro-1.47/tidyMicro/R/micro_otu.R |only tidyMicro-1.47/tidyMicro/R/micro_pca.R | 37 +- tidyMicro-1.47/tidyMicro/R/micro_rank_sum.R | 13 tidyMicro-1.47/tidyMicro/R/micro_rocky_mtn.R | 14 - tidyMicro-1.47/tidyMicro/R/nb_bars.R | 9 tidyMicro-1.47/tidyMicro/R/nb_mods.R | 14 - tidyMicro-1.47/tidyMicro/R/pca_3d.R | 159 +++++++---- tidyMicro-1.47/tidyMicro/R/pca_helper.R | 10 tidyMicro-1.47/tidyMicro/R/ra_bars.R | 7 tidyMicro-1.47/tidyMicro/R/taxa_summary.R | 7 tidyMicro-1.47/tidyMicro/R/three_mode_pca.R | 134 ++++------ tidyMicro-1.47/tidyMicro/R/tidy_micro.R | 50 ++- tidyMicro-1.47/tidyMicro/R/tidy_micro_helper.R | 6 tidyMicro-1.47/tidyMicro/README.md | 39 +- tidyMicro-1.47/tidyMicro/build/vignette.rds |binary tidyMicro-1.47/tidyMicro/data/bpd_cla.rda |only tidyMicro-1.47/tidyMicro/data/bpd_clin.rda |only tidyMicro-1.47/tidyMicro/data/bpd_fam.rda |only tidyMicro-1.47/tidyMicro/data/bpd_ord.rda |only tidyMicro-1.47/tidyMicro/data/bpd_phy.rda |only tidyMicro-1.47/tidyMicro/data/mrsa_clin.rda |only tidyMicro-1.47/tidyMicro/data/mrsa_gen.rda |only tidyMicro-1.47/tidyMicro/inst/doc/tidy_micro_vignette.R |only tidyMicro-1.47/tidyMicro/inst/doc/tidy_micro_vignette.Rmd |only tidyMicro-1.47/tidyMicro/inst/doc/tidy_micro_vignette.html |only tidyMicro-1.47/tidyMicro/man/alpha_div.Rd | 7 tidyMicro-1.47/tidyMicro/man/bb_bars.Rd | 7 tidyMicro-1.47/tidyMicro/man/bb_mods.Rd | 7 tidyMicro-1.47/tidyMicro/man/beta_div.Rd | 7 tidyMicro-1.47/tidyMicro/man/beta_heatmap.Rd | 7 tidyMicro-1.47/tidyMicro/man/bpd_cla.Rd |only tidyMicro-1.47/tidyMicro/man/bpd_clin.Rd |only tidyMicro-1.47/tidyMicro/man/bpd_fam.Rd |only tidyMicro-1.47/tidyMicro/man/bpd_ord.Rd |only tidyMicro-1.47/tidyMicro/man/bpd_phy.Rd |only tidyMicro-1.47/tidyMicro/man/cor_heatmap.Rd | 8 tidyMicro-1.47/tidyMicro/man/cor_rocky_mtn.Rd | 9 tidyMicro-1.47/tidyMicro/man/micro_PERMANOVA.Rd | 8 tidyMicro-1.47/tidyMicro/man/micro_alpha_reg.Rd | 8 tidyMicro-1.47/tidyMicro/man/micro_chisq.Rd | 4 tidyMicro-1.47/tidyMicro/man/micro_forest.Rd | 7 tidyMicro-1.47/tidyMicro/man/micro_heatmap.Rd | 7 tidyMicro-1.47/tidyMicro/man/micro_otu.Rd |only tidyMicro-1.47/tidyMicro/man/micro_pca.Rd | 22 - tidyMicro-1.47/tidyMicro/man/micro_rank_sum.Rd | 4 tidyMicro-1.47/tidyMicro/man/micro_rocky_mtn.Rd | 7 tidyMicro-1.47/tidyMicro/man/mrsa_clin.Rd |only tidyMicro-1.47/tidyMicro/man/mrsa_gen.Rd |only tidyMicro-1.47/tidyMicro/man/nb_bars.Rd | 8 tidyMicro-1.47/tidyMicro/man/nb_mods.Rd | 7 tidyMicro-1.47/tidyMicro/man/otu_filter.Rd | 7 tidyMicro-1.47/tidyMicro/man/pca_3d.Rd | 40 +- tidyMicro-1.47/tidyMicro/man/ra_bars.Rd | 7 tidyMicro-1.47/tidyMicro/man/taxa_boxplot.Rd | 8 tidyMicro-1.47/tidyMicro/man/taxa_summary.Rd | 7 tidyMicro-1.47/tidyMicro/man/three_mode.Rd | 19 - tidyMicro-1.47/tidyMicro/man/tidy_micro.Rd | 32 +- tidyMicro-1.47/tidyMicro/tests |only tidyMicro-1.47/tidyMicro/vignettes/tidy_micro_vignette.Rmd |only 104 files changed, 638 insertions(+), 469 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 1.0.2 dated 2020-07-05 and 1.0.3 dated 2020-09-13
ubiquity-1.0.2/ubiquity/inst/ubinc/systems/system-one_cmt_macro.txt |only ubiquity-1.0.2/ubiquity/inst/ubinc/systems/system-two_cmt_macro.txt |only ubiquity-1.0.3/ubiquity/DESCRIPTION | 18 ubiquity-1.0.3/ubiquity/MD5 | 74 - ubiquity-1.0.3/ubiquity/NAMESPACE | 6 ubiquity-1.0.3/ubiquity/R/ubiquity.r | 370 ++++--- ubiquity-1.0.3/ubiquity/README.md | 15 ubiquity-1.0.3/ubiquity/build/vignette.rds |binary ubiquity-1.0.3/ubiquity/inst/doc/Deployment.Rmd | 4 ubiquity-1.0.3/ubiquity/inst/doc/Deployment.html | 126 +- ubiquity-1.0.3/ubiquity/inst/doc/Estimation.Rmd | 4 ubiquity-1.0.3/ubiquity/inst/doc/Estimation.html | 518 +++++----- ubiquity-1.0.3/ubiquity/inst/doc/Language.Rmd | 8 ubiquity-1.0.3/ubiquity/inst/doc/Language.html | 37 ubiquity-1.0.3/ubiquity/inst/doc/NCA.Rmd | 2 ubiquity-1.0.3/ubiquity/inst/doc/NCA.html | 212 ++-- ubiquity-1.0.3/ubiquity/inst/doc/Reporting.html | 418 ++++---- ubiquity-1.0.3/ubiquity/inst/doc/Simulation.Rmd | 4 ubiquity-1.0.3/ubiquity/inst/doc/Simulation.html | 186 +-- ubiquity-1.0.3/ubiquity/inst/doc/Titration.Rmd | 4 ubiquity-1.0.3/ubiquity/inst/doc/Titration.html | 292 ++--- ubiquity-1.0.3/ubiquity/inst/ubinc/scripts/analysis_multiple_file.r | 7 ubiquity-1.0.3/ubiquity/inst/ubinc/scripts/make_report_PowerPoint.R | 191 +++ ubiquity-1.0.3/ubiquity/inst/ubinc/scripts/make_report_Word.R | 228 ++++ ubiquity-1.0.3/ubiquity/inst/ubinc/scripts/ubiquity_fcns.R | 370 ++++--- ubiquity-1.0.3/ubiquity/inst/ubinc/systems/system-one_cmt_cl.txt |only ubiquity-1.0.3/ubiquity/inst/ubinc/systems/system-two_cmt_cl.txt |only ubiquity-1.0.3/ubiquity/inst/ubinc/templates/r_components.R | 2 ubiquity-1.0.3/ubiquity/inst/ubinc/templates/r_nca.R | 2 ubiquity-1.0.3/ubiquity/inst/ubinc/templates/r_simulation_driver.R | 1 ubiquity-1.0.3/ubiquity/inst/ubinc/templates/ubiquity_server.R | 4 ubiquity-1.0.3/ubiquity/man/system_load_data.Rd | 2 ubiquity-1.0.3/ubiquity/man/system_new.Rd | 6 ubiquity-1.0.3/ubiquity/man/system_set_option.Rd | 11 ubiquity-1.0.3/ubiquity/vignettes/Deployment.Rmd | 4 ubiquity-1.0.3/ubiquity/vignettes/Estimation.Rmd | 4 ubiquity-1.0.3/ubiquity/vignettes/Language.Rmd | 8 ubiquity-1.0.3/ubiquity/vignettes/NCA.Rmd | 2 ubiquity-1.0.3/ubiquity/vignettes/Simulation.Rmd | 4 ubiquity-1.0.3/ubiquity/vignettes/Titration.Rmd | 4 40 files changed, 1907 insertions(+), 1241 deletions(-)
Title: Tidy RSS for R
Description: With the objective of including data from RSS feeds into your analysis,
'tidyRSS' parses RSS, Atom and JSON feeds and returns a tidy data frame.
Author: Robert Myles McDonnell [aut, cre],
Jonathan Carroll [ctb],
Mike Smith [ctb],
Joseph Stachelek [ctb]
Maintainer: Robert Myles McDonnell <robertmylesmcdonnell@gmail.com>
Diff between tidyRSS versions 2.0.2 dated 2020-06-01 and 2.0.3 dated 2020-09-13
DESCRIPTION | 21 +++++++++++++++------ MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 7 +++++++ R/clean_up.R | 6 +++++- R/tidyfeed.R | 1 + tests/testthat/test_general.R | 2 ++ 7 files changed, 37 insertions(+), 13 deletions(-)
Title: Obtaining Star Schemas from Flat Tables
Description: Data in multidimensional systems is obtained from
operational systems and is transformed to adapt it to the new
structure. Frequently, the operations to be performed aim to
transform a flat table into a star schema. Transformations can
be carried out using professional ETL (extract, transform and
load) tools or tools intended for data transformation for end
users. With the tools mentioned, this transformation can be
carried out, but it requires a lot of work. The main objective
this package is to define transformations that allow obtaining
star schemas from flat tables easily. In addition, it includes
basic data cleaning, dimension enrichment, incremental data
refresh and query operations, adapted to this context.
Author: Jose Samos [aut, cre, cph] (<https://orcid.org/0000-0002-4457-3439>)
Maintainer: Jose Samos <jsamos@ugr.es>
Diff between starschemar versions 1.0.0 dated 2020-08-07 and 1.1.0 dated 2020-09-13
DESCRIPTION | 12 MD5 | 108 + NAMESPACE | 34 NEWS.md | 14 R/common.R | 10 R/constellation_purge_dimensions.R |only R/data.R | 48 R/dimensional_model_define_fact.R | 2 R/dimensional_query.R |only R/dimensional_query_filter_dimension.R |only R/dimensional_query_run_query.R |only R/dimensional_query_select_dimension.R |only R/dimensional_query_select_fact.R |only R/fact_table.R | 31 R/multistar.R | 4 R/multistar_as_flat_table.R |only R/star_schema_enrich_dimension.R |only R/star_schema_filter_fact_rows.R |only R/star_schema_purge_dimensions.R |only R/star_schema_rename.R |only R/starschemar.R | 60 README.md | 11 data/ft_datagov_uk.rda |only data/ms_mrs.rda |only data/ms_mrs_test.rda |only inst/doc/starschemar.R | 249 ++++ inst/doc/starschemar.Rmd | 426 ++++++ inst/doc/starschemar.html | 1178 ++++++++++++++----- man/constellation_as_multistar.Rd | 1 man/constellation_as_tibble_list.Rd | 1 man/define_fact.Rd | 2 man/define_selected_dimensions.Rd |only man/define_selected_facts.Rd |only man/delete_unused_foreign_keys.Rd |only man/dimensional_query.Rd |only man/enrich_dimension_export.Rd |only man/enrich_dimension_import.Rd |only man/filter_dimension.Rd |only man/filter_fact_rows.Rd |only man/filter_selected_instances.Rd |only man/ft_datagov_uk.Rd |only man/get_dimension_attribute_names.Rd |only man/get_measure_names.Rd |only man/get_role_dimension_names.Rd |only man/group_facts.Rd |only man/incremental_refresh_constellation.Rd | 5 man/incremental_refresh_star_schema.Rd | 5 man/ms_mrs.Rd |only man/ms_mrs_test.Rd |only man/multistar_as_flat_table.Rd |only man/new_dimensional_query.Rd |only man/purge_dimensions_constellation.Rd |only man/purge_dimensions_star_schema.Rd |only man/remove_duplicate_dimension_rows.Rd |only man/rename_dimension.Rd |only man/rename_dimension_attributes.Rd |only man/rename_fact.Rd |only man/rename_measures.Rd |only man/run_query.Rd |only man/select_dimension.Rd |only man/select_fact.Rd |only man/set_fact_name.Rd |only man/star_schema_as_flat_table.Rd | 1 man/star_schema_as_multistar.Rd | 1 man/star_schema_as_tibble_list.Rd | 1 man/starschemar.Rd | 73 + man/unify_facts_by_grain.Rd |only tests/testthat/test-dimensional_query.R |only tests/testthat/test-enrich_dimension_export.R |only tests/testthat/test-enrich_dimension_import.R |only tests/testthat/test-filter_dimension.R |only tests/testthat/test-filter_fact_rows.R |only tests/testthat/test-get_dimension_attribute_names.R |only tests/testthat/test-get_measure_names.R |only tests/testthat/test-multistar_as_flat_table.R |only tests/testthat/test-purge_dimensions.R |only tests/testthat/test-purge_dimensions_constellation.R |only tests/testthat/test-purge_dimensions_star_schema.R |only tests/testthat/test-rename_dimension.R |only tests/testthat/test-rename_dimension_attributes.R |only tests/testthat/test-rename_fact.R |only tests/testthat/test-rename_measures.R |only tests/testthat/test-run_query.R |only tests/testthat/test-select_dimension.R |only tests/testthat/test-select_fact.R |only vignettes/starschemar.Rmd | 426 ++++++ 86 files changed, 2369 insertions(+), 334 deletions(-)
Title: The Moving Epidemic Method
Description: The Moving Epidemic Method, created by T Vega and JE Lozano (2012, 2015) <doi:10.1111/j.1750-2659.2012.00422.x>, <doi:10.1111/irv.12330>, allows the weekly assessment of the epidemic and intensity status to help in routine respiratory infections surveillance in health systems. Allows the comparison of different epidemic indicators, timing and shape with past epidemics and across different regions or countries with different surveillance systems. Also, it gives a measure of the performance of the method in terms of sensitivity and specificity of the alert week.
Author: Jose E. Lozano [aut, cre]
Maintainer: Jose E. Lozano <lozalojo@gmail.com>
Diff between mem versions 2.15 dated 2019-05-28 and 2.16 dated 2020-09-13
DESCRIPTION | 12 MD5 | 98 +++---- NAMESPACE | 4 R/calcular.map.R | 2 R/create.calendar.R |only R/flucyl.R | 6 R/flucylraw.R | 6 R/full.series.graph.R | 6 R/get.dates.R |only R/get.epiweek.R |only R/memgoodness.R | 2 R/memsurveillance.R | 44 +-- R/memsurveillance.animated.R | 14 - R/optimum.by.inspection.R | 8 R/percentage.added.R | 7 R/processPlots.R | 6 R/transformdata.R | 13 R/transformseries.multiple.R | 474 ++++++++++++++++++++-------------- man/calcular.indicadores.2.timings.Rd | 38 +- man/calcular.indicadores.Rd | 42 +-- man/create.calendar.Rd |only man/epimem.Rd | 74 ++--- man/epitiming.Rd | 50 +-- man/flucyl.Rd | 104 +++---- man/flucylraw.Rd | 92 +++--- man/full.series.graph.Rd | 210 ++++++++------- man/get.dates.Rd |only man/get.epiweek.Rd |only man/iconfianza.Rd | 13 man/iconfianza.aritmetica.Rd | 3 man/iconfianza.geometrica.Rd | 3 man/iconfianza.percentil.boot.Rd | 11 man/iconfianza.percentil.eqnpar.Rd | 3 man/iconfianza.percentil.kc.Rd | 10 man/mem-package.Rd | 46 +-- man/memevolution.Rd | 176 ++++++------ man/memgoodness.Rd | 350 +++++++++++++------------ man/memintensity.Rd | 174 ++++++------ man/memmodel.Rd | 418 +++++++++++++++-------------- man/memstability.Rd | 122 ++++---- man/memsurveillance.Rd | 310 +++++++++++----------- man/memsurveillance.animated.Rd | 180 ++++++------ man/memtiming.Rd | 227 ++++++++-------- man/memtrend.Rd | 179 ++++++------ man/optimal.tickmarks.Rd | 39 +- man/optimum.by.inspection.Rd | 149 +++++----- man/processPlots.Rd | 108 ++++--- man/roc.analysis.Rd | 173 ++++++------ man/transformdata.Rd | 129 ++++----- man/transformdata.back.Rd | 123 ++++---- man/transformseries.Rd | 152 +++++----- man/transformseries.multiple.Rd | 39 +- man/transformseries.twowaves.Rd | 10 53 files changed, 2390 insertions(+), 2069 deletions(-)
Title: DTR Estimation and Inference via G-Estimation, Dynamic WOLS,
Q-Learning, and Dynamic Weighted Survival Modeling (DWSurv)
Description: Dynamic treatment regime estimation and inference via G-estimation, dynamic weighted ordinary least squares (dWOLS) and Q-learning. Inference via bootstrap and (for G-estimation) recursive sandwich estimation. Estimation and inference for survival outcomes via Dynamic Weighted Survival Modeling (DWSurv). Extension to continuous treatment variables (gdwols). Wallace et al. (2017) <DOI:10.18637/jss.v080.i02>; Simoneau et al. (2020) <DOI:10.1080/00949655.2020.1793341>.
Author: Michael Wallace, Erica E M Moodie, David A Stephens, Gabrielle Simoneau and Juliana Schulz
Maintainer: Michael Wallace <michael.wallace@uwaterloo.ca>
Diff between DTRreg versions 1.6 dated 2020-08-11 and 1.7 dated 2020-09-13
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/confint.DTRreg.Rd | 5 +---- 3 files changed, 7 insertions(+), 10 deletions(-)
Title: Learning Sparse Bayesian Networks from High-Dimensional Data
Description: Fast methods for learning sparse Bayesian networks from high-dimensional data using sparse regularization, as described in Aragam, Gu, and Zhou (2017) <arXiv:1703.04025>. Designed to handle mixed experimental and observational data with thousands of variables with either continuous or discrete observations.
Author: Bryon Aragam [aut, cre],
Jiaying Gu [aut],
Dacheng Zhang [aut],
Qing Zhou [aut]
Maintainer: Bryon Aragam <sparsebn@gmail.com>
Diff between sparsebn versions 0.1.1 dated 2020-09-10 and 0.1.2 dated 2020-09-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 2 +- data/cytometryContinuous.rda |binary inst/doc/sparsebn-vignette.html | 22 +++++++++++----------- man/cytometryContinuous.Rd | 6 ++---- man/cytometryDiscrete.Rd | 6 ++---- man/pathfinder.Rd | 8 ++------ 8 files changed, 29 insertions(+), 37 deletions(-)
Title: Policy Learning via Doubly Robust Empirical Welfare Maximization
over Trees
Description: Learn optimal policies via doubly robust empirical
welfare maximization over trees. This package implements the multi-action doubly
robust approach of Zhou, Athey and Wager (2018) <arXiv:1810.04778> in the case where
we want to learn policies that belong to the class of depth k decision trees.
Author: Zhengyuan Zhou [aut],
Susan Athey [aut],
Stefan Wager [aut],
Ayush Kanodia [aut],
Erik Sverdrup [cre]
Maintainer: Erik Sverdrup <erikcs@stanford.edu>
Diff between policytree versions 1.0.2 dated 2020-09-09 and 1.0.3 dated 2020-09-13
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Rcppbindings.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Disciplined Convex Optimization
Description: An object-oriented modeling language for disciplined
convex programming (DCP) as described in Fu, Narasimhan, and Boyd
(2020, <doi:10.18637/jss.v094.i14>). It allows the user to
formulate convex optimization problems in a natural way following
mathematical convention and DCP rules. The system analyzes the
problem, verifies its convexity, converts it into a canonical
form, and hands it off to an appropriate solver to obtain the
solution. Interfaces to solvers on CRAN and elsewhere are
provided, both commercial and open source.
Author: Anqi Fu [aut, cre],
Balasubramanian Narasimhan [aut],
David W Kang [aut],
Steven Diamond [aut],
John Miller [aut],
Stephen Boyd [ctb],
Paul Kunsberg Rosenfield [ctb]
Maintainer: Anqi Fu <anqif@stanford.edu>
Diff between CVXR versions 1.0-1 dated 2020-04-02 and 1.0-8 dated 2020-09-13
DESCRIPTION | 30 MD5 | 55 - NEWS.md | 20 R/conic_solvers.R | 146 ++- R/reduction_solvers.R | 21 R/solver_utilities.R | 3 R/utilities.R | 3 README.md | 19 build/vignette.rds |binary inst/CITATION |only inst/doc/cvxr_intro.html | 23 inst/doc/version1.html | 19 man/CVXOPT-class.Rd | 30 src/RcppExports.cpp | 1 tests/testthat/test-g01-constraints.R | 34 tests/testthat/test-g01-convolution.R | 2 tests/testthat/test-g01-curvature.R | 9 tests/testthat/test-g01-domain.R | 27 tests/testthat/test-g01-expressions.R | 132 +- tests/testthat/test-g01-grad.R | 25 tests/testthat/test-g01-lin_ops.R | 9 tests/testthat/test-g01-linear_cone.R | 2 tests/testthat/test-g01-matrices.R | 5 tests/testthat/test-g01-monotonicity.R | 36 tests/testthat/test-g01-mosek_conif.R | 84 - tests/testthat/test-g01-nonlinear_atoms.R | 6 tests/testthat/test-g01-problem.R | 57 + tests/testthat/test-g01-solvers.R | 1407 +++++++++++++----------------- tests/testthat/test-g05-solver_tests.R | 11 29 files changed, 1232 insertions(+), 984 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to
encode spatial vector data. Binds to 'GDAL' for reading and writing
data, to 'GEOS' for geometrical operations, and to 'PROJ' for
projection conversions and datum transformations. Optionally uses the 's2'
package for spherical geometry operations on geographic coordinates.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>),
Etienne Racine [ctb],
Michael Sumner [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Kirill Müller [ctb],
Thomas Lin Pedersen [ctb],
Dan Baston [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 0.9-5 dated 2020-07-14 and 0.9-6 dated 2020-09-13
DESCRIPTION | 8 MD5 | 136 +++---- NAMESPACE | 3 NEWS.md | 26 + R/RcppExports.R | 56 ++- R/crs.R | 11 R/gdal_utils.R | 38 +- R/geom-predicates.R | 62 +-- R/geom-transformers.R | 60 ++- R/init.R | 16 R/make_grid.R | 20 - R/plot.R | 4 R/read.R | 2 R/s2.R | 7 R/sample.R | 49 +- R/sfc.R | 8 R/sp.R | 7 R/tidyverse.R | 16 R/transform.R | 10 R/wkt.R | 6 configure | 14 inst/doc/sf1.R | 2 inst/doc/sf1.Rmd | 27 - inst/doc/sf1.html | 764 +++++++++++++++----------------------------- inst/doc/sf2.R | 2 inst/doc/sf2.Rmd | 17 inst/doc/sf2.html | 518 ++++++++--------------------- inst/doc/sf3.Rmd | 13 inst/doc/sf3.html | 704 +++++++++++++--------------------------- inst/doc/sf4.Rmd | 13 inst/doc/sf4.html | 443 ++++++------------------- inst/doc/sf5.R | 14 inst/doc/sf5.Rmd | 17 inst/doc/sf5.html | 522 ++++++++---------------------- inst/doc/sf6.Rmd | 13 inst/doc/sf6.html | 399 +++++----------------- inst/doc/sf7.R | 90 ++++- inst/doc/sf7.Rmd | 238 ++++++++++--- inst/doc/sf7.html | 599 +++++++++++++--------------------- inst/docker/static |only man/gdal_utils.Rd | 10 man/geos_binary_ops.Rd | 16 man/geos_binary_pred.Rd | 6 man/geos_combine.Rd | 4 man/geos_unary.Rd | 4 man/plot.Rd | 2 man/s2.Rd | 3 man/sf_proj_search_paths.Rd |only man/sfc.Rd | 7 man/st_as_sfc.Rd | 2 man/st_as_text.Rd | 4 man/st_make_grid.Rd | 12 man/st_sample.Rd | 22 - man/st_write.Rd | 2 man/stars.Rd | 1 src/RcppExports.cpp | 144 +++++--- src/gdal.cpp | 41 +- src/gdal_utils.cpp | 263 +++++++++++---- src/geos.cpp | 15 src/stars.cpp | 7 tests/crs.R | 10 tests/s2.R | 18 + tests/testthat/test_geos.R | 17 vignettes/sf1.Rmd | 27 - vignettes/sf2.Rmd | 17 vignettes/sf3.Rmd | 13 vignettes/sf4.Rmd | 13 vignettes/sf5.Rmd | 17 vignettes/sf6.Rmd | 13 vignettes/sf7.Rmd | 238 ++++++++++--- 70 files changed, 2570 insertions(+), 3332 deletions(-)
Title: Rho for Inter Rater Reliability
Description: Rho is used to test the generalization of inter rater reliability
(IRR) statistics. Calculating rho starts by generating a large number of
simulated, fully-coded data sets: a sizable collection of hypothetical
populations, all of which have a kappa value below a given threshold -- which
indicates unacceptable agreement. Then kappa is calculated on a sample from
each of those sets in the collection to see if it is equal to or higher than
the kappa in then real sample. If less than five percent of the distribution
of samples from the simulated data sets is greater than actual observed kappa,
the null hypothesis is rejected and one can conclude that if the two raters had
coded the rest of the data, we would have acceptable agreement (kappa above the
threshold).
Author: Brendan Eagan [aut],
Brad Rogers [aut],
Rebecca Pozen [aut],
Cody L Marquart [cre, aut] (<https://orcid.org/0000-0002-3387-6792>),
David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
Diff between rhoR versions 1.3.0.2 dated 2019-12-06 and 1.3.0.3 dated 2020-09-13
rhoR-1.3.0.2/rhoR/data/codeSet.csv.gz |only rhoR-1.3.0.2/rhoR/data/contingencyTable.csv.gz |only rhoR-1.3.0.2/rhoR/inst/coverage |only rhoR-1.3.0.3/rhoR/DESCRIPTION | 10 ++- rhoR-1.3.0.3/rhoR/MD5 | 65 ++++++---------------- rhoR-1.3.0.3/rhoR/NEWS.md | 5 + rhoR-1.3.0.3/rhoR/R/rhoR.R | 2 rhoR-1.3.0.3/rhoR/README.md | 13 +--- rhoR-1.3.0.3/rhoR/data/codeSet.csv |only rhoR-1.3.0.3/rhoR/data/contingencyTable.csv |only rhoR-1.3.0.3/rhoR/inst/_pkgdown.yml | 5 + rhoR-1.3.0.3/rhoR/man/codeSet.Rd | 4 + rhoR-1.3.0.3/rhoR/man/contingencyTable.Rd | 4 + rhoR-1.3.0.3/rhoR/man/createSimulatedCodeSet.Rd | 12 +++- rhoR-1.3.0.3/rhoR/man/generateKPs_c.Rd | 12 +++- rhoR-1.3.0.3/rhoR/man/random_contingency_table.Rd | 10 ++- rhoR-1.3.0.3/rhoR/man/rho.Rd | 16 ++++- rhoR-1.3.0.3/rhoR/man/rho.file.Rd | 17 ++++- rhoR-1.3.0.3/rhoR/man/rhoCT.Rd | 14 +++- rhoR-1.3.0.3/rhoR/man/rhoK.Rd | 17 ++++- rhoR-1.3.0.3/rhoR/man/rhoR.Rd | 2 rhoR-1.3.0.3/rhoR/man/rhoSet.Rd | 14 +++- rhoR-1.3.0.3/rhoR/tests/testthat/test-rhoFile.R | 4 - 23 files changed, 134 insertions(+), 92 deletions(-)
Title: Project MOSAIC Data Sets
Description: Data sets from Project MOSAIC (<http://mosaic-web.org>) used
to teach mathematics, statistics, computation and modeling. Funded by the
NSF, Project MOSAIC is a community of educators working to tie together
aspects of quantitative work that students in science, technology,
engineering and mathematics will need in their professional lives, but
which are usually taught in isolation, if at all.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel Kaplan
<kaplan@macalester.edu>, Nicholas Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between mosaicData versions 0.18.0 dated 2020-05-15 and 0.20.1 dated 2020-09-13
DESCRIPTION | 9 ++--- MD5 | 42 ++++++++++++------------- NEWS.md | 6 +++ R/SaratogaHousesDoc.R | 2 - R/Weather.R | 2 - R/datasetsDoc.R | 82 ++++++++++++++++++++++++++------------------------ data/Alcohol.rda |binary data/Gestation.rda |binary data/HELPmiss.rda |binary data/HELPrct.rda |binary data/Marriage.rda |binary data/Weather.rda |binary man/Alcohol.Rd | 2 - man/CPS85.Rd | 2 - man/Gestation.Rd | 41 ++++++++++--------------- man/HELPrct.Rd | 1 man/HeatX.Rd | 13 ++++--- man/Marriage.Rd | 5 +-- man/Mites.Rd | 8 ++++ man/SaratogaHouses.Rd | 2 - man/SnowGR.Rd | 10 +++--- man/Weather.Rd | 2 - 22 files changed, 121 insertions(+), 108 deletions(-)
Title: Common Utilities for Other MOSAIC-Family Packages
Description: Common utilities used in other MOSAIC-family packages are
collected here.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel T. Kaplan
<kaplan@macalester.edu>, Nicholas J. Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between mosaicCore versions 0.6.0 dated 2018-06-24 and 0.8.0 dated 2020-09-13
DESCRIPTION | 11 +-- MD5 | 62 +++++++++-------- NAMESPACE | 8 +- NEWS.md | 14 +++- R/ashplots.R | 1 R/df_stats.R | 142 ++++++++++++++++++++++++++++++++--------- R/ediff.R | 5 - R/formulas.R | 20 ++--- R/inspect.R | 10 +- R/interval-statistics.R | 2 R/makeFun.R | 2 R/nmissing.R | 4 - R/parse_call.R |only R/tally.R | 37 ++++------ README.md | 1 man/coef.Rd | 2 man/df_stats.Rd | 54 ++++++++++----- man/ediff.Rd | 16 ++-- man/evalFormula.Rd | 2 man/formularise.Rd | 7 +- man/inspect.Rd | 3 man/interval_statistics.Rd | 12 ++- man/makeFun.Rd | 21 ++++-- man/mosaicformula.Rd | 18 ++++- man/msummary.Rd | 16 +++- man/n_missing.Rd | 4 - man/na.warn.Rd | 2 man/prop.Rd | 16 +++- man/props.Rd | 4 - man/rhs_or_expr.Rd |only man/tally.Rd | 24 ++++-- tests/testthat/test-df-stats.R | 58 ++++++++++------ tests/testthat/test-tally.R | 23 ++++++ 33 files changed, 395 insertions(+), 206 deletions(-)
Title: Functions for Plotting Graphical Shapes, Colors
Description: Functions for plotting graphical shapes
such as ellipses, circles, cylinders, arrows, ...
Author: Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between shape versions 1.4.4 dated 2018-02-07 and 1.4.5 dated 2020-09-13
DESCRIPTION | 11 MD5 | 16 R/Arrowhead.R | 4 R/Arrows.R | 3 build/vignette.rds |binary inst/doc/shape.R | 1113 ++++++++++++++++++++++++++--------------------------- inst/doc/shape.pdf |binary man/Arrowhead.Rd | 2 man/Arrows.Rd | 2 9 files changed, 577 insertions(+), 574 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>),
Giuseppe Casalicchio [ctb] (<https://orcid.org/0000-0001-5324-5966>),
Stefan Coors [ctb] (<https://orcid.org/0000-0002-7465-2146>),
Quay Au [ctb] (<https://orcid.org/0000-0002-5252-8902>),
Martin Binder [aut]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3 versions 0.5.0 dated 2020-08-07 and 0.6.0 dated 2020-09-13
DESCRIPTION | 20 +- MD5 | 164 +++++++++++---------- NAMESPACE | 32 +++- NEWS.md | 10 + R/BenchmarkResult.R | 217 +++++++++++++++++++--------- R/Learner.R | 32 ++-- R/LearnerClassifDebug.R | 2 R/LearnerClassifFeatureless.R | 4 R/LearnerClassifRpart.R | 9 - R/LearnerRegrFeatureless.R | 2 R/LearnerRegrRpart.R | 2 R/Measure.R | 77 +++++++-- R/MeasureClassifCosts.R | 2 R/MeasureSelectedFeatures.R | 2 R/Prediction.R | 28 ++- R/PredictionClassif.R | 102 ++----------- R/PredictionData.R |only R/PredictionDataClassif.R |only R/PredictionDataRegr.R |only R/PredictionRegr.R | 100 ++---------- R/ResampleResult.R | 185 ++++++++++++++--------- R/ResamplingCV.R | 2 R/ResamplingRepeatedCV.R | 2 R/Task.R | 17 +- R/TaskClassif.R | 11 + R/TaskClassif_breast_cancer.R | 4 R/TaskGenerator2DNormals.R | 2 R/TaskGeneratorCassini.R | 2 R/TaskGeneratorCircle.R | 2 R/TaskGeneratorMoons.R | 4 R/TaskGeneratorSimplex.R | 2 R/TaskGeneratorSmiley.R | 2 R/TaskGeneratorSpirals.R | 2 R/TaskGeneratorXor.R | 2 R/TaskRegr.R | 7 R/TaskRegr_boston_housing.R | 5 R/TaskRegr_mtcars.R | 2 R/TaskSupervised.R | 5 R/as_data_backend.R | 5 R/benchmark.R | 11 - R/helper.R | 62 ++------ R/helper_R6.R |only R/helper_future.R |only R/mlr_coercions.R | 2 R/mlr_resamplings.R | 11 + R/mlr_tasks.R | 8 - R/resample.R | 13 + R/task_converters.R |only R/worker.R | 42 +---- R/zzz.R | 3 README.md | 210 +++++++++++++-------------- build/partial.rdb |binary inst/references.bib | 2 inst/testthat/helper_expectations.R | 21 ++ man/BenchmarkResult.Rd | 51 ++++-- man/Learner.Rd | 5 man/Measure.Rd | 8 - man/PredictionClassif.Rd | 9 - man/PredictionData.Rd |only man/PredictionRegr.Rd | 9 - man/ResampleResult.Rd | 73 ++++++--- man/Task.Rd | 10 + man/TaskClassif.Rd | 6 man/TaskRegr.Rd | 6 man/TaskSupervised.Rd | 6 man/as_data_backend.Rd | 3 man/as_resample_result.Rd |only man/convert_task.Rd |only man/figures/mlr3verse.svg | 2 man/mlr_coercions.Rd | 2 man/mlr_learners_classif.featureless.Rd | 2 man/mlr_task_generators_2dnormals.Rd | 2 man/mlr_task_generators_cassini.Rd | 2 man/mlr_task_generators_circle.Rd | 2 man/mlr_task_generators_moons.Rd | 2 man/mlr_task_generators_simplex.Rd | 2 man/mlr_task_generators_smiley.Rd | 2 man/mlr_task_generators_spirals.Rd | 2 man/mlr_task_generators_xor.Rd | 2 man/mlr_tasks_breast_cancer.Rd | 1 tests/testthat/test_DataBackendMatrix.R | 11 - tests/testthat/test_Learner.R | 3 tests/testthat/test_PredictionClassif.R | 4 tests/testthat/test_PredictionDataClassif.R |only tests/testthat/test_PredictionDataRegr.R |only tests/testthat/test_PredictionRegr.R | 6 tests/testthat/test_benchmark.R | 20 +- tests/testthat/test_convert_task.R |only tests/testthat/test_resample.R | 17 -- 89 files changed, 976 insertions(+), 747 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects from statistical models and returns the
result as tidy data frames. These data frames are ready to use with the
'ggplot2'-package. Marginal effects can be calculated for many different
models. Interaction terms, splines and polynomial terms are also supported.
The main functions are ggpredict(), ggemmeans() and ggeffect(). There is a
generic plot()-method to plot the results using 'ggplot2'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Sam Crawley [ctb] (<https://orcid.org/0000-0002-7847-0411>),
Mattan S. Ben-Shachar [ctb] (<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between ggeffects versions 0.15.1 dated 2020-07-27 and 0.16.0 dated 2020-09-13
DESCRIPTION | 16 MD5 | 86 +- NAMESPACE | 5 NEWS.md | 20 R/get_predictions_mlogit.R |only R/get_predictions_stan.R | 3 R/getter.R | 2 R/ggeffect.R | 7 R/ggemmeans.R | 2 R/ggpredict.R | 2 R/plot.R | 426 ++++++++--- R/post_processing_predictions.R | 2 R/predict_zero_inflation.R | 48 - R/predictions.R | 2 R/print.R | 8 R/residualize_over_grid.R |only R/utils.R | 17 R/utils_check_transformations.R | 9 R/utils_get_data_grid.R | 30 R/utils_model_function.R | 11 README.md | 17 build/partial.rdb |binary build/vignette.rds |binary inst/doc/ggeffects.html | 830 +++++++++++------------ inst/doc/introduction_effectsatvalues.R | 8 inst/doc/introduction_effectsatvalues.Rmd | 13 inst/doc/introduction_effectsatvalues.html | 491 ++++++------- inst/doc/introduction_partial_residuals.R |only inst/doc/introduction_partial_residuals.Rmd |only inst/doc/introduction_partial_residuals.html |only inst/doc/introduction_plotcustomize.html | 132 +-- inst/doc/introduction_plotmethod.html | 214 ++--- inst/doc/introduction_randomeffects.html | 464 ++++++------ inst/doc/practical_logisticmixedmodel.html | 250 +++--- inst/doc/practical_robustestimation.html | 230 ++---- inst/doc/technical_differencepredictemmeans.html | 310 +++----- inst/doc/technical_stata.html | 104 +- man/get_title.Rd | 2 man/plot.Rd | 372 +++++----- tests/testthat/test-glmrob_base.R | 4 tests/testthat/test-ivreg.R | 4 tests/testthat/test-lrm.R | 2 tests/testthat/test-rq.R | 2 tests/testthat/test-survreg.R | 2 tests/testthat/test-tobit.R | 1 vignettes/introduction_effectsatvalues.Rmd | 13 vignettes/introduction_partial_residuals.Rmd |only 47 files changed, 2039 insertions(+), 2122 deletions(-)
Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
Description: Calculates the Delaunay triangulation and the Dirichlet
or Voronoi tessellation (with respect to the entire plane) of
a planar point set. Plots triangulations and tessellations in
various ways. Clips tessellations to sub-windows. Calculates
perimeters of tessellations. Summarises information about the
tiles of the tessellation.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between deldir versions 0.1-28 dated 2020-07-15 and 0.1-29 dated 2020-09-13
ChangeLog | 31 ++++++++++ DESCRIPTION | 8 +- MD5 | 16 ++--- R/First.R | 9 +++ R/deldir.R | 6 +- R/plot.deldir.R | 124 ++++++++++++++++++++++++++++++++++------- man/deldir.Rd | 10 +-- man/plot.deldir.Rd | 158 ++++++++++++++++++++++++++++++++++++++++------------- man/triMat.Rd | 2 9 files changed, 285 insertions(+), 79 deletions(-)
Title: Causal Modeling with Coincidence Analysis
Description: Provides comprehensive functionalities for causal modeling with Coincidence Analysis (CNA), which is a configurational comparative method of causal data analysis that was first introduced in Baumgartner (2009) <doi:10.1177/0049124109339369>, and generalized in Baumgartner & Ambuehl (2018) <doi:10.1017/psrm.2018.45>. CNA is designed to recover INUS-causation from data, which is particularly relevant for analyzing processes featuring conjunctural causation (component causation) and equifinality (alternative causation). CNA is currently the only method for INUS-discovery that allows for multiple effects (outcomes/endogenous factors), meaning it can analyze common-cause and causal chain structures.
Author: Mathias Ambuehl [aut, cre, cph],
Michael Baumgartner [aut, cph],
Ruedi Epple [ctb],
Veli-Pekka Parkkinen [ctb],
Alrik Thiem [ctb]
Maintainer: Mathias Ambuehl <mathias.ambuehl@consultag.ch>
Diff between cna versions 2.2.3 dated 2020-05-13 and 3.0.0 dated 2020-09-13
cna-2.2.3/cna/R/full.tt.R |only cna-2.2.3/cna/R/qcondtype.R |only cna-2.2.3/cna/R/truthTab.r |only cna-2.2.3/cna/R/tt2df.r |only cna-2.2.3/cna/man/full.tt.Rd |only cna-2.2.3/cna/man/truthTab.Rd |only cna-2.2.3/cna/man/tt2df.Rd |only cna-3.0.0/cna/DESCRIPTION | 14 cna-3.0.0/cna/MD5 | 142 - cna-3.0.0/cna/NAMESPACE | 59 cna-3.0.0/cna/R/RcppExports.R | 4 cna-3.0.0/cna/R/allCombs_makefuzzy.r | 10 cna-3.0.0/cna/R/cna-deprecated.R |only cna-3.0.0/cna/R/cna.r | 158 +- cna-3.0.0/cna/R/cna_aux.r | 92 - cna-3.0.0/cna/R/coherence.r | 43 cna-3.0.0/cna/R/condTbl.r | 53 cna-3.0.0/cna/R/condition.r | 115 - cna-3.0.0/cna/R/condition_aux.R | 2 cna-3.0.0/cna/R/configTable.R |only cna-3.0.0/cna/R/csf.R | 202 ++ cna-3.0.0/cna/R/ct2df.r |only cna-3.0.0/cna/R/cyclic.R | 88 - cna-3.0.0/cna/R/details.R | 101 - cna-3.0.0/cna/R/equivClass.R | 4 cna-3.0.0/cna/R/exfaith.R | 50 cna-3.0.0/cna/R/exhaustive.R | 30 cna-3.0.0/cna/R/full.ct.R |only cna-3.0.0/cna/R/getCondtype.R |only cna-3.0.0/cna/R/is.inus.R | 257 ++- cna-3.0.0/cna/R/is.submodel.R | 6 cna-3.0.0/cna/R/minimalize.R | 23 cna-3.0.0/cna/R/minimalizeCsf.R | 98 - cna-3.0.0/cna/R/misc_aux.R | 8 cna-3.0.0/cna/R/print.cna.r | 45 cna-3.0.0/cna/R/print.condList.R | 6 cna-3.0.0/cna/R/print.condition.R | 16 cna-3.0.0/cna/R/qcond.R | 11 cna-3.0.0/cna/R/randomConds.R | 14 cna-3.0.0/cna/R/redundant.R | 55 cna-3.0.0/cna/R/rreduce.R | 24 cna-3.0.0/cna/R/selectCases.r | 22 cna-3.0.0/cna/R/some.r | 10 cna-3.0.0/cna/R/standard.R | 1 cna-3.0.0/cna/build/vignette.rds |binary cna-3.0.0/cna/inst/NEWS | 13 cna-3.0.0/cna/inst/doc/cna_vignette.R | 242 +-- cna-3.0.0/cna/inst/doc/cna_vignette.Rnw | 2426 ++++++++++++++++--------------- cna-3.0.0/cna/inst/doc/cna_vignette.pdf |binary cna-3.0.0/cna/man/allCombs.Rd | 148 - cna-3.0.0/cna/man/cna-deprecated.Rd |only cna-3.0.0/cna/man/cna-package.Rd | 33 cna-3.0.0/cna/man/cna.Rd | 962 ++++++------ cna-3.0.0/cna/man/coherence.Rd | 89 - cna-3.0.0/cna/man/condTbl.Rd | 108 - cna-3.0.0/cna/man/condition.Rd | 473 +++--- cna-3.0.0/cna/man/configTable.Rd |only cna-3.0.0/cna/man/ct2df.Rd |only cna-3.0.0/cna/man/cyclic.Rd | 196 +- cna-3.0.0/cna/man/d.autonomy.Rd | 84 - cna-3.0.0/cna/man/d.educate.Rd | 62 cna-3.0.0/cna/man/d.jobsecurity.Rd | 88 - cna-3.0.0/cna/man/d.minaret.Rd | 76 cna-3.0.0/cna/man/d.pban.Rd | 66 cna-3.0.0/cna/man/d.women.Rd | 64 cna-3.0.0/cna/man/full.ct.Rd |only cna-3.0.0/cna/man/is.inus.Rd | 269 ++- cna-3.0.0/cna/man/is.submodel.Rd | 6 cna-3.0.0/cna/man/makeFuzzy.Rd | 125 - cna-3.0.0/cna/man/minimalize.Rd | 161 +- cna-3.0.0/cna/man/minimalizeCsf.Rd | 180 +- cna-3.0.0/cna/man/randomConds.Rd | 325 ++-- cna-3.0.0/cna/man/redundant.Rd | 158 +- cna-3.0.0/cna/man/selectCases.Rd | 176 +- cna-3.0.0/cna/man/some.Rd | 141 - cna-3.0.0/cna/src/RcppExports.cpp | 12 cna-3.0.0/cna/src/cna_init.c | 2 cna-3.0.0/cna/src/minimal_submodel.cpp | 1 cna-3.0.0/cna/src/utils.cpp | 32 cna-3.0.0/cna/vignettes/cna_vignette.Rnw | 2426 ++++++++++++++++--------------- 80 files changed, 5907 insertions(+), 5000 deletions(-)
Title: Bivariate Probability Distributions
Description: Convenience functions for plotting/evaluating bivariate (uniform, binomial, Poisson, categorical, normal and bimodal) distributions, trivariate (normal and Dirichlet) distributions, bivariate kernel density estimates and bivariate empirical cumulative distribution functions. Supports their probability mass functions (PMFs), probability density functions (PDFs) and cumulative distribution functions (CDFs), generally where applicable.
Author: Abby Spurdle
Maintainer: Abby Spurdle <spurdle.a@gmail.com>
Diff between bivariate versions 0.5.0 dated 2020-02-26 and 0.6.0 dated 2020-09-13
bivariate-0.5.0/bivariate/R/bimodal.r |only bivariate-0.5.0/bivariate/R/binomial.r |only bivariate-0.5.0/bivariate/R/categorical.r |only bivariate-0.5.0/bivariate/R/cu.r |only bivariate-0.5.0/bivariate/R/dirichlet.r |only bivariate-0.5.0/bivariate/R/du.r |only bivariate-0.5.0/bivariate/R/empirical.r |only bivariate-0.5.0/bivariate/R/kernel.r |only bivariate-0.5.0/bivariate/R/normal.r |only bivariate-0.5.0/bivariate/R/other.r |only bivariate-0.5.0/bivariate/R/poisson.r |only bivariate-0.5.0/bivariate/man/01_uniform.Rd |only bivariate-0.5.0/bivariate/man/02_binomial.Rd |only bivariate-0.5.0/bivariate/man/03_poisson.Rd |only bivariate-0.5.0/bivariate/man/04_categorical.Rd |only bivariate-0.5.0/bivariate/man/05_normal.Rd |only bivariate-0.5.0/bivariate/man/06_bimodal.Rd |only bivariate-0.5.0/bivariate/man/07_dirichlet.Rd |only bivariate-0.5.0/bivariate/man/08_kernel_and_empicial.Rd |only bivariate-0.5.0/bivariate/man/09_print_method.Rd |only bivariate-0.5.0/bivariate/man/10_plot_methods.Rd |only bivariate-0.6.0/bivariate/DESCRIPTION | 13 bivariate-0.6.0/bivariate/MD5 | 58 - bivariate-0.6.0/bivariate/NAMESPACE | 60 + bivariate-0.6.0/bivariate/R/bv0.r |only bivariate-0.6.0/bivariate/R/bv1_u.r |only bivariate-0.6.0/bivariate/R/bv2_bnp.r |only bivariate-0.6.0/bivariate/R/bv3_nbm.r |only bivariate-0.6.0/bivariate/R/bv4_gdke.r |only bivariate-0.6.0/bivariate/R/outer.r |only bivariate-0.6.0/bivariate/R/plots.r |only bivariate-0.6.0/bivariate/R/plots2.r |only bivariate-0.6.0/bivariate/build/vignette.rds |binary bivariate-0.6.0/bivariate/inst/doc/bivariate.R | 291 ++++---- bivariate-0.6.0/bivariate/inst/doc/bivariate.Rnw | 391 ++++++------ bivariate-0.6.0/bivariate/inst/doc/bivariate.pdf |binary bivariate-0.6.0/bivariate/man/11_PD_uniform.Rd |only bivariate-0.6.0/bivariate/man/12_PD_binomial.Rd |only bivariate-0.6.0/bivariate/man/13_PD_poisson.Rd |only bivariate-0.6.0/bivariate/man/14_PD_categorical.Rd |only bivariate-0.6.0/bivariate/man/15_PD_normal.Rd |only bivariate-0.6.0/bivariate/man/16_PD_bimodal.Rd |only bivariate-0.6.0/bivariate/man/17_PD_dirichlet.Rd |only bivariate-0.6.0/bivariate/man/18_PD_kernel_and_empicial.Rd |only bivariate-0.6.0/bivariate/man/21_mockup_function_objects.Rd |only bivariate-0.6.0/bivariate/man/31_new_generics.Rd |only bivariate-0.6.0/bivariate/man/32_supporting_methods.Rd |only bivariate-0.6.0/bivariate/man/41_main_plotting_functions.Rd |only bivariate-0.6.0/bivariate/man/42_random_numbers.Rd |only bivariate-0.6.0/bivariate/man/43_density_matrices.Rd |only bivariate-0.6.0/bivariate/man/51_color_functions.Rd |only bivariate-0.6.0/bivariate/vignettes/bivariate.Rnw | 391 ++++++------ 52 files changed, 636 insertions(+), 568 deletions(-)
Title: Fast Generators and Iterators for Permutations, Combinations,
Integer Partitions and Compositions
Description: Fast generators and iterators for permutations, combinations,
integer partitions and compositions. The arrangements are in
lexicographical order and generated iteratively in a memory efficient manner.
It has been demonstrated that 'arrangements' outperforms most existing
packages of similar kind. Benchmarks could be found at
<https://randy3k.github.io/arrangements/articles/benchmark.html>.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between arrangements versions 1.1.8 dated 2020-01-08 and 1.1.9 dated 2020-09-13
DESCRIPTION | 10 +++---- MD5 | 20 +++++++------- README.md | 14 +++++++--- src/combinations/combinations-multiset.c | 12 ++++++++ src/combinations/combinations-ordinary.c | 12 ++++++++ src/combinations/combinations-replacement.c | 12 ++++++++ src/macros.h | 38 ++++++++++++++++++++++++++++ src/permutations/permutations-k.c | 12 ++++++++ src/permutations/permutations-multiset.c | 12 ++++++++ src/permutations/permutations-ordinary.c | 12 ++++++++ src/permutations/permutations-replacement.c | 12 ++++++++ 11 files changed, 147 insertions(+), 19 deletions(-)
Title: A Sample Size Calculator for Micro-Randomized Trials
Description: Provide a sample size calculator for micro-randomized trials (MRTs) based on methodology developed in Sample Size Calculations for Micro-randomized Trials in mHealth by Liao et al. (2016) <DOI:10.1002/sim.6847>.
Author: Peng Liao [aut, cre],
Liying Huang [aut],
Nicholas J. Seewald [aut],
Ji Sun [aut]
Maintainer: Peng Liao <pengliao@umich.edu>
Diff between MRTSampleSize versions 0.2.0 dated 2020-05-20 and 0.3.0 dated 2020-09-13
DESCRIPTION | 27 - MD5 | 18 - NAMESPACE | 24 - R/CalculatePower.R | 316 ++++++++++---------- R/CalculateSampleSize.R | 379 ++++++++++-------------- R/internal.R | 708 ++++++++++++++++++++++----------------------- man/calculatePower.Rd | 245 +++++++-------- man/calculateSampleSize.Rd | 243 +++++++-------- man/plotExpectAvail.Rd | 116 +++---- man/plotProximalEffect.Rd | 118 +++---- 10 files changed, 1082 insertions(+), 1112 deletions(-)
Title: Longitudinal Concordance Correlation
Description: Estimates the longitudinal concordance correlation to access the longitudinal agreement profile. The estimation approach implemented is variance components approach based on polynomial mixed effects regression model, as proposed by Oliveira, Hinde and Zocchi (2018) <doi:10.1007/s13253-018-0321-1>. In addition, non-parametric confidence intervals were implemented using percentile method or normal-approximation based on Fisher Z-transformation.
Author: Thiago de Paula Oliveira [aut, cre],
Rafael de Andrade Moral [aut],
Silvio Sandoval Zocchi [ctb],
Clarice Garcia Borges Demetrio [ctb],
John Hinde [aut]
Maintainer: Thiago de Paula Oliveira <thiago.paula.oliveira@alumni.usp.br>
Diff between lcc versions 1.1.0 dated 2020-05-22 and 1.1.1 dated 2020-09-13
DESCRIPTION | 14 +-- MD5 | 67 +++++++------- NAMESPACE | 6 - R/CCC.R | 2 R/ciBuilder.R | 2 R/ciCompute.R | 2 R/dataBuilder.R | 2 R/fittedBuilder.R | 2 R/getDelta.R | 2 R/init.R | 63 +++++++++++++ R/laBuilder.R | 2 R/laWrapper.R | 2 R/lcc.R | 37 +++++--- R/lccBootstrap.R | 10 +- R/lccBuilder.R | 2 R/lccModel.R | 2 R/lccSummary.R | 2 R/lccWrapper.R | 2 R/lcc_internal.R | 2 R/lcc_intervals.R | 2 R/lpcBuilder.R | 2 R/lpcWrapper.R | 2 R/methods.R | 30 +++--- R/plotBuilder_la.R | 238 ++++++++++++++++++++-------------------------------- R/plotBuilder_lcc.R | 238 ++++++++++++++++++++-------------------------------- R/plotBuilder_lpc.R | 229 +++++++++++++++++++------------------------------- R/plotControl.R | 23 ----- R/plot_la.R | 10 +- R/plot_lcc.R | 15 +-- R/plot_lpc.R | 10 +- R/plotmethod_lcc.R | 45 ++++++--- man/lcc.Rd | 35 +++++-- man/lccPlot.Rd | 19 +++- man/plotControl.Rd | 13 -- man/rename.vars.Rd |only 35 files changed, 533 insertions(+), 601 deletions(-)
Title: Loading Screen for 'Shiny'
Description: Full screen and partial loading screens for 'Shiny' with spinners, progress bars, and notifications.
Author: John Coene [aut, cre],
Jinhwan Kim [ctb]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between waiter versions 0.1.2 dated 2020-07-12 and 0.1.3 dated 2020-09-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/waiter.R | 13 +++++++++++-- inst/assets/waiter/custom.js | 15 ++++++++++----- inst/assets/waiter/waiter.js | 31 ++++++++++++++++++++++++++++--- man/waiterClass.Rd | 7 ++++++- 7 files changed, 70 insertions(+), 21 deletions(-)
Title: Graphical User Interface ('Shiny' App) for Package 'brms'
Description: A graphical user interface (GUI) for fitting Bayesian
regression models using the package 'brms' which in turn relies on
'Stan' (<https://mc-stan.org/>). The 'shinybrms' GUI is a 'Shiny'
(<https://shiny.rstudio.com/>) app.
Author: Frank Weber [aut, cre] (<https://orcid.org/0000-0002-4842-7922>)
Maintainer: Frank Weber <fweber144@protonmail.com>
Diff between shinybrms versions 1.3.0 dated 2020-08-06 and 1.4.0 dated 2020-09-13
DESCRIPTION | 13 - LICENSE |only MD5 | 92 ++++++++++++ NEWS.md | 68 +++++++-- README.md | 57 +++---- inst/shinybrms_app/app.R | 343 +++++++++++++++++++++++++++++++++-------------- inst/shinybrms_app/tests |only inst/shinybrms_app/www |only tests |only 9 files changed, 421 insertions(+), 152 deletions(-)
Title: Visualisation Toolbox for 'easystats' and Extra Geoms, Themes
and Color Palettes for 'ggplot2'
Description: Provides plotting utilities supporting easystats-packages (<https://github.com/easystats/easystats>)
and some extra themes, geoms, and scales for 'ggplot2'. Color scales are
based on <https://www.materialui.co/colors>.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, inv] (<https://orcid.org/0000-0001-5375-9967>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>),
Brenton M. Wiernik [ctb] (<https://orcid.org/0000-0001-9560-6336>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between see versions 0.5.2 dated 2020-07-27 and 0.6.0 dated 2020-09-13
DESCRIPTION | 16 ++- MD5 | 102 +++++++++++---------- NAMESPACE | 13 ++ NEWS.md | 22 ++++ R/geom_point2.R | 35 ++++++- R/plot.bayesfactor_models.R | 4 R/plot.bayesfactor_parameters.R | 6 - R/plot.check_distribution.R | 8 - R/plot.check_heteroscedasticity.R | 2 R/plot.check_normality.R | 13 +- R/plot.check_outliers.R | 42 ++++---- R/plot.cluster_analysis.R | 5 - R/plot.compare_performance.R | 4 R/plot.describe_distribution.R | 13 +- R/plot.easycormatrix.R | 7 - R/plot.easycorrelation.R | 5 - R/plot.effectsize_table.R | 4 R/plot.equivalence_test.R | 4 R/plot.estimate_density.R | 106 +++++++++++++--------- R/plot.hdi.R | 25 +++-- R/plot.n_factors.R | 1 R/plot.parameters_brms_meta.R |only R/plot.parameters_model.R | 151 ++++++++++++++++++++++++-------- R/plot.parameters_pca.R | 5 - R/plot.parameters_sem.R | 4 R/plot.parameters_simulate.R | 17 ++- R/plot.performance_pp_check.R |only R/plot.performance_roc.R | 4 R/plot.point_estimates.R | 14 +- R/print.check_model.R | 52 +++++------ R/utils_add_prior_layer.R | 76 +++++++++++----- inst/CITATION | 4 man/geom_point2.Rd | 22 ++++ man/plot.see_bayesfactor_models.Rd | 4 man/plot.see_bayesfactor_parameters.Rd | 4 man/plot.see_check_distribution.Rd | 4 man/plot.see_check_normality.Rd | 9 - man/plot.see_check_outliers.Rd | 4 man/plot.see_cluster_analysis.Rd | 5 - man/plot.see_compare_performance.Rd | 5 - man/plot.see_easycormatrix.Rd | 9 - man/plot.see_easycorrelation.Rd | 5 - man/plot.see_equivalence_test.Rd | 4 man/plot.see_estimate_density.Rd | 23 +++- man/plot.see_n_factors.Rd | 3 man/plot.see_p_direction.Rd | 3 man/plot.see_p_significance.Rd | 3 man/plot.see_parameters_brms_meta.Rd |only man/plot.see_parameters_distribution.Rd | 5 - man/plot.see_parameters_model.Rd | 21 ++-- man/plot.see_parameters_pca.Rd | 7 - man/plot.see_parameters_simulate.Rd | 21 ++++ man/plot.see_point_estimate.Rd | 11 +- man/print.see_performance_pp_check.Rd |only 54 files changed, 604 insertions(+), 332 deletions(-)
Title: A Framework for Data-Driven Stochastic Disease Spread
Simulations
Description: Provides an efficient and very flexible framework to
conduct data-driven epidemiological modeling in realistic large
scale disease spread simulations. The framework integrates
infection dynamics in subpopulations as continuous-time Markov
chains using the Gillespie stochastic simulation algorithm and
incorporates available data such as births, deaths and movements
as scheduled events at predefined time-points. Using C code for
the numerical solvers and 'OpenMP' (if available) to divide work
over multiple processors ensures high performance when simulating
a sample outcome. One of our design goals was to make the package
extendable and enable usage of the numerical solvers from other R
extension packages in order to facilitate complex epidemiological
research. The package contains template models and can be extended
with user-defined models. For more details see the paper by
Widgren, Bauer, Eriksson and Engblom (2019)
<doi:10.18637/jss.v091.i12>.
Author: Stefan Widgren [aut, cre] (<https://orcid.org/0000-0001-5745-2284>),
Robin Eriksson [aut] (<https://orcid.org/0000-0002-4291-712X>),
Stefan Engblom [aut] (<https://orcid.org/0000-0002-3614-1732>),
Pavol Bauer [aut] (<https://orcid.org/0000-0003-4328-7171>),
Thomas Rosendal [ctb] (<https://orcid.org/0000-0002-6576-9668>),
Attractive Chaos [cph] (Author of 'kvec.h'.)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between SimInf versions 7.0.1 dated 2020-06-18 and 8.0.0 dated 2020-09-13
SimInf-7.0.1/SimInf/R/formula.R |only SimInf-7.0.1/SimInf/man/Nn.Rd |only SimInf-8.0.0/SimInf/DESCRIPTION | 10 SimInf-8.0.0/SimInf/MD5 | 117 +++--- SimInf-8.0.0/SimInf/NAMESPACE | 7 SimInf-8.0.0/SimInf/NEWS.md | 40 ++ SimInf-8.0.0/SimInf/R/SEIR.R | 6 SimInf-8.0.0/SimInf/R/SIR.R | 6 SimInf-8.0.0/SimInf/R/SISe.R | 8 SimInf-8.0.0/SimInf/R/SISe3.R | 2 SimInf-8.0.0/SimInf/R/SimInf.R | 2 SimInf-8.0.0/SimInf/R/SimInf_model.R | 38 -- SimInf-8.0.0/SimInf/R/check_arguments.R | 22 - SimInf-8.0.0/SimInf/R/degree.R | 2 SimInf-8.0.0/SimInf/R/match_compartments.R |only SimInf-8.0.0/SimInf/R/n.R |only SimInf-8.0.0/SimInf/R/plot.R | 279 ++++++++-------- SimInf-8.0.0/SimInf/R/prevalence.R | 238 +++++++------ SimInf-8.0.0/SimInf/R/print.R | 80 ++-- SimInf-8.0.0/SimInf/R/punchcard.R | 4 SimInf-8.0.0/SimInf/R/run.R | 133 ++++--- SimInf-8.0.0/SimInf/R/trajectory.R | 259 ++++++-------- SimInf-8.0.0/SimInf/build/vignette.rds |binary SimInf-8.0.0/SimInf/configure | 66 ++- SimInf-8.0.0/SimInf/configure.ac | 44 +- SimInf-8.0.0/SimInf/inst/doc/SimInf.R | 23 - SimInf-8.0.0/SimInf/inst/doc/SimInf.Rnw | 26 - SimInf-8.0.0/SimInf/inst/doc/SimInf.pdf |binary SimInf-8.0.0/SimInf/man/boxplot-SimInf_model-method.Rd | 19 - SimInf-8.0.0/SimInf/man/examples |only SimInf-8.0.0/SimInf/man/n_nodes.Rd |only SimInf-8.0.0/SimInf/man/nodes.Rd | 2 SimInf-8.0.0/SimInf/man/pairs-SimInf_model-method.Rd | 20 + SimInf-8.0.0/SimInf/man/prevalence.Rd | 55 +-- SimInf-8.0.0/SimInf/man/trajectory.Rd | 54 +-- SimInf-8.0.0/SimInf/man/u0_SISe.Rd | 2 SimInf-8.0.0/SimInf/man/u0_SISe3.Rd | 2 SimInf-8.0.0/SimInf/src/SimInf.c | 2 SimInf-8.0.0/SimInf/src/init.c | 4 SimInf-8.0.0/SimInf/src/misc/SimInf_openmp.c | 3 SimInf-8.0.0/SimInf/src/misc/SimInf_trajectory.c | 166 +++++---- SimInf-8.0.0/SimInf/src/solvers/SimInf_solver.c | 8 SimInf-8.0.0/SimInf/src/solvers/aem/SimInf_solver_aem.c | 36 +- SimInf-8.0.0/SimInf/src/solvers/ssm/SimInf_solver_ssm.c | 36 +- SimInf-8.0.0/SimInf/tests/SEIR.R | 37 +- SimInf-8.0.0/SimInf/tests/SIR.R | 6 SimInf-8.0.0/SimInf/tests/SISe.R | 27 - SimInf-8.0.0/SimInf/tests/SISe3.R | 4 SimInf-8.0.0/SimInf/tests/SISe3_sp.R | 4 SimInf-8.0.0/SimInf/tests/SISe_sp.R | 4 SimInf-8.0.0/SimInf/tests/SimInf.R | 60 ++- SimInf-8.0.0/SimInf/tests/SimInf_events.R | 7 SimInf-8.0.0/SimInf/tests/SimInf_model.R | 50 +- SimInf-8.0.0/SimInf/tests/match_compartments.R |only SimInf-8.0.0/SimInf/tests/measures.R | 86 ++-- SimInf-8.0.0/SimInf/tests/mparse.R | 14 SimInf-8.0.0/SimInf/tests/phi.R | 12 SimInf-8.0.0/SimInf/tests/prevalence.R | 15 SimInf-8.0.0/SimInf/tests/priors.R | 3 SimInf-8.0.0/SimInf/tests/punchcard.R | 9 SimInf-8.0.0/SimInf/tests/sample_select.R | 20 - SimInf-8.0.0/SimInf/tests/solver_aem.R | 18 - SimInf-8.0.0/SimInf/vignettes/SimInf.Rnw | 26 - 63 files changed, 1225 insertions(+), 998 deletions(-)
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates
graphics with details from statistical tests included in the plots
themselves. It provides easier API to generate information-rich plots
for statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports only the most common types of
statistical tests: parametric, nonparametric, robust, and Bayesian
versions of t-test/ANOVA, correlation analyses, contingency table
analysis, meta-analysis, and regression analyses.
Author: Indrajeet Patil [cre, aut, cph]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 0.5.0 dated 2020-05-30 and 0.6.0 dated 2020-09-13
ggstatsplot-0.5.0/ggstatsplot/data/intent_morality.rdata |only ggstatsplot-0.5.0/ggstatsplot/man/intent_morality.Rd |only ggstatsplot-0.6.0/ggstatsplot/DESCRIPTION | 40 ggstatsplot-0.6.0/ggstatsplot/MD5 | 186 - ggstatsplot-0.6.0/ggstatsplot/NAMESPACE | 28 ggstatsplot-0.6.0/ggstatsplot/NEWS.md | 39 ggstatsplot-0.6.0/ggstatsplot/R/data.R | 62 ggstatsplot-0.6.0/ggstatsplot/R/ggbarstats.R | 33 ggstatsplot-0.6.0/ggstatsplot/R/ggbetweenstats.R | 92 ggstatsplot-0.6.0/ggstatsplot/R/ggcoefstats.R | 265 - ggstatsplot-0.6.0/ggstatsplot/R/ggcorrmat.R | 31 ggstatsplot-0.6.0/ggstatsplot/R/ggdotplotstats.R | 12 ggstatsplot-0.6.0/ggstatsplot/R/gghistostats.R | 133 ggstatsplot-0.6.0/ggstatsplot/R/ggpiestats.R | 97 ggstatsplot-0.6.0/ggstatsplot/R/ggscatterstats.R | 28 ggstatsplot-0.6.0/ggstatsplot/R/ggwithinstats.R | 40 ggstatsplot-0.6.0/ggstatsplot/R/global_vars.R | 4 ggstatsplot-0.6.0/ggstatsplot/R/grouped_ggcorrmat.R | 7 ggstatsplot-0.6.0/ggstatsplot/R/grouped_ggscatterstats.R | 2 ggstatsplot-0.6.0/ggstatsplot/R/helpers_ggbetweenstats_graphics.R | 104 ggstatsplot-0.6.0/ggstatsplot/R/helpers_ggcatstats_graphics.R | 149 - ggstatsplot-0.6.0/ggstatsplot/R/helpers_ggcoefstats_graphics.R | 287 + ggstatsplot-0.6.0/ggstatsplot/R/reexports.R | 4 ggstatsplot-0.6.0/ggstatsplot/README.md | 1392 ++++----- ggstatsplot-0.6.0/ggstatsplot/build/vignette.rds |binary ggstatsplot-0.6.0/ggstatsplot/inst/WORDLIST | 11 ggstatsplot-0.6.0/ggstatsplot/inst/doc/additional.html | 17 ggstatsplot-0.6.0/ggstatsplot/man/aesthetic_addon.Rd | 9 ggstatsplot-0.6.0/ggstatsplot/man/combine_plots.Rd | 1 ggstatsplot-0.6.0/ggstatsplot/man/figures/README-ggbarstats1-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-ggbarstats2-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-ggbetweenstats1-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-ggbetweenstats2-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-ggbetweenstats3-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-ggdotplotstats1-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-gghistostats1-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-gghistostats2-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-ggpiestats1-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-ggpiestats2-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-ggpiestats3-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-ggscatterstats1-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-ggscatterstats3-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-ggwithinstats1-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-ggwithinstats2-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/figures/README-ridgeplot-1.png |binary ggstatsplot-0.6.0/ggstatsplot/man/ggbarstats.Rd | 55 ggstatsplot-0.6.0/ggstatsplot/man/ggbetweenstats.Rd | 29 ggstatsplot-0.6.0/ggstatsplot/man/ggcoefstats.Rd | 133 ggstatsplot-0.6.0/ggstatsplot/man/ggcoefstats_label_maker.Rd | 9 ggstatsplot-0.6.0/ggstatsplot/man/ggcorrmat.Rd | 31 ggstatsplot-0.6.0/ggstatsplot/man/ggdotplotstats.Rd | 4 ggstatsplot-0.6.0/ggstatsplot/man/gghistostats.Rd | 4 ggstatsplot-0.6.0/ggstatsplot/man/ggpiestats.Rd | 60 ggstatsplot-0.6.0/ggstatsplot/man/ggscatterstats.Rd | 26 ggstatsplot-0.6.0/ggstatsplot/man/ggsignif_adder.Rd | 4 ggstatsplot-0.6.0/ggstatsplot/man/ggwithinstats.Rd | 19 ggstatsplot-0.6.0/ggstatsplot/man/grouped_ggbarstats.Rd | 27 ggstatsplot-0.6.0/ggstatsplot/man/grouped_ggbetweenstats.Rd | 23 ggstatsplot-0.6.0/ggstatsplot/man/grouped_ggcorrmat.Rd | 29 ggstatsplot-0.6.0/ggstatsplot/man/grouped_ggdotplotstats.Rd | 2 ggstatsplot-0.6.0/ggstatsplot/man/grouped_gghistostats.Rd | 2 ggstatsplot-0.6.0/ggstatsplot/man/grouped_ggpiestats.Rd | 27 ggstatsplot-0.6.0/ggstatsplot/man/grouped_ggscatterstats.Rd | 12 ggstatsplot-0.6.0/ggstatsplot/man/grouped_ggwithinstats.Rd | 13 ggstatsplot-0.6.0/ggstatsplot/man/grouped_proptest.Rd |only ggstatsplot-0.6.0/ggstatsplot/man/lm_effsize_standardizer.Rd |only ggstatsplot-0.6.0/ggstatsplot/man/movies_long.Rd | 10 ggstatsplot-0.6.0/ggstatsplot/man/movies_wide.Rd | 10 ggstatsplot-0.6.0/ggstatsplot/man/reexports.Rd | 5 ggstatsplot-0.6.0/ggstatsplot/tests/testthat/test-ggbarstats.R | 86 ggstatsplot-0.6.0/ggstatsplot/tests/testthat/test-ggbetweenstats.R | 128 ggstatsplot-0.6.0/ggstatsplot/tests/testthat/test-ggcoefstats.R | 568 ++- ggstatsplot-0.6.0/ggstatsplot/tests/testthat/test-ggcorrmat.R | 4 ggstatsplot-0.6.0/ggstatsplot/tests/testthat/test-ggdotplotstats.R | 22 ggstatsplot-0.6.0/ggstatsplot/tests/testthat/test-gghistostats.R | 38 ggstatsplot-0.6.0/ggstatsplot/tests/testthat/test-ggpiestats.R | 215 + ggstatsplot-0.6.0/ggstatsplot/tests/testthat/test-ggscatterstats.R | 42 ggstatsplot-0.6.0/ggstatsplot/tests/testthat/test-ggwithinstats.R | 99 ggstatsplot-0.6.0/ggstatsplot/tests/testthat/test-grouped_ggpiestats.R | 1 ggstatsplot-0.6.0/ggstatsplot/tests/testthat/test-grouped_ggscatterstats.R | 4 ggstatsplot-0.6.0/ggstatsplot/tests/testthat/test-pairwise_ggsignif.R | 30 ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/combine_plots.Rmd | 4 ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/effsize_interpretation.Rmd | 2 ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/faq.Rmd | 97 ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/gallery.Rmd | 33 ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/ggbetweenstats.Rmd | 11 ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/ggcoefstats.Rmd | 1442 ++++++---- ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/ggcorrmat.Rmd | 5 ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/ggdotplotstats.Rmd | 6 ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/gghistostats.Rmd | 22 ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/ggpiestats.Rmd | 17 ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/ggscatterstats.Rmd | 2 ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/ggwithinstats.Rmd | 89 ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/other_resources.Rmd | 14 ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/purrr_examples.Rmd | 69 ggstatsplot-0.6.0/ggstatsplot/vignettes/web_only/session_info.Rmd | 1 96 files changed, 3608 insertions(+), 3050 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-31 0.0.2
Title: Plot a Model's Residuals, Response, and Partial Dependence Plots
Description: Plot model surfaces for a wide variety of models
using partial dependence plots and other techniques.
Also plot model residuals and other information on the model.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between plotmo versions 3.5.7 dated 2020-04-15 and 3.6.0 dated 2020-09-13
plotmo-3.5.7/plotmo/inst/slowtests/test.emma.R |only plotmo-3.5.7/plotmo/inst/slowtests/test.emma.Rout.save |only plotmo-3.5.7/plotmo/inst/slowtests/test.emma.bat |only plotmo-3.6.0/plotmo/DESCRIPTION | 12 plotmo-3.6.0/plotmo/MD5 | 200 - plotmo-3.6.0/plotmo/NEWS | 24 plotmo-3.6.0/plotmo/R/as.char.R | 15 plotmo-3.6.0/plotmo/R/bx.R | 9 plotmo-3.6.0/plotmo/R/caret.R | 12 plotmo-3.6.0/plotmo/R/check.index.R | 29 plotmo-3.6.0/plotmo/R/dotlib.R | 2 plotmo-3.6.0/plotmo/R/grid.R | 6 plotmo-3.6.0/plotmo/R/lib.R | 159 - plotmo-3.6.0/plotmo/R/meta.R | 12 plotmo-3.6.0/plotmo/R/methods.R | 23 plotmo-3.6.0/plotmo/R/naken.R |only plotmo-3.6.0/plotmo/R/partdep.R | 4 plotmo-3.6.0/plotmo/R/partykit.R | 2 plotmo-3.6.0/plotmo/R/pint.R | 4 plotmo-3.6.0/plotmo/R/plotmo.R | 40 plotmo-3.6.0/plotmo/R/plotres.R | 19 plotmo-3.6.0/plotmo/R/plotresids.R | 12 plotmo-3.6.0/plotmo/R/pre.R | 2 plotmo-3.6.0/plotmo/R/predict.R | 4 plotmo-3.6.0/plotmo/R/prolog.R | 3 plotmo-3.6.0/plotmo/R/residuals.R | 10 plotmo-3.6.0/plotmo/R/response.R | 4 plotmo-3.6.0/plotmo/R/singles.R | 50 plotmo-3.6.0/plotmo/R/type.R | 2 plotmo-3.6.0/plotmo/R/xy.R | 270 +- plotmo-3.6.0/plotmo/README.md | 4 plotmo-3.6.0/plotmo/inst/doc/modguide.pdf |binary plotmo-3.6.0/plotmo/inst/doc/plotmo-notes.pdf |binary plotmo-3.6.0/plotmo/inst/doc/plotres-notes.pdf |binary plotmo-3.6.0/plotmo/inst/slowtests/linmod.R | 31 plotmo-3.6.0/plotmo/inst/slowtests/make.README.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/make.bat | 84 plotmo-3.6.0/plotmo/inst/slowtests/test.c50.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.caret.R | 35 plotmo-3.6.0/plotmo/inst/slowtests/test.caret.Rout.save | 145 - plotmo-3.6.0/plotmo/inst/slowtests/test.caret.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.center.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.degree.R | 28 plotmo-3.6.0/plotmo/inst/slowtests/test.degree.Rout.save | 60 plotmo-3.6.0/plotmo/inst/slowtests/test.degree.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.dots.R | 6 plotmo-3.6.0/plotmo/inst/slowtests/test.dots.Rout.save | 146 - plotmo-3.6.0/plotmo/inst/slowtests/test.dots.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.fac.Rout.save | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.fac.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.gbm.R | 53 plotmo-3.6.0/plotmo/inst/slowtests/test.gbm.Rout.save | 70 plotmo-3.6.0/plotmo/inst/slowtests/test.gbm.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.glmnet.R | 56 plotmo-3.6.0/plotmo/inst/slowtests/test.glmnet.Rout.save | 91 plotmo-3.6.0/plotmo/inst/slowtests/test.glmnet.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.glmnetUtils.R | 9 plotmo-3.6.0/plotmo/inst/slowtests/test.glmnetUtils.Rout.save | 17 plotmo-3.6.0/plotmo/inst/slowtests/test.glmnetUtils.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.linmod.R | 274 +- plotmo-3.6.0/plotmo/inst/slowtests/test.linmod.Rout.save | 650 +++-- plotmo-3.6.0/plotmo/inst/slowtests/test.linmod.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.mlr.R | 13 plotmo-3.6.0/plotmo/inst/slowtests/test.mlr.Rout.save | 48 plotmo-3.6.0/plotmo/inst/slowtests/test.mlr.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.modguide.R | 1 plotmo-3.6.0/plotmo/inst/slowtests/test.modguide.Rout.save | 51 plotmo-3.6.0/plotmo/inst/slowtests/test.modguide.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.non.earth.R | 80 plotmo-3.6.0/plotmo/inst/slowtests/test.non.earth.Rout.save | 358 ++- plotmo-3.6.0/plotmo/inst/slowtests/test.non.earth.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.parsnip.R |only plotmo-3.6.0/plotmo/inst/slowtests/test.parsnip.Rout.save |only plotmo-3.6.0/plotmo/inst/slowtests/test.parsnip.bat |only plotmo-3.6.0/plotmo/inst/slowtests/test.partdep.R | 16 plotmo-3.6.0/plotmo/inst/slowtests/test.partdep.Rout.save | 18 plotmo-3.6.0/plotmo/inst/slowtests/test.partdep.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.partykit.Rout.save | 1109 +++++----- plotmo-3.6.0/plotmo/inst/slowtests/test.partykit.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo.R | 34 plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo.Rout.save | 216 + plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo.args.R | 5 plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo.args.Rout.save | 19 plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo.args.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo.dots.R | 6 plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo.dots.Rout.save | 16 plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo.dots.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo.x.R | 5 plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo.x.Rout.save | 185 - plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo.x.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo3.R | 84 plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo3.Rout.save | 722 +++--- plotmo-3.6.0/plotmo/inst/slowtests/test.plotmo3.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.plotres.R | 10 plotmo-3.6.0/plotmo/inst/slowtests/test.plotres.Rout.save | 22 plotmo-3.6.0/plotmo/inst/slowtests/test.plotres.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.pre.R | 7 plotmo-3.6.0/plotmo/inst/slowtests/test.pre.Rout.save | 11 plotmo-3.6.0/plotmo/inst/slowtests/test.pre.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.printcall.bat | 2 plotmo-3.6.0/plotmo/inst/slowtests/test.prolog.R | 15 plotmo-3.6.0/plotmo/inst/slowtests/test.unusual.vars.R |only plotmo-3.6.0/plotmo/inst/slowtests/test.unusual.vars.Rout.save |only plotmo-3.6.0/plotmo/inst/slowtests/test.unusual.vars.bat |only plotmo-3.6.0/plotmo/man/plotmo.Rd | 4 106 files changed, 3283 insertions(+), 2510 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation and
statistical computing in R that is extremely fast, flexible and
parsimonious to code with and programmer friendly.
It is well integrated with 'dplyr', 'plm' and 'data.table'.
--- Key Features: ---
(1) Advanced statistical programming: A full set of fast statistical functions
supporting grouped and weighted computations on vectors, matrices and
data frames. Fast and programmable grouping, ordering, unique values / rows,
factor generation and interactions. Fast and flexible functions for data
manipulation and data object conversions.
(2) Advanced aggregation: Fast and easy multi-data-type, multi-function,
weighted, parallelized and fully customized data aggregation.
(3) Advanced transformations: Fast (grouped) replacing and sweeping out of
statistics, and (grouped, weighted) scaling / standardizing, between
(averaging) and (quasi-)within (centering / demeaning) transformations,
higher-dimensional centering (i.e. multiple fixed effects transformations),
linear prediction and partialling-out.
(4) Advanced time-computations: Fast (sequences of) lags / leads, and
(lagged / leaded, iterated, quasi-, log-) differences and growth
rates on (unordered) time series and panel data. Multivariate auto-,
partial- and cross-correlation functions for panel data.
Panel data to (ts-)array conversions.
(5) List processing: (Recursive) list search / identification, extraction /
subsetting, data-apply, and generalized row-binding / unlisting in 2D.
(6) Advanced data exploration: Fast (grouped, weighted, panel-decomposed)
summary statistics for complex multilevel / panel data.
Author: Sebastian Krantz [aut, cre],
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Simen Gaure [ctb],
Dirk Eddelbuettel [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999-2016 The R Core Team [cph]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 1.3.1 dated 2020-08-27 and 1.3.2 dated 2020-09-13
DESCRIPTION | 10 MD5 | 106 NAMESPACE | 4 NEWS.md | 15 R/fsubset_ftransform.R | 124 R/global_macros.R | 22 R/recode_replace.R | 2 R/roworder_colorder_rename.R | 14 R/select_replace_add_vars.R | 2 R/small_helper.R | 4 inst/doc/collapse_and_dplyr.R | 16 inst/doc/collapse_and_dplyr.Rmd | 21 inst/doc/collapse_and_dplyr.html | 2140 +++++------ inst/doc/collapse_and_plm.html | 116 inst/doc/collapse_intro.R | 22 inst/doc/collapse_intro.Rmd | 32 inst/doc/collapse_intro.html | 3871 ++++++++++----------- man/collapse-documentation.Rd | 2 man/collapse-package.Rd | 13 man/fast-data-manipulation.Rd | 2 man/frename.Rd | 3 man/ftransform.Rd | 140 src/Makevars | 14 src/fNdistinct.cpp | 70 tests/testthat.R | 1 tests/testthat/test-BY.R | 9 tests/testthat/test-GRP.R | 2 tests/testthat/test-TRA.R | 2 tests/testthat/test-collap.R | 2 tests/testthat/test-dapply.R | 3 tests/testthat/test-fHDbetween-fHDwithin-HDB-HDW.R | 2 tests/testthat/test-fNobs-fNdistinct.R | 2 tests/testthat/test-fbetween-fwithin-B-W.R | 2 tests/testthat/test-fdiff-fgrowth-D-G.R | 2 tests/testthat/test-ffirst-flast.R | 2 tests/testthat/test-flag-L-F.R | 2 tests/testthat/test-fmean.R | 2 tests/testthat/test-fmedian.R | 2 tests/testthat/test-fmin-fmax.R | 2 tests/testthat/test-fmode.R | 10 tests/testthat/test-fprod.R | 2 tests/testthat/test-fscale-STD.R | 2 tests/testthat/test-fsubset-ftransform.R | 2 tests/testthat/test-fsum.R | 2 tests/testthat/test-fvar-fsd.R | 2 tests/testthat/test-miscellaneous-issues.R | 2 tests/testthat/test-psmat-psacf.R | 2 tests/testthat/test-qsu.R | 2 tests/testthat/test-quick-conversion.R | 2 tests/testthat/test-select-replace-vars.R | 2 tests/testthat/test-seqid-groupid.R | 2 tests/testthat/test-varying.R | 2 vignettes/collapse_and_dplyr.Rmd | 21 vignettes/collapse_intro.Rmd | 32 54 files changed, 3588 insertions(+), 3301 deletions(-)