Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of R documentation objects,
including functions reprompt() and ereprompt() for updating 'Rd'
documentation for functions, methods and classes; 'Rd' macros for
citations and import of references from 'bibtex' files for use in
'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and
inserting snippets of 'R' code and the results of its evaluation or
creating graphics on the fly; and many functions for manipulation of
references and Rd files.
Author: Georgi N. Boshnakov [aut, cre],
Duncan Murdoch [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between Rdpack versions 0.11-0 dated 2019-04-14 and 0.11-1 dated 2019-12-14
Rdpack-0.11-0/Rdpack/inst/auto |only Rdpack-0.11-0/Rdpack/vignettes/auto |only Rdpack-0.11-1/Rdpack/DESCRIPTION | 8 Rdpack-0.11-1/Rdpack/MD5 | 235 - Rdpack-0.11-1/Rdpack/NAMESPACE | 256 - Rdpack-0.11-1/Rdpack/NEWS.md | 991 ++-- Rdpack-0.11-1/Rdpack/R/RStudio.R | 86 Rdpack-0.11-1/Rdpack/R/Rdo2Rdf.R | 436 +- Rdpack-0.11-1/Rdpack/R/alias.R | 48 Rdpack-0.11-1/Rdpack/R/bib.R | 2164 +++++----- Rdpack-0.11-1/Rdpack/R/elements.R | 284 - Rdpack-0.11-1/Rdpack/R/f_usage.R | 302 - Rdpack-0.11-1/Rdpack/R/inspect.R | 424 - Rdpack-0.11-1/Rdpack/R/manip.R | 656 +-- Rdpack-0.11-1/Rdpack/R/parse.R | 126 Rdpack-0.11-1/Rdpack/R/predefined.R | 158 Rdpack-0.11-1/Rdpack/R/promptSexpr.R | 152 Rdpack-0.11-1/Rdpack/R/repromptAny.R | 515 +- Rdpack-0.11-1/Rdpack/R/runexamples.R | 428 - Rdpack-0.11-1/Rdpack/R/sections.R | 430 - Rdpack-0.11-1/Rdpack/R/signature.R | 448 +- Rdpack-0.11-1/Rdpack/R/slots.R | 100 Rdpack-0.11-1/Rdpack/R/threedots.R | 164 Rdpack-0.11-1/Rdpack/R/usage.R | 827 +-- Rdpack-0.11-1/Rdpack/R/utils.R | 572 +- Rdpack-0.11-1/Rdpack/R/yytransient.R | 246 - Rdpack-0.11-1/Rdpack/R/zzobsolete.R | 698 +-- Rdpack-0.11-1/Rdpack/README.md | 1048 ++-- Rdpack-0.11-1/Rdpack/build/partial.rdb |binary Rdpack-0.11-1/Rdpack/build/vignette.rds |binary Rdpack-0.11-1/Rdpack/inst/REFERENCES.bib | 74 Rdpack-0.11-1/Rdpack/inst/RStudio/addins.dcf | 8 Rdpack-0.11-1/Rdpack/inst/doc/Inserting_bibtex_references.R | 36 Rdpack-0.11-1/Rdpack/inst/doc/Inserting_bibtex_references.pdf |binary Rdpack-0.11-1/Rdpack/inst/doc/Inserting_figures_and_evaluated_examples.R | 18 Rdpack-0.11-1/Rdpack/inst/doc/Inserting_figures_and_evaluated_examples.pdf |binary Rdpack-0.11-1/Rdpack/inst/examples/RdpackTester/DESCRIPTION | 26 Rdpack-0.11-1/Rdpack/inst/examples/RdpackTester/NAMESPACE | 2 Rdpack-0.11-1/Rdpack/inst/examples/RdpackTester/R/RdpackTester-internal.R | 6 Rdpack-0.11-1/Rdpack/inst/examples/RdpackTester/inst/REFERENCES.bib | 244 - Rdpack-0.11-1/Rdpack/inst/examples/RdpackTester/inst/auto/REFERENCES.el | 32 Rdpack-0.11-1/Rdpack/inst/examples/RdpackTester/man/RdpackTester-package.Rd | 112 Rdpack-0.11-1/Rdpack/inst/examples/journal_with_percents.bib | 18 Rdpack-0.11-1/Rdpack/inst/examples/tz.Rd | 108 Rdpack-0.11-1/Rdpack/inst/examples/url_with_percents.bib | 18 Rdpack-0.11-1/Rdpack/man/RStudio_reprompt.Rd | 84 Rdpack-0.11-1/Rdpack/man/Rd_combo.Rd | 118 Rdpack-0.11-1/Rdpack/man/Rdapply.Rd | 252 - Rdpack-0.11-1/Rdpack/man/Rdo2Rdf.Rd | 220 - Rdpack-0.11-1/Rdpack/man/Rdo_append_argument.Rd | 113 Rdpack-0.11-1/Rdpack/man/Rdo_collect_metadata.Rd | 122 Rdpack-0.11-1/Rdpack/man/Rdo_empty_sections.Rd | 148 Rdpack-0.11-1/Rdpack/man/Rdo_fetch.Rd | 174 Rdpack-0.11-1/Rdpack/man/Rdo_flatinsert.Rd | 72 Rdpack-0.11-1/Rdpack/man/Rdo_get_argument_names.Rd | 98 Rdpack-0.11-1/Rdpack/man/Rdo_get_insert_pos.Rd | 106 Rdpack-0.11-1/Rdpack/man/Rdo_get_item_labels.Rd | 82 Rdpack-0.11-1/Rdpack/man/Rdo_insert.Rd | 134 Rdpack-0.11-1/Rdpack/man/Rdo_insert_element.Rd | 130 Rdpack-0.11-1/Rdpack/man/Rdo_is_newline.Rd | 114 Rdpack-0.11-1/Rdpack/man/Rdo_locate.Rd | 182 Rdpack-0.11-1/Rdpack/man/Rdo_locate_leaves.Rd | 111 Rdpack-0.11-1/Rdpack/man/Rdo_macro.Rd | 192 Rdpack-0.11-1/Rdpack/man/Rdo_modify.Rd | 242 - Rdpack-0.11-1/Rdpack/man/Rdo_modify_simple.Rd | 90 Rdpack-0.11-1/Rdpack/man/Rdo_piecetag.Rd | 152 Rdpack-0.11-1/Rdpack/man/Rdo_remove_srcref.Rd | 62 Rdpack-0.11-1/Rdpack/man/Rdo_reparse.Rd | 116 Rdpack-0.11-1/Rdpack/man/Rdo_sections.Rd | 198 Rdpack-0.11-1/Rdpack/man/Rdo_set_section.Rd | 164 Rdpack-0.11-1/Rdpack/man/Rdo_show.Rd | 74 Rdpack-0.11-1/Rdpack/man/Rdo_tag.Rd | 156 Rdpack-0.11-1/Rdpack/man/Rdo_tags.Rd | 114 Rdpack-0.11-1/Rdpack/man/Rdo_which.Rd | 162 Rdpack-0.11-1/Rdpack/man/Rdpack-package.Rd | 898 ++-- Rdpack-0.11-1/Rdpack/man/Rdpack_bibstyles.Rd | 138 Rdpack-0.11-1/Rdpack/man/Rdreplace_section.Rd | 124 Rdpack-0.11-1/Rdpack/man/S4formals.Rd | 96 Rdpack-0.11-1/Rdpack/man/append_to_Rd_list.Rd | 182 Rdpack-0.11-1/Rdpack/man/bibentry_key.Rd | 60 Rdpack-0.11-1/Rdpack/man/c_Rd.Rd | 138 Rdpack-0.11-1/Rdpack/man/char2Rdpiece.Rd | 160 Rdpack-0.11-1/Rdpack/man/compare_usage1.Rd | 118 Rdpack-0.11-1/Rdpack/man/deparse_usage.Rd | 184 Rdpack-0.11-1/Rdpack/man/ereprompt.Rd | 106 Rdpack-0.11-1/Rdpack/man/format_funusage.Rd | 144 Rdpack-0.11-1/Rdpack/man/get_bibentries.Rd | 252 - Rdpack-0.11-1/Rdpack/man/get_sig_text.Rd | 260 - Rdpack-0.11-1/Rdpack/man/get_usage_text.Rd | 138 Rdpack-0.11-1/Rdpack/man/insert_all_ref.Rd | 150 Rdpack-0.11-1/Rdpack/man/insert_ref.Rd | 360 - Rdpack-0.11-1/Rdpack/man/inspect_Rd.Rd | 186 Rdpack-0.11-1/Rdpack/man/inspect_args.Rd | 146 Rdpack-0.11-1/Rdpack/man/inspect_signatures.Rd | 150 Rdpack-0.11-1/Rdpack/man/inspect_slots.Rd | 56 Rdpack-0.11-1/Rdpack/man/inspect_usage.Rd | 138 Rdpack-0.11-1/Rdpack/man/list_Rd.Rd | 126 Rdpack-0.11-1/Rdpack/man/macros/refmacros.Rd | 42 Rdpack-0.11-1/Rdpack/man/makeVignetteReference.Rd | 222 - Rdpack-0.11-1/Rdpack/man/parse_Rdname.Rd | 136 Rdpack-0.11-1/Rdpack/man/parse_Rdpiece.Rd | 197 Rdpack-0.11-1/Rdpack/man/parse_Rdtext.Rd | 148 Rdpack-0.11-1/Rdpack/man/parse_pairlist.Rd | 188 Rdpack-0.11-1/Rdpack/man/parse_text.Rd | 104 Rdpack-0.11-1/Rdpack/man/parse_usage_text.Rd | 102 Rdpack-0.11-1/Rdpack/man/predefined.Rd | 202 Rdpack-0.11-1/Rdpack/man/promptPackageSexpr.Rd | 166 Rdpack-0.11-1/Rdpack/man/promptUsage.Rd | 318 - Rdpack-0.11-1/Rdpack/man/rdo_text_restore.Rd | 110 Rdpack-0.11-1/Rdpack/man/rebib.Rd | 256 - Rdpack-0.11-1/Rdpack/man/reprompt.Rd | 640 +- Rdpack-0.11-1/Rdpack/man/set_Rdpack_bibstyle.Rd | 80 Rdpack-0.11-1/Rdpack/man/update_aliases_tmp.Rd | 98 Rdpack-0.11-1/Rdpack/man/viewRd.Rd | 94 Rdpack-0.11-1/Rdpack/man/zzasym_compare.Rd | 152 Rdpack-0.11-1/Rdpack/man/zzbsdup.Rd | 116 Rdpack-0.11-1/Rdpack/man/zzcapture_promptany.Rd | 170 Rdpack-0.11-1/Rdpack/tests/testthat.R | 8 Rdpack-0.11-1/Rdpack/tests/testthat/test-char2Rdpiece.R | 180 119 files changed, 12298 insertions(+), 12227 deletions(-)
Title: Generate Postestimation Quantities for Bayesian MCMC Estimation
Description: An implementation of functions to generate and plot postestimation quantities after estimating Bayesian regression models using Markov chain Monte Carlo (MCMC). Functionality includes the estimation of the Precision-Recall curves (see Beger, 2016 <doi:10.2139/ssrn.2765419>), the implementation of the observed values method of calculating predicted probabilities by Hanmer and Kalkan (2013) <doi:10.1111/j.1540-5907.2012.00602.x>, the implementation of the average value method of calculating predicted probabilities (see King, Tomz, and Wittenberg, 2000 <doi:10.2307/2669316>), and the generation and plotting of first differences to summarize typical effects across covariates (see Long 1997, ISBN:9780803973749; King, Tomz, and Wittenberg, 2000 <doi:10.2307/2669316>). This package can be used with MCMC output generated by any Bayesian estimation tool including 'JAGS', 'BUGS', 'MCMCpack', and 'Stan'.
Author: Johannes Karreth [aut] (<https://orcid.org/0000-0003-4586-7153>),
Shana Scogin [aut, cre] (<https://orcid.org/0000-0002-7801-853X>),
Rob Williams [aut] (<https://orcid.org/0000-0001-9259-3883>),
Andreas Beger [aut] (<https://orcid.org/0000-0003-1883-3169>),
Myunghee Lee [ctb],
Neil Williams [ctb]
Maintainer: Shana Scogin <shanarscogin@gmail.com>
Diff between BayesPostEst versions 0.1.0 dated 2019-10-06 and 0.2.0 dated 2019-12-14
DESCRIPTION | 12 +-- MD5 | 45 +++++++---- NAMESPACE | 5 + NEWS.md | 7 + R/BayesPostEst.R | 3 R/data.R | 145 +++++++++++++++++++++++++++++++++++++ R/mcmcCoefPlot.R |only R/mcmcMargEff.R |only R/mcmcReg.R | 19 ++-- R/mcmcRocPrc.R | 4 - R/mcmcRocPrcGen.R |only README.md | 2 data/jags_interactive.rda |only data/jags_interactive_cat.rda |only data/sim_data_interactive.rda |only data/sim_data_interactive_cat.rda |only inst/doc/getting_started.Rmd | 2 inst/doc/getting_started.html | 14 +-- man/jags_interactive.Rd |only man/jags_interactive_cat.Rd |only man/mcmcCoefPlot.Rd |only man/mcmcMargEff.Rd |only man/mcmcReg.Rd | 13 +-- man/mcmcRocPrc.Rd | 4 - man/mcmcRocPrcGen.Rd |only man/sim_data_interactive.Rd |only man/sim_data_interactive_cat.Rd |only tests/testthat/test_mcmcCoefPlot.R |only tests/testthat/test_mcmcMargEff.R |only tests/testthat/test_mcmcReg.R | 24 +++--- vignettes/getting_started.Rmd | 2 vignettes/mod.rds |only 32 files changed, 242 insertions(+), 59 deletions(-)
Title: Understanding Suppression of HIV
Description: Analyzes longitudinal data of HIV decline in patients on antiretroviral therapy using the canonical biphasic exponential decay model (pioneered, for example, by work in Perelson et al. (1997) <doi:10.1038/387188a0>; and Wu and Ding (1999) <doi:10.1111/j.0006-341X.1999.00410.x>). Model fitting and parameter estimation are performed, with additional options to calculate the time to viral suppression. Plotting and summary tools are also provided for fast assessment of model results.
Author: Sinead E. Morris [aut, cre] (<https://orcid.org/0000-0001-8626-1698>),
Luise Dziobek-Garrett [ctb],
Andrew Yates [ctb]
Maintainer: Sinead E. Morris <sinead.morris@columbia.edu>
Diff between ushr versions 0.1.0 dated 2019-10-09 and 0.2.0 dated 2019-12-14
DESCRIPTION | 11 MD5 | 53 NAMESPACE | 5 NEWS.md | 11 R/fitting_fns.R | 2 R/fitting_fns_triphasic.R |only R/get_TTS.R | 41 R/globals.R | 3 R/input_processing.R | 8 R/master_fn.R | 15 R/master_fn_triphasic.R |only R/model_fns.R | 2 R/output_processing.R | 286 +++- inst/doc/Vignette.Rmd | 20 inst/doc/Vignette.html | 20 man/filter_data.Rd | 6 man/filter_dataTTS.Rd | 4 man/fit_model_triphasic.Rd |only man/get_TTS.Rd | 6 man/get_biphasic.Rd | 2 man/get_error_triphasic.Rd |only man/get_optim_fit_triphasic.Rd |only man/get_triphasic.Rd |only man/plot_model.Rd | 2 man/plot_pairs.Rd |only man/tri_switch_params.Rd |only man/triphasic_root.Rd |only man/ushr.Rd | 6 man/ushr_triphasic.Rd |only tests/testthat/test-filtering.R | 3 tests/testthat/test-fitting.R |only vignettes/HIV.bib | 2540 ++++++++++++++++++++-------------------- vignettes/Vignette.Rmd | 20 33 files changed, 1723 insertions(+), 1343 deletions(-)
Title: Manage Competition Results
Description: Tools for storing and managing competition results.
Competition is understood as a set of games in which players gain some
abstract scores. There are two ways for storing results: in long (one
row per game-player) and wide (one row per game with fixed amount of
players) formats. This package provides functions for creation and
conversion between them. Also there are functions for computing their
summary and Head-to-Head values for players. They leverage grammar of
data manipulation from 'dplyr'.
Author: Evgeni Chasnovski [aut, cre]
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>
Diff between comperes versions 0.2.2 dated 2019-01-12 and 0.2.3 dated 2019-12-14
DESCRIPTION | 30 - MD5 | 34 - NAMESPACE | 52 -- NEWS.md | 5 R/data.R | 6 R/outer-methods.R | 55 -- R/pairgames.R | 2 R/zzz.R |only build/vignette.rds |binary inst/doc/formats.R | 18 inst/doc/formats.html | 496 +++++++++++++++++------- inst/doc/manipulation.R | 28 - inst/doc/manipulation.html | 739 +++++++++++++++++++++++------------- man/convert-pair-value.Rd | 3 man/hp_survey.Rd | 6 man/reexports.Rd | 5 tests/testthat/test-head-to-head.R | 14 tests/testthat/test-outer-methods.R | 11 tests/testthat/test-zzz.R |only 19 files changed, 915 insertions(+), 589 deletions(-)
Title: Data on Base Packages for Current and Previous Versions of R
Description: Provides a dataset of functions in all base packages of R versions 1.0.1 onwards.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between rcheology versions 3.6.1.0 dated 2019-07-07 and 3.6.2.0 dated 2019-12-14
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ README.md | 2 +- data/Rversions.rda |binary data/rcheology.rda |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary 8 files changed, 15 insertions(+), 11 deletions(-)
Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Description: Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
Author: Guangchuang Yu [aut, cre, cph]
(<https://orcid.org/0000-0002-6485-8781>),
Bradley Jones [ctb],
Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between tidytree versions 0.3.0 dated 2019-11-21 and 0.3.1 dated 2019-12-14
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 7 ++++++- R/groupOTU.R | 5 +++++ build/vignette.rds |binary inst/doc/tidytree.R | 2 +- inst/doc/tidytree.html | 4 ++-- 7 files changed, 23 insertions(+), 13 deletions(-)
Title: Sequential Parameter Optimization Toolbox
Description: A set of tools for model based optimization and tuning of
algorithms. It includes surrogate models, optimizers and design of experiment
approaches. The main interface is spot, which uses sequentially updated
surrogate models for the purpose of efficient optimization. The main goal is
to ease the burden of objective function evaluations, when a single evaluation
requires a significant amount of resources.
Author: Thomas Bartz-Beielstein [aut],
Joerg Stork [aut],
Martin Zaefferer [aut, cre],
Margarita Rebolledo [ctb],
Christian Lasarczyk [ctb],
Joerg Ziegenhirt [ctb],
Wolfgang Konen [ctb],
Oliver Flasch [ctb],
Patrick Koch [ctb],
Martina Friese [ctb],
Lorenzo Gentile [ctb],
Frederik Rehbach [aut]
Maintainer: Martin Zaefferer <martin.zaefferer@gmx.de>
Diff between SPOT versions 2.0.4 dated 2019-05-17 and 2.0.5 dated 2019-12-14
DESCRIPTION | 20 MD5 | 256 +- NAMESPACE | 21 R/buildCVModel.R |only R/buildKrigingDACE.R | 2902 ++++++++++++------------ R/buildKrigingForrester.R | 24 R/buildRandomForest.R | 4 R/buildRanger.R |only R/cyclone.R | 2 R/evaluate.R | 43 R/funOptimLecture.R |only R/infillExpectedImprovement.R |only R/infillGetFullPrediction.R |only R/package.R | 4 R/plotFunction.R | 6 R/plotModel.R | 114 R/plotSingleDimFunction.R |only R/satter.R | 78 R/spot.R | 660 ++--- R/wrapper.R | 116 README.md |only data/dataGasSensor.RData |binary inst/consoleCallTrialScript.R |only man/OCBA.Rd | 84 man/SPOT-package.Rd | 126 - man/buildCVModel.Rd |only man/buildEnsembleStack.Rd | 108 man/buildKriging.Rd | 236 - man/buildKrigingDACE.Rd | 134 - man/buildLM.Rd | 104 man/buildLOESS.Rd | 100 man/buildRSM.Rd | 100 man/buildRandomForest.Rd | 90 man/buildRanger.Rd |only man/calculationBarthMuschelknautz.Rd | 48 man/calculationMothes.Rd | 44 man/checkForNAs.Rd | 38 man/checkFunEvalsDesignSize.Rd | 46 man/checkInputDimensionsionalityCorrect.Rd | 38 man/checkInputTypesInControl.Rd | 30 man/checkLowerNotEqualsUpper.Rd | 36 man/checkLowerSmallerThanUpper.Rd | 34 man/checkTypesOfInput.Rd | 42 man/corrcubic.Rd | 72 man/correxp.Rd | 72 man/correxpg.Rd | 72 man/corrgauss.Rd | 72 man/corrkriging.Rd | 70 man/corrlin.Rd | 72 man/corrnoisygauss.Rd | 70 man/corrnoisykriging.Rd | 70 man/corrspherical.Rd | 72 man/corrspline.Rd | 72 man/daceEvalFit.Rd | 46 man/daceFixTheta.Rd | 64 man/daceGetFit.Rd | 84 man/daceLikelihood.Rd | 50 man/daceObjfunc.Rd | 78 man/dacePrepareFit.Rd | 68 man/daceStartParameters.Rd | 62 man/dataGasSensor.Rd | 94 man/descentSpotRSM.Rd | 52 man/designLHD.Rd | 106 man/designLHDNorm.Rd | 79 man/designUniformRandom.Rd | 84 man/duplicateAndReplicateHandling.Rd | 64 man/evaluateModel.Rd | 46 man/expectedImprovement.Rd | 64 man/funCyclone.Rd | 121 - man/funOptimLecture.Rd |only man/funSphere.Rd | 40 man/infillExpectedImprovement.Rd |only man/infillGetFullPrediction.Rd |only man/initialInputCheck.Rd | 56 man/krigingLikelihood.Rd | 70 man/linearAdaptedSE.Rd |only man/maxNearestNeighbourDistance.Rd |only man/normalizeMatrix.Rd | 50 man/normalizeMatrix2.Rd | 58 man/objectiveFunctionEvaluation.Rd | 72 man/optimDE.Rd | 88 man/optimES.Rd | 124 - man/optimGenoud.Rd | 88 man/optimLBFGSB.Rd | 92 man/optimLHD.Rd | 92 man/optimNLOPTR.Rd | 120 man/plot.spotRSM.Rd | 34 man/plotData.Rd | 131 - man/plotFunction.Rd | 172 - man/plotModel.Rd | 111 man/plotSingleDimFunction.Rd |only man/predict.cvModel.Rd |only man/predict.dace.Rd | 122 - man/predict.ensembleStack.Rd | 50 man/predict.kriging.Rd | 86 man/predict.spotLOESS.Rd | 54 man/predict.spotLinearModel.Rd | 38 man/predict.spotRSM.Rd | 50 man/predict.spotRandomForest.Rd | 38 man/predict.spotRanger.Rd |only man/predictKrigingReinterpolation.Rd | 114 man/print.Rd | 48 man/print.spotLOESS.Rd | 41 man/print.spotLinearModel.Rd | 34 man/print.spotRSM.Rd | 40 man/print.spotRandomForest.Rd | 34 man/print.spotRanger.Rd |only man/regpoly0.Rd | 60 man/regpoly1.Rd | 64 man/regpoly2.Rd | 62 man/repairNonNumeric.Rd | 44 man/repeatsOCBA.Rd | 64 man/repmat.Rd | 44 man/satter.Rd | 68 man/spot.Rd | 228 - man/spotAlgEs.Rd | 163 - man/spotAlgEsDominantReco.Rd | 53 man/spotAlgEsGetSuccessRate.Rd | 48 man/spotAlgEsHps.Rd | 44 man/spotAlgEsIndividualInitial.Rd | 92 man/spotAlgEsInitParentPop.Rd | 92 man/spotAlgEsInterReco.Rd | 52 man/spotAlgEsInterRecoBeSw02.Rd | 48 man/spotAlgEsMarriage.Rd | 48 man/spotAlgEsMarriageWithReplace.Rd | 48 man/spotAlgEsObjMutation.Rd | 34 man/spotAlgEsSelection.Rd | 50 man/spotAlgEsStratMutation.Rd | 54 man/spotAlgEsTermination.Rd | 66 man/spotControl.Rd | 125 - man/spotFillControlList.Rd |only man/spotHelpBslash.Rd | 40 man/spotLoop.Rd | 104 man/wrapBatchTools.Rd |only man/wrapFunction.Rd | 76 man/wrapFunctionParallel.Rd |only man/wrapSystemCommand.Rd |only man/wrapSystem_parseMatrixToString.Rd |only tests/testthat.R | 4 tests/testthat/test.000TestSetup.R |only tests/testthat/test.buildCVModel.R |only tests/testthat/test.infillExpectedImprovement.R |only tests/testthat/test.plots.R |only 143 files changed, 5974 insertions(+), 5612 deletions(-)
Title: Robust Methods for High-Dimensional Data
Description: Robust methods for high-dimensional data, in particular linear
model selection techniques based on least angle regression and sparse
regression.
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robustHD versions 0.6.0 dated 2019-12-09 and 0.6.1 dated 2019-12-14
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 5 +++++ R/fastLasso.R | 4 ++-- R/test.R | 15 ++++++++------- build/partial.rdb |binary src/fastSparseLTS.h | 4 ++-- src/robustHD_init.c | 8 ++++---- 8 files changed, 32 insertions(+), 26 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code
ported from S-PLUS. A modern 'MySQL' client based on 'Rcpp' is available
from the 'RMariaDB' package.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between RMySQL versions 0.10.17 dated 2019-03-04 and 0.10.18 dated 2019-12-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ configure | 3 --- 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Respondent-Driven Sampling
Description: Provides functionality for carrying out estimation
with data collected using Respondent-Driven Sampling. This includes
Heckathorn's RDS-I and RDS-II estimators as well as Gile's Sequential
Sampling estimator. The package is part of the "RDS Analyst" suite of
packages for the analysis of respondent-driven sampling data.
See Gile and Handcock (2010) <doi:10.1111/j.1467-9531.2010.01223.x> and
Gile and Handcock (2015) <doi:10.1111/rssa.12091>.
Author: Mark S. Handcock [aut, cre],
Krista J. Gile [aut],
Ian E. Fellows [aut],
W. Whipple Neely [aut]
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between RDS versions 0.9-0 dated 2019-05-31 and 0.9-2 dated 2019-12-14
DESCRIPTION | 10 +-- MD5 | 94 ++++++++++++++++----------------- NAMESPACE | 3 + R/MA.sampling-c.R | 61 ++++++++++----------- R/MA.util.R | 6 +- R/bootstrap-intervals.R | 1 R/bootstrap.contingency.test.R | 2 R/control.rds.estimates.R | 21 +++++++ R/control.utilities.R | 46 ++++++++++------ R/hcg-bootstrap.R | 16 +++-- R/hcg-util.R | 22 ++++--- R/rds.interval.estimate.R | 41 ++++++++++++-- R/weights.R | 12 +++- man/LRT.trend.test.Rd | 13 +++- man/MA.estimates.Rd | 31 ++++++++-- man/RDS.HCG.estimates.Rd | 13 +++- man/RDS.I.estimates.Rd | 13 +++- man/RDS.II.estimates.Rd | 10 ++- man/RDS.Rd | 1 man/RDS.SS.estimates.Rd | 16 ++++- man/RDS.bootstrap.intervals.Rd | 23 +++++--- man/RDS.compare.two.proportions.Rd | 10 ++- man/as.rds.data.frame.Rd | 26 +++++---- man/bootstrap.contingency.test.Rd | 13 +++- man/bootstrap.incidence.Rd | 23 +++++--- man/bottleneck.plot.Rd | 10 ++- man/compute.weights.Rd | 12 +++- man/control.rds.estimates.Rd | 25 +++++++- man/convergence.plot.Rd | 10 ++- man/cumulative.estimate.Rd | 9 ++- man/differential.activity.estimates.Rd | 10 ++- man/get.h.hat.Rd | 7 +- man/get.recruitment.time.Rd | 8 ++ man/gile.ss.weights.Rd | 13 +++- man/hcg.weights.Rd | 20 ++++++- man/homophily.estimates.Rd | 18 ++++-- man/impute.degree.Rd | 12 +++- man/impute.visibility_mle.Rd | 18 ++++-- man/plot.rds.data.frame.Rd | 10 ++- man/print.rds.interval.estimate.Rd | 7 ++ man/print.summary.svyglm.RDS.Rd | 10 ++- man/rds.I.weights.Rd | 3 - man/rds.interval.estimate.Rd | 12 +++- man/rdssampleC.Rd |only man/reingold.tilford.plot.Rd | 19 ++++-- man/rid.from.coupons.Rd | 9 ++- man/set.control.class.Rd | 10 +-- man/summary.svyglm.RDS.Rd | 3 - man/ult.Rd |only 49 files changed, 544 insertions(+), 238 deletions(-)
Title: Import 'OpenStreetMap' Data as Simple Features or Spatial
Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp'
objects. 'OSM' data are extracted from the 'Overpass' web server and
processed with very fast 'C++' routines for return to 'R'.
Author: Mark Padgham [aut, cre],
Bob Rudis [aut],
Robin Lovelace [aut],
Maƫlle Salmon [aut],
Andrew Smith [ctb],
James Smith [ctb],
Marcin Kalicinski [ctb, cph] (Author of included RapidXML code),
Finkelstein Noam [ctb, cph] (Author of included stub.R code),
Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between osmdata versions 0.1.1 dated 2019-05-22 and 0.1.2 dated 2019-12-14
DESCRIPTION | 11 +- MD5 | 88 +++++++++-------- NAMESPACE | 1 NEWS.md | 18 +++ R/features.R | 20 ++- R/get-osmdata.R | 56 ++++++++--- R/getbb.R | 36 +++---- R/opq.R | 89 ++++++++++------- R/overpass-query.R | 14 +- R/poly2line.R | 12 +- R/trim-osmdata.R | 91 +++++++++++++++++- R/utils.R |only R/zzz.R | 20 +-- build/vignette.rds |binary inst/doc/osm-sf-translation.R | 16 +-- inst/doc/osm-sf-translation.Rmd | 8 - inst/doc/osm-sf-translation.html | 135 ++++++++++++++------------ inst/doc/osmdata-sc.R | 20 +-- inst/doc/osmdata-sc.Rmd | 10 - inst/doc/osmdata-sc.html | 117 ++++++++++++----------- inst/doc/osmdata.R | 128 ++++++++++++------------- inst/doc/osmdata.Rmd | 107 ++++++++++----------- inst/doc/osmdata.html | 197 ++++++++++++++++++++------------------- inst/figures |only man/add_osm_feature.Rd | 38 +++++-- man/available_features.Rd | 2 man/available_tags.Rd | 2 man/figures/osmhex.png |only man/get_overpass_url.Rd | 2 man/getbb.Rd | 21 ++-- man/opq.Rd | 36 +++---- man/osm_poly2line.Rd | 12 +- man/osmdata.Rd | 14 +- man/set_overpass_url.Rd | 12 +- man/unique_osmdata.Rd | 6 - man/unname_osmdata_sf.Rd |only src/convert-osm-rcpp.cpp | 3 tests/testthat/test-elevation.R |only tests/testthat/test-extract.R | 8 - tests/testthat/test-features.R | 2 tests/testthat/test-getbb.R | 22 ++++ tests/testthat/test-osmdata.R | 103 ++++++++++---------- tests/testthat/test-trim.R | 9 + tests/valgrind-test.R |only vignettes/osm-sf-translation.Rmd | 8 - vignettes/osmdata-refs.bib | 4 vignettes/osmdata-sc.Rmd | 10 - vignettes/osmdata.Rmd | 107 ++++++++++----------- 48 files changed, 928 insertions(+), 687 deletions(-)
Title: Multilevel Networks Analysis
Description: Analyze multilevel networks as described in Lazega et al (2008)
<doi:10.1016/j.socnet.2008.02.001> and in Lazega and Snijders
(2016, ISBN:978-3-319-24520-1). The package was developed essentially as an
extension to 'igraph'.
Author: Neylson Crepalde [aut, cre]
Maintainer: Neylson Crepalde <neylsoncrepalde@gmail.com>
Diff between multinets versions 0.2.1 dated 2018-07-07 and 0.2.2 dated 2019-12-14
DESCRIPTION | 12 +- MD5 | 68 ++++++------ NAMESPACE | 26 ++-- NEWS.md | 59 ++++++----- R/RcppExports.R | 38 +++---- R/extract_highlevel.R | 78 +++++++------- R/extract_lowlevel.R | 78 +++++++------- R/extract_mesolevel.R | 104 +++++++++---------- R/is_multilevel.R | 126 ++++++++++++------------ R/layout_multilevel.R | 154 ++++++++++++++--------------- R/linked_sim.R | 72 ++++++------- R/mode_transformation.R | 116 +++++++++++----------- R/rcpp_roxy.R | 6 - R/set_color_multilevel.R | 139 +++++++++++++------------- R/set_shape_multilevel.R | 84 ++++++++-------- R/zzz.R | 14 +- README.md | 157 ++++++++++++++---------------- man/extract_highlevel.Rd | 78 +++++++------- man/extract_lowlevel.Rd | 78 +++++++------- man/extract_mesolevel.Rd | 78 +++++++------- man/figures/README-example-1.png |binary man/is_multilevel.Rd | 94 ++++++++--------- man/layout_multilevel.Rd | 100 +++++++++---------- man/linked_sim.Rd | 86 ++++++++-------- man/mode_transformation.Rd | 96 +++++++++--------- man/set_color_multilevel.Rd | 88 ++++++++-------- man/set_shape_multilevel.Rd | 76 +++++++------- src/RcppExports.cpp | 4 src/get_edge_color.cpp | 10 - src/open_plot.cpp | 4 tests/testthat.R | 8 - tests/testthat/test-extraction.R | 26 ++-- tests/testthat/test-is_multilevel.R | 28 ++--- tests/testthat/test-layout_conditions.R | 22 ++-- tests/testthat/test-mode_transformation.R | 44 ++++---- 35 files changed, 1129 insertions(+), 1122 deletions(-)
Title: Analyze Multinomial Processing Tree Models
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, this package can fit a wide variety of other cognitive models such as SDT models (see fit.model). It also supports multicore fitting and FIA calculation (using the snowfall package), can generate or bootstrap data for simulations, and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre],
David Kellen [aut],
Quentin Gronau [aut],
Christian Mueller [ctb],
Akhil S Bhel [ctb]
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between MPTinR versions 1.11.0 dated 2018-06-23 and 1.12.0 dated 2019-12-14
DESCRIPTION | 10 ++--- MD5 | 38 +++++++++++----------- NAMESPACE | 21 +++++++++++- NEWS | 22 +++++++++++++ R/RcppExports.R | 8 ++-- R/bmpt.fia.R | 4 +- R/prediction.plot.R | 2 - R/select.mpt.R | 3 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/mptinr_introduction.R | 64 +++++++++++++++++++------------------- inst/doc/mptinr_introduction.Rnw | 2 - inst/doc/mptinr_introduction.pdf |binary man/check.mpt.Rd | 1 man/fit.mpt.Rd | 4 -- man/fit.mpt.old.Rd | 4 -- man/make.eqn.Rd | 2 - man/make.mpt.cf.Rd | 2 - src/RcppExports.cpp | 20 +++++------ vignettes/mptinr_introduction.Rnw | 2 - 20 files changed, 122 insertions(+), 87 deletions(-)
Title: Identify Similar Cases for Qualitative Case Studies
Description: Allows users to identify similar cases for qualitative case studies using statistical matching methods.
Author: Rich Nielsen
Maintainer: Rich Nielsen <rnielsen@mit.edu>
Diff between caseMatch versions 1.0.7 dated 2017-01-06 and 1.0.8 dated 2019-12-14
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/case.match.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Convert Statistical Analysis Objects into Tidy Tibbles
Description: Summarizes key information about statistical
objects in tidy tibbles. This makes it easy to report results, create
plots and consistently work with large numbers of models at once.
Broom provides three verbs that each provide different types of
information about a model. tidy() summarizes information about model
components such as coefficients of a regression. glance() reports
information about an entire model, such as goodness of fit measures
like AIC and BIC. augment() adds information about individual
observations to a dataset, such as fitted values or influence
measures.
Author: David Robinson [aut],
Alex Hayes [aut, cre] (<https://orcid.org/0000-0002-4985-5160>),
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Dieter Menne [ctb],
Benjamin Nutter [ctb],
Luke Johnston [ctb],
Ben Bolker [ctb],
Francois Briatte [ctb],
Jeffrey Arnold [ctb],
Jonah Gabry [ctb],
Luciano Selzer [ctb],
Gavin Simpson [ctb],
Jens Preussner [ctb],
Jay Hesselberth [ctb],
Hadley Wickham [ctb],
Matthew Lincoln [ctb],
Alessandro Gasparini [ctb],
Lukasz Komsta [ctb],
Frederick Novometsky [ctb],
Wilson Freitas [ctb],
Michelle Evans [ctb],
Jason Cory Brunson [ctb],
Simon Jackson [ctb],
Ben Whalley [ctb],
Michael Kuehn [ctb],
Jorge Cimentada [ctb],
Erle Holgersen [ctb],
Karl Dunkle Werner [ctb]
Maintainer: Alex Hayes <alexpghayes@gmail.com>
Diff between broom versions 0.5.2 dated 2019-04-07 and 0.5.3 dated 2019-12-14
DESCRIPTION | 9 MD5 | 410 ++++++++++++++++++++-------------------- NAMESPACE | 2 NEWS.md | 4 R/caret-tidiers.R | 2 R/lmodel2-tidiers.R | 19 - R/stats-loess-tidiers.R | 4 README.md | 125 +++++++----- build/vignette.rds |binary inst/doc/adding-tidiers.R | 8 inst/doc/adding-tidiers.html | 95 ++++----- inst/doc/available-methods.R | 4 inst/doc/available-methods.html | 11 - inst/doc/bootstrapping.R | 22 +- inst/doc/bootstrapping.html | 271 +++++++++++++------------- inst/doc/broom.R | 22 +- inst/doc/broom.html | 197 +++++++++---------- inst/doc/broom_and_dplyr.R | 30 +- inst/doc/broom_and_dplyr.html | 337 ++++++++++++++++---------------- inst/doc/glossary.R | 6 inst/doc/glossary.html | 11 - inst/doc/kmeans.R | 22 +- inst/doc/kmeans.html | 228 +++++++++++----------- man/argument_glossary.Rd | 44 ++-- man/augment.Mclust.Rd | 163 ++++++++------- man/augment.betareg.Rd | 194 +++++++++--------- man/augment.coxph.Rd | 260 +++++++++++++------------ man/augment.decomposed.ts.Rd | 255 ++++++++++++------------ man/augment.factanal.Rd | 171 ++++++++-------- man/augment.felm.Rd | 165 ++++++++-------- man/augment.glm.Rd | 139 ++++++------- man/augment.glmRob.Rd | 147 +++++++------- man/augment.htest.Rd | 171 ++++++++-------- man/augment.ivreg.Rd | 221 ++++++++++----------- man/augment.kmeans.Rd | 161 +++++++-------- man/augment.lm.Rd | 257 ++++++++++++------------- man/augment.lmRob.Rd | 147 +++++++------- man/augment.loess.Rd | 163 +++++++-------- man/augment.mjoint.Rd | 178 ++++++++--------- man/augment.nlrq.Rd | 108 +++++----- man/augment.nls.Rd | 177 ++++++++--------- man/augment.plm.Rd | 167 ++++++++-------- man/augment.poLCA.Rd | 177 ++++++++--------- man/augment.prcomp.Rd | 172 ++++++++-------- man/augment.rlm.Rd | 143 +++++++------ man/augment.rq.Rd | 231 +++++++++++----------- man/augment.rqs.Rd | 233 +++++++++++----------- man/augment.smooth.spline.Rd | 129 ++++++------ man/augment.speedlm.Rd | 170 ++++++++-------- man/augment.stl.Rd | 163 ++++++++------- man/augment.survreg.Rd | 260 +++++++++++++------------ man/augment_columns.Rd | 84 ++++---- man/bootstrap.Rd | 70 +++--- man/brms_tidiers.Rd | 186 +++++++++--------- man/broom.Rd | 32 +-- man/column_glossary.Rd | 48 ++-- man/confint_tidy.Rd | 68 +++--- man/data.frame_tidiers.Rd | 170 ++++++++-------- man/durbinWatsonTest_tidiers.Rd | 100 ++++----- man/emmeans_tidiers.Rd | 190 +++++++++--------- man/finish_glance.Rd | 72 +++---- man/fix_data_frame.Rd | 44 ++-- man/geeglm_tidiers.Rd | 184 +++++++++-------- man/glance.Arima.Rd | 101 ++++----- man/glance.Gam.Rd | 111 +++++----- man/glance.Mclust.Rd | 96 ++++----- man/glance.aareg.Rd | 132 ++++++------ man/glance.betareg.Rd | 132 ++++++------ man/glance.biglm.Rd | 101 ++++----- man/glance.binDesign.Rd | 133 ++++++------ man/glance.cch.Rd | 141 +++++++------ man/glance.coxph.Rd | 127 ++++++------ man/glance.cv.glmnet.Rd | 104 +++++----- man/glance.ergm.Rd | 115 +++++------ man/glance.factanal.Rd | 117 +++++------ man/glance.felm.Rd | 94 ++++----- man/glance.fitdistr.Rd | 99 ++++----- man/glance.garch.Rd | 104 +++++----- man/glance.glm.Rd | 125 ++++++------ man/glance.glmRob.Rd | 105 +++++----- man/glance.glmnet.Rd | 98 ++++----- man/glance.gmm.Rd | 99 ++++----- man/glance.ivreg.Rd | 175 ++++++++--------- man/glance.kmeans.Rd | 103 +++++----- man/glance.lavaan.Rd | 165 ++++++++-------- man/glance.lm.Rd | 129 ++++++------ man/glance.lmRob.Rd | 107 +++++----- man/glance.lmodel2.Rd | 101 +++++---- man/glance.mjoint.Rd | 101 ++++----- man/glance.muhaz.Rd | 103 +++++----- man/glance.multinom.Rd | 99 ++++----- man/glance.nlrq.Rd | 112 +++++----- man/glance.nls.Rd | 111 +++++----- man/glance.orcutt.Rd | 109 +++++----- man/glance.plm.Rd | 109 +++++----- man/glance.poLCA.Rd | 161 +++++++-------- man/glance.pyears.Rd | 131 ++++++------ man/glance.ridgelm.Rd | 105 +++++----- man/glance.rlm.Rd | 137 ++++++------- man/glance.rq.Rd | 126 ++++++------ man/glance.smooth.spline.Rd | 91 ++++---- man/glance.speedlm.Rd | 117 +++++------ man/glance.survdiff.Rd | 132 ++++++------ man/glance.survexp.Rd | 132 ++++++------ man/glance.survfit.Rd | 146 +++++++------- man/glance.survreg.Rd | 144 +++++++------- man/glance_optim.Rd | 105 +++++----- man/insert_NAs.Rd | 30 +- man/list_tidiers.Rd | 77 +++---- man/lme4_tidiers.Rd | 257 ++++++++++++------------- man/matrix_tidiers.Rd | 98 ++++----- man/mcmc_tidiers.Rd | 205 +++++++++++--------- man/mgcv_glance_gam.Rd | 111 +++++----- man/mgcv_tidy_gam.Rd | 111 +++++----- man/nlme_tidiers.Rd | 220 ++++++++++----------- man/null_tidiers.Rd | 64 +++--- man/ordinal_tidiers.Rd | 300 ++++++++++++++++------------- man/reexports.Rd | 50 ++-- man/rowwise_df_tidiers.Rd | 182 ++++++++--------- man/rstanarm_tidiers.Rd | 223 ++++++++++----------- man/sp_tidiers.Rd | 96 ++++----- man/sparse_tidiers.Rd | 60 ++--- man/summary_tidiers.Rd | 116 +++++------ man/tidy.Arima.Rd | 123 ++++++------ man/tidy.Gam.Rd | 107 +++++----- man/tidy.Kendall.Rd | 122 +++++------ man/tidy.Mclust.Rd | 155 +++++++-------- man/tidy.TukeyHSD.Rd | 118 +++++------ man/tidy.aareg.Rd | 156 ++++++++------- man/tidy.acf.Rd | 102 +++++---- man/tidy.anova.Rd | 118 +++++------ man/tidy.aov.Rd | 116 +++++------ man/tidy.aovlist.Rd | 118 +++++------ man/tidy.betareg.Rd | 162 +++++++-------- man/tidy.biglm.Rd | 189 +++++++++--------- man/tidy.binDesign.Rd | 117 +++++------ man/tidy.binWidth.Rd | 135 ++++++------- man/tidy.boot.Rd | 159 +++++++-------- man/tidy.btergm.Rd | 181 ++++++++--------- man/tidy.cch.Rd | 200 ++++++++++--------- man/tidy.cld.Rd | 78 +++---- man/tidy.coeftest.Rd | 106 +++++----- man/tidy.confint.glht.Rd | 78 +++---- man/tidy.confusionMatrix.Rd | 160 +++++++-------- man/tidy.coxph.Rd | 237 +++++++++++------------ man/tidy.cv.glmnet.Rd | 202 +++++++++---------- man/tidy.density.Rd | 81 ++++--- man/tidy.dist.Rd | 134 ++++++------- man/tidy.ergm.Rd | 172 ++++++++-------- man/tidy.factanal.Rd | 113 +++++------ man/tidy.felm.Rd | 196 +++++++++---------- man/tidy.fitdistr.Rd | 113 +++++------ man/tidy.ftable.Rd | 93 ++++----- man/tidy.gamlss.Rd | 120 +++++------ man/tidy.garch.Rd | 117 +++++------ man/tidy.glht.Rd | 135 ++++++------- man/tidy.glm.Rd | 129 ++++++------ man/tidy.glmRob.Rd | 163 ++++++++------- man/tidy.glmnet.Rd | 188 +++++++++--------- man/tidy.gmm.Rd | 283 ++++++++++++++------------- man/tidy.htest.Rd | 157 +++++++-------- man/tidy.ivreg.Rd | 178 ++++++++--------- man/tidy.kappa.Rd | 128 ++++++------ man/tidy.kde.Rd | 132 ++++++------ man/tidy.kmeans.Rd | 99 ++++----- man/tidy.lavaan.Rd | 149 +++++++------- man/tidy.lm.Rd | 277 +++++++++++++-------------- man/tidy.lmRob.Rd | 165 ++++++++-------- man/tidy.lmodel2.Rd | 150 +++++++------- man/tidy.manova.Rd | 129 ++++++------ man/tidy.map.Rd | 102 ++++----- man/tidy.mjoint.Rd | 237 +++++++++++------------ man/tidy.mle2.Rd | 110 +++++----- man/tidy.muhaz.Rd | 103 +++++----- man/tidy.multinom.Rd | 160 +++++++-------- man/tidy.nlrq.Rd | 128 ++++++------ man/tidy.nls.Rd | 166 ++++++++-------- man/tidy.orcutt.Rd | 117 +++++------ man/tidy.pairwise.htest.Rd | 142 +++++++------ man/tidy.plm.Rd | 168 ++++++++-------- man/tidy.poLCA.Rd | 217 ++++++++++----------- man/tidy.power.htest.Rd | 107 +++++----- man/tidy.prcomp.Rd | 238 +++++++++++------------ man/tidy.pyears.Rd | 170 ++++++++-------- man/tidy.rcorr.Rd | 162 +++++++-------- man/tidy.ridgelm.Rd | 141 ++++++------- man/tidy.rlm.Rd | 133 ++++++------ man/tidy.roc.Rd | 146 +++++++------- man/tidy.rq.Rd | 135 ++++++------- man/tidy.rqs.Rd | 139 ++++++------- man/tidy.spec.Rd | 100 ++++----- man/tidy.speedlm.Rd | 147 +++++++------- man/tidy.summary.glht.Rd | 78 +++---- man/tidy.survdiff.Rd | 150 +++++++------- man/tidy.survexp.Rd | 158 ++++++++------- man/tidy.survfit.Rd | 179 +++++++++-------- man/tidy.survreg.Rd | 188 +++++++++--------- man/tidy.table.Rd | 96 ++++----- man/tidy.ts.Rd | 110 +++++----- man/tidy.zoo.Rd | 146 +++++++------- man/tidy_irlba.Rd | 177 ++++++++--------- man/tidy_optim.Rd | 131 ++++++------ man/tidy_svd.Rd | 249 ++++++++++++------------ man/tidy_xyz.Rd | 125 ++++++------ man/vector_tidiers.Rd | 74 +++---- tests/testthat/test-lfe.R | 2 206 files changed, 13953 insertions(+), 13456 deletions(-)
Title: Performs Common Linear Algebra Operations Used in Quantum
Computing and Implements Quantum Algorithms
Description: Contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help learn quantum mechanics and algorithms. Can create arbitrarily sized kets and bras and implements quantum gates, inner products, and tensor products. Creates arbitrarily controlled versions of all gates and can simulate complete or partial measurements of kets. Has functionality to convert functions into equivalent quantum gates and model quantum noise. Includes larger applications, such as Steane error correction <DOI:10.1103/physrevlett.77.793>, Quantum Fourier Transform and Shor's algorithm (Shor 1999), Grover's algorithm (1996), Quantum Approximation Optimization Algorithm (QAOA) (Farhi, Goldstone, and Gutmann 2014) <arXiv:1411.4028>, and a variational quantum classifier (Schuld 2018) <arXiv:1804.00633>.
Author: Salonik Resch
Maintainer: Salonik Resch <resc0059@umn.edu>
Diff between QuantumOps versions 2.5.3 dated 2019-08-30 and 3.0.0 dated 2019-12-14
DESCRIPTION | 10 +- MD5 | 50 ++++++++++---- NAMESPACE | 12 +++ NEWS.md | 18 +++++ R/AmplitudeDamping.R |only R/CoherentNoise.R |only R/DecomposeGate.R |only R/FullAdder.R |only R/PauliNoise.R |only R/PauliOperators.R |only R/QAOA.R | 48 ++++++++++--- R/QFT.R | 57 ++++++++++++++-- R/QuantumClassifier.R | 162 +++++++++++++++++++++++++++++++++-------------- R/RandomizeCompile.R |only R/SynthesizeCircuit.R |only R/TOFFOLI.R | 59 +++++++++++++---- R/convert_ket2DM.R |only R/many.R | 5 - R/nBitAddition.R |only R/opDM.R |only R/ranket.R |only R/single.R | 6 + man/AmplitudeDamping.Rd |only man/CoherentNoise.Rd |only man/DecomposeGate.Rd |only man/FullAdder.Rd |only man/PauliNoise.Rd |only man/PauliOperators.Rd |only man/QAOA.Rd | 4 - man/QFT.Rd | 10 ++ man/QuantumClassifier.Rd | 18 +++-- man/RandomizeCompile.Rd |only man/SynthesizeCircuit.Rd |only man/TOFFOLI.Rd | 10 ++ man/convert_ket2DM.Rd |only man/nBitAddition.Rd |only man/opDM.Rd |only man/ranket.Rd |only 38 files changed, 355 insertions(+), 114 deletions(-)
Title: Three Dimensional PCA Plots
Description: Functions simplifying presentation of PCA models in a 3D interactive representation using 'rgl'.
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between pca3d versions 0.10 dated 2017-02-17 and 0.10.1 dated 2019-12-14
DESCRIPTION | 7 ++++--- MD5 | 16 ++++++++-------- R/helpers.R | 19 +++++++++++-------- R/pca2d.R | 2 +- R/pca3d.R | 2 +- build/vignette.rds |binary data/metabo.rda |binary inst/doc/pca3d.R | 20 ++++++++++---------- inst/doc/pca3d.pdf |binary 9 files changed, 35 insertions(+), 31 deletions(-)
Title: Statistical Framework to Define Subgroups in Complex Datasets
Description: High-dimensional datasets that do not exhibit a clear intrinsic clustered structure pose a challenge to conventional clustering algorithms. For this reason, we developed an unsupervised framework that helps scientists to better subgroup their datasets based on visual cues, please see Gao S, Mutter S, Casey A, Makinen V-P (2019) Numero: a statistical framework to define multivariable subgroups in complex population-based datasets, Int J Epidemiology, 48:369-37, <doi:10.1093/ije/dyy113>. The framework includes the necessary functions to construct a self-organizing map of the data, to evaluate the statistical significance of the observed data patterns, and to visualize the results.
Author: Song Gao [aut],
Stefan Mutter [aut],
Aaron E. Casey [aut],
Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine@gmail.com>
Diff between Numero versions 1.3.3 dated 2019-10-31 and 1.4.0 dated 2019-12-14
Numero-1.3.3/Numero/inst/extcode/circus.js |only Numero-1.3.3/Numero/inst/extcode/examples.R |only Numero-1.4.0/Numero/DESCRIPTION | 8 Numero-1.4.0/Numero/MD5 | 71 ++- Numero-1.4.0/Numero/NAMESPACE | 5 Numero-1.4.0/Numero/R/nroAggregate.R | 4 Numero-1.4.0/Numero/R/nroDestratify.R | 15 Numero-1.4.0/Numero/R/nroImpute.R | 6 Numero-1.4.0/Numero/R/nroKmeans.R | 4 Numero-1.4.0/Numero/R/nroKohonen.R | 2 Numero-1.4.0/Numero/R/nroLabel.R | 2 Numero-1.4.0/Numero/R/nroMatch.R | 2 Numero-1.4.0/Numero/R/nroPair.R | 23 - Numero-1.4.0/Numero/R/nroPermute.R | 2 Numero-1.4.0/Numero/R/nroPlot.save.R | 10 Numero-1.4.0/Numero/R/nroStatistic.R |only Numero-1.4.0/Numero/R/nroTrain.R | 7 Numero-1.4.0/Numero/R/numero.clean.R | 46 +- Numero-1.4.0/Numero/inst/doc/intro.html | 351 +++++++++------- Numero-1.4.0/Numero/inst/extcode/a_globals.js |only Numero-1.4.0/Numero/inst/extcode/createhoverdistrict.js |only Numero-1.4.0/Numero/inst/extcode/createsymbol.js |only Numero-1.4.0/Numero/inst/extcode/downloadregions.js |only Numero-1.4.0/Numero/inst/extcode/getdistrictdata.js |only Numero-1.4.0/Numero/inst/extcode/initmenu.js |only Numero-1.4.0/Numero/inst/extcode/initpage.js |only Numero-1.4.0/Numero/inst/extcode/initregions.js |only Numero-1.4.0/Numero/inst/extcode/locatesubplot.js |only Numero-1.4.0/Numero/inst/extcode/pointerdowndistrict.js |only Numero-1.4.0/Numero/inst/extcode/pointerdownsymbol.js |only Numero-1.4.0/Numero/inst/extcode/pointeroverdistrict.js |only Numero-1.4.0/Numero/inst/extcode/pointeroversymbol.js |only Numero-1.4.0/Numero/inst/extcode/refreshmenu.js |only Numero-1.4.0/Numero/inst/extcode/removehovers.js |only Numero-1.4.0/Numero/inst/extcode/updatehighlights.js |only Numero-1.4.0/Numero/man/nroPair.Rd | 15 Numero-1.4.0/Numero/man/nroStatistic.Rd |only Numero-1.4.0/Numero/man/numero.clean.Rd | 46 +- Numero-1.4.0/Numero/src/Numero_init.c | 2 Numero-1.4.0/Numero/src/abacus.h | 10 Numero-1.4.0/Numero/src/abacus.matrix.add.cpp | 25 + Numero-1.4.0/Numero/src/abacus.matrix.insert.cpp | 23 + Numero-1.4.0/Numero/src/abacus.statistic.cpp | 71 ++- Numero-1.4.0/Numero/src/abacus.version.cpp | 2 Numero-1.4.0/Numero/src/nro_diffuse.cpp | 14 Numero-1.4.0/Numero/src/nro_statistic.cpp |only Numero-1.4.0/Numero/src/nro_train.cpp | 4 47 files changed, 512 insertions(+), 258 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-18 1.0
Title: Syntax Highlighter
Description: Syntax highlighter for R code based
on the results of the R parser. Rendering in HTML and latex
markup. Custom Sweave driver performing syntax highlighting
of R code chunks.
Author: Romain Francois [aut, cre],
Andre Simon [ctb]
Maintainer: ORPHANED
Diff between highlight versions 0.4.7.3 dated 2019-12-01 and 0.4.7.4 dated 2019-12-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/Makevars | 1 + src/Makevars.win | 1 + 4 files changed, 8 insertions(+), 6 deletions(-)