Title: Common Plots for Analysis
Description: Select data analysis plots, under a standardized calling interface implemented on top of 'ggplot2' and 'plotly'.
Plots of interest include: 'ROC', gain curve, scatter plot with marginal distributions,
conditioned scatter plot with marginal densities,
box and stem with matching theoretical distribution, and density with matching theoretical distribution.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between WVPlots versions 1.2.5 dated 2020-05-01 and 1.2.6 dated 2020-08-11
WVPlots-1.2.5/WVPlots/R/wrapr_exports.R |only WVPlots-1.2.5/WVPlots/man/reexports.Rd |only WVPlots-1.2.6/WVPlots/DESCRIPTION | 18 WVPlots-1.2.6/WVPlots/MD5 | 99 - WVPlots-1.2.6/WVPlots/NAMESPACE | 26 WVPlots-1.2.6/WVPlots/NEWS.md | 7 WVPlots-1.2.6/WVPlots/R/ConditionalSmoothedScatterPlot.R | 2 WVPlots-1.2.6/WVPlots/R/DistributionPlot.R | 5 WVPlots-1.2.6/WVPlots/R/DoubleDensity.R | 2 WVPlots-1.2.6/WVPlots/R/DoubleHistogram.R | 2 WVPlots-1.2.6/WVPlots/R/FitHistoryPlot.R | 4 WVPlots-1.2.6/WVPlots/R/GainCurve.R | 2 WVPlots-1.2.6/WVPlots/R/LogLogPlot.R | 2 WVPlots-1.2.6/WVPlots/R/PRPlot.R | 4 WVPlots-1.2.6/WVPlots/R/PRTPlot.R | 4 WVPlots-1.2.6/WVPlots/R/PairPlot.R | 8 WVPlots-1.2.6/WVPlots/R/ROC.R | 26 WVPlots-1.2.6/WVPlots/R/ScatterHist.R | 4 WVPlots-1.2.6/WVPlots/R/ScatterHistC.R | 4 WVPlots-1.2.6/WVPlots/R/ShadowHist.R | 2 WVPlots-1.2.6/WVPlots/R/ShadowPlot.R | 2 WVPlots-1.2.6/WVPlots/R/ThresholdPlot.R |only WVPlots-1.2.6/WVPlots/README.md | 11 WVPlots-1.2.6/WVPlots/build/vignette.rds |binary WVPlots-1.2.6/WVPlots/inst/doc/WVPlots_concept.Rmd | 2 WVPlots-1.2.6/WVPlots/inst/doc/WVPlots_concept.html | 196 +-- WVPlots-1.2.6/WVPlots/inst/doc/WVPlots_examples.R | 29 WVPlots-1.2.6/WVPlots/inst/doc/WVPlots_examples.Rmd | 42 WVPlots-1.2.6/WVPlots/inst/doc/WVPlots_examples.html | 644 ++++++------ WVPlots-1.2.6/WVPlots/man/ConditionalSmoothedScatterPlot.Rd | 2 WVPlots-1.2.6/WVPlots/man/DoubleDensityPlot.Rd | 2 WVPlots-1.2.6/WVPlots/man/DoubleHistogramPlot.Rd | 2 WVPlots-1.2.6/WVPlots/man/GainCurvePlotWithNotation.Rd | 2 WVPlots-1.2.6/WVPlots/man/LogLogPlot.Rd | 2 WVPlots-1.2.6/WVPlots/man/MetricPairPlot.Rd |only WVPlots-1.2.6/WVPlots/man/PRPlot.Rd | 2 WVPlots-1.2.6/WVPlots/man/PRTPlot.Rd | 2 WVPlots-1.2.6/WVPlots/man/PairPlot.Rd | 8 WVPlots-1.2.6/WVPlots/man/PlotDistCountNormal.Rd | 2 WVPlots-1.2.6/WVPlots/man/PlotDistDensityNormal.Rd | 2 WVPlots-1.2.6/WVPlots/man/ROCPlot.Rd | 4 WVPlots-1.2.6/WVPlots/man/ROCPlotPair.Rd | 2 WVPlots-1.2.6/WVPlots/man/ROCPlotPair2.Rd | 2 WVPlots-1.2.6/WVPlots/man/ScatterHist.Rd | 2 WVPlots-1.2.6/WVPlots/man/ScatterHistC.Rd | 2 WVPlots-1.2.6/WVPlots/man/ScatterHistN.Rd | 2 WVPlots-1.2.6/WVPlots/man/ShadowHist.Rd | 2 WVPlots-1.2.6/WVPlots/man/ShadowPlot.Rd | 2 WVPlots-1.2.6/WVPlots/man/ThresholdPlot.Rd |only WVPlots-1.2.6/WVPlots/man/plot_Keras_fit_trajectory.Rd | 2 WVPlots-1.2.6/WVPlots/man/plot_fit_trajectory.Rd | 2 WVPlots-1.2.6/WVPlots/vignettes/WVPlots_concept.Rmd | 2 WVPlots-1.2.6/WVPlots/vignettes/WVPlots_examples.Rmd | 42 53 files changed, 688 insertions(+), 551 deletions(-)
Title: Mixed-Effect Models, Particularly Spatial Models
Description: Inference based on mixed-effect models, including generalized linear mixed models with spatial correlations and models with non-Gaussian random effects (e.g., Beta). Various approximations of likelihood or restricted likelihood are implemented, in particular Laplace approximation and h-likelihood (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>). Both classical geostatistical models, and Markov random field models on irregular grids (as considered in the 'INLA' package, <http://www.r-inla.org>), can be fitted. Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model.
Author: François Rousset [aut, cre, cph]
(<https://orcid.org/0000-0003-4670-0371>),
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [aut] (<https://orcid.org/0000-0003-0637-2959>),
GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 3.3.0 dated 2020-05-30 and 3.4.1 dated 2020-08-11
DESCRIPTION | 12 - MD5 | 116 ++++++------- NAMESPACE | 2 R/HLCor.R | 6 R/HLCor_body.R | 7 R/HLFactorList.R | 62 ++++-- R/HLfit.R | 5 R/HLfit_Internals.R | 31 ++- R/HLfit_b_internals.R | 3 R/HLfit_body.R | 16 + R/HLfit_body_augZXy.R | 8 R/HLframes.R | 23 +- R/MakeCovEst.R | 2 R/confint.R | 76 +++++--- R/corrHLfit-internals.R | 8 R/corrHLfit.R | 7 R/corrHLfit_body.R | 7 R/correlationFns.R | 4 R/cov_new_fix.R | 59 ++++-- R/extractors.R | 10 - R/fit_as_ZX.R | 81 ++++++--- R/fit_as_sparsePrecision.R | 97 +++++++--- R/fitme.R | 16 + R/fitme_body.R | 7 R/fitmecorrHLfit_body_internals.R | 10 - R/geo_info.R | 177 ++++++++++++++++--- R/get_inits_by_glm.R |only R/multiFRK.R | 83 ++++++--- R/predict.R | 25 ++ R/preprocess.R | 206 +++++------------------ R/preprocess_internals.R | 33 +++ R/sXaug_sparsePrecisions.R | 50 +++-- R/safe_opt.R | 2 R/separator.R | 1 R/simulate.HL.R | 5 R/source_MV.R | 213 +++++++++++++++++++++--- R/spaMM.data.R | 4 R/summary.HL.R | 27 +++ R/update.HL.R | 2 R/utils.R | 41 +++- build/partial.rdb |binary inst/NEWS.Rd | 38 ++++ man/HLCor.Rd | 27 +-- man/HLfit.Rd | 2 man/IMRF.Rd | 14 + man/confint.Rd | 19 +- man/div_info.Rd |only man/dopar.Rd | 2 man/fitme.Rd | 2 man/get_ranPars.Rd | 7 man/good-practice.Rd | 20 ++ man/inverse.Gamma.Rd | 2 man/mapMM.Rd | 2 man/predict.Rd | 2 man/seaMask.Rd | 4 man/spaMM-S3.Rd | 3 tests/testthat/test-IMRF.R | 3 tests/testthat/test-confint-spprec.R |only tests/testthat/test-confint.R | 12 + tests/testthat/test-distMatrix.R |only tests/testthat/test-predVar-Matern-corrMatrix.R | 85 +++++---- 61 files changed, 1191 insertions(+), 597 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>),
Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>),
Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>),
Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>),
Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>),
Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>),
Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>),
Joseph Larmarange [ctb] (<https://orcid.org/0000-0001-7097-700X>),
Stephanie Lobaugh [ctb],
Gustavo Zapata Wainberg [ctb] (<https://orcid.org/0000-0002-2524-3637>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 1.3.2 dated 2020-06-14 and 1.3.3 dated 2020-08-11
gtsummary-1.3.2/gtsummary/R/as_flextable.R |only gtsummary-1.3.2/gtsummary/R/as_huxtable.R |only gtsummary-1.3.2/gtsummary/R/gtsummary_logo.R |only gtsummary-1.3.2/gtsummary/R/modify_footnote.R |only gtsummary-1.3.2/gtsummary/R/modify_header.R |only gtsummary-1.3.2/gtsummary/R/modify_spanning_header.R |only gtsummary-1.3.2/gtsummary/R/other_exports.R |only gtsummary-1.3.2/gtsummary/man/all_of.Rd |only gtsummary-1.3.2/gtsummary/man/any_of.Rd |only gtsummary-1.3.2/gtsummary/man/as_flextable.Rd |only gtsummary-1.3.2/gtsummary/man/contains.Rd |only gtsummary-1.3.2/gtsummary/man/ends_with.Rd |only gtsummary-1.3.2/gtsummary/man/everything.Rd |only gtsummary-1.3.2/gtsummary/man/figures/modify_footnote_ex1.png |only gtsummary-1.3.2/gtsummary/man/figures/modify_footnote_ex2.png |only gtsummary-1.3.2/gtsummary/man/figures/modify_footnote_ex3.png |only gtsummary-1.3.2/gtsummary/man/figures/modify_header_ex1.png |only gtsummary-1.3.2/gtsummary/man/figures/modify_header_ex2.png |only 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gtsummary-1.3.3/gtsummary/R/reexport.R | 44 gtsummary-1.3.3/gtsummary/R/set_gtsummary_theme.R | 4 gtsummary-1.3.3/gtsummary/R/style_number.R |only gtsummary-1.3.3/gtsummary/R/style_percent.R | 13 gtsummary-1.3.3/gtsummary/R/style_pvalue.R | 60 gtsummary-1.3.3/gtsummary/R/style_ratio.R | 9 gtsummary-1.3.3/gtsummary/R/style_sigfig.R | 38 gtsummary-1.3.3/gtsummary/R/sysdata.rda |binary gtsummary-1.3.3/gtsummary/R/tbl_cross.R | 2 gtsummary-1.3.3/gtsummary/R/tbl_merge.R | 15 gtsummary-1.3.3/gtsummary/R/tbl_regression.R | 37 gtsummary-1.3.3/gtsummary/R/tbl_stack.R | 37 gtsummary-1.3.3/gtsummary/R/tbl_summary.R | 194 gtsummary-1.3.3/gtsummary/R/tbl_survfit.R | 464 gtsummary-1.3.3/gtsummary/R/tbl_survival.R | 2 gtsummary-1.3.3/gtsummary/R/tbl_svysummary.R |only gtsummary-1.3.3/gtsummary/R/tbl_uvregression.R | 20 gtsummary-1.3.3/gtsummary/R/theme_gtsummary.R | 190 gtsummary-1.3.3/gtsummary/R/utils-add_p.R | 166 gtsummary-1.3.3/gtsummary/R/utils-gtsummary_core.R | 13 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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 1.5 dated 2019-10-17 and 1.6 dated 2020-08-11
DESCRIPTION | 19 +- MD5 | 13 - NAMESPACE | 9 - R/DTRreg.R | 369 +++++++++++++++++++++++++++++++++++++------------- man/DWSurv.Rd | 47 ++++-- man/confint.DTRreg.Rd | 12 - man/gdwols.Rd |only man/plot.DTRreg.Rd | 5 8 files changed, 339 insertions(+), 135 deletions(-)
Title: Stylometric Multivariate Analyses
Description: Supervised and unsupervised multivariate methods, supplemented by GUI and some visualizations, to perform various analyses in the field of computational stylistics, authorship attribution, etc. For further reference, see Eder et al. (2016), <https://journal.r-project.org/archive/2016/RJ-2016-007/index.html>. You are also encouraged to visit the Computational Stylistics Group's website <https://computationalstylistics.github.io/>, where a reasonable amount of information about the package and related projects are provided.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont, Steffen Pielstroem
Maintainer: Maciej Eder <maciejeder@gmail.com>
Diff between stylo versions 0.7.2 dated 2020-04-20 and 0.7.3 dated 2020-08-11
DESCRIPTION | 8 ++-- MD5 | 28 +++++++------- NEWS.md | 11 +++++ R/load.corpus.R | 8 ++-- R/oppose.R | 4 +- R/perform.svm.R | 2 + R/rolling.classify.r | 90 +++++++++++++++++++++++++++++++++++++++++------- R/stylo.pronouns.R | 2 - man/delete.markup.Rd | 2 - man/dist.cosine.Rd | 7 +-- man/dist.delta.Rd | 9 ++-- man/dist.wurzburg.Rd | 7 +-- man/make.ngrams.Rd | 2 - man/perform.svm.Rd | 3 - man/rolling.classify.Rd | 8 +++- 15 files changed, 135 insertions(+), 56 deletions(-)
Title: Succinct and Correct Statistical Summaries for Reports
Description: Succinctly and correctly format statistical summaries of
various models and tests (F-test, Chi-Sq-test, Fisher-test, T-test, and rank-significance). The main purpose is unified reporting
of experimental results, working around issue such as the difficulty of
extracting model summary facts (such as with 'lm'/'glm'). This package also
includes empirical tests, such as bootstrap estimates.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between sigr versions 1.0.6 dated 2019-07-24 and 1.0.8 dated 2020-08-11
DESCRIPTION | 12 +-- MD5 | 110 ++++++++++++++++----------------- NEWS.md | 5 + R/fns.R | 2 R/run_sigr_tests.R | 2 README.md | 28 +++----- build/vignette.rds |binary inst/doc/lmExample.R | 10 +-- inst/doc/lmExample.html | 21 +++--- inst/doc/sigrFormatting.R | 32 ++++----- inst/doc/sigrFormatting.Rmd | 4 - inst/doc/sigrFormatting.html | 25 +++---- man/TInterval.data.frame.Rd | 3 man/TIntervalS.Rd | 10 ++- man/calcAUC.Rd | 2 man/permTestAUC.Rd | 13 +++ man/permutationScoreModel.Rd | 12 +++ man/reexports.Rd | 2 man/render.Rd | 11 ++- man/render.sigr_Bernoulli_diff_test.Rd | 12 ++- man/render.sigr_aucpairtest.Rd | 11 ++- man/render.sigr_aucpermtest.Rd | 11 ++- man/render.sigr_aucresamptest.Rd | 12 ++- man/render.sigr_binomtest.Rd | 11 ++- man/render.sigr_chisqtest.Rd | 11 ++- man/render.sigr_cohend.Rd | 11 ++- man/render.sigr_cortest.Rd | 11 ++- man/render.sigr_emptest.Rd | 11 ++- man/render.sigr_fishertest.Rd | 11 ++- man/render.sigr_ftest.Rd | 11 ++- man/render.sigr_permtest.Rd | 11 ++- man/render.sigr_pwr_htest.Rd | 11 ++- man/render.sigr_significance.Rd | 12 ++- man/render.sigr_tinterval.Rd | 11 ++- man/render.sigr_ttest.Rd | 11 ++- man/resampleScoreModel.Rd | 12 +++ man/resampleScoreModelPair.Rd | 15 +++- man/resampleTestAUC.Rd | 14 +++- man/run_sigr_tests.Rd | 19 +++-- man/sigr.Rd | 1 man/testAUCpair.Rd | 15 +++- man/wrapBinomTest.data.frame.Rd | 13 +++ man/wrapBinomTest.logical.Rd | 11 ++- man/wrapBinomTest.numeric.Rd | 12 ++- man/wrapBinomTestS.Rd | 10 ++- man/wrapChiSqTest.data.frame.Rd | 13 +++ man/wrapCohenD.data.frame.Rd | 3 man/wrapCorTest.data.frame.Rd | 14 +++- man/wrapFTest.data.frame.Rd | 16 +++- man/wrapFTest.lm.Rd | 3 man/wrapFTest.summary.lm.Rd | 3 man/wrapFisherTest.data.frame.Rd | 21 ++++-- man/wrapFisherTest.table.Rd | 17 +++-- man/wrapTTest.data.frame.Rd | 17 +++-- man/wrapTTest.numeric.Rd | 16 +++- vignettes/sigrFormatting.Rmd | 4 - 56 files changed, 498 insertions(+), 234 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut],
Namita Gupta [aut],
Susanna Marquez [aut],
Julian Zhou [aut],
Nima Nouri [aut],
Ang Cui [ctb],
Jason Vander Heiden [aut, cre],
Gur Yaari [aut],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@gmail.com>
Diff between shazam versions 1.0.1 dated 2020-07-19 and 1.0.2 dated 2020-08-11
DESCRIPTION | 12 ++++++------ MD5 | 32 ++++++++++++++++---------------- NEWS.md | 15 +++++++++++++++ R/DistToNearest.R | 1 + R/MutationDefinitions.R | 1 + R/MutationProfiling.R | 7 +++++-- R/RegionDefinitions.R | 1 + R/Shmulate.R | 3 ++- R/TargetingModels.R | 22 +++++++++++++--------- build/vignette.rds |binary inst/doc/Baseline-Vignette.pdf |binary inst/doc/DistToNearest-Vignette.pdf |binary inst/doc/Mutation-Vignette.pdf |binary inst/doc/Shmulate-Vignette.pdf |binary inst/doc/Targeting-Vignette.pdf |binary man/createMutabilityMatrix.Rd | 5 +++-- man/createTargetingModel.Rd | 10 +++++----- 17 files changed, 68 insertions(+), 41 deletions(-)
Title: Univariate Bootstrapping and Other Things
Description: Primarily devoted to implementing the Univariate Bootstrap (as well as the Traditional Bootstrap). In addition there are multiple functions for DeFries-Fulker behavioral genetics models. The univariate bootstrapping functions, DeFries-Fulker functions, regression and traditional bootstrapping functions form the original core. Additional features may come online later, however this software is a work in progress. For more information about univariate bootstrapping see: Lee and Rodgers (1998) and Beasley et al (2007) <doi.org/10.1037/1082-989X.12.4.414>.
Author: Patrick O'Keefe
Maintainer: Patrick O'Keefe <patrick.okeefe@vanderbilt.edu>
Diff between Omisc versions 0.1.2 dated 2019-07-03 and 0.1.3 dated 2020-08-11
DESCRIPTION | 8 +- MD5 | 88 +++++++++++++++--------------- NAMESPACE | 2 R/DFanalysis.R | 29 ++++++++-- R/standardBootIntervals.R | 2 man/AllBootResults.Rd | 66 +++++++++++----------- man/BCa.Rd | 81 +++++++++++++++------------- man/BarebonesBetas.Rd | 50 ++++++++--------- man/DFSimulated.Rd | 52 +++++++++--------- man/DFSimulatedChisq.Rd | 56 +++++++++---------- man/DFSimulatedChisqNew.Rd | 57 +++++++++---------- man/DFanalysis.Rd | 94 ++++++++++++++++++-------------- man/Group_function.Rd | 88 ++++++++++++++++-------------- man/HoffPseudoStandard.Rd | 48 ++++++++-------- man/MyLM.Rd | 60 ++++++++++---------- man/NaiveBoot.Rd | 58 ++++++++++---------- man/NaiveBoot_dep.Rd | 59 ++++++++++---------- man/RK.Rd | 54 +++++++++--------- man/Sfunc.Rd | 42 +++++++------- man/TestData.Rd | 61 ++++++++++----------- man/aCalc.Rd | 42 +++++++------- man/aboot.Rd | 48 ++++++++-------- man/add.Rd | 40 ++++++------- man/ajack.Rd | 50 ++++++++--------- man/bias.Rd | 52 +++++++++--------- man/bootAnalysis.Rd | 60 ++++++++++---------- man/bootsample.Rd | 44 +++++++-------- man/cent.Rd | 40 ++++++------- man/centerData.Rd | 40 ++++++------- man/cholcors.Rd | 50 ++++++++--------- man/cholcovs.Rd | 50 ++++++++--------- man/doubleEnter.Rd | 48 ++++++++-------- man/findSa.Rd | 124 +++++++++++++++++++++---------------------- man/jackknife.Rd | 44 +++++++-------- man/justBetas.Rd | 62 ++++++++++----------- man/lbind.Rd | 54 +++++++++--------- man/leave1out.Rd | 46 +++++++-------- man/resample.Rd | 44 +++++++-------- man/standardBootIntervals.Rd | 56 +++++++++---------- man/uniboot.Rd | 86 ++++++++++++++++------------- man/unibootVar.Rd | 50 ++++++++--------- man/uniboot_dep.Rd | 80 +++++++++++++++------------ man/unibootsample.Rd | 50 ++++++++--------- man/zScore.Rd | 44 +++++++-------- man/zScoreData.Rd | 40 ++++++------- 45 files changed, 1230 insertions(+), 1169 deletions(-)
Title: A Seamless Integration of 'R' and 'Dynare'
Description: It allows running 'Dynare' program from R Markdown. 'Dynare' is a software platform for handling a wide class of economic models, in particular dynamic stochastic general equilibrium ('DSGE') and overlapping generations ('OLG') models. This package serves as a 'Dynare' Knit-Engine for 'knitr' package. The package requires 'Dynare' 4.6.1 (<https://www.dynare.org/>) and 'Octave' 5.2.0 (<https://www.gnu.org/software/octave/download.html>). Write all your 'Dynare' commands in R Markdown chunk.
Author: Sagiru Mati [aut, cre]
Maintainer: Sagiru Mati <smati@smati.com.ng>
Diff between DynareR versions 0.1.0 dated 2020-06-25 and 0.1.1 dated 2020-08-11
DynareR-0.1.0/DynareR/inst/examples/BKK |only DynareR-0.1.0/DynareR/inst/examples/DynareR.pdf |only DynareR-0.1.1/DynareR/DESCRIPTION | 10 DynareR-0.1.1/DynareR/MD5 | 100 ++--- DynareR-0.1.1/DynareR/NAMESPACE | 5 DynareR-0.1.1/DynareR/NEWS.md |only DynareR-0.1.1/DynareR/R/eng_dynare.R | 29 + DynareR-0.1.1/DynareR/R/include_IRF.R |only DynareR-0.1.1/DynareR/R/run_dynare.R |only DynareR-0.1.1/DynareR/R/run_model.R |only DynareR-0.1.1/DynareR/R/run_models.R |only DynareR-0.1.1/DynareR/R/write_dyn.R |only DynareR-0.1.1/DynareR/R/write_mod.R |only DynareR-0.1.1/DynareR/README.md | 270 ++++++++++++++- DynareR-0.1.1/DynareR/demo |only DynareR-0.1.1/DynareR/inst/doc/DynareR.R | 168 +++++++++ DynareR-0.1.1/DynareR/inst/doc/DynareR.Rmd | 237 ++++++++++++- DynareR-0.1.1/DynareR/inst/doc/DynareR.html | 189 ++++++++++ DynareR-0.1.1/DynareR/inst/examples/Ramsey_Example.R |only DynareR-0.1.1/DynareR/inst/examples/agtrend.R |only DynareR-0.1.1/DynareR/inst/examples/bkk.R |only DynareR-0.1.1/DynareR/inst/examples/example1.R |only DynareR-0.1.1/DynareR/inst/examples/example1_reporting.R |only DynareR-0.1.1/DynareR/inst/examples/example2.R |only DynareR-0.1.1/DynareR/inst/examples/example3.R |only DynareR-0.1.1/DynareR/inst/examples/ramst.R |only DynareR-0.1.1/DynareR/inst/examples/run_dynare.R |only DynareR-0.1.1/DynareR/inst/examples/run_model.R |only DynareR-0.1.1/DynareR/inst/examples/run_models.R |only DynareR-0.1.1/DynareR/inst/examples/write_dyn.R |only DynareR-0.1.1/DynareR/inst/examples/write_mod.R |only DynareR-0.1.1/DynareR/inst/rmarkdown |only DynareR-0.1.1/DynareR/man/eng_dynare.Rd | 44 +- DynareR-0.1.1/DynareR/man/include_IRF.Rd |only DynareR-0.1.1/DynareR/man/run_dynare.Rd |only DynareR-0.1.1/DynareR/man/run_model.Rd |only DynareR-0.1.1/DynareR/man/run_models.Rd |only DynareR-0.1.1/DynareR/man/write_dyn.Rd |only DynareR-0.1.1/DynareR/man/write_mod.Rd |only DynareR-0.1.1/DynareR/vignettes/DynareR.Rmd | 237 ++++++++++++- 40 files changed, 1168 insertions(+), 121 deletions(-)
Title: Heteroskedasticity Diagnostics for Linear Regression Models
Description: Implements numerous methods for detecting heteroskedasticity
(sometimes called heteroscedasticity) in the classical linear regression
model. These include a test based on Anscombe (1961)
<https://projecteuclid.org/ euclid.bsmsp/1200512155>, Ramsey's (1969)
BAMSET Test <doi:10.1111/j.2517-6161.1969.tb00796.x>, the tests of Bickel
(1978) <doi:10.1214/aos/1176344124>, Breusch and Pagan (1979)
<doi:10.2307/1911963> with and without the modification
proposed by Koenker (1981) <doi:10.1016/0304-4076(81)90062-2>, Carapeto and
Holt (2003) <doi:10.1080/0266476022000018475>, Cook and Weisberg (1983)
<doi:10.1093/biomet/70.1.1> (including their graphical methods), Diblasi
and Bowman (1997) <doi:10.1016/S0167-7152(96)00115-0>, Dufour, Khalaf,
Bernard, and Genest (2004) <doi:10.1016/j.jeconom.2003.10.024>, Evans and
King (1985) <doi:10.1016/0304-4076(85)90085-5> and Evans and King (1988)
<doi:10.1016/0304-4076(88)90006-1>, Glejser (1969)
<doi:10.1080/01621459.1969.10500976> as formulated by
Mittelhammer, Judge and Miller (2000, ISBN: 0-521-62394-4), Godfrey and
Orme (1999) <doi:10.1080/07474939908800438>, Goldfeld and Quandt
(1965) <doi:10.1080/01621459.1965.10480811>, Harvey (1976)
<doi:10.2307/1913974>, Honda (1989)
<doi:10.1111/j.2517-6161.1989.tb01749.x>, Horn (1981)
<doi:10.1080/03610928108828074>, Li and Yao (2019)
<doi:10.1016/j.ecosta.2018.01.001> with and without the modification of
Bai, Pan, and Yin (2016) <doi:10.1007/s11749-017-0575-x>, Rackauskas and
Zuokas (2007) <doi:10.1007/s10986-007-0018-6>, Simonoff and Tsai (1994)
<doi:10.2307/2986026> with and without the modification of Ferrari,
Cysneiros, and Cribari-Neto (2004) <doi:10.1016/S0378-3758(03)00210-6>,
Szroeter (1978) <doi:10.2307/1913831>, Verbyla (1993)
<doi:10.1111/j.2517-6161.1993.tb01918.x>, White (1980)
<doi:10.2307/1912934>, Wilcox and Keselman (2006)
<doi:10.1080/10629360500107923>, and Zhou, Song, and Thompson (2015)
<doi:10.1002/cjs.11252>. Besides these heteroskedasticity tests, there are
supporting functions that compute the BLUS residuals of Theil (1965)
<doi:10.1080/01621459.1965.10480851>, the conditional two-sided p-values of
Kulinskaya (2008) <arXiv:0810.2124v1>, and probabilities for the
nonparametric trend statistic of Lehmann (1975, ISBN: 0-816-24996-1).
Homoskedasticity refers to the assumption of constant variance that is
imposed on the model errors (disturbances); heteroskedasticity is the
violation of this assumption.
Author: Thomas Farrar [aut, cre] (<https://orcid.org/0000-0003-0744-6972>),
University of the Western Cape [cph]
Maintainer: Thomas Farrar <tjfarrar@alumni.uwaterloo.ca>
Diff between skedastic versions 0.1.0 dated 2020-01-10 and 1.0.0 dated 2020-08-11
DESCRIPTION | 78 ++++++++----- MD5 | 141 +++++++++++++++++------ NAMESPACE | 21 +++ R/anscombe.R |only R/bamset.R | 96 +++++----------- R/bickel.R |only R/blus.R | 98 +++++++--------- R/breusch_pagan.R | 69 ++++++----- R/carapeto_holt.R |only R/cook_weisberg.R | 89 +++++++------- R/data.R | 24 +++- R/diblasi_bowman.R |only R/dufour_etal.R |only R/evans_king.R |only R/glejser.R | 59 +++++---- R/globals.R | 3 R/godfrey_orme.R |only R/goldfeld_quandt.R | 228 +++++++++++++++++++++----------------- R/harvey.R | 35 ++--- R/hetplot.R | 143 +++++++++++------------ R/honda.R |only R/horn.R |only R/li_yao.R | 68 +++++++---- R/myutils.R | 281 +++++++++++++++++++++++++++++++++++++++++++++-- R/pRQF.R |only R/peaks.R | 174 ++++++++++++++++++----------- R/rackauskas_zuokas.R |only R/simonoff_tsai.R |only R/szroeter.R |only R/trend.R |only R/twosidedpval.R |only R/verbyla.R |only R/white_lm.R | 34 +---- R/wilcox_keselman.R |only R/zhou_etal.R |only README.md | 30 +---- build/partial.rdb |binary data/T_alpha.rda |only data/dpeakdat.rda |binary inst/CITATION | 8 - inst/REFERENCES.bib | 162 +++++++++++++++++++++++++-- man/T_alpha.Rd |only man/anscombe.Rd |only man/bamset.Rd | 41 ++++-- man/bickel.Rd |only man/blus.Rd | 46 +++++-- man/breusch_pagan.Rd | 35 +++-- man/carapeto_holt.Rd |only man/cook_weisberg.Rd | 72 +++++++----- man/countpeaks.Rd | 66 +++++------ man/dDtrend.Rd |only man/diblasi_bowman.Rd |only man/dpeak.Rd | 36 +++--- man/dpeakdat.Rd | 10 + man/dufour_etal.Rd |only man/evans_king.Rd |only man/glejser.Rd | 45 +++++-- man/godfrey_orme.Rd |only man/goldfeld_quandt.Rd | 113 ++++++++++++------ man/harvey.Rd | 32 +++-- man/hetplot.Rd | 67 ++++++----- man/honda.Rd |only man/horn.Rd |only man/li_yao.Rd | 47 +++++-- man/pDtrend.Rd |only man/pRQF.Rd |only man/ppeak.Rd | 40 +++--- man/rackauskas_zuokas.Rd |only man/simonoff_tsai.Rd |only man/szroeter.Rd |only man/twosidedpval.Rd |only man/verbyla.Rd |only man/white_lm.Rd | 30 +++-- man/wilcox_keselman.Rd |only man/zhou_etal.Rd |only tests |only 76 files changed, 1632 insertions(+), 889 deletions(-)
Title: 'Rcpp' Bindings for the 'simdjson' Header-Only Library for
'JSON' Parsing
Description: The 'JSON' format is ubiquitous for data interchange, and the
'simdjson' library written by Daniel Lemire (and many contributors) provides
a high-performance parser for these files which by relying on parallel 'SIMD'
instruction manages to parse these files as faster than disk speed. See the
<arXiv:1902.08318> paper for more details about 'simdjson'. This package is
at present still a fairly thin and not fully complete wrapper that does not
aim to replace the existing and excellent 'JSON' packages for R.
Author: Dirk Eddelbuettel, Brendan Knapp
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSimdJson versions 0.1.0 dated 2020-07-07 and 0.1.1 dated 2020-08-11
ChangeLog | 318 ++++++----- DESCRIPTION | 8 MD5 | 56 + R/RcppExports.R | 20 R/fload.R | 334 +++++------ R/fparse.R | 175 +++--- R/utils.R | 85 ++ README.md | 51 - build/partial.rdb |binary demo/00Index | 1 demo/simpleBenchmark.R | 20 demo/simpleParseBenchmark.R |only inst/NEWS.Rd | 28 inst/include/RcppSimdJson/deserialize.hpp | 519 +++++++++++++++++- inst/include/RcppSimdJson/deserialize/Type_Doctor.hpp | 204 ++----- inst/include/RcppSimdJson/deserialize/dataframe.hpp | 8 inst/include/RcppSimdJson/deserialize/matrix.hpp | 100 +-- inst/include/RcppSimdJson/deserialize/scalar.hpp | 2 inst/include/RcppSimdJson/deserialize/simplify.hpp | 4 inst/include/RcppSimdJson/deserialize/vector.hpp | 37 - inst/include/RcppSimdJson/utils.hpp | 159 +++++ inst/include/simdjson.cpp | 2 inst/tinytest/test_compressed_files.R |only inst/tinytest/test_deserialization.R | 14 inst/tinytest/test_encoding.R |only inst/tinytest/test_fparse_fload.R | 76 +- inst/tinytest/test_issues.R |only inst/tinytest/test_query.R |only man/fparse.Rd | 156 +++-- src/RcppExports.cpp | 76 ++ src/deserialize.cpp | 441 +++++---------- src/internal-utils.cpp |only 32 files changed, 1815 insertions(+), 1079 deletions(-)
Title: Mendelian Randomization Package
Description: Encodes several methods for performing Mendelian randomization
analyses with summarized data. Summarized data on genetic associations with the
exposure and with the outcome can be obtained from large consortia. These data
can be used for obtaining causal estimates using instrumental variable methods.
Author: Olena Yavorska <olena.yavorska@ludwig.ox.ac.uk>
James Staley <james.staley@bristol.ac.uk>
Maintainer: Stephen Burgess <sb452@medschl.cam.ac.uk>
Diff between MendelianRandomization versions 0.4.2 dated 2020-02-25 and 0.4.3 dated 2020-08-11
DESCRIPTION | 10 MD5 | 24 NEWS | 4 R/pheno_input-function.R | 23 build/vignette.rds |binary inst/doc/Vignette_MR.R | 462 +++++------ inst/doc/Vignette_MR.Rmd | 2 man/calcium.Rd | 12 man/coursedata.Rd | 28 man/ldlc.Rd | 24 man/simpleCap.Rd | 48 - vignettes/Vignette_MR.Rmd | 2 vignettes/Vignette_MR.html | 1858 ++++++++++++++++++++++----------------------- 13 files changed, 1269 insertions(+), 1228 deletions(-)
More information about MendelianRandomization at CRAN
Permanent link
Title: Autocorrelation Function for Functional Time Series
Description: Quantify the serial correlation across lags of a given functional
time series using an autocorrelation function and a partial autocorrelation
function for functional time series.
The autocorrelation functions are based on the L2 norm of the lagged covariance
operators of the series. Functions are available for estimating the
distribution of the autocorrelation functions under the assumption
of strong functional white noise.
Author: Guillermo Mestre Marcos [aut, cre],
José Portela González [aut],
Gregory Rice [aut],
Antonio Muñoz San Roque [ctb],
Estrella Alonso Pérez [ctb]
Maintainer: Guillermo Mestre Marcos <guillermo.mestre@comillas.edu>
Diff between fdaACF versions 0.1.0 dated 2020-01-24 and 0.2.0 dated 2020-08-11
DESCRIPTION | 22 MD5 | 37 - NAMESPACE | 29 - NEWS.md |only R/estimate_distribution.R | 716 +++++++++++++++---------------- R/fdaACF.R | 26 - R/functional_autocorrelation.R | 828 ++++++++++++++++++++++-------------- R/misc.R |only R/plotting_functions.R | 276 ++++++------ man/estimate_iid_distr_Imhof.Rd | 3 man/estimate_iid_distr_MC.Rd | 11 man/fdaACF.Rd | 1 man/fit_ARHp_FPCA.Rd |only man/integral_operator.Rd |only man/mat2fd.Rd |only man/obtain_FACF.Rd | 17 man/obtain_FPACF.Rd |only man/obtain_autocorrelation.Rd | 9 man/obtain_autocov_eigenvalues.Rd | 3 man/obtain_autocovariance.Rd | 2 man/reconstruct_fd_from_PCA.Rd |only man/simulate_iid_brownian_bridge.Rd | 7 man/simulate_iid_brownian_motion.Rd | 7 23 files changed, 1119 insertions(+), 875 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 1.2.1 dated 2020-05-26 and 1.3.0 dated 2020-08-11
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Title: Sound Synthesis and Acoustic Analysis
Description: Performs parametric synthesis of sounds with harmonic and noise
components such as animal vocalizations or human voice. Also offers tools
for spectral analysis, audio segmentation, self-similarity matrices,
modulation spectra, morphing, etc., as well as interactive web apps for
manually corrected pitch tracking and formant measurement. Reference:
Anikin (2019) <doi:10.3758/s13428-018-1095-7>.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <rty.anik@rambler.ru>
Diff between soundgen versions 1.7.0 dated 2020-05-24 and 1.8.0 dated 2020-08-11
soundgen-1.7.0/soundgen/DESCRIPTION |only soundgen-1.7.0/soundgen/MD5 |only soundgen-1.7.0/soundgen/NEWS |only soundgen-1.7.0/soundgen/R |only soundgen-1.7.0/soundgen/build |only soundgen-1.7.0/soundgen/inst |only soundgen-1.7.0/soundgen/man/HzToSemitones.Rd |only soundgen-1.7.0/soundgen/man/addFormants.Rd |only soundgen-1.7.0/soundgen/man/convert_sec_to_hms.Rd |only soundgen-1.7.0/soundgen/man/divideIntoSyllables.Rd |only soundgen-1.7.0/soundgen/man/evaluatePars.Rd |only soundgen-1.7.0/soundgen/man/fart.Rd |only soundgen-1.7.0/soundgen/man/filterMS.Rd |only soundgen-1.7.0/soundgen/man/findGrad.Rd |only soundgen-1.7.0/soundgen/man/findVoicedSegments.Rd |only soundgen-1.7.0/soundgen/man/forcePerPath.Rd |only soundgen-1.7.0/soundgen/man/ftwindow_modif.Rd |only soundgen-1.7.0/soundgen/man/gaussian.w.Rd |only soundgen-1.7.0/soundgen/man/generateEpoch.Rd |only soundgen-1.7.0/soundgen/man/generateGC.Rd |only soundgen-1.7.0/soundgen/man/generateNoise.Rd |only soundgen-1.7.0/soundgen/man/generatePath.Rd |only soundgen-1.7.0/soundgen/man/getBandwidth.Rd |only soundgen-1.7.0/soundgen/man/getDiscreteContour.Rd |only soundgen-1.7.0/soundgen/man/getGlottalCycles.Rd |only soundgen-1.7.0/soundgen/man/getIntegerRandomWalk.Rd |only soundgen-1.7.0/soundgen/man/getMelSpec.Rd |only soundgen-1.7.0/soundgen/man/getPitchSpec.Rd |only soundgen-1.7.0/soundgen/man/getRMS.Rd |only soundgen-1.7.0/soundgen/man/getRandomWalk.Rd |only soundgen-1.7.0/soundgen/man/getSmoothContour.Rd |only soundgen-1.7.0/soundgen/man/getSpectralEnvelope.Rd |only soundgen-1.7.0/soundgen/man/harmEnergy.Rd |only soundgen-1.7.0/soundgen/man/harmHeight_dif.Rd |only soundgen-1.7.0/soundgen/man/htmlPlots.Rd |only soundgen-1.7.0/soundgen/man/interpolate.Rd |only soundgen-1.7.0/soundgen/man/intplPitch.Rd |only soundgen-1.7.0/soundgen/man/lockToFormants.Rd |only soundgen-1.7.0/soundgen/man/matchLengths.Rd |only soundgen-1.7.0/soundgen/man/matchPars.Rd |only soundgen-1.7.0/soundgen/man/mergeSyllables.Rd |only soundgen-1.7.0/soundgen/man/modulationSpectrumFolder.Rd |only soundgen-1.7.0/soundgen/man/morphDF.Rd |only soundgen-1.7.0/soundgen/man/morphFormants.Rd |only soundgen-1.7.0/soundgen/man/normalizeFolder.Rd |only soundgen-1.7.0/soundgen/man/notesDict.Rd |only soundgen-1.7.0/soundgen/man/optimizePars.Rd |only soundgen-1.7.0/soundgen/man/osc_dB.Rd |only soundgen-1.7.0/soundgen/man/parabPeakInterpol.Rd |only soundgen-1.7.0/soundgen/man/pathfinder.Rd |only soundgen-1.7.0/soundgen/man/pathfinding_slow.Rd |only soundgen-1.7.0/soundgen/man/permittedValues.Rd |only soundgen-1.7.0/soundgen/man/pitchManual.Rd |only soundgen-1.7.0/soundgen/man/pitch_app.Rd |only soundgen-1.7.0/soundgen/man/reportCI.Rd |only soundgen-1.7.0/soundgen/man/reportTime.Rd |only soundgen-1.7.0/soundgen/man/rnorm_truncated.Rd |only soundgen-1.7.0/soundgen/man/segmentFolder.Rd |only soundgen-1.7.0/soundgen/man/segmentManual.Rd |only soundgen-1.7.0/soundgen/man/snake.Rd |only soundgen-1.7.0/soundgen/man/soundgen_app.Rd |only soundgen-1.7.0/soundgen/man/spectrogram.Rd |only soundgen-1.7.0/soundgen/man/ssm.Rd |only soundgen-1.7.0/soundgen/man/switchColorTheme.Rd |only soundgen-1.7.0/soundgen/man/transplantFormants.Rd |only soundgen-1.7.0/soundgen/man/upsample.Rd |only soundgen-1.7.0/soundgen/man/validatePars.Rd |only soundgen-1.7.0/soundgen/man/wiggleAnchors.Rd |only soundgen-1.7.0/soundgen/man/wiggleGC.Rd |only soundgen-1.7.0/soundgen/man/wigglePars.Rd |only soundgen-1.7.0/soundgen/vignettes |only soundgen-1.8.0/soundgen/NAMESPACE | 2 soundgen-1.8.0/soundgen/README.md | 126 ++++++++++++---- soundgen-1.8.0/soundgen/data/def_form.rda |only soundgen-1.8.0/soundgen/data/defaults_analyze.rda |binary soundgen-1.8.0/soundgen/data/permittedValues.rda |binary soundgen-1.8.0/soundgen/man/analyze.Rd | 83 ++++++---- soundgen-1.8.0/soundgen/man/analyzeFolder.Rd | 29 ++- soundgen-1.8.0/soundgen/man/drawContour.Rd | 5 soundgen-1.8.0/soundgen/man/estimateVTL.Rd | 29 ++- soundgen-1.8.0/soundgen/man/filterSoundByMS.Rd | 70 -------- soundgen-1.8.0/soundgen/man/formant_app.Rd |only soundgen-1.8.0/soundgen/man/generateHarmonics.Rd | 5 soundgen-1.8.0/soundgen/man/getFormantDispersion.Rd | 12 + soundgen-1.8.0/soundgen/man/getFrameBank.Rd | 5 soundgen-1.8.0/soundgen/man/getLoudness.Rd | 5 soundgen-1.8.0/soundgen/man/getLoudnessFolder.Rd | 29 ++- soundgen-1.8.0/soundgen/man/getRMSFolder.Rd | 14 - soundgen-1.8.0/soundgen/man/getRough.Rd | 2 soundgen-1.8.0/soundgen/man/modulationSpectrum.Rd | 80 ++++++---- soundgen-1.8.0/soundgen/man/msToSpec.Rd | 2 soundgen-1.8.0/soundgen/man/segment.Rd | 21 +- soundgen-1.8.0/soundgen/man/soundgen.Rd | 29 +-- soundgen-1.8.0/soundgen/man/spectrogramFolder.Rd | 10 - soundgen-1.8.0/soundgen/man/splitContour.Rd | 12 - soundgen-1.8.0/soundgen/man/updateAnalyze.Rd | 4 96 files changed, 326 insertions(+), 248 deletions(-)
Title: Bayesian Age-Depth Modelling of Cores Dated by Pb-210
Description: An approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for 210Pb-dated deposits using prior information. It can combine 210Pb, radiocarbon, and other dates in the chronologies. See Aquino et al. (2018) <doi:10.1007/s13253-018-0328-7>. Note that parts of the code underlying 'rplum' are derived from the 'rbacon' package by the same authors. Subsequent versions of 'rplum' and 'rbacon' are planned to reduce duplication, with 'rplum' importing 'rbacon' instead.
Author: Maarten Blaauw [aut, cre],
J. Andres Christen [aut, ctb, cph],
Marco A. Aquino-Lopez [aut],
Judith Esquivel-Vazquez [ctb],
Oscar M. Gonzalez V. [ctb],
Ted Belding [cph],
James Theiler [cph],
Brian Gough [cph],
Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rplum versions 0.1.4 dated 2020-05-04 and 0.1.5.1 dated 2020-08-11
rplum-0.1.4/rplum/inst/extdata/Cores/MSB2K |only rplum-0.1.4/rplum/inst/extdata/Cores/RLGH3 |only rplum-0.1.4/rplum/inst/extdata/Curves/3Col_intcal13.14C |only rplum-0.1.4/rplum/inst/extdata/Curves/3Col_marine13.14C |only rplum-0.1.4/rplum/inst/extdata/Curves/3Col_shcal13.14C |only rplum-0.1.4/rplum/inst/extdata/Curves/TranslateCal13.R |only rplum-0.1.4/rplum/inst/extdata/Curves/intcal13.14c |only rplum-0.1.4/rplum/inst/extdata/Curves/marine13.14c |only rplum-0.1.4/rplum/inst/extdata/Curves/shcal13.14c |only rplum-0.1.5.1/rplum/DESCRIPTION | 14 rplum-0.1.5.1/rplum/MD5 | 111 rplum-0.1.5.1/rplum/NAMESPACE | 1 rplum-0.1.5.1/rplum/NEWS.md | 9 rplum-0.1.5.1/rplum/R/Bacon.R | 54 rplum-0.1.5.1/rplum/R/MCMC.R | 35 rplum-0.1.5.1/rplum/R/Plum.R | 110 rplum-0.1.5.1/rplum/R/accrate.R | 35 rplum-0.1.5.1/rplum/R/agedepth.R | 57 rplum-0.1.5.1/rplum/R/calc.R | 101 rplum-0.1.5.1/rplum/R/calibrate.R | 341 rplum-0.1.5.1/rplum/R/calibrate_plum.R | 151 rplum-0.1.5.1/rplum/R/internal_plots.R | 9 rplum-0.1.5.1/rplum/R/plots.R | 12 rplum-0.1.5.1/rplum/R/read_write.R | 23 rplum-0.1.5.1/rplum/R/read_write_plum.R | 453 rplum-0.1.5.1/rplum/inst/extdata/Cores/HP1C/HP1C_30.out | 6018 +++++------ rplum-0.1.5.1/rplum/inst/extdata/Cores/HP1C/HP1C_30_ages.txt | 60 rplum-0.1.5.1/rplum/inst/extdata/Curves/3Col_intcal20.14C |only rplum-0.1.5.1/rplum/inst/extdata/Curves/3Col_marine20.14C |only rplum-0.1.5.1/rplum/inst/extdata/Curves/3Col_shcal20.14C |only rplum-0.1.5.1/rplum/inst/extdata/Curves/TranslateCal20.R |only rplum-0.1.5.1/rplum/man/A.modelled.Rd | 17 rplum-0.1.5.1/rplum/man/AgesOfEvents.Rd | 7 rplum-0.1.5.1/rplum/man/Bacon.Age.d.Rd | 6 rplum-0.1.5.1/rplum/man/Bacon.Rd | 53 rplum-0.1.5.1/rplum/man/Bacon.cleanup.Rd | 4 rplum-0.1.5.1/rplum/man/Bacon.hist.Rd | 6 rplum-0.1.5.1/rplum/man/Plum.Rd | 59 rplum-0.1.5.1/rplum/man/Plum.cleanup.Rd |only rplum-0.1.5.1/rplum/man/Plum_runs.Rd | 4 rplum-0.1.5.1/rplum/man/accrate.age.Rd | 7 rplum-0.1.5.1/rplum/man/accrate.age.ghost.Rd | 6 rplum-0.1.5.1/rplum/man/accrate.depth.Rd | 8 rplum-0.1.5.1/rplum/man/accrate.depth.ghost.Rd | 6 rplum-0.1.5.1/rplum/man/add.dates.Rd | 9 rplum-0.1.5.1/rplum/man/agedepth.Rd | 15 rplum-0.1.5.1/rplum/man/agemodel.it.Rd | 5 rplum-0.1.5.1/rplum/man/bacon2clam.Rd | 9 rplum-0.1.5.1/rplum/man/calib.plot.Rd | 5 rplum-0.1.5.1/rplum/man/calib.plumbacon.plot.Rd | 52 rplum-0.1.5.1/rplum/man/clam2bacon.Rd | 2 rplum-0.1.5.1/rplum/man/copyCalibrationCurve.Rd | 7 rplum-0.1.5.1/rplum/man/draw.pbmodelled.Rd | 30 rplum-0.1.5.1/rplum/man/flux.age.ghost.Rd | 8 rplum-0.1.5.1/rplum/man/mix.curves.Rd | 11 rplum-0.1.5.1/rplum/man/proxy.ghost.Rd | 7 rplum-0.1.5.1/rplum/man/scissors.Rd | 13 rplum-0.1.5.1/rplum/man/thinner.Rd | 13 rplum-0.1.5.1/rplum/src/cal.h | 430 rplum-0.1.5.1/rplum/src/input.cpp | 12 60 files changed, 4542 insertions(+), 3863 deletions(-)
Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on 'Windows',
'Linux' and 'macOS'.
Author: Jay Loden [aut],
Dave Daeschler [aut],
Giampaolo Rodola' [aut],
Gábor Csárdi [aut, cre],
RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between ps versions 1.3.3 dated 2020-05-08 and 1.3.4 dated 2020-08-11
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/low-level.R | 2 +- man/ps_memory_info.Rd | 2 +- src/api-linux.c | 8 +++++--- src/api-windows.c | 14 +++----------- src/arch/windows/process_handles.h | 1 - src/windows.c | 10 ++++++---- 9 files changed, 33 insertions(+), 32 deletions(-)
Title: Motif-Based Spectral Clustering of Weighted Directed Networks
Description: Tools for spectral clustering of weighted directed networks using motif
adjacency matrices. Methods perform well on large and sparse networks, and
random sampling methods for generating weighted directed networks are also
provided. Based on methodology detailed in Underwood, Elliott and Cucuringu
(2020) <arXiv:2004.01293>.
Author: William George Underwood [aut, cre]
Maintainer: William George Underwood <wgu2@princeton.edu>
Diff between motifcluster versions 0.1.0 dated 2020-05-18 and 0.1.1 dated 2020-08-11
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 4 ++++ README.md | 2 +- build/vignette.rds |binary inst/doc/motifcluster_vignette.pdf |binary vignettes/motifcluster_vignette.html |only 7 files changed, 14 insertions(+), 9 deletions(-)
Title: Interactive Viewing of Spatial Data in R
Description: Quickly and conveniently create interactive
visualisations of spatial data with or without background maps.
Attributes of displayed features are fully queryable via pop-up
windows. Additional functionality includes methods to visualise true-
and false-color raster images and bounding boxes.
Author: Tim Appelhans [cre, aut],
Florian Detsch [aut],
Christoph Reudenbach [aut],
Stefan Woellauer [aut],
Spaska Forteva [ctb],
Thomas Nauss [ctb],
Edzer Pebesma [ctb],
Kenton Russell [ctb],
Michael Sumner [ctb],
Jochen Darley [ctb],
Pierre Roudier [ctb],
Patrick Schratz [ctb],
Environmental Informatics Marburg [ctb],
Lorenzo Busetto [ctb]
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between mapview versions 2.7.8 dated 2020-04-07 and 2.9.0 dated 2020-08-11
mapview-2.7.8/mapview/R/mapview-deprecated.R |only mapview-2.7.8/mapview/R/plus.R |only mapview-2.7.8/mapview/inst/htmlwidgets/cubeView.js |only mapview-2.7.8/mapview/inst/htmlwidgets/cubeView.yaml |only mapview-2.7.8/mapview/inst/htmlwidgets/lib/HomeButton |only mapview-2.7.8/mapview/inst/htmlwidgets/lib/Leaflet.Sync |only mapview-2.7.8/mapview/inst/htmlwidgets/lib/TrackballControls-r74 |only mapview-2.7.8/mapview/inst/htmlwidgets/lib/cubeView_style |only mapview-2.7.8/mapview/inst/htmlwidgets/lib/joda |only mapview-2.7.8/mapview/inst/htmlwidgets/lib/pane |only mapview-2.7.8/mapview/inst/htmlwidgets/lib/popup |only mapview-2.7.8/mapview/inst/htmlwidgets/lib/three.js-r74 |only mapview-2.7.8/mapview/inst/htmlwidgets/slideView.js |only mapview-2.7.8/mapview/inst/htmlwidgets/slideView.yaml |only mapview-2.7.8/mapview/man/addFeatures.Rd |only mapview-2.7.8/mapview/man/addHomeButton.Rd |only mapview-2.7.8/mapview/man/addImageQuery.Rd |only mapview-2.7.8/mapview/man/addLogo.Rd |only mapview-2.7.8/mapview/man/addMouseCoordinates.Rd |only mapview-2.7.8/mapview/man/addStarsImage.Rd |only mapview-2.7.8/mapview/man/addStaticLabels.Rd |only mapview-2.7.8/mapview/man/cubeView.Rd |only mapview-2.7.8/mapview/man/cubeViewOutput.Rd |only mapview-2.7.8/mapview/man/garnishMap.Rd |only mapview-2.7.8/mapview/man/latticeView.Rd |only mapview-2.7.8/mapview/man/mapview-deprecated.Rd |only mapview-2.7.8/mapview/man/plainView.Rd |only mapview-2.7.8/mapview/man/plus.Rd |only mapview-2.7.8/mapview/man/popup.Rd |only mapview-2.7.8/mapview/man/renderCubeView.Rd |only mapview-2.7.8/mapview/man/renderslideView.Rd |only mapview-2.7.8/mapview/man/slideView.Rd |only mapview-2.7.8/mapview/man/slideViewOutput.Rd |only mapview-2.9.0/mapview/DESCRIPTION | 18 mapview-2.9.0/mapview/MD5 | 141 - mapview-2.9.0/mapview/NAMESPACE | 29 mapview-2.9.0/mapview/NEWS | 18 mapview-2.9.0/mapview/NEWS.md | 18 mapview-2.9.0/mapview/R/AAAmapviewClasses.R | 1 mapview-2.9.0/mapview/R/burst.R | 167 - mapview-2.9.0/mapview/R/color.R | 8 mapview-2.9.0/mapview/R/cubeView.R | 332 -- mapview-2.9.0/mapview/R/extensions.R | 1228 ++-------- mapview-2.9.0/mapview/R/extent.R | 42 mapview-2.9.0/mapview/R/fgb.R |only mapview-2.9.0/mapview/R/files.R | 15 mapview-2.9.0/mapview/R/garnishMap.R | 119 mapview-2.9.0/mapview/R/initpkg.R |only mapview-2.9.0/mapview/R/leafletControls.R | 39 mapview-2.9.0/mapview/R/legend.R | 75 mapview-2.9.0/mapview/R/mapView.R | 577 ++-- mapview-2.9.0/mapview/R/mapshot.R | 254 +- mapview-2.9.0/mapview/R/mapview-defunct.R |only mapview-2.9.0/mapview/R/mapview-package.R | 10 mapview-2.9.0/mapview/R/mapviewControls.R | 86 mapview-2.9.0/mapview/R/missing.R | 10 mapview-2.9.0/mapview/R/ops.R |only mapview-2.9.0/mapview/R/options.R | 172 + mapview-2.9.0/mapview/R/plainView.R | 364 -- mapview-2.9.0/mapview/R/popup.R | 602 ---- mapview-2.9.0/mapview/R/print.R | 31 mapview-2.9.0/mapview/R/raster.R | 83 mapview-2.9.0/mapview/R/sf.R | 584 ++++ mapview-2.9.0/mapview/R/shiny-mapview.R |only mapview-2.9.0/mapview/R/slideView.R | 656 +---- mapview-2.9.0/mapview/R/stars.R | 204 - mapview-2.9.0/mapview/R/sync.R | 241 - mapview-2.9.0/mapview/R/viewRGB.R | 7 mapview-2.9.0/mapview/R/watch.R | 12 mapview-2.9.0/mapview/README.md | 34 mapview-2.9.0/mapview/data/breweries.rda |binary mapview-2.9.0/mapview/data/franconia.rda |binary mapview-2.9.0/mapview/data/trails.rda |binary mapview-2.9.0/mapview/inst/htmlwidgets/lib/css |only mapview-2.9.0/mapview/man/breweries.Rd | 6 mapview-2.9.0/mapview/man/franconia.Rd | 8 mapview-2.9.0/mapview/man/mapView.Rd | 109 mapview-2.9.0/mapview/man/mapshot.Rd | 59 mapview-2.9.0/mapview/man/mapview-defunct.Rd |only mapview-2.9.0/mapview/man/mapviewOptions.Rd | 20 mapview-2.9.0/mapview/man/mapviewOutput.Rd | 2 mapview-2.9.0/mapview/man/ops.Rd |only mapview-2.9.0/mapview/man/removeMapJunk.Rd |only mapview-2.9.0/mapview/man/renderMapview.Rd | 2 mapview-2.9.0/mapview/man/trails.Rd | 6 mapview-2.9.0/mapview/man/viewExtent.Rd | 12 mapview-2.9.0/mapview/man/viewRGB.Rd | 6 mapview-2.9.0/mapview/tests/testthat/test-mapviewControls.R | 2 88 files changed, 2510 insertions(+), 3899 deletions(-)
Title: Linear Regression by Gibbs Sampling
Description: Implements a Gibbs sampler to do linear regression with multiple covariates, multiple responses, Gaussian measurement errors on covariates and responses, Gaussian intrinsic scatter, and a covariate prior distribution which is given by either a Gaussian mixture of specified size or a Dirichlet process with a Gaussian base distribution. Described further in Mantz (2016) <DOI:10.1093/mnras/stv3008>.
Author: Adam Mantz
Maintainer: Adam Mantz <amantz@slac.stanford.edu>
Diff between lrgs versions 0.5.3 dated 2017-12-01 and 0.5.4 dated 2020-08-11
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/lrgs.R | 6 ++++-- man/lrgs-package.Rd | 4 ++-- 4 files changed, 14 insertions(+), 12 deletions(-)
Title: Calling Copy Number Alterations in Amplicon Sequencing Data
Description: Method for the calculation of copy numbers and calling of copy number alterations. The algorithm uses coverage data from amplicon sequencing of a sample cohort as input. The method includes significance assessment, correction for multiple testing and does not depend on normal DNA controls. Budczies (2016 Mar 15) <doi:10.18632/oncotarget.7451>.
Author: Jan Budczies, Eva Romanovsky
Maintainer: Jan Budczies <jan.budczies@med.uni-heidelberg.de>
Diff between ioncopy versions 2.1.1 dated 2018-03-23 and 2.2.2 dated 2020-08-11
ioncopy-2.1.1/ioncopy/R/ioncopy-internal.R |only ioncopy-2.1.1/ioncopy/inst/doc/Ioncopy_manual.pdf |only ioncopy-2.1.1/ioncopy/inst/doc/Thumbs.db |only ioncopy-2.1.1/ioncopy/inst/doc/index.html |only ioncopy-2.2.2/ioncopy/DESCRIPTION | 12 - ioncopy-2.2.2/ioncopy/MD5 | 19 - ioncopy-2.2.2/ioncopy/NAMESPACE | 30 +- ioncopy-2.2.2/ioncopy/R/heatmap.CNA.R | 11 + ioncopy-2.2.2/ioncopy/R/summarize.CNA.R | 8 ioncopy-2.2.2/ioncopy/inst/doc/Ioncopy_2.2_manual.pdf |only ioncopy-2.2.2/ioncopy/inst/shiny/ioncopy/server.R | 185 +++++++++++++++++- ioncopy-2.2.2/ioncopy/inst/shiny/ioncopy/ui.R | 3 ioncopy-2.2.2/ioncopy/man/ioncopy-package.Rd | 6 13 files changed, 232 insertions(+), 42 deletions(-)
Title: Calculates Goodness of Fit Statistics
Description: Calculates 15 different goodness of fit criteria. These are; standard deviation ratio (SDR), coefficient of variation (CV), relative root mean square error (RRMSE), Pearson's correlation coefficients (PC), root mean square error (RMSE), performance index (PI), mean error (ME), global relative approximation error (RAE), mean relative approximation error (MRAE), mean absolute percentage error (MAPE), mean absolute deviation (MAD), coefficient of determination (R-squared), adjusted coefficient of determination (adjusted R-squared), Akaike's information criterion (AIC), corrected Akaike's information criterion (CAIC), Mean Square Error (MSE), Bayesian Information Criterion (BIC) and Normalized Mean Square Error (NMSE).
Author: Alper Gulbe [cre],
Ecevit Eyduran [aut]
Maintainer: Alper Gulbe <alper.gulbe@igdir.edu.tr>
Diff between ehaGoF versions 0.1.0 dated 2019-11-19 and 0.1.1 dated 2020-08-11
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/hello.R | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Calculates Disproportionate Impact When Binary Success Data are
Disaggregated by Subgroups
Description: Implements methods for calculating disproportionate impact: the percentage point gap, proportionality index, and the 80% index.
California Community Colleges Chancellor's Office (2017). Percentage Point Gap Method. <https://www.cccco.edu/-/media/CCCCO-Website/About-Us/Divisions/Digital-Innovation-and-Infrastructure/Research/Files/PercentagePointGapMethod2017.ashx>.
California Community Colleges Chancellor's Office (2014). Guidelines for Measuring Disproportionate Impact in Equity Plans. <https://www.cccco.edu/-/media/CCCCO-Website/Files/DII/guidelines-for-measuring-disproportionate-impact-in-equity-plans-tfa-ada.pdf>.
Author: Vinh Nguyen [aut, cre]
Maintainer: Vinh Nguyen <nguyenvq714@gmail.com>
Diff between DisImpact versions 0.0.10 dated 2020-08-10 and 0.0.11 dated 2020-08-11
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 2 ++ R/di_iterate.R | 19 +++++++++++-------- inst/doc/Tutorial.html | 26 +++++++++++++------------- man/di_iterate.Rd | 5 ++++- 6 files changed, 38 insertions(+), 30 deletions(-)
Title: Network Analysis of Dependencies of CRAN Packages
Description: The dependencies of CRAN packages can be analysed in a network fashion. For each package we can obtain the packages that it depends, imports, suggests, etc. By iterating this procedure over a number of packages, we can build, visualise, and analyse the dependency network, enabling us to have a bird's-eye view of the CRAN ecosystem. One aspect of interest is the number of reverse dependencies of the packages, or equivalently the in-degree distribution of the dependency network. This can be fitted by the power law and/or an extreme value mixture distribution <arXiv:2008.03073>, of which functions are provided.
Author: Clement Lee [aut, cre]
Maintainer: Clement Lee <clement.lee.tm@outlook.com>
Diff between crandep versions 0.0.2 dated 2020-07-19 and 0.1.0 dated 2020-08-11
crandep-0.0.2/crandep/R/topo_order.R |only crandep-0.0.2/crandep/man/get_dep_all.Rd |only crandep-0.1.0/crandep/DESCRIPTION | 12 crandep-0.1.0/crandep/MD5 | 54 +-- crandep-0.1.0/crandep/NAMESPACE | 6 crandep-0.1.0/crandep/NEWS.md | 22 - crandep-0.1.0/crandep/R/cleaning.R | 170 ++------- crandep-0.1.0/crandep/R/data.R | 2 crandep-0.1.0/crandep/R/get_dep.R |only crandep-0.1.0/crandep/R/graph.R |only crandep-0.1.0/crandep/README.md | 321 +++++++++++++++--- crandep-0.1.0/crandep/build/vignette.rds |binary crandep-0.1.0/crandep/data/cran_dependencies.rda |binary crandep-0.1.0/crandep/inst/doc/cran.R |only crandep-0.1.0/crandep/inst/doc/cran.Rmd |only crandep-0.1.0/crandep/inst/doc/cran.html |only crandep-0.1.0/crandep/inst/doc/degree.R | 88 +++-- crandep-0.1.0/crandep/inst/doc/degree.Rmd | 110 ++++-- crandep-0.1.0/crandep/inst/doc/degree.html | 254 +++++++------- crandep-0.1.0/crandep/inst/doc/introduction.R | 82 ---- crandep-0.1.0/crandep/inst/doc/introduction.Rmd | 130 +------ crandep-0.1.0/crandep/inst/doc/introduction.html | 346 ++++++-------------- crandep-0.1.0/crandep/man/check_dep_word.Rd |only crandep-0.1.0/crandep/man/cran_dependencies.Rd | 2 crandep-0.1.0/crandep/man/df_to_graph.Rd | 4 crandep-0.1.0/crandep/man/get_dep.Rd |only crandep-0.1.0/crandep/man/get_dep_all_packages.Rd | 14 crandep-0.1.0/crandep/man/get_dep_df.Rd | 15 crandep-0.1.0/crandep/man/get_graph_all_packages.Rd |only crandep-0.1.0/crandep/man/reshape_dep.Rd |only crandep-0.1.0/crandep/man/topo_sort_kahn.Rd | 2 crandep-0.1.0/crandep/vignettes/cran.Rmd |only crandep-0.1.0/crandep/vignettes/degree.Rmd | 110 ++++-- crandep-0.1.0/crandep/vignettes/introduction.Rmd | 130 +------ 34 files changed, 886 insertions(+), 988 deletions(-)
Title: A C++11 Interface for R's C Interface
Description: Provides a header only, C++11 interface to R's C
interface. Compared to other approaches 'cpp11' strives to be safe
against long jumps from the C API as well as C++ exceptions, conform
to normal R function semantics and supports interaction with 'ALTREP'
vectors.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>),
Romain François [ctb],
Benjamin Kietzman [ctb],
RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between cpp11 versions 0.2.0 dated 2020-08-10 and 0.2.1 dated 2020-08-11
DESCRIPTION | 6 MD5 | 26 - NEWS.md | 6 R/zzz.R | 6 inst/doc/cpp11.R | 344 ++++++++++---------- inst/doc/cpp11.Rmd | 4 inst/doc/cpp11.html | 608 +++++++++++++++++++----------------- inst/doc/motivations.R | 108 +++--- inst/doc/motivations.html | 361 ++++++++++++++++++++- inst/include/cpp11/as.hpp | 8 inst/include/cpp11/declarations.hpp | 7 inst/include/cpp11/r_vector.hpp | 1 inst/include/cpp11/strings.hpp | 6 vignettes/cpp11.Rmd | 4 14 files changed, 955 insertions(+), 540 deletions(-)
Title: k-Nearest Neighbor Join for Spatial Data
Description: K-nearest neighbor search for projected and non-projected 'sf' spatial layers. Nearest neighbor search uses (1) C code from 'GeographicLib' for lon-lat point layers, (2) function nn2() from package 'RANN' for projected point layers, or (3) function st_distance() from package 'sf' for line or polygon layers. The package also includes several other utility functions for spatial analysis.
Author: Michael Dorman [aut, cre],
Johnathan Rush [ctb],
Ian Hough [ctb],
Dominic Russel [ctb],
Charles F.F Karney [ctb, cph] (Author of included C code from
'GeographicLib' for geodesic distance)
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between nngeo versions 0.3.8 dated 2020-06-10 and 0.3.9 dated 2020-08-11
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 7 ++++++- R/st_nn.R | 14 ++------------ build/vignette.rds |binary inst/doc/intro.pdf |binary inst/tinytest/test_st_nn.R | 23 +++++++++++++++++++++++ man/st_nn.Rd | 2 +- 8 files changed, 43 insertions(+), 25 deletions(-)
More information about KnockoffScreen at CRAN
Permanent link
Title: General-to-Specific (GETS) Modelling and Indicator Saturation
Methods
Description: Automated General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting and testing for structural breaks in the mean, see Pretis, Reade and Sucarrat (2018) <doi:10.18637/jss.v086.i03>.
Author: Genaro Sucarrat [aut, cre], Felix Pretis [aut], James Reade [aut], Jonas Kurle [ctb], Moritz Schwarz [ctb]
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between gets versions 0.24 dated 2020-07-28 and 0.25 dated 2020-08-11
DESCRIPTION | 10 ++--- MD5 | 46 +++++++++++++------------- NEWS | 36 ++++++++++---------- R/biascorr.R | 4 +- R/diagnostics.R | 19 ++++------ R/gets-internal.R | 2 - R/getsm.R | 4 +- R/getsv.R | 5 +- R/isat.R | 7 +++- R/ols.R | 10 ++--- R/plot.isat.R | 2 - R/predict.arx.R | 91 +++++++++++++++++++++++++++++++++------------------- R/print.arx.R | 1 R/print.isat.R | 9 +++-- man/coef.arx.Rd | 4 +- man/coef.gets.Rd | 4 +- man/coef.isat.Rd | 4 +- man/gets-package.Rd | 8 ++-- man/gets.Rd | 1 man/getsFun.Rd | 6 +-- man/getsm.Rd | 11 +++--- man/hpdata.Rd | 6 ++- man/infldata.Rd | 17 +++++++-- man/predict.arx.Rd | 2 - 24 files changed, 177 insertions(+), 132 deletions(-)
Title: Bayesian Quantile Regression for Ordinal Models
Description: Provides an estimation technique for Bayesian quantile
regression in ordinal models. Two algorithms are considered - one
for an ordinal model with three outcomes and the other for an ordinal
model with more than 3 outcomes. It further provides model performance
criteria and trace plots for Markov chain Monte Carlo (MCMC) draws.
Rahman, M. A. (2016) <doi:10.1214/15-BA939>.
Greenberg, E. (2012) <doi:10.1017/CBO9781139058414>.
Spiegelhalter, D. J., Best, N. G., Carlin B. P. and Linde A. (2002) <doi:10.1111/1467-9868.00353>.
Author: Dr. Mohammad Arshad Rahman Developer [aut],
Prajual Maheshwari [cre]
Maintainer: Prajual Maheshwari <prajual1391@gmail.com>
Diff between bqror versions 0.1.0 dated 2020-02-26 and 0.1.1 dated 2020-08-11
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/ODRI.R | 2 +- R/ODRII.R | 4 ++-- 4 files changed, 9 insertions(+), 9 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 0.1-20 dated 2016-04-27 and 0.1.21 dated 2020-08-11
ggdendro-0.1-20/ggdendro/tests/testthat/Rplots.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots1.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots10.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots11.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots12.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots13.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots14.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots15.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots16.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots2.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots3.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots4.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots5.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots6.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots7.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots8.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots9.pdf |only ggdendro-0.1.21/ggdendro/DESCRIPTION | 32 ggdendro-0.1.21/ggdendro/MD5 | 112 - ggdendro-0.1.21/ggdendro/NEWS | 74 - ggdendro-0.1.21/ggdendro/R/dendro_data.R | 108 - ggdendro-0.1.21/ggdendro/R/dendro_rpart.R | 116 - ggdendro-0.1.21/ggdendro/R/dendro_tree.R | 173 +- ggdendro-0.1.21/ggdendro/R/dendrogram.R | 474 +++--- ggdendro-0.1.21/ggdendro/R/ggdendro-package.R | 50 ggdendro-0.1.21/ggdendro/R/ggdendrogram.R | 92 - ggdendro-0.1.21/ggdendro/R/rpart.R | 448 +++--- ggdendro-0.1.21/ggdendro/build/vignette.rds |binary ggdendro-0.1.21/ggdendro/inst/WORDLIST |only ggdendro-0.1.21/ggdendro/inst/doc/ggdendro.R | 22 ggdendro-0.1.21/ggdendro/inst/doc/ggdendro.Rmd | 30 ggdendro-0.1.21/ggdendro/inst/doc/ggdendro.html | 693 +++++----- ggdendro-0.1.21/ggdendro/inst/examples/example_dendro_data.R | 34 ggdendro-0.1.21/ggdendro/inst/examples/example_dendro_rpart.R | 17 ggdendro-0.1.21/ggdendro/inst/examples/example_dendro_tree.R | 24 ggdendro-0.1.21/ggdendro/inst/examples/example_dendro_twins.R | 5 ggdendro-0.1.21/ggdendro/inst/examples/example_ggdendrogram.R | 7 ggdendro-0.1.21/ggdendro/inst/examples/example_twins.R |only ggdendro-0.1.21/ggdendro/man/as.dendro.Rd | 7 ggdendro-0.1.21/ggdendro/man/dendro_data.Rd | 93 - ggdendro-0.1.21/ggdendro/man/dendro_data.rpart.Rd | 88 - ggdendro-0.1.21/ggdendro/man/dendro_data.tree.Rd | 58 ggdendro-0.1.21/ggdendro/man/dendrogram_data.Rd | 16 ggdendro-0.1.21/ggdendro/man/figures |only ggdendro-0.1.21/ggdendro/man/get_data_tree_leaf_labels.Rd | 16 ggdendro-0.1.21/ggdendro/man/ggdendro-package.Rd | 46 ggdendro-0.1.21/ggdendro/man/ggdendrogram.Rd | 32 ggdendro-0.1.21/ggdendro/man/is.dendro.Rd | 3 ggdendro-0.1.21/ggdendro/man/labels.rpart.Rd | 14 ggdendro-0.1.21/ggdendro/man/rpart_labels.Rd | 24 ggdendro-0.1.21/ggdendro/man/rpart_segments.Rd | 9 ggdendro-0.1.21/ggdendro/man/rpartco.Rd | 3 ggdendro-0.1.21/ggdendro/man/segment.Rd | 8 ggdendro-0.1.21/ggdendro/man/theme_dendro.Rd | 5 ggdendro-0.1.21/ggdendro/man/tree_labels.Rd | 17 ggdendro-0.1.21/ggdendro/man/tree_segments.Rd | 17 ggdendro-0.1.21/ggdendro/man/treeco.Rd | 1 ggdendro-0.1.21/ggdendro/tests/spelling.R |only ggdendro-0.1.21/ggdendro/tests/testthat.R | 2 ggdendro-0.1.21/ggdendro/tests/testthat/test-1-dendrogram.R | 32 ggdendro-0.1.21/ggdendro/tests/testthat/test-2-hclust.R | 11 ggdendro-0.1.21/ggdendro/tests/testthat/test-3-rpart.R | 9 ggdendro-0.1.21/ggdendro/tests/testthat/test-3-tree.R | 10 ggdendro-0.1.21/ggdendro/tests/testthat/test-4-clusterplots.R | 19 ggdendro-0.1.21/ggdendro/tests/testthat/test-6-ggdendrogram.R | 10 ggdendro-0.1.21/ggdendro/vignettes/ggdendro.Rmd | 30 66 files changed, 1701 insertions(+), 1390 deletions(-)
Title: SOM Bound to Realize Euclidean and Relational Outputs
Description: The stochastic (also called on-line) version of the Self-Organising
Map (SOM) algorithm is provided. Different versions of the
algorithm are implemented, for numeric and relational data and for
contingency tables as described, respectively, in Kohonen (2001)
<isbn:3-540-67921-9>, Olteanu & Villa-Vialaneix (2005)
<doi:10.1016/j.neucom.2013.11.047> and Cottrell et al (2004)
<doi:10.1016/j.neunet.2004.07.010>. The package also contains many
plotting features (to help the user interpret the results) and a
graphical user interface based on 'shiny'.
Author: Nathalie Vialaneix [aut, cre],
Elise Maigne [aut],
Jerome Mariette [aut],
Madalina Olteanu [aut],
Fabrice Rossi [aut],
Laura Bendhaiba [ctb],
Julien Boelaert [ctb]
Maintainer: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Diff between SOMbrero versions 1.3 dated 2020-06-08 and 1.3-1 dated 2020-08-11
DESCRIPTION | 14 ++-- MD5 | 65 ++++++++++++-------- NAMESPACE | 7 ++ NEWS | 8 ++ R/SOMbrero-package.R | 5 - R/data.R | 7 -- R/som.R | 42 +++++++++++++ R/sombreroGUI.R | 2 build/vignette.rds |binary inst/doc/a-doc-SOMbrero-package.R | 4 - inst/doc/a-doc-SOMbrero-package.html | 35 +++++----- inst/doc/b-doc-grids.R | 14 ++-- inst/doc/b-doc-grids.html | 48 +++++++------- inst/doc/c-doc-numericSOM.R | 78 ++++++++++++------------ inst/doc/c-doc-numericSOM.Rmd | 2 inst/doc/c-doc-numericSOM.html | 113 +++++++++++++++++------------------ inst/doc/d-doc-korrespSOM.R | 42 ++++++------- inst/doc/d-doc-korrespSOM.html | 71 ++++++++++----------- inst/doc/e-doc-relationalSOM.R | 34 +++++----- inst/doc/e-doc-relationalSOM.Rmd | 13 ++-- inst/doc/e-doc-relationalSOM.html | 101 +++++++++++++++++++++---------- man/SOMbrero-package.Rd | 4 - man/presidentielles2002.Rd | 7 -- man/sombreroGUI.Rd | 2 vignettes/c-doc-numericSOM.Rmd | 2 vignettes/c-doc-numericSOM_cache |only vignettes/d-doc-korrespSOM_cache |only vignettes/e-doc-relationalSOM.Rmd | 13 ++-- vignettes/e-doc-relationalSOM_cache |only 29 files changed, 420 insertions(+), 313 deletions(-)
Title: Create Future 'EnergyPlus' Weather Files using 'CMIP6' Data
Description: Query, download climate change projection data from the 'CMIP6' (Coupled
Model Intercomparison Project Phase 6) project
<https://pcmdi.llnl.gov/CMIP6/> in the 'ESGF' (Earth System Grid Federation)
platform <https://esgf.llnl.gov>, and create future 'EnergyPlus'
<https://energyplus.net> Weather ('EPW') files adjusted from climate changes
using data from Global Climate Models ('GCM').
Author: Hongyuan Jia [aut, cre] (<https://orcid.org/0000-0002-0075-8183>),
Adrian Chong [aut] (<https://orcid.org/0000-0002-9486-4728>)
Maintainer: Hongyuan Jia <hongyuan.jia@bears-berkeley.sg>
Diff between epwshiftr versions 0.1.0 dated 2020-07-07 and 0.1.1 dated 2020-08-11
DESCRIPTION | 23 +- LICENSE | 4 MD5 | 27 +-- NEWS.md | 9 + R/coord.R | 4 R/epwshiftr-package.R | 2 R/esgf.R | 7 R/netcdf.R | 68 ++++---- README.md | 382 +++++++++++++++++++++------------------------ man/epwshiftr-package.Rd | 2 man/extract_data.Rd | 4 man/figures |only man/match_coord.Rd | 4 man/summary_database.Rd | 4 tests/testthat/test-esgf.R | 147 +++++++++-------- 15 files changed, 356 insertions(+), 331 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. 4. Overlaying those maps over reference maps from
Google Maps.
Author: Ari Lamstein [aut, cre],
Brian Johnson [ctb],
Trulia, Inc. [cph]
Maintainer: Ari Lamstein <ari@lamsteinconsulting.com>
Diff between choroplethr versions 3.6.4 dated 2020-07-25 and 3.7.0 dated 2020-08-11
DESCRIPTION | 13 ++++--- MD5 | 23 +++++++++---- NAMESPACE | 16 +++++++++ NEWS | 8 ++++ R/data.R | 42 ++++++++++++++++++++++-- R/get_congress_116_party_data.R |only R/get_congressional_demographics.R |only README.md | 2 - data/congress116.regions.rdata |only data/df_congress116_demographics.rdata |only data/df_congress116_party.rdata |only man/congress116.regions.Rd |only man/df_congress116_demographics.Rd |only man/df_congress116_party.Rd |only man/df_japan_census.Rd | 2 - man/filter_to_voting_congressional_districts.Rd |only man/get_congressional_district_demographics.Rd |only man/visualize_df_by_race_ethnicity_party.Rd |only 18 files changed, 91 insertions(+), 15 deletions(-)
Title: Goodman-Weare Affine-Invariant Sampling
Description: Implementation of the affine-invariant method of Goodman & Weare (2010) <DOI:10.2140/camcos.2010.5.65>, a method of producing Monte-Carlo samples from a target distribution.
Author: Adam Mantz
Maintainer: Adam Mantz <amantz@slac.stanford.edu>
Diff between rgw versions 0.1.0 dated 2016-10-10 and 0.3.0 dated 2020-08-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + R/rgw.R | 17 ++++++++++++++++- man/GoodmanWeare.rem.Rd | 42 ++++++++++++++++++++++++++++++++++++------ man/rgw-package.Rd | 4 ++-- 6 files changed, 64 insertions(+), 18 deletions(-)
Title: Parse Darwin Core Files
Description: Parse and create Darwin Core (<http://rs.tdwg.org/dwc/>) Simple
and Archives. Functionality includes reading and parsing all the
files in a Darwin Core Archive, including the datasets and metadata;
read and parse simple Darwin Core files; and validation of Darwin
Core Archives.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between finch versions 0.3.0 dated 2019-04-25 and 0.4.0 dated 2020-08-11
DESCRIPTION | 18 +++++++++------- LICENSE | 2 - MD5 | 16 +++++++------- NAMESPACE | 5 ++-- NEWS.md | 8 +++++++ R/dwca_validate.R | 3 -- R/finch-package.R | 9 ++++---- README.md | 56 +++++++++++++++++++++++++-------------------------- man/finch-package.Rd | 2 - 9 files changed, 64 insertions(+), 55 deletions(-)
Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description: Graphical and tabular effect displays, e.g., of interactions, for
various statistical models with linear predictors.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Brad Price [aut],
Michael Friendly [aut],
Jangman Hong [aut],
Robert Andersen [ctb],
David Firth [ctb],
Steve Taylor [ctb],
R Core Team [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between effects versions 4.1-4 dated 2019-11-15 and 4.2-0 dated 2020-08-11
effects-4.1-4/effects/inst/doc/adding-Effect-methods.R |only effects-4.1-4/effects/inst/doc/adding-Effect-methods.Rnw |only effects-4.1-4/effects/inst/doc/adding-Effect-methods.pdf |only effects-4.1-4/effects/man/effect-methods.Rd |only effects-4.1-4/effects/vignettes/adding-Effect-methods.Rnw |only effects-4.1-4/effects/vignettes/adding-Effect-methods.bib |only effects-4.2-0/effects/DESCRIPTION | 16 effects-4.2-0/effects/MD5 | 59 effects-4.2-0/effects/NAMESPACE | 34 effects-4.2-0/effects/NEWS | 712 +-- effects-4.2-0/effects/R/Effect-methods.R | 91 effects-4.2-0/effects/R/Effect.R | 1389 +++---- effects-4.2-0/effects/R/Effect.mlm.R | 120 effects-4.2-0/effects/R/effectspoLCA.R | 136 effects-4.2-0/effects/R/plot.effpoly.R | 1950 +++++----- effects-4.2-0/effects/R/predictorEffects.R | 28 effects-4.2-0/effects/R/utilities.R | 1295 +++--- effects-4.2-0/effects/build/vignette.rds |binary effects-4.2-0/effects/inst/CITATION | 158 effects-4.2-0/effects/inst/doc/methods-supported-by-effects.R |only effects-4.2-0/effects/inst/doc/methods-supported-by-effects.Rnw |only effects-4.2-0/effects/inst/doc/methods-supported-by-effects.pdf |only effects-4.2-0/effects/inst/doc/partial-residuals.pdf |binary effects-4.2-0/effects/inst/doc/predictor-effects-gallery.R | 4 effects-4.2-0/effects/inst/doc/predictor-effects-gallery.Rnw | 40 effects-4.2-0/effects/inst/doc/predictor-effects-gallery.pdf |binary effects-4.2-0/effects/man/effCoef.Rd |only effects-4.2-0/effects/man/effSources.Rd |only effects-4.2-0/effects/man/effect.Rd | 1128 ++--- effects-4.2-0/effects/man/effects-package.Rd | 164 effects-4.2-0/effects/man/effectsTheme.Rd | 102 effects-4.2-0/effects/man/plot.effect.Rd | 6 effects-4.2-0/effects/man/predictorEffects.Rd | 58 effects-4.2-0/effects/tests/regression-tests.R |only effects-4.2-0/effects/tests/regression-tests.RData |only effects-4.2-0/effects/vignettes/methods-supported-by-effects.Rnw |only effects-4.2-0/effects/vignettes/methods-supported-by-effects.bib |only effects-4.2-0/effects/vignettes/predictor-effects-gallery.Rnw | 40 38 files changed, 3775 insertions(+), 3755 deletions(-)
Title: Companion to Applied Regression
Description: Functions to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Third Edition, Sage, 2019.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Brad Price [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Ben Bolker [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Pavel Krivitsky [ctb],
Rafael Laboissiere [ctb],
Martin Maechler [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
Steve Walker [ctb],
David Winsemius [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between car versions 3.0-8 dated 2020-05-21 and 3.0-9 dated 2020-08-11
DESCRIPTION | 14 MD5 | 98 +- NAMESPACE | 7 NEWS | 1766 +++++++++++++++++++++--------------------- R/Anova.R | 15 R/avPlots.R | 6 R/ceresPlots.R | 369 ++++---- R/crPlots.R | 299 +++---- R/deltaMethod.R | 8 R/hccm.R | 4 R/linearHypothesis.R | 8 R/mcPlots.R | 7 R/residualPlots.R | 626 +++++++------- R/scatterplotMatrix.R | 3 inst/doc/embedding.pdf |binary man/Anova.Rd | 756 ++++++++--------- man/Boot.Rd | 12 man/Contrasts.Rd | 4 man/Ellipses.Rd | 10 man/Export.Rd | 10 man/Import.Rd | 10 man/S.Rd | 2 man/ScatterplotSmoothers.Rd | 280 +++--- man/TransformationAxes.Rd | 2 man/avPlots.Rd | 12 man/boxCoxVariable.Rd | 2 man/ceresPlots.Rd | 11 man/crPlots.Rd | 11 man/deltaMethod.Rd | 396 ++++----- man/hist.boot.Rd | 318 +++---- man/influence-mixed-models.Rd | 228 ++--- man/influencePlot.Rd | 4 man/leveragePlots.Rd | 2 man/linearHypothesis.Rd | 815 +++++++++---------- man/mcPlots.Rd | 7 man/ncvTest.Rd | 2 man/outlierTest.Rd | 160 +-- man/panel.car.Rd | 2 man/poTest.Rd | 4 man/qqPlot.Rd | 282 +++--- man/recode.Rd | 165 ++- man/regLine.Rd | 8 man/scatter3d.Rd | 4 man/scatterplot.Rd | 14 man/scatterplotMatrix.Rd | 6 man/some.Rd | 2 man/spreadLevelPlot.Rd | 8 man/subsets.Rd | 2 man/symbox.Rd | 116 +- man/wcrossprod.Rd | 4 50 files changed, 3497 insertions(+), 3404 deletions(-)