Title: Clustering and Visualizing Distance Matrices
Description: Defines the classes used to explore, cluster and
visualize distance matrices, especially those arising from binary data.
Author: Kevin R. Coombes, Caitlin E. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Mercator versions 0.10.0 dated 2020-03-06 and 0.11.2 dated 2020-08-24
DESCRIPTION | 10 MD5 | 43 +- NAMESPACE | 4 NEWS | 24 + R/02-binaryMatrix.R | 12 R/04-vis.R | 51 ++- TODO | 4 build/vignette.rds |binary data/CML1000.rda |binary data/CML500.rda |binary data/datalist |only data/fakedata.rda |only data/lgfFeatures.rda |binary inst/Examples/makeFake.R |only inst/doc/mercVis.R |only inst/doc/mercVis.Rmd |only inst/doc/mercVis.html |only inst/doc/mercator.R | 121 +++---- inst/doc/mercator.Rmd | 232 ++++++++------ inst/doc/mercator.html | 727 +++++++++++++++++++++++++++++++++-------------- man/Mercator-class.Rd | 4 man/binaryMatrix.Rd | 10 man/coloring.Rd | 8 man/datasets.Rd | 27 + vignettes/mercVis.Rmd |only vignettes/mercator.Rmd | 232 ++++++++------ 26 files changed, 968 insertions(+), 541 deletions(-)
Title: Data Package for the 2016 United States Federal Elections
Description: Easily analyze relational data from the United States 2016 federal
election cycle as reported by the Federal Election Commission.
This package contains data about candidates, committees, and a
variety of different financial expenditures. Data is from <https://www.fec.gov/data/browse-data/?tab=bulk-data>.
Author: Marium Tapal [aut, cre] (<https://orcid.org/0000-0001-5093-6462>),
Rana Gahwagy [aut],
Irene Ryan [aut],
Benjamin S. Baumer [aut] (<https://orcid.org/0000-0002-3279-0516>)
Maintainer: Marium Tapal <mariumtapal@gmail.com>
Diff between fec16 versions 0.1.0 dated 2020-07-30 and 0.1.1 dated 2020-08-24
DESCRIPTION | 16 +++--- MD5 | 31 ++++++------- NEWS.md | 8 +++ R/data.R | 6 +- R/fn_contributions.R | 16 +++--- R/fn_expenditures.R | 3 - R/fn_individuals.R | 5 -- R/fn_transactions.R | 3 - README.md | 52 +++++++++++----------- inst/doc/fec_vignette.R | 46 +++++++++++-------- inst/doc/fec_vignette.Rmd | 13 ++++- inst/doc/fec_vignette.html | 85 ++++++++++++++++++------------------ man/expenditures.Rd | 4 - man/figures/README-party-plot-1.png |binary man/transactions.Rd | 2 vignettes/fec_vignette.Rmd | 13 ++++- vignettes/results_by_cand.Rda |only 17 files changed, 167 insertions(+), 136 deletions(-)
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 1.2.6 dated 2020-08-11 and 1.2.7 dated 2020-08-24
DESCRIPTION | 8 MD5 | 22 +- NEWS.md | 4 R/ROC.R | 4 R/ThresholdPlot.R | 32 +-- inst/doc/WVPlots_concept.html | 4 inst/doc/WVPlots_examples.R | 29 +++ inst/doc/WVPlots_examples.Rmd | 35 ++++ inst/doc/WVPlots_examples.html | 351 ++++++++++++++++++++++------------------- man/ThresholdPlot.Rd | 2 man/plotlyROC.Rd | 5 vignettes/WVPlots_examples.Rmd | 35 ++++ 12 files changed, 330 insertions(+), 201 deletions(-)
Title: Test and Item Analysis via Shiny
Description: Interactive shiny application for analysis of educational tests and
their items.
Author: Patricia Martinkova [aut, cre],
Adela Hladka [aut],
Ondrej Leder [ctb],
Jakub Houdek [ctb],
Lubomir Stepanek [ctb],
Tomas Jurica [ctb],
Jana Vorlickova [ctb],
Jan Netik [ctb]
Maintainer: Patricia Martinkova <martinkova@cs.cas.cz>
Diff between ShinyItemAnalysis versions 1.3.3 dated 2020-05-04 and 1.3.4 dated 2020-08-24
ShinyItemAnalysis-1.3.3/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/www/author_adela.jpg |only ShinyItemAnalysis-1.3.3/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/www/author_jakub.png |only ShinyItemAnalysis-1.3.3/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/www/author_lubos.jpg |only ShinyItemAnalysis-1.3.3/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/www/author_ondra.png |only ShinyItemAnalysis-1.3.3/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/www/author_patricia.png |only ShinyItemAnalysis-1.3.3/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/www/author_tomas.jpg |only ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/DESCRIPTION | 18 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/MD5 | 88 - ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/NAMESPACE | 3 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/NEWS.md | 31 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/R/DDplot.R | 173 +- ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/R/ItemAnalysis.R | 97 - ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/R/ShinyItemAnalysis-package.R | 6 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/R/ggWrightMap.R | 3 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/R/recode_nr.R |only ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/R/startShinyItemAnalysis.R | 66 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/README.md | 22 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/CITATION | 2 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/reporthtml.Rmd | 2 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/server.R | 18 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/server/DIF.R | 694 +++++++++- ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/server/Data.R | 14 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/server/IRT.R | 28 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/server/Regression.R | 107 - ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/server/Reliability.R | 2 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/server/Summary.R | 2 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/server/TraditionalAnalysis.R | 248 ++- ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/server/Validity.R | 53 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/ui.R | 4 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/ui/uiAbout.R | 7 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/ui/uiDIF.R | 103 + ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/ui/uiData.R | 3 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/ui/uiIRT.R | 58 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/ui/uiIRT/uiDIRT.R | 7 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/ui/uiReferences.R | 2 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/ui/uiRegression.R | 42 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/ui/uiReliability.R | 12 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/ui/uiSetting.R | 2 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/ui/uiSummary.R | 8 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/ui/uiTraditionalAnalysis.R | 62 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/ui/uiValidity.R | 81 + ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/www/bootstrap.css | 2 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/www/bootstrap_for_ss.css |only ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/inst/shiny-examples/ShinyItemAnalysis/www/bootstrap_print.css |only ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/man/DDplot.Rd | 92 - ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/man/ItemAnalysis.Rd | 56 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/man/ShinyItemAnalysis-package.Rd | 4 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/man/ggWrightMap.Rd | 3 ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/man/recode_nr.Rd |only ShinyItemAnalysis-1.3.4/ShinyItemAnalysis/man/startShinyItemAnalysis.Rd | 18 50 files changed, 1740 insertions(+), 503 deletions(-)
More information about ShinyItemAnalysis at CRAN
Permanent link
Title: Analysis of Longitudinal Data with Irregular Observation Times
Description: Analysis of longitudinal data for which the times of observation are random variables that are potentially associated with the outcome process. The package includes inverse-intensity weighting methods (Lin H, Scharfstein DO, Rosenheck RA (2004) <doi:10.1111/j.1467-9868.2004.b5543.x>) and multiple outputation (Pullenayegum EM (2016) <doi:10.1002/sim.6829>).
Author: Eleanor Pullenayegum
Maintainer: Eleanor Pullenayegum <eleanor.pullenayegum@sickkids.ca>
Diff between IrregLong versions 0.3.2 dated 2020-06-24 and 0.3.3 dated 2020-08-24
DESCRIPTION | 10 - MD5 | 22 +-- NAMESPACE | 1 R/IIWcode.R | 100 +++++-------- build/vignette.rds |binary inst/doc/Irreglong-vignette.R | 15 -- inst/doc/Irreglong-vignette.Rmd | 18 +- inst/doc/Irreglong-vignette.html | 284 +++++++++++++++++++-------------------- man/Liang.Rd | 12 - man/extent.of.irregularity.Rd | 14 - man/iiw.weights.Rd | 5 vignettes/Irreglong-vignette.Rmd | 18 +- 12 files changed, 222 insertions(+), 277 deletions(-)
Title: A Package to Visualize Linear Models Features and Play with Them
Description: Contains a suite of shiny applications
meant to explore linear model inference feature through simulation
and games.
Author: Francesco Pauli (see file LICENSEMEDIA for credits on sounds and images)
Maintainer: Francesco Pauli <francesco.pauli@deams.units.it>
Diff between lmviz versions 0.1.2 dated 2019-05-15 and 0.2.0 dated 2020-08-24
DESCRIPTION | 17 - MD5 | 68 ++++-- NAMESPACE | 15 + NEWS.md | 11 - R/BadLM.r | 6 R/Collin.r |only R/ComputerDecision.default.r | 23 +- R/ConfInt.r |only R/GuessTheLine.r |only R/GuessThePoints.r |only R/LMBoard.R |only R/MultipleLM.R |only R/Prediction.r |only R/SampleDist.R |only R/SimpleLM.R | 5 R/Simulation.default.r | 5 R/SlopeTest.R |only R/checksim.r | 2 R/lmviz-package.r | 13 + inst/BadLMApp.r | 416 ++++++++++++++++++++-------------------- inst/CollinLMApp.r |only inst/ConfintLMApp.r |only inst/GuessTheLineApp.r |only inst/GuessTheNonLinLine.r |only inst/GuessTheNonLinLine2.r |only inst/GuessThePointsApp.r |only inst/LMboardApp.r |only inst/MultipleLMApp.r |only inst/PredictionLMApp.r |only inst/QuizResidualApp.r | 55 +++-- inst/SampleDistLMApp.r |only inst/SimpleLMApp.r | 145 +++++++------ inst/SlopeTestLMApp.r |only inst/rsconnect |only man/BadLM.Rd | 9 man/Collin.Rd |only man/ComputerDecision.default.Rd | 5 man/ConfInt.Rd |only man/GuessTheLine.Rd |only man/GuessThePoints.Rd |only man/LMBoard.Rd |only man/MultipleLM.Rd |only man/Prediction.Rd |only man/QuizResidual.Rd | 9 man/SampleDist.Rd |only man/SimpleLM.Rd | 3 man/Simulation.default.Rd | 5 man/SlopeTest.Rd |only man/checksim.Rd | 7 man/lmviz.Rd | 14 + 50 files changed, 494 insertions(+), 339 deletions(-)
More information about sparklyr.flint at CRAN
Permanent link
Title: Variable Life Adjusted Display and Other Risk-Adjusted Quality
Control Charts
Description: Contains functions to set up risk-adjusted quality control charts in health care. For the variable life adjusted display (VLAD) proposed by Lovegrove et al. (1997) <doi:10.1016/S0140-6736(97)06507-0> signaling rules derived in Wittenberg et al. (2018) <doi:10.1002/sim.7647> are implemented. Additionally, for the risk-adjusted cumulative sum chart based on log-likelihood ratio statistic introduced by Steiner et al. (2000) <doi:10.1093/biostatistics/1.4.441> average run length and control limits can be computed with fast and accurate Markov chain approximations developed in Knoth et al. (2019) <doi:10.1002/sim.8104>.
Author: Philipp Wittenberg [aut, cre] (<https://orcid.org/0000-0001-7151-8243>),
Sven Knoth [aut, ths] (<https://orcid.org/0000-0002-9666-5554>)
Maintainer: Philipp Wittenberg <pwitten@hsu-hh.de>
Diff between vlad versions 0.2.0 dated 2018-12-06 and 0.2.1 dated 2020-08-24
vlad-0.2.0/vlad/build |only vlad-0.2.0/vlad/man/calceo.Rd |only vlad-0.2.0/vlad/man/cusum_arl_h_sim.Rd |only vlad-0.2.0/vlad/man/cusum_arl_sim.Rd |only vlad-0.2.0/vlad/man/eocusum_adoc_sim.Rd |only vlad-0.2.0/vlad/man/eocusum_arl_h_sim.Rd |only vlad-0.2.0/vlad/man/eocusum_arloc_h_sim.Rd |only vlad-0.2.0/vlad/man/eocusum_arloc_sim.Rd |only vlad-0.2.0/vlad/man/gettherisk.Rd |only vlad-0.2.0/vlad/man/racusum_adoc_sim.Rd |only vlad-0.2.0/vlad/man/racusum_arl_h_sim.Rd |only vlad-0.2.0/vlad/man/racusum_arloc_h_sim.Rd |only vlad-0.2.0/vlad/man/racusum_arloc_sim.Rd |only vlad-0.2.0/vlad/tests/testthat/test-eocusum_arloc_h_sim.R |only vlad-0.2.0/vlad/tests/testthat/test-eocusum_arloc_sim.R |only vlad-0.2.0/vlad/tests/testthat/test-racusum_arloc_h_sim.R |only vlad-0.2.0/vlad/tests/testthat/test-racusum_arloc_sim.R |only vlad-0.2.1/vlad/DESCRIPTION | 24 vlad-0.2.1/vlad/MD5 | 148 +- vlad-0.2.1/vlad/NAMESPACE | 28 vlad-0.2.1/vlad/NEWS.md | 26 vlad-0.2.1/vlad/R/RcppExports.R | 66 - vlad-0.2.1/vlad/R/eocusum_sim.R | 463 ++------- vlad-0.2.1/vlad/R/misc.R | 36 vlad-0.2.1/vlad/R/package.R | 18 vlad-0.2.1/vlad/R/racusum_beta_int.R |only vlad-0.2.1/vlad/R/racusum_beta_mc.R |only vlad-0.2.1/vlad/R/racusum_beta_sim.R |only vlad-0.2.1/vlad/R/racusum_betabinomial_sim.R |only vlad-0.2.1/vlad/R/racusum_discretebeta_sim.R |only vlad-0.2.1/vlad/R/racusum_mc.R | 61 - vlad-0.2.1/vlad/R/racusum_sim.R | 501 ++-------- vlad-0.2.1/vlad/README.md | 326 +++--- vlad-0.2.1/vlad/inst/CITATION | 4 vlad-0.2.1/vlad/inst/VLAD.bib |only vlad-0.2.1/vlad/inst/ims.csl |only vlad-0.2.1/vlad/inst/include/eocusum_sim.h | 24 vlad-0.2.1/vlad/inst/include/misc.h | 1 vlad-0.2.1/vlad/inst/include/racusum_beta_int.h |only vlad-0.2.1/vlad/inst/include/racusum_beta_mc.h |only vlad-0.2.1/vlad/inst/include/racusum_beta_sim.h |only vlad-0.2.1/vlad/inst/include/racusum_betabinomial_sim.h |only vlad-0.2.1/vlad/inst/include/racusum_discretebeta_sim.h |only vlad-0.2.1/vlad/inst/include/racusum_mc.h | 1 vlad-0.2.1/vlad/inst/include/racusum_sim.h | 15 vlad-0.2.1/vlad/man/bcusum_crit_sim.Rd | 12 vlad-0.2.1/vlad/man/eocusum_ad_sim.Rd | 20 vlad-0.2.1/vlad/man/eocusum_arl_sim.Rd | 15 vlad-0.2.1/vlad/man/eocusum_crit_sim.Rd | 89 + vlad-0.2.1/vlad/man/eocusum_scores.Rd | 28 vlad-0.2.1/vlad/man/optimal_k.Rd | 68 - vlad-0.2.1/vlad/man/racusum_ad_sim.Rd |only vlad-0.2.1/vlad/man/racusum_arl_mc.Rd | 13 vlad-0.2.1/vlad/man/racusum_arl_sim.Rd | 78 - vlad-0.2.1/vlad/man/racusum_beta_arl_int.Rd |only vlad-0.2.1/vlad/man/racusum_beta_arl_mc.Rd |only vlad-0.2.1/vlad/man/racusum_beta_arl_sim.Rd |only vlad-0.2.1/vlad/man/racusum_beta_crit_mc.Rd |only vlad-0.2.1/vlad/man/racusum_beta_crit_sim.Rd |only vlad-0.2.1/vlad/man/racusum_betabinomial_arl_sim.Rd |only vlad-0.2.1/vlad/man/racusum_betabinomial_crit_sim.Rd |only vlad-0.2.1/vlad/man/racusum_crit_mc.Rd | 21 vlad-0.2.1/vlad/man/racusum_crit_sim.Rd | 68 - vlad-0.2.1/vlad/man/racusum_discretebeta_arl_sim.Rd |only vlad-0.2.1/vlad/man/racusum_discretebeta_crit_sim.Rd |only vlad-0.2.1/vlad/man/racusum_scores.Rd | 2 vlad-0.2.1/vlad/man/search_delta.Rd | 5 vlad-0.2.1/vlad/man/vlad-package.Rd | 15 vlad-0.2.1/vlad/src/RcppExports.cpp | 315 ++++-- vlad-0.2.1/vlad/src/eocusum_sim.cpp | 260 ++--- vlad-0.2.1/vlad/src/racusum_beta_int.cpp |only vlad-0.2.1/vlad/src/racusum_beta_mc.cpp |only vlad-0.2.1/vlad/src/racusum_beta_sim.cpp |only vlad-0.2.1/vlad/src/racusum_betabinomial_sim.cpp |only vlad-0.2.1/vlad/src/racusum_discretebeta_sim.cpp |only vlad-0.2.1/vlad/src/racusum_mc.cpp | 203 +--- vlad-0.2.1/vlad/src/racusum_sim.cpp | 98 - vlad-0.2.1/vlad/tests/testthat.R | 2 vlad-0.2.1/vlad/tests/testthat/helper-racusum_arloc_h_sim.R | 2 vlad-0.2.1/vlad/tests/testthat/test-QQ.R |only vlad-0.2.1/vlad/tests/testthat/test-bcusum_arl_sim.R | 17 vlad-0.2.1/vlad/tests/testthat/test-ell.R |only vlad-0.2.1/vlad/tests/testthat/test-eocusum_ad_sim.R | 100 + vlad-0.2.1/vlad/tests/testthat/test-eocusum_arl_sim.R | 165 ++- vlad-0.2.1/vlad/tests/testthat/test-eocusum_crit_sim.R | 59 + vlad-0.2.1/vlad/tests/testthat/test-eocusum_scores.R |only vlad-0.2.1/vlad/tests/testthat/test-llr_score.R | 125 +- vlad-0.2.1/vlad/tests/testthat/test-optimal_k.R | 14 vlad-0.2.1/vlad/tests/testthat/test-racusum_ad_sim.R |only vlad-0.2.1/vlad/tests/testthat/test-racusum_arl_mc.R | 215 ++-- vlad-0.2.1/vlad/tests/testthat/test-racusum_arl_sim.R | 148 +- vlad-0.2.1/vlad/tests/testthat/test-racusum_beta_arl_int.R |only vlad-0.2.1/vlad/tests/testthat/test-racusum_beta_arl_mc.R |only vlad-0.2.1/vlad/tests/testthat/test-racusum_beta_arl_sim.R |only vlad-0.2.1/vlad/tests/testthat/test-racusum_beta_crit_mc.R |only vlad-0.2.1/vlad/tests/testthat/test-racusum_beta_crit_sim.R |only vlad-0.2.1/vlad/tests/testthat/test-racusum_betabinomial_arl_sim.R |only vlad-0.2.1/vlad/tests/testthat/test-racusum_betabinomial_crit_sim.R |only vlad-0.2.1/vlad/tests/testthat/test-racusum_crit_mc.R | 153 +-- vlad-0.2.1/vlad/tests/testthat/test-racusum_crit_sim.R | 152 +-- vlad-0.2.1/vlad/tests/testthat/test-racusum_discretebeta_arl_sim.R |only vlad-0.2.1/vlad/tests/testthat/test-racusum_discretebeta_crit_sim.R |only vlad-0.2.1/vlad/tests/testthat/test-racusum_scores.R | 22 vlad-0.2.1/vlad/tests/testthat/test-search_delta.R |only 104 files changed, 2017 insertions(+), 2209 deletions(-)
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Creates matrix population models for use in population ecological
analyses. Specializes on the construction of historical matrices,
which are 2d matrices comprising 3 time intervals of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. Methodology based on
Ehrlen (2000) <doi:10.1890/0012-9658(2000)081[1675:TDOPPD]2.0.CO;2>.
Author: Richard P. Shefferson [aut, cre]
(<https://orcid.org/0000-0002-5234-3131>),
Johan Ehrlen [aut] (<https://orcid.org/0000-0001-8539-8967>)
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 2.2.2 dated 2020-08-03 and 2.3.0 dated 2020-08-24
lefko3-2.2.2/lefko3/src/RateFunctions.cpp |only lefko3-2.3.0/lefko3/DESCRIPTION | 20 lefko3-2.3.0/lefko3/MD5 | 62 lefko3-2.3.0/lefko3/NAMESPACE | 1 lefko3-2.3.0/lefko3/R/RcppExports.R | 306 + lefko3-2.3.0/lefko3/R/datamanag.R | 1618 +------ lefko3-2.3.0/lefko3/R/matrixcreation.R | 1792 -------- lefko3-2.3.0/lefko3/R/modelselection.R | 197 lefko3-2.3.0/lefko3/R/popchar.R | 1 lefko3-2.3.0/lefko3/build/vignette.rds |binary lefko3-2.3.0/lefko3/inst/doc/Chapter1.Rmd | 145 lefko3-2.3.0/lefko3/inst/doc/Chapter1.html | 144 lefko3-2.3.0/lefko3/inst/doc/Chapter2.Rmd | 3056 ++++++-------- lefko3-2.3.0/lefko3/inst/doc/Chapter2.html | 4136 ++++++++----------- lefko3-2.3.0/lefko3/inst/doc/Chapter3.Rmd | 1470 +++--- lefko3-2.3.0/lefko3/inst/doc/Chapter3.html | 1856 ++++---- lefko3-2.3.0/lefko3/man/flefko2.Rd | 10 lefko3-2.3.0/lefko3/man/flefko3.Rd | 10 lefko3-2.3.0/lefko3/man/historicalize3.Rd | 27 lefko3-2.3.0/lefko3/man/summary.lefkoMat.Rd | 2 lefko3-2.3.0/lefko3/man/verticalize3.Rd | 15 lefko3-2.3.0/lefko3/src/DataManagement.cpp |only lefko3-2.3.0/lefko3/src/MatrixEstimators.cpp |only lefko3-2.3.0/lefko3/src/PopDynamics.cpp |only lefko3-2.3.0/lefko3/src/RcppExports.cpp | 158 lefko3-2.3.0/lefko3/vignettes/Ch2an2st1ln383-1.png |binary lefko3-2.3.0/lefko3/vignettes/Ch2an2st1ln389-1.png |binary lefko3-2.3.0/lefko3/vignettes/Ch3an1st1aln79pl-1.png |binary lefko3-2.3.0/lefko3/vignettes/Ch3an2st5ln710-1.png |binary lefko3-2.3.0/lefko3/vignettes/Chapter1.Rmd | 145 lefko3-2.3.0/lefko3/vignettes/Chapter2.Rmd | 3056 ++++++-------- lefko3-2.3.0/lefko3/vignettes/Chapter2.Rmd.orig | 183 lefko3-2.3.0/lefko3/vignettes/Chapter3.Rmd | 1470 +++--- lefko3-2.3.0/lefko3/vignettes/Chapter3.Rmd.orig | 120 34 files changed, 8623 insertions(+), 11377 deletions(-)
Title: Bridge to System Package Manager
Description: Enables binary package installations on Linux distributions.
Provides functions to manage packages via the distribution's package
manager. Also provides transparent integration with R's install.packages()
and a fallback mechanism. When installed as a system package, interacts
with the system's package manager without requiring administrative
privileges via an integrated D-Bus service; otherwise, uses sudo.
Currently, the following backends are supported: DNF, APT.
Author: Iñaki Ucar [aut, cph, cre] (<https://orcid.org/0000-0001-6403-5550>)
Maintainer: Iñaki Ucar <iucar@fedoraproject.org>
Diff between bspm versions 0.3.4 dated 2020-08-03 and 0.3.5 dated 2020-08-24
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 9 +++++++++ R/bridge.R | 24 +++++++++++++++++------- README.md | 1 + inst/service/backend/apt.py | 6 ++++++ inst/service/bspm.py | 16 ++++++---------- 7 files changed, 48 insertions(+), 26 deletions(-)
Title: Graphical Elements of the University of Konstanz's Corporate
Design
Description: Define and use graphical elements of corporate design manuals in R. The 'unikn' package provides color functions (by defining dedicated colors and color palettes, and commands for changing, viewing, and using them) and styled text elements (e.g., for marking, underlining, or plotting colored titles). The pre-defined range of colors and text functions is based on the corporate design of the University of Konstanz <https://www.uni-konstanz.de/>, but can be adapted and extended for other institutions and purposes.
Author: Hansjoerg Neth [aut, cre] (<https://orcid.org/0000-0001-5427-3141>),
Nico Gradwohl [aut] (<https://orcid.org/0000-0002-8703-905X>)
Maintainer: Hansjoerg Neth <h.neth@uni.kn>
Diff between unikn versions 0.2.0 dated 2019-09-25 and 0.3.0 dated 2020-08-24
unikn-0.2.0/unikn/inst/pix/README-col_scale_1-1.png |only unikn-0.2.0/unikn/inst/pix/README-col_scale_2-1.png |only unikn-0.2.0/unikn/inst/pix/README-col_scale_3-1.png |only unikn-0.2.0/unikn/inst/pix/README-compare_custom_pals-1.png |only unikn-0.2.0/unikn/inst/pix/README-heading_demo-1.png |only unikn-0.2.0/unikn/inst/pix/README-mark_new_plot-1.png |only unikn-0.2.0/unikn/inst/pix/README-others_txt_demo-1.png |only unikn-0.2.0/unikn/inst/pix/README-pal_n-1.png |only unikn-0.2.0/unikn/inst/pix/README-post-demo-1.png |only unikn-0.2.0/unikn/inst/pix/README-seecol_freiburg-1.png |only unikn-0.2.0/unikn/inst/pix/README-seecol_pref-1.png |only unikn-0.2.0/unikn/inst/pix/README-uline_demo-1.png |only unikn-0.2.0/unikn/inst/pix/README-url_post-1.png |only unikn-0.2.0/unikn/inst/pix/README-use_pal_demo_image-1.png |only unikn-0.2.0/unikn/inst/pix/README-use_pal_demo_mpg-1.png |only unikn-0.2.0/unikn/inst/pix/README-usepal_demo_barplot_1-1.png |only unikn-0.2.0/unikn/inst/pix/README-usepal_demo_barplot_2-1.png |only unikn-0.2.0/unikn/inst/pix/README-usepal_demo_scatter-1.png |only unikn-0.3.0/unikn/DESCRIPTION | 18 unikn-0.3.0/unikn/MD5 | 148 +- unikn-0.3.0/unikn/NAMESPACE | 1 unikn-0.3.0/unikn/NEWS.md | 25 unikn-0.3.0/unikn/R/color_fun.R | 561 +++++----- unikn-0.3.0/unikn/R/color_util.R | 11 unikn-0.3.0/unikn/R/plot_box_calls.R | 2 unikn-0.3.0/unikn/R/plot_themes.R | 154 ++ unikn-0.3.0/unikn/README.md | 116 +- unikn-0.3.0/unikn/build/vignette.rds |binary unikn-0.3.0/unikn/inst/CITATION | 8 unikn-0.3.0/unikn/inst/WORDLIST |only unikn-0.3.0/unikn/inst/doc/colors.R | 118 +- unikn-0.3.0/unikn/inst/doc/colors.Rmd | 201 ++- unikn-0.3.0/unikn/inst/doc/colors.html | 141 +- unikn-0.3.0/unikn/inst/doc/text.R | 61 - unikn-0.3.0/unikn/inst/doc/text.Rmd | 72 - unikn-0.3.0/unikn/inst/doc/text.html | 51 unikn-0.3.0/unikn/inst/pix/README-col-scale-1-1.png |only unikn-0.3.0/unikn/inst/pix/README-col-scale-2-1.png |only unikn-0.3.0/unikn/inst/pix/README-col-scale-3-1.png |only unikn-0.3.0/unikn/inst/pix/README-compare-custom-pals-1.png |only unikn-0.3.0/unikn/inst/pix/README-heading-demo-1.png |only unikn-0.3.0/unikn/inst/pix/README-mark-new-plot-1.png |only unikn-0.3.0/unikn/inst/pix/README-mpg-use-pal-1.png |only unikn-0.3.0/unikn/inst/pix/README-others-txt-demo-1.png |only unikn-0.3.0/unikn/inst/pix/README-pal-n-1.png |only unikn-0.3.0/unikn/inst/pix/README-post-demo-1-1.png |only unikn-0.3.0/unikn/inst/pix/README-seecol-pref-1.png |only unikn-0.3.0/unikn/inst/pix/README-uline-demo-1.png |only unikn-0.3.0/unikn/inst/pix/README-uni-freiburg-seecol-1.png |only unikn-0.3.0/unikn/inst/pix/README-url-post-1.png |only unikn-0.3.0/unikn/inst/pix/README-use-pal-demo-image-1.png |only unikn-0.3.0/unikn/inst/pix/README-use_ggplot2_princeton-1.png |binary unikn-0.3.0/unikn/inst/pix/README-usepal-demo-barplot-1-1.png |only unikn-0.3.0/unikn/inst/pix/README-usepal-demo-barplot-2-1.png |only unikn-0.3.0/unikn/inst/pix/README-usepal-demo-scatter-1.png |only unikn-0.3.0/unikn/man/Bordeaux.Rd | 18 unikn-0.3.0/unikn/man/Grau.Rd | 18 unikn-0.3.0/unikn/man/Karpfenblau.Rd | 18 unikn-0.3.0/unikn/man/Peach.Rd | 18 unikn-0.3.0/unikn/man/Petrol.Rd | 18 unikn-0.3.0/unikn/man/Pinky.Rd | 18 unikn-0.3.0/unikn/man/Seeblau.Rd | 18 unikn-0.3.0/unikn/man/Seegruen.Rd | 18 unikn-0.3.0/unikn/man/Signal.Rd | 18 unikn-0.3.0/unikn/man/heading.Rd | 15 unikn-0.3.0/unikn/man/mark.Rd | 23 unikn-0.3.0/unikn/man/newpal.Rd | 6 unikn-0.3.0/unikn/man/pal_bordeaux.Rd | 30 unikn-0.3.0/unikn/man/pal_grau.Rd | 30 unikn-0.3.0/unikn/man/pal_karpfenblau.Rd | 30 unikn-0.3.0/unikn/man/pal_peach.Rd | 30 unikn-0.3.0/unikn/man/pal_petrol.Rd | 30 unikn-0.3.0/unikn/man/pal_pinky.Rd | 30 unikn-0.3.0/unikn/man/pal_seeblau.Rd | 30 unikn-0.3.0/unikn/man/pal_seegruen.Rd | 30 unikn-0.3.0/unikn/man/pal_signal.Rd | 30 unikn-0.3.0/unikn/man/pal_unikn.Rd | 34 unikn-0.3.0/unikn/man/pal_unikn_dark.Rd | 30 unikn-0.3.0/unikn/man/pal_unikn_light.Rd | 30 unikn-0.3.0/unikn/man/pal_unikn_pair.Rd | 30 unikn-0.3.0/unikn/man/pal_unikn_ppt.Rd | 30 unikn-0.3.0/unikn/man/pal_unikn_pref.Rd | 30 unikn-0.3.0/unikn/man/pal_unikn_web.Rd | 32 unikn-0.3.0/unikn/man/post.Rd | 23 unikn-0.3.0/unikn/man/seecol.Rd | 72 - unikn-0.3.0/unikn/man/slide.Rd | 6 unikn-0.3.0/unikn/man/theme_grau.Rd |only unikn-0.3.0/unikn/man/theme_unikn.Rd | 30 unikn-0.3.0/unikn/man/uline.Rd | 23 unikn-0.3.0/unikn/man/url_unikn.Rd | 6 unikn-0.3.0/unikn/man/usecol.Rd | 42 unikn-0.3.0/unikn/man/xbox.Rd | 6 unikn-0.3.0/unikn/vignettes/colors.Rmd | 201 ++- unikn-0.3.0/unikn/vignettes/text.Rmd | 72 - 94 files changed, 1763 insertions(+), 1098 deletions(-)
Title: Visualization and Analysis of Statistical Measures of Confidence
Description: Enables: (1) plotting two-dimensional confidence regions, (2) coverage analysis
of confidence region simulations and (3) calculating confidence intervals and the associated
actual coverage for binomial proportions. Each is given in greater detail next.
(1) Plots the two-dimensional confidence region for probability distribution parameters
(supported distribution suffixes: cauchy, gamma, invgauss, logis, llogis, lnorm, norm, unif,
weibull) corresponding to a user-given complete or right-censored dataset and level of
significance. The crplot() algorithm plots more points in areas of greater curvature to
ensure a smooth appearance throughout the confidence region boundary. An alternative
heuristic plots a specified number of points at roughly uniform intervals along its boundary.
Both heuristics build upon the radial profile log-likelihood ratio technique for plotting
confidence regions given by Jaeger (2016) <doi:10.1080/00031305.2016.1182946>, and
are detailed in a publication by Weld (2019) <doi:10.1080/00031305.2018.1564696>.
(2) Performs confidence region coverage simulations for a random sample drawn from a user-
specified parametric population distribution, or for a user-specified dataset and point of
interest with coversim(). (3) Calculates confidence interval bounds for a binomial proportion
with binomTest(), calculates the actual coverage with binomTestCoverage(), and plots the
actual coverage with binomTestCoveragePlot(). Calculates confidence interval bounds for the
binomial proportion using an ensemble of constituent confidence intervals with
binomTestEnsemble(). Calculates confidence interval bounds for the binomial proportion using
a complete enumeration of all possible transitions from one actual coverage acceptance curve
to another which minimizes the root mean square error for n <= 15 and follows the transitions
for well-known confidence intervals for n > 15 using binomTestMSE().
Author: Christopher Weld [aut, cre] (<https://orcid.org/0000-0001-5902-9738>),
Hayeon Park [aut],
Kexin Feng [aut],
Heather Sasinowska [aut],
Lawrence Leemis [aut],
Andrew Loh [ctb],
Yuan Chang [ctb],
Brock Crook [ctb],
Xin Zhang [ctb]
Maintainer: Christopher Weld <ceweld@email.wm.edu>
Diff between conf versions 1.6.3 dated 2020-03-13 and 1.7.0 dated 2020-08-24
DESCRIPTION | 30 +++++++++++++++++++----------- MD5 | 20 +++++++++++--------- NAMESPACE | 3 +++ R/binomTestMSE.R |only inst/CITATION | 25 ++++++++++++++++--------- inst/doc/coversim.R | 26 +++++++++++++------------- inst/doc/coversim.html | 15 ++++++--------- inst/doc/crplot.R | 32 ++++++++++++++++---------------- inst/doc/crplot.html | 15 ++++++--------- inst/doc/crplot_advanced.R | 34 +++++++++++++++++----------------- inst/doc/crplot_advanced.html | 15 ++++++--------- man/binomTestMSE.Rd |only 12 files changed, 113 insertions(+), 102 deletions(-)
Title: Reimplementations of Functions Introduced Since R-3.0.0
Description: Functions introduced or changed since R v3.0.0 are re-implemented in this
package. The backports are conditionally exported in order to let R resolve
the function name to either the implemented backport, or the respective base
version, if available. Package developers can make use of new functions or
arguments by selectively importing specific backports to
support older installations.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
R Core Team [aut]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between backports versions 1.1.8 dated 2020-06-17 and 1.1.9 dated 2020-08-24
DESCRIPTION | 8 ++++---- MD5 | 16 +++++++++++----- NAMESPACE | 4 +++- NEWS.md | 5 +++++ R/import.R | 22 ++++++++++++++-------- R/str2expression.R |only R/str2lang.R |only R/zzz.R | 2 +- man/str2expression.Rd |only man/str2lang.Rd |only tests/test_str2expression.R |only tests/test_str2lang.R |only 12 files changed, 38 insertions(+), 19 deletions(-)
Title: Spatially Balanced Sampling
Description: Selection of spatially balanced samples. In particular, the implemented sampling designs allow to select probability samples well spread over the population of interest, in any dimension and using any distance function (e.g. Euclidean distance, Manhattan distance). For more details, Benedetti R and Piersimoni F (2017) <doi:10.1002/bimj.201600194> and Benedetti R and Piersimoni F (2017) <arXiv:1710.09116>. The implementation has been done in C++ through the use of 'Rcpp' and 'RcppArmadillo'.
Author: Francesco Pantalone [aut, cre],
Roberto Benedetti [aut],
Federica Piersimoni [aut]
Maintainer: Francesco Pantalone <pantalone.fra@gmail.com>
Diff between Spbsampling versions 1.3.3 dated 2020-03-31 and 1.3.4 dated 2020-08-24
DESCRIPTION | 8 ++++---- MD5 | 44 ++++++++++++++++++++++---------------------- NEWS.md | 8 ++++++++ R/RcppExports.R | 48 +++++++++++++++++++++++++++++++++--------------- man/Spbsampling.Rd | 1 - man/hpwd.Rd | 4 ++-- man/income_emilia.Rd | 6 ++++-- man/lucas_abruzzo.Rd | 6 ++++-- man/pwd.Rd | 14 +++++++++----- man/sbi.Rd | 2 +- man/simul1.Rd | 6 ++++-- man/simul2.Rd | 6 ++++-- man/simul3.Rd | 6 ++++-- man/stprod.Rd | 7 ++++++- man/stsum.Rd | 7 ++++++- man/swd.Rd | 14 +++++++++----- src/RcppExports.cpp | 8 ++++---- src/hpwd.cpp | 4 ++-- src/pwd.cpp | 20 +++++++++++++------- src/sbi.cpp | 2 +- src/stprod.cpp | 11 ++++++++--- src/stsum.cpp | 11 ++++++++--- src/swd.cpp | 20 +++++++++++++------- 23 files changed, 169 insertions(+), 94 deletions(-)
Title: A Biomarker Validation Approach for Classification and
Predicting Survival Using Metabolomics Signature
Description: An approach to identifies metabolic biomarker signature for metabolic data by discovering predictive metabolite for predicting survival and classifying patients into risk groups.
Classifiers are constructed as a linear combination of predictive/important metabolites, prognostic factors and treatment effects if necessary.
Several methods were implemented to reduce the metabolomics matrix such as the principle component analysis of Wold Svante et al. (1987) <doi:10.1016/0169-7439(87)80084-9> ,
the LASSO method by Robert Tibshirani (1998) <doi:10.1002/(SICI)1097-0258(19970228)16:4%3C385::AID-SIM380%3E3.0.CO;2-3>, the
elastic net approach by Hui Zou and Trevor Hastie (2005) <doi:10.1111/j.1467-9868.2005.00503.x>.
Sensitivity analysis on the quantile used for the classification can also be accessed to check the deviation of the classification group based on the quantile specified.
Large scale cross validation can be performed in order to investigate the mostly selected predictive metabolites and for internal validation. During the evaluation process, validation is accessed using the hazard ratios (HR) distribution of the test set and inference is mainly based on resampling and permutations technique.
Author: Olajumoke Evangelina Owokotomo [aut, cre],
Ziv Shkedy [aut]
Maintainer: Olajumoke Evangelina Owokotomo <olajumoke.owokotomo@uhasselt.be>
Diff between MetabolicSurv versions 1.1.0 dated 2019-08-05 and 1.1.1 dated 2020-08-24
DESCRIPTION | 12 - INDEX |only MD5 | 105 ++++---- NAMESPACE | 2 R/CVLasoelascox.R | 514 ++++++++++++++++++++++---------------------- R/CVPcaPls.R | 318 +++++++++++++-------------- R/EstimateHR.R | 204 ++++++++--------- R/Lasoelascox.R | 447 +++++++++++++++++++------------------- R/MetFreq.R | 112 ++++----- R/MspecificCoxph.R | 226 +++++++++---------- R/SIMet.R | 230 +++++++++---------- R/SurvPcaClass.R | 254 ++++++++++----------- R/cvle-class.R | 342 ++++++++++++++--------------- R/cvmm-class.R | 253 ++++++++++----------- R/cvmv-class.R | 255 ++++++++++----------- R/cvpp-class.R | 209 ++++++++--------- R/cvsim-class.R | 286 +++++++++++------------- R/fcv-class.R | 264 +++++++++++----------- R/ms-class.R | 280 +++++++++++------------ R/perm-class.R | 238 +++++++++----------- README.md | 176 +++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/MetabolicSurv.R | 2 inst/doc/MetabolicSurv.Rmd | 1 inst/doc/MetabolicSurv.html | 35 ++ man/CVLasoelacox.Rd | 188 ++++++++-------- man/CVMajorityvotes.Rd | 142 ++++++------ man/CVMetSpecificCoxPh.Rd | 153 ++++++------- man/CVPcaPls.Rd | 155 ++++++------- man/CVSim.Rd | 119 +++++----- man/DataHR.Rd | 58 ++-- man/DistHR.Rd | 147 ++++++------ man/EstimateHR.Rd | 109 ++++----- man/Icvlasoel.Rd | 172 +++++++------- man/Lasoelacox.Rd | 172 +++++++------- man/MSData.Rd | 96 ++++---- man/MSpecificCoxPh.Rd | 141 ++++++------ man/Majorityvotes.Rd | 134 +++++------ man/MetFreq.Rd | 104 ++++---- man/MetabolicSurv.Rd | 53 ++-- man/QuantileAnalysis.Rd | 152 ++++++------- man/SIMet.Rd | 150 ++++++------ man/SurvPcaClass.Rd | 160 +++++++------ man/SurvPlsClass.Rd | 160 +++++++------ man/cvle-class.Rd | 163 +++++++------ man/cvmm-class.Rd | 163 +++++++------ man/cvmv-class.Rd | 141 ++++++------ man/cvpp-class.Rd | 141 ++++++------ man/cvsim-class.Rd | 153 ++++++------- man/fcv-class.Rd | 159 ++++++------- man/ms-class.Rd | 150 ++++++------ man/perm-class.Rd | 147 ++++++------ vignettes/MetabolicSurv.Rmd | 1 54 files changed, 4325 insertions(+), 4223 deletions(-)
Title: Matrices in Data Frames
Description: Provides functions to collapse a tidy data frame into matrices in a data frame
and expand a data frame of matrices into a tidy data frame.
Author: Matthew Heun [aut, cre] (<https://orcid.org/0000-0002-7438-214X>)
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between matsindf versions 0.3.4 dated 2020-03-21 and 0.3.6 dated 2020-08-24
DESCRIPTION | 13 +-- MD5 | 62 +++++++++--------- NEWS.md | 13 +++ R/collapse.R | 2 R/matsindf_apply.R | 118 +++++++++++++++++------------------ R/utilities.R | 10 +- R/utils-.data.R | 2 R/utils-pipe.R | 2 R/utils-qqassign.R | 2 README.md | 5 + build/vignette.rds |binary inst/CITATION | 8 +- inst/doc/matsindf.Rmd | 26 +++---- inst/doc/matsindf.html | 49 +++++++++----- inst/doc/midf_apply_primer.Rmd | 4 - inst/doc/midf_apply_primer.html | 29 ++++++-- man/UKEnergy2000.Rd | 14 ++-- man/add_UKEnergy2000_row_col_meta.Rd | 4 - man/data.Rd | 2 man/group_by_everything_except.Rd | 10 +- man/index_column.Rd | 2 man/matsindf_apply.Rd | 6 - man/matsindf_apply_types.Rd | 4 - man/pipe.Rd | 2 man/quasi-quote-assign.Rd | 2 man/rowcolval_to_mat.Rd | 4 - man/verify_cols_missing.Rd | 4 - tests/testthat.R | 1 vignettes/References.bib | 6 - vignettes/matsindf.Rmd | 26 +++---- vignettes/matsindf.md | 24 +++---- vignettes/midf_apply_primer.Rmd | 4 - 32 files changed, 253 insertions(+), 207 deletions(-)
Title: In-place Operators for R
Description: It provides in-place operators for R
that are equivalent to '+=', '-=', '*=', '/=' in C++.
Those can be applied on integer|double vectors|matrices.
You have also access to sweep operations (in-place).
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between inplace versions 0.1.1 dated 2020-08-13 and 0.1.2 dated 2020-08-24
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- tests/testthat/test-operators.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Authentication Management for 'Shiny' Applications
Description: Simple and secure authentification mechanism for single 'Shiny' applications.
Credentials are stored in an encrypted 'SQLite' database. Source code of main application
is protected until authentication is successful.
Author: Benoit Thieurmel [aut, cre],
Victor Perrier [aut]
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>
Diff between shinymanager versions 1.0.200 dated 2020-02-28 and 1.0.300 dated 2020-08-24
DESCRIPTION | 10 MD5 | 62 ++--- NAMESPACE | 12 + NEWS.md | 12 + R/check_credentials.R | 31 ++ R/credentials-db.R | 17 + R/language.R | 471 ++++++++++++++++++++++++------------------- R/module-admin.R | 149 ++++++++----- R/module-auth.R | 132 +++++++++--- R/module-edit_user.R | 9 R/module-pwd.R | 32 +- R/modules-logs.R | 26 +- R/secure-app.R | 61 +++-- R/shiny-utils.R | 36 ++- R/utils.R | 4 README.md | 93 ++++++++ build/vignette.rds |binary inst/assets/bindEnter.js | 8 inst/doc/SQLite_Admin.R | 2 inst/doc/SQLite_Admin.Rmd | 25 ++ inst/doc/SQLite_Admin.html | 407 ++++++++++++++++++++++++++++--------- inst/sticker/build_sticker.R | 2 man/check_credentials.Rd | 140 +++++++----- man/create_db.Rd | 118 +++++----- man/custom-labels.Rd |only man/db-crypted.Rd | 184 ++++++++-------- man/fab_button.Rd | 150 ++++++------- man/figures/shinymanager.png |only man/generate_pwd.Rd | 42 +-- man/module-authentication.Rd | 339 ++++++++++++++++-------------- man/module-password.Rd | 197 +++++++++-------- man/secure-app.Rd | 256 ++++++++++++----------- vignettes/SQLite_Admin.Rmd | 25 ++ 33 files changed, 1898 insertions(+), 1154 deletions(-)
Title: Tools for Handling Spatial Objects
Description: Set of tools for manipulating geographic data. It includes binary access to 'GSHHG' shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as 'PBSmapping', 'spatstat', 'maps', and others.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Nicholas Lewin-Koh [aut],
Edzer Pebesma [ctb],
Eric Archer [ctb],
Adrian Baddeley [ctb],
Nick Bearman [ctb],
Hans-Jörg Bibiko [ctb],
Steven Brey [ctb],
Jonathan Callahan [ctb],
German Carrillo [ctb],
Stéphane Dray [ctb],
David Forrest [ctb],
Michael Friendly [ctb],
Patrick Giraudoux [ctb],
Duncan Golicher [ctb],
Virgilio Gómez Rubio [ctb],
Patrick Hausmann [ctb],
Karl Ove Hufthammer [ctb],
Thomas Jagger [ctb],
Kent Johnson [ctb],
Matthew Lewis [ctb] (<https://orcid.org/0000-0003-2244-4078>),
Sebastian Luque [ctb],
Don MacQueen [ctb],
Andrew Niccolai [ctb],
Edzer Pebesma [ctb],
Oscar Perpiñán Lamigueiro [ctb],
Ethan Plunkett [ctb],
Ege Rubak [ctb] (<https://orcid.org/0000-0002-6675-533X>),
Tom Short [ctb],
Greg Snow [ctb],
Ben Stabler [ctb],
Murray Stokely [ctb],
Rolf Turner [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between maptools versions 1.0-1 dated 2020-05-14 and 1.0-2 dated 2020-08-24
ChangeLog | 18 ++++++++++ DESCRIPTION | 14 +++++--- MD5 | 35 ++++++++++---------- R/sp_spat1.R | 73 ++++++++++++++++++++++++++++++++---------- build/vignette.rds |binary data/SplashDams.rda |binary data/datalist |only data/wrld_simpl.rda |binary inst/ChangeLog | 30 +++++++++++++++++ inst/doc/combine_maptools.pdf |binary man/ContourLines2SLDF.Rd | 2 - man/SplashDams.Rd | 2 - man/as.im.Rd | 25 +++++++++++++- man/gcDestination.Rd | 2 - man/pointLabelBase.Rd | 4 +- man/readGPS.Rd | 2 - man/sp2tmap.Rd | 2 - man/state.vbm.Rd | 2 - man/sun-methods.Rd | 6 +-- 19 files changed, 166 insertions(+), 51 deletions(-)
Title: Credible Visualization for Two-Dimensional Projections of Data
Description: Projections are common dimensionality reduction methods, which represent high-dimensional data in a two-dimensional space. However, when restricting the output space to two dimensions, which results in a two dimensional scatter plot (projection) of the data, low dimensional similarities do not represent high dimensional distances coercively [Thrun, 2018]. This could lead to a misleading interpretation of the underlying structures [Thrun, 2018]. By means of the 3D topographic map the generalized Umatrix is able to depict errors of these two-dimensional scatter plots. The package is based on the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9>.
Author: Michael Thrun [aut, cre, cph] (<https://orcid.org/0000-0001-9542-5543>),
Felix Pape [ctb, ctr],
Tim Schreier [ctb, ctr],
Luis Winckelman [ctb, ctr],
Alfred Ultsch [ths]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between GeneralizedUmatrix versions 1.1.9 dated 2020-03-23 and 1.2.0 dated 2020-08-24
DESCRIPTION | 15 MD5 | 34 + NAMESPACE | 6 R/EsomNeuronsAsList.R |only R/GeneratePmatrix.R | 23 - R/ListAsEsomNeurons.R |only R/TopviewTopographicMap.R | 677 ++++++++++++++++++++++----------------- R/plotTopographicMap.R | 212 +++++++----- R/setdiffMatrix.R |only R/tileGUM.R |only R/upscaleUmatrix.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/GeneralizedUmatrix.html | 109 +++--- man/EsomNeuronsAsList.Rd |only man/GeneralizedUmatrix.Rd | 12 man/ListAsEsomNeurons.Rd |only man/TopviewTopographicMap.Rd | 176 +++++----- man/addRowWiseC.Rd |only man/plotTopographicMap.Rd | 230 +++++++------ man/setdiffMatrix.Rd |only man/upscaleUmatrix.Rd | 3 22 files changed, 857 insertions(+), 642 deletions(-)
More information about GeneralizedUmatrix at CRAN
Permanent link
Title: DIF and DDF Detection by Non-Linear Regression Models
Description: Detection of differential item functioning (DIF) among dichotomously scored items and differential distractor functioning (DDF) among unscored items with non-linear regression procedures based on generalized logistic regression models (Drabinova and Martinkova, 2017, doi:10.1111/jedm.12158).
Author: Adela Hladka [aut, cre],
Patricia Martinkova [aut],
Karel Zvara [ctb]
Maintainer: Adela Hladka <hladka@cs.cas.cz>
Diff between difNLR versions 1.3.3 dated 2020-05-04 and 1.3.5 dated 2020-08-24
DESCRIPTION | 8 ++--- MD5 | 18 +++++------ NEWS.md | 13 ++++++++ R/NLR.R | 77 +++++++++++++++++++++++++++----------------------- R/ddfMLR.R | 3 + R/difNLR-package.R | 4 +- README.md | 10 +++--- inst/CITATION | 4 +- man/ddfMLR.Rd | 3 + man/difNLR-package.Rd | 4 +- 10 files changed, 84 insertions(+), 60 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-06-06 1.1.1
2015-10-06 1.1
2015-07-17 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-08 1.0.1
2016-07-20 1.0.0
Title: The Flexible Spatial Scan Statistic
Description: Functions for the detection of spatial clusters using the flexible
spatial scan statistic developed by Tango and Takahashi (2005) <doi:10.1186/1476-072X-4-11>.
This package implements a wrapper for the C routine used in the FleXScan 3.1.2
<https://sites.google.com/site/flexscansoftware/home> developed by Takahashi,
Yokoyama, and Tango.
Author: Takahiro Otani,
Kunihiko Takahashi
Maintainer: Takahiro Otani <otani@med.nagoya-cu.ac.jp>
Diff between rflexscan versions 0.3.0 dated 2020-06-23 and 0.3.1 dated 2020-08-24
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/flexscan.R | 13 ++++++++++--- man/rflexscan.Rd | 13 ++++++++++--- 4 files changed, 28 insertions(+), 14 deletions(-)
Title: Connector Between 'mlr3' and 'OpenML'
Description: Provides an interface to 'OpenML.org' to list and
download machine learning data and tasks. Data and tasks can be
automatically converted to 'mlr3' tasks. For a more sophisticated
interface which also allows uploading experiments, see the 'OpenML'
package.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3oml versions 0.1.0 dated 2020-08-07 and 0.2.0 dated 2020-08-24
mlr3oml-0.1.0/mlr3oml/R/download_task_description.R |only mlr3oml-0.2.0/mlr3oml/DESCRIPTION | 10 - mlr3oml-0.2.0/mlr3oml/MD5 | 47 ++++---- mlr3oml-0.2.0/mlr3oml/NEWS.md |only mlr3oml-0.2.0/mlr3oml/R/OMLData.R | 14 +- mlr3oml-0.2.0/mlr3oml/R/OMLTask.R | 7 - mlr3oml-0.2.0/mlr3oml/R/as_data_backend.R | 4 mlr3oml-0.2.0/mlr3oml/R/download_data.R | 2 mlr3oml-0.2.0/mlr3oml/R/download_data_desc.R | 3 mlr3oml-0.2.0/mlr3oml/R/download_task_desc.R |only mlr3oml-0.2.0/mlr3oml/R/helper_download.R | 16 ++ mlr3oml-0.2.0/mlr3oml/R/helper_query.R | 13 +- mlr3oml-0.2.0/mlr3oml/R/list_oml_data_sets.R | 42 ++----- mlr3oml-0.2.0/mlr3oml/R/list_oml_tasks.R | 26 ++-- mlr3oml-0.2.0/mlr3oml/R/zzz.R | 12 +- mlr3oml-0.2.0/mlr3oml/README.md | 79 +++++++++++--- mlr3oml-0.2.0/mlr3oml/build/partial.rdb |binary mlr3oml-0.2.0/mlr3oml/man/OMLData.Rd | 7 + mlr3oml-0.2.0/mlr3oml/man/list_oml_data_sets.Rd | 6 - mlr3oml-0.2.0/mlr3oml/man/list_oml_tasks.Rd | 6 - mlr3oml-0.2.0/mlr3oml/src/parse_arff_levels.cpp | 2 mlr3oml-0.2.0/mlr3oml/src/remove_comments.cpp | 4 mlr3oml-0.2.0/mlr3oml/tests/testthat/test_OMLData.R | 10 + mlr3oml-0.2.0/mlr3oml/tests/testthat/test_list_oml_data.R | 6 - mlr3oml-0.2.0/mlr3oml/tests/testthat/test_list_oml_task.R | 7 - mlr3oml-0.2.0/mlr3oml/tests/testthat/test_manual.R | 4 26 files changed, 220 insertions(+), 107 deletions(-)
Title: Distributions Hermite Polynomial Approximation
Description: Multivariate conditional and marginal densities, moments, cumulative distribution functions as well as binary choice and sample selection models based on hermite polynomial approximation which was proposed and described by A. Gallant and D. W. Nychka (1987) <doi:10.2307/1913241>.
Author: Potanin Bogdan
Maintainer: Potanin Bogdan <bogdanpotanin@gmail.com>
Diff between hpa versions 1.1.1 dated 2020-07-01 and 1.1.2 dated 2020-08-24
DESCRIPTION | 8 MD5 | 84 +- NAMESPACE | 4 R/RcppExports.R | 129 ++-- R/hpaBinary_generics.R | 48 + R/hpaML_generics.R | 171 +++++ R/hpaSelection_generics.R | 45 + man/dhpa.Rd | 55 + man/dhpaDiff.Rd | 86 ++ man/dnorm_parallel.Rd | 13 man/dtrhpa.Rd | 71 +- man/ehpa.Rd | 61 +- man/etrhpa.Rd | 49 - man/hpaBinary.Rd | 190 +++--- man/hpaML.Rd | 118 ++-- man/hpaSelection.Rd | 94 +-- man/ihpa.Rd | 79 +- man/ihpaDiff.Rd | 100 ++- man/itrhpa.Rd | 82 +- man/normalMoment.Rd | 31 - man/phpa.Rd | 68 +- man/plot.hpaML.Rd |only man/polynomialIndex.Rd | 5 man/predict.hpaBinary.Rd | 7 man/predict.hpaML.Rd | 7 man/predict.hpaSelection.Rd | 7 man/predict_hpaBinary.Rd | 7 man/predict_hpaML.Rd | 7 man/predict_hpaSelection.Rd | 7 man/print.hpaBinary.Rd |only man/print.hpaML.Rd |only man/print.hpaSelection.Rd |only man/print.summary.hpaBinary.Rd | 6 man/print.summary.hpaSelection.Rd | 4 man/printPolynomial.Rd | 2 man/truncatedNormalMoment.Rd | 75 +- src/ParallelFunctions.cpp | 1 src/RcppExports.cpp | 90 +-- src/hpaBinary.cpp | 448 ++++++--------- src/hpaML.cpp | 287 ++++------ src/hpaMain.cpp | 1090 ++++++++++++++++++++++++++++++++++---- src/hpaMain.h | 24 src/hpaSelection.cpp | 627 ++++++++++----------- src/normalMoments.cpp | 332 ++++++++++- src/normalMoments.h | 6 45 files changed, 3090 insertions(+), 1535 deletions(-)
Title: Power Analyses for SEM
Description: Provides a-priori, post-hoc, and compromise power-analyses for structural equation models (SEM). Moshagen & Erdfelder (2016) <doi:10.1080/10705511.2014.950896>.
Author: Morten Moshagen
Maintainer: Morten Moshagen <morten.moshagen@uni-ulm.de>
Diff between semPower versions 1.0.1 dated 2020-05-17 and 1.1.0 dated 2020-08-24
DESCRIPTION | 8 MD5 | 48 +- R/aPriori.R | 95 +++- R/compromise.R | 49 +- R/helperFunctions.R | 136 +++++- R/postHoc.R | 47 +- R/semPower-package.R | 2 R/validator.R | 113 ++++- README.md | 12 build/vignette.rds |binary inst/doc/semPower.R | 111 ++++- inst/doc/semPower.Rmd | 119 +++++- inst/doc/semPower.pdf |binary man/checkBounded.Rd | 2 man/checkPositive.Rd | 2 man/checkPositiveDefinite.Rd | 2 man/getBetadiff.Rd | 4 man/getCFI.Sigma.mgroups.Rd |only man/getIndices.F.Rd | 4 man/getRMSEA.F.Rd | 4 man/getSRMR.Sigma.mgroups.Rd |only man/semPower.aPriori.Rd | 12 man/semPower.compromise.Rd | 8 man/semPower.postHoc.Rd | 11 vignettes/semPower.Rmd | 119 +++++- vignettes/semPower.html | 848 +++++++++++++++++++++++++++---------------- 26 files changed, 1264 insertions(+), 492 deletions(-)
Title: SA Counterparty Credit Risk under CRR2
Description: Computes the Exposure-At-Default based on the standardized approach
of CRR2 (SA-CCR). The simplified version of SA-CCR has been included, as well as the OEM methodology.
Multiple trade types of all the five major asset classes are being supported including the 'Other' Exposure and, given the inheritance-
based structure of the application, the addition of further trade types
is straightforward. The application returns a list of trees per Counterparty and CSA after
automatically separating the trades based on the Counterparty, the CSAs, the hedging sets, the
netting sets and the risk factors. The basis and volatility transactions are
also identified and treated in specific hedging sets whereby the corresponding
penalty factors are applied. All the examples appearing on the
regulatory papers (both for the margined and the un-margined workflow) have been
implemented including the latest CRR2 developments.
Author: Tasos Grivas
Maintainer: Tasos Grivas <info@openriskcalculator.com>
Diff between SACCR versions 2.3 dated 2019-01-13 and 3.0 dated 2020-08-24
SACCR-2.3/SACCR/inst/extdata/example_trades.csv |only SACCR-3.0/SACCR/DESCRIPTION | 33 +-- SACCR-3.0/SACCR/MD5 | 75 ++++--- SACCR-3.0/SACCR/NAMESPACE | 10 - SACCR-3.0/SACCR/R/CalcAddon.R | 138 +++++++++++--- SACCR-3.0/SACCR/R/CalcEAD.R | 4 SACCR-3.0/SACCR/R/CalcPFE.R | 24 +- SACCR-3.0/SACCR/R/CalcRC.R | 17 + SACCR-3.0/SACCR/R/CalculateFactorMult.R | 2 SACCR-3.0/SACCR/R/CreateTradeGraph.R | 29 +-- SACCR-3.0/SACCR/R/DetermineCCRMethodology.R |only SACCR-3.0/SACCR/R/ExampleBasisVol.R | 6 SACCR-3.0/SACCR/R/ExampleCredit.R | 6 SACCR-3.0/SACCR/R/ExampleFX.R | 10 - SACCR-3.0/SACCR/R/ExampleIRDCredit.R | 6 SACCR-3.0/SACCR/R/GroupEquityTrades.R | 4 SACCR-3.0/SACCR/R/GroupOtherTrades.R |only SACCR-3.0/SACCR/R/HandleBasisVol.R | 8 SACCR-3.0/SACCR/R/LoadSupervisoryData.R | 4 SACCR-3.0/SACCR/R/SACCRCalculator.R | 104 ++++++++--- SACCR-3.0/SACCR/R/SingleTradeAddon.R | 17 + SACCR-3.0/SACCR/R/onLoad.R |only SACCR-3.0/SACCR/R/runExampleCalcs.R | 179 ++++++++++++++----- SACCR-3.0/SACCR/inst/extdata/supervisory_factors.csv | 4 SACCR-3.0/SACCR/man/CalcAddon.Rd | 15 - SACCR-3.0/SACCR/man/CalcEAD.Rd | 9 SACCR-3.0/SACCR/man/CalcPFE.Rd | 15 - SACCR-3.0/SACCR/man/CalcRC.Rd | 13 - SACCR-3.0/SACCR/man/CreateTradeGraph.Rd | 1 SACCR-3.0/SACCR/man/DetermineCCRMethodology.Rd |only SACCR-3.0/SACCR/man/ExampleBasisVol.Rd | 9 SACCR-3.0/SACCR/man/ExampleComm.Rd | 7 SACCR-3.0/SACCR/man/ExampleCredit.Rd | 7 SACCR-3.0/SACCR/man/ExampleFX.Rd | 7 SACCR-3.0/SACCR/man/ExampleIRD.Rd | 7 SACCR-3.0/SACCR/man/ExampleIRDCommMargined.Rd | 7 SACCR-3.0/SACCR/man/ExampleIRDCredit.Rd | 7 SACCR-3.0/SACCR/man/HandleBasisVol.Rd | 9 SACCR-3.0/SACCR/man/LoadSupervisoryData.Rd | 9 SACCR-3.0/SACCR/man/SACCRCalculator.Rd | 29 ++- SACCR-3.0/SACCR/man/SingleTradeAddon.Rd | 9 41 files changed, 551 insertions(+), 289 deletions(-)
Title: 'sf'-Based Interface to the 'HERE' REST APIs
Description: Interface to the 'HERE' REST APIs <https://developer.here.com/develop/rest-apis>:
(1) geocode and autocomplete addresses or reverse geocode POIs using the 'Geocoder' API;
(2) route directions, travel distance or time matrices and isolines using the 'Routing' API;
(3) request real-time traffic flow and incident information from the 'Traffic' API;
(4) find request public transport connections and nearby stations from the 'Public Transit' API;
(5) request intermodal routes using the 'Intermodal Routing' API;
(6) get weather forecasts, reports on current weather conditions, astronomical
information and alerts at a specific location from the 'Destination Weather' API.
Locations, routes and isolines are returned as 'sf' objects.
Author: Merlin Unterfinger [aut, cre] (<https://orcid.org/0000-0003-2020-2366>),
Daniel Possenriede [ctb] (<https://orcid.org/0000-0002-6738-9845>,
Geocode return options)
Maintainer: Merlin Unterfinger <info@munterfinger.ch>
Diff between hereR versions 0.4.0 dated 2020-07-05 and 0.4.1 dated 2020-08-24
DESCRIPTION | 18 MD5 | 64 NEWS.md | 6 R/intermodal_route.R | 14 R/sysdata.rda |binary README.md | 7 build/vignette.rds |binary inst/doc/authentication.html | 14 inst/doc/geocoder.R | 41 inst/doc/geocoder.Rmd | 5 inst/doc/geocoder.html | 5046 ----------------------------------------- inst/doc/intermodal.R | 32 inst/doc/intermodal.Rmd | 20 inst/doc/intermodal.html | 5118 ----------------------------------------- inst/doc/routing.R | 41 inst/doc/routing.Rmd | 5 inst/doc/routing.html | 5126 ----------------------------------------- inst/doc/traffic.R | 33 inst/doc/traffic.Rmd | 5 inst/doc/traffic.html | 4986 ---------------------------------------- inst/doc/transit.R | 49 inst/doc/transit.Rmd | 5 inst/doc/transit.html | 5116 ----------------------------------------- inst/doc/weather.R | 75 inst/doc/weather.Rmd | 5 inst/doc/weather.html | 5250 +------------------------------------------ man/intermodal_route.Rd | 14 vignettes/geocoder.Rmd | 5 vignettes/intermodal.Rmd | 20 vignettes/routing.Rmd | 5 vignettes/traffic.Rmd | 5 vignettes/transit.Rmd | 5 vignettes/weather.Rmd | 5 33 files changed, 717 insertions(+), 30423 deletions(-)
Title: Estimate Gaussian Mixture Vector Autoregressive Model
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive (GMVAR) model, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (2020) <arXiv:2007.04713>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 1.1.3 dated 2020-03-12 and 1.2.0 dated 2020-08-24
DESCRIPTION | 24 + MD5 | 211 +++++++++------- NAMESPACE | 11 NEWS.md | 16 + R/GIRF.R |only R/GMVARconstruction.R | 354 +++++++++++++++++++++++++--- R/MAINest.R | 160 +++++++++--- R/WaldAndLR.R |only R/argumentChecks.R | 199 ++++++++++++--- R/diagnosticPlot.R | 113 ++++++-- R/generateParams.R | 284 +++++++++++++++------- R/geneticAlgorithm.R | 164 +++++++++--- R/loglikelihood.R | 103 ++++++-- R/matcal.R | 90 +++++++ R/parameterReforms.R | 253 ++++++++++++++++---- R/pickParams.R | 195 +++++++++++---- R/plotMethods.R | 61 ++++ R/predictMethod.R | 25 + R/printMethods.R | 152 ++++++++++-- R/quantileResidualTests.R | 33 +- R/quantileResiduals.R | 41 +-- R/simulateGMVAR.R | 189 +++++++++++++- R/standardErrors.R | 123 +++++++-- R/uncondMoments.R | 69 +++-- README.md | 40 ++- build/vignette.rds |binary inst/doc/intro-to-gmvarkit.Rmd | 167 ++++++++++--- inst/doc/intro-to-gmvarkit.html | 187 +++++++++++--- man/GAfit.Rd | 93 ++++++- man/GIRF.Rd |only man/GMVAR.Rd | 77 ++++-- man/LR_test.Rd |only man/Wald_test.Rd |only man/Wvec.Rd |only man/add_data.Rd | 13 + man/alt_gmvar.Rd | 32 +- man/change_parametrization.Rd | 54 +++- man/change_regime.Rd | 59 ++++ man/check_constraints.Rd | 21 + man/check_gmvar.Rd | 10 man/check_parameters.Rd | 67 ++++- man/cond_moments.Rd | 54 +++- man/diag_Omegas.Rd |only man/diagnostic_plot.Rd | 4 man/eurusd.Rd | 8 man/fitGMVAR.Rd | 126 +++++++-- man/form_boldA.Rd | 4 man/format_valuef.Rd | 2 man/get_boldA_eigens.Rd | 10 man/get_omega_eigens.Rd | 9 man/get_regime_autocovs.Rd | 12 man/get_regime_autocovs_int.Rd | 62 ++++ man/get_regime_means.Rd | 14 - man/get_regime_means_int.Rd | 56 +++- man/get_test_Omega.Rd | 52 +++- man/get_unconstrained_structural_pars.Rd |only man/gmvar_to_sgmvar.Rd |only man/in_paramspace.Rd | 61 ++++ man/in_paramspace_int.Rd | 52 ++++ man/is_stationary.Rd | 55 +++- man/iterate_more.Rd | 13 + man/loglikelihood.Rd | 63 ++++ man/loglikelihood_int.Rd | 56 +++- man/n_params.Rd | 23 + man/pick_Am.Rd | 51 +++- man/pick_Ami.Rd | 54 +++- man/pick_Omegas.Rd | 42 ++- man/pick_W.Rd |only man/pick_allA.Rd | 44 +++ man/pick_all_phi0_A.Rd | 50 +++ man/pick_alphas.Rd | 25 + man/pick_lambdas.Rd |only man/pick_phi0.Rd | 44 +++ man/pick_regime.Rd | 63 ++++ man/plot.gmvarpred.Rd | 2 man/predict.gmvar.Rd | 14 + man/print.gmvarpred.Rd | 2 man/print_std_errors.Rd | 2 man/profile_logliks.Rd | 15 + man/quantile_residual_tests.Rd | 21 + man/quantile_residuals.Rd | 14 - man/quantile_residuals_int.Rd | 54 +++- man/random_covmat.Rd | 67 ++++- man/random_ind.Rd | 78 +++++- man/random_ind2.Rd | 78 +++++- man/reform_constrained_pars.Rd | 61 ++++ man/reform_structural_pars.Rd |only man/regime_distance.Rd | 2 man/reorder_W_columns.Rd |only man/simulateGMVAR.Rd | 35 ++ man/smart_covmat.Rd | 56 +++- man/smart_ind.Rd | 95 ++++++- man/sort_components.Rd | 90 +++++-- man/standard_errors.Rd | 54 +++- man/swap_W_signs.Rd |only man/swap_parametrization.Rd | 26 +- man/unWvec.Rd |only man/uncond_moments.Rd | 12 man/uncond_moments_int.Rd | 56 +++- tests/testthat/test_GIRF.R |only tests/testthat/test_MAINest.R | 27 +- tests/testthat/test_S3methods.R | 24 - tests/testthat/test_argumentChecks.R | 223 +++++++++++++++++ tests/testthat/test_generateParams.R |only tests/testthat/test_gmvarConstruction.R |only tests/testthat/test_loglikelihood.R | 131 ++++++++++ tests/testthat/test_matcal.R | 44 +++ tests/testthat/test_parameterReforms.R | 309 +++++++++++++++++++++++- tests/testthat/test_pickParams.R | 267 ++++++++++++++++++++- tests/testthat/test_quantileResidualTests.R | 92 +++++-- tests/testthat/test_quantileResiduals.R | 65 ++++- tests/testthat/test_simulateGMVAR.R | 10 tests/testthat/test_standardErrors.R | 53 +++- tests/testthat/test_uncondMoments.R | 225 +++++++++++++++++ tests/testthat/test_waldAndLR.R |only vignettes/intro-to-gmvarkit.Rmd | 167 ++++++++++--- 116 files changed, 6103 insertions(+), 1167 deletions(-)
Title: Easily Extracting Information About Your Data
Description: Makes it easy to display descriptive information on
a data set. Getting an easy overview of a data set by displaying and
visualizing sample information in different tables (e.g., time and
scope conditions). The package also provides publishable 'LaTeX' code
to present the sample information.
Author: Cosima Meyer [cre, aut],
Dennis Hammerschmidt [aut]
Maintainer: Cosima Meyer <cosima.meyer@gmail.com>
Diff between overviewR versions 0.0.4 dated 2020-06-30 and 0.0.6 dated 2020-08-24
DESCRIPTION | 14 +-- MD5 | 43 ++++++--- NAMESPACE | 6 + NEWS.md | 23 ++++ R/globals.R | 15 +++ R/overview_heat.R |only R/overview_na.R |only R/overview_plot.R |only R/overview_tab.R | 10 +- README.md | 129 +++++++++++++++++++++++++-- build/vignette.rds |binary inst/doc/overviewR_vignette.R | 44 ++++++++- inst/doc/overviewR_vignette.Rmd | 88 ++++++++++++++++++ inst/doc/overviewR_vignette.html | 163 ++++++++++++++++++++--------------- man/figures/CheatSheet_overviewR.pdf |only man/figures/unnamed-chunk-22-1.png |only man/figures/unnamed-chunk-23-1.png |only man/figures/unnamed-chunk-24-1.png |only man/figures/unnamed-chunk-25-1.png |only man/figures/unnamed-chunk-27-1.png |only man/figures/unnamed-chunk-28-1.png |only man/overview_heat.Rd |only man/overview_na.Rd |only man/overview_plot.Rd |only tests/testthat/test-check_output.R | 19 ++++ vignettes/overviewR_vignette.Rmd | 88 ++++++++++++++++++ vignettes/unnamed-chunk-22-1.png |only vignettes/unnamed-chunk-23-1.png |only vignettes/unnamed-chunk-24-1.png |only vignettes/unnamed-chunk-25-1.png |only vignettes/unnamed-chunk-27-1.png |only vignettes/unnamed-chunk-28-1.png |only 32 files changed, 531 insertions(+), 111 deletions(-)
Title: Log-Multiplicative Models, Including Association Models
Description: Functions to fit log-multiplicative models using 'gnm', with
support for convenient printing, plots, and jackknife/bootstrap
standard errors. For complex survey data, models can be fitted from
design objects from the 'survey' package. Currently supported models
include UNIDIFF (Erikson & Goldthorpe), a.k.a. log-multiplicative
layer effect model (Xie), and several association models: Goodman's
row-column association models of the RC(M) and RC(M)-L families
with one or several dimensions; two skew-symmetric association
models proposed by Yamaguchi and by van der Heijden & Mooijaart.
Functions allow computing the intrinsic association coefficient
(and therefore the Altham index), including via the Bayes shrinkage
estimator proposed by Zhou; and the RAS/IPF/Deming-Stephan algorithm.
Author: Milan Bouchet-Valat [aut, cre],
Heather Turner [ctb],
Michael Friendly [ctb],
Jim Lemon [cph],
Gabor Csardi [cph]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between logmult versions 0.7.1 dated 2019-02-13 and 0.7.2 dated 2020-08-24
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 3 +++ R/iac.R | 20 +++++++++++--------- build/vignette.rds |binary inst/doc/logmult.html | 8 ++++---- tests/iac.R | 6 +++--- 7 files changed, 31 insertions(+), 26 deletions(-)
Title: Flexible Regression Models for Survival Data
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression
Models for Survival Data', Springer Verlag. Plus more recent developments.
Additive survival model, semiparametric proportional odds model, fast
cumulative residuals, excess risk models and more. Flexible competing risks
regression including GOF-tests. Two-stage frailty modelling. PLS for the
additive risk model. Lasso in the 'ahaz' package.
Author: Thomas Scheike with contributions from Torben Martinussen, Jeremy
Silver and Klaus Holst
Maintainer: Thomas Scheike <ts@biostat.ku.dk>
Diff between timereg versions 1.9.6 dated 2020-07-16 and 1.9.7 dated 2020-08-24
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- inst/CITATION | 4 ++-- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Sparse Matrix Format with Data on Disk
Description: Provides a sparse matrix format with data stored on disk, to be
used in both R and C++. This is intended for more efficient use of sparse
data in C++ and also when parallelizing, since data on disk does not need
copying. Only a limited number of features will be implemented. For now,
conversion can be performed from a 'dgCMatrix' or a 'dsCMatrix' from R
package 'Matrix'.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigsparser versions 0.3.1 dated 2020-07-26 and 0.4.0 dated 2020-08-24
DESCRIPTION | 9 +-- MD5 | 25 ++++---- NAMESPACE | 2 R/RcppExports.R | 12 +++- R/SFBM.R | 46 +++++++++++---- README.md | 2 inst/include/bigsparser/SFBM.h | 4 - man/SFBM-class.Rd | 111 +++++++++++++++++++------------------- man/bigsparser-package.Rd | 55 +++++++++--------- src/RcppExports.cpp | 41 ++++++++++++-- src/write-indval.cpp | 104 ++++++++++++++++++++++++++++++++++- tests/testthat/test-SFBM.R | 26 +++++++- tests/testthat/test-add-columns.R | 28 +++++++++ tests/testthat/test-utils-sym.R |only 14 files changed, 338 insertions(+), 127 deletions(-)
Title: Easy Parallel Tools
Description: Utility functions for easy parallelism in R. Include some reexports
from other packages, utility functions for splitting and parallelizing over
blocks, and choosing and setting the number of cores used.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigparallelr versions 0.2.3 dated 2020-01-09 and 0.2.5 dated 2020-08-24
DESCRIPTION | 8 +- MD5 | 31 ++++---- NAMESPACE | 5 + R/bigparallelr-package.R | 2 R/nb-cores.R | 14 +-- R/split-parapply.R | 16 +++- R/split.R | 129 +++++++++++++++++++++++++++-------- man/assert_cores.Rd | 14 +-- man/get_blas_ncores.Rd | 38 +++++----- man/nb_cores.Rd | 34 ++++----- man/plus.Rd | 38 +++++----- man/reexports.Rd | 2 man/split_costs.Rd |only man/split_len.Rd | 5 - man/split_parapply.Rd | 8 +- tests/testthat/test-split-parapply.R | 17 ++++ tests/testthat/test-split.R | 33 +++++++- 17 files changed, 264 insertions(+), 130 deletions(-)