Title: Clustering Algorithm for Data Integration and Disease Subtyping
Description: Provides a robust approach for omics data integration and disease subtyping. 'PINSPlus' supports both single and multiple data types. The software automatically determines the optimal number of clusters and then partitions the samples in a way such that the results are robust to noise and data perturbation. 'PINSPlus' is fast and it supports parallel computing on Windows, Linux, and Mac OS.
Author: Hung Nguyen, Sangam Shrestha and Tin Nguyen
Maintainer: Hung Nguyen <hungnp@nevada.unr.edu>
Diff between PINSPlus versions 1.0.1 dated 2018-05-06 and 1.0.2 dated 2018-07-16
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/perturb-functions.R | 8 -------- R/perturbation-clustering-helpers.R | 9 ++------- R/subtyping-omics-data.R | 6 +++--- inst/doc/PINSPlus.R | 3 --- inst/doc/PINSPlus.Rmd | 4 ---- inst/doc/PINSPlus.pdf |binary vignettes/PINSPlus.Rmd | 4 ---- vignettes/PINSPlus.html | 24 ++++++++++-------------- 10 files changed, 29 insertions(+), 57 deletions(-)
Title: Miscellaneous Functions for Panel Data, Quantiles, and Printing
Results
Description: These are miscellaneous functions for working with panel data, quantiles, and printing results. For panel data, the package includes functions for making a panel data balanced (that is, dropping missing individuals that have missing observations in any time period), converting id numbers to row numbers, and to treat repeated cross sections as panel data under the assumption of rank invariance. For quantiles, there are functions to make distribution functions from a set of data points (this is particularly useful when a distribution function is created in several steps), to combine distribution functions based on some external weights, and to invert distribution functions. Finally, there are several other miscellaneous functions for obtaining weighted means, weighted distribution functions, and weighted quantiles; to generate summary statistics and their differences for two groups; and to add or drop covariates from formulas.
Author: Brantly Callaway [aut, cre]
Maintainer: Brantly Callaway <brantly.callaway@temple.edu>
Diff between BMisc versions 1.2.0 dated 2018-02-27 and 1.3.0 dated 2018-07-16
DESCRIPTION | 10 +-- MD5 | 15 +++-- NAMESPACE | 5 + NEWS.md | 6 ++ R/BMisc.R | 147 ++++++++++++++++++++++++++++++++++++++++++++------ man/addCovToFormla.Rd | 2 man/invertEcdf.Rd |only man/lhs.vars.Rd |only man/rhs.Rd |only man/rhs.vars.Rd |only man/toformula.Rd |only 11 files changed, 158 insertions(+), 27 deletions(-)
Title: Access to Current and Historical Basketball Data
Description: Provides simple functions for accessing data/tables on
<http://www.basketball-reference.com>.
Author: Ryan Elmore [cre, aut],
Peter DeWitt [ctb]
Maintainer: Ryan Elmore <rtelmore@gmail.com>
Diff between ballr versions 0.2.0 dated 2018-03-26 and 0.2.1 dated 2018-07-16
DESCRIPTION | 10 +- MD5 | 11 +- R/nba-standings-by-date.R | 4 build/vignette.rds |binary inst/doc/use-ballr.html | 194 +++++++++++++++++++++++----------------------- man/NBAStandingsByDate.Rd | 4 vignettes/use-ballr.md |only 7 files changed, 112 insertions(+), 111 deletions(-)
Title: eXtensible Time Series
Description: Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.
Author: Jeffrey A. Ryan [aut, cph],
Joshua M. Ulrich [cre, aut],
Ross Bennett [ctb],
Corwin Joy [ctb]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>
Diff between xts versions 0.10-2 dated 2018-03-14 and 0.11-0 dated 2018-07-16
xts-0.10-2/xts/src/leadingNA.c |only xts-0.10-2/xts/src/period.max.f |only xts-0.10-2/xts/src/period.min.f |only xts-0.10-2/xts/src/period.prod.f |only xts-0.10-2/xts/src/period.sum.f |only xts-0.11-0/xts/DESCRIPTION | 13 xts-0.11-0/xts/MD5 | 104 ++--- xts-0.11-0/xts/NAMESPACE | 2 xts-0.11-0/xts/NEWS | 41 + xts-0.11-0/xts/R/adj.time.R | 21 + xts-0.11-0/xts/R/align.time.R | 21 + xts-0.11-0/xts/R/as.environment.xts.R | 21 + xts-0.11-0/xts/R/axTicksByTime.R | 131 +++--- xts-0.11-0/xts/R/dimnames.R | 19 xts-0.11-0/xts/R/first.R | 37 - xts-0.11-0/xts/R/last.R | 29 - xts-0.11-0/xts/R/merge.R | 2 xts-0.11-0/xts/R/na.R | 21 - xts-0.11-0/xts/R/parse8601.R | 27 + xts-0.11-0/xts/R/period.R | 56 +- xts-0.11-0/xts/R/period.apply.R |only xts-0.11-0/xts/R/periodicity.R | 114 +---- xts-0.11-0/xts/R/plot.R | 204 +++------ xts-0.11-0/xts/R/utils.R | 60 -- xts-0.11-0/xts/R/xts.R | 44 -- xts-0.11-0/xts/R/xts.methods.R | 164 ++++++- xts-0.11-0/xts/R/zzz.R | 21 + xts-0.11-0/xts/build/vignette.rds |binary xts-0.11-0/xts/inst/benchmarks |only xts-0.11-0/xts/inst/doc/xts-faq.pdf |binary xts-0.11-0/xts/inst/doc/xts.pdf |binary xts-0.11-0/xts/inst/include/xts.h | 8 xts-0.11-0/xts/inst/unitTests/runit.align.time.R |only xts-0.11-0/xts/inst/unitTests/runit.binsearch.R |only xts-0.11-0/xts/inst/unitTests/runit.data.frame.R | 24 - xts-0.11-0/xts/inst/unitTests/runit.first-last.R |only xts-0.11-0/xts/inst/unitTests/runit.merge.R | 8 xts-0.11-0/xts/inst/unitTests/runit.na.locf.R | 152 ++++++- xts-0.11-0/xts/inst/unitTests/runit.period.apply.R | 54 ++ xts-0.11-0/xts/inst/unitTests/runit.periodicity.R |only xts-0.11-0/xts/inst/unitTests/runit.subset.R | 83 +++- xts-0.11-0/xts/inst/unitTests/runit.tclass.R |only xts-0.11-0/xts/inst/unitTests/runit.xts.R | 7 xts-0.11-0/xts/inst/unitTests/runit.xts.methods.R | 435 +++++++++++---------- xts-0.11-0/xts/man/addPanel.Rd | 2 xts-0.11-0/xts/man/addSeries.Rd | 2 xts-0.11-0/xts/man/plot.xts.Rd | 27 - xts-0.11-0/xts/man/window.xts.Rd |only xts-0.11-0/xts/src/any.c | 22 + xts-0.11-0/xts/src/binsearch.c | 258 ++++++------ xts-0.11-0/xts/src/dimnames.c | 17 xts-0.11-0/xts/src/endpoints.c | 22 + xts-0.11-0/xts/src/extract_col.c | 22 + xts-0.11-0/xts/src/init.c | 14 xts-0.11-0/xts/src/merge.c | 10 xts-0.11-0/xts/src/migrate_index_attrib.c |only xts-0.11-0/xts/src/na.c |only xts-0.11-0/xts/src/period_apply.c |only xts-0.11-0/xts/src/period_arithmetic.c |only xts-0.11-0/xts/src/period_quantile.c |only xts-0.11-0/xts/src/subset.c | 22 + xts-0.11-0/xts/src/unique.time.c | 59 +- 62 files changed, 1456 insertions(+), 944 deletions(-)
Title: A Time Series Toolbox for Official Statistics
Description: Plot official statistics' time series conveniently: automatic legends, highlight windows, stacked bar chars with positive and negative contributions, sum-as-line option, two y-axes with automatic horizontal grids that fit both axes and other popular chart types. 'tstools' comes with a plethora of defaults to let you plot without setting an abundance of parameters first, but gives you the flexibility to tweak the defaults. In addition to charts, 'tstools' provides a super fast, 'data.table' backed time series I/O that allows the user to export / import long format, wide format and transposed wide format data to various file types.
Author: Matthias Bannert [aut, cre],
Severin Thoeni [aut]
Maintainer: Matthias Bannert <bannert@kof.ethz.ch>
Diff between tstools versions 0.3.6.1 dated 2018-04-24 and 0.3.7 dated 2018-07-16
DESCRIPTION | 10 MD5 | 53 ++--- NAMESPACE | 12 + R/KOF.R | 7 R/add_legend.R | 230 ++++++++++++---------- R/add_title.R | 33 ++- R/create_dummies.R | 2 R/draw_ts_ci.R |only R/generate_random_ts.R |only R/import_helpers.R | 13 + R/low_level_bar_plots.R | 5 R/read_swissdata.R |only R/regularize.R | 2 R/set_month_to_NA.R | 1 R/themes.R | 320 ++++++++++++++++++------------ R/tsplot.R | 333 +++++++++++++++++++++++++------- R/utils.R | 172 ++++++++++++---- build/vignette.rds |binary data/KOF.rda |binary inst/doc/tstools.R | 152 +++++++++++--- inst/doc/tstools.Rmd | 349 +++++++++++++++++++++++---------- inst/doc/tstools.html | 478 ++++++++++++++++++++++++++++------------------ inst/example_data |only inst/marc_vja_examples.R |only inst/vja.xlsx |only man/KOF.Rd | 7 man/generate_random_ts.Rd |only man/getCiLegendColors.Rd |only man/init_tsplot_theme.Rd | 239 ++++++++++++++--------- man/read_swissdata.Rd |only man/tsplot.Rd | 45 +++- vignettes/tstools.Rmd | 349 +++++++++++++++++++++++---------- 32 files changed, 1909 insertions(+), 903 deletions(-)
Title: General-Purpose MCMC and SMC Samplers and Tools for Bayesian
Statistics
Description: General-purpose MCMC and SMC samplers, as well as plot and
diagnostic functions for Bayesian statistics, with a particular focus on
calibrating complex system models. Implemented samplers include various
Metropolis MCMC variants (including adaptive and/or delayed rejection MH), the
T-walk, two differential evolution MCMCs, two DREAM MCMCs, and a sequential
Monte Carlo (SMC) particle filter.
Author: Florian Hartig [aut, cre],
Francesco Minunno [aut],
Stefan Paul [aut],
David Cameron [ctb],
Tankred Ott [ctb],
Maximilian Pichler [ctb]
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Diff between BayesianTools versions 0.1.4 dated 2017-12-20 and 0.1.5 dated 2018-07-16
BayesianTools-0.1.4/BayesianTools/inst/examples/plotCorrelationDensity.R |only BayesianTools-0.1.4/BayesianTools/inst/examples/plotMarginals.R |only BayesianTools-0.1.4/BayesianTools/man/createBreakMat.Rd |only BayesianTools-0.1.4/BayesianTools/man/histMarginal.Rd |only BayesianTools-0.1.4/BayesianTools/man/plotHist.Rd |only BayesianTools-0.1.4/BayesianTools/man/violinPlot.Rd |only BayesianTools-0.1.4/BayesianTools/tests/manualTests |only BayesianTools-0.1.5/BayesianTools/DESCRIPTION | 21 BayesianTools-0.1.5/BayesianTools/MD5 | 205 +-- BayesianTools-0.1.5/BayesianTools/NAMESPACE | 5 BayesianTools-0.1.5/BayesianTools/NEWS | 46 BayesianTools-0.1.5/BayesianTools/R/BayesianTools.R | 2 BayesianTools-0.1.5/BayesianTools/R/WAIC.R | 10 BayesianTools-0.1.5/BayesianTools/R/blockUpdate.R | 29 BayesianTools-0.1.5/BayesianTools/R/classBayesianOutput.R | 2 BayesianTools-0.1.5/BayesianTools/R/classBayesianSetup.R | 162 +- BayesianTools-0.1.5/BayesianTools/R/classLikelihood.R | 7 BayesianTools-0.1.5/BayesianTools/R/classMcmcSampler.R | 5 BayesianTools-0.1.5/BayesianTools/R/classPrior.R | 42 BayesianTools-0.1.5/BayesianTools/R/codaFunctions.R | 27 BayesianTools-0.1.5/BayesianTools/R/diagnosticsGelman.R | 4 BayesianTools-0.1.5/BayesianTools/R/marginalLikelihood.R | 41 BayesianTools-0.1.5/BayesianTools/R/mcmcDEzs.R | 15 BayesianTools-0.1.5/BayesianTools/R/mcmcDREAM_helperFunctions.R | 28 BayesianTools-0.1.5/BayesianTools/R/mcmcDREAMzs.R | 10 BayesianTools-0.1.5/BayesianTools/R/mcmcFrancesco.R | 4 BayesianTools-0.1.5/BayesianTools/R/mcmcMetropolis.R | 5 BayesianTools-0.1.5/BayesianTools/R/mcmcMultipleChains.R | 12 BayesianTools-0.1.5/BayesianTools/R/mcmcRun.R | 29 BayesianTools-0.1.5/BayesianTools/R/mcmcTwalk_helperFunctions.R | 107 - BayesianTools-0.1.5/BayesianTools/R/plotCorrelationDensity.r | 10 BayesianTools-0.1.5/BayesianTools/R/plotDiagnostic.R |only BayesianTools-0.1.5/BayesianTools/R/plotMarginals.R | 659 ++++------ BayesianTools-0.1.5/BayesianTools/R/plotTimeSeries.R | 29 BayesianTools-0.1.5/BayesianTools/R/proposalGenerator.R | 17 BayesianTools-0.1.5/BayesianTools/R/utils-Numerics.R | 3 BayesianTools-0.1.5/BayesianTools/R/utils.R | 40 BayesianTools-0.1.5/BayesianTools/build/vignette.rds |binary BayesianTools-0.1.5/BayesianTools/inst/doc/BayesianTools.R | 94 + BayesianTools-0.1.5/BayesianTools/inst/doc/BayesianTools.Rmd | 119 + BayesianTools-0.1.5/BayesianTools/inst/doc/BayesianTools.html | 305 +++- BayesianTools-0.1.5/BayesianTools/inst/examples/SMCHelp.R | 65 BayesianTools-0.1.5/BayesianTools/inst/examples/VSEMHelp.R | 2 BayesianTools-0.1.5/BayesianTools/inst/examples/bridgesampleHelp.R | 3 BayesianTools-0.1.5/BayesianTools/inst/examples/classBayesianSetup.R | 4 BayesianTools-0.1.5/BayesianTools/inst/examples/correlationPlotHelp.R |only BayesianTools-0.1.5/BayesianTools/inst/examples/createPriorDensity.R | 10 BayesianTools-0.1.5/BayesianTools/inst/examples/marginalLikelihoodHelp.R | 42 BayesianTools-0.1.5/BayesianTools/inst/examples/marginalPlotHelp.R |only BayesianTools-0.1.5/BayesianTools/inst/examples/plotDiagnosticHelp.R |only BayesianTools-0.1.5/BayesianTools/inst/examples/plotTimeSeriesHelp.R | 1 BayesianTools-0.1.5/BayesianTools/inst/examples/plotTimeSeriesResultsHelp.R | 69 + BayesianTools-0.1.5/BayesianTools/inst/examples/tracePlotHelp.R | 5 BayesianTools-0.1.5/BayesianTools/man/AM.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/AdaptpCR.Rd |only BayesianTools-0.1.5/BayesianTools/man/BayesianTools.Rd | 2 BayesianTools-0.1.5/BayesianTools/man/DEzs.Rd | 2 BayesianTools-0.1.5/BayesianTools/man/DR.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/DRAM.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/Gfun.Rd |only BayesianTools-0.1.5/BayesianTools/man/M.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/TwalkMove.Rd |only BayesianTools-0.1.5/BayesianTools/man/Twalksteps.Rd |only BayesianTools-0.1.5/BayesianTools/man/VSEM.Rd | 2 BayesianTools-0.1.5/BayesianTools/man/WAIC.Rd | 2 BayesianTools-0.1.5/BayesianTools/man/betaFun.Rd |only BayesianTools-0.1.5/BayesianTools/man/bridgesample.Rd | 8 BayesianTools-0.1.5/BayesianTools/man/combineChains.Rd |only BayesianTools-0.1.5/BayesianTools/man/correctThin.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/correlationPlot.Rd | 31 BayesianTools-0.1.5/BayesianTools/man/createBayesianSetup.Rd | 21 BayesianTools-0.1.5/BayesianTools/man/createPriorDensity.Rd | 10 BayesianTools-0.1.5/BayesianTools/man/factorMatrice.Rd |only BayesianTools-0.1.5/BayesianTools/man/generateCRvalues.Rd |only BayesianTools-0.1.5/BayesianTools/man/getBlock.Rd |only BayesianTools-0.1.5/BayesianTools/man/getBlockSettings.Rd |only BayesianTools-0.1.5/BayesianTools/man/getMetropolisDefaultSettings.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/getPanels.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/getRmvnorm.Rd |only BayesianTools-0.1.5/BayesianTools/man/getSetup.Rd |only BayesianTools-0.1.5/BayesianTools/man/logSumExp.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/makeObjectClassCodaMCMC.Rd |only BayesianTools-0.1.5/BayesianTools/man/marginalLikelihood.Rd | 59 BayesianTools-0.1.5/BayesianTools/man/marginalPlot.Rd | 76 - BayesianTools-0.1.5/BayesianTools/man/marginalPlotDensity.Rd |only BayesianTools-0.1.5/BayesianTools/man/marginalPlotViolin.Rd |only BayesianTools-0.1.5/BayesianTools/man/mcmcMultipleChains.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/metropolisRatio.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/plotDiagnostic.Rd |only BayesianTools-0.1.5/BayesianTools/man/plotTimeSeries.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/plotTimeSeriesResults.Rd | 20 BayesianTools-0.1.5/BayesianTools/man/propFun.Rd |only BayesianTools-0.1.5/BayesianTools/man/rescale.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/runMCMC.Rd | 4 BayesianTools-0.1.5/BayesianTools/man/sampleEquallySpaced.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/sampleMetropolis.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/scaleMatrix.Rd |only BayesianTools-0.1.5/BayesianTools/man/setupStartProposal.Rd | 1 BayesianTools-0.1.5/BayesianTools/man/smcSampler.Rd | 65 BayesianTools-0.1.5/BayesianTools/man/sumSquare.Rd |only BayesianTools-0.1.5/BayesianTools/man/thinMatrix.Rd |only BayesianTools-0.1.5/BayesianTools/man/tracePlot.Rd | 5 BayesianTools-0.1.5/BayesianTools/man/updateGroups.Rd |only BayesianTools-0.1.5/BayesianTools/tests/testthat/test-convergence.R | 4 BayesianTools-0.1.5/BayesianTools/tests/testthat/test-correlationPlot.R |only BayesianTools-0.1.5/BayesianTools/tests/testthat/test-createBayesianSetup.R |only BayesianTools-0.1.5/BayesianTools/tests/testthat/test-marginalLikelihood.R | 2 BayesianTools-0.1.5/BayesianTools/tests/testthat/test-marginalPlot.R | 36 BayesianTools-0.1.5/BayesianTools/tests/testthat/test-plotDiagnostic.R |only BayesianTools-0.1.5/BayesianTools/tests/testthat/test-plotTimeSeriesResults.R | 2 BayesianTools-0.1.5/BayesianTools/tests/testthat/test-samplers.R | 5 BayesianTools-0.1.5/BayesianTools/tests/testthat/test-settingsDefault.R | 3 BayesianTools-0.1.5/BayesianTools/tests/testthat/test-startValues.R |only BayesianTools-0.1.5/BayesianTools/tests/testthat/test-tracePlot.R | 2 BayesianTools-0.1.5/BayesianTools/tests/testthat/test-utilities.R | 19 BayesianTools-0.1.5/BayesianTools/tests/testthat/test-workflow.R | 14 BayesianTools-0.1.5/BayesianTools/vignettes/BayesianTools.Rmd | 119 + 117 files changed, 1802 insertions(+), 1021 deletions(-)
Title: Modelling and Validation of Non Homogeneous Poisson Processes
Description: Tools for modelling, ML estimation, validation analysis and simulation of non homogeneous Poisson processes in time.
Author: Ana C. Cebrian <acebrian@unizar.es>
Maintainer: Ana C. Cebrian <acebrian@unizar.es>
Diff between NHPoisson versions 3.1 dated 2015-03-15 and 3.2 dated 2018-07-16
DESCRIPTION | 12 ++++----- MD5 | 58 +++++++++++++++++++++++------------------------ NAMESPACE | 17 +++++++++---- inst/CITATION | 2 - man/BarTxTn.Rd | 2 - man/CIdelta.fun.Rd | 2 - man/CItran.fun.Rd | 2 - man/CalcRes.fun.Rd | 4 +-- man/CalcResD.fun.Rd | 2 - man/GenEnv.fun.Rd | 2 - man/LRTpv.fun.Rd | 8 +++--- man/NHPoisson-package.Rd | 4 +-- man/POTevents.fun.Rd | 2 - man/VARbeta.fun.Rd | 4 +-- man/addAIC.fun.Rd | 2 - man/confintAsin.fun.Rd | 10 ++++---- man/dropAIC.fun.Rd | 2 - man/fitPP.fun.Rd | 4 +-- man/globalval.fun.Rd | 7 ++--- man/graphResCov.fun.Rd | 8 +++--- man/graphResX.fun.Rd | 4 +-- man/graphrate.fun.Rd | 4 +-- man/graphres.fun.Rd | 8 +++--- man/graphresU.fun.Rd | 2 - man/resQQplot.fun.Rd | 4 +-- man/simNHP.fun.Rd | 4 +-- man/stepAICmle.fun.Rd | 8 +++--- man/testlik.fun.Rd | 8 ++---- man/transfH.fun.Rd | 4 +-- man/unifres.fun.Rd | 4 +-- 30 files changed, 105 insertions(+), 99 deletions(-)
Title: Using KEEL in R Code
Description: 'KEEL' is a popular Java software for a large number of different knowledge data discovery tasks.
This package takes the advantages of 'KEEL' and R, allowing to use 'KEEL' algorithms in simple R code.
The implemented R code layer between R and 'KEEL' makes easy both using 'KEEL' algorithms in R as implementing new algorithms for 'RKEEL' in a very simple way.
It includes more than 100 algorithms for classification, regression, preprocess, association rules and imbalance learning, which allows a more complete experimentation process.
For more information about KEEL, see <http://www.keel.es/>.
Author: Jose M. Moyano [aut, cre],
Luciano Sanchez Ramos [aut],
Oliver Sanchez Marin [ctb]
Maintainer: Jose M. Moyano <jmoyano@uco.es>
Diff between RKEEL versions 1.2.1 dated 2018-07-06 and 1.2.2 dated 2018-07-16
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/KeelAlgorithm.R | 10 ++++++++-- 3 files changed, 13 insertions(+), 7 deletions(-)
Title: Fast Nearest Neighbour Search (Wraps ANN Library) Using L2
Metric
Description: Finds the k nearest neighbours for every point in a given dataset
in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is
support for approximate as well as exact searches, fixed radius searches
and 'bd' as well as 'kd' trees. The distance is computed using the L2
(Euclidean) metric. Please see package 'RANN.L1' for the same
functionality using the L1 (Manhattan, taxicab) metric.
Author: Sunil Arya and David Mount (for ANN), Samuel E. Kemp, Gregory Jefferis
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between RANN versions 2.5.1 dated 2017-05-21 and 2.6 dated 2018-07-16
RANN-2.5.1/RANN/NEWS |only RANN-2.6/RANN/DESCRIPTION | 6 +++--- RANN-2.6/RANN/MD5 | 18 +++++++++--------- RANN-2.6/RANN/NEWS.md |only RANN-2.6/RANN/src/ANN.cpp | 6 +++--- RANN-2.6/RANN/src/kd_fix_rad_search.cpp | 10 +++++----- RANN-2.6/RANN/src/kd_pr_search.cpp | 12 ++++++------ RANN-2.6/RANN/src/kd_search.cpp | 12 ++++++------ RANN-2.6/RANN/src/kd_util.cpp | 10 +++++----- RANN-2.6/RANN/src/pr_queue.h | 10 +++++----- RANN-2.6/RANN/src/pr_queue_k.h | 2 +- 11 files changed, 43 insertions(+), 43 deletions(-)
Title: A Set of Tools for Calculating Spatial Synchrony Between
Tree-Ring Chronologies
Description: Provides functions for the calculation and plotting of synchrony in
tree growth from tree-ring width chronologies (TRW index). It combines
variance-covariance (VCOV) mixed modelling with functions that quantify
the degree to which the TRW chronologies contain a common temporal
signal. It also implements temporal trends in spatial synchrony using a
moving window. These methods can also be used with other kind of ecological
variables that have temporal autocorrelation corrected.
Author: Josu G. Alday, Tatiana A. Shestakova, Victor Resco de Dios, Jordi Voltas
Maintainer: Josu G. Alday <josucham@gmail.com>
Diff between DendroSync versions 0.1.1 dated 2018-06-22 and 0.1.2 dated 2018-07-16
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++-- R/sync.trend.plot.R | 10 ++++++---- README.md | 2 +- man/sync.trend.plot.Rd | 2 +- 6 files changed, 19 insertions(+), 17 deletions(-)
Title: Bayesian Spectral Inference for Stationary Time Series
Description: Implementations of a Bayesian parametric (autoregressive), a Bayesian nonparametric (Whittle likelihood with Bernstein-Dirichlet prior) and a Bayesian semiparametric (autoregressive likelihood with Bernstein-Dirichlet correction) procedure are provided. The work is based on the corrected parametric likelihood by C. Kirch et al (2017) <arXiv:1701.04846>. It was supported by DFG grant KI 1443/3-1.
Author: Alexander Meier [aut, cre],
Claudia Kirch [aut],
Matthew C. Edwards [aut],
Renate Meyer [aut]
Maintainer: Alexander Meier <alexander.meier@ovgu.de>
Diff between beyondWhittle versions 0.18.1 dated 2017-04-07 and 1.0 dated 2018-07-16
beyondWhittle-0.18.1/beyondWhittle/R/intern__gibbs_pacf.R |only beyondWhittle-0.18.1/beyondWhittle/R/intern__gibbs_toggle_ar.R |only beyondWhittle-0.18.1/beyondWhittle/man/Cn.Rd |only beyondWhittle-0.18.1/beyondWhittle/man/arma_partial.Rd |only beyondWhittle-0.18.1/beyondWhittle/man/gibbs_pacf.Rd |only beyondWhittle-0.18.1/beyondWhittle/man/gibbs_toggle_ar.Rd |only beyondWhittle-0.18.1/beyondWhittle/man/llike_full.Rd |only beyondWhittle-0.18.1/beyondWhittle/man/llike_pacf.Rd |only beyondWhittle-0.18.1/beyondWhittle/man/lpost_pacf.Rd |only beyondWhittle-0.18.1/beyondWhittle/man/lprior_pacf.Rd |only beyondWhittle-1.0/beyondWhittle/DESCRIPTION | 10 beyondWhittle-1.0/beyondWhittle/MD5 | 80 ++- beyondWhittle-1.0/beyondWhittle/NAMESPACE | 5 beyondWhittle-1.0/beyondWhittle/R/RcppExports.R | 31 - beyondWhittle-1.0/beyondWhittle/R/gibbs_AR.R | 116 ++--- beyondWhittle-1.0/beyondWhittle/R/gibbs_AR_nuisance.R |only beyondWhittle-1.0/beyondWhittle/R/gibbs_NP.R | 62 +- beyondWhittle-1.0/beyondWhittle/R/gibbs_NPC.R | 109 +++-- beyondWhittle-1.0/beyondWhittle/R/gibbs_NPC_nuisance.R |only beyondWhittle-1.0/beyondWhittle/R/gibbs_NP_nuisance.R |only beyondWhittle-1.0/beyondWhittle/R/intern__gibbs_AR_nuisance.R |only beyondWhittle-1.0/beyondWhittle/R/intern__gibbs_core.R | 208 ++++------ beyondWhittle-1.0/beyondWhittle/R/intern__gibbs_nuisance.R |only beyondWhittle-1.0/beyondWhittle/R/intern__gibbs_util.R | 90 ++++ beyondWhittle-1.0/beyondWhittle/R/nuisance_models.R |only beyondWhittle-1.0/beyondWhittle/R/scree_type.R |only beyondWhittle-1.0/beyondWhittle/man/ar_lik.Rd | 10 beyondWhittle-1.0/beyondWhittle/man/ar_screeType.Rd | 2 beyondWhittle-1.0/beyondWhittle/man/arma_conditional.Rd | 2 beyondWhittle-1.0/beyondWhittle/man/betaBasis_k.Rd |only beyondWhittle-1.0/beyondWhittle/man/coarsened_bernstein.Rd |only beyondWhittle-1.0/beyondWhittle/man/coarsened_bernstein_i.Rd |only beyondWhittle-1.0/beyondWhittle/man/dbList.Rd |only beyondWhittle-1.0/beyondWhittle/man/gibbs_AR.Rd | 30 + beyondWhittle-1.0/beyondWhittle/man/gibbs_AR_nuisance.Rd |only beyondWhittle-1.0/beyondWhittle/man/gibbs_AR_nuisance_intern.Rd |only beyondWhittle-1.0/beyondWhittle/man/gibbs_NP.Rd | 23 - beyondWhittle-1.0/beyondWhittle/man/gibbs_NPC.Rd | 37 + beyondWhittle-1.0/beyondWhittle/man/gibbs_NPC_nuisance.Rd |only beyondWhittle-1.0/beyondWhittle/man/gibbs_NP_nuisance.Rd |only beyondWhittle-1.0/beyondWhittle/man/gibbs_nuisance.Rd |only beyondWhittle-1.0/beyondWhittle/man/llike.Rd | 4 beyondWhittle-1.0/beyondWhittle/man/llike_AR.Rd |only beyondWhittle-1.0/beyondWhittle/man/logDet_stickBreaking.Rd |only beyondWhittle-1.0/beyondWhittle/man/logfuller.Rd | 2 beyondWhittle-1.0/beyondWhittle/man/lpost.Rd | 4 beyondWhittle-1.0/beyondWhittle/man/lpost_AR.Rd |only beyondWhittle-1.0/beyondWhittle/man/lprior.Rd | 5 beyondWhittle-1.0/beyondWhittle/man/lprior_AR.Rd |only beyondWhittle-1.0/beyondWhittle/man/my_ddirichlet_unnormalized.Rd |only beyondWhittle-1.0/beyondWhittle/man/my_rdirichlet.Rd |only beyondWhittle-1.0/beyondWhittle/man/nuisanceModel_linearTrend.Rd |only beyondWhittle-1.0/beyondWhittle/man/nuisanceModel_mean.Rd |only beyondWhittle-1.0/beyondWhittle/man/print_warn.Rd |only beyondWhittle-1.0/beyondWhittle/man/psd_dummy_model.Rd |only beyondWhittle-1.0/beyondWhittle/man/qpsd.Rd |only beyondWhittle-1.0/beyondWhittle/man/vFromP.Rd |only beyondWhittle-1.0/beyondWhittle/src/RcppExports.cpp | 58 ++ beyondWhittle-1.0/beyondWhittle/src/gibbs_core.cpp | 16 beyondWhittle-1.0/beyondWhittle/src/gibbs_util.cpp | 12 60 files changed, 582 insertions(+), 334 deletions(-)
Title: Average Positive Predictive Values (AP) for Binary Outcomes and
Censored Event Times
Description: We provide tools to estimate two prediction performance metrics,
the average positive predictive values (AP) as well as the well-known AUC
(the area under the receiver operator characteristic curve) for risk scores
or marker. The outcome of interest is either binary or censored event time.
Note that for censored event time, our functions estimate the AP and the
AUC are time-dependent for pre-specified time interval(s). A function that
compares the APs of two risk scores/markers is also included. Optional
outputs include positive predictive values and true positive fractions at
the specified marker cut-off values, and a plot of the time-dependent AP
versus time (available for event time data).
Author: Hengrui Cai <hengruicai@gmail.com>, Yan Yuan <yyuan@ualberta.ca>, Qian
Michelle Zhou <qz70@msstate.edu>, Bingying Li<dorisli1120@gmail.com>
Maintainer: Hengrui Cai <hengruicai@gmail.com>
Diff between APtools versions 3.0 dated 2016-08-05 and 5.1 dated 2018-07-16
DESCRIPTION | 13 MD5 | 12 NAMESPACE | 26 - R/APBinary.R | 17 - R/APSurv.R | 572 ++++++++++++++++++++-------------------- R/CompareAP.R | 789 +++++++++++++++++++++++++++----------------------------- man/APBinary.Rd | 151 +++++----- 7 files changed, 792 insertions(+), 788 deletions(-)
Title: Wrapper to the 'spaCy' 'NLP' Library
Description: An R wrapper to the 'Python' 'spaCy' 'NLP' library,
from <http://spacy.io>.
Author: Kenneth Benoit [aut, cre, cph],
Akitaka Matsuo [aut]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between spacyr versions 0.9.9 dated 2018-04-17 and 0.9.91 dated 2018-07-16
DESCRIPTION | 8 +-- MD5 | 15 +++-- NEWS.md | 2 README.md | 82 +++++++++++++++---------------- inst/doc/VS_Installer_screenshot.png |only inst/doc/WINDOWS.Rmd | 59 ++++++++++++++-------- inst/doc/WINDOWS.md | 79 +++++++++++++++++++---------- inst/python/initialize_spacyPython.py | 10 +++ tests/testthat/test-4-quanteda-methods.R | 1 9 files changed, 155 insertions(+), 101 deletions(-)
Title: R Speaks 'Monolix'
Description: Provides methods for model building and model evaluation of mixed effects models using
'Monolix' <http://monolix.lixoft.com>. 'Monolix' is a software tool for nonlinear mixed effects
modeling that must have been installed in order to use 'Rsmlx'.
Among other tasks, 'Rsmlx' provides a powerful tool for automatic PK model building, performs
statistical tests for model assessment, bootstrap simulation and likelihood profiling for
computing confidence intervals. 'Rsmlx' also proposes several automatic covariate search methods for
mixed effects models.
Author: Marc Lavielle [aut, cre],
Jonathan Chauvin [aut],
Duc-Dung Tran [ctb]
Maintainer: Marc Lavielle <Marc.Lavielle@inria.fr>
Diff between Rsmlx versions 1.0.1 dated 2018-06-21 and 1.1.0 dated 2018-07-16
DESCRIPTION | 18 ++-- MD5 | 25 ++++-- NAMESPACE | 6 + R/ProjectManagement.R | 91 ------------------------ R/RsmlxTools.R |only R/bootstrap.R | 15 ++- R/buildmlx.R | 159 +++++++++++++++++++++++------------------- R/correlationModelSelection.R | 6 - R/newConnectors.R | 94 ++++++++++++++++++++++++ R/pkbuild.R |only R/pkpopini.R |only R/readdatamlx.R |only R/setSettings.R | 1 R/whichPKmodel.R |only man/pkbuild.Rd |only man/pkpopini.Rd |only man/readDatamlx.Rd |only man/whichPKmodel.Rd |only 18 files changed, 226 insertions(+), 189 deletions(-)
Title: Random Ferns Classifier
Description: Provides the random ferns classifier by Ozuysal, Calonder, Lepetit and Fua (2009) <doi:10.1109/TPAMI.2009.23>, modified for generic and multi-label classification and featuring OOB error approximation and importance measure as introduced in Kursa (2014) <doi:10.18637/jss.v061.i10>.
Author: Miron Bartosz Kursa [aut, cre]
(<https://orcid.org/0000-0001-7672-648X>)
Maintainer: Miron Bartosz Kursa <M.Kursa@icm.edu.pl>
Diff between rFerns versions 2.0.3 dated 2017-11-15 and 3.0.0 dated 2018-07-16
DESCRIPTION | 27 +++++-- MD5 | 28 ++++---- R/ferns.R | 89 +++++++++++-------------- R/naivewrapper.R | 54 ++++++++------- R/tools.R | 81 +++++++++++------------ inst/NEWS | 20 +++-- man/merge.rFerns.Rd | 9 -- man/naiveWrapper.Rd | 17 +++- man/predict.rFerns.Rd | 3 man/rFerns.Rd | 18 +---- src/Makevars | 3 src/fern.h | 15 ++-- src/ferns.c | 68 ++++++++----------- src/forest.h | 173 ++++++++++++++++++++------------------------------ src/tools.h | 27 +++++-- 15 files changed, 308 insertions(+), 324 deletions(-)
Title: Analysis of RD Designs with Multiple Cutoffs or Scores
Description: The regression discontinuity (RD) design is a popular quasi-experimental design for causal inference and policy evaluation. The 'rdmulti' package provides tools to analyze RD designs with multiple cutoffs or scores: rdmc() estimates pooled and cutoff specific effects for multi-cutoff designs, rdmcplot() draws RD plots for multi-cutoff designs and rdms() estimates effects in cumulative cutoffs or multi-score designs. See Cattaneo, Titiunik and Vazquez-Bare (2018) <https://sites.google.com/site/rdpackages/rdmulti/Cattaneo-Titiunik-VazquezBare_2018_rdmulti.pdf> for further methodological details.
Author: Matias D. Cattaneo, Rocio Titiunik, Gonzalo Vazquez-Bare
Maintainer: Gonzalo Vazquez-Bare <gvazquez@umich.edu>
Diff between rdmulti versions 0.1 dated 2018-04-23 and 0.2 dated 2018-07-16
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/rdmc.R | 25 +++++++++++++------------ R/rdmcplot.R | 2 +- R/rdms.R | 14 +++++++------- R/rdmulti_package.R | 2 +- 6 files changed, 30 insertions(+), 29 deletions(-)
Title: Fitting Markov Switching Models
Description: Estimation, inference and diagnostics for Univariate Autoregressive Markov Switching Models for Linear and Generalized Models. Distributions for the series include gaussian, Poisson, binomial and gamma cases. The EM algorithm is used for estimation (see Perlin (2012) <doi:10.2139/ssrn.1714016>).
Author: Josep A. Sanchez-Espigares, Alberto Lopez-Moreno
Maintainer: Josep A. Sanchez-Espigares <josep.a.sanchez@upc.edu>
Diff between MSwM versions 1.3 dated 2018-06-12 and 1.4 dated 2018-07-16
DESCRIPTION | 14 ++++++++------ MD5 | 18 +++++++++--------- NAMESPACE | 14 +++----------- R/1global.r | 1 + R/2MSM.r | 23 ++++++++++++----------- build/vignette.rds |binary inst/doc/examples.R | 4 ++-- inst/doc/examples.pdf |binary inst/doc/examples.rnw | 4 ++-- vignettes/examples.rnw | 4 ++-- 10 files changed, 39 insertions(+), 43 deletions(-)
Title: Amend, Augment and Aid Analysis of John Snow's Cholera Map
Description: Amends errors, augments data and aids analysis of John Snow's map
of the 1854 London cholera outbreak.
Author: Peter Li [aut, cre]
Maintainer: Peter Li <lindbrook@gmail.com>
Diff between cholera versions 0.4.0 dated 2018-04-01 and 0.5.0 dated 2018-07-16
cholera-0.4.0/cholera/man/plot.euclidean_distance.Rd |only cholera-0.4.0/cholera/man/plot.walking_distance.Rd |only cholera-0.4.0/cholera/man/print.euclidean_distance.Rd |only cholera-0.4.0/cholera/man/print.walking_distance.Rd |only cholera-0.5.0/cholera/DESCRIPTION | 12 cholera-0.5.0/cholera/MD5 | 242 +- cholera-0.5.0/cholera/NAMESPACE | 19 cholera-0.5.0/cholera/NEWS | 76 cholera-0.5.0/cholera/R/addCases.R |only cholera-0.5.0/cholera/R/addEuclideanPath.R |only cholera-0.5.0/cholera/R/addIndexCase.R | 2 cholera-0.5.0/cholera/R/addKernelDensity.R | 9 cholera-0.5.0/cholera/R/addLandmarks.R | 105 - cholera-0.5.0/cholera/R/addMilePosts.R |only cholera-0.5.0/cholera/R/addNeighborhood.R | 413 ++-- cholera-0.5.0/cholera/R/addPlaguePit.R | 1 cholera-0.5.0/cholera/R/addPump.R | 56 cholera-0.5.0/cholera/R/addVoronoi.R | 2 cholera-0.5.0/cholera/R/addWalkingPath.R |only cholera-0.5.0/cholera/R/addWhitehead.R | 19 cholera-0.5.0/cholera/R/cholera.R | 20 cholera-0.5.0/cholera/R/classifierAudit.R | 34 cholera-0.5.0/cholera/R/data.R | 45 cholera-0.5.0/cholera/R/distanceTime.R |only cholera-0.5.0/cholera/R/euclidean.R |only cholera-0.5.0/cholera/R/euclideanDistance.R | 261 +-- cholera-0.5.0/cholera/R/euclideanPath.R |only cholera-0.5.0/cholera/R/multiCore.R |only cholera-0.5.0/cholera/R/nearestPump.R | 34 cholera-0.5.0/cholera/R/neighborhoodData.R | 120 - cholera-0.5.0/cholera/R/pearlString.R |only cholera-0.5.0/cholera/R/pumpCase.R | 25 cholera-0.5.0/cholera/R/pumpData.R | 11 cholera-0.5.0/cholera/R/roadSegments.R | 4 cholera-0.5.0/cholera/R/segmentLength.R | 16 cholera-0.5.0/cholera/R/segmentLocator.R | 36 cholera-0.5.0/cholera/R/simulateFatalities.R | 81 cholera-0.5.0/cholera/R/snowMap.R | 51 cholera-0.5.0/cholera/R/streetLength.R | 17 cholera-0.5.0/cholera/R/streetNameLocator.R | 110 - cholera-0.5.0/cholera/R/streetNumberLocator.R | 130 + cholera-0.5.0/cholera/R/timeSeries.R | 2 cholera-0.5.0/cholera/R/unitMeter.R | 25 cholera-0.5.0/cholera/R/unstack.R | 4 cholera-0.5.0/cholera/R/voronoi.R | 149 - cholera-0.5.0/cholera/R/walking.R | 832 ++------- cholera-0.5.0/cholera/R/walkingAuxillaryFunctions.R |only cholera-0.5.0/cholera/R/walkingDistance.R | 317 --- cholera-0.5.0/cholera/R/walkingPath.R |only cholera-0.5.0/cholera/README.md | 41 cholera-0.5.0/cholera/build/vignette.rds |binary cholera-0.5.0/cholera/data/regular.cases.RData |binary cholera-0.5.0/cholera/data/road.segments.RData |binary cholera-0.5.0/cholera/data/sim.ortho.proj.RData |binary cholera-0.5.0/cholera/inst/doc/duplicate.missing.cases.R | 766 -------- cholera-0.5.0/cholera/inst/doc/duplicate.missing.cases.Rmd | 866 ---------- cholera-0.5.0/cholera/inst/doc/duplicate.missing.cases.html | 136 - cholera-0.5.0/cholera/inst/doc/kernel.density.Rmd | 4 cholera-0.5.0/cholera/inst/doc/kernel.density.html | 14 cholera-0.5.0/cholera/inst/doc/pump.neighborhoods.R | 3 cholera-0.5.0/cholera/inst/doc/pump.neighborhoods.Rmd | 34 cholera-0.5.0/cholera/inst/doc/pump.neighborhoods.html | 45 cholera-0.5.0/cholera/inst/doc/roads.Rmd | 2 cholera-0.5.0/cholera/inst/doc/roads.html | 6 cholera-0.5.0/cholera/inst/doc/time.series.Rmd | 2 cholera-0.5.0/cholera/inst/doc/time.series.html | 6 cholera-0.5.0/cholera/inst/doc/unstacking.bars.R | 420 ---- cholera-0.5.0/cholera/inst/doc/unstacking.bars.Rmd | 466 ----- cholera-0.5.0/cholera/inst/doc/unstacking.bars.html | 55 cholera-0.5.0/cholera/man/addCases.Rd |only cholera-0.5.0/cholera/man/addEuclideanPath.Rd |only cholera-0.5.0/cholera/man/addIndexCase.Rd | 2 cholera-0.5.0/cholera/man/addKernelDensity.Rd | 9 cholera-0.5.0/cholera/man/addLandmarks.Rd | 8 cholera-0.5.0/cholera/man/addMilePosts.Rd |only cholera-0.5.0/cholera/man/addNeighborhood.Rd | 33 cholera-0.5.0/cholera/man/addPlaguePit.Rd | 3 cholera-0.5.0/cholera/man/addPump.Rd | 8 cholera-0.5.0/cholera/man/addVoronoi.Rd | 5 cholera-0.5.0/cholera/man/addWalkingPath.Rd |only cholera-0.5.0/cholera/man/addWhitehead.Rd | 13 cholera-0.5.0/cholera/man/anchor.case.Rd | 5 cholera-0.5.0/cholera/man/cholera-package.Rd | 19 cholera-0.5.0/cholera/man/classifierAudit.Rd | 2 cholera-0.5.0/cholera/man/distanceTime.Rd |only cholera-0.5.0/cholera/man/euclideanDistance.Rd | 21 cholera-0.5.0/cholera/man/euclideanPath.Rd |only cholera-0.5.0/cholera/man/fatalities.Rd | 7 cholera-0.5.0/cholera/man/fatalities.address.Rd | 7 cholera-0.5.0/cholera/man/fatalities.unstacked.Rd | 7 cholera-0.5.0/cholera/man/figures/README-expected-1.png |binary cholera-0.5.0/cholera/man/figures/README-expected_area_polygons-1.png |binary cholera-0.5.0/cholera/man/figures/README-unnamed-chunk-3-1.png |only cholera-0.5.0/cholera/man/fixFatalities.Rd | 4 cholera-0.5.0/cholera/man/nearestPump.Rd | 15 cholera-0.5.0/cholera/man/neighborhoodEuclidean.Rd |only cholera-0.5.0/cholera/man/neighborhoodVoronoi.Rd | 2 cholera-0.5.0/cholera/man/neighborhoodWalking.Rd | 7 cholera-0.5.0/cholera/man/ortho.proj.Rd | 5 cholera-0.5.0/cholera/man/ortho.proj.pump.Rd | 5 cholera-0.5.0/cholera/man/ortho.proj.pump.vestry.Rd | 5 cholera-0.5.0/cholera/man/plot.classifier_audit.Rd | 6 cholera-0.5.0/cholera/man/plot.euclidean.Rd |only cholera-0.5.0/cholera/man/plot.euclidean_path.Rd |only cholera-0.5.0/cholera/man/plot.voronoi.Rd | 7 cholera-0.5.0/cholera/man/plot.walking.Rd | 5 cholera-0.5.0/cholera/man/plot.walking_path.Rd |only cholera-0.5.0/cholera/man/print.euclidean.Rd |only cholera-0.5.0/cholera/man/print.euclidean_path.Rd |only cholera-0.5.0/cholera/man/print.walking.Rd | 4 cholera-0.5.0/cholera/man/print.walking_path.Rd |only cholera-0.5.0/cholera/man/pumpCase.Rd | 11 cholera-0.5.0/cholera/man/pumpData.Rd | 9 cholera-0.5.0/cholera/man/pumps.Rd | 5 cholera-0.5.0/cholera/man/pumps.vestry.Rd | 5 cholera-0.5.0/cholera/man/regular.cases.Rd | 9 cholera-0.5.0/cholera/man/road.segments.Rd | 5 cholera-0.5.0/cholera/man/roadSegments.Rd | 7 cholera-0.5.0/cholera/man/segmentLength.Rd | 10 cholera-0.5.0/cholera/man/segmentLocator.Rd | 16 cholera-0.5.0/cholera/man/sim.ortho.proj.Rd | 14 cholera-0.5.0/cholera/man/sim.pump.case.Rd | 7 cholera-0.5.0/cholera/man/simulateFatalities.Rd | 11 cholera-0.5.0/cholera/man/snowMap.Rd | 15 cholera-0.5.0/cholera/man/streetLength.Rd | 8 cholera-0.5.0/cholera/man/streetNameLocator.Rd | 11 cholera-0.5.0/cholera/man/streetNumberLocator.Rd | 18 cholera-0.5.0/cholera/man/timeSeries.Rd | 5 cholera-0.5.0/cholera/man/unitMeter.Rd | 10 cholera-0.5.0/cholera/man/walkingDistance.Rd | 41 cholera-0.5.0/cholera/man/walkingPath.Rd |only cholera-0.5.0/cholera/vignettes/duplicate.missing.cases.Rmd | 866 ---------- cholera-0.5.0/cholera/vignettes/kernel.density.Rmd | 4 cholera-0.5.0/cholera/vignettes/pump.neighborhoods.Rmd | 34 cholera-0.5.0/cholera/vignettes/roads.Rmd | 2 cholera-0.5.0/cholera/vignettes/time.series.Rmd | 2 cholera-0.5.0/cholera/vignettes/unstacking.bars.Rmd | 466 ----- 137 files changed, 1816 insertions(+), 6135 deletions(-)
Title: Tools and Classes for Statistical Models
Description: A collection of tools to deal with statistical models.
The functionality is experimental and the user interface is likely to
change in the future. The documentation is rather terse, but packages `coin'
and `party' have some working examples. However, if you find the
implemented ideas interesting we would be very interested in a discussion
of this proposal. Contributions are more than welcome!
Author: Torsten Hothorn, Friedrich Leisch, Achim Zeileis
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between modeltools versions 0.2-21 dated 2013-09-02 and 0.2-22 dated 2018-07-16
modeltools-0.2-21/modeltools/NEWS |only modeltools-0.2-22/modeltools/DESCRIPTION | 8 ++++---- modeltools-0.2-22/modeltools/MD5 | 5 ++--- modeltools-0.2-22/modeltools/inst/NEWS | 4 ++++ 4 files changed, 10 insertions(+), 7 deletions(-)
Title: S3 Infrastructure for Regular and Irregular Time Series (Z's
Ordered Observations)
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>),
Gabor Grothendieck [aut],
Jeffrey A. Ryan [aut],
Joshua M. Ulrich [ctb],
Felix Andrews [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between zoo versions 1.8-2 dated 2018-06-11 and 1.8-3 dated 2018-07-16
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NEWS | 12 ++++++++++++ R/rollapply.R | 10 ++++++++-- R/rollmean.R | 8 ++++---- demo/zoo-overplot.R | 6 ++---- inst/doc/zoo-design.pdf | 14 +++++++------- inst/doc/zoo-faq.R | 8 ++++---- inst/doc/zoo-faq.Rnw | 8 ++++---- inst/doc/zoo-faq.pdf |binary inst/doc/zoo-quickref.pdf |binary inst/doc/zoo-read.pdf |binary inst/doc/zoo.pdf |binary man/yearmon.Rd | 2 +- tests/Examples/zoo-Ex.Rout.save | 2 +- vignettes/zoo-faq.Rnw | 8 ++++---- 16 files changed, 66 insertions(+), 50 deletions(-)
Title: Tables so Beautifully Fine-Tuned You Will Believe It's Magic
Description: The introduction of the 'broom' package has made converting model
objects into data frames as simple as a single function. While the 'broom'
package focuses on providing tidy data frames that can be used in advanced
analysis, it deliberately stops short of providing functionality for reporting
models in publication-ready tables. 'pixiedust' provides this functionality with
a programming interface intended to be similar to 'ggplot2's system of layers
with fine tuned control over each cell of the table. Options for output include
printing to the console and to the common markdown formats (markdown, HTML, and
LaTeX). With a little 'pixiedust' (and happy thoughts) tables can really fly.
Author: Benjamin Nutter [aut, cre],
David Kretch [ctb]
Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>
Diff between pixiedust versions 0.8.4 dated 2018-06-29 and 0.8.5 dated 2018-07-16
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/dust.R | 6 +++--- R/gaze.R | 2 +- inst/doc/advancedMagic.html | 4 ++-- inst/doc/pixiedust.html | 4 ++-- inst/doc/sprinkles.html | 4 ++-- tests/testthat/test-dust.R | 2 +- tests/testthat/test-gaze.R | 4 ++-- 9 files changed, 24 insertions(+), 24 deletions(-)
Title: Calculate Physiological Characteristics of Adults, Children and
Infants
Description: A variety of formulae are provided for estimation
of physiologic characteristics of infants, children, and adults. For
example, calculations of ideal weight, airway dead-space, and the
alveolar gas equation. Each formula is referenced to the original
publication. Future functions will cover more material with a focus
on anaesthesia, critical care and peri-operative medicine.
Author: Jack O. Wasey [aut, cre, cph]
Maintainer: Jack O. Wasey <jack@jackwasey.com>
Diff between physiology versions 0.2.2 dated 2015-01-06 and 1.0.1 dated 2018-07-16
physiology-0.2.2/physiology/R/util.R |only physiology-0.2.2/physiology/man/ideal_weight_Straub.Rd |only physiology-0.2.2/physiology/tests/testthat/test-util.R |only physiology-1.0.1/physiology/DESCRIPTION | 43 physiology-1.0.1/physiology/MD5 | 90 + physiology-1.0.1/physiology/NAMESPACE | 60 physiology-1.0.1/physiology/NEWS.md |only physiology-1.0.1/physiology/R/RcppExports.R |only physiology-1.0.1/physiology/R/acidbase.R |only physiology-1.0.1/physiology/R/age.R |only physiology-1.0.1/physiology/R/bmi.R | 617 ++++------ physiology-1.0.1/physiology/R/physics.R |only physiology-1.0.1/physiology/R/physiology-package.R | 20 physiology-1.0.1/physiology/R/pulmonary.R |only physiology-1.0.1/physiology/R/units.R |only physiology-1.0.1/physiology/R/valid.R |only physiology-1.0.1/physiology/R/ventilation.R |only physiology-1.0.1/physiology/README.md | 50 physiology-1.0.1/physiology/build/vignette.rds |binary physiology-1.0.1/physiology/inst/WORDLIST |only physiology-1.0.1/physiology/inst/doc/Everest.R |only physiology-1.0.1/physiology/inst/doc/Everest.Rmd |only physiology-1.0.1/physiology/inst/doc/Everest.html |only physiology-1.0.1/physiology/inst/doc/IdealWeightComparison.R | 58 physiology-1.0.1/physiology/inst/doc/IdealWeightComparison.Rmd | 86 - physiology-1.0.1/physiology/inst/doc/IdealWeightComparison.html | 292 +++- physiology-1.0.1/physiology/inst/doc/NeonatalVentilation.R |only physiology-1.0.1/physiology/inst/doc/NeonatalVentilation.Rmd |only physiology-1.0.1/physiology/inst/doc/NeonatalVentilation.html |only physiology-1.0.1/physiology/man/Pa_to_torr.Rd |only physiology-1.0.1/physiology/man/adj_weight_adult.Rd | 49 physiology-1.0.1/physiology/man/age_from_dates.Rd | 63 - physiology-1.0.1/physiology/man/age_m.Rd |only physiology-1.0.1/physiology/man/alveolar_PAO2_mmHg.Rd |only physiology-1.0.1/physiology/man/bloodvol.Rd | 138 +- physiology-1.0.1/physiology/man/bmi.Rd | 59 physiology-1.0.1/physiology/man/bsa_adult.Rd | 51 physiology-1.0.1/physiology/man/deadspace_total.Rd |only physiology-1.0.1/physiology/man/french_to_diameter_mm.Rd |only physiology-1.0.1/physiology/man/getStandardTemperature.Rd |only physiology-1.0.1/physiology/man/henderson_hasselbalch.Rd |only physiology-1.0.1/physiology/man/ideal_weight.Rd | 209 +-- physiology-1.0.1/physiology/man/ideal_weight_Traub.Rd |only physiology-1.0.1/physiology/man/is_adult.Rd |only physiology-1.0.1/physiology/man/physiology-package.Rd | 34 physiology-1.0.1/physiology/man/pres_atm_kPa.Rd |only physiology-1.0.1/physiology/man/svp_sea_level.Rd |only physiology-1.0.1/physiology/man/temp_c_to_k.Rd |only physiology-1.0.1/physiology/man/valid_height.Rd |only physiology-1.0.1/physiology/src |only physiology-1.0.1/physiology/tests/spelling.R |only physiology-1.0.1/physiology/tests/test-all.R | 6 physiology-1.0.1/physiology/tests/testthat/test-NadlerBloodVolume.R | 135 +- physiology-1.0.1/physiology/tests/testthat/test-acidbase.R |only physiology-1.0.1/physiology/tests/testthat/test-age.R |only physiology-1.0.1/physiology/tests/testthat/test-atm-pressure.R |only physiology-1.0.1/physiology/tests/testthat/test-bmi.R | 310 ++++- physiology-1.0.1/physiology/tests/testthat/test-examples.R |only physiology-1.0.1/physiology/tests/testthat/test-physics.R |only physiology-1.0.1/physiology/tests/testthat/test-pulmonary.R |only physiology-1.0.1/physiology/tests/testthat/test-units.R |only physiology-1.0.1/physiology/tests/testthat/test-ventilation.R |only physiology-1.0.1/physiology/vignettes/Everest.Rmd |only physiology-1.0.1/physiology/vignettes/IdealWeightComparison.Rmd | 86 - physiology-1.0.1/physiology/vignettes/IdealWeightComparison.md | 48 physiology-1.0.1/physiology/vignettes/NeonatalVentilation.Rmd |only physiology-1.0.1/physiology/vignettes/altitude.bib |only 67 files changed, 1527 insertions(+), 977 deletions(-)
Title: Ordinal Regression for High-Dimensional Data
Description: Provides a function for fitting cumulative link, adjacent category, forward and backward continuation ratio, and stereotype ordinal response models when the number of parameters exceeds the sample size, using the the generalized monotone incremental forward stagewise method.
Author: Kellie J. Archer, Jiayi Hou, Qing Zhou, Kyle Ferber, John G. Layne, Amanda Gentry
Maintainer: Kellie J. Archer <archer.43@osu.edu>
Diff between ordinalgmifs versions 1.0.4 dated 2018-06-12 and 1.0.5 dated 2018-07-16
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/ordinalgmifs.R | 4 ++-- build/partial.rdb |binary inst/NEWS.Rd | 5 +++++ inst/doc/ordinalgmifs.pdf |binary man/ordinalgmifs.Rd | 2 +- 7 files changed, 18 insertions(+), 13 deletions(-)
Title: Ordinal Forests: Prediction and Variable Ranking with Ordinal
Target Variables
Description: The ordinal forest (OF) method allows ordinal regression with high-dimensional
and low-dimensional data. After having constructed an OF prediction rule using a training dataset,
it can be used to predict the values of the ordinal target variable for new observations.
Moreover, by means of the (permutation-based) variable importance measure of OF, it is also
possible to rank the covariates with respect to their importances in the prediction of the
values of the ordinal target variable.
OF is presented in Hornung (2017).
The main functions of the package are: ordfor() (construction of OF) and predict.ordfor()
(prediction of the target variable values of new observations).
References:
Hornung R. (2017) Ordinal Forests. Tech. Rep. 212, Department of Statistics,
University of Munich.
Author: Roman Hornung
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between ordinalForest versions 2.1 dated 2017-10-20 and 2.2 dated 2018-07-16
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/hearth.R | 1 + R/predict.ordfor.R | 3 +-- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory
factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre] (<https://orcid.org/0000-0002-4129-4477>),
Daniel Oberski [ctb],
Jarrett Byrnes [ctb],
Leonard Vanbrabant [ctb],
Victoria Savalei [ctb],
Ed Merkle [ctb],
Michael Hallquist [ctb],
Mijke Rhemtulla [ctb],
Myrsini Katsikatsou [ctb],
Mariska Barendse [ctb],
Michael Chow [ctb],
Terrence D. Jorgensen [ctb]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>
Diff between lavaan versions 0.6-1 dated 2018-05-22 and 0.6-2 dated 2018-07-16
lavaan-0.6-1/lavaan/R/lav_fabin.R |only lavaan-0.6-2/lavaan/DESCRIPTION | 17 lavaan-0.6-2/lavaan/MD5 | 258 ++++---- lavaan-0.6-2/lavaan/NAMESPACE | 8 lavaan-0.6-2/lavaan/R/00class.R | 12 lavaan-0.6-2/lavaan/R/00generic.R | 6 lavaan-0.6-2/lavaan/R/01RefClass_00lavRefModel.R | 2 lavaan-0.6-2/lavaan/R/01RefClass_01lavOptim.R | 22 lavaan-0.6-2/lavaan/R/01RefClass_02lavML.R | 2 lavaan-0.6-2/lavaan/R/ctr_estfun.R | 22 lavaan-0.6-2/lavaan/R/ctr_informative_testing.R | 294 ++++----- lavaan-0.6-2/lavaan/R/ctr_modelcov.R | 6 lavaan-0.6-2/lavaan/R/ctr_mplus2lavaan.R | 420 +++++++------- lavaan-0.6-2/lavaan/R/ctr_pairwise_fit.R | 12 lavaan-0.6-2/lavaan/R/ctr_pairwise_table.R | 50 - lavaan-0.6-2/lavaan/R/ctr_pml_plrt.R | 37 - lavaan-0.6-2/lavaan/R/ctr_pml_plrt2.R | 24 lavaan-0.6-2/lavaan/R/ctr_pml_plrt_nested.R | 98 +-- lavaan-0.6-2/lavaan/R/ctr_pml_utils.R | 152 ++--- lavaan-0.6-2/lavaan/R/lav_binorm.R | 22 lavaan-0.6-2/lavaan/R/lav_bootstrap.R | 97 +-- lavaan-0.6-2/lavaan/R/lav_bootstrap_lrt.R | 183 +++--- lavaan-0.6-2/lavaan/R/lav_cfa_1fac.R |only lavaan-0.6-2/lavaan/R/lav_constraints.R | 28 lavaan-0.6-2/lavaan/R/lav_cor.R | 26 lavaan-0.6-2/lavaan/R/lav_data.R | 248 ++++---- lavaan-0.6-2/lavaan/R/lav_dataframe.R | 16 lavaan-0.6-2/lavaan/R/lav_export.R | 18 lavaan-0.6-2/lavaan/R/lav_export_bugs.R | 38 - lavaan-0.6-2/lavaan/R/lav_export_mplus.R | 26 lavaan-0.6-2/lavaan/R/lav_fiml.R | 14 lavaan-0.6-2/lavaan/R/lav_fit.R | 8 lavaan-0.6-2/lavaan/R/lav_fit_measures.R | 41 - lavaan-0.6-2/lavaan/R/lav_fsr.R | 4 lavaan-0.6-2/lavaan/R/lav_func_deriv.R | 24 lavaan-0.6-2/lavaan/R/lav_h1_logl.R | 4 lavaan-0.6-2/lavaan/R/lav_integrate.R | 6 lavaan-0.6-2/lavaan/R/lav_lavaanList_inspect.R | 22 lavaan-0.6-2/lavaan/R/lav_lavaanList_methods.R | 22 lavaan-0.6-2/lavaan/R/lav_lavaanList_multipleGroups.R | 6 lavaan-0.6-2/lavaan/R/lav_lavaanList_multipleImputation.R | 4 lavaan-0.6-2/lavaan/R/lav_lavaanList_simulate.R | 14 lavaan-0.6-2/lavaan/R/lav_matrix.R | 125 ++-- lavaan-0.6-2/lavaan/R/lav_model.R | 34 - lavaan-0.6-2/lavaan/R/lav_model_compute.R | 42 - lavaan-0.6-2/lavaan/R/lav_model_estimate.R | 360 +++++++++--- lavaan-0.6-2/lavaan/R/lav_model_gradient.R | 132 ++-- lavaan-0.6-2/lavaan/R/lav_model_gradient_mml.R | 16 lavaan-0.6-2/lavaan/R/lav_model_gradient_pml.R | 64 +- lavaan-0.6-2/lavaan/R/lav_model_h1_information.R | 73 +- lavaan-0.6-2/lavaan/R/lav_model_hessian.R | 40 - lavaan-0.6-2/lavaan/R/lav_model_implied.R | 2 lavaan-0.6-2/lavaan/R/lav_model_information.R | 48 - lavaan-0.6-2/lavaan/R/lav_model_lik.R | 10 lavaan-0.6-2/lavaan/R/lav_model_loglik.R | 4 lavaan-0.6-2/lavaan/R/lav_model_objective.R | 32 - lavaan-0.6-2/lavaan/R/lav_model_utils.R | 14 lavaan-0.6-2/lavaan/R/lav_model_vcov.R | 196 ++++-- lavaan-0.6-2/lavaan/R/lav_model_wls.R | 12 lavaan-0.6-2/lavaan/R/lav_modification.R | 68 +- lavaan-0.6-2/lavaan/R/lav_mplus.R | 2 lavaan-0.6-2/lavaan/R/lav_muthen1984.R | 36 - lavaan-0.6-2/lavaan/R/lav_mvnorm.R | 86 +- lavaan-0.6-2/lavaan/R/lav_mvnorm_cluster.R | 58 - lavaan-0.6-2/lavaan/R/lav_mvnorm_h1.R | 54 - lavaan-0.6-2/lavaan/R/lav_mvnorm_missing.R | 221 +++++-- lavaan-0.6-2/lavaan/R/lav_mvnorm_missing_h1.R | 16 lavaan-0.6-2/lavaan/R/lav_mvreg.R | 46 - lavaan-0.6-2/lavaan/R/lav_nlminb_constr.R | 30 - lavaan-0.6-2/lavaan/R/lav_object_generate.R | 36 - lavaan-0.6-2/lavaan/R/lav_object_inspect.R | 303 +++++----- lavaan-0.6-2/lavaan/R/lav_object_methods.R | 55 + lavaan-0.6-2/lavaan/R/lav_object_post_check.R | 8 lavaan-0.6-2/lavaan/R/lav_object_print.R | 45 + lavaan-0.6-2/lavaan/R/lav_objective.R | 125 ++-- lavaan-0.6-2/lavaan/R/lav_ols.R | 12 lavaan-0.6-2/lavaan/R/lav_options.R | 173 +++-- lavaan-0.6-2/lavaan/R/lav_partable.R | 84 +- lavaan-0.6-2/lavaan/R/lav_partable_attributes.R | 2 lavaan-0.6-2/lavaan/R/lav_partable_check.R | 6 lavaan-0.6-2/lavaan/R/lav_partable_complete.R | 10 lavaan-0.6-2/lavaan/R/lav_partable_constraints.R | 26 lavaan-0.6-2/lavaan/R/lav_partable_flat.R | 28 lavaan-0.6-2/lavaan/R/lav_partable_from_lm.R | 4 lavaan-0.6-2/lavaan/R/lav_partable_full.R | 18 lavaan-0.6-2/lavaan/R/lav_partable_independence.R | 2 lavaan-0.6-2/lavaan/R/lav_partable_merge.R | 10 lavaan-0.6-2/lavaan/R/lav_partable_subset.R | 14 lavaan-0.6-2/lavaan/R/lav_partable_unrestricted.R | 46 - lavaan-0.6-2/lavaan/R/lav_partable_utils.R | 10 lavaan-0.6-2/lavaan/R/lav_partable_vnames.R | 12 lavaan-0.6-2/lavaan/R/lav_pearson.R | 20 lavaan-0.6-2/lavaan/R/lav_polychor.R | 36 - lavaan-0.6-2/lavaan/R/lav_polyserial.R | 22 lavaan-0.6-2/lavaan/R/lav_predict.R | 164 +++-- lavaan-0.6-2/lavaan/R/lav_prelis.R | 10 lavaan-0.6-2/lavaan/R/lav_print.R | 170 +++-- lavaan-0.6-2/lavaan/R/lav_probit.R | 22 lavaan-0.6-2/lavaan/R/lav_representation_lisrel.R | 274 ++++----- lavaan-0.6-2/lavaan/R/lav_residuals.R | 77 +- lavaan-0.6-2/lavaan/R/lav_samplestats.R | 130 +--- lavaan-0.6-2/lavaan/R/lav_samplestats_gamma.R | 71 +- lavaan-0.6-2/lavaan/R/lav_samplestats_icov.R | 6 lavaan-0.6-2/lavaan/R/lav_samplestats_igamma.R | 10 lavaan-0.6-2/lavaan/R/lav_samplestats_step1.R | 14 lavaan-0.6-2/lavaan/R/lav_samplestats_step2.R | 10 lavaan-0.6-2/lavaan/R/lav_samplestats_wls_obs.R | 16 lavaan-0.6-2/lavaan/R/lav_simulate.R | 28 lavaan-0.6-2/lavaan/R/lav_simulate_old.R | 38 - lavaan-0.6-2/lavaan/R/lav_standardize.R | 351 +++++++---- lavaan-0.6-2/lavaan/R/lav_start.R | 314 ++++++---- lavaan-0.6-2/lavaan/R/lav_syntax.R | 123 ++-- lavaan-0.6-2/lavaan/R/lav_syntax_independence.R | 12 lavaan-0.6-2/lavaan/R/lav_tables.R | 130 ++-- lavaan-0.6-2/lavaan/R/lav_tables_mvb.R | 10 lavaan-0.6-2/lavaan/R/lav_test.R | 42 - lavaan-0.6-2/lavaan/R/lav_test_LRT.R | 36 - lavaan-0.6-2/lavaan/R/lav_test_Wald.R | 4 lavaan-0.6-2/lavaan/R/lav_test_diff.R | 40 - lavaan-0.6-2/lavaan/R/lav_test_satorra_bentler.R | 24 lavaan-0.6-2/lavaan/R/lav_test_score.R | 18 lavaan-0.6-2/lavaan/R/lav_test_yuan_bentler.R | 65 -- lavaan-0.6-2/lavaan/R/lav_utils.R | 40 - lavaan-0.6-2/lavaan/R/lavaan-deprecated.R | 2 lavaan-0.6-2/lavaan/R/xxx_fsr.R | 60 +- lavaan-0.6-2/lavaan/R/xxx_lavaan.R | 81 +- lavaan-0.6-2/lavaan/R/xxx_lavaanList.R | 66 +- lavaan-0.6-2/lavaan/R/xxx_prelav.R | 6 lavaan-0.6-2/lavaan/R/xxx_twostep.R | 22 lavaan-0.6-2/lavaan/man/lavOptions.Rd | 24 lavaan-0.6-2/lavaan/man/parameterEstimates.Rd | 2 131 files changed, 4435 insertions(+), 3318 deletions(-)
Title: Check if the Title of a Package is Available, Appropriate and
Interesting
Description: Check if a given package name is available to use. It checks the
name's validity. Checks if it is used on 'GitHub', 'CRAN' and 'Bioconductor'. Checks
for unintended meanings by querying Urban Dictionary, 'Wiktionary' and Wikipedia.
Author: Carl Ganz [aut],
Gábor Csárdi [aut],
Jim Hester [aut, cre],
Molly Lewis [aut],
Rachael Tatman [aut]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between available versions 1.0.0 dated 2017-11-17 and 1.0.1 dated 2018-07-16
DESCRIPTION | 10 +++++----- MD5 | 24 +++++++++++++----------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/bad_words.R | 4 ++-- R/bioc.R | 3 +-- R/get_urban_data.R | 9 ++++----- R/github.R | 15 ++++++++++++++- R/name_to_search_terms.R | 2 +- R/namr.R | 16 ++++++++-------- R/utils.R | 15 +++++++++++++++ R/zzz.R |only README.md | 25 +++++++++++++------------ tests/testthat/test-name_to_search_terms.R |only 14 files changed, 84 insertions(+), 47 deletions(-)
Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Specialization of method ggplot(): accept and convert on the fly
time series data. Geom: "table", adds tables to plots. Statistics: locate
and tag peaks and valleys in 2D plots; count observations in different
quadrants of a plot; select observations based on 2D density; label with the
equation of a polynomial fitted with lm() or other types of models; labels
with P-value, R^2 or adjusted R^2 or information criteria for fitted models;
label with ANOVA table for fitted models; label with summary for fitted
models. Model fit classes for which suitable methods are provided by package
'broom' are supported.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Kamil Slowikowski [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpmisc versions 0.2.17 dated 2018-05-06 and 0.3.0 dated 2018-07-16
ggpmisc-0.2.17/ggpmisc/R/geom-debug.R |only ggpmisc-0.2.17/ggpmisc/R/layer-manip.R |only ggpmisc-0.2.17/ggpmisc/R/stat-debug-group.R |only ggpmisc-0.2.17/ggpmisc/R/stat-debug-panel.R |only ggpmisc-0.2.17/ggpmisc/R/stat-quadrat-counts.R |only ggpmisc-0.2.17/ggpmisc/inst/doc/user-guide-1.R |only ggpmisc-0.2.17/ggpmisc/inst/doc/user-guide-1.Rmd |only ggpmisc-0.2.17/ggpmisc/inst/doc/user-guide-1.html |only ggpmisc-0.2.17/ggpmisc/inst/doc/user-guide-2.R |only ggpmisc-0.2.17/ggpmisc/inst/doc/user-guide-2.Rmd |only ggpmisc-0.2.17/ggpmisc/inst/doc/user-guide-2.html |only ggpmisc-0.2.17/ggpmisc/inst/doc/user-guide-3.R |only ggpmisc-0.2.17/ggpmisc/inst/doc/user-guide-3.Rmd |only ggpmisc-0.2.17/ggpmisc/inst/doc/user-guide-3.html |only ggpmisc-0.2.17/ggpmisc/inst/doc/user-guide-4.R |only ggpmisc-0.2.17/ggpmisc/inst/doc/user-guide-4.Rmd |only ggpmisc-0.2.17/ggpmisc/inst/doc/user-guide-4.html |only ggpmisc-0.2.17/ggpmisc/man/delete_layers.Rd |only ggpmisc-0.2.17/ggpmisc/man/edit_layers.Rd |only ggpmisc-0.2.17/ggpmisc/man/geom_debug.Rd |only ggpmisc-0.2.17/ggpmisc/man/geom_null.Rd |only ggpmisc-0.2.17/ggpmisc/man/stat_debug_group.Rd |only ggpmisc-0.2.17/ggpmisc/man/stat_debug_panel.Rd |only ggpmisc-0.2.17/ggpmisc/man/stat_quadrat_counts.Rd |only ggpmisc-0.2.17/ggpmisc/vignettes/user-guide-1.Rmd |only ggpmisc-0.2.17/ggpmisc/vignettes/user-guide-2.Rmd |only ggpmisc-0.2.17/ggpmisc/vignettes/user-guide-3.Rmd |only ggpmisc-0.2.17/ggpmisc/vignettes/user-guide-4.Rmd |only ggpmisc-0.3.0/ggpmisc/DESCRIPTION | 43 ++-- ggpmisc-0.3.0/ggpmisc/MD5 | 105 +++++------- ggpmisc-0.3.0/ggpmisc/NAMESPACE | 27 --- ggpmisc-0.3.0/ggpmisc/NEWS | 26 ++ ggpmisc-0.3.0/ggpmisc/R/geom-table.R |only ggpmisc-0.3.0/ggpmisc/R/ggpmisc.R | 48 +++-- ggpmisc-0.3.0/ggpmisc/R/moved-to-gginnards.R |only ggpmisc-0.3.0/ggpmisc/R/on-attach.R | 4 ggpmisc-0.3.0/ggpmisc/R/renamed.R |only ggpmisc-0.3.0/ggpmisc/R/stat-dens2d-filter.r | 4 ggpmisc-0.3.0/ggpmisc/R/stat-dens2d-labels.r | 4 ggpmisc-0.3.0/ggpmisc/R/stat-fit-broom-tb.R |only ggpmisc-0.3.0/ggpmisc/R/stat-fit-broom.R | 46 ++++- ggpmisc-0.3.0/ggpmisc/R/stat-fit-deviations.R | 8 ggpmisc-0.3.0/ggpmisc/R/stat-fit-residuals.R | 4 ggpmisc-0.3.0/ggpmisc/R/stat-fmt-tb.R |only ggpmisc-0.3.0/ggpmisc/R/stat-peaks.R | 18 +- ggpmisc-0.3.0/ggpmisc/R/stat-poly-eq.R | 126 ++++++++------ ggpmisc-0.3.0/ggpmisc/R/stat-quadrant-counts.R |only ggpmisc-0.3.0/ggpmisc/R/try-data-frame.R | 6 ggpmisc-0.3.0/ggpmisc/README.md | 191 +++++++++++++++++----- ggpmisc-0.3.0/ggpmisc/build/vignette.rds |binary ggpmisc-0.3.0/ggpmisc/inst/doc/user-guide.R |only ggpmisc-0.3.0/ggpmisc/inst/doc/user-guide.Rmd |only ggpmisc-0.3.0/ggpmisc/inst/doc/user-guide.html |only ggpmisc-0.3.0/ggpmisc/man/figures |only ggpmisc-0.3.0/ggpmisc/man/find_peaks.Rd | 2 ggpmisc-0.3.0/ggpmisc/man/geom_table.Rd |only ggpmisc-0.3.0/ggpmisc/man/ggplot.Rd | 2 ggpmisc-0.3.0/ggpmisc/man/ggpmisc-ggproto.Rd | 22 +- ggpmisc-0.3.0/ggpmisc/man/ggpmisc-package.Rd | 71 +++++--- ggpmisc-0.3.0/ggpmisc/man/moved-to-gginnards.Rd |only ggpmisc-0.3.0/ggpmisc/man/renamed.Rd |only ggpmisc-0.3.0/ggpmisc/man/stat_dens2d_filter.Rd | 4 ggpmisc-0.3.0/ggpmisc/man/stat_dens2d_labels.Rd | 4 ggpmisc-0.3.0/ggpmisc/man/stat_fit_augment.Rd | 4 ggpmisc-0.3.0/ggpmisc/man/stat_fit_deviations.Rd | 4 ggpmisc-0.3.0/ggpmisc/man/stat_fit_glance.Rd | 41 ++++ ggpmisc-0.3.0/ggpmisc/man/stat_fit_residuals.Rd | 4 ggpmisc-0.3.0/ggpmisc/man/stat_fit_tb.Rd |only ggpmisc-0.3.0/ggpmisc/man/stat_fit_tidy.Rd | 4 ggpmisc-0.3.0/ggpmisc/man/stat_fmt_tb.Rd |only ggpmisc-0.3.0/ggpmisc/man/stat_peaks.Rd | 4 ggpmisc-0.3.0/ggpmisc/man/stat_poly_eq.Rd | 119 ++++++++----- ggpmisc-0.3.0/ggpmisc/man/stat_quadrant_counts.Rd |only ggpmisc-0.3.0/ggpmisc/man/try_data_frame.Rd | 4 ggpmisc-0.3.0/ggpmisc/vignettes/user-guide.Rmd |only 75 files changed, 607 insertions(+), 342 deletions(-)
Title: Geometric Morphometrics Analyses
Description: Tools for geometric morphometric analysis. The package includes tools of virtual anthropology to align two not articulated parts belonging to the same specimen, to build virtual cavities as endocast (Profico et al, 2018 <doi:10.1002/ajpa.23493>), and functions to import and export the coordinates of landmarks and 3D paths into 'landmarkAscii' and 'am' format files.
Author: Antonio Profico, Alessio Veneziano, Marina Melchionna, Pasquale Raia
Maintainer: Antonio Profico <antonio.profico@uniroma1.it>
Diff between Arothron versions 1.0.1 dated 2018-06-14 and 1.0.2 dated 2018-07-16
DESCRIPTION | 12 ++++++------ MD5 | 14 ++++++++++---- R/MAs_sets.R |only R/SM_set.R |only R/out.inn.mesh.R | 4 +++- data/MAs_sets.rda |only data/SM_set.rda |only data/datalist | 2 ++ man/MAs_sets.Rd |only man/SM_set.Rd |only man/out.inn.mesh.Rd | 4 +++- 11 files changed, 24 insertions(+), 12 deletions(-)
Title: Access the System Credential Store from R
Description: Platform independent 'API' to access the operating system's
credential store. Currently supports: 'Keychain' on 'macOS', Credential
Store on 'Windows', the Secret Service 'API' on 'Linux', and a simple,
platform independent store implemented with environment variables.
Additional storage back-ends can be added easily.
Author: Gábor Csárdi [aut, cre],
RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between keyring versions 1.0.0 dated 2017-09-09 and 1.1.0 dated 2018-07-16
DESCRIPTION | 15 +++---- MD5 | 53 +++++++++++++++---------- NAMESPACE | 10 ---- NEWS.md | 26 ++++++++++++ R/assertions.R | 27 ++++++++++++- R/backend-env.R | 22 ++++++++++ R/backend-file.R |only R/backend-secret-service.R | 2 R/backend-wincred.R | 66 +++++++++++++++++--------------- R/default_backend.R | 7 +-- R/pass.R | 10 +++- R/utils.R | 20 +++++++++ README.md | 25 +++++++++--- configure | 7 +-- man/backend_env.Rd | 3 - man/backend_file.Rd |only man/backend_macos.Rd | 1 man/backend_secret_service.Rd | 2 man/backend_wincred.Rd | 2 man/backends.Rd | 4 - src/keyring_macos.c | 4 - src/keyring_secret_service.c | 26 ++++++++++++ tests/testthat/RkeyringtestAInJgFhN.lck |only tests/testthat/RkeyringtestJjqIoCFx |only tests/testthat/RkeyringtestJjqIoCFx.lck |only tests/testthat/RkeyringtestUStFddkA.lck |only tests/testthat/RkeyringtestoOrHMNgB.lck |only tests/testthat/RkeyringtestqEwLpisK.lck |only tests/testthat/helper.R | 7 +++ tests/testthat/test-env.R | 9 ---- tests/testthat/test-file.R |only tests/testthat/test-wincred.R | 2 32 files changed, 250 insertions(+), 100 deletions(-)
Title: Reading Annual Financial Reports from Bovespa's DFP, FRE and FCA
System
Description: Reads annual financial reports including assets, liabilities, dividends history, stockholder composition and much more from Bovespa's DFP, FRE and FCA systems <http://www.bmfbovespa.com.br/en_us/products/listed-equities-and-derivatives/equities/listed-companies.htm>.
These are web based interfaces for all financial reports of companies traded at Bovespa. The package is specially designed for large scale data importation, keeping a tabular (long) structure for easier processing.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetDFPData versions 0.7 dated 2018-05-06 and 0.8 dated 2018-07-16
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/gdfpd_GetDFPData.R | 6 +++--- R/gdfpd_fct_get_files_from_bovespa.R | 2 +- build/vignette.rds |binary inst/doc/gdfpd-vignette-introduction.html | 4 ++-- man/gdfpd.GetDFPData.Rd | 4 ++-- 8 files changed, 23 insertions(+), 19 deletions(-)
Title: Visual Data Mining Tools
Description: This provides web-based visual data-mining tools by adding
interactive functions to 'ggplot2' graphics. Brushing and linking between the
multiple plots is one of the main feature of this package. Currently scatter
plots, histograms, parallel coordinate plots and choropleth maps are supported.
Author: Tomokazu Fujino
Maintainer: Tomokazu Fujino <fujino@fwu.ac.jp>
Diff between vdmR versions 0.2.5 dated 2017-11-24 and 0.2.6 dated 2018-07-16
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/vhist.R | 22 ++++++++++++++++++---- R/vlaunch.R | 2 ++ R/vsfuk2012-data.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/vdmR-vignette.pdf |binary man/vhist.Rd | 2 ++ man/vlaunch.Rd | 2 ++ man/vsfuk2012.Rd | 2 +- 11 files changed, 40 insertions(+), 20 deletions(-)
Title: Clinical Trial Simulations
Description: Provides a general framework for clinical trial simulations based
on the Clinical Scenario Evaluation (CSE) approach. The package supports a
broad class of data models (including clinical trials with continuous, binary,
survival-type and count-type endpoints as well as multivariate outcomes that are
based on combinations of different endpoints), analysis strategies and commonly
used evaluation criteria.
Author: Gautier Paux, Alex Dmitrienko.
Maintainer: Gautier Paux <gautier@paux.fr>
Diff between Mediana versions 1.0.6 dated 2018-02-13 and 1.0.7 dated 2018-07-16
DESCRIPTION | 10 - MD5 | 29 +-- NEWS.md | 20 +- R/GenerateReport.R | 10 - R/GenerateReport.default.R | 142 ++++++++-------- build/vignette.rds |binary inst/doc/adjusted-pvalues.Rmd | 2 inst/doc/adjusted-pvalues.html | 30 +-- inst/doc/case-studies.html | 357 +++++++++++++++++++++-------------------- inst/doc/mediana.Rmd | 14 - inst/doc/mediana.html | 101 +++++------ inst/template |only man/GenerateReport.Rd | 2 man/Mediana-package.Rd | 4 vignettes/adjusted-pvalues.Rmd | 2 vignettes/mediana.Rmd | 14 - 16 files changed, 380 insertions(+), 357 deletions(-)
Title: Simple Peak Alignment for Gas-Chromatography Data
Description: Aligns peak based on peak retention times and matches homologous peaks
across samples. The underlying alignment procedure comprises three sequential steps.
(1) Full alignment of samples by linear transformation of retention times to
maximise similarity among homologous peaks (2) Partial alignment of peaks within
a user-defined retention time window to cluster homologous peaks (3) Merging rows
that are likely representing homologous substances (i.e. no sample shows peaks in
both rows and the rows have similar retention time means). The algorithm is described in detail
in Ottensmann et al., 2018 <doi:10.1371/journal.pone.0198311>.
Author: Meinolf Ottensmann [aut, cre],
Martin Stoffel [aut],
Hazel J. Nichols [aut],
Joseph I. Hoffman [aut]
Maintainer: Meinolf Ottensmann <meinolf.ottensmann@web.de>
Diff between GCalignR versions 1.0.1 dated 2018-01-16 and 1.0.2 dated 2018-07-16
GCalignR-1.0.1/GCalignR/inst/doc/GCalignR_How_does_the_Algorithm_works.R |only GCalignR-1.0.1/GCalignR/inst/doc/GCalignR_How_does_the_Algorithm_works.Rmd |only GCalignR-1.0.1/GCalignR/inst/doc/GCalignR_How_does_the_Algorithm_works.html |only GCalignR-1.0.1/GCalignR/vignettes/GCalignR_How_does_the_Algorithm_works.Rmd |only GCalignR-1.0.2/GCalignR/DESCRIPTION | 10 - GCalignR-1.0.2/GCalignR/MD5 | 46 ++++---- GCalignR-1.0.2/GCalignR/NAMESPACE | 1 GCalignR-1.0.2/GCalignR/R/align_chromatograms.R | 12 +- GCalignR-1.0.2/GCalignR/R/check_input.R | 56 +++++----- GCalignR-1.0.2/GCalignR/R/draw_chromatogram.R | 2 GCalignR-1.0.2/GCalignR/R/read_empower2.R |only GCalignR-1.0.2/GCalignR/R/remove_singletons.R | 2 GCalignR-1.0.2/GCalignR/README.md | 52 ++++++--- GCalignR-1.0.2/GCalignR/build/vignette.rds |binary GCalignR-1.0.2/GCalignR/inst/CITATION | 17 +-- GCalignR-1.0.2/GCalignR/inst/doc/GCalignR_How_does_the_Algorithm_work.R |only GCalignR-1.0.2/GCalignR/inst/doc/GCalignR_How_does_the_Algorithm_work.Rmd |only GCalignR-1.0.2/GCalignR/inst/doc/GCalignR_How_does_the_Algorithm_work.html |only GCalignR-1.0.2/GCalignR/inst/doc/GCalignR_step_by_step.Rmd | 3 GCalignR-1.0.2/GCalignR/inst/doc/GCalignR_step_by_step.html | 8 - GCalignR-1.0.2/GCalignR/man/align_chromatograms.Rd | 7 - GCalignR-1.0.2/GCalignR/man/as.data.frame.GCalign.Rd | 3 GCalignR-1.0.2/GCalignR/man/check_input.Rd | 2 GCalignR-1.0.2/GCalignR/man/choose_optimal_reference.Rd | 2 GCalignR-1.0.2/GCalignR/man/peak_interspace.Rd | 2 GCalignR-1.0.2/GCalignR/man/read_empower2.Rd |only GCalignR-1.0.2/GCalignR/man/remove_singletons.Rd | 2 GCalignR-1.0.2/GCalignR/vignettes/GCalignR_How_does_the_Algorithm_work.Rmd |only GCalignR-1.0.2/GCalignR/vignettes/GCalignR_step_by_step.Rmd | 3 29 files changed, 131 insertions(+), 99 deletions(-)
Title: Tools to Conduct Meteorological Normalisation on Air Quality
Data
Description: An integrated set of tools to allow data users to conduct
meteorological normalisation on air quality data. This meteorological
normalisation technique uses predictive random forest models to remove
variation of pollutant concentrations so trends and interventions can be
explored in a robust way. For an example, see Grange et al. (2018)
<doi:10.5194/acp-18-6223-2018>.
Author: Stuart K. Grange [cre, aut]
Maintainer: Stuart K. Grange <stuart.grange@york.ac.uk>
Diff between rmweather versions 0.1.1 dated 2018-05-08 and 0.1.2 dated 2018-07-16
rmweather-0.1.1/rmweather/R/release_questions.R |only rmweather-0.1.1/rmweather/R/stats_re_exports.R |only rmweather-0.1.1/rmweather/man/release_questions.Rd |only rmweather-0.1.2/rmweather/DESCRIPTION | 12 - rmweather-0.1.2/rmweather/MD5 | 44 ++-- rmweather-0.1.2/rmweather/NEWS.md | 18 + rmweather-0.1.2/rmweather/R/base_re_exports.R |only rmweather-0.1.2/rmweather/R/no_global_variable_notes.R | 2 rmweather-0.1.2/rmweather/R/rmw_do_all.R | 38 +++ rmweather-0.1.2/rmweather/R/rmw_normalise.R | 65 ++++-- rmweather-0.1.2/rmweather/R/rmw_predict.R | 50 ++++- rmweather-0.1.2/rmweather/R/rmw_prepare_data.R | 69 ++++-- rmweather-0.1.2/rmweather/R/rmw_train_model.R | 8 rmweather-0.1.2/rmweather/R/rmweather_plotting_functions.R | 42 +++- rmweather-0.1.2/rmweather/README.md | 17 + rmweather-0.1.2/rmweather/data/model_london.rda |binary rmweather-0.1.2/rmweather/man/rmw_do_all.Rd | 21 +- rmweather-0.1.2/rmweather/man/rmw_normalise.Rd | 8 rmweather-0.1.2/rmweather/man/rmw_plot_importance.Rd | 4 rmweather-0.1.2/rmweather/man/rmw_plot_normalised.Rd | 6 rmweather-0.1.2/rmweather/man/rmw_predict.Rd | 16 + rmweather-0.1.2/rmweather/man/rmw_prepare_data.Rd | 8 rmweather-0.1.2/rmweather/man/rmw_train_model.Rd | 6 rmweather-0.1.2/rmweather/tests/testthat/test_01_utilities.R | 2 rmweather-0.1.2/rmweather/tests/testthat/test_02_rmw_functions.R | 100 +++++++++- 25 files changed, 428 insertions(+), 108 deletions(-)
Title: Dyadic Mixed Model for Pedigree Data
Description: Dyadic mixed model analysis with multi-trait responses and
pedigree-based partitioning of individual variation into a range of
environmental and genetic variance components for individual and
maternal effects.
Author: Neville Jackson
Maintainer: Neville Jackson <nanddjackson@bigpond.com>
Diff between dmm versions 2.1-4 dated 2018-06-16 and 2.1-5 dated 2018-07-16
dmm-2.1-4/dmm/R/match.crosseffect.vars.R |only dmm-2.1-4/dmm/R/match.vars.R |only dmm-2.1-4/dmm/R/vc.posdef.R |only dmm-2.1-5/dmm/DESCRIPTION | 8 +-- dmm-2.1-5/dmm/MD5 | 60 ++++++++++++++-------------- dmm-2.1-5/dmm/R/comtopar.specific.R | 6 +- dmm-2.1-5/dmm/R/dmesolve.R | 21 +++++++-- dmm-2.1-5/dmm/R/genericvarvcnames.R | 4 + dmm-2.1-5/dmm/R/genericvcnames.R | 4 + dmm-2.1-5/dmm/R/gls.iter.b.R | 13 +++++- dmm-2.1-5/dmm/R/make.ctable.R | 2 dmm-2.1-5/dmm/R/match.cecov.nonspecific.R |only dmm-2.1-5/dmm/R/match.cecov.specific.R |only dmm-2.1-5/dmm/R/match.var.specific.R |only dmm-2.1-5/dmm/R/print.dmm.R | 3 + dmm-2.1-5/dmm/R/siga.posdef.specific.R | 6 +- dmm-2.1-5/dmm/R/sigatovc.R | 32 +++++++------- dmm-2.1-5/dmm/inst/doc/bugs.txt | 19 ++++++++ dmm-2.1-5/dmm/inst/doc/dmmClassSpecific.pdf |binary dmm-2.1-5/dmm/inst/doc/dmmOverview.pdf |binary dmm-2.1-5/dmm/inst/doc/mods.txt | 18 ++++++++ dmm-2.1-5/dmm/man/condense.dmmarray.Rd | 3 - dmm-2.1-5/dmm/man/condense.dmmblockarray.Rd | 5 +- dmm-2.1-5/dmm/man/dmm-internal.Rd | 13 ++---- dmm-2.1-5/dmm/man/dmm-package.Rd | 7 +-- dmm-2.1-5/dmm/man/dmm.Rd | 17 +++++-- dmm-2.1-5/dmm/man/gprint.Rd | 3 - dmm-2.1-5/dmm/man/gprint.dmm.Rd | 3 - dmm-2.1-5/dmm/man/plot.dmm.Rd | 4 + dmm-2.1-5/dmm/man/print.dmm.Rd | 10 ++-- dmm-2.1-5/dmm/man/print.gresponse.dmm.Rd | 3 - dmm-2.1-5/dmm/man/print.gsummary.dmm.Rd | 3 - dmm-2.1-5/dmm/man/print.summary.dmm.Rd | 3 - dmm-2.1-5/dmm/man/summary.gresponse.dmm.Rd | 3 - 34 files changed, 181 insertions(+), 92 deletions(-)
Title: Weighted Regression for Water Quality Evaluation in Tidal Waters
Description: An adaptation for estuaries (tidal waters) of weighted regression
on time, discharge, and season to evaluate trends in water quality time series.
Author: Marcus W. Beck [aut, cre]
Maintainer: Marcus W. Beck <marcusb@sccwrp.org>
Diff between WRTDStidal versions 1.1.0 dated 2017-06-23 and 1.1.1 dated 2018-07-16
DESCRIPTION | 16 ++++++++-------- MD5 | 14 +++++++++----- NAMESPACE | 13 ++++++++++++- R/globalVariables.R | 5 +++-- R/kendallSeasonalTrendTest.R |only R/kendallTrendTest.R |only R/wrtdstrnd_sk.R | 5 ++--- man/kendallSeasonalTrendTest.Rd |only man/kendallTrendTest.Rd |only man/wrtdstrnd_sk.Rd | 4 ++-- 10 files changed, 36 insertions(+), 21 deletions(-)
Title: Spatio-Temporal Under-Five Mortality Methods for Estimation
Description: Provides methods for estimating, projecting, and plotting spatio-temporal
under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>.
Author: Bryan D Martin [cre, aut],
Zehang R Li [aut],
Yuan Hsiao [aut],
Jessica Godwin [aut],
Jon Wakefield [aut],
Samuel J Clark [aut]
Maintainer: Bryan D Martin <bmartin6@uw.edu>
Diff between SUMMER versions 0.2.0 dated 2018-04-20 and 0.2.1 dated 2018-07-16
DESCRIPTION | 13 ++++++------- MD5 | 12 +++++++----- R/fitINLA.R | 2 +- R/fitspace.R | 23 +++++++++++++++-------- R/simRandom.R |only build/vignette.rds |binary man/fitSpace.Rd | 7 ++++++- man/rst.Rd |only 8 files changed, 35 insertions(+), 22 deletions(-)
Title: Randomer Forest
Description: Random Forester (RerF) is an algorithm developed by Tomita
(2016) <arXiv:1506.03410v2> which is similar to Random Forest - Random
Combination (Forest-RC) developed by Breiman (2001)
<doi:10.1023/A:1010933404324>. Random Forests create axis-parallel, or
orthogonal trees. That is, the feature space is recursively split along
directions parallel to the axes of the feature space. Thus, in cases in
which the classes seem inseparable along any single dimension, Random
Forests may be suboptimal. To address this, Breiman also proposed and
characterized Forest-RC, which uses linear combinations of coordinates
rather than individual coordinates, to split along. This package,
'rerf', implements RerF which is similar to Forest-RC. The difference
between the two algorithms is where the random linear combinations
occur: Forest-RC combines features at the per tree level whereas RerF
takes linear combinations of coordinates at every node in the tree.
Author: James Browne [aut, cre],
Tyler Tomita [aut],
Joshua Vogelstein [ths]
Maintainer: James Browne <jbrowne6@jhu.edu>
Diff between rerf versions 1.1.1 dated 2018-07-10 and 1.1.2 dated 2018-07-16
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: A Package for Graphical Modelling in R
Description: The 'gRbase' package provides general features
which are used by other graphical modelling packages, in particular
by the packages 'gRain', 'gRim' and 'gRc'.
'gRbase' contains several data sets relevant for use in connection with
graphical models. Almost all data sets used in the book Graphical
Models with R (2012) are contained in 'gRbase'.
'gRbase' implements several graph algorithms (based mainly on
representing graphs as adjacency matrices - either in the form
of a standard matrix or a sparse matrix). Some graph
algorithms are:
(i) maximum cardinality search (for marked and unmarked graphs).
(ii) moralize.
(iii) triangulate.
(iv) junction tree.
'gRbase' facilitates array operations,
'gRbase' implements functions for testing for conditional independence.
'gRbase' illustrates how hierarchical log-linear models may be
implemented and describes concept of graphical meta
data. These features, however, are not maintained anymore and
remains in 'gRbase' only because there exists a paper describing
these facilities: A Common Platform for Graphical Models in R:
The 'gRbase' Package, Journal of Statistical Software, Vol 14,
No 17, 2005.
NOTICE Proper functionality of 'gRbase' requires that the packages graph,
'Rgraphviz' and 'RBGL' are installed from 'bioconductor'; for
installation instructions please refer to the web page given below.
Author: Søren Højsgaard <sorenh@math.aau.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between gRbase versions 1.8-3 dated 2017-03-20 and 1.8-3.1 dated 2018-07-16
DESCRIPTION | 6 ++--- MD5 | 52 ++++++++++++++++++++++---------------------- data/BodyFat.RData |binary data/Nutrimouse.rda |binary data/ashtrees.RData |binary data/breastcancer.rda |binary data/cad1.RData |binary data/cad2.RData |binary data/carcass.RData |binary data/carcassall.RData |binary data/chestSim1000.RData |binary data/chestSim10000.rda |binary data/chestSim100000.rda |binary data/chestSim500.RData |binary data/chestSim50000.rda |binary data/dietox.RData |binary data/dumping.RData |binary data/lizard.RData |binary data/math.RData |binary data/mathmark.RData |binary data/mildew.RData |binary data/milkcomp.RData |binary data/milkcomp1.RData |binary data/rats.RData |binary data/reinis.RData |binary data/wine.RData |binary src/_t_array_properties.cpp | 2 - 27 files changed, 30 insertions(+), 30 deletions(-)
Title: Visualization and Analysis of Statistical Measures of Confidence
Description: Enables: (1) plotting two-dimensional confidence regions, and (2) calculating
confidence intervals and the associated actual coverage for binomial proportions. Both
are given in greater detail next. (1) Plots the two-dimensional confidence region for
probability distribution parameters (supported distribution suffixes: gamma, invgauss,
llogis, lnorm, norm, unif, weibull) corresponding to a user given 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 two-dimensional confidence regions given by Jaeger (2016)
<doi:10.1080/00031305.2016.1182946>. (2) 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().
Author: Christopher Weld [aut, cre] (<https://orcid.org/0000-0001-5902-9738>),
Hayeon Park [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 1.2 dated 2018-05-14 and 1.3 dated 2018-07-16
DESCRIPTION | 6 MD5 | 16 +- R/coversim.R | 46 ++++- R/crplot.R | 403 +++++++++++++++++++++++++++++++++++++++------------ inst/doc/crplot.R | 30 +++ inst/doc/crplot.Rmd | 65 +++++++- inst/doc/crplot.html | 100 ++++++++++-- man/crplot.Rd | 9 + vignettes/crplot.Rmd | 65 +++++++- 9 files changed, 586 insertions(+), 154 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-28 0.8.10
2018-01-08 0.8.9
2017-01-09 0.8.8
2016-11-05 0.8.7
2016-03-08 0.8.6
2016-02-26 0.8.5
2015-08-03 0.8.2
2015-03-06 0.7.8
2015-03-05 0.7.7
2014-12-09 0.7.2
2014-11-20 0.7.0
2014-08-13 0.6.0
2014-06-06 0.5.5
2014-04-23 0.5.2
2014-03-03 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-11-12 0.1.5
2015-03-24 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-28 0.0.4
2018-01-08 0.0.3
2014-08-13 0.0.2
2014-03-03 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-03 1.1
2017-12-18 1.0
2016-05-10 0.3
2016-04-03 0.2
2016-03-12 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-11 0.2
2016-11-12 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-04 0.6
2017-07-18 0.5
2016-10-10 0.4
2016-09-26 0.3
2016-09-09 0.2
2016-08-09 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-11 0.9.4
2016-09-26 0.9.3
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2016-08-01 0.7
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2016-06-17 0.5
2015-11-18 0.4
2015-11-03 0.3
2015-10-22 0.2
2015-10-14 0.1