Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>;
- net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>;
- measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>;
- ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>;
- partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Bruggemann, 2014) <DOI:10.1002/cem.2569>;
- split direct and indirect evidence to check consistency (Dias et al., 2010) <DOI:10.1002/sim.3767>;
- automated drawing of network graphs described in Rücker & Schwarzer (2016) <DOI:10.1002/jrsm.1143>.
Author: Gerta Rücker [aut],
Guido Schwarzer [aut, cre],
Ulrike Krahn [aut],
Jochem König [aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 0.9-3 dated 2017-03-12 and 0.9-4 dated 2017-04-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 10 ++++++++++ R/netmeasures.R | 3 +++ R/netsplit.R | 5 +++-- 5 files changed, 24 insertions(+), 10 deletions(-)
Title: Data Validation Infrastructure
Description: Declare data validation rules and data quality indicators; confront
data with them and analyze or visualize the results. The package supports
rules that are per-field, in-record, cross-record or cross-dataset. Rules
can be automatically analyzed for rule type and connectivity.
Author: Mark van der Loo [cre, aut],
Edwin de Jonge [aut],
Paul Hsieh [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between validate versions 0.1.5 dated 2016-06-24 and 0.1.7 dated 2017-04-07
DESCRIPTION | 10 +++--- MD5 | 40 ++++++++++++++------------- NAMESPACE | 5 ++- NEWS | 10 ++++++ R/confrontation.R | 5 ++- R/expressionset.R | 13 ++++++++- R/functions.R | 32 +++++++++++++--------- R/indicator.R | 5 --- R/parse.R | 24 +++++++++++----- R/rule.R | 2 - R/validate_pkg.R | 2 - build/vignette.rds |binary inst/doc/intro.Rmd | 2 - inst/doc/intro.html | 19 ++++++++----- inst/doc/rule-files.html | 17 +++++++---- man/nofun.Rd |only man/syntax.Rd | 59 +++++++---------------------------------- man/validate_extend.Rd | 7 ++++ man/voptions.Rd | 12 +++++--- src/R_register_native.c |only tests/testthat/testValidator.R | 13 +++++++++ vignettes/intro.Rmd | 2 - 22 files changed, 155 insertions(+), 124 deletions(-)
Title: 'Htmlwidget' for 'Kerry Rodden' 'd3.js' Sequence Sunburst
Description: Make interactive 'd3.js' sequence sunburst diagrams in R with the
convenience and infrastructure of an 'htmlwidget'.
Author: Mike Bostock [aut, cph] (d3.js library, http://d3js.org),
Kerry Rodden [aut, cph] (sequences library in htmlwidgets/lib,
https://gist.github.com/kerryrodden/7090426),
Kent Russell [aut, cre] (R interface),
Florian Breitwieser [ctb] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between sunburstR versions 0.6.3 dated 2016-10-15 and 0.6.4 dated 2017-04-07
DESCRIPTION | 11 +++--- LICENSE | 2 - MD5 | 19 ++++++------ NEWS.md | 10 ++++++ R/sunburst.R | 8 ++++- inst/examples/example_baseball_shiny.R |only inst/examples/example_baseball_shiny.Rmd |only inst/examples/example_treemap.R |only inst/htmlwidgets/sunburst.js | 49 ++++++++++++++++++------------- man/add_shiny.Rd | 1 man/sunburst-shiny.Rd | 3 - man/sunburst.Rd | 39 +++++++++++++++++++++--- 12 files changed, 100 insertions(+), 42 deletions(-)
Title: El Nino/Southern Oscillation (ENSO) Index
Description: Downloads Southern Oscillation Index from <https://www.ncdc.noaa.gov/teleconnections/enso/indicators/soi/> and Oceanic Nino Index data from <http://www.cpc.ncep.noaa.gov/products/analysis_monitoring/ensostuff/detrend.nino34.ascii.txt>.
Author: Sam Albers [aut, cre]
Maintainer: Sam Albers <sam.albers@gmail.com>
Diff between rsoi versions 0.1.0 dated 2017-04-04 and 0.2.1 dated 2017-04-07
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/download-enso.R | 2 +- README.md | 9 +++++++-- man/download_enso.Rd | 2 +- tests/testthat/test_download_soi.R | 1 + 6 files changed, 20 insertions(+), 14 deletions(-)
Title: Plot Raster Map Tiles from Open Street Map and Other Sources
Description: Download and plot Open Street Map <http://www.openstreetmap.org/>,
Bing Maps <http://www.bing.com/maps> and other tiled map sources in a way
that works seamlessly with plotting from the 'sp' package. Use to create
high-resolution basemaps and add hillshade to vector-based maps.
Author: Dewey Dunnington [aut, cre],
Timothée Giraud [ctb]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between rosm versions 0.2.1 dated 2017-04-01 and 0.2.2 dated 2017-04-07
DESCRIPTION | 8 +- MD5 | 16 ++-- NAMESPACE | 2 R/1_tiles.R | 9 +- R/cachedir.R |only R/commonplot.R | 2 R/extract.R | 2 R/osmplot.R | 27 +++---- man/set_default_cachedir.Rd |only tests/manual/tests.R | 152 ++++++++++++++++++++++++++++++++++++++++++++ 10 files changed, 186 insertions(+), 32 deletions(-)
Title: Scale Bar, North Arrow, and Pretty Margins in R
Description: Automates the process of creating a scale bar and north arrow in
any package that uses base graphics to plot in R. Bounding box tools help find
and manipulate extents. Finally, there is a function to automate the process
of setting margins, plotting the map, scale bar, and north arrow, and resetting
graphic parameters upon completion.
Author: Dewey Dunnington <dewey@fishandwhistle.net>
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between prettymapr versions 0.2 dated 2017-04-01 and 0.2.1 dated 2017-04-07
DESCRIPTION | 8 +-- MD5 | 11 ++-- NAMESPACE | 2 R/geocode.R | 93 ++++++++++++++++++++++++++++++++++++------ man/geocode.Rd | 10 +++- man/get_default_geocoder.Rd |only tests/testthat/test_geocode.R | 56 +++++++++++++++++++++++-- 7 files changed, 150 insertions(+), 30 deletions(-)
Title: Item Response Theory via Shiny
Description: Interactive shiny application for running Item Response Theory
analysis. Provides graphics for characteristic and information curves.
Author: W. Kyle Hamilton <kyle.hamilton@gmail.com>, Atsushi Mizumoto
<atsushi@mizumot.com>
Maintainer: W. Kyle Hamilton <kyle.hamilton@gmail.com>
Diff between IRTShiny versions 1.1 dated 2015-09-20 and 1.2 dated 2017-04-07
DESCRIPTION | 14 +++++++------- MD5 | 6 +++--- NEWS | 6 ++++++ inst/IRT/ui.R | 21 ++++++++++++++------- 4 files changed, 30 insertions(+), 17 deletions(-)
Title: A Flexible Container to Transport and Manipulate Data and
Associated Resources
Description: Provides a flexible container to transport and
manipulate complex sets of data. These data may consist of multiple data files and
associated meta data and ancillary files. Individual data objects have
associated system level meta data, and data files are linked together using
the OAI-ORE standard resource map which describes the relationships between the files.
The OAI-ORE standard is described at <https://www.openarchives.org/ore>. Data packages
can be serialized and transported as structured files that have been created following
the BagIt specification. The BagIt specification is described at
<https://tools.ietf.org/html/draft-kunze-bagit-08>.
Author: Matthew B. Jones [aut, cre],
Peter Slaughter [aut],
Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between datapack versions 1.0.1 dated 2016-05-20 and 1.2.0 dated 2017-04-07
DESCRIPTION | 14 MD5 | 118 +++--- NAMESPACE | 3 NEWS | 34 + R/Constants.R |only R/DataObject.R | 68 +++ R/DataPackage.R | 411 +++++++++++++++++++++-- R/ResourceMap.R | 28 + R/SystemMetadata.R | 84 ++++ R/zzz.R |only README.md | 14 build/vignette.rds |binary inst/doc/datapack-overview.R | 54 ++- inst/doc/datapack-overview.Rmd | 245 +++++++++---- inst/doc/datapack-overview.html | 189 +++++++--- inst/extdata/filter-species.R |only inst/extdata/pkg-example |only inst/extdata/sample-data-filtered.csv |only inst/testfiles/sysmeta-v2-repfalse-zero-reps.xml |only inst/testfiles/sysmeta-v2-repfalse.xml |only inst/testfiles/sysmeta-v2.xml | 4 inst/tests/test.ResourceMap.R | 2 inst/tests/test.SystemMetadata.R | 82 +++- inst/tests/test_DataObject.R | 2 inst/tests/test_DataPackage.R | 222 +++++++++++- man/DataObject-class.Rd | 3 man/DataObject-initialize.Rd | 7 man/DataPackage-class.Rd | 52 ++ man/DataPackage-initialize.Rd | 3 man/ResourceMap-class.Rd | 3 man/ResourceMap-initialize.Rd | 3 man/SystemMetadata-class.Rd | 6 man/SystemMetadata-initialize.Rd | 10 man/SystemMetadata.Rd | 2 man/addAccessRule.Rd | 3 man/addData.Rd | 1 man/canRead.Rd | 1 man/clearAccessPolicy.Rd |only man/containsId.Rd | 1 man/createFromTriples.Rd | 5 man/datapack-deprecated.Rd |only man/datapack.Rd | 2 man/describeWorkflow.Rd |only man/dmsg.Rd | 1 man/freeResourceMap.Rd | 1 man/getData.Rd | 2 man/getFormatId.Rd | 2 man/getIdentifier.Rd | 2 man/getIdentifiers.Rd | 1 man/getMember.Rd | 1 man/getRelationships.Rd | 5 man/getSize.Rd | 1 man/hasAccessRule.Rd | 1 man/insertRelationship.Rd | 1 man/parseSystemMetadata.Rd | 1 man/recordDerivation.Rd | 7 man/removeMember.Rd | 1 man/serializePackage.Rd | 3 man/serializeRDF.Rd | 1 man/serializeSystemMetadata.Rd | 1 man/serializeToBagIt.Rd | 3 man/setPublicAccess.Rd | 2 man/validate.Rd | 1 vignettes/datapack-overview.Rmd | 245 +++++++++---- 64 files changed, 1509 insertions(+), 450 deletions(-)
Title: Bayesian Object Oriented Modeling
Description: A C++ library for Bayesian modeling, with an emphasis on
Markov chain Monte Carlo. Although boom contains a few R utilities
(mainly plotting functions), its primary purpose is to install the
BOOM C++ library on your system so that other packages can link
against it.
Author: Steven L. Scott is the sole author and creator of the BOOM
project. Some code in the BOOM libraries has been modified from
other open source projects. These include Cephes (obtained from
Netlib, written by Stephen L. Moshier), NEWUOA (M.J.D Powell,
obtained from Powell's web site), and a modified version of the R
math libraries (R core development team). Original copyright
notices have been maintained in all source files. In these cases,
copyright claimed by Steven L. Scott is limited to modifications
made to the original code.
Maintainer: Steve Scott <stevescott@google.com>
Diff between Boom versions 0.5 dated 2016-08-18 and 0.6 dated 2017-04-07
Boom-0.5/Boom/inst/include/Models/CompositeVectorModel.hpp |only Boom-0.5/Boom/inst/include/Models/ProductModel.hpp |only Boom-0.5/Boom/inst/include/Models/StateSpace/StateModels/LocalLinearTrendMeanRevertingSlope.hpp |only Boom-0.5/Boom/inst/include/distributions/ks.hpp |only Boom-0.5/Boom/src/Models/CompositeVectorModel.cpp |only Boom-0.5/Boom/src/Models/StateSpace/StateModels/LocalLinearTrendMeanRevertingSlope.cpp |only Boom-0.6/Boom/DESCRIPTION | 8 Boom-0.6/Boom/MD5 | 721 ++-- Boom-0.6/Boom/NAMESPACE | 8 Boom-0.6/Boom/R/compare.vector.distribution.R | 5 Boom-0.6/Boom/R/dirichlet.R |only Boom-0.6/Boom/R/dmvn.R |only Boom-0.6/Boom/R/format.R |only Boom-0.6/Boom/R/inverse.wishart.R |only Boom-0.6/Boom/R/lmgamma.R |only Boom-0.6/Boom/R/mscan.R |only Boom-0.6/Boom/R/plot.many.ts.R | 15 Boom-0.6/Boom/R/prior_specification.R | 148 - Boom-0.6/Boom/R/rmvn.R |only Boom-0.6/Boom/R/suggest_burn_log_likelihood.R | 13 Boom-0.6/Boom/R/thin.matrix.R |only Boom-0.6/Boom/inst/include/LinAlg/Array.hpp | 187 - Boom-0.6/Boom/inst/include/LinAlg/Matrix.hpp | 7 Boom-0.6/Boom/inst/include/LinAlg/SpdMatrix.hpp | 12 Boom-0.6/Boom/inst/include/LinAlg/Vector.hpp | 14 Boom-0.6/Boom/inst/include/LinAlg/VectorView.hpp | 2 Boom-0.6/Boom/inst/include/Models/Bart/Bart.hpp | 10 Boom-0.6/Boom/inst/include/Models/Bart/PosteriorSamplers/BartPosteriorSampler.hpp | 4 Boom-0.6/Boom/inst/include/Models/Bart/PosteriorSamplers/GaussianBartPosteriorSampler.hpp | 6 Boom-0.6/Boom/inst/include/Models/Bart/PosteriorSamplers/LogitBartPosteriorSampler.hpp | 6 Boom-0.6/Boom/inst/include/Models/Bart/PosteriorSamplers/PoissonBartPosteriorSampler.hpp | 6 Boom-0.6/Boom/inst/include/Models/Bart/PosteriorSamplers/ProbitBartPosteriorSampler.hpp | 4 Boom-0.6/Boom/inst/include/Models/BetaModel.hpp | 26 Boom-0.6/Boom/inst/include/Models/DataTypes.hpp | 16 Boom-0.6/Boom/inst/include/Models/DirichletModel.hpp | 3 Boom-0.6/Boom/inst/include/Models/DoubleModel.hpp | 52 Boom-0.6/Boom/inst/include/Models/ExponentialModel.hpp | 29 Boom-0.6/Boom/inst/include/Models/FiniteMixtureModel.hpp | 32 Boom-0.6/Boom/inst/include/Models/GammaModel.hpp | 75 Boom-0.6/Boom/inst/include/Models/GaussianModelBase.hpp | 4 Boom-0.6/Boom/inst/include/Models/Glm/AggregatedRegressionModel.hpp | 5 Boom-0.6/Boom/inst/include/Models/Glm/BinomialLogitModel.hpp | 29 Boom-0.6/Boom/inst/include/Models/Glm/BinomialProbitModel.hpp | 2 Boom-0.6/Boom/inst/include/Models/Glm/LogisticRegressionModel.hpp | 31 Boom-0.6/Boom/inst/include/Models/Glm/MultinomialLogitModel.hpp | 6 Boom-0.6/Boom/inst/include/Models/Glm/MvReg2.hpp | 1 Boom-0.6/Boom/inst/include/Models/Glm/MvnGivenXandSigma.hpp | 123 Boom-0.6/Boom/inst/include/Models/Glm/OrdinalCutpointModel.hpp | 54 Boom-0.6/Boom/inst/include/Models/Glm/PoissonRegressionData.hpp | 4 Boom-0.6/Boom/inst/include/Models/Glm/PoissonRegressionModel.hpp | 12 Boom-0.6/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.hpp | 172 - Boom-0.6/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitSamplerRwm.hpp | 2 Boom-0.6/Boom/inst/include/Models/Glm/PosteriorSamplers/MLVS.hpp | 29 Boom-0.6/Boom/inst/include/Models/Glm/PosteriorSamplers/MLVS_data_imputer.hpp | 24 Boom-0.6/Boom/inst/include/Models/Glm/PosteriorSamplers/MultinomialLogitCompleteDataSuf.hpp | 49 Boom-0.6/Boom/inst/include/Models/Glm/PosteriorSamplers/NonconjugateRegressionSampler.hpp |only Boom-0.6/Boom/inst/include/Models/Glm/PosteriorSamplers/NormalMixtureApproximation.hpp | 109 Boom-0.6/Boom/inst/include/Models/Glm/PosteriorSamplers/PoissonDataImputer.hpp | 17 Boom-0.6/Boom/inst/include/Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.hpp | 60 Boom-0.6/Boom/inst/include/Models/Glm/PosteriorSamplers/QuantileRegressionPosteriorSampler.hpp |only Boom-0.6/Boom/inst/include/Models/Glm/PosteriorSamplers/poisson_mixture_approximation_table.hpp | 3 Boom-0.6/Boom/inst/include/Models/Glm/ProbitRegression.hpp | 1 Boom-0.6/Boom/inst/include/Models/Glm/QuantileRegressionModel.hpp |only Boom-0.6/Boom/inst/include/Models/Glm/RegressionModel.hpp | 15 Boom-0.6/Boom/inst/include/Models/Glm/TRegression.hpp | 4 Boom-0.6/Boom/inst/include/Models/Glm/VariableSelectionPrior.hpp | 4 Boom-0.6/Boom/inst/include/Models/Glm/WeightedRegressionModel.hpp | 26 Boom-0.6/Boom/inst/include/Models/Glm/ZeroInflatedPoissonRegression.hpp | 26 Boom-0.6/Boom/inst/include/Models/HMM/PosteriorSamplers/HmmPosteriorSampler.hpp | 2 Boom-0.6/Boom/inst/include/Models/IRT/DafePcrRwm.hpp | 31 Boom-0.6/Boom/inst/include/Models/IRT/Item.hpp | 11 Boom-0.6/Boom/inst/include/Models/IRT/PartialCreditModel.hpp | 4 Boom-0.6/Boom/inst/include/Models/IRT/SubjectSliceSampler.hpp | 9 Boom-0.6/Boom/inst/include/Models/LognormalModel.hpp | 7 Boom-0.6/Boom/inst/include/Models/Mixtures/DirichletProcessMvnModel.hpp | 9 Boom-0.6/Boom/inst/include/Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.hpp | 49 Boom-0.6/Boom/inst/include/Models/ModelTypes.hpp | 57 Boom-0.6/Boom/inst/include/Models/MultinomialModel.hpp | 3 Boom-0.6/Boom/inst/include/Models/MvnBase.hpp | 76 Boom-0.6/Boom/inst/include/Models/MvnGivenSigma.hpp | 19 Boom-0.6/Boom/inst/include/Models/MvnModel.hpp | 3 Boom-0.6/Boom/inst/include/Models/MvtModel.hpp | 49 Boom-0.6/Boom/inst/include/Models/Nonparametric/BayesRules.hpp | 1 Boom-0.6/Boom/inst/include/Models/ParamTypes.hpp | 13 Boom-0.6/Boom/inst/include/Models/PointProcess/BoundedPoissonProcessSimulator.hpp | 3 Boom-0.6/Boom/inst/include/Models/PointProcess/CosinePoissonProcess.hpp | 4 Boom-0.6/Boom/inst/include/Models/PointProcess/HomogeneousPoissonProcess.hpp | 4 Boom-0.6/Boom/inst/include/Models/PointProcess/MarkovModulatedPoissonProcess.hpp | 4 Boom-0.6/Boom/inst/include/Models/PointProcess/PoissonClusterProcess.hpp | 11 Boom-0.6/Boom/inst/include/Models/PointProcess/PoissonProcess.hpp | 3 Boom-0.6/Boom/inst/include/Models/PointProcess/WeeklyCyclePoissonProcess.hpp | 10 Boom-0.6/Boom/inst/include/Models/Policies/CompositeParamPolicy.hpp | 11 Boom-0.6/Boom/inst/include/Models/Policies/ManyParamPolicy.hpp | 4 Boom-0.6/Boom/inst/include/Models/Policies/NonparametricParamPolicy.hpp | 8 Boom-0.6/Boom/inst/include/Models/Policies/NullParamPolicy.hpp | 11 Boom-0.6/Boom/inst/include/Models/Policies/ParamPolicy_1.hpp | 8 Boom-0.6/Boom/inst/include/Models/Policies/ParamPolicy_2.hpp | 4 Boom-0.6/Boom/inst/include/Models/Policies/ParamPolicy_3.hpp | 4 Boom-0.6/Boom/inst/include/Models/Policies/ParamPolicy_4.hpp | 4 Boom-0.6/Boom/inst/include/Models/PosteriorSamplers/GenericGaussianVarianceSampler.hpp | 3 Boom-0.6/Boom/inst/include/Models/PosteriorSamplers/Imputer.hpp | 547 ++- Boom-0.6/Boom/inst/include/Models/PosteriorSamplers/PoissonGammaPosteriorSampler.hpp | 3 Boom-0.6/Boom/inst/include/Models/PosteriorSamplers/PosteriorSampler.hpp | 41 Boom-0.6/Boom/inst/include/Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.hpp | 29 Boom-0.6/Boom/inst/include/Models/ProductVectorModel.hpp |only Boom-0.6/Boom/inst/include/Models/ScaledChisqModel.hpp | 4 Boom-0.6/Boom/inst/include/Models/SpdData.hpp | 106 Boom-0.6/Boom/inst/include/Models/StateSpace/AggregatedStateSpaceRegression.hpp | 7 Boom-0.6/Boom/inst/include/Models/StateSpace/Filters/ScalarKalmanStorage.hpp | 5 Boom-0.6/Boom/inst/include/Models/StateSpace/Filters/SparseMatrix.hpp | 240 + Boom-0.6/Boom/inst/include/Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.hpp | 44 Boom-0.6/Boom/inst/include/Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.hpp | 8 Boom-0.6/Boom/inst/include/Models/StateSpace/StateModels/ArStateModel.hpp | 10 Boom-0.6/Boom/inst/include/Models/StateSpace/StateModels/DynamicRegressionStateModel.hpp | 6 Boom-0.6/Boom/inst/include/Models/StateSpace/StateModels/LocalLevelStateModel.hpp | 8 Boom-0.6/Boom/inst/include/Models/StateSpace/StateModels/LocalLinearTrend.hpp | 8 Boom-0.6/Boom/inst/include/Models/StateSpace/StateModels/RandomWalkHolidayStateModel.hpp | 8 Boom-0.6/Boom/inst/include/Models/StateSpace/StateModels/SeasonalStateModel.hpp | 17 Boom-0.6/Boom/inst/include/Models/StateSpace/StateModels/SemilocalLinearTrend.hpp |only Boom-0.6/Boom/inst/include/Models/StateSpace/StateModels/StateModel.hpp | 21 Boom-0.6/Boom/inst/include/Models/StateSpace/StateModels/StudentLocalLinearTrend.hpp | 2 Boom-0.6/Boom/inst/include/Models/StateSpace/StateModels/TrigStateModel.hpp | 14 Boom-0.6/Boom/inst/include/Models/StateSpace/StateSpaceLogitModel.hpp | 131 Boom-0.6/Boom/inst/include/Models/StateSpace/StateSpaceModel.hpp | 61 Boom-0.6/Boom/inst/include/Models/StateSpace/StateSpaceModelBase.hpp | 621 +++- Boom-0.6/Boom/inst/include/Models/StateSpace/StateSpaceNormalMixture.hpp | 2 Boom-0.6/Boom/inst/include/Models/StateSpace/StateSpacePoissonModel.hpp | 107 Boom-0.6/Boom/inst/include/Models/StateSpace/StateSpaceRegressionModel.hpp | 44 Boom-0.6/Boom/inst/include/Models/StateSpace/StateSpaceStudentRegressionModel.hpp | 70 Boom-0.6/Boom/inst/include/Models/Sufstat.hpp | 1 Boom-0.6/Boom/inst/include/Models/TruncatedGammaModel.hpp | 32 Boom-0.6/Boom/inst/include/Models/UniformModel.hpp | 6 Boom-0.6/Boom/inst/include/Models/VectorModel.hpp | 81 Boom-0.6/Boom/inst/include/Models/WishartModel.hpp | 10 Boom-0.6/Boom/inst/include/Models/ZeroInflatedGammaModel.hpp | 35 Boom-0.6/Boom/inst/include/Models/ZeroInflatedLognormalModel.hpp | 16 Boom-0.6/Boom/inst/include/Models/ZeroInflatedPoissonModel.hpp | 2 Boom-0.6/Boom/inst/include/Models/ZeroMeanGaussianModel.hpp | 3 Boom-0.6/Boom/inst/include/Samplers/MetropolisHastings.hpp | 6 Boom-0.6/Boom/inst/include/Samplers/MoveAccounting.hpp | 28 Boom-0.6/Boom/inst/include/Samplers/ScalarSliceSampler.hpp | 4 Boom-0.6/Boom/inst/include/Samplers/SliceSampler.hpp | 4 Boom-0.6/Boom/inst/include/Samplers/TIM.hpp | 3 Boom-0.6/Boom/inst/include/Samplers/UnivariateSliceSampler.hpp | 18 Boom-0.6/Boom/inst/include/TargetFun/LogPost.hpp | 5 Boom-0.6/Boom/inst/include/TargetFun/TargetFun.hpp | 15 Boom-0.6/Boom/inst/include/cpputil/ParamFileIoManager.hpp | 6 Boom-0.6/Boom/inst/include/cpputil/ProgramOptions.hpp | 7 Boom-0.6/Boom/inst/include/cpputil/Ptr.hpp | 14 Boom-0.6/Boom/inst/include/cpputil/RefCounted.hpp | 59 Boom-0.6/Boom/inst/include/cpputil/ThreadTools.hpp |only Boom-0.6/Boom/inst/include/cpputil/stream.hpp | 2 Boom-0.6/Boom/inst/include/cpputil/string_utils.hpp | 18 Boom-0.6/Boom/inst/include/distributions.hpp | 43 Boom-0.6/Boom/inst/include/distributions/BoundedAdaptiveRejectionSampler.hpp | 4 Boom-0.6/Boom/inst/include/distributions/DoublyBoundedAdaptiveRejectionSampler.hpp | 4 Boom-0.6/Boom/inst/include/distributions/inverse_gaussian.hpp | 19 Boom-0.6/Boom/inst/include/numopt.hpp | 279 + Boom-0.6/Boom/inst/include/numopt/Integral.hpp | 4 Boom-0.6/Boom/inst/include/numopt/NelderMead.hpp | 3 Boom-0.6/Boom/inst/include/r_interface/boom_r_tools.hpp | 55 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Boom-0.6/Boom/man/suggest.burn.log.likelihood.Rd | 10 Boom-0.6/Boom/man/thin.matrix.Rd |only Boom-0.6/Boom/man/traceproduct.Rd |only Boom-0.6/Boom/man/wishart.Rd |only Boom-0.6/Boom/src/Bmath/d1mach.cpp | 4 Boom-0.6/Boom/src/Bmath/fprec.cpp | 2 Boom-0.6/Boom/src/Bmath/fround.cpp | 2 Boom-0.6/Boom/src/Bmath/gamma_cody.cpp | 4 Boom-0.6/Boom/src/Bmath/i1mach.cpp | 4 Boom-0.6/Boom/src/Bmath/mlutils.cpp | 13 Boom-0.6/Boom/src/Bmath/pf.cpp | 2 Boom-0.6/Boom/src/Bmath/pgamma.cpp | 7 Boom-0.6/Boom/src/Bmath/pnorm.cpp | 5 Boom-0.6/Boom/src/Bmath/pnt.cpp | 16 Boom-0.6/Boom/src/Bmath/polygamma.cpp | 8 Boom-0.6/Boom/src/Bmath/qbinom.cpp | 4 Boom-0.6/Boom/src/Bmath/qf.cpp | 2 Boom-0.6/Boom/src/Bmath/qgamma.cpp | 2 Boom-0.6/Boom/src/Bmath/qhyper.cpp | 2 Boom-0.6/Boom/src/Bmath/qnbinom.cpp | 5 Boom-0.6/Boom/src/Bmath/qpois.cpp | 5 Boom-0.6/Boom/src/Bmath/rbeta.cpp | 4 Boom-0.6/Boom/src/Bmath/rgamma.cpp | 24 Boom-0.6/Boom/src/Bmath/rloggamma_small_alpha.cpp |only Boom-0.6/Boom/src/Bmath/snorm.cpp | 3 Boom-0.6/Boom/src/Interfaces/R/BoomInterface/test/dirichlet_test.R |only Boom-0.6/Boom/src/Interfaces/R/BoomInterface/test/dmvn_test.R |only Boom-0.6/Boom/src/Interfaces/R/BoomInterface/test/format_test.R |only Boom-0.6/Boom/src/Interfaces/R/BoomInterface/test/mvn_test.R |only Boom-0.6/Boom/src/Interfaces/R/BoomInterface/test/wishart_test.R |only Boom-0.6/Boom/src/LinAlg/Array.cpp | 76 Boom-0.6/Boom/src/LinAlg/Matrix.cpp | 5 Boom-0.6/Boom/src/LinAlg/SpdMatrix.cpp | 1470 +++++----- Boom-0.6/Boom/src/LinAlg/Vector.cpp | 20 Boom-0.6/Boom/src/LinAlg/VectorView.cpp | 2 Boom-0.6/Boom/src/Makevars | 3 Boom-0.6/Boom/src/Models/Bart/Bart.cpp | 4 Boom-0.6/Boom/src/Models/Bart/PosteriorSamplers/BartPosteriorSampler.cpp | 4 Boom-0.6/Boom/src/Models/Bart/PosteriorSamplers/GaussianBartPosteriorSampler.cpp | 4 Boom-0.6/Boom/src/Models/Bart/PosteriorSamplers/LogitBartPosteriorSampler.cpp | 4 Boom-0.6/Boom/src/Models/Bart/PosteriorSamplers/PoissonBartPosteriorSampler.cpp | 4 Boom-0.6/Boom/src/Models/Bart/PosteriorSamplers/ProbitBartPosteriorSampler.cpp | 4 Boom-0.6/Boom/src/Models/BetaModel.cpp | 147 - Boom-0.6/Boom/src/Models/CategoricalData.cpp | 265 - Boom-0.6/Boom/src/Models/ConstrainedVectorParams.cpp | 2 Boom-0.6/Boom/src/Models/FiniteMixtureModel.cpp | 111 Boom-0.6/Boom/src/Models/GammaModel.cpp | 270 - Boom-0.6/Boom/src/Models/Glm/GlmCoefs.cpp | 1 Boom-0.6/Boom/src/Models/Glm/MultinomialLogitModel.cpp | 6 Boom-0.6/Boom/src/Models/Glm/MvReg2.cpp | 1 Boom-0.6/Boom/src/Models/Glm/MvnGivenXandSigma.cpp | 153 - Boom-0.6/Boom/src/Models/Glm/OrdinalCutpointModel.cpp | 6 Boom-0.6/Boom/src/Models/Glm/PoissonRegressionData.cpp | 4 Boom-0.6/Boom/src/Models/Glm/PoissonRegressionModel.cpp | 10 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/BinomialLogitAuxmixSampler.cpp | 185 - Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/BinomialLogitSamplerTim.cpp | 14 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/BregVsSampler.cpp | 2 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/CumulativeLogitSampler.cpp | 4 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/CumulativeProbitSampler.cpp | 4 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/DAFE_MLM.cpp | 9 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/MLVS.cpp | 30 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/MLVS_data_imputer.cpp | 17 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/MultinomialLogitCompleteDataSuf.cpp | 8 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/NonconjugateRegressionSampler.cpp |only Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/NormalMixtureApproximation.cpp | 133 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/PoissonDataImputer.cpp | 10 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/PoissonRegressionAuxMixSampler.cpp | 60 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/PoissonRegressionSpikeSlabSampler.cpp | 22 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/QuantileRegressionPosteriorSampler.cpp |only Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/RegressionConjSampler.cpp | 2 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/SpikeSlabDaRegressionSampler.cpp | 14 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/TRegressionSampler.cpp | 2 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/ZeroInflatedPoissonRegressionSampler.cpp | 12 Boom-0.6/Boom/src/Models/Glm/PosteriorSamplers/poisson_mixture_approximation_table.cpp | 2 Boom-0.6/Boom/src/Models/Glm/ProbitRegression.cpp | 11 Boom-0.6/Boom/src/Models/Glm/QuantileRegressionModel.cpp |only Boom-0.6/Boom/src/Models/Glm/RegressionModel.cpp | 39 Boom-0.6/Boom/src/Models/Glm/TRegression.cpp | 4 Boom-0.6/Boom/src/Models/Glm/VariableSelectionPrior.cpp | 22 Boom-0.6/Boom/src/Models/Glm/ZeroInflatedPoissonRegression.cpp | 18 Boom-0.6/Boom/src/Models/HMM/Clickstream/NestedHmm.cpp | 2 Boom-0.6/Boom/src/Models/HMM/HmmFilter.cpp | 32 Boom-0.6/Boom/src/Models/HMM/PosteriorSamplers/HmmPosteriorSampler.cpp | 2 Boom-0.6/Boom/src/Models/Hierarchical/HierarchicalGammaModel.cpp | 4 Boom-0.6/Boom/src/Models/Hierarchical/PosteriorSamplers/HierarchicalPoissonSampler.cpp | 9 Boom-0.6/Boom/src/Models/IRT/DafePcrDataImputer.cpp | 31 Boom-0.6/Boom/src/Models/IRT/DafePcrItemSampler.cpp | 21 Boom-0.6/Boom/src/Models/IRT/DafePcrRwmItemSampler.cpp | 9 Boom-0.6/Boom/src/Models/IRT/DafePcrRwmSubject.cpp | 23 Boom-0.6/Boom/src/Models/IRT/DafePcrSubject.cpp | 16 Boom-0.6/Boom/src/Models/IRT/IrtModel.cpp | 5 Boom-0.6/Boom/src/Models/IRT/Item.cpp | 38 Boom-0.6/Boom/src/Models/IRT/PartialCreditModel.cpp | 28 Boom-0.6/Boom/src/Models/IRT/Subject.cpp | 2 Boom-0.6/Boom/src/Models/MarkovModel.cpp | 52 Boom-0.6/Boom/src/Models/Mixtures/DirichletProcessMvnModel.cpp | 39 Boom-0.6/Boom/src/Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.cpp | 147 - Boom-0.6/Boom/src/Models/ModelTypes.cpp | 49 Boom-0.6/Boom/src/Models/MultinomialModel.cpp | 4 Boom-0.6/Boom/src/Models/MvnBase.cpp | 81 Boom-0.6/Boom/src/Models/MvnGivenSigma.cpp | 117 Boom-0.6/Boom/src/Models/MvnModel.cpp | 2 Boom-0.6/Boom/src/Models/MvtModel.cpp | 153 - Boom-0.6/Boom/src/Models/PointProcess/BoundedPoissonProcessSimulator.cpp | 2 Boom-0.6/Boom/src/Models/PointProcess/CosinePoissonProcess.cpp | 2 Boom-0.6/Boom/src/Models/PointProcess/HomogeneousPoissonProcess.cpp | 2 Boom-0.6/Boom/src/Models/PointProcess/PointProcess.cpp | 2 Boom-0.6/Boom/src/Models/PointProcess/PoissonClusterProcess.cpp | 9 Boom-0.6/Boom/src/Models/PointProcess/WeeklyCyclePoissonProcess.cpp | 5 Boom-0.6/Boom/src/Models/Policies/CompositeParamPolicy.cpp | 11 Boom-0.6/Boom/src/Models/Policies/ManyParamPolicy.cpp | 4 Boom-0.6/Boom/src/Models/Policies/NullParamPolicy.cpp | 4 Boom-0.6/Boom/src/Models/PosteriorSamplers/BetaBinomialPosteriorSampler.cpp | 11 Boom-0.6/Boom/src/Models/PosteriorSamplers/BetaBinomialSampler.cpp | 8 Boom-0.6/Boom/src/Models/PosteriorSamplers/BetaPosteriorSampler.cpp | 5 Boom-0.6/Boom/src/Models/PosteriorSamplers/DirichletPosteriorSampler.cpp | 6 Boom-0.6/Boom/src/Models/PosteriorSamplers/GammaPosteriorSampler.cpp | 20 Boom-0.6/Boom/src/Models/PosteriorSamplers/GaussianConjSampler.cpp | 5 Boom-0.6/Boom/src/Models/PosteriorSamplers/GaussianVarSampler.cpp | 2 Boom-0.6/Boom/src/Models/PosteriorSamplers/GenericGaussianVarianceSampler.cpp | 7 Boom-0.6/Boom/src/Models/PosteriorSamplers/IndependentMvnConjSampler.cpp | 2 Boom-0.6/Boom/src/Models/PosteriorSamplers/IndependentMvnVarSampler.cpp | 2 Boom-0.6/Boom/src/Models/PosteriorSamplers/MvnIndependentVarianceSampler.cpp | 2 Boom-0.6/Boom/src/Models/PosteriorSamplers/PoissonGammaPosteriorSampler.cpp | 20 Boom-0.6/Boom/src/Models/PosteriorSamplers/PoissonGammaSampler.cpp | 15 Boom-0.6/Boom/src/Models/PosteriorSamplers/PosteriorSampler.cpp | 15 Boom-0.6/Boom/src/Models/PosteriorSamplers/SharedSigsqSampler.cpp | 3 Boom-0.6/Boom/src/Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.cpp | 55 Boom-0.6/Boom/src/Models/PosteriorSamplers/ZeroMeanMvnIndependenceSampler.cpp | 4 Boom-0.6/Boom/src/Models/ProductVectorModel.cpp |only Boom-0.6/Boom/src/Models/SpdData.cpp | 312 +- Boom-0.6/Boom/src/Models/StateSpace/AggregatedStateSpaceRegression.cpp | 9 Boom-0.6/Boom/src/Models/StateSpace/Filters/SparseMatrix.cpp | 8 Boom-0.6/Boom/src/Models/StateSpace/PosteriorSamplers/DynamicRegressionPosteriorSampler.cpp | 2 Boom-0.6/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.cpp | 43 Boom-0.6/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.cpp | 87 Boom-0.6/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.cpp | 140 Boom-0.6/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.cpp | 63 Boom-0.6/Boom/src/Models/StateSpace/PosteriorSamplers/StudentLocalLinearTrendPosteriorSampler.cpp | 83 Boom-0.6/Boom/src/Models/StateSpace/StateModels/ArStateModel.cpp | 34 Boom-0.6/Boom/src/Models/StateSpace/StateModels/DynamicRegressionStateModel.cpp | 22 Boom-0.6/Boom/src/Models/StateSpace/StateModels/LocalLevelStateModel.cpp | 26 Boom-0.6/Boom/src/Models/StateSpace/StateModels/LocalLinearTrend.cpp | 34 Boom-0.6/Boom/src/Models/StateSpace/StateModels/RandomWalkHolidayStateModel.cpp | 10 Boom-0.6/Boom/src/Models/StateSpace/StateModels/SeasonalStateModel.cpp | 32 Boom-0.6/Boom/src/Models/StateSpace/StateModels/SemilocalLinearTrend.cpp |only Boom-0.6/Boom/src/Models/StateSpace/StateModels/StateModel.cpp | 9 Boom-0.6/Boom/src/Models/StateSpace/StateModels/StudentLocalLinearTrend.cpp | 8 Boom-0.6/Boom/src/Models/StateSpace/StateModels/TrigStateModel.cpp | 6 Boom-0.6/Boom/src/Models/StateSpace/StateSpaceLogitModel.cpp | 97 Boom-0.6/Boom/src/Models/StateSpace/StateSpaceModel.cpp | 110 Boom-0.6/Boom/src/Models/StateSpace/StateSpaceModelBase.cpp | 559 +++ Boom-0.6/Boom/src/Models/StateSpace/StateSpacePoissonModel.cpp | 98 Boom-0.6/Boom/src/Models/StateSpace/StateSpaceRegressionModel.cpp | 130 Boom-0.6/Boom/src/Models/StateSpace/StateSpaceStudentRegressionModel.cpp | 93 Boom-0.6/Boom/src/Models/Sufstat.cpp | 7 Boom-0.6/Boom/src/Models/TimeSeries/ArModel.cpp | 10 Boom-0.6/Boom/src/Models/TimeSeries/PosteriorSamplers/ArPosteriorSampler.cpp | 2 Boom-0.6/Boom/src/Models/TimeSeries/PosteriorSamplers/ArSpikeSlabSampler.cpp | 2 Boom-0.6/Boom/src/Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.cpp | 2 Boom-0.6/Boom/src/Models/TruncatedGammaModel.cpp | 58 Boom-0.6/Boom/src/Models/UniformCorrelationModel.cpp | 1 Boom-0.6/Boom/src/Models/UniformModel.cpp | 115 Boom-0.6/Boom/src/Models/WishartModel.cpp | 110 Boom-0.6/Boom/src/Models/ZeroInflatedGammaModel.cpp | 99 Boom-0.6/Boom/src/Models/ZeroInflatedLognormalModel.cpp | 99 Boom-0.6/Boom/src/Models/ZeroInflatedPoissonModel.cpp | 84 Boom-0.6/Boom/src/Models/ZeroMeanGaussianModel.cpp | 9 Boom-0.6/Boom/src/Samplers/MetropolisHastings.cpp | 5 Boom-0.6/Boom/src/Samplers/MoveAccounting.cpp | 20 Boom-0.6/Boom/src/Samplers/SliceSampler.cpp | 19 Boom-0.6/Boom/src/Samplers/TIM.cpp | 19 Boom-0.6/Boom/src/Samplers/UnivariateSliceSampler.cpp | 49 Boom-0.6/Boom/src/TargetFun/TargetFun.cpp | 5 Boom-0.6/Boom/src/boom_r_tools.cpp | 184 - Boom-0.6/Boom/src/cpputil/ThreadTools.cpp |only Boom-0.6/Boom/src/cpputil/cat_string.cpp | 14 Boom-0.6/Boom/src/cpputil/parse_range.cpp | 2 Boom-0.6/Boom/src/cpputil/split.cpp | 2 Boom-0.6/Boom/src/cpputil/strip.cpp | 2 Boom-0.6/Boom/src/create_mixture_component.cpp | 11 Boom-0.6/Boom/src/create_state_model.cpp | 98 Boom-0.6/Boom/src/distributions/mvn.cpp | 103 Boom-0.6/Boom/src/extract_mixture_data.cpp | 8 Boom-0.6/Boom/src/list_io.cpp | 144 Boom-0.6/Boom/src/math/lmultigamma.cpp |only Boom-0.6/Boom/src/math/special_functions.hpp | 37 Boom-0.6/Boom/src/numopt/Brent.cpp | 33 Boom-0.6/Boom/src/numopt/Integral.cpp | 6 Boom-0.6/Boom/src/numopt/NelderMead.cpp | 210 - Boom-0.6/Boom/src/numopt/bfgs.cpp | 7 Boom-0.6/Boom/src/numopt/conj_grad.cpp | 85 Boom-0.6/Boom/src/numopt/max_nd.cpp | 110 Boom-0.6/Boom/src/numopt/nelder_mead.cpp | 43 Boom-0.6/Boom/src/prior_specification.cpp | 128 Boom-0.6/Boom/src/spike_slab_prior.cpp | 7 Boom-0.6/Boom/src/stats/Bspline.cpp | 65 Boom-0.6/Boom/src/stats/DataTable.cpp | 6 Boom-0.6/Boom/src/stats/ECDF.cpp | 22 Boom-0.6/Boom/src/stats/IQagent.cpp | 31 Boom-0.6/Boom/src/stats/Mspline.cpp |only Boom-0.6/Boom/src/stats/Spline.cpp | 143 Boom-0.6/Boom/src/stats/moments.cpp | 6 385 files changed, 9116 insertions(+), 5556 deletions(-)
Title: Stochastic Process Model for Analysis of Longitudinal and
Time-to-Event Outcomes
Description: Utilities to estimate parameters of the models with survival functions
induced by stochastic covariates. Miscellaneous functions for data preparation
and simulation are also provided. For more information, see:
(i)"Stochastic model for analysis of longitudinal data on aging and mortality"
by Yashin A. et al. (2007),
Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>;
(ii) "Health decline, aging and mortality: how are they related?"
by Yashin A. et al. (2007),
Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.
Author: I. Y. Zhbannikov, Liang He, K. G. Arbeev, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between stpm versions 1.6.4 dated 2017-03-05 and 1.6.6 dated 2017-04-07
stpm-1.6.4/stpm/man/getNextY.Rd |only stpm-1.6.6/stpm/DESCRIPTION | 8 stpm-1.6.6/stpm/MD5 | 10 stpm-1.6.6/stpm/R/spm.impute.R | 1204 +++++++++++++++------------- stpm-1.6.6/stpm/inst/NEWS | 5 stpm-1.6.6/stpm/inst/doc/stpm-vignette.html | 1081 ++++++++++--------------- stpm-1.6.6/stpm/man/getNextY.cont2.Rd |only 7 files changed, 1100 insertions(+), 1208 deletions(-)
Title: Sequential Co-Sparse Factor Regression
Description: Sequential factor extraction via co-sparse unit-rank estimation (SeCURE).
Author: Aditya Mishra [aut, cre], Kun Chen [aut, cre]
Maintainer: Aditya Mishra <aditya.mishra@uconn.edu>
Diff between secure versions 0.3 dated 2017-04-01 and 0.5 dated 2017-04-07
secure-0.3/secure/R/CellCycleX.R |only secure-0.3/secure/R/CellCycleY.R |only secure-0.3/secure/data/CellCycleX.RData |only secure-0.3/secure/data/CellCycleY.RData |only secure-0.3/secure/man/CellCycleX.Rd |only secure-0.3/secure/man/CellCycleY.Rd |only secure-0.3/secure/man/bregpcdenet_Rcpp.Rd |only secure-0.3/secure/man/bregpcdenetdiag_Rcpp.Rd |only secure-0.3/secure/man/rfit.Rd |only secure-0.3/secure/man/secure.init.Rd |only secure-0.3/secure/man/secure.miss.init.Rd |only secure-0.3/secure/man/sefar_SURR_Rcpp.Rd |only secure-0.3/secure/man/sefar_SURR_Rcpp_ortho.Rd |only secure-0.3/secure/man/sefar_SURR_miss_Rcpp.Rd |only secure-0.3/secure/src/sefar_SURR_fit.cpp |only secure-0.5/secure/DESCRIPTION | 8 secure-0.5/secure/MD5 | 42 secure-0.5/secure/NAMESPACE | 22 secure-0.5/secure/R/CellCycle.R |only secure-0.5/secure/R/DLBCL.R | 23 secure-0.5/secure/R/RcppExports.R | 86 - secure-0.5/secure/R/secure.R | 1143 ++++++++++++------------- secure-0.5/secure/data/CellCycle.RData |only secure-0.5/secure/data/DLBCL.RData |binary secure-0.5/secure/man/CellCycle.Rd |only secure-0.5/secure/man/DLBCL.Rd | 64 - secure-0.5/secure/man/rrr.fit.Rd |only secure-0.5/secure/man/secure.control.Rd | 2 secure-0.5/secure/man/secure.path.Rd | 244 ++--- secure-0.5/secure/man/secure.sim.Rd | 114 +- secure-0.5/secure/src/RcppExports.cpp | 24 secure-0.5/secure/src/secure_SURR_fit.cpp |only 32 files changed, 884 insertions(+), 888 deletions(-)
Title: Performs Bayesian Variable Selection on the Covariates in a
Semi-Competing Risks Model
Description: Contains four functions used in the DIC-tau_g procedure. SCRSELECT() and SCRSELECTRUN() uses Stochastic Search Variable Selection to select important
covariates in the three hazard functions of a semi-competing risks model. These functions perform the Gibbs sampler for variable selection and a Metropolis-Hastings-Green sampler for the number of split points and parameters for the
three baseline hazard function. The function SCRSELECT() returns the posterior sample of all quantities sampled in the Gibbs sampler after a burn-in period to a desired
file location, while the function SCRSELECTRUN() returns posterior values of important quantities to the DIC-Tau_g procedure in a list.
The function DICTAUG() returns a list containing the DIC values for the unique models visited by the DIC-Tau_g grid search.
The function ReturnModel() uses SCRSELECTRUN() and DICTAUG() to return a summary of the posterior coefficient vectors for the optimal model along with saving this posterior sample to a desired path location.
Author: Andrew Chapple [aut, cre]
Maintainer: Andrew Chapple <Andrew.G.Chapple@rice.edu>
Diff between SCRSELECT versions 1.1-0 dated 2016-09-28 and 1.1-1 dated 2017-04-07
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/DICTAUG.R | 5 +++++ R/ReturnModel.R | 14 ++++++++++---- R/SCRSELECT.R | 21 ++++++--------------- man/DICTAUG.Rd | 5 ++++- man/ReturnModel.Rd | 7 +++++-- man/SCRSELECT.Rd | 4 ++-- man/SCRSELECTRUN.Rd | 1 - 9 files changed, 44 insertions(+), 37 deletions(-)
Title: R Client for Adobe Analytics API V1.4
Description: Functions for interacting with the Adobe Analytics API V1.4
(<https://api.omniture.com/admin/1.4/rest/>).
Author: Willem Paling, Randy Zwitch & Jowanza Joseph
Maintainer: Randy Zwitch <rzwitch+rsitecatalyst@gmail.com>
Diff between RSiteCatalyst versions 1.4.11 dated 2017-03-04 and 1.4.12 dated 2017-04-07
DESCRIPTION | 10 +- MD5 | 52 ++++++------- NAMESPACE | 1 NEWS | 11 ++ R/GetLogin.R | 6 + R/GetMarketingChannelRules.R | 94 +++++++++++++++---------- R/QueueDataWarehouse.R | 18 +++- R/QueueFallout.R | 2 R/QueueOvertime.R | 2 R/QueuePathing.R | 2 R/QueueRanked.R | 2 R/QueueSummary.R | 2 R/QueueTrended.R | 2 R/RSiteCatalyst.R | 4 - R/SubmitJsonQueueReport.R | 2 R/ViewProcessingRules.R | 27 +++++-- man/QueueDataWarehouse.Rd | 6 + man/QueueFallout.Rd | 2 man/QueueOvertime.Rd | 2 man/QueuePathing.Rd | 2 man/QueueRanked.Rd | 2 man/QueueSummary.Rd | 2 man/QueueTrended.Rd | 2 man/RSiteCatalyst.Rd | 4 - man/SubmitJsonQueueReport.Rd | 2 tests/testthat/test-getmarketingchannelrules.R | 5 + tests/testthat/test-queuedatawarehouse.R | 12 +++ 27 files changed, 182 insertions(+), 96 deletions(-)
Title: Download NRCS Data
Description: Downloads Natural Resources Conservation Service (NRCS) data for sites in the Soil Climate Analysis Network (SCAN) <https://www.wcc.nrcs.usda.gov/scan/>, and Snow Telemetry (SNOTEL and SNOLITE) <https://www.wcc.nrcs.usda.gov/snow/> networks. Metadata can be returned for all sites in the NRCS' Air and Water Data Base (AWDB) <https://www.wcc.nrcs.usda.gov/report_generator/AWDB_Network_Codes.pdf>.
Author: Robert Lee <rhlee@colorado.edu>, Josh Roberti <jaroberti87@gmail.com>,
Maintainer: Robert Lee <rhlee@colorado.edu>
Diff between RNRCS versions 0.1.0 dated 2017-04-06 and 0.1.1 dated 2017-04-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/grabNRCSdata.R | 6 +++--- man/grabNRCS.data.Rd | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Psychometric Mixture Models
Description: Psychometric mixture models based on 'flexmix' infrastructure. At the moment Rasch mixture models
with different parameterizations of the score distribution (saturated vs. mean/variance specification),
Bradley-Terry mixture models, and MPT mixture models are implemented. These mixture models can be estimated
with or without concomitant variables. See vignette('raschmix', package = 'psychomix') for details on the
Rasch mixture models.
Author: Hannah Frick [aut, cre],
Friedrich Leisch [aut],
Carolin Strobl [aut],
Florian Wickelmaier [aut],
Achim Zeileis [aut]
Maintainer: Hannah Frick <hannah.frick@gmail.com>
Diff between psychomix versions 1.1-3 dated 2015-09-09 and 1.1-4 dated 2017-04-07
DESCRIPTION | 28 ++++++++++++++------------- MD5 | 35 +++++++++++++++++++--------------- NAMESPACE | 11 ++++++++++ NEWS | 9 ++++++++ R/allClasses.R | 21 ++++++++++++++++++++ R/effects.R | 7 ++++-- R/mptmix.R |only R/mptmixPlot.R |only R/raschmixPlot.R | 2 - build/partial.rdb |only build/vignette.rds |binary inst/doc/raschmix.pdf |binary inst/doc/scores.pdf |binary man/btmix.Rd | 2 - man/btmixClass.Rd | 4 +-- man/effectsplot.Rd | 9 +++++--- man/mptmix.Rd |only man/mptmixClass.Rd |only man/raschmixClass.Rd | 2 - man/raschmixPlotMethod.Rd | 2 - tests/Examples/psychomix-Ex.Rout.save | 29 +++++++++++++++++++++++----- 21 files changed, 117 insertions(+), 44 deletions(-)
Title: Calculate Accurate Precision-Recall and ROC (Receiver Operator
Characteristics) Curves
Description: Accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics)
curves.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between precrec versions 0.6.2 dated 2017-01-18 and 0.7.1 dated 2017-04-07
DESCRIPTION | 10 +- MD5 | 75 +++++++++-------- NAMESPACE | 2 NEWS.md | 8 + R/RcppExports.R | 8 - R/etc_utils_autoplot.R | 69 +++++++++++++++- R/etc_utils_dataframe.R | 14 ++- R/etc_utils_fortify.R | 4 R/g_autoplot.R | 24 +++-- R/g_fortify.R | 44 ++++++---- build/vignette.rds |binary inst/doc/introduction.R | 14 +++ inst/doc/introduction.Rmd | 17 ++++ inst/doc/introduction.html | 135 +++++++++++++++++--------------- man/B1000.Rd | 1 man/B500.Rd | 1 man/IB1000.Rd | 1 man/IB500.Rd | 1 man/P10N10.Rd | 1 man/as.data.frame.Rd | 11 +- man/auc.Rd | 1 man/autoplot.Rd | 60 ++++++++++++-- man/create_sim_samples.Rd | 1 man/evalmod.Rd | 1 man/fortify.Rd | 39 +++++---- man/join_labels.Rd | 1 man/join_scores.Rd | 1 man/mmdata.Rd | 1 man/part.Rd | 5 - man/pauc.Rd | 1 man/plot.Rd | 11 +- src/RcppExports.cpp | 14 +-- src/conv_vec.cpp | 60 ++++++++++++-- src/conv_vec.h | 17 +++- src/convert_curve_avg_df.cpp | 61 +++++++++++--- src/convert_curve_df.cpp | 61 +++++++++++--- src/precrec_init.c |only tests/testthat/test_g_fortify2_curves.R | 96 ++++++++++++++++++++++ vignettes/introduction.Rmd | 17 ++++ 39 files changed, 658 insertions(+), 230 deletions(-)
Title: Automatic Parallelized Monte Carlo Simulations
Description: Simplifies Monte Carlo simulation studies by automatically
setting up loops to run over parameter grids and parallelising
the Monte Carlo repetitions. It also generates LaTeX tables.
Author: Christian Hendrik Leschinski
Maintainer: Christian Hendrik Leschinski <leschinski@statistik.uni-hannover.de>
Diff between MonteCarlo versions 1.0.0 dated 2017-03-17 and 1.0.1 dated 2017-04-07
DESCRIPTION | 13 ++++++------- MD5 | 8 ++++---- NAMESPACE | 2 ++ R/MonteCarlo.R | 2 ++ inst/doc/MonteCarlo-Vignette.html | 6 +++--- 5 files changed, 17 insertions(+), 14 deletions(-)
Title: Modelling Microbial Populations
Description: Modelling interacting microbial populations - example applications include human gut microbiota, rumen microbiota and phytoplankton. Solves a system of ordinary differential equations to simulate microbial growth and resource uptake over time.
Author: Helen Kettle [aut, cre]
Maintainer: Helen Kettle <Helen.Kettle@bioss.ac.uk>
Diff between microPop versions 1.0 dated 2017-03-29 and 1.1 dated 2017-04-07
microPop-1.0/microPop/inst/DemoFiles/microbeSysInfoRumen.csv |only microPop-1.0/microPop/inst/DemoFiles/resourceSysInfoRumen.csv |only microPop-1.0/microPop/inst/DemoFiles/strainParams.csv |only microPop-1.0/microPop/inst/DemoFiles/systemInfoMicrobesPhyto.csv |only microPop-1.0/microPop/inst/DemoFiles/systemInfoMicrobesVirus.csv |only microPop-1.0/microPop/inst/DemoFiles/systemInfoResourcesPhyto.csv |only microPop-1.0/microPop/inst/DemoFiles/systemInfoResourcesVirus.csv |only microPop-1.1/microPop/DESCRIPTION | 8 microPop-1.1/microPop/MD5 | 124 +++++----- microPop-1.1/microPop/NAMESPACE | 14 + microPop-1.1/microPop/R/combineGrowthLimFuncDefault.R | 3 microPop-1.1/microPop/R/combinePathsFuncDefault.R | 2 microPop-1.1/microPop/R/data.R | 83 ++++++ microPop-1.1/microPop/R/entryRateFuncDefault.R | 3 microPop-1.1/microPop/R/extraGrowthLimFuncDefault.R | 2 microPop-1.1/microPop/R/getStrainParamsFromFile.R | 29 +- microPop-1.1/microPop/R/growthLimFuncDefault.R | 1 microPop-1.1/microPop/R/massBalanceFuncDefault.R | 3 microPop-1.1/microPop/R/microPopModel.R | 21 - microPop-1.1/microPop/R/pHFuncDefault.R | 3 microPop-1.1/microPop/R/pHLimFuncDefault.R | 2 microPop-1.1/microPop/R/plotTraitChange.R | 3 microPop-1.1/microPop/R/productionFuncDefault.R | 2 microPop-1.1/microPop/R/rateFuncsDefault.R | 1 microPop-1.1/microPop/R/removalRateFuncDefault.R | 1 microPop-1.1/microPop/R/uptakeFuncDefault.R | 2 microPop-1.1/microPop/data/Acetogens.RData |binary microPop-1.1/microPop/data/ButyrateProducers1.RData |binary microPop-1.1/microPop/data/ButyrateProducers2.RData |binary microPop-1.1/microPop/data/ButyrateProducers3.RData |binary microPop-1.1/microPop/data/LactateProducers.RData |binary microPop-1.1/microPop/data/Methanogens.RData |binary microPop-1.1/microPop/data/NoButyFibreDeg.RData |binary microPop-1.1/microPop/data/NoButyStarchDeg.RData |binary microPop-1.1/microPop/data/PropionateProducers.RData |binary microPop-1.1/microPop/data/Xaa.RData |binary microPop-1.1/microPop/data/Xh2.RData |binary microPop-1.1/microPop/data/Xsu.RData |binary microPop-1.1/microPop/data/microbeSysInfoRumen.RData |only microPop-1.1/microPop/data/resourceSysInfoRumen.RData |only microPop-1.1/microPop/data/strainParams.RData |only microPop-1.1/microPop/data/systemInfoMicrobesPhyto.RData |only microPop-1.1/microPop/data/systemInfoMicrobesVirus.RData |only microPop-1.1/microPop/data/systemInfoResourcesPhyto.RData |only microPop-1.1/microPop/data/systemInfoResourcesVirus.RData |only microPop-1.1/microPop/inst/DemoFiles/human4.R | 7 microPop-1.1/microPop/inst/DemoFiles/phages.R | 4 microPop-1.1/microPop/inst/DemoFiles/phyto.R | 4 microPop-1.1/microPop/inst/DemoFiles/rumen.R | 81 +++++- microPop-1.1/microPop/inst/doc/microPop.pdf |binary microPop-1.1/microPop/inst/extdata/Acetogens.csv | 42 +-- microPop-1.1/microPop/inst/extdata/ButyrateProducers1.csv | 20 - microPop-1.1/microPop/inst/extdata/ButyrateProducers2.csv | 20 - microPop-1.1/microPop/inst/extdata/ButyrateProducers3.csv | 30 +- microPop-1.1/microPop/inst/extdata/LactateProducers.csv | 18 - microPop-1.1/microPop/inst/extdata/Methanogens.csv | 31 +- microPop-1.1/microPop/inst/extdata/NoButyFibreDeg.csv | 18 - microPop-1.1/microPop/inst/extdata/NoButyStarchDeg.csv | 18 - microPop-1.1/microPop/inst/extdata/PropionateProducers.csv | 30 +- microPop-1.1/microPop/inst/extdata/Xaa.csv | 16 - microPop-1.1/microPop/inst/extdata/Xh2.csv | 16 - microPop-1.1/microPop/inst/extdata/Xsu.csv | 4 microPop-1.1/microPop/inst/extdata/microbeSysInfoRumen.csv |only microPop-1.1/microPop/inst/extdata/resourceSysInfoRumen.csv |only microPop-1.1/microPop/inst/extdata/strainParams.csv |only microPop-1.1/microPop/inst/extdata/systemInfoMicrobesPhyto.csv |only microPop-1.1/microPop/inst/extdata/systemInfoMicrobesVirus.csv |only microPop-1.1/microPop/inst/extdata/systemInfoResourcesPhyto.csv |only microPop-1.1/microPop/inst/extdata/systemInfoResourcesVirus.csv |only microPop-1.1/microPop/man/microPopModel.Rd | 12 microPop-1.1/microPop/man/microbeSysInfoRumen.Rd |only microPop-1.1/microPop/man/resourceSysInfoRumen.Rd |only microPop-1.1/microPop/man/strainParams.Rd |only microPop-1.1/microPop/man/systemInfoMicrobesPhyto.Rd |only microPop-1.1/microPop/man/systemInfoMicrobesVirus.Rd |only microPop-1.1/microPop/man/systemInfoResourcesPhyto.Rd |only microPop-1.1/microPop/man/systemInfoResourcesVirus.Rd |only 77 files changed, 424 insertions(+), 254 deletions(-)
Title: Models for Health Economic Evaluation
Description: Health Economic Evaluation Modelling:
decision trees and cohort simulations. Provides a simple
and consistent interface for Markov models specification,
comparison, sensitivity and probabilistic analysis, input of
survival models, etc. Models with time varying properties
(non-homogeneous Markov models and semi-Markov models)
are supported.
Author: Antoine Filipovic-Pierucci [aut, cre],
Kevin Zarca [aut],
Matthew Wiener [ctb],
Zdenek Kabat [ctb],
Vojtech Filipec [ctb],
Jordan Amdahl [ctb]
Maintainer: Antoine Filipovic-Pierucci <pierucci@gmail.com>
Diff between heemod versions 0.8.0 dated 2017-02-10 and 0.9.0 dated 2017-04-07
heemod-0.8.0/heemod/R/survival.R |only heemod-0.8.0/heemod/inst/tmp |only heemod-0.8.0/heemod/man/get_probs_from_surv.Rd |only heemod-0.8.0/heemod/tests/testthat/test_survival.R |only heemod-0.9.0/heemod/DESCRIPTION | 23 heemod-0.9.0/heemod/MD5 | 369 +++++----- heemod-0.9.0/heemod/NAMESPACE | 43 + heemod-0.9.0/heemod/NEWS.md | 123 ++- heemod-0.9.0/heemod/R/acceptability_curve.R | 8 heemod-0.9.0/heemod/R/calibration.R |only heemod-0.9.0/heemod/R/cluster.R | 28 heemod-0.9.0/heemod/R/combine.R | 15 heemod-0.9.0/heemod/R/correct_counts.R |only heemod-0.9.0/heemod/R/density.R | 8 heemod-0.9.0/heemod/R/dispatch_strategy.R | 14 heemod-0.9.0/heemod/R/efficiency_frontier.R | 2 heemod-0.9.0/heemod/R/evpi.R | 6 heemod-0.9.0/heemod/R/expand.R | 28 heemod-0.9.0/heemod/R/get_code.R | 12 heemod-0.9.0/heemod/R/gho_mortality.R | 141 ++- heemod-0.9.0/heemod/R/heemod.R | 12 heemod-0.9.0/heemod/R/look_up.R | 4 heemod-0.9.0/heemod/R/matrix_define.R | 39 - heemod-0.9.0/heemod/R/matrix_eval.R | 16 heemod-0.9.0/heemod/R/newdata.R | 12 heemod-0.9.0/heemod/R/param_define.R | 155 +++- heemod-0.9.0/heemod/R/param_eval.R | 14 heemod-0.9.0/heemod/R/part_surv.R | 126 ++- heemod-0.9.0/heemod/R/resamp_define.R | 18 heemod-0.9.0/heemod/R/resamp_eval.R | 18 heemod-0.9.0/heemod/R/resamp_print.R | 20 heemod-0.9.0/heemod/R/run_model_define.R | 175 ++-- heemod-0.9.0/heemod/R/run_model_summary.R | 42 - heemod-0.9.0/heemod/R/sensitivity_define.R | 2 heemod-0.9.0/heemod/R/sensitivity_eval.R | 54 + heemod-0.9.0/heemod/R/sensitivity_print.R | 84 +- heemod-0.9.0/heemod/R/states_define.R | 34 heemod-0.9.0/heemod/R/states_eval.R | 25 heemod-0.9.0/heemod/R/strategy_define.R | 20 heemod-0.9.0/heemod/R/strategy_eval.R | 176 ++-- heemod-0.9.0/heemod/R/strategy_print.R | 14 heemod-0.9.0/heemod/R/survival_define.R |only heemod-0.9.0/heemod/R/survival_eval.R |only heemod-0.9.0/heemod/R/survival_operations.R |only heemod-0.9.0/heemod/R/tabular_input.R | 312 ++++++-- heemod-0.9.0/heemod/R/update.R | 38 - heemod-0.9.0/heemod/R/utils.R | 64 + heemod-0.9.0/heemod/README.md | 28 heemod-0.9.0/heemod/build/vignette.rds |binary heemod-0.9.0/heemod/inst/CITATION |only heemod-0.9.0/heemod/inst/doc/a-introduction.html | 11 heemod-0.9.0/heemod/inst/doc/b-time-dependency.Rmd | 4 heemod-0.9.0/heemod/inst/doc/b-time-dependency.html | 10 heemod-0.9.0/heemod/inst/doc/c-homogeneous.Rmd | 2 heemod-0.9.0/heemod/inst/doc/c-homogeneous.html | 17 heemod-0.9.0/heemod/inst/doc/d-non-homogeneous.html | 17 heemod-0.9.0/heemod/inst/doc/e-probabilistic.html | 43 - heemod-0.9.0/heemod/inst/doc/f-sensitivity.R | 7 heemod-0.9.0/heemod/inst/doc/f-sensitivity.Rmd | 9 heemod-0.9.0/heemod/inst/doc/f-sensitivity.html | 85 +- heemod-0.9.0/heemod/inst/doc/g-heterogeneity.html | 158 ++-- heemod-0.9.0/heemod/inst/doc/h-tabular.Rmd | 1 heemod-0.9.0/heemod/inst/doc/h-tabular.html | 34 heemod-0.9.0/heemod/inst/doc/i-reproduction.Rmd | 2 heemod-0.9.0/heemod/inst/doc/i-reproduction.html | 28 heemod-0.9.0/heemod/inst/doc/j-survival.R | 126 ++- heemod-0.9.0/heemod/inst/doc/j-survival.Rmd | 165 +++- heemod-0.9.0/heemod/inst/doc/j-survival.html | 157 +++- heemod-0.9.0/heemod/inst/doc/k-calibration.R |only heemod-0.9.0/heemod/inst/doc/k-calibration.Rmd |only heemod-0.9.0/heemod/inst/doc/k-calibration.html |only heemod-0.9.0/heemod/inst/examples/example_calibration.R |only heemod-0.9.0/heemod/inst/examples/example_define_calibration_fn.R |only heemod-0.9.0/heemod/inst/examples/example_eval_strategy.R | 8 heemod-0.9.0/heemod/inst/tabular/surv |only heemod-0.9.0/heemod/inst/tabular/test/REFERENCE_missingfunctions.csv |only heemod-0.9.0/heemod/inst/tabular/test/THR_parameters.csv |only heemod-0.9.0/heemod/inst/tabular/test/example_multinom_params.csv | 3 heemod-0.9.0/heemod/inst/tabular/test/example_multinom_params_dup_name.csv |only heemod-0.9.0/heemod/inst/tabular/thr/output/dsa.csv | 50 - heemod-0.9.0/heemod/inst/tabular/thr/output/icer_by_group.csv | 34 heemod-0.9.0/heemod/inst/tabular/thr/output/psa_values.csv | 42 - heemod-0.9.0/heemod/man/acceptability_curve.Rd | 14 heemod-0.9.0/heemod/man/add_hazards.Rd |only heemod-0.9.0/heemod/man/apply_af.Rd |only heemod-0.9.0/heemod/man/apply_hr.Rd |only heemod-0.9.0/heemod/man/apply_or.Rd |only heemod-0.9.0/heemod/man/as_expr_list.Rd | 2 heemod-0.9.0/heemod/man/calc_prob_from_surv.Rd |only heemod-0.9.0/heemod/man/calc_surv_from_prob.Rd |only heemod-0.9.0/heemod/man/calibrate_model.Rd |only heemod-0.9.0/heemod/man/check_cycle_inputs.Rd |only heemod-0.9.0/heemod/man/check_matrix.Rd | 6 heemod-0.9.0/heemod/man/check_names.Rd | 2 heemod-0.9.0/heemod/man/check_strategy_index.Rd | 2 heemod-0.9.0/heemod/man/cluster.Rd | 24 heemod-0.9.0/heemod/man/combine_models.Rd | 8 heemod-0.9.0/heemod/man/combine_probs.Rd | 2 heemod-0.9.0/heemod/man/compute_counts.Rd | 14 heemod-0.9.0/heemod/man/compute_icer.Rd | 6 heemod-0.9.0/heemod/man/compute_surv.Rd |only heemod-0.9.0/heemod/man/compute_values.Rd | 6 heemod-0.9.0/heemod/man/create_df_from_tabular.Rd | 6 heemod-0.9.0/heemod/man/create_matrix_from_tabular.Rd | 26 heemod-0.9.0/heemod/man/create_model_from_tabular.Rd | 12 heemod-0.9.0/heemod/man/create_parameters_from_tabular.Rd | 10 heemod-0.9.0/heemod/man/create_states_from_tabular.Rd | 30 heemod-0.9.0/heemod/man/define_calibration_fn.Rd |only heemod-0.9.0/heemod/man/define_correlation.Rd | 8 heemod-0.9.0/heemod/man/define_dsa.Rd | 6 heemod-0.9.0/heemod/man/define_inflow.Rd | 18 heemod-0.9.0/heemod/man/define_init.Rd |only heemod-0.9.0/heemod/man/define_multinom.Rd | 4 heemod-0.9.0/heemod/man/define_parameters.Rd | 40 - heemod-0.9.0/heemod/man/define_part_surv.Rd | 26 heemod-0.9.0/heemod/man/define_psa.Rd | 20 heemod-0.9.0/heemod/man/define_spline_survival.Rd |only heemod-0.9.0/heemod/man/define_state.Rd | 12 heemod-0.9.0/heemod/man/define_state_list.Rd | 12 heemod-0.9.0/heemod/man/define_strategy.Rd | 14 heemod-0.9.0/heemod/man/define_survival.Rd | 7 heemod-0.9.0/heemod/man/define_transition.Rd | 38 - heemod-0.9.0/heemod/man/discount.Rd | 7 heemod-0.9.0/heemod/man/discount_hack.Rd | 2 heemod-0.9.0/heemod/man/dispatch_strategy_hack.Rd | 6 heemod-0.9.0/heemod/man/distributions.Rd | 6 heemod-0.9.0/heemod/man/eval_models_from_tabular.Rd | 26 heemod-0.9.0/heemod/man/eval_parameters.Rd | 8 heemod-0.9.0/heemod/man/eval_resample.Rd | 10 heemod-0.9.0/heemod/man/eval_state_list.Rd | 14 heemod-0.9.0/heemod/man/eval_strategy.Rd | 37 - heemod-0.9.0/heemod/man/eval_strategy_newdata.Rd | 20 heemod-0.9.0/heemod/man/eval_surv.Rd |only heemod-0.9.0/heemod/man/eval_transition.Rd | 4 heemod-0.9.0/heemod/man/expand_state.Rd | 8 heemod-0.9.0/heemod/man/export_savi.Rd | 4 heemod-0.9.0/heemod/man/extract_params.Rd |only heemod-0.9.0/heemod/man/extract_strata.Rd |only heemod-0.9.0/heemod/man/extract_stratum.Rd |only heemod-0.9.0/heemod/man/file-checkers.Rd | 2 heemod-0.9.0/heemod/man/filter_blanks.Rd | 4 heemod-0.9.0/heemod/man/gather_model_info.Rd | 14 heemod-0.9.0/heemod/man/get_counts.Rd | 4 heemod-0.9.0/heemod/man/get_frontier.Rd | 2 heemod-0.9.0/heemod/man/get_parameter_names.Rd | 6 heemod-0.9.0/heemod/man/get_transition.Rd | 6 heemod-0.9.0/heemod/man/get_values.Rd | 4 heemod-0.9.0/heemod/man/heemod.Rd | 4 heemod-0.9.0/heemod/man/heemod_scale.Rd | 10 heemod-0.9.0/heemod/man/insert.Rd | 2 heemod-0.9.0/heemod/man/interp_heemod.Rd | 6 heemod-0.9.0/heemod/man/is.wholenumber.Rd | 2 heemod-0.9.0/heemod/man/look_up.Rd | 14 heemod-0.9.0/heemod/man/make_names.Rd | 2 heemod-0.9.0/heemod/man/modify.Rd | 2 heemod-0.9.0/heemod/man/parse_multi_spec.Rd | 26 heemod-0.9.0/heemod/man/plot.dsa.Rd | 19 heemod-0.9.0/heemod/man/plot.psa.Rd | 10 heemod-0.9.0/heemod/man/plot.run_model.Rd | 4 heemod-0.9.0/heemod/man/plot.surv_obj.Rd |only heemod-0.9.0/heemod/man/pool.Rd |only heemod-0.9.0/heemod/man/probability.Rd | 2 heemod-0.9.0/heemod/man/project.Rd |only heemod-0.9.0/heemod/man/project_fn.Rd |only heemod-0.9.0/heemod/man/reexports.Rd |only heemod-0.9.0/heemod/man/rescale_discount_rate.Rd | 6 heemod-0.9.0/heemod/man/run_dsa.Rd | 8 heemod-0.9.0/heemod/man/run_model.Rd | 59 - heemod-0.9.0/heemod/man/run_model_tabular.Rd | 28 heemod-0.9.0/heemod/man/run_psa.Rd | 10 heemod-0.9.0/heemod/man/save_outputs.Rd | 4 heemod-0.9.0/heemod/man/set_covariates.Rd |only heemod-0.9.0/heemod/man/summary.run_model.Rd | 4 heemod-0.9.0/heemod/man/update-model.Rd | 18 heemod-0.9.0/heemod/man/who-mortality.Rd | 37 - heemod-0.9.0/heemod/man/wtd_summary.Rd | 2 heemod-0.9.0/heemod/tests/testthat/Rplots.pdf |binary heemod-0.9.0/heemod/tests/testthat/test_get_code.R | 15 heemod-0.9.0/heemod/tests/testthat/test_gho.R | 73 + heemod-0.9.0/heemod/tests/testthat/test_heterogeneity.R | 6 heemod-0.9.0/heemod/tests/testthat/test_model.R | 33 heemod-0.9.0/heemod/tests/testthat/test_parallel.R | 9 heemod-0.9.0/heemod/tests/testthat/test_part_surv.R |only heemod-0.9.0/heemod/tests/testthat/test_probabilistic.R | 2 heemod-0.9.0/heemod/tests/testthat/test_run_model.R | 9 heemod-0.9.0/heemod/tests/testthat/test_sensitivity.R | 7 heemod-0.9.0/heemod/tests/testthat/test_surv_eval.R |only heemod-0.9.0/heemod/tests/testthat/test_tabular_input.R | 121 ++- heemod-0.9.0/heemod/vignettes/b-time-dependency.Rmd | 4 heemod-0.9.0/heemod/vignettes/c-homogeneous.Rmd | 2 heemod-0.9.0/heemod/vignettes/f-sensitivity.Rmd | 9 heemod-0.9.0/heemod/vignettes/h-tabular.Rmd | 1 heemod-0.9.0/heemod/vignettes/i-reproduction.Rmd | 2 heemod-0.9.0/heemod/vignettes/j-survival.Rmd | 165 +++- heemod-0.9.0/heemod/vignettes/k-calibration.Rmd |only 195 files changed, 2892 insertions(+), 1749 deletions(-)
Title: Simple Key-Value Database
Description: Implements a simple key-value style database where character string keys
are associated with data values that are stored on the disk. A simple interface is provided for inserting,
retrieving, and deleting data from the database. Utilities are provided that allow 'filehash' databases to be
treated much like environments and lists are already used in R. These utilities are provided to encourage
interactive and exploratory analysis on large datasets. Three different file formats for representing the
database are currently available and new formats can easily be incorporated by third parties for use in the
'filehash' framework.
Author: Roger D. Peng <rdpeng@jhu.edu>
Maintainer: Roger D. Peng <rdpeng@jhu.edu>
Diff between filehash versions 2.3 dated 2015-08-16 and 2.4-1 dated 2017-04-07
DESCRIPTION | 7 +++---- MD5 | 19 ++++++++++--------- NAMESPACE | 2 +- R/filehash-DB1.R | 6 +++--- R/hash.R | 4 ++-- R/zzz.R | 4 ++-- build/vignette.rds |binary inst/CITATION | 2 +- inst/doc/filehash.pdf |binary man/dbInit.Rd | 4 ---- src/init.c |only 11 files changed, 22 insertions(+), 26 deletions(-)
Title: Install Packages from Snapshots on the Checkpoint Server for
Reproducibility
Description: The goal of checkpoint is to solve the problem of package
reproducibility in R. Specifically, checkpoint allows you to install packages
as they existed on CRAN on a specific snapshot date as if you had a CRAN time
machine. To achieve reproducibility, the checkpoint() function installs the
packages required or called by your project and scripts to a local library
exactly as they existed at the specified point in time. Only those packages
are available to your project, thereby avoiding any package updates that came
later and may have altered your results. In this way, anyone using checkpoint's
checkpoint() can ensure the reproducibility of your scripts or projects at any
time. To create the snapshot archives, once a day (at midnight UTC) Microsoft
refreshes the Austria CRAN mirror on the "Microsoft R Archived Network"
server (<https://mran.microsoft.com/>). Immediately after completion
of the rsync mirror process, the process takes a snapshot, thus creating the
archive. Snapshot archives exist starting from 2014-09-17.
Author: Microsoft Corporation
Maintainer: Andrie de Vries <adevries@microsoft.com>
Diff between checkpoint versions 0.3.18 dated 2016-10-31 and 0.3.22 dated 2017-04-07
DESCRIPTION | 17 - MD5 | 79 +++-- NAMESPACE | 3 R/access_date.R |only R/checkpoint-package.R | 24 + R/checkpoint.R | 238 ++++++++--------- R/checkpoint_internals.R |only R/checkpoint_log.R | 1 R/checkpoint_paths.R | 56 ++-- R/checkpoint_remove.R | 72 ++++- R/fixRstudioBug.R | 143 ++++++---- R/installMissingBasePackages.R | 16 - R/mock-install-packages.R |only R/mranUrl.R | 100 ++----- R/scanRepoPackages.R | 64 ++-- R/setSnapshot.R | 36 ++ build/vignette.rds |binary inst/doc/checkpoint.R | 13 inst/doc/checkpoint.Rmd | 19 - inst/doc/checkpoint.html | 136 ++++++++-- inst/doc/managing-checkpoint-archives.R |only inst/doc/managing-checkpoint-archives.Rmd |only inst/doc/managing-checkpoint-archives.html |only inst/doc/using-checkpoint-with-knitr.R |only inst/doc/using-checkpoint-with-knitr.Rmd |only inst/doc/using-checkpoint-with-knitr.html |only inst/examples/example_mranurl.R |only man/checkpoint-package.Rd | 27 +- man/checkpoint.Rd | 71 +++-- man/checkpointArchives.Rd | 10 man/checkpointRemove.Rd | 22 + man/getAccessDate.Rd |only man/getValidSnapshots.Rd | 18 - man/mranUrl.Rd |only man/setSnapshot.Rd | 14 - man/unCheckpoint.Rd |only tests/test-all.R | 5 tests/testthat/helper.R |only tests/testthat/test-0-is-404.R | 60 +--- tests/testthat/test-0-snapshots.R | 111 ++++---- tests/testthat/test-1-scan.R | 176 ++++++------- tests/testthat/test-2-snapshot-dates.R | 72 ++--- tests/testthat/test-3-checkpoint.R | 337 +++++++++++++------------ tests/testthat/test-4-mranUrl.R |only tests/testthat/test-5-search-detach.R |only tests/testthat/test-6-accessdate.R |only tests/testthat/test-7-anyRfiles.R |only tests/testthat/test-8-authoriseFileSystemUse.R |only vignettes/checkpoint.Rmd | 19 - vignettes/managing-checkpoint-archives.Rmd |only vignettes/using-checkpoint-with-knitr.Rmd |only 51 files changed, 1116 insertions(+), 843 deletions(-)
Title: Calculate TL-Moments and Convert Them to Distribution Parameters
Description: Calculates empirical TL-moments (trimmed L-moments) of arbitrary
order and trimming, and converts them to distribution parameters.
Author: Jona Lilienthal
Maintainer: Jona Lilienthal <lilienthal@statistik.tu-dortmund.de>
Diff between TLMoments versions 0.6.3.1 dated 2017-01-18 and 0.7.2.1 dated 2017-04-07
DESCRIPTION | 16 - MD5 | 110 +++++------ NAMESPACE | 18 + R/PWM.R | 1 R/PWMs.R | 2 R/TLMoment.R | 1 R/TLMoments.R | 7 R/as.PWMs.R | 1 R/as.TLMoments.R | 1 R/as.parameters.R | 23 +- R/covfunctions.R | 9 R/distribution_functions.R |only R/est_cov.R | 256 ++++++++++++++++--------- R/est_paramcov.R | 82 +++++--- R/est_pwmcov.R | 24 +- R/est_quancov.R | 86 ++++++-- R/est_tlmcov.R | 105 +++++++--- R/helper.R | 57 +++-- R/parameters.R | 251 +++++++++++++++---------- R/quantiles.R | 17 - R/regionalize.R | 5 R/summary.PWMs.R | 15 + R/summary.TLMoments.R | 57 ++--- R/summary.parameters.R | 32 ++- R/summary.quantiles.R | 23 +- R/zzz.R | 4 build/vignette.rds |binary inst/doc/comparison_of_computation_time.R | 23 +- inst/doc/comparison_of_computation_time.Rmd | 25 +- inst/doc/comparison_of_computation_time.html | 99 +++++---- inst/doc/short_introduction.R | 14 + inst/doc/short_introduction.Rmd | 49 +++- inst/doc/short_introduction.html | 269 ++++++++++++++++----------- man/PWM.Rd | 4 man/PWMs.Rd | 9 man/TLMoment.Rd | 4 man/TLMoments.Rd | 13 - man/as.PWMs.Rd | 11 - man/as.TLMoments.Rd | 11 - man/as.parameters.Rd | 27 +- man/est_cov.Rd | 162 +++++++++------- man/est_paramcov.Rd | 21 +- man/est_pwmcov.Rd | 9 man/est_quancov.Rd | 19 + man/est_tlmcov.Rd | 34 +-- man/gev.Rd |only man/gpd.Rd |only man/gum.Rd |only man/ln3.Rd |only man/parameters.Rd | 58 +++-- man/quantiles.Rd | 20 -- man/regionalize.Rd | 5 man/summary.PWMs.Rd | 8 man/summary.TLMoments.Rd | 20 +- man/summary.parameters.Rd | 12 - man/summary.quantiles.Rd | 12 - src/init.c |only vignettes/comparison_of_computation_time.Rmd | 25 +- vignettes/short_introduction.Rmd | 49 +++- 59 files changed, 1356 insertions(+), 859 deletions(-)
Title: Character String Processing Facilities
Description: Allows for fast, correct, consistent, portable,
as well as convenient character string/text processing in every locale
and any native encoding. Owing to the use of the ICU library,
the package provides R users with platform-independent functions
known to Java, Perl, Python, PHP, and Ruby programmers. Available
features include: pattern searching (e.g., with ICU Java-like regular
expressions or the Unicode Collation Algorithm), random string generation,
case mapping, string transliteration, concatenation,
Unicode normalization, date-time formatting and parsing, etc.
Author: Marek Gagolewski [aut, cre], Bartek Tartanus [ctb],
and other contributors (stringi source code);
IBM and other contributors (ICU4C 55.1 source code);
Unicode, Inc. (Unicode Character Database)
Maintainer: Marek Gagolewski <gagolews@rexamine.com>
Diff between stringi versions 1.1.3 dated 2017-03-21 and 1.1.5 dated 2017-04-07
DESCRIPTION | 21 ++- INSTALL | 10 - MD5 | 214 +++++++++++++++++++-------------------- NEWS | 22 +++- R/draft_encdetect.R | 22 ++-- R/draft_files.R | 10 - R/encoding_management.R | 8 - R/install.R | 33 ++++-- configure | 130 +++++++++++++++++------ inst/AUTHORS | 2 man/oper_comparison.Rd | 25 ++-- man/oper_plus.Rd | 1 man/stri_compare.Rd | 11 -- man/stri_count.Rd | 1 man/stri_count_boundaries.Rd | 7 - man/stri_datetime_add.Rd | 5 man/stri_datetime_create.Rd | 1 man/stri_datetime_fields.Rd | 1 man/stri_datetime_format.Rd | 2 man/stri_datetime_fstr.Rd | 1 man/stri_datetime_now.Rd | 1 man/stri_datetime_symbols.Rd | 1 man/stri_detect.Rd | 3 man/stri_dup.Rd | 1 man/stri_duplicated.Rd | 1 man/stri_enc_detect.Rd | 15 +- man/stri_enc_detect2.Rd | 21 +-- man/stri_enc_fromutf32.Rd | 1 man/stri_enc_info.Rd | 3 man/stri_enc_isascii.Rd | 1 man/stri_enc_isutf16.Rd | 1 man/stri_enc_isutf8.Rd | 1 man/stri_enc_list.Rd | 1 man/stri_enc_mark.Rd | 3 man/stri_enc_set.Rd | 7 - man/stri_enc_toascii.Rd | 1 man/stri_enc_tonative.Rd | 1 man/stri_enc_toutf32.Rd | 1 man/stri_enc_toutf8.Rd | 1 man/stri_encode.Rd | 3 man/stri_escape_unicode.Rd | 1 man/stri_extract.Rd | 21 +-- man/stri_extract_boundaries.Rd | 13 +- man/stri_flatten.Rd | 1 man/stri_info.Rd | 1 man/stri_isempty.Rd | 1 man/stri_join.Rd | 3 man/stri_join_list.Rd | 3 man/stri_length.Rd | 1 man/stri_list2matrix.Rd | 1 man/stri_locale_info.Rd | 1 man/stri_locale_list.Rd | 1 man/stri_locale_set.Rd | 3 man/stri_locate.Rd | 27 ++-- man/stri_locate_boundaries.Rd | 13 +- man/stri_match.Rd | 7 - man/stri_numbytes.Rd | 1 man/stri_opts_brkiter.Rd | 1 man/stri_opts_collator.Rd | 1 man/stri_opts_fixed.Rd | 1 man/stri_opts_regex.Rd | 1 man/stri_order.Rd | 1 man/stri_pad.Rd | 3 man/stri_rand_lipsum.Rd | 1 man/stri_rand_shuffle.Rd | 1 man/stri_rand_strings.Rd | 1 man/stri_read_lines.Rd | 5 man/stri_read_raw.Rd | 7 - man/stri_replace.Rd | 19 +-- man/stri_replace_na.Rd | 1 man/stri_reverse.Rd | 1 man/stri_split.Rd | 5 man/stri_split_boundaries.Rd | 7 - man/stri_split_lines.Rd | 2 man/stri_startsendswith.Rd | 9 - man/stri_stats_general.Rd | 1 man/stri_stats_latex.Rd | 1 man/stri_sub.Rd | 1 man/stri_subset.Rd | 5 man/stri_timezone_info.Rd | 1 man/stri_timezone_list.Rd | 1 man/stri_timezone_set.Rd | 1 man/stri_trans_casemap.Rd | 13 +- man/stri_trans_char.Rd | 1 man/stri_trans_general.Rd | 1 man/stri_trans_list.Rd | 1 man/stri_trans_nf.Rd | 13 +- man/stri_trim.Rd | 10 - man/stri_unescape_unicode.Rd | 1 man/stri_unique.Rd | 1 man/stri_width.Rd | 1 man/stri_wrap.Rd | 1 man/stri_write_lines.Rd | 1 man/stringi-arguments.Rd | 2 man/stringi-encoding.Rd | 34 +++--- man/stringi-locale.Rd | 2 man/stringi-package.Rd | 18 +-- man/stringi-search-boundaries.Rd | 19 +-- man/stringi-search-charclass.Rd | 2 man/stringi-search-coll.Rd | 8 - man/stringi-search-fixed.Rd | 2 man/stringi-search-regex.Rd | 2 man/stringi-search.Rd | 47 ++++---- src/Makevars.win | 4 src/stri_brkiter.cpp | 2 src/stri_brkiter.h | 10 - src/stri_external.h | 1 src/stri_stringi.cpp | 6 - 108 files changed, 493 insertions(+), 482 deletions(-)
Title: Serializable Representations
Description: String and binary representations of objects for several formats /
mime types.
Author: Philipp Angerer [aut, cre],
Thomas Kluyver [aut],
Jan Schulz [aut],
abielr [ctb],
Denilson Figueiredo de Sa [ctb],
Jim Hester [ctb],
karldw [ctb]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>
Diff between repr versions 0.10 dated 2016-11-25 and 0.12.0 dated 2017-04-07
DESCRIPTION | 12 +++---- MD5 | 46 ++++++++++++++-------------- NAMESPACE | 5 +++ R/repr_datatable.r |only R/repr_htmlwidget.r | 13 +++++++ R/repr_recordedplot.r | 2 - R/repr_vector.r | 3 + R/utils.r | 2 - man/repr-generics.Rd | 17 ++++------ man/repr-options.Rd | 2 - man/repr-package.Rd | 1 man/repr.Rd | 1 man/repr_-times-.data.table.Rd |only man/repr_-times-.function.Rd | 1 man/repr_-times-.help_files_with_topic.Rd | 3 - man/repr_-times-.htmlwidget.Rd | 9 ++++- man/repr_-times-.list.Rd | 3 - man/repr_-times-.matrix-slash-data.frame.Rd | 9 ++--- man/repr_-times-.packageIQR.Rd | 3 - man/repr_-times-.recordedplot.Rd | 9 ++--- man/repr_-times-.vector.Rd | 39 +++++++++++------------ man/repr_text.Rd | 1 man/times-2repr.Rd | 3 - tests/testthat/test_escaping.r | 4 ++ tests/testthat/test_vector.r | 10 ++++++ 25 files changed, 112 insertions(+), 86 deletions(-)
Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt,
Pierre Legendre, Dan McGlinn, Peter R. Minchin, R. B. O'Hara,
Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs,
Helene Wagner
Maintainer: Jari Oksanen <jari.oksanen@oulu.fi>
Diff between vegan versions 2.4-2 dated 2017-01-17 and 2.4-3 dated 2017-04-07
DESCRIPTION | 8 ++-- MD5 | 64 ++++++++++++++++++++------------------- NAMESPACE | 2 - R/as.mlm.cca.R | 10 +++--- R/as.mlm.rda.R | 7 ++-- R/biplot.rda.R | 2 - R/cca.default.R | 6 ++- R/envfit.default.R | 2 - R/intersetcor.R | 15 ++++++--- R/ordiParseFormula.R | 13 ++++++-- R/ordiR2step.R | 55 ++++++++++++++++------------------ R/ordiTerminfo.R | 5 +-- R/ordiYbar.R |only R/ordispider.R | 11 ++++-- R/ordisurf.R | 9 +++-- R/spenvcor.R | 10 +++--- R/tolerance.cca.R | 23 +++++++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 69 ++++++++++++++++++++++++++++++++++++++++++- inst/doc/FAQ-vegan.Rmd | 12 +++---- inst/doc/FAQ-vegan.html | 12 +++---- inst/doc/decision-vegan.pdf |binary inst/doc/diversity-vegan.pdf |binary inst/doc/intro-vegan.pdf |binary inst/doc/partitioning.pdf |binary man/MOStest.Rd | 2 - man/cca.object.Rd | 32 +++++++++++++------ man/envfit.Rd | 22 ++++++------- man/mso.Rd | 2 - man/ordistep.Rd | 64 +++++++++++++++++++-------------------- man/ordisurf.Rd | 2 - src/init.c |only vignettes/FAQ-vegan.Rmd | 12 +++---- 34 files changed, 294 insertions(+), 177 deletions(-)
Title: A Two-Stage Approach to Maximize Interpretability of Drug
Response Models Based on Multiple Molecular Data Types
Description: A two-stage regression method that can be used when various input data types are correlated, for example gene expression and methylation in drug response prediction. In the first stage it uses the upstream features (such as methylation) to predict the response variable (such as drug response), and in the second stage it uses the downstream features (such as gene expression) to predict the residuals of the first stage. In our manuscript (Aben et al., 2016, <doi:10.1093/bioinformatics/btw449>), we show that using TANDEM prevents the model from being dominated by gene expression and that the features selected by TANDEM are more interpretable.
Author: Nanne Aben
Maintainer: Nanne Aben <nanne.aben@gmail.com>
Diff between TANDEM versions 1.0.0 dated 2016-09-19 and 1.0.1 dated 2017-04-07
DESCRIPTION | 12 ++--- MD5 | 26 ++++++------ NEWS.md |only R/functions.R | 9 ++-- README.md |only build/vignette.rds |binary inst/doc/my-vignette.Rmd | 2 inst/doc/my-vignette.html | 86 ++++++++++++++++++++++++------------------ man/coef.tandem.Rd | 1 man/example_data.Rd | 1 man/nested.cv.Rd | 1 man/predict.tandem.Rd | 1 man/relative.contributions.Rd | 7 ++- man/tandem.Rd | 1 vignettes/my-vignette.Rmd | 2 15 files changed, 84 insertions(+), 65 deletions(-)
Title: Rank Preserving Structural Failure Time Models
Description: Implements methods described by the paper Robins and Tsiatis (1991) <DOI:10.1080/03610929108830654>. These use g-estimation to estimate the causal effect of a treatment in a two-armed randomised control trial where non-compliance exists and is measured, under an assumption of an accelerated failure time model and no unmeasured confounders.
Author: Simon Bond [aut, cre] (primary author of code, secondary author of
vignette),
Annabel Allison [aut] (primary author of vignette, secondary author of
code)
Maintainer: Simon Bond <simon.bond@addenbrookes.nhs.uk>
Diff between rpsftm versions 1.0.2 dated 2016-11-25 and 1.1.0 dated 2017-04-07
DESCRIPTION | 8 MD5 | 84 ++- NAMESPACE | 34 - NEWS.md | 49 +- R/data.R | 42 - R/est_eqn.R | 80 +-- R/extract_z.R | 118 ++--- R/plot.rpsftm.R | 46 +- R/print.rpsftm.R | 159 ++++++- R/rand.R | 48 +- R/rpsftm-package.R | 36 - R/rpsftm.R | 595 ++++++++++++++------------- R/summary.rpsftm.R | 177 ++++++-- R/terms.inner.R | 56 +- R/untreated.R | 96 ++-- README.md | 68 +-- build/vignette.rds |binary inst/doc/rpsftm_vignette.R | 138 +++--- inst/doc/rpsftm_vignette.Rmd | 578 +++++++++++++-------------- inst/doc/rpsftm_vignette.html | 716 ++++++++++++++++----------------- man/est_eqn.Rd | 82 +-- man/extract_z.Rd | 90 ++-- man/immdef.Rd | 62 +- man/plot.rpsftm.Rd | 46 +- man/print.coxph.Rd |only man/print.rpsftm.Rd | 46 +- man/print.summary.coxph.Rd |only man/print.summary.survreg.Rd |only man/print.survreg.Rd |only man/rand.Rd | 50 +- man/rpsftm-package.Rd | 52 +- man/rpsftm.Rd | 179 ++++---- man/summary.rpsftm.Rd | 46 +- man/terms.inner.Rd | 42 - man/untreated.Rd | 72 +-- tests/testthat.R | 8 tests/testthat/test_errors.R | 379 +++++++++-------- tests/testthat/test_rpsftm.R | 605 +++++++++++++++------------- tools |only vignettes/dev/adjustedHR.Rmd | 216 +++++----- vignettes/dev/rpsftm_vignette_v1.Rmd | 574 +++++++++++++-------------- vignettes/dev/rpsftm_vignette_v2.Rmd | 744 +++++++++++++++++------------------ vignettes/rpsftm_vignette.Rmd | 578 +++++++++++++-------------- vignettes/rpsftm_vignette_files |only 44 files changed, 3672 insertions(+), 3327 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-02 2160.2
2012-03-27 2160.1
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression are covered in
this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>
Diff between sdcTable versions 0.22.1 dated 2017-02-23 and 0.22.4 dated 2017-04-07
DESCRIPTION | 8 ++-- MD5 | 21 ++++++------ NAMESPACE | 1 R/export_functions.r | 73 ++++++++++++++++++++++++++++++++++++++++--- R/helper_functions.r | 40 +++++++++++++++++------ R/methods_class_sdcProblem.r | 10 ++++- R/tauBatch_helpers.R | 49 +++++++++++----------------- build/vignette.rds |binary inst/doc/sdcTable.pdf |binary man/makeProblem.Rd | 11 ++++-- man/sdcProb2df.Rd |only src/suppMultDimTable.cpp | 2 - 12 files changed, 149 insertions(+), 66 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu, Simon Firestone and Ryan Kyle
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 0.9-79 dated 2016-07-18 and 0.9-82 dated 2017-04-07
DESCRIPTION | 8 +- MD5 | 40 +++++------ NAMESPACE | 2 R/epi.2by2.R | 51 ++++++-------- R/epi.ccc.R | 173 ++++++++++++++++++++++++++++++-------------------- R/epi.conf.R | 36 ++++++---- R/epi.dsl.R | 28 ++++---- R/epi.iv.R | 28 ++++---- R/epi.kappa.R | 37 ++++++---- R/epi.mh.R | 28 ++++---- R/epi.nomogram.R | 4 - R/epi.smd.R | 13 ++- R/epi.tests.R | 38 ++++++---- man/epi.betabuster.Rd | 17 +++- man/epi.ccc.Rd | 89 +++++++++++++++++-------- man/epi.dsl.Rd | 8 +- man/epi.edr.Rd | 34 +++++++-- man/epi.empbayes.Rd | 32 ++++++--- man/epi.iv.Rd | 8 +- man/epi.mh.Rd | 8 +- man/epi.nomogram.Rd | 10 ++ 21 files changed, 410 insertions(+), 282 deletions(-)
Title: Submit R Calculations to a 'SLURM' Cluster
Description: Functions that simplify the R interface the 'SLURM' cluster
workload manager, and automate the process of dividing a parallel calculation
across cluster nodes.
Author: Philippe Marchand [aut],
Mike Smorul [ctb],
Ian Carroll [ctb, cre]
Maintainer: Ian Carroll <icarroll@sesync.org>
Diff between rslurm versions 0.3.1 dated 2016-06-18 and 0.3.2 dated 2017-04-07
rslurm-0.3.1/rslurm/inst/doc/rslurm-vignette.Rmd |only rslurm-0.3.1/rslurm/inst/doc/rslurm-vignette.html |only rslurm-0.3.1/rslurm/vignettes/rslurm-vignette.Rmd |only rslurm-0.3.2/rslurm/DESCRIPTION | 28 - rslurm-0.3.2/rslurm/MD5 | 53 +-- rslurm-0.3.2/rslurm/NEWS.md | 16 rslurm-0.3.2/rslurm/R/cancel_print_cleanup.R | 4 rslurm-0.3.2/rslurm/R/get_slurm_out.R | 19 - rslurm-0.3.2/rslurm/R/rslurm.R | 2 rslurm-0.3.2/rslurm/R/slurm_apply.R | 32 + rslurm-0.3.2/rslurm/R/slurm_call.R | 32 + rslurm-0.3.2/rslurm/R/slurm_job.R | 5 rslurm-0.3.2/rslurm/R/slurm_utils.R | 33 + rslurm-0.3.2/rslurm/README.md | 235 -------------- rslurm-0.3.2/rslurm/build/vignette.rds |binary rslurm-0.3.2/rslurm/inst/doc/overview.R |only rslurm-0.3.2/rslurm/inst/doc/overview.Rmd |only rslurm-0.3.2/rslurm/inst/doc/overview.html |only rslurm-0.3.2/rslurm/inst/templates/slurm_run_R.txt | 4 rslurm-0.3.2/rslurm/inst/templates/slurm_run_single_R.txt | 4 rslurm-0.3.2/rslurm/man/cancel_slurm.Rd | 1 rslurm-0.3.2/rslurm/man/cleanup_files.Rd | 5 rslurm-0.3.2/rslurm/man/get_slurm_out.Rd | 5 rslurm-0.3.2/rslurm/man/print_job_status.Rd | 1 rslurm-0.3.2/rslurm/man/rslurm-package.Rd | 6 rslurm-0.3.2/rslurm/man/slurm_apply.Rd | 12 rslurm-0.3.2/rslurm/man/slurm_call.Rd | 12 rslurm-0.3.2/rslurm/man/slurm_job.Rd | 5 rslurm-0.3.2/rslurm/tests/testthat/test_slurm_apply.R | 20 - rslurm-0.3.2/rslurm/tests/testthat/test_slurm_call.R | 15 rslurm-0.3.2/rslurm/vignettes/overview.Rmd |only 31 files changed, 197 insertions(+), 352 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-12 1.1.2
2014-12-12 1.0.3
2014-07-22 1.0.0
Title: Spatial Methods and Indices
Description: Functions for spatial methods based on generalized estimating equations (GEE) and
wavelet-revised methods (WRM), functions for scaling by wavelet multiresolution regression (WMRR),
conducting multi-model inference, and stepwise model selection. Further, contains functions
for spatially corrected model accuracy measures.
Author: Gudrun Carl [cre, aut], Ingolf Kuehn [aut], Sam Levin [aut]
Maintainer: Sam Levin <levisc8@gmail.com>
Diff between spind versions 2.0.0 dated 2017-04-04 and 2.0.1 dated 2017-04-07
DESCRIPTION | 6 MD5 | 11 inst/CITATION |only inst/doc/spind_vignette.R | 108 ++++- inst/doc/spind_vignette.Rmd | 185 +++++++-- inst/doc/spind_vignette.html | 836 +++++++++++++++++++++++++++---------------- vignettes/spind_vignette.Rmd | 2 7 files changed, 768 insertions(+), 380 deletions(-)
Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended
for people coming from other statistical software packages like 'SPSS', and/
or who are new to R), supporting following common tasks when working with
data : 1) Reading and writing data between R and other statistical software
packages like 'SPSS', 'SAS' or 'Stata' and working with labelled data; this
includes easy ways to get and set label attributes, to convert labelled
vectors into factors (and vice versa), or to deal with multiple declared
missing values etc. 2) Data transformation tasks like recoding,
dichotomizing or grouping variables, setting and replacing missing values.
The data transformation functions also support labelled data, and all integrate
seamlessly into a 'tidyverse'-workflow.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 2.3.1 dated 2017-03-06 and 2.4.0 dated 2017-04-07
DESCRIPTION | 21 MD5 | 250 ++++---- NAMESPACE | 315 +++++----- NEWS | 464 +++++++-------- NEWS.md | 340 ++++++----- R/add_columns.R | 318 +++++----- R/add_labels.R | 39 - R/as_labelled.R | 256 ++++---- R/copy_labels.R | 3 R/dicho.R | 281 ++++----- R/drop_labels.R | 10 R/fill_labels.R | 3 R/find_var.R | 338 +++++----- R/get_labels.R | 587 +++++++++---------- R/get_na.R | 9 R/get_note.R | 156 ++--- R/get_values.R | 191 +++--- R/group_str.R | 34 - R/group_var.R | 505 ++++++++-------- R/helpfunctions.R | 329 +++++----- R/is_crossed.R | 167 ++--- R/is_empty.R | 282 ++++----- R/is_num_fac.R | 2 R/notin.R |only R/read_write.R | 609 +++++++++---------- R/rec.R | 854 ++++++++++++++------------- R/rec_pattern.R | 136 ++-- R/recode_to.R | 268 ++++---- R/ref_lvl.R | 243 ++++--- R/remove_all_labels.R | 119 ++- R/remove_labels.R | 2 R/replace_na.R | 319 +++++----- R/row_sums.R |only R/set_label.R | 2 R/set_labels.R | 5 R/set_na.R | 10 R/split_var.R | 275 ++++---- R/spread_coef.R | 27 R/std.R | 228 +++---- R/str_pos.R | 270 ++++---- R/to_factor.R | 291 ++++----- R/to_label.R | 612 +++++++++---------- R/to_long.R | 5 R/to_value.R | 322 +++++----- R/unlabel.R | 111 +-- R/var_labels.R | 155 +++-- R/word_wrap.R | 133 ++-- R/zap_labels.R | 601 +++++++++---------- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/design_philosophy.R | 104 +-- inst/doc/design_philosophy.Rmd | 24 inst/doc/design_philosophy.html | 591 +++++++++---------- inst/doc/exploringdatasets.R | 144 ++-- inst/doc/exploringdatasets.Rmd | 2 inst/doc/exploringdatasets.html | 519 ++++++++-------- inst/doc/intro_sjmisc.R | 566 +++++++++--------- inst/doc/intro_sjmisc.Rmd | 18 inst/doc/intro_sjmisc.html | 1231 +++++++++++++++++++--------------------- inst/doc/labelleddata.R | 110 +-- inst/doc/labelleddata.Rmd | 3 inst/doc/labelleddata.html | 734 +++++++++++------------ man/add_columns.Rd | 226 +++---- man/add_labels.Rd | 244 +++---- man/as_labelled.Rd | 112 +-- man/big_mark.Rd | 66 +- man/copy_labels.Rd | 94 +-- man/count_na.Rd | 112 +-- man/descr.Rd | 122 +-- man/dicho.Rd | 188 +++--- man/efc.Rd | 64 +- man/empty_cols.Rd | 98 +-- man/find_var.Rd | 197 +++--- man/flat_table.Rd | 140 ++-- man/frq.Rd | 164 ++--- man/get_label.Rd | 162 ++--- man/get_labels.Rd | 334 +++++----- man/get_na.Rd | 132 ++-- man/get_note.Rd | 74 +- man/get_values.Rd | 122 +-- man/grapes-nin-grapes.Rd |only man/group_str.Rd | 140 ++-- man/group_var.Rd | 278 ++++----- man/is_crossed.Rd | 146 ++-- man/is_empty.Rd | 116 +-- man/is_even.Rd | 68 +- man/is_labelled.Rd | 36 - man/is_num_fac.Rd | 66 +- man/lbl_df.Rd | 72 +- man/merge_df.Rd | 118 +-- man/merge_imputations.Rd | 130 ++-- man/read_spss.Rd | 144 ++-- man/rec.Rd | 347 +++++------ man/rec_pattern.Rd | 108 +-- man/recode_to.Rd | 187 +++--- man/reexports.Rd | 32 - man/ref_lvl.Rd | 124 ++-- man/remove_all_labels.Rd | 64 +- man/replace_na.Rd | 210 +++--- man/row_sums.Rd |only man/set_label.Rd | 228 +++---- man/set_labels.Rd | 344 +++++------ man/set_na.Rd | 256 ++++---- man/set_note.Rd | 74 +- man/split_var.Rd | 218 +++---- man/spread_coef.Rd | 222 +++---- man/std.Rd | 148 ++-- man/str_contains.Rd | 166 ++--- man/str_pos.Rd | 156 ++--- man/to_character.Rd | 232 +++---- man/to_dummy.Rd | 118 +-- man/to_factor.Rd | 208 +++--- man/to_label.Rd | 280 ++++----- man/to_long.Rd | 192 +++--- man/to_value.Rd | 180 ++--- man/trim.Rd | 64 +- man/unlabel.Rd | 78 +- man/var_rename.Rd | 64 +- man/word_wrap.Rd | 64 +- man/write_spss.Rd | 72 +- man/zap_inf.Rd | 98 +-- man/zap_labels.Rd | 278 ++++----- man/zap_na_tags.Rd | 94 +-- vignettes/design_philosophy.Rmd | 24 vignettes/exploringdatasets.Rmd | 2 vignettes/intro_sjmisc.Rmd | 18 vignettes/labelleddata.Rmd | 3 128 files changed, 11912 insertions(+), 11551 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 0.17 dated 2017-01-23 and 0.18.1 dated 2017-04-07
DESCRIPTION | 12 +-- MD5 | 119 ++++++++++++++++++------------------ NAMESPACE | 2 R/gibbs_AR.R | 4 - R/gibbs_NP.R | 4 - R/gibbs_NPC.R | 8 +- R/intern__gibbs_core.R | 109 ++++++++++++++++++++++++-------- R/intern__gibbs_toggle_ar.R | 16 ++-- R/intern__gibbs_util.R | 44 ++++++------- man/Cn.Rd | 1 man/acceptanceRate.Rd | 1 man/acvMatrix.Rd | 1 man/ar_lik.Rd | 1 man/ar_screeType.Rd | 1 man/arma_conditional.Rd | 1 man/arma_partial.Rd | 1 man/densityMixture.Rd | 1 man/dtex.kurt.Rd | 1 man/fast_ft.Rd | 1 man/fast_ift.Rd | 1 man/fast_mean.Rd | 1 man/filenameMCMC.Rd | 1 man/genEpsARC.Rd | 1 man/genEpsARMAC.Rd | 1 man/genEpsMAC.Rd | 1 man/generalizedGaussian.alpha.Rd | 1 man/generalizedGaussian.kurtosis.Rd | 1 man/gibbs_AR.Rd | 3 man/gibbs_NP.Rd | 3 man/gibbs_NPC.Rd | 7 -- man/gibbs_pacf.Rd | 1 man/gibbs_toggle_ar.Rd | 1 man/l_generalizedGaussian.Rd | 1 man/llike.Rd | 1 man/llike_full.Rd | 1 man/llike_pacf.Rd | 1 man/logfuller.Rd | 1 man/logrosenthal.Rd | 1 man/lpost.Rd | 1 man/lpost_pacf.Rd | 1 man/lprior.Rd | 1 man/lprior_pacf.Rd | 1 man/mixtureWeight.Rd | 1 man/nll_generalizedGaussian.Rd | 1 man/nll_norm.Rd | 1 man/nll_norm_unnormalized.Rd | 1 man/nll_t.Rd | 1 man/omegaFreq.Rd | 1 man/pFromV.Rd | 1 man/pacf2AR.Rd | 1 man/pacf2ARacv.Rd | 1 man/pacfToAR.Rd | 1 man/plotMCMC.Rd | 1 man/plotPsdEstimate.Rd | 1 man/psd_arma.Rd | 1 man/reduceMemoryStorageMCMC.Rd | 1 man/se_kurt.Rd | 1 man/uniformmax.Rd | 1 man/unrollPsd.Rd | 1 src/gibbs_core.cpp | 9 +- src/registerDynamicSymbol.c |only 61 files changed, 195 insertions(+), 192 deletions(-)
Title: Structural Equation Modelling in R with 'OpenMx'
Description: Quickly create, run, and report structural equation and twin models.
See '?umx' to learn more.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 1.5.5 dated 2017-03-21 and 1.7.5 dated 2017-04-07
umx-1.5.5/umx/man/umx_cov_diag.Rd |only umx-1.7.5/umx/DESCRIPTION | 12 umx-1.7.5/umx/MD5 | 158 ++-- umx-1.7.5/umx/NAMESPACE | 8 umx-1.7.5/umx/NEWS | 120 ++- umx-1.7.5/umx/R/build_run_modify.r | 617 ++++++++++------ umx-1.7.5/umx/R/fit_and_reporting.r | 48 - umx-1.7.5/umx/R/misc_and_utility.r | 515 +++++++++---- umx-1.7.5/umx/R/umxCF_SexLim.R | 2 umx-1.7.5/umx/R/xmu.r | 10 umx-1.7.5/umx/README.md | 12 umx-1.7.5/umx/man/install.OpenMx.Rd | 13 umx-1.7.5/umx/man/plot.MxModel.Rd | 2 umx-1.7.5/umx/man/umx.Rd | 21 umx-1.7.5/umx/man/umxACE.Rd | 101 +- umx-1.7.5/umx/man/umxACESexLim.Rd | 2 umx-1.7.5/umx/man/umxACEcov.Rd | 39 - umx-1.7.5/umx/man/umxCF_SexLim.Rd | 2 umx-1.7.5/umx/man/umxCP.Rd | 20 umx-1.7.5/umx/man/umxCovData.Rd | 1 umx-1.7.5/umx/man/umxFactor.Rd | 1 umx-1.7.5/umx/man/umxGxE.Rd | 2 umx-1.7.5/umx/man/umxGxE_window.Rd | 2 umx-1.7.5/umx/man/umxHetCor.Rd | 1 umx-1.7.5/umx/man/umxIP.Rd | 9 umx-1.7.5/umx/man/umxLabel.Rd | 22 umx-1.7.5/umx/man/umxMatrix.Rd | 4 umx-1.7.5/umx/man/umxModel.Rd |only umx-1.7.5/umx/man/umxPadAndPruneForDefVars.Rd | 1 umx-1.7.5/umx/man/umxPath.Rd | 2 umx-1.7.5/umx/man/umxPlotACEcov.Rd | 2 umx-1.7.5/umx/man/umxPlotCP.Rd | 2 umx-1.7.5/umx/man/umxPlotGxE.Rd | 2 umx-1.7.5/umx/man/umxPlotIP.Rd | 2 umx-1.7.5/umx/man/umxRAM.Rd | 60 + umx-1.7.5/umx/man/umxSummary.MxModel.Rd | 28 umx-1.7.5/umx/man/umxSummaryACE.Rd | 3 umx-1.7.5/umx/man/umxSummaryACEcov.Rd | 2 umx-1.7.5/umx/man/umxSummaryCP.Rd | 3 umx-1.7.5/umx/man/umxSummaryGxE.Rd | 3 umx-1.7.5/umx/man/umxSummaryIP.Rd | 3 umx-1.7.5/umx/man/umxVersion.Rd |only umx-1.7.5/umx/man/umx_as_numeric.Rd | 1 umx-1.7.5/umx/man/umx_check_names.Rd | 4 umx-1.7.5/umx/man/umx_cont_2_quantiles.Rd | 46 - umx-1.7.5/umx/man/umx_cov2raw.Rd | 1 umx-1.7.5/umx/man/umx_fun_mean_sd.Rd | 3 umx-1.7.5/umx/man/umx_is_MxData.Rd | 2 umx-1.7.5/umx/man/umx_is_ordered.Rd | 2 umx-1.7.5/umx/man/umx_lower2full.Rd | 1 umx-1.7.5/umx/man/umx_make.Rd | 3 umx-1.7.5/umx/man/umx_make_MR_data.Rd | 1 umx-1.7.5/umx/man/umx_make_TwinData.Rd | 122 ++- umx-1.7.5/umx/man/umx_make_bin_cont_pair_data.Rd | 1 umx-1.7.5/umx/man/umx_make_fake_data.Rd | 3 umx-1.7.5/umx/man/umx_merge_CIs.Rd | 1 umx-1.7.5/umx/man/umx_paste_names.Rd | 53 + umx-1.7.5/umx/man/umx_read_lower.Rd | 1 umx-1.7.5/umx/man/umx_reorder.Rd | 1 umx-1.7.5/umx/man/umx_residualize.Rd | 1 umx-1.7.5/umx/man/umx_round.Rd | 1 umx-1.7.5/umx/man/umx_scale.Rd | 1 umx-1.7.5/umx/man/umx_scale_wide_twin_data.Rd | 1 umx-1.7.5/umx/man/umx_swap_a_block.Rd | 1 umx-1.7.5/umx/man/umx_var.Rd |only umx-1.7.5/umx/man/umx_write_to_clipboard.Rd | 3 umx-1.7.5/umx/man/xmuHasSquareBrackets.Rd | 3 umx-1.7.5/umx/man/xmuLabel_MATRIX_Model.Rd | 3 umx-1.7.5/umx/man/xmuLabel_Matrix.Rd | 3 umx-1.7.5/umx/man/xmuLabel_RAM_Model.Rd | 7 umx-1.7.5/umx/man/xmuMI.Rd | 3 umx-1.7.5/umx/man/xmuMakeDeviationThresholdsMatrices.Rd | 3 umx-1.7.5/umx/man/xmuMakeOneHeadedPathsFromPathList.Rd | 3 umx-1.7.5/umx/man/xmuMakeTwoHeadedPathsFromPathList.Rd | 3 umx-1.7.5/umx/man/xmuMaxLevels.Rd | 3 umx-1.7.5/umx/man/xmuMinLevels.Rd | 3 umx-1.7.5/umx/man/xmuPropagateLabels.Rd | 3 umx-1.7.5/umx/man/xmu_check_levels_identical.Rd | 3 umx-1.7.5/umx/man/xmu_dot_make_paths.Rd | 3 umx-1.7.5/umx/man/xmu_dot_make_residuals.Rd | 3 umx-1.7.5/umx/man/xmu_start_value_list.Rd | 3 umx-1.7.5/umx/tests/testthat/ACE.gv |only umx-1.7.5/umx/tests/testthat/test_umxACE.r |only 83 files changed, 1446 insertions(+), 714 deletions(-)
Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that
should be familiar to experienced R users. Provides a wrapper for several
topic models that take similarly-formatted input and give similarly-formatted
output. Has additional functionality for analyzing and diagnostics for
topic models.
Author: Thomas Jones [aut, cre],
William Doane [ctb]
Maintainer: Thomas Jones <jones.thos.w@gmail.com>
Diff between textmineR versions 2.0.4 dated 2016-11-03 and 2.0.5 dated 2017-04-07
DESCRIPTION | 19 ++++++++---- MD5 | 69 ++++++++++++++++++++++++---------------------- NAMESPACE | 2 - R/CreateDtm.R | 7 +++- R/CreateTcm.R | 10 ++++-- R/GetVocabFromDtm.R |only README.md | 2 - man/CalcHellingerDist.Rd | 1 man/CalcJSDivergence.Rd | 1 man/CalcLikelihood.Rd | 1 man/CalcPhiPrime.Rd | 1 man/CalcProbCoherence.Rd | 1 man/CalcTopicModelR2.Rd | 1 man/Cluster2TopicModel.Rd | 1 man/CorrectS.Rd | 1 man/CreateDtm.Rd | 6 ++-- man/CreateTcm.Rd | 6 ++-- man/DepluralizeDtm.Rd | 1 man/Dtm2Docs.Rd | 1 man/Dtm2Tcm.Rd | 1 man/Files2Vec.Rd | 1 man/FitCtmModel.Rd | 1 man/FitLdaModel.Rd | 1 man/FitLsaModel.Rd | 1 man/FormatRawLdaOutput.Rd | 1 man/GetPhiPrime.Rd | 1 man/GetProbableTerms.Rd | 1 man/GetTopTerms.Rd | 1 man/GetVocabFromDtm.Rd |only man/HellDist.Rd | 1 man/JSD.Rd | 1 man/LabelTopics.Rd | 1 man/RecursiveRbind.Rd | 1 man/TermDocFreq.Rd | 1 man/TmParallelApply.Rd | 1 man/Vec2Dtm.Rd | 1 src/textmineR_init.cpp |only 37 files changed, 70 insertions(+), 77 deletions(-)
Title: Latent Variable Analysis with Shiny
Description: Interactive shiny application for working with different kinds of
latent variable analysis, with the 'lavaan' package. Graphical output for models
are provided and different estimators are supported.
Author: W. Kyle Hamilton <kyle.hamilton@gmail.com>
Maintainer: W. Kyle Hamilton <kyle.hamilton@gmail.com>
Diff between lavaan.shiny versions 1.1 dated 2016-06-24 and 1.2 dated 2017-04-07
lavaan.shiny-1.1/lavaan.shiny/NEWS |only lavaan.shiny-1.2/lavaan.shiny/DESCRIPTION | 8 ++++---- lavaan.shiny-1.2/lavaan.shiny/MD5 | 9 ++++----- lavaan.shiny-1.2/lavaan.shiny/NAMESPACE | 3 ++- lavaan.shiny-1.2/lavaan.shiny/README.md | 3 --- lavaan.shiny-1.2/lavaan.shiny/inst/shiny/server.R | 12 ++++++------ 6 files changed, 16 insertions(+), 19 deletions(-)
Title: Use and Explore CRU CL v. 2.0 Climatology Elements in R
Description: Provides functions that automate downloading and importing
University of East Anglia Climate Research Unit (CRU) CL v. 2.0 climatology
data into R, facilitates the calculation of minimum temperature and maximum
temperature and formats the data into a tidy data frame as a tibble or a
list of raster stack objects for use in an R session. CRU CL v. 2.0 data
are a gridded climatology of 1961-1990 monthly means released in 2002 and
cover all land areas (excluding Antarctica) at 10 arcminutes
(0.1666667 degree) resolution. For more information see the description of
the data provided by the University of East Anglia Climate Research Unit,
<https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.
Author: Adam Sparks [aut, cre]
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between getCRUCLdata versions 0.1.4 dated 2017-02-03 and 0.1.5 dated 2017-04-07
getCRUCLdata-0.1.4/getCRUCLdata/R/calculate_T.R |only getCRUCLdata-0.1.4/getCRUCLdata/R/tidy_df.R |only getCRUCLdata-0.1.4/getCRUCLdata/man/getCRUdata.Rd |only getCRUCLdata-0.1.5/getCRUCLdata/DESCRIPTION | 41 getCRUCLdata-0.1.5/getCRUCLdata/MD5 | 71 getCRUCLdata-0.1.5/getCRUCLdata/NAMESPACE | 7 getCRUCLdata-0.1.5/getCRUCLdata/NEWS.md | 16 getCRUCLdata-0.1.5/getCRUCLdata/R/create_CRU_df.R | 118 - getCRUCLdata-0.1.5/getCRUCLdata/R/create_CRU_stack.R | 271 -- getCRUCLdata-0.1.5/getCRUCLdata/R/create_df.R |only getCRUCLdata-0.1.5/getCRUCLdata/R/create_stacks.R |only getCRUCLdata-0.1.5/getCRUCLdata/R/getCRUCLdata.R | 16 getCRUCLdata-0.1.5/getCRUCLdata/R/get_CRU.R | 219 +- getCRUCLdata-0.1.5/getCRUCLdata/R/get_CRU_df.R |only getCRUCLdata-0.1.5/getCRUCLdata/R/get_CRU_stack.R |only getCRUCLdata-0.1.5/getCRUCLdata/R/manage_cached_files.R |only getCRUCLdata-0.1.5/getCRUCLdata/R/validate_dsn.R |only getCRUCLdata-0.1.5/getCRUCLdata/README.md | 238 +- getCRUCLdata-0.1.5/getCRUCLdata/build/vignette.rds |binary getCRUCLdata-0.1.5/getCRUCLdata/inst/CITATION | 27 getCRUCLdata-0.1.5/getCRUCLdata/inst/doc/getCRUCLdata.R | 110 - getCRUCLdata-0.1.5/getCRUCLdata/inst/doc/getCRUCLdata.Rmd | 223 +- getCRUCLdata-0.1.5/getCRUCLdata/inst/doc/getCRUCLdata.html | 214 + getCRUCLdata-0.1.5/getCRUCLdata/inst/paper/paper.bib | 23 getCRUCLdata-0.1.5/getCRUCLdata/inst/paper/paper.md | 8 getCRUCLdata-0.1.5/getCRUCLdata/inst/paper/paper.pdf |binary getCRUCLdata-0.1.5/getCRUCLdata/man/create_CRU_df.Rd | 39 getCRUCLdata-0.1.5/getCRUCLdata/man/create_CRU_stack.Rd | 87 getCRUCLdata-0.1.5/getCRUCLdata/man/figures |only getCRUCLdata-0.1.5/getCRUCLdata/man/getCRUCLdata.Rd |only getCRUCLdata-0.1.5/getCRUCLdata/man/get_CRU_df.Rd |only getCRUCLdata-0.1.5/getCRUCLdata/man/get_CRU_stack.Rd |only getCRUCLdata-0.1.5/getCRUCLdata/man/manage_CRU_cache.Rd |only getCRUCLdata-0.1.5/getCRUCLdata/tests/testthat/test-create_CRU_df.R | 1052 ++++----- getCRUCLdata-0.1.5/getCRUCLdata/tests/testthat/test-create_CRU_stack.R | 1091 ++++------ getCRUCLdata-0.1.5/getCRUCLdata/tests/testthat/test-create_df.R |only getCRUCLdata-0.1.5/getCRUCLdata/tests/testthat/test-create_stack.R |only getCRUCLdata-0.1.5/getCRUCLdata/tests/testthat/test-get_CRU.R | 66 getCRUCLdata-0.1.5/getCRUCLdata/tests/testthat/test-get_CRU_df.R |only getCRUCLdata-0.1.5/getCRUCLdata/tests/testthat/test-get_CRU_stack.R |only getCRUCLdata-0.1.5/getCRUCLdata/tests/testthat/test-validate_dsn.R |only getCRUCLdata-0.1.5/getCRUCLdata/tests/testthat/test_get_local.R |only getCRUCLdata-0.1.5/getCRUCLdata/vignettes/README-unnamed-chunk-10-1.png |only getCRUCLdata-0.1.5/getCRUCLdata/vignettes/README-unnamed-chunk-11-1.png |only getCRUCLdata-0.1.5/getCRUCLdata/vignettes/README-unnamed-chunk-6-1.png |only getCRUCLdata-0.1.5/getCRUCLdata/vignettes/README-unnamed-chunk-7-1.png |only getCRUCLdata-0.1.5/getCRUCLdata/vignettes/getCRUCLdata.Rmd | 223 +- 47 files changed, 2281 insertions(+), 1879 deletions(-)
Title: Miscellaneous Tools for Chinese Text Mining and More
Description: Efforts are made to make Chinese text mining easier, faster, and robust to errors.
Document term matrix can be generated by only one line of code; detecting encoding,
segmenting and removing stop words are done automatically.
Some convenient tools are also supplied.
Author: Jiang Wu [aut, cre] (from Tsinghua University)
Maintainer: Jiang Wu <textidea@sina.com>
Diff between chinese.misc versions 0.1.4 dated 2017-03-23 and 0.1.5 dated 2017-04-07
DESCRIPTION | 8 +++--- MD5 | 20 ++++++++-------- NAMESPACE | 1 NEWS | 9 +++++++ R/create_ttm.R | 2 - R/csv2txt.R | 6 ++++ R/dictionary_dtm.R |only R/output_dtm.R | 3 +- R/sort_tf.R | 22 +++++++++++------ R/word_cor.R | 62 +++++++++++++++++++++++++++++++------------------- man/dictionary_dtm.Rd |only man/word_cor.Rd | 2 - 12 files changed, 87 insertions(+), 48 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-05-02 2.0-5
2012-04-25 2.0-1
2009-04-15 1.3-1
2009-03-20 1.2-0
2008-10-30 1.0-12
2008-10-17 1.0-11
2008-10-14 1.0-9
2008-08-14 1.0-6