PReMiuM: Dirichlet Process Bayesian Clustering, Profile Regression

Bayesian clustering using a Dirichlet process mixture model. This model is an alternative to regression models, non-parametrically linking a response vector to covariate data through cluster membership. The package allows Bernoulli, Binomial, Poisson, Normal, survival and categorical response, as well as Normal and discrete covariates. It also allows for fixed effects in the response model, where a spatial CAR (conditional autoregressive) term can be also included. Additionally, predictions may be made for the response, and missing values for the covariates are handled. Several samplers and label switching moves are implemented along with diagnostic tools to assess convergence. A number of R functions for post-processing of the output are also provided. In addition to fitting mixtures, it may additionally be of interest to determine which covariates actively drive the mixture components. This is implemented in the package as variable selection.

AuthorDavid I. Hastie <david.hastie@rsimony.com>, Silvia Liverani <liveranis@gmail.com> and Sylvia Richardson <sylvia.richardson@mrc-bsu.cam.ac.uk> with contributions from Aurore J. Lavigne, Lucy Leigh, Lamiae Azizi
Date of publication2016-12-28 18:03:52
MaintainerSilvia Liverani <liveranis@gmail.com>
LicenseGPL-2
Version3.1.4
http://www.silvialiverani.com/software/

View on CRAN

Functions

calcAvgRiskAndProfile Man page
calcDissimilarityMatrix Man page
calcOptimalClustering Man page
calcPredictions Man page
clusSummaryBernoulliDiscrete Man page
clusSummaryBernoulliDiscreteSmall Man page
clusSummaryBernoulliMixed Man page
clusSummaryBernoulliNormal Man page
clusSummaryBinomialNormal Man page
clusSummaryCategoricalDiscrete Man page
clusSummaryNormalDiscrete Man page
clusSummaryNormalNormal Man page
clusSummaryNormalNormalSpatial Man page
clusSummaryPoissonDiscrete Man page
clusSummaryPoissonNormal Man page
clusSummaryPoissonNormalSpatial Man page
clusSummaryQuantileNormal Man page
clusSummaryVarSelectBernoulliDiscrete Man page
clusSummaryWeibullDiscrete Man page
computeRatioOfVariance Man page
generateSampleDataFile Man page
globalParsTrace Man page
heatDissMat Man page
is.wholenumber Man page
mapforGeneratedData Man page
margModelPosterior Man page
plotPredictions Man page
plotRiskProfile Man page
PReMiuM Man page
PReMiuMpackage Man page
profRegr Man page
setHyperparams Man page
summariseVarSelectRho Man page
vec2mat Man page

Files

PReMiuM
PReMiuM/inst
PReMiuM/inst/CITATION
PReMiuM/src
PReMiuM/src/Makevars
PReMiuM/src/postProcess.cpp
PReMiuM/src/PReMiuM.cpp
PReMiuM/src/Makevars.win
PReMiuM/src/include
PReMiuM/src/include/postProcess.h
PReMiuM/src/include/PReMiuMData.h
PReMiuM/src/include/PReMiuMOptions.h
PReMiuM/src/include/PReMiuMArs.h
PReMiuM/src/include/PReMiuMModel.h
PReMiuM/src/include/PReMiuMProposals.h
PReMiuM/src/include/MCMC
PReMiuM/src/include/MCMC/model.h
PReMiuM/src/include/MCMC/chain.h
PReMiuM/src/include/MCMC/state.h
PReMiuM/src/include/MCMC/proposal.h
PReMiuM/src/include/MCMC/sampler.h
PReMiuM/src/include/PReMiuMArs.cpp
PReMiuM/src/include/PReMiuMIO.h
PReMiuM/src/include/Math
PReMiuM/src/include/Math/random.h
PReMiuM/src/include/Math/Error.h
PReMiuM/src/include/Math/ars2.h
PReMiuM/src/include/Math/mathfunctions.h
PReMiuM/src/include/Math/distribution.h
PReMiuM/NAMESPACE
PReMiuM/R
PReMiuM/R/postProcess.R PReMiuM/R/generateData.R
PReMiuM/MD5
PReMiuM/DESCRIPTION
PReMiuM/ChangeLog
PReMiuM/man
PReMiuM/man/computeRatioOfVariance.Rd PReMiuM/man/vec2mat.Rd PReMiuM/man/setHyperparams.Rd PReMiuM/man/margModelPosterior.Rd PReMiuM/man/globalParsTrace.Rd PReMiuM/man/PReMiuM-package.Rd PReMiuM/man/is.wholenumber.Rd PReMiuM/man/clusSummaryBernoulliDiscrete.Rd PReMiuM/man/calcAvgRiskAndProfile.Rd PReMiuM/man/mapforGeneratedData.Rd PReMiuM/man/plotPredictions.Rd PReMiuM/man/heatDissMat.Rd PReMiuM/man/generateSampleDataFile.Rd PReMiuM/man/calcOptimalClustering.Rd PReMiuM/man/calcDissimilarityMatrix.Rd PReMiuM/man/profRegr.Rd PReMiuM/man/calcPredictions.Rd PReMiuM/man/plotRiskProfile.Rd PReMiuM/man/summariseVarSelectRho.Rd

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