DPpackage: Bayesian nonparametric modeling in R

This package contains functions to perform inference via simulation from the posterior distributions for Bayesian nonparametric and semiparametric models. Although the name of the package was motivated by the Dirichlet Process prior, the package considers and will consider other priors on functional spaces. So far, DPpackage includes models considering Dirichlet Processes, Dependent Dirichlet Processes, Dependent Poisson- Dirichlet Processes, Hierarchical Dirichlet Processes, Polya Trees, Linear Dependent Tailfree Processes, Mixtures of Triangular distributions, Random Bernstein polynomials priors and Dependent Bernstein Polynomials. The package also includes models considering Penalized B-Splines. Currently the package includes semiparametric models for marginal and conditional density estimation, ROC curve analysis, interval censored data, binary regression models, generalized linear mixed models, IRT type models, and generalized additive models. The package also contains functions to compute Pseudo-Bayes factors for model comparison, and to elicitate the precision parameter of the Dirichlet Process. To maximize computational efficiency, the actual sampling for each model is done in compiled FORTRAN. The functions return objects which can be subsequently analyzed with functions provided in the coda package.

Author
Alejandro Jara [aut, cre], Timothy Hanson [ctb], Fernando Quintana [ctb], Peter Mueller [ctb], Gary Rosner [ctb]
Date of publication
2012-09-14 04:32:15
Maintainer
Alejandro Jara <atjara@uc.cl>
License
GPL (>= 2)
Version
1.1-6
URLs

View on CRAN

Man pages

BDPdensity
Semiparametric Bayesian density estimation using Bernstein...
bir
British Institute of Radiology Fractionation Studies
calgb
Cancer and Leukemia Group B (CALGB) Data
calgb.pred
Cancer and Leukemia Group B (CALGB) Data for Prediction
CSDPbinary
Bayesian analysis for a semiparametric logistic regression...
deterioration
Time to Cosmetic Deterioration of Breast Cancer Patients
DPbetabinom
Bayesian Semiparametric Beta-Binomial Model using a DP prior
DPbinary
Bayesian analysis for a semiparametric Bernoulli regression...
DPcaterpillar
Caterpillar Plots for Random Effects
DPcdensity
Bayesian Semiparametric Conditional Density Estimation using...
DPdensity
Semiparametric Bayesian density estimation using a DPM of...
DPelicit
Performs a prior elicitation for the precision parameter of a...
DPglmm
Bayesian analysis for a semiparametric generalized linear...
DPlmm
Bayesian analysis for a semiparametric linear mixed model...
DPMdencens
Bayesian density estimation for interval-censored data using...
DPmeta
Bayesian analysis for a semiparametric linear mixed effects...
DPMglmm
Bayesian analysis for a semiparametric generalized linear...
DPMlmm
Bayesian analysis for a semiparametric linear mixed model...
DPMmeta
Bayesian analysis for a semiparametric linear mixed effects...
DPMolmm
Bayesian analysis for a semiparametric ordinal linear mixed...
DPMrandom
Extracts Random Effects
DPMrasch
Bayesian analysis for a semiparametric Rasch model
DPMraschpoisson
Bayesian analysis for a semiparametric Rasch Poisson model
DPmultmeta
Bayesian analysis for a semiparametric random effects...
DPolmm
Bayesian analysis for a semiparametric ordinal linear mixed...
DPpsBF
Computes Pseudo Bayes Factors from DPpackage output
DPrandom
Extracts Random Effects
DPrasch
Bayesian analysis for a semiparametric Rasch model
DPraschpoisson
Bayesian analysis for a semiparametric Rasch Poisson model
DProc
Semiparametric Bayesian ROC curve analysis using DPM of...
DPsurvint
Bayesian analysis for a semiparametric AFT regression model
fleabeetles
Flea-beetles
FPTbinary
Bayesian analysis for a Finite Polya Tree Bernoulli...
FPTrasch
Bayesian analysis for a Finite Polya Tree Rasch model
FPTraschpoisson
Bayesian analysis for a Finite Polya Tree Rasch Poisson model
fractionation
British Institute of Radiology Fractionation Studies
galaxy
Galaxy velocities
HDPMcdensity
Bayesian analysis for a hierarchical Dirichlet Process...
HDPMdensity
Bayesian analysis for a hierarchical Dirichlet Process...
hiv
HIV-AIDS data
igg
Immunoglobulin G concentrations
indon
Indonesian Children's Health Study
LDBDPdensity
Bounded Density Regression using Dependent Bernstein...
LDDPdensity
Bayesian analysis for a Linear Dependent Dirichlet Process...
LDDPrasch
Bayesian analysis for a dependent semiparametric Rasch model
LDDPraschpoisson
Bayesian analysis for a dependent semiparametric Rasch...
LDDProc
Linear dependent DP model for conditional ROC curve...
LDDPsurvival
Bayesian analysis for a Linear Dependent Dirichlet Process...
LDDPtwopl
Bayesian analysis for a dependent semiparametric two...
LDPDdoublyint
Bayesian analysis for a Linear Dependent Poisson Dirichlet...
LDTFPdensity
Density Regression using Linear Dependent Tailfree Processes
LDTFPglmm
Generalized linear mixed model using a linear dependent...
LDTFPsurvival
Survival Regression using Linear Dependent Tailfree Processes
nodal
Nodal Involvement Data
orings
Challenger Space Shuttle O-Ring Data
Pbinary
Bayesian analysis for a parametric Bernoulli regression model
Plm
Bayesian analysis for a parametric linear regression model
predict.DPsurvint
Computes the Survival Curve in a Bayesian analysis for a...
predict.HDPMcdensity
Predictive Information for the Dependent Random Probability...
predict.HDPMdensity
Predictive Information for the Dependent Random Probability...
ps
Specify a smoothing spline fit in a PSgam formula
PSgam
Bayesian analysis for a semiparametric generalized additive...
psychiatric
Psychiatric Clinical Trial
PTdensity
Nonparametric Bayesian density estimation using Mixtures of...
PTglmm
Bayesian analysis for a semiparametric generalized linear...
PTlm
Bayesian analysis for a semiparametric linear regression...
PTlmm
Bayesian analysis for a semiparametric linear mixed model...
PTmeta
Bayesian analysis for a semiparametric linear mixed effects...
PTolmm
Bayesian analysis for a semiparametric ordinal linear mixed...
PTrandom
Extracts Random Effects
PTsampler
Polya Tree sampler function
rats
Rats
rolling
Rolling Thumbtacks Data
schoolgirls
The Heights of Schoolgirls
seizures
Epileptic seizures
sports
The Australian Athletes Data
TDPdensity
Semiparametric Bayesian density estimation using DP Mixtures...
toenail
Toenail data
uniond
Union Membership

Files in this package

DPpackage
DPpackage/MD5
DPpackage/src
DPpackage/src/ToolsTDP.f
DPpackage/src/ToolsSweep.f
DPpackage/src/ToolsStat.f
DPpackage/src/ToolsSplines.f
DPpackage/src/ToolsSparseMatrix.f
DPpackage/src/ToolsSlice.f
DPpackage/src/ToolsSB.f
DPpackage/src/ToolsRSBA.f
DPpackage/src/ToolsRnumbers.f
DPpackage/src/ToolsRfun.c
DPpackage/src/ToolsRandlib.f
DPpackage/src/ToolsPTsampler.f
DPpackage/src/ToolsPT.f
DPpackage/src/ToolsProbf90.f90
DPpackage/src/ToolsPolynomials.f
DPpackage/src/ToolsMatrix.f
DPpackage/src/ToolsLDTFP.f
DPpackage/src/ToolsIntegrate.f
DPpackage/src/ToolsHMM.f
DPpackage/src/ToolsDPM.f
DPpackage/src/ToolsDP.f
DPpackage/src/ToolsDistributions.f
DPpackage/src/ToolsDDP.f
DPpackage/src/ToolsCdflib.f
DPpackage/src/ToolsCDF.f
DPpackage/src/ToolsBDP.f
DPpackage/src/TDPdensitypl.f
DPpackage/src/TDPdensity.f
DPpackage/src/PTudensityp.f
DPpackage/src/PTudensity.f
DPpackage/src/PTsurv.f
DPpackage/src/PTraschpoisson.f
DPpackage/src/PTrasch.f
DPpackage/src/PTolmmp.f
DPpackage/src/PTmeta.f
DPpackage/src/PTmdensityp.f
DPpackage/src/PTmdensityf.f
DPpackage/src/PTmdensity.f
DPpackage/src/PTlmp.f
DPpackage/src/PTlmm.f
DPpackage/src/PTlm.f
DPpackage/src/PTglmmprob.f
DPpackage/src/PTglmmpois.f
DPpackage/src/PTglmmlogit.f
DPpackage/src/PTglmmgam.f
DPpackage/src/PSgamprob.f
DPpackage/src/PSgampois.f
DPpackage/src/PSgamlogit.f
DPpackage/src/PSgamgauss.f
DPpackage/src/PSgamgam.f
DPpackage/src/Plm.f
DPpackage/src/Pbinary.f
DPpackage/src/Makevars
DPpackage/src/LDTFPsurvival.f
DPpackage/src/LDTFPglmmpois.f
DPpackage/src/LDTFPdensity.f
DPpackage/src/LDPDdoublyintsba.f
DPpackage/src/LDDPtwopl.f
DPpackage/src/LDDPsurvival.f
DPpackage/src/LDDPraschpoisson.f
DPpackage/src/LDDPrasch.f
DPpackage/src/LDDPdensity.f
DPpackage/src/LDBDPdensity.f
DPpackage/src/HDPMdensity.f
DPpackage/src/HDPMcdensity.f
DPpackage/src/FPTbinaryl.f
DPpackage/src/DPsurvint.f
DPpackage/src/DPraschpoisson.f
DPpackage/src/DPrasch.f
DPpackage/src/DPolmmp.f
DPpackage/src/DPmultmeta.f
DPpackage/src/DPMraschpoissonh.f
DPpackage/src/DPMraschpoisson.f
DPpackage/src/DPMrasch.f
DPpackage/src/DPMolmmp.f
DPpackage/src/DPMmeta.f
DPpackage/src/DPMlmm.f
DPpackage/src/DPMlm.f
DPpackage/src/DPMglmmprob.f
DPpackage/src/DPMglmmpois.f
DPpackage/src/DPMglmmlogit.f
DPpackage/src/DPMglmmgam.f
DPpackage/src/DPmeta.f
DPpackage/src/DPMdencens.f
DPpackage/src/DPlmm.f
DPpackage/src/DPglmmprob.f
DPpackage/src/DPglmmpois.f
DPpackage/src/DPglmmlogita.f
DPpackage/src/DPglmmlogit.f
DPpackage/src/DPglmmgam.f
DPpackage/src/DPdensityreg.f
DPpackage/src/DPdensityn.f
DPpackage/src/DPdensityg.f
DPpackage/src/DPbivdensityn.f
DPpackage/src/DPbivdensityg.f
DPpackage/src/DPbinaryp.f
DPpackage/src/DPbinaryl.f
DPpackage/src/DPbinaryc.f
DPpackage/src/DPbetabinom.f
DPpackage/src/CSDPbinaryl.f
DPpackage/src/BDPdensity.f
DPpackage/R
DPpackage/R/TDPdensity.R
DPpackage/R/PTsampler.R
DPpackage/R/PTrandom.R
DPpackage/R/PTolmm.R
DPpackage/R/PTmeta.R
DPpackage/R/PTlmm.R
DPpackage/R/PTlm.R
DPpackage/R/PTglmm.R
DPpackage/R/PTdensity.R
DPpackage/R/PSgam.R
DPpackage/R/ps.R
DPpackage/R/Plm.R
DPpackage/R/Pbinary.R
DPpackage/R/LDTFPsurvival.R
DPpackage/R/LDTFPglmm.R
DPpackage/R/LDTFPdensity.R
DPpackage/R/LDPDdoublyint.R
DPpackage/R/LDDPtwopl.R
DPpackage/R/LDDPsurvival.R
DPpackage/R/LDDProc.R
DPpackage/R/LDDPraschpoisson.R
DPpackage/R/LDDPrasch.R
DPpackage/R/LDDPdensity.R
DPpackage/R/LDBDPdensity.R
DPpackage/R/hidden.R
DPpackage/R/HDPMdensity.R
DPpackage/R/HDPMcdensity.R
DPpackage/R/FPTraschpoisson.R
DPpackage/R/FPTrasch.R
DPpackage/R/FPTbinary.R
DPpackage/R/DPsurvint.R
DPpackage/R/DProc.R
DPpackage/R/DPraschpoisson.R
DPpackage/R/DPrasch.R
DPpackage/R/DPrandom.R
DPpackage/R/DPpsBF.R
DPpackage/R/DPolmm.R
DPpackage/R/DPmultmeta.R
DPpackage/R/DPMraschpoisson.R
DPpackage/R/DPMrasch.R
DPpackage/R/DPMrandom.R
DPpackage/R/DPMolmm.R
DPpackage/R/DPMmeta.R
DPpackage/R/DPMlmm.R
DPpackage/R/DPMglmm.R
DPpackage/R/DPmeta.R
DPpackage/R/DPMdencens.R
DPpackage/R/DPlmm.R
DPpackage/R/DPglmm.R
DPpackage/R/DPelicit.R
DPpackage/R/DPdensity.R
DPpackage/R/DPcdensity.R
DPpackage/R/DPcaterpillar.R
DPpackage/R/DPbinary.R
DPpackage/R/DPbetabinom.R
DPpackage/R/CSDPbinary.R
DPpackage/R/BDPdensity.R
DPpackage/NAMESPACE
DPpackage/man
DPpackage/man/uniond.Rd
DPpackage/man/toenail.Rd
DPpackage/man/TDPdensity.Rd
DPpackage/man/sports.Rd
DPpackage/man/seizures.Rd
DPpackage/man/schoolgirls.Rd
DPpackage/man/rolling.Rd
DPpackage/man/rats.Rd
DPpackage/man/PTsampler.Rd
DPpackage/man/PTrandom.Rd
DPpackage/man/PTolmm.Rd
DPpackage/man/PTmeta.Rd
DPpackage/man/PTlmm.Rd
DPpackage/man/PTlm.Rd
DPpackage/man/PTglmm.Rd
DPpackage/man/PTdensity.Rd
DPpackage/man/psychiatric.Rd
DPpackage/man/PSgam.Rd
DPpackage/man/ps.Rd
DPpackage/man/predict.HDPMdensity.Rd
DPpackage/man/predict.HDPMcdensity.Rd
DPpackage/man/predict.DPsurvint.Rd
DPpackage/man/Plm.Rd
DPpackage/man/Pbinary.Rd
DPpackage/man/orings.Rd
DPpackage/man/nodal.Rd
DPpackage/man/LDTFPsurvival.Rd
DPpackage/man/LDTFPglmm.Rd
DPpackage/man/LDTFPdensity.Rd
DPpackage/man/LDPDdoublyint.Rd
DPpackage/man/LDDPtwopl.Rd
DPpackage/man/LDDPsurvival.Rd
DPpackage/man/LDDProc.Rd
DPpackage/man/LDDPraschpoisson.Rd
DPpackage/man/LDDPrasch.Rd
DPpackage/man/LDDPdensity.Rd
DPpackage/man/LDBDPdensity.Rd
DPpackage/man/indon.Rd
DPpackage/man/igg.Rd
DPpackage/man/hiv.Rd
DPpackage/man/HDPMdensity.Rd
DPpackage/man/HDPMcdensity.Rd
DPpackage/man/galaxy.Rd
DPpackage/man/fractionation.Rd
DPpackage/man/FPTraschpoisson.Rd
DPpackage/man/FPTrasch.Rd
DPpackage/man/FPTbinary.Rd
DPpackage/man/fleabeetles.Rd
DPpackage/man/DPsurvint.Rd
DPpackage/man/DProc.Rd
DPpackage/man/DPraschpoisson.Rd
DPpackage/man/DPrasch.Rd
DPpackage/man/DPrandom.Rd
DPpackage/man/DPpsBF.Rd
DPpackage/man/DPolmm.Rd
DPpackage/man/DPmultmeta.Rd
DPpackage/man/DPMraschpoisson.Rd
DPpackage/man/DPMrasch.Rd
DPpackage/man/DPMrandom.Rd
DPpackage/man/DPMolmm.Rd
DPpackage/man/DPMmeta.Rd
DPpackage/man/DPMlmm.Rd
DPpackage/man/DPMglmm.Rd
DPpackage/man/DPmeta.Rd
DPpackage/man/DPMdencens.Rd
DPpackage/man/DPlmm.Rd
DPpackage/man/DPglmm.Rd
DPpackage/man/DPelicit.Rd
DPpackage/man/DPdensity.Rd
DPpackage/man/DPcdensity.Rd
DPpackage/man/DPcaterpillar.Rd
DPpackage/man/DPbinary.Rd
DPpackage/man/DPbetabinom.Rd
DPpackage/man/deterioration.Rd
DPpackage/man/CSDPbinary.Rd
DPpackage/man/calgb.Rd
DPpackage/man/calgb.pred.Rd
DPpackage/man/bir.Rd
DPpackage/man/BDPdensity.Rd
DPpackage/LICENSE
DPpackage/inst
DPpackage/inst/CITATION
DPpackage/DESCRIPTION
DPpackage/data
DPpackage/data/uniond.rda
DPpackage/data/toenail.rda
DPpackage/data/sports.rda
DPpackage/data/seizures.rda
DPpackage/data/schoolgirls.rda
DPpackage/data/rolling.rda
DPpackage/data/rats.rda
DPpackage/data/psychiatric.rda
DPpackage/data/orings.rda
DPpackage/data/nodal.rda
DPpackage/data/indon.rda
DPpackage/data/igg.rda
DPpackage/data/hiv.rda
DPpackage/data/galaxy.rda
DPpackage/data/fractionation.rda
DPpackage/data/fleabeetles.rda
DPpackage/data/deterioration.rda
DPpackage/data/calgb.rda
DPpackage/data/calgb.pred.rda
DPpackage/data/bir.rda