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.

AuthorAlejandro Jara [aut, cre], Timothy Hanson [ctb], Fernando Quintana [ctb], Peter Mueller [ctb], Gary Rosner [ctb]
Date of publication2012-09-14 04:32:15
MaintainerAlejandro Jara <atjara@uc.cl>
LicenseGPL (>= 2)
Version1.1-6
http://www.mat.puc.cl/~ajara

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

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