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

Functions

BDPdensity Man page
BDPdensity.default Man page
bir Man page
calgb Man page
calgb.pred Man page
CSDPbinary Man page
CSDPbinary.default Man page
deterioration Man page
DPbetabinom Man page
DPbetabinom.default Man page
DPbinary Man page
DPbinary.default Man page
DPcaterpillar Man page
DPcdensity Man page
DPcdensity.default Man page
DPdensity Man page
DPdensity.default Man page
DPelicit Man page
DPelicit.default Man page
DPglmm Man page
DPglmm.default Man page
DPlmm Man page
DPlmm.default Man page
DPMdencens Man page
DPMdencens.default Man page
DPmeta Man page
DPmeta.default Man page
DPMglmm Man page
DPMglmm.default Man page
DPMlmm Man page
DPMlmm.default Man page
DPMmeta Man page
DPMmeta.default Man page
DPMolmm Man page
DPMolmm.default Man page
DPMrandom Man page
DPMrandom.default Man page
DPMrasch Man page
DPMrasch.default Man page
DPMraschpoisson Man page
DPMraschpoisson.default Man page
DPmultmeta Man page
DPmultmeta.default Man page
DPolmm Man page
DPolmm.default Man page
DPpsBF Man page
DPrandom Man page
DPrandom.default Man page
DPrasch Man page
DPrasch.default Man page
DPraschpoisson Man page
DPraschpoisson.default Man page
DProc Man page
DProc.default Man page
DPsurvint Man page
DPsurvint.default Man page
fleabeetles Man page
FPTbinary Man page
FPTbinary.default Man page
FPTrasch Man page
FPTrasch.default Man page
FPTraschpoisson Man page
FPTraschpoisson.default Man page
fractionation Man page
galaxy Man page
HDPMcdensity Man page
HDPMcdensity.default Man page
HDPMdensity Man page
HDPMdensity.default Man page
hiv Man page
igg Man page
indon Man page
LDBDPdensity Man page
LDBDPdensity.default Man page
LDDPdensity Man page
LDDPdensity.default Man page
LDDPrasch Man page
LDDPrasch.default Man page
LDDPraschpoisson Man page
LDDPraschpoisson.default Man page
LDDProc Man page
LDDProc.default Man page
LDDPsurvival Man page
LDDPsurvival.default Man page
LDDPtwopl Man page
LDDPtwopl.default Man page
LDPDdoublyint Man page
LDPDdoublyint.default Man page
LDTFPdensity Man page
LDTFPdensity.default Man page
LDTFPglmm Man page
LDTFPglmm.default Man page
LDTFPsurvival Man page
LDTFPsurvival.default Man page
nodal Man page
orings Man page
Pbinary Man page
Pbinary.default Man page
Plm Man page
Plm.default Man page
predict.DPsurvint Man page
predict.HDPMcdensity Man page
predict.HDPMdensity Man page
ps Man page
PSgam Man page
PSgam.default Man page
psychiatric Man page
PTdensity Man page
PTdensity.default Man page
PTglmm Man page
PTglmm.default Man page
PTlm Man page
PTlm.default Man page
PTlmm Man page
PTlmm.default Man page
PTmeta Man page
PTmeta.default Man page
PTolmm Man page
PTolmm.default Man page
PTrandom Man page
PTrandom.default Man page
PTsampler Man page
PTsampler.default Man page
rats Man page
rolling Man page
schoolgirls Man page
seizures Man page
sports Man page
TDPdensity Man page
TDPdensity.default Man page
toenail Man page
uniond Man page

Files

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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