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MCMCpack (version 1.4-9)

Markov Chain Monte Carlo (MCMC) Package

Description

Contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library Version 1.0.3. All models return 'coda' mcmc objects that can then be summarized using the 'coda' package. Some useful utility functions such as density functions, pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization are provided.

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Version

Install

install.packages('MCMCpack')

Monthly Downloads

18,466

Version

1.4-9

License

GPL-3

Maintainer

Jong Hee Park

Last Published

August 2nd, 2020

Functions in MCMCpack (1.4-9)

HMMpanelRE

Markov Chain Monte Carlo for the Hidden Markov Random-effects Model
InvGamma

The Inverse Gamma Distribution
InvWishart

The Inverse Wishart Distribution
MCMCSVDreg

Markov Chain Monte Carlo for SVD Regression
HDPHSMMnegbin

Markov Chain Monte Carlo for HDP-HSMM with a Negative Binomial outcome distribution
HMMpanelFE

Markov Chain Monte Carlo for the Hidden Markov Fixed-effects Model
HDPHMMpoisson

Markov Chain Monte Carlo for sticky HDP-HMM with a Poisson outcome distribution
HDPHMMnegbin

Markov Chain Monte Carlo for sticky HDP-HMM with a Negative Binomial outcome distribution
Dirichlet

The Dirichlet Distribution
BayesFactor

Create an object of class BayesFactor from MCMCpack output
MCMCbinaryChange

Markov Chain Monte Carlo for a Binary Multiple Changepoint Model
MCMCirtHier1d

Markov Chain Monte Carlo for Hierarchical One Dimensional Item Response Theory Model, Covariates Predicting Latent Ideal Point (Ability)
MCMCdynamicIRT1d_b

Markov Chain Monte Carlo for Dynamic One Dimensional Item Response Theory Model
MCMCirt1d

Markov Chain Monte Carlo for One Dimensional Item Response Theory Model
MCMChierEI

Markov Chain Monte Carlo for Wakefield's Hierarchial Ecological Inference Model
MCMChregress

Markov Chain Monte Carlo for the Hierarchical Gaussian Linear Regression Model
MCMChpoisson

Markov Chain Monte Carlo for the Hierarchical Poisson Linear Regression Model using the log link function
MCMCdynamicEI

Markov Chain Monte Carlo for Quinn's Dynamic Ecological Inference Model
MCMChlogit

Markov Chain Monte Carlo for the Hierarchical Binomial Linear Regression Model using the logit link function
MCMCfactanal

Markov Chain Monte Carlo for Normal Theory Factor Analysis Model
MCMCnegbin

Markov Chain Monte Carlo for Negative Binomial Regression
MCMCmixfactanal

Markov Chain Monte Carlo for Mixed Data Factor Analysis Model
MCMCoprobit

Markov Chain Monte Carlo for Ordered Probit Regression
MCMCmnl

Markov Chain Monte Carlo for Multinomial Logistic Regression
MCMCirtKdRob

Markov Chain Monte Carlo for Robust K-Dimensional Item Response Theory Model
MCMCmetrop1R

Metropolis Sampling from User-Written R function
MCMCoprobitChange

Markov Chain Monte Carlo for Ordered Probit Changepoint Regression Model
MCMCnegbinChange

Markov Chain Monte Carlo for Negative Binomial Regression Changepoint Model
MCMClogit

Markov Chain Monte Carlo for Logistic Regression
MCMCresidualBreakAnalysis

Break Analysis of Univariate Time Series using Markov Chain Monte Carlo
MCMCirtKd

Markov Chain Monte Carlo for K-Dimensional Item Response Theory Model
MCMCordfactanal

Markov Chain Monte Carlo for Ordinal Data Factor Analysis Model
MCMCregress

Markov Chain Monte Carlo for Gaussian Linear Regression
MCMCregressChange

Markov Chain Monte Carlo for a linear Gaussian Multiple Changepoint Model
MCMCquantreg

Bayesian quantile regression using Gibbs sampling
PErisk

Political Economic Risk Data from 62 Countries in 1987
MCMCprobit

Markov Chain Monte Carlo for Probit Regression
PostProbMod

Calculate Posterior Probability of Model
Rehnquist

U.S. Supreme Court Vote Matrix, Rehnquist Court (1994-2004)
MCMCprobitChange

Markov Chain Monte Carlo for a linear Gaussian Multiple Changepoint Model
plotChangepoint

Posterior Density of Regime Change Plot
MCMCpoissonChange

Markov Chain Monte Carlo for a Poisson Regression Changepoint Model
MCnormalnormal

Monte Carlo Simulation from a Normal Likelihood (with known variance) with a Normal Prior
MCbinomialbeta

Monte Carlo Simulation from a Binomial Likelihood with a Beta Prior
MCMCpoisson

Markov Chain Monte Carlo for Poisson Regression
SSVSquantreg

Stochastic search variable selection for quantile regression
plotHDPChangepoint

Posterior Changepoint Probabilities from HDP-HMM
MCmultinomdirichlet

Monte Carlo Simulation from a Multinomial Likelihood with a Dirichlet Prior
read.Scythe

Read a Matrix from a File written by Scythe
summaryqrssvs

Summarising the results of quantile regression stochastic search variable selection (QR-SSVS).
plot.qrssvs

Plot output from quantile regression stochastic search variable selection (QR-SSVS).
SupremeCourt

U.S. Supreme Court Vote Matrix
Senate

106th U.S. Senate Roll Call Vote Matrix
mptable

Calculate the marginal posterior probabilities of predictors being included in a quantile regression model.
testpanelGroupBreak

A Test for the Group-level Break using a Multivariate Linear Regression Model with Breaks
xpnd

Expand a Vector into a Symmetric Matrix
testpanelSubjectBreak

A Test for the Subject-level Break using a Unitivariate Linear Regression Model with Breaks
MCMCtobit

Markov Chain Monte Carlo for Gaussian Linear Regression with a Censored Dependent Variable
Nethvote

Dutch Voting Behavior in 1989
tomogplot

Tomography Plot
topmodels

Shows an ordered list of the most frequently visited models sampled during quantile regression stochastic search variable selection (QR-SSVS).
choicevar

Handle Choice-Specific Covariates in Multinomial Choice Models
Wishart

The Wishart Distribution
MCpoissongamma

Monte Carlo Simulation from a Poisson Likelihood with a Gamma Prior
NoncenHypergeom

The Noncentral Hypergeometric Distribution
vech

Extract Lower Triangular Elements from a Symmetric Matrix
dtomogplot

Dynamic Tomography Plot
make.breaklist

Vector of break numbers
write.Scythe

Write a Matrix to a File to be Read by Scythe
procrustes

Procrustes Transformation
plotState

Changepoint State Plot