coda v0.10-1

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by Martyn Plummer

Output analysis and diagnostics for MCMC

Output analysis and diagnostics for Markov Chain Monte Carlo simulations.

Functions in coda

Name Description
spectrum0.ar Estimate spectral density at zero
codamenu Main menu driver for the coda package
read.and.check Read data interactively and check that it satisfies conditions
line Simple linear regression example
read.coda.interactive Read CODA output files interactively
spectrum0 Estimate spectral density at zero
Cramer The Cramer-von Mises Distribution
coda.options Options settings for the codamenu driver
crosscorr Cross correlations for MCMC output
rejectionRate Rejection Rate for Metropolis--Hastings chains
cumuplot Cumulative quantile plot
varnames Named dimensions of MCMC objects
heidel.diag Heidelberger and Welch's convergence diagnostic
geweke.diag Geweke's convergence diagnostic
effectiveSize Effective sample size for estimating the mean
thin Thinning interval
autocorr.diag Autocorrelation function for Markov chains
mcpar Mcpar attribute of MCMC objects
mcmc Markov Chain Monte Carlo Objects
gelman.diag Gelman and Rubin's convergence diagnostic
multi.menu Choose multiple options from a menu
nchain Dimensions of MCMC objects
crosscorr.plot Plot image of correlation matrix
summary.mcmc Summary statistics for Markov Chain Monte Carlo chains
bugs2jags Convert WinBUGS data file to JAGS data file
gelman.plot Gelman-Rubin-Brooks plot
raftery.diag Raftery and Lewis's diagnostic
time.mcmc Time attributes for mcmc objects
plot.mcmc Summary plots of mcmc objects
window.mcmc Time windows for mcmc objects
trellisplots Trellis plots for mcmc objects
mcmcUpgrade Upgrade mcmc objects in obsolete format
autocorr.plot Plot autocorrelations for Markov Chains
autocorr Autocorrelation function for Markov chains
HPDinterval Highest Posterior Density intervals
mcmc.list Replicated Markov Chain Monte Carlo Objects
mcmc.subset Extract or replace parts of MCMC objects
read.openbugs Read CODA output files produced by OpenBUGS
geweke.plot Geweke-Brooks plot
batchSE Batch Standard Error
read.coda Read output files in CODA format
mcmc.convert Conversions of MCMC objects
as.ts.mcmc Coerce mcmc object to time series
densplot Probability density function estimate from MCMC output
traceplot Trace plot of MCMC output
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Date 2005-11-07
License GPL Version 2 or later.
Packaged Mon Nov 7 13:24:29 2005; deepayan

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