Output analysis and diagnostics for MCMC


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Documentation for package `coda' version 0.8-3

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.Coda.Options Options settings for the codamenu driver
as.array.mcmc.list Conversions of MCMC objects
as.matrix.mcmc Conversions of MCMC objects
as.mcmc Markov Chain Monte Carlo Objects
as.mcmc.list Replicated Markov Chain Monte Carlo Objects
as.mcmc.mcmc.list Conversions of MCMC objects
as.ts.mcmc Coerce mcmc object to time series
autocorr Autocorrelation function for Markov chains
autocorr.plot Plot autocorrelations for Markov Chains
bugs2jags Convert WinBUGS data file to JAGS data file
chanames Named dimensions of MCMC objects
coda.options Options settings for the codamenu driver
codamenu Main menu driver for the coda package
crosscorr Cross correlations for MCMC output
crosscorr.plot Plot image of correlation matrix
cumuplot Cumulative quantile plot
densplot Probability density function estimate from MCMC output
display.coda.options Options settings for the codamenu driver
effectiveSize Effective sample size for estimating the mean
end.mcmc Time attributes for mcmc objects
frequency.mcmc Time attributes for mcmc objects
gelman.diag Gelman and Rubin's convergence diagnostic
gelman.plot Gelman-Rubin-Brooks plot
geweke.diag Geweke's convergence diagnostic
geweke.plot Geweke-Brooks plot
heidel.diag Heidelberger and Welch's convergence diagnostic
is.mcmc Markov Chain Monte Carlo Objects
is.mcmc.list Replicated Markov Chain Monte Carlo Objects
line Simple linear regression example
mcmc Markov Chain Monte Carlo Objects
mcmc.list Replicated Markov Chain Monte Carlo Objects
mcmcUpgrade Upgrade mcmc objects in obsolete format
mcpar Mcpar attribute of MCMC objects
multi.menu Choose multiple options from a menu
nchain Dimensions of MCMC objects
niter Dimensions of MCMC objects
nvar Dimensions of MCMC objects
pcramer The Cramer-von Mises Distribution
plot.mcmc Summary plots of mcmc objects
plot.mcmc.list Replicated Markov Chain Monte Carlo Objects
print.mcmc Markov Chain Monte Carlo Objects
raftery.diag Raftery and Lewis's diagnostic
read.and.check Read data interactively and check that it satisfies conditions
read.bugs Read BUGS output files
read.bugs.interactive Read BUGS output files interactively
read.coda Read BUGS output files
read.jags Read BUGS output files
spectrum0 Estimate spectral density at zero
spectrum0.ar Estimate spectral density at zero
start.mcmc Time attributes for mcmc objects
summary.mcmc Summary statistics for Markov Chain Monte Carlo chains
thin Thinning interval
thin.mcmc Time attributes for mcmc objects
time.mcmc Time attributes for mcmc objects
traceplot Trace plot of MCMC output
varnames Named dimensions of MCMC objects
window.mcmc Time windows for mcmc objects
[.mcmc Extract or replace parts of MCMC objects