# Output Analysis and Diagnostics for MCMC

## Documentation for package ‘coda’ version 0.19-4

- DESCRIPTION file.

## Help Pages

.Coda.Options | Options settings for the codamenu driver
.Coda.Options.Default | Options settings for the codamenu driver
acfplot | Trellis plots for mcmc objects
acfplot.mcmc | Trellis plots for mcmc objects
acfplot.mcmc.list | Trellis plots for mcmc objects
as.array.mcmc.list | Conversions of MCMC objects
as.matrix.mcmc | Conversions of MCMC objects
as.matrix.mcmc.list | Conversions of MCMC objects
as.mcmc | Markov Chain Monte Carlo Objects
as.mcmc.default | Markov Chain Monte Carlo Objects
as.mcmc.list | Replicated Markov Chain Monte Carlo Objects
as.mcmc.list.default | 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.diag | Autocorrelation function for Markov chains
autocorr.diag.mcmc | Autocorrelation function for Markov chains
autocorr.diag.mcmc.list | Autocorrelation function for Markov chains
autocorr.plot | Plot autocorrelations for Markov Chains
batchSE | Batch Standard Error
bugs2jags | Convert WinBUGS data file to JAGS data file
chanames | Named dimensions of MCMC objects
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
densityplot.mcmc | Trellis plots for mcmc objects
densityplot.mcmc.list | Trellis plots for mcmc objects
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
end.mcmc.list | 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
HPDinterval | Highest Posterior Density intervals
HPDinterval.mcmc | Highest Posterior Density intervals
HPDinterval.mcmc.list | Highest Posterior Density intervals
is.mcmc | Markov Chain Monte Carlo Objects
is.mcmc.list | Replicated Markov Chain Monte Carlo Objects
levelplot.mcmc | Trellis plots for mcmc objects
levelplot.mcmc.list | Trellis plots for mcmc 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
qqmath.mcmc | Trellis plots for mcmc objects
qqmath.mcmc.list | Trellis plots for mcmc objects
raftery.diag | Raftery and Lewis's diagnostic
read.and.check | Read data interactively and check that it satisfies conditions
read.coda | Read output files in CODA format
read.coda.interactive | Read CODA output files interactively
read.jags | Read output files in CODA format
read.openbugs | Read CODA output files produced by OpenBUGS
rejectionRate | Rejection Rate for Metropolis-Hastings chains
rejectionRate.mcmc | Rejection Rate for Metropolis-Hastings chains
rejectionRate.mcmc.list | Rejection Rate for Metropolis-Hastings chains
spectrum0 | Estimate spectral density at zero
spectrum0.ar | Estimate spectral density at zero
start.mcmc | Time attributes for mcmc objects
start.mcmc.list | Time attributes for mcmc objects
summary.mcmc | Summary statistics for Markov Chain Monte Carlo chains
summary.mcmc.list | Summary statistics for Markov Chain Monte Carlo chains
thin | Thinning interval
thin.mcmc | Time attributes for mcmc objects
thin.mcmc.list | Time attributes for mcmc objects
time.mcmc | Time attributes for mcmc objects
time.mcmc.list | Time attributes for mcmc objects
traceplot | Trace plot of MCMC output
varnames | Named dimensions of MCMC objects
varnames<- | Named dimensions of MCMC objects
window.mcmc | Time windows for mcmc objects
window.mcmc.list | Time windows for mcmc objects
xyplot.mcmc | Trellis plots for mcmc objects
xyplot.mcmc.list | Trellis plots for mcmc objects
[.mcmc | Extract or replace parts of MCMC objects
[.mcmc.list | Extract or replace parts of MCMC objects