Package index • coda

All functions
`pcramer()`	The Cramer-von Mises Distribution
`HPDinterval()`	Highest Posterior Density intervals
`as.ts(<mcmc>)`	Coerce mcmc object to time series
`autocorr()`	Autocorrelation function for Markov chains
`autocorr.diag()`	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
`coda.options()` `display.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
`effectiveSize()`	Effective sample size for estimating the mean
`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
`line`	Simple linear regression example
`mcmc()` `as.mcmc()` `is.mcmc()`	Markov Chain Monte Carlo Objects
`as.matrix(<mcmc>)` `as.matrix(<mcmc.list>)` `as.array(<mcmc.list>)`	Conversions of MCMC objects
`mcmc.list()` `as.mcmc.list()` `is.mcmc.list()`	Replicated Markov Chain Monte Carlo Objects
`[`(<mcmc>) `[`(<mcmc.list>)	Extract or replace parts of MCMC objects
`mcmcUpgrade()`	Upgrade mcmc objects in obsolete format
`mcpar()`	Mcpar attribute of MCMC objects
`multi.menu()`	Choose multiple options from a menu
`niter()` `nvar()` `nchain()`	Dimensions of MCMC objects
`plot(<mcmc>)`	Summary plots of mcmc objects
`raftery.diag()`	Raftery and Lewis's diagnostic
`read.and.check()`	Read data interactively and check that it satisfies conditions
`read.coda()` `read.jags()`	Read output files in CODA format
`read.coda.interactive()`	Read CODA output files interactively
`read.openbugs()`	Read CODA output files produced by OpenBUGS
`rejectionRate()`	Rejection Rate for Metropolis–Hastings chains
`spectrum0()`	Estimate spectral density at zero
`spectrum0.ar()`	Estimate spectral density at zero
`summary(<mcmc>)`	Summary statistics for Markov Chain Monte Carlo chains
`thin()`	Thinning interval
`time(<mcmc>)` `start(<mcmc>)` `end(<mcmc>)` `thin(<mcmc>)`	Time attributes for mcmc objects
`traceplot()`	Trace plot of MCMC output
`densityplot(<mcmc>)` `densityplot(<mcmc.list>)` `levelplot(<mcmc>)` `qqmath(<mcmc>)` `qqmath(<mcmc.list>)` `xyplot(<mcmc>)` `xyplot(<mcmc.list>)` `acfplot()`	Trellis plots for mcmc objects
`varnames()` `chanames()` `varnames<-`() `chanames<-`()	Named dimensions of MCMC objects
`window(<mcmc>)`	Time windows for mcmc objects

Reference

All functions