Output Analysis and Diagnostics for MCMC
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Documentation for package ‘coda’ version 0.19-4.1
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 |