coda v0.19-3
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Output Analysis and Diagnostics for MCMC
Provides functions for summarizing and plotting the
output from Markov Chain Monte Carlo (MCMC) simulations, as
well as diagnostic tests of convergence to the equilibrium
distribution of the Markov chain.
Functions in coda
| Name | Description | |
| effectiveSize | Effective sample size for estimating the mean | |
| plot.mcmc | Summary plots of mcmc objects | |
| gelman.diag | Gelman and Rubin's convergence diagnostic | |
| nchain | Dimensions of MCMC objects | |
| spectrum0 | Estimate spectral density at zero | |
| cumuplot | Cumulative quantile plot | |
| densplot | Probability density function estimate from MCMC output | |
| bugs2jags | Convert WinBUGS data file to JAGS data file | |
| spectrum0.ar | Estimate spectral density at zero | |
| mcmcUpgrade | Upgrade mcmc objects in obsolete format | |
| mcmc.subset | Extract or replace parts of MCMC objects | |
| rejectionRate | Rejection Rate for Metropolis--Hastings chains | |
| trellisplots | Trellis plots for mcmc objects | |
| read.openbugs | Read CODA output files produced by OpenBUGS | |
| time.mcmc | Time attributes for mcmc objects | |
| traceplot | Trace plot of MCMC output | |
| gelman.plot | Gelman-Rubin-Brooks plot | |
| geweke.diag | Geweke's convergence diagnostic | |
| read.coda.interactive | Read CODA output files interactively | |
| line | Simple linear regression example | |
| read.coda | Read output files in CODA format | |
| crosscorr | Cross correlations for MCMC output | |
| varnames | Named dimensions of MCMC objects | |
| mcmc | Markov Chain Monte Carlo Objects | |
| mcpar | Mcpar attribute of MCMC objects | |
| crosscorr.plot | Plot image of correlation matrix | |
| summary.mcmc | Summary statistics for Markov Chain Monte Carlo chains | |
| thin | Thinning interval | |
| mcmc.list | Replicated Markov Chain Monte Carlo Objects | |
| geweke.plot | Geweke-Brooks plot | |
| mcmc.convert | Conversions of MCMC objects | |
| heidel.diag | Heidelberger and Welch's convergence diagnostic | |
| read.and.check | Read data interactively and check that it satisfies conditions | |
| multi.menu | Choose multiple options from a menu | |
| raftery.diag | Raftery and Lewis's diagnostic | |
| window.mcmc | Time windows for mcmc objects | |
| codamenu | Main menu driver for the coda package | |
| autocorr.diag | Autocorrelation function for Markov chains | |
| as.ts.mcmc | Coerce mcmc object to time series | |
| batchSE | Batch Standard Error | |
| coda.options | Options settings for the codamenu driver | |
| Cramer | The Cramer-von Mises Distribution | |
| autocorr | Autocorrelation function for Markov chains | |
| autocorr.plot | Plot autocorrelations for Markov Chains | |
| HPDinterval | Highest Posterior Density intervals | |
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Details
| Date | 2019-07-05 |
| License | GPL (>= 2) |
| NeedsCompilation | no |
| Packaged | 2019-07-05 12:32:44 UTC; martyn |
| Repository | CRAN |
| Date/Publication | 2019-07-05 13:30:03 UTC |
| imports | lattice |
| depends | R (>= 2.14.0) |
| Contributors | Karen Vines, Douglas Bates, Deepayan Sarkar, Arni Magnusson, Kate Cowles, Nicky Best, Russell Almond |
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