coda v0.17-1
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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 | |
| HPDinterval | Highest Posterior Density intervals | |
| as.ts.mcmc | Coerce mcmc object to time series | |
| gelman.diag | Gelman and Rubin's convergence diagnostic | |
| bugs2jags | Convert WinBUGS data file to JAGS data file | |
| batchSE | Batch Standard Error | |
| mcmc.list | Replicated Markov Chain Monte Carlo Objects | |
| cumuplot | Cumulative quantile plot | |
| mcmc.subset | Extract or replace parts of MCMC objects | |
| autocorr.plot | Plot autocorrelations for Markov Chains | |
| autocorr | Autocorrelation function for Markov chains | |
| time.mcmc | Time attributes for mcmc objects | |
| spectrum0.ar | Estimate spectral density at zero | |
| Cramer | The Cramer-von Mises Distribution | |
| mcpar | Mcpar attribute of MCMC objects | |
| crosscorr.plot | Plot image of correlation matrix | |
| effectiveSize | Effective sample size for estimating the mean | |
| coda.options | Options settings for the codamenu driver | |
| multi.menu | Choose multiple options from a menu | |
| crosscorr | Cross correlations for MCMC output | |
| read.and.check | Read data interactively and check that it satisfies conditions | |
| geweke.diag | Geweke's convergence diagnostic | |
| raftery.diag | Raftery and Lewis's diagnostic | |
| traceplot | Trace plot of MCMC output | |
| mcmcUpgrade | Upgrade mcmc objects in obsolete format | |
| gelman.plot | Gelman-Rubin-Brooks plot | |
| summary.mcmc | Summary statistics for Markov Chain Monte Carlo chains | |
| mcmc.convert | Conversions of MCMC objects | |
| mcmc | Markov Chain Monte Carlo Objects | |
| plot.mcmc | Summary plots of mcmc objects | |
| window.mcmc | Time windows for mcmc objects | |
| line | Simple linear regression example | |
| read.coda | Read output files in CODA format | |
| spectrum0 | Estimate spectral density at zero | |
| thin | Thinning interval | |
| heidel.diag | Heidelberger and Welch's convergence diagnostic | |
| trellisplots | Trellis plots for mcmc objects | |
| densplot | Probability density function estimate from MCMC output | |
| geweke.plot | Geweke-Brooks plot | |
| rejectionRate | Rejection Rate for Metropolis--Hastings chains | |
| varnames | Named dimensions of MCMC objects | |
| autocorr.diag | Autocorrelation function for Markov chains | |
| read.coda.interactive | Read CODA output files interactively | |
| codamenu | Main menu driver for the coda package | |
| nchain | Dimensions of MCMC objects | |
| read.openbugs | Read CODA output files produced by OpenBUGS | |
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Details
| Date | 2015-03-02 |
| License | GPL (>= 2) |
| Packaged | 2015-03-03 17:21:11 UTC; martyn |
| NeedsCompilation | no |
| Repository | CRAN |
| Date/Publication | 2015-03-03 19:25:43 |
| depends | base (>= 2.14.0) , R (>= 2.14.0) |
| imports | lattice |
| Contributors | Karen Vines, Martyn Plummer, Douglas Bates, Deepayan Sarkar, Kate Cowles, Nicky Best, Russell Almond |
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