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coda (version 0.16-1)
Output analysis and diagnostics for MCMC
Description
Output analysis and diagnostics for Markov Chain Monte Carlo simulations.
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Install
install.packages('coda')
Monthly Downloads
214,045
Version
0.16-1
License
GPL (>= 2)
Maintainer
Martyn Plummer
Last Published
November 6th, 2012
Functions in coda (0.16-1)
Search all functions
codamenu2
Submenus for the coda package
coda.options
Options settings for the codamenu driver
mcmc
Markov Chain Monte Carlo Objects
multi.menu
Choose multiple options from a menu
nchain
Dimensions of MCMC objects
mcmcUpgrade
Upgrade mcmc objects in obsolete format
autocorr
Autocorrelation function for Markov chains
Cramer
The Cramer-von Mises Distribution
autocorr.plot
Plot autocorrelations for Markov Chains
effectiveSize
Effective sample size for estimating the mean
trellisplots
Trellis plots for mcmc objects
cumuplot
Cumulative quantile plot
rejectionRate
Rejection Rate for Metropolis--Hastings chains
window.mcmc
Time windows for mcmc objects
codamenu
Main menu driver for the coda package
mcmc.subset
Extract or replace parts of MCMC objects
densplot
Probability density function estimate from MCMC output
bugs2jags
Convert WinBUGS data file to JAGS data file
mcpar
Mcpar attribute of MCMC objects
change.tfoption
Interactively modify logical codamenu options.
gelman.diag
Gelman and Rubin's convergence diagnostic
read.openbugs
Read CODA output files produced by OpenBUGS
set.mfrow
Set layout for graphical plots
raftery.diag
Raftery and Lewis's diagnostic
spectrum0
Estimate spectral density at zero
as.ts.mcmc
Coerce mcmc object to time series
time.mcmc
Time attributes for mcmc objects
mcmc.convert
Conversions of MCMC objects
spectrum0.ar
Estimate spectral density at zero
read.coda.interactive
Read CODA output files interactively
autocorr.diag
Autocorrelation function for Markov chains
mcmc.list
Replicated Markov Chain Monte Carlo Objects
gelman.plot
Gelman-Rubin-Brooks plot
traceplot
Trace plot of MCMC output
geweke.diag
Geweke's convergence diagnostic
read.and.check
Read data interactively and check that it satisfies conditions
line
Simple linear regression example
plot.mcmc
Summary plots of mcmc objects
summary.mcmc
Summary statistics for Markov Chain Monte Carlo chains
crosscorr
Cross correlations for MCMC output
HPDinterval
Highest Posterior Density intervals
read.yesno
Read logical values from the command line
batchSE
Batch Standard Error
geweke.plot
Geweke-Brooks plot
varnames
Named dimensions of MCMC objects
heidel.diag
Heidelberger and Welch's convergence diagnostic
thin
Thinning interval
read.coda
Read output files in CODA format
crosscorr.plot
Plot image of correlation matrix