Output analysis and diagnostics for MCMC


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A B C D E F G H I L M N P R S T V W misc

.Coda.Options Options settings for the codamenu driver

-- A --

as.array.mcmc.list Conversions of MCMC objects
as.matrix.mcmc Conversions of MCMC objects
as.mcmc Markov Chain Monte Carlo Objects
as.mcmc.list 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.plot Plot autocorrelations for Markov Chains

-- B --

bugs2jags Convert WinBUGS data file to JAGS data file

-- C --

chanames Named dimensions of MCMC objects
change.tfoption Interactively modify logical codamenu options.
coda.global.assign Cross-platform assignment to global environment
coda.options Options settings for the codamenu driver
codamenu Main menu driver for the coda package
codamenu.anal Submenus for the coda package
codamenu.diags Submenus for the coda package
codamenu.main Submenus for the coda package
codamenu.options Submenus for the coda package
codamenu.options.geweke.bin Submenus for the coda package
codamenu.options.geweke.win Submenus for the coda package
codamenu.options.heidel Submenus for the coda package
codamenu.options.plot Submenus for the coda package
codamenu.options.raftery Submenus for the coda package
codamenu.options.stats Submenus for the coda package
codamenu.output.header Submenus for the coda package
codamenu.ps Submenus for the coda package
crosscorr Cross correlations for MCMC output
crosscorr.plot Plot image of correlation matrix
cumuplot Cumulative quantile plot

-- D --

densplot Probability density function estimate from MCMC output
display.coda.options Options settings for the codamenu driver

-- E --

effectiveSize Effective sample size for estimating the mean
end.mcmc Time attributes for mcmc objects

-- F --

frequency.mcmc Time attributes for mcmc objects

-- G --

gelman.diag Gelman and Rubin's convergence diagnostic
gelman.mv.diag Gelman and Rubin's convergence diagnostic
gelman.plot Gelman-Rubin-Brooks plot
gelman.preplot Gelman-Rubin-Brooks plot
gelman.transform Gelman and Rubin's convergence diagnostic
geweke.diag Geweke's convergence diagnostic
geweke.plot Geweke-Brooks plot

-- H --

heidel.diag Heidelberger and Welch's convergence diagnostic

-- I --

is.mcmc Markov Chain Monte Carlo Objects
is.mcmc.list Replicated Markov Chain Monte Carlo Objects

-- L --

line Simple linear regression example

-- M --

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

-- N --

nchain Dimensions of MCMC objects
niter Dimensions of MCMC objects
nvar Dimensions of MCMC objects

-- P --

pcramer The Cramer-von Mises Distribution
plot.mcmc Summary plots of mcmc objects
plot.mcmc.list Replicated Markov Chain Monte Carlo Objects
print.gelman.diag Gelman and Rubin's convergence diagnostic
print.geweke.diag Geweke's convergence diagnostic
print.heidel.diag Heidelberger and Welch's convergence diagnostic
print.mcmc Markov Chain Monte Carlo Objects
print.raftery.diag Raftery and Lewis's diagnostic
print.summary.mcmc Summary statistics for Markov Chain Monte Carlo chains

-- R --

raftery.diag Raftery and Lewis's diagnostic
read.and.check Read data interactively and check that it satisfies conditions
read.bugs Read BUGS output files
read.bugs.interactive Read BUGS output files interactively
read.coda Read BUGS output files
read.jags Read BUGS output files
read.yesno Read logical values from the command line

-- S --

set.mfrow Set layout for graphical plots
spectrum0 Estimate spectral density at zero
spectrum0.ar Estimate spectral density at zero
start.mcmc Time attributes for mcmc objects
summary.mcmc Summary statistics for Markov Chain Monte Carlo chains

-- T --

thin Thinning interval
thin.mcmc Time attributes for mcmc objects
tidy.up Submenus for the coda package
time.mcmc Time attributes for mcmc objects
traceplot Trace plot of MCMC output

-- V --

varnames Named dimensions of MCMC objects

-- W --

window.mcmc Time windows for mcmc objects

-- misc --

[.mcmc Extract or replace parts of MCMC objects