coda: read.coda – R documentation

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read.coda

Read output files in CODA format

Description

read.coda reads Markov Chain Monte Carlo output in the CODA format produced by OpenBUGS and JAGS. By default, all of the data in the file is read, but the arguments start, end and thin may be used to read a subset of the data. If the arguments given to start, end or thin are incompatible with the data, they are ignored.

Usage

read.coda(output.file, index.file, start, end, thin, quiet=FALSE)
read.jags(file = "jags.out", start, end, thin, quiet=FALSE)

Arguments

`output.file`	The name of the file containing the monitored output
`index.file`	The name of the file containing the index, showing which rows of the output file correspond to which variables
`file`	For JAGS output, the name of the output file. The extension ".out" may be omitted. There must be a corresponding ".ind" file with the same file stem.
`start`	First iteration of chain
`end`	Last iteration of chain
`thin`	Thinning interval for chain
`quiet`	Logical flag. If true, a progress summary will be printed

Value

An object of class mcmc containing a representation of the data in the file.

Author(s)

Karen Vines, Martyn Plummer

References

Spiegelhalter DJ, Thomas A, Best NG and Gilks WR (1995). BUGS: Bayesian inference Using Gibbs Sampling, Version 0.50. MRC Biostatistics Unit, Cambridge.