0th

Percentile

##### Read output files in CODA format

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.

Keywords
file
##### 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.

##### References

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

mcmc, read.coda.interactive, read.openbugs.