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
thin may be used to read a subset of the
data. If the arguments given to
thin are incompatible with the data, they are ignored.
read.coda(output.file, index.file, start, end, thin, quiet=FALSE) read.jags(file = "jags.out", start, end, thin, quiet=FALSE)
- The name of the file containing the monitored output
- The name of the file containing the index, showing which rows of the output file correspond to which variables
- 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.
- First iteration of chain
- Last iteration of chain
- Thinning interval for chain
- Logical flag. If true, a progress summary will be printed
- An object of class
mcmccontaining a representation of the data in the file.
Spiegelhalter DJ, Thomas A, Best NG and Gilks WR (1995). BUGS: Bayesian inference Using Gibbs Sampling, Version 0.50. MRC Biostatistics Unit, Cambridge.