Editing Software Plugins and Codes (section)

===OBSOLETE: JAGS run script===

This is not required when running JAGS from within R, which seems to be the best way to run JAGS.

Here is the script I used to run JAGS, fnbmd10.jags.  Of course, you could enter all these commands interactively into JAGS as well.  You probably want to customize this.  For example, I just guessed at the number of iterations.  There are also several output options.  Probably you want to use the coda command to save the monitor values in files that can be read by the coda package of R, and then do some sort of statistical analysis on the convergence.

<source lang=text>
# Read in the model and the data
model in findcp.model
data in fnbmd10.R

# Required stuff
compile
initialize

# Do some iterations
# (The adaptive part of the iterating needs to be done before monitors can be set)
update 500

# Now set some monitors to track parameters over iterations 
monitor b.cutoff, thin(50)
monitor b.intercept, thin(50)
monitor b.slope, thin(50)

# Do lots of iterations
update 10000

# Save parameters and monitors.
# There are other kinds of outputs and files you can write; refer to the
# JAGS documentation
parameters to parameters.out
monitors to monitors.out

# Bye
exit
</source>


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