emacs syntax highlighting for jags / bugs

Question

Are there packages to color-highlight jags amd bugs model files? I have ESS installed, but it doesn't seem to recognize .bug files or jags/bugs syntax out of the box.

Answer 1

Syntax highlighting

I'm using ESS 5.14 (from ELPA) and syntax highlighting or smart underscore works fine for me with GNU Emacs 24.1.1. If you want to highlight a given file, you can try M-x ess-jags-mode or add a hook to highlight JAGS file each time, e.g.

(add-to-list 'auto-mode-alist '("\\.jag\\'" . jags-mode))

However, that is not really needed since you can simply

(require 'ess-jags-d)

in your .emacs. There's a corresponding mode for BUGS file. This file was already included in earlier release (at least 5.13), and it comes with the corresponding auto-mode-alist (for "\\.[jJ][aA][gG]\\'" extension).
(Please note that there seems to exist subtle issue with using both JAGS and BUGS, but I can't tell more because I only use JAGS.)

Running command file

If you want to stick with Emacs for running JAGS (i.e., instead of rjags or other R interfaces to JAGS/BUGS), there's only one command to know: As described in the ESS manual, when working on a command file, C-c C-c should create a .jmd file, and then C-c C-c'ing again should submit this command file to Emacs *shell* (in a new buffer), and call jags in batch mode. Internally, this command is binded to a 'Next Action' instruction (ess-*-next-action). For example, using the mice data that comes with JAGS sample files, you should get a mice.jmd that looks like that:

model in "mice.jag"
data in "mice.jdt"
compile, nchains(1)
parameters in "mice.in1", chain(1)
initialize
update 10000
update 10000
#
parameters to "mice.to1", chain(1)
coda \*, stem("mice")
system rm -f mice.ind
system ln -s miceindex.txt mice.ind
system rm -f mice1.out
system ln -s micechain1.txt mice1.out
exit
Local Variables:
ess-jags-chains:1
ess-jags-command:"jags"
End:

Be careful with default filenames! Here, data are assumed to be in file mice.jdt and initial values for parameters in mice.in1. You can change this in the Emacs buffer if you want, as well as modify the number of chains to use.