running COMDYN and/or SPECRICH in some kind of "batch m

questions concerning analysis/theory using software from the Patuxent Software Archive

running COMDYN and/or SPECRICH in some kind of "batch m

Postby giancarlo » Thu Jan 21, 2010 9:58 pm

I'm interested in generating the kinds of parameter estimates produced by SPECRICHs (e.g., jackknife spp. richness estimates) and COMDYN4 (e.g., same as those in SPECRICH4, plus PHI, GAMMA, etc) for a large number of sites.

I understand the jackknife estimator underlying these estimates is the same as that of the M(h) model (individual/spp. heterogeneity) in other capture-recapture software (e.g. MARK).

Has anyone developed a "batch COMDYN" or have any suggestions for how it might be implemented (perhaps in MARK?) to generate estimates for lots of sites? The web and standalone interfaces of SPECRICH and COMDYN are clear and great, but only allow one site at a time.

Thanks in advance for any help!

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running COMDYN and/or SPECRICH in some kind of "batch m

Postby jhines » Thu Jan 21, 2010 11:19 pm

If you downloaded, you'll see two application files, comdyn08.exe, and comdyn4.exe. The first one is a windows GUI program which gets the input from the user, then submits the data to the 2nd program for analysis. After running a dummy data-set, there will be a text file generated containing the input data, comdyn4.dat. The trick to running comdyn in batch mode will be to create a script which generates the input text file, then make the script call the 2nd application (comdyn4.exe) and save the output file. I usually use 'gawk', 'perl', or 'R' (free versions available on web) to create these types of scripts, but you can use any scripting language which allows you to call another program.

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