Analysis methods in program GENPRES

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

Analysis methods in program GENPRES

Postby Matthew Bowser » Fri Nov 30, 2007 6:44 pm

When detection probability is small, the results yielded by the two analysis methods available in GENPRES ("Analyze w/ expected values" or "Analyze w/ simulated values") can be quite different. In design of a study, which method is more reliable?

I found empirically that the results of the "Analyze w/ expected values" option were equivalent to the equations for asymptotic variance calculation from MacKenzie and Royle (2005). Is there any guidance in the literature for deciding whether asymptotic variance calculations or simulation studies are more appropriate for use in designing occupancy studies?
Matthew Bowser
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Joined: Wed Nov 28, 2007 5:18 pm

Helpful Reference

Postby Matthew Bowser » Mon Dec 03, 2007 7:19 pm

I later found help relevant to my question as well as good examples of the use of GENPRES in the article below. I request that the citation for this article be included in the Help -> Overview document of GENPRES.

Bailey LL, Hines JE, Nichols JD, MacKenzie DI (2007) SAMPLING DESIGN TRADE-OFFS IN OCCUPANCY STUDIES WITH IMPERFECT DETECTION: EXAMPLES AND SOFTWARE. Ecological Applications: Vol. 17, No. 1 pp. 281–290
Matthew Bowser
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Joined: Wed Nov 28, 2007 5:18 pm

GENPRES from the command line?

Postby Matthew Bowser » Tue Dec 04, 2007 7:00 pm

Through fiddling with GENPRES, reading over its (limited) documentation, and by studying the reference above, I was able to assess the expected precision of estimators given a variety of sampling scenarios: standard designs, double sampling designs, and multi-season panel designs.

In my situation, I am concerned about multi-species monitoring. Especially in multi-season situations where rates of colonization and extinction may vary, the number of permutations of potential scenarios that I would like to consider becomes very large. Is there any documentation for using genpres2.exe via the command line so that this process could be automated? Simply running

C:\Program Files\PRESENCE>genpres2.exe

returns some basic help, but the meaning of options is not explained.

C:\Program Files\PRESENCE>genpres2.exe 1 5 60 .75 .5 .5 .5 .5 .5 0 0 0 0

yielded a terse summary of an analysis of the default GENPRES dataset. Implementing more complicated sampling regimes seems to be straightforward. It is not clear how much of the functionality of the GENPRES GUI can be accessed through the command line, for example it is not apparent how input files could be entered, how models could be specified, how an analysis method can be selected (asymptotic variance estimates or simulations), or how output could be sent to a file or files.

Might MARK serve better for this purpose?
Matthew Bowser
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Joined: Wed Nov 28, 2007 5:18 pm

GENPRES from command line

Postby jhines » Wed Dec 05, 2007 12:52 am

GENPRES2.EXE generates expected or simulated data under several model types. The GUI program, GENPRES2_INT.EXE, takes care of gathering input, calling GENPRES2.EXE, running the selected model(s), and presenting/summarizing the output. As you have discovered, you can call GENPRES2.EXE from a command window, and if you call it without any arguments, it will list the format it expects for input. All input is via arguments to the command. No input file needs to be created. The program creates expected value data unless 'STOCHASTIC' is specified as an argument of the command.

The models used to analyze the data generated by GENPRES2.EXE are created in the GUI program. Actually, the GUI calls MARK for many expected value data-sets, and PRESENCE for some others. It sounds like you wish to automate the process of the GUI program, which would involve writing a 'script', or program to do what the GUI program does. If you would like help with this, contact me directly.

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