Species richness occupancy models

questions concerning analysis/theory using program PRESENCE

Species richness occupancy models

Postby amielle » Thu Dec 13, 2007 2:16 pm

I'm trying to run species richness occupancy models for 10 breeding birds at 75 locations (6 visits, 1 season) with 3 covariates in PRESENCE. I am comfortable running single species/season models, but would prefer not to run each species on its own. I've been trying to find the mechanics of doing multiple species in PRESENCE with the Donovan + Hines book and with the MacKenzie et al. but haven't been able to find a description. Can someone provide me with a quick and dirty explanation? Let me know if I need to provide more info- Thanks, Amielle
amielle
 
Posts: 1
Joined: Mon Nov 26, 2007 12:04 pm

Postby darryl » Thu Dec 13, 2007 3:27 pm

Amielle,
It depends exactly what you're trying to do, but one option is to append all your data from all locations and species in 1 file (so it's 750 rows), and define a series of site-specific covariates that denote each species to 'species effects'.
Darryl
darryl
 
Posts: 495
Joined: Thu Jun 12, 2003 3:04 pm
Location: Dunedin, New Zealand

PRESENCE w/ multiple groups

Postby jhines » Thu Dec 13, 2007 3:34 pm

To model 10 species in PRESENCE, construct the data such that each site/species combination is a separate record. Then construct site covariates with one column for each species, where the column would contain '0' if the particular record did not corresponded to that species, and '1' if the record did correspond to that species.

So, if the first 5 histories were observations for species1, then the first species covariate column would contain '1' and the other 9 species covariates would contain '0' for the first 5 records. If histories 6-10 were observations (at the same or different sites) for species2, then the first species covariate column would contain '0', the 2nd covariate would contain '1', and the rest would contain '0' for records 6-10.

To build a model where all 10 species have the same occupancy(psi) and detection(p), run a single-season model as you would for only one species, ignoring the 10 new covariates.

To build a model where each of the 10 species has a different psi, add a 9 columns in the 'psi' page of the design matrix, and enter the name of each of the species covariates (except the first) in the newly created cells (click blank cell, goto 'Init' menu, select covariate name). This causes PRESENCE to compute occupancy as a function of an 'intercept' term plus a term for each species (except the first). Since the covariates are either zero or one, occupancy will be computed as:

psi(species1) = f(1*a1) { since all covariates for spec2-spec10 are zero}
psi(species2) = f(1*a1+1*a2) { since covariate for spec2=1, others=0}
psi(species3) = f(1*a1+1*a3) { since covariate for spec3=1, others=0}
psi(species4) = f(1*a1+1*a4) { since covariate for spec3=1, others=0}

PRESENCE will estimate a1,a2,...a10, and compute a different psi for each species. Detection probabilities would be done the same way, except that you have the possibility of different estimates for each survey (in combination with each species). For a survey-specific p and different p for each species, you would need 2 columns (one intercept and 9 columns for each species covariate) for each survey.

More documentation on building models with a design matrix is available in the Cooch's online MARK book.

Jim
jhines
 
Posts: 599
Joined: Fri May 16, 2003 9:24 am
Location: Laurel, MD, USA


Return to analysis help

Who is online

Users browsing this forum: No registered users and 7 guests