Small-scale covariates in mutli-method occupancy

questions concerning analysis/theory using program PRESENCE

Small-scale covariates in mutli-method occupancy

Postby bam59 » Mon Jun 11, 2018 2:30 pm

Hi all,
I'm working on a multi-method (a la Nichols et al. 2008) analysis in PRESENCE and am wondering how I can incorporate a covariate that is specific to the small-scale occupancy parameter (theta).

In my example, the study sites are wetlands where up to 10 amphibians per site are sampled for a pathogen (the number of sampled amphibians is equivalent to the number of 'surveys'). Each individual is sampled three times using tissue samples (equivalent to the number of methods/survey), and the pathogen is either detected (1) or not (0). In this case, the interpretation of theta is the pathogen prevalence (the proportion of infected individuals). I believe this set-up to be appropriate because conditional upon the pathogen occurring at the site (psi), individual amphibians may be infected or uninfected.

Say I have a continuous covariate like the weight of each animal sampled. How would I add this kind of covariate to the input data?

Here are my ideas:
1 - Paste/enter the covariate values directly into the design matrix
2 - Specify the survey covariate as a sampling covariate, but only fill in the first (nSurvey) columns

I think these will work, but I'm wondering if there might be something more efficient out there. Thanks for any thoughts you have.
Brittany :D
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Re: Small-scale covariates in mutli-method occupancy

Postby jhines » Mon Jun 11, 2018 7:44 pm

Hi Brittney,

To use a covariate on theta for the multi-method model, you'll need to use a 'survey' covariate, however that model treats each method-survey combination as a survey when estimating theta. So, you need to duplicate the covariate for each method. For example, if you have 3 methods and 10 surveys, the number of columns in the detection-history matrix is 30 and the number of columns in your survey covariate must be 30. You should replicate the covariate for the 1st survey 3 times, then replicate the covariate for the 2nd survey 3 times,...etc.

You won't be able to enter values directly into the design matrix because the design matrix isn't site-specific.

Presence will use the 3rd, 6th, 9th,...etc. columns in the survey covariate matrix to get the covariate value for theta for each survey. So you don't want to fill in only the 1st nSurvey columns.

Jim
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Re: Small-scale covariates in mutli-method occupancy

Postby bam59 » Fri Jun 15, 2018 9:59 am

Hi Jim,
Thanks for that explanation. I was wondering if Presence might be clever enough to grab one entry from each survey/method string to use for modeling theta. When I inserted the individual covariate in the design matrix for theta, the names that were imported were "cov" rather than cov3, cov6, cov9 which is why I assumed it was collecting the first nSurvey entries. What you have coded into Presence makes sense and is much easier than the user having to do bookkeeping!

Thanks again,
Brittany
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Posts: 6
Joined: Wed Jul 03, 2013 6:24 pm
Location: Colorado State University


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