Recovery rate individual covariates for Brownie model

questions concerning analysis/theory using program MARK

Recovery rate individual covariates for Brownie model

Postby wil_16 » Fri Oct 08, 2021 4:06 pm

Hello,
I am having difficulty with my individual covariate for my Brownie model.

The data set I am working with is a fishery based dead-recovery tagging study spanning 18 years, with both adult and juvenile tagged fish. The juveniles become adults after 1 year. The Brownie model I am building in RMark has an age variable and I am looking to add an individual covariate. This individual covariate is an efficiency rate of detection of fish recoveries that applies only to recovered fish, and I will be looking to make my recovery rate a function of this efficiency rate covariate. Currently, this efficiency rate is not time-varying.

However, because this covariate only applies to recovered fish (which is a small portion of the data set), most of my individuals have NA in the cov column, which RMark does not like.
How would I go about applying this covariate to my recovery rate parameters? I would like to avoid the multistrata method, as I have 11 different efficiency rates.

Would I be fine with the standardized covariates method, and just changing all those individuals with NA's to 0?

I have read Catchpole et al., 2008 and as far as I can tell (which admittedly may not be very far) they only deal with survival based parameters for the missing covariates.


Thank you very much for any advice.
wil_16
 
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Joined: Fri Oct 08, 2021 11:56 am

Re: Recovery rate individual covariates for Brownie model

Postby sbonner » Thu Oct 14, 2021 10:32 am

Hi Catherine,

If I'm understanding correctly then you want to model the recovery probability for fish
Code: Select all
i
in year
Code: Select all
t
as something like
Code: Select all
logit(lambda[i,t])=beta0 + beta1 * x[t]

where
Code: Select all
x[t]
is a measure of effort in year
Code: Select all
t
that varies by year but is the same for all fish. Is that right?

If so, then the covariate in any given year is the same for all fish and doesn't depend on whether or not they are recovered. The recovery probability applies to all fish that die in a given year, and all fish would be exposed to the same probability of recovery if they were to die.

You say that the efficiency rate is not time-varying. In this case, you would want to include a single covariate for efficiency and it would have the same value for all of the fish. However, I'm confused because you say later that there are 11 different efficiency rates, and I'm not sure what that refers to. Are the fish recovered in different locations with different amounts of effort? If that's the case then you will need to allow for different strata with different recovery rates that depend on the location specific efficiency values. I'm sure this can be done, though I need to look into how this would be formulated in RMark.

I hope that helps.

Cheers,

Simon
sbonner
 
Posts: 70
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Location: University of Western Ontario, Canada

Re: Recovery rate individual covariates for Brownie model

Postby wil_16 » Tue Oct 19, 2021 2:41 pm

The 'effort' does not vary by year - it just varies by the way the fish is recovered (the fish are recovered at different facilities - 11 facilities - and those facilities have a unique efficiency rate that for my purpose stays the same each year).
So these fish are harvested each year in the commercial fishery, and those fish that are caught are brought in for processing, where their tags are recovered. Each facility has a different efficiency rate of recovery of the tags. So only the fish that are brought into the facility have the covariate of the facility efficiency rate. Those not caught and/or detected do not have a facility efficiency rate covariate.
wil_16
 
Posts: 2
Joined: Fri Oct 08, 2021 11:56 am


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