species-level covariates

[Oscar Morton]

Hi all,

I'm working on fitting a multi-species, multi-season occupancy model. One of the things I'd like to be able to incorporate is if average occurrence probabilities vary through seasons by some trait intrinsic to species e.g. species habitat preference, to evaluate whether more broad species groups share a common temporal trend.

I can see in tMsPGOcc() the occurrence covariates can vary by site or site/primary time period level, and the detection covariates can vary the same or additionally at the observation level. Does that mean it's not currently possible to include species-level covariates (traits etc.) in the occurrence model? Or have I missed something?

If that is the case, would an alternative be to extract this from the posterior post-fitting, e.g. if I have a trait with two levels, I could feasibly compare the average species-level trends for species of each level or the proportion with x-directional temporal change per trait level or the like.

Thank you in advance for any guidance or support!

All the best,

Oscar

[Jeffrey Doser]

Hi Oscar,

You are correct that spOccupancy does not directly support including species-level covariates in the multi-species model functions (including tMsPGOcc()). However, the alternative you propose there is a completely valid option, and the function postHocLM() in spOccupancy is designed exactly for that purpose. You could take the species-specific posterior samples from tMsPGOcc() and use those as the response in a subsequent linear model, testing the impact of species-traits on those species-specific effects. postHocLM() allows you to take the full posterior distribution of those effects and propagate that uncertainty into the subsequent regression. This is perhaps a bit less elegant than directly allowing for species-level effects when fitting the model, but it gets the job done.

Kind regards,

Jeff

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Jeffrey W. Doser, Ph.D.

Assistant Professor

Department of Forestry and Environmental Resources

North Carolina State University

Statistical Ecology and Forest Science Lab

Pronouns: he/him/his

[Oscar Morton]

Hi Jeff, 

Thanks for the fast reply, and sorry I missed postHocLM(), that looks like it will work great.

Many thanks,

Oscar