RMark - 2SpecOccup - mlogit link function

posts related to the RMark library, which may not be of general interest to users of 'classic' MARK

RMark - 2SpecOccup - mlogit link function

Postby bgerber » Mon Apr 06, 2020 10:18 am

RMark won't allow an mlogit link function for the 2 species occupancy model (original specification).
However, r detection parameters rAb, raB, rAB, rab, need to be constrained to sum to 1. See,
See, https://sites.warnercnr.colostate.edu/g ... o-species/


RMark error:
"Error in make.mark.model(data.proc, title = title, parameters = model.parameters, :
Mlogit link not allowed with parameter rAB
Error in mark(dp, ddl, model.parameters = list(PsiAB = PsiAB, PsiA = PsiA, :
Misspecification of model or internal error in code"

Thanks
cheers, Brian
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Re: RMark - 2SpecOccup - mlogit link function

Postby jlaake » Mon Apr 06, 2020 1:33 pm

The following is all explained in the documentation but 'll give an overview here.

RMark was designed to work with individual parameters (eg. rAB) rather than across parameters (rAB, RAb,...). I started off with CJS models because that's what I needed for my work. In that model Phi and p are very different parameters and you would never share the same column of a design matrix for Phi and p so the design matrices are constructed such that the DM for Phi is separate from the DM for p and the complete DM is built in blocks like

DMPhi 0
0 DMp

This works well for most of the models in MARK. But when I encountered the Closed models parameters p and c, it did make sense to have the columns shared across parameters so I created the Share argument in the formula where it made sense.

In a moment of weakness I added some of the occupancy models to RMark even though I haven't ever used them for my own work. With more requests I added even added more models (in a moment of weakness). But there are limits to what you can do with the occupancy models with the structure I started with in RMark. In particular, only sharing pairs of parameters doesn't always work when you have so many parameters that are related. And as you found you can't use an mlogit across types of parameters like you would want. Again RMark is designed around individual parameters and using rAB with an mlogit would be using an mlogit within rAB and not be creating an mlogit across parameters. If you want to do that I suggest using MARK directly or Presence or RPresence. Or use the alternate conditional 2 species occupancy which is better behaved from what is implied in the link you gave.
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