spOccupancy tMsPGOcc() worked example?

[Jarrad Barnes]

Hi all, I'm dipping my toe into the spOccupancy package as I'm interested in developing a multi-species multi-season occupancy model, but I'm swimming a bit. I'm familiar with occupancy models through other packages (notably unmarked and camtrapR), but spOccupancy is a bit of a different beast for me. I've played through the simulated data for tMsPGOcc() but I would really like to see a worked example with real data so I can see how I might shape my own dataset to this function. I haven't had any luck online finding one, but I'm hoping there might be someone or something that can provide a direction with this. Thanks for any help/insight. Jarrad

[Jeff Doser]

Hi Jarrad,

I've attached a script that walks through an example using tMsPGOcc() with the Hubbard Brook bird data that is included as part of the package. I'm hoping at some point to put together a vignette on the package website that walks through the multi-species, multi-season models, but in the meantime, you might also take a look at this data formatting vignette (which is for single-season models but could be adapted accordingly) and this vignette on single-species multi-season models (which are very similar in form to the multi-species functions).

Hope that helps!

Jeff

On Mon, Mar 25, 2024 at 8:54 PM Jarrad Barnes <jarrad...@gmail.com> wrote:

Hi all, I'm dipping my toe into the spOccupancy package as I'm interested in developing a multi-species multi-season occupancy model, but I'm swimming a bit. I'm familiar with occupancy models through other packages (notably unmarked and camtrapR), but spOccupancy is a bit of a different beast for me. I've played through the simulated data for tMsPGOcc() but I would really like to see a worked example with real data so I can see how I might shape my own dataset to this function. I haven't had any luck online finding one, but I'm hoping there might be someone or something that can provide a direction with this. Thanks for any help/insight. Jarrad

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[Jarrad Barnes]

Thanks Jeff, appreciate you replying to this so quickly. I'll take a good look at everything you've sent/suggested. Jarrad

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[Jarrad Barnes]

Hi Jeff, I've managed to work through and adapt the code you've provided right up to running the tMsPGOcc function and I'm running across two issues:

1) I get an "error in colMeans [...] x must be numeric" error. As far as I can tell this is because several of my occupancy covariates are factors. I assume it is possible to use factors in the model, as for other occupancy models, and I'm just missing something?

2) When I try to run the function without factors, it begins to run but R Studio terminates as soon as the first chain begins. Is this a common occurrence? Happy to provide any code, data, etc. that might help pinpoint the problem. For what it's worth, in case it's a memory issue, I'm working with a dataset of 17 species, over 9 primary sampling periods, with 21 secondary sampling periods per primary.

Thanks,

Jarrad

[Jeff Doser]

Hi Jarrad,

Yes, you should be able to include factors in the model. They can either be supplied as a factor directly in "occ.covs" or "det.covs", or you can specify them as a numeric or categorical in "occ.covs"/"det.covs" and then include them in the model formula with the factor() function (e.g., occ.formula = ~ factor(habitatType)).

As far as the second problem goes, that could be related to a problem in an older version in the package. Under certain circumstances, the model could fail to run across multiple chains when specifying the MCMC criteria in a specific manner (see this github issue here). If you install the latest spOccupancy version from CRAN then I think that should go away.

Feel free to send me your code/data and I can try and debug if you still can't get it to work. There could potentially be other formatting issues that are leading to the problems.

Jeff

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[Jarrad Barnes]

Thanks Jeff, I'll give those things a try and see how I get on. Hopefully it will all be smooth sailing, otherwise you may hear from me one more time ... !

Jarrad