Estimating species distributions with occupancy models #836
Description
Notebook proposal
Title: Estimating species distributions with occupancy models
Why should this notebook be added to pymc-examples?
There are few notebooks on ecology in the examples gallery. While most ecologists do Bayesian statistics via R (e.g., with Stan, Nimble, or BUGS/JAGS), some might be interested in what PyMC has to offer. Moreover, many ecological models involve discrete latent states, and thus might be a good examples for showcasing pymc_extras.marginalize(). I have several such notebooks hosted on my personal webpage, including ones on species distribution modeling, distance sampling, capture-recapture, spatial capture-recapture, and estimating species richness.
I propose adding a notebook on estimating species distributions with occupancy models. This is pretty standard model in ecology and would be a good way to showcase marginalize and ZeroInflatedBinomial. Also, for what it's worth, @jessegrabowski suggested that it would be a good case study for pymc-examples.
Suggested categories:
- Level: Intermediate
- Diataxis type: How-to
Related notebooks
The closest notebook is probably the guide on automated marginalization of discrete latent states. But would be more of a case study that applies automated marginalization, rather than a general purpose guide.
References
I would be adapting the notebook on my personal website.
MacKenzie, D.I., Nichols, J.D., Lachman, G.B., Droege, S., Royle, J.A. and Langtimm, C.A., 2002. Estimating site occupancy rates when detection probabilities are less than one. Ecology, 83(8), pp.2248-2255.