The purpose of this post is to raise awareness of my occupancy modeling work with RStan, help people find my work, and seek out possible collaborators to help other avoid reinventing the wheel. I also hope others would please add links to your own tutorials on occupancy modeling with Stan.
I am writing a set of tutorials on doing Occupancy Modeling with RStan. The tutorials are on GitHub (link here). I am also in the process of putting the tutorials into an R Package (currently in rough shape on GitHub). My long term goal is to put all of the tutorials as Vignettes in the R Package.
I am motivated for my project by environmental DNA (eDNA) occupancy modeling (or occupancy modeling with sub-sampling). The models require at least 3-levels: Molecular detection (e.g., did qPCR detect the eDNA?); Sample capture (e.g., did you get eDNA in your water bottle?); and Site-level occupancy (e.g., is eDNA at the site?). I am currently working with USGS and USFWS scientists who use these 3-level models for their work and my tutorials builds up to them, starting with
glm() in R before moving to Stan and occupancy models.
I have found that @jsocolar has posted a nice tutorial comparing JAGS to RStan (and @jsocolar, I invite you (and anyone else!) to collaborate with me on my projects). I also know that @mbjoseph has a nice tutorial on Dynamic occupancy models in Stan and a paper using SEM models with occupancy models in Stan.