This repo contains code to run capture-recapture model to determine the status of jaguars in Corcovado National Park, Costa Rica.
We implemented a (spatially-explicit) Jolly-Seber model with habitat selection in Stan. (See the stan folder). Since Stan does not allow discrete parameters, the state of the individual was manually marginalized during posterior sampling via a forward algorithm and the sample back using forward filtering backward sampling (FFBS) algorithm. One can use make to run part of all of the work flow
