Description
This is a tutorial that I developed with Ana Miller-ter Kuile to provide a more detailed description of the modelling approaches in our paper. In the tutorial, we walk through the Bayesian models for species abundance or occupancy that lead to an output of “latent” abundance or occupancy, which one could consider the “true” abundance or occupancy given some variables influencing detection.
The latent abundances (or occupancies) then get fed into calculations of commonly used indices of diversity like Shannon diversity (for abundance) or species richness (for occupancy).
Then, we built models to determine how environmental variables influence abundance/occupancy using the observed (original) datasets and the “latent” datasets to compare the interpretations of each environmental variable on diversity indices.