How does habitat diversity affect species richness? Perhaps intuition suggests that habitat diversity increases species richness by facilitating niche or resource partitioning among species. But, for a fixed area, as habitat heterogeneity increases, the area that can be allocated to each habitat type decreases. In a recent paper, Allouche and colleagues (2012) provide a theoretical and empirical treatment...
This post is intended to provide a simple example of how to construct and make inferences on a multi-species multi-year occupancy model using R, JAGS, and the ‘rjags’ package. This is not intended to be a standalone tutorial on dynamic community occupancy modeling. Useful primary literature references include MacKenzie et al. (2002), Kery and Royle (2007), Royle and Kery...
This is an example of interfacing R, shiny, and deSolve to produce an interactive environment where users can explore model behavior by altering parameters in an easy to use GUI.
The model tracks the number of susceptible, infectious, and recovered individuals in two co-occuring host species. The rates of change for each class are represented as a system of...
This is an example of interfacing R and shiny to allow users to explore a biological model often encountered in an introductory ecology class. We are interested the growth of a population that is composed of multiple, discrete stages or age classes. Patrick H. Leslie provides an in-depth derivation of the model in his 1945 paper “On the...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
