R code supporting: Detecting disease progression from animal movement using hidden Markov models

Abstract

This repository contains R code supporting: Detecting disease progression from animal movement using hidden Markov models (HMMs). We provide a series of .Rmd files that can be compiled to form a transferable workflow for detecting infection from animal movement. We demonstrate the flexibility of (H)HMMs in capturing different disease scenarios and a workflow for appropriate model selection. Our approach has the potential to improve wildlife disease surveillance, inform management of vulnerable populations, and enhance understanding of disease dynamics.