patter: Particle algorithms for animal tracking in R and Julia

Abstract

Abstract State‐space models are a powerful modelling framework in movement ecology that represents individual movements and the processes connecting movements to observations. However, fitting state‐space models to animal‐tracking data can be difficult and computationally expensive. Here, we introduce patter, a package that provides particle filtering and smoothing algorithms that fit Bayesian state‐space models to tracking data, with a focus on data from aquatic animals in receiver arrays. patter is written in R, with a performant Julia backend. Package functionality supports data simulation, preparation, filtering, smoothing and mapping. In two examples, we demonstrate how to implement patter to reconstruct the movements of a tagged animal in an acoustic telemetry system from acoustic detections and ancillary observations. With perfect information, the particle filter reconstructs the true (unobserved) movement path (Example One). More generally, particle algorithms represent an individual's possible location probabilistically as a weighted series of samples (‘particles’). In our illustration, we resolve an individual's (unobserved) location every 2 min during 1 month and use particles to visualise movements, map space use and quantify residency (Example Two). patter facilitates robust, flexible and efficient analyses of animal‐tracking data. The methods are widely applicable and enable refined analyses of space use, home ranges and residency.

Keywords

• Bayesian inference
• movement ecology
• package
• particle filter
• passive acoustic telemetry
• state‐space model