Inference in MCMC step selection models

Abstract: Habitat selection models are used in ecology to link the distribution of animals to environmental covariates, and identify habitats that are important for conservation. The most widely used models of this type, resource selection functions, assume independence between the observed locations of an animal. This is unrealistic when location data display spatio-temporal autocorrelation. Alternatively, step selection functions embed habitat selection in a model of animal movement, to account for the autocorrelation. However, inferences from step selection functions depend on the movement model, and they cannot readily be used to predict long-term space use. We recently suggested that a Markov chain Monte Carlo (MCMC) algorithm could define a step selection model with an explicit stationary distribution: the target distribution. Here, we explain how the likelihood of a MCMC step selection model is derived, and how maximum likelihood estimation can be used for inference about parameters of movement and habitat selection. We describe the local Gibbs sampler, a rejection-free MCMC scheme designed to capture important features of real animal movement. The sampler can be used as the basis for a flexible class of movement models, and we derive the likelihood function for several important special cases. In a simulation study, we verify that maximum likelihood estimation can be used to recover all model parameters. We illustrate the application of the method with data from a plains zebra.