Fitting occupancy models with E-SURGE: Hidden Markov modelling of presence-absence data

1. Occupancy – the proportion of area occupied by a species – is a key notion for addressing important questions in ecology, biogeography and conservation biology. Occupancy models allow estimating and inferring about species occurrence while accounting for false absences (or imperfect species detection). 2. Most occupancy models can be formulated as hidden Markov models (HMM) in which the state process captures the Markovian dynamic of the actual but latent states while the observation process consists of observations that are made from these underlying states. 3. We show how occupancy models can be implemented in program E-SURGE, which was initially developed to analyse capture-recapture data in the HMM framework. Replacing individuals by sites provides the user with access to several features of E-SURGE that are not available altogether or just not available in standard occupancy software: i) user-friendly model specification through a SAS/R-like syntax without having to write custom code, ii) decomposition of the observation and state processes in several steps to provide flexible parameterisation, iii) up-to-date diagnostics of model identifiability and iv) advanced numerical algorithms to produce fast and reliable results (including site random effects). 4. To illustrate E-SURGE features, we provide simulated data and the details of the implementation on the analysis of several occupancy models. These detailed examples are gathered in a companion wiki platform http://occupancyinesurge.wikidot.com/ .