Markov modulated poisson processes for clustered line transect data

We model the points of the detection along the transect line by a Markov modulated Poisson process (MMPP). The MMPP can accommodate the spatial cluster structure typical of many line transect surveys. The basic idea is that animal density switches between a low and a high level according to a latent Markov process. The MMPP is attractive from a mathematical point of view, as it provides an explicit expression for the likelihood function and other important quantities. We focus on estimating the level of overdispersion in the number of detected animals, as this is important for quantifying the precision of the line transect estimator of animal abundance. The approach is illustrated using both simulated data and data from a minke whale sighting survey conducted in the North Atlantic.