1. Tracking technologies have widely expanded our understanding of bird migration routes, destinations, and underlying strategies. However, determining the entire trajectory of small birds equipped with lightweight geolocators remains a challenge. Statistical trajectory models that incorporate both flight behaviour and sensor information provide the most accurate estimates of a bird’s full trajectory.
2. We develop a highly optimized hidden Markov model (HMM) for reconstructing bird trajectories. The observation model is defined by pressure and, optionally, light measurements, while the movement model incorporates wind data to constrain consecutive positions based on realistic airspeeds. Due to the large state space, the computational requirements for HMM calculations are high and may exceed available memory. We prune the HMM states and transitions based on flight and observation constraints to efficiently model the entire trajectory.
3. The approach presented is based on a mathematically exact procedure and is fast to compute. We demonstrate how to compute: (1) the most likely trajectory, (2) the marginal probability map of each stopover, (3) simulated trajectories, and (4) the wind conditions (wind support/drift) encountered by the bird during each migratory flight.
4. We construct a version of an HMM optimized for reconstructing a bird’s migration trajectory based on lightweight geolocator data. The focus of this work is to render this approach easily accessible to researchers through the dedicated R package GeoPressureR (https://raphaelnussbaumer.com/GeoPressureR/).