title: A hidden Markov model for reconstructing animal paths from solar geolocation loggers using templates for light intensity.
abstract: BACKGROUND
  Solar archival tags (henceforth called geolocators) are tracking devices deployed on animals to reconstruct their long-distance movements on the basis of locations inferred post hoc with reference to the geographical and seasonal variations in the timing and speeds of sunrise and sunset. The increased use of geolocators has created a need for analytical tools to produce accurate and objective estimates of migration routes that are explicit in their uncertainty about the position estimates.
  
  
  RESULTS
  We developed a hidden Markov chain model for the analysis of geolocator data. This model estimates tracks for animals with complex migratory behaviour by combining: (1) a shading-insensitive, template-fit physical model, (2) an uncorrelated random walk movement model that includes migratory and sedentary behavioural states, and (3) spatially explicit behavioural masks. The model is implemented in a specially developed open source R package FLightR. We used the particle filter (PF) algorithm to provide relatively fast model posterior computation. We illustrate our modelling approach with analysis of simulated data for stationary tags and of real tracks of both a tree swallow Tachycineta bicolor migrating along the east and a golden-crowned sparrow Zonotrichia atricapilla migrating along the west coast of North America.
  
  
  CONCLUSIONS
  We provide a model that increases accuracy in analyses of noisy data and movements of animals with complicated migration behaviour. It provides posterior distributions for the positions of animals, their behavioural states (e.g., migrating or sedentary), and distance and direction of movement. Our approach allows biologists to estimate locations of animals with complex migratory behaviour based on raw light data. This model advances the current methods for estimating migration tracks from solar geolocation, and will benefit a fast-growing number of tracking studies with this technology.
authors.affiliation: Department of Ecology and Evolutionary Biology and Laboratory of Ornithology, Cornell University, Ithaca, 14853 USA ; Department of Marine Ecology, NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, The Netherlands ; Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, 119991 Russia.
authors.forename: Eldar
authors.identifier: 0000-0001-6357-6187
authors.initials: E
authors.lastname: Rakhimberdiev
authors.affiliation: Department of Ecology and Evolutionary Biology and Laboratory of Ornithology, Cornell University, Ithaca, 14853 USA.
authors.forename: David W
authors.initials: DW
authors.lastname: Winkler
authors.affiliation: Oklahoma Biological Survey, University of Oklahoma, 111 E Chesapeake St., Norman, OK 73019 USA.
authors.forename: Eli
authors.initials: E
authors.lastname: Bridge
authors.affiliation: Point Blue Conservation Science, 3820 Cypress Drive, Suite 11, Petaluma, CA 94954 USA.
authors.forename: Nathaniel E
authors.initials: NE
authors.lastname: Seavy
authors.affiliation: College of Information and Computer Sciences, University of Massachusetts, Amherst, MA 01003 USA ; Department of Computer Science, Mount Holyoke College, South Hadley, MA 01075 USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Sheldon
authors.affiliation: Department of Marine Ecology, NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790 AB Den Burg, The Netherlands ; Chair in Global Flyway Ecology, Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103, Groningen, 9700 CC The Netherlands.
authors.forename: Theunis
authors.initials: T
authors.lastname: Piersma
authors.affiliation: Department of Ecological Systems Modelling, Institute of Environmental Sciences, Kazan Federal University, 5 Tovarisheskaya, Kazan, 420008 Russia.
authors.forename: Anatoly
authors.initials: A
authors.lastname: Saveliev
keywords: Bird migration; FLightR; Hidden Markov models; Particle filter; Solar geolocation; Template fitting