HMMoce : an R package for improved geolocation of archival-tagged fishes using a hidden Markov method
Braun, Camrin D.
Thorrold, Simon R.
MetadataShow full item record
Electronic tagging of marine fishes is commonly achieved with archival tags that rely on light levels and sea surface temperatures to retrospectively estimate movements. However, methodological issues associated with light-level geolocation have constrained meaningful inference to species where it is possible to accurately estimate time of sunrise and sunset. Most studies have largely ignored the oceanographic profiles collected by the tag as a potential way to refine light-level geolocation estimates. Open-source oceanographic measurements and outputs from high-resolution models are increasingly available and accessible. Temperature and depth profiles recorded by electronic tags can be integrated with these empirical data and model outputs to construct likelihoods and improve geolocation estimates. The R package HMMoce leverages available tag and oceanographic data to improve position estimates derived from electronic tags using a hidden Markov approach. We illustrate the use of the model and test its performance using example blue and mako shark archival tag data. Model results were validated using independent, known tracks and compared to results from other geolocation approaches. HMMoce exhibited as much as 6-fold improvement in pointwise error as compared to traditional light-level geolocation approaches. The results demonstrated the general applicability of HMMoce to marine animals, particularly those that do not frequent surface waters during crepuscular periods.
Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Methods in Ecology and Evolution 9 (2018): 1212-1220, doi:10.1111/2041-210X.12959.
Suggested CitationPreprint: Braun, Camrin D., Galuardi, Benjamin, Thorrold, Simon R., "HMMoce : an R package for improved geolocation of archival-tagged fishes using a hidden Markov method", 2017-11, https://doi.org/10.1111/2041-210X.12959, https://hdl.handle.net/1912/10390
Showing items related by title, author, creator and subject.
Land carbon sequestration within the conterminous United States : regional- and state-level analyses Lu, Xiaoliang; Kicklighter, David W.; Melillo, Jerry M.; Reilly, John M.; Xu, Liyi (John Wiley & Sons, 2015-02-28)A quantitative understanding of the rate at which land ecosystems are sequestering or losing carbon at national-, regional-, and state-level scales is needed to develop policies to mitigate climate change. In this study, ...
The Southern Ocean meridional overturning circulation as diagnosed from an eddy permitting state estimate Mazloff, Matthew R. (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2008-09)A modern general circulation model of the Southern Ocean with one-sixth of a degree resolution is optimized to the observed ocean in a weighted least squares sense. Convergence to the state estimate solution is carried ...
Schanze, Julian J.; Schmitt, Raymond W.; Yu, Lisan (Sears Foundation for Marine Research, 2010-05-01)The current capabilities of quantifying the oceanic freshwater cycle are shown based on new observations from satellite data and re-analysis models for evaporation and precipitation over the ocean. For this purpose, we ...