Spatiotemporal modelling of marine movement data using Template Model Builder (TMB)
Tracking of marine animals has increased exponentially in the past decade, and the resulting data could lead to an in-depth understanding of the causes and consequences of movement in the ocean. However, most common marine tracking systems are associated with large measurement errors. Accounting for...
Published in: | Marine Ecology Progress Series |
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2017
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ftdtupubl:oai:pure.atira.dk:publications/06ae7fc0-1497-4f60-aadf-a1eabf71f628 2024-06-09T07:49:09+00:00 Spatiotemporal modelling of marine movement data using Template Model Builder (TMB) Auger-Méthé, Marie Albertsen, Christoffer Moesgaard Jonsen, Ian D. Derocher, Andrew E. Lidgard, Damian C. Studholme, Katharine R. Bowen, W. Don Crossin, Glenn T. Flemming, Joanna Mills 2017 application/pdf https://orbit.dtu.dk/en/publications/06ae7fc0-1497-4f60-aadf-a1eabf71f628 https://doi.org/10.3354/meps12019 https://backend.orbit.dtu.dk/ws/files/128932523/Publishers_version.pdf eng eng https://orbit.dtu.dk/en/publications/06ae7fc0-1497-4f60-aadf-a1eabf71f628 info:eu-repo/semantics/openAccess Auger-Méthé , M , Albertsen , C M , Jonsen , I D , Derocher , A E , Lidgard , D C , Studholme , K R , Bowen , W D , Crossin , G T & Flemming , J M 2017 , ' Spatiotemporal modelling of marine movement data using Template Model Builder (TMB) ' , Marine Ecology - Progress Series , vol. 565 , pp. 237-249 . https://doi.org/10.3354/meps12019 /dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water article 2017 ftdtupubl https://doi.org/10.3354/meps12019 2024-05-15T00:04:04Z Tracking of marine animals has increased exponentially in the past decade, and the resulting data could lead to an in-depth understanding of the causes and consequences of movement in the ocean. However, most common marine tracking systems are associated with large measurement errors. Accounting for these errors requires the use of hierarchical models, which are often difficult to fit to data. Using 3 case studies, we demonstrate that Template Model Builder (TMB), a new R package, is an accurate, efficient and flexible framework for modelling movement data. First, to demonstrate that TMB is as accurate but 30 times faster than bsam, a popular R package used to apply state-space models to Argos data, we modelled polar bear Ursus maritimus Argos data and compared the locations estimated by the models to GPS locations of these same bears. Second, to demonstrate how TMB’s gain in efficiency and frequentist framework facilitate model comparison, we developed models with different error structures and compared them to find the most effective model for light-based geolocations of rhinoceros auklets Cerorhinca monocerata. Finally, to maximize efficiency through TMB’s use of the Laplace approximation of the marginal likelihood, we modelled behavioural changes with continuous rather than discrete states. This new model directly accounts for the irregular sampling intervals characteristic of Fastloc-GPS data of grey seals Halichoerus grypus. Using real and simulated data, we show that TMB is a fast and powerful tool for modelling marine movement data. We discuss how TMB’s potential reaches beyond marine movement studies Article in Journal/Newspaper polar bear Ursus maritimus Technical University of Denmark: DTU Orbit Laplace ENVELOPE(141.467,141.467,-66.782,-66.782) Marine Ecology Progress Series 565 237 249 |
institution |
Open Polar |
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Technical University of Denmark: DTU Orbit |
op_collection_id |
ftdtupubl |
language |
English |
topic |
/dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water |
spellingShingle |
/dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water Auger-Méthé, Marie Albertsen, Christoffer Moesgaard Jonsen, Ian D. Derocher, Andrew E. Lidgard, Damian C. Studholme, Katharine R. Bowen, W. Don Crossin, Glenn T. Flemming, Joanna Mills Spatiotemporal modelling of marine movement data using Template Model Builder (TMB) |
topic_facet |
/dk/atira/pure/sustainabledevelopmentgoals/life_below_water name=SDG 14 - Life Below Water |
description |
Tracking of marine animals has increased exponentially in the past decade, and the resulting data could lead to an in-depth understanding of the causes and consequences of movement in the ocean. However, most common marine tracking systems are associated with large measurement errors. Accounting for these errors requires the use of hierarchical models, which are often difficult to fit to data. Using 3 case studies, we demonstrate that Template Model Builder (TMB), a new R package, is an accurate, efficient and flexible framework for modelling movement data. First, to demonstrate that TMB is as accurate but 30 times faster than bsam, a popular R package used to apply state-space models to Argos data, we modelled polar bear Ursus maritimus Argos data and compared the locations estimated by the models to GPS locations of these same bears. Second, to demonstrate how TMB’s gain in efficiency and frequentist framework facilitate model comparison, we developed models with different error structures and compared them to find the most effective model for light-based geolocations of rhinoceros auklets Cerorhinca monocerata. Finally, to maximize efficiency through TMB’s use of the Laplace approximation of the marginal likelihood, we modelled behavioural changes with continuous rather than discrete states. This new model directly accounts for the irregular sampling intervals characteristic of Fastloc-GPS data of grey seals Halichoerus grypus. Using real and simulated data, we show that TMB is a fast and powerful tool for modelling marine movement data. We discuss how TMB’s potential reaches beyond marine movement studies |
format |
Article in Journal/Newspaper |
author |
Auger-Méthé, Marie Albertsen, Christoffer Moesgaard Jonsen, Ian D. Derocher, Andrew E. Lidgard, Damian C. Studholme, Katharine R. Bowen, W. Don Crossin, Glenn T. Flemming, Joanna Mills |
author_facet |
Auger-Méthé, Marie Albertsen, Christoffer Moesgaard Jonsen, Ian D. Derocher, Andrew E. Lidgard, Damian C. Studholme, Katharine R. Bowen, W. Don Crossin, Glenn T. Flemming, Joanna Mills |
author_sort |
Auger-Méthé, Marie |
title |
Spatiotemporal modelling of marine movement data using Template Model Builder (TMB) |
title_short |
Spatiotemporal modelling of marine movement data using Template Model Builder (TMB) |
title_full |
Spatiotemporal modelling of marine movement data using Template Model Builder (TMB) |
title_fullStr |
Spatiotemporal modelling of marine movement data using Template Model Builder (TMB) |
title_full_unstemmed |
Spatiotemporal modelling of marine movement data using Template Model Builder (TMB) |
title_sort |
spatiotemporal modelling of marine movement data using template model builder (tmb) |
publishDate |
2017 |
url |
https://orbit.dtu.dk/en/publications/06ae7fc0-1497-4f60-aadf-a1eabf71f628 https://doi.org/10.3354/meps12019 https://backend.orbit.dtu.dk/ws/files/128932523/Publishers_version.pdf |
long_lat |
ENVELOPE(141.467,141.467,-66.782,-66.782) |
geographic |
Laplace |
geographic_facet |
Laplace |
genre |
polar bear Ursus maritimus |
genre_facet |
polar bear Ursus maritimus |
op_source |
Auger-Méthé , M , Albertsen , C M , Jonsen , I D , Derocher , A E , Lidgard , D C , Studholme , K R , Bowen , W D , Crossin , G T & Flemming , J M 2017 , ' Spatiotemporal modelling of marine movement data using Template Model Builder (TMB) ' , Marine Ecology - Progress Series , vol. 565 , pp. 237-249 . https://doi.org/10.3354/meps12019 |
op_relation |
https://orbit.dtu.dk/en/publications/06ae7fc0-1497-4f60-aadf-a1eabf71f628 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.3354/meps12019 |
container_title |
Marine Ecology Progress Series |
container_volume |
565 |
container_start_page |
237 |
op_container_end_page |
249 |
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1801381374524915712 |