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Dhanjal-Adams KL, Willener AST, Liechti F. sspamlr: a toolbox for analysing animal behaviour using pressure, acceleration, temperature, magnetic or light data in R. J Anim Ecol 2022; 91:1345-1360. [PMID: 35362103 PMCID: PMC9542251 DOI: 10.1111/1365-2656.13695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 03/09/2022] [Indexed: 11/28/2022]
Abstract
Light‐level geolocators have revolutionised the study of animal behaviour. However, lacking spatial precision, their usage has been primary targeted towards the analysis of large‐scale movements. Recent technological developments have allowed the integration of magnetometers and accelerometers into geolocator tags in addition to barometers and thermometers, offering new behavioural insights. Here, we introduce an R toolbox for identifying behavioural patterns from multisensor geolocator tags, with functions specifically designed for data visualisation, calibration, classification and error estimation. More specifically, the package allows for the flexible analysis of any combination of sensor data using k‐means clustering, expectation maximisation binary clustering, hidden Markov models and changepoint analyses. Furthermore, the package integrates tailored algorithms for identifying periods of prolonged high activity (most commonly used for identifying migratory flapping flight), and pressure changes (most commonly used for identifying dive or flight events). Finally, we highlight some of the limitations, implications and opportunities of using these methods.
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Affiliation(s)
- Kiran L Dhanjal-Adams
- Swiss ornithological institute, Seerose 1, 6204, Sempach, Switzerland.,Centre for the Advanced Study of Collective Behavior, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany.,Max Planck Institute of Animal Behavior, Bücklestraße 5, 78467, Konstanz, Germany
| | | | - Felix Liechti
- Swiss ornithological institute, Seerose 1, 6204, Sempach, Switzerland
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Nathan R, Monk CT, Arlinghaus R, Adam T, Alós J, Assaf M, Baktoft H, Beardsworth CE, Bertram MG, Bijleveld AI, Brodin T, Brooks JL, Campos-Candela A, Cooke SJ, Gjelland KØ, Gupte PR, Harel R, Hellström G, Jeltsch F, Killen SS, Klefoth T, Langrock R, Lennox RJ, Lourie E, Madden JR, Orchan Y, Pauwels IS, Říha M, Roeleke M, Schlägel UE, Shohami D, Signer J, Toledo S, Vilk O, Westrelin S, Whiteside MA, Jarić I. Big-data approaches lead to an increased understanding of the ecology of animal movement. Science 2022; 375:eabg1780. [PMID: 35175823 DOI: 10.1126/science.abg1780] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Understanding animal movement is essential to elucidate how animals interact, survive, and thrive in a changing world. Recent technological advances in data collection and management have transformed our understanding of animal "movement ecology" (the integrated study of organismal movement), creating a big-data discipline that benefits from rapid, cost-effective generation of large amounts of data on movements of animals in the wild. These high-throughput wildlife tracking systems now allow more thorough investigation of variation among individuals and species across space and time, the nature of biological interactions, and behavioral responses to the environment. Movement ecology is rapidly expanding scientific frontiers through large interdisciplinary and collaborative frameworks, providing improved opportunities for conservation and insights into the movements of wild animals, and their causes and consequences.
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Affiliation(s)
- Ran Nathan
- Movement Ecology Lab, A. Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel.,Minerva Center for Movement Ecology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Christopher T Monk
- Institute of Marine Research, His, Norway.,Centre for Coastal Research (CCR), Department of Natural Sciences, University of Agder, Kristiansand, Norway.,Department of Fish Biology, Fisheries and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Robert Arlinghaus
- Department of Fish Biology, Fisheries and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Division of Integrative Fisheries Management, Faculty of Life Sciences and Integrative Research Institute on Transformations of Human-Environment Systems (IRI THESys), Humboldt-Universität zu Berlin, Berlin, Germany
| | - Timo Adam
- Centre for Research into Ecological and Environmental Modelling, School of Mathematics and Statistics, University of St Andrews, St Andrews, UK
| | - Josep Alós
- Instituto Mediterráneo de Estudios Avanzados, IMEDEA (CSIC-UIB), Esporles, Spain
| | - Michael Assaf
- Racah Institute of Physics, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Henrik Baktoft
- National Institute of Aquatic Resources, Section for Freshwater Fisheries and Ecology, Technical University of Denmark, Silkeborg, Denmark
| | - Christine E Beardsworth
- NIOZ Royal Netherlands Institute for Sea Research, Department of Coastal Systems, Den Burg, The Netherlands.,Centre for Research in Animal Behaviour, Psychology, University of Exeter, Exeter, UK
| | - Michael G Bertram
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Allert I Bijleveld
- NIOZ Royal Netherlands Institute for Sea Research, Department of Coastal Systems, Den Burg, The Netherlands
| | - Tomas Brodin
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Jill L Brooks
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Andrea Campos-Candela
- Department of Fish Biology, Fisheries and Aquaculture, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Instituto Mediterráneo de Estudios Avanzados, IMEDEA (CSIC-UIB), Esporles, Spain
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, ON, Canada
| | | | - Pratik R Gupte
- NIOZ Royal Netherlands Institute for Sea Research, Department of Coastal Systems, Den Burg, The Netherlands.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Roi Harel
- Movement Ecology Lab, A. Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel.,Minerva Center for Movement Ecology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gustav Hellström
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Florian Jeltsch
- Plant Ecology and Nature Conservation, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Shaun S Killen
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow UK
| | - Thomas Klefoth
- Ecology and Conservation, Faculty of Nature and Engineering, Hochschule Bremen, City University of Applied Sciences, Bremen, Germany
| | - Roland Langrock
- Department of Business Administration and Economics, Bielefeld University, Bielefeld, Germany
| | - Robert J Lennox
- NORCE Norwegian Research Centre, Laboratory for Freshwater Ecology and Inland Fisheries, Bergen, Norway
| | - Emmanuel Lourie
- Movement Ecology Lab, A. Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel.,Minerva Center for Movement Ecology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joah R Madden
- Centre for Research in Animal Behaviour, Psychology, University of Exeter, Exeter, UK
| | - Yotam Orchan
- Movement Ecology Lab, A. Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel.,Minerva Center for Movement Ecology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ine S Pauwels
- Research Institute for Nature and Forest (INBO), Brussels, Belgium
| | - Milan Říha
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czech Republic
| | - Manuel Roeleke
- Plant Ecology and Nature Conservation, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ulrike E Schlägel
- Plant Ecology and Nature Conservation, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - David Shohami
- Movement Ecology Lab, A. Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel.,Minerva Center for Movement Ecology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Johannes Signer
- Wildlife Sciences, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Göttingen, Germany
| | - Sivan Toledo
- Minerva Center for Movement Ecology, The Hebrew University of Jerusalem, Jerusalem, Israel.,Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Ohad Vilk
- Movement Ecology Lab, A. Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel.,Minerva Center for Movement Ecology, The Hebrew University of Jerusalem, Jerusalem, Israel.,Racah Institute of Physics, Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Samuel Westrelin
- INRAE, Aix Marseille Univ, Pôle R&D ECLA, RECOVER, Aix-en-Provence, France
| | - Mark A Whiteside
- Centre for Research in Animal Behaviour, Psychology, University of Exeter, Exeter, UK.,School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, UK
| | - Ivan Jarić
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czech Republic.,University of South Bohemia, Faculty of Science, Department of Ecosystem Biology, České Budějovice, Czech Republic
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