Animal movement tools (amt): R package for managing tracking data and conducting habitat selection analyses.

Johannes Signer, John Fieberg, Tal Avgar
Author Information
  1. Johannes Signer: Wildlife Sciences University of Goettingen Göttingen Germany. ORCID
  2. John Fieberg: Department of Fisheries, Wildlife and Conservation Biology University of Minnesota St. Paul Minnesota. ORCID
  3. Tal Avgar: Department of Integrative Biology University of Guelph Guelph Ontario Canada. ORCID

Abstract

Advances in tracking technology have led to an exponential increase in animal location data, greatly enhancing our ability to address interesting questions in movement ecology, but also presenting new challenges related to data management and analysis. Step-selection functions (SSFs) are commonly used to link environmental covariates to animal location data collected at fine temporal resolution. SSFs are estimated by comparing observed steps connecting successive animal locations to random steps, using a likelihood equivalent of a Cox proportional hazards model. By using common statistical distributions to model step length and turn angle distributions, and including habitat- and movement-related covariates (functions of distances between points, angular deviations), it is possible to make inference regarding habitat selection and movement processes or to control one process while investigating the other. The fitted model can also be used to estimate utilization distributions and mechanistic home ranges. Here, we present the R package amt (animal movement tools) that allows users to fit SSFs to data and to simulate space use of animals from fitted models. The amt package also provides tools for managing telemetry data. Using fisher () data as a case study, we illustrate a four-step approach to the analysis of animal movement data, consisting of data management, exploratory data analysis, fitting of models, and simulating from fitted models.

Keywords

References

  1. Ecology. 2016 May;97(5):1113-22 [PMID: 27349089]
  2. Ecol Evol. 2019 Feb 05;9(2):880-890 [PMID: 30766677]
  3. Ecol Lett. 2009 May;12(5):395-408 [PMID: 19379134]
  4. Trends Ecol Evol. 1999 Jul;14(7):268-272 [PMID: 10370262]
  5. Philos Trans R Soc Lond B Biol Sci. 2010 Jul 27;365(1550):2233-44 [PMID: 20566500]
  6. Mov Ecol. 2018 Jan 05;6:1 [PMID: 29318021]
  7. Mov Ecol. 2014 Feb 07;2(1):4 [PMID: 25520815]
  8. Ecology. 2009 Dec;90(12):3554-65 [PMID: 20120822]
  9. Philos Trans R Soc Lond B Biol Sci. 2010 Jul 27;365(1550):2245-54 [PMID: 20566501]
  10. J Math Biol. 2008 Jul;57(1):139-59 [PMID: 18064464]
  11. Biometrics. 2008 Sep;64(3):968-976 [PMID: 18047525]
  12. Philos Trans R Soc Lond B Biol Sci. 2010 Jul 27;365(1550):2157-62 [PMID: 20566493]
  13. Ecology. 2015 Oct;96(10):2590-7 [PMID: 26649380]
  14. Ecology. 2013 Jul;94(7):1456-63 [PMID: 23951705]
  15. Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19052-9 [PMID: 19060196]
  16. J Anim Ecol. 2013 Nov;82(6):1155-64 [PMID: 23800202]
  17. Ecol Evol. 2017 Jun 14;7(14):5322-5330 [PMID: 28770070]
  18. Science. 2015 Jun 12;348(6240):aaa2478 [PMID: 26068858]
  19. PLoS One. 2015 Apr 21;10(4):e0122947 [PMID: 25898019]

Word Cloud

Created with Highcharts 10.0.0datamovementanimalalsoanalysisSSFsmodeldistributionshabitatselectionfittedpackageamttoolsmodelstrackinglocationecologymanagementfunctionsusedcovariatesstepsusinghomeRmanagingtelemetryfunctionAdvancestechnologyledexponentialincreasegreatlyenhancingabilityaddressinterestingquestionspresentingnewchallengesrelatedStep-selectioncommonlylinkenvironmentalcollectedfinetemporalresolutionestimatedcomparingobservedconnectingsuccessivelocationsrandomlikelihoodequivalentCoxproportionalhazardscommonstatisticalsteplengthturnangleincludinghabitat-movement-relateddistancespointsangulardeviationspossiblemakeinferenceregardingprocessescontroloneprocessinvestigatingcanestimateutilizationmechanisticrangespresentallowsusersfitsimulatespaceuseanimalsprovidesUsingfishercasestudyillustratefour-stepapproachconsistingexploratoryfittingsimulatingAnimal:conductinganalysesrangeresource‐selectionstep‐selection

Similar Articles

Cited By