Title
Navigating through the r packages for movement
Date Issued
01 January 2020
Access level
open access
Resource Type
review
Author(s)
Boone M.E.
Clay T.A.
Patrick S.C.
Clusella-Trullas S.
Basille M.
University of Florida
Publisher(s)
Blackwell Publishing Ltd
Abstract
The advent of miniaturized biologging devices has provided ecologists with unprecedented opportunities to record animal movement across scales, and led to the collection of ever-increasing quantities of tracking data. In parallel, sophisticated tools have been developed to process, visualize and analyse tracking data; however, many of these tools have proliferated in isolation, making it challenging for users to select the most appropriate method for the question in hand. Indeed, within the r software alone, we listed 58 packages created to deal with tracking data or ‘tracking packages’. Here, we reviewed and described each tracking package based on a workflow centred around tracking data (i.e. spatio-temporal locations (x, y, t)), broken down into three stages: pre-processing, post-processing and analysis, the latter consisting of data visualization, track description, path reconstruction, behavioural pattern identification, space use characterization, trajectory simulation and others. Supporting documentation is key to render a package accessible for users. Based on a user survey, we reviewed the quality of packages' documentation and identified 11 packages with good or excellent documentation. Links between packages were assessed through a network graph analysis. Although a large group of packages showed some degree of connectivity (either depending on functions or suggesting the use of another tracking package), one third of the packages worked in isolation, reflecting a fragmentation in the r movement-ecology programming community. Finally, we provide recommendations for users when choosing packages, and for developers to maximize the usefulness of their contribution and strengthen the links within the programming community.
Start page
248
End page
267
Volume
89
Issue
1
Language
English
OCDE Knowledge area
Zoología, Ornitología, Entomología, ciencias biológicas del comportamiento
Scopus EID
2-s2.0-85074648216
PubMed ID
Source
Journal of Animal Ecology
ISSN of the container
00218790
Sponsor(s)
The authors (RJ, TAC, SCP, SCT and MB) were funded by a Human Frontier Science Program Young Investigator Grant (SeabirdSound – /2017). We are grateful to Guillaume Bastille‐Rousseau, Clément Calenge, Christen H. Fleming, Devin Johnson, Bart Kranstauber, Simeon Lisovski, Brett McClintock, Benjamin Merkel, Théo Michelot, Anders Nielsen, Eldar Rakhimberdiev, Henry Scharf, Jakob Schwalb‐Willmann, Takashiro Shimada, Derek Spitz and Michael Sumner for enlightening discussions and additional information about their packages. Special thanks to Simon Benhamou for discussions about accelerometers, magnetometers and gyroscopes, and reviewing the corresponding sections of the manuscript. During review, constructive comments and suggestions of Johannes Signer and Luca Borger (associated editor) have significantly contributed to the quality of this work. We also thank the anonymous survey participants and everyone who suggested packages for this review.
Sources of information: Directorio de Producción Científica Scopus