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mangal - making ecological network analysis simple

View ORCID ProfileTimothée Poisot, View ORCID ProfileBenjamin Baiser, View ORCID ProfileJennifer A. Dunne, View ORCID ProfileSonia Kéfi, View ORCID ProfileFrançois Massol, View ORCID ProfileNicolas Mouquet, View ORCID ProfileTamara N. Romanuk, View ORCID ProfileDaniel B. Stouffer, View ORCID ProfileSpencer A. Wood, View ORCID ProfileDominique Gravel
doi: https://doi.org/10.1101/002634
Timothée Poisot
1University of Canterbury, School of Biological Sciences, Christchurch, New Zealand
2Québec Centre for Biodiversity Sciences, Montréal (QC), Canada
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Benjamin Baiser
3Department of Wildlife Ecology and Conservation, University of Florida, Gainesville
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Jennifer A. Dunne
4Sante Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501
5Pacific Ecoinformatics and Computational Ecology Lab, 1604 McGee Ave., Berkeley, CA 94703
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Sonia Kéfi
6Institut des Sciences de l’Évolution, UMR CRNS 5554, Université Montpellier 2, 3405 Montpellier, France
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François Massol
7Laboratoire Génétique et Evolution des Populations Végétales, CNRS UMR 8198, Université Lille 1, Bâtiment SN2, F-59655 Villeneuve d’Ascq cedex, France
8UMR 5175 CEFE – Centre d’Ecologie Fonctionnelle et Evolutive (CNRS), 1919 Route de Mende, F-34293 Montpellier cedex 05, France
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Nicolas Mouquet
6Institut des Sciences de l’Évolution, UMR CRNS 5554, Université Montpellier 2, 3405 Montpellier, France
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Tamara N. Romanuk
9Department of Biology, Dalhousie University
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Daniel B. Stouffer
1University of Canterbury, School of Biological Sciences, Christchurch, New Zealand
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Spencer A. Wood
10Natural Capital Project, School of Environmental and Forest Sciences, University of Washington, Seattle, WA 19 98195, USA
11Department of Biological Sciences, Idaho State University Pocatello, ID 83209, USA
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Dominique Gravel
12Université du Québec à Rimouski, Département de Biologie, 300 Allées des Ursulines, Rimouski (QC) G5L 3A1, Canada
2Québec Centre for Biodiversity Sciences, Montréal (QC), Canada
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Abstract

The study of ecological networks is severely limited by (i) the difficulty to access data, (ii) the lack of a standardized way to link meta-data with interactions, and (iii) the disparity of formats in which ecological networks themselves are represented. To overcome these limitations, we conceived a data specification for ecological networks. We implemented a database respecting this standard, and released a R package (rmangal) allowing users to programmatically access, curate, and deposit data on ecological interactions. In this article, we show how these tools, in conjunctions with other frameworks for the programmatic manipulation of open ecological data, streamlines the analysis process, and improves eplicability and reproducibility of ecological networks studies.

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Posted February 24, 2015.
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mangal - making ecological network analysis simple
Timothée Poisot, Benjamin Baiser, Jennifer A. Dunne, Sonia Kéfi, François Massol, Nicolas Mouquet, Tamara N. Romanuk, Daniel B. Stouffer, Spencer A. Wood, Dominique Gravel
bioRxiv 002634; doi: https://doi.org/10.1101/002634
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mangal - making ecological network analysis simple
Timothée Poisot, Benjamin Baiser, Jennifer A. Dunne, Sonia Kéfi, François Massol, Nicolas Mouquet, Tamara N. Romanuk, Daniel B. Stouffer, Spencer A. Wood, Dominique Gravel
bioRxiv 002634; doi: https://doi.org/10.1101/002634

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