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speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution

Alexander Zizka, Alexandre Antonelli
doi: https://doi.org/10.1101/032755
Alexander Zizka
1University of Gothenburg, Department of Biological and Environmental Sciences, Carl Skottsbergs gata 22B, P.O. Box 461, SE 405 30, Göteborg, Sweden
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  • For correspondence: alexander.zizka@bioenv.gu.se
Alexandre Antonelli
1University of Gothenburg, Department of Biological and Environmental Sciences, Carl Skottsbergs gata 22B, P.O. Box 461, SE 405 30, Göteborg, Sweden
2Gothenburg Botanical Garden, Department of Biological and Environmental Sciences, Carl Skottsbergs gata 22A, SE 41319, Göteborg, Sweden
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Abstract

1. Large-scale species occurrence data from geo-referenced observations and collected specimens are crucial for analyses in ecology, evolution and biogeography. Despite the rapidly growing availability of such data, their use in evolutionary analyses is often hampered by tedious manual classification of point occurrences into operational areas, leading to a lack of reproducibility and concerns regarding data quality.

2. Here we present speciesgeocodeR, a user-friendly R-package for data cleaning, data exploration and data visualization of species point occurrences using discrete operational areas, and linking them to analyses invoking phylogenetic trees.

3. The three core functions of the package are 1) automated and reproducible data cleaning, 2) rapid and reproducible classification of point occurrences into discrete operational areas in an adequate format for subsequent biogeographic analyses, and 3) a comprehensive summary and visualization of species distributions to explore large datasets and ensure data quality. In addition, speciesgeocodeR facilitates the access and analysis of publicly available species occurrence data, widely used operational areas and elevation ranges. Other functionalities include the implementation of minimum occurrence thresholds and the visualization of coexistence patterns and range sizes. SpeciesgeocodeR accompanies a richly illustrated and easy-to-follow tutorial and help functions.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted November 24, 2015.
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speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution
Alexander Zizka, Alexandre Antonelli
bioRxiv 032755; doi: https://doi.org/10.1101/032755
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speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution
Alexander Zizka, Alexandre Antonelli
bioRxiv 032755; doi: https://doi.org/10.1101/032755

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