RT Journal Article
SR Electronic
T1 speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 032755
DO 10.1101/032755
A1 Alexander Zizka
A1 Alexandre Antonelli
YR 2015
UL http://biorxiv.org/content/early/2015/11/24/032755.abstract
AB 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.