SpeciesGeoCoder: fast categorization of species occurrences for analyses of biodiversity, biogeography, ecology and evolution

Understanding the patterns and processes underlying the uneven distribution of biodiversity across space constitutes a major scientific challenge in systematic biology and biogeography, which largely relies on effectively mapping and making sense of rapidly increasing species occurrence data. There is thus an urgent need for making the process of coding species into spatial units faster, automated, transparent, and reproducible. Here we present SpeciesGeoCoder, an open-source software package written in Python and R, that allows for easy coding of species into user-defined operational units. These units may be of any size and be purely spatial (i.e., polygons) such as countries and states, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include elevation ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. In addition, SpeciesGeoCode...理解生物多样性在空间分布上的不均格局及其内在过程，是系统生物学（systematic biology）与生物地理学（biogeography）领域的一项重大科学挑战，该领域的研究高度依赖对快速增长的物种出现数据（species occurrence data）进行有效映射与解析。因此，亟需将物种编码至空间单元的流程实现提速、自动化、透明化及可重复。本文介绍了SpeciesGeoCoder这一基于Python与R语言编写的开源软件包，其可便捷地将物种编码至用户自定义的空间操作单元（operational units）。此类单元尺寸不限，既可为纯空间单元（即多边形区域），例如国家、行政区、保护地、生物群区（biome）、岛屿、生物多样性热点地区（biodiversity hotspot）以及特有分布区（area of endemism），也可包含海拔梯度范围。这种灵活性支持将物种归类至复杂分类类别中，例如在地形与生态异质性较强的景观中所涉及的类别。此外，SpeciesGeoCode……