subsppLabelR: a wrapper package in R to automatically label and filter subspecies occurrence data

Abstract

O_LIOccurrence data is the basis for many fundamental ecoevolutionary analyses, and many ways of filtering them to be robust enough for analysis have been developed. One issue that still remains is separating out the boundaries of taxa, especially taxa below the species level which often have vague definitions. C_LIO_LIsubsppLabelR is an R package that uses labeled data on taxa to automatically define boundaries between them, with various levels of uncertainty. I tested the features of the package on three species of bird that vary in the number and location of subspecies, as well as one sister-species pair with a known overlap in their distribution. I then used existing ecological niche modeling software to compare and contrast their niche space. C_LIO_LIsubsppLabelR performs well in scenarios where subspecies are well-sampled and cover large geographic areas, but rare or highly endemic subspecies are difficult to resolve without further input. C_LIO_LIThis package serves to automatically define geographic boundaries of taxa, identifying any sympatric overlaps, and provides an alternate way to clean occurrence data for ecological and evolutionary analyses. C_LI Data/Code for peer review statementCode and data are available with peer review. Raw Data and the package are available as .ZIP files as well as an R script.