spThin: an R package for spatial thinning of species occurrence records for use in ecological niche models

Abstract

Spatial thinning of species occurrence records can help address problems associated with spatial sampling biases. Ideally, thinning removes the fewest records necessary to substantially reduce the effects of sampling bias, while simultaneously retaining the greatest amount of useful information. Spatial thinning can be done manually; however, this is prohibitively time consuming for large datasets. Using a randomization approach, the ‘thin’ function in the spThin R package returns a dataset with the maximum number of records for a given thinning distance, when run for sufficient iterations. We here provide a worked example for the Caribbean spiny pocket mouse, where the results obtained match those of manual thinning.

Are fundamental niches larger than the realized? Testing a 50-year-old prediction by Hutchinson

“…We kept only 14,051 non-redundant (at 10 km) [39, 40] georeferenced records from this database (S1 File, Fig A2). Obvious georeferencing problems were detected by checking the presence of GBIF records within the recorded borders of countries (Environmental Systems Research Institute; http://www.esri.com/) and excluding them from the database.…”

Contextualized niche shifts upon independent invasions by the dung beetle Onthophagus taurus

“…We assembled 1272 records for O. taurus. We applied a 10 km buffer around each one to minimize geographical sampling biases, using the spThin R package (Aiello-Lammens et al 2015), which resulted in 1058 geographically unique occurrences considering the thinning distance applied in our analyses. Then, we considered a minimum convex polygon around the occurrences and the estimated annual dispersion rates for O. taurus (130-200 km; Hanski and Cambefort 1991) to define five different geographical backgrounds, as the region defined by a buffer of one degree width around the occurrences in each separate region.…”

Fifty-seventh Supplement to the American Ornithologists' UnionCheck-list of North American Birds

“…Occurrence records were spatially thinned to a nearest-neighbor distance of 3 km using spThin (Aiello-Lammens et al 2015). We selected a 3 km thinning distance based on the home range of the Shaft-tailed Whydah (V. regia), a congener of the Pin-tailed Whydah (Barnard 1990).…”