r.niche.similarity computes two metrics to quantify niche
similarity or overlap between all pairs of input raster layers.
One is the niche equivalency or similarity for two species following
Warren et al. (2008) based on Schoeners D (Schoener, 1968). This metric
ranges from 0 to 1, representing respectively no overlap and an
The other is the niche overlap metric which indicates the niche
overlap from predictions of species distributions with the I similarity
statistic of Warren et al. (2009), which is based on Hellinger
Distances (van der Vaart, 1998). The statistic ranges from 0 (no
overlap) to 1 (the distributions are identical).
By default the results are written to screen, but they can also be
written to a text file with two columns for the names of each pair of
rasters, a third column for the type of statistic (D or I) and a fourth
column for the D or I statistic.
This implementation is especially suitable if you are working with very
large data sets. Results are checked against the niche.overlap function
in the phyloclim package for R.
I would like to thank Christoph Heibl, author of the phyloclim package,
for pointing me out the corrected formulation of I, published in an
erratum of the article by Warren et al (2008).
- Warren, D. L., Glor, R. E., & Turelli, M. 2008. Environmental Niche Equivalency Versus Conservatism: Quantitative Approaches to Niche Evolution. Evolution 62(11): 2868–2883
- Warren, D. L., R. E. Glor, and M. Turelli. 2010. ENMTools: a toolbox for comparative studies of environmental niche models. Ecography 33:607–611.
- Robert J. Hijmans, Steven Phillips, John Leathwick and Jane Elith (2013). dismo: Species distribution
modeling. R package version 0.8-5. http://CRAN.R-project.org/package=dismo
- Christoph Heibl and Clement Calenge (2012). phyloclim: Integrating Phylogenetics and Climatic Niche
Modeling. R package version 0.9-0. http://CRAN.R-project.org/package=phyloclim
Contact: Paulo van Breugel
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