- Computes niche overlap or similarity
, niche modelling
r.niche.similarity [-idc] maps=name[,name,...] [output=name] [--overwrite] [--help] [--verbose] [--quiet] [--ui]
- I niche similarity
- D niche similarity
- Allow output files to overwrite existing files
- Print usage summary
- Verbose module output
- Quiet module output
- Force launching GUI dialog
- maps=name[,name,...] [required]
- Input maps
- Name of output text file
A module to compute 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 identical distribution.
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 were checked against the
niche.overlap function in the phyloclim package for R, which also uses
the corrected formulation of I as 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
- Robert J. Hijmans, Steven Phillips, John
Leathwick and Jane Elith (2013). dismo: Species distribution
modeling. R package version 0.8-5.
- Christoph Heibl and Clement Calenge (2012). phyloclim: Integrating
Phylogenetics and Climatic Niche Modeling. R package version 0.9-0.
Paulo van Breugel, paulo at ecodiv.org
Available at: r.niche.similarity source code (history)
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