r.niche.similarity - GRASS GIS manual

NAME

r.niche.similarity - Computes niche overlap or similarity

KEYWORDS

SYNOPSIS

r.niche.similarity

r.niche.similarity --help

r.niche.similarity [-idc] maps=name[,name,...] [output=name] [--overwrite] [--help] [--verbose] [--quiet] [--ui]

Flags:

-i: I niche similarity
-d: D niche similarity
-c: Correlation
--overwrite: Allow output files to overwrite existing files
--help: Print usage summary
--verbose: Verbose module output
--quiet: Quiet module output
--ui: Force launching GUI dialog

Parameters:

maps=name[,name,...] [required]: Input maps
output=name: Name of output text file

DESCRIPTION
Notes
REFERENCES
AUTHOR

DESCRIPTION

r.niche.similarity

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.

Notes

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).

REFERENCES

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

AUTHOR

Paulo van Breugel, paulo at ecodiv.org

SOURCE CODE

Available at: r.niche.similarity source code (history)