hypothesis.testing {phyloclim}R Documentation

Niche equivalency and background similarity test

Description

Hypothesis testing as proposed by Warren et al. (2008) based on the generation of pseudoreplicate datasets. The niche equivaleny (or identity) test asks whether the ecological niche models (ENMs) of two are more different than expected if they are drawn from the same underlying distribution. The background similarity test asks whether ENMs drawn from populations with partially or entirely non-overlapping distributions are any more different from one another than expected by random chance.

Usage

niche.equivalency.test(spec, n, maxent)

bg.similarity.test(spec, n, maxent)

Arguments

spec A vector of mode character and length = 2 that corresponds to two species names in the sample file (see details).
n An integer given the number of permutations of the original data.
maxent A list containing the location of the MAXENT application and its input files (see details).

Details

An installation of MAXENT (Phillips et al., 2006; http://www.cs.princeton.edu/~schapire/maxent/) is required in order to run niche.equivalency.test and bg.similarity.test. The maxent argument of both functions is a list of four elements:

app
The path to the MAXENT application.
samples
The path to a SWD-formatted file with sample points.
background
The path to a SWD-formatted file with background points.
projections
The path to a folder containing environmental GIS layers to be used for projection of the MAXENT models.

For an explanation of SWD-formatted (=Samples-With-Data) files and model projection see the MAXENT tutorial.

Value

A list containing five elements:

test Name of the test.
spec Names of the two species compared.
D Measure of niche overlap D based on Schoeners D together with p-values.
I Measure of niche overlap I based on Hellinger distances together with p-values.
null.distribution Null distributions of D and I derived from randomization.

Note

These functions have been developed and tested with MAXENT version 3.3.1.

Author(s)

Christoph Heibl (heibl@lmu.de)

References

Phillips, S.J, M. Dudik, & R.E. Schapire. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modeling 190: 231-259.

Warren, D., R.E. Glor, & M. Turelli. 2008. Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution. 62: 2868-2883.

See Also

niche.overlap


[Package phyloclim version 0.0.1 Index]