hypothesis.testing {phyloclim} | R Documentation |
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.
niche.equivalency.test(spec, n, maxent) bg.similarity.test(spec, n, maxent)
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). |
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:
For an explanation of SWD-formatted (=Samples-With-Data) files and model projection see the MAXENT tutorial.
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. |
These functions have been developed and tested with MAXENT version 3.3.1.
Christoph Heibl (heibl@lmu.de)
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.