Run a niche similarity test (see Warren et al 2008) based on two species occurrence density grids.
ecospat.niche.similarity.test (z1, z2, rep, intersection = NA,
rand.type = 1, ncores= 1, overlap.alternative = "higher",
expansion.alternative = "lower", stability.alternative = "higher",
unfilling.alternative = "lower")a list with $obs = observed overlap and dynamic indices, $sim = simulated overlap and dynamic indices, $p.D = p-value of the test on D, $p.I = p-value of the test on I, $p.expansion = p-value for the test on expansion, $p.stability = p-value for the test on stability, $p.unfilling = p-value for the test on unfilling.
Species 1 occurrence density grid created by ecospat.grid.clim.
Species 2 occurrence density grid created by ecospat.grid.clim.
Number of replications to perform.
Quantile of the environmental density used to remove marginal climates. See Details.
Type of randomization on the density grids (1 or 2).
Number of cores used for parallelisation.
Alternative hypothesis of the test. See Details.
Alternative hypothesis of the expansion test. See Details.
Alternative hypothesis of the stability test. See Details.
Alternative hypothesis of the unfilling test. See Details.
Olivier Broennimann olivier.broennimann@unil.ch with contributions of Blaise Petitpierre bpetitpierre@gmail.com
Compares the observed niche overlap between z1 and z2 to overlaps between z1 and random niches (z2.sim) as available in the range of z2 (z2$Z). z2.sim has the same pattern as z2 but the center is randomly translatated in the availabe z2$Z space and weighted by z2$Z densities.
intersection allows setting if the niche dynamic indices (expansion, stability and unfilling) are measured across the full extent pooling the two study areas or not. If intersection = NA, the analysis is performed on the whole environmental extent (native and invaded). If instersection = 0, the analysis is performed at the intersection between native and invaded range. If instersection = 0.05, the analysis is performed at the intersection of the 5th quantile of both native and invaded environmental densities. Etc...
If rand.type = 1, both z1 and z2 are randomly shifted, if rand.type = 2, only z2 is randomly shifted.
overlap.alternative specifies if you want to test for niche conservatism (overlap.alternative = "higher", i.e. the niche overlap is more equivalent/similar than random) or for niche divergence (overlap.alternative = "lower", i.e. the niche overlap is less equivalent/similar than random). You can also specifiy if you want to test if you have more, less or different observed niche dynamics than random niches(with expansion.alternative, stabilty.alternative and unfilling.alternative). If you want to test for niche conservatism, we recommande to set these niche dynamic hypotheses to "lower", "higher" and "lower" respectively for expansion, stability and unfilling.
If you encounter a problem during your analyses, please first read the FAQ section of "Niche overlap" in http://www.unil.ch/ecospat/home/menuguid/ecospat-resources/tools.html
The arguments ncores allows choosing the number of cores used to parallelize the computation. The default value is 1. On multicore computers, the optimal would be ncores = detectCores() - 1.
Broennimann, O., M.C. Fitzpatrick, P.B. Pearman, B. Petitpierre, L. Pellissier, N.G. Yoccoz, W. Thuiller, M.J. Fortin, C. Randin, N.E. Zimmermann, C.H. Graham and A. Guisan. 2012. Measuring ecological niche overlap from occurrence and spatial environmental data. Global Ecology and Biogeography, 21, 481-497.
Warren, D.L., R.E. Glor and M. Turelli. 2008. Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution, 62, 2868-2883.
ecospat.grid.clim.dyn, ecospat.niche.equivalency.test