phyloclim (version 0.9.5)

niche.overlap: Quantification of Niche Overlap

Description

This function quantifies the degree of niche overlap using the statistics D and I (as proposed by Warren et al., 2008) based on Schoeners D (Schoener, 1968) and Hellinger Distances (van der Vaart, 1998). Niche overlap can be calculated either from the probability surfaces of entire ecological niche models (Warren et al., 2008) or from single dimensions of the climatic niches (Evans et al., 2009).

Usage

niche.overlap(x)

Arguments

x

Might take one of the follwing forms: (1) a data frame containing predicted niche occupancy (PNO) profiles, e.g., as derived by pno; (2) a vector of filenames referencing to probability surfaces saved in ASCII-format with an ArcGIS-compatible header; (3) a list containing probability surfaces stored as objects of class SpatialGrid.

Value

A matrix of class "niolap". The upper triangle contains pairwise comparisons of niche overlap in terms of D, whereas the lower triangle contains values of I.

References

Evans, M. E. K., S. A. Smith, R. S. Flynn, and M. J. Donoghue. 2009. Climate, niche evolution, and diversification of the 'bird-cage evening primroses' (Oenothera, sections Anogra and Kleinia). Am. Nat. 173: 225-240.

Schoener, T.W. 1968. Anolis lizards in Bimini: resource partitioning in a complex fauna. Ecology 49: 704-726.

Van der Vaart, A.W. 1998. Asymptotic statistics. Cambridge University Press, U.K.

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

See Also

pno, niche.equivalency.test, bg.similarity.test, age.range.correlation

Examples

# NOT RUN {
# load PNOs for Oxalis sect. Palmatifoliae
data(PNO)

# niche overlap on a annual precipitation gradient:
no <- niche.overlap(PNO$AnnualPrecipitation)

# upper triangle: based on Schoeners D
# lower triangle: based on Hellinger distances
print(no)	
# }