niche.overlap: Quantification of Niche Overlap

In phyloclim: Integrating Phylogenetics and Climatic Niche Modeling

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.

Author(s)

Christoph Heibl

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

# 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)	

Example output

Loading required package: ape
Loading required package: raster
Loading required package: sp

Attaching package: 'raster'

The following objects are masked from 'package:ape':

    rotate, zoom

            adenophylla  arenaria enneaphylla laciniata  loricata
adenophylla          NA 0.7660363   0.5847042 0.6914690 0.8731398
arenaria      0.9580793        NA   0.7416155 0.6200435 0.7760373
enneaphylla   0.8703467 0.9460834          NA 0.4686174 0.5828796
laciniata     0.9306613 0.9010384   0.8015475        NA 0.7185989
loricata      0.9752528 0.9392395   0.8599603 0.9494476        NA
attr(,"class")
[1] "niolap"

phyloclim documentation built on May 2, 2019, 8:07 a.m.