ENMeval: calc.niche.overlap – R documentation

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calc.niche.overlap

Calculate Similarity of ENMs in Geographic Space

Description

Compute pairwise "niche overlap" in geographic space for Maxent predictions. The value ranges from 0 (no overlap) to 1 (identical predictions). The function uses the nicheOverlap function of the dismo package (Hijmans et al. 2011).

Usage

calc.niche.overlap(predictive.maps, stat = "D", maxent.args)

Arguments

`predictive.maps`	A rasterStack of at least 2 Maxent predictive raster layers.
`stat`	The statistic calculated by the `nicheOverlap` function of the dismo package. Defaults to Schoener's D (Schoener 1968) but can also accept `"I"` to calculate the I similarity statistic from Warren et al. (2008).
`maxent.args`	A list of (1) feature classes, and (2) regularization multiplier values that describe model settings for each predictive map provided in `predictive.maps`. This is generated by the function `make.args(..., labels=TRUE)`.

Value

A matrix with the lower triangle giving values of pairwise "niche overlap" in geographic space. Row and column names are given by the make.args argument when run by the ENMevaluate function.

Author(s)

Based on dismo::nicheOverlap, which is based on SDMTools::Istat

Robert Muscarella <bob.muscarella@gmail.com>

References

Hijmans, R. J., Phillips, S., Leathwick, J. and Elith, J. (2011) dismo package for R. Available online at: https://cran.r-project.org/package=dismo.

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

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