calc.niche.overlap: Calculate Similarity of ENMs in Geographic Space

In jamiemkass/ENMeval: Automated Tuning and Evaluations of Ecological Niche Models

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(predictors, overlapStat, quiet = FALSE)

Arguments

predictors	SpatRaster: at least 2 Maxent raster predictions
overlapStat	character: either "D" or "I", the statistic calculated by the nicheOverlap function of the dismo package (default: "D"), which we updated for terra as no correlate currently exists in the new predicts package
quiet	boolean: if TRUE, silence all function messages (but not errors)

Details

"D" refers to Schoeners D (Schoener 1968), while "I" refers to the I similarity statistic from Warren et al. (2008).

Value

A matrix with the lower triangle giving values of pairwise "niche overlap" in geographic space. Row and column names correspond to the results table output by ENMevaluate().

Author(s)

Based on dismo::nicheOverlap, which is based on SDMTools::Istat, updated for terra package Robert Muscarella <[e-mail]>

References

Hijmans, R. J., Phillips, S., Leathwick, J. & 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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.2307/1935534")}

Warren, D. L., Glor, R. E., Turelli, M. & Funk, D. (2008) Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution, 62: 2868-2883. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/j.1558-5646.2008.00482.x")}

See Also

'nicheOverlap' in the dismo package

jamiemkass/ENMeval documentation built on Jan. 19, 2025, 4:33 a.m.