dot-rast.geo.phylo: Calculate phylogenetic community metrics for raster data

In phyloraster: Evolutionary Diversity Metrics for Raster Data

Calculate phylogenetic community metrics for raster data

Description

Calculate species richness, phylogenetic diversity, evolutionary distinctiveness, phylogenetic endemism and weighted endemism using rasters as input

Usage

.rast.geo.phylo(
  x,
  inv.R,
  edge.path,
  branch.length,
  n.descen,
  filename = "",
  ...
)

Arguments

x	SpatRaster. A SpatRaster containing presence-absence data (0 or 1) for a set of species. The layers (species) must be sorted according to the tree order. See the phylo.pres function.
inv.R	SpatRaster. inverse of range size calculated from inv.range
edge.path	matrix. Matrix representing the paths through the tree from root to each tip. See phylo.pres
branch.length	numeric. A named numerical vector containing the branch length for each species.
n.descen	numeric. A Named numeric vector of number of descendants for each branch
filename	character. Output filename
...	additional arguments passed for terra::app

Details

Community metrics calculated:

• Phylogenetic diversity (Faith 1992)

• Species Richness

• Evolutionary distinctiveness by fair-proportion (Isaac et al. 2007)

• Phylogenetic endemism (Rosauer et al. 2009)

• Weighted endemism (Crisp et al. 2001, Williams et al. 1994)

Value

SpatRaster with one layer for each metric

Author(s)

Neander Marcel Heming

References

Rosauer, D. A. N., Laffan, S. W., Crisp, M. D., Donnellan, S. C. and Cook, L. G. (2009). Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history. Molecular ecology, 18(19), 4061-4072.

Faith, D. P. (1992). Conservation evaluation and phylogenetic diversity. Biological conservation, 61(1), 1-10.

Williams, P.H., Humphries, C.J., Forey, P.L., Humphries, C.J. and VaneWright, R.I. (1994). Biodiversity, taxonomic relatedness, and endemism in conservation. In: Systematics and Conservation Evaluation (eds Forey PL, Humphries C.J., Vane-Wright RI), p. 438. Oxford University Press, Oxford.

Crisp, M., Laffan, S., Linder, H. and Monro, A. (2001). Endemism in the Australian flora. Journal of Biogeography, 28, 183–198.

Isaac, N. J., Turvey, S. T., Collen, B., Waterman, C. and Baillie, J. E. (2007). Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS ONE 2, e296.

Laffan, S. W., Rosauer, D. F., Di Virgilio, G., Miller, J. T., González‐Orozco, C. E., Knerr, N., ... & Mishler, B. D. (2016). Range‐weighted metrics of species and phylogenetic turnover can better resolve biogeographic transition zones. Methods in Ecology and Evolution, 7(5), 580-588.

phyloraster documentation built on April 3, 2025, 8:45 p.m.