.rast.pe.B {phyloraster}R Documentation

Calculate phylogenetic endemism for a raster

Description

Calculate phylogenetic endemism using rasters as input and output.

Usage

.rast.pe.B(
  x,
  inv.R,
  branch.length,
  branch.length.alt,
  metric = c("pe", "pe.alt", "rpe", "all")[1],
  filename = "",
  overwrite = TRUE,
  ...
)

Arguments

x

SpatRaster. A SpatRaster containing presence-absence data (0 or 1) for a set of species. The layers (species) will be sorted according to the tree order. See the phylo.pres function.

inv.R

SpatRaster. Inverse of range size. See inv.range

branch.length

numeric. A Named numeric vector of branch length for each species. See phylo.pres

branch.length.alt

numeric. Branch length calculated by using an alternative phylogeny with non-zero branch lengths converted to a constant value (1) and rescaled so the sum of all branch lengths is 1.

metric

character. Names of the biodiversity metrics to calculate. Available options are: "pe", "pe.alt", "rpe", or "all". See details.

filename

character. Output filename

overwrite

logical. If TRUE, filename is overwritten

...

additional arguments passed for terra::app

Details

Metrics available are:

Value

SpatRaster

Author(s)

Gabriela Alves-Ferreira and Neander Heming

References

Mishler, B. D., Knerr, N., González-Orozco, C. E., Thornhill, A. H., Laffan, S. W. and Miller, J. T. 2014. Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian Acacia. – Nat. Commun. 5: 4473.

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


[Package phyloraster version 2.2.0 Index]