dot-rast.pe.B: Calculate phylogenetic endemism for a raster

In phyloraster: Evolutionary Diversity Metrics for Raster Data

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:

• pe: Phylogenetic endemism (Rosauer et al., 2009)

• pe.alt: Alternate Phylogenetic endemism (Mishler et al., 2014)

• rpe: Relative Phylogenetic endemism (Mishler et al., 2014)

• all: Calculate all available metrics Alternate phylogenetic endemism (PE.alt, Mishler et al., 2014) is calculated using an alternate phylogeny with non-zero branch lengths converted to a constant value (here we use 1) and rescaled so the sum of all branch lengths is 1. Relative phylogenetic endemism (RPE, Mishler et al., 2014) is the ratio of phylogenetic endemism (PE, Rosauer et al., 2009) measured on the original tree versus PE measured on a alternate tree (PE.alt).

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.

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