Calculate phylogenetic community metrics for raster data

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

Usage

geo.phylo(
  x,
  tree,
  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) will be sorted according to the tree order. See the phylo.pres function.
tree: phylo. A dated tree.
inv.R: SpatRaster. Inverse of range size. See inv.range
edge.path: matrix representing the paths through the tree from root to each tip. See phylo.pres
branch.length: numeric. A Named numeric vector of branch length for each species. See phylo.pres
n.descen: numeric. A Named numeric vector of number of descendants for each branch. See phylo.pres
filename: character. Output filename
...: additional arguments passed for terra::app

Value

SpatRaster with one layer for each metric

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)

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.

Author

Neander Marcel Heming

Examples

# \donttest{
library(terra)
#> terra 1.7.83
library(phyloraster)
x <- terra::rast(system.file("extdata", "rast.presab.tif",
package="phyloraster"))[[1:10]]
tree <- ape::read.tree(system.file("extdata", "tree.nex",
package="phyloraster"))
data <- phylo.pres(x, tree)
#> Warning: Some species in the phylogeny 'tree' are missing from the
#>                   SpatRaster 'x' and were dropped: Litoria_nigrofrenata, Litoria_bicolor, Litoria_fallax, Litoria_genimaculata, Litoria_andiirrmalin, Litoria_wilcoxii, Litoria_jungguy, Litoria_caerulea, Litoria_gracilenta, Litoria_chloris, Litoria_xanthomera, Cyclorana_brevipes, Cyclorana_novaehollandiae, Cyclorana_manya, Cyclorana_cultripes, Litoria_alboguttata, Cyclorana_longipes, Nyctimystes_dayi, Litoria_nannotis, Litoria_lorica, Litoria_rheocola, Litoria_nyakalensis, Litoria_infrafrenata
inv.R <- inv.range(data$x)
t <- geo.phylo(data$x, inv.R = inv.R, edge.path = data$edge.path,
branch.length = data$branch.length, n.descen = data$n.descendants)
terra::plot(t)

# }