Phylogenetic diversity standardized for species richness

Calculates the standardized effect size for phylogenetic diversity. See Details for more information.

Usage

rast.pd.ses(
  x,
  tree,
  edge.path,
  branch.length,
  spat_alg = "bootspat_str",
  spat_alg_args = list(rprob = NULL, rich = NULL, fr_prob = NULL),
  random = c("tip", "spat")[2],
  aleats = 10,
  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.

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

spat_alg

A function with the algorithm implementing the desired randomization method. It must work with SpatRaster objects. See examples. Example of functions that work are: bootspat_naive, bootspat_str, bootspat_ff.

spat_alg_args

List of arguments passed to the randomization method chosen in 'spat_alg'. See bootspat_naive, bootspat_str, bootspat_ff

random

character. A character indicating the type of randomization. The currently available randomization methods are "tip", "site", "species" or "both" (site and species).

aleats

positive integer. A positive integer indicating how many times the calculation should be repeated.

filename

character. Output filename

...

additional arguments passed for terra::app

Value

SpatRaster

SpatRaster. The function returns the observed phylogenetic diversity, the mean of the simulations calculated over n times, the standard deviation of the simulations, and the standardized effect size (SES) for the phylogenetic diversity.

Details

The spatial randomization (spat) keeps the richness exact and samples species presences proportionally to their observed frequency (i.e. number of occupied pixels). The randomization will not assign values to cells with nodata. The phylogenetic randomization shuffles taxa names across all taxa included in phylogeny.

The spatial randomization (spat) keeps the richness exact and samples species presences proportionally to their observed frequency (i.e. number of occupied pixels). The randomization will not assign values to cells with nodata. The phylogenetic randomization shuffles taxa names across all taxa included in phylogeny.

References

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

See also

phylo.pres, inv.range, geo.phylo.ses, rast.ed.ses, rast.pd.ses, rast.we.ses, rast.pe.ses, bootspat_str, bootspat_naive, bootspat_ff, SESraster

Author

Gabriela Alves-Ferreira and Neander Heming

Examples

# \donttest{
library(terra)
library(phyloraster)
library(SESraster)
x <- rast(system.file("extdata", "rast.presab.tif",
package="phyloraster"))
tree <- ape::read.tree(system.file("extdata", "tree.nex",
package="phyloraster"))
data <- phylo.pres(x[[1:10]], 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
t <- rast.pd.ses(data$x, edge.path = data$edge.path,
                branch.length = data$branch.length, aleats = 3,
                random = "spat")
plot(t)

# }