geo.phylo.ses {phyloraster} | R Documentation |
Calculates the standardized effect size for phylogenetic community metrics. See Details for more information.
geo.phylo.ses(
x,
tree,
inv.R,
edge.path,
branch.length,
n.descen,
spat_alg = "bootspat_str",
spat_alg_args = list(rprob = NULL, rich = NULL, fr_prob = NULL),
random = c("tip", "spat")[2],
aleats = 10,
cores = 1,
filename = "",
...
)
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 |
edge.path |
matrix representing the paths through the tree from root
to each tip. See |
branch.length |
numeric. A Named numeric vector of branch length for
each species. See |
n.descen |
numeric. A Named numeric vector of number of descendants for
each branch. See |
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: |
spat_alg_args |
List of arguments passed to the randomization method
chosen in 'spat_alg'. See |
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. |
cores |
positive integer. If |
filename |
character. Output filename |
... |
additional arguments passed for terra::app |
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.
SpatRaster
Neander Marcel Heming
Williams, P.H., Humphries, C.J., Forey, P.L., Humphries, C.J., 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., Monro, A. (2001). Endemism in the Australian flora. Journal of Biogeography, 28, 183–198.
phylo.pres
,
inv.range
,
geo.phylo
,
rast.ed.ses
,
rast.pd.ses
,
rast.we.ses
,
rast.pe.ses
,
bootspat_str
,
bootspat_naive
,
bootspat_ff
,
SESraster
library(terra)
library(phyloraster)
require("SESraster")
x <- terra::rast(system.file("extdata", "rast.presab.tif",
package="phyloraster"))
tree <- ape::read.tree(system.file("extdata", "tree.nex",
package="phyloraster"))
tses <- geo.phylo.ses(x = x,
tree = tree,
# FUN_args = list(range.BL=area.branch$range.BL,
# inv.R=area.branch$inv.R,
# branch.length=data$branch.length,
# n.descen = data$n.descendants),
spat_alg = "bootspat_str",
spat_alg_args = list(rprob = NULL,
rich = NULL,
fr_prob = NULL),
aleats = 2)
terra::plot(tses)