canape.rast: Classify Phylogenetic Endemism using rasters

In phyloraster: Evolutionary Diversity Metrics for Raster Data

Classify Phylogenetic Endemism using rasters

Description

Use the results of rast.pe.ses() to identify centers of paleo-, neo-, super-, and mixed- endemism following the CANAPE scheme of Mishler et al., 2014.

Usage

canape.rast(
  pe.obs.p.upper,
  pe.alt.obs.p.upper,
  rpe.obs.p.upper,
  rpe.obs.p.lower,
  filename = NULL,
  overwrite = FALSE
)

Arguments

pe.obs.p.upper	SpatRaster. Upper p-value comparing the observed phylogenetic endemism and the randomized phylogenetic endemism values
pe.alt.obs.p.upper	SpatRaster. Upper p-value comparing the alternate phylogenetic endemism and the randomized alternate phylogenetic endemism
rpe.obs.p.upper	SpatRaster. Upper p-value comparing the relative phylogenetic endemism and the randomized relative phylogenetic endemism
rpe.obs.p.lower	SpatRaster. Lower p-value comparing the relative phylogenetic endemism and the randomized relative phylogenetic endemism
filename	character. Output filename
overwrite	logical. If TRUE, filename is overwritten

Value

SpatRaster

See Also

rast.pe.ses, SESraster

Examples

library(SESraster)
library(terra)
library(phyloraster)
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, tree)
ses <- rast.pe.ses(x = data$x, data$tree,
                aleats = 5, metric = "all")
# CANAPE
canape <- canape.rast(ses$p.upper.PE, ses$p.upper.PE.alt,
                   ses$p.upper.RPE, ses$p.lower.RPE)
unique(canape)
plot(canape)

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