extract_endemic_clade {DAISIEprep} | R Documentation |
Extracts the information for an endemic clade (i.e. more than one species on
the island more closely related to each other than other mainland species)
from a phylogeny (specifically phylo4d
object from phylobase
package)
and stores it in an Island_colonist
class
Description
Extracts the information for an endemic clade (i.e. more than one species on
the island more closely related to each other than other mainland species)
from a phylogeny (specifically phylo4d
object from phylobase
package)
and stores it in an Island_colonist
class
Usage
extract_endemic_clade(phylod, species_label, unique_clade_name)
Arguments
phylod |
A |
species_label |
The tip label of the species of interest. |
unique_clade_name |
Boolean determining whether a unique species identifier is used as the clade name in the Island_tbl object or a genus name which may not be unique if that genus has several independent island colonisations |
Value
An object of Island_colonist
class
Examples
set.seed(
3,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
"bird_f", "bird_g", "bird_h", "bird_i", "bird_j")
phylo <- methods::as(phylo, "phylo4")
endemicity_status <- sample(
x = c("not_present", "endemic", "nonendemic"),
size = length(phylobase::tipLabels(phylo)),
replace = TRUE,
prob = c(0.7, 0.3, 0)
)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
island_colonist <- extract_endemic_clade(
phylod = phylod,
species_label = "bird_i",
unique_clade_name = TRUE
)
[Package DAISIEprep version 0.4.0 Index]