extract_multi_tip_species {DAISIEprep} | R Documentation |
Extracts the information for a species (endemic or non-endemic) which has
multiple tips in the phylogeny (i.e. more than one sample per species) from
a phylogeny (specifically phylo4d
object from phylobase
package)
and stores it in an Island_colonist
class
Description
Extracts the information for a species (endemic or non-endemic) which has
multiple tips in the phylogeny (i.e. more than one sample per species) from
a phylogeny (specifically phylo4d
object from phylobase
package)
and stores it in an Island_colonist
class
Usage
extract_multi_tip_species(phylod, species_label, species_endemicity)
Arguments
phylod |
A |
species_label |
The tip label of the species of interest. |
species_endemicity |
A character string with the endemicity, either "endemic" or "nonendemic" of an island species, or "not_present" if not on the island. |
Value
An object of Island_colonist
class
Examples
set.seed(
1,
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_1", "bird_h_2", "bird_i")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- c("not_present", "not_present", "not_present",
"not_present", "not_present", "not_present",
"not_present", "endemic", "endemic", "not_present")
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
extract_multi_tip_species(
phylod = phylod,
species_label = "bird_h_1",
species_endemicity = "endemic"
)
[Package DAISIEprep version 0.4.0 Index]