Extracts the colonisation, diversification, and endemicty data from phylogenetic and endemicity data and stores it in an Island_tbl
object
Source: R/extract_island_species.R
extract_island_species.Rd
Extracts the colonisation, diversification, and endemicty data from
phylogenetic and endemicity data and stores it in an Island_tbl
object
Usage
extract_island_species(
phylod,
extraction_method,
island_tbl = NULL,
include_not_present = FALSE,
unique_clade_name = TRUE
)
Arguments
- phylod
A
phylo4d
object from the packagephylobase
containing phylogenetic and endemicity data for each species.- extraction_method
A character string specifying whether the colonisation time extracted is the minimum time (
min
) (before the present), or the most probable time under ancestral state reconstruction (asr
).- island_tbl
An instance of the
Island_tbl
class.- include_not_present
A boolean determining whether species not present on the island should be included in island colonist when embedded within an island clade. Default is FALSE.
- 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
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", "bird_i", "bird_j")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- sample(
c("not_present", "endemic", "nonendemic"),
size = length(phylobase::tipLabels(phylo)),
replace = TRUE,
prob = c(0.6, 0.2, 0.2)
)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
extract_island_species(phylod, extraction_method = "min")
#> Class: Island_tbl
#> clade_name status missing_species col_time col_max_age branching_times
#> 1 bird_g nonendemic 0 0.38003405 FALSE NA
#> 2 bird_i endemic 0 0.04960523 FALSE NA
#> min_age species clade_type
#> 1 NA bird_g 1
#> 2 NA bird_i 1