is_back_colonisation: Checks whether species has undergone back-colonisation from

In DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees

Checks whether species has undergone back-colonisation from

Description

Checks whether species has undergone back-colonisation from

Usage

is_back_colonisation(phylod, node_label)

Arguments

phylod	A phylo4d object from the package phylobase containing phylogenetic and endemicity data for each species.
node_label	A numeric label for a node within a phylogeny.

Value

A character string or FALSE. Character string is in the format ancestral_node -> focal_node, where the ancestral node is not on mainland but the focal node is.

Examples

set.seed(
3,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
phylo <- ape::rcoal(5)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- c("endemic", "endemic", "not_present",
                       "endemic", "not_present")
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
phylod <- add_asr_node_states(phylod = phylod, asr_method = "parsimony")
# aritificially modify data to produce back-colonisation
phylobase::tdata(phylod)$island_status[8] <- "endemic"
# Example without back colonisation
is_back_colonisation(phylod = phylod, node_label = 2)
# Example with back colonisation
is_back_colonisation(phylod = phylod, node_label = 3)

DAISIEprep documentation built on April 3, 2025, 9:26 p.m.