select_endemicity_status: Select endemicity status from ancestral states probabilities

In DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees

Select endemicity status from ancestral states probabilities

Description

Selects a state for each node (both internal nodes, i.e. ancestral states, and tips, if included) from a table of probabilities.

Usage

select_endemicity_status(asr_df, method = "max")

Arguments

asr_df	a data frame containing at least these three columns: not_present_prob | endemic_prob | nonendemic_prob (in any order). Each column should contain the estimated probability of the state for each node (rows) and these columns should sum to 1.
method	"max" or "random". "max" will select the state with highest probability (selecting last state in event of a tie), while "random" will sample the states randomly with the probabilities as weight for each state.

Value

a character vector, with the selected endemicity status for each node.

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