multi_extract_island_species {DAISIEprep}

Extracts the colonisation, diversification, and endemicty data from multiple phylod (phylo4d class from phylobase) objects (composed of phylogenetic and endemicity data) and stores each in an Island_tbl object which are stored in a Multi_island_tbl object.

Description

Extracts the colonisation, diversification, and endemicty data from multiple phylod (phylo4d class from phylobase) objects (composed of phylogenetic and endemicity data) and stores each in an Island_tbl object which are stored in a Multi_island_tbl object.

Usage

multi_extract_island_species(
  multi_phylod,
  extraction_method,
  island_tbl = NULL,
  include_not_present = FALSE,
  verbose = FALSE,
  unique_clade_name = TRUE
)

Arguments

multi_phylod

A list of phylod objects.

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.

verbose

Boolean. States if intermediate results should be printed to console. Defaults to 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

Value

An object of Multi_island_tbl class

Examples

multi_phylod <- list()
multi_phylod[[1]] <- create_test_phylod(test_scenario = 1)
multi_phylod[[2]] <- create_test_phylod(test_scenario = 2)
multi_island_tbl <- multi_extract_island_species(
  multi_phylod = multi_phylod,
  extraction_method = "min",
  island_tbl = NULL,
  include_not_present = FALSE
)