all_endemic_clades: Checks if all island species are endemic clades. Clade are...

In joshwlambert/DAISIEmainland: Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics

Checks if all island species are endemic clades. Clade are colonisations that have formed an island clade of two or more species surviving to the present.

Description

Checks if all island species are endemic clades. Clade are colonisations that have formed an island clade of two or more species surviving to the present.

Usage

all_endemic_clades(daisie_data)

Arguments

daisie_data

a DAISIE datalist, as can be checked by check_daisie_data. To quote the DAISE doc: A datalist is an object containing information on colonisation and branching times. This object can be generated using DAISIE_dataprep, which converts a user-specified data table into a datalist, but the object can of course also be entered directly. A datalist is a list with the following elements: The first element of the list has two or three components: $island_age - the island age Then, depending on whether a distinction between types is made, we have: $not_present - the number of mainland lineages that are not present on the island or: $not_present_type1 - the number of mainland lineages of type 1 that are not present on the island $not_present_type2 - the number of mainland lineages of type 2 that are not present on the island The remaining elements of the datalist each contains information on a single colonist lineage on the island and has 5 components: $colonist_name - the name of the species or clade that colonized the island $branching_times - island age followed by stem age of the population/species in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close relatives on the island. For endemic clades with more than one species on the island (cladogenetic clades/ radiations) these should be island age followed by the branching times of the island clade including the stem age of the clade $stac - the status of the colonist, see stac_to_str for values and descriptions $missing_species - number of island species that were not sampled for particular clade (only applicable for endemic clades) $type1or2 - whether the colonist belongs to type 1 or type 2

Value

Boolean

Author(s)

Joshua W. Lambert

Examples

## Not run: 
island <- DAISIEmainland::sim_island_with_mainland(
  total_time = 1,
  m = 100,
  island_pars = c(1, 1, 10, 0.1, 1),
  mainland_ex = 0.1,
  mainland_sample_prob = 1,
  mainland_sample_type = "complete",
  replicates = 2,
  verbose = FALSE
)
bool <- all_endemic_clades(island$ideal_islands[[1]])

## End(Not run)

joshwlambert/DAISIEmainland documentation built on July 14, 2024, 5:40 p.m.