DAISIEprep (version 1.0.1)

island_colonist: Constructor for Island_colonist

Description

Constructor for Island_colonist

Usage

island_colonist(
  clade_name = NA_character_,
  status = NA_character_,
  missing_species = NA_real_,
  col_time = NA_real_,
  col_max_age = NA,
  branching_times = NA_real_,
  min_age = NA_real_,
  species = NA_character_,
  clade_type = NA_integer_
)

Value

Object of Island_colonist class.

Arguments

clade_name

Character name of the colonising clade.

status

Character endemicity status of the colonising clade. Either "endemic" or "nonendemic".

missing_species

Numeric number of missing species from the phylogeny that belong to the colonising clade. For a clade with missing species this is \(n - 1\), where \(n\) is the number of missing species in the clade. If the clade is an island singleton, the number of missing species is 0 because by adding the colonist it already counts as one automatically. If the clade has more than one species, the missing_species is \(n - 1\) because adding the lineage already counts as one.

col_time

Numeric with the colonisation time of the island colonist

col_max_age

Boolean determining whether colonisation time should be considered a precise time of colonisation or a maximum time of colonisation

branching_times

Numeric vector of one or more elements which are the branching times on the island.

min_age

Numeric minimum age (time before the present) that the species must have colonised the island by. This is known when there is a branching on the island, either in species or subspecies.

species

Character vector of one or more elements containing the name of the species included in the colonising clade.

clade_type

Numeric determining which type of clade the island colonist is, this determines which macroevolutionary regime (parameter set) the island colonist is in. After formatting the island_tbl to a DAISIE data list, the clade type can be used to conduct a 2-type analysis (see https://CRAN.R-project.org/package=DAISIE/vignettes/demo_optimize.html for more information)

Examples

# Without initial values
colonist <- island_colonist()

# With initial values
colonist <- island_colonist(
  clade_name = "bird",
  status = "endemic",
  missing_species = 0,
  col_time = 0.5,
  col_max_age = FALSE,
  branching_times = 0.5,
  min_age = NA_real_,
  species = "bird_a",
  clade_type = 1
)