Adds an island colonists (can be either a singleton lineage or an island clade) to the island community (island_tbl).

Usage

add_island_colonist(
  island_tbl,
  clade_name,
  status,
  missing_species,
  col_time,
  col_max_age,
  branching_times,
  min_age,
  species,
  clade_type
)

Arguments

island_tbl: An instance of the Island_tbl class.
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)

Value

An object of Island_tbl class

Examples

# create an empty island_tbl to add to
island_tbl <- island_tbl()

# add a new island colonist
island_tbl <- add_island_colonist(
  island_tbl,
  clade_name = "new_clade",
  status = "endemic",
  missing_species = 0,
  col_time = 1,
  col_max_age = FALSE,
  branching_times = NA,
  min_age = NA,
  species = "new_clade",
  clade_type = 1
)