add_island_colonist {DAISIEprep}

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

Description

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
)