create_daisie_data {DAISIEprep}

This is a wrapper function for DAISIE::DAISIE_dataprep(). It allows the final DAISIE data structure to be produced from within DAISIEprep. For detailed documentation see the help documentation in the DAISIE package (?DAISIE::DAISIE_dataprep).

Description

This is a wrapper function for DAISIE::DAISIE_dataprep(). It allows the final DAISIE data structure to be produced from within DAISIEprep. For detailed documentation see the help documentation in the DAISIE package (?DAISIE::DAISIE_dataprep).

Usage

create_daisie_data(
  data,
  island_age,
  num_mainland_species,
  num_clade_types = 1,
  list_type2_clades = NA,
  prop_type2_pool = "proportional",
  epss = 1e-05,
  verbose = FALSE,
  precise_col_time = TRUE
)

Arguments

data

Either an object of class Island_tbl or a DAISIE data table object (output from as_daisie_datatable()).

island_age

Age of the island in appropriate units.

num_mainland_species

The size of the mainland pool, i.e. the number of species that can potentially colonise the island.

num_clade_types

Number of clade types. Default num_clade_types = 1 all species are considered to belong to the same macroevolutionary process. If num_clade_types = 2, there are two types of clades with distinct macroevolutionary processes.

list_type2_clades

If num_clade_types = 2, list_type2_clades specifies the names of the clades that have a distinct macroevolutionary process. The names must match those in the "Clade_name" column of the source data table. If num_clade_types = 1, then list_type2_clades = NA should be specified (default).

prop_type2_pool

Specifies the fraction of potential mainland colonists that have a distinct macroevolutionary process. Applies only if number_clade_types = 2. Default "proportional" sets the fraction to be proportional to the number of clades of distinct macroevolutionary process that have colonised the island. Alternatively, the user can specify a value between 0 and 1 (e.g. if the mainland pool size is 1000 and prop_type2_pool = 0.02 then the number of type 2 species is 20).

epss

Default = 1e-5 should be appropriate in most cases. This value is used to set the maximum age of colonisation of "Non_endemic_MaxAge" and "Endemic_MaxAge" species to an age that is slightly younger than the island for cases when the age provided for that species is older than the island. The new maximum age is then used as an upper bound to integrate over all possible colonisation times.

verbose

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

precise_col_time

Boolean, TRUE uses the precise times of colonisation, FALSE makes every colonist a max age colonistion and uses minimum age of colonisation if available.

Value

DAISIE data list

Examples

phylod <- create_test_phylod(3)
island_tbl <- extract_island_species(
  phylod = phylod,
  extraction_method = "min"
)
daisie_datatable <- as_daisie_datatable(island_tbl, island_age = 10)
daisie_data_list <- create_daisie_data(
  data = daisie_datatable,
  island_age = 10,
  num_mainland_species = 1000,
  num_clade_types = 1,
  list_type2_clades = NA,
  prop_type2_pool = NA,
  epss = 1e-5,
  verbose = FALSE
)