as_daisie_datatable: Converts the 'Island_tbl' class to a data frame in the format...

In DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees

Converts the Island_tbl class to a data frame in the format of a DAISIE data table (see DAISIE R package for details). This can then be input into DAISIEprep::create_daisie_data() function which creates the list input into the DAISIE ML models.

Description

Converts the Island_tbl class to a data frame in the format of a DAISIE data table (see DAISIE R package for details). This can then be input into DAISIEprep::create_daisie_data() function which creates the list input into the DAISIE ML models.

Usage

as_daisie_datatable(island_tbl, island_age, precise_col_time = TRUE)

Arguments

island_tbl	An instance of the Island_tbl class.
island_age	Age of the island in appropriate units.
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

A data frame in the format of a DAISIE data table

Author(s)

Joshua W. Lambert, Pedro Neves

Examples

phylod <- create_test_phylod(10)
island_tbl <- extract_island_species(
  phylod = phylod,
  extraction_method = "asr"
)

# Example where precise colonisation times are known
daisie_datatable <- as_daisie_datatable(
  island_tbl = island_tbl,
  island_age = 0.2,
  precise_col_time = TRUE
)

# Example where colonisation times are uncertain and set to max ages
daisie_datatable <- as_daisie_datatable(
  island_tbl = island_tbl,
  island_age = 0.2,
  precise_col_time = FALSE
)

DAISIEprep documentation built on April 3, 2025, 9:26 p.m.