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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.

Source: R/as_daisie_datatable.R
as_daisie_datatable.Rd

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

Details

When the colonisation time of an island colonist is older than island_age (either because col_max_age = TRUE in the island_tbl, because precise_col_time = FALSE, or because the extracted colonisation time itself exceeds island_age), the colonist's status is appended with _MaxAge. This tells the downstream create_daisie_data() step to treat the colonisation time as an upper bound and integrate over possible colonisation times between the island age and the present.

If the island colonist additionally contains one or more in-island branching times that are also older than island_age, those branching events cannot represent on-island cladogenesis (the island did not yet exist). In that case the clade is split:

  • each branching time older than island_age is written as its own _MaxAge singleton row, with the clade name suffixed _1, _2, ...; and

  • the colonisation time together with any remaining (valid, in-island) branching times stays as the main _MaxAge row under the original clade name.

If all branching times exceed island_age, the main row contains only the colonisation time. The numeric values written to Branching_times are not clamped to island_age at this stage; clamping (to island_age - epss) happens in create_daisie_data(), which treats the _MaxAge flag as an instruction to integrate up to the island age.

Author

Joshua W. Lambert, Pedro Neves

Examples

phylod <- create_test_phylod(10)
island_tbl <- extract_island_species(
  phylod = phylod,
  extraction_method = "asr"
)
#> Warning: Root of the phylogeny is on the island so the colonisation
#>               time from the stem age cannot be collected, colonisation time
#>               will be set to infinite.

# 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
)