joshwlambert / DAISIEprep

Extracts phylogenetic island community data from phylogenetic trees
https://joshwlambert.github.io/DAISIEprep
GNU General Public License v3.0
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min_age in add_island_colonist: how is it handled? #40

Open luislvalente opened 2 days ago

luislvalente commented 2 days ago

In the following code:

island_tbl <- add_island_colonist(
  island_tbl = island_tbl,
  clade_name = "Bird_e",
  status = "endemic",
  # clade with just 1 species, missing_species = 0
  # because adding the lineage already counts as 1
  missing_species = 0,
  col_time = NA_real_,
  col_max_age = FALSE,
  branching_times = NA_real_,
  min_age = NA_real_,
  clade_type = 1,
  species = "Bird_e"
)

how is min_age considered? If we are adding a singleton (no branching times), adding a min_age would tell DAISIE inference to use that age (potentially turning it to stac=8). But if we are adding a clade (potentially with branching times). Would the min_age override the crown age? Would this be stac=9 and how would it be treated in the inferecence?