beast.fbd.format: Transforms a tree and fossils into a sampled tree in...

In rachelwarnock/fossilsim: Simulation and Plots for Fossil and Taxonomy Data

Transforms a tree and fossils into a sampled tree in BEAST-usable format and writes it in Newick format.

Description

For each species, removes all the intermediate fossils and leave only the youngest and oldest. The oldest and youngest of each species will be labelled according to the 'tip_order' argument.

Usage

beast.fbd.format(
  tree,
  fossils,
  rho = 1,
  sampled_tips = NULL,
  tip_order = "oldest_first",
  ...
)

Arguments

tree	Complete tree.
fossils	fossils dataframe.
rho	Sampling probability of extant tips. Default 1, will be disregarded if sampled_tips is not null.
sampled_tips	List of tip labels corresponding to sampled extant tips.
tip_order	Order of indexes to assign to the tips, either 'oldest_first' (by default, first = oldest and last = youngest) or 'youngest_first' (reversed).
...	Additional parameters will be passed to ape::write.tree

Value

Output of write.tree.

Examples

# simulate tree
t = ape::rtree(6)

# simulate fossils
f = sim.fossils.poisson(rate = 2, tree = t)

# output for BEAST
beast.fbd.format(t, f) # output on the console
## Not run: 
beast.fbd.format(t, f, file="example.tre") # output in file

## End(Not run)

rachelwarnock/fossilsim documentation built on June 2, 2025, 9:34 a.m.