beast.fbd.format: Transforms a tree and fossils into a sampled tree in...
In rachelwarnock/fossilsim: Simulation of Fossil and Taxonomy Data

Description Usage Arguments Value Examples

Transforms a tree and fossils into a sampled tree in beast-usable format and writes it in Newick format. Designed to work with FBD.

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

`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.
`...`	Additional parameters will be passed to ape::write.tree

Output of write.tree.

# 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
beast.fbd.format(t, f, file="example.tre") # output in file