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

In 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. Designed to work with FBD.

Description

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

Usage

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

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.
...	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)

FossilSim documentation built on Oct. 3, 2024, 1:07 a.m.