prune.fossils: Removes all intermediate fossils from a combined tree and...

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

Removes all intermediate fossils from a combined tree and labels the first and last fossils of each lineage.

Description

First and last are based on the order used in the 'SAtree.from.fossils' function, i.e. youngest first or oldest first. Can be used with sampled or complete trees. If only one fossil is present for a particular species it is labelled as first.

Usage

prune.fossils(tree)

Arguments

tree	Combined tree with fossils.

Value

Tree with pruned fossils.

Examples

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

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

# transform format
t2 = SAtree.from.fossils(t,f)$tree

# prune fossils
t4 = prune.fossils(t2)

# or transform to sampled tree first
t3 = sampled.tree.from.combined(t2)
t4 = prune.fossils(t3)
plot(t4)

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