prune.fossils function

Removes all intermediate fossils from a combined tree and labels the first and last fossils of each lineage. Can be used with sampled or complete trees. If only one fossil is present for a particular species it is labelled as first.

prune.fossils(tree)

Arguments

• tree: Combined tree with fossils.

Returns

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)