reconstructed.tree.fossils.objects: Returns tree and fossil objects that you can use to plot the...

In FossilSim: Simulation and Plots for Fossil and Taxonomy Data

Returns tree and fossil objects that you can use to plot the reconstructed tree.

Description

Note that for datasets containing extinct only samples (& rho = 0) the ages output are scaled so that the youngest sample = 0.

Usage

reconstructed.tree.fossils.objects(
  fossils,
  tree,
  rho = 1,
  tip_order = c("oldest_first", "youngest_first")
)

Arguments

fossils	Fossils object.
tree	Tree object.
rho	Extant species sampling probability. Default = 1, will be disregarded if fossils object already contains extant samples.
tip_order	Order of indexes to assign to the tips in the SA tree, either 'oldest_first' (by default, indexes increase towards the present) or 'youngest_first' (indexes increase towards the past).

Value

A list containing the reconstructed SA tree and fossil objects.

Examples

# simulate tree
birth = 0.1
death = 0.05
tips = 10
t = TreeSim::sim.bd.taxa(tips, 1, birth, death)[[1]]

# simulate fossils
f = sim.fossils.poisson(rate = 0.3, tree = t)

# simulate extant samples
f = sim.extant.samples(f, tree = t, rho = 0.5)

# plot the complete tree
plot(f,t)

# generate tree & fossil objects corresponding to the reconstructed tree
out = reconstructed.tree.fossils.objects(f, t)
f.reconst = out$fossils
t.reconst = out$tree

# plot the reconstructed tree
plot(f.reconst, t.reconst)

FossilSim documentation built on Nov. 5, 2025, 7:05 p.m.