reconcile.fossils.taxonomy: Reconcile existing fossil and taxonomy objects

In FossilSim: Simulation and Plots for Fossil and Taxonomy Data

Reconcile existing fossil and taxonomy objects

Description

This function uses edge identifiers (edge) and fossil sampling times (hmin) to reassign fossil species identifiers (sp, origin) using an existing taxonomy object. It can only be used if exact fossil sampling times are known (i.e. hmin = hmax), otherwise edges containing multiple species may be indistinguishable.

Usage

reconcile.fossils.taxonomy(fossils, taxonomy)

Arguments

fossils	Fossils object.
taxonomy	Taxonomy object.

Value

An object of class fossils.

Examples

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

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

# simulate fossils using taxonomy
s = sim.taxonomy(t, 0.5, 1, 0.5)
f = reconcile.fossils.taxonomy(f, s)
plot(f, t)

FossilSim documentation built on Nov. 6, 2025, 5:07 p.m.