reconstructed.tree.fossils.objects | R Documentation |
Note that for datasets containing extinct only samples (& rho = 0) the ages output are scaled so that the youngest sample = 0.
reconstructed.tree.fossils.objects(fossils, tree, rho = 1)
fossils |
Fossils object. |
tree |
Tree object. |
rho |
Extant species sampling probability. Default = 1, will be disregarded if fossils object already contains extant samples. |
A list containing the tree and fossil objects.
# 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)
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