Process fossilized birth-death sample of lineages

Takes output from GetFossils and places extinct lineages in the tree and produces a properly formatted table of fossil samples from lineages that survive to the present (k fossils).

ProcessSimSample(phy, f)

Arguments

phy

a complete phylogeny that includes both extant and extinct lineages.

f

the table of sampled lineages under the fossilized birth-death process obtained from GetFossils.

Value

Returns an object that contains:

$phy

a tree of extant taxa and sampled extinct tips.

$k.samples

a table of k fossils sampled, formatted to be input into MiSSE, hisse, MuHiSSE.