Integration with the FossilSim package
admtools can transform phylogenetic trees coded as
phylo objects as well as fossils and
taxonomy objects as defined by the FossilSim
package. This allows to transform phylogenetic trees with their
associated taxonomic information and fossil locations between the time
and the stratigraphic domain. We give an example of this workflow
set.seed(42)
# construct age-depth model
my_adm = tp_to_adm(t = CarboCATLite_data$time_myr,
h = CarboCATLite_data$height_2_km_offshore_m,
L_unit = "m",
T_unit = "Myr")
# simulate phylogenetic tree
t = ape::rbdtree(birth = 3, death = 1, Tmax = 2)
# simulate taxonomy along the tree
s = FossilSim::sim.taxonomy(tree = t)
# simulate fossils based on taxonomy
f = FossilSim::sim.fossils.poisson(rate = 4, taxonomy = s)
# plot tree with taxonomy and fossil times
FossilSim:::plot.fossils(f, tree = t, taxonomy = s, show.taxonomy = TRUE)
## transform everything into the strat domain
t_strat = time_to_strat(t, my_adm)
s_strat = time_to_strat(s, my_adm, destructive = FALSE)
f_strat = time_to_strat(f, my_adm, destructive = FALSE)
FossilSim:::plot.fossils(f_strat, tree = t_strat, taxonomy = s_strat, show.taxonomy = TRUE)