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Integration with the FossilSim and paleotree packages

Source: vignettes/FossilSim_integration.Rmd
FossilSim_integration.Rmd

This vignette explains the integration of admtools with the FossilSim and paleotree packages.

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)

Integration with paleotree

To combine the admtools package with the paleotree package, please convert the paleotree format into the FossilSim format as described in the paleotree vignette of the FossilSim vignette:

vignette("paleotree", package = "FossilSim")

After conversion you can proceed as described in the section Integration with the FossilSim package

References