This vignette explains the integration of admtools with
the FossilSim and paleotree packages.
FossilSim packageadmtools 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.
In contrast to admtools, FossilSim uses age
(time before the present) instead of time. To successfully transform
data generated by FossilSim, this must be reversed using
rev_dir.
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) # no transformation of time to age required
s_strat = s |> # taxonomy object in the time domain
rev_dir(ref = max_time(my_adm)) |> # convert age to time
time_to_strat( my_adm, destructive = FALSE) |> # transform using age-depth model
rev_dir(ref = max_height(my_adm)) # transform back into age
f_strat = f |> # same here
rev_dir(ref = max_time(my_adm)) |>
time_to_strat( my_adm, destructive = TRUE)|> # destroy fossils coinciding with gaps
rev_dir(ref = max_height(my_adm))
FossilSim:::plot.fossils(f_strat, tree = t_strat, taxonomy = s_strat, show.taxonomy = TRUE)Important point are
rev_dir must be applied directly after data was
generated and and directly before the data is further processed using
FossilSim. As a principle, use rev_dir before
data from FossilSim enters the admtools and
StratPal ecosystem, and as it leaves the
ecosystem.
By default, FossilSim plots have axis labels “Time
before present”, although the trees after the transformation can be
trees in the stratigraphic domain. Because of this fixed reference point
used, 0 in the above plot represents the uppermost height of the
section, the axis units are lengths and not times, and the “Age” is
stratigraphic position below the top of the section.
paleotreeTo 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:
After conversion you can proceed as described in the section
Integration with the FossilSim package