knitr::opts_chunk$set(echo = TRUE) library(FossilSim) if(!require(paleotree)) knitr::opts_chunk$set(eval = FALSE)
Objects produced by FossilSim
contain all the information required by the paleotree
format and vice-versa, thus these two packages are fully compatible.
Converting from paleotree
is done using the paleotree.record.to.fossils
function, which returns a list of the corresponding phylo
, taxonomy
and fossils
objects.
record = paleotree::simFossilRecord(p = 0.1, q = 0.1, r = 0.1, nruns = 1, nTotalTaxa = c(30,40), nExtant = 0, nSamp = c(5,25)) converted_record = paleotree.record.to.fossils(record = record) converted_record
If the paleotree
record is fully extinct, i.e contains no extant samples, the age of the record will be encoded in the field origin.time
of the tree.
converted_record$tree$origin.time
Similarly, converting from the FossilSim
objects to paleotree
format is done using the fossils.to.paleotree.record
function, which requires a fossils
object and either a phylo
or taxonomy
object. If no taxonomy is provided, all speciation events in the tree will be assumed to be symmetric (bifurcating).
t = ape::rtree(6) f = sim.fossils.poisson(rate = 2, tree = t) converted_record = fossils.to.paleotree.record(fossils = f, tree = t) converted_record
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