Compatibility with paleotree

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 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 = = 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.


Similarly, converting from the FossilSim objects to paleotree format is done using the 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 = = f, tree = t)