Objects produced by
FossilSim contain all the
information required by the
paleotree format and
vice-versa, thus these two packages are fully compatible.
paleotree is done using the
paleotree.record.to.fossils function, which returns a list
of the corresponding
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
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
fossils.to.paleotree.record function, which requires a
fossils object and either a
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