The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.
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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.