beast.fbd.format | R Documentation |
Transforms a tree and fossils into a sampled tree in beast-usable format and writes it in Newick format. Designed to work with FBD.
beast.fbd.format(tree, fossils, rho = 1, sampled_tips = NULL, ...)
tree |
Complete tree. |
fossils |
fossils dataframe. |
rho |
Sampling probability of extant tips. Default 1, will be disregarded if sampled_tips is not null. |
sampled_tips |
List of tip labels corresponding to sampled extant tips. |
... |
Additional parameters will be passed to ape::write.tree |
Output of write.tree.
# simulate tree t = ape::rtree(6) # simulate fossils f = sim.fossils.poisson(rate = 2, tree = t) # output for BEAST beast.fbd.format(t, f) # output on the console ## Not run: beast.fbd.format(t, f, file="example.tre") # output in file ## End(Not run)
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