add.species.to.genus adds an additional species to a genus on a phylogeny.
genus.to.species.tree simulates pure-birth subtrees and then binds them at a random height along the terminal edge leading to each corresponding genus on a genus-level backbone tree.
add.species.to.genus(tree, species, genus=NULL, where=c("root","random")) genus.to.species.tree(tree, species)
an object of class
string contain species name in the format
genus contains only one species and
species will be attached midway along the branch leading to the one species. If
species will be added at a random position along the edge. If
genus cannot be found in the tree, then the original tree is returned and a warning printed. If the tree is not ultrametric, then the resultant tree may not contain branch lengths and a warning will be printed. Note that for some cases in which a tree is read in from file, R may initially think it is ultrametric, but then later (as tips are added) decide that it is not due to rounding of the edge lengths when it was written to file. This can most likely be resolved by using
force.ultrametric to coerce the tree to be exactly ultrametric (to the maximum numerical precision permitted by R) before adding tips to the tree. If
genus is non-monophyletic then
species will be attached to the most inclusive group containing members of
genus and a warning will be printed.
An object of class
Liam Revell email@example.com
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
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