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 "phylo".
an object of class "phylo". In the case of genus.to.species.tree this should be a genus-level backbone tree.
string contain species name in the format "Genus_species" or "Genus species".
for add.species.to.genus, optional argument containing the genus to which species is to be attached. If NULL then genus will be extracted from species.
for add.species.to.genus, the location to attach species to the tree. where= "root" will cause the species to be attached to the MRCA of all members of genus. where="random" will cause species to be attached at random to the subtree descended from the MRCA of all members of genus.
Liam Revell liam.revell@umb.edu
For add.species.to.genus, if genus contains only one species and where="root", then species will be attached midway along the branch leading to the one species. If where="random" then 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.
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
add.random, bind.tip