Dear R-sig-phylo,
I have been working with a mammalian phylogeny I recently downloaded from
VertLife (http://vertlife.org/phylosubsets/). Unfortunately, the phylogeny
is missing a large number of species, so I am trying to manually add these
taxa to the phylogeny. I have a series of 100 trees that I am using to do
things such as test for phylogenetic signal. I know how to use bind.tip to
add new taxa to a single tree, but I am having more trouble with a
multiPhylo object. I am primarily adding these taxa by placing them as
sister to their nearest included relative (since most of them are elevated
former subspecies), but the issue here is that in the 100 trees in the
multiPhylo object the node representing the taxon to bind these taxa to is
not the same across all trees due to shifting topologies.
This is an example of the code I have been using, in which "tree" is the
tree object. This works for a single 'phylo' tree but not 'multiphylo'.
```
newtree<-lapply(tree,bind.tip,tip.label="Cercopithecus_albogularis",
position=0.59,edge.length = 0.59,
where=mrca(tree)["Cercopithecus_mitis","Cercopithecus_mitis"])
```
Now, this code will not work, but I know exactly why: 'tree' is a
multiPhylo object and so the 'where' argument cannot find the node for the
terminal taxon. However, the issue is how can I tell R to repeat this
'where' argument for each of the 100 trees, since the node in question is
not identical across these trees? Is there an easier way to do this than
using the 'mrca' call for each terminal taxon? I've noticed adding a 'mrca'
argument also increases computation time and if I am reinventing the wheel
it would be nice to know if I am overthinking things.
Sincerely,
Russell
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