I just updated the phytools function locate.yeti (a method to attach a missing tip to an ultrametric base tree using continuous character data) so that the missing leaf is now permitted to attach below the root node.
When I first started working on this, I initially mistakenly thought that I would have to add one additional parameter to when attaching a new leaf to the root node - that being the length of the edge leading to the tip. Actually, this is not the case. Whereas for a leaf attached to an edge we have to optimize the position along the edge from whence the lineage splits; in the case of a leaf attached to the root we only have to optimize its total length. Since our tree is invariably ultrametric - the lengths of the root stem and the terminal edge can be found by simply midpoint rooting our phylogeny.
The new version of locate.yeti is here; however since locate.yeti uses phytools internal functions it is probably best & easiest to simply install the latest non-CRAN phytools version.
Here's a quick demo using a phylogeny in which the true position of the missing lineage is sister to our ultrametric base tree:
> ## this is the full true tree
> ## place our missing taxon
Optimizing the phylogenetic position of Missing-lineage. Please wait....
Although it's pretty obvious that we have the correct tree in this case, we can also quantify it:
Loading required package: phangorn
Loading required package: Rphylip
That's pretty much it for now.
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