Rob Lanfear has identified a problem with the function ltt() in "phytools" when the tree includes extinct lineages. For instance, take the following tree with 20 extant taxa:
With the present version of ltt(), we get:
which is obviously incorrect. We can substituted v0.3 of the function and try again:
and this seems to solve the problem. I will try and fix the most recent version (which corrected some bugs from v0.3 as well as adding additional functionality) and this will be included in the next version of "phytools." Thanks to Rob for finding this problem.
Note that the tree above was simulated using Tanja Stadler's neat package "TreeSim."