drop.tip function in
R to prune all the taxa that need to be pruned from all the source trees. There is a nice way to loop this through any number of trees with drop.tip but it doesn't work for me. I suspect it's because in perhaps many trees the tips I want to drop my make up 100% of the tree.
drop.tip on each individual tree reveals that standard use of
drop.tip can only successfully remove tips from 421/924 of the source trees. There are a variety of error messages for the others.
drop.tip error messages encountered:
Error in kids[[parent[i]]] : subscript out of bounds
Others have also encountered this error using the
Error in phy$edge[, 1] <- newNb[phy$edge[, 1]] :
number of items to replace is not a multiple of replacement length
I have not yet found ways around these problems or what is causing them. Still investigating.