Hi again,
I realized this was a misunderstanding on my end - it seems to be working
fine.
Best,
-mpn.
On Thu, May 22, 2014 at 1:59 PM, Matthew Nelsen <mpnel...@gmail.com> wrote:
> Hi All,
>
> I'm encountering some unexpected results when using the
> trim.internal=FALSE argument in the drop.tip function in ape 3.1-1.
> Basically, I take a tree and drop the tips for a clade while preserving
> internal branches (as I'd like to retain all info up to the MRCA). It is
> dropping all the taxa in the clade of interest, but the branch length
> leading up to the MRCA of the clade I just dropped doesn't seem correct.
> I've provided an example below. Essentially, I'd expect the cut to be
> made at 1.14⦠(depth of node 21 in the original tree, the MRCA of the clade
> of interest), but instead, the depth is different (1.06â¦, a depth
> corresponding with that of node 23 in the original tree). Am I
> misunderstanding things, or overlooking something obvious? Thanks for any
> help,
>
> -Matt
>
> test.tree<-read.tree(text=
> "(((t4:0.7304771217,t5:0.7304771217):0.3471362426,t1:1.077613364):0.1974721889,((((t11:0.1192444999,t12:0.1192444999):0.6281874858,t3:0.7474319857):0.1048044294,t2:0.8522364151):0.05863278219,(t6:0.3575242818,(((t9:0.1323304724,t10:0.1323304724):0.06068353401,t8:0.1930140064):0.01819581885,t7:0.2112098252):0.1463144566):0.5533449155):0.3642163558);"
> )
>
>
> depths<-node.depth.edgelength(test.tree)
>
> depths
>
>
> #assign taxa to clade of interest
>
> taxa<-c("t7","t8","t10","t9")
>
>
> #get node that is mrca of clade
>
> clade.mrca<-getMRCA(test.tree,taxa)
>
>
> #depth of clade of interest...1.063876
>
> depths[clade.mrca]
>
>
> #drop clade of interest from starting tree and do NOT trim internal
> branches
>
> tree.wo.clade<-drop.tip(test.tree,taxa,trim.internal=FALSE)
>
>
> #now take a look at can see depth where cut was made...can see cut (node 9
> in new tree) was made at 1.1427551 instead of at 1.063876 (depth of node 23
> in test.tree)...
>
> node.depth.edgelength(tree.wo.clade)
>
>
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