(Posted to: r-sig-phylo and GitHub)
Hi all,
is.monophyletic() does not work correctly when some tip labels are
duplicated. Here's a simple example:
R> tr <- read.tree(text = "((A,B),(A,C));")
The two tips labelled "A" are not sister-lineages, but the current
version of ape gives:
R> is.monophyletic(tr, "A")
[1] TRUE
R> is.monophyletic(tr, c("A", "A")) # <- must interrupt
^C
The reason for this is that the function looks for the first occurrence
of "A" in the tip labels of 'tr', even with duplicated labels. By
contrast, drop.tip() looks for all occurrences; the following command
drops 2 tips even if a single label is given:
R> drop.tip(tr, "A")
Phylogenetic tree with 2 tips and 1 internal nodes.
Tip labels:
B, C
Rooted; no branch lengths.
The version of ape on GH (will be submitted to CRAN next week) now
returns FALSE in both above commands. I assume this change will create
no problem for the packages that use this function, but I thought it may
be worth explaining this issue ahead of the CRAN submission. As usual,
any feedback welcome.
Best,
Emmanuel
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