Hi Bret,
This is fixed and will be in the next release. In the meantime, you can edit
the function and change the last line to:
all.equal(tips, desc)
Thanks for the report.
Cheers,
Emmanuel
-----Original Message-----
From: Bret Larget <lar...@stat.wisc.edu>
Sender: r-sig-phylo-boun...@r-project.org
Date: Thu, 22 Mar 2012 18:05:24
To: <jnylan...@users.sourceforge.net>
Cc: <r-sig-phylo@r-project.org>
Subject: [R-sig-phylo] behavior of is.monophyletic()
Please note the following discrepency in the behavior of
is.monophyletic().
------------------------------------------------------------------
> foo = read.tree(text="((1:2.0,(2:1.0,3:1.0):1.0):1.0,4:3.0);")
> is.monophyletic(foo,tips=2:3)
[1] TRUE
> is.monophyletic(foo,tips=c(2,3))
[1] FALSE
-----------------------------------------------------------------
I am aware that the function works properly when tips are specified as
characters. However, the documentation states that tips may be specified
as numeric. The difference between c(2,3) and 2:3 is that the former is
class numeric and the latter is class integer. I cannot think of any good
reason for why this distinction should result in different behavior of the
function. It would be best if the function worked correctly in all
situations, but in particular when the input matches the usage specified
by the documentation.
--------------------------------------------------------------------------
Usage
is.monophyletic(phy, tips, reroot = !is.rooted(phy), plot = FALSE, ...)
Arguments
phy a phylogenetic tree description of class "phylo".
tips a vector of mode numeric or character specifying the tips to be
^^^^^^^
tested.
reroot a logical. If FALSE, then the input tree is not unrooted before
the test.
plot a logical. If TRUE, then the tree is plotted with the specified
group tips highlighted.
... further arguments passed to plot.
-------------------------------------------------------------------------
I hope that this can be corrected in a future version of ape.
-Bret Larget
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