Message-ID: <935B7252-F93A-4914-BB88-FEDD96F9A236@gmx.net>
Date: 2008-09-04T06:45:00Z
From: Christoph Heibl
Subject: Binary Tree Testing in "ape" package (a bug?)
In-Reply-To: <73f827b50809032027u34f594fewf0b5b8fc7277888@mail.gmail.com>
If I am right informed, 'is.binary.tree' cannot test for root
polytomies.
Consider this example:
tree.hiv <- read.tree(text="((rat,mouse,(human,chimp)), kangaroo);")
is.binary.tree(tree.hiv) # will yield 'FALSE'
For further questions you might be better advised to use the 'R-sig-
phylo' mailing list.
________________________________________________________
Christoph Heibl
Systematic Botany
Ludwig-Maximilians-Universit?t M?nchen
Menzinger Str. 67
D-80638 M?nchen
GERMANY
phone: +49-(0)89-17861-251
e-mail: heibl at lmu.de
http://www.christophheibl.de/ch-home.html
On Sep 4, 2008, at 5:27 AM, Gundala Viswanath wrote:
> Dear all,
>
> I was testing the wonderful package APE.
>
> However upon testing a particular Newick's format
> tree - which I think to be a non-binary tree -
> it yields different result as expected.
>
>> library(ape)
>> tree.hiv <- read.tree(text="(rat,mouse,(human,chimp));")
>> is.binary.tree(tree.hiv)
> [1] TRUE
>
> Was that a bug in APE package?
>
> - Gundala Viswanath
> Jakarta - Indonesia
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.