Dear Joseph,
thanks so much. This is exactly what I need!
I am running into some problems that I don’t understand though. In my case,
rootID is 18, and max(phy$edge[,1]) is 33. When I try to execute your loop,
this happens:
> extract.clade(phy, 18)
Phylogenetic tree with 17 tips and 16 internal nodes.
Tip labels:
X1, X8, X9, X10 ...
Rooted; includes branch lengths.
So far so good… but then I keep getting these errors:
> extract.clade(phy, 19)
Error in phy$edge[, 2] : incorrect number of dimensions
> extract.clade(phy, 20)
Error in phy$edge[, 2] : incorrect number of dimensions
Not sure why extract.clade produces these errors. 19-23 don’t work, 24-26 work,
27 produces the error again, 28 works etc.
Thanks again.
Kamila
> On Jan 5, 2017, at 4:12 PM, Joseph W. Brown <josep...@umich.edu> wrote:
>
> Not sure if I understand the problem completely, but this should allow you to
> examine all of the clades (and should work if polytomies are involved):
>
> # for tree phy
> rootID <- length(phy$tip.label) + 1;
> for (i in rootID:max(phy$edge[,1])) {
> clade <- extract.clade(phy, i);
> # do something
> }
>
> This includes the root node (i.e. whole tree), but that can be changed. This
> can be rewritten as an lapply if necessary.
>
> HTH.
> JWB
> ________________________________________
> Joseph W. Brown
> Post-doctoral Researcher, Smith Laboratory
> University of Michigan
> Department of Ecology & Evolutionary Biology
> Room 2071, Kraus Natural Sciences Building
> Ann Arbor MI 48109-1079
> josep...@umich.edu <mailto:josep...@umich.edu>
>
>
>
>> On 5 Jan, 2017, at 15:50, Kamila Naxerova <knaxer...@partners.org
>> <mailto:knaxer...@partners.org>> wrote:
>>
>> Hi all,
>>
>> I would like to break a phylogenetic tree into all possible clades and then
>> examine each one of them for certain characteristics.
>>
>> I am writing some code to do this from scratch, but it’s getting pretty
>> cumbersome quickly.
>>
>> I was wondering whether there are some functions out there already that
>> could help me with this task?
>>
>> Thanks so much for any help.
>>
>> Cheers,
>> Kamila
>>
>>
>> The information in this e-mail is intended only for t...{{dropped:24}}
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