Re: [R-sig-phylo] Extract all possible clades from a tree

[Joseph W. Brown]

Hmm. Maybe something wonky with your tree? I simulated a 17-tip tree and tried 
things out:

phy <- rtree(17);
rootID <- length(phy$tip.label) + 1;
counter <- 1;
for (i in rootID:max(phy$edge[,1])) {
  clade <- extract.clade(phy, i);
  # do something. just printing clade properties here
  print(paste0("clade ", counter, " (node ", i, ") has ", 
length(clade$tip.label), " tips."));
  counter <- counter + 1;
}

[1] "clade 1 (node 18) has 17 tips."
[1] "clade 2 (node 19) has 11 tips."
[1] "clade 3 (node 20) has 10 tips."
[1] "clade 4 (node 21) has 4 tips."
[1] "clade 5 (node 22) has 3 tips."
[1] "clade 6 (node 23) has 2 tips."
[1] "clade 7 (node 24) has 6 tips."
[1] "clade 8 (node 25) has 5 tips."
[1] "clade 9 (node 26) has 3 tips."
[1] "clade 10 (node 27) has 2 tips."
[1] "clade 11 (node 28) has 2 tips."
[1] "clade 12 (node 29) has 6 tips."
[1] "clade 13 (node 30) has 2 tips."
[1] "clade 14 (node 31) has 4 tips."
[1] "clade 15 (node 32) has 3 tips."
[1] "clade 16 (node 33) has 2 tips."

and had no problem. Maybe post your tree here?

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



> On 5 Jan, 2017, at 17:18, Kamila Naxerova  wrote:
> 
> 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$edge[, 2] : incorrect number of dimensions
> 
> Not sure why extract.clade produces these errors. 19-23 don’t work, 24-26 
> work, 27 produces the error again, 28 works etc. 
> 
> Thanks again. 
> 
> Kamila
> 
> 
>> On Jan 5, 2017, at 4:12 PM, Joseph W. Brown > > wrote:
>> 
>> Not sure if I understand the problem completely, but this should allow you 
>> to examine all of the clades (and should work if polytomies are involved):
>> 
>> # for tree phy
>> rootID <- length(phy$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 
>> 
>> 
>> 
>>> On 5 Jan, 2017, at 15:50, Kamila Naxerova >> > 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
>>> 
>>> 
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>>> addressed. If you believe this e-mail was sent to you in error and the 
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>>> HelpLine at
>>> http://www.partners.org/complianceline 
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>>> 
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>>> 
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>>> http://www.mail-archive.com/r-sig-phylo@r-project.org/ 
>>> 
> 


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Re: [R-sig-phylo] Extract all possible clades from a tree

[Kamila Naxerova]

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  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 
> 
> 
> 
>> On 5 Jan, 2017, at 15:50, Kamila Naxerova > > 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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Re: [R-sig-phylo] Extract all possible clades from a tree

[Joseph W. Brown]

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



> On 5 Jan, 2017, at 15:50, Kamila Naxerova  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 th...{{dropped:21}}

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[R-sig-phylo] Extract all possible clades from a tree

[Kamila Naxerova]

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 the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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