Re: [R-sig-phylo] identify duplicate topologies and add corresponding values

2016-05-30 Thread Liam J. Revell 
Here is a solution to identify the unique topologies in your dataset and 
then average some quantity over them. Let us know if it works:


http://blog.phytools.org/2016/05/identifying-unique-tree-topologies-in.html

All the best, Liam

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: [email protected]
blog: http://blog.phytools.org

On 5/30/2016 1:52 PM, John Denton wrote:

Hi Liam,

Thanks for this. Yes, it looked back at the script and it is actually a data 
frame. I realized my question wasn't clear. Th second column has the actual 
trees as each entry (not just A, B, C, etc), which I suppose makes it more 
complicated--isn't an RF.dist/multiRF call needed?

Best,

~John

John S. S. Denton, Ph.D.
Department of Vertebrate Paleontology
American Museum of Natural History
www.johnssdenton.com

From: Liam J. Revell [[email protected]]
Sent: Monday, May 30, 2016 12:53 PM
To: John Denton; [email protected]
Subject: Re: [R-sig-phylo] identify duplicate topologies and add corresponding 
values

Hi John.

This would have to be a data frame (not a matrix) as you could not have
different data types in your matrix. Try the function aggregate, e.g.:

obj<-data.frame(number=c(1,1.5,0.2,0.8,1.0,3.2),
 tree=factor(c("A","A","B","C","A","B")))
obj ## data frame
aggregate(obj$number,by=list(obj$tree),sum)

- Liam

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: [email protected]
blog: http://blog.phytools.org

On 5/30/2016 12:13 PM, John Denton wrote:

Hi all,

I have a two-column matrix, containing trees in one column and a numeric value 
associated with each tree in the other column. I would like to go through the 
list to identify any duplicated topologies, and for each set of duplicates sum 
the corresponding numeric values and prune away the duplicate trees.

For example,

1.0   A
1.5   A
0.2  B
0.8.  C
1.0.  A
3.2.  B

Would become

3.5.  A
3.4. B
0.8.  C

Any help would be great!

Thanks,

~John
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Re: [R-sig-phylo] identify duplicate topologies and add corresponding values

2016-05-30 Thread Emmanuel Paradis 

Hi John,

Something like this does what you are looking for:

z <- tapply(X[, 1], X[, 2], sum)

To have it in a matrix-like layout (similar to X):

data.frame(z, names(z))

Best,

Emmanuel

Le 30/05/2016 18:13, John Denton a écrit :

Hi all,

I have a two-column matrix, containing trees in one column and a numeric
value associated with each tree in the other column. I would like to go
through the list to identify any duplicated topologies, and for each set
of duplicates sum the corresponding numeric values and prune away the
duplicate trees.





For example,

1.0   A
1.5   A
0.2  B
0.8.  C
1.0.  A
3.2.  B

Would become

3.5.  A
3.4. B
0.8.  C

Any help would be great!

Thanks,

~John


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Re: [R-sig-phylo] identify duplicate topologies and add corresponding values

2016-05-30 Thread Liam J. Revell 

Hi John.

This would have to be a data frame (not a matrix) as you could not have 
different data types in your matrix. Try the function aggregate, e.g.:


obj<-data.frame(number=c(1,1.5,0.2,0.8,1.0,3.2),
tree=factor(c("A","A","B","C","A","B")))
obj ## data frame
aggregate(obj$number,by=list(obj$tree),sum)

- Liam

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: [email protected]
blog: http://blog.phytools.org

On 5/30/2016 12:13 PM, John Denton wrote:

Hi all,

I have a two-column matrix, containing trees in one column and a numeric value 
associated with each tree in the other column. I would like to go through the 
list to identify any duplicated topologies, and for each set of duplicates sum 
the corresponding numeric values and prune away the duplicate trees.

For example,

1.0   A
1.5   A
0.2  B
0.8.  C
1.0.  A
3.2.  B

Would become

3.5.  A
3.4. B
0.8.  C

Any help would be great!

Thanks,

~John
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Searchable archive at http://www.mail-archive.com/[email protected]/



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[R-sig-phylo] identify duplicate topologies and add corresponding values

2016-05-30 Thread John Denton 
Hi all,

I have a two-column matrix, containing trees in one column and a numeric value 
associated with each tree in the other column. I would like to go through the 
list to identify any duplicated topologies, and for each set of duplicates sum 
the corresponding numeric values and prune away the duplicate trees.

For example,

1.0   A
1.5   A
0.2  B
0.8.  C
1.0.  A
3.2.  B

Would become

3.5.  A
3.4. B
0.8.  C

Any help would be great!

Thanks,

~John
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