## Tuesday, February 23, 2016

### Extracting the terminal edge lengths for a set of tips

A phytools user asked the following:

Is there a good way to extract the branch length for a given set of tips? For a given tree, we would like to calculate the mean and variance for the terminal branch lengths leading to a specific set of tips. Is there a way in phytools to target a set of tips and extract those branch lengths?

If I understand the question properly, then what we have is a tree:

``````tree
``````
``````##
## Phylogenetic tree with 26 tips and 25 internal nodes.
##
## Tip labels:
##  A, B, C, D, E, F, ...
##
## Rooted; includes branch lengths.
``````

and a set of tips:

``````tips
``````
``````##   "K" "V" "P" "S" "J" "Q" "X" "B" "H" "D"
``````

and we want to extract the set of terminal edge lengths associated with these tips. This is easy.

``````## first get the node numbers of the tips
nodes<-sapply(tips,function(x,y) which(y==x),y=tree\$tip.label)
## then get the edge lengths for those nodes
edge.lengths<-setNames(tree\$edge.length[sapply(nodes,
function(x,y) which(y==x),y=tree\$edge[,2])],names(nodes))
``````

We can check as follows:

``````## our edge lengths
edge.lengths
``````
``````##          K          V          P          S          J          Q
## 0.26489330 0.76661579 0.04553788 0.15279683 0.13592584 0.04553788
##          X          B          H          D
## 0.05511474 0.59774131 1.28135176 0.83764106
``````
``````plotTree(tree)
edgelabels(round(tree\$edge.length,3),cex=0.7)
`````` That's all there is to it.

The data used for this exercise were simulated as follows:

``````library(phytools)
tree<-pbtree(n=26,tip.label=LETTERS)
tips<-sample(LETTERS,10)
``````

1. Hi Liam,

How would it change in case of a multiphylo object?

Cheers

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