Liam,
Your solution worked as well! Thanks for the help and your wonderful blog
post.
BL
On Thu, Sep 15, 2016 at 8:55 AM, Liam J. Revell wrote:
> I'm sure Florian's solution works, though I haven't tried it.
>
> Here is another one that may work that I just posted to my blog:
>
> http://blog.p
Florian and list,
Great ideas to use getDescendants! Worked as advertised. Thanks for the
help!
BL
On Thu, Sep 15, 2016 at 8:55 AM, Liam J. Revell wrote:
> I'm sure Florian's solution works, though I haven't tried it.
>
> Here is another one that may work that I just posted to my blog:
>
> ht
I'm sure Florian's solution works, though I haven't tried it.
Here is another one that may work that I just posted to my blog:
http://blog.phytools.org/2016/09/collapsing-clades-of-foo-huh.html
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
I don't really know what you mean by 'hard-coding', but here is what I
could think of (it is probably not optimal, but should work pretty quickly
if your tree does not have thousands of tips):
First, borrow 'getDescendants' from phytools:
getDescendants<-function(tree,node,curr=NULL){
if(is.nul
Florian and list,
What is your preferred method to go about this? phy$tip.label? If so, how
would one label a tip label from each clade of foo's without having to hard
code the clade number? I am trying to prevent any hard coding.
BL
On Wed, Sep 14, 2016 at 3:46 PM, Florian Boucher
wrote:
> Hi
Hi Branchlizard and list,
in order to do this you would first need to rename one of the foo's in each
clade (I would always rename the first one) as '6 foo's', '4 foo's', etc.
Then you can apply drop.tip on all the foos, as you did before.
I hope this helps.
Cheers,
Florian
2016-09-14 21:32 GMT
I would like to turn this
http://i.imgur.com/chLdFmZ.jpg
into this
http://i.imgur.com/vSoe6mu.jpg
My dataset and phylogeny is much more complex than this, but this is the
basic idea.
BL
On Mon, Sep 12, 2016 at 8:16 PM, Liam J. Revell wrote:
> I'm sure this is possible, but I really don'
I'm sure this is possible, but I really don't understand the question.
Maybe you could draw what you have in mind on a piece of paper and post
a picture of the paper
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb
Hello Hilmar,
Thank you for your suggestion.
Below is the url to the stack overflow question. As of now, it has received
no answers.
http://stackoverflow.com/questions/39403443/collapse-a-clade-by-tip-labels-while-maintaining-phylogenetic-position
BranchLizard
On Mon, Sep 12, 2016 at 3:58 PM,
Hi BranchLizard,
> On Sep 12, 2016, at 3:46 PM, branchlizard . wrote:
>
> I have posted this question at Stack Overflow. I hope this doesn't violate
> any community rules about double posting.
It doesn’t, but why not include the URL so that people can avoid answering what
may already have been
I have posted this question at Stack Overflow. I hope this doesn't violate
any community rules about double posting.
I probably could have worded the title better, but I am wanting to collapse
any clade within a phylogenetic tree (even if the clade has one member)
which has a tip label of "foo" an
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