Emmanuel,
Thanks! I actually realized that the reason this wasn’t working was because
there were a few tiny differences between the taxon names in my two trees. Once
I corrected this the rotateConstr() function works great, as does Liam’s
solution. Thanks both!
Jake
> On Apr 8, 2015, at 1:08
Strange... here's some code that seems to do what you describe but I
don't see something unexpected in the output.
A <- rcoal(200)
B <- A
NODES <- Ntip(B) + seq_len(B$Nnode)
for (i in 1:100) B <- rotate(B, sample(NODES, size = 1))
## to avoid line-crossing when plotting:
B <- read.tree(text = wr
The rotateConstr() function does not give me any errors -
Here is how I was trying to use it:
With a 200 taxon tree (tree A), I rotated ~50 nodes using rotate() to get it
how I wanted.
With a mostly similar (topologically identical, but different branch lengths,
so node numbers are not exactl
Hi Jacob,
Can you send an example of your output with rotateConstr()? Thanks.
Best,
Emmanuel
Le 08/04/2015 06:41, Jacob Berv a écrit :
Hi all,
Is there an easy way to get R to automatically rotate the nodes of a phylogeny
to match an arbitrary ordering of the tips?
Consider the following t
Hi Jacob.
There is a function in phytools that does something like this. It is
called minRotate and it was designed to be used internally by
phylo.to.map but can also be used on its own. I have blogged about your
question and the function here:
http://blog.phytools.org/2015/04/finding-closest
Hi all,
Is there an easy way to get R to automatically rotate the nodes of a phylogeny
to match an arbitrary ordering of the tips?
Consider the following two situations -
Situation 1:
Say I have a particular taxonomic order, such as
SpeciesA, SpeciesC, SpeciesB
And I want to rotate the node
