Dear R-sig-phylo,
I am looking for a method to plot an unrooted tre/phylo object e in the
reverse order (of the tip labels). Like all the nodes would have
rotated.
Any of you has an idea?
Kind regards,
Thierry
Thierry Janssens
Postdoctoral researcher
Delft University of
Hi Thierry,
There might be a more elegant way to do this, but you can just apply the
ape function rotate() to each node number of the tree (excluding tips).
I.e.
tr2-tree
for(i in length(tr2$tip)+1:tr2$Nnode) tr2-rotate(tr2,i)
plot(tr2)
[rotate() may also be able to take a vector of
Hi Scott,
I don't think MPD and MNTD are appropriate measures of tree shape, since
factors other than tree shape including the number of tips on the tree and the
branch length distribution influence those statistics. I would recommend one of
the metrics of tree shape that you mentioned, most of
Hi Scott-
There are lots of indices to quantify tree shape differences, both in terms of
topology (Colless etc) and temporal differences (e.g., Pybus and Harvey's
gamma). MNTD and MPD will largely capture the temporal dimension of your trees
and will be highly correlated with gamma. For
Hi Liam,
Thanks for the help. It works partially, one clade remains at the
bottom of the plot, but since it is an unrooted tree there is no node to
rotate anymore.
But can you explain to me what is the rationale behind this? There are
only 47 nodes and 54 tips. How can the nodes from 55 to 47
But can you explain to me what is the rationale behind this? There are
only 47 nodes and 54 tips. How can the nodes from 55 to 47 than be
rotated?
Liam's code is rotating nodes 55+(1:47), rather than 55 to 47. The internal
node indexing in ape's phylo class starts with number of tips plus
Dan is right on - and I also suspect that the issue of the non-rotating
node is probably due to a polytomy at that node.
Thanks for the insight Dan.
- Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog:
Thanks much Dan and Steve.
Scott
On Thursday, March 17, 2011 at 11:05 AM, Dan Rabosky wrote:
Hi Scott-
There are lots of indices to quantify tree shape differences, both in terms
of topology (Colless etc) and temporal differences (e.g., Pybus and Harvey's
gamma). MNTD and MPD will
Hi all,
My understanding of lambda is that it is a scalar multiplier for the
off-diagonal elements of the variance covariance matrix computed from
your tree. When lambda = 1, then the trait is evolving according to
Brownian motion, when lambda = 0 there is no phylogenetic signal in
the data.
Hi Andrew,
The lambda value estimated for your dependent variable and the lambda value you
get from the gls analyses differ because the second is the lambda of the
residuals of your model. The lambda value of the model (which is estimated when
you fit the gls) is a measure of the covariance in
Dear Daniel,
OK, then I think your results make sense. You have, in fact, designed
a comparative study in which the power to detect a statistical effect of
Habitat (i.e., a group difference) will be higher if analyzed phylogenetically
than if analyzed in the conventional fashion
Dear all,
ape 2.7 has been on CRAN since yesterday. A bug has been introduced in
read.nexus. You can find how to fix it on ape's web site:
http://ape.mpl.ird.fr/
You don't need this fix if you don't use read.nexus, or if you have not
updated to ape 2.7 and can wait until version 2.7-1
12 matches
Mail list logo
