Hi everybody !
I have a tree with 235 tips with branchs length.
I would like use ape package (v. 2.4) to construct a circular tree
with the type fan, by keeping branchs length.
My trouble is that the tip label appears vertical and not axial, so
it's bearly readable.
I tried radial type, but
Hello,
I am desperately looking for a program or an R function that can
simulate the evolution of 2 continuous characters (with a given
correlation between the two characters) on a phylogenetic tree. I am
aware of the sim.char function of the GEIGER package; however, this
function only
Hi Christian (and everyone else),
You can do that with geiger, you just need to transform the tree
first. For example:
originalTree-birthdeath.tree(b=0.1, d=0, taxa.stop=10)
transformedTree-ouTree(originalTree, alpha=0.4)
sim.char(transformedTree, model.matrix=cbind(c(1, 0.5), c(0.5, 1)))
You
Hi Claire,
Have you tried with a random tree to check? eg:
tr - rcoal(235)
plot(tr, f)
If the results are different with your tree, this might a bug that
occurs with your particular tree.
EP
Quoting claire.ho...@inserm.fr:
Hi everybody !
I have a tree with 235 tips with branchs length.
Much of this can be done in our DOS PDSIMUL.EXE program, which I would be happy
to
send you. Reference is Garland et al. (1993) Systematic Biology, posted on my
website. It
outputs plain text ASCII files, which can be read into R using phylogr.
Cheers,
Ted
Theodore Garland, Jr., Ph.D.
We discussed on the list a few months ago about using any correlation
matrix to simulate characters. At the moment, it's tedious to get the
correlation matrix from a corStruct object in ape, but I'll improve
that soon (following several requests) so that it'll be
straightforward to
Emmanuel said --
We discussed on the list a few months ago about using any
correlation matrix to simulate characters. At the moment, it's
tedious to get the correlation matrix from a corStruct object in
ape, but I'll improve that soon (following several requests) so
that it'll be
Quoting Joe Felsenstein j...@gs.washington.edu:
Emmanuel said --
We discussed on the list a few months ago about using any
correlation matrix to simulate characters. At the moment, it's
tedious to get the correlation matrix from a corStruct object in
ape, but I'll improve that soon
