Quoting Joe Felsenstein :
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 reques
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 straigh
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 simulate
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.
Profe
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
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)))
Yo
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 implem
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, b