Dear R community,
I would like to simulate discrete characters on a randomly generated tree.
However, I would like to create different sets of trees and associated
characters at certain levels of phylogenetic signal.
Can someone point me in the right direction?
I am familiar with sim.char from geiger package for simulating characters, and
rcoal for simulating the ultrametric trees that I want, but I don't know how I
could, if at all, simulate characters that have a particular a priori set
phylogenetic signal.
As a simple example, the following example gets phylogenetic signal (K) that is
all over the map in different runs:
q <- list(rbind(c(-.5, .5), c(.5, -.5)))
traits <- sim.char(tree, q, model = "discrete", n = 1)
traits_ <- as.data.frame(traits[,,1])
traitsvec <- traits_[,1]
names(traitsvec) <- rownames(traits_)
phylosignal(traitsvec, tree, reps = 100)
Sincerely,
Scott Chamberlain
Rice University, EEB Dept.
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