Hi Everyone,
I was wondering if anyone knows if it is possible to set up a custom rate model
to represent a binary discrete Dollo character with ace or make.simmap?
Thanks,
Graeme
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Graeme,
You can simulate characters (and associated tree) in the package
diversitree. For a binary character, the parameters specified are the
speciation rates, extinction rates, and transition rates between the two
states. If you want to simulate unidirectional evolution, you can just
specify
Hi Graeme,
I am not sure what you want to do with this but...it is straightforward to
disallow reverse transitions in diversitree
## Simulate a dollo character
library(diversitree)
set.seed(1)
t <- tree.bd(c(1,0), max.taxa=100)
d <- sim.character(t, c(0.1, 0), model="mk2")
## make a likelihood
Hi Graeme.
What Matt says is correct, of course, but it is also true that you can
do this with ace or make.simmap.
That would look like:
model<-matrix(c(0,0,1,0),2,2)
rownames(model)<-colnames(model)<-0:1
## ace
fit<-ace(x,tree,type="discrete",model=model)
## make.simmap
Hi Everyone,
Thanks for your responses. I guess I failed to explain what I really meant.
Apologies.
I have a time-scaled ultrametric tree and a binary character (and no missing
data) and I want to fit a true Dollo character (exactly as Brian describes
with: 1) a root state of zero, 2) a
