
Experimental phenogram plotting function for set of model of model parameters
OUphenogram(pars, tree, dat, SE = 0, regime.col = NULL, ...)
No return value. This function generates a phenogram plot as a side effect.
A bayou formatted parameter list
A tree of class 'phylo'
A named vector of tip data
Standard error of the tip states
A named vector of colors equal in length to the number of regimes
Optional arguments passed to phenogram()
This is an experimental plotting utility that can plot a phenogram with a given regime painting from a parameter list. Note that it uses optimization of internal node states using matrix inversion, which is very slow for large trees. However, what is returned is the maximum likelihood estimate of the internal node states given the model, data and the parameter values.
# \donttest{
tree <- sim.bdtree(n=50)
tree$edge.length <- tree$edge.length/max(branching.times(tree))
prior <- make.prior(tree, dists=list(dk="cdpois", dsig2="dnorm",
dtheta="dnorm"), param=list(dk=list(lambda=5, kmax=10),
dsig2=list(mean=1, sd=0.01), dtheta=list(mean=0, sd=3)),
plot.prior=FALSE)
pars <- priorSim(prior, tree, plot=FALSE, nsim=1)$pars[[1]]
pars$alpha <- 4
dat <- dataSim(pars, model="OU", phenogram=FALSE, tree)$dat
OUphenogram(pars, tree, dat, ftype="off")
# }
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