Description Usage Arguments Details Examples
Experimental phenogram plotting function for set of model of model parameters
1 | OUphenogram(pars, tree, dat, SE = 0, regime.col = NULL, ...)
|
pars |
A bayou formatted parameter list |
tree |
A tree of class 'phylo' |
dat |
A named vector of tip data |
SE |
Standard error of the tip states |
regime.col |
A named vector of colors equal in length to the number of regimes |
... |
Optional arguments passed to |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## Not run:
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")
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.