OUphenogram: Experimental phenogram plotting function for set of model of...

In uyedaj/bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Experimental phenogram plotting function for set of model of model parameters

Description

Experimental phenogram plotting function for set of model of model parameters

Usage

OUphenogram(pars, tree, dat, SE = 0, regime.col = NULL, ...)

Arguments

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 phenogram()

Details

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.

Examples

## 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)

uyedaj/bayou documentation built on Jan. 28, 2024, 5:09 a.m.