paint: Painting selective regimes on a phylogenetic tree.
In ouch: Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses

Description Usage Arguments Details Value Author(s) See Also Examples

Function to paint selective regimes on a phylogenetic tree.

1	paint(tree, subtree, branch, which = 1)

`tree`	An object of class `ouchtree`.
`subtree`	An optional named vector specifying the root nodes of subtrees. Each branch that descends from this node will be painted with the specified regime.
`branch`	An optional named vector specifying the end nodes of branches. The unique branch that terminates at the named node will be painted with the specified regime.
`which`	integer; if `tree` is a `hansentree`, start not with a blank canvas but with the regime specifications `tree` contains for the character indicated by `which`.

The names of subtree and branch must be the names of nodes of tree. The painting proceeds in a particular order: one can overpaint a branch. The subtrees indicated by the elements of subtree are painted first, in order. Then the branches indicated by branch are painted. If tree is a simple ouchtree object, then paint begins with a blank canvas, i.e., a tree painted with the single regime "nonspec". If tree inherits class hansentree, then paint begins with the regimes specified in the regimes slot of tree. Note that, if tree is a multivariate hansentree, then there are multiple regime specifications contained in tree. In this case, the argument which lets you pick which one you wish to begin with; by default, the first is used.

A vector of class 'factor' with names corresponding to the nodes in tree, specifying selective regimes.

Aaron A. King kingaa at umich dot edu

ouchtree, hansen

data(bimac)
x <- with(bimac,ouchtree(nodes=node,times=time/max(time),ancestors=ancestor,labels=species))
r <- paint(x,subtree=c("1"="medium","9"="large","2"="small"),branch=c("38"="large","2"="medium"))
plot(x,regimes=r,node.names=TRUE)
# compare to bimac['OU.LP']
h5 <- hansen(data=log(bimac['size']),tree=x,regimes=bimac['OU.LP'],sqrt.alpha=1,sigma=1,reltol=1e-5)
r <- paint(h5,branch=c("18"="large"),subtree=c("9"="small"))
plot(x,regimes=r,node.names=TRUE)