Painting selective regimes on a phylogenetic tree.
Function to paint selective regimes on a phylogenetic tree.
An object of class
An optional named vector specifying the root nodes of subtrees. Each branch that descends from this node will be painted with the specified regime.
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.
The names of
branch must be the names of nodes of
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.
tree is a simple
ouchtree object, then
paint begins with a blank canvas, i.e., a tree painted with the single regime "nonspec".
tree inherits class
paint begins with the regimes specified in the
regimes slot of
Note that, if
tree is a multivariate
hansentree, then there are multiple regime specifications contained in
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
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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)