paint {ouch} | R Documentation |
Function to paint selective regimes on a phylogenetic tree.
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'],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)