Description Usage Arguments Value Author(s) Examples
These hidden functions are utils for adephylo, used by other
functions. Regular users can use them as well, but no validity checks
are performed for the arguments: speed is here favored over safety.
Most of these functions handle trees inheriting phylo4
class.
.tipToRoot
finds the set of nodes between a tip and the root of
a tree.
1 | .tipToRoot(x, tip, root, include.root=FALSE)
|
x |
A valid tree of class phylo4. |
tip |
An integer identifying a tip by its numbers. |
root |
An integer identifying the root of the tree by its number. |
include.root |
a logical stating whether the root must be included as a node of the path from tip to root (TRUE), or not (FALSE, default). |
.tipToRoot
: a vector of named integers identifying nodes.
Thibaut Jombart tjombart@imperial.ac.uk
1 2 3 4 5 6 7 8 9 10 | if(require(ape) & require(phylobase)){
## make a tree
x <- as(rtree(20),"phylo4")
plot(x,show.node=TRUE)
## .tipToRoot
root <- rootNode(x)
.tipToRoot(x, 1, root)
lapply(1:nTips(x), function(i) .tipToRoot(x, i, root))
}
|
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