Description Usage Arguments Details Value Author(s) References See Also Examples
The function distRoot
computes the distance of a set of tips to
the root. Several distances can be used, defaulting to the sum of
branch lengths.
1 |
x |
a tree of class |
tips |
A vector of integers identifying tips by their numbers, or a vector of characters identifying tips by their names. |
method |
a character string (full or abbreviated without
ambiguity) specifying the method used to compute distances ;
possible values are: |
Abouheif
distance refers to the phylogenetic distance
underlying the test of Abouheif (see references). Let P be the set of
all the nodes in the path going from node1
to node2
. Let
DDP be the number of direct descendants from each node in P. Then, the
so-called 'Abouheif' distance is the product of all terms in DDP.
sumDD
refers to a phylogenetic distance quite similar to that
of Abouheif. We consider the same sets P and DDP. But instead of
computing the product of all terms in DDP, this distance computes the
sum of all terms in DDP.
A numeric vector containing one distance value for each tip.
Thibaut Jombart tjombart@imperial.ac.uk
Pavoine, S.; Ollier, S.; Pontier, D. & Chessel, D. (2008) Testing for phylogenetic signal in life history variable: Abouheif's test revisited. Theoretical Population Biology: 73, 79-91.
distTips
which computes the same phylogenetic
distances, but between tips.
1 2 3 4 5 6 7 8 9 10 11 12 13 | if(require(ape) & require(phylobase)){
## make a tree
x <- as(rtree(50),"phylo4")
## compute 4 different distances
met <- c("patristic","nNodes","Abouheif","sumDD")
D <- lapply(met, function(e) distRoot(x, method=e) )
names(D) <- met
D <- as.data.frame(D)
## plot these distances along with the tree
temp <- phylo4d(x, D)
table.phylo4d(temp, show.node=FALSE, cex.lab=.6)
}
|
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