distRoot | R Documentation |
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.
distRoot(
x,
tips = "all",
method = c("patristic", "nNodes", "Abouheif", "sumDD")
)
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.
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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