distTips {adephylo} | R Documentation |
The function distTips
computes a given distance between a set
of tips of a phylogeny. A vector of tips is supplied: distances
between all possible pairs of these tips are computed.
The distances are computed from the shortest path
between the tips. Several distances can be used, defaulting to the
sum of branch lengths (see argument method
).
distTips(x, tips, method=c("patristic","nNodes","Abouheif","sumDD"))
x |
a tree of class phylo ,
phylo4 or phylo4d. |
tips |
A vector of integers identifying tips by their numbers, or a vector of characters identifying tips by their names. Distances will be computed between all possible pairs of tips. |
method |
a character string (full or abbreviated without
ambiguity) specifying the method used to compute distances ;
possible values are: - patristic : patristic distance, i.e. sum of branch lengths - nNodes : number of nodes on the path between the nodes - Abouheif : Abouheif's distance (see details) - sumDD : sum of direct descendants of all nodes on the path
(see details) |
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.
An object of class dist
, containing phylogenetic distances.
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 several phylogenetic
distances between tips.
if(require(ape) & require(phylobase)){ ## make a tree x <- as(rtree(10),"phylo4") plot(x, show.node=TRUE) axisPhylo() ## compute different distances distTips(x, 1:3) distTips(x, 1:3, "nNodes") distTips(x, 1:3, "Abouheif") distTips(x, 1:3, "sumDD") }