adephylo: distRoot – R documentation

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distRoot

Compute the distance of tips to the root

Description

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.

Usage

distRoot(x, tips = "all", method = c("patristic", "nNodes", "Abouheif",
  "sumDD"))

Arguments

`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.
`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)

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.

Value

A numeric vector containing one distance value for each tip.

Author(s)

Thibaut Jombart tjombart@imperial.ac.uk

References

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.

Examples

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)
}

adephylo

Exploratory Analyses for the Phylogenetic Comparative Method

v1.1-11

GPL (>= 2)

Authors

Thibaut Jombart <t.jombart@imperial.ac.uk>, Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anders Ellern Bilgrau <abilgrau@math.aau.dk>

Initial release

2017-12-18