adephylo (version 1.1-16)

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")
)

Value

A numeric vector containing one distance value for each tip.

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)

Author

Thibaut Jombart

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.

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.

See Also

distTips which computes the same phylogenetic distances, but between tips.

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)
}