# distRoot: Compute the distance of tips to the root In adephylo: Exploratory Analyses for the Phylogenetic Comparative Method

 distRoot R Documentation

## 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.

`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)
}

```

adephylo documentation built on Oct. 19, 2022, 5:15 p.m.