Description Usage Arguments Details Value Author(s) References See Also Examples

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.

1 2 |

`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.

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
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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