Linear MRCA function

Function to make the most recent common ancestor (MRCA) matrix of a tree, where entry (i,j) gives the MRCA of tips i and j. The function is linear, exploiting the fact that the tree is rooted.

linearMrca(tree, k = 0)

Arguments

tree

an object of the class phylo which should be rooted.

k

(optional) number of tips in tree, for faster computation

Author

Michelle Kendall michelle.louise.kendall@gmail.com

Examples

## generate a random tree
x <- rtree(6)

## create matrix of MRCAs: entry (i,j) is the node number of the MRCA of tips i and j
linearMrca(x,6)
#>      [,1] [,2] [,3] [,4] [,5] [,6]
#> [1,]    1    9    8    8    7    7
#> [2,]    9    2    8    8    7    7
#> [3,]    8    8    3   10    7    7
#> [4,]    8    8   10    4    7    7
#> [5,]    7    7    7    7    5   11
#> [6,]    7    7    7    7   11    6