R: Convert phylogenetic tree to 'ClusterTable'

ClusterTable {TreeTools} | R Documentation

## Convert phylogenetic tree to `ClusterTable`

### Description

`as.ClusterTable()` converts a phylogenetic tree to a `ClusterTable` object, which is an internal representation of its splits suitable for rapid tree distance calculation (per Day, 1985).

### Usage

    as.ClusterTable(x, tipLabels = NULL, ...)

    ## S3 method for class 'phylo'
    as.ClusterTable(x, tipLabels = NULL, ...)

    ## S3 method for class 'list'
    as.ClusterTable(x, tipLabels = NULL, ...)

    ## S3 method for class 'multiPhylo'
    as.ClusterTable(x, tipLabels = NULL, ...)

### Arguments

`x` | Object to convert into `ClusterTable`: perhaps a tree of class `phylo`.
`tipLabels` | Character vector specifying sequence in which to order tip labels.
`...` | Presently unused.

### Details

Each row of a cluster table relates to a clade on a tree rooted on tip 1. Tips are numbered according to the order in which they are visited in preorder: i.e., if plotted using `plot(x)`, from the top of the page downwards. A clade containing the tips 2 .. 5 would be denoted by the entry `2, 5`, in either row 2 or row 5 of the cluster table.

### Value

`as.ClusterTable()` returns an object of class `ClusterTable`.

### Author(s)

Martin R. Smith (martin.smith@durham.ac.uk)

### References

Day WHE (1985). “Optimal algorithms for comparing trees with labeled leaves.” Journal of Classification, 2(1), 7–28. doi: 10.1007/BF01908061.

### See Also

S3 methods for `ClusterTable` objects.

### Examples

    tree1 <- ape::read.tree(text = "(A, (B, (C, (D, E))));");
    tree2 <- ape::read.tree(text = "(A, (B, (D, (C, E))));");
    ct1 <- as.ClusterTable(tree1)
    summary(ct1)
    as.matrix(ct1)

    # Tip label order must match ct1 to allow comparison
    ct2 <- as.ClusterTable(tree2, tipLabels = LETTERS[1:5])

[Package TreeTools version 1.7.2 Index]