R: Constrained neighbour-joining tree

ConstrainedNJ {TreeTools} | R Documentation

## Constrained neighbour-joining tree

### Description

Constructs an approximation to a neighbour-joining tree, modified in order to be consistent with a constraint. Zero-length branches are collapsed at random.

### Usage

    ConstrainedNJ(dataset, constraint, weight = 1L, ratio = TRUE, ambig = "mean")

### Arguments

`dataset` | A phylogenetic data matrix of class `phyDat`, whose names correspond to the labels of any accompanying tree.
`constraint` | An object of class `phyDat`; returned trees will be perfectly compatible with each character in `constraint`. See vignette for further examples.
`weight` | Numeric specifying degree to up-weight characters in `constraint`.
`ratio` | Settings of `ambig` and `ratio` to be used when computing `Hamming()` distances between sequences.
`ambig` | Settings of `ambig` and `ratio` to be used when computing `Hamming()` distances between sequences.

### Value

`ConstrainedNJ()` returns a tree of class `phylo`.

### Author(s)

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

### See Also

Other tree generation functions: `GenerateTree`, `NJTree()`, `SingleTaxonTree()`, `TreeNumber`

### Examples

    dataset <- MatrixToPhyDat(matrix(
      c(0, 1, 1, 1, 0, 1,
        0, 1, 1, 0, 0, 1), ncol = 2,
      dimnames = list(letters[1:6], NULL)))
    constraint <- MatrixToPhyDat(
      c(a = 0, b = 0, c = 0, d = 0, e = 1, f = 1))
    plot(ConstrainedNJ(dataset, constraint))

[Package TreeTools version 1.7.0 Index]