R: Position Leverage

position.leverage {distory} | R Documentation

## Position Leverage

### Description

Provides a rough heuristic for determining the degree to which each position in the DNA matrix affects the resulting tree.

### Usage

    position.leverage(data, F, to = NULL, rep = 50, by = 1)

### Arguments

`data` | A DNA matrix in `DNAbin` format.
`F` | A tree estimation function, accepting a DNA matrix of class `DNAbin` and returning a tree of class `phylo`.
`to` | The tree with which distances are measured in respect to, or `NULL` to indicate the tree estimated by `F` for the starting DNA matrix.
`rep` | The number of times to replicate the position in question.
`by` | The function will perform the calculation on every `by`-th position (that is, on `seq(1, N, by)`).

### Details

This function takes a DNA matrix and, for every `by`-th position, replicates that position `rep` times, randomly removing `rep` other positions to keep all sequences the same length other positions to keep all sequences the same length. For each new DNA matrix created in this way, `F` is used to estimate the corresponding tree, and the distance to tree `to` is computed and stored. This distance can be thought of as somewhat analogous to the leverage of that position.

### Value

Returns a numeric vector of distances from tree `to` for each position sampled.

### Author(s)

John Chakerian

### References

Chakerian, J. and Holmes, S. P. Computational Tools for Evaluating Phylogenetic and Heirarchical Clustering Trees. arXiv:1006.1015v1.

### See Also

`dist.multiPhylo`

### Examples

    data(woodmouse)
    f.est <- function(x) root(nj(dist.dna(x)), "No305", resolve.root = TRUE)
    position.leverage(woodmouse, f.est, by = 10)

[Package distory version 1.4.4 Index]