R: Shimodaira-Hasegawa Test

SH.test {phangorn} | R Documentation

## Shimodaira-Hasegawa Test

### Description

This function computes the Shimodaira–Hasegawa test for a set of trees.

### Usage

    SH.test(..., B = 10000, data = NULL, weight = NULL)

### Arguments

`...` | either a series of objects of class `"pml"` separated by commas, a list containing such objects or an object of class `"pmlPart"` or a matrix containing the site-wise likelihoods in columns.
`B` | the number of bootstrap replicates.
`data` | an object of class `"phyDat"`.
`weight` | if a matrix with site (log-)likelihoods is is supplied an optional vector containing the number of occurances of each site pattern.

### Value

a numeric vector with the P-value associated with each tree given in `...`.

### Author(s)

Klaus Schliep klaus.schliep@gmail.com

### References

Shimodaira, H. and Hasegawa, M. (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16, 1114–1116.

### See Also

`pml`, `pmlPart`, `pmlCluster`, `SOWH.test`

### Examples

    data(Laurasiatherian)
    dm <- dist.logDet(Laurasiatherian)
    tree1 <- NJ(dm)
    tree2 <- unroot(upgma(dm))
    fit1 <- pml(tree1, Laurasiatherian)
    fit2 <- pml(tree2, Laurasiatherian)
    fit1 <- optim.pml(fit1) # optimize edge weights
    fit2 <- optim.pml(fit2)
    # with pml objects as input
    SH.test(fit1, fit2, B=1000)
    # in real analysis use larger B, e.g. 10000

    # with matrix as input
    X <- matrix(c(fit1$siteLik, fit2$siteLik), ncol=2)
    SH.test(X, weight=attr(Laurasiatherian, "weight"), B=1000)
    ## Not run:
    example(pmlPart)
    SH.test(sp, B=1000)

    ## End(Not run)

[Package phangorn version 2.6.2 Index]