R: Swofford-Olsen-Waddell-Hillis Test

SOWH.test {phangorn} | R Documentation

## Swofford-Olsen-Waddell-Hillis Test

### Description

This function computes the Swofford–Olsen–Waddell–Hillis (SOWH) test, a parametric bootstrap test. The function is computational very demanding and likely to be very slow.

### Usage

    SOWH.test(x, n = 100, restricted = list(optNni = FALSE), optNni = TRUE,
      trace = 1, ...)

### Arguments

`x` | an object of class `"pml"`.
`n` | the number of bootstrap replicates.
`restricted` | list of restricted parameter settings.
`optNni` | Logical value indicating whether topology gets optimized (NNI).
`trace` | Show output during computations.
`...` | Further arguments passed to `"optim.pml"`.

### Details

`SOWH.test` performs a parametric bootstrap test to compare two trees. It makes extensive use `simSeq` and `optim.pml` and can take quite long.

### Value

an object of class SOWH. That is a list with three elements, one is a matrix containing for each bootstrap replicate the (log-) likelihood of the restricted and unrestricted estimate and two pml objects of the restricted and unrestricted model.

### Author(s)

Klaus Schliep klaus.schliep@gmail.com

### References

Goldman, N., Anderson, J. P., and Rodrigo, A. G. (2000) Likelihood -based tests of topologies in phylogenetics. Systematic Biology 49 652-670.

Swofford, D.L., Olsen, G.J., Waddell, P.J. and Hillis, D.M. (1996) Phylogenetic Inference in Hillis, D.M., Moritz, C. and Mable, B.K. (Eds.) Molecular Systematics (2nd ed.) 407-514, Sunderland, MA: Sinauer

### See Also

`pml`, `pmlPart`, `pmlCluster`, `simSeq`, `SH.test`

### Examples

    # in real analysis use larger n, e.g. 500 preferably more
    ## Not run:
    data(Laurasiatherian)
    dm <- dist.logDet(Laurasiatherian)
    tree <- NJ(dm)
    fit <- pml(tree, Laurasiatherian)
    fit <- optim.pml(fit, TRUE)
    set.seed(6)
    tree <- rNNI(fit$tree, 1)
    fit <- update(fit, tree = tree)
    (res <- SOWH.test(fit, n=100))
    summary(res)

    ## End(Not run)

[Package phangorn version 2.6.2 Index]