phangorn: SOWH.test – R documentation

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SOWH.test

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

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)

phangorn

Phylogenetic Reconstruction and Analysis

v2.7.0

GPL (>= 2)

Authors

Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>), Leonardo de Oliveira Martins [aut] (<https://orcid.org/0000-0001-5247-1320>), Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam Revell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb], Brian O'Meara [ctb], Long Qu [ctb]

Initial release