phangorn (version 2.0.3)

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".

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 objetcs of the restricted and unrestricted model.

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.

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
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)