sh.test {ape}R Documentation

Shimodaira-Hasegawa Test

Description

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

Usage

sh.test(..., x, model = DNAmodel(), B = 100)

Arguments

... either a series of objects of class "phylo" separated by commas, or a list containing such objects.
x a list, a matrix, or a data frame containing the (aligned) DNA sequences.
model the model to be fitted to each tree (as an object of "DNAmodel").
B the number of bootstrap replicates.

Details

The present implementation follows the original formulation of Shimodaira and Hasegawa (1999). A difference is that the bootstrap resampling is done on the original sequence data rather than the RELL method as sugested by Shimodaira and Hasegawa.

Value

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

Author(s)

Emmanuel Paradis Emmanuel.Paradis@mpl.ird.fr

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

mlphylo, DNAmodel

Examples

data(woodmouse)
t1 <- nj(dist.dna(woodmouse))
t2 <- rtree(15, tip.label = t1$tip.label)
t3 <- rtree(15, tip.label = t1$tip.label)
### Are the NJ tree and two random tress significantly different?
## Not run: sh.test(t1, t2, t3, x = woodmouse, B = 100)

[Package ape version 1.10-1 Index]