ape (version 1.9-1)

sh.test: 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.

Value

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

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.

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

Run this code
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?
sh.test(t1, t2, t3, x = woodmouse, B = 100)

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