sh.test

0th

Percentile

Shimodaira-Hasegawa Test

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

Keywords
models
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 ....

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

Aliases
  • sh.test
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?
sh.test(t1, t2, t3, x = woodmouse, B = 100)
Documentation reproduced from package ape, version 2.1-1, License: GPL (>= 2)

Community examples

Looks like there are no examples yet.