sh.test {ape} | R Documentation |
This function computes the Shimodaira–Hasegawa test for a set of trees.
sh.test(..., x, model = DNAmodel(), B = 100)
... |
either a series of objects of class "phylo"
separated by commas, or a list containing such objects. |
x |
a list or a matrix 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. |
The present implementation follows the original formulation of Shimodaira and Hasegawa (1999) with the difference that the bootstrap resampling is done on the original sequence data rather than the RELL method suggested by Shimodaira and Hasegawa.
a numeric vector with the P-value associated with each tree given in
...
.
Emmanuel Paradis Emmanuel.Paradis@mpl.ird.fr
Shimodaira, H. and Hasegawa, M. (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16, 1114–1116.
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)