| SH.test {phangorn} | R Documentation |
This function computes the Shimodaira–Hasegawa test for a set of trees.
SH.test(..., B = 10000, data = NULL)
... |
either a series of objects of class |
B |
the number of bootstrap replicates. |
data |
an object of class |
a numeric vector with the P-value associated with each tree given in
....
Klaus Schliep klaus.schliep@gmail.com
Shimodaira, H. and Hasegawa, M. (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16, 1114–1116.
pml, pmlPart, pmlCluster,
SOWH.test
data(Laurasiatherian) dm <- dist.logDet(Laurasiatherian) tree1 <- NJ(dm) tree2 <- unroot(upgma(dm)) fit1 <- pml(tree1, Laurasiatherian) fit2 <- pml(tree2, Laurasiatherian) fit1 <- optim.pml(fit1) # optimize edge weights fit2 <- optim.pml(fit2) SH.test(fit1, fit2, B=500) # in real analysis use larger B, e.g. 10000 ## Not run: example(pmlPart) SH.test(sp, B=1000) ## End(Not run)