Collapse and Resolve Multichotomies
These two functions collapse or resolve multichotomies in phylogenetic trees.
multi2di(phy, ...) ## S3 method for class 'phylo' multi2di(phy, random = TRUE, equiprob = TRUE, ...) ## S3 method for class 'multiPhylo' multi2di(phy, random = TRUE, equiprob = TRUE, ...) di2multi(phy, ...) ## S3 method for class 'phylo' di2multi(phy, tol = 1e-08, ...) ## S3 method for class 'multiPhylo' di2multi(phy, tol = 1e-08, ...)
phy |
an object of class |
random |
a logical value specifying whether to resolve the
multichotomies randomly (the default) or in the order they appear in
the tree (if |
equiprob |
a logical value: should topologies generated in equal
probabilities; see details in |
tol |
a numeric value giving the tolerance to consider a branch length significantly greater than zero. |
... |
arguments passed among methods. |
multi2di
transforms all multichotomies into a series of
dichotomies with one (or several) branch(es) of length zero.
di2multi
deletes all branches smaller than tol
and
collapses the corresponding dichotomies into a multichotomy.
an object of the same class than the input.
Emmanuel Paradis
data(bird.families) is.binary(bird.families) is.binary(multi2di(bird.families)) all.equal(di2multi(multi2di(bird.families)), bird.families) ### To see the results of randomly resolving a trichotomy: tr <- read.tree(text = "(a:1,b:1,c:1);") layout(matrix(1:4, 2, 2)) for (i in 1:4) plot(multi2di(tr), use.edge.length = FALSE, cex = 1.5) layout(1)
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