multi2di: Collapse and Resolve Multichotomies In ape: Analyses of Phylogenetics and Evolution

Description

These two functions collapse or resolve multichotomies in phylogenetic trees.

Usage

 1 2 3 4 5 6 7 8 9 10 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, ...)

Arguments

 phy an object of class "phylo" or "multiPhylo". random a logical value specifying whether to resolve the multichotomies randomly (the default) or in the order they appear in the tree (if random = FALSE). equiprob a logical value: should topologies generated in equal probabilities; see details in rtree (ignored if random = FALSE). tol a numeric value giving the tolerance to consider a branch length significantly greater than zero. ... arguments passed among methods.

Details

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.

Value

an object of the same class than the input.

is.binary

Examples

 1 2 3 4 5 6 7 8 9 10 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)

Example output FALSE
 TRUE
 TRUE

ape documentation built on Jan. 7, 2022, 5:14 p.m.