Wednesday, June 21, 2017

Generating a set of random resolutions of all the nodes in a tree with multifurcations

Today, an R-sig-phylo list member asked:

“I am using the ape package to randomly resolve polytomies using 'multi2di' and wondering if there is a way to use this function to get a single output tree file that contains multiple different randomly resolved trees using some number of resamplings?”

This can be done using the phytools function resolveNode, which returns all possible resolutions of a given node. We just iterate over all the nodes of the tree pick a random resolution each time.

Here's a function to do that:

resolveRandom<-function(tree){
    while(!is.binary(tree)){
        nodes<-1:tree$Nnode+Ntip(tree)
        Nchildren<-function(node,tree) length(Children(tree,node))
        nchilds<-sapply(nodes,Nchildren,tree=tree)
        node<-nodes[which(nchilds>2)[1]]
        tree<-sample(resolveNode(tree,node),1)[[1]]
    }
    tree
}

Here's a quick demo:

library(phytools)
library(phangorn)
tree<-read.tree(text="(((A1,A2),(B1,B2,B3),C,D),E,F);")
plotTree(tree,type="cladogram",nodes="centered")

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## now some random resolutions
plotTree(resolveRandom(tree),type="cladogram",nodes="centered")

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plotTree(resolveRandom(tree),type="cladogram",nodes="centered")

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plotTree(resolveRandom(tree),type="cladogram",nodes="centered")

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plotTree(resolveRandom(tree),type="cladogram",nodes="centered")

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We can also generate a set of resolutions using replicate:

trees<-replicate(36,resolveRandom(tree),simplify=FALSE)
class(trees)<-"multiPhylo"
par(mfrow=c(6,6))
plotTree(trees,type="cladogram",nodes="centered")

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That's it.

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