equiv.nodes: Get equivalences of nodes between phylogenies

In jacobmaugoust/ULT: Useful Little Things

Get equivalences of nodes between phylogenies

Description

For a given set of trees of close construction (i.e., tips in common), this function returns the equivalences in node labels (or numbers if no node labels are provided) for each node given the subtaxa of each

Usage

equiv.nodes(trees,nodes,equitips=NULL,out=c("matrix","vector"),out.collapse="/")

Arguments

trees	Phylogenetic trees to consider
nodes	Optional. The nodes to be compared; without specifying it, all nodes of all trees are compared. Can be the node number (from 1 to the number of nodes, or from the number of tips +1 to the number of tips + number of nodes)
equitips	Optional. If there are "equivalent tips" between phylogenies (i.e., same tip but not same label for that tip), they should be provided as a list of vectors, each containing the equivalent labels (the first one being to be used)
out	The type of output. Can be a matrix (if out="matrix", the default) with nodes as columns, phylogenies as rows, and node labels (or numbers) of the corresponding node for the given "global" node and phylogeny. Can be a vector (if out="vector") collating node labels (or numbers).
out.collapse	The way to collate node labels (or numbers) if a vector is desired as output. Default is set to "/"

Examples

require(ape)
require(phytools)
# Get three random trees of 20, 19, and 21 tips (hence with some tips not present in all trees)
## Start by having the larger tree, of 21 tips
set.seed(1)
tree<-rtree(21)
plot(tree)
axisPhylo()
## Removing taxon #10 to get the first other tree
arrows(nodeHeights(tree)[tree$edge[,2]==10,2]+0.3,10,nodeHeights(tree)[tree$edge[,2]==10,2]+0.13,10,length=0.1,lwd=3,col="red")
## Removing the taxa #5 and #14 for the second other tree
for(i in c(5,14)){
  arrows(nodeHeights(tree)[tree$edge[,2]==i,2]+0.3,i,nodeHeights(tree)[tree$edge[,2]==i,2]+0.13,i,length=0.1,lwd=3,col="green3")
}
trees<-c(drop.tip(tree,10),drop.tip(tree,c(5,14)),tree)

# Getting node equivalences
equiv.nodes(trees)
# Checking node names and equivalence
par(mfrow=c(1,3),mar=rep(0,4))
for(i in 1:3){
  plot(trees[[i]],show.tip.label = FALSE)
  nodelabels()
  tiplabels()
}

jacobmaugoust/ULT documentation built on May 16, 2023, 1:29 p.m.