fixNodes: Standard Node Numbering in Phylo Objects

In heibl/ips: Interfaces to Phylogenetic Software in R

Standard Node Numbering in Phylo Objects

Description

(Re-)establishes the standard numbering of terminal and internal nodes in phylogenies represented as objects of class phylo.

Usage

fixNodes(phy)

Arguments

phy	An object of class phylo.

Details

Internal and terminal nodes of phylo objects have a standard, "canonical" node numbering. It consists of the following rules:

1. Number tip nodes from left/bottom to right/top by 1 to ntip()

2. Number internal nodes by preorder traversal (see Examples) consecutively from ntip() + 1 to nnode() + 1

When reading phylogenetic trees from a NEXUS file that contains a translate section, it can happen that the terminal nodes (tips, leaves) of the corresponding phylo object are not numbered consecutively, which can be a problem in some downstream applications. You can use fixNodes to get the correct order of terminal node numbers.

fixNodes is also intended to re-establish the standard numbering of internal nodes and reorder all node value elements (e.g. node.label, posterior, ...) if a phylo object has been modified by either root, ladderize, or rotate.

Value

An object of class phylo.

Note

fixNodes has been completely rewritten for ips version 1.0-0. It should now run absolutely stable and is much quicker. Nevertheless, I recommend checking carefully the results of fixNodes, until the function has been tested by a number of users. Then this comment will be removed.

See Also

read.tree, read.nexus, read.beast for reading trees in NEWICK and NEXUS format; ladderize and rotate for tree manipulation; node.support for plotting node support values has been moved to package viper. non-standard node elements in class phylo.

Examples

set.seed(9999)

# Create random topology with random node numbering
phy1 <- rtopology(10)

# Impose 'canonical' node numbering
phy2 <- fixNodes(phy1)

# Compare node numbering schemes
op = par(no.readonly = TRUE)
par(mfcol = c(1, 2), mar = c(0, 0, 3, 0))
plot(phy1, use.edge.length = FALSE, show.tip.label = FALSE)
nodelabels(); tiplabels()
title("random node numbers")
plot(phy2, use.edge.length = FALSE, show.tip.label = FALSE)
nodelabels(); tiplabels()
title("preorder traversal of internal nodes")
par(op)

heibl/ips documentation built on Feb. 20, 2025, 12:08 p.m.