extractClade: Extract multiple subclades from a phylogeny based on node...

In eliotmiller/addTaxa: An R package for adding missing taxa to phylogenies

Extract multiple subclades from a phylogeny based on node numbers

Description

Given a tree and a vector or list of nodes, this function extracts subclades and returns a list of smaller trees.

Usage

extractClade(tree, nodes, root.edge = 0)

Arguments

tree	An ape-style phylogenetic tree.
nodes	A named list or vector of node numbers that subtend the clade in question to extract. Can extract and create single species trees with appropriate branch length. The input vector or list must have names!
root.edge	Default is 0, meaning that no stem is left below the node from which the subclade is extracted. If root.edge is 1, then a root edge (stem) is also included with the extracted clade.

Details

Given a named list or vector of node numbers that subtend one or more clades, extracts those clades and returns a list of trees. The nodes provided must have names, though the tree itself does not need to have named nodes. This is because the output trees are provided with these names, which are used in further downstream analyses. If the node provided relates to a tip, then the tree that is returned contains the stem length from the ancestor of that species to the tip in question.

Value

A named list of trees.

References

Mast et al. 2015. Paraphyly changes understanding of timing and tempo of diversification in subtribe Hakeinae (Proteaceae), a giant Australian plant radiation. American Journal of Botany.

Examples

#load a molecular tree up
data(bird.families)

#define a named vector of node numbers, including a root
temp <- c()
temp[1] <- length(bird.families$tip.label) + 1
names(temp) <- "root"

#create a data frame of all taxa from the phylogeny, and make up clade memberships
#for each. note that the names on this data frame differ from "groupings" in other
#functions
dummy.frame <- data.frame(species=bird.families$tip.label, 
clade=c(rep("nonPasserine", 95), rep("suboscine", 9), rep("basalOscine", 13), 
rep("oscine", 20)))

#use the function getMRCAs() to determine the nodes subtending these named clades
nodes <- getMRCAs(bird.families, dummy.frame)
#unlist the results and append to the root node defined above
nodes <- append(temp, nodes)

#use the function. note the effect of including a root edge or not. also note that 
#because non-passerines are not monophyletic, the "subtree" corresponding to that
#"clade" is the whole tree
temp1 <- extractClade(bird.families, nodes)
temp2 <- extractClade(bird.families, nodes, root.edge=1)
plot(temp1$oscine, root.edge=TRUE)
plot(temp2$oscine, root.edge=TRUE)

eliotmiller/addTaxa documentation built on Feb. 3, 2024, 12:19 a.m.