checkTips: Rboreturm Tip Checker (X)

In BobLiterman/Rboretum: Compare Phylogenetic Trees and Alignment Support Values

Rboreturm Tip Checker (X)

Description

This function returns TRUE if all 'taxa' are present in 'tree' (or a multiPhylo of trees); FALSE otherwise. If multiPhylo, all comparisons are made on the common set of taxa.

Usage

checkTips(tree, taxa, check_mono, check_root)

Arguments

tree	Tree(s) to check. Options include: A phylo object A multiPhylo object where all trees share 3+ taxa
taxa	Taxon labels to check. Can be: A character vector of tip labels A semicolon-separated list of labels
check_mono	OPTIONAL: If TRUE, also query whether 'taxa' are monophyletic in tree(s) [Default: FALSE]
check_root	OPTIONAL: If TRUE, also query whether 'taxa' are monophyletic and make up one of the two root splits in tree(s) [Default: FALSE]

Value

TRUE if all 'taxa' in 'tree'; else, FALSE (barring other selected options)

Examples

# Check if all labels in 'myTaxa' are present in phylo object 'myTree'
myTaxa <- c('Species_1','Species_2','Species_3')
checkTips(myTree,myTaxa)
# Check if all labels in 'myTaxa' are present in all trees in multiPhylo object 'myTrees'
checkTips(myTrees,myTaxa)
# Check if clade 'myTaxa' are monophyletic in phylo object 'myTree'
checkTips(myTree,myTaxa,check_mono=TRUE)
# Check if clade 'myTaxa' are one of the two root splits in phylo object 'myTree' 
checkTips(myTree,myTaxa,check_root=TRUE)

BobLiterman/Rboretum documentation built on July 6, 2023, 7:46 p.m.