getTreeClades: Rboretum Clade Fetcher

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

Rboretum Clade Fetcher

Description

This function breaks down a rooted phylo or multiPhylo object into its respective monophyletic groups, sorted alphanumerically.

Usage

getTreeClades(tree, include_root, print_counts, return_counts, return_shared)

Arguments

tree	Tree(s) to split. Options include: A rooted phylo object A rooted multiPhylo object where all trees share 3+ taxa
include_root	OPTIONAL: If FALSE, don't include root clades as part of the return (Automatic if tree is rooted on a single taxon) [Default: TRUE, include root clades]
print_counts	OPTIONAL: If TRUE, print a summary table of unique splits and how many/which trees contain them [Default: FALSE, no printing]
return_counts	OPTIONAL: If TRUE, instead of returning a vector of clades, return a summary table of unique splits and how many/which trees contain them [Default: FALSE, return clades as sorted vector]
return_shared	OPTIONAL: If TRUE, instead of returning a vector of clades, return a vector of only those clades present in all trees [Default: FALSE, return all clades]

Value

Either:

• A character vector of monophyletic groups; or,

• A dataframe containing information about clades and their occurrence among trees

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