countTrees: Calculate the number of times a set of topologies occur

In coleoguy/evobir: Evolutionary Biology in R

Calculate the number of times a set of topologies occur

Description

This function counts the number of times that a set of topologies is present in a collection of trees.

Usage

countTrees(collection = NULL, ref = NULL, classes = T, verbose=T)

Arguments

collection	path to a collection of trees in a Newick format file
ref	path to a Newick format file with the topologies of interest
classes	if T then will return a vector with classification of each tree
verbose	returns intermediate progress messages if TRUE

Value

If classes is T returns a list with the first element being a numeric vector of the same length as the number of trees in the ref file. The elements of the returned vector correspond to the occurences of trees in the collection file that match the topologies supplied in the ref file. The second element is a vector the same length as the input tree collection and each tree is assigned a number based on the topology it matches.

Author(s)

Heath Blackmon

References

http://coleoguy.github.io/

coleoguy/evobir documentation built on May 8, 2024, 6:57 p.m.