choose_cluster: Choose an ultrametric phylo object from...

In datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

Choose an ultrametric phylo object from cluster_patristicmatrix() obtained with a particular clustering method, or the next best tree. If there are no ultrametric trees, it does not force them to be ultrametric.

Description

Choose an ultrametric phylo object from cluster_patristicmatrix() obtained with a particular clustering method, or the next best tree. If there are no ultrametric trees, it does not force them to be ultrametric.

Usage

choose_cluster(phycluster, clustering_method = "nj")

Arguments

phycluster

An output from cluster_patristicmatrix()

clustering_method

A character vector indicating the method to construct the tree. Options are: nj Neighbor-Joining method applied with ape::nj(). upgma Unweighted Pair Group Method with Arithmetic Mean method applied with phangorn::upgma(). bionj An improved version of the Neighbor-Joining method applied with ape::bionj(). triangle Triangles method applied with ape::triangMtd() mvr Minimum Variance Reduction method applied with ape::mvr().

Value

A phylo object or NA.

datelife documentation built on July 10, 2023, 2:02 a.m.