geodesic_MDS: Geodesic implementation Calculates the geodesic distance...

In svteichman/TreeVizPackage: Tree Visualization Package

Geodesic implementation Calculates the geodesic distance between each tree

Description

Geodesic implementation Calculates the geodesic distance between each tree

Usage

geodesic_MDS(
  tree_path,
  nf = 2,
  names = NULL,
  consensus = "consensus",
  mds_package = "ade4"
)

Arguments

tree_path	The file path to a txt file containing phylogenetic trees in a multiPhylo object.
nf	The number of axes in the MDS to keep.
names	Optional tree names to use.
consensus	Optional name of the consensus tree.
mds_package	The default is to run classical MDS using ade4. To change this to metric MDS using the package smacof, use the argument mds_package = "smacof".

Value

A list containing an object 'dist_mat' containing geodesic distances between each phylogenetic tree in the multiPhylo object, and an object 'df' containing the desired number of axes in the MDS of the trees.

svteichman/TreeVizPackage documentation built on June 22, 2022, 11:21 p.m.