clustPAM: Cluster phylogenetic tree using PAM

In rainali475/ClustPhy: Phylogenetic Trees Clustering

Description

A function that calculates optimal tree clustering scheme using PAM method given the number of clusters, file directory for a phylogenetic tree or a newick tree character string.

Usage

clustPAM(k, file = "", text = NULL)

Arguments

k	A positive integer greater than 1 indicating the number of clusters.
file	A character string indicating the path to the newick tree. Default value is "".
text	A character string of the tree in newick format. Default value is NULL. By default, this is ignored. When this argument is assigned a value, the argument file is ignored.

Value

Returns an S3 object of class PAMclusts with results.

• distM - A distance matrix of tree leaves.

• phyloTree - An S3 object of class phylo, containing tree information.

• clustering - A positive integer vector indicating the clusters assigned to each leaf.

• medoids - A character vector indicating names of leaves that have been assigned as cluster centers.

• stats - A matrix containing parameters for each cluster. The columns are "size", "max_diss", "av_diss", "diameter", and "separation". Each row represents a computed cluster.

  • size - number of leaves in the cluster.

  • max_diss - maximum dissimilarity between leaves in the cluster and center of the cluster.

  • av_diss - average dissimilarity between leaves in the cluster and center of the cluster.

  • diameter - maximum dissimilarity between two leaves in the cluster.

  • separation - minimum dissimilarity between one leaf of this cluster and one leaf of another cluster.

References

Kaufman, L., & Rousseeuw, P. J. (2005). Finding groups in data: An introduction to cluster analysis. Wiley.

Examples

# Make 6 clusters from a newick tree using PAM
pam <- clustPAM(6, text = NwkTree2)

rainali475/ClustPhy documentation built on Dec. 22, 2021, 12:03 p.m.