step.cluster: Obtain paraphyletic clusters

In PoonLab/clustuneR: Molecular clustering implementation and predictive optimization

Obtain paraphyletic clusters

Description

Clusters are defined as a group of tips diverging from a high confidence common ancestor. Divergence must be done through a series of short branches, which the branch.thresh constrains.

Usage

step.cluster(obj, branch.thresh = 0.03, boot.thresh = 0, setID = 0)

Arguments

obj:	S3 object of class "phylo". The input tree file, extended to be annotated with vertex, edge and growth information.
branch.thresh:	The maximum branch length criterion defining clusters. A branch exceeding this value separates the tip from it's ancestor's cluster. Higher values imply larger average cluster sizes.
boot.thresh:	The minimum bootstrap criterion defining clusters. Lower values imply larger average cluster size
setID:	A numeric identifier for this cluster set.

Value

: A set of clusters as a data.table. See example cluster.ex object documentation for an example of clustered sequence data + meta data

Examples

step.cluster.set <- step.cluster(extended.tree.ex, branch.thresh = 0.03, boot.thresh = 0)

step.cluster.set[which.max(Size), ]

PoonLab/clustuneR documentation built on Jan. 29, 2024, 2:40 a.m.