split_clusters_3

Peform an iteration of the third move in the algorithm. That is split cluster in two
and re-allocate one sub-cluster.

Implements the hierarchical Bayesian analysis of populations structure (hierBAPS)
algorithm of Cheng et al. (2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences
from multiple sequence alignments in FASTA format.
The implementation includes improved defaults and plotting capabilities
and unlike the original 'MATLAB' version removes singleton SNPs by default.

Gerry Tonkin-Hill

rhierbaps

Clustering Genetic Sequence Data Using the HierBAPS Algorithm

split_clusters_3 function

<dl><dt>snp.object</dt>
<dd>A snp.object containing the processed SNP data.</dd>
<dt>partition</dt>
<dd>An integer vector indicating an initial partition of the isolates.</dd>
<dt>threshold</dt>
<dd>The increase in marginal log likelihood required to accept a move.</dd>
<dt>min.clust.size</dt>
<dd>Clusters smaller than min.clust.size will not be split.</dd>
<dt>n.cores</dt>
<dd>The number of cores to use.</dd></dl>

Arguments

split_clusters_3 — split_clusters_3

<dl>

<dt>snp.object</dt>
<dd>A snp.object containing the processed SNP data.</dd>


<dt>partition</dt>
<dd>An integer vector indicating an initial partition of the isolates.</dd>


<dt>threshold</dt>
<dd>The increase in marginal log likelihood required to accept a move.</dd>


<dt>min.clust.size</dt>
<dd>Clusters smaller than min.clust.size will not be split.</dd>


<dt>n.cores</dt>
<dd>The number of cores to use.</dd>

</dl>

split_clusters_3: split_clusters_3

Description

Usage

Value

Arguments