calc_change_in_ml

Calculate the change in the log marginal likelihood after moving index to each possible 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

calc_change_in_ml function

<dl><dt>snp.object</dt>
<dd>A snp.object containing the processed SNP data.</dd>
<dt>partition</dt>
<dd>An integer vector indicating a partition of the isolates.</dd>
<dt>indexes</dt>
<dd>Indexes of the isolates to be moved (must come from one cluster.)</dd></dl>

Arguments

calc_change_in_ml — calc_change_in_ml

<dl>

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


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


<dt>indexes</dt>
<dd>Indexes of the isolates to be moved (must come from one cluster.)</dd>

</dl>

calc_change_in_ml: calc_change_in_ml

Description

Usage

Value

Arguments