calc_log_ml

Calculate the log marginal likelihood assuming a Multinomial-Dirichlet distribution

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_log_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></dl>

Arguments

calc_log_ml — calc_log_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>

</dl>

calc_log_ml: calc_log_ml

Description

Usage

Value

Arguments