model_search_parallel

Clusters DNA alignment using independent loci model

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

model_search_parallel 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 starting partition.</dd>
<dt>round.types</dt>
<dd>A vector indicating which series of moves to make.</dd>
<dt>quiet</dt>
<dd>Whether to suppress progress information (default=FALSE).</dd>
<dt>n.extra.rounds</dt>
<dd>The number of additional rounds to perform after the default hierBAPS
settings (default=0). If set to Inf it will run until a local optimum is reached
(this might take a long time).</dd>
<dt>n.cores</dt>
<dd>The number of cores to use.</dd></dl>

Arguments

model_search_parallel — model_search_parallel

<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 starting partition.</dd>


<dt>round.types</dt>
<dd>A vector indicating which series of moves to make.</dd>


<dt>quiet</dt>
<dd>Whether to suppress progress information (default=FALSE).</dd>


<dt>n.extra.rounds</dt>
<dd>The number of additional rounds to perform after the default hierBAPS
settings (default=0). If set to Inf it will run until a local optimum is reached
(this might take a long time).</dd>


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

</dl>

model_search_parallel: model_search_parallel

Description

Usage

Value

Arguments