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<title>Genotype likelihood ratio distance (Dlr) — dlr • assigner</title>

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    <h1>Genotype likelihood ratio distance (Dlr)</h1>
    <small class="dont-index">Source: <a href='https://github.com/thierrygosselin/assigner/blob/master/R/dlr.R'><code>R/dlr.R</code></a></small>
    <div class="hidden name"><code>dlr.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>The function computes Paetkau's et al. (1997) genotype likelihood
ratio distance (Dlr).</p>
    </div>

    <pre class="usage"><span class='fu'>dlr</span><span class='op'>(</span>
  <span class='va'>data</span>,
  <span class='va'>strata</span>,
  plots <span class='op'>=</span> <span class='cn'>FALSE</span>,
  filename <span class='op'>=</span> <span class='cn'>NULL</span>,
  parallel.core <span class='op'>=</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>1</span>
<span class='op'>)</span></pre>

    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
    <table class="ref-arguments">
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>data</th>
      <td><p>The output assignment file (home likelihood or
likelihood ratio statistics) from GENODIVE.</p></td>
    </tr>
    <tr>
      <th>strata</th>
      <td><p>A tab delimited file with 2 columns with header:
<code>INDIVIDUALS</code> and <code>STRATA</code>.
The <code>STRATA</code> column is used here as the populations id of your sample.</p></td>
    </tr>
    <tr>
      <th>plots</th>
      <td><p>(optional) Generate Dlr plots for all the pairwise populations
in the dataset. The plots are <code>ggplot2</code> objects that can be modified with
the proper <code>ggplot2</code> syntax. Default: <code>plots = FALSE</code>.</p></td>
    </tr>
    <tr>
      <th>filename</th>
      <td><p>(optional) Name of the file prefix for
the matrix and the table written in the working directory.</p></td>
    </tr>
    <tr>
      <th>parallel.core</th>
      <td><p>(optional) The number of core for parallel computation.
Default: <code>parallel.core = parallel::detectCores() - 1</code>.</p></td>
    </tr>
    </table>

    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

    <p>A list with 5 objects:</p><ol>
<li><p>the assignment results ($assignment),</p></li>
<li><p>the dlr pairwise table ($dlr.table),</p></li>
<li><p>the lower diagonal dlr distance matrix ($dlr.dist),</p></li>
<li><p>a data.frame with the dlr distance mirrored ($dlr.matrix),</p></li>
<li><p>the list of dlr plots ($dlr.plots)</p></li>
</ol>

    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>

    <p>Paetkau D, Slade R, Burden M, Estoup A (2004)
Genetic assignment methods for the direct, real-time estimation of
migration rate: a simulation-based exploration of accuracy and power.
Molecular Ecology, 13, 55-65.</p>
<p>Paetkau D, Waits LP, Clarkson PL, Craighead L, Strobeck C (1997)
 An empirical evaluation of genetic distance statistics using microsatellite
  data from bear (Ursidae) populations. Genetics, 147, 1943-1957.</p>
<p>Meirmans PG, Van Tienderen PH (2004) genotype and genodive:
two programs for the analysis of genetic diversity of asexual organisms.
Molecular Ecology Notes, 4, 792-794.</p>
    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>

    <p>Thierry Gosselin <a href='mailto:thierrygosselin@icloud.com'>thierrygosselin@icloud.com</a></p>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='cn'>FALSE</span><span class='op'>)</span> <span class='op'>{</span>
<span class='va'>dlr</span> <span class='op'>&lt;-</span> <span class='fu'>assigner</span><span class='fu'>::</span><span class='fu'>dlr</span><span class='op'>(</span>
data <span class='op'>=</span> <span class='st'>"assignment.gdv"</span>, strata <span class='op'>=</span> <span class='st'>"my.strata.tsv"</span>, plots <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>

<span class='co'># to get the plots list:</span>
<span class='va'>plot.list</span> <span class='op'>&lt;-</span> <span class='va'>dlr</span><span class='op'>$</span><span class='va'>dlr.plots</span>
<span class='co'># access and isolate in different object a plot with $</span>
<span class='op'>}</span>
</div></pre>
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