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<title>A class for dataset groups for mkin — mkindsg • mkin</title>


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    <h1>A class for dataset groups for mkin</h1>
    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinds.R'><code>R/mkinds.R</code></a></small>
    <div class="hidden name"><code>mkindsg.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>A container for working with datasets that share at least one compound,
so that combined evaluations are desirable.</p>
<p>Time normalisation factors are initialised with a value of 1 for each
dataset if no data are supplied.</p>
    </div>

    <pre class="usage"><span class='co'># S3 method for mkindsg</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span>, verbose <span class='op'>=</span> <span class='va'>data</span>, <span class='va'>...</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>x</th>
      <td><p>An mkindsg object.</p></td>
    </tr>
    <tr>
      <th>data</th>
      <td><p>Should the mkinds objects be printed with their data?</p></td>
    </tr>
    <tr>
      <th>verbose</th>
      <td><p>Should the mkinds objects be printed?</p></td>
    </tr>
    <tr>
      <th>...</th>
      <td><p>Not used.</p></td>
    </tr>
    </table>

    <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>

    <p><div class="r6-fields"></p><dl>
<dt><code>title</code></dt><dd><p>A title for the dataset group</p></dd>

<dt><code>ds</code></dt><dd><p>A list of mkinds objects</p></dd>

<dt><code>observed_n</code></dt><dd><p>Occurrence counts of compounds in datasets</p></dd>

<dt><code>f_time_norm</code></dt><dd><p>Time normalisation factors</p></dd>

<dt><code>meta</code></dt><dd><p>A data frame with a row for each dataset,
containing additional information in the form
of categorical data (factors) or numerical data
(e.g. temperature, moisture,
or covariates like soil pH).</p></dd>

</dl><p></div></p>
    <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>

    
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Public methods</h3>

<ul>
<li><p><a href='#method-new'><code>mkindsg$new()</code></a></p></li>
<li><p><a href='#method-clone'><code>mkindsg$clone()</code></a></p></li>
</ul>
<p><hr>
<a id="method-new"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>new()</code></h3>
<p>Create a new mkindsg object</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>mkindsg</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span>title <span class='op'>=</span> <span class='st'>""</span>, <span class='va'>ds</span>, f_time_norm <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>meta</span><span class='op'>)</span></pre><p></div></p>

<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4>
<p><div class="arguments"></p><dl>
<dt><code>title</code></dt><dd><p>The title</p></dd>

<dt><code>ds</code></dt><dd><p>A list of mkinds objects</p></dd>

<dt><code>f_time_norm</code></dt><dd><p>Time normalisation factors</p></dd>

<dt><code>meta</code></dt><dd><p>The meta data</p></dd>

</dl><p></div></p>
<p><hr>
<a id="method-clone"></a></p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Method <code>clone()</code></h3>
<p>The objects of this class are cloneable with this method.</p><h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Usage</h4>
<p><div class="r"></p><pre><span class='va'>mkindsg</span><span class='op'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>

<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4>
<p><div class="arguments"></p><dl>
<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>

</dl><p></div></p>



    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'>
<span class='va'>mdsg</span> <span class='op'>&lt;-</span> <span class='va'>mkindsg</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"Experimental X"</span>, <span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span><span class='op'>)</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>mdsg</span><span class='op'>)</span>
</div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 5 mkinds objects
#&gt; Title $title:  Experimental X 
#&gt; Occurrence of observed compounds $observed_n:
#&gt; parent     A1 
#&gt;      5      5 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>mdsg</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 5 mkinds objects
#&gt; Title $title:  Experimental X 
#&gt; Occurrence of observed compounds $observed_n:
#&gt; parent     A1 
#&gt;      5      5 
#&gt; 
#&gt; Datasets $ds:
#&gt; &lt;mkinds&gt; with $title:  Soil 6 
#&gt; Observed compounds $observed:  parent, A1 
#&gt; Sampling times $sampling_times:
#&gt; 0, 3, 6, 10, 20, 34, 55, 90, 112, 132 
#&gt; With a maximum of  2  replicates
#&gt; Time unit:  days 
#&gt; Observation unit:  \%AR 
#&gt; 
#&gt; &lt;mkinds&gt; with $title:  Soil 7 
#&gt; Observed compounds $observed:  parent, A1 
#&gt; Sampling times $sampling_times:
#&gt; 0, 3, 7, 14, 30, 60, 90, 120, 180 
#&gt; With a maximum of  2  replicates
#&gt; Time unit:  days 
#&gt; Observation unit:  \%AR 
#&gt; 
#&gt; &lt;mkinds&gt; with $title:  Soil 8 
#&gt; Observed compounds $observed:  parent, A1 
#&gt; Sampling times $sampling_times:
#&gt; 0, 1, 3, 8, 14, 27, 48, 70 
#&gt; With a maximum of  2  replicates
#&gt; Time unit:  days 
#&gt; Observation unit:  \%AR 
#&gt; 
#&gt; &lt;mkinds&gt; with $title:  Soil 9 
#&gt; Observed compounds $observed:  parent, A1 
#&gt; Sampling times $sampling_times:
#&gt; 0, 1, 3, 8, 14, 27, 48, 70, 91, 120 
#&gt; With a maximum of  2  replicates
#&gt; Time unit:  days 
#&gt; Observation unit:  \%AR 
#&gt; 
#&gt; &lt;mkinds&gt; with $title:  Soil 10 
#&gt; Observed compounds $observed:  parent, A1 
#&gt; Sampling times $sampling_times:
#&gt; 0, 8, 14, 21, 41, 63, 91, 120 
#&gt; With a maximum of  2  replicates
#&gt; Time unit:  days 
#&gt; Observation unit:  \%AR </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>mdsg</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 5 mkinds objects
#&gt; Title $title:  Experimental X 
#&gt; Occurrence of observed compounds $observed_n:
#&gt; parent     A1 
#&gt;      5      5 
#&gt; 
#&gt; Datasets $ds:
#&gt; &lt;mkinds&gt; with $title:  Soil 6 
#&gt; Observed compounds $observed:  parent, A1 
#&gt; Sampling times $sampling_times:
#&gt; 0, 3, 6, 10, 20, 34, 55, 90, 112, 132 
#&gt; With a maximum of  2  replicates
#&gt; Time unit:  days 
#&gt; Observation unit:  \%AR 
#&gt;    time parent   A1
#&gt; 1     0   97.2   NA
#&gt; 2     0   96.4   NA
#&gt; 3     3   71.1  4.3
#&gt; 4     3   69.2  4.6
#&gt; 5     6   58.1  7.0
#&gt; 6     6   56.6  7.2
#&gt; 7    10   44.4  8.2
#&gt; 8    10   43.4  8.0
#&gt; 9    20   33.3 11.0
#&gt; 10   20   29.2 13.7
#&gt; 11   34   17.6 11.5
#&gt; 12   34   18.0 12.7
#&gt; 13   55   10.5 14.9
#&gt; 14   55    9.3 14.5
#&gt; 15   90    4.5 12.1
#&gt; 16   90    4.7 12.3
#&gt; 17  112    3.0  9.9
#&gt; 18  112    3.4 10.2
#&gt; 19  132    2.3  8.8
#&gt; 20  132    2.7  7.8
#&gt; 
#&gt; &lt;mkinds&gt; with $title:  Soil 7 
#&gt; Observed compounds $observed:  parent, A1 
#&gt; Sampling times $sampling_times:
#&gt; 0, 3, 7, 14, 30, 60, 90, 120, 180 
#&gt; With a maximum of  2  replicates
#&gt; Time unit:  days 
#&gt; Observation unit:  \%AR 
#&gt;    time parent   A1
#&gt; 1     0   93.6   NA
#&gt; 2     0   92.3   NA
#&gt; 3     3   87.0  3.9
#&gt; 4     3   82.2  3.1
#&gt; 5     7   74.0  6.9
#&gt; 6     7   73.9  6.6
#&gt; 7    14   64.2 10.4
#&gt; 8    14   69.5  8.3
#&gt; 9    30   54.0 14.4
#&gt; 10   30   54.6 13.7
#&gt; 11   60   41.1 22.1
#&gt; 12   60   38.4 22.3
#&gt; 13   90   32.5 27.5
#&gt; 14   90   35.5 25.4
#&gt; 15  120   28.1 28.0
#&gt; 16  120   29.0 26.6
#&gt; 17  180   26.5 25.8
#&gt; 18  180   27.6 25.3
#&gt; 
#&gt; &lt;mkinds&gt; with $title:  Soil 8 
#&gt; Observed compounds $observed:  parent, A1 
#&gt; Sampling times $sampling_times:
#&gt; 0, 1, 3, 8, 14, 27, 48, 70 
#&gt; With a maximum of  2  replicates
#&gt; Time unit:  days 
#&gt; Observation unit:  \%AR 
#&gt;    time parent   A1
#&gt; 1     0   91.9   NA
#&gt; 2     0   90.8   NA
#&gt; 3     1   64.9  9.6
#&gt; 4     1   66.2  7.7
#&gt; 5     3   43.5 15.0
#&gt; 6     3   44.1 15.1
#&gt; 7     8   18.3 21.2
#&gt; 8     8   18.1 21.1
#&gt; 9    14   10.2 19.7
#&gt; 10   14   10.8 18.9
#&gt; 11   27    4.9 17.5
#&gt; 12   27    3.3 15.9
#&gt; 13   48    1.6  9.5
#&gt; 14   48    1.5  9.8
#&gt; 15   70    1.1  6.2
#&gt; 16   70    0.9  6.1
#&gt; 
#&gt; &lt;mkinds&gt; with $title:  Soil 9 
#&gt; Observed compounds $observed:  parent, A1 
#&gt; Sampling times $sampling_times:
#&gt; 0, 1, 3, 8, 14, 27, 48, 70, 91, 120 
#&gt; With a maximum of  2  replicates
#&gt; Time unit:  days 
#&gt; Observation unit:  \%AR 
#&gt;    time parent   A1
#&gt; 1     0   99.8   NA
#&gt; 2     0   98.3   NA
#&gt; 3     1   77.1  4.2
#&gt; 4     1   77.2  3.9
#&gt; 5     3   59.0  7.4
#&gt; 6     3   58.1  7.9
#&gt; 7     8   27.4 14.5
#&gt; 8     8   29.2 13.7
#&gt; 9    14   19.1 14.2
#&gt; 10   14   29.6 12.2
#&gt; 11   27   10.1 13.7
#&gt; 12   27   18.2 13.2
#&gt; 13   48    4.5 13.6
#&gt; 14   48    9.1 15.4
#&gt; 15   70    2.3 10.4
#&gt; 16   70    2.9 11.6
#&gt; 17   91    2.0 10.0
#&gt; 18   91    1.8  9.5
#&gt; 19  120    2.0  9.1
#&gt; 20  120    2.2  9.0
#&gt; 
#&gt; &lt;mkinds&gt; with $title:  Soil 10 
#&gt; Observed compounds $observed:  parent, A1 
#&gt; Sampling times $sampling_times:
#&gt; 0, 8, 14, 21, 41, 63, 91, 120 
#&gt; With a maximum of  2  replicates
#&gt; Time unit:  days 
#&gt; Observation unit:  \%AR 
#&gt;    time parent   A1
#&gt; 1     0   96.1   NA
#&gt; 2     0   94.3   NA
#&gt; 3     8   73.9  3.3
#&gt; 4     8   73.9  3.4
#&gt; 5    14   69.4  3.9
#&gt; 6    14   73.1  2.9
#&gt; 7    21   65.6  6.4
#&gt; 8    21   65.3  7.2
#&gt; 9    41   55.9  9.1
#&gt; 10   41   54.4  8.5
#&gt; 11   63   47.0 11.7
#&gt; 12   63   49.3 12.0
#&gt; 13   91   44.7 13.3
#&gt; 14   91   46.7 13.2
#&gt; 15  120   42.1 14.3
#&gt; 16  120   41.3 12.1</div><div class='input'>
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