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<!DOCTYPE html>
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so that combined evaluations are desirable.
Time normalisation factors are initialised with a value of 1 for each
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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/HEAD/R/mkinds.R" class="external-link"><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>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mkindsg</span>
<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">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></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<dd><p>An mkindsg object.</p></dd>
<dt>data</dt>
<dd><p>Should the mkinds objects be printed with their data?</p></dd>
<dt>verbose</dt>
<dd><p>Should the mkinds objects be printed?</p></dd>
<dt>...</dt>
<dd><p>Not used.</p></dd>
</dl></div>
<div id="public-fields">
<h2>Public fields</h2>
<p></p><div class="r6-fields"><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></p></div>
</div>
<div id="methods">
<h2>Methods</h2>
<div class="section">
<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
<ul><li><p><a href="#method-mkindsg-new"><code>mkindsg$new()</code></a></p></li>
<li><p><a href="#method-mkindsg-clone"><code>mkindsg$clone()</code></a></p></li>
</ul></div><p></p><hr><a id="method-mkindsg-new"></a><div class="section">
<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
<p>Create a new mkindsg object</p><div class="section">
<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span class="va"><a href="../reference/mkindsg.html">mkindsg</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span>title <span class="op">=</span> <span class="st">""</span>, <span class="va">ds</span>, f_time_norm <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span><span class="op">)</span>, <span class="va">meta</span><span class="op">)</span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
<p></p><div class="arguments"><dl><dt><code>title</code></dt>
<dd><p>The title</p></dd>
<dt><code>ds</code></dt>
<dd><p>A list of mkinds objects</p></dd>
<dt><code>f_time_norm</code></dt>
<dd><p>Time normalisation factors</p></dd>
<dt><code>meta</code></dt>
<dd><p>The meta data</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-mkindsg-clone"></a><div class="section">
<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
<p>The objects of this class are cloneable with this method.</p><div class="section">
<h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span class="va">mkindsg</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4>
<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
<dd><p>Whether to make a deep clone.</p></dd>
</dl><p></p></div>
</div>
</div>
</div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span>
<span class="r-in"><span class="va">mdsg</span> <span class="op"><-</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>
<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">mdsg</span><span class="op">)</span></span>
<span class="r-out co"><span class="r-pr">#></span> <mkindsg> holding 5 mkinds objects</span>
<span class="r-out co"><span class="r-pr">#></span> Title $title: Experimental X </span>
<span class="r-out co"><span class="r-pr">#></span> Occurrence of observed compounds $observed_n:</span>
<span class="r-out co"><span class="r-pr">#></span> parent A1 </span>
<span class="r-out co"><span class="r-pr">#></span> 5 5 </span>
<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">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></span>
<span class="r-out co"><span class="r-pr">#></span> <mkindsg> holding 5 mkinds objects</span>
<span class="r-out co"><span class="r-pr">#></span> Title $title: Experimental X </span>
<span class="r-out co"><span class="r-pr">#></span> Occurrence of observed compounds $observed_n:</span>
<span class="r-out co"><span class="r-pr">#></span> parent A1 </span>
<span class="r-out co"><span class="r-pr">#></span> 5 5 </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Datasets $ds:</span>
<span class="r-out co"><span class="r-pr">#></span> <mkinds> with $title: Soil 6 </span>
<span class="r-out co"><span class="r-pr">#></span> Observed compounds $observed: parent, A1 </span>
<span class="r-out co"><span class="r-pr">#></span> Sampling times $sampling_times:</span>
<span class="r-out co"><span class="r-pr">#></span> 0, 3, 6, 10, 20, 34, 55, 90, 112, 132 </span>
<span class="r-out co"><span class="r-pr">#></span> With a maximum of 2 replicates</span>
<span class="r-out co"><span class="r-pr">#></span> Time unit: days </span>
<span class="r-out co"><span class="r-pr">#></span> Observation unit: \%AR </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> <mkinds> with $title: Soil 7 </span>
<span class="r-out co"><span class="r-pr">#></span> Observed compounds $observed: parent, A1 </span>
<span class="r-out co"><span class="r-pr">#></span> Sampling times $sampling_times:</span>
<span class="r-out co"><span class="r-pr">#></span> 0, 3, 7, 14, 30, 60, 90, 120, 180 </span>
<span class="r-out co"><span class="r-pr">#></span> With a maximum of 2 replicates</span>
<span class="r-out co"><span class="r-pr">#></span> Time unit: days </span>
<span class="r-out co"><span class="r-pr">#></span> Observation unit: \%AR </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> <mkinds> with $title: Soil 8 </span>
<span class="r-out co"><span class="r-pr">#></span> Observed compounds $observed: parent, A1 </span>
<span class="r-out co"><span class="r-pr">#></span> Sampling times $sampling_times:</span>
<span class="r-out co"><span class="r-pr">#></span> 0, 1, 3, 8, 14, 27, 48, 70 </span>
<span class="r-out co"><span class="r-pr">#></span> With a maximum of 2 replicates</span>
<span class="r-out co"><span class="r-pr">#></span> Time unit: days </span>
<span class="r-out co"><span class="r-pr">#></span> Observation unit: \%AR </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> <mkinds> with $title: Soil 9 </span>
<span class="r-out co"><span class="r-pr">#></span> Observed compounds $observed: parent, A1 </span>
<span class="r-out co"><span class="r-pr">#></span> Sampling times $sampling_times:</span>
<span class="r-out co"><span class="r-pr">#></span> 0, 1, 3, 8, 14, 27, 48, 70, 91, 120 </span>
<span class="r-out co"><span class="r-pr">#></span> With a maximum of 2 replicates</span>
<span class="r-out co"><span class="r-pr">#></span> Time unit: days </span>
<span class="r-out co"><span class="r-pr">#></span> Observation unit: \%AR </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> <mkinds> with $title: Soil 10 </span>
<span class="r-out co"><span class="r-pr">#></span> Observed compounds $observed: parent, A1 </span>
<span class="r-out co"><span class="r-pr">#></span> Sampling times $sampling_times:</span>
<span class="r-out co"><span class="r-pr">#></span> 0, 8, 14, 21, 41, 63, 91, 120 </span>
<span class="r-out co"><span class="r-pr">#></span> With a maximum of 2 replicates</span>
<span class="r-out co"><span class="r-pr">#></span> Time unit: days </span>
<span class="r-out co"><span class="r-pr">#></span> Observation unit: \%AR </span>
<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">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></span>
<span class="r-out co"><span class="r-pr">#></span> <mkindsg> holding 5 mkinds objects</span>
<span class="r-out co"><span class="r-pr">#></span> Title $title: Experimental X </span>
<span class="r-out co"><span class="r-pr">#></span> Occurrence of observed compounds $observed_n:</span>
<span class="r-out co"><span class="r-pr">#></span> parent A1 </span>
<span class="r-out co"><span class="r-pr">#></span> 5 5 </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Datasets $ds:</span>
<span class="r-out co"><span class="r-pr">#></span> <mkinds> with $title: Soil 6 </span>
<span class="r-out co"><span class="r-pr">#></span> Observed compounds $observed: parent, A1 </span>
<span class="r-out co"><span class="r-pr">#></span> Sampling times $sampling_times:</span>
<span class="r-out co"><span class="r-pr">#></span> 0, 3, 6, 10, 20, 34, 55, 90, 112, 132 </span>
<span class="r-out co"><span class="r-pr">#></span> With a maximum of 2 replicates</span>
<span class="r-out co"><span class="r-pr">#></span> Time unit: days </span>
<span class="r-out co"><span class="r-pr">#></span> Observation unit: \%AR </span>
<span class="r-out co"><span class="r-pr">#></span> time parent A1</span>
<span class="r-out co"><span class="r-pr">#></span> 1 0 97.2 NA</span>
<span class="r-out co"><span class="r-pr">#></span> 2 0 96.4 NA</span>
<span class="r-out co"><span class="r-pr">#></span> 3 3 71.1 4.3</span>
<span class="r-out co"><span class="r-pr">#></span> 4 3 69.2 4.6</span>
<span class="r-out co"><span class="r-pr">#></span> 5 6 58.1 7.0</span>
<span class="r-out co"><span class="r-pr">#></span> 6 6 56.6 7.2</span>
<span class="r-out co"><span class="r-pr">#></span> 7 10 44.4 8.2</span>
<span class="r-out co"><span class="r-pr">#></span> 8 10 43.4 8.0</span>
<span class="r-out co"><span class="r-pr">#></span> 9 20 33.3 11.0</span>
<span class="r-out co"><span class="r-pr">#></span> 10 20 29.2 13.7</span>
<span class="r-out co"><span class="r-pr">#></span> 11 34 17.6 11.5</span>
<span class="r-out co"><span class="r-pr">#></span> 12 34 18.0 12.7</span>
<span class="r-out co"><span class="r-pr">#></span> 13 55 10.5 14.9</span>
<span class="r-out co"><span class="r-pr">#></span> 14 55 9.3 14.5</span>
<span class="r-out co"><span class="r-pr">#></span> 15 90 4.5 12.1</span>
<span class="r-out co"><span class="r-pr">#></span> 16 90 4.7 12.3</span>
<span class="r-out co"><span class="r-pr">#></span> 17 112 3.0 9.9</span>
<span class="r-out co"><span class="r-pr">#></span> 18 112 3.4 10.2</span>
<span class="r-out co"><span class="r-pr">#></span> 19 132 2.3 8.8</span>
<span class="r-out co"><span class="r-pr">#></span> 20 132 2.7 7.8</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> <mkinds> with $title: Soil 7 </span>
<span class="r-out co"><span class="r-pr">#></span> Observed compounds $observed: parent, A1 </span>
<span class="r-out co"><span class="r-pr">#></span> Sampling times $sampling_times:</span>
<span class="r-out co"><span class="r-pr">#></span> 0, 3, 7, 14, 30, 60, 90, 120, 180 </span>
<span class="r-out co"><span class="r-pr">#></span> With a maximum of 2 replicates</span>
<span class="r-out co"><span class="r-pr">#></span> Time unit: days </span>
<span class="r-out co"><span class="r-pr">#></span> Observation unit: \%AR </span>
<span class="r-out co"><span class="r-pr">#></span> time parent A1</span>
<span class="r-out co"><span class="r-pr">#></span> 1 0 93.6 NA</span>
<span class="r-out co"><span class="r-pr">#></span> 2 0 92.3 NA</span>
<span class="r-out co"><span class="r-pr">#></span> 3 3 87.0 3.9</span>
<span class="r-out co"><span class="r-pr">#></span> 4 3 82.2 3.1</span>
<span class="r-out co"><span class="r-pr">#></span> 5 7 74.0 6.9</span>
<span class="r-out co"><span class="r-pr">#></span> 6 7 73.9 6.6</span>
<span class="r-out co"><span class="r-pr">#></span> 7 14 64.2 10.4</span>
<span class="r-out co"><span class="r-pr">#></span> 8 14 69.5 8.3</span>
<span class="r-out co"><span class="r-pr">#></span> 9 30 54.0 14.4</span>
<span class="r-out co"><span class="r-pr">#></span> 10 30 54.6 13.7</span>
<span class="r-out co"><span class="r-pr">#></span> 11 60 41.1 22.1</span>
<span class="r-out co"><span class="r-pr">#></span> 12 60 38.4 22.3</span>
<span class="r-out co"><span class="r-pr">#></span> 13 90 32.5 27.5</span>
<span class="r-out co"><span class="r-pr">#></span> 14 90 35.5 25.4</span>
<span class="r-out co"><span class="r-pr">#></span> 15 120 28.1 28.0</span>
<span class="r-out co"><span class="r-pr">#></span> 16 120 29.0 26.6</span>
<span class="r-out co"><span class="r-pr">#></span> 17 180 26.5 25.8</span>
<span class="r-out co"><span class="r-pr">#></span> 18 180 27.6 25.3</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> <mkinds> with $title: Soil 8 </span>
<span class="r-out co"><span class="r-pr">#></span> Observed compounds $observed: parent, A1 </span>
<span class="r-out co"><span class="r-pr">#></span> Sampling times $sampling_times:</span>
<span class="r-out co"><span class="r-pr">#></span> 0, 1, 3, 8, 14, 27, 48, 70 </span>
<span class="r-out co"><span class="r-pr">#></span> With a maximum of 2 replicates</span>
<span class="r-out co"><span class="r-pr">#></span> Time unit: days </span>
<span class="r-out co"><span class="r-pr">#></span> Observation unit: \%AR </span>
<span class="r-out co"><span class="r-pr">#></span> time parent A1</span>
<span class="r-out co"><span class="r-pr">#></span> 1 0 91.9 NA</span>
<span class="r-out co"><span class="r-pr">#></span> 2 0 90.8 NA</span>
<span class="r-out co"><span class="r-pr">#></span> 3 1 64.9 9.6</span>
<span class="r-out co"><span class="r-pr">#></span> 4 1 66.2 7.7</span>
<span class="r-out co"><span class="r-pr">#></span> 5 3 43.5 15.0</span>
<span class="r-out co"><span class="r-pr">#></span> 6 3 44.1 15.1</span>
<span class="r-out co"><span class="r-pr">#></span> 7 8 18.3 21.2</span>
<span class="r-out co"><span class="r-pr">#></span> 8 8 18.1 21.1</span>
<span class="r-out co"><span class="r-pr">#></span> 9 14 10.2 19.7</span>
<span class="r-out co"><span class="r-pr">#></span> 10 14 10.8 18.9</span>
<span class="r-out co"><span class="r-pr">#></span> 11 27 4.9 17.5</span>
<span class="r-out co"><span class="r-pr">#></span> 12 27 3.3 15.9</span>
<span class="r-out co"><span class="r-pr">#></span> 13 48 1.6 9.5</span>
<span class="r-out co"><span class="r-pr">#></span> 14 48 1.5 9.8</span>
<span class="r-out co"><span class="r-pr">#></span> 15 70 1.1 6.2</span>
<span class="r-out co"><span class="r-pr">#></span> 16 70 0.9 6.1</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> <mkinds> with $title: Soil 9 </span>
<span class="r-out co"><span class="r-pr">#></span> Observed compounds $observed: parent, A1 </span>
<span class="r-out co"><span class="r-pr">#></span> Sampling times $sampling_times:</span>
<span class="r-out co"><span class="r-pr">#></span> 0, 1, 3, 8, 14, 27, 48, 70, 91, 120 </span>
<span class="r-out co"><span class="r-pr">#></span> With a maximum of 2 replicates</span>
<span class="r-out co"><span class="r-pr">#></span> Time unit: days </span>
<span class="r-out co"><span class="r-pr">#></span> Observation unit: \%AR </span>
<span class="r-out co"><span class="r-pr">#></span> time parent A1</span>
<span class="r-out co"><span class="r-pr">#></span> 1 0 99.8 NA</span>
<span class="r-out co"><span class="r-pr">#></span> 2 0 98.3 NA</span>
<span class="r-out co"><span class="r-pr">#></span> 3 1 77.1 4.2</span>
<span class="r-out co"><span class="r-pr">#></span> 4 1 77.2 3.9</span>
<span class="r-out co"><span class="r-pr">#></span> 5 3 59.0 7.4</span>
<span class="r-out co"><span class="r-pr">#></span> 6 3 58.1 7.9</span>
<span class="r-out co"><span class="r-pr">#></span> 7 8 27.4 14.5</span>
<span class="r-out co"><span class="r-pr">#></span> 8 8 29.2 13.7</span>
<span class="r-out co"><span class="r-pr">#></span> 9 14 19.1 14.2</span>
<span class="r-out co"><span class="r-pr">#></span> 10 14 29.6 12.2</span>
<span class="r-out co"><span class="r-pr">#></span> 11 27 10.1 13.7</span>
<span class="r-out co"><span class="r-pr">#></span> 12 27 18.2 13.2</span>
<span class="r-out co"><span class="r-pr">#></span> 13 48 4.5 13.6</span>
<span class="r-out co"><span class="r-pr">#></span> 14 48 9.1 15.4</span>
<span class="r-out co"><span class="r-pr">#></span> 15 70 2.3 10.4</span>
<span class="r-out co"><span class="r-pr">#></span> 16 70 2.9 11.6</span>
<span class="r-out co"><span class="r-pr">#></span> 17 91 2.0 10.0</span>
<span class="r-out co"><span class="r-pr">#></span> 18 91 1.8 9.5</span>
<span class="r-out co"><span class="r-pr">#></span> 19 120 2.0 9.1</span>
<span class="r-out co"><span class="r-pr">#></span> 20 120 2.2 9.0</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> <mkinds> with $title: Soil 10 </span>
<span class="r-out co"><span class="r-pr">#></span> Observed compounds $observed: parent, A1 </span>
<span class="r-out co"><span class="r-pr">#></span> Sampling times $sampling_times:</span>
<span class="r-out co"><span class="r-pr">#></span> 0, 8, 14, 21, 41, 63, 91, 120 </span>
<span class="r-out co"><span class="r-pr">#></span> With a maximum of 2 replicates</span>
<span class="r-out co"><span class="r-pr">#></span> Time unit: days </span>
<span class="r-out co"><span class="r-pr">#></span> Observation unit: \%AR </span>
<span class="r-out co"><span class="r-pr">#></span> time parent A1</span>
<span class="r-out co"><span class="r-pr">#></span> 1 0 96.1 NA</span>
<span class="r-out co"><span class="r-pr">#></span> 2 0 94.3 NA</span>
<span class="r-out co"><span class="r-pr">#></span> 3 8 73.9 3.3</span>
<span class="r-out co"><span class="r-pr">#></span> 4 8 73.9 3.4</span>
<span class="r-out co"><span class="r-pr">#></span> 5 14 69.4 3.9</span>
<span class="r-out co"><span class="r-pr">#></span> 6 14 73.1 2.9</span>
<span class="r-out co"><span class="r-pr">#></span> 7 21 65.6 6.4</span>
<span class="r-out co"><span class="r-pr">#></span> 8 21 65.3 7.2</span>
<span class="r-out co"><span class="r-pr">#></span> 9 41 55.9 9.1</span>
<span class="r-out co"><span class="r-pr">#></span> 10 41 54.4 8.5</span>
<span class="r-out co"><span class="r-pr">#></span> 11 63 47.0 11.7</span>
<span class="r-out co"><span class="r-pr">#></span> 12 63 49.3 12.0</span>
<span class="r-out co"><span class="r-pr">#></span> 13 91 44.7 13.3</span>
<span class="r-out co"><span class="r-pr">#></span> 14 91 46.7 13.2</span>
<span class="r-out co"><span class="r-pr">#></span> 15 120 42.1 14.3</span>
<span class="r-out co"><span class="r-pr">#></span> 16 120 41.3 12.1</span>
<span class="r-in"></span>
</code></pre></div>
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