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charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>A class for dataset groups for mkin — mkindsg • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="A class for dataset groups for mkin — mkindsg"><meta property="og:description" content="A container for working with datasets that share at least one compound, so that combined evaluations are desirable. Time normalisation factors are initialised with a value of 1 for each -dataset if no data are supplied." /> - - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +dataset if no data are supplied."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -75,13 +20,12 @@ dataset if no data are supplied." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> @@ -90,8 +34,7 @@ dataset if no data are supplied." /> <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -101,6 +44,9 @@ dataset if no data are supplied." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> @@ -115,34 +61,27 @@ dataset if no data are supplied." /> <li> <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> </li> - </ul> -</li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <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> + <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> @@ -153,308 +92,329 @@ so that combined evaluations are desirable.</p> 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, + <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></div></p> - <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> +</dl><p></p></div> + </div> + <div id="methods"> + <h2>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'><-</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'>#> <mkindsg> holding 5 mkinds objects -#> Title $title: Experimental X -#> Occurrence of observed compounds $observed_n: -#> parent A1 -#> 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'>#> <mkindsg> holding 5 mkinds objects -#> Title $title: Experimental X -#> Occurrence of observed compounds $observed_n: -#> parent A1 -#> 5 5 -#> -#> Datasets $ds: -#> <mkinds> with $title: Soil 6 -#> Observed compounds $observed: parent, A1 -#> Sampling times $sampling_times: -#> 0, 3, 6, 10, 20, 34, 55, 90, 112, 132 -#> With a maximum of 2 replicates -#> Time unit: days -#> Observation unit: \%AR -#> -#> <mkinds> with $title: Soil 7 -#> Observed compounds $observed: parent, A1 -#> Sampling times $sampling_times: -#> 0, 3, 7, 14, 30, 60, 90, 120, 180 -#> With a maximum of 2 replicates -#> Time unit: days -#> Observation unit: \%AR -#> -#> <mkinds> with $title: Soil 8 -#> Observed compounds $observed: parent, A1 -#> Sampling times $sampling_times: -#> 0, 1, 3, 8, 14, 27, 48, 70 -#> With a maximum of 2 replicates -#> Time unit: days -#> Observation unit: \%AR -#> -#> <mkinds> with $title: Soil 9 -#> Observed compounds $observed: parent, A1 -#> Sampling times $sampling_times: -#> 0, 1, 3, 8, 14, 27, 48, 70, 91, 120 -#> With a maximum of 2 replicates -#> Time unit: days -#> Observation unit: \%AR -#> -#> <mkinds> with $title: Soil 10 -#> Observed compounds $observed: parent, A1 -#> Sampling times $sampling_times: -#> 0, 8, 14, 21, 41, 63, 91, 120 -#> With a maximum of 2 replicates -#> Time unit: days -#> 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'>#> <mkindsg> holding 5 mkinds objects -#> Title $title: Experimental X -#> Occurrence of observed compounds $observed_n: -#> parent A1 -#> 5 5 -#> -#> Datasets $ds: -#> <mkinds> with $title: Soil 6 -#> Observed compounds $observed: parent, A1 -#> Sampling times $sampling_times: -#> 0, 3, 6, 10, 20, 34, 55, 90, 112, 132 -#> With a maximum of 2 replicates -#> Time unit: days -#> Observation unit: \%AR -#> time parent A1 -#> 1 0 97.2 NA -#> 2 0 96.4 NA -#> 3 3 71.1 4.3 -#> 4 3 69.2 4.6 -#> 5 6 58.1 7.0 -#> 6 6 56.6 7.2 -#> 7 10 44.4 8.2 -#> 8 10 43.4 8.0 -#> 9 20 33.3 11.0 -#> 10 20 29.2 13.7 -#> 11 34 17.6 11.5 -#> 12 34 18.0 12.7 -#> 13 55 10.5 14.9 -#> 14 55 9.3 14.5 -#> 15 90 4.5 12.1 -#> 16 90 4.7 12.3 -#> 17 112 3.0 9.9 -#> 18 112 3.4 10.2 -#> 19 132 2.3 8.8 -#> 20 132 2.7 7.8 -#> -#> <mkinds> with $title: Soil 7 -#> Observed compounds $observed: parent, A1 -#> Sampling times $sampling_times: -#> 0, 3, 7, 14, 30, 60, 90, 120, 180 -#> With a maximum of 2 replicates -#> Time unit: days -#> Observation unit: \%AR -#> time parent A1 -#> 1 0 93.6 NA -#> 2 0 92.3 NA -#> 3 3 87.0 3.9 -#> 4 3 82.2 3.1 -#> 5 7 74.0 6.9 -#> 6 7 73.9 6.6 -#> 7 14 64.2 10.4 -#> 8 14 69.5 8.3 -#> 9 30 54.0 14.4 -#> 10 30 54.6 13.7 -#> 11 60 41.1 22.1 -#> 12 60 38.4 22.3 -#> 13 90 32.5 27.5 -#> 14 90 35.5 25.4 -#> 15 120 28.1 28.0 -#> 16 120 29.0 26.6 -#> 17 180 26.5 25.8 -#> 18 180 27.6 25.3 -#> -#> <mkinds> with $title: Soil 8 -#> Observed compounds $observed: parent, A1 -#> Sampling times $sampling_times: -#> 0, 1, 3, 8, 14, 27, 48, 70 -#> With a maximum of 2 replicates -#> Time unit: days -#> Observation unit: \%AR -#> time parent A1 -#> 1 0 91.9 NA -#> 2 0 90.8 NA -#> 3 1 64.9 9.6 -#> 4 1 66.2 7.7 -#> 5 3 43.5 15.0 -#> 6 3 44.1 15.1 -#> 7 8 18.3 21.2 -#> 8 8 18.1 21.1 -#> 9 14 10.2 19.7 -#> 10 14 10.8 18.9 -#> 11 27 4.9 17.5 -#> 12 27 3.3 15.9 -#> 13 48 1.6 9.5 -#> 14 48 1.5 9.8 -#> 15 70 1.1 6.2 -#> 16 70 0.9 6.1 -#> -#> <mkinds> with $title: Soil 9 -#> Observed compounds $observed: parent, A1 -#> Sampling times $sampling_times: -#> 0, 1, 3, 8, 14, 27, 48, 70, 91, 120 -#> With a maximum of 2 replicates -#> Time unit: days -#> Observation unit: \%AR -#> time parent A1 -#> 1 0 99.8 NA -#> 2 0 98.3 NA -#> 3 1 77.1 4.2 -#> 4 1 77.2 3.9 -#> 5 3 59.0 7.4 -#> 6 3 58.1 7.9 -#> 7 8 27.4 14.5 -#> 8 8 29.2 13.7 -#> 9 14 19.1 14.2 -#> 10 14 29.6 12.2 -#> 11 27 10.1 13.7 -#> 12 27 18.2 13.2 -#> 13 48 4.5 13.6 -#> 14 48 9.1 15.4 -#> 15 70 2.3 10.4 -#> 16 70 2.9 11.6 -#> 17 91 2.0 10.0 -#> 18 91 1.8 9.5 -#> 19 120 2.0 9.1 -#> 20 120 2.2 9.0 -#> -#> <mkinds> with $title: Soil 10 -#> Observed compounds $observed: parent, A1 -#> Sampling times $sampling_times: -#> 0, 8, 14, 21, 41, 63, 91, 120 -#> With a maximum of 2 replicates -#> Time unit: days -#> Observation unit: \%AR -#> time parent A1 -#> 1 0 96.1 NA -#> 2 0 94.3 NA -#> 3 8 73.9 3.3 -#> 4 8 73.9 3.4 -#> 5 14 69.4 3.9 -#> 6 14 73.1 2.9 -#> 7 21 65.6 6.4 -#> 8 21 65.3 7.2 -#> 9 41 55.9 9.1 -#> 10 41 54.4 8.5 -#> 11 63 47.0 11.7 -#> 12 63 49.3 12.0 -#> 13 91 44.7 13.3 -#> 14 91 46.7 13.2 -#> 15 120 42.1 14.3 -#> 16 120 41.3 12.1</div><div class='input'> -</div></pre> +<div class="section"> +<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> + +<ul><li><p><a href="#method-new"><code>mkindsg$new()</code></a></p></li> +<li><p><a href="#method-clone"><code>mkindsg$clone()</code></a></p></li> +</ul></div><p></p><hr><a id="method-new"></a><div class="section"> +<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> +<p>Create a new mkindsg object</p><div class="section"> +<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span class="va"><a href="../reference/mkindsg.html">mkindsg</a></span><span class="op">$</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-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> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> |