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| author | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-03 16:41:31 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-03 18:18:19 +0100 |
| commit | f0ef23a7598e5d19648ae4edc2b74e0fba27a41c (patch) | |
| tree | 03af20e730330e148acf3a7c008d82387dbe52eb /docs/reference/mkindsg.html | |
| parent | 82814b17ec182467c25325d747fffa8ffbe4bb33 (diff) | |
Prepare for v1.0.0v1.0.0
- Improve authorship and copyright information
- Prepare pkgdown config
- Remove dependence on saemix as we need the development version which
is not ready for CRAN
- Temporarily remove saemix interface to check code coverage of the rest
Diffstat (limited to 'docs/reference/mkindsg.html')
| -rw-r--r-- | docs/reference/mkindsg.html | 460 |
1 files changed, 460 insertions, 0 deletions
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class="icon-bar"></span> + </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">1.0.0</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </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/"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </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> + <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'><-</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> + <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> +</div> + + + <footer> + <div class="copyright"> + <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> +</div> + + </footer> + </div> + + + + + </body> 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