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@@ -74,23 +19,21 @@ may depend on the predicted value and is specified as a standard deviation." />
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@@ -100,195 +43,203 @@ may depend on the predicted value and is specified as a standard deviation." />
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
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- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
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+ </li>
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<h1>Add normally distributed errors to simulated kinetic degradation data</h1>
- <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/add_err.R'><code>R/add_err.R</code></a></small>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/add_err.R" class="external-link"><code>R/add_err.R</code></a></small>
<div class="hidden name"><code>add_err.Rd</code></div>
</div>
<div class="ref-description">
<p>Normally distributed errors are added to data predicted for a specific
-degradation model using <code><a href='mkinpredict.html'>mkinpredict</a></code>. The variance of the error
+degradation model using <code><a href="mkinpredict.html">mkinpredict</a></code>. The variance of the error
may depend on the predicted value and is specified as a standard deviation.</p>
</div>
- <pre class="usage"><span class='fu'>add_err</span><span class='op'>(</span>
- <span class='va'>prediction</span>,
- <span class='va'>sdfunc</span>,
- secondary <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span>,
- n <span class='op'>=</span> <span class='fl'>10</span>,
- LOD <span class='op'>=</span> <span class='fl'>0.1</span>,
- reps <span class='op'>=</span> <span class='fl'>2</span>,
- digits <span class='op'>=</span> <span class='fl'>1</span>,
- seed <span class='op'>=</span> <span class='cn'>NA</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>prediction</th>
- <td><p>A prediction from a kinetic model as produced by
-<code><a href='mkinpredict.html'>mkinpredict</a></code>.</p></td>
- </tr>
- <tr>
- <th>sdfunc</th>
- <td><p>A function taking the predicted value as its only argument and
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">add_err</span><span class="op">(</span></span>
+<span> <span class="va">prediction</span>,</span>
+<span> <span class="va">sdfunc</span>,</span>
+<span> secondary <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span>
+<span> n <span class="op">=</span> <span class="fl">10</span>,</span>
+<span> LOD <span class="op">=</span> <span class="fl">0.1</span>,</span>
+<span> reps <span class="op">=</span> <span class="fl">2</span>,</span>
+<span> digits <span class="op">=</span> <span class="fl">1</span>,</span>
+<span> seed <span class="op">=</span> <span class="cn">NA</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+ </div>
+
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>prediction</dt>
+<dd><p>A prediction from a kinetic model as produced by
+<code><a href="mkinpredict.html">mkinpredict</a></code>.</p></dd>
+
+
+<dt>sdfunc</dt>
+<dd><p>A function taking the predicted value as its only argument and
returning a standard deviation that should be used for generating the
-random error terms for this value.</p></td>
- </tr>
- <tr>
- <th>secondary</th>
- <td><p>The names of state variables that should have an initial
-value of zero</p></td>
- </tr>
- <tr>
- <th>n</th>
- <td><p>The number of datasets to be generated.</p></td>
- </tr>
- <tr>
- <th>LOD</th>
- <td><p>The limit of detection (LOD). Values that are below the LOD after
-adding the random error will be set to NA.</p></td>
- </tr>
- <tr>
- <th>reps</th>
- <td><p>The number of replicates to be generated within the datasets.</p></td>
- </tr>
- <tr>
- <th>digits</th>
- <td><p>The number of digits to which the values will be rounded.</p></td>
- </tr>
- <tr>
- <th>seed</th>
- <td><p>The seed used for the generation of random numbers. If NA, the
-seed is not set.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>A list of datasets compatible with <code><a href='mmkin.html'>mmkin</a></code>, i.e. the
-components of the list are datasets compatible with <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
- <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+random error terms for this value.</p></dd>
+
+
+<dt>secondary</dt>
+<dd><p>The names of state variables that should have an initial
+value of zero</p></dd>
+
+
+<dt>n</dt>
+<dd><p>The number of datasets to be generated.</p></dd>
+
+
+<dt>LOD</dt>
+<dd><p>The limit of detection (LOD). Values that are below the LOD after
+adding the random error will be set to NA.</p></dd>
+
+<dt>reps</dt>
+<dd><p>The number of replicates to be generated within the datasets.</p></dd>
+
+
+<dt>digits</dt>
+<dd><p>The number of digits to which the values will be rounded.</p></dd>
+
+
+<dt>seed</dt>
+<dd><p>The seed used for the generation of random numbers. If NA, the
+seed is not set.</p></dd>
+
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
+
+
+<p>A list of datasets compatible with <code><a href="mmkin.html">mmkin</a></code>, i.e. the
+components of the list are datasets compatible with <code><a href="mkinfit.html">mkinfit</a></code>.</p>
+ </div>
+ <div id="references">
+ <h2>References</h2>
<p>Ranke J and Lehmann R (2015) To t-test or not to t-test, that is
the question. XV Symposium on Pesticide Chemistry 2-4 September 2015,
Piacenza, Italy
https://jrwb.de/posters/piacenza_2015.pdf</p>
- <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
-
+ </div>
+ <div id="author">
+ <h2>Author</h2>
<p>Johannes Ranke</p>
+ </div>
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'>
-<span class='co'># The kinetic model</span>
-<span class='va'>m_SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M1"</span><span class='op'>)</span>,
- M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
-<span class='co'># Generate a prediction for a specific set of parameters</span>
-<span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span>
-
-<span class='co'># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span>
-<span class='co'># from 2015</span>
-<span class='va'>d_SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_SFO_SFO</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.1</span>, f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.5</span>,
- k_M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span><span class='op'>/</span><span class='fl'>1000</span><span class='op'>)</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>,
- <span class='va'>sampling_times</span><span class='op'>)</span>
-
-<span class='co'># Add an error term with a constant (independent of the value) standard deviation</span>
-<span class='co'># of 10, and generate three datasets</span>
-<span class='va'>d_SFO_SFO_err</span> <span class='op'>&lt;-</span> <span class='fu'>add_err</span><span class='op'>(</span><span class='va'>d_SFO_SFO</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fl'>10</span>, n <span class='op'>=</span> <span class='fl'>3</span>, seed <span class='op'>=</span> <span class='fl'>123456789</span> <span class='op'>)</span>
-
-<span class='co'># Name the datasets for nicer plotting</span>
-<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>d_SFO_SFO_err</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>)</span>
-
-<span class='co'># Name the model in the list of models (with only one member in this case) for</span>
-<span class='co'># nicer plotting later on. Be quiet and use only one core not to offend CRAN</span>
-<span class='co'># checks</span>
-<span class='co'># \dontrun{</span>
-<span class='va'>f_SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_SFO_SFO</span><span class='op'>)</span>,
- <span class='va'>d_SFO_SFO_err</span>, cores <span class='op'>=</span> <span class='fl'>1</span>,
- quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_SFO_SFO</span><span class='op'>)</span>
-</div><div class='img'><img src='add_err-1.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='co'># We would like to inspect the fit for dataset 3 more closely</span>
-<span class='co'># Using double brackets makes the returned object an mkinfit object</span>
-<span class='co'># instead of a list of mkinfit objects, so plot.mkinfit is used</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_SFO_SFO</span><span class='op'>[[</span><span class='fl'>3</span><span class='op'>]</span><span class='op'>]</span>, show_residuals <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='img'><img src='add_err-2.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='co'># If we use single brackets, we should give two indices (model and dataset),</span>
-<span class='co'># and plot.mmkin is used</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_SFO_SFO</span><span class='op'>[</span><span class='fl'>1</span>, <span class='fl'>3</span><span class='op'>]</span><span class='op'>)</span>
-</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
-
-</div></pre>
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># The kinetic model</span></span></span>
+<span class="r-in"><span><span class="va">m_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Generate a prediction for a specific set of parameters</span></span></span>
+<span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span></span></span>
+<span class="r-in"><span><span class="co"># from 2015</span></span></span>
+<span class="r-in"><span><span class="va">d_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span>, f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>,</span></span>
+<span class="r-in"><span> k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Add an error term with a constant (independent of the value) standard deviation</span></span></span>
+<span class="r-in"><span><span class="co"># of 10, and generate three datasets</span></span></span>
+<span class="r-in"><span><span class="va">d_SFO_SFO_err</span> <span class="op">&lt;-</span> <span class="fu">add_err</span><span class="op">(</span><span class="va">d_SFO_SFO</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">10</span>, n <span class="op">=</span> <span class="fl">3</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Name the datasets for nicer plotting</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">d_SFO_SFO_err</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Name the model in the list of models (with only one member in this case) for</span></span></span>
+<span class="r-in"><span><span class="co"># nicer plotting later on. Be quiet and use only one core not to offend CRAN</span></span></span>
+<span class="r-in"><span><span class="co"># checks</span></span></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">f_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">m_SFO_SFO</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="va">d_SFO_SFO_err</span>, cores <span class="op">=</span> <span class="fl">1</span>,</span></span>
+<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="add_err-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># We would like to inspect the fit for dataset 3 more closely</span></span></span>
+<span class="r-in"><span><span class="co"># Using double brackets makes the returned object an mkinfit object</span></span></span>
+<span class="r-in"><span><span class="co"># instead of a list of mkinfit objects, so plot.mkinfit is used</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="add_err-2.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># If we use single brackets, we should give two indices (model and dataset),</span></span></span>
+<span class="r-in"><span><span class="co"># and plot.mmkin is used</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">3</span><span class="op">]</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="add_err-3.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+ </div>
</div>
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