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diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html
index 69345b2f..19b8e2c1 100644
--- a/docs/dev/reference/plot.mixed.mmkin.html
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@@ -1,67 +1,12 @@
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@@ -77,8 +22,7 @@
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<h1>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</h1>
- <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.mixed.mmkin.R'><code>R/plot.mixed.mmkin.R</code></a></small>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mixed.mmkin.R" class="external-link"><code>R/plot.mixed.mmkin.R</code></a></small>
<div class="hidden name"><code>plot.mixed.mmkin.Rd</code></div>
</div>
@@ -147,193 +83,158 @@
<p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p>
</div>
- <pre class="usage"><span class='co'># S3 method for mixed.mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
- <span class='va'>x</span>,
- i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>,
- obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
- standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
- xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
- xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
- resplot <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'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>,
- pred_over <span class='op'>=</span> <span class='cn'>NULL</span>,
- test_log_parms <span class='op'>=</span> <span class='cn'>FALSE</span>,
- conf.level <span class='op'>=</span> <span class='fl'>0.6</span>,
- ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
- maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
- ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>,
- nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>,
- rel.height.legend <span class='op'>=</span> <span class='fl'>0.02</span> <span class='op'>+</span> <span class='fl'>0.07</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>,
- rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>,
- pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>,
- col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>,
- lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>,
- frame <span class='op'>=</span> <span class='cn'>TRUE</span>,
- <span class='va'>...</span>
-<span class='op'>)</span></pre>
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mixed.mmkin</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">x</span>,
+ i <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">ncol</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">mmkin</span><span class="op">)</span>,
+ obs_vars <span class="op">=</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">x</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,
+ standardized <span class="op">=</span> <span class="cn">TRUE</span>,
+ xlab <span class="op">=</span> <span class="st">"Time"</span>,
+ xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span>,
+ resplot <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">"predicted"</span>, <span class="st">"time"</span><span class="op">)</span>,
+ pred_over <span class="op">=</span> <span class="cn">NULL</span>,
+ test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,
+ conf.level <span class="op">=</span> <span class="fl">0.6</span>,
+ ymax <span class="op">=</span> <span class="st">"auto"</span>,
+ maxabs <span class="op">=</span> <span class="st">"auto"</span>,
+ ncol.legend <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</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">i</span><span class="op">)</span> <span class="op">&lt;=</span> <span class="fl">3</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">i</span><span class="op">)</span> <span class="op">+</span> <span class="fl">1</span>, <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</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">i</span><span class="op">)</span> <span class="op">&lt;=</span> <span class="fl">8</span>, <span class="fl">3</span>, <span class="fl">4</span><span class="op">)</span><span class="op">)</span>,
+ nrow.legend <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">ceiling</a></span><span class="op">(</span><span class="op">(</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">i</span><span class="op">)</span> <span class="op">+</span> <span class="fl">1</span><span class="op">)</span><span class="op">/</span><span class="va">ncol.legend</span><span class="op">)</span>,
+ rel.height.legend <span class="op">=</span> <span class="fl">0.02</span> <span class="op">+</span> <span class="fl">0.07</span> <span class="op">*</span> <span class="va">nrow.legend</span>,
+ rel.height.bottom <span class="op">=</span> <span class="fl">1.1</span>,
+ pch_ds <span class="op">=</span> <span class="fl">1</span><span class="op">:</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">i</span><span class="op">)</span>,
+ col_ds <span class="op">=</span> <span class="va">pch_ds</span> <span class="op">+</span> <span class="fl">1</span>,
+ lty_ds <span class="op">=</span> <span class="va">col_ds</span>,
+ frame <span class="op">=</span> <span class="cn">TRUE</span>,
+ <span class="va">...</span>
+<span class="op">)</span></code></pre></div>
+ </div>
- <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 object of class <a href='mixed.html'>mixed.mmkin</a>, <a href='saem.html'>saem.mmkin</a> or <a href='nlme.mmkin.html'>nlme.mmkin</a></p></td>
- </tr>
- <tr>
- <th>i</th>
- <td><p>A numeric index to select datasets for which to plot the individual predictions,
-in case plots get too large</p></td>
- </tr>
- <tr>
- <th>obs_vars</th>
- <td><p>A character vector of names of the observed variables for
+ <div id="arguments">
+ <h2>Arguments</h2>
+ <dl><dt>x</dt>
+<dd><p>An object of class <a href="mixed.html">mixed.mmkin</a>, <a href="saem.html">saem.mmkin</a> or <a href="nlme.mmkin.html">nlme.mmkin</a></p></dd>
+<dt>i</dt>
+<dd><p>A numeric index to select datasets for which to plot the individual predictions,
+in case plots get too large</p></dd>
+<dt>obs_vars</dt>
+<dd><p>A character vector of names of the observed variables for
which the data and the model should be plotted. Defauls to all observed
-variables in the model.</p></td>
- </tr>
- <tr>
- <th>standardized</th>
- <td><p>Should the residuals be standardized? Only takes effect if
-<code>resplot = "time"</code>.</p></td>
- </tr>
- <tr>
- <th>xlab</th>
- <td><p>Label for the x axis.</p></td>
- </tr>
- <tr>
- <th>xlim</th>
- <td><p>Plot range in x direction.</p></td>
- </tr>
- <tr>
- <th>resplot</th>
- <td><p>Should the residuals plotted against time or against
-predicted values?</p></td>
- </tr>
- <tr>
- <th>pred_over</th>
- <td><p>Named list of alternative predictions as obtained
-from <a href='mkinpredict.html'>mkinpredict</a> with a compatible <a href='mkinmod.html'>mkinmod</a>.</p></td>
- </tr>
- <tr>
- <th>test_log_parms</th>
- <td><p>Passed to <a href='mean_degparms.html'>mean_degparms</a> in the case of an
-<a href='mixed.html'>mixed.mmkin</a> object</p></td>
- </tr>
- <tr>
- <th>conf.level</th>
- <td><p>Passed to <a href='mean_degparms.html'>mean_degparms</a> in the case of an
-<a href='mixed.html'>mixed.mmkin</a> object</p></td>
- </tr>
- <tr>
- <th>ymax</th>
- <td><p>Vector of maximum y axis values</p></td>
- </tr>
- <tr>
- <th>maxabs</th>
- <td><p>Maximum absolute value of the residuals. This is used for the
-scaling of the y axis and defaults to "auto".</p></td>
- </tr>
- <tr>
- <th>ncol.legend</th>
- <td><p>Number of columns to use in the legend</p></td>
- </tr>
- <tr>
- <th>nrow.legend</th>
- <td><p>Number of rows to use in the legend</p></td>
- </tr>
- <tr>
- <th>rel.height.legend</th>
- <td><p>The relative height of the legend shown on top</p></td>
- </tr>
- <tr>
- <th>rel.height.bottom</th>
- <td><p>The relative height of the bottom plot row</p></td>
- </tr>
- <tr>
- <th>pch_ds</th>
- <td><p>Symbols to be used for plotting the data.</p></td>
- </tr>
- <tr>
- <th>col_ds</th>
- <td><p>Colors used for plotting the observed data and the
-corresponding model prediction lines for the different datasets.</p></td>
- </tr>
- <tr>
- <th>lty_ds</th>
- <td><p>Line types to be used for the model predictions.</p></td>
- </tr>
- <tr>
- <th>frame</th>
- <td><p>Should a frame be drawn around the plots?</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
+variables in the model.</p></dd>
+<dt>standardized</dt>
+<dd><p>Should the residuals be standardized? Only takes effect if
+<code>resplot = "time"</code>.</p></dd>
+<dt>xlab</dt>
+<dd><p>Label for the x axis.</p></dd>
+<dt>xlim</dt>
+<dd><p>Plot range in x direction.</p></dd>
+<dt>resplot</dt>
+<dd><p>Should the residuals plotted against time or against
+predicted values?</p></dd>
+<dt>pred_over</dt>
+<dd><p>Named list of alternative predictions as obtained
+from <a href="mkinpredict.html">mkinpredict</a> with a compatible <a href="mkinmod.html">mkinmod</a>.</p></dd>
+<dt>test_log_parms</dt>
+<dd><p>Passed to <a href="mean_degparms.html">mean_degparms</a> in the case of an
+<a href="mixed.html">mixed.mmkin</a> object</p></dd>
+<dt>conf.level</dt>
+<dd><p>Passed to <a href="mean_degparms.html">mean_degparms</a> in the case of an
+<a href="mixed.html">mixed.mmkin</a> object</p></dd>
+<dt>ymax</dt>
+<dd><p>Vector of maximum y axis values</p></dd>
+<dt>maxabs</dt>
+<dd><p>Maximum absolute value of the residuals. This is used for the
+scaling of the y axis and defaults to "auto".</p></dd>
+<dt>ncol.legend</dt>
+<dd><p>Number of columns to use in the legend</p></dd>
+<dt>nrow.legend</dt>
+<dd><p>Number of rows to use in the legend</p></dd>
+<dt>rel.height.legend</dt>
+<dd><p>The relative height of the legend shown on top</p></dd>
+<dt>rel.height.bottom</dt>
+<dd><p>The relative height of the bottom plot row</p></dd>
+<dt>pch_ds</dt>
+<dd><p>Symbols to be used for plotting the data.</p></dd>
+<dt>col_ds</dt>
+<dd><p>Colors used for plotting the observed data and the
+corresponding model prediction lines for the different datasets.</p></dd>
+<dt>lty_ds</dt>
+<dd><p>Line types to be used for the model predictions.</p></dd>
+<dt>frame</dt>
+<dd><p>Should a frame be drawn around the plots?</p></dd>
+<dt>...</dt>
+<dd><p>Further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd>
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
<p>The function is called for its side effect.</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='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</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='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</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='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"ds "</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span>
-<span class='va'>dfop_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'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
- A1 <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>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='co'># \dontrun{</span>
-<span class='va'>f</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'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</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</span><span class='op'>[</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='img'><img src='plot.mixed.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='co'># For this fit we need to increase pnlsMaxiter, and we increase the</span>
-<span class='co'># tolerance in order to speed up the fit for this example evaluation</span>
-<span class='co'># It still takes 20 seconds to run</span>
-<span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-3</span><span class='op'>)</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_nlme</span><span class='op'>)</span>
-</div><div class='img'><img src='plot.mixed.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span>, transformations <span class='op'>=</span> <span class='st'>"saemix"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in saem(f, transformations = "saemix"): unused argument (transformations = "saemix")</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in plot(f_saem): object 'f_saem' not found</span></div><div class='input'>
-<span class='va'>f_obs</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'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span>
-<span class='va'>f_nlmix</span> <span class='op'>&lt;-</span> <span class='fu'>nlmix</span><span class='op'>(</span><span class='va'>f_obs</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in nlmix(f_obs): could not find function "nlmix"</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlmix</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in plot(f_nlmix): object 'f_nlmix' not found</span></div><div class='input'>
-<span class='co'># We can overlay the two variants if we generate predictions</span>
-<span class='va'>pred_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span>,
- <span class='va'>f_nlme</span><span class='op'>$</span><span class='va'>bparms.optim</span><span class='op'>[</span><span class='op'>-</span><span class='fl'>1</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='va'>f_nlme</span><span class='op'>$</span><span class='va'>bparms.optim</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>, A1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>180</span>, by <span class='op'>=</span> <span class='fl'>0.2</span><span class='op'>)</span><span class='op'>)</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span>, pred_over <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>nlme <span class='op'>=</span> <span class='va'>pred_nlme</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='error'>Error in plot(f_saem, pred_over = list(nlme = pred_nlme)): object 'f_saem' not found</span></div><div class='input'><span class='co'># }</span>
-</div></pre>
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">ds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span>
+<span class="r-in"> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</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="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span></span>
+<span class="r-in"><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">ds</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">paste0</a></span><span class="op">(</span><span class="st">"ds "</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span></span>
+<span class="r-in"><span class="va">dfop_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">"DFOP"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span>
+<span class="r-in"> A1 <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>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span class="r-in"><span class="co"># \dontrun{</span></span>
+<span class="r-in"><span class="va">f</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">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span class="r-in"><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</span><span class="op">[</span>, <span class="fl">3</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>, standardized <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span class="r-plt img"><img src="plot.mixed.mmkin-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"></span>
+<span class="r-in"><span class="co"># For this fit we need to increase pnlsMaxiter, and we increase the</span></span>
+<span class="r-in"><span class="co"># tolerance in order to speed up the fit for this example evaluation</span></span>
+<span class="r-in"><span class="co"># It still takes 20 seconds to run</span></span>
+<span class="r-in"><span class="va">f_nlme</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span>, control <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>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-in"><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_nlme</span><span class="op">)</span></span>
+<span class="r-plt img"><img src="plot.mixed.mmkin-2.png" alt="" width="700" height="433"></span>
+<span class="r-in"></span>
+<span class="r-in"><span class="va">f_saem</span> <span class="op">&lt;-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in saem(f, transformations = "saemix"):</span> unused argument (transformations = "saemix")</span>
+<span class="r-in"><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_saem</span><span class="op">)</span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in plot(f_saem):</span> object 'f_saem' not found</span>
+<span class="r-in"></span>
+<span class="r-in"><span class="va">f_obs</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">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span>
+<span class="r-in"><span class="va">f_nlmix</span> <span class="op">&lt;-</span> <span class="fu">nlmix</span><span class="op">(</span><span class="va">f_obs</span><span class="op">)</span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in nlmix(f_obs):</span> could not find function "nlmix"</span>
+<span class="r-in"><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_nlmix</span><span class="op">)</span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in plot(f_nlmix):</span> object 'f_nlmix' not found</span>
+<span class="r-in"></span>
+<span class="r-in"><span class="co"># We can overlay the two variants if we generate predictions</span></span>
+<span class="r-in"><span class="va">pred_nlme</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">dfop_sfo</span>,</span>
+<span class="r-in"> <span class="va">f_nlme</span><span class="op">$</span><span class="va">bparms.optim</span><span class="op">[</span><span class="op">-</span><span class="fl">1</span><span class="op">]</span>,</span>
+<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="va">f_nlme</span><span class="op">$</span><span class="va">bparms.optim</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, A1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span>
+<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">180</span>, by <span class="op">=</span> <span class="fl">0.2</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-in"><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_saem</span>, pred_over <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>nlme <span class="op">=</span> <span class="va">pred_nlme</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in plot(f_saem, pred_over = list(nlme = pred_nlme)):</span> object 'f_saem' not found</span>
+<span class="r-in"><span class="co"># }</span></span>
+</code></pre></div>
+ </div>
</div>
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