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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/HEAD/R/plot.mixed.mmkin.R" class="external-link"><code>R/plot.mixed.mmkin.R</code></a></small>
+      <div class="d-none name"><code>plot.mixed.mmkin.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class 'mixed.mmkin'</span></span>
+<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>
+<span>  <span class="va">x</span>,</span>
+<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">$</span><span class="va">mmkin</span><span class="op">)</span>,</span>
+<span>  obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span>
+<span>  standardized <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  covariates <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  covariate_quantiles <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">0.05</span>, <span class="fl">0.95</span><span class="op">)</span>,</span>
+<span>  xlab <span class="op">=</span> <span class="st">"Time"</span>,</span>
+<span>  xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span>,</span>
+<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>,</span>
+<span>  pop_curves <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  pred_over <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span>
+<span>  default_log_parms <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span>  ymax <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  maxabs <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<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>,</span>
+<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>,</span>
+<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>,</span>
+<span>  rel.height.bottom <span class="op">=</span> <span class="fl">1.1</span>,</span>
+<span>  pch_ds <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">1</span><span class="op">:</span><span class="fl">25</span>, <span class="fl">33</span>, <span class="fl">35</span><span class="op">:</span><span class="fl">38</span>, <span class="fl">40</span><span class="op">:</span><span class="fl">41</span>, <span class="fl">47</span><span class="op">:</span><span class="fl">57</span>, <span class="fl">60</span><span class="op">:</span><span class="fl">90</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/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>
+<span>  col_ds <span class="op">=</span> <span class="va">pch_ds</span> <span class="op">+</span> <span class="fl">1</span>,</span>
+<span>  lty_ds <span class="op">=</span> <span class="va">col_ds</span>,</span>
+<span>  frame <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></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 id="arg-i">i<a class="anchor" aria-label="anchor" href="#arg-i"></a></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 id="arg-obs-vars">obs_vars<a class="anchor" aria-label="anchor" href="#arg-obs-vars"></a></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></dd>
+
+
+<dt id="arg-standardized">standardized<a class="anchor" aria-label="anchor" href="#arg-standardized"></a></dt>
+<dd><p>Should the residuals be standardized? Only takes effect if
+<code>resplot = "time"</code>.</p></dd>
+
+
+<dt id="arg-covariates">covariates<a class="anchor" aria-label="anchor" href="#arg-covariates"></a></dt>
+<dd><p>Data frame with covariate values for all variables in
+any covariate models in the object. If given, it overrides 'covariate_quantiles'.
+Each line in the data frame will result in a line drawn for the population.
+Rownames are used in the legend to label the lines.</p></dd>
+
+
+<dt id="arg-covariate-quantiles">covariate_quantiles<a class="anchor" aria-label="anchor" href="#arg-covariate-quantiles"></a></dt>
+<dd><p>This argument only has an effect if the fitted
+object has covariate models. If so, the default is to show three population
+curves, for the 5th percentile, the 50th percentile and the 95th percentile
+of the covariate values used for fitting the model.</p></dd>
+
+
+<dt id="arg-xlab">xlab<a class="anchor" aria-label="anchor" href="#arg-xlab"></a></dt>
+<dd><p>Label for the x axis.</p></dd>
+
+
+<dt id="arg-xlim">xlim<a class="anchor" aria-label="anchor" href="#arg-xlim"></a></dt>
+<dd><p>Plot range in x direction.</p></dd>
+
+
+<dt id="arg-resplot">resplot<a class="anchor" aria-label="anchor" href="#arg-resplot"></a></dt>
+<dd><p>Should the residuals plotted against time or against
+predicted values?</p></dd>
+
+
+<dt id="arg-pop-curves">pop_curves<a class="anchor" aria-label="anchor" href="#arg-pop-curves"></a></dt>
+<dd><p>Per default, one population curve is drawn in case
+population parameters are fitted by the model, e.g. for saem objects.
+In case there is a covariate model, the behaviour depends on the value
+of 'covariates'</p></dd>
+
+
+<dt id="arg-pred-over">pred_over<a class="anchor" aria-label="anchor" href="#arg-pred-over"></a></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 id="arg-test-log-parms">test_log_parms<a class="anchor" aria-label="anchor" href="#arg-test-log-parms"></a></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 id="arg-conf-level">conf.level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></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 id="arg-default-log-parms">default_log_parms<a class="anchor" aria-label="anchor" href="#arg-default-log-parms"></a></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 id="arg-ymax">ymax<a class="anchor" aria-label="anchor" href="#arg-ymax"></a></dt>
+<dd><p>Vector of maximum y axis values</p></dd>
+
+
+<dt id="arg-maxabs">maxabs<a class="anchor" aria-label="anchor" href="#arg-maxabs"></a></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 id="arg-ncol-legend">ncol.legend<a class="anchor" aria-label="anchor" href="#arg-ncol-legend"></a></dt>
+<dd><p>Number of columns to use in the legend</p></dd>
+
+
+<dt id="arg-nrow-legend">nrow.legend<a class="anchor" aria-label="anchor" href="#arg-nrow-legend"></a></dt>
+<dd><p>Number of rows to use in the legend</p></dd>
+
+
+<dt id="arg-rel-height-legend">rel.height.legend<a class="anchor" aria-label="anchor" href="#arg-rel-height-legend"></a></dt>
+<dd><p>The relative height of the legend shown on top</p></dd>
+
+
+<dt id="arg-rel-height-bottom">rel.height.bottom<a class="anchor" aria-label="anchor" href="#arg-rel-height-bottom"></a></dt>
+<dd><p>The relative height of the bottom plot row</p></dd>
+
+
+<dt id="arg-pch-ds">pch_ds<a class="anchor" aria-label="anchor" href="#arg-pch-ds"></a></dt>
+<dd><p>Symbols to be used for plotting the data.</p></dd>
+
+
+<dt id="arg-col-ds">col_ds<a class="anchor" aria-label="anchor" href="#arg-col-ds"></a></dt>
+<dd><p>Colors used for plotting the observed data and the
+corresponding model prediction lines for the different datasets.</p></dd>
+
+
+<dt id="arg-lty-ds">lty_ds<a class="anchor" aria-label="anchor" href="#arg-lty-ds"></a></dt>
+<dd><p>Line types to be used for the model predictions.</p></dd>
+
+
+<dt id="arg-frame">frame<a class="anchor" aria-label="anchor" href="#arg-frame"></a></dt>
+<dd><p>Should a frame be drawn around the plots?</p></dd>
+
+
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></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 class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <p>The function is called for its side effect.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <p>Covariate models are currently only supported for saem.mmkin objects.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
+    <p>Johannes Ranke</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><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>
+<span class="r-in"><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" 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>
+<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">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>
+<span class="r-in"><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>,</span></span>
+<span class="r-in"><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></span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><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" 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>
+<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</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>
+<span class="r-plt img"><img src="plot.mixed.mmkin-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># For this fit we need to increase pnlsMaxiter, and we increase the</span></span></span>
+<span class="r-in"><span><span class="co"># tolerance in order to speed up the fit for this example evaluation</span></span></span>
+<span class="r-in"><span><span class="co"># It still takes 20 seconds to run</span></span></span>
+<span class="r-in"><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" 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>
+<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_nlme</span><span class="op">)</span></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></span>
+<span class="r-in"><span><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>
+<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_saem</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.mixed.mmkin-3.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><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>
+<span class="r-in"><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></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><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>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error:</span> object 'f_nlmix' not found</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># We can overlay the two variants if we generate predictions</span></span></span>
+<span class="r-in"><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></span>
+<span class="r-in"><span>  <span class="va">f_nlme</span><span class="op">$</span><span class="va">bparms.optim</span><span class="op">[</span><span class="op">-</span><span class="fl">1</span><span class="op">]</span>,</span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="va">f_nlme</span><span class="op">$</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>
+<span class="r-in"><span>  <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>
+<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_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>
+<span class="r-plt img"><img src="plot.mixed.mmkin-4.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+</code></pre></div>
+    </div>
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