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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="hidden name"><code>plot.mixed.mmkin.Rd</code></div>
</div>
<div class="ref-description">
<p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for 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"><=</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"><=</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="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>
<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 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></dd>
<dt>standardized</dt>
<dd><p>Should the residuals be standardized? Only takes effect if
<code>resplot = "time"</code>.</p></dd>
<dt>covariates</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>covariate_quantiles</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>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>pop_curves</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>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>default_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>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>
</div>
<div id="note">
<h2>Note</h2>
<p>Covariate models are currently only supported for saem.mmkin objects.</p>
</div>
<div id="author">
<h2>Author</h2>
<p>Johannes Ranke</p>
</div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">ds</span> <span class="op"><-</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"><-</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"><-</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"><-</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"><-</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"><-</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"><-</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"><-</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">#></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">#></span> <span class="error">Error in eval(expr, envir, enclos):</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"><-</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>
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