Merge branch 'main' into custom_lsoda_call

1 files changed, 117 insertions, 59 deletions

diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html
index 2af2328d..b1083204 100644
--- a/docs/reference/plot.mixed.mmkin.html
+++ b/docs/reference/plot.mixed.mmkin.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
       </span>
     </div>
 
@@ -44,19 +44,25 @@
       <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
     </li>
     <li>
       <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
       <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
     </li>
     <li>
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul></li>
 <li>
@@ -87,94 +93,146 @@
     </div>
 
     <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>,
-  default_log_parms <span class="op">=</span> <span class="cn">NA</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 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>  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_curve <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="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>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_curve</dt>
+<dd><p>Per default, a 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, no population curve is currently shown.</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>
+    
+
+<p>The function is called for its side effect.</p>
     </div>
     <div id="author">
     <h2>Author</h2>
@@ -183,41 +241,41 @@ corresponding model prediction lines for the different datasets.</p></dd>
 
     <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>
+    <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 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-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 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-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-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 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-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 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-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 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-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 class="co"># }</span></span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
   </div>
@@ -232,7 +290,7 @@ corresponding model prediction lines for the different datasets.</p></dd>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
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