Plot method for nlme.mmkin objects

Update docs

11 files changed, 351 insertions, 76 deletions

diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 190bfe87..c29e413d 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -146,7 +146,9 @@
 <a href="#mkin-0-9-50-4-unreleased" class="anchor"></a>mkin 0.9.50.4 (unreleased)<small> Unreleased </small>
 </h1>
 <ul>
-<li>‘saemix_model’, ‘saemix_data’: Helper functions to fit nonlinear mixed-effects models for mmkin row objects using the saemix package</li>
+<li><p>‘plot’ method for ‘nlme.mmkin’ objects</p></li>
+<li><p>‘print’ method for ‘mmkin’ objects</p></li>
+<li><p>‘saemix_model’, ‘saemix_data’: Helper functions to fit nonlinear mixed-effects models for mmkin row objects using the saemix package</p></li>
 </ul>
 </div>
     <div id="mkin-0-9-50-3-2020-10-08" class="section level1">
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index 4bca36e6..8c97cd7c 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   web_only/NAFTA_examples: NAFTA_examples.html
   web_only/benchmarks: benchmarks.html
   web_only/compiled_models: compiled_models.html
-last_built: 2020-10-22T11:16Z
+last_built: 2020-10-23T22:30Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/Extract.mmkin.html b/docs/dev/reference/Extract.mmkin.html
index c69259b6..0c02355f 100644
--- a/docs/dev/reference/Extract.mmkin.html
+++ b/docs/dev/reference/Extract.mmkin.html
@@ -40,7 +40,7 @@
 
 
 <meta property="og:title" content="Subsetting method for mmkin objects — [.mmkin" />
-<meta property="og:description" content="Subsetting method for mmkin objects." />
+<meta property="og:description" content="Subsetting method for mmkin objects" />
 
 
 <meta name="robots" content="noindex">
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -120,7 +120,7 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -139,12 +139,12 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Subsetting method for mmkin objects</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small>
     <div class="hidden name"><code>Extract.mmkin.Rd</code></div>
     </div>
 
     <div class="ref-description">
-    <p>Subsetting method for mmkin objects.</p>
+    <p>Subsetting method for mmkin objects</p>
     </div>
 
     <pre class="usage"># S3 method for mmkin
@@ -179,30 +179,46 @@ either a list of mkinfit objects or a single mkinfit object.</p></td>
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>An object of class <code><a href='mmkin.html'>mmkin</a></code>.</p>
+    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+
+    <p>Johannes Ranke</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>
   <span class='co'># Only use one core, to pass R CMD check --as-cran</span>
-  <span class='no'>fits</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>B</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>),
-                <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-  <span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#&gt;       dataset
-#&gt; model  B       C      
-#&gt;   FOMC List,39 List,39
-#&gt; attr(,"class")
-#&gt; [1] "mmkin"</div><div class='input'>  <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#&gt;       dataset
-#&gt; model  B      
-#&gt;   SFO  List,39
-#&gt;   FOMC List,39
-#&gt; attr(,"class")
-#&gt; [1] "mmkin"</div><div class='input'>  <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#&gt;      dataset
-#&gt; model B      
-#&gt;   SFO List,39
-#&gt; attr(,"class")
-#&gt; [1] "mmkin"</div><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(
+  <span class='va'>fits</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/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>B <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, C <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>,
+                cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+  <span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>
+</div><div class='output co'>#&gt; &lt;mmkin&gt; object
+#&gt; Status of individual fits:
+#&gt; 
+#&gt;       dataset
+#&gt; model  B  C 
+#&gt;   FOMC OK OK
+#&gt; 
+#&gt; OK: No warnings</div><div class='input'>  <span class='va'>fits</span><span class='op'>[</span>, <span class='st'>"B"</span><span class='op'>]</span>
+</div><div class='output co'>#&gt; &lt;mmkin&gt; object
+#&gt; Status of individual fits:
+#&gt; 
+#&gt;       dataset
+#&gt; model  B 
+#&gt;   SFO  OK
+#&gt;   FOMC OK
+#&gt; 
+#&gt; OK: No warnings</div><div class='input'>  <span class='va'>fits</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='st'>"B"</span><span class='op'>]</span>
+</div><div class='output co'>#&gt; &lt;mmkin&gt; object
+#&gt; Status of individual fits:
+#&gt; 
+#&gt;      dataset
+#&gt; model B 
+#&gt;   SFO OK
+#&gt; 
+#&gt; OK: No warnings</div><div class='input'>
+  <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span><span class='op'>(</span>
     <span class='co'># This extracts an mkinfit object with lots of components</span>
-    <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span>]]
-  )</div><div class='output co'>#&gt; $par
+    <span class='va'>fits</span><span class='op'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span><span class='op'>]</span><span class='op'>]</span>
+  <span class='op'>)</span>
+</div><div class='output co'>#&gt; $par
 #&gt;  parent_0 log_alpha  log_beta     sigma 
 #&gt; 99.666193  2.549849  5.050586  1.890202 
 #&gt; 
@@ -217,12 +233,11 @@ either a list of mkinfit objects or a single mkinfit object.</p></td>
 #&gt; 
 #&gt; $evaluations
 #&gt; function gradient 
-#&gt;       25       72 
+#&gt;       25       78 
 #&gt; 
 #&gt; $message
 #&gt; [1] "both X-convergence and relative convergence (5)"
-#&gt; </div><div class='input'>
-</div></pre>
+#&gt; </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -238,7 +253,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index 9c8f80fc..cfc5bc2b 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png
index 1b15782a..71c768bd 100644
--- a/docs/dev/reference/Rplot002.png
+++ b/docs/dev/reference/Rplot002.png
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index 5d70a450..24056025 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -297,6 +297,12 @@ of an mmkin object</p></td>
           <p><code><a href="AIC.mmkin.html">AIC(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i>&lt;mmkin&gt;</i>)</a></code> </p>
         </td>
         <td><p>Calculate the AIC for a column of an mmkin object</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="print.mmkin.html">print(<i>&lt;mmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Print method for mmkin objects</p></td>
       </tr>
     </tbody><tbody>
       <tr>
@@ -334,6 +340,12 @@ of an mmkin object</p></td>
           <p><code><a href="get_deg_func.html">get_deg_func()</a></code> </p>
         </td>
         <td><p>Retrieve a degradation function from the mmkin namespace</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="saemix.html">saemix_model()</a></code> <code><a href="saemix.html">saemix_data()</a></code> </p>
+        </td>
+        <td><p>Create saemix models from mmkin row objects</p></td>
       </tr>
     </tbody><tbody>
       <tr>
diff --git a/docs/dev/reference/plot.nlme.mmkin-1.png b/docs/dev/reference/plot.nlme.mmkin-1.png
index fe2ef7d3..91e3ca52 100644
--- a/docs/dev/reference/plot.nlme.mmkin-1.png
+++ b/docs/dev/reference/plot.nlme.mmkin-1.png
diff --git a/docs/dev/reference/plot.nlme.mmkin-2.png b/docs/dev/reference/plot.nlme.mmkin-2.png
index 265fd2e0..57128ade 100644
--- a/docs/dev/reference/plot.nlme.mmkin-2.png
+++ b/docs/dev/reference/plot.nlme.mmkin-2.png
diff --git a/docs/dev/reference/plot.nlme.mmkin.html b/docs/dev/reference/plot.nlme.mmkin.html
index 7e6124a1..f17a23e3 100644
--- a/docs/dev/reference/plot.nlme.mmkin.html
+++ b/docs/dev/reference/plot.nlme.mmkin.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
       </span>
     </div>
 
@@ -120,7 +120,7 @@
       </ul>
       <ul class="nav navbar-nav navbar-right">
         <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -139,7 +139,7 @@
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Plot a fitted nonlinear mixed model obtained via an mmkin row object</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/plot.nlme.mmkin.R'><code>R/plot.nlme.mmkin.R</code></a></small>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.nlme.mmkin.R'><code>R/plot.nlme.mmkin.R</code></a></small>
     <div class="hidden name"><code>plot.nlme.mmkin.Rd</code></div>
     </div>
 
@@ -148,21 +148,29 @@
     </div>
 
     <pre class="usage"><span class='co'># S3 method for nlme.mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(
-  <span class='no'>x</span>,
-  <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span>(<span class='no'>x</span>$<span class='no'>mmkin_orig</span>),
-  <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
-  <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>,
-  <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"time"</span>, <span class='st'>"errmod"</span>),
-  <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>,
-  <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>,
-  <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>,
-  <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>,
-  <span class='kw'>ymax</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
-  <span class='no'>...</span>
-)</pre>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
+  <span class='va'>x</span>,
+  i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin_orig</span><span class='op'>)</span>,
+  main <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin_orig</span><span class='op'>)</span>,
+  obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
+  standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
+  ylab <span class='op'>=</span> <span class='st'>"Observed"</span>,
+  xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
+  legends <span class='op'>=</span> <span class='fl'>1</span>,
+  lpos <span class='op'>=</span> <span class='st'>"topright"</span>,
+  inset <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.05</span>, <span class='fl'>0.05</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>,
+  ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
+  maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
+  cex <span class='op'>=</span> <span class='fl'>0.7</span>,
+  rel.height.middle <span class='op'>=</span> <span class='fl'>0.9</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>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -181,35 +189,55 @@ in case plots get too large</p></td>
       <td><p>The main title placed on the outer margin of the plot.</p></td>
     </tr>
     <tr>
+      <th>obs_vars</th>
+      <td><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>ylab</th>
+      <td><p>Label for the y axis.</p></td>
+    </tr>
+    <tr>
+      <th>xlim</th>
+      <td><p>Plot range in x direction.</p></td>
+    </tr>
+    <tr>
       <th>legends</th>
       <td><p>An index for the fits for which legends should be shown.</p></td>
     </tr>
     <tr>
-      <th>resplot</th>
-      <td><p>Should the residuals plotted against time, using
-<code><a href='mkinresplot.html'>mkinresplot</a></code>, or as squared residuals against predicted
-values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td>
+      <th>lpos</th>
+      <td><p>Position(s) of the legend(s). Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> as
+the first argument.  If not length one, this should be of the same length
+as the obs_var argument.</p></td>
     </tr>
     <tr>
-      <th>standardized</th>
-      <td><p>Should the residuals be standardized? This option
-is passed to <code><a href='mkinresplot.html'>mkinresplot</a></code>, it only takes effect if
-<code>resplot = "time"</code>.</p></td>
+      <th>inset</th>
+      <td><p>Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> if applicable.</p></td>
     </tr>
     <tr>
-      <th>show_errmin</th>
-      <td><p>Should the chi2 error level be shown on top of the plots
-to the left?</p></td>
+      <th>resplot</th>
+      <td><p>Should the residuals plotted against time or against
+predicted values?</p></td>
     </tr>
     <tr>
-      <th>errmin_var</th>
-      <td><p>The variable for which the FOCUS chi2 error value should
-be shown.</p></td>
+      <th>ymax</th>
+      <td><p>Vector of maximum y axis values</p></td>
     </tr>
     <tr>
-      <th>errmin_digits</th>
-      <td><p>The number of significant digits for rounding the FOCUS
-chi2 error percentage.</p></td>
+      <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>cex</th>
@@ -221,8 +249,21 @@ chi2 error percentage.</p></td>
 than two rows of plots are shown.</p></td>
     </tr>
     <tr>
-      <th>ymax</th>
-      <td><p>Maximum y axis value for <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p></td>
+      <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>
@@ -234,16 +275,24 @@ than two rows of plots are shown.</p></td>
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>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>
+
+    <p>Johannes Ranke</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='no'>ds</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>],
- <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)], <span class='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>))
-<span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='st'>"SFO"</span>, <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.0195</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p =  0.011</span></div><div class='input'><span class='co'>#plot(f) # too many panels for pkgdown</span>
-<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f</span>[, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='plot.nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>)
-<span class='no'>f_nlme</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>)
-
-<span class='co'>#plot(f_nlme) # too many panels for pkgdown</span>
-<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='plot.nlme.mmkin-2.png' alt='' width='700' height='433' /></div></pre>
+    <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='mkinsub.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='mkinsub.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='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>, cores <span class='op'>=</span> <span class='fl'>1</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.nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span>
+<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='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-4</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.nlme.mmkin-2.png' alt='' width='700' height='433' /></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
@@ -259,7 +308,7 @@ than two rows of plots are shown.</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/reference/print.mmkin.html b/docs/dev/reference/print.mmkin.html
new file mode 100644
index 00000000..12c67d86
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@@ -0,0 +1,194 @@
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Print method for mmkin objects</h1>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small>
+    <div class="hidden name"><code>print.mmkin.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Print method for mmkin objects</p>
+    </div>
+
+    <pre class="usage"><span class='co'># S3 method for mmkin</span>
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre>
+
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>x</th>
+      <td><p>An <a href='mmkin.html'>mmkin</a> object.</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>Not used.</p></td>
+    </tr>
+    </table>
+
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
+</div>
+
+
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+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
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+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml
index e284abf6..8c4d8cbe 100644
--- a/docs/dev/sitemap.xml
+++ b/docs/dev/sitemap.xml
@@ -166,6 +166,9 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/print.mkinmod.html</loc>
   </url>
   <url>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/print.mmkin.html</loc>
+  </url>
+  <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/reexports.html</loc>
   </url>
   <url>