saemix.mmkin and nlme.mmkin inherit from mixed.mmkin

With a plot method. The class mixed.mmkin is currently only a virtual
class created to unify the plotting method.

13 files changed, 370 insertions, 55 deletions

diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index cfc5bc2b..fc26276a 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 8ada7133..48e8698c 100644
--- a/docs/dev/reference/Rplot002.png
+++ b/docs/dev/reference/Rplot002.png
diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png
index cd2014eb..b4581e35 100644
--- a/docs/dev/reference/Rplot003.png
+++ b/docs/dev/reference/Rplot003.png
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index 5ed2044b..ada9fb24 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -325,21 +325,21 @@ of an mmkin object</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="plot_mixed.html">plot(<i>&lt;saem.mmkin&gt;</i>)</a></code> <code><a href="plot_mixed.html">plot(<i>&lt;nlme.mmkin&gt;</i>)</a></code> </p>
+          <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p>
         </td>
-        <td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td>
+        <td><p>Fit nonlinear mixed models with SAEM</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="summary.nlme.mmkin.html">summary(<i>&lt;nlme.mmkin&gt;</i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i>&lt;summary.nlme.mmkin&gt;</i>)</a></code> </p>
+          <p><code><a href="plot.mixed.mmkin.html">plot(<i>&lt;mixed.mmkin&gt;</i>)</a></code> </p>
         </td>
-        <td><p>Summary method for class "nlme.mmkin"</p></td>
+        <td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p>
+          <p><code><a href="summary.nlme.mmkin.html">summary(<i>&lt;nlme.mmkin&gt;</i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i>&lt;summary.nlme.mmkin&gt;</i>)</a></code> </p>
         </td>
-        <td><p>Fit nonlinear mixed models with SAEM</p></td>
+        <td><p>Summary method for class "nlme.mmkin"</p></td>
       </tr><tr>
         
         <td>
diff --git a/docs/dev/reference/nlme.mmkin-1.png b/docs/dev/reference/nlme.mmkin-1.png
index 04d8b234..25bebeca 100644
--- a/docs/dev/reference/nlme.mmkin-1.png
+++ b/docs/dev/reference/nlme.mmkin-1.png
diff --git a/docs/dev/reference/nlme.mmkin-3.png b/docs/dev/reference/nlme.mmkin-3.png
index 281d6024..46846067 100644
--- a/docs/dev/reference/nlme.mmkin-3.png
+++ b/docs/dev/reference/nlme.mmkin-3.png
diff --git a/docs/dev/reference/nlme.mmkin-4.png b/docs/dev/reference/nlme.mmkin-4.png
index d504e8f0..6724163f 100644
--- a/docs/dev/reference/nlme.mmkin-4.png
+++ b/docs/dev/reference/nlme.mmkin-4.png
diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html
index c3cc53ff..defef75d 100644
--- a/docs/dev/reference/nlme.mmkin.html
+++ b/docs/dev/reference/nlme.mmkin.html
@@ -152,7 +152,7 @@ have been obtained by fitting the same model to a list of datasets.</p>
     </div>
 
     <pre class="usage"><span class='co'># S3 method for mmkin</span>
-<span class='fu'>nlme</span><span class='op'>(</span>
+<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span>
   <span class='va'>model</span>,
   data <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.frame</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.parent</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>,
   <span class='va'>fixed</span>,
@@ -253,8 +253,8 @@ parameters taken from the mmkin object are used</p></td>
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>Upon success, a fitted nlme.mmkin object, which is an nlme object
-with additional elements</p>
+    <p>Upon success, a fitted 'nlme.mmkin' object, which is an nlme object
+with additional elements. It also inherits from 'mixed.mmkin'.</p>
     <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
 
     <p>As the object inherits from <a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme::nlme</a>, there is a wealth of
@@ -262,7 +262,8 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <code><a href='https://rdrr.io/pkg/nlme/man/intervals.html'>nlme::intervals()</a></code>, <code><a href='https://rdrr.io/pkg/nlme/man/anova.lme.html'>nlme::anova.lme()</a></code> and <code><a href='https://rdrr.io/pkg/nlme/man/coef.lme.html'>nlme::coef.lme()</a></code>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <div class='dont-index'><p><code><a href='nlme_function.html'>nlme_function()</a></code></p></div>
+    <div class='dont-index'><p><code><a href='nlme_function.html'>nlme_function()</a></code>, <a href='plot.mixed.mmkin.html'>plot.mixed.mmkin</a>, <a href='summary.nlme.mmkin.html'>summary.nlme.mmkin</a>,
+parms.nlme.mmkin</p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>,
@@ -288,21 +289,21 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 #&gt; Log-likelihood: -238.5635
 #&gt; 
 #&gt; Fixed effects:
-#&gt;  list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) 
-#&gt;    parent_0      log_k1      log_k2       g_ilr 
-#&gt; 94.17015133 -1.80015306 -4.14738870  0.02290935 
+#&gt;  list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) 
+#&gt;    parent_0      log_k1      log_k2    g_qlogis 
+#&gt; 94.17015185 -1.80015278 -4.14738834  0.03239833 
 #&gt; 
 #&gt; Random effects:
-#&gt;  Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1)
+#&gt;  Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)
 #&gt;  Level: ds
 #&gt;  Structure: Diagonal
-#&gt;         parent_0    log_k1  log_k2     g_ilr Residual
-#&gt; StdDev: 2.488249 0.8447273 1.32965 0.3289311 2.321364
+#&gt;         parent_0    log_k1  log_k2  g_qlogis Residual
+#&gt; StdDev: 2.488249 0.8447275 1.32965 0.4651789 2.321364
 #&gt; </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
 </div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; $distimes
 #&gt;            DT50     DT90 DT50back  DT50_k1  DT50_k2
-#&gt; parent 10.79857 100.7937 30.34193 4.193938 43.85443
+#&gt; parent 10.79857 100.7937 30.34192 4.193937 43.85442
 #&gt; </div><div class='input'>
 <span class='co'># \dontrun{</span>
   <span class='va'>f_nlme_2</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><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span>, start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, log_k_parent <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span>
@@ -353,35 +354,35 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
     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'>5e-4</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; 
 #&gt; **Iteration 1
-#&gt; LME step: Loglik: -404.9582, nlminb iterations: 1
+#&gt; LME step: Loglik: -404.9583, nlminb iterations: 1
 #&gt; reStruct  parameters:
 #&gt;        ds1        ds2        ds3        ds4        ds5        ds6 
-#&gt; -0.4114355  0.9798697  1.6990037  0.7293315  0.3354323  1.7113046 
+#&gt; -0.4114356  0.9798646  1.3524300  0.7293315  0.3354323  1.3647313 
 #&gt;  Beginning PNLS step: ..  completed fit_nlme() step.
-#&gt; PNLS step: RSS =  630.3644 
-#&gt;  fixed effects: 93.82269  -5.455991  -0.6788957  -1.862196  -4.199671  0.05532828  
+#&gt; PNLS step: RSS =  630.3633 
+#&gt;  fixed effects: 93.82269  -5.455993  -0.9601037  -1.862196  -4.199671  0.07824609  
 #&gt;  iterations: 120 
 #&gt; Convergence crit. (must all become &lt;= tolerance = 0.0005):
 #&gt;     fixed  reStruct 
-#&gt; 0.7885368 0.5822683 
+#&gt; 0.7897284 0.5822782 
 #&gt; 
 #&gt; **Iteration 2
 #&gt; LME step: Loglik: -407.7755, nlminb iterations: 11
 #&gt; reStruct  parameters:
-#&gt;          ds1          ds2          ds3          ds4          ds5          ds6 
-#&gt; -0.371224133  0.003056179  1.789939402  0.724671158  0.301602977  1.754200729 
+#&gt;         ds1         ds2         ds3         ds4         ds5         ds6 
+#&gt; -0.37122411  0.00305562  1.44336560  0.72467122  0.30160310  1.40762692 
 #&gt;  Beginning PNLS step: ..  completed fit_nlme() step.
-#&gt; PNLS step: RSS =  630.3633 
-#&gt;  fixed effects: 93.82269  -5.455992  -0.6788958  -1.862196  -4.199671  0.05532831  
+#&gt; PNLS step: RSS =  630.3637 
+#&gt;  fixed effects: 93.82269  -5.455992  -0.9601036  -1.862196  -4.199671  0.0782462  
 #&gt;  iterations: 120 
 #&gt; Convergence crit. (must all become &lt;= tolerance = 0.0005):
 #&gt;        fixed     reStruct 
-#&gt; 4.789774e-07 2.200661e-05 </div><div class='input'>
+#&gt; 1.375673e-06 9.758294e-06 </div><div class='input'>
   <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span>
 </div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'>
   <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
 </div><div class='output co'>#&gt;                 Model df       AIC       BIC    logLik   Test  L.Ratio p-value
-#&gt; f_nlme_dfop_sfo     1 13  843.8547  884.6201 -408.9273                        
+#&gt; f_nlme_dfop_sfo     1 13  843.8547  884.6201 -408.9274                        
 #&gt; f_nlme_sfo_sfo      2  9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274  &lt;.0001</div><div class='input'>
   <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; $ff
@@ -400,7 +401,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 #&gt; $distimes
 #&gt;             DT50     DT90 DT50back  DT50_k1  DT50_k2
 #&gt; parent  11.07091 104.6320 31.49738 4.462384 46.20825
-#&gt; A1     162.30536 539.1667       NA       NA       NA
+#&gt; A1     162.30523 539.1663       NA       NA       NA
 #&gt; </div><div class='input'>
   <span class='kw'>if</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='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>&gt;</span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span> <span class='co'># tc error model for nlme available</span>
     <span class='co'># Attempts to fit metabolite kinetics with the tc error model are possible,</span>
@@ -425,23 +426,23 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 #&gt; Log-likelihood: -238.4298
 #&gt; 
 #&gt; Fixed effects:
-#&gt;  list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) 
-#&gt;    parent_0      log_k1      log_k2       g_ilr 
-#&gt; 94.04774463 -1.82339924 -4.16715509  0.04020161 
+#&gt;  list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) 
+#&gt;    parent_0      log_k1      log_k2    g_qlogis 
+#&gt; 94.04774566 -1.82339808 -4.16715311  0.05685186 
 #&gt; 
 #&gt; Random effects:
-#&gt;  Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1)
+#&gt;  Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)
 #&gt;  Level: ds
 #&gt;  Structure: Diagonal
-#&gt;         parent_0    log_k1   log_k2     g_ilr Residual
-#&gt; StdDev: 2.473883 0.8499901 1.337187 0.3294411        1
+#&gt;         parent_0    log_k1   log_k2  g_qlogis Residual
+#&gt; StdDev: 2.473881 0.8499884 1.337185 0.4659005        1
 #&gt; 
 #&gt; Variance function:
 #&gt;  Structure: Constant plus proportion of variance covariate
 #&gt;  Formula: ~fitted(.) 
 #&gt;  Parameter estimates:
 #&gt;      const       prop 
-#&gt; 2.23222625 0.01262414 </div><div class='input'>
+#&gt; 2.23224114 0.01262341 </div><div class='input'>
   <span class='va'>f_2_obs</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>,
    <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>,
     <span class='va'>ds_2</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>
diff --git a/docs/dev/reference/plot.mixed.mmkin-1.png b/docs/dev/reference/plot.mixed.mmkin-1.png
new file mode 100644
index 00000000..5cb33214
--- /dev/null
+++ b/docs/dev/reference/plot.mixed.mmkin-1.png
diff --git a/docs/dev/reference/plot.mixed.mmkin-2.png b/docs/dev/reference/plot.mixed.mmkin-2.png
new file mode 100644
index 00000000..c0d67204
--- /dev/null
+++ b/docs/dev/reference/plot.mixed.mmkin-2.png
diff --git a/docs/dev/reference/plot.mixed.mmkin-3.png b/docs/dev/reference/plot.mixed.mmkin-3.png
new file mode 100644
index 00000000..67058e6c
--- /dev/null
+++ b/docs/dev/reference/plot.mixed.mmkin-3.png
diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html
new file mode 100644
index 00000000..4108aea3
--- /dev/null
+++ b/docs/dev/reference/plot.mixed.mmkin.html
@@ -0,0 +1,313 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
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+
+
+<!-- jquery -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
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+
+      
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+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</h1>
+    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.mixed.mmkin.R'><code>R/plot.mixed.mmkin.R</code></a></small>
+    <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>
+
+    <pre class="usage"><span class='co'># S3 method for mixed.mmkin</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
+  <span class='va'>x</span>,
+  i <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>,
+  obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>,
+  standardized <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  xlab <span class='op'>=</span> <span class='st'>"Time"</span>,
+  xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>,
+  resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>,
+  ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
+  maxabs <span class='op'>=</span> <span class='st'>"auto"</span>,
+  ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>&lt;=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>,
+  nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>,
+  rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>,
+  rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>,
+  pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>,
+  col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>,
+  lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>,
+  frame <span class='op'>=</span> <span class='cn'>TRUE</span>,
+  <span class='va'>...</span>
+<span class='op'>)</span></pre>
+
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>x</th>
+      <td><p>An object of class <a href='saem.html'>saem.mmkin</a> or <a href='nlme.mmkin.html'>nlme.mmkin</a></p></td>
+    </tr>
+    <tr>
+      <th>i</th>
+      <td><p>A numeric index to select datasets for which to plot the individual predictions,
+in case plots get too large</p></td>
+    </tr>
+    <tr>
+      <th>obs_vars</th>
+      <td><p>A character vector of names of the observed variables for
+which the data and the model should be plotted. Defauls to all observed
+variables in the model.</p></td>
+    </tr>
+    <tr>
+      <th>standardized</th>
+      <td><p>Should the residuals be standardized? Only takes effect if
+<code>resplot = "time"</code>.</p></td>
+    </tr>
+    <tr>
+      <th>xlab</th>
+      <td><p>Label for the x axis.</p></td>
+    </tr>
+    <tr>
+      <th>xlim</th>
+      <td><p>Plot range in x direction.</p></td>
+    </tr>
+    <tr>
+      <th>resplot</th>
+      <td><p>Should the residuals plotted against time or against
+predicted values?</p></td>
+    </tr>
+    <tr>
+      <th>ymax</th>
+      <td><p>Vector of maximum y axis values</p></td>
+    </tr>
+    <tr>
+      <th>maxabs</th>
+      <td><p>Maximum absolute value of the residuals. This is used for the
+scaling of the y axis and defaults to "auto".</p></td>
+    </tr>
+    <tr>
+      <th>ncol.legend</th>
+      <td><p>Number of columns to use in the legend</p></td>
+    </tr>
+    <tr>
+      <th>nrow.legend</th>
+      <td><p>Number of rows to use in the legend</p></td>
+    </tr>
+    <tr>
+      <th>rel.height.legend</th>
+      <td><p>The relative height of the legend shown on top</p></td>
+    </tr>
+    <tr>
+      <th>rel.height.bottom</th>
+      <td><p>The relative height of the bottom plot row</p></td>
+    </tr>
+    <tr>
+      <th>pch_ds</th>
+      <td><p>Symbols to be used for plotting the data.</p></td>
+    </tr>
+    <tr>
+      <th>col_ds</th>
+      <td><p>Colors used for plotting the observed data and the
+corresponding model prediction lines for the different datasets.</p></td>
+    </tr>
+    <tr>
+      <th>lty_ds</th>
+      <td><p>Line types to be used for the model predictions.</p></td>
+    </tr>
+    <tr>
+      <th>frame</th>
+      <td><p>Should a frame be drawn around the plots?</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <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='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='co'># \dontrun{</span>
+<span class='va'>f</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='img'><img src='plot.mixed.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='co'># For this fit we need to increase pnlsMaxiter, and we increase the</span>
+<span class='co'># tolerance in order to speed up the fit for this example evaluation</span>
+<span class='va'>f_nlme</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-3</span><span class='op'>)</span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span>
+</div><div class='img'><img src='plot.mixed.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='va'>f_saem</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Running main SAEM algorithm
+#&gt; [1] "Mon Nov  9 17:18:17 2020"
+#&gt; ....
+#&gt;     Minimisation finished
+#&gt; [1] "Mon Nov  9 17:18:26 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span>
+</div><div class='img'><img src='plot.mixed.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>
+</div></pre>
+  </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>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index 26f4c3e3..f1b4c421 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -206,7 +206,8 @@ by the saemix function?</p></td>
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>An S3 object of class 'saem.mmkin', containing the fitted
-<a href='https://rdrr.io/pkg/saemix/man/SaemixObject-class.html'>saemix::SaemixObject</a> as a list component named 'so'.</p>
+<a href='https://rdrr.io/pkg/saemix/man/SaemixObject-class.html'>saemix::SaemixObject</a> as a list component named 'so'. The
+object also inherits from 'mixed.mmkin'.</p>
 <p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixModel-class.html'>saemix::SaemixModel</a> object.</p>
 <p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixData-class.html'>saemix::SaemixData</a> object.</p>
     <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
@@ -218,7 +219,7 @@ psi0 of <code><a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix::
 using <a href='mmkin.html'>mmkin</a>.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <div class='dont-index'><p><a href='summary.saem.mmkin.html'>summary.saem.mmkin</a></p></div>
+    <div class='dont-index'><p><a href='summary.saem.mmkin.html'>summary.saem.mmkin</a> <a href='plot.mixed.mmkin.html'>plot.mixed.mmkin</a></p></div>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
@@ -229,27 +230,27 @@ using <a href='mmkin.html'>mmkin</a>.</p>
   state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='va'>f_saem_p0_fixed</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov  9 09:03:11 2020"
+#&gt; [1] "Mon Nov  9 17:18:28 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Mon Nov  9 09:03:13 2020"</div><div class='input'>
+#&gt; [1] "Mon Nov  9 17:18:30 2020"</div><div class='input'>
 <span class='va'>f_mmkin_parent</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='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='va'>f_saem_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov  9 09:03:14 2020"
+#&gt; [1] "Mon Nov  9 17:18:31 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Mon Nov  9 09:03:16 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Mon Nov  9 17:18:33 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov  9 09:03:16 2020"
+#&gt; [1] "Mon Nov  9 17:18:33 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Mon Nov  9 09:03:18 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Mon Nov  9 17:18:35 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov  9 09:03:19 2020"
+#&gt; [1] "Mon Nov  9 17:18:36 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Mon Nov  9 09:03:22 2020"</div><div class='input'>
+#&gt; [1] "Mon Nov  9 17:18:39 2020"</div><div class='input'>
 <span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span>
 <span class='co'># functions from saemix</span>
 <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span>
@@ -295,10 +296,10 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 <span class='va'>f_mmkin_parent_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
 <span class='va'>f_saem_fomc_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov  9 09:03:24 2020"
+#&gt; [1] "Mon Nov  9 17:18:41 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Mon Nov  9 09:03:29 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</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='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
+#&gt; [1] "Mon Nov  9 17:18:46 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</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='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Likelihoods computed by importance sampling </div><div class='output co'>#&gt;        AIC      BIC
 #&gt; 1 467.7644 465.0305
 #&gt; 2 469.4862 466.3617</div><div class='input'>
@@ -318,20 +319,20 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 <span class='co'># solutions written for mkin this took around four minutes</span>
 <span class='va'>f_saem_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov  9 09:03:31 2020"
+#&gt; [1] "Mon Nov  9 17:18:48 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Mon Nov  9 09:03:36 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Mon Nov  9 17:18:53 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov  9 09:03:37 2020"
+#&gt; [1] "Mon Nov  9 17:18:54 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Mon Nov  9 09:03:46 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
+#&gt; [1] "Mon Nov  9 17:19:03 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; saemix version used for fitting:      3.1.9000 
 #&gt; mkin version used for pre-fitting:  0.9.50.4 
 #&gt; R version used for fitting:         4.0.3 
-#&gt; Date of fit:     Mon Nov  9 09:03:47 2020 
-#&gt; Date of summary: Mon Nov  9 09:03:47 2020 
+#&gt; Date of fit:     Mon Nov  9 17:19:04 2020 
+#&gt; Date of summary: Mon Nov  9 17:19:04 2020 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -346,7 +347,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted in 9.758 s using 300, 100 iterations
+#&gt; Fitted in 9.941 s using 300, 100 iterations
 #&gt; 
 #&gt; Variance model: Constant variance 
 #&gt;