Merge branch 'dmta_vignette'

13 files changed, 36 insertions, 25 deletions

diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html
index 7650f06f..0c51cd50 100644
--- a/docs/articles/web_only/dimethenamid_2018.html
+++ b/docs/articles/web_only/dimethenamid_2018.html
@@ -105,7 +105,7 @@
       <h1 data-toc-skip>Example evaluations of the dimethenamid data from 2018</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 7 March 2022, built on 18 May 2022</h4>
+            <h4 data-toc-skip class="date">Last change 7 March 2022, built on 30 Jun 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/dimethenamid_2018.rmd" class="external-link"><code>vignettes/web_only/dimethenamid_2018.rmd</code></a></small>
       <div class="hidden name"><code>dimethenamid_2018.rmd</code></div>
@@ -155,20 +155,20 @@
   error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <p>The plot of the individual SFO fits shown below suggests that at least in some datasets the degradation slows down towards later time points, and that the scatter of the residuals error is smaller for smaller values (panel to the right):</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></code></pre></div>
 <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_sfo_const-1.png" width="700"></p>
 <p>Using biexponential decline (DFOP) results in a slightly more random scatter of the residuals:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></code></pre></div>
 <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const-1.png" width="700"></p>
 <p>The population curve (bold line) in the above plot results from taking the mean of the individual transformed parameters, i.e. of log k1 and log k2, as well as of the logit of the g parameter of the DFOP model). Here, this procedure does not result in parameters that represent the degradation well, because in some datasets the fitted value for k2 is extremely close to zero, leading to a log k2 value that dominates the average. This is alleviated if only rate constants that pass the t-test for significant difference from zero (on the untransformed scale) are considered in the averaging:</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const_test-1.png" width="700"></p>
 <p>While this is visually much more satisfactory, such an average procedure could introduce a bias, as not all results from the individual fits enter the population curve with the same weight. This is where nonlinear mixed-effects models can help out by treating all datasets with equally by fitting a parameter distribution model together with the degradation model and the error model (see below).</p>
 <p>The remaining trend of the residuals to be higher for higher predicted residues is reduced by using the two-component error model:</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
 <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_tc_test-1.png" width="700"></p>
 <p>However, note that in the case of using this error model, the fits to the Flaach and BBA 2.3 datasets appear to be ill-defined, indicated by the fact that they did not converge:</p>
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
@@ -222,7 +222,7 @@ f_parent_nlme_dfop_tc       3 10 671.91 702.34 -325.96 2 vs 3  134.69  &lt;.0001
 <p>While the SFO variants converge fast, the additional parameters introduced by this lead to convergence warnings for the DFOP model. The model comparison clearly show that adding correlations between random effects does not improve the fits.</p>
 <p>The selected model (DFOP with two-component error) fitted to the data assuming no correlations between random effects is shown below.</p>
 <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><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_parent_nlme_dfop_tc</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_nlme_dfop_tc</span><span class="op">)</span></code></pre></div>
 <p><img src="dimethenamid_2018_files/figure-html/plot_parent_nlme-1.png" width="700"></p>
 </div>
 <div class="section level4">
@@ -380,8 +380,8 @@ DFOP tc more iterations    NaN    NaN</code></pre>
 <div class="section level3">
 <h3 id="comparison">Comparison<a class="anchor" aria-label="anchor" href="#comparison"></a>
 </h3>
-<p>The following table gives the AIC values obtained with both backend packages using the same control parameters (800 iterations burn-in, 300 iterations second phase, 15 chains). Note that</p>
-<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
+<p>The following table gives the AIC values obtained with both backend packages using the same control parameters (800 iterations burn-in, 300 iterations second phase, 15 chains).</p>
+<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">AIC_all</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>
   check.names <span class="op">=</span> <span class="cn">FALSE</span>,
   <span class="st">"Degradation model"</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">"SFO"</span>, <span class="st">"SFO"</span>, <span class="st">"DFOP"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index e653e88e..9912aeb2 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
   benchmarks: web_only/benchmarks.html
   compiled_models: web_only/compiled_models.html
   dimethenamid_2018: web_only/dimethenamid_2018.html
-last_built: 2022-05-18T19:26Z
+last_built: 2022-06-30T07:49Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
index ca982688..17a35806 100644
--- a/docs/reference/Rplot001.png
+++ b/docs/reference/Rplot001.png
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
index de2d61aa..f06a860e 100644
--- a/docs/reference/Rplot002.png
+++ b/docs/reference/Rplot002.png
diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png
index 014bf258..cb419daa 100644
--- a/docs/reference/Rplot005.png
+++ b/docs/reference/Rplot005.png
diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html
index 36b054fe..b85acb7a 100644
--- a/docs/reference/create_deg_func.html
+++ b/docs/reference/create_deg_func.html
@@ -119,7 +119,12 @@
 <span class="r-in">    deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
 <span class="r-in">    replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: rbenchmark</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>there is no package called ‘rbenchmark’</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>         test replications elapsed relative user.self sys.self user.child</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical            2   0.401     1.00     0.401    0.000          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   1.211     3.02     1.210    0.002          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   sys.child</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1         0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2         0</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></span>
 <span class="r-in">    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">"m1"</span><span class="op">)</span>,</span>
 <span class="r-in">    m1 <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><span class="op">)</span></span>
@@ -128,7 +133,12 @@
 <span class="r-in">    analytical <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
 <span class="r-in">    deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
 <span class="r-in">    replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in benchmark(analytical = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "analytical",     quiet = TRUE), deSolve = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "deSolve",     quiet = TRUE), replications = 2):</span> could not find function "benchmark"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>         test replications elapsed relative user.self sys.self user.child</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical            2    0.84    1.000     0.839    0.001          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2    3.19    3.798     3.188    0.001          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   sys.child</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1         0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2         0</span>
 <span class="r-in"><span class="co"># }</span></span>
 </code></pre></div>
     </div>
diff --git a/docs/reference/dimethenamid_2018-3.png b/docs/reference/dimethenamid_2018-3.png
index 339aaef6..7c876208 100644
--- a/docs/reference/dimethenamid_2018-3.png
+++ b/docs/reference/dimethenamid_2018-3.png
diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html
index a3cfc271..431e5c34 100644
--- a/docs/reference/dimethenamid_2018.html
+++ b/docs/reference/dimethenamid_2018.html
@@ -202,9 +202,9 @@ specific pieces of information in the comments.</p>
 <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting:      3.0 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.1.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.2.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Wed May 18 20:37:14 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed May 18 20:37:14 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.2.1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Thu Jun 30 10:21:01 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Jun 30 10:21:01 2022 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_DMTA/dt = - k_DMTA * DMTA</span>
@@ -217,7 +217,7 @@ specific pieces of information in the comments.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type deSolve </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 1660.941 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 1845.619 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 9 chains</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Two-component variance function </span>
diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png
index fe1ff61d..45e4eebe 100644
--- a/docs/reference/nlme.mmkin-1.png
+++ b/docs/reference/nlme.mmkin-1.png
diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png
index 2ab51f97..2a724bed 100644
--- a/docs/reference/nlme.mmkin-3.png
+++ b/docs/reference/nlme.mmkin-3.png
diff --git a/docs/reference/saem.html b/docs/reference/saem.html
index 7e22e839..e9898a73 100644
--- a/docs/reference/saem.html
+++ b/docs/reference/saem.html
@@ -303,9 +303,9 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting:      3.0 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.1.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.2.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Wed May 18 20:41:57 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed May 18 20:41:57 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.2.1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Thu Jun 30 10:23:53 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Jun 30 10:23:53 2022 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
@@ -320,7 +320,7 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 9.745 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 8.85 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 10 chains</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Constant variance </span>
diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html
index 8440e8c2..ff014cc1 100644
--- a/docs/reference/summary.nlme.mmkin.html
+++ b/docs/reference/summary.nlme.mmkin.html
@@ -198,12 +198,13 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span>
 <span class="r-in"><span class="va">f_mmkin</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds_sfo_syn</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</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_mmkin</span><span class="op">)</span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span>
 <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> nlme version used for fitting:      3.1.157 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> nlme version used for fitting:      3.1.155 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.1.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.2.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Wed May 18 20:42:02 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed May 18 20:42:02 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.2.1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Thu Jun 30 10:23:57 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Jun 30 10:23:57 2022 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - k_parent * parent</span>
@@ -213,7 +214,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 0.516 s using 4 iterations</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 0.538 s using 4 iterations</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Two-component variance function </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
diff --git a/vignettes/web_only/dimethenamid_2018.rmd b/vignettes/web_only/dimethenamid_2018.rmd
index f34ca3ae..41681d45 100644
--- a/vignettes/web_only/dimethenamid_2018.rmd
+++ b/vignettes/web_only/dimethenamid_2018.rmd
@@ -362,7 +362,7 @@ print(AIC_parent_saemix_methods_defaults)
 
 The following table gives the AIC values obtained with both backend packages
 using the same control parameters (800 iterations burn-in, 300 iterations
-second phase, 15 chains). Note that
+second phase, 15 chains).
 
 ```{r AIC_all, cache = FALSE}
 AIC_all <- data.frame(