Remove stray sentence from vignette, update docs

15 files changed, 22 insertions, 19 deletions

diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
index fa5f3834..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 3caf465f..f06a860e 100644
--- a/docs/reference/Rplot002.png
+++ b/docs/reference/Rplot002.png
diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png
index 88ebd2d4..f8bf10bb 100644
--- a/docs/reference/Rplot003.png
+++ b/docs/reference/Rplot003.png
diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png
index 7e87d63d..12d337a4 100644
--- a/docs/reference/Rplot004.png
+++ b/docs/reference/Rplot004.png
diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png
index 76f25647..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 2516edff..1c70a094 100644
--- a/docs/reference/create_deg_func.html
+++ b/docs/reference/create_deg_func.html
@@ -120,8 +120,8 @@
 <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-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   0.394    1.000     0.393        0          0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   0.678    1.721     0.677        0          0</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>
@@ -134,8 +134,8 @@
 <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-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   0.829    1.000     0.829        0          0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   1.559    1.881     1.559        0          0</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>
diff --git a/docs/reference/dimethenamid_2018-3.png b/docs/reference/dimethenamid_2018-3.png
index efb89bdb..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 d2ed8647..e913fa27 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:         4.1.3 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Sat Apr  9 18:03:34 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Sat Apr  9 18:03:34 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 787.836 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 d93b0950..45e4eebe 100644
--- a/docs/reference/nlme.mmkin-1.png
+++ b/docs/reference/nlme.mmkin-1.png
diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png
index 5afccfbb..b9a68e92 100644
--- a/docs/reference/nlme.mmkin-2.png
+++ b/docs/reference/nlme.mmkin-2.png
diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png
index bf3aac6c..2a724bed 100644
--- a/docs/reference/nlme.mmkin-3.png
+++ b/docs/reference/nlme.mmkin-3.png
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 4c2ff570..b74d1e7b 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -155,7 +155,8 @@ variables in the model.</p></dd>
 <dt>xlim</dt>
 <dd><p>Plot range in x direction.</p></dd>
 <dt>ylim</dt>
-<dd><p>Plot range in y direction.</p></dd>
+<dd><p>Plot range in y direction. If given as a list, plot ranges
+for the different plot rows can be given for row layout.</p></dd>
 <dt>col_obs</dt>
 <dd><p>Colors used for plotting the observed data and the
 corresponding model prediction lines.</p></dd>
@@ -237,7 +238,9 @@ latex is being used for the formatting of the chi2 error level, if
 <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>, full <span class="op">=</span> <span class="st">"Metabolite M1"</span> <span class="op">)</span><span class="op">)</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
 <span class="r-in"><span class="va">fit</span> <span class="op">&lt;-</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_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
 <span class="r-in"><span class="va">fit</span> <span class="op">&lt;-</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_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
 <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span>
 <span class="r-plt img"><img src="plot.mkinfit-1.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span class="fu">plot_res</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span>
diff --git a/docs/reference/saem-4.png b/docs/reference/saem-4.png
index 5f65ba2e..bb775c25 100644
--- a/docs/reference/saem-4.png
+++ b/docs/reference/saem-4.png
diff --git a/docs/reference/saem.html b/docs/reference/saem.html
index cc597665..f9e6565f 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:         4.1.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Mon Mar  7 13:15:26 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Mon Mar  7 13:15:26 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 8.741 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 3f98bec7..4879269e 100644
--- a/docs/reference/summary.nlme.mmkin.html
+++ b/docs/reference/summary.nlme.mmkin.html
@@ -96,7 +96,7 @@ endpoints such as formation fractions and DT50 values. Optionally
 
     <div id="ref-usage">
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for nlme.mmkin</span>
-<span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span>
+<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">object</span>,
   data <span class="op">=</span> <span class="cn">FALSE</span>,
   verbose <span class="op">=</span> <span class="cn">FALSE</span>,
@@ -201,12 +201,12 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> iteration limit reached without convergence (10)</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/r/base/summary.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-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:      3.1.155 </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:         4.1.3 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Mon Mar 14 08:58:29 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Mon Mar 14 08:58:29 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>
@@ -216,7 +216,7 @@ 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 0.527 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>