Merge branch 'dmta_vignette'

10 files changed, 26 insertions, 15 deletions

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>