Import saemix for easier profiling, update online docs

7 files changed, 52 insertions, 37 deletions

diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html
index cb048453..5c7aa3dc 100644
--- a/docs/dev/articles/web_only/benchmarks.html
+++ b/docs/dev/articles/web_only/benchmarks.html
@@ -78,7 +78,10 @@
       <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul>
 </li>
@@ -109,7 +112,7 @@
       <h1 data-toc-skip>Benchmark timings for mkin</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-11-14)</h4>
+            <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-11-15)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small>
       <div class="hidden name"><code>benchmarks.rmd</code></div>
@@ -348,8 +351,8 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.2</td>
 <td align="left">1.2.0</td>
-<td align="right">2.030</td>
-<td align="right">3.791</td>
+<td align="right">2.129</td>
+<td align="right">3.784</td>
 </tr>
 </tbody>
 </table>
@@ -527,9 +530,9 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.2</td>
 <td align="left">1.2.0</td>
-<td align="right">1.579</td>
-<td align="right">6.591</td>
-<td align="right">3.107</td>
+<td align="right">1.559</td>
+<td align="right">6.097</td>
+<td align="right">2.841</td>
 </tr>
 </tbody>
 </table>
@@ -761,12 +764,12 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.2</td>
 <td align="left">1.2.0</td>
-<td align="right">0.915</td>
-<td align="right">1.426</td>
-<td align="right">1.613</td>
-<td align="right">3.224</td>
-<td align="right">2.068</td>
-<td align="right">2.962</td>
+<td align="right">0.911</td>
+<td align="right">1.328</td>
+<td align="right">1.519</td>
+<td align="right">2.986</td>
+<td align="right">1.957</td>
+<td align="right">2.769</td>
 </tr>
 </tbody>
 </table>
diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html
index 97ea6fd4..e54bc38c 100644
--- a/docs/dev/articles/web_only/saem_benchmarks.html
+++ b/docs/dev/articles/web_only/saem_benchmarks.html
@@ -78,7 +78,10 @@
       <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul>
 </li>
@@ -109,7 +112,7 @@
       <h1 data-toc-skip>Benchmark timings for saem.mmkin</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-14)</h4>
+            <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-15)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small>
       <div class="hidden name"><code>saem_benchmarks.rmd</code></div>
@@ -306,10 +309,10 @@
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">2.589</td>
-<td align="right">4.945</td>
-<td align="right">4.786</td>
-<td align="right">4.484</td>
+<td align="right">2.11</td>
+<td align="right">4.632</td>
+<td align="right">4.264</td>
+<td align="right">4.93</td>
 </tr></tbody>
 </table>
 <p>Two-component error fits for SFO, DFOP, SFORB and HS.</p>
@@ -329,10 +332,10 @@
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">5.645</td>
-<td align="right">8.115</td>
-<td align="right">7.737</td>
-<td align="right">7.782</td>
+<td align="right">5.602</td>
+<td align="right">7.373</td>
+<td align="right">7.815</td>
+<td align="right">7.831</td>
 </tr></tbody>
 </table>
 </div>
@@ -354,8 +357,8 @@
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">25.921</td>
-<td align="right">766.034</td>
+<td align="right">24.014</td>
+<td align="right">749.699</td>
 </tr></tbody>
 </table>
 </div>
@@ -376,7 +379,7 @@
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">1269.799</td>
+<td align="right">1249.834</td>
 </tr></tbody>
 </table>
 </div>
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index ad0d8b19..e0c11a84 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -13,7 +13,7 @@ articles:
   dimethenamid_2018: web_only/dimethenamid_2018.html
   multistart: web_only/multistart.html
   saem_benchmarks: web_only/saem_benchmarks.html
-last_built: 2022-11-14T20:49Z
+last_built: 2022-11-14T23:45Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index 17a35806..b3448db0 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
diff --git a/docs/dev/reference/logLik.saem.mmkin.html b/docs/dev/reference/logLik.saem.mmkin.html
index b1ea22ef..ebef3b10 100644
--- a/docs/dev/reference/logLik.saem.mmkin.html
+++ b/docs/dev/reference/logLik.saem.mmkin.html
@@ -59,7 +59,10 @@
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul></li>
 <li>
diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html
index 14f2b75b..37930912 100644
--- a/docs/dev/reference/mkinpredict.html
+++ b/docs/dev/reference/mkinpredict.html
@@ -61,7 +61,10 @@ kinetic parameters and initial values for the state variables."><meta name="robo
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul></li>
 <li>
@@ -371,10 +374,10 @@ as these always return mapped output.</p></dd>
 <span class="r-in"><span><span class="op">}</span></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 relative elapsed</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled     1.00   0.004</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4       analytical     5.25   0.021</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1            eigen     6.00   0.024</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3          deSolve    52.50   0.210</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled      1.0   0.005</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1            eigen      4.2   0.021</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4       analytical      4.2   0.021</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3          deSolve     40.8   0.204</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span>  <span class="co"># Predict from a fitted model</span></span></span>
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index 968dc68c..73382cba 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -61,7 +61,10 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul></li>
 <li>
@@ -429,8 +432,8 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting:      3.2 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.2.0 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.2.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Mon Nov 14 21:06:30 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Mon Nov 14 21:06:30 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Tue Nov 15 00:45:58 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Tue Nov 15 00:45:58 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>
@@ -445,7 +448,7 @@ 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 9.625 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 9.189 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>