Merge branch 'main' into custom_lsoda_call

1 files changed, 19 insertions, 13 deletions

diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 0b78bb2e..d17d7aeb 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
       </span>
     </div>
 
@@ -62,19 +62,25 @@
       <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
     </li>
     <li>
-      <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a>
     </li>
     <li>
       <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
+      <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
       <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
     </li>
     <li>
       <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>
@@ -105,7 +111,7 @@
       <h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">2022-10-29</h4>
+            <h4 data-toc-skip class="date">2022-11-17</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/compiled_models.rmd" class="external-link"><code>vignettes/web_only/compiled_models.rmd</code></a></small>
       <div class="hidden name"><code>compiled_models.rmd</code></div>
@@ -163,10 +169,10 @@
 <span>  <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span></span>
 <span><span class="op">}</span></span></code></pre></div>
 <pre><code><span><span class="co">##                    test replications relative elapsed</span></span>
-<span><span class="co">## 4            analytical            1    1.000   0.188</span></span>
-<span><span class="co">## 3     deSolve, compiled            1    1.628   0.306</span></span>
-<span><span class="co">## 2      Eigenvalue based            1    2.064   0.388</span></span>
-<span><span class="co">## 1 deSolve, not compiled            1   38.894   7.312</span></span></code></pre>
+<span><span class="co">## 4            analytical            1    1.000   0.218</span></span>
+<span><span class="co">## 3     deSolve, compiled            1    1.550   0.338</span></span>
+<span><span class="co">## 2      Eigenvalue based            1    1.950   0.425</span></span>
+<span><span class="co">## 1 deSolve, not compiled            1   33.041   7.203</span></span></code></pre>
 <p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p>
 </div>
 <div class="section level2">
@@ -193,11 +199,11 @@
 <span><span class="op">}</span></span></code></pre></div>
 <pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
 <pre><code><span><span class="co">##                    test replications relative elapsed</span></span>
-<span><span class="co">## 2     deSolve, compiled            1     1.00   0.441</span></span>
-<span><span class="co">## 1 deSolve, not compiled            1    30.68  13.530</span></span></code></pre>
-<p>Here we get a performance benefit of a factor of 31 using the version of the differential equation model compiled from C code!</p>
-<p>This vignette was built with mkin 1.1.2 on</p>
-<pre><code><span><span class="co">## R version 4.2.1 (2022-06-23)</span></span>
+<span><span class="co">## 2     deSolve, compiled            1    1.000   0.510</span></span>
+<span><span class="co">## 1 deSolve, not compiled            1   26.247  13.386</span></span></code></pre>
+<p>Here we get a performance benefit of a factor of 26 using the version of the differential equation model compiled from C code!</p>
+<p>This vignette was built with mkin 1.2.0 on</p>
+<pre><code><span><span class="co">## R version 4.2.2 (2022-10-31)</span></span>
 <span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span>
 <span><span class="co">## Running under: Debian GNU/Linux 11 (bullseye)</span></span></code></pre>
 <pre><code><span><span class="co">## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</span></span></code></pre>