WIP adapting to new deSolve with faster lsoda

2 files changed, 83 insertions, 16 deletions

diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html
index 451d8afe..fb799462 100644
--- a/vignettes/web_only/benchmarks.html
+++ b/vignettes/web_only/benchmarks.html
@@ -1592,7 +1592,7 @@ div.tocify {
 
 <h1 class="title toc-ignore">Benchmark timings for mkin</h1>
 <h4 class="author">Johannes Ranke</h4>
-<h4 class="date">Last change 14 July 2022 (rebuilt 2023-01-05)</h4>
+<h4 class="date">Last change 14 July 2022 (rebuilt 2023-02-13)</h4>
 
 </div>
 
@@ -1636,11 +1636,31 @@ FOMC_SFO &lt;- mkinmod(
 DFOP_SFO &lt;- mkinmod(
   parent = mkinsub(&quot;FOMC&quot;, &quot;m1&quot;), # erroneously used FOMC twice, not fixed for consistency
   m1 = mkinsub(&quot;SFO&quot;))
-t3 &lt;- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[[&quot;elapsed&quot;]]
-t4 &lt;- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
-    error_model = &quot;tc&quot;))[[&quot;elapsed&quot;]]
-t5 &lt;- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
+t3 &lt;- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[[&quot;elapsed&quot;]]</code></pre>
+<pre><code>## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable
+## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable</code></pre>
+<pre class="r"><code>t4 &lt;- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
+    error_model = &quot;tc&quot;))[[&quot;elapsed&quot;]]</code></pre>
+<pre><code>## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable
+## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable
+## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable
+## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable</code></pre>
+<pre class="r"><code>t5 &lt;- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
     error_model = &quot;obs&quot;))[[&quot;elapsed&quot;]]</code></pre>
+<pre><code>## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable
+## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable
+## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable
+## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable</code></pre>
 <p>Two metabolites, synthetic data:</p>
 <pre class="r"><code>m_synth_SFO_lin &lt;- mkinmod(parent = mkinsub(&quot;SFO&quot;, &quot;M1&quot;),
                            M1 = mkinsub(&quot;SFO&quot;, &quot;M2&quot;),
@@ -1656,18 +1676,36 @@ SFO_lin_a &lt;- synthetic_data_for_UBA_2014[[1]]$data
 
 DFOP_par_c &lt;- synthetic_data_for_UBA_2014[[12]]$data
 
-t6 &lt;- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))[[&quot;elapsed&quot;]]
-t7 &lt;- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))[[&quot;elapsed&quot;]]
-
-t8 &lt;- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
-    error_model = &quot;tc&quot;))[[&quot;elapsed&quot;]]
-t9 &lt;- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
-    error_model = &quot;tc&quot;))[[&quot;elapsed&quot;]]
-
-t10 &lt;- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
-    error_model = &quot;obs&quot;))[[&quot;elapsed&quot;]]
-t11 &lt;- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
+t6 &lt;- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))[[&quot;elapsed&quot;]]</code></pre>
+<pre><code>## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable</code></pre>
+<pre class="r"><code>t7 &lt;- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))[[&quot;elapsed&quot;]]</code></pre>
+<pre><code>## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable</code></pre>
+<pre class="r"><code>t8 &lt;- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
+    error_model = &quot;tc&quot;))[[&quot;elapsed&quot;]]</code></pre>
+<pre><code>## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable
+## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable</code></pre>
+<pre class="r"><code>t9 &lt;- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
+    error_model = &quot;tc&quot;))[[&quot;elapsed&quot;]]</code></pre>
+<pre><code>## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable
+## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable</code></pre>
+<pre class="r"><code>t10 &lt;- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
+    error_model = &quot;obs&quot;))[[&quot;elapsed&quot;]]</code></pre>
+<pre><code>## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable
+## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable</code></pre>
+<pre class="r"><code>t11 &lt;- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
     error_model = &quot;obs&quot;))[[&quot;elapsed&quot;]]</code></pre>
+<pre><code>## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable
+## Error in mkinmod[[&quot;symbols&quot;]] : 
+##   object of type &#39;closure&#39; is not subsettable</code></pre>
 </div>
 <div id="results" class="section level2">
 <h2>Results</h2>
@@ -1858,6 +1896,14 @@ models fitted to two datasets, i.e. eight fits for each test.</p>
 <td align="right">1.308</td>
 <td align="right">1.793</td>
 </tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X 16-Core Processor</td>
+<td align="left">4.2.2</td>
+<td align="left">1.3.0</td>
+<td align="right">1.271</td>
+<td align="right">1.787</td>
+</tr>
 </tbody>
 </table>
 </div>
@@ -2068,6 +2114,15 @@ for each test.</p>
 <td align="right">2.364</td>
 <td align="right">1.230</td>
 </tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X 16-Core Processor</td>
+<td align="left">4.2.2</td>
+<td align="left">1.3.0</td>
+<td align="right">0.526</td>
+<td align="right">0.623</td>
+<td align="right">0.631</td>
+</tr>
 </tbody>
 </table>
 </div>
@@ -2344,6 +2399,18 @@ dataset, i.e. one fit for each test.</p>
 <td align="right">0.801</td>
 <td align="right">1.093</td>
 </tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 9 7950X 16-Core Processor</td>
+<td align="left">4.2.2</td>
+<td align="left">1.3.0</td>
+<td align="right">0.242</td>
+<td align="right">0.237</td>
+<td align="right">0.238</td>
+<td align="right">0.239</td>
+<td align="right">0.237</td>
+<td align="right">0.237</td>
+</tr>
 </tbody>
 </table>
 </div>
diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda
index 64ac2680..93138541 100644
--- a/vignettes/web_only/mkin_benchmarks.rda
+++ b/vignettes/web_only/mkin_benchmarks.rda