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-rw-r--r--vignettes/compiled_models.html42
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diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 2f2a6edb..e6f21b09 100644
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+++ b/vignettes/compiled_models.html
@@ -77,7 +77,7 @@ img {
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<div id="benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues" class="section level1">
<h1>Benchmark for a model that can also be solved with Eigenvalues</h1>
-<p>This evaluation is taken from the example section of mkinfit. When using an mkin version greater than 0.9-36 and the ccSolve package is installed and functional, you will get a message that the model is being compiled when defining a model using mkinmod.</p>
+<p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a compiler (gcc) is installed, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod.</p>
<pre class="r"><code>library(&quot;mkin&quot;)
SFO_SFO &lt;- mkinmod(
parent = list(type = &quot;SFO&quot;, to = &quot;m1&quot;, sink = TRUE),
@@ -94,20 +94,20 @@ mb.1 &lt;- microbenchmark(
smb.1 &lt;- summary(mb.1)[-1]
rownames(smb.1) &lt;- c(&quot;deSolve, not compiled&quot;, &quot;Eigenvalue based&quot;, &quot;deSolve, compiled&quot;)
print(smb.1)</code></pre>
-<pre><code>## min lq mean median uq
-## deSolve, not compiled 6192.0125 6195.3470 6211.0309 6198.6816 6220.5401
-## Eigenvalue based 956.7604 1008.7224 1026.2572 1060.6844 1061.0055
-## deSolve, compiled 869.6880 871.9315 883.4929 874.1751 890.3953
+<pre><code>## min lq mean median uq
+## deSolve, not compiled 4969.585 5033.7311 5092.7389 5097.8773 5154.3160
+## Eigenvalue based 868.731 891.7239 909.6449 914.7169 930.1018
+## deSolve, compiled 4935.049 4935.4796 4968.2150 4935.9097 4984.7978
## max neval
-## deSolve, not compiled 6242.3986 3
-## Eigenvalue based 1061.3266 3
-## deSolve, compiled 906.6155 3</code></pre>
+## deSolve, not compiled 5210.7547 3
+## Eigenvalue based 945.4867 3
+## deSolve, compiled 5033.6858 3</code></pre>
<p>We see that using the compiled model is almost a factor of 8 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p>
<pre class="r"><code>smb.1[&quot;median&quot;]/smb.1[&quot;deSolve, compiled&quot;, &quot;median&quot;]</code></pre>
-<pre><code>## median
-## deSolve, not compiled 7.120877
-## Eigenvalue based 1.205328
-## deSolve, compiled 1.000000</code></pre>
+<pre><code>## median
+## deSolve, not compiled 1.0328141
+## Eigenvalue based 0.1853188
+## deSolve, compiled 1.0000000</code></pre>
</div>
<div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level1">
<h1>Benchmark for a model that can not be solved with Eigenvalues</h1>
@@ -124,16 +124,16 @@ smb.2 &lt;- summary(mb.2)[-1]
rownames(smb.2) &lt;- c(&quot;deSolve, not compiled&quot;, &quot;deSolve, compiled&quot;)
print(smb.2)</code></pre>
<pre><code>## min lq mean median uq
-## deSolve, not compiled 13.297283 13.427702 13.481155 13.558121 13.573092
-## deSolve, compiled 1.486926 1.526887 1.546851 1.566848 1.576813
-## max neval
-## deSolve, not compiled 13.588063 3
-## deSolve, compiled 1.586778 3</code></pre>
+## deSolve, not compiled 11.745276 11.754288 11.820726 11.763300 11.858451
+## deSolve, compiled 1.385829 1.386407 1.400841 1.386985 1.408347
+## max neval
+## deSolve, not compiled 11.95360 3
+## deSolve, compiled 1.42971 3</code></pre>
<pre class="r"><code>smb.2[&quot;median&quot;]/smb.2[&quot;deSolve, compiled&quot;, &quot;median&quot;]</code></pre>
-<pre><code>## median
-## deSolve, not compiled 8.653119
-## deSolve, compiled 1.000000</code></pre>
-<p>Here we get a performance benefit of more than a factor of 8 using the version of the differential equation model compiled from C code using the ccSolve package!</p>
+<pre><code>## median
+## deSolve, not compiled 8.4812
+## deSolve, compiled 1.0000</code></pre>
+<p>Here we get a performance benefit of more than a factor of 10 using the version of the differential equation model compiled from C code using the inline package!</p>
</div>

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