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-rw-r--r--docs/articles/FOCUS_D.html15
-rw-r--r--docs/articles/FOCUS_L.html43
-rw-r--r--docs/articles/mkin.html9
-rw-r--r--docs/articles/twa.html9
-rw-r--r--docs/articles/web_only/FOCUS_Z.html9
-rw-r--r--docs/articles/web_only/NAFTA_examples.html9
-rw-r--r--docs/articles/web_only/benchmarks.html24
-rw-r--r--docs/articles/web_only/compiled_models.html23
8 files changed, 81 insertions, 60 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 10b8f685..243ebee1 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -68,6 +68,9 @@
<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>
+ </li>
</ul>
</li>
<li>
@@ -97,10 +100,10 @@
<h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-12</h4>
+ <h4 class="date">2020-05-14</h4>
- <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.Rmd"><code>vignettes/FOCUS_D.Rmd</code></a></small>
- <div class="hidden name"><code>FOCUS_D.Rmd</code></div>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.rmd"><code>vignettes/FOCUS_D.rmd</code></a></small>
+ <div class="hidden name"><code>FOCUS_D.rmd</code></div>
</div>
@@ -177,8 +180,8 @@
<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">fit</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:36 2020
-## Date of summary: Tue May 12 15:31:36 2020
+## Date of fit: Thu May 14 17:07:12 2020
+## Date of summary: Thu May 14 17:07:12 2020
##
## Equations:
## d_parent/dt = - k_parent * parent
@@ -186,7 +189,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 421 model solutions performed in 0.165 s
+## Fitted using 421 model solutions performed in 0.167 s
##
## Error model: Constant variance
##
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 742718cb..df5c77c4 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -68,6 +68,9 @@
<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>
+ </li>
</ul>
</li>
<li>
@@ -97,10 +100,10 @@
<h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-12</h4>
+ <h4 class="date">2020-05-14</h4>
- <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_L.Rmd"><code>vignettes/FOCUS_L.Rmd</code></a></small>
- <div class="hidden name"><code>FOCUS_L.Rmd</code></div>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_L.rmd"><code>vignettes/FOCUS_L.rmd</code></a></small>
+ <div class="hidden name"><code>FOCUS_L.rmd</code></div>
</div>
@@ -123,15 +126,15 @@
<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L1.SFO</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:38 2020
-## Date of summary: Tue May 12 15:31:38 2020
+## Date of fit: Thu May 14 17:07:14 2020
+## Date of summary: Thu May 14 17:07:14 2020
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 133 model solutions performed in 0.03 s
+## Fitted using 133 model solutions performed in 0.032 s
##
## Error model: Constant variance
##
@@ -224,8 +227,8 @@
## doubtful</code></pre>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:38 2020
-## Date of summary: Tue May 12 15:31:38 2020
+## Date of fit: Thu May 14 17:07:14 2020
+## Date of summary: Thu May 14 17:07:14 2020
##
##
## Warning: Optimisation did not converge:
@@ -332,8 +335,8 @@
<div class="sourceCode" id="cb17"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L2.FOMC</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:39 2020
-## Date of summary: Tue May 12 15:31:39 2020
+## Date of fit: Thu May 14 17:07:15 2020
+## Date of summary: Thu May 14 17:07:15 2020
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -411,8 +414,8 @@
<div class="sourceCode" id="cb20"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L2.DFOP</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:39 2020
-## Date of summary: Tue May 12 15:31:39 2020
+## Date of fit: Thu May 14 17:07:15 2020
+## Date of summary: Thu May 14 17:07:15 2020
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -421,7 +424,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 572 model solutions performed in 0.13 s
+## Fitted using 572 model solutions performed in 0.131 s
##
## Error model: Constant variance
##
@@ -514,8 +517,8 @@
<div class="sourceCode" id="cb24"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L3</span><span class="kw">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span>]])</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:39 2020
-## Date of summary: Tue May 12 15:31:40 2020
+## Date of fit: Thu May 14 17:07:16 2020
+## Date of summary: Thu May 14 17:07:16 2020
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -623,8 +626,8 @@
<div class="sourceCode" id="cb29"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L4</span><span class="kw">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span>]], <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:40 2020
-## Date of summary: Tue May 12 15:31:40 2020
+## Date of fit: Thu May 14 17:07:16 2020
+## Date of summary: Thu May 14 17:07:16 2020
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
@@ -687,15 +690,15 @@
<div class="sourceCode" id="cb31"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L4</span><span class="kw">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span>]], <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
<pre><code>## mkin version used for fitting: 0.9.50.2
## R version used for fitting: 4.0.0
-## Date of fit: Tue May 12 15:31:40 2020
-## Date of summary: Tue May 12 15:31:40 2020
+## Date of fit: Thu May 14 17:07:16 2020
+## Date of summary: Thu May 14 17:07:16 2020
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 224 model solutions performed in 0.044 s
+## Fitted using 224 model solutions performed in 0.043 s
##
## Error model: Constant variance
##
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 0d4ced0f..37b7b1a1 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -68,6 +68,9 @@
<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>
+ </li>
</ul>
</li>
<li>
@@ -97,10 +100,10 @@
<h1 data-toc-skip>Introduction to mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-12</h4>
+ <h4 class="date">2020-05-14</h4>
- <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/mkin.Rmd"><code>vignettes/mkin.Rmd</code></a></small>
- <div class="hidden name"><code>mkin.Rmd</code></div>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/mkin.rmd"><code>vignettes/mkin.rmd</code></a></small>
+ <div class="hidden name"><code>mkin.rmd</code></div>
</div>
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index b58306f1..c231e17d 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -68,6 +68,9 @@
<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>
+ </li>
</ul>
</li>
<li>
@@ -97,10 +100,10 @@
<h1 data-toc-skip>Calculation of time weighted average concentrations with mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-12</h4>
+ <h4 class="date">2020-05-14</h4>
- <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/twa.Rmd"><code>vignettes/twa.Rmd</code></a></small>
- <div class="hidden name"><code>twa.Rmd</code></div>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/twa.rmd"><code>vignettes/twa.rmd</code></a></small>
+ <div class="hidden name"><code>twa.rmd</code></div>
</div>
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 0c34d77d..3427afb6 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -68,6 +68,9 @@
<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>
+ </li>
</ul>
</li>
<li>
@@ -97,10 +100,10 @@
<h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-12</h4>
+ <h4 class="date">2020-05-14</h4>
- <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/FOCUS_Z.Rmd"><code>vignettes/web_only/FOCUS_Z.Rmd</code></a></small>
- <div class="hidden name"><code>FOCUS_Z.Rmd</code></div>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/FOCUS_Z.rmd"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small>
+ <div class="hidden name"><code>FOCUS_Z.rmd</code></div>
</div>
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index 411341b8..46cb7aa5 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -68,6 +68,9 @@
<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>
+ </li>
</ul>
</li>
<li>
@@ -97,10 +100,10 @@
<h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-12</h4>
+ <h4 class="date">2020-05-14</h4>
- <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.Rmd"><code>vignettes/web_only/NAFTA_examples.Rmd</code></a></small>
- <div class="hidden name"><code>NAFTA_examples.Rmd</code></div>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.rmd"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small>
+ <div class="hidden name"><code>NAFTA_examples.rmd</code></div>
</div>
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 202ec25f..97e22303 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -100,7 +100,7 @@
<h1 data-toc-skip>Benchmark timings for mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-13</h4>
+ <h4 class="date">2020-05-14</h4>
<small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/benchmarks.rmd"><code>vignettes/web_only/benchmarks.rmd</code></a></small>
<div class="hidden name"><code>benchmarks.rmd</code></div>
@@ -210,8 +210,8 @@
</tr>
<tr class="even">
<td align="left">0.9.50.2</td>
-<td align="right">1.704</td>
-<td align="right">3.909</td>
+<td align="right">1.714</td>
+<td align="right">3.971</td>
</tr>
</tbody>
</table>
@@ -260,9 +260,9 @@
</tr>
<tr class="even">
<td align="left">0.9.50.2</td>
-<td align="right">1.370</td>
-<td align="right">6.147</td>
-<td align="right">2.747</td>
+<td align="right">1.402</td>
+<td align="right">6.174</td>
+<td align="right">2.764</td>
</tr>
</tbody>
</table>
@@ -329,12 +329,12 @@
</tr>
<tr class="even">
<td align="left">0.9.50.2</td>
-<td align="right">0.761</td>
-<td align="right">1.213</td>
-<td align="right">1.287</td>
-<td align="right">2.886</td>
-<td align="right">2.054</td>
-<td align="right">2.984</td>
+<td align="right">0.777</td>
+<td align="right">1.236</td>
+<td align="right">1.332</td>
+<td align="right">2.872</td>
+<td align="right">2.069</td>
+<td align="right">2.987</td>
</tr>
</tbody>
</table>
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 85134720..837b288b 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -68,6 +68,9 @@
<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>
+ </li>
</ul>
</li>
<li>
@@ -97,10 +100,10 @@
<h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-05-12</h4>
+ <h4 class="date">2020-05-14</h4>
- <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/compiled_models.Rmd"><code>vignettes/web_only/compiled_models.Rmd</code></a></small>
- <div class="hidden name"><code>compiled_models.Rmd</code></div>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/compiled_models.rmd"><code>vignettes/web_only/compiled_models.rmd</code></a></small>
+ <div class="hidden name"><code>compiled_models.rmd</code></div>
</div>
@@ -149,10 +152,10 @@
<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="st">"R package rbenchmark is not available"</span>)
}</pre></body></html></div>
<pre><code>## test replications relative elapsed
-## 4 analytical 1 1.000 0.190
-## 3 deSolve, compiled 1 1.774 0.337
-## 2 Eigenvalue based 1 2.105 0.400
-## 1 deSolve, not compiled 1 42.763 8.125</code></pre>
+## 4 analytical 1 1.000 0.191
+## 3 deSolve, compiled 1 1.801 0.344
+## 2 Eigenvalue based 1 2.105 0.402
+## 1 deSolve, not compiled 1 42.864 8.187</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 id="model-without-analytical-solution" class="section level2">
@@ -178,9 +181,9 @@
}</pre></body></html></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<pre><code>## test replications relative elapsed
-## 2 deSolve, compiled 1 1.000 0.476
-## 1 deSolve, not compiled 1 30.103 14.329</code></pre>
-<p>Here we get a performance benefit of a factor of 30 using the version of the differential equation model compiled from C code!</p>
+## 2 deSolve, compiled 1 1.000 0.466
+## 1 deSolve, not compiled 1 30.942 14.419</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 0.9.50.2 on</p>
<pre><code>## R version 4.0.0 (2020-04-24)
## Platform: x86_64-pc-linux-gnu (64-bit)

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