aboutsummaryrefslogtreecommitdiff
path: root/docs/articles
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2018-03-09 23:14:39 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2018-03-09 23:14:39 +0100
commit0b677308e3ffbf742880f05cc54da469f3ecc854 (patch)
tree26dab561d6f5a31923b28b5fdf6c1859727dfe7f /docs/articles
parent5aec8e34680e05671347f7577ae36c9ad8e37063 (diff)
Another rebuild of the static docs
Now with rbenchmark installed, to get results for the compiled_models vignette
Diffstat (limited to 'docs/articles')
-rw-r--r--docs/articles/FOCUS_D.html13
-rw-r--r--docs/articles/FOCUS_D_files/figure-html/plot-1.pngbin96321 -> 98934 bytes
-rw-r--r--docs/articles/FOCUS_D_files/figure-html/plot_2-1.pngbin14047 -> 14308 bytes
-rw-r--r--docs/articles/FOCUS_L.html47
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.pngbin28683 -> 29157 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.pngbin52097 -> 54520 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.pngbin21427 -> 21712 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.pngbin36600 -> 38347 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.pngbin23247 -> 23493 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.pngbin14668 -> 14866 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.pngbin23624 -> 23973 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.pngbin27537 -> 27988 bytes
-rw-r--r--docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.pngbin27959 -> 28412 bytes
-rw-r--r--docs/articles/FOCUS_Z.html7
-rw-r--r--docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.pngbin83846 -> 85456 bytes
-rw-r--r--docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.pngbin123289 -> 128546 bytes
-rw-r--r--docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.pngbin122641 -> 128162 bytes
-rw-r--r--docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.pngbin96633 -> 101891 bytes
-rw-r--r--docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.pngbin22186 -> 22697 bytes
-rw-r--r--docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.pngbin84217 -> 86036 bytes
-rw-r--r--docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.pngbin83907 -> 85658 bytes
-rw-r--r--docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.pngbin96969 -> 101516 bytes
-rw-r--r--docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.pngbin123363 -> 129164 bytes
-rw-r--r--docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.pngbin123396 -> 128994 bytes
-rw-r--r--docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.pngbin103846 -> 108244 bytes
-rw-r--r--docs/articles/compiled_models.html37
-rw-r--r--docs/articles/index.html1
-rw-r--r--docs/articles/mkin.html7
-rw-r--r--docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.pngbin110404 -> 114757 bytes
-rw-r--r--docs/articles/twa.html7
30 files changed, 54 insertions, 65 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index af04f755..d85246f8 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -9,10 +9,7 @@
<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS Example Dataset D">
-<meta property="og:description" content="">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
@@ -80,7 +77,7 @@
<h1>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-03-01</h4>
+ <h4 class="date">2018-03-09</h4>
</div>
@@ -155,8 +152,8 @@
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div>
<pre><code>## mkin version: 0.9.46.3
## R version: 3.4.3
-## Date of fit: Thu Mar 1 14:17:55 2018
-## Date of summary: Thu Mar 1 14:17:55 2018
+## Date of fit: Fri Mar 9 23:09:48 2018
+## Date of summary: Fri Mar 9 23:09:48 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -164,7 +161,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.993 s
+## Fitted with method Port using 153 model solutions performed in 0.99 s
##
## Weighting: none
##
diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png
index b4fa2ff4..c0fab72d 100644
--- a/docs/articles/FOCUS_D_files/figure-html/plot-1.png
+++ b/docs/articles/FOCUS_D_files/figure-html/plot-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png
index ba06ce31..47916477 100644
--- a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png
+++ b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 5de06ad5..196a0c4f 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -9,10 +9,7 @@
<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS Laboratory Data L1 to L3">
-<meta property="og:description" content="">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
@@ -80,7 +77,7 @@
<h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-03-01</h4>
+ <h4 class="date">2018-03-09</h4>
</div>
@@ -103,15 +100,15 @@ FOCUS_<span class="dv">2006</span>_L1_mkin &lt;-<span class="st"> </span><span c
<span class="kw">summary</span>(m.L1.SFO)</code></pre></div>
<pre><code>## mkin version: 0.9.46.3
## R version: 3.4.3
-## Date of fit: Thu Mar 1 14:31:57 2018
-## Date of summary: Thu Mar 1 14:31:57 2018
+## Date of fit: Fri Mar 9 23:09:50 2018
+## Date of summary: Fri Mar 9 23:09:50 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.24 s
+## Fitted with method Port using 37 model solutions performed in 0.264 s
##
## Weighting: none
##
@@ -194,15 +191,15 @@ FOCUS_<span class="dv">2006</span>_L1_mkin &lt;-<span class="st"> </span><span c
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.46.3
## R version: 3.4.3
-## Date of fit: Thu Mar 1 14:31:59 2018
-## Date of summary: Thu Mar 1 14:32:00 2018
+## Date of fit: Fri Mar 9 23:09:52 2018
+## Date of summary: Fri Mar 9 23:09:52 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 611 model solutions performed in 1.375 s
+## Fitted with method Port using 611 model solutions performed in 1.451 s
##
## Weighting: none
##
@@ -289,15 +286,15 @@ FOCUS_<span class="dv">2006</span>_L2_mkin &lt;-<span class="st"> </span><span c
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.46.3
## R version: 3.4.3
-## Date of fit: Thu Mar 1 14:32:00 2018
-## Date of summary: Thu Mar 1 14:32:00 2018
+## Date of fit: Fri Mar 9 23:09:53 2018
+## Date of summary: Fri Mar 9 23:09:53 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 81 model solutions performed in 0.158 s
+## Fitted with method Port using 81 model solutions performed in 0.175 s
##
## Weighting: none
##
@@ -360,8 +357,8 @@ FOCUS_<span class="dv">2006</span>_L2_mkin &lt;-<span class="st"> </span><span c
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.46.3
## R version: 3.4.3
-## Date of fit: Thu Mar 1 14:32:01 2018
-## Date of summary: Thu Mar 1 14:32:01 2018
+## Date of fit: Fri Mar 9 23:09:54 2018
+## Date of summary: Fri Mar 9 23:09:54 2018
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -370,7 +367,7 @@ FOCUS_<span class="dv">2006</span>_L2_mkin &lt;-<span class="st"> </span><span c
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.708 s
+## Fitted with method Port using 336 model solutions performed in 0.739 s
##
## Weighting: none
##
@@ -452,8 +449,8 @@ mm.L3 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</code></pre></div>
<pre><code>## mkin version: 0.9.46.3
## R version: 3.4.3
-## Date of fit: Thu Mar 1 14:32:02 2018
-## Date of summary: Thu Mar 1 14:32:02 2018
+## Date of fit: Fri Mar 9 23:09:55 2018
+## Date of summary: Fri Mar 9 23:09:55 2018
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -462,7 +459,7 @@ mm.L3 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.287 s
+## Fitted with method Port using 137 model solutions performed in 0.293 s
##
## Weighting: none
##
@@ -553,15 +550,15 @@ mm.L4 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.46.3
## R version: 3.4.3
-## Date of fit: Thu Mar 1 14:32:03 2018
-## Date of summary: Thu Mar 1 14:32:03 2018
+## Date of fit: Fri Mar 9 23:09:55 2018
+## Date of summary: Fri Mar 9 23:09:56 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.089 s
+## Fitted with method Port using 46 model solutions performed in 0.09 s
##
## Weighting: none
##
@@ -613,8 +610,8 @@ mm.L4 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.46.3
## R version: 3.4.3
-## Date of fit: Thu Mar 1 14:32:03 2018
-## Date of summary: Thu Mar 1 14:32:03 2018
+## Date of fit: Fri Mar 9 23:09:56 2018
+## Date of summary: Fri Mar 9 23:09:56 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png
index c9da66ac..f5f45ac6 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png
index aa728f0f..22f3a530 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png
index 4eb7f3b1..9eb0378f 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png
index 56654730..d8e58169 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png
index b143282b..1a9c8457 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png
index a4753a7e..12b4beea 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png
index 50528c8a..ee225461 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png
index 95a5bc5c..7b8e7f95 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png
index 745477a3..49c48168 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html
index 52a1db77..606121ff 100644
--- a/docs/articles/FOCUS_Z.html
+++ b/docs/articles/FOCUS_Z.html
@@ -9,10 +9,7 @@
<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS dataset Z">
-<meta property="og:description" content="">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
@@ -80,7 +77,7 @@
<h1>Example evaluation of FOCUS dataset Z</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-03-01</h4>
+ <h4 class="date">2018-03-09</h4>
</div>
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png
index b66289d9..cb32b3c6 100644
--- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png
+++ b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png
index af26f416..7ce8a39c 100644
--- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png
+++ b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png
index d4e7a647..7a8f3fad 100644
--- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png
+++ b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png
index 8c6d81ef..b61de1fc 100644
--- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png
+++ b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png
index fffb4892..1e4c541d 100644
--- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png
+++ b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png
index 0ac5b6ce..dfe447ed 100644
--- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png
+++ b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png
index 87226454..8f7102aa 100644
--- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png
+++ b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png
index 58241d1d..a0a00abb 100644
--- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png
+++ b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png
index 381e7df5..783f7954 100644
--- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png
+++ b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png
index 19e73f1c..29824228 100644
--- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png
+++ b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
index 891d8d92..8eb7e968 100644
--- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
+++ b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
Binary files differ
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 9f0b5708..915e5474 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -9,10 +9,7 @@
<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Performance benefit by using compiled model definitions in mkin">
-<meta property="og:description" content="">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
@@ -80,7 +77,7 @@
<h1>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-03-01</h4>
+ <h4 class="date">2018-03-09</h4>
</div>
@@ -101,7 +98,7 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) {
- b<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw">benchmark</span>(
+ b<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(
<span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,
<span class="dt">solution_type =</span> <span class="st">"deSolve"</span>,
<span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),
@@ -117,10 +114,15 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
<span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>)
}</code></pre></div>
<pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
-<pre><code>## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'</code></pre>
-<pre><code>## [1] "R package benchmark is not available"</code></pre>
-<p>We see that using the compiled model is by a factor of around NA 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><code>## test replications elapsed relative user.self sys.self
+## 3 deSolve, compiled 3 2.044 1.000 2.042 0
+## 1 deSolve, not compiled 3 14.198 6.946 14.185 0
+## 2 Eigenvalue based 3 2.751 1.346 2.747 0
+## user.child sys.child
+## 3 0 0
+## 1 0 0
+## 2 0 0</code></pre>
+<p>We see that using the compiled model is by a factor of around 7 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>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
<h2 class="hasAnchor">
@@ -131,7 +133,7 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),
<span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>))
- b<span class="fl">.2</span> &lt;-<span class="st"> </span><span class="kw">benchmark</span>(
+ b<span class="fl">.2</span> &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(
<span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D,
<span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),
<span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),
@@ -142,11 +144,14 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
factor_FOMC_SFO &lt;-<span class="st"> </span><span class="ot">NA</span>
<span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>)
}</code></pre></div>
-<pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
-<pre><code>## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'</code></pre>
-<pre><code>## [1] "R package benchmark is not available"</code></pre>
-<p>Here we get a performance benefit of a factor of NA using the version of the differential equation model compiled from C code!</p>
+<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<pre><code>## test replications elapsed relative user.self sys.self
+## 2 deSolve, compiled 3 3.695 1.000 3.692 0
+## 1 deSolve, not compiled 3 31.143 8.428 31.114 0
+## user.child sys.child
+## 2 0 0
+## 1 0 0</code></pre>
+<p>Here we get a performance benefit of a factor of 8 using the version of the differential equation model compiled from C code!</p>
<p>This vignette was built with mkin 0.9.46.3 on</p>
<pre><code>## R version 3.4.3 (2017-11-30)
## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 2b16580a..c0c5864b 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -27,7 +27,6 @@
<script src="../pkgdown.js"></script>
-<meta property="og:title" content="Articles" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index a91da0a4..f668b500 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -9,10 +9,7 @@
<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Introduction to mkin">
-<meta property="og:description" content="">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
@@ -80,7 +77,7 @@
<h1>Introduction to mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-03-01</h4>
+ <h4 class="date">2018-03-09</h4>
</div>
diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
index 5a3e3b6c..fafe8afd 100644
--- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
+++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
Binary files differ
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 400b1383..e5b68cfe 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -9,10 +9,7 @@
<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Calculation of time weighted average concentrations with mkin">
-<meta property="og:description" content="">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
@@ -80,7 +77,7 @@
<h1>Calculation of time weighted average concentrations with mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-03-01</h4>
+ <h4 class="date">2018-03-09</h4>
</div>

Contact - Imprint