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authorJohannes Ranke <jranke@uni-bremen.de>2018-01-14 18:37:07 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2018-01-14 18:37:07 +0100
commit373d98038c514c5152478127a8a2b9b390ee1b58 (patch)
tree5b3e2852caca2856e0d42c87149e865ed22d841d /vignettes/compiled_models.html
parent6860dea6d5ef9dd9375a1cf98cc0bacfaea2dcb4 (diff)
Load mkin quietly in vignettes
Static documentation articles rebuilt by pkgdown::build_articles()
Diffstat (limited to 'vignettes/compiled_models.html')
-rw-r--r--vignettes/compiled_models.html27
1 files changed, 11 insertions, 16 deletions
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 30f29699..8aaa70d6 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -12,7 +12,7 @@
<meta name="author" content="Johannes Ranke" />
-<meta name="date" content="2017-07-21" />
+<meta name="date" content="2018-01-14" />
<title>Performance benefit by using compiled model definitions in mkin</title>
@@ -70,7 +70,7 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<h1 class="title toc-ignore">Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author"><em>Johannes Ranke</em></h4>
-<h4 class="date"><em>2017-07-21</em></h4>
+<h4 class="date"><em>2018-01-14</em></h4>
@@ -81,13 +81,8 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<pre><code>## gcc
## &quot;/usr/bin/gcc&quot;</code></pre>
<p>First, we build a simple degradation model for a parent compound with one metabolite.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">&quot;mkin&quot;</span>)</code></pre></div>
-<pre><code>## Loading required package: minpack.lm</code></pre>
-<pre><code>## Loading required package: rootSolve</code></pre>
-<pre><code>## Loading required package: inline</code></pre>
-<pre><code>## Loading required package: methods</code></pre>
-<pre><code>## Loading required package: parallel</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">SFO_SFO &lt;-<span class="st"> </span><span class="kw">mkinmod</span>(
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">&quot;mkin&quot;</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)
+SFO_SFO &lt;-<span class="st"> </span><span class="kw">mkinmod</span>(
<span class="dt">parent =</span> <span class="kw">mkinsub</span>(<span class="st">&quot;SFO&quot;</span>, <span class="st">&quot;m1&quot;</span>),
<span class="dt">m1 =</span> <span class="kw">mkinsub</span>(<span class="st">&quot;SFO&quot;</span>))</code></pre></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
@@ -110,9 +105,9 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
}</code></pre></div>
<pre><code>## Loading required package: rbenchmark</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 3 deSolve, compiled 3 2.140 1.000 2.140 0
-## 1 deSolve, not compiled 3 15.070 7.042 15.068 0
-## 2 Eigenvalue based 3 2.577 1.204 2.576 0
+## 3 deSolve, compiled 3 2.005 1.000 2.000 0.004
+## 1 deSolve, not compiled 3 14.202 7.083 14.196 0.000
+## 2 Eigenvalue based 3 2.427 1.210 2.428 0.000
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -140,14 +135,14 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
}</code></pre></div>
<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 3.646 1.000 3.644 0
-## 1 deSolve, not compiled 3 30.752 8.434 30.752 0
+## 2 deSolve, compiled 3 3.489 1.000 3.488 0
+## 1 deSolve, not compiled 3 28.906 8.285 28.904 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 0.9.45.2 on</p>
-<pre><code>## R version 3.4.1 (2017-06-30)
+<p>This vignette was built with mkin 0.9.47.1 on</p>
+<pre><code>## R version 3.4.3 (2017-11-30)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 9 (stretch)</code></pre>
<pre><code>## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre>

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