diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-01-14 18:37:07 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-01-14 18:37:07 +0100 |
| commit | 373d98038c514c5152478127a8a2b9b390ee1b58 (patch) | |
| tree | 5b3e2852caca2856e0d42c87149e865ed22d841d /vignettes/compiled_models.html | |
| parent | 6860dea6d5ef9dd9375a1cf98cc0bacfaea2dcb4 (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.html | 27 |
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 ## "/usr/bin/gcc"</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">"mkin"</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 <-<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">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>) +SFO_SFO <-<span class="st"> </span><span class="kw">mkinmod</span>( <span class="dt">parent =</span> <span class="kw">mkinsub</span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw">mkinsub</span>(<span class="st">"SFO"</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> |