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authorJohannes Ranke <jranke@uni-bremen.de>2018-07-18 15:18:30 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2018-07-18 15:58:46 +0200
commit0b98c459c30a0629a728acf6b311de035c55fb64 (patch)
treef146faf4802da38862aa14b0268265f3fad9ba34 /vignettes/compiled_models.html
parentd3ed95f2a0a43ed74b02ea90e35d043ed4e1e72f (diff)
Correct references to the Rocke and Lorenzato model
Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y. Rebuild static documentation.
Diffstat (limited to 'vignettes/compiled_models.html')
-rw-r--r--vignettes/compiled_models.html20
1 files changed, 10 insertions, 10 deletions
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index d8c5b19b..81bff548 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="2018-03-09" />
+<meta name="date" content="2018-07-17" />
<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>2018-03-09</em></h4>
+<h4 class="date"><em>2018-07-17</em></h4>
@@ -105,14 +105,14 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw">mkinmod</span>(
}</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 1.980 1.000 1.979 0
-## 1 deSolve, not compiled 3 13.926 7.033 13.914 0
-## 2 Eigenvalue based 3 2.362 1.193 2.360 0
+## 3 deSolve, compiled 3 2.116 1.000 2.115 0
+## 1 deSolve, not compiled 3 16.563 7.828 16.555 0
+## 2 Eigenvalue based 3 2.599 1.228 2.597 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>
+<p>We see that using the compiled model is by a factor of around 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>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
<h2>Model that can not be solved with Eigenvalues</h2>
@@ -135,14 +135,14 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw">mkinmod</span>(
}</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 3.437 1.000 3.433 0
-## 1 deSolve, not compiled 3 30.406 8.847 30.380 0
+## 2 deSolve, compiled 3 3.809 1.000 3.806 0
+## 1 deSolve, not compiled 3 35.885 9.421 35.866 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
<p>Here we get a performance benefit of a factor of 9 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)
+<p>This vignette was built with mkin 0.9.47.1 on</p>
+<pre><code>## R version 3.5.1 (2018-07-02)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 9 (stretch)</code></pre>
<pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre>

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