Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge

1 files changed, 21 insertions, 21 deletions

diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 8fb08136..814f3a52 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -10,7 +10,7 @@
 
 <meta name="author" content="Johannes Ranke" />
 
-<meta name="date" content="2015-06-22" />
+<meta name="date" content="2015-06-23" />
 
 <title>Performance benefit by using compiled model definitions in mkin</title>
 
@@ -65,7 +65,7 @@ img {
 <div id="header">
 <h1 class="title">Performance benefit by using compiled model definitions in mkin</h1>
 <h4 class="author"><em>Johannes Ranke</em></h4>
-<h4 class="date"><em>2015-06-22</em></h4>
+<h4 class="date"><em>2015-06-23</em></h4>
 </div>
 
 <div id="TOC">
@@ -77,7 +77,7 @@ img {
 
 <div id="benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues" class="section level2">
 <h2>Benchmark for a model that can also be solved with Eigenvalues</h2>
-<p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a compiler (gcc) is installed, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The package tests for presence of the gcc compiler using</p>
+<p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The <code>mkinmod()</code> function checks for presence of the gcc compiler using</p>
 <pre class="r"><code>Sys.which(&quot;gcc&quot;)</code></pre>
 <pre><code>##            gcc 
 ## &quot;/usr/bin/gcc&quot;</code></pre>
@@ -86,7 +86,7 @@ img {
 SFO_SFO &lt;- mkinmod(
   parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;),
   m1 = mkinsub(&quot;SFO&quot;))</code></pre>
-<pre><code>## Compiling differential equation model from auto-generated C code...</code></pre>
+<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 microbenchmark package.</p>
 <pre class="r"><code>library(&quot;microbenchmark&quot;)
 mb.1 &lt;- microbenchmark(
@@ -99,18 +99,18 @@ smb.1 &lt;- summary(mb.1)[-1]
 rownames(smb.1) &lt;- c(&quot;deSolve, not compiled&quot;, &quot;Eigenvalue based&quot;, &quot;deSolve, compiled&quot;)
 print(smb.1)</code></pre>
 <pre><code>##                             min        lq      mean    median        uq
-## deSolve, not compiled 6896.8680 6933.3330 6963.5277 6969.7979 6996.8575
-## Eigenvalue based       933.0581  937.8984  963.5002  942.7388  978.7213
-## deSolve, compiled      784.9729  807.9919  822.4500  831.0110  841.1886
+## deSolve, not compiled 6650.2684 6684.4530 6774.1607 6718.6377 6836.1068
+## Eigenvalue based       903.5520  916.8598  927.3873  930.1676  939.3049
+## deSolve, compiled      751.1205  752.5239  756.1227  753.9273  758.6238
 ##                             max neval
-## deSolve, not compiled 7023.9171     3
-## Eigenvalue based      1014.7039     3
-## deSolve, compiled      851.3663     3</code></pre>
-<p>We see that using the compiled model is by a factor of 8.4 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>
+## deSolve, not compiled 6953.5760     3
+## Eigenvalue based       948.4423     3
+## deSolve, compiled      763.3202     3</code></pre>
+<p>We see that using the compiled model is by a factor of 8.9 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 class="r"><code>smb.1[&quot;median&quot;]/smb.1[&quot;deSolve, compiled&quot;, &quot;median&quot;]</code></pre>
 <pre><code>##                         median
-## deSolve, not compiled 8.387131
-## Eigenvalue based      1.134448
+## deSolve, not compiled 8.911519
+## Eigenvalue based      1.233763
 ## deSolve, compiled     1.000000</code></pre>
 </div>
 <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -119,7 +119,7 @@ print(smb.1)</code></pre>
 <pre class="r"><code>FOMC_SFO &lt;- mkinmod(
   parent = mkinsub(&quot;FOMC&quot;, &quot;m1&quot;),
   m1 = mkinsub( &quot;SFO&quot;))</code></pre>
-<pre><code>## Compiling differential equation model from auto-generated C code...</code></pre>
+<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
 <pre class="r"><code>mb.2 &lt;- microbenchmark(
   mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = TRUE),
   mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
@@ -127,17 +127,17 @@ print(smb.1)</code></pre>
 smb.2 &lt;- summary(mb.2)[-1]
 rownames(smb.2) &lt;- c(&quot;deSolve, not compiled&quot;, &quot;deSolve, compiled&quot;)
 print(smb.2)</code></pre>
-<pre><code>##                             min        lq      mean    median        uq
-## deSolve, not compiled 14.661881 14.668453 14.701870 14.675025 14.721864
-## deSolve, compiled      1.393051  1.394908  1.415653  1.396764  1.426953
+<pre><code>##                            min        lq      mean    median        uq
+## deSolve, not compiled 14.32061 14.336413 14.380847 14.352216 14.410966
+## deSolve, compiled      1.34366  1.344778  1.371116  1.345897  1.384844
 ##                             max neval
-## deSolve, not compiled 14.768704     3
-## deSolve, compiled      1.457143     3</code></pre>
+## deSolve, not compiled 14.469716     3
+## deSolve, compiled      1.423791     3</code></pre>
 <pre class="r"><code>smb.2[&quot;median&quot;]/smb.2[&quot;deSolve, compiled&quot;, &quot;median&quot;]</code></pre>
 <pre><code>##                         median
-## deSolve, not compiled 10.50644
+## deSolve, not compiled 10.66368
 ## deSolve, compiled      1.00000</code></pre>
-<p>Here we get a performance benefit of a factor of 10.5 using the version of the differential equation model compiled from C code using the inline package!</p>
+<p>Here we get a performance benefit of a factor of 10.7 using the version of the differential equation model compiled from C code using the inline package!</p>
 <p>This vignette was built with mkin 0.9.37 on</p>
 <pre><code>## R version 3.2.1 (2015-06-18)
 ## Platform: x86_64-pc-linux-gnu (64-bit)