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-rw-r--r--docs/articles/FOCUS_D.html6
-rw-r--r--docs/articles/FOCUS_L.html40
-rw-r--r--docs/articles/compiled_models.html28
-rw-r--r--docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.pngbin10199 -> 9755 bytes
-rw-r--r--docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.pngbin12764 -> 11237 bytes
5 files changed, 37 insertions, 37 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index de1e1072..50b3d00a 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -132,8 +132,8 @@
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div>
<pre><code>## mkin version: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 09:23:12 2016
-## Date of summary: Thu Dec 8 09:23:13 2016
+## Date of fit: Thu Dec 8 09:39:23 2016
+## Date of summary: Thu Dec 8 09:39:24 2016
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -141,7 +141,7 @@
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.639 s
+## Fitted with method Port using 153 model solutions performed in 0.627 s
##
## Weighting: none
##
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index a6ec5532..366a0e46 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -79,15 +79,15 @@ FOCUS_2006_L1_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<span class="kw">summary</span>(m.L1.SFO)</code></pre></div>
<pre><code>## mkin version: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 09:23:13 2016
-## Date of summary: Thu Dec 8 09:23:13 2016
+## Date of fit: Thu Dec 8 09:39:24 2016
+## Date of summary: Thu Dec 8 09:39:24 2016
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.088 s
+## Fitted with method Port using 37 model solutions performed in 0.084 s
##
## Weighting: none
##
@@ -172,8 +172,8 @@ FOCUS_2006_L1_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<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: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 09:23:14 2016
-## Date of summary: Thu Dec 8 09:23:14 2016
+## Date of fit: Thu Dec 8 09:39:25 2016
+## Date of summary: Thu Dec 8 09:39:25 2016
##
##
## Warning: Optimisation by method Port did not converge.
@@ -269,15 +269,15 @@ FOCUS_2006_L2_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<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: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 09:23:14 2016
-## Date of summary: Thu Dec 8 09:23:14 2016
+## Date of fit: Thu Dec 8 09:39:26 2016
+## Date of summary: Thu Dec 8 09:39:26 2016
##
## 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 0.185 s
+## Fitted with method Port using 81 model solutions performed in 0.183 s
##
## Weighting: none
##
@@ -339,8 +339,8 @@ FOCUS_2006_L2_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
<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: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 09:23:15 2016
-## Date of summary: Thu Dec 8 09:23:15 2016
+## Date of fit: Thu Dec 8 09:39:27 2016
+## Date of summary: Thu Dec 8 09:39:27 2016
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -349,7 +349,7 @@ FOCUS_2006_L2_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.765 s
+## Fitted with method Port using 336 model solutions performed in 0.771 s
##
## Weighting: none
##
@@ -428,8 +428,8 @@ 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: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 09:23:17 2016
-## Date of summary: Thu Dec 8 09:23:17 2016
+## Date of fit: Thu Dec 8 09:39:28 2016
+## Date of summary: Thu Dec 8 09:39:28 2016
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -438,7 +438,7 @@ 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 0.309 s
+## Fitted with method Port using 137 model solutions performed in 0.304 s
##
## Weighting: none
##
@@ -528,15 +528,15 @@ 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: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 09:23:17 2016
-## Date of summary: Thu Dec 8 09:23:17 2016
+## Date of fit: Thu Dec 8 09:39:28 2016
+## Date of summary: Thu Dec 8 09:39:29 2016
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.106 s
+## Fitted with method Port using 46 model solutions performed in 0.107 s
##
## Weighting: none
##
@@ -588,15 +588,15 @@ 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">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
<pre><code>## mkin version: 0.9.45
## R version: 3.3.2
-## Date of fit: Thu Dec 8 09:23:17 2016
-## Date of summary: Thu Dec 8 09:23:17 2016
+## Date of fit: Thu Dec 8 09:39:28 2016
+## Date of summary: Thu Dec 8 09:39:29 2016
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 66 model solutions performed in 0.148 s
+## Fitted with method Port using 66 model solutions performed in 0.145 s
##
## Weighting: none
##
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 660af1d1..457f5a1d 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -99,21 +99,21 @@ mb<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw">micr
<span class="kw">print</span>(mb<span class="fl">.1</span>)</code></pre></div>
<pre><code>## Unit: milliseconds
## expr min lq mean median uq
-## deSolve, not compiled 5006.3815 5014.4629 5112.7115 5022.5443 5165.8765
-## Eigenvalue based 840.3027 874.3549 892.0593 908.4071 917.9376
-## deSolve, compiled 706.9909 712.8031 723.4380 718.6154 731.6615
+## deSolve, not compiled 5185.0893 5231.5690 5266.8769 5278.0487 5307.7706
+## Eigenvalue based 843.3153 847.1503 876.5398 850.9853 893.1520
+## deSolve, compiled 723.0636 740.5682 755.9995 758.0729 772.4674
## max neval cld
-## 5309.2087 3 b
-## 927.4680 3 a
-## 744.7077 3 a</code></pre>
+## 5337.4926 3 b
+## 935.3187 3 a
+## 786.8620 3 a</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.1</span>)</code></pre></div>
<p><img src="compiled_models_files/figure-html/benchmark_SFO_SFO-1.png" width="672"></p>
<p>We see that using the compiled model is by a factor of 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 class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rownames</span>(smb<span class="fl">.1</span>) &lt;-<span class="st"> </span>smb<span class="fl">.1</span>$expr
smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="fl">.1</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div>
<pre><code>## median
-## deSolve, not compiled 6.989197
-## Eigenvalue based 1.264108
+## deSolve, not compiled 6.962456
+## Eigenvalue based 1.122564
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -134,19 +134,19 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span> &lt;-<span class="st"> </span><span class="kw">summary</span>(mb<span class="fl">.2</span>)
<span class="kw">print</span>(mb<span class="fl">.2</span>)</code></pre></div>
<pre><code>## Unit: seconds
-## expr min lq mean median uq
-## deSolve, not compiled 11.015990 11.17783 11.24827 11.339674 11.364403
-## deSolve, compiled 1.285264 1.29794 1.32988 1.310616 1.352189
+## expr min lq mean median uq
+## deSolve, not compiled 10.963655 10.992677 11.033360 11.02170 11.068212
+## deSolve, compiled 1.287898 1.309754 1.322972 1.33161 1.340509
## max neval cld
-## 11.389132 3 b
-## 1.393762 3 a</code></pre>
+## 11.114726 3 b
+## 1.349408 3 a</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span>[<span class="st">"median"</span>]/smb<span class="fl">.2</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div>
<pre><code>## median
## 1 NA
## 2 NA</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.2</span>)</code></pre></div>
<p><img src="compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png" width="672"></p>
-<p>Here we get a performance benefit of a factor of 8.7 using the version of the differential equation model compiled from C code!</p>
+<p>Here we get a performance benefit of a factor of 8.3 using the version of the differential equation model compiled from C code!</p>
<p>This vignette was built with mkin 0.9.45 on</p>
<pre><code>## R version 3.3.2 (2016-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
index 53ff97f7..dae2c9d4 100644
--- a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
+++ b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
Binary files differ
diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
index d3a507bd..696236dc 100644
--- a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
+++ b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
Binary files differ

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