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-rw-r--r--docs/articles/FOCUS_L.html42
-rw-r--r--docs/articles/compiled_models.html37
-rw-r--r--docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.pngbin9742 -> 9519 bytes
-rw-r--r--docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.pngbin10742 -> 10832 bytes
-rw-r--r--docs/articles/index.html2
5 files changed, 43 insertions, 38 deletions
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 6a25282b..feceab6f 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -76,15 +76,15 @@ 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: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Thu Dec 8 07:59:15 2016
-## Date of summary: Thu Dec 8 07:59:15 2016
+## Date of fit: Thu Dec 8 08:18:47 2016
+## Date of summary: Thu Dec 8 08:18:47 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 0.087 s
+## Fitted with method Port using 37 model solutions performed in 0.084 s
##
## Weighting: none
##
@@ -169,8 +169,8 @@ 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: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Thu Dec 8 07:59:15 2016
-## Date of summary: Thu Dec 8 07:59:15 2016
+## Date of fit: Thu Dec 8 08:18:47 2016
+## Date of summary: Thu Dec 8 08:18:47 2016
##
##
## Warning: Optimisation by method Port did not converge.
@@ -182,7 +182,7 @@ FOCUS_2006_L1_mkin &lt;-<span class="st"> </span><span class="kw"><a href="../re
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 188 model solutions performed in 0.436 s
+## Fitted with method Port using 188 model solutions performed in 0.462 s
##
## Weighting: none
##
@@ -266,15 +266,15 @@ 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: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Thu Dec 8 07:59:16 2016
-## Date of summary: Thu Dec 8 07:59:16 2016
+## Date of fit: Thu Dec 8 08:18:48 2016
+## Date of summary: Thu Dec 8 08:18:48 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 0.19 s
+## Fitted with method Port using 81 model solutions performed in 0.201 s
##
## Weighting: none
##
@@ -336,8 +336,8 @@ 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: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Thu Dec 8 07:59:17 2016
-## Date of summary: Thu Dec 8 07:59:17 2016
+## Date of fit: Thu Dec 8 08:18:49 2016
+## Date of summary: Thu Dec 8 08:18:49 2016
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -346,7 +346,7 @@ 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 0.785 s
+## Fitted with method Port using 336 model solutions performed in 0.767 s
##
## Weighting: none
##
@@ -425,8 +425,8 @@ 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: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Thu Dec 8 07:59:18 2016
-## Date of summary: Thu Dec 8 07:59:18 2016
+## Date of fit: Thu Dec 8 08:18:50 2016
+## Date of summary: Thu Dec 8 08:18:51 2016
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -435,7 +435,7 @@ 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 0.319 s
+## Fitted with method Port using 137 model solutions performed in 0.311 s
##
## Weighting: none
##
@@ -525,15 +525,15 @@ 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: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Thu Dec 8 07:59:19 2016
-## Date of summary: Thu Dec 8 07:59:19 2016
+## Date of fit: Thu Dec 8 08:18:51 2016
+## Date of summary: Thu Dec 8 08:18:51 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 0.107 s
+## Fitted with method Port using 46 model solutions performed in 0.118 s
##
## Weighting: none
##
@@ -585,15 +585,15 @@ 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: 0.9.44.9000
## R version: 3.3.2
-## Date of fit: Thu Dec 8 07:59:19 2016
-## Date of summary: Thu Dec 8 07:59:19 2016
+## Date of fit: Thu Dec 8 08:18:51 2016
+## Date of summary: Thu Dec 8 08:18:51 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 0.152 s
+## Fitted with method Port using 66 model solutions performed in 0.151 s
##
## Weighting: none
##
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index d39caf12..2850a9ae 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -67,8 +67,13 @@
<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>)
-SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(
+<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 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(
<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),
<span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</code></pre></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
@@ -91,21 +96,21 @@ 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 6263.2932 6273.5107 6286.8574 6283.7283 6298.6394
-## Eigenvalue based 865.5257 872.4146 892.2705 879.3036 905.6429
-## deSolve, compiled 716.7534 717.9075 724.6869 719.0617 728.6537
+## deSolve, not compiled 4973.8901 4975.2320 5000.4065 4976.5739 5013.6648
+## Eigenvalue based 848.4335 859.7111 886.9766 870.9887 906.2481
+## deSolve, compiled 702.8916 705.1930 706.2696 707.4944 707.9587
## max neval cld
-## 6313.5506 3 c
-## 931.9821 3 b
-## 738.2457 3 a</code></pre>
+## 5050.7556 3 c
+## 941.5075 3 b
+## 708.4229 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 8.7 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 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 8.738789
-## Eigenvalue based 1.222849
+## deSolve, not compiled 7.034082
+## Eigenvalue based 1.231089
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -127,18 +132,18 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="
<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 13.487097 13.492149 13.528060 13.497201 13.548541
-## deSolve, compiled 1.307845 1.318979 1.322967 1.330114 1.330528
+## deSolve, not compiled 10.819486 10.846433 10.863732 10.873381 10.885855
+## deSolve, compiled 1.300192 1.301168 1.304769 1.302144 1.307058
## max neval cld
-## 13.599881 3 b
-## 1.330941 3 a</code></pre>
+## 10.898330 3 b
+## 1.311972 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 10.1 using the version of the differential equation model compiled from C code!</p>
+<p>Here we get a performance benefit of a factor of 8.4 using the version of the differential equation model compiled from C code!</p>
<p>This vignette was built with mkin 0.9.44.9000 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 d881a0a2..c30550c9 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 b3faa16f..5f95613a 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
diff --git a/docs/articles/index.html b/docs/articles/index.html
index de5643c2..20792ba1 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -90,7 +90,7 @@
</header>
<div class="page-header">
- <h1>Vignette reference <small>version&nbsp;0.9.44.9000</small></h1>
+ <h1>Vignette reference <small>version&nbsp;0.9.45</small></h1>
</div>
<div class="row">

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