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-rw-r--r--docs/articles/FOCUS_D.html2
-rw-r--r--docs/articles/FOCUS_D_cache/html/__packages2
-rw-r--r--docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RDatabin0 -> 2756 bytes
-rw-r--r--docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb0
-rw-r--r--docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdxbin0 -> 113 bytes
-rw-r--r--docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RDatabin0 -> 2786 bytes
-rw-r--r--docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb0
-rw-r--r--docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdxbin0 -> 113 bytes
-rw-r--r--docs/articles/FOCUS_D_files/figure-html/plot-1.pngbin95834 -> 38557 bytes
-rw-r--r--docs/articles/FOCUS_D_files/figure-html/plot_2-1.pngbin14059 -> 6091 bytes
-rw-r--r--docs/articles/FOCUS_L.html44
-rw-r--r--docs/articles/compiled_models.html28
-rw-r--r--docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.pngbin9514 -> 10757 bytes
-rw-r--r--docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.pngbin11028 -> 10610 bytes
-rw-r--r--docs/articles/mkin.html2
-rw-r--r--docs/articles/mkin_cache/html/__packages2
-rw-r--r--docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.RDatabin0 -> 3367 bytes
-rw-r--r--docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdbbin0 -> 20287 bytes
-rw-r--r--docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdxbin0 -> 225 bytes
-rw-r--r--docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.pngbin112161 -> 45379 bytes
20 files changed, 38 insertions, 42 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 776e1093..0ce7bd07 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -41,7 +41,7 @@
<h1>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2016-11-17</h4>
+ <h4 class="date">2016-11-18</h4>
</div>
diff --git a/docs/articles/FOCUS_D_cache/html/__packages b/docs/articles/FOCUS_D_cache/html/__packages
index f8bbf624..c3c384b1 100644
--- a/docs/articles/FOCUS_D_cache/html/__packages
+++ b/docs/articles/FOCUS_D_cache/html/__packages
@@ -8,5 +8,3 @@ inline
mkin
rmarkdown
knitr
-microbenchmark
-ggplot2
diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData
new file mode 100644
index 00000000..36a4095f
--- /dev/null
+++ b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData
Binary files differ
diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb
diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx
new file mode 100644
index 00000000..20f10d9f
--- /dev/null
+++ b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx
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diff --git a/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData
new file mode 100644
index 00000000..b0731d7b
--- /dev/null
+++ b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData
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diff --git a/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb
diff --git a/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx
new file mode 100644
index 00000000..20f10d9f
--- /dev/null
+++ b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx
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diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png
index fc237898..e44c1374 100644
--- a/docs/articles/FOCUS_D_files/figure-html/plot-1.png
+++ b/docs/articles/FOCUS_D_files/figure-html/plot-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png
index b0a7c26b..c7df3486 100644
--- a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png
+++ b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png
Binary files differ
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index e7ec5308..c3009e4d 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -41,7 +41,7 @@
<h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2016-11-17</h4>
+ <h4 class="date">2016-11-18</h4>
</div>
@@ -63,15 +63,15 @@ 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 Nov 17 22:58:18 2016
-## Date of summary: Thu Nov 17 22:58:18 2016
+## Date of fit: Fri Nov 18 15:22:03 2016
+## Date of summary: Fri Nov 18 15:22:03 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 0.103 s
+## Fitted with method Port using 37 model solutions performed in 0.09 s
##
## Weighting: none
##
@@ -156,8 +156,8 @@ 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 Nov 17 22:58:19 2016
-## Date of summary: Thu Nov 17 22:58:19 2016
+## Date of fit: Fri Nov 18 15:22:04 2016
+## Date of summary: Fri Nov 18 15:22:04 2016
##
##
## Warning: Optimisation by method Port did not converge.
@@ -169,7 +169,7 @@ 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 0.462 s
+## Fitted with method Port using 188 model solutions performed in 0.445 s
##
## Weighting: none
##
@@ -253,15 +253,15 @@ 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 Nov 17 22:58:20 2016
-## Date of summary: Thu Nov 17 22:58:20 2016
+## Date of fit: Fri Nov 18 15:22:05 2016
+## Date of summary: Fri Nov 18 15:22:05 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 0.195 s
+## Fitted with method Port using 81 model solutions performed in 0.19 s
##
## Weighting: none
##
@@ -323,8 +323,8 @@ 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 Nov 17 22:58:21 2016
-## Date of summary: Thu Nov 17 22:58:21 2016
+## Date of fit: Fri Nov 18 15:22:06 2016
+## Date of summary: Fri Nov 18 15:22:06 2016
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -333,7 +333,7 @@ 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 0.882 s
+## Fitted with method Port using 336 model solutions performed in 0.803 s
##
## Weighting: none
##
@@ -412,8 +412,8 @@ 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 Nov 17 22:58:22 2016
-## Date of summary: Thu Nov 17 22:58:22 2016
+## Date of fit: Fri Nov 18 15:22:07 2016
+## Date of summary: Fri Nov 18 15:22:07 2016
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -422,7 +422,7 @@ 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 0.338 s
+## Fitted with method Port using 137 model solutions performed in 0.329 s
##
## Weighting: none
##
@@ -512,15 +512,15 @@ 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 Nov 17 22:58:22 2016
-## Date of summary: Thu Nov 17 22:58:23 2016
+## Date of fit: Fri Nov 18 15:22:08 2016
+## Date of summary: Fri Nov 18 15:22:08 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 0.114 s
+## Fitted with method Port using 46 model solutions performed in 0.109 s
##
## Weighting: none
##
@@ -572,15 +572,15 @@ 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 Nov 17 22:58:23 2016
-## Date of summary: Thu Nov 17 22:58:23 2016
+## Date of fit: Fri Nov 18 15:22:08 2016
+## Date of summary: Fri Nov 18 15:22:08 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 0.151 s
+## Fitted with method Port using 66 model solutions performed in 0.15 s
##
## Weighting: none
##
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 1446a357..ce149bc5 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -41,7 +41,7 @@
<h1>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2016-11-17</h4>
+ <h4 class="date">2016-11-18</h4>
</div>
@@ -78,21 +78,21 @@ 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 6251.2433 6291.2435 6315.5160 6331.2438 6347.6524
-## Eigenvalue based 858.2035 903.1770 926.2132 948.1505 960.2181
-## deSolve, compiled 721.0067 739.1361 745.9964 757.2656 758.4913
+## deSolve, not compiled 6341.1795 6363.5977 6373.7748 6386.0158 6390.0724
+## Eigenvalue based 907.1699 908.8498 921.8335 910.5297 929.1653
+## deSolve, compiled 747.5311 752.3718 754.2086 757.2125 757.5474
## max neval cld
-## 6364.0611 3 c
-## 972.2856 3 b
-## 759.7171 3 a</code></pre>
+## 6394.1290 3 c
+## 947.8008 3 b
+## 757.8823 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 8.4 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>
<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 8.360665
-## Eigenvalue based 1.252071
+## deSolve, not compiled 8.433585
+## Eigenvalue based 1.202476
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -114,11 +114,11 @@ 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 13.601046 13.602861 13.619563 13.604676 13.628821
-## deSolve, compiled 1.341581 1.346263 1.348298 1.350944 1.351657
-## max neval cld
-## 13.65297 3 b
-## 1.35237 3 a</code></pre>
+## deSolve, not compiled 13.214250 13.248908 13.384577 13.283565 13.469740
+## deSolve, compiled 1.303868 1.307484 1.332879 1.311099 1.347384
+## max neval cld
+## 13.655915 3 b
+## 1.383669 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
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 3c3b9c54..53b631b1 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 0ec027f1..6d78194f 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/mkin.html b/docs/articles/mkin.html
index 4eed053a..8134287b 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -41,7 +41,7 @@
<h1>mkin - Kinetic evaluation of chemical degradation data</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2016-11-17</h4>
+ <h4 class="date">2016-11-18</h4>
</div>
diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages
index ff62e6df..ae46e2d7 100644
--- a/docs/articles/mkin_cache/html/__packages
+++ b/docs/articles/mkin_cache/html/__packages
@@ -8,5 +8,3 @@ colorout
setwidth
nvimcom
rmarkdown
-microbenchmark
-ggplot2
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.RData
new file mode 100644
index 00000000..fbc45b28
--- /dev/null
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.RData
Binary files differ
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdb
new file mode 100644
index 00000000..2b71e52b
--- /dev/null
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdb
Binary files differ
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdx
new file mode 100644
index 00000000..bee3222a
--- /dev/null
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdx
Binary files differ
diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
index d34e3805..2e7e2244 100644
--- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
+++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png
Binary files differ

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