aboutsummaryrefslogtreecommitdiff
path: root/docs/articles
diff options
context:
space:
mode:
Diffstat (limited to 'docs/articles')
-rw-r--r--docs/articles/FOCUS_L.html42
-rw-r--r--docs/articles/compiled_models.html26
-rw-r--r--docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.pngbin9973 -> 10652 bytes
-rw-r--r--docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.pngbin12199 -> 11994 bytes
-rw-r--r--docs/articles/mkin_cache/html/__packages9
-rw-r--r--docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RDatabin0 -> 3274 bytes
-rw-r--r--docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdbbin0 -> 20269 bytes
-rw-r--r--docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdxbin0 -> 226 bytes
-rw-r--r--docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.pngbin112161 -> 45379 bytes
9 files changed, 41 insertions, 36 deletions
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 2244a359..4c3e5c9b 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -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: Fri Nov 4 16:56:21 2016
-## Date of summary: Fri Nov 4 16:56:21 2016
+## Date of fit: Fri Nov 4 17:13:56 2016
+## Date of summary: Fri Nov 4 17:13:56 2016
##
## Equations:
## d_parent = - 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 0.089 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: Fri Nov 4 16:56:21 2016
-## Date of summary: Fri Nov 4 16:56:21 2016
+## Date of fit: Fri Nov 4 17:13:57 2016
+## Date of summary: Fri Nov 4 17:13:57 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 0.46 s
+## Fitted with method Port using 188 model solutions performed in 0.444 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: Fri Nov 4 16:56:22 2016
-## Date of summary: Fri Nov 4 16:56:22 2016
+## Date of fit: Fri Nov 4 17:13:58 2016
+## Date of summary: Fri Nov 4 17:13:58 2016
##
## Equations:
## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 81 model solutions performed in 0.199 s
+## Fitted with method Port using 81 model solutions performed in 0.194 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: Fri Nov 4 16:56:23 2016
-## Date of summary: Fri Nov 4 16:56:23 2016
+## Date of fit: Fri Nov 4 17:13:59 2016
+## Date of summary: Fri Nov 4 17:13:59 2016
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -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 0.81 s
+## Fitted with method Port using 336 model solutions performed in 0.82 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: Fri Nov 4 16:56:24 2016
-## Date of summary: Fri Nov 4 16:56:25 2016
+## Date of fit: Fri Nov 4 17:14:00 2016
+## Date of summary: Fri Nov 4 17:14:00 2016
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -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 0.335 s
+## Fitted with method Port using 137 model solutions performed in 0.336 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: Fri Nov 4 16:56:25 2016
-## Date of summary: Fri Nov 4 16:56:25 2016
+## Date of fit: Fri Nov 4 17:14:01 2016
+## Date of summary: Fri Nov 4 17:14:01 2016
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.109 s
+## Fitted with method Port using 46 model solutions performed in 0.114 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: Fri Nov 4 16:56:25 2016
-## Date of summary: Fri Nov 4 16:56:25 2016
+## Date of fit: Fri Nov 4 17:14:01 2016
+## Date of summary: Fri Nov 4 17:14:01 2016
##
## Equations:
## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 66 model solutions performed in 0.16 s
+## Fitted with method Port using 66 model solutions performed in 0.162 s
##
## Weighting: none
##
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index e1572b17..153841ae 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -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 6326.4518 6378.7429 6476.2219 6431.0341 6551.1069
-## Eigenvalue based 925.7797 935.9924 939.8725 946.2051 946.9189
-## deSolve, compiled 740.2821 750.0017 767.8440 759.7212 781.6249
+## deSolve, not compiled 6282.2220 6293.7637 6323.0479 6305.3053 6343.4608
+## Eigenvalue based 873.2553 886.5949 903.6178 899.9345 918.7990
+## deSolve, compiled 737.7899 738.8794 752.3343 739.9689 759.6065
## max neval cld
-## 6671.1797 3 b
-## 947.6327 3 a
-## 803.5287 3 a</code></pre>
+## 6381.6162 3 c
+## 937.6634 3 b
+## 779.2441 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 8.5 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 8.464993
-## Eigenvalue based 1.245464
+## deSolve, not compiled 8.521041
+## Eigenvalue based 1.216179
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -114,18 +114,18 @@ 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 13.619556 13.761382 13.825679 13.903207 13.928741
-## deSolve, compiled 1.316871 1.322577 1.358847 1.328283 1.379834
+## deSolve, not compiled 13.644880 13.648332 13.835874 13.651784 13.931372
+## deSolve, compiled 1.422381 1.448574 1.495091 1.474767 1.531446
## max neval cld
-## 13.954275 3 b
-## 1.431386 3 a</code></pre>
+## 14.210959 3 b
+## 1.588125 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 10.5 using the version of the differential equation model compiled from C code!</p>
+<p>Here we get a performance benefit of a factor of 9.3 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 57730131..c52ccd5d 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 50adff32..c89ef9a5 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_cache/html/__packages b/docs/articles/mkin_cache/html/__packages
index c8b1e877..03ece635 100644
--- a/docs/articles/mkin_cache/html/__packages
+++ b/docs/articles/mkin_cache/html/__packages
@@ -1,8 +1,13 @@
base
+datasets
+utils
+grDevices
+graphics
+stats
knitr
minpack.lm
rootSolve
+methods
inline
+parallel
mkin
-microbenchmark
-ggplot2
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData
new file mode 100644
index 00000000..d11ccf31
--- /dev/null
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData
Binary files differ
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb
new file mode 100644
index 00000000..5ac4f484
--- /dev/null
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb
Binary files differ
diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx
new file mode 100644
index 00000000..8983f69e
--- /dev/null
+++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.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

Contact - Imprint