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authorJohannes Ranke <jranke@uni-bremen.de>2015-06-23 11:44:00 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-06-23 11:44:00 +0200
commitc6759635fbea7f541d421b3de78f0d8868856486 (patch)
tree7a6d602aa505aedf6ef35a0afb2541e67b245ee1 /vignettes
parent6c62c42eb57631aa0f4ab7e008621ffb519bd7be (diff)
Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge
Diffstat (limited to 'vignettes')
-rw-r--r--vignettes/FOCUS_D.html14
-rw-r--r--vignettes/FOCUS_L.html60
-rw-r--r--vignettes/FOCUS_Z.pdfbin224278 -> 225020 bytes
-rw-r--r--vignettes/compiled_models.html42
-rw-r--r--vignettes/mkin.pdfbin160260 -> 160260 bytes
5 files changed, 58 insertions, 58 deletions
diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html
index 45c5810a..099004ad 100644
--- a/vignettes/FOCUS_D.html
+++ b/vignettes/FOCUS_D.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>Example evaluation of FOCUS Example Dataset D</title>
@@ -64,7 +64,7 @@ img {
<div id="header">
<h1 class="title">Example evaluation of FOCUS Example Dataset D</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>
@@ -117,9 +117,9 @@ print(FOCUS_2006_D)</code></pre>
## 43 m1 120 25.15
## 44 m1 120 33.31</code></pre>
<p>Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.</p>
-<p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If the gcc compiler is installed and functional, the differential equation model will be compiled from auto-generated C code.</p>
+<p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p>
<pre class="r"><code>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>
<pre class="r"><code>print(SFO_SFO$diffs)</code></pre>
<pre><code>## parent
## &quot;d_parent = - k_parent_sink * parent - k_parent_m1 * parent&quot;
@@ -137,8 +137,8 @@ print(FOCUS_2006_D)</code></pre>
<pre class="r"><code>summary(fit)</code></pre>
<pre><code>## mkin version: 0.9.37
## R version: 3.2.1
-## Date of fit: Mon Jun 22 23:02:24 2015
-## Date of summary: Mon Jun 22 23:02:25 2015
+## Date of fit: Tue Jun 23 11:42:55 2015
+## Date of summary: Tue Jun 23 11:42:55 2015
##
## Equations:
## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -146,7 +146,7 @@ print(FOCUS_2006_D)</code></pre>
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.772 s
+## Fitted with method Port using 153 model solutions performed in 0.719 s
##
## Weighting: none
##
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 7ea5d342..ec4203b7 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.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>Example evaluation of FOCUS Laboratory Data L1 to L3</title>
@@ -65,7 +65,7 @@ img {
<div id="header">
<h1 class="title">Example evaluation of FOCUS Laboratory Data L1 to L3</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">
@@ -93,15 +93,15 @@ FOCUS_2006_L1_mkin &lt;- mkin_wide_to_long(FOCUS_2006_L1)</code></pre>
summary(m.L1.SFO)</code></pre>
<pre><code>## mkin version: 0.9.37
## R version: 3.2.1
-## Date of fit: Mon Jun 22 23:02:25 2015
-## Date of summary: Mon Jun 22 23:02:25 2015
+## Date of fit: Tue Jun 23 11:42:56 2015
+## Date of summary: Tue Jun 23 11:42:56 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.097 s
+## Fitted with method Port using 37 model solutions performed in 0.096 s
##
## Weighting: none
##
@@ -183,8 +183,8 @@ summary(m.L1.SFO)</code></pre>
<pre class="r"><code>summary(m.L1.FOMC, data = FALSE)</code></pre>
<pre><code>## mkin version: 0.9.37
## R version: 3.2.1
-## Date of fit: Mon Jun 22 23:02:26 2015
-## Date of summary: Mon Jun 22 23:02:26 2015
+## Date of fit: Tue Jun 23 11:42:57 2015
+## Date of summary: Tue Jun 23 11:42:57 2015
##
##
## Warning: Optimisation by method Port did not converge.
@@ -196,7 +196,7 @@ summary(m.L1.SFO)</code></pre>
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 188 model solutions performed in 0.492 s
+## Fitted with method Port using 188 model solutions performed in 0.466 s
##
## Weighting: none
##
@@ -263,15 +263,15 @@ FOCUS_2006_L2_mkin &lt;- mkin_wide_to_long(FOCUS_2006_L2)</code></pre>
summary(m.L2.SFO)</code></pre>
<pre><code>## mkin version: 0.9.37
## R version: 3.2.1
-## Date of fit: Mon Jun 22 23:02:26 2015
-## Date of summary: Mon Jun 22 23:02:26 2015
+## Date of fit: Tue Jun 23 11:42:57 2015
+## Date of summary: Tue Jun 23 11:42:57 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 41 model solutions performed in 0.111 s
+## Fitted with method Port using 41 model solutions performed in 0.108 s
##
## Weighting: none
##
@@ -351,15 +351,15 @@ mkinresplot(m.L2.FOMC)</code></pre>
<pre class="r"><code>summary(m.L2.FOMC, data = FALSE)</code></pre>
<pre><code>## mkin version: 0.9.37
## R version: 3.2.1
-## Date of fit: Mon Jun 22 23:02:27 2015
-## Date of summary: Mon Jun 22 23:02:27 2015
+## Date of fit: Tue Jun 23 11:42:57 2015
+## Date of summary: Tue Jun 23 11:42:57 2015
##
## 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 0.217 s
+## Fitted with method Port using 81 model solutions performed in 0.214 s
##
## Weighting: none
##
@@ -423,8 +423,8 @@ plot(m.L2.DFOP)</code></pre>
<pre class="r"><code>summary(m.L2.DFOP, data = FALSE)</code></pre>
<pre><code>## mkin version: 0.9.37
## R version: 3.2.1
-## Date of fit: Mon Jun 22 23:02:29 2015
-## Date of summary: Mon Jun 22 23:02:29 2015
+## Date of fit: Tue Jun 23 11:43:00 2015
+## Date of summary: Tue Jun 23 11:43:00 2015
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -433,7 +433,7 @@ plot(m.L2.DFOP)</code></pre>
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.967 s
+## Fitted with method Port using 336 model solutions performed in 0.917 s
##
## Weighting: none
##
@@ -500,8 +500,8 @@ plot(m.L3.SFO)</code></pre>
<pre class="r"><code>summary(m.L3.SFO)</code></pre>
<pre><code>## mkin version: 0.9.37
## R version: 3.2.1
-## Date of fit: Mon Jun 22 23:02:29 2015
-## Date of summary: Mon Jun 22 23:02:29 2015
+## Date of fit: Tue Jun 23 11:43:00 2015
+## Date of summary: Tue Jun 23 11:43:00 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
@@ -576,15 +576,15 @@ plot(m.L3.FOMC)</code></pre>
<pre class="r"><code>summary(m.L3.FOMC, data = FALSE)</code></pre>
<pre><code>## mkin version: 0.9.37
## R version: 3.2.1
-## Date of fit: Mon Jun 22 23:02:30 2015
-## Date of summary: Mon Jun 22 23:02:30 2015
+## Date of fit: Tue Jun 23 11:43:00 2015
+## Date of summary: Tue Jun 23 11:43:00 2015
##
## Equations:
## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 83 model solutions performed in 0.243 s
+## Fitted with method Port using 83 model solutions performed in 0.207 s
##
## Weighting: none
##
@@ -642,8 +642,8 @@ plot(m.L3.DFOP)</code></pre>
<pre class="r"><code>summary(m.L3.DFOP, data = FALSE)</code></pre>
<pre><code>## mkin version: 0.9.37
## R version: 3.2.1
-## Date of fit: Mon Jun 22 23:02:30 2015
-## Date of summary: Mon Jun 22 23:02:30 2015
+## Date of fit: Tue Jun 23 11:43:01 2015
+## Date of summary: Tue Jun 23 11:43:01 2015
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -724,15 +724,15 @@ plot(m.L4.SFO)</code></pre>
<pre class="r"><code>summary(m.L4.SFO, data = FALSE)</code></pre>
<pre><code>## mkin version: 0.9.37
## R version: 3.2.1
-## Date of fit: Mon Jun 22 23:02:31 2015
-## Date of summary: Mon Jun 22 23:02:31 2015
+## Date of fit: Tue Jun 23 11:43:01 2015
+## Date of summary: Tue Jun 23 11:43:01 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.151 s
+## Fitted with method Port using 46 model solutions performed in 0.114 s
##
## Weighting: none
##
@@ -789,15 +789,15 @@ plot(m.L4.FOMC)</code></pre>
<pre class="r"><code>summary(m.L4.FOMC, data = FALSE)</code></pre>
<pre><code>## mkin version: 0.9.37
## R version: 3.2.1
-## Date of fit: Mon Jun 22 23:02:31 2015
-## Date of summary: Mon Jun 22 23:02:31 2015
+## Date of fit: Tue Jun 23 11:43:02 2015
+## Date of summary: Tue Jun 23 11:43:02 2015
##
## 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 0.186 s
+## Fitted with method Port using 66 model solutions performed in 0.166 s
##
## Weighting: none
##
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 98cf0c4d..1ac6002b 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
Binary files differ
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)
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index f7795162..7534bc6d 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf
Binary files differ

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