aboutsummaryrefslogtreecommitdiff
path: root/vignettes
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2015-06-22 20:47:13 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-06-22 20:47:13 +0200
commit97725f51ad869b7338208c19c33c8fbf5db29d18 (patch)
tree87b2133eddef1fcc0691a706953d6e4e0d88bdd0 /vignettes
parent01d9de6ff165c64ffc4366f2eeb3d2649b5c74c0 (diff)
Vignettes rebuilt by staticdocs::build_site() for r-forge
Diffstat (limited to 'vignettes')
-rw-r--r--vignettes/FOCUS_L.html68
-rw-r--r--vignettes/FOCUS_Z.pdfbin225699 -> 224268 bytes
-rw-r--r--vignettes/compiled_models.html32
-rw-r--r--vignettes/mkin.pdfbin160260 -> 160260 bytes
4 files changed, 48 insertions, 52 deletions
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 153be558..488d5dc8 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -80,12 +80,8 @@ img {
<div id="laboratory-data-l1" class="section level2">
<h2>Laboratory Data L1</h2>
<p>The following code defines example dataset L1 from the FOCUS kinetics report, p. 284:</p>
-<pre class="r"><code>library(&quot;mkin&quot;)</code></pre>
-<pre><code>## Loading required package: minpack.lm
-## Loading required package: rootSolve
-## Loading required package: inline
-## Loading required package: methods</code></pre>
-<pre class="r"><code>FOCUS_2006_L1 = data.frame(
+<pre class="r"><code>library(&quot;mkin&quot;)
+FOCUS_2006_L1 = data.frame(
t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6,
72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
@@ -97,15 +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 18:38:53 2015
-## Date of summary: Mon Jun 22 18:38:53 2015
+## Date of fit: Mon Jun 22 20:44:34 2015
+## Date of summary: Mon Jun 22 20:44:34 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.089 s
+## Fitted with method Port using 37 model solutions performed in 0.093 s
##
## Weighting: none
##
@@ -187,8 +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 18:38:54 2015
-## Date of summary: Mon Jun 22 18:38:54 2015
+## Date of fit: Mon Jun 22 20:44:35 2015
+## Date of summary: Mon Jun 22 20:44:35 2015
##
##
## Warning: Optimisation by method Port did not converge.
@@ -200,7 +196,7 @@ summary(m.L1.SFO)</code></pre>
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 188 model solutions performed in 0.397 s
+## Fitted with method Port using 188 model solutions performed in 0.48 s
##
## Weighting: none
##
@@ -267,15 +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 18:38:54 2015
-## Date of summary: Mon Jun 22 18:38:54 2015
+## Date of fit: Mon Jun 22 20:44:35 2015
+## Date of summary: Mon Jun 22 20:44:35 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 41 model solutions performed in 0.086 s
+## Fitted with method Port using 41 model solutions performed in 0.104 s
##
## Weighting: none
##
@@ -355,15 +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 18:38:54 2015
-## Date of summary: Mon Jun 22 18:38:54 2015
+## Date of fit: Mon Jun 22 20:44:36 2015
+## Date of summary: Mon Jun 22 20:44:36 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 0.175 s
+## Fitted with method Port using 81 model solutions performed in 0.203 s
##
## Weighting: none
##
@@ -427,8 +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 18:38:56 2015
-## Date of summary: Mon Jun 22 18:38:56 2015
+## Date of fit: Mon Jun 22 20:44:38 2015
+## Date of summary: Mon Jun 22 20:44:38 2015
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -437,7 +433,7 @@ plot(m.L2.DFOP)</code></pre>
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.751 s
+## Fitted with method Port using 336 model solutions performed in 0.926 s
##
## Weighting: none
##
@@ -504,15 +500,15 @@ 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 18:38:56 2015
-## Date of summary: Mon Jun 22 18:38:56 2015
+## Date of fit: Mon Jun 22 20:44:38 2015
+## Date of summary: Mon Jun 22 20:44:38 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 43 model solutions performed in 0.088 s
+## Fitted with method Port using 43 model solutions performed in 0.132 s
##
## Weighting: none
##
@@ -580,15 +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 18:38:57 2015
-## Date of summary: Mon Jun 22 18:38:57 2015
+## Date of fit: Mon Jun 22 20:44:39 2015
+## Date of summary: Mon Jun 22 20:44:39 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 0.178 s
+## Fitted with method Port using 83 model solutions performed in 0.221 s
##
## Weighting: none
##
@@ -646,8 +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 18:38:57 2015
-## Date of summary: Mon Jun 22 18:38:57 2015
+## Date of fit: Mon Jun 22 20:44:39 2015
+## Date of summary: Mon Jun 22 20:44:39 2015
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -656,7 +652,7 @@ plot(m.L3.DFOP)</code></pre>
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.292 s
+## Fitted with method Port using 137 model solutions performed in 0.372 s
##
## Weighting: none
##
@@ -728,15 +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 18:38:57 2015
-## Date of summary: Mon Jun 22 18:38:57 2015
+## Date of fit: Mon Jun 22 20:44:40 2015
+## Date of summary: Mon Jun 22 20:44:40 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.102 s
+## Fitted with method Port using 46 model solutions performed in 0.115 s
##
## Weighting: none
##
@@ -793,15 +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 18:38:58 2015
-## Date of summary: Mon Jun 22 18:38:58 2015
+## Date of fit: Mon Jun 22 20:44:40 2015
+## Date of summary: Mon Jun 22 20:44:40 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 0.137 s
+## Fitted with method Port using 66 model solutions performed in 0.169 s
##
## Weighting: none
##
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 95d5f949..d75b1288 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 fc71debe..ed61b47a 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -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 5379.4269 5431.6605 5455.0396 5483.8940 5492.8460
-## Eigenvalue based 930.6245 951.6701 959.4653 972.7157 973.8857
-## deSolve, compiled 755.9828 771.1000 794.1810 786.2172 813.2800
+## deSolve, not compiled 6585.7039 6651.4937 6685.6248 6717.2836 6735.5853
+## Eigenvalue based 971.2893 981.5618 998.2746 991.8344 1011.7673
+## deSolve, compiled 760.5522 765.4274 780.3243 770.3026 790.2103
## max neval
-## deSolve, not compiled 5501.7979 3
-## Eigenvalue based 975.0556 3
-## deSolve, compiled 840.3428 3</code></pre>
-<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>
+## deSolve, not compiled 6753.8871 3
+## Eigenvalue based 1031.7003 3
+## deSolve, compiled 810.1179 3</code></pre>
+<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>
<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 6.975037
-## Eigenvalue based 1.237210
+## deSolve, not compiled 8.720318
+## Eigenvalue based 1.287591
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -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 11.815894 11.84960 12.03290 11.883305 12.141404
-## deSolve, compiled 1.387086 1.43514 1.45956 1.483194 1.495796
+<pre><code>## min lq mean median uq
+## deSolve, not compiled 14.271472 14.285039 14.303450 14.298607 14.319440
+## deSolve, compiled 1.350642 1.390549 1.412823 1.430456 1.443914
## max neval
-## deSolve, not compiled 12.399502 3
-## deSolve, compiled 1.508399 3</code></pre>
+## deSolve, not compiled 14.340272 3
+## deSolve, compiled 1.457372 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 8.011968
+## deSolve, not compiled 9.995841
## deSolve, compiled 1.000000</code></pre>
-<p>Here we get a performance benefit of a factor of 8 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 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 11da2863..d7381e6f 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf
Binary files differ

Contact - Imprint