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authorJohannes Ranke <jranke@uni-bremen.de>2015-06-22 23:03:28 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-06-22 23:03:28 +0200
commit00d164d6d40172c6f8b83578fd30ca28f8c378c7 (patch)
treecf00069a265ddd8fc0ef40cd871f95d572187fd0 /vignettes
parent4a2809943b4bcb234f1eb979619c8cd27341c124 (diff)
Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge
Diffstat (limited to 'vignettes')
-rw-r--r--vignettes/FOCUS_D.Rmd6
-rw-r--r--vignettes/FOCUS_D.html6
-rw-r--r--vignettes/FOCUS_L.Rmd4
-rw-r--r--vignettes/FOCUS_L.html60
-rw-r--r--vignettes/FOCUS_Z.pdfbin224263 -> 224278 bytes
-rw-r--r--vignettes/compiled_models.Rmd4
-rw-r--r--vignettes/compiled_models.html34
-rw-r--r--vignettes/mkin.pdfbin160260 -> 160260 bytes
8 files changed, 57 insertions, 57 deletions
diff --git a/vignettes/FOCUS_D.Rmd b/vignettes/FOCUS_D.Rmd
index ec0c9040..38613082 100644
--- a/vignettes/FOCUS_D.Rmd
+++ b/vignettes/FOCUS_D.Rmd
@@ -1,13 +1,13 @@
---
-title: "`r (vignette_title <- 'Example evaluation of FOCUS Example Dataset D')`"
-author: "Johannes Ranke"
+title: Example evaluation of FOCUS Example Dataset D
+author: Johannes Ranke
date: "`r Sys.Date()`"
output:
html_document:
mathjax: null
theme: united
vignette: >
- %\VignetteIndexEntry{`r vignette_title`}
+ %\VignetteIndexEntry{Example evaluation of FOCUS Example Dataset D}
%\VignetteEngine{knitr::rmarkdown}
\usepackage[utf8]{inputenc}
---
diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html
index 58399198..45c5810a 100644
--- a/vignettes/FOCUS_D.html
+++ b/vignettes/FOCUS_D.html
@@ -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 22:17:05 2015
-## Date of summary: Mon Jun 22 22:17:05 2015
+## Date of fit: Mon Jun 22 23:02:24 2015
+## Date of summary: Mon Jun 22 23:02:25 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 0.744 s
+## Fitted with method Port using 153 model solutions performed in 0.772 s
##
## Weighting: none
##
diff --git a/vignettes/FOCUS_L.Rmd b/vignettes/FOCUS_L.Rmd
index 584c43eb..f2981c10 100644
--- a/vignettes/FOCUS_L.Rmd
+++ b/vignettes/FOCUS_L.Rmd
@@ -1,5 +1,5 @@
---
-title: "`r (vignette_title <- 'Example evaluation of FOCUS Laboratory Data L1 to L3')`"
+title: "Example evaluation of FOCUS Laboratory Data L1 to L3"
author: "Johannes Ranke"
date: "`r Sys.Date()`"
output:
@@ -9,7 +9,7 @@ output:
mathjax: null
theme: united
vignette: >
- %\VignetteIndexEntry{`r vignette_title`}
+ %\VignetteIndexEntry{Example evaluation of FOCUS Laboratory Data L1 to L3}
%\VignetteEngine{knitr::rmarkdown}
\usepackage[utf8]{inputenc}
---
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 276c7c35..7ea5d342 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -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 22:17:06 2015
-## Date of summary: Mon Jun 22 22:17:06 2015
+## Date of fit: Mon Jun 22 23:02:25 2015
+## Date of summary: Mon Jun 22 23:02:25 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.09 s
+## Fitted with method Port using 37 model solutions performed in 0.097 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 22:17:07 2015
-## Date of summary: Mon Jun 22 22:17:07 2015
+## Date of fit: Mon Jun 22 23:02:26 2015
+## Date of summary: Mon Jun 22 23:02:26 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 0.476 s
+## Fitted with method Port using 188 model solutions performed in 0.492 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 22:17:07 2015
-## Date of summary: Mon Jun 22 22:17:07 2015
+## Date of fit: Mon Jun 22 23:02:26 2015
+## Date of summary: Mon Jun 22 23:02:26 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 41 model solutions performed in 0.099 s
+## Fitted with method Port using 41 model solutions performed in 0.111 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 22:17:07 2015
-## Date of summary: Mon Jun 22 22:17:07 2015
+## Date of fit: Mon Jun 22 23:02:27 2015
+## Date of summary: Mon Jun 22 23:02:27 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 0.237 s
+## Fitted with method Port using 81 model solutions performed in 0.217 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 22:17:10 2015
-## Date of summary: Mon Jun 22 22:17:10 2015
+## Date of fit: Mon Jun 22 23:02:29 2015
+## Date of summary: Mon Jun 22 23:02:29 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 0.841 s
+## Fitted with method Port using 336 model solutions performed in 0.967 s
##
## Weighting: none
##
@@ -500,15 +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 22:17:10 2015
-## Date of summary: Mon Jun 22 22:17:10 2015
+## Date of fit: Mon Jun 22 23:02:29 2015
+## Date of summary: Mon Jun 22 23:02:29 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 43 model solutions performed in 0.11 s
+## Fitted with method Port using 43 model solutions performed in 0.108 s
##
## Weighting: none
##
@@ -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 22:17:10 2015
-## Date of summary: Mon Jun 22 22:17:10 2015
+## Date of fit: Mon Jun 22 23:02:30 2015
+## Date of summary: Mon Jun 22 23:02:30 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 0.2 s
+## Fitted with method Port using 83 model solutions performed in 0.243 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 22:17:11 2015
-## Date of summary: Mon Jun 22 22:17:11 2015
+## Date of fit: Mon Jun 22 23:02:30 2015
+## Date of summary: Mon Jun 22 23:02:30 2015
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -652,7 +652,7 @@ plot(m.L3.DFOP)</code></pre>
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.423 s
+## Fitted with method Port using 137 model solutions performed in 0.349 s
##
## Weighting: none
##
@@ -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 22:17:11 2015
-## Date of summary: Mon Jun 22 22:17:11 2015
+## Date of fit: Mon Jun 22 23:02:31 2015
+## Date of summary: Mon Jun 22 23:02:31 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.113 s
+## Fitted with method Port using 46 model solutions performed in 0.151 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 22:17:12 2015
-## Date of summary: Mon Jun 22 22:17:12 2015
+## Date of fit: Mon Jun 22 23:02:31 2015
+## Date of summary: Mon Jun 22 23:02:31 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 0.179 s
+## Fitted with method Port using 66 model solutions performed in 0.186 s
##
## Weighting: none
##
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 94084bca..98cf0c4d 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
Binary files differ
diff --git a/vignettes/compiled_models.Rmd b/vignettes/compiled_models.Rmd
index 9aa8b133..5ee3f7bc 100644
--- a/vignettes/compiled_models.Rmd
+++ b/vignettes/compiled_models.Rmd
@@ -1,5 +1,5 @@
---
-title: "`r (vignette_title <- 'Performance benefit by using compiled model definitions in mkin')`"
+title: "Performance benefit by using compiled model definitions in mkin"
author: "Johannes Ranke"
date: "`r Sys.Date()`"
output:
@@ -9,7 +9,7 @@ output:
mathjax: null
theme: united
vignette: >
- %\VignetteIndexEntry{`r vignette_title`}
+ %\VignetteIndexEntry{Performance benefit by using compiled model definitions in mkin}
%\VignetteEngine{knitr::rmarkdown}
\usepackage[utf8]{inputenc}
---
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 0b77f1c2..8fb08136 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -98,19 +98,19 @@ mb.1 &lt;- microbenchmark(
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 6737.589 6818.2149 6911.3916 6898.8407 6998.2929
-## Eigenvalue based 945.433 968.8592 979.7477 992.2854 996.9051
-## deSolve, compiled 744.785 748.8107 770.7521 752.8364 783.7357
-## max neval
-## deSolve, not compiled 7097.745 3
-## Eigenvalue based 1001.525 3
-## deSolve, compiled 814.635 3</code></pre>
-<p>We see that using the compiled model is by a factor of 9.2 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><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
+## 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>
<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 9.163798
-## Eigenvalue based 1.318062
+## deSolve, not compiled 8.387131
+## Eigenvalue based 1.134448
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -128,16 +128,16 @@ 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 13.955273 13.961009 14.041563 13.966745 14.084708
-## deSolve, compiled 1.350567 1.371225 1.381397 1.391882 1.396812
+## 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
## max neval
-## deSolve, not compiled 14.202672 3
-## deSolve, compiled 1.401743 3</code></pre>
+## deSolve, not compiled 14.768704 3
+## deSolve, compiled 1.457143 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 10.03443
+## deSolve, not compiled 10.50644
## deSolve, compiled 1.00000</code></pre>
-<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>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>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 f2178a99..f7795162 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf
Binary files differ

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