Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge

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
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