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

5 files changed, 54 insertions, 69 deletions

diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html
index e8ab70de..6b4d8b95 100644
--- a/vignettes/FOCUS_D.html
+++ b/vignettes/FOCUS_D.html
@@ -69,13 +69,8 @@ img {
 
 
 <p>This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using <code>mkin</code>. After loading the library we look a the data. We have observed concentrations in the column named <code>value</code> at the times specified in column <code>time</code> for the two observed variables named <code>parent</code> and <code>m1</code>.</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
-## Loading required package: parallel</code></pre>
-<pre class="r"><code>print(FOCUS_2006_D)</code></pre>
+<pre class="r"><code>library(&quot;mkin&quot;)
+print(FOCUS_2006_D)</code></pre>
 <pre><code>##      name time  value
 ## 1  parent    0  99.46
 ## 2  parent    0 102.04
@@ -142,8 +137,8 @@ img {
 <pre class="r"><code>summary(fit)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 14:41:39 2015 
-## Date of summary: Fri Jun 26 14:41:40 2015 
+## Date of fit:     Fri Jun 26 16:06:46 2015 
+## Date of summary: Fri Jun 26 16:06:47 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -151,7 +146,7 @@ img {
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.629 s
+## Fitted with method Port using 153 model solutions performed in 0.741 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 7e0ef4dd..7fb65960 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -80,13 +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
-## Loading required package: parallel</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,
@@ -98,15 +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:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 14:41:41 2015 
-## Date of summary: Fri Jun 26 14:41:41 2015 
+## Date of fit:     Fri Jun 26 16:06:47 2015 
+## Date of summary: Fri Jun 26 16:06:47 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.08 s
+## Fitted with method Port using 37 model solutions performed in 0.096 s
 ## 
 ## Weighting: none
 ## 
@@ -188,8 +183,8 @@ summary(m.L1.SFO)</code></pre>
 <pre class="r"><code>summary(m.L1.FOMC, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 14:41:41 2015 
-## Date of summary: Fri Jun 26 14:41:41 2015 
+## Date of fit:     Fri Jun 26 16:06:48 2015 
+## Date of summary: Fri Jun 26 16:06:48 2015 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -201,7 +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 0.555 s
 ## 
 ## Weighting: none
 ## 
@@ -268,15 +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:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 14:41:42 2015 
-## Date of summary: Fri Jun 26 14:41:42 2015 
+## Date of fit:     Fri Jun 26 16:06:48 2015 
+## Date of summary: Fri Jun 26 16:06:48 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.087 s
+## Fitted with method Port using 41 model solutions performed in 0.112 s
 ## 
 ## Weighting: none
 ## 
@@ -356,15 +351,15 @@ mkinresplot(m.L2.FOMC)</code></pre>
 <pre class="r"><code>summary(m.L2.FOMC, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 14:41:42 2015 
-## Date of summary: Fri Jun 26 14:41:42 2015 
+## Date of fit:     Fri Jun 26 16:06:49 2015 
+## Date of summary: Fri Jun 26 16:06:49 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 0.21 s
 ## 
 ## Weighting: none
 ## 
@@ -428,8 +423,8 @@ plot(m.L2.DFOP)</code></pre>
 <pre class="r"><code>summary(m.L2.DFOP, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 14:41:44 2015 
-## Date of summary: Fri Jun 26 14:41:44 2015 
+## Date of fit:     Fri Jun 26 16:06:52 2015 
+## Date of summary: Fri Jun 26 16:06:52 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -438,7 +433,7 @@ plot(m.L2.DFOP)</code></pre>
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.744 s
+## Fitted with method Port using 336 model solutions performed in 0.945 s
 ## 
 ## Weighting: none
 ## 
@@ -505,15 +500,15 @@ plot(m.L3.SFO)</code></pre>
 <pre class="r"><code>summary(m.L3.SFO)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 14:41:44 2015 
-## Date of summary: Fri Jun 26 14:41:44 2015 
+## Date of fit:     Fri Jun 26 16:06:52 2015 
+## Date of summary: Fri Jun 26 16:06:52 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.087 s
+## Fitted with method Port using 43 model solutions performed in 0.122 s
 ## 
 ## Weighting: none
 ## 
@@ -581,15 +576,15 @@ plot(m.L3.FOMC)</code></pre>
 <pre class="r"><code>summary(m.L3.FOMC, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 14:41:44 2015 
-## Date of summary: Fri Jun 26 14:41:44 2015 
+## Date of fit:     Fri Jun 26 16:06:52 2015 
+## Date of summary: Fri Jun 26 16:06:52 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 0.235 s
 ## 
 ## Weighting: none
 ## 
@@ -647,8 +642,8 @@ plot(m.L3.DFOP)</code></pre>
 <pre class="r"><code>summary(m.L3.DFOP, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 14:41:45 2015 
-## Date of summary: Fri Jun 26 14:41:45 2015 
+## Date of fit:     Fri Jun 26 16:06:53 2015 
+## Date of summary: Fri Jun 26 16:06:53 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -657,7 +652,7 @@ plot(m.L3.DFOP)</code></pre>
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.287 s
+## Fitted with method Port using 137 model solutions performed in 0.385 s
 ## 
 ## Weighting: none
 ## 
@@ -729,15 +724,15 @@ plot(m.L4.SFO)</code></pre>
 <pre class="r"><code>summary(m.L4.SFO, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 14:41:45 2015 
-## Date of summary: Fri Jun 26 14:41:45 2015 
+## Date of fit:     Fri Jun 26 16:06:53 2015 
+## Date of summary: Fri Jun 26 16:06:53 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.097 s
+## Fitted with method Port using 46 model solutions performed in 0.116 s
 ## 
 ## Weighting: none
 ## 
@@ -794,15 +789,15 @@ plot(m.L4.FOMC)</code></pre>
 <pre class="r"><code>summary(m.L4.FOMC, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.39 
 ## R version:       3.2.1 
-## Date of fit:     Fri Jun 26 14:41:45 2015 
-## Date of summary: Fri Jun 26 14:41:45 2015 
+## Date of fit:     Fri Jun 26 16:06:54 2015 
+## Date of summary: Fri Jun 26 16:06:54 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 0.143 s
+## Fitted with method Port using 66 model solutions performed in 0.175 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index d03b7e01..3245544c 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 12454559..a62f3826 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -82,13 +82,8 @@ img {
 <pre><code>##            gcc 
 ## &quot;/usr/bin/gcc&quot;</code></pre>
 <p>First, we build a simple degradation model for a parent compound with one metabolite.</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
-## Loading required package: parallel</code></pre>
-<pre class="r"><code>SFO_SFO &lt;- mkinmod(
+<pre class="r"><code>library(&quot;mkin&quot;)
+SFO_SFO &lt;- mkinmod(
   parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;),
   m1 = mkinsub(&quot;SFO&quot;))</code></pre>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
@@ -104,18 +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 5292.0165 5313.7620 5364.5733 5335.5075 5400.8517
-## Eigenvalue based       893.9459  921.1984  936.1750  948.4509  957.2895
-## deSolve, compiled      742.7723  745.4243  750.1963  748.0763  753.9083
+## deSolve, not compiled 7047.6039 7083.3201 7123.5962 7119.0364 7161.5924
+## Eigenvalue based       901.5593  924.3357  968.8689  947.1121 1002.5238
+## deSolve, compiled      765.7604  770.7657  786.8638  775.7709  797.4156
 ##                             max neval
-## deSolve, not compiled 5466.1959     3
-## Eigenvalue based       966.1282     3
-## deSolve, compiled      759.7404     3</code></pre>
-<p>We see that using the compiled model is by a factor of 7.1 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 7204.1483     3
+## Eigenvalue based      1057.9355     3
+## deSolve, compiled      819.0602     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 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 7.132304
-## Eigenvalue based      1.267853
+## deSolve, not compiled 9.176725
+## Eigenvalue based      1.220866
 ## deSolve, compiled     1.000000</code></pre>
 </div>
 <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -133,16 +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 11.277340 11.336373 11.392883 11.395407 11.450654
-## deSolve, compiled      1.339204  1.342662  1.350783  1.346121  1.356573
+## deSolve, not compiled 14.080456 14.209689 14.287313 14.338922 14.390742
+## deSolve, compiled      1.467266  1.521451  1.555168  1.575636  1.599119
 ##                             max neval
-## deSolve, not compiled 11.505901     3
-## deSolve, compiled      1.367025     3</code></pre>
+## deSolve, not compiled 14.442561     3
+## deSolve, compiled      1.622601     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 8.465368
+## deSolve, not compiled 9.100402
 ## deSolve, compiled     1.000000</code></pre>
-<p>Here we get a performance benefit of a factor of 8.5 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 9.1 using the version of the differential equation model compiled from C code using the inline package!</p>
 <p>This vignette was built with mkin 0.9.39 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 be82f41f..76426c30 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf