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

5 files changed, 52 insertions, 55 deletions

diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html
index 53711e88..58399198 100644
--- a/vignettes/FOCUS_D.html
+++ b/vignettes/FOCUS_D.html
@@ -69,11 +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</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
@@ -140,8 +137,8 @@ img {
 <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 18:45:34 2015 
-## Date of summary: Mon Jun 22 18:45:34 2015 
+## Date of fit:     Mon Jun 22 22:17:05 2015 
+## Date of summary: Mon Jun 22 22:17:05 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -149,7 +146,7 @@ img {
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.609 s
+## Fitted with method Port using 153 model solutions performed in 0.744 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 488d5dc8..276c7c35 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 20:44:34 2015 
-## Date of summary: Mon Jun 22 20:44:34 2015 
+## Date of fit:     Mon Jun 22 22:17:06 2015 
+## Date of summary: Mon Jun 22 22:17:06 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.093 s
+## Fitted with method Port using 37 model solutions performed in 0.09 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 20:44:35 2015 
-## Date of summary: Mon Jun 22 20:44:35 2015 
+## Date of fit:     Mon Jun 22 22:17:07 2015 
+## Date of summary: Mon Jun 22 22:17:07 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 0.48 s
+## Fitted with method Port using 188 model solutions performed in 0.476 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 20:44:35 2015 
-## Date of summary: Mon Jun 22 20:44:35 2015 
+## Date of fit:     Mon Jun 22 22:17:07 2015 
+## Date of summary: Mon Jun 22 22:17:07 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.104 s
+## Fitted with method Port using 41 model solutions performed in 0.099 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 20:44:36 2015 
-## Date of summary: Mon Jun 22 20:44:36 2015 
+## Date of fit:     Mon Jun 22 22:17:07 2015 
+## Date of summary: Mon Jun 22 22:17:07 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 0.203 s
+## Fitted with method Port using 81 model solutions performed in 0.237 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 20:44:38 2015 
-## Date of summary: Mon Jun 22 20:44:38 2015 
+## Date of fit:     Mon Jun 22 22:17:10 2015 
+## Date of summary: Mon Jun 22 22:17:10 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 0.926 s
+## Fitted with method Port using 336 model solutions performed in 0.841 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 20:44:38 2015 
-## Date of summary: Mon Jun 22 20:44:38 2015 
+## Date of fit:     Mon Jun 22 22:17:10 2015 
+## Date of summary: Mon Jun 22 22:17:10 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.132 s
+## Fitted with method Port using 43 model solutions performed in 0.11 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 20:44:39 2015 
-## Date of summary: Mon Jun 22 20:44:39 2015 
+## Date of fit:     Mon Jun 22 22:17:10 2015 
+## Date of summary: Mon Jun 22 22:17:10 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 0.221 s
+## Fitted with method Port using 83 model solutions performed in 0.2 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 20:44:39 2015 
-## Date of summary: Mon Jun 22 20:44:39 2015 
+## Date of fit:     Mon Jun 22 22:17:11 2015 
+## Date of summary: Mon Jun 22 22:17:11 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 0.372 s
+## Fitted with method Port using 137 model solutions performed in 0.423 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 20:44:40 2015 
-## Date of summary: Mon Jun 22 20:44:40 2015 
+## Date of fit:     Mon Jun 22 22:17:11 2015 
+## Date of summary: Mon Jun 22 22:17:11 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.115 s
+## Fitted with method Port using 46 model solutions performed in 0.113 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 20:44:40 2015 
-## Date of summary: Mon Jun 22 20:44:40 2015 
+## Date of fit:     Mon Jun 22 22:17:12 2015 
+## Date of summary: Mon Jun 22 22:17:12 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 0.169 s
+## Fitted with method Port using 66 model solutions performed in 0.179 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index d75b1288..94084bca 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index ed61b47a..0b77f1c2 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 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 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><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 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 8.720318
-## Eigenvalue based      1.287591
+## deSolve, not compiled 9.163798
+## Eigenvalue based      1.318062
 ## deSolve, compiled     1.000000</code></pre>
 </div>
 <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -128,15 +128,15 @@ 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 14.271472 14.285039 14.303450 14.298607 14.319440
-## deSolve, compiled      1.350642  1.390549  1.412823  1.430456  1.443914
+## 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
 ##                             max neval
-## deSolve, not compiled 14.340272     3
-## deSolve, compiled      1.457372     3</code></pre>
+## deSolve, not compiled 14.202672     3
+## deSolve, compiled      1.401743     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 9.995841
-## deSolve, compiled     1.000000</code></pre>
+## deSolve, not compiled 10.03443
+## 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>This vignette was built with mkin 0.9.37 on</p>
 <pre><code>## R version 3.2.1 (2015-06-18)
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index d7381e6f..f2178a99 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf