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

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
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