Implement the NAFTA evaluation scheme

3 files changed, 30 insertions, 30 deletions

diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 38e59d9d..ad8413dc 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -163,8 +163,8 @@
 <div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 09:51:20 2019 
-## Date of summary: Fri Feb 22 09:51:21 2019 
+## Date of fit:     Fri Feb 22 20:48:30 2019 
+## Date of summary: Fri Feb 22 20:48:31 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -172,7 +172,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.693 s
+## Fitted with method Port using 153 model solutions performed in 0.731 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 13131315..17c7bf59 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -111,15 +111,15 @@
 <a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 09:51:22 2019 
-## Date of summary: Fri Feb 22 09:51:22 2019 
+## Date of fit:     Fri Feb 22 20:48:32 2019 
+## Date of summary: Fri Feb 22 20:48:32 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.095 s
+## Fitted with method Port using 37 model solutions performed in 0.105 s
 ## 
 ## Weighting: none
 ## 
@@ -202,15 +202,15 @@
 <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 09:51:24 2019 
-## Date of summary: Fri Feb 22 09:51:24 2019 
+## Date of fit:     Fri Feb 22 20:48:34 2019 
+## Date of summary: Fri Feb 22 20:48:34 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 611 model solutions performed in 1.515 s
+## Fitted with method Port using 611 model solutions performed in 1.604 s
 ## 
 ## Weighting: none
 ## 
@@ -297,15 +297,15 @@
 <div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 09:51:25 2019 
-## Date of summary: Fri Feb 22 09:51:25 2019 
+## Date of fit:     Fri Feb 22 20:48:35 2019 
+## Date of summary: Fri Feb 22 20:48:35 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.198 s
+## Fitted with method Port using 81 model solutions performed in 0.216 s
 ## 
 ## Weighting: none
 ## 
@@ -368,8 +368,8 @@
 <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 09:51:26 2019 
-## Date of summary: Fri Feb 22 09:51:26 2019 
+## Date of fit:     Fri Feb 22 20:48:36 2019 
+## Date of summary: Fri Feb 22 20:48:36 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -378,7 +378,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.847 s
+## Fitted with method Port using 336 model solutions performed in 0.864 s
 ## 
 ## Weighting: none
 ## 
@@ -460,8 +460,8 @@
 <div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 09:51:27 2019 
-## Date of summary: Fri Feb 22 09:51:27 2019 
+## Date of fit:     Fri Feb 22 20:48:37 2019 
+## Date of summary: Fri Feb 22 20:48:38 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -470,7 +470,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.347 s
+## Fitted with method Port using 137 model solutions performed in 0.362 s
 ## 
 ## Weighting: none
 ## 
@@ -561,15 +561,15 @@
 <div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 09:51:27 2019 
-## Date of summary: Fri Feb 22 09:51:28 2019 
+## Date of fit:     Fri Feb 22 20:48:38 2019 
+## Date of summary: Fri Feb 22 20:48:38 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.112 s
+## Fitted with method Port using 46 model solutions performed in 0.123 s
 ## 
 ## Weighting: none
 ## 
@@ -621,15 +621,15 @@
 <div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Fri Feb 22 09:51:28 2019 
-## Date of summary: Fri Feb 22 09:51:28 2019 
+## Date of fit:     Fri Feb 22 20:48:38 2019 
+## Date of summary: Fri Feb 22 20:48:38 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.165 s
+## Fitted with method Port using 66 model solutions performed in 0.184 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index e9f8fa99..fbf2de33 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -126,14 +126,14 @@
 <a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div>
 <pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
 <pre><code>##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.336    1.000     2.335        0
-## 1 deSolve, not compiled            3  17.610    7.539    17.602        0
-## 2      Eigenvalue based            3   2.899    1.241     2.897        0
+## 3     deSolve, compiled            3   2.484    1.000     2.483        0
+## 1 deSolve, not compiled            3  17.963    7.231    17.951        0
+## 2      Eigenvalue based            3   3.146    1.267     3.144        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
 ## 2          0         0</code></pre>
-<p>We see that using the compiled model is by a factor of around 8 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>
+<p>We see that using the compiled model is by a factor of around 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>
 </div>
 <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
 <h2 class="hasAnchor">
@@ -157,8 +157,8 @@
 <a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
 <pre><code>##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.122    1.000     4.119        0
-## 1 deSolve, not compiled            3  37.359    9.063    37.343        0
+## 2     deSolve, compiled            3   4.232    1.000     4.226    0.004
+## 1 deSolve, not compiled            3  37.946    8.966    37.924    0.000
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0</code></pre>