Correct references to the Rocke and Lorenzato model

Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y.
Rebuild static documentation.

7 files changed, 52 insertions, 52 deletions

diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 8a1f51d1..630b1d02 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -29,7 +29,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
       </span>
     </div>
 
@@ -84,7 +84,7 @@
       <h1>Example evaluation of FOCUS Example Dataset D</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2018-06-06</h4>
+            <h4 class="date">2018-07-18</h4>
       
       
       <div class="hidden name"><code>FOCUS_D.Rmd</code></div>
@@ -161,9 +161,9 @@
 <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.47.1 
-## R version used for fitting:       3.5.0 
-## Date of fit:     Wed Jun  6 01:21:49 2018 
-## Date of summary: Wed Jun  6 01:21:50 2018 
+## R version used for fitting:       3.5.1 
+## Date of fit:     Wed Jul 18 14:52:30 2018 
+## Date of summary: Wed Jul 18 14:52:31 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -171,7 +171,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.633 s
+## Fitted with method Port using 153 model solutions performed in 0.604 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index fcd0719d..72c293b9 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -29,7 +29,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
       </span>
     </div>
 
@@ -84,7 +84,7 @@
       <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2018-06-06</h4>
+            <h4 class="date">2018-07-18</h4>
       
       
       <div class="hidden name"><code>FOCUS_L.Rmd</code></div>
@@ -109,16 +109,16 @@ FOCUS_<span class="dv">2006</span>_L1_mkin &lt;-<span class="st"> </span><span c
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m.L1.SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_<span class="dv">2006</span>_L1_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)
 <span class="kw">summary</span>(m.L1.SFO)</code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.47.1 
-## R version used for fitting:       3.5.0 
-## Date of fit:     Wed Jun  6 01:21:52 2018 
-## Date of summary: Wed Jun  6 01:21:52 2018 
+## R version used for fitting:       3.5.1 
+## Date of fit:     Wed Jul 18 15:16:17 2018 
+## Date of summary: Wed Jul 18 15:16:17 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.094 s
+## Fitted with method Port using 37 model solutions performed in 0.081 s
 ## 
 ## Weighting: none
 ## 
@@ -200,16 +200,16 @@ FOCUS_<span class="dv">2006</span>_L1_mkin &lt;-<span class="st"> </span><span c
 <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.47.1 
-## R version used for fitting:       3.5.0 
-## Date of fit:     Wed Jun  6 01:21:53 2018 
-## Date of summary: Wed Jun  6 01:21:53 2018 
+## R version used for fitting:       3.5.1 
+## Date of fit:     Wed Jul 18 15:16:19 2018 
+## Date of summary: Wed Jul 18 15:16:19 2018 
 ## 
 ## 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 1.369 s
+## Fitted with method Port using 611 model solutions performed in 1.304 s
 ## 
 ## Weighting: none
 ## 
@@ -295,16 +295,16 @@ FOCUS_<span class="dv">2006</span>_L2_mkin &lt;-<span class="st"> </span><span c
 <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.47.1 
-## R version used for fitting:       3.5.0 
-## Date of fit:     Wed Jun  6 01:21:54 2018 
-## Date of summary: Wed Jun  6 01:21:54 2018 
+## R version used for fitting:       3.5.1 
+## Date of fit:     Wed Jul 18 15:16:19 2018 
+## Date of summary: Wed Jul 18 15:16:19 2018 
 ## 
 ## 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 0.173 s
+## Fitted with method Port using 81 model solutions performed in 0.175 s
 ## 
 ## Weighting: none
 ## 
@@ -366,9 +366,9 @@ FOCUS_<span class="dv">2006</span>_L2_mkin &lt;-<span class="st"> </span><span c
 <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.47.1 
-## R version used for fitting:       3.5.0 
-## Date of fit:     Wed Jun  6 01:21:55 2018 
-## Date of summary: Wed Jun  6 01:21:55 2018 
+## R version used for fitting:       3.5.1 
+## Date of fit:     Wed Jul 18 15:16:20 2018 
+## Date of summary: Wed Jul 18 15:16:20 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -377,7 +377,7 @@ FOCUS_<span class="dv">2006</span>_L2_mkin &lt;-<span class="st"> </span><span c
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.76 s
+## Fitted with method Port using 336 model solutions performed in 0.721 s
 ## 
 ## Weighting: none
 ## 
@@ -458,9 +458,9 @@ mm.L3 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
 <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.47.1 
-## R version used for fitting:       3.5.0 
-## Date of fit:     Wed Jun  6 01:21:56 2018 
-## Date of summary: Wed Jun  6 01:21:56 2018 
+## R version used for fitting:       3.5.1 
+## Date of fit:     Wed Jul 18 15:16:21 2018 
+## Date of summary: Wed Jul 18 15:16:21 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -469,7 +469,7 @@ mm.L3 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.33 s
+## Fitted with method Port using 137 model solutions performed in 0.294 s
 ## 
 ## Weighting: none
 ## 
@@ -559,16 +559,16 @@ mm.L4 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
 <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.47.1 
-## R version used for fitting:       3.5.0 
-## Date of fit:     Wed Jun  6 01:21:56 2018 
-## Date of summary: Wed Jun  6 01:21:57 2018 
+## R version used for fitting:       3.5.1 
+## Date of fit:     Wed Jul 18 15:16:22 2018 
+## Date of summary: Wed Jul 18 15:16:22 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.099 s
+## Fitted with method Port using 46 model solutions performed in 0.092 s
 ## 
 ## Weighting: none
 ## 
@@ -619,16 +619,16 @@ mm.L4 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mmkin
 ## parent  106  352</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.47.1 
-## R version used for fitting:       3.5.0 
-## Date of fit:     Wed Jun  6 01:21:57 2018 
-## Date of summary: Wed Jun  6 01:21:57 2018 
+## R version used for fitting:       3.5.1 
+## Date of fit:     Wed Jul 18 15:16:22 2018 
+## Date of summary: Wed Jul 18 15:16:22 2018 
 ## 
 ## 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 0.146 s
+## Fitted with method Port using 66 model solutions performed in 0.137 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html
index 61425745..d8b9c961 100644
--- a/docs/articles/FOCUS_Z.html
+++ b/docs/articles/FOCUS_Z.html
@@ -29,7 +29,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
       </span>
     </div>
 
@@ -84,7 +84,7 @@
       <h1>Example evaluation of FOCUS dataset Z</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2018-06-06</h4>
+            <h4 class="date">2018-07-18</h4>
       
       
       <div class="hidden name"><code>FOCUS_Z.Rmd</code></div>
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 379176bf..183c9658 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -29,7 +29,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
       </span>
     </div>
 
@@ -84,7 +84,7 @@
       <h1>Performance benefit by using compiled model definitions in mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2018-06-06</h4>
+            <h4 class="date">2018-07-18</h4>
       
       
       <div class="hidden name"><code>compiled_models.Rmd</code></div>
@@ -125,14 +125,14 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
 }</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   2.335    1.000     2.333        0
-## 1 deSolve, not compiled            3  16.810    7.199    16.801        0
-## 2      Eigenvalue based            3   2.882    1.234     2.879        0
+## 3     deSolve, compiled            3   2.044    1.000     2.043        0
+## 1 deSolve, not compiled            3  16.571    8.107    16.565        0
+## 2      Eigenvalue based            3   2.499    1.223     2.496        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 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>
+<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>
 </div>
 <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
 <h2 class="hasAnchor">
@@ -156,14 +156,14 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
 }</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   3.766    1.000     3.764        0
-## 1 deSolve, not compiled            3  37.119    9.856    37.097        0
+## 2     deSolve, compiled            3   3.592    1.000     3.589        0
+## 1 deSolve, not compiled            3  35.340    9.839    35.324        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0</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!</p>
 <p>This vignette was built with mkin 0.9.47.1 on</p>
-<pre><code>## R version 3.5.0 (2018-04-23)
+<pre><code>## R version 3.5.1 (2018-07-02)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 9 (stretch)</code></pre>
 <pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 59bd221d..7902c611 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -58,7 +58,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
       </span>
     </div>
 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 28186062..14a2f9b9 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -29,7 +29,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
       </span>
     </div>
 
@@ -84,7 +84,7 @@
       <h1>Introduction to mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2018-06-06</h4>
+            <h4 class="date">2018-07-18</h4>
       
       
       <div class="hidden name"><code>mkin.Rmd</code></div>
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 53afcca3..0c5fe558 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -29,7 +29,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.2</span>
       </span>
     </div>
 
@@ -84,7 +84,7 @@
       <h1>Calculation of time weighted average concentrations with mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2018-06-06</h4>
+            <h4 class="date">2018-07-18</h4>
       
       
       <div class="hidden name"><code>twa.Rmd</code></div>