Static documentation rebuilt by pkgdown

Also update test log

7 files changed, 47 insertions, 47 deletions

diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 0afabe7f..195570b1 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">0.9.47.2</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</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">2018-09-06</h4>
+            <h4 class="date">2018-09-14</h4>
       
       
       <div class="hidden name"><code>FOCUS_D.Rmd</code></div>
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index a42c6e38..f7bbf961 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">0.9.47.2</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</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">2018-09-06</h4>
+            <h4 class="date">2018-09-14</h4>
       
       
       <div class="hidden name"><code>FOCUS_L.Rmd</code></div>
@@ -108,17 +108,17 @@
 <p>Since mkin version 0.9-32 (July 2014), we can use shorthand notation like <code>"SFO"</code> for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.</p>
 <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">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>)</a>
 <a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw">summary</span>(m.L1.SFO)</a></code></pre></div>
-<pre><code>## mkin version used for fitting:    0.9.47.2 
+<pre><code>## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 13:35:50 2018 
-## Date of summary: Thu Sep  6 13:35:50 2018 
+## Date of fit:     Fri Sep 14 06:39:28 2018 
+## Date of summary: Fri Sep 14 06:39:28 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 0.086 s
+## Fitted with method Port using 37 model solutions performed in 0.091 s
 ## 
 ## Weighting: none
 ## 
@@ -199,17 +199,17 @@
 <a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw">plot</span>(m.L1.FOMC, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - FOMC"</span>)</a></code></pre></div>
 <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p>
 <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">summary</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:    0.9.47.2 
+<pre><code>## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 13:35:52 2018 
-## Date of summary: Thu Sep  6 13:35:52 2018 
+## Date of fit:     Fri Sep 14 06:39:30 2018 
+## Date of summary: Fri Sep 14 06:39:30 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 1.35 s
+## Fitted with method Port using 611 model solutions performed in 1.333 s
 ## 
 ## Weighting: none
 ## 
@@ -294,17 +294,17 @@
 <a class="sourceLine" id="cb11-3" data-line-number="3">     <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</a></code></pre></div>
 <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p>
 <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">summary</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:    0.9.47.2 
+<pre><code>## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 13:35:52 2018 
-## Date of summary: Thu Sep  6 13:35:53 2018 
+## Date of fit:     Fri Sep 14 06:39:30 2018 
+## Date of summary: Fri Sep 14 06:39:30 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 0.175 s
+## Fitted with method Port using 81 model solutions performed in 0.172 s
 ## 
 ## Weighting: none
 ## 
@@ -365,10 +365,10 @@
 <a class="sourceLine" id="cb14-3" data-line-number="3">     <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</a></code></pre></div>
 <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p>
 <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">summary</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:    0.9.47.2 
+<pre><code>## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 13:35:53 2018 
-## Date of summary: Thu Sep  6 13:35:53 2018 
+## Date of fit:     Fri Sep 14 06:39:31 2018 
+## Date of summary: Fri Sep 14 06:39:31 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -377,7 +377,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.746 s
+## Fitted with method Port using 336 model solutions performed in 0.742 s
 ## 
 ## Weighting: none
 ## 
@@ -457,10 +457,10 @@
 <p>The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.</p>
 <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" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
-<pre><code>## mkin version used for fitting:    0.9.47.2 
+<pre><code>## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 13:35:54 2018 
-## Date of summary: Thu Sep  6 13:35:55 2018 
+## Date of fit:     Fri Sep 14 06:39:32 2018 
+## Date of summary: Fri Sep 14 06:39:32 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -469,7 +469,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.324 s
+## Fitted with method Port using 137 model solutions performed in 0.312 s
 ## 
 ## Weighting: none
 ## 
@@ -558,17 +558,17 @@
 <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="700"></p>
 <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" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><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>)</a></code></pre></div>
-<pre><code>## mkin version used for fitting:    0.9.47.2 
+<pre><code>## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 13:35:55 2018 
-## Date of summary: Thu Sep  6 13:35:55 2018 
+## Date of fit:     Fri Sep 14 06:39:33 2018 
+## Date of summary: Fri Sep 14 06:39:33 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 0.107 s
+## Fitted with method Port using 46 model solutions performed in 0.097 s
 ## 
 ## Weighting: none
 ## 
@@ -618,17 +618,17 @@
 ##        DT50 DT90
 ## parent  106  352</code></pre>
 <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">summary</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:    0.9.47.2 
+<pre><code>## mkin version used for fitting:    0.9.47.3 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 13:35:55 2018 
-## Date of summary: Thu Sep  6 13:35:55 2018 
+## Date of fit:     Fri Sep 14 06:39:33 2018 
+## Date of summary: Fri Sep 14 06:39:33 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 0.161 s
+## Fitted with method Port using 66 model solutions performed in 0.143 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html
index 6e7707f8..9753abd6 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">0.9.47.2</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
       </span>
     </div>
 
@@ -84,7 +84,7 @@
       <h1>Example evaluation of FOCUS dataset Z</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2018-09-06</h4>
+            <h4 class="date">2018-09-14</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 16059fcb..d93fe9e1 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">0.9.47.2</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</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">2018-09-06</h4>
+            <h4 class="date">2018-09-14</h4>
       
       
       <div class="hidden name"><code>compiled_models.Rmd</code></div>
@@ -125,9 +125,9 @@
 <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   2.218    1.000     2.217        0
-## 1 deSolve, not compiled            3  16.654    7.509    16.646        0
-## 2      Eigenvalue based            3   2.724    1.228     2.722        0
+## 3     deSolve, compiled            3   2.110    1.000     2.108        0
+## 1 deSolve, not compiled            3  16.442    7.792    16.433        0
+## 2      Eigenvalue based            3   2.593    1.229     2.592        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -156,13 +156,13 @@
 <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   3.780    1.000     3.777        0
-## 1 deSolve, not compiled            3  35.169    9.304    35.152        0
+## 2     deSolve, compiled            3   3.781    1.000     3.778        0
+## 1 deSolve, not compiled            3  34.742    9.189    34.725        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0</code></pre>
 <p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!</p>
-<p>This vignette was built with mkin 0.9.47.2 on</p>
+<p>This vignette was built with mkin 0.9.47.3 on</p>
 <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>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 7902c611..dcaf33b8 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">0.9.47.2</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
       </span>
     </div>
 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 234c6885..4d62b50d 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">0.9.47.2</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span>
       </span>
     </div>
 
@@ -84,7 +84,7 @@
       <h1>Introduction to mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2018-09-06</h4>
+            <h4 class="date">2018-09-14</h4>
       
       
       <div class="hidden name"><code>mkin.Rmd</code></div>
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 1a8a7eb2..2952e887 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">0.9.47.2</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</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">2018-09-06</h4>
+            <h4 class="date">2018-09-14</h4>
       
       
       <div class="hidden name"><code>twa.Rmd</code></div>