Merge branch 'algorithm'

1 files changed, 52 insertions, 45 deletions

diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 6771bf63..4388edd2 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -30,7 +30,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span>
       </span>
     </div>
 
@@ -88,7 +88,7 @@
       <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2019-05-08</h4>
+            <h4 class="date">2019-06-05</h4>
       
       
       <div class="hidden name"><code>FOCUS_L.Rmd</code></div>
@@ -112,20 +112,21 @@
 <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" title="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" title="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:    0.9.49.4 
+<pre><code>## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:29 2019 
-## Date of summary: Wed May  8 20:52:29 2019 
+## Date of fit:     Wed Jun  5 15:10:52 2019 
+## Date of summary: Wed Jun  5 15:10:52 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.276 s
+## Fitted using 133 model solutions performed in 0.277 s
 ## 
-## Error model:
-## Constant variance 
+## Error model: Constant variance 
+## 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##                   value   type
@@ -213,10 +214,10 @@
 <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre>
 <pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
 ## finite result is doubtful</code></pre>
-<pre><code>## mkin version used for fitting:    0.9.49.4 
+<pre><code>## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:31 2019 
-## Date of summary: Wed May  8 20:52:31 2019 
+## Date of fit:     Wed Jun  5 15:10:54 2019 
+## Date of summary: Wed Jun  5 15:10:54 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -228,10 +229,11 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 899 model solutions performed in 1.868 s
+## Fitted using 899 model solutions performed in 1.877 s
+## 
+## Error model: Constant variance 
 ## 
-## Error model:
-## Constant variance 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##              value   type
@@ -317,20 +319,21 @@
 <a class="sourceLine" id="cb16-3" title="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="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="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:    0.9.49.4 
+<pre><code>## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:32 2019 
-## Date of summary: Wed May  8 20:52:32 2019 
+## Date of fit:     Wed Jun  5 15:10:55 2019 
+## Date of summary: Wed Jun  5 15:10:55 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.483 s
+## Fitted using 239 model solutions performed in 0.492 s
 ## 
-## Error model:
-## Constant variance 
+## Error model: Constant variance 
+## 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##              value   type
@@ -392,10 +395,10 @@
 <a class="sourceLine" id="cb19-3" title="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="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="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:    0.9.49.4 
+<pre><code>## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:33 2019 
-## Date of summary: Wed May  8 20:52:33 2019 
+## Date of fit:     Wed Jun  5 15:10:56 2019 
+## Date of summary: Wed Jun  5 15:10:56 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -404,10 +407,11 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 572 model solutions performed in 1.185 s
+## Fitted using 572 model solutions performed in 1.183 s
+## 
+## Error model: Constant variance 
 ## 
-## Error model:
-## Constant variance 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##              value   type
@@ -491,10 +495,10 @@
 <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="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="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:    0.9.49.4 
+<pre><code>## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:35 2019 
-## Date of summary: Wed May  8 20:52:35 2019 
+## Date of fit:     Wed Jun  5 15:10:58 2019 
+## Date of summary: Wed Jun  5 15:10:58 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -503,10 +507,11 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 373 model solutions performed in 0.768 s
+## Fitted using 373 model solutions performed in 0.773 s
 ## 
-## Error model:
-## Constant variance 
+## Error model: Constant variance 
+## 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##              value   type
@@ -596,20 +601,21 @@
 <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="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="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:    0.9.49.4 
+<pre><code>## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:36 2019 
-## Date of summary: Wed May  8 20:52:37 2019 
+## Date of fit:     Wed Jun  5 15:10:59 2019 
+## Date of summary: Wed Jun  5 15:10:59 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.289 s
+## Fitted using 142 model solutions performed in 0.288 s
+## 
+## Error model: Constant variance 
 ## 
-## Error model:
-## Constant variance 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##                  value   type
@@ -660,20 +666,21 @@
 ##        DT50 DT90
 ## parent  106  352</code></pre>
 <div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="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:    0.9.49.4 
+<pre><code>## mkin version used for fitting:    0.9.49.5 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Wed May  8 20:52:36 2019 
-## Date of summary: Wed May  8 20:52:37 2019 
+## Date of fit:     Wed Jun  5 15:10:59 2019 
+## Date of summary: Wed Jun  5 15:10:59 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.45 s
+## Fitted using 224 model solutions performed in 0.453 s
+## 
+## Error model: Constant variance 
 ## 
-## Error model:
-## Constant variance 
+## Error model algorithm: d_3 
 ## 
 ## Starting values for parameters to be optimised:
 ##              value   type
@@ -769,7 +776,7 @@
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