From b9be19af5e3085216d0cd5af439332f631fa8b92 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 15 Feb 2021 17:36:12 +0100
Subject: Fully rebuild docs, rerun tests and check

---
 docs/dev/articles/FOCUS_L.html | 129 ++++++++++++++++++++---------------------
 1 file changed, 64 insertions(+), 65 deletions(-)

(limited to 'docs/dev/articles/FOCUS_L.html')

diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html
index 2695db5e..547ec630 100644
--- a/docs/dev/articles/FOCUS_L.html
+++ b/docs/dev/articles/FOCUS_L.html
@@ -32,7 +32,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
       </span>
     </div>
 
@@ -81,7 +81,7 @@
 <ul class="nav navbar-nav navbar-right">
 <li>
   <a href="https://github.com/jranke/mkin/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
@@ -95,14 +95,13 @@
 
       
 
-      </header><link href="FOCUS_L_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="FOCUS_L_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="FOCUS_L_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_L_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2020-11-30</h4>
+            <h4 class="date">Last change 17 November 2016 (rebuilt 2021-02-15)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/FOCUS_L.rmd"><code>vignettes/FOCUS_L.rmd</code></a></small>
       <div class="hidden name"><code>FOCUS_L.rmd</code></div>
@@ -128,10 +127,10 @@
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">m.L1.SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
 <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></code></pre></div>
-<pre><code>## mkin version used for fitting:    0.9.50.4 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:52 2020 
-## Date of summary: Mon Nov 30 16:01:52 2020 
+## Date of fit:     Mon Feb 15 17:13:39 2021 
+## Date of summary: Mon Feb 15 17:13:39 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -234,17 +233,17 @@
 <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
 <pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
 ## doubtful</code></pre>
-<pre><code>## mkin version used for fitting:    0.9.50.4 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:53 2020 
-## Date of summary: Mon Nov 30 16:01:53 2020 
+## Date of fit:     Mon Feb 15 17:13:40 2021 
+## Date of summary: Mon Feb 15 17:13:40 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 380 model solutions performed in 0.087 s
+## Fitted using 369 model solutions performed in 0.084 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -272,22 +271,22 @@
 ## 
 ## Results:
 ## 
-##        AIC      BIC    logLik
-##   95.88778 99.44927 -43.94389
+##        AIC      BIC   logLik
+##   95.88781 99.44929 -43.9439
 ## 
 ## Optimised, transformed parameters with symmetric confidence intervals:
 ##           Estimate Std. Error  Lower  Upper
 ## parent_0     92.47     1.2820 89.720 95.220
-## log_alpha    16.92        NaN    NaN    NaN
-## log_beta     19.26        NaN    NaN    NaN
-## sigma         2.78     0.4501  1.814  3.745
+## log_alpha    13.78        NaN    NaN    NaN
+## log_beta     16.13        NaN    NaN    NaN
+## sigma         2.78     0.4598  1.794  3.766
 ## 
 ## Parameter correlation:
-##           parent_0 log_alpha log_beta    sigma
-## parent_0  1.000000       NaN      NaN 0.002218
-## log_alpha      NaN         1      NaN      NaN
-## log_beta       NaN       NaN        1      NaN
-## sigma     0.002218       NaN      NaN 1.000000
+##            parent_0 log_alpha log_beta     sigma
+## parent_0  1.0000000       NaN      NaN 0.0001671
+## log_alpha       NaN         1      NaN       NaN
+## log_beta        NaN       NaN        1       NaN
+## sigma     0.0001671       NaN      NaN 1.0000000
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -295,9 +294,9 @@
 ## for estimators of untransformed parameters.
 ##           Estimate t value Pr(&gt;t)  Lower  Upper
 ## parent_0 9.247e+01      NA     NA 89.720 95.220
-## alpha    2.223e+07      NA     NA     NA     NA
-## beta     2.325e+08      NA     NA     NA     NA
-## sigma    2.780e+00      NA     NA  1.814  3.745
+## alpha    9.658e+05      NA     NA     NA     NA
+## beta     1.010e+07      NA     NA     NA     NA
+## sigma    2.780e+00      NA     NA  1.794  3.766
 ## 
 ## FOCUS Chi2 error levels in percent:
 ##          err.min n.optim df
@@ -346,10 +345,10 @@
 <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
-<pre><code>## mkin version used for fitting:    0.9.50.4 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:54 2020 
-## Date of summary: Mon Nov 30 16:01:54 2020 
+## Date of fit:     Mon Feb 15 17:13:40 2021 
+## Date of summary: Mon Feb 15 17:13:40 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -391,10 +390,10 @@
 ## 
 ## Parameter correlation:
 ##             parent_0  log_alpha   log_beta      sigma
-## parent_0   1.000e+00 -1.151e-01 -2.085e-01 -7.436e-09
-## log_alpha -1.151e-01  1.000e+00  9.741e-01 -1.617e-07
-## log_beta  -2.085e-01  9.741e-01  1.000e+00 -1.386e-07
-## sigma     -7.436e-09 -1.617e-07 -1.386e-07  1.000e+00
+## parent_0   1.000e+00 -1.151e-01 -2.085e-01 -7.828e-09
+## log_alpha -1.151e-01  1.000e+00  9.741e-01 -1.602e-07
+## log_beta  -2.085e-01  9.741e-01  1.000e+00 -1.372e-07
+## sigma     -7.828e-09 -1.602e-07 -1.372e-07  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -427,10 +426,10 @@
 <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p>
 <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
-<pre><code>## mkin version used for fitting:    0.9.50.4 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:54 2020 
-## Date of summary: Mon Nov 30 16:01:54 2020 
+## Date of fit:     Mon Feb 15 17:13:41 2021 
+## Date of summary: Mon Feb 15 17:13:41 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -439,7 +438,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 581 model solutions performed in 0.136 s
+## Fitted using 581 model solutions performed in 0.134 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -470,18 +469,18 @@
 ## Optimised, transformed parameters with symmetric confidence intervals:
 ##          Estimate Std. Error      Lower     Upper
 ## parent_0   93.950  9.998e-01    91.5900   96.3100
-## log_k1      3.117  1.929e+03 -4558.0000 4564.0000
+## log_k1      3.112  1.842e+03 -4353.0000 4359.0000
 ## log_k2     -1.088  6.285e-02    -1.2370   -0.9394
 ## g_qlogis   -0.399  9.946e-02    -0.6342   -0.1638
 ## sigma       1.414  2.886e-01     0.7314    2.0960
 ## 
 ## Parameter correlation:
-##           parent_0     log_k1     log_k2   g_qlogis      sigma
-## parent_0 1.000e+00  6.459e-07  9.147e-11  2.665e-01  8.413e-11
-## log_k1   6.459e-07  1.000e+00  1.061e-04 -2.087e-04 -9.802e-06
-## log_k2   9.147e-11  1.061e-04  1.000e+00 -7.903e-01 -2.429e-09
-## g_qlogis 2.665e-01 -2.087e-04 -7.903e-01  1.000e+00  4.049e-09
-## sigma    8.413e-11 -9.802e-06 -2.429e-09  4.049e-09  1.000e+00
+##            parent_0     log_k1     log_k2   g_qlogis      sigma
+## parent_0  1.000e+00  6.783e-07 -3.390e-10  2.665e-01 -2.967e-10
+## log_k1    6.783e-07  1.000e+00  1.116e-04 -2.196e-04 -1.031e-05
+## log_k2   -3.390e-10  1.116e-04  1.000e+00 -7.903e-01  2.917e-09
+## g_qlogis  2.665e-01 -2.196e-04 -7.903e-01  1.000e+00 -4.408e-09
+## sigma    -2.967e-10 -1.031e-05  2.917e-09 -4.408e-09  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -489,7 +488,7 @@
 ## for estimators of untransformed parameters.
 ##          Estimate   t value    Pr(&gt;t)   Lower   Upper
 ## parent_0  93.9500 9.397e+01 2.036e-12 91.5900 96.3100
-## k1        22.5800 5.303e-04 4.998e-01  0.0000     Inf
+## k1        22.4800 5.553e-04 4.998e-01  0.0000     Inf
 ## k2         0.3369 1.591e+01 4.697e-07  0.2904  0.3909
 ## g          0.4016 1.680e+01 3.238e-07  0.3466  0.4591
 ## sigma      1.4140 4.899e+00 8.776e-04  0.7314  2.0960
@@ -501,7 +500,7 @@
 ## 
 ## Estimated disappearance times:
 ##          DT50  DT90 DT50back DT50_k1 DT50_k2
-## parent 0.5335 5.311    1.599  0.0307   2.058</code></pre>
+## parent 0.5335 5.311    1.599 0.03084   2.058</code></pre>
 <p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the chi^2 error level criterion. However, the failure to calculate the covariance matrix indicates that the parameter estimates correlate excessively. Therefore, the FOMC model may be preferred for this dataset.</p>
 </div>
 </div>
@@ -533,10 +532,10 @@
 <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="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
-<pre><code>## mkin version used for fitting:    0.9.50.4 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:55 2020 
-## Date of summary: Mon Nov 30 16:01:55 2020 
+## Date of fit:     Mon Feb 15 17:13:41 2021 
+## Date of summary: Mon Feb 15 17:13:42 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -545,7 +544,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 376 model solutions performed in 0.081 s
+## Fitted using 376 model solutions performed in 0.082 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -583,11 +582,11 @@
 ## 
 ## Parameter correlation:
 ##            parent_0     log_k1     log_k2   g_qlogis      sigma
-## parent_0  1.000e+00  1.732e-01  2.282e-02  4.009e-01 -9.671e-08
-## log_k1    1.732e-01  1.000e+00  4.945e-01 -5.809e-01  7.148e-07
+## parent_0  1.000e+00  1.732e-01  2.282e-02  4.009e-01 -9.664e-08
+## log_k1    1.732e-01  1.000e+00  4.945e-01 -5.809e-01  7.147e-07
 ## log_k2    2.282e-02  4.945e-01  1.000e+00 -6.812e-01  1.022e-06
-## g_qlogis  4.009e-01 -5.809e-01 -6.812e-01  1.000e+00 -7.929e-07
-## sigma    -9.671e-08  7.148e-07  1.022e-06 -7.929e-07  1.000e+00
+## g_qlogis  4.009e-01 -5.809e-01 -6.812e-01  1.000e+00 -7.926e-07
+## sigma    -9.664e-08  7.147e-07  1.022e-06 -7.926e-07  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -646,10 +645,10 @@
 <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="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
-<pre><code>## mkin version used for fitting:    0.9.50.4 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:55 2020 
-## Date of summary: Mon Nov 30 16:01:55 2020 
+## Date of fit:     Mon Feb 15 17:13:42 2021 
+## Date of summary: Mon Feb 15 17:13:42 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -711,17 +710,17 @@
 ## parent  106  352</code></pre>
 <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div>
-<pre><code>## mkin version used for fitting:    0.9.50.4 
+<pre><code>## mkin version used for fitting:    1.0.3.9000 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Mon Nov 30 16:01:55 2020 
-## Date of summary: Mon Nov 30 16:01:56 2020 
+## Date of fit:     Mon Feb 15 17:13:42 2021 
+## Date of summary: Mon Feb 15 17:13:42 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.045 s
+## Fitted using 224 model solutions performed in 0.046 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -756,10 +755,10 @@
 ## 
 ## Parameter correlation:
 ##             parent_0  log_alpha   log_beta      sigma
-## parent_0   1.000e+00 -4.696e-01 -5.543e-01 -2.456e-07
-## log_alpha -4.696e-01  1.000e+00  9.889e-01  2.169e-08
-## log_beta  -5.543e-01  9.889e-01  1.000e+00  4.910e-08
-## sigma     -2.456e-07  2.169e-08  4.910e-08  1.000e+00
+## parent_0   1.000e+00 -4.696e-01 -5.543e-01 -2.468e-07
+## log_alpha -4.696e-01  1.000e+00  9.889e-01  2.478e-08
+## log_beta  -5.543e-01  9.889e-01  1.000e+00  5.211e-08
+## sigma     -2.468e-07  2.478e-08  5.211e-08  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -783,7 +782,7 @@
 <div id="references" class="section level1 unnumbered">
 <h1 class="hasAnchor">
 <a href="#references" class="anchor"></a>References</h1>
-<div id="refs" class="references">
+<div id="refs" class="references hanging-indent">
 <div id="ref-ranke2014">
 <p>Ranke, Johannes. 2014. “Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0.” Umweltbundesamt Projektnummer 27452.</p>
 </div>
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