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authorJohannes Ranke <jranke@uni-bremen.de>2021-02-15 17:36:12 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-02-15 17:36:12 +0100
commitb9be19af5e3085216d0cd5af439332f631fa8b92 (patch)
treee10511f60e7f1713b781d5ea2acf885f3d1e6767 /docs/dev/articles/FOCUS_L.html
parent11c7f26dd6c532d977d9875f3c16952c7bba37ca (diff)
Fully rebuild docs, rerun tests and check
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-rw-r--r--docs/dev/articles/FOCUS_L.html129
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+++ 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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