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authorJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
commit8d1a84ac2190538ed3bac53a303064e281595868 (patch)
treeacb894d85ab7ec87c4911c355a5264a77e08e34b /docs/dev/articles/FOCUS_D.html
parent51d63256a7b3020ee11931d61b4db97b9ded02c0 (diff)
parent4200e566ad2600f56bc3987669aeab88582139eb (diff)
Merge branch 'main' into custom_lsoda_call
Diffstat (limited to 'docs/dev/articles/FOCUS_D.html')
-rw-r--r--docs/dev/articles/FOCUS_D.html411
1 files changed, 213 insertions, 198 deletions
diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html
index a35a255a..a7617d55 100644
--- a/docs/dev/articles/FOCUS_D.html
+++ b/docs/dev/articles/FOCUS_D.html
@@ -20,6 +20,8 @@
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
+
+
<div class="container template-article">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
@@ -32,7 +34,7 @@
</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">1.0.3.9000</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
</span>
</div>
@@ -42,7 +44,7 @@
<a href="../reference/index.html">Functions and data</a>
</li>
<li class="dropdown">
- <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Articles
<span class="caret"></span>
@@ -58,19 +60,28 @@
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
</li>
<li>
<a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
<a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
</li>
<li>
<a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
<li>
- <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+ <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
</li>
</ul>
</li>
@@ -80,7 +91,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
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- <a href="https://github.com/jranke/mkin/">
+ <a href="https://github.com/jranke/mkin/" class="external-link">
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</a>
@@ -95,15 +106,15 @@
- </header><script src="FOCUS_D_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
+ </header><script src="FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
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<div class="page-header toc-ignore">
<h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1>
- <h4 class="author">Johannes Ranke</h4>
+ <h4 data-toc-skip class="author">Johannes Ranke</h4>
- <h4 class="date">Last change 31 January 2019 (rebuilt 2021-02-15)</h4>
+ <h4 data-toc-skip class="date">Last change 31 January 2019 (rebuilt 2022-11-24)</h4>
- <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.rmd"><code>vignettes/FOCUS_D.rmd</code></a></small>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_D.rmd" class="external-link"><code>vignettes/FOCUS_D.rmd</code></a></small>
<div class="hidden name"><code>FOCUS_D.rmd</code></div>
</div>
@@ -112,207 +123,207 @@
<p>This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using <code>mkin</code>. After loading the library we look at the data. We have observed concentrations in the column named <code>value</code> at the times specified in column <code>time</code> for the two observed variables named <code>parent</code> and <code>m1</code>.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></code></pre></div>
-<pre><code>## name time value
-## 1 parent 0 99.46
-## 2 parent 0 102.04
-## 3 parent 1 93.50
-## 4 parent 1 92.50
-## 5 parent 3 63.23
-## 6 parent 3 68.99
-## 7 parent 7 52.32
-## 8 parent 7 55.13
-## 9 parent 14 27.27
-## 10 parent 14 26.64
-## 11 parent 21 11.50
-## 12 parent 21 11.64
-## 13 parent 35 2.85
-## 14 parent 35 2.91
-## 15 parent 50 0.69
-## 16 parent 50 0.63
-## 17 parent 75 0.05
-## 18 parent 75 0.06
-## 19 parent 100 NA
-## 20 parent 100 NA
-## 21 parent 120 NA
-## 22 parent 120 NA
-## 23 m1 0 0.00
-## 24 m1 0 0.00
-## 25 m1 1 4.84
-## 26 m1 1 5.64
-## 27 m1 3 12.91
-## 28 m1 3 12.96
-## 29 m1 7 22.97
-## 30 m1 7 24.47
-## 31 m1 14 41.69
-## 32 m1 14 33.21
-## 33 m1 21 44.37
-## 34 m1 21 46.44
-## 35 m1 35 41.22
-## 36 m1 35 37.95
-## 37 m1 50 41.19
-## 38 m1 50 40.01
-## 39 m1 75 40.09
-## 40 m1 75 33.85
-## 41 m1 100 31.04
-## 42 m1 100 33.13
-## 43 m1 120 25.15
-## 44 m1 120 33.31</code></pre>
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## name time value</span></span>
+<span><span class="co">## 1 parent 0 99.46</span></span>
+<span><span class="co">## 2 parent 0 102.04</span></span>
+<span><span class="co">## 3 parent 1 93.50</span></span>
+<span><span class="co">## 4 parent 1 92.50</span></span>
+<span><span class="co">## 5 parent 3 63.23</span></span>
+<span><span class="co">## 6 parent 3 68.99</span></span>
+<span><span class="co">## 7 parent 7 52.32</span></span>
+<span><span class="co">## 8 parent 7 55.13</span></span>
+<span><span class="co">## 9 parent 14 27.27</span></span>
+<span><span class="co">## 10 parent 14 26.64</span></span>
+<span><span class="co">## 11 parent 21 11.50</span></span>
+<span><span class="co">## 12 parent 21 11.64</span></span>
+<span><span class="co">## 13 parent 35 2.85</span></span>
+<span><span class="co">## 14 parent 35 2.91</span></span>
+<span><span class="co">## 15 parent 50 0.69</span></span>
+<span><span class="co">## 16 parent 50 0.63</span></span>
+<span><span class="co">## 17 parent 75 0.05</span></span>
+<span><span class="co">## 18 parent 75 0.06</span></span>
+<span><span class="co">## 19 parent 100 NA</span></span>
+<span><span class="co">## 20 parent 100 NA</span></span>
+<span><span class="co">## 21 parent 120 NA</span></span>
+<span><span class="co">## 22 parent 120 NA</span></span>
+<span><span class="co">## 23 m1 0 0.00</span></span>
+<span><span class="co">## 24 m1 0 0.00</span></span>
+<span><span class="co">## 25 m1 1 4.84</span></span>
+<span><span class="co">## 26 m1 1 5.64</span></span>
+<span><span class="co">## 27 m1 3 12.91</span></span>
+<span><span class="co">## 28 m1 3 12.96</span></span>
+<span><span class="co">## 29 m1 7 22.97</span></span>
+<span><span class="co">## 30 m1 7 24.47</span></span>
+<span><span class="co">## 31 m1 14 41.69</span></span>
+<span><span class="co">## 32 m1 14 33.21</span></span>
+<span><span class="co">## 33 m1 21 44.37</span></span>
+<span><span class="co">## 34 m1 21 46.44</span></span>
+<span><span class="co">## 35 m1 35 41.22</span></span>
+<span><span class="co">## 36 m1 35 37.95</span></span>
+<span><span class="co">## 37 m1 50 41.19</span></span>
+<span><span class="co">## 38 m1 50 40.01</span></span>
+<span><span class="co">## 39 m1 75 40.09</span></span>
+<span><span class="co">## 40 m1 75 33.85</span></span>
+<span><span class="co">## 41 m1 100 31.04</span></span>
+<span><span class="co">## 42 m1 100 33.13</span></span>
+<span><span class="co">## 43 m1 120 25.15</span></span>
+<span><span class="co">## 44 m1 120 33.31</span></span></code></pre>
<p>Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.</p>
<p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<pre><code>## Temporary DLL for differentials generated and loaded</code></pre>
+<code class="sourceCode R"><span><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">diffs</span><span class="op">)</span></code></pre></div>
-<pre><code>## parent
-## "d_parent = - k_parent * parent"
-## m1
-## "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1"</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">diffs</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## parent </span></span>
+<span><span class="co">## "d_parent = - k_parent * parent" </span></span>
+<span><span class="co">## m1 </span></span>
+<span><span class="co">## "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1"</span></span></code></pre>
<p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value
-## of zero were removed from the data</code></pre>
+<code class="sourceCode R"><span><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value</span></span>
+<span><span class="co">## of zero were removed from the data</span></span></code></pre>
<p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot_sep</code> method for <code>mkinfit</code> objects, which shows separate graphs for all compounds and their residuals.</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<p><img src="FOCUS_D_files/figure-html/plot-1.png" width="768"></p>
<p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div>
<p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p>
<p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p>
<div class="sourceCode" id="cb11"><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">fit</span><span class="op">)</span></code></pre></div>
-<pre><code>## mkin version used for fitting: 1.0.3.9000
-## R version used for fitting: 4.0.3
-## Date of fit: Mon Feb 15 17:13:36 2021
-## Date of summary: Mon Feb 15 17:13:37 2021
-##
-## Equations:
-## d_parent/dt = - k_parent * parent
-## d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
-##
-## Model predictions using solution type analytical
-##
-## Fitted using 401 model solutions performed in 0.161 s
-##
-## Error model: Constant variance
-##
-## Error model algorithm: OLS
-##
-## Starting values for parameters to be optimised:
-## value type
-## parent_0 100.7500 state
-## k_parent 0.1000 deparm
-## k_m1 0.1001 deparm
-## f_parent_to_m1 0.5000 deparm
-##
-## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 100.750000 -Inf Inf
-## log_k_parent -2.302585 -Inf Inf
-## log_k_m1 -2.301586 -Inf Inf
-## f_parent_qlogis 0.000000 -Inf Inf
-##
-## Fixed parameter values:
-## value type
-## m1_0 0 state
-##
-##
-## Warning(s):
-## Observations with value of zero were removed from the data
-##
-## Results:
-##
-## AIC BIC logLik
-## 204.4486 212.6365 -97.22429
-##
-## Optimised, transformed parameters with symmetric confidence intervals:
-## Estimate Std. Error Lower Upper
-## parent_0 99.60000 1.57000 96.4000 102.8000
-## log_k_parent -2.31600 0.04087 -2.3990 -2.2330
-## log_k_m1 -5.24700 0.13320 -5.5180 -4.9770
-## f_parent_qlogis 0.05792 0.08926 -0.1237 0.2395
-## sigma 3.12600 0.35850 2.3960 3.8550
-##
-## Parameter correlation:
-## parent_0 log_k_parent log_k_m1 f_parent_qlogis sigma
-## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.172e-06
-## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.483e-07
-## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.205e-07
-## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.305e-06
-## sigma -1.172e-06 -8.483e-07 8.205e-07 1.305e-06 1.000e+00
-##
-## Backtransformed parameters:
-## Confidence intervals for internally transformed parameters are asymmetric.
-## t-test (unrealistically) based on the assumption of normal distribution
-## for estimators of untransformed parameters.
-## Estimate t value Pr(&gt;t) Lower Upper
-## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02
-## k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01
-## k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03
-## f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01
-## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00
-##
-## FOCUS Chi2 error levels in percent:
-## err.min n.optim df
-## All data 6.398 4 15
-## parent 6.459 2 7
-## m1 4.690 2 8
-##
-## Resulting formation fractions:
-## ff
-## parent_m1 0.5145
-## parent_sink 0.4855
-##
-## Estimated disappearance times:
-## DT50 DT90
-## parent 7.023 23.33
-## m1 131.761 437.70
-##
-## Data:
-## time variable observed predicted residual
-## 0 parent 99.46 99.59848 -1.385e-01
-## 0 parent 102.04 99.59848 2.442e+00
-## 1 parent 93.50 90.23787 3.262e+00
-## 1 parent 92.50 90.23787 2.262e+00
-## 3 parent 63.23 74.07319 -1.084e+01
-## 3 parent 68.99 74.07319 -5.083e+00
-## 7 parent 52.32 49.91207 2.408e+00
-## 7 parent 55.13 49.91207 5.218e+00
-## 14 parent 27.27 25.01258 2.257e+00
-## 14 parent 26.64 25.01258 1.627e+00
-## 21 parent 11.50 12.53462 -1.035e+00
-## 21 parent 11.64 12.53462 -8.946e-01
-## 35 parent 2.85 3.14787 -2.979e-01
-## 35 parent 2.91 3.14787 -2.379e-01
-## 50 parent 0.69 0.71624 -2.624e-02
-## 50 parent 0.63 0.71624 -8.624e-02
-## 75 parent 0.05 0.06074 -1.074e-02
-## 75 parent 0.06 0.06074 -7.382e-04
-## 1 m1 4.84 4.80296 3.704e-02
-## 1 m1 5.64 4.80296 8.370e-01
-## 3 m1 12.91 13.02400 -1.140e-01
-## 3 m1 12.96 13.02400 -6.400e-02
-## 7 m1 22.97 25.04476 -2.075e+00
-## 7 m1 24.47 25.04476 -5.748e-01
-## 14 m1 41.69 36.69003 5.000e+00
-## 14 m1 33.21 36.69003 -3.480e+00
-## 21 m1 44.37 41.65310 2.717e+00
-## 21 m1 46.44 41.65310 4.787e+00
-## 35 m1 41.22 43.31313 -2.093e+00
-## 35 m1 37.95 43.31313 -5.363e+00
-## 50 m1 41.19 41.21832 -2.832e-02
-## 50 m1 40.01 41.21832 -1.208e+00
-## 75 m1 40.09 36.44704 3.643e+00
-## 75 m1 33.85 36.44704 -2.597e+00
-## 100 m1 31.04 31.98162 -9.416e-01
-## 100 m1 33.13 31.98162 1.148e+00
-## 120 m1 25.15 28.78984 -3.640e+00
-## 120 m1 33.31 28.78984 4.520e+00</code></pre>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## mkin version used for fitting: 1.2.2 </span></span>
+<span><span class="co">## R version used for fitting: 4.2.2 </span></span>
+<span><span class="co">## Date of fit: Thu Nov 24 08:12:04 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:05 2022 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Equations:</span></span>
+<span><span class="co">## d_parent/dt = - k_parent * parent</span></span>
+<span><span class="co">## d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Model predictions using solution type analytical </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Fitted using 401 model solutions performed in 0.152 s</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Error model: Constant variance </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Error model algorithm: OLS </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Starting values for parameters to be optimised:</span></span>
+<span><span class="co">## value type</span></span>
+<span><span class="co">## parent_0 100.7500 state</span></span>
+<span><span class="co">## k_parent 0.1000 deparm</span></span>
+<span><span class="co">## k_m1 0.1001 deparm</span></span>
+<span><span class="co">## f_parent_to_m1 0.5000 deparm</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Starting values for the transformed parameters actually optimised:</span></span>
+<span><span class="co">## value lower upper</span></span>
+<span><span class="co">## parent_0 100.750000 -Inf Inf</span></span>
+<span><span class="co">## log_k_parent -2.302585 -Inf Inf</span></span>
+<span><span class="co">## log_k_m1 -2.301586 -Inf Inf</span></span>
+<span><span class="co">## f_parent_qlogis 0.000000 -Inf Inf</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Fixed parameter values:</span></span>
+<span><span class="co">## value type</span></span>
+<span><span class="co">## m1_0 0 state</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Warning(s): </span></span>
+<span><span class="co">## Observations with value of zero were removed from the data</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Results:</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## AIC BIC logLik</span></span>
+<span><span class="co">## 204.4486 212.6365 -97.22429</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Optimised, transformed parameters with symmetric confidence intervals:</span></span>
+<span><span class="co">## Estimate Std. Error Lower Upper</span></span>
+<span><span class="co">## parent_0 99.60000 1.57000 96.4000 102.8000</span></span>
+<span><span class="co">## log_k_parent -2.31600 0.04087 -2.3990 -2.2330</span></span>
+<span><span class="co">## log_k_m1 -5.24700 0.13320 -5.5180 -4.9770</span></span>
+<span><span class="co">## f_parent_qlogis 0.05792 0.08926 -0.1237 0.2395</span></span>
+<span><span class="co">## sigma 3.12600 0.35850 2.3960 3.8550</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameter correlation:</span></span>
+<span><span class="co">## parent_0 log_k_parent log_k_m1 f_parent_qlogis sigma</span></span>
+<span><span class="co">## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.172e-06</span></span>
+<span><span class="co">## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.483e-07</span></span>
+<span><span class="co">## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.205e-07</span></span>
+<span><span class="co">## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.305e-06</span></span>
+<span><span class="co">## sigma -1.172e-06 -8.483e-07 8.205e-07 1.305e-06 1.000e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Backtransformed parameters:</span></span>
+<span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span>
+<span><span class="co">## t-test (unrealistically) based on the assumption of normal distribution</span></span>
+<span><span class="co">## for estimators of untransformed parameters.</span></span>
+<span><span class="co">## Estimate t value Pr(&gt;t) Lower Upper</span></span>
+<span><span class="co">## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02</span></span>
+<span><span class="co">## k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01</span></span>
+<span><span class="co">## k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03</span></span>
+<span><span class="co">## f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01</span></span>
+<span><span class="co">## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## FOCUS Chi2 error levels in percent:</span></span>
+<span><span class="co">## err.min n.optim df</span></span>
+<span><span class="co">## All data 6.398 4 15</span></span>
+<span><span class="co">## parent 6.459 2 7</span></span>
+<span><span class="co">## m1 4.690 2 8</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Resulting formation fractions:</span></span>
+<span><span class="co">## ff</span></span>
+<span><span class="co">## parent_m1 0.5145</span></span>
+<span><span class="co">## parent_sink 0.4855</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Estimated disappearance times:</span></span>
+<span><span class="co">## DT50 DT90</span></span>
+<span><span class="co">## parent 7.023 23.33</span></span>
+<span><span class="co">## m1 131.761 437.70</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Data:</span></span>
+<span><span class="co">## time variable observed predicted residual</span></span>
+<span><span class="co">## 0 parent 99.46 99.59848 -1.385e-01</span></span>
+<span><span class="co">## 0 parent 102.04 99.59848 2.442e+00</span></span>
+<span><span class="co">## 1 parent 93.50 90.23787 3.262e+00</span></span>
+<span><span class="co">## 1 parent 92.50 90.23787 2.262e+00</span></span>
+<span><span class="co">## 3 parent 63.23 74.07319 -1.084e+01</span></span>
+<span><span class="co">## 3 parent 68.99 74.07319 -5.083e+00</span></span>
+<span><span class="co">## 7 parent 52.32 49.91207 2.408e+00</span></span>
+<span><span class="co">## 7 parent 55.13 49.91207 5.218e+00</span></span>
+<span><span class="co">## 14 parent 27.27 25.01258 2.257e+00</span></span>
+<span><span class="co">## 14 parent 26.64 25.01258 1.627e+00</span></span>
+<span><span class="co">## 21 parent 11.50 12.53462 -1.035e+00</span></span>
+<span><span class="co">## 21 parent 11.64 12.53462 -8.946e-01</span></span>
+<span><span class="co">## 35 parent 2.85 3.14787 -2.979e-01</span></span>
+<span><span class="co">## 35 parent 2.91 3.14787 -2.379e-01</span></span>
+<span><span class="co">## 50 parent 0.69 0.71624 -2.624e-02</span></span>
+<span><span class="co">## 50 parent 0.63 0.71624 -8.624e-02</span></span>
+<span><span class="co">## 75 parent 0.05 0.06074 -1.074e-02</span></span>
+<span><span class="co">## 75 parent 0.06 0.06074 -7.382e-04</span></span>
+<span><span class="co">## 1 m1 4.84 4.80296 3.704e-02</span></span>
+<span><span class="co">## 1 m1 5.64 4.80296 8.370e-01</span></span>
+<span><span class="co">## 3 m1 12.91 13.02400 -1.140e-01</span></span>
+<span><span class="co">## 3 m1 12.96 13.02400 -6.400e-02</span></span>
+<span><span class="co">## 7 m1 22.97 25.04476 -2.075e+00</span></span>
+<span><span class="co">## 7 m1 24.47 25.04476 -5.748e-01</span></span>
+<span><span class="co">## 14 m1 41.69 36.69003 5.000e+00</span></span>
+<span><span class="co">## 14 m1 33.21 36.69003 -3.480e+00</span></span>
+<span><span class="co">## 21 m1 44.37 41.65310 2.717e+00</span></span>
+<span><span class="co">## 21 m1 46.44 41.65310 4.787e+00</span></span>
+<span><span class="co">## 35 m1 41.22 43.31313 -2.093e+00</span></span>
+<span><span class="co">## 35 m1 37.95 43.31313 -5.363e+00</span></span>
+<span><span class="co">## 50 m1 41.19 41.21832 -2.832e-02</span></span>
+<span><span class="co">## 50 m1 40.01 41.21832 -1.208e+00</span></span>
+<span><span class="co">## 75 m1 40.09 36.44704 3.643e+00</span></span>
+<span><span class="co">## 75 m1 33.85 36.44704 -2.597e+00</span></span>
+<span><span class="co">## 100 m1 31.04 31.98162 -9.416e-01</span></span>
+<span><span class="co">## 100 m1 33.13 31.98162 1.148e+00</span></span>
+<span><span class="co">## 120 m1 25.15 28.78984 -3.640e+00</span></span>
+<span><span class="co">## 120 m1 33.31 28.78984 4.520e+00</span></span></code></pre>
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@@ -324,11 +335,13 @@
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- <p>Developed by Johannes Ranke.</p>
+ <p></p>
+<p>Developed by Johannes Ranke.</p>
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- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+ <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
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@@ -337,5 +350,7 @@
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