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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/reference/test_data_from_UBA_2014.html
parent51d63256a7b3020ee11931d61b4db97b9ded02c0 (diff)
parent4200e566ad2600f56bc3987669aeab88582139eb (diff)
Merge branch 'main' into custom_lsoda_call
Diffstat (limited to 'docs/dev/reference/test_data_from_UBA_2014.html')
-rw-r--r--docs/dev/reference/test_data_from_UBA_2014.html292
1 files changed, 125 insertions, 167 deletions
diff --git a/docs/dev/reference/test_data_from_UBA_2014.html b/docs/dev/reference/test_data_from_UBA_2014.html
index 539b8287..05529e0e 100644
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+ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
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<h1>Three experimental datasets from two water sediment systems and one soil</h1>
@@ -149,113 +94,126 @@
software packages (Ranke, 2014).</p>
</div>
- <pre class="usage"><span class='va'>test_data_from_UBA_2014</span></pre>
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">test_data_from_UBA_2014</span></span></code></pre></div>
+ </div>
+ <div id="format">
+ <h2>Format</h2>
+ <p>A list containing three datasets as an R6 class defined by <code><a href="mkinds.html">mkinds</a></code>.
+ Each dataset has, among others, the following components</p><dl><dt><code>title</code></dt>
+<dd><p>The name of the dataset, e.g. <code>UBA_2014_WS_river</code></p></dd>
- <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+ <dt><code>data</code></dt>
+<dd><p>A data frame with the data in the form expected by <code><a href="mkinfit.html">mkinfit</a></code></p></dd>
- <p>A list containing three datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>.
- Each dataset has, among others, the following components</p><dl>
- <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>UBA_2014_WS_river</code></p></dd>
- <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd>
-</dl>
-
- <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
-
+</dl></div>
+ <div id="source">
+ <h2>Source</h2>
<p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative
zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p>
+ </div>
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='co'># \dontrun{</span>
- <span class='co'># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span>
- <span class='co'># guidance. Due to the strong correlation of the parameter estimates, the</span>
- <span class='co'># covariance matrix is not returned. Note that level P-II evaluations are</span>
- <span class='co'># generally considered deprecated due to the frequent occurrence of such</span>
- <span class='co'># large parameter correlations, among other reasons (e.g. the adequacy of the</span>
- <span class='co'># model).</span>
- <span class='va'>m_ws</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent_w <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span><span class='op'>)</span>,
- parent_s <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>f_river</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_ws</span>, <span class='va'>test_data_from_UBA_2014</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>f_river</span><span class='op'>)</span>
-</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'>
- <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_river</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
-#&gt; parent_w_0 95.91998118 NA NA NA NA NA
-#&gt; k_parent_w 0.41145375 NA NA NA NA NA
-#&gt; k_parent_s 0.04663944 NA NA NA NA NA
-#&gt; f_parent_w_to_parent_s 0.12467894 NA NA NA NA NA
-#&gt; f_parent_s_to_parent_w 0.50000000 NA NA NA NA NA
-#&gt; sigma 3.13612618 NA NA NA NA NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span><span class='op'>(</span><span class='va'>f_river</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; err.min n.optim df
-#&gt; All data 0.1090929 5 6
-#&gt; parent_w 0.0817436 3 3
-#&gt; parent_s 0.1619965 2 3</div><div class='input'>
- <span class='co'># This is the evaluation used for the validation of software packages</span>
- <span class='co'># in the expertise from 2014</span>
- <span class='va'>m_soil</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>,
- M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M3"</span><span class='op'>)</span>,
- M2 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M3"</span><span class='op'>)</span>,
- M3 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>,
- use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>
- <span class='va'>f_soil</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_soil</span>, <span class='va'>test_data_from_UBA_2014</span><span class='op'>[[</span><span class='fl'>3</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>f_soil</span>, lpos <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_soil</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span>
-</div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
-#&gt; parent_0 76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418
-#&gt; k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575
-#&gt; k_M1 0.84258615 0.806160102 1.0451846 1.545268e-01 0.113779609
-#&gt; k_M2 0.04210880 0.017083034 2.4649483 1.170188e-02 0.018013857
-#&gt; k_M3 0.01122918 0.007245856 1.5497385 6.885052e-02 0.002909431
-#&gt; f_parent_to_M1 0.32240200 0.240783943 1.3389680 9.819076e-02 NA
-#&gt; f_parent_to_M2 0.16099855 0.033691952 4.7785464 6.531136e-05 NA
-#&gt; f_M1_to_M3 0.27921507 0.269423780 1.0363416 1.565267e-01 0.022978205
-#&gt; f_M2_to_M3 0.55641252 0.595119966 0.9349586 1.807707e-01 0.008002509
-#&gt; sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778
-#&gt; Upper
-#&gt; parent_0 78.35255358
-#&gt; k_parent 0.13084582
-#&gt; k_M1 6.23970702
-#&gt; k_M2 0.09843260
-#&gt; k_M3 0.04333992
-#&gt; f_parent_to_M1 NA
-#&gt; f_parent_to_M2 NA
-#&gt; f_M1_to_M3 0.86450775
-#&gt; f_M2_to_M3 0.99489895
-#&gt; sigma 1.45337221</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span><span class='op'>(</span><span class='va'>f_soil</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; err.min n.optim df
-#&gt; All data 0.09649963 9 20
-#&gt; parent 0.04721283 2 6
-#&gt; M1 0.26551208 2 5
-#&gt; M2 0.20327575 2 5
-#&gt; M3 0.05196550 3 4</div><div class='input'> <span class='co'># }</span>
-</div></pre>
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span> <span class="co"># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span></span></span>
+<span class="r-in"><span> <span class="co"># guidance. Due to the strong correlation of the parameter estimates, the</span></span></span>
+<span class="r-in"><span> <span class="co"># covariance matrix is not returned. Note that level P-II evaluations are</span></span></span>
+<span class="r-in"><span> <span class="co"># generally considered deprecated due to the frequent occurrence of such</span></span></span>
+<span class="r-in"><span> <span class="co"># large parameter correlations, among other reasons (e.g. the adequacy of the</span></span></span>
+<span class="r-in"><span> <span class="co"># model).</span></span></span>
+<span class="r-in"><span> <span class="va">m_ws</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent_w <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"parent_s"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> parent_s <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"parent_w"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"><span> <span class="va">f_river</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_ws</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
+<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="test_data_from_UBA_2014-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Could not calculate correlation; no covariance matrix</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Estimate se_notrans t value Pr(&gt;t) Lower Upper</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_w_0 95.91998118 NA NA NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_w 0.41145375 NA NA NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_s 0.04663944 NA NA NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_w_to_parent_s 0.12467894 NA NA NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_s_to_parent_w 0.50000000 NA NA NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 3.13612618 NA NA NA NA NA</span>
+<span class="r-in"><span> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> err.min n.optim df</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> All data 0.1090929 5 6</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_w 0.0817436 3 3</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_s 0.1619965 2 3</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="co"># This is the evaluation used for the validation of software packages</span></span></span>
+<span class="r-in"><span> <span class="co"># in the expertise from 2014</span></span></span>
+<span class="r-in"><span> <span class="va">m_soil</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</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">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> M3 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="va">f_soil</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_soil</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
+<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_soil</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="test_data_from_UBA_2014-2.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Estimate se_notrans t value Pr(&gt;t) Lower</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_M1 0.84258615 0.806160102 1.0451846 1.545268e-01 0.113779609</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_M2 0.04210880 0.017083034 2.4649483 1.170188e-02 0.018013857</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_M3 0.01122918 0.007245856 1.5497385 6.885052e-02 0.002909431</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_M1 0.32240200 0.240783943 1.3389680 9.819076e-02 NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_M2 0.16099855 0.033691952 4.7785464 6.531136e-05 NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_M1_to_M3 0.27921507 0.269423780 1.0363416 1.565267e-01 0.022978205</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_M2_to_M3 0.55641252 0.595119966 0.9349586 1.807707e-01 0.008002509</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Upper</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 78.35255358</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent 0.13084582</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_M1 6.23970702</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_M2 0.09843260</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_M3 0.04333992</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_M1 NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_M2 NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_M1_to_M3 0.86450775</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_M2_to_M3 0.99489895</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma 1.45337221</span>
+<span class="r-in"><span> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> err.min n.optim df</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> All data 0.09649963 9 20</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent 0.04721283 2 6</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> M1 0.26551208 2 5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> M2 0.20327575 2 5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> M3 0.05196550 3 4</span>
+<span class="r-in"><span> <span class="co"># }</span></span></span>
+</code></pre></div>
+ </div>
</div>
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