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diff --git a/docs/dev/reference/test_data_from_UBA_2014.html b/docs/dev/reference/test_data_from_UBA_2014.html new file mode 100644 index 00000000..0d6b8105 --- /dev/null +++ b/docs/dev/reference/test_data_from_UBA_2014.html @@ -0,0 +1,195 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014 • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link 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were used for the comparative validation of several kinetic evaluation + software packages (Ranke, 2014)."><meta name="robots" content="noindex"></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">mkin</a> + + <small class="nav-text text-info me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">1.2.10</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" 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NAFTA SOP Attachment examples</a></li> + </ul></li> +<li class="nav-item"><a class="nav-link" href="../coverage/coverage.html">Test coverage</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">News</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + + <h1>Three experimental datasets from two water sediment systems and one soil</h1> + + <div class="d-none name"><code>test_data_from_UBA_2014.Rd</code></div> + </div> + + <div class="ref-description section level2"> + <p>The datasets were used for the comparative validation of several kinetic evaluation + software packages (Ranke, 2014).</p> + </div> + + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">test_data_from_UBA_2014</span></span></code></pre></div> + </div> + + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></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> + + <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></div> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> + <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative + zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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"><-</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">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="va">f_river</span> <span class="op"><-</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">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="test_data_from_UBA_2014-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t)</span> +<span class="r-out co"><span class="r-pr">#></span> parent_w_0 95.98567441 2.16285684 44.3791159 1.245593e-17</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_w 0.42068803 0.05573864 7.5475120 8.752928e-07</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_s 0.07419672 0.10108562 0.7339987 2.371337e-01</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_w_to_parent_s 0.14336920 0.05809346 2.4679062 1.305295e-02</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_s_to_parent_w 1.00000000 3.13868615 0.3186046 3.772097e-01</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.98287858 0.68923267 4.3278253 2.987160e-04</span> +<span class="r-out co"><span class="r-pr">#></span> Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_w_0 91.48420501 100.4871438</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_w 0.36593946 0.4836276</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_s 0.02289956 0.2404043</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_w_to_parent_s 0.08180934 0.2391848</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_s_to_parent_w 0.00000000 1.0000000</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.00184022 3.9639169</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">#></span> err.min n.optim df</span> +<span class="r-out co"><span class="r-pr">#></span> All data 0.09246946 5 6</span> +<span class="r-out co"><span class="r-pr">#></span> parent_w 0.06377096 3 3</span> +<span class="r-out co"><span class="r-pr">#></span> parent_s 0.20882325 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"><-</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">#></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"><-</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">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_soil</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="test_data_from_UBA_2014-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 76.55425650 0.859186398 89.1008711 1.113861e-26 74.755959420</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.84258615 0.806159719 1.0451851 1.545266e-01 0.113779564</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.04210880 0.017083034 2.4649483 1.170188e-02 0.018013857</span> +<span class="r-out co"><span class="r-pr">#></span> k_M3 0.01122918 0.007245855 1.5497385 6.885051e-02 0.002909431</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.32240200 0.240783878 1.3389684 9.819070e-02 NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.16099855 0.033691952 4.7785463 6.531136e-05 NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_to_M3 0.27921507 0.269423709 1.0363419 1.565266e-01 0.022978202</span> +<span class="r-out co"><span class="r-pr">#></span> f_M2_to_M3 0.55641252 0.595119937 0.9349586 1.807707e-01 0.008002509</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778</span> +<span class="r-out co"><span class="r-pr">#></span> Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 78.35255358</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.13084582</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 6.23970946</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.09843260</span> +<span class="r-out co"><span class="r-pr">#></span> k_M3 0.04333992</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_to_M3 0.86450778</span> +<span class="r-out co"><span class="r-pr">#></span> f_M2_to_M3 0.99489895</span> +<span class="r-out co"><span class="r-pr">#></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">#></span> err.min n.optim df</span> +<span class="r-out co"><span class="r-pr">#></span> All data 0.09649963 9 20</span> +<span class="r-out co"><span class="r-pr">#></span> parent 0.04721283 2 6</span> +<span class="r-out co"><span class="r-pr">#></span> M1 0.26551208 2 5</span> +<span class="r-out co"><span class="r-pr">#></span> M2 0.20327575 2 5</span> +<span class="r-out co"><span class="r-pr">#></span> M3 0.05196550 3 4</span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +</code></pre></div> + </div> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + 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