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diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index fcf37ee4..10239ccb 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -1,5 +1,18 @@ <!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>Short introduction to mkin • 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 href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Short introduction to mkin"></head><body> +<!-- 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>Short introduction to mkin • 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 href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"> +<link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"> +<script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Short introduction to mkin"> +</head> +<body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -7,7 +20,7 @@ <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released 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"> @@ -15,10 +28,12 @@ </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> -<li class="nav-item dropdown"> + <ul class="navbar-nav me-auto"> +<li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="active nav-item dropdown"> <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button> - <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/mkin.html">Introduction to mkin</a></li> + <ul class="dropdown-menu" aria-labelledby="dropdown-articles"> +<li><a class="dropdown-item" href="../articles/mkin.html">Introduction to mkin</a></li> <li><hr class="dropdown-divider"></li> <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6></li> <li><a class="dropdown-item" href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li> @@ -41,13 +56,18 @@ <li><h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6></li> <li><a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a></li> <li><a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a></li> - </ul></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> + </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> + </ul> +</div> </div> @@ -64,7 +84,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 18 May 2023 -(rebuilt 2025-02-13)</h4> +(rebuilt 2025-05-12)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/mkin.rmd" class="external-link"><code>vignettes/mkin.rmd</code></a></small> <div class="d-none name"><code>mkin.rmd</code></div> @@ -72,11 +92,12 @@ Ranke</h4> -<p><a href="https://www.jrwb.de">Wissenschaftlicher Berater, Kronacher -Str. 12, 79639 Grenzach-Wyhlen, Germany</a><br /> Privatdozent at the +<p><a href="https://www.jrwb.de" class="external-link">Wissenschaftlicher Berater, Kronacher +Str. 12, 79639 Grenzach-Wyhlen, Germany</a><br> Privatdozent at the University of Freiburg</p> -<div id="abstract" class="section level1"> -<h1>Abstract</h1> +<div class="section level2"> +<h2 id="abstract">Abstract<a class="anchor" aria-label="anchor" href="#abstract"></a> +</h2> <p>In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide @@ -86,38 +107,40 @@ nonlinear optimisation. The <code>R</code> add-on package this guidance from within R and calculates some statistical measures for data series within one or more compartments, for parent and metabolites.</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(<span class="st">"mkin"</span>, <span class="at">quietly =</span> <span class="cn">TRUE</span>)</span> -<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="co"># Define the kinetic model</span></span> -<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>m_SFO_SFO_SFO <span class="ot"><-</span> <span class="fu">mkinmod</span>(<span class="at">parent =</span> <span class="fu">mkinsub</span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</span> -<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> <span class="at">M1 =</span> <span class="fu">mkinsub</span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</span> -<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a> <span class="at">M2 =</span> <span class="fu">mkinsub</span>(<span class="st">"SFO"</span>),</span> -<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a> <span class="at">use_of_ff =</span> <span class="st">"max"</span>, <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span> -<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a></span> -<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a></span> -<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="co"># Produce model predictions using some arbitrary parameters</span></span> -<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a>sampling_times <span class="ot">=</span> <span class="fu">c</span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">28</span>, <span class="dv">60</span>, <span class="dv">90</span>, <span class="dv">120</span>)</span> -<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a>d_SFO_SFO_SFO <span class="ot"><-</span> <span class="fu">mkinpredict</span>(m_SFO_SFO_SFO,</span> -<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(<span class="at">k_parent =</span> <span class="fl">0.03</span>,</span> -<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a> <span class="at">f_parent_to_M1 =</span> <span class="fl">0.5</span>, <span class="at">k_M1 =</span> <span class="fu">log</span>(<span class="dv">2</span>)<span class="sc">/</span><span class="dv">100</span>,</span> -<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a> <span class="at">f_M1_to_M2 =</span> <span class="fl">0.9</span>, <span class="at">k_M2 =</span> <span class="fu">log</span>(<span class="dv">2</span>)<span class="sc">/</span><span class="dv">50</span>),</span> -<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(<span class="at">parent =</span> <span class="dv">100</span>, <span class="at">M1 =</span> <span class="dv">0</span>, <span class="at">M2 =</span> <span class="dv">0</span>),</span> -<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a> sampling_times)</span> -<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a></span> -<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a><span class="co"># Generate a dataset by adding normally distributed errors with</span></span> -<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a><span class="co"># standard deviation 3, for two replicates at each sampling time</span></span> -<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a>d_SFO_SFO_SFO_err <span class="ot"><-</span> <span class="fu">add_err</span>(d_SFO_SFO_SFO, <span class="at">reps =</span> <span class="dv">2</span>,</span> -<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a> <span class="at">sdfunc =</span> <span class="cf">function</span>(x) <span class="dv">3</span>,</span> -<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a> <span class="at">n =</span> <span class="dv">1</span>, <span class="at">seed =</span> <span class="dv">123456789</span> )</span> -<span id="cb1-23"><a href="#cb1-23" aria-hidden="true" tabindex="-1"></a></span> -<span id="cb1-24"><a href="#cb1-24" aria-hidden="true" tabindex="-1"></a><span class="co"># Fit the model to the dataset</span></span> -<span id="cb1-25"><a href="#cb1-25" aria-hidden="true" tabindex="-1"></a>f_SFO_SFO_SFO <span class="ot"><-</span> <span class="fu">mkinfit</span>(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[<span class="dv">1</span>]], <span class="at">quiet =</span> <span class="cn">TRUE</span>)</span> -<span id="cb1-26"><a href="#cb1-26" aria-hidden="true" tabindex="-1"></a></span> -<span id="cb1-27"><a href="#cb1-27" aria-hidden="true" tabindex="-1"></a><span class="co"># Plot the results separately for parent and metabolites</span></span> -<span id="cb1-28"><a href="#cb1-28" aria-hidden="true" tabindex="-1"></a><span class="fu">plot_sep</span>(f_SFO_SFO_SFO, <span class="at">lpos =</span> <span class="fu">c</span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</span></code></pre></div> -<p><img src="/home/jranke/git/mkin/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png" width="768" /></p> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<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="st"><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="co"># Define the kinetic model</span></span> +<span><span class="va">m_SFO_SFO_SFO</span> <span class="op"><-</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>,</span> +<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="st">"M2"</span><span class="op">)</span>,</span> +<span> M2 <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> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span></span> +<span></span> +<span><span class="co"># Produce model predictions using some arbitrary parameters</span></span> +<span><span class="va">sampling_times</span> <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="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> +<span><span class="va">d_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>,</span> +<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.03</span>,</span> +<span> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>, k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">100</span>,</span> +<span> f_M1_to_M2 <span class="op">=</span> <span class="fl">0.9</span>, k_M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">50</span><span class="op">)</span>,</span> +<span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> +<span> <span class="va">sampling_times</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># Generate a dataset by adding normally distributed errors with</span></span> +<span><span class="co"># standard deviation 3, for two replicates at each sampling time</span></span> +<span><span class="va">d_SFO_SFO_SFO_err</span> <span class="op"><-</span> <span class="fu"><a href="../reference/add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_SFO_SFO</span>, reps <span class="op">=</span> <span class="fl">2</span>,</span> +<span> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">3</span>,</span> +<span> n <span class="op">=</span> <span class="fl">1</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span></span> +<span></span> +<span><span class="co"># Fit the model to the dataset</span></span> +<span><span class="va">f_SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>, <span class="va">d_SFO_SFO_SFO_err</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># Plot the results separately for parent and metabolites</span></span> +<span><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_SFO_SFO_SFO</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="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> </div> -<div id="background" class="section level1"> -<h1>Background</h1> +<div class="section level2"> +<h2 id="background">Background<a class="anchor" aria-label="anchor" href="#background"></a> +</h2> <p>The <code>mkin</code> package <span class="citation">(J. Ranke 2021)</span> implements the approach to degradation kinetics recommended in the kinetics report provided by the FOrum for Co-ordination of @@ -138,8 +161,7 @@ purpose compartment based tool providing infrastructure for fitting dynamic simulation models based on differential equations to data.</p> <p>The ‘mkin’ code was first uploaded to the BerliOS development platform. When this was taken down, the version control history was -imported into the R-Forge site (see <em>e.g.</em> <a -href="https://cgit.jrwb.de/mkin/commit/?id=30cbb4092f6d2d3beff5800603374a0d009ad770">the +imported into the R-Forge site (see <em>e.g.</em> <a href="https://cgit.jrwb.de/mkin/commit/?id=30cbb4092f6d2d3beff5800603374a0d009ad770" class="external-link">the initial commit on 11 May 2010</a>), where the code is still being updated.</p> <p>At that time, the R package <code>FME</code> (Flexible Modelling @@ -162,8 +184,9 @@ times.</p> <p>The possibility to specify back-reactions and a biphasic model (SFORB) for metabolites were present in <code>mkin</code> from the very beginning.</p> -<div id="derived-software-tools" class="section level2"> -<h2>Derived software tools</h2> +<div class="section level3"> +<h3 id="derived-software-tools">Derived software tools<a class="anchor" aria-label="anchor" href="#derived-software-tools"></a> +</h3> <p>Soon after the publication of <code>mkin</code>, two derived tools were published, namely KinGUII (developed at Bayer Crop Science) and CAKE (commissioned to Tessella by Syngenta), which added a graphical @@ -184,50 +207,44 @@ be specified for transformation products. Starting with KinGUII version KinGUII.</p> <p>A further graphical user interface (GUI) that has recently been brought to a decent degree of maturity is the browser based GUI named -<code>gmkin</code>. Please see its <a -href="https://pkgdown.jrwb.de/gmkin/">documentation page</a> and <a -href="https://pkgdown.jrwb.de/gmkin/articles/gmkin_manual.html">manual</a> +<code>gmkin</code>. Please see its <a href="https://pkgdown.jrwb.de/gmkin/" class="external-link">documentation page</a> and <a href="https://pkgdown.jrwb.de/gmkin/articles/gmkin_manual.html" class="external-link">manual</a> for further information.</p> <p>A comparison of scope, usability and numerical results obtained with -these tools has been recently been published by <span -class="citation">Johannes Ranke, Wöltjen, and Meinecke +these tools has been recently been published by <span class="citation">Johannes Ranke, Wöltjen, and Meinecke (2018)</span>.</p> </div> </div> -<div id="unique-features" class="section level1"> -<h1>Unique features</h1> +<div class="section level2"> +<h2 id="unique-features">Unique features<a class="anchor" aria-label="anchor" href="#unique-features"></a> +</h2> <p>Currently, the main unique features available in <code>mkin</code> are</p> <ul> -<li>the <a -href="https://pkgdown.jrwb.de/mkin/articles/web_only/compiled_models.html">speed +<li>the <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/compiled_models.html">speed increase</a> by using compiled code when a compiler is present,</li> -<li>parallel model fitting on multicore machines using the <a -href="https://pkgdown.jrwb.de/mkin/reference/mmkin.html"><code>mmkin</code> +<li>parallel model fitting on multicore machines using the <a href="https://pkgdown.jrwb.de/mkin/reference/mmkin.html"><code>mmkin</code> function</a>,</li> <li>the estimation of parameter confidence intervals based on transformed parameters (see below) and</li> -<li>the possibility to use the <a -href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">two-component -error model</a></li> +<li>the possibility to use the <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">two-component +error model</a> +</li> </ul> <p>The iteratively reweighted least squares fitting of different variances for each variable as introduced by <span class="citation">Gao -et al. (2011)</span> has been available in mkin since <a -href="https://pkgdown.jrwb.de/mkin/news/index.html#mkin-0-9-22-2013-10-26">version -0.9-22</a>. With <a -href="https://pkgdown.jrwb.de/mkin/news/index.html#mkin-0-9-49-5-2019-07-04">release +et al. (2011)</span> has been available in mkin since <a href="https://pkgdown.jrwb.de/mkin/news/index.html#mkin-0-9-22-2013-10-26">version +0.9-22</a>. With <a href="https://pkgdown.jrwb.de/mkin/news/index.html#mkin-0-9-49-5-2019-07-04">release 0.9.49.5</a>, the IRLS algorithm has been complemented by direct or step-wise maximisation of the likelihood function, which makes it possible not only to fit the variance by variable error model but also a -<a -href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">two-component +<a href="https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html">two-component error model</a> inspired by error models developed in analytical chemistry <span class="citation">(Johannes Ranke and Meinecke 2019)</span>.</p> </div> -<div id="internal-parameter-transformations" class="section level1"> -<h1>Internal parameter transformations</h1> +<div class="section level2"> +<h2 id="internal-parameter-transformations">Internal parameter transformations<a class="anchor" aria-label="anchor" href="#internal-parameter-transformations"></a> +</h2> <p>For rate constants, the log transformation is used, as proposed by Bates and Watts <span class="citation">(1988, 77, 149)</span>. Approximate intervals are constructed for the transformed rate constants @@ -252,9 +269,9 @@ well as in the subsequent calculation of parameter confidence intervals. In the current version of mkin, a logit transformation is used for parameters that are bound between 0 and 1, such as the g parameter of the DFOP model.</p> -<div id="confidence-intervals-based-on-transformed-parameters" -class="section level2"> -<h2>Confidence intervals based on transformed parameters</h2> +<div class="section level3"> +<h3 id="confidence-intervals-based-on-transformed-parameters">Confidence intervals based on transformed parameters<a class="anchor" aria-label="anchor" href="#confidence-intervals-based-on-transformed-parameters"></a> +</h3> <p>In the first attempt at providing improved parameter confidence intervals introduced to <code>mkin</code> in 2013, confidence intervals obtained from FME on the transformed parameters were simply all @@ -276,14 +293,13 @@ are considered by the author of this vignette to be more accurate than those obtained using a re-estimation of the Hessian matrix after backtransformation, as implemented in the FME package.</p> </div> -<div id="parameter-t-test-based-on-untransformed-parameters" -class="section level2"> -<h2>Parameter t-test based on untransformed parameters</h2> +<div class="section level3"> +<h3 id="parameter-t-test-based-on-untransformed-parameters">Parameter t-test based on untransformed parameters<a class="anchor" aria-label="anchor" href="#parameter-t-test-based-on-untransformed-parameters"></a> +</h3> <p>The standard output of many nonlinear regression software packages includes the results from a test for significant difference from zero for all parameters. Such a test is also recommended to check the -validity of rate constants in the FOCUS guidance <span -class="citation">(FOCUS Work Group on Degradation Kinetics 2014, +validity of rate constants in the FOCUS guidance <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 96ff)</span>.</p> <p>It has been argued that the precondition for this test, <em>i.e.</em> normal distribution of the estimator for the parameters, is not @@ -304,8 +320,9 @@ t-test is based on the unjustified assumption of normal distribution of the parameter estimators.</p> </div> </div> -<div id="references" class="section level1"> -<h1>References</h1> +<div class="section level2"> +<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> +</h2> <!-- vim: set foldmethod=syntax: --> <div id="refs" class="references csl-bib-body hanging-indent"> <div id="ref-bates1988" class="csl-entry"> @@ -316,14 +333,12 @@ Applications</em>. Wiley-Interscience. FOCUS Work Group on Degradation Kinetics. 2006. <em>Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration. Report of the FOCUS Work Group -on Degradation Kinetics</em>. <a -href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>. +on Degradation Kinetics</em>. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>. </div> <div id="ref-FOCUSkinetics2014" class="csl-entry"> ———. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU -Registration</em>. 1.1 ed. <a -href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>. +Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>. </div> <div id="ref-gao11" class="csl-entry"> Gao, Z., J. W. Green, J. Vanderborght, and W. Schmitt. 2011. @@ -333,34 +348,29 @@ Science and Technology</em> 45: 4429–37. </div> <div id="ref-pkg:mkin" class="csl-entry"> Ranke, J. 2021. <em>‘<span class="nocase">mkin</span>‘: -<span>K</span>inetic Evaluation of Chemical Degradation Data</em>. <a -href="https://CRAN.R-project.org/package=mkin">https://CRAN.R-project.org/package=mkin</a>. +<span>K</span>inetic Evaluation of Chemical Degradation Data</em>. <a href="https://CRAN.R-project.org/package=mkin" class="external-link">https://CRAN.R-project.org/package=mkin</a>. </div> <div id="ref-ranke2012" class="csl-entry"> Ranke, J., and R. Lehmann. 2012. <span>“Parameter Reliability in Kinetic Evaluation of Environmental Metabolism Data - Assessment and the Influence of Model Specification.”</span> In <em>SETAC World 20-24 -May</em>. Berlin. <a -href="https://jrwb.de/posters/Poster_SETAC_2012_Kinetic_parameter_uncertainty_model_parameterization_Lehmann_Ranke.pdf">https://jrwb.de/posters/Poster_SETAC_2012_Kinetic_parameter_uncertainty_model_parameterization_Lehmann_Ranke.pdf</a>. +May</em>. Berlin. <a href="https://jrwb.de/posters/Poster_SETAC_2012_Kinetic_parameter_uncertainty_model_parameterization_Lehmann_Ranke.pdf" class="external-link">https://jrwb.de/posters/Poster_SETAC_2012_Kinetic_parameter_uncertainty_model_parameterization_Lehmann_Ranke.pdf</a>. </div> <div id="ref-ranke2015" class="csl-entry"> ———. 2015. <span>“To t-Test or Not to t-Test, That Is the Question.”</span> In <em>XV Symposium on Pesticide Chemistry 2-4 -September 2015</em>. Piacenza. <a -href="https://jrwb.de/posters/piacenza_2015.pdf">https://jrwb.de/posters/piacenza_2015.pdf</a>. +September 2015</em>. Piacenza. <a href="https://jrwb.de/posters/piacenza_2015.pdf" class="external-link">https://jrwb.de/posters/piacenza_2015.pdf</a>. </div> <div id="ref-ranke2019" class="csl-entry"> Ranke, Johannes, and Stefan Meinecke. 2019. <span>“Error Models for the Kinetic Evaluation of Chemical Degradation Data.”</span> -<em>Environments</em> 6 (12). <a -href="https://doi.org/10.3390/environments6120124">https://doi.org/10.3390/environments6120124</a>. +<em>Environments</em> 6 (12). <a href="https://doi.org/10.3390/environments6120124" class="external-link">https://doi.org/10.3390/environments6120124</a>. </div> <div id="ref-ranke2018" class="csl-entry"> Ranke, Johannes, Janina Wöltjen, and Stefan Meinecke. 2018. <span>“Comparison of Software Tools for Kinetic Evaluation of Chemical Degradation Data.”</span> <em>Environmental Sciences Europe</em> 30 (1): -17. <a -href="https://doi.org/10.1186/s12302-018-0145-1">https://doi.org/10.1186/s12302-018-0145-1</a>. +17. <a href="https://doi.org/10.1186/s12302-018-0145-1" class="external-link">https://doi.org/10.1186/s12302-018-0145-1</a>. </div> <div id="ref-schaefer2007" class="csl-entry"> Schäfer, D., B. Mikolasch, P. Rainbird, and B. Harvey. 2007. @@ -374,13 +384,13 @@ Piacenza. Soetaert, Karline, and Thomas Petzoldt. 2010. <span>“Inverse Modelling, Sensitivity and Monte Carlo Analysis in <span>R</span> Using Package <span>FME</span>.”</span> <em>Journal of Statistical Software</em> 33 -(3): 1–28. <a -href="https://doi.org/10.18637/jss.v033.i03">https://doi.org/10.18637/jss.v033.i03</a>. +(3): 1–28. <a href="https://doi.org/10.18637/jss.v033.i03" class="external-link">https://doi.org/10.18637/jss.v033.i03</a>. </div> </div> </div> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> - </nav></aside></div> + </nav></aside> +</div> @@ -392,10 +402,12 @@ href="https://doi.org/10.18637/jss.v033.i03">https://doi.org/10.18637/jss.v033.i <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> - </footer></div> + </footer> +</div> - </body></html> + </body> +</html> |