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Diffstat (limited to 'docs/dev/articles/twa.html')
| -rw-r--r-- | docs/dev/articles/twa.html | 114 |
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diff --git a/docs/dev/articles/twa.html b/docs/dev/articles/twa.html index 673d753a..4aa8f5b1 100644 --- a/docs/dev/articles/twa.html +++ b/docs/dev/articles/twa.html @@ -34,14 +34,14 @@ </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">1.2.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -53,6 +53,9 @@ <li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -60,22 +63,31 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li class="divider"> </li> +<li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + </li> +<li class="dropdown-header">Performance</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/benchmarks.html">Benchmark timings for mkin</a> @@ -83,6 +95,15 @@ <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Miscellaneous</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> </ul> </li> <li> @@ -106,13 +127,16 @@ - </header><script src="twa_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> - <h1 data-toc-skip>Calculation of time weighted average concentrations with mkin</h1> - <h4 data-toc-skip class="author">Johannes Ranke</h4> + <h1 data-toc-skip>Calculation of time weighted average +concentrations with mkin</h1> + <h4 data-toc-skip class="author">Johannes +Ranke</h4> - <h4 data-toc-skip class="date">Last change 18 September 2019 (rebuilt 2022-11-24)</h4> + <h4 data-toc-skip class="date">Last change 18 September 2019 +(rebuilt 2023-04-16)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/twa.rmd" class="external-link"><code>vignettes/twa.rmd</code></a></small> <div class="hidden name"><code>twa.rmd</code></div> @@ -121,13 +145,25 @@ -<p>Since version 0.9.45.1 of the ‘mkin’ package, a function for calculating time weighted average concentrations for decline kinetics (<em>i.e.</em> only for the compound applied in the experiment) is included. Strictly speaking, they are maximum moving window time weighted average concentrations, <em>i.e.</em> the maximum time weighted average concentration that can be found when moving a time window of a specified width over the decline curve.</p> -<p>Time weighted average concentrations for the SFO, FOMC and the DFOP model are calculated using the formulas given in the FOCUS kinetics guidance <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 251)</span>:</p> +<p>Since version 0.9.45.1 of the ‘mkin’ package, a function for +calculating time weighted average concentrations for decline kinetics +(<em>i.e.</em> only for the compound applied in the experiment) is +included. Strictly speaking, they are maximum moving window time +weighted average concentrations, <em>i.e.</em> the maximum time weighted +average concentration that can be found when moving a time window of a +specified width over the decline curve.</p> +<p>Time weighted average concentrations for the SFO, FOMC and the DFOP +model are calculated using the formulas given in the FOCUS kinetics +guidance <span class="citation">(FOCUS Work Group on Degradation +Kinetics 2014, 251)</span>:</p> <p>SFO:</p> -<p><span class="math display">\[c_\textrm{twa} = c_0 \frac{\left( 1 - e^{- k t} \right)}{ k t} \]</span></p> +<p><span class="math display">\[c_\textrm{twa} = c_0 \frac{\left( 1 - +e^{- k t} \right)}{ k t} \]</span></p> <p>FOMC:</p> -<p><span class="math display">\[c_\textrm{twa} = c_0 \frac{\beta}{t (1 - \alpha)} - \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha} - 1 \right) \]</span></p> +<p><span class="math display">\[c_\textrm{twa} = c_0 \frac{\beta}{t (1 - +\alpha)} + \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha} +- 1 \right) \]</span></p> <p>DFOP:</p> <p><span class="math display">\[c_\textrm{twa} = \frac{c_0}{t} \left( \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) + @@ -135,15 +171,25 @@ <p>HS for <span class="math inline">\(t > t_b\)</span>:</p> <p><span class="math display">\[c_\textrm{twa} = \frac{c_0}{t} \left( \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) + - \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right) \right) \]</span></p> -<p>Often, the ratio between the time weighted average concentration <span class="math inline">\(c_\textrm{twa}\)</span> and the initial concentration <span class="math inline">\(c_0\)</span></p> -<p><span class="math display">\[f_\textrm{twa} = \frac{c_\textrm{twa}}{c_0}\]</span></p> -<p>is needed. This can be calculated from the fitted initial concentration <span class="math inline">\(c_0\)</span> and the time weighted average concentration <span class="math inline">\(c_\textrm{twa}\)</span>, or directly from the model parameters using the following formulas:</p> + \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} +\right) \right) \]</span></p> +<p>Often, the ratio between the time weighted average concentration +<span class="math inline">\(c_\textrm{twa}\)</span> and the initial +concentration <span class="math inline">\(c_0\)</span></p> +<p><span class="math display">\[f_\textrm{twa} = +\frac{c_\textrm{twa}}{c_0}\]</span></p> +<p>is needed. This can be calculated from the fitted initial +concentration <span class="math inline">\(c_0\)</span> and the time +weighted average concentration <span class="math inline">\(c_\textrm{twa}\)</span>, or directly from the +model parameters using the following formulas:</p> <p>SFO:</p> -<p><span class="math display">\[f_\textrm{twa} = \frac{\left( 1 - e^{- k t} \right)}{k t} \]</span></p> +<p><span class="math display">\[f_\textrm{twa} = \frac{\left( 1 - e^{- k +t} \right)}{k t} \]</span></p> <p>FOMC:</p> -<p><span class="math display">\[f_\textrm{twa} = \frac{\beta}{t (1 - \alpha)} - \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha} - 1 \right) \]</span></p> +<p><span class="math display">\[f_\textrm{twa} = \frac{\beta}{t (1 - +\alpha)} + \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha} +- 1 \right) \]</span></p> <p>DFOP:</p> <p><span class="math display">\[f_\textrm{twa} = \frac{1}{t} \left( \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) + @@ -151,11 +197,19 @@ <p>HS for <span class="math inline">\(t > t_b\)</span>:</p> <p><span class="math display">\[f_\textrm{twa} = \frac{1}{t} \left( \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) + - \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right) \right) \]</span></p> -<p>Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the <code><a href="../reference/max_twa_parent.html">max_twa_parent()</a></code> function. If the same is needed for metabolites, the function <code><a href="https://pkgdown.jrwb.de/pfm/reference/max_twa.html" class="external-link">pfm::max_twa()</a></code> from the ‘pfm’ package can be used.</p> -<div id="refs" class="references hanging-indent"> -<div id="ref-FOCUSkinetics2014"> -<p>FOCUS Work Group on Degradation Kinetics. 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" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> + \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} +\right) \right) \]</span></p> +<p>Note that a method for calculating maximum moving window time +weighted average concentrations for a model fitted by ‘mkinfit’ or from +parent decline model parameters is included in the +<code><a href="../reference/max_twa_parent.html">max_twa_parent()</a></code> function. If the same is needed for +metabolites, the function <code><a href="https://pkgdown.jrwb.de/pfm/reference/max_twa.html" class="external-link">pfm::max_twa()</a></code> from the ‘pfm’ +package can be used.</p> +<div id="refs" class="references csl-bib-body hanging-indent"> +<div id="ref-FOCUSkinetics2014" class="csl-entry"> +FOCUS Work Group on Degradation Kinetics. 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" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>. </div> </div> </div> @@ -175,7 +229,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer> |