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diff --git a/docs/index.html b/docs/index.html index e13f573e..ef4fc650 100644 --- a/docs/index.html +++ b/docs/index.html @@ -4,148 +4,82 @@ <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=1.0"> +<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <title>Kinetic Evaluation of Chemical Degradation Data • mkin</title> -<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"> -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"> -<script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"> -<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> -<script src="pkgdown.js"></script><meta property="og:title" content="Kinetic Evaluation of Chemical Degradation Data"> -<meta property="og:description" content="Calculation routines based on the FOCUS Kinetics Report (2006, - 2014). Includes a function for conveniently defining differential equation - models, model solution based on eigenvalues if possible or using numerical - solvers. If a C compiler (on windows: Rtools) is installed, differential - equation models are solved using automatically generated C functions. - Heteroscedasticity can be taken into account using variance by variable or - two-component error models as described by Ranke and Meinecke (2018) - <doi:10.3390/environments6120124>. Hierarchical degradation models can - be fitted using nonlinear mixed-effects model packages as a back end as - described by Ranke et al. (2021) <doi:10.3390/environments8080071>. Please - note that no warranty is implied for correctness of results or fitness for a - particular purpose."> -<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> +<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="Kinetic Evaluation of Chemical Degradation Data"> +<meta name="description" content="Calculation routines based on the FOCUS Kinetics Report (2006, 2014). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers. If a C compiler (on windows: Rtools) is installed, differential equation models are solved using automatically generated C functions. Non-constant errors can be taken into account using variance by variable or two-component error models <doi:10.3390/environments6120124>. Hierarchical degradation models can be fitted using nonlinear mixed-effects model packages as a back end <doi:10.3390/environments8080071>. Please note that no warranty is implied for correctness of results or fitness for a particular purpose."> +<meta property="og:description" content="Calculation routines based on the FOCUS Kinetics Report (2006, 2014). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers. If a C compiler (on windows: Rtools) is installed, differential equation models are solved using automatically generated C functions. Non-constant errors can be taken into account using variance by variable or two-component error models <doi:10.3390/environments6120124>. Hierarchical degradation models can be fitted using nonlinear mixed-effects model packages as a back end <doi:10.3390/environments8080071>. Please note that no warranty is implied for correctness of results or fitness for a particular purpose."> </head> -<body data-spy="scroll" data-target="#toc"> - +<body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-home"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.5</span> - </span> - </div> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> -<li> - 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<a href="news/index.html">News</a> -</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="nav navbar-nav navbar-right"> -<li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> - - </a> -</li> +<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> -<!--/.nav-collapse --> - </div> -<!--/.container --> -</div> -<!--/.navbar --> - - </header><div class="row"> - <div class="contents col-md-9"> -<div class="section level1"> + </div> +</nav><div class="container template-home"> +<div class="row"> + <main id="main" class="col-md-9"><div class="section level1"> <div class="page-header"><h1 id="mkin">mkin<a class="anchor" aria-label="anchor" href="#mkin"></a> </h1></div> -<p><a href="https://cran.r-project.org/package=mkin" class="external-link"><img src="https://www.r-pkg.org/badges/version/mkin"></a> <a href="https://jranke.r-universe.dev/ui/#package:mkin" class="external-link"><img src="https://jranke.r-universe.dev/badges/mkin" alt="mkin status badge"></a> <a href="https://app.travis-ci.com/github/jranke/mkin" class="external-link"><img src="https://travis-ci.com/jranke/mkin.svg?branch=main" alt="Build Status"></a> <a href="https://app.codecov.io/gh/jranke/mkin" class="external-link"><img src="https://codecov.io/github/jranke/mkin/branch/main/graphs/badge.svg" alt="codecov"></a></p> +<!-- badges: start --> + <p>The <a href="https://www.r-project.org" class="external-link">R</a> package <strong>mkin</strong> provides calculation routines for the analysis of chemical degradation data, including <b>m</b>ulticompartment <b>kin</b>etics as needed for modelling the formation and decline of transformation products, or if several degradation compartments are involved. It provides stable functionality for kinetic evaluations according to the FOCUS guidance (see below for details). In addition, it provides functionality to do hierarchical kinetics based on nonlinear mixed-effects models.</p> <div class="section level2"> <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a> @@ -242,6 +176,7 @@ </ul> <p>Thanks to everyone involved for collaboration and support!</p> <p>Thanks are due also to Emmanuelle Comets, maintainer of the saemix package, for her interest and support for using the SAEM algorithm and its implementation in saemix for the evaluation of chemical degradation data.</p> +<p>Regarding the application of nonlinear mixed-effects models to degradation data, von Götz et al (1999) have already proposed to use this technique in the context of environmental risk assessments of pesticides. However, this work was apparently not followed up, which is why we had to independently arrive at the idea and missed to cite this previous work on the topic in our first publications.</p> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> @@ -249,6 +184,11 @@ <table class="table"> <tr> <td> +Ranke J (2023) Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data - Guidance for the use of an R markdown template file. <a href="https://www.umweltbundesamt.de/publikationen/application-of-nonlinear-hierarchical-models-to-the" class="external-link">Umweltbundesamt TEXTE 151/2023</a> +</td> +</tr> +<tr> +<td> Ranke J, Wöltjen J, Schmidt J, and Comets E (2021) Taking kinetic evaluations of degradation data to the next level with nonlinear mixed-effects models. <i>Environments</i> <b>8</b> (8) 71 <a href="https://doi.org/10.3390/environments8080071" class="external-link">doi:10.3390/environments8080071</a> </td> </tr> @@ -262,6 +202,11 @@ Ranke J, Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical D Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic evaluation of chemical degradation data <i>Environmental Sciences Europe</i> <b>30</b> 17 <a href="https://doi.org/10.1186/s12302-018-0145-1" class="external-link">doi:10.1186/s12302-018-0145-1</a> </td> </tr> +<tr> +<td> +Von Götz N, Nörtersheuser P, Richter O (1999) Population based analysis of pesticide kinetics <i>Chemosphere</i> <b>38</b> 7 <a href="https://doi.org/10.1016/S0045-6535(98)00388-9" class="external-link">doi:10.1016/S0045-6535(98)00388-9</a> +</td> +</tr> </table> </div> <div class="section level2"> @@ -270,10 +215,7 @@ Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic <p>Contributions are welcome!</p> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <div class="links"> + </main><aside class="col-md-3"><div class="links"> <h2 data-toc-skip>Links</h2> <ul class="list-unstyled"> <li><a href="https://cloud.r-project.org/package=mkin" class="external-link">View on CRAN</a></li> @@ -307,27 +249,24 @@ Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic - </div> + </aside> </div> - <footer><div class="copyright"> - <p></p> -<p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> - </footer> + </footer> </div> - - + </body> </html> |