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| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 18:03:54 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 18:03:54 +0100 |
| commit | 2bb59c88d49b193f278916ad9cc4de83c0de9604 (patch) | |
| tree | f286bba254d7c5f2d32eeb2b11f6148938b0e1e1 /docs/reference/SFORB.solution.html | |
| parent | 351248d07f810ccb6c497633a02cd48ee35526e6 (diff) | |
Make tests more platform independent, update docs
Diffstat (limited to 'docs/reference/SFORB.solution.html')
| -rw-r--r-- | docs/reference/SFORB.solution.html | 215 |
1 files changed, 73 insertions, 142 deletions
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index b2062e30..45933071 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Single First-Order Reversible Binding kinetics — SFORB.solution • 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="Single First-Order Reversible Binding kinetics — SFORB.solution" /> -<meta property="og:description" content="Function describing the solution of the differential equations describing +<!-- 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=1.0"><title>Single First-Order Reversible Binding kinetics — SFORB.solution • 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="Single First-Order Reversible Binding kinetics — SFORB.solution"><meta property="og:description" content="Function describing the solution of the differential equations describing the kinetic model with first-order terms for a two-way transfer from a free to a bound fraction, and a first-order degradation term for the free fraction. The initial condition is a defined amount in the free fraction -and no substance in the bound fraction." /> - - - - -<!-- 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]> +and no substance in the bound fraction."><!-- 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]--> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -76,13 +21,12 @@ and no substance in the bound fraction." /> </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">1.0.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> @@ -91,8 +35,7 @@ and no substance in the bound fraction." /> <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,6 +45,9 @@ and no substance in the bound fraction." /> <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> + </li> + <li> <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> @@ -116,34 +62,27 @@ and no substance in the bound fraction." /> <li> <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> </li> - </ul> -</li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </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> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Single First-Order Reversible Binding kinetics</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parent_solutions.R" class="external-link"><code>R/parent_solutions.R</code></a></small> <div class="hidden name"><code>SFORB.solution.Rd</code></div> </div> @@ -155,90 +94,82 @@ fraction. The initial condition is a defined amount in the free fraction and no substance in the bound fraction.</p> </div> - <pre class="usage"><span class='fu'>SFORB.solution</span><span class='op'>(</span><span class='va'>t</span>, <span class='va'>parent_0</span>, <span class='va'>k_12</span>, <span class='va'>k_21</span>, <span class='va'>k_1output</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>t</th> - <td><p>Time.</p></td> - </tr> - <tr> - <th>parent_0</th> - <td><p>Starting value for the response variable at time zero.</p></td> - </tr> - <tr> - <th>k_12</th> - <td><p>Kinetic constant describing transfer from free to bound.</p></td> - </tr> - <tr> - <th>k_21</th> - <td><p>Kinetic constant describing transfer from bound to free.</p></td> - </tr> - <tr> - <th>k_1output</th> - <td><p>Kinetic constant describing degradation of the free -fraction.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">SFORB.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k_12</span>, <span class="va">k_21</span>, <span class="va">k_1output</span><span class="op">)</span></code></pre></div> + </div> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>t</dt> +<dd><p>Time.</p></dd> +<dt>parent_0</dt> +<dd><p>Starting value for the response variable at time zero.</p></dd> +<dt>k_12</dt> +<dd><p>Kinetic constant describing transfer from free to bound.</p></dd> +<dt>k_21</dt> +<dd><p>Kinetic constant describing transfer from bound to free.</p></dd> +<dt>k_1output</dt> +<dd><p>Kinetic constant describing degradation of the free +fraction.</p></dd> +</dl></div> + <div id="value"> + <h2>Value</h2> <p>The value of the response variable, which is the sum of free and bound fractions at time <code>t</code>.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - - <p>FOCUS (2006) “Guidance Document on Estimating Persistence + </div> + <div id="references"> + <h2>References</h2> + <p>FOCUS (2006) “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, +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, -<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a> -FOCUS (2014) “Generic guidance for Estimating Persistence +<a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a> +FOCUS (2014) “Generic guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in -EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 -<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p>Other parent solutions: -<code><a href='DFOP.solution.html'>DFOP.solution</a>()</code>, -<code><a href='FOMC.solution.html'>FOMC.solution</a>()</code>, -<code><a href='HS.solution.html'>HS.solution</a>()</code>, -<code><a href='IORE.solution.html'>IORE.solution</a>()</code>, -<code><a href='SFO.solution.html'>SFO.solution</a>()</code>, -<code><a href='logistic.solution.html'>logistic.solution</a>()</code></p></div> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'>SFORB.solution</span><span class='op'>(</span><span class='va'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span><span class='op'>)</span>, <span class='fl'>0</span>, <span class='fl'>2</span><span class='op'>)</span> -</div><div class='img'><img src='SFORB.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> -</div></pre> +<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> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p>Other parent solutions: +<code><a href="DFOP.solution.html">DFOP.solution</a>()</code>, +<code><a href="FOMC.solution.html">FOMC.solution</a>()</code>, +<code><a href="HS.solution.html">HS.solution</a>()</code>, +<code><a href="IORE.solution.html">IORE.solution</a>()</code>, +<code><a href="SFO.solution.html">SFO.solution</a>()</code>, +<code><a href="logistic.solution.html">logistic.solution</a>()</code></p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> +<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">SFORB.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.5</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span><span class="op">)</span></span> +<span class="r-plt img"><img src="SFORB.solution-1.png" alt="" width="700" height="433"></span> +<span class="r-in"></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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