Initialize dev docsHEAD dev

author: Johannes Ranke <johannes.ranke@jrwb.de> 2025-02-14 09:15:20 +0100
committer: Johannes Ranke <johannes.ranke@jrwb.de> 2025-02-14 09:15:20 +0100
commit: 91a5834dd701211f929fd25419dc34561ce3b4e7 (patch)
tree: 860862d680fea23581d08b2948c5ac3e922a8447 /docs/dev/reference/IORE.solution.html
parent: b0f08271d1dae8ffaf57f557c27eba1314ece1d5 (diff)
1 files changed, 171 insertions, 0 deletions
diff --git a/docs/dev/reference/IORE.solution.html b/docs/dev/reference/IORE.solution.html
new file mode 100644
index 00000000..47cc1e3d
--- /dev/null
+++ b/docs/dev/reference/IORE.solution.html
@@ -0,0 +1,171 @@
+<!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>Indeterminate order rate equation kinetics — IORE.solution • 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="Indeterminate order rate equation kinetics — IORE.solution"><meta name="description" content="Function describing exponential decline from a defined starting value, with
+a concentration dependent rate constant."><meta property="og:description" content="Function describing exponential decline from a defined starting value, with
+a concentration dependent rate constant."><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" href="../reference/index.html">Reference</a></li>
+<li class="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>
+    <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>
+    <li><a class="dropdown-item" href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li>
+    <li><a class="dropdown-item" href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a></li>
+    <li><hr class="dropdown-divider"></li>
+    <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li>
+    <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li>
+    <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li>
+    <li><a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li>
+    <li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li>
+    <li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li>
+    <li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li>
+    <li><hr class="dropdown-divider"></li>
+    <li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li>
+    <li><a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li>
+    <li><a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li>
+    <li><a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li>
+    <li><hr class="dropdown-divider"></li>
+    <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>
+<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>Indeterminate order rate equation kinetics</h1>
+      <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="d-none name"><code>IORE.solution.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Function describing exponential decline from a defined starting value, with
+a concentration dependent rate constant.</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="fu">IORE.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k__iore</span>, <span class="va">N</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+
+
+<dl><dt id="arg-t">t<a class="anchor" aria-label="anchor" href="#arg-t"></a></dt>
+<dd><p>Time.</p></dd>
+
+
+<dt id="arg-parent-">parent_0<a class="anchor" aria-label="anchor" href="#arg-parent-"></a></dt>
+<dd><p>Starting value for the response variable at time zero.</p></dd>
+
+
+<dt id="arg-k-iore">k__iore<a class="anchor" aria-label="anchor" href="#arg-k-iore"></a></dt>
+<dd><p>Rate constant. Note that this depends on the concentration
+units used.</p></dd>
+
+
+<dt id="arg-n">N<a class="anchor" aria-label="anchor" href="#arg-n"></a></dt>
+<dd><p>Exponent describing the nonlinearity of the rate equation</p></dd>
+
+</dl></div>
+    <div class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <p>The value of the response variable at time <code>t</code>.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
+    <p>The solution of the IORE kinetic model reduces to the
+<code><a href="SFO.solution.html">SFO.solution</a></code> if N = 1.  The parameters of the IORE model can
+be transformed to equivalent parameters of the FOMC mode - see the NAFTA
+guidance for details.</p>
+    </div>
+    <div class="section level2">
+    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
+    <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance
+for Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
+    </div>
+    <div class="section level2">
+    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></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="SFO.solution.html">SFO.solution</a>()</code>,
+<code><a href="SFORB.solution.html">SFORB.solution</a>()</code>,
+<code><a href="logistic.solution.html">logistic.solution</a>()</code></p></div>
+    </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></span>
+<span class="r-in"><span>  <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">IORE.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.2</span>, <span class="fl">1.3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span>, ylim <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">100</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="IORE.solution-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span>  <span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span>    <span class="va">fit.fomc</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span>    <span class="va">fit.iore</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"IORE"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span>    <span class="va">fit.iore.deS</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"IORE"</span>, <span class="va">FOCUS_2006_C</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Error in is.loaded(initfunc, PACKAGE = dllname, type = "") : </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   invalid 'PACKAGE' argument</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span>    <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span><span class="va">fit.fomc</span><span class="op">$</span><span class="va">par</span>, <span class="va">fit.iore</span><span class="op">$</span><span class="va">par</span>, <span class="va">fit.iore.deS</span><span class="op">$</span><span class="va">par</span>,</span></span>
+<span class="r-in"><span>                     row.names <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"model par"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>             fit.fomc.par fit.iore.par fit.iore.deS.par</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> model par 1  85.87489063    85.874890        85.874890</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> model par 2   0.05192238    -4.826631        -4.826631</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> model par 3   0.65096665     1.949403         1.949403</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> model par 4   1.85744396     1.857444         1.857444</span>
+<span class="r-in"><span>    <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span>fomc <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.fomc</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span>, iore <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.iore</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span>,</span></span>
+<span class="r-in"><span>                iore.deS <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.iore</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>              DT50    DT90 DT50back</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> fomc     1.785233 15.1479 4.559973</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> iore     1.785233 15.1479 4.559973</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> iore.deS 1.785233 15.1479 4.559973</span>
+<span class="r-in"><span>  <span class="co"># }</span></span></span>
+<span class="r-in"><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>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<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></div>
+
+
+
+
+
+  </body></html>
+
author	Johannes Ranke <johannes.ranke@jrwb.de>	2025-02-14 09:15:20 +0100
committer	Johannes Ranke <johannes.ranke@jrwb.de>	2025-02-14 09:15:20 +0100
commit	91a5834dd701211f929fd25419dc34561ce3b4e7 (patch)
tree	860862d680fea23581d08b2948c5ac3e922a8447 /docs/dev/reference/IORE.solution.html
parent	b0f08271d1dae8ffaf57f557c27eba1314ece1d5 (diff)