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diff --git a/docs/dev/reference/mccall81_245T.html b/docs/dev/reference/mccall81_245T.html new file mode 100644 index 00000000..996e9fc2 --- /dev/null +++ b/docs/dev/reference/mccall81_245T.html @@ -0,0 +1,201 @@ +<!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>Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • 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 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corresponding + 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether + extracts."><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" 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</div> + + <div class="ref-description section level2"> + <p>Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding + 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether + extracts.</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="va">mccall81_245T</span></span></code></pre></div> + </div> + + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> + <p>A dataframe containing the following variables.</p><dl><dt><code>name</code></dt> +<dd><p>the name of the compound observed. Note that T245 is used as + an acronym for 2,4,5-T. T245 is a legitimate object name + in R, which is necessary for specifying models using + <code><a href="mkinmod.html">mkinmod</a></code>.</p></dd> + + <dt><code>time</code></dt> +<dd><p>a numeric vector containing sampling times in days after + treatment</p></dd> + + <dt><code>value</code></dt> +<dd><p>a numeric vector containing concentrations in percent of applied radioactivity</p></dd> + + <dt><code>soil</code></dt> +<dd><p>a factor containing the name of the soil</p></dd> + + +</dl></div> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> + <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labelled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 + <a href="https://doi.org/10.1021/jf00103a026" class="external-link">doi:10.1021/jf00103a026</a></p> + </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 class="va">SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>T245 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"phenol"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> phenol <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"anisole"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> anisole <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit.1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t)</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1847074943 47.537272 4.472189e-18</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050581e-01 0.2986993738 1.356073 9.756990e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.3985340721 1.562626 6.949414e-02</span> +<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 1.000000e+00 0.6718440131 1.488441 7.867790e-02</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.4907558973 5.123989 6.233159e-05</span> +<span class="r-out co"><span class="r-pr">#></span> Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 99.246061490 1.084640e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 0.039631621 4.746194e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.218013879 7.525762e-01</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 0.005370739 8.305299e-03</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.547559080 6.924813e-01</span> +<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 0.000000000 1.000000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.706607296 3.322649e+00</span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $ff</span> +<span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.072478e-10 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $distimes</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> T245 15.982025 53.09114</span> +<span class="r-out co"><span class="r-pr">#></span> phenol 1.711229 5.68458</span> +<span class="r-out co"><span class="r-pr">#></span> anisole 103.784093 344.76329</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span> <span class="co"># formation fraction from phenol to anisol is practically 1. As we cannot</span></span></span> +<span class="r-in"><span> <span class="co"># fix formation fractions when using the ilr transformation, we can turn of</span></span></span> +<span class="r-in"><span> <span class="co"># the sink in the model generation</span></span></span> +<span class="r-in"><span> <span class="va">SFO_SFO_SFO_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>T245 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"phenol"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> phenol <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"anisole"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> anisole <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="va">fit.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO_2</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1623653059 48.028439 4.993108e-19 99.271020328</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050582e-01 0.1177237651 3.440752 1.679255e-03 0.218746589</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.0342197873 18.198824 2.039411e-12 0.547975634</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655</span> +<span class="r-out co"><span class="r-pr">#></span> Upper</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 108.43904079</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 0.04743877</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.75005593</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 0.00829550</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.69212307</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.31827222</span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $ff</span> +<span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.072478e-10 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $distimes</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> T245 15.982025 53.09114</span> +<span class="r-out co"><span class="r-pr">#></span> phenol 1.711229 5.68458</span> +<span class="r-out co"><span class="r-pr">#></span> anisole 103.784093 344.76329</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mccall81_245T-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="co"># }</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> + |